diff --git a/.gene_requests_cache.sqlite b/.gene_requests_cache.sqlite deleted file mode 100644 index 357053d74..000000000 Binary files a/.gene_requests_cache.sqlite and /dev/null differ diff --git a/CITATION.cff b/CITATION.cff deleted file mode 100644 index 765af3219..000000000 --- a/CITATION.cff +++ /dev/null @@ -1,86 +0,0 @@ -cff-version: 1.2.0 -message: "If you use OntoGPT, please cite it as follows." -authors: -- family-names: "Caufield" - given-names: "J. Harry" - orcid: "https://orcid.org/0000-0001-5705-7831" -- family-names: "Hegde" - given-names: "Harshad" - orcid: "https://orcid.org/0000-0002-2411-565X" -- family-names: "Emonet" - given-names: "Vincent" - orcid: "https://orcid.org/0000-0002-1501-1082" -- family-names: "Harris" - given-names: "Nomi L." - orcid: "https://orcid.org/0000-0001-6315-3707" -- family-names: "Joachimiak" - given-names: "Marcin P." - orcid: "https://orcid.org/0000-0001-8175-045X" -- family-names: "Matentzoglu" - given-names: "Nicolas" - orcid: "https://orcid.org/0000-0002-7356-1779" -- family-names: "Kim" - given-names: "HyeongSik" - orcid: "https://orcid.org/0000-0002-3002-9838" -- family-names: "Moxon" - given-names: "Sierra A.T." - orcid: "https://orcid.org/0000-0002-8719-7760" -- family-names: "Reese" - given-names: "Justin T." - orcid: "https://orcid.org/0000-0002-2170-2250" -- family-names: "Haendel" - given-names: "Melissa A." - orcid: "https://orcid.org/0000-0001-9114-8737" -- family-names: "Robinson" - given-names: "Peter N." - orcid: "https://orcid.org/0000-0002-0736-9199" -- family-names: "Mungall" - given-names: "Christopher J." - orcid: "https://orcid.org/0000-0002-6601-2165" -title: "OntoGPT" -version: 0.2.1 -date-released: 2023-04-06 -url: "https://github.com/monarch-initiative/ontogpt" -preferred-citation: - type: article - authors: - - family-names: "Caufield" - given-names: "J. Harry" - orcid: "https://orcid.org/0000-0001-5705-7831" - - family-names: "Hegde" - given-names: "Harshad" - orcid: "https://orcid.org/0000-0002-2411-565X" - - family-names: "Emonet" - given-names: "Vincent" - orcid: "https://orcid.org/0000-0002-1501-1082" - - family-names: "Harris" - given-names: "Nomi L." - orcid: "https://orcid.org/0000-0001-6315-3707" - - family-names: "Joachimiak" - given-names: "Marcin P." - orcid: "https://orcid.org/0000-0001-8175-045X" - - family-names: "Matentzoglu" - given-names: "Nicolas" - orcid: "https://orcid.org/0000-0002-7356-1779" - - family-names: "Kim" - given-names: "HyeongSik" - orcid: "https://orcid.org/0000-0002-3002-9838" - - family-names: "Moxon" - given-names: "Sierra A.T." - orcid: "https://orcid.org/0000-0002-8719-7760" - - family-names: "Reese" - given-names: "Justin T." - orcid: "https://orcid.org/0000-0002-2170-2250" - - family-names: "Haendel" - given-names: "Melissa A." - orcid: "https://orcid.org/0000-0001-9114-8737" - - family-names: "Robinson" - given-names: "Peter N." - orcid: "https://orcid.org/0000-0002-0736-9199" - - family-names: "Mungall" - given-names: "Christopher J." - orcid: "https://orcid.org/0000-0002-6601-2165" - doi: "10.48550/arXiv.2304.02711" - journal: "arXiv [cs.AI]" - title: "Structured prompt interrogation and recursive extraction of semantics (SPIRES): A method for populating knowledge bases using zero-shot learning" - year: 2023 diff --git a/README.md b/README.md index a44345ef7..f0d28b779 100644 --- a/README.md +++ b/README.md @@ -1,88 +1,21 @@ -# OntoGPT - -[![DOI](https://zenodo.org/badge/13996/monarch-initiative/ontogpt.svg)](https://zenodo.org/badge/latestdoi/13996/monarch-initiative/ontogpt) -![PyPI](https://img.shields.io/pypi/v/ontogpt) +# TALISMAN ## Introduction -_OntoGPT_ is a Python package for extracting structured information from text with large language models (LLMs), _instruction prompts_, and ontology-based grounding. +_TALISMAN_ is a Python package for summarizing gene set functions using large language models (LLMs). -Two different strategies for knowledge extraction are currently implemented in OntoGPT: +It uses the OntoGPT package to interface with LLMs. -[For more details, please see the full documentation.](https://monarch-initiative.github.io/ontogpt/) +[For more details, please see the full documentation.](https://monarch-initiative.github.io/talisman/) ## Quick Start -OntoGPT runs on the command line, though there's also a minimal web app interface (see `Web Application` section below). - -1. Ensure you have Python 3.9 or greater installed. -2. Install with `pip`: - - ```bash - pip install ontogpt - ``` - -3. Set your OpenAI API key: - - ```bash - runoak set-apikey -e openai - ``` - -4. See the list of all OntoGPT commands: - - ```bash - ontogpt --help - ``` - -5. Try a simple example of information extraction: - - ```bash - echo "One treatment for high blood pressure is carvedilol." > example.txt - ontogpt extract -i example.txt -t drug - ``` - - OntoGPT will retrieve the necessary ontologies and output results to the command line. Your output will provide all extracted objects under the heading `extracted_object`. - -## Web Application - -There is a bare bones web application for running OntoGPT and viewing results. - -First, install the required dependencies with `pip` by running the following command: - -```bash -pip install ontogpt[web] -``` - -Then run this command to start the web application: - -```bash -web-ontogpt -``` - -NOTE: We do not recommend hosting this webapp publicly without authentication. - -## Evaluations - -OpenAI's functions have been evaluated on test data. Please see the full documentation for details on these evaluations and how to reproduce them. - -## Tutorials and Presentations - -- Presentation: "Staying grounded: assembling structured biological knowledge with help from large language models" - presented by Harry Caufield as part of the AgBioData Consortium webinar series (September 2023) - - [Slides](https://docs.google.com/presentation/d/1rMQVWaMju-ucYFif5nx4Xv3bNX2SVI_w89iBIT1bkV4/edit?usp=sharing) - - [Video](https://www.youtube.com/watch?v=z38lI6WyBsY) -- Presentation: "Transforming unstructured biomedical texts with large language models" - presented by Harry Caufield as part of the BOSC track at ISMB/ECCB 2023 (July 2023) - - [Slides](https://docs.google.com/presentation/d/1LsOTKi-rXYczL9vUTHB1NDkaEqdA9u3ZFC5ANa0x1VU/edit?usp=sharing) - - [Video](https://www.youtube.com/watch?v=a34Yjz5xPp4) -- Presentation: "OntoGPT: A framework for working with ontologies and large language models" - talk by Chris Mungall at Joint Food Ontology Workgroup (May 2023) - - [Slides](https://docs.google.com/presentation/d/1CosJJe8SqwyALyx85GWkw9eOT43B4HwDlAY2CmkmJgU/edit) - - [Video](https://www.youtube.com/watch?v=rt3wobA9hEs&t=1955s) +TBD ## Citation -The information extraction approach used in OntoGPT, SPIRES, is described further in: Caufield JH, Hegde H, Emonet V, Harris NL, Joachimiak MP, Matentzoglu N, et al. Structured prompt interrogation and recursive extraction of semantics (SPIRES): A method for populating knowledge bases using zero-shot learning. arXiv publication: - -The gene summarization approach used in OntoGPT, SPINDOCTOR, is described further in: Joachimiak MP, Caufield JH, Harris NL, Kim H, Mungall CJ. Gene Set Summarization using Large Language Models. arXiv publication: +The gene summarization approach used in TALISMAN is described further in: Joachimiak MP, Caufield JH, Harris NL, Kim H, Mungall CJ. Gene Set Summarization using Large Language Models. arXiv publication: ## Acknowledgements -This project is part of the [Monarch Initiative](https://monarchinitiative.org/). We also gratefully acknowledge [Bosch Research](https://www.bosch.com/research) for their support of this research project. +This project is part of the [Monarch Initiative](https://monarchinitiative.org/). diff --git a/disease_cp_output.yaml b/disease_cp_output.yaml deleted file mode 100644 index 5a68599fe..000000000 --- a/disease_cp_output.yaml +++ /dev/null @@ -1,612 +0,0 @@ -input_text: |- - Title: Symptoms of anxiety and depression associated with steroid efficacy and clinical outcomes in patients with inflammatory bowel disease. - Keywords: HADS; anxiety; depression; inflammatory bowel disease; steroid resistance - PMID: 37547213 - Abstract: Anxiety and depression symptoms are very common in patients with inflammatory bowel disease (IBD). We aimed to explore the impact of anxiety and depression on the efficacy of medications, as well as IBD-related poor outcomes.This was a prospective longitudinal observational study. Hospital Anxiety and Depression Scale was used to assess anxiety and depression symptoms. Logistic regression analyses were used to assess the association between anxiety/depression and the response to different medications. Kaplan-Meier survival analysis and Cox regression model were applied to analyze the relationship between anxiety/depression and IBD-related poor outcomes, which were defined as urgent IBD-related hospitalization, IBD-related surgery, or death.A total of 325 IBD patients were enrolled, 118 of whom were treated with corticosteroids, 88 with azathioprine/6-mercaptopurine (AZA/6-MP), and 147 with anti-TNF agents. Anxiety/depression symptoms were found to be significantly related to steroid resistance, but independent of AZA/6-MP and anti-TNF agents nonresponse. There was a significant association between anxiety/depression symptoms and IBD-related poor outcomes. Coexisting with anxiety/depression symptoms was an independent influencing factor of steroid resistance and IBD-related poor outcomes.IBD patients with anxiety/depression symptoms were at a higher risk of developing steroid resistance and IBD-related poor outcomes. Future studies are needed to explore whether interventions for anxiety and depression will improve their response to medications and change their prognosis.Copyright © 2023 Duan, Yang, Cao, Chen, Liang and Zhang. -raw_completion_output: |- - genes: N/A - exposures: corticosteroids, azathioprine/6-mercaptopurine (AZA/6-MP), anti-TNF agents - gene_exposures_relationships: N/A - diseases: inflammatory bowel disease - cellular_process: N/A - disease_cellular_process_relationships: N/A -prompt: |+ - Split the following piece of text into fields in the following format: - - subject: - predicate: - object: - qualifier: - subject_qualifier: - object_qualifier: - - - Text: - N/A - - === - -extracted_object: - genes: - - N/A - exposures: - - corticosteroids, azathioprine/6-mercaptopurine (AZA/6-MP), anti-TNF agents - gene_exposures_relationships: - - subject: N/A - predicate: N/A - object: N/A - qualifier: N/A - subject_qualifier: N/A - object_qualifier: N/A - diseases: - - MONDO:0005265 - cellular_process: - - N/A - disease_cellular_process_relationships: - - subject: N/A - predicate: N/A - object: N/A - qualifier: N/A - subject_qualifier: N/A - object_qualifier: N/A -named_entities: - - id: MONDO:0005265 - label: inflammatory bowel disease -input_text: |- - Title: Hypoxia-sensing by the Histone Demethylase UTX ( KDM6A ) Controls Colitogenic CD4 + T cell Fate and Mucosal Inflammation. - Keywords: - PMID: 37546969 - Abstract: Hypoxia is a feature of inflammatory conditions [e.g., inflammatory bowel disease (IBD)] and can exacerbate tissue damage in these diseases. To counteract hypoxia's deleterious effects, adaptive responses have evolved which protect against hypoxia-associated tissue injury. To date, much attention has focused on hypoxia-activated HIF (hypoxia-inducible factor) transcription factors in these responses. However, recent work has identified epigenetic regulators that are also oxygen-sensitive, but their role in adaptation to hypoxic inflammation is currently unclear. Here, we show that the oxygen-sensing epigenetic regulator UTX is a critical modulator of colitis severity. Unlike HIF transcription factors that act on gut epithelial cells, UTX functions in colitis through its effects on immune cells. Hypoxia results in decreased CD4 + T cell IFN-γ production and increased CD4 + regulatory T cells, and these findings are recapitulated by T cell-specific UTX deficiency. Hypoxia impairs the histone demethylase activity of UTX, and loss of UTX function leads to accumulation of repressive H3K27me3 epigenetic marks at IL12/STAT4 pathway genes ( Il12rb2, Tbx21, and Ifng ). In a colitis mouse model, T cell-specific UTX deletion ameliorates colonic inflammation, protects against weight loss, and increases survival. Together these findings implicate UTX's oxygen-sensitive histone demethylase activity in mediating protective, hypoxia-induced pathways in colitis. -raw_completion_output: |- - genes: UTX, HIF, IL12rb2, Tbx21, Ifng - exposures: hypoxia - gene_exposures_relationships: UTX - hypoxia - diseases: inflammatory bowel disease (IBD), colitis - cellular_process: CD4 + T cell IFN-γ production, CD4 + regulatory T cells - disease_cellular_process_relationships: colitis - CD4 + T cell IFN-γ production, CD4 + regulatory T cells -prompt: |+ - From the text below, extract the following entities in the following format: - - subject: - predicate: - object: - qualifier: - subject_qualifier: - object_qualifier: - - - Text: - colitis - CD4 + T cell IFN-γ production, CD4 + regulatory T cells - - === - -extracted_object: - genes: - - UTX, HIF, IL12rb2, Tbx21, Ifng - exposures: - - hypoxia - gene_exposures_relationships: - - subject: UTX - predicate: hypoxia - object: None - qualifier: None - subject_qualifier: None - object_qualifier: None - diseases: - - MONDO:0005052 - cellular_process: - - CD4 + T cell IFN-γ production, CD4 + regulatory T cells - disease_cellular_process_relationships: - - subject: MONDO:0005292 - predicate: regulatory - object: CD4 + T cells - subject_qualifier: None - object_qualifier: None -named_entities: - - id: MONDO:0005052 - label: inflammatory bowel disease (IBD), colitis - - id: MONDO:0005292 - label: colitis -input_text: |- - Title: Iranian Consensus Guideline for Pharmacotherapy with Biologics and Small Molecules Drugs in Adults with Inflammatory Bowel Diseases. - Keywords: Biologic drugs; Consensus guideline; Pharmacotherapy; Small therapeutic molecules - PMID: 37546508 - Abstract: Background: Pharmacotherapy with biologics and small molecules, as the more effective therapies for moderate to severe ulcerative colitis (UC) and Crohn's disease (CD), is complex. Choosing the best methods for their utilization in order to induce and maintain remission are critical for practicing gastroenterologists. We aimed to develop an Iranian consensus on the management of inflammatory bowel disease (IBD) patients with biologics and small molecules. Methods: A Delphi consensus was undertaken by experts who performed a literature summary and voting process. Quality of evidence was assessed using the Grading and Recommendations Assessment, Development, and Evaluation; and an additional risk of bias-protocol. Results: Following an extensive search of the literature, 219 studies were used to determine the quality of the evidence. After three rounds of voting, consensus (defined as≥80% agreement) was reached for 87 statements. Conclusion: We considered different aspects of pharmacotherapy in this consensus. This guideline, along with clinical judgment, can be used to optimize management of IBD patients.© 2023 Middle East Journal of Digestive Diseases. -raw_completion_output: |- - genes: None mentioned in the text - exposures: Biologic drugs; Small therapeutic molecules - gene_exposures_relationships: None mentioned in the text - diseases: Inflammatory bowel disease (IBD); Ulcerative colitis (UC); Crohn's disease (CD) - cellular_process: None mentioned in the text - disease_cellular_process_relationships: None mentioned in the text -prompt: |+ - Split the following piece of text into fields in the following format: - - subject: - predicate: - object: - qualifier: - subject_qualifier: - object_qualifier: - - - Text: - None mentioned in the text - - === - -extracted_object: - genes: - - None mentioned in the text - exposures: - - Biologic drugs - - Small therapeutic molecules - gene_exposures_relationships: - - subject: None mentioned in the text - predicate: None mentioned in the text - object: None mentioned in the text - qualifier: None mentioned in the text - subject_qualifier: None mentioned in the text - object_qualifier: None mentioned in the text - diseases: - - MONDO:0005052 - - MONDO:0005101 - - MONDO:0016063 - cellular_process: - - None mentioned in the text - disease_cellular_process_relationships: - - subject: None mentioned in the text - predicate: None mentioned in the text - object: None mentioned in the text - qualifier: None mentioned in the text - subject_qualifier: None mentioned in the text - object_qualifier: None mentioned in the text -named_entities: - - id: MONDO:0005052 - label: Inflammatory bowel disease (IBD) - - id: MONDO:0005101 - label: Ulcerative colitis (UC) - - id: MONDO:0016063 - label: Crohn's disease (CD) -input_text: |- - Title: Whipple's Disease; An Overlooked Diagnosis. - Keywords: COVID-19; Malabsorption syndrome; Whipple disease - PMID: 37546505 - Abstract: Whipple disease is a rare multisystem inflammatory disease. Because fewer than 1000 reported cases have been described, clinical experience with this disorder is sparse. We are reporting a case of a 46-year-old man who presented with fever, weight loss, and polyarthralgia for 2 months, and 1 month of diarrhea. The patient was thoroughly investigated for collagen diseases and COVID-19, with no definite diagnosis. A therapeutic trial by immunosuppressive drugs provided partial remission followed by a marked rebound of the symptoms. His occult blood in stool was positive and subsequent upper endoscopy with proximal small intestinal biopsies showed the pathological features of Whipple's disease. The patient showed a dramatic improvement following treatment with ceftriaxone and trimethoprim-sulfamethoxazole. Despite the rarity of Whipple's disease, its course mimics many rheumatological diseases, inflammatory bowel disease, and COVID-19 disease. It should always be a part of the differential diagnosis of obscure polyarthralgia and chronic diarrhea.© 2023 Middle East Journal of Digestive Diseases. -raw_completion_output: |- - genes: not mentioned in the text - exposures: not mentioned in the text - gene_exposures_relationships: not mentioned in the text - diseases: Whipple's disease; COVID-19; Malabsorption syndrome - cellular_process: not mentioned in the text - disease_cellular_process_relationships: not mentioned in the text -prompt: |+ - Split the following piece of text into fields in the following format: - - subject: - predicate: - object: - qualifier: - subject_qualifier: - object_qualifier: - - - Text: - not mentioned in the text - - === - -extracted_object: - genes: - - not mentioned in the text - exposures: - - not mentioned in the text - gene_exposures_relationships: - - subject: not mentioned in the text - predicate: not mentioned in the text - object: not mentioned in the text - qualifier: not mentioned in the text - subject_qualifier: not mentioned in the text - object_qualifier: not mentioned in the text - diseases: - - MONDO:0005116 - - MONDO:0100096 - - MONDO:0020598 - cellular_process: - - not mentioned in the text - disease_cellular_process_relationships: - - subject: not mentioned - predicate: not mentioned - object: not mentioned - qualifier: not mentioned - subject_qualifier: not mentioned - object_qualifier: not mentioned -named_entities: - - id: MONDO:0005116 - label: Whipple's disease - - id: MONDO:0100096 - label: COVID-19 - - id: MONDO:0020598 - label: Malabsorption syndrome -input_text: |- - Title: Bowel-associated dermatosis-arthritis syndrome (BADAS): a narrative review. - Keywords: bacterial translocation; bariatric surgery; bowel-associated dermatosis-arthritis syndrome; inflammatory bowel disease; neutrophilic dermatosis - PMID: 37545820 - Abstract: Bowel-associated dermatosis-arthritis syndrome is a neutrophilic dermatosis presenting with flu-like symptoms, arthritis and skin lesions. The type of skin presentation varies although typically consists of red patches progressing into papulopustular-type lesions. Initially, the pathogenesis of the disease was linked exclusively to bariatric surgery, but more recent reports indicate the role of gastrointestinal diseases resulting in bacterial overgrowth and consequent translocation of bacteria into the bloodstream. The disease may resolve spontaneously, however sometimes requires a treatment aimed at managing inflammation and excessive bacterial overgrowth, and therefore antibiotic therapy, immunosuppressive drugs, biological treatment and sometimes intestinal surgeries are applied.Copyright: © 2023 Termedia Sp. z o. o. -raw_completion_output: |- - genes: Not mentioned in the text - exposures: bacterial translocation; bariatric surgery; inflammatory bowel disease; gastrointestinal diseases; bacterial overgrowth - gene_exposures_relationships: Not mentioned in the text - diseases: Bowel-associated dermatosis-arthritis syndrome; neutrophilic dermatosis - cellular_process: Not mentioned in the text - disease_cellular_process_relationships: Not mentioned in the text -prompt: |+ - Split the following piece of text into fields in the following format: - - subject: - predicate: - object: - qualifier: - subject_qualifier: - object_qualifier: - - - Text: - Not mentioned in the text - - === - -extracted_object: - genes: - - Not mentioned in the text - exposures: - - bacterial translocation - - bariatric surgery - - inflammatory bowel disease - - gastrointestinal diseases - - bacterial overgrowth - gene_exposures_relationships: - - subject: Not mentioned in the text - predicate: Not mentioned in the text - object: Not mentioned in the text - qualifier: Not mentioned in the text - subject_qualifier: Not mentioned in the text - object_qualifier: Not mentioned in the text - diseases: - - Bowel-associated dermatosis-arthritis syndrome - - neutrophilic dermatosis - cellular_process: - - Not mentioned in the text -input_text: |- - Title: Stigma and its correlates among patients with Crohn's disease: A cross-sectional study in China. - Keywords: China; Crohn’s disease; Self-efficacy; Social support; Stigma - PMID: 37545781 - Abstract: Crohn's disease is an incurable disease characterized by unpredictable intestinal symptoms, which unavoidably affect patients' lives and contribute to feelings of stigma. This study aimed to explore the status and its correlates of stigma among patients with Crohn's disease.Using a convenience sampling, 146 hospitalized patients with Crohn's disease were recruited in a tertiary hospital in Southern China from October 2020 to March 2021. The participants were assessed by demographic and disease-related questionnaires, the Social Impact Scale (SIS), Inflammatory Bowel Disease-Self-Efficacy Scale (IBD-SES), and Social Support Rating Scale (SSRS). Multivariate linear regression analysis was conducted to explore the influencing factors of stigma among patients with Crohn's disease.The mean SIS score was 58.14 ± 10.74, representing a moderate effect of stigma, and 85.6% (125/146) of the patients experienced moderate to high levels of stigma. The multiple linear regression analysis showed that perceived public awareness of the disease, family income, age, and self-efficacy were the main influencing factors of stigma, which could explain 52% of the total variation of stigma among patients with Crohn's disease.Stigma among patients with Crohn's disease is influenced by perceived public awareness of the disease, family income, age, and self-efficacy. Interventions aimed at improving self-efficacy and public awareness should be considered to alleviate the level of stigma, especially for those aged 40 years or older or low-income patients.© 2023 The Authors. -raw_completion_output: |- - genes: No genes mentioned in the text. - exposures: No exposures mentioned in the text. - gene_exposures_relationships: No gene-exposure relationships mentioned in the text. - diseases: Crohn's disease - cellular_process: No cellular processes mentioned in the text. - disease_cellular_process_relationships: No disease-cellular process relationships mentioned in the text. -prompt: |+ - From the text below, extract the following entities in the following format: - - subject: - predicate: - object: - qualifier: - subject_qualifier: - object_qualifier: - - - Text: - No disease-cellular process relationships mentioned in the text. - - === - -extracted_object: - genes: - - No genes mentioned in the text. - exposures: - - No exposures mentioned in the text. - gene_exposures_relationships: - - subject: No gene-exposure relationships mentioned in the text. - predicate: None - object: None - qualifier: None - subject_qualifier: None - object_qualifier: None - diseases: - - MONDO:0005011 - cellular_process: - - No cellular processes mentioned in the text. - disease_cellular_process_relationships: - - subject: None - predicate: None - object: None - qualifier: None - subject_qualifier: None - object_qualifier: None -named_entities: - - id: MONDO:0005011 - label: Crohn's disease -input_text: |- - Title: Bile acids and their receptors: Potential therapeutic targets in inflammatory bowel disease. - Keywords: Bile acid metabolism; Bile acid receptors; Bile acids; Gut microbiota; Inflammatory bowel disease; Intestinal immunology - PMID: 37545642 - Abstract: Chronic and recurrent inflammatory disorders of the gastrointestinal tract caused by a complex interplay between genetics and intestinal dysbiosis are called inflammatory bowel disease. As a result of the interaction between the liver and the gut microbiota, bile acids are an atypical class of steroids produced in mammals and traditionally known for their function in food absorption. With the development of genomics and metabolomics, more and more data suggest that the pathophysiological mechanisms of inflammatory bowel disease are regulated by bile acids and their receptors. Bile acids operate as signalling molecules by activating a variety of bile acid receptors that impact intestinal flora, epithelial barrier function, and intestinal immunology. Inflammatory bowel disease can be treated in new ways by using these potential molecules. This paper mainly discusses the increasing function of bile acids and their receptors in inflammatory bowel disease and their prospective therapeutic applications. In addition, we explore bile acid metabolism and the interaction of bile acids and the gut microbiota.©The Author(s) 2023. Published by Baishideng Publishing Group Inc. All rights reserved. -raw_completion_output: |- - genes: N/A - exposures: bile acids; gut microbiota - gene_exposures_relationships: N/A - diseases: inflammatory bowel disease - cellular_process: bile acid metabolism; epithelial barrier function; intestinal immunology - disease_cellular_process_relationships: inflammatory bowel disease to bile acid metabolism; inflammatory bowel disease to epithelial barrier function; inflammatory bowel disease to intestinal immunology -prompt: |+ - Split the following piece of text into fields in the following format: - - subject: - predicate: - object: - qualifier: - subject_qualifier: - object_qualifier: - - - Text: - inflammatory bowel disease to intestinal immunology - - === - -extracted_object: - genes: - - N/A - exposures: - - CHEBI:3098 - - gut microbiota - gene_exposures_relationships: - - subject: N/A - predicate: N/A - object: N/A - qualifier: N/A - subject_qualifier: N/A - object_qualifier: N/A - diseases: - - MONDO:0005265 - cellular_process: - - GO:0008206 - - epithelial barrier function - - intestinal immunology - disease_cellular_process_relationships: - - subject: MONDO:0005265 - predicate: to - object: GO:0008206 - - subject: MONDO:0005265 - predicate: to - object: epithelial barrier function - qualifier: N/A - subject_qualifier: N/A - object_qualifier: N/A - - subject: MONDO:0005265 - predicate: to - object: intestinal immunology -named_entities: - - id: CHEBI:3098 - label: bile acids - - id: MONDO:0005265 - label: inflammatory bowel disease - - id: GO:0008206 - label: bile acid metabolism -input_text: |- - Title: Azathioprine monotherapy withdrawal in inflammatory bowel diseases: A retrospective mono-centric study. - Keywords: Azathioprine; Crohn's Disease; Inflammatory bowel diseases; Relapse; Side effects; Ulcerative Colitis - PMID: 37545640 - Abstract: There is no consensus on the recommended duration of and optimal time to stop azathioprine (AZA) therapy in inflammatory bowel disease (IBD). Determining the optimal duration and cessation time can help to balance the risks of long-term intake with the possibility of relapse after cessation.To describe the events following AZA cessation.Retrospective analysis was performed to examine data from adult patients affected by IBD who were followed at the University of Padua and had started but then discontinued AZA between 1995 and 2022. Data on therapy duration, reasons for cessation, and type of relapse after cessation were collected. Cox regression models were used to estimate the risk of relapse in different subgroups.A total of 133 ulcerative colitis patients and 141 Crohn's disease patients were included. Therapy with AZA was stopped in the 1st year in approximately 34% of patients but was continued for more than 10 years in approximately 10% of cases. AZA discontinuation was due to primary failure or disease relapse in 30% of patients and due to disease remission in 25.2% of patients. Most of the remaining cases stopped AZA therapy due to side effects (primarily clinical intolerance, cytopenia, and pancreatic disease). Patients who stopped AZA for clinical remission had an 83% lower risk of relapse during the observation time than other groups, with a relapse-free rate of 89% after 1 year and 79% after 2 years.AZA administration is effective and safe, but it requires careful monitoring for potential minor and major side effects. Only 10% of patients who achieved remission with AZA needed a new treatment within 1 year of drug interruption.©The Author(s) 2023. Published by Baishideng Publishing Group Inc. All rights reserved. -raw_completion_output: |- - genes: N/A - exposures: Azathioprine - gene_exposures_relationships: N/A - diseases: Crohn's Disease, Inflammatory bowel diseases, Ulcerative Colitis - cellular_process: N/A - disease_cellular_process_relationships: N/A -prompt: |+ - Split the following piece of text into fields in the following format: - - subject: - predicate: - object: - qualifier: - subject_qualifier: - object_qualifier: - - - Text: - N/A - - === - -extracted_object: - genes: - - N/A - exposures: - - CHEBI:2948 - gene_exposures_relationships: - - subject: N/A - predicate: N/A - object: N/A - qualifier: N/A - subject_qualifier: N/A - object_qualifier: N/A - diseases: - - Crohn's Disease, Inflammatory bowel diseases, Ulcerative Colitis - cellular_process: - - N/A - disease_cellular_process_relationships: - - subject: N/A - predicate: N/A - object: N/A - qualifier: N/A - subject_qualifier: N/A - object_qualifier: N/A -named_entities: - - id: CHEBI:2948 - label: Azathioprine -input_text: |- - Title: Niacin modulates depressive-like behavior in experimental colitis through GPR109A-dependent mechanisms. - Keywords: BBB; DSS; Depression; GPR109A; Niacin; Sirt1 - PMID: 37544378 - Abstract: Depression is one of the common neurological comorbidities in patients with inflammatory bowel disease (IBD). The current study aimed to investigate the potential impact of niacin on colitis-induced depressive-like behavior in rats.Animals were given 5 % dextran sulfate sodium (DSS) in drinking water for one week to induce colitis. Niacin (80 mg/kg), with or without mepenzolate bromide (GPR109A blocker), was administered once per day throughout the experimental period. Rats were tested for behavioral changes using open field and forced swimming tests.Niacin significantly ameliorated DSS-induced behavioral deficits and alleviated macroscopic and microscopic colonic inflammatory changes. It also augmented the hippocampal levels of ZO-1, occludin, and claudin-5 proteins, indicating the ability of niacin to restore the blood-brain barrier (BBB) integrity. Moreover, niacin decreased hippocampal IL-1ꞵ and NF-ĸB contents but increased GSH, Sirt-1, Nrf-2, HO-1 concentrations. All these beneficial effects were partially abolished by the co-administration of mepenzolate bromide.The neuroprotective effect of niacin against DSS-induced depressive-like behavior was partially mediated through GPR109A-mediated mechanisms. Such mechanisms are also involved in modulating neuronal oxidative stress and inflammation via Sirt-1/Nrf-2/HO-1 signaling pathways.Copyright © 2023. Published by Elsevier Inc. -raw_completion_output: |- - genes: Sirt1, Nrf-2, HO-1, IL-1ꞵ, NF-ĸB - exposures: niacin, mepenzolate bromide, dextran sulfate sodium (DSS) - gene_exposures_relationships: niacin-GPR109A; mepenzolate bromide-GPR109A; DSS-colitis - diseases: depression, inflammatory bowel disease (IBD) - cellular_process: blood-brain barrier (BBB) integrity, oxidative stress, inflammation - disease_cellular_process_relationships: depression-BBB integrity, depression-oxidative stress, depression-inflammation, IBD-BBB integrity, IBD-oxidative stress, IBD-inflammation -prompt: |+ - From the text below, extract the following entities in the following format: - - subject: - predicate: - object: - qualifier: - subject_qualifier: - object_qualifier: - - - Text: - depression-BBB integrity, depression-oxidative stress, depression-inflammation, IBD-BBB integrity, IBD-oxidative stress, IBD-inflammation - - === - -extracted_object: - genes: - - Sirt1, Nrf-2, HO-1, IL-1ꞵ, NF-ĸB - exposures: - - CHEBI:191875 - gene_exposures_relationships: - - subject: niacin-GPR109A - object: HGNC:24827 - subject_qualifier: niacin - - subject: CHEBI:6753 - predicate: '-' - object: HGNC:24827 - qualifier: '-' - subject_qualifier: '-' - object_qualifier: '-' - - subject: DSS-colitis - diseases: - - MONDO:0005052 - cellular_process: - - blood-brain barrier (BBB) integrity, oxidative stress, inflammation - disease_cellular_process_relationships: - - subject: MONDO:0005052 - predicate: inflammation -named_entities: - - id: CHEBI:191875 - label: niacin, mepenzolate bromide, dextran sulfate sodium (DSS) - - id: HGNC:24827 - label: GPR109A - - id: CHEBI:6753 - label: mepenzolate bromide - - id: MONDO:0005052 - label: depression, inflammatory bowel disease (IBD) -input_text: |- - Title: Body Composition in Inflammatory Bowel Disease. - Keywords: Body composition; Clinical outcomes; Inflammatory bowel disease; Treatment strategies - PMID: 37543940 - Abstract: Inflammatory bowel disease (IBD) is associated with body composition changes, which are associated with clinical prognosis, response to therapy, and quality of life in IBD patients. Therefore, it is critical to review the body composition distribution in IBD, summarize the potential factors affecting body composition distribution, and take steps to improve the body composition distribution of IBD patients as early as possible. In the current review, we searched PubMed via keywords 'inflammatory bowel disease', or 'IBD', or 'Crohn's disease', or 'CD', or 'ulcerative colitis', or 'UC', and 'body composition'. Malnutrition and sarcopenia are common in IBD patients and are associated with the clinical course, prognosis, and need for surgery. Disease activity, reduced nutrition intake, vitamin D deficiency, and intestinal dysbiosis are factors contributing to changed body composition. Early use of biological agents to induce remission is critical to improving body composition distribution in IBD patients, supplementation of vitamin D is also important, and moderate physical activity is recommended in IBD patients with clinical remission.© 2023 The Author(s). This is an open-access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. -raw_completion_output: |- - genes: Not mentioned in the text - exposures: vitamin D deficiency, intestinal dysbiosis - gene_exposures_relationships: Not mentioned in the text - diseases: Inflammatory bowel disease, Crohn's disease, ulcerative colitis - cellular_process: Not mentioned in the text - disease_cellular_process_relationships: Not mentioned in the text -prompt: |+ - Split the following piece of text into fields in the following format: - - subject: - predicate: - object: - qualifier: - subject_qualifier: - object_qualifier: - - - Text: - Not mentioned in the text - - === - -extracted_object: - genes: - - Not mentioned in the text - exposures: - - vitamin D deficiency, intestinal dysbiosis - gene_exposures_relationships: - - subject: Not mentioned in the text - predicate: Not mentioned in the text - object: Not mentioned in the text - qualifier: Not mentioned in the text - subject_qualifier: Not mentioned in the text - object_qualifier: Not mentioned in the text - diseases: - - Inflammatory bowel disease, Crohn's disease, ulcerative colitis - cellular_process: - - Not mentioned in the text -input_text: |- - Title: Economic Burden of Inflammatory Bowel Disease in Shiraz, Iran. - Keywords: Direct costs; Economic burden; Indirect costs; Inflammatory bowel diseases - PMID: 37543918 - Abstract: The epidemiological burden of chronic diseases and their risk factors is increasing all over the world, especially in developing and low-income countries. Inflammatory bowel disease (IBD) is one of the chronic diseases which has imposed a great financial burden on individuals and the society.The current study aimed at estimating the economic burden of IBD among 90 patients with IBD who referred to Namazi hospital and Motahari clinic of Shiraz in 2019. The costs to patients were monitored for a year to detect their expenses.This study is descriptive cross-sectional and from a social perspective. The cost-of-illness method, based on the human capital theory, has been used. Both direct and indirect costs have been estimated using a prevalence approach and bottom-up method. Hospital costs were extracted from patients' records and the accounting system of Namazi Hospital. Outpatient expenses were obtained according to the number of outpatient visits and the average cost of visit were obtained by interviewing patients. Socio-economic status, medical expenses and number of days absent from work were determined using a valid and reliable questionnaire. Assessment of the cost of hospital care was made on the basis of the average daily. Non-medical direct costs such as transportation and residence, etc. were also calculated.The total annual economic costs of IBD per patient were estimated at 1229.74 USD. Finally, increased use of health care as well as lost productivity leads to increased disease costs.IBD imposes a substantial economic burden on patients, families and the society. Establishing a correct diagnosis early, management of IBD worsening, and appropriate treatment can reduce the costs of treatment and lost production to some extent. Therefore, policymakers should take this into consideration and according to available health resources, provide services and facilities for the prevention and treatment of the disease.© 2023 The Author(s). This is an open-access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. -raw_completion_output: |- - genes: N/A - exposures: N/A - gene_exposures_relationships: N/A - diseases: Inflammatory bowel disease (IBD) - cellular_process: N/A - disease_cellular_process_relationships: N/A -prompt: |+ - Split the following piece of text into fields in the following format: - - subject: - predicate: - object: - qualifier: - subject_qualifier: - object_qualifier: - - - Text: - N/A - - === - -extracted_object: - genes: - - N/A - exposures: - - N/A - gene_exposures_relationships: - - subject: N/A - predicate: N/A - object: N/A - qualifier: N/A - subject_qualifier: N/A - object_qualifier: N/A - diseases: - - MONDO:0005052 - cellular_process: - - N/A - disease_cellular_process_relationships: - - subject: N/A - predicate: N/A - object: N/A - qualifier: N/A - subject_qualifier: N/A - object_qualifier: N/A -named_entities: - - id: MONDO:0005052 - label: Inflammatory bowel disease (IBD) diff --git a/docs/custom.md b/docs/custom.md deleted file mode 100644 index 648c5b6f7..000000000 --- a/docs/custom.md +++ /dev/null @@ -1,481 +0,0 @@ -# Custom Schemas - -## Build a custom schema - -Define a schema (using a subset of [LinkML](https://linkml.io)) that describes the structure in which you want to extract knowledge from your text. - -There are a number of pre-defined LinkML data models already developed here - [src/ontogpt/templates/](src/ontogpt/templates/) which you can use as reference when creating your own data models. - -### The header - -The header of the schema defines metadata, parameters instructing LinkML to interpret prefixes in specific ways, and names of imports. - -You will find these fields in the schema header: - -* `id`: A unique identifier for the schema. These may take the form of W3IDs like `http://w3id.org/ontogpt/schemaname`. -* `name`: Name of the schema. Should resemble the filename. -* `title`: Title of the schema for human readability. -* `description`: A human readable description of the schema. Detail is welcome! -* `license`: A license indicating reusability of the schema. We prefer a [CC0 license](https://creativecommons.org/publicdomain/zero/1.0/). -* `prefixes`: This is a list (actually a dictionary, as each item contains a key and a value) of short prefixes for the identifier namespaces used in the schema along with their corresponding identifier prefixes. At minimum, this shoulc include `linkml: https://w3id.org/linkml/` and the prefix for your schema itself. If the schema is named `salmon`, this will be something like `salmon: http://w3id.org/ontogpt/salmon/`. If you're using Gene Ontology identifiers, specify their prefixes as `GO: http://purl.obolibrary.org/obo/GO_`, because each Gene Ontology term has an identifier prefixed with `GO:`. -* `default_prefix`: This is the prefix for your schema. It should match what you used in the `prefixes` list, so following the above example, that would be `salmon`. -* `default_range`: This is the default data type LinkML will assume each class should be unless specified otherwise. Using `string` is usually safe. - -* `imports`: A list of other schemas to import types from. These may be any schemas in the same directory (e.g., if you have another schema named `francine` then you may simply include `francine` in the list of imports) but note that LinkML will raise an error if multiple classes have the same name across the imports. Minimally, this list should include `linkml:types` and `core` to import the base LinkML data types and the generic OntoGPT classes, respectively. - -An example: - -```yaml -id: http://w3id.org/ontogpt/gocam -name: gocam-template -title: GO-CAM Template -description: >- - A template for GO-CAMs -license: https://creativecommons.org/publicdomain/zero/1.0/ -prefixes: - linkml: https://w3id.org/linkml/ - gocam: http://w3id.org/ontogpt/gocam/ - GO: http://purl.obolibrary.org/obo/GO_ - CL: http://purl.obolibrary.org/obo/CL_ - -default_prefix: gocam -default_range: string - -imports: - - linkml:types - - core -``` - -### The classes - -The classes in the schema define the "things" you are interested in extracting. LinkML doesn't make many assumptions about the difference between a class and a relationship, a node and an edge, or a relation and a property. It's designed to be flexibile enough to handle a variety of data models. - -The start of this section is indicated by `classes:`. - -A minimal class may look like this: - -```yaml - ClassName: - is_a: NamedEntity - attributes: - entity: - range: string - description: >- - A named entity. -``` - -In practice, this class won't do much, as it doesn't contain much for OntoGPT to work with or many instructions to form an LLM prompt out of. And that's fine, because we can do more. - -These fields may be used in classes: - -* `is_a`: This describes a hierarchical structure, so the value of this slot is the name of a LinkML class. `NamedEntity` is defined in OntoGPT's core schema and is will ensure extracted objects of this class have both unique identifiers and human readable labels. -* `tree_root`: If `true`, this class will be treated as the root of the data hierarchy. If you're planning to extract specific objects from a full text document, for example, it may be useful to define a class for the document to contain its metadata. This parent class could then be the `tree_root`. -* `attributes`: This slot defines all class attributes, and in OntoGPT, that means each will be included in a prompt for the LLM. Each attribute should have a unique, lowercased name. Attributes have their own slots: - * `description`: The attribute description to be *passed as part of the prompt*. This should describe the attribute and how it should be formatted in the generated output. Do not include references to specific identifiers here. - * `multivalued`: If `true`, any value for this attribute will be interpreted as a list. This is cruical if you expect multiple values in the extracted output and should be reflected in the description by indicating how each value should be separated. OntoGPT prefers semicolons. - * `range`: The class to restrict the object to. This may be an abstract data type like `string` or another class defined elsewhere in your schema, like `Gene` in the example below. -* `id_prefixes`: A list of identifiers to ground values of this class to. Usually specific to a class rather than an attribute. Use capitalized forms and omit the colon. If you want to ground to MeSH terms, for example, include the prefix `MESH`. -* `annotations`: This slot contains specific instructions for OntoGPT in its annotation and grounding operations. The heading `annotators`, placed under this slot, must contain a comma separated list of value annotators provided by the Ontology Access Kit (OAK). [In OAK these are called *implementations* or *adapters* and there are many of them available.](https://incatools.github.io/ontology-access-kit/packages/implementations/index.html). Annotators are responsible for bridging the gap between raw text and unique identifier, though that process may involve searching a combination of term lists along with their synonyms and equivalents. - * OBO Foundry ontologies make great annotators. To use CHEBI for chemical names, for example, use the annotator `sqlite:obo:chebi` and include `CHEBI` in the `id_prefixes` list. - * Ontologies in BioPortal work well, too. They may be specified with the BioPortal ID. To use the EnvThes ecological thesaurus, for example, use the annotator `bioportal:ENVTHES` and the prefix `ENVTHES`. -* `slot_usage`: This slot can contain rules about how another slot may be restricted. In the example below, `GeneLocation` has values for its `id` slot restricted to values within two different *enums*. See the next section for more information on how to use enums. - -An example, continuing from where the header left off: - -```yaml -classes: - GoCamAnnotations: - tree_root: true - attributes: - genes: - description: semicolon-separated list of genes - multivalued: true - range: Gene - organisms: - description: semicolon-separated list of organism taxons - multivalued: true - range: Organism - gene_organisms: - annotations: - prompt: semicolon-separated list of asterisk separated gene to organism relationships - multivalued: true - range: GeneOrganismRelationship - activities: - description: semicolon-separated list of molecular activities - multivalued: true - range: MolecularActivity - gene_functions: - description: semicolon-separated list of gene to molecular activity relationships - multivalued: true - range: GeneMolecularActivityRelationship - cellular_processes: - description: semicolon-separated list of cellular processes - multivalued: true - range: CellularProcess - pathways: - description: semicolon-separated list of pathways - multivalued: true - range: Pathway - gene_gene_interactions: - description: semicolon-separated list of gene to gene interactions - multivalued: true - range: GeneGeneInteraction - gene_localizations: - description: >- - semicolon-separated list of genes plus their location in the cell; - for example, "gene1 / cytoplasm; gene2 / mitochondrion" - multivalued: true - range: GeneSubcellularLocalizationRelationship - - Gene: - is_a: NamedEntity - id_prefixes: - - HGNC - - PR - - UniProtKB - annotations: - annotators: gilda:, bioportal:hgnc-nr - Pathway: - is_a: NamedEntity - id_prefixes: - - GO - - PW - annotations: - annotators: sqlite:obo:go, sqlite:obo:pw - CellularProcess: - is_a: NamedEntity - id_prefixes: - - GO - annotations: - annotators: sqlite:obo:go - MolecularActivity: - is_a: NamedEntity - id_prefixes: - - GO - annotations: - annotators: sqlite:obo:go - GeneLocation: - is_a: NamedEntity - id_prefixes: - - GO - - CL - - UBERON - annotations: - annotators: "sqlite:obo:go, sqlite:obo:cl" - slot_usage: - id: - values_from: - - GOCellComponentType - - CellType - Organism: - is_a: NamedEntity - id_prefixes: - - NCBITaxon - - EFO - annotations: - annotators: gilda:, sqlite:obo:ncbitaxon - Molecule: - is_a: NamedEntity - id_prefixes: - - CHEBI - - PR - annotations: - annotators: gilda:, sqlite:obo:chebi - - GeneOrganismRelationship: - is_a: CompoundExpression - attributes: - gene: - range: Gene - organism: - range: Organism - - GeneMolecularActivityRelationship: - is_a: CompoundExpression - attributes: - gene: - range: Gene - annotations: - prompt: the name of the gene in the pair. This comes first. - molecular_activity: - range: MolecularActivity - annotations: - prompt: the name of the molecular function in the pair. This comes second. May be a GO term. - - GeneMolecularActivityRelationship2: - is_a: CompoundExpression - attributes: - gene: - range: Gene - annotations: - prompt: the name of the gene. - molecular_activity: - range: MolecularActivity - annotations: - prompt: the name of the molecular activity, for example, ubiquitination. May be a GO term. - target: - range: Molecule - annotations: - prompt: the name of the molecular entity that is the target of the molecular activity. - - GeneSubcellularLocalizationRelationship: - is_a: CompoundExpression - attributes: - gene: - range: Gene - location: - range: GeneLocation - - GeneGeneInteraction: - is_a: CompoundExpression - attributes: - gene1: - range: Gene - gene2: - range: Gene -``` - -### Enums - -LinkML supports defining *enums*, or sets of values. In OntoGPT this allows schemas to work with subsets of identifiers. Enums have their own hierarchy. In the example below, the `reachable_from` slot is used to define sets of values: in `GOCellComponentType` these are all children of the GO term with the ID `GO:0005575` (cellular component), so restricting a set of identifiers based on this enum will ensure they all correspond to cellular components. - -Example, starting where the classes left off above: - -```yaml -enums: - - GeneLocationEnum: - inherits: - - GOCellComponent - - CellType - - GOCellComponentType: - reachable_from: - source_ontology: obo:go - source_nodes: - - GO:0005575 ## cellular_component - CellType: - reachable_from: - source_ontology: obo:cl - source_nodes: - - CL:0000000 ## cell -``` - -### Schema design tips - -It helps to have an understanding of the [LinkML](https://linkml.io) schema language, but it should be possible to define your own schemas using the examples in [src/ontogpt/templates](src/ontogpt/templates/) as a guide. - -* Prompt hints can be specified using the `prompt` annotation (otherwise description is used) -* Multivalued fields are supported -* The default range is string — these are not grounded. Ex.: disease name, synonyms -* Define a class for each `NamedEntity` -* For any `NamedEntity`, you can specify a preferred annotator using the `annotators` annotation - -We recommend following an established schema like [BioLink Model](https://github.com/biolink/biolink-model), but you can define your own. - -Once you have defined your own schema / data model and placed in the correct directory, you can run the `extract` command. - -Ex.: - -```bash -ontogpt extract -t mendelian_disease.MendelianDisease -i marfan-wikipedia.txt -``` - -OntoGPT-specific extensions are specified as *annotations*. - -You can specify a set of annotators for a field using the `annotators` annotation. - -Ex.: - -```yaml - Gene: - is_a: NamedThing - id_prefixes: - - HGNC - annotations: - annotators: gilda:, bioportal:hgnc-nr, obo:pr -``` - -The annotators are applied in order. - -Additionally, when performing grounding, the following measures can be taken to improve accuracy: - -* Specify the valid set of ID prefixes using `id_prefixes` -* Some vocabularies have structural IDs that are amenable to regexes, you can specify these using `pattern` -* You can make use of `values_from` slot to specify a [Dynamic Value Set](https://linkml.io/linkml/schemas/enums.html#dynamic-enums) - * For example, you can constrain the set of valid locations for a gene product to be subclasses of `cellular_component` in GO or `cell` in CL - -Ex.: - -```yaml -classes: - ... - GeneLocation: - is_a: NamedEntity - id_prefixes: - - GO - - CL - annotations: - annotators: "sqlite:obo:go, sqlite:obo:cl" - slot_usage: - id: - values_from: - - GOCellComponentType - - CellType - -enums: - GOCellComponentType: - reachable_from: - source_ontology: obo:go - source_nodes: - - GO:0005575 ## cellular_component - CellType: - reachable_from: - source_ontology: obo:cl - source_nodes: - - CL:0000000 ## cell -``` - -#### Multiple levels of nesting - -Currently no more than two levels of nesting are recommended. - -If a field has a range which is itself a class and not a primitive, it will attempt to nest. - -Ex. the `gocam` schema has an attribute: - -```yaml - attributes: - ... - gene_functions: - description: semicolon-separated list of gene to molecular activity relationships - multivalued: true - range: GeneMolecularActivityRelationship -``` - -The range `GeneMolecularActivityRelationship` has been specified *inline*, so it will nest. - -The generated prompt is: - -```bash -gene_functions : -``` - -The output of this is then passed through further SPIRES iterations. - -#### Text length limit - -LLMs have context sizes limiting the combined length of their inputs and outputs. The `gpt-3.5-turbo` model, for example, has a 4,096 token limit (prompt + completion), while the `gpt-3.5-turbo-16k` model has a larger context of 16,384 tokens. - -## Advanced functionality with linkml-owl - -A LinkML schema used in OntoGPT may include annotations describing how each component relates to OWL syntax. - -This level of detail may be necessary if your data model includes complex logic beyond simple hierarchical relationships. - -For example, if you are extracting details of chemical reactions, it may be necessary to keep track of details like stoichiometry or charge. [See a relevant example here](https://linkml.io/linkml-owl/templates/). - -Incorporating OWL annotations into the custom schema (remember to export using the `-O owl` option) also supports importing the results into an ontology editor like Protege, at which point it may be reasoned over. - -The `recipe` template in OntoGPT incorporates several OWL annotations: - -```yaml -classes: - Recipe: - tree_root: true - close_mappings: - - FOODON:00004081 - attributes: - url: - identifier: true - range: uriorcurie - slot_uri: rdf:Resource - annotations: - prompt.skip: true - label: - description: the name of the recipe - slot_uri: rdfs:label - annotations: - owl: AnnotationProperty, AnnotationAssertion - description: - description: a brief textual description of the recipe - slot_uri: dcterms:description - annotations: - owl: AnnotationProperty, AnnotationAssertion - categories: - description: a semicolon separated list of the categories to which this recipe belongs - range: RecipeCategory - multivalued: true - slot_uri: dcterms:subject - annotations: - owl: AnnotationAssertion - ingredients: - description: a semicolon separated list of the ingredients plus quantities of the recipe - multivalued: true - range: Ingredient - slot_uri: FOODON:00002420 - annotations: - owl: ObjectProperty, ObjectSomeValuesFrom - steps: - description: a semicolon separated list of the individual steps involved in this recipe - multivalued: true - range: Step - annotations: - owl: ObjectProperty, ObjectSomeValuesFrom - annotations: - owl: Class - owl.template: | - EquivalentClasses( - {{url}} - ObjectIntersectionOf( - recipe:Recipe - - {% for step in steps %} - ObjectSomeValuesFrom( - recipe:steps - {{tr(step)}} - ) - {% endfor %} - {% for ingredient in ingredients %} - ObjectSomeValuesFrom( - FOODON:00002420 - {{tr(ingredient)}} - ) - {% endfor %} - ) - ) -... -``` - -Several of the slots above, like `close_mappings` and `slot_uri`, aren't exclusive to OWL but define the parts of this data model in terms of existing vocabularies, so the schema and any extracted results will be more compatible with other models and methods. Here, `close_mappings` is used to show that the `Recipe` class is close but not necessarily identical to `FOODON:00004081`, or "food recipe". - -The `owl` slot under `annotations` for these attributes defines one or more corresponding OWL axiom types. Because the `label` attribute may be `AnnotationProperty, AnnotationAssertion` in OWL ([see the OWL2 syntax on Annotations](https://www.w3.org/TR/owl2-syntax/#Annotations)) we know it can be applied as a property for something else, like an axiom or a specific entity with an IRI. This is how the `rdfs:label` annotation property usually works so this isn't surprising. - -The `owl.template` slot defines template logic relating a Recipe to its component objects: steps and ingredients. It begins with an `EquivalentClasses` axiom to define the identifier of the recipe, which we assume to be a URL, as identical to the class expression in subsequent lines. Specifically, that `Recipe` must include both a series of steps (e.g., "fry", "chop", etc.) and a series of ingredients. The ingredients relate to the recipe through the property `FOODON:00002420`, or "has ingredient". - -Note that everything in {curly brackets} is a template of some kind. The Jinja template system is used in the example in lines like `{% for step in steps %}` where a loop is used. Template slots like `{{url}}` may be accessed directly with their names. So what makes `{{tr(step)}}` different from `{{step}}`? The `tr()` function used here translates its input into an OWL entity so it may be used to generate valid OWL axioms. - -See also: the [documentation page on OWL exports](owl_exports.md) and the [linkml-owl documentation](https://linkml.io/linkml-owl/). - -## Install a custom schema - -If you have installed OntoGPT directly from its GitHub repository, then you may install a custom schema like this: - -1. Move the schema file to the `src/ontogpt/templates` directory. -2. Run `make` from the root of the repository to generate Pydantic versions of the schema. - -If you have installed OntoGPT from `pip`, *or* if you can't use the `make` command, the process is similar, though it will depend on where the package is installed. - -1. Use the LinkML `gen-pydantic` tool to generate Pydantic classes. If your schema is named `alfred.yaml`, then run the following: - - ```bash - gen-pydantic --pydantic_version 2 alfred.yaml > alfred.py - ``` - -2. Move both the .yaml and the .py versions of your schema to the `templates` directory of wherever OntoGPT is installed. In a virtual environment named `temp` that may be something like `/temp/lib/python3.9/site-packages/ontogpt/templates`. - -You may then use the schema like any other. For example, if your schema is named `albatross.yaml`, then an extract command is: - -```bash -ontogpt extract -t albatross -i input.txt -``` diff --git a/docs/evaluations.md b/docs/evaluations.md index ccacb8f79..2a8c7a390 100644 --- a/docs/evaluations.md +++ b/docs/evaluations.md @@ -1,199 +1,3 @@ # Evaluations -OpenAI's functions have been evaluated on test data sets. - -All evaluation results include OpenAI cache databases (`openai_cache.db.gz`) as a reference of the prompts and responses obtained during the evaluation. This may be used by extracting the cache database to the root directory of the project. - -Tests may be run with the `eval` command followed by the test name, e.g., for the BC5CDR test below: - -```bash -ontogpt eval EvalCTD -``` - -By default, the evaluation will only be executed over a subset of the test corpus. - -The exact number of inputs to run the test over can be controlled with the `--num-tests` option, like this: - -```bash -ontogpt eval --num-tests 1 EvalCTD -``` - -To run the full set of tests, set `num-tests` to the input count for a given evaluation, as defined below. - -For each document, the evaluation process will attempt to process the full text without preprocessing. - -If the `--chunking` option is used, then the input text will instead be chunked into segments of a few tokens each, essentially creating new queries for each segment. This alternate strategy may impact test results and will result in longer run time. - -## BC5CDR - -*Test Name:* EvalCTD -*Input Count:* 500 - -Results for OntoGPT on the [BioCreative V Chemical Disease Relation Task (BC5CDR)](https://biocreative.bioinformatics.udel.edu/media/store/files/2015/BC5CDR_overview.final.pdf) are available on Zenodo here: - -Evaluation functions for BC5CDR are available in `src/ontogpt/evaluation/ctd/eval_ctd.py`. - -Note that the project also includes test and train data (`CDR_TestSet.BioC.xml.gz` and `CDR_TrainSet.BioC.xml.gz`, respectively) as well as a set of synonyms for MeSH terms (see `synonyms.yaml`). - -### Template - -This evaluation uses the following schema template: - -```yaml -id: http://w3id.org/ontogpt/ctd -name: ctd -title: Chemical to Disease Template -description: >- - A template for Chemical to Disease associations. - - This template is intended to represent associations between chemicals and diseases, - and for evaluating Semantic Llama against BioCreative V Chemical Disease - Relation (CDR) Task (BC5CDR). -see_also: - - https://biocreative.bioinformatics.udel.edu/media/store/files/2015/BC5CDR_overview.final.pdf - - https://academic.oup.com/database/article/doi/10.1093/database/baw068/2630414 -source: https://biocreative.bioinformatics.udel.edu/tasks/biocreative-v/track-3-cdr/ -license: https://creativecommons.org/publicdomain/zero/1.0/ -prefixes: - linkml: https://w3id.org/linkml/ - drug: http://w3id.org/ontogpt/drug/ - -default_prefix: drug -default_range: string - -imports: - - linkml:types - - core - -classes: - - ChemicalToDiseaseDocument: - description: A document that contains chemical to disease relations. - is_a: TextWithTriples - slot_usage: - triples: - range: ChemicalToDiseaseRelationship - annotations: - prompt: >- - A semi-colon separated list of chemical to disease relationships, where the relationship is either INDUCES - or TREATS. - for example: Lidocaine INDUCES cardiac asystole; - Hydroxychloroquine NOT TREATS COVID-19; - Methyldopa INDUCES Hypotension; - Monosodium Glutamate NOT INDUCES Headache; - Imatinib TREATS cancer - exclude: Lidocaine, cardiac asystole, Hydroxychloroquine, COVID-19, Methyldopa, Headache, Imatinib, cancer - - - ChemicalToDiseaseRelationship: - is_a: Triple - description: A triple where the subject is a chemical and the object is a disease. - slot_usage: - subject: - range: Chemical - description: >- - The chemical substance, drug, or small molecule. - For example: Lidocaine, Monosodium Glutamate, Imatinib. - object: - range: Disease - description: >- - The disease or condition that is being treated or induced by the chemical. - For example, asthma, cancer, covid-19, cardiac asystole, Hypotension, Headache. - predicate: - range: ChemicalToDiseasePredicate - description: The relationship type, e.g. INDUCES, TREATS. - subject_qualifier: - range: NamedEntity - description: >- - An optional qualifier or modifier for the chemical, e.g. "high dose" or "intravenously administered" - object_qualifier: - range: NamedEntity - description: >- - An optional qualifier or modifier for the disease, e.g. "severe" or "with additional complications" - - Disease: - is_a: NamedEntity - annotations: - annotators: "sqlite:obo:mesh, sqlite:obo:mondo, sqlite:obo:hp, sqlite:obo:ncit, sqlite:obo:doid, bioportal:meddra" - prompt.examples: cardiac asystole, COVID-19, Headache, cancer - id_prefixes: - - MESH - slot_usage: - id: - pattern: "^MESH:[CD][0-9]{6}$" - values_from: - - MeshDiseaseIdentifier - - Chemical: - is_a: NamedEntity - annotations: - annotators: "sqlite:obo:mesh, sqlite:obo:chebi, sqlite:obo:ncit, bioportal:mdm, sqlite:obo:drugbank, gilda:" - prompt.examples: Lidocaine, Hydroxychloroquine, Methyldopa, Imatinib - id_prefixes: - - MESH - slot_usage: - id: - pattern: "^MESH:[CD][0-9]{6}$" - values_from: - - MeshChemicalIdentifier - - ChemicalToDiseasePredicate: - is_a: RelationshipType - description: >- - A predicate for chemical to disease relationships - comments: - - for the purposes of evaluation against BC5CDR, any predicate other than INDUCES is ignored. - -enums: - - MeshChemicalIdentifier: - reachable_from: - source_ontology: obo:mesh - source_nodes: - - MESH:D000602 ## Amino Acids, Peptides, and Proteins - - MESH:D001685 ## Biological Factors - - MESH:D002241 ## Carbohydrates - - MESH:D004364 ## Pharmaceutical Preparations - - MESH:D006571 ## Heterocyclic Compounds - - MESH:D007287 ## Inorganic Chemicals - - MESH:D008055 ## Lipids - - MESH:D009706 ## Nucleic Acids, Nucleotides, and Nucleosides - - MESH:D009930 ## Organic Chemicals - - MESH:D011083 ## Polycyclic Compounds - - MESH:D013812 ## Therapeutics - - MESH:D019602 ## Food and Beverages - - MESH:D045424 ## Complex Mixtures - - MESH:D045762 ## Enzymes and Coenzymes - - MESH:D046911 ## Macromolecular Substances - MeshDiseaseIdentifier: - reachable_from: - source_ontology: obo:mesh - source_nodes: - - MESH:D001423 ## Bacterial Infections and Mycoses - - MESH:D001523 ## Mental Disorders - - MESH:D002318 ## Cardiovascular Diseases - - MESH:D002943 ## Circulatory and Respiratory Physiological Phenomena - - MESH:D004066 ## Digestive System Diseases - - MESH:D004700 ## Endocrine System Diseases - - MESH:D005128 ## Eye Diseases - - MESH:D005261 ## Female Urogenital Diseases and Pregnancy Complications - - MESH:D006425 ## Hemic and Lymphatic Diseases - - MESH:D007154 ## Immune System Diseases - - MESH:D007280 ## Disorders of Environmental Origin - - MESH:D009057 ## Stomatognathic Diseases - - MESH:D009140 ## Musculoskeletal Diseases - - MESH:D009358 ## Congenital, Hereditary, and Neonatal Diseases and Abnormalities - - MESH:D009369 ## Neoplasms - - MESH:D009422 ## Nervous System Diseases - - MESH:D009750 ## Nutritional and Metabolic Diseases - - MESH:D009784 ## Occupational Diseases - - MESH:D010038 ## Otorhinolaryngologic Diseases - - MESH:D010272 ## Parasitic Diseases - - MESH:D012140 ## Respiratory Tract Diseases - - MESH:D013568 ## Pathological Conditions, Signs and Symptoms - - MESH:D014777 ## Virus Diseases - - MESH:D014947 ## Wounds and Injuries - - MESH:D017437 ## Skin and Connective Tissue Diseases - - MESH:D052801 ## Male Urogenital Diseases - - MESH:D064419 ## Chemically-Induced Disorders -``` +TODO diff --git a/docs/functions.md b/docs/functions.md index a38e48b21..2a6e3e5fe 100644 --- a/docs/functions.md +++ b/docs/functions.md @@ -1,796 +1,3 @@ -# OntoGPT Functions +# TALISMAN Functions -All OntoGPT functions are run from the command line. - -Precede all commands with `ontogpt`. - -To see the full list of available commands, run this: - -```bash -ontogpt --help -``` - -## Basic Parameters - -To see verbose output, run: - -```bash -ontogpt -v -``` - -The options `-vv` and `-vvv` will enable progressively more verbose output. - -### cache-db - -Use the option `--cache-db` to specify a path to a sqlite database to cache the prompt-completion results. - -### skip-annotator - -Use the option `--skip-annotator` to skip one or more annotators (e.g. `--skip-annotator gilda`). - -## Common Parameters - -The following options are available for most functions unless stated otherwise. - -### inputfile - -Use the option `--inputfile` to specify a path to a file containing input text. - -For the `extract` command, this may be a single file or a directory of files. - -In the latter case, all .txt files will be assumed to be input, and the path will *not* be parsed recursively. - -### template - -Use the option `--template` to specify a template to use. This is a required parameter. - -Only the name is required, without any filename suffix. - -To use the `gocam` template, for example, the parameter will be `--template gocam` - -This may be one of the templates included with OntoGPT or a custom template, but in the latter case, the schema, generated Pydantic classes, and any imported schemas should be present in the same location. - -### target-class - -Use the option `--target-class` to specify a class in a schema to treat as the root. - -If a schema does not already specify a root class, this is required. - -Alternatively, the target class can be specified as part of the `--template` option, like so: `--template mendelian_disease.MendelianDisease` - -### model - -Use the option `model` to specify the name of a large language model to be used. - -For example, this may be `--model gpt-4`. - -Consult the full list of available models with: - -```bash -ontogpt list-models -``` - -### recurse - -Use the option `recurse` to specify whether recursion should be used when parsing the schema. - -Recursion is on by default. - -Disable it with `--no-recurse`. - -### use-textract - -Use the option `use-textract` to specify whether to use the [textract](https://textract.readthedocs.io/en/stable/) package to extract text from the input document. Textract supports retrieving raw text from PDFs, images, audio, and a variety of other formats. - -Textract extraction is off by default. - -Enable it with `--use-textract`. - -### output - -Use the option `output` to provide a path to write an output file to. - -If this path is not provided, OntoGPT will write to stdout. - -### output-format - -Use the option `output-format` to specify the desired output file format. - -This may be one of: - -* html -* json -* jsonl -* md -* owl -* pickle -* turtle -* yaml - -### auto-prefix - -Use the option `auto-prefix` to define a prefix to use for entities without a matching namespace. - -When OntoGPT's extract functions find an entity matching the input schema but cannot ground it, the entity will still be included in the output. - -By default, these entities will be assigned identifiers like `AUTO:tangerine`. If you ground this term to the [Food Ontology](https://foodon.org), however, the entity may be `FOODON:00003488` instead. - -### show-prompt - -Use the option `show-prompt` to show _all_ prompts constructed and sent to the model. Otherwise, only the final prompt will be shown. - -Showing the full prompt is off by default. - -Enable it by using `--show-prompt` and setting the verbosity level to high (`-vvv`). - -## Functions - -### categorize-mappings - -Categorize a collection of mappings in the Simple Standard for Sharing Ontological Mappings (SSSOM) format. - -Mappings in this format may not include their specific mapping types (e.g., broad or close mappings). - -This function will attempt to apply more specific mappings wherever possible. - -Example: - -Using an [example SSSOM mapping collection](https://github.com/mapping-commons/sssom/blob/master/examples/embedded/mp-hp-exact-0.0.1.sssom.tsv) - -```bash -ontogpt categorize-mappings -i mp-hp-exact-0.0.1.sssom.tsv -``` - -Note that OntoGPT will attempt to retrieve the resources specified in the mapping (in the above example, that will include HP and MP). If it cannot find a corresponding resource it will raise a HTTP 404 error. - -### clinical-notes - -Create mock clinical notes. - -Options: - -* `-d`, `--description TEXT` - a text description of the contents of the generated notes. -* `--sections TEXT` - sections to include in the generated notes, for example, medications, vital signs. Use multiple times for multiple sections, e.g., `--sections medications --sections "vital signs"` - -Example: - -```bash -ontogpt clinical-notes -d "middle-aged female patient with syncope and recent travel to the Amazon rainforest" -``` - -### complete - -Prompt completion. - -Given the path to a file containing text to continue, this command will simply pass it to the model as a completion task. - -Example: - -The file `example2.txt` contains the text "Here's a good joke about high blood pressure:" - -```bash -ontogpt complete example2.txt -``` - -We take no responsibility for joke quality or lack thereof. - -### convert - -Convert output format. - -Rather than a direct format translation, this function performs a full SPIRES extraction on the input file and writes the output in the specified format. - -Example: - -```bash -ontogpt convert -o outputfile.md -O md inputfile.yaml -``` - -### convert-examples - -Convert training examples from YAML. - -This can be necessary for performing evaluations. - -Given the path to a YAML-format input file containing training examples in a format like this: - -```yaml ---- -examples: - - prompt: - completion: - - prompt: - completion: -``` - -the function will convert it to equivalent JSON. - -Example: - -```bash -ontogpt convert-examples inputfile.yaml -``` - -### convert-geneset - -Convert gene set to YAML. - -The gene set may be in JSON (msigdb format) or text (one gene symbol per line) format. - -See also the `create-gene-set` command (see below). - -Options: - -* `--fill` / `--no-fill` - Defaults to False (`--no-fill`). If True (`--fill`), the function will attempt to fill in missing gene values. -* `-U`, `--input-file TEXT` - Path to a file with gene IDs to enrich (if not passed as arguments). - -Example: - -```bash -ontogpt convert-geneset -U inputfile.json -``` - -### create-gene-set - -Create a gene set. - -This is primarily relevant to the TALISMAN method for creating gene set summaries. - -It creates a gene set given a set of gene annotations in two-column TSV or GAF format. - -The function also requires a single argument for the term to create the gene set with. - -The output is provided in YAML format. - -Options: - -* `-A`, `--annotation-path TEXT` - Path to a file containing annotations. - -Example: - -```bash -ontogpt create-gene-set -A inputfile.tsv "positive regulation of mitotic cytokinesis" -``` - -### diagnose - -Diagnose a clinical case represented as one or more [Phenopackets](http://phenopackets.org/). - -This function takes one or more file paths as arguments, where each must contain a phenopacket in JSON format. - -Example inputs may be found at the [Phenomics Exchange repository](https://github.com/phenopackets/phenomics-exchange-ig). - -Example: - -```bash -ontogpt diagnose case1.json case2.json -``` - -### dump-completions - -Dump cached completions. - -OntoGPT saves queries and successful text completions to an sqlite database. - -Caching is not currently supported for local models. - -Use this function to retrieve the contents of this database. - -See also: the `cache-db` parameter described above. - -Options: - -* `-m TEXT` - Match string to use for filtering. -* `-D TEXT` - Path to sqlite database. - -Example: - -```bash -ontogpt dump-completions -m "soup" -``` - -### embed - -Embed text. - -This function will return an embedding vector for the input text or texts. - -Embedding retrieval is not currently supported for local models. - -Options: - -* `-C`, `--context TEXT` - domain e.g. anatomy, industry, health-related - -Example: - -```bash -ontogpt embed "obstreperous muskrat" -``` - -For OpenAI's "text-embedding-ada-002" model, the output will be a vector of length 1536, like so: - -```bash -[-0.015013165771961212, -0.013102399185299873, -0.005333086010068655, ...] -``` - -### enrichment - -Gene class summary enriching. This is OntoGPT's implementation of TALISMAN. - -The goal of gene summary enrichment is to assemble a textual summary of the functions of a set of genes and their products. - -TALISMAN can run in three different ways: - -1. Map gene symbols to IDs using the resolver (unless IDs are specified) -2. Fetch gene descriptions using Alliance API -3. Create a prompt using descriptions - -Options: - -* `-r`, `--resolver TEXT` - OAK selector for the gene ID resolver, e.g., `sqlite:obo:hgnc` for HGNC gene IDs. -* `-C`, `--context TEXT` - domain, e.g., anatomy, industry, health-related -* `--strict` / `--no-strict` - If set, there must be a unique mappings from labels to IDs. Defaults to True. -* `-U`, `--input-file TEXT` - Path to a file with gene IDs to enrich if not passed as arguments. -* `--randomize-gene-descriptions-using-file TEXT` - For evaluation only. Path to a file containing gene identifiers and descriptions; if this option is used, TALISMAN will swap out gene descriptions with those from this gene set file. -* `--ontological-synopsis` / `--no-ontological-synopsis` - If set, use automated rather than manual gene descriptions. Defaults to True. -* `--combined-synopsis` / `--no-combined-synopsis` - If set, combine gene descriptions. Defaults to False. -* `--end-marker TEXT` - Specify a character or string to end prompts with. For testing minor variants of prompts. -* `--annotations` / `--no-annotations` - If set, include annotations in the prompt. Defaults to True. -* `--prompt-template TEXT` - Path to a file containing the prompt. -* `--interactive` / `--no-interactive` - Interactive mode - rather than call the API, the function will present a walkthrough process. Defaults to False. - -Example: - -```bash -ontogpt enrichment -r sqlite:obo:hgnc -U tests/input/genesets/EDS.yaml -``` - -In this case, the prompt will include gene summaries retrieved from the database. - -The response text will include, among other fields, a summary like this: - -```text -Summary: The common function among these genes is their involvement in the regulation and organization of the extracellular matrix, particularly collagen fibril organization and biosynthesis. -``` - -### entity-similarity - -Determine similarity between ontology entities by comparing their embeddings. - -Options: - -* `-r`, `--ontology TEXT` - name of the ontology to use. This should be an OAK adapter name such as "sqlite:obo:hp". -* `--definitions` / `--no-definitions` - Include text definitions in the text to embed. Defaults to True. -* `--parents` / `--no-parents` - Include is-a parent terms in the text to embed. Defaults to True. -* `--ancestors` / `--no-ancestors` - Include all ancestors in the text to embed. Defaults to True. -* `--logical-definitions` / `--no-logical-definitions`- Include logical definitions in the text to embed. Defaults to True. -* `--autolabel` / `--no-autolabel` - Add labels to each subject and object identifier. Defaults to True. -* `--synonyms` / `--no-synonyms` - Include synonyms in the text to embed. Defaults to True. - -Example: - -```bash -ontogpt entity-similarity -r sqlite:obo:hp HP:0012228 HP:0000629 -``` - -In this case, the output will look like this: - -```text -subject_id subject_label object_id object_label embedding_cosine_similarity object_rank_for_subject -HP:0012228 Tension-type headache HP:0012228 Tension-type headache 0.9999999999999999 0 -HP:0012228 Tension-type headache HP:0000629 Periorbital fullness 0.7755551231762359 1 -HP:0000629 Periorbital fullness HP:0000629 Periorbital fullness 1.0000000000000002 0 -HP:0000629 Periorbital fullness HP:0012228 Tension-type headache 0.7755551231762359 1 -``` - -### eval - -Evaluate an extractor. - -See the Evaluations section for more details. - -Options: - -* `--num-tests INTEGER` - number of test iterations to cycle through. Defaults to 5. -* `--chunking` / `--no-chunking` - If set, chunk input text, then prepare a separate prompt for each chunk. Otherwise the full input text is passed. Defaults to False. - -Example: - -```bash -ontogpt eval --num-tests 1 EvalCTD -``` - -### eval-enrichment - -Run enrichment (TALISMAN) using multiple methods. - -This function runs a set of evaluations specific to the TALISMAN gene set summary process. - -It will iterate through all relevant models to compare results. - -The function assumes genes will have HGNC identifiers. - -Options: - -* `--strict` / `--no-strict` - If set, there must be a unique mappings from labels to IDs. Defaults to True. -* `-U`, `--input-file TEXT` - Path to a file with gene IDs to enrich (if not passed as arguments) -* `--ontological-synopsis` / `--no-ontological-synopsis` - If set, use automated rather than manual gene descriptions. Defaults to True. -* `--combined-synopsis` / `--no-combined-synopsis` - If set, combine gene descriptions. Defaults to False. -* `--annotations` / `--no-annotations` - If set, include annotations in the prompt. Defaults to True. -* `-n`, `--number-to-drop INTEGER` - Maximum number of genes to drop if necessary. -* `-A`, `--annotations-path TEXT` - Path to file containing annotations. - -Example: - -```bash -ontogpt enrichment -U tests/input/genesets/EDS.yaml -``` - -### extract - -Extract knowledge from text guided by a schema. - -This is OntoGPT's implementation of SPIRES. - -Output includes the input text (or a truncated part), the raw completion output, the prompt (specifically, the last iteration of the prompts used), and an extracted object containing all parts identified in the input text, as well as a list of named entities and their labels. - -Options: - -* `-S`, `--set-slot-value TEXT` - Set slot value manually, e.g., `--set-slot-value has_participant=protein` - -Examples: - -```bash -ontogpt extract -t gocam.GoCamAnnotations -i tests/input/cases/gocam-33246504.txt -``` - -In this case, you will an extracted object in the output like: - -```yaml -extracted_object: - genes: - - HGNC:5992 - - AUTO:F4/80 - - HGNC:16400 - - HGNC:1499 - - HGNC:5992 - - HGNC:5993 - organisms: - - NCBITaxon:10088 - - AUTO:bone%20marrow-derived%20macrophages - - AUTO:astrocytes - - AUTO:bipolar%20cells - - AUTO:vascular%20cells - - AUTO:perivascular%20MPs - gene_organisms: - - gene: HGNC:5992 - organism: AUTO:mononuclear%20phagocytes - - gene: HGNC:16400 - organism: AUTO:F4/80%2B%20mononuclear%20phagocytes - - gene: HGNC:1499 - organism: AUTO:F4/80%2B%20mononuclear%20phagocytes - - gene: HGNC:5992 - organism: AUTO:perivascular%20macrophages - - gene: HGNC:5993 - organism: AUTO:None - activities: - - GO:0006954 - - AUTO:photoreceptor%20death - - AUTO:retinal%20function - gene_functions: - - gene: HGNC:5992 - molecular_activity: GO:0006954 - - gene: AUTO:F4/80 - molecular_activity: AUTO:mononuclear%20phagocyte%20recruitment - - gene: HGNC:1499 - molecular_activity: GO:0006954 - - gene: HGNC:5992 - molecular_activity: AUTO:immune-specific%20expression - - gene: HGNC:5993 - molecular_activity: AUTO:IL-1%CE%B2%20receptor - - gene: AUTO:rytvela - molecular_activity: AUTO:IL-1R%20modulation - - gene: AUTO:Kineret - molecular_activity: AUTO:IL-1R%20antagonism - cellular_processes: - - AUTO:macrophage-induced%20photoreceptor%20death - gene_localizations: - - gene: HGNC:5992 - location: AUTO:subretinal%20space -``` - -Or, we can extract information about a drug and specify which model to use: - -```bash -ontogpt extract -t drug -i tests/input/cases/drug-DB00316-moa.txt --auto-prefix UNKNOWN -m gpt-4 -``` - -The `ontology_class` schema may be used to perform more domain-agnostic entity recognition, though this is generally incompatible with grounding. - -```bash -ontogpt extract -t ontology_class -i tests/input/cases/human_urban_green_space.txt -``` - -### fill - -Fill in missing values. - -Requires the path to a file containing a data object to be passed (as an argument) and a set of examples as an input file. - -Options: - -* `-E`, `--examples FILENAME` - Path to a file of example objects. - -### generate-extract - -Generate text and then extract knowledge from it. - -This command runs two operations: - -1. Generate a natural language description of something -2. Parse the generated description using SPIRES - -For example, given a cell type such as [Acinar Cell Of Salivary Gland](https://cellxgene.cziscience.com/cellguide/CL_0002623), generate a description using GPT describing many aspects of the cell type, from its marker genes through to its function and diseases it is implicated in. - -After that, use the [cell-type schema](https://w3id.org/ontogpt/cell_type) to extract this into structured form. - -As an optional next step use [linkml-owl](https://github.com/linkml/linkml-owl) to generate OWL TBox axioms. - -See also: `iteratively-generate-extract` below. - -Example: - -```bash -ontogpt generate-extract -t cell_type CL:0002623 -``` - -### iteratively-generate-extract - -Iterate through generate-extract. - -This runs the `generate-extract` command in iterative mode. It will traverse the extracted subtypes with each iteration, gradually building up an ontology that is entirely generated from the "latent knowledge" in the LLM. - -Currently each iteration is independent so the method remains unaware as to whether it has already made a concept. Ungrounded concepts may indicate gaps in available knowledgebases. - -Unlike the `generate-extract` command, this command requires some additional parameters to be specified. - -Please specify the input ontology and the output path. - -Options: - -* `-r`, `--ontology TEXT` - Ontology to use. Use the OAK selector format, e.g., "sqlite:obo:cl" -* `-M`, `--max-iterations INTEGER` - Maximum number of iterations. -* `-I`, `--iteration-slot TEXT` - Slots to iterate over. -* `-D`, `--db TEXT` - Path to the output, in YAML format. -* `--clear` / `--no-clear` - If set, clear the output database before starting. Defaults to False. - -Example: - -```bash -ontogpt iteratively-generate-extract -t cell_type -r sqlite:obo:cl -D cells.yaml CL:0002623 -``` - -### list-models - -List all available models. - -Example: - -```bash -ontogpt list-models -``` - -### list-templates - -List the templates. - -Alternatively, run `make list_templates`. - -Example: - -```bash -ontogpt list-templates -``` - -### pubmed-annotate - -Retrieve a collection of PubMed IDs for a given search, then perform extraction on them with SPIRES. - -The search argument will accept all parameters known to PubMed search, such as filtering by publication year. - -Works for single publications, too - set the `--limit` parameter to 1 and specify a PubMed ID as the search argument. - -Options: - -* `--limit INTEGER` - Total number of citation records to return. Limited by the NCBI API. -* `--get-pmc` / `--no-get-pmc` - Attempt to parse PubMed Central full text(s) rather than abstract(s) alone. - -Examples: - -```bash -ontogpt pubmed-annotate -t phenotype "Takotsubo Cardiomyopathy: A Brief Review" --get-pmc --model gpt-3.5-turbo-16k --limit 3 -``` - -```bash -ontogpt pubmed-annotate -t environmental_sample "33126925" --limit 1 -``` - -```bash -ontogpt pubmed-annotate -t composite_disease "(earplugs) AND (("1950"[Date - Publication] : "1990"[Date - Publication]))" --limit 4 -``` - -### pubmed-extract - -Extract knowledge from a single PubMed ID. - -_DEPRECATED_ - use `pubmed-annotate` instead. - -### recipe-extract - -Extract from a recipe on the web. - -This uses the `recipe` template and the [recipe_scrapers](https://github.com/hhursev/recipe-scrapers) package. The latter supports many different recipe web sites, so give your favorite a try. - -Pass a URL as the argument, or use the -R option to specify the path to a file containing one URL per line. - -Options: - -* `-R`, `--recipes-urls-file TEXT` - File with URLs to recipes to use for extraction. - -Example: - -```bash -ontogpt recipe-extract https://www.allrecipes.com/recipe/17445/grilled-asparagus/ -``` - -In this case, expect an extracted object like the following: - -```yaml -extracted_object: - url: https://www.allrecipes.com/recipe/17445/grilled-asparagus/ - label: Grilled Asparagus - description: Grilled asparagus with olive oil, salt, and pepper. - categories: - - AUTO:None - ingredients: - - food_item: - food: FOODON:03311349 - state: fresh, spears - amount: - value: '1' - unit: UO:0010034 - - food_item: - food: FOODON:03301826 - amount: - value: '1' - unit: UO:0010042 - - food_item: - food: AUTO:salt - state: and pepper - amount: - value: N/A - unit: AUTO:N/A - steps: - - action: AUTO:Preheat - inputs: - - food: AUTO:outdoor%20grill - state: None - outputs: - - food: AUTO:None - state: None - utensils: - - AUTO:None - - action: dbpediaont:season - inputs: - - food: FOODON:00003458 - state: coated - - food: AUTO:salt - state: None - - food: FOODON:00003520 - outputs: - - food: FOODON:00003458 - state: seasoned - utensils: - - AUTO:None - - action: AUTO:cook - inputs: - - food: FOODON:03311349 - state: None - outputs: - - food: FOODON:03311349 - state: cooked - utensils: - - AUTO:grill -``` - -### synonyms - -Extract synonyms, based on embeddings. - -The context parameter is required. - -Options: - -* `-C`, `--context TEXT` - domain, e.g., anatomy, industry, health-related - -Example: - -```bash -ontogpt synonyms --context astronomy star -``` - -### text-distance - -Embed text and calculate euclidian distance between the embeddings. - -The terms must be separated by an `@` character. - -Options: - -* `-C`, `--context TEXT` - domain, e.g., anatomy, industry, health-related - -Example: - -```bash -ontogpt text-distance pancakes @ syrup -``` - -### text-similarity - -Like `text-distance`, this command compares the embeddings of input terms. - -This command returns the cosine similarity of the embedding vectors. - -Options: - -* `-C`, `--context TEXT` - domain, e.g., anatomy, industry, health-related - -Example: - -```bash -ontogpt text-similarity basketball @ basket-weaving -``` - -### web-extract - -Extract knowledge from web page. - -Pass a URL as an argument and OntoGPT will use the SPIRES method to extract information based on the specified template. - -Because this depends upon scraping a page, results may vary depending on a site's complexity and structure. - -Even relatively short pages may exceed a model's context size, so larger context models may be necessary. - -Example: - -```bash -ontogpt web-extract -t reaction.Reaction -m gpt-3.5-turbo-16k https://www.scienceofcooking.com/maillard_reaction.htm -``` - -### wikipedia-extract - -Extract knowledge from a Wikipedia page. - -Pass an article title as an argument and OntoGPT will use the SPIRES method to extract information based on the specified template. - -Even relatively short pages may exceed a model's context size, so larger context models may be necessary. - -Example: - -```bash -ontogpt wikipedia-extract -t mendelian_disease.MendelianDisease -m gpt-3.5-turbo-16k "Cartilage–hair hypoplasia" -``` - -### wikipedia-search - -Extract knowledge from Wikipedia pages based on a search. - -Pass a search phrase as an argument and OntoGPT will use the SPIRES method to extract information based on the specified template. - -Even relatively short pages may exceed a model's context size, so larger context models may be necessary. - -Example: - -```bash -ontogpt wikipedia-search -t biological_process -m gpt-3.5-turbo-16k "digestion" -``` +TODO diff --git a/docs/index.md b/docs/index.md index 98cff3672..6d9f63937 100644 --- a/docs/index.md +++ b/docs/index.md @@ -1,89 +1,13 @@ # Introduction -_OntoGPT_ is a Python package for extracting structured information from text with large language models (LLMs), _instruction prompts_, and ontology-based grounding. It works well with OpenAI's GPT-3.5 and GPT-4 models as well as a selection of other LLMs. OntoGPT's output can be used for general-purpose natural language tasks (e.g., named entity recognition and relation extraction), summarization, knowledge base and knowledge graph construction, and more. +_TALISMAN_ is a Python package for summarizing gene set functions using large language models (LLMs). -## Methods - -Two different strategies for knowledge extraction are currently implemented in OntoGPT: - -* SPIRES: *Structured Prompt Interrogation and Recursive Extraction of Semantics* - * A Zero-shot learning (ZSL) approach to extracting nested semantic structures from text - * This approach takes two inputs - 1) LinkML schema 2) free text, and outputs knowledge in a structure conformant with the supplied schema in JSON, YAML, RDF or OWL formats - * Uses GPT-3.5-turbo, GPT-4, or one of a variety of open LLMs on your local machine -* SPINDOCTOR: *Structured Prompt Interpolation of Narrative Descriptions Or Controlled Terms for Ontological Reporting* - * Summarizes gene set descriptions (pseudo gene-set enrichment) - * Uses GPT-3.5-turbo or GPT-4 - -## Quick Start - -Please see the Setup page on the left for more detailed instructions. - -OntoGPT runs on the command line, though there's also a minimal web app interface (see `Web Application` section below). - -1. Ensure you have Python 3.9 or greater installed. -2. Install with `pip`: - - ```bash - pip install ontogpt - ``` - -3. Set your OpenAI API key: - - ```bash - runoak set-apikey -e openai - ``` - -4. See the list of all OntoGPT commands: - - ```bash - ontogpt --help - ``` - -5. Try a simple example of information extraction: - - ```bash - echo "One treatment for high blood pressure is carvedilol." > example.txt - ontogpt extract -i example.txt -t drug - ``` - - OntoGPT will retrieve the necessary ontologies and output results to the command line. Your output will provide all extracted objects under the heading `extracted_object`. - -## Web Applications - -There is a bare bones web application for running OntoGPT and viewing results. - -First, install the required dependencies with `pip` by running the following command: - -```bash -pip install ontogpt[web] -``` - -Then run this command to start the web application: - -```bash -web-ontogpt -``` - -NOTE: We do not recommend hosting this webapp publicly without authentication. - -Gene enrichment has its own webapp powered by Streamlit: - -```bash -streamlit run src/ontogpt/streamlit/spindoctor.py -``` +It uses the OntoGPT package to interface with LLMs. ## Citation -SPIRES is described further in: Caufield JH, Hegde H, Emonet V, Harris NL, Joachimiak MP, Matentzoglu N, et al. Structured prompt interrogation and recursive extraction of semantics (SPIRES): A method for populating knowledge bases using zero-shot learning. arXiv publication: - -SPINDOCTOR is described further in: Joachimiak MP, Caufield JH, Harris NL, Kim H, Mungall CJ. Gene Set Summarization using Large Language Models. arXiv publication: +TALISMAN is described further in: Joachimiak MP, Caufield JH, Harris NL, Kim H, Mungall CJ. Gene Set Summarization using Large Language Models. arXiv publication: ## Contributing -Contributions are welcome! One way to get started with contributing to OntoGPT is to submit an - -Contributions on recipes to test welcome from anyone! Just make a PR [here](https://github.com/monarch-initiative/ontogpt/blob/main/tests/input/recipe-urls.csv). See [this list](https://github.com/hhursev/recipe-scrapers) for accepted URLs - -## Acknowledgements - -We gratefully acknowledge [Bosch Research](https://www.bosch.com/research) for their support of this research project. +Contributions are welcome! One way to get started with contributing to OntoGPT is to submit an issue. diff --git a/docs/operation.md b/docs/operation.md index 76384713c..8531cec50 100644 --- a/docs/operation.md +++ b/docs/operation.md @@ -1,136 +1,3 @@ # Operation -## Getting Started - -OntoGPT is run from the command line. See the full list of commands with: - -```bash -ontogpt --help -``` - -For a simple example of text completion and testing to ensure OntoGPT is set up correctly, create a text file containing the following, saving the file as `example.txt`: - -```bash -Why did the squid cross the coral reef? -``` - -Then try the following command: - -```bash -ontogpt complete example.txt -``` - -You should get text output like the following: - -```bash -Perhaps the squid crossed the coral reef for a variety of reasons: - -1. Food: Squids are known to feed on small fish and other marine organisms, and there could have been a rich food source on the other side of the reef. - -... -``` - -OntoGPT is intended to be used for information extraction. The following examples show how to accomplish this. - -### Strategy 1: Knowledge extraction using SPIRES - -#### Working Mechanism - -1. You provide an arbitrary data model, describing the structure you want to extract text into. This can be nested (but see limitations below). The predefined [templates](src/ontogpt/templates/) may be used. -2. Provide your preferred annotations for grounding `NamedEntity` fields -3. OntoGPT will: - * Generate a prompt - * Feed the prompt to a language model - * Parse the results into a dictionary structure - * Ground the results using a preferred annotator (e.g., an ontology) - -#### Input - -Consider some text from one of the input files being used in the OntoGPT test suite. You can find the text file [here](tests/input/cases/gocam-betacat.txt). You can download the raw file from the GitHub link to that input text file, or copy its contents over into another file, say, `abstract.txt`. An excerpt: - - > The cGAS/STING-mediated DNA-sensing signaling pathway is crucial - for interferon (IFN) production and host antiviral - responses - > - > ... - > [snip] - > ... - > - > The underlying mechanism was the - interaction of US3 with β-catenin and its hyperphosphorylation of - β-catenin at Thr556 to block its nuclear translocation - > ... - > ... - -We can extract knowledge from the above text this into the [GO pathway datamodel](src/ontogpt/templates/gocam.yaml) by running the following command: - -#### Command - -```bash -ontogpt extract -t gocam.GoCamAnnotations -i ~/path/to/abstract.txt -``` - -Note: The value accepted by the `-t` / `--template` argument is the base name of one of the LinkML schema / data model which can be found in the [templates](src/ontogpt/templates/) folder. - -#### Output - -The output returned from the above command can be optionally redirected into an output file using the `-o` / `--output`. - -The following is a small part of what the larger schema-compliant output looks like: - -```yaml -genes: -- HGNC:2514 -- HGNC:21367 -- HGNC:27962 -- US3 -- FPLX:Interferon -- ISG -gene_gene_interactions: -- gene1: US3 - gene2: HGNC:2514 -gene_localizations: -- gene: HGNC:2514 - location: Nuclear -gene_functions: -- gene: HGNC:2514 - molecular_activity: Transcription -- gene: HGNC:21367 - molecular_activity: Production -... -``` - -#### Local Models - -To use a local model, specify it with the `-m` or `--model` option. - -Example: - -```bash -ontogpt extract -t drug -i ~/path/to/abstract.txt -m nous-hermes-13b -``` - -See the list of all available models with this command: - -```bash -ontogpt list-models -``` - -When specifying a local model for the first time, it will be downloaded to your local system. - -## Strategy 2: Gene Enrichment using SPINDOCTOR - -Given a set of genes, OntoGPT can find similarities among them. - -Ex.: - -```bash -ontogpt enrichment -U tests/input/genesets/sensory-ataxia.yaml -``` - -The default is to use ontological gene function synopses (via the Alliance API). - -* To use narrative/RefSeq summaries, use the `--no-ontological-synopses` flag -* To run without any gene descriptions, use the `--no-annotations` flag - -This strategy does not currently support using local models. +TODO diff --git a/docs/owl_exports.md b/docs/owl_exports.md deleted file mode 100644 index 9ccf099bd..000000000 --- a/docs/owl_exports.md +++ /dev/null @@ -1,20 +0,0 @@ -# OWL Exports - -The `extract` command will let you export the results as OWL axioms, utilizing [linkml-owl](https://linkml.io/linkml-owl) mappings in the schema. - -Ex.: - -```bash -ontogpt extract -t recipe -i recipe-spaghetti.txt -o recipe-spaghetti.owl -O owl -``` - -[src/ontogpt/templates/recipe.yaml](src/ontogpt/templates/recipe.yaml) is an example schema that uses linkml-owl mappings. - -See the [Makefile](Makefile) for a full pipeline that involves using robot to extract a subset of FOODON -and merge in the extracted results. This uses [recipe-scrapers](https://github.com/hhursev/recipe-scrapers). - -OWL output: [recipe-all-merged.owl](tests/output/owl/merged/recipe-all-merged.owl) - -Classification: - -![OWL in the Protege editor](https://user-images.githubusercontent.com/50745/230427663-20d845e9-f1d5-490e-b1ad-cdccdd0dca70.png "OWL in the Protege editor") diff --git a/docs/setup.md b/docs/setup.md index 62887f04a..2cb618917 100644 --- a/docs/setup.md +++ b/docs/setup.md @@ -1,79 +1,3 @@ # Setup -## Prerequisites - -OntoGPT may be installed through `pip` or used directly from the GitHub repository. In the latter case, you will need to install the `poetry` dependency manager and precede commands with `poetry run`. [See the poetry installation documentation for more details.](https://python-poetry.org/docs/#installation) - -### Additional requirements and options - -* Python 3.9+ - -* OpenAI API key: necessary for using OpenAI's GPT models. This is a paid API and you will be charged based on usage. If you do not have an OpenAI account, [you may sign up here](https://platform.openai.com/signup). - -You may also set additional API keys for optional resources: - -* [BioPortal](https://bioportal.bioontology.org/) account (for grounding). The BioPortal key is necessary for using ontologies from [BioPortal](https://bioportal.bioontology.org/). You may get a key by signing up for an account on their web site. -* [NCBI E-utilities](https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/). The NCBI email address and API key are used for retrieving text and metadata from PubMed. You may still access these resources without identifying yourself, but you may encounter rate limiting and errors. -* [HuggingFace Hub](https://huggingface.co/docs/api-inference/quicktour#get-your-api-token). This API key is necessary to retrieve models from the HuggingFace Hub service. - -## Installation - -To simply start using the package in your workspace: - -```bash -pip install ontogpt -``` - -Note that some features require installing additional, optional dependencies. These may be installed as: - -```bash -pip install ontogpt[extra_name] -``` - -where `extra_name` is one of the following: - -* `docs` - dependencies for building documentation -* `gpt4all` - dependencies for running local models -* `huggingface` - dependencies for accessing LLMs from HuggingFace Hub, remotely or locally -* `recipes` - dependencies for recipe scraping and parsing -* `textract` - the textract plugin -* `web` - dependencies for the web application - -For installation from the GitHub repository, particularly if you plan to contribute to feature development or other package code: - -```bash -git clone https://github.com/monarch-initiative/ontogpt.git -cd ontogpt/ -poetry install -``` - -Extras listed above may be installed as: - -```bash -poetry install --extras extra_name -``` - -All commands should then be preceded by `poetry run`, or simply run `poetry shell` to create and enter a virtual environment for the project. - -### Setting API keys - -One OntoGPT and all of its dependencies are installed, you will need to set your API keys using the [Ontology Access Kit](https://github.com/INCATools/ontology-access-kit): - -```bash -runoak set-apikey -e openai -``` - -The optional keys may be set as follows: - -```bash -runoak set-apikey -e bioportal -runoak set-apikey -e ncbi-email -runoak set-apikey -e ncbi-key -runoak set-apikey -e hfhub-key -``` - -### Running local models - -Using local models currently depends upon using the `gpt4all` package and may require additional setup steps specific to your computing environment. - -See the [gpt4all documentation](https://docs.gpt4all.io/) for more details. +TODO diff --git a/docs/start_with_owl.md b/docs/start_with_owl.md deleted file mode 100644 index f3402e932..000000000 --- a/docs/start_with_owl.md +++ /dev/null @@ -1,92 +0,0 @@ -# Starting with OWL - -OWL, or Web Ontology Language, is a popular format for ontologies, so what is the best way to start working with OntoGPT if you have an OWL ontology already? - -OWL is a data model for expressing ontologies, oriented around set-theoretic logical Axioms. OWL is not strictly an ontology format, but it may be represented in the RDF language, among others. [Much, much more detail here](https://oboacademy.github.io/obook/explanation/owl-format-variants/). - -OWL *may* encode a data schema, or it may encode something else. In the latter case, think very carefully about what data you wish to extract and how it relates to what is present in your OWL. - -The crucial question is this: does your OWL literally contain a set of terms you wish to ground extractions to, or does it define a set of concepts and their relationships you would like to extract? - -For example, let's use this very simple example ontology: - -```xml - - - - - - - - - - - - - Apple - - - - Orange - - - -``` - -If you want to extract entities from text (and they may be anything - foods, flavors, etc.) and then ground them to individuals in the ontology, then continue to Option 1. - -If you want to extract *all* Fruit entities from input text while also recognizing that some of them may be CitrusFruit, then continue to Option 2. - -## Option 1 - grounding to a set of terms - -You may use an OWL file the same way as any other annotator. - -Note that the example ontology above doesn't use prefixes, so let us imagine that each named individual has an identifier like `FRUIT:12345`. - -If your input text contains the word "orange", then it will be grounded based on the provided OWL, but any terms *not* in the OWL, like ["snakeskin fruit"](https://en.wikipedia.org/wiki/Salak) will not be grounded unless you provide additional annotators capable of grounding the term. - -If your ontology is in `fruit.owl`, then your schema may define a class like this: - -```yaml - Fruit: - is_a: NamedEntity - id_prefixes: - - FRUIT - annotations: - annotators: fruit.owl -``` - -The OWL file should be in the same path as where you will run `ontogpt` from. - -If your ontology is already in the [OBO Foundry](http://obofoundry.org/), then you may also specify the annotator as something like `sqlite:obo:fruit` (that's just an example, but try something like the Food Ontology with `sqlite:obo:foodon` for an equivalent). - -## Option 2 - transforming an OWL into OntoGPT schema - -This path is a bit more complicated. - -If you'd rather use the OWL more like a schema to develop a corresponding extraction schema for OntoGPT, you may be able to do so with the [schema-automator tool](https://github.com/linkml/schema-automator). - -After installing the tool, try something like this: - -```bash -$ schemauto import-owl fruit.owl -... schema-automator attempts to transform the OWL ... -``` - -This process may encounter some errors along the way. One frequent issue is that the input ontology may not be in *functional syntax*, but may be converted using the [robot tool](http://robot.obolibrary.org/) like this: - -```bash -$ robot convert -i fruit.owl -o fruit.ofn -... a magical transformation happens ... -$ schemauto import-owl fruit.ofn -``` - -The process may still go poorly if the input ontology is heavily dependent on imports. - -If everything goes well, however, you should get a LinkML YAML version of the ontology. It will still require addition of `description` and `annotation` slots to each class before it will be useful for extraction operations. - -Overall, you may find that it is easier to modify an existing OntoGPT schema to fit your schema. diff --git a/docs/troubleshooting.md b/docs/troubleshooting.md index 473a335e5..10a4dd066 100644 --- a/docs/troubleshooting.md +++ b/docs/troubleshooting.md @@ -1,39 +1,3 @@ # Troubleshooting -Encountering an error, mystery, or other unexplained oddity? Open a ticket on the GitHub repository: - -## I get an error like `TypeError: ConfiguredBaseModel.__init_subclass__() takes no keyword arguments` - -This can happen if you have installed a version of the Pydantic package older than version 2 and/or if you're using a schema generated for Pydantic v1. Versions of OntoGPT of v0.3.3 and above should prevent this from happening, but if you're still seeing the error, then running `make` again may fix it. - -## I get an error like `urllib.error.HTTPError: HTTP Error 404: Not Found` - -There are a variety of reasons why this may happen, but one cause is if your schema specifies an annotator which does not exist. If the stack trace of the error includes the `get_adapter` method from `oaklib`, then this is a likely cause, and you may want to verify that all annotators are accessible to OAK. - -## I get a lot of warnings like `WARNING:root:Could not find any mappings for ...` and I don't get the expected identifiers in my extracted object - -Verify that the `id_prefixes` you specify in your schema correspond to those provided by the annotator. If your annotator is `sqlite:obo:hp`, for example, the prefix will be `HP` rather than `HPO`. - -## I need to store the annotator files OntoGPT downloads somewhere other than `~/.data/oaklib` - -OntoGPT uses `oaklib` to handle the ontologies it uses as annotators, and `oaklib` uses the `pystow` package to determine where downloads should go. - -To change the download location, set the `PYSTOW_HOME` variable in your environment to your preferred path. - -For example, to save downloads to `/tmp/oaklib`, set the varible like this: - -```bash -export PYSTOW_HOME='/tmp/' -``` - -You may then reset that variable with this command: - -```bash -unset PYSTOW_HOME -``` - -Or make the change more permanent by adding it to your `.bashrc` file and then run - -```bash -source ~/.bashrc -``` +TODO diff --git a/images/ontogpt_logo_2.jpg b/images/ontogpt_logo_2.jpg deleted file mode 100644 index b3594b10d..000000000 Binary files a/images/ontogpt_logo_2.jpg and /dev/null differ diff --git a/images/ontogpt_logo_2.svg b/images/ontogpt_logo_2.svg deleted file mode 100644 index 70ccf5599..000000000 --- a/images/ontogpt_logo_2.svg +++ /dev/null @@ -1,46 +0,0 @@ - - - - - - - - - - diff --git a/images/spires_logo.png b/images/spires_logo.png deleted file mode 100644 index b4e4535c8..000000000 Binary files a/images/spires_logo.png and /dev/null differ diff --git a/images/spires_logo.svg b/images/spires_logo.svg deleted file mode 100644 index dcc6755df..000000000 --- a/images/spires_logo.svg +++ /dev/null @@ -1,48 +0,0 @@ - - - - - - - - - - diff --git a/long_output.yaml b/long_output.yaml deleted file mode 100644 index 5a32e1bb0..000000000 --- a/long_output.yaml +++ /dev/null @@ -1,2873 +0,0 @@ -input_text: |- - Title: Relationship between disease activity index and sleep disorders in children with inflammatory bowel diseases. - Abstract: The aim of the study was to assess the prevalence of sleep disturbance in pediatric IBD patients and evaluate the relationship between clinical features of IBD, disease activity, inflammatory markers and quality of sleep. A total of 99 patients who were followed-up with the diagnosis of IBD (44 Crohn's disease (CD), 55 Ulcerative colitis (UC)) between 2015-2020 and 80 healthy controls were enrolled in the study. The clinical and demographic characteristics, laboratory parameters and disease activities were obtained from medical reports retrospectively. Pittsburgh sleep quality index (PSQI) was administered to all participants. PSQI score was significantly higher in patient group than the control group (P < 0.001). The sleep time of patient group, especially patients with UC was later than the control group (P = 0.008). Sleep duration was longer in control group than the patient group (P < 0.001). A positive strong correlation was obtained in disease activity index (r = 0.886; P < 0.001) and abdominal pain (r = 0.781; P < 0.001) with PSQI scores of CD patients. Disease activity index, rectal bleeding, diarrhea and number of stool had statistically significant positive strong correlation with PSQI scores of UC patients (P < 0.001). Pediatric Crohn's disease activity index and Pediatric ulcerative colitis activity index were the only independent risk factors affecting sleep disturbances (80% sensitivity and 91.67% specificity, 93.1% sensitivity and %96.15 specificity, respectively).   Conclusion: Increased disease activity has adverse effects on sleep quality. PSQI and PCDAI were strong tests for predicting sleep disorders in pediatric patients with IBD. What is Known: • Sleep disturbances are common complaint in inflammatory bowel disease (IBD), even in clinical remission. • Pittsburgh sleep quality index (PSQI) was used to evaluate the subjective sleep quality of patients. What is New: • PSQI and Pediatric Crohn Disease Activity index (PCDAI) were strong tests for predicting sleep disorders in pediatric patients with IBD. • PSQI and PCDAI scores correlated significantly with the severity of the sleep disturbances.© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature. - Keywords: Children; Crohn’s disease; Inflammatory bowel disease; Pittsburgh sleep quality index; Ulcerative colitis -raw_completion_output: |- - genes: None mentioned in the text - exposures: disease activity; inflammatory markers - gene_exposures_relationships: None mentioned in the text -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - None mentioned in the text - - === - -extracted_object: - genes: - - None mentioned in the text - exposures: - - disease activity - - inflammatory markers - gene_exposures_relationships: - - molecular_activity: None mentioned in the text - gene: None mentioned in the text -input_text: |- - Title: Current and Emerging Targeted Therapies for Ulcerative Colitis. - Abstract: Ulcerative colitis is one of the main entities of inflammatory bowel diseases. The clinical course of this immune-mediated disorder is marked by unpredictable exacerbations and asymptomatic remission, causing lifelong morbidity. Optimized anti-inflammatory treatment is a prerequisite to not only restore the quality of life of the affected patients but also halt progressive bowel damage and reduce the risk for colitis-associated neoplasia. Advances in understanding the underlying immunopathogenesis of ulcerative colitis have led to the advent of targeted therapies that selectively inhibit crucial molecular structures or signaling pathways that perpetuate the inflammatory reaction.We will delineate the mode of action and summarize efficacy and safety data of current and emerging targeted therapies in ulcerative colitis, which encompasses representatives of the drug classes of antibodies, small molecules, and oligonucleotides. These substances have already been approved for induction and maintenance treatment or are being tested in late-stage clinical trials in moderately-to-severely active ulcerative colitis patients. These advanced therapies have enabled us to define and achieve novel therapeutic outcomes, such as clinical and endoscopic remission, histological remission, mucosal healing, and recently, also barrier healing as an emerging outcome measure.Established and emerging targeted therapies and monitoring modalities broaden our therapeutic armamentarium and have enabled us to define novel therapeutic outcomes that have the potential to modify the individual disease course of patients with ulcerative colitis.© 2023 S. Karger AG, Basel. - Keywords: Anti-tumor necrosis factor antibody; IL-23; Molecular resistance; Therapy; Ulcerative colitis -raw_completion_output: |- - genes: IL-23 - exposures: Anti-tumor necrosis factor antibody - gene_exposures_relationships: IL-23 to Anti-tumor necrosis factor antibody -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - IL-23 to Anti-tumor necrosis factor antibody - - === - -extracted_object: - genes: - - HGNC:15488 - exposures: - - Anti-tumor necrosis factor antibody - gene_exposures_relationships: - - molecular_activity: IL-23 - gene: Anti-tumor necrosis factor antibody -named_entities: - - id: HGNC:15488 - label: IL-23 -input_text: |- - Title: Intrahepatic cholangiocarcinoma in patients with primary sclerosing cholangitis and ulcerative colitis: Two case reports. - Abstract: Primary sclerosing cholangitis (PSC) is an extraintestinal manifestation of ulcerative colitis (UC). PSC is a well-known risk factor for intrahepatic cholangiocarcinoma (ICC), and ICC is known to have a poor prognosis.We present two cases of ICC in patients with PSC associated with UC. In the first case, a tumor was found by magnetic resonance imaging (MRI) in the liver of a patient with PSC and UC who presented to our hospital with right-sided rib pain. The second patient was asymptomatic, but we unexpectedly detected two liver tumors in an MRI performed to evaluate bile duct stenosis associated with PSC. ICC was strongly suspected by computed tomography and MRI in both cases, and surgery was performed, but unfortunately, the first patient died of ICC recurrence 16 mo postoperatively, and the second patient died of liver failure 14 mo postoperatively.Careful follow-up of patients with UC and PSC with imaging and blood tests is necessary for early detection of ICC.©The Author(s) 2023. Published by Baishideng Publishing Group Inc. All rights reserved. - Keywords: Case report; Hepatic lobectomy; Inflammatory bowel disease; Intrahepatic cholangiocarcinoma; Primary sclerosing cholangitis; Ulcerative colitis -raw_completion_output: |- - genes: None mentioned in the text - exposures: primary sclerosing cholangitis (PSC), ulcerative colitis (UC) - gene_exposures_relationships: None mentioned in the text -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - None mentioned in the text - - === - -extracted_object: - genes: - - None mentioned in the text - exposures: - - primary sclerosing cholangitis (PSC), ulcerative colitis (UC) - gene_exposures_relationships: - - molecular_activity: None mentioned in the text - gene: None mentioned in the text -input_text: |- - Title: Surgical management of duodenal Crohn's disease. - Abstract: The case of Crohn's disease involving the duodenum is rare, and its surgical management requires a thorough understanding.To investigate the surgical management of duodenal Crohn's disease.We systematically reviewed patients diagnosed with duodenal Crohn's disease who underwent surgery in the Department of Geriatrics Surgery of the Second Xiangya Hospital of Central South University from January 1, 2004, to August 31, 2022. The general information, surgical procedures, prognosis, and other information of these patients were collected and summarized.A total of 16 patients were diagnosed with duodenal Crohn's disease, where 6 cases had primary duodenal Crohn's disease, and 10 had secondary duodenal Crohn's disease. Among patients with primary disease, 5 underwent duodenal bypass and gastrojejunostomy, and 1 received pancreaticoduodenectomy. Among those with a secondary disease, 6 underwent closure of duodenal defect and colectomy, 3 received duodenal lesion exclusion and right hemicolectomy, and 1 underwent duodenal lesion exclusion and double-lumen ileostomy.Crohn's disease involving the duodenum is a rare condition. Different surgical management should be applied for patients with Crohn's disease presenting with different clinical manifestations.©The Author(s) 2023. Published by Baishideng Publishing Group Inc. All rights reserved. - Keywords: Crohn’s disease; Duodenum; Inflammatory bowel disease; Surgical treatment -raw_completion_output: |- - genes: N/A - exposures: surgical management - gene_exposures_relationships: N/A -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - N/A - - === - -extracted_object: - genes: - - N/A - exposures: - - surgical management - gene_exposures_relationships: - - molecular_activity: N/A - gene: N/A -input_text: |- - Title: Editorial: Game changers in inflammatory bowel diseases, volume II. - Abstract: - Keywords: EIM; IBD; markers; systemic inflammation; tailored therapy -raw_completion_output: 'genes: Not mentioned in the text' -prompt: |+ - From the text below, extract the following entities in the following format: - - genes: - exposures: - gene_exposures_relationships: - - - Text: - Title: Editorial: Game changers in inflammatory bowel diseases, volume II. - Abstract: - Keywords: EIM; IBD; markers; systemic inflammation; tailored therapy - - === - -extracted_object: - genes: - - Not mentioned in the text -input_text: |- - Title: Administration of Bifidobacterium pseudolongum suppresses the increase of colonic serotonin and alleviates symptoms in dextran sodium sulfate-induced colitis in mice. - Abstract: Previous studies suggested that altered gut serotonin (5-HT) signaling is implicated in the pathophysiology of inflammatory bowel disease (IBD). Indeed, 5-HT administration reportedly exacerbated the severity of murine dextran sodium sulfate (DSS)-induced colitis that mimics human IBD. Our recent study suggested that Bifidobacterium pseudolongum, one of the most predominant bifidobacterial species in various mammals, reduces the colonic 5-HT content in mice. The present study thus tested whether the administration of B. pseudolongum prevents DSS-induced colitis in mice. Colitis was induced by administering 3% DSS in drinking water in female BALB/c mice, and B. pseudolongum (109 CFU/day) or 5-aminosalicylic acid (5-ASA, 200 mg/kg body weight) was intragastrically administered once daily throughout the experimental period. B. pseudolongum administration reduced body weight loss, diarrhea, fecal bleeding, colon shortening, spleen enlargement, and colon tissue damage and increased colonic mRNA levels of cytokine genes (Il1b, Il6, Il10, and Tnf) almost to an extent similar to 5-ASA administration in DSS-treated mice. B. pseudolongum administration also reduced the increase of colonic 5-HT content, whereas it did not alter the colonic mRNA levels of genes that encode the 5-HT synthesizing enzyme, 5-HT reuptake transporter, 5-HT metabolizing enzyme, and tight junction-associated proteins. We propose that B. pseudolongum is as beneficial against murine DSS-induced colitis as the widely used anti-inflammatory agent 5-ASA. However, further studies are needed to clarify the causal relationship between the reduced colonic 5-HT content and reduced severity of DSS-induced colitis caused by B. pseudolongum administration.©2023 BMFH Press. - Keywords: Bifidobacterium pseudolongum; dextran sodium sulfate (DSS)-induced colitis; erotonin; inflammation -raw_completion_output: |- - genes: Il1b; Il6; Il10; Tnf - exposures: Bifidobacterium pseudolongum; dextran sodium sulfate (DSS); 5-aminosalicylic acid (5-ASA) - gene_exposures_relationships: Bifidobacterium pseudolongum - reduction of colonic 5-HT content; Bifidobacterium pseudolongum - prevention of DSS-induced colitis -prompt: |+ - From the text below, extract the following entities in the following format: - - molecular_activity: - gene: - - - Text: - Bifidobacterium pseudolongum - prevention of DSS-induced colitis - - === - -extracted_object: - genes: - - HGNC:5992 - - HGNC:6018 - - HGNC:5962 - - HGNC:11892 - exposures: - - Bifidobacterium pseudolongum - - dextran sodium sulfate (DSS) - - 5-aminosalicylic acid (5-ASA) - gene_exposures_relationships: - - molecular_activity: reduction - gene: colonic 5-HT - - molecular_activity: prevention of DSS-induced colitis - gene: Bifidobacterium pseudolongum -named_entities: - - id: HGNC:5992 - label: Il1b - - id: HGNC:6018 - label: Il6 - - id: HGNC:5962 - label: Il10 - - id: HGNC:11892 - label: Tnf -input_text: |- - Title: A Systematic Review of Self-Management Interventions for Patients with Inflammatory Bowel Disease. - Abstract: Previous studies have reported the effectiveness of inflammatory bowel disease (IBD) self-management. However, it is unclear which types of self-management interventions are effective. We conducted a systematic literature review to clarify the status and efficacy of self-management interventions for IBD.Searches were performed in databases including Embase, Medline, and Cochrane Library. Randomized, controlled studies of interventions in adult human participants with IBD involving a self-management component published in English from 2000 to 2020 were included. Studies were stratified based on study design, baseline demographic characteristics, methodological quality, and how outcomes were measured and analyzed for statistically significant improvements in outcomes, such as psychological health, quality of life, and healthcare resource usage.Among 50 studies included, 31 considered patients with IBD and 14 and 5 focused on patients with ulcerative colitis and Crohn's disease, respectively. Improvements in an outcome were reported in 33 (66%) studies. Most of the interventions that significantly improved an outcome index were based on symptom management and many of these were also delivered in combination with provision of information. We also note that among effective interventions, many were conducted with individualized and patient-participatory activities, and multidisciplinary healthcare practitioners were responsible for delivery of the interventions.Ongoing interventions that focus on symptom management with provision of information may support self-management behavior in patients with IBD. A participatory intervention targeting individuals was suggested to be an effective intervention method.© 2023 The Author(s). Published by S. Karger AG, Basel. - Keywords: Inflammatory bowel disease; Quality of life; Remote monitoring; Self-management; Symptom management -raw_completion_output: |- - genes: Not mentioned - exposures: Not mentioned - gene_exposures_relationships: Not mentioned -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - Not mentioned - - === - -extracted_object: - genes: - - Not mentioned - exposures: - - Not mentioned - gene_exposures_relationships: - - molecular_activity: Not mentioned - gene: Not mentioned -input_text: |- - Title: Construction of an Explanatory Model for Quality of Life in Outpatients with Ulcerative Colitis. - Abstract: To date, no studies have reported explanatory models of health-related quality of life (HRQoL) in patients with ulcerative colitis. Therefore, this study aimed to examine HRQoL and its related factors in outpatients with ulcerative colitis to construct an explanatory model.We conducted a cross-sectional survey at a clinic in Japan. The HRQoL was evaluated using the 32-item Inflammatory Bowel Disease Questionnaire. We extracted explanatory variables of HRQoL from demographic, physical, psychological, and social factors reported in previous studies and created a predictive explanatory model. The relationship between explanatory variables and the questionnaire total score was examined using Spearman's rank correlation coefficient, the Mann-Whitney test, or the Kruskal-Wallis test. We conducted multiple regression and path analyses to examine the effect of explanatory variables on the total score.We included 203 patients. Variables that were associated with the total score were the partial Mayo score (r = -0.451), treatment side effects (p = 0.004), the Hospital Anxiety and Depression Scale-Anxiety score (r = -0.678), the Hospital Anxiety and Depression Scale-Depression score (r = -0.528), and the availability of an advisor during difficult times (p = 0.001). The model included the partial Mayo score, treatment side effects, the Hospital Anxiety and Depression Scale-Anxiety score, and the availability of an advisor during difficult times as explanatory variables of the total score that showed the best goodness-of-fit (adjusted R2 = 0.597). The anxiety score exerted the greatest negative effect on the questionnaire total score (β = -0.586), followed by the partial Mayo score (β = -0.373), treatment side effects (β = 0.121), and availability of an advisor during difficult times (β = -0.101).Psychological symptoms exerted the strongest direct effect on HRQoL in outpatients with ulcerative colitis and mediated the relationship between social support and HRQoL. Nurses should listen carefully to the concerns and anxieties of patients to ensure that a social support system is provided by leveraging multidisciplinary collaborations.© 2023 The Author(s). Published by S. Karger AG, Basel. - Keywords: Psychological symptoms; Quality of life; Ulcerative colitis -raw_completion_output: |- - genes: - - exposures: - - gene_exposures_relationships: -prompt: |+ - From the text below, extract the following entities in the following format: - - genes: - exposures: - gene_exposures_relationships: - - - Text: - Title: Construction of an Explanatory Model for Quality of Life in Outpatients with Ulcerative Colitis. - Abstract: To date, no studies have reported explanatory models of health-related quality of life (HRQoL) in patients with ulcerative colitis. Therefore, this study aimed to examine HRQoL and its related factors in outpatients with ulcerative colitis to construct an explanatory model.We conducted a cross-sectional survey at a clinic in Japan. The HRQoL was evaluated using the 32-item Inflammatory Bowel Disease Questionnaire. We extracted explanatory variables of HRQoL from demographic, physical, psychological, and social factors reported in previous studies and created a predictive explanatory model. The relationship between explanatory variables and the questionnaire total score was examined using Spearman's rank correlation coefficient, the Mann-Whitney test, or the Kruskal-Wallis test. We conducted multiple regression and path analyses to examine the effect of explanatory variables on the total score.We included 203 patients. Variables that were associated with the total score were the partial Mayo score (r = -0.451), treatment side effects (p = 0.004), the Hospital Anxiety and Depression Scale-Anxiety score (r = -0.678), the Hospital Anxiety and Depression Scale-Depression score (r = -0.528), and the availability of an advisor during difficult times (p = 0.001). The model included the partial Mayo score, treatment side effects, the Hospital Anxiety and Depression Scale-Anxiety score, and the availability of an advisor during difficult times as explanatory variables of the total score that showed the best goodness-of-fit (adjusted R2 = 0.597). The anxiety score exerted the greatest negative effect on the questionnaire total score (β = -0.586), followed by the partial Mayo score (β = -0.373), treatment side effects (β = 0.121), and availability of an advisor during difficult times (β = -0.101).Psychological symptoms exerted the strongest direct effect on HRQoL in outpatients with ulcerative colitis and mediated the relationship between social support and HRQoL. Nurses should listen carefully to the concerns and anxieties of patients to ensure that a social support system is provided by leveraging multidisciplinary collaborations.© 2023 The Author(s). Published by S. Karger AG, Basel. - Keywords: Psychological symptoms; Quality of life; Ulcerative colitis - - === - -extracted_object: {} -input_text: |- - Title: Smoking Is Not an Independent Risk Factor for Surgery in Patients with Crohn's Disease on Biologic Therapy. - Abstract: The development and course of inflammatory bowel disease appear to be influenced by environmental factors. Particularly, smoking has been shown to assume a harmful role in Crohn's disease (CD) and a protective role in ulcerative colitis. This study aims to examine the effect of smoking on need for surgery in patients with moderate to severe CD receiving biologic therapy.This was a retrospective study of adult patients with CD at a University Medical Center over a 20-year period.A total of 251 patients were included (mean age 36.0 ± 15.0; 70.1% males; current, former, and nonsmokers: 44.2%, 11.6%, and 43.8%, respectively). Mean duration on biologics was 5.0 ± 3.1 years (>2/3 received anti-TNFs, followed by ustekinumab in 25.9%) and a third of patients (29.5%) received more than one biologic. Disease-related surgeries (abdominal, perianal, or both) occurred in 97 patients (38.6%): 50 patients had surgeries prior to starting biologics only, 41 had some surgeries after, and 6 had insufficient information. There was no significant difference in surgeries between ever-smokers (current or previous) versus nonsmokers in the overall study group. On logistic regression, the odds of having any CD surgery were higher in patients with longer disease duration (OR = 1.05, 95% CI = 1.01, 1.09) and in those receiving more than one biologic (OR = 2.31, 95% CI = 1.16, 4.59). However, among patients who had surgery prior to biologic therapy, smokers were more likely to have perianal surgery compared to nonsmokers (OR = 10.6, 95% CI = 2.0, 57.4; p = 0.006).In biologic-naive CD patients requiring surgery, smoking is an independent predictor of perianal surgery. Smoking, however, is not an independent risk factor for surgery in this cohort after starting biologics. The risk of surgery in those patients is primarily associated with disease duration and the use of more than one biologic.© 2023 The Author(s). Published by S. Karger AG, Basel. - Keywords: Abdominal surgery; Adalimumab; Anti-Tumor necrosis factor; Crohn’s disease; Fistula; Infliximab; Perianal; Tobacco; Ustekinumab; Vedolizumab -raw_completion_output: |- - genes: None mentioned in the text. - exposures: smoking - gene_exposures_relationships: None mentioned in the text. -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - None mentioned in the text. - - === - -extracted_object: - genes: - - None mentioned in the text. - exposures: - - NCIT:C154329 - gene_exposures_relationships: - - molecular_activity: None mentioned in the text. - gene: None mentioned in the text. -named_entities: - - id: NCIT:C154329 - label: smoking -input_text: |- - Title: Gene-based microbiome representation enhances host phenotype classification. - Abstract: With the concomitant advances in both the microbiome and machine learning fields, the gut microbiome has become of great interest for the potential discovery of biomarkers to be used in the classification of the host health status. Shotgun metagenomics data derived from the human microbiome is composed of a high-dimensional set of microbial features. The use of such complex data for the modeling of host-microbiome interactions remains a challenge as retaining de novo content yields a highly granular set of microbial features. In this study, we compared the prediction performances of machine learning approaches according to different types of data representations derived from shotgun metagenomics. These representations include commonly used taxonomic and functional profiles and the more granular gene cluster approach. For the five case-control datasets used in this study (Type 2 diabetes, obesity, liver cirrhosis, colorectal cancer, and inflammatory bowel disease), gene-based approaches, whether used alone or in combination with reference-based data types, allowed improved or similar classification performances as the taxonomic and functional profiles. In addition, we show that using subsets of gene families from specific functional categories of genes highlight the importance of these functions on the host phenotype. This study demonstrates that both reference-free microbiome representations and curated metagenomic annotations can provide relevant representations for machine learning based on metagenomic data. IMPORTANCE Data representation is an essential part of machine learning performance when using metagenomic data. In this work, we show that different microbiome representations provide varied host phenotype classification performance depending on the dataset. In classification tasks, untargeted microbiome gene content can provide similar or improved classification compared to taxonomical profiling. Feature selection based on biological function also improves classification performance for some pathologies. Function-based feature selection combined with interpretable machine learning algorithms can generate new hypotheses that can potentially be assayed mechanistically. This work thus proposes new approaches to represent microbiome data for machine learning that can potentiate the findings associated with metagenomic data. - Keywords: endocannabinoidome; feature selection; gene clusters; gut-brain axis; interpretable models; machine learning; metabolic health; metagenomics; microbiome; shotgun microbiome -raw_completion_output: |- - genes: gene-based approaches, gene families - exposures: gut microbiome, taxonomic and functional profiles, gene cluster approach, reference-based data types, metagenomic annotations, metagenomic data - gene_exposures_relationships: reference-based data types - gene-based approaches; gene families - specific functional categories of genes -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - gene families - specific functional categories of genes - - === - -extracted_object: - genes: - - gene-based approaches, gene families - exposures: - - gut microbiome, taxonomic and functional profiles, gene cluster approach, reference-based - data types, metagenomic annotations, metagenomic data - gene_exposures_relationships: - - molecular_activity: reference-based data types - gene: gene-based approaches - - molecular_activity: specific functional categories of genes - gene: gene families -input_text: |- - Title: Development of the intestinal microbiome in cystic fibrosis in early life. - Abstract: Cystic fibrosis (CF) is a heritable disease that causes altered physiology at mucosal sites; these changes result in chronic infections in the lung, significant gastrointestinal complications as well as dysbiosis of the gut microbiome, although the latter has been less well explored. Here, we describe the longitudinal development of the gut microbiome in a cohort of children with CF (cwCF) from birth through early childhood (0-4 years of age) using 16S rRNA gene amplicon sequencing of stool samples as a surrogate for the gut microbiota. Similar to healthy populations, alpha diversity of the gut microbiome increases significantly with age, but diversity plateaus at ~2 years of age for this CF cohort. Several taxa that have been associated with dysbiosis in CF change with age toward a more healthy-like composition; notable exceptions include Akkermansia, which decreases with age, and Blautia, which increases with age. We also examined the relative abundance and prevalence of nine taxa associated with CF lung disease, several of which persist across early life, highlighting the possibility of the lung being seeded directly from the gut early in life. Finally, we applied the Crohn's Dysbiosis Index to each sample, and found that high Crohn's-associated dysbiosis early in life (<2 years) was associated with significantly lower Bacteroides in samples collected from 2 to 4 years of age. Together, these data comprise an observational study that describes the longitudinal development of the CF-associated gut microbiota and suggest that early markers associated with inflammatory bowel disease may shape the later gut microbiota of cwCF. IMPORTANCE Cystic fibrosis is a heritable disease that disrupts ion transport at mucosal surfaces, causing a buildup of mucus and dysregulation of microbial communities in both the lungs and the intestines. Persons with CF are known to have dysbiotic gut microbial communities, but the development of these communities over time beginning at birth has not been thoroughly studied. Here, we describe an observation study following the development of the gut microbiome of cwCF throughout the first 4 years of life, during the critical window of both gut microbiome and immune development. Our findings indicate the possibility of the gut microbiota as a reservoir of airway pathogens and a surprisingly early indication of a microbiota associated with inflammatory bowel disease. - Keywords: Crohn’s disease; cystic fibrosis; gut; microbiome -raw_completion_output: |- - genes: N/A - exposures: Crohn's disease; cystic fibrosis - gene_exposures_relationships: N/A -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - N/A - - === - -extracted_object: - genes: - - N/A - exposures: - - Crohn's disease - - cystic fibrosis - gene_exposures_relationships: - - molecular_activity: N/A - gene: N/A -input_text: |- - Title: Frail Phenotype in Patients With Inflammatory Bowel Disease. - Abstract: - Keywords: -raw_completion_output: |- - genes: - exposures: - gene_exposures_relationships: -prompt: |+ - From the text below, extract the following entities in the following format: - - genes: - exposures: - gene_exposures_relationships: - - - Text: - Title: Frail Phenotype in Patients With Inflammatory Bowel Disease. - Abstract: - Keywords: - - === - -extracted_object: {} -input_text: |- - Title: Physical activity, quality of diet and bone mineral density in patients with inflammatory bowel disease. - Abstract: The aim of this study was to find an association between moderate, vigorous and total physical activity (PA); diet quality; and bone mineral density (BMD) among patients suffering from inflammatory bowel disease (IBD).We enrolled 54 IBD patients, including those with Crohn's disease (CD) and ulcerative colitis (UC), and 24 healthy adults. All subjects completed the Questionnaire of Eating Behaviour based on which prohealthy and nonhealthy diet indexes were calculated, and the questionnaire included questions from the International Physical Activity Questionnaire. Prohealthy and nonhealthy diet indexes were divided into low-, medium- and high scores. BMD and T- and Z-scores of the lumbar spine (L1-L4) and femoral neck (FN) were assessed using dual-energy X-ray absorptiometry method.BMD, T- and Z-scores of the FN and the Z-score of L1-L4 were significantly lower among patients with CD and UC than healthy controls. We did not find any differences in the time of PA among CD, UC and control groups (CG). The prohealthy diet index was higher among healthy subjects than the CD and UC groups. The nonhealthy diet index was lower among UC patients compared with the CG or CD patients. Prohealthy diet index positively correlated with BMD and T- and Z-scores of L1-L4 and FN in IBD. The prohealthy diet index correlated negatively with C-reactive protein and positively with body mass index. The prohealthy diet index correlated only with total PA in the CD group.A well-balanced diet and proper PA may decrease the risk of osteoporosis in IBD, so education of patients referring to nutrition and PA is needed.© 2023 British Dietetic Association. - Keywords: bone mineral density; diet quality; inflammatory bowel disease; osteoporosis; physical activity -raw_completion_output: |- - genes: N/A - exposures: diet quality; physical activity - gene_exposures_relationships: N/A -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - N/A - - === - -extracted_object: - genes: - - N/A - exposures: - - diet quality - - NCIT:C17708 - gene_exposures_relationships: - - molecular_activity: N/A - gene: N/A -named_entities: - - id: NCIT:C17708 - label: physical activity -input_text: |- - Title: Sweet Syndrome Associated with Active Inflammatory Bowel Disease: A Case Series of a Rare Extra-intestinal Manifestation. - Abstract: Cutaneous extra-intestinal manifestations (EIM) occur in up to 20% of patients with IBD. Information about Sweet syndrome (SS)'s clinical course as a rare cutaneous EIM in IBD is limited to case reports. We present the largest retrospective cohort on the occurrence and management of SS in IBD.Electronic medical records and paper charts since 1980 were retrospectively reviewed at a large quaternary medical center to identify all adult IBD patients with histopathology-proven SS. Patient characteristics and clinical outcomes were evaluated.25 IBD patients with SS were identified; 3 patients were assessed to have AZA-induced SS. The majority of SS patients were female. Median age at diagnosis was 47 years (IQR 33-54 years) and SS appeared at a median of 6.4 years after IBD diagnosis. IBD patients with SS had a high rate of complicated IBD phenotypes (75% extensive colitis in UC and 73% stricturing or penetrating disease in CD, with 100% colonic involvement), as well as frequent co-occurring EIMs (60%). SS correlated with global IBD disease activity. Corticosteroids were an effective therapy for SS in IBD. Recurrence rate of SS was 36%.Contrary to previous case reports, SS was a cutaneous EIM occurring late after diagnosis of IBD in our cohort, with occurrences paralleling global IBD disease activity. Although AZA-induced and IBD-associated SS were both effectively treated with corticosteroids, distinguishing them is relevant for future IBD treatment strategies.© 2023. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature. - Keywords: Azathioprine; Colitis; Cutaneous manifestations; Extra-intestinal manifestation; Inflammatory bowel disease; Sweet syndrome -raw_completion_output: |- - genes: Not mentioned in the text - exposures: Azathioprine - gene_exposures_relationships: Azathioprine -> Sweet syndrome -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - Azathioprine -> Sweet syndrome - - === - -extracted_object: - genes: - - Not mentioned in the text - exposures: - - Azathioprine - gene_exposures_relationships: - - molecular_activity: Azathioprine - gene: Sweet syndrome -input_text: |- - Title: Decreased Risk of Preeclampsia in Women with Inflammatory Bowel Disease on Anti-Tumor Necrosis Factor Therapy. - Abstract: Evidence suggests that upregulation of tumor necrosis factor-alpha (TNF-α) plays a role in immune dysregulation in both preeclampsia and inflammatory bowel disease (IBD).We aimed to investigate whether anti-TNF therapy during pregnancy decreases the risk of preeclampsia in women with IBD.The study population included women with IBD and pregnancies who were followed at a tertiary care center from 2007 to 2021. Cases of preeclampsia were compared with controls with a normotensive pregnancy. Data on patient demographics, disease type and activity, pregnancy complications, and additional risk factors for preeclampsia were collected. The association between anti-TNF therapy and preeclampsia was analyzed using univariate analysis and multivariate logistic regression.Women with preeclampsia were more likely to have a preterm delivery (44% vs. 12%, p < 0.001). More women without preeclampsia were exposed to anti-TNF therapy during pregnancy than women with preeclampsia (55% vs. 30%, p = 0.029). The majority of women (32/44) on anti-TNF therapy, either adalimumab or infliximab, continued to have some degree of exposure during the third trimester. Though not significant, multivariate analysis showed a trend towards a protective effect of anti-TNF therapy against developing preeclampsia if exposed during the third trimester (OR 0.39; 95% CI 0.14-1.12, p = 0.08).In this study, anti-TNF therapy exposure was higher in IBD patients who did not develop preeclampsia than in those who did. While not significant, there was a trend towards a protective effect of anti-TNF therapy against preeclampsia if exposed during the third trimester.© 2023. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature. - Keywords: Anti-TNF; Crohn’s disease; Inflammatory bowel disease; Preeclampsia; Pregnancy; TNF-α; Ulcerative colitis -raw_completion_output: |- - genes: TNF-α - - exposures: anti-TNF therapy - - gene_exposures_relationships: TNF-α to anti-TNF therapy -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - TNF-α to anti-TNF therapy - - === - -extracted_object: - genes: - - TNF-α - exposures: - - anti-TNF therapy - gene_exposures_relationships: - - molecular_activity: TNF-α - gene: anti-TNF therapy -input_text: |- - Title: Inflammatory bowel disease is not linked to a higher rate of adverse events in colonoscopy - a nationwide population-based study in Sweden. - Abstract: Inflammatory bowel disease may cause long-standing inflammation and fibrosis and may increase the risk of adverse events in colonoscopy. We evaluated whether inflammatory bowel disease and other potential risk factors are associated with bleeding or perforation in a nationwide population-based Swedish study.Data from 969,532 colonoscopies, including 164,012 (17%) on inflammatory bowel disease patients, between 2003 and 2019 were retrieved from the National Patient Registers. ICD-10 codes for bleeding (T810) and perforation (T812) within 30 days of the colonoscopy were recorded. Multivariable logistic regression was used to test if inflammatory bowel disease status, inpatient setting, time period, general anesthesia, age, sex, endoscopic procedures and antithrombotic treatment were associated with higher odds for bleeding and perforation.Bleeding and perforation were reported in 0.19% and 0.11% of all colonoscopies, respectively. Bleeding (Odds Ratio 0.66, p < 0.001) and perforation (Odds Ratio 0.79, p < 0.033) were less likely in colonoscopies in individuals with inflammatory bowel disease status. Bleeding and perforation were more common in inpatient inflammatory bowel disease colonoscopies compared with outpatient. The odds for bleeding but not perforation increased between 2003 to 2019. General anesthesia was associated with double the odds for perforation.Individuals with inflammatory bowel disease did not have more adverse events compared with individuals without inflammatory bowel disease status. However, inpatient setting was associated with more adverse events, especially in inflammatory bowel disease status. General anesthesia was associated with a greater risk of perforation.© The Author(s) 2023. Published by Oxford University Press on behalf of European Crohn’s and Colitis Organisation. All rights reserved. For permissions, please email: journals.permissions@oup.com. - Keywords: Gastrointestinal Bleeding; Inflammatory Bowel Disease; Perforation -raw_completion_output: |- - genes: - - exposures: inflammatory bowel disease, general anesthesia, antithrombotic treatment - - gene_exposures_relationships: inflammatory bowel disease - bleeding, perforation; general anesthesia - perforation -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - general anesthesia - perforation - - === - -extracted_object: - exposures: - - inflammatory bowel disease, general anesthesia, antithrombotic treatment - gene_exposures_relationships: - - molecular_activity: inflammatory bowel disease - gene: perforation - - molecular_activity: general anesthesia - gene: perforation -input_text: |- - Title: Major Adverse Cardiovascular Events by Baseline Cardiovascular Risk in Patients with Ulcerative Colitis Treated with Tofacitinib: Data from the OCTAVE Clinical Programme. - Abstract: Patients with inflammatory bowel disease have increased risk of atherosclerotic cardiovascular [CV] disease [ASCVD]. Tofacitinib is an oral small molecule Janus kinase inhibitor for treatment of ulcerative colitis [UC]. We report major adverse CV events [MACE] in the UC OCTAVE programme, stratified by baseline CV risk.Rates of MACE were analysed by baseline [first tofacitinib exposure] CV risk profile: prior ASCVD, or 10-year ASCVD risk categories [low, borderline, intermediate, high].Of 1157 patients [2814.4 patient-years' exposure; ≤7.8 years' tofacitinib treatment], 4% had prior ASCVD and 83% had no prior ASCVD and low-borderline baseline 10-year ASCVD risk. Eight patients [0.7%] developed MACE; one had prior ASCVD. Incidence rates [unique patients with events/100 patient-years of exposure; 95% confidence intervals] for MACE were: 0.95 [0.02-5.27] in patients with prior ASCVD; and 1.81 [0.05-10.07], 1.54 [0.42-3.95], 0.00 [0.00-2.85], and 0.09 [0.01-0.32] in patients without prior ASCVD and with high, intermediate, borderline, and low baseline 10year ASCVD risk, respectively. For the 5/7 patients with MACE and without prior ASCVD, 10year ASCVD risk scores were numerically higher [>1%] prior to MACE versus at baseline, primarily due to increasing age.Most patients receiving tofacitinib in the UC OCTAVE programme had low baseline 10-year ASCVD risk. MACE were more frequent in patients with prior ASCVD and higher baseline CV risk. This analysis demonstrates potential associations between baseline CV risk and MACE in patients with UC, suggesting CV risk should be assessed individually in clinical practice.© The Author(s) 2023. Published by Oxford University Press on behalf of European Crohn’s and Colitis Organisation. - Keywords: cardiovascular risk; inflammatory bowel disease; ulcerative colitis -raw_completion_output: |- - genes: None mentioned in the given text - exposures: Tofacitinib - gene_exposures_relationships: None mentioned in the given text -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - None mentioned in the given text - - === - -extracted_object: - genes: - - None mentioned in the given text - exposures: - - Tofacitinib - gene_exposures_relationships: - - molecular_activity: None mentioned in the given text - gene: None mentioned in the given text -input_text: |- - Title: Relevance of sonographic parameters for inflammatory bowel disease in children. - Abstract: Intestinal ultrasound (IUS) is widely used as the first exam in patients with suspected inflammatory bowel disease (IBD). This study investigated the accuracy of several IUS parameters, including increased bowel wall thickening (BWT), in detecting IBD in a paediatric population.The study included an unselected series of 113 patients aged 2-18 years (mean age 10.8 years, 65 male), referred for recurrent abdominal pain or altered bowel habits, without known organic diseases, to perform an IUS as first investigation of a diagnostic workup. Patients with full systematic IUS examination, clinical and biochemical exams, and ileocolonoscopy or an uneventful follow-up at least one year follow up were eligible.23 IBD patients (20.4%; 8 ulcerative colitis, 12 Crohn's disease and 3 indeterminate colitis) were diagnosed. We found that increased BWT > 3 mm (OR 5.4), altered IUS bowel pattern (IUS-BP, OR 9.8) and mesenteric hypertrophy (MH, OR 5.2) accurately identified IBD at the multivariate analysis. IUS-BP, MH and BWT > 3 mm had a sensitivity of 78.3%, 65.2% and 69.6% and a specificity of 93.3%, 92.2% and 96.7%, respectively. The combination of these three alterations increased the specificity up to 100%, whilst decreased sensitivity to 56.5%.Among several US parameters suggestive of IBD, the increased BWT, MH and altered echopattern are independent predictors of IBD. The ultrasonographic diagnosis of IBD could be more accurate if relied on combination of different sonographic parameters, than on the sole BWT evaluation.© 2023. The Author(s). - Keywords: Bowel wall thickness; Children; Fecal calprotectin; Inflammatory bowel diseases; Intestinal ultrasound; Ultrasound -raw_completion_output: |- - genes: None mentioned in the text - exposures: Fecal calprotectin - gene_exposures_relationships: None mentioned in the text -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - None mentioned in the text - - === - -extracted_object: - genes: - - None mentioned in the text - exposures: - - Fecal calprotectin - gene_exposures_relationships: - - molecular_activity: None mentioned in the text - gene: None mentioned in the text -input_text: |- - Title: Fecal acute phase proteins in cats with chronic enteropathies. - Abstract: Chronic enteropathies (CE) are common in cats and reliable biomarkers that can distinguish different causes and predict or monitor response to treatment are currently lacking.To evaluate certain acute phase proteins in feces that could potentially be used as biomarkers in cats with CE.Twenty-eight cats with either inflammatory bowel disease (IBD; n = 13), food-responsive enteropathy (FRE; n = 3) or small cell gastrointestinal lymphoma (SCGL; n = 12) and 29 healthy control cats were prospectively enrolled.Fecal concentrations of haptoglobin, alpha-1-acid-glycoprotein (AGP), pancreatitis-associated protein-1 (PAP-1), ceruloplasmin, and C-reactive protein (CRP) were measured using Spatial Proximity Analyte Reagent Capture Luminescence (SPARCL) immunoassays before and after initiation of treatment. Cats were treated with diet and/or prednisolone (IBD cats), plus chlorambucil (SCGL cats).Compared with controls, median fecal AGP concentrations were significantly lower (25.1 vs 1.8 μg/g; P = .003) and median fecal haptoglobin (0.17 vs 0.5 μg/g), PAP-1 (0.04 vs 0.4 μg/g) and ceruloplasmin (0.15 vs 4.2 μg/g) concentrations were significantly higher (P < .001) in cats with CE. Median fecal AGP concentrations were significantly lower (P = .01) in cats with IBD and FRE (0.6 μg/g) compared with cats with SCGL (10.75 μg/g). A significant reduction was found in CE cats after treatment for median fecal ceruloplasmin concentrations (6.36 vs 1.16 μg/g; P = .04).Fecal AGP concentration shows promise to differentiate cats with SCGL from cats with IBD and FRE. Fecal ceruloplasmin concentrations may be useful to objectively monitor response to treatment in cats with CE.© 2023 The Authors. Journal of Veterinary Internal Medicine published by Wiley Periodicals LLC on behalf of American College of Veterinary Internal Medicine. - Keywords: AGP; PAP-1; ceruloplasmin; fecal biomarkers; haptoglobin -raw_completion_output: |- - genes: - - exposures: PAP-1; ceruloplasmin; haptoglobin; alpha-1-acid-glycoprotein (AGP); C-reactive protein (CRP) - - gene_exposures_relationships: PAP-1 to molecular activity; ceruloplasmin to molecular activity; haptoglobin to molecular activity; alpha-1-acid-glycoprotein (AGP) to molecular activity; C-reactive protein (CRP) to molecular activity -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - C-reactive protein (CRP) to molecular activity - - === - -extracted_object: - exposures: - - PAP-1 - - ceruloplasmin - - haptoglobin - - alpha-1-acid-glycoprotein (AGP) - - C-reactive protein (CRP) - gene_exposures_relationships: - - molecular_activity: PAP-1 - gene: molecular activity - - molecular_activity: exposure to a chemical toxin - gene: ceruloplasmin - - molecular_activity: molecular activity - gene: haptoglobin - - molecular_activity: molecular activity - gene: HGNC:30889 - - molecular_activity: C-reactive protein (CRP) - gene: molecular activity -named_entities: - - id: HGNC:30889 - label: alpha-1-acid-glycoprotein (AGP) -input_text: |- - Title: Does intestinal obstruction influence hypo-albuminemia: assessment of the physio-pathogenesis of protein-losing enteropathy with literature review. - Abstract: Non-steroidal anti-inflammatory drug (NSAID) use may cause diaphragm-like lesions in the bowel. Although NSAID-enteropathy is among the causes of protein-losing enteropathy (PLE), intractable hypoalbuminemia is rare.Here, we discuss a case of NSAID-enteropathy with a diaphragm-like disease that presented with Protein Losing Enteropathy (PLE) rather than obstruction. The hypoalbuminemia recovered immediately after resection of the obstructive segment, despite ongoing annular ulcerations in the early postoperative period. Thus, it was not clear whether obstructive mechanisms influenced resistant hypoalbuminemia besides the ulcers. We also reviewed the English-written literature for "diaphragm-type lesion, NSAID-enteropathy, obstruction, and protein-losing enteropathy". We noted that the role of obstruction in the pathophysiology of PLE was not clear.As our case and a couple of cases reported in literature, slow-onset obstructive pathology seems to contribute to well-known factors: inflammatory response, exudation, tight-junction dysfunction, and increase in permeability in the physiopathology of NSAID-induced PLE. Factors such as distention-induced low-flow ischemia and reperfusion, cholecystectomy-related continuous bile flow, bacterial overgrowth-related bile deconjugation and concomitant inflammation are among other potential influencers. The possible role of a slow-onset obstructive pathology in the physiopathology of NSAID-induced and other PLE needs to be further elucidated. - Keywords: -raw_completion_output: |- - genes: not mentioned in the text - exposures: non-steroidal anti-inflammatory drug (NSAID) - gene_exposures_relationships: not mentioned in the text -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - not mentioned in the text - - === - -extracted_object: - genes: - - not mentioned in the text - exposures: - - CHEBI:35475 - gene_exposures_relationships: - - molecular_activity: not mentioned in the text - gene: not mentioned in the text -named_entities: - - id: CHEBI:35475 - label: non-steroidal anti-inflammatory drug (NSAID) -input_text: |- - Title: Comparison of infliximab with adalimumab in biologic-naïve patients with Crohn's disease: a single-center 13-year experience. - Abstract: Long-term comparison studies between infliximab (IFX) and adalimumab (ADA) with or without immunomodulator therapy are still needed in Crohn's disease (CD). In this study, we evaluated IFX and ADA for long-term clinical effectiveness and safety in CD patients who had not previously received a biologic treatment.The data of adult CD patients were collected retrospectively between December 2007 and February 2021. We compared CD-related hospitalization, CD-related abdominal surgery, steroid use, and serious infections.Out of 224 CD patients, 101 started IFX first (median age: 38.12 years, 61.4% male), while 123 started ADA first (median age: 30.2 years, 64.2% male). The disease durations were 7.01 years and 6.91 years for IFX and ADA, respectively. There were no significant differences between the two groups with respect to age, gender, smoking, immunomodulator usage, and disease activity score at the onset of anti-TNF therapy (p>0.05). Overall, the median follow-up time was 2.36 and 1.86 years after starting anti-tumor necrosis factor-alpha (anti-TNF) therapy in the IFX and ADA groups, respectively. Steroid use (4.0% vs. 10.6%, p=0.109), hospitalization for CD (13.9% vs. 22.8%, p=0.127), abdominal surgery for CD (9.9% vs. 13.0%, p=0.608), and major infections (1.0% vs. 0.8%, p>0.999) did not differ significantly from one another. There were also no significant differences in the rates of these outcomes between concomitant immunomodulator therapy and monotherapy (p>0.05).In this study, we observed no significant differences in the long-term effectiveness and safety of IFX and ADA in biologic-naïve patients with CD. - Keywords: -raw_completion_output: |- - genes: IFX, ADA, CD - - exposures: immunomodulator therapy, anti-TNF therapy - - gene_exposures_relationships: IFX - immunomodulator therapy; ADA - immunomodulator therapy; IFX - anti-TNF therapy; ADA - anti-TNF therapy -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - ADA - anti-TNF therapy - - === - -extracted_object: - genes: - - IFX, ADA, CD - exposures: - - immunomodulator therapy, anti-TNF therapy - gene_exposures_relationships: - - molecular_activity: immunomodulator therapy - gene: IFX - - molecular_activity: immunomodulator therapy - gene: HGNC:186 - - molecular_activity: anti-TNF therapy - gene: IFX - - molecular_activity: anti-TNF therapy - gene: HGNC:186 -named_entities: - - id: HGNC:186 - label: ADA -input_text: |- - Title: Disease clearance in ulcerative colitis: Is the ultimate therapeutic target? - Abstract: - Keywords: IBD; gastroenterology; inflammation; inflammatory bowel disease; ulcerative colitis -raw_completion_output: |- - genes: none mentioned - exposures: none mentioned - gene_exposures_relationships: none mentioned -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - none mentioned - - === - -extracted_object: - genes: - - none mentioned - exposures: - - none mentioned - gene_exposures_relationships: - - molecular_activity: none mentioned - gene: none mentioned -input_text: |- - Title: Dissecting the effect of ileal faecal diversion on the intestine using single-cell sequencing. - Abstract: Although ileal faecal diversion is commonly used in clinical settings, complications accompany it. Elucidating the intestinal changes caused by ileal faecal diversion will help resolve postoperative complications and elucidate the pathogenic mechanisms of associated intestinal disorders, such as Crohn's disease (CD). Therefore, our study aimed to provide new insights into the effects of ileal faecal diversion on the intestine and the potential mechanisms.Single-cell RNA sequencing was performed on proximal functional and paired distal defunctioned intestinal mucosae from three patients with ileal faecal diversion. We also performed in vitro cellular and animal experiments, tissue staining and analysed public datasets to validate our findings.We found that the epithelium in the defunctioned intestine tended to be immature, with defective mechanical and mucous barriers. However, the innate immune barrier in the defunctioned intestine was enhanced. Focusing on the changes in goblet cells, we demonstrated that mechanical stimulation promotes the differentiation and maturation of goblet cells through the TRPA1-ERK pathway, indicating that the absence of mechanical stimulation may be the main cause of defects in the goblet cells of the defunctioned intestine. Furthermore, we found obvious fibrosis with a pro-fibrotic microenvironment in the defunctioned intestine and identified that monocytes may be important targets for faecal diversion to alleviate CD.This study revealed the different transcription landscapes of various cell subsets and the potential underlying mechanisms within the defunctioned intestine, when compared to the functional intestine, based on the background of ileal faecal diversion. These findings provide novel insights for understanding the physiological and pathological roles of the faecal stream in the intestine.© 2023 The Authors. Clinical and Translational Medicine published by John Wiley & Sons Australia, Ltd on behalf of Shanghai Institute of Clinical Bioinformatics. - Keywords: Crohn's disease; TRPA1; fibrosis; ileal faecal diversion; intestinal goblet cells; single-cell RNA sequencing -raw_completion_output: |- - genes: TRPA1 - exposures: ileal faecal diversion - gene_exposures_relationships: TRPA1-ERK pathway; faecal diversion -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - faecal diversion - - === - -extracted_object: - genes: - - HGNC:497 - exposures: - - ileal faecal diversion - gene_exposures_relationships: - - molecular_activity: TRPA1-ERK pathway - gene: None - - molecular_activity: exposure to a chemical toxin. - gene: faecal diversion -named_entities: - - id: HGNC:497 - label: TRPA1 -input_text: |- - Title: Diet high in linoleic acid dysregulates the intestinal endocannabinoid system and increases susceptibility to colitis in Mice. - Abstract: Inflammatory bowel disease (IBD) is a multifactorial disease with increasing incidence in the U.S. suggesting that environmental factors, including diet, are involved. It has been suggested that excessive consumption of linoleic acid (LA, C18:2 omega-6), which must be obtained from the diet, may promote the development of IBD in humans. To demonstrate a causal link between LA and IBD, we show that a high fat diet (HFD) based on soybean oil (SO), which is comprised of ~55% LA, increases susceptibility to colitis in several models, including IBD-susceptible IL10 knockout mice. This effect was not observed with low-LA HFDs derived from genetically modified soybean oil or olive oil. The conventional SO HFD causes classical IBD symptoms including immune dysfunction, increased intestinal epithelial barrier permeability, and disruption of the balance of isoforms from the IBD susceptibility gene Hepatocyte Nuclear Factor 4α (HNF4α). The SO HFD causes gut dysbiosis, including increased abundance of an endogenous adherent invasive Escherichia coli (AIEC), which can use LA as a carbon source. Metabolomic analysis shows that in the mouse gut, even in the absence of bacteria, the presence of soybean oil increases levels of LA, oxylipins and prostaglandins. Many compounds in the endocannabinoid system, which are protective against IBD, are decreased by SO both in vivo and in vitro. These results indicate that a high LA diet increases susceptibility to colitis via microbial and host-initiated pathways involving alterations in the balance of bioactive metabolites of omega-6 and omega-3 polyunsaturated fatty acids, as well as HNF4α isoforms. - Keywords: HNF4α; IBD; PUFAs; adherent invasive E.Coli; epithelial barrier function; gut microbiome; metabolomics; olive oil; oxylipins; soybean oil -raw_completion_output: |- - genes: IL10, Hepatocyte Nuclear Factor 4α (HNF4α) - exposures: linoleic acid (LA), soybean oil (SO), omega-6 and omega-3 polyunsaturated fatty acids, adherent invasive Escherichia coli (AIEC) - gene_exposures_relationships: IL10 - linoleic acid (LA); Hepatocyte Nuclear Factor 4α (HNF4α) - linoleic acid (LA), soybean oil (SO) -prompt: |+ - From the text below, extract the following entities in the following format: - - molecular_activity: - gene: - - - Text: - Hepatocyte Nuclear Factor 4α (HNF4α) - linoleic acid (LA), soybean oil (SO) - - === - -extracted_object: - genes: - - IL10, Hepatocyte Nuclear Factor 4α (HNF4α) - exposures: - - CHEBI:17351 - gene_exposures_relationships: - - molecular_activity: CHEBI:17351 - gene: HGNC:5962 - - molecular_activity: exposure to a chemical toxin. - gene: Hepatocyte Nuclear Factor 4α (HNF4α) -named_entities: - - id: CHEBI:17351 - label: linoleic acid (LA), soybean oil (SO), omega-6 and omega-3 polyunsaturated - fatty acids, adherent invasive Escherichia coli (AIEC) - - id: HGNC:5962 - label: IL10 -input_text: |- - Title: A catalog of bacterial reference genomes from cultivated human oral bacteria. - Abstract: The oral cavity harbors highly diverse communities of microorganisms. However, the number of isolated species and high-quality genomes is limited. Here we present a Cultivated Oral Bacteria Genome Reference (COGR), comprising 1089 high-quality genomes based on large-scale aerobic and anaerobic cultivation of human oral bacteria isolated from dental plaques, tongue, and saliva. COGR covers five phyla and contains 195 species-level clusters of which 95 include 315 genomes representing species with no taxonomic annotation. The oral microbiota differs markedly between individuals, with 111 clusters being person-specific. Genes encoding CAZymes are abundant in the genomes of COGR. Members of the Streptococcus genus make up the largest proportion of COGR and many of these harbor entire pathways for quorum sensing important for biofilm formation. Several clusters containing unknown bacteria are enriched in individuals with rheumatoid arthritis, emphasizing the importance of culture-based isolation for characterizing and exploiting oral bacteria.© 2023. The Author(s). - Keywords: -raw_completion_output: |- - genes: Streptococcus - exposures: quorum sensing - gene_exposures_relationships: Streptococcus-gene expression in quorum sensing -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - Streptococcus-gene expression in quorum sensing - - === - -extracted_object: - genes: - - Streptococcus - exposures: - - quorum sensing - gene_exposures_relationships: - - molecular_activity: quorum sensing - gene: Streptococcus -input_text: |- - Title: Letter to Editor in Response to: The Use of Perioperative Nutrition Score in Postoperative Pediatric Inflammatory Bowel Disease. - Abstract: - Keywords: -raw_completion_output: |- - genes: Not mentioned in the text - exposures: Not mentioned in the text - gene_exposures_relationships: Not mentioned in the text -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - Not mentioned in the text - - === - -extracted_object: - genes: - - Not mentioned in the text - exposures: - - Not mentioned in the text - gene_exposures_relationships: - - molecular_activity: Not mentioned in the text - gene: Not mentioned in the text -input_text: |- - Title: Assessing Serious Infections in Children Exposed In Utero to Ustekinumab. - Abstract: Chronic inflammatory conditions, including inflammatory bowel disease (IBD), psoriasis (PsO), and psoriatic arthritis (PsA), have a high burden among women of reproductive age. There has been significant interest in finding safe ways of controlling disease activity during pregnancy without adversely affecting the pregnancy or offspring. - Keywords: -raw_completion_output: |- - genes: None mentioned in the text - exposures: Ustekinumab - gene_exposures_relationships: None mentioned in the text -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - None mentioned in the text - - === - -extracted_object: - genes: - - None mentioned in the text - exposures: - - Ustekinumab - gene_exposures_relationships: - - molecular_activity: None mentioned in the text - gene: None mentioned in the text -input_text: |- - Title: Impact of the Affordable Care Act on Providing Equitable Healthcare Access for Inflammatory Bowel Disease in the Kentucky Appalachian Region. - Abstract: Medicaid expansion improved insurance coverage for patients with chronic conditions and low income. The effect of Medicaid expansion on patients with inflammatory bowel disease from high-poverty communities is unknown.This study aimed to evaluate the impact of Medicaid expansion in Kentucky on care for inflammatory bowel disease patients from the Eastern-Kentucky Appalachian community, a historically impoverished area.This study was a retrospective, descriptive, ecological study.This study was conducted in Kentucky using the Hospital Inpatient Discharge and Outpatient Services Database.All encounters for inflammatory bowel disease care for 2009-2020 for patients from the Eastern-Kentucky Appalachian region were included.The primary outcomes measured were proportions of inpatient and emergency encounters, total hospital charge, and hospital length of stay.825 pre-expansion and 5726 post-expansion encounters were identified. Post-expansion demonstrated decreases in the uninsured (9.2% to 1.0%, p < 0.001), inpatient encounters (42.7% to 8.1%, p < 0.001), emergency admissions (36.7% to 12.3%, p < 0.001), admission from the emergency department (8.0% to 0.2%, p < 0.001), median total hospital charge ($7080 to $3260, p < 0.001), and median total hospital length of stay (4 to 3 days, p < 0.001). Similarly, Medicaid coverage (18.8% to 27.7%, p < 0.001), outpatient encounters (57.3% to 91.9%, p < 0.001), elective admissions (46.9% to 76.2%, p < 0.001), admissions from clinic (78.4% to 90.2%, p < 0.001), and discharges to home (43.8% to 88.2%, p < 0.001) increased post-expansion.This study is subject to the limitations inherent of being retrospective and using a partially-deidentified database.This study is the first to demonstrate the changes in trends in care following Medicaid expansion for patients with inflammatory bowel disease in the Commonwealth of Kentucky, especially Appalachian Kentucky, showing significantly increased outpatient care utilization, reduced emergency department encounters, and decreased length of stays.Copyright © The ASCRS 2023. - Keywords: -raw_completion_output: |- - genes: - exposures: Medicaid expansion - gene_exposures_relationships: Medicaid expansion -> improved insurance coverage -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - Medicaid expansion -> improved insurance coverage - - === - -extracted_object: - exposures: - - Medicaid expansion - gene_exposures_relationships: - - molecular_activity: Medicaid expansion - gene: improved insurance coverage -input_text: |- - Title: Prognostic role of intestinal ultrasound in Crohn's disease. - Abstract: The majority of patients affected by Crohn's disease (CD) develop a chronic condition with persistent inflammation and relapses that may cause progressive and irreversible damage to the bowel, resulting in stricturing or penetrating complications in around 50% of patients during the natural history of the disease. Surgery is frequently needed to treat complicated disease when pharmacological therapy failes, with a high risk of repeated operations in time. Intestinal ultrasound (IUS), a non-invasive, cost-effective, radiation free and reproducible method for the diagnosis and follow-up of CD, in expert hands, allow a precise assessment of all the disease manifestations: Bowel characteristics, retrodilation, wrapping fat, fistulas and abscesses. Moreover, IUS is able to assess bowel wall thickness, bowel wall stratification (echo-pattern), vascularization and elasticity, as well as mesenteric hypertrophy, lymph-nodes and mesenteric blood flow. Its role in the disease evaluation and behaviour description is well assessed in literature, but less is known about the potential space of IUS as predictor of prognostic factors suggesting response to a medical treatment or postoperative recurrence. The availability of a low cost exam as IUS, able to recognize which patients are more likely to respond to a specific therapy and which patients are at high risk of surgery or complications, could be a very useful instrument in the hands of IBD physician. The aim of this review is to present current evidence about the prognostic role that IUS can show in predicting response to treatment, disease progression, risk of surgery and risk of post-surgical recurrence in CD.©The Author(s) 2023. Published by Baishideng Publishing Group Inc. All rights reserved. - Keywords: Bowel wall thickness; Crohn’s disease; Intestinal surgery; Intestinal ultrasound; Postoperative recurrence; Remission -raw_completion_output: |- - genes: None mentioned in the text - exposures: Baishideng Publishing Group Inc. - gene_exposures_relationships: None mentioned in the text -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - None mentioned in the text - - === - -extracted_object: - genes: - - None mentioned in the text - exposures: - - Baishideng Publishing Group Inc. - gene_exposures_relationships: - - molecular_activity: None mentioned in the text - gene: None mentioned in the text -input_text: |- - Title: Spatial cluster mapping and environmental modeling in pediatric inflammatory bowel disease. - Abstract: Geographical (geospatial) clusters have been observed in inflammatory bowel disease (IBD) incidence and linked to environmental determinants of disease, but pediatric spatial patterns in North America are unknown. We hypothesized that we would identify geospatial clusters in the pediatric IBD (PIBD) population of British Columbia (BC), Canada and associate incidence with ethnicity and environmental exposures.To identify PIBD clusters and model how spatial patterns are associated with population ethnicity and environmental exposures.One thousand one hundred eighty-three patients were included from a BC Children's Hospital clinical registry who met the criteria of diagnosis with IBD ≤ age 16.9 from 2001-2016 with a valid postal code on file. A spatial cluster detection routine was used to identify areas with similar incidence. An ecological analysis employed Poisson rate models of IBD, Crohn's disease (CD), and ulcerative colitis (UC) cases as functions of areal population ethnicity, rurality, average family size and income, average population exposure to green space, air pollution, and vitamin-D weighted ultraviolet light from the Canadian Environmental Health Research Consortium, and pesticide applications.Hot spots (high incidence) were identified in Metro Vancouver (IBD, CD, UC), southern Okanagan regions (IBD, CD), and Vancouver Island (CD). Cold spots (low incidence) were identified in Southeastern BC (IBD, CD, UC), Northern BC (IBD, CD), and on BC's coast (UC). No high incidence hot spots were detected in the densest urban areas. Modeling results were represented as incidence rate ratios (IRR) with 95%CI. Novel risk factors for PIBD included fine particulate matter (PM2.5) pollution (IRR = 1.294, CI = 1.113-1.507, P < 0.001) and agricultural application of petroleum oil to orchards and grapes (IRR = 1.135, CI = 1.007-1.270, P = 0.033). South Asian population (IRR = 1.020, CI = 1.011-1.028, P < 0.001) was a risk factor and Indigenous population (IRR = 0.956, CI = 0.941-0.971, P < 0.001), family size (IRR = 0.467, CI = 0.268-0.816, P = 0.007), and summer ultraviolet (IBD = 0.9993, CI = 0.9990-0.9996, P < 0.001) were protective factors as previously established. Novel risk factors for CD, as for PIBD, included: PM2.5 air pollution (IRR = 1.230, CI = 1 .056-1.435, P = 0.008) and agricultural petroleum oil (IRR = 1.159, CI = 1.002-1.326, P = 0.038). Indigenous population (IRR = 0.923, CI = 0.895-0.951, P < 0.001), as previously established, was a protective factor. For UC, rural population (UC IRR = 0.990, CI = 0.983-0.996, P = 0.004) was a protective factor and South Asian population (IRR = 1.054, CI = 1.030-1.079, P < 0.001) a risk factor as previously established.PIBD spatial clusters were identified and associated with known and novel environmental determinants. The identification of agricultural pesticides and PM2.5 air pollution need -raw_completion_output: |- - genes: IBD, CD, UC - exposures: fine particulate matter (PM2.5) pollution, agricultural application of petroleum oil to orchards and grapes - gene_exposures_relationships: IBD - PM2.5 pollution, IBD - agricultural application of petroleum oil to orchards and grapes -prompt: |+ - From the text below, extract the following entities in the following format: - - molecular_activity: - gene: - - - Text: - IBD - PM2.5 pollution, IBD - agricultural application of petroleum oil to orchards and grapes - - === - -extracted_object: - genes: - - IBD, CD, UC - exposures: - - fine particulate matter (PM2.5) pollution, agricultural application of petroleum - oil to orchards and grapes - gene_exposures_relationships: - - molecular_activity: agricultural application of petroleum oil - gene: HGNC:87 -named_entities: - - id: HGNC:87 - label: IBD -input_text: |- - Title: Low vaccination and infection rate of Omicron in patients with inflammatory bowel disease: a comparative study of three unique cohorts. - Abstract: The SARS-CoV-2 Omicron variant caused a large-scale outbreak of COVID-19 in Shanghai, China. Patients with inflammatory bowel disease (IBD) are at high risk of infection due to immunosuppressive interventions. We aimed to investigate the vaccination information of patients with IBD and update a vaccination guide based on a comparison of vaccination in asymptomatic carriers and healthy individuals.This retrospective study was conducted during an Omicron variant wave. We assessed the vaccination status in patients with IBD, asymptomatic carriers and healthy individuals. Factors with unvaccinated status and adverse events following vaccination were also determined in patients with IBD.The vaccination rate was 51.2% in patients with IBD, 73.2% in asymptomatic carriers, and 96.1% in healthy individuals. Female sex (p = 0.012), Crohn's disease (p = 0.026), and disease behavior of B3 (p = 0.029) were factors that indicated a lower vaccination rate. A significantly higher proportion of healthy individuals had received one booster dose (76.8%) than asymptomatic carriers (43.4%) and patients with IBD (26.2%). Patients with IBD received vaccination without an increased risk of adverse events (p = 0.768).The vaccination rate of patients with IBD remains much lower than that of asymptomatic carriers and healthy individuals. The COVID-19 vaccine has been found to be safe among all three groups and patients with IBD are not more susceptible to adverse events.Copyright © 2023 Feng, Yang, Yao, Feng, Hao, Qiao, Tong and Shen. - Keywords: Omicron; asymptomatic; coronavirus disease-19 (COVID-19); inflammatory bowel disease (IBD); severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) -raw_completion_output: |- - genes: None mentioned in the text - exposures: Omicron variant, SARS-CoV-2, COVID-19 vaccine - gene_exposures_relationships: None mentioned in the text -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - None mentioned in the text - - === - -extracted_object: - genes: - - None mentioned in the text - exposures: - - Omicron variant, SARS-CoV-2, COVID-19 vaccine - gene_exposures_relationships: - - molecular_activity: None mentioned in the text - gene: None mentioned in the text -input_text: |- - Title: Inappropriate Multi-Target Stool DNA Use for Colorectal Cancer Screening: Risks, Compliance, and Outcomes. - Abstract: Background Inappropriate or "off-label" use of multi-target stool DNA (mt-sDNA) tests refers to their use in patients for whom colonoscopy or no testing at all is warranted. Examples include a positive family history of colorectal cancer, a history of inflammatory bowel disease, or medical issues necessitating diagnostic colonoscopy, among others. Current understanding of off-label mt-sDNA use for colorectal cancer screening, its associated risks, and outcomes is lacking. We examined off-label mt-sDNA prescription and compliance with testing in an outpatient setting in southeast Michigan. Aims The primary aims of the study were determining the extent of off-label mt-sDNA testing and compliance, and results of all testing, as well as demographic factors associated with off-label prescriptions. The secondary aims were to examine explanations for incomplete testing and factors contributing to successful completion. Methods Using a retrospective design, we identified mt-sDNA orders from outpatient internal medicine clinics between January 1, 2018, to July 31, 2019, to evaluate the proportion of off-label mt-sDNA, results of testing, and follow-up colonoscopies up to one year after order placement. Patients were categorized as "off-label" if any inappropriate criteria were met. Statistical analysis was performed for primary and secondary outcomes. Results From 679 mt-sDNA orders within the study period, 81 (12.1%) had at least one off-label criterion for testing. In total, 404/679 (59.5%) patients completed testing. Lack of follow-up comprised the majority of incompletions (216/275; 78.6%). Only 52 (70.3%) out of 74 positive results were followed by diagnostic colonoscopy. Retired employment status (OR = 1.87; 95%CI, 1.17-2.98; P = 0.008) and age of 76 years or older (OR = 2.28; 95%CI, 0.99-5.21; P = 0.044) were significantly associated with increased risk of off-label mt-sDNA prescription. Increasing age range was associated with higher test completion (χ2 (5) = 12.085, p = 0.034). Multinomial logistic regression revealed an increasing age range (OR = 1.29; 95% CI, 1.09-1.54; P = 0.004), predictive of a positive mt-sDNA result for both groups. There was no significant difference between off-label or on-label groups in the mean number of resected polyps or pathology scores on follow-up colonoscopy. Conclusions Off-label mt-sDNA use remains a concern in the outpatient setting. Compliance for test completion and follow-up colonoscopy for positive results require further improvement. Our findings shed new light on the factors associated with off-label testing while reiterating its burden. We also describe common reasons for incomplete tests in an attempt to augment future colorectal cancer (CRC) screening initiatives.Copyright © 2023, Lazar et al. - Keywords: cologuard®; colon cancer prevention; colon cancer screening; colorectal canc -raw_completion_output: |- - genes: None mentioned - exposures: multi-target stool DNA (mt-sDNA) tests - gene_exposures_relationships: None mentioned -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - None mentioned - - === - -extracted_object: - genes: - - None mentioned - exposures: - - multi-target stool DNA (mt-sDNA) tests - gene_exposures_relationships: - - molecular_activity: None mentioned - gene: None mentioned -input_text: |- - Title: Protective effects of IRG1/itaconate on acute colitis through the inhibition of gasdermins-mediated pyroptosis and inflammation response. - Abstract: Inflammatory bowel disease (IBD) is a chronic relapsing gastrointestinal disorder, while the treatment effect is not satisfactory. Immune responsive gene 1 (IRG1) is a highly expressed gene in macrophage in response to inflammatory response and catalyzes the production of itaconate. Studies have reported that IRG1/itaconate has a significant antioxidant effect. This study aimed to investigate the effect and mechanism of IRG1/itaconate on dextran sulfate sodium (DSS)-induced colitis in vivo and in vitro. In vivo experiments, we found IRG1/itaconate exerted protective effects against acute colitis by increasing mice weight, the length of colon, reducing disease activity index and colonic inflammation. Meanwhile, IRG1 deletion aggravated the macrophages/CD4+/CD8+ T-cell accumulation, and increased the release of interleukin (IL)-1β, tumor necrosis factor-α (TNF-α), IL-6, the activation of nuclear factor-κB (NF-κB)/mitogen-activated protein kinase (MAPK) signaling pathway, and gasdermin D (GSDMD) mediated pyroptosis. Four-octyl itaconate (4-OI), a derivative of itaconate, attenuated these changes, therefore relieved DSS-induced colitis. In vitro experiment, we found 4-OI inhibited the reactive oxygen species production, thereby inhibiting the activation of MAPK/NF-κB signaling pathway in RAW264.7 and murine bone-marrow-derived macrophages. Simultaneously, we found 4-OI inhibited caspase1/GSDMD-mediated pyroptosis to reduce the release of cytokines. Finally, we found anti-TNF-α agent reduced the severity of DSS-induced colitis and inhibited gasdermin E (GSDME)-mediated pyroptosis in vivo. Meanwhile, our study revealed that 4-OI inhibited caspase3/GSDME-mediated pyroptosis induced by TNF-α in vitro. Taken together, IRG1/itaconate exerted a protective role in DSS-induced colitis by inhibiting inflammatory response and GSDMD/GSDME-mediated pyroptosis, which could be a promising candidate for IBD therapy.© 2022 The Authors. Publishing services by Elsevier B.V. on behalf of KeAi Communications Co., Ltd. - Keywords: Colitis; Gasdermin D; Gasdermin E; IRG1; Inflammation -raw_completion_output: |- - genes: IRG1, GSDMD, GSDME - exposures: itaconate, DSS (dextran sulfate sodium), IL-1β, TNF-α, IL-6, NF-κB (nuclear factor-κB), MAPK (mitogen-activated protein kinase), 4-OI (four-octyl itaconate), caspase1, caspase3 - gene_exposures_relationships: IRG1/itaconate inhibits gasdermin D (GSDMD)-mediated pyroptosis; IRG1/itaconate inhibits gasdermin E (GSDME)-mediated pyroptosis; 4-OI attenuates the effects of DSS-induced colitis; 4-OI inhibits the activation of MAPK/NF-κB signaling pathway; 4-OI inhibits caspase1/GSDMD-mediated pyroptosis; 4-OI inhibits caspase3/GSDME-mediated pyroptosis; TNF-α agent reduces the severity of DSS-induced colitis; TNF-α agent inhibits gasdermin E (GSDME)-mediated pyroptosis. -prompt: |+ - From the text below, extract the following entities in the following format: - - molecular_activity: - gene: - - - Text: - TNF-α agent inhibits gasdermin E (GSDME)-mediated pyroptosis. - - === - -extracted_object: - genes: - - IRG1, GSDMD, GSDME - exposures: - - itaconate, DSS (dextran sulfate sodium), IL-1β, TNF-α, IL-6, NF-κB (nuclear - factor-κB), MAPK (mitogen-activated protein kinase), 4-OI (four-octyl itaconate), - caspase1, caspase3 - gene_exposures_relationships: - - molecular_activity: pyroptosis - gene: HGNC:25697 - - molecular_activity: inhibits gasdermin E (GSDME)-mediated pyroptosis - gene: HGNC:33904 - - molecular_activity: effects - gene: DSS-induced colitis - - molecular_activity: activation - gene: MAPK/NF-κB - - molecular_activity: pyroptosis - gene: HGNC:25697 - - molecular_activity: pyroptosis - gene: caspase3/GSDME - - molecular_activity: DSS-induced colitis - gene: TNF-α agent - - molecular_activity: inhibits - gene: HGNC:2810 -named_entities: - - id: HGNC:25697 - label: GSDMD - - id: HGNC:33904 - label: IRG1 - - id: HGNC:2810 - label: GSDME -input_text: |- - Title: Autophagy in intestinal fibrosis: relevance in inflammatory bowel disease. - Abstract: Chronic inflammation is often associated with fibrotic disorders in which an excessive deposition of extracellular matrix is a hallmark. Long-term fibrosis starts with tissue hypofunction and finally ends in organ failure. Intestinal fibrosis is not an exception, and it is a frequent complication of inflammatory bowel disease (IBD). Several studies have confirmed the link between deregulated autophagy and fibrosis and the presence of common prognostic markers; indeed, both up- and downregulation of autophagy are presumed to be implicated in the progression of fibrosis. A better knowledge of the role of autophagy in fibrosis may lead to it becoming a potential target of antifibrotic therapy. In this review we explore novel advances in the field that highlight the relevance of autophagy in fibrosis, and give special focus to fibrosis in IBD patients.Copyright © 2023 Macias-Ceja, Barrachina and Ortiz-Masià. - Keywords: Crohn’s disease; autophagy; colitis; fibrosis; inflammatory bowel disease; intestinal fibrosis -raw_completion_output: |- - genes: N/A - exposures: autophagy - gene_exposures_relationships: N/A -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - N/A - - === - -extracted_object: - genes: - - N/A - exposures: - - autophagy - gene_exposures_relationships: - - molecular_activity: N/A - gene: N/A -input_text: |- - Title: Provincial variation in colorectal cancer screening adherence in Canada; evidence from the Canadian Partnership for Tomorrow's Health. - Abstract: Although colorectal cancer (CRC) screening program is proven to reduce CRC incidence and mortality, understanding patterns and predictors of suboptimal adherence in screening program requires further investigation in Canada.We used self-reported data from five regional cohorts of the Canadian Partnership for Tomorrow's Health (CanPath), namely the BC Generations Project (BCGP), Alberta's Tomorrow Project (ATP), the Ontario Health Study (OHS), Quebec's CARTaGENE, and the Atlantic Partnership for Tomorrow's Health Study (Atlantic PATH). We stratified participants into the following four risk categories: 1) age 50-74 years, 2) family history in a first-degree relative, 3) personal history of chronic inflammatory bowel disease and/or polyps, and 4) co-existence of personal risk and family history. Multivariable logistic regression was used to identify predictors of adherence to the screening guidelines.Adherence to CRC screening varied considerably between regions, ranging from 16.6% in CARTaGENE to 47.7% in OHS. Compared to the largest cohort OHS, the likelihood of non-adherence to CRC screening was significantly higher in BCGP (OR 1.15, 95% CI 1.11-1.19), the Atlantic PATH (OR 1.90, 95% CI 1.82-1.99) and CARTaGENE (OR 5.10, 95% CI 4.85-5.36). Low physical activity, current smoking, presence of personal risk, family history of CRC significantly reduced the likelihood of adherence to screening recommendations.Compared to the national target of ≥ 60% for participation in CRC screening, adherence to regular CRC screening was suboptimal in this cohort of Canadians and varied by region. Further efforts are needed to identify the specific barriers to screening adherence in different provinces and across risk categories.Copyright © 2023 Darvishian, Moustaqim-Barrette, Awadalla, Bhatti, Broet, McDonald, Murphy, Skead, Urquhart, Vena and Dummer. - Keywords: CanPath cohort; Canada; adherence; colorectal cancer; screening -raw_completion_output: |- - genes: Not mentioned - exposures: None mentioned - gene_exposures_relationships: Not applicable -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - Not applicable - - === - -extracted_object: - genes: - - Not mentioned - exposures: - - None mentioned - gene_exposures_relationships: - - molecular_activity: Not applicable - gene: Not applicable -input_text: |- - Title: 3D printed infliximab suppositories for rectal biologic delivery. - Abstract: Infliximab is a monoclonal antibody that plays an important role in the management and treatment of chronic inflammatory bowel diseases (IBD). Due to its macromolecular structure, its delivery through the oral route is challenging, limiting its administration to only via the parenteral route. The rectal route offers an alternative way for administering infliximab, allowing it to be localised at the disease site and circumventing its passage across the alimentary canal and thus, maintaining its integrity and bioactivity. Three-dimensional (3D) printing is an advanced production technology that permits the creation of dose-flexible drug products from digital designs. The current study assessed the feasibility of utilising semi-solid extrusion 3D printing for the fabrication of infliximab-loaded suppositories for the local treatment of IBD. Various printing inks composed of Gelucire® (48/16 or 44/14) mixed with coconut oil and/or purified water were investigated. It was shown that following reconstitution in water, the infliximab solution can be directly incorporated into the printing ink of Gelucire® 48/16 and can withstand the extrusion process, resulting in well-defined suppositories. Since water content and temperature are critical for safeguarding infliximab's potency, the effect of changing the composition of the printing inks and printing parameters on infliximab's biologic efficiency was evaluated by measuring its binding capacity (i.e., the amount of infliximab that actively binds to its antigen to exert an effect). Despite drug loading assays showing that infliximab remains intact following printing, it was found that the incorporation of water in isolation results in only ∼65% binding capacity. However, when oil is added to the mixture, infliximab's binding capacity increases up to ∼85%. These promising results demonstrate that 3D printing has the potential to be exploited as a novel platform for fabricating dosage forms containing biopharmaceuticals, avoiding patients' compliance issues observed with injectables and addressing their unmet needs.© 2023 The Authors. - Keywords: Biologicals and monoclonal antibodies; Digital medicine production; Extrusion-assisted additve manufacturing of a suppository formulation; Pressure-assisted syringe; Rectal drug delivery; Tumour necrosis factor-alpha (TNF-alpha) inhibitors; Ulcerative colitis (UC) and Crohn's disease (CD) -raw_completion_output: |- - genes: None mentioned in the text - exposures: infliximab - gene_exposures_relationships: None mentioned in the text -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - None mentioned in the text - - === - -extracted_object: - genes: - - None mentioned in the text - exposures: - - infliximab - gene_exposures_relationships: - - molecular_activity: None mentioned in the text - gene: None mentioned in the text -input_text: |- - Title: Serum amyloid A and metabolic disease: evidence for a critical role in chronic inflammatory conditions. - Abstract: Serum amyloid A (SAA) subtypes 1-3 are well-described acute phase reactants that are elevated in acute inflammatory conditions such as infection, tissue injury, and trauma, while SAA4 is constitutively expressed. SAA subtypes also have been implicated as playing roles in chronic metabolic diseases including obesity, diabetes, and cardiovascular disease, and possibly in autoimmune diseases such as systemic lupus erythematosis, rheumatoid arthritis, and inflammatory bowel disease. Distinctions between the expression kinetics of SAA in acute inflammatory responses and chronic disease states suggest the potential for differentiating SAA functions. Although circulating SAA levels can rise up to 1,000-fold during an acute inflammatory event, elevations are more modest (∼5-fold) in chronic metabolic conditions. The majority of acute-phase SAA derives from the liver, while in chronic inflammatory conditions SAA also derives from adipose tissue, the intestine, and elsewhere. In this review, roles for SAA subtypes in chronic metabolic disease states are contrasted to current knowledge about acute phase SAA. Investigations show distinct differences between SAA expression and function in human and animal models of metabolic disease, as well as sexual dimorphism of SAA subtype responses.© 2023 den Hartigh, May, Zhang, Chait and Blaser. - Keywords: SAA; adipocytes, macrophages; cardiovascular disease; diabetes; intestine; liver; obesity -raw_completion_output: |- - genes: SAA - - exposures: not mentioned - - gene_exposures_relationships: not mentioned -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - not mentioned - - === - -extracted_object: - genes: - - SAA - exposures: - - not mentioned - gene_exposures_relationships: - - molecular_activity: not mentioned - gene: not mentioned -input_text: |- - Title: Probiotic lactic acid bacteria alleviate pediatric IBD and remodel gut microbiota by modulating macrophage polarization and suppressing epithelial apoptosis. - Abstract: The incidence of pediatric inflammatory bowel disease (PIBD) continues to rise. It was reported that the probiotic lactic acid bacteria Pediococcus pentosaceus (P. pentosaceus) can interfere with intestinal immunity, but it is still unknown whether it can alleviate PIBD and the concrete mechanism of immune regulation is unclear.For this study, 3-week-old juvenile mice were selected for modeling the development of PIBD. The mice treated with 2% DSS were randomly divided into two groups, which were given P. pentosaceus CECT8330 and equal amounts of solvent, respectively. The feces and intestinal tissue were collected for the mechanism exploration in vivo. THP-1 and NCM460 cells were used to investigate the effects of P. pentosaceus CECT8330 on macrophage polarization, epithelial cell apoptosis, and their crosstalk in vitro.P. pentosaceus CECT8330 obviously alleviated colitis symptoms of juvenile mice, including weight loss, colon length shortening, spleen swelling, and intestinal barrier function. Mechanistically, P. pentosaceus CECT8330 could inhibit intestinal epithelial apoptosis by suppressing the NF-κB signaling pathway. Meanwhile, it reprogramed macrophages from a pro-inflammatory M1 phenotype to an anti-inflammatory M2 phenotype, leading to a decreased secretion of IL-1β which contributes to the reduction in ROS production and epithelial apoptosis. Additionally, the 16S rRNA sequence analysis revealed that P. pentosaceus CECT8330 could recover the balance of gut microbiota, and a significantly increased content of Akkermansia muciniphila was particularly observed.P. pentosaceus CECT8330 shifts macrophage polarization toward an anti-inflammatory M2 phenotype. The decreased production of IL-1β leads to a reduction in ROS, NF-κB activation, and apoptosis in the intestinal epithelium, all of which help to repair the intestinal barrier and adjust gut microbiota in juvenile colitis mice.Copyright © 2023 Hua, Pan, Chen, Jing, Xie, Gao, Huang, Chen, Gao, Xu and Li. - Keywords: Akkermansia muciniphila; Pediococcus pentosaceus CECT8330; intestinal epithelium apoptosis; macrophage polarization; pediatric IBD -raw_completion_output: |- - genes: NF-κB - exposures: Pediococcus pentosaceus CECT8330; IL-1β; ROS - gene_exposures_relationships: NF-κB and Pediococcus pentosaceus CECT8330; IL-1β and ROS -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - IL-1β and ROS - - === - -extracted_object: - genes: - - NF-κB - exposures: - - Pediococcus pentosaceus CECT8330 - - IL-1β - - CHEBI:26523 - gene_exposures_relationships: - - molecular_activity: undeclared - gene: Pediococcus pentosaceus CECT8330 - - molecular_activity: IL-1β - gene: HGNC:1455 -named_entities: - - id: CHEBI:26523 - label: ROS - - id: HGNC:1455 - label: ROS -input_text: |- - Title: Comparison of the gut virus communities between patients with Crohn's disease and healthy individuals. - Abstract: The escalating incidence of Crohn's disease (CD), a debilitating ailment that ravages individuals and their families, has become a formidable issue over recent decades.In this study, fecal samples from patients with CD and healthy individuals were investigated by means of viral metagenomics.The fecal virome was analyzed and some suspected disease-causing viruses were described. A polyomavirus named HuPyV with 5,120 base pairs (bp) was found in the disease group. In a preliminary analysis employing large T region-specific primers, it was found that HuPyV was present in 3.2% (1/31) of healthy samples and 43.2% (16/37) of disease samples. Additionally, two other viruses from the anellovirus and CRESS-DNA virus families were found in fecal samples from CD patients. The complete genome sequences of these two viruses were described respectively, and the phylogenetic trees have been built using the anticipated amino acid sequences of the viral proteins.Further research is required to elucidate the relationship between these viruses and the onset and development of Crohn's disease.Copyright © 2023 Ding, Wan, Li, Ma, Zhang and Xu. - Keywords: CRESS-DNA virus; Crohn’s disease; anellovirus; inflammatory bowel disease; polyomavirus; viral metagenomics method -raw_completion_output: |- - genes: HuPyV - exposures: CRESS-DNA virus, anellovirus - gene_exposures_relationships: HuPyV - viral metagenomics method; CRESS-DNA virus - fecal samples from CD patients; anellovirus - fecal samples from CD patients -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - anellovirus - fecal samples from CD patients - - === - -extracted_object: - genes: - - HuPyV - exposures: - - CRESS-DNA virus, anellovirus - gene_exposures_relationships: - - molecular_activity: viral metagenomics method - gene: HuPyV - - molecular_activity: CRESS-DNA virus - gene: fecal samples from CD patients - - molecular_activity: exposure to anellovirus - gene: fecal samples -input_text: |- - Title: Combination therapy is not associated with improved rates of clinical or endoscopic remission in patients with inflammatory bowel disease treated with ustekinumab or vedolizumab: a retrospective study. - Abstract: Management of inflammatory bowel disease (IBD) involves biological agents, often in combination with thiopurines or methotrexate. The aim of our study was to compare clinical and endoscopic outcomes in IBD patients treated with vedolizumab or ustekinumab, as monotherapy or in combination with thiopurines or methotrexate.We conducted a retrospective cohort study of all patients aged ≥18 years with a diagnosis of ulcerative colitis or Crohn's disease, commenced on vedolizumab or ustekinumab between October 2015 and March 2022. Primary outcome was clinical remission or response calculated by partial Mayo score (remission: <3; response: improvement >1) for ulcerative colitis or Harvey-Bradshaw index (<5, >2 respectively) for Crohn's disease over 1 year. Secondary endpoints were treatment failure, relapse, endoscopic remission at 1 year. Statistical analysis was done using 2-sample Student's t and chi-square tests.A total of 159 IBD patients were included in the study, 85 (53%) on vedolizumab and 74 (47%) on ustekinumab. For those on vedolizumab, 61 (72%) patients had ulcerative colitis, and 24 (28%) has Crohn's disease. All patients on ustekinumab had Crohn's disease. Mean disease duration in was 9.4 and 13.5 years respectively. There was no difference in clinical response or remission for vedolizumab or ustekinumab monotherapy compared to combination therapy at 1 year. There was also no difference in treatment failure, relapse or endoscopic remission.Combining vedolizumab or ustekinumab with an immunomodulator is not superior to monotherapy in terms of clinical response or endoscopic remission up to 1 year in IBD.Copyright: © Hellenic Society of Gastroenterology. - Keywords: Crohn’s disease; Ulcerative colitis; biologics; thiopurines -raw_completion_output: |- - genes: None mentioned in the text - exposures: vedolizumab, ustekinumab, thiopurines, methotrexate - gene_exposures_relationships: None mentioned in the text -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - None mentioned in the text - - === - -extracted_object: - genes: - - None mentioned in the text - exposures: - - vedolizumab, ustekinumab, thiopurines, methotrexate - gene_exposures_relationships: - - molecular_activity: None mentioned in the text - gene: None mentioned in the text -input_text: |- - Title: Association of serum IgG4 and disease outcomes in patients with inflammatory bowel disease. - Abstract: The etiology of inflammatory bowel disease (IBD) is multifactorial and thought to be influenced by inappropriate activation of the gut mucosal immune system. As the only immunoglobulin G (IgG) subclass unable to activate the classical complement cascade, the role of IgG4 in IBD pathophysiology as an immunomodulator is controversial. This study aimed to determine the association of low, normal and high IgG4 levels with the outcomes of IBD patients.This was a retrospective study of a multisite tertiary care center database evaluating patients with IBD who had an IgG4 level drawn between 2014 and 2021. Subjects were divided into low, normal, and high IgG4 level groups for evaluation of demographic and clinical indicators of IBD activity and severity.Of 284 patients with IBD, 22 had low (7.7%), 16 high (5.6%), and 246 (86.6%) normal IgG4 levels. There was no difference in IBD subtype, mean age, age at IBD diagnosis, or smoking between the 3 groups. There was no difference in number of hospitalizations (P=0.20), C-reactive protein levels, need for intestinal resection (P=0.85), or presence of primary sclerosing cholangitis (P=0.15), pancreatitis (P=0.70), or perianal disease (P=0.68) between the groups. Significantly more patients in the low IgG4 group had previous exposure to vedolizumab compared to the other groups and more patients in the low IgG4 group received vedolizumab (P=0.04), azathioprine (P=0.04) and prednisone (P=0.03) during the 5-year follow up.In this study, a low serum IgG4 level was associated with higher rates of vedolizumab, azathioprine, and steroid use.Copyright: © Hellenic Society of Gastroenterology. - Keywords: IgG4; disease outcomes; disease severity; inflammatory bowel disease -raw_completion_output: |- - genes: None - exposures: IgG4, vedolizumab, azathioprine, prednisone - gene_exposures_relationships: None -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - None - - === - -extracted_object: - genes: - - None - exposures: - - IgG4, vedolizumab, azathioprine, prednisone - gene_exposures_relationships: - - molecular_activity: None - gene: None -input_text: |- - Title: Alexithymic characteristics and interoceptive abilities are associated with disease severity and levels of C-reactive protein and cytokines in patients with inflammatory bowel disease. - Abstract: Alexithymia and atypical gut-brain signaling have been linked to the pathophysiology of inflammatory bowel disease (IBD). We herein assessed IBD patients' alexithymia levels and interoceptive abilities, and detected potential correlations with psychological distress, symptom severity and disease activity, and inflammation indices.Adult IBD outpatients and healthy controls were recruited. Alexithymia was assessed using the Toronto Alexithymia Scale, interoceptive accuracy using the Heartbeat Counting Test (cardiac interoception) and the Water Load Test-II (gastric interoception), and interoceptive sensibility using the Multidimensional Assessment of Interoceptive Awareness (MAIA).Forty-one patients with Crohn's disease (CD), 16 with ulcerative colitis (UC), and 50 healthy controls were included. In CD patients, the level of externally oriented thinking and total alexithymia score were correlated with disease activity (P=0.027 and P=0.047, respectively), while in UC patients difficulties in identifying emotions were linked to disease activity (P=0.007). In CD patients, the Noticing, Not-Worrying and Emotional Awareness MAIA subscale score were correlated with C-reactive protein levels (P=0.005, P=0.048 and P=0.005), the Noticing subscale score with interleukin (IL)-1β levels (r=-0.350, P=0.039), the Not-Distracting subscale score with IL-6 levels (r=-0.402, P=0.017), and the Emotional Awareness subscale score with IL-1β (r=-0.367, P=0.030) and IL-6 (r=-0.379, P=0.025) levels. Finally, in UC patients, the Not-Worrying subscale score was significantly associated with IL-6 levels (r=-0.532, P=0.049), while difficulties in identifying emotions were linked to IL-8 levels (r=0.604, P=0.022).Emotional and interoceptive processing is associated with IBD disease activity, suggesting a potential implication for IBD pathophysiology.Copyright: © Hellenic Society of Gastroenterology. - Keywords: Alexithymia; cytokines; inflammatory bowel disease; interoception -raw_completion_output: |- - genes: N/A - exposures: cytokines - gene_exposures_relationships: N/A -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - N/A - - === - -extracted_object: - genes: - - N/A - exposures: - - cytokines - gene_exposures_relationships: - - molecular_activity: N/A - gene: N/A -input_text: |- - Title: Cutaneous Crohn's disease after proctocolectomy for medically refractory colonic Crohn's disease: a case series and review of the literature. - Abstract: Cutaneous Crohn's disease (CCD), also known as metastatic Crohn's disease (CD), is one of the rarest and most challenging cutaneous manifestations of CD. It is characterized by non-caseating granulomatous inflammation of the skin at sites that are non-contiguous with the gastrointestinal (GI) tract. Diagnosis of CCD needs a high clinical suspicion since morphological presentation varies widely and lacks an apparent correlation to the activity of the luminal CD. The onset of CCD in patients without active GI CD is a particularly understudied phenomenon.We present a case series of a unique patient group who developed CCD while in remission from a luminal CD perspective, mainly after a proctocolectomy for Crohn's colitis. We also provide a literature review and summary of case reports of CCD after proctocolectomy.Our 4 adult patients diagnosed with CCD after proctocolectomy presented herein, were successfully treated with high-dose corticosteroids, followed by biologic therapy. Furthermore, a comprehensive review of CCD is provided regarding its pathogenesis, clinical presentation, differential diagnosis, and the evidence behind the available treatments.CCD should be considered in any CD patient presenting with skin lesions regardless of their disease activity status and history of proctocolectomy. The treatment remains challenging; biologics remain the cornerstone and a multidisciplinary approach is recommended. Larger randomized clinical trials are essential to determine the optimal treatment protocol and to improve outcomes.Copyright: © Hellenic Society of Gastroenterology. - Keywords: Cutaneous Crohn’s disease; dermatologic manifestations; inflammatory bowel disease; metastatic Crohn’s disease; proctocolectomy -raw_completion_output: |- - genes: None mentioned in the text. - exposures: high-dose corticosteroids, biologic therapy, proctocolectomy. - gene_exposures_relationships: None mentioned in the text. -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - None mentioned in the text. - - === - -extracted_object: - genes: - - None mentioned in the text. - exposures: - - high-dose corticosteroids, biologic therapy, proctocolectomy. - gene_exposures_relationships: - - molecular_activity: None mentioned in the text. - gene: None mentioned in the text. -input_text: |- - Title: Outcome of inflammatory bowel disease patients with prior malignancy. - Abstract: Inflammatory bowel disease (IBD) treatment options, such as anti-tumor necrosis factor (TNF) agents and thiopurines, are associated with an increased risk of certain malignancies. However, the management of IBD patients with prior malignancy is not well defined and the literature is scarce. The main aim of this study was to describe the outcome of IBD patients with prior malignancy, or malignancy before first exposure to IBD-related biologic or immunosuppressive treatment.The study cohort included adult IBD patients followed in a tertiary academic center, with at least one malignancy diagnosed before IBD diagnosis or before initiation of IBD-related treatment. The main outcome of interest was a relapse of the previous malignancy or development of a second malignancy.Our database included 1112 patients with both IBD and malignancy. Of these, 86 (9%) who had their malignancy diagnosed before IBD-related treatment initiation were identified, while 10/86 patients (9%) were further diagnosed with a second primary malignancy. Twenty patients, (20/86, 23%) had recurrence of a previous malignancy, most commonly non-melanoma skin cancer (NMSC), found in 9/20 patients (45%). Treatment with infliximab was found to be significantly associated with recurrence of NMSC (P=0.003).Anti-TNF treatment may be associated with an increased risk of NMSC recurrence. This underscores the importance of rigorous dermatological follow up in IBD patients with previous NMSC treated with anti-TNFs.Copyright: © Hellenic Society of Gastroenterology. - Keywords: Inflammatory bowel disease; malignancy; recurrent; secondary; therapy -raw_completion_output: |- - genes: TNF - exposures: anti-TNF agents, thiopurines, infliximab - gene_exposures_relationships: TNF - infliximab -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - TNF - infliximab - - === - -extracted_object: - genes: - - HGNC:11892 - exposures: - - anti-TNF agents, thiopurines, infliximab - gene_exposures_relationships: - - molecular_activity: infliximab - gene: HGNC:11892 -named_entities: - - id: HGNC:11892 - label: TNF -input_text: |- - Title: Knowledge mapping of COVID-19 and autoimmune diseases: a visual and bibliometric analysis. - Abstract: Many studies have shown an association between COVID-19 and autoimmune diseases (ADs). Studies on COVID-19 and ADs have also increased significantly, but there is no bibliometric analysis to summarize the association between COVID-19 and ADs. The purpose of this study was to perform a bibliometric and visual analysis of published studies related to COVID-19 and ADs.Based on the Web of Science Core Collection SCI-Expanded database, we utilize Excel 2019 and visualization analysis tools Co-Occurrence13.2 (COOC13.2), VOSviewer, CiteSpace, and HistCite for analysis.A total of 1736 related kinds of papers were included, and the number of papers presented an overall increasing trend. The country/region with the most publications is the USA, the institution is the Harvard Medical School, the author is Yehuda Shoenfeld from Israel, and the journal is Frontiers in Immunology. Research hotspots include immune responses (such as cytokines storm), multisystem ADs (such as systemic lupus erythematosus, rheumatoid arthritis, and multiple sclerosis), treatment modalities (such as hydroxychloroquine, rituximab), vaccination and autoimmune mechanisms (such as autoantibodies, molecular mimicry). The future research direction may be the mechanisms and treatment ideas of the association between ADs and COVID-19 (such as NF-κB, hyperinflammation, antiphospholipid antibodies, neutrophil extracellular traps, granulocyte-macrophage colony-stimulating factor), other cross-diseases of COVID-19 and ADs (such as inflammatory bowel disease, chronic mucocutaneous candidiasis, acute respiratory distress syndrome).The growth rate of publications regarding ADs and COVID-19 has risen sharply. Our research results can help researchers grasp the current status of ADs and COVID-19 research and find new research directions in the future.© 2023. The Author(s). - Keywords: Autoimmune diseases; COVID-19; Frontiers; Hotspots; Keywords analysis -raw_completion_output: |- - genes: NF-κB - exposures: hydroxychloroquine, rituximab - gene_exposures_relationships: NF-κB - hydroxychloroquine; NF-κB - rituximab -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - NF-κB - rituximab - - === - -extracted_object: - genes: - - NF-κB - exposures: - - hydroxychloroquine, rituximab - gene_exposures_relationships: - - molecular_activity: hydroxychloroquine - gene: NF-κB - - molecular_activity: NF-kB - gene: rituximab -input_text: |- - Title: Lymphogranuloma venereum and CMV co-infection mimicking ulcerative proctitis in a non-immunocompromised patient. - Abstract: - Keywords: -raw_completion_output: |- - genes: N/A - exposures: Lymphogranuloma venereum, CMV - gene_exposures_relationships: N/A -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - N/A - - === - -extracted_object: - genes: - - N/A - exposures: - - Lymphogranuloma venereum, CMV - gene_exposures_relationships: - - molecular_activity: N/A - gene: N/A -input_text: |- - Title: Mechanism by which oleracein E alleviates TNBS-induced ulcerative colitis. - Abstract: This study aimed to investigate the effect of oleracein E (OE) in improving 2,4,6-trinitrobenzene sulfonic acid (TNBS)-induced ulcerative colitis (UC).Lipopolysaccharide (LPS) was used to induce a UC cell model, and TNBS was used to induce a UC rat model. ELISA was performed to assess the levels of inflammatory factors (IL-1β, TNF-α, and IL-6). Moreover, the activities of catalase (CAT), myeloperoxidase (MPO), and malonaldehyde (MDA) were detected by kits. Western blotting was performed to assess related proteins of the Nrf2/HO-1 signaling pathway, tight junction protein (ZO-1, Occludin, and claudin-2) expression levels, and apoptosis-related proteins (Bcl2, Bax, and cleaved caspase 3). Flow cytometry was used to analyze ROS levels. The morphology of colon tissues and the apoptosis of cells were detected by HE and TUNEL staining, respectively.OE significantly increased the activity of CAT and decreased the activity of MPO in LPS-induced Caco-2 cells and TNBS-induced UC rats. However, the levels of IL-1β, IL-6, and TNF-α were markedly reduced both in vivo and in vitro. In addition, OE significantly increased the levels of Nrf2/HO-1 signaling pathway-related proteins and tight junction proteins and inhibited cell apoptosis. HE staining showed that OE significantly decreased the severity of acute TNBS-induced colitis in rats.OE may exert a regulatory effect on ameliorating intestinal barrier injury and reducing inflammation and oxidative stress levels by activating the Nrf2/HO-1 pathway.Copyright © 2023 The Author(s). Published by Wolters Kluwer Health, Inc. - Keywords: -raw_completion_output: |- - genes: Nrf2, HO-1, ZO-1, Occludin, claudin-2, Bcl2, Bax, cleaved caspase 3 - - exposures: oleracein E (OE), 2,4,6-trinitrobenzene sulfonic acid (TNBS), Lipopolysaccharide (LPS) - - gene_exposures_relationships: OE to Nrf2/HO-1 pathway -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - OE to Nrf2/HO-1 pathway - - === - -extracted_object: - genes: - - Nrf2, HO-1, ZO-1, Occludin, claudin-2, Bcl2, Bax, cleaved caspase 3 - exposures: - - CHEBI:48113 - gene_exposures_relationships: - - molecular_activity: OE to Nrf2/HO-1 pathway - gene: HGNC:4071 -named_entities: - - id: CHEBI:48113 - label: oleracein E (OE), 2,4,6-trinitrobenzene sulfonic acid (TNBS), Lipopolysaccharide - (LPS) - - id: HGNC:4071 - label: Nrf2 -input_text: |- - Title: Protective effect of Arum maculatum against dextran sulfate sodium induced colitis in rats. - Abstract: Ulcerative colitis (UC) is an inflammatory disease of the large intestine that is characterized by diarrhea, bloody stools, abdominal pain and mucosal ulceration. UC is treated with nonsteroidal anti-inflammatory drugs, corticosteroids or immunosuppressants, but long-term use of these drugs can cause adverse effects. Arum maculatum is used as a traditional treatment for digestive system disorders, but its use for treatment of UC has not been investigated rigorously. We investigated the possible protective effect of a methanol extract of A. maculatum against dextran sulfate sodium (DSS) induced experimental UC in rats. Total phenolic and flavonoid contents of the extract were 32.919 ± 1.125 mg gallic acid equivalent (GAE)/g and 52.045 ± 7.902 µg rutin equivalent (RE)/mg, respectively. The half-maximal inhibitory concentration (IC50) for the extract was 105.76 µg/ml according to the 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical scavenging activity assay. Effects of A. maculatum extract on UC induced by DSS were assessed both macroscopically and histologically. We also investigated effects of A. maculatum extract on malondialdehyde (MDA) levels and the oxidative stress index (OSI) in normal rats and rats with UC. We found that treatment with A. maculatum extract protected the colon against DSS induced UC in a dose-dependent manner. - Keywords: Arum maculatum; inflammatory bowel disease; medicinal plant; rats; ulcerative colitis -raw_completion_output: |- - genes: None mentioned in the text. - exposures: dextran sulfate sodium - gene_exposures_relationships: None mentioned in the text. -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - None mentioned in the text. - - === - -extracted_object: - genes: - - None mentioned in the text. - exposures: - - dextran sulfate sodium - gene_exposures_relationships: - - molecular_activity: None mentioned in the text. - gene: None mentioned in the text. -input_text: |- - Title: Reporting of endoscopy and histology of ulcerative colitis in routine clinical practice: How far we are! - Abstract: - Keywords: clinical practice; endoscopy; histology; inflammatory bowel disease; ulcerative colitis -raw_completion_output: |- - genes: - exposures: - gene_exposures_relationships: -prompt: |+ - From the text below, extract the following entities in the following format: - - genes: - exposures: - gene_exposures_relationships: - - - Text: - Title: Reporting of endoscopy and histology of ulcerative colitis in routine clinical practice: How far we are! - Abstract: - Keywords: clinical practice; endoscopy; histology; inflammatory bowel disease; ulcerative colitis - - === - -extracted_object: {} -input_text: |- - Title: Clinical features analysis of Kawasaki disease with abdominal symptoms as the first manifestation. - Abstract: To investigate the clinical characteristics of Kawasaki disease (KD) presenting with abdominal manifestation as the first manifestation. Our findings may help improve the cognition of KD with abdominal complications, and avoid misdiagnosis and missed diagnosis. A retrospective analysis was conducted of 1490 KD patients admitted to Shengjing Hospital between January 2019 and March 2022. Clinical characteristics, related factors, and prognosis of KD with abdominal manifestation as first manifestation were analyzed. Based on the presenting symptoms, patients were divided into gastrointestinal symptom group (n = 141), liver dysfunction group (n = 55), and control group (n = 1294). In the gastrointestinal group, diarrhea [100 cases (70.9%)], vomiting [55 cases (39.0%)], and abdominal pain [34 cases (24.1%)] were the most common symptoms at onset. 8 cases (5.7%) were complicated with pseudo-intestinal obstruction, 6 cases (4.3%) with ischemic colitis, 5 cases (3.5%) with pancreatitis, 2 cases (1.4%) with appendicitis, and 1 case (0.7%) with cholecystitis. Comparied to ordinary gastroenteritis caused by infection, gastroenteritis with KD has longer fever duration before treatment, higher WBC, PLT, CRP, AST levels and lower albumin levels. All patients in the liver dysfunction group had elevated transaminases, and 19 patients (34.5%) presented with jaundice. In the gastrointestinal group, the average hospital stay was 10.3 days, and the incidence of IVIG unresponsiveness and coronary artery lesion were 18.4% and 19.9%, respectively, which were significantly higher than that in the control group. In the liver dysfunction group, the average hospital stay (11.18 days), incidence of IVIG unresponsiveness (25.5%), and incidence of coronary artery lesion (29.1%) were significantly higher than that in the control group. On multivariate logistic regression analysis, gastrointestinal involvement, fever duration, ALT, PLT, and CRP were identified as risk factors for CAL, younger age, gastrointestinal involvement and fever duration were risk factors for IVIG unresponsiveness.  Conclusion: KD with gastrointestinal involvement is associated with a higher risk of IVIG unresponsiveness and coronary artery lesion. KD should be considered in the differential diagnosis of children with acute fever, especially those with gastrointestinal involvement and liver dysfunction. What is Known: • Fever duration, PLT, and CRP were identified as risk factors for CAL. Timely diagnosis and application of IVIG treatment can avoid exploratory laparotomy for ileus, appendectomy for misdiagnosed appendicitis, colonoscopy for misdiagnosed inflammatory bowel disease, and reduce the complications of CAL and IVIG unresponsiveness. What is New: • Abdominal symptoms as the first manifestation can be an independent risk factor for CAL and IVIG unresponsiveness. KD should be conside -raw_completion_output: |- - genes: None mentioned in the text. - exposures: infection, pseudointestinal obstruction, ischemic colitis, pancreatitis, appendicitis, cholecystitis, gastroenteritis, IVIG treatment, fever, ALT, CRP. - gene_exposures_relationships: None mentioned in the text. -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - None mentioned in the text. - - === - -extracted_object: - genes: - - None mentioned in the text. - exposures: - - infection, pseudointestinal obstruction, ischemic colitis, pancreatitis, appendicitis, - cholecystitis, gastroenteritis, IVIG treatment, fever, ALT, CRP. - gene_exposures_relationships: - - molecular_activity: None mentioned in the text. - gene: None mentioned in the text. -input_text: |- - Title: Decoding the microbiome: advances in genetic manipulation for gut bacteria. - Abstract: Studies of the gut microbiota have revealed associations between specific bacterial species or community compositions with health and disease, yet the causal mechanisms underlying microbiota gene-host interactions remain poorly understood. This is partly due to limited genetic manipulation (GM) tools for gut bacteria. Here, we review current advances and challenges in the development of GM approaches, including clustered regularly interspaced short palindromic repeats (CRISPR)-Cas and transposase-based systems in either model or non-model gut bacteria. By overcoming barriers to 'taming' the gut microbiome, GM tools allow molecular understanding of host-microbiome associations and accelerate microbiome engineering for clinical treatment of cancer and metabolic disorders. Finally, we provide perspectives on the future development of GM for gut microbiome species, where more effort should be placed on assembling a generalized GM pipeline to accelerate the application of groundbreaking GM tools in non-model gut bacteria towards both basic understanding and clinical translation.Copyright © 2023 Elsevier Ltd. All rights reserved. - Keywords: CRISPR-Cas; genetic manipulation tools; gut microbiome; host–microbe interactions; transposon -raw_completion_output: |- - genes: Not mentioned in the text. - - exposures: CRISPR-Cas, transposase-based systems - - gene_exposures_relationships: CRISPR-Cas to genetic manipulation tools; transposase-based systems to genetic manipulation tools -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - transposase-based systems to genetic manipulation tools - - === - -extracted_object: - genes: - - Not mentioned in the text. - exposures: - - CRISPR-Cas, transposase-based systems - gene_exposures_relationships: - - molecular_activity: genetic manipulation tools - gene: CRISPR-Cas - - molecular_activity: transposase-based systems - gene: genetic manipulation tools -input_text: |- - Title: Heterogeneity in protocols and outcomes to study the effect of renin-angiotensin system blockers in inflammatory bowel disease: A systematic review. - Abstract: The renin-angiotensin system (RAS) has been associated with inflammatory bowel disease (IBD), supporting translational relevance of RAS blockers. Comparability of study design/outcomes is fundamental for data analysis/discussion.We aimed at evaluating the heterogeneity among protocols and outcomes to study the effect of angiotensin-converting enzyme inhibitors or angiotensin receptor blockers in IBD.This study was performed and reported in accordance with the Cochrane recommendations and PRISMA (PROSPERO-CRD42022323853). Systematic searches were performed in PubMed, Scopus and Web of Science. Studies that met the inclusion criteria were selected. Quality assessment of the studies was done with the SYRCLES's risk of bias tools for animal studies.Thirty-five pre-clinical studies and six clinical studies were included. Chemical induction of colitis was the most used model, but variable doses of the induction agent were reported. All studies reported at least a disease activity index, a macroscopic score, or a histologic assessment, but these scores were methodologically heterogeneous and reported for different characteristics. Great heterogeneity was also found in drug interventions. Inflammatory markers assessed as outcomes were different across studies.Lack of standardization of protocols and outcomes among studies threatens the evidence on how RAS blockers influence IBD outcomes.© 2023 Société Française de Pharmacologie et de Thérapeutique. Published by John Wiley & Sons Ltd. - Keywords: angiotensin-converting enzyme; colitis; heterogeneity; inflammatory bowel disease; renin-angiotensin system blockers; variability -raw_completion_output: |- - genes: none mentioned in the text - - exposures: renin-angiotensin system blockers; angiotensin-converting enzyme inhibitors; angiotensin receptor blockers - - gene_exposures_relationships: none mentioned in the text -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - none mentioned in the text - - === - -extracted_object: - genes: - - none mentioned in the text - exposures: - - renin-angiotensin system blockers - - CHEBI:35457 - - angiotensin receptor blockers - gene_exposures_relationships: - - molecular_activity: none mentioned in the text - gene: none mentioned in the text -named_entities: - - id: CHEBI:35457 - label: angiotensin-converting enzyme inhibitors -input_text: |- - Title: Antimicrobial therapies for chronic pain (part 2): the prevention and treatment of chronic pain. - Abstract: The discovery and development of antimicrobial therapies represents one of the most significant advancements in modern medicine. Although the primary therapeutic intent of antimicrobials is to eliminate their target pathogens, several antimicrobials have been shown to provide analgesia as a secondary benefit. Antimicrobials have demonstrated analgesic effects in conditions that involve dysbiosis or potential subclinical infection (e.g ., chronic low back pain with Modic type 1 changes; chronic prostatitis/chronic pelvic pain; irritable bowel syndrome; inflammatory bowel disease; functional gastrointestinal disorders/dyspepsia; myalgic encephalomyelitis/chronic fatigue syndrome), and might even prevent the chronification of pain after acute infections that are associated with excessive systemic inflammation (e.g ., post COVID-19 condition/long Covid, rheumatic fever). Clinical studies often assess the analgesic effects of antimicrobial therapies in an observational manner, without the ability to identify causative relationships, and significant gaps in the understanding remain regarding the analgesic potential of antimicrobials. Numerous interrelated patient-specific, antimicrobial-specific, and disease-specific factors altogether contribute to the perception and experience of pain, and each of these requires further study. Given worldwide concerns regarding antimicrobial resistance, antimicrobials must continue to be used judiciously and are unlikely to be repurposed as primary analgesic medications. However, when equipoise exists among several antimicrobial treatment options, the potential analgesic benefits of certain antimicrobial agents might be a valuable aspect to consider in clinical decision-making. This article (the second in a two-part series) aims to comprehensively review the evidence on the prevention and treatment of chronic pain using antimicrobial therapies and suggest a framework for future studies on this topic. - Keywords: Analgesia; Anti-Bacterial Agents; Anti-Infective Agents; Antiviral Agents; Central Nervous System Sensitization; Chronic Pain; Infections; Neuralgia; Nociceptive Pain; Pain Management -raw_completion_output: |- - genes: - - exposures: Antimicrobials, pathogens, dysbiosis, subclinical infection, excessive systemic inflammation, post COVID-19 condition/long Covid, rheumatic fever, antimicrobial resistance - - gene_exposures_relationships: Not mentioned in the text. -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - Not mentioned in the text. - - === - -extracted_object: - exposures: - - Antimicrobials, pathogens, dysbiosis, subclinical infection, excessive systemic - inflammation, post COVID-19 condition/long Covid, rheumatic fever, antimicrobial - resistance - gene_exposures_relationships: - - molecular_activity: Not mentioned in the text. - gene: Not mentioned in the text. -input_text: |- - Title: Antimicrobial therapies for chronic pain (part 1): analgesic mechanisms. - Abstract: There is increasing evidence that the relationship between chronic pain and infections is complex and intertwined. Bacterial and viral infections can cause pain through numerous mechanisms such as direct tissue damage and inflammation, the induction of excessive immunologic activity, and the development of peripheral or central sensitization. Treating infections might relieve pain by attenuating these processes, but a growing body of literature suggests that some antimicrobial therapies confer analgesic effects, including for nociceptive and neuropathic pain symptoms, and affective components of pain. The analgesic mechanisms of antimicrobials are indirect, but might be conceptualized into two broad categories: 1) the reduction of the infectious burden and associated pro-inflammatory processes; and 2) the inhibition of signaling processes (e.g., enzymatic and cytokine activity) necessary for nociception and maladaptive neuroplastic changes via off-target effects (unintended binding sites). For the former, there is evidence that symptoms of chronic low back pain (when associated with Modic type 1 changes), irritable bowel syndrome, inflammatory bowel disease, chronic pelvic pain, and functional dyspepsia might be improved after antibiotic treatment, though significant questions remain regarding specific regimens and dose, and which subpopulations are most likely to benefit. For the latter, there is evidence that several antimicrobial classes and medications exert analgesic effects independent of their reduction of infectious burden, and these include cephalosporins, ribavirin, chloroquine derivatives, rapalogues, minocycline, dapsone, and piscidin-1. This article aims to comprehensively review the existing literature for antimicrobial agents that have demonstrated analgesic efficacy in preclinical or clinical studies. - Keywords: Analgesia; Anti-Bacterial Agents; Anti-Infective Agents; Antiviral Agents; Central Nervous System Sensitization; Chronic Pain; Infections; Neuralgia; Nociceptive Pain; Pain Management -raw_completion_output: |- - genes: - exposures: antimicrobial therapies - gene_exposures_relationships: antimicrobial therapies have analgesic effects; antimicrobial therapies reduce infectious burden and associated pro-inflammatory processes; antimicrobial therapies inhibit signaling processes necessary for nociception and maladaptive neuroplastic changes -prompt: |+ - From the text below, extract the following entities in the following format: - - molecular_activity: - gene: - - - Text: - antimicrobial therapies inhibit signaling processes necessary for nociception and maladaptive neuroplastic changes - - === - -extracted_object: - exposures: - - antimicrobial therapies - gene_exposures_relationships: - - molecular_activity: antimicrobial therapies - gene: analgesic effects - - molecular_activity: antimicrobial therapies - gene: N/A - - molecular_activity: inhibit signaling processes - gene: antimicrobial therapies -input_text: |- - Title: Spondyloarthritides. - Abstract: The spondyloarthritides are a diverse group of distinct yet interrelated disease processes with overlapping clinical features. They are ankylosing spondylitis, reactive arthritis, inflammatory bowel disease-associated arthritis, and psoriatic arthritis. Genetically, these disease processes have been linked by the presence of HLA-B27. They manifest with axial and peripheral symptoms, such as inflammatory back pain, enthesitis, oligoarthritis, and dactylitis. The onset of symptoms can begin before the age of 45; however, because of the wide range of signs and symptoms, diagnosis can be delayed, leading to unchecked inflammation, structural damage, and later, restriction in physical mobility.Copyright © 2022 Elsevier Inc. All rights reserved. - Keywords: Ankylosing spondylitis; Axial spondylitis; Inflammatory bowel disease–associated spondyloarthritis; Psoriatic arthritis; Reactive arthritis; Spondyloarthritides -raw_completion_output: |- - genes: HLA-B27 - exposures: Not mentioned in the provided text. - gene_exposures_relationships: Not applicable (N/A) as no specific gene-exposure relationships are mentioned in the text. -prompt: |+ - From the text below, extract the following entities in the following format: - - molecular_activity: - gene: - - - Text: - Not applicable (N/A) as no specific gene-exposure relationships are mentioned in the text. - - === - -extracted_object: - genes: - - HLA-B27 - exposures: - - Not mentioned in the provided text. - gene_exposures_relationships: - - molecular_activity: N/A - gene: N/A -input_text: |- - Title: Combining ultrasound radiomics, complete blood count, and serum biochemical biomarkers for diagnosing intestinal disorders in cats using machine learning. - Abstract: This retrospective analytical observational cohort study aimed to model and predict the classification of feline intestinal diseases from segmentations of a transverse section from small intestine ultrasound (US) image, complete blood count (CBC), and serum biochemical profile data using a variety of machine-learning approaches. In 149 cats from three institutions, images were obtained from cats with biopsy-confirmed small cell epitheliotropic lymphoma (lymphoma), inflammatory bowel disease (IBD), no pathology ("healthy"), and other conditions (warrant a biopsy for further diagnosis). CBC, blood serum chemistry, small intestinal ultrasound, and small intestinal biopsy were obtained within a 2-week interval. CBC and serum biomarkers and radiomic features were combined for modeling. Four classification schemes were investigated: (1) normal versus abnormal; (2) warranting or not warranting a biopsy; (3) lymphoma, IBD, healthy, or other conditions; and (4) lymphoma, IBD, or other conditions. Two feature selection methods were used to identify the top 3, 5, 10, and 20 features, and six machine learning models were trained. The average (95% CI) performance of models for all combinations of features, numbers of features, and types of classifiers was 0.886 (0.871-0.912) for Model 1 (normal vs. abnormal), 0.751 (0.735-0.818) for Model 2 (biopsy vs. no biopsy), 0.504 (0.450-0.556) for Model 3 (lymphoma, IBD, healthy, or other), and 0.531 (0.426-0.589), for Model 4 (lymphoma, IBD, or other). Our findings suggest model accuracies above 0.85 can be achieved in Model 1 and 2, and that including CBC and biochemistry data with US radiomics data did not significantly improve accuracy in our models.© 2023 The Authors. Veterinary Radiology & Ultrasound published by Wiley Periodicals LLC on behalf of American College of Veterinary Radiology. - Keywords: artificial intelligence; feline; intestine; lymphoma -raw_completion_output: |- - genes: No genes mentioned in the text. - exposures: No exposures mentioned in the text. - gene_exposures_relationships: No gene-exposures relationships mentioned in the text. -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - No gene-exposures relationships mentioned in the text. - - === - -extracted_object: - genes: - - No genes mentioned in the text. - exposures: - - No exposures mentioned in the text. - gene_exposures_relationships: - - molecular_activity: No mention of gene-exposures relationships - gene: No mention of gene-exposures relationships -input_text: |- - Title: Increasing Dietary Nutrient Levels Modulates Colon Immune Adaptation and Alleviates Inflammation in the Epithelial Heterogeneous Nuclear Ribonucleoprotein I (Hnrnp I) Knockout Mice. - Abstract: Heterogeneous nuclear ribonucleoprotein I (HNRNP I) is an RNA-binding protein essential for neonatal immune adaptation by downregulating interleukin-1 receptor-associated kinase (IRAK1) in toll-like receptor (TLR)-mediated NF-κB signaling pathways. TLR-mediated NF-κB is associated with chronic inflammation, including the development of inflammatory bowel diseases. Therefore, dietary protein intake is one of the major concerns for individuals with inflammatory bowel diseases. The present study aims to investigate the effects of a protein-enriched diet on intestinal inflammation and immune responses in a mouse model with aberrant NF-κB signaling in the colon.A transgenic mouse model with intestinal-epithelial-cell (IEC) specific Hnrnp I knocked out was used to investigate the effects of protein intake on the immune system in the colon. A control diet (CON) and a nutrient-dense modified diet (MOD) were fed to both the wild-type (WT) and the knockout (KO) male mice for 14 weeks. Inflammatory markers and colonic immune responses were examined, with gene expression and protein expression levels analyzed. IEC-specific Hnrnp I knocked out mice had significantly increased expression of the active NF-κB subunit, P65, in their colons. There was a concomitant induction of mRNA expression of Il1β, Il6, Cxcl1, and Ccl2. The number of CD4+ T cells in the distal colon was also increased in the KO mice. The results confirmed that KO mice had pro-inflammatory responses with aberrant NF-κB signaling in the colon. Importantly, increased nutrient density in their diets attenuated colon inflammation by decreasing the expression of pro-inflammatory cytokines, reducing P65 translocation, downregulating IRAK1, and limiting the number of CD4+ T cells recruited in Hnrnp I KO mice colon.A diet with increased nutrient density relieved the inflammation induced by knockout of Hnrnp I, attributable partially to the reduced expression of inflammatory and immune-modulating cytokines in the mouse distal colon.Copyright © 2023. Published by Elsevier Inc. - Keywords: Hnrnp I; Inflammation; colon immunity; dietary protein -raw_completion_output: |- - genes: Hnrnp I, IRAK1, Il1β, Il6, Cxcl1, Ccl2 - exposures: dietary protein, nutrient-dense modified diet - gene_exposures_relationships: Hnrnp I - downregulates IRAK1; nutrient-dense modified diet - attenuated colon inflammation -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - nutrient-dense modified diet - attenuated colon inflammation - - === - -extracted_object: - genes: - - Hnrnp I, IRAK1, Il1β, Il6, Cxcl1, Ccl2 - exposures: - - dietary protein, nutrient-dense modified diet - gene_exposures_relationships: - - molecular_activity: downregulates - gene: Hnrnp I - - molecular_activity: attenuated colon inflammation - gene: nutrient-dense modified diet -input_text: |- - Title: Prior Authorizations Delay Therapy, Impact Decision Making, and Lead to Adverse Events in IBD: 2022 Provider Survey. - Abstract: - Keywords: Crohn’s disease; Prior authorization; biologics; inflammatory bowel disease; ulcerative colitis -raw_completion_output: |- - genes: None given in the text - exposures: biologics - gene_exposures_relationships: None mentioned in the text -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - None mentioned in the text - - === - -extracted_object: - genes: - - None given in the text - exposures: - - biologics - gene_exposures_relationships: - - molecular_activity: None mentioned in the text - gene: None mentioned in the text -input_text: |- - Title: High Frequency of Deep Infiltrating Endometriosis in Patients with Inflammatory Bowel Disease: A Nested Case-Control Study. - Abstract: Inflammatory bowel disease (IBD) and endometriosis are chronic inflammatory diseases occurring in young women, sharing some clinical manifestations. In a multidisciplinary approach, we aimed to investigate symptoms, type, and site of pelvic endometriosis in IBD patients versus non-IBD controls with endometriosis.In a prospective nested case-control study, all female premenopausal IBD patients showing symptoms compatible with endometriosis were enrolled. Patients were referred to dedicated gynecologists for assessing pelvic endometriosis by transvaginal sonography (TVS). Each IBD patient with endometriosis (cases) was retrospectively matched for age (±5 years) and body mass index (±1) with 4 patients with endometriosis at TVS but no-IBD (controls). Data were expressed as median [range]; the Mann-Whitney or Student t and χ2 tests were used for comparisons.Endometriosis was diagnosed in 25 (71%) out of 35 IBD patients with compatible symptoms including 12 (52.6%) Crohn's disease and 13 (47.4%) ulcerative colitis patients. Dyspareunia and dyschezia were significantly more frequent in cases versus controls (25 [73.7%] vs. 26 [45.6%]; p = 0.03). At TVS, deep infiltrating endometriosis (DIE) and posterior adenomyosis were significantly more frequently observed in cases versus controls (25 [100%] vs. 80 [80%]; p = 0.03 and 19 [76%] vs. 48 [48%]; p = 0.02).Endometriosis was detected in two-thirds of IBD patients with compatible symptoms. The frequency of DIE and posterior adenomyosis was higher in IBD than in controls. A diagnosis of endometriosis, often mimicking IBD activity, should be considered in subgroups of female patients with IBD.© 2023 S. Karger AG, Basel. - Keywords: Deep infiltrating endometriosis; Endometriosis; Inflammatory bowel disease -raw_completion_output: |- - genes: None mentioned in the text - exposures: None mentioned in the text - gene_exposures_relationships: None mentioned in the text -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - None mentioned in the text - - === - -extracted_object: - genes: - - None mentioned in the text - exposures: - - None mentioned in the text - gene_exposures_relationships: - - molecular_activity: None mentioned in the text - gene: None mentioned in the text -input_text: |- - Title: Manifestation of acute appendicitis as known but paradox visceral side effect of ulcerative colitis anti-inflammatory therapy with januskinase-inhibitor Tofacitinib (Xeljanz™). - Abstract: The etiopathogenesis of accompanying inflammatory phenomena and consequences of immunomodulation constitute a challenging and innovative field in the medical treatment of patients with autoimmune diseases.Based on i) clinical management experience gained from this challenging clinical case and ii) selective references of reports published in the scientific medical literature, we present an unusual counterfactual scientific case report. A patient diagnosed with ulcerative colitis undergoing januskinase (JAK)-inhibitor therapy developed acuteappendicitis as an unusual complication or as a visceral side effect of immunosuppressive/anti-inflammatory therapy.Scientific case report.(case description): Medical history: A 52-year-old male presented with spasmodic pain in the right lower abdomen lasting for two days (no fever, no bowel movement changes (no stool irregularities), no vomiting).Steroid-resistant ulcerative colitis treated with immunosuppressive therapy (Adalimumab administered for 10 months [next generation anti-TNFα mAb], Vendolizumab for 9 months [α4β7 integrin antagonist], Tofacitinib for 6 months); fructose intolerance, no previous abdominal surgery; medication: XeljanzTM (Tofacitinib, 5 mg 2x1; JAK-inhibitor; PFIZER PHARMA GmbH, Berlin,Germany); MutaflorTM (1x1; Ardeypharm GmbH, Herdecke, Germany).Pressure pain in the right lower abdomen with local muscular defense (Mc-Burney's/Lanz's point positive), no peritonism, Psoas-muscle sign positive.Laboratory parameters: standard value of white blood cell count, CrP: 25 mg/l.-Transabdominal ultrasound revealed hypertrophic 'appendix vermiformis' with detectable target-phenomenon and surrounding fluid.Indication for laparoscopic exploration.Under perioperative single-shot antibiotic administration with UnacidTM, the patient underwent emergency laparoscopic appendectomy due to confirmed acute appendicitis with additional lavage and placement of local drainage.The postoperative phase was uneventful (sufficient analgetic therapy, removal of local drainage on the 2nd postoperative day). The patient was discharged four days after surgery. Histopathology confirmed ulcero-phlegmonous, acute purulent appendicitis with fibrinous purulent mesenteriolitis.Immunosuppressive therapy was continued.Based on the paradoxon of an acute inflammatory disease (acute appendicitis) seen in the case of a patient undergoing immunosuppressive/anti-inflammatory treatment using a JAK-Inhibitor for ulcerative colitis, we consider this case worthy of publication although this side effect has previously been described in patients with rheumatoid arthritis. This might be the manifestation of i) an immunomodulatory effect that reduced or at least altered mucosal defense, including an increased risk of opportunistic infections, presenti -raw_completion_output: |- - genes: januskinase (JAK) - exposures: Tofacitinib (Xeljanz™) - gene_exposures_relationships: januskinase (JAK) - Tofacitinib (Xeljanz™) -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - januskinase (JAK) - Tofacitinib (Xeljanz™) - - === - -extracted_object: - genes: - - januskinase (JAK) - exposures: - - Tofacitinib (Xeljanz™) - gene_exposures_relationships: - - molecular_activity: exposure to a chemical toxin - gene: JAK -input_text: |- - Title: Prevention of colitis-induced liver oxidative stress and inflammation in a transgenic mouse model with increased omega-3 polyunsaturated fatty acids. - Abstract: Inflammatory bowel disease (IBD) is an immune-mediated gut dysfunction, which might also be associated with an inflammatory phenotype in the liver. It is known that the nutritional intake of omega-3 polyunsaturated fatty acids (n-3 PUFA) is inversely correlated to the severity and occurrence of IBD. In order to investigate whether n-3 PUFA can also reduce liver inflammation and oxidative liver damage due to colon inflammation, we explored the dextran sulfate sodium (DSS)-induced colitis model in wild-type and fat-1 mice with endogenously increased n-3 PUFA tissue content. Besides confirming previous data of alleviated DSS-induced colitis in the fat-1 mouse model, the increase of n-3 PUFA also resulted in a significant reduction of liver inflammation and oxidative damage in colitis-affected fat-1 mice as compared to wild-type littermates. This was accompanied by a remarkable increase of established inflammation-dampening n-3 PUFA oxylipins, namely docosahexaenoic acid-derived 19,20-epoxydocosapentaenoic acid and eicosapentaenoic acid-derived 15-hydroxyeicosapentaenoic acid and 17,18-epoxyeicosatetraenoic acid. Taken together, these observations demonstrate a strong inverse correlation between the anti-inflammatory lipidome derived from n-3 PUFA and the colitis-triggered inflammatory changes in the liver by reducing oxidative liver stress.Copyright © 2023 The Authors. Published by Elsevier B.V. All rights reserved. - Keywords: Colitis; Fat-1 mice; Liver inflammation; Liver oxidative stress; n-3 PUFA -raw_completion_output: |- - genes: No gene mentioned in the text. - - exposures: omega-3 polyunsaturated fatty acids (n-3 PUFA), dextran sulfate sodium (DSS) - - gene_exposures_relationships: No gene to molecular activity relationships mentioned in the text. -prompt: |+ - From the text below, extract the following entities in the following format: - - molecular_activity: - gene: - - - Text: - No gene to molecular activity relationships mentioned in the text. - - === - -extracted_object: - genes: - - No gene mentioned in the text. - exposures: - - omega-3 polyunsaturated fatty acids (n-3 PUFA), dextran sulfate sodium (DSS) -input_text: |- - Title: Borrelia Burgdorferi, a Root Cause of Inflammatory Bowel Disease: A Case Report of Successful Treatment and Remission. - Abstract: The Borrelia species is recognized to cause a myriad of non-specific symptoms among Lyme patients. It has also been documented in the literature to have the ability to incite autoimmune responses. Despite this, very few clinical cases have ever put together the autoimmune connection to such infections, including in Crohn's disease.A 14-year-old adolescent male with a previous diagnosis of Crohn's disease was discovered to have underlying Lyme disease caused by Borrelia burgdorferi infection. Identifying this as a potential cause of his autoimmune condition, an integrative medical approach was initiated, resulting in successful treatment and complete remission.Lyme disease should be recognized as a potential trigger of autoimmune conditions, especially Crohn's disease. This underlying cause is novel to the literature and may help many patients obtain the proper diagnosis so that curative treatment may be received. - Keywords: -raw_completion_output: |- - genes: Borrelia burgdorferi - - exposures: Lyme disease, Borrelia burgdorferi - - gene_exposures_relationships: Borrelia burgdorferi -> autoimmune responses -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - Borrelia burgdorferi -> autoimmune responses - - === - -extracted_object: - genes: - - Borrelia burgdorferi - exposures: - - Lyme disease, Borrelia burgdorferi - gene_exposures_relationships: - - molecular_activity: autoimmune responses - gene: Borrelia burgdorferi -input_text: |- - Title: Clinical Features and Natural History of Paediatric Patients with Ulcerative Proctitis: A Multicentre Study from the Paediatric IBD Porto Group of ESPGHAN. - Abstract: Ulcerative proctitis (UP) is an uncommon presentation in paediatric patients with ulcerative colitis. We aimed to characterize the clinical features and natural history of UP in children, and identify predictors of poor outcomes.Retrospective study involving 37 sites affiliated with the IBD Porto Group of ESPGHAN. Data were collected from patients aged<18 years diagnosed with UP between 01/01/2016-31/12/2020.We identified 196 patients with UP (median age at diagnosis 14.6 [IQR 12.5-16.0] years), with a median follow-up of 2.7 (IQR 1.7-3.8) years. The most common presenting symptoms were bloody stools (95%), abdominal pain (61%) and diarrhea )47%). At diagnosis, the median paediatric ulcerative colitis activity index (PUCAI) score was 25 (IQR 20-35), but most patients exhibited moderate-severe endoscopic inflammation. By the end-of-induction, 5-aminosalicylic acid administration orally, topically or both resulted in clinical remission rates of 48%, 48% and 73%, respectively. The rates of treatment escalation to biologics at 1, 3 and 5 years were 10%, 22% and 43%, respectively. In multivariate analysis, the PUCAI score at diagnosis was significantly associated with initiation of systemic steroids, or biologics, and subsequent acute severe colitis events and IBD-associated admission, with a score≥35 providing increased risk for poor outcomes. By the end of follow-up, 3.1% of patients underwent colectomy. Patients with proximal disease progression (48%) had significantly higher rates of cecal patch at diagnosis and higher PUCAI score by end-of-induction, compared to those without progression.Paediatric patients with UP exhibit high rates of treatment escalation and proximal disease extension.© The Author(s) 2023. Published by Oxford University Press on behalf of European Crohn’s and Colitis Organisation. All rights reserved. For permissions, please email: journals.permissions@oup.com. - Keywords: children; inflammatory bowel disease; proctitis; ulcerative colitis -raw_completion_output: |- - genes: None mentioned in the text - exposures: 5-aminosalicylic acid - gene_exposures_relationships: None mentioned in the text -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - None mentioned in the text - - === - -extracted_object: - genes: - - None mentioned in the text - exposures: - - 5-aminosalicylic acid - gene_exposures_relationships: - - molecular_activity: None mentioned in the text - gene: None mentioned in the text -input_text: |- - Title: Smoking and colorectal cancer in inflammatory bowel disease: Quantity matters? - Abstract: - Keywords: -raw_completion_output: |- - genes: - - exposures: smoking; - - gene_exposures_relationships: smoking and colorectal cancer; -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - smoking and colorectal cancer - - === - -extracted_object: - exposures: - - NCIT:C154329 - gene_exposures_relationships: - - molecular_activity: NCIT:C154329 - gene: colorectal cancer -named_entities: - - id: NCIT:C154329 - label: smoking -input_text: |- - Title: Recent developments on BMPs and their antagonists in inflammatory bowel diseases. - Abstract: Inflammatory bowel diseases (IBDs), including ulcerative colitis, and Crohn's disease, are intestinal disorders characterized by chronic relapsing inflammation. A large proportion of patients with IBD will progress to develop colitis-associated colorectal cancer due to the chronic intestinal inflammation. Biologic agents that target tumour necrosis factor-α, integrin α4β7, and interleukin (IL)12/23p40 have been more successful than conventional therapies in treating IBD. However, drug intolerance and loss of response are serious drawbacks of current biologics, necessitating the development of novel drugs that target specific pathways in IBD pathogenesis. One promising group of candidate molecules are bone morphogenetic proteins (BMPs), members of the TGF-β family involved in regulating morphogenesis, homeostasis, stemness, and inflammatory responses in the gastrointestinal tract. Also worth examining are BMP antagonists, major regulators of these proteins. Evidence has shown that BMPs (especially BMP4/6/7) and BMP antagonists (especially Gremlin1 and follistatin-like protein 1) play essential roles in IBD pathogenesis. In this review, we provide an updated overview on the involvement of BMPs and BMP antagonists in IBD pathogenesis and in regulating the fate of intestinal stem cells. We also described the expression patterns of BMPs and BMP antagonists along the intestinal crypt-villus axis. Lastly, we synthesized available research on negative regulators of BMP signalling. This review summarizes recent developments on BMPs and BMP antagonists in IBD pathogenesis, which provides novel insights into future therapeutic strategies.© 2023. The Author(s). - Keywords: -raw_completion_output: |- - genes: BMP4, BMP6, BMP7, Gremlin1, follistatin-like protein 1 - exposures: bone morphogenetic proteins (BMPs) - gene_exposures_relationships: BMP4/6/7 are BMPs involved in IBD pathogenesis; Gremlin1 and follistatin-like protein 1 are BMP antagonists -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - Gremlin1 and follistatin-like protein 1 are BMP antagonists - - === - -extracted_object: - genes: - - BMP4, BMP6, BMP7, Gremlin1, follistatin-like protein 1 - exposures: - - bone morphogenetic proteins (BMPs) - gene_exposures_relationships: - - molecular_activity: BMPs involved in IBD pathogenesis - gene: BMP4/6/7 - - molecular_activity: BMP antagonists - gene: Gremlin1 and follistatin-like protein 1 -input_text: |- - Title: 7TSG6 hyaluronan matrix remodeling dampens the inflammatory response during colitis. - Abstract: In response to tissue injury, changes in the extracellular matrix (ECM) can directly affect the inflammatory response and contribute to disease progression or resolution. During inflammation, the glycosaminoglycan hyaluronan (HA) becomes modified by tumor necrosis factor stimulated gene-6 (TSG6). TSG6 covalently transfers heavy chain (HC) proteins from inter-α-trypsin inhibitor (IαI) to HA in a transesterification reaction and is to date is the only known HC-transferase. By modifying the HA matrix, TSG6 generates HC:HA complexes that are implicated in mediating both protective and pathological responses. Inflammatory bowel disease (IBD) is a lifelong chronic disorder with well-described remodeling of the ECM and increased mononuclear leukocyte influx into the intestinal mucosa. Deposition of HC:HA matrices is an early event in inflamed gut tissue that precedes and promotes leukocyte infiltration. However, the mechanisms by which TSG6 contributes to intestinal inflammation are not well understood. The aim of our study was to understand how the TSG6 and its enzymatic activity contributes to the inflammatory response in colitis. Our findings indicate that inflamed tissues of IBD patients show an elevated level of TSG6 and increased HC deposition and that levels of HA strongly associate with TSG6 levels in patient colon tissue specimens. Additionally, we observed that mice lacking TSG6 are more vulnerable to acute colitis and exhibit an aggravated macrophage-associated mucosal immune response characterized by elevated pro-inflammatory cytokines and chemokines and diminished anti-inflammatory mediators including IL-10. Surprisingly, along with significantly increased levels of inflammation in the absence of TSG6, tissue HA levels in mice were found to be significantly reduced and disorganized, absent of typical "HA-cable" structures. Inhibition of TSG6 HC-transferase activity leads to a loss of cell surface HA and leukocyte adhesion, indicating that the enzymatic functions of TSG6 are a major contributor to stability of the HA ECM during inflammation. Finally, using biochemically generated HC:HA matrices derived by TSG6, we show that HC:HA complexes can attenuate the inflammatory response of activated monocytes. In conclusion, our data suggests that TSG6 exerts a tissue-protective, anti-inflammatory effect via the generation of HC:HA complexes that become dysregulated in IBD.Copyright © 2023. Published by Elsevier B.V. - Keywords: Colitis; Extracellular matrix; Hyaluronan; IBD; TSG6 -raw_completion_output: |- - genes: TSG6, IL-10 - exposures: tumor necrosis factor, inter-α-trypsin inhibitor, hyaluronan - gene_exposures_relationships: TSG6 with tumor necrosis factor, TSG6 with inter-α-trypsin inhibitor, TSG6 with hyaluronan -prompt: |+ - From the text below, extract the following entities in the following format: - - molecular_activity: - gene: - - - Text: - TSG6 with tumor necrosis factor, TSG6 with inter-α-trypsin inhibitor, TSG6 with hyaluronan - - === - -extracted_object: - genes: - - TSG6, IL-10 - exposures: - - tumor necrosis factor, inter-α-trypsin inhibitor, hyaluronan - gene_exposures_relationships: - - molecular_activity: hyaluronan - gene: HGNC:11898 -named_entities: - - id: HGNC:11898 - label: TSG6 -input_text: |- - Title: Delayed Ustekinumab Responders in Ulcerative Colitis Have Greater Inflammatory Burden but Similar Outcomes as Early Responders. - Abstract: Differences in one-year outcomes among early compared to delayed responders to vedolizumab have been demonstrated in ulcerative colitis. However, it is unclear whether similar differences exist with ustekinumab, and what factors differentiate delayed responders from non-responders.This was a post-hoc analysis of patient-level data from the UNIFI clinical trial. Ustekinumab-treated patients with clinical response, defined as reduction in total Mayo score ≥30% and ≥3 points from baseline with reduction in rectal bleeding subscore (RBS)≥1 or RBS≤1, at week 8 were deemed early responders and their outcomes were compared with delayed responders (week 8 non-responders who subsequently responded at week 16). The primary outcome assessed was one-year clinical remission (CR), defined as total Mayo score ≤2 and no subscore >1.We included 642 ustekinumab-treated patients, including 321 (50%) early responders, 115 (17.9%) delayed responders, and 205 (32.1%) non-responders. No differences were observed for one-year CR among early vs. delayed responders [132/321 (41.1%) vs. 40/115 (34.8%), p=0.233], nor for other outcomes assessed regardless of induction dose. Compared to early responders, delayed responders had more severe baseline Mayo endoscopic disease [88/115 (76.5%) vs. 206/321 (64.2%), p=0.015] and abnormal baseline CRP >3mg/L [83/115 (72.2%) vs. 183/321 (57%), p=0.004]. Compared to non-responders, delayed responders had a significant decline in CRP (F(4, 844), p<0.0001) and fecal calprotectin (F(4, 818), p<0.0001) through week 16.Compared with early ustekinumab responders, delayed responders had greater inflammatory burden at baseline. Early and delayed responders have similar one-year outcomes. Biomarker decline observed in delayed responders can help differentiate them from non-responders.Copyright © 2023 AGA Institute. Published by Elsevier Inc. All rights reserved. - Keywords: Endoscopic Improvement; Inflammatory Bowel Disease; Ulcerative Colitis -raw_completion_output: |- - genes: N/A - exposures: ustekinumab, vedolizumab - gene_exposures_relationships: N/A -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - N/A - - === - -extracted_object: - genes: - - N/A - exposures: - - ustekinumab, vedolizumab - gene_exposures_relationships: - - molecular_activity: N/A - gene: N/A -input_text: |- - Title: Eriocalyxin B ameliorated Crohn's disease-like colitis by restricting M1 macrophage polarization through JAK2/STAT1 signalling. - Abstract: M1 polarization of macrophages in the intestine is an important maintenance factor of the inflammatory response in Crohn's disease (CD). Eriocalyxin B (EriB) is a natural medicine that antagonizes inflammation. Our study aimed to determine the effects of EriB on CD-like colitis in mice, as well as the possible mechanism.2,4,6-trinitrobenzene sulfonic acid (TNBS) mice and Il-10-/- mice were used as CD animal models, and the therapeutic effect of EriB on CD-like colitis in mice was addressed by the disease activity index (DAI) score, weight change, histological analysis and flow cytometry assay. To assess the direct role of EriB in regulating macrophage polarization, bone marrow-derived macrophages (BMDMs) were induced to M1 or M2 polarization separately. Molecular docking simulations and blocking experiments were performed to explore the potential mechanisms by which EriB regulates the macrophage polarization.EriB treatment reduced body weight loss, DAI score and histological score, demonstrating the improvement of colitis symptoms in mice. In vivo and in vitro experiments both showed that EriB decreased the M1 polarization of macrophages, and suppressed the release of proinflammatory cytokines (IL-1β, TNF-α and IL-6) in mouse colons and BMDMs. The activation of Janus kinase 2/signal transducer and activator of transcription 1 (JAK2/STAT1) signals could be inhibited by EriB, which may be related to the regulation of EriB on M1 polarization.EriB inhibits the M1 polarization of macrophages by attenuating the JAK2/STAT1 pathway, which partially explains the potential mechanism by which EriB ameliorates colitis in mice, and provides a new regimen for the clinical treatment of CD.Copyright © 2023 The Authors. Published by Elsevier B.V. All rights reserved. - Keywords: Colitis; Crohn's disease; Eriocalyxin B; JAK2/STAT1; macrophage -raw_completion_output: |- - genes: JAK2, STAT1 - exposures: Eriocalyxin B, 2,4,6-trinitrobenzene sulfonic acid (TNBS), IL-1β, TNF-α, IL-6 - gene_exposures_relationships: JAK2/STAT1 to Eriocalyxin B -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - JAK2/STAT1 to Eriocalyxin B - - === - -extracted_object: - genes: - - JAK2, STAT1 - exposures: - - CHEBI:48113 - gene_exposures_relationships: - - molecular_activity: JAK2/STAT1 - gene: Eriocalyxin B -named_entities: - - id: CHEBI:48113 - label: Eriocalyxin B, 2,4,6-trinitrobenzene sulfonic acid (TNBS), IL-1β, TNF-α, - IL-6 -input_text: |- - Title: Lack of Seroconversion Following COVID-19 Vaccination Is an Independent Risk Factor for SARS-CoV-2 Infection in Patients With Inflammatory Bowel Disease: Data from ESCAPE-IBD, an IG-IBD Study. - Abstract: - Keywords: SARS-CoV-2; Seroconversion; biologics; vaccine -raw_completion_output: |- - genes: none mentioned in the text - - exposures: SARS-CoV-2, biologics, vaccine - - gene_exposures_relationships: none mentioned in the text -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - none mentioned in the text - - === - -extracted_object: - genes: - - none mentioned in the text - exposures: - - SARS-CoV-2, biologics, vaccine - gene_exposures_relationships: - - molecular_activity: none mentioned in the text - gene: none mentioned in the text -input_text: |- - Title: Neutrophil-only histological assessment of ulcerative colitis correlates with endoscopic activity and predicts long-term outcomes in a multicenter study. - Abstract: Absence of neutrophils is the minimum standard to consider histological remission of ulcerative colitis (UC). The PICaSSO Histological remission Index (PHRI) is a new simple index for UC based only on the detection of neutrophils. We evaluate PHRI's correlation with endoscopy and its prognostic value compared to other established indices.Consecutive patients with UC underwent colonoscopy at 2 referral centres (Birmingham, UK and Milan, Italy) and were followed up for 2 years. Correlation between histology (PHRI, Nancy [NHI] and Robarts [RHI]) and endoscopy (Mayo Endoscopic Score [MES]; Ulcerative Colitis Severity Endoscopic Index of Severity [UCEIS], and PICaSSO score) was calculated as Spearman coefficients. Diagnostic performance of endoscopy was assessed with ROC curves and outcome stratification with Kaplan-meier curves.192 patients with UC were enrolled, representing all grades of endoscopic severity. Correlation between histology and endoscopy did not differ significantly when using PHRI instead of NHI or RHI. In particular, PHRI's correlation with MES, UCEIS and PICaSSO was 0.745, 0.718, and 0.694, respectively. Endoscopically-assessed remission reflected the absence of neutrophils (PHRI = 0) with areas under the ROC curve of 0.905, 0.906, and 0.877 for MES, UCEIS, and PICaSSO, respectively. The hazard ratio for disease flare between patients in histological activity/remission was statistically similar (p>0.05) across indexes (2.752, 2.706, and 2.871 for RHI, NHI, and PHRI, respectively).PHRI correlates with endoscopy and stratifies risk of relapse similarly to RHI and NHI. Neutrophil-only assessment of UC is a simple yet viable alternative to established histological scores.© The Author(s) 2023. Published by Oxford University Press on behalf of European Crohn’s and Colitis Organisation. All rights reserved. For permissions, please email: journals.permissions@oup.com. - Keywords: PHRI; PICaSSO; endoscopic remission; histological remission; inflammatory bowel diseases; neutrophils -raw_completion_output: |- - genes: None mentioned - exposures: PICaSSO, Nancy, Robarts, Mayo Endoscopic Score, Ulcerative Colitis Severity Endoscopic Index of Severity, PICaSSO score, RHI, NHI - gene_exposures_relationships: PHRI correlates with MES, UCEIS, PICaSSO; RHI, NHI, and PHRI reflect histological activity/remission; endoscopically-assessed remission reflects the absence of neutrophils (PHRI = 0) -prompt: |+ - From the text below, extract the following entities in the following format: - - molecular_activity: - gene: - - - Text: - endoscopically-assessed remission reflects the absence of neutrophils (PHRI = 0) - - === - -extracted_object: - genes: - - None mentioned - exposures: - - PICaSSO, Nancy, Robarts, Mayo Endoscopic Score, Ulcerative Colitis Severity - Endoscopic Index of Severity, PICaSSO score, RHI, NHI - gene_exposures_relationships: - - molecular_activity: PHRI - gene: PICaSSO - - molecular_activity: histological activity/remission - gene: RHI - - molecular_activity: exposure to a chemical toxin - gene: PHRI -input_text: |- - Title: Effect of Bariatric Surgery on Disease Outcomes in Patients with Inflammatory Bowel Disease: A US-based Propensity Matched Cohort Study. - Abstract: A growing body of evidence suggests a negative impact of obesity on the disease activity of inflammatory bowel disease (IBD). The primary aim of the study was to evaluate disease outcomes of IBD in patients after bariatric surgery (BS).Patients with IBD and morbid obesity who underwent BS were compared with patients with IBD and morbid obesity without BS in a retrospective, propensity-score matched cohort study using TriNetX, a multi-institutional database. The primary aim was to assess the 2-year risk of a composite of disease-related complications, which included intravenous steroid use or IBD-related surgery. Risk was expressed as adjusted odds ratios (aOR) with 95% confidence intervals (CI).In all, 482 patients (3.4%) with IBD and morbid obesity underwent BS (mean age 46.9±11.2 y old, mean BMI 42.1±7.72 kg/m2, Crohn's disease 60%). After propensity-score matching, the BS cohort had a lower risk (aOR 0.31, 95% CI 0.17-0.56) of a composite of IBD-related complications compared with the control cohort. After propensity-score matching, the BS cohort with sleeve gastrectomy had a decreased risk (aOR 0.45, 95% CI 0.31-0.66) of a composite of IBD-related complications. There was no difference in the risk (aOR 0.77, 95% CI 0.45-1.31) of a composite of IBD-related complications between the BS cohort with Roux-en-Y gastric bypass (RYGB) compared with the control cohort.Sleeve gastrectomy but not Roux-en-Y gastric bypass is associated with improved disease-specific outcomes in patients with IBD and morbid obesity.Copyright © 2023 Wolters Kluwer Health, Inc. All rights reserved. - Keywords: -raw_completion_output: |- - genes: N/A - exposures: Bariatric surgery - gene_exposures_relationships: N/A -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - N/A - - === - -extracted_object: - genes: - - N/A - exposures: - - Bariatric surgery - gene_exposures_relationships: - - molecular_activity: N/A - gene: N/A -input_text: |- - Title: The Effect of Renin-Angiotensin-Aldosterone System Blocking Agents on the Long-term Disease Course of Patients With Crohn's Disease. - Abstract: The renin-angiotensin-aldosterone system (RAAS) has been associated with gastrointestinal inflammation and fibrosis, suggesting that RAAS blockade may be beneficial in patients with inflammatory bowel disease. Using retrospective analysis, we aimed to compare the disease course of patients with Crohn's disease (CD) taking two commonly prescribed classes of RAAS-blocking agents.Patients with CD initiated on an angiotensin-converting enzyme inhibitor (ACEI) or angiotensin receptor blocker (ARB) between 2000 and 2016 were enrolled. Data on clinical, radiologic, and procedural surrogate markers of inflammatory bowel disease were collected in the subsequent 3, 5, and 10 years and compared with matched controls using univariate and multivariate analyses.Compared with controls, patients taking ARBs had fewer instances of corticosteroid use (1.06 vs 2.88, P < 0.01) at 10 years. Patients taking ACEIs had an overall worse disease course, with more imaging studies (3.00 vs 1.75, P = 0.03) and endoscopic procedures (2.70 vs 1.78, P = 0.01) at 5 years, and more imaging studies (6.19 vs 3.50, P < 0.01), endoscopic procedures (5.91 vs 3.78, P < 0.01), and gastrointestinal operations (0.59 vs 0.18, P < 0.02) at 10 years. Results remained significant on multivariate analysis, adjusting for CD characteristics and the use of other antihypertensive medications.Our study provides insight into the long-term use of RAAS-blocking agents in patients with CD, suggesting that differences exist among commonly prescribed medication classes. While ACEIs were associated with an overall worse disease course at 5 and 10 years, patients taking ARBs were noted to have fewer instances of corticosteroid use at 10 years. Future large-scale studies are needed to further explore this association.Copyright © 2023 Wolters Kluwer Health, Inc. All rights reserved. - Keywords: -raw_completion_output: |- - genes: N/A (no genes mentioned in the text) - exposures: angiotensin-converting enzyme inhibitor (ACEI), angiotensin receptor blocker (ARB) - gene_exposures_relationships: N/A (no gene-molecular activity relationships mentioned in the text) -prompt: |+ - From the text below, extract the following entities in the following format: - - molecular_activity: - gene: - - - Text: - N/A (no gene-molecular activity relationships mentioned in the text) - - === - -extracted_object: - genes: - - N/A (no genes mentioned in the text) - exposures: - - angiotensin-converting enzyme inhibitor (ACEI), angiotensin receptor blocker - (ARB) - gene_exposures_relationships: - - molecular_activity: N/A - gene: N/A -input_text: |- - Title: The role of complex interactions between the intestinal flora and host in regulating intestinal homeostasis and inflammatory bowel disease. - Abstract: Pharmacological treatment of inflammatory bowel disease (IBD) is inefficient and difficult to discontinue appropriately, and enterobacterial interactions are expected to provide a new target for the treatment of IBD. We collected recent studies on the enterobacterial interactions among the host, enterobacteria, and their metabolite products and discuss potential therapeutic options. Intestinal flora interactions in IBD are affected in the reduced bacterial diversity, impact the immune system and are influenced by multiple factors such as host genetics and diet. Enterobacterial metabolites such as SCFAs, bile acids, and tryptophan also play important roles in enterobacterial interactions, especially in the progression of IBD. Therapeutically, a wide range of sources of probiotics and prebiotics exhibit potential therapeutic benefit in IBD through enterobacterial interactions, and some have gained wide recognition as adjuvant drugs. Different dietary patterns and foods, especially functional foods, are novel therapeutic modalities that distinguish pro-and prebiotics from traditional medications. Combined studies with food science may significantly improve the therapeutic experience of patients with IBD. In this review, we provide a brief overview of the role of enterobacteria and their metabolites in enterobacterial interactions, discuss the advantages and disadvantages of the potential therapeutic options derived from such metabolites, and postulate directions for further research.Copyright © 2023 Li, Xu, Cheng, Chen, Yi, Xiao, Zhao, Chen, Tian, Meng, Tang, Zhou, Ruan and Wei. - Keywords: IBD therapies; functional foods; gut metabolome; inflammatory bowel disease; intestinal flora; intestinal homeostasis; short chain fatty acids (SCFAs) -raw_completion_output: |- - genes: N/A - exposures: intestinal flora, enterobacteria, metabolite products, SCFAs, bile acids, tryptophan, probiotics, prebiotics, dietary patterns, functional foods, gut metabolome - gene_exposures_relationships: N/A -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - N/A - - === - -extracted_object: - genes: - - N/A - exposures: - - intestinal flora, enterobacteria, metabolite products, SCFAs, bile acids, tryptophan, - probiotics, prebiotics, dietary patterns, functional foods, gut metabolome - gene_exposures_relationships: - - molecular_activity: N/A - gene: N/A -input_text: |- - Title: Study of the roles of caspase-3 and nuclear factor kappa B in myenteric neurons in a P2X7 receptor knockout mouse model of ulcerative colitis. - Abstract: The literature indicates that the enteric nervous system is affected in inflammatory bowel diseases (IBDs) and that the P2X7 receptor triggers neuronal death. However, the mechanism by which enteric neurons are lost in IBDs is unknown.To study the role of the caspase-3 and nuclear factor kappa B (NF-κB) pathways in myenteric neurons in a P2X7 receptor knockout (KO) mouse model of IBDs.Forty male wild-type (WT) C57BL/6 and P2X7 receptor KO mice were euthanized 24 h or 4 d after colitis induction by 2,4,6-trinitrobenzene sulfonic acid (colitis group). Mice in the sham groups were injected with vehicle. The mice were divided into eight groups (n = 5): The WT sham 24 h and 4 d groups, the WT colitis 24 h and 4 d groups, the KO sham 24 h and 4 d groups, and the KO colitis 24 h and 4 d groups. The disease activity index (DAI) was analyzed, the distal colon was collected for immunohistochemistry analyses, and immunofluorescence was performed to identify neurons immunoreactive (ir) for calretinin, P2X7 receptor, cleaved caspase-3, total caspase-3, phospho-NF-κB, and total NF-κB. We analyzed the number of calretinin-ir and P2X7 receptor-ir neurons per ganglion, the neuronal profile area (µm²), and corrected total cell fluorescence (CTCF).Cells double labeled for calretinin and P2X7 receptor, cleaved caspase-3, total caspase-3, phospho-NF-κB, or total NF-κB were observed in the WT colitis 24 h and 4 d groups. The number of calretinin-ir neurons per ganglion was decreased in the WT colitis 24 h and 4 d groups compared to the WT sham 24 h and 4 d groups, respectively (2.10 ± 0.13 vs 3.33 ± 0.17, P < 0.001; 2.92 ± 0.12 vs 3.70 ± 0.11, P < 0.05), but was not significantly different between the KO groups. The calretinin-ir neuronal profile area was increased in the WT colitis 24 h group compared to the WT sham 24 h group (312.60 ± 7.85 vs 278.41 ± 6.65, P < 0.05), and the nuclear profile area was decreased in the WT colitis 4 d group compared to the WT sham 4 d group (104.63 ± 2.49 vs 117.41 ± 1.14, P < 0.01). The number of P2X7 receptor-ir neurons per ganglion was decreased in the WT colitis 24 h and 4 d groups compared to the WT sham 24 h and 4 d groups, respectively (19.49 ± 0.35 vs 22.21 ± 0.18, P < 0.001; 20.35 ± 0.14 vs 22.75 ± 0.51, P < 0.001), and no P2X7 receptor-ir neurons were observed in the KO groups. Myenteric neurons showed ultrastructural changes in the WT colitis 24 h and 4 d groups and in the KO colitis 24 h group. The cleaved caspase-3 CTCF was increased in the WT colitis 24 h and 4 d groups compared to the WT sham 24 h and 4 d groups, respectively (485949 ± 14140 vs 371371 ± 16426, P < 0.001; 480381 ± 11336 vs 378365 ± 4053, P < 0.001), but was not significantly different between the KO groups. The total caspase-3 CTCF, phospho-NF-κB CTCF, and total NF-κB CTCF were not significantly d -raw_completion_output: |- - genes: caspase-3, nuclear factor kappa B (NF-κB), P2X7 receptor - exposures: 2,4,6-trinitrobenzene sulfonic acid - gene_exposures_relationships: P2X7 receptor triggers neuronal death -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - P2X7 receptor triggers neuronal death - - === - -extracted_object: - genes: - - caspase-3, nuclear factor kappa B (NF-κB), P2X7 receptor - exposures: - - 2,4,6-trinitrobenzene sulfonic acid - gene_exposures_relationships: - - molecular_activity: triggers neuronal death - gene: P2X7 receptor -input_text: |- - Title: Crohn's disease in human immunodeficiency virus-infected patient: A case report. - Abstract: Inflammatory bowel disease (IBD) is an autoimmune condition treated with immunosuppressive drugs. However, the need for immune system suppression becomes questionable when infection with the human immunodeficiency virus (HIV) occurs simultaneously and impacts the course of IBD. Our reported case represents the clinical course, prescribed treatment and its effect, as well as clinical challenges faced by physicians in a combination of such diseases. We also present a comprehensive literature review of similar cases.A 49-year-old woman suffering from a newly diagnosed Crohn's disease was hospitalized due to exacerbated symptoms (abdominal pain, fever, and weight loss). During her hospital stay, she tested positive for HIV. With conservative treatment, the patient improved and was discharged. In the outpatient clinic, her HIV infection was confirmed as stage C3, and antiretroviral treatment was initiated immediately. That notwithstanding, soon the patient was rehospitalized with pulmonary embolism and developed a series of complications because of the subsequent coexistence of IBD and HIV. After intensive and meticulous treatment, the patient's condition has improved and she remains in remission.The paucity of studies and data on the coexistence of HIV and IBD leaves clinicians doubting the optimal treatment options.©The Author(s) 2023. Published by Baishideng Publishing Group Inc. All rights reserved. - Keywords: Case report; Crohn’s disease; Human immunodeficiency virus; Immunocompromised patient; Inflammatory bowel disease -raw_completion_output: |- - genes: None mentioned in the text - exposures: immunosuppressive drugs, human immunodeficiency virus (HIV), antiretroviral treatment - gene_exposures_relationships: None mentioned in the text -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - None mentioned in the text - - === - -extracted_object: - genes: - - None mentioned in the text - exposures: - - immunosuppressive drugs, human immunodeficiency virus (HIV), antiretroviral - treatment - gene_exposures_relationships: - - molecular_activity: None mentioned in the text - gene: None mentioned in the text -input_text: |- - Title: A peculiar case of intususception in a pregnant woman: A diagnostic challenge. - Abstract: Adult intussusception presents a diagnostic challenge given its non-specific symptoms. It is not as common as in infants and young children. Traditionally, diagnostic steps are invariably fit for normal adults, but not in pregnancy which faces certain limitations. A 40-year-old pregnant mother, gravida 9 para 8 at 34-week gestation, complained of intermittent epigastric pain for 2 days, requiring hospitalization. She soon developed minimal per rectal bleeding that was ruled out as hemorrhoid. Imaging was limited due to her pregnancy status. She later developed spontaneous delivery to a premature baby. Computed tomography (CT) revealed an ileocolic intussusception, which was confirmed via exploratory laparotomy. Histology was consistent with inflammatory fibroid polyp. Acute abdomen in pregnancy can be due to various causes, thus a high index of suspicion and early CT abdomen might help in early diagnosis and treatment. The benefit of doing CT on the mother and the risk of CT on the fetus is to be weighed as the timely diagnosis can prevent bowel ischemia and reduce maternal morbidity and mortality. Surgery remains the definite management in adult intussusception and an exact diagnosis can be made during the operation.© 2023 The Authors. Published by Elsevier Inc. on behalf of University of Washington. - Keywords: Abdominal neoplasms; Cecal diseases; Ileal diseases; Intussusception; Pregnant; case report -raw_completion_output: |- - genes: None mentioned in the text - exposures: None mentioned in the text - gene_exposures_relationships: None mentioned in the text -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - None mentioned in the text - - === - -extracted_object: - genes: - - None mentioned in the text - exposures: - - None mentioned in the text - gene_exposures_relationships: - - molecular_activity: None mentioned in the text - gene: None mentioned in the text -input_text: |- - Title: DietaAnti-Inflamatoria or DAIN: A Crohn's disease management strategy tailored for Puerto Ricans. - Abstract: Diet has been increasingly shown to be of therapeutic benefit for patients with inflammatory bowel diseases (IBD), especially Crohn's disease (CD). Yet dietary guidelines are nonexistent. Moreover, diets tailored to Puerto Ricans with IBD living on the island, have not been developed and tested. The rising prevalence of IBD in Puerto Rico warrants exploring the use of diet as part of the treatment strategies for these patients [1]. Here, we describe the study design of "Dieta Anti-Inflamatoria" or DAIN, a parallel two-arm randomized pilot trial aiming at testing the efficacy of IBD-Anti-inflammatory diet (IBD-AID) adapted for adults with CD living in Puerto Rico (clinical trial registration number: NCT05627128). We tailored the IBD-AID to the local cuisine preferences and food availability by creating and adapting recipes consistent with the IBD-AID principles [2,3]. In focus groups with a Community Research Advisory Panel and one-on-one consultations with implementation experts, we identified several aspects of the intervention to adapt before the implementation. The objectives of the stakeholder/expert-informed adaptation were to improve feasibility and compliance while developing the culturally tailored dietary intervention. DAIN was designed for adults living in Puerto Rico with CD and geared to be affordable, appropriate, and acceptable for patients with mild-to-moderate CD. The significance of this work is the validation of culturally appropriate nutritional guidelines to help manage CD symptoms. DAIN provides a blueprint for a comprehensive nutritional program that can be adapted to regional preferences and local food availability allowing wider implementation of diet as an adjunct treatment in diverse clinical settings.© 2023 The Authors. Published by Elsevier Inc. - Keywords: -raw_completion_output: |- - genes: None mentioned in the text - exposures: diet, IBD-Anti-inflammatory diet (IBD-AID), local cuisine, food availability, culturally tailored dietary intervention - gene_exposures_relationships: None mentioned in the text -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - None mentioned in the text - - === - -extracted_object: - genes: - - None mentioned in the text - exposures: - - diet, IBD-Anti-inflammatory diet (IBD-AID), local cuisine, food availability, - culturally tailored dietary intervention - gene_exposures_relationships: - - molecular_activity: None mentioned in the text - gene: None mentioned in the text -input_text: |- - Title: Time to incorporate pre-emptive NUDT15 testing before starting thiopurines in inflammatory bowel disease in Asia and beyond: a review. - Abstract: Thiopurine toxicity is related to genetic polymorphism. Thiopurine methyltransferase (TPMT) variants do not explain thiopurine toxicity in more than half of patients. Asian people, despite the low prevalence of TPMT variants, are more susceptible to thiopurine toxicity. Since 2014, studies from many Asian countries have shown a strong association between nucleoside diphosphate-linked moiety X-type motif (NUDT) 15 polymorphism and thiopurine-induced myelotoxicity.An English language literature search was performed for TPMT and NUDT15 genetic variants in inflammatory bowel disease and other diseases. This article discusses the merits of preemptive NUDT15 and TPMT testing in Asian and non-Asian IBD populations.The NUDT polymorphism occurs in up to 27% of the Asian and Hispanic population. The hematological toxicity occurs in up to a third of patients with this genetic variant. Given this, preemptive testing for NUDT15 variant is worthwhile and is probably more cost-effective than TPMT testing in these groups. Prevalence of NUDT15 variants is low in non-Finnish European population but NUDT15 variants have been linked to myelotoxicity along with TPMT genetic variants. NUDT15 preemptive testing should be considered in the migrant Asian population in Europe and North America and in Caucasian populations who develop myelotoxicity. - Keywords: Crohn’s disease; Inflammatory bowel disease; Thiopurine toxicity in asian; Ulcerative colitis; thiopurine metabolism; thiopurine toxicity; thiopurines -raw_completion_output: |- - genes: TPMT, NUDT15 - exposures: nucleoside diphosphate-linked moiety X-type motif (NUDT) 15 polymorphism, thiopurines - gene_exposures_relationships: TPMT variants and thiopurine toxicity, NUDT15 polymorphism and thiopurine-induced myelotoxicity -prompt: |+ - From the text below, extract the following entities in the following format: - - molecular_activity: - gene: - - - Text: - TPMT variants and thiopurine toxicity, NUDT15 polymorphism and thiopurine-induced myelotoxicity - - === - -extracted_object: - genes: - - TPMT, NUDT15 - exposures: - - nucleoside diphosphate-linked moiety X-type motif (NUDT) 15 polymorphism, thiopurines - gene_exposures_relationships: - - molecular_activity: thiopurine-induced myelotoxicity - gene: HGNC:23063 -named_entities: - - id: HGNC:23063 - label: NUDT15 -input_text: |- - Title: Langerhans Cell Histiocytosis Caused by Adalimumab for Crohn's Disease: A Case Report. - Abstract: - Keywords: -raw_completion_output: |- - genes: not mentioned in the text - exposures: Adalimumab - gene_exposures_relationships: not mentioned in the text -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - not mentioned in the text - - === - -extracted_object: - genes: - - not mentioned in the text - exposures: - - Adalimumab - gene_exposures_relationships: - - molecular_activity: not mentioned in the text - gene: not mentioned in the text -input_text: |- - Title: Bakdrive: identifying a minimum set of bacterial species driving interactions across multiple microbial communities. - Abstract: Interactions among microbes within microbial communities have been shown to play crucial roles in human health. In spite of recent progress, low-level knowledge of bacteria driving microbial interactions within microbiomes remains unknown, limiting our ability to fully decipher and control microbial communities.We present a novel approach for identifying species driving interactions within microbiomes. Bakdrive infers ecological networks of given metagenomic sequencing samples and identifies minimum sets of driver species (MDS) using control theory. Bakdrive has three key innovations in this space: (i) it leverages inherent information from metagenomic sequencing samples to identify driver species, (ii) it explicitly takes host-specific variation into consideration, and (iii) it does not require a known ecological network. In extensive simulated data, we demonstrate identifying driver species identified from healthy donor samples and introducing them to the disease samples, we can restore the gut microbiome in recurrent Clostridioides difficile (rCDI) infection patients to a healthy state. We also applied Bakdrive to two real datasets, rCDI and Crohn's disease patients, uncovering driver species consistent with previous work. Bakdrive represents a novel approach for capturing microbial interactions.Bakdrive is open-source and available at: https://gitlab.com/treangenlab/bakdrive.© The Author(s) 2023. Published by Oxford University Press. - Keywords: -raw_completion_output: |- - genes: Not mentioned in the text. - - exposures: Not mentioned in the text. - - gene_exposures_relationships: Not mentioned in the text. -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - Not mentioned in the text. - - === - -extracted_object: - genes: - - Not mentioned in the text. - exposures: - - Not mentioned in the text. - gene_exposures_relationships: - - molecular_activity: Not mentioned in the text. - gene: Not mentioned in the text. -input_text: |- - Title: Efficacy of Crohn's disease exclusion diet in treatment -naïve children and children progressed on biological therapy: a retrospective chart review. - Abstract: Recent trials suggested that the Crohn's disease (CD) exclusion diet (CDED) plus partial enteral nutrition (PEN) is a safe and effective strategy in remission induction of paediatric-onset CD. However, real-world evidence regarding the safety and efficacy of the CDED plus PEN approach is still lacking. The present case-series study reported our experience with the outcomes of CDED plus PEN in the paediatric-onset CD at disease onset and after the loss of response to biologics.We conducted a retrospective chart review on children who were treated with CDED plus PEN through the period from July 2019 and December 2020. Clinical and laboratory data were retrieved and compared at baseline, 6, 12, and 24 weeks of treatment. The primary endpoint of the present study was the rate of clinical remission.The present study retrieved the data from 15 patients. Of them, nine patients were treatment naïve at the time of initiation of CDED plus PEN (group A) and the remaining patients relapsed on biologics before treatment. All patients in groups A and B exhibited clinical remission in week six, which was sustained until week 12. At the end of the follow-up, the clinical remission rate was 87% and 60% in groups A and B, respectively. No side effects were observed in both groups. In group A, the faecal calprotectin (FC) and albumin improved at week six, week 12, and week 24 (p < 0.05). The erythrocyte sedimentation rate (ESR) improved significantly at week 12 (p = 0.021) and week 24 (p = 0.027). At the same time, the haemoglobin and iron levels showed significant improvement only at week 24. For group B, only FC showed numerical reductions over time that did not reach the level of statistical significance.Treatment with CDED plus PEN was well tolerated and achieved an excellent clinical remission rate in treatment-naive patients. However, the benefit of CDED plus PEN was less in patients who initiated the strategy after losing the response to biologics.© 2023. The Author(s). - Keywords: Crohn’s disease; Crohn’s disease exclusion diet; Paediatrics; Partial enteral nutrition; Remission -raw_completion_output: |- - genes: CD - exposures: Crohn's disease exclusion diet (CDED), partial enteral nutrition (PEN), biologics - gene_exposures_relationships: CD-CDED, CD-PEN, CD-biologics -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - CD-CDED, CD-PEN, CD-biologics - - === - -extracted_object: - genes: - - HGNC:2505 - exposures: - - Crohn's disease exclusion diet (CDED), partial enteral nutrition (PEN), biologics - gene_exposures_relationships: - - molecular_activity: CD-biologics - gene: biologics -named_entities: - - id: HGNC:2505 - label: CD -input_text: |- - Title: Spondyloarthritis with inflammatory bowel disease: the latest on biologic and targeted therapies. - Abstract: Spondyloarthritis (SpA) encompasses a heterogeneous group of chronic inflammatory diseases that can affect both axial and peripheral joints, tendons and entheses. Among the extra-articular manifestations, inflammatory bowel disease (IBD) is associated with considerable morbidity and effects on quality of life. In everyday clinical practice, treatment of these conditions requires a close collaboration between gastroenterologists and rheumatologists to enable early detection of joint and intestinal manifestations during follow-up and to choose the most effective therapeutic regimen, implementing precision medicine for each patient's subtype of SpA and IBD. The biggest issue in this field is the dearth of drugs that are approved for both diseases, as only TNF inhibitors are currently approved for the treatment of full-spectrum SpA-IBD. Janus tyrosine kinase inhibitors are among the most promising drugs for the treatment of peripheral and axial SpA, as well as for intestinal manifestations. Other therapies such as inhibitors of IL-23 and IL-17, phosphodiesterase 4 inhibitor, α4β7 integrin blockers and faecal microbiota transplantation seem to only be able to control some disease domains, or require further studies. Given the growing interest in the development of novel drugs to treat both conditions, it is important to understand the current state of the art and the unmet needs in the management of SpA-IBD.© 2023. Springer Nature Limited. - Keywords: -raw_completion_output: |- - genes: TNF, Janus tyrosine kinase, IL-23, IL-17, phosphodiesterase 4, α4β7 integrin - exposures: TNF inhibitors, Janus tyrosine kinase inhibitors, inhibitors of IL-23 and IL-17, phosphodiesterase 4 inhibitor, α4β7 integrin blockers, faecal microbiota transplantation - gene_exposures_relationships: TNF inhibitors - SpA-IBD treatment; Janus tyrosine kinase inhibitors - peripheral and axial SpA treatment and treatment of intestinal manifestations; inhibitors of IL-23 and IL-17 - control of some disease domains, potential treatment but require further studies; phosphodiesterase 4 inhibitor - potential treatment but require further studies; α4β7 integrin blockers - potential treatment but require further studies; faecal microbiota transplantation - potential treatment but require further studies -prompt: |+ - From the text below, extract the following entities in the following format: - - molecular_activity: - gene: - - - Text: - faecal microbiota transplantation - potential treatment but require further studies - - === - -extracted_object: - genes: - - TNF, Janus tyrosine kinase, IL-23, IL-17, phosphodiesterase 4, α4β7 integrin - exposures: - - TNF inhibitors, Janus tyrosine kinase inhibitors, inhibitors of IL-23 and IL-17, - phosphodiesterase 4 inhibitor, α4β7 integrin blockers, faecal microbiota transplantation - gene_exposures_relationships: - - molecular_activity: TNF inhibitors - gene: SpA-IBD treatment - - molecular_activity: Janus tyrosine kinase inhibitors - gene: not mentioned in the text - - molecular_activity: inhibitors of IL-23 and IL-17 - gene: HGNC:5981 - - molecular_activity: phosphodiesterase 4 inhibitor - gene: None - - molecular_activity: α4β7 integrin blockers - gene: N/A -named_entities: - - id: HGNC:5981 - label: IL-17 -input_text: |- - Title: [Mechanism of intestinal injury induced by WNT2B high-expressed fibroblasts in Crohn's disease]. - Abstract: Objective: To explore the mechanism of intestinal tissue damage induced by macrophages activated by WNT2B high-expressed fibroblasts. Methods: This study involved biological information analysis, pathological tissue research and cell experimental research. The biological information of the colon tissue from the children with inflammatory bowel disease in previous study was analyzed again with single-cell sequencing. The pathological tissues were collected by colonoscopy from 10 children with Crohn's disease treated in the Department of Gastroenterology of Guangzhou Women and Children's Medical Center from July 2022 to September 2022. According to the findings of colonoscopy, tissues with obvious inflammation or ulceration were classified as the inflammatory group, while tissues with slight inflammation and no ulceration were classified as the non-inflammatory group. HE staining was performed to observe the pathological changes of the colon tissues. Macrophage infiltration and CXCL12 expression were detected by immunofluorescence. In terms of cell experiments, fibroblasts transfected with WNT2B plasmid or empty plasmid were co-cultured with salinomycin treated or non-treated macrophages, respectively; the expression of proteins through Wnt classical pathway were detected by western blotting. Macrophages treated with SKL2001 were used as the experimental group, and those with phosphate buffer as the control group. The expression and secretion of CXCL12 in macrophages were detected by quantitative Real-time PCR and enzyme-linked immunosorbent assay (ELISA). T-test or rank sum test were used for the comparison between groups. Results: Single-cell sequencing analysis suggested that macrophages were the main cells in inflammatory bowel disease colon tissue, and there was interaction between WNT2B high-expressed fibroblasts and macrophages. HE staining of the 10 patients ((9.3±3.8) years old, 7 males and 3 females) showed that the pathological score of colon tissue in the inflammatory group was higher than that in the non-inflammatory group (4 (3, 4) vs. 2 (1, 2) points, Z=3.05, P=0.002). Tissue immunofluorescence indicated that the number of infiltrating macrophages in the inflammatory group was significantly higher than that in the non-inflammatory group under high power field of view (72.8±10.4 vs.8.4±3.5, t=25.10, P<0.001), as well as the number of cells expressing CXCL12 (14.0±3.5 vs. 4.7±1.9, t=14.68, P<0.001). In cell experiments, western blotting suggested an elevated level of glycogen synthase kinase-3β phosphorylation in macrophages co-cultured with fibroblast transfected with WNT2B plasmid, and salinmycin could reverse this change. Real-time PCR suggested that the transcription level of CXCL12 in the experimental group was higher than that in the control group (6.42±0.04 vs. 1.00±0.03, t=183.00, P<0.001), as well as the expression -raw_completion_output: |- - genes: WNT2B, CXCL12, glycogen synthase kinase-3β - exposures: salinomycin, SKL2001, phosphate buffer - gene_exposures_relationships: WNT2B to macrophage activation, fibroblast transfected with WNT2B plasmid to elevated level of glycogen synthase kinase-3β phosphorylation, salinomycin to reversal of glycogen synthase kinase-3β phosphorylation change, SKL2001 to macrophage treatment, phosphate buffer as control group. -prompt: |+ - From the text below, extract the following entities in the following format: - - molecular_activity: - gene: - - - Text: - WNT2B to macrophage activation, fibroblast transfected with WNT2B plasmid to elevated level of glycogen synthase kinase-3β phosphorylation, salinomycin to reversal of glycogen synthase kinase-3β phosphorylation change, SKL2001 to macrophage treatment, phosphate buffer as control group. - - === - -extracted_object: - genes: - - WNT2B, CXCL12, glycogen synthase kinase-3β - exposures: - - salinomycin, SKL2001, phosphate buffer - gene_exposures_relationships: - - molecular_activity: macrophage treatment - gene: SKL2001 -input_text: |- - Title: Sialylation shapes mucus architecture inhibiting bacterial invasion in the colon. - Abstract: In the intestine, Mucin 2 (Muc2) forms a network structure and prevents bacterial invasion. Glycans are indispensable for Muc2 barrier function. Among various glycosylation patterns of Muc2, sialylation inhibits a bacteria-dependent Muc2 degradation. However, the mechanisms by which Muc2 creates the network structure and sialylation prevents the mucin degradation remain unknown. Here, by focusing on two colon-specific glycosyltransferases, St6galnac6 and B3galt5, mediating the generation of disialylated glycans, we show that sialylation forms the network structure of Muc2 by providing negative charge and hydrophilicity. The colonic mucus of mice lacking St6galnac6 and B3galt5 was less sialylated, thinner, and more permeable to microbiota, resulting in high susceptibility to intestinal inflammation. Mice with a B3galt5 mutation associated with inflammatory bowel disease (IBD) also showed the loss of disialylated glycans of mucus and the high susceptibility to intestinal inflammation, suggesting that the reduced sialylation of Muc2 is associated with the pathogenesis of IBD. In mucins of mice with reduced sialylation, negative charge was reduced, the network structure was disturbed, and many bacteria invaded. Thus, sialylation mediates the negative charging of Muc2 and facilitates crosslinking of Muc2 polymers to form the network structure, and thereby inhibits bacterial invasion in the colon to maintain gut homeostasis.Copyright © 2023 The Author(s). Published by Elsevier Inc. All rights reserved. - Keywords: -raw_completion_output: |- - genes: Mucin 2 (Muc2), St6galnac6, B3galt5 - - exposures: sialylation - - gene_exposures_relationships: Muc2 to sialylation -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - Muc2 to sialylation - - === - -extracted_object: - genes: - - HGNC:7512 - exposures: - - sialylation - gene_exposures_relationships: - - molecular_activity: sialylation - gene: HGNC:7512 -named_entities: - - id: HGNC:7512 - label: Mucin 2 (Muc2), St6galnac6, B3galt5 -input_text: |- - Title: Adiponectin Levels in Inflammatory Bowel Disease - A Systematic Review and Meta-analysis. - Abstract: Adipose tissue plays an important role in the pathogenesis of inflammatory conditions. The role of adipokines in inflammatory bowel disease (IBD) has been evaluated in the current literature with conflicting results. The aim of this study was to evaluate adiponectin levels in IBD patients, including Crohn's disease (CD) and ulcerative colitis (UC), compared to controls, as well as further subgroup analyses. Hence, assessing the potential role of adiponectin as a surrogate marker.We performed a systematic electronic search on PubMed, EMBASE, Scopus and Cochrane Library, including observational or interventional studies evaluating serum or plasma adiponectin levels in IBD patients on humans. The primary summary outcome was the mean difference (MD) in serum or plasma adiponectin levels between IBD patients vs. controls. Subgroups analyses were conducted involving adiponectin levels in CD and UC compared to controls, as well as CD compared to UC.A total of 20 studies were included in our qualitative synthesis and 14 studies in our quantitative synthesis, with a total population sample of 2,085 subjects. No significant MD in serum adiponectin levels was observed between IBD patients vs. controls (-1.331 [95% CI -3.135-0.472]), UC patients vs. controls (-0.213 [95% CI -1.898-1.472]), and CD patients vs. controls (-0.851 [95% CI -2.263-0.561]). Nevertheless, a significant MD was found between UC patients vs. CD patients (0.859 [95% CI 0.097-1.622]).Serum adiponectin levels were not able to differentiate between IBD, UC and CD patients compared to controls. However, significantly higher serum adiponectin levels were observed in UC compared to CD patients.S. Karger AG, Basel. - Keywords: -raw_completion_output: |- - genes: None mentioned in the text - exposures: adiponectin - gene_exposures_relationships: None mentioned in the text -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - None mentioned in the text - - === - -extracted_object: - genes: - - None mentioned in the text - exposures: - - adiponectin - gene_exposures_relationships: - - molecular_activity: None mentioned in the text - gene: None mentioned in the text -input_text: |- - Title: Clinical course of new-onset Crohn's disease in children and adolescents in dependency of age, initial location, initial severity level and therapy over the period 2000-2014 based on the Saxon Pediatric IBD-Registry in Germany. - Abstract: In Saxony, the incidence of Crohn's disease (CD) in children and adolescents increased significantly from 3.3 per 100,000 person-years in 2000 to 5.1 in 2014. The aim of this study was to describe the initial characteristics and the clinical course of CD in children and adolescents and to identify drug treatment options associated with an advantage for a mild course or remission.Clinical data were collected from patients who suffered from inflammatory bowel disease (IBD) and were recruited in the Saxon Pediatric IBD-Registry. All children newly diagnosed with CD in this registry in Saxony between 2000 and 2014 were included in this registry study. Characteristics such as age, disease location and extra-intestinal manifestations at diagnosis were accessed. The severity level of the disease at diagnosis as well as at follow-up were analysed by PCDAI index. Patients were divided into 3 groups according to length of follow-up: 1-3 years, 4-6 years and 7-9 years after diagnosis. A logistic regression model was conducted to examine which baseline parameters are associated with disease progression.There were 338 children and adolescents with CD included in this registry study. At diagnosis, the median age of patients was 12.0 (0.7-14.9), 61.5% (n = 208) of the patients were male. The most common disease location observed in pediatric CD patients was the L3 (55%, n = 176). Patients aged 10-14 years were significantly more likely to present an L2 than patients aged 0-4 years (80.3%, n = 53 vs. 19.7%, n = 13, p = 0.01). During the follow-up, data from 71.3% (n = 241) othe patients were available. Disease activity measured by PCDAI decreased in 47.7% (n = 115) of the patients, 40.7% (n = 98) of the patients were stable and increased in 11.6% (n = 28) of the patients. Patients with intermediate/severe disease at onset were more likely to have an active disease at the end of follow up, too (p = 0.00). Logistic regression analysis of the initial characteristics showed that the age at diagnosis, gender, initial location and initial extra-intestinal manifestation are not associated with the progression of the disease (p>0.05). Furthermore, drug treatment options could be identified from our data, which are associated with benefits for a milder course or remission.From 2000 to 2014, the health status of most pediatric patients with CD had improved or remained stable. Initial characteristics including age at diagnosis, initial localization and initial extra-intestinal manifestation are not associated with the progression of the disease, only the initial activity by PCDAI.Copyright: © 2023 Dong et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestr -raw_completion_output: |- - genes: None mentioned in the text - exposures: drug treatment options - gene_exposures_relationships: None relevant -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - None relevant - - === - -extracted_object: - genes: - - None mentioned in the text - exposures: - - drug treatment options - gene_exposures_relationships: - - molecular_activity: None relevant - gene: None relevant -input_text: |- - Title: Nutritional aspects of inflammatory bowel disease. - Abstract: The number of people diagnosed with inflammatory bowel disease (IBD) continues to increase in most parts of the world. Although the exact etiology of this chronic intestinal disease is not fully understood, nutritional factors appear to play key roles. Furthermore, individuals with IBD are at increased risk of adverse nutritional impacts, including micronutrient deficiencies.This review aims to summarize recent reports focusing on nutritional factors relevant to the development of IBD and to also review data on nutritional deficiencies seen in individuals with IBD.The typical Western diet, characterized by high-fat/high-sugar foods, along with food additives, appears to contribute to the etiopathogenesis of IBD. In contrast, some reports indicate that some foods are likely protective. However, there are inconsistencies in the currently available data, reflecting study design and other confounding factors. Furthermore, some of the conclusions are inferred from animal or in vitro studies. The presence of IBD can compromise the nutrition of individuals with one of these disorders: ongoing monitoring is critical. Nutrition and diet in the setting of IBD remain key areas for further and ongoing study. - Keywords: Crohn disease; Diet; Inflammation; Inflammatory bowel disease; Nutrition; ulcerative colitis -raw_completion_output: |- - genes: Crohn disease; ulcerative colitis - exposures: nutritional factors; high-fat/high-sugar foods; food additives - gene_exposures_relationships: Crohn disease - nutrition; ulcerative colitis - nutrition -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - ulcerative colitis - nutrition - - === - -extracted_object: - genes: - - Crohn disease - - ulcerative colitis - exposures: - - nutritional factors - - high-fat/high-sugar foods - - CHEBI:64047 - gene_exposures_relationships: - - molecular_activity: nutrition - gene: Crohn disease - - molecular_activity: nutrition - gene: ulcerative colitis -named_entities: - - id: CHEBI:64047 - label: food additives -input_text: |- - Title: Incisional hernia rates between intracorporeal and extracorporeal anastomosis in minimally invasive ileocolic resection for Crohn's disease. - Abstract: One-third of patients with Crohn's disease (CD) require multiple surgeries during their lifetime. So, reducing the incisional hernia rate is crucial. We aimed to define incisional hernia rates after minimally invasive ileocolic resection for CD, comparing intracorporeal anastomosis with Pfannenstiel incision (ICA-P) versus extracorporeal anastomosis with midline vertical incision (ECA-M).This retrospective cohort compares ICA-P versus ECA-M from a prospectively maintained database of consecutive minimally invasive ileocolic resections for CD performed between 2014 and 2021 in a referral center.Of the 249 patients included: 59 were in the ICA-P group, 190 in the ECA-M group. Both groups were similar according to baseline and preoperative characteristics. Overall, 22 (8.8%) patients developed an imaging-proven incisional hernia: seven at the port-site and 15 at the extraction-site. All 15 extraction-site incisional hernias were midline vertical incisions [7.9%; p = 0.025], and 8 patients (53%) required surgical repair. Time-to-event analysis showed a 20% rate of extraction-site incisional hernia in the ECA-M group after 48 months (p = 0.037). The length of stay was lower in the intracorporeal anastomosis with Pfannenstiel incision group [ICA-P: 3.3 ± 2.5 vs. ECA-M: 4.1 ± 2.4 days; p = 0.02] with similar 30-day postoperative complication [11(18.6) vs. 59(31.1); p = 0.064] and readmission rates [7(11.9) vs. 18(9.5); p = 0.59].Patients in the ICA-P group did not encounter any incisional hernias while having shorter hospital length of stay and similar 30-day postoperative complications or readmission compared to ECA-M. Therefore, more consideration should be given to performing intracorporeal anastomosis with Pfannenstiel incision during Ileocolic resection in patients with CD to reduce hernia risk.© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature. - Keywords: Anastomosis; Crohn disease; Ileocolic resection; Incisional hernia; Minimally invasive surgery -raw_completion_output: |- - genes: N/A - exposures: Pfannenstiel incision, midline vertical incision, intracorporeal anastomosis, extracorporeal anastomosis - gene_exposures_relationships: N/A -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - N/A - - === - -extracted_object: - genes: - - N/A - exposures: - - Pfannenstiel incision, midline vertical incision, intracorporeal anastomosis, - extracorporeal anastomosis - gene_exposures_relationships: - - molecular_activity: N/A - gene: N/A -input_text: |- - Title: The Tolerance of Gut Commensal Faecalibacterium to Oxidative Stress Is Strain Dependent and Relies on Detoxifying Enzymes. - Abstract: Obligate anaerobic bacteria in genus Faecalibacterium are among the most dominant taxa in the colon of healthy individuals and contribute to intestinal homeostasis. A decline in the abundance of this genus is associated with the occurrence of various gastrointestinal disorders, including inflammatory bowel diseases. In the colon, these diseases are accompanied by an imbalance between the generation and elimination of reactive oxygen species (ROS), and oxidative stress is closely linked to disruptions in anaerobiosis. In this work, we explored the impact of oxidative stress on several strains of faecalibacteria. An in silico analysis of complete genomes of faecalibacteria revealed the presence of genes encoding O2- and/or ROS-detoxifying enzymes, including flavodiiron proteins, rubrerythrins, reverse rubrerythrins, superoxide reductases, and alkyl peroxidase. However, the presence and the number of these detoxification systems varied greatly among faecalibacteria. These results were confirmed by O2 stress survival tests, in which we found that strains differed widely in their sensitivity. We showed the protective role of cysteine, which limited the production of extracellular O2•- and improved the survival of Faecalibacterium longum L2-6 under high O2 tension. In the strain F. longum L2-6, we observed that the expression of genes encoding detoxifying enzymes was upregulated in the response to O2 or H2O2 stress but with different patterns of regulation. Based on these results, we propose a first model of the gene regulatory network involved in the response to oxidative stress in F. longum L2-6. IMPORTANCE Commensal bacteria in the genus Faecalibacterium have been proposed for use as next-generation probiotics, but efforts to cultivate and exploit the potential of these strains have been limited by their sensitivity to O2. More broadly, little is known about how commensal and health-associated bacterial species in the human microbiome respond to the oxidative stress that occurs as a result of inflammation in the colon. In this work, we provide insights regarding the genes that encode potential mechanisms of protection against O2 or ROS stress in faecalibacteria, which may facilitate future advances in work with these important bacteria. - Keywords: Faecalibacterium; oxidative stress; oxygen sensitivity; transcriptional regulation -raw_completion_output: |- - genes: flavodiiron proteins; rubrerythrins; reverse rubrerythrins; superoxide reductases; alkyl peroxidase - exposures: oxidative stress; reactive oxygen species (ROS); cysteine; O2 tension; O2; H2O2 stress - gene_exposures_relationships: faecalibacteria have genes encoding O2- and/or ROS-detoxifying enzymes; cysteine limits the production of extracellular O2•- and improves the survival of Faecalibacterium longum L2-6 under high O2 tension; genes encoding detoxifying enzymes are upregulated in response to O2 or H2O2 stress with different patterns of regulation; the genes encode potential mechanisms of protection against O2 or ROS stress in faecalibacteria -prompt: |+ - From the text below, extract the following entities in the following format: - - molecular_activity: - gene: - - - Text: - the genes encode potential mechanisms of protection against O2 or ROS stress in faecalibacteria - - === - -extracted_object: - genes: - - flavodiiron proteins - - rubrerythrins - - reverse rubrerythrins - - superoxide reductases - - alkyl peroxidase - exposures: - - oxidative stress - - CHEBI:26523 - - CHEBI:15356 - - O2 tension - - CHEBI:15379 - - H2O2 stress - gene_exposures_relationships: - - molecular_activity: exposure to high O2 tension. - gene: Faecalibacterium longum L2-6. - - molecular_activity: O2 or H2O2 stress - gene: detoxifying enzymes - - molecular_activity: O2 or ROS stress - gene: faecalibacteria -named_entities: - - id: CHEBI:26523 - label: reactive oxygen species (ROS) - - id: CHEBI:15356 - label: cysteine - - id: CHEBI:15379 - label: O2 -input_text: |- - Title: Review article: Translating STRIDE-II into clinical reality - Opportunities and challenges. - Abstract: With the introduction of novel therapies for inflammatory bowel diseases (IBD), 'treat-to-target' strategies are increasingly discussed to improve the short- and long-term outcomes in IBD patients.To discuss opportunities and challenges of a treat-to-target approach in light of the current 'Selecting Therapeutic Targets in Inflammatory Bowel Disease' (STRIDE-II) consensus.The 2021 update of STRIDE-II encompasses 13 evidence- and consensus-based recommendations for treat-to-target strategies in adults and children with IBD. We highlight the potential implications and limitations of these recommendations for clinical practice.STRIDE-II provides valuable guidance for personalised IBD management. It reflects scientific progress as well as increased evidence of improved outcomes when more ambitious treatment goals such as mucosal healing are achieved.Prospective studies, objective criteria for risk stratification, and better predictors of therapeutic response are needed to potentially render 'treating to target' more effective in the future.© 2023 The Authors. Alimentary Pharmacology & Therapeutics published by John Wiley & Sons Ltd. - Keywords: Crohn’s disease < disease-based; biologics (IBD) < topics; inflammatory bowel disease < disease-based; ulcerative colitis < disease-based -raw_completion_output: |- - genes: - exposures: novel therapies, treatments, therapeutic response - gene_exposures_relationships: None mentioned in the text. -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - None mentioned in the text. - - === - -extracted_object: - exposures: - - novel therapies, treatments, therapeutic response - gene_exposures_relationships: - - molecular_activity: None mentioned in the text. - gene: None mentioned in the text. -input_text: |- - Title: Real-world experience with subcutaneous infliximab: broadening treatment strategies for inflammatory bowel disease. - Abstract: The first subcutaneous (SC) formulation of infliximab (IFX), CT‑P13 SC, has been approved in Europe and Australia, including for the treatment of inflammatory bowel disease (IBD).We provide a comprehensive overview of available clinical trial and real-world data for IFX SC treatment of IBD, focusing on potential benefits of switching from IFX intravenous (IV) to IFX SC. We evaluate emerging evidence for IFX SC treatment for difficult-to-treat IBD, use as monotherapy, and suitability for patients receiving escalated IFX IV. Therapeutic drug monitoring approaches and patient and healthcare system perspectives on IFX SC are also discussed.IFX SC represents a significant treatment innovation in the tumor necrosis factor inhibitor class after approximately 20 years of IFX IV availability. Evidence suggests that IFX SC is well tolerated and is associated with high patient acceptance and satisfaction. In addition, effectiveness is maintained in patients with stable disease following switch from IFX IV. Switching may be advisable, given the clinical benefits of IFX SC and its potential to improve healthcare service capacity. There are several areas requiring further research, including the role of IFX SC in difficult-to-treat and refractory disease, and the feasibility of IFX SC monotherapy. - Keywords: Anti-TNF; Crohn’s disease; biologics; inflammatory bowel disease; infliximab; subcutaneous; ulcerative colitis -raw_completion_output: |- - genes: No genes mentioned - exposures: infliximab (IFX), CT‑P13 SC - gene_exposures_relationships: No gene to molecular activity relationships mentioned -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - No gene to molecular activity relationships mentioned - - === - -extracted_object: - genes: - - No genes mentioned - exposures: - - infliximab (IFX), CT‑P13 SC -input_text: |- - Title: Posttranslational modifications of NLRP3 and their regulatory roles in inflammasome activation. - Abstract: The NACHT, LRR, and PYD domains-containing protein 3 (NLRP3) inflammasome is a multimolecular complex that plays a fundamental role in inflammation. Optimal activation of NLRP3 inflammasome is crucial for host defense against pathogens and the maintenance of immune homeostasis. Aberrant NLRP3 inflammasome activity has been implicated in various inflammatory diseases. Posttranslational modifications (PTMs) of NLRP3, a key inflammasome sensor, play critical roles in directing inflammasome activation and controlling the severity of inflammation and inflammatory diseases, such as arthritis, peritonitis, inflammatory bowel disease, atherosclerosis, and Parkinson's disease. Various NLRP3 PTMs, including phosphorylation, ubiquitination, and SUMOylation, could direct inflammasome activation and control inflammation severity by affecting the protein stability, ATPase activity, subcellular localization, and oligomerization of NLRP3 as well as the association between NLRP3 and other inflammasome components. Here, we provide an overview of the PTMs of NLRP3 and their roles in controlling inflammation and summarize potential anti-inflammatory drugs targeting NLRP3 PTMs.© 2023 Wiley-VCH GmbH. - Keywords: NLRP3; inflammasome; inflammation; posttranslational modifications; ubiquitination -raw_completion_output: |- - genes: NLRP3 - exposures: posttranslational modifications - gene_exposures_relationships: NLRP3 to posttranslational modifications -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - NLRP3 to posttranslational modifications - - === - -extracted_object: - genes: - - HGNC:16400 - exposures: - - posttranslational modifications - gene_exposures_relationships: - - molecular_activity: posttranslational modifications - gene: HGNC:16400 -named_entities: - - id: HGNC:16400 - label: NLRP3 -input_text: |- - Title: Chitinase 3-Like-1 Expression Is Upregulated Under Inflammatory Conditions in Human Oral Epithelial Cells. - Abstract: Chitinase 3-like-1 (CHI3L1), also known as YKL-40, is a partially secreted glycoprotein and is involved in inflammatory disorders, including inflammatory bowel diseases. CHI3L1 is known to play a role in biological responses such as cell proliferation, tissue remodeling, and inflammation. CHI3L1 forms an immune complex (known as a Chitosome complex) with IL-13 receptor alpha 2 (IL-13 Rα2) and transmembrane protein 219 (TMEM219) to activate the MAPK/ERK and PKB/AKT signaling pathways. The objective of this study is to investigate how the expressions of CHI3L1 and a Chitosome complex in human oral cavity epithelial cells are linked with intraoral inflammatory diseases.CHI3L1 and Chitosome complex mRNA expressions were analyzed using human oral squamous cancer cell lines, HSC3 and HSC4 cells. Signaling activation in HSC4 cells was analyzed by using the western blot technique. Immunohistological analysis was performed using surgical samples obtained from patients with benign oral cavity tumors and cysts.Increased expression of CHI3L1 was observed in both HSC3 and HSC4 cells after TNFα stimulation. The expression of Chitosome complex factors increased as CHI3L1 levels increased, resulting in the activation of a downstream signaling pathway. Among the intraoral tissues, the epithelial cells from inflammatory lesions, but not benign tumors, were found to be intensively stained with the anti-CHI3L1 antibody.It was indicated that the formation of a Chitosome complex is induced during inflammation, leading to the activation of signaling pathways. - Keywords: chitinase 3-like-1; chitosome complex; inflammation; oral epithelial cells -raw_completion_output: |- - genes: CHI3L1, IL-13 Rα2, TMEM219 - exposures: TNFα, Chitosome complex - gene_exposures_relationships: CHI3L1 - TNFα stimulation; CHI3L1 - Chitosome complex; Chitosome complex - activation of signaling pathways -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - Chitosome complex - activation of signaling pathways - - === - -extracted_object: - genes: - - CHI3L1, IL-13 Rα2, TMEM219 - exposures: - - TNFα, Chitosome complex - gene_exposures_relationships: - - molecular_activity: TNFα stimulation - gene: HGNC:1932 - - molecular_activity: Chitosome complex - gene: HGNC:1932 - - molecular_activity: activation of signaling pathways - gene: Chitosome complex -named_entities: - - id: HGNC:1932 - label: CHI3L1 -input_text: |- - Title: Drug rediscovery in gastroenterology: from off-label to on-label use of thioguanine in inflammatory bowel disease. - Abstract: Drug rediscovery refers to the principle of using 'old' drugs outside the indications mentioned in the summary of product characteristics. In the past decades, several drugs were rediscovered in a wide variety of medical fields. One of the most recent examples is the unconditional registration of thioguanine (TG), a thiopurine derivative, in patients with inflammatory bowel disease in the Netherlands. In this paper, we aim to visualise potential hurdles that hamper drug rediscovery in general, emphasise the global need for optimal use and development of potentially useful drugs, and provide an overview of the registration process for TG in the Netherlands. With this summary, we aim to guide drug rediscovery trajectories in the near future.© Author(s) (or their employer(s)) 2023. No commercial re-use. See rights and permissions. Published by BMJ. - Keywords: azathioprine; crohn's disease; drug development; drug metabolism; inflammatory bowel disease -raw_completion_output: |- - genes: N/A - exposures: thioguanine (TG), thiopurine derivative - gene_exposures_relationships: N/A -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - N/A - - === - -extracted_object: - genes: - - N/A - exposures: - - CHEBI:9516 - gene_exposures_relationships: - - molecular_activity: N/A - gene: N/A -named_entities: - - id: CHEBI:9516 - label: thioguanine (TG), thiopurine derivative -input_text: |- - Title: Author's Reply: ``Use of biologics for the management of Crohn's disease''. - Abstract: - Keywords: -raw_completion_output: |- - genes: None - exposures: None - gene_exposures_relationships: None -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - None - - === - -extracted_object: - genes: - - None - exposures: - - None - gene_exposures_relationships: - - molecular_activity: None - gene: None diff --git a/mkdocs.yml b/mkdocs.yml index 0f7711124..1a4600d33 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -1,5 +1,5 @@ --- -site_name: "OntoGPT" +site_name: "TALISMAN" theme: name: material analytics: @@ -7,14 +7,14 @@ theme: palette: - media: '(prefers-color-scheme: light)' scheme: default - primary: teal + primary: green accent: amber toggle: icon: material/lightbulb name: Switch to light mode - media: '(prefers-color-scheme: dark)' scheme: slate - primary: teal + primary: green accent: amber toggle: icon: material/lightbulb-outline @@ -29,32 +29,8 @@ nav: - Introduction: index.md - Setup: setup.md - Operation: operation.md - - Custom Schemas: custom.md - - OWL Exports: owl_exports.md - Evaluations: evaluations.md - Functions: functions.md - - Starting with OWL: start_with_owl.md - Troubleshooting: troubleshooting.md - - SPIRES Templates: # Note these are autogenerated - - Core Upper Level Schema: core/index.md - - Biochemical Reactions: reaction/index.md - - Biological Processes: biological_process/index.md - - Biotic Interactions: biotic_interaction/index.md - - Cell Types: cell_type/index.md - - Chemical to Disease: ctd/index.md - - Diagnostic Procedures: diagnostic_procedure/index.md - - Drugs and Mechanisms: drug/index.md - - Environmental Samples: environmental_sample/index.md - - GO-CAMs and Pathways: gocam/index.md - - Irritable Bowel Diseases and Literature: ibd_literature/index.md - - Mendelian Diseases: mendelian_disease/index.md - - Metabolic Processes: metabolic_process/index.md - - Metagenome Studies: metagenome_study/index.md - - Ontology Classes: ontology_class/index.md - - Ontology Issues: ontology_issue/index.md - - Recipes: recipe/index.md - - Traits of a Taxon: traits/index.md - - Treatments: treatment/index.md - - HALO Schema: halo/index.md -site_url: https://monarch-initiative.github.io/ontogpt/ -repo_url: https://github.com/monarch-initiative/ontogpt/ +site_url: https://monarch-initiative.github.io/talisman/ +repo_url: https://github.com/monarch-initiative/talisman/ diff --git a/notebooks/Enrichment-Results-Analysis.ipynb b/notebooks/Enrichment-Results-Analysis.ipynb deleted file mode 100644 index 6580c33f5..000000000 --- a/notebooks/Enrichment-Results-Analysis.ipynb +++ /dev/null @@ -1,71259 +0,0 @@ -{ - "cells": [ - { - "cell_type": "markdown", - "id": "4327d3f7", - "metadata": {}, - "source": [ - "# Enrichment Analysis Notebook\n", - "\n", - "Compares the results of SPINDOCTOR gene set summarization vs statistical ontological enrichment.\n", - "\n", - "Draft: https://docs.google.com/document/d/1H103ux6Dd1_bPM0un4RwutBLcYJx-0ybil2AwlAvG_Q/edit#" - ] - }, - { - "cell_type": "markdown", - "id": "32c9fa1d", - "metadata": {}, - "source": [ - "## Initial setup\n", - "\n", - "Here we take care of imports, defining the data dictionary for the pandas dataframes" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "id": "3452b4b0", - "metadata": { - "tags": [ - "parameters" - ] - }, - "outputs": [], - "source": [ - "# parameters\n", - "experiment_results = \"analysis/enrichment-summary.yaml\"" - ] - }, - { - "cell_type": "code", - "execution_count": 5, - "id": "97e39d4a", - "metadata": {}, - "outputs": [], - "source": [ - "import yaml\n", - "from yaml import Loader\n", - "from collections import defaultdict\n", - "import pandas as pd\n", - "from oaklib import get_adapter\n", - "from oaklib.datamodels.vocabulary import IS_A, PART_OF\n", - "from ontogpt.evaluation.enrichment.eval_enrichment import EvalEnrichment\n", - "go = get_adapter(\"sqlite:obo:go\")\n", - "hgnc = get_adapter(\"sqlite:obo:hgnc\")" - ] - }, - { - "cell_type": "code", - "execution_count": 6, - "id": "293db399", - "metadata": {}, - "outputs": [], - "source": [ - "#from ontogpt.utils.gene_set_utils import populate_ids_and_symbols, GeneSet\n", - "#ee = EvalEnrichment()\n", - "#ee.ontology = go\n", - "#ee.load_annotations(\"../tests/input/genes2go.tsv.gz\")" - ] - }, - { - "cell_type": "code", - "execution_count": 7, - "id": "a988de3f", - "metadata": {}, - "outputs": [], - "source": [ - "TURBO = \"gpt-3.5-turbo\"\n", - "DAVINCI = \"text-davinci-003\"\n", - "GPT4 = \"gpt-4\"\n", - "MODELS = [TURBO, DAVINCI, GPT4]" - ] - }, - { - "cell_type": "code", - "execution_count": 8, - "id": "9b0990c0", - "metadata": {}, - "outputs": [], - "source": [ - "# data dictionary\n", - "MODEL = \"model\"\n", - "METHOD = \"method\"\n", - "HAS_TOP_HIT = \"has top term\"\n", - "IN_TOP_5 = \"in top 5\"\n", - "IN_TOP_10 = \"in top 10\"\n", - "RANK = \"rank\"\n", - "SIZE_OVERLAP = \"size overlap\"\n", - "SIMILARITY = \"similarity\"\n", - "NR_SIZE_OVERLAP = \"nr size overlap\"\n", - "NR_SIMILARITY = \"nr similarity\"\n", - "GENESET = \"geneset\"\n", - "PROMPT_VARIANT = \"prompt_variant\"\n", - "SOURCE_GENESET = \"source geneset\"\n", - "GENESET_DESCRIPTION = \"description\"\n", - "GENESET_SIZE = \"geneset_size\"\n", - "TRUNCATION_FACTOR = \"truncation factor\"\n", - "NUM_TERMS = \"num terms\"\n", - "NUM_GO_TERMS = \"num GO terms\"\n", - "NUM_UNPARSED = \"num unparsed\"\n", - "TERM_IDS = \"term ids\"\n", - "GO_TERM_IDS = \"go term ids\"\n", - "GO_TERM_P_VALUES = \"go term p values\"\n", - "MAX_P_VALUE = \"max p value\"\n", - "MIN_P_VALUE = \"min p value\"\n", - "MEAN_P_VALUE = \"mean p value\"\n", - "PROPOTION_SIGNIFICANT = \"proportion significant\"\n", - "NOVEL = \"unannotated\"\n", - "NOVEL_LABELS = \"unannotated labels\"\n", - "NUM_NOVEL = \"num unannotated\"\n", - "GENE_RANDOMIZATION_FACTOR = \"gene_randomization_factor\"\n", - "SUMMARY = \"summary\"\n", - "\n", - "\n" - ] - }, - { - "cell_type": "code", - "execution_count": 9, - "id": "e16189b3", - "metadata": {}, - "outputs": [], - "source": [ - "from ontogpt.evaluation.enrichment.eval_enrichment import GeneSetComparison" - ] - }, - { - "cell_type": "code", - "execution_count": 10, - "id": "ca76b18a", - "metadata": {}, - "outputs": [], - "source": [ - "# assumes comparisons have been run and concatenated (see Makefile) \n", - "def load_comparisons():\n", - " with open(f\"../{experiment_results}\") as f:\n", - " obj = yaml.load(f, Loader)\n", - " comps = [GeneSetComparison(**x) for x in obj]\n", - " return comps" - ] - }, - { - "cell_type": "code", - "execution_count": 11, - "id": "ebab4da5", - "metadata": {}, - "outputs": [], - "source": [ - "comps = load_comparisons()" - ] - }, - { - "cell_type": "code", - "execution_count": 12, - "id": "1eec3e01", - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "['GO:0005773', 'GO:0005634', 'GO:0008150']" - ] - }, - "execution_count": 12, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "\n", - "def filter_redundant(term_ids):\n", - " \"\"\"\n", - " find leaf nodes in a set of term ids\n", - " \"\"\"\n", - " cumulative_ancs = set()\n", - " visited = set()\n", - " for t in term_ids:\n", - " visited.add(t)\n", - " if t in cumulative_ancs:\n", - " # a descendant of t has been encountered\n", - " continue\n", - " ancs = list(go.ancestors(t, [IS_A, PART_OF]))\n", - " cumulative_ancs.update(ancs)\n", - " if (visited-{t}).intersection(ancs):\n", - " # t is a descendant of a term that has been encountered\n", - " continue\n", - " yield t\n", - "\n", - "# test\n", - "list(filter_redundant([\"GO:0005773\", \"GO:0005634\", \"GO:0031965\", \"GO:0008150\"]))" - ] - }, - { - "cell_type": "code", - "execution_count": 13, - "id": "1ad7746a", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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modelmethodgenesettruncation factorprompt_variantsummarysource genesetgene_randomization_factorhas top termrank...num termsnum unparsedgo term p valuesmax p valuemin p valuemean p valueproportion significantunannotatedunannotated labelsnum unannotated
0gpt-3.5-turbono_synopsisEDS-01.0v1Summary: The common function of the genes is r...EDS0True1.0...33[3.341122685366184e-06, 5.591343976855226e-11,...0.0003215.591344e-110.0001081.000000[][]0
1gpt-3.5-turbono_synopsisEDS-01.0v2Summary: Extracellular matrix organization and...EDS0True2.0...66[3.341122685366184e-06, 3.4271478353194616e-06...1.0000005.591344e-110.5000010.500000[][]0
2gpt-3.5-turboontological_synopsisEDS-01.0v1Summary: The enriched terms are related to the...EDS0True0.0...44[5.591343976855226e-11, 3.341122685366184e-06,...1.0000005.591344e-110.2500810.750000[][]0
3gpt-3.5-turboontological_synopsisEDS-01.0v2Summary: The common function of the listed gen...EDS0True0.0...55[5.591343976855226e-11, 1.0, 2.2177237867319e-...1.0000005.591344e-110.2000650.800000[][]0
4gpt-3.5-turbonarrative_synopsisEDS-01.0v1Summary: Genes involved in connective tissue d...EDS0FalseNaN...77[1.0, 3.341122685366184e-06, 1.0, 1.0, 1.0, 1....1.0000003.341123e-060.8571430.142857[GO:0010712, GO:0043687][regulation of collagen metabolic process, pos...2
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2409N/Astandardtf-downreg-colorectal-11.0NoneNonetf-downreg-colorectal1True0.0...180180[2.463439488461684e-28, 2.511460888299925e-28,...0.0476702.463439e-280.0034281.000000[][]0
2410N/Astandard_no_ontologytf-downreg-colorectal-11.0NoneNonetf-downreg-colorectal1FalseNaN...4040[1.0670949536417977e-21, 6.368123603602858e-19...1.0000006.758362e-270.1539150.850000[][]0
2411N/Arandomtf-downreg-colorectal-11.0NoneNonetf-downreg-colorectal1FalseNaN...4242[1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 6.26342211...1.0000006.263422e-130.9523810.047619[GO:2000095, GO:0006869, GO:0004721, GO:001513...[regulation of Wnt signaling pathway, planar c...25
2412N/Arank_basedtf-downreg-colorectal-11.0NoneNonetf-downreg-colorectal1FalseNaN...4646[4.966218259085737e-14, 1.0, 1.0, 1.0, 1.0, 6....1.0000006.758362e-270.6739240.326087[GO:0004930, GO:0005509, GO:0007186, GO:000013...[G protein-coupled receptor activity, calcium ...5
2413N/Aclosuretf-downreg-colorectal-11.0NoneNonetf-downreg-colorectal1True505.0...35233523[1.0, 1.0, 1.0, 3.405746031985595e-10, 1.0, 1....1.0000002.463439e-280.9302240.070029[][]0
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" - ], - "text/plain": [ - " model method geneset \\\n", - "0 gpt-3.5-turbo no_synopsis EDS-0 \n", - "1 gpt-3.5-turbo no_synopsis EDS-0 \n", - "2 gpt-3.5-turbo ontological_synopsis EDS-0 \n", - "3 gpt-3.5-turbo ontological_synopsis EDS-0 \n", - "4 gpt-3.5-turbo narrative_synopsis EDS-0 \n", - "... ... ... ... \n", - "2409 N/A standard tf-downreg-colorectal-1 \n", - "2410 N/A standard_no_ontology tf-downreg-colorectal-1 \n", - "2411 N/A random tf-downreg-colorectal-1 \n", - "2412 N/A rank_based tf-downreg-colorectal-1 \n", - "2413 N/A closure tf-downreg-colorectal-1 \n", - "\n", - " truncation factor prompt_variant \\\n", - "0 1.0 v1 \n", - "1 1.0 v2 \n", - "2 1.0 v1 \n", - "3 1.0 v2 \n", - "4 1.0 v1 \n", - "... ... ... \n", - "2409 1.0 None \n", - "2410 1.0 None \n", - "2411 1.0 None \n", - "2412 1.0 None \n", - "2413 1.0 None \n", - "\n", - " summary \\\n", - "0 Summary: The common function of the genes is r... \n", - "1 Summary: Extracellular matrix organization and... \n", - "2 Summary: The enriched terms are related to the... \n", - "3 Summary: The common function of the listed gen... \n", - "4 Summary: Genes involved in connective tissue d... \n", - "... ... \n", - "2409 None \n", - "2410 None \n", - "2411 None \n", - "2412 None \n", - "2413 None \n", - "\n", - " source geneset gene_randomization_factor has top term rank \\\n", - "0 EDS 0 True 1.0 \n", - "1 EDS 0 True 2.0 \n", - "2 EDS 0 True 0.0 \n", - "3 EDS 0 True 0.0 \n", - "4 EDS 0 False NaN \n", - "... ... ... ... ... \n", - "2409 tf-downreg-colorectal 1 True 0.0 \n", - "2410 tf-downreg-colorectal 1 False NaN \n", - "2411 tf-downreg-colorectal 1 False NaN \n", - "2412 tf-downreg-colorectal 1 False NaN \n", - "2413 tf-downreg-colorectal 1 True 505.0 \n", - "\n", - " ... num terms num unparsed \\\n", - "0 ... 3 3 \n", - "1 ... 6 6 \n", - "2 ... 4 4 \n", - "3 ... 5 5 \n", - "4 ... 7 7 \n", - "... ... ... ... \n", - "2409 ... 180 180 \n", - "2410 ... 40 40 \n", - "2411 ... 42 42 \n", - "2412 ... 46 46 \n", - "2413 ... 3523 3523 \n", - "\n", - " go term p values max p value \\\n", - "0 [3.341122685366184e-06, 5.591343976855226e-11,... 0.000321 \n", - "1 [3.341122685366184e-06, 3.4271478353194616e-06... 1.000000 \n", - "2 [5.591343976855226e-11, 3.341122685366184e-06,... 1.000000 \n", - "3 [5.591343976855226e-11, 1.0, 2.2177237867319e-... 1.000000 \n", - "4 [1.0, 3.341122685366184e-06, 1.0, 1.0, 1.0, 1.... 1.000000 \n", - "... ... ... \n", - "2409 [2.463439488461684e-28, 2.511460888299925e-28,... 0.047670 \n", - "2410 [1.0670949536417977e-21, 6.368123603602858e-19... 1.000000 \n", - "2411 [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 6.26342211... 1.000000 \n", - "2412 [4.966218259085737e-14, 1.0, 1.0, 1.0, 1.0, 6.... 1.000000 \n", - "2413 [1.0, 1.0, 1.0, 3.405746031985595e-10, 1.0, 1.... 1.000000 \n", - "\n", - " min p value mean p value proportion significant \\\n", - "0 5.591344e-11 0.000108 1.000000 \n", - "1 5.591344e-11 0.500001 0.500000 \n", - "2 5.591344e-11 0.250081 0.750000 \n", - "3 5.591344e-11 0.200065 0.800000 \n", - "4 3.341123e-06 0.857143 0.142857 \n", - "... ... ... ... \n", - "2409 2.463439e-28 0.003428 1.000000 \n", - "2410 6.758362e-27 0.153915 0.850000 \n", - "2411 6.263422e-13 0.952381 0.047619 \n", - "2412 6.758362e-27 0.673924 0.326087 \n", - "2413 2.463439e-28 0.930224 0.070029 \n", - "\n", - " unannotated \\\n", - "0 [] \n", - "1 [] \n", - "2 [] \n", - "3 [] \n", - "4 [GO:0010712, GO:0043687] \n", - "... ... \n", - "2409 [] \n", - "2410 [] \n", - "2411 [GO:2000095, GO:0006869, GO:0004721, GO:001513... \n", - "2412 [GO:0004930, GO:0005509, GO:0007186, GO:000013... \n", - "2413 [] \n", - "\n", - " unannotated labels num unannotated \n", - "0 [] 0 \n", - "1 [] 0 \n", - "2 [] 0 \n", - "3 [] 0 \n", - "4 [regulation of collagen metabolic process, pos... 2 \n", - "... ... ... \n", - "2409 [] 0 \n", - "2410 [] 0 \n", - "2411 [regulation of Wnt signaling pathway, planar c... 25 \n", - "2412 [G protein-coupled receptor activity, calcium ... 5 \n", - "2413 [] 0 \n", - "\n", - "[2414 rows x 32 columns]" - ] - }, - "execution_count": 13, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "import statistics\n", - "import re\n", - "def eval_payload(comp, payload, expected, closure):\n", - " \"\"\"\n", - " Create a dataframe row from a payload in a comparison\n", - " \"\"\"\n", - " expected_nr_ids = list(filter_redundant(expected.term_ids))\n", - " name = comp.name\n", - " model = payload.model\n", - " method = payload.method\n", - " if not model:\n", - " model = \"N/A\"\n", - " tf = payload.truncation_factor\n", - " if not tf:\n", - " tf = 1.0\n", - " unparsed_term_ids = [t for t in payload.term_ids if not re.match(r'^\\S+:w+$', t)]\n", - " go_term_ids = [t for t in payload.term_ids if t.startswith(\"GO:\")]\n", - " nr_term_ids = list(filter_redundant(go_term_ids))\n", - " obj = {MODEL: model, METHOD: method, GENESET: name, TRUNCATION_FACTOR: tf, PROMPT_VARIANT: payload.prompt_variant}\n", - " obj[SUMMARY] = payload.summary\n", - " name_toks = name.split(\"-\")\n", - " obj[SOURCE_GENESET] = \"-\".join(name_toks[0:-1])\n", - " # obj[GENESET_DESCRIPTION] = comp.\n", - " obj[GENE_RANDOMIZATION_FACTOR] = int(name_toks[-1])\n", - " if not expected.term_ids:\n", - " #print(f\"Nothing expected for {name}\")\n", - " # top_term_id = \"FAKE:123\"\n", - " return\n", - " else:\n", - " top_term_id = expected.term_ids[0]\n", - " obj[HAS_TOP_HIT] = top_term_id in payload.term_ids\n", - " in_top_5 = False\n", - " in_top_10 = False\n", - " if top_term_id in payload.term_ids:\n", - " rank = payload.term_ids.index(top_term_id)\n", - " obj[RANK] = rank\n", - " in_top_5 = rank < 5\n", - " in_top_10 = rank < 10\n", - " obj[IN_TOP_5] = in_top_5\n", - " obj[IN_TOP_10] = in_top_10\n", - " overlap = set(go_term_ids).intersection(expected.term_ids)\n", - " obj[SIZE_OVERLAP] = len(overlap)\n", - " nr_overlap = set(nr_term_ids).intersection(expected_nr_ids)\n", - " obj[NR_SIZE_OVERLAP] = len(nr_overlap)\n", - " size_union = len(set(go_term_ids).union(expected.term_ids))\n", - " if size_union:\n", - " obj[SIMILARITY] = len(overlap) / len(set(go_term_ids).union(expected.term_ids))\n", - " nr_size_union = len(set(nr_term_ids).union(expected_nr_ids))\n", - " if nr_size_union:\n", - " obj[NR_SIMILARITY] = len(nr_overlap) / len(set(nr_term_ids).union(expected_nr_ids))\n", - " obj['number_of_terms'] = len(payload.term_ids)\n", - " obj[NUM_GO_TERMS] = len(go_term_ids)\n", - " obj[GENESET_SIZE] = len(comp.gene_symbols)\n", - " obj[TERM_IDS] = payload.term_ids\n", - " obj['term_strings'] = payload.term_strings\n", - " obj[GO_TERM_IDS] = go_term_ids\n", - " obj[NUM_TERMS] = len(payload.term_ids)\n", - " obj[NUM_UNPARSED] = len(unparsed_term_ids)\n", - " p_vals = []\n", - " for t in go_term_ids:\n", - " p_val = 1.0\n", - " for e in expected.enrichment_results:\n", - " if e.class_id == t:\n", - " p_val = e.p_value_adjusted\n", - " break\n", - " p_vals.append(p_val)\n", - " obj[GO_TERM_P_VALUES] = p_vals\n", - " if p_vals:\n", - " obj[MAX_P_VALUE] = max(p_vals)\n", - " obj[MIN_P_VALUE] = min(p_vals)\n", - " obj[MEAN_P_VALUE] = statistics.mean(p_vals)\n", - " obj[PROPOTION_SIGNIFICANT] = len([v for v in p_vals if v<=0.05]) / len(p_vals)\n", - " novel = []\n", - " novel_labels = []\n", - " # enriched_terms = [e.class_id for e in expected.enrichment_results]\n", - " for t in go_term_ids:\n", - " if t not in closure:\n", - " novel.append(t)\n", - " novel_labels.append(go.label(t))\n", - " obj[NOVEL] = novel\n", - " obj[NOVEL_LABELS] = novel_labels\n", - " obj[NUM_NOVEL] = len(novel)\n", - " return obj\n", - "\n", - "objs = []\n", - "for comp in comps:\n", - " expected = comp.payloads[\"standard\"]\n", - " closure = comp.payloads[\"closure\"].term_ids\n", - " #gene_set = GeneSet(name=comp.name, gene_symbols=comp.gene_symbols)\n", - " #populate_ids_and_symbols(gene_set, hgnc)\n", - " \n", - " for method, payload in comp.payloads.items():\n", - " obj = eval_payload(comp, payload, expected, closure)\n", - " if obj:\n", - " objs.append(obj)\n", - " # temp\n", - " if not obj[METHOD]:\n", - " obj[METHOD] = method\n", - "df = pd.DataFrame(objs)\n", - "df.to_csv(\"enr.csv\")\n", - "df" - ] - }, - { - "cell_type": "markdown", - "id": "23f78d45", - "metadata": {}, - "source": [ - "The above data frame has one row per run of a method" - ] - }, - { - "cell_type": "code", - "execution_count": 14, - "id": "b377198f", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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modelmethod
0gpt-3.5-turbono_synopsis
2gpt-3.5-turboontological_synopsis
4gpt-3.5-turbonarrative_synopsis
6text-davinci-003no_synopsis
8text-davinci-003ontological_synopsis
10text-davinci-003narrative_synopsis
12N/Astandard
13N/Astandard_no_ontology
14N/Arandom
15N/Arank_based
16N/Aclosure
\n", - "
" - ], - "text/plain": [ - " model method\n", - "0 gpt-3.5-turbo no_synopsis\n", - "2 gpt-3.5-turbo ontological_synopsis\n", - "4 gpt-3.5-turbo narrative_synopsis\n", - "6 text-davinci-003 no_synopsis\n", - "8 text-davinci-003 ontological_synopsis\n", - "10 text-davinci-003 narrative_synopsis\n", - "12 N/A standard\n", - "13 N/A standard_no_ontology\n", - "14 N/A random\n", - "15 N/A rank_based\n", - "16 N/A closure" - ] - }, - "execution_count": 14, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "df[[MODEL, METHOD]].drop_duplicates()" - ] - }, - { - "cell_type": "code", - "execution_count": 15, - "id": "c7263499", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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source geneset
0EDS
34FA
68HALLMARK_ADIPOGENESIS
102HALLMARK_ALLOGRAFT_REJECTION
136HALLMARK_ANDROGEN_RESPONSE
......
2244peroxisome
2278progeria
2312regulation of presynaptic membrane potential
2346sensory ataxia
2380tf-downreg-colorectal
\n", - "

71 rows × 1 columns

\n", - "
" - ], - "text/plain": [ - " source geneset\n", - "0 EDS\n", - "34 FA\n", - "68 HALLMARK_ADIPOGENESIS\n", - "102 HALLMARK_ALLOGRAFT_REJECTION\n", - "136 HALLMARK_ANDROGEN_RESPONSE\n", - "... ...\n", - "2244 peroxisome\n", - "2278 progeria\n", - "2312 regulation of presynaptic membrane potential\n", - "2346 sensory ataxia\n", - "2380 tf-downreg-colorectal\n", - "\n", - "[71 rows x 1 columns]" - ] - }, - "execution_count": 15, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "df[[SOURCE_GENESET]].drop_duplicates()" - ] - }, - { - "cell_type": "markdown", - "id": "1a11ded7", - "metadata": {}, - "source": [ - "## TABLE: All gene sets and their sizes\n", - "\n", - "Copy this to [gene set](https://docs.google.com/spreadsheets/d/1gGO5IHEg-N0hivtHBO6-rdXtin8hPhw-zv6eYOBgXcE/edit#gid=1762479413) tab" - ] - }, - { - "cell_type": "code", - "execution_count": 1, - "id": "30174f04", - "metadata": {}, - "outputs": [ - { - "ename": "NameError", - "evalue": "name 'df' is not defined", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mNameError\u001b[0m Traceback (most recent call last)", - "Cell \u001b[0;32mIn[1], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[43mdf\u001b[49m[[SOURCE_GENESET, GENESET_SIZE]]\u001b[38;5;241m.\u001b[39mdrop_duplicates()\u001b[38;5;241m.\u001b[39mhide_index()\n", - "\u001b[0;31mNameError\u001b[0m: name 'df' is not defined" - ] - } - ], - "source": [ - "df[[SOURCE_GENESET, GENESET_SIZE]].drop_duplicates().style.hide_index()" - ] - }, - { - "cell_type": "code", - "execution_count": 17, - "id": "0c34babb", - "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "/var/folders/nc/m4tx21912kv1b8nk3zzx9plr0000gn/T/ipykernel_27125/2185383538.py:1: FutureWarning: this method is deprecated in favour of `Styler.hide(axis=\"index\")`\n", - " df[[MODEL, METHOD]].drop_duplicates().style.hide_index()\n" - ] - }, - { - "data": { - "text/html": [ - "\n", - "\n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - "
modelmethod
gpt-3.5-turbono_synopsis
gpt-3.5-turboontological_synopsis
gpt-3.5-turbonarrative_synopsis
text-davinci-003no_synopsis
text-davinci-003ontological_synopsis
text-davinci-003narrative_synopsis
N/Astandard
N/Astandard_no_ontology
N/Arandom
N/Arank_based
N/Aclosure
\n" - ], - "text/plain": [ - "" - ] - }, - "execution_count": 17, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "df[[MODEL, METHOD]].drop_duplicates().style.hide_index()" - ] - }, - { - "cell_type": "code", - "execution_count": 18, - "id": "33b27486", - "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "/var/folders/nc/m4tx21912kv1b8nk3zzx9plr0000gn/T/ipykernel_27125/1312593990.py:1: FutureWarning: this method is deprecated in favour of `Styler.hide(axis=\"index\")`\n", - " df[[MODEL, METHOD, PROMPT_VARIANT]].drop_duplicates().style.hide_index()\n" - ] - }, - { - "data": { - "text/html": [ - "\n", - "\n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - "
modelmethodprompt_variant
gpt-3.5-turbono_synopsisv1
gpt-3.5-turbono_synopsisv2
gpt-3.5-turboontological_synopsisv1
gpt-3.5-turboontological_synopsisv2
gpt-3.5-turbonarrative_synopsisv1
gpt-3.5-turbonarrative_synopsisv2
text-davinci-003no_synopsisv1
text-davinci-003no_synopsisv2
text-davinci-003ontological_synopsisv1
text-davinci-003ontological_synopsisv2
text-davinci-003narrative_synopsisv1
text-davinci-003narrative_synopsisv2
N/AstandardNone
N/Astandard_no_ontologyNone
N/ArandomNone
N/Arank_basedNone
N/AclosureNone
\n" - ], - "text/plain": [ - "" - ] - }, - "execution_count": 18, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "df[[MODEL, METHOD, PROMPT_VARIANT]].drop_duplicates().style.hide_index()" - ] - }, - { - "cell_type": "markdown", - "id": "f8ac06b4", - "metadata": {}, - "source": [ - "## Subset Analysis" - ] - }, - { - "cell_type": "code", - "execution_count": 19, - "id": "a15bf2ee", - "metadata": {}, - "outputs": [], - "source": [ - "\n", - "go = get_adapter(\"sqlite:obo:go\")\n", - "subsets = list(go.subsets())\n", - "subsets_by_term = defaultdict(list)\n", - "for subset in subsets:\n", - " members = [m for m in go.subset_members(subset) if m.startswith(\"GO:\")]\n", - " for t in members:\n", - " subsets_by_term[t].append(subset)\n", - " members_ancs = go.ancestors(members)\n", - " anc_subset = f\"anc_of_{subset}\"\n", - " for a in members_ancs:\n", - " if a not in members:\n", - " subsets_by_term[a].append(anc_subset)" - ] - }, - { - "cell_type": "code", - "execution_count": 20, - "id": "854ea86d", - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "756445\n" - ] - }, - { - "data": { - "text/html": [ - "
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modelmethodtermlabelgoslim_chemblgoslim_genericgoslim_drosophilagoslim_piranc_of_goslim_chemblanc_of_goslim_generic...anc_of_goslim_flybase_ribbonanc_of_goslim_agrgoslim_mouseanc_of_goslim_plantanc_of_goslim_pombeanc_of_gocheck_do_not_manually_annotateanc_of_goslim_mousegocheck_do_not_annotategocheck_do_not_manually_annotategoslim_synapse
0gpt-3.5-turbono_synopsisGO:0030198extracellular matrix organization1.01.01.0NaNNaNNaN...NaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
1gpt-3.5-turbono_synopsisGO:0030199collagen fibril organizationNaNNaNNaNNaNNaNNaN...NaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
2gpt-3.5-turbono_synopsisGO:0006024glycosaminoglycan biosynthetic processNaNNaNNaNNaNNaNNaN...NaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
3gpt-3.5-turbono_synopsisGO:0030198extracellular matrix organization1.01.01.0NaNNaNNaN...NaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
4gpt-3.5-turbono_synopsisGO:0043062extracellular structure organizationNaNNaNNaN1.01.01.0...NaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
..................................................................
756440N/AclosureGO:0032106positive regulation of response to extracellul...NaNNaNNaNNaNNaNNaN...NaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
756441N/AclosureGO:0032109positive regulation of response to nutrient le...NaNNaNNaNNaNNaNNaN...NaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
756442N/AclosureGO:0045848positive regulation of nitrogen utilizationNaNNaNNaNNaNNaNNaN...NaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
756443N/AclosureGO:2001248regulation of ammonia assimilation cycleNaNNaNNaNNaNNaNNaN...NaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
756444N/AclosureGO:2001250positive regulation of ammonia assimilation cycleNaNNaNNaNNaNNaNNaN...NaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
\n", - "

756445 rows × 36 columns

\n", - "
" - ], - "text/plain": [ - " model method term \\\n", - "0 gpt-3.5-turbo no_synopsis GO:0030198 \n", - "1 gpt-3.5-turbo no_synopsis GO:0030199 \n", - "2 gpt-3.5-turbo no_synopsis GO:0006024 \n", - "3 gpt-3.5-turbo no_synopsis GO:0030198 \n", - "4 gpt-3.5-turbo no_synopsis GO:0043062 \n", - "... ... ... ... \n", - "756440 N/A closure GO:0032106 \n", - "756441 N/A closure GO:0032109 \n", - "756442 N/A closure GO:0045848 \n", - "756443 N/A closure GO:2001248 \n", - "756444 N/A closure GO:2001250 \n", - "\n", - " label goslim_chembl \\\n", - "0 extracellular matrix organization 1.0 \n", - "1 collagen fibril organization NaN \n", - "2 glycosaminoglycan biosynthetic process NaN \n", - "3 extracellular matrix organization 1.0 \n", - "4 extracellular structure organization NaN \n", - "... ... ... \n", - "756440 positive regulation of response to extracellul... NaN \n", - "756441 positive regulation of response to nutrient le... NaN \n", - "756442 positive regulation of nitrogen utilization NaN \n", - "756443 regulation of ammonia assimilation cycle NaN \n", - "756444 positive regulation of ammonia assimilation cycle NaN \n", - "\n", - " goslim_generic goslim_drosophila goslim_pir anc_of_goslim_chembl \\\n", - "0 1.0 1.0 NaN NaN \n", - "1 NaN NaN NaN NaN \n", - "2 NaN NaN NaN NaN \n", - "3 1.0 1.0 NaN NaN \n", - "4 NaN NaN 1.0 1.0 \n", - "... ... ... ... ... \n", - "756440 NaN NaN NaN NaN \n", - "756441 NaN NaN NaN NaN \n", - "756442 NaN NaN NaN NaN \n", - "756443 NaN NaN NaN NaN \n", - "756444 NaN NaN NaN NaN \n", - "\n", - " anc_of_goslim_generic ... anc_of_goslim_flybase_ribbon \\\n", - "0 NaN ... NaN \n", - "1 NaN ... NaN \n", - "2 NaN ... NaN \n", - "3 NaN ... NaN \n", - "4 1.0 ... NaN \n", - "... ... ... ... \n", - "756440 NaN ... NaN \n", - "756441 NaN ... NaN \n", - "756442 NaN ... NaN \n", - "756443 NaN ... NaN \n", - "756444 NaN ... NaN \n", - "\n", - " anc_of_goslim_agr goslim_mouse anc_of_goslim_plant \\\n", - "0 NaN NaN NaN \n", - "1 NaN NaN NaN \n", - "2 NaN NaN NaN \n", - "3 NaN NaN NaN \n", - "4 NaN NaN NaN \n", - "... ... ... ... \n", - "756440 NaN NaN NaN \n", - "756441 NaN NaN NaN \n", - "756442 NaN NaN NaN \n", - "756443 NaN NaN NaN \n", - "756444 NaN NaN NaN \n", - "\n", - " anc_of_goslim_pombe anc_of_gocheck_do_not_manually_annotate \\\n", - "0 NaN NaN \n", - "1 NaN NaN \n", - "2 NaN NaN \n", - "3 NaN NaN \n", - "4 NaN NaN \n", - "... ... ... \n", - "756440 NaN NaN \n", - "756441 NaN NaN \n", - "756442 NaN NaN \n", - "756443 NaN NaN \n", - "756444 NaN NaN \n", - "\n", - " anc_of_goslim_mouse gocheck_do_not_annotate \\\n", - "0 NaN NaN \n", - "1 NaN NaN \n", - "2 NaN NaN \n", - "3 NaN NaN \n", - "4 NaN NaN \n", - "... ... ... \n", - "756440 NaN NaN \n", - "756441 NaN NaN \n", - "756442 NaN NaN \n", - "756443 NaN NaN \n", - "756444 NaN NaN \n", - "\n", - " gocheck_do_not_manually_annotate goslim_synapse \n", - "0 NaN NaN \n", - "1 NaN NaN \n", - "2 NaN NaN \n", - "3 NaN NaN \n", - "4 NaN NaN \n", - "... ... ... \n", - "756440 NaN NaN \n", - "756441 NaN NaN \n", - "756442 NaN NaN \n", - "756443 NaN NaN \n", - "756444 NaN NaN \n", - "\n", - "[756445 rows x 36 columns]" - ] - }, - "execution_count": 20, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "objs = []\n", - "for row in df.to_dict(orient=\"records\"):\n", - " for t in row[GO_TERM_IDS]:\n", - " obj = {MODEL: row.get(MODEL), METHOD: row.get(METHOD) , \"term\": t, \"label\": go.label(t)}\n", - " for s in subsets_by_term.get(t, []):\n", - " obj[s] = 1\n", - " objs.append(obj)\n", - "print(len(objs))\n", - "subsets_df=pd.DataFrame(objs) \n", - "pd.set_option('display.max_rows', 10)\n", - "subsets_df" - ] - }, - { - "cell_type": "markdown", - "id": "8e09a4a1", - "metadata": {}, - "source": [ - "### All subsets" - ] - }, - { - "cell_type": "code", - "execution_count": 21, - "id": "9745fa79", - "metadata": {}, - "outputs": [ - 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" \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - "
  goslim_chemblgoslim_genericgoslim_drosophilagoslim_piranc_of_goslim_chemblanc_of_goslim_genericanc_of_goslim_drosophilaprokaryote_subsetgoslim_yeastgoslim_pombegoslim_metagenomicsgoslim_candidaanc_of_goslim_piranc_of_goslim_synapseanc_of_goslim_yeastanc_of_gocheck_do_not_annotateanc_of_goslim_candidagoslim_plantanc_of_goslim_metagenomicsanc_of_prokaryote_subsetgoslim_flybase_ribbongoslim_agranc_of_goslim_flybase_ribbonanc_of_goslim_agrgoslim_mouseanc_of_goslim_plantanc_of_goslim_pombeanc_of_gocheck_do_not_manually_annotateanc_of_goslim_mousegocheck_do_not_annotategocheck_do_not_manually_annotategoslim_synapse
modelmethod                                
N/Aclosure0.0500.0270.0350.0510.0550.0470.0540.0170.0300.0090.0180.0180.0790.0940.0520.0430.0310.0220.0360.0330.0130.0150.0120.0200.0130.0270.0380.0320.0210.0080.0080.012
random0.1670.0990.1120.1090.0470.0570.0680.0560.1040.0170.0690.0850.1110.1640.0510.0850.0270.1020.0390.0350.0570.0710.0260.0360.0620.0240.0770.0650.0380.0010.0010.016
rank_based0.3340.1860.2210.2180.1080.1290.1620.1000.2040.0240.1180.1650.2120.3150.1120.1660.0710.2000.0960.0820.1110.1510.0460.0800.1280.0650.1420.1260.0840.0000.0040.022
standard0.0870.0490.0550.0950.1630.1420.1600.0350.0440.0130.0430.0370.1730.2160.1390.1160.0980.0610.1040.1060.0310.0360.0450.0770.0320.0870.1030.1190.0840.0360.0370.007
standard_no_ontology0.1070.0620.0630.0680.0270.0340.0370.0340.0590.0140.0340.0420.0740.0930.0280.0490.0120.0510.0310.0210.0300.0350.0080.0130.0320.0100.0420.0310.0130.0010.0010.014
gpt-3.5-turbonarrative_synopsis0.2650.2100.2530.2420.0830.1070.1110.1550.1940.1130.1400.1670.1700.2390.1060.1580.0540.1300.0760.0990.0280.0570.0240.0660.0420.0290.0680.0760.0740.0220.0090.006
no_synopsis0.1950.1780.2150.1910.0880.1020.0960.1180.1540.0980.0920.1020.1390.1980.1120.1270.0550.0800.0820.0860.0280.0500.0200.0480.0360.0360.0900.0550.0480.0210.0230.007
ontological_synopsis0.2540.1330.1800.1630.0710.0950.1210.0970.1550.0570.1340.1220.1690.2140.1010.1340.0640.1250.0770.0880.0510.0740.0360.0660.0640.0350.0380.0670.0730.0130.0090.009
text-davinci-003narrative_synopsis0.3960.2450.2890.3150.1150.2120.2120.2310.2250.1410.2440.2630.2360.2720.2190.2330.1200.2520.1180.1620.1080.1280.0850.1410.1090.0670.1360.1170.1490.0310.0340.002
no_synopsis0.3280.2310.3100.3550.1740.2300.2410.2110.1880.1500.2160.2130.2420.3030.2490.2930.1480.2190.1130.1570.0780.1160.0590.1250.0740.0980.2250.1590.1520.0470.0360.007
ontological_synopsis0.2950.1440.1850.1460.1030.1100.1260.1240.1520.0380.1350.1300.1830.1980.1180.1330.0780.1290.0800.0930.0710.0840.0390.0730.0710.0440.0410.0820.0820.0120.0040.004
\n" - ], - "text/plain": [ - "" - ] - }, - "execution_count": 21, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "subsets_df.fillna(0).groupby([MODEL, METHOD]).mean(numeric_only=True).style.highlight_max(axis=1, props='font-weight:bold').format(precision=3)" - ] - }, - { - "cell_type": "markdown", - "id": "1b96e626", - "metadata": {}, - "source": [ - "### Core subsets\n", - "\n", - "Copy this to [subsets tab](https://docs.google.com/spreadsheets/d/1gGO5IHEg-N0hivtHBO6-rdXtin8hPhw-zv6eYOBgXcE/edit#gid=669935942)" - ] - }, - { - "cell_type": "code", - "execution_count": 22, - "id": "9f53fd9c", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "\n", - "\n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - "
  goslim_genericanc_of_goslim_genericgoslim_agranc_of_goslim_agrclosure_of_goslim_genericclosure_of_goslim_agr
modelmethod      
N/Aclosure0.0270.0470.0150.0200.0740.035
random0.0990.0570.0710.0360.1560.108
rank_based0.1860.1290.1510.0800.3150.231
standard0.0490.1420.0360.0770.1900.113
standard_no_ontology0.0620.0340.0350.0130.0960.048
gpt-3.5-turbonarrative_synopsis0.2100.1070.0570.0660.3170.123
no_synopsis0.1780.1020.0500.0480.2810.098
ontological_synopsis0.1330.0950.0740.0660.2270.140
text-davinci-003narrative_synopsis0.2450.2120.1280.1410.4560.268
no_synopsis0.2310.2300.1160.1250.4610.241
ontological_synopsis0.1440.1100.0840.0730.2540.157
\n" - ], - "text/plain": [ - "" - ] - }, - "execution_count": 22, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "subsets_cols = [MODEL, METHOD, \"goslim_generic\", \"anc_of_goslim_generic\", \"goslim_agr\", \"anc_of_goslim_agr\"]\n", - "subsets_grouped = subsets_df.fillna(0).groupby([MODEL, METHOD])[subsets_cols]\n", - "means = subsets_grouped.mean(numeric_only=True)\n", - "means[\"closure_of_goslim_generic\"] = means[\"goslim_generic\"] + means[\"anc_of_goslim_generic\"]\n", - "means[\"closure_of_goslim_agr\"] = means[\"goslim_agr\"] + means[\"anc_of_goslim_agr\"]\n", - "means.style.highlight_max(axis=0, props='font-weight:bold').format(precision=3)" - ] - }, - { - "cell_type": "markdown", - "id": "68c23cd9", - "metadata": {}, - "source": [ - "### TABLE: Above the shoreline in key subsets\n", - "\n", - "[anc subsets tab](https://docs.google.com/spreadsheets/d/1gGO5IHEg-N0hivtHBO6-rdXtin8hPhw-zv6eYOBgXcE/edit#gid=345667144)" - ] - }, - { - "cell_type": "code", - "execution_count": 23, - "id": "b6b4f797", - "metadata": { - "scrolled": true - }, - "outputs": [ - { - "data": { - "text/html": [ - "\n", - "\n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - "
  anc_of_goslim_genericanc_of_goslim_agr
modelmethod  
text-davinci-003no_synopsis0.2300.125
narrative_synopsis0.2120.141
N/Astandard0.1420.077
rank_based0.1290.080
text-davinci-003ontological_synopsis0.1100.073
gpt-3.5-turbonarrative_synopsis0.1070.066
no_synopsis0.1020.048
ontological_synopsis0.0950.066
N/Arandom0.0570.036
closure0.0470.020
standard_no_ontology0.0340.013
\n" - ], - "text/plain": [ - "" - ] - }, - "execution_count": 23, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "sorted_means = means.sort_values(\"anc_of_goslim_generic\", ascending=False)\n", - "filtered = sorted_means[[\"anc_of_goslim_generic\", \"anc_of_goslim_agr\"]]\n", - "filtered.style.highlight_max(axis=0, props='font-weight:bold').format(precision=3)" - ] - }, - { - "cell_type": "code", - "execution_count": 24, - "id": "bd90d757", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "\n", - "\n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - "
  anc_of_goslim_genericanc_of_goslim_agr
modelmethod  
N/Astandard_no_ontology0.0340.013
closure0.0470.020
random0.0570.036
gpt-3.5-turbono_synopsis0.1020.048
narrative_synopsis0.1070.066
ontological_synopsis0.0950.066
text-davinci-003ontological_synopsis0.1100.073
N/Astandard0.1420.077
rank_based0.1290.080
text-davinci-003no_synopsis0.2300.125
narrative_synopsis0.2120.141
\n" - ], - "text/plain": [ - "" - ] - }, - "execution_count": 24, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "means[[\"anc_of_goslim_generic\", \"anc_of_goslim_agr\"]].sort_values(\"anc_of_goslim_agr\", ascending=True).style.highlight_min(axis=0, props='font-weight:bold').format(precision=3)" - ] - }, - { - "cell_type": "code", - "execution_count": 25, - "id": "18ccc356", - "metadata": {}, - "outputs": [], - "source": [ - "# Reset the index of the pivoted DataFrame to have 'profession' as a column\n", - "#subsets_df = subsets_df.fillna(0).groupby([MODEL, METHOD])[subsets_cols].mean(numeric_only=True).reset_index()\n", - "\n", - "# Melt the DataFrame to have 'category', 'profession', and 'percentage' columns\n", - "#melted_df = subsets_df.melt(id_vars=[MODEL, METHOD], var_name='subset', value_name='proportion')\n", - "#melted_df[\"mm\"] = melted_df[MODEL] + melted_df[METHOD]\n", - "#melted_df\n", - "# Create a bar plot using Seaborn\n", - "#plt.figure(figsize=(10, 6))\n", - "#sns.barplot(x='subset', y='proportion', hue=\"mm\", data=melted_df)\n", - "#plt.title('Subsets by method')\n", - "#plt.xlabel('Subset')\n", - "#plt.ylabel('Proportion')\n", - "#plt.legend(title='Subsets')\n", - "#plt.show()" - ] - }, - { - "cell_type": "markdown", - "id": "a5502e7b", - "metadata": {}, - "source": [ - "## Evaluation" - ] - }, - { - "cell_type": "code", - "execution_count": 26, - "id": "6a587eee", - "metadata": {}, - "outputs": [], - "source": [ - "def agg_table(this_df, cols, exclude=[None]):\n", - " qcols = [MODEL, METHOD] + cols\n", - " agg_df = this_df.replace(r\"_\", \" \", regex=True)[qcols].groupby([MODEL, METHOD]).mean(numeric_only=True)\n", - " for x in exclude:\n", - " agg_df= agg_df.query(f\"method != '{x}'\")\n", - " return agg_df.style.highlight_max(axis=0, props='font-weight:bold').format(precision=3)\n", - "\n", - "pd.options.display.precision = 2\n", - "pd.set_option(\"display.precision\", 2)" - ] - }, - { - "cell_type": "code", - "execution_count": 27, - "id": "d59a8dfe", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "\n", - "\n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - "
  num GO termssize overlapnr size overlap
modelmethod   
N/Aclosure4781.408229.6832.261
random96.3106.9860.549
rank based109.15515.1270.852
standard no ontology56.50046.8384.915
gpt-3.5-turbonarrative synopsis3.9652.5110.518
no synopsis4.9543.1230.599
ontological synopsis3.6872.1620.472
text-davinci-003narrative synopsis4.0281.4650.335
no synopsis3.4611.3420.296
ontological synopsis6.9152.0560.338
\n" - ], - "text/plain": [ - "" - ] - }, - "execution_count": 27, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "agg_table(df, [NUM_GO_TERMS, SIZE_OVERLAP, NR_SIZE_OVERLAP], [\"standard\"])" - ] - }, - { - "cell_type": "code", - "execution_count": 28, - "id": "35fddeb4", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "\n", - "\n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - "
  has top termin top 5in top 10size overlapsimilaritynum termsnum GO termsnr size overlapnr similaritymean p valuemin p valuemax p valueproportion significantnum unannotated
modelmethod              
N/Aclosure1.0000.0140.028229.6830.0724842.8384781.4082.2610.0110.9260.0001.0000.0750.000
random0.0350.0000.0006.9860.01796.31096.3100.5490.0070.9380.1421.0000.06240.282
rank based0.1550.0140.02815.1270.036109.155109.1550.8520.0140.8780.0921.0000.1238.803
standard1.0001.0001.000229.6830.970236.077229.68317.5850.9670.0070.0000.0471.0000.000
standard no ontology0.5420.3730.41546.8380.19556.50056.5004.9150.1390.2300.0001.0000.7750.000
gpt-3.5-turbonarrative synopsis0.1410.1300.1412.5110.0155.5993.9650.5180.0290.3440.1260.6200.6570.180
no synopsis0.1900.1650.1903.1230.0186.8844.9540.5990.0300.3610.1220.6980.6400.225
ontological synopsis0.1480.1340.1482.1620.0176.1873.6870.4720.0290.4050.1620.6710.5970.102
text-davinci-003narrative synopsis0.0950.0810.0951.4650.00811.9014.0280.3350.0160.6210.2920.8830.3800.342
no synopsis0.0850.0770.0851.3420.00710.0183.4610.2960.0140.5650.2840.8020.4360.285
ontological synopsis0.0990.0600.0812.0560.01313.6236.9150.3380.0160.6920.2860.9460.3090.408
\n" - ], - "text/plain": [ - "" - ] - }, - "execution_count": 28, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "eval_summary_cols = [HAS_TOP_HIT, IN_TOP_5, IN_TOP_10, SIZE_OVERLAP, SIMILARITY, NUM_TERMS, NUM_GO_TERMS, NR_SIZE_OVERLAP, NR_SIMILARITY, MEAN_P_VALUE, MIN_P_VALUE, MAX_P_VALUE, PROPOTION_SIGNIFICANT, NUM_NOVEL]\n", - "agg_table(df, eval_summary_cols)" - ] - }, - { - "cell_type": "markdown", - "id": "8efddbe7", - "metadata": {}, - "source": [ - "## TABLE: MAIN RESULTS" - ] - }, - { - "cell_type": "code", - "execution_count": 30, - "id": "8c00964a", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "\n", - "\n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - "
  proportion significanthas top termnum GO termsnum unannotatednum unparsed
modelmethod     
gpt-3.5-turbonarrative synopsis0.6570.1413.9650.1805.599
no synopsis0.6400.1904.9540.2256.884
ontological synopsis0.5970.1483.6870.1026.187
text-davinci-003narrative synopsis0.3800.0954.0280.34211.901
no synopsis0.4360.0853.4610.28510.018
ontological synopsis0.3090.0996.9150.40813.623
\n" - ], - "text/plain": [ - "" - ] - }, - "execution_count": 30, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "CORE_METRICS = [PROPOTION_SIGNIFICANT, HAS_TOP_HIT, NUM_GO_TERMS, NUM_NOVEL, NUM_UNPARSED]\n", - "EXCLUDE = [\"standard\", \"standard no ontology\", \"random\", \"rank based\", \"closure\"]\n", - "agg_table(df, CORE_METRICS, EXCLUDE)\n", - "#means.query(\"method != 'standard'\").style.highlight_max(axis=0, props='font-weight:bold').format(precision=3)" - ] - }, - { - "cell_type": "markdown", - "id": "63b34e0b", - "metadata": {}, - "source": [ - "## as above, no perturbation" - ] - }, - { - "cell_type": "code", - "execution_count": 31, - "id": "c7487343", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "\n", - "\n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - "
  proportion significanthas top termnum GO termsnum unannotatednum unparsed
modelmethod     
gpt-3.5-turbonarrative synopsis0.6610.1343.7820.1975.500
no synopsis0.6340.2184.6900.2187.246
ontological synopsis0.6120.1483.4080.0855.838
text-davinci-003narrative synopsis0.3720.0853.9150.33111.359
no synopsis0.4140.0923.0630.22510.324
ontological synopsis0.3160.0996.5630.33813.070
\n" - ], - "text/plain": [ - "" - ] - }, - "execution_count": 31, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "df_no_perturb = df.query(f\"{GENE_RANDOMIZATION_FACTOR} == 0\")\n", - "agg_table(df_no_perturb, CORE_METRICS, EXCLUDE)\n" - ] - }, - { - "cell_type": "markdown", - "id": "ace58328", - "metadata": {}, - "source": [ - "## Maximums" - ] - }, - { - "cell_type": "code", - "execution_count": 32, - "id": "bd936323", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "\n", - "\n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - "
  has top termin top 5in top 10size overlapsimilaritynum termsnum GO termsnr size overlapnr similaritymean p valuemin p valuemax p valueproportion significantnum unannotated
modelmethod              
N/AclosureTrueTrueTrue8720.2399056897790.1400.9960.0111.0000.2660
randomTrueFalseFalse330.04318118130.0621.0001.0001.0000.18698
rank_basedTrueTrueTrue580.09020020070.0711.0001.0001.0000.34361
standardTrueTrueTrue8721.000873872401.0000.0240.0110.0501.0000
standard_no_ontologyTrueTrueTrue1990.449227227180.8000.8770.0231.0000.9690
gpt-3.5-turbonarrative_synopsisTrueTrueTrue150.333202040.5001.0001.0001.0001.0002
no_synopsisTrueTrueTrue160.200531950.2501.0001.0001.0001.0003
ontological_synopsisTrueTrueTrue100.200391930.6671.0001.0001.0001.0002
text-davinci-003narrative_synopsisTrueTrueTrue90.111481520.1251.0001.0001.0001.0003
no_synopsisTrueTrueTrue60.083601730.1671.0001.0001.0001.0005
ontological_synopsisTrueTrueTrue120.103362540.3331.0001.0001.0001.0007
\n" - ], - "text/plain": [ - "" - ] - }, - "execution_count": 32, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "df[[MODEL, METHOD] + eval_summary_cols].groupby([MODEL, METHOD]).max(numeric_only=True).style.highlight_max(axis=0, props='font-weight:bold').format(precision=3)" - ] - }, - { - "cell_type": "markdown", - "id": "4064f765", - "metadata": {}, - "source": [ - "### Effect of truncation\n", - "\n", - "Larger gene sets penalize annotation-based GPT methods due to the necessity to truncate to fit in the window size.\n", - "\n" - ] - }, - { - "cell_type": "code", - "execution_count": 33, - "id": "6f79eece", - "metadata": {}, - "outputs": [ - { - "data": { - "image/png": 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", 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" - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "import numpy as np\n", - "import matplotlib as mpl\n", - "import matplotlib.pyplot as plt\n", - "import seaborn as sns\n", - "sns.set(color_codes=True)\n", - "np.random.seed(sum(map(ord, \"regression\")))\n", - "sns.lmplot(x=GENESET_SIZE, y=TRUNCATION_FACTOR, data=df.query(\"method=='ontological_synopsis'\"))\n", - "plt.show()" - ] - }, - { - "cell_type": "code", - "execution_count": 34, - "id": "f2e1f5ce", - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "" - ] - }, - "execution_count": 34, - "metadata": {}, - "output_type": "execute_result" - }, - { - "data": { - "image/png": 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" - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "dftups = [(method, df.query(f\"method=='{method}'\")) for method in [\"ontological_synopsis\", \"narrative_synopsis\"]]\n", - "for m, mdf in dftups:\n", - " mdf.assign(dataset=m)\n", - "concatenated = pd.concat([mdf.assign(dataset=m) for m, mdf in dftups])\n", - "sns.scatterplot(x=GENESET_SIZE, y=TRUNCATION_FACTOR, data=concatenated, style='dataset', hue='model')" - ] - }, - { - "cell_type": "code", - "execution_count": 35, - "id": "324b3c1d", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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source geneset
0EDS
34FA
170HALLMARK_ANGIOGENESIS
238HALLMARK_APICAL_SURFACE
714HALLMARK_HEDGEHOG_SIGNALING
......
2244peroxisome
2278progeria
2312regulation of presynaptic membrane potential
2346sensory ataxia
2397tf-downreg-colorectal
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" - ], - "text/plain": [ - " source geneset\n", - "0 EDS\n", - "34 FA\n", - "170 HALLMARK_ANGIOGENESIS\n", - "238 HALLMARK_APICAL_SURFACE\n", - "714 HALLMARK_HEDGEHOG_SIGNALING\n", - "... ...\n", - "2244 peroxisome\n", - "2278 progeria\n", - "2312 regulation of presynaptic membrane potential\n", - "2346 sensory ataxia\n", - "2397 tf-downreg-colorectal\n", - "\n", - "[25 rows x 1 columns]" - ] - }, - "execution_count": 35, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "df.query(f\"{GENESET_SIZE} < 50\")[[SOURCE_GENESET]].drop_duplicates()" - ] - }, - { - "cell_type": "code", - "execution_count": 36, - "id": "2ab6ac9f", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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has top termin top 5in top 10size overlapsimilaritynum termsnum GO termsnr size overlapnr similaritymean p valuemin p valuemax p valueproportion significantnum unannotated
modelmethod
N/Aclosure1.000.040.09132.617.95e-022389.762346.593.412.27e-029.15e-012.59e-041.000.090.00
random0.000.000.001.417.41e-0326.0726.070.266.58e-039.54e-013.71e-011.000.0514.74
rank_based0.040.040.042.851.70e-0226.7226.720.288.75e-039.11e-012.62e-011.000.092.70
standard1.001.001.00132.619.83e-01135.43132.6115.709.78e-018.28e-032.59e-040.051.000.00
standard_no_ontology0.630.540.5728.802.14e-0138.3738.375.631.92e-012.96e-017.75e-041.000.710.00
................................................
gpt-3.5-turbono_synopsis0.200.180.202.452.44e-025.274.330.714.12e-024.27e-011.48e-010.750.570.33
ontological_synopsis0.340.340.342.273.10e-025.353.900.775.47e-023.90e-011.16e-010.690.610.12
text-davinci-003narrative_synopsis0.120.120.121.181.07e-0211.343.350.351.97e-026.75e-013.87e-010.900.330.33
no_synopsis0.120.110.121.007.48e-037.362.620.281.57e-025.95e-013.95e-010.790.410.25
ontological_synopsis0.220.120.172.512.36e-0212.597.910.522.67e-026.63e-012.13e-010.940.340.45
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11 rows × 14 columns

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" - ], - "text/plain": [ - " has top term in top 5 in top 10 \\\n", - "model method \n", - "N/A closure 1.00 0.04 0.09 \n", - " random 0.00 0.00 0.00 \n", - " rank_based 0.04 0.04 0.04 \n", - " standard 1.00 1.00 1.00 \n", - " standard_no_ontology 0.63 0.54 0.57 \n", - "... ... ... ... \n", - "gpt-3.5-turbo no_synopsis 0.20 0.18 0.20 \n", - " ontological_synopsis 0.34 0.34 0.34 \n", - "text-davinci-003 narrative_synopsis 0.12 0.12 0.12 \n", - " no_synopsis 0.12 0.11 0.12 \n", - " ontological_synopsis 0.22 0.12 0.17 \n", - "\n", - " size overlap similarity num terms \\\n", - "model method \n", - "N/A closure 132.61 7.95e-02 2389.76 \n", - " random 1.41 7.41e-03 26.07 \n", - " rank_based 2.85 1.70e-02 26.72 \n", - " standard 132.61 9.83e-01 135.43 \n", - " standard_no_ontology 28.80 2.14e-01 38.37 \n", - "... ... ... ... \n", - "gpt-3.5-turbo no_synopsis 2.45 2.44e-02 5.27 \n", - " ontological_synopsis 2.27 3.10e-02 5.35 \n", - "text-davinci-003 narrative_synopsis 1.18 1.07e-02 11.34 \n", - " no_synopsis 1.00 7.48e-03 7.36 \n", - " ontological_synopsis 2.51 2.36e-02 12.59 \n", - "\n", - " num GO terms nr size overlap \\\n", - "model method \n", - "N/A closure 2346.59 3.41 \n", - " random 26.07 0.26 \n", - " rank_based 26.72 0.28 \n", - " standard 132.61 15.70 \n", - " standard_no_ontology 38.37 5.63 \n", - "... ... ... \n", - "gpt-3.5-turbo no_synopsis 4.33 0.71 \n", - " ontological_synopsis 3.90 0.77 \n", - "text-davinci-003 narrative_synopsis 3.35 0.35 \n", - " no_synopsis 2.62 0.28 \n", - " ontological_synopsis 7.91 0.52 \n", - "\n", - " nr similarity mean p value \\\n", - "model method \n", - "N/A closure 2.27e-02 9.15e-01 \n", - " random 6.58e-03 9.54e-01 \n", - " rank_based 8.75e-03 9.11e-01 \n", - " standard 9.78e-01 8.28e-03 \n", - " standard_no_ontology 1.92e-01 2.96e-01 \n", - "... ... ... \n", - "gpt-3.5-turbo no_synopsis 4.12e-02 4.27e-01 \n", - " ontological_synopsis 5.47e-02 3.90e-01 \n", - "text-davinci-003 narrative_synopsis 1.97e-02 6.75e-01 \n", - " no_synopsis 1.57e-02 5.95e-01 \n", - " ontological_synopsis 2.67e-02 6.63e-01 \n", - "\n", - " min p value max p value \\\n", - "model method \n", - "N/A closure 2.59e-04 1.00 \n", - " random 3.71e-01 1.00 \n", - " rank_based 2.62e-01 1.00 \n", - " standard 2.59e-04 0.05 \n", - " standard_no_ontology 7.75e-04 1.00 \n", - "... ... ... \n", - "gpt-3.5-turbo no_synopsis 1.48e-01 0.75 \n", - " ontological_synopsis 1.16e-01 0.69 \n", - "text-davinci-003 narrative_synopsis 3.87e-01 0.90 \n", - " no_synopsis 3.95e-01 0.79 \n", - " ontological_synopsis 2.13e-01 0.94 \n", - "\n", - " proportion significant num unannotated \n", - "model method \n", - "N/A closure 0.09 0.00 \n", - " random 0.05 14.74 \n", - " rank_based 0.09 2.70 \n", - " standard 1.00 0.00 \n", - " standard_no_ontology 0.71 0.00 \n", - "... ... ... \n", - "gpt-3.5-turbo no_synopsis 0.57 0.33 \n", - " ontological_synopsis 0.61 0.12 \n", - "text-davinci-003 narrative_synopsis 0.33 0.33 \n", - " no_synopsis 0.41 0.25 \n", - " ontological_synopsis 0.34 0.45 \n", - "\n", - "[11 rows x 14 columns]" - ] - }, - "execution_count": 36, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "df_small = df.query(f\"{GENESET_SIZE} < 50\")\n", - "means = df_small[[MODEL, METHOD] + eval_summary_cols].groupby(['model', 'method']).mean(numeric_only=True)\n", - "means" - ] - }, - { - "cell_type": "code", - "execution_count": 37, - "id": "7ec9701c", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "\n", - "\n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - 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  has top termin top 5in top 10size overlapsimilaritynum termsnum GO termsnr size overlapnr similaritymean p valuemin p valuemax p valueproportion significantnum unannotated
modelmethod              
N/Aclosure1.0000.0430.087132.6090.0802389.7612346.5873.4130.0230.9150.0001.0000.0850.000
random0.0000.0000.0001.4130.00726.06526.0650.2610.0070.9540.3711.0000.04614.739
rank_based0.0430.0430.0432.8480.01726.71726.7170.2830.0090.9110.2621.0000.0902.696
standard_no_ontology0.6300.5430.56528.8040.21438.37038.3705.6300.1920.2960.0011.0000.7100.000
gpt-3.5-turbonarrative_synopsis0.1630.1520.1631.6630.0214.9353.0430.5870.0430.4000.1520.6220.6020.228
no_synopsis0.1960.1850.1962.4460.0245.2724.3260.7070.0410.4270.1480.7500.5740.326
ontological_synopsis0.3370.3370.3372.2720.0315.3483.9020.7720.0550.3900.1160.6920.6110.120
text-davinci-003narrative_synopsis0.1200.1200.1201.1850.01111.3373.3480.3480.0200.6750.3870.9040.3260.326
no_synopsis0.1200.1090.1201.0000.0077.3592.6200.2830.0160.5950.3950.7860.4060.250
ontological_synopsis0.2170.1200.1742.5110.02412.5877.9130.5220.0270.6630.2130.9450.3380.446
\n" - ], - "text/plain": [ - "" - ] - }, - "execution_count": 37, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "means.query(\"method != 'standard'\").style.highlight_max(axis=0, props='font-weight:bold').format(precision=3)" - ] - }, - { - "cell_type": "markdown", - "id": "aa429ba1", - "metadata": {}, - "source": [ - "## TABLE: evaluation for gene sets < 75" - ] - }, - { - "cell_type": "code", - "execution_count": 39, - "id": "ec20a512", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "\n", - "\n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - "
  proportion significanthas top termnum GO termsnum unannotatednum unparsed
modelmethod     
gpt-3.5-turbonarrative synopsis0.6020.1633.0430.2284.935
no synopsis0.5740.1964.3260.3265.272
ontological synopsis0.6110.3373.9020.1205.348
text-davinci-003narrative synopsis0.3260.1203.3480.32611.337
no synopsis0.4060.1202.6200.2507.359
ontological synopsis0.3380.2177.9130.44612.587
\n" - ], - "text/plain": [ - "" - ] - }, - "execution_count": 39, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "agg_table(df_small, CORE_METRICS, EXCLUDE)" - ] - }, - { - "cell_type": "markdown", - "id": "80244ec5", - "metadata": {}, - "source": [ - "## Looking at individual gene sets" - ] - }, - { - "cell_type": "code", - "execution_count": 35, - "id": "f97cd9a4", - "metadata": {}, - "outputs": [], - "source": [ - "\n", - "def terms_summary(df, variant=\"v1\", max_rows=9999):\n", - " term_dict = {}\n", - " n = 0\n", - " for _, row in df.iterrows():\n", - " if row[PROMPT_VARIANT] and row[PROMPT_VARIANT] != variant:\n", - " continue\n", - " n += 1\n", - " if n > max_rows:\n", - " break\n", - " model = row['model'] \n", - " if \"turbo\" in model:\n", - " model = \"turbo\"\n", - " elif \"davinci\" in model:\n", - " model = \"dav\"\n", - " else:\n", - " model = \"\"\n", - " method = str(row['method']).replace('_', ' ')\n", - " if method in [\"closure\", \"rank_based\", \"random\"]:\n", - " continue\n", - " mm = f\"{model} {method}\"\n", - " if method == \"standard\":\n", - " nr_term_ids = list(filter_redundant(row[TERM_IDS]))\n", - " else:\n", - " nr_term_ids = None\n", - " for ix, t_id in enumerate(row[TERM_IDS]):\n", - " if t_id not in term_dict:\n", - " t = {\"id\": t_id, \"label\": go.label(t_id), \"redundant\": False}\n", - " term_dict[t_id] = t\n", - " else:\n", - " t = term_dict[t_id]\n", - " t[mm] = ix\n", - " if nr_term_ids and t_id not in nr_term_ids:\n", - " t[\"redundant\"] = True\n", - " objs = list(term_dict.values())\n", - " return pd.DataFrame(objs)" - ] - }, - { - "cell_type": "code", - "execution_count": 36, - "id": "14e27208", - "metadata": {}, - "outputs": [], - "source": [ - "import oaklib.datamodels.obograph as og\n", - "from oaklib.utilities.obograph_utils import graph_to_image, default_stylemap_path\n", - "!mkdir -p output\n", - "\n", - "MMAP = {\"standard\": None, \n", - " \"gpt-3.5-turbo.no_synopsis\": \"NS\",\n", - " \"gpt-3.5-turbo.ontological_synopsis\": \"ONT\",\n", - " \"gpt-3.5-turbo.narrative_synopsis\": \"NAR\",\n", - " }\n", - "\n", - "def viz(geneset, include_std=True, mmap = MMAP, variant=\"v1\"):\n", - " methods = mmap.keys()\n", - " [gsobj] = [c for c in comps if c.name == geneset]\n", - " std = gsobj.payloads[\"standard\"]\n", - " t2p = {e.class_id : e.p_value_adjusted for e in std.enrichment_results}\n", - " terms = set()\n", - " terms.add(\"GO:0008150\")\n", - " terms.add(\"GO:0003674\")\n", - " terms.add(\"GO:0005575\")\n", - " m2t = defaultdict(list)\n", - " t2m = defaultdict(set)\n", - " seeds = []\n", - " for m in methods:\n", - " if m == \"standard\":\n", - " mv = m\n", - " else:\n", - " mv = f\"{m}.{variant}\"\n", - " p = gsobj.payloads[mv]\n", - " if include_std or m != \"standard\":\n", - " terms.update(p.term_ids)\n", - " for t in p.term_ids:\n", - " if t.startswith(\"MONDO:\"):\n", - " continue\n", - " m2t[m].append(t)\n", - " t2m[t].add(m)\n", - " if m == \"standard\":\n", - " seeds.append(t)\n", - " # rels = go.gap_fill_relationships(list(terms), predicates=[IS_A, PART_OF, \"RO:0002211\", \"RO:0002212\", RO:0002213\"])\n", - " rels = go.gap_fill_relationships(list(terms), predicates=[IS_A, PART_OF])\n", - " g = go.relationships_to_graph(rels)\n", - " for n in g.nodes:\n", - " if not n.lbl:\n", - " n.lbl = go.label(n.id)\n", - " if not n.lbl:\n", - " n.lbl = n.id\n", - " if n.id in t2p:\n", - " n.lbl += f\" {t2p[n.id]:.2e}\"\n", - " #for m in t2m[n.id]:\n", - " # n.lbl += f\" [{m}]\"\n", - " for m in m2t.keys():\n", - " if m == \"standard\":\n", - " continue\n", - " for t in m2t[m]:\n", - " n = og.Node(id=f\"{mmap[m]}:{t}\", lbl=mmap[m])\n", - " g.nodes.append(n)\n", - " g.edges.append(og.Edge(n.id, \"has\", t))\n", - " outfile = f\"output/{geneset.replace(' ', '_')}-{include_std}-{variant}.png\"\n", - " graph_to_image(g, seeds=seeds, imgfile=outfile, stylemap=\"input/enr-style.json\")\n", - " graph_to_image(g, seeds=seeds, imgfile=outfile, stylemap=\"input/enr-style.json\")\n", - " #return g\n", - " \n", - "viz('peroxisome-0')\n", - "viz('peroxisome-0', variant=\"v2\")" - ] - }, - { - "cell_type": "code", - "execution_count": 37, - "id": "be9a09e7", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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idlabelredundantstandardstandard no ontologyturbo no synopsisturbo narrative synopsisdav ontological synopsisturbo ontological synopsisdav no synopsisdav narrative synopsisrank basedp_label
0GO:0006625protein targeting to peroxisomeFalse0.010.0NaNNaNNaNNaNNaNNaNNaNprotein targeting to peroxisome 1.983967326142...
1GO:0072663establishment of protein localization to perox...True1.0NaNNaNNaNNaNNaNNaNNaNNaNestablishment of protein localization to perox...
2GO:0072662protein localization to peroxisomeTrue2.0NaNNaNNaNNaNNaNNaNNaNNaNprotein localization to peroxisome 1.983967326...
3GO:0015919peroxisomal membrane transportFalse3.0NaNNaNNaNNaNNaNNaNNaNNaNperoxisomal membrane transport 3.8191371028307...
4GO:0043574peroxisomal transportTrue4.0NaNNaNNaNNaNNaNNaNNaNNaNperoxisomal transport 6.889423793379416e-16
..........................................
92GO:0016020membraneFalseNaNNaNNaNNaNNaNNaNNaNNaN3.0membrane
93GO:0005829cytosolFalseNaNNaNNaNNaNNaNNaNNaNNaN4.0cytosol
94GO:0005634nucleusFalseNaNNaNNaNNaNNaNNaNNaNNaN5.0nucleus
95GO:0005654nucleoplasmFalseNaNNaNNaNNaNNaNNaNNaNNaN6.0nucleoplasm
96GO:0046872metal ion bindingFalseNaNNaNNaNNaNNaNNaNNaNNaN7.0metal ion binding
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97 rows × 13 columns

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" - ], - "text/plain": [ - " id label redundant \\\n", - "0 GO:0006625 protein targeting to peroxisome False \n", - "1 GO:0072663 establishment of protein localization to perox... True \n", - "2 GO:0072662 protein localization to peroxisome True \n", - "3 GO:0015919 peroxisomal membrane transport False \n", - "4 GO:0043574 peroxisomal transport True \n", - ".. ... ... ... \n", - "92 GO:0016020 membrane False \n", - "93 GO:0005829 cytosol False \n", - "94 GO:0005634 nucleus False \n", - "95 GO:0005654 nucleoplasm False \n", - "96 GO:0046872 metal ion binding False \n", - "\n", - " standard standard no ontology turbo no synopsis \\\n", - "0 0.0 10.0 NaN \n", - "1 1.0 NaN NaN \n", - "2 2.0 NaN NaN \n", - "3 3.0 NaN NaN \n", - "4 4.0 NaN NaN \n", - ".. ... ... ... \n", - "92 NaN NaN NaN \n", - "93 NaN NaN NaN \n", - "94 NaN NaN NaN \n", - "95 NaN NaN NaN \n", - "96 NaN NaN NaN \n", - "\n", - " turbo narrative synopsis dav ontological synopsis \\\n", - "0 NaN NaN \n", - "1 NaN NaN \n", - "2 NaN NaN \n", - "3 NaN NaN \n", - "4 NaN NaN \n", - ".. ... ... \n", - "92 NaN NaN \n", - "93 NaN NaN \n", - "94 NaN NaN \n", - "95 NaN NaN \n", - "96 NaN NaN \n", - "\n", - " turbo ontological synopsis dav no synopsis dav narrative synopsis \\\n", - "0 NaN NaN NaN \n", - "1 NaN NaN NaN \n", - "2 NaN NaN NaN \n", - "3 NaN NaN NaN \n", - "4 NaN NaN NaN \n", - ".. ... ... ... \n", - "92 NaN NaN NaN \n", - "93 NaN NaN NaN \n", - "94 NaN NaN NaN \n", - "95 NaN NaN NaN \n", - "96 NaN NaN NaN \n", - "\n", - " rank based p_label \n", - "0 NaN protein targeting to peroxisome 1.983967326142... \n", - "1 NaN establishment of protein localization to perox... \n", - "2 NaN protein localization to peroxisome 1.983967326... \n", - "3 NaN peroxisomal membrane transport 3.8191371028307... \n", - "4 NaN peroxisomal transport 6.889423793379416e-16 \n", - ".. ... ... \n", - "92 3.0 membrane \n", - "93 4.0 cytosol \n", - "94 5.0 nucleus \n", - "95 6.0 nucleoplasm \n", - "96 7.0 metal ion binding \n", - "\n", - "[97 rows x 13 columns]" - ] - }, - "execution_count": 37, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "def geneset_summary(df, geneset):\n", - " sdf = terms_summary(df.query(f\"{GENESET} == '{geneset}'\").sort_values(\"similarity\", ascending=False))\n", - " [gsobj] = [c for c in comps if c.name == geneset]\n", - " std = gsobj.payloads[\"standard\"]\n", - " t2p = {e.class_id : e.p_value_adjusted for e in std.enrichment_results}\n", - " sdf[\"p_label\"] = sdf.apply(lambda row: str(row.label) + \" \" + str(t2p.get(row.id, \"\")), axis=1)\n", - " return sdf\n", - "\n", - "geneset_summary(df, 'peroxisome-0')" - ] - }, - { - "cell_type": "markdown", - "id": "df5e1e69", - "metadata": {}, - "source": [ - "### Peroxisome" - ] - }, - { - "cell_type": "code", - "execution_count": 38, - "id": "7d7f78b2", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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modelmethodhas top termin top 5in top 10size overlapsimilaritynum termsnum GO termsnr size overlapnr similaritymean p valuemin p valuemax p valueproportion significantnum unannotated
2256N/AstandardTrueTrueTrue621.006262101.005.64e-031.98e-160.041.000
2257N/Astandard_no_ontologyTrueFalseFalse150.22212170.412.89e-011.98e-161.000.710
2260N/AclosureTrueTrueTrue620.1941939170.148.02e-011.98e-161.000.200
2252text-davinci-003ontological_synopsisFalseFalseFalse50.0810640.331.73e-012.87e-041.000.830
2253text-davinci-003ontological_synopsisTrueFalseTrue40.0610620.153.33e-011.98e-161.000.670
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2254text-davinci-003narrative_synopsisFalseFalseFalse00.008000.00NaNNaNNaNNaN0
2255text-davinci-003narrative_synopsisFalseFalseFalse00.003000.00NaNNaNNaNNaN0
2247gpt-3.5-turboontological_synopsisFalseFalseFalse00.003100.001.00e+001.00e+001.000.001
2258N/ArandomFalseFalseFalse00.008800.001.00e+001.00e+001.000.007
2259N/Arank_basedFalseFalseFalse00.008800.001.00e+001.00e+001.000.001
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17 rows × 16 columns

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" - ], - "text/plain": [ - " model method has top term in top 5 \\\n", - "2256 N/A standard True True \n", - "2257 N/A standard_no_ontology True False \n", - "2260 N/A closure True True \n", - "2252 text-davinci-003 ontological_synopsis False False \n", - "2253 text-davinci-003 ontological_synopsis True False \n", - "... ... ... ... ... \n", - "2254 text-davinci-003 narrative_synopsis False False \n", - "2255 text-davinci-003 narrative_synopsis False False \n", - "2247 gpt-3.5-turbo ontological_synopsis False False \n", - "2258 N/A random False False \n", - "2259 N/A rank_based False False \n", - "\n", - " in top 10 size overlap similarity num terms num GO terms \\\n", - "2256 True 62 1.00 62 62 \n", - "2257 False 15 0.22 21 21 \n", - "2260 True 62 0.19 419 391 \n", - "2252 False 5 0.08 10 6 \n", - "2253 True 4 0.06 10 6 \n", - "... ... ... ... ... ... \n", - "2254 False 0 0.00 8 0 \n", - "2255 False 0 0.00 3 0 \n", - "2247 False 0 0.00 3 1 \n", - "2258 False 0 0.00 8 8 \n", - "2259 False 0 0.00 8 8 \n", - "\n", - " nr size overlap nr similarity mean p value min p value max p value \\\n", - "2256 10 1.00 5.64e-03 1.98e-16 0.04 \n", - "2257 7 0.41 2.89e-01 1.98e-16 1.00 \n", - "2260 7 0.14 8.02e-01 1.98e-16 1.00 \n", - "2252 4 0.33 1.73e-01 2.87e-04 1.00 \n", - "2253 2 0.15 3.33e-01 1.98e-16 1.00 \n", - "... ... ... ... ... ... \n", - "2254 0 0.00 NaN NaN NaN \n", - "2255 0 0.00 NaN NaN NaN \n", - "2247 0 0.00 1.00e+00 1.00e+00 1.00 \n", - "2258 0 0.00 1.00e+00 1.00e+00 1.00 \n", - "2259 0 0.00 1.00e+00 1.00e+00 1.00 \n", - "\n", - " proportion significant num unannotated \n", - "2256 1.00 0 \n", - "2257 0.71 0 \n", - "2260 0.20 0 \n", - "2252 0.83 0 \n", - "2253 0.67 0 \n", - "... ... ... \n", - "2254 NaN 0 \n", - "2255 NaN 0 \n", - "2247 0.00 1 \n", - "2258 0.00 7 \n", - "2259 0.00 1 \n", - "\n", - "[17 rows x 16 columns]" - ] - }, - "execution_count": 38, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "peroxisome = df.query(f\"{GENESET} == 'peroxisome-0'\").sort_values(\"similarity\", ascending=False)\n", - "peroxisome[[MODEL, METHOD] + eval_summary_cols]" - ] - }, - { - "cell_type": "code", - "execution_count": 39, - "id": "149cb60b", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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idlabelredundantstandardstandard no ontologyturbo no synopsisturbo narrative synopsisdav ontological synopsisturbo ontological synopsisdav no synopsisdav narrative synopsisrank based
0GO:0006625protein targeting to peroxisomeFalse0.010.0NaNNaNNaNNaNNaNNaNNaN
1GO:0072663establishment of protein localization to perox...True1.0NaNNaNNaNNaNNaNNaNNaNNaN
2GO:0072662protein localization to peroxisomeTrue2.0NaNNaNNaNNaNNaNNaNNaNNaN
3GO:0015919peroxisomal membrane transportFalse3.0NaNNaNNaNNaNNaNNaNNaNNaN
4GO:0043574peroxisomal transportTrue4.0NaNNaNNaNNaNNaNNaNNaNNaN
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92GO:0016020membraneFalseNaNNaNNaNNaNNaNNaNNaNNaN3.0
93GO:0005829cytosolFalseNaNNaNNaNNaNNaNNaNNaNNaN4.0
94GO:0005634nucleusFalseNaNNaNNaNNaNNaNNaNNaNNaN5.0
95GO:0005654nucleoplasmFalseNaNNaNNaNNaNNaNNaNNaNNaN6.0
96GO:0046872metal ion bindingFalseNaNNaNNaNNaNNaNNaNNaNNaN7.0
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97 rows × 12 columns

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" - ], - "text/plain": [ - " id label redundant \\\n", - "0 GO:0006625 protein targeting to peroxisome False \n", - "1 GO:0072663 establishment of protein localization to perox... True \n", - "2 GO:0072662 protein localization to peroxisome True \n", - "3 GO:0015919 peroxisomal membrane transport False \n", - "4 GO:0043574 peroxisomal transport True \n", - ".. ... ... ... \n", - "92 GO:0016020 membrane False \n", - "93 GO:0005829 cytosol False \n", - "94 GO:0005634 nucleus False \n", - "95 GO:0005654 nucleoplasm False \n", - "96 GO:0046872 metal ion binding False \n", - "\n", - " standard standard no ontology turbo no synopsis \\\n", - "0 0.0 10.0 NaN \n", - "1 1.0 NaN NaN \n", - "2 2.0 NaN NaN \n", - "3 3.0 NaN NaN \n", - "4 4.0 NaN NaN \n", - ".. ... ... ... \n", - "92 NaN NaN NaN \n", - "93 NaN NaN NaN \n", - "94 NaN NaN NaN \n", - "95 NaN NaN NaN \n", - "96 NaN NaN NaN \n", - "\n", - " turbo narrative synopsis dav ontological synopsis \\\n", - "0 NaN NaN \n", - "1 NaN NaN \n", - "2 NaN NaN \n", - "3 NaN NaN \n", - "4 NaN NaN \n", - ".. ... ... \n", - "92 NaN NaN \n", - "93 NaN NaN \n", - "94 NaN NaN \n", - "95 NaN NaN \n", - "96 NaN NaN \n", - "\n", - " turbo ontological synopsis dav no synopsis dav narrative synopsis \\\n", - "0 NaN NaN NaN \n", - "1 NaN NaN NaN \n", - "2 NaN NaN NaN \n", - "3 NaN NaN NaN \n", - "4 NaN NaN NaN \n", - ".. ... ... ... \n", - "92 NaN NaN NaN \n", - "93 NaN NaN NaN \n", - "94 NaN NaN NaN \n", - "95 NaN NaN NaN \n", - "96 NaN NaN NaN \n", - "\n", - " rank based \n", - "0 NaN \n", - "1 NaN \n", - "2 NaN \n", - "3 NaN \n", - "4 NaN \n", - ".. ... \n", - "92 3.0 \n", - "93 4.0 \n", - "94 5.0 \n", - "95 6.0 \n", - "96 7.0 \n", - "\n", - "[97 rows x 12 columns]" - ] - }, - "execution_count": 39, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "# terms_summary(peroxisome).style.highlight_min(axis=1, props='font-weight:bold', numeric_only=True)\n", - "terms_summary(peroxisome)" - ] - }, - { - "cell_type": "code", - "execution_count": 40, - "id": "68176c92", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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idlabelredundantstandardstandard no ontologydav ontological synopsisturbo no synopsisturbo narrative synopsisdav no synopsisdav narrative synopsisturbo ontological synopsisrank based
0GO:0006625protein targeting to peroxisomeFalse0.010.08.0NaNNaNNaNNaNNaNNaN
1GO:0072663establishment of protein localization to perox...True1.0NaNNaNNaNNaNNaNNaNNaNNaN
2GO:0072662protein localization to peroxisomeTrue2.0NaNNaNNaNNaNNaNNaNNaNNaN
3GO:0015919peroxisomal membrane transportFalse3.0NaNNaNNaNNaNNaNNaNNaNNaN
4GO:0043574peroxisomal transportTrue4.0NaNNaNNaNNaNNaNNaNNaNNaN
.......................................
95GO:0016020membraneFalseNaNNaNNaNNaNNaNNaNNaNNaN3.0
96GO:0005829cytosolFalseNaNNaNNaNNaNNaNNaNNaNNaN4.0
97GO:0005634nucleusFalseNaNNaNNaNNaNNaNNaNNaNNaN5.0
98GO:0005654nucleoplasmFalseNaNNaNNaNNaNNaNNaNNaNNaN6.0
99GO:0046872metal ion bindingFalseNaNNaNNaNNaNNaNNaNNaNNaN7.0
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100 rows × 12 columns

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" - ], - "text/plain": [ - " id label redundant \\\n", - "0 GO:0006625 protein targeting to peroxisome False \n", - "1 GO:0072663 establishment of protein localization to perox... True \n", - "2 GO:0072662 protein localization to peroxisome True \n", - "3 GO:0015919 peroxisomal membrane transport False \n", - "4 GO:0043574 peroxisomal transport True \n", - ".. ... ... ... \n", - "95 GO:0016020 membrane False \n", - "96 GO:0005829 cytosol False \n", - "97 GO:0005634 nucleus False \n", - "98 GO:0005654 nucleoplasm False \n", - "99 GO:0046872 metal ion binding False \n", - "\n", - " standard standard no ontology dav ontological synopsis \\\n", - "0 0.0 10.0 8.0 \n", - "1 1.0 NaN NaN \n", - "2 2.0 NaN NaN \n", - "3 3.0 NaN NaN \n", - "4 4.0 NaN NaN \n", - ".. ... ... ... \n", - "95 NaN NaN NaN \n", - "96 NaN NaN NaN \n", - "97 NaN NaN NaN \n", - "98 NaN NaN NaN \n", - "99 NaN NaN NaN \n", - "\n", - " turbo no synopsis turbo narrative synopsis dav no synopsis \\\n", - "0 NaN NaN NaN \n", - "1 NaN NaN NaN \n", - "2 NaN NaN NaN \n", - "3 NaN NaN NaN \n", - "4 NaN NaN NaN \n", - ".. ... ... ... \n", - "95 NaN NaN NaN \n", - "96 NaN NaN NaN \n", - "97 NaN NaN NaN \n", - "98 NaN NaN NaN \n", - "99 NaN NaN NaN \n", - "\n", - " dav narrative synopsis turbo ontological synopsis rank based \n", - "0 NaN NaN NaN \n", - "1 NaN NaN NaN \n", - "2 NaN NaN NaN \n", - "3 NaN NaN NaN \n", - "4 NaN NaN NaN \n", - ".. ... ... ... \n", - "95 NaN NaN 3.0 \n", - "96 NaN NaN 4.0 \n", - "97 NaN NaN 5.0 \n", - "98 NaN NaN 6.0 \n", - "99 NaN NaN 7.0 \n", - "\n", - "[100 rows x 12 columns]" - ] - }, - "execution_count": 40, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "terms_summary(peroxisome, \"v2\")" - ] - }, - { - "cell_type": "markdown", - "id": "ccb68aa7", - "metadata": {}, - "source": [ - "## Sensory Ataxia" - ] - }, - { - "cell_type": "code", - "execution_count": 41, - "id": "8562caa4", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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modelmethodhas top termin top 5in top 10size overlapsimilaritynum termsnum GO termsnr size overlapnr similaritymean p valuemin p valuemax p valueproportion significantnum unannotated
2358N/AstandardTrueTrueTrue91.009931.000.011.95e-050.041.000
2359N/Astandard_no_ontologyFalseFalseFalse30.304410.200.263.13e-041.000.750
2348gpt-3.5-turboontological_synopsisTrueTrueTrue20.205320.670.331.95e-051.000.670
2349gpt-3.5-turboontological_synopsisTrueTrueTrue20.187420.400.501.95e-051.000.500
2351gpt-3.5-turbonarrative_synopsisFalseFalseFalse10.115110.330.032.80e-020.031.000
...................................................
2357text-davinci-003narrative_synopsisFalseFalseFalse00.0011400.001.001.00e+001.000.001
2356text-davinci-003narrative_synopsisFalseFalseFalse00.008200.001.001.00e+001.000.000
2353text-davinci-003no_synopsisFalseFalseFalse00.005300.001.001.00e+001.000.001
2352text-davinci-003no_synopsisFalseFalseFalse00.005300.001.001.00e+001.000.000
2354text-davinci-003ontological_synopsisFalseFalseFalse00.009600.001.001.00e+001.000.000
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" - ], - "text/plain": [ - " model method has top term in top 5 \\\n", - "2358 N/A standard True True \n", - "2359 N/A standard_no_ontology False False \n", - "2348 gpt-3.5-turbo ontological_synopsis True True \n", - "2349 gpt-3.5-turbo ontological_synopsis True True \n", - "2351 gpt-3.5-turbo narrative_synopsis False False \n", - "... ... ... ... ... \n", - "2357 text-davinci-003 narrative_synopsis False False \n", - "2356 text-davinci-003 narrative_synopsis False False \n", - "2353 text-davinci-003 no_synopsis False False \n", - "2352 text-davinci-003 no_synopsis False False \n", - "2354 text-davinci-003 ontological_synopsis False False \n", - "\n", - " in top 10 size overlap similarity num terms num GO terms \\\n", - "2358 True 9 1.00 9 9 \n", - "2359 False 3 0.30 4 4 \n", - "2348 True 2 0.20 5 3 \n", - "2349 True 2 0.18 7 4 \n", - "2351 False 1 0.11 5 1 \n", - "... ... ... ... ... ... \n", - "2357 False 0 0.00 11 4 \n", - "2356 False 0 0.00 8 2 \n", - "2353 False 0 0.00 5 3 \n", - "2352 False 0 0.00 5 3 \n", - "2354 False 0 0.00 9 6 \n", - "\n", - " nr size overlap nr similarity mean p value min p value max p value \\\n", - "2358 3 1.00 0.01 1.95e-05 0.04 \n", - "2359 1 0.20 0.26 3.13e-04 1.00 \n", - "2348 2 0.67 0.33 1.95e-05 1.00 \n", - "2349 2 0.40 0.50 1.95e-05 1.00 \n", - "2351 1 0.33 0.03 2.80e-02 0.03 \n", - "... ... ... ... ... ... \n", - "2357 0 0.00 1.00 1.00e+00 1.00 \n", - "2356 0 0.00 1.00 1.00e+00 1.00 \n", - "2353 0 0.00 1.00 1.00e+00 1.00 \n", - "2352 0 0.00 1.00 1.00e+00 1.00 \n", - "2354 0 0.00 1.00 1.00e+00 1.00 \n", - "\n", - " proportion significant num unannotated \n", - "2358 1.00 0 \n", - "2359 0.75 0 \n", - "2348 0.67 0 \n", - "2349 0.50 0 \n", - "2351 1.00 0 \n", - "... ... ... \n", - "2357 0.00 1 \n", - "2356 0.00 0 \n", - "2353 0.00 1 \n", - "2352 0.00 0 \n", - "2354 0.00 0 \n", - "\n", - "[17 rows x 16 columns]" - ] - }, - "execution_count": 41, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "ataxia = df.query(f\"{GENESET} == 'sensory ataxia-0'\").sort_values(\"similarity\", ascending=False)\n", - "ataxia[[MODEL, METHOD] + eval_summary_cols] " - ] - }, - { - "cell_type": "code", - "execution_count": 42, - "id": "a744a21e", - "metadata": {}, - "outputs": [], - "source": [ - "pd.set_option('display.max_colwidth', None)\n", - "pd.set_option('display.max_rows', None)\n" - ] - }, - { - "cell_type": "code", - "execution_count": 43, - "id": "884f460d", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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modelmethodprompt_variantgo term idsunannotated labels
2358N/AstandardNone[GO:0042552, GO:0008366, GO:0007272, GO:0007422, GO:0014037, GO:0010001, GO:0032287, GO:0006264, GO:0042063][]
2359N/Astandard_no_ontologyNone[GO:0021680, GO:0032287, GO:0006264, GO:0007422][]
2348gpt-3.5-turboontological_synopsisv1[GO:0042552, GO:0007422, GO:0022011][]
2349gpt-3.5-turboontological_synopsisv2[GO:0042552, GO:0007422, GO:0006457, GO:0007600][]
2351gpt-3.5-turbonarrative_synopsisv2[GO:0006264][]
2350gpt-3.5-turbonarrative_synopsisv1[GO:0043209, GO:0006264][]
2347gpt-3.5-turbono_synopsisv2[GO:0042552, GO:0007411, GO:0007399, GO:0008104, GO:0031175][]
2355text-davinci-003ontological_synopsisv2[GO:0031625, GO:0003677, GO:0006027, GO:0043583, GO:0045475, GO:0007399, GO:0006457, GO:0043066, GO:0010595, GO:0002639, GO:0034214, GO:0050974, GO:0006812, GO:0015886, GO:0071260, GO:0042552, GO:0098742, GO:0006839, GO:0019226, GO:0008380, GO:0003774, GO:0061608, GO:0006607, GO:0003887, GO:0006284][glycosaminoglycan catabolic process, transmission of nerve impulse, RNA splicing, cytoskeletal motor activity]
2362N/AclosureNone[GO:0005654, GO:0140018, GO:0008381, GO:0032060, GO:0009611, GO:0006915, GO:0043484, GO:0006400, GO:0046620, GO:0035994, GO:0071310, GO:0043139, GO:0048168, GO:0055085, GO:0005760, GO:0032963, GO:0042982, GO:0030278, GO:0043218, GO:0000981, GO:0061608, GO:0032570, GO:0032868, GO:0034975, GO:0048536, GO:0006959, GO:0000976, GO:0008270, GO:0003158, GO:0034101, GO:0009612, GO:0060173, GO:0042391, GO:0033157, GO:0021675, GO:0004860, GO:0042564, GO:0099022, GO:0006611, GO:0043565, GO:0002020, GO:0006094, GO:0045182, GO:0046872, GO:0005576, GO:0007165, GO:0035264, GO:0010595, GO:0016597, GO:0014037, GO:0032496, GO:0032355, GO:0002161, GO:0006914, GO:0007399, GO:0034142, GO:0106074, GO:1904390, GO:0050885, GO:0043154, GO:0002639, GO:0006096, GO:0006259, GO:0098743, GO:0035284, GO:0007611, GO:0006390, GO:0035640, GO:0014040, GO:0033574, GO:0006801, GO:0071260, GO:0031069, GO:0006287, GO:0007268, GO:0001701, GO:0007040, GO:0005739, GO:0035578, GO:0006419, GO:0005759, GO:0035633, GO:0034774, GO:0097577, GO:0046548, GO:0005783, GO:0001707, GO:0031625, GO:0051787, GO:0005125, GO:0051607, GO:0004561, GO:0030201, GO:0003697, GO:0008366, GO:0008033, GO:0008408, GO:0005643, GO:0003700, GO:0006812, ...][]
2361N/Arank_basedNone[GO:0005654, GO:0006357, GO:0070062, GO:0042802, GO:0016020, GO:0046872, GO:0005576, GO:0005737, GO:0005829, GO:0005634, GO:0005739, GO:0005615, GO:0005524, GO:0005886, GO:0003723][]
2360N/ArandomNone[GO:0007169, GO:0042132, GO:0007207, GO:0045944, GO:0001916, GO:0007229, GO:1990889, GO:0097546, GO:0050878, GO:0044772, GO:0006413, GO:0001525, GO:0005615, GO:0036064, GO:0072686][transmembrane receptor protein tyrosine kinase signaling pathway, fructose 1,6-bisphosphate 1-phosphatase activity, phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway, positive regulation of T cell mediated cytotoxicity, integrin-mediated signaling pathway, H4K20me3 modified histone binding, ciliary base, mitotic cell cycle phase transition, translational initiation, angiogenesis, ciliary basal body, mitotic spindle]
2346gpt-3.5-turbono_synopsisv1[GO:0006457, GO:0030163, GO:0055085][]
2357text-davinci-003narrative_synopsisv2[GO:0000981, GO:0009056, GO:0002377, GO:0005643][immunoglobulin production]
2356text-davinci-003narrative_synopsisv1[GO:0030218, GO:0036211][]
2353text-davinci-003no_synopsisv2[GO:0006412, GO:0008152, GO:0006936][muscle contraction]
2352text-davinci-003no_synopsisv1[GO:0015031, GO:0006629, GO:0009653][]
2354text-davinci-003ontological_synopsisv1[GO:0046872, GO:0031625, GO:0045944, GO:0002639, GO:1901184, GO:0033157][]
\n", - "
" - ], - "text/plain": [ - " model method prompt_variant \\\n", - "2358 N/A standard None \n", - "2359 N/A standard_no_ontology None \n", - "2348 gpt-3.5-turbo ontological_synopsis v1 \n", - "2349 gpt-3.5-turbo ontological_synopsis v2 \n", - "2351 gpt-3.5-turbo narrative_synopsis v2 \n", - "2350 gpt-3.5-turbo narrative_synopsis v1 \n", - "2347 gpt-3.5-turbo no_synopsis v2 \n", - "2355 text-davinci-003 ontological_synopsis v2 \n", - "2362 N/A closure None \n", - "2361 N/A rank_based None \n", - "2360 N/A random None \n", - "2346 gpt-3.5-turbo no_synopsis v1 \n", - "2357 text-davinci-003 narrative_synopsis v2 \n", - "2356 text-davinci-003 narrative_synopsis v1 \n", - "2353 text-davinci-003 no_synopsis v2 \n", - "2352 text-davinci-003 no_synopsis v1 \n", - "2354 text-davinci-003 ontological_synopsis v1 \n", - "\n", - " go term ids \\\n", - "2358 [GO:0042552, GO:0008366, GO:0007272, GO:0007422, GO:0014037, GO:0010001, GO:0032287, GO:0006264, GO:0042063] \n", - "2359 [GO:0021680, GO:0032287, GO:0006264, GO:0007422] \n", - "2348 [GO:0042552, GO:0007422, GO:0022011] \n", - "2349 [GO:0042552, GO:0007422, GO:0006457, GO:0007600] \n", - "2351 [GO:0006264] \n", - "2350 [GO:0043209, GO:0006264] \n", - "2347 [GO:0042552, GO:0007411, GO:0007399, GO:0008104, GO:0031175] \n", - "2355 [GO:0031625, GO:0003677, GO:0006027, GO:0043583, GO:0045475, GO:0007399, GO:0006457, GO:0043066, GO:0010595, GO:0002639, GO:0034214, GO:0050974, GO:0006812, GO:0015886, GO:0071260, GO:0042552, GO:0098742, GO:0006839, GO:0019226, GO:0008380, GO:0003774, GO:0061608, GO:0006607, GO:0003887, GO:0006284] \n", - "2362 [GO:0005654, GO:0140018, GO:0008381, GO:0032060, GO:0009611, GO:0006915, GO:0043484, GO:0006400, GO:0046620, GO:0035994, GO:0071310, GO:0043139, GO:0048168, GO:0055085, GO:0005760, GO:0032963, GO:0042982, GO:0030278, GO:0043218, GO:0000981, GO:0061608, GO:0032570, GO:0032868, GO:0034975, GO:0048536, GO:0006959, GO:0000976, GO:0008270, GO:0003158, GO:0034101, GO:0009612, GO:0060173, GO:0042391, GO:0033157, GO:0021675, GO:0004860, GO:0042564, GO:0099022, GO:0006611, GO:0043565, GO:0002020, GO:0006094, GO:0045182, GO:0046872, GO:0005576, GO:0007165, GO:0035264, GO:0010595, GO:0016597, GO:0014037, GO:0032496, GO:0032355, GO:0002161, GO:0006914, GO:0007399, GO:0034142, GO:0106074, GO:1904390, GO:0050885, GO:0043154, GO:0002639, GO:0006096, GO:0006259, GO:0098743, GO:0035284, GO:0007611, GO:0006390, GO:0035640, GO:0014040, GO:0033574, GO:0006801, GO:0071260, GO:0031069, GO:0006287, GO:0007268, GO:0001701, GO:0007040, GO:0005739, GO:0035578, GO:0006419, GO:0005759, GO:0035633, GO:0034774, GO:0097577, GO:0046548, GO:0005783, GO:0001707, GO:0031625, GO:0051787, GO:0005125, GO:0051607, GO:0004561, GO:0030201, GO:0003697, GO:0008366, GO:0008033, GO:0008408, GO:0005643, GO:0003700, GO:0006812, ...] \n", - "2361 [GO:0005654, GO:0006357, GO:0070062, GO:0042802, GO:0016020, GO:0046872, GO:0005576, GO:0005737, GO:0005829, GO:0005634, GO:0005739, GO:0005615, GO:0005524, GO:0005886, GO:0003723] \n", - "2360 [GO:0007169, GO:0042132, GO:0007207, GO:0045944, GO:0001916, GO:0007229, GO:1990889, GO:0097546, GO:0050878, GO:0044772, GO:0006413, GO:0001525, GO:0005615, GO:0036064, GO:0072686] \n", - "2346 [GO:0006457, GO:0030163, GO:0055085] \n", - "2357 [GO:0000981, GO:0009056, GO:0002377, GO:0005643] \n", - "2356 [GO:0030218, GO:0036211] \n", - "2353 [GO:0006412, GO:0008152, GO:0006936] \n", - "2352 [GO:0015031, GO:0006629, GO:0009653] \n", - "2354 [GO:0046872, GO:0031625, GO:0045944, GO:0002639, GO:1901184, GO:0033157] \n", - "\n", - " unannotated labels \n", - "2358 [] \n", - "2359 [] \n", - "2348 [] \n", - "2349 [] \n", - "2351 [] \n", - "2350 [] \n", - "2347 [] \n", - "2355 [glycosaminoglycan catabolic process, transmission of nerve impulse, RNA splicing, cytoskeletal motor activity] \n", - "2362 [] \n", - "2361 [] \n", - "2360 [transmembrane receptor protein tyrosine kinase signaling pathway, fructose 1,6-bisphosphate 1-phosphatase activity, phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway, positive regulation of T cell mediated cytotoxicity, integrin-mediated signaling pathway, H4K20me3 modified histone binding, ciliary base, mitotic cell cycle phase transition, translational initiation, angiogenesis, ciliary basal body, mitotic spindle] \n", - "2346 [] \n", - "2357 [immunoglobulin production] \n", - "2356 [] \n", - "2353 [muscle contraction] \n", - "2352 [] \n", - "2354 [] " - ] - }, - "execution_count": 43, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "ataxia[[MODEL, METHOD, PROMPT_VARIANT, GO_TERM_IDS, NOVEL_LABELS]]" - ] - }, - { - "cell_type": "code", - "execution_count": 44, - "id": "a2a0cd0a", - "metadata": {}, - "outputs": [], - "source": [ - "viz('sensory ataxia-0')" - ] - }, - { - "cell_type": "markdown", - "id": "9677d6c9", - "metadata": {}, - "source": [ - "![img](output/sensory_ataxia-0-True-v1.png)" - ] - }, - { - "cell_type": "code", - "execution_count": 45, - "id": "66960fba", - "metadata": {}, - "outputs": [], - "source": [ - "viz('sensory ataxia-0', variant=\"v2\")" - ] - }, - { - "cell_type": "markdown", - "id": "c30b0077", - "metadata": {}, - "source": [ - "![img](output/sensory_ataxia-0-True-v2.png)" - ] - }, - { - "cell_type": "code", - "execution_count": 46, - "id": "06560bd8", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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idlabelredundantstandardturbo ontological synopsisstandard no ontologyturbo narrative synopsisrank baseddav ontological synopsisturbo no synopsisdav narrative synopsisdav no synopsis
0GO:0042552myelinationFalse0.00.0NaNNaNNaNNaNNaNNaNNaN
1GO:0008366axon ensheathmentTrue1.0NaNNaNNaNNaNNaNNaNNaNNaN
2GO:0007272ensheathment of neuronsTrue2.0NaNNaNNaNNaNNaNNaNNaNNaN
3GO:0007422peripheral nervous system developmentFalse3.01.03.0NaNNaNNaNNaNNaNNaN
4GO:0014037Schwann cell differentiationTrue4.0NaNNaNNaNNaNNaNNaNNaNNaN
5GO:0010001glial cell differentiationTrue5.0NaNNaNNaNNaNNaNNaNNaNNaN
6GO:0032287peripheral nervous system myelin maintenanceTrue6.0NaN1.0NaNNaNNaNNaNNaNNaN
7GO:0006264mitochondrial DNA replicationFalse7.0NaN2.04.0NaNNaNNaNNaNNaN
8GO:0042063gliogenesisTrue8.0NaNNaNNaNNaNNaNNaNNaNNaN
9GO:0021680cerebellar Purkinje cell layer developmentFalseNaNNaN0.0NaNNaNNaNNaNNaNNaN
10MONDO:0005071NoneFalseNaN2.0NaNNaNNaNNaNNaNNaNNaN
11GO:0022011myelination in peripheral nervous systemFalseNaN3.0NaNNaNNaNNaNNaNNaNNaN
12MONDO:0005244NoneFalseNaN4.0NaN1.0NaNNaNNaNNaNNaN
13MONDO:0015626NoneFalseNaNNaNNaN0.0NaNNaNNaNNaNNaN
14MONDO:0007790NoneFalseNaNNaNNaN2.0NaNNaNNaNNaNNaN
15GO:0043209myelin sheathFalseNaNNaNNaN3.0NaNNaNNaNNaNNaN
16tetratricopeptide repeatNoneFalseNaNNaNNaN5.0NaNNaNNaNNaNNaN
17transporter protein\\n\\nmechanism: these genes are involved in myelin upkeep and various neurological diseases associated with defects in myelin sheath synthesis and functions. they play roles in mitochondrial dna replication and transport, as well as protein transportation across the nuclear membrane. the presence of tetratricopeptide repeat motifs in these genes suggests their roles in protein-protein interactions and chaperone functionsNoneFalseNaNNaNNaN6.0NaNNaNNaNNaNNaN
18GO:0005654nucleoplasmFalseNaNNaNNaNNaN0.0NaNNaNNaNNaN
19GO:0006357regulation of transcription by RNA polymerase IIFalseNaNNaNNaNNaN1.0NaNNaNNaNNaN
20GO:0070062extracellular exosomeFalseNaNNaNNaNNaN2.0NaNNaNNaNNaN
21GO:0042802identical protein bindingFalseNaNNaNNaNNaN3.0NaNNaNNaNNaN
22GO:0016020membraneFalseNaNNaNNaNNaN4.0NaNNaNNaNNaN
23GO:0046872metal ion bindingFalseNaNNaNNaNNaN5.02.0NaNNaNNaN
24GO:0005576extracellular regionFalseNaNNaNNaNNaN6.0NaNNaNNaNNaN
25GO:0005737cytoplasmFalseNaNNaNNaNNaN7.0NaNNaNNaNNaN
26GO:0005829cytosolFalseNaNNaNNaNNaN8.0NaNNaNNaNNaN
27GO:0005634nucleusFalseNaNNaNNaNNaN9.0NaNNaNNaNNaN
28GO:0005739mitochondrionFalseNaNNaNNaNNaN10.0NaNNaNNaNNaN
29GO:0005615extracellular spaceFalseNaNNaNNaNNaN11.0NaNNaNNaNNaN
30GO:0005524ATP bindingFalseNaNNaNNaNNaN12.0NaNNaNNaNNaN
31GO:0005886plasma membraneFalseNaNNaNNaNNaN13.0NaNNaNNaNNaN
32GO:0003723RNA bindingFalseNaNNaNNaNNaN14.0NaNNaNNaNNaN
33mitochondrial functionNoneFalseNaNNaNNaNNaNNaNNaN0.0NaNNaN
34GO:0006457protein foldingFalseNaNNaNNaNNaNNaNNaN1.0NaNNaN
35GO:0030163protein catabolic processFalseNaNNaNNaNNaNNaNNaN2.0NaNNaN
36GO:0055085transmembrane transportFalseNaNNaNNaNNaNNaNNaN3.0NaNNaN
37transcriptional regulationNoneFalseNaNNaNNaNNaNNaNNaNNaN0.0NaN
38mitochondrial rna synthesisNoneFalseNaNNaNNaNNaNNaNNaNNaN1.0NaN
39neurodevelopmentNoneFalseNaNNaNNaNNaNNaNNaNNaN2.0NaN
40GO:0030218erythrocyte differentiationFalseNaNNaNNaNNaNNaNNaNNaN3.0NaN
41GO:0036211protein modification processFalseNaNNaNNaNNaNNaNNaNNaN4.0NaN
42nucleolar functionNoneFalseNaNNaNNaNNaNNaNNaNNaN5.0NaN
43neuronal network formationNoneFalseNaNNaNNaNNaNNaNNaNNaN6.0NaN
44sensory receptor functionNoneFalseNaNNaNNaNNaNNaNNaNNaN7.0NaN
45MESH:D024510NoneFalseNaNNaNNaNNaNNaNNaNNaNNaN0.0
46neuronal developmentNoneFalseNaNNaNNaNNaNNaNNaNNaNNaN1.0
47GO:0015031protein transportFalseNaNNaNNaNNaNNaNNaNNaNNaN2.0
48GO:0006629lipid metabolic processFalseNaNNaNNaNNaNNaNNaNNaNNaN3.0
49GO:0009653anatomical structure morphogenesisFalseNaNNaNNaNNaNNaNNaNNaNNaN4.0
50dna-bindingNoneFalseNaNNaNNaNNaNNaN0.0NaNNaNNaN
51rna polymerase ii-specific activityNoneFalseNaNNaNNaNNaNNaN1.0NaNNaNNaN
52GO:0031625ubiquitin protein ligase bindingFalseNaNNaNNaNNaNNaN3.0NaNNaNNaN
53GO:0045944positive regulation of transcription by RNA polymerase IIFalseNaNNaNNaNNaNNaN4.0NaNNaNNaN
54GO:0002639positive regulation of immunoglobulin productionFalseNaNNaNNaNNaNNaN5.0NaNNaNNaN
55GO:1901184regulation of ERBB signaling pathwayFalseNaNNaNNaNNaNNaN6.0NaNNaNNaN
56GO:0033157regulation of intracellular protein transportFalseNaNNaNNaNNaNNaN7.0NaNNaNNaN
57monoatomic cationNoneFalseNaNNaNNaNNaNNaN8.0NaNNaNNaN
\n", - "
" - ], - "text/plain": [ - " id \\\n", - "0 GO:0042552 \n", - "1 GO:0008366 \n", - "2 GO:0007272 \n", - "3 GO:0007422 \n", - "4 GO:0014037 \n", - "5 GO:0010001 \n", - "6 GO:0032287 \n", - "7 GO:0006264 \n", - "8 GO:0042063 \n", - "9 GO:0021680 \n", - "10 MONDO:0005071 \n", - "11 GO:0022011 \n", - "12 MONDO:0005244 \n", - "13 MONDO:0015626 \n", - "14 MONDO:0007790 \n", - "15 GO:0043209 \n", - "16 tetratricopeptide repeat \n", - "17 transporter protein\\n\\nmechanism: these genes are involved in myelin upkeep and various neurological diseases associated with defects in myelin sheath synthesis and functions. they play roles in mitochondrial dna replication and transport, as well as protein transportation across the nuclear membrane. the presence of tetratricopeptide repeat motifs in these genes suggests their roles in protein-protein interactions and chaperone functions \n", - "18 GO:0005654 \n", - "19 GO:0006357 \n", - "20 GO:0070062 \n", - "21 GO:0042802 \n", - "22 GO:0016020 \n", - "23 GO:0046872 \n", - "24 GO:0005576 \n", - "25 GO:0005737 \n", - "26 GO:0005829 \n", - "27 GO:0005634 \n", - "28 GO:0005739 \n", - "29 GO:0005615 \n", - "30 GO:0005524 \n", - "31 GO:0005886 \n", - "32 GO:0003723 \n", - "33 mitochondrial function \n", - "34 GO:0006457 \n", - "35 GO:0030163 \n", - "36 GO:0055085 \n", - "37 transcriptional regulation \n", - "38 mitochondrial rna synthesis \n", - "39 neurodevelopment \n", - "40 GO:0030218 \n", - "41 GO:0036211 \n", - "42 nucleolar function \n", - "43 neuronal network formation \n", - "44 sensory receptor function \n", - "45 MESH:D024510 \n", - "46 neuronal development \n", - "47 GO:0015031 \n", - "48 GO:0006629 \n", - "49 GO:0009653 \n", - "50 dna-binding \n", - "51 rna polymerase ii-specific activity \n", - "52 GO:0031625 \n", - "53 GO:0045944 \n", - "54 GO:0002639 \n", - "55 GO:1901184 \n", - "56 GO:0033157 \n", - "57 monoatomic cation \n", - "\n", - " label redundant \\\n", - "0 myelination False \n", - "1 axon ensheathment True \n", - "2 ensheathment of neurons True \n", - "3 peripheral nervous system development False \n", - "4 Schwann cell differentiation True \n", - "5 glial cell differentiation True \n", - "6 peripheral nervous system myelin maintenance True \n", - "7 mitochondrial DNA replication False \n", - "8 gliogenesis True \n", - "9 cerebellar Purkinje cell layer development False \n", - "10 None False \n", - "11 myelination in peripheral nervous system False \n", - "12 None False \n", - "13 None False \n", - "14 None False \n", - "15 myelin sheath False \n", - "16 None False \n", - "17 None False \n", - "18 nucleoplasm False \n", - "19 regulation of transcription by RNA polymerase II False \n", - "20 extracellular exosome False \n", - "21 identical protein binding False \n", - "22 membrane False \n", - "23 metal ion binding False \n", - "24 extracellular region False \n", - "25 cytoplasm False \n", - "26 cytosol False \n", - "27 nucleus False \n", - "28 mitochondrion False \n", - "29 extracellular space False \n", - "30 ATP binding False \n", - "31 plasma membrane False \n", - "32 RNA binding False \n", - "33 None False \n", - "34 protein folding False \n", - "35 protein catabolic process False \n", - "36 transmembrane transport False \n", - "37 None False \n", - "38 None False \n", - "39 None False \n", - "40 erythrocyte differentiation False \n", - "41 protein modification process False \n", - "42 None False \n", - "43 None False \n", - "44 None False \n", - "45 None False \n", - "46 None False \n", - "47 protein transport False \n", - "48 lipid metabolic process False \n", - "49 anatomical structure morphogenesis False \n", - "50 None False \n", - "51 None False \n", - "52 ubiquitin protein ligase binding False \n", - "53 positive regulation of transcription by RNA polymerase II False \n", - "54 positive regulation of immunoglobulin production False \n", - "55 regulation of ERBB signaling pathway False \n", - "56 regulation of intracellular protein transport False \n", - "57 None False \n", - "\n", - " standard turbo ontological synopsis standard no ontology \\\n", - "0 0.0 0.0 NaN \n", - "1 1.0 NaN NaN \n", - "2 2.0 NaN NaN \n", - "3 3.0 1.0 3.0 \n", - "4 4.0 NaN NaN \n", - "5 5.0 NaN NaN \n", - "6 6.0 NaN 1.0 \n", - "7 7.0 NaN 2.0 \n", - "8 8.0 NaN NaN \n", - "9 NaN NaN 0.0 \n", - "10 NaN 2.0 NaN \n", - "11 NaN 3.0 NaN \n", - "12 NaN 4.0 NaN \n", - "13 NaN NaN NaN \n", - "14 NaN NaN NaN \n", - "15 NaN NaN NaN \n", - "16 NaN NaN NaN \n", - "17 NaN NaN NaN \n", - "18 NaN NaN NaN \n", - "19 NaN NaN NaN \n", - "20 NaN NaN NaN \n", - "21 NaN NaN NaN \n", - "22 NaN NaN NaN \n", - "23 NaN NaN NaN \n", - "24 NaN NaN NaN \n", - "25 NaN NaN NaN \n", - "26 NaN NaN NaN \n", - "27 NaN NaN NaN \n", - "28 NaN NaN NaN \n", - "29 NaN NaN NaN \n", - "30 NaN NaN NaN \n", - "31 NaN NaN NaN \n", - "32 NaN NaN NaN \n", - "33 NaN NaN NaN \n", - "34 NaN NaN NaN \n", - "35 NaN NaN NaN \n", - "36 NaN NaN NaN \n", - "37 NaN NaN NaN \n", - "38 NaN NaN NaN \n", - "39 NaN NaN NaN \n", - "40 NaN NaN NaN \n", - "41 NaN NaN NaN \n", - "42 NaN NaN NaN \n", - "43 NaN NaN NaN \n", - "44 NaN NaN NaN \n", - "45 NaN NaN NaN \n", - "46 NaN NaN NaN \n", - "47 NaN NaN NaN \n", - "48 NaN NaN NaN \n", - "49 NaN NaN NaN \n", - "50 NaN NaN NaN \n", - "51 NaN NaN NaN \n", - "52 NaN NaN NaN \n", - "53 NaN NaN NaN \n", - "54 NaN NaN NaN \n", - "55 NaN NaN NaN \n", - "56 NaN NaN NaN \n", - "57 NaN NaN NaN \n", - "\n", - " turbo narrative synopsis rank based dav ontological synopsis \\\n", - "0 NaN NaN NaN \n", - "1 NaN NaN NaN \n", - "2 NaN NaN NaN \n", - "3 NaN NaN NaN \n", - "4 NaN NaN NaN \n", - "5 NaN NaN NaN \n", - "6 NaN NaN NaN \n", - "7 4.0 NaN NaN \n", - "8 NaN NaN NaN \n", - "9 NaN NaN NaN \n", - "10 NaN NaN NaN \n", - "11 NaN NaN NaN \n", - "12 1.0 NaN NaN \n", - "13 0.0 NaN NaN \n", - "14 2.0 NaN NaN \n", - "15 3.0 NaN NaN \n", - "16 5.0 NaN NaN \n", - "17 6.0 NaN NaN \n", - "18 NaN 0.0 NaN \n", - "19 NaN 1.0 NaN \n", - "20 NaN 2.0 NaN \n", - "21 NaN 3.0 NaN \n", - "22 NaN 4.0 NaN \n", - "23 NaN 5.0 2.0 \n", - "24 NaN 6.0 NaN \n", - "25 NaN 7.0 NaN \n", - "26 NaN 8.0 NaN \n", - "27 NaN 9.0 NaN \n", - "28 NaN 10.0 NaN \n", - "29 NaN 11.0 NaN \n", - "30 NaN 12.0 NaN \n", - "31 NaN 13.0 NaN \n", - "32 NaN 14.0 NaN \n", - "33 NaN NaN NaN \n", - "34 NaN NaN NaN \n", - "35 NaN NaN NaN \n", - "36 NaN NaN NaN \n", - "37 NaN NaN NaN \n", - "38 NaN NaN NaN \n", - "39 NaN NaN NaN \n", - "40 NaN NaN NaN \n", - "41 NaN NaN NaN \n", - "42 NaN NaN NaN \n", - "43 NaN NaN NaN \n", - "44 NaN NaN NaN \n", - "45 NaN NaN NaN \n", - "46 NaN NaN NaN \n", - "47 NaN NaN NaN \n", - "48 NaN NaN NaN \n", - "49 NaN NaN NaN \n", - "50 NaN NaN 0.0 \n", - "51 NaN NaN 1.0 \n", - "52 NaN NaN 3.0 \n", - "53 NaN NaN 4.0 \n", - "54 NaN NaN 5.0 \n", - "55 NaN NaN 6.0 \n", - "56 NaN NaN 7.0 \n", - "57 NaN NaN 8.0 \n", - "\n", - " turbo no synopsis dav narrative synopsis dav no synopsis \n", - "0 NaN NaN NaN \n", - "1 NaN NaN NaN \n", - "2 NaN NaN NaN \n", - "3 NaN NaN NaN \n", - "4 NaN NaN NaN \n", - "5 NaN NaN NaN \n", - "6 NaN NaN NaN \n", - "7 NaN NaN NaN \n", - "8 NaN NaN NaN \n", - "9 NaN NaN NaN \n", - "10 NaN NaN NaN \n", - "11 NaN NaN NaN \n", - "12 NaN NaN NaN \n", - "13 NaN NaN NaN \n", - "14 NaN NaN NaN \n", - "15 NaN NaN NaN \n", - "16 NaN NaN NaN \n", - "17 NaN NaN NaN \n", - "18 NaN NaN NaN \n", - "19 NaN NaN NaN \n", - "20 NaN NaN NaN \n", - "21 NaN NaN NaN \n", - "22 NaN NaN NaN \n", - "23 NaN NaN NaN \n", - "24 NaN NaN NaN \n", - "25 NaN NaN NaN \n", - "26 NaN NaN NaN \n", - "27 NaN NaN NaN \n", - "28 NaN NaN NaN \n", - "29 NaN NaN NaN \n", - "30 NaN NaN NaN \n", - "31 NaN NaN NaN \n", - "32 NaN NaN NaN \n", - "33 0.0 NaN NaN \n", - "34 1.0 NaN NaN \n", - "35 2.0 NaN NaN \n", - "36 3.0 NaN NaN \n", - "37 NaN 0.0 NaN \n", - "38 NaN 1.0 NaN \n", - "39 NaN 2.0 NaN \n", - "40 NaN 3.0 NaN \n", - "41 NaN 4.0 NaN \n", - "42 NaN 5.0 NaN \n", - "43 NaN 6.0 NaN \n", - "44 NaN 7.0 NaN \n", - "45 NaN NaN 0.0 \n", - "46 NaN NaN 1.0 \n", - "47 NaN NaN 2.0 \n", - "48 NaN NaN 3.0 \n", - "49 NaN NaN 4.0 \n", - "50 NaN NaN NaN \n", - "51 NaN NaN NaN \n", - "52 NaN NaN NaN \n", - "53 NaN NaN NaN \n", - "54 NaN NaN NaN \n", - "55 NaN NaN NaN \n", - "56 NaN NaN NaN \n", - "57 NaN NaN NaN " - ] - }, - "execution_count": 46, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "terms_summary(ataxia)" - ] - }, - { - "cell_type": "code", - "execution_count": 47, - "id": "76c0b8ee", - "metadata": {}, - "outputs": [], - "source": [ - "def retrieve_payload(geneset, method):\n", - " for comp in comps:\n", - " if comp.name == geneset:\n", - " return comp.payloads[method]" - ] - }, - { - "cell_type": "code", - "execution_count": 48, - "id": "17c4d4f6", - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Summary: Genes are primarily involved in the peripheral nervous system, myelination, and neurological disorders.\n", - "Mechanism: The enriched terms suggest that these genes primarily function in the peripheral nervous system and myelination.\n", - "Enriched Terms: myelination; peripheral nervous system development; neurological disorder; peripheral nervous system myelination; and neuropathy. \n", - "Hypothesis: These genes are all involved in the development and maintenance of the peripheral nervous system and myelination. Dysregulation or mutation of these genes likely leads to neuropathic disorders.\n" - ] - } - ], - "source": [ - "print(retrieve_payload(\"sensory ataxia-0\", \"gpt-3.5-turbo.ontological_synopsis.v1\").response_text)" - ] - }, - { - "cell_type": "code", - "execution_count": 49, - "id": "2fb5f713", - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Summary: Myelin upkeep and neurological diseases\n", - "Enriched Terms: Charcot-Marie-Tooth disease; peripheral neuropathy; Dejerine-Sottas syndrome; myelin sheath; mitochondrial DNA replication; tetratricopeptide repeat; transporter protein\n", - "\n", - "Mechanism: These genes are involved in myelin upkeep and various neurological diseases associated with defects in myelin sheath synthesis and functions. They play roles in mitochondrial DNA replication and transport, as well as protein transportation across the nuclear membrane. The presence of tetratricopeptide repeat motifs in these genes suggests their roles in protein-protein interactions and chaperone functions.\n", - "\n", - "Hypothesis: Dysregulation of the myelin upkeep pathways can lead to mitochondrial dysfunction, accumulations of toxic metabolites, and impaired protein processing, which contribute to the development of neurological diseases. Dysfunction of the transporter proteins and nuclear membrane transporters can further exacerbate cell dysfunction and death. Treatment strategies aimed at restoring mitochondrial function and enhancing myelin synthesis and repair may alleviate symptoms of these diseases.\n" - ] - } - ], - "source": [ - "print(retrieve_payload(\"sensory ataxia-0\", \"gpt-3.5-turbo.narrative_synopsis.v1\").response_text)" - ] - }, - { - "cell_type": "code", - "execution_count": 50, - "id": "652ef2a2", - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Summary: The enriched terms found among the listed human genes suggest a common involvement in cellular metabolism, particularly in mitochondrial function, protein folding and degradation, and transportation across cellular membranes.\n", - "Mechanism: These genes may be involved in the maintenance of cellular homeostasis and energy production.\n", - "Enriched Terms: Mitochondrial function; Protein folding; Protein degradation; Membrane transport. \n", - "\n", - "Hypothesis: Many of the enriched terms are related to cellular stress pathways, suggesting that these genes may be involved in the response to stress and cellular damage. Additionally, the involvement of several genes related to mitochondrial function suggests that there may be a common underlying mechanism related to energy production and metabolism.\n" - ] - } - ], - "source": [ - "print(retrieve_payload(\"sensory ataxia-0\", \"gpt-3.5-turbo.no_synopsis.v1\").response_text)" - ] - }, - { - "cell_type": "markdown", - "id": "90fecbd6", - "metadata": {}, - "source": [ - "## T cell proliferation" - ] - }, - { - "cell_type": "code", - "execution_count": 51, - "id": "76a06931", - "metadata": { - "scrolled": true - }, - "outputs": [ - { - "data": { - "text/html": [ - "
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modelmethodhas top termin top 5in top 10size overlapsimilaritynum termsnum GO termsnr size overlapnr similaritymean p valuemin p valuemax p valueproportion significantnum unannotated
1746N/AstandardTrueTrueTrue4911.00e+00491491151.00e+002.96e-032.66e-1934.96e-021.000
1747N/Astandard_no_ontologyTrueTrueTrue791.56e-01959534.62e-021.71e-012.66e-1931.00e+000.830
1750N/AclosureTrueFalseFalse4911.11e-016315625511.47e-038.93e-012.66e-1931.00e+000.110
1749N/Arank_basedFalseFalseFalse152.74e-02727212.63e-027.92e-013.40e-191.00e+000.214
1736gpt-3.5-turboontological_synopsisFalseFalseFalse51.02e-028500.00e+001.08e-021.22e-284.94e-021.000
1735gpt-3.5-turbono_synopsisFalseFalseFalse51.02e-026600.00e+001.67e-014.13e-1261.00e+000.830
1748N/ArandomFalseFalseFalse47.22e-03676700.00e+009.41e-011.18e-031.00e+000.0629
1741text-davinci-003no_synopsisFalseFalseFalse36.11e-035300.00e+009.86e-041.59e-142.96e-031.000
1738gpt-3.5-turbonarrative_synopsisFalseFalseFalse36.10e-035400.00e+002.50e-011.50e-181.00e+000.750
1740text-davinci-003no_synopsisFalseFalseFalse36.07e-0310600.00e+005.00e-011.50e-181.00e+000.500
1743text-davinci-003ontological_synopsisFalseFalseFalse36.06e-0315700.00e+005.75e-017.76e-051.00e+000.430
1737gpt-3.5-turboontological_synopsisFalseFalseFalse24.07e-035200.00e+003.88e-057.43e-137.76e-051.000
1734gpt-3.5-turbono_synopsisFalseFalseFalse12.04e-033100.00e+004.13e-1264.13e-1264.13e-1261.000
1742text-davinci-003ontological_synopsisFalseFalseFalse12.02e-036400.00e+007.50e-018.79e-091.00e+000.250
1745text-davinci-003narrative_synopsisFalseFalseFalse00.00e+0017000.00e+00NaNNaNNaNNaN0
1744text-davinci-003narrative_synopsisFalseFalseFalse00.00e+0010600.00e+001.00e+001.00e+001.00e+000.000
1739gpt-3.5-turbonarrative_synopsisFalseFalseFalse00.00e+009400.00e+001.00e+001.00e+001.00e+000.002
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idlabelredundantstandardstandard no ontologyturbo ontological synopsisdav narrative synopsisdav ontological synopsisturbo no synopsisturbo narrative synopsisdav no synopsisrank based
0GO:0006907pinocytosisFalse0.01.0NaNNaNNaNNaNNaNNaNNaN
1GO:0006897endocytosisTrue1.06.00.00.05.00.00.0NaNNaN
2GO:0044351macropinocytosisTrue2.00.0NaN4.0NaNNaNNaNNaNNaN
3GO:0016192vesicle-mediated transportTrue3.0NaNNaNNaNNaN1.0NaNNaNNaN
4GO:0030100regulation of endocytosisFalse4.0NaNNaNNaNNaNNaNNaNNaNNaN
5GO:0006810transportTrue5.0NaNNaNNaNNaNNaNNaNNaNNaN
6GO:0051234establishment of localizationTrue6.0NaNNaNNaNNaNNaNNaNNaNNaN
7GO:0045807positive regulation of endocytosisTrue7.0NaNNaNNaNNaNNaNNaNNaNNaN
8GO:0060627regulation of vesicle-mediated transportTrue8.0NaNNaNNaNNaNNaNNaNNaNNaN
9GO:0051179localizationTrue9.0NaNNaNNaNNaNNaNNaNNaNNaN
10GO:0031410cytoplasmic vesicleFalse10.0NaNNaNNaNNaNNaNNaNNaNNaN
11GO:0097708intracellular vesicleTrue11.0NaNNaNNaNNaNNaNNaNNaNNaN
12GO:0050766positive regulation of phagocytosisTrue12.04.0NaNNaNNaNNaNNaNNaNNaN
13GO:0048518positive regulation of biological processTrue13.0NaNNaNNaNNaNNaNNaNNaNNaN
14GO:0050764regulation of phagocytosisTrue14.0NaNNaNNaNNaNNaNNaNNaNNaN
15GO:0051128regulation of cellular component organizationTrue15.0NaNNaNNaNNaNNaNNaNNaNNaN
16GO:0031982vesicleTrue16.0NaNNaNNaNNaNNaNNaNNaNNaN
17GO:0150094amyloid-beta clearance by cellular catabolic processFalse17.03.0NaNNaNNaNNaNNaNNaNNaN
18GO:0006909phagocytosisTrue18.017.0NaNNaNNaNNaNNaNNaNNaN
19GO:0051049regulation of transportTrue19.0NaNNaNNaNNaNNaNNaNNaNNaN
20GO:0006898receptor-mediated endocytosisTrue20.02.02.0NaN6.0NaNNaNNaNNaN
21GO:0051050positive regulation of transportTrue21.0NaNNaNNaNNaNNaNNaNNaNNaN
22GO:0005041low-density lipoprotein particle receptor activityTrue22.05.0NaNNaNNaNNaNNaNNaNNaN
23GO:0030139endocytic vesicleTrue23.0NaNNaNNaNNaNNaNNaNNaNNaN
24GO:0030228lipoprotein particle receptor activityTrue24.0NaNNaNNaNNaNNaNNaNNaNNaN
25GO:0030666endocytic vesicle membraneTrue25.018.0NaNNaNNaNNaNNaNNaNNaN
26GO:0097242amyloid-beta clearanceTrue26.022.0NaNNaNNaNNaNNaNNaNNaN
27GO:0051130positive regulation of cellular component organizationTrue27.0NaNNaNNaNNaNNaNNaNNaNNaN
28GO:0060907positive regulation of macrophage cytokine productionTrue28.08.0NaNNaNNaNNaNNaNNaNNaN
29GO:0032879regulation of localizationTrue29.0NaNNaNNaNNaNNaNNaNNaNNaN
30GO:0048522positive regulation of cellular processTrue30.0NaNNaNNaNNaNNaNNaNNaNNaN
31GO:0002277myeloid dendritic cell activation involved in immune responseFalse31.09.0NaNNaNNaNNaNNaNNaNNaN
32GO:0030659cytoplasmic vesicle membraneTrue32.0NaNNaNNaNNaNNaNNaNNaNNaN
33GO:0012506vesicle membraneTrue33.0NaNNaNNaNNaNNaNNaNNaNNaN
34GO:0061081positive regulation of myeloid leukocyte cytokine production involved in immune responseTrue34.0NaNNaNNaNNaNNaNNaNNaNNaN
35GO:0010935regulation of macrophage cytokine productionTrue35.0NaNNaNNaNNaNNaNNaNNaNNaN
36GO:0048583regulation of response to stimulusFalse36.0NaNNaNNaNNaNNaNNaNNaNNaN
37GO:1905167positive regulation of lysosomal protein catabolic processTrue37.010.0NaNNaNNaNNaNNaNNaNNaN
38GO:0009894regulation of catabolic processTrue38.0NaNNaNNaNNaNNaNNaNNaNNaN
39GO:0023051regulation of signalingFalse39.0NaNNaNNaNNaNNaNNaNNaNNaN
40GO:0051641cellular localizationTrue40.0NaNNaNNaNNaNNaNNaNNaNNaN
41GO:1904352positive regulation of protein catabolic process in the vacuoleTrue41.0NaNNaNNaNNaNNaNNaNNaNNaN
42GO:0070508cholesterol importTrue42.013.0NaNNaNNaNNaNNaNNaNNaN
43GO:0031347regulation of defense responseTrue43.0NaNNaNNaNNaNNaNNaNNaNNaN
44GO:0005794Golgi apparatusFalse44.014.0NaNNaNNaNNaNNaNNaNNaN
45GO:1901700response to oxygen-containing compoundFalse45.0NaNNaNNaNNaNNaNNaNNaNNaN
46GO:0061024membrane organizationFalse46.0NaNNaNNaNNaNNaNNaNNaNNaN
47GO:0009966regulation of signal transductionTrue47.0NaNNaNNaNNaNNaNNaNNaNNaN
48GO:0015031protein transportTrue48.0NaN1.01.03.0NaNNaNNaNNaN
49GO:0048523negative regulation of cellular processFalse49.0NaNNaNNaNNaNNaNNaNNaNNaN
50GO:0032429regulation of phospholipase A2 activityFalseNaN7.0NaNNaNNaNNaNNaNNaNNaN
51GO:0034381plasma lipoprotein particle clearanceFalseNaN11.0NaNNaNNaNNaNNaNNaNNaN
52GO:0031623receptor internalizationFalseNaN12.0NaNNaNNaNNaNNaNNaNNaN
53GO:0009931calcium-dependent protein serine/threonine kinase activityFalseNaN15.0NaNNaNNaNNaNNaNNaNNaN
54GO:0005905clathrin-coated pitFalseNaN16.0NaNNaNNaNNaNNaNNaNNaN
55GO:0032050clathrin heavy chain bindingFalseNaN19.0NaNNaNNaNNaNNaNNaNNaN
56GO:0030299intestinal cholesterol absorptionFalseNaN20.0NaNNaNNaNNaNNaNNaNNaN
57GO:0001540amyloid-beta bindingFalseNaN21.0NaNNaNNaNNaNNaNNaNNaN
58GO:0034383low-density lipoprotein particle clearanceFalseNaN23.0NaNNaNNaNNaNNaNNaNNaN
59GO:0032760positive regulation of tumor necrosis factor productionFalseNaN24.0NaNNaNNaNNaNNaNNaNNaN
60GO:0071404cellular response to low-density lipoprotein particle stimulusFalseNaN25.0NaNNaNNaNNaNNaNNaNNaN
61GO:0042953lipoprotein transportFalseNaN26.0NaNNaNNaNNaNNaNNaNNaN
62GO:0030169low-density lipoprotein particle bindingFalseNaN27.0NaNNaNNaNNaNNaNNaNNaN
63GO:0051639actin filament network formationFalseNaNNaNNaN2.0NaNNaNNaNNaNNaN
64endoplasmic reticulum and recycling endosome membrane organizationNoneFalseNaNNaNNaN3.0NaNNaNNaNNaNNaN
65GO:0016043cellular component organizationFalseNaNNaNNaN5.0NaNNaNNaNNaNNaN
66intracellular signalingNoneFalseNaNNaNNaN6.0NaNNaNNaNNaNNaN
67GO:0051260protein homooligomerizationFalseNaNNaNNaN7.0NaNNaNNaNNaNNaN
68protein signalingNoneFalseNaNNaNNaNNaN0.0NaNNaNNaNNaN
69GO:0006468protein phosphorylationFalseNaNNaNNaNNaN1.0NaNNaNNaNNaN
70GO:0016567protein ubiquitinationFalseNaNNaNNaNNaN2.0NaNNaNNaNNaN
71GO:0030030cell projection organizationFalseNaNNaNNaNNaN4.0NaNNaNNaNNaN
72GO:0035091phosphatidylinositol bindingFalseNaNNaNNaNNaN7.0NaNNaNNaNNaN
73GO:0001766membrane raft polarizationFalseNaNNaNNaNNaN8.0NaNNaNNaNNaN
74GO:0097320plasma membrane tubulationFalseNaNNaNNaNNaN9.0NaNNaNNaNNaN
75GO:0007041lysosomal transportFalseNaNNaNNaNNaNNaN2.0NaNNaNNaN
76GO:0007032endosome organizationFalseNaNNaNNaNNaNNaN3.0NaNNaNNaN
77GO:0030163protein catabolic processFalseNaNNaNNaNNaNNaN4.0NaNNaNNaN
78intracellular traffickingNoneFalseNaNNaNNaNNaNNaNNaN1.0NaNNaN
79cytoskeleton reorganizationNoneFalseNaNNaNNaNNaNNaNNaN2.0NaNNaN
80GO:0007165signal transductionFalseNaNNaNNaNNaNNaNNaNNaN0.0NaN
81vesicle/lipid traffickingNoneFalseNaNNaNNaNNaNNaNNaNNaN1.0NaN
82cellular adhesionNoneFalseNaNNaNNaNNaNNaNNaNNaN2.0NaN
83nutrient regulationNoneFalseNaNNaNNaNNaNNaNNaNNaN3.0NaN
84cell metabolismNoneFalseNaNNaNNaNNaNNaNNaNNaN4.0NaN
85cytoskeletal organizationNoneFalseNaNNaNNaNNaNNaNNaNNaN5.0NaN
86endocytosis/exocytosisNoneFalseNaNNaNNaNNaNNaNNaNNaN6.0NaN
87intercellular adhesion/motilityNoneFalseNaNNaNNaNNaNNaNNaNNaN7.0NaN
88GO:0005654nucleoplasmFalseNaNNaNNaNNaNNaNNaNNaNNaN0.0
89GO:0005634nucleusFalseNaNNaNNaNNaNNaNNaNNaNNaN1.0
90GO:0046872metal ion bindingFalseNaNNaNNaNNaNNaNNaNNaNNaN2.0
91GO:0005886plasma membraneFalseNaNNaNNaNNaNNaNNaNNaNNaN3.0
92GO:0005524ATP bindingFalseNaNNaNNaNNaNNaNNaNNaNNaN4.0
93GO:0045944positive regulation of transcription by RNA polymerase IIFalseNaNNaNNaNNaNNaNNaNNaNNaN5.0
94GO:0070062extracellular exosomeFalseNaNNaNNaNNaNNaNNaNNaNNaN6.0
95GO:0005576extracellular regionFalseNaNNaNNaNNaNNaNNaNNaNNaN7.0
96GO:0042802identical protein bindingFalseNaNNaNNaNNaNNaNNaNNaNNaN8.0
97GO:0005829cytosolFalseNaNNaNNaNNaNNaNNaNNaNNaN9.0
98GO:0006357regulation of transcription by RNA polymerase IIFalseNaNNaNNaNNaNNaNNaNNaNNaN10.0
99GO:0005739mitochondrionFalseNaNNaNNaNNaNNaNNaNNaNNaN11.0
100GO:0005737cytoplasmFalseNaNNaNNaNNaNNaNNaNNaNNaN12.0
101GO:0016020membraneFalseNaNNaNNaNNaNNaNNaNNaNNaN13.0
102GO:0003723RNA bindingFalseNaNNaNNaNNaNNaNNaNNaNNaN14.0
103GO:0005615extracellular spaceFalseNaNNaNNaNNaNNaNNaNNaNNaN15.0
\n", - "
" - ], - "text/plain": [ - " id \\\n", - "0 GO:0006907 \n", - "1 GO:0006897 \n", - "2 GO:0044351 \n", - "3 GO:0016192 \n", - "4 GO:0030100 \n", - "5 GO:0006810 \n", - "6 GO:0051234 \n", - "7 GO:0045807 \n", - "8 GO:0060627 \n", - "9 GO:0051179 \n", - "10 GO:0031410 \n", - "11 GO:0097708 \n", - "12 GO:0050766 \n", - "13 GO:0048518 \n", - "14 GO:0050764 \n", - "15 GO:0051128 \n", - "16 GO:0031982 \n", - "17 GO:0150094 \n", - "18 GO:0006909 \n", - "19 GO:0051049 \n", - "20 GO:0006898 \n", - "21 GO:0051050 \n", - "22 GO:0005041 \n", - "23 GO:0030139 \n", - "24 GO:0030228 \n", - "25 GO:0030666 \n", - "26 GO:0097242 \n", - "27 GO:0051130 \n", - "28 GO:0060907 \n", - "29 GO:0032879 \n", - "30 GO:0048522 \n", - "31 GO:0002277 \n", - "32 GO:0030659 \n", - "33 GO:0012506 \n", - "34 GO:0061081 \n", - "35 GO:0010935 \n", - "36 GO:0048583 \n", - "37 GO:1905167 \n", - "38 GO:0009894 \n", - "39 GO:0023051 \n", - "40 GO:0051641 \n", - "41 GO:1904352 \n", - "42 GO:0070508 \n", - "43 GO:0031347 \n", - "44 GO:0005794 \n", - "45 GO:1901700 \n", - "46 GO:0061024 \n", - "47 GO:0009966 \n", - "48 GO:0015031 \n", - "49 GO:0048523 \n", - "50 GO:0032429 \n", - "51 GO:0034381 \n", - "52 GO:0031623 \n", - "53 GO:0009931 \n", - "54 GO:0005905 \n", - "55 GO:0032050 \n", - "56 GO:0030299 \n", - "57 GO:0001540 \n", - "58 GO:0034383 \n", - "59 GO:0032760 \n", - "60 GO:0071404 \n", - "61 GO:0042953 \n", - "62 GO:0030169 \n", - "63 GO:0051639 \n", - "64 endoplasmic reticulum and recycling endosome membrane organization \n", - "65 GO:0016043 \n", - "66 intracellular signaling \n", - "67 GO:0051260 \n", - "68 protein signaling \n", - "69 GO:0006468 \n", - "70 GO:0016567 \n", - "71 GO:0030030 \n", - "72 GO:0035091 \n", - "73 GO:0001766 \n", - "74 GO:0097320 \n", - "75 GO:0007041 \n", - "76 GO:0007032 \n", - "77 GO:0030163 \n", - "78 intracellular trafficking \n", - "79 cytoskeleton reorganization \n", - "80 GO:0007165 \n", - "81 vesicle/lipid trafficking \n", - "82 cellular adhesion \n", - "83 nutrient regulation \n", - "84 cell metabolism \n", - "85 cytoskeletal organization \n", - "86 endocytosis/exocytosis \n", - "87 intercellular adhesion/motility \n", - "88 GO:0005654 \n", - "89 GO:0005634 \n", - "90 GO:0046872 \n", - "91 GO:0005886 \n", - "92 GO:0005524 \n", - "93 GO:0045944 \n", - "94 GO:0070062 \n", - "95 GO:0005576 \n", - "96 GO:0042802 \n", - "97 GO:0005829 \n", - "98 GO:0006357 \n", - "99 GO:0005739 \n", - "100 GO:0005737 \n", - "101 GO:0016020 \n", - "102 GO:0003723 \n", - "103 GO:0005615 \n", - "\n", - " label \\\n", - "0 pinocytosis \n", - "1 endocytosis \n", - "2 macropinocytosis \n", - "3 vesicle-mediated transport \n", - "4 regulation of endocytosis \n", - "5 transport \n", - "6 establishment of localization \n", - "7 positive regulation of endocytosis \n", - "8 regulation of vesicle-mediated transport \n", - "9 localization \n", - "10 cytoplasmic vesicle \n", - "11 intracellular vesicle \n", - "12 positive regulation of phagocytosis \n", - "13 positive regulation of biological process \n", - "14 regulation of phagocytosis \n", - "15 regulation of cellular component organization \n", - "16 vesicle \n", - "17 amyloid-beta clearance by cellular catabolic process \n", - "18 phagocytosis \n", - "19 regulation of transport \n", - "20 receptor-mediated endocytosis \n", - "21 positive regulation of transport \n", - "22 low-density lipoprotein particle receptor activity \n", - "23 endocytic vesicle \n", - "24 lipoprotein particle receptor activity \n", - "25 endocytic vesicle membrane \n", - "26 amyloid-beta clearance \n", - "27 positive regulation of cellular component organization \n", - "28 positive regulation of macrophage cytokine production \n", - "29 regulation of localization \n", - "30 positive regulation of cellular process \n", - "31 myeloid dendritic cell activation involved in immune response \n", - "32 cytoplasmic vesicle membrane \n", - "33 vesicle membrane \n", - "34 positive regulation of myeloid leukocyte cytokine production involved in immune response \n", - "35 regulation of macrophage cytokine production \n", - "36 regulation of response to stimulus \n", - "37 positive regulation of lysosomal protein catabolic process \n", - "38 regulation of catabolic process \n", - "39 regulation of signaling \n", - "40 cellular localization \n", - "41 positive regulation of protein catabolic process in the vacuole \n", - "42 cholesterol import \n", - "43 regulation of defense response \n", - "44 Golgi apparatus \n", - "45 response to oxygen-containing compound \n", - "46 membrane organization \n", - "47 regulation of signal transduction \n", - "48 protein transport \n", - "49 negative regulation of cellular process \n", - "50 regulation of phospholipase A2 activity \n", - "51 plasma lipoprotein particle clearance \n", - "52 receptor internalization \n", - "53 calcium-dependent protein serine/threonine kinase activity \n", - "54 clathrin-coated pit \n", - "55 clathrin heavy chain binding \n", - "56 intestinal cholesterol absorption \n", - "57 amyloid-beta binding \n", - "58 low-density lipoprotein particle clearance \n", - "59 positive regulation of tumor necrosis factor production \n", - "60 cellular response to low-density lipoprotein particle stimulus \n", - "61 lipoprotein transport \n", - "62 low-density lipoprotein particle binding \n", - "63 actin filament network formation \n", - "64 None \n", - "65 cellular component organization \n", - "66 None \n", - "67 protein homooligomerization \n", - "68 None \n", - "69 protein phosphorylation \n", - "70 protein ubiquitination \n", - "71 cell projection organization \n", - "72 phosphatidylinositol binding \n", - "73 membrane raft polarization \n", - "74 plasma membrane tubulation \n", - "75 lysosomal transport \n", - "76 endosome organization \n", - "77 protein catabolic process \n", - "78 None \n", - "79 None \n", - "80 signal transduction \n", - "81 None \n", - "82 None \n", - "83 None \n", - "84 None \n", - "85 None \n", - "86 None \n", - "87 None \n", - "88 nucleoplasm \n", - "89 nucleus \n", - "90 metal ion binding \n", - "91 plasma membrane \n", - "92 ATP binding \n", - "93 positive regulation of transcription by RNA polymerase II \n", - "94 extracellular exosome \n", - "95 extracellular region \n", - "96 identical protein binding \n", - "97 cytosol \n", - "98 regulation of transcription by RNA polymerase II \n", - "99 mitochondrion \n", - "100 cytoplasm \n", - "101 membrane \n", - "102 RNA binding \n", - "103 extracellular space \n", - "\n", - " redundant standard standard no ontology turbo ontological synopsis \\\n", - "0 False 0.0 1.0 NaN \n", - "1 True 1.0 6.0 0.0 \n", - "2 True 2.0 0.0 NaN \n", - "3 True 3.0 NaN NaN \n", - "4 False 4.0 NaN NaN \n", - "5 True 5.0 NaN NaN \n", - "6 True 6.0 NaN NaN \n", - "7 True 7.0 NaN NaN \n", - "8 True 8.0 NaN NaN \n", - "9 True 9.0 NaN NaN \n", - "10 False 10.0 NaN NaN \n", - "11 True 11.0 NaN NaN \n", - "12 True 12.0 4.0 NaN \n", - "13 True 13.0 NaN NaN \n", - "14 True 14.0 NaN NaN \n", - "15 True 15.0 NaN NaN \n", - "16 True 16.0 NaN NaN \n", - "17 False 17.0 3.0 NaN \n", - "18 True 18.0 17.0 NaN \n", - "19 True 19.0 NaN NaN \n", - "20 True 20.0 2.0 2.0 \n", - "21 True 21.0 NaN NaN \n", - "22 True 22.0 5.0 NaN \n", - "23 True 23.0 NaN NaN \n", - "24 True 24.0 NaN NaN \n", - "25 True 25.0 18.0 NaN \n", - "26 True 26.0 22.0 NaN \n", - "27 True 27.0 NaN NaN \n", - "28 True 28.0 8.0 NaN \n", - "29 True 29.0 NaN NaN \n", - "30 True 30.0 NaN NaN \n", - "31 False 31.0 9.0 NaN \n", - "32 True 32.0 NaN NaN \n", - "33 True 33.0 NaN NaN \n", - "34 True 34.0 NaN NaN \n", - "35 True 35.0 NaN NaN \n", - "36 False 36.0 NaN NaN \n", - "37 True 37.0 10.0 NaN \n", - "38 True 38.0 NaN NaN \n", - "39 False 39.0 NaN NaN \n", - "40 True 40.0 NaN NaN \n", - "41 True 41.0 NaN NaN \n", - "42 True 42.0 13.0 NaN \n", - "43 True 43.0 NaN NaN \n", - "44 False 44.0 14.0 NaN \n", - "45 False 45.0 NaN NaN \n", - "46 False 46.0 NaN NaN \n", - "47 True 47.0 NaN NaN \n", - "48 True 48.0 NaN 1.0 \n", - "49 False 49.0 NaN NaN \n", - "50 False NaN 7.0 NaN \n", - "51 False NaN 11.0 NaN \n", - "52 False NaN 12.0 NaN \n", - "53 False NaN 15.0 NaN \n", - "54 False NaN 16.0 NaN \n", - "55 False NaN 19.0 NaN \n", - "56 False NaN 20.0 NaN \n", - "57 False NaN 21.0 NaN \n", - "58 False NaN 23.0 NaN \n", - "59 False NaN 24.0 NaN \n", - "60 False NaN 25.0 NaN \n", - "61 False NaN 26.0 NaN \n", - "62 False NaN 27.0 NaN \n", - "63 False NaN NaN NaN \n", - "64 False NaN NaN NaN \n", - "65 False NaN NaN NaN \n", - "66 False NaN NaN NaN \n", - "67 False NaN NaN NaN \n", - "68 False NaN NaN NaN \n", - "69 False NaN NaN NaN \n", - "70 False NaN NaN NaN \n", - "71 False NaN NaN NaN \n", - "72 False NaN NaN NaN \n", - "73 False NaN NaN NaN \n", - "74 False NaN NaN NaN \n", - "75 False NaN NaN NaN \n", - "76 False NaN NaN NaN \n", - "77 False NaN NaN NaN \n", - "78 False NaN NaN NaN \n", - "79 False NaN NaN NaN \n", - "80 False NaN NaN NaN \n", - "81 False NaN NaN NaN \n", - "82 False NaN NaN NaN \n", - "83 False NaN NaN NaN \n", - "84 False NaN NaN NaN \n", - "85 False NaN NaN NaN \n", - "86 False NaN NaN NaN \n", - "87 False NaN NaN NaN \n", - "88 False NaN NaN NaN \n", - "89 False NaN NaN NaN \n", - "90 False NaN NaN NaN \n", - "91 False NaN NaN NaN \n", - "92 False NaN NaN NaN \n", - "93 False NaN NaN NaN \n", - "94 False NaN NaN NaN \n", - "95 False NaN NaN NaN \n", - "96 False NaN NaN NaN \n", - "97 False NaN NaN NaN \n", - "98 False NaN NaN NaN \n", - "99 False NaN NaN NaN \n", - "100 False NaN NaN NaN \n", - "101 False NaN NaN NaN \n", - "102 False NaN NaN NaN \n", - "103 False NaN NaN NaN \n", - "\n", - " dav narrative synopsis dav ontological synopsis turbo no synopsis \\\n", - "0 NaN NaN NaN \n", - "1 0.0 5.0 0.0 \n", - "2 4.0 NaN NaN \n", - "3 NaN NaN 1.0 \n", - "4 NaN NaN NaN \n", - "5 NaN NaN NaN \n", - "6 NaN NaN NaN \n", - "7 NaN NaN NaN \n", - "8 NaN NaN NaN \n", - "9 NaN NaN NaN \n", - "10 NaN NaN NaN \n", - "11 NaN NaN NaN \n", - "12 NaN NaN NaN \n", - "13 NaN NaN NaN \n", - "14 NaN NaN NaN \n", - "15 NaN NaN NaN \n", - "16 NaN NaN NaN \n", - "17 NaN NaN NaN \n", - "18 NaN NaN NaN \n", - "19 NaN NaN NaN \n", - "20 NaN 6.0 NaN \n", - "21 NaN NaN NaN \n", - "22 NaN NaN NaN \n", - "23 NaN NaN NaN \n", - "24 NaN NaN NaN \n", - "25 NaN NaN NaN \n", - "26 NaN NaN NaN \n", - "27 NaN NaN NaN \n", - "28 NaN NaN NaN \n", - "29 NaN NaN NaN \n", - "30 NaN NaN NaN \n", - "31 NaN NaN NaN \n", - "32 NaN NaN NaN \n", - "33 NaN NaN NaN \n", - "34 NaN NaN NaN \n", - "35 NaN NaN NaN \n", - "36 NaN NaN NaN \n", - "37 NaN NaN NaN \n", - "38 NaN NaN NaN \n", - "39 NaN NaN NaN \n", - "40 NaN NaN NaN \n", - "41 NaN NaN NaN \n", - "42 NaN NaN NaN \n", - "43 NaN NaN NaN \n", - "44 NaN NaN NaN \n", - "45 NaN NaN NaN \n", - "46 NaN NaN NaN \n", - "47 NaN NaN NaN \n", - "48 1.0 3.0 NaN \n", - "49 NaN NaN NaN \n", - "50 NaN NaN NaN \n", - "51 NaN NaN NaN \n", - "52 NaN NaN NaN \n", - "53 NaN NaN NaN \n", - "54 NaN NaN NaN \n", - "55 NaN NaN NaN \n", - "56 NaN NaN NaN \n", - "57 NaN NaN NaN \n", - "58 NaN NaN NaN \n", - "59 NaN NaN NaN \n", - "60 NaN NaN NaN \n", - "61 NaN NaN NaN \n", - "62 NaN NaN NaN \n", - "63 2.0 NaN NaN \n", - "64 3.0 NaN NaN \n", - "65 5.0 NaN NaN \n", - "66 6.0 NaN NaN \n", - "67 7.0 NaN NaN \n", - "68 NaN 0.0 NaN \n", - "69 NaN 1.0 NaN \n", - "70 NaN 2.0 NaN \n", - "71 NaN 4.0 NaN \n", - "72 NaN 7.0 NaN \n", - "73 NaN 8.0 NaN \n", - "74 NaN 9.0 NaN \n", - "75 NaN NaN 2.0 \n", - "76 NaN NaN 3.0 \n", - "77 NaN NaN 4.0 \n", - "78 NaN NaN NaN \n", - "79 NaN NaN NaN \n", - "80 NaN NaN NaN \n", - "81 NaN NaN NaN \n", - "82 NaN NaN NaN \n", - "83 NaN NaN NaN \n", - "84 NaN NaN NaN \n", - "85 NaN NaN NaN \n", - "86 NaN NaN NaN \n", - "87 NaN NaN NaN \n", - "88 NaN NaN NaN \n", - "89 NaN NaN NaN \n", - "90 NaN NaN NaN \n", - "91 NaN NaN NaN \n", - "92 NaN NaN NaN \n", - "93 NaN NaN NaN \n", - "94 NaN NaN NaN \n", - "95 NaN NaN NaN \n", - "96 NaN NaN NaN \n", - "97 NaN NaN NaN \n", - "98 NaN NaN NaN \n", - "99 NaN NaN NaN \n", - "100 NaN NaN NaN \n", - "101 NaN NaN NaN \n", - "102 NaN NaN NaN \n", - "103 NaN NaN NaN \n", - "\n", - " turbo narrative synopsis dav no synopsis rank based \n", - "0 NaN NaN NaN \n", - "1 0.0 NaN NaN \n", - "2 NaN NaN NaN \n", - "3 NaN NaN NaN \n", - "4 NaN NaN NaN \n", - "5 NaN NaN NaN \n", - "6 NaN NaN NaN \n", - "7 NaN NaN NaN \n", - "8 NaN NaN NaN \n", - "9 NaN NaN NaN \n", - "10 NaN NaN NaN \n", - "11 NaN NaN NaN \n", - "12 NaN NaN NaN \n", - "13 NaN NaN NaN \n", - "14 NaN NaN NaN \n", - "15 NaN NaN NaN \n", - "16 NaN NaN NaN \n", - "17 NaN NaN NaN \n", - "18 NaN NaN NaN \n", - "19 NaN NaN NaN \n", - "20 NaN NaN NaN \n", - "21 NaN NaN NaN \n", - "22 NaN NaN NaN \n", - "23 NaN NaN NaN \n", - "24 NaN NaN NaN \n", - "25 NaN NaN NaN \n", - "26 NaN NaN NaN \n", - "27 NaN NaN NaN \n", - "28 NaN NaN NaN \n", - "29 NaN NaN NaN \n", - "30 NaN NaN NaN \n", - "31 NaN NaN NaN \n", - "32 NaN NaN NaN \n", - "33 NaN NaN NaN \n", - "34 NaN NaN NaN \n", - "35 NaN NaN NaN \n", - "36 NaN NaN NaN \n", - "37 NaN NaN NaN \n", - "38 NaN NaN NaN \n", - "39 NaN NaN NaN \n", - "40 NaN NaN NaN \n", - "41 NaN NaN NaN \n", - "42 NaN NaN NaN \n", - "43 NaN NaN NaN \n", - "44 NaN NaN NaN \n", - "45 NaN NaN NaN \n", - "46 NaN NaN NaN \n", - "47 NaN NaN NaN \n", - "48 NaN NaN NaN \n", - "49 NaN NaN NaN \n", - "50 NaN NaN NaN \n", - "51 NaN NaN NaN \n", - "52 NaN NaN NaN \n", - "53 NaN NaN NaN \n", - "54 NaN NaN NaN \n", - "55 NaN NaN NaN \n", - "56 NaN NaN NaN \n", - "57 NaN NaN NaN \n", - "58 NaN NaN NaN \n", - "59 NaN NaN NaN \n", - "60 NaN NaN NaN \n", - "61 NaN NaN NaN \n", - "62 NaN NaN NaN \n", - "63 NaN NaN NaN \n", - "64 NaN NaN NaN \n", - "65 NaN NaN NaN \n", - "66 NaN NaN NaN \n", - "67 NaN NaN NaN \n", - "68 NaN NaN NaN \n", - "69 NaN NaN NaN \n", - "70 NaN NaN NaN \n", - "71 NaN NaN NaN \n", - "72 NaN NaN NaN \n", - "73 NaN NaN NaN \n", - "74 NaN NaN NaN \n", - "75 NaN NaN NaN \n", - "76 NaN NaN NaN \n", - "77 NaN NaN NaN \n", - "78 1.0 NaN NaN \n", - "79 2.0 NaN NaN \n", - "80 NaN 0.0 NaN \n", - "81 NaN 1.0 NaN \n", - "82 NaN 2.0 NaN \n", - "83 NaN 3.0 NaN \n", - "84 NaN 4.0 NaN \n", - "85 NaN 5.0 NaN \n", - "86 NaN 6.0 NaN \n", - "87 NaN 7.0 NaN \n", - "88 NaN NaN 0.0 \n", - "89 NaN NaN 1.0 \n", - "90 NaN NaN 2.0 \n", - "91 NaN NaN 3.0 \n", - "92 NaN NaN 4.0 \n", - "93 NaN NaN 5.0 \n", - "94 NaN NaN 6.0 \n", - "95 NaN NaN 7.0 \n", - "96 NaN NaN 8.0 \n", - "97 NaN NaN 9.0 \n", - "98 NaN NaN 10.0 \n", - "99 NaN NaN 11.0 \n", - "100 NaN NaN 12.0 \n", - "101 NaN NaN 13.0 \n", - "102 NaN NaN 14.0 \n", - "103 NaN NaN 15.0 " - ] - }, - "execution_count": 54, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "endocytosis = df.query(f\"{GENESET} == 'endocytosis-0'\").sort_values(\"similarity\", ascending=False)\n", - "terms_summary(endocytosis)" - ] - }, - { - "cell_type": "code", - "execution_count": 55, - "id": "e9c3c720", - "metadata": {}, - "outputs": [ - { - "ename": "KeyError", - "evalue": "'gpt-3.5-turbo.narrative_synopsis'", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mKeyError\u001b[0m Traceback (most recent call last)", - "Cell \u001b[0;32mIn[55], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[38;5;28mprint\u001b[39m(\u001b[43mretrieve_payload\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mendocytosis-0\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mgpt-3.5-turbo.narrative_synopsis\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m)\u001b[49m\u001b[38;5;241m.\u001b[39mprompt)\n", - "Cell \u001b[0;32mIn[47], line 4\u001b[0m, in \u001b[0;36mretrieve_payload\u001b[0;34m(geneset, method)\u001b[0m\n\u001b[1;32m 2\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m comp \u001b[38;5;129;01min\u001b[39;00m comps:\n\u001b[1;32m 3\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m comp\u001b[38;5;241m.\u001b[39mname \u001b[38;5;241m==\u001b[39m geneset:\n\u001b[0;32m----> 4\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mcomp\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mpayloads\u001b[49m\u001b[43m[\u001b[49m\u001b[43mmethod\u001b[49m\u001b[43m]\u001b[49m\n", - "\u001b[0;31mKeyError\u001b[0m: 'gpt-3.5-turbo.narrative_synopsis'" - ] - } - ], - "source": [ - "print(retrieve_payload(\"endocytosis-0\", \"gpt-3.5-turbo.narrative_synopsis\").prompt)" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "6357dffb", - "metadata": {}, - "outputs": [], - "source": [ - "print(retrieve_payload(\"endocytosis-0\", \"gpt-3.5-turbo.narrative_synopsis\").response_text)" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "4f101e21", - "metadata": {}, - "outputs": [], - "source": [ - "print(retrieve_payload(\"endocytosis-0\", \"gpt-3.5-turbo.ontological_synopsis\").prompt)" - ] - }, - { - "cell_type": "markdown", - "id": "ba1d59a2", - "metadata": {}, - "source": [ - "## Hydrolysis" - ] - }, - { - "cell_type": "code", - "execution_count": 56, - "id": "77d2a353", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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idlabelredundantstandardstandard no ontologydav ontological synopsisdav narrative synopsisturbo narrative synopsisturbo no synopsisturbo ontological synopsisrank baseddav no synopsis
0GO:0004553hydrolase activity, hydrolyzing O-glycosyl compoundsFalse0.062.014.0NaNNaNNaNNaNNaNNaN
1GO:0016798hydrolase activity, acting on glycosyl bondsTrue1.0NaNNaN0.0NaNNaNNaNNaNNaN
2GO:0005975carbohydrate metabolic processFalse2.00.0NaNNaN2.01.0NaNNaNNaN
3GO:0016787hydrolase activityTrue3.0NaNNaNNaN3.0NaNNaNNaNNaN
4GO:1901136carbohydrate derivative catabolic processFalse4.0NaNNaNNaNNaNNaNNaNNaNNaN
5GO:0009311oligosaccharide metabolic processTrue5.022.0NaNNaNNaN3.0NaNNaNNaN
6GO:1901135carbohydrate derivative metabolic processTrue6.0NaNNaNNaNNaNNaNNaNNaNNaN
7GO:0003824catalytic activityTrue7.0NaNNaNNaNNaNNaNNaNNaNNaN
8GO:0006026aminoglycan catabolic processTrue8.0NaNNaNNaNNaNNaNNaNNaNNaN
9GO:0009313oligosaccharide catabolic processTrue9.01.0NaNNaNNaNNaNNaNNaNNaN
10GO:0015929hexosaminidase activityTrue10.0NaNNaNNaN7.0NaNNaNNaNNaN
11GO:0015923mannosidase activityTrue11.0NaNNaNNaNNaNNaNNaNNaNNaN
12GO:0016052carbohydrate catabolic processTrue12.0NaNNaNNaNNaNNaNNaNNaNNaN
13GO:1901575organic substance catabolic processTrue13.0NaNNaNNaNNaNNaNNaNNaNNaN
14GO:0004559alpha-mannosidase activityTrue14.09.0NaNNaNNaNNaNNaNNaNNaN
15GO:0015926glucosidase activityTrue15.0NaNNaNNaNNaNNaNNaNNaNNaN
16GO:0019377glycolipid catabolic processTrue16.070.0NaNNaNNaNNaNNaNNaNNaN
17GO:0046514ceramide catabolic processTrue17.059.0NaNNaNNaNNaNNaNNaNNaN
18GO:0046466membrane lipid catabolic processTrue18.0NaNNaNNaNNaNNaNNaNNaNNaN
19GO:0006022aminoglycan metabolic processTrue19.0NaNNaNNaNNaNNaNNaNNaNNaN
20GO:0009056catabolic processTrue20.0NaNNaNNaNNaNNaNNaNNaNNaN
21GO:1901565organonitrogen compound catabolic processTrue21.0NaNNaNNaNNaNNaNNaNNaNNaN
22GO:0046479glycosphingolipid catabolic processTrue22.0NaNNaNNaNNaNNaN0.0NaNNaN
23GO:0006027glycosaminoglycan catabolic processTrue23.015.0NaNNaN4.02.0NaNNaNNaN
24GO:0030149sphingolipid catabolic processTrue24.0NaNNaNNaNNaNNaNNaNNaNNaN
25GO:0009100glycoprotein metabolic processTrue25.0NaNNaNNaNNaNNaNNaNNaNNaN
26GO:0006516glycoprotein catabolic processTrue26.049.0NaN2.0NaNNaN1.0NaNNaN
27GO:0043202lysosomal lumenFalse27.02.0NaNNaNNaNNaNNaNNaNNaN
28GO:0005775vacuolar lumenTrue28.0NaNNaNNaNNaNNaNNaNNaNNaN
29GO:0006517protein deglycosylationTrue29.026.0NaNNaNNaNNaNNaNNaNNaN
30GO:0009057macromolecule catabolic processTrue30.0NaNNaNNaNNaNNaNNaNNaNNaN
31GO:0008152metabolic processTrue31.024.0NaNNaNNaNNaNNaNNaNNaN
32GO:0015924mannosyl-oligosaccharide mannosidase activityTrue32.0NaNNaNNaNNaNNaNNaNNaNNaN
33GO:0003796lysozyme activityTrue33.03.020.0NaNNaNNaNNaNNaNNaN
34GO:0030203glycosaminoglycan metabolic processTrue34.0NaNNaNNaNNaNNaNNaNNaNNaN
35GO:0006672ceramide metabolic processTrue35.0NaNNaNNaNNaNNaNNaNNaNNaN
36GO:0006687glycosphingolipid metabolic processTrue36.021.0NaNNaNNaNNaNNaNNaNNaN
37GO:0005764lysosomeTrue37.04.0NaNNaN0.04.0NaNNaNNaN
38GO:0000323lytic vacuoleTrue38.0NaNNaNNaNNaNNaNNaNNaNNaN
39GO:0030214hyaluronan catabolic processTrue39.05.0NaNNaNNaNNaN3.0NaNNaN
40GO:0006664glycolipid metabolic processTrue40.0NaNNaNNaNNaNNaNNaNNaNNaN
41GO:1903509liposaccharide metabolic processTrue41.0NaNNaNNaNNaNNaNNaNNaNNaN
42GO:0005773vacuoleTrue42.050.0NaNNaNNaNNaNNaNNaNNaN
43GO:0006643membrane lipid metabolic processTrue43.0NaNNaNNaNNaNNaNNaNNaNNaN
44GO:0004415hyalurononglucosaminidase activityTrue44.06.07.0NaNNaNNaNNaNNaNNaN
45GO:0061783peptidoglycan muralytic activityTrue45.0NaNNaNNaNNaNNaNNaNNaNNaN
46GO:0006665sphingolipid metabolic processTrue46.0NaNNaNNaNNaNNaNNaNNaNNaN
47GO:0044242cellular lipid catabolic processTrue47.0NaNNaNNaNNaNNaNNaNNaNNaN
48GO:0005576extracellular regionFalse48.038.0NaNNaNNaNNaNNaN42.0NaN
49GO:0071704organic substance metabolic processTrue49.0NaNNaNNaNNaNNaNNaNNaNNaN
50GO:1903510mucopolysaccharide metabolic processTrue50.0NaNNaNNaNNaNNaNNaNNaNNaN
51GO:0006689ganglioside catabolic processTrue51.07.0NaNNaN6.0NaNNaNNaNNaN
52GO:0004571mannosyl-oligosaccharide 1,2-alpha-mannosidase activityTrue52.08.0NaNNaNNaNNaNNaNNaNNaN
53GO:0090599alpha-glucosidase activityTrue53.076.0NaNNaNNaNNaNNaNNaNNaN
54GO:0015925galactosidase activityTrue54.0NaNNaNNaNNaNNaNNaNNaNNaN
55GO:0030212hyaluronan metabolic processTrue55.0NaNNaNNaNNaNNaNNaNNaNNaN
56GO:0005984disaccharide metabolic processTrue56.0NaNNaNNaNNaNNaNNaNNaNNaN
57GO:0044238primary metabolic processTrue57.0NaNNaNNaNNaNNaNNaNNaNNaN
58GO:0016139glycoside catabolic processTrue58.012.0NaNNaNNaNNaNNaNNaNNaN
59GO:0016042lipid catabolic processTrue59.0NaNNaNNaNNaNNaNNaNNaNNaN
60GO:0006032chitin catabolic processTrue60.011.0NaNNaNNaNNaN2.0NaNNaN
61GO:0006030chitin metabolic processTrue61.0NaNNaNNaNNaNNaNNaNNaNNaN
62GO:0016160amylase activityTrue62.0NaNNaNNaNNaNNaNNaNNaNNaN
63GO:0006491N-glycan processingTrue63.010.0NaNNaNNaNNaNNaNNaNNaN
64GO:1901564organonitrogen compound metabolic processTrue64.0NaNNaNNaNNaNNaNNaNNaNNaN
65GO:0044273sulfur compound catabolic processTrue65.0NaNNaNNaNNaNNaNNaNNaNNaN
66GO:0030246carbohydrate bindingFalse66.013.0NaNNaNNaNNaNNaNNaNNaN
67GO:0005996monosaccharide metabolic processTrue67.0NaNNaNNaNNaNNaNNaNNaNNaN
68GO:0008061chitin bindingFalse68.014.0NaNNaNNaNNaNNaNNaNNaN
69GO:0031982vesicleFalse69.0NaNNaNNaNNaNNaNNaNNaNNaN
70GO:0001573ganglioside metabolic processTrue70.0NaNNaNNaNNaNNaNNaNNaNNaN
71GO:0036508protein alpha-1,2-demannosylationTrue71.0NaNNaNNaNNaNNaNNaNNaNNaN
72GO:0036507protein demannosylationTrue72.0NaNNaNNaNNaNNaNNaNNaNNaN
73GO:1901072glucosamine-containing compound catabolic processTrue73.0NaNNaNNaNNaNNaNNaNNaNNaN
74GO:1903561extracellular vesicleTrue74.0NaNNaNNaNNaNNaNNaNNaNNaN
75GO:0065010extracellular membrane-bounded organelleTrue75.0NaNNaNNaNNaNNaNNaNNaNNaN
76GO:0043230extracellular organelleTrue76.0NaNNaNNaNNaNNaNNaNNaNNaN
77CL:0000775neutrophilFalse77.0NaNNaNNaNNaNNaNNaNNaNNaN
78CL:0000094granulocyteTrue78.0NaNNaNNaNNaNNaNNaNNaNNaN
79CL:0000766myeloid leukocyteTrue79.0NaNNaNNaNNaNNaNNaNNaNNaN
80CL:0000738leukocyteTrue80.0NaNNaNNaNNaNNaNNaNNaNNaN
81CL:0002242nucleate cellTrue81.0NaNNaNNaNNaNNaNNaNNaNNaN
82CL:0000219motile cellTrue82.0NaNNaNNaNNaNNaNNaNNaNNaN
83UBERON:0002405immune systemTrue83.0NaNNaNNaNNaNNaNNaNNaNNaN
84GO:0030141secretory granuleTrue84.0NaNNaNNaNNaNNaNNaNNaNNaN
85UBERON:0015203non-connected functional systemTrue85.0NaNNaNNaNNaNNaNNaNNaNNaN
86UBERON:0034923disconnected anatomical groupTrue86.0NaNNaNNaNNaNNaNNaNNaNNaN
87GO:1904382mannose trimming involved in glycoprotein ERAD pathwayTrue87.019.0NaNNaNNaNNaNNaNNaNNaN
88GO:0097466ubiquitin-dependent glycoprotein ERAD pathwayTrue88.067.0NaNNaNNaNNaNNaNNaNNaN
89GO:0046477glycosylceramide catabolic processTrue89.042.0NaNNaNNaNNaNNaNNaNNaN
90GO:0035977protein deglycosylation involved in glycoprotein catabolic processTrue90.0NaNNaNNaNNaNNaNNaNNaNNaN
91GO:0004558alpha-1,4-glucosidase activityTrue91.020.0NaNNaNNaNNaNNaNNaNNaN
92GO:0004563beta-N-acetylhexosaminidase activityTrue92.035.016.0NaNNaNNaNNaNNaNNaN
93GO:0004565beta-galactosidase activityTrue93.016.0NaNNaNNaNNaNNaNNaNNaN
94GO:0008422beta-glucosidase activityTrue94.017.011.0NaNNaNNaNNaNNaNNaN
95GO:0004556alpha-amylase activityTrue95.018.05.0NaNNaNNaNNaNNaNNaN
96GO:0016137glycoside metabolic processTrue96.0NaNNaNNaNNaNNaNNaNNaNNaN
97GO:0005615extracellular spaceTrue97.065.0NaNNaNNaNNaNNaN77.0NaN
98GO:0042582azurophil granuleTrue98.0NaNNaNNaNNaNNaNNaNNaNNaN
99GO:0005766primary lysosomeTrue99.0NaNNaNNaNNaNNaNNaNNaNNaN
100GO:0044248cellular catabolic processTrue100.0NaNNaNNaNNaNNaNNaNNaNNaN
101GO:1901071glucosamine-containing compound metabolic processTrue101.0NaNNaNNaNNaNNaNNaNNaNNaN
102GO:0070062extracellular exosomeTrue102.023.0NaNNaNNaNNaNNaN64.0NaN
103CL:0000763myeloid cellTrue103.0NaNNaNNaNNaNNaNNaNNaNNaN
104CL:0000081blood cellTrue104.0NaNNaNNaNNaNNaNNaNNaNNaN
105CL:0000988hematopoietic cellTrue105.0NaNNaNNaNNaNNaNNaNNaNNaN
106GO:0046348amino sugar catabolic processTrue106.0NaNNaNNaNNaNNaNNaNNaNNaN
107GO:0099503secretory vesicleTrue107.0NaNNaNNaNNaNNaNNaNNaNNaN
108GO:1901658glycosyl compound catabolic processTrue108.0NaNNaNNaNNaNNaNNaNNaNNaN
109GO:0030200heparan sulfate proteoglycan catabolic processTrue109.027.0NaNNaNNaNNaNNaNNaNNaN
110GO:0006013mannose metabolic processTrue110.025.0NaNNaNNaNNaNNaNNaNNaN
111GO:1904587response to glycoproteinTrue111.0NaNNaNNaNNaNNaNNaNNaNNaN
112GO:0034774secretory granule lumenTrue112.0NaNNaNNaNNaNNaNNaNNaNNaN
113GO:0060205cytoplasmic vesicle lumenTrue113.0NaNNaNNaNNaNNaNNaNNaNNaN
114GO:0012505endomembrane systemTrue114.0NaNNaNNaNNaNNaNNaNNaNNaN
115GO:0031983vesicle lumenTrue115.0NaNNaNNaNNaNNaNNaNNaNNaN
116GO:0035578azurophil granule lumenTrue116.028.0NaNNaNNaNNaNNaNNaNNaN
117GO:0006029proteoglycan metabolic processTrue117.0NaNNaNNaNNaNNaNNaNNaNNaN
118GO:0030207chondroitin sulfate catabolic processTrue118.031.0NaNNaNNaNNaNNaNNaNNaN
119GO:0046352disaccharide catabolic processTrue119.0NaNNaNNaNNaNNaNNaNNaNNaN
120GO:0052795exo-alpha-(2->6)-sialidase activityTrue120.033.0NaNNaNNaNNaNNaNNaNNaN
121GO:0052794exo-alpha-(2->3)-sialidase activityTrue121.030.0NaNNaNNaNNaNNaNNaNNaN
122GO:0052796exo-alpha-(2->8)-sialidase activityTrue122.034.0NaNNaNNaNNaNNaNNaNNaN
123GO:0004308exo-alpha-sialidase activityTrue123.032.0NaNNaNNaNNaNNaNNaNNaN
124GO:0004336galactosylceramidase activityTrue124.029.013.0NaNNaNNaNNaNNaNNaN
125GO:0016997alpha-sialidase activityTrue125.073.0NaNNaNNaNNaNNaNNaNNaN
126GO:0004568chitinase activityTrue126.036.08.0NaNNaNNaNNaNNaNNaN
127GO:0044245polysaccharide digestionFalse127.037.0NaNNaNNaNNaNNaNNaNNaN
128GO:0030167proteoglycan catabolic processTrue128.0NaNNaNNaNNaNNaNNaNNaNNaN
129GO:0006040amino sugar metabolic processTrue129.0NaNNaNNaNNaNNaNNaNNaNNaN
130GO:0006677glycosylceramide metabolic processTrue130.0NaNNaNNaNNaNNaNNaNNaNNaN
131GO:0000272polysaccharide catabolic processTrue131.069.0NaNNaNNaNNaNNaNNaNNaN
132GO:0031410cytoplasmic vesicleTrue132.0NaNNaNNaNNaNNaNNaNNaNNaN
133GO:0097708intracellular vesicleTrue133.0NaNNaNNaNNaNNaNNaNNaNNaN
134GO:0070085glycosylationTrue134.0NaNNaNNaNNaNNaNNaNNaNNaN
135GO:0044255cellular lipid metabolic processTrue135.0NaNNaNNaNNaNNaNNaNNaNNaN
136GO:0019318hexose metabolic processTrue136.0NaNNaNNaNNaNNaNNaNNaNNaN
137GO:0006486protein glycosylationTrue137.039.0NaNNaNNaNNaNNaNNaNNaN
138GO:0043413macromolecule glycosylationTrue138.0NaNNaNNaNNaNNaNNaNNaNNaN
139GO:0032450maltose alpha-glucosidase activityTrue139.041.0NaNNaNNaNNaNNaNNaNNaN
140GO:0036510trimming of terminal mannose on C branchTrue140.044.0NaNNaNNaNNaNNaNNaNNaN
141GO:1904381Golgi apparatus mannose trimmingTrue141.045.0NaNNaNNaNNaNNaNNaNNaN
142GO:0071633dihydroceramidase activityTrue142.047.0NaNNaNNaNNaNNaNNaNNaN
143GO:0000023maltose metabolic processTrue143.077.0NaNNaNNaNNaNNaNNaNNaN
144GO:0004566beta-glucuronidase activityTrue144.040.0NaNNaNNaNNaNNaNNaNNaN
145GO:0102148N-acetyl-beta-D-galactosaminidase activityTrue145.046.0NaNNaNNaNNaNNaNNaNNaN
146GO:0004348glucosylceramidase activityTrue146.043.012.0NaNNaNNaNNaNNaNNaN
147GO:0007342fusion of sperm to egg plasma membrane involved in single fertilizationFalse147.048.0NaNNaNNaNNaNNaNNaNNaN
148GO:1901657glycosyl compound metabolic processTrue148.0NaNNaNNaNNaNNaNNaNNaNNaN
149GO:0045026plasma membrane fusionTrue149.0NaNNaNNaNNaNNaNNaNNaNNaN
150GO:0030209dermatan sulfate catabolic processTrue150.051.0NaNNaNNaNNaNNaNNaNNaN
151GO:0052782amino disaccharide catabolic processTrue151.0NaNNaNNaNNaNNaNNaNNaNNaN
152GO:1904380endoplasmic reticulum mannose trimmingTrue152.053.0NaNNaNNaNNaNNaNNaNNaN
153GO:0031404chloride ion bindingFalse153.054.0NaNNaNNaNNaNNaNNaNNaN
154GO:0007338single fertilizationTrue154.0NaNNaNNaNNaNNaNNaNNaNNaN
155GO:0009101glycoprotein biosynthetic processTrue155.0NaNNaNNaNNaNNaNNaNNaNNaN
156GO:0043603amide metabolic processTrue156.0NaNNaNNaNNaNNaNNaNNaNNaN
157GO:0102121ceramidase activityTrue157.056.0NaNNaNNaNNaNNaNNaNNaN
158GO:0006629lipid metabolic processTrue158.0NaNNaNNaNNaNNaNNaNNaNNaN
159CL:0000096mature neutrophilTrue159.0NaNNaNNaNNaNNaNNaNNaNNaN
160CL:0000234phagocyteTrue160.0NaNNaNNaNNaNNaNNaNNaNNaN
161CL:0000473defensive cellTrue161.0NaNNaNNaNNaNNaNNaNNaNNaN
162GO:0009566fertilizationTrue162.0NaNNaNNaNNaNNaNNaNNaNNaN
163GO:0017040N-acylsphingosine amidohydrolase activityTrue163.058.01.0NaNNaNNaNNaNNaNNaN
164GO:1901137carbohydrate derivative biosynthetic processTrue164.0NaNNaNNaNNaNNaNNaNNaNNaN
165GO:0005509calcium ion bindingFalse165.060.0NaNNaNNaNNaNNaN45.0NaN
166GO:0001669acrosomal vesicleTrue166.055.0NaNNaNNaNNaNNaNNaNNaN
167GO:0044322endoplasmic reticulum quality control compartmentTrue167.061.0NaNNaNNaNNaNNaNNaNNaN
168GO:0003674molecular_functionTrue168.0NaNNaNNaNNaNNaNNaN47.0NaN
169CL:0000325stuff accumulating cellTrue169.0NaNNaNNaNNaNNaNNaNNaNNaN
170GO:0030205dermatan sulfate metabolic processTrue170.0NaNNaNNaNNaNNaNNaNNaNNaN
171GO:0052779amino disaccharide metabolic processTrue171.0NaNNaNNaNNaNNaNNaNNaNNaN
172GO:0035580specific granule lumenTrue172.063.0NaNNaNNaNNaNNaNNaNNaN
173GO:0030163protein catabolic processTrue173.0NaNNaNNaNNaNNaNNaNNaNNaN
174GO:0030204chondroitin sulfate metabolic processTrue174.0NaNNaNNaNNaNNaNNaNNaNNaN
175GO:0019082viral protein processingFalse175.064.0NaNNaNNaNNaNNaNNaNNaN
176GO:0006790sulfur compound metabolic processTrue176.0NaNNaNNaNNaNNaNNaNNaNNaN
177GO:0006807nitrogen compound metabolic processTrue177.0NaNNaNNaNNaNNaNNaNNaNNaN
178GO:0005976polysaccharide metabolic processTrue178.0NaNNaNNaNNaNNaNNaNNaNNaN
179GO:0071493cellular response to UV-BFalse179.066.0NaNNaNNaNNaNNaNNaNNaN
180GO:0050655dermatan sulfate proteoglycan metabolic processTrue180.0NaNNaNNaNNaNNaNNaNNaNNaN
181GO:0006683galactosylceramide catabolic processTrue181.082.0NaNNaNNaNNaNNaNNaNNaN
182GO:0006680glucosylceramide catabolic processTrue182.084.0NaNNaNNaNNaNNaNNaNNaN
183GO:0036511trimming of first mannose on A branchTrue183.074.0NaNNaNNaNNaNNaNNaNNaN
184GO:0036509trimming of terminal mannose on B branchTrue184.087.0NaNNaNNaNNaNNaNNaNNaN
185GO:0036512trimming of second mannose on A branchTrue185.071.0NaNNaNNaNNaNNaNNaNNaN
186GO:0046373L-arabinose metabolic processTrue186.075.0NaNNaNNaNNaNNaNNaNNaN
187GO:0019566arabinose metabolic processTrue187.0NaNNaNNaNNaNNaNNaNNaNNaN
188GO:0004572mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activityTrue188.079.0NaNNaNNaNNaNNaNNaNNaN
189GO:0004339glucan 1,4-alpha-glucosidase activityTrue189.080.0NaNNaNNaNNaNNaNNaNNaN
190GO:0004557alpha-galactosidase activityTrue190.088.0NaNNaNNaNNaNNaNNaNNaN
191GO:0004560alpha-L-fucosidase activityTrue191.081.0NaNNaNNaNNaNNaNNaNNaN
192GO:0033906hyaluronoglucuronidase activityTrue192.089.0NaNNaNNaNNaNNaNNaNNaN
193GO:0030305heparanase activityTrue193.068.0NaNNaNNaNNaNNaNNaNNaN
194GO:0017042glycosylceramidase activityTrue194.072.0NaNNaNNaNNaNNaNNaNNaN
195GO:1905379beta-N-acetylhexosaminidase complexFalse195.083.0NaNNaNNaNNaNNaNNaNNaN
196GO:0015928fucosidase activityTrue196.0NaNNaNNaNNaNNaNNaNNaNNaN
197GO:0046556alpha-L-arabinofuranosidase activityTrue197.085.0NaNNaNNaNNaNNaNNaNNaN
198GO:0004649poly(ADP-ribose) glycohydrolase activityTrue198.078.0NaNNaNNaNNaNNaNNaNNaN
199GO:0050654chondroitin sulfate proteoglycan metabolic processTrue199.0NaNNaNNaNNaNNaNNaNNaNNaN
200GO:0046512sphingosine biosynthetic processTrue200.090.0NaNNaNNaNNaNNaNNaNNaN
201GO:0046520sphingoid biosynthetic processTrue201.0NaNNaNNaNNaNNaNNaNNaNNaN
202GO:0009251glucan catabolic processTrue202.0NaNNaNNaNNaNNaNNaNNaNNaN
203GO:0030433ubiquitin-dependent ERAD pathwayTrue203.0NaNNaNNaNNaNNaNNaNNaNNaN
204GO:0051651maintenance of location in cellFalseNaN52.0NaNNaNNaNNaNNaNNaNNaN
205GO:0007040lysosome organizationFalseNaN57.0NaNNaNNaNNaNNaNNaNNaN
206GO:0016799hydrolase activity, hydrolyzing N-glycosyl compoundsFalseNaN86.0NaNNaNNaNNaNNaNNaNNaN
207GO:0050885neuromuscular process controlling balanceFalseNaN91.0NaNNaNNaNNaNNaNNaNNaN
208GO:1904154positive regulation of retrograde protein transport, ER to cytosolFalseNaN92.0NaNNaNNaNNaNNaNNaNNaN
209GO:0042552myelinationFalseNaN93.0NaNNaNNaNNaNNaNNaNNaN
210the genes in this list share functions involving glycoprotein and carbohydrate metabolic processes and structural functions related to extracellular matrix organization. enriched terms include: dihydroceramidase activityNoneFalseNaNNaN0.0NaNNaNNaNNaNNaNNaN
211GO:0061463O-acetyl-ADP-ribose deacetylase activityFalseNaNNaN2.0NaNNaNNaNNaNNaNNaN
212GO:00041344-alpha-glucanotransferase activityFalseNaNNaN3.0NaNNaNNaNNaNNaNNaN
213GO:0004135amylo-alpha-1,6-glucosidase activityFalseNaNNaN4.0NaNNaNNaNNaNNaNNaN
214hyaluronic acid binding activityNoneFalseNaNNaN6.0NaNNaNNaNNaNNaNNaN
215GO:0008843endochitinase activityFalseNaNNaN9.0NaNNaNNaNNaNNaNNaN
216clathrin heavy chain binding activityNoneFalseNaNNaN10.0NaNNaNNaNNaNNaNNaN
217GO:0008375acetylglucosaminyltransferase activityFalseNaNNaN15.0NaNNaNNaNNaNNaNNaN
218identical protein binding activityNoneFalseNaNNaN17.0NaNNaNNaNNaNNaNNaN
219syndecan binding activityNoneFalseNaNNaN18.0NaNNaNNaNNaNNaNNaN
220heparan sulfate proteoglycan binding activityNoneFalseNaNNaN19.0NaNNaNNaNNaNNaNNaN
221GO:0004567beta-mannosidase activityFalseNaNNaN21.0NaNNaNNaNNaNNaNNaN
222glycoside hydrolase activityNoneFalseNaNNaNNaNNaN1.00.0NaNNaNNaN
223GO:0005980glycogen catabolic processFalseNaNNaNNaN1.05.0NaNNaNNaNNaN
224acid hydrolase activityNoneFalseNaNNaNNaNNaN8.0NaNNaNNaNNaN
225chitin catabolic process\\n\\nmechanism: these genes participate in the lysosomal degradation of various carbohydrate molecules, breaking them down into their component parts for further processing by the cellNoneFalseNaNNaNNaNNaN9.0NaNNaNNaNNaN
226GO:0005783endoplasmic reticulumFalseNaNNaNNaNNaNNaN5.0NaN28.0NaN
227catabolism of carbohydrateNoneFalseNaNNaNNaNNaNNaN6.0NaNNaNNaN
228MONDO:0019249NoneFalseNaNNaNNaNNaNNaN7.0NaNNaNNaN
229GO:0007155cell adhesionFalseNaNNaNNaNNaNNaNNaNNaN0.0NaN
230GO:0007399nervous system developmentFalseNaNNaNNaNNaNNaNNaNNaN1.0NaN
231GO:0009986cell surfaceFalseNaNNaNNaNNaNNaNNaNNaN2.0NaN
232GO:0046872metal ion bindingFalseNaNNaNNaNNaNNaNNaNNaN3.0NaN
233GO:0008270zinc ion bindingFalseNaNNaNNaNNaNNaNNaNNaN4.0NaN
234GO:0043066negative regulation of apoptotic processFalseNaNNaNNaNNaNNaNNaNNaN5.0NaN
235GO:0045087innate immune responseFalseNaNNaNNaNNaNNaNNaNNaN6.0NaN
236GO:0042803protein homodimerization activityFalseNaNNaNNaNNaNNaNNaNNaN7.0NaN
237GO:0005654nucleoplasmFalseNaNNaNNaNNaNNaNNaNNaN8.0NaN
238GO:0019899enzyme bindingFalseNaNNaNNaNNaNNaNNaNNaN9.0NaN
239GO:0006954inflammatory responseFalseNaNNaNNaNNaNNaNNaNNaN10.0NaN
240GO:0008284positive regulation of cell population proliferationFalseNaNNaNNaNNaNNaNNaNNaN11.0NaN
241GO:0004984olfactory receptor activityFalseNaNNaNNaNNaNNaNNaNNaN12.0NaN
242GO:0016607nuclear speckFalseNaNNaNNaNNaNNaNNaNNaN13.0NaN
243GO:0000785chromatinFalseNaNNaNNaNNaNNaNNaNNaN14.0NaN
244GO:0051301cell divisionFalseNaNNaNNaNNaNNaNNaNNaN15.0NaN
245GO:0042802identical protein bindingFalseNaNNaNNaNNaNNaNNaNNaN16.0NaN
246GO:0045944positive regulation of transcription by RNA polymerase IIFalseNaNNaNNaNNaNNaNNaNNaN17.0NaN
247GO:0106310protein serine kinase activityFalseNaNNaNNaNNaNNaNNaNNaN18.0NaN
248GO:0043231intracellular membrane-bounded organelleFalseNaNNaNNaNNaNNaNNaNNaN19.0NaN
249GO:0043025neuronal cell bodyFalseNaNNaNNaNNaNNaNNaNNaN20.0NaN
250GO:0010628positive regulation of gene expressionFalseNaNNaNNaNNaNNaNNaNNaN21.0NaN
251GO:0016020membraneFalseNaNNaNNaNNaNNaNNaNNaN22.0NaN
252GO:0008150biological_processFalseNaNNaNNaNNaNNaNNaNNaN23.0NaN
253GO:0006508proteolysisFalseNaNNaNNaNNaNNaNNaNNaN24.0NaN
254GO:0005524ATP bindingFalseNaNNaNNaNNaNNaNNaNNaN25.0NaN
255GO:0005856cytoskeletonFalseNaNNaNNaNNaNNaNNaNNaN26.0NaN
256GO:0061630ubiquitin protein ligase activityFalseNaNNaNNaNNaNNaNNaNNaN27.0NaN
257GO:0016567protein ubiquitinationFalseNaNNaNNaNNaNNaNNaNNaN29.0NaN
258GO:0006357regulation of transcription by RNA polymerase IIFalseNaNNaNNaNNaNNaNNaNNaN30.0NaN
259GO:0030154cell differentiationFalseNaNNaNNaNNaNNaNNaNNaN31.0NaN
260GO:0003723RNA bindingFalseNaNNaNNaNNaNNaNNaNNaN32.0NaN
261GO:0016887ATP hydrolysis activityFalseNaNNaNNaNNaNNaNNaNNaN33.0NaN
262GO:0006355regulation of DNA-templated transcriptionFalseNaNNaNNaNNaNNaNNaNNaN34.0NaN
263GO:0000981DNA-binding transcription factor activity, RNA polymerase II-specificFalseNaNNaNNaNNaNNaNNaNNaN35.0NaN
264GO:0005765lysosomal membraneFalseNaNNaNNaNNaNNaNNaNNaN36.0NaN
265GO:0005739mitochondrionFalseNaNNaNNaNNaNNaNNaNNaN37.0NaN
266GO:0005102signaling receptor bindingFalseNaNNaNNaNNaNNaNNaNNaN38.0NaN
267GO:0044877protein-containing complex bindingFalseNaNNaNNaNNaNNaNNaNNaN39.0NaN
268GO:0048471perinuclear region of cytoplasmFalseNaNNaNNaNNaNNaNNaNNaN40.0NaN
269GO:0006915apoptotic processFalseNaNNaNNaNNaNNaNNaNNaN41.0NaN
270GO:0005743mitochondrial inner membraneFalseNaNNaNNaNNaNNaNNaNNaN43.0NaN
271GO:0009897external side of plasma membraneFalseNaNNaNNaNNaNNaNNaNNaN44.0NaN
272GO:0003682chromatin bindingFalseNaNNaNNaNNaNNaNNaNNaN46.0NaN
273GO:0002250adaptive immune responseFalseNaNNaNNaNNaNNaNNaNNaN48.0NaN
274GO:0008285negative regulation of cell population proliferationFalseNaNNaNNaNNaNNaNNaNNaN49.0NaN
275GO:0045892negative regulation of DNA-templated transcriptionFalseNaNNaNNaNNaNNaNNaNNaN50.0NaN
276GO:0001228DNA-binding transcription activator activity, RNA polymerase II-specificFalseNaNNaNNaNNaNNaNNaNNaN51.0NaN
277GO:0050911detection of chemical stimulus involved in sensory perception of smellFalseNaNNaNNaNNaNNaNNaNNaN52.0NaN
278GO:0062023collagen-containing extracellular matrixFalseNaNNaNNaNNaNNaNNaNNaN53.0NaN
279GO:0035556intracellular signal transductionFalseNaNNaNNaNNaNNaNNaNNaN54.0NaN
280GO:0005925focal adhesionFalseNaNNaNNaNNaNNaNNaNNaN55.0NaN
281GO:0006468protein phosphorylationFalseNaNNaNNaNNaNNaNNaNNaN56.0NaN
282GO:0004674protein serine/threonine kinase activityFalseNaNNaNNaNNaNNaNNaNNaN57.0NaN
283GO:0005886plasma membraneFalseNaNNaNNaNNaNNaNNaNNaN58.0NaN
284GO:0006955immune responseFalseNaNNaNNaNNaNNaNNaNNaN59.0NaN
285GO:0005575cellular_componentFalseNaNNaNNaNNaNNaNNaNNaN60.0NaN
286GO:0007165signal transductionFalseNaNNaNNaNNaNNaNNaNNaN61.0NaN
287GO:0005813centrosomeFalseNaNNaNNaNNaNNaNNaNNaN62.0NaN
288GO:0005730nucleolusFalseNaNNaNNaNNaNNaNNaNNaN63.0NaN
289GO:0007186G protein-coupled receptor signaling pathwayFalseNaNNaNNaNNaNNaNNaNNaN65.0NaN
290GO:0004930G protein-coupled receptor activityFalseNaNNaNNaNNaNNaNNaNNaN66.0NaN
291GO:1990837sequence-specific double-stranded DNA bindingFalseNaNNaNNaNNaNNaNNaNNaN67.0NaN
292GO:0015031protein transportFalseNaNNaNNaNNaNNaNNaNNaN68.0NaN
293GO:0019901protein kinase bindingFalseNaNNaNNaNNaNNaNNaNNaN69.0NaN
294GO:0005829cytosolFalseNaNNaNNaNNaNNaNNaNNaN70.0NaN
295GO:0000978RNA polymerase II cis-regulatory region sequence-specific DNA bindingFalseNaNNaNNaNNaNNaNNaNNaN71.0NaN
296GO:0045893positive regulation of DNA-templated transcriptionFalseNaNNaNNaNNaNNaNNaNNaN72.0NaN
297GO:0005737cytoplasmFalseNaNNaNNaNNaNNaNNaNNaN73.0NaN
298GO:0016324apical plasma membraneFalseNaNNaNNaNNaNNaNNaNNaN74.0NaN
299GO:0007283spermatogenesisFalseNaNNaNNaNNaNNaNNaNNaN75.0NaN
300GO:0005794Golgi apparatusFalseNaNNaNNaNNaNNaNNaNNaN76.0NaN
301GO:0003677DNA bindingFalseNaNNaNNaNNaNNaNNaNNaN78.0NaN
302GO:0003700DNA-binding transcription factor activityFalseNaNNaNNaNNaNNaNNaNNaN79.0NaN
303GO:0098978glutamatergic synapseFalseNaNNaNNaNNaNNaNNaNNaN80.0NaN
304GO:0005759mitochondrial matrixFalseNaNNaNNaNNaNNaNNaNNaN81.0NaN
305GO:0000122negative regulation of transcription by RNA polymerase IIFalseNaNNaNNaNNaNNaNNaNNaN82.0NaN
306GO:0032991protein-containing complexFalseNaNNaNNaNNaNNaNNaNNaN83.0NaN
307GO:0045202synapseFalseNaNNaNNaNNaNNaNNaNNaN84.0NaN
308GO:0005789endoplasmic reticulum membraneFalseNaNNaNNaNNaNNaNNaNNaN85.0NaN
309GO:0005525GTP bindingFalseNaNNaNNaNNaNNaNNaNNaN86.0NaN
310GO:0000139Golgi membraneFalseNaNNaNNaNNaNNaNNaNNaN87.0NaN
311GO:0016604nuclear bodyFalseNaNNaNNaNNaNNaNNaNNaN88.0NaN
312GO:0030425dendriteFalseNaNNaNNaNNaNNaNNaNNaN89.0NaN
313GO:0005634nucleusFalseNaNNaNNaNNaNNaNNaNNaN90.0NaN
314GO:0051787misfolded protein bindingFalseNaNNaNNaN3.0NaNNaNNaNNaNNaN
315GO:0036503ERAD pathwayFalseNaNNaNNaN4.0NaNNaNNaNNaNNaN
316glycosaminoglycan hydrolysisNoneFalseNaNNaNNaN5.0NaNNaNNaNNaNNaN
317heparan sulfate hydrolysisNoneFalseNaNNaNNaN6.0NaNNaNNaNNaNNaN
318cell surface hyaluronidase.\\nhpyothesis: the genes listed serve key roles in the degradation of polysaccharides and glycoproteins, the recognition of misfolded proteins and their subsequent degradation by endoplasmic reticulum-associated degradation, the hydrolysis of glycosaminoglycans, and the hydrolysis of heparan sulfate for the maintenance of cell proteins and structureNoneFalseNaNNaNNaN7.0NaNNaNNaNNaNNaN
319carbohydrate digestion and absorption; glycosaminoglycan and glycan metabolism; lysosomalNoneFalseNaNNaNNaNNaNNaNNaNNaNNaN0.0
320GO:0005777peroxisomeFalseNaNNaNNaNNaNNaNNaNNaNNaN1.0
321and catabolic processes; digitNoneFalseNaNNaNNaNNaNNaNNaNNaNNaN2.0
322skeletalNoneFalseNaNNaNNaNNaNNaNNaNNaNNaN3.0
323GO:0035108limb morphogenesisFalseNaNNaNNaNNaNNaNNaNNaNNaN4.0
\n", - "
" - ], - "text/plain": [ - " id \\\n", - "0 GO:0004553 \n", - "1 GO:0016798 \n", - "2 GO:0005975 \n", - "3 GO:0016787 \n", - "4 GO:1901136 \n", - "5 GO:0009311 \n", - "6 GO:1901135 \n", - "7 GO:0003824 \n", - "8 GO:0006026 \n", - "9 GO:0009313 \n", - "10 GO:0015929 \n", - "11 GO:0015923 \n", - "12 GO:0016052 \n", - "13 GO:1901575 \n", - "14 GO:0004559 \n", - "15 GO:0015926 \n", - "16 GO:0019377 \n", - "17 GO:0046514 \n", - "18 GO:0046466 \n", - "19 GO:0006022 \n", - "20 GO:0009056 \n", - "21 GO:1901565 \n", - "22 GO:0046479 \n", - "23 GO:0006027 \n", - "24 GO:0030149 \n", - "25 GO:0009100 \n", - "26 GO:0006516 \n", - "27 GO:0043202 \n", - "28 GO:0005775 \n", - "29 GO:0006517 \n", - "30 GO:0009057 \n", - "31 GO:0008152 \n", - "32 GO:0015924 \n", - "33 GO:0003796 \n", - "34 GO:0030203 \n", - "35 GO:0006672 \n", - "36 GO:0006687 \n", - "37 GO:0005764 \n", - "38 GO:0000323 \n", - "39 GO:0030214 \n", - "40 GO:0006664 \n", - "41 GO:1903509 \n", - "42 GO:0005773 \n", - "43 GO:0006643 \n", - "44 GO:0004415 \n", - "45 GO:0061783 \n", - "46 GO:0006665 \n", - "47 GO:0044242 \n", - "48 GO:0005576 \n", - "49 GO:0071704 \n", - "50 GO:1903510 \n", - "51 GO:0006689 \n", - "52 GO:0004571 \n", - "53 GO:0090599 \n", - "54 GO:0015925 \n", - "55 GO:0030212 \n", - "56 GO:0005984 \n", - "57 GO:0044238 \n", - "58 GO:0016139 \n", - "59 GO:0016042 \n", - "60 GO:0006032 \n", - "61 GO:0006030 \n", - "62 GO:0016160 \n", - "63 GO:0006491 \n", - "64 GO:1901564 \n", - "65 GO:0044273 \n", - "66 GO:0030246 \n", - "67 GO:0005996 \n", - "68 GO:0008061 \n", - "69 GO:0031982 \n", - "70 GO:0001573 \n", - "71 GO:0036508 \n", - "72 GO:0036507 \n", - "73 GO:1901072 \n", - "74 GO:1903561 \n", - "75 GO:0065010 \n", - "76 GO:0043230 \n", - "77 CL:0000775 \n", - "78 CL:0000094 \n", - "79 CL:0000766 \n", - "80 CL:0000738 \n", - "81 CL:0002242 \n", - "82 CL:0000219 \n", - "83 UBERON:0002405 \n", - "84 GO:0030141 \n", - "85 UBERON:0015203 \n", - "86 UBERON:0034923 \n", - "87 GO:1904382 \n", - "88 GO:0097466 \n", - "89 GO:0046477 \n", - "90 GO:0035977 \n", - "91 GO:0004558 \n", - "92 GO:0004563 \n", - "93 GO:0004565 \n", - "94 GO:0008422 \n", - "95 GO:0004556 \n", - "96 GO:0016137 \n", - "97 GO:0005615 \n", - "98 GO:0042582 \n", - "99 GO:0005766 \n", - "100 GO:0044248 \n", - "101 GO:1901071 \n", - "102 GO:0070062 \n", - "103 CL:0000763 \n", - "104 CL:0000081 \n", - "105 CL:0000988 \n", - "106 GO:0046348 \n", - "107 GO:0099503 \n", - "108 GO:1901658 \n", - "109 GO:0030200 \n", - "110 GO:0006013 \n", - "111 GO:1904587 \n", - "112 GO:0034774 \n", - "113 GO:0060205 \n", - "114 GO:0012505 \n", - "115 GO:0031983 \n", - "116 GO:0035578 \n", - "117 GO:0006029 \n", - "118 GO:0030207 \n", - "119 GO:0046352 \n", - "120 GO:0052795 \n", - "121 GO:0052794 \n", - "122 GO:0052796 \n", - "123 GO:0004308 \n", - "124 GO:0004336 \n", - "125 GO:0016997 \n", - "126 GO:0004568 \n", - "127 GO:0044245 \n", - "128 GO:0030167 \n", - "129 GO:0006040 \n", - "130 GO:0006677 \n", - "131 GO:0000272 \n", - "132 GO:0031410 \n", - "133 GO:0097708 \n", - "134 GO:0070085 \n", - "135 GO:0044255 \n", - "136 GO:0019318 \n", - "137 GO:0006486 \n", - "138 GO:0043413 \n", - "139 GO:0032450 \n", - "140 GO:0036510 \n", - "141 GO:1904381 \n", - "142 GO:0071633 \n", - "143 GO:0000023 \n", - "144 GO:0004566 \n", - "145 GO:0102148 \n", - "146 GO:0004348 \n", - "147 GO:0007342 \n", - "148 GO:1901657 \n", - "149 GO:0045026 \n", - "150 GO:0030209 \n", - "151 GO:0052782 \n", - "152 GO:1904380 \n", - "153 GO:0031404 \n", - "154 GO:0007338 \n", - "155 GO:0009101 \n", - "156 GO:0043603 \n", - "157 GO:0102121 \n", - "158 GO:0006629 \n", - "159 CL:0000096 \n", - "160 CL:0000234 \n", - "161 CL:0000473 \n", - "162 GO:0009566 \n", - "163 GO:0017040 \n", - "164 GO:1901137 \n", - "165 GO:0005509 \n", - "166 GO:0001669 \n", - "167 GO:0044322 \n", - "168 GO:0003674 \n", - "169 CL:0000325 \n", - "170 GO:0030205 \n", - "171 GO:0052779 \n", - "172 GO:0035580 \n", - "173 GO:0030163 \n", - "174 GO:0030204 \n", - "175 GO:0019082 \n", - "176 GO:0006790 \n", - "177 GO:0006807 \n", - "178 GO:0005976 \n", - "179 GO:0071493 \n", - "180 GO:0050655 \n", - "181 GO:0006683 \n", - "182 GO:0006680 \n", - "183 GO:0036511 \n", - "184 GO:0036509 \n", - "185 GO:0036512 \n", - "186 GO:0046373 \n", - "187 GO:0019566 \n", - "188 GO:0004572 \n", - "189 GO:0004339 \n", - "190 GO:0004557 \n", - "191 GO:0004560 \n", - "192 GO:0033906 \n", - "193 GO:0030305 \n", - "194 GO:0017042 \n", - "195 GO:1905379 \n", - "196 GO:0015928 \n", - "197 GO:0046556 \n", - "198 GO:0004649 \n", - "199 GO:0050654 \n", - "200 GO:0046512 \n", - "201 GO:0046520 \n", - "202 GO:0009251 \n", - "203 GO:0030433 \n", - "204 GO:0051651 \n", - "205 GO:0007040 \n", - "206 GO:0016799 \n", - "207 GO:0050885 \n", - "208 GO:1904154 \n", - "209 GO:0042552 \n", - "210 the genes in this list share functions involving glycoprotein and carbohydrate metabolic processes and structural functions related to extracellular matrix organization. enriched terms include: dihydroceramidase activity \n", - "211 GO:0061463 \n", - "212 GO:0004134 \n", - "213 GO:0004135 \n", - "214 hyaluronic acid binding activity \n", - "215 GO:0008843 \n", - "216 clathrin heavy chain binding activity \n", - "217 GO:0008375 \n", - "218 identical protein binding activity \n", - "219 syndecan binding activity \n", - "220 heparan sulfate proteoglycan binding activity \n", - "221 GO:0004567 \n", - "222 glycoside hydrolase activity \n", - "223 GO:0005980 \n", - "224 acid hydrolase activity \n", - "225 chitin catabolic process\\n\\nmechanism: these genes participate in the lysosomal degradation of various carbohydrate molecules, breaking them down into their component parts for further processing by the cell \n", - "226 GO:0005783 \n", - "227 catabolism of carbohydrate \n", - "228 MONDO:0019249 \n", - "229 GO:0007155 \n", - "230 GO:0007399 \n", - "231 GO:0009986 \n", - "232 GO:0046872 \n", - "233 GO:0008270 \n", - "234 GO:0043066 \n", - "235 GO:0045087 \n", - "236 GO:0042803 \n", - "237 GO:0005654 \n", - "238 GO:0019899 \n", - "239 GO:0006954 \n", - "240 GO:0008284 \n", - "241 GO:0004984 \n", - "242 GO:0016607 \n", - "243 GO:0000785 \n", - "244 GO:0051301 \n", - "245 GO:0042802 \n", - "246 GO:0045944 \n", - "247 GO:0106310 \n", - "248 GO:0043231 \n", - "249 GO:0043025 \n", - "250 GO:0010628 \n", - "251 GO:0016020 \n", - "252 GO:0008150 \n", - "253 GO:0006508 \n", - "254 GO:0005524 \n", - "255 GO:0005856 \n", - "256 GO:0061630 \n", - "257 GO:0016567 \n", - "258 GO:0006357 \n", - "259 GO:0030154 \n", - "260 GO:0003723 \n", - "261 GO:0016887 \n", - "262 GO:0006355 \n", - "263 GO:0000981 \n", - "264 GO:0005765 \n", - "265 GO:0005739 \n", - "266 GO:0005102 \n", - "267 GO:0044877 \n", - "268 GO:0048471 \n", - "269 GO:0006915 \n", - "270 GO:0005743 \n", - "271 GO:0009897 \n", - "272 GO:0003682 \n", - "273 GO:0002250 \n", - "274 GO:0008285 \n", - "275 GO:0045892 \n", - "276 GO:0001228 \n", - "277 GO:0050911 \n", - "278 GO:0062023 \n", - "279 GO:0035556 \n", - "280 GO:0005925 \n", - "281 GO:0006468 \n", - "282 GO:0004674 \n", - "283 GO:0005886 \n", - "284 GO:0006955 \n", - "285 GO:0005575 \n", - "286 GO:0007165 \n", - "287 GO:0005813 \n", - "288 GO:0005730 \n", - "289 GO:0007186 \n", - "290 GO:0004930 \n", - "291 GO:1990837 \n", - "292 GO:0015031 \n", - "293 GO:0019901 \n", - "294 GO:0005829 \n", - "295 GO:0000978 \n", - "296 GO:0045893 \n", - "297 GO:0005737 \n", - "298 GO:0016324 \n", - "299 GO:0007283 \n", - "300 GO:0005794 \n", - "301 GO:0003677 \n", - "302 GO:0003700 \n", - "303 GO:0098978 \n", - "304 GO:0005759 \n", - "305 GO:0000122 \n", - "306 GO:0032991 \n", - "307 GO:0045202 \n", - "308 GO:0005789 \n", - "309 GO:0005525 \n", - "310 GO:0000139 \n", - "311 GO:0016604 \n", - "312 GO:0030425 \n", - "313 GO:0005634 \n", - "314 GO:0051787 \n", - "315 GO:0036503 \n", - "316 glycosaminoglycan hydrolysis \n", - "317 heparan sulfate hydrolysis \n", - "318 cell surface hyaluronidase.\\nhpyothesis: the genes listed serve key roles in the degradation of polysaccharides and glycoproteins, the recognition of misfolded proteins and their subsequent degradation by endoplasmic reticulum-associated degradation, the hydrolysis of glycosaminoglycans, and the hydrolysis of heparan sulfate for the maintenance of cell proteins and structure \n", - "319 carbohydrate digestion and absorption; glycosaminoglycan and glycan metabolism; lysosomal \n", - "320 GO:0005777 \n", - "321 and catabolic processes; digit \n", - "322 skeletal \n", - "323 GO:0035108 \n", - "\n", - " label \\\n", - "0 hydrolase activity, hydrolyzing O-glycosyl compounds \n", - "1 hydrolase activity, acting on glycosyl bonds \n", - "2 carbohydrate metabolic process \n", - "3 hydrolase activity \n", - "4 carbohydrate derivative catabolic process \n", - "5 oligosaccharide metabolic process \n", - "6 carbohydrate derivative metabolic process \n", - "7 catalytic activity \n", - "8 aminoglycan catabolic process \n", - "9 oligosaccharide catabolic process \n", - "10 hexosaminidase activity \n", - "11 mannosidase activity \n", - "12 carbohydrate catabolic process \n", - "13 organic substance catabolic process \n", - "14 alpha-mannosidase activity \n", - "15 glucosidase activity \n", - "16 glycolipid catabolic process \n", - "17 ceramide catabolic process \n", - "18 membrane lipid catabolic process \n", - "19 aminoglycan metabolic process \n", - "20 catabolic process \n", - "21 organonitrogen compound catabolic process \n", - "22 glycosphingolipid catabolic process \n", - "23 glycosaminoglycan catabolic process \n", - "24 sphingolipid catabolic process \n", - "25 glycoprotein metabolic process \n", - "26 glycoprotein catabolic process \n", - "27 lysosomal lumen \n", - "28 vacuolar lumen \n", - "29 protein deglycosylation \n", - "30 macromolecule catabolic process \n", - "31 metabolic process \n", - "32 mannosyl-oligosaccharide mannosidase activity \n", - "33 lysozyme activity \n", - "34 glycosaminoglycan metabolic process \n", - "35 ceramide metabolic process \n", - "36 glycosphingolipid metabolic process \n", - "37 lysosome \n", - "38 lytic vacuole \n", - "39 hyaluronan catabolic process \n", - "40 glycolipid metabolic process \n", - "41 liposaccharide metabolic process \n", - "42 vacuole \n", - "43 membrane lipid metabolic process \n", - "44 hyalurononglucosaminidase activity \n", - "45 peptidoglycan muralytic activity \n", - "46 sphingolipid metabolic process \n", - "47 cellular lipid catabolic process \n", - "48 extracellular region \n", - "49 organic substance metabolic process \n", - "50 mucopolysaccharide metabolic process \n", - "51 ganglioside catabolic process \n", - "52 mannosyl-oligosaccharide 1,2-alpha-mannosidase activity \n", - "53 alpha-glucosidase activity \n", - "54 galactosidase activity \n", - "55 hyaluronan metabolic process \n", - "56 disaccharide metabolic process \n", - "57 primary metabolic process \n", - "58 glycoside catabolic process \n", - "59 lipid catabolic process \n", - "60 chitin catabolic process \n", - "61 chitin metabolic process \n", - "62 amylase activity \n", - "63 N-glycan processing \n", - "64 organonitrogen compound metabolic process \n", - "65 sulfur compound catabolic process \n", - "66 carbohydrate binding \n", - "67 monosaccharide metabolic process \n", - "68 chitin binding \n", - "69 vesicle \n", - "70 ganglioside metabolic process \n", - "71 protein alpha-1,2-demannosylation \n", - "72 protein demannosylation \n", - "73 glucosamine-containing compound catabolic process \n", - "74 extracellular vesicle \n", - "75 extracellular membrane-bounded organelle \n", - "76 extracellular organelle \n", - "77 neutrophil \n", - "78 granulocyte \n", - "79 myeloid leukocyte \n", - "80 leukocyte \n", - "81 nucleate cell \n", - "82 motile cell \n", - "83 immune system \n", - "84 secretory granule \n", - "85 non-connected functional system \n", - "86 disconnected anatomical group \n", - "87 mannose trimming involved in glycoprotein ERAD pathway \n", - "88 ubiquitin-dependent glycoprotein ERAD pathway \n", - "89 glycosylceramide catabolic process \n", - "90 protein deglycosylation involved in glycoprotein catabolic process \n", - "91 alpha-1,4-glucosidase activity \n", - "92 beta-N-acetylhexosaminidase activity \n", - "93 beta-galactosidase activity \n", - "94 beta-glucosidase activity \n", - "95 alpha-amylase activity \n", - "96 glycoside metabolic process \n", - "97 extracellular space \n", - "98 azurophil granule \n", - "99 primary lysosome \n", - "100 cellular catabolic process \n", - "101 glucosamine-containing compound metabolic process \n", - "102 extracellular exosome \n", - "103 myeloid cell \n", - "104 blood cell \n", - "105 hematopoietic cell \n", - "106 amino sugar catabolic process \n", - "107 secretory vesicle \n", - "108 glycosyl compound catabolic process \n", - "109 heparan sulfate proteoglycan catabolic process \n", - "110 mannose metabolic process \n", - "111 response to glycoprotein \n", - "112 secretory granule lumen \n", - "113 cytoplasmic vesicle lumen \n", - "114 endomembrane system \n", - "115 vesicle lumen \n", - "116 azurophil granule lumen \n", - "117 proteoglycan metabolic process \n", - "118 chondroitin sulfate catabolic process \n", - "119 disaccharide catabolic process \n", - "120 exo-alpha-(2->6)-sialidase activity \n", - "121 exo-alpha-(2->3)-sialidase activity \n", - "122 exo-alpha-(2->8)-sialidase activity \n", - "123 exo-alpha-sialidase activity \n", - "124 galactosylceramidase activity \n", - "125 alpha-sialidase activity \n", - "126 chitinase activity \n", - "127 polysaccharide digestion \n", - "128 proteoglycan catabolic process \n", - "129 amino sugar metabolic process \n", - "130 glycosylceramide metabolic process \n", - "131 polysaccharide catabolic process \n", - "132 cytoplasmic vesicle \n", - "133 intracellular vesicle \n", - "134 glycosylation \n", - "135 cellular lipid metabolic process \n", - "136 hexose metabolic process \n", - "137 protein glycosylation \n", - "138 macromolecule glycosylation \n", - "139 maltose alpha-glucosidase activity \n", - "140 trimming of terminal mannose on C branch \n", - "141 Golgi apparatus mannose trimming \n", - "142 dihydroceramidase activity \n", - "143 maltose metabolic process \n", - "144 beta-glucuronidase activity \n", - "145 N-acetyl-beta-D-galactosaminidase activity \n", - "146 glucosylceramidase activity \n", - "147 fusion of sperm to egg plasma membrane involved in single fertilization \n", - "148 glycosyl compound metabolic process \n", - "149 plasma membrane fusion \n", - "150 dermatan sulfate catabolic process \n", - "151 amino disaccharide catabolic process \n", - "152 endoplasmic reticulum mannose trimming \n", - "153 chloride ion binding \n", - "154 single fertilization \n", - "155 glycoprotein biosynthetic process \n", - "156 amide metabolic process \n", - "157 ceramidase activity \n", - "158 lipid metabolic process \n", - "159 mature neutrophil \n", - "160 phagocyte \n", - "161 defensive cell \n", - "162 fertilization \n", - "163 N-acylsphingosine amidohydrolase activity \n", - "164 carbohydrate derivative biosynthetic process \n", - "165 calcium ion binding \n", - "166 acrosomal vesicle \n", - "167 endoplasmic reticulum quality control compartment \n", - "168 molecular_function \n", - "169 stuff accumulating cell \n", - "170 dermatan sulfate metabolic process \n", - "171 amino disaccharide metabolic process \n", - "172 specific granule lumen \n", - "173 protein catabolic process \n", - "174 chondroitin sulfate metabolic process \n", - "175 viral protein processing \n", - "176 sulfur compound metabolic process \n", - "177 nitrogen compound metabolic process \n", - "178 polysaccharide metabolic process \n", - "179 cellular response to UV-B \n", - "180 dermatan sulfate proteoglycan metabolic process \n", - "181 galactosylceramide catabolic process \n", - "182 glucosylceramide catabolic process \n", - "183 trimming of first mannose on A branch \n", - "184 trimming of terminal mannose on B branch \n", - "185 trimming of second mannose on A branch \n", - "186 L-arabinose metabolic process \n", - "187 arabinose metabolic process \n", - "188 mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity \n", - "189 glucan 1,4-alpha-glucosidase activity \n", - "190 alpha-galactosidase activity \n", - "191 alpha-L-fucosidase activity \n", - "192 hyaluronoglucuronidase activity \n", - "193 heparanase activity \n", - "194 glycosylceramidase activity \n", - "195 beta-N-acetylhexosaminidase complex \n", - "196 fucosidase activity \n", - "197 alpha-L-arabinofuranosidase activity \n", - "198 poly(ADP-ribose) glycohydrolase activity \n", - "199 chondroitin sulfate proteoglycan metabolic process \n", - "200 sphingosine biosynthetic process \n", - "201 sphingoid biosynthetic process \n", - "202 glucan catabolic process \n", - "203 ubiquitin-dependent ERAD pathway \n", - "204 maintenance of location in cell \n", - "205 lysosome organization \n", - "206 hydrolase activity, hydrolyzing N-glycosyl compounds \n", - "207 neuromuscular process controlling balance \n", - "208 positive regulation of retrograde protein transport, ER to cytosol \n", - "209 myelination \n", - "210 None \n", - "211 O-acetyl-ADP-ribose deacetylase activity \n", - "212 4-alpha-glucanotransferase activity \n", - "213 amylo-alpha-1,6-glucosidase activity \n", - "214 None \n", - "215 endochitinase activity \n", - "216 None \n", - "217 acetylglucosaminyltransferase activity \n", - "218 None \n", - "219 None \n", - "220 None \n", - "221 beta-mannosidase activity \n", - "222 None \n", - "223 glycogen catabolic process \n", - "224 None \n", - "225 None \n", - "226 endoplasmic reticulum \n", - "227 None \n", - "228 None \n", - "229 cell adhesion \n", - "230 nervous system development \n", - "231 cell surface \n", - "232 metal ion binding \n", - "233 zinc ion binding \n", - "234 negative regulation of apoptotic process \n", - "235 innate immune response \n", - "236 protein homodimerization activity \n", - "237 nucleoplasm \n", - "238 enzyme binding \n", - "239 inflammatory response \n", - "240 positive regulation of cell population proliferation \n", - "241 olfactory receptor activity \n", - "242 nuclear speck \n", - "243 chromatin \n", - "244 cell division \n", - "245 identical protein binding \n", - "246 positive regulation of transcription by RNA polymerase II \n", - "247 protein serine kinase activity \n", - "248 intracellular membrane-bounded organelle \n", - "249 neuronal cell body \n", - "250 positive regulation of gene expression \n", - "251 membrane \n", - "252 biological_process \n", - "253 proteolysis \n", - "254 ATP binding \n", - "255 cytoskeleton \n", - "256 ubiquitin protein ligase activity \n", - "257 protein ubiquitination \n", - "258 regulation of transcription by RNA polymerase II \n", - "259 cell differentiation \n", - "260 RNA binding \n", - "261 ATP hydrolysis activity \n", - "262 regulation of DNA-templated transcription \n", - "263 DNA-binding transcription factor activity, RNA polymerase II-specific \n", - "264 lysosomal membrane \n", - "265 mitochondrion \n", - "266 signaling receptor binding \n", - "267 protein-containing complex binding \n", - "268 perinuclear region of cytoplasm \n", - "269 apoptotic process \n", - "270 mitochondrial inner membrane \n", - "271 external side of plasma membrane \n", - "272 chromatin binding \n", - "273 adaptive immune response \n", - "274 negative regulation of cell population proliferation \n", - "275 negative regulation of DNA-templated transcription \n", - "276 DNA-binding transcription activator activity, RNA polymerase II-specific \n", - "277 detection of chemical stimulus involved in sensory perception of smell \n", - "278 collagen-containing extracellular matrix \n", - "279 intracellular signal transduction \n", - "280 focal adhesion \n", - "281 protein phosphorylation \n", - "282 protein serine/threonine kinase activity \n", - "283 plasma membrane \n", - "284 immune response \n", - "285 cellular_component \n", - "286 signal transduction \n", - "287 centrosome \n", - "288 nucleolus \n", - "289 G protein-coupled receptor signaling pathway \n", - "290 G protein-coupled receptor activity \n", - "291 sequence-specific double-stranded DNA binding \n", - "292 protein transport \n", - "293 protein kinase binding \n", - "294 cytosol \n", - "295 RNA polymerase II cis-regulatory region sequence-specific DNA binding \n", - "296 positive regulation of DNA-templated transcription \n", - "297 cytoplasm \n", - "298 apical plasma membrane \n", - "299 spermatogenesis \n", - "300 Golgi apparatus \n", - "301 DNA binding \n", - "302 DNA-binding transcription factor activity \n", - "303 glutamatergic synapse \n", - "304 mitochondrial matrix \n", - "305 negative regulation of transcription by RNA polymerase II \n", - "306 protein-containing complex \n", - "307 synapse \n", - "308 endoplasmic reticulum membrane \n", - "309 GTP binding \n", - "310 Golgi membrane \n", - "311 nuclear body \n", - "312 dendrite \n", - "313 nucleus \n", - "314 misfolded protein binding \n", - "315 ERAD pathway \n", - "316 None \n", - "317 None \n", - "318 None \n", - "319 None \n", - "320 peroxisome \n", - "321 None \n", - "322 None \n", - "323 limb morphogenesis \n", - "\n", - " redundant standard standard no ontology dav ontological synopsis \\\n", - "0 False 0.0 62.0 14.0 \n", - "1 True 1.0 NaN NaN \n", - "2 False 2.0 0.0 NaN \n", - "3 True 3.0 NaN NaN \n", - "4 False 4.0 NaN NaN \n", - "5 True 5.0 22.0 NaN \n", - "6 True 6.0 NaN NaN \n", - "7 True 7.0 NaN NaN \n", - "8 True 8.0 NaN NaN \n", - "9 True 9.0 1.0 NaN \n", - "10 True 10.0 NaN NaN \n", - "11 True 11.0 NaN NaN \n", - "12 True 12.0 NaN NaN \n", - 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"212 False NaN NaN 3.0 \n", - "213 False NaN NaN 4.0 \n", - "214 False NaN NaN 6.0 \n", - "215 False NaN NaN 9.0 \n", - "216 False NaN NaN 10.0 \n", - "217 False NaN NaN 15.0 \n", - "218 False NaN NaN 17.0 \n", - "219 False NaN NaN 18.0 \n", - "220 False NaN NaN 19.0 \n", - "221 False NaN NaN 21.0 \n", - "222 False NaN NaN NaN \n", - "223 False NaN NaN NaN \n", - "224 False NaN NaN NaN \n", - "225 False NaN NaN NaN \n", - "226 False NaN NaN NaN \n", - "227 False NaN NaN NaN \n", - "228 False NaN NaN NaN \n", - "229 False NaN NaN NaN \n", - "230 False NaN NaN NaN \n", - "231 False NaN NaN NaN \n", - "232 False NaN NaN NaN \n", - "233 False NaN NaN NaN \n", - "234 False NaN NaN NaN \n", - "235 False NaN NaN NaN \n", - "236 False NaN NaN NaN \n", - "237 False NaN NaN NaN \n", - "238 False NaN NaN NaN \n", - "239 False NaN NaN NaN \n", - "240 False NaN NaN NaN \n", - "241 False NaN NaN NaN \n", - "242 False NaN NaN NaN \n", - "243 False NaN NaN NaN \n", - "244 False NaN NaN NaN \n", - "245 False NaN NaN NaN \n", - "246 False NaN NaN NaN \n", - "247 False NaN NaN NaN \n", - "248 False NaN NaN NaN \n", - "249 False NaN NaN NaN \n", - "250 False NaN NaN NaN \n", - "251 False NaN NaN NaN \n", - "252 False NaN NaN NaN \n", - "253 False NaN NaN NaN \n", - "254 False NaN NaN NaN \n", - "255 False NaN NaN NaN \n", - "256 False NaN NaN NaN \n", - "257 False NaN NaN NaN \n", - "258 False NaN NaN NaN \n", - "259 False NaN NaN NaN \n", - "260 False NaN NaN NaN \n", - "261 False NaN NaN NaN \n", - "262 False NaN NaN NaN \n", - "263 False NaN NaN NaN \n", - "264 False NaN NaN NaN \n", - "265 False NaN NaN NaN \n", - "266 False NaN NaN NaN \n", - "267 False NaN NaN NaN \n", - "268 False NaN NaN NaN \n", - "269 False NaN NaN NaN \n", - "270 False NaN NaN NaN \n", - "271 False NaN NaN NaN \n", - "272 False NaN NaN NaN \n", - "273 False NaN NaN NaN \n", - "274 False NaN NaN NaN \n", - "275 False NaN NaN NaN \n", - "276 False NaN NaN NaN \n", - "277 False NaN NaN NaN \n", - "278 False NaN NaN NaN \n", - "279 False NaN NaN NaN \n", - "280 False NaN NaN NaN \n", - "281 False NaN NaN NaN \n", - "282 False NaN NaN NaN \n", - "283 False NaN NaN NaN \n", - "284 False NaN NaN NaN \n", - "285 False NaN NaN NaN \n", - "286 False NaN NaN NaN \n", - "287 False NaN NaN NaN \n", - "288 False NaN NaN NaN \n", - "289 False NaN NaN NaN \n", - "290 False NaN NaN NaN \n", - "291 False NaN NaN NaN \n", - "292 False NaN NaN NaN \n", - "293 False NaN NaN NaN \n", - "294 False NaN NaN NaN \n", - "295 False NaN NaN NaN \n", - "296 False NaN NaN NaN \n", - "297 False NaN NaN NaN \n", - "298 False NaN NaN NaN \n", - "299 False NaN NaN NaN \n", - "300 False NaN NaN NaN \n", - "301 False NaN NaN NaN \n", - "302 False NaN NaN NaN \n", - "303 False NaN NaN NaN \n", - "304 False NaN NaN NaN \n", - "305 False NaN NaN NaN \n", - "306 False NaN NaN NaN \n", - "307 False NaN NaN NaN \n", - "308 False NaN NaN NaN \n", - "309 False NaN NaN NaN \n", - "310 False NaN NaN NaN \n", - "311 False NaN NaN NaN \n", - "312 False NaN NaN NaN \n", - "313 False NaN NaN NaN \n", - "314 False NaN NaN NaN \n", - "315 False NaN NaN NaN \n", - "316 False NaN NaN NaN \n", - "317 False NaN NaN NaN \n", - "318 False NaN NaN NaN \n", - "319 False NaN NaN NaN \n", - "320 False NaN NaN NaN \n", - "321 False NaN NaN NaN \n", - "322 False NaN NaN NaN \n", - "323 False NaN NaN NaN \n", - "\n", - " dav narrative synopsis turbo narrative synopsis turbo no synopsis \\\n", - "0 NaN NaN NaN \n", - "1 0.0 NaN NaN \n", - "2 NaN 2.0 1.0 \n", - "3 NaN 3.0 NaN \n", - "4 NaN NaN NaN \n", - "5 NaN NaN 3.0 \n", - "6 NaN NaN NaN \n", - "7 NaN NaN NaN \n", - "8 NaN NaN NaN \n", - "9 NaN NaN NaN \n", - "10 NaN 7.0 NaN \n", - "11 NaN NaN NaN \n", - "12 NaN NaN NaN \n", - "13 NaN NaN NaN \n", - "14 NaN NaN NaN \n", - "15 NaN NaN NaN \n", - "16 NaN NaN NaN \n", - "17 NaN NaN NaN \n", - "18 NaN NaN NaN \n", - "19 NaN NaN NaN \n", - "20 NaN NaN NaN \n", - "21 NaN NaN NaN \n", - "22 NaN NaN NaN \n", - "23 NaN 4.0 2.0 \n", - "24 NaN NaN NaN \n", - "25 NaN NaN NaN \n", - "26 2.0 NaN NaN \n", - "27 NaN NaN NaN \n", - "28 NaN NaN NaN \n", - "29 NaN NaN NaN \n", - "30 NaN NaN NaN \n", - "31 NaN NaN NaN \n", - "32 NaN NaN NaN \n", - "33 NaN NaN NaN \n", - "34 NaN NaN NaN \n", - "35 NaN NaN NaN \n", - "36 NaN NaN NaN \n", - "37 NaN 0.0 4.0 \n", - "38 NaN NaN NaN \n", - "39 NaN NaN NaN \n", - "40 NaN NaN NaN \n", - "41 NaN NaN NaN \n", - "42 NaN NaN NaN \n", - "43 NaN NaN NaN \n", - "44 NaN NaN NaN \n", - "45 NaN NaN NaN \n", - "46 NaN NaN NaN \n", - "47 NaN NaN NaN \n", - "48 NaN NaN NaN \n", - "49 NaN NaN NaN \n", - "50 NaN NaN NaN \n", - "51 NaN 6.0 NaN \n", - "52 NaN NaN NaN \n", - "53 NaN NaN NaN \n", - "54 NaN NaN NaN \n", - "55 NaN NaN NaN \n", - "56 NaN NaN NaN \n", - "57 NaN NaN NaN \n", - "58 NaN NaN NaN \n", - "59 NaN NaN NaN \n", - "60 NaN NaN NaN \n", - "61 NaN NaN NaN \n", - "62 NaN NaN NaN \n", - "63 NaN NaN NaN \n", - "64 NaN NaN NaN \n", - "65 NaN NaN NaN \n", - "66 NaN NaN NaN \n", - "67 NaN NaN NaN \n", - "68 NaN NaN NaN \n", - "69 NaN NaN NaN \n", - "70 NaN NaN NaN \n", - "71 NaN NaN NaN \n", - "72 NaN NaN NaN \n", - "73 NaN NaN NaN \n", - "74 NaN NaN NaN \n", - "75 NaN NaN NaN \n", - "76 NaN NaN NaN \n", - "77 NaN NaN NaN \n", - "78 NaN NaN NaN \n", - "79 NaN NaN NaN \n", - "80 NaN NaN NaN \n", - "81 NaN NaN NaN \n", - "82 NaN NaN NaN \n", - "83 NaN NaN NaN \n", - "84 NaN NaN NaN \n", - "85 NaN NaN NaN \n", - "86 NaN NaN NaN \n", - "87 NaN NaN NaN \n", - "88 NaN NaN NaN \n", - "89 NaN NaN NaN \n", - "90 NaN NaN NaN \n", - "91 NaN NaN NaN \n", - "92 NaN NaN NaN \n", - "93 NaN NaN NaN \n", - "94 NaN NaN NaN \n", - "95 NaN NaN NaN \n", - "96 NaN NaN NaN \n", - "97 NaN NaN NaN \n", - "98 NaN NaN NaN \n", - "99 NaN NaN NaN \n", - "100 NaN NaN NaN \n", - "101 NaN NaN NaN \n", - "102 NaN NaN NaN \n", - "103 NaN NaN NaN \n", - "104 NaN NaN NaN \n", - "105 NaN NaN NaN \n", - "106 NaN NaN NaN \n", - "107 NaN NaN NaN \n", - "108 NaN NaN NaN \n", - "109 NaN NaN NaN \n", - "110 NaN NaN NaN \n", - "111 NaN NaN NaN \n", - "112 NaN NaN NaN \n", - "113 NaN NaN NaN \n", - "114 NaN NaN NaN \n", - "115 NaN NaN NaN \n", - "116 NaN NaN NaN \n", - "117 NaN NaN NaN \n", - "118 NaN NaN NaN \n", - "119 NaN NaN NaN \n", - "120 NaN NaN NaN \n", - "121 NaN NaN NaN \n", - "122 NaN NaN NaN \n", - "123 NaN NaN NaN \n", - "124 NaN NaN NaN \n", - "125 NaN NaN NaN \n", - "126 NaN NaN NaN \n", - "127 NaN NaN NaN \n", - "128 NaN NaN NaN \n", - "129 NaN NaN NaN \n", - "130 NaN NaN NaN \n", - "131 NaN NaN NaN \n", - "132 NaN NaN NaN \n", - "133 NaN NaN NaN \n", - "134 NaN NaN NaN \n", - "135 NaN NaN NaN \n", - "136 NaN NaN NaN \n", - "137 NaN NaN NaN \n", - "138 NaN NaN NaN \n", - "139 NaN NaN NaN \n", - "140 NaN NaN NaN \n", - "141 NaN NaN NaN \n", - "142 NaN NaN NaN \n", - "143 NaN NaN NaN \n", - "144 NaN NaN NaN \n", - "145 NaN NaN NaN \n", - "146 NaN NaN NaN \n", - "147 NaN NaN NaN \n", - "148 NaN NaN NaN \n", - "149 NaN NaN NaN \n", - "150 NaN NaN NaN \n", - "151 NaN NaN NaN \n", - "152 NaN NaN NaN \n", - "153 NaN NaN NaN \n", - "154 NaN NaN NaN \n", - "155 NaN NaN NaN \n", - "156 NaN NaN NaN \n", - "157 NaN NaN NaN \n", - "158 NaN NaN NaN \n", - "159 NaN NaN NaN \n", - "160 NaN NaN NaN \n", - "161 NaN NaN NaN \n", - "162 NaN NaN NaN \n", - "163 NaN NaN NaN \n", - "164 NaN NaN NaN \n", - "165 NaN NaN NaN \n", - "166 NaN NaN NaN \n", - "167 NaN NaN NaN \n", - "168 NaN NaN NaN \n", - "169 NaN NaN NaN \n", - "170 NaN NaN NaN \n", - "171 NaN NaN NaN \n", - "172 NaN NaN NaN \n", - "173 NaN NaN NaN \n", - "174 NaN NaN NaN \n", - "175 NaN NaN NaN \n", - "176 NaN NaN NaN \n", - "177 NaN NaN NaN \n", - "178 NaN NaN NaN \n", - "179 NaN NaN NaN \n", - "180 NaN NaN NaN \n", - "181 NaN NaN NaN \n", - "182 NaN NaN NaN \n", - "183 NaN NaN NaN \n", - "184 NaN NaN NaN \n", - "185 NaN NaN NaN \n", - "186 NaN NaN NaN \n", - "187 NaN NaN NaN \n", - "188 NaN NaN NaN \n", - "189 NaN NaN NaN \n", - "190 NaN NaN NaN \n", - "191 NaN NaN NaN \n", - "192 NaN NaN NaN \n", - "193 NaN NaN NaN \n", - "194 NaN NaN NaN \n", - "195 NaN NaN NaN \n", - "196 NaN NaN NaN \n", - "197 NaN NaN NaN \n", - "198 NaN NaN NaN \n", - "199 NaN NaN NaN \n", - "200 NaN NaN NaN \n", - "201 NaN NaN NaN \n", - "202 NaN NaN NaN \n", - "203 NaN NaN NaN \n", - "204 NaN NaN NaN \n", - "205 NaN NaN NaN \n", - "206 NaN NaN NaN \n", - "207 NaN NaN NaN \n", - "208 NaN NaN NaN \n", - "209 NaN NaN NaN \n", - "210 NaN NaN NaN \n", - "211 NaN NaN NaN \n", - "212 NaN NaN NaN \n", - "213 NaN NaN NaN \n", - "214 NaN NaN NaN \n", - "215 NaN NaN NaN \n", - "216 NaN NaN NaN \n", - "217 NaN NaN NaN \n", - "218 NaN NaN NaN \n", - "219 NaN NaN NaN \n", - "220 NaN NaN NaN \n", - "221 NaN NaN NaN \n", - "222 NaN 1.0 0.0 \n", - "223 1.0 5.0 NaN \n", - "224 NaN 8.0 NaN \n", - "225 NaN 9.0 NaN \n", - "226 NaN NaN 5.0 \n", - "227 NaN NaN 6.0 \n", - "228 NaN NaN 7.0 \n", - "229 NaN NaN NaN \n", - "230 NaN NaN NaN \n", - "231 NaN NaN NaN \n", - "232 NaN NaN NaN \n", - "233 NaN NaN NaN \n", - "234 NaN NaN NaN \n", - "235 NaN NaN NaN \n", - "236 NaN NaN NaN \n", - "237 NaN NaN NaN \n", - "238 NaN NaN NaN \n", - "239 NaN NaN NaN \n", - "240 NaN NaN NaN \n", - "241 NaN NaN NaN \n", - "242 NaN NaN NaN \n", - "243 NaN NaN NaN \n", - "244 NaN NaN NaN \n", - "245 NaN NaN NaN \n", - "246 NaN NaN NaN \n", - "247 NaN NaN NaN \n", - "248 NaN NaN NaN \n", - "249 NaN NaN NaN \n", - "250 NaN NaN NaN \n", - "251 NaN NaN NaN \n", - "252 NaN NaN NaN \n", - "253 NaN NaN NaN \n", - "254 NaN NaN NaN \n", - "255 NaN NaN NaN \n", - "256 NaN NaN NaN \n", - "257 NaN NaN NaN \n", - "258 NaN NaN NaN \n", - "259 NaN NaN NaN \n", - "260 NaN NaN NaN \n", - "261 NaN NaN NaN \n", - "262 NaN NaN NaN \n", - "263 NaN NaN NaN \n", - "264 NaN NaN NaN \n", - "265 NaN NaN NaN \n", - "266 NaN NaN NaN \n", - "267 NaN NaN NaN \n", - "268 NaN NaN NaN \n", - "269 NaN NaN NaN \n", - "270 NaN NaN NaN \n", - "271 NaN NaN NaN \n", - "272 NaN NaN NaN \n", - "273 NaN NaN NaN \n", - "274 NaN NaN NaN \n", - "275 NaN NaN NaN \n", - "276 NaN NaN NaN \n", - "277 NaN NaN NaN \n", - "278 NaN NaN NaN \n", - "279 NaN NaN NaN \n", - "280 NaN NaN NaN \n", - "281 NaN NaN NaN \n", - "282 NaN NaN NaN \n", - "283 NaN NaN NaN \n", - "284 NaN NaN NaN \n", - "285 NaN NaN NaN \n", - "286 NaN NaN NaN \n", - "287 NaN NaN NaN \n", - "288 NaN NaN NaN \n", - "289 NaN NaN NaN \n", - "290 NaN NaN NaN \n", - "291 NaN NaN NaN \n", - "292 NaN NaN NaN \n", - "293 NaN NaN NaN \n", - "294 NaN NaN NaN \n", - "295 NaN NaN NaN \n", - "296 NaN NaN NaN \n", - "297 NaN NaN NaN \n", - "298 NaN NaN NaN \n", - "299 NaN NaN NaN \n", - "300 NaN NaN NaN \n", - "301 NaN NaN NaN \n", - "302 NaN NaN NaN \n", - "303 NaN NaN NaN \n", - "304 NaN NaN NaN \n", - "305 NaN NaN NaN \n", - "306 NaN NaN NaN \n", - "307 NaN NaN NaN \n", - "308 NaN NaN NaN \n", - "309 NaN NaN NaN \n", - "310 NaN NaN NaN \n", - "311 NaN NaN NaN \n", - "312 NaN NaN NaN \n", - "313 NaN NaN NaN \n", - "314 3.0 NaN NaN \n", - "315 4.0 NaN NaN \n", - "316 5.0 NaN NaN \n", - "317 6.0 NaN NaN \n", - "318 7.0 NaN NaN \n", - "319 NaN NaN NaN \n", - "320 NaN NaN NaN \n", - "321 NaN NaN NaN \n", - "322 NaN NaN NaN \n", - "323 NaN NaN NaN \n", - "\n", - " turbo ontological synopsis rank based dav no synopsis \n", - "0 NaN NaN NaN \n", - "1 NaN NaN NaN \n", - "2 NaN NaN NaN \n", - "3 NaN NaN NaN \n", - "4 NaN NaN NaN \n", - "5 NaN NaN NaN \n", - "6 NaN NaN NaN \n", - "7 NaN NaN NaN \n", - "8 NaN NaN NaN \n", - "9 NaN NaN NaN \n", - "10 NaN NaN NaN \n", - "11 NaN NaN NaN \n", - "12 NaN NaN NaN \n", - "13 NaN NaN NaN \n", - "14 NaN NaN NaN \n", - "15 NaN NaN NaN \n", - "16 NaN NaN NaN \n", - "17 NaN NaN NaN \n", - "18 NaN NaN NaN \n", - "19 NaN NaN NaN \n", - "20 NaN NaN NaN \n", - "21 NaN NaN NaN \n", - "22 0.0 NaN NaN \n", - "23 NaN NaN NaN \n", - "24 NaN NaN NaN \n", - "25 NaN NaN NaN \n", - "26 1.0 NaN NaN \n", - "27 NaN NaN NaN \n", - "28 NaN NaN NaN \n", - "29 NaN NaN NaN \n", - "30 NaN NaN NaN \n", - "31 NaN NaN NaN \n", - "32 NaN NaN NaN \n", - "33 NaN NaN NaN \n", - "34 NaN NaN NaN \n", - "35 NaN NaN NaN \n", - "36 NaN NaN NaN \n", - "37 NaN NaN NaN \n", - "38 NaN NaN NaN \n", - "39 3.0 NaN NaN \n", - "40 NaN NaN NaN \n", - "41 NaN NaN NaN \n", - "42 NaN NaN NaN \n", - "43 NaN NaN NaN \n", - "44 NaN NaN NaN \n", - "45 NaN NaN NaN \n", - "46 NaN NaN NaN \n", - "47 NaN NaN NaN \n", - "48 NaN 42.0 NaN \n", - "49 NaN NaN NaN \n", - "50 NaN NaN NaN \n", - "51 NaN NaN NaN \n", - "52 NaN NaN NaN \n", - "53 NaN NaN NaN \n", - "54 NaN NaN NaN \n", - "55 NaN NaN NaN \n", - "56 NaN NaN NaN \n", - "57 NaN NaN NaN \n", - "58 NaN NaN NaN \n", - "59 NaN NaN NaN \n", - "60 2.0 NaN NaN \n", - "61 NaN NaN NaN \n", - "62 NaN NaN NaN \n", - "63 NaN NaN NaN \n", - "64 NaN NaN NaN \n", - "65 NaN NaN NaN \n", - "66 NaN NaN NaN \n", - "67 NaN NaN NaN \n", - "68 NaN NaN NaN \n", - "69 NaN NaN NaN \n", - "70 NaN NaN NaN \n", - "71 NaN NaN NaN \n", - "72 NaN NaN NaN \n", - "73 NaN NaN NaN \n", - "74 NaN NaN NaN \n", - "75 NaN NaN NaN \n", - "76 NaN NaN NaN \n", - "77 NaN NaN NaN \n", - "78 NaN NaN NaN \n", - "79 NaN NaN NaN \n", - "80 NaN NaN NaN \n", - "81 NaN NaN NaN \n", - "82 NaN NaN NaN \n", - "83 NaN NaN NaN \n", - "84 NaN NaN NaN \n", - "85 NaN NaN NaN \n", - "86 NaN NaN NaN \n", - "87 NaN NaN NaN \n", - "88 NaN NaN NaN \n", - "89 NaN NaN NaN \n", - "90 NaN NaN NaN \n", - "91 NaN NaN NaN \n", - "92 NaN NaN NaN \n", - "93 NaN NaN NaN \n", - "94 NaN NaN NaN \n", - "95 NaN NaN NaN \n", - "96 NaN NaN NaN \n", - "97 NaN 77.0 NaN \n", - "98 NaN NaN NaN \n", - "99 NaN NaN NaN \n", - "100 NaN NaN NaN \n", - "101 NaN NaN NaN \n", - "102 NaN 64.0 NaN \n", - "103 NaN NaN NaN \n", - "104 NaN NaN NaN \n", - "105 NaN NaN NaN \n", - "106 NaN NaN NaN \n", - "107 NaN NaN NaN \n", - "108 NaN NaN NaN \n", - "109 NaN NaN NaN \n", - "110 NaN NaN NaN \n", - "111 NaN NaN NaN \n", - "112 NaN NaN NaN \n", - "113 NaN NaN NaN \n", - "114 NaN NaN NaN \n", - "115 NaN NaN NaN \n", - "116 NaN NaN NaN \n", - "117 NaN NaN NaN \n", - "118 NaN NaN NaN \n", - "119 NaN NaN NaN \n", - "120 NaN NaN NaN \n", - "121 NaN NaN NaN \n", - "122 NaN NaN NaN \n", - "123 NaN NaN NaN \n", - "124 NaN NaN NaN \n", - "125 NaN NaN NaN \n", - "126 NaN NaN NaN \n", - "127 NaN NaN NaN \n", - "128 NaN NaN NaN \n", - "129 NaN NaN NaN \n", - "130 NaN NaN NaN \n", - "131 NaN NaN NaN \n", - "132 NaN NaN NaN \n", - "133 NaN NaN NaN \n", - "134 NaN NaN NaN \n", - "135 NaN NaN NaN \n", - "136 NaN NaN NaN \n", - "137 NaN NaN NaN \n", - "138 NaN NaN NaN \n", - "139 NaN NaN NaN \n", - "140 NaN NaN NaN \n", - "141 NaN NaN NaN \n", - "142 NaN NaN NaN \n", - "143 NaN NaN NaN \n", - "144 NaN NaN NaN \n", - "145 NaN NaN NaN \n", - "146 NaN NaN NaN \n", - "147 NaN NaN NaN \n", - "148 NaN NaN NaN \n", - "149 NaN NaN NaN \n", - "150 NaN NaN NaN \n", - "151 NaN NaN NaN \n", - "152 NaN NaN NaN \n", - "153 NaN NaN NaN \n", - "154 NaN NaN NaN \n", - "155 NaN NaN NaN \n", - "156 NaN NaN NaN \n", - "157 NaN NaN NaN \n", - "158 NaN NaN NaN \n", - "159 NaN NaN NaN \n", - "160 NaN NaN NaN \n", - "161 NaN NaN NaN \n", - "162 NaN NaN NaN \n", - "163 NaN NaN NaN \n", - "164 NaN NaN NaN \n", - "165 NaN 45.0 NaN \n", - "166 NaN NaN NaN \n", - "167 NaN NaN NaN \n", - "168 NaN 47.0 NaN \n", - "169 NaN NaN NaN \n", - "170 NaN NaN NaN \n", - "171 NaN NaN NaN \n", - "172 NaN NaN NaN \n", - 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"296 NaN 72.0 NaN \n", - "297 NaN 73.0 NaN \n", - "298 NaN 74.0 NaN \n", - "299 NaN 75.0 NaN \n", - "300 NaN 76.0 NaN \n", - "301 NaN 78.0 NaN \n", - "302 NaN 79.0 NaN \n", - "303 NaN 80.0 NaN \n", - "304 NaN 81.0 NaN \n", - "305 NaN 82.0 NaN \n", - "306 NaN 83.0 NaN \n", - "307 NaN 84.0 NaN \n", - "308 NaN 85.0 NaN \n", - "309 NaN 86.0 NaN \n", - "310 NaN 87.0 NaN \n", - "311 NaN 88.0 NaN \n", - "312 NaN 89.0 NaN \n", - "313 NaN 90.0 NaN \n", - "314 NaN NaN NaN \n", - "315 NaN NaN NaN \n", - "316 NaN NaN NaN \n", - "317 NaN NaN NaN \n", - "318 NaN NaN NaN \n", - "319 NaN NaN 0.0 \n", - "320 NaN NaN 1.0 \n", - "321 NaN NaN 2.0 \n", - "322 NaN NaN 3.0 \n", - "323 NaN NaN 4.0 " - ] - }, - "execution_count": 56, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "hydrolysis = df.query(f\"{GENESET} == 'hydrolase activity, hydrolyzing O-glycosyl compounds-0'\").sort_values(\"similarity\", ascending=False)\n", - "terms_summary(hydrolysis)" - ] - }, - { - "cell_type": "code", - "execution_count": 57, - "id": "6c079a29", - "metadata": {}, - "outputs": [], - "source": [ - "viz('hydrolase activity, hydrolyzing O-glycosyl compounds-0')" - ] - }, - { - "cell_type": "markdown", - "id": "d98d0174", - "metadata": {}, - "source": [ - "## Variability" - ] - }, - { - "cell_type": "code", - "execution_count": 58, - "id": "bd0dc703", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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prompt_variantv1v2diff
modelmethodgeneset
gpt-3.5-turbonarrative_synopsisEDS-00.140.50-0.36
EDS-10.500.250.25
FA-01.001.000.00
FA-11.001.000.00
HALLMARK_ADIPOGENESIS-01.000.670.33
HALLMARK_ADIPOGENESIS-10.331.00-0.67
HALLMARK_ALLOGRAFT_REJECTION-01.000.870.13
HALLMARK_ALLOGRAFT_REJECTION-11.001.000.00
HALLMARK_ANDROGEN_RESPONSE-00.000.000.00
HALLMARK_ANDROGEN_RESPONSE-10.200.000.20
HALLMARK_ANGIOGENESIS-00.500.330.17
HALLMARK_ANGIOGENESIS-10.500.500.00
HALLMARK_APICAL_JUNCTION-01.001.000.00
HALLMARK_APICAL_JUNCTION-10.800.670.13
HALLMARK_APICAL_SURFACE-00.250.080.17
HALLMARK_APICAL_SURFACE-10.330.000.33
HALLMARK_APOPTOSIS-01.001.000.00
HALLMARK_APOPTOSIS-1NaN0.71NaN
HALLMARK_BILE_ACID_METABOLISM-01.000.600.40
HALLMARK_BILE_ACID_METABOLISM-10.831.00-0.17
HALLMARK_CHOLESTEROL_HOMEOSTASIS-00.670.670.00
HALLMARK_CHOLESTEROL_HOMEOSTASIS-10.670.75-0.08
HALLMARK_COAGULATION-01.001.000.00
HALLMARK_COAGULATION-10.501.00-0.50
HALLMARK_COMPLEMENT-01.001.000.00
HALLMARK_COMPLEMENT-10.800.800.00
HALLMARK_DNA_REPAIR-00.671.00-0.33
HALLMARK_DNA_REPAIR-10.381.00-0.62
HALLMARK_E2F_TARGETS-01.001.000.00
HALLMARK_E2F_TARGETS-10.751.00-0.25
HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-01.000.790.21
HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-10.830.670.17
HALLMARK_ESTROGEN_RESPONSE_EARLY-00.000.000.00
HALLMARK_ESTROGEN_RESPONSE_EARLY-10.000.000.00
HALLMARK_ESTROGEN_RESPONSE_LATE-00.000.38-0.38
HALLMARK_ESTROGEN_RESPONSE_LATE-10.200.170.03
HALLMARK_FATTY_ACID_METABOLISM-00.801.00-0.20
HALLMARK_FATTY_ACID_METABOLISM-11.000.880.12
HALLMARK_G2M_CHECKPOINT-01.001.000.00
HALLMARK_G2M_CHECKPOINT-10.831.00-0.17
HALLMARK_GLYCOLYSIS-00.641.00-0.36
HALLMARK_GLYCOLYSIS-10.400.50-0.10
HALLMARK_HEDGEHOG_SIGNALING-01.000.800.20
HALLMARK_HEDGEHOG_SIGNALING-11.001.000.00
HALLMARK_HEME_METABOLISM-00.000.000.00
HALLMARK_HEME_METABOLISM-10.100.000.10
HALLMARK_HYPOXIA-00.671.00-0.33
HALLMARK_HYPOXIA-10.500.400.10
HALLMARK_IL2_STAT5_SIGNALING-01.000.200.80
HALLMARK_IL2_STAT5_SIGNALING-10.670.75-0.08
HALLMARK_IL6_JAK_STAT3_SIGNALING-0NaN0.80NaN
HALLMARK_IL6_JAK_STAT3_SIGNALING-11.001.000.00
HALLMARK_INFLAMMATORY_RESPONSE-00.331.00-0.67
HALLMARK_INFLAMMATORY_RESPONSE-11.000.800.20
HALLMARK_INTERFERON_ALPHA_RESPONSE-00.751.00-0.25
HALLMARK_INTERFERON_ALPHA_RESPONSE-11.001.000.00
HALLMARK_INTERFERON_GAMMA_RESPONSE-0NaN1.00NaN
HALLMARK_INTERFERON_GAMMA_RESPONSE-10.751.00-0.25
HALLMARK_KRAS_SIGNALING_DN-00.200.120.08
HALLMARK_KRAS_SIGNALING_DN-10.000.000.00
HALLMARK_KRAS_SIGNALING_UP-00.200.33-0.13
HALLMARK_KRAS_SIGNALING_UP-10.25NaNNaN
HALLMARK_MITOTIC_SPINDLE-00.801.00-0.20
HALLMARK_MITOTIC_SPINDLE-11.001.000.00
HALLMARK_MTORC1_SIGNALING-00.600.600.00
HALLMARK_MTORC1_SIGNALING-10.500.67-0.17
HALLMARK_MYC_TARGETS_V1-00.830.800.03
HALLMARK_MYC_TARGETS_V1-11.000.750.25
HALLMARK_MYC_TARGETS_V2-01.000.670.33
HALLMARK_MYC_TARGETS_V2-11.000.750.25
HALLMARK_MYOGENESIS-00.781.00-0.22
HALLMARK_MYOGENESIS-11.001.000.00
HALLMARK_NOTCH_SIGNALING-00.750.330.42
HALLMARK_NOTCH_SIGNALING-11.000.670.33
HALLMARK_OXIDATIVE_PHOSPHORYLATION-01.001.000.00
HALLMARK_OXIDATIVE_PHOSPHORYLATION-11.001.000.00
HALLMARK_P53_PATHWAY-00.670.250.42
HALLMARK_P53_PATHWAY-10.750.670.08
HALLMARK_PANCREAS_BETA_CELLS-01.000.400.60
HALLMARK_PANCREAS_BETA_CELLS-10.000.000.00
HALLMARK_PEROXISOME-00.600.80-0.20
HALLMARK_PEROXISOME-11.001.000.00
HALLMARK_PI3K_AKT_MTOR_SIGNALING-01.001.000.00
HALLMARK_PI3K_AKT_MTOR_SIGNALING-11.001.000.00
HALLMARK_PROTEIN_SECRETION-00.670.83-0.17
HALLMARK_PROTEIN_SECRETION-11.000.830.17
HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-01.00NaNNaN
HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-11.001.000.00
HALLMARK_SPERMATOGENESIS-00.250.60-0.35
HALLMARK_SPERMATOGENESIS-10.000.33-0.33
HALLMARK_TGF_BETA_SIGNALING-0NaN1.00NaN
HALLMARK_TGF_BETA_SIGNALING-11.000.670.33
HALLMARK_TNFA_SIGNALING_VIA_NFKB-01.000.830.17
HALLMARK_TNFA_SIGNALING_VIA_NFKB-11.000.500.50
HALLMARK_UNFOLDED_PROTEIN_RESPONSE-01.000.670.33
HALLMARK_UNFOLDED_PROTEIN_RESPONSE-11.000.860.14
HALLMARK_UV_RESPONSE_DN-00.000.75-0.75
HALLMARK_UV_RESPONSE_DN-10.670.600.07
HALLMARK_UV_RESPONSE_UP-00.300.67-0.37
HALLMARK_UV_RESPONSE_UP-10.200.000.20
HALLMARK_WNT_BETA_CATENIN_SIGNALING-00.001.00-1.00
HALLMARK_WNT_BETA_CATENIN_SIGNALING-11.000.500.50
T cell proliferation-00.750.000.75
T cell proliferation-11.000.670.33
Yamanaka-TFs-0NaN0.00NaN
Yamanaka-TFs-10.000.000.00
amigo-example-00.200.33-0.13
amigo-example-10.500.67-0.17
bicluster_RNAseqDB_0-00.000.000.00
bicluster_RNAseqDB_0-10.000.000.00
bicluster_RNAseqDB_1002-00.550.400.15
bicluster_RNAseqDB_1002-10.670.170.50
endocytosis-01.000.200.80
endocytosis-11.001.000.00
glycolysis-gocam-0NaN1.00NaN
glycolysis-gocam-11.000.400.60
go-postsynapse-calcium-transmembrane-01.001.000.00
go-postsynapse-calcium-transmembrane-10.670.670.00
go-reg-autophagy-pkra-00.500.67-0.17
go-reg-autophagy-pkra-10.670.170.50
hydrolase activity, hydrolyzing O-glycosyl compounds-00.860.750.11
hydrolase activity, hydrolyzing O-glycosyl compounds-10.751.00-0.25
ig-receptor-binding-2022-00.330.330.00
ig-receptor-binding-2022-11.001.000.00
meiosis I-0NaN1.00NaN
meiosis I-11.001.000.00
molecular sequestering-00.000.000.00
molecular sequestering-10.000.33-0.33
mtorc1-00.600.600.00
mtorc1-11.000.600.40
peroxisome-01.00NaNNaN
peroxisome-1NaN0.50NaN
progeria-01.000.330.67
progeria-10.000.000.00
regulation of presynaptic membrane potential-01.000.750.25
regulation of presynaptic membrane potential-10.671.00-0.33
sensory ataxia-00.501.00-0.50
sensory ataxia-10.000.67-0.67
term-GO:0007212-01.001.000.00
term-GO:0007212-10.670.500.17
tf-downreg-colorectal-00.501.00-0.50
tf-downreg-colorectal-11.001.000.00
no_synopsisEDS-01.000.500.50
EDS-10.671.00-0.33
FA-0NaN0.67NaN
FA-11.001.000.00
HALLMARK_ADIPOGENESIS-00.640.88-0.24
HALLMARK_ADIPOGENESIS-10.361.00-0.64
HALLMARK_ALLOGRAFT_REJECTION-01.001.000.00
HALLMARK_ALLOGRAFT_REJECTION-11.001.000.00
HALLMARK_ANDROGEN_RESPONSE-00.000.000.00
HALLMARK_ANDROGEN_RESPONSE-10.000.000.00
HALLMARK_ANGIOGENESIS-00.330.75-0.42
HALLMARK_ANGIOGENESIS-10.500.67-0.17
HALLMARK_APICAL_JUNCTION-00.750.500.25
HALLMARK_APICAL_JUNCTION-10.891.00-0.11
HALLMARK_APICAL_SURFACE-00.140.33-0.19
HALLMARK_APICAL_SURFACE-10.120.100.02
HALLMARK_APOPTOSIS-00.701.00-0.30
HALLMARK_APOPTOSIS-11.000.700.30
HALLMARK_BILE_ACID_METABOLISM-00.500.500.00
HALLMARK_BILE_ACID_METABOLISM-11.000.750.25
HALLMARK_CHOLESTEROL_HOMEOSTASIS-00.670.80-0.13
HALLMARK_CHOLESTEROL_HOMEOSTASIS-10.881.00-0.12
HALLMARK_COAGULATION-01.000.750.25
HALLMARK_COAGULATION-11.001.000.00
HALLMARK_COMPLEMENT-00.400.75-0.35
HALLMARK_COMPLEMENT-10.891.00-0.11
HALLMARK_DNA_REPAIR-00.800.750.05
HALLMARK_DNA_REPAIR-10.750.80-0.05
HALLMARK_E2F_TARGETS-01.001.000.00
HALLMARK_E2F_TARGETS-11.001.000.00
HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-00.821.00-0.18
HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-10.890.860.03
HALLMARK_ESTROGEN_RESPONSE_EARLY-00.000.000.00
HALLMARK_ESTROGEN_RESPONSE_EARLY-10.500.090.41
HALLMARK_ESTROGEN_RESPONSE_LATE-00.200.25-0.05
HALLMARK_ESTROGEN_RESPONSE_LATE-10.300.000.30
HALLMARK_FATTY_ACID_METABOLISM-0NaN1.00NaN
HALLMARK_FATTY_ACID_METABOLISM-11.001.000.00
HALLMARK_G2M_CHECKPOINT-01.00NaNNaN
HALLMARK_G2M_CHECKPOINT-11.001.000.00
HALLMARK_GLYCOLYSIS-0NaN0.50NaN
HALLMARK_GLYCOLYSIS-10.500.430.07
HALLMARK_HEDGEHOG_SIGNALING-00.800.250.55
HALLMARK_HEDGEHOG_SIGNALING-11.001.000.00
HALLMARK_HEME_METABOLISM-00.330.000.33
HALLMARK_HEME_METABOLISM-10.381.00-0.62
HALLMARK_HYPOXIA-00.560.440.11
HALLMARK_HYPOXIA-11.00NaNNaN
HALLMARK_IL2_STAT5_SIGNALING-10.670.330.33
HALLMARK_IL6_JAK_STAT3_SIGNALING-01.000.440.56
HALLMARK_IL6_JAK_STAT3_SIGNALING-11.001.000.00
HALLMARK_INFLAMMATORY_RESPONSE-00.711.00-0.29
HALLMARK_INFLAMMATORY_RESPONSE-10.670.92-0.25
HALLMARK_INTERFERON_ALPHA_RESPONSE-01.001.000.00
HALLMARK_INTERFERON_ALPHA_RESPONSE-10.291.00-0.71
HALLMARK_INTERFERON_GAMMA_RESPONSE-01.000.630.37
HALLMARK_INTERFERON_GAMMA_RESPONSE-11.000.860.14
HALLMARK_KRAS_SIGNALING_DN-00.500.000.50
HALLMARK_KRAS_SIGNALING_DN-10.000.000.00
HALLMARK_KRAS_SIGNALING_UP-00.860.500.36
HALLMARK_KRAS_SIGNALING_UP-10.400.000.40
HALLMARK_MITOTIC_SPINDLE-01.001.000.00
HALLMARK_MITOTIC_SPINDLE-11.000.940.06
HALLMARK_MTORC1_SIGNALING-00.75NaNNaN
HALLMARK_MTORC1_SIGNALING-10.500.75-0.25
HALLMARK_MYC_TARGETS_V1-01.001.000.00
HALLMARK_MYC_TARGETS_V1-11.000.890.11
HALLMARK_MYC_TARGETS_V2-00.670.600.07
HALLMARK_MYC_TARGETS_V2-10.670.78-0.11
HALLMARK_MYOGENESIS-00.601.00-0.40
HALLMARK_MYOGENESIS-1NaN1.00NaN
HALLMARK_NOTCH_SIGNALING-00.450.71-0.26
HALLMARK_NOTCH_SIGNALING-10.250.250.00
HALLMARK_OXIDATIVE_PHOSPHORYLATION-00.670.670.00
HALLMARK_OXIDATIVE_PHOSPHORYLATION-11.000.890.11
HALLMARK_P53_PATHWAY-01.001.000.00
HALLMARK_P53_PATHWAY-10.500.60-0.10
HALLMARK_PANCREAS_BETA_CELLS-00.670.75-0.08
HALLMARK_PANCREAS_BETA_CELLS-10.500.57-0.07
HALLMARK_PEROXISOME-00.500.60-0.10
HALLMARK_PEROXISOME-10.500.71-0.21
HALLMARK_PI3K_AKT_MTOR_SIGNALING-00.001.00-1.00
HALLMARK_PI3K_AKT_MTOR_SIGNALING-11.000.750.25
HALLMARK_PROTEIN_SECRETION-01.001.000.00
HALLMARK_PROTEIN_SECRETION-10.621.00-0.38
HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-00.801.00-0.20
HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-10.331.00-0.67
HALLMARK_SPERMATOGENESIS-00.800.400.40
HALLMARK_SPERMATOGENESIS-10.170.000.17
HALLMARK_TGF_BETA_SIGNALING-00.860.830.02
HALLMARK_TGF_BETA_SIGNALING-10.501.00-0.50
HALLMARK_TNFA_SIGNALING_VIA_NFKB-00.000.42-0.42
HALLMARK_TNFA_SIGNALING_VIA_NFKB-10.670.80-0.13
HALLMARK_UNFOLDED_PROTEIN_RESPONSE-01.000.600.40
HALLMARK_UNFOLDED_PROTEIN_RESPONSE-10.530.75-0.22
HALLMARK_UV_RESPONSE_DN-01.000.670.33
HALLMARK_UV_RESPONSE_DN-10.400.50-0.10
HALLMARK_UV_RESPONSE_UP-00.500.75-0.25
HALLMARK_UV_RESPONSE_UP-10.330.43-0.10
HALLMARK_WNT_BETA_CATENIN_SIGNALING-01.000.001.00
HALLMARK_WNT_BETA_CATENIN_SIGNALING-10.751.00-0.25
T cell proliferation-01.000.830.17
T cell proliferation-11.001.000.00
Yamanaka-TFs-00.000.000.00
Yamanaka-TFs-10.000.000.00
amigo-example-00.43NaNNaN
amigo-example-10.500.71-0.21
bicluster_RNAseqDB_0-00.000.12-0.12
bicluster_RNAseqDB_0-10.000.000.00
bicluster_RNAseqDB_1002-00.500.75-0.25
bicluster_RNAseqDB_1002-11.000.400.60
endocytosis-00.400.250.15
endocytosis-10.570.60-0.03
glycolysis-gocam-01.001.000.00
glycolysis-gocam-11.000.750.25
go-postsynapse-calcium-transmembrane-00.801.00-0.20
go-postsynapse-calcium-transmembrane-10.560.75-0.19
go-reg-autophagy-pkra-01.000.600.40
go-reg-autophagy-pkra-10.331.00-0.67
hydrolase activity, hydrolyzing O-glycosyl compounds-00.800.86-0.06
hydrolase activity, hydrolyzing O-glycosyl compounds-10.751.00-0.25
ig-receptor-binding-2022-00.000.60-0.60
ig-receptor-binding-2022-10.330.000.33
meiosis I-01.000.690.31
meiosis I-10.801.00-0.20
molecular sequestering-00.120.000.12
molecular sequestering-10.000.000.00
mtorc1-00.75NaNNaN
mtorc1-10.330.67-0.33
peroxisome-01.001.000.00
peroxisome-10.000.50-0.50
progeria-00.000.25-0.25
progeria-10.330.000.33
regulation of presynaptic membrane potential-00.860.800.06
regulation of presynaptic membrane potential-10.860.800.06
sensory ataxia-00.000.20-0.20
sensory ataxia-1NaN0.00NaN
term-GO:0007212-00.800.500.30
term-GO:0007212-1NaN0.75NaN
tf-downreg-colorectal-01.000.250.75
tf-downreg-colorectal-11.000.890.11
ontological_synopsisEDS-00.750.80-0.05
EDS-10.750.80-0.05
FA-01.001.000.00
FA-11.001.000.00
HALLMARK_ADIPOGENESIS-00.000.50-0.50
HALLMARK_ADIPOGENESIS-11.000.500.50
HALLMARK_ALLOGRAFT_REJECTION-00.751.00-0.25
HALLMARK_ALLOGRAFT_REJECTION-10.600.570.03
HALLMARK_ANDROGEN_RESPONSE-00.500.000.50
HALLMARK_ANDROGEN_RESPONSE-10.00NaNNaN
HALLMARK_ANGIOGENESIS-1NaN1.00NaN
HALLMARK_APICAL_JUNCTION-01.000.330.67
HALLMARK_APICAL_SURFACE-00.000.43-0.43
HALLMARK_APICAL_SURFACE-10.430.000.43
HALLMARK_APOPTOSIS-01.000.750.25
HALLMARK_APOPTOSIS-11.001.000.00
HALLMARK_BILE_ACID_METABOLISM-01.000.800.20
HALLMARK_BILE_ACID_METABOLISM-10.801.00-0.20
HALLMARK_CHOLESTEROL_HOMEOSTASIS-00.330.80-0.47
HALLMARK_CHOLESTEROL_HOMEOSTASIS-10.250.67-0.42
HALLMARK_COAGULATION-00.671.00-0.33
HALLMARK_COAGULATION-11.001.000.00
HALLMARK_COMPLEMENT-00.000.67-0.67
HALLMARK_COMPLEMENT-11.000.500.50
HALLMARK_DNA_REPAIR-01.001.000.00
HALLMARK_DNA_REPAIR-11.000.750.25
HALLMARK_E2F_TARGETS-01.000.880.12
HALLMARK_E2F_TARGETS-1NaN0.00NaN
HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-01.001.000.00
HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-10.500.250.25
HALLMARK_ESTROGEN_RESPONSE_EARLY-00.000.000.00
HALLMARK_ESTROGEN_RESPONSE_EARLY-10.000.33-0.33
HALLMARK_ESTROGEN_RESPONSE_LATE-00.000.000.00
HALLMARK_ESTROGEN_RESPONSE_LATE-1NaN0.00NaN
HALLMARK_FATTY_ACID_METABOLISM-00.290.80-0.51
HALLMARK_FATTY_ACID_METABOLISM-11.001.000.00
HALLMARK_G2M_CHECKPOINT-01.000.500.50
HALLMARK_G2M_CHECKPOINT-11.000.750.25
HALLMARK_GLYCOLYSIS-00.670.80-0.13
HALLMARK_GLYCOLYSIS-10.670.400.27
HALLMARK_HEDGEHOG_SIGNALING-00.291.00-0.71
HALLMARK_HEDGEHOG_SIGNALING-11.001.000.00
HALLMARK_HEME_METABOLISM-00.330.000.33
HALLMARK_HEME_METABOLISM-1NaN0.00NaN
HALLMARK_HYPOXIA-00.200.000.20
HALLMARK_HYPOXIA-10.330.170.17
HALLMARK_IL2_STAT5_SIGNALING-00.800.250.55
HALLMARK_IL2_STAT5_SIGNALING-10.120.50-0.38
HALLMARK_IL6_JAK_STAT3_SIGNALING-01.001.000.00
HALLMARK_IL6_JAK_STAT3_SIGNALING-11.001.000.00
HALLMARK_INFLAMMATORY_RESPONSE-01.001.000.00
HALLMARK_INFLAMMATORY_RESPONSE-11.001.000.00
HALLMARK_INTERFERON_ALPHA_RESPONSE-00.671.00-0.33
HALLMARK_INTERFERON_ALPHA_RESPONSE-10.500.55-0.05
HALLMARK_INTERFERON_GAMMA_RESPONSE-00.330.330.00
HALLMARK_INTERFERON_GAMMA_RESPONSE-11.001.000.00
HALLMARK_KRAS_SIGNALING_DN-00.000.000.00
HALLMARK_KRAS_SIGNALING_DN-10.000.000.00
HALLMARK_KRAS_SIGNALING_UP-0NaN0.33NaN
HALLMARK_KRAS_SIGNALING_UP-10.400.000.40
HALLMARK_MITOTIC_SPINDLE-01.001.000.00
HALLMARK_MITOTIC_SPINDLE-11.001.000.00
HALLMARK_MTORC1_SIGNALING-00.330.000.33
HALLMARK_MTORC1_SIGNALING-10.000.75-0.75
HALLMARK_MYC_TARGETS_V1-01.000.670.33
HALLMARK_MYC_TARGETS_V1-11.000.800.20
HALLMARK_MYC_TARGETS_V2-00.331.00-0.67
HALLMARK_MYC_TARGETS_V2-11.001.000.00
HALLMARK_MYOGENESIS-00.00NaNNaN
HALLMARK_MYOGENESIS-1NaN0.50NaN
HALLMARK_NOTCH_SIGNALING-01.001.000.00
HALLMARK_NOTCH_SIGNALING-1NaN1.00NaN
HALLMARK_OXIDATIVE_PHOSPHORYLATION-01.000.500.50
HALLMARK_OXIDATIVE_PHOSPHORYLATION-10.50NaNNaN
HALLMARK_P53_PATHWAY-00.500.250.25
HALLMARK_P53_PATHWAY-10.000.50-0.50
HALLMARK_PANCREAS_BETA_CELLS-00.670.75-0.08
HALLMARK_PANCREAS_BETA_CELLS-10.000.000.00
HALLMARK_PEROXISOME-00.600.80-0.20
HALLMARK_PEROXISOME-10.400.50-0.10
HALLMARK_PI3K_AKT_MTOR_SIGNALING-00.500.60-0.10
HALLMARK_PI3K_AKT_MTOR_SIGNALING-10.671.00-0.33
HALLMARK_PROTEIN_SECRETION-00.620.330.29
HALLMARK_PROTEIN_SECRETION-10.400.75-0.35
HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-00.750.83-0.08
HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-10.881.00-0.12
HALLMARK_SPERMATOGENESIS-00.400.250.15
HALLMARK_SPERMATOGENESIS-10.000.000.00
HALLMARK_TGF_BETA_SIGNALING-01.001.000.00
HALLMARK_TGF_BETA_SIGNALING-1NaN1.00NaN
HALLMARK_TNFA_SIGNALING_VIA_NFKB-01.001.000.00
HALLMARK_TNFA_SIGNALING_VIA_NFKB-11.000.860.14
HALLMARK_UNFOLDED_PROTEIN_RESPONSE-00.75NaNNaN
HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1NaN0.67NaN
HALLMARK_UV_RESPONSE_DN-00.501.00-0.50
HALLMARK_UV_RESPONSE_DN-10.500.500.00
HALLMARK_UV_RESPONSE_UP-00.000.000.00
HALLMARK_UV_RESPONSE_UP-10.000.000.00
HALLMARK_WNT_BETA_CATENIN_SIGNALING-00.331.00-0.67
HALLMARK_WNT_BETA_CATENIN_SIGNALING-10.401.00-0.60
T cell proliferation-01.001.000.00
T cell proliferation-10.470.88-0.41
Yamanaka-TFs-00.670.250.42
Yamanaka-TFs-10.250.000.25
amigo-example-01.000.250.75
amigo-example-10.750.330.42
bicluster_RNAseqDB_0-00.000.000.00
bicluster_RNAseqDB_0-10.000.25-0.25
bicluster_RNAseqDB_1002-01.000.670.33
bicluster_RNAseqDB_1002-10.500.67-0.17
endocytosis-01.000.200.80
endocytosis-10.251.00-0.75
glycolysis-gocam-00.500.67-0.17
glycolysis-gocam-10.670.75-0.08
go-postsynapse-calcium-transmembrane-01.000.750.25
go-postsynapse-calcium-transmembrane-10.291.00-0.71
go-reg-autophagy-pkra-00.600.600.00
go-reg-autophagy-pkra-10.600.80-0.20
hydrolase activity, hydrolyzing O-glycosyl compounds-01.001.000.00
hydrolase activity, hydrolyzing O-glycosyl compounds-10.801.00-0.20
ig-receptor-binding-2022-01.00NaNNaN
ig-receptor-binding-2022-10.140.50-0.36
meiosis I-01.001.000.00
meiosis I-11.001.000.00
molecular sequestering-00.330.50-0.17
molecular sequestering-10.250.000.25
mtorc1-00.330.000.33
mtorc1-10.580.330.25
peroxisome-00.500.000.50
peroxisome-10.600.330.27
progeria-00.000.000.00
progeria-10.250.000.25
regulation of presynaptic membrane potential-01.001.000.00
regulation of presynaptic membrane potential-10.801.00-0.20
sensory ataxia-00.670.500.17
sensory ataxia-10.250.50-0.25
term-GO:0007212-01.000.500.50
term-GO:0007212-10.130.29-0.15
tf-downreg-colorectal-01.001.000.00
tf-downreg-colorectal-10.601.00-0.40
text-davinci-003narrative_synopsisEDS-00.330.000.33
EDS-10.500.000.50
FA-00.671.00-0.33
FA-11.001.000.00
HALLMARK_ADIPOGENESIS-00.800.310.49
HALLMARK_ADIPOGENESIS-10.330.140.19
HALLMARK_ALLOGRAFT_REJECTION-00.330.50-0.17
HALLMARK_ALLOGRAFT_REJECTION-10.501.00-0.50
HALLMARK_ANDROGEN_RESPONSE-00.000.000.00
HALLMARK_ANDROGEN_RESPONSE-10.000.000.00
HALLMARK_ANGIOGENESIS-00.000.30-0.30
HALLMARK_ANGIOGENESIS-10.50NaNNaN
HALLMARK_APICAL_JUNCTION-00.500.000.50
HALLMARK_APICAL_JUNCTION-11.000.750.25
HALLMARK_APICAL_SURFACE-00.000.20-0.20
HALLMARK_APICAL_SURFACE-10.140.000.14
HALLMARK_APOPTOSIS-01.000.500.50
HALLMARK_APOPTOSIS-11.001.000.00
HALLMARK_BILE_ACID_METABOLISM-00.330.40-0.07
HALLMARK_BILE_ACID_METABOLISM-10.431.00-0.57
HALLMARK_CHOLESTEROL_HOMEOSTASIS-0NaN0.25NaN
HALLMARK_CHOLESTEROL_HOMEOSTASIS-10.500.330.17
HALLMARK_COAGULATION-01.000.001.00
HALLMARK_COAGULATION-10.000.000.00
HALLMARK_COMPLEMENT-00.750.330.42
HALLMARK_COMPLEMENT-11.000.670.33
HALLMARK_DNA_REPAIR-00.001.00-1.00
HALLMARK_DNA_REPAIR-10.360.170.20
HALLMARK_E2F_TARGETS-00.700.670.03
HALLMARK_E2F_TARGETS-10.710.80-0.09
HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-01.000.500.50
HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-10.000.67-0.67
HALLMARK_ESTROGEN_RESPONSE_EARLY-00.000.20-0.20
HALLMARK_ESTROGEN_RESPONSE_EARLY-10.330.000.33
HALLMARK_ESTROGEN_RESPONSE_LATE-00.00NaNNaN
HALLMARK_ESTROGEN_RESPONSE_LATE-10.200.200.00
HALLMARK_FATTY_ACID_METABOLISM-00.400.67-0.27
HALLMARK_FATTY_ACID_METABOLISM-10.250.33-0.08
HALLMARK_G2M_CHECKPOINT-00.670.600.07
HALLMARK_G2M_CHECKPOINT-10.620.570.05
HALLMARK_GLYCOLYSIS-00.500.000.50
HALLMARK_GLYCOLYSIS-10.460.200.26
HALLMARK_HEDGEHOG_SIGNALING-00.330.330.00
HALLMARK_HEDGEHOG_SIGNALING-10.600.500.10
HALLMARK_HEME_METABOLISM-00.000.000.00
HALLMARK_HEME_METABOLISM-10.000.000.00
HALLMARK_HYPOXIA-00.120.000.12
HALLMARK_HYPOXIA-10.250.250.00
HALLMARK_IL2_STAT5_SIGNALING-00.000.50-0.50
HALLMARK_IL2_STAT5_SIGNALING-10.380.330.04
HALLMARK_IL6_JAK_STAT3_SIGNALING-00.33NaNNaN
HALLMARK_IL6_JAK_STAT3_SIGNALING-10.400.50-0.10
HALLMARK_INFLAMMATORY_RESPONSE-00.33NaNNaN
HALLMARK_INFLAMMATORY_RESPONSE-10.670.500.17
HALLMARK_INTERFERON_ALPHA_RESPONSE-00.250.000.25
HALLMARK_INTERFERON_ALPHA_RESPONSE-10.220.220.00
HALLMARK_INTERFERON_GAMMA_RESPONSE-00.250.67-0.42
HALLMARK_INTERFERON_GAMMA_RESPONSE-10.250.000.25
HALLMARK_KRAS_SIGNALING_DN-00.000.000.00
HALLMARK_KRAS_SIGNALING_DN-10.000.50-0.50
HALLMARK_KRAS_SIGNALING_UP-00.000.11-0.11
HALLMARK_KRAS_SIGNALING_UP-10.27NaNNaN
HALLMARK_MITOTIC_SPINDLE-00.00NaNNaN
HALLMARK_MITOTIC_SPINDLE-10.500.400.10
HALLMARK_MTORC1_SIGNALING-00.250.44-0.19
HALLMARK_MTORC1_SIGNALING-10.431.00-0.57
HALLMARK_MYC_TARGETS_V1-00.500.60-0.10
HALLMARK_MYC_TARGETS_V1-10.620.64-0.01
HALLMARK_MYC_TARGETS_V2-00.200.33-0.13
HALLMARK_MYC_TARGETS_V2-10.000.33-0.33
HALLMARK_MYOGENESIS-01.001.000.00
HALLMARK_MYOGENESIS-10.000.50-0.50
HALLMARK_NOTCH_SIGNALING-00.801.00-0.20
HALLMARK_NOTCH_SIGNALING-11.000.750.25
HALLMARK_OXIDATIVE_PHOSPHORYLATION-01.000.800.20
HALLMARK_OXIDATIVE_PHOSPHORYLATION-11.000.670.33
HALLMARK_P53_PATHWAY-00.500.67-0.17
HALLMARK_P53_PATHWAY-10.380.290.09
HALLMARK_PANCREAS_BETA_CELLS-00.000.33-0.33
HALLMARK_PANCREAS_BETA_CELLS-10.000.33-0.33
HALLMARK_PEROXISOME-00.001.00-1.00
HALLMARK_PEROXISOME-10.500.200.30
HALLMARK_PI3K_AKT_MTOR_SIGNALING-00.670.000.67
HALLMARK_PI3K_AKT_MTOR_SIGNALING-10.671.00-0.33
HALLMARK_PROTEIN_SECRETION-00.670.500.17
HALLMARK_PROTEIN_SECRETION-10.500.170.33
HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-00.200.33-0.13
HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-10.000.000.00
HALLMARK_SPERMATOGENESIS-00.120.000.12
HALLMARK_SPERMATOGENESIS-10.000.000.00
HALLMARK_TGF_BETA_SIGNALING-00.000.000.00
HALLMARK_TGF_BETA_SIGNALING-1NaN0.50NaN
HALLMARK_TNFA_SIGNALING_VIA_NFKB-00.500.67-0.17
HALLMARK_TNFA_SIGNALING_VIA_NFKB-11.000.600.40
HALLMARK_UNFOLDED_PROTEIN_RESPONSE-00.401.00-0.60
HALLMARK_UNFOLDED_PROTEIN_RESPONSE-10.600.500.10
HALLMARK_UV_RESPONSE_DN-01.000.250.75
HALLMARK_UV_RESPONSE_DN-10.330.50-0.17
HALLMARK_UV_RESPONSE_UP-00.001.00-1.00
HALLMARK_UV_RESPONSE_UP-10.330.000.33
HALLMARK_WNT_BETA_CATENIN_SIGNALING-00.600.000.60
HALLMARK_WNT_BETA_CATENIN_SIGNALING-10.000.20-0.20
T cell proliferation-00.00NaNNaN
T cell proliferation-10.670.200.47
Yamanaka-TFs-00.000.000.00
Yamanaka-TFs-10.000.000.00
amigo-example-00.400.50-0.10
amigo-example-10.330.50-0.17
bicluster_RNAseqDB_0-00.000.000.00
bicluster_RNAseqDB_0-10.000.000.00
bicluster_RNAseqDB_1002-00.330.270.07
bicluster_RNAseqDB_1002-10.000.57-0.57
endocytosis-00.500.250.25
endocytosis-10.401.00-0.60
glycolysis-gocam-00.500.440.06
glycolysis-gocam-10.500.500.00
go-postsynapse-calcium-transmembrane-00.50NaNNaN
go-postsynapse-calcium-transmembrane-11.001.000.00
go-reg-autophagy-pkra-00.500.400.10
go-reg-autophagy-pkra-10.600.200.40
hydrolase activity, hydrolyzing O-glycosyl compounds-00.40NaNNaN
ig-receptor-binding-2022-00.500.000.50
ig-receptor-binding-2022-10.500.500.00
meiosis I-00.800.750.05
meiosis I-10.670.75-0.08
molecular sequestering-00.000.000.00
molecular sequestering-10.200.000.20
mtorc1-00.250.44-0.19
mtorc1-10.000.40-0.40
peroxisome-10.00NaNNaN
progeria-00.000.000.00
progeria-10.000.000.00
regulation of presynaptic membrane potential-10.000.50-0.50
sensory ataxia-00.000.000.00
sensory ataxia-10.000.000.00
term-GO:0007212-00.670.000.67
term-GO:0007212-1NaN0.25NaN
tf-downreg-colorectal-01.001.000.00
tf-downreg-colorectal-10.000.000.00
no_synopsisEDS-01.000.001.00
EDS-11.000.001.00
FA-0NaN0.50NaN
FA-11.000.001.00
HALLMARK_ADIPOGENESIS-00.250.000.25
HALLMARK_ADIPOGENESIS-10.500.290.21
HALLMARK_ALLOGRAFT_REJECTION-01.000.001.00
HALLMARK_ALLOGRAFT_REJECTION-11.001.000.00
HALLMARK_ANDROGEN_RESPONSE-00.120.25-0.12
HALLMARK_ANDROGEN_RESPONSE-10.080.000.08
HALLMARK_ANGIOGENESIS-0NaN0.50NaN
HALLMARK_ANGIOGENESIS-10.80NaNNaN
HALLMARK_APICAL_JUNCTION-00.000.50-0.50
HALLMARK_APICAL_JUNCTION-10.501.00-0.50
HALLMARK_APICAL_SURFACE-00.200.25-0.05
HALLMARK_APICAL_SURFACE-10.501.00-0.50
HALLMARK_APOPTOSIS-01.000.500.50
HALLMARK_APOPTOSIS-10.330.56-0.22
HALLMARK_BILE_ACID_METABOLISM-00.670.670.00
HALLMARK_BILE_ACID_METABOLISM-10.000.50-0.50
HALLMARK_CHOLESTEROL_HOMEOSTASIS-00.330.330.00
HALLMARK_CHOLESTEROL_HOMEOSTASIS-10.330.330.00
HALLMARK_COAGULATION-10.600.67-0.07
HALLMARK_COMPLEMENT-00.000.75-0.75
HALLMARK_COMPLEMENT-10.400.360.04
HALLMARK_DNA_REPAIR-00.600.430.17
HALLMARK_DNA_REPAIR-10.330.290.05
HALLMARK_E2F_TARGETS-00.500.500.00
HALLMARK_E2F_TARGETS-10.550.75-0.20
HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0NaN1.00NaN
HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-10.671.00-0.33
HALLMARK_ESTROGEN_RESPONSE_EARLY-0NaN0.00NaN
HALLMARK_ESTROGEN_RESPONSE_EARLY-10.000.33-0.33
HALLMARK_ESTROGEN_RESPONSE_LATE-00.000.000.00
HALLMARK_ESTROGEN_RESPONSE_LATE-10.250.120.12
HALLMARK_FATTY_ACID_METABOLISM-00.571.00-0.43
HALLMARK_FATTY_ACID_METABOLISM-11.000.800.20
HALLMARK_G2M_CHECKPOINT-01.000.570.43
HALLMARK_G2M_CHECKPOINT-11.001.000.00
HALLMARK_GLYCOLYSIS-00.401.00-0.60
HALLMARK_GLYCOLYSIS-10.330.60-0.27
HALLMARK_HEDGEHOG_SIGNALING-00.861.00-0.14
HALLMARK_HEDGEHOG_SIGNALING-10.711.00-0.29
HALLMARK_HEME_METABOLISM-00.000.50-0.50
HALLMARK_HEME_METABOLISM-10.000.10-0.10
HALLMARK_HYPOXIA-00.430.000.43
HALLMARK_HYPOXIA-10.120.33-0.21
HALLMARK_IL2_STAT5_SIGNALING-00.250.000.25
HALLMARK_IL2_STAT5_SIGNALING-11.000.750.25
HALLMARK_IL6_JAK_STAT3_SIGNALING-00.750.000.75
HALLMARK_IL6_JAK_STAT3_SIGNALING-11.001.000.00
HALLMARK_INFLAMMATORY_RESPONSE-01.00NaNNaN
HALLMARK_INFLAMMATORY_RESPONSE-10.670.670.00
HALLMARK_INTERFERON_ALPHA_RESPONSE-00.00NaNNaN
HALLMARK_INTERFERON_ALPHA_RESPONSE-10.000.33-0.33
HALLMARK_INTERFERON_GAMMA_RESPONSE-01.000.670.33
HALLMARK_INTERFERON_GAMMA_RESPONSE-11.001.000.00
HALLMARK_KRAS_SIGNALING_DN-00.200.000.20
HALLMARK_KRAS_SIGNALING_DN-11.000.001.00
HALLMARK_KRAS_SIGNALING_UP-00.500.500.00
HALLMARK_KRAS_SIGNALING_UP-10.80NaNNaN
HALLMARK_MITOTIC_SPINDLE-00.000.50-0.50
HALLMARK_MITOTIC_SPINDLE-10.500.75-0.25
HALLMARK_MTORC1_SIGNALING-00.000.000.00
HALLMARK_MTORC1_SIGNALING-10.140.33-0.19
HALLMARK_MYC_TARGETS_V1-00.500.330.17
HALLMARK_MYC_TARGETS_V1-10.501.00-0.50
HALLMARK_MYC_TARGETS_V2-0NaN0.25NaN
HALLMARK_MYC_TARGETS_V2-10.000.000.00
HALLMARK_MYOGENESIS-0NaN0.00NaN
HALLMARK_MYOGENESIS-10.750.250.50
HALLMARK_NOTCH_SIGNALING-00.000.50-0.50
HALLMARK_NOTCH_SIGNALING-10.330.50-0.17
HALLMARK_OXIDATIVE_PHOSPHORYLATION-01.000.500.50
HALLMARK_OXIDATIVE_PHOSPHORYLATION-11.001.000.00
HALLMARK_P53_PATHWAY-00.670.500.17
HALLMARK_P53_PATHWAY-10.400.67-0.27
HALLMARK_PANCREAS_BETA_CELLS-00.670.400.27
HALLMARK_PANCREAS_BETA_CELLS-10.000.33-0.33
HALLMARK_PEROXISOME-0NaN0.25NaN
HALLMARK_PEROXISOME-10.670.110.56
HALLMARK_PI3K_AKT_MTOR_SIGNALING-00.000.000.00
HALLMARK_PI3K_AKT_MTOR_SIGNALING-10.400.57-0.17
HALLMARK_PROTEIN_SECRETION-0NaN1.00NaN
HALLMARK_PROTEIN_SECRETION-10.330.200.13
HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0NaN0.20NaN
HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-10.000.000.00
HALLMARK_SPERMATOGENESIS-00.000.17-0.17
HALLMARK_SPERMATOGENESIS-10.000.000.00
HALLMARK_TGF_BETA_SIGNALING-00.330.000.33
HALLMARK_TGF_BETA_SIGNALING-11.000.670.33
HALLMARK_TNFA_SIGNALING_VIA_NFKB-01.000.400.60
HALLMARK_TNFA_SIGNALING_VIA_NFKB-10.250.000.25
HALLMARK_UNFOLDED_PROTEIN_RESPONSE-00.670.500.17
HALLMARK_UNFOLDED_PROTEIN_RESPONSE-10.200.33-0.13
HALLMARK_UV_RESPONSE_DN-01.001.000.00
HALLMARK_UV_RESPONSE_DN-10.800.500.30
HALLMARK_UV_RESPONSE_UP-00.330.40-0.07
HALLMARK_UV_RESPONSE_UP-10.170.33-0.17
HALLMARK_WNT_BETA_CATENIN_SIGNALING-01.000.500.50
HALLMARK_WNT_BETA_CATENIN_SIGNALING-10.670.670.00
T cell proliferation-00.501.00-0.50
T cell proliferation-10.500.67-0.17
Yamanaka-TFs-00.500.500.00
Yamanaka-TFs-10.000.000.00
amigo-example-00.500.000.50
amigo-example-10.000.33-0.33
bicluster_RNAseqDB_0-00.000.000.00
bicluster_RNAseqDB_0-10.500.000.50
bicluster_RNAseqDB_1002-0NaN0.33NaN
bicluster_RNAseqDB_1002-10.200.000.20
endocytosis-00.000.000.00
endocytosis-10.000.50-0.50
glycolysis-gocam-01.000.500.50
glycolysis-gocam-10.500.500.00
go-postsynapse-calcium-transmembrane-00.001.00-1.00
go-postsynapse-calcium-transmembrane-11.001.000.00
go-reg-autophagy-pkra-00.17NaNNaN
go-reg-autophagy-pkra-10.000.000.00
hydrolase activity, hydrolyzing O-glycosyl compounds-00.001.00-1.00
hydrolase activity, hydrolyzing O-glycosyl compounds-10.000.000.00
ig-receptor-binding-2022-00.50NaNNaN
ig-receptor-binding-2022-10.330.000.33
meiosis I-01.000.750.25
meiosis I-11.001.000.00
molecular sequestering-00.000.000.00
molecular sequestering-10.000.000.00
mtorc1-00.000.000.00
mtorc1-11.00NaNNaN
peroxisome-00.000.000.00
peroxisome-1NaN1.00NaN
progeria-00.000.000.00
progeria-10.000.000.00
regulation of presynaptic membrane potential-01.001.000.00
regulation of presynaptic membrane potential-10.751.00-0.25
sensory ataxia-00.000.000.00
sensory ataxia-10.000.000.00
term-GO:0007212-10.500.500.00
tf-downreg-colorectal-00.501.00-0.50
tf-downreg-colorectal-10.000.40-0.40
ontological_synopsisEDS-00.180.170.02
EDS-10.330.80-0.47
FA-0NaN0.83NaN
FA-10.380.230.15
HALLMARK_ADIPOGENESIS-00.250.000.25
HALLMARK_ADIPOGENESIS-10.000.000.00
HALLMARK_ALLOGRAFT_REJECTION-00.750.400.35
HALLMARK_ALLOGRAFT_REJECTION-10.500.500.00
HALLMARK_ANDROGEN_RESPONSE-00.000.09-0.09
HALLMARK_ANDROGEN_RESPONSE-10.000.000.00
HALLMARK_ANGIOGENESIS-00.200.000.20
HALLMARK_ANGIOGENESIS-10.330.290.05
HALLMARK_APICAL_JUNCTION-01.000.800.20
HALLMARK_APICAL_JUNCTION-10.000.000.00
HALLMARK_APICAL_SURFACE-00.000.000.00
HALLMARK_APICAL_SURFACE-10.500.000.50
HALLMARK_APOPTOSIS-00.500.60-0.10
HALLMARK_APOPTOSIS-11.000.330.67
HALLMARK_BILE_ACID_METABOLISM-00.330.50-0.17
HALLMARK_BILE_ACID_METABOLISM-10.400.50-0.10
HALLMARK_CHOLESTEROL_HOMEOSTASIS-00.080.25-0.17
HALLMARK_CHOLESTEROL_HOMEOSTASIS-10.330.50-0.17
HALLMARK_COAGULATION-00.501.00-0.50
HALLMARK_COAGULATION-10.500.330.17
HALLMARK_COMPLEMENT-00.330.50-0.17
HALLMARK_COMPLEMENT-10.560.70-0.14
HALLMARK_DNA_REPAIR-00.250.000.25
HALLMARK_DNA_REPAIR-10.000.33-0.33
HALLMARK_E2F_TARGETS-00.830.500.33
HALLMARK_E2F_TARGETS-10.400.86-0.46
HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-01.000.001.00
HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-10.000.50-0.50
HALLMARK_ESTROGEN_RESPONSE_EARLY-00.000.000.00
HALLMARK_ESTROGEN_RESPONSE_EARLY-10.000.000.00
HALLMARK_ESTROGEN_RESPONSE_LATE-0NaN0.05NaN
HALLMARK_ESTROGEN_RESPONSE_LATE-10.000.000.00
HALLMARK_FATTY_ACID_METABOLISM-00.260.200.06
HALLMARK_FATTY_ACID_METABOLISM-10.140.60-0.46
HALLMARK_G2M_CHECKPOINT-00.500.67-0.17
HALLMARK_G2M_CHECKPOINT-10.250.73-0.48
HALLMARK_GLYCOLYSIS-00.140.000.14
HALLMARK_GLYCOLYSIS-10.000.11-0.11
HALLMARK_HEDGEHOG_SIGNALING-00.600.110.49
HALLMARK_HEDGEHOG_SIGNALING-10.000.33-0.33
HALLMARK_HEME_METABOLISM-00.000.000.00
HALLMARK_HEME_METABOLISM-10.000.000.00
HALLMARK_HYPOXIA-00.000.50-0.50
HALLMARK_HYPOXIA-10.000.000.00
HALLMARK_IL2_STAT5_SIGNALING-00.330.43-0.10
HALLMARK_IL2_STAT5_SIGNALING-10.080.33-0.25
HALLMARK_IL6_JAK_STAT3_SIGNALING-00.330.67-0.33
HALLMARK_IL6_JAK_STAT3_SIGNALING-11.000.600.40
HALLMARK_INFLAMMATORY_RESPONSE-00.750.430.32
HALLMARK_INFLAMMATORY_RESPONSE-10.400.250.15
HALLMARK_INTERFERON_ALPHA_RESPONSE-00.000.25-0.25
HALLMARK_INTERFERON_ALPHA_RESPONSE-10.820.250.57
HALLMARK_INTERFERON_GAMMA_RESPONSE-00.270.000.27
HALLMARK_INTERFERON_GAMMA_RESPONSE-10.000.20-0.20
HALLMARK_KRAS_SIGNALING_DN-00.000.000.00
HALLMARK_KRAS_SIGNALING_DN-10.330.000.33
HALLMARK_KRAS_SIGNALING_UP-00.000.67-0.67
HALLMARK_KRAS_SIGNALING_UP-10.000.000.00
HALLMARK_MITOTIC_SPINDLE-00.330.44-0.11
HALLMARK_MITOTIC_SPINDLE-1NaN0.29NaN
HALLMARK_MTORC1_SIGNALING-00.200.120.08
HALLMARK_MTORC1_SIGNALING-10.080.000.08
HALLMARK_MYC_TARGETS_V1-00.400.71-0.31
HALLMARK_MYC_TARGETS_V1-10.330.100.23
HALLMARK_MYC_TARGETS_V2-00.140.25-0.11
HALLMARK_MYC_TARGETS_V2-10.200.25-0.05
HALLMARK_MYOGENESIS-00.430.000.43
HALLMARK_MYOGENESIS-10.330.000.33
HALLMARK_NOTCH_SIGNALING-00.800.88-0.07
HALLMARK_NOTCH_SIGNALING-10.330.62-0.29
HALLMARK_OXIDATIVE_PHOSPHORYLATION-00.500.500.00
HALLMARK_OXIDATIVE_PHOSPHORYLATION-10.270.33-0.06
HALLMARK_P53_PATHWAY-00.00NaNNaN
HALLMARK_P53_PATHWAY-10.080.50-0.42
HALLMARK_PANCREAS_BETA_CELLS-00.330.080.26
HALLMARK_PANCREAS_BETA_CELLS-10.000.000.00
HALLMARK_PEROXISOME-00.500.430.07
HALLMARK_PEROXISOME-1NaN0.08NaN
HALLMARK_PI3K_AKT_MTOR_SIGNALING-00.311.00-0.69
HALLMARK_PI3K_AKT_MTOR_SIGNALING-11.000.620.38
HALLMARK_PROTEIN_SECRETION-00.400.000.40
HALLMARK_PROTEIN_SECRETION-10.000.25-0.25
HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-00.080.000.08
HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-10.550.64-0.09
HALLMARK_SPERMATOGENESIS-00.000.12-0.12
HALLMARK_SPERMATOGENESIS-10.110.000.11
HALLMARK_TGF_BETA_SIGNALING-01.000.560.44
HALLMARK_TGF_BETA_SIGNALING-10.000.70-0.70
HALLMARK_TNFA_SIGNALING_VIA_NFKB-01.000.001.00
HALLMARK_TNFA_SIGNALING_VIA_NFKB-10.250.75-0.50
HALLMARK_UNFOLDED_PROTEIN_RESPONSE-00.450.000.45
HALLMARK_UNFOLDED_PROTEIN_RESPONSE-10.000.17-0.17
HALLMARK_UV_RESPONSE_DN-00.00NaNNaN
HALLMARK_UV_RESPONSE_DN-10.000.29-0.29
HALLMARK_UV_RESPONSE_UP-00.170.000.17
HALLMARK_UV_RESPONSE_UP-10.000.000.00
HALLMARK_WNT_BETA_CATENIN_SIGNALING-00.170.170.00
HALLMARK_WNT_BETA_CATENIN_SIGNALING-10.670.440.22
T cell proliferation-00.250.43-0.18
T cell proliferation-10.000.000.00
Yamanaka-TFs-00.000.000.00
Yamanaka-TFs-10.080.11-0.03
amigo-example-00.250.44-0.19
amigo-example-10.400.300.10
bicluster_RNAseqDB_0-00.000.000.00
bicluster_RNAseqDB_0-10.000.000.00
bicluster_RNAseqDB_1002-00.380.50-0.12
bicluster_RNAseqDB_1002-10.670.000.67
endocytosis-00.330.200.13
endocytosis-10.170.000.17
glycolysis-gocam-00.000.33-0.33
glycolysis-gocam-10.260.190.08
go-postsynapse-calcium-transmembrane-00.471.00-0.53
go-postsynapse-calcium-transmembrane-11.001.000.00
go-reg-autophagy-pkra-00.000.25-0.25
go-reg-autophagy-pkra-10.331.00-0.67
hydrolase activity, hydrolyzing O-glycosyl compounds-00.620.75-0.12
hydrolase activity, hydrolyzing O-glycosyl compounds-10.350.70-0.35
ig-receptor-binding-2022-00.000.000.00
ig-receptor-binding-2022-10.140.110.03
meiosis I-00.250.67-0.42
meiosis I-10.710.73-0.01
molecular sequestering-00.170.170.00
molecular sequestering-10.330.140.19
mtorc1-00.200.120.08
mtorc1-11.000.220.78
peroxisome-00.830.670.17
peroxisome-10.430.140.29
progeria-00.000.07-0.07
progeria-10.000.000.00
regulation of presynaptic membrane potential-00.560.90-0.34
regulation of presynaptic membrane potential-11.000.600.40
sensory ataxia-00.000.04-0.04
sensory ataxia-1NaN0.11NaN
term-GO:0007212-00.200.140.06
term-GO:0007212-10.430.220.21
tf-downreg-colorectal-00.570.330.24
tf-downreg-colorectal-10.800.500.30
\n", - "
" - ], - "text/plain": [ - "prompt_variant v1 \\\n", - "model method geneset \n", - "gpt-3.5-turbo narrative_synopsis EDS-0 0.14 \n", - " EDS-1 0.50 \n", - " FA-0 1.00 \n", - " FA-1 1.00 \n", - " HALLMARK_ADIPOGENESIS-0 1.00 \n", - " HALLMARK_ADIPOGENESIS-1 0.33 \n", - " HALLMARK_ALLOGRAFT_REJECTION-0 1.00 \n", - " HALLMARK_ALLOGRAFT_REJECTION-1 1.00 \n", - " HALLMARK_ANDROGEN_RESPONSE-0 0.00 \n", - " HALLMARK_ANDROGEN_RESPONSE-1 0.20 \n", - " HALLMARK_ANGIOGENESIS-0 0.50 \n", - " HALLMARK_ANGIOGENESIS-1 0.50 \n", - " HALLMARK_APICAL_JUNCTION-0 1.00 \n", - " HALLMARK_APICAL_JUNCTION-1 0.80 \n", - " HALLMARK_APICAL_SURFACE-0 0.25 \n", - " HALLMARK_APICAL_SURFACE-1 0.33 \n", - " HALLMARK_APOPTOSIS-0 1.00 \n", - " HALLMARK_APOPTOSIS-1 NaN \n", - " HALLMARK_BILE_ACID_METABOLISM-0 1.00 \n", - " HALLMARK_BILE_ACID_METABOLISM-1 0.83 \n", - " HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 0.67 \n", - " HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 0.67 \n", - " HALLMARK_COAGULATION-0 1.00 \n", - " HALLMARK_COAGULATION-1 0.50 \n", - " HALLMARK_COMPLEMENT-0 1.00 \n", - " HALLMARK_COMPLEMENT-1 0.80 \n", - " HALLMARK_DNA_REPAIR-0 0.67 \n", - " HALLMARK_DNA_REPAIR-1 0.38 \n", - " HALLMARK_E2F_TARGETS-0 1.00 \n", - " HALLMARK_E2F_TARGETS-1 0.75 \n", - " HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 1.00 \n", - " HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 0.83 \n", - " HALLMARK_ESTROGEN_RESPONSE_EARLY-0 0.00 \n", - " HALLMARK_ESTROGEN_RESPONSE_EARLY-1 0.00 \n", - " HALLMARK_ESTROGEN_RESPONSE_LATE-0 0.00 \n", - " HALLMARK_ESTROGEN_RESPONSE_LATE-1 0.20 \n", - " HALLMARK_FATTY_ACID_METABOLISM-0 0.80 \n", - " HALLMARK_FATTY_ACID_METABOLISM-1 1.00 \n", - " HALLMARK_G2M_CHECKPOINT-0 1.00 \n", - " HALLMARK_G2M_CHECKPOINT-1 0.83 \n", - " HALLMARK_GLYCOLYSIS-0 0.64 \n", - " HALLMARK_GLYCOLYSIS-1 0.40 \n", - " HALLMARK_HEDGEHOG_SIGNALING-0 1.00 \n", - " HALLMARK_HEDGEHOG_SIGNALING-1 1.00 \n", - " HALLMARK_HEME_METABOLISM-0 0.00 \n", - " HALLMARK_HEME_METABOLISM-1 0.10 \n", - " HALLMARK_HYPOXIA-0 0.67 \n", - " HALLMARK_HYPOXIA-1 0.50 \n", - " HALLMARK_IL2_STAT5_SIGNALING-0 1.00 \n", - " HALLMARK_IL2_STAT5_SIGNALING-1 0.67 \n", - " HALLMARK_IL6_JAK_STAT3_SIGNALING-0 NaN \n", - " HALLMARK_IL6_JAK_STAT3_SIGNALING-1 1.00 \n", - " HALLMARK_INFLAMMATORY_RESPONSE-0 0.33 \n", - " HALLMARK_INFLAMMATORY_RESPONSE-1 1.00 \n", - " HALLMARK_INTERFERON_ALPHA_RESPONSE-0 0.75 \n", - " HALLMARK_INTERFERON_ALPHA_RESPONSE-1 1.00 \n", - " HALLMARK_INTERFERON_GAMMA_RESPONSE-0 NaN \n", - " HALLMARK_INTERFERON_GAMMA_RESPONSE-1 0.75 \n", - " HALLMARK_KRAS_SIGNALING_DN-0 0.20 \n", - " HALLMARK_KRAS_SIGNALING_DN-1 0.00 \n", - " HALLMARK_KRAS_SIGNALING_UP-0 0.20 \n", - " HALLMARK_KRAS_SIGNALING_UP-1 0.25 \n", - " HALLMARK_MITOTIC_SPINDLE-0 0.80 \n", - " HALLMARK_MITOTIC_SPINDLE-1 1.00 \n", - " HALLMARK_MTORC1_SIGNALING-0 0.60 \n", - " HALLMARK_MTORC1_SIGNALING-1 0.50 \n", - " HALLMARK_MYC_TARGETS_V1-0 0.83 \n", - " HALLMARK_MYC_TARGETS_V1-1 1.00 \n", - " HALLMARK_MYC_TARGETS_V2-0 1.00 \n", - " HALLMARK_MYC_TARGETS_V2-1 1.00 \n", - " HALLMARK_MYOGENESIS-0 0.78 \n", - " HALLMARK_MYOGENESIS-1 1.00 \n", - " HALLMARK_NOTCH_SIGNALING-0 0.75 \n", - " HALLMARK_NOTCH_SIGNALING-1 1.00 \n", - " HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 1.00 \n", - " HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 1.00 \n", - " HALLMARK_P53_PATHWAY-0 0.67 \n", - " HALLMARK_P53_PATHWAY-1 0.75 \n", - " HALLMARK_PANCREAS_BETA_CELLS-0 1.00 \n", - " HALLMARK_PANCREAS_BETA_CELLS-1 0.00 \n", - " HALLMARK_PEROXISOME-0 0.60 \n", - " HALLMARK_PEROXISOME-1 1.00 \n", - " HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 1.00 \n", - " HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 1.00 \n", - " HALLMARK_PROTEIN_SECRETION-0 0.67 \n", - " HALLMARK_PROTEIN_SECRETION-1 1.00 \n", - " HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 1.00 \n", - " HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 1.00 \n", - " HALLMARK_SPERMATOGENESIS-0 0.25 \n", - " HALLMARK_SPERMATOGENESIS-1 0.00 \n", - " HALLMARK_TGF_BETA_SIGNALING-0 NaN \n", - " HALLMARK_TGF_BETA_SIGNALING-1 1.00 \n", - " HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 1.00 \n", - " HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 1.00 \n", - " HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 1.00 \n", - " HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 1.00 \n", - " HALLMARK_UV_RESPONSE_DN-0 0.00 \n", - " HALLMARK_UV_RESPONSE_DN-1 0.67 \n", - " HALLMARK_UV_RESPONSE_UP-0 0.30 \n", - " HALLMARK_UV_RESPONSE_UP-1 0.20 \n", - " HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 0.00 \n", - " HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 1.00 \n", - " T cell proliferation-0 0.75 \n", - " T cell proliferation-1 1.00 \n", - " Yamanaka-TFs-0 NaN \n", - " Yamanaka-TFs-1 0.00 \n", - " amigo-example-0 0.20 \n", - " amigo-example-1 0.50 \n", - " bicluster_RNAseqDB_0-0 0.00 \n", - " bicluster_RNAseqDB_0-1 0.00 \n", - " bicluster_RNAseqDB_1002-0 0.55 \n", - " bicluster_RNAseqDB_1002-1 0.67 \n", - " endocytosis-0 1.00 \n", - " endocytosis-1 1.00 \n", - " glycolysis-gocam-0 NaN \n", - " glycolysis-gocam-1 1.00 \n", - " go-postsynapse-calcium-transmembrane-0 1.00 \n", - " go-postsynapse-calcium-transmembrane-1 0.67 \n", - " go-reg-autophagy-pkra-0 0.50 \n", - " go-reg-autophagy-pkra-1 0.67 \n", - " hydrolase activity, hydrolyzing O-glycosyl compounds-0 0.86 \n", - " hydrolase activity, hydrolyzing O-glycosyl compounds-1 0.75 \n", - " ig-receptor-binding-2022-0 0.33 \n", - " ig-receptor-binding-2022-1 1.00 \n", - " meiosis I-0 NaN \n", - " meiosis I-1 1.00 \n", - " molecular sequestering-0 0.00 \n", - " molecular sequestering-1 0.00 \n", - " mtorc1-0 0.60 \n", - " mtorc1-1 1.00 \n", - " peroxisome-0 1.00 \n", - " peroxisome-1 NaN \n", - " progeria-0 1.00 \n", - " progeria-1 0.00 \n", - " regulation of presynaptic membrane potential-0 1.00 \n", - " regulation of presynaptic membrane potential-1 0.67 \n", - " sensory ataxia-0 0.50 \n", - " sensory ataxia-1 0.00 \n", - " term-GO:0007212-0 1.00 \n", - " term-GO:0007212-1 0.67 \n", - " tf-downreg-colorectal-0 0.50 \n", - " tf-downreg-colorectal-1 1.00 \n", - " no_synopsis EDS-0 1.00 \n", - " EDS-1 0.67 \n", - " FA-0 NaN \n", - " FA-1 1.00 \n", - " HALLMARK_ADIPOGENESIS-0 0.64 \n", - " HALLMARK_ADIPOGENESIS-1 0.36 \n", - " HALLMARK_ALLOGRAFT_REJECTION-0 1.00 \n", - " HALLMARK_ALLOGRAFT_REJECTION-1 1.00 \n", - " HALLMARK_ANDROGEN_RESPONSE-0 0.00 \n", - " HALLMARK_ANDROGEN_RESPONSE-1 0.00 \n", - " HALLMARK_ANGIOGENESIS-0 0.33 \n", - " HALLMARK_ANGIOGENESIS-1 0.50 \n", - " HALLMARK_APICAL_JUNCTION-0 0.75 \n", - " HALLMARK_APICAL_JUNCTION-1 0.89 \n", - " HALLMARK_APICAL_SURFACE-0 0.14 \n", - " HALLMARK_APICAL_SURFACE-1 0.12 \n", - " HALLMARK_APOPTOSIS-0 0.70 \n", - " HALLMARK_APOPTOSIS-1 1.00 \n", - " HALLMARK_BILE_ACID_METABOLISM-0 0.50 \n", - " HALLMARK_BILE_ACID_METABOLISM-1 1.00 \n", - " HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 0.67 \n", - " HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 0.88 \n", - " HALLMARK_COAGULATION-0 1.00 \n", - " HALLMARK_COAGULATION-1 1.00 \n", - " HALLMARK_COMPLEMENT-0 0.40 \n", - " HALLMARK_COMPLEMENT-1 0.89 \n", - " HALLMARK_DNA_REPAIR-0 0.80 \n", - " HALLMARK_DNA_REPAIR-1 0.75 \n", - " HALLMARK_E2F_TARGETS-0 1.00 \n", - " HALLMARK_E2F_TARGETS-1 1.00 \n", - " HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 0.82 \n", - " HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 0.89 \n", - " HALLMARK_ESTROGEN_RESPONSE_EARLY-0 0.00 \n", - " HALLMARK_ESTROGEN_RESPONSE_EARLY-1 0.50 \n", - " HALLMARK_ESTROGEN_RESPONSE_LATE-0 0.20 \n", - " HALLMARK_ESTROGEN_RESPONSE_LATE-1 0.30 \n", - " HALLMARK_FATTY_ACID_METABOLISM-0 NaN \n", - " HALLMARK_FATTY_ACID_METABOLISM-1 1.00 \n", - " HALLMARK_G2M_CHECKPOINT-0 1.00 \n", - " HALLMARK_G2M_CHECKPOINT-1 1.00 \n", - " HALLMARK_GLYCOLYSIS-0 NaN \n", - " HALLMARK_GLYCOLYSIS-1 0.50 \n", - " HALLMARK_HEDGEHOG_SIGNALING-0 0.80 \n", - " HALLMARK_HEDGEHOG_SIGNALING-1 1.00 \n", - " HALLMARK_HEME_METABOLISM-0 0.33 \n", - " HALLMARK_HEME_METABOLISM-1 0.38 \n", - " HALLMARK_HYPOXIA-0 0.56 \n", - " HALLMARK_HYPOXIA-1 1.00 \n", - " HALLMARK_IL2_STAT5_SIGNALING-1 0.67 \n", - " HALLMARK_IL6_JAK_STAT3_SIGNALING-0 1.00 \n", - " HALLMARK_IL6_JAK_STAT3_SIGNALING-1 1.00 \n", - " HALLMARK_INFLAMMATORY_RESPONSE-0 0.71 \n", - " HALLMARK_INFLAMMATORY_RESPONSE-1 0.67 \n", - " HALLMARK_INTERFERON_ALPHA_RESPONSE-0 1.00 \n", - " HALLMARK_INTERFERON_ALPHA_RESPONSE-1 0.29 \n", - " HALLMARK_INTERFERON_GAMMA_RESPONSE-0 1.00 \n", - " HALLMARK_INTERFERON_GAMMA_RESPONSE-1 1.00 \n", - " HALLMARK_KRAS_SIGNALING_DN-0 0.50 \n", - " HALLMARK_KRAS_SIGNALING_DN-1 0.00 \n", - " HALLMARK_KRAS_SIGNALING_UP-0 0.86 \n", - " HALLMARK_KRAS_SIGNALING_UP-1 0.40 \n", - " HALLMARK_MITOTIC_SPINDLE-0 1.00 \n", - " HALLMARK_MITOTIC_SPINDLE-1 1.00 \n", - " HALLMARK_MTORC1_SIGNALING-0 0.75 \n", - " HALLMARK_MTORC1_SIGNALING-1 0.50 \n", - " HALLMARK_MYC_TARGETS_V1-0 1.00 \n", - " HALLMARK_MYC_TARGETS_V1-1 1.00 \n", - " HALLMARK_MYC_TARGETS_V2-0 0.67 \n", - " HALLMARK_MYC_TARGETS_V2-1 0.67 \n", - " HALLMARK_MYOGENESIS-0 0.60 \n", - " HALLMARK_MYOGENESIS-1 NaN \n", - " HALLMARK_NOTCH_SIGNALING-0 0.45 \n", - " HALLMARK_NOTCH_SIGNALING-1 0.25 \n", - " HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 0.67 \n", - " HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 1.00 \n", - " HALLMARK_P53_PATHWAY-0 1.00 \n", - " HALLMARK_P53_PATHWAY-1 0.50 \n", - " HALLMARK_PANCREAS_BETA_CELLS-0 0.67 \n", - " HALLMARK_PANCREAS_BETA_CELLS-1 0.50 \n", - " HALLMARK_PEROXISOME-0 0.50 \n", - " HALLMARK_PEROXISOME-1 0.50 \n", - " HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 0.00 \n", - " HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 1.00 \n", - " HALLMARK_PROTEIN_SECRETION-0 1.00 \n", - " HALLMARK_PROTEIN_SECRETION-1 0.62 \n", - " HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 0.80 \n", - " HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 0.33 \n", - " HALLMARK_SPERMATOGENESIS-0 0.80 \n", - " HALLMARK_SPERMATOGENESIS-1 0.17 \n", - " HALLMARK_TGF_BETA_SIGNALING-0 0.86 \n", - " HALLMARK_TGF_BETA_SIGNALING-1 0.50 \n", - " HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 0.00 \n", - " HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 0.67 \n", - " HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 1.00 \n", - " HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 0.53 \n", - " HALLMARK_UV_RESPONSE_DN-0 1.00 \n", - " HALLMARK_UV_RESPONSE_DN-1 0.40 \n", - " HALLMARK_UV_RESPONSE_UP-0 0.50 \n", - " HALLMARK_UV_RESPONSE_UP-1 0.33 \n", - " HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 1.00 \n", - " HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 0.75 \n", - " T cell proliferation-0 1.00 \n", - " T cell proliferation-1 1.00 \n", - " Yamanaka-TFs-0 0.00 \n", - " Yamanaka-TFs-1 0.00 \n", - " amigo-example-0 0.43 \n", - " amigo-example-1 0.50 \n", - " bicluster_RNAseqDB_0-0 0.00 \n", - " bicluster_RNAseqDB_0-1 0.00 \n", - " bicluster_RNAseqDB_1002-0 0.50 \n", - " bicluster_RNAseqDB_1002-1 1.00 \n", - " endocytosis-0 0.40 \n", - " endocytosis-1 0.57 \n", - " glycolysis-gocam-0 1.00 \n", - " glycolysis-gocam-1 1.00 \n", - " go-postsynapse-calcium-transmembrane-0 0.80 \n", - " go-postsynapse-calcium-transmembrane-1 0.56 \n", - " go-reg-autophagy-pkra-0 1.00 \n", - " go-reg-autophagy-pkra-1 0.33 \n", - " hydrolase activity, hydrolyzing O-glycosyl compounds-0 0.80 \n", - " hydrolase activity, hydrolyzing O-glycosyl compounds-1 0.75 \n", - " ig-receptor-binding-2022-0 0.00 \n", - " ig-receptor-binding-2022-1 0.33 \n", - " meiosis I-0 1.00 \n", - " meiosis I-1 0.80 \n", - " molecular sequestering-0 0.12 \n", - " molecular sequestering-1 0.00 \n", - " mtorc1-0 0.75 \n", - " mtorc1-1 0.33 \n", - " peroxisome-0 1.00 \n", - " peroxisome-1 0.00 \n", - " progeria-0 0.00 \n", - " progeria-1 0.33 \n", - " regulation of presynaptic membrane potential-0 0.86 \n", - " regulation of presynaptic membrane potential-1 0.86 \n", - " sensory ataxia-0 0.00 \n", - " sensory ataxia-1 NaN \n", - " term-GO:0007212-0 0.80 \n", - " term-GO:0007212-1 NaN \n", - " tf-downreg-colorectal-0 1.00 \n", - " tf-downreg-colorectal-1 1.00 \n", - " ontological_synopsis EDS-0 0.75 \n", - " EDS-1 0.75 \n", - " FA-0 1.00 \n", - " FA-1 1.00 \n", - " HALLMARK_ADIPOGENESIS-0 0.00 \n", - " HALLMARK_ADIPOGENESIS-1 1.00 \n", - " HALLMARK_ALLOGRAFT_REJECTION-0 0.75 \n", - " HALLMARK_ALLOGRAFT_REJECTION-1 0.60 \n", - " HALLMARK_ANDROGEN_RESPONSE-0 0.50 \n", - " HALLMARK_ANDROGEN_RESPONSE-1 0.00 \n", - " HALLMARK_ANGIOGENESIS-1 NaN \n", - " HALLMARK_APICAL_JUNCTION-0 1.00 \n", - " HALLMARK_APICAL_SURFACE-0 0.00 \n", - " HALLMARK_APICAL_SURFACE-1 0.43 \n", - " HALLMARK_APOPTOSIS-0 1.00 \n", - " HALLMARK_APOPTOSIS-1 1.00 \n", - " HALLMARK_BILE_ACID_METABOLISM-0 1.00 \n", - " HALLMARK_BILE_ACID_METABOLISM-1 0.80 \n", - " HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 0.33 \n", - " HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 0.25 \n", - " HALLMARK_COAGULATION-0 0.67 \n", - " HALLMARK_COAGULATION-1 1.00 \n", - " HALLMARK_COMPLEMENT-0 0.00 \n", - " HALLMARK_COMPLEMENT-1 1.00 \n", - " HALLMARK_DNA_REPAIR-0 1.00 \n", - " HALLMARK_DNA_REPAIR-1 1.00 \n", - " HALLMARK_E2F_TARGETS-0 1.00 \n", - " HALLMARK_E2F_TARGETS-1 NaN \n", - " HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 1.00 \n", - " HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 0.50 \n", - " HALLMARK_ESTROGEN_RESPONSE_EARLY-0 0.00 \n", - " HALLMARK_ESTROGEN_RESPONSE_EARLY-1 0.00 \n", - " HALLMARK_ESTROGEN_RESPONSE_LATE-0 0.00 \n", - " HALLMARK_ESTROGEN_RESPONSE_LATE-1 NaN \n", - " HALLMARK_FATTY_ACID_METABOLISM-0 0.29 \n", - " HALLMARK_FATTY_ACID_METABOLISM-1 1.00 \n", - " HALLMARK_G2M_CHECKPOINT-0 1.00 \n", - " HALLMARK_G2M_CHECKPOINT-1 1.00 \n", - " HALLMARK_GLYCOLYSIS-0 0.67 \n", - " HALLMARK_GLYCOLYSIS-1 0.67 \n", - " HALLMARK_HEDGEHOG_SIGNALING-0 0.29 \n", - " HALLMARK_HEDGEHOG_SIGNALING-1 1.00 \n", - " HALLMARK_HEME_METABOLISM-0 0.33 \n", - " HALLMARK_HEME_METABOLISM-1 NaN \n", - " HALLMARK_HYPOXIA-0 0.20 \n", - " HALLMARK_HYPOXIA-1 0.33 \n", - " HALLMARK_IL2_STAT5_SIGNALING-0 0.80 \n", - " HALLMARK_IL2_STAT5_SIGNALING-1 0.12 \n", - " HALLMARK_IL6_JAK_STAT3_SIGNALING-0 1.00 \n", - " HALLMARK_IL6_JAK_STAT3_SIGNALING-1 1.00 \n", - " HALLMARK_INFLAMMATORY_RESPONSE-0 1.00 \n", - " HALLMARK_INFLAMMATORY_RESPONSE-1 1.00 \n", - " HALLMARK_INTERFERON_ALPHA_RESPONSE-0 0.67 \n", - " HALLMARK_INTERFERON_ALPHA_RESPONSE-1 0.50 \n", - " HALLMARK_INTERFERON_GAMMA_RESPONSE-0 0.33 \n", - " HALLMARK_INTERFERON_GAMMA_RESPONSE-1 1.00 \n", - " HALLMARK_KRAS_SIGNALING_DN-0 0.00 \n", - " HALLMARK_KRAS_SIGNALING_DN-1 0.00 \n", - " HALLMARK_KRAS_SIGNALING_UP-0 NaN \n", - " HALLMARK_KRAS_SIGNALING_UP-1 0.40 \n", - " HALLMARK_MITOTIC_SPINDLE-0 1.00 \n", - " HALLMARK_MITOTIC_SPINDLE-1 1.00 \n", - " HALLMARK_MTORC1_SIGNALING-0 0.33 \n", - " HALLMARK_MTORC1_SIGNALING-1 0.00 \n", - " HALLMARK_MYC_TARGETS_V1-0 1.00 \n", - " HALLMARK_MYC_TARGETS_V1-1 1.00 \n", - " HALLMARK_MYC_TARGETS_V2-0 0.33 \n", - " HALLMARK_MYC_TARGETS_V2-1 1.00 \n", - " HALLMARK_MYOGENESIS-0 0.00 \n", - " HALLMARK_MYOGENESIS-1 NaN \n", - " HALLMARK_NOTCH_SIGNALING-0 1.00 \n", - " HALLMARK_NOTCH_SIGNALING-1 NaN \n", - " HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 1.00 \n", - " HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 0.50 \n", - " HALLMARK_P53_PATHWAY-0 0.50 \n", - " HALLMARK_P53_PATHWAY-1 0.00 \n", - " HALLMARK_PANCREAS_BETA_CELLS-0 0.67 \n", - " HALLMARK_PANCREAS_BETA_CELLS-1 0.00 \n", - " HALLMARK_PEROXISOME-0 0.60 \n", - " HALLMARK_PEROXISOME-1 0.40 \n", - " HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 0.50 \n", - " HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 0.67 \n", - " HALLMARK_PROTEIN_SECRETION-0 0.62 \n", - " HALLMARK_PROTEIN_SECRETION-1 0.40 \n", - " HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 0.75 \n", - " HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 0.88 \n", - " HALLMARK_SPERMATOGENESIS-0 0.40 \n", - " HALLMARK_SPERMATOGENESIS-1 0.00 \n", - " HALLMARK_TGF_BETA_SIGNALING-0 1.00 \n", - " HALLMARK_TGF_BETA_SIGNALING-1 NaN \n", - " HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 1.00 \n", - " HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 1.00 \n", - " HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 0.75 \n", - " HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 NaN \n", - " HALLMARK_UV_RESPONSE_DN-0 0.50 \n", - " HALLMARK_UV_RESPONSE_DN-1 0.50 \n", - " HALLMARK_UV_RESPONSE_UP-0 0.00 \n", - " HALLMARK_UV_RESPONSE_UP-1 0.00 \n", - " HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 0.33 \n", - " HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 0.40 \n", - " T cell proliferation-0 1.00 \n", - " T cell proliferation-1 0.47 \n", - " Yamanaka-TFs-0 0.67 \n", - " Yamanaka-TFs-1 0.25 \n", - " amigo-example-0 1.00 \n", - " amigo-example-1 0.75 \n", - " bicluster_RNAseqDB_0-0 0.00 \n", - " bicluster_RNAseqDB_0-1 0.00 \n", - " bicluster_RNAseqDB_1002-0 1.00 \n", - " bicluster_RNAseqDB_1002-1 0.50 \n", - " endocytosis-0 1.00 \n", - " endocytosis-1 0.25 \n", - " glycolysis-gocam-0 0.50 \n", - " glycolysis-gocam-1 0.67 \n", - " go-postsynapse-calcium-transmembrane-0 1.00 \n", - " go-postsynapse-calcium-transmembrane-1 0.29 \n", - " go-reg-autophagy-pkra-0 0.60 \n", - " go-reg-autophagy-pkra-1 0.60 \n", - " hydrolase activity, hydrolyzing O-glycosyl compounds-0 1.00 \n", - " hydrolase activity, hydrolyzing O-glycosyl compounds-1 0.80 \n", - " ig-receptor-binding-2022-0 1.00 \n", - " ig-receptor-binding-2022-1 0.14 \n", - " meiosis I-0 1.00 \n", - " meiosis I-1 1.00 \n", - " molecular sequestering-0 0.33 \n", - " molecular sequestering-1 0.25 \n", - " mtorc1-0 0.33 \n", - " mtorc1-1 0.58 \n", - " peroxisome-0 0.50 \n", - " peroxisome-1 0.60 \n", - " progeria-0 0.00 \n", - " progeria-1 0.25 \n", - " regulation of presynaptic membrane potential-0 1.00 \n", - " regulation of presynaptic membrane potential-1 0.80 \n", - " sensory ataxia-0 0.67 \n", - " sensory ataxia-1 0.25 \n", - " term-GO:0007212-0 1.00 \n", - " term-GO:0007212-1 0.13 \n", - " tf-downreg-colorectal-0 1.00 \n", - " tf-downreg-colorectal-1 0.60 \n", - "text-davinci-003 narrative_synopsis EDS-0 0.33 \n", - " EDS-1 0.50 \n", - " FA-0 0.67 \n", - " FA-1 1.00 \n", - " HALLMARK_ADIPOGENESIS-0 0.80 \n", - " HALLMARK_ADIPOGENESIS-1 0.33 \n", - " HALLMARK_ALLOGRAFT_REJECTION-0 0.33 \n", - " HALLMARK_ALLOGRAFT_REJECTION-1 0.50 \n", - " HALLMARK_ANDROGEN_RESPONSE-0 0.00 \n", - " HALLMARK_ANDROGEN_RESPONSE-1 0.00 \n", - " HALLMARK_ANGIOGENESIS-0 0.00 \n", - " HALLMARK_ANGIOGENESIS-1 0.50 \n", - " HALLMARK_APICAL_JUNCTION-0 0.50 \n", - " HALLMARK_APICAL_JUNCTION-1 1.00 \n", - " HALLMARK_APICAL_SURFACE-0 0.00 \n", - " HALLMARK_APICAL_SURFACE-1 0.14 \n", - " HALLMARK_APOPTOSIS-0 1.00 \n", - " HALLMARK_APOPTOSIS-1 1.00 \n", - " HALLMARK_BILE_ACID_METABOLISM-0 0.33 \n", - " HALLMARK_BILE_ACID_METABOLISM-1 0.43 \n", - " HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 NaN \n", - " HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 0.50 \n", - " HALLMARK_COAGULATION-0 1.00 \n", - " HALLMARK_COAGULATION-1 0.00 \n", - " HALLMARK_COMPLEMENT-0 0.75 \n", - " HALLMARK_COMPLEMENT-1 1.00 \n", - " HALLMARK_DNA_REPAIR-0 0.00 \n", - " HALLMARK_DNA_REPAIR-1 0.36 \n", - " HALLMARK_E2F_TARGETS-0 0.70 \n", - " HALLMARK_E2F_TARGETS-1 0.71 \n", - " HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 1.00 \n", - " HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 0.00 \n", - " HALLMARK_ESTROGEN_RESPONSE_EARLY-0 0.00 \n", - " HALLMARK_ESTROGEN_RESPONSE_EARLY-1 0.33 \n", - " HALLMARK_ESTROGEN_RESPONSE_LATE-0 0.00 \n", - " HALLMARK_ESTROGEN_RESPONSE_LATE-1 0.20 \n", - " HALLMARK_FATTY_ACID_METABOLISM-0 0.40 \n", - " HALLMARK_FATTY_ACID_METABOLISM-1 0.25 \n", - " HALLMARK_G2M_CHECKPOINT-0 0.67 \n", - " HALLMARK_G2M_CHECKPOINT-1 0.62 \n", - " HALLMARK_GLYCOLYSIS-0 0.50 \n", - " HALLMARK_GLYCOLYSIS-1 0.46 \n", - " HALLMARK_HEDGEHOG_SIGNALING-0 0.33 \n", - " HALLMARK_HEDGEHOG_SIGNALING-1 0.60 \n", - " HALLMARK_HEME_METABOLISM-0 0.00 \n", - " HALLMARK_HEME_METABOLISM-1 0.00 \n", - " HALLMARK_HYPOXIA-0 0.12 \n", - " HALLMARK_HYPOXIA-1 0.25 \n", - " HALLMARK_IL2_STAT5_SIGNALING-0 0.00 \n", - " HALLMARK_IL2_STAT5_SIGNALING-1 0.38 \n", - " HALLMARK_IL6_JAK_STAT3_SIGNALING-0 0.33 \n", - " HALLMARK_IL6_JAK_STAT3_SIGNALING-1 0.40 \n", - " HALLMARK_INFLAMMATORY_RESPONSE-0 0.33 \n", - " HALLMARK_INFLAMMATORY_RESPONSE-1 0.67 \n", - " HALLMARK_INTERFERON_ALPHA_RESPONSE-0 0.25 \n", - " HALLMARK_INTERFERON_ALPHA_RESPONSE-1 0.22 \n", - " HALLMARK_INTERFERON_GAMMA_RESPONSE-0 0.25 \n", - " HALLMARK_INTERFERON_GAMMA_RESPONSE-1 0.25 \n", - " HALLMARK_KRAS_SIGNALING_DN-0 0.00 \n", - " HALLMARK_KRAS_SIGNALING_DN-1 0.00 \n", - " HALLMARK_KRAS_SIGNALING_UP-0 0.00 \n", - " HALLMARK_KRAS_SIGNALING_UP-1 0.27 \n", - " HALLMARK_MITOTIC_SPINDLE-0 0.00 \n", - " HALLMARK_MITOTIC_SPINDLE-1 0.50 \n", - " HALLMARK_MTORC1_SIGNALING-0 0.25 \n", - " HALLMARK_MTORC1_SIGNALING-1 0.43 \n", - " HALLMARK_MYC_TARGETS_V1-0 0.50 \n", - " HALLMARK_MYC_TARGETS_V1-1 0.62 \n", - " HALLMARK_MYC_TARGETS_V2-0 0.20 \n", - " HALLMARK_MYC_TARGETS_V2-1 0.00 \n", - " HALLMARK_MYOGENESIS-0 1.00 \n", - " HALLMARK_MYOGENESIS-1 0.00 \n", - " HALLMARK_NOTCH_SIGNALING-0 0.80 \n", - " HALLMARK_NOTCH_SIGNALING-1 1.00 \n", - " HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 1.00 \n", - " HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 1.00 \n", - " HALLMARK_P53_PATHWAY-0 0.50 \n", - " HALLMARK_P53_PATHWAY-1 0.38 \n", - " HALLMARK_PANCREAS_BETA_CELLS-0 0.00 \n", - " HALLMARK_PANCREAS_BETA_CELLS-1 0.00 \n", - " HALLMARK_PEROXISOME-0 0.00 \n", - " HALLMARK_PEROXISOME-1 0.50 \n", - " HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 0.67 \n", - " HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 0.67 \n", - " HALLMARK_PROTEIN_SECRETION-0 0.67 \n", - " HALLMARK_PROTEIN_SECRETION-1 0.50 \n", - " HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 0.20 \n", - " HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 0.00 \n", - " HALLMARK_SPERMATOGENESIS-0 0.12 \n", - " HALLMARK_SPERMATOGENESIS-1 0.00 \n", - " HALLMARK_TGF_BETA_SIGNALING-0 0.00 \n", - " HALLMARK_TGF_BETA_SIGNALING-1 NaN \n", - " HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 0.50 \n", - " HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 1.00 \n", - " HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 0.40 \n", - " HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 0.60 \n", - " HALLMARK_UV_RESPONSE_DN-0 1.00 \n", - " HALLMARK_UV_RESPONSE_DN-1 0.33 \n", - " HALLMARK_UV_RESPONSE_UP-0 0.00 \n", - " HALLMARK_UV_RESPONSE_UP-1 0.33 \n", - " HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 0.60 \n", - " HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 0.00 \n", - " T cell proliferation-0 0.00 \n", - " T cell proliferation-1 0.67 \n", - " Yamanaka-TFs-0 0.00 \n", - " Yamanaka-TFs-1 0.00 \n", - " amigo-example-0 0.40 \n", - " amigo-example-1 0.33 \n", - " bicluster_RNAseqDB_0-0 0.00 \n", - " bicluster_RNAseqDB_0-1 0.00 \n", - " bicluster_RNAseqDB_1002-0 0.33 \n", - " bicluster_RNAseqDB_1002-1 0.00 \n", - " endocytosis-0 0.50 \n", - " endocytosis-1 0.40 \n", - " glycolysis-gocam-0 0.50 \n", - " glycolysis-gocam-1 0.50 \n", - " go-postsynapse-calcium-transmembrane-0 0.50 \n", - " go-postsynapse-calcium-transmembrane-1 1.00 \n", - " go-reg-autophagy-pkra-0 0.50 \n", - " go-reg-autophagy-pkra-1 0.60 \n", - " hydrolase activity, hydrolyzing O-glycosyl compounds-0 0.40 \n", - " ig-receptor-binding-2022-0 0.50 \n", - " ig-receptor-binding-2022-1 0.50 \n", - " meiosis I-0 0.80 \n", - " meiosis I-1 0.67 \n", - " molecular sequestering-0 0.00 \n", - " molecular sequestering-1 0.20 \n", - " mtorc1-0 0.25 \n", - " mtorc1-1 0.00 \n", - " peroxisome-1 0.00 \n", - " progeria-0 0.00 \n", - " progeria-1 0.00 \n", - " regulation of presynaptic membrane potential-1 0.00 \n", - " sensory ataxia-0 0.00 \n", - " sensory ataxia-1 0.00 \n", - " term-GO:0007212-0 0.67 \n", - " term-GO:0007212-1 NaN \n", - " tf-downreg-colorectal-0 1.00 \n", - " tf-downreg-colorectal-1 0.00 \n", - " no_synopsis EDS-0 1.00 \n", - " EDS-1 1.00 \n", - " FA-0 NaN \n", - " FA-1 1.00 \n", - " HALLMARK_ADIPOGENESIS-0 0.25 \n", - " HALLMARK_ADIPOGENESIS-1 0.50 \n", - " HALLMARK_ALLOGRAFT_REJECTION-0 1.00 \n", - " HALLMARK_ALLOGRAFT_REJECTION-1 1.00 \n", - " HALLMARK_ANDROGEN_RESPONSE-0 0.12 \n", - " HALLMARK_ANDROGEN_RESPONSE-1 0.08 \n", - " HALLMARK_ANGIOGENESIS-0 NaN \n", - " HALLMARK_ANGIOGENESIS-1 0.80 \n", - " HALLMARK_APICAL_JUNCTION-0 0.00 \n", - " HALLMARK_APICAL_JUNCTION-1 0.50 \n", - " HALLMARK_APICAL_SURFACE-0 0.20 \n", - " HALLMARK_APICAL_SURFACE-1 0.50 \n", - " HALLMARK_APOPTOSIS-0 1.00 \n", - " HALLMARK_APOPTOSIS-1 0.33 \n", - " HALLMARK_BILE_ACID_METABOLISM-0 0.67 \n", - " HALLMARK_BILE_ACID_METABOLISM-1 0.00 \n", - " HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 0.33 \n", - " HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 0.33 \n", - " HALLMARK_COAGULATION-1 0.60 \n", - " HALLMARK_COMPLEMENT-0 0.00 \n", - " HALLMARK_COMPLEMENT-1 0.40 \n", - " HALLMARK_DNA_REPAIR-0 0.60 \n", - " HALLMARK_DNA_REPAIR-1 0.33 \n", - " HALLMARK_E2F_TARGETS-0 0.50 \n", - " HALLMARK_E2F_TARGETS-1 0.55 \n", - " HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 NaN \n", - " HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 0.67 \n", - " HALLMARK_ESTROGEN_RESPONSE_EARLY-0 NaN \n", - " HALLMARK_ESTROGEN_RESPONSE_EARLY-1 0.00 \n", - " HALLMARK_ESTROGEN_RESPONSE_LATE-0 0.00 \n", - " HALLMARK_ESTROGEN_RESPONSE_LATE-1 0.25 \n", - " HALLMARK_FATTY_ACID_METABOLISM-0 0.57 \n", - " HALLMARK_FATTY_ACID_METABOLISM-1 1.00 \n", - " HALLMARK_G2M_CHECKPOINT-0 1.00 \n", - " HALLMARK_G2M_CHECKPOINT-1 1.00 \n", - " HALLMARK_GLYCOLYSIS-0 0.40 \n", - " HALLMARK_GLYCOLYSIS-1 0.33 \n", - " HALLMARK_HEDGEHOG_SIGNALING-0 0.86 \n", - " HALLMARK_HEDGEHOG_SIGNALING-1 0.71 \n", - " HALLMARK_HEME_METABOLISM-0 0.00 \n", - " HALLMARK_HEME_METABOLISM-1 0.00 \n", - " HALLMARK_HYPOXIA-0 0.43 \n", - " HALLMARK_HYPOXIA-1 0.12 \n", - " HALLMARK_IL2_STAT5_SIGNALING-0 0.25 \n", - " HALLMARK_IL2_STAT5_SIGNALING-1 1.00 \n", - " HALLMARK_IL6_JAK_STAT3_SIGNALING-0 0.75 \n", - " HALLMARK_IL6_JAK_STAT3_SIGNALING-1 1.00 \n", - " HALLMARK_INFLAMMATORY_RESPONSE-0 1.00 \n", - " HALLMARK_INFLAMMATORY_RESPONSE-1 0.67 \n", - " HALLMARK_INTERFERON_ALPHA_RESPONSE-0 0.00 \n", - " HALLMARK_INTERFERON_ALPHA_RESPONSE-1 0.00 \n", - " HALLMARK_INTERFERON_GAMMA_RESPONSE-0 1.00 \n", - " HALLMARK_INTERFERON_GAMMA_RESPONSE-1 1.00 \n", - " HALLMARK_KRAS_SIGNALING_DN-0 0.20 \n", - " HALLMARK_KRAS_SIGNALING_DN-1 1.00 \n", - " HALLMARK_KRAS_SIGNALING_UP-0 0.50 \n", - " HALLMARK_KRAS_SIGNALING_UP-1 0.80 \n", - " HALLMARK_MITOTIC_SPINDLE-0 0.00 \n", - " HALLMARK_MITOTIC_SPINDLE-1 0.50 \n", - " HALLMARK_MTORC1_SIGNALING-0 0.00 \n", - " HALLMARK_MTORC1_SIGNALING-1 0.14 \n", - " HALLMARK_MYC_TARGETS_V1-0 0.50 \n", - " HALLMARK_MYC_TARGETS_V1-1 0.50 \n", - " HALLMARK_MYC_TARGETS_V2-0 NaN \n", - " HALLMARK_MYC_TARGETS_V2-1 0.00 \n", - " HALLMARK_MYOGENESIS-0 NaN \n", - " HALLMARK_MYOGENESIS-1 0.75 \n", - " HALLMARK_NOTCH_SIGNALING-0 0.00 \n", - " HALLMARK_NOTCH_SIGNALING-1 0.33 \n", - " HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 1.00 \n", - " HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 1.00 \n", - " HALLMARK_P53_PATHWAY-0 0.67 \n", - " HALLMARK_P53_PATHWAY-1 0.40 \n", - " HALLMARK_PANCREAS_BETA_CELLS-0 0.67 \n", - " HALLMARK_PANCREAS_BETA_CELLS-1 0.00 \n", - " HALLMARK_PEROXISOME-0 NaN \n", - " HALLMARK_PEROXISOME-1 0.67 \n", - " HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 0.00 \n", - " HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 0.40 \n", - " HALLMARK_PROTEIN_SECRETION-0 NaN \n", - " HALLMARK_PROTEIN_SECRETION-1 0.33 \n", - " HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 NaN \n", - " HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 0.00 \n", - " HALLMARK_SPERMATOGENESIS-0 0.00 \n", - " HALLMARK_SPERMATOGENESIS-1 0.00 \n", - " HALLMARK_TGF_BETA_SIGNALING-0 0.33 \n", - " HALLMARK_TGF_BETA_SIGNALING-1 1.00 \n", - " HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 1.00 \n", - " HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 0.25 \n", - " HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 0.67 \n", - " HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 0.20 \n", - " HALLMARK_UV_RESPONSE_DN-0 1.00 \n", - " HALLMARK_UV_RESPONSE_DN-1 0.80 \n", - " HALLMARK_UV_RESPONSE_UP-0 0.33 \n", - " HALLMARK_UV_RESPONSE_UP-1 0.17 \n", - " HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 1.00 \n", - " HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 0.67 \n", - " T cell proliferation-0 0.50 \n", - " T cell proliferation-1 0.50 \n", - " Yamanaka-TFs-0 0.50 \n", - " Yamanaka-TFs-1 0.00 \n", - " amigo-example-0 0.50 \n", - " amigo-example-1 0.00 \n", - " bicluster_RNAseqDB_0-0 0.00 \n", - " bicluster_RNAseqDB_0-1 0.50 \n", - " bicluster_RNAseqDB_1002-0 NaN \n", - " bicluster_RNAseqDB_1002-1 0.20 \n", - " endocytosis-0 0.00 \n", - " endocytosis-1 0.00 \n", - " glycolysis-gocam-0 1.00 \n", - " glycolysis-gocam-1 0.50 \n", - " go-postsynapse-calcium-transmembrane-0 0.00 \n", - " go-postsynapse-calcium-transmembrane-1 1.00 \n", - " go-reg-autophagy-pkra-0 0.17 \n", - " go-reg-autophagy-pkra-1 0.00 \n", - " hydrolase activity, hydrolyzing O-glycosyl compounds-0 0.00 \n", - " hydrolase activity, hydrolyzing O-glycosyl compounds-1 0.00 \n", - " ig-receptor-binding-2022-0 0.50 \n", - " ig-receptor-binding-2022-1 0.33 \n", - " meiosis I-0 1.00 \n", - " meiosis I-1 1.00 \n", - " molecular sequestering-0 0.00 \n", - " molecular sequestering-1 0.00 \n", - " mtorc1-0 0.00 \n", - " mtorc1-1 1.00 \n", - " peroxisome-0 0.00 \n", - " peroxisome-1 NaN \n", - " progeria-0 0.00 \n", - " progeria-1 0.00 \n", - " regulation of presynaptic membrane potential-0 1.00 \n", - " regulation of presynaptic membrane potential-1 0.75 \n", - " sensory ataxia-0 0.00 \n", - " sensory ataxia-1 0.00 \n", - " term-GO:0007212-1 0.50 \n", - " tf-downreg-colorectal-0 0.50 \n", - " tf-downreg-colorectal-1 0.00 \n", - " ontological_synopsis EDS-0 0.18 \n", - " EDS-1 0.33 \n", - " FA-0 NaN \n", - " FA-1 0.38 \n", - " HALLMARK_ADIPOGENESIS-0 0.25 \n", - " HALLMARK_ADIPOGENESIS-1 0.00 \n", - " HALLMARK_ALLOGRAFT_REJECTION-0 0.75 \n", - " HALLMARK_ALLOGRAFT_REJECTION-1 0.50 \n", - " HALLMARK_ANDROGEN_RESPONSE-0 0.00 \n", - " HALLMARK_ANDROGEN_RESPONSE-1 0.00 \n", - " HALLMARK_ANGIOGENESIS-0 0.20 \n", - " HALLMARK_ANGIOGENESIS-1 0.33 \n", - " HALLMARK_APICAL_JUNCTION-0 1.00 \n", - " HALLMARK_APICAL_JUNCTION-1 0.00 \n", - " HALLMARK_APICAL_SURFACE-0 0.00 \n", - " HALLMARK_APICAL_SURFACE-1 0.50 \n", - " HALLMARK_APOPTOSIS-0 0.50 \n", - " HALLMARK_APOPTOSIS-1 1.00 \n", - " HALLMARK_BILE_ACID_METABOLISM-0 0.33 \n", - " HALLMARK_BILE_ACID_METABOLISM-1 0.40 \n", - " HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 0.08 \n", - " HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 0.33 \n", - " HALLMARK_COAGULATION-0 0.50 \n", - " HALLMARK_COAGULATION-1 0.50 \n", - " HALLMARK_COMPLEMENT-0 0.33 \n", - " HALLMARK_COMPLEMENT-1 0.56 \n", - " HALLMARK_DNA_REPAIR-0 0.25 \n", - " HALLMARK_DNA_REPAIR-1 0.00 \n", - " HALLMARK_E2F_TARGETS-0 0.83 \n", - " HALLMARK_E2F_TARGETS-1 0.40 \n", - " HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 1.00 \n", - " HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 0.00 \n", - " HALLMARK_ESTROGEN_RESPONSE_EARLY-0 0.00 \n", - " HALLMARK_ESTROGEN_RESPONSE_EARLY-1 0.00 \n", - " HALLMARK_ESTROGEN_RESPONSE_LATE-0 NaN \n", - " HALLMARK_ESTROGEN_RESPONSE_LATE-1 0.00 \n", - " HALLMARK_FATTY_ACID_METABOLISM-0 0.26 \n", - " HALLMARK_FATTY_ACID_METABOLISM-1 0.14 \n", - " HALLMARK_G2M_CHECKPOINT-0 0.50 \n", - " HALLMARK_G2M_CHECKPOINT-1 0.25 \n", - " HALLMARK_GLYCOLYSIS-0 0.14 \n", - " HALLMARK_GLYCOLYSIS-1 0.00 \n", - " HALLMARK_HEDGEHOG_SIGNALING-0 0.60 \n", - " HALLMARK_HEDGEHOG_SIGNALING-1 0.00 \n", - " HALLMARK_HEME_METABOLISM-0 0.00 \n", - " HALLMARK_HEME_METABOLISM-1 0.00 \n", - " HALLMARK_HYPOXIA-0 0.00 \n", - " HALLMARK_HYPOXIA-1 0.00 \n", - " HALLMARK_IL2_STAT5_SIGNALING-0 0.33 \n", - " HALLMARK_IL2_STAT5_SIGNALING-1 0.08 \n", - " HALLMARK_IL6_JAK_STAT3_SIGNALING-0 0.33 \n", - " HALLMARK_IL6_JAK_STAT3_SIGNALING-1 1.00 \n", - " HALLMARK_INFLAMMATORY_RESPONSE-0 0.75 \n", - " HALLMARK_INFLAMMATORY_RESPONSE-1 0.40 \n", - " HALLMARK_INTERFERON_ALPHA_RESPONSE-0 0.00 \n", - " HALLMARK_INTERFERON_ALPHA_RESPONSE-1 0.82 \n", - " HALLMARK_INTERFERON_GAMMA_RESPONSE-0 0.27 \n", - " HALLMARK_INTERFERON_GAMMA_RESPONSE-1 0.00 \n", - " HALLMARK_KRAS_SIGNALING_DN-0 0.00 \n", - " HALLMARK_KRAS_SIGNALING_DN-1 0.33 \n", - " HALLMARK_KRAS_SIGNALING_UP-0 0.00 \n", - " HALLMARK_KRAS_SIGNALING_UP-1 0.00 \n", - " HALLMARK_MITOTIC_SPINDLE-0 0.33 \n", - " HALLMARK_MITOTIC_SPINDLE-1 NaN \n", - " HALLMARK_MTORC1_SIGNALING-0 0.20 \n", - " HALLMARK_MTORC1_SIGNALING-1 0.08 \n", - " HALLMARK_MYC_TARGETS_V1-0 0.40 \n", - " HALLMARK_MYC_TARGETS_V1-1 0.33 \n", - " HALLMARK_MYC_TARGETS_V2-0 0.14 \n", - " HALLMARK_MYC_TARGETS_V2-1 0.20 \n", - " HALLMARK_MYOGENESIS-0 0.43 \n", - " HALLMARK_MYOGENESIS-1 0.33 \n", - " HALLMARK_NOTCH_SIGNALING-0 0.80 \n", - " HALLMARK_NOTCH_SIGNALING-1 0.33 \n", - " HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 0.50 \n", - " HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 0.27 \n", - " HALLMARK_P53_PATHWAY-0 0.00 \n", - " HALLMARK_P53_PATHWAY-1 0.08 \n", - " HALLMARK_PANCREAS_BETA_CELLS-0 0.33 \n", - " HALLMARK_PANCREAS_BETA_CELLS-1 0.00 \n", - " HALLMARK_PEROXISOME-0 0.50 \n", - " HALLMARK_PEROXISOME-1 NaN \n", - " HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 0.31 \n", - " HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 1.00 \n", - " HALLMARK_PROTEIN_SECRETION-0 0.40 \n", - " HALLMARK_PROTEIN_SECRETION-1 0.00 \n", - " HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 0.08 \n", - " HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 0.55 \n", - " HALLMARK_SPERMATOGENESIS-0 0.00 \n", - " HALLMARK_SPERMATOGENESIS-1 0.11 \n", - " HALLMARK_TGF_BETA_SIGNALING-0 1.00 \n", - " HALLMARK_TGF_BETA_SIGNALING-1 0.00 \n", - " HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 1.00 \n", - " HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 0.25 \n", - " HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 0.45 \n", - " HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 0.00 \n", - " HALLMARK_UV_RESPONSE_DN-0 0.00 \n", - " HALLMARK_UV_RESPONSE_DN-1 0.00 \n", - " HALLMARK_UV_RESPONSE_UP-0 0.17 \n", - " HALLMARK_UV_RESPONSE_UP-1 0.00 \n", - " HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 0.17 \n", - " HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 0.67 \n", - " T cell proliferation-0 0.25 \n", - " T cell proliferation-1 0.00 \n", - " Yamanaka-TFs-0 0.00 \n", - " Yamanaka-TFs-1 0.08 \n", - " amigo-example-0 0.25 \n", - " amigo-example-1 0.40 \n", - " bicluster_RNAseqDB_0-0 0.00 \n", - " bicluster_RNAseqDB_0-1 0.00 \n", - " bicluster_RNAseqDB_1002-0 0.38 \n", - " bicluster_RNAseqDB_1002-1 0.67 \n", - " endocytosis-0 0.33 \n", - " endocytosis-1 0.17 \n", - " glycolysis-gocam-0 0.00 \n", - " glycolysis-gocam-1 0.26 \n", - " go-postsynapse-calcium-transmembrane-0 0.47 \n", - " go-postsynapse-calcium-transmembrane-1 1.00 \n", - " go-reg-autophagy-pkra-0 0.00 \n", - " go-reg-autophagy-pkra-1 0.33 \n", - " hydrolase activity, hydrolyzing O-glycosyl compounds-0 0.62 \n", - " hydrolase activity, hydrolyzing O-glycosyl compounds-1 0.35 \n", - " ig-receptor-binding-2022-0 0.00 \n", - " ig-receptor-binding-2022-1 0.14 \n", - " meiosis I-0 0.25 \n", - " meiosis I-1 0.71 \n", - " molecular sequestering-0 0.17 \n", - " molecular sequestering-1 0.33 \n", - " mtorc1-0 0.20 \n", - " mtorc1-1 1.00 \n", - " peroxisome-0 0.83 \n", - " peroxisome-1 0.43 \n", - " progeria-0 0.00 \n", - " progeria-1 0.00 \n", - " regulation of presynaptic membrane potential-0 0.56 \n", - " regulation of presynaptic membrane potential-1 1.00 \n", - " sensory ataxia-0 0.00 \n", - " sensory ataxia-1 NaN \n", - " term-GO:0007212-0 0.20 \n", - " term-GO:0007212-1 0.43 \n", - " tf-downreg-colorectal-0 0.57 \n", - " tf-downreg-colorectal-1 0.80 \n", - "\n", - "prompt_variant v2 \\\n", - "model method geneset \n", - "gpt-3.5-turbo narrative_synopsis EDS-0 0.50 \n", - " EDS-1 0.25 \n", - " FA-0 1.00 \n", - " FA-1 1.00 \n", - " HALLMARK_ADIPOGENESIS-0 0.67 \n", - " HALLMARK_ADIPOGENESIS-1 1.00 \n", - " HALLMARK_ALLOGRAFT_REJECTION-0 0.87 \n", - " HALLMARK_ALLOGRAFT_REJECTION-1 1.00 \n", - " HALLMARK_ANDROGEN_RESPONSE-0 0.00 \n", - " HALLMARK_ANDROGEN_RESPONSE-1 0.00 \n", - " HALLMARK_ANGIOGENESIS-0 0.33 \n", - " HALLMARK_ANGIOGENESIS-1 0.50 \n", - " HALLMARK_APICAL_JUNCTION-0 1.00 \n", - " HALLMARK_APICAL_JUNCTION-1 0.67 \n", - " HALLMARK_APICAL_SURFACE-0 0.08 \n", - " HALLMARK_APICAL_SURFACE-1 0.00 \n", - " HALLMARK_APOPTOSIS-0 1.00 \n", - " HALLMARK_APOPTOSIS-1 0.71 \n", - " HALLMARK_BILE_ACID_METABOLISM-0 0.60 \n", - " HALLMARK_BILE_ACID_METABOLISM-1 1.00 \n", - " HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 0.67 \n", - " HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 0.75 \n", - " HALLMARK_COAGULATION-0 1.00 \n", - " HALLMARK_COAGULATION-1 1.00 \n", - " HALLMARK_COMPLEMENT-0 1.00 \n", - " HALLMARK_COMPLEMENT-1 0.80 \n", - " HALLMARK_DNA_REPAIR-0 1.00 \n", - " HALLMARK_DNA_REPAIR-1 1.00 \n", - " HALLMARK_E2F_TARGETS-0 1.00 \n", - " HALLMARK_E2F_TARGETS-1 1.00 \n", - " HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 0.79 \n", - " HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 0.67 \n", - " HALLMARK_ESTROGEN_RESPONSE_EARLY-0 0.00 \n", - " HALLMARK_ESTROGEN_RESPONSE_EARLY-1 0.00 \n", - " HALLMARK_ESTROGEN_RESPONSE_LATE-0 0.38 \n", - " HALLMARK_ESTROGEN_RESPONSE_LATE-1 0.17 \n", - " HALLMARK_FATTY_ACID_METABOLISM-0 1.00 \n", - " HALLMARK_FATTY_ACID_METABOLISM-1 0.88 \n", - " HALLMARK_G2M_CHECKPOINT-0 1.00 \n", - " HALLMARK_G2M_CHECKPOINT-1 1.00 \n", - " HALLMARK_GLYCOLYSIS-0 1.00 \n", - " HALLMARK_GLYCOLYSIS-1 0.50 \n", - " HALLMARK_HEDGEHOG_SIGNALING-0 0.80 \n", - " HALLMARK_HEDGEHOG_SIGNALING-1 1.00 \n", - " HALLMARK_HEME_METABOLISM-0 0.00 \n", - " HALLMARK_HEME_METABOLISM-1 0.00 \n", - " HALLMARK_HYPOXIA-0 1.00 \n", - " HALLMARK_HYPOXIA-1 0.40 \n", - " HALLMARK_IL2_STAT5_SIGNALING-0 0.20 \n", - " HALLMARK_IL2_STAT5_SIGNALING-1 0.75 \n", - " HALLMARK_IL6_JAK_STAT3_SIGNALING-0 0.80 \n", - " HALLMARK_IL6_JAK_STAT3_SIGNALING-1 1.00 \n", - " HALLMARK_INFLAMMATORY_RESPONSE-0 1.00 \n", - " HALLMARK_INFLAMMATORY_RESPONSE-1 0.80 \n", - " HALLMARK_INTERFERON_ALPHA_RESPONSE-0 1.00 \n", - " HALLMARK_INTERFERON_ALPHA_RESPONSE-1 1.00 \n", - " HALLMARK_INTERFERON_GAMMA_RESPONSE-0 1.00 \n", - " HALLMARK_INTERFERON_GAMMA_RESPONSE-1 1.00 \n", - " HALLMARK_KRAS_SIGNALING_DN-0 0.12 \n", - " HALLMARK_KRAS_SIGNALING_DN-1 0.00 \n", - " HALLMARK_KRAS_SIGNALING_UP-0 0.33 \n", - " HALLMARK_KRAS_SIGNALING_UP-1 NaN \n", - " HALLMARK_MITOTIC_SPINDLE-0 1.00 \n", - " HALLMARK_MITOTIC_SPINDLE-1 1.00 \n", - " HALLMARK_MTORC1_SIGNALING-0 0.60 \n", - " HALLMARK_MTORC1_SIGNALING-1 0.67 \n", - " HALLMARK_MYC_TARGETS_V1-0 0.80 \n", - " HALLMARK_MYC_TARGETS_V1-1 0.75 \n", - " HALLMARK_MYC_TARGETS_V2-0 0.67 \n", - " HALLMARK_MYC_TARGETS_V2-1 0.75 \n", - " HALLMARK_MYOGENESIS-0 1.00 \n", - " HALLMARK_MYOGENESIS-1 1.00 \n", - " HALLMARK_NOTCH_SIGNALING-0 0.33 \n", - " HALLMARK_NOTCH_SIGNALING-1 0.67 \n", - " HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 1.00 \n", - " HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 1.00 \n", - " HALLMARK_P53_PATHWAY-0 0.25 \n", - " HALLMARK_P53_PATHWAY-1 0.67 \n", - " HALLMARK_PANCREAS_BETA_CELLS-0 0.40 \n", - " HALLMARK_PANCREAS_BETA_CELLS-1 0.00 \n", - " HALLMARK_PEROXISOME-0 0.80 \n", - " HALLMARK_PEROXISOME-1 1.00 \n", - " HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 1.00 \n", - " HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 1.00 \n", - " HALLMARK_PROTEIN_SECRETION-0 0.83 \n", - " HALLMARK_PROTEIN_SECRETION-1 0.83 \n", - " HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 NaN \n", - " HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 1.00 \n", - " HALLMARK_SPERMATOGENESIS-0 0.60 \n", - " HALLMARK_SPERMATOGENESIS-1 0.33 \n", - " HALLMARK_TGF_BETA_SIGNALING-0 1.00 \n", - " HALLMARK_TGF_BETA_SIGNALING-1 0.67 \n", - " HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 0.83 \n", - " HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 0.50 \n", - " HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 0.67 \n", - " HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 0.86 \n", - " HALLMARK_UV_RESPONSE_DN-0 0.75 \n", - " HALLMARK_UV_RESPONSE_DN-1 0.60 \n", - " HALLMARK_UV_RESPONSE_UP-0 0.67 \n", - " HALLMARK_UV_RESPONSE_UP-1 0.00 \n", - " HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 1.00 \n", - " HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 0.50 \n", - " T cell proliferation-0 0.00 \n", - " T cell proliferation-1 0.67 \n", - " Yamanaka-TFs-0 0.00 \n", - " Yamanaka-TFs-1 0.00 \n", - " amigo-example-0 0.33 \n", - " amigo-example-1 0.67 \n", - " bicluster_RNAseqDB_0-0 0.00 \n", - " bicluster_RNAseqDB_0-1 0.00 \n", - " bicluster_RNAseqDB_1002-0 0.40 \n", - " bicluster_RNAseqDB_1002-1 0.17 \n", - " endocytosis-0 0.20 \n", - " endocytosis-1 1.00 \n", - " glycolysis-gocam-0 1.00 \n", - " glycolysis-gocam-1 0.40 \n", - " go-postsynapse-calcium-transmembrane-0 1.00 \n", - " go-postsynapse-calcium-transmembrane-1 0.67 \n", - " go-reg-autophagy-pkra-0 0.67 \n", - " go-reg-autophagy-pkra-1 0.17 \n", - " hydrolase activity, hydrolyzing O-glycosyl compounds-0 0.75 \n", - " hydrolase activity, hydrolyzing O-glycosyl compounds-1 1.00 \n", - " ig-receptor-binding-2022-0 0.33 \n", - " ig-receptor-binding-2022-1 1.00 \n", - " meiosis I-0 1.00 \n", - " meiosis I-1 1.00 \n", - " molecular sequestering-0 0.00 \n", - " molecular sequestering-1 0.33 \n", - " mtorc1-0 0.60 \n", - " mtorc1-1 0.60 \n", - " peroxisome-0 NaN \n", - " peroxisome-1 0.50 \n", - " progeria-0 0.33 \n", - " progeria-1 0.00 \n", - " regulation of presynaptic membrane potential-0 0.75 \n", - " regulation of presynaptic membrane potential-1 1.00 \n", - " sensory ataxia-0 1.00 \n", - " sensory ataxia-1 0.67 \n", - " term-GO:0007212-0 1.00 \n", - " term-GO:0007212-1 0.50 \n", - " tf-downreg-colorectal-0 1.00 \n", - " tf-downreg-colorectal-1 1.00 \n", - " no_synopsis EDS-0 0.50 \n", - " EDS-1 1.00 \n", - " FA-0 0.67 \n", - " FA-1 1.00 \n", - " HALLMARK_ADIPOGENESIS-0 0.88 \n", - " HALLMARK_ADIPOGENESIS-1 1.00 \n", - " HALLMARK_ALLOGRAFT_REJECTION-0 1.00 \n", - " HALLMARK_ALLOGRAFT_REJECTION-1 1.00 \n", - " HALLMARK_ANDROGEN_RESPONSE-0 0.00 \n", - " HALLMARK_ANDROGEN_RESPONSE-1 0.00 \n", - " HALLMARK_ANGIOGENESIS-0 0.75 \n", - " HALLMARK_ANGIOGENESIS-1 0.67 \n", - " HALLMARK_APICAL_JUNCTION-0 0.50 \n", - " HALLMARK_APICAL_JUNCTION-1 1.00 \n", - " HALLMARK_APICAL_SURFACE-0 0.33 \n", - " HALLMARK_APICAL_SURFACE-1 0.10 \n", - " HALLMARK_APOPTOSIS-0 1.00 \n", - " HALLMARK_APOPTOSIS-1 0.70 \n", - " HALLMARK_BILE_ACID_METABOLISM-0 0.50 \n", - " HALLMARK_BILE_ACID_METABOLISM-1 0.75 \n", - " HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 0.80 \n", - " HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 1.00 \n", - " HALLMARK_COAGULATION-0 0.75 \n", - " HALLMARK_COAGULATION-1 1.00 \n", - " HALLMARK_COMPLEMENT-0 0.75 \n", - " HALLMARK_COMPLEMENT-1 1.00 \n", - " HALLMARK_DNA_REPAIR-0 0.75 \n", - " HALLMARK_DNA_REPAIR-1 0.80 \n", - " HALLMARK_E2F_TARGETS-0 1.00 \n", - " HALLMARK_E2F_TARGETS-1 1.00 \n", - " HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 1.00 \n", - " HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 0.86 \n", - " HALLMARK_ESTROGEN_RESPONSE_EARLY-0 0.00 \n", - " HALLMARK_ESTROGEN_RESPONSE_EARLY-1 0.09 \n", - " HALLMARK_ESTROGEN_RESPONSE_LATE-0 0.25 \n", - " HALLMARK_ESTROGEN_RESPONSE_LATE-1 0.00 \n", - " HALLMARK_FATTY_ACID_METABOLISM-0 1.00 \n", - " HALLMARK_FATTY_ACID_METABOLISM-1 1.00 \n", - " HALLMARK_G2M_CHECKPOINT-0 NaN \n", - " HALLMARK_G2M_CHECKPOINT-1 1.00 \n", - " HALLMARK_GLYCOLYSIS-0 0.50 \n", - " HALLMARK_GLYCOLYSIS-1 0.43 \n", - " HALLMARK_HEDGEHOG_SIGNALING-0 0.25 \n", - " HALLMARK_HEDGEHOG_SIGNALING-1 1.00 \n", - " HALLMARK_HEME_METABOLISM-0 0.00 \n", - " HALLMARK_HEME_METABOLISM-1 1.00 \n", - " HALLMARK_HYPOXIA-0 0.44 \n", - " HALLMARK_HYPOXIA-1 NaN \n", - " HALLMARK_IL2_STAT5_SIGNALING-1 0.33 \n", - " HALLMARK_IL6_JAK_STAT3_SIGNALING-0 0.44 \n", - " HALLMARK_IL6_JAK_STAT3_SIGNALING-1 1.00 \n", - " HALLMARK_INFLAMMATORY_RESPONSE-0 1.00 \n", - " HALLMARK_INFLAMMATORY_RESPONSE-1 0.92 \n", - " HALLMARK_INTERFERON_ALPHA_RESPONSE-0 1.00 \n", - " HALLMARK_INTERFERON_ALPHA_RESPONSE-1 1.00 \n", - " HALLMARK_INTERFERON_GAMMA_RESPONSE-0 0.63 \n", - " HALLMARK_INTERFERON_GAMMA_RESPONSE-1 0.86 \n", - " HALLMARK_KRAS_SIGNALING_DN-0 0.00 \n", - " HALLMARK_KRAS_SIGNALING_DN-1 0.00 \n", - " HALLMARK_KRAS_SIGNALING_UP-0 0.50 \n", - " HALLMARK_KRAS_SIGNALING_UP-1 0.00 \n", - " HALLMARK_MITOTIC_SPINDLE-0 1.00 \n", - " HALLMARK_MITOTIC_SPINDLE-1 0.94 \n", - " HALLMARK_MTORC1_SIGNALING-0 NaN \n", - " HALLMARK_MTORC1_SIGNALING-1 0.75 \n", - " HALLMARK_MYC_TARGETS_V1-0 1.00 \n", - " HALLMARK_MYC_TARGETS_V1-1 0.89 \n", - " HALLMARK_MYC_TARGETS_V2-0 0.60 \n", - " HALLMARK_MYC_TARGETS_V2-1 0.78 \n", - " HALLMARK_MYOGENESIS-0 1.00 \n", - " HALLMARK_MYOGENESIS-1 1.00 \n", - " HALLMARK_NOTCH_SIGNALING-0 0.71 \n", - " HALLMARK_NOTCH_SIGNALING-1 0.25 \n", - " HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 0.67 \n", - " HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 0.89 \n", - " HALLMARK_P53_PATHWAY-0 1.00 \n", - " HALLMARK_P53_PATHWAY-1 0.60 \n", - " HALLMARK_PANCREAS_BETA_CELLS-0 0.75 \n", - " HALLMARK_PANCREAS_BETA_CELLS-1 0.57 \n", - " HALLMARK_PEROXISOME-0 0.60 \n", - " HALLMARK_PEROXISOME-1 0.71 \n", - " HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 1.00 \n", - " HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 0.75 \n", - " HALLMARK_PROTEIN_SECRETION-0 1.00 \n", - " HALLMARK_PROTEIN_SECRETION-1 1.00 \n", - " HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 1.00 \n", - " HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 1.00 \n", - " HALLMARK_SPERMATOGENESIS-0 0.40 \n", - " HALLMARK_SPERMATOGENESIS-1 0.00 \n", - " HALLMARK_TGF_BETA_SIGNALING-0 0.83 \n", - " HALLMARK_TGF_BETA_SIGNALING-1 1.00 \n", - " HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 0.42 \n", - " HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 0.80 \n", - " HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 0.60 \n", - " HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 0.75 \n", - " HALLMARK_UV_RESPONSE_DN-0 0.67 \n", - " HALLMARK_UV_RESPONSE_DN-1 0.50 \n", - " HALLMARK_UV_RESPONSE_UP-0 0.75 \n", - " HALLMARK_UV_RESPONSE_UP-1 0.43 \n", - " HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 0.00 \n", - " HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 1.00 \n", - " T cell proliferation-0 0.83 \n", - " T cell proliferation-1 1.00 \n", - " Yamanaka-TFs-0 0.00 \n", - " Yamanaka-TFs-1 0.00 \n", - " amigo-example-0 NaN \n", - " amigo-example-1 0.71 \n", - " bicluster_RNAseqDB_0-0 0.12 \n", - " bicluster_RNAseqDB_0-1 0.00 \n", - " bicluster_RNAseqDB_1002-0 0.75 \n", - " bicluster_RNAseqDB_1002-1 0.40 \n", - " endocytosis-0 0.25 \n", - " endocytosis-1 0.60 \n", - " glycolysis-gocam-0 1.00 \n", - " glycolysis-gocam-1 0.75 \n", - " go-postsynapse-calcium-transmembrane-0 1.00 \n", - " go-postsynapse-calcium-transmembrane-1 0.75 \n", - " go-reg-autophagy-pkra-0 0.60 \n", - " go-reg-autophagy-pkra-1 1.00 \n", - " hydrolase activity, hydrolyzing O-glycosyl compounds-0 0.86 \n", - " hydrolase activity, hydrolyzing O-glycosyl compounds-1 1.00 \n", - " ig-receptor-binding-2022-0 0.60 \n", - " ig-receptor-binding-2022-1 0.00 \n", - " meiosis I-0 0.69 \n", - " meiosis I-1 1.00 \n", - " molecular sequestering-0 0.00 \n", - " molecular sequestering-1 0.00 \n", - " mtorc1-0 NaN \n", - " mtorc1-1 0.67 \n", - " peroxisome-0 1.00 \n", - " peroxisome-1 0.50 \n", - " progeria-0 0.25 \n", - " progeria-1 0.00 \n", - " regulation of presynaptic membrane potential-0 0.80 \n", - " regulation of presynaptic membrane potential-1 0.80 \n", - " sensory ataxia-0 0.20 \n", - " sensory ataxia-1 0.00 \n", - " term-GO:0007212-0 0.50 \n", - " term-GO:0007212-1 0.75 \n", - " tf-downreg-colorectal-0 0.25 \n", - " tf-downreg-colorectal-1 0.89 \n", - " ontological_synopsis EDS-0 0.80 \n", - " EDS-1 0.80 \n", - " FA-0 1.00 \n", - " FA-1 1.00 \n", - " HALLMARK_ADIPOGENESIS-0 0.50 \n", - " HALLMARK_ADIPOGENESIS-1 0.50 \n", - " HALLMARK_ALLOGRAFT_REJECTION-0 1.00 \n", - " HALLMARK_ALLOGRAFT_REJECTION-1 0.57 \n", - " HALLMARK_ANDROGEN_RESPONSE-0 0.00 \n", - " HALLMARK_ANDROGEN_RESPONSE-1 NaN \n", - " HALLMARK_ANGIOGENESIS-1 1.00 \n", - " HALLMARK_APICAL_JUNCTION-0 0.33 \n", - " HALLMARK_APICAL_SURFACE-0 0.43 \n", - " HALLMARK_APICAL_SURFACE-1 0.00 \n", - " HALLMARK_APOPTOSIS-0 0.75 \n", - " HALLMARK_APOPTOSIS-1 1.00 \n", - " HALLMARK_BILE_ACID_METABOLISM-0 0.80 \n", - " HALLMARK_BILE_ACID_METABOLISM-1 1.00 \n", - " HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 0.80 \n", - " HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 0.67 \n", - " HALLMARK_COAGULATION-0 1.00 \n", - " HALLMARK_COAGULATION-1 1.00 \n", - " HALLMARK_COMPLEMENT-0 0.67 \n", - " HALLMARK_COMPLEMENT-1 0.50 \n", - " HALLMARK_DNA_REPAIR-0 1.00 \n", - " HALLMARK_DNA_REPAIR-1 0.75 \n", - " HALLMARK_E2F_TARGETS-0 0.88 \n", - " HALLMARK_E2F_TARGETS-1 0.00 \n", - " HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 1.00 \n", - " HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 0.25 \n", - " HALLMARK_ESTROGEN_RESPONSE_EARLY-0 0.00 \n", - " HALLMARK_ESTROGEN_RESPONSE_EARLY-1 0.33 \n", - " HALLMARK_ESTROGEN_RESPONSE_LATE-0 0.00 \n", - " HALLMARK_ESTROGEN_RESPONSE_LATE-1 0.00 \n", - " HALLMARK_FATTY_ACID_METABOLISM-0 0.80 \n", - " HALLMARK_FATTY_ACID_METABOLISM-1 1.00 \n", - " HALLMARK_G2M_CHECKPOINT-0 0.50 \n", - " HALLMARK_G2M_CHECKPOINT-1 0.75 \n", - " HALLMARK_GLYCOLYSIS-0 0.80 \n", - " HALLMARK_GLYCOLYSIS-1 0.40 \n", - " HALLMARK_HEDGEHOG_SIGNALING-0 1.00 \n", - " HALLMARK_HEDGEHOG_SIGNALING-1 1.00 \n", - " HALLMARK_HEME_METABOLISM-0 0.00 \n", - " HALLMARK_HEME_METABOLISM-1 0.00 \n", - " HALLMARK_HYPOXIA-0 0.00 \n", - " HALLMARK_HYPOXIA-1 0.17 \n", - " HALLMARK_IL2_STAT5_SIGNALING-0 0.25 \n", - " HALLMARK_IL2_STAT5_SIGNALING-1 0.50 \n", - " HALLMARK_IL6_JAK_STAT3_SIGNALING-0 1.00 \n", - " HALLMARK_IL6_JAK_STAT3_SIGNALING-1 1.00 \n", - " HALLMARK_INFLAMMATORY_RESPONSE-0 1.00 \n", - " HALLMARK_INFLAMMATORY_RESPONSE-1 1.00 \n", - " HALLMARK_INTERFERON_ALPHA_RESPONSE-0 1.00 \n", - " HALLMARK_INTERFERON_ALPHA_RESPONSE-1 0.55 \n", - " HALLMARK_INTERFERON_GAMMA_RESPONSE-0 0.33 \n", - " HALLMARK_INTERFERON_GAMMA_RESPONSE-1 1.00 \n", - " HALLMARK_KRAS_SIGNALING_DN-0 0.00 \n", - " HALLMARK_KRAS_SIGNALING_DN-1 0.00 \n", - " HALLMARK_KRAS_SIGNALING_UP-0 0.33 \n", - " HALLMARK_KRAS_SIGNALING_UP-1 0.00 \n", - " HALLMARK_MITOTIC_SPINDLE-0 1.00 \n", - " HALLMARK_MITOTIC_SPINDLE-1 1.00 \n", - " HALLMARK_MTORC1_SIGNALING-0 0.00 \n", - " HALLMARK_MTORC1_SIGNALING-1 0.75 \n", - " HALLMARK_MYC_TARGETS_V1-0 0.67 \n", - " HALLMARK_MYC_TARGETS_V1-1 0.80 \n", - " HALLMARK_MYC_TARGETS_V2-0 1.00 \n", - " HALLMARK_MYC_TARGETS_V2-1 1.00 \n", - " HALLMARK_MYOGENESIS-0 NaN \n", - " HALLMARK_MYOGENESIS-1 0.50 \n", - " HALLMARK_NOTCH_SIGNALING-0 1.00 \n", - " HALLMARK_NOTCH_SIGNALING-1 1.00 \n", - " HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 0.50 \n", - " HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 NaN \n", - " HALLMARK_P53_PATHWAY-0 0.25 \n", - " HALLMARK_P53_PATHWAY-1 0.50 \n", - " HALLMARK_PANCREAS_BETA_CELLS-0 0.75 \n", - " HALLMARK_PANCREAS_BETA_CELLS-1 0.00 \n", - " HALLMARK_PEROXISOME-0 0.80 \n", - " HALLMARK_PEROXISOME-1 0.50 \n", - " HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 0.60 \n", - " HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 1.00 \n", - " HALLMARK_PROTEIN_SECRETION-0 0.33 \n", - " HALLMARK_PROTEIN_SECRETION-1 0.75 \n", - " HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 0.83 \n", - " HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 1.00 \n", - " HALLMARK_SPERMATOGENESIS-0 0.25 \n", - " HALLMARK_SPERMATOGENESIS-1 0.00 \n", - " HALLMARK_TGF_BETA_SIGNALING-0 1.00 \n", - " HALLMARK_TGF_BETA_SIGNALING-1 1.00 \n", - " HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 1.00 \n", - " HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 0.86 \n", - " HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 NaN \n", - " HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 0.67 \n", - " HALLMARK_UV_RESPONSE_DN-0 1.00 \n", - " HALLMARK_UV_RESPONSE_DN-1 0.50 \n", - " HALLMARK_UV_RESPONSE_UP-0 0.00 \n", - " HALLMARK_UV_RESPONSE_UP-1 0.00 \n", - " HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 1.00 \n", - " HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 1.00 \n", - " T cell proliferation-0 1.00 \n", - " T cell proliferation-1 0.88 \n", - " Yamanaka-TFs-0 0.25 \n", - " Yamanaka-TFs-1 0.00 \n", - " amigo-example-0 0.25 \n", - " amigo-example-1 0.33 \n", - " bicluster_RNAseqDB_0-0 0.00 \n", - " bicluster_RNAseqDB_0-1 0.25 \n", - " bicluster_RNAseqDB_1002-0 0.67 \n", - " bicluster_RNAseqDB_1002-1 0.67 \n", - " endocytosis-0 0.20 \n", - " endocytosis-1 1.00 \n", - " glycolysis-gocam-0 0.67 \n", - " glycolysis-gocam-1 0.75 \n", - " go-postsynapse-calcium-transmembrane-0 0.75 \n", - " go-postsynapse-calcium-transmembrane-1 1.00 \n", - " go-reg-autophagy-pkra-0 0.60 \n", - " go-reg-autophagy-pkra-1 0.80 \n", - " hydrolase activity, hydrolyzing O-glycosyl compounds-0 1.00 \n", - " hydrolase activity, hydrolyzing O-glycosyl compounds-1 1.00 \n", - " ig-receptor-binding-2022-0 NaN \n", - " ig-receptor-binding-2022-1 0.50 \n", - " meiosis I-0 1.00 \n", - " meiosis I-1 1.00 \n", - " molecular sequestering-0 0.50 \n", - " molecular sequestering-1 0.00 \n", - " mtorc1-0 0.00 \n", - " mtorc1-1 0.33 \n", - " peroxisome-0 0.00 \n", - " peroxisome-1 0.33 \n", - " progeria-0 0.00 \n", - " progeria-1 0.00 \n", - " regulation of presynaptic membrane potential-0 1.00 \n", - " regulation of presynaptic membrane potential-1 1.00 \n", - " sensory ataxia-0 0.50 \n", - " sensory ataxia-1 0.50 \n", - " term-GO:0007212-0 0.50 \n", - " term-GO:0007212-1 0.29 \n", - " tf-downreg-colorectal-0 1.00 \n", - " tf-downreg-colorectal-1 1.00 \n", - "text-davinci-003 narrative_synopsis EDS-0 0.00 \n", - " EDS-1 0.00 \n", - " FA-0 1.00 \n", - " FA-1 1.00 \n", - " HALLMARK_ADIPOGENESIS-0 0.31 \n", - " HALLMARK_ADIPOGENESIS-1 0.14 \n", - " HALLMARK_ALLOGRAFT_REJECTION-0 0.50 \n", - " HALLMARK_ALLOGRAFT_REJECTION-1 1.00 \n", - " HALLMARK_ANDROGEN_RESPONSE-0 0.00 \n", - " HALLMARK_ANDROGEN_RESPONSE-1 0.00 \n", - " HALLMARK_ANGIOGENESIS-0 0.30 \n", - " HALLMARK_ANGIOGENESIS-1 NaN \n", - " HALLMARK_APICAL_JUNCTION-0 0.00 \n", - " HALLMARK_APICAL_JUNCTION-1 0.75 \n", - " HALLMARK_APICAL_SURFACE-0 0.20 \n", - " HALLMARK_APICAL_SURFACE-1 0.00 \n", - " HALLMARK_APOPTOSIS-0 0.50 \n", - " HALLMARK_APOPTOSIS-1 1.00 \n", - " HALLMARK_BILE_ACID_METABOLISM-0 0.40 \n", - " HALLMARK_BILE_ACID_METABOLISM-1 1.00 \n", - " HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 0.25 \n", - " HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 0.33 \n", - " HALLMARK_COAGULATION-0 0.00 \n", - " HALLMARK_COAGULATION-1 0.00 \n", - " HALLMARK_COMPLEMENT-0 0.33 \n", - " HALLMARK_COMPLEMENT-1 0.67 \n", - " HALLMARK_DNA_REPAIR-0 1.00 \n", - " HALLMARK_DNA_REPAIR-1 0.17 \n", - " HALLMARK_E2F_TARGETS-0 0.67 \n", - " HALLMARK_E2F_TARGETS-1 0.80 \n", - " HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 0.50 \n", - " HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 0.67 \n", - " HALLMARK_ESTROGEN_RESPONSE_EARLY-0 0.20 \n", - " HALLMARK_ESTROGEN_RESPONSE_EARLY-1 0.00 \n", - " HALLMARK_ESTROGEN_RESPONSE_LATE-0 NaN \n", - " HALLMARK_ESTROGEN_RESPONSE_LATE-1 0.20 \n", - " HALLMARK_FATTY_ACID_METABOLISM-0 0.67 \n", - " HALLMARK_FATTY_ACID_METABOLISM-1 0.33 \n", - " HALLMARK_G2M_CHECKPOINT-0 0.60 \n", - " HALLMARK_G2M_CHECKPOINT-1 0.57 \n", - " HALLMARK_GLYCOLYSIS-0 0.00 \n", - " HALLMARK_GLYCOLYSIS-1 0.20 \n", - " HALLMARK_HEDGEHOG_SIGNALING-0 0.33 \n", - " HALLMARK_HEDGEHOG_SIGNALING-1 0.50 \n", - " HALLMARK_HEME_METABOLISM-0 0.00 \n", - " HALLMARK_HEME_METABOLISM-1 0.00 \n", - " HALLMARK_HYPOXIA-0 0.00 \n", - " HALLMARK_HYPOXIA-1 0.25 \n", - " HALLMARK_IL2_STAT5_SIGNALING-0 0.50 \n", - " HALLMARK_IL2_STAT5_SIGNALING-1 0.33 \n", - " HALLMARK_IL6_JAK_STAT3_SIGNALING-0 NaN \n", - " HALLMARK_IL6_JAK_STAT3_SIGNALING-1 0.50 \n", - " HALLMARK_INFLAMMATORY_RESPONSE-0 NaN \n", - " HALLMARK_INFLAMMATORY_RESPONSE-1 0.50 \n", - " HALLMARK_INTERFERON_ALPHA_RESPONSE-0 0.00 \n", - " HALLMARK_INTERFERON_ALPHA_RESPONSE-1 0.22 \n", - " HALLMARK_INTERFERON_GAMMA_RESPONSE-0 0.67 \n", - " HALLMARK_INTERFERON_GAMMA_RESPONSE-1 0.00 \n", - " HALLMARK_KRAS_SIGNALING_DN-0 0.00 \n", - " HALLMARK_KRAS_SIGNALING_DN-1 0.50 \n", - " HALLMARK_KRAS_SIGNALING_UP-0 0.11 \n", - " HALLMARK_KRAS_SIGNALING_UP-1 NaN \n", - " HALLMARK_MITOTIC_SPINDLE-0 NaN \n", - " HALLMARK_MITOTIC_SPINDLE-1 0.40 \n", - " HALLMARK_MTORC1_SIGNALING-0 0.44 \n", - " HALLMARK_MTORC1_SIGNALING-1 1.00 \n", - " HALLMARK_MYC_TARGETS_V1-0 0.60 \n", - " HALLMARK_MYC_TARGETS_V1-1 0.64 \n", - " HALLMARK_MYC_TARGETS_V2-0 0.33 \n", - " HALLMARK_MYC_TARGETS_V2-1 0.33 \n", - " HALLMARK_MYOGENESIS-0 1.00 \n", - " HALLMARK_MYOGENESIS-1 0.50 \n", - " HALLMARK_NOTCH_SIGNALING-0 1.00 \n", - " HALLMARK_NOTCH_SIGNALING-1 0.75 \n", - " HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 0.80 \n", - " HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 0.67 \n", - " HALLMARK_P53_PATHWAY-0 0.67 \n", - " HALLMARK_P53_PATHWAY-1 0.29 \n", - " HALLMARK_PANCREAS_BETA_CELLS-0 0.33 \n", - " HALLMARK_PANCREAS_BETA_CELLS-1 0.33 \n", - " HALLMARK_PEROXISOME-0 1.00 \n", - " HALLMARK_PEROXISOME-1 0.20 \n", - " HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 0.00 \n", - " HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 1.00 \n", - " HALLMARK_PROTEIN_SECRETION-0 0.50 \n", - " HALLMARK_PROTEIN_SECRETION-1 0.17 \n", - " HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 0.33 \n", - " HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 0.00 \n", - " HALLMARK_SPERMATOGENESIS-0 0.00 \n", - " HALLMARK_SPERMATOGENESIS-1 0.00 \n", - " HALLMARK_TGF_BETA_SIGNALING-0 0.00 \n", - " HALLMARK_TGF_BETA_SIGNALING-1 0.50 \n", - " HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 0.67 \n", - " HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 0.60 \n", - " HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 1.00 \n", - " HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 0.50 \n", - " HALLMARK_UV_RESPONSE_DN-0 0.25 \n", - " HALLMARK_UV_RESPONSE_DN-1 0.50 \n", - " HALLMARK_UV_RESPONSE_UP-0 1.00 \n", - " HALLMARK_UV_RESPONSE_UP-1 0.00 \n", - " HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 0.00 \n", - " HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 0.20 \n", - " T cell proliferation-0 NaN \n", - " T cell proliferation-1 0.20 \n", - " Yamanaka-TFs-0 0.00 \n", - " Yamanaka-TFs-1 0.00 \n", - " amigo-example-0 0.50 \n", - " amigo-example-1 0.50 \n", - " bicluster_RNAseqDB_0-0 0.00 \n", - " bicluster_RNAseqDB_0-1 0.00 \n", - " bicluster_RNAseqDB_1002-0 0.27 \n", - " bicluster_RNAseqDB_1002-1 0.57 \n", - " endocytosis-0 0.25 \n", - " endocytosis-1 1.00 \n", - " glycolysis-gocam-0 0.44 \n", - " glycolysis-gocam-1 0.50 \n", - " go-postsynapse-calcium-transmembrane-0 NaN \n", - " go-postsynapse-calcium-transmembrane-1 1.00 \n", - " go-reg-autophagy-pkra-0 0.40 \n", - " go-reg-autophagy-pkra-1 0.20 \n", - " hydrolase activity, hydrolyzing O-glycosyl compounds-0 NaN \n", - " ig-receptor-binding-2022-0 0.00 \n", - " ig-receptor-binding-2022-1 0.50 \n", - " meiosis I-0 0.75 \n", - " meiosis I-1 0.75 \n", - " molecular sequestering-0 0.00 \n", - " molecular sequestering-1 0.00 \n", - " mtorc1-0 0.44 \n", - " mtorc1-1 0.40 \n", - " peroxisome-1 NaN \n", - " progeria-0 0.00 \n", - " progeria-1 0.00 \n", - " regulation of presynaptic membrane potential-1 0.50 \n", - " sensory ataxia-0 0.00 \n", - " sensory ataxia-1 0.00 \n", - " term-GO:0007212-0 0.00 \n", - " term-GO:0007212-1 0.25 \n", - " tf-downreg-colorectal-0 1.00 \n", - " tf-downreg-colorectal-1 0.00 \n", - " no_synopsis EDS-0 0.00 \n", - " EDS-1 0.00 \n", - " FA-0 0.50 \n", - " FA-1 0.00 \n", - " HALLMARK_ADIPOGENESIS-0 0.00 \n", - " HALLMARK_ADIPOGENESIS-1 0.29 \n", - " HALLMARK_ALLOGRAFT_REJECTION-0 0.00 \n", - " HALLMARK_ALLOGRAFT_REJECTION-1 1.00 \n", - " HALLMARK_ANDROGEN_RESPONSE-0 0.25 \n", - " HALLMARK_ANDROGEN_RESPONSE-1 0.00 \n", - " HALLMARK_ANGIOGENESIS-0 0.50 \n", - " HALLMARK_ANGIOGENESIS-1 NaN \n", - " HALLMARK_APICAL_JUNCTION-0 0.50 \n", - " HALLMARK_APICAL_JUNCTION-1 1.00 \n", - " HALLMARK_APICAL_SURFACE-0 0.25 \n", - " HALLMARK_APICAL_SURFACE-1 1.00 \n", - " HALLMARK_APOPTOSIS-0 0.50 \n", - " HALLMARK_APOPTOSIS-1 0.56 \n", - " HALLMARK_BILE_ACID_METABOLISM-0 0.67 \n", - " HALLMARK_BILE_ACID_METABOLISM-1 0.50 \n", - " HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 0.33 \n", - " HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 0.33 \n", - " HALLMARK_COAGULATION-1 0.67 \n", - " HALLMARK_COMPLEMENT-0 0.75 \n", - " HALLMARK_COMPLEMENT-1 0.36 \n", - " HALLMARK_DNA_REPAIR-0 0.43 \n", - " HALLMARK_DNA_REPAIR-1 0.29 \n", - " HALLMARK_E2F_TARGETS-0 0.50 \n", - " HALLMARK_E2F_TARGETS-1 0.75 \n", - " HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 1.00 \n", - " HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 1.00 \n", - " HALLMARK_ESTROGEN_RESPONSE_EARLY-0 0.00 \n", - " HALLMARK_ESTROGEN_RESPONSE_EARLY-1 0.33 \n", - " HALLMARK_ESTROGEN_RESPONSE_LATE-0 0.00 \n", - " HALLMARK_ESTROGEN_RESPONSE_LATE-1 0.12 \n", - " HALLMARK_FATTY_ACID_METABOLISM-0 1.00 \n", - " HALLMARK_FATTY_ACID_METABOLISM-1 0.80 \n", - " HALLMARK_G2M_CHECKPOINT-0 0.57 \n", - " HALLMARK_G2M_CHECKPOINT-1 1.00 \n", - " HALLMARK_GLYCOLYSIS-0 1.00 \n", - " HALLMARK_GLYCOLYSIS-1 0.60 \n", - " HALLMARK_HEDGEHOG_SIGNALING-0 1.00 \n", - " HALLMARK_HEDGEHOG_SIGNALING-1 1.00 \n", - " HALLMARK_HEME_METABOLISM-0 0.50 \n", - " HALLMARK_HEME_METABOLISM-1 0.10 \n", - " HALLMARK_HYPOXIA-0 0.00 \n", - " HALLMARK_HYPOXIA-1 0.33 \n", - " HALLMARK_IL2_STAT5_SIGNALING-0 0.00 \n", - " HALLMARK_IL2_STAT5_SIGNALING-1 0.75 \n", - " HALLMARK_IL6_JAK_STAT3_SIGNALING-0 0.00 \n", - " HALLMARK_IL6_JAK_STAT3_SIGNALING-1 1.00 \n", - " HALLMARK_INFLAMMATORY_RESPONSE-0 NaN \n", - " HALLMARK_INFLAMMATORY_RESPONSE-1 0.67 \n", - " HALLMARK_INTERFERON_ALPHA_RESPONSE-0 NaN \n", - " HALLMARK_INTERFERON_ALPHA_RESPONSE-1 0.33 \n", - " HALLMARK_INTERFERON_GAMMA_RESPONSE-0 0.67 \n", - " HALLMARK_INTERFERON_GAMMA_RESPONSE-1 1.00 \n", - " HALLMARK_KRAS_SIGNALING_DN-0 0.00 \n", - " HALLMARK_KRAS_SIGNALING_DN-1 0.00 \n", - " HALLMARK_KRAS_SIGNALING_UP-0 0.50 \n", - " HALLMARK_KRAS_SIGNALING_UP-1 NaN \n", - " HALLMARK_MITOTIC_SPINDLE-0 0.50 \n", - " HALLMARK_MITOTIC_SPINDLE-1 0.75 \n", - " HALLMARK_MTORC1_SIGNALING-0 0.00 \n", - " HALLMARK_MTORC1_SIGNALING-1 0.33 \n", - " HALLMARK_MYC_TARGETS_V1-0 0.33 \n", - " HALLMARK_MYC_TARGETS_V1-1 1.00 \n", - " HALLMARK_MYC_TARGETS_V2-0 0.25 \n", - " HALLMARK_MYC_TARGETS_V2-1 0.00 \n", - " HALLMARK_MYOGENESIS-0 0.00 \n", - " HALLMARK_MYOGENESIS-1 0.25 \n", - " HALLMARK_NOTCH_SIGNALING-0 0.50 \n", - " HALLMARK_NOTCH_SIGNALING-1 0.50 \n", - " HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 0.50 \n", - " HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 1.00 \n", - " HALLMARK_P53_PATHWAY-0 0.50 \n", - " HALLMARK_P53_PATHWAY-1 0.67 \n", - " HALLMARK_PANCREAS_BETA_CELLS-0 0.40 \n", - " HALLMARK_PANCREAS_BETA_CELLS-1 0.33 \n", - " HALLMARK_PEROXISOME-0 0.25 \n", - " HALLMARK_PEROXISOME-1 0.11 \n", - " HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 0.00 \n", - " HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 0.57 \n", - " HALLMARK_PROTEIN_SECRETION-0 1.00 \n", - " HALLMARK_PROTEIN_SECRETION-1 0.20 \n", - " HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 0.20 \n", - " HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 0.00 \n", - " HALLMARK_SPERMATOGENESIS-0 0.17 \n", - " HALLMARK_SPERMATOGENESIS-1 0.00 \n", - " HALLMARK_TGF_BETA_SIGNALING-0 0.00 \n", - " HALLMARK_TGF_BETA_SIGNALING-1 0.67 \n", - " HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 0.40 \n", - " HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 0.00 \n", - " HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 0.50 \n", - " HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 0.33 \n", - " HALLMARK_UV_RESPONSE_DN-0 1.00 \n", - " HALLMARK_UV_RESPONSE_DN-1 0.50 \n", - " HALLMARK_UV_RESPONSE_UP-0 0.40 \n", - " HALLMARK_UV_RESPONSE_UP-1 0.33 \n", - " HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 0.50 \n", - " HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 0.67 \n", - " T cell proliferation-0 1.00 \n", - " T cell proliferation-1 0.67 \n", - " Yamanaka-TFs-0 0.50 \n", - " Yamanaka-TFs-1 0.00 \n", - " amigo-example-0 0.00 \n", - " amigo-example-1 0.33 \n", - " bicluster_RNAseqDB_0-0 0.00 \n", - " bicluster_RNAseqDB_0-1 0.00 \n", - " bicluster_RNAseqDB_1002-0 0.33 \n", - " bicluster_RNAseqDB_1002-1 0.00 \n", - " endocytosis-0 0.00 \n", - " endocytosis-1 0.50 \n", - " glycolysis-gocam-0 0.50 \n", - " glycolysis-gocam-1 0.50 \n", - " go-postsynapse-calcium-transmembrane-0 1.00 \n", - " go-postsynapse-calcium-transmembrane-1 1.00 \n", - " go-reg-autophagy-pkra-0 NaN \n", - " go-reg-autophagy-pkra-1 0.00 \n", - " hydrolase activity, hydrolyzing O-glycosyl compounds-0 1.00 \n", - " hydrolase activity, hydrolyzing O-glycosyl compounds-1 0.00 \n", - " ig-receptor-binding-2022-0 NaN \n", - " ig-receptor-binding-2022-1 0.00 \n", - " meiosis I-0 0.75 \n", - " meiosis I-1 1.00 \n", - " molecular sequestering-0 0.00 \n", - " molecular sequestering-1 0.00 \n", - " mtorc1-0 0.00 \n", - " mtorc1-1 NaN \n", - " peroxisome-0 0.00 \n", - " peroxisome-1 1.00 \n", - " progeria-0 0.00 \n", - " progeria-1 0.00 \n", - " regulation of presynaptic membrane potential-0 1.00 \n", - " regulation of presynaptic membrane potential-1 1.00 \n", - " sensory ataxia-0 0.00 \n", - " sensory ataxia-1 0.00 \n", - " term-GO:0007212-1 0.50 \n", - " tf-downreg-colorectal-0 1.00 \n", - " tf-downreg-colorectal-1 0.40 \n", - " ontological_synopsis EDS-0 0.17 \n", - " EDS-1 0.80 \n", - " FA-0 0.83 \n", - " FA-1 0.23 \n", - " HALLMARK_ADIPOGENESIS-0 0.00 \n", - " HALLMARK_ADIPOGENESIS-1 0.00 \n", - " HALLMARK_ALLOGRAFT_REJECTION-0 0.40 \n", - " HALLMARK_ALLOGRAFT_REJECTION-1 0.50 \n", - " HALLMARK_ANDROGEN_RESPONSE-0 0.09 \n", - " HALLMARK_ANDROGEN_RESPONSE-1 0.00 \n", - " HALLMARK_ANGIOGENESIS-0 0.00 \n", - " HALLMARK_ANGIOGENESIS-1 0.29 \n", - " HALLMARK_APICAL_JUNCTION-0 0.80 \n", - " HALLMARK_APICAL_JUNCTION-1 0.00 \n", - " HALLMARK_APICAL_SURFACE-0 0.00 \n", - " HALLMARK_APICAL_SURFACE-1 0.00 \n", - " HALLMARK_APOPTOSIS-0 0.60 \n", - " HALLMARK_APOPTOSIS-1 0.33 \n", - " HALLMARK_BILE_ACID_METABOLISM-0 0.50 \n", - " HALLMARK_BILE_ACID_METABOLISM-1 0.50 \n", - " HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 0.25 \n", - " HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 0.50 \n", - " HALLMARK_COAGULATION-0 1.00 \n", - " HALLMARK_COAGULATION-1 0.33 \n", - " HALLMARK_COMPLEMENT-0 0.50 \n", - " HALLMARK_COMPLEMENT-1 0.70 \n", - " HALLMARK_DNA_REPAIR-0 0.00 \n", - " HALLMARK_DNA_REPAIR-1 0.33 \n", - " HALLMARK_E2F_TARGETS-0 0.50 \n", - " HALLMARK_E2F_TARGETS-1 0.86 \n", - " HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 0.00 \n", - " HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 0.50 \n", - " HALLMARK_ESTROGEN_RESPONSE_EARLY-0 0.00 \n", - " HALLMARK_ESTROGEN_RESPONSE_EARLY-1 0.00 \n", - " HALLMARK_ESTROGEN_RESPONSE_LATE-0 0.05 \n", - " HALLMARK_ESTROGEN_RESPONSE_LATE-1 0.00 \n", - " HALLMARK_FATTY_ACID_METABOLISM-0 0.20 \n", - " HALLMARK_FATTY_ACID_METABOLISM-1 0.60 \n", - " HALLMARK_G2M_CHECKPOINT-0 0.67 \n", - " HALLMARK_G2M_CHECKPOINT-1 0.73 \n", - " HALLMARK_GLYCOLYSIS-0 0.00 \n", - " HALLMARK_GLYCOLYSIS-1 0.11 \n", - " HALLMARK_HEDGEHOG_SIGNALING-0 0.11 \n", - " HALLMARK_HEDGEHOG_SIGNALING-1 0.33 \n", - " HALLMARK_HEME_METABOLISM-0 0.00 \n", - " HALLMARK_HEME_METABOLISM-1 0.00 \n", - " HALLMARK_HYPOXIA-0 0.50 \n", - " HALLMARK_HYPOXIA-1 0.00 \n", - " HALLMARK_IL2_STAT5_SIGNALING-0 0.43 \n", - " HALLMARK_IL2_STAT5_SIGNALING-1 0.33 \n", - " HALLMARK_IL6_JAK_STAT3_SIGNALING-0 0.67 \n", - " HALLMARK_IL6_JAK_STAT3_SIGNALING-1 0.60 \n", - " HALLMARK_INFLAMMATORY_RESPONSE-0 0.43 \n", - " HALLMARK_INFLAMMATORY_RESPONSE-1 0.25 \n", - " HALLMARK_INTERFERON_ALPHA_RESPONSE-0 0.25 \n", - " HALLMARK_INTERFERON_ALPHA_RESPONSE-1 0.25 \n", - " HALLMARK_INTERFERON_GAMMA_RESPONSE-0 0.00 \n", - " HALLMARK_INTERFERON_GAMMA_RESPONSE-1 0.20 \n", - " HALLMARK_KRAS_SIGNALING_DN-0 0.00 \n", - " HALLMARK_KRAS_SIGNALING_DN-1 0.00 \n", - " HALLMARK_KRAS_SIGNALING_UP-0 0.67 \n", - " HALLMARK_KRAS_SIGNALING_UP-1 0.00 \n", - " HALLMARK_MITOTIC_SPINDLE-0 0.44 \n", - " HALLMARK_MITOTIC_SPINDLE-1 0.29 \n", - " HALLMARK_MTORC1_SIGNALING-0 0.12 \n", - " HALLMARK_MTORC1_SIGNALING-1 0.00 \n", - " HALLMARK_MYC_TARGETS_V1-0 0.71 \n", - " HALLMARK_MYC_TARGETS_V1-1 0.10 \n", - " HALLMARK_MYC_TARGETS_V2-0 0.25 \n", - " HALLMARK_MYC_TARGETS_V2-1 0.25 \n", - " HALLMARK_MYOGENESIS-0 0.00 \n", - " HALLMARK_MYOGENESIS-1 0.00 \n", - " HALLMARK_NOTCH_SIGNALING-0 0.88 \n", - " HALLMARK_NOTCH_SIGNALING-1 0.62 \n", - " HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 0.50 \n", - " HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 0.33 \n", - " HALLMARK_P53_PATHWAY-0 NaN \n", - " HALLMARK_P53_PATHWAY-1 0.50 \n", - " HALLMARK_PANCREAS_BETA_CELLS-0 0.08 \n", - " HALLMARK_PANCREAS_BETA_CELLS-1 0.00 \n", - " HALLMARK_PEROXISOME-0 0.43 \n", - " HALLMARK_PEROXISOME-1 0.08 \n", - " HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 1.00 \n", - " HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 0.62 \n", - " HALLMARK_PROTEIN_SECRETION-0 0.00 \n", - " HALLMARK_PROTEIN_SECRETION-1 0.25 \n", - " HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 0.00 \n", - " HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 0.64 \n", - " HALLMARK_SPERMATOGENESIS-0 0.12 \n", - " HALLMARK_SPERMATOGENESIS-1 0.00 \n", - " HALLMARK_TGF_BETA_SIGNALING-0 0.56 \n", - " HALLMARK_TGF_BETA_SIGNALING-1 0.70 \n", - " HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 0.00 \n", - " HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 0.75 \n", - " HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 0.00 \n", - " HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 0.17 \n", - " HALLMARK_UV_RESPONSE_DN-0 NaN \n", - " HALLMARK_UV_RESPONSE_DN-1 0.29 \n", - " HALLMARK_UV_RESPONSE_UP-0 0.00 \n", - " HALLMARK_UV_RESPONSE_UP-1 0.00 \n", - " HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 0.17 \n", - " HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 0.44 \n", - " T cell proliferation-0 0.43 \n", - " T cell proliferation-1 0.00 \n", - " Yamanaka-TFs-0 0.00 \n", - " Yamanaka-TFs-1 0.11 \n", - " amigo-example-0 0.44 \n", - " amigo-example-1 0.30 \n", - " bicluster_RNAseqDB_0-0 0.00 \n", - " bicluster_RNAseqDB_0-1 0.00 \n", - " bicluster_RNAseqDB_1002-0 0.50 \n", - " bicluster_RNAseqDB_1002-1 0.00 \n", - " endocytosis-0 0.20 \n", - " endocytosis-1 0.00 \n", - " glycolysis-gocam-0 0.33 \n", - " glycolysis-gocam-1 0.19 \n", - " go-postsynapse-calcium-transmembrane-0 1.00 \n", - " go-postsynapse-calcium-transmembrane-1 1.00 \n", - " go-reg-autophagy-pkra-0 0.25 \n", - " go-reg-autophagy-pkra-1 1.00 \n", - " hydrolase activity, hydrolyzing O-glycosyl compounds-0 0.75 \n", - " hydrolase activity, hydrolyzing O-glycosyl compounds-1 0.70 \n", - " ig-receptor-binding-2022-0 0.00 \n", - " ig-receptor-binding-2022-1 0.11 \n", - " meiosis I-0 0.67 \n", - " meiosis I-1 0.73 \n", - " molecular sequestering-0 0.17 \n", - " molecular sequestering-1 0.14 \n", - " mtorc1-0 0.12 \n", - " mtorc1-1 0.22 \n", - " peroxisome-0 0.67 \n", - " peroxisome-1 0.14 \n", - " progeria-0 0.07 \n", - " progeria-1 0.00 \n", - " regulation of presynaptic membrane potential-0 0.90 \n", - " regulation of presynaptic membrane potential-1 0.60 \n", - " sensory ataxia-0 0.04 \n", - " sensory ataxia-1 0.11 \n", - " term-GO:0007212-0 0.14 \n", - " term-GO:0007212-1 0.22 \n", - " tf-downreg-colorectal-0 0.33 \n", - " tf-downreg-colorectal-1 0.50 \n", - "\n", - "prompt_variant diff \n", - "model method geneset \n", - "gpt-3.5-turbo narrative_synopsis EDS-0 -0.36 \n", - " EDS-1 0.25 \n", - " FA-0 0.00 \n", - " FA-1 0.00 \n", - " HALLMARK_ADIPOGENESIS-0 0.33 \n", - " HALLMARK_ADIPOGENESIS-1 -0.67 \n", - " HALLMARK_ALLOGRAFT_REJECTION-0 0.13 \n", - " HALLMARK_ALLOGRAFT_REJECTION-1 0.00 \n", - " HALLMARK_ANDROGEN_RESPONSE-0 0.00 \n", - " HALLMARK_ANDROGEN_RESPONSE-1 0.20 \n", - " HALLMARK_ANGIOGENESIS-0 0.17 \n", - " HALLMARK_ANGIOGENESIS-1 0.00 \n", - " HALLMARK_APICAL_JUNCTION-0 0.00 \n", - " HALLMARK_APICAL_JUNCTION-1 0.13 \n", - " HALLMARK_APICAL_SURFACE-0 0.17 \n", - " HALLMARK_APICAL_SURFACE-1 0.33 \n", - " HALLMARK_APOPTOSIS-0 0.00 \n", - " HALLMARK_APOPTOSIS-1 NaN \n", - " HALLMARK_BILE_ACID_METABOLISM-0 0.40 \n", - " HALLMARK_BILE_ACID_METABOLISM-1 -0.17 \n", - " HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 0.00 \n", - " HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 -0.08 \n", - " HALLMARK_COAGULATION-0 0.00 \n", - " HALLMARK_COAGULATION-1 -0.50 \n", - " HALLMARK_COMPLEMENT-0 0.00 \n", - " HALLMARK_COMPLEMENT-1 0.00 \n", - " HALLMARK_DNA_REPAIR-0 -0.33 \n", - " HALLMARK_DNA_REPAIR-1 -0.62 \n", - " HALLMARK_E2F_TARGETS-0 0.00 \n", - " HALLMARK_E2F_TARGETS-1 -0.25 \n", - " HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 0.21 \n", - " HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 0.17 \n", - " HALLMARK_ESTROGEN_RESPONSE_EARLY-0 0.00 \n", - " HALLMARK_ESTROGEN_RESPONSE_EARLY-1 0.00 \n", - " HALLMARK_ESTROGEN_RESPONSE_LATE-0 -0.38 \n", - " HALLMARK_ESTROGEN_RESPONSE_LATE-1 0.03 \n", - " HALLMARK_FATTY_ACID_METABOLISM-0 -0.20 \n", - " HALLMARK_FATTY_ACID_METABOLISM-1 0.12 \n", - " HALLMARK_G2M_CHECKPOINT-0 0.00 \n", - " HALLMARK_G2M_CHECKPOINT-1 -0.17 \n", - " HALLMARK_GLYCOLYSIS-0 -0.36 \n", - " HALLMARK_GLYCOLYSIS-1 -0.10 \n", - " HALLMARK_HEDGEHOG_SIGNALING-0 0.20 \n", - " HALLMARK_HEDGEHOG_SIGNALING-1 0.00 \n", - " HALLMARK_HEME_METABOLISM-0 0.00 \n", - " HALLMARK_HEME_METABOLISM-1 0.10 \n", - " HALLMARK_HYPOXIA-0 -0.33 \n", - " HALLMARK_HYPOXIA-1 0.10 \n", - " HALLMARK_IL2_STAT5_SIGNALING-0 0.80 \n", - " HALLMARK_IL2_STAT5_SIGNALING-1 -0.08 \n", - " HALLMARK_IL6_JAK_STAT3_SIGNALING-0 NaN \n", - " HALLMARK_IL6_JAK_STAT3_SIGNALING-1 0.00 \n", - " HALLMARK_INFLAMMATORY_RESPONSE-0 -0.67 \n", - " HALLMARK_INFLAMMATORY_RESPONSE-1 0.20 \n", - " HALLMARK_INTERFERON_ALPHA_RESPONSE-0 -0.25 \n", - " HALLMARK_INTERFERON_ALPHA_RESPONSE-1 0.00 \n", - " HALLMARK_INTERFERON_GAMMA_RESPONSE-0 NaN \n", - " HALLMARK_INTERFERON_GAMMA_RESPONSE-1 -0.25 \n", - " HALLMARK_KRAS_SIGNALING_DN-0 0.08 \n", - " HALLMARK_KRAS_SIGNALING_DN-1 0.00 \n", - " HALLMARK_KRAS_SIGNALING_UP-0 -0.13 \n", - " HALLMARK_KRAS_SIGNALING_UP-1 NaN \n", - " HALLMARK_MITOTIC_SPINDLE-0 -0.20 \n", - " HALLMARK_MITOTIC_SPINDLE-1 0.00 \n", - " HALLMARK_MTORC1_SIGNALING-0 0.00 \n", - " HALLMARK_MTORC1_SIGNALING-1 -0.17 \n", - " HALLMARK_MYC_TARGETS_V1-0 0.03 \n", - " HALLMARK_MYC_TARGETS_V1-1 0.25 \n", - " HALLMARK_MYC_TARGETS_V2-0 0.33 \n", - " HALLMARK_MYC_TARGETS_V2-1 0.25 \n", - " HALLMARK_MYOGENESIS-0 -0.22 \n", - " HALLMARK_MYOGENESIS-1 0.00 \n", - " HALLMARK_NOTCH_SIGNALING-0 0.42 \n", - " HALLMARK_NOTCH_SIGNALING-1 0.33 \n", - " HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 0.00 \n", - " HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 0.00 \n", - " HALLMARK_P53_PATHWAY-0 0.42 \n", - " HALLMARK_P53_PATHWAY-1 0.08 \n", - " HALLMARK_PANCREAS_BETA_CELLS-0 0.60 \n", - " HALLMARK_PANCREAS_BETA_CELLS-1 0.00 \n", - " HALLMARK_PEROXISOME-0 -0.20 \n", - " HALLMARK_PEROXISOME-1 0.00 \n", - " HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 0.00 \n", - " HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 0.00 \n", - " HALLMARK_PROTEIN_SECRETION-0 -0.17 \n", - " HALLMARK_PROTEIN_SECRETION-1 0.17 \n", - " HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 NaN \n", - " HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 0.00 \n", - " HALLMARK_SPERMATOGENESIS-0 -0.35 \n", - " HALLMARK_SPERMATOGENESIS-1 -0.33 \n", - " HALLMARK_TGF_BETA_SIGNALING-0 NaN \n", - " HALLMARK_TGF_BETA_SIGNALING-1 0.33 \n", - " HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 0.17 \n", - " HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 0.50 \n", - " HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 0.33 \n", - " HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 0.14 \n", - " HALLMARK_UV_RESPONSE_DN-0 -0.75 \n", - " HALLMARK_UV_RESPONSE_DN-1 0.07 \n", - " HALLMARK_UV_RESPONSE_UP-0 -0.37 \n", - " HALLMARK_UV_RESPONSE_UP-1 0.20 \n", - " HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 -1.00 \n", - " HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 0.50 \n", - " T cell proliferation-0 0.75 \n", - " T cell proliferation-1 0.33 \n", - " Yamanaka-TFs-0 NaN \n", - " Yamanaka-TFs-1 0.00 \n", - " amigo-example-0 -0.13 \n", - " amigo-example-1 -0.17 \n", - " bicluster_RNAseqDB_0-0 0.00 \n", - " bicluster_RNAseqDB_0-1 0.00 \n", - " bicluster_RNAseqDB_1002-0 0.15 \n", - " bicluster_RNAseqDB_1002-1 0.50 \n", - " endocytosis-0 0.80 \n", - " endocytosis-1 0.00 \n", - " glycolysis-gocam-0 NaN \n", - " glycolysis-gocam-1 0.60 \n", - " go-postsynapse-calcium-transmembrane-0 0.00 \n", - " go-postsynapse-calcium-transmembrane-1 0.00 \n", - " go-reg-autophagy-pkra-0 -0.17 \n", - " go-reg-autophagy-pkra-1 0.50 \n", - " hydrolase activity, hydrolyzing O-glycosyl compounds-0 0.11 \n", - " hydrolase activity, hydrolyzing O-glycosyl compounds-1 -0.25 \n", - " ig-receptor-binding-2022-0 0.00 \n", - " ig-receptor-binding-2022-1 0.00 \n", - " meiosis I-0 NaN \n", - " meiosis I-1 0.00 \n", - " molecular sequestering-0 0.00 \n", - " molecular sequestering-1 -0.33 \n", - " mtorc1-0 0.00 \n", - " mtorc1-1 0.40 \n", - " peroxisome-0 NaN \n", - " peroxisome-1 NaN \n", - " progeria-0 0.67 \n", - " progeria-1 0.00 \n", - " regulation of presynaptic membrane potential-0 0.25 \n", - " regulation of presynaptic membrane potential-1 -0.33 \n", - " sensory ataxia-0 -0.50 \n", - " sensory ataxia-1 -0.67 \n", - " term-GO:0007212-0 0.00 \n", - " term-GO:0007212-1 0.17 \n", - " tf-downreg-colorectal-0 -0.50 \n", - " tf-downreg-colorectal-1 0.00 \n", - " no_synopsis EDS-0 0.50 \n", - " EDS-1 -0.33 \n", - " FA-0 NaN \n", - " FA-1 0.00 \n", - " HALLMARK_ADIPOGENESIS-0 -0.24 \n", - " HALLMARK_ADIPOGENESIS-1 -0.64 \n", - " HALLMARK_ALLOGRAFT_REJECTION-0 0.00 \n", - " HALLMARK_ALLOGRAFT_REJECTION-1 0.00 \n", - " HALLMARK_ANDROGEN_RESPONSE-0 0.00 \n", - " HALLMARK_ANDROGEN_RESPONSE-1 0.00 \n", - " HALLMARK_ANGIOGENESIS-0 -0.42 \n", - " HALLMARK_ANGIOGENESIS-1 -0.17 \n", - " HALLMARK_APICAL_JUNCTION-0 0.25 \n", - " HALLMARK_APICAL_JUNCTION-1 -0.11 \n", - " HALLMARK_APICAL_SURFACE-0 -0.19 \n", - " HALLMARK_APICAL_SURFACE-1 0.02 \n", - " HALLMARK_APOPTOSIS-0 -0.30 \n", - " HALLMARK_APOPTOSIS-1 0.30 \n", - " HALLMARK_BILE_ACID_METABOLISM-0 0.00 \n", - " HALLMARK_BILE_ACID_METABOLISM-1 0.25 \n", - " HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 -0.13 \n", - " HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 -0.12 \n", - " HALLMARK_COAGULATION-0 0.25 \n", - " HALLMARK_COAGULATION-1 0.00 \n", - " HALLMARK_COMPLEMENT-0 -0.35 \n", - " HALLMARK_COMPLEMENT-1 -0.11 \n", - " HALLMARK_DNA_REPAIR-0 0.05 \n", - " HALLMARK_DNA_REPAIR-1 -0.05 \n", - " HALLMARK_E2F_TARGETS-0 0.00 \n", - " HALLMARK_E2F_TARGETS-1 0.00 \n", - " HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 -0.18 \n", - " HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 0.03 \n", - " HALLMARK_ESTROGEN_RESPONSE_EARLY-0 0.00 \n", - " HALLMARK_ESTROGEN_RESPONSE_EARLY-1 0.41 \n", - " HALLMARK_ESTROGEN_RESPONSE_LATE-0 -0.05 \n", - " HALLMARK_ESTROGEN_RESPONSE_LATE-1 0.30 \n", - " HALLMARK_FATTY_ACID_METABOLISM-0 NaN \n", - " HALLMARK_FATTY_ACID_METABOLISM-1 0.00 \n", - " HALLMARK_G2M_CHECKPOINT-0 NaN \n", - " HALLMARK_G2M_CHECKPOINT-1 0.00 \n", - " HALLMARK_GLYCOLYSIS-0 NaN \n", - " HALLMARK_GLYCOLYSIS-1 0.07 \n", - " HALLMARK_HEDGEHOG_SIGNALING-0 0.55 \n", - " HALLMARK_HEDGEHOG_SIGNALING-1 0.00 \n", - " HALLMARK_HEME_METABOLISM-0 0.33 \n", - " HALLMARK_HEME_METABOLISM-1 -0.62 \n", - " HALLMARK_HYPOXIA-0 0.11 \n", - " HALLMARK_HYPOXIA-1 NaN \n", - " HALLMARK_IL2_STAT5_SIGNALING-1 0.33 \n", - " HALLMARK_IL6_JAK_STAT3_SIGNALING-0 0.56 \n", - " HALLMARK_IL6_JAK_STAT3_SIGNALING-1 0.00 \n", - " HALLMARK_INFLAMMATORY_RESPONSE-0 -0.29 \n", - " HALLMARK_INFLAMMATORY_RESPONSE-1 -0.25 \n", - " HALLMARK_INTERFERON_ALPHA_RESPONSE-0 0.00 \n", - " HALLMARK_INTERFERON_ALPHA_RESPONSE-1 -0.71 \n", - " HALLMARK_INTERFERON_GAMMA_RESPONSE-0 0.37 \n", - " HALLMARK_INTERFERON_GAMMA_RESPONSE-1 0.14 \n", - " HALLMARK_KRAS_SIGNALING_DN-0 0.50 \n", - " HALLMARK_KRAS_SIGNALING_DN-1 0.00 \n", - " HALLMARK_KRAS_SIGNALING_UP-0 0.36 \n", - " HALLMARK_KRAS_SIGNALING_UP-1 0.40 \n", - " HALLMARK_MITOTIC_SPINDLE-0 0.00 \n", - " HALLMARK_MITOTIC_SPINDLE-1 0.06 \n", - " HALLMARK_MTORC1_SIGNALING-0 NaN \n", - " HALLMARK_MTORC1_SIGNALING-1 -0.25 \n", - " HALLMARK_MYC_TARGETS_V1-0 0.00 \n", - " HALLMARK_MYC_TARGETS_V1-1 0.11 \n", - " HALLMARK_MYC_TARGETS_V2-0 0.07 \n", - " HALLMARK_MYC_TARGETS_V2-1 -0.11 \n", - " HALLMARK_MYOGENESIS-0 -0.40 \n", - " HALLMARK_MYOGENESIS-1 NaN \n", - " HALLMARK_NOTCH_SIGNALING-0 -0.26 \n", - " HALLMARK_NOTCH_SIGNALING-1 0.00 \n", - " HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 0.00 \n", - " HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 0.11 \n", - " HALLMARK_P53_PATHWAY-0 0.00 \n", - " HALLMARK_P53_PATHWAY-1 -0.10 \n", - " HALLMARK_PANCREAS_BETA_CELLS-0 -0.08 \n", - " HALLMARK_PANCREAS_BETA_CELLS-1 -0.07 \n", - " HALLMARK_PEROXISOME-0 -0.10 \n", - " HALLMARK_PEROXISOME-1 -0.21 \n", - " HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 -1.00 \n", - " HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 0.25 \n", - " HALLMARK_PROTEIN_SECRETION-0 0.00 \n", - " HALLMARK_PROTEIN_SECRETION-1 -0.38 \n", - " HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 -0.20 \n", - " HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 -0.67 \n", - " HALLMARK_SPERMATOGENESIS-0 0.40 \n", - " HALLMARK_SPERMATOGENESIS-1 0.17 \n", - " HALLMARK_TGF_BETA_SIGNALING-0 0.02 \n", - " HALLMARK_TGF_BETA_SIGNALING-1 -0.50 \n", - " HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 -0.42 \n", - " HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 -0.13 \n", - " HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 0.40 \n", - " HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 -0.22 \n", - " HALLMARK_UV_RESPONSE_DN-0 0.33 \n", - " HALLMARK_UV_RESPONSE_DN-1 -0.10 \n", - " HALLMARK_UV_RESPONSE_UP-0 -0.25 \n", - " HALLMARK_UV_RESPONSE_UP-1 -0.10 \n", - " HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 1.00 \n", - " HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 -0.25 \n", - " T cell proliferation-0 0.17 \n", - " T cell proliferation-1 0.00 \n", - " Yamanaka-TFs-0 0.00 \n", - " Yamanaka-TFs-1 0.00 \n", - " amigo-example-0 NaN \n", - " amigo-example-1 -0.21 \n", - " bicluster_RNAseqDB_0-0 -0.12 \n", - " bicluster_RNAseqDB_0-1 0.00 \n", - " bicluster_RNAseqDB_1002-0 -0.25 \n", - " bicluster_RNAseqDB_1002-1 0.60 \n", - " endocytosis-0 0.15 \n", - " endocytosis-1 -0.03 \n", - " glycolysis-gocam-0 0.00 \n", - " glycolysis-gocam-1 0.25 \n", - " go-postsynapse-calcium-transmembrane-0 -0.20 \n", - " go-postsynapse-calcium-transmembrane-1 -0.19 \n", - " go-reg-autophagy-pkra-0 0.40 \n", - " go-reg-autophagy-pkra-1 -0.67 \n", - " hydrolase activity, hydrolyzing O-glycosyl compounds-0 -0.06 \n", - " hydrolase activity, hydrolyzing O-glycosyl compounds-1 -0.25 \n", - " ig-receptor-binding-2022-0 -0.60 \n", - " ig-receptor-binding-2022-1 0.33 \n", - " meiosis I-0 0.31 \n", - " meiosis I-1 -0.20 \n", - " molecular sequestering-0 0.12 \n", - " molecular sequestering-1 0.00 \n", - " mtorc1-0 NaN \n", - " mtorc1-1 -0.33 \n", - " peroxisome-0 0.00 \n", - " peroxisome-1 -0.50 \n", - " progeria-0 -0.25 \n", - " progeria-1 0.33 \n", - " regulation of presynaptic membrane potential-0 0.06 \n", - " regulation of presynaptic membrane potential-1 0.06 \n", - " sensory ataxia-0 -0.20 \n", - " sensory ataxia-1 NaN \n", - " term-GO:0007212-0 0.30 \n", - " term-GO:0007212-1 NaN \n", - " tf-downreg-colorectal-0 0.75 \n", - " tf-downreg-colorectal-1 0.11 \n", - " ontological_synopsis EDS-0 -0.05 \n", - " EDS-1 -0.05 \n", - " FA-0 0.00 \n", - " FA-1 0.00 \n", - " HALLMARK_ADIPOGENESIS-0 -0.50 \n", - " HALLMARK_ADIPOGENESIS-1 0.50 \n", - " HALLMARK_ALLOGRAFT_REJECTION-0 -0.25 \n", - " HALLMARK_ALLOGRAFT_REJECTION-1 0.03 \n", - " HALLMARK_ANDROGEN_RESPONSE-0 0.50 \n", - " HALLMARK_ANDROGEN_RESPONSE-1 NaN \n", - " HALLMARK_ANGIOGENESIS-1 NaN \n", - " HALLMARK_APICAL_JUNCTION-0 0.67 \n", - " HALLMARK_APICAL_SURFACE-0 -0.43 \n", - " HALLMARK_APICAL_SURFACE-1 0.43 \n", - " HALLMARK_APOPTOSIS-0 0.25 \n", - " HALLMARK_APOPTOSIS-1 0.00 \n", - " HALLMARK_BILE_ACID_METABOLISM-0 0.20 \n", - " HALLMARK_BILE_ACID_METABOLISM-1 -0.20 \n", - " HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 -0.47 \n", - " HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 -0.42 \n", - " HALLMARK_COAGULATION-0 -0.33 \n", - " HALLMARK_COAGULATION-1 0.00 \n", - " HALLMARK_COMPLEMENT-0 -0.67 \n", - " HALLMARK_COMPLEMENT-1 0.50 \n", - " HALLMARK_DNA_REPAIR-0 0.00 \n", - " HALLMARK_DNA_REPAIR-1 0.25 \n", - " HALLMARK_E2F_TARGETS-0 0.12 \n", - " HALLMARK_E2F_TARGETS-1 NaN \n", - " HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 0.00 \n", - " HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 0.25 \n", - " HALLMARK_ESTROGEN_RESPONSE_EARLY-0 0.00 \n", - " HALLMARK_ESTROGEN_RESPONSE_EARLY-1 -0.33 \n", - " HALLMARK_ESTROGEN_RESPONSE_LATE-0 0.00 \n", - " HALLMARK_ESTROGEN_RESPONSE_LATE-1 NaN \n", - " HALLMARK_FATTY_ACID_METABOLISM-0 -0.51 \n", - " HALLMARK_FATTY_ACID_METABOLISM-1 0.00 \n", - " HALLMARK_G2M_CHECKPOINT-0 0.50 \n", - " HALLMARK_G2M_CHECKPOINT-1 0.25 \n", - " HALLMARK_GLYCOLYSIS-0 -0.13 \n", - " HALLMARK_GLYCOLYSIS-1 0.27 \n", - " HALLMARK_HEDGEHOG_SIGNALING-0 -0.71 \n", - " HALLMARK_HEDGEHOG_SIGNALING-1 0.00 \n", - " HALLMARK_HEME_METABOLISM-0 0.33 \n", - " HALLMARK_HEME_METABOLISM-1 NaN \n", - " HALLMARK_HYPOXIA-0 0.20 \n", - " HALLMARK_HYPOXIA-1 0.17 \n", - " HALLMARK_IL2_STAT5_SIGNALING-0 0.55 \n", - " HALLMARK_IL2_STAT5_SIGNALING-1 -0.38 \n", - " HALLMARK_IL6_JAK_STAT3_SIGNALING-0 0.00 \n", - " HALLMARK_IL6_JAK_STAT3_SIGNALING-1 0.00 \n", - " HALLMARK_INFLAMMATORY_RESPONSE-0 0.00 \n", - " HALLMARK_INFLAMMATORY_RESPONSE-1 0.00 \n", - " HALLMARK_INTERFERON_ALPHA_RESPONSE-0 -0.33 \n", - " HALLMARK_INTERFERON_ALPHA_RESPONSE-1 -0.05 \n", - " HALLMARK_INTERFERON_GAMMA_RESPONSE-0 0.00 \n", - " HALLMARK_INTERFERON_GAMMA_RESPONSE-1 0.00 \n", - " HALLMARK_KRAS_SIGNALING_DN-0 0.00 \n", - " HALLMARK_KRAS_SIGNALING_DN-1 0.00 \n", - " HALLMARK_KRAS_SIGNALING_UP-0 NaN \n", - " HALLMARK_KRAS_SIGNALING_UP-1 0.40 \n", - " HALLMARK_MITOTIC_SPINDLE-0 0.00 \n", - " HALLMARK_MITOTIC_SPINDLE-1 0.00 \n", - " HALLMARK_MTORC1_SIGNALING-0 0.33 \n", - " HALLMARK_MTORC1_SIGNALING-1 -0.75 \n", - " HALLMARK_MYC_TARGETS_V1-0 0.33 \n", - " HALLMARK_MYC_TARGETS_V1-1 0.20 \n", - " HALLMARK_MYC_TARGETS_V2-0 -0.67 \n", - " HALLMARK_MYC_TARGETS_V2-1 0.00 \n", - " HALLMARK_MYOGENESIS-0 NaN \n", - " HALLMARK_MYOGENESIS-1 NaN \n", - " HALLMARK_NOTCH_SIGNALING-0 0.00 \n", - " HALLMARK_NOTCH_SIGNALING-1 NaN \n", - " HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 0.50 \n", - " HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 NaN \n", - " HALLMARK_P53_PATHWAY-0 0.25 \n", - " HALLMARK_P53_PATHWAY-1 -0.50 \n", - " HALLMARK_PANCREAS_BETA_CELLS-0 -0.08 \n", - " HALLMARK_PANCREAS_BETA_CELLS-1 0.00 \n", - " HALLMARK_PEROXISOME-0 -0.20 \n", - " HALLMARK_PEROXISOME-1 -0.10 \n", - " HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 -0.10 \n", - " HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 -0.33 \n", - " HALLMARK_PROTEIN_SECRETION-0 0.29 \n", - " HALLMARK_PROTEIN_SECRETION-1 -0.35 \n", - " HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 -0.08 \n", - " HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 -0.12 \n", - " HALLMARK_SPERMATOGENESIS-0 0.15 \n", - " HALLMARK_SPERMATOGENESIS-1 0.00 \n", - " HALLMARK_TGF_BETA_SIGNALING-0 0.00 \n", - " HALLMARK_TGF_BETA_SIGNALING-1 NaN \n", - " HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 0.00 \n", - " HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 0.14 \n", - " HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 NaN \n", - " HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 NaN \n", - " HALLMARK_UV_RESPONSE_DN-0 -0.50 \n", - " HALLMARK_UV_RESPONSE_DN-1 0.00 \n", - " HALLMARK_UV_RESPONSE_UP-0 0.00 \n", - " HALLMARK_UV_RESPONSE_UP-1 0.00 \n", - " HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 -0.67 \n", - " HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 -0.60 \n", - " T cell proliferation-0 0.00 \n", - " T cell proliferation-1 -0.41 \n", - " Yamanaka-TFs-0 0.42 \n", - " Yamanaka-TFs-1 0.25 \n", - " amigo-example-0 0.75 \n", - " amigo-example-1 0.42 \n", - " bicluster_RNAseqDB_0-0 0.00 \n", - " bicluster_RNAseqDB_0-1 -0.25 \n", - " bicluster_RNAseqDB_1002-0 0.33 \n", - " bicluster_RNAseqDB_1002-1 -0.17 \n", - " endocytosis-0 0.80 \n", - " endocytosis-1 -0.75 \n", - " glycolysis-gocam-0 -0.17 \n", - " glycolysis-gocam-1 -0.08 \n", - " go-postsynapse-calcium-transmembrane-0 0.25 \n", - " go-postsynapse-calcium-transmembrane-1 -0.71 \n", - " go-reg-autophagy-pkra-0 0.00 \n", - " go-reg-autophagy-pkra-1 -0.20 \n", - " hydrolase activity, hydrolyzing O-glycosyl compounds-0 0.00 \n", - " hydrolase activity, hydrolyzing O-glycosyl compounds-1 -0.20 \n", - " ig-receptor-binding-2022-0 NaN \n", - " ig-receptor-binding-2022-1 -0.36 \n", - " meiosis I-0 0.00 \n", - " meiosis I-1 0.00 \n", - " molecular sequestering-0 -0.17 \n", - " molecular sequestering-1 0.25 \n", - " mtorc1-0 0.33 \n", - " mtorc1-1 0.25 \n", - " peroxisome-0 0.50 \n", - " peroxisome-1 0.27 \n", - " progeria-0 0.00 \n", - " progeria-1 0.25 \n", - " regulation of presynaptic membrane potential-0 0.00 \n", - " regulation of presynaptic membrane potential-1 -0.20 \n", - " sensory ataxia-0 0.17 \n", - " sensory ataxia-1 -0.25 \n", - " term-GO:0007212-0 0.50 \n", - " term-GO:0007212-1 -0.15 \n", - " tf-downreg-colorectal-0 0.00 \n", - " tf-downreg-colorectal-1 -0.40 \n", - "text-davinci-003 narrative_synopsis EDS-0 0.33 \n", - " EDS-1 0.50 \n", - " FA-0 -0.33 \n", - " FA-1 0.00 \n", - " HALLMARK_ADIPOGENESIS-0 0.49 \n", - " HALLMARK_ADIPOGENESIS-1 0.19 \n", - " HALLMARK_ALLOGRAFT_REJECTION-0 -0.17 \n", - " HALLMARK_ALLOGRAFT_REJECTION-1 -0.50 \n", - " HALLMARK_ANDROGEN_RESPONSE-0 0.00 \n", - " HALLMARK_ANDROGEN_RESPONSE-1 0.00 \n", - " HALLMARK_ANGIOGENESIS-0 -0.30 \n", - " HALLMARK_ANGIOGENESIS-1 NaN \n", - " HALLMARK_APICAL_JUNCTION-0 0.50 \n", - " HALLMARK_APICAL_JUNCTION-1 0.25 \n", - " HALLMARK_APICAL_SURFACE-0 -0.20 \n", - " HALLMARK_APICAL_SURFACE-1 0.14 \n", - " HALLMARK_APOPTOSIS-0 0.50 \n", - " HALLMARK_APOPTOSIS-1 0.00 \n", - " HALLMARK_BILE_ACID_METABOLISM-0 -0.07 \n", - " HALLMARK_BILE_ACID_METABOLISM-1 -0.57 \n", - " HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 NaN \n", - " HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 0.17 \n", - " HALLMARK_COAGULATION-0 1.00 \n", - " HALLMARK_COAGULATION-1 0.00 \n", - " HALLMARK_COMPLEMENT-0 0.42 \n", - " HALLMARK_COMPLEMENT-1 0.33 \n", - " HALLMARK_DNA_REPAIR-0 -1.00 \n", - " HALLMARK_DNA_REPAIR-1 0.20 \n", - " HALLMARK_E2F_TARGETS-0 0.03 \n", - " HALLMARK_E2F_TARGETS-1 -0.09 \n", - " HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 0.50 \n", - " HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 -0.67 \n", - " HALLMARK_ESTROGEN_RESPONSE_EARLY-0 -0.20 \n", - " HALLMARK_ESTROGEN_RESPONSE_EARLY-1 0.33 \n", - " HALLMARK_ESTROGEN_RESPONSE_LATE-0 NaN \n", - " HALLMARK_ESTROGEN_RESPONSE_LATE-1 0.00 \n", - " HALLMARK_FATTY_ACID_METABOLISM-0 -0.27 \n", - " HALLMARK_FATTY_ACID_METABOLISM-1 -0.08 \n", - " HALLMARK_G2M_CHECKPOINT-0 0.07 \n", - " HALLMARK_G2M_CHECKPOINT-1 0.05 \n", - " HALLMARK_GLYCOLYSIS-0 0.50 \n", - " HALLMARK_GLYCOLYSIS-1 0.26 \n", - " HALLMARK_HEDGEHOG_SIGNALING-0 0.00 \n", - " HALLMARK_HEDGEHOG_SIGNALING-1 0.10 \n", - " HALLMARK_HEME_METABOLISM-0 0.00 \n", - " HALLMARK_HEME_METABOLISM-1 0.00 \n", - " HALLMARK_HYPOXIA-0 0.12 \n", - " HALLMARK_HYPOXIA-1 0.00 \n", - " HALLMARK_IL2_STAT5_SIGNALING-0 -0.50 \n", - " HALLMARK_IL2_STAT5_SIGNALING-1 0.04 \n", - " HALLMARK_IL6_JAK_STAT3_SIGNALING-0 NaN \n", - " HALLMARK_IL6_JAK_STAT3_SIGNALING-1 -0.10 \n", - " HALLMARK_INFLAMMATORY_RESPONSE-0 NaN \n", - " HALLMARK_INFLAMMATORY_RESPONSE-1 0.17 \n", - " HALLMARK_INTERFERON_ALPHA_RESPONSE-0 0.25 \n", - " HALLMARK_INTERFERON_ALPHA_RESPONSE-1 0.00 \n", - " HALLMARK_INTERFERON_GAMMA_RESPONSE-0 -0.42 \n", - " HALLMARK_INTERFERON_GAMMA_RESPONSE-1 0.25 \n", - " HALLMARK_KRAS_SIGNALING_DN-0 0.00 \n", - " HALLMARK_KRAS_SIGNALING_DN-1 -0.50 \n", - " HALLMARK_KRAS_SIGNALING_UP-0 -0.11 \n", - " HALLMARK_KRAS_SIGNALING_UP-1 NaN \n", - " HALLMARK_MITOTIC_SPINDLE-0 NaN \n", - " HALLMARK_MITOTIC_SPINDLE-1 0.10 \n", - " HALLMARK_MTORC1_SIGNALING-0 -0.19 \n", - " HALLMARK_MTORC1_SIGNALING-1 -0.57 \n", - " HALLMARK_MYC_TARGETS_V1-0 -0.10 \n", - " HALLMARK_MYC_TARGETS_V1-1 -0.01 \n", - " HALLMARK_MYC_TARGETS_V2-0 -0.13 \n", - " HALLMARK_MYC_TARGETS_V2-1 -0.33 \n", - " HALLMARK_MYOGENESIS-0 0.00 \n", - " HALLMARK_MYOGENESIS-1 -0.50 \n", - " HALLMARK_NOTCH_SIGNALING-0 -0.20 \n", - " HALLMARK_NOTCH_SIGNALING-1 0.25 \n", - " HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 0.20 \n", - " HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 0.33 \n", - " HALLMARK_P53_PATHWAY-0 -0.17 \n", - " HALLMARK_P53_PATHWAY-1 0.09 \n", - " HALLMARK_PANCREAS_BETA_CELLS-0 -0.33 \n", - " HALLMARK_PANCREAS_BETA_CELLS-1 -0.33 \n", - " HALLMARK_PEROXISOME-0 -1.00 \n", - " HALLMARK_PEROXISOME-1 0.30 \n", - " HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 0.67 \n", - " HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 -0.33 \n", - " HALLMARK_PROTEIN_SECRETION-0 0.17 \n", - " HALLMARK_PROTEIN_SECRETION-1 0.33 \n", - " HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 -0.13 \n", - " HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 0.00 \n", - " HALLMARK_SPERMATOGENESIS-0 0.12 \n", - " HALLMARK_SPERMATOGENESIS-1 0.00 \n", - " HALLMARK_TGF_BETA_SIGNALING-0 0.00 \n", - " HALLMARK_TGF_BETA_SIGNALING-1 NaN \n", - " HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 -0.17 \n", - " HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 0.40 \n", - " HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 -0.60 \n", - " HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 0.10 \n", - " HALLMARK_UV_RESPONSE_DN-0 0.75 \n", - " HALLMARK_UV_RESPONSE_DN-1 -0.17 \n", - " HALLMARK_UV_RESPONSE_UP-0 -1.00 \n", - " HALLMARK_UV_RESPONSE_UP-1 0.33 \n", - " HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 0.60 \n", - " HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 -0.20 \n", - " T cell proliferation-0 NaN \n", - " T cell proliferation-1 0.47 \n", - " Yamanaka-TFs-0 0.00 \n", - " Yamanaka-TFs-1 0.00 \n", - " amigo-example-0 -0.10 \n", - " amigo-example-1 -0.17 \n", - " bicluster_RNAseqDB_0-0 0.00 \n", - " bicluster_RNAseqDB_0-1 0.00 \n", - " bicluster_RNAseqDB_1002-0 0.07 \n", - " bicluster_RNAseqDB_1002-1 -0.57 \n", - " endocytosis-0 0.25 \n", - " endocytosis-1 -0.60 \n", - " glycolysis-gocam-0 0.06 \n", - " glycolysis-gocam-1 0.00 \n", - " go-postsynapse-calcium-transmembrane-0 NaN \n", - " go-postsynapse-calcium-transmembrane-1 0.00 \n", - " go-reg-autophagy-pkra-0 0.10 \n", - " go-reg-autophagy-pkra-1 0.40 \n", - " hydrolase activity, hydrolyzing O-glycosyl compounds-0 NaN \n", - " ig-receptor-binding-2022-0 0.50 \n", - " ig-receptor-binding-2022-1 0.00 \n", - " meiosis I-0 0.05 \n", - " meiosis I-1 -0.08 \n", - " molecular sequestering-0 0.00 \n", - " molecular sequestering-1 0.20 \n", - " mtorc1-0 -0.19 \n", - " mtorc1-1 -0.40 \n", - " peroxisome-1 NaN \n", - " progeria-0 0.00 \n", - " progeria-1 0.00 \n", - " regulation of presynaptic membrane potential-1 -0.50 \n", - " sensory ataxia-0 0.00 \n", - " sensory ataxia-1 0.00 \n", - " term-GO:0007212-0 0.67 \n", - " term-GO:0007212-1 NaN \n", - " tf-downreg-colorectal-0 0.00 \n", - " tf-downreg-colorectal-1 0.00 \n", - " no_synopsis EDS-0 1.00 \n", - " EDS-1 1.00 \n", - " FA-0 NaN \n", - " FA-1 1.00 \n", - " HALLMARK_ADIPOGENESIS-0 0.25 \n", - " HALLMARK_ADIPOGENESIS-1 0.21 \n", - " HALLMARK_ALLOGRAFT_REJECTION-0 1.00 \n", - " HALLMARK_ALLOGRAFT_REJECTION-1 0.00 \n", - " HALLMARK_ANDROGEN_RESPONSE-0 -0.12 \n", - " HALLMARK_ANDROGEN_RESPONSE-1 0.08 \n", - " HALLMARK_ANGIOGENESIS-0 NaN \n", - " HALLMARK_ANGIOGENESIS-1 NaN \n", - " HALLMARK_APICAL_JUNCTION-0 -0.50 \n", - " HALLMARK_APICAL_JUNCTION-1 -0.50 \n", - " HALLMARK_APICAL_SURFACE-0 -0.05 \n", - " HALLMARK_APICAL_SURFACE-1 -0.50 \n", - " HALLMARK_APOPTOSIS-0 0.50 \n", - " HALLMARK_APOPTOSIS-1 -0.22 \n", - " HALLMARK_BILE_ACID_METABOLISM-0 0.00 \n", - " HALLMARK_BILE_ACID_METABOLISM-1 -0.50 \n", - " HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 0.00 \n", - " HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 0.00 \n", - " HALLMARK_COAGULATION-1 -0.07 \n", - " HALLMARK_COMPLEMENT-0 -0.75 \n", - " HALLMARK_COMPLEMENT-1 0.04 \n", - " HALLMARK_DNA_REPAIR-0 0.17 \n", - " HALLMARK_DNA_REPAIR-1 0.05 \n", - " HALLMARK_E2F_TARGETS-0 0.00 \n", - " HALLMARK_E2F_TARGETS-1 -0.20 \n", - " HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 NaN \n", - " HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 -0.33 \n", - " HALLMARK_ESTROGEN_RESPONSE_EARLY-0 NaN \n", - " HALLMARK_ESTROGEN_RESPONSE_EARLY-1 -0.33 \n", - " HALLMARK_ESTROGEN_RESPONSE_LATE-0 0.00 \n", - " HALLMARK_ESTROGEN_RESPONSE_LATE-1 0.12 \n", - " HALLMARK_FATTY_ACID_METABOLISM-0 -0.43 \n", - " HALLMARK_FATTY_ACID_METABOLISM-1 0.20 \n", - " HALLMARK_G2M_CHECKPOINT-0 0.43 \n", - " HALLMARK_G2M_CHECKPOINT-1 0.00 \n", - " HALLMARK_GLYCOLYSIS-0 -0.60 \n", - " HALLMARK_GLYCOLYSIS-1 -0.27 \n", - " HALLMARK_HEDGEHOG_SIGNALING-0 -0.14 \n", - " HALLMARK_HEDGEHOG_SIGNALING-1 -0.29 \n", - " HALLMARK_HEME_METABOLISM-0 -0.50 \n", - " HALLMARK_HEME_METABOLISM-1 -0.10 \n", - " HALLMARK_HYPOXIA-0 0.43 \n", - " HALLMARK_HYPOXIA-1 -0.21 \n", - " HALLMARK_IL2_STAT5_SIGNALING-0 0.25 \n", - " HALLMARK_IL2_STAT5_SIGNALING-1 0.25 \n", - " HALLMARK_IL6_JAK_STAT3_SIGNALING-0 0.75 \n", - " HALLMARK_IL6_JAK_STAT3_SIGNALING-1 0.00 \n", - " HALLMARK_INFLAMMATORY_RESPONSE-0 NaN \n", - " HALLMARK_INFLAMMATORY_RESPONSE-1 0.00 \n", - " HALLMARK_INTERFERON_ALPHA_RESPONSE-0 NaN \n", - " HALLMARK_INTERFERON_ALPHA_RESPONSE-1 -0.33 \n", - " HALLMARK_INTERFERON_GAMMA_RESPONSE-0 0.33 \n", - " HALLMARK_INTERFERON_GAMMA_RESPONSE-1 0.00 \n", - " HALLMARK_KRAS_SIGNALING_DN-0 0.20 \n", - " HALLMARK_KRAS_SIGNALING_DN-1 1.00 \n", - " HALLMARK_KRAS_SIGNALING_UP-0 0.00 \n", - " HALLMARK_KRAS_SIGNALING_UP-1 NaN \n", - " HALLMARK_MITOTIC_SPINDLE-0 -0.50 \n", - " HALLMARK_MITOTIC_SPINDLE-1 -0.25 \n", - " HALLMARK_MTORC1_SIGNALING-0 0.00 \n", - " HALLMARK_MTORC1_SIGNALING-1 -0.19 \n", - " HALLMARK_MYC_TARGETS_V1-0 0.17 \n", - " HALLMARK_MYC_TARGETS_V1-1 -0.50 \n", - " HALLMARK_MYC_TARGETS_V2-0 NaN \n", - " HALLMARK_MYC_TARGETS_V2-1 0.00 \n", - " HALLMARK_MYOGENESIS-0 NaN \n", - " HALLMARK_MYOGENESIS-1 0.50 \n", - " HALLMARK_NOTCH_SIGNALING-0 -0.50 \n", - " HALLMARK_NOTCH_SIGNALING-1 -0.17 \n", - " HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 0.50 \n", - " HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 0.00 \n", - " HALLMARK_P53_PATHWAY-0 0.17 \n", - " HALLMARK_P53_PATHWAY-1 -0.27 \n", - " HALLMARK_PANCREAS_BETA_CELLS-0 0.27 \n", - " HALLMARK_PANCREAS_BETA_CELLS-1 -0.33 \n", - " HALLMARK_PEROXISOME-0 NaN \n", - " HALLMARK_PEROXISOME-1 0.56 \n", - " HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 0.00 \n", - " HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 -0.17 \n", - " HALLMARK_PROTEIN_SECRETION-0 NaN \n", - " HALLMARK_PROTEIN_SECRETION-1 0.13 \n", - " HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 NaN \n", - " HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 0.00 \n", - " HALLMARK_SPERMATOGENESIS-0 -0.17 \n", - " HALLMARK_SPERMATOGENESIS-1 0.00 \n", - " HALLMARK_TGF_BETA_SIGNALING-0 0.33 \n", - " HALLMARK_TGF_BETA_SIGNALING-1 0.33 \n", - " HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 0.60 \n", - " HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 0.25 \n", - " HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 0.17 \n", - " HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 -0.13 \n", - " HALLMARK_UV_RESPONSE_DN-0 0.00 \n", - " HALLMARK_UV_RESPONSE_DN-1 0.30 \n", - " HALLMARK_UV_RESPONSE_UP-0 -0.07 \n", - " HALLMARK_UV_RESPONSE_UP-1 -0.17 \n", - " HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 0.50 \n", - " HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 0.00 \n", - " T cell proliferation-0 -0.50 \n", - " T cell proliferation-1 -0.17 \n", - " Yamanaka-TFs-0 0.00 \n", - " Yamanaka-TFs-1 0.00 \n", - " amigo-example-0 0.50 \n", - " amigo-example-1 -0.33 \n", - " bicluster_RNAseqDB_0-0 0.00 \n", - " bicluster_RNAseqDB_0-1 0.50 \n", - " bicluster_RNAseqDB_1002-0 NaN \n", - " bicluster_RNAseqDB_1002-1 0.20 \n", - " endocytosis-0 0.00 \n", - " endocytosis-1 -0.50 \n", - " glycolysis-gocam-0 0.50 \n", - " glycolysis-gocam-1 0.00 \n", - " go-postsynapse-calcium-transmembrane-0 -1.00 \n", - " go-postsynapse-calcium-transmembrane-1 0.00 \n", - " go-reg-autophagy-pkra-0 NaN \n", - " go-reg-autophagy-pkra-1 0.00 \n", - " hydrolase activity, hydrolyzing O-glycosyl compounds-0 -1.00 \n", - " hydrolase activity, hydrolyzing O-glycosyl compounds-1 0.00 \n", - " ig-receptor-binding-2022-0 NaN \n", - " ig-receptor-binding-2022-1 0.33 \n", - " meiosis I-0 0.25 \n", - " meiosis I-1 0.00 \n", - " molecular sequestering-0 0.00 \n", - " molecular sequestering-1 0.00 \n", - " mtorc1-0 0.00 \n", - " mtorc1-1 NaN \n", - " peroxisome-0 0.00 \n", - " peroxisome-1 NaN \n", - " progeria-0 0.00 \n", - " progeria-1 0.00 \n", - " regulation of presynaptic membrane potential-0 0.00 \n", - " regulation of presynaptic membrane potential-1 -0.25 \n", - " sensory ataxia-0 0.00 \n", - " sensory ataxia-1 0.00 \n", - " term-GO:0007212-1 0.00 \n", - " tf-downreg-colorectal-0 -0.50 \n", - " tf-downreg-colorectal-1 -0.40 \n", - " ontological_synopsis EDS-0 0.02 \n", - " EDS-1 -0.47 \n", - " FA-0 NaN \n", - " FA-1 0.15 \n", - " HALLMARK_ADIPOGENESIS-0 0.25 \n", - " HALLMARK_ADIPOGENESIS-1 0.00 \n", - " HALLMARK_ALLOGRAFT_REJECTION-0 0.35 \n", - " HALLMARK_ALLOGRAFT_REJECTION-1 0.00 \n", - " HALLMARK_ANDROGEN_RESPONSE-0 -0.09 \n", - " HALLMARK_ANDROGEN_RESPONSE-1 0.00 \n", - " HALLMARK_ANGIOGENESIS-0 0.20 \n", - " HALLMARK_ANGIOGENESIS-1 0.05 \n", - " HALLMARK_APICAL_JUNCTION-0 0.20 \n", - " HALLMARK_APICAL_JUNCTION-1 0.00 \n", - " HALLMARK_APICAL_SURFACE-0 0.00 \n", - " HALLMARK_APICAL_SURFACE-1 0.50 \n", - " HALLMARK_APOPTOSIS-0 -0.10 \n", - " HALLMARK_APOPTOSIS-1 0.67 \n", - " HALLMARK_BILE_ACID_METABOLISM-0 -0.17 \n", - " HALLMARK_BILE_ACID_METABOLISM-1 -0.10 \n", - " HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 -0.17 \n", - " HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 -0.17 \n", - " HALLMARK_COAGULATION-0 -0.50 \n", - " HALLMARK_COAGULATION-1 0.17 \n", - " HALLMARK_COMPLEMENT-0 -0.17 \n", - " HALLMARK_COMPLEMENT-1 -0.14 \n", - " HALLMARK_DNA_REPAIR-0 0.25 \n", - " HALLMARK_DNA_REPAIR-1 -0.33 \n", - " HALLMARK_E2F_TARGETS-0 0.33 \n", - " HALLMARK_E2F_TARGETS-1 -0.46 \n", - " HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 1.00 \n", - " HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 -0.50 \n", - " HALLMARK_ESTROGEN_RESPONSE_EARLY-0 0.00 \n", - " HALLMARK_ESTROGEN_RESPONSE_EARLY-1 0.00 \n", - " HALLMARK_ESTROGEN_RESPONSE_LATE-0 NaN \n", - " HALLMARK_ESTROGEN_RESPONSE_LATE-1 0.00 \n", - " HALLMARK_FATTY_ACID_METABOLISM-0 0.06 \n", - " HALLMARK_FATTY_ACID_METABOLISM-1 -0.46 \n", - " HALLMARK_G2M_CHECKPOINT-0 -0.17 \n", - " HALLMARK_G2M_CHECKPOINT-1 -0.48 \n", - " HALLMARK_GLYCOLYSIS-0 0.14 \n", - " HALLMARK_GLYCOLYSIS-1 -0.11 \n", - " HALLMARK_HEDGEHOG_SIGNALING-0 0.49 \n", - " HALLMARK_HEDGEHOG_SIGNALING-1 -0.33 \n", - " HALLMARK_HEME_METABOLISM-0 0.00 \n", - " HALLMARK_HEME_METABOLISM-1 0.00 \n", - " HALLMARK_HYPOXIA-0 -0.50 \n", - " HALLMARK_HYPOXIA-1 0.00 \n", - " HALLMARK_IL2_STAT5_SIGNALING-0 -0.10 \n", - " HALLMARK_IL2_STAT5_SIGNALING-1 -0.25 \n", - " HALLMARK_IL6_JAK_STAT3_SIGNALING-0 -0.33 \n", - " HALLMARK_IL6_JAK_STAT3_SIGNALING-1 0.40 \n", - " HALLMARK_INFLAMMATORY_RESPONSE-0 0.32 \n", - " HALLMARK_INFLAMMATORY_RESPONSE-1 0.15 \n", - " HALLMARK_INTERFERON_ALPHA_RESPONSE-0 -0.25 \n", - " HALLMARK_INTERFERON_ALPHA_RESPONSE-1 0.57 \n", - " HALLMARK_INTERFERON_GAMMA_RESPONSE-0 0.27 \n", - " HALLMARK_INTERFERON_GAMMA_RESPONSE-1 -0.20 \n", - " HALLMARK_KRAS_SIGNALING_DN-0 0.00 \n", - " HALLMARK_KRAS_SIGNALING_DN-1 0.33 \n", - " HALLMARK_KRAS_SIGNALING_UP-0 -0.67 \n", - " HALLMARK_KRAS_SIGNALING_UP-1 0.00 \n", - " HALLMARK_MITOTIC_SPINDLE-0 -0.11 \n", - " HALLMARK_MITOTIC_SPINDLE-1 NaN \n", - " HALLMARK_MTORC1_SIGNALING-0 0.08 \n", - " HALLMARK_MTORC1_SIGNALING-1 0.08 \n", - " HALLMARK_MYC_TARGETS_V1-0 -0.31 \n", - " HALLMARK_MYC_TARGETS_V1-1 0.23 \n", - " HALLMARK_MYC_TARGETS_V2-0 -0.11 \n", - " HALLMARK_MYC_TARGETS_V2-1 -0.05 \n", - " HALLMARK_MYOGENESIS-0 0.43 \n", - " HALLMARK_MYOGENESIS-1 0.33 \n", - " HALLMARK_NOTCH_SIGNALING-0 -0.07 \n", - " HALLMARK_NOTCH_SIGNALING-1 -0.29 \n", - " HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 0.00 \n", - " HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 -0.06 \n", - " HALLMARK_P53_PATHWAY-0 NaN \n", - " HALLMARK_P53_PATHWAY-1 -0.42 \n", - " HALLMARK_PANCREAS_BETA_CELLS-0 0.26 \n", - " HALLMARK_PANCREAS_BETA_CELLS-1 0.00 \n", - " HALLMARK_PEROXISOME-0 0.07 \n", - " HALLMARK_PEROXISOME-1 NaN \n", - " HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 -0.69 \n", - " HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 0.38 \n", - " HALLMARK_PROTEIN_SECRETION-0 0.40 \n", - " HALLMARK_PROTEIN_SECRETION-1 -0.25 \n", - " HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 0.08 \n", - " HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 -0.09 \n", - " HALLMARK_SPERMATOGENESIS-0 -0.12 \n", - " HALLMARK_SPERMATOGENESIS-1 0.11 \n", - " HALLMARK_TGF_BETA_SIGNALING-0 0.44 \n", - " HALLMARK_TGF_BETA_SIGNALING-1 -0.70 \n", - " HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 1.00 \n", - " HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 -0.50 \n", - " HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 0.45 \n", - " HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 -0.17 \n", - " HALLMARK_UV_RESPONSE_DN-0 NaN \n", - " HALLMARK_UV_RESPONSE_DN-1 -0.29 \n", - " HALLMARK_UV_RESPONSE_UP-0 0.17 \n", - " HALLMARK_UV_RESPONSE_UP-1 0.00 \n", - " HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 0.00 \n", - " HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 0.22 \n", - " T cell proliferation-0 -0.18 \n", - " T cell proliferation-1 0.00 \n", - " Yamanaka-TFs-0 0.00 \n", - " Yamanaka-TFs-1 -0.03 \n", - " amigo-example-0 -0.19 \n", - " amigo-example-1 0.10 \n", - " bicluster_RNAseqDB_0-0 0.00 \n", - " bicluster_RNAseqDB_0-1 0.00 \n", - " bicluster_RNAseqDB_1002-0 -0.12 \n", - " bicluster_RNAseqDB_1002-1 0.67 \n", - " endocytosis-0 0.13 \n", - " endocytosis-1 0.17 \n", - " glycolysis-gocam-0 -0.33 \n", - " glycolysis-gocam-1 0.08 \n", - " go-postsynapse-calcium-transmembrane-0 -0.53 \n", - " go-postsynapse-calcium-transmembrane-1 0.00 \n", - " go-reg-autophagy-pkra-0 -0.25 \n", - " go-reg-autophagy-pkra-1 -0.67 \n", - " hydrolase activity, hydrolyzing O-glycosyl compounds-0 -0.12 \n", - " hydrolase activity, hydrolyzing O-glycosyl compounds-1 -0.35 \n", - " ig-receptor-binding-2022-0 0.00 \n", - " ig-receptor-binding-2022-1 0.03 \n", - " meiosis I-0 -0.42 \n", - " meiosis I-1 -0.01 \n", - " molecular sequestering-0 0.00 \n", - " molecular sequestering-1 0.19 \n", - " mtorc1-0 0.08 \n", - " mtorc1-1 0.78 \n", - " peroxisome-0 0.17 \n", - " peroxisome-1 0.29 \n", - " progeria-0 -0.07 \n", - " progeria-1 0.00 \n", - " regulation of presynaptic membrane potential-0 -0.34 \n", - " regulation of presynaptic membrane potential-1 0.40 \n", - " sensory ataxia-0 -0.04 \n", - " sensory ataxia-1 NaN \n", - " term-GO:0007212-0 0.06 \n", - " term-GO:0007212-1 0.21 \n", - " tf-downreg-colorectal-0 0.24 \n", - " tf-downreg-colorectal-1 0.30 " - ] - }, - "execution_count": 58, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "pv_pivot = df.pivot_table(index=[MODEL, METHOD, GENESET], columns=PROMPT_VARIANT, values=PROPOTION_SIGNIFICANT)\n", - "# Calculate differences between run \"1\" and run \"2\"\n", - "pv_pivot['diff'] = pv_pivot[\"v1\"] - pv_pivot[\"v2\"]\n", - "pv_pivot" - ] - }, - { - "cell_type": "code", - "execution_count": 59, - "id": "1c862cee", - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "mean 3.45e-04\n", - "std 3.26e-01\n", - "var 1.06e-01\n", - "min -1.00e+00\n", - "max 1.00e+00\n", - "range 2.00e+00\n", - "Name: diff, dtype: float64" - ] - }, - "execution_count": 59, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "\n", - "# Now you can perform statistics on the 'diff' column\n", - "df_diff_stats = pv_pivot['diff'].agg(['mean', 'std', 'var', 'min', 'max'])\n", - "df_diff_stats['range'] = df_diff_stats['max'] - df_diff_stats['min']\n", - "df_diff_stats" - ] - }, - { - "cell_type": "code", - "execution_count": 60, - "id": "927c6577", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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prompt_variantv1v2
modelmethodgeneset
gpt-3.5-turbonarrative_synopsisEDS-0[[GO:0032964, GO:0030198, GO:0010712, GO:0043687, GO:0006493, GO:0006508, GO:0008270]][[GO:0032964, matrix maturation, GO:0031012, MESH:D006023, MESH:D015238, zinc finger proteins, proteolytic subunits, MESH:D057057, MESH:M0465019]]
EDS-1[[GO:0032964, GO:0061448, GO:0030198, GO:0030166]][[GO:0032964, GO:0030198, GO:0006457, GO:0006955]]
FA-0[[GO:0006281, GO:0035825, GO:0006302, chromosome stability \\n\\nhypotheses: the enriched terms suggest that the common function of these genes is dna repair, specifically in the context of homologous recombination and double-strand break repair. the genes are part of a complex network involved in maintaining chromosome stability, which is critical for preventing mutations and malignant transformation. mutations in these genes have been linked to various forms of cancer and the fanconi anemia disorder. understanding the mechanisms by which these genes function in dna repair could provide insights into cancer development and potential therapeutic targets]][[GO:0006281, GO:0035825, fanconi anemia pathway]]
FA-1[[GO:0006281, fanconi anemia pathway, GO:0035825, MESH:M0443452, genome maintenance, GO:0006302]][[GO:0006281, GO:0035825, MESH:D051856, rad51 family proteins, chromosome stability maintenance\\n\\nmechanism: these genes are involved in dna damage repair and maintenance of genome stability, particularly through homologous recombination and the formation of the fanconi anemia complementation group proteins. the rad51 family proteins and chromosomal stability maintenance are also important in these processes]]
HALLMARK_ADIPOGENESIS-0[[GO:0005739, GO:0006119, GO:0022900, GO:0006091, MESH:M0496924, GO:0006631, GO:0006099, GO:0006635]][[mitochondrial function, GO:0008152, GO:0006118, GO:0006631, redox reactions]]
HALLMARK_ADIPOGENESIS-1[[mitochondrial function, GO:0070469, energy production, GO:0006629, GO:0006869, GO:0005515, GO:0016049, GO:0051301, antioxidant enzyme. \\n\\nmechanism/]][[mitochondrial function; energy metabolism; lipid metabolism; electron transport chain. \\n\\nmechanism: these genes likely contribute to the production and regulation of energy in the form of atp through processes including beta-oxidation of lipids, GO:0006119, and electron transport chain activity. dysfunction or dysregulation of these genes may lead to mitochondrial dysfunction and impaired energy metabolism, which have been implicated in various diseases including neurodegenerative disorders, MONDO:0004995, MONDO:0005066]]
HALLMARK_ALLOGRAFT_REJECTION-0[[chemokine signaling pathway, cytokine-cytokine receptor interaction, GO:0006955, GO:0042110, GO:0050776, GO:0006954, GO:0050900]][[GO:0005125, GO:0042110, GO:0042379, GO:0002429, GO:0032623, GO:0032609, GO:0002504, GO:0050776, GO:0030217, GO:0050900, GO:0060333, GO:0001819, GO:0002685, GO:0070098, GO:0050852]]
HALLMARK_ALLOGRAFT_REJECTION-1[[MESH:D018925, MESH:D016207, t cell-mediated immunity, interferon signaling, GO:0006954, tgf-beta signaling, toll-like receptor signaling, tnf signaling]][[GO:0008009, cytokine signaling, GO:0019882]]
HALLMARK_ANDROGEN_RESPONSE-0[[protein kinase activity; membrane transport; enzyme catalysis\\n\\nmechanism: these genes are involved in signal transduction and cellular metabolism, with a focus on protein kinase activity, GO:0055085, and enzyme catalysis. they play roles in the transport of various molecules across biological membranes, including fatty acids, sugars, and ions. they are also important in regulating cellular responses to extracellular stimuli, such as growth factors, MESH:D006728, and cytokines. additionally, they catalyze metabolic reactions and contribute to various metabolic pathways]][[GO:0004672, GO:0031344, GO:0008285, GO:0010468, regulation of cellular protein localization and movement]]
HALLMARK_ANDROGEN_RESPONSE-1[[GO:0004672, GO:0008134, GO:0005515, GO:0007165, GO:0003824]][[GO:0004672, GO:0008134, GO:0006810, enzymatic activity, GO:0006511, GO:0061024, GO:0042445, GO:0016567]]
HALLMARK_ANGIOGENESIS-0[[GO:0031012, GO:0007155, tissue development and regeneration, growth factor signaling, endothelial-specific signaling, cytokine signaling]][[GO:0030198, GO:0007155, GO:0030199, GO:0006029, GO:0045765, GO:0009611]]
HALLMARK_ANGIOGENESIS-1[[ecm organization, GO:0031589, GO:0016477]][[GO:0030198, GO:0007155, GO:0007088, protein kinase activity regulation, GO:0070848, cellular response to transforming growth factor beta stimulus\\n\\nmechanism: the genes listed are involved in the organization of the extracellular matrix and cell adhesion. specifically, they play roles in binding to and regulating the spacing of collagen fibrils, inhibiting proteases, promoting cell-cell and cell-matrix interactions, and regulating mitosis and protein kinase activity. growth factors and transforming growth factor beta are also involved in signal transduction pathways that are regulated by these genes]]
HALLMARK_APICAL_JUNCTION-0[[GO:0005884, GO:0007155, GO:0007010, GO:0008360, GO:0007165]][[GO:0007155, GO:0007010, GO:0005925, GO:0070160]]
HALLMARK_APICAL_JUNCTION-1[[GO:0070160, GO:0031012, GO:0005604, GO:0007155, adhesion junction, GO:0007160]][[GO:0070160, GO:0007155, GO:0008014, integrin, GO:0007165, adhesion g-protein coupled receptor (gpcr), GO:0015629, UBERON:4000022, protein tyrosine kinase (ptk), GO:0016303, map kinase, MESH:D016212]]
HALLMARK_APICAL_SURFACE-0[[GO:0007155, GO:0007165, GO:0061024, GO:0015031]][[GO:0007166, GO:0007169, GO:1901796, GO:0019048, GO:0045785, GO:0043408, GO:2000145, GO:0032956, GO:0051897, GO:0048015, GO:0010810, GO:0030334, regulation of cell growth\\n\\nmechanism and hypotheses: the enriched terms suggest a common mechanism involving transmembrane signaling pathways, with a focus on cell adhesion, migration, and growth regulation. several of the genes are involved in the regulation of the mapk signaling pathway, which is known to play a central role in cellular processes such as proliferation, differentiation, and apoptosis. pathway analysis of these genes may further elucidate the specific regulatory mechanisms at play]]
HALLMARK_APICAL_SURFACE-1[[GO:0007155, GO:0007165, GO:0007154]][[GO:0007160, GO:0006811, GO:0007165, GO:0098631, insulin regulation, GO:0016485]]
HALLMARK_APOPTOSIS-0[[GO:0006915, GO:0008219, GO:0043067, GO:0097153, binding of proteins involved in cell death.\\n\\nmechanism: the majority of the genes on the list are involved in apoptotic processes or regulate cell death. many of these genes belong to the bcl-2 protein family, which regulate apoptosis by either inhibiting or promoting cell death. other gene products, such as the caspases, also play a crucial role in the apoptotic process by cleaving proteins involved in cell death, ultimately leading to cell death. the enrichment of this theme in the gene list suggests that the regulation of apoptosis and programmed cell death is a significant biological mechanism that the genes in the list are involved in]][[GO:0006915, GO:0008219, GO:0007165]]
HALLMARK_APOPTOSIS-1[[apoptosis regulation, cytokine signaling, growth factor regulation]][[GO:0097153, GO:0042981, positive regulation of dna fragmentation, GO:0043067, GO:0010941, GO:1901796, GO:0006974, GO:0070613]]
HALLMARK_BILE_ACID_METABOLISM-0[[GO:0140359, long-chain fatty-acid metabolism, GO:0008203, GO:0006629, GO:0006637]][[GO:0006869, GO:0008203, GO:0006631, peroxisomal biogenesis, GO:0004448, GO:0008146]]
HALLMARK_BILE_ACID_METABOLISM-1[[peroxisome biogenesis, GO:0006631, GO:0006699, GO:0008203, GO:0140359, GO:0016491, atp-binding cassette, GO:0005490]][[GO:0007031, GO:0001676, GO:0006699, GO:0008202, GO:0008203, GO:0001523, GO:0006635, alpha-oxidation, GO:0006720, lipid metabolic process \\n\\nmechanism: these genes function in a variety of processes involved in lipid metabolism and peroxisome biogenesis. peroxisomes are intracellular organelles involved in many metabolic pathways, including fatty acid beta-oxidation, which our enriched terms suggest is a common theme among these genes. additionally, these genes are involved in the synthesis of bile acids, steroid hormones, and retinoids, highlighting the importance of lipid metabolism in cellular function]]
HALLMARK_CHOLESTEROL_HOMEOSTASIS-0[[GO:0006695, GO:0006633, GO:0006629, regulation of cholesterol levels, transport across cell membranes]][[GO:0006629, GO:0006869, GO:0008610]]
HALLMARK_CHOLESTEROL_HOMEOSTASIS-1[[GO:0006695, GO:0006629, GO:0007165]][[GO:0006695, GO:0006644, GO:0006633, GO:0016125]]
HALLMARK_COAGULATION-0[[GO:0006956, GO:0007596, GO:0006508, GO:0030198]][[GO:0007596, extracellular matrix remodeling, GO:0030449]]
HALLMARK_COAGULATION-1[[blood coagulation cascade; complement activation, classical pathway; extracellular matrix disassembly; calcium ion binding. \\n\\nmechanism: these genes are involved in the regulation and activation of different pathways implicated in blood coagulation, GO:0006956, and extracellular matrix remodelling. blood coagulation involves the conversion of prothrombin to thrombin by coagulation factors, which leads to the formation of a fibrin clot. complement activation is a cascade resulting in the removal of damaged cells and pathogens. extracellular matrix disassembly and remodelling are implicated in cellular processes such as tissue repair, GO:0001525, metastasis. calcium-binding proteins play a vital role in signalling pathways regulation of enzymatic activities]][[extracellular matrix breakdown, GO:0007596, protein inhibition]]
HALLMARK_COMPLEMENT-0[[GO:0006956, GO:0006955, GO:0030162, GO:0030168]][[GO:0008233, GO:0007596, GO:0006956]]
HALLMARK_COMPLEMENT-1[[GO:0006956, GO:0007596, cytokine signaling, GO:0006468, GO:0006955, GO:0006954]][[GO:0006956, GO:0007596, GO:0006955, GO:0030168, cytokine signaling, GO:0002685, response to virus.\\n\\nmechanism: these genes are involved in regulating different aspects of immune response, including complement activation, platelet activation, cytokine signaling, and leukocyte migration. they are also involved in blood coagulation, which can be activated during an immune response to prevent pathogen spread. the over-representation of these genes suggests that immune activation and regulation are key to the identified biological process]]
HALLMARK_DNA_REPAIR-0[[GO:0006281, transcription initiation, GO:0006396, GO:0009117]][[GO:0006281, transcription initiation, GO:0009117]]
HALLMARK_DNA_REPAIR-1[[GO:0006270, GO:0006261, GO:0006297, transcription, dna-template-dependent, GO:0045893, GO:0000122, GO:0006281, GO:0000723, GO:0065004]][[GO:0006281, transcription regulation]]
HALLMARK_E2F_TARGETS-0[[GO:0006260, GO:0006281, GO:0051726]][[GO:0006260, GO:0006281, GO:0051276]]
HALLMARK_E2F_TARGETS-1[[GO:0006260, GO:0006281, dna polymerase, GO:0009117, GO:0006298, chromatin structure\\n\\nmechanism: the genes on this list primarily function in dna replication and repair. many of them are involved in dna polymerase activity, nucleotide metabolism, mismatch repair, and chromatin structure. it is likely that these genes work together in a coordinated manner to ensure accurate dna replication and repair, and that defects in these processes can lead to genetic instability and cancer development]][[GO:0006260, GO:0006281, cell-cycle checkpoint regulation]]
HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0[[GO:0030198, GO:0030199, GO:0048251, GO:0071711, regulation of protein localization to extracellular matrix, GO:0043236, GO:0001968, GO:0005518]][[GO:0030198, GO:0007155, GO:0005518, actin binding activity, GO:0007229, GO:0001501, GO:0005201, GO:0006936, GO:0005604, GO:0031012, GO:0008009, GO:0008083, GO:0016860, GO:0006508, GO:0005125]]
HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1[[GO:0030198, GO:0005518, GO:0051015, GO:0005125, GO:0007155, GO:0016477]][[GO:0030198, GO:0006936, GO:0007155]]
HALLMARK_ESTROGEN_RESPONSE_EARLY-0[[membrane-bound proteins, MESH:D004798, GO:0000981]][[MESH:D002352, MESH:D004798, MESH:D008565, GO:0000981, receptors, MESH:D003598]]
HALLMARK_ESTROGEN_RESPONSE_EARLY-1[[GO:0055085, cell signaling, GO:0004672, GO:1904659, GO:0006811]][[GO:0006631, GO:0006811, GO:0010468]]
HALLMARK_ESTROGEN_RESPONSE_LATE-0[[membrane-associated protein complex, GO:0019899, GO:0034220, transcriptional regulation]][[GO:0005515, GO:0007165, GO:0019899, GO:0005737, GO:0043687, GO:0006355, GO:0006915, GO:0045860, positive regulation of cell proliferation.\\n\\nmechanism/]]
HALLMARK_ESTROGEN_RESPONSE_LATE-1[[GO:0005515, GO:0003824, GO:0008134, GO:0006355, GO:0007165, cytokine signaling pathway, regulation of cell growth and differentiation]][[GO:0007165, GO:0004672, g-protein coupled receptor signaling pathway, GO:0055085, GO:0035556, GO:0004721, GO:0006468, zinc ion binding. \\n\\nhypotheses: the enriched terms suggest that the genes in this list are involved in regulatory mechanisms that help to control intracellular signaling cascades and protein expression through phosphorylation and dephosphorylation of proteins, and zinc ion binding. additionally, these genes may play a role in transmembrane transport and regulation of ion channels]]
HALLMARK_FATTY_ACID_METABOLISM-0[[GO:0006629, mitochondrial function, GO:0003824, GO:0006631, oxidation-reduction process, metabolism of carboxylic acid, GO:0006118, GO:0006082]][[GO:0006631, GO:0005975, amino acid metabolism, mitochondrial function, oxidative stress response]]
HALLMARK_FATTY_ACID_METABOLISM-1[[GO:0006629, oxidation-reduction process, energy production, metabolism of fatty acids, mitochondrial function, GO:0045333]][[GO:0006631, energy production, mitochondrial function, GO:0006629, oxidation-reduction process, GO:0006637, GO:0006099, MESH:D014451, GO:0019752, GO:0015936, GO:0006084, GO:0022900]]
HALLMARK_G2M_CHECKPOINT-0[[GO:0051301, GO:0006260, GO:0007059, GO:0000910]][[GO:0051726, GO:0006260, GO:0006281]]
HALLMARK_G2M_CHECKPOINT-1[[GO:0006270, GO:0007059, GO:0000075, GO:0007052, GO:0007346, GO:0065004]][[GO:0006260, GO:0051726, GO:0006281, GO:0007059, GO:0000910]]
HALLMARK_GLYCOLYSIS-0[[GO:0070085, GO:0005975, fructose-bisphosphate metabolism, GO:0006098, GO:0006006, GO:0006012, GO:0006090, GO:0006089, GO:0019319, GO:0006011, GO:0052573, GO:0004332]][[GO:0006096, GO:0005975]]
HALLMARK_GLYCOLYSIS-1[[GO:0006096, GO:0005975, GO:0007165, GO:1904659, GO:0033554]][[GO:0052574, GO:0006006, protein kinase binding activity, GO:0006090, GO:0006024, GO:0015012, GO:0006098, GO:0006096, rna polymerase iii transcription initiation, GO:0051287, GO:0022618, GO:0030199, GO:0008408, GO:0042803, atp-binding cassette transporter activity]]
HALLMARK_HEDGEHOG_SIGNALING-0[[GO:0007411, GO:0007155, transcriptional regulation, cell communication. \\n\\nhypotheses: \\nthese genes may be involved in regulating the formation of neural circuits and maintaining neural plasticity through dynamic regulation of gene expression and protein signaling. the enriched terms suggest that the neural development process involves complex regulation of cell-cell communication and adhesion, as well as transcriptional control of gene expression. axon guidance is critical for the proper formation of neural circuits, and dysregulation of this process may lead to neural disorders]][[neuronal development, GO:0007155, GO:0007165, GO:0016477, GO:0010977, GO:0001525, MESH:D018121, transcriptional regulation]]
HALLMARK_HEDGEHOG_SIGNALING-1[[GO:0007411, GO:0007155, transcription regulation, neuro-endocrine signaling, protein cleavage, cell migration.\\n\\nmechanism: these genes are involved in various aspects of neuronal development and signaling, including axon guidance, neuron migration, cell adhesion and communication, transcription regulation, and protein cleavage. these processes are critical for proper central nervous system development and function]][[GO:0007155, GO:0007411, neuronal proliferation and differentiation, GO:0007165, GO:0001525]]
HALLMARK_HEME_METABOLISM-0[[GO:0006811, GO:0010468, protein turnover, GO:0061024]][[GO:0006810, GO:0005488, MESH:D008565, MONDO:0018815, solute carrier (slc) family of transporters]]
HALLMARK_HEME_METABOLISM-1[[GO:0005515, GO:0003824, GO:0008152, GO:0006082, GO:0006810, GO:0006811, GO:0006820, GO:0044281, GO:0019538, GO:0006357, GO:0003924, GO:0016740, GO:0000166, GO:0003677, GO:0000988, GO:0006163, GO:0008643, GO:0050801, GO:0003723, GO:0019899]][[GO:1904659, GO:0003723, GO:0003677, GO:0000988, GO:0006811, GO:0019899, GO:0042826, GO:0140657, GO:0003824, GO:0008270]]
HALLMARK_HYPOXIA-0[[GO:0006096, GO:0006006, GO:0006000, GO:0005975, MESH:D004734, GO:0045333, GO:0019318, GO:0019682, triose-phosphate metabolic process, GO:0006090, GO:0006754]][[GO:0006096, GO:0006006, GO:0005515, transcription regulation]]
HALLMARK_HYPOXIA-1[[GO:0006006, insulin signaling pathway, GO:0051726, transcriptional regulation]][[GO:0006096, GO:0016310, GO:0006006, GO:0051726, GO:0007165, transcriptional regulation, heparan sulfate biosynthesis]]
HALLMARK_IL2_STAT5_SIGNALING-0[[cytokine, receptor, t-cell, GO:0006955, GO:0065007]][[cytokine signaling, GO:0042110, GO:0042113, GO:0007159, GO:0030593, GO:0050900]]
HALLMARK_IL2_STAT5_SIGNALING-1[[GO:0004896, GO:0002224, GO:0002685, GO:0002521, GO:0002682, GO:0046649, GO:0019221, GO:0007159, GO:0051249, positive regulation of leukocyte proliferation\\n\\nmechanism: these genes are involved in the immune system response and regulation, specifically in the activation, differentiation, and migration of leukocytes. they are also involved in cytokine-mediated signaling pathways and toll-like receptor signaling pathways. the enriched terms suggest that these genes are involved in the regulation of various aspects of immune system processes, including leukocyte proliferation and adhesion]][[GO:0004896, GO:0007166, GO:0045321, GO:0050900, GO:0006955, GO:0006954, GO:0002250, GO:0070663, GO:0002521, GO:0042110, GO:0042113, GO:0046649]]
HALLMARK_IL6_JAK_STAT3_SIGNALING-0[[cytokine receptor activity; signal transduction; jak-stat cascade; cytokine-mediated signaling pathway\\n\\nmechanism: the enriched terms suggest that the commonality in gene function is the involvement of cytokine receptors and signaling pathways, particularly the jak-stat cascade, in cytokine-mediated signaling. this pathway is activated by cytokine binding to their respective receptors, leading to activation of the jak family of tyrosine kinases, which then phosphorylate and activate stat transcription factors to induce gene expression changes and cellular responses. the presence of these genes in the list suggests a potential role in regulating immune responses and inflammation through cytokine signaling]][[GO:0004896, GO:0050778, GO:0007155, GO:0019221, GO:0002687]]
HALLMARK_IL6_JAK_STAT3_SIGNALING-1[[GO:0005126, GO:0002376, GO:0001817, GO:0050776, cytokine-mediated signaling pathway\\n\\nmechanism]][[GO:0004896, GO:0019221, GO:0050776, GO:0050900, apoptosis regulation, GO:0006954, antimicrobial response]]
HALLMARK_INFLAMMATORY_RESPONSE-0[[cytokine signaling, GO:0004950, GO:0004930, GO:0050900, GO:0004908, GO:0002224, GO:0005164]][[GO:0005125, GO:0008009, GO:0004930, GO:0050900, inflammation\\n\\nmechanism]]
HALLMARK_INFLAMMATORY_RESPONSE-1[[GO:0004896, GO:0004930, GO:0042379, GO:0006955, GO:0006954, GO:0019221, GO:0050900, GO:0002694, GO:0002682, GO:0001819, GO:0009617, GO:0032496, GO:0070555, GO:0034612, GO:0042110]][[GO:0004896, GO:0004930, GO:0004950, GO:0004888, GO:0004896]]
HALLMARK_INTERFERON_ALPHA_RESPONSE-0[[interferon-induced protein, GO:0051607, GO:0006955, nucleotide-binding domain, leucine-rich repeat-containing receptor signaling, GO:0005764, GO:0019882, cytokine]][[interferon response, GO:0051607, GO:0006955]]
HALLMARK_INTERFERON_ALPHA_RESPONSE-1[[GO:0140888, cytokine signaling pathway, GO:0045087, GO:0009615, GO:0006952]][[GO:0140888, GO:0045087, GO:0051607, cytokine signaling, GO:0019882, ubiquitin-mediated proteolysis\\n\\nmechanism: these genes are involved in the innate immune response and antiviral activity, particularly in the interferon signaling pathway. they encode proteins that regulate cytokine signaling, antigen processing and presentation, and ubiquitin-mediated proteolysis. the functions of these genes suggest a coordinated response to viral infection, with the interferon signaling pathway acting as a central mediator of the antiviral response]]
HALLMARK_INTERFERON_GAMMA_RESPONSE-0[[interferon signaling, immune response regulation, cytokine signaling, tnf-receptor superfamily, protein tyrosine phosphatase, ubiquitin-proteasome system, MONDO:0007435]][[GO:0006955, GO:0019221, chemokine signaling pathway, GO:0019882]]
HALLMARK_INTERFERON_GAMMA_RESPONSE-1[[GO:0006955, cytokine signaling, GO:0030163, GO:0000502, ubiquitin system, viral rna sensing, MESH:D018925, GO:0019882]][[GO:0045087, GO:0051607, GO:0005125, GO:0009615, GO:0001817, GO:0051607, GO:0032481, type i interferon signaling pathway. \\n\\nmechanism/]]
HALLMARK_KRAS_SIGNALING_DN-0[[GO:0005509, GO:0055085, GO:0007155, GO:0004672, GO:0007186]][[GO:0005509, GO:0005245, GO:0006811, GO:0015085, GO:0005388, GO:0019722, GO:0055074, GO:0048306]]
HALLMARK_KRAS_SIGNALING_DN-1[[cytokine signaling, g-protein coupled receptor signaling, GO:0019722, protein metabolism and processing]][[GO:0005509, GO:0042981, GO:0055085, GO:0006811, GO:0006468]]
HALLMARK_KRAS_SIGNALING_UP-0[[receptor signaling pathway, GO:0006468, negative regulation of transcription, GO:0031396, GO:0071345, GO:0032880, GO:0070374]][[GO:0044425, GO:0007165, GO:0003824]]
HALLMARK_KRAS_SIGNALING_UP-1[[signal transduction; cytokine activity; coagulation; ion transport; extracellular matrix organization. \\n\\nmechanism: the enriched terms suggest that the commonality in the function of these genes is related to signal transduction and regulation of various biological processes, such as coagulation, GO:0005125, GO:0030198, and ion transport. specifically, these genes are involved in regulating signaling pathways that are critical for these biological processes. there are several pathways known to contribute to these enriched terms, including the jak/stat, MESH:D016328, mapk/erk, and pi3k pathways. these pathways play important roles in cell signaling, GO:0006954, GO:0006955, other cellular processes]][[cytokine signaling, growth factor signaling, coagulation and complement activation, enzymatic activity regulation]]
HALLMARK_MITOTIC_SPINDLE-0[[GO:0008017, GO:0007010, regulation of protein activity, GO:0051301, GO:0019894, GO:0003779]][[microtubule organization, GO:0007098, GO:0030036, GO:0051726, GO:0071539]]
HALLMARK_MITOTIC_SPINDLE-1[[microtubule organization, GO:0140014, GO:0051301]][[GO:0008017, GO:0008574, GO:0007098, GO:0051225, GO:0003774, GO:0007010]]
HALLMARK_MTORC1_SIGNALING-0[[GO:0046034, GO:0006629, GO:0006006, GO:0006457, GO:0046907]][[GO:0006457, GO:0006006, microtubule organization and biogenesis, GO:0000502, GO:0043043, GO:0042254]]
HALLMARK_MTORC1_SIGNALING-1[[GO:0051087, GO:0005515, GO:0006457, GO:0043161]][[GO:0008152, GO:0009117, GO:0006629, GO:0005975, GO:0006457, GO:0030163, GO:0010468, GO:0000988, GO:0003682]]
HALLMARK_MYC_TARGETS_V1-0[[GO:0006413, GO:0042254, GO:0006260, GO:0006281, GO:0008380, GO:0009117]][[GO:0042254, GO:0000394, GO:0006412, GO:0006412, GO:0006457, chaperonin-mediated protein folding]]
HALLMARK_MYC_TARGETS_V1-1[[GO:0006413, GO:0006412, GO:0042254]][[GO:0042254, GO:0006413, GO:0006414, GO:0006397]]
HALLMARK_MYC_TARGETS_V2-0[[GO:0006396, GO:0042254, rrna maturation]][[GO:0006364, ribosomal subunit biogenesis, GO:0003723, nucleolar function, GO:0006412]]
HALLMARK_MYC_TARGETS_V2-1[[GO:0006364, nucleolar rna processing, GO:0042273, GO:0003723]][[GO:0006364, GO:0005730, GO:0003723, ribosomal biogenesis, GO:0051726]]
HALLMARK_MYOGENESIS-0[[GO:0003779, GO:0006936, sarcomere assembly, GO:0005509, GO:0005861, GO:0005523, MESH:D024510, GO:0005524, GO:0004672, GO:0005515, GO:0032982]][[GO:0006936, muscle metabolism, GO:0007010]]
HALLMARK_MYOGENESIS-1[[GO:0006936, GO:0005861, GO:0005509, GO:0003779, sarcomere organization and biogenesis]][[GO:0005861, MESH:M0013780, MESH:D018995, GO:0006936, GO:0005509, sarcomere assembly, MESH:D024510]]
HALLMARK_NOTCH_SIGNALING-0[[GO:0007219, GO:0016567, GO:0001709, GO:0016055]][[GO:0007219, basic helix-loop-helix transcription factor activity, GO:0016567, GO:0016563, GO:0005102, GO:0097153, GO:0006468]]
HALLMARK_NOTCH_SIGNALING-1[[GO:0007219, GO:0016567]][[GO:0007219, GO:0016567, transcriptional regulation, GO:0001709]]
HALLMARK_OXIDATIVE_PHOSPHORYLATION-0[[GO:0006754, GO:0022900, GO:0005746, GO:0006119]][[GO:0005739, GO:0006119, GO:0022900, MESH:D004734, GO:0031966, MESH:D024101]]
HALLMARK_OXIDATIVE_PHOSPHORYLATION-1[[GO:0005746, GO:0006119, mitochondrial metabolism, complex i-v, energy production]][[GO:0005746, GO:0006754, GO:0022900, GO:0006119]]
HALLMARK_P53_PATHWAY-0[[GO:0006281, GO:0010468, GO:0008083]][[cyclin family, GO:0006281, GO:0008083, GO:0004672, GO:0000988, zinc finger protein]]
HALLMARK_P53_PATHWAY-1[[GO:0006281, GO:0051726, GO:0007165, GO:0006915, MESH:D016207]][[GO:0008083, transcriptional regulation, GO:0006915, GO:0006281]]
HALLMARK_PANCREAS_BETA_CELLS-0[[GO:0006006, insulin signaling, pancreatic development, neuroendocrine regulation]][[GO:0006006, insulin regulation, GO:0031016, GO:0006096, GO:0006094, GO:0030073, hormone regulation]]
HALLMARK_PANCREAS_BETA_CELLS-1[[GO:0006006, pancreatic islet development, neuroendocrine differentiation, GO:0007269, MESH:D009473]][[GO:0006006, GO:0030073, pancreatic islet development, neuroendocrine differentiation]]
HALLMARK_PEROXISOME-0[[atp binding cassette transporter activity, GO:0006631, GO:0042445, GO:0008289, GO:0043574, GO:0005502]][[GO:0140359, GO:0055085, atp-binding cassette, GO:0043574, GO:0006631, GO:0006839]]
HALLMARK_PEROXISOME-1[[GO:0005777, GO:0006635, antioxidant response, mitochondrial carrier protein]][[GO:0005777, GO:0006631, beta-oxidation, MESH:D018384, antioxidant defense mechanism, coenzyme a ligase, aldehyde dehydrogenase family, MESH:D009195]]
HALLMARK_PI3K_AKT_MTOR_SIGNALING-0[[GO:0004672, GO:0035556, GO:1902531, GO:0050794, GO:0003824, cytoskeletal regulation]][[GO:0004672, intracellular signaling, GO:0050794]]
HALLMARK_PI3K_AKT_MTOR_SIGNALING-1[[GO:0004672, GO:0007165, GO:0006468, GO:0035556]][[GO:0016301, GO:0006468, GO:0007165]]
HALLMARK_PROTEIN_SECRETION-0[[GO:0005794, GO:0005480, GO:0005764]][[GO:0005794, membrane trafficking, GO:0016192, GO:0015031, GO:0006906, GO:0035493, GO:0005793]]
HALLMARK_PROTEIN_SECRETION-1[[golgi transport, GO:0016192, GO:0015031, GO:0008104, GO:0032880, GO:0006886, GO:0016197]][[GO:0007030, GO:0006888, GO:0016192, GO:0007040, sorting nexin-containing complex, GO:0030665, GO:0032880]]
HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0[[GO:0016209, GO:0006749, GO:0016491]][[antioxidant activity; redox regulation; catalytic activity, UBERON:0035930, such as water and oxygen. the over-representation of terms related to antioxidant activity, redox regulation, and responding to oxidative stress suggest that these genes are involved in maintaining the balance between oxidants and antioxidants in the body, help protect against oxidative damage]]
HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1[[GO:0016209, redox regulation, MESH:D018384]][[oxidative stress response, antioxidant defense, regulation of reactive oxygen species, GO:0006749, superoxide anion radical metabolism, peroxiredoxin-mediated detoxification]]
HALLMARK_SPERMATOGENESIS-0[[GO:0051726, GO:0003677, GO:0003723, GO:0016301, transcription regulation, chromatin organization and modification]][[GO:0008584, GO:0007283, GO:0097722, GO:0007340, GO:0048232, testicular germ cell proliferation\\n\\nmechanism and]]
HALLMARK_SPERMATOGENESIS-1[[GO:0005515, enzymatic activity, GO:0006811]][[GO:0006811, GO:0006468, MESH:D054875, GO:0007283, receptor signaling]]
HALLMARK_TGF_BETA_SIGNALING-0[[growth factor signaling, transcriptional regulation, smad/tgf-beta signaling pathway, cellular differentiation]][[tgf-beta signaling pathway, transcriptional regulation, GO:0007165, cell growth and differentiation]]
HALLMARK_TGF_BETA_SIGNALING-1[[GO:0005024, GO:0060395, GO:0030509]][[tgf-beta signaling pathway, GO:0030509, GO:0071141, GO:0004674, GO:0008134, GO:0006468, GO:0030154, GO:0060348, GO:0042981, GO:0034436]]
HALLMARK_TNFA_SIGNALING_VIA_NFKB-0[[GO:0006955, cytokine signaling pathway, transcription regulation. \\n\\nmechanism: these genes are primarily involved in regulating the immune response through the cytokine signaling pathway. they also play a role in transcriptional regulation of genes involved in these pathways. overall, these genes are important in regulating the response to pathogens and maintaining immune homeostasis]][[GO:0004950, GO:0005125, GO:0006955, GO:0006954, GO:0050900, GO:0007165]]
HALLMARK_TNFA_SIGNALING_VIA_NFKB-1[[cytokine signaling pathway, GO:0002682, GO:0006351, GO:0006355, GO:0050900, GO:0006954, GO:0050727, GO:0032496, GO:0002237, GO:0009615, GO:0045893, GO:0045892]][[interleukin signaling, GO:0032602, GO:0006955]]
HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0[[GO:0044183, GO:0006457, GO:0006396, cellular stress response, GO:0006401]][[endoplasmic reticulum stress response, GO:0006457, GO:0008380, GO:0006402, mrna localization, translation regulation, stress response]]
HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1[[GO:0006457, GO:0006396, GO:0006413, endoplasmic reticulum stress response, GO:0042254]][[GO:0006457, GO:0061077, GO:0015031, GO:0006413, GO:0003723, MESH:D020365, GO:0042254, aminoacyl-trna synthesis, GO:0005783, MESH:D005786]]
HALLMARK_UV_RESPONSE_DN-0[[GO:0006816, cytoskeletal organization, cell signaling, protein regulation]][[GO:0030198, GO:0007155, GO:0006811, GO:0004672, transcription regulation, receptor signaling pathway]]
HALLMARK_UV_RESPONSE_DN-1[[GO:0030198, GO:0007165, GO:0006811]][[GO:0030198, GO:0030155, GO:0006468, positive regulation of cellular signaling pathway activity, GO:0022604, GO:0072659]]
HALLMARK_UV_RESPONSE_UP-0[[GO:0006810, GO:0003824, regulation of transcription, GO:0016310, GO:0005515, GO:0006950, GO:0006915, GO:0006811, GO:0005524, GO:0007165, GO:0005975]][[GO:0006810, GO:0008152, GO:0003824]]
HALLMARK_UV_RESPONSE_UP-1[[GO:0008152, GO:0005515, GO:0007165, GO:0009165, GO:0006468, transcription factor activity\\n\\nmechanism: these enriched terms suggest that the commonality between these genes is their involvement in fundamental biological processes required for normal cell function. these include metabolism, signal transduction, and protein biosynthesis and regulation. the transcription factor activity term suggests that some of these genes may be transcriptional regulators, controlling the expression of other genes involved in these processes. overall, these genes likely work together to maintain cellular homeostasis and respond to internal and external cues]][[GO:0003723, GO:0003677, GO:0000166, GO:0006396, GO:0006260]]
HALLMARK_WNT_BETA_CATENIN_SIGNALING-0[[wnt signaling pathway regulation, transcriptional regulation, GO:0051726]][[GO:0016055, transcriptional regulation, cell cycle progression]]
HALLMARK_WNT_BETA_CATENIN_SIGNALING-1[[GO:0016055, GO:0008013, transcription regulation]][[GO:0016055, GO:0051726, transcriptional regulation]]
T cell proliferation-0[[GO:0006955, GO:0007165, GO:0001816, cell proliferation and differentiation, GO:0042981]][[cytokine, MESH:D007378, MESH:D011948, GO:0005530, GO:0008180, GO:0000502, protein tyrosine phosphatase, MESH:D010770, GO:0000981]]
T cell proliferation-1[[cytokine, GO:0006955, GO:0023052, receptor, t cell]][[cytokine signaling, tnf-receptor superfamily, GO:0006955, GO:0007165, GO:0019882, cell proliferation and survival, protein phosphorylation and kinase activity]]
Yamanaka-TFs-0[[MESH:D047108, stem cell pluripotency, MESH:D063646, cell cycle progression]][[MESH:D047108, GO:0001709, cell cycle progression]]
Yamanaka-TFs-1[[MESH:D047108, stem cell maintenance, GO:0010468]][[MESH:D047108, GO:0048863, pluripotent stem cell, transcription factor regulation, homeobox protein]]
amigo-example-0[[GO:0030198, GO:0007155, GO:0007229, GO:0051495, GO:0002576]][[GO:0031012, GO:0007155, MESH:D011509, GO:0005202, integrin]]
amigo-example-1[[GO:0030198, GO:0007155, GO:0006029, GO:0042339, GO:0007229, GO:0030168]][[GO:0030198, GO:0007155, GO:0016477, GO:0009888, GO:0042246, signaling pathway regulation, GO:0030168]]
bicluster_RNAseqDB_0-0[[GO:0055085, GO:0006811, GO:0005524, zinc finger domain binding, GO:0007186, GO:0000988]][[GO:0006351, GO:0005515, MESH:D016335, GO:0005509, MESH:D008565]]
bicluster_RNAseqDB_0-1[[GO:0019722, GO:0000988, GO:0055085]][[calcium binding, receptor protein activity, GO:0000988, GO:0005515]]
bicluster_RNAseqDB_1002-0[[GO:0006936, GO:0007015, GO:0032972, GO:0005509, GO:0005861, GO:0005865, GO:0003779, GO:0045214, GO:0005523, GO:0017022, GO:0045932, skeletal muscle thin filament, cardiac muscle thin filament]][[GO:0006936, GO:0005509, GO:0043269, GO:0032516, GO:0051015]]
bicluster_RNAseqDB_1002-1[[GO:0006936, GO:0051015, GO:0005523, calcium binding, myofibril assembly.\\n\\nmechanism: these genes are involved in the regulation and maintenance of muscle structure and the contraction cycle. they act through the interaction of actin and myosin filaments, with the regulation of calcium ions controlling muscle contraction. the proteins encoded by these genes are involved in ion channel regulation, protein binding and modification, and energy metabolism]][[GO:0006936, GO:0005509, GO:0051015, GO:0043462, GO:0097009, GO:0006811]]
endocytosis-0[[GO:0006897, intracellular trafficking, cytoskeleton reorganization]][[GO:0006897, GO:0007010, GO:0007165, GO:0006629, GO:0060348, brain development. \\n\\nhypotheses: these genes may be involved in common pathways related to endocytic vesicle trafficking, cytoskeletal organization, and signal transduction. some of the genes are associated with lipid metabolism and bone and brain development, suggesting their potential roles in cellular processes related to these functions]]
endocytosis-1[[GO:0006897, GO:0016192, intracellular signaling, GO:0015031, cytoskeletal organization]][[GO:0006897, intracellular trafficking, cytoskeletal reorganization]]
glycolysis-gocam-0[[glucose metabolism; glycolysis\\n\\nmechanism: these genes play a role in converting glucose to produce energy in the form of atp. hexokinase (hk1) and glucose phosphate isomerase (gpi) are involved in the initial steps of glucose metabolism, while phosphofructokinase (pfkm), MESH:D005634, and pyruvate kinase (pkm) are involved in glycolysis. triosephosphate isomerase (tpi1) and glyceraldehyde-3-phosphate dehydrogenase (gapdh) are also involved in glycolysis and produce atp by oxidizing glucose. phosphoglycerate mutase (pgam2) and enolase (eno3) are also involved in glycolysis and help convert glucose to pyruvate, which can then be converted to atp]][[GO:0006096, GO:0006006, MESH:D004734]]
glycolysis-gocam-1[[GO:0006096, GO:0005975, energy pathway]][[GO:0006096, GO:0006006, GO:0004743, GO:0019682, GO:0006000, phosphoenolpyruvate metabolic process]]
go-postsynapse-calcium-transmembrane-0[[GO:0006816, GO:0004970, n-methyl-d-aspartate receptor complex, GO:0043269, GO:0014069, GO:0007165]][[GO:0006816, intracellular calcium homeostasis, ionotropic glutamate receptor regulation, nmda receptor subunits, sodium/calcium exchanger proteins, trp ion channel family]]
go-postsynapse-calcium-transmembrane-1[[GO:0006816, GO:0005509, GO:0005216, GO:0005102, GO:0007268, GO:0030594]][[GO:0005509, GO:0005262, GO:0004970, calcium-mediated signaling pathway, GO:0007268, GO:0031175, GO:0005216]]
go-reg-autophagy-pkra-0[[summary: regulation of cellular processes, including cell growth and metabolism, GO:0006915, GO:0006955, and regulation of chromatin remodeling and transcription.\\n\\nmechanism: these genes function in various pathways involved in the regulation of cellular processes. akt1 and pik3ca are involved in the pi3k/akt/mtor signaling pathway, which regulates cell growth, MESH:D013534, and metabolism. casp3 is a protease involved in the execution-phase of cell apoptosis. ccny and cdk5r1 are involved in the regulation of cell division cycles and the development of the central nervous system. hspb1 plays an important role in cell differentiation, but its overexpression may promote cancer cell proliferation and metastasis while protecting cancer cells from apoptosis. irgm regulates autophagy formation in response to intracellular pathogens. kat5 is a histone acetylase that has a role in dna repair and apoptosis and is thought to play an important role in signal transduction. mlst8, rptor, and smcr8 are involved in the torc1 signaling pathway, which regulates protein synthesis and cell growth in response to nutrient and insulin levels. nod2 is a pattern recognition receptor that detects cytosolic nucleic acids and trans]][[MESH:D002470, GO:0016301, GO:0009966, GO:0001558, GO:0042981, GO:0010506, GO:0032006]]
go-reg-autophagy-pkra-1[[GO:0038202, GO:0032006, GO:0010605, activation of map3k7/tak1]][[GO:0016049, GO:0004672, GO:0006955, GO:0007165, GO:0000988, neuronal development, GO:0006468]]
hydrolase activity, hydrolyzing O-glycosyl compounds-0[[GO:0005764, glycoside hydrolase activity, GO:0005975, GO:0016787, GO:0006027, GO:0005980, GO:0006689, GO:0015929, acid hydrolase activity, chitin catabolic process\\n\\nmechanism: these genes participate in the lysosomal degradation of various carbohydrate molecules, breaking them down into their component parts for further processing by the cell]][[glycosyl hydrolase activity, degradation of carbohydrates, GO:0006032, GO:0030211, GO:0003796, GO:0030214]]
hydrolase activity, hydrolyzing O-glycosyl compounds-1[[GO:0004559, GO:0004415, lysosomal enzyme activity, GO:0016798, GO:0006487]][[GO:0016787, GO:0044248, GO:0006027, GO:0005764]]
ig-receptor-binding-2022-0[[immunoglobulin receptor binding activity, GO:0002253, GO:0098542, GO:0002922, b cell-mediated immunity]][[GO:0019731, GO:0098542, GO:0002253, immunoglobulin receptor binding activity]]
ig-receptor-binding-2022-1[[GO:0002250, GO:0002376, antigen binding activity, immunoglobulin receptor binding activity. \\n\\nmechanism: the enriched terms suggest that these genes are involved in the recognition and response to specific foreign antigens encountered by the immune system. antigen binding activity enables the binding of specific antigens, while immunoglobulin receptor binding activity allows for the activation and signaling of immune cells. together, these genes contribute to the adaptive immune response and immune system processes by recognizing and responding to diverse foreign antigens]][[antigen binding activity, immunoglobulin receptor binding activity, GO:0002253]]
meiosis I-0[[meiotic recombination; homologous recombination; chromosome segregation during meiosis; double-strand break repair via homologous recombination.\\n\\nmechanism: these genes are all involved in the meiotic cell cycle process, specifically in events related to recombination, repair, and segregation of chromosomes during meiosis. the proteins encoded by these genes interact with each other to form protein complexes that are essential for proper meiotic division. the enriched terms indicate a strong association with meiotic recombination and double-strand break repair via homologous recombination. additionally, they suggest a role in chromosome segregation during meiosis]][[GO:0140013, GO:0035825, GO:0007059, GO:0006281, GO:0000795]]
meiosis I-1[[meiotic recombination, GO:0006281, GO:0035825, GO:0007059, GO:0006302, holliday junction, rad51, GO:0007127]][[meiotic recombination, GO:0006281, GO:0007059, GO:0035825, holliday junction resolution, double-strand dna binding, GO:0007276, GO:0007130]]
molecular sequestering-0[[GO:0005515, GO:0006955, intracellular transport\\n\\nmechanism/]][[GO:0006955, GO:0051726, GO:0046907]]
molecular sequestering-1[[GO:0006810, regulation of cell growth and survival, GO:0010468, GO:0006915]][[GO:0051726, GO:0006955, GO:0005515]]
mtorc1-0[[GO:0046034, GO:0006629, GO:0006006, GO:0006457, GO:0046907]][[GO:0006457, GO:0006006, microtubule organization and biogenesis, GO:0000502, GO:0043043, GO:0042254]]
mtorc1-1[[GO:0000502, GO:0030163]][[GO:0000502, GO:1904659, GO:0008152, GO:0003676, GO:0044183, GO:0005524, GO:0005783, GO:0005739, GO:0006096, GO:0006631]]
peroxisome-0[[peroxisome biogenesis, GO:0016558, peroxin]][[peroxisome biogenesis, peroxisomal protein import, peroxin proteins, MONDO:0019234, neonatal adrenoleukodystrophy, MONDO:0019609, MONDO:0009959, MONDO:0008972, MONDO:0009958]]
peroxisome-1[[peroxisome biogenesis, matrix protein import, MONDO:0009279, peroxin (pex) family]][[peroxisome biogenesis, GO:0005777, GO:0017038]]
progeria-0[[GO:0006998, chromatin organization and maintenance, dna repair and recombination]][[GO:0005652, GO:0005635, GO:0006281]]
progeria-1[[GO:0006325, GO:0006281, nuclear stability]][[GO:0006997, GO:0006281, chromatin structure organization, GO:0000723]]
regulation of presynaptic membrane potential-0[[GO:0007268, GO:0005216, neurological function]][[GO:0005216, GO:0031175, GO:0007268, GO:0042391]]
regulation of presynaptic membrane potential-1[[GO:0005216, GO:0048666, GO:0007268]][[GO:0005267, chloride ion transmembrane transport, GO:0042391, GO:0034220, GO:0030594]]
sensory ataxia-0[[MONDO:0015626, MONDO:0005244, MONDO:0007790, GO:0043209, GO:0006264, tetratricopeptide repeat, transporter protein\\n\\nmechanism: these genes are involved in myelin upkeep and various neurological diseases associated with defects in myelin sheath synthesis and functions. they play roles in mitochondrial dna replication and transport, as well as protein transportation across the nuclear membrane. the presence of tetratricopeptide repeat motifs in these genes suggests their roles in protein-protein interactions and chaperone functions]][[MONDO:0015626, MONDO:0007790, MONDO:0005244, myelin sheath maintenance, GO:0006264]]
sensory ataxia-1[[MONDO:0011890, MONDO:0007790, MONDO:0011527, GO:0043217, peripheral myelin sheath, n-acetyl-d-glucosamine residue degradation, MESH:D008565, GO:0007399, nervous system myelination, GO:0006260]][[GO:0042552, GO:0007422, GO:0016567, er-associated protein degradation.\\n\\nmechanism/]]
term-GO:0007212-0[[GO:0007186, GO:0007189, regulation of cyclic nucleotide metabolic process, regulation of camp metabolic process]][[g-protein signaling, GO:0007165, neurotransmitter activity]]
term-GO:0007212-1[[GO:0007186, GO:0019932, GO:0007212]][[g-protein signaling pathway, GO:0030594, GO:1902531]]
tf-downreg-colorectal-0[[transcriptional regulation, GO:0006338, GO:0000988, GO:0003700, rna polymerase ii regulatory region sequence-specific dna binding, zinc finger domain, GO:0042393, nucleosome binding.\\n\\nmechanism: the enriched functions suggest that the given set of genes are involved in transcriptional regulation and chromatin remodeling. transcription factors bind to specific dna sequences and regulate gene expression, while chromatin remodeling alters the structure of chromatin to allow or prevent access to the dna by transcriptional machinery. zinc finger domain-containing proteins are involved in dna binding, and histone binding proteins facilitate the formation of transcriptionally active or inactive chromatin structures. the enriched functions suggest the potential involvement of these genes in both gene activation and repression, which may have important implications in cellular differentiation, development, and disease]][[transcription regulation, GO:0006338, GO:0003700]]
tf-downreg-colorectal-1[[transcription regulation, chromatin structure alteration, cell cycle progression, GO:0003682]][[GO:0003700, GO:0006355, GO:0006325, GO:0010468, transcription factor complex\\n\\nmechanism: these genes all play a role in regulating transcription, primarily at the level of dna binding and chromatin organization. they are involved in the regulation of gene expression and the formation of transcription factor complexes]]
no_synopsisEDS-0[[GO:0030198, GO:0030199, GO:0006024]][[GO:0030198, GO:0043062, GO:0030199, GO:0006486, GO:0008233, GO:0008270]]
EDS-1[[GO:0030199, GO:0030198, GO:0032964]][[GO:0032963, GO:0030198, GO:0031012]]
FA-0[[fanconi anemia pathway, homologous recombination repair pathway, dna double-strand break repair]][[GO:0006281, GO:0006325, GO:0006312, GO:0006302, GO:0035825, GO:0006260]]
FA-1[[GO:0006281, GO:0006302, GO:0035825, mitotic cell-cycle checkpoint, GO:0006974]][[fanconi anemia pathway, GO:0035825, GO:0006302]]
HALLMARK_ADIPOGENESIS-0[[GO:0006631, GO:0006869, GO:0005746, GO:0006637, GO:0032000, GO:0016042, GO:0019216, GO:0033108, GO:0035336, GO:0033539, GO:0051791]][[GO:0006629, GO:0006631, mitochondrial function, GO:0006119, GO:0006099, beta-oxidation of fatty acids, GO:0006084, GO:0006637, GO:0015980, GO:0005975]]
HALLMARK_ADIPOGENESIS-1[[GO:0006119, GO:0006631, GO:0006457, GO:0030301, GO:0019915, stress response, GO:0045333, mitochondrial metabolism, energy generation, GO:0006986, GO:0046890, GO:0032368, GO:0033344, GO:0007517, GO:0006979, GO:0001666, regulation of fatty acid catabolic process, GO:0019216]][[GO:0005740, GO:0006122]]
HALLMARK_ALLOGRAFT_REJECTION-0[[GO:0042110, GO:0030098, GO:0019221, GO:0002682, GO:0050776]][[GO:0002376, GO:0042110, GO:0019221, GO:0019882, GO:0030098, GO:0050900, GO:0050778, GO:0050777, GO:0001817]]
HALLMARK_ALLOGRAFT_REJECTION-1[[GO:0005125, GO:0008009, GO:0034341, GO:0042110, GO:0050727]][[GO:0042110, cytokine signaling, GO:0019882, GO:0006955, chemokine signaling, interferon signaling, GO:0030183, GO:0050900]]
HALLMARK_ANDROGEN_RESPONSE-0[[GO:0006351, regulation of transcription, GO:0006629, GO:0030163]][[GO:0016567, GO:0036211, GO:0008134, GO:0045892, GO:0071535, GO:0031647, GO:0043161]]
HALLMARK_ANDROGEN_RESPONSE-1[[GO:0006508, GO:0004672, GO:0007010, GO:0006695, GO:0045944, GO:0043066]][[regulation of transcription, GO:0005515, GO:0007155, GO:0007165, GO:0016126]]
HALLMARK_ANGIOGENESIS-0[[GO:0030198, GO:0007267, GO:0043405, GO:0042127, GO:0030155, GO:0002576]][[GO:0030198, GO:0070848, GO:1903010, GO:0042060]]
HALLMARK_ANGIOGENESIS-1[[GO:0030198, GO:0001525, vascular development, GO:0030335, GO:0001938, GO:0017015, GO:0007155]][[GO:0030198, GO:0001525, GO:0007155]]
HALLMARK_APICAL_JUNCTION-0[[GO:0098609, GO:0034332, GO:0002159, GO:0030198]][[GO:0007155, GO:0007010, GO:0048041, regulation of actin cytoskeleton, GO:0051017, GO:0046847, GO:0035023]]
HALLMARK_APICAL_JUNCTION-1[[GO:0070160, GO:0007155, GO:0007154, GO:0022407, GO:0043542, GO:0030198, cell junction organization and biogenesis, GO:0032956, GO:0001525, GO:0010810]][[GO:0007155, GO:0016477, GO:0048870, GO:0007229, GO:0008360, focal adhesion\\n\\nmechanism: the enriched terms suggest that the common function of these genes is involved in cell adhesion and migration. these processes are essential for various biological functions such as wound healing, inflammation, and embryonic development. integrin-mediated signaling pathway and focal adhesion are two crucial pathways in cell adhesion and migration, which are perturbed in many types of cancer and autoimmune diseases. these findings may shed light on the underlying mechanism and potential targets for drug development]]
HALLMARK_APICAL_SURFACE-0[[GO:0051716, GO:0005515, GO:0035556, GO:0007155, GO:0055085, GO:0061024, GO:0015031]][[GO:0007155, GO:0023052, GO:0006810]]
HALLMARK_APICAL_SURFACE-1[[GO:0007155, GO:0016477, GO:0007165, GO:0038023, GO:0006468, GO:0008104, GO:0055085, GO:0003824]][[GO:0007155, GO:0007186, GO:0010906, GO:0050796, GO:0070528, GO:0043406, GO:0050731, GO:0051897, GO:0061024, GO:0043066]]
HALLMARK_APOPTOSIS-0[[GO:0006915, GO:0043123, GO:0050855, GO:0001817, GO:0002697, GO:0050670, GO:0051249, GO:0050856, GO:0034097, GO:0032496]][[GO:0006915, GO:0012501, regulation of cell death\\n\\nmechanism: these genes are involved in various processes that regulate cell death. they participate in the apoptotic process, the programmed cell death that occurs in multicellular organisms. apoptosis is a complex physiological process that is essential for development and homeostasis in healthy adult tissues. these genes also contribute to the regulation of cell death, preventing or promoting apoptosis under specific conditions]]
HALLMARK_APOPTOSIS-1[[cellular stress response, GO:0006915, GO:0006954, GO:0043067, negative regulation of nf-kappab transcription factor, GO:0043280]][[GO:0097153, GO:0006915, GO:0006954, GO:0008285, GO:0050871, GO:0001819, GO:0045944, GO:0004672, GO:0046328, GO:0010803]]
HALLMARK_BILE_ACID_METABOLISM-0[[GO:0006695, GO:0006699, peroxisome biogenesis]][[peroxisome organization; steroid metabolic process; cholesterol metabolic process; fatty acid metabolic process; lipid metabolic process\\n\\nmechanism: \\n\\nthese genes are involved in various metabolic pathways, especially those related to lipid and sterol metabolism. many of these genes are involved in the transport of lipids and cholesterol, including the abc transporters abca1, abca2, abca3, abca4, abca5, abca6, abca8, abca9, and abcg4. other genes such as cat, ch25h, crot, cyp7a1, GO:0033783, MESH:D013253, dhcr24, and hsd17b6 are involved in the synthesis, GO:0009056, and modification of cholesterol and sterols. \\n\\nadditionally, these genes are also involved in peroxisome biogenesis and function, with genes such as pex1, pex11a, pex11g, pex12, pex13, pex16, pex19, pex26, MESH:D010758]]
HALLMARK_BILE_ACID_METABOLISM-1[[GO:0006629, GO:0006869, GO:0005777, mitochondrial function]][[GO:0006695, GO:0006629, GO:0007031, peroxisome biogenesis, GO:0008202, GO:0006635, GO:0006699, GO:0015908, GO:0006886]]
HALLMARK_CHOLESTEROL_HOMEOSTASIS-0[[GO:0016126, GO:0006695, GO:0030301, GO:0006629, GO:0008202, GO:0042632]][[GO:0006695, GO:0006629, GO:0045540, GO:0019216, GO:0016126]]
HALLMARK_CHOLESTEROL_HOMEOSTASIS-1[[GO:0006695, GO:0006629, GO:0008203, GO:0016126, GO:0008299, GO:0042632, GO:0045540, GO:0019216]][[GO:0006695, GO:0006694, GO:0006629]]
HALLMARK_COAGULATION-0[[GO:0007596, GO:0006956, GO:0030168, GO:0042730, GO:0042060]][[GO:0030198, GO:0030574, GO:0007596, GO:0042730, GO:0002576, GO:0052547, GO:0045055, GO:0045862]]
HALLMARK_COAGULATION-1[[GO:0030198, GO:0007596, GO:0006508, GO:0006955]][[GO:0007596, GO:0006955]]
HALLMARK_COMPLEMENT-0[[c1q binding, GO:0006958, GO:0010951, GO:0043154, GO:2001237, GO:1903051]][[GO:0006956, GO:0002576, GO:0050776, GO:0009611, blood coagulation\\n\\nmechanism: genes involved in complement activation, platelet degranulation, regulation of immune response, response to wounding, and blood coagulation are enriched in this gene set. these functions are related to the prevention of thrombosis and regulation of the immune system]]
HALLMARK_COMPLEMENT-1[[GO:0006955, GO:0007596, GO:0030163, GO:0006508, GO:0010951, GO:0071345, GO:0010952, GO:0030194, GO:0030449]][[GO:0006955, GO:0007596, GO:0006508, GO:0030168, GO:0006954, GO:0010952]]
HALLMARK_DNA_REPAIR-0[[GO:0006260, GO:0006281, GO:0006397, GO:0006351, GO:0042278]][[GO:0006260, GO:0006281, dna binding and packaging, GO:0009117, GO:0006338]]
HALLMARK_DNA_REPAIR-1[[GO:0097747, GO:0003677, GO:0006397, GO:0006281]][[GO:0006260, GO:0006281, transcription elongation, GO:0006396, GO:0009117, GO:0003682]]
HALLMARK_E2F_TARGETS-0[[GO:0006260, GO:0007049, GO:0051301, GO:0140014, GO:0006281]][[GO:0006260, GO:0007049, GO:0007052, GO:0007059, GO:0007346, GO:0006281, GO:0006334]]
HALLMARK_E2F_TARGETS-1[[GO:0006260, GO:0006281, GO:0071897, GO:0006302, GO:0022616, GO:0006974, GO:0000075, dna damage recognition and signaling]][[GO:0006260, GO:0006281, GO:0051726, GO:0007059]]
HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0[[GO:0030198, GO:0043062, GO:0042277, GO:0030199, GO:0007155, GO:0007229, GO:0043410, GO:0005125, GO:0043498, GO:0010646, GO:0071711, GO:0007166, GO:0008285, GO:0070374, GO:0043236, GO:0005509, GO:0030335]][[GO:0030198, GO:0030199, GO:0032964, GO:0071711, regulation of growth factor signaling, regulation of bmp signaling, regulation of tgf-beta signaling]]
HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1[[GO:0030198, GO:0007155, GO:0005604, GO:0005581, GO:0007229, GO:0005925, GO:0005515, ecm-receptor interaction, GO:0030334, GO:0007010]][[GO:0030198, GO:0007155, GO:0007229, GO:0030574, GO:0009888, GO:0016477, GO:0071711]]
HALLMARK_ESTROGEN_RESPONSE_EARLY-0[[GO:0006811, GO:0006631, GO:0006006, GO:0032870, GO:0008203, drug binding]][[GO:0005509, GO:0006816, GO:0005516, GO:0010857, GO:0055074, GO:0005262, GO:0030899]]
HALLMARK_ESTROGEN_RESPONSE_EARLY-1[[GO:0006629, GO:0007165, transcriptional regulation]][[GO:0006811, GO:0023051, transport of small molecules, GO:0072657, GO:0009966, GO:0008202, GO:0010817, GO:0048522, GO:0010468, GO:0043066, GO:0051246, GO:0071363]]
HALLMARK_ESTROGEN_RESPONSE_LATE-0[[GO:0006351, GO:0008152, GO:0008283, GO:0006955, GO:0007165]][[GO:0005509, GO:0051302, GO:0042981, GO:0006816]]
HALLMARK_ESTROGEN_RESPONSE_LATE-1[[GO:0008152, GO:0007165, GO:0032502, GO:0006955, GO:0006351, GO:0019538, GO:0006810, GO:0001558, GO:0042981, GO:0006811]][[GO:0051726, GO:0008283, GO:0006260, GO:0051301, cancer progression]]
HALLMARK_FATTY_ACID_METABOLISM-0[[1. metabolic process \\n2. oxidation-reduction process \\n3. response to oxidative stress \\n4. lipid metabolic process \\n5. carbohydrate metabolic process \\n6. amino acid metabolic process \\n7. detoxification \\n8. fatty acid beta-oxidation \\n9. tca cycle \\n10. electron transport chain \\n11. glucose homeostasis \\n12. protein folding and stabilization \\n13. ion homeostasis]][[GO:0006635, mitochondrial beta-oxidation of fatty acids, GO:0015980, GO:0008152, GO:0044255, GO:0006084, coenzyme metabolic process, GO:0001676, GO:0019752, GO:0006099]]
HALLMARK_FATTY_ACID_METABOLISM-1[[GO:0006629, oxidative stress response, energy production]][[GO:0006631, MESH:D004734, mitochondrial function, GO:0016042, oxidative stress response]]
HALLMARK_G2M_CHECKPOINT-0[[GO:0022402, GO:0140014, GO:0007059, GO:0007052, GO:0000226, GO:0006260]][[cdc20, cdc25a, cdc25b, cdc27, cdc45, cdc6, cdc7, cdk1, cenpa, cenpe, cenpf, chek1, cks1b, cks2, dbf4, e2f1, e2f2, e2f3, e2f4, espl1, exo1, fbxo5, gins2, h2ax, h2az1, h2az2, h2bc12, hmmr, hus1, ilf3, incenp, katna1, kif11, kif15, kif20b, kif22, kif23, kif2c, kif4a, kif5b, kpna2, kpnb1, lig3, mad2l1, map3k20, mcm2, mcm3, mcm5, mcm6, ne]]
HALLMARK_G2M_CHECKPOINT-1[[GO:0006260, GO:0007049, GO:0006281, GO:0140014, GO:0007059]][[GO:0051726, GO:0006260, chromosomal segregation, GO:0051276, GO:0006281]]
HALLMARK_GLYCOLYSIS-0[[1. glycosylation\\n2. glycolysis\\n3. pentose phosphate pathway]][[GO:0006096, GO:0005978, glycosylation pathway]]
HALLMARK_GLYCOLYSIS-1[[GO:0006006, energy generation, GO:0016052, GO:0006096, GO:0006090, GO:0006099, GO:0022900, GO:0006119, GO:0006754]][[GO:0008152, GO:0006796, molecular function regulation, GO:0033554, GO:0031323, GO:0019538, GO:0050794, GO:0044281]]
HALLMARK_HEDGEHOG_SIGNALING-0[[GO:0030182, GO:0007411, GO:0016477, GO:0007155, GO:0008283]][[GO:0007399, nervous system neuron differentiation, nervous system development and angiogenesis, GO:0045765, GO:0023056, GO:0048598]]
HALLMARK_HEDGEHOG_SIGNALING-1[[GO:0007399, GO:0007165, GO:0007155]][[GO:0031175, GO:0007411, GO:0051960, GO:0007165, GO:0007267]]
HALLMARK_HEME_METABOLISM-0[[GO:0006811, GO:0005515, GO:0008152]][[GO:0015886, GO:0051536, [2fe-2s] cluster binding]]
HALLMARK_HEME_METABOLISM-1[[GO:0048821, GO:0045646, GO:0042541, GO:0015671, GO:0020037, GO:0005506, GO:0043496, GO:0046982]][[gene expression regulation; metabolism; transport\\n\\nmechanism and hypotheses:\\nthe genes in this list are involved in various cellular processes, including gene expression regulation, GO:0008152, and transport. gene expression regulation may be a mechanism by which these genes function, possibly through the involvement of transcription factors such as foxo3 and klf3. metabolism may also be a key mechanism, as many of these genes are involved in metabolic pathways, such as fech and alas2 in heme synthesis, and gclc and gclm in glutathione metabolism. transport may also be a contributing mechanism, as several genes in this list, such as slc2a1 and slc6a9, are involved in membrane transport of various molecules. overall, the commonality in function among these genes may be attributed to their roles in regulating cellular metabolism and transporting molecules across various membranes]]
HALLMARK_HYPOXIA-0[[GO:0008152, GO:0006096, GO:0006979, GO:0080135, GO:1901031, GO:0046324, GO:0006006, GO:0005975, GO:0006974]][[GO:0006110, GO:0051246, GO:0010628, GO:0030198, GO:0006006, GO:0009749, GO:0001558, GO:0008284, GO:0051094]]
HALLMARK_HYPOXIA-1[[glycolysis; gluconeogenesis; citrate cycle; pyruvate metabolism; atp production\\n\\nmechanism: these genes are enriched in functions related to energy metabolism, including glycolysis, GO:0006094, the citrate cycle, GO:0006090, and atp production. they are involved in various aspects of energy metabolism, such as glucose uptake and metabolism, GO:0005980, atp synthesis. the over-representation of these functions suggests that these genes may play a role in the regulation of energy metabolism at the cellular organismal level]][[hk1, hk2, pfkl, pfkfb3, gys1, pklr, pgk1, tpi1, aldoa, eno2, pgam2, pgm2, fbp1, eno1, ndst1, ndst2]]
HALLMARK_IL2_STAT5_SIGNALING-0[[il10ra, tnfrsf18, il18r1, il1r2, il1rl1, il2ra, il2rb, il4r, MESH:D016753, MESH:D018793, tnfrsf1b, tnfrsf21, tnfrsf4, tnfrsf8, tnfrsf9, tnfsf11, tnfsf10, ifngr1, ccr4, ctla4, cxcl10, icos, irf4, irf6, irf8, socs1, socs2, ager, cish, gata1, gbp4, spp1, bcl2, bcl2l1, bmpr2, ccnd2, ccne1, cd79b, galm, glipr2, gpx4, hk2, MESH:D016753, itga6, itgae, itih5, klf6, lif, lrig1, ltb, mxd1, myc]][[il2ra, il1r2, il2rb, il10ra, ctla4, cd44, MESH:D016753, il1rl1, il18r1, icos, tnfrsf4, tnfrsf18, tnfrsf8, tnfrsf21, tnfsf11, tnfrsf9, tnfsf10, tnfrsf1b, cd48, tnfrsf4, cxcl10, MESH:D018793, selp, ccne1, MESH:D047990, socs1, socs2]]
HALLMARK_IL2_STAT5_SIGNALING-1[[cytokine signaling pathway, GO:0006955, GO:0002682, GO:0006954, leukocyte migration and chemotaxis, GO:0002694, GO:0071347, GO:0032680]][[GO:0006955, cell signaling, GO:0005125, GO:0008009, GO:0008083, GO:0007166, GO:0002250, GO:0030595, GO:0050900, GO:0006954]]
HALLMARK_IL6_JAK_STAT3_SIGNALING-0[[GO:0006955, cytokine signaling pathway, GO:0060333, positive regulation of interleukin production, GO:0032729]][[GO:0019221, GO:0002757, GO:0007259, GO:0002694, regulation of leukocyte migration and chemotaxis, GO:0035456, GO:0034341, GO:0070555, GO:0070671, GO:0070741, response to tumor necrosis factor. \\n\\nhypotheses: these genes are involved in activating immune responses and cytokine-mediated signaling pathways. the enrichment of terms related to leukocyte activation and chemotaxis suggests an increased focus on the recruitment of immune cells to sites of infection and inflammation. the involvement of genes related to cytokine signaling, such as jak-stat cascade, suggests that the activation of immune responses may be regulated by cytokines released in response to infection or inflammation. overall, these genes are likely involved in the regulation of immune system activation and inflammation]]
HALLMARK_IL6_JAK_STAT3_SIGNALING-1[[GO:0005126, GO:0006955, GO:0050900, jak-stat signaling pathway, GO:0034341, GO:0002690, GO:0051249, GO:0001817, GO:0050863, GO:0019221, GO:1902105]][[cytokine signaling, GO:0006954, GO:0006955, interleukin signaling, GO:0008009, jak-stat signaling, toll-like receptor signaling]]
HALLMARK_INFLAMMATORY_RESPONSE-0[[GO:0050900, cytokine signaling, GO:0002224, GO:0006954, GO:0032729, GO:0045087, GO:0032733, GO:0030595]][[cytokine signaling, GO:0006955, GO:0006954]]
HALLMARK_INFLAMMATORY_RESPONSE-1[[cytokine signaling, chemokine signaling, GO:0050900, GO:0002250, GO:0045087]][[GO:0004896, GO:0042379, GO:0050900, GO:0002694, GO:0050778, GO:0045088, GO:0005149, GO:0042110, GO:0006952, GO:0006954, GO:0002685, GO:0034097]]
HALLMARK_INTERFERON_ALPHA_RESPONSE-0[[interferon signaling, GO:0045087, antiviral defense]][[GO:0051607, GO:0045087, interferon signaling, type i interferon response, viral defense]]
HALLMARK_INTERFERON_ALPHA_RESPONSE-1[[GO:0034341, GO:0002718, GO:0060333, GO:0045070, GO:0032897, innate immune response-activating signal transduction, GO:0060337, GO:0035457, antiviral mechanism by interferon-stimulated genes (isg)]][[GO:0051607, GO:0002376, GO:0140888]]
HALLMARK_INTERFERON_GAMMA_RESPONSE-0[[GO:0051607, GO:0035458, GO:0071357, GO:0045071, GO:0031323, GO:0002682, GO:0034097, GO:0034340]][[GO:0060337, GO:0006955, GO:0002579, GO:0051607, GO:0046596, GO:0032481, GO:0045087, GO:0034341, GO:0032727, GO:0002504, GO:0002479, GO:0032728, GO:0071357, GO:0043331, GO:0016032, GO:0045859, GO:0006954, GO:0060333, GO:0038187]]
HALLMARK_INTERFERON_GAMMA_RESPONSE-1[[interferon signaling, GO:0019882, GO:0045321]][[GO:0019882, interferon response, GO:0001816, GO:0006954, GO:0002376, GO:0050776, GO:0006952, GO:0009615, response to interferon]]
HALLMARK_KRAS_SIGNALING_DN-0[[GO:0005509, contractile fiber part, GO:0006936]][[GO:0005509, GO:0070588, GO:0051924, GO:0051899, GO:0042391, GO:0071277]]
HALLMARK_KRAS_SIGNALING_DN-1[[GO:0043167, GO:0007165, GO:0019222, GO:0050794, g protein-coupled receptor signaling, GO:0035556, GO:0031325, GO:0043066, metabolic process regulation, GO:0005509, GO:0034765, GO:0001932, GO:0043169, GO:0045859, GO:0051716]][[GO:0006811, neurological signaling, tissue development.\\n\\nmechanism]]
HALLMARK_KRAS_SIGNALING_UP-0[[GO:0006955, GO:0007165, GO:0050794, cytokine signaling, GO:0006954, GO:0006935, GO:0008284, GO:0043066]][[GO:0006955, cellular signaling, GO:0001525]]
HALLMARK_KRAS_SIGNALING_UP-1[[GO:0006955, GO:0006954, GO:0002694, GO:0001817, interleukin-10 signaling, tumor necrosis factor (tnf) signaling, GO:0006956, platelet activation and aggregation, eicosanoid synthesis]][[1. immune response\\n2. inflammatory response\\n3. coagulation\\n4. positive regulation of endothelial cell migration \\n5. cell adhesion\\n6. positive regulation of cell migration \\n7. signal transduction \\n8. negative regulation of apoptotic process \\n9. regulation of angiogenesis \\n10. positive regulation of protein serine/threonine kinase activity \\n11. positive regulation of transcription from rna polymerase ii promoter \\n\\nmechanism: the enriched functions suggest that these genes play an important role in innate and adaptive immune responses, inflammatory processes, GO:0007596, cell adhesion and migration, GO:0001525, and signal transduction pathways. they could be involved in regulating the expression and activity of various immune cells, MESH:D016207, chemokines to modulate immunity inflammation. the coagulation-related genes may contribute to thrombotic disorders cardiovascular diseases by affecting blood clot formation fibrinolysis. the cell adhesion migration-related genes are potentially involved in tumor metastasis progression through facilitating cell invasion motility. the signal]]
HALLMARK_MITOTIC_SPINDLE-0[[GO:0007018, GO:0007052, cell division, chromosome separation]][[GO:0007052, GO:0007017, GO:0051301, GO:0007010, GO:0030029]]
HALLMARK_MITOTIC_SPINDLE-1[[kinesin family members, microtubule formation and stabilization, spindle formation and assembly, GO:0000910, GO:0051726, gene expression and chromosome segregation]][[GO:0007051, GO:0031023, GO:0007059, GO:0071173, GO:0051382, GO:0007052, GO:0000226, GO:0007098, GO:0007020, GO:0000075, GO:0007018, GO:0007346, GO:0000070, GO:0001578, GO:0008017, GO:0000910, GO:0030953]]
HALLMARK_MTORC1_SIGNALING-0[[GO:0006457, GO:0050776, GO:0009117, GO:0006629, gluconeogenesis and glycolysis, mrna processing and splicing]][[glycolysis; tca cycle; cholesterol biosynthesis; pentose phosphate pathway\\n\\nmechanism and hypotheses:\\nthe enriched terms suggest that these genes are involved in various aspects of cellular metabolism. glycolysis is the central pathway for glucose metabolism, converting glucose into pyruvate. the tca cycle is responsible for generating energy from the breakdown of carbohydrates, MESH:D005227, and amino acids. the cholesterol biosynthesis pathway is responsible for producing cholesterol, which is involved in membrane structure, steroid hormone synthesis, and bile salt production. the pentose phosphate pathway is involved in the production of nadph, which is critical for many cellular processes, including antioxidant defense and biosynthesis.\\n\\noverall, these genes are likely involved in regulating various aspects of cellular metabolism, including energy production, biosynthesis of important molecules like cholesterol and nadph, mediating the cellular response to oxidative stress]]
HALLMARK_MTORC1_SIGNALING-1[[GO:0044237, protein regulation, transcriptional regulation, translation regulation, GO:0006281, stress response.\\n\\nmechanism: these enriched terms suggest that the identified genes are involved in several pathways, including maintaining cellular metabolism and homeostasis, regulating transcription and translation of proteins, repairing dna in response to damage, and responding to cellular stress]][[GO:0051087, GO:0006457, co-factor binding, GO:0008152, GO:0005524]]
HALLMARK_MYC_TARGETS_V1-0[[GO:0006412, GO:0006457, GO:1990904, u4/u6.u5 tri-snrnp, chaperone-mediated protein folding.\\n\\nmechanism: these genes are involved in protein synthesis and processing, including translation and ribosome biogenesis. many of them are also involved in protein folding and chaperone-mediated protein folding. the u4/u6.u5 tri-snrnp is also highly represented, indicating these genes may be involved in splicing]][[GO:0006397, GO:0006413, GO:0042254]]
HALLMARK_MYC_TARGETS_V1-1[[GO:0006396, GO:0006413, GO:0006446, GO:0042254, GO:0008380, GO:0006397]][[GO:0006396, GO:0006412, GO:0042254, GO:0006402, GO:0043488, regulation of mrna splicing, GO:0043393, GO:0008380, GO:0006417, GO:0003723]]
HALLMARK_MYC_TARGETS_V2-0[[GO:0042254, GO:0008033, GO:0006364, GO:0016072, GO:0009451, GO:0022613]][[GO:0042254, GO:0006364, GO:0003723, GO:0005681, GO:0006413]]
HALLMARK_MYC_TARGETS_V2-1[[GO:0042254, GO:0006364, GO:0000394, rna polymerase ii regulation, rna processing and modification]][[GO:0006396, GO:0022613, GO:0042254, GO:0000166, GO:0003723, GO:0090304, GO:0042273, GO:0006364, GO:0065004]]
HALLMARK_MYOGENESIS-0[[GO:0006936, GO:0006816, z-disc, UBERON:0002036, GO:0030017, MESH:D014335, GO:0005861, GO:0071689]][[muscle filament sliding; sarcomere organization; muscle system process\\n\\nmechanism: the majority of the listed genes are involved in muscle contraction and development, specifically in the organization and structure of the sarcomere. the enriched terms - muscle filament sliding, GO:0045214, muscle system process - all relate to the mechanisms of muscle contraction the intricate process of sarcomere formation]]
HALLMARK_MYOGENESIS-1[[UBERON:0001630, MESH:D009218, MESH:D000199, MESH:D014336, filament]][[GO:0003012, GO:0006936, GO:0045214, GO:0030029]]
HALLMARK_NOTCH_SIGNALING-0[[GO:0007219, GO:0045165, GO:0022008, GO:0030154, GO:0045893, GO:0043066, GO:0008285, GO:0043065, GO:0045747, GO:0016055, GO:0007268]][[GO:0007219, GO:0008593, GO:0016055, GO:0030111, GO:0045944, GO:0045596, GO:0045597]]
HALLMARK_NOTCH_SIGNALING-1[[GO:0051726, GO:0030154, GO:0001709, transcriptional regulation, GO:0016567]][[GO:0007219, GO:0005515, GO:0000122, GO:0000988]]
HALLMARK_OXIDATIVE_PHOSPHORYLATION-0[[GO:0022900, GO:0045333, GO:0002082]][[GO:0042773, mitochondrial atp synthesis coupled electron transport in respiratory chain, GO:0033108, GO:0006979]]
HALLMARK_OXIDATIVE_PHOSPHORYLATION-1[[GO:0006119, GO:0005746, GO:0070469, GO:0005739, MESH:D004734, GO:0031966, GO:0006099, GO:0006635, citrate cycle, GO:0098798, GO:0006754, GO:0051536]][[GO:0003954, GO:0022900, GO:0042773, GO:0005743, GO:0007005, GO:0006119, GO:0033108, respiratory chain complex i, ii, iii, iv, v, vi, GO:0006743, GO:0006631]]
HALLMARK_P53_PATHWAY-0[[GO:0006974, GO:0051726, cell growth and proliferation]][[GO:0051726, GO:0006915, GO:0008285, GO:0006974, negative regulation of cellular process.\\n\\nmechanism: the genes in this list are enriched in functions that regulate the cell cycle and cell death. specifically, they are involved in cell cycle arrest, apoptosis, negative regulation of cell proliferation, and response to dna damage stimulus]]
HALLMARK_P53_PATHWAY-1[[GO:0051726, GO:0006281, GO:0030330, GO:0000082, response to dna damage]][[GO:0006974, GO:0051726, GO:0006915, GO:0006281, MESH:D002470, p53 signaling, checkpoint regulation, transcriptional regulation, GO:0006338]]
HALLMARK_PANCREAS_BETA_CELLS-0[[pancreatic development, beta cell differentiation, GO:0030073, GO:0042593, GO:0006006]][[GO:0030073, GO:0042593, GO:0003309, GO:0003323, pancreatic beta cell function, pancreatic islet cell development]]
HALLMARK_PANCREAS_BETA_CELLS-1[[GO:0003323, GO:0030073, glucose regulation, diabetes-related pathways]][[GO:0003323, GO:0030073, GO:0042593, GO:0031018, GO:0050796, GO:0006006, positive regulation of pancreatic beta cell differentiation, GO:0010827, regulation of insulin secretion by glucose]]
HALLMARK_PEROXISOME-0[[GO:0006631, GO:0006805, steroid hormone biosynthesis]][[GO:0140359, GO:0006631, GO:0006695, GO:0035357, GO:0005777]]
HALLMARK_PEROXISOME-1[[GO:0006631, GO:0007031, GO:0015721, GO:0006282]][[GO:0006631, GO:0006629, GO:0008202, GO:0030301, GO:0006641, GO:0008206, GO:0005777]]
HALLMARK_PI3K_AKT_MTOR_SIGNALING-0[[mapk cascade; pi3k-akt signaling pathway; regulation of cell proliferation\\n\\nmechanism: the enriched terms suggest that the common function of the listed genes is to regulate cellular processes related to signal transduction and cell cycle/apoptosis. the mapk cascade is a crucial signaling pathway that controls the expression of genes required for cellular proliferation, differentiation, and survival. pi3k-akt signaling pathway controls cell survival, GO:0040007, and metabolism. the enriched term \"regulation of cell proliferation\" suggests that the listed genes contribute to regulating the balance between cell growth and division. these genes could affect the rate of cellular proliferation, arresting or promoting the cell cycle or modulating apoptotic signal transduction]][[GO:0016301, GO:0006468, GO:0010646, GO:0035556, regulation of map kinase activity\\n\\nmechanism: these genes are involved in several signaling pathways and primarily regulate protein kinase activity and phosphorylation. they are involved in the regulation of cell communication and intracellular signaling cascades, including the map kinase cascade]]
HALLMARK_PI3K_AKT_MTOR_SIGNALING-1[[GO:0033554, GO:0035556, GO:0006468, GO:0042981, GO:0080135]][[GO:0007165, GO:0006468, GO:0008152, GO:0001558, GO:0042127, GO:0042981, GO:0045859, GO:0043408, GO:0032024, GO:0005975, GO:0010906, GO:0010604]]
HALLMARK_PROTEIN_SECRETION-0[[GO:0016192, GO:0046907, GO:0006897, GO:0061024, GO:0008104, GO:0048193]][[GO:0016192, endosome to golgi transport, GO:0006886, GO:0008104, GO:0015031, regulation of membrane organization and biogenesis]]
HALLMARK_PROTEIN_SECRETION-1[[GO:0048193, GO:0005768, GO:0005764, GO:0006612, GO:0006886, GO:0042391, GO:0034765, GO:0005773]][[GO:0006886, GO:0006891, GO:0007030, GO:0072583]]
HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0[[GO:0016209, GO:0051920, GO:0006749, GO:0006979, GO:0070301]][[GO:0016209, redox regulation, GO:0006749, oxidation-reduction process, GO:0006979]]
HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1[[GO:0016209, regulation of iron ion binding, GO:0006979, GO:0048821, GO:2000378, GO:0006282, GO:0070301, GO:0050790, GO:0032092, regulation of thiol-dependent ubiquitinyl hydrolase activity, GO:0034599]][[oxidative stress response, redox regulation, GO:0006749, GO:0016209, GO:0000302]]
HALLMARK_SPERMATOGENESIS-0[[GO:0007283, GO:0140013, GO:0007130, GO:0007281, GO:0097722, oocyte meiosis]][[GO:0140013, GO:0007283, GO:0007059, GO:0051301, GO:0140014]]
HALLMARK_SPERMATOGENESIS-1[[GO:1903047, GO:0010971, regulation of spindle assembly checkpoint, GO:0034501, GO:0090234, GO:0051985, GO:0110028]][[GO:0007052, GO:0007059, GO:0007094]]
HALLMARK_TGF_BETA_SIGNALING-0[[tgf-beta signaling pathway, GO:0030514, GO:0090287, GO:0030513, GO:0006351, GO:0006355, GO:0045893, GO:0000122]][[GO:0030509, GO:0000122, GO:0045944, GO:0048705, GO:0007183, GO:0007179]]
HALLMARK_TGF_BETA_SIGNALING-1[[tgf-beta signaling pathway, GO:0030509, GO:0030513, GO:0030198, GO:0060391]][[GO:0007179, GO:0030514, GO:0010990]]
HALLMARK_TNFA_SIGNALING_VIA_NFKB-0[[ccl2, ccl20, ccl4, ccl5, ccn1, ccnd1, ccrl2, cd44, cd69, cd80, cd83, cdkn1a, icam1, icoslg, ifih1, ifit2, ifngr2, GO:0043514, il15ra, MESH:D020382, il1a, il1b, GO:0070743, MESH:D015850, il6st, il7r, inhba, irf1, jag1, nfkb1, nfkb2, nfkbia, nfkbie, nr4a1, nr4a2, nr4a3, ptger4, MESH:D051546, rel, rela, relb, ripk2, stat5a, tlr2, tnf, tnfaip2, tnfaip3, tnfaip6, tnfaip8, tnfrsf9, tnfsf9, tnip1, tnip]][[GO:0006955, GO:0006954, GO:0034097, GO:0050865, GO:0071624, GO:0032855, GO:0010552, GO:0051092, GO:0043406, GO:0007259, GO:0043065, GO:0004672]]
HALLMARK_TNFA_SIGNALING_VIA_NFKB-1[[cytokine signaling, GO:0000988, stress response, GO:0050776, GO:0006954]][[GO:0006955, GO:0006954, GO:0032680, GO:0001816, GO:0032496, negative regulation of nf-kappab transcription factor activity.\\n\\nmechanism and]]
HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0[[GO:0006457, GO:0036503, upr signaling pathway]][[GO:0006457, MESH:M0354322, ubiquitin-mediated proteolysis, GO:0034976, GO:0006986, GO:0006397, GO:0008380]]
HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1[[GO:0006457, GO:0006605, GO:0006396, GO:0006950, GO:0006417, GO:0016481, GO:0006986, GO:0006913, GO:0008380, GO:1903021, GO:0016032, GO:0032496, GO:0072659, GO:0017148, GO:0022613, negative regulation of transcription by rna polymerase]][[GO:0006457, chaperone-mediated protein processing, GO:0015031, GO:0007029, GO:0006986]]
HALLMARK_UV_RESPONSE_DN-0[[tgf-beta signaling pathway, GO:0030198, GO:0007155, GO:0030334, GO:0042127]][[GO:0004672, GO:0003700, GO:0006355, GO:0035556, cytoplasmic membrane-bounded vesicle, receptor protein signaling pathway, GO:0007155, GO:0001932, GO:0007399, GO:0007498, GO:0045666]]
HALLMARK_UV_RESPONSE_DN-1[[GO:0030198, GO:0030036, GO:0030155, GO:0007160, GO:0016477, GO:0007229, GO:0030199, GO:0035023, GO:0030178, basement membrane formation, GO:0014909]][[GO:0030198, GO:0007165, GO:0008083, neural development, GO:0022008]]
HALLMARK_UV_RESPONSE_UP-0[[GO:0006355, regulation of transcription, dna-templated; go:0044267, cellular protein metabolic process; go:0009968, GO:0009968]][[GO:0033554, GO:0031323, GO:0051050, GO:0009966]]
HALLMARK_UV_RESPONSE_UP-1[[GO:0006955, GO:0008104, GO:0051726]][[GO:0008104, GO:0006950, GO:0042981, GO:0008283, GO:0006979, regulation of transcription, GO:0006974, GO:0007049, response to hypoxia.\\n\\nmechanism]]
HALLMARK_WNT_BETA_CATENIN_SIGNALING-0[[GO:0016055, GO:0007219, transcriptional regulation, GO:0030154, GO:0008283]][[cellular response to wnt stimulus, GO:0090263, GO:0045746]]
HALLMARK_WNT_BETA_CATENIN_SIGNALING-1[[GO:0007219, GO:0045747, GO:0045746, GO:0045165]][[GO:0016055, GO:0007219, GO:0005515, GO:0008134]]
T cell proliferation-0[[cd28 co-stimulation, il-2 signaling, GO:0042110]][[GO:0002376, GO:0042110, GO:0001816, GO:0046649, GO:0006955, GO:0007166]]
T cell proliferation-1[[GO:0042110, GO:0051247, GO:0001817]][[t cell activation; cytokine signaling; lymphocyte proliferation; immune response\\n\\nmechanism: these genes are all involved in the regulation and function of the immune system, specifically in t cell activation, GO:0046651, and cytokine signaling pathways. they play a role in immune responses to pathogens, MONDO:0007179, MONDO:0004992]]
Yamanaka-TFs-0[[GO:0000988, transcriptional regulation, GO:0030154, GO:0008283, stem cell maintenance, MESH:D047108]][[GO:0000988, GO:0003677, GO:0048863]]
Yamanaka-TFs-1[[MESH:D047108, regulation of transcription, GO:0048863]][[pluripotency, self-renewal, GO:0048863]]
amigo-example-0[[GO:0030198, GO:0030199, GO:0001525, GO:0001568, GO:0030168, GO:0001666, GO:0001936]][[extracellular matrix organization; angiogenesis; positive regulation of cell migration; positive regulation of endothelial cell migration; positive regulation of sprouting angiogenesis; positive regulation of angiogenesis; positive regulation of vascular endothelial cell migration; positive regulation of smooth muscle cell migration; positive regulation of vascular smooth muscle cell migration; positive regulation of tube formation; positive regulation of endothelial cell proliferation; positive regulation of vascular endothelial growth factor production. \\n\\nhypotheses: several of the genes in the list encode for extracellular matrix components or regulators of matrix organization, including col3a1, col5a2, lum, postn, and vcan. others, such as cxcl6, pdgfa, pf4, and vegfa, encode for angiogenic growth factors. itgav is a common denominator and is associated with integrin-mediated signaling that regulates cell adhesion, migration, angiogenesis. fgfr1 has also been shown to play a critical role in angiogenesis extracellular matrix organization by regulating downstream signaling pathways such as pi3k mapk]]
amigo-example-1[[GO:0030198, GO:0030155, regulation of cell substrate adhesion, GO:0045785, GO:0043062]][[GO:0030198, GO:0007155, GO:0001525, GO:0016477, GO:0030334, GO:0008284, GO:0043410]]
bicluster_RNAseqDB_0-0[[GO:0005509, GO:0050804, transcriptional regulation, GO:0050808]][[GO:0030182, GO:0006811, GO:0000988, GO:0005509, GO:0007399, GO:0007267, synapse assembly and organization, g protein-coupled receptor signaling, GO:0003723, GO:0005515]]
bicluster_RNAseqDB_0-1[[GO:0007186, GO:0010468, GO:0007154, GO:0006355, GO:0005515, GO:0007155, GO:0001932, GO:0016055, GO:0030334, GO:0007165, GO:0043408, GO:0003677, GO:0006357, GO:0005543, GO:0051493, GO:0006811]][[GO:0006396, GO:0008134, GO:0006355, GO:0003682, GO:0005634, GO:0003723, GO:0006397, transcriptional regulation, GO:0061629]]
bicluster_RNAseqDB_1002-0[[atp hydrolysis coupled calcium ion transport, GO:0030036, GO:0006936, GO:0033365, GO:0051147, GO:0014743, GO:0045214]][[GO:0006936, GO:0045214, GO:0006941, GO:0060048]]
bicluster_RNAseqDB_1002-1[[GO:0006936, MESH:D024510, GO:0007519, GO:0055001, GO:0030239, GO:0007517]][[GO:0006936, GO:0033275, GO:0031034, GO:0005509, GO:0045214, MESH:D024510]]
endocytosis-0[[GO:0006897, GO:0016192, GO:0007041, GO:0007032, GO:0030163]][[GO:0030301, GO:0006629, GO:0006897, GO:0030163]]
endocytosis-1[[GO:0006897, GO:0006898, GO:0016197, GO:0015031, GO:0006886, GO:0007032, GO:0016192, endosomal sorting]][[GO:0006897, GO:0007032, GO:0036010, GO:0006898, GO:0016192]]
glycolysis-gocam-0[[GO:0006096, GO:0005975, GO:0006006, GO:0019318]][[GO:0006006, GO:0006096]]
glycolysis-gocam-1[[GO:0006096, GO:0006006, GO:0006007]][[GO:0005975, GO:0006006, GO:0006096, GO:0006754]]
go-postsynapse-calcium-transmembrane-0[[GO:0005509, GO:0005262, GO:0019722, GO:0006874, GO:0034765]][[GO:0006816, GO:0015075, GO:0099601, GO:0007268, GO:0034765]]
go-postsynapse-calcium-transmembrane-1[[GO:0005509, GO:0004970, GO:0051966, GO:0046928, GO:0005216, GO:0034765, GO:0004672, GO:0051924, GO:0051247]][[GO:0005216, neurotransmitter signaling, GO:0050804, GO:0005509, GO:0008066]]
go-reg-autophagy-pkra-0[[GO:0033554, GO:0010506, GO:0007165]][[GO:0006950, GO:0006915, GO:0042981, GO:0043123, GO:0046330]]
go-reg-autophagy-pkra-1[[GO:0097190, GO:0016485, GO:0031323]][[autophagy regulation, GO:0033554, GO:0006915]]
hydrolase activity, hydrolyzing O-glycosyl compounds-0[[glycoside hydrolase activity, GO:0005975, GO:0006027, GO:0009311, GO:0005764, GO:0005783, catabolism of carbohydrate, MONDO:0019249]][[GO:0005975, GO:0005764, GO:0016798, glycoside hydrolase activity, GO:0004556, GO:0008422, acid alpha-glucosidase activity, GO:0004565, GO:0015929, GO:0015923, n-acetylglucosaminidase activity, GO:0004308, GO:0015926, GO:0005980, GO:0006027, mucopolysaccharide catabolic process, GO:0016266, GO:0006491]]
hydrolase activity, hydrolyzing O-glycosyl compounds-1[[GO:0006096, metabolism of carbohydrates, GO:0019318, GO:0006013, GO:0009311, chitin catabolic/metabolic process, hyaluronan catabolic/metabolic process, glycosphingolipid metabolic/catabolic process, sialic acid catabolic/metabolic process]][[GO:0005975, GO:0070085, GO:0000272, GO:0004553, GO:0015929, GO:0004556, GO:0004565]]
ig-receptor-binding-2022-0[[GO:0002377, t cell receptor signaling, GO:0042113, t cell activation. \\n\\nhypotheses: this list of genes is heavily enriched in those involved in the function and development of b cells and t cells. specifically, they play a role in the production and function of immunoglobulins and t cell receptors, as well as the activation of these cell types. this suggests that these genes are integral to the proper functioning of the immune system]][[GO:0002376, GO:0046649, GO:0002250, GO:0042113, GO:0003823, antibody-mediated immunity\\n\\nmechanism]]
ig-receptor-binding-2022-1[[GO:0006955, GO:0046649, GO:0030098]][[GO:0002377, GO:0042113, GO:0016064]]
meiosis I-0[[meiotic recombination, crossover formation, GO:0007130, GO:0006281, GO:0035825]][[GO:0006281, GO:0035825, GO:0140013, GO:0007059, GO:0007129, GO:0006974, m phase of meiosis, dna replication-independent nucleosome assembly, crossover junction formation, GO:0007281, GO:0036093, GO:0009994, GO:0007283, GO:0071173, GO:0006298, GO:0033554]]
meiosis I-1[[GO:0007059, GO:0051321, GO:0006310, synapsis of chromosomes, GO:0051276, GO:0051177]][[GO:0140013, GO:0006281, GO:0007059, MESH:D011995, GO:0035825, GO:0006302, GO:0007129, crossing-over, GO:0051276]]
molecular sequestering-0[[GO:0002376, GO:0006950, GO:0006457, GO:0051641, GO:0006396, GO:0006829, GO:0010467, GO:0007165]][[GO:0034599, GO:0001558, GO:0032088, GO:0043066, GO:0051726, GO:0010468, GO:0008285]]
molecular sequestering-1[[GO:0006979, GO:0032088, GO:0055072, GO:0016567, GO:0043066]][[GO:0006979, GO:0006974, GO:0080135, regulation of protein localization to organelles, GO:0043065, GO:0043066, GO:0008285, GO:0050821]]
mtorc1-0[[GO:0006457, GO:0050776, GO:0009117, GO:0006629, gluconeogenesis and glycolysis, mrna processing and splicing]][[glycolysis; tca cycle; cholesterol biosynthesis; pentose phosphate pathway\\n\\nmechanism and hypotheses:\\nthe enriched terms suggest that these genes are involved in various aspects of cellular metabolism. glycolysis is the central pathway for glucose metabolism, converting glucose into pyruvate. the tca cycle is responsible for generating energy from the breakdown of carbohydrates, MESH:D005227, and amino acids. the cholesterol biosynthesis pathway is responsible for producing cholesterol, which is involved in membrane structure, steroid hormone synthesis, and bile salt production. the pentose phosphate pathway is involved in the production of nadph, which is critical for many cellular processes, including antioxidant defense and biosynthesis.\\n\\noverall, these genes are likely involved in regulating various aspects of cellular metabolism, including energy production, biosynthesis of important molecules like cholesterol and nadph, mediating the cellular response to oxidative stress]]
mtorc1-1[[GO:0006457, GO:0015031, GO:0042254]][[GO:0006810, GO:0008152, GO:0006457]]
peroxisome-0[[GO:0005778, peroxisome targeting, GO:0007031]][[GO:0007031, peroxisome biogenesis, protein import into peroxisome, peroxisome membrane organization, peroxisomal matrix organization]]
peroxisome-1[[peroxisome biogenesis, peroxisome membrane organization, GO:0016559]][[GO:0007031, peroxisome biogenesis, GO:0016559]]
progeria-0[[GO:0006281, GO:0051276, regulation of transcription]][[GO:0006281, GO:0006997, GO:0010467, GO:0007568]]
progeria-1[[GO:0006281, GO:0006325, GO:0090398]][[GO:0006325, GO:0006281, GO:0000723, nuclear localization, nuclear lamina organization, genome stability regulation]]
regulation of presynaptic membrane potential-0[[GO:0004970, GO:0099536, GO:0001505, GO:0007268, GO:0043269, GO:0005244, GO:0042391]][[GO:0006811, GO:0048666, GO:0007268, GO:0042391, GO:0034765]]
regulation of presynaptic membrane potential-1[[GO:0005216, GO:0007268, GO:0005261, GO:0007215, GO:0019228, GO:0006813, GO:0060080, MESH:D005680, sodium ion transport. \\n\\nhypotheses: \\n1. the enrichment of ion channel activity-related terms suggests that the genes play a crucial role in regulating ion transport during neuronal signaling, which in turn influences synaptic plasticity and memory formation.\\n2. the enrichment of synaptic transmission-related terms points towards the involvement of the genes in various aspects of synaptic signaling, including the glutamate and gaba receptor signaling pathways, inhibition of neuronal activity, and modulation of action potential generation. \\n3. overall, the enrichment of these terms hints at a potential interaction between the listed genes in regulating various aspects of neural signal processing, synaptic transmission, and plasticity]][[GO:0005216, GO:0042803, GO:0008066, GO:0016917, GO:0005261]]
sensory ataxia-0[[mitochondrial function, GO:0006457, GO:0030163, GO:0055085]][[GO:0042552, GO:0007411, GO:0007399, GO:0008104, GO:0031175]]
sensory ataxia-1[[\"nervous system development\", \"axon guidance\", \"myelination\", \"neuron projection\", \"synaptic transmission\"]][[GO:0044237, neurological development, myelin sheath formation]]
term-GO:0007212-0[[GO:0030594, GO:0007186, GO:0046928, GO:0007212, GO:0007188]][[GO:0007186, GO:0007188, GO:0046928, GO:0032225, positive regulation of camp biosynthetic process, GO:0007194, GO:0007212, prostaglandin receptor signaling pathway]]
term-GO:0007212-1[[g protein coupled receptor signaling pathway, g protein beta/gamma subunit complex binding]][[GO:0007186, dopamine receptor activity, GO:0007188, GO:0004952, GO:0099528, d1 dopamine receptor signaling pathway]]
tf-downreg-colorectal-0[[transcriptional regulation, GO:0006325]][[transcription regulation, GO:0016569, GO:0032502, GO:0065004, GO:0006950]]
tf-downreg-colorectal-1[[GO:0003677, regulation of transcription, GO:0003682, GO:0008134, GO:0003713, negative regulation of transcription]][[GO:0003677, transcriptional regulation, GO:0010468, GO:0000988, GO:0003682, GO:0006357, GO:0006355, GO:0000977, GO:0043565, GO:0051090]]
ontological_synopsisEDS-0[[GO:0030199, GO:0030198, GO:0006024, GO:0061448]][[GO:0030199, GO:0061448, GO:0062023, GO:0030198, GO:0006024]]
EDS-1[[GO:0030199, GO:0030198, GO:0030166, GO:0061448]][[GO:0030198, GO:0030199, GO:0030166, GO:0006024, GO:0061448]]
FA-0[[GO:0006281, GO:0000724, GO:0006513, fanconi anemia complementation group]][[GO:0006281, GO:0006513]]
FA-1[[GO:0006281, GO:0006513, GO:0000724, fanconi anemia complementation group, GO:0000785, GO:0005654, GO:0140513]][[GO:0006281, GO:0006513]]
HALLMARK_ADIPOGENESIS-0[[fad binding activity, GO:0016407, lipid binding activity, coenzyme binding, identical protein binding activity, citrate biosynthetic process]][[mitochondrial function, GO:0006754, GO:0006629, GO:0005515, GO:0023052]]
HALLMARK_ADIPOGENESIS-1[[mitochondrial respiration, mitochondrial function, GO:0008152, energy production, GO:0022900, GO:0006629, GO:0006631, GO:0006637]][[GO:0005746, GO:0022900, GO:0006754, GO:0006631, GO:0015746, GO:0016746, dehydrogenase activity, GO:0016491, GO:0022857]]
HALLMARK_ALLOGRAFT_REJECTION-0[[GO:0005125, GO:0004896, integrin binding activity, GO:0004672, GO:0000988, t-cell receptor binding activity, abc-type peptide antigen transporter activity.\\n\\nmechanism: these genes are involved in various aspects of immune response, including cytokine activity, cytokine receptor activity, and t-cell receptor binding activity. they also play a role in antigen processing and presentation through the abc-type peptide antigen transporter activity. the integrin binding activity reflects the involvement of integrins in leukocyte adhesion and migration. finally, the transcription factor activity reflects the importance of transcriptional regulation in immune responses]][[GO:0005125, chemokine receptor binding activity, interleukin receptor binding activity, mhc class protein complex binding activity, identical protein binding activity\\n\\nmechanism: these genes are involved in the regulation of the immune response, including the production of cytokines and chemokines, binding to immune receptors, and mhc class protein complex binding. their common function is likely related to the regulation of the immune system and the activation of the immune response against foreign invaders]]
HALLMARK_ALLOGRAFT_REJECTION-1[[GO:0005125, GO:0008009, mhc class ii protein complex binding activity, signaling receptor binding activity, protein kinase binding activity, integrin binding activity, identical protein binding activity, sh2 domain binding activity, GO:0004252, rna binding activity, GO:0046982, GO:0008083]][[GO:0005125, chemokine receptor binding activity, GO:0004672, GO:0004896, identical protein binding activity, integrin binding activity, GO:0002376, GO:0005840, GO:0042803, GO:0042110, transcription activator activity, rna polymerase ii-specific. \\n\\nmechanism and hypotheses: these enriched terms suggest that the identified genes are involved in immune system processes such as cytokine signaling, chemokine receptor binding, and t cell activation. protein kinase activity may be involved in signaling pathways downstream of cytokine receptors or chemokine receptors. the presence of ribosome-related terms suggests these genes may play a role in protein synthesis in immune cells. the identified enriched terms point to a central role of the immune system in the functions of these genes, with potential impacts on inflammation, infection, and other immune-related diseases]]
HALLMARK_ANDROGEN_RESPONSE-0[[binding activity, GO:0008152, GO:0043167, nucleic acid binding. \\n\\nmechanism: the enriched terms suggest that the listed genes have a common function in binding and metabolic processes. it is possible that these genes are involved in regulating the flow and utilization of energy and molecules within cells]][[GO:0006468, GO:0035556, GO:0010604]]
HALLMARK_ANDROGEN_RESPONSE-1[[GO:0004672, GO:0035556, GO:0000079, GO:0007166]][[1. binding of metal ions \\n2. protein kinase activity \\n3. positive regulation of protein kinase activity \\n4. cytoskeletal protein binding activity \\n5. signal transduction \\n\\nmechanism: these enriched terms indicate that the genes have a role in signal transduction pathways and cytoskeletal organization. the genes are involved in the binding of metal ions and protein kinases, which are important components of these pathways. additionally, the positive regulation of protein kinase activity suggests that these genes have a role in the amplification of signal transduction through cascade-like pathways]]
HALLMARK_ANGIOGENESIS-0[[extracellular matrix organization; cell adhesion; protein binding; signaling pathway; regulation of cell proliferation.\\n\\nmechanism: the enriched terms suggest that these genes are involved in extracellular matrix organization and cell signaling pathways that regulate cell proliferation and adhesion. many of the genes are structural constituents of the extracellular matrix and influence cell-matrix interactions. others are involved in cell signaling pathways, such as the notch and fibroblast growth factor pathways, that play critical roles in cell proliferation and differentiation. some of the genes have also been implicated in diseases involving abnormal extracellular matrix formation or cell signaling dysregulation, such as ehlers-danlos syndrome, MONDO:0004975, MONDO:0004992]][[extracellular matrix organization; cell signaling; blood coagulation; lipid metabolism; immunity.\\n\\nmechanism and hypotheses: these genes appear to be involved in a variety of pathways related to extracellular matrix organization, cell signaling, and intercellular communication. specifically, several genes encode proteins that are structural components of the extracellular matrix or interact with extracellular matrix proteins, suggesting a role in tissue development, remodeling, or repair. many of these genes also participate in signaling pathways that control cell proliferation, differentiation, and migration. additionally, several genes are involved in blood coagulation and lipid metabolism, which may be related to their roles in cardiovascular disease. finally, some genes have roles in immunity and host defense against infectious pathogens, possibly contributing to susceptibility or resistance to infectious diseases. overall, these common functions may point to a greater role for extracellular matrix and signaling pathways in disease pathogenesis]]
HALLMARK_ANGIOGENESIS-1[[UBERON:4000022, binding activity]][[GO:0030198, cell signaling, protein binding activity, GO:1902533, GO:0062023]]
HALLMARK_APICAL_JUNCTION-0[[GO:0007010, GO:0007155, GO:0005102, kinase activity.\\n\\nmechanism: these genes are involved in the maintenance of cell structure and organization through regulation of the cytoskeleton. they also contribute to cell-cell interactions and signaling through receptor binding and kinase activity. a biological pathway that might be involved is the rho gtpase signaling pathway, which regulates actin cytoskeleton dynamics and cell adhesion]][[actin filament binding activity, integrin binding activity, protein kinase binding activity, sh2 domain binding activity, cell adhesion molecule binding activity, identical protein binding activity, GO:0005096, atp binding activity, cadherin binding activity, collagen binding activity, GO:0051219, GO:0042803]]
HALLMARK_APICAL_JUNCTION-1[[cell adhesion: cdh3, cdh4, cdh6, cdh11, cdh15, cd276, cd209, icam5, icam2, icam1, itga3, itga9, itga10, itgb1, cldn4, cldn5, cldn6, cldn7, cldn8, cldn9, cldn11, cldn14, cldn18, cldn19\\n- protein kinase activity: cdk8, ptk2, syk, taok2, vav2, src\\n- actin filament binding: actn1, actn3, lima1, nexn, calb2, pfn1\\n- metalloendopeptidase activity: adamts5, adam23, mmp2, mmp9\\n- integrin binding: jup, vcam1, slit2]][[integrin binding activity, cell adhesion molecule binding activity, sh3 domain binding activity, identical protein binding activity, actin filament binding activity, protein kinase binding activity]]
HALLMARK_APICAL_SURFACE-0[[GO:0007165, cell surface receptor activity, protein binding activity]][[GO:0005886, GO:0005615, signaling receptor binding activity, protein domain specific binding activity, protein kinase binding activity, GO:0006811, GO:0051247, GO:0010468, GO:0007155, GO:1902531]]
HALLMARK_APICAL_SURFACE-1[[GO:0005886, GO:0009986, GO:0055085, GO:0038023, positive regulation of transcription, GO:0010468, GO:0006468, GO:0005615]][[GO:0010468, signaling receptor binding activity, GO:0045944, GO:2001234, GO:0006811, GO:0060244, GO:0051965, carbohydrate binding activity, GO:1902531, GO:1904054]]
HALLMARK_APOPTOSIS-0[[GO:0006915, GO:0005125, transcription factor binding activity. \\n\\nmechanism/]][[GO:0097190, GO:0006955, GO:0005125, identical protein binding activity, protease binding activity, enzyme binding activity, GO:0000988, dna binding activity]]
HALLMARK_APOPTOSIS-1[[GO:0006915, GO:0005125, GO:0010941, GO:2001233, GO:0001819, GO:0042981, GO:0043067, positive regulation of apoptotic process.\\n\\nmechanism: these genes are involved in apoptotic signaling and cytokine activity, which suggests that they play a role in regulating cell death and programmed cell death. the enriched terms suggest that these genes may be regulated by shared signaling pathways or transcriptional programs that control apoptosis and cytokine production. one potential underlying mechanism could involve the activation of pro-apoptotic proteins in response to cellular stress or damage, leading to the release of cytokines that further promote cell death. alternatively, these genes may be involved in controlling the balance between cell survival and death in response to external cues such as cytokine signaling or nutrient availability. further research is needed to fully elucidate the molecular mechanisms underlying these gene functions]][[apoptotic process; cytokine activity; protein binding activity.\\n\\nmechanism: the genes in this list are involved in processes related to cell death, GO:0006955, and molecular interactions. the enriched terms suggest that these genes may be involved in pathways related to apoptosis, cytokine signaling, protein interactions. it is possible that these genes contribute to the regulation of cell death through cytokine-mediated signaling pathways protein-protein interactions]]
HALLMARK_BILE_ACID_METABOLISM-0[[GO:0006629, GO:0030301, GO:0006633]][[cholesterol binding activity, GO:0016887, GO:0005319, GO:0008559, atp binding activity, GO:0007031, vitamin d receptor binding activity, GO:0042626]]
HALLMARK_BILE_ACID_METABOLISM-1[[GO:0030301, GO:0015908, GO:0007031, GO:0004467, GO:0008123, atp binding activity, ubiquitin-dependent protein binding activity. \\n\\nmechanism: these genes are likely involved in the regulation and transport of lipids, particularly cholesterol and long-chain fatty acids, in cells and tissues. peroxisomal proteins and functions may also play a role in this process, including in the regulation of lipid metabolism]][[GO:0008610, GO:0006631, GO:0008203, GO:0007031, GO:0015908, peroxisome matrix targeting, abc-type transporter activity. \\n\\nmechanism]]
HALLMARK_CHOLESTEROL_HOMEOSTASIS-0[[GO:0042632, GO:0008610, GO:0010883, phospholipid binding activity, fatty acid binding activity, low-density lipoprotein particle binding activity, more]][[GO:0006695, GO:0008610, GO:0019216, GO:0042632, GO:0090181]]
HALLMARK_CHOLESTEROL_HOMEOSTASIS-1[[GO:0006695, GO:0008299, GO:0055088, GO:0006646, GO:0000122, GO:0045944, GO:0070458, GO:0001676]][[GO:0006695, GO:0008299, GO:0006633]]
HALLMARK_COAGULATION-0[[GO:0006508, complement pathways, GO:0007596, GO:0007155]][[GO:0006956, GO:0050817, GO:0008237]]
HALLMARK_COAGULATION-1[[GO:0006508, GO:0007596, GO:0006956, negative regulation of proteolysis. \\n\\nmechanism: the enriched terms suggest that these genes are involved in the regulation of proteolytic activity in several biological processes, including blood coagulation and immune response]][[metalloendopeptidase activity; serine-type endopeptidase activity; protease binding activity; identical protein binding activity; complement binding activity \\n\\nmechanism and hypotheses: these enriched terms suggest that the common mechanism or pathway involves the regulation of proteolysis and immune response, particularly the complement system. metalloendopeptidase and serine-type endopeptidase activity are involved in the proteolytic degradation of various extracellular matrix components including collagen, GO:0005577, and proteoglycan, as well as destruction of pathogenic microorganisms during immune response. protease binding activity, identical protein binding activity, and complement binding activity are involved in protein-protein interactions that regulate proteolysis and activation of complement components. therefore, the hypothesis is that the common mechanism of these genes is related to the regulation of proteolysis and complement system activity]]
HALLMARK_COMPLEMENT-0[[GO:0004867, protease binding activity, enzyme binding activity, calcium ion binding activity]][[GO:0005515, GO:0046872, GO:0019899, GO:0042802, GO:0005524, GO:0003677, calcium ion binding. \\n\\nmechanism]]
HALLMARK_COMPLEMENT-1[[GO:0005515, GO:0019899, GO:0005488, GO:0004175, metal ion binding.\\n\\nmechanism: the enriched terms suggest that these genes play a role in protein-protein interactions and enzymatic reactions involving metal ions]][[GO:0004222, GO:0004252, complement binding activity, heparin binding activity, GO:0008234, GO:0004869, GO:0005201, serine-type endopeptidase inhibitor activity involved in apoptotic process, GO:0004722, MESH:D011809]]
HALLMARK_DNA_REPAIR-0[[GO:0006281, GO:0097747, nucleotide metabolism. \\n\\nmechanism: these genes are predominantly involved in regulating dna replication, transcription, and repair. they may also play roles in the metabolism of nucleotides and nucleotide analogs that target dna synthesis. the enrichment of terms related to rna polymerase may reflect the closely intertwined nature of dna and rna synthesis]][[dna binding activity, transcription initiation, rna binding activity, GO:0009117, rna splicing. \\n\\nmechanism: these genes are likely involved in regulating dna replication, transcription, and various steps in rna processing, including splicing and export from the nucleus. they could also be involved in nucleotide metabolism and/or maintaining genomic stability]]
HALLMARK_DNA_REPAIR-1[[GO:0006260, GO:0006281, rna transcription]][[GO:0003677, GO:0003723, GO:0009117, GO:0006281, transcription initiation, protein-macromolecule adaptor activity.\\n\\nmechanism: these genes work together to maintain the integrity and expression of genetic information, with a focus on dna-related processes]]
HALLMARK_E2F_TARGETS-0[[GO:0006260, GO:0051726, GO:0006325]][[GO:0006260, GO:0006281, GO:0051726, GO:0003682, GO:0005524, GO:0019899, GO:0042393, GO:0043130]]
HALLMARK_E2F_TARGETS-1[[dna binding activity, protein binding activity, enzyme binding activity, chromatin binding activity, atp binding activity, histone binding activity, rna binding activity, identical protein binding activity]][[dna binding activity, chromatin binding activity, rna binding activity, enzyme binding activity, GO:0042803, single-stranded dna binding activity, identical protein binding activity, histone binding activity, atp binding activity, cyclin binding activity, nucleic acid binding activity]]
HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0[[GO:0005201, integrin binding activity, collagen binding activity, identical protein binding activity, fibrinogen binding activity, protease binding activity]][[GO:0005201, collagen binding activity, heparin binding activity, GO:0005125, GO:0008083, signaling receptor binding activity, wnt-protein binding activity]]
HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1[[GO:0005201, collagen binding activity, integrin binding activity, heparin binding activity, GO:0008237, signaling receptor binding activity.\\n\\nmechanism: these genes are involved in the maintenance and formation of the extracellular matrix, which provides structural support to cells and tissues. they play a role in cell adhesion, signaling, and migration through interactions with the extracellular matrix. the enriched binding activities suggest that these genes are involved in extracellular matrix remodeling and regulation of growth factor signaling. metallopeptidase activity may be involved in the degradation of extracellular matrix components]][[collagen binding activity, integrin binding activity, heparin binding activity, GO:0005201, GO:0008237, platelet-derived growth factor binding activity, GO:0008009, fibronectin binding activity, GO:0004867]]
HALLMARK_ESTROGEN_RESPONSE_EARLY-0[[GO:0005509, GO:0000166, enzyme binding activity, MESH:D048788, gene transcription, GO:0006811]][[GO:0004888, GO:0022857, GO:0001216]]
HALLMARK_ESTROGEN_RESPONSE_EARLY-1[[GO:0005515, GO:0000988, transmembrane transporter activity.\\n\\nmechanism: the enriched terms suggest that the genes on the list are involved in various cellular processes that require protein-protein interaction, transcriptional regulation, and transmembrane transport of substances. a possible hypothesis is that these genes play a role in signal transduction and regulation of gene expression]][[GO:0007165, transcriptional regulation, GO:0003824, GO:0038023, GO:0003676, GO:0007154, GO:0042445, protein-protein interaction\\n\\nhypotheses: the enriched terms suggest that the genes in this list are involved in various aspects of signaling and transcriptional regulation. they may function in pathways such as cell signaling, hormone metabolism, and protein-protein interaction. this list includes genes encoding enzymes with specific activities, as well as receptor and nucleic acid binding proteins that are crucial for signaling and transcriptional regulation]]
HALLMARK_ESTROGEN_RESPONSE_LATE-0[[GO:0022857, protein binding activity]][[enzyme binding activity, identical protein binding activity, calcium ion binding activity, GO:0005215, phosphorylation-dependent protein binding activity, atpase binding activity, GO:0004930, GO:0004712, nucleotide binding activity, ubiquitin protein ligase binding activity, transcription factor binding activity, histone deacetylase binding activity, GO:0016787, GO:0016491]]
HALLMARK_ESTROGEN_RESPONSE_LATE-1[[(1) enzymatic activity; (2) binding activity; (3) transcription regulation. \\n\\nmechanism: these genes likely play roles in various biological pathways, such as metabolism, cell signaling, and gene expression regulation. given the enrichment in enzymatic activity, it is possible that some of these genes are involved in metabolic pathways, such as lipid metabolism. the enrichment in binding activity may reflect the importance of protein-protein interactions and signaling cascades in cellular processes. the enrichment in transcription regulation suggests that many of these genes may be key players in regulating gene expression and ultimately cell fate]][[binding activity, GO:0005215, enzyme binding activity, identical protein binding activity, protein kinase binding activity, GO:0004930]]
HALLMARK_FATTY_ACID_METABOLISM-0[[GO:0047617, GO:0006631, GO:0120227, GO:0008289, GO:0004467, GO:0006099, GO:0046356]][[fatty acid-coa ligase activity, GO:0003995, long-chain fatty acid binding activity, GO:0003985, GO:0016615, GO:0000104, GO:0016616]]
HALLMARK_FATTY_ACID_METABOLISM-1[[GO:0016491, binding activity, GO:0006631, GO:0006084, heme-binding activity]][[GO:0003824, GO:0016491, GO:0006631, GO:0006629, metabolic pathways. \\n\\nmechanism: these genes may be involved in the regulation of lipid and fatty acid metabolism, potentially through oxidation-reduction processes and metabolic pathways]]
HALLMARK_G2M_CHECKPOINT-0[[dna binding activity, chromatin binding activity, protein binding activity, enzyme binding activity, histone binding activity, GO:0003714]][[dna binding activity, transcription regulation, GO:0004672, protein binding activity, GO:0016570]]
HALLMARK_G2M_CHECKPOINT-1[[dna-binding transcription factor activity; protein kinase activity; microtubule binding activity. \\n\\nmechanism: these genes are likely involved in the regulation of gene expression, cell cycle progression, and cytoskeletal dynamics through the binding and modification of dna, MESH:D011506, and microtubules. specifically, they may be involved in processes such as transcriptional regulation, dna replication and repair, GO:0007059, GO:0051301]][[dna-binding transcription factor, GO:0004672, protein binding activity, GO:0140014, GO:0006260, GO:0010467]]
HALLMARK_GLYCOLYSIS-0[[GO:0008378, GO:0015020, n-acetylglucosamine sulfotransferase activity, GO:0035250, glucosaminyl-proteoglycan 3-beta-glucosyltransferase activity, GO:0016758, GO:0045130, GO:0016779]][[GO:0008194, GO:0008146, GO:0008378, GO:0015020, GO:0004553, heparan sulfate binding activity, several others]]
HALLMARK_GLYCOLYSIS-1[[GO:0005975, GO:0006024, GO:0006493]][[enzyme binding activity, GO:0008194, atp binding activity, GO:0008378, GO:0004340, fructose binding activity, heme binding activity, GO:0016787, rna binding activity, identical protein binding activity, GO:0046983, nucleoside triphosphate activity]]
HALLMARK_HEDGEHOG_SIGNALING-0[[GO:0006357, GO:0016525, GO:0007155, GO:0030036, GO:0010604, GO:0007411, GO:0030336]][[GO:0032502, GO:0007165, MESH:D005786]]
HALLMARK_HEDGEHOG_SIGNALING-1[[GO:0007165, GO:0007155, GO:0007399, transcription regulation]][[GO:0007155, transcription regulation, GO:0007165, negative regulation, positive regulation]]
HALLMARK_HEME_METABOLISM-0[[GO:0020037, GO:0015075, protein binding activity, GO:0000988]][[GO:0005215, binding activity, GO:0003824]]
HALLMARK_HEME_METABOLISM-1[[transmembrane transport; protein binding activity; metal ion binding activity; dna-binding transcription activator activity\\n\\nmechanism: these genes are involved in various transport and binding activities, especially transmembrane transport, indicating a possible importance in cellular trafficking and signaling pathways. additionally, they exhibit a significant enrichment in protein and metal ion binding activities, which may suggest a role in protein-protein interactions and redox reactions, respectively. finally, dna-binding transcription activator activity is found to be enriched, indicating that these genes may regulate gene expression]][[enzyme binding activity, protein domain specific binding activity, GO:0046982, identical protein binding activity, GO:0042803]]
HALLMARK_HYPOXIA-0[[enzyme binding activity, GO:0005515, GO:0003700, carbohydrate binding activity, signaling receptor binding activity, identical protein binding activity, atp binding activity, nad binding activity, phosphoprotein binding activity, metal ion binding activity, GO:0003924, GO:0008083, GO:0008194, phospholipid binding activity, platelet-derived growth factor binding activity]][[enzyme binding activity, protein kinase binding activity, identical protein binding activity, GO:0003700, GO:0004674, calcium ion binding activity, nucleic acid binding activity, atp binding activity, GO:0060422, gtp binding activity, GO:0004340, GO:0005353, GO:0008459, heparin binding activity, apolipoprotein binding activity]]
HALLMARK_HYPOXIA-1[[GO:0006006, GO:0016301, transcriptional regulation, GO:0023052]][[GO:0042802, GO:0019899, GO:0005524, GO:0019901, GO:0005509, GO:0005102, GO:0015035, GO:0016538, GO:0008083, GO:0005353, GO:0004347, nadph binding activity, GO:0042803, MESH:D013213]]
HALLMARK_IL2_STAT5_SIGNALING-0[[GO:0005125, interleukin receptor binding activity, cytokine binding activity, GO:0031295, GO:0051250, GO:0006952, GO:0006955, interleukin binding activity]][[GO:0042802, GO:0003700, GO:0005125, GO:0005096, interleukin receptor binding activity, ubiquitin protein ligase activity.\\n\\nmechanism: these genes likely play a role in regulating various cell signaling pathways, including cytokine and growth factor signaling, as well as intracellular protein degradation via ubiquitin-proteasome system]]
HALLMARK_IL2_STAT5_SIGNALING-1[[GO:0004896, interleukin binding activity, identical protein binding activity, gtp binding activity, GO:0001216, protein kinase binding activity, atp binding activity, GO:0016787, collagen binding activity, small gtpase binding activity, GO:0061630, GO:0004197, GO:0005215, rna binding activity, calcium ion binding activity, signaling receptor binding activity, GO:0005125, GO:0008083, enzyme binding activity, several others.\\n\\nmechanism: these genes are involved in immune response cytokine activity. many of them encode for cytokine receptors, transcription factors, enzymes involved in immune system pathways processes. the enrichment of terms related to protein binding, including dna binding identical protein binding, may suggest that many of these genes act as transcriptional regulators in immune cells, coordinating the expression of genes involved in immune function. the enrichment of transporter activity may indicate that some of these genes are involved in cell migration or trafficking of immune cells to sites of inflammation or infection. additionally, the enrichment of terms related to enzyme activity may suggest that some of]][[GO:0004896, protein binding activity, GO:0003824, dna binding activity, rna binding activity, apoptosis. \\n\\nmechanism: these genes are involved in various cellular processes such as signaling and cytokine receptor activity, where they play a role in transmitting signals from the outside to the inside of the cell, as well as in regulating the immune system. they are also involved in enzyme activity, dna and rna binding activity, and apoptosis, playing a role in various pathways such as the regulation of gene expression and programmed cell death]]
HALLMARK_IL6_JAK_STAT3_SIGNALING-0[[GO:0005125, GO:0004896, protein kinase binding activity, GO:0006954, GO:0006955, GO:0007165]][[GO:0004896, GO:0004896, growth factor receptor binding activity]]
HALLMARK_IL6_JAK_STAT3_SIGNALING-1[[GO:0004896, interleukin binding activity, GO:0008009, GO:0001819, GO:0050778, GO:0098542, GO:0010604]][[GO:0005125, signaling receptor binding activity, GO:0001819, GO:0019221, GO:0009967, GO:0004896, GO:0050776]]
HALLMARK_INFLAMMATORY_RESPONSE-0[[GO:0005125, GO:0008009, identical protein binding activity, GO:0038023, GO:0006811]][[GO:0005125, GO:0004896, GO:0004930, GO:0002376, GO:0006954, GO:0008009]]
HALLMARK_INFLAMMATORY_RESPONSE-1[[GO:0004930, GO:0004896, enzyme binding activity, identical protein binding activity, GO:0007165, calcium ion binding activity, protease binding activity, transporter activity.\\n\\nmechanism: these genes are involved in various mechanisms related to cell signaling and transport. one hypothesis is that these genes may collectively contribute to the regulation of calcium levels and calcium-dependent signaling pathways, as well as cytokine-mediated signaling pathways involved in immune response]][[GO:0004896, GO:0004930, signaling receptor binding activity, identical protein binding activity, enzyme binding activity]]
HALLMARK_INTERFERON_ALPHA_RESPONSE-0[[GO:0005125, GO:0098542, GO:0046597, rna binding activity, identical protein binding activity]][[GO:0006955, GO:0019882, cytokines/chemokines, interferon-related genes, rna processing/editing]]
HALLMARK_INTERFERON_ALPHA_RESPONSE-1[[GO:0098542, GO:0050709, GO:0046597, GO:0045071, GO:0030501, GO:0002688, regulation of transcription]][[GO:0098542, GO:0045071, GO:0035458, GO:0071345, GO:0042590, GO:0006469, GO:0010604, GO:0046597, GO:0019221, GO:0045669, GO:0052548]]
HALLMARK_INTERFERON_GAMMA_RESPONSE-0[[GO:0004896, GO:0000981, identical protein binding activity, enzyme binding activity, GO:0042110, cell adhesion molecule binding activity, positive regulation of activated cd8-positive t cell proliferation, GO:0038187, GO:0061630, GO:0000166, GO:0004930, protein kinase binding activity, calcium ion binding activity, complement binding activity, GO:0004867, GO:0008009, integrin binding activity.\\n\\nmechanism: these genes predominantly function in the immune system and are related to the activation and proliferation of t cells, cytokine signaling, pattern recognition, and complement cascades. the enriched terms suggest an association with signaling cascades, receptor binding, enzyme activity, and immune response to pathogens]][[GO:0005125, GO:0008009, GO:0001216, enzyme binding activity, identical protein binding activity, protease binding activity, GO:0042803, rna binding activity, GO:0050852, GO:0061630]]
HALLMARK_INTERFERON_GAMMA_RESPONSE-1[[GO:0019882, GO:0045087, cytokine signaling, GO:0045321, antiviral defense]][[GO:0019882, cytokine signaling, antiviral defense]]
HALLMARK_KRAS_SIGNALING_DN-0[[calcium ion binding activity, atp binding activity, GO:0008511, GO:0004930, GO:0004888, GO:0016887, identical protein binding activity, protein kinase binding activity]][[GO:0003824, protein binding activity, GO:0000988, identical protein binding activity, ion binding activity.\\n\\nmechanism]]
HALLMARK_KRAS_SIGNALING_DN-1[[protein binding activity, calcium ion binding activity, atp binding activity, identical protein binding activity, GO:0008507, GO:0005337, GO:0043273, GO:0003924, GO:0015432]][[GO:0005488, GO:0003824, GO:0004930, GO:0000988, GO:0005509, GO:0005524, protein homodimerization activity.\\n\\nmechanism: the enriched terms suggest that these genes are involved in cellular regulation and signaling processes through binding and enzymatic activities, particularly involving calcium ions and atp. many genes also have transcription factor activity, indicating a role in gene expression regulation. g protein-coupled receptor activity is also overrepresented, suggesting a role in cellular signaling processes]]
HALLMARK_KRAS_SIGNALING_UP-0[[binding activity; enzyme activity; transcription activator activity. \\n\\nmechanism: these enriched terms suggest that the commonality among these genes is that they are involved in various types of binding and enzymatic activities, as well as regulating transcription. it is possible that these genes work together in regulatory pathways to bind to specific targets, catalyze reactions, modulate transcriptional activity in the cell]][[GO:0005515, enzyme binding activity, transcriptional regulation, ion binding activity, dna binding activity, GO:0004930, GO:0005125, identical protein binding activity]]
HALLMARK_KRAS_SIGNALING_UP-1[[GO:0005178, GO:0005515, GO:0005524, GO:0071345, GO:0043167, ubiquitin protein ligase binding. \\n\\nmechanism: the shared function of binding among the enriched terms suggests that these genes may play a role in mediating protein regulation and signal transduction pathways through protein-protein or protein-ligand interactions. the involvement in cellular response to cytokine stimulus may suggest a potential role in modulating immune responses]][[enzymatic activity, GO:0019901, binding activity\\n\\nmechanism: the enriched functions suggest that these genes may be involved in the regulation of cellular processes through protein-protein interactions, including enzymatic activities and binding activities. this could involve pathways such as signal transduction or gene expression regulation]]
HALLMARK_MITOTIC_SPINDLE-0[[microtubule binding activity, GO:0005096, actin filament binding activity, microtubule plus-end binding activity, identical protein binding activity, protein kinase binding activity, kinetochore binding activity, cytoskeletal protein binding activity, gamma-tubulin binding activity]][[microtubule binding activity, actin binding activity, GO:0005096]]
HALLMARK_MITOTIC_SPINDLE-1[[microtubule binding activity, GO:0007052, GO:0000226]][[GO:0008017, mitotic processes, GO:0000910, GO:0007018, spindle organization. \\n\\nmechanism: these genes play important roles in the regulation and organization of microtubules, which are key components of the cytoskeleton involved in cell division processes such as mitosis and cytokinesis. the enrichment of terms related to microtubule binding and regulation suggest that these genes may function together in a pathway that regulates the dynamics and organization of microtubules during these cellular processes. they may also be involved in microtubule-based movement, which is crucial for various cellular activities such as intracellular transport and cell migration]]
HALLMARK_MTORC1_SIGNALING-0[[binding activity, enzymatic activity, GO:0006412, GO:0023052, GO:0008152]][[GO:0005515, GO:0003723, enzymatic activity, structural constituent of cytoskeleton. \\n\\nmechanism: these genes likely play a role in cellular processes such as transcription, translation, protein folding, and cytoskeletal organization]]
HALLMARK_MTORC1_SIGNALING-1[[GO:0005515, enzyme activity. \\n\\nmechanism: the enriched terms suggest that these genes play a role in protein-protein interactions and enzymatic reactions, potentially involved in metabolic pathways or signal transduction cascades]][[GO:0006457, GO:0005783, ubiquitin-proteasome system, GO:0015031, GO:0030163]]
HALLMARK_MYC_TARGETS_V1-0[[ribosome binding activity; rna binding activity; translation initiation factor activity; protein folding chaperone activity\\n\\nmechanism: these genes are involved in different aspects of protein synthesis, such as ribosome binding, GO:0006413, and rna binding. they also contribute to protein folding processes as chaperones. the enrichment of these terms suggests that these genes function together to ensure proper protein synthesis and folding, which are vital to numerous cellular processes]][[GO:0003743, ribosome binding activity, rna binding activity, GO:0003735, protein folding chaperone activity, GO:0140713]]
HALLMARK_MYC_TARGETS_V1-1[[GO:0006396, GO:0003676, GO:0006457, ribosomal structural activity. \\n\\nmechanism: these genes likely function together in the post-transcriptional regulation of gene expression, from rna splicing to translation initiation and ribosome assembly]][[GO:0000394, GO:0006413, GO:0003723, GO:0003676, GO:0006457, ribosome structure\\n\\nmechanism: these genes are involved in rna processing, including mrna splicing and translation initiation, as well as binding to rna and nucleic acids. some genes also play roles in protein folding and ribosome structure. the underlying biological mechanism or pathway is likely related to rna processing and regulation of gene expression]]
HALLMARK_MYC_TARGETS_V2-0[[GO:0006364, rna binding activity, GO:0046982, mitochondrial function, GO:0051726]][[GO:0006364, GO:0042273, snorna binding activity, GO:0005730, rna binding activity]]
HALLMARK_MYC_TARGETS_V2-1[[GO:0006364, snorna binding activity, GO:0042273, rna binding activity, GO:0005730]][[GO:0006364, ribosomal biogenesis, rna binding activity, GO:0005730]]
HALLMARK_MYOGENESIS-0[[cytoskeletal protein binding activity, actin binding activity, atp binding activity, calcium ion binding activity, identical protein binding activity, enzyme binding activity, GO:0042803]][[actin binding activity, calcium ion binding activity, atp binding activity, identical protein binding activity, cytoskeletal protein binding activity, enzyme binding activity, UBERON:0005090]]
HALLMARK_MYOGENESIS-1[[actin binding activity, cytoskeletal protein binding activity, calcium ion binding activity, myosin binding activity, atp binding activity, kinase binding activity, muscle structure development. \\n\\nmechanism: these genes are involved in muscle structure and function as they encode proteins that bind to actin, myosin, and other cytoskeletal proteins to form the muscle fibers. they also bind to calcium ions and atp, which are necessary for muscle contraction, and contribute to the development of muscle structure]][[GO:0006936, GO:0030036, GO:0006600, GO:0032956, regulation of muscle contraction.\\n\\nmechanism: these genes are involved in the regulation of muscle contraction and actin cytoskeleton organization, likely through their roles in calcium ion binding, myosin light chain kinase activity, and actin filament binding. several of the genes are also involved in creatine metabolism, which is important for energy generation in muscle tissues]]
HALLMARK_NOTCH_SIGNALING-0[[GO:0007219, GO:0016567]][[GO:0007219, GO:0016567, GO:0006357, GO:0051247, GO:0016055, scf-dependent proteasomal ubiquitin-dependent protein catabolic process, cyclin-dependent protein kinase holoenzyme complex]]
HALLMARK_NOTCH_SIGNALING-1[[\"notch signaling pathway,\" \"protein ubiquitination,\" \"negative regulation of cell differentiation,\" \"regulation of dna-templated transcription.\"]][[GO:0007219, GO:0016567]]
HALLMARK_OXIDATIVE_PHOSPHORYLATION-0[[GO:0022900, GO:0006119, mitochondrial metabolism, GO:0006637, ketone body metabolism.\\n\\nmechanism and]][[GO:0009055, ubiquitin protein ligase binding activity, MESH:D014451, rna binding activity, GO:0042803, metal ion binding activity.\\n\\nmechanism and]]
HALLMARK_OXIDATIVE_PHOSPHORYLATION-1[[GO:0005746, GO:0006118, GO:0006754, MESH:D009245, MESH:D003576, GO:0016467, flavin adenine dinucleotide]][[mitochondria\\n- atp synthesis\\n- respiratory chain complex\\n- electron transfer\\n- oxidoreductase activity\\n- iron-sulfur cluster binding\\n\\nmechanism: these genes are involved in the regulation of metabolic processes and energy production in the mitochondria. they play important roles in cellular respiration, which involves the conversion of nutrients into energy necessary for cellular activities. the enriched terms suggest that these genes are closely related to the function of the mitochondrial respiratory chain complex and atp synthase, both of which are necessary for energy production in the form of atp. additionally, several of these genes are involved in electron transfer and oxidoreductase activity, which are also important in metabolic processes that lead to energy production. finally, there is a common theme of iron-sulfur cluster binding, which suggests a common mechanism in the regulation of metabolic processes and energy production]]
HALLMARK_P53_PATHWAY-0[[GO:0042981, protein binding activity, GO:0003700]][[GO:0003677, GO:0005515, GO:0003824, GO:0000988, growth factor activity. \\n\\nmechanism: these genes likely play roles in regulating transcription, protein-protein interactions, metabolism, and growth factor signaling pathways]]
HALLMARK_P53_PATHWAY-1[[GO:0000988, rna binding activity, enzyme binding activity, identical protein binding activity, dna binding activity, histone binding activity]][[GO:0005515, dna binding activity, GO:0016301]]
HALLMARK_PANCREAS_BETA_CELLS-0[[GO:0006006, GO:0030073, GO:0006357]][[GO:0042593, GO:0050796, GO:0046326, GO:0006006]]
HALLMARK_PANCREAS_BETA_CELLS-1[[GO:0006006, GO:0030073, glucose homeostasis.\\n\\nmechanism]][[GO:0030073, GO:0006006, transcriptional regulation, transcription factor binding activity, rna polymerase ii-specific dna binding activity, GO:0000122, positive regulation of transcription by rna polymerase ii. \\n\\nmechanism and]]
HALLMARK_PEROXISOME-0[[GO:0006629, GO:0006631, GO:0006810, GO:0003824, GO:0005501, steroid binding.\\n\\nmechanism and]][[GO:0001676, GO:0043574, GO:0008203, GO:0006633, lipid binding activity, atp binding activity, GO:0016491]]
HALLMARK_PEROXISOME-1[[GO:0004467, GO:0016401, GO:0047676, GO:0031957, peroxisome targeting sequence binding activity, GO:0006633]][[GO:0006629, mitochondrial function, GO:0006281]]
HALLMARK_PI3K_AKT_MTOR_SIGNALING-0[[GO:0004672, cytoskeleton structure, GO:0006629, protein binding activity]][[GO:0004672, g protein-coupled receptor binding activity, transcription factor binding activity, enzyme binding activity, GO:0007166, GO:0035556, GO:0032007, GO:0010971, negative regulation of vasc, negative regulation of nitrogen com, actin filament binding activity, cytoskeletal protein binding activity]]
HALLMARK_PI3K_AKT_MTOR_SIGNALING-1[[GO:0006468, intracellular signaling, GO:0016301, GO:0016791, enzyme binding activity. \\n\\nmechanism: the enriched terms suggest that many of the genes are involved in regulatory processes related to protein modification through phosphorylation and dephosphorylation. this could implicate several signaling pathways, such as mapk, pi3k/akt, and nf-kappab pathways]][[GO:0006468, GO:0035556, GO:0016301, enzyme binding activity, GO:0004672, identical protein binding activity, scaffold protein binding activity]]
HALLMARK_PROTEIN_SECRETION-0[[GO:0007030, GO:0006888, retrograde transport, vesicle recycling, GO:0090110, GO:0006891, GO:0008333, GO:0006893, GO:0048488, GO:0016192, vesicle recycling]][[GO:0007030, GO:0048193, GO:0090110, GO:0006888, retrograde transport, vesicle recycling, GO:0034260, negative regulation of autophagosome formation and maturation, GO:1905604, GO:1905280, GO:0002091, GO:0009967]]
HALLMARK_PROTEIN_SECRETION-1[[GO:0048193, GO:0032456, GO:0035493, GO:0006891, GO:0070836]][[GO:0006888, GO:0048193, GO:0006891, GO:0034067, snare complex assembly.\\n\\nmechanism and]]
HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0[[GO:0098869, GO:0006750, GO:0042744, oxidation-reduction process, GO:0006979]][[cellular redox homeostasis, GO:0006979, protein disulfide reduction, GO:0006749, GO:0003954, GO:0004601, GO:0006826, GO:0016209, MESH:D015227]]
HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1[[GO:0045454, GO:0006979, GO:0016209, GO:0004602, GO:0004784, GO:0004601, GO:0003954, GO:0032981]][[GO:0045454, GO:0006979]]
HALLMARK_SPERMATOGENESIS-0[[GO:0005515, GO:0005524, GO:0042802, GO:0016301, GO:0000166]][[GO:0005515, GO:0016301, GO:0051726, GO:0010467]]
HALLMARK_SPERMATOGENESIS-1[[identical protein binding activity, protein folding chaperone binding activity, GO:0004672, rna binding activity, chromatin binding activity, atp binding activity, nucleotide binding activity, GO:0004722, GO:0061630, calcium ion binding activity, rna polymerase iii binding activity, cytokine binding activity, GO:0004930, integrin binding activity, many others]][[GO:0005515, GO:0008047, atp binding activity]]
HALLMARK_TGF_BETA_SIGNALING-0[[GO:0007178, GO:0010862, GO:0010991, GO:0045668, GO:0030512, GO:0010604, GO:0009967]][[GO:0060395, GO:0006357, GO:0010604, GO:0090101, GO:0045668, establishment of sert, positive regulation of vascular associated smooth muscle cell proliferat, several others]]
HALLMARK_TGF_BETA_SIGNALING-1[[signal transduction; regulation of gene expression; transcription regulation; protein phosphorylation; smad protein signal transduction.\\n\\nmechanism: these genes are involved in various aspects of signal transduction, including regulation of gene expression, transcription regulation, MESH:D016212, where they regulate transcription of target genes. genes in this list may activate or inhibit smad signaling and affect downstream transcriptional regulation. additionally, many of these genes play roles in other signaling pathways and regulatory processes, such as the wnt signaling pathway and negative regulation of protein degradation]][[GO:0005024, GO:0046332, GO:0009967, GO:0006357, GO:0000122, GO:0007166, GO:0010604, nucleic acid binding activity]]
HALLMARK_TNFA_SIGNALING_VIA_NFKB-0[[GO:0005125, GO:0003700, enzyme binding activity, GO:0006955]][[GO:0003700, rna polymerase ii-specific; cytokine activity; protein binding activity.\\n\\nmechanism: these genes are involved in the regulation of transcription and cytokine activity, likely playing a role in immune responses and cellular differentiation. they are involved in binding to dna and rna polymerases to regulate the expression of genes, as well as in the production and regulation of cytokines and growth factors that play a role in cell signaling and differentiation]]
HALLMARK_TNFA_SIGNALING_VIA_NFKB-1[[cytokine activity; dna-binding transcription factor activity; enzyme binding activity; phosphatidylinositol-3,4-bisphosphate binding activity; g protein-coupled receptor activity.\\n\\nmechanism: the enriched terms suggest that the genes on the list are involved in signaling pathways that regulate gene expression and cellular responses through cytokine receptors, GO:0035556, and various enzymatic activities. these pathways play essential roles in several biological processes, including immune responses, cell differentiation and development, cell survival death]][[GO:0005125, GO:0008009, GO:0001216, GO:0006955, interleukin-12 alpha subunit binding activity, GO:0004707, protein kinase binding activity, GO:0001817, GO:0002682, smad binding activity, transcription factor binding activity]]
HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0[[protein folding and processing, GO:0015031, GO:0003723, GO:0043022, GO:0003743]][[protein folding and chaperone activity, rna binding and transcriptional regulation, rna processing and degradation]]
HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1[[rna binding activity, protein folding chaperone binding activity, ribosome binding activity, histone binding activity, dna-binding transcription factor binding activity, ubiquitin protein ligase binding activity]][[GO:0003723, GO:0051087, GO:0090304, endoplasmic reticulum stress response pathway]]
HALLMARK_UV_RESPONSE_DN-0[[extracellular matrix organization; growth factor signaling; regulation of transcription, dna-templated; positive regulation of protein kinase activity; organic acid metabolic process.\\n\\nmechanism: these genes are involved in extracellular matrix structural constituent, growth factor signaling, GO:0000988, GO:0005515, and nucleotide binding. this suggests that they may be involved in the regulation of gene transcription, cellular growth and differentiation, and the organization of extracellular matrices. a hypothesis for the underlying biological mechanism or pathway is that these genes may be involved in the regulation of extracellular matrix formation and growth factor signaling pathways, which then contribute to cellular differentiation and growth. additionally, the binding of proteins with transcription factor activity and nucleotide binding activity suggests that these genes are involved in the regulation of gene transcription, which may have downstream effects on cellular function and behavior]][[GO:0005201, identical protein binding activity, enzyme binding activity, smad binding activity]]
HALLMARK_UV_RESPONSE_DN-1[[GO:0005201, GO:0005178, identical protein binding activity, protease binding activity, calcium binding, platelet-derived growth factor binding activity]][[GO:0005201, GO:0005515, GO:0016563, GO:0005102]]
HALLMARK_UV_RESPONSE_UP-0[[enzyme binding activity, protein kinase binding activity, GO:0042803, rna binding activity, atp binding activity, identical protein binding activity, ubiquitin protein ligase binding activity, GO:0001228, ion binding activity, g protein-coupled receptor binding activity, dna polymerase binding activity, peptide hormone receptor binding activity. \\n\\nmechanism: these genes are involved in a variety of molecular activities, including enzyme activity, protein binding, and transcription factor activity. one potential underlying biological mechanism is the regulation and interaction of proteins in various cellular processes]][[enzyme binding activity, GO:0003700, protein kinase binding activity, identical protein binding activity, rna binding activity, atp binding activity, ubiquitin protein ligase binding activity]]
HALLMARK_UV_RESPONSE_UP-1[[atp binding activity, GO:0001216, identical protein binding activity, rna binding activity, protein kinase binding activity, cysteine-type endopeptidase activity involvement in apoptotic signaling, GO:0004602, histone binding activity, GO:0030594, glucagon receptor binding activity, GO:0004499, peptide hormone receptor binding activity, gtp binding activity, more]][[enzyme binding activity, GO:0006508, protein phosphatase binding activity, GO:0004725]]
HALLMARK_WNT_BETA_CATENIN_SIGNALING-0[[GO:0090090, regulation of transcription, GO:0000981, histone deacetylase binding activity, ubiquitin protein ligase binding activity, notch binding activity, protein kinase binding activity, GO:0003713, identical protein binding activity]][[GO:0060070, transcription regulation, MESH:D012319, transcription activator, beta-catenin complex, GO:0007219]]
HALLMARK_WNT_BETA_CATENIN_SIGNALING-1[[GO:0060070, GO:0031398, GO:0090090, GO:0031397, GO:0030162]][[GO:0060070, GO:0010468]]
T cell proliferation-0[[GO:0050776, intracellular signaling, GO:0008037, GO:0009617, GO:0008284, GO:0005125, protein kinase binding activity, identical protein binding activity]][[GO:0050852, GO:0005125, interleukin-2 receptor binding activity, negative regulation of peptid, intracellular signal transduction\\n\\nmechanism: the genes analyzed in this study are primarily involved in signaling and receptor binding activities. this suggests that these genes may play an important role in the communication between cells and regulation of immune response. \\n\\n t cell receptor signaling pathway, cytokine activity, interleukin-2 receptor binding activity, negative regulation of peptid..., and intracellular signal transduction]]
T cell proliferation-1[[GO:0042110, GO:0001816, GO:0010468, GO:0050671, GO:0001819, GO:0001933, GO:0045840, protein kinase binding activity, GO:0004697, GO:0004911, GO:0004896, GO:0097190, GO:0007005, GO:0043065, GO:0042100, GO:0004931]][[GO:0050863, GO:0001819, GO:0006468, GO:0043066, GO:0002687, GO:0030890, GO:0006879, GO:0010468]]
Yamanaka-TFs-0[[transcription regulation, GO:0010468, GO:0045944, GO:0003700, cellular differentiation]][[transcriptional regulation, GO:0010467, GO:0003700, GO:0009889, GO:0019219]]
Yamanaka-TFs-1[[GO:0010468, transcriptional regulation, GO:0003700, GO:0001714, GO:0045944]][[GO:0010467, transcription regulation, dna binding activity, rna polymerase ii-specific, GO:0010468, transcription cis-regulatory region binding activity]]
amigo-example-0[[GO:0030198, GO:0007165, GO:0007596]][[GO:0007160, GO:0030198, GO:0030199, GO:0008034]]
amigo-example-1[[GO:0005178, GO:0005201, GO:0008083, platelet-derived growth factor binding activity, GO:0030199]][[GO:0007160, GO:0030199, GO:0030198, GO:1902533, GO:0010604, GO:0030334]]
bicluster_RNAseqDB_0-0[[GO:0005515, GO:0005216, transcriptional regulation, ubiquitin-protein ligase activity]][[GO:0003700, identical protein binding activity, protein kinase binding activity, actin binding activity, sequence-specific double-stranded dna binding activity, metal ion binding activity, calcium ion binding activity, chromatin binding activity, rna binding activity]]
bicluster_RNAseqDB_0-1[[metal ion binding activity, calcium ion binding activity, GO:0000981, g protein-coupled receptor binding activity, enzyme binding activity, sequence-specific double-stranded dna binding activity, cytoskeletal protein binding activity, GO:0061630]][[binding activity, GO:0003700, GO:0046872, GO:0019904, GO:0061630]]
bicluster_RNAseqDB_1002-0[[GO:0006936, GO:0030239, GO:0043502, GO:0051015, GO:0005523]][[GO:0006936, GO:0043502, GO:0016567]]
bicluster_RNAseqDB_1002-1[[GO:0003009, GO:0060048, GO:0010628, actin filament binding activity, GO:0008307]][[GO:0006936, GO:0003009, GO:0016567, ion channel activity.\\n\\nmechanism: these genes likely play a role in muscle contraction and structure, possibly through the regulation of ion channels and protein ubiquitination]]
endocytosis-0[[GO:0006897, GO:0015031, GO:0006898]][[GO:0006897, GO:0007165, cellular adhesion, GO:0006869, GO:0030163, GO:0007009]]
endocytosis-1[[GO:0006897, lysosomal function, GO:0038023, GO:0006955, GO:0008152]][[GO:0006897, membrane traffic, GO:0015031]]
glycolysis-gocam-0[[GO:0006006, GO:0005975, GO:0019725, GO:0008104, GO:0070062, GO:0005634]][[GO:0006096, GO:0005975, GO:0006000, metabolic homeostasis]]
glycolysis-gocam-1[[GO:0006096, GO:0005975, GO:0006000, cell development.\\n\\nhypotheses: the enriched terms suggest that these genes are involved in the glycolysis pathway, contributing to carbohydrate metabolic processes and the production of energy for cellular development. specifically, fructose metabolic processes are enriched, indicating that the genes may play a role in the conversion of fructose to glucose during glycolysis]][[GO:0006096, GO:0005975, GO:0006002, GO:0005945]]
go-postsynapse-calcium-transmembrane-0[[GO:0006816, GO:0007268, GO:0005245, GO:0098978, GO:0004972]][[GO:0006816, GO:0005245, GO:0008066, GO:0005892]]
go-postsynapse-calcium-transmembrane-1[[GO:0005509, GO:0006836, GO:0001505, GO:0016079, GO:0035235, GO:0007186, GO:0071318]][[GO:0019722, voltage-gated calcium channel, GO:0051480, GO:0008066, GO:0017146, GO:0007268, GO:0051899, g-protein coupled receptor signaling pathway]]
go-reg-autophagy-pkra-0[[GO:0006468, GO:0010604, GO:0038202, GO:0032006, GO:0016241, positive regulation of cyclin-dependent protein serine/threonine kinase activity.\\n\\nmechanism and]][[GO:0006468, GO:0035556, GO:0031929, GO:0097190, kinase activity regulation, GO:0010604]]
go-reg-autophagy-pkra-1[[intracellular signaling, pathway regulation, GO:0006915, GO:0004672, GO:0006468, GO:0010604, GO:0045859]][[GO:0035556, protein kinase activity regulation, GO:0010604, GO:0038202, GO:0032008, GO:0045859, apoptosis signaling pathway, chromatin binding activity]]
hydrolase activity, hydrolyzing O-glycosyl compounds-0[[GO:0046479, GO:0006516, GO:0006032, GO:0030214]][[GO:0016052, GO:0006516, GO:0006032, GO:0030214]]
hydrolase activity, hydrolyzing O-glycosyl compounds-1[[GO:0005975, MESH:D054794, glycan catabolism, GO:0006516, GO:0019377, GO:0006032, GO:0006004]][[GO:0016052, GO:0030214, GO:0006516, GO:0019377, GO:0006032, GO:0006491, GO:0006517, mannose trimming involved in glycoprotein erad pathway.\\n\\nmechanism: one potential underlying biological mechanism is the regulation of cell surface and extracellular matrix composition, as well as the breakdown and recycling of molecules within these structures. glycosidases play a key role in breaking down complex carbohydrates into smaller subunits, which can then be reassembled into new molecules. the ability to break down specific types of carbohydrates, such as hyaluronic acid and chitin, may also be important for cellular processes such as cell migration and host defense]]
ig-receptor-binding-2022-0[[antigen binding activity, immunoglobulin receptor binding activity, GO:0002253]][[immunoglobulin receptor binding activity, antigen binding activity]]
ig-receptor-binding-2022-1[[GO:0002253, GO:0098542, GO:0019731, GO:0006959, GO:0002377, GO:0051130, GO:0045657]][[GO:0006955, GO:0006952, antigen binding activity]]
meiosis I-0[[GO:0061982, GO:0007131, GO:0007129, GO:0000712, GO:0000724]][[homologous chromosome pairing, GO:0042138, GO:0000706, GO:0007131, GO:0000724, GO:0000712, GO:0000795]]
meiosis I-1[[meiotic recombination, GO:0035825, GO:0006302]][[meiotic recombination, GO:0006302, GO:0035825, chromosomal segregation, GO:0007130]]
molecular sequestering-0[[molecular sequestering, protein binding activity, transport of metal ions, GO:0048523, response to infection and stress, GO:0010468, GO:0019722, regulation of transcription]][[GO:0140313, GO:0140311, identical protein binding activity, GO:0060090, ubiquitin protein ligase binding activity, GO:0016567]]
molecular sequestering-1[[GO:0140311, GO:0010468, GO:0031398, GO:0051238]][[GO:0010468, GO:0042742, GO:0045185, GO:0002376, GO:0009267, GO:0032387, GO:0035556]]
mtorc1-0[[binding activity, enzymatic activity, GO:0006412, GO:0023052, GO:0008152]][[GO:0005515, GO:0003723, enzymatic activity, structural constituent of cytoskeleton. \\n\\nmechanism: these genes likely play a role in cellular processes such as transcription, translation, protein folding, and cytoskeletal organization]]
mtorc1-1[[GO:0005515, GO:0042802, GO:0019899, GO:0043167, GO:0005524, GO:0031625, GO:0003723, GO:0003677, GO:0097159, GO:0017076, GO:0051015, GO:0042802, GO:0016491, phosphoprotein binding activity, GO:0005215, GO:0006793, GO:0044237, GO:0006457, GO:0003677, GO:0008380]][[GO:0005515, GO:0003824, GO:0005215]]
peroxisome-0[[GO:0017038, peroxisomal biogenesis, GO:0140036, atp binding and hydrolysis activity, lipid binding activity]][[peroxisome biogenesis, peroxisome matrix targeting, GO:0017038]]
peroxisome-1[[GO:0007031, GO:0016558, GO:0005778, peroxisomal biogenesis disorder, GO:0008611, lipid binding activity, atp binding activity, GO:0016887, ubiquitin-dependent protein binding activity, enzyme binding activity]][[peroxisome biogenesis, GO:0017038, GO:0005778, ubiquitin-dependent protein binding activity, atp binding activity, GO:0016887]]
progeria-0[[GO:0006259, GO:0006325, GO:0033554, GO:0006281, GO:0007568]][[GO:0006259, GO:0006325, GO:0033554]]
progeria-1[[GO:0006281, GO:0006950, GO:0090398, GO:0000723, chromatin condensation]][[GO:0006281, GO:0000723, GO:0007568]]
regulation of presynaptic membrane potential-0[[GO:0015276, GO:0099505, GO:0060078, GO:0071805, GO:0035725, GO:0035235]][[GO:0007214, GO:0022849, GO:0005242, GO:0035235, GO:0015276, GO:0071805, GO:0005244]]
regulation of presynaptic membrane potential-1[[GO:0007214, GO:0007215, GO:0006811, GO:0006836, GO:0007268]][[GO:0006811, GO:0007268, membrane potential regulation, GO:0008066, GO:0007214]]
sensory ataxia-0[[GO:0042552, GO:0007422, MONDO:0005071, GO:0022011, MONDO:0005244]][[MONDO:0015626, GO:0042552, GO:0007422, GO:0006457, GO:0007600, nucleic acid metabolism, mitochondrial function]]
sensory ataxia-1[[GO:0007399, GO:0042552, mitochondrial metabolism, GO:0030163, protein regulation, GO:0071260]][[GO:0007399, MONDO:0015626, GO:0042552, UBERON:0000010, mitochondrial dysfunction, protein ubiquitination.\\n\\nmechanism]]
term-GO:0007212-0[[GO:0007186, GO:0007212]][[GO:0007212, GO:0007190, calcium ion regulation, g protein-coupled receptor pathway]]
term-GO:0007212-1[[GO:0007212, GO:0007186, GO:0051480, GO:0004016, GO:0006469, GO:0050821, GO:0060828, GO:0007220, GO:0034205, GO:0006508, GO:0046325, GO:1904227, GO:0051247, GO:0015171, GO:0015108]][[GO:0007186, GO:0004952, GO:0004016, GO:0051480, negative regulation of glycogen synthase activity, GO:0004672, GO:0019538, GO:0006468]]
tf-downreg-colorectal-0[[dna-binding transcription factor, rna polymerase ii-specific transcription regulation, GO:0000122, GO:0045944, GO:0006355]][[GO:0001216, rna polymerase ii transcription regulatory region sequence-specific dna binding activity, GO:0045944, GO:0000122, GO:0006355, transcription factor binding activity, nucleic acid binding activity, chromatin binding activity, GO:0003713]]
tf-downreg-colorectal-1[[GO:0000988, GO:0006355, GO:0045893, GO:0045892, dna-binding, GO:0003702]][[GO:0003700, GO:0006355, GO:0010468, GO:0006337]]
text-davinci-003narrative_synopsisEDS-0[[connective tissue formation and repair, protein binding and folding, GO:0006955, GO:0042060, GO:0006024]][[GO:0032964, collagen fiber formation, extracellular matrix maturation, transcriptional regulation, procollagen protein, MESH:D006025, metalloproteinase, proteolytic processing, peptidyl prolyl cis-trans isomerase, MESH:M0465019, tumor-rejection antigen, sulfotransferase, transmembrane protein, beta-1,3 galactosyltransferase]]
EDS-1[[collagen maturation, GO:0006024, transcriptional regulation, GO:0006829]][[GO:0006486, extracellular matrix remodeling, collagen production, GO:0061448, immunity response, GO:0006508, tumor rejection, MESH:M0465019, MESH:D008565, transcriptional repressor, peptidyl-prolyl isomerase, complement system, GO:0004226, peptidase s1]]
FA-0[[GO:0006281, GO:0035825, GO:0016310, nucleoprotein complex assembly, formation of nuclear foci, double-strand dna repair, holliday junction resolution, function in tumor suppression, reca/rad51-related protein family, dna lesions, structural specific endonucleases, rad51 family, cellular responses to replication fork failure, brc motif]][[GO:0006281, genome maintenance, MESH:D004249, nucleoprotein complex, GO:0035825, double-strand dna repair, holliday junction resolution, monoubiquinated, MESH:D051135, nuclear foci, structure-specific endonucleases, MESH:D051135, recq deah helicase, tumor suppression, ssdna-binding proteins]]
FA-1[[GO:0006281, GO:0035825, monoubiquitination, holliday junction resolution, rad51 binding]][[GO:0006281, nucleoprotein complex, GO:0035825, dna lesion, MESH:M0443450, fanconi anemia complementation group (fanc), GO:0006302]]
HALLMARK_ADIPOGENESIS-0[[GO:0006629, GO:0006633, GO:0022900, GO:0005739, MESH:D000975, GO:0045333, MESH:D010084, acyltransferase, carboxylase, acyl-coenzyme a synthetase, ubiquitin protease, MESH:C021451, MESH:D010743, oxidoreductase, plasma lipase, hydratase]][[GO:0010467, GO:0140657, GO:0006468, ubiquitin-mediated degradation, GO:0051726, GO:0005525, GO:0006839, GO:0006118, GO:0006119, MESH:D004789, enzyme inhibition, GO:0016491, GO:0016482, GO:0005515, GO:0006629, GO:0036211, ubiquitinylation]]
HALLMARK_ADIPOGENESIS-1[[GO:0005515, transcription regulation, atpase, MESH:D020558, transcript processing, protein transduction, MESH:D014451, GO:0044237, energy production, GO:0006508]][[atp production, GO:0005746, GO:0006118, GO:0030497, rna/dna binding, GO:0015031, MESH:D054875, GO:0016310, GO:0008017, GO:0006869]]
HALLMARK_ALLOGRAFT_REJECTION-0[[immune/cytokine responses, GO:0006412, GO:0006351, cell surface signaling, receptor activation, MESH:D054875, MONDO:0002123, GO:0005524]][[cell signalling, cytokine production/regulation, chemokine production/regulation, antimicrobial defence, plasma protein regulation, immune regulation, inflammatory regulation, transcriptional regulation, GO:0004672, GO:0008233, glycoprotein activity, receptor protein activity]]
HALLMARK_ALLOGRAFT_REJECTION-1[[GO:0006412, cellular regulation, GO:0008152, cell signaling, GO:0006351, immunoregulation, stability, GO:0005515, GO:0016310, GO:0010467, g-protein coupled receptor, transmembrane protein, t-cell development]][[integrin, cytokine, g-protein coupled receptor, MESH:D007372, MESH:D018124, MESH:D008562, MESH:D011494, chemokine, transmembrane receptor, GO:0007165, transcriptional regulation, GO:0006412, GO:0006955]]
HALLMARK_ANDROGEN_RESPONSE-0[[MESH:D011494, GO:0000981, GO:0005530, adhesion molecule, GO:0016538, MESH:D016601, protein tyrosine phosphatase, g protein, serine/threonine protein kinase, MESH:D008565, MESH:D006657, ubiquitin ligase, MESH:C052123, microtubule-associated protein, atp-binding cassette, alpha/beta-hydrolase, integrin alpha-chain, signal transducion, protein inhibitor of activated stat]][[GO:0005524, GO:0006351, GO:0016310, MESH:D011494, protein tyrosine phosphatase, GO:0065007, GO:0005515, hydrolase, ribosomal s6 kinase, GO:0016192, regulatory subunit, acetyltransferase, modulation, GO:0005509, GO:0005783, GO:0000981, GO:0003723, n-myc downregulated, polypeptide, GO:0016125, MESH:D006657, protein inhibitor, MESH:D051116, structural fibre, disulfide oxidoreductase, adenine dinucleotide, non-sterol metabolism, calcium-induced, GO:0042593]]
HALLMARK_ANDROGEN_RESPONSE-1[[GO:0008283, GO:0006351, GO:0007165, structural components, metabolism of proteins, GO:0006629, GO:0005975, GO:0007155, binding activity, GO:0010467, GO:0003677, MESH:D011494, oxidoreductase, anchoring kinase to microtubules, GO:0005102, molecule transport, MESH:D010455]][[transcriptional regulation, GO:0004672, GO:0005515, GO:0003723, GO:0007165, proteolytic enzyme activity, GO:0003677]]
HALLMARK_ANGIOGENESIS-0[[this is a list of genes involved in a variety of pathways and processes related to cell adhesion, GO:0040007, GO:0008152, and other physiologic functions. the terms “cell adhesion”, “cell signaling”, “extracellular matrix”, “transcriptional regulation”, and “cell cycle progression and differentiation” are all enriched among this group of genes. a hypothesis of the underlying biological mechanism at work is that these genes work together to promote cell growth and regulation, that many of these genes interact to achieve greater cellular complexity]][[GO:0042157, GO:0050817, GO:0007599, MESH:D016207, MESH:D018925, receptors, transporters, secreted extracellular matrix proteins, GO:0004868, MESH:D011509, GO:0007155, GO:0016477, GO:0023052, GO:0008283, GO:0006915, transcriptional regulation, tissue development and regeneration, GO:0006955]]
HALLMARK_ANGIOGENESIS-1[[GO:0007155, extracellular matrix remodeling, GO:0007165, protease inhibition, transcriptional regulation]][[cell-cell interactions, cell-matrix interactions, extracellular matrix production, processing of proteoglycans and glycoproteins]]
HALLMARK_APICAL_JUNCTION-0[[GO:0005207, GO:0007155, calcium-dependent proteins, MESH:D008565, intronless proteins, intracellular scaffolding proteins, fibrillin proteins, signaling receptors, MESH:D051193, MESH:D003598, tubulin proteins, type ii membrane proteins, MESH:D006023]][[integrin, GO:0008014, GO:0005530, MESH:C119025, map kinase, protein tyrosine kinase, guanine nucleotide binding protein, MESH:D020558, act]]
HALLMARK_APICAL_JUNCTION-1[[GO:0007155, GO:0007165, actin binding and assembly, membrane localization, ecm protein binding and assembly]][[GO:0007155, GO:0023052, scaffolding, cytoskeleton maintenance, GO:0031012, MESH:D016023, MESH:D057167, MESH:C119025, MESH:D011494, GO:0008014]]
HALLMARK_APICAL_SURFACE-0[[GO:0007160, GO:0007165, MESH:D008565, transcriptional coactivation, signal recognition, GO:0055085, GO:0006898]][[GO:0007155, GO:0006457, GO:0007154, GO:0006898, gpi-anchored cell surface proteins, cation transport atpase, transcriptional coactivation, interleukin signaling, hormone-dependence, MESH:D019812, heparin-binding, GO:0007160]]
HALLMARK_APICAL_SURFACE-1[[GO:0007160, cell-matrix interactions, carbohydrate binding activity, GO:0007155, GO:0038023, GO:0007165, GO:0008284, GO:0048681, GO:0030506, protein tyrosine kinase, sh2 domain binding activity, sh3 domain binding activity]][[cell signal transduction, GO:0007160, GO:0006457, GO:0030308, ligand binding, cell-surface glycoprotein, cation transmembrane transporter, growth arrest, MESH:D051246, transmembrane protein, regulatory subunit, membrane-bound glycoprotein, ammonium transmembrane transporter, cell surface receptor, insulin-regulated facilitative glucose transporter, cell surface adhesion molecule, GO:0140326, glycosylphosphatidylinositol-anchored protein]]
HALLMARK_APOPTOSIS-0[[GO:0006915, cytoplasmic signaling, transcriptional regulation, GO:0005515, cellular organization]][[GO:0006915, transcriptional regulation, GO:0003677, tnf receptor superfamily, bcl-2 protein family]]
HALLMARK_APOPTOSIS-1[[cell death processes, GO:0023052, cytoplasmic proteins, MESH:M0015044, MESH:D015533, MESH:D004798, toxin removal, GO:0005102]][[the genes summarized are involved in a wide range of processes, including apoptosis, tumor suppression, inflammation, thioredoxin binding, cytoplasmic protein and membrane glycoprotein regulation, dna topoisomerase and transcriptional activation. the commonalities that emerge from the enrichment test point to a specific biological pathway known as cell death regulation and signal transduction. this involves the interconnected network of genes that regulate apoptosis and maintain genetic stability, as well as others involved in the modulation of immune response pathways. enriched terms include apoptosis, cytoplasmic protein regulation, transcriptional regulation, tumor suppression, GO:0006954, MESH:D004264, thioredoxin binding, membrane glycoprotein regulation, transcriptional coactivation, death agonist, GO:0048018, serine/threonine phosphatase, voltage-dependent anion channel, MESH:D006136, class-1 polypeptide chain release factor, proapoptotic, nf-kappa-b.\\n\\nsummary: genes related to cell death regulation signal transduction pathways.\\nmechanism: interconnected network of genes that regulate apoptosis maintain genetic stability, as well as those involved in the modulation]]
HALLMARK_BILE_ACID_METABOLISM-0[[atp-binding, GO:0006810, GO:0004768, MESH:D010084, enzyme catalysis, GO:0000981]][[GO:0006629, atp binding cassette, MESH:M0011631, GO:0005490, peroxin, gamma-glutamylcysteine synthetase, GO:0050632, MESH:D002785, flavoenzymes, GO:0042446, GO:0016209]]
HALLMARK_BILE_ACID_METABOLISM-1[[GO:0015031, GO:0006412, GO:0006629, MESH:D010084, hormone regulation, transcription regulation, GO:0006805, calcium binding, GO:0005524, MESH:D005982, GO:0008203, MESH:M0011631, sulfate conjugation, 2-hydroxyacid oxidase, MESH:D000214, MESH:D000215, coenzyme a ligase, natriuretic peptide, peroxisome biogenesis, tgf-beta ligand, adrenal steroid synthesis, nuclear receptor, copper zinc binding, GO:0050632, MESH:D012319, gamma-glut]][[GO:0006629, GO:0006810, oxidation, bile acids synthesis, GO:0006790, GO:0005777, oxidative stress response]]
HALLMARK_CHOLESTEROL_HOMEOSTASIS-0[[MESH:D008565, MONDO:0018815, acetoacetyl-coa thiolase, cytosolic enzyme, actin isoforms, activation transcription factor (creb), annexin family, fructose-biphosphate aldolase, immunoglobulin superfamily, g-protein coupled receptor (gpcr), homotetramer, hydratase/isomerase superfamily, MESH:C022503, mal proteolipid, MESH:M0476528, sre-binding proteins (srebp), peroxisomal enzyme, transmembrane 4 superfamily, transmembrane protein, multispan transmembrane protein, tetr]][[GO:0048870, energy generation, GO:0008652, GO:0009063, GO:0009101, GO:0016126, GO:0016127, GO:0006629, GO:0006869, transcriptional regulation]]
HALLMARK_CHOLESTEROL_HOMEOSTASIS-1[[GO:0006629, GO:0005543, GO:0004768, atp-binding cassette, GO:0016126, cytochrome p450 family proteins]][[GO:0006695, GO:0006629, GO:0006636, cell growth/regulation, GO:0051726, GO:0005515, mhc class ii presentation, cellular antioxidant activity, GO:0000988]]
HALLMARK_COAGULATION-0[[complement system, GO:0007596, peptide hydrolysis, GO:0016485, inflammation regulation]][[analysis of this set of human genes revealed high enrichment for terms related to proteases and protease inhibitors, GO:0005209, MESH:D006023, and serine proteinases. of particular note is the abundance of genes related to the regulation of the complement system and to the coagulation cascade, GO:0004235, there appears to be a strong emphasis on proteins that are involved in the maintenance of cellular integrity and in the regulation of inflammatory and immune responses. in particular, it appears that the presence of proteases, MESH:D011480, GO:0005209, MESH:D006023, and serine proteinases is significantly enriched. this suggests that these proteins are involved in the regulation of a variety of processes, including the complement system and the coagulation cascade. furthermore, the presence of various mmps suggests a regulatory role in the breakdown of proteins in the extracellular matrix, which is important for tissue remodeling and wound healing]]
HALLMARK_COAGULATION-1[[matrix metalloproteinase, cysteine-rich protein, serine protease inhibitor, transforming growth factor-beta, MESH:D054834, guanine nucleotide-binding proteins, peptidase s1 family, integrin beta chain, MESH:D001779, dipeptidyl peptidase, vitamin k-dependent glycoprotein, vitamin k-dependent coagulation factor, regulator of complement activation, protein tyrosine kinase, MESH:D006904, iron-sulfur cluster scaffold, disulfide bridge, kunitz-type serine protease, MESH:D042962, MESH:D037601, g-protein coupled receptor, cytosolic peptidase, GO:0030165, basic leucine zipper, a disintegrin and metalloprote]][[cysteine-aspartic acid protease, MESH:D020782, peptidase, guanine nucleotide-binding proteins, GO:0030165, metalloproteinase, MESH:D042962, regulator of complement activation, regulator of g protein signal transduction, rnase a superfamily, MESH:D011505, subtilisin-like proprotein convertase, MESH:D011973, vitamin k-dependent plasma glycoprotein, vitamin k-dependent coagulation factor, GO:0005161, lysosomal cysteine proteinase, MESH:D015842, transforming growth factor-beta, MESH:D006904, kunitz-type serine protease, integ]]
HALLMARK_COMPLEMENT-0[[cell signaling, cell structure/stability, GO:0008152, vitamin k/clotting, GO:0005856, GO:0005886, GO:0006954]][[MESH:D010770, GO:0000502, GO:0004868, cysteine-aspartic acid protease (caspase), GO:0006915, inflammation signalling, MESH:D005165, factor]]
HALLMARK_COMPLEMENT-1[[protein production, cell surface glycoprotein regulation, GO:0006956, GO:0007165, heat shock protein, MESH:D003564, metalloproteinase, guanine nucleotide-binding protein, lysosomal cysteine protease, zinc finger protein, cysteine-aspartic acid protease, MESH:D001053, metallothionein.\\nmechanism: the genes may be involved in various signalling pathways to facilitate the regulation of cell surface glycoprotein as well as the production of proteins. cytidine deaminase, metalloproteinase, guanine nucleotide-binding protein and cysteine-aspartic acid protease are likely enzymes that the list of genes may be involved in. heat shock proteins and zinc finger proteins, in addition to apolipoproteins and metallothionein, may be involved in the regulation and transportation of cell proteins]][[cell signaling, GO:0007155, GO:0008233, transcriptional regulation, GO:0008152, cytoskeletal functions]]
HALLMARK_DNA_REPAIR-0[[summary: this enrichment test provides evidence of a common biological mechanism underlying many genes in human genetics: dna repair, replication, and transcription.\\n\\nmechanism: the mechanism underlying this term enrichment is the need for accurate dna repair, replication, and transcription, which all require the co-ordinated efforts of many protein families, such as those encoded by the wd-repeat, MESH:D000262, argonaute, MESH:D000263, purine/pyrimidine phosphoribosyltransferase, b-cell receptor associated proteins, MESH:C056608, clp1, GO:0016538, MESH:C010098, dna helicase, MESH:M0251357, general transcription factor (gtf) ii, MESH:D005979, histone-fold proteins, mhc, MESH:C110617, GO:0005662, saccharomyces cerevisiae rad52, schizosaccharomyces pombe rae1, splicing factor (sf3a), GO:0003734, MESH:D011988, transcription factor b (tfb4), trans]][[GO:0003677, transcription control, post-splicing, MESH:D012319, GO:0006281, GO:0071897]]
HALLMARK_DNA_REPAIR-1[[GO:0003677, transcription regulation, GO:0006281, GO:0000394, GO:0006397, GO:0003723, GO:0003682, GO:0019899, GO:0003684, general transcription factor, transcription/repair factors, MESH:M0006668, hypothalamic hormone receptor binding, GO:0004016, nuclear cap-binding protein, GO:0016567, transcription initiation, dna polymerase, GO:0006605]][[GO:0019899, GO:0003723, GO:0003677, GO:0005515, chromosomal binding, dna polymerase, MESH:D012321, phosphorolysis, GO:0010629, GO:0016567]]
HALLMARK_E2F_TARGETS-0[[GO:0006260, GO:0006281, GO:0006351, GO:0003682, GO:0016569, GO:0051726, ran binding, GO:0000808, atpase, GO:0016538, cyclin-dependent kinase, polycomb, dead box protein, gtpase activating protein, GO:0042393, GO:0003723, nucleolar protein, ubiquitously expressed protein, smc subfamily protein, pp2c family, elongation of primed dna template synthesis, dna interstrand cross-linking, import of proteins into nucleus, MESH:D004264, tumor suppressor protein, MESH:D051981, ubr box protein, p80 autoantigen]][[dna replication/repair, chromatin regulation, GO:0006396, ser/thr protein kinase, MESH:D063146, nuclear transport and export, GO:0016567, gtpase activation, GO:0006413, GO:0003723, GO:0003677, GO:0042393, ubiquitin protein ligase, cyclin-dependent kinase, MESH:D000251, MESH:D003842]]
HALLMARK_E2F_TARGETS-1[[GO:0003676, GO:0006260, GO:0036211, GO:0006259, GO:0000785, GO:0051726, GO:0016570, protein assembly and disassembly]][[GO:0006260, nuclear import/export, GO:0003723, chromatin regulation/modification, GO:0030163, GO:1901987, GO:0006281]]
HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0[[cell signaling, extracellular matrix formation, GO:0007155, connective tissue formation, GO:0001525, metabolic regulation, MESH:D016207, tissue repair]][[GO:0003779, actin regulation, GO:0007155, cell signaling, GO:0005518, cytokine regulation and signaling, GO:0005207, growth factor family members, peptidase genes]]
HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1[[MESH:D016326, GO:0005202, MESH:D007797, MESH:D005353, MESH:D014841, integrin, MESH:D016189, fibulin proteins]][[GO:0007155, GO:0005518, GO:0003779, MESH:D024022, MESH:D016326, cytoskeletal components, cell signalling]]
HALLMARK_ESTROGEN_RESPONSE_EARLY-0[[GO:0042277, membrane structure modification, GO:0003677, GO:0006631, GO:0051427, signalling transcription, gtpase activation, adenylate cyclase modulation, GO:0016301, GO:0006897, glycoprotein production, GO:0019838, GO:0016570, GO:0006644, zinc-binding]][[GO:0007165, GO:0010467, GO:0006810, MESH:D008565, GO:0043687, GO:0005515, ligand binding, acyltransferase]]
HALLMARK_ESTROGEN_RESPONSE_EARLY-1[[dna-binding, GO:0005515, GO:0043687, GO:0007165, metabolic activity]][[cytoskeletal organization, dna-binding transcription regulation, GO:0055085, membrane-associated signaling, receptor activation and signaling, cytokine and growth factor signaling]]
HALLMARK_ESTROGEN_RESPONSE_LATE-0[[MESH:D011494, GO:0000981, GO:0005509, MESH:D054794, hormone receptors, GO:0007155, GO:0006457, GO:0010467]][[g-protein signaling, ion channel transport, membrane receptor signalling, cytoskeletal protein scaffolding, enzyme regulation, glycoprotein modulation.\\nmechanism: the genes identified as being related to these topics are involved in the regulation of cell signalling pathways and the transport of ions across cellular membranes. in addition, the genes are involved in biochemical processes such as enzyme regulation and glycoprotein modulation, which may be important in modulating the amount or type of molecules entering the cell and in organizing the cytoskeleton]]
HALLMARK_ESTROGEN_RESPONSE_LATE-1[[membrane processes, transmembrane processes, GO:0006811, GO:0007155, GO:0016049, GO:0008152, MESH:D011506, GO:0023052, processing, MESH:D048788, reparative pathways, immune pathways, disease pathways]][[GO:0007165, gene transcription, ion transport and binding, protein-protein interaction, GO:0043687, GO:0007155, MESH:M0518050, GO:0016310, MESH:D011494, membrane recognition, GO:0003676, MESH:D018118, enzymatic reactions, lipid transport, glucose transport, cytokine receptor, molybdenum cofactor biosynthesis]]
HALLMARK_FATTY_ACID_METABOLISM-0[[GO:0006732, GO:0006754, GO:0006096, oxidative decarboxylation, GO:0006631, nad/nadh-dependent oxidation, pyridine nucleotide oxidation, amino acid oxidation, glycerol-3-phosphate dehydrogenase activity, GO:0022900, MESH:D042942, nadp-dependent oxidation, l-amino acid oxidation, endogenous and xenobiotic n-methylation, conversion of pyruvate to acetyl coa, 2-oxoglutarate catabolism, galectin family activity]][[GO:0008152, GO:0009117, GO:0006631, GO:0006096, oxidation-reduction processes, GO:0006595, GO:0003824, amino acid metabolism, protein homodimerization, protein biotransformation, protein-macromolecule adaptor, protein-tat binding]]
HALLMARK_FATTY_ACID_METABOLISM-1[[GO:0008152, fatty acid transport and processing, oxidoreductase, GO:0009653, GO:0030154, GO:0030674]][[GO:0006099, GO:0006118, GO:0005504, MESH:D042964, pyruvate dehydrogenase, nad-dependent glycerol-3-phosphate dehydrogenase, nad-dependent dehydrogenase, MESH:D013385, MESH:D000154, lyase, flavin adenine dinucleotide-dependent oxidoreductase, gtp-specific beta subunit, MESH:D006631, nad-retinol dehydrogenase, hydratase/isomerase, MESH:D006631, carnitine o]]
HALLMARK_G2M_CHECKPOINT-0[[GO:0006325, GO:0051726, GO:0016570, MESH:D011494, atp-binding, rna-binding]][[transcriptional regulation, epigenetic regulation, GO:0051169, GO:0043687, dna replication and repair, chromatin structure, GO:0140014, GO:0036211, GO:0006397]]
HALLMARK_G2M_CHECKPOINT-1[[GO:0051301, GO:0003677, GO:0003723, transcriptional regulation, chromatin restructuring, GO:0004672, GO:0051169, cytoplasmic transport, nucleic acid metabolism, GO:0016570, GO:0016310, GO:0032259, MESH:D000107, MESH:D054875]][[GO:0006913, GO:0016573, chromatin-associated processes, GO:0051726, transcriptional regulation, signal- and energy- dependent processes, nuclear phosphoproteins, GO:0006334, dna unwinding enzymes, protein heterodimers, GO:0000910, GO:0000398, MESH:D004264, GO:0035064, rna binding proteins, microtubule polymersization, nuclear localization, ubiquitin modification, mitosis regulation, centromere-interacting proteins.\\nmechanism: the genes in this list participate in a wide variety of mechanisms in the context of cellular development, including nucleocytoplasmic transport, histone acetylation, chromatin-associated processes, cell cycle regulation, and transcriptional regulation. these mechanisms are often interdependent and]]
HALLMARK_GLYCOLYSIS-0[[GO:0016310, GO:0009100, GO:0007155, transcription regulation, GO:0009117, energy production]][[MESH:D006023, transmembrane protein, cell-surface protein, enzymes plus coenzymes, GO:0000981, hormones, cytokines, and growth factors, ligand-receptor interaction, regulatory proteins, cargo-binding proteins, cell adhesion and morphogenesis, MESH:D000604, metabolism and transport within the cell, metabolism of macromolecules, cellular energy metabolism, cellular homeostasis and signaling, cell signaling and transcription, protein modification and degradation, GO:0007049, dna replication and repair, GO:0008219, enzyme-substrate interaction\\n\\nmechanism:\\nthis list of genes is primarily involved in cellular metabolism, ligand-receptor interactions, and cell signaling and transcription. there are a variety of molecules that are acted upon, such as glycoproteins, transmembrane proteins, hormones, enzymes, and transcription factors. in terms of metabolic functions, the gene list includes proteins for metabolic control, cargo-binding proteins, and enzymes involved in macromolecule metabolism and transport within the cell. additionally, many of these genes are involved in the regulation of cell cycle and homeostasis, as]]
HALLMARK_GLYCOLYSIS-1[[GO:0008152, GO:0005975, GO:0048468, GO:0009100, GO:0006629, GO:0015031, nucleic acid metabolism, GO:0009117, GO:0070085, ferric ion binding, GO:0016491, GO:0003677, GO:0000988, GO:0031545, GO:0004736]][[enzyme function, GO:0005488, GO:0006810, GO:0008152, MESH:D007477, sugars, GO:0006351, cytoskeleton structure, GO:0007155]]
HALLMARK_HEDGEHOG_SIGNALING-0[[GO:0007155, GO:0007165, GO:0000981, MESH:D018121, MESH:D039921, rho-gtpase-activating protein, transmembrane protein, GO:1902911, transduction pathway, growth factor, g protein-coupled receptor, cadherin superfamily, basic helix-loop-helix, phosphoprotein, zinc finger protein, cytoplasmic domain, dna-binding, GO:0005886, neurotransmitter, MESH:D057057, coiled-coil, pdz binding motif, cholesterol moiety, fibronectin-like repeat, MESH:D000070557, GO:0016604, MESH:D006655, collapsin response mediator, tripartite motif, hedgehog signaling.\\nmechanism: the genes seem to be primarily involved in regulating signal transduction pathways that control cell migration, proliferation and differentiation, by modulating transcription, cell adhesion and receptor activities. the proteins encoded by these genes interact]][[GO:0006897, GO:0019838, receptor-mediated pathways;neuron survival;neuron differentiation;neuronal development;cell adhesion, transcription factor regulation, GO:0007165, extracellular protein interaction]]
HALLMARK_HEDGEHOG_SIGNALING-1[[GO:0007155, GO:0007165, neuron signalling, regulatory activity, GO:0009987, GO:0040007, differentiation, motility, GO:0032502]][[structure-specific proteins, GO:0006898, g-protein coupled receptors, GO:0007155, gene transcription, post-translational regulation]]
HALLMARK_HEME_METABOLISM-0[[GO:0005515, GO:0000910, transcription regulation, metabolic & enzymatic function, cell cortex formation, GO:0006810, GO:0016310, MESH:D000107, protein formation & modification]][[GO:0005515, GO:0006351, catalyzing reactions, gtpase activating protein activation, GO:0016575, carbohydrate & lipid metabolism, receptor binding & signaling, GO:0005574]]
HALLMARK_HEME_METABOLISM-1[[GO:0006351, GO:0003723, post-transcriptional regulation, GO:0006096, GO:0006090, GO:0006749, GO:0006508, transcriptional regulation, MESH:D054875, GO:0003677, MESH:D006655, GO:0006915, cytoskeletal protein, atp-binding, GO:0048870, ubiquitin specific protease, MESH:D015220, voltage-gated chloride channel, GO:0004384, GO:0023052, GO:0051726, cation transporters]][[GO:0003677, GO:0016573, GO:0005515, transcription regulation, leucine residue modification, GO:0003729, zinc metalloenzymes, atp-binding, protein serine/threonin, endoribonuclease, GO:0031545, 6-phosphogluconate dehydrase, GO:0003723, dynein heavy chain, MESH:C052997, chloride intracellular channel, GO:0003779, MESH:D051528, hexameric atpase, GO:0006814, rho gtpase, inositol polyphosphate, MESH:D011766, selenium-binding protein, clathrin assembly, c-myc, dual specificity protein kinase, MESH:D006021, gtpase-activating-protein, GO:0006914, ring between two helices]]
HALLMARK_HYPOXIA-0[[GO:0006096, GO:0016310, GO:0004672, GO:0006508, GO:0085029, transcription regulation, GO:0051726, GO:0097009, GO:0006954, cell-cell communication, oxidative stress response]][[cell signaling, metabolic regulation, GO:0043687]]
HALLMARK_HYPOXIA-1[[GO:0006915, GO:0016310, MESH:D011494, GO:0005515, GO:0006351, GO:0031005, glycolytic enzyme, carboyhydrate binding, cell binding, GO:0042157, GO:0007165, UBERON:2000098, GO:0040007]][[cellular transport, GO:0008152, scaffolding, transcriptional regulation, GO:1901987, transcription activity, GO:0016310, cysteine-aspartic acid, GO:0016020, cell surface heparan sulfate, glycosyl hydrolase family, MESH:D000263, MESH:D000262, glyceraldehyde-3-phosphate, cytokine, glycosyltransferase, MESH:D000070778, sulfatase, sulfotransferase, serine/threonine kinase, MESH:D016232, MESH:D008668, MESH:D011973, basic helix-loop-helix]]
HALLMARK_IL2_STAT5_SIGNALING-0[[GO:0051726, receptor signaling, MESH:D008565, GO:0000981]][[GO:0005515, GO:0005102, transcription regulation, enzyme regulation, GO:0001816, GO:0007155, structure, membrane-associated]]
HALLMARK_IL2_STAT5_SIGNALING-1[[GO:0007165, protein homodimerization, GO:0005525, GO:0003676, GO:0055085, GO:0004672, GO:0007049, GO:0006955, GO:0006915]][[an underlying biological mechanism of intracellular signaling and cell adhesion proteins working together to regulate gene expression and control cell functions was identified. enriched terms related to this mechanism include gtpases, MESH:D008565, intracellular signaling, calcium-dependent proteins, rna and dna binding, GO:0007155, GO:0000981, enzyme regulation, GO:0005515]]
HALLMARK_IL6_JAK_STAT3_SIGNALING-0[[MESH:D016207, GO:0016049, GO:0048468, transmembrane proteins, MESH:D011494, GO:0000981, cell cycle progression]][[MESH:D018121, MESH:D018925, tgf-beta superfamily, transcriptional regulation, MESH:D017027, MESH:D011494]]
HALLMARK_IL6_JAK_STAT3_SIGNALING-1[[the list of gene summaries reveals a group of genes involved in cell trafficking, GO:0007165, GO:0007155, ligand binding, and regulation of the immune response. enriched terms include cytokine, chemokine, MESH:D007378, receptor, GO:0007155, ligand binding, GO:0007165, and regulation of the immune response.\\n\\nmechanism: the mechanism involving these genes involve ligand binding to cytokine, chemokine, or other receptors, resulting in the activation of intracellular pathways leading to signal transduction, GO:0007155, regulation of the immune response]][[the genes identified are part of the cytokine signaling system and its related pathways involved in immune response and regulation. more specifically, they belong to the type i cytokine receptor family, the phospholipase a2 family, the tumor necrosis factor receptor superfamily, the gp130 family of cytokine receptors, the toll-like receptor family, the interferon regulatory factor family, the bcl2 protein family, the reg gene family, the type ii membrane protein of the tnf family, the ring finger e3 ubiquitin ligase family, the protein tyrosine phosphatase family, the tgf-beta superfamily proteins, the hemopoietin receptor superfamily, the chemokine family, the integrin alpha chain family of proteins and the adapter protein family. there is a common function of these genes in the signaling of cell growth, UBERON:2000098, GO:0006915, migration, and differentiation, as well as the regulation of gene transcription, apoptosis and immune response. \\n\\nmechanism:\\nthe genes identified are part of a gene network that functions together to allow for cell signaling, GO:0040007, and differentiation, as well as inflammatory and immune responses. the various cytokine receptors, protein ty]]
HALLMARK_INFLAMMATORY_RESPONSE-0[[GO:0005102, cytokine signalling, GO:0016049, cellular function regulation, immune signalling, inflammation regulation, GO:0051726, apoptosis coordination]][[MESH:D008565, g protein-coupled receptors, MESH:D018121, interferon-induced proteins, MESH:M0013343, MESH:D051116, MESH:D018925, MESH:D016023, MESH:D020782, MESH:D061566, tol-like receptors]]
HALLMARK_INFLAMMATORY_RESPONSE-1[[interactions, GO:0023052, MESH:D008055, GO:0000981, MESH:D016207, MESH:D006728, MESH:D021381, receptors, GO:0007165]][[GO:0005102, GO:0023052, GO:0055085, calcium binding, GO:0055085]]
HALLMARK_INTERFERON_ALPHA_RESPONSE-0[[protein-binding, subunit-binding, rna-binding, transcriptional regulation, GO:0007165, GO:0006955, ligand binding, GO:0032991, GO:0036211]][[ligand binding, GO:0005102, GO:0003824, GO:0003677, GO:0003723, protein activation, GO:0030163, MESH:D054875]]
HALLMARK_INTERFERON_ALPHA_RESPONSE-1[[transcriptional regulation, GO:0008181, MESH:D010447, cytoplasmic proteins, antiviral, MESH:M0369740, GO:0009165, chemokine receptor, dna-binding, rna-binding, lipid-binding, protein adp-ribosylation, GO:0016567, GO:0048255, GO:0016556, GO:0006479, gtp-metabolizing, GO:0008283, GO:0006955, GO:0006952]][[these genes are connected by their participation in immune regulation and defense, either directly regulating the innate and acquired immune response, or acting as downstream inhibitors and activators of such responses. specific enriched terms include interferon regulation, transcriptional regulation, tumor suppression, MESH:D054875, chemokine receptor signaling, GO:0003723, GO:0009165, GO:0051607, GO:0048255, GO:0005525, GO:0008289, viral invasion, GO:0045087, GO:0030701, GO:0008134, and antigen presentation.\\n\\nmechanism: the commonalities between these genes suggest that they act at various levels of a complex innate and acquired immune response, controlling transcriptional regulation, protein modification and silencing, viral response, and antigen presentation. there are multiple pathways overlapping or influencing each gene's particular role in the overall immune defense, merging into a greater shared mechanism of host immunity]]
HALLMARK_INTERFERON_GAMMA_RESPONSE-0[[immune regulation, GO:0003677, GO:0003723, GO:0016567, anti-viral response, cytokine signaling, GO:0006954]][[the genes in the list encode proteins involved in a variety of processes including immunity, GO:0006954, GO:0006351, GO:0007165, and protein folding and assembly. these processes are typically carried out by two main classes of molecules; ubiquitin ligases and cytokines. the genes in this list are enriched for terms including \"signal transduction\", \"ubiquitin ligases\", \"immune modulation\", \"cytokine activity\", \"transcription regulation\", \"proteasome activity\", \"rna binding\", and \"metallothionein\".\\n\\nmechanism:\\nthe genes in this list encode proteins involved in a variety of processes, with an emphasis on immunity and inflammation. these processes are typically mediated by ubiquitin ligases, MESH:D016207, and other signal transduction proteins. ubiquitin ligases mark target proteins for ubiquitination and other modifications, while cytokines affect the activity of multiple cells. signal transduction proteins transmit signals across cell membranes, affecting the activity of cells. metallothioneins play a role in detoxification and protein folding and assembly, while proteasomes carry out protein degradation within the cell. transcripts are regulated by transcription factors, many genes contain rna binding domains]]
HALLMARK_INTERFERON_GAMMA_RESPONSE-1[[GO:0006954, immune cell signaling and development, immune regulation, GO:0044237, regulation of innate and adaptive immunity, metabolic and transcriptional regulation, GO:0003677, GO:0003723]][[transcriptional regulation, GO:0003824, binding ability, protein structure, cell signalling, MESH:D016207, growth factor signalling, MESH:D007109, GO:0000981, MESH:D054875, MESH:D006136, tripartite motif, GO:0070085, atpase, intracellular sensor, MESH:D015088, GO:0003723, calcium-binding, GO:0004930, MESH:M0476528, cysteine-aspartic acid protease, regulator of complement activation, protein tyrosine phosphatase, ubiquitin-specific protease, antiviral activity, inter]]
HALLMARK_KRAS_SIGNALING_DN-0[[protein-binding, transcriptional regulation, GO:0007155, cell membrane channel activity, protein metabolism/modification, receptor signalling]][[ion channels & transporters, receptor proteins, MESH:D002135, MESH:D004798, cell signaling, hormone regulation, GO:0008152]]
HALLMARK_KRAS_SIGNALING_DN-1[[MESH:D011506, GO:0016049, cellular development, MESH:D009068, GO:0001508, calcium binding, GO:0005496, GO:0008152, GO:0006351, GO:0005488, MESH:C062738, GO:0005562, g proteins, dna-binding]][[catalyzing reactions, GO:0055085, GO:0023052, dna-binding, GO:0006351, extracellular signaling, calcium-ion binding, immune system signaling, cell growth/maintenance, GO:0007154, hormone regulation, GO:0032502, GO:0008152]]
HALLMARK_KRAS_SIGNALING_UP-0[[GO:0007155, regulation of growth factors, cytokine regulation, calcium activation, transcriptional regulation]][[MESH:D008565, MESH:D010447, receptor proteins, MESH:D004268, MESH:D010770, GO:0000981, GO:0008217, MESH:M0022898, GO:0007165, transcriptional regulation, GO:0006811, GO:0006936, immunologic regulation, GO:0001816, GO:1901987, GO:0006915, GO:0007155, MESH:D063646]]
HALLMARK_KRAS_SIGNALING_UP-1[[GO:0003677, MESH:D015533, cytokine regulation, GO:0008083, GO:0005515, GO:0007165, transmembrane protein activity, GO:0004930, GO:0003723, GO:0003924, GO:0005509, GO:0016571, glutamine-fructose-6-phosphate transaminase activity, cell growth control, GO:0019725, GO:0016491]][[receptor functions]]
HALLMARK_MITOTIC_SPINDLE-0[[cytoskeletal organization, GO:0003677, microtubule organization, gtpase regulation, centrosome interaction, chromatin structure, protein homodimerization]][[cytoskeleton regulation, cellular communication, gtpase regulation, actin-binding, dna-dependent protein binding, microtubule-associated protein, filamentous cytoskeletal protein, 14-3-3 family protein, MESH:D020662]]
HALLMARK_MITOTIC_SPINDLE-1[[MESH:D020558, nucleotide exchange regulation, cellular signaling, GO:0006338, cytoskeleton structure, GO:0006260, GO:0007155, GO:0003779, actin regulation]][[gtpase activation, GO:0005525, structural maintenance, GO:0003677, GO:0005856, GO:0006915, GO:0007049]]
HALLMARK_MTORC1_SIGNALING-0[[GO:0006412, GO:0015031, protein signaling, GO:0008152, GO:0010467]][[GO:0006412, GO:0008152, GO:0006457, MESH:D054875, GO:0006351, GO:0003677, damage control, GO:0032502, cellular pathway regulation, GO:0006915, GO:0007049, GO:0030163]]
HALLMARK_MTORC1_SIGNALING-1[[GO:0005515, MESH:D054875, GO:0006351, GO:0003824, GO:0006457, chaperoning, GO:0051726, GO:0006629, GO:0046323, cytoskeleton formation]][[atp production, amino acid homeostasis and metabolism, stress response, transcription and mrna regulation, chaperones and proteasome degradation pathways, GO:0006629]]
HALLMARK_MYC_TARGETS_V1-0[[GO:0006351, GO:0006412, GO:0003729, MESH:D054657, MESH:D000072260, GO:0043687, cytoplasmic proteins, MESH:M0015044, GO:0003677, GO:0032508, GO:0005652, GO:0005681]][[GO:0006351, GO:0006412, GO:0006413, GO:0003723, MESH:D054875, GO:0005840, GO:0006412, GO:0032508, MESH:D039102, GO:0003734, GO:0045292, heat shock proteins, MESH:D006655, MESH:D011073, MESH:D000604, GO:0043687]]
HALLMARK_MYC_TARGETS_V1-1[[GO:0009299, GO:0042254, GO:0006412, MESH:D049148, GO:0003723, GO:0043687, GO:0045292, polymerase, GO:0006913, MESH:D054875, GO:0006457, 14-3-3 family proteins]][[poly(a)-binding, GO:0003723, GO:0032508, GO:0006913, GO:0032183, GO:0000394, GO:0003676, GO:0006473, GO:0006413, GO:0036211, GO:0006457, MESH:D014176, GO:0006412, MESH:D018832, peptidyl-prolyl cis-trans isomerization, antioxidant function, heat shock protein, ubiquitin protein ligase, 14-3-3 family, dna-unwinding enzymes, dna polymerase, voltage-dependent anion]]
HALLMARK_MYC_TARGETS_V2-0[[GO:0003723, ribosomal biogenesis, GO:0008283, GO:0006335, GO:0007165, cell cycle progression, GO:0003682]][[GO:0005515, transcriptional regulation, cell cycle progression, protein chaperoning, GO:0008283, nuclear localization, rna binding activity, pre-rrna processing, GO:0042254]]
HALLMARK_MYC_TARGETS_V2-1[[GO:0006351, rna binding activity, GO:0006457, cell cycle progression, GO:0006281, protein homodimerization, GO:0006468, GO:0065003, protein kinase/phosphatase activity, mitochondrial mrna processing. mechanism: this list of genes encodes proteins which work together to regulate key cellular activities such as dna replication, transcription, cell cycle progression, and rna processing. these proteins can either complex together or work in tandem to form kinase/phosphatase complexes, which control phosphorylation of key substrates and regulate protein folding to ensure proper protein function. these proteins also interact with dna to regulate genomic activities such as dna replication, transcription, and repair processes]][[rna binding activity, GO:0006364, protein homodimerization, GO:0008283, GO:0007165, GO:0042254, GO:0006457, GO:0034246]]
HALLMARK_MYOGENESIS-0[[motor protein activity, GO:0019722, GO:0006936, transcriptional regulation, intracellular fatty acid-binding, ligand binding, MESH:D007473, GO:0005884, MESH:D008565, regulation of transcription, phosphorylation of proteins]][[GO:0006936, calcium channel regulation, ion channel regulation, protein ubiquitination/degradation, actin-based motor proteins, GO:0007165, MESH:D004734]]
HALLMARK_MYOGENESIS-1[[MESH:M0496924, protein regulation, ion channeling, cellular transport, GO:0006629, GO:0010468, neurotransmitter signaling, small molecules, large molecules]][[summary: the list of genes provided contains components of muscle formation, GO:0023052, and growth.\\nmechanism: the genes encode the components of signaling pathways and physical structures involved in the formation of muscle, including proteins that serve as receptors, binders, MESH:D004798, and structural components like spectrins, GO:0005202, laminin.\\nenriche terms: muscular development; musculosketetal function; signal transduction; protein phosphorylation degradation; cytoplasmic proteins; structural proteins; cytochrome oxidase]]
HALLMARK_NOTCH_SIGNALING-0[[cell fate decisions, GO:0007219, GO:0007165, wnt signalling pathway, cell-cell interaction, GO:0016567, GO:0006355, protein ligase activity, GO:0006468]][[GO:0007219, GO:0016055, GO:0016567, transcriptional repressor, MESH:D015533, cell fate decisions, MESH:D044767, MESH:D011494]]
HALLMARK_NOTCH_SIGNALING-1[[notch signaling, GO:0016567, cell-cycle regulation, protein breakdown and turnover, intracellular signalling pathways, cell fate]][[GO:0007219, GO:0016567, GO:0001709, transcriptional regulation, GO:0031146, gamma secretase complex, MESH:D011493, wnt family, basic helix-loop-helix family of transcription factors]]
HALLMARK_OXIDATIVE_PHOSPHORYLATION-0[[GO:0005739, MESH:D004798, MESH:D010088, MESH:D010088, GO:0006754]][[GO:0006006, GO:0006631, amino acid metabolism, GO:0005746, MESH:D007506, nadh-ubiquinone oxidoreductase, MESH:D009245, pyruvate dehydrogenase, GO:0022900, oxidative decarboxylation, nad+/nadh oxidoreductase, GO:0016467, MESH:D003576, MESH:D063988, matrix processing, shuttling mechanism.\\n\\nmechanism: the gene products involved in this metabolic pathways work to convert small molecules such as glucose and fatty acids into energy-containing molecules, such as atp and nadh, through a combination of redox reactions, electron transfer processes, and other catalytic systems. these processes involve the participation of numerous proteins, including membrane-associated proteins, enzymes, and enzyme complexes. these proteins form a complex network of interactions that enable the conversion of energy from one form to another, ultimately leading to atp production]]
HALLMARK_OXIDATIVE_PHOSPHORYLATION-1[[oxidative decarboxylation, MESH:D010088, MESH:D010084, GO:0006754, mitochondrial respiration, GO:0008152, MESH:D003580, MESH:D000214, pyruvate dehydrogenase, MESH:D005420, hydratase/isomerase, leucine-rich protein, 3-hydroxyacyl-coa]][[terminal enzyme, GO:0006754, GO:0005746, nad/nadh-dependent, cytochrome c oxidase (cox), GO:0006118]]
HALLMARK_P53_PATHWAY-0[[GO:0007049, GO:0006351, GO:0023052, GO:0006412, GO:0065007, GO:0042592]][[GO:0005515, GO:0003677, transcriptional regulation, GO:0051726, cell signaling]]
HALLMARK_P53_PATHWAY-1[[GO:0051726, GO:0016049, GO:0006915, GO:0007165, GO:0006281, transcriptional regulation, chromatin structure, tumor suppression, enzymatic activity, GO:0000988, GO:0004725, GO:0003925]][[MESH:D011494, GO:0000981, GO:0007049, GO:0006281, GO:0003677, GO:0006412, tnf receptor superfamily, zinc finger, calcium-activated, cyclin dependent, iron-sulfur, GO:0015629, GO:0007165]]
HALLMARK_PANCREAS_BETA_CELLS-0[[analysis of the human genes abcc8, akt3, chga, dcx, dpp4, elp4, foxa2, foxo1, g6pc2, gcg, gck, hnf1a, iapp, UBERON:0002876, insm1, isl1, lmo2, mafb, neurod1, neurog3, nkx2-2, nkx6-1, pak3, pax4, pax6, pcsk1, pcsk2, pdx1, pklr, scgn, sec11a, slc2a2, spcs1, srp14, srp9, srprb, UBERON:0035931, stxbp1, syt13, vdr was performed to determine commonalities in gene function. term enrichment indicated a commonalty in genes that are involved in the regulation of glucose and insulin metabolism, GO:0008283, differentiation and apoptosis, as well as glycogen synthesis and glucose uptake. additionally, many of the genes are involved in the development of neural tissues and the regulation of gene transcription. the underlying biological mechanism could involve alterations in the phosphorylation of proteins and signaling pathways,]][[GO:0000981, homeobox domain, signal peptide cleavage, MESH:D011494, atp-binding, chromogranin/secretogranin, GO:0005180, protease, MESH:D011770, MESH:D005952, MESH:D000243, MESH:D006593, nuclear receptor, dna-binding, g-protein linked receptor, cysteine-rich protein, gtp-bound proteins, GO:0048500, bhlh transcription factor, doublecortin, calcium-binding protein\\n\\nsummary: genes identified in this list facilitate a variety of essential biological processes, particularly in terms of cell signaling and transcription regulation. among these processes are signal peptide cleavage, atp-binding, peptide hormone secretion and regulation, protease activity, glucose metabolism, adenosine deaminase, gtp-bound protein binding, and transcription factor actions. \\n\\nmechanism: these genes are involved in transcriptional regulation and signaling processes through binding of dna and g-protein linked receptors, homeobox domains, cysteine-rich proteins]]
HALLMARK_PANCREAS_BETA_CELLS-1[[this analysis identifies the common functions of 18 human genes: dpp4, scgn, pklr, pax4, neurod1, srprb, srp14, isl1, insm1, pak3, pax6, elp4, dcx, iapp, lmo2, neurog3, gck, stxbp1, nkx2-2, pdx1, UBERON:0035931, pcsk1, nkx6-1, UBERON:0002876, pcsk2, spcs1, g6pc2, foxo1, sec11a, vdr, foxa2, slc2a2, mafb. they are related to metabolic regulation (glucose, GO:0016088, MESH:D004837, citrate), developmental regulation (neural tissues, UBERON:0001264, UBERON:0002107, lymph nodes), signal transduction (g proteins, ace, atp binding proteins) and hormone regulation related (somatostatin, GO:0016088, vitamin d3). these factors likely work in concert to control and maintain metabolic parameters throughout the body. mechanism: these genes act through various methods including transcriptional regulation, protein interactions, protein cleavage, signaling casc]][[transcriptional regulation, MESH:M0496924, endocrine system regulation, GO:0006006, cell signalling, MESH:D020558, GO:0000981, GO:0005180, MONDO:0018815, MESH:D043484]]
HALLMARK_PEROXISOME-0[[MONDO:0018815, an antioxidant enzyme, a hormone binding protein, a nuclear receptor transcription factor, a fatty acid desaturase, a carnitine acyltransferase, an isocalate dehydrogenase, a peroxisomal membrane protein, MESH:D005182, antioxidant enzyme, hormone binding protein, nuclear receptor transcription factor, GO:0004768, carnitine acyltransferase, isocalate dehydrogenase, peroxisomal membrane protein, and fad-dependent oxidoreductase.\\n\\nmechanism: many of the genes are involved in regulating the production and movement of lipids and fatty acids, as well as the synthesis of hormones, MESH:D000305, and signalling receptors. the underlying biological mechanism is that these genes act as regulators of metabolic pathways, ensuring that their respective pathways are functioning correctly and that metabolites are transported correctly]][[GO:0140359, oxidoreductase, dehydrogenase/reductase, hydratase/isomerase, enzymes responsible for fatty acid beta-oxidation, enzymes catalyzing the]]
HALLMARK_PEROXISOME-1[[GO:0006629, GO:0006635, GO:0006281, transcription and replication, MESH:D018384, GO:0006536, GO:0005502, GO:0008202]][[MESH:D018384, MONDO:0018815, atpases associated with diverse cellular activities, vitamin a family, GO:0004879, nad-dependent oxidoreductases, GO:0005783, MESH:D015238, cyclin-dependent protein kinase, hydratase/isomerase superfamily, GO:0005515, GO:0003677, GO:0050632, carnitine acyltransferase, MESH:D011960]]
HALLMARK_PI3K_AKT_MTOR_SIGNALING-0[[GO:0016310, GO:0006412, mrna expression, GO:0005515, cell signalling, MESH:D054875, protein phosphatase]][[MESH:D011494, GO:0016791, GO:0005525, protein-protein interaction, GO:0030552, GO:0000981, peptidyl-prolyl cis/trans isomerase, cytoskeletal function, protein tyrosine phosphatase, protein phosphatase, GO:0140597, MESH:D020662, receptor interacting protein, transmembrane glycoprotein, MESH:D018123, MESH:D054387, inositol trisphosphate receptor, plexin domain, phosphoinositide 3-kinase, ubiquitin activation/conjugation, GO:0003925]]
HALLMARK_PI3K_AKT_MTOR_SIGNALING-1[[GO:0007165, MESH:D011494, GO:0004707, MONDO:0008383, gpcr, GO:0016791, MESH:D020662, endoplasmic reticulum chaperone protein]][[MESH:D011494, guanine nucleotide-binding protein, receptor-interacting protein, chaperone protein, protein tyrosine kinase, MESH:D020558, MESH:D000262, protein phosphatase, cytoplasmic face, GO:0006468, GO:0007165, GO:0036211]]
HALLMARK_PROTEIN_SECRETION-0[[GO:0005480, GO:0006897, GO:0006887, intracellular trafficking, MESH:D001678, MESH:D008565, GO:0005906, MESH:D020558, GO:0005794, GO:0005484]][[MESH:D008565, MESH:D020558, coatomer complex, GO:0016192, MESH:D001678, GO:0035091, GO:0065007, MESH:D002966, GO:0005906, GO:0005794, GO:0030136, MONDO:0018815, GO:0042393, GO:0005802, MESH:M0013340, GO:0006811, GO:0005159, GO:0005783, MESH:D057056, GO:0005483, GO:0005764, GO:0005794, multifunctional proteins]]
HALLMARK_PROTEIN_SECRETION-1[[GO:0003924, snare binding activity, GO:0005484, phosphoinositide-binding, coatomer protein complex, MESH:D052067, protein kinase binding activity, adaptor complexes, atpases associated with diverse cellular activities, snare recognition molecules, gold domain, GO:0030136, transmembrane 4 superfamily, GO:0070273, sec7 domain, membrane mannose-specific lectin, signal-transducing adaptor molecule, identical protein binding activity]][[this list of genes codes for proteins of various functions, primarily related to organelle trafficking, membrane associations, and receptor binding activities. these proteins are involved in the regulation of intracellular vesicles, endoplasmic reticulum and golgi organization, protein sorting and secretion, cell surface receptor binding, cell-signaling and immunity, protein phosphorylation and kinase binding, and lipid protein modifications. the enriched terms found in the functions of these genes include vesicular transport, MESH:M0354322, organelle trafficking, GO:0007030, GO:0005102, GO:0006457, GO:0006468, snare recognition molecules, clathrin coated vesicles, endoplasmic reticulum-golgi transport, MESH:D025262, GO:0005906, and dystrophin-glycoprotein complex. \\n\\nmechanism: the enriched terms in the gene functions indicate that these proteins are involved in various pathways and process of intracellular cargo trafficking, where proteins, membranes and signaling molecules are sorted, distributed and regulated. the processes are involved with vesicular transport, protein co-translocation, GO:0030258, and protein phosphorylation, which coordinate the mobilization and distribution of proteins, MESH:D008055]]
HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0[[MONDO:0018815, copper chaperone, MESH:D002374, GO:0004861, hypoxia inducible factor (hif), nucleotide excision repair pathway, GO:0004672, GO:0009487, MESH:D005979, MESH:D009195, MESH:D010758, phosphofructokinase, MESH:D054464, GO:0050115, arginine/serine-rich splicing factor, iron/manganese superoxide dismutase, GO:0016491, germinal centre kinase iii (gck iii) subfamily, thioredoxin (trx) system]][[this list of genes were found to be involved in oxidoreductase activity, intracellular binding and catalytic activity, cellular response regulation, dna and transcription regulation, membrane function, mitochondrial function and antioxidant activity. the enriched terms include oxidoreductase activity, intracellular binding, GO:0003824, cell growth regulation, transcription regulation, membrane function, mitochondrial function, GO:0016209, GO:0020037, GO:0005507, GO:0003677, GO:0043565, tyrosine-specific protein kinase activity, f-actin binding. the underlying biological mechanism is probable related to redox homeostasis, the oxygen metabolism pathway, the cell cycle dna repair pathways, the regulation of transcription membrane function]]
HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1[[GO:0016049, GO:0007049, GO:0006351, redox regulation, MESH:D018384, MESH:D005721, hydroxylase, protease, free-radical scavenging, protein phosphatase]][[redox processes, MESH:D018384, GO:0006281, GO:0008152, cell growth regulation, inflammation control, cellular defense, MESH:D006419, MESH:D005980, superoxide dism]]
HALLMARK_SPERMATOGENESIS-0[[protein binding activity, GO:0003714, dna binding activity, rna binding activity, zinc ion binding activity, GO:0004596, serine/threonine-protein kinase activity, GO:0004016, snare binding activity, clathrin binding activity, myosin light chain binding activity, double-stranded dna binding activity, phosphatidic acid phosphohydrolase activity, ubiquitin-protein ligase activity, rna polymerase binding activity, GO:1990817, GO:1990817, GO:0060090, phosphatase binding activity, atp-ases associated activity, GO:0044183, GO:0016165, adp-ribosylation factor-like activity]][[cell cycle regulatory proteins and kinases, dna binding proteins and chaperones, nucleotide and polypeptide binding proteins, GO:0016791, proteins involved in transcription, gene transcription, GO:0051276, apoptosis regulation, GO:0006281, protein folding and transport, cell signaling and growth regulation, MESH:D004734, cytoskeletal organization, vesicular trafficking\\n\\nmechanism: the underlying biological mechanism is likely involved in multiple steps in cell division and the regulation of gene expression, and in the maintenance of cell homeostasis]]
HALLMARK_SPERMATOGENESIS-1[[GO:0006457, transcriptional regulation, GO:0007165, GO:0051726, chromatin structure and nuclear envelop function, cell adhesion and motility, GO:0008152, GO:0016567, detection and binding, enzymatic activity, GO:0042311]][[this list of genes is associated with a range of diverse functions, including intracellular and intercellular trafficking, adhesion, enzyme regulation, transcriptional regulation, ion channel and receptor regulation, and processes related to stress, GO:0007568, and metabolism. common enriched terms include protein kinase and phosphatase, GO:0140359, g-protein coupled receptors, receptors, transcriptional regulation, GO:0016569, GO:0051726, heat shock, GO:0005515, ubiquitin-protein ligase and ubiquitin protease, zinc metalloproteases, and peptide n-acetyltransferase. the underlying biological mechanism or pathway associated with these genes may involve signal transduction as mediated by enzyme activity, MESH:D007473, receptors, and other proteins, as well as cell-to-cell adhesion and trafficking processes involved in membrane dynamics.\\n\\nsummary: list of genes associated with diverse functions including intracellular and intercellluar trafficking, adhesion, regulation of enzymes, GO:0006351, ion channels and receptors, and processes related to stress, GO:0007568, and metabolism.\\nmechanism: signal transduction as mediated by enzyme activity, MESH:D007473, receptors, and other proteins, as well as cell-to]]
HALLMARK_TGF_BETA_SIGNALING-0[[transmembrane proteins, receptor signaling pathways, transcription regulation, cell signaling, GO:0007155, GO:0016049, tgf-beta superfamily, MESH:D010749, ubiquitin ligases, tight junction adaptors]][[the human gene summaries represent a variety of cell signaling, cell growth and differentiation, transcription regulation, adhesion and migration, and apoptosis-related functions. several genes in the list (acvr1, GO:0005680, arid4b, bmpr1a, bmpr2, cdh1, ifngr2, junb, lefty2, map3k7, ncor2, ppm1a, pp1ca, rahb, smad1, smad3, smad6, smurf1, smurf2, tgfb1, tgfbr1, MESH:D016212, cdk9, cdkn1c, ctnnb1, eng, fnta, MESH:D045683, hipk2, id1-3, klf10, ltbp2, pmepa1, ppp1r15a, serpine1, ski, skil, slc20a]]
HALLMARK_TGF_BETA_SIGNALING-1[[transmembrane serine/threonine kinases, transcriptional repressors, transforming growth factor (tgf)-beta superfamily, rho family of small gtpases, smad family, c2h2-type zinc finger domains, MESH:M0460357, caax geranylgeranyltransferase, smad interacting motif (sim), homeodomain-interacting protein kinase, MESH:D004122, transforming growth factor-beta (tgfb) signal transduction, MESH:D018398, MESH:D054645, protein folding and trafficking]][[GO:0007165, transcription regulation, cell-to-cell communication, MESH:D018398, serine/threonine protein kinase, disulfide-linked homotrimeric proteins, protein phosphatase, transmembrane proteins, smurf protein, cystein-rich motif, GO:0006457]]
HALLMARK_TNFA_SIGNALING_VIA_NFKB-0[[GO:0006351, cytokine, inflammatory, UBERON:2000098, GO:0006915, cell signalling, receptor regulation, GO:0003924, GO:0003723]][[transcriptional regulation, GO:0005125, GO:0008283, GO:0006629]]
HALLMARK_TNFA_SIGNALING_VIA_NFKB-1[[MESH:D016207, MESH:D018925, MESH:D010770, GO:0000981, MESH:D016212, nf-kappa-b, myc/max/mad, jagged 1, stat-regulated pathways, MESH:D008074, MESH:M0496065]][[GO:0006954, GO:0007165, transcriptional regulation, GO:1901987, cytokine, MESH:D011506, receptor, GO:0000981, enzyme, growth factor, MESH:D019204, chemokine, MESH:D008074, pentraxin protein, GO:0016791, MESH:D010770, stress response]]
HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0[[rna-binding, protein-binding, GO:0019538, GO:0009058, GO:0044183, GO:0000981, GO:0006457]][[GO:0003723, transcription regulation, GO:0006457, protein targeting and covalent modifications, endoplasmic reticulum function, GO:0006413]]
HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1[[GO:0003723, GO:0005783, transcriptional regulation, GO:0006457, GO:0140597, mrna decapping, MESH:M0465019, GO:0030163, MESH:D021381]][[GO:0006412, endoplasmic reticulum stress response, GO:0003723, protein expression, conformation folding]]
HALLMARK_UV_RESPONSE_DN-0[[cellular response regulation, GO:0007165, transcriptional regulations, MESH:D011956, GO:0016310, calcium binding, MESH:D011494, transmembrane proteins, protein tyrosine kinases, MESH:D017027, MESH:M0015044, protein inhibitor of activated stats, integrin beta, annexin family, adp-binding cassette family, MESH:D020690, arfaptin family, wd repeat proteins, maguk family, camp-dependent pathways, MESH:D000071377, MESH:D008869, pak family, MESH:D015220, mitogen-responsive phosphoproteins, nuclear histone/protein, celf/brunol family, four-and-a-half-lim-only proteins]][[GO:0007155, GO:0005207, nuclear phosphoprotein, phosphoprotein, cytoplasmic receptor, MESH:D020558, GO:0016791, receptor tyrosine kinase, GO:0006351, camp, ion transport atpase, transmembrane protein]]
HALLMARK_UV_RESPONSE_DN-1[[GO:0007165, MESH:D016326, cellular adhesion, GO:0000981, MESH:D011494, MESH:D020558, camp, calcium-dependent phospholipid binding protein, MESH:D011505, MESH:D017868, scaffolding protein, MESH:D020690, MESH:D010711, protein tyrosine phosphatase, rho-like gtpase, calcium-activated bk channel, cyclin-dependent kinase, n6-methyladenosine-containig protein, helix-loop-helix proteins, MESH:D016601, atpase, guanine nucleotide-binding protein, cytoplasmic surface protein, serine protease inhibitor, protein inhibitor of activated stat, GO:0004384, mitogen-responsive]][[GO:0000981, receptor, GO:0005488, growth factor, phosphoprotein, MESH:D010770, cytoplasmic surface, nuclear histone/protein methyltransferase, MESH:D020558, wd repeat protein, protein tyrosine phosphatase, serine/threonine kinase, caveolae plasma membrane, g-protein coupled receptor, MESH:D000071377, ab hydrolase superfamily, microtubule-associated protein, protein-tyros]]
HALLMARK_UV_RESPONSE_UP-0[[cell regulation, GO:0055085, metabolic catabolism, transcription support, GO:0006468, non-classical heavy chain, GO:0020037, GO:0007165, cytoskeleton formation, GO:0030163, cell signaling, GO:0006412, GO:0010467]][[GO:0005515, MESH:D002384, transcriptional regulation, cell signaling, metabolic reactions]]
HALLMARK_UV_RESPONSE_UP-1[[GO:0005515, GO:0005525, GO:0005215, reactive catalysis, cell signaling, membrane-associated functions]][[regulatory proteins, GO:0000981, membrane and transport proteins, structural proteins, MESH:D004798, biosynthesis of heme, cellular signaling, transcription control, GO:0008152, GO:0006955]]
HALLMARK_WNT_BETA_CATENIN_SIGNALING-0[[wnt signalling pathway, transmembrane glycoprotein, MESH:D006655, GO:0000981, GO:0007219, GO:0005515, GO:0007165, GO:0006511, transcriptional regulation, dna replication and repair]][[cell-cell interactions, MESH:D047108, transcriptional regulation, GO:0006281, wnt signaling, notch signaling, hedgehog signaling, MESH:D044783]]
HALLMARK_WNT_BETA_CATENIN_SIGNALING-1[[wnt signaling, notch signaling, hedgehog signaling, transcriptional regulation, cell cycle progression, developmental events, dna replication and repair, transcriptional silencing, GO:0043161]][[transcriptional regulation, GO:0001709, signaling pathway activation, MESH:D060449, notch pathway, hedgehog pathway, protein interactions, cell growth regulation, GO:0004672, GO:0030163, cell-cell interaction, cell-matrix interaction, protein ligase binding activity, GO:0004842, membrane-bound protease activity, transcriptional repressor, GO:0006338, notch receptor cleavage, intracellular domain formation, ectodomain shedding, MESH:D015533, nuclear receptor co-repressor]]
T cell proliferation-0[[GO:0004888, calmodulin binding activity, GO:0061630, GO:0033192, GO:0004721, GO:0004725, GO:0004672, MESH:D015533, guanine nucleotide exchange activity, ligand binding activity]][[the provided list of genes and associated descriptions demonstrates variation in generic cellular processes like protein degradation, protein and nucleic acid binding and kinase activity, as well as specific pathways involving cytokine and chemokine signaling, transcriptional regulation and regulation of immune cell activity. across these processes, the significant terms enriched across the genes include: protein tyrosine kinase activity; protein/nucleic acid/oligomeric binding activities; protein ubiquitination; transcriptional and immune cell activation and proliferation; intracellular receptor signaling and nf-kappab pathways; and cell cycle regulation.\\n\\nmechanism:\\nthe identified genes likely affect several common pathways, including signaling pathways that mediate cell division, motility, adhesion, chemokine- and cytokine-mediated responses, and immune cell function. in particular, the proteins encoded by these genes likely play roles in the regulation of post-translational modifications, such as protein ubiquitination, and the regulation of gene transcription, likely in response to extracellular cues. additionally, the identified proteins may mediate the recruitment of the cbm signalosome, leading to the activation of nf-kappab pathways. finally, cell cycle-related processes]]
T cell proliferation-1[[transcriptional regulation, cellular signaling pathways and processes, GO:0016049, differentiation, GO:0006950, GO:0006955, protein folding and trafficking, MESH:D051192, transmembrane proteins, receptor tyrosine kinases, ubiquitin e3 ligases, MESH:D020134, cgmp-binding phosphodiesterase]][[GO:0007165, GO:0008037, GO:0004721, GO:0061630, lipid enzyme, MESH:D011505, cgmp kinases, GO:0000981, protein scaffold, cytokine, adaptor protein, GO:0051301, adhesion, differentiation, GO:0006950, negatively regulated, MESH:D021381, cell fate and patterning, MESH:D002470, ligand-gated ion channel, GO:0051092, GO:0006569, er stress-induced protection, transmembrane glycoprotein, MESH:D050503, wnt gene family, GO:0016020]]
Yamanaka-TFs-0[[this set of genes is involved in embryonic development, stem cell pluripotency, stem-cell maintenance, and dna damage response. commonly enriched terms include cell cycle regulation, transcription regulation, GO:0006915, cellular transformation, and dna damage repair. mechanism:these genes control critical functions of cell cycle progression, gene transcription, and dna repair, providing the necessary foundation for the development of the organism. these pathways provide the structural and biochemical features of embryonic development, maintenance of stem cells and pluripotency, response to cellular damage]][[genes in this list are transcription factors involved in the development of various organ systems, such as the skin and cns, as well as responding to dna damage, GO:0006915, and cellular transformation. the enriched terms are transcription factor activity; gene expression regulation; cell cycle regulation; dna damage response; pluripotency; and embryo development.\\n\\nmechanism: the transcription factors in this list interact with dna, regulate gene expression, and influence cell cycle progression, GO:0006915, and cellular transformation. combined, these genes are thought to play a role in creating and maintaining cellular and tissue identity, as well as responding to environmental changes. this could be part of a larger mechanism that governs organism development and homeostasis]]
Yamanaka-TFs-1[[GO:0000981, MESH:D047108, stem cell maintenance, MESH:D063646, GO:0030154]][[GO:0000981, zinc finger proteins, GO:0007049, MESH:D004249, MESH:D016147, MESH:D047108, stem cell maintenance, translocation, homeodomain]]
amigo-example-0[[GO:0007155, MESH:D016326, MESH:M0023728, cellular communication, GO:0042592, GO:0042060, GO:0006915, motility, GO:0001525]][[GO:0007155, GO:0016477, cell signalling, GO:0008152, GO:0006915, GO:0009653, GO:0007599, MESH:D007109, extracellular matrix maintenance]]
amigo-example-1[[GO:0007219, osteoclast attachment/mineralized bone matrix, jagged 1/notch 1 signaling, GO:0007155, GO:0006915]][[GO:0048729, matrix metalloproteinase inhibitor, regulated cell adhesion, cytoplasmic protein tyrosine kinase, GO:0005161, cytokine-induced gene expression, GO:0005583, cell signaling pathway, MESH:D015533, antimicrobial activity, GO:0031012, GO:0016477, GO:0008283]]
bicluster_RNAseqDB_0-0[[GO:0055085, growth factor regulation, calcium regulation, transcription regulation, MESH:D007473, calcium-dependent processes, protein binding activity, chromatin binding activity, gtpase activating protein binding activity, histone binding activity, dna-binding activity, sequence-specific double-stranded dna binding activity, GO:0000988]][[GO:0007165, transcription regulation, ion regulation, GO:0005515, cytoskeletal adaptor, MESH:D006023]]
bicluster_RNAseqDB_0-1[[this list of genes is involved predominantly in processes related to binding activities, dna-binding transcription factor activities, chromatin binding activities, and protein domain-specific binding. the underlying biological mechanism involves pathways that regulate cell morphology and cytoskeletal adaptor proteins. the enriched terms include: binding activity, GO:0003700, chromatin binding activity, protein domain-specific binding activity, cell morphology, MESH:D051179]][[GO:0000988, metal ion binding activity, dna binding activity, chromatin binding activity, rna binding activity, protein domain-specific binding activity, histone binding activity, methylated histone binding activity]]
bicluster_RNAseqDB_1002-0[[GO:0007165, protein-protein interactions, MESH:D004734, GO:0051015, troponin binding, GO:0005523, GO:0051219, GO:0032515, GO:0043531, atp binding. mechanism: these genes are involved in pathways of signal transduction, protein-protein interactions, and energy metabolism, which lead to muscle contraction and tissue development. activation of these pathways leads to calcium release, which in turn activates contractile proteins such as troponin, tropomyosin, and actin. these proteins act together to promote muscle contraction and cytoskeletal structure]][[GO:0051015, GO:0048870, GO:0004722, myosin-binding proteins, MESH:D002154, GO:0045010, GO:0005523, calcium sensitivity, MESH:D044767, GO:0003735, GO:0004930, GO:0042923, GO:0050262, GO:0061769, GO:0019674, GO:0007015, GO:0006936, GO:0055008, GO:0030838]]
bicluster_RNAseqDB_1002-1[[MESH:D024510, actin and tropomyosin binding, calcium- and energy-regulation, ion channeling, negative regulation of cytokine signaling pathways, GO:0033173]][[actin filament binding activity, muscle alpha-actinin binding activity, actin monomer binding activity, tropomyosin binding activity, GO:0006936, GO:0045214, GO:0071691, GO:0045010, GO:0030838, muscle excitation-contraction coupling, calcium release complex, muscle associated proteins, GO:0030036, GO:0007507]]
endocytosis-0[[GO:0006897, GO:0015031, GO:0051639, endoplasmic reticulum and recycling endosome membrane organization, GO:0044351, GO:0016043, intracellular signaling, GO:0051260]][[GO:0030030, MESH:D021381, MESH:D011494, GO:0048870, membrane reorganization, GO:0006897, cytoskeletal reorganization, mitogen-activated protein kinase, lysosomal degradation, GO:0051168]]
endocytosis-1[[GO:0015031, GO:0006897, GO:0006898, GO:0051260, GO:0007155, GO:0048870, amino acid residues, MESH:D054875, GO:0015908, cytoskeletal reorganization, GO:0016192, signaling complex regulation, GO:0140014, GO:0006919]][[GO:0006897, lysosomal degradation, GO:0015031, GO:0006898, membrane processes, gtpase regulation, MESH:D044767, death domain-fold]]
glycolysis-gocam-0[[GO:0006096, GO:0016310, MESH:D006593, glucose phosphate isomerase, phosphofructokinase, MESH:D005634, fructose-1,6-bisphosphate, MESH:D014305, glyceraldehyde-3-phosphate dehydrogenase, MESH:D010736, MESH:D011770, MESH:D010751]][[GO:0006006, GO:0006096, GO:0016310, GO:0006000, GO:0006094, GO:0004332, glycogen storage, GO:0016853, GO:0004743, GO:0004396]]
glycolysis-gocam-1[[muscle maturation, MESH:D024510, GO:0001525, GO:0006096, MONDO:0003664, MONDO:0002412, plasmin regulation]][[GO:0006096, GO:0008152, regulation of energy conversion, MESH:D024510, tumor progression, GO:0006094, GO:0001525, neurotrophic factor, MESH:M0025255]]
go-postsynapse-calcium-transmembrane-0[[GO:0006816, calcium ion regulation, postsynaptic ion channel, GO:0005892, glutamate receptor channel, g protein-coupled receptor, plasma membrane protein, ligand-gated ion channel]][[calcium homeostasis, calcium-channel activity, MESH:D007473, g-protein coupled receptor, ligand-gated ion channel]]
go-postsynapse-calcium-transmembrane-1[[calcium ion regulation, GO:0006816, n-methyl-d-aspartate receptor family, MESH:C413185, MESH:D011954, p-type primary ion transport atpases]][[calcium homeostasis, calcium influx, GO:0007268, neuronal development, MESH:D058446, purinergic receptor, GO:0004972, MESH:C413185, g-protein coupled receptor]]
go-reg-autophagy-pkra-0[[GO:0043539, protein serine/threonine kinase binding activity, GO:0004860, GO:0005085, GO:0032008, GO:0010605, GO:0032956, GO:0032006, GO:0016241, regulation of nf-kappab activation, GO:0001558, regulation of cell survival, GO:0038187, GO:0006281, GO:0045087]][[GO:0016049, GO:0006915, GO:0007165, serine/threonine kinase activator activity, GO:0035004, GO:0005085]]
go-reg-autophagy-pkra-1[[this term enrichment test looked at a list of human genes together with their functions. it found that the genes have functions related to cell cycle regulation, GO:0007165, GO:0043170, protein kinase binding and regulating chromatin remodeling and transcription. the enriched terms include cell cycle regulation, GO:0007165, GO:0043170, GO:0019901, GO:0016310, chromatin remodeling and transcriptional regulation.\\n\\nmechanism: the genes in this list are involved in processes such as cell cycle regulation, GO:0007165, GO:0043170, GO:0019901, phosphorylation and chromatin remodeling and transcription, which are interconnected. these processes all depend on the activity of various protein kinases and their activation by various components, including snca, MESH:D053148, trib3, ccny, pik3ca, akt1, nod2, kat5, rptor, smcr8, mlst8, tab2, hspb1, irgm, GO:0033868, cdk5r1 and other proteins. they interact and cooperate with each other to form pathways and complexes responsible for cell cycle regulation and activation or inhibition of specific genes. ph]][[GO:0006281, apoptosis regulation, GO:0007165, GO:0016049, nutrient and insulin levels, macromolecule metabolic process regulation, GO:1901987, GO:0006338]]
hydrolase activity, hydrolyzing O-glycosyl compounds-0[[GO:0016798, GO:0005980, GO:0006516, GO:0051787, GO:0036503, glycosaminoglycan hydrolysis, heparan sulfate hydrolysis, cell surface hyaluronidase.\\nhpyothesis: the genes listed serve key roles in the degradation of polysaccharides and glycoproteins, the recognition of misfolded proteins and their subsequent degradation by endoplasmic reticulum-associated degradation, the hydrolysis of glycosaminoglycans, and the hydrolysis of heparan sulfate for the maintenance of cell proteins and structure]][[glycosyl hydrolase, glycosyl bond hydrolysis, oligosaccharide processing, MESH:D006023, MESH:D011134, n-linked oligosaccharide, o-linked n-acetylglucosamine, β-1,4-glucosidase, β-glucosidase, β-hexosaminidase]]
hydrolase activity, hydrolyzing O-glycosyl compounds-1[[glycohydrolase enzymes, glycosaminoglycans (gag]][[glycosyl hydrolase, glycohydrolytic enzyme, MESH:D006821, MESH:D005644, lysosomal hydrolase, n-linked oligosaccharide processing, MESH:D001616, MESH:D001619, MESH:D001617, MESH:D009113, alpha-1,4-glucosidase, MESH:D043323, MESH:D000520, MESH:D055572, mannosidase, MESH:M0012138, alpha-l-iduronic acid, alpha]]
ig-receptor-binding-2022-0[[antigen binding activity, immunoglobulin receptor binding activity, GO:0002377, GO:0002250, protein homodimerization]][[antigen binding activity, immunoglobulin receptor binding activity, activated/inactivated immune response, GO:0042803, peptidoglycan binding activity]]
ig-receptor-binding-2022-1[[immunoglobulin receptor binding activity, GO:0002253, antigen binding activity, GO:0042803, immunoglobulin lambda-like polypeptides, preb cell receptor, src family of protein tyrosine kinases, c-type lectin/c-type lectin-like domain]][[antigen binding activity, immunoglobulin receptor binding activity, GO:0002253, GO:0042803, peptidoglycan binding activity, phosphatidylcholine binding activity, transduction of signals, allelic exclusion, myristylation, palmitylation, protein tyrosine kinases, sh2 and sh3 domains, MESH:D008285, MESH:D010455, antigen presenting cells, preb cells, src family of protein tyrosine kinases (ptks), c-type lectin domain]]
meiosis I-0[[GO:0004519, bcl-2 homology domain 3 binding, GO:0003682, GO:0003677, GO:0003678, GO:0003697, 3'-5' exode]][[the gene summaries indicate that most of the genes are involved in processes related to dna binding, GO:0006281, GO:0006310, and meiotic processes. the enriched terms include \"dna binding\", \"dna repair\", \"dna recombination\", \"meiosis\", \"double-stranded dna binding\", \"single-stranded dna binding\", GO:0003682, GO:0004519, dead-like helicase activity, and bcl-2 homology domain activity.\\n\\nmechanism: the mechanism underlying the enrichment of these gene functions appears to be related to the repair and maintenance of chromosomal integrity as well as the regulation of cell division, differentiation, and development. through their combined activities, the genes appear to be involved in the maintenance of genome stability and the efficient transmission of genetic information from one generation to the next]]
meiosis I-1[[meiotic recombination, GO:0006281, GO:0007059, double-strand dna break repair, homologous chromosome pairing, dna binding activity, GO:0051289]][[GO:0006281, meiotic recombination, GO:0006302, GO:0035825, chromosome synapsis, GO:0007059, MESH:D023902, holliday junction resolution, dna strand-exchange, reciprocal recombination, GO:0007130, GO:2000816, positive regulation of response to dna damage, GO:0006611, GO:0031297, GO:0000712, GO:0060629, GO:0003677, GO:0003697, single-str]]
molecular sequestering-0[[this list of genes encodes proteins involved in a range of cellular processes such as cell cycle progression, GO:0006897, iron storage and regulation, cellular response to stress and inflammation, GO:0006915, transcriptional regulation, GO:0046907, GO:0016567, and toxic metal and cytosolic signaling. enriched terms include protein binding, lipid and hormone transport, GO:0003779, GO:0003724, GO:0006511, cell cycle progression, and negative regulation of nitrogen compound metabolic process. mechanism: these genes are involved in a wide range of processes related to regulating cell growth, GO:0032502, and homeostasis. they play a role in pathways such as the cell cycle, GO:0006915, inflammatory metabolic processes]][[GO:0005515, GO:0046907, GO:0043161, GO:0051726, regulation of cell growth and survival, cholesterol and lipids metabolism, nf-κb inhibiting proteins, GO:0009792, GO:0007283, GO:0045087, cytokines and growth factors, antioxidant enzymes, GO:0030097]]
molecular sequestering-1[[GO:0005515, MESH:D015533, GO:0008152, MESH:D007109, GO:0006915, GO:0007049, GO:0016310]][[GO:0006897, iron storage, GO:0008610, GO:0006915, GO:0008283, GO:0030154, defense from bacterial infection, transcription regulation, translation regulation]]
mtorc1-0[[GO:0006412, GO:0015031, protein signaling, GO:0008152, GO:0010467]][[GO:0006412, GO:0008152, GO:0006457, MESH:D054875, GO:0006351, GO:0003677, damage control, GO:0032502, cellular pathway regulation, GO:0006915, GO:0007049, GO:0030163]]
mtorc1-1[[metabolic reactions, GO:0051726, energy production, MESH:D011494, GO:0016791, MESH:D003577, MESH:D000604, peptidase c1 family, GO:0031545, ion transporter, ubiquitin-like proteases, ubiquitin ligases, serine/threonine protein kinases, glyceraldehyde-3-phosphate dehydrogenase, nadp-dependent dehydrogenases, rna binding protein, GO:0016467, pyruvate dehydrogenase, MESH:D012321, GO:0016538, MESH:D005634, heat shock protein, hetero trimeric co-factors, MESH:D050603, MESH:D000263, MESH:D013762, MONDO:0008090]][[GO:0008152, GO:0023036, GO:0007165, transcriptional regulation, epigenetic regulation, GO:0044183, proteolytic activity, GO:0051726]]
peroxisome-0[[this set of genes are enriched for terms related to peroxisomal biogenesis and peroxisomal protein import. the aaa atpase family, peroxisomal membrane proteins, c-terminal pts1-type tripeptide peroxisomal targeting signals, and peroxisomal targeting signal 2 are all over-represented in the gene list.\\n\\nmechanism: the mechanism behind these genes is the import of proteins into peroxisomes, resulting in peroxisomal biogenesis. the aaa atpases, peroxisomal membrane proteins, c-terminal pts1-type tripeptide peroxisomal targeting signals, peroxisomal targeting signal 2 are all involved in either targeting or catalyzing this protein import]][[peroxisome biogenesis, peroxisomal protein import, tripeptide peroxis]]
peroxisome-1[[this set of genes is related to the function of peroxisome biogenesis and associated disorders. the enriched terms are peroxisome biogenesis, GO:0017038, peroxisomal matrix proteins, atpase family, and pti2 receptor/pex7.\\n\\nmechanism: peroxisomes are important organelles for a variety of metabolic functions, and the synthesis and organization of these organelles is mediated by the pex genes. pex6 and pex2 are involved in protein import, where the pex2 protein forms a membrane-restricted complex, and pex6 is predominantly cytoplasmic and plays a direct role in peroxisomal protein import and receptor activity. pex3 and pex7 are required for peroxisomal biogenesis, and pex7 is the cytosolic receptor for the set of peroxisomal matrix enzymes targeted to the organelle by the peroxisome targeting signal 2. lastly, pex1 forms a heteromeric complex and plays a role in the import of proteins into peroxisomes and peroxisome biogenesis]][[aaa atpase family, MONDO:0019234, peroxisomal protein import, peroxisomal matrix protein import, heteromeric complex, peroxisome targeting signal 2]]
progeria-0[[GO:0000785, nuclear membr]][[the genes in this list are associated with post-translational proteolytic cleavage, intermolecular integration, dna repair and dna helicase activity, and nuclear stability and chromatin structure. the underlying mechanism is likely related to protein modification and regulation of cellular components involved in dna metabolism and gene expression. the enriched terms include protein modification, proteolytic cleavage, GO:0003678, intermolecular integration, GO:0006281, chromatin structure, nuclear stability]]
progeria-1[[these genes are all related to essential functions that facilitate the proper structure and organization of the nucleus and genome, primarily through the formation and maintenance of nuclear lamin, dna helicases and chromatin structures. there is evidence that all of these genes are involved in the proper functioning of cell division, GO:0006281, and transcription, as well as the maintenance of genome stability. the most enriched terms related to the functions of these genes are nuclear lamina, dna helicase, chromatin structure, GO:0006281, GO:0006351, genome stability, GO:0051301, nuclear membrane proteins, and nuclear localization signal. \\n\\nmechanism: the genes may be involved in pathways that coordinate the formation and maintenance of nuclear lamin, dna helicase, and chromatin structures, which are necessary for cell division and transcription, as well as the maintenance of genome stability. these pathways may involve the direct interactions between the gene products, as well as the recruitment of nuclear membrane proteins and signals involved in maintaining nuclear organization]][[this set of genes is involved in the maintenance of genome stability and chromosome integrity, likely in terms of forming the nuclear lamina and promoting nuclear reassembly. the enriched terms are genome stability, chromosome integrity, GO:0005652, nuclear reassembly.\\n\\nmechanism: the set of genes are likely working together to form and maintain a matrix of proteins which form the nuclear lamina next to the inner nuclear membrane, thus providing stability to the genome and the chromosomes by helping to organize the dna within the nucleus. this is achieved through binding with both dna and inner nuclear membrane proteins and recruiting chromatin to the nuclear periphery to achieve nuclear reassembly]]
regulation of presynaptic membrane potential-0[[neuronal signaling, neuron communication, MESH:D007473, excitatory dependent channels, inhibitory neurotransmitter, ligand-gated ion channel, g protein-coupled membrane receptor]][[MESH:D007473, voltage-gated ion channel, MESH:D015221, ligand-gated ion channel, MESH:D018079, MESH:D017470, MESH:D015222]]
regulation of presynaptic membrane potential-1[[MESH:D017981, MESH:D058446, GO:0009451, voltage-gated ion channels, channel subunits, channel polymorphisms, g-protein-coupled transmembrane receptors, MESH:D017470, MESH:D018079, MESH:D015221]][[GO:0007268, MESH:D009482, inhibitory, excitatory, MESH:D017981, MESH:D015221, MESH:D018079, MESH:D017470, MESH:D007649, GO:0009451, voltage-gated, MESH:D007473, MESH:D058446, MESH:D019204]]
sensory ataxia-0[[transcriptional regulation, mitochondrial rna synthesis, neurodevelopment, GO:0030218, GO:0036211, nucleolar function, neuronal network formation, sensory receptor function]][[GO:0000981, GO:0009056, moonlighting proteins, GO:0002377, adapter molecules, heme transporter, myelin upkeep, GO:0005643, mitochondrial dna polymerase, ubiquitin ligase, aminoacyl-trna synthetase.\\n\\nmechanism: these genes work together in a joint mechanism to regulate biological processes like cell replication, neuronal development, protein folding, and enzymatic activity. in particular, their collective involvement in the coordination of transcriptional activity, ion transport, and dna-binding suggests a complex integrated process by which these genes serve to facilitate normal cell functions]]
sensory ataxia-1[[GO:0000981, dna helicase, hexameric dna helicase, neurotrophic factor, pdz domain, ma cation channels, MESH:D005956, protein synthetase, mitochondrial dna polymerase, heme transporter, GO:0005643, MESH:D044767, transmembrane glycoprotein]][[GO:0000981, dna helicase, nerve myelin maintenance, mechanically-activated cations channels, nerve motor neuron survival, MESH:D054875]]
term-GO:0007212-0[[g-protein coupled receptor signaling, g-protein subunit signaling, GO:0004016, phospholipase c-beta activity, GO:0005102, GO:0007165, second messenger synthesis, transmembrane signaling]][[the summaries of the provided gene functions describe proteins linked to the activity and regulation of g-protein coupled receptor signaling pathways, including dopamine, MESH:D016232, and serotonin receptors, as well as proteins involved in calcium ion regulation, GO:0003677, and apoptosis. statistically over-represented terms include: g-protein coupled signaling; calcium ion regulation; transmembrane signaling; dna binding; and apoptotic process. \\n\\nmechanism:\\nthe common function of these genes is likely to be linked to the regulation of g-protein coupled signaling pathways, which regulate a variety of cellular processes, including cellular signaling and growth, neuronal development, apoptosis. calcium ion regulation transmembrane signaling are also likely to be important for the functioning of these genes. dna binding proteins proteins that enable clathrin light chain binding activity may be involved in the transcriptional regulation of these signals]]
term-GO:0007212-1[[the list of human genes supplied involves several different cell signaling pathways, including the dopamine receptor (drd1, drd2, drd3 and drd5) pathway, g-protein coupled receptor (gpcr) signalling pathway (gnas, gnai3, gnaq, gna11, gna14, gna15, gnb1, gnb5, gnao1, gng2, sl]][[this gene set was comprised of dopamine and g-protein coupled receptors that participate in cellular signaling pathways and influence cellular functions such as metabolism and behavior. the genes are involved in a wide range of pathways such as signal transduction, transcriptional regulation, memory and behavior, GO:0007612, neural development and synaptic plasticity. the enriched terms in this list include: signal transduction, g protein-coupled receptor, camp, MESH:D000262, MESH:D054799, MESH:D017868, calcium ions, transcriptional regulation, GO:0000981, MESH:D011954, wnt and pi3k signaling pathways, neuronal growth and development, GO:0010467, and synaptic receptors.\\n\\nmechanism: this gene set is involved in many pathways such as signal transduction, transcriptional regulation, and synaptic organization. signal transduction occurs through g-protein coupled receptors and camp, which in turn regulate downstream effectors including adenylyl cyclase, MESH:D017868, and calcium ions. furthermore, transcriptional regulation occurs through various receptor signaling pathways, such as those related to the wnt and pi3k pathways, while dopamine receptors regulate neuronal growth and development, GO:0010467, and behavior. finally, synaptic receptors enable]]
tf-downreg-colorectal-0[[transcriptional regulation, GO:0006338, GO:0003677, GO:0000981, coactivator, heterodimer, response element]][[dna-binding, chromatin-binding, transcriptional regulation, e-box dna consensus sequence binding, dna damage response regulation, dna damage response maintenance, phosphoprotein shutting, MESH:D016335, interaction with cellular retinol-binding protein, hormone-dependent transcription, receptor-dependent transcription, nuclear hormone receptor-dependent transcription, transcriptional coactivator complex recruitment, GO:0000785]]
tf-downreg-colorectal-1[[transcription factor regulation, GO:0016569, dna-binding activity, zinc-finger binding, GO:0032183, retinoid x receptor responsive element binding]][[transcriptional regulation, dna-binding, chromatin binding activity, histone binding activity, GO:0000988]]
no_synopsisEDS-0[[GO:0031012, ecm components, matrix components, ecm regulators]][[GO:0001501, GO:0032964, cell-matrix interactions, extracellular matrix remodeling, cell signaling]]
EDS-1[[extracellular matrix protein network, collagen fibril formation, GO:0030199, ecm protein network assembly, UBERON:2007004]][[collagen production, GO:0061448, matrix remodeling, zinc finger protein regulation]]
FA-0[[MONDO:0100339, \"double strand break repair\", \"fanconi anemia protein complex\", \"ubiquitin ligase complex formation\"]][[GO:0006281, homologous recomination, MESH:M0006667, GO:0004518]]
FA-1[[GO:0006974, dna damage recognition, GO:0006281, GO:0035825, double-stranded break repair, double-stranded break recognition]][[MONDO:0100339, dna/rna damage response, dna/rna metabolism, GO:0051726, genome stability, MONDO:0019391]]
HALLMARK_ADIPOGENESIS-0[[MESH:D004734, GO:0006631, GO:0045444, GO:0006695, GO:0006699]][[metabolic regulation, GO:0050658, GO:0006412, cell membrane transport, transcription regulation, GO:0006915, GO:0006457, GO:0019432, GO:0003676, GO:0006633, GO:0006096, GO:0045454]]
HALLMARK_ADIPOGENESIS-1[[MESH:D004734, cell death regulation, cell proliferation signaling, dna replication/remodeling, GO:0006396, GO:0006629]][[GO:0008152, MESH:D004734, GO:0007165, GO:0006119, transcriptional regulation, GO:0006468, GO:0051726, GO:0006629, GO:0006457, protein assembly, mitochondrial function, GO:0006915, GO:0006839, GO:0055085, GO:0007010, GO:0006094, GO:0006096, GO:0042632]]
HALLMARK_ALLOGRAFT_REJECTION-0[[cell surface molecules, MESH:D016207, MESH:M0000731, receptor signalling, transcriptional regulation, GO:0006915]][[immune signalling, GO:0051726, cellular differentiation, transcriptional regulation]]
HALLMARK_ALLOGRAFT_REJECTION-1[[GO:0019882, GO:0007165, b and t cell metabolism, GO:0001816, GO:0006935]][[genes in this list are representative of various pathways involved in cell movement, GO:0019882, GO:0006954, immune regulation, and cell signaling events including jak-stat and mapk- pi3k pathways. enriched terms include “immune system processes”; “immune recognition pathways”; “cytokine-mediated signaling pathways”; “inflammatory response”; “cellular immune activation”; “intestinal immune network for iga production”; “cytokine secretion”; “tcr signaling pathway”; “cd4 t cell activation”; “t lymphocyte differentiation”; “innate immune response”; and “cytokine-cytokine receptor interaction”.\\n\\nmechanism: the genes are involved in pathways that affect cell movement, GO:0019882, GO:0006954, immune regulation, and cell signaling. these pathways control the activation, response, differentiation, and survival of t cells by regulating cytokine expression, activation of specific receptors, production of antibodies, regulation of transcription factors and their binding to promoters, other immune system processes]]
HALLMARK_ANDROGEN_RESPONSE-0[[genes in this list are involved in developmental processes, metabolism, and the inflammatory response. the terms enriched in these genes include: cell cycle regulation, GO:0008152, GO:0006260, GO:0015031, receptor signaling, GO:0006954, GO:0006915, GO:0006351, GO:0006457, GO:0016477, developmental processes.\\n\\nmechanism: these genes appear to work together to regulate a variety of cellular processes, such as cellular metabolism, transcription, growth, and differentiation, as well as communication between cells and the environment. these genes likely act in concert to coordinate the intricate interplay between these processes and respond to changes in the environment. furthermore, they likely play a role in the body’s inflammatory response when faced with a variety of external stimuli]][[genes in this list are mainly involved in regulation of skeletal tissue formation and development, signal cascade activation, protein folding, cellular metabolism and movement, cell cycle regulation, and transcriptional regulation. the underlying biological mechanism may be related to the complex network of interactions among these genes in controlling the basic functions of a cell. the enriched terms are: bone morphogenesis, GO:0001501, signal cascade activation, GO:0006457, GO:0044237, cellular movement, GO:0051726, transcriptional regulation, chromatin and dna modification]]
HALLMARK_ANDROGEN_RESPONSE-1[[GO:0065007, GO:0023052, GO:0019538, GO:0051726, transcription regulation, MESH:D021381, GO:0007165, membrane trafficking, protein kinase regulation, GO:0044237, GO:0006259, GO:0006468, GO:0030163, mitochondrial function, GO:0006629, cytoskeleton regulation, GO:0007155, GO:0009117]][[gene transcription and regulation, protein translation and metabolism, cytoskeletal organization, GO:0006629]]
HALLMARK_ANGIOGENESIS-0[[extracellular matrix formation and maintenance, fibrous tissue development, vascular development, cell-cell communication and migration, extracellular secreted signaling, collagen and laminin-fibrillin proteins]][[GO:0030198, vascularization, endothelial cell aggregation, GO:0007155, cell surface interactions]]
HALLMARK_ANGIOGENESIS-1[[GO:0032502, GO:0009653, GO:0009888, GO:0030198, GO:0006954, MESH:D066253, cell-cell communication]][[cytokine receptor signaling, growth factor signal transduction, transmembrane and extracellular matrix proteins, development of muscle, bone, and neuronal networks]]
HALLMARK_APICAL_JUNCTION-0[[this term enrichment test suggests that the genes provided are involved in cell adhesion, GO:0006955, and tissue morphogenesis. specifically, the adhesion-associated genes enriched in this dataset include icam1, icam2, icam4, icam5, nectin1, nectin2, nectin3, nectin4, nrxn2, ptprc, sdc3, thy1, vcam1, and vwf. the immune response-associated genes enriched in this dataset include cd34, cd86, cd209, ctnna1, icam2, icam4, icam5, map4k2, msn, pard6g, and tnfrsf11b. lastly, the tissue morphogenesis-associated genes enriched in this dataset include acta1, actb, actc1, actg1, actn1, actn2, actn4, adam15, adra1b, akt2, alox15b, amigo2, baiap2, cadm2, cadm3, MESH:M0359286, col9a1, MONDO:0011642, ctnnd1, MESH:C040896]][[GO:0060348, joint development, MESH:D024510, GO:0061448, GO:0007155, adhesion receptor complex formation, GO:0007165, receptor-mediated signaling cascades]]
HALLMARK_APICAL_JUNCTION-1[[GO:0009653, GO:0016049, MESH:D047108, cellular signaling, GO:0031012, cytoskeletal organization, basal membrane assembly, GO:0098609, GO:0006915, GO:0016477, GO:0001816, growth factor production, tyrosine kinase activity, g-protein coupled receptor signaling pathway, nuclear receptor signaling pathway, GO:0016055, phosphatidylinositol 3-kinase signaling pathway, protein kinase b signaling pathway, map kinase signaling pathway, cell adhesion molecule signaling pathway, focal adhesion signaling pathway]][[GO:0007155, GO:0016477, migration and interaction, cytoskeletal organization, actin cytoskeletal regulation, GO:0007165, regulation of actin cytoskeletal organization]]
HALLMARK_APICAL_SURFACE-0[[GO:0016477, membrane receptor signaling, GO:0009100, protein tyrosine kinases, GO:0007155, cytoskeletal dynamics, receptor-mediated lectin binding, GO:0006629, GO:0007015]][[cell regulation, GO:0007165, GO:0007155, GO:0006457, GO:0030198]]
HALLMARK_APICAL_SURFACE-1[[cell signaling, GO:0032502, transcription regulation, GO:0008152, MESH:D049109, MESH:D005786]][[cell adhesion and migration, cell signaling, GO:0030154, protein kinase and phosphatase activities, transcription and dna metabolism, MESH:D056747, glycosylation and carbohydrate metabolism, cell growth and proliferation]]
HALLMARK_APOPTOSIS-0[[transcriptional regulation/control, cell cycle/apoptosis, GO:0006955]][[GO:0006915, transcription regulation, cell cycle progression, GO:0006954, GO:0006260, GO:0006281, oxidative stress response, immune system activation]]
HALLMARK_APOPTOSIS-1[[the genes listed are mainly involved in the regulation and expression of genes, inflammation pathways and cell cycle regulation. specifically, enriched terms include gene expression and transcriptional regulation, dna damage and repair, GO:0007165, GO:1901987, metabolism and apoptosis.\\n\\nmechanism: the commonality in the function of these genes is likely related to the roles they play in the regulation of gene expression by affecting signal transduction, GO:0008152, cell cycle control and apoptosis. these gene functions may lead to a variety of processes, including inflammation pathways related to immunity, UBERON:2000098, MESH:D002470]][[cell death regulation, GO:0006954, immune reaction, growth and morphogenesis, UBERON:2000098, GO:0006915, GO:0006281, GO:0030217, GO:0001816, GO:0051726, fast axonal transport, extracellular proteolysis, GO:0007155, GO:0042060, MESH:D009362, MESH:D063646, GO:0016477, regulation of nf-kb pathway]]
HALLMARK_BILE_ACID_METABOLISM-0[[MESH:M0496924, GO:0006869, development of connective tissues, GO:0006633, GO:0006699, GO:0006805, GO:0006694, cellular transport, MESH:M0023727, connective tissue formation, digit development, GO:0060173]][[GO:0006629, GO:0006869, organ development, cell signaling, GO:0006412, transport processes]]
HALLMARK_BILE_ACID_METABOLISM-1[[this set of genes is related to lipid metabolism and lipid transport, protein homeostasis, retinol metabolism, developmental processes, and transportation of lysosomal hydrolases and oxygen-carrying molecules. the set includes genes involved in lipid metabolism (aqp9, atxn1, GO:0033781, abcg4, acsl1, fdxr, aldh8a1, hsd17b11, aldh9a1, aldh1a1, cyp7a1, cp25h, gstk1, MONDO:0100102, acsl5), lipid transport (abca1, abca2, abca3, abca4, abca5, abca8, abca9, abcg8), protein homeostasis (pex12, pex16, pex19, pex11a, pex11g, GO:0005053, pex6, pex26), retinol metabolism (abcd1, abcd2, abcd3), developmental processes (lck, nr3c2, retsat, klf1, ephx2, phyh, bbox1, MONDO:0004277]][[GO:0006629, GO:0006536, serine metabolism, transcription factor regulation, oxidative stress response]]
HALLMARK_CHOLESTEROL_HOMEOSTASIS-0[[transcriptional regulation, MESH:D006026, GO:0006629, GO:0005509, GO:0001525, MESH:D016326, receptor signaling; transcription regulators; calcium signaling; glycoside hydrolases; lipid metabolism; cell adhesion; extracellular matrix proteins; signaling receptor molecules.\\n\\nmechanism: this set of genes is likely involved in regulating transcriptional responses, MESH:D006026, GO:0006629, GO:0005509, GO:0001525, MESH:D016326, and receptor signaling. many of these genes interact with each other, forming complex cellular networks and pathways. the particular genes identified in this list are likely related to stimulating or inhibiting the expression of specific genes or pathways, as well as modulating or mediating responses to various environmental signals or stimuli. these gene functions likely interact to maintain homeostasis, contribute to cellular development and processes, promote angiogenesis, and provide a structural and functional framework for the extracellular matrix. furthermore, these genes may be involved in signaling pathways that involve receptor molecules by modulating intracellular calcium levels]][[GO:0006629, GO:0008203, cell signaling and regulation, GO:0032502, GO:0007155, GO:0006915, GO:0006351]]
HALLMARK_CHOLESTEROL_HOMEOSTASIS-1[[GO:0006629, transcriptional regulation, cellular adhesion, GO:0032502, GO:0042592]][[GO:0006629, cholesterol control, GO:0009062, GO:0006699, hmgcr regulation, pmvk regulation, fads2 regulation, srebf2 regulation, s100a11 regulation, mvk regulation]]
HALLMARK_COAGULATION-0[[inflammatory response regulation, extracellular matrix formation regulation, proteolytic activities]][[extracellular matrix remodeling; angiogenesis and vascular development; immune response and platelet activation; collagen and fibronectin metabolism and regulation; endocytosis and signal transduction; \\nmechanism: the genes in this list work together to control and regulate multiple relevant processes, such as extracellular matrix remodeling, which is the process of breaking down and reorganizing the components of the extracellular matrix in order to facilitate tissue development and repair, angiogenesis and vascular development, which regulate the formation of new blood vessels and ensure proper blood flow throughout the body, immune response and platelet activation, which are necessary to protect the body from foreign agents and to form healthy blood clots, collagen and fibronectin metabolism and regulation, which are important for tissue integrity and structure, and endocytosis and signal transduction, which are necessary for cellular communication and regulation]]
HALLMARK_COAGULATION-1[[GO:0007165, GO:0030198, matrix molecular regulation, GO:0006508, GO:0050817, matrix remodeling, GO:0009653]][[GO:0007155, proteolysis regulation, extracellular protein-cell interaction, migration, GO:0050817, GO:0006956]]
HALLMARK_COMPLEMENT-0[[GO:0030198, immune system/inflammation/interferon response, GO:0000988]][[development of tissue and organs, GO:0007165, cell surface receptor binding, GO:0050896, UBERON:0002405, GO:0006955, GO:0005125]]
HALLMARK_COMPLEMENT-1[[immunoglobulin like domains, GO:0042113, GO:0050852, integrin mediated cell adhesion, GO:0006915, regulation of transcription, GO:0007165, receptor mediated endocytosis and exocytosis, GO:0030198, calcium mediated signaling]][[cellular signalling, GO:0006954, cell stress response, cell-cell interaction, GO:0007165, GO:0045087, cytoskeletal remodelling, GO:0006457, GO:0050900, GO:0004672, GO:0007155, MESH:D005786, GO:0006260, protein activation, GO:0019763, GO:0002377, GO:0016791]]
HALLMARK_DNA_REPAIR-0[[GO:0006259, GO:0016070, GO:0006412, dna damage repair, GO:0006351, GO:0006325]][[GO:0032502, GO:0006260, MESH:D047108, GO:0030154, transcription regulation, GO:0006335, nuclear mrna surveillance pathway, GO:0016070, GO:0006281, GO:0140014, rna-dependent dna replication]]
HALLMARK_DNA_REPAIR-1[[GO:0006260, transcription regulation, GO:0006412, GO:0043687, nucleic acid metabolism, GO:0010467, GO:0006397, GO:0006412]][[nucleic acid metabolism, GO:0006351, post-transcriptional modifications, GO:0006338, GO:0000398, GO:0006281, rna polymerization, GO:0006397, GO:0051028, GO:0006413]]
HALLMARK_E2F_TARGETS-0[[GO:0006260, GO:0006281, gene transcription, GO:0006412, GO:0016569, GO:0007049, GO:0010468]][[transcriptional regulation, GO:0016569, mitotic division, GO:0051726, MESH:D004268, MESH:D006657, GO:0000981, MESH:D004259, MESH:D012321, chromatin remodeling proteins, ubiquitin ligases, nucleosome assembly proteins, helicases, motor proteins, GO:0000075]]
HALLMARK_E2F_TARGETS-1[[GO:0006260, GO:0006351, GO:0030261, transcriptional regulation, GO:0006338, GO:0006974, chromatin structure modifications, GO:0006281, GO:0006306, GO:0030163, GO:0007094, GO:1901987, GO:0006468]][[GO:0006260, GO:0006281, GO:0016569, transcription regulation, translation regulation, protein-protein networks, GO:0051225, kinesin motor proteins, dynein motor proteins]]
HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0[[genes in this list are enriched for functions related to modulating extracellular matrix, cell adhesion and morphogenesis, as well as playing roles in development, growth and signal transduction pathways. enriched terms include:extracellular matrix modulation; cell adhesion; morphogenesis; development; growth; signal transduction.\\n\\nmechanism: many of the genes listed are involved in the signaling, development and maintenance of the extracellular matrix, cell adhesion and morphogenesis, which can be regulated through diverse pathways involving the growth factors (bdnf, MESH:D016222, igfbp2, igfbp3, igfbp4, wnt5a), proteoglycans (comp, cspg4, MONDO:0021055, lamc1, lamc2, dcn, has3, sdc1) and adhesion molecules and receptors (acta2, abi3bp, cadm1, cap2, capg, cd44, cdh11, cdh2, cdh6, fn1, grem1, itga2, itga5, itgav, itgb1, itgb3, itgb5, lrp1, tagl]][[GO:0031012, GO:0007155, GO:0048870, cell-matrix interaction, growth factor signaling, cytokine signaling, matrix remodeling]]
HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1[[GO:0030198, GO:0009653, collagen production, matrix metalloproteinase activity, GO:0009100, cytoskeletal component organization, regulation of growth and reproduction, regulation of skin morphogenesis]][[GO:0048705, cell-cell adhesion and motility, extracellular matrix production and remodeling, connective tissue development and differentiation, collagen production and turnover, cytokine and chemokine signaling]]
HALLMARK_ESTROGEN_RESPONSE_EARLY-0[[cell morphology; homeostasis & regulation; innervation; cellular metabolism.\\nmechanism: the genes are likely to be involved in various pathways, such as the regulation of gene expression, protein synthesis and structure, cell motility and differentiation, tissue repair regeneration]][[GO:0006260, GO:0006351, GO:0010467, GO:0016049, differentiation, GO:0016485, trafficking, GO:0060349, cancer-related pathways, GO:0098609, matrix remodeling, intracellular signaling, external signals, internal signals]]
HALLMARK_ESTROGEN_RESPONSE_EARLY-1[[immunological response, GO:0007155, transcription regulation, GO:0016477, GO:0008544, GO:0060348, MESH:D024510, GO:0015031, GO:0006915]][[transcriptional regulation, GO:0007165, protein-protein interactions, GO:0055085, GO:0008610]]
HALLMARK_ESTROGEN_RESPONSE_LATE-0[[MESH:D023281, cytoskeletal processes, GO:0006955, extracellular modification]][[GO:0030198, GO:0007155, GO:0016477, GO:0048870, growth factor signaling, cytoskeletal organization]]
HALLMARK_ESTROGEN_RESPONSE_LATE-1[[the commonalities in the functions of these genes are involved in transcription, post-transcriptional regulation, GO:0009966, and cell-cycle related processes. the enriched terms are: transcription; post-transcriptional regulation; signal transduction; cell cycle; dna binding; regulation of transcription; regulation of protein abundance; chromatin remodeling; ubiquitination; and protein-protein interaction.\\n\\nmechanism: the underlying mechanism may be related to the regulation of intricate pathways leading to the expression of specific genes in conversion of genetic information into protein-based processes. these genes may be involved in a variety of biological processes, such as transcriptional and post-transcriptional regulation of gene expression, GO:0007165, cell-cycle related processes, GO:0003677, regulation of transcription, regulation of protein abundance, GO:0006338, MESH:D054875, protein-protein interaction]][[GO:0030198, GO:0000988, receptor signaling pathway, GO:0007269, GO:0019725, GO:0006508, immunological responses, GO:0016049, GO:0003677, GO:0006629]]
HALLMARK_FATTY_ACID_METABOLISM-0[[GO:0006631, oxidation of lipids, GO:0006695, GO:0005977, GO:0009117, GO:0006862, GO:0009165, electron transport activity, enzyme regulation, regulation of metabolic pathways, GO:0006915]][[metabolic pathways; cellular functions; energy metabolism; lipid metabolism; amino acid metabolism; dna damage repair; cell signaling.\\nmechanism: the genes listed here are likely involved in the various metabolic pathways and cellular functions, perhaps through the production of enzymes, MESH:D011506, or other molecules that contribute to energy metabolism, GO:0006629, amino acid metabolism, dna damage repair, cell signaling]]
HALLMARK_FATTY_ACID_METABOLISM-1[[GO:0008152, energy production and storage, lipid metabolism and transport, acetyl-coa biosynthesis and catalysis, oxidation, GO:0006631]][[GO:0006629, cell cytoskeleton, GO:0008610, GO:0016042, lipid transportation, GO:0034440, cell membrane biogenesis, GO:0048870, cell traffic, cell signaling]]
HALLMARK_G2M_CHECKPOINT-0[[GO:0051726, GO:0006260, GO:0006338, cyclin b-cdk1 activation, cks1b, cdc25a, wee1, cdc20, apc/]][[GO:0006260, GO:0006351, GO:0051726, protein binding/interaction, chromatin modifiers/modification, GO:0006281, GO:0000988, GO:0006397, GO:0006915, ubiquitination and proteasomal degradation]]
HALLMARK_G2M_CHECKPOINT-1[[nuclear processes, GO:0006260, gene transcription, GO:0006338, GO:1901987, GO:0006281, GO:0010467, GO:0010468]][[genes involved in the list are mainly associated with dna replication, cell division and related functions. enriched terms include \"cell cycle\", \"dna replication\", \"chromatin modification\", \"transcription regulation\", \"cell division\", \"dna repair\", \"transcriptional regulation\", \"chromosome segregation\".\\n\\nmechanism: these genes likely play a role in the coordination of the many steps and activities involved in dna replication, GO:0051301, and related cellular processes. the cell cycle is an area of particular interest due to its critical role in the growth and division of cells. dna replication, modification, repair occur during cell division in order to produce maintain copies of genetic information. chromatin modifications occur during cell division in order to package regulate genomic information. transcriptional regulation involves the control of gene expression the production of proteins other materials essential for the maintenance of cellular functions. chromosome segregation cell division serve to divide replicated genetic material into daughter cells]]
HALLMARK_GLYCOLYSIS-0[[developmental process: digit development, GO:0001525, GO:0030154, GO:0005488, transporting, GO:0008152, GO:0008152, cell signalling]][[the genes in this list are involved in a variety of cellular processes including protein translation, GO:0070085, regulation of ion channels, gene transcription and dna replication. the enriched terms identified are: translation; glycosylation; ion channels; gene transcription; and dna replication.\\n\\nmechanism: the common underlying mechanisms of the genes in this list likely involve cellular processes such as protein translation, GO:0070085, regulation of ion channels, gene transcription and dna replication. these processes are essential for the regulation of cell functions and the maintenance of a stable organism]]
HALLMARK_GLYCOLYSIS-1[[GO:0005975, MESH:D004734, GO:0046785, dna binding and replication, actin cytoskeleton dynamics, ion channel regulation, transcriptional regulation, GO:0007155]][[structural proteins, GO:0006096, GO:0006098, GO:0006099, GO:0007155, GO:0030166, extracellular matrix formation, cytoskeletal assembly]]
HALLMARK_HEDGEHOG_SIGNALING-0[[GO:0009653, GO:0022008, GO:0016049, GO:0030154, GO:0001764, thalamocortical pathway development, GO:0001764, GO:0007399, neural crest migration]][[the provided genes are involved in a variety of different processes ranging from morphogenesis, development and growth of the digits/limbs, neuronal migration and regulation of cell proliferation. the underlying biological mechanism might be related to the modulation of cell migration, development of neural connections, formation of complex structures, maintenance of body plan and tissue development. enriched terms are: morphogenesis, digit/limb development, GO:0001764, GO:0042127, modulation of cell migration, development of neural connections, formation of complex structures, maintenance of body plan, GO:0009888]]
HALLMARK_HEDGEHOG_SIGNALING-1[[GO:0009653, GO:0007155, GO:0032502, GO:0007268, GO:0008283, GO:0016477, GO:0030154, MESH:D009473]][[neuron formation, GO:0007155, migration, GO:0007165, GO:0048729, GO:0007399]]
HALLMARK_HEME_METABOLISM-0[[GO:0055085, MESH:D004734, GO:0003735, GO:0003676, GO:0015031, negative regulation of transcription, regulation of transcription, positive regulation of transcription, GO:0071840, iron metabolism, GO:0007165, GO:0045087, GO:0042803, GO:0051276, GO:0050794, GO:0016569, GO:0008380, GO:0005515, GO:0000075, GO:0006006, GO:0000088, GO:0009116]][[GO:0044237, energy production and transport, cytoskeleton modification, cytoskeleton remodelling, GO:0007155, MESH:D004735, MESH:M0496924, cellular transport, cellular reorganization]]
HALLMARK_HEME_METABOLISM-1[[GO:0048468, GO:0010467, GO:0048513, nucleic acid metabolism, transcriptional regulation, GO:0006259, GO:0016070, cytoskeletal dynamics, GO:0007165, GO:0006412]][[MESH:D047108, GO:0001501, GO:0048513, GO:0009653, GO:0040007, GO:0002376, GO:0048870, GO:0003707, receptor signaling pathway, GO:0006810, GO:0006897, GO:0019725]]
HALLMARK_HYPOXIA-0[[gene enrichment analysis of the gene list showed that the majority of genes are involved in cellular proliferation, GO:0006915, GO:0006811, GO:0005102, and development. the enriched terms associated with this list include cell proliferation, GO:0006915, GO:0006811, GO:0005102, cell signaling, transcriptional regulation, and development.\\n\\nmechanism: the genes are likely involved in an intricate, interconnected biological network that involves numerous signaling pathways and transcription factors necessary for cellular proliferation, GO:0006915, ion transport and receptor binding. these gene functions result in the regulation of numerous cellular processes and ultimately the development of various diseases. in addition, the genes may be regulating a number of other processes such as metabolism, cell-cell communication, energy production]][[GO:0007049, remodeling proteins, stress response proteins, calcium signaling proteins, hypoxia-inducible factor proteins, GO:0000981, chromatin-associated proteins, MESH:D010770]]
HALLMARK_HYPOXIA-1[[GO:0048468, cell metabolism, transcription regulation, GO:0010468, GO:0006974, GO:0007155, GO:0030154, GO:0042440, MESH:M0352612, GO:0006412, GO:0051726, MESH:D004734]][[GO:0032502, cell structure and movement, cell cycle and division, GO:0007165, GO:0006810, energy production]]
HALLMARK_IL2_STAT5_SIGNALING-0[[GO:0016049, cell regulation, GO:0009988, MESH:D007109, signal transduction and regulation, GO:0032502, transcriptional regulation, GO:0030198, cytokine-receptor-mediated signaling pathway]][[immunological function, GO:0030036, MESH:D011956, pro-inflammatory regulation]]
HALLMARK_IL2_STAT5_SIGNALING-1[[this list of genes are involved in developmental processes, GO:0006955, GO:0006954, GO:0007165, and cell adhesion functions. the enriched terms are \"development\"; \"signal transduction\"; \"cell adhesion\"; \"immune response\"; \"inflammation\"; \"transmembrane transport\"; \"protein metabolism\"; \"cardiovascular function\".\\n\\nmechanism: the underlying biological mechanisms involves the coordination of different pathways, genes and proteins. these genes are involved in cellular processes and regulation, including cell proliferation, differentiation, adhesion and migration, GO:0007165, and immunity. the genes also influence signaling pathways, protein metabolism and other functions that have roles in cardiovascular and carcinogenesis. the mechanisms through which these genes affect development, GO:0006954, other immunological responses are complex dependent on the coordination between multiple pathways]][[MESH:D007109, GO:0006954, GO:0016049, differentiation, GO:0032502, GO:0007165]]
HALLMARK_IL6_JAK_STAT3_SIGNALING-0[[pain sensing and signal transduction, GO:0006935, GO:0019221, leukocyte transendothelial migration, GO:0006955, GO:0030168]][[cell signaling, GO:0001816, cytokine regulation, MESH:D005786, transcription regulation, GO:0007155]]
HALLMARK_IL6_JAK_STAT3_SIGNALING-1[[GO:0007165, MESH:D056747, immune signaling, transcription regulation, cytokine regulation, GO:0030155, MESH:D005786, cell growth regulation, metabolism regulation, MESH:D002470, cell death regulation, antifungal immunity]][[cytokine regulation, chemokine regulation, interleukin regulation, cellular differentiation, cell motility and adhesion, GO:0007165, GO:0006954]]
HALLMARK_INFLAMMATORY_RESPONSE-0[[MESH:M0000731, GO:0006954, GO:0007165, transcription regulation, intercellular signaling, GO:0045087, MESH:D056704]][[this list of genes is significantly enriched for the functions of cell signalling, cytokine mediated immunity, receptor signalling, and tissue morphogenesis. furthermore, the list contains several genes associated with the immune response, including tlrs and ifns, as well as cytokines and chemokines such as ccl17, ccl20, cxcl10, cxcl9, ifnar1, tnfrsf1b, and tnfsf10. in addition, several receptors were found to be enriched on the list, including gpr132, axl, c3ar1, MONDO:0043317, and ccr7. finally, key genes involved in tissue morphogenesis were also found on the list, such as adgre1, edn1, btg2, ccl2, tacr1, and cxcr6.\\n\\nmechanism: \\nthe underlying mechanism for this enrichment of genes is likely related to the common activities of cell signalling, cytokine mediated immunity and tissue morphogenesis. the list of genes is likely regulating common processes such as cell-cell communication and inflammation. additionally, the list of genes may be involved in the development and maintenance of tissue structures, such as muscle tissue]]
HALLMARK_INFLAMMATORY_RESPONSE-1[[immune cell signaling, GO:0006928, cell surface receptor activity, GO:0006954, GO:0016477, cell–cell interactions, immune cell receptor-mediated signaling]][[GO:0006955, cellular activation, receptor-coupled pathways, transcriptional regulation, cytokine and cytokine receptor binding, GO:0006629, GO:0007155]]
HALLMARK_INTERFERON_ALPHA_RESPONSE-0[[GO:0006954, neutroph]][[analysis of this list of genes reveals that they are all involved in the functioning of the immune system in some way, either through regulation of inflammatory response pathways, recognition of foreign agents, or production of molecules defending against potentially harmful intruders. the enriched terms include \"immune system regulation\"; \"inflammatory response\"; \"foreign agent recognition\"; \"antimicrobial defense\"; \"interferon signaling\"; \"antiviral defense\". \\n\\nmechanism: the genes in this list combined likely regulate a wide variety of immune system functions, including modulating inflammation, recognizing and responding to foreign antigens, producing effector molecules against potentially harmful microorganisms, promoting interferon signaling cascades to defend from viral invasion]]
HALLMARK_INTERFERON_ALPHA_RESPONSE-1[[interferon signalling pathway, interferon gamma activity, interferon regulatory factor activity, status response to interferon, GO:0006915, GO:0008289, GO:0005509, GO:0002446]][[GO:0006955, GO:0006954, cytokine signaling, interferon response, GO:0006355, interferon-stimulated genes]]
HALLMARK_INTERFERON_GAMMA_RESPONSE-0[[GO:0006955, cell signaling, cytokine response, interferon response, nuclear factor kappab-dependent transcriptional regulation]][[MESH:M0000731, GO:0019882, GO:0006954, chemokine signaling, GO:0007155, cytokine interactions]]
HALLMARK_INTERFERON_GAMMA_RESPONSE-1[[MESH:D007109, interleukin regulation, transcription regulation, GO:0006954, cell signaling, GO:0006915]][[interferon signaling, antigen processing, presentation, and recognition, cytokine signaling, cell cycle and dna damage response, GO:0006915]]
HALLMARK_KRAS_SIGNALING_DN-0[[GO:0060348, GO:0009653, growth maintenance, GO:0007267, cell-cell communication, GO:0036211, GO:0006810]][[digit development, neural development, GO:0002520, transcriptional regulation, g-protein coupled receptors, MESH:D011494, MESH:D020662]]
HALLMARK_KRAS_SIGNALING_DN-1[[GO:0009653, cell-cell communication, GO:0032502, hormone regulation, cellular differentiation, cell-cycle, cell-signalling]][[our analysis revealed the enrichment of the gene functions related to development, GO:0007165, transcription and metabolism. specifically, some of the enriched terms include cellular development, GO:0016049, GO:0001501, GO:0048598, cell junction organization and assembly, GO:0007165, GO:0007049, GO:0006351, and cellular metabolism.\\n\\nmechanism: these gene functions may be related to the biological mechanism of growth, differentiation, and development of cells. the signals and transcription are likely involved in regulating and controlling these processes, as well as providing energy through metabolic pathways. additionally, the cell junction processes are likely involved in the coordination and communication between cells, which is essential to development]]
HALLMARK_KRAS_SIGNALING_UP-0[[GO:0007165, GO:0000902, GO:0050896, GO:0001525, GO:0065009, GO:0030198]][[GO:0007165, GO:1901987, cell-to-cell adhesion]]
HALLMARK_KRAS_SIGNALING_UP-1[[GO:0009653, GO:0009888, cell signaling, immune regulation, transcription modulation, GO:0007165, GO:0007155, GO:0016477]][[integrin, chemokine receptor, MESH:D011494, g-protein-coupled receptor, cytoskeleton proteins, cell-extracellular matrix interaction, type i ifn-mediated innate immunity, wnt signaling, MESH:D020558, MESH:D010740, MESH:D008565, MESH:D016326, receptor tyrosine kinase, toll-like receptor signaling, tlr adaptor proteins]]
HALLMARK_MITOTIC_SPINDLE-0[[the human genes abi1, abl1, abr, actn4, akap13, alms1, MONDO:0008780, anln, GO:0005680, arap3, arf6, arfgef1, arfip2, arhgap10, arhgap27, arhgap29, arhgap4, arhgap5, arhgdia, arhgef11, arhgef12, arhgef2, arhgef3, arhgef7, arl8a, atg4b, MESH:D064096, bcar1, bcl2l11, bcr, bin1, birc5, brca2, bub1, capzb, ccdc88a, ccnb2, cd2ap, cdc27, cdc42, cdc42bpa, cdc42ep1, cdc42ep2, cdc42ep4, cdk1, cdk5rap2, cenpe, cenpf, cenpj, cep131, cep192, cep250, cep57, GO:0047849]][[GO:0007049, GO:0007155, cytoskeletal organization, GO:0004672, GO:0003924]]
HALLMARK_MITOTIC_SPINDLE-1[[cytoskeletal organization, GO:0016477, GO:0051301, GO:0006260, GO:0006281, GO:0006605, GO:0065007]][[GO:0051301, GO:0006468, GO:0006338, GO:0008017, microtubule organization, GO:0051225, GO:0007059, GO:0051305, cell-cycle control, GO:0140014]]
HALLMARK_MTORC1_SIGNALING-0[[the human genes abcf2, acaca, acly, acsl3, actr2, actr3, add3, adipor2, ak4, aldoa, arpc5l, asns, atp2a2, atp5mc1, atp6v1d, MESH:D064096, bcat1, bhlhe40, btg2, bub1, cacybp, calr, canx, ccnf, ccng1, cct6a, cd9, cdc25a, cdkn1a, cfp, cops5, coro1a, cth, ctsc, GO:0038147, cyb5b, cyp51a1, dapp1, ddit3, ddit4, ddx39a, dhcr24, dhcr7, GO:0004146, ebp, edem1, eef1e1, egln3, eif2s2, elovl5, elovl6, eno1, eprs1, ero1a, etf1, MONDO:0100101, MONDO:0100102, fdxr, fgl2, MESH:D010649]][[genes in this list are involved in various aspects of cellular metabolism, GO:0065007, and development.a number of the genes have roles in energy production and metabolism such as, atp2a2, aldoa, MONDO:0009214, fao1, fgl2, gapdh, gbe1, MONDO:0015408, glrx, MONDO:0005775, me1, phgdh, and pgm1. there is a strong presence of genes involved in protein synthesis and transport, including the ribosomal proteins, the eukaryotic translation factors and initiation factors (eif2s2, eif1e1, elovl5, and elovl6). this gene set is also enriched for a number of ubiquitin and ubiquitin-like proteins (ube2d3, ufm1, uso1, tomm40, hspd1, hspe1, sytl2, nherf1, and hk2). many of these genes are involved in regulation through multiple pathways including regulation of transcription (add3, actr2, actr3, cct6a, gga2, gdh2, mef2b, ykt]]
HALLMARK_MTORC1_SIGNALING-1[[GO:0006412, MESH:D004734, cellular transport, GO:0006955, GO:0035194, mitochondrial oxidative phosphorylation, GO:0006915, GO:0016310, GO:0006096, GO:0006914]][[GO:0006412, transcription regulation, GO:0009653, GO:0016049, GO:0007165, GO:0008152, GO:0006629, cellular translation]]
HALLMARK_MYC_TARGETS_V1-0[[rna biogenesis, protein synthesis biosynthesis, atp-binding, cytoskeleton organization and assembly, GO:0006351, GO:0006338, GO:0007165, GO:0010467, GO:0006413, MESH:M0439896, GO:0006260]][[GO:0006412, GO:0036211, GO:0006260, GO:0051726, transcription regulation, GO:0016049, GO:0048468, gene expression.\\nmechanism: the genes may constitute a pathway in which they coordinate together to regulate cell growth, development, and gene expression]]
HALLMARK_MYC_TARGETS_V1-1[[GO:0000394, GO:0051028, MESH:M0439896, GO:0006412, GO:0042254, GO:0035194, GO:0006338]][[developmental regulation, energy production, GO:0006412, structural maintenance of cell components, GO:0006260, transcription regulation, protein assembly]]
HALLMARK_MYC_TARGETS_V2-0[[genes in this list are primarily involved in cell development, including the processes of rna metabolism, dna replication and cell cycle control. enriched terms include: rna metabolism; dna replication; cell cycle control; chromatin regulation; transcription regulation; cell differentiation; gene expression; and protein synthesis.\\n\\nmechanism: the genes in this list are part of a complex network of molecular pathways involved in regulating the expression, replication and maintenance of genetic material. this includes the transcription, splicing and translation of rnas as well as the replication and repair of dna. the multiple genes in this list suggest coordination and control of various steps in these processes, such as chromatin regulation, which is directly responsible for how genetic material is packaged and regulated. additionally, the genes may be involved in regulating cell cycle progression, transcription regulation and cell differentiation]][[protein post translational modification, GO:0016310, GO:0006351, GO:0006412, GO:0042254]]
HALLMARK_MYC_TARGETS_V2-1[[GO:0001775, GO:0008283, GO:0006260, dna transcription, rna translation.\\nmechanism: the genes may indicate an underlying biological pathway involving the coordinated expression of these gene sets to regulate the cell cycle, dna replication, transcription, and translation in order to enable cell proliferation]][[transcription regulation, GO:0006338, nucleosome remodeling, GO:0006260, nuclear localization, GO:0007165, GO:0016567, GO:0006468]]
HALLMARK_MYOGENESIS-0[[gene expression and structure, cytoskeletal structure and dynamics, calcium regulation and signaling, cell adhesion and migration, cell death biochemistry, metabolic regulation]][[genes in this list are associated with various cellular functions, including cell cycle regulation, developmental pathways, contractile force generation, protein synthesis and degradation, GO:0006915, GO:0000988, and metabolic processes. enriched terms include: cell cycle; cell differentiation; transcriptional regulation; intracellular signaling; muscle contraction; metabolism; apoptosis; protein synthesis; protein degradation.\\n\\nmechanism:\\n\\nthe genes in this list code for proteins involved in a range of cellular processes, including transcription factors that regulate gene expression, receptors that initiate intracellular signaling cascades, enzymes involved in metabolic pathways or apoptosis, and ion channels involved in muscle contraction and cell cycle regulation. these proteins interact to regulate the expression and activity of other proteins, impacting the activity of many important pathways that together coordinate cell growth, differentiation, MESH:D009068, GO:0008152]]
HALLMARK_MYOGENESIS-1[[GO:0031012, GO:0005856, UBERON:0005090, GO:0032502, neuromuscular structure, MESH:D007473, GO:0006811]][[the genes that were analyzed were related to development, cell signalling, GO:0008152, GO:0065007, GO:0006936, MESH:D055550, and transport. the enriched terms were cellular development, actin cytoskeleton regulation, cell migration and adhesion, GO:0051726, calcium homeostasis and signaling, GO:0006936, GO:0006119, receptor tyrosine kinase signaling, apoptosis and programmed cell death, GO:0030198, GO:0016567, GO:0042632, metabolism and energy production, cell death and apoptosis, cytoskeletal protein binding and regulation of transcription and translation.\\n\\nmechanism: the underlying biological mechanism or pathways involved in these genes include regulation of muscle contraction, cell adhesion and migration, calcium homeostasis, protein ubiquitination and stability, receptor signaling, GO:0051726, GO:0006119, GO:0008219, and regulation of transcription and translation. these mechanisms are essential for cellular development and function, and thus, are enriched in these gene list]]
HALLMARK_NOTCH_SIGNALING-0[[MESH:D047108, GO:0051726, GO:0019722, notch signaling down-regulation, wnt signaling, hedgehog signaling, GO:0000902]][[GO:0009653, GO:0048513, GO:0009888, GO:0001709, MESH:D002450, notch receptor signaling, wnt signaling, transcription factor signaling]]
HALLMARK_NOTCH_SIGNALING-1[[these genes are involved in a wide range of functions related to signaling, development, and transcriptional regulation, indicating an involvement in a variety of cellular pathways. enriched terms include: cell signaling, GO:0007399, GO:0030154, wnt signaling, notch signaling, hedgehog signaling, transcription factor regulation, GO:0006338, e3 ubiquitin ligase.\\n\\nmechanism: the likely underlying biological mechanism is a complex network of interactions between these genes and their pathways, forming a web of signaling molecules that regulate cell growth, differentiation, apoptosis and other cellular processes. the genes and pathways involved in the network are likely to interact in a dynamic manner]][[GO:0008283, GO:0009653, GO:0032502, nerve system differentiation, transcription regulation, wnt signalling pathway, GO:0007219]]
HALLMARK_OXIDATIVE_PHOSPHORYLATION-0[[mitochondrial activity, GO:0022900, GO:0006119, metabolic regulation, MESH:D065767]][[the list of genes provided are primarily involved in energy metabolism, GO:0007585, and the electron transport chain. specifically, terms such as \"oxidative phosphorylation\", \"mitochondrial electron transport chain\", and \"tricarboxylic acid cycle\" are found to be significantly over-represented.\\n\\nmechanism: the genes provided are involved in the production of atp through metabolic pathways such as oxidative phosphorylation, GO:0005746, and the tricarboxylic acid cycle. these molecules, along with other regulatory proteins, facilitate the flow of electrons to generate energy in the form of atp. this energy is used by cells to carry out metabolic reactions and various cellular processes]]
HALLMARK_OXIDATIVE_PHOSPHORYLATION-1[[GO:0005746, electron transfer proteins, proton ion transportation proteins, oxidative phosphorylation proteins, metabolite-binding proteins, atp synthesis proteins]][[mitochondrial electron transport chain complex activity, GO:0006120, GO:0005747]]
HALLMARK_P53_PATHWAY-0[[cytoskeletal reorganization, calcium homeostasis, ubiquitin-proteasome pathway, GO:1901987, transcriptional regulation, GO:0006397, GO:0006974]][[analysis of this list of genes suggests a function related to cell cycle regulation, GO:0006915, and protein translation. the enriched terms include 'cell cycle regulation', 'apoptosis', 'protein translation', 'transcription regulation', 'intracellular protein transport', 'protein synthesis', and 'dna repair'.\\n\\nmechanism: the list of genes may be associated with a mechanism related to the regulation of cell cycle transitions and the integration of external signals to regulate gene transcription, protein translation and stability, and cellular apoptosis. this could involve some combination of signal transduction, GO:0006355, GO:0043687, GO:0006281]]
HALLMARK_P53_PATHWAY-1[[GO:0006351, chromatin dynamics, GO:0007155, MESH:D016207, GO:0007049, dna damage repair, cell signaling, GO:0016049, GO:0006915, immune modulation]][[gene expression and protein metabolism are likely to be enriched. specifically, the genes are likely involved in protein folding and transport, GO:0016567, transcriptional regulation, GO:0051726, protein-protein interactions, and signal transduction. \\nmechanism: these genes likely play a role in common metabolic, GO:0023052, and regulatory pathways.\\nubiqutination terms: rchy1, hexim1, upp1, pom121, procr, tap1, phlda3, wwp11; \\ntranscription factors:cd81, sat1, ercc5, ralgdh, irak1, aen, tob1, stom, MONDO:0100339, rap2b, tm7sf3, lif, MESH:C058179, ccp110, baiap2, tnfsf9, dcxr, eps8l2, ifi30, fdxr, elp1, itgb4, hbegf, irag2, ccnd2, sertad3, mknk2, retsat, ip6k2, hmox1, zfp36l1, epha2, tpd]]
HALLMARK_PANCREAS_BETA_CELLS-0[[GO:0031016, GO:0006006, GO:0048870, neural development]][[GO:0031016, GO:0007399, development of neural structures, GO:0048513, transcription regulation, GO:0009653, cell-to-cell adhesion, GO:0006412, hormonal metabolism, hormonal signaling]]
HALLMARK_PANCREAS_BETA_CELLS-1[[GO:0009653, neuronal development, GO:0007165, GO:0030073, transcription regulation, GO:0000988]][[GO:0022008, GO:0008152, GO:0006355, GO:0006412, GO:0009653, body patterning and organization, neurological system development, GO:0030154]]
HALLMARK_PEROXISOME-0[[enrichment test suggested genes are skewed towards genes involved in development, metabolic control, transport, cell cycle and homeostasis, as well as transcriptional regulation.\\n\\nmechanism: these genes appear to be involved in a diverse range of processes, suggesting multiple pathways contributing to the physiological functions of these genes. for instance, abcb1, abcb4 and abcb9 are involved in medication transport, abcc5 and abcc8 are involved in atp coupling, acaa1 is involved in fatty acid metabolism, alb is involved in heme metabolism, aldh1a1, aldh9a1, atxn1 and bcl10 are involved in transcriptional regulation, ctbp1 and ctps1 are involved in ubiquitination, dhcr24 and dhrs3 are involved in cholesterol biosynthesis, fabp6 is involved in bile acid transport, fads1 is involved in fatty acid desaturase, fis1 and gnpat are involved in lipoic acid synthesis and mitochondrial fatty acid metabolism, gstk1 is involved in gst-mediated detoxification, hmgcl is involved in steroidogenesis, hras, hsd11b2, hsd17b11]][[GO:0006629, stress response, GO:0009299, GO:0006281, skeletal and cartilage development, GO:0016477, metabolic enzymes, MESH:D002352]]
HALLMARK_PEROXISOME-1[[GO:0006629, GO:0008202, transcription regulation, GO:0051726]][[GO:0008152, GO:0006351, GO:0065007, GO:0006810, GO:0007165, GO:0006412, GO:0030154, GO:0006260, GO:0036211, membrane trafficking]]
HALLMARK_PI3K_AKT_MTOR_SIGNALING-0[[GO:0010467, dna repair & maintenance, MESH:M0496065, cellular signaling pathways, GO:0006629]][[MESH:M0023730, GO:0009653, GO:0030154, tyrosine kinase activity, GO:0038023]]
HALLMARK_PI3K_AKT_MTOR_SIGNALING-1[[GO:0051726, gene transcription, transcription factor activation, MESH:M0023730, MESH:D011494, receptor proteins, GO:0006412, GO:0016049, GO:0008283, GO:0030154]][[cell signaling, GO:0019538, GO:0006629, transcription regulation, GO:1901987, GO:0007165, receptor signaling, GO:0070085, GO:0016301, GO:0006915, g-protein interactions, transcriptional regulation]]
HALLMARK_PROTEIN_SECRETION-0[[gene expression regulation; co-translational protein targeting; clathrin-mediated endocytosis; endosomal protein trafficking; vesicle transport; exocytosis; receptor and ligand-mediated signaling; development and organ morphogenesis.\\nmechanism: the identified genes are likely involved in a variety of biological processes related to endocytosis, vesicle trafficking and transport, receptor and ligand-mediated signaling, MESH:D005786, co-translational protein targeting, and organ morphogenesis. these processes can be clustered into several pathways, including the calcineurin-mediated endocytosis pathway, the mapk signaling pathway, the wnt/beta-catenin signaling pathway, the clathrin-mediated endocytosis pathway, the endosomal protein trafficking pathway, the vesicle transport pathway, the exocytosis pathway, the receptor ligand-mediated signaling pathways]][[cell membrane fusion, GO:0016192, intracellular trafficking, predominant cargo proteins, GO:0006900, membrane remodeling]]
HALLMARK_PROTEIN_SECRETION-1[[genes belonging to this list are mainly involved in endocytosis, GO:0016192, MESH:D021381, and membrane fusion. the enriched terms include: endocytosis; vesicle trafficking; protein trafficking; membrane fusion; membrane transport; cytoskeleton organization; signal transduction; receptor internalization; and protein trafficking pathways.\\n\\nmechanism: the common characteristics shared by the genes suggest that they are all involved in some aspect of the endocytosis pathway. this biological mechanism involves signal transduction by which a signal (chemical or physical) can pass through a cell membrane and allow the cell to take up extracellular substances. through receptor internalization, molecules, like hormones, can be shuttled into intracellular vesicles and undergo further signaling events. the sequential vesicle trafficking steps then enable the cargo to be transported to their final destination. the proteins play various roles in facilitating membrane fusion, GO:0036211, GO:0007010, and vesicle transport. all of these activities act in concert to usher signals, MESH:D011506, other substances into the cell]][[GO:0043687, GO:0006457, GO:0006412, GO:0006897, GO:0009311, lysosomal trafficking]]
HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0[[redox regulation, antioxidant defense, detoxification of reactive oxygen species, peroxisomal biogenesis, MESH:M0572479, cell metabolism]][[GO:0008152, oxidative damage resistance, GO:0006281, cellular metabolic regulation, GO:0006915, regulatory pathway, GO:0006457, GO:0006749]]
HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1[[redox balance regulation, GO:0008152, GO:0051726, transcriptional regulation]][[this list of genes is enriched for terms related to oxidative stress, GO:0008152, and immune system function. specifically, the genes represent proteins involved in oxygen-sensing, anti-oxidation, redox regulation, GO:0006281, the stress response, and cytokine signaling.\\n\\nmechanism:\\nthe underlying biological mechanism of the gene list is likely the cellular response to oxidative stress. oxidative stress is a term used to describe a disruption in the balance of antioxidant molecules and reactive oxygen species. these reactive molecules can cause damage to the cell, and thus the relevant genes likely help the cell to counteract this damage by regulating redox status, mediating oxidant stress, and participating in dna repair and other defense mechanisms. additionally, some of these genes are involved in cytokine signaling, which helps to aid the immune system in defending against potential oxidative insults]]
HALLMARK_SPERMATOGENESIS-0[[cell signaling, protein regulation, GO:1901987, GO:0009653, GO:0048513, cytoskeletal regulation]][[GO:1901987, GO:0006338, GO:0016567, GO:0006260, GO:0051225, GO:0006997]]
HALLMARK_SPERMATOGENESIS-1[[cell cycle checkpoint regulation, GO:0009653, cell signaling, MESH:D003598, organ development]][[the list of genes provided are involved in diverse processes, such as cell structure and organization, GO:0007165, transcriptional regulation and other metabolic activities. the enriched terms from performing a term enrichment test are cell cycle, GO:0051301, GO:0016569, development and differentiation, cell signaling and signal transduction, GO:0006397, transcriptional regulation, and metabolic processes.\\n\\nmechanism:\\nthe genes provided are believed to be involved in a general mechanism of cell organization and function. the enriched terms are suggestive of the genes being related to fundamental processes such as cell cycle regulation, GO:0051301, transcriptional regulation, GO:0016569, and signal transduction. through the regulation of the genes, they are thought to be capable of controlling the organization and structure of cells, as well as metabolism and other cellular activities. furthermore, these pathways likely interact with each other in a complex manner, thereby allowing for intricate coordination between the genes in order to precisely tune process]]
HALLMARK_TGF_BETA_SIGNALING-0[[mapk pathway, tgf-β signaling pathway, wnt/β-catenin pathway, GO:0035329, transcriptional regulation, muscle morphogenesis, GO:0048729, regulation of g-protein signaling, GO:0006954]][[genes in this set are related to morphogenesis, GO:0007155, immune signaling, and transcriptional regulation. enriched terms include: morphogenesis, GO:0007155, immune signaling, transcriptional regulation, digit development, GO:0007049, protein-protein interaction, GO:0008083, and regulation of transcriptional activity.\\n\\nmechanism: morphogenesis can be regulated by the activity of kinases, cell adhesion can be mediated by the expression of cell adhesion molecules, and immune signaling can be regulated by the activity of cytokines, MESH:D018121, and transcription factors. the transcriptional regulation of these genes can be mediated by transcription factors and the regulation of transcriptional activity can be mediated by modulators of tfs, such as kinases and ubiquitin ligases. protein-protein interactions can occur between the different genes, signaling from growth factors can affect the expression of genes in this set]]
HALLMARK_TGF_BETA_SIGNALING-1[[these genes are involved in processes related to cell development, GO:0009653, calcium and calcium-dependent signaling, MESH:D017978, smad pathway and extracellular matrix proteins.\\n\\nmechanism: the mechanism underlying this gene list is likely related to signal transduction pathways. these may involve cell surface receptors which bind growth factors, such as tgfb1 and bmpr2, and transduce the signal through the smad pathway via the fkbp1a, bmpr1a, smurf1, smad1, ltbp2, thbs1, arid4b, ppm1a, and ctnnb1 proteins to influence the regulation of gene expression and cell fate. moreover, other molecules such as xiap, ube2d3, nog, slc20a1, serpine1, bcar3, rhoa, MESH:D045683, hipk2, ppp1ca, smad7, junb, smad6, ppp1r15a, tjp1, and ifngr2 may be involved in the signal transduction pathway. in addition, the calcium and calcium-dependent signaling by the tg]][[transcriptional regulation, GO:0007165, GO:0051726, protein kinase pathways, GO:0006412, GO:0048468, GO:0008283, GO:0030054, cytoskeletal organization]]
HALLMARK_TNFA_SIGNALING_VIA_NFKB-0[[GO:0032502, GO:0006954, MESH:D056747, cell signaling, MESH:M0496924, GO:0009653, GO:0009888, GO:0008283, GO:0006915, immune system response, MESH:M0496924]][[GO:0002224, GO:0032502, GO:0006954, immune-response regulation, nfkb, GO:0004707, GO:0010467, pro-inflammatory molecules]]
HALLMARK_TNFA_SIGNALING_VIA_NFKB-1[[gene transcription, actin maturation, cytoskeleton formation, signaling complex assembly, interleukin receptor signaling, GO:0051170, cytokine receptor signaling, nf-kappab signaling pathway, cytokine-mediated signal transduction, GO:0006367, MESH:D005786, cytokine receptor signaling pathway, GO:0010737, GO:0035556]][[cytokine-mediated signaling, antigen-receptor mediated signaling, GO:0042100, cytokine expression and release, immunoregulatory interactions, GO:0051092, interferon (ifn) signaling]]
HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0[[GO:0009299, GO:0042254, GO:0006457, nucleolar activity, spliceosomal activity, protein production, GO:0015031, GO:0006396, GO:1901987]][[GO:0006412, GO:0042254, GO:0006413, GO:0006457, GO:0006414, GO:0015833, peptide assembly, chaperone mediated protein folding]]
HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1[[GO:0008152, GO:0006412, GO:0043687, GO:0016310, pepetide binding and metabolism, protein structure and folding, rna synthesis and processing, GO:0000394, GO:0010467, GO:0051726, GO:0006915, GO:0007165, GO:0006281]][[analysis of this gene list has revealed that the functions enriched in the gene set include translation and translation initiation (exosc2, eif4a3, MESH:D039561, eif4g1, eif4a2); ubiquitination (ern1, skp1, herpud1, ube2g2, ube2l3); and protein folding and stability (atf3, fkbp14, dnajb9, calr, preb, hspa5, hsp90b1).\\n\\nmechanism: the enriched functions imply a complex network of processes that is likely to involve translation initiation of mrna, GO:0016567, and chaperone activity that facilitates protein folding, stability and degradation. it is possible that this gene set is associated with a variety of cellular pathways, including those related to gene expression, GO:0007165, GO:0008152]]
HALLMARK_UV_RESPONSE_DN-0[[MESH:D011494, cellular signaling pathways, GO:0001501, GO:0031012, transcriptional regulation, post-translational phosphorylation, growth regulation, development regulation, remodeling]][[cell signaling, structural proteins, MESH:D004798, GO:0009653]]
HALLMARK_UV_RESPONSE_DN-1[[mitotic regulation, GO:0060349, morphogenesis of specific organs and tissues, GO:0009966, regulation of transcription, GO:0042127, cellular responses to external stimuli, GO:0006468, GO:0003677]][[the above list of genes is significantly enriched for terms related to the development of the connective tissue, including morphogenesis, GO:0007049, regulation of transcription, and extracellular matrix organization; as well as the regulation of cell migration, matricellular protein signaling, GO:0007165, and calcium ion binding.\\n\\nmechanism: the enriched terms suggest that these genes work together in a common and interconnected pathway to control the formation, MESH:D009068, and functioning of the connective tissue. this pathway likely involves interactions among signal transduction pathways mediated by protein-protein interactions, transcriptional regulation, and calcium ion binding. these interactions would likely affect the structure and organization of the extracellular matrix, the migration of cells, the cell cycle, signalling through matricellular proteins]]
HALLMARK_UV_RESPONSE_UP-0[[GO:0032502, GO:0016049, gene transcription, GO:0008152, MESH:D011506, GO:0006412, GO:0007049, cell signaling, transcriptional regulation, MESH:D021381, GO:0010468]][[MESH:D021381, organelle trafficking, GO:0006306, transcription regulation, GO:0003677, GO:0006338, GO:0051726, GO:0008152]]
HALLMARK_UV_RESPONSE_UP-1[[GO:0008283, GO:0051726, dna replication and repair, GO:0007165, GO:0019722, GO:0006915, GO:0006629, oxygen pathway]][[genes in this list are generally involved in the regulation of cell growth and development, in particular related to apoptosis, signaling and transcriptional pathways. enriched terms include: transcriptional regulation; cell cycle regulation; apoptosis regulation; signal transduction; dna damage response; and cellular metabolism.\\n\\nmechanism: the molecular and cellular mechanisms underlying cell growth and development are complex and interconnected. genes in this list are believed to be involved in several pathways, such as transcriptional regulation, GO:0051726, apoptosis regulation, GO:0007165, GO:0006974, and cellular metabolism. these pathways interact and regulate each other in order to ensure the healthy functioning of cells. transcriptional regulation is key in regulating gene expression, while the cell cycle is tightly regulated by the activation of cell cycle control proteins and anti-apoptotic pathways. signal transduction pathways are essential for the proper coordination of cellular responses to external stimuli, and dna damage response allows for the repair of any irregularities. cellular metabolism is necessary for providing energy for growth and repair, for controlling the production of proteins]]
HALLMARK_WNT_BETA_CATENIN_SIGNALING-0[[this examination of human genes reveals a number of gene functions that are significantly enriched and related to developmental processes, including cell proliferation and differentiation, GO:0048729, and wnt signalling pathways. \\nmechanism: cell proliferation and differentiation, GO:0048729, wnt signalling pathways are all important in the normal healthy development of cells organs. these genes provide important functions that act in cooperative downstream pathways to enable promote these developmental processes.\\nthe enriched terms are: cellular differentiation; cellular proliferation; digit development; tissue morphogenesis; wnt signalling pathway]][[the genes in this list are associated with the wnt signaling pathway, modulating cell growth and mophogenesis. the enrichment terms corresponding to this list are wnt signaling, GO:0016049, GO:0009653, transcriptional regulation, and epigenetics.\\n\\nmechanism: the wnt signaling pathway activates nuclear proteins such as lef1 and tcf7, which then activate transcription of genes involved in cell growth and morphogenesis. the genes on the listed are associated with modulating the wnt pathway, including epigenetic regulation and cell cycle regulation]]
HALLMARK_WNT_BETA_CATENIN_SIGNALING-1[[wnt signaling, notch signaling, transcription regulation, GO:0051726, GO:0009653, GO:0032502]][[GO:0009653, GO:0006351, GO:0032502, MESH:D060449]]
T cell proliferation-0[[cell signalling, protein interaction, GO:0007165, GO:0032502, regulatory role in immunity, GO:0030163, receptor-mediated signaling, GO:0016049, GO:0030154, GO:0006396]][[GO:0009653, GO:0048468, cell signaling, receptor-mediated signaling, GO:0010468]]
T cell proliferation-1[[cell signaling, immune regulation, GO:0007165, growth factor production and response, immune response and modulation, calcium homeostasis, GO:0000981, development and differentiation, GO:0005102, GO:0001816]][[GO:0005126, GO:0007155, immunoreceptor-antigen complex binding, regulation of the ubiquitin-proteasome pathway, transcription factor regulator activity, gtp-binding protein binding, GO:0030154]]
Yamanaka-TFs-0[[the enrichment test results reveal that the list of genes are all involved in stem cell pluripotency and early embryonic development. enriched terms include pluripotency, stem cell morphology, MESH:D047108, GO:0000981, GO:0016049, differentiation, cell proliferation.\\n\\nmechanism: the genes focus on the regulation of the pluripotency and early embryonic developmental program. they regulate various aspects such as transcription factors, cell growth, morphogenesis, differentiation and cell proliferation. by acting in concert, they maintain the pluripotency of stem cells and initiate the processes of early morphogenesis. it is hypothesized that these genes are part of a large regulatory network which facilitates the pluripotency of the progenitor cells and the successful orchestration of early embryonic development]][[GO:0000988, embryonic stem cell differentiation, cell pluripotency, dna-binding, MESH:D005786, GO:0140110, transcription factor complex formation.\\nmechanism: these genes are known to be involved in the regulation of gene expression, and thus serve an important role in directing the biological activities associated with embryonic stem cell differentiation and pluripotency. they are likely to form complexes, interact with dna, and/or bind to components of the transcription machinery to regulate gene expression at the transcriptional level]]
Yamanaka-TFs-1[[GO:0009792, GO:0048864, GO:0000981, GO:0009653]][[GO:0048863, GO:0048468, embryonic stem cell differentiation, transcriptional regulation, pluripotency, transcription factor regulation.\\n\\nmechanism: the genes klf4, pou5f1, and sox2 act in concert to regulate the expression of developmental proteins that are involved in forming stem cells. this trio of transcription factors plays a key role in regulating cell differentiation and pluripotency, thus influencing the direction of embryonic stem cell development by regulating gene expression of proteins involved in stem cell formation]]
amigo-example-0[[GO:0030198, GO:0007155, GO:0009653, cell signaling, cytoskeletal organization, GO:0030154, MESH:D002470]][[GO:0008283, GO:0048729, motility regulation, vascular development, GO:0098868, UBERON:0002405]]
amigo-example-1[[our term enrichment analysis suggests that the human genes jag2, spp1, jag1, vcan, olr1, col5a2, app, UBERON:0003010, postn, tnfrsf21, apoh, pglyrp1, vav2, fstl1, nrp1, s100a4, lrpap1, vtn, timp1, itgav, lum, pf4, cxcl6, col3a1, stc1, kcnj8, msx1, ptk2, prg2, pdgfa, serpina5, and vegfa are related to processes in growth and differentiation, including transcriptional network maintenance, cell adhesion and motility, GO:0006915, and extracellular matrix component formation.\\n\\nmechanism: \\nthese genes may be involved in a complex network of signaling pathways that regulate cell growth and differentiation, cell adhesion and migration, GO:0006915, and matrix component formation. they may be involved in the reception and transduction of growth and differentiation signals, could facilitate the assembly of extracellular matrix components to form the microenvironment necessary to prompt and]][[GO:0001525, GO:0008283, GO:0016477, matrix remodeling, GO:0048771, jagged-mediated signaling, transcriptional regulation, GO:0030168, GO:0070527, immune regulation, extracellular matrix formation]]
bicluster_RNAseqDB_0-0[[GO:0009653, GO:0032502, transcription regulation, cell signalling, GO:0006811]][[GO:0016049, differentiation, migration, chromatin modulation, transcription regulation, cytoskeletal organization, intracellular trafficking, GO:0007155, GO:0007165, dna/rna metabolic processes, GO:0009653, GO:0001525, muscle growth, GO:0032502]]
bicluster_RNAseqDB_0-1[[GO:0009653, neuronal growth, neuronal system development, cell-cell communication, cell signaling, GO:0009888, organ development]][[chromatin regulation, GO:0048468, GO:0006412, GO:0006811, GO:0000981, GO:0043687]]
bicluster_RNAseqDB_1002-0[[analysis of the gene list shows that they are all associated with sarcomere function, MESH:D009119, skeletal muscles and thermogenesis. the enriched terms include sarcomere function, MESH:D009119, UBERON:0001134, MESH:D022722, actin-myosin interaction, calcium handling, muscle development and differentiation, and mitochondrial function. \\n\\nmechanism: the underlying biological mechanism is associated with the activation of genes that are linked to the assembly, maintenance and contraction of the sarcomere, which is the fundamental unit of muscle contraction, as well as muscle development and differentiation, calcium handling, mitochondrial fluctuation, thermogenesis. this contributes to the generation of force within the skeletal muscles]][[MESH:M0370791, GO:0007015, GO:0006936, z-disc formation, GO:0007097, muscle fiber organization, ion channel influx/efflux]]
bicluster_RNAseqDB_1002-1[[skeletogenesis, MESH:D024510, GO:0048740, GO:0001501, GO:0006936, GO:0006412, GO:0009058, MESH:D009126]][[MESH:D024510, GO:0048740, GO:0021675, calcium distribution, actin proteins, cardiac contractile proteins, sarcomeric proteins, membrane protein transport, ion channel proteins, enzyme regulation.\\nmechanism: this list of genes are likely to be involved in the regulation of muscle structures and contractions, organization of calcium distribution throughout the cell, nerve development, and support of membrane protein transport and enzymatic activities. these processes are important for maintaining muscle contraction and activity]]
endocytosis-0[[GO:0007165, vesicle/lipid trafficking, cellular adhesion, nutrient regulation, cell metabolism, cytoskeletal organization, endocytosis/exocytosis, intercellular adhesion/motility]][[GO:0006629, cell signaling, GO:0007049, cytoskeletal dynamics]]
endocytosis-1[[membrane trafficking, GO:0007165, protein proteolysis, GO:0006629, receptor signaling, GO:0055088]][[GO:0006897, intracellular signaling, GO:0016310, protein interactions, receptor trafficking]]
glycolysis-gocam-0[[GO:0006096, aerobic glycolysis, GO:0006094]][[GO:0006754, GO:0006096, MESH:D004734, MESH:M0496924]]
glycolysis-gocam-1[[GO:0008152, GO:0006096, GO:0006098, GO:0006006, MESH:D004734]][[metabolic pathway, GO:0006096, glucose oxidation, pyruvic acid production, GO:0006754]]
go-postsynapse-calcium-transmembrane-0[[these genes appear to be involved in the development, functioning and regulation of the nervous system, specifically neurons and their associated pathways and processes. the terms \"neurotransmission\"; \"neuronal cell membrane regulation\"; \"neurotransmitter release\"; \"calcium signaling\"; \"neuronal ion channel regulation\"; and \"neuronal excitability regulation\" are significantly enriched in this gene set.\\n\\nmechanism: it appears that this gene set may be involved in a broad range of processes related to neurophysiology, including the regulation of neuronal membrane excitability and ion channels, neuronal cell membrane regulation, GO:0007269, and calcium signaling. these processes are all complex and interrelated, are likely to have a direct impact on neural development function]][[summary: the enriched terms of the human genes atp2b1, atp2b2, cacna1c, cacng2, cacng3, cacng4, cacng5, cacng7, cacng8, chrna10, chrna7, chrna9, drd2, f2r, gpm6a, grin1, grin2a, grin2b, grin2c, grin2d, grin3a, grin3b, htr2a, itpr1, ncs1, p2rx4, p2rx7, plcb1, psen1, slc8a1, slc8a2, slc8a3, trpv1 include neuron development; neurotransmitter signaling; signal transduction; transmembrane transport; neural plasticity; ion transport; calcium signaling; glutamate receptor signaling; and synaptic signaling. \\n\\nmechanism: these genes are believed to act in concert to regulate and coordinate the various stages of neuron development, such as neurotransmitter signaling, GO:0007165, GO:0055085, neural]]
go-postsynapse-calcium-transmembrane-1[[the term enrichment test reveals that the genes in the list are mainly involved in neuronal ion channels and calcium signalling pathways. enriched terms included calcium channel activity, GO:0005244, GO:0038023, GO:0015276, and g-protein coupled receptor activity. \\n\\nmechanism: the genes in the list form ion channels and g-protein coupled receptors within neuronal cells, which facilitates the communication of neurotransmitters between neurons. several of the genes are involved in calcium signalling pathways, which regulate various cellular pathways involved in the development and maintenance of neurons]][[neuronal function, GO:0006811, ion channel regulation, neurotransmitter regulation, calcium regulation, potassium regulation, GO:0007268, membrane potential regulation]]
go-reg-autophagy-pkra-0[[GO:0016049, GO:0048468, GO:0006915, GO:0006955, GO:0030163, GO:0006508]][[this set of genes is associated with cellular functions related to metabolic homeostasis and activation of the pi3k/akt signaling pathway. the enriched terms associated with the genes include cell cycle regulation, protein kinase regulation, mitochondrial regulation, and mitochondrial stress response.\\n\\nmechanism: the metabolic homeostasis and activation of the pi3k/akt pathway are mediated by these genes, which affect the regulation of cell cycle, protein kinase regulation, mitochondrial regulation, and mitochondrial stress response. these genes have roles in regulating metabolic processes as well as responding to external stressors. their involvement in cell cycle regulation and protein kinase regulation ensures the healthy development and maintenance of the cell, while their role in mitochondrial regulation and mitochondrial stress response plays an important role in maintaining the cell's energy production]]
go-reg-autophagy-pkra-1[[phosphatidylinositol signalling, vascular endothelial growth factor receptor signalling, progesterone-mediated oocyte maturation, nf-kb signaling, GO:0043526]][[cell signaling, transcription regulation, GO:0006468, ras activation, akt activation, calcium-associated kinases, GO:0019722]]
hydrolase activity, hydrolyzing O-glycosyl compounds-0[[carbohydrate digestion and absorption; glycosaminoglycan and glycan metabolism; lysosomal, GO:0005777, and catabolic processes; digit, skeletal, GO:0035108]][[MESH:D009113, MESH:D009077, glycosyltransferase, MESH:D006821, GO:0070085, enzyme, MESH:D011506]]
hydrolase activity, hydrolyzing O-glycosyl compounds-1[[glycoside hydrolase (gh) activity, mucin biosynthesis, GO:0006031, MESH:D057056, lysosomal enzyme activity.\\nmechanism: glycoside hydrolase (gh) and lysosomal enzymes play important roles in the process of glycostasis, and are involved in a variety of metabolic activities such as the breakdown of polysaccharides, the synthesis of glycolipids and glycoproteins, and the degradation of other macromolecules. chitin and mucin biosynthesis also involve glycosylation and enzymatic modification of sugars and polysaccharides to form polymeric molecules. cysteine protease are involved in the hydrolysis of proteins, while lysosomal enzymes aid in the breakdown of molecules in the l]][[the gene functions that were found to be enriched amongst this set of genes were predominantly related to carbohydrate metabolism, including glycosaminoglycan and glycosphingolipid biosynthesis as well as lysosomal enzyme activity.\\n\\nmechanism:\\nthe mechanism most likely lies in the pathway of glycoconjugation, which helps to regulate important processes such as cell adhesion, GO:0006955, and signal transduction. the pathway is integral to the proper formation and function of the extracellular matrix, which is important for cellular differentiation and tissue organization. the enriched terms found here likely represent genes that are involved in the biosynthesis and metabolism of various glycoconjugates, in addition to the regulation of lysosomal enzymes involved in the degradation of complex carbohydrates]]
ig-receptor-binding-2022-0[[members of the immunoglobulin (ig) gene superfamily - specifically, igh, GO:0033984, MESH:C014609, GO:0042571, response and maintenance of the adaptive immune system at different levels, likely via antigen binding, signal transduction and b cell activation]][[immunoglobulin heavy chain combination, immunoglobulin light chain combination, j-chain, antigen-specific receptor, t-lymphocyte receptor, regulation of immune function]]
ig-receptor-binding-2022-1[[GO:0003823, b cell receptors, GO:0007596, GO:0005577, MESH:D001779, clec4d]][[genes related to immunoglobulins, transcripts associated with immunoglobulin transcription and splicing, immunoglobulin gene expression, proteins involved in immunoglobulin regulation and processing, GO:0002637, GO:0002637, mhc class i antigen processing and presentation, cytokine-mediated signaling, GO:0002544, limit degranulation. \\n\\nmechanism: these genes are associated with immunoglobulin production, processing, and regulation. this includes genes related to immunoglobulins, transcripts involved in transcription and splicing, and proteins that are involved in the regulation and processing of immunoglobulins. additionally, genes related to mhc class i antigen processing, cytokine-mediated signaling, chronic inflammatory response, and limit degranulation are also expressed. these genes interact to form an integrated pathway that is involved in the regulation of the immune response and the formation of immunoglobulins]]
meiosis I-0[[dna damage recognition, GO:0006281, GO:0006302, meiotic recombination, GO:0007059, GO:0035825, rad51 family proteins, dna end-protection, mus81-mms4 complex, muts family proteins, dna proofreading, spo11-associated pathway]][[GO:0006260, GO:0006281, replication fidelity, GO:0007049, GO:0071897, dna prioritization]]
meiosis I-1[[GO:0006281, GO:0006260, gene splicing]][[this enrichment test on the list of human genes suggests a central role for dna damage repair and cell cycle regulation in the common functionalities of the genes. enriched terms found include \"dna repair\", \"cell cycle\", \"chromatin remodelling\", \"recombinational repair\", \"steroid hormone receptor\", \"centromere\", GO:0000724]]
molecular sequestering-0[[GO:0000075, cell adhesion/motility complex, transcriptional complex, GO:0036211, rna processing complex]][[GO:0019722, calcium buffering, GO:0006816, regulation of calcification, protection against calcium overload, calcium-v influx/efflux]]
molecular sequestering-1[[calcium binding, apoptotic regulation, immune modulation, MESH:D018384, GO:0051726, stress-response regulation]][[cell morphology regulation, GO:0008152, GO:0006915, GO:0006412, GO:0036211, GO:0006811, GO:0023052, stress response, GO:0006351, cell surface interactions, chromatin regulation]]
mtorc1-0[[the human genes abcf2, acaca, acly, acsl3, actr2, actr3, add3, adipor2, ak4, aldoa, arpc5l, asns, atp2a2, atp5mc1, atp6v1d, MESH:D064096, bcat1, bhlhe40, btg2, bub1, cacybp, calr, canx, ccnf, ccng1, cct6a, cd9, cdc25a, cdkn1a, cfp, cops5, coro1a, cth, ctsc, GO:0038147, cyb5b, cyp51a1, dapp1, ddit3, ddit4, ddx39a, dhcr24, dhcr7, GO:0004146, ebp, edem1, eef1e1, egln3, eif2s2, elovl5, elovl6, eno1, eprs1, ero1a, etf1, MONDO:0100101, MONDO:0100102, fdxr, fgl2, MESH:D010649]][[genes in this list are involved in various aspects of cellular metabolism, GO:0065007, and development.a number of the genes have roles in energy production and metabolism such as, atp2a2, aldoa, MONDO:0009214, fao1, fgl2, gapdh, gbe1, MONDO:0015408, glrx, MONDO:0005775, me1, phgdh, and pgm1. there is a strong presence of genes involved in protein synthesis and transport, including the ribosomal proteins, the eukaryotic translation factors and initiation factors (eif2s2, eif1e1, elovl5, and elovl6). this gene set is also enriched for a number of ubiquitin and ubiquitin-like proteins (ube2d3, ufm1, uso1, tomm40, hspd1, hspe1, sytl2, nherf1, and hk2). many of these genes are involved in regulation through multiple pathways including regulation of transcription (add3, actr2, actr3, cct6a, gga2, gdh2, mef2b, ykt]]
mtorc1-1[[energy production, GO:0008152, protein biosynthesis and folding, cell regulation, MESH:D048788, protein turnover]][[genes related to metabolism and biosynthesis (acly, aldoa, atp2a2, atp6v1d, cacybp, coro1a, dhcr24, MONDO:0100101, MONDO:0100102, gbe1, MESH:C066524, gsr, hmgcs1, hspa9, lgmn, me1, mthfd2l, nampt, pgm1, pgk1, psat1, psma3, psma4, psmg1, psmc2, psmc4, psmd12, psmd13, psmd14, stc1, stip1, and ufm1), protein folding/interaction (act2, actr2, actr3, add3, elovl5, eno1, ero1a, eif2s2, fgl2, insig1, itgb2, map2k3, mcm2, mcm4, nufip1, p4ha1, pdk1, pitpnb, pnp, psme3, sec11a, shmt2, slc2a1, slc2a3]]
peroxisome-0[[peroxisome biogenesis, peroxisome formation, membrane protein trafficking, GO:0044255, mitochondrial-peroxisomal crosstalk]][[protein homeostasis, peroxisome biogenesis, peroxisome assembly, peroxisome maintenance, protein regulation, GO:0050821]]
peroxisome-1[[peroxisomal biogenesis, peroxisomal protein transport, oxidative damage resistance]][[peroxisomal biogenesis, peroxisome assembly, peroxisome regulation, GO:0015031, membrane trafficking]]
progeria-0[[cell structural element development, gene transcription, GO:0016070, GO:0006259, transcriptional regulation]][[after performing the enrichment test on the genes zmpste24, banf1, MONDO:0010196, and lmna, we identified that all of the genes have a role in the regulation of nuclear and chromatin structures. the individual genes are involved in a wide range of processes in these two areas. this includes gene expression, GO:0006260, GO:0006338, GO:0000723, as well as cell cycle checkpoints.\\n\\nthe enriched terms are 'nuclear structure regulation'; 'chromatin structure regulation'; 'gene expression regulation'; 'dna replication regulation'; 'chromatin remodeling'; 'telomere maintenance'; and 'cell cycle checkpoint regulation'. \\n\\nmechanism: the underlying biological mechanism that our gene list points to is one involving the regulation of nuclear and chromatin structures. in order to maintain the stability of the genome and ensure its accurate transmission, molecules encoded by the four genes could be involved in key activities such as gene expression, GO:0006260, GO:0006338, GO:0000723, as well as cell cycle checkpoints]]
progeria-1[[dna replication and repair, GO:0006334, GO:0000723, transcriptional regulation]][[transcriptional regulation, GO:0006281, GO:0051726, GO:0030154]]
regulation of presynaptic membrane potential-0[[GO:0007165, GO:0006811, regulation of neurotransmitter release]][[MESH:D007473, MESH:D008565, synapse formation, GO:0007268, MESH:D009473, neuronal excitability, voltage-gated ion channels, MESH:D058446]]
regulation of presynaptic membrane potential-1[[analysis of these genes show that they are involved in human neurological structure and function. enriched terms include neuron activity, GO:0005216, GO:0008066, GO:0004930, MESH:D005680, GO:0005267, MESH:D005680]][[ion-channel function, neuron excitability, GO:0007268, MESH:D018079, MESH:D017470, MESH:D015221, MESH:D015222]]
sensory ataxia-0[[MESH:D024510, neuronal development, GO:0015031, GO:0006629, GO:0009653]][[GO:0006412, GO:0008152, ion channel transport, GO:0006936, MESH:D024510]]
sensory ataxia-1[[GO:0015031, MONDO:0008090, GO:0048705, MESH:D024510, GO:0005783, mitochondrial protein transport, cytoskeletal organization]][[nucleic acid metabolism, GO:0003676, GO:0050657, GO:0019538, GO:0005515, GO:0015031]]
term-GO:0007212-0[[g alpha subunit signaling, gpcr activation and signaling, gpcr function, MESH:D019281]][[g-protein coupled receptor (gpcr), g-protein subunit, MESH:D000262, MESH:D015220, MESH:D010770]]
term-GO:0007212-1[[cellular signaling, g protein signaling pathway, calcium signaling pathway, GO:0007399, GO:0007268, phosphorylation cascade, nerve morphogenesis, indoleamine metabolism]][[GO:0007165, cellular growth & differentiation, GO:0007010, endocrine system regulation, transcriptional regulation]]
tf-downreg-colorectal-0[[nuclear receptor superfamily, transcription regulation, epigenetic regulation, GO:0051726, GO:0003677, GO:0006338, GO:0032502, cell signaling pathways, GO:0005652, GO:0016363]][[genes such as hira, cebpb, e2f3, hmga1, znf263, tfdp1, trib3, bhlhe40, smarca4, slc26a3, nfe2l3, ssbp2, gtf3a, npm1, trip13, mef2c, nr3c2, foxm1, vdr, hand1, klf4, hexim1, tgif1, med24, tead4, smarcc1, scml1, MESH:D024243, myc, foxa2, bmal2, spib, nme2, phb1, cbx4, runx1, ppargc1a, polr3k, nr5a2, maf, nr1h4, sox9, dnmt1, cbfb, znf593, mta1, zbtb18 are all involved in the regulation of transcription, GO:0006338, GO:0003677, and epigenetics. of this group, genes involved in transcription are significantly enriched (e.g. hira, cebpb, e2f3,]]
tf-downreg-colorectal-1[[transcriptional regulation, GO:0016569, GO:0009653, cardiovascular development, differentiation, MESH:M0464910, MESH:M0030450, GO:0048863]][[GO:0016049, transcriptional regulation, GO:0006338, GO:0051726, GO:0006351, GO:0016569]]
ontological_synopsisEDS-0[[GO:0032963, GO:0030198, GO:0004222, GO:0030206, GO:0008378, GO:0005509, GO:0008270, platelet derived growth factor binding, GO:0002020, GO:0035987, GO:0007266, GO:0007160, hypoxia response, epidrmis development, peptidyl-lysine hydroxyl]][[collagen or extracellular matrix structural constituent, collagen metabolic process or biosynthetic process, proteoglycan metabolic process or biosynthetic process, GO:0006024, dna-binding transcription factor binding activity, GO:0001217, rna polymerase ii transcription regulatory region sequence-specific dna binding activity, metal ion binding activity, GO:0003755, GO:0035987, GO:0004252, GO:1904028, protein peptidyl-prolyl is]]
EDS-1[[GO:0030198, GO:0030199, GO:0043589, GO:0042060, GO:0043588, GO:0032964, GO:0006024, GO:0003755, GO:0035987]][[GO:0030198, GO:0030199, GO:0032964, GO:0030166, GO:0006024]]
FA-0[[analysis of the above genes shows that they are all involved in dna repair and involved in the fanconi anaemia nuclear complex, which is a critical part of the fanconi anaemia disease pathway. the list of enriched terms includes \"protein monoubiquitination\", \"dna repair complex\", \"fanconi anaemia nuclear complex\", \"double-strand break repair via homologous recombination\", \"response to intra-s dna damage checkpoint signaling\", \"telomere maintenance\", \"positive regulation of g2/m transition of mitotic cell cycle\", \"regulation of transcription by rna polymerase ii\".\\n\\nmechanism: the underlying biological mechanism is the fanconi anaemia pathway, where the defective genes of the path have the potential to lead to cancer or other fanconi anaemia-related illnesses. this dna repair pathway relies heavily on the fanconi anaemia nuclear complex, which involves the processes of monoubiquitination, involving the above genes, double-strbreak repair via homologous recombination. in addition, the regulation of telomere maintenance, positive regulation of g2/m transition of mitotic cell cycle regulation of transcription by rna polymerase ii are essential for proper dna repair]][[GO:0006281, GO:0006513, GO:0043240, GO:0000785, GO:0005634, GO:0005829]]
FA-1[[this group of genes are involved in a range of dna repair processes, including protein monoubiquitination and double-strand break repair via homologous recombination. they are all localized in different components of the cell (e.g. chromatin, GO:0005634, GO:0005829, GO:0005657, GO:0005694, etc.) and are part of several complexes/hierarchies (e.g. fanconi anaemia nuclear complex, GO:0033063, GO:0048476, GO:0033557, GO:0033593, etc.). enriched terms includes: dna repair; protein monoubiquitination; double-strand break repair via homologous recombination; regulation of dna metabolic process; negative regulation of double-stranded telomeric dna binding activity; response to gamma radiation; regulation of telomere maintenance; establishment of protein localization to telomere; and regulation of protein metabolic process.\\n\\nmechanism: these genes are involved in a range of complex and interrelated biochemical pathways, which utilize a variety of enzymatic activities (e.g. ubiqu]][[GO:0006513, GO:0006281, GO:0003682, GO:0000400, GO:0003684, GO:0003697, GO:1990599, GO:0004520, GO:0006310, GO:0005524, GO:0006259, GO:0072757, GO:0051052, GO:0003691, GO:0000723, GO:0019219, GO:0051246, GO:0070200, GO:0016573, GO:0004402, gamma-tubulin binding activity, identical protein binding activity, jun kinase binding activity, rna polymerase ii-specific dna-binding transcription factor binding activity, GO:0061630, GO:0031386]]
HALLMARK_ADIPOGENESIS-0[[GO:0005515, protein homodimerization, GO:0005524, GO:0003677, GO:0003824, MONDO:0016019]][[protein binding activity, MESH:D010758, atp binding activity, gtp binding activity, GO:0022857, dna binding activity, receptor binding activity, GO:0004869, caspase binding activity, rna binding activity]]
HALLMARK_ADIPOGENESIS-1[[protein homodimerization, GO:0019899, GO:0140657, GO:0005102, ligase binding, GO:0003924, GO:0046872, dna-binding, rna-binding, oxidase activity, MESH:D010758, GO:0120227, transportase activity, dehydrogenase activity, GO:0016791, GO:0016301, GO:0004175, GO:0022857, chemotactic receptor activity, GO:0017077]][[protein binding activity, enzyme binding activity, atp binding activity, rna binding activity, gtp binding activity, identical protein binding activity, gtp-dependent protein binding activity, transition metal ion binding activity, GO:0016615, aldehyde dehydrogenase activity, GO:0008097, GO:0052650, fad binding activity, MESH:D010758, heme binding activity, GO:0003872, GO:0004609, GO:0003873, GO:0004144, GO:0003994, GO:0004784, GO:0004129, molybdenum ion binding activity]]
HALLMARK_ALLOGRAFT_REJECTION-0[[receptor binding activity, signaling receptor binding activity, protein binding activity, dna-binding, GO:0016563, GO:0005125, GO:0008083, GO:0042605, enzyme binding activity, chemical binding activity, protein complex binding activity]][[protein homodimerization, protein heterodimerization, GO:0042802, GO:0019901, dna-binding, rna-binding, GO:0017124, GO:0019958, GO:0008201, ubiquitin-protein ligase binding]]
HALLMARK_ALLOGRAFT_REJECTION-1[[enzyme binding activity, rna binding activity, protein binding activity, chemokine receptor binding activity, GO:0004712, GO:0042803, identical protein binding activity, GO:0008083, interleukin binding activity, cell-cell adhesion mediation, dna-binding transcription activity, GO:0015026, cytoplasmic factor activity, metal ion binding activity, polypeptide antigen transporter activity]][[GO:0007155, GO:0005102, GO:0007165, GO:0001228, chemokine receptor binding activity, enzyme binding activity, GO:0008083, GO:0005125, degradation of redundant or damaged proteins and peptides, GO:0046983, metal ion binding activity, peptide antigen binding activity, GO:0004888, GO:0004712, GO:0042803, ubiquitin binding activity]]
HALLMARK_ANDROGEN_RESPONSE-0[[protein binding activity, enzyme binding activity, transcription factor binding activity, GO:0016787, GO:0004721, GO:0003714, GO:0003713, atp binding activity, GO:0004672, GO:0016563, GO:0003924, nad+ binding activity, ring-like zinc finger domain binding activity, GO:0061656, small protein activating enzyme binding activity, GO:0000224, GO:0062076, GO:0004383, GO:0004222, 17-beta-dehydrogen]][[GO:0005215, GO:0005515, GO:0004672, GO:0038023, GO:0006351, GO:0044237, GO:0006974, GO:0007010, GO:0016787, GO:0046872, GO:0003924]]
HALLMARK_ANDROGEN_RESPONSE-1[[protein binding activity, GO:0004672, GO:0006351, GO:0038023, enzymatic activity, GO:0016310, GO:0097472, GO:0003677, GO:0006351, postsynaptic organization, GO:0016887, nucleic acid binding activity, ubiquitin protein ligase binding activity, fad binding activity, MESH:D009249, GO:0061665, enzyme binding activity, GO:0022857, endopeptidase activator]][[GO:0005515, GO:0016887, GO:0016563, GO:0003677, GO:0004674, GO:0022857, GO:0016787, GO:0061631, cis-regulatory region sequence-specific dna binding activity, GO:0061665, GO:0034594, GO:0007165, GO:0043027, GO:0003924, GO:0042803, nucleic acid binding activity, GO:0003713, GO:0003714, enzyme binding activity, calmodulin binding activity, metalloendope]]
HALLMARK_ANGIOGENESIS-0[[GO:0030021, collagen binding activity, integrin binding activity, GO:0060090, identical protein binding activity, fibronectin binding activity, GO:0046983, heparan sulfate proteoglycan binding activity, GO:0007160, GO:0010810]][[summary: the list of genes provided appear to be involved in a variety of unrelated processes, but when grouped by shared activities, several functions in common can be identified. these common functions include protein binding activity, GO:0060230, phospholipid binding activity, platelet-derived growth factor binding activity, GO:0046983, signaling receptor binding activity, collagen binding activity, atp activated inward rectifier potassium channel activity, voltage gated monoatomic ion channel activity, GO:0005249, GO:0016298, heparan sulfate proteoglycan binding activity, heparin binding activity, multiple growth factor activities, peptidoglycan binding activity, GO:0016019, platelet derived growth factor binding activity, non membrane spanning protein tyrosine kinase activity, GO:0005096, vascular endothelial growth factor binding activity, metal ion binding activity, small molecule binding activity, enzyme binding activity, retinoic acid binding activity, cxcr3 chemokine receptor binding activity, prostaglandin transmembrane transporter activity and sodium-independent organic anion transmembrane transporter activity. \\nmechanism: the genes in the list appear]]
HALLMARK_ANGIOGENESIS-1[[GO:0007166, GO:0006468, GO:0045861, GO:0007160, GO:1902533, GO:0010604, transmem]][[GO:0005515, GO:0006468, GO:0016477, GO:0008283, GO:0045861, GO:1902533, GO:0009966, GO:0010604, GO:0019901, GO:0008191, ion binding activity, small molecule binding activity, GO:0035987, GO:0005096, platelet-derived growth factor binding activity, GO:0046983, calcium ion binding activity, sympathetic nerve activity, GO:0051336]]
HALLMARK_APICAL_JUNCTION-0[[GO:0098609, agonist binding activity, cytoplasmic matrix binding, protein homodimerization, GO:0005102]][[GO:0007155, GO:0005178, gtp binding activity, collagen binding activity, atp binding activity, phospholipase binding activity, GO:0007160, GO:0050839, GO:0017124]]
HALLMARK_APICAL_JUNCTION-1[[binding activities, GO:0003824, involvement in biological processes, structural roles]][[extracellular matrix structure, GO:0038023, cell adhesion molecule binding activity, small gtpase binding activity, GO:0042803, identical protein binding activity, collagen binding activity, actin binding activity, atp binding activity, protein kinase binding activity, sh3 domain binding activity, integrin binding activity, GO:0005096]]
HALLMARK_APICAL_SURFACE-0[[GO:0061024, protein organization, GO:0036211, GO:0015031, GO:0006897, GO:0007165, GO:0006915]][[GO:0005480, cell structure maintenance, GO:0046872, GO:0016477, plasmamembrane transport, GO:0005515, GO:0043170, GO:0030296, endolemmal transport, GO:0016485, GO:0010467, GO:0006915, lipoprotein particle receptor catabolic process, peptide chain release, protein homodimerization, GO:0007165, GO:0048870, GO:1902600, GO:0000785, GO:0005654, GO:0031410, GO:0042552, GO:0044183]]
HALLMARK_APICAL_SURFACE-1[[GO:0007155, protein folding and regulation, GO:0050801, MESH:D005786]][[genes in this list are primarily involved in regulation of transcription, GO:0007165, membrane management, protein folding and binding, cell surface receptor signaling and adhesion, and cellular extravasation. enriched terms include: transcription, GO:0007165, protein-folding and binding, cell-surface receptor signaling, adhesion, GO:0045123, GO:0061024, extracellular matrix structural components, genetic expression, apoptotic pathways, and intracellular ion homeostasis. \\n\\nmechanism: genes on this list are primarily involved in several processes that coordinate essential cellular functions by dynamically managing activity of proteins at the surface of the cell, within underlying membrane layers, extracellularly and within dna. these genes manage the way cells communicate within their environment, interact with extracellular components, respond to stimuli, and extravasate. they code for proteins involved in transcription, GO:0007165, protein folding and binding, adhesion, apoptotic pathways, intracellular ion homeostasis, extracellular matrix structural components that have pleiotropic roles in modulating gene expression functioning of cellular components]]
HALLMARK_APOPTOSIS-0[[dna binding activity, protein binding activity, enzyme binding activity, GO:0004197, identical protein binding activity, signaling receptor binding activity, calcium ion binding activity, protein kinase binding activity, GO:0000988, bh3 domain binding activity]][[dna binding activity, GO:0046983, protein binding activity, enzyme binding activity, protein kinase binding activity, GO:0004197, GO:0003714, phosphoprotein binding activity, mhc class i protein binding activity, GO:0003700, signaling receptor binding activity, GO:0042803]]
HALLMARK_APOPTOSIS-1[[calcium ion binding activity, protein binding activity, identical protein binding activity, chromatin dna binding activity, dna-binding transcription factor binding activity, ig domain binding activity, sh2 domain binding activity, bh3 domain binding activity, cyclin binding activity, rna binding activity, GO:0004197, metalloprotease inhibitor activity, phospholipid binding activity, lipopeptide binding activity, lysophosphatidic acid binding activity, sulfatide binding activity, atpase binding activity, pdz domain binding activity]][[protein binding activity, identical protein binding activity, enzyme binding activity, GO:0003700, rna polymerase ii-specific transcriptional activity, GO:0004197, GO:0004896]]
HALLMARK_BILE_ACID_METABOLISM-0[[atp binding activity, GO:0016887, protein binding activity, signaling receptor binding activity, enzyme binding activity, GO:0042803, GO:0016791, GO:0000988, GO:0022857, ubiquitin-dependent protein binding activity, cholesterol binding activity, GO:0019871, phosphotyrosine residue binding activity]][[atp binding activity, GO:0016887, cholesterol binding activity, GO:0022857, GO:0046982, GO:0000981, enzyme binding activity, GO:0016491, peptide antifungal protein binding activity, acyl-coa hydroxyacyltransferase activity, GO:0019145]]
HALLMARK_BILE_ACID_METABOLISM-1[[GO:0140657, GO:0016887, GO:0008233, enzyme binding activity, GO:0003700, GO:0042803, identical protein binding activity, signaling receptor binding activity]][[this gene list is associated with multiple functions in various metabolic processes, from binding and transporter activity to atpase activity, homodimerization activity, and various hydrolytic activities. enriched terms include: protein binding activity; atp hydrolysis activity; protein homodimerization activity; atpase binding activity; atpase-coupled transmembrane transporter activity; transcription regulatory region sequence-specific dna binding activity; and transmembrane transporter activity. mechanism: this set of genes acts as part of multiple metabolic processes, such as lipid and fatty acid metabolism, GO:0042632, GO:0140327, and hormone regulation. these genes facilitate enzymatic activity and activity in transporting molecules, such as fatty acids, MESH:D002784, MESH:D014815, hormones. the processes activities these genes are involved in suggest a coordination of metabolic cell stimulation processes]]
HALLMARK_CHOLESTEROL_HOMEOSTASIS-0[[atp binding activity, protein kinase binding activity, GO:0042803, GO:0003700, low-density lipoprotein particle binding activity, GO:0005041, GO:0030229, GO:0004602, GO:0004364, GO:0016491, GO:0004496, GO:0004631, GO:0047598, GO:0047024, MESH:D010758, GO:0060090, cholesterol binding activity, GO:0120020, isopentenyl]][[atp binding activity, protein binding activity, GO:0007155, GO:0007165, GO:0006915, dna-binding, GO:0006695, cell structure organization, GO:0003985, GO:0008610, GO:0000988, GO:0015631, protein homodimerization]]
HALLMARK_CHOLESTEROL_HOMEOSTASIS-1[[GO:0042632, MESH:D055438, GO:0005515, GO:0006351, GO:0010468, dna-binding, GO:0007165, negative regulation, positive regulation, GO:0016491, GO:0008610, GO:0003723, ldl particle binding, GO:0019901, phosphotransferase activity, acetyl-coa ligase activity, endopeptidase activity, etc]][[GO:0006695, GO:0008610, positive regulation of transcription, GO:2001234, GO:0031647, regulation of cell adhesion/migration, atp binding activity, transcription factor binding activity, protein binding activity, protein kinase binding activity, signaling receptor binding activity, ion/metal binding activity, endopeptidase regulator activity, etc]]
HALLMARK_COAGULATION-0[[the provided list of human genes are mainly involved in metabolism, adjustment of the immune system and coagulation, and development of cells and organs. in particular, they are found to be involved in binding activities and endopeptidase activities such as post-translational modification, transcription and regulation of protein. the enriched terms include calcium-dependent protein/phospholipid/lipoprotein binding activity, GO:0004197, protein homodimerization/homooligomerization activity, identical protein binding activity, and serine-type endopeptidase activity. \\n\\nmechanism: the expression and activities of these genes may play important roles in the development and metabolism of cells and organs by facilitating protein folding, GO:0043687, cell-matrix adhesion and crosstalk between proteins. the binding activities of these genes towards phospholipid, lipoprotein and other molecules mediate the interaction between cells and extracellular environment, and regulate blood coagulation and formation of extracellular matrix. the endopeptidase activities of these genes degrade and modulate proteins, which are essential for various biological processes]][[protein binding activity, collagen binding activity, identical protein binding activity, integrin binding activity, phospholipid binding activity, atp binding activity, fibronectin binding activity, GO:0008237, GO:0004252, metaloendopeptidase activity, calcium ion binding activity]]
HALLMARK_COAGULATION-1[[protein binding activity, domain specific binding activity, disordered domain specific binding activity, GO:0008233, GO:0004252, GO:0005125, signaling receptor binding activity, identical protein binding activity, GO:0004222, GO:0003924, receptor tyrosine kinase binding activity, GO:0004421, phospholipid binding activity, amyloid-beta]][[the genes in this list are predicted to enable various calcium-dependent functions related to protein binding, GO:0019899, and peptidase activity, typically related to blood coagulation, GO:0007155, endodermal cell fate, and negative regulation of protein-regulating processes. these genes are involved in various activities across multiple cellular pathways, including cellular response to uv-a, GO:0030155, and blood coagulation. the enriched terms include “calcium-dependent functions”, “protein binding activity”, “enzme binding activity”, “peptidase activity”, “blood coagulation”, “cell adhesion”, “endodermal cell fate”, “negative regulation of protein-regulating processes”, “cellular response to uv-a”, and “regulation of cell adhesion”.\\n\\nmechanism: the mechanism underlying this list of genes is likely related to calcium-dependent regulation of proteins and peptides, which acts to control various cellular processes. calcium can act as a negative regulator of proteins, through calcium binding to proteins and preventing their activity, or as a]]
HALLMARK_COMPLEMENT-0[[enriched functions observed in the genes include binding activitiy (for various ligands, such as dna, GO:0005562, MESH:C062738, calcium ions, heparin/heparan sulphate, MESH:D019204, c5l2 anaphylatiotaxin, MESH:M0028275, mhc, amyloid-beta, cytokine, opsonin, MESH:D005227, MESH:D011494, etc.), enzyme activity (such as deubiquitinase, lck, atpase, aminopeptidase, peptidase, etc.), GO:0044183, cysteine type endopeptidase inhibitor activity and endopeptidase activity, phospholipid binding activity, transcription factor activity and transcription regulatory region sequence-specific dna binding activitiy. the underlying mechanism could be related to signal transduction, functional process, dna/rna transcription, protein degradation and signalling pathways such as cell killing and apoptotic signalling pathways.\\n\\nsummary: enriched functions include multiple binding activities, GO:0003824, and transcription regulatory activities for signal transduction, functional processes, and signalling pathways. \\nmechanism: signal transduction, functional processes, dna/rna transcription, protein degradation,]][[protein binding activity, GO:0001216, enzyme binding activity, metal ion binding activity, sh2 domain binding activity, GO:0004197, phosphoprotein binding activity, actin binding activity, cation binding activity, lipid binding activity, GO:0004252, GO:0008092, cell killing activity, protein kinase binding activity]]
HALLMARK_COMPLEMENT-1[[enzyme binding activity, GO:0101005, GO:0004197, GO:0005102, GO:0019901, sh2 domain binding activity, GO:0004435, GO:0003924, GO:0004222, atpase binding activity, integrin binding activity, dna binding activity, lipoprotein receptor binding activity, GO:0007165, GO:0006915, MESH:D015850]][[dna-binding, GO:0005543, GO:0005515, GO:0005102, GO:0019899, inhibitor activities, GO:0003924, GO:0046872, protein activities, GO:0023052, transcription regulation, GO:0006281, GO:0008219, GO:0006955]]
HALLMARK_DNA_REPAIR-0[[the given list of human genes are primarily involved in dna binding, transcription and translational activities, rna binding, enzyme binding activities, and identical protein and nucleic acid binding activities. there is also evidence of involvement in activities such as transcription co-activator activity, nuclear localization, cytochrome-c oxidase activity, atp-dependent activities and endopeptidase activator activity. enriched terms include dna binding, GO:0003723, GO:0003887, GO:0046983, identical protein binding activity, transcription factor binding activity, GO:0003700, zinc ion binding activity, atp binding activity, protein binding activity]][[dna binding activity, rna binding activity, enzyme binding activity, protein binding activity, calcium ion binding activity, GO:0140612, GO:0003713, zinc ion binding activity]]
HALLMARK_DNA_REPAIR-1[[dna binding activity, rna binding activity, transcription activity, enzyme binding activity, GO:0042803]][[dna binding activity, enzyme binding activity, GO:0016887, rna binding activity, protein binding activity, GO:0003887, GO:0004518, mrna regulatory element binding]]
HALLMARK_E2F_TARGETS-0[[GO:0007049, GO:0006260, transcriptional regulation, post-transcriptional regulation, GO:0003682, GO:0140014, GO:0051169, GO:0046931]][[chromatin binding activity, GO:0006260, GO:0006281, GO:0006351, GO:0016570, nuclear import/export, dna/rna binding, protein-macromolecule binding, GO:0051726, protein homodimerization, GO:0006200, GO:0000287, MESH:D011494, GO:0004518]]
HALLMARK_E2F_TARGETS-1[[dna binding activity, protein binding activity, histone binding activity, GO:0016887, enzyme binding activity, GO:0006260, GO:0006306, chromatin binding activity, GO:0042803, GO:0003887, rna binding activity]][[nuclear pore remodeling, GO:0065003, GO:0003677, transcriptional regulation, GO:0006260, GO:0006913, chromatin modification and repair, cell cycle progression, GO:0140014, GO:0019899, GO:0042393, protein homod]]
HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0[[extracellular matrix structural components, GO:0007160, protein domain specific binding activity, identical protein binding activity, GO:0048018, signaling receptor binding activity, metal ion binding activity, peptide hormone receptor binding activity, heparin binding activity, collagen binding activity, GO:0007165, GO:0005125]][[protein binding activity, identical protein binding activity, collagen binding activity, integrin binding activity, heparin binding activity, phosphatidylinositol binding activity, cell adhesion molecule binding activity, extracellular matrix binding activity, signaling receptor binding activity, GO:0008009, gene transcriotion activity, metal ion binding activity]]
HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1[[protein binding activity, identical protein binding activity, metal ion binding activity, ion binding activity, actin binding activity, small molecule binding activity, fibronectin binding activity, collagen binding activity, integrin binding activity, procollagen binding activity, cadherin binding activity, phosphatidylinositol-3,4,5-trisphosphate binding activity, substrate-binding activity, GO:0005096, GO:0004867, GO:0005006, GO:0005024, GO:0004896, platelet-derived growth factor binding activity, nucleotide-binding transcription factor activity]][[GO:0005201, collagen binding activity, cell adhesion molecule binding activity, dna binding activity, gtp binding activity, GO:0042803, platelet-derived growth factor binding activity, platelet-derived growth factor binding activity, calcium ion binding activity, signaling receptor binding activity, identical protein binding activity]]
HALLMARK_ESTROGEN_RESPONSE_EARLY-0[[binding activity, transport activity, GO:0003824, adhesion activity, intracellular signaling, GO:0006351, neuronal development]][[dna binding activity, protein binding activity, enzyme binding activity, GO:0022857, transcription activity, GO:0003924, atpase binding activity, mrna binding activity, protein homodimerization, GO:0042169, GO:0016922, GO:0030165]]
HALLMARK_ESTROGEN_RESPONSE_EARLY-1[[GO:0003677, GO:0051117, GO:0005515, GO:0016791, dehydrogenase activity, GO:0004016, GO:0055085, transcriptional regulation, GO:0007155, GO:0006915]][[GO:0003677, GO:0000981, GO:0003723, protein binding/dimerization, transmembrane transporter, GO:0005509, GO:0019899, GO:0003924]]
HALLMARK_ESTROGEN_RESPONSE_LATE-0[[protein binding activity, dna-binding, domain binding activity, carbohydrate binding activity, enzyme binding activity, ligand binding activity, transmembr]][[GO:0050839, GO:0003677, transfacmembrane receptor protein tyrosine kinase activity, ligand binding, ca2+ ion binding, GO:0005543, GO:0019899, GO:0016563, GO:0005243, GO:0003682, GO:0032794, GO:0048018, GO:0005242, GO:0004930, GO:0060089, calcium-dependent exonuclease activity, GO:0003779, GO:0007165, GO:0004672, GO:0016310, sh2 domain binding activity, heme binding activity, GO:0042803, hsp90 protein binding activity, GO:0017002, GO:0004957, ww domain binding activity, pdz domain binding activity, sh3 domain binding activity]]
HALLMARK_ESTROGEN_RESPONSE_LATE-1[[dna-binding, GO:0016563, GO:0005515, membrane transporter activity, GO:0016787, GO:0016310, ligand-mediated activity]][[GO:0008134, GO:0019899, GO:0005515, GO:0007155, ligand-gated ion transporter activity, GO:0001216, GO:0050839, protein domain specificity, GO:0030742, GO:0003677, GO:0019003, GO:0005525, GO:0051117, GO:0030165, GO:0005509, phosphotransfer, GO:0031490, GO:0001217]]
HALLMARK_FATTY_ACID_METABOLISM-0[[GO:0006631, GO:0006629, GO:0005975, GO:0003677, GO:0003723, protein homodimerization, GO:0000287, GO:0005524, GO:0046872, GO:0047617, GO:0003995, fad binding activity, nadph binding activity, homodimerization activity, GO:0000774, GO:0015254, GO:0004497, 5alpha-androstane-3alpha,17beta-diol dehydrogenase activity, GO:0008170, identical protein binding activity, GO:0016860, enzyme binding activity, GO:0004674, GO:0042803, GO:0004351, GO:0004222, ubiquitin binding activity, dna-binding]][[protein binding activity, identical protein binding activity, metal ion binding activity, atp binding activity;lipid transport activity, fatty acid binding activity, fad binding activity, pdz domain binding activity;transmembrane transporter activity, ubiquitin binding activity, nucleotide binding activity, GO:0004080, GO:0004738, enoyl-coa hydratase activity;amino-acid oxidase activity, GO:0003979, GO:0009055, GO:0004853, 5alpha-reductase activity, rna-binding]]
HALLMARK_FATTY_ACID_METABOLISM-1[[GO:0016491, enzyme binding activity, dna binding activity, GO:0004090, GO:0052650, GO:0015245, nadph binding activity, GO:0042803, atp binding activity, receptor ligand binding activity, nad+ binding activity, smad binding activity, rna polymerase ii-specific transcription factor activity, atp-dependent protease activity, GO:0016404, GO:0004672, ubiquitin conjugating]][[GO:0003824, GO:0016491, protein binding activity, hydratase activity, GO:0003997, lipid binding activity, dna binding activity, ubiquitin binding activity, atp binding activity, flavine adenine dinucleotide binding activity, nadp+ binding activity, GO:0042803, smad binding activity, GO:0004466]]
HALLMARK_G2M_CHECKPOINT-0[[GO:0003677, transcription binding, GO:0046872, GO:0005515, GO:0019899, MESH:D020558, GO:0003682, GO:0042826, GO:0046983, sumo-dependent ubiquitination, GO:0003723, GO:0005524, GO:0042054, GO:0008017, GO:0010997, boxh/aca snorna binding, GO:0043515, GO:0070840, m7gpppn-cap structure binding, GO:0008270, GO:0003697, GO:0038024, GO:0006200, GO:0051536, GO:0005884]][[dna binding activity, rna binding activity, protein kinase binding activity, protein folding activity, enzyme binding activity, transcription factor binding activity, chromatin binding activity, protein domain specific binding activity, nucleic acid binding activity, atp binding activity, identical protein binding activity, GO:0140110, GO:0046983, histone binding activity, anaphase-promoting complex binding activity, cytoplasmic release activity, metal ion binding activity, GO:0016887, histone deacetylase binding activity, telomere binding activity]]
HALLMARK_G2M_CHECKPOINT-1[[GO:0005515, GO:0003677, GO:0006351, GO:0019904, GO:0042054, GO:0004402, GO:0004674, GO:0030374, GO:0005049, GO:0016887, zinc ion binding activity, GO:0140037, GO:0036310, sumo polymer binding activity, nuclear receptor binding activity, dna topoisomerase binding activity, GO:0010997, GO:0000774, GO:0005096, microtubule binding activity, dna replication origin binding activity, GO:0000987, rna polymerase ii-specific transcription]][[GO:0005515, GO:0003677, GO:0008134, MESH:D019098, GO:0003723, GO:0006260, GO:0051726, GO:0003682, GO:0010467, GO:0006457, regulation of chromosome structure, GO:0019904, GO:0005524, GO:0019900, GO:0035402, GO:0031267, MESH:M0518050, protein homodimerization, GO:0043130, atp-dependent dna/dna annealing]]
HALLMARK_GLYCOLYSIS-0[[GO:0003676, GO:0005515, GO:0005524, metabolic activity, GO:0016310, MESH:D010084, GO:0005975, GO:0005125, GO:0008083]][[the list of genes represent a range of molecular, metabolic, and protein regulatory processes, including atpase activity, glucose binding activity, GO:0004672, transcriptional activity and activity from receptors, transporters, and enzymes. the enriched terms are \"protein binding activity\"; \"atpase activity\"; \"transcriptional activity\"; \"receptor activity\"; \"transporter activity\"; \"enzyme activity\"; and \"glucose binding activity\".\\n\\nmechanism: the genes in the list encode proteins involved in a range of processes, such as structural support, GO:0007165, regulation of transcription, metabolic pathways and transport of molecules. the underlying biological mechanism is likely related to the coordinated expression of these genes in response to a particular stimulus, or to maintain cellular homeostasis]]
HALLMARK_GLYCOLYSIS-1[[protein binding activity, identical protein binding activity, enzyme binding activity, atp binding activity, transcription activation activity, dna-binding transcription activity, heparin binding activity, cytoplasmic protein binding activity, signalling receptor binding activity, cytoskeletal protein binding activity, GO:0042803, GO:0060422, rna binding activity, GO:0140677, GO:0004689, phosphotransferase activity, heme binding activity, calcium ion binding activity]][[enzyme binding activity, identical protein binding activity, dna binding activity, GO:0042803, heparin binding activity, atp binding activity, protein kinase binding activity, phosphatase binding activity, cyclin binding activity, protein phosphatase binding activity, GO:0004722, actin binding activity, lbd domain binding activity, actin filament binding activity, GO:0008083, chromatin binding activity, hyaluronic acid binding activity, GO:0004197, ubiquitin binding activity, cyclosporin a binding activity, mannose-binding activity, heparan sulfate binding activity, heme binding activity, GO:0016887, transition metal ion binding activity, GO:0031545, GO:0016615, GO:0004148, GO:0004784, transcription core]]
HALLMARK_HEDGEHOG_SIGNALING-0[[GO:0007155, GO:0007165, epithelial-mesenchymal interaction, GO:0006898, GO:0001525, GO:0001843]][[protein/lipid binding activity, GO:0003700, GO:0010468, GO:0051246, positive/negative regulation of cellular component organization, GO:0030036, GO:0030833, GO:0001525, GO:0090630, GO:0019219, GO:0007160]]
HALLMARK_HEDGEHOG_SIGNALING-1[[GO:0003700, rna polymerase ii transcription regulatory region sequence-specific dna binding activity, chromatin binding activity, receptor binding activity, GO:0005096, gtpase binding activity, phospholipid binding activity, calcium ion binding activity, zinc ion binding activity, identical protein binding activity, apolipoprotein binding activity, phosphotyrosine residue binding activity, very-low-density lipoprotein particle binding activity, phosphatidylcholine binding activity, phosphatidylethanolamine binding activity, adenyl ribonucleotide]][[acetylcholine binding activity, GO:0003990, GO:0005096, rna polymerase ii-specific dna-binding transcription factor binding activity, GO:0003714, GO:0017053, GO:0007165, GO:0006351, GO:0007155, GO:0016477, GO:0001525, GO:0035556, GO:0019219, GO:0006468]]
HALLMARK_HEME_METABOLISM-0[[identical protein binding activity, dna binding activity, rna binding activity, GO:0000988, GO:0003714, GO:0016564, GO:0016563, GO:0016791, protein kinase binding activity, GO:0006865, GO:0006811, heme binding activity, oxygen binding activity, protein-fructose gamma-glutamyltransferase activity, GO:0042803, lamin binding activity, chromatin binding activity and ubiquitin ligase activity]][[dna-binding, rna-binding, GO:0019899, GO:0019901, GO:0019903, protein homodimerization, GO:0048729, GO:0006468]]
HALLMARK_HEME_METABOLISM-1[[transcription activity, dna binding activity;rna binding activity, protein kinase binding activity, atp binding activity, protein binding activity, identical protein binding activity, GO:0042803, GO:0004197, GO:0015075, protein domain specific binding activity, GO:0032452, GO:0004674, GO:0016564, GO:0061630, lamin binding activity, GO:0004521, GO:0038023, GO:0004602, phosphoprotein binding activity, molecule adaptation, enzyme binding activity, protein phosphatase binding activity, GO:0004418, ubiquitin conjugating enzyme binding activity, GO:0004842, ap-2 adapt]][[GO:0003677, GO:0005515, GO:0016310, GO:0003824, GO:0005215, MESH:M0496924, vesicular pathways, cytoskeletal pathways, GO:0046872, GO:0003723, GO:0030544, GO:0042802, GO:0008013, phosphatidylinositol-4 binding, GO:0035612, rna polymerase ii dna binding, GO:0042393, GO:0019901, tyrosine-protein kinase activity, GO:0061630, GO:0003713, fibronectin leucine-rich-repeat sense-specific binding, endothelial differentiation-specific factor binding, fatty-acid binding, heme-binding, GO:0051537, GO:0050661, GO:0070742, MESH:D012330]]
HALLMARK_HYPOXIA-0[[dna-binding transcription activity, enzyme binding activity, protein binding activity, ligand-binding activity, atp binding activity, nadp binding activity, metal ion binding activity, carbohydrate binding activity, signaling receptor binding activity, GO:0003714, GO:0001217, GO:0008160, heparin binding activity, n-acetylglucosamine n-sulfotransferase activity, MESH:D006497]][[this is a list of genes of known or suspected functions in a variety of processes, ranging from dna binding and transcription regulation to enzyme binding, metabolic activity, GO:0005102, and structural protein formation. commonly enriched terms include dna binding, transcription regulation, GO:0019899, and protein binding. mechanism: a variety of processes are involved in these gene functions, including dna replication and repair, protein folding and conformational change, receptor binding and signal transduction, metabolic activity, structural protein formation]]
HALLMARK_HYPOXIA-1[[dna binding activity, rna binding activity, protein binding activity, GO:0004672, GO:0019887, GO:0016407, GO:0016301, GO:0008233, GO:0004197, GO:0004252, ubiquitin binding activity, GO:0042803, GO:0000988, GO:0016563, GO:0016564, apolipoprotein binding activity, phosphatase binding activity, disordered domain specific binding activity, chromatin binding activity, GO:0016303, GO:0030701, GO:0004693, GO:0004396, actinin binding activity, 14-3-3 protein binding activity, gtp binding activity, MESH:D009584]][[dna-binding transcription activity, GO:0003714, GO:0016564, GO:0016563, rna polymerase ii-specific, protein binding activity, GO:0042803, platelet-derived growth factor binding activity, GO:0030291, GO:0046982, GO:0004197, protein kinase binding activity, GO:0019887, GO:0004725, cyclin binding activity, GO:0004693, GO:0035403, phosphatidylinositol-3-kinase activity, nad+]]
HALLMARK_IL2_STAT5_SIGNALING-0[[ligand binding, GO:0019899, GO:0005102, MESH:M0518050, GO:0003700, rna-binding, protein homodimerization, protein-kinase binding activity, identical protein binding activity, GO:0004896, c-c chemokine binding activity, GO:0004197, GO:0022857, gtp binding activity, protease binding activity]][[GO:0005096, dna-binding transcription activator/repressor activity, protein binding activity, ligand binding activity, identical protein binding activity, bh3 domain binding activity, phosphatidylinositol binding activity, GO:0016787, atp binding activity, atpase-coupled intramembrane lipid transport activity, amyloid-beta binding activity, hsp90 protein binding activity, s100 protein binding activity, cadherin binding activity, GO:0038023, GO:0005125, GO:0005021, GO:0004896, identical protein binding activity, GO:0008233, heat shock protein]]
HALLMARK_IL2_STAT5_SIGNALING-1[[dna-binding, transcriptional activity, GO:0006355, GO:0005515, protein homodimerization, GO:0003924, GO:0005102, ligand-activated transcription, GO:0019900, GO:0002020, GO:0004674, GO:0004175, cystein-type endopeptidase activity, GO:0005102, GO:0061630, GO:0005125, GO:0008083, leukemia inhibitory factor activity, 5'-deoxyn]][[dna-binding transcription activity, protein kinase binding activity, small gtpase binding activity, interleukin-binding activity, GO:0004896, signaling receptor binding activity, rna binding activity, gtp binding activity, GO:0004197, identical protein binding activity, protein domain specific binding activity, GO:0046982]]
HALLMARK_IL6_JAK_STAT3_SIGNALING-0[[GO:0038023, binding activity, MESH:D016207, MESH:M0496065, MESH:D008074, MESH:D010455, MESH:D011506, GO:0019900, GO:0005524]][[cytokine binding activity, protein binding activity, kinase binding activity, signaling receptor binding activity, GO:0004675, cell adhesion molecule binding activity, interleukin-receptor activity, GO:0004725, tir domain binding activity, ubiquitin protein ligase binding activity, GO:0008284, GO:0032768, GO:0009966, GO:0090276, GO:0045597, GO:0010604, GO:0098542, GO:0009612, GO:0001819, GO:0031349]]
HALLMARK_IL6_JAK_STAT3_SIGNALING-1[[GO:0004896, cxcr chemokine receptor binding activity, interleukin-binding activity, GO:0006952, GO:0010605, GO:0051247]][[cytokine binding activity, GO:0004896, GO:0008083, cell adhesion molecule binding activity, chemokine (c-x3-c) binding activity, GO:0006952, signaling receptor binding activity, GO:0000988, identical protein binding activity, phosphatidylinositol binding activity, heparin binding activity, lipid binding activity, c-c chemokine binding activity, dna binding activity, GO:0005096, sh3 domain binding activity, ephrin receptor binding activity, transforming growth factor beta receptor binding activity, ubiquitin-like protein ligase binding activity, enzyme binding activity, calcium-dependent protein binding activity, protease binding activity]]
HALLMARK_INFLAMMATORY_RESPONSE-0[[protein binding activity, GO:0005125, GO:0004930, dna-binding transcription activity, lipopolysaccharide binding activity, atp binding activity, integrin binding activity, GO:0048018, GO:0022857, signaling receptor binding activity, extracellular atp-gated channel activity, phosphatidylinositol- 3-kinase activity, metallod]][[GO:0004930, GO:0005125, GO:0003700, GO:0005216, receptor binding activity, GO:0008083, cell adhesion molecule binding activity, signalling receptor binding activity, GO:0003714, enzymatic activity, phospholipid binding activity, peptide hormone receptor binding activity, GO:0003924]]
HALLMARK_INFLAMMATORY_RESPONSE-1[[GO:0038023, binding activity, GO:0003824, GO:0008083, GO:0005215, GO:0000988]][[atp binding activity, chemokine/chemokine receptor/chemokine receptor binding activity, cytokine/cytokine binding activity/cytokine receptor activity, dna binding activity/dna-binding transcription factor activity, GO:0004930, identical protein binding activity, ion transport/ion transporter activity, peptide/peptide receptor binding activity, phospholipid binding activity, GO:0019887, signaling receptor binding activity, GO:0000988, GO:0022857]]
HALLMARK_INTERFERON_ALPHA_RESPONSE-0[[signaling receptor binding activity, GO:0003713, regulation of transcription, dna-binding activity, rna binding activity, metal ion binding activity, identical protein binding activity, GO:0042803]][[immunologic processes, GO:0098609, GO:0006952, cellular response, positive regulation, rna polymerase ii specific, GO:0003677, GO:0003723, protein homodimer]]
HALLMARK_INTERFERON_ALPHA_RESPONSE-1[[GO:0098542, GO:0006955, GO:0046718, GO:0032020, GO:0019882, GO:0019221, GO:0045087, GO:0007166, GO:0030225, GO:0032722, GO:0001961, cell-cell adhesion mediated by plasma membrane cell adhesion molecules]][[GO:0003713, rna binding activity, dna binding activity, identical protein binding activity, GO:0061630, zinc ion binding activity, GO:0042803, double-stranded rna binding activity, heparin binding activity, GO:0030701, GO:0004175, cxcr chemokine receptor binding activity, tap binding activity, peptide antigen binding activity, gtp binding activity, GO:0033862, GO:0004197, amyloid-beta binding activity, macrophage migration inhibitory factor binding activity, GO:0004550, GO:0016064, GO:0140374, GO:0071345, GO:0046597, positive regulation of]]
HALLMARK_INTERFERON_GAMMA_RESPONSE-0[[the list of genes are discovered to be enriched in terms like dna binding activities, GO:0042803, GO:0000988, GO:0004672, GO:0004725, GO:0016887, enzyme binding activity, phosphatidylinositol phosphate binding activity, GO:0030528, GO:0008009, and cytokine receptor activity.\\n\\nmechanism: the biological mechanism underlying the enriched terms is most likely associated with cell and immune response. these genes are involved in various processes related to cell signaling, detection, recognition, GO:0006351, and expression. through these processes, the genes regulate important functions such as cell adhesion, GO:0005515, GO:0019899, GO:0005125, and transcription factor activation. in addition, several of these genes are also involved in apoptotic and other cell regulation pathways]][[protein binding activity, enzyme binding activity, dna-binding transcription activity, GO:0006200, protein homodimerization, kinase regulation, protein dimerization.\\nmechanism: these genes are likely involved in the regulation of gene expression cell signaling pathways, enabling an array of signaling activities that help to maintain cellular homeostasis]]
HALLMARK_INTERFERON_GAMMA_RESPONSE-1[[binding activity, GO:0003824, protein activity, GO:0000981]][[GO:0016887, dna binding activity, gtp binding activity, peptide antigen binding activity, GO:0004252, dna-binding transcription activity, GO:0005125, GO:0008009, GO:0004896, GO:0038023, GO:0004930, rna binding activity, enzyme binding activity, GO:0046983, phosphorylation-dependent protein binding activity, GO:0019887, GO:0140311, toll-interleukin receptor (tir) domain binding activity, signaling receptor binding activity, and]]
HALLMARK_KRAS_SIGNALING_DN-0[[protein binding activity, transmembrane activity, GO:0003700, sequence-specific double-stranded dna binding activity, GO:0004930, identical protein binding activity, calcium ion binding activity, scaffold protein binding activity, transcription cis-regulatory region binding activity]][[GO:0004930, GO:0042803, calcium ion binding activity, sodium:potassium:chloride transporter activity, GO:0004683, platelet-derived growth factor activity, GO:0005007, cytoskeletal protein binding activity, GO:0015171, n6-threonylcarbamylade adenine dinucleotide synthetase activity, GO:0043273, intracellular transport activity, signal transduction activity, GO:0016887, GO:0004175, GO:0016491, GO:1990817, GO:0004958, beta-caten]]
HALLMARK_KRAS_SIGNALING_DN-1[[dna-binding activity, transcription activity, calcium ion binding activity, atp-binding activity, protein binding activity, GO:0004930, cell death regulation, GO:0009653, GO:0042445]][[the list of genes is significantly enriched for dna-binding activities, calcium ion binding activities, identical protein-binding activities, GO:0046982, GO:0016887, and g protein-coupled receptor activities.\\n\\nmechanism:\\nthe underlying biological mechanism likely involves a complex, dynamic interaction between various proteins, MESH:D004798, and ions, driven by a variety of dna-binding, calcium-binding, and atp-binding activities, resulting in the recruitment of additional proteins to form heterodimers, thereby leading to protein synapsis cell signaling]]
HALLMARK_KRAS_SIGNALING_UP-0[[cell adhesion molecule binding activity, atpase-coupled intramembrane transport, GO:0004222, GO:0042803, signal receptor binding activity, GO:0003700, MESH:D006493]][[atp binding activity, atpase-coupled intramembrane transport, GO:0048018, dna-binding transcription regulation, protein domain binding activity, enzyme binding activity, GO:0005125, GO:0007165, GO:0007155, GO:0016477, GO:0030154, MESH:D048788]]
HALLMARK_KRAS_SIGNALING_UP-1[[GO:0005125, protein domain specific binding activity, protein kinase binding activity, cell adhesion molecule binding activity, signaling receptor binding activity, GO:0004222, GO:0001217, rna binding activity, gtpase binding activity, structural proteins, atp binding activity]][[receptor binding activity, identical protein binding activity, GO:0001216, enzyme binding activity, protein domain specific binding activity, protein kinase binding activity, ligand binding activity, atp binding activity, cytoskeletal protein binding activity, cell adhesion molecule binding activity, GO:0004930, transmembrane transporter binding activity, GO:0008233, dna binding activity, GO:0004252, histone binding activity, signal transduction activity]]
HALLMARK_MITOTIC_SPINDLE-0[[protein binding activity, cytoskeleton binding activity, GO:0005096, atpase binding activity, GO:0042030, adenyl ribonucleotide binding activity, calmodulin binding activity, cadherin binding activity, gamma-tubulin binding activity, integrin binding activity, kinetochore binding activity, molecular function adaptor activity, GO:0042803, protein kinase binding activity, protein phosphatase binding activity, sh2 domain binding activity, sh3 domain binding activity, small gtpase binding activity, beta-catenin binding activity, beta-tubulin binding activity, dynein complex binding activity, identical protein binding activity, phosphatidylcholine binding activity, protein domain specific binding activity, protein tyrosine kinase binding activity]][[actin binding activity, atp binding activity, atpase binding activity, GO:0098632, dynein complex binding activity, gamma-tubulin binding activity, gtp binding activity, gtpase binding activity, guanyl ribonucleotide binding activity, GO:0003924, GO:0005085, kinetochore binding activity, GO:0060090, GO:0140677, myosin binding activity, phosphatidylcholine binding activity, GO:0019904, GO:0042803, GO:0004672, GO:0004674, small gtpase binding activity]]
HALLMARK_MITOTIC_SPINDLE-1[[MESH:D020558, atpase, tubulin binding activity, microtubule binding activity, actin filament binding activity, kinesin binding activity, dynein binding activity, g protein-coupled receptor binding activity]][[this set of genes are involved in activities, processes and signaling pathways related to intracellular motion such as transport within cells (microtubule/kinesin/dynein binding, GO:0005096, GO:0008092, motor protein activity), cell cycle activities (centrosome duplication, GO:0019899, protein homodimerization, GO:0019902, GO:0003682, GO:0043515, GO:0005516, formin binding, atpase/atp hydrolysis regulatory activity), and cell-cell signaling (jun kinase kinase kinase activity, map-kinase scaffolding, GO:0042608, GO:0045296, GO:0051879, GO:0097016, GO:0005680, GO:0051059, rna binding).\\n\\nmechanism: these genes enable a wide range of activities and processes related to intracellular motion and cell-cell signaling that are either directly or indirectly connected to the assembly, MESH:M0030663, and disassembly of cytoskeletal structures, MESH:D014404, and cellular organelles. these activities can promote cell cycle progression, GO:0008283, and/or cell-cell signaling]]
HALLMARK_MTORC1_SIGNALING-0[[enzyme binding activity, acid binding activity, molecule transport, adapter binding activity, receptor binding activity, dna binding activity, protein binding activity, GO:0003824, GO:0016787, GO:0016491, anion binding activity, GO:0008233, GO:0140657, thioredoxin activity, translocation, GO:0061630, cysteine endopeptidase activity, GO:0004738, GO:0004618, magnesium ion binding activity, GO:0004340, GO:0003924]][[protein binding activity, dna binding activity, enzyme binding activity, GO:0060090, GO:0140677, GO:0042803, domain binding activity, GO:0016491, protein kinase binding activity, phosphatidylinositol binding activity, GO:0016504, GO:0003714, nuclear androgen receptor binding activity, nf-kappab binding activity, ubiquitin protein ligase binding activity, phosphotyrosine residue binding activity, GO:0016564, GO:0003743, peptidyl-proinalyl cistrans isomerase activity]]
HALLMARK_MTORC1_SIGNALING-1[[protein binding activity, identical protein binding activity, GO:0008233, GO:0003824, GO:0005884, dna-binding, rna-binding, GO:0016922, MESH:D054875, anion binding activity, atp binding activity, GO:0016887, protein kinase binding activity, phosphotyrosine residue binding activity, e3 ubiquitin-protein ligase binding activity, mdm2 binding activity, GO:0060090, GO:0140677, GO:0098772, GO:0003713, GO:0003714, GO:0016564, GO:0042803, k63]][[protein-protein interaction, atp binding activity, GO:0042803, GO:0016887, protein kinase binding activity, ubiquitin protein ligase binding activity, GO:0060090, anion binding activity, chemical oxidoreductase activity, protein domain specific binding activity, gtp binding activity, dna binding activity, rna binding activity, transcription regulation activity, GO:0007165, chromatin binding activity, phospholipid binding activity, GO:0004017, lipoprotein particle binding activity, GO:0008233, actin filament binding activity, fad binding activity, steroid hydrolase activity, rna stem-loop binding activity, GO:0022857, nf-kappab binding activity, coenzyme a binding activity, protein n-terminal phospho-seryl-prolyl pept]]
HALLMARK_MYC_TARGETS_V1-0[[GO:0003677, GO:0003723, GO:0003682, GO:0006351, GO:0006412, GO:0045292, atpase binding activity, enzyme binding activity, GO:0044183, ubiquitin protein ligase, MESH:C021362, nf-kappab binding activity, GO:0140693, nucleic acid binding activity, heparan sulfate binding activity, biopolymer binding activity, GO:0060090, GO:0140678, g-protein beta-subunit binding activity, molecular sequence recognition, complementary rna strand recognition, mrna 3'-utr]][[GO:0003723, GO:0044183, dna binding/recognition, protein homodimerization, GO:0003678, GO:0019904, MONDO:0000179, GO:0042393, cytoplasmic protein binding, GO:0005524, GO:0006281]]
HALLMARK_MYC_TARGETS_V1-1[[rna binding activity, identical protein binding activity, mrna 3' utr binding activity, GO:0000900, dna binding activity, ubiquitin protein ligase binding activity, protein domain specific binding activity, GO:0006457, dna replication origin binding activity, dna-binding transcription factor binding activity, GO:0042803]][[GO:0003677, GO:0003723, GO:0019904, GO:0003682, GO:0019899, protein folding chaperone activities, atp binding activity, mrna 3'-utr binding activity, identical protein binding activity, GO:0004869, GO:0140693, GO:0140713, heparan sulfate binding activity, peptidyl-prolyl isomerase activity, cyclin binding activity, GO:0004693, nuclear localization sequence binding activity, magnetic ion binding activity, histone methyltransferase binding activity, mrna 5'-utr binding activity, GO:0033677, MESH:D012321]]
HALLMARK_MYC_TARGETS_V2-0[[GO:0006351, GO:0006351, GO:0008284, GO:0071824, GO:0019219, rna binding activity, GO:0010468, GO:0006364]][[rna-binding, GO:0036211, GO:0015031, cell signaling, GO:0006412, genetic information regulation, protein bridging, chromatin regulation, transcription regulation, GO:0003676, mitochondrial functions]]
HALLMARK_MYC_TARGETS_V2-1[[rna binding activity, dna binding activity, protein binding activity, GO:0006364, GO:0019538, GO:0006351, transcription coregulator binding activity, GO:0022402, GO:0003682, mitochondria regulation, cyclin binding activity, cyclin-dependent protein serine/threonine kin]][[rna binding activity, ribosomal rrna processing, mrna and/or rrna catabolism/stability, regulation of transcription/translation, regulation of signal transduction and metabolism processes, regulation of cell cycle/proliferation, protein modification/regulation, GO:0005634, GO:0005829, GO:0005840, GO:0005739]]
HALLMARK_MYOGENESIS-0[[GO:0008092, GO:0005201, GO:0044325, ion channel regulator, GO:0003779, GO:0005096, GO:0051879, GO:0017046, GO:0003677, signalling receptor binding, GO:0042802, GO:0048306, GO:0019899, GO:0005509, GO:0005524, GO:0006200, GO:0051117, GO:0004017, GO:0008195, GO:0051015, microfilament binding, GO:0003872, GO:0043138, GO:0004517, MESH:D009243]][[calcium ion binding activity, identical protein binding activity, actin filament binding activity, GO:0042803, signaling receptor binding activity, atp binding activity, gtp binding activity, dna binding activity, GO:0019887]]
HALLMARK_MYOGENESIS-1[[GO:0005509, GO:0004129, GO:0003677, GO:0005524, GO:0003779, abnormal growth and development, GO:0002020, structural constituent]][[calcium binding activity, enzyme binding activity, dna binding activity, atp binding activity, GO:0042803, protein domain-specific binding activity, gtp binding activity, actin binding activity, GO:0008160, small gtpase activator activity, transmembrane transporter binding activity, GO:0004016, c3hc4-type ring finger domain-binding activity, GO:0060090, GO:0005096]]
HALLMARK_NOTCH_SIGNALING-0[[GO:0036211, MESH:D005786, signal transduction regulation, dna-templated transcription regulation, GO:0007219, GO:0016567, GO:0031146, GO:0045893]][[this list of genes is associated with several biological processes related to the regulation of gene expression, such as notch receptor processing, amyloid-beta formation, proteolysis, regulation of cell differentiation, canonical wnt signaling pathway, protein ubiquitination, scf-dependent proteasomal ubiquitin-dependent protein catabolic process, and positive regulation of transcription by rna polymerase ii. the underlying biological mechanism is likely related to the role of these genes in transcription and post-transcriptional gene regulation. enriched terms include: gene expression regulation, GO:0007220, GO:0034205, GO:0006508, GO:0045595, GO:0060070, GO:0016567, GO:0031146, GO:0045944]]
HALLMARK_NOTCH_SIGNALING-1[[GO:0006351, GO:0036211, MESH:D054875, GO:0065007, GO:0007219, GO:0031146, wnt, GO:0016567, GO:0043543, GO:0004879, GO:0003714, transcription corepressor binding activity, GO:0006351, rna polymerase ii-specific dna-binding transcription repressor activity, GO:0045893, GO:0000122, GO:0045737, GO:0010604, GO:0010628, negative regulation of cell different]][[GO:0016567, GO:0031146, GO:0007219, GO:0036211, GO:0010468, GO:0030335, GO:0008284, GO:0045596]]
HALLMARK_OXIDATIVE_PHOSPHORYLATION-0[[GO:0006118, GO:0020037, GO:0005515, GO:0016491, atpase activity & binding activity, GO:0060090, acyl binding activity, GO:0003954, gtp binding activity, iron-sulfur cluster binding activity, fad binding activity, MESH:D010758, GO:0019395, rna binding activity, 4 iron, 4 sulfur cluster binding activity, ubiquitin protein ligase binding activity, GO:0004129, proton-transporting atp synthase activity, lipoic acid binding activity, mhc class i protein binding activity, angiostatin binding activity, deltarasin binding activity, ubiquitin protein binding activity, nadp binding activity]][[acetyl-coa transferase activity, GO:0003995, aldehyde dehydrogenase activity, atpase binding activity, GO:0004129, GO:0009055, GO:0004300, fad binding activity, GO:0003924, heme binding activity, identical protein binding activity, lipid binding activity, metal ion binding activity, GO:0003958, GO:0016491, GO:0004738, pro]]
HALLMARK_OXIDATIVE_PHOSPHORYLATION-1[[GO:0140657, GO:0009055, GO:0008553, ubiquitin protein ligase binding activity, MESH:D014451, heme binding activity, protein homodimerization, mhc class i protein binding activity, metal ion binding activity, angiostatin binding activity, mitochondrion targeting sequence binding activity, GO:0015227, rna binding activity, 4 iron, 4 sulfur cluster binding activity, GO:0000295, GO:0004129, fatselytranstransferase activity, GO:0003925, acyl-coa c-acetyltransferase activity, GO:0004774, GO:0003994, GO:0004095, GO:0003958, acetate coa-transfer]][[GO:0009055, protein homodimerization, GO:0003924, GO:0000295, phosphoprotein binding activity, mitochondrial respiratory chain activity, proton-transporting atp synthase activity, mitochondrial ribosome binding activity]]
HALLMARK_P53_PATHWAY-0[[GO:0003700, protein binding activity, protein kinase binding activity, GO:0042803, enzyme binding activity, GO:0098631, signaling receptor binding activity, actin binding activity, cyclin binding activity, GO:0005198, GO:0030695]][[dna binding activity, rna polymerase ii-specific dna-binding transcription factor binding activity, transcription regulation, protein binding activity, enzyme binding activity]]
HALLMARK_P53_PATHWAY-1[[dna binding activity, rna binding activity, rna polymerase binding activity, GO:0004672, GO:0042803, protein kinase binding activity, GO:0000988, GO:0003924, GO:0098631, cell signaling receptor binding activity, enzyme binding activity, heme binding activity, collagen binding activity, GO:0004392, GO:0060090, GO:0004527, GO:0042803, g protein-coupled receptor binding activity, GO:0022857, identical protein binding activity, GO:0016787, GO:0008083]][[GO:0007165, MESH:D005786, GO:0005515, GO:0019899, GO:0016791, GO:0000988, GO:0007155, growth factor binding. \\nmechanism: these genes are involved in the regulation of gene expression and cellular processes by modulating signal transduction, binding proteins, and enzymes, as well as activating phosphatase activity, transcription factor activity and growth factor binding]]
HALLMARK_PANCREAS_BETA_CELLS-0[[GO:0006351, GO:0016563, atpase-coupled ion transport, GO:0004672, GO:0008233, dna binding activity, GO:0017156, GO:1903530]][[atp binding activity, GO:0019829, GO:0016477, GO:0044249, GO:0071333, GO:0090398, GO:0042742, GO:0005789, e-box binding activity, GO:0015149, GO:0002551, GO:0043303, GO:0008233, GO:0008607, GO:0045597, positively regulation of cellular biosynthetic process, positively regulation of glycolytic process, positively regulation of insulin secretion, positively regulation of macromolecule metabolic process, positively regulation of type b pancreatic cell development, positive regulation of cellular]]
HALLMARK_PANCREAS_BETA_CELLS-1[[transcription regulation, GO:0098609, GO:0007165, GO:0045047, GO:0030041, GO:0051594, GO:0060291, GO:1903561, GO:0030027, GO:0005881, GO:0043195, GO:0005829, GO:0030425, MESH:D012319, dna-templated trans]][[GO:0098609, GO:0032502, differentiation, UBERON:0000061, transcription regulation, MESH:D012319, GO:0007165, GO:0043170, protein expression, cell signaling, protein production]]
HALLMARK_PEROXISOME-0[[molecular binding activity, GO:0003824, GO:0005215, domain binding activity, GO:0006869, GO:0015031, GO:0006259, GO:0016070]][[after term enrichment analysis on the gene summaries, the following terms were found to be enriched: atp binding activity, atpase-coupled activity, GO:0042803, identical protein binding activity, enzyme binding activity, GO:0005319, GO:0016887, and metal ion binding activity.\\n\\nmechanism: the enriched terms suggest a biological mechanism that involves energy production and transport, GO:0007165, and protein interactions and formation of protein complexes. these processes are necessary for various cellular processes such as metabolism, GO:0007585, GO:0098754, GO:0040007]]
HALLMARK_PEROXISOME-1[[genes involved in this list are primarily associated with the metabolic or structural processes needed for cellular development and homeostasis. enriched terms include fatty acid metabolism, protein homodimerization, MESH:D010084, dna and rna binding, enzyme/acyl-coa/gtpase binding/hydrolase activity, transport/export/import, and regulation of transcription by rna polymerase ii. mechanism: these genes act together to provide a plethora of functions that are integral to the growth, maintenance and protection of cells. fatty acids are transported, oxidized, and bound to proteins or phospholipids in the membrane, proteins interact with atp and gtp and undergo homodimerization, transcriptional activity is regulated by heterodimerizing with transcription factor proteins]][[cell metabolic process, GO:0090304, GO:0005515, GO:0003677, GO:0016485, GO:0042446, GO:0006694, GO:0005524, GO:0006200, protein homodimerization, GO:0019901, GO:0003714, GO:0003712, cyclin binding activity, rna binding activity, protein phosphatase binding activity, sulphatide binding activity, magnesium ion binding activity, GO:0043621, MESH:M0518050, protein transmembrane]]
HALLMARK_PI3K_AKT_MTOR_SIGNALING-0[[protein binding activity, GO:0016301, GO:0005048, GO:0005102, GO:0051726, apoptosis regulation, GO:0007165, rna binding activity, GO:0004721, GO:0004620, GO:0003924, 1-phosphatidylinositol phospholipase activity, phosphotyrosine residue binding activity, GO:0000774, guanyl ribonucleotide binding activity, GO:0004869, GO:0051219, GO:0044325, GO:0008092, GO:0050750, GO:0003713, GO:0050681, nuclear receptor coactiv]][[cellular process regulations, GO:0003824, protein and peptide regulation, protein domain modification]]
HALLMARK_PI3K_AKT_MTOR_SIGNALING-1[[the genes in this list are involved in several biological functions, including signal transduction, GO:0006915, cellular response to stimuli, response to dna damage, GO:0051726, and regulation of protein phosphorylation and ubiquitination. the terms \"protein phosphorylation\"; \"ubiquitination\"; \"signal transduction\"; \"cellular response to stimulus\"; \"dna damage response\"; \"regulation of cell cycle\"; \"intrinsic apoptosis\"; and \"scaffold protein\" are all statistically over-represented.\\n\\nmechanism: signaling pathways and cellular processes are intricately regulated and require the coordinated participation of different proteins. by performing a term enrichment analysis, we see that the genes in this list are involved in a variety of molecular pathways, including signal transduction, GO:0006915, cellular response to stimuli, response to dna damage, GO:0051726, and regulation of protein phosphorylation and ubiquitination. this suggests that the gene products help coordinate these pathways by forming complexes, binding to signaling molecules, or carrying out the necessary enzyme activities. this suggests the underlying biological mechanism may involve interplay between specific gene products, MESH:D011506, signaling molecules to ensure efficient functioning of the cell]][[GO:0007165, GO:0019900, GO:0003924, GO:0004721, transcription factor activation, GO:0004620, GO:0005102, MESH:D054875, MESH:D000107, GO:0006915, GO:0016477, negative regulation of proliferation]]
HALLMARK_PROTEIN_SECRETION-0[[protein binding activity, GO:0003924, gtp-dependent protein binding activity, snare binding activity, enzyme binding activity, protein kinase binding activity, clathrin binding activity, GO:0006897, retrograde transport, GO:0006893, GO:0006888, GO:0006622]][[protein binding activity, atp binding activity, gtp-dependent protein binding activity, GO:0003924, signal sequence binding activity, clathrin binding activity, small gtpase binding activity]]
HALLMARK_PROTEIN_SECRETION-1[[protein binding activity, activity, GO:0042803, enzyme binding activity, scaffold protein binding activity, snare receptor activity, syntaxin binding activity, GO:0016887, GO:0008553, GO:0008320, metal ion binding activity, protein foldinactivity, GO:0003924, protein kinase binding activity, phosphat]][[atp binding activity, GO:0042803, smarc protein binding activity, GO:0003924, gtp binding activity, GO:0005096, enzyme binding activity, GO:0004197, protein domain specific binding activity, phosphatidylinositol-4-phosphate binding activity, protein kinase binding activity, GO:0008320, calcium-dependent protein binding activity, metal ion binding activity, dopaminergic receptor binding activity, ubiquitin-like protein ligase binding activity, GO:0005484, phosphatidylinositol-3,4,5-trisphosphate binding activity, phosphatidylinositol-3,5-bisphosphate binding activity, signaling receptor binding activity, GO:0005198, syntaxin binding activity, GO:0005484]]
HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0[[oxidative stress defense, GO:0098754, dna/rna binding, GO:0006351, GO:0098609, GO:0016043, GO:0019722, GO:0006468, GO:0010731, GO:0004392, GO:0019511, GO:0061621, GO:0005886, GO:0006750, GO:0006082]][[the human genes provided are mostly involved in redox homeostasis, GO:0006952, and cell organization. there is also involvement in processes related to the maintenance of the blood-brain barrier, GO:0009650, and metabolism of hormones, MESH:D008055, and glucose. there are an abundance of terms related to transmembrane transport, MESH:D010088, heme and iron metabolism, GO:0019511, and gluthathione metabolism.\\n\\nmechanism:\\nredox homeostasis is regulated by a network of enzymatic and substrate-dependent processes. these processes include cellular antioxidant defense, removal of superoxide radicals and peroxides, GO:0061691, and regulation of the balance between oxidant production and scavenging. transport genes are employed to promote transmembrane transport of xenobiotics and lipids, like abcc1, atox1, and glrx. iron and heme metabolism is facilitated by genes like ftl, hmox2, and mpo. peptidyl-proline hydroxylation is regulated by genes like egln2 and mgst1, while glutathione metabolism is controlled by genes like g]]
HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1[[MESH:D004734, oxidative stress response, GO:0042803, protein phosphatase 2a binding activity, GO:0004601, GO:0004602, GO:0047499, GO:0003954, chromatin dna binding activity, GO:0004861, GO:0004784, GO:0047184, GO:0015038, GO:0015035, phosphatidylinositol binding activity, GO:0004096, heme binding activity]][[GO:0045454, GO:0019899, protein homodimerization, GO:0015035, GO:0004602, GO:0003954, atp binding activity, identical protein binding activity, transition metal ion binding activity, GO:0016209, heme binding activity, ubiquitin-specific protease binding activity, GO:0047499, heparin binding activity, GO:0004601, GO:0004784, GO:0008811, GO:0004096]]
HALLMARK_SPERMATOGENESIS-0[[GO:0003723, GO:0031491, transcription and regulation, GO:0003677, GO:0004672, protein folding and chaperoning, metabolic regulation, MESH:D054875]][[GO:0140677, GO:0004672, cellular component activity, binding activity, GO:0008233, nucleosome binding activity, ion binding activity, phosphatase binding activity, GO:0051726, apoptosis regulation, GO:0007155, GO:0007399, transcription regulation, GO:0015031, GO:0009988, MESH:D005786]]
HALLMARK_SPERMATOGENESIS-1[[GO:0019899, GO:0005515, ligand binding, GO:0005509, GO:0000166, GO:0008134, GO:0003677, GO:0005525, GO:0042562, GO:0006200, GO:0004672, GO:0003723, GO:0008047, GO:0044183, GO:0003682, GO:0019903, GO:0019212, GO:0008233, GO:0022890]][[all of the genes are involved in regulation of various metabolic processes and signaling pathways, with most of them associated with binding activities and regulation of protein activities. enriched terms include: protein binding activity, atp binding activity, protein-folding chaperone binding activity, chromatin binding activity, GO:0046976, transcription corepressor binding activity, GO:0004672, GO:0060090, enzyme binding activity, GO:0140677, GO:0098632, GO:0004888, gtp binding activity, signaling receptor binding activity, ribonucleoprotein complex binding activity, myosin light chain binding activity, GO:0017116, GO:0003689, GO:0051131, peptide alpha-n-acetyltransferase activity. mechanism: the genes are involved in various metabolic processes and signaling pathways, by regulating protein activities through different binding activities and histone methyltransferase activity. some of these activities regulate certain processes based on gtp binding, while others are involved in cell-cell adhesion, transmembrane signaling and chaperone-mediated protein complex assembly]]
HALLMARK_TGF_BETA_SIGNALING-0[[GO:0007165, regulation of transcription, GO:0051246, regulation of macromolecule metabolism, GO:0050794, interaction with transcription factors, interaction with smad proteins]][[GO:0005524, GO:0048185, GO:0046332, protein phosphatase/kinase activity, smad signaling, bmp signaling, GO:0006351, MESH:D012319, GO:0005515, GO:0007165, GO:0007049, GO:0008152, GO:0007155]]
HALLMARK_TGF_BETA_SIGNALING-1[[tgf binding activity, dna-binding transcription factor binding activity, smad binding activity, GO:0019211, GO:0004674, GO:0004869, GO:0061631, myosin binding activity, r-smad binding activity, beta-catenin binding activity, cadherin binding activity, gtp binding activity, i-smad binding activity, GO:0003924, GO:0003714, GO:0042803, nucleic acid binding activity, serine-type endope]][[dna-binding activity, transcription regulation, GO:0035556, GO:0004674, smad binding activity, positive/negative regulation of rna/protein metabolic process, GO:0006468, receptor tyrosine kinase binding activity, GO:0007165, GO:0042803, GO:0061630, GO:0031326, GO:0009966, GO:0006357, GO:0090092]]
HALLMARK_TNFA_SIGNALING_VIA_NFKB-0[[dna binding transcription factor, GO:0005102, GO:0019899, GO:0005126, growth factor, transmembrane receptor]][[the list of genes provided are involved in a broad set of functions related to gene transcription or regulation of transcription factors, cell signaling, binding activities and metabolic processes. the enriched terms for this gene set include dna-binding transcription factor activity, rna polymerase ii transcription regulatory region sequence-specific binding, GO:0003924, chemokine receptor binding activity, signaling receptor binding activity, protein kinase binding activity, enzyme binding activity, identical protein binding activity and protease binding activity.\\n\\nmechanism: the underlying biological mechanism for this list of genes is likely related to control of gene expression, as well as control of protein interactions that mediate cell signaling and metabolic processes. additionally, the functions related to binding activities suggest many of the genes are involved in cell-to-cell communication and cell adhesion]]
HALLMARK_TNFA_SIGNALING_VIA_NFKB-1[[GO:0000988, rna polymerase ii-specific, dna-binding, identical protein binding activity, enzyme binding activity, signaling receptor binding activity, GO:0004672, GO:0005125, GO:0008083, GO:0098631, GO:0022857, GO:0016791, gtp binding activity, GO:0140657]][[GO:0001216, transcription regulatory region sequence-specific dna-binding, gtp binding activity, enzyme binding activity, identical protein binding activity, signal receptor binding activity, GO:0016791, protein kinase binding activity, GO:0005125, GO:0008083]]
HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0[[GO:0006457, GO:0003723, transcription activator, GO:0003677, GO:0051082, GO:0003720, GO:0003676, GO:0044325, GO:0005524, GO:0006402, translation regulation, GO:0003755, GO:0035925]][[rna binding activity, dna binding activity, protein binding activity, GO:0140693, identical protein binding activity, dna-binding transcription factor binding activity, GO:0042803, atpase binding activity, GO:0016887, enzymatic activity, GO:0003713, GO:0008494, protein phosphatase binding activity, peptidyl-prolyl primase activity, transcription cis-regulatory region sequence-specific activity]]
HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1[[atp binding activity, GO:0016887, enzyme binding activity, identical protein binding activity, GO:0060090, GO:0140678, nucleic acid binding activity, GO:0046983, protein folding chaperone binding activity, ribosome binding activity, rna binding activity, snare binding activity, transcription corepressor binding activity, transcription regulator]][[enzyme binding activity, rna binding activity, protein binding activity, transmembrane transporter binding activity, dna binding activity, protein kinase binding activity, box h/aca snorna binding activity, protein phosphatase binding activity, telomerase rna binding activity, GO:0042803, GO:0046982, transcription factor binding activity, atp binding activity, GO:0016887, GO:0003724, GO:0003756, ubiquitin protein ligase binding activity, GO:0004518, adenyl ribonucleotide binding activity, heat shock protein binding activity]]
HALLMARK_UV_RESPONSE_DN-0[[genes included in this set are involved in various cellular functions such as enzyme binding activity, GO:0003924, lipoprotein binding activity, GO:0004620, and other related activities. common enriched terms across these genes include protein binding activity, smad binding activity, dna-binding activity, phosphotyrosine residue binding activity, GO:0003824, GO:0003924, and enzymatic inhibitor activity. mechanism: these genes are likely to be involved in regulation and control of cellular functions and processes through various proteins. this regulation and control is likely being done through interaction of the proteins encoded by these genes with other proteins and structurally with dna, as well as through the enzymatic activities of the encoded proteins]][[gtp binding activity, enzyme binding activity, dna-binding transcription factor binding activity, phosphotyrosine residue binding activity, cyclin binding activity, receptor-ligand interaction, protein-protein interaction, smad binding protein, nf-kappab binding protein, growth factor binding protein]]
HALLMARK_UV_RESPONSE_DN-1[[dna binding activity, GO:0000988, protein binding activity, smad binding activity, GO:0005096, MESH:C062738]][[GO:0001216, rna polymerase ii-specific activity, nf-kappab binding activity, microtubule binding activity, actin binding activity, identical protein binding activity, smad binding activity, GO:0005243, GO:0005388, receptor binding activity, GO:0005096, histone binding activity, ap-1 transcription factor binding activity, vitamin d receptor binding activity, cytoplasmic protein binding activity, GO:0004930, platelet-derived growth factor binding activity, enzyme binding activity, protease binding activity, phospholipid binding activity, GO:0004672, GO:0004674, intracellular protein binding activity]]
HALLMARK_UV_RESPONSE_UP-0[[GO:0005515, GO:0003677, binding activity, receptor binding activity, GO:0004672, GO:0007155, GO:0023052, GO:0010468]][[protein binding activity, atp binding activity, rna binding activity, dna binding activity, receptor binding activity, enzyme binding activity, GO:0005548, GO:0098609, GO:0007268, GO:0097190, GO:0005138, GO:0042110, overall cellular metabolism, MESH:D005786]]
HALLMARK_UV_RESPONSE_UP-1[[gtp binding activity, dna binding activity, GO:0016563, protein kinase binding activity, GO:0004175]][[enzyme binding activity, GO:0016787, GO:0016740, GO:0038023, dna binding activity, rna binding activity, GO:0000988, protein binding activity]]
HALLMARK_WNT_BETA_CATENIN_SIGNALING-0[[the genes summarized above are all involved in developmental processes, such as organizing and regulating cell adhesion, components of the wnt pathway and regulation of gene expression. the enriched terms for these genes would be development-related terms, such as cell adhesion, GO:0060070, GO:0006468, GO:0016567, GO:0006351, GO:0006476, GO:0006351, and protein stability.\\n\\nmechanism: the underlying biological mechanism involves the involvement of many of these genes in the wnt pathway, which is a conserved signaling pathway involved in cell-cell communication and a variety of developmental processes. another mechanism involves the regulation of gene expression and the binding of dna-binding transcription factors, as well as protein ubiquitination and deacetylation which also control gene expression]][[protein binding activity, GO:0003700, rna polymerase ii-specific dna-binding transcription factor binding activity, notch binding activity, pdz domain binding activity, GO:0042813, ubiquitin protein ligase binding activity, beta-catenin binding activity, GO:0003713, histone deacetylase binding activity, GO:0048019, transcription corepressor binding activity, GO:0060090, GO:0004407, cholesterol binding activity]]
HALLMARK_WNT_BETA_CATENIN_SIGNALING-1[[GO:0005515, transcription regulation, GO:0051726, GO:0007165, response pathways]][[GO:0007165, GO:0010468, GO:0006351, GO:0001932, GO:0031647, GO:0016477, GO:0008283, GO:0032502, GO:0006508]]
T cell proliferation-0[[signaling receptor binding activity, protein kinase binding activity, GO:0061630, GO:0035556, GO:0001816, GO:0010467]][[protein binding activity, enzyme binding activity, protein kinase binding activity, interleukin binding activity, phosphorylation-dependent protein binding activity, GO:0001216, GO:0042803, nucleic acid binding activity, GO:0005001, GO:0048018, GO:0004725, GO:0005125, cytoskeletal protein binding activity, cytokin receptor activity, GO:0030335]]
T cell proliferation-1[[GO:0048018, phosphotyrosine residue binding activity, cytoskeletal protein binding activity, GO:0005574]][[cation binding activity, diacylglycerol binding activity, enzyme binding activity, GO:0046982, receptor binding activity, protein kinase binding activity, phosphorylation-dependent protein binding activity, phosphotyrosine residue binding activity, GO:0005001, protease binding activity, cytoskeletal protein binding activity, phosphatidylinositol 3-kinase binding activity, GO:0061630, GO:0004888, GO:0043621, GO:0004697, zinc ion binding activity, transmembrane atp-gated monoatomic cation channel activity, purin]]
Yamanaka-TFs-0[[transcription repressor and activator activities, rna polymerase ii-specific, nucleic acid binding activity, GO:0009889, GO:0009966, GO:0010468, GO:0045765, and protein-dna complex organization, GO:0042127]][[dna-binding, GO:0000988, rna polymerase ii-specific, nucleic acid binding activity, transcription cis-regulatory region binding activity, GO:0010468, GO:0009889]]
Yamanaka-TFs-1[[dna-binding, GO:0016563, GO:0016564, GO:0000988, rna binding activity, ubiquitin protein ligase binding activity, GO:0010628, GO:0010629, GO:0009889, GO:0045765, GO:0060828, GO:0009966, transcription cis-regulatory region binding activity, GO:0045944, GO:0003130, GO:0001714]][[GO:0006351, GO:0010468, dna-binding, GO:0000785, GO:0005829, GO:0005654, GO:0005667, GO:0009966, GO:0045944, GO:0001714]]
amigo-example-0[[GO:0005515, GO:0060230, GO:0005543, MESH:M0518050, GO:0050804]][[the list of genes provided is involved in multiple processes related to cell adhesion, growth factor binding, protein phosphorylation, tissue development, and regulation of cholesterol homeostatis and transcytosis. the underlying biological mechanism likely involves multiple pathways, including cellular response to lipopolysaccharide, cell-matrix adhesion, and negative regulation of low-density lipoprotein. enriched terms include cell adhesion, cell surface receptor signaling, collagen binding activity, GO:0019838, GO:0042157, GO:1902533, GO:0046983, GO:0006468, regulation of bmp signaling, GO:0042127, GO:0010468, GO:0009966, regulation of very-low-density lipoproten particle clearance, GO:0045056]]
amigo-example-1[[GO:0005515, GO:0043167, GO:0008009, GO:0019838, signal receptor binding, GO:0019902, GO:0016477, GO:0086009, GO:0007165, GO:0065007, GO:0006952]][[GO:0051246, GO:0001952, GO:0042127, GO:0042981, GO:0043269, GO:0030193, GO:0007166, GO:0050804, GO:0005201, GO:0007160, organ development and differentiation, regulation of hormone pathways]]
bicluster_RNAseqDB_0-0[[GO:0005509, double-stranded dna-binding, cell adhesion and migration, transcriptional regulation]][[genes in this list are involved in a range of activities, including calcium ion binding activity, metal ion binding activity, protein domain specific binding activity, identical protein binding activity, dna-binding transcription factor activity, and several others. the underlying biological mechanism appears to be related to structural support and regulation of cellular processes. enriched terms include: metal ion binding, GO:0005509, GO:0005515, GO:0000988, dna-binding, GO:0042802, domain specific protein binding]]
bicluster_RNAseqDB_0-1[[metal ion binding activity, protein binding activity, rna binding activity, GO:0019208, GO:0005243, GO:0042803, calcium ion binding activity, MESH:C086554]][[GO:0001216, protein kinase binding activity, metal ion binding activity, calcium ion binding activity, transcription co-regulator activity, responsive to stimuli]]
bicluster_RNAseqDB_1002-0[[UBERON:0001134, GO:0006936, GO:0016567, GO:0045010, calcium-dependent signaling, GO:0010468, GO:0006468, GO:0043687, GO:0042692, GO:0060537, MONDO:0020121, muscle organelle organization]][[GO:0051015, GO:0000146, GO:0051371, GO:0003785, GO:0005523, GO:0017022, GO:0031432, GO:0004111]]
bicluster_RNAseqDB_1002-1[[actin binding activity, GO:0007015, muscle alpha-actinin binding activity, GO:0006936, GO:0060415, GO:0071689, GO:0004672, protein phosphatase binding activity, GO:0043502, tropomyosin binding activity, troponin binding activity, troponin complex activities]][[calcium-dependent protein binding activity, atp binding activity, actin filament binding activity, actin monomer binding activity, transmembrane transporter binding activity, GO:0016567, GO:0061630, tropomyosin binding activity, identical protein binding activity, GO:0008375, protein phosphatase 1 binding activity, zinc ion binding activity, troponin c binding activity, troponin i binding activity, actin binding activity, tropomyosin binding activity, GO:0001216, sequence-specific double-stranded dna binding activity]]
endocytosis-0[[protein signaling, GO:0006468, GO:0016567, GO:0015031, GO:0030030, GO:0006897, GO:0006898, GO:0035091, GO:0001766, GO:0097320]][[GO:0004674, lysophosphatidic acid binding activity, sulfatide binding activity, GO:0016790, cadherin binding activity, GO:0032456, sh3 domain binding activity, GO:0051260, macropinosome formation, GO:0031623, transferring transport, t cell receptor binding activity, GO:0005085, GO:0044351, GO:0001773, GO:0007520, GO:0018105, GO:0010468, vascular endothelial growth factor receptor signalling pathway, GO:0051128, GO:0007042, GO:0045807, GO:0051090]]
endocytosis-1[[GO:0006897, GO:0005515, GO:0006869, GO:0016567, GO:0042632, GO:0035727]][[GO:0006468, GO:0051260, cell signaling, GO:0005480, GO:0016567, endocytosis/exocytosis, GO:0005102, GO:0010468, vesicle buddying, GO:0007165, GO:0050727, GO:0035556, gtp-dependent pathways, receptor signaling, canonical inflammasome signaling]]
glycolysis-gocam-0[[GO:0019538, enzymatic activity, protein transcription, cell metabolism, carbohydrate phosphorylation and metabolism, protein homeostasis, cell signaling, GO:0008104, cell homeostasis, cellular energy production]][[protein binding activity, atp binding activity, peptidoglycan binding activity, GO:0051156, GO:0002639, GO:0010595, GO:0006002, GO:0061615, GO:0030388, GO:0046166, fructose binding activity, GO:0004332, MONDO:0009295, GO:0004807, disordered domain specific binding activity, GO:0004866, GO:0046835, GO:0072655, maintenance of protein location in]]
glycolysis-gocam-1[[GO:0003824, GO:0031625, protein homodimerization, GO:0016310, GO:0006096, GO:1904659, GO:0070061, GO:0004332, GO:0004618, GO:0004619, GO:0004396, peptidoglycan binding activity, GO:0003872, GO:0004807, GO:0004347, GO:0021762, binding activity of sperm to zona pellucida, GO:0030388, GO:0019725, GO:0046716, GO:0071456, GO:0016525, UBERON:2005050]][[protein binding activity, atp binding activity, ubiquitin protein ligase binding activity, fructose binding activity, GO:0042803, GO:0004618, GO:0004619, GO:0004807, GO:0004396, GO:0004332, GO:0004634, GO:0003872, GO:0004347, GO:0006096, GO:0006002, GO:0046166, GO:0046835, GO:0072655, GO:0072656, GO:0071456, negative regulation of]]
go-postsynapse-calcium-transmembrane-0[[GO:0097553, GO:1990034, GO:0071318, GO:0007186, GO:0035235, GO:1990454, GO:0017146, GO:0014066, GO:1900274, GO:0099509, GO:2000300, GO:0032680, GO:0005245, GO:2000311, GO:0080164]][[GO:0005262, GO:0005245, regulation of intracellular calcium concentrations, GO:0098960, GO:2000311, g protein-coupled receptor signaling, GO:0070588, GO:0015276]]
go-postsynapse-calcium-transmembrane-1[[GO:0006816, regulation of calcium]][[GO:0005261, acetylcholine-gated channel activity, GO:0022849, nmda selective glutamate receptor activity, GO:0005245, GO:1990454, GO:0035235, GO:0071318, regulation of]]
go-reg-autophagy-pkra-0[[these genes are involved in several cellular activities, primarily in their roles in signal transduction pathways, GO:0036211, protein folding and stability, GO:0051726, and apoptosis. the terms enriched are: signaling receptor activity; protein phosphorylation; regulation of macromolecule biosynthetic process; autophagy; g2/m transition of mitotic cell cycle; chromosome segregation; cytoplasmic stress granule; torc1 signaling; defense response; anoikis; protein folding chaperone; histone acetylation; i-kappab kinase/nf-kappab signaling; k63-linked polyubiquitin modification-dependent protein binding activity.\\n\\nmechanism: these genes participate in a variety of biological processes, including signal transduction pathways, GO:0036211, GO:0051726, apoptosis and dna-templated transcription, answering to different external and internal stimuli as well as aiding in cell survival and death. the enriched terms involve protein-protein interactions and modifications, as well as involvement in akt/pi3k, tor, and nf-kb pathways that are essential for cell signaling, typical in response to bacterial infection and the activation of pro-survival mechanisms]][[protein kinase binding activity, GO:0004672, GO:0004674, GO:0001934, GO:0010556]]
go-reg-autophagy-pkra-1[[protein binding activity, metal ion binding activity, protein kinase binding activity, GO:0030295, protein folding chaperone activity, GO:0042803, chromatin binding activity, GO:0003713, GO:0016410, GO:0016538, GO:0016303, card domain binding activity, heat shock protein binding activity, muramyl dipeptide binding activity, 14-3-3 protein binding activity, rna polymerase iii cis-regulatory region sequence-specific dna binding activity]][[the genes listed above are involved in a variety of processes, including negative and positive regulation of transport, GO:0051246, cell surface receptor signaling, and regulation of gene expression. these genes also have a variety of functions, including protein kinase binding activity, chromatin binding activity, GO:0030295, and metal ion binding activity. the enriched terms that describe these genes include: protein binding activity; protein kinase binding activity; signal transduction; positive and negative regulation of transport; chromatin binding activity; and protein serine/threonine kinase activity.\\n\\nmechanism: these gene products are part of, or act upstream of a variety of signaling pathways, all of which are involved in cell growth, MESH:D008283, and response to environmental stimuli. the pathways typically involve post-translational modifications of target proteins by phosphorylation, as well as formation or breakdown of protein-containing complexes. these signaling pathways ultimately affect gene expression and determine the type of output which a particular cell will produce]]
hydrolase activity, hydrolyzing O-glycosyl compounds-0[[the genes in this list share functions involving glycoprotein and carbohydrate metabolic processes and structural functions related to extracellular matrix organization. enriched terms include: dihydroceramidase activity, GO:0017040, GO:0061463, GO:0004134, GO:0004135, GO:0004556, hyaluronic acid binding activity, GO:0004415, GO:0004568, GO:0008843, clathrin heavy chain binding activity, GO:0008422, GO:0004348, GO:0004336, GO:0004553, GO:0008375, GO:0004563, identical protein binding activity, syndecan binding activity, heparan sulfate proteoglycan binding activity, GO:0003796, GO:0004567]][[the genes in the list are involved in many processes relating to glycan metabolism and synthesis, such as glycoside catabolic process, GO:0006027, GO:0019377, GO:0005980, and sucrose catabolic process. other enriched terms are dihydroceramidase activity, hyaluronic acid binding activity, GO:0004415, GO:0030212, GO:0046373, GO:0004571, GO:0006487, and protein homodimerization activity.\\n\\nmechanism: glycan metabolism and synthesis involves several enzymes with diverse activities such as alpha-glucosidases, MESH:D043323, MESH:D001617, MESH:D001619, n-acetylglucosaminyltransferases. these enzymes hydrolyze transfer carbohydrate building blocks to form modify carbohydrates for a variety of cellular functions]]
hydrolase activity, hydrolyzing O-glycosyl compounds-1[[GO:0006516, GO:0006027, heparan sulfate catabolism, glucoside catabolism, GO:0036508, GO:0006517, GO:0005975, GO:0006869, GO:0030214, receptor signaling, GO:0031589, GO:0009313, GO:0004672, GO:0008283, GO:0019915, GO:0050885, GO:0042742, GO:0005989, GO:0008344, GO:0007605, GO:0006487, GO:0006281, GO:0071451, peptidyl-serine]][[GO:0005975, GO:0046477, GO:0006516, oligo-saccharide catabolic process, GO:0006869, GO:0015144, GO:0046982, protein domain specific binding activity, GO:0006629, GO:0016139, GO:0030214, GO:0006032]]
ig-receptor-binding-2022-0[[immunoglobulin receptor binding activity, antigen binding activity, fc-gamma receptor i complex binding activity, GO:0004715, phosphotyrosine residue binding activity, peptidoglycan binding activity, phosphatidylcholine binding activity. mechanism: the genes listed appear to be involved in the regulation of the immune response. they likely aid in the recognition of pathogens, binding to the appropriate receptors, triggering a signal for an immune response. they may also play a role in enabling the recognition of self-antigens inhibiting a response to them]][[immunoglobulin receptor binding activity, antigen binding activity, GO:0004715, phosphatidylcholine binding activity, phosphotyrosine residue binding activity]]
ig-receptor-binding-2022-1[[antigen binding activity, immunoglobulin receptor binding activity, GO:0098542, GO:0002253, fc-gamma receptor i complex binding activity, GO:0004715, peptidoglycan binding activity, phosphatidylcholine binding activity, GO:0007229, GO:0038187, mannose binding activity, phosphotyrosine residue binding activity, GO:0051130, GO:0045657, protection of host from foreign agent]][[GO:0042803, GO:0007160, phosphorylation-dependent signaling, GO:0019901, GO:0034988, GO:0030098, GO:0098609, GO:0001784, GO:0042834, integrin signaling, GO:0006909]]
meiosis I-0[[these genes are involved in processes related to dna binding, repair, replication, recombination, and regulation thereof. the enriched terms would be: dna binding, GO:0003690, dna damage repair, GO:0006310, GO:0005515, meiotic recombination, GO:0007059, GO:0000278, GO:0071173, GO:0051289, GO:0003682, resolution of meiotic recombination intermediates. \\nmechanism: the underlying biological mechanism is that these proteins work together to maintain genomic stability, regulate gene expression, promote proper cell division, germline cell development, meiosis]][[GO:0003677, atp dependent activity, GO:0003682, GO:0005634, protein export, transcriptional regulation, GO:0003690, GO:0003697, GO:0006281, GO:0004518, MESH:D011995, GO:0007059, GO:0000278, intrinsic apoptotic signaling, regulation of telomere maintenance.\\nmechanism: the genes identified are likely playing roles in a variety of dna metabolic pathways, including dna repair, double-stranded dna break repair, homologous recombination, transcriptional regulation, and mitotic cell cycle processes. these pathways likely enable cellular replication and maintenance of genomic integrity, as well as control of gene expression and apoptosis]]
meiosis I-1[[GO:0140013, dna binding activity, GO:0006259, GO:0035825, telomere attachment, GO:0000785, GO:0000795, GO:0005694, GO:0005737]][[GO:0003677, GO:0003690, GO:0042802, GO:0006259, GO:0006302, GO:0007131, meiotic chromosome segregation and pairing, GO:0007283, GO:0000712, GO:0051026, GO:0016925, GO:0007130]]
molecular sequestering-0[[calcium ion binding activity, identical protein binding activity, GO:0004252, GO:0140314, calcium-dependent protein binding activity, arginine binding activity, GO:0140313, enzyme binding activity, GO:0019887, nf-κb binding activity, nuclear localization sequence binding activity, oxysterol binding activity, rage receptor binding activity, ubiquitin protein ligase binding activity, actin binding activity, rig-i binding activity, GO:0003713, zinc ion binding activity, GO:1903231]][[calcium ion binding activity, identical protein binding activity, GO:0140311, ubiquitin protein ligase binding activity, cellular response, GO:0001932, GO:0010359, GO:0097214, GO:0010468, GO:0035456]]
molecular sequestering-1[[protein binding activity, GO:0140313, GO:0000988, GO:0019887, calcium ion binding activity, dna-binding activity, ubiquitin protein ligase binding activity, tumor necrosis factor binding activity, regulatory pathway activity]][[GO:0005515, GO:0046872, GO:0043167, GO:0010468, GO:0001932, cell death pathways, GO:0009059, GO:0046907, cellular response to infection and inflammation]]
mtorc1-0[[enzyme binding activity, acid binding activity, molecule transport, adapter binding activity, receptor binding activity, dna binding activity, protein binding activity, GO:0003824, GO:0016787, GO:0016491, anion binding activity, GO:0008233, GO:0140657, thioredoxin activity, translocation, GO:0061630, cysteine endopeptidase activity, GO:0004738, GO:0004618, magnesium ion binding activity, GO:0004340, GO:0003924]][[protein binding activity, dna binding activity, enzyme binding activity, GO:0060090, GO:0140677, GO:0042803, domain binding activity, GO:0016491, protein kinase binding activity, phosphatidylinositol binding activity, GO:0016504, GO:0003714, nuclear androgen receptor binding activity, nf-kappab binding activity, ubiquitin protein ligase binding activity, phosphotyrosine residue binding activity, GO:0016564, GO:0003743, peptidyl-proinalyl cistrans isomerase activity]]
mtorc1-1[[cytoskeleton protein binding, phosphatase binding activity, GO:0016491, cell development and signaling activity, dna binding activity, cellular transporter activity, protein kinase binding activity]][[protein binding activity, GO:0005215, dna binding activity, rna binding activity, atp binding activity, peptide activity, GO:0003824, enzyme binding activity, phosphoprotein binding activity, GO:0016563, GO:0016787, GO:0016491, GO:0004017, identical protein binding activity, GO:0060090, GO:0007165, signal receiving activity, GO:1901987, metabolism regulation, cell growth control]]
peroxisome-0[[peroxisome biogenesis, protein import into peroxisome, GO:0000425, GO:0000268, GO:0140036, GO:0006631, protein homodimerization, enzyme binding activity, GO:0050821, GO:0043335]][[peroxisome biogenesis, atp binding activity, GO:0016887, ubiquitin-dependent protein binding activity, GO:0016558, GO:0050821, GO:0043335, GO:0000425, GO:0006625, protein tetramerization.\\n\\nmechanism: these gene functions are involved in a complex process involving the biogenesis and maintenance of peroxisomes, which are subcellular organelles that contain a variety of enzymes involved in metabolic processes. this process entails the function of multiple proteins working together to ferry important proteins into the peroxisomal membrane, where these proteins will become functional components of the organelle]]
peroxisome-1[[GO:0016558, GO:0050821, GO:0042127, protein-lipid binding, GO:0007031, GO:0008611, GO:0001881, GO:0006631]][[protein binding activity, GO:0016558, peroxisome matrix targeting signal-2 binding activity, GO:0042803, GO:0008611, GO:0006631, GO:0008285, GO:0000425, GO:0032994, microtubule-based peroxisome localization.\\nmechanism: based on the functions that these genes carry out, it is likely that the genes are involved in a mechanism whereby proteins are imported into the peroxisome matrix, and the peroxisome matrix is organized, stabilized, and/or maintained in order to carry out fatty acid metabolism and pexophagy. the receptor recycling and microtubule-based localization also likely play a role in this mechanism]]
progeria-0[[GO:0003677, GO:0005515, GO:0046872, cellular response to radiation, hypoxia, and starvation, GO:0042981, GO:0032204, GO:0010835, GO:0045069]][[protein binding activity, dna binding activity, metal ion binding activity, GO:0003678, GO:0042803, GO:0071480, GO:0010836, GO:0007084, GO:0045071, GO:0032392, GO:0006259, GO:0009267, GO:1902570, GO:0042981, GO:0071456, GO:0032204, GO:0004222, GO:0050688, with a positive effect]]
progeria-1[[dna damage and repair, GO:0005515, GO:0046872, homodimerization, GO:0006915, MESH:D016922, GO:0001666]][[GO:2000772, dna binding and metabolic processes, dna helicase and metal ion binding activities, protein localization to nucleolus and regulation of apoptotic processes appear to be enriched terms common to the three genes given.\\n\\nmechanism: the three genes appear to be involved in similar nucleic acid binding and regulation activities that enable the maintenance and regulation of cellular processes. this suggests an underlying molecular mechanism in which these genes interact directly to modulate a variety of cellular processes related to senescence, GO:0003677, GO:0008152, GO:0006915]]
regulation of presynaptic membrane potential-0[[GO:0005216, GO:0016917, GO:0008066, GO:0007186, GO:0007214, GO:0006836, GO:0005249, GO:0005248, GO:0007193]][[voltage-gated potassium/sodium channel activity, GO:0015276, transmembrane transporter binding activity, GO:0004930, GO:0004971, GO:0015277, GO:0035235, GO:1902476, GO:0007214, GO:0019228, GO:0042391, GO:0007268, regulation of]]
regulation of presynaptic membrane potential-1[[GO:0005216, membrane potential regulation, GO:0015276, g protein-coupled receptor signaling, GO:1902476, GO:0007214, GO:0071805]][[GO:0005216, GO:0015276, membrane potential regulation, GO:0005249, GO:0005248, GO:0008066, GO:0004890, GO:0055074, GO:0022851, ionotropic glutamate receptor signaling, GO:1902476, GO:0051932, GO:0048167, negative regulation of smooth muscle apoptotic process, GO:0051924, GO:0086009, GO:0035249, GO:0060292, GO:0006836, GO:0050804, GO:0034220, GO:0051205, GO:0060079]]
sensory ataxia-0[[dna-binding, rna polymerase ii-specific activity, GO:0046872, GO:0031625, GO:0045944, GO:0002639, GO:1901184, GO:0033157, monoatomic cation]][[transcription regulation, GO:0031625, GO:0003677, GO:0006027, GO:0043583, GO:0045475, GO:0007399, GO:0006457, GO:0043066, GO:0010595, GO:0002639, GO:0034214, GO:0050974, GO:0006812, GO:0015886, GO:0071260, GO:0042552, GO:0098742, GO:0006839, GO:0019226, GO:0008380, GO:0003774, GO:0061608, nuclear localization sequence binding activity, GO:0006607, GO:0003887, GO:0006284, gap-filling, protein ubiquitination.\\n\\nmechanism: analysis of the given list of genes suggests that there]]
sensory ataxia-1[[transcription regulation, nucleic acid metabol]][[MESH:D015533, dna-binding, rna polymrease ii-specific, dna binding activity, GO:0034214, GO:0061608, protein folding chaperone binding activity, GO:0016567, cell aggregration, GO:0098609, GO:0042552, GO:0005886, GO:0034220, GO:0030218, GO:0015886, mitochondrial transport.\\nmechanism: the eighteen human genes are involved in a variety of complex biological processes, from transcriptional regulation, through to cellular adhesion and the transport of macromolecules, including proteins, nucleic acids and heme. there is likely significant cross-talk between these various processes, particularly at the level of dna binding proteins, transcription activators, and nuclear receptor activities. this suggests that these genes are likely playing a role in the coordination of cellular processes to facilitate proper neural development and maintenance of peripheral nerve function]]
term-GO:0007212-0[[g protein-coupled receptor binding activity, GO:0003924, enzyme binding activity, GO:0042803, signaling receptor binding activity, GO:0004016, g-protein beta/gamma-subunit complex binding activity, signaling receptor binding activity, clathrin light chain binding activity, sequence-specific double-stranded dna binding activity, GO:0004672, nf-kappab binding activity, protein kinase a catalytic subunit binding activity, GO:0004674]][[GO:0007186, GO:0051480, GO:0006357, GO:1901214, GO:0006915, GO:0006171, GO:0006468]]
term-GO:0007212-1[[GO:0004672, g-protein activity, g-protein beta/gamma- subunit complex binding activity, atpase binding activity, GO:0004016, protein-folding chaperone binding activity, signal receptor binding activity, GO:0071333, GO:0007165, negative regulation of nf-kappa b transcription factor activity, GO:2000394, GO:0007212, cellular response to prostaglandin e, GO:0007204]][[GO:0007186, GO:0043087, GO:0060170, GO:0006171, GO:0005783, membrane localization, transcriptional regulation, GO:0007212, GO:0006874, GO:0046039, GO:0098843, protein kinase activity. \\n\\nmechanism:\\nthe g protein-coupled receptor signaling pathway is a general pathway that mediates the effects of hormones, neurotransmitters other extracellular signals in cells across a variety of tissues organs. signaling through gpcrs involves activation of g proteins, which in turn activate or inhibit effector enzymes ion channels. the commonality among these genes is that they are involved in mechanisms of gpcr signaling downstream processes such as regulation of gtpase activity, camp synthesis regulation of calcium ion concentration. the genes may also participate in membrane localization, transcriptional regulation postsynaptic endocytic zone functions. other associated activities]]
tf-downreg-colorectal-0[[GO:0003677, GO:0003723, GO:0003682, GO:0008134, GO:0003713, GO:0016564, MESH:M0518050, GO:0019899]][[transcription activation/repression, GO:0007165, GO:0006351, GO:0007049, MESH:D012319, GO:0003682, GO:0008270, GO:0016575, protein ligase/cofactor binding]]
tf-downreg-colorectal-1[[GO:0006351, dna-binding, rna polymerase ii-specific, transcription activator/transcription repressor, cis-regulatory region sequence-specific, GO:0001221, GO:0006355, GO:0006337, GO:0009966]][[dna-binding transcription, GO:0016563, rna polymerase ii-specific, GO:0016564, positive/negative regulation of transcription, GO:0006351, GO:0010468, nucleic acid binding activity, sequence-specific double-stranded dna binding activity, protein kinase binding activity]]
\n", - "
" - ], - "text/plain": [ - "prompt_variant v1 \\\n", - "model method geneset \n", - "gpt-3.5-turbo narrative_synopsis EDS-0 [[GO:0032964, GO:0030198, GO:0010712, GO:0043687, GO:0006493, GO:0006508, GO:0008270]] \n", - " EDS-1 [[GO:0032964, GO:0061448, GO:0030198, GO:0030166]] \n", - " FA-0 [[GO:0006281, GO:0035825, GO:0006302, chromosome stability \\n\\nhypotheses: the enriched terms suggest that the common function of these genes is dna repair, specifically in the context of homologous recombination and double-strand break repair. the genes are part of a complex network involved in maintaining chromosome stability, which is critical for preventing mutations and malignant transformation. mutations in these genes have been linked to various forms of cancer and the fanconi anemia disorder. understanding the mechanisms by which these genes function in dna repair could provide insights into cancer development and potential therapeutic targets]] \n", - " FA-1 [[GO:0006281, fanconi anemia pathway, GO:0035825, MESH:M0443452, genome maintenance, GO:0006302]] \n", - " HALLMARK_ADIPOGENESIS-0 [[GO:0005739, GO:0006119, GO:0022900, GO:0006091, MESH:M0496924, GO:0006631, GO:0006099, GO:0006635]] \n", - " HALLMARK_ADIPOGENESIS-1 [[mitochondrial function, GO:0070469, energy production, GO:0006629, GO:0006869, GO:0005515, GO:0016049, GO:0051301, antioxidant enzyme. \\n\\nmechanism/]] \n", - " HALLMARK_ALLOGRAFT_REJECTION-0 [[chemokine signaling pathway, cytokine-cytokine receptor interaction, GO:0006955, GO:0042110, GO:0050776, GO:0006954, GO:0050900]] \n", - " HALLMARK_ALLOGRAFT_REJECTION-1 [[MESH:D018925, MESH:D016207, t cell-mediated immunity, interferon signaling, GO:0006954, tgf-beta signaling, toll-like receptor signaling, tnf signaling]] \n", - " HALLMARK_ANDROGEN_RESPONSE-0 [[protein kinase activity; membrane transport; enzyme catalysis\\n\\nmechanism: these genes are involved in signal transduction and cellular metabolism, with a focus on protein kinase activity, GO:0055085, and enzyme catalysis. they play roles in the transport of various molecules across biological membranes, including fatty acids, sugars, and ions. they are also important in regulating cellular responses to extracellular stimuli, such as growth factors, MESH:D006728, and cytokines. additionally, they catalyze metabolic reactions and contribute to various metabolic pathways]] \n", - " HALLMARK_ANDROGEN_RESPONSE-1 [[GO:0004672, GO:0008134, GO:0005515, GO:0007165, GO:0003824]] \n", - " HALLMARK_ANGIOGENESIS-0 [[GO:0031012, GO:0007155, tissue development and regeneration, growth factor signaling, endothelial-specific signaling, cytokine signaling]] \n", - " HALLMARK_ANGIOGENESIS-1 [[ecm organization, GO:0031589, GO:0016477]] \n", - " HALLMARK_APICAL_JUNCTION-0 [[GO:0005884, GO:0007155, GO:0007010, GO:0008360, GO:0007165]] \n", - " HALLMARK_APICAL_JUNCTION-1 [[GO:0070160, GO:0031012, GO:0005604, GO:0007155, adhesion junction, GO:0007160]] \n", - " HALLMARK_APICAL_SURFACE-0 [[GO:0007155, GO:0007165, GO:0061024, GO:0015031]] \n", - " HALLMARK_APICAL_SURFACE-1 [[GO:0007155, GO:0007165, GO:0007154]] \n", - " HALLMARK_APOPTOSIS-0 [[GO:0006915, GO:0008219, GO:0043067, GO:0097153, binding of proteins involved in cell death.\\n\\nmechanism: the majority of the genes on the list are involved in apoptotic processes or regulate cell death. many of these genes belong to the bcl-2 protein family, which regulate apoptosis by either inhibiting or promoting cell death. other gene products, such as the caspases, also play a crucial role in the apoptotic process by cleaving proteins involved in cell death, ultimately leading to cell death. the enrichment of this theme in the gene list suggests that the regulation of apoptosis and programmed cell death is a significant biological mechanism that the genes in the list are involved in]] \n", - " HALLMARK_APOPTOSIS-1 [[apoptosis regulation, cytokine signaling, growth factor regulation]] \n", - " HALLMARK_BILE_ACID_METABOLISM-0 [[GO:0140359, long-chain fatty-acid metabolism, GO:0008203, GO:0006629, GO:0006637]] \n", - " HALLMARK_BILE_ACID_METABOLISM-1 [[peroxisome biogenesis, GO:0006631, GO:0006699, GO:0008203, GO:0140359, GO:0016491, atp-binding cassette, GO:0005490]] \n", - " HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 [[GO:0006695, GO:0006633, GO:0006629, regulation of cholesterol levels, transport across cell membranes]] \n", - " HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 [[GO:0006695, GO:0006629, GO:0007165]] \n", - " HALLMARK_COAGULATION-0 [[GO:0006956, GO:0007596, GO:0006508, GO:0030198]] \n", - " HALLMARK_COAGULATION-1 [[blood coagulation cascade; complement activation, classical pathway; extracellular matrix disassembly; calcium ion binding. \\n\\nmechanism: these genes are involved in the regulation and activation of different pathways implicated in blood coagulation, GO:0006956, and extracellular matrix remodelling. blood coagulation involves the conversion of prothrombin to thrombin by coagulation factors, which leads to the formation of a fibrin clot. complement activation is a cascade resulting in the removal of damaged cells and pathogens. extracellular matrix disassembly and remodelling are implicated in cellular processes such as tissue repair, GO:0001525, metastasis. calcium-binding proteins play a vital role in signalling pathways regulation of enzymatic activities]] \n", - " HALLMARK_COMPLEMENT-0 [[GO:0006956, GO:0006955, GO:0030162, GO:0030168]] \n", - " HALLMARK_COMPLEMENT-1 [[GO:0006956, GO:0007596, cytokine signaling, GO:0006468, GO:0006955, GO:0006954]] \n", - " HALLMARK_DNA_REPAIR-0 [[GO:0006281, transcription initiation, GO:0006396, GO:0009117]] \n", - " HALLMARK_DNA_REPAIR-1 [[GO:0006270, GO:0006261, GO:0006297, transcription, dna-template-dependent, GO:0045893, GO:0000122, GO:0006281, GO:0000723, GO:0065004]] \n", - " HALLMARK_E2F_TARGETS-0 [[GO:0006260, GO:0006281, GO:0051726]] \n", - " HALLMARK_E2F_TARGETS-1 [[GO:0006260, GO:0006281, dna polymerase, GO:0009117, GO:0006298, chromatin structure\\n\\nmechanism: the genes on this list primarily function in dna replication and repair. many of them are involved in dna polymerase activity, nucleotide metabolism, mismatch repair, and chromatin structure. it is likely that these genes work together in a coordinated manner to ensure accurate dna replication and repair, and that defects in these processes can lead to genetic instability and cancer development]] \n", - " HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 [[GO:0030198, GO:0030199, GO:0048251, GO:0071711, regulation of protein localization to extracellular matrix, GO:0043236, GO:0001968, GO:0005518]] \n", - " HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 [[GO:0030198, GO:0005518, GO:0051015, GO:0005125, GO:0007155, GO:0016477]] \n", - " HALLMARK_ESTROGEN_RESPONSE_EARLY-0 [[membrane-bound proteins, MESH:D004798, GO:0000981]] \n", - " HALLMARK_ESTROGEN_RESPONSE_EARLY-1 [[GO:0055085, cell signaling, GO:0004672, GO:1904659, GO:0006811]] \n", - " HALLMARK_ESTROGEN_RESPONSE_LATE-0 [[membrane-associated protein complex, GO:0019899, GO:0034220, transcriptional regulation]] \n", - " HALLMARK_ESTROGEN_RESPONSE_LATE-1 [[GO:0005515, GO:0003824, GO:0008134, GO:0006355, GO:0007165, cytokine signaling pathway, regulation of cell growth and differentiation]] \n", - " HALLMARK_FATTY_ACID_METABOLISM-0 [[GO:0006629, mitochondrial function, GO:0003824, GO:0006631, oxidation-reduction process, metabolism of carboxylic acid, GO:0006118, GO:0006082]] \n", - " HALLMARK_FATTY_ACID_METABOLISM-1 [[GO:0006629, oxidation-reduction process, energy production, metabolism of fatty acids, mitochondrial function, GO:0045333]] \n", - " HALLMARK_G2M_CHECKPOINT-0 [[GO:0051301, GO:0006260, GO:0007059, GO:0000910]] \n", - " HALLMARK_G2M_CHECKPOINT-1 [[GO:0006270, GO:0007059, GO:0000075, GO:0007052, GO:0007346, GO:0065004]] \n", - " HALLMARK_GLYCOLYSIS-0 [[GO:0070085, GO:0005975, fructose-bisphosphate metabolism, GO:0006098, GO:0006006, GO:0006012, GO:0006090, GO:0006089, GO:0019319, GO:0006011, GO:0052573, GO:0004332]] \n", - " HALLMARK_GLYCOLYSIS-1 [[GO:0006096, GO:0005975, GO:0007165, GO:1904659, GO:0033554]] \n", - " HALLMARK_HEDGEHOG_SIGNALING-0 [[GO:0007411, GO:0007155, transcriptional regulation, cell communication. \\n\\nhypotheses: \\nthese genes may be involved in regulating the formation of neural circuits and maintaining neural plasticity through dynamic regulation of gene expression and protein signaling. the enriched terms suggest that the neural development process involves complex regulation of cell-cell communication and adhesion, as well as transcriptional control of gene expression. axon guidance is critical for the proper formation of neural circuits, and dysregulation of this process may lead to neural disorders]] \n", - " HALLMARK_HEDGEHOG_SIGNALING-1 [[GO:0007411, GO:0007155, transcription regulation, neuro-endocrine signaling, protein cleavage, cell migration.\\n\\nmechanism: these genes are involved in various aspects of neuronal development and signaling, including axon guidance, neuron migration, cell adhesion and communication, transcription regulation, and protein cleavage. these processes are critical for proper central nervous system development and function]] \n", - " HALLMARK_HEME_METABOLISM-0 [[GO:0006811, GO:0010468, protein turnover, GO:0061024]] \n", - " HALLMARK_HEME_METABOLISM-1 [[GO:0005515, GO:0003824, GO:0008152, GO:0006082, GO:0006810, GO:0006811, GO:0006820, GO:0044281, GO:0019538, GO:0006357, GO:0003924, GO:0016740, GO:0000166, GO:0003677, GO:0000988, GO:0006163, GO:0008643, GO:0050801, GO:0003723, GO:0019899]] \n", - " HALLMARK_HYPOXIA-0 [[GO:0006096, GO:0006006, GO:0006000, GO:0005975, MESH:D004734, GO:0045333, GO:0019318, GO:0019682, triose-phosphate metabolic process, GO:0006090, GO:0006754]] \n", - " HALLMARK_HYPOXIA-1 [[GO:0006006, insulin signaling pathway, GO:0051726, transcriptional regulation]] \n", - " HALLMARK_IL2_STAT5_SIGNALING-0 [[cytokine, receptor, t-cell, GO:0006955, GO:0065007]] \n", - " HALLMARK_IL2_STAT5_SIGNALING-1 [[GO:0004896, GO:0002224, GO:0002685, GO:0002521, GO:0002682, GO:0046649, GO:0019221, GO:0007159, GO:0051249, positive regulation of leukocyte proliferation\\n\\nmechanism: these genes are involved in the immune system response and regulation, specifically in the activation, differentiation, and migration of leukocytes. they are also involved in cytokine-mediated signaling pathways and toll-like receptor signaling pathways. the enriched terms suggest that these genes are involved in the regulation of various aspects of immune system processes, including leukocyte proliferation and adhesion]] \n", - " HALLMARK_IL6_JAK_STAT3_SIGNALING-0 [[cytokine receptor activity; signal transduction; jak-stat cascade; cytokine-mediated signaling pathway\\n\\nmechanism: the enriched terms suggest that the commonality in gene function is the involvement of cytokine receptors and signaling pathways, particularly the jak-stat cascade, in cytokine-mediated signaling. this pathway is activated by cytokine binding to their respective receptors, leading to activation of the jak family of tyrosine kinases, which then phosphorylate and activate stat transcription factors to induce gene expression changes and cellular responses. the presence of these genes in the list suggests a potential role in regulating immune responses and inflammation through cytokine signaling]] \n", - " HALLMARK_IL6_JAK_STAT3_SIGNALING-1 [[GO:0005126, GO:0002376, GO:0001817, GO:0050776, cytokine-mediated signaling pathway\\n\\nmechanism]] \n", - " HALLMARK_INFLAMMATORY_RESPONSE-0 [[cytokine signaling, GO:0004950, GO:0004930, GO:0050900, GO:0004908, GO:0002224, GO:0005164]] \n", - " HALLMARK_INFLAMMATORY_RESPONSE-1 [[GO:0004896, GO:0004930, GO:0042379, GO:0006955, GO:0006954, GO:0019221, GO:0050900, GO:0002694, GO:0002682, GO:0001819, GO:0009617, GO:0032496, GO:0070555, GO:0034612, GO:0042110]] \n", - " HALLMARK_INTERFERON_ALPHA_RESPONSE-0 [[interferon-induced protein, GO:0051607, GO:0006955, nucleotide-binding domain, leucine-rich repeat-containing receptor signaling, GO:0005764, GO:0019882, cytokine]] \n", - " HALLMARK_INTERFERON_ALPHA_RESPONSE-1 [[GO:0140888, cytokine signaling pathway, GO:0045087, GO:0009615, GO:0006952]] \n", - " HALLMARK_INTERFERON_GAMMA_RESPONSE-0 [[interferon signaling, immune response regulation, cytokine signaling, tnf-receptor superfamily, protein tyrosine phosphatase, ubiquitin-proteasome system, MONDO:0007435]] \n", - " HALLMARK_INTERFERON_GAMMA_RESPONSE-1 [[GO:0006955, cytokine signaling, GO:0030163, GO:0000502, ubiquitin system, viral rna sensing, MESH:D018925, GO:0019882]] \n", - " HALLMARK_KRAS_SIGNALING_DN-0 [[GO:0005509, GO:0055085, GO:0007155, GO:0004672, GO:0007186]] \n", - " HALLMARK_KRAS_SIGNALING_DN-1 [[cytokine signaling, g-protein coupled receptor signaling, GO:0019722, protein metabolism and processing]] \n", - " HALLMARK_KRAS_SIGNALING_UP-0 [[receptor signaling pathway, GO:0006468, negative regulation of transcription, GO:0031396, GO:0071345, GO:0032880, GO:0070374]] \n", - " HALLMARK_KRAS_SIGNALING_UP-1 [[signal transduction; cytokine activity; coagulation; ion transport; extracellular matrix organization. \\n\\nmechanism: the enriched terms suggest that the commonality in the function of these genes is related to signal transduction and regulation of various biological processes, such as coagulation, GO:0005125, GO:0030198, and ion transport. specifically, these genes are involved in regulating signaling pathways that are critical for these biological processes. there are several pathways known to contribute to these enriched terms, including the jak/stat, MESH:D016328, mapk/erk, and pi3k pathways. these pathways play important roles in cell signaling, GO:0006954, GO:0006955, other cellular processes]] \n", - " HALLMARK_MITOTIC_SPINDLE-0 [[GO:0008017, GO:0007010, regulation of protein activity, GO:0051301, GO:0019894, GO:0003779]] \n", - " HALLMARK_MITOTIC_SPINDLE-1 [[microtubule organization, GO:0140014, GO:0051301]] \n", - " HALLMARK_MTORC1_SIGNALING-0 [[GO:0046034, GO:0006629, GO:0006006, GO:0006457, GO:0046907]] \n", - " HALLMARK_MTORC1_SIGNALING-1 [[GO:0051087, GO:0005515, GO:0006457, GO:0043161]] \n", - " HALLMARK_MYC_TARGETS_V1-0 [[GO:0006413, GO:0042254, GO:0006260, GO:0006281, GO:0008380, GO:0009117]] \n", - " HALLMARK_MYC_TARGETS_V1-1 [[GO:0006413, GO:0006412, GO:0042254]] \n", - " HALLMARK_MYC_TARGETS_V2-0 [[GO:0006396, GO:0042254, rrna maturation]] \n", - " HALLMARK_MYC_TARGETS_V2-1 [[GO:0006364, nucleolar rna processing, GO:0042273, GO:0003723]] \n", - " HALLMARK_MYOGENESIS-0 [[GO:0003779, GO:0006936, sarcomere assembly, GO:0005509, GO:0005861, GO:0005523, MESH:D024510, GO:0005524, GO:0004672, GO:0005515, GO:0032982]] \n", - " HALLMARK_MYOGENESIS-1 [[GO:0006936, GO:0005861, GO:0005509, GO:0003779, sarcomere organization and biogenesis]] \n", - " HALLMARK_NOTCH_SIGNALING-0 [[GO:0007219, GO:0016567, GO:0001709, GO:0016055]] \n", - " HALLMARK_NOTCH_SIGNALING-1 [[GO:0007219, GO:0016567]] \n", - " HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 [[GO:0006754, GO:0022900, GO:0005746, GO:0006119]] \n", - " HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 [[GO:0005746, GO:0006119, mitochondrial metabolism, complex i-v, energy production]] \n", - " HALLMARK_P53_PATHWAY-0 [[GO:0006281, GO:0010468, GO:0008083]] \n", - " HALLMARK_P53_PATHWAY-1 [[GO:0006281, GO:0051726, GO:0007165, GO:0006915, MESH:D016207]] \n", - " HALLMARK_PANCREAS_BETA_CELLS-0 [[GO:0006006, insulin signaling, pancreatic development, neuroendocrine regulation]] \n", - " HALLMARK_PANCREAS_BETA_CELLS-1 [[GO:0006006, pancreatic islet development, neuroendocrine differentiation, GO:0007269, MESH:D009473]] \n", - " HALLMARK_PEROXISOME-0 [[atp binding cassette transporter activity, GO:0006631, GO:0042445, GO:0008289, GO:0043574, GO:0005502]] \n", - " HALLMARK_PEROXISOME-1 [[GO:0005777, GO:0006635, antioxidant response, mitochondrial carrier protein]] \n", - " HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 [[GO:0004672, GO:0035556, GO:1902531, GO:0050794, GO:0003824, cytoskeletal regulation]] \n", - " HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 [[GO:0004672, GO:0007165, GO:0006468, GO:0035556]] \n", - " HALLMARK_PROTEIN_SECRETION-0 [[GO:0005794, GO:0005480, GO:0005764]] \n", - " HALLMARK_PROTEIN_SECRETION-1 [[golgi transport, GO:0016192, GO:0015031, GO:0008104, GO:0032880, GO:0006886, GO:0016197]] \n", - " HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 [[GO:0016209, GO:0006749, GO:0016491]] \n", - " HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 [[GO:0016209, redox regulation, MESH:D018384]] \n", - " HALLMARK_SPERMATOGENESIS-0 [[GO:0051726, GO:0003677, GO:0003723, GO:0016301, transcription regulation, chromatin organization and modification]] \n", - " HALLMARK_SPERMATOGENESIS-1 [[GO:0005515, enzymatic activity, GO:0006811]] \n", - " HALLMARK_TGF_BETA_SIGNALING-0 [[growth factor signaling, transcriptional regulation, smad/tgf-beta signaling pathway, cellular differentiation]] \n", - " HALLMARK_TGF_BETA_SIGNALING-1 [[GO:0005024, GO:0060395, GO:0030509]] \n", - " HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 [[GO:0006955, cytokine signaling pathway, transcription regulation. \\n\\nmechanism: these genes are primarily involved in regulating the immune response through the cytokine signaling pathway. they also play a role in transcriptional regulation of genes involved in these pathways. overall, these genes are important in regulating the response to pathogens and maintaining immune homeostasis]] \n", - " HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 [[cytokine signaling pathway, GO:0002682, GO:0006351, GO:0006355, GO:0050900, GO:0006954, GO:0050727, GO:0032496, GO:0002237, GO:0009615, GO:0045893, GO:0045892]] \n", - " HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 [[GO:0044183, GO:0006457, GO:0006396, cellular stress response, GO:0006401]] \n", - " HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 [[GO:0006457, GO:0006396, GO:0006413, endoplasmic reticulum stress response, GO:0042254]] \n", - " HALLMARK_UV_RESPONSE_DN-0 [[GO:0006816, cytoskeletal organization, cell signaling, protein regulation]] \n", - " HALLMARK_UV_RESPONSE_DN-1 [[GO:0030198, GO:0007165, GO:0006811]] \n", - " HALLMARK_UV_RESPONSE_UP-0 [[GO:0006810, GO:0003824, regulation of transcription, GO:0016310, GO:0005515, GO:0006950, GO:0006915, GO:0006811, GO:0005524, GO:0007165, GO:0005975]] \n", - " HALLMARK_UV_RESPONSE_UP-1 [[GO:0008152, GO:0005515, GO:0007165, GO:0009165, GO:0006468, transcription factor activity\\n\\nmechanism: these enriched terms suggest that the commonality between these genes is their involvement in fundamental biological processes required for normal cell function. these include metabolism, signal transduction, and protein biosynthesis and regulation. the transcription factor activity term suggests that some of these genes may be transcriptional regulators, controlling the expression of other genes involved in these processes. overall, these genes likely work together to maintain cellular homeostasis and respond to internal and external cues]] \n", - " HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 [[wnt signaling pathway regulation, transcriptional regulation, GO:0051726]] \n", - " HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 [[GO:0016055, GO:0008013, transcription regulation]] \n", - " T cell proliferation-0 [[GO:0006955, GO:0007165, GO:0001816, cell proliferation and differentiation, GO:0042981]] \n", - " T cell proliferation-1 [[cytokine, GO:0006955, GO:0023052, receptor, t cell]] \n", - " Yamanaka-TFs-0 [[MESH:D047108, stem cell pluripotency, MESH:D063646, cell cycle progression]] \n", - " Yamanaka-TFs-1 [[MESH:D047108, stem cell maintenance, GO:0010468]] \n", - " amigo-example-0 [[GO:0030198, GO:0007155, GO:0007229, GO:0051495, GO:0002576]] \n", - " amigo-example-1 [[GO:0030198, GO:0007155, GO:0006029, GO:0042339, GO:0007229, GO:0030168]] \n", - " bicluster_RNAseqDB_0-0 [[GO:0055085, GO:0006811, GO:0005524, zinc finger domain binding, GO:0007186, GO:0000988]] \n", - " bicluster_RNAseqDB_0-1 [[GO:0019722, GO:0000988, GO:0055085]] \n", - " bicluster_RNAseqDB_1002-0 [[GO:0006936, GO:0007015, GO:0032972, GO:0005509, GO:0005861, GO:0005865, GO:0003779, GO:0045214, GO:0005523, GO:0017022, GO:0045932, skeletal muscle thin filament, cardiac muscle thin filament]] \n", - " bicluster_RNAseqDB_1002-1 [[GO:0006936, GO:0051015, GO:0005523, calcium binding, myofibril assembly.\\n\\nmechanism: these genes are involved in the regulation and maintenance of muscle structure and the contraction cycle. they act through the interaction of actin and myosin filaments, with the regulation of calcium ions controlling muscle contraction. the proteins encoded by these genes are involved in ion channel regulation, protein binding and modification, and energy metabolism]] \n", - " endocytosis-0 [[GO:0006897, intracellular trafficking, cytoskeleton reorganization]] \n", - " endocytosis-1 [[GO:0006897, GO:0016192, intracellular signaling, GO:0015031, cytoskeletal organization]] \n", - " glycolysis-gocam-0 [[glucose metabolism; glycolysis\\n\\nmechanism: these genes play a role in converting glucose to produce energy in the form of atp. hexokinase (hk1) and glucose phosphate isomerase (gpi) are involved in the initial steps of glucose metabolism, while phosphofructokinase (pfkm), MESH:D005634, and pyruvate kinase (pkm) are involved in glycolysis. triosephosphate isomerase (tpi1) and glyceraldehyde-3-phosphate dehydrogenase (gapdh) are also involved in glycolysis and produce atp by oxidizing glucose. phosphoglycerate mutase (pgam2) and enolase (eno3) are also involved in glycolysis and help convert glucose to pyruvate, which can then be converted to atp]] \n", - " glycolysis-gocam-1 [[GO:0006096, GO:0005975, energy pathway]] \n", - " go-postsynapse-calcium-transmembrane-0 [[GO:0006816, GO:0004970, n-methyl-d-aspartate receptor complex, GO:0043269, GO:0014069, GO:0007165]] \n", - " go-postsynapse-calcium-transmembrane-1 [[GO:0006816, GO:0005509, GO:0005216, GO:0005102, GO:0007268, GO:0030594]] \n", - " go-reg-autophagy-pkra-0 [[summary: regulation of cellular processes, including cell growth and metabolism, GO:0006915, GO:0006955, and regulation of chromatin remodeling and transcription.\\n\\nmechanism: these genes function in various pathways involved in the regulation of cellular processes. akt1 and pik3ca are involved in the pi3k/akt/mtor signaling pathway, which regulates cell growth, MESH:D013534, and metabolism. casp3 is a protease involved in the execution-phase of cell apoptosis. ccny and cdk5r1 are involved in the regulation of cell division cycles and the development of the central nervous system. hspb1 plays an important role in cell differentiation, but its overexpression may promote cancer cell proliferation and metastasis while protecting cancer cells from apoptosis. irgm regulates autophagy formation in response to intracellular pathogens. kat5 is a histone acetylase that has a role in dna repair and apoptosis and is thought to play an important role in signal transduction. mlst8, rptor, and smcr8 are involved in the torc1 signaling pathway, which regulates protein synthesis and cell growth in response to nutrient and insulin levels. nod2 is a pattern recognition receptor that detects cytosolic nucleic acids and trans]] \n", - " go-reg-autophagy-pkra-1 [[GO:0038202, GO:0032006, GO:0010605, activation of map3k7/tak1]] \n", - " hydrolase activity, hydrolyzing O-glycosyl compounds-0 [[GO:0005764, glycoside hydrolase activity, GO:0005975, GO:0016787, GO:0006027, GO:0005980, GO:0006689, GO:0015929, acid hydrolase activity, chitin catabolic process\\n\\nmechanism: these genes participate in the lysosomal degradation of various carbohydrate molecules, breaking them down into their component parts for further processing by the cell]] \n", - " hydrolase activity, hydrolyzing O-glycosyl compounds-1 [[GO:0004559, GO:0004415, lysosomal enzyme activity, GO:0016798, GO:0006487]] \n", - " ig-receptor-binding-2022-0 [[immunoglobulin receptor binding activity, GO:0002253, GO:0098542, GO:0002922, b cell-mediated immunity]] \n", - " ig-receptor-binding-2022-1 [[GO:0002250, GO:0002376, antigen binding activity, immunoglobulin receptor binding activity. \\n\\nmechanism: the enriched terms suggest that these genes are involved in the recognition and response to specific foreign antigens encountered by the immune system. antigen binding activity enables the binding of specific antigens, while immunoglobulin receptor binding activity allows for the activation and signaling of immune cells. together, these genes contribute to the adaptive immune response and immune system processes by recognizing and responding to diverse foreign antigens]] \n", - " meiosis I-0 [[meiotic recombination; homologous recombination; chromosome segregation during meiosis; double-strand break repair via homologous recombination.\\n\\nmechanism: these genes are all involved in the meiotic cell cycle process, specifically in events related to recombination, repair, and segregation of chromosomes during meiosis. the proteins encoded by these genes interact with each other to form protein complexes that are essential for proper meiotic division. the enriched terms indicate a strong association with meiotic recombination and double-strand break repair via homologous recombination. additionally, they suggest a role in chromosome segregation during meiosis]] \n", - " meiosis I-1 [[meiotic recombination, GO:0006281, GO:0035825, GO:0007059, GO:0006302, holliday junction, rad51, GO:0007127]] \n", - " molecular sequestering-0 [[GO:0005515, GO:0006955, intracellular transport\\n\\nmechanism/]] \n", - " molecular sequestering-1 [[GO:0006810, regulation of cell growth and survival, GO:0010468, GO:0006915]] \n", - " mtorc1-0 [[GO:0046034, GO:0006629, GO:0006006, GO:0006457, GO:0046907]] \n", - " mtorc1-1 [[GO:0000502, GO:0030163]] \n", - " peroxisome-0 [[peroxisome biogenesis, GO:0016558, peroxin]] \n", - " peroxisome-1 [[peroxisome biogenesis, matrix protein import, MONDO:0009279, peroxin (pex) family]] \n", - " progeria-0 [[GO:0006998, chromatin organization and maintenance, dna repair and recombination]] \n", - " progeria-1 [[GO:0006325, GO:0006281, nuclear stability]] \n", - " regulation of presynaptic membrane potential-0 [[GO:0007268, GO:0005216, neurological function]] \n", - " regulation of presynaptic membrane potential-1 [[GO:0005216, GO:0048666, GO:0007268]] \n", - " sensory ataxia-0 [[MONDO:0015626, MONDO:0005244, MONDO:0007790, GO:0043209, GO:0006264, tetratricopeptide repeat, transporter protein\\n\\nmechanism: these genes are involved in myelin upkeep and various neurological diseases associated with defects in myelin sheath synthesis and functions. they play roles in mitochondrial dna replication and transport, as well as protein transportation across the nuclear membrane. the presence of tetratricopeptide repeat motifs in these genes suggests their roles in protein-protein interactions and chaperone functions]] \n", - " sensory ataxia-1 [[MONDO:0011890, MONDO:0007790, MONDO:0011527, GO:0043217, peripheral myelin sheath, n-acetyl-d-glucosamine residue degradation, MESH:D008565, GO:0007399, nervous system myelination, GO:0006260]] \n", - " term-GO:0007212-0 [[GO:0007186, GO:0007189, regulation of cyclic nucleotide metabolic process, regulation of camp metabolic process]] \n", - " term-GO:0007212-1 [[GO:0007186, GO:0019932, GO:0007212]] \n", - " tf-downreg-colorectal-0 [[transcriptional regulation, GO:0006338, GO:0000988, GO:0003700, rna polymerase ii regulatory region sequence-specific dna binding, zinc finger domain, GO:0042393, nucleosome binding.\\n\\nmechanism: the enriched functions suggest that the given set of genes are involved in transcriptional regulation and chromatin remodeling. transcription factors bind to specific dna sequences and regulate gene expression, while chromatin remodeling alters the structure of chromatin to allow or prevent access to the dna by transcriptional machinery. zinc finger domain-containing proteins are involved in dna binding, and histone binding proteins facilitate the formation of transcriptionally active or inactive chromatin structures. the enriched functions suggest the potential involvement of these genes in both gene activation and repression, which may have important implications in cellular differentiation, development, and disease]] \n", - " tf-downreg-colorectal-1 [[transcription regulation, chromatin structure alteration, cell cycle progression, GO:0003682]] \n", - " no_synopsis EDS-0 [[GO:0030198, GO:0030199, GO:0006024]] \n", - " EDS-1 [[GO:0030199, GO:0030198, GO:0032964]] \n", - " FA-0 [[fanconi anemia pathway, homologous recombination repair pathway, dna double-strand break repair]] \n", - " FA-1 [[GO:0006281, GO:0006302, GO:0035825, mitotic cell-cycle checkpoint, GO:0006974]] \n", - " HALLMARK_ADIPOGENESIS-0 [[GO:0006631, GO:0006869, GO:0005746, GO:0006637, GO:0032000, GO:0016042, GO:0019216, GO:0033108, GO:0035336, GO:0033539, GO:0051791]] \n", - " HALLMARK_ADIPOGENESIS-1 [[GO:0006119, GO:0006631, GO:0006457, GO:0030301, GO:0019915, stress response, GO:0045333, mitochondrial metabolism, energy generation, GO:0006986, GO:0046890, GO:0032368, GO:0033344, GO:0007517, GO:0006979, GO:0001666, regulation of fatty acid catabolic process, GO:0019216]] \n", - " HALLMARK_ALLOGRAFT_REJECTION-0 [[GO:0042110, GO:0030098, GO:0019221, GO:0002682, GO:0050776]] \n", - " HALLMARK_ALLOGRAFT_REJECTION-1 [[GO:0005125, GO:0008009, GO:0034341, GO:0042110, GO:0050727]] \n", - " HALLMARK_ANDROGEN_RESPONSE-0 [[GO:0006351, regulation of transcription, GO:0006629, GO:0030163]] \n", - " HALLMARK_ANDROGEN_RESPONSE-1 [[GO:0006508, GO:0004672, GO:0007010, GO:0006695, GO:0045944, GO:0043066]] \n", - " HALLMARK_ANGIOGENESIS-0 [[GO:0030198, GO:0007267, GO:0043405, GO:0042127, GO:0030155, GO:0002576]] \n", - " HALLMARK_ANGIOGENESIS-1 [[GO:0030198, GO:0001525, vascular development, GO:0030335, GO:0001938, GO:0017015, GO:0007155]] \n", - " HALLMARK_APICAL_JUNCTION-0 [[GO:0098609, GO:0034332, GO:0002159, GO:0030198]] \n", - " HALLMARK_APICAL_JUNCTION-1 [[GO:0070160, GO:0007155, GO:0007154, GO:0022407, GO:0043542, GO:0030198, cell junction organization and biogenesis, GO:0032956, GO:0001525, GO:0010810]] \n", - " HALLMARK_APICAL_SURFACE-0 [[GO:0051716, GO:0005515, GO:0035556, GO:0007155, GO:0055085, GO:0061024, GO:0015031]] \n", - " HALLMARK_APICAL_SURFACE-1 [[GO:0007155, GO:0016477, GO:0007165, GO:0038023, GO:0006468, GO:0008104, GO:0055085, GO:0003824]] \n", - " HALLMARK_APOPTOSIS-0 [[GO:0006915, GO:0043123, GO:0050855, GO:0001817, GO:0002697, GO:0050670, GO:0051249, GO:0050856, GO:0034097, GO:0032496]] \n", - " HALLMARK_APOPTOSIS-1 [[cellular stress response, GO:0006915, GO:0006954, GO:0043067, negative regulation of nf-kappab transcription factor, GO:0043280]] \n", - " HALLMARK_BILE_ACID_METABOLISM-0 [[GO:0006695, GO:0006699, peroxisome biogenesis]] \n", - " HALLMARK_BILE_ACID_METABOLISM-1 [[GO:0006629, GO:0006869, GO:0005777, mitochondrial function]] \n", - " HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 [[GO:0016126, GO:0006695, GO:0030301, GO:0006629, GO:0008202, GO:0042632]] \n", - " HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 [[GO:0006695, GO:0006629, GO:0008203, GO:0016126, GO:0008299, GO:0042632, GO:0045540, GO:0019216]] \n", - " HALLMARK_COAGULATION-0 [[GO:0007596, GO:0006956, GO:0030168, GO:0042730, GO:0042060]] \n", - " HALLMARK_COAGULATION-1 [[GO:0030198, GO:0007596, GO:0006508, GO:0006955]] \n", - " HALLMARK_COMPLEMENT-0 [[c1q binding, GO:0006958, GO:0010951, GO:0043154, GO:2001237, GO:1903051]] \n", - " HALLMARK_COMPLEMENT-1 [[GO:0006955, GO:0007596, GO:0030163, GO:0006508, GO:0010951, GO:0071345, GO:0010952, GO:0030194, GO:0030449]] \n", - " HALLMARK_DNA_REPAIR-0 [[GO:0006260, GO:0006281, GO:0006397, GO:0006351, GO:0042278]] \n", - " HALLMARK_DNA_REPAIR-1 [[GO:0097747, GO:0003677, GO:0006397, GO:0006281]] \n", - " HALLMARK_E2F_TARGETS-0 [[GO:0006260, GO:0007049, GO:0051301, GO:0140014, GO:0006281]] \n", - " HALLMARK_E2F_TARGETS-1 [[GO:0006260, GO:0006281, GO:0071897, GO:0006302, GO:0022616, GO:0006974, GO:0000075, dna damage recognition and signaling]] \n", - " HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 [[GO:0030198, GO:0043062, GO:0042277, GO:0030199, GO:0007155, GO:0007229, GO:0043410, GO:0005125, GO:0043498, GO:0010646, GO:0071711, GO:0007166, GO:0008285, GO:0070374, GO:0043236, GO:0005509, GO:0030335]] \n", - " HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 [[GO:0030198, GO:0007155, GO:0005604, GO:0005581, GO:0007229, GO:0005925, GO:0005515, ecm-receptor interaction, GO:0030334, GO:0007010]] \n", - " HALLMARK_ESTROGEN_RESPONSE_EARLY-0 [[GO:0006811, GO:0006631, GO:0006006, GO:0032870, GO:0008203, drug binding]] \n", - " HALLMARK_ESTROGEN_RESPONSE_EARLY-1 [[GO:0006629, GO:0007165, transcriptional regulation]] \n", - " HALLMARK_ESTROGEN_RESPONSE_LATE-0 [[GO:0006351, GO:0008152, GO:0008283, GO:0006955, GO:0007165]] \n", - " HALLMARK_ESTROGEN_RESPONSE_LATE-1 [[GO:0008152, GO:0007165, GO:0032502, GO:0006955, GO:0006351, GO:0019538, GO:0006810, GO:0001558, GO:0042981, GO:0006811]] \n", - " HALLMARK_FATTY_ACID_METABOLISM-0 [[1. metabolic process \\n2. oxidation-reduction process \\n3. response to oxidative stress \\n4. lipid metabolic process \\n5. carbohydrate metabolic process \\n6. amino acid metabolic process \\n7. detoxification \\n8. fatty acid beta-oxidation \\n9. tca cycle \\n10. electron transport chain \\n11. glucose homeostasis \\n12. protein folding and stabilization \\n13. ion homeostasis]] \n", - " HALLMARK_FATTY_ACID_METABOLISM-1 [[GO:0006629, oxidative stress response, energy production]] \n", - " HALLMARK_G2M_CHECKPOINT-0 [[GO:0022402, GO:0140014, GO:0007059, GO:0007052, GO:0000226, GO:0006260]] \n", - " HALLMARK_G2M_CHECKPOINT-1 [[GO:0006260, GO:0007049, GO:0006281, GO:0140014, GO:0007059]] \n", - " HALLMARK_GLYCOLYSIS-0 [[1. glycosylation\\n2. glycolysis\\n3. pentose phosphate pathway]] \n", - " HALLMARK_GLYCOLYSIS-1 [[GO:0006006, energy generation, GO:0016052, GO:0006096, GO:0006090, GO:0006099, GO:0022900, GO:0006119, GO:0006754]] \n", - " HALLMARK_HEDGEHOG_SIGNALING-0 [[GO:0030182, GO:0007411, GO:0016477, GO:0007155, GO:0008283]] \n", - " HALLMARK_HEDGEHOG_SIGNALING-1 [[GO:0007399, GO:0007165, GO:0007155]] \n", - " HALLMARK_HEME_METABOLISM-0 [[GO:0006811, GO:0005515, GO:0008152]] \n", - " HALLMARK_HEME_METABOLISM-1 [[GO:0048821, GO:0045646, GO:0042541, GO:0015671, GO:0020037, GO:0005506, GO:0043496, GO:0046982]] \n", - " HALLMARK_HYPOXIA-0 [[GO:0008152, GO:0006096, GO:0006979, GO:0080135, GO:1901031, GO:0046324, GO:0006006, GO:0005975, GO:0006974]] \n", - " HALLMARK_HYPOXIA-1 [[glycolysis; gluconeogenesis; citrate cycle; pyruvate metabolism; atp production\\n\\nmechanism: these genes are enriched in functions related to energy metabolism, including glycolysis, GO:0006094, the citrate cycle, GO:0006090, and atp production. they are involved in various aspects of energy metabolism, such as glucose uptake and metabolism, GO:0005980, atp synthesis. the over-representation of these functions suggests that these genes may play a role in the regulation of energy metabolism at the cellular organismal level]] \n", - " HALLMARK_IL2_STAT5_SIGNALING-0 [[il10ra, tnfrsf18, il18r1, il1r2, il1rl1, il2ra, il2rb, il4r, MESH:D016753, MESH:D018793, tnfrsf1b, tnfrsf21, tnfrsf4, tnfrsf8, tnfrsf9, tnfsf11, tnfsf10, ifngr1, ccr4, ctla4, cxcl10, icos, irf4, irf6, irf8, socs1, socs2, ager, cish, gata1, gbp4, spp1, bcl2, bcl2l1, bmpr2, ccnd2, ccne1, cd79b, galm, glipr2, gpx4, hk2, MESH:D016753, itga6, itgae, itih5, klf6, lif, lrig1, ltb, mxd1, myc]] \n", - " HALLMARK_IL2_STAT5_SIGNALING-1 [[cytokine signaling pathway, GO:0006955, GO:0002682, GO:0006954, leukocyte migration and chemotaxis, GO:0002694, GO:0071347, GO:0032680]] \n", - " HALLMARK_IL6_JAK_STAT3_SIGNALING-0 [[GO:0006955, cytokine signaling pathway, GO:0060333, positive regulation of interleukin production, GO:0032729]] \n", - " HALLMARK_IL6_JAK_STAT3_SIGNALING-1 [[GO:0005126, GO:0006955, GO:0050900, jak-stat signaling pathway, GO:0034341, GO:0002690, GO:0051249, GO:0001817, GO:0050863, GO:0019221, GO:1902105]] \n", - " HALLMARK_INFLAMMATORY_RESPONSE-0 [[GO:0050900, cytokine signaling, GO:0002224, GO:0006954, GO:0032729, GO:0045087, GO:0032733, GO:0030595]] \n", - " HALLMARK_INFLAMMATORY_RESPONSE-1 [[cytokine signaling, chemokine signaling, GO:0050900, GO:0002250, GO:0045087]] \n", - " HALLMARK_INTERFERON_ALPHA_RESPONSE-0 [[interferon signaling, GO:0045087, antiviral defense]] \n", - " HALLMARK_INTERFERON_ALPHA_RESPONSE-1 [[GO:0034341, GO:0002718, GO:0060333, GO:0045070, GO:0032897, innate immune response-activating signal transduction, GO:0060337, GO:0035457, antiviral mechanism by interferon-stimulated genes (isg)]] \n", - " HALLMARK_INTERFERON_GAMMA_RESPONSE-0 [[GO:0051607, GO:0035458, GO:0071357, GO:0045071, GO:0031323, GO:0002682, GO:0034097, GO:0034340]] \n", - " HALLMARK_INTERFERON_GAMMA_RESPONSE-1 [[interferon signaling, GO:0019882, GO:0045321]] \n", - " HALLMARK_KRAS_SIGNALING_DN-0 [[GO:0005509, contractile fiber part, GO:0006936]] \n", - " HALLMARK_KRAS_SIGNALING_DN-1 [[GO:0043167, GO:0007165, GO:0019222, GO:0050794, g protein-coupled receptor signaling, GO:0035556, GO:0031325, GO:0043066, metabolic process regulation, GO:0005509, GO:0034765, GO:0001932, GO:0043169, GO:0045859, GO:0051716]] \n", - " HALLMARK_KRAS_SIGNALING_UP-0 [[GO:0006955, GO:0007165, GO:0050794, cytokine signaling, GO:0006954, GO:0006935, GO:0008284, GO:0043066]] \n", - " HALLMARK_KRAS_SIGNALING_UP-1 [[GO:0006955, GO:0006954, GO:0002694, GO:0001817, interleukin-10 signaling, tumor necrosis factor (tnf) signaling, GO:0006956, platelet activation and aggregation, eicosanoid synthesis]] \n", - " HALLMARK_MITOTIC_SPINDLE-0 [[GO:0007018, GO:0007052, cell division, chromosome separation]] \n", - " HALLMARK_MITOTIC_SPINDLE-1 [[kinesin family members, microtubule formation and stabilization, spindle formation and assembly, GO:0000910, GO:0051726, gene expression and chromosome segregation]] \n", - " HALLMARK_MTORC1_SIGNALING-0 [[GO:0006457, GO:0050776, GO:0009117, GO:0006629, gluconeogenesis and glycolysis, mrna processing and splicing]] \n", - " HALLMARK_MTORC1_SIGNALING-1 [[GO:0044237, protein regulation, transcriptional regulation, translation regulation, GO:0006281, stress response.\\n\\nmechanism: these enriched terms suggest that the identified genes are involved in several pathways, including maintaining cellular metabolism and homeostasis, regulating transcription and translation of proteins, repairing dna in response to damage, and responding to cellular stress]] \n", - " HALLMARK_MYC_TARGETS_V1-0 [[GO:0006412, GO:0006457, GO:1990904, u4/u6.u5 tri-snrnp, chaperone-mediated protein folding.\\n\\nmechanism: these genes are involved in protein synthesis and processing, including translation and ribosome biogenesis. many of them are also involved in protein folding and chaperone-mediated protein folding. the u4/u6.u5 tri-snrnp is also highly represented, indicating these genes may be involved in splicing]] \n", - " HALLMARK_MYC_TARGETS_V1-1 [[GO:0006396, GO:0006413, GO:0006446, GO:0042254, GO:0008380, GO:0006397]] \n", - " HALLMARK_MYC_TARGETS_V2-0 [[GO:0042254, GO:0008033, GO:0006364, GO:0016072, GO:0009451, GO:0022613]] \n", - " HALLMARK_MYC_TARGETS_V2-1 [[GO:0042254, GO:0006364, GO:0000394, rna polymerase ii regulation, rna processing and modification]] \n", - " HALLMARK_MYOGENESIS-0 [[GO:0006936, GO:0006816, z-disc, UBERON:0002036, GO:0030017, MESH:D014335, GO:0005861, GO:0071689]] \n", - " HALLMARK_MYOGENESIS-1 [[UBERON:0001630, MESH:D009218, MESH:D000199, MESH:D014336, filament]] \n", - " HALLMARK_NOTCH_SIGNALING-0 [[GO:0007219, GO:0045165, GO:0022008, GO:0030154, GO:0045893, GO:0043066, GO:0008285, GO:0043065, GO:0045747, GO:0016055, GO:0007268]] \n", - " HALLMARK_NOTCH_SIGNALING-1 [[GO:0051726, GO:0030154, GO:0001709, transcriptional regulation, GO:0016567]] \n", - " HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 [[GO:0022900, GO:0045333, GO:0002082]] \n", - " HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 [[GO:0006119, GO:0005746, GO:0070469, GO:0005739, MESH:D004734, GO:0031966, GO:0006099, GO:0006635, citrate cycle, GO:0098798, GO:0006754, GO:0051536]] \n", - " HALLMARK_P53_PATHWAY-0 [[GO:0006974, GO:0051726, cell growth and proliferation]] \n", - " HALLMARK_P53_PATHWAY-1 [[GO:0051726, GO:0006281, GO:0030330, GO:0000082, response to dna damage]] \n", - " HALLMARK_PANCREAS_BETA_CELLS-0 [[pancreatic development, beta cell differentiation, GO:0030073, GO:0042593, GO:0006006]] \n", - " HALLMARK_PANCREAS_BETA_CELLS-1 [[GO:0003323, GO:0030073, glucose regulation, diabetes-related pathways]] \n", - " HALLMARK_PEROXISOME-0 [[GO:0006631, GO:0006805, steroid hormone biosynthesis]] \n", - " HALLMARK_PEROXISOME-1 [[GO:0006631, GO:0007031, GO:0015721, GO:0006282]] \n", - " HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 [[mapk cascade; pi3k-akt signaling pathway; regulation of cell proliferation\\n\\nmechanism: the enriched terms suggest that the common function of the listed genes is to regulate cellular processes related to signal transduction and cell cycle/apoptosis. the mapk cascade is a crucial signaling pathway that controls the expression of genes required for cellular proliferation, differentiation, and survival. pi3k-akt signaling pathway controls cell survival, GO:0040007, and metabolism. the enriched term \"regulation of cell proliferation\" suggests that the listed genes contribute to regulating the balance between cell growth and division. these genes could affect the rate of cellular proliferation, arresting or promoting the cell cycle or modulating apoptotic signal transduction]] \n", - " HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 [[GO:0033554, GO:0035556, GO:0006468, GO:0042981, GO:0080135]] \n", - " HALLMARK_PROTEIN_SECRETION-0 [[GO:0016192, GO:0046907, GO:0006897, GO:0061024, GO:0008104, GO:0048193]] \n", - " HALLMARK_PROTEIN_SECRETION-1 [[GO:0048193, GO:0005768, GO:0005764, GO:0006612, GO:0006886, GO:0042391, GO:0034765, GO:0005773]] \n", - " HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 [[GO:0016209, GO:0051920, GO:0006749, GO:0006979, GO:0070301]] \n", - " HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 [[GO:0016209, regulation of iron ion binding, GO:0006979, GO:0048821, GO:2000378, GO:0006282, GO:0070301, GO:0050790, GO:0032092, regulation of thiol-dependent ubiquitinyl hydrolase activity, GO:0034599]] \n", - " HALLMARK_SPERMATOGENESIS-0 [[GO:0007283, GO:0140013, GO:0007130, GO:0007281, GO:0097722, oocyte meiosis]] \n", - " HALLMARK_SPERMATOGENESIS-1 [[GO:1903047, GO:0010971, regulation of spindle assembly checkpoint, GO:0034501, GO:0090234, GO:0051985, GO:0110028]] \n", - " HALLMARK_TGF_BETA_SIGNALING-0 [[tgf-beta signaling pathway, GO:0030514, GO:0090287, GO:0030513, GO:0006351, GO:0006355, GO:0045893, GO:0000122]] \n", - " HALLMARK_TGF_BETA_SIGNALING-1 [[tgf-beta signaling pathway, GO:0030509, GO:0030513, GO:0030198, GO:0060391]] \n", - " HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 [[ccl2, ccl20, ccl4, ccl5, ccn1, ccnd1, ccrl2, cd44, cd69, cd80, cd83, cdkn1a, icam1, icoslg, ifih1, ifit2, ifngr2, GO:0043514, il15ra, MESH:D020382, il1a, il1b, GO:0070743, MESH:D015850, il6st, il7r, inhba, irf1, jag1, nfkb1, nfkb2, nfkbia, nfkbie, nr4a1, nr4a2, nr4a3, ptger4, MESH:D051546, rel, rela, relb, ripk2, stat5a, tlr2, tnf, tnfaip2, tnfaip3, tnfaip6, tnfaip8, tnfrsf9, tnfsf9, tnip1, tnip]] \n", - " HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 [[cytokine signaling, GO:0000988, stress response, GO:0050776, GO:0006954]] \n", - " HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 [[GO:0006457, GO:0036503, upr signaling pathway]] \n", - " HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 [[GO:0006457, GO:0006605, GO:0006396, GO:0006950, GO:0006417, GO:0016481, GO:0006986, GO:0006913, GO:0008380, GO:1903021, GO:0016032, GO:0032496, GO:0072659, GO:0017148, GO:0022613, negative regulation of transcription by rna polymerase]] \n", - " HALLMARK_UV_RESPONSE_DN-0 [[tgf-beta signaling pathway, GO:0030198, GO:0007155, GO:0030334, GO:0042127]] \n", - " HALLMARK_UV_RESPONSE_DN-1 [[GO:0030198, GO:0030036, GO:0030155, GO:0007160, GO:0016477, GO:0007229, GO:0030199, GO:0035023, GO:0030178, basement membrane formation, GO:0014909]] \n", - " HALLMARK_UV_RESPONSE_UP-0 [[GO:0006355, regulation of transcription, dna-templated; go:0044267, cellular protein metabolic process; go:0009968, GO:0009968]] \n", - " HALLMARK_UV_RESPONSE_UP-1 [[GO:0006955, GO:0008104, GO:0051726]] \n", - " HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 [[GO:0016055, GO:0007219, transcriptional regulation, GO:0030154, GO:0008283]] \n", - " HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 [[GO:0007219, GO:0045747, GO:0045746, GO:0045165]] \n", - " T cell proliferation-0 [[cd28 co-stimulation, il-2 signaling, GO:0042110]] \n", - " T cell proliferation-1 [[GO:0042110, GO:0051247, GO:0001817]] \n", - " Yamanaka-TFs-0 [[GO:0000988, transcriptional regulation, GO:0030154, GO:0008283, stem cell maintenance, MESH:D047108]] \n", - " Yamanaka-TFs-1 [[MESH:D047108, regulation of transcription, GO:0048863]] \n", - " amigo-example-0 [[GO:0030198, GO:0030199, GO:0001525, GO:0001568, GO:0030168, GO:0001666, GO:0001936]] \n", - " amigo-example-1 [[GO:0030198, GO:0030155, regulation of cell substrate adhesion, GO:0045785, GO:0043062]] \n", - " bicluster_RNAseqDB_0-0 [[GO:0005509, GO:0050804, transcriptional regulation, GO:0050808]] \n", - " bicluster_RNAseqDB_0-1 [[GO:0007186, GO:0010468, GO:0007154, GO:0006355, GO:0005515, GO:0007155, GO:0001932, GO:0016055, GO:0030334, GO:0007165, GO:0043408, GO:0003677, GO:0006357, GO:0005543, GO:0051493, GO:0006811]] \n", - " bicluster_RNAseqDB_1002-0 [[atp hydrolysis coupled calcium ion transport, GO:0030036, GO:0006936, GO:0033365, GO:0051147, GO:0014743, GO:0045214]] \n", - " bicluster_RNAseqDB_1002-1 [[GO:0006936, MESH:D024510, GO:0007519, GO:0055001, GO:0030239, GO:0007517]] \n", - " endocytosis-0 [[GO:0006897, GO:0016192, GO:0007041, GO:0007032, GO:0030163]] \n", - " endocytosis-1 [[GO:0006897, GO:0006898, GO:0016197, GO:0015031, GO:0006886, GO:0007032, GO:0016192, endosomal sorting]] \n", - " glycolysis-gocam-0 [[GO:0006096, GO:0005975, GO:0006006, GO:0019318]] \n", - " glycolysis-gocam-1 [[GO:0006096, GO:0006006, GO:0006007]] \n", - " go-postsynapse-calcium-transmembrane-0 [[GO:0005509, GO:0005262, GO:0019722, GO:0006874, GO:0034765]] \n", - " go-postsynapse-calcium-transmembrane-1 [[GO:0005509, GO:0004970, GO:0051966, GO:0046928, GO:0005216, GO:0034765, GO:0004672, GO:0051924, GO:0051247]] \n", - " go-reg-autophagy-pkra-0 [[GO:0033554, GO:0010506, GO:0007165]] \n", - " go-reg-autophagy-pkra-1 [[GO:0097190, GO:0016485, GO:0031323]] \n", - " hydrolase activity, hydrolyzing O-glycosyl compounds-0 [[glycoside hydrolase activity, GO:0005975, GO:0006027, GO:0009311, GO:0005764, GO:0005783, catabolism of carbohydrate, MONDO:0019249]] \n", - " hydrolase activity, hydrolyzing O-glycosyl compounds-1 [[GO:0006096, metabolism of carbohydrates, GO:0019318, GO:0006013, GO:0009311, chitin catabolic/metabolic process, hyaluronan catabolic/metabolic process, glycosphingolipid metabolic/catabolic process, sialic acid catabolic/metabolic process]] \n", - " ig-receptor-binding-2022-0 [[GO:0002377, t cell receptor signaling, GO:0042113, t cell activation. \\n\\nhypotheses: this list of genes is heavily enriched in those involved in the function and development of b cells and t cells. specifically, they play a role in the production and function of immunoglobulins and t cell receptors, as well as the activation of these cell types. this suggests that these genes are integral to the proper functioning of the immune system]] \n", - " ig-receptor-binding-2022-1 [[GO:0006955, GO:0046649, GO:0030098]] \n", - " meiosis I-0 [[meiotic recombination, crossover formation, GO:0007130, GO:0006281, GO:0035825]] \n", - " meiosis I-1 [[GO:0007059, GO:0051321, GO:0006310, synapsis of chromosomes, GO:0051276, GO:0051177]] \n", - " molecular sequestering-0 [[GO:0002376, GO:0006950, GO:0006457, GO:0051641, GO:0006396, GO:0006829, GO:0010467, GO:0007165]] \n", - " molecular sequestering-1 [[GO:0006979, GO:0032088, GO:0055072, GO:0016567, GO:0043066]] \n", - " mtorc1-0 [[GO:0006457, GO:0050776, GO:0009117, GO:0006629, gluconeogenesis and glycolysis, mrna processing and splicing]] \n", - " mtorc1-1 [[GO:0006457, GO:0015031, GO:0042254]] \n", - " peroxisome-0 [[GO:0005778, peroxisome targeting, GO:0007031]] \n", - " peroxisome-1 [[peroxisome biogenesis, peroxisome membrane organization, GO:0016559]] \n", - " progeria-0 [[GO:0006281, GO:0051276, regulation of transcription]] \n", - " progeria-1 [[GO:0006281, GO:0006325, GO:0090398]] \n", - " regulation of presynaptic membrane potential-0 [[GO:0004970, GO:0099536, GO:0001505, GO:0007268, GO:0043269, GO:0005244, GO:0042391]] \n", - " regulation of presynaptic membrane potential-1 [[GO:0005216, GO:0007268, GO:0005261, GO:0007215, GO:0019228, GO:0006813, GO:0060080, MESH:D005680, sodium ion transport. \\n\\nhypotheses: \\n1. the enrichment of ion channel activity-related terms suggests that the genes play a crucial role in regulating ion transport during neuronal signaling, which in turn influences synaptic plasticity and memory formation.\\n2. the enrichment of synaptic transmission-related terms points towards the involvement of the genes in various aspects of synaptic signaling, including the glutamate and gaba receptor signaling pathways, inhibition of neuronal activity, and modulation of action potential generation. \\n3. overall, the enrichment of these terms hints at a potential interaction between the listed genes in regulating various aspects of neural signal processing, synaptic transmission, and plasticity]] \n", - " sensory ataxia-0 [[mitochondrial function, GO:0006457, GO:0030163, GO:0055085]] \n", - " sensory ataxia-1 [[\"nervous system development\", \"axon guidance\", \"myelination\", \"neuron projection\", \"synaptic transmission\"]] \n", - " term-GO:0007212-0 [[GO:0030594, GO:0007186, GO:0046928, GO:0007212, GO:0007188]] \n", - " term-GO:0007212-1 [[g protein coupled receptor signaling pathway, g protein beta/gamma subunit complex binding]] \n", - " tf-downreg-colorectal-0 [[transcriptional regulation, GO:0006325]] \n", - " tf-downreg-colorectal-1 [[GO:0003677, regulation of transcription, GO:0003682, GO:0008134, GO:0003713, negative regulation of transcription]] \n", - " ontological_synopsis EDS-0 [[GO:0030199, GO:0030198, GO:0006024, GO:0061448]] \n", - " EDS-1 [[GO:0030199, GO:0030198, GO:0030166, GO:0061448]] \n", - " FA-0 [[GO:0006281, GO:0000724, GO:0006513, fanconi anemia complementation group]] \n", - " FA-1 [[GO:0006281, GO:0006513, GO:0000724, fanconi anemia complementation group, GO:0000785, GO:0005654, GO:0140513]] \n", - " HALLMARK_ADIPOGENESIS-0 [[fad binding activity, GO:0016407, lipid binding activity, coenzyme binding, identical protein binding activity, citrate biosynthetic process]] \n", - " HALLMARK_ADIPOGENESIS-1 [[mitochondrial respiration, mitochondrial function, GO:0008152, energy production, GO:0022900, GO:0006629, GO:0006631, GO:0006637]] \n", - " HALLMARK_ALLOGRAFT_REJECTION-0 [[GO:0005125, GO:0004896, integrin binding activity, GO:0004672, GO:0000988, t-cell receptor binding activity, abc-type peptide antigen transporter activity.\\n\\nmechanism: these genes are involved in various aspects of immune response, including cytokine activity, cytokine receptor activity, and t-cell receptor binding activity. they also play a role in antigen processing and presentation through the abc-type peptide antigen transporter activity. the integrin binding activity reflects the involvement of integrins in leukocyte adhesion and migration. finally, the transcription factor activity reflects the importance of transcriptional regulation in immune responses]] \n", - " HALLMARK_ALLOGRAFT_REJECTION-1 [[GO:0005125, GO:0008009, mhc class ii protein complex binding activity, signaling receptor binding activity, protein kinase binding activity, integrin binding activity, identical protein binding activity, sh2 domain binding activity, GO:0004252, rna binding activity, GO:0046982, GO:0008083]] \n", - " HALLMARK_ANDROGEN_RESPONSE-0 [[binding activity, GO:0008152, GO:0043167, nucleic acid binding. \\n\\nmechanism: the enriched terms suggest that the listed genes have a common function in binding and metabolic processes. it is possible that these genes are involved in regulating the flow and utilization of energy and molecules within cells]] \n", - " HALLMARK_ANDROGEN_RESPONSE-1 [[GO:0004672, GO:0035556, GO:0000079, GO:0007166]] \n", - " HALLMARK_ANGIOGENESIS-0 [[extracellular matrix organization; cell adhesion; protein binding; signaling pathway; regulation of cell proliferation.\\n\\nmechanism: the enriched terms suggest that these genes are involved in extracellular matrix organization and cell signaling pathways that regulate cell proliferation and adhesion. many of the genes are structural constituents of the extracellular matrix and influence cell-matrix interactions. others are involved in cell signaling pathways, such as the notch and fibroblast growth factor pathways, that play critical roles in cell proliferation and differentiation. some of the genes have also been implicated in diseases involving abnormal extracellular matrix formation or cell signaling dysregulation, such as ehlers-danlos syndrome, MONDO:0004975, MONDO:0004992]] \n", - " HALLMARK_ANGIOGENESIS-1 [[UBERON:4000022, binding activity]] \n", - " HALLMARK_APICAL_JUNCTION-0 [[GO:0007010, GO:0007155, GO:0005102, kinase activity.\\n\\nmechanism: these genes are involved in the maintenance of cell structure and organization through regulation of the cytoskeleton. they also contribute to cell-cell interactions and signaling through receptor binding and kinase activity. a biological pathway that might be involved is the rho gtpase signaling pathway, which regulates actin cytoskeleton dynamics and cell adhesion]] \n", - " HALLMARK_APICAL_JUNCTION-1 [[cell adhesion: cdh3, cdh4, cdh6, cdh11, cdh15, cd276, cd209, icam5, icam2, icam1, itga3, itga9, itga10, itgb1, cldn4, cldn5, cldn6, cldn7, cldn8, cldn9, cldn11, cldn14, cldn18, cldn19\\n- protein kinase activity: cdk8, ptk2, syk, taok2, vav2, src\\n- actin filament binding: actn1, actn3, lima1, nexn, calb2, pfn1\\n- metalloendopeptidase activity: adamts5, adam23, mmp2, mmp9\\n- integrin binding: jup, vcam1, slit2]] \n", - " HALLMARK_APICAL_SURFACE-0 [[GO:0007165, cell surface receptor activity, protein binding activity]] \n", - " HALLMARK_APICAL_SURFACE-1 [[GO:0005886, GO:0009986, GO:0055085, GO:0038023, positive regulation of transcription, GO:0010468, GO:0006468, GO:0005615]] \n", - " HALLMARK_APOPTOSIS-0 [[GO:0006915, GO:0005125, transcription factor binding activity. \\n\\nmechanism/]] \n", - " HALLMARK_APOPTOSIS-1 [[GO:0006915, GO:0005125, GO:0010941, GO:2001233, GO:0001819, GO:0042981, GO:0043067, positive regulation of apoptotic process.\\n\\nmechanism: these genes are involved in apoptotic signaling and cytokine activity, which suggests that they play a role in regulating cell death and programmed cell death. the enriched terms suggest that these genes may be regulated by shared signaling pathways or transcriptional programs that control apoptosis and cytokine production. one potential underlying mechanism could involve the activation of pro-apoptotic proteins in response to cellular stress or damage, leading to the release of cytokines that further promote cell death. alternatively, these genes may be involved in controlling the balance between cell survival and death in response to external cues such as cytokine signaling or nutrient availability. further research is needed to fully elucidate the molecular mechanisms underlying these gene functions]] \n", - " HALLMARK_BILE_ACID_METABOLISM-0 [[GO:0006629, GO:0030301, GO:0006633]] \n", - " HALLMARK_BILE_ACID_METABOLISM-1 [[GO:0030301, GO:0015908, GO:0007031, GO:0004467, GO:0008123, atp binding activity, ubiquitin-dependent protein binding activity. \\n\\nmechanism: these genes are likely involved in the regulation and transport of lipids, particularly cholesterol and long-chain fatty acids, in cells and tissues. peroxisomal proteins and functions may also play a role in this process, including in the regulation of lipid metabolism]] \n", - " HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 [[GO:0042632, GO:0008610, GO:0010883, phospholipid binding activity, fatty acid binding activity, low-density lipoprotein particle binding activity, more]] \n", - " HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 [[GO:0006695, GO:0008299, GO:0055088, GO:0006646, GO:0000122, GO:0045944, GO:0070458, GO:0001676]] \n", - " HALLMARK_COAGULATION-0 [[GO:0006508, complement pathways, GO:0007596, GO:0007155]] \n", - " HALLMARK_COAGULATION-1 [[GO:0006508, GO:0007596, GO:0006956, negative regulation of proteolysis. \\n\\nmechanism: the enriched terms suggest that these genes are involved in the regulation of proteolytic activity in several biological processes, including blood coagulation and immune response]] \n", - " HALLMARK_COMPLEMENT-0 [[GO:0004867, protease binding activity, enzyme binding activity, calcium ion binding activity]] \n", - " HALLMARK_COMPLEMENT-1 [[GO:0005515, GO:0019899, GO:0005488, GO:0004175, metal ion binding.\\n\\nmechanism: the enriched terms suggest that these genes play a role in protein-protein interactions and enzymatic reactions involving metal ions]] \n", - " HALLMARK_DNA_REPAIR-0 [[GO:0006281, GO:0097747, nucleotide metabolism. \\n\\nmechanism: these genes are predominantly involved in regulating dna replication, transcription, and repair. they may also play roles in the metabolism of nucleotides and nucleotide analogs that target dna synthesis. the enrichment of terms related to rna polymerase may reflect the closely intertwined nature of dna and rna synthesis]] \n", - " HALLMARK_DNA_REPAIR-1 [[GO:0006260, GO:0006281, rna transcription]] \n", - " HALLMARK_E2F_TARGETS-0 [[GO:0006260, GO:0051726, GO:0006325]] \n", - " HALLMARK_E2F_TARGETS-1 [[dna binding activity, protein binding activity, enzyme binding activity, chromatin binding activity, atp binding activity, histone binding activity, rna binding activity, identical protein binding activity]] \n", - " HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 [[GO:0005201, integrin binding activity, collagen binding activity, identical protein binding activity, fibrinogen binding activity, protease binding activity]] \n", - " HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 [[GO:0005201, collagen binding activity, integrin binding activity, heparin binding activity, GO:0008237, signaling receptor binding activity.\\n\\nmechanism: these genes are involved in the maintenance and formation of the extracellular matrix, which provides structural support to cells and tissues. they play a role in cell adhesion, signaling, and migration through interactions with the extracellular matrix. the enriched binding activities suggest that these genes are involved in extracellular matrix remodeling and regulation of growth factor signaling. metallopeptidase activity may be involved in the degradation of extracellular matrix components]] \n", - " HALLMARK_ESTROGEN_RESPONSE_EARLY-0 [[GO:0005509, GO:0000166, enzyme binding activity, MESH:D048788, gene transcription, GO:0006811]] \n", - " HALLMARK_ESTROGEN_RESPONSE_EARLY-1 [[GO:0005515, GO:0000988, transmembrane transporter activity.\\n\\nmechanism: the enriched terms suggest that the genes on the list are involved in various cellular processes that require protein-protein interaction, transcriptional regulation, and transmembrane transport of substances. a possible hypothesis is that these genes play a role in signal transduction and regulation of gene expression]] \n", - " HALLMARK_ESTROGEN_RESPONSE_LATE-0 [[GO:0022857, protein binding activity]] \n", - " HALLMARK_ESTROGEN_RESPONSE_LATE-1 [[(1) enzymatic activity; (2) binding activity; (3) transcription regulation. \\n\\nmechanism: these genes likely play roles in various biological pathways, such as metabolism, cell signaling, and gene expression regulation. given the enrichment in enzymatic activity, it is possible that some of these genes are involved in metabolic pathways, such as lipid metabolism. the enrichment in binding activity may reflect the importance of protein-protein interactions and signaling cascades in cellular processes. the enrichment in transcription regulation suggests that many of these genes may be key players in regulating gene expression and ultimately cell fate]] \n", - " HALLMARK_FATTY_ACID_METABOLISM-0 [[GO:0047617, GO:0006631, GO:0120227, GO:0008289, GO:0004467, GO:0006099, GO:0046356]] \n", - " HALLMARK_FATTY_ACID_METABOLISM-1 [[GO:0016491, binding activity, GO:0006631, GO:0006084, heme-binding activity]] \n", - " HALLMARK_G2M_CHECKPOINT-0 [[dna binding activity, chromatin binding activity, protein binding activity, enzyme binding activity, histone binding activity, GO:0003714]] \n", - " HALLMARK_G2M_CHECKPOINT-1 [[dna-binding transcription factor activity; protein kinase activity; microtubule binding activity. \\n\\nmechanism: these genes are likely involved in the regulation of gene expression, cell cycle progression, and cytoskeletal dynamics through the binding and modification of dna, MESH:D011506, and microtubules. specifically, they may be involved in processes such as transcriptional regulation, dna replication and repair, GO:0007059, GO:0051301]] \n", - " HALLMARK_GLYCOLYSIS-0 [[GO:0008378, GO:0015020, n-acetylglucosamine sulfotransferase activity, GO:0035250, glucosaminyl-proteoglycan 3-beta-glucosyltransferase activity, GO:0016758, GO:0045130, GO:0016779]] \n", - " HALLMARK_GLYCOLYSIS-1 [[GO:0005975, GO:0006024, GO:0006493]] \n", - " HALLMARK_HEDGEHOG_SIGNALING-0 [[GO:0006357, GO:0016525, GO:0007155, GO:0030036, GO:0010604, GO:0007411, GO:0030336]] \n", - " HALLMARK_HEDGEHOG_SIGNALING-1 [[GO:0007165, GO:0007155, GO:0007399, transcription regulation]] \n", - " HALLMARK_HEME_METABOLISM-0 [[GO:0020037, GO:0015075, protein binding activity, GO:0000988]] \n", - " HALLMARK_HEME_METABOLISM-1 [[transmembrane transport; protein binding activity; metal ion binding activity; dna-binding transcription activator activity\\n\\nmechanism: these genes are involved in various transport and binding activities, especially transmembrane transport, indicating a possible importance in cellular trafficking and signaling pathways. additionally, they exhibit a significant enrichment in protein and metal ion binding activities, which may suggest a role in protein-protein interactions and redox reactions, respectively. finally, dna-binding transcription activator activity is found to be enriched, indicating that these genes may regulate gene expression]] \n", - " HALLMARK_HYPOXIA-0 [[enzyme binding activity, GO:0005515, GO:0003700, carbohydrate binding activity, signaling receptor binding activity, identical protein binding activity, atp binding activity, nad binding activity, phosphoprotein binding activity, metal ion binding activity, GO:0003924, GO:0008083, GO:0008194, phospholipid binding activity, platelet-derived growth factor binding activity]] \n", - " HALLMARK_HYPOXIA-1 [[GO:0006006, GO:0016301, transcriptional regulation, GO:0023052]] \n", - " HALLMARK_IL2_STAT5_SIGNALING-0 [[GO:0005125, interleukin receptor binding activity, cytokine binding activity, GO:0031295, GO:0051250, GO:0006952, GO:0006955, interleukin binding activity]] \n", - " HALLMARK_IL2_STAT5_SIGNALING-1 [[GO:0004896, interleukin binding activity, identical protein binding activity, gtp binding activity, GO:0001216, protein kinase binding activity, atp binding activity, GO:0016787, collagen binding activity, small gtpase binding activity, GO:0061630, GO:0004197, GO:0005215, rna binding activity, calcium ion binding activity, signaling receptor binding activity, GO:0005125, GO:0008083, enzyme binding activity, several others.\\n\\nmechanism: these genes are involved in immune response cytokine activity. many of them encode for cytokine receptors, transcription factors, enzymes involved in immune system pathways processes. the enrichment of terms related to protein binding, including dna binding identical protein binding, may suggest that many of these genes act as transcriptional regulators in immune cells, coordinating the expression of genes involved in immune function. the enrichment of transporter activity may indicate that some of these genes are involved in cell migration or trafficking of immune cells to sites of inflammation or infection. additionally, the enrichment of terms related to enzyme activity may suggest that some of]] \n", - " HALLMARK_IL6_JAK_STAT3_SIGNALING-0 [[GO:0005125, GO:0004896, protein kinase binding activity, GO:0006954, GO:0006955, GO:0007165]] \n", - " HALLMARK_IL6_JAK_STAT3_SIGNALING-1 [[GO:0004896, interleukin binding activity, GO:0008009, GO:0001819, GO:0050778, GO:0098542, GO:0010604]] \n", - " HALLMARK_INFLAMMATORY_RESPONSE-0 [[GO:0005125, GO:0008009, identical protein binding activity, GO:0038023, GO:0006811]] \n", - " HALLMARK_INFLAMMATORY_RESPONSE-1 [[GO:0004930, GO:0004896, enzyme binding activity, identical protein binding activity, GO:0007165, calcium ion binding activity, protease binding activity, transporter activity.\\n\\nmechanism: these genes are involved in various mechanisms related to cell signaling and transport. one hypothesis is that these genes may collectively contribute to the regulation of calcium levels and calcium-dependent signaling pathways, as well as cytokine-mediated signaling pathways involved in immune response]] \n", - " HALLMARK_INTERFERON_ALPHA_RESPONSE-0 [[GO:0005125, GO:0098542, GO:0046597, rna binding activity, identical protein binding activity]] \n", - " HALLMARK_INTERFERON_ALPHA_RESPONSE-1 [[GO:0098542, GO:0050709, GO:0046597, GO:0045071, GO:0030501, GO:0002688, regulation of transcription]] \n", - " HALLMARK_INTERFERON_GAMMA_RESPONSE-0 [[GO:0004896, GO:0000981, identical protein binding activity, enzyme binding activity, GO:0042110, cell adhesion molecule binding activity, positive regulation of activated cd8-positive t cell proliferation, GO:0038187, GO:0061630, GO:0000166, GO:0004930, protein kinase binding activity, calcium ion binding activity, complement binding activity, GO:0004867, GO:0008009, integrin binding activity.\\n\\nmechanism: these genes predominantly function in the immune system and are related to the activation and proliferation of t cells, cytokine signaling, pattern recognition, and complement cascades. the enriched terms suggest an association with signaling cascades, receptor binding, enzyme activity, and immune response to pathogens]] \n", - " HALLMARK_INTERFERON_GAMMA_RESPONSE-1 [[GO:0019882, GO:0045087, cytokine signaling, GO:0045321, antiviral defense]] \n", - " HALLMARK_KRAS_SIGNALING_DN-0 [[calcium ion binding activity, atp binding activity, GO:0008511, GO:0004930, GO:0004888, GO:0016887, identical protein binding activity, protein kinase binding activity]] \n", - " HALLMARK_KRAS_SIGNALING_DN-1 [[protein binding activity, calcium ion binding activity, atp binding activity, identical protein binding activity, GO:0008507, GO:0005337, GO:0043273, GO:0003924, GO:0015432]] \n", - " HALLMARK_KRAS_SIGNALING_UP-0 [[binding activity; enzyme activity; transcription activator activity. \\n\\nmechanism: these enriched terms suggest that the commonality among these genes is that they are involved in various types of binding and enzymatic activities, as well as regulating transcription. it is possible that these genes work together in regulatory pathways to bind to specific targets, catalyze reactions, modulate transcriptional activity in the cell]] \n", - " HALLMARK_KRAS_SIGNALING_UP-1 [[GO:0005178, GO:0005515, GO:0005524, GO:0071345, GO:0043167, ubiquitin protein ligase binding. \\n\\nmechanism: the shared function of binding among the enriched terms suggests that these genes may play a role in mediating protein regulation and signal transduction pathways through protein-protein or protein-ligand interactions. the involvement in cellular response to cytokine stimulus may suggest a potential role in modulating immune responses]] \n", - " HALLMARK_MITOTIC_SPINDLE-0 [[microtubule binding activity, GO:0005096, actin filament binding activity, microtubule plus-end binding activity, identical protein binding activity, protein kinase binding activity, kinetochore binding activity, cytoskeletal protein binding activity, gamma-tubulin binding activity]] \n", - " HALLMARK_MITOTIC_SPINDLE-1 [[microtubule binding activity, GO:0007052, GO:0000226]] \n", - " HALLMARK_MTORC1_SIGNALING-0 [[binding activity, enzymatic activity, GO:0006412, GO:0023052, GO:0008152]] \n", - " HALLMARK_MTORC1_SIGNALING-1 [[GO:0005515, enzyme activity. \\n\\nmechanism: the enriched terms suggest that these genes play a role in protein-protein interactions and enzymatic reactions, potentially involved in metabolic pathways or signal transduction cascades]] \n", - " HALLMARK_MYC_TARGETS_V1-0 [[ribosome binding activity; rna binding activity; translation initiation factor activity; protein folding chaperone activity\\n\\nmechanism: these genes are involved in different aspects of protein synthesis, such as ribosome binding, GO:0006413, and rna binding. they also contribute to protein folding processes as chaperones. the enrichment of these terms suggests that these genes function together to ensure proper protein synthesis and folding, which are vital to numerous cellular processes]] \n", - " HALLMARK_MYC_TARGETS_V1-1 [[GO:0006396, GO:0003676, GO:0006457, ribosomal structural activity. \\n\\nmechanism: these genes likely function together in the post-transcriptional regulation of gene expression, from rna splicing to translation initiation and ribosome assembly]] \n", - " HALLMARK_MYC_TARGETS_V2-0 [[GO:0006364, rna binding activity, GO:0046982, mitochondrial function, GO:0051726]] \n", - " HALLMARK_MYC_TARGETS_V2-1 [[GO:0006364, snorna binding activity, GO:0042273, rna binding activity, GO:0005730]] \n", - " HALLMARK_MYOGENESIS-0 [[cytoskeletal protein binding activity, actin binding activity, atp binding activity, calcium ion binding activity, identical protein binding activity, enzyme binding activity, GO:0042803]] \n", - " HALLMARK_MYOGENESIS-1 [[actin binding activity, cytoskeletal protein binding activity, calcium ion binding activity, myosin binding activity, atp binding activity, kinase binding activity, muscle structure development. \\n\\nmechanism: these genes are involved in muscle structure and function as they encode proteins that bind to actin, myosin, and other cytoskeletal proteins to form the muscle fibers. they also bind to calcium ions and atp, which are necessary for muscle contraction, and contribute to the development of muscle structure]] \n", - " HALLMARK_NOTCH_SIGNALING-0 [[GO:0007219, GO:0016567]] \n", - " HALLMARK_NOTCH_SIGNALING-1 [[\"notch signaling pathway,\" \"protein ubiquitination,\" \"negative regulation of cell differentiation,\" \"regulation of dna-templated transcription.\"]] \n", - " HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 [[GO:0022900, GO:0006119, mitochondrial metabolism, GO:0006637, ketone body metabolism.\\n\\nmechanism and]] \n", - " HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 [[GO:0005746, GO:0006118, GO:0006754, MESH:D009245, MESH:D003576, GO:0016467, flavin adenine dinucleotide]] \n", - " HALLMARK_P53_PATHWAY-0 [[GO:0042981, protein binding activity, GO:0003700]] \n", - " HALLMARK_P53_PATHWAY-1 [[GO:0000988, rna binding activity, enzyme binding activity, identical protein binding activity, dna binding activity, histone binding activity]] \n", - " HALLMARK_PANCREAS_BETA_CELLS-0 [[GO:0006006, GO:0030073, GO:0006357]] \n", - " HALLMARK_PANCREAS_BETA_CELLS-1 [[GO:0006006, GO:0030073, glucose homeostasis.\\n\\nmechanism]] \n", - " HALLMARK_PEROXISOME-0 [[GO:0006629, GO:0006631, GO:0006810, GO:0003824, GO:0005501, steroid binding.\\n\\nmechanism and]] \n", - " HALLMARK_PEROXISOME-1 [[GO:0004467, GO:0016401, GO:0047676, GO:0031957, peroxisome targeting sequence binding activity, GO:0006633]] \n", - " HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 [[GO:0004672, cytoskeleton structure, GO:0006629, protein binding activity]] \n", - " HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 [[GO:0006468, intracellular signaling, GO:0016301, GO:0016791, enzyme binding activity. \\n\\nmechanism: the enriched terms suggest that many of the genes are involved in regulatory processes related to protein modification through phosphorylation and dephosphorylation. this could implicate several signaling pathways, such as mapk, pi3k/akt, and nf-kappab pathways]] \n", - " HALLMARK_PROTEIN_SECRETION-0 [[GO:0007030, GO:0006888, retrograde transport, vesicle recycling, GO:0090110, GO:0006891, GO:0008333, GO:0006893, GO:0048488, GO:0016192, vesicle recycling]] \n", - " HALLMARK_PROTEIN_SECRETION-1 [[GO:0048193, GO:0032456, GO:0035493, GO:0006891, GO:0070836]] \n", - " HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 [[GO:0098869, GO:0006750, GO:0042744, oxidation-reduction process, GO:0006979]] \n", - " HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 [[GO:0045454, GO:0006979, GO:0016209, GO:0004602, GO:0004784, GO:0004601, GO:0003954, GO:0032981]] \n", - " HALLMARK_SPERMATOGENESIS-0 [[GO:0005515, GO:0005524, GO:0042802, GO:0016301, GO:0000166]] \n", - " HALLMARK_SPERMATOGENESIS-1 [[identical protein binding activity, protein folding chaperone binding activity, GO:0004672, rna binding activity, chromatin binding activity, atp binding activity, nucleotide binding activity, GO:0004722, GO:0061630, calcium ion binding activity, rna polymerase iii binding activity, cytokine binding activity, GO:0004930, integrin binding activity, many others]] \n", - " HALLMARK_TGF_BETA_SIGNALING-0 [[GO:0007178, GO:0010862, GO:0010991, GO:0045668, GO:0030512, GO:0010604, GO:0009967]] \n", - " HALLMARK_TGF_BETA_SIGNALING-1 [[signal transduction; regulation of gene expression; transcription regulation; protein phosphorylation; smad protein signal transduction.\\n\\nmechanism: these genes are involved in various aspects of signal transduction, including regulation of gene expression, transcription regulation, MESH:D016212, where they regulate transcription of target genes. genes in this list may activate or inhibit smad signaling and affect downstream transcriptional regulation. additionally, many of these genes play roles in other signaling pathways and regulatory processes, such as the wnt signaling pathway and negative regulation of protein degradation]] \n", - " HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 [[GO:0005125, GO:0003700, enzyme binding activity, GO:0006955]] \n", - " HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 [[cytokine activity; dna-binding transcription factor activity; enzyme binding activity; phosphatidylinositol-3,4-bisphosphate binding activity; g protein-coupled receptor activity.\\n\\nmechanism: the enriched terms suggest that the genes on the list are involved in signaling pathways that regulate gene expression and cellular responses through cytokine receptors, GO:0035556, and various enzymatic activities. these pathways play essential roles in several biological processes, including immune responses, cell differentiation and development, cell survival death]] \n", - " HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 [[protein folding and processing, GO:0015031, GO:0003723, GO:0043022, GO:0003743]] \n", - " HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 [[rna binding activity, protein folding chaperone binding activity, ribosome binding activity, histone binding activity, dna-binding transcription factor binding activity, ubiquitin protein ligase binding activity]] \n", - " HALLMARK_UV_RESPONSE_DN-0 [[extracellular matrix organization; growth factor signaling; regulation of transcription, dna-templated; positive regulation of protein kinase activity; organic acid metabolic process.\\n\\nmechanism: these genes are involved in extracellular matrix structural constituent, growth factor signaling, GO:0000988, GO:0005515, and nucleotide binding. this suggests that they may be involved in the regulation of gene transcription, cellular growth and differentiation, and the organization of extracellular matrices. a hypothesis for the underlying biological mechanism or pathway is that these genes may be involved in the regulation of extracellular matrix formation and growth factor signaling pathways, which then contribute to cellular differentiation and growth. additionally, the binding of proteins with transcription factor activity and nucleotide binding activity suggests that these genes are involved in the regulation of gene transcription, which may have downstream effects on cellular function and behavior]] \n", - " HALLMARK_UV_RESPONSE_DN-1 [[GO:0005201, GO:0005178, identical protein binding activity, protease binding activity, calcium binding, platelet-derived growth factor binding activity]] \n", - " HALLMARK_UV_RESPONSE_UP-0 [[enzyme binding activity, protein kinase binding activity, GO:0042803, rna binding activity, atp binding activity, identical protein binding activity, ubiquitin protein ligase binding activity, GO:0001228, ion binding activity, g protein-coupled receptor binding activity, dna polymerase binding activity, peptide hormone receptor binding activity. \\n\\nmechanism: these genes are involved in a variety of molecular activities, including enzyme activity, protein binding, and transcription factor activity. one potential underlying biological mechanism is the regulation and interaction of proteins in various cellular processes]] \n", - " HALLMARK_UV_RESPONSE_UP-1 [[atp binding activity, GO:0001216, identical protein binding activity, rna binding activity, protein kinase binding activity, cysteine-type endopeptidase activity involvement in apoptotic signaling, GO:0004602, histone binding activity, GO:0030594, glucagon receptor binding activity, GO:0004499, peptide hormone receptor binding activity, gtp binding activity, more]] \n", - " HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 [[GO:0090090, regulation of transcription, GO:0000981, histone deacetylase binding activity, ubiquitin protein ligase binding activity, notch binding activity, protein kinase binding activity, GO:0003713, identical protein binding activity]] \n", - " HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 [[GO:0060070, GO:0031398, GO:0090090, GO:0031397, GO:0030162]] \n", - " T cell proliferation-0 [[GO:0050776, intracellular signaling, GO:0008037, GO:0009617, GO:0008284, GO:0005125, protein kinase binding activity, identical protein binding activity]] \n", - " T cell proliferation-1 [[GO:0042110, GO:0001816, GO:0010468, GO:0050671, GO:0001819, GO:0001933, GO:0045840, protein kinase binding activity, GO:0004697, GO:0004911, GO:0004896, GO:0097190, GO:0007005, GO:0043065, GO:0042100, GO:0004931]] \n", - " Yamanaka-TFs-0 [[transcription regulation, GO:0010468, GO:0045944, GO:0003700, cellular differentiation]] \n", - " Yamanaka-TFs-1 [[GO:0010468, transcriptional regulation, GO:0003700, GO:0001714, GO:0045944]] \n", - " amigo-example-0 [[GO:0030198, GO:0007165, GO:0007596]] \n", - " amigo-example-1 [[GO:0005178, GO:0005201, GO:0008083, platelet-derived growth factor binding activity, GO:0030199]] \n", - " bicluster_RNAseqDB_0-0 [[GO:0005515, GO:0005216, transcriptional regulation, ubiquitin-protein ligase activity]] \n", - " bicluster_RNAseqDB_0-1 [[metal ion binding activity, calcium ion binding activity, GO:0000981, g protein-coupled receptor binding activity, enzyme binding activity, sequence-specific double-stranded dna binding activity, cytoskeletal protein binding activity, GO:0061630]] \n", - " bicluster_RNAseqDB_1002-0 [[GO:0006936, GO:0030239, GO:0043502, GO:0051015, GO:0005523]] \n", - " bicluster_RNAseqDB_1002-1 [[GO:0003009, GO:0060048, GO:0010628, actin filament binding activity, GO:0008307]] \n", - " endocytosis-0 [[GO:0006897, GO:0015031, GO:0006898]] \n", - " endocytosis-1 [[GO:0006897, lysosomal function, GO:0038023, GO:0006955, GO:0008152]] \n", - " glycolysis-gocam-0 [[GO:0006006, GO:0005975, GO:0019725, GO:0008104, GO:0070062, GO:0005634]] \n", - " glycolysis-gocam-1 [[GO:0006096, GO:0005975, GO:0006000, cell development.\\n\\nhypotheses: the enriched terms suggest that these genes are involved in the glycolysis pathway, contributing to carbohydrate metabolic processes and the production of energy for cellular development. specifically, fructose metabolic processes are enriched, indicating that the genes may play a role in the conversion of fructose to glucose during glycolysis]] \n", - " go-postsynapse-calcium-transmembrane-0 [[GO:0006816, GO:0007268, GO:0005245, GO:0098978, GO:0004972]] \n", - " go-postsynapse-calcium-transmembrane-1 [[GO:0005509, GO:0006836, GO:0001505, GO:0016079, GO:0035235, GO:0007186, GO:0071318]] \n", - " go-reg-autophagy-pkra-0 [[GO:0006468, GO:0010604, GO:0038202, GO:0032006, GO:0016241, positive regulation of cyclin-dependent protein serine/threonine kinase activity.\\n\\nmechanism and]] \n", - " go-reg-autophagy-pkra-1 [[intracellular signaling, pathway regulation, GO:0006915, GO:0004672, GO:0006468, GO:0010604, GO:0045859]] \n", - " hydrolase activity, hydrolyzing O-glycosyl compounds-0 [[GO:0046479, GO:0006516, GO:0006032, GO:0030214]] \n", - " hydrolase activity, hydrolyzing O-glycosyl compounds-1 [[GO:0005975, MESH:D054794, glycan catabolism, GO:0006516, GO:0019377, GO:0006032, GO:0006004]] \n", - " ig-receptor-binding-2022-0 [[antigen binding activity, immunoglobulin receptor binding activity, GO:0002253]] \n", - " ig-receptor-binding-2022-1 [[GO:0002253, GO:0098542, GO:0019731, GO:0006959, GO:0002377, GO:0051130, GO:0045657]] \n", - " meiosis I-0 [[GO:0061982, GO:0007131, GO:0007129, GO:0000712, GO:0000724]] \n", - " meiosis I-1 [[meiotic recombination, GO:0035825, GO:0006302]] \n", - " molecular sequestering-0 [[molecular sequestering, protein binding activity, transport of metal ions, GO:0048523, response to infection and stress, GO:0010468, GO:0019722, regulation of transcription]] \n", - " molecular sequestering-1 [[GO:0140311, GO:0010468, GO:0031398, GO:0051238]] \n", - " mtorc1-0 [[binding activity, enzymatic activity, GO:0006412, GO:0023052, GO:0008152]] \n", - " mtorc1-1 [[GO:0005515, GO:0042802, GO:0019899, GO:0043167, GO:0005524, GO:0031625, GO:0003723, GO:0003677, GO:0097159, GO:0017076, GO:0051015, GO:0042802, GO:0016491, phosphoprotein binding activity, GO:0005215, GO:0006793, GO:0044237, GO:0006457, GO:0003677, GO:0008380]] \n", - " peroxisome-0 [[GO:0017038, peroxisomal biogenesis, GO:0140036, atp binding and hydrolysis activity, lipid binding activity]] \n", - " peroxisome-1 [[GO:0007031, GO:0016558, GO:0005778, peroxisomal biogenesis disorder, GO:0008611, lipid binding activity, atp binding activity, GO:0016887, ubiquitin-dependent protein binding activity, enzyme binding activity]] \n", - " progeria-0 [[GO:0006259, GO:0006325, GO:0033554, GO:0006281, GO:0007568]] \n", - " progeria-1 [[GO:0006281, GO:0006950, GO:0090398, GO:0000723, chromatin condensation]] \n", - " regulation of presynaptic membrane potential-0 [[GO:0015276, GO:0099505, GO:0060078, GO:0071805, GO:0035725, GO:0035235]] \n", - " regulation of presynaptic membrane potential-1 [[GO:0007214, GO:0007215, GO:0006811, GO:0006836, GO:0007268]] \n", - " sensory ataxia-0 [[GO:0042552, GO:0007422, MONDO:0005071, GO:0022011, MONDO:0005244]] \n", - " sensory ataxia-1 [[GO:0007399, GO:0042552, mitochondrial metabolism, GO:0030163, protein regulation, GO:0071260]] \n", - " term-GO:0007212-0 [[GO:0007186, GO:0007212]] \n", - " term-GO:0007212-1 [[GO:0007212, GO:0007186, GO:0051480, GO:0004016, GO:0006469, GO:0050821, GO:0060828, GO:0007220, GO:0034205, GO:0006508, GO:0046325, GO:1904227, GO:0051247, GO:0015171, GO:0015108]] \n", - " tf-downreg-colorectal-0 [[dna-binding transcription factor, rna polymerase ii-specific transcription regulation, GO:0000122, GO:0045944, GO:0006355]] \n", - " tf-downreg-colorectal-1 [[GO:0000988, GO:0006355, GO:0045893, GO:0045892, dna-binding, GO:0003702]] \n", - "text-davinci-003 narrative_synopsis EDS-0 [[connective tissue formation and repair, protein binding and folding, GO:0006955, GO:0042060, GO:0006024]] \n", - " EDS-1 [[collagen maturation, GO:0006024, transcriptional regulation, GO:0006829]] \n", - " FA-0 [[GO:0006281, GO:0035825, GO:0016310, nucleoprotein complex assembly, formation of nuclear foci, double-strand dna repair, holliday junction resolution, function in tumor suppression, reca/rad51-related protein family, dna lesions, structural specific endonucleases, rad51 family, cellular responses to replication fork failure, brc motif]] \n", - " FA-1 [[GO:0006281, GO:0035825, monoubiquitination, holliday junction resolution, rad51 binding]] \n", - " HALLMARK_ADIPOGENESIS-0 [[GO:0006629, GO:0006633, GO:0022900, GO:0005739, MESH:D000975, GO:0045333, MESH:D010084, acyltransferase, carboxylase, acyl-coenzyme a synthetase, ubiquitin protease, MESH:C021451, MESH:D010743, oxidoreductase, plasma lipase, hydratase]] \n", - " HALLMARK_ADIPOGENESIS-1 [[GO:0005515, transcription regulation, atpase, MESH:D020558, transcript processing, protein transduction, MESH:D014451, GO:0044237, energy production, GO:0006508]] \n", - " HALLMARK_ALLOGRAFT_REJECTION-0 [[immune/cytokine responses, GO:0006412, GO:0006351, cell surface signaling, receptor activation, MESH:D054875, MONDO:0002123, GO:0005524]] \n", - " HALLMARK_ALLOGRAFT_REJECTION-1 [[GO:0006412, cellular regulation, GO:0008152, cell signaling, GO:0006351, immunoregulation, stability, GO:0005515, GO:0016310, GO:0010467, g-protein coupled receptor, transmembrane protein, t-cell development]] \n", - " HALLMARK_ANDROGEN_RESPONSE-0 [[MESH:D011494, GO:0000981, GO:0005530, adhesion molecule, GO:0016538, MESH:D016601, protein tyrosine phosphatase, g protein, serine/threonine protein kinase, MESH:D008565, MESH:D006657, ubiquitin ligase, MESH:C052123, microtubule-associated protein, atp-binding cassette, alpha/beta-hydrolase, integrin alpha-chain, signal transducion, protein inhibitor of activated stat]] \n", - " HALLMARK_ANDROGEN_RESPONSE-1 [[GO:0008283, GO:0006351, GO:0007165, structural components, metabolism of proteins, GO:0006629, GO:0005975, GO:0007155, binding activity, GO:0010467, GO:0003677, MESH:D011494, oxidoreductase, anchoring kinase to microtubules, GO:0005102, molecule transport, MESH:D010455]] \n", - " HALLMARK_ANGIOGENESIS-0 [[this is a list of genes involved in a variety of pathways and processes related to cell adhesion, GO:0040007, GO:0008152, and other physiologic functions. the terms “cell adhesion”, “cell signaling”, “extracellular matrix”, “transcriptional regulation”, and “cell cycle progression and differentiation” are all enriched among this group of genes. a hypothesis of the underlying biological mechanism at work is that these genes work together to promote cell growth and regulation, that many of these genes interact to achieve greater cellular complexity]] \n", - " HALLMARK_ANGIOGENESIS-1 [[GO:0007155, extracellular matrix remodeling, GO:0007165, protease inhibition, transcriptional regulation]] \n", - " HALLMARK_APICAL_JUNCTION-0 [[GO:0005207, GO:0007155, calcium-dependent proteins, MESH:D008565, intronless proteins, intracellular scaffolding proteins, fibrillin proteins, signaling receptors, MESH:D051193, MESH:D003598, tubulin proteins, type ii membrane proteins, MESH:D006023]] \n", - " HALLMARK_APICAL_JUNCTION-1 [[GO:0007155, GO:0007165, actin binding and assembly, membrane localization, ecm protein binding and assembly]] \n", - " HALLMARK_APICAL_SURFACE-0 [[GO:0007160, GO:0007165, MESH:D008565, transcriptional coactivation, signal recognition, GO:0055085, GO:0006898]] \n", - " HALLMARK_APICAL_SURFACE-1 [[GO:0007160, cell-matrix interactions, carbohydrate binding activity, GO:0007155, GO:0038023, GO:0007165, GO:0008284, GO:0048681, GO:0030506, protein tyrosine kinase, sh2 domain binding activity, sh3 domain binding activity]] \n", - " HALLMARK_APOPTOSIS-0 [[GO:0006915, cytoplasmic signaling, transcriptional regulation, GO:0005515, cellular organization]] \n", - " HALLMARK_APOPTOSIS-1 [[cell death processes, GO:0023052, cytoplasmic proteins, MESH:M0015044, MESH:D015533, MESH:D004798, toxin removal, GO:0005102]] \n", - " HALLMARK_BILE_ACID_METABOLISM-0 [[atp-binding, GO:0006810, GO:0004768, MESH:D010084, enzyme catalysis, GO:0000981]] \n", - " HALLMARK_BILE_ACID_METABOLISM-1 [[GO:0015031, GO:0006412, GO:0006629, MESH:D010084, hormone regulation, transcription regulation, GO:0006805, calcium binding, GO:0005524, MESH:D005982, GO:0008203, MESH:M0011631, sulfate conjugation, 2-hydroxyacid oxidase, MESH:D000214, MESH:D000215, coenzyme a ligase, natriuretic peptide, peroxisome biogenesis, tgf-beta ligand, adrenal steroid synthesis, nuclear receptor, copper zinc binding, GO:0050632, MESH:D012319, gamma-glut]] \n", - " HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 [[MESH:D008565, MONDO:0018815, acetoacetyl-coa thiolase, cytosolic enzyme, actin isoforms, activation transcription factor (creb), annexin family, fructose-biphosphate aldolase, immunoglobulin superfamily, g-protein coupled receptor (gpcr), homotetramer, hydratase/isomerase superfamily, MESH:C022503, mal proteolipid, MESH:M0476528, sre-binding proteins (srebp), peroxisomal enzyme, transmembrane 4 superfamily, transmembrane protein, multispan transmembrane protein, tetr]] \n", - " HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 [[GO:0006629, GO:0005543, GO:0004768, atp-binding cassette, GO:0016126, cytochrome p450 family proteins]] \n", - " HALLMARK_COAGULATION-0 [[complement system, GO:0007596, peptide hydrolysis, GO:0016485, inflammation regulation]] \n", - " HALLMARK_COAGULATION-1 [[matrix metalloproteinase, cysteine-rich protein, serine protease inhibitor, transforming growth factor-beta, MESH:D054834, guanine nucleotide-binding proteins, peptidase s1 family, integrin beta chain, MESH:D001779, dipeptidyl peptidase, vitamin k-dependent glycoprotein, vitamin k-dependent coagulation factor, regulator of complement activation, protein tyrosine kinase, MESH:D006904, iron-sulfur cluster scaffold, disulfide bridge, kunitz-type serine protease, MESH:D042962, MESH:D037601, g-protein coupled receptor, cytosolic peptidase, GO:0030165, basic leucine zipper, a disintegrin and metalloprote]] \n", - " HALLMARK_COMPLEMENT-0 [[cell signaling, cell structure/stability, GO:0008152, vitamin k/clotting, GO:0005856, GO:0005886, GO:0006954]] \n", - " HALLMARK_COMPLEMENT-1 [[protein production, cell surface glycoprotein regulation, GO:0006956, GO:0007165, heat shock protein, MESH:D003564, metalloproteinase, guanine nucleotide-binding protein, lysosomal cysteine protease, zinc finger protein, cysteine-aspartic acid protease, MESH:D001053, metallothionein.\\nmechanism: the genes may be involved in various signalling pathways to facilitate the regulation of cell surface glycoprotein as well as the production of proteins. cytidine deaminase, metalloproteinase, guanine nucleotide-binding protein and cysteine-aspartic acid protease are likely enzymes that the list of genes may be involved in. heat shock proteins and zinc finger proteins, in addition to apolipoproteins and metallothionein, may be involved in the regulation and transportation of cell proteins]] \n", - " HALLMARK_DNA_REPAIR-0 [[summary: this enrichment test provides evidence of a common biological mechanism underlying many genes in human genetics: dna repair, replication, and transcription.\\n\\nmechanism: the mechanism underlying this term enrichment is the need for accurate dna repair, replication, and transcription, which all require the co-ordinated efforts of many protein families, such as those encoded by the wd-repeat, MESH:D000262, argonaute, MESH:D000263, purine/pyrimidine phosphoribosyltransferase, b-cell receptor associated proteins, MESH:C056608, clp1, GO:0016538, MESH:C010098, dna helicase, MESH:M0251357, general transcription factor (gtf) ii, MESH:D005979, histone-fold proteins, mhc, MESH:C110617, GO:0005662, saccharomyces cerevisiae rad52, schizosaccharomyces pombe rae1, splicing factor (sf3a), GO:0003734, MESH:D011988, transcription factor b (tfb4), trans]] \n", - " HALLMARK_DNA_REPAIR-1 [[GO:0003677, transcription regulation, GO:0006281, GO:0000394, GO:0006397, GO:0003723, GO:0003682, GO:0019899, GO:0003684, general transcription factor, transcription/repair factors, MESH:M0006668, hypothalamic hormone receptor binding, GO:0004016, nuclear cap-binding protein, GO:0016567, transcription initiation, dna polymerase, GO:0006605]] \n", - " HALLMARK_E2F_TARGETS-0 [[GO:0006260, GO:0006281, GO:0006351, GO:0003682, GO:0016569, GO:0051726, ran binding, GO:0000808, atpase, GO:0016538, cyclin-dependent kinase, polycomb, dead box protein, gtpase activating protein, GO:0042393, GO:0003723, nucleolar protein, ubiquitously expressed protein, smc subfamily protein, pp2c family, elongation of primed dna template synthesis, dna interstrand cross-linking, import of proteins into nucleus, MESH:D004264, tumor suppressor protein, MESH:D051981, ubr box protein, p80 autoantigen]] \n", - " HALLMARK_E2F_TARGETS-1 [[GO:0003676, GO:0006260, GO:0036211, GO:0006259, GO:0000785, GO:0051726, GO:0016570, protein assembly and disassembly]] \n", - " HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 [[cell signaling, extracellular matrix formation, GO:0007155, connective tissue formation, GO:0001525, metabolic regulation, MESH:D016207, tissue repair]] \n", - " HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 [[MESH:D016326, GO:0005202, MESH:D007797, MESH:D005353, MESH:D014841, integrin, MESH:D016189, fibulin proteins]] \n", - " HALLMARK_ESTROGEN_RESPONSE_EARLY-0 [[GO:0042277, membrane structure modification, GO:0003677, GO:0006631, GO:0051427, signalling transcription, gtpase activation, adenylate cyclase modulation, GO:0016301, GO:0006897, glycoprotein production, GO:0019838, GO:0016570, GO:0006644, zinc-binding]] \n", - " HALLMARK_ESTROGEN_RESPONSE_EARLY-1 [[dna-binding, GO:0005515, GO:0043687, GO:0007165, metabolic activity]] \n", - " HALLMARK_ESTROGEN_RESPONSE_LATE-0 [[MESH:D011494, GO:0000981, GO:0005509, MESH:D054794, hormone receptors, GO:0007155, GO:0006457, GO:0010467]] \n", - " HALLMARK_ESTROGEN_RESPONSE_LATE-1 [[membrane processes, transmembrane processes, GO:0006811, GO:0007155, GO:0016049, GO:0008152, MESH:D011506, GO:0023052, processing, MESH:D048788, reparative pathways, immune pathways, disease pathways]] \n", - " HALLMARK_FATTY_ACID_METABOLISM-0 [[GO:0006732, GO:0006754, GO:0006096, oxidative decarboxylation, GO:0006631, nad/nadh-dependent oxidation, pyridine nucleotide oxidation, amino acid oxidation, glycerol-3-phosphate dehydrogenase activity, GO:0022900, MESH:D042942, nadp-dependent oxidation, l-amino acid oxidation, endogenous and xenobiotic n-methylation, conversion of pyruvate to acetyl coa, 2-oxoglutarate catabolism, galectin family activity]] \n", - " HALLMARK_FATTY_ACID_METABOLISM-1 [[GO:0008152, fatty acid transport and processing, oxidoreductase, GO:0009653, GO:0030154, GO:0030674]] \n", - " HALLMARK_G2M_CHECKPOINT-0 [[GO:0006325, GO:0051726, GO:0016570, MESH:D011494, atp-binding, rna-binding]] \n", - " HALLMARK_G2M_CHECKPOINT-1 [[GO:0051301, GO:0003677, GO:0003723, transcriptional regulation, chromatin restructuring, GO:0004672, GO:0051169, cytoplasmic transport, nucleic acid metabolism, GO:0016570, GO:0016310, GO:0032259, MESH:D000107, MESH:D054875]] \n", - " HALLMARK_GLYCOLYSIS-0 [[GO:0016310, GO:0009100, GO:0007155, transcription regulation, GO:0009117, energy production]] \n", - " HALLMARK_GLYCOLYSIS-1 [[GO:0008152, GO:0005975, GO:0048468, GO:0009100, GO:0006629, GO:0015031, nucleic acid metabolism, GO:0009117, GO:0070085, ferric ion binding, GO:0016491, GO:0003677, GO:0000988, GO:0031545, GO:0004736]] \n", - " HALLMARK_HEDGEHOG_SIGNALING-0 [[GO:0007155, GO:0007165, GO:0000981, MESH:D018121, MESH:D039921, rho-gtpase-activating protein, transmembrane protein, GO:1902911, transduction pathway, growth factor, g protein-coupled receptor, cadherin superfamily, basic helix-loop-helix, phosphoprotein, zinc finger protein, cytoplasmic domain, dna-binding, GO:0005886, neurotransmitter, MESH:D057057, coiled-coil, pdz binding motif, cholesterol moiety, fibronectin-like repeat, MESH:D000070557, GO:0016604, MESH:D006655, collapsin response mediator, tripartite motif, hedgehog signaling.\\nmechanism: the genes seem to be primarily involved in regulating signal transduction pathways that control cell migration, proliferation and differentiation, by modulating transcription, cell adhesion and receptor activities. the proteins encoded by these genes interact]] \n", - " HALLMARK_HEDGEHOG_SIGNALING-1 [[GO:0007155, GO:0007165, neuron signalling, regulatory activity, GO:0009987, GO:0040007, differentiation, motility, GO:0032502]] \n", - " HALLMARK_HEME_METABOLISM-0 [[GO:0005515, GO:0000910, transcription regulation, metabolic & enzymatic function, cell cortex formation, GO:0006810, GO:0016310, MESH:D000107, protein formation & modification]] \n", - " HALLMARK_HEME_METABOLISM-1 [[GO:0006351, GO:0003723, post-transcriptional regulation, GO:0006096, GO:0006090, GO:0006749, GO:0006508, transcriptional regulation, MESH:D054875, GO:0003677, MESH:D006655, GO:0006915, cytoskeletal protein, atp-binding, GO:0048870, ubiquitin specific protease, MESH:D015220, voltage-gated chloride channel, GO:0004384, GO:0023052, GO:0051726, cation transporters]] \n", - " HALLMARK_HYPOXIA-0 [[GO:0006096, GO:0016310, GO:0004672, GO:0006508, GO:0085029, transcription regulation, GO:0051726, GO:0097009, GO:0006954, cell-cell communication, oxidative stress response]] \n", - " HALLMARK_HYPOXIA-1 [[GO:0006915, GO:0016310, MESH:D011494, GO:0005515, GO:0006351, GO:0031005, glycolytic enzyme, carboyhydrate binding, cell binding, GO:0042157, GO:0007165, UBERON:2000098, GO:0040007]] \n", - " HALLMARK_IL2_STAT5_SIGNALING-0 [[GO:0051726, receptor signaling, MESH:D008565, GO:0000981]] \n", - " HALLMARK_IL2_STAT5_SIGNALING-1 [[GO:0007165, protein homodimerization, GO:0005525, GO:0003676, GO:0055085, GO:0004672, GO:0007049, GO:0006955, GO:0006915]] \n", - " HALLMARK_IL6_JAK_STAT3_SIGNALING-0 [[MESH:D016207, GO:0016049, GO:0048468, transmembrane proteins, MESH:D011494, GO:0000981, cell cycle progression]] \n", - " HALLMARK_IL6_JAK_STAT3_SIGNALING-1 [[the list of gene summaries reveals a group of genes involved in cell trafficking, GO:0007165, GO:0007155, ligand binding, and regulation of the immune response. enriched terms include cytokine, chemokine, MESH:D007378, receptor, GO:0007155, ligand binding, GO:0007165, and regulation of the immune response.\\n\\nmechanism: the mechanism involving these genes involve ligand binding to cytokine, chemokine, or other receptors, resulting in the activation of intracellular pathways leading to signal transduction, GO:0007155, regulation of the immune response]] \n", - " HALLMARK_INFLAMMATORY_RESPONSE-0 [[GO:0005102, cytokine signalling, GO:0016049, cellular function regulation, immune signalling, inflammation regulation, GO:0051726, apoptosis coordination]] \n", - " HALLMARK_INFLAMMATORY_RESPONSE-1 [[interactions, GO:0023052, MESH:D008055, GO:0000981, MESH:D016207, MESH:D006728, MESH:D021381, receptors, GO:0007165]] \n", - " HALLMARK_INTERFERON_ALPHA_RESPONSE-0 [[protein-binding, subunit-binding, rna-binding, transcriptional regulation, GO:0007165, GO:0006955, ligand binding, GO:0032991, GO:0036211]] \n", - " HALLMARK_INTERFERON_ALPHA_RESPONSE-1 [[transcriptional regulation, GO:0008181, MESH:D010447, cytoplasmic proteins, antiviral, MESH:M0369740, GO:0009165, chemokine receptor, dna-binding, rna-binding, lipid-binding, protein adp-ribosylation, GO:0016567, GO:0048255, GO:0016556, GO:0006479, gtp-metabolizing, GO:0008283, GO:0006955, GO:0006952]] \n", - " HALLMARK_INTERFERON_GAMMA_RESPONSE-0 [[immune regulation, GO:0003677, GO:0003723, GO:0016567, anti-viral response, cytokine signaling, GO:0006954]] \n", - " HALLMARK_INTERFERON_GAMMA_RESPONSE-1 [[GO:0006954, immune cell signaling and development, immune regulation, GO:0044237, regulation of innate and adaptive immunity, metabolic and transcriptional regulation, GO:0003677, GO:0003723]] \n", - " HALLMARK_KRAS_SIGNALING_DN-0 [[protein-binding, transcriptional regulation, GO:0007155, cell membrane channel activity, protein metabolism/modification, receptor signalling]] \n", - " HALLMARK_KRAS_SIGNALING_DN-1 [[MESH:D011506, GO:0016049, cellular development, MESH:D009068, GO:0001508, calcium binding, GO:0005496, GO:0008152, GO:0006351, GO:0005488, MESH:C062738, GO:0005562, g proteins, dna-binding]] \n", - " HALLMARK_KRAS_SIGNALING_UP-0 [[GO:0007155, regulation of growth factors, cytokine regulation, calcium activation, transcriptional regulation]] \n", - " HALLMARK_KRAS_SIGNALING_UP-1 [[GO:0003677, MESH:D015533, cytokine regulation, GO:0008083, GO:0005515, GO:0007165, transmembrane protein activity, GO:0004930, GO:0003723, GO:0003924, GO:0005509, GO:0016571, glutamine-fructose-6-phosphate transaminase activity, cell growth control, GO:0019725, GO:0016491]] \n", - " HALLMARK_MITOTIC_SPINDLE-0 [[cytoskeletal organization, GO:0003677, microtubule organization, gtpase regulation, centrosome interaction, chromatin structure, protein homodimerization]] \n", - " HALLMARK_MITOTIC_SPINDLE-1 [[MESH:D020558, nucleotide exchange regulation, cellular signaling, GO:0006338, cytoskeleton structure, GO:0006260, GO:0007155, GO:0003779, actin regulation]] \n", - " HALLMARK_MTORC1_SIGNALING-0 [[GO:0006412, GO:0015031, protein signaling, GO:0008152, GO:0010467]] \n", - " HALLMARK_MTORC1_SIGNALING-1 [[GO:0005515, MESH:D054875, GO:0006351, GO:0003824, GO:0006457, chaperoning, GO:0051726, GO:0006629, GO:0046323, cytoskeleton formation]] \n", - " HALLMARK_MYC_TARGETS_V1-0 [[GO:0006351, GO:0006412, GO:0003729, MESH:D054657, MESH:D000072260, GO:0043687, cytoplasmic proteins, MESH:M0015044, GO:0003677, GO:0032508, GO:0005652, GO:0005681]] \n", - " HALLMARK_MYC_TARGETS_V1-1 [[GO:0009299, GO:0042254, GO:0006412, MESH:D049148, GO:0003723, GO:0043687, GO:0045292, polymerase, GO:0006913, MESH:D054875, GO:0006457, 14-3-3 family proteins]] \n", - " HALLMARK_MYC_TARGETS_V2-0 [[GO:0003723, ribosomal biogenesis, GO:0008283, GO:0006335, GO:0007165, cell cycle progression, GO:0003682]] \n", - " HALLMARK_MYC_TARGETS_V2-1 [[GO:0006351, rna binding activity, GO:0006457, cell cycle progression, GO:0006281, protein homodimerization, GO:0006468, GO:0065003, protein kinase/phosphatase activity, mitochondrial mrna processing. mechanism: this list of genes encodes proteins which work together to regulate key cellular activities such as dna replication, transcription, cell cycle progression, and rna processing. these proteins can either complex together or work in tandem to form kinase/phosphatase complexes, which control phosphorylation of key substrates and regulate protein folding to ensure proper protein function. these proteins also interact with dna to regulate genomic activities such as dna replication, transcription, and repair processes]] \n", - " HALLMARK_MYOGENESIS-0 [[motor protein activity, GO:0019722, GO:0006936, transcriptional regulation, intracellular fatty acid-binding, ligand binding, MESH:D007473, GO:0005884, MESH:D008565, regulation of transcription, phosphorylation of proteins]] \n", - " HALLMARK_MYOGENESIS-1 [[MESH:M0496924, protein regulation, ion channeling, cellular transport, GO:0006629, GO:0010468, neurotransmitter signaling, small molecules, large molecules]] \n", - " HALLMARK_NOTCH_SIGNALING-0 [[cell fate decisions, GO:0007219, GO:0007165, wnt signalling pathway, cell-cell interaction, GO:0016567, GO:0006355, protein ligase activity, GO:0006468]] \n", - " HALLMARK_NOTCH_SIGNALING-1 [[notch signaling, GO:0016567, cell-cycle regulation, protein breakdown and turnover, intracellular signalling pathways, cell fate]] \n", - " HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 [[GO:0005739, MESH:D004798, MESH:D010088, MESH:D010088, GO:0006754]] \n", - " HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 [[oxidative decarboxylation, MESH:D010088, MESH:D010084, GO:0006754, mitochondrial respiration, GO:0008152, MESH:D003580, MESH:D000214, pyruvate dehydrogenase, MESH:D005420, hydratase/isomerase, leucine-rich protein, 3-hydroxyacyl-coa]] \n", - " HALLMARK_P53_PATHWAY-0 [[GO:0007049, GO:0006351, GO:0023052, GO:0006412, GO:0065007, GO:0042592]] \n", - " HALLMARK_P53_PATHWAY-1 [[GO:0051726, GO:0016049, GO:0006915, GO:0007165, GO:0006281, transcriptional regulation, chromatin structure, tumor suppression, enzymatic activity, GO:0000988, GO:0004725, GO:0003925]] \n", - " HALLMARK_PANCREAS_BETA_CELLS-0 [[analysis of the human genes abcc8, akt3, chga, dcx, dpp4, elp4, foxa2, foxo1, g6pc2, gcg, gck, hnf1a, iapp, UBERON:0002876, insm1, isl1, lmo2, mafb, neurod1, neurog3, nkx2-2, nkx6-1, pak3, pax4, pax6, pcsk1, pcsk2, pdx1, pklr, scgn, sec11a, slc2a2, spcs1, srp14, srp9, srprb, UBERON:0035931, stxbp1, syt13, vdr was performed to determine commonalities in gene function. term enrichment indicated a commonalty in genes that are involved in the regulation of glucose and insulin metabolism, GO:0008283, differentiation and apoptosis, as well as glycogen synthesis and glucose uptake. additionally, many of the genes are involved in the development of neural tissues and the regulation of gene transcription. the underlying biological mechanism could involve alterations in the phosphorylation of proteins and signaling pathways,]] \n", - " HALLMARK_PANCREAS_BETA_CELLS-1 [[this analysis identifies the common functions of 18 human genes: dpp4, scgn, pklr, pax4, neurod1, srprb, srp14, isl1, insm1, pak3, pax6, elp4, dcx, iapp, lmo2, neurog3, gck, stxbp1, nkx2-2, pdx1, UBERON:0035931, pcsk1, nkx6-1, UBERON:0002876, pcsk2, spcs1, g6pc2, foxo1, sec11a, vdr, foxa2, slc2a2, mafb. they are related to metabolic regulation (glucose, GO:0016088, MESH:D004837, citrate), developmental regulation (neural tissues, UBERON:0001264, UBERON:0002107, lymph nodes), signal transduction (g proteins, ace, atp binding proteins) and hormone regulation related (somatostatin, GO:0016088, vitamin d3). these factors likely work in concert to control and maintain metabolic parameters throughout the body. mechanism: these genes act through various methods including transcriptional regulation, protein interactions, protein cleavage, signaling casc]] \n", - " HALLMARK_PEROXISOME-0 [[MONDO:0018815, an antioxidant enzyme, a hormone binding protein, a nuclear receptor transcription factor, a fatty acid desaturase, a carnitine acyltransferase, an isocalate dehydrogenase, a peroxisomal membrane protein, MESH:D005182, antioxidant enzyme, hormone binding protein, nuclear receptor transcription factor, GO:0004768, carnitine acyltransferase, isocalate dehydrogenase, peroxisomal membrane protein, and fad-dependent oxidoreductase.\\n\\nmechanism: many of the genes are involved in regulating the production and movement of lipids and fatty acids, as well as the synthesis of hormones, MESH:D000305, and signalling receptors. the underlying biological mechanism is that these genes act as regulators of metabolic pathways, ensuring that their respective pathways are functioning correctly and that metabolites are transported correctly]] \n", - " HALLMARK_PEROXISOME-1 [[GO:0006629, GO:0006635, GO:0006281, transcription and replication, MESH:D018384, GO:0006536, GO:0005502, GO:0008202]] \n", - " HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 [[GO:0016310, GO:0006412, mrna expression, GO:0005515, cell signalling, MESH:D054875, protein phosphatase]] \n", - " HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 [[GO:0007165, MESH:D011494, GO:0004707, MONDO:0008383, gpcr, GO:0016791, MESH:D020662, endoplasmic reticulum chaperone protein]] \n", - " HALLMARK_PROTEIN_SECRETION-0 [[GO:0005480, GO:0006897, GO:0006887, intracellular trafficking, MESH:D001678, MESH:D008565, GO:0005906, MESH:D020558, GO:0005794, GO:0005484]] \n", - " HALLMARK_PROTEIN_SECRETION-1 [[GO:0003924, snare binding activity, GO:0005484, phosphoinositide-binding, coatomer protein complex, MESH:D052067, protein kinase binding activity, adaptor complexes, atpases associated with diverse cellular activities, snare recognition molecules, gold domain, GO:0030136, transmembrane 4 superfamily, GO:0070273, sec7 domain, membrane mannose-specific lectin, signal-transducing adaptor molecule, identical protein binding activity]] \n", - " HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 [[MONDO:0018815, copper chaperone, MESH:D002374, GO:0004861, hypoxia inducible factor (hif), nucleotide excision repair pathway, GO:0004672, GO:0009487, MESH:D005979, MESH:D009195, MESH:D010758, phosphofructokinase, MESH:D054464, GO:0050115, arginine/serine-rich splicing factor, iron/manganese superoxide dismutase, GO:0016491, germinal centre kinase iii (gck iii) subfamily, thioredoxin (trx) system]] \n", - " HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 [[GO:0016049, GO:0007049, GO:0006351, redox regulation, MESH:D018384, MESH:D005721, hydroxylase, protease, free-radical scavenging, protein phosphatase]] \n", - " HALLMARK_SPERMATOGENESIS-0 [[protein binding activity, GO:0003714, dna binding activity, rna binding activity, zinc ion binding activity, GO:0004596, serine/threonine-protein kinase activity, GO:0004016, snare binding activity, clathrin binding activity, myosin light chain binding activity, double-stranded dna binding activity, phosphatidic acid phosphohydrolase activity, ubiquitin-protein ligase activity, rna polymerase binding activity, GO:1990817, GO:1990817, GO:0060090, phosphatase binding activity, atp-ases associated activity, GO:0044183, GO:0016165, adp-ribosylation factor-like activity]] \n", - " HALLMARK_SPERMATOGENESIS-1 [[GO:0006457, transcriptional regulation, GO:0007165, GO:0051726, chromatin structure and nuclear envelop function, cell adhesion and motility, GO:0008152, GO:0016567, detection and binding, enzymatic activity, GO:0042311]] \n", - " HALLMARK_TGF_BETA_SIGNALING-0 [[transmembrane proteins, receptor signaling pathways, transcription regulation, cell signaling, GO:0007155, GO:0016049, tgf-beta superfamily, MESH:D010749, ubiquitin ligases, tight junction adaptors]] \n", - " HALLMARK_TGF_BETA_SIGNALING-1 [[transmembrane serine/threonine kinases, transcriptional repressors, transforming growth factor (tgf)-beta superfamily, rho family of small gtpases, smad family, c2h2-type zinc finger domains, MESH:M0460357, caax geranylgeranyltransferase, smad interacting motif (sim), homeodomain-interacting protein kinase, MESH:D004122, transforming growth factor-beta (tgfb) signal transduction, MESH:D018398, MESH:D054645, protein folding and trafficking]] \n", - " HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 [[GO:0006351, cytokine, inflammatory, UBERON:2000098, GO:0006915, cell signalling, receptor regulation, GO:0003924, GO:0003723]] \n", - " HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 [[MESH:D016207, MESH:D018925, MESH:D010770, GO:0000981, MESH:D016212, nf-kappa-b, myc/max/mad, jagged 1, stat-regulated pathways, MESH:D008074, MESH:M0496065]] \n", - " HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 [[rna-binding, protein-binding, GO:0019538, GO:0009058, GO:0044183, GO:0000981, GO:0006457]] \n", - " HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 [[GO:0003723, GO:0005783, transcriptional regulation, GO:0006457, GO:0140597, mrna decapping, MESH:M0465019, GO:0030163, MESH:D021381]] \n", - " HALLMARK_UV_RESPONSE_DN-0 [[cellular response regulation, GO:0007165, transcriptional regulations, MESH:D011956, GO:0016310, calcium binding, MESH:D011494, transmembrane proteins, protein tyrosine kinases, MESH:D017027, MESH:M0015044, protein inhibitor of activated stats, integrin beta, annexin family, adp-binding cassette family, MESH:D020690, arfaptin family, wd repeat proteins, maguk family, camp-dependent pathways, MESH:D000071377, MESH:D008869, pak family, MESH:D015220, mitogen-responsive phosphoproteins, nuclear histone/protein, celf/brunol family, four-and-a-half-lim-only proteins]] \n", - " HALLMARK_UV_RESPONSE_DN-1 [[GO:0007165, MESH:D016326, cellular adhesion, GO:0000981, MESH:D011494, MESH:D020558, camp, calcium-dependent phospholipid binding protein, MESH:D011505, MESH:D017868, scaffolding protein, MESH:D020690, MESH:D010711, protein tyrosine phosphatase, rho-like gtpase, calcium-activated bk channel, cyclin-dependent kinase, n6-methyladenosine-containig protein, helix-loop-helix proteins, MESH:D016601, atpase, guanine nucleotide-binding protein, cytoplasmic surface protein, serine protease inhibitor, protein inhibitor of activated stat, GO:0004384, mitogen-responsive]] \n", - " HALLMARK_UV_RESPONSE_UP-0 [[cell regulation, GO:0055085, metabolic catabolism, transcription support, GO:0006468, non-classical heavy chain, GO:0020037, GO:0007165, cytoskeleton formation, GO:0030163, cell signaling, GO:0006412, GO:0010467]] \n", - " HALLMARK_UV_RESPONSE_UP-1 [[GO:0005515, GO:0005525, GO:0005215, reactive catalysis, cell signaling, membrane-associated functions]] \n", - " HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 [[wnt signalling pathway, transmembrane glycoprotein, MESH:D006655, GO:0000981, GO:0007219, GO:0005515, GO:0007165, GO:0006511, transcriptional regulation, dna replication and repair]] \n", - " HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 [[wnt signaling, notch signaling, hedgehog signaling, transcriptional regulation, cell cycle progression, developmental events, dna replication and repair, transcriptional silencing, GO:0043161]] \n", - " T cell proliferation-0 [[GO:0004888, calmodulin binding activity, GO:0061630, GO:0033192, GO:0004721, GO:0004725, GO:0004672, MESH:D015533, guanine nucleotide exchange activity, ligand binding activity]] \n", - " T cell proliferation-1 [[transcriptional regulation, cellular signaling pathways and processes, GO:0016049, differentiation, GO:0006950, GO:0006955, protein folding and trafficking, MESH:D051192, transmembrane proteins, receptor tyrosine kinases, ubiquitin e3 ligases, MESH:D020134, cgmp-binding phosphodiesterase]] \n", - " Yamanaka-TFs-0 [[this set of genes is involved in embryonic development, stem cell pluripotency, stem-cell maintenance, and dna damage response. commonly enriched terms include cell cycle regulation, transcription regulation, GO:0006915, cellular transformation, and dna damage repair. mechanism:these genes control critical functions of cell cycle progression, gene transcription, and dna repair, providing the necessary foundation for the development of the organism. these pathways provide the structural and biochemical features of embryonic development, maintenance of stem cells and pluripotency, response to cellular damage]] \n", - " Yamanaka-TFs-1 [[GO:0000981, MESH:D047108, stem cell maintenance, MESH:D063646, GO:0030154]] \n", - " amigo-example-0 [[GO:0007155, MESH:D016326, MESH:M0023728, cellular communication, GO:0042592, GO:0042060, GO:0006915, motility, GO:0001525]] \n", - " amigo-example-1 [[GO:0007219, osteoclast attachment/mineralized bone matrix, jagged 1/notch 1 signaling, GO:0007155, GO:0006915]] \n", - " bicluster_RNAseqDB_0-0 [[GO:0055085, growth factor regulation, calcium regulation, transcription regulation, MESH:D007473, calcium-dependent processes, protein binding activity, chromatin binding activity, gtpase activating protein binding activity, histone binding activity, dna-binding activity, sequence-specific double-stranded dna binding activity, GO:0000988]] \n", - " bicluster_RNAseqDB_0-1 [[this list of genes is involved predominantly in processes related to binding activities, dna-binding transcription factor activities, chromatin binding activities, and protein domain-specific binding. the underlying biological mechanism involves pathways that regulate cell morphology and cytoskeletal adaptor proteins. the enriched terms include: binding activity, GO:0003700, chromatin binding activity, protein domain-specific binding activity, cell morphology, MESH:D051179]] \n", - " bicluster_RNAseqDB_1002-0 [[GO:0007165, protein-protein interactions, MESH:D004734, GO:0051015, troponin binding, GO:0005523, GO:0051219, GO:0032515, GO:0043531, atp binding. mechanism: these genes are involved in pathways of signal transduction, protein-protein interactions, and energy metabolism, which lead to muscle contraction and tissue development. activation of these pathways leads to calcium release, which in turn activates contractile proteins such as troponin, tropomyosin, and actin. these proteins act together to promote muscle contraction and cytoskeletal structure]] \n", - " bicluster_RNAseqDB_1002-1 [[MESH:D024510, actin and tropomyosin binding, calcium- and energy-regulation, ion channeling, negative regulation of cytokine signaling pathways, GO:0033173]] \n", - " endocytosis-0 [[GO:0006897, GO:0015031, GO:0051639, endoplasmic reticulum and recycling endosome membrane organization, GO:0044351, GO:0016043, intracellular signaling, GO:0051260]] \n", - " endocytosis-1 [[GO:0015031, GO:0006897, GO:0006898, GO:0051260, GO:0007155, GO:0048870, amino acid residues, MESH:D054875, GO:0015908, cytoskeletal reorganization, GO:0016192, signaling complex regulation, GO:0140014, GO:0006919]] \n", - " glycolysis-gocam-0 [[GO:0006096, GO:0016310, MESH:D006593, glucose phosphate isomerase, phosphofructokinase, MESH:D005634, fructose-1,6-bisphosphate, MESH:D014305, glyceraldehyde-3-phosphate dehydrogenase, MESH:D010736, MESH:D011770, MESH:D010751]] \n", - " glycolysis-gocam-1 [[muscle maturation, MESH:D024510, GO:0001525, GO:0006096, MONDO:0003664, MONDO:0002412, plasmin regulation]] \n", - " go-postsynapse-calcium-transmembrane-0 [[GO:0006816, calcium ion regulation, postsynaptic ion channel, GO:0005892, glutamate receptor channel, g protein-coupled receptor, plasma membrane protein, ligand-gated ion channel]] \n", - " go-postsynapse-calcium-transmembrane-1 [[calcium ion regulation, GO:0006816, n-methyl-d-aspartate receptor family, MESH:C413185, MESH:D011954, p-type primary ion transport atpases]] \n", - " go-reg-autophagy-pkra-0 [[GO:0043539, protein serine/threonine kinase binding activity, GO:0004860, GO:0005085, GO:0032008, GO:0010605, GO:0032956, GO:0032006, GO:0016241, regulation of nf-kappab activation, GO:0001558, regulation of cell survival, GO:0038187, GO:0006281, GO:0045087]] \n", - " go-reg-autophagy-pkra-1 [[this term enrichment test looked at a list of human genes together with their functions. it found that the genes have functions related to cell cycle regulation, GO:0007165, GO:0043170, protein kinase binding and regulating chromatin remodeling and transcription. the enriched terms include cell cycle regulation, GO:0007165, GO:0043170, GO:0019901, GO:0016310, chromatin remodeling and transcriptional regulation.\\n\\nmechanism: the genes in this list are involved in processes such as cell cycle regulation, GO:0007165, GO:0043170, GO:0019901, phosphorylation and chromatin remodeling and transcription, which are interconnected. these processes all depend on the activity of various protein kinases and their activation by various components, including snca, MESH:D053148, trib3, ccny, pik3ca, akt1, nod2, kat5, rptor, smcr8, mlst8, tab2, hspb1, irgm, GO:0033868, cdk5r1 and other proteins. they interact and cooperate with each other to form pathways and complexes responsible for cell cycle regulation and activation or inhibition of specific genes. ph]] \n", - " hydrolase activity, hydrolyzing O-glycosyl compounds-0 [[GO:0016798, GO:0005980, GO:0006516, GO:0051787, GO:0036503, glycosaminoglycan hydrolysis, heparan sulfate hydrolysis, cell surface hyaluronidase.\\nhpyothesis: the genes listed serve key roles in the degradation of polysaccharides and glycoproteins, the recognition of misfolded proteins and their subsequent degradation by endoplasmic reticulum-associated degradation, the hydrolysis of glycosaminoglycans, and the hydrolysis of heparan sulfate for the maintenance of cell proteins and structure]] \n", - " hydrolase activity, hydrolyzing O-glycosyl compounds-1 [[glycohydrolase enzymes, glycosaminoglycans (gag]] \n", - " ig-receptor-binding-2022-0 [[antigen binding activity, immunoglobulin receptor binding activity, GO:0002377, GO:0002250, protein homodimerization]] \n", - " ig-receptor-binding-2022-1 [[immunoglobulin receptor binding activity, GO:0002253, antigen binding activity, GO:0042803, immunoglobulin lambda-like polypeptides, preb cell receptor, src family of protein tyrosine kinases, c-type lectin/c-type lectin-like domain]] \n", - " meiosis I-0 [[GO:0004519, bcl-2 homology domain 3 binding, GO:0003682, GO:0003677, GO:0003678, GO:0003697, 3'-5' exode]] \n", - " meiosis I-1 [[meiotic recombination, GO:0006281, GO:0007059, double-strand dna break repair, homologous chromosome pairing, dna binding activity, GO:0051289]] \n", - " molecular sequestering-0 [[this list of genes encodes proteins involved in a range of cellular processes such as cell cycle progression, GO:0006897, iron storage and regulation, cellular response to stress and inflammation, GO:0006915, transcriptional regulation, GO:0046907, GO:0016567, and toxic metal and cytosolic signaling. enriched terms include protein binding, lipid and hormone transport, GO:0003779, GO:0003724, GO:0006511, cell cycle progression, and negative regulation of nitrogen compound metabolic process. mechanism: these genes are involved in a wide range of processes related to regulating cell growth, GO:0032502, and homeostasis. they play a role in pathways such as the cell cycle, GO:0006915, inflammatory metabolic processes]] \n", - " molecular sequestering-1 [[GO:0005515, MESH:D015533, GO:0008152, MESH:D007109, GO:0006915, GO:0007049, GO:0016310]] \n", - " mtorc1-0 [[GO:0006412, GO:0015031, protein signaling, GO:0008152, GO:0010467]] \n", - " mtorc1-1 [[metabolic reactions, GO:0051726, energy production, MESH:D011494, GO:0016791, MESH:D003577, MESH:D000604, peptidase c1 family, GO:0031545, ion transporter, ubiquitin-like proteases, ubiquitin ligases, serine/threonine protein kinases, glyceraldehyde-3-phosphate dehydrogenase, nadp-dependent dehydrogenases, rna binding protein, GO:0016467, pyruvate dehydrogenase, MESH:D012321, GO:0016538, MESH:D005634, heat shock protein, hetero trimeric co-factors, MESH:D050603, MESH:D000263, MESH:D013762, MONDO:0008090]] \n", - " peroxisome-0 [[this set of genes are enriched for terms related to peroxisomal biogenesis and peroxisomal protein import. the aaa atpase family, peroxisomal membrane proteins, c-terminal pts1-type tripeptide peroxisomal targeting signals, and peroxisomal targeting signal 2 are all over-represented in the gene list.\\n\\nmechanism: the mechanism behind these genes is the import of proteins into peroxisomes, resulting in peroxisomal biogenesis. the aaa atpases, peroxisomal membrane proteins, c-terminal pts1-type tripeptide peroxisomal targeting signals, peroxisomal targeting signal 2 are all involved in either targeting or catalyzing this protein import]] \n", - " peroxisome-1 [[this set of genes is related to the function of peroxisome biogenesis and associated disorders. the enriched terms are peroxisome biogenesis, GO:0017038, peroxisomal matrix proteins, atpase family, and pti2 receptor/pex7.\\n\\nmechanism: peroxisomes are important organelles for a variety of metabolic functions, and the synthesis and organization of these organelles is mediated by the pex genes. pex6 and pex2 are involved in protein import, where the pex2 protein forms a membrane-restricted complex, and pex6 is predominantly cytoplasmic and plays a direct role in peroxisomal protein import and receptor activity. pex3 and pex7 are required for peroxisomal biogenesis, and pex7 is the cytosolic receptor for the set of peroxisomal matrix enzymes targeted to the organelle by the peroxisome targeting signal 2. lastly, pex1 forms a heteromeric complex and plays a role in the import of proteins into peroxisomes and peroxisome biogenesis]] \n", - " progeria-0 [[GO:0000785, nuclear membr]] \n", - " progeria-1 [[these genes are all related to essential functions that facilitate the proper structure and organization of the nucleus and genome, primarily through the formation and maintenance of nuclear lamin, dna helicases and chromatin structures. there is evidence that all of these genes are involved in the proper functioning of cell division, GO:0006281, and transcription, as well as the maintenance of genome stability. the most enriched terms related to the functions of these genes are nuclear lamina, dna helicase, chromatin structure, GO:0006281, GO:0006351, genome stability, GO:0051301, nuclear membrane proteins, and nuclear localization signal. \\n\\nmechanism: the genes may be involved in pathways that coordinate the formation and maintenance of nuclear lamin, dna helicase, and chromatin structures, which are necessary for cell division and transcription, as well as the maintenance of genome stability. these pathways may involve the direct interactions between the gene products, as well as the recruitment of nuclear membrane proteins and signals involved in maintaining nuclear organization]] \n", - " regulation of presynaptic membrane potential-0 [[neuronal signaling, neuron communication, MESH:D007473, excitatory dependent channels, inhibitory neurotransmitter, ligand-gated ion channel, g protein-coupled membrane receptor]] \n", - " regulation of presynaptic membrane potential-1 [[MESH:D017981, MESH:D058446, GO:0009451, voltage-gated ion channels, channel subunits, channel polymorphisms, g-protein-coupled transmembrane receptors, MESH:D017470, MESH:D018079, MESH:D015221]] \n", - " sensory ataxia-0 [[transcriptional regulation, mitochondrial rna synthesis, neurodevelopment, GO:0030218, GO:0036211, nucleolar function, neuronal network formation, sensory receptor function]] \n", - " sensory ataxia-1 [[GO:0000981, dna helicase, hexameric dna helicase, neurotrophic factor, pdz domain, ma cation channels, MESH:D005956, protein synthetase, mitochondrial dna polymerase, heme transporter, GO:0005643, MESH:D044767, transmembrane glycoprotein]] \n", - " term-GO:0007212-0 [[g-protein coupled receptor signaling, g-protein subunit signaling, GO:0004016, phospholipase c-beta activity, GO:0005102, GO:0007165, second messenger synthesis, transmembrane signaling]] \n", - " term-GO:0007212-1 [[the list of human genes supplied involves several different cell signaling pathways, including the dopamine receptor (drd1, drd2, drd3 and drd5) pathway, g-protein coupled receptor (gpcr) signalling pathway (gnas, gnai3, gnaq, gna11, gna14, gna15, gnb1, gnb5, gnao1, gng2, sl]] \n", - " tf-downreg-colorectal-0 [[transcriptional regulation, GO:0006338, GO:0003677, GO:0000981, coactivator, heterodimer, response element]] \n", - " tf-downreg-colorectal-1 [[transcription factor regulation, GO:0016569, dna-binding activity, zinc-finger binding, GO:0032183, retinoid x receptor responsive element binding]] \n", - " no_synopsis EDS-0 [[GO:0031012, ecm components, matrix components, ecm regulators]] \n", - " EDS-1 [[extracellular matrix protein network, collagen fibril formation, GO:0030199, ecm protein network assembly, UBERON:2007004]] \n", - " FA-0 [[MONDO:0100339, \"double strand break repair\", \"fanconi anemia protein complex\", \"ubiquitin ligase complex formation\"]] \n", - " FA-1 [[GO:0006974, dna damage recognition, GO:0006281, GO:0035825, double-stranded break repair, double-stranded break recognition]] \n", - " HALLMARK_ADIPOGENESIS-0 [[MESH:D004734, GO:0006631, GO:0045444, GO:0006695, GO:0006699]] \n", - " HALLMARK_ADIPOGENESIS-1 [[MESH:D004734, cell death regulation, cell proliferation signaling, dna replication/remodeling, GO:0006396, GO:0006629]] \n", - " HALLMARK_ALLOGRAFT_REJECTION-0 [[cell surface molecules, MESH:D016207, MESH:M0000731, receptor signalling, transcriptional regulation, GO:0006915]] \n", - " HALLMARK_ALLOGRAFT_REJECTION-1 [[GO:0019882, GO:0007165, b and t cell metabolism, GO:0001816, GO:0006935]] \n", - " HALLMARK_ANDROGEN_RESPONSE-0 [[genes in this list are involved in developmental processes, metabolism, and the inflammatory response. the terms enriched in these genes include: cell cycle regulation, GO:0008152, GO:0006260, GO:0015031, receptor signaling, GO:0006954, GO:0006915, GO:0006351, GO:0006457, GO:0016477, developmental processes.\\n\\nmechanism: these genes appear to work together to regulate a variety of cellular processes, such as cellular metabolism, transcription, growth, and differentiation, as well as communication between cells and the environment. these genes likely act in concert to coordinate the intricate interplay between these processes and respond to changes in the environment. furthermore, they likely play a role in the body’s inflammatory response when faced with a variety of external stimuli]] \n", - " HALLMARK_ANDROGEN_RESPONSE-1 [[GO:0065007, GO:0023052, GO:0019538, GO:0051726, transcription regulation, MESH:D021381, GO:0007165, membrane trafficking, protein kinase regulation, GO:0044237, GO:0006259, GO:0006468, GO:0030163, mitochondrial function, GO:0006629, cytoskeleton regulation, GO:0007155, GO:0009117]] \n", - " HALLMARK_ANGIOGENESIS-0 [[extracellular matrix formation and maintenance, fibrous tissue development, vascular development, cell-cell communication and migration, extracellular secreted signaling, collagen and laminin-fibrillin proteins]] \n", - " HALLMARK_ANGIOGENESIS-1 [[GO:0032502, GO:0009653, GO:0009888, GO:0030198, GO:0006954, MESH:D066253, cell-cell communication]] \n", - " HALLMARK_APICAL_JUNCTION-0 [[this term enrichment test suggests that the genes provided are involved in cell adhesion, GO:0006955, and tissue morphogenesis. specifically, the adhesion-associated genes enriched in this dataset include icam1, icam2, icam4, icam5, nectin1, nectin2, nectin3, nectin4, nrxn2, ptprc, sdc3, thy1, vcam1, and vwf. the immune response-associated genes enriched in this dataset include cd34, cd86, cd209, ctnna1, icam2, icam4, icam5, map4k2, msn, pard6g, and tnfrsf11b. lastly, the tissue morphogenesis-associated genes enriched in this dataset include acta1, actb, actc1, actg1, actn1, actn2, actn4, adam15, adra1b, akt2, alox15b, amigo2, baiap2, cadm2, cadm3, MESH:M0359286, col9a1, MONDO:0011642, ctnnd1, MESH:C040896]] \n", - " HALLMARK_APICAL_JUNCTION-1 [[GO:0009653, GO:0016049, MESH:D047108, cellular signaling, GO:0031012, cytoskeletal organization, basal membrane assembly, GO:0098609, GO:0006915, GO:0016477, GO:0001816, growth factor production, tyrosine kinase activity, g-protein coupled receptor signaling pathway, nuclear receptor signaling pathway, GO:0016055, phosphatidylinositol 3-kinase signaling pathway, protein kinase b signaling pathway, map kinase signaling pathway, cell adhesion molecule signaling pathway, focal adhesion signaling pathway]] \n", - " HALLMARK_APICAL_SURFACE-0 [[GO:0016477, membrane receptor signaling, GO:0009100, protein tyrosine kinases, GO:0007155, cytoskeletal dynamics, receptor-mediated lectin binding, GO:0006629, GO:0007015]] \n", - " HALLMARK_APICAL_SURFACE-1 [[cell signaling, GO:0032502, transcription regulation, GO:0008152, MESH:D049109, MESH:D005786]] \n", - " HALLMARK_APOPTOSIS-0 [[transcriptional regulation/control, cell cycle/apoptosis, GO:0006955]] \n", - " HALLMARK_APOPTOSIS-1 [[the genes listed are mainly involved in the regulation and expression of genes, inflammation pathways and cell cycle regulation. specifically, enriched terms include gene expression and transcriptional regulation, dna damage and repair, GO:0007165, GO:1901987, metabolism and apoptosis.\\n\\nmechanism: the commonality in the function of these genes is likely related to the roles they play in the regulation of gene expression by affecting signal transduction, GO:0008152, cell cycle control and apoptosis. these gene functions may lead to a variety of processes, including inflammation pathways related to immunity, UBERON:2000098, MESH:D002470]] \n", - " HALLMARK_BILE_ACID_METABOLISM-0 [[MESH:M0496924, GO:0006869, development of connective tissues, GO:0006633, GO:0006699, GO:0006805, GO:0006694, cellular transport, MESH:M0023727, connective tissue formation, digit development, GO:0060173]] \n", - " HALLMARK_BILE_ACID_METABOLISM-1 [[this set of genes is related to lipid metabolism and lipid transport, protein homeostasis, retinol metabolism, developmental processes, and transportation of lysosomal hydrolases and oxygen-carrying molecules. the set includes genes involved in lipid metabolism (aqp9, atxn1, GO:0033781, abcg4, acsl1, fdxr, aldh8a1, hsd17b11, aldh9a1, aldh1a1, cyp7a1, cp25h, gstk1, MONDO:0100102, acsl5), lipid transport (abca1, abca2, abca3, abca4, abca5, abca8, abca9, abcg8), protein homeostasis (pex12, pex16, pex19, pex11a, pex11g, GO:0005053, pex6, pex26), retinol metabolism (abcd1, abcd2, abcd3), developmental processes (lck, nr3c2, retsat, klf1, ephx2, phyh, bbox1, MONDO:0004277]] \n", - " HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 [[transcriptional regulation, MESH:D006026, GO:0006629, GO:0005509, GO:0001525, MESH:D016326, receptor signaling; transcription regulators; calcium signaling; glycoside hydrolases; lipid metabolism; cell adhesion; extracellular matrix proteins; signaling receptor molecules.\\n\\nmechanism: this set of genes is likely involved in regulating transcriptional responses, MESH:D006026, GO:0006629, GO:0005509, GO:0001525, MESH:D016326, and receptor signaling. many of these genes interact with each other, forming complex cellular networks and pathways. the particular genes identified in this list are likely related to stimulating or inhibiting the expression of specific genes or pathways, as well as modulating or mediating responses to various environmental signals or stimuli. these gene functions likely interact to maintain homeostasis, contribute to cellular development and processes, promote angiogenesis, and provide a structural and functional framework for the extracellular matrix. furthermore, these genes may be involved in signaling pathways that involve receptor molecules by modulating intracellular calcium levels]] \n", - " HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 [[GO:0006629, transcriptional regulation, cellular adhesion, GO:0032502, GO:0042592]] \n", - " HALLMARK_COAGULATION-0 [[inflammatory response regulation, extracellular matrix formation regulation, proteolytic activities]] \n", - " HALLMARK_COAGULATION-1 [[GO:0007165, GO:0030198, matrix molecular regulation, GO:0006508, GO:0050817, matrix remodeling, GO:0009653]] \n", - " HALLMARK_COMPLEMENT-0 [[GO:0030198, immune system/inflammation/interferon response, GO:0000988]] \n", - " HALLMARK_COMPLEMENT-1 [[immunoglobulin like domains, GO:0042113, GO:0050852, integrin mediated cell adhesion, GO:0006915, regulation of transcription, GO:0007165, receptor mediated endocytosis and exocytosis, GO:0030198, calcium mediated signaling]] \n", - " HALLMARK_DNA_REPAIR-0 [[GO:0006259, GO:0016070, GO:0006412, dna damage repair, GO:0006351, GO:0006325]] \n", - " HALLMARK_DNA_REPAIR-1 [[GO:0006260, transcription regulation, GO:0006412, GO:0043687, nucleic acid metabolism, GO:0010467, GO:0006397, GO:0006412]] \n", - " HALLMARK_E2F_TARGETS-0 [[GO:0006260, GO:0006281, gene transcription, GO:0006412, GO:0016569, GO:0007049, GO:0010468]] \n", - " HALLMARK_E2F_TARGETS-1 [[GO:0006260, GO:0006351, GO:0030261, transcriptional regulation, GO:0006338, GO:0006974, chromatin structure modifications, GO:0006281, GO:0006306, GO:0030163, GO:0007094, GO:1901987, GO:0006468]] \n", - " HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 [[genes in this list are enriched for functions related to modulating extracellular matrix, cell adhesion and morphogenesis, as well as playing roles in development, growth and signal transduction pathways. enriched terms include:extracellular matrix modulation; cell adhesion; morphogenesis; development; growth; signal transduction.\\n\\nmechanism: many of the genes listed are involved in the signaling, development and maintenance of the extracellular matrix, cell adhesion and morphogenesis, which can be regulated through diverse pathways involving the growth factors (bdnf, MESH:D016222, igfbp2, igfbp3, igfbp4, wnt5a), proteoglycans (comp, cspg4, MONDO:0021055, lamc1, lamc2, dcn, has3, sdc1) and adhesion molecules and receptors (acta2, abi3bp, cadm1, cap2, capg, cd44, cdh11, cdh2, cdh6, fn1, grem1, itga2, itga5, itgav, itgb1, itgb3, itgb5, lrp1, tagl]] \n", - " HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 [[GO:0030198, GO:0009653, collagen production, matrix metalloproteinase activity, GO:0009100, cytoskeletal component organization, regulation of growth and reproduction, regulation of skin morphogenesis]] \n", - " HALLMARK_ESTROGEN_RESPONSE_EARLY-0 [[cell morphology; homeostasis & regulation; innervation; cellular metabolism.\\nmechanism: the genes are likely to be involved in various pathways, such as the regulation of gene expression, protein synthesis and structure, cell motility and differentiation, tissue repair regeneration]] \n", - " HALLMARK_ESTROGEN_RESPONSE_EARLY-1 [[immunological response, GO:0007155, transcription regulation, GO:0016477, GO:0008544, GO:0060348, MESH:D024510, GO:0015031, GO:0006915]] \n", - " HALLMARK_ESTROGEN_RESPONSE_LATE-0 [[MESH:D023281, cytoskeletal processes, GO:0006955, extracellular modification]] \n", - " HALLMARK_ESTROGEN_RESPONSE_LATE-1 [[the commonalities in the functions of these genes are involved in transcription, post-transcriptional regulation, GO:0009966, and cell-cycle related processes. the enriched terms are: transcription; post-transcriptional regulation; signal transduction; cell cycle; dna binding; regulation of transcription; regulation of protein abundance; chromatin remodeling; ubiquitination; and protein-protein interaction.\\n\\nmechanism: the underlying mechanism may be related to the regulation of intricate pathways leading to the expression of specific genes in conversion of genetic information into protein-based processes. these genes may be involved in a variety of biological processes, such as transcriptional and post-transcriptional regulation of gene expression, GO:0007165, cell-cycle related processes, GO:0003677, regulation of transcription, regulation of protein abundance, GO:0006338, MESH:D054875, protein-protein interaction]] \n", - " HALLMARK_FATTY_ACID_METABOLISM-0 [[GO:0006631, oxidation of lipids, GO:0006695, GO:0005977, GO:0009117, GO:0006862, GO:0009165, electron transport activity, enzyme regulation, regulation of metabolic pathways, GO:0006915]] \n", - " HALLMARK_FATTY_ACID_METABOLISM-1 [[GO:0008152, energy production and storage, lipid metabolism and transport, acetyl-coa biosynthesis and catalysis, oxidation, GO:0006631]] \n", - " HALLMARK_G2M_CHECKPOINT-0 [[GO:0051726, GO:0006260, GO:0006338, cyclin b-cdk1 activation, cks1b, cdc25a, wee1, cdc20, apc/]] \n", - " HALLMARK_G2M_CHECKPOINT-1 [[nuclear processes, GO:0006260, gene transcription, GO:0006338, GO:1901987, GO:0006281, GO:0010467, GO:0010468]] \n", - " HALLMARK_GLYCOLYSIS-0 [[developmental process: digit development, GO:0001525, GO:0030154, GO:0005488, transporting, GO:0008152, GO:0008152, cell signalling]] \n", - " HALLMARK_GLYCOLYSIS-1 [[GO:0005975, MESH:D004734, GO:0046785, dna binding and replication, actin cytoskeleton dynamics, ion channel regulation, transcriptional regulation, GO:0007155]] \n", - " HALLMARK_HEDGEHOG_SIGNALING-0 [[GO:0009653, GO:0022008, GO:0016049, GO:0030154, GO:0001764, thalamocortical pathway development, GO:0001764, GO:0007399, neural crest migration]] \n", - " HALLMARK_HEDGEHOG_SIGNALING-1 [[GO:0009653, GO:0007155, GO:0032502, GO:0007268, GO:0008283, GO:0016477, GO:0030154, MESH:D009473]] \n", - " HALLMARK_HEME_METABOLISM-0 [[GO:0055085, MESH:D004734, GO:0003735, GO:0003676, GO:0015031, negative regulation of transcription, regulation of transcription, positive regulation of transcription, GO:0071840, iron metabolism, GO:0007165, GO:0045087, GO:0042803, GO:0051276, GO:0050794, GO:0016569, GO:0008380, GO:0005515, GO:0000075, GO:0006006, GO:0000088, GO:0009116]] \n", - " HALLMARK_HEME_METABOLISM-1 [[GO:0048468, GO:0010467, GO:0048513, nucleic acid metabolism, transcriptional regulation, GO:0006259, GO:0016070, cytoskeletal dynamics, GO:0007165, GO:0006412]] \n", - " HALLMARK_HYPOXIA-0 [[gene enrichment analysis of the gene list showed that the majority of genes are involved in cellular proliferation, GO:0006915, GO:0006811, GO:0005102, and development. the enriched terms associated with this list include cell proliferation, GO:0006915, GO:0006811, GO:0005102, cell signaling, transcriptional regulation, and development.\\n\\nmechanism: the genes are likely involved in an intricate, interconnected biological network that involves numerous signaling pathways and transcription factors necessary for cellular proliferation, GO:0006915, ion transport and receptor binding. these gene functions result in the regulation of numerous cellular processes and ultimately the development of various diseases. in addition, the genes may be regulating a number of other processes such as metabolism, cell-cell communication, energy production]] \n", - " HALLMARK_HYPOXIA-1 [[GO:0048468, cell metabolism, transcription regulation, GO:0010468, GO:0006974, GO:0007155, GO:0030154, GO:0042440, MESH:M0352612, GO:0006412, GO:0051726, MESH:D004734]] \n", - " HALLMARK_IL2_STAT5_SIGNALING-0 [[GO:0016049, cell regulation, GO:0009988, MESH:D007109, signal transduction and regulation, GO:0032502, transcriptional regulation, GO:0030198, cytokine-receptor-mediated signaling pathway]] \n", - " HALLMARK_IL2_STAT5_SIGNALING-1 [[this list of genes are involved in developmental processes, GO:0006955, GO:0006954, GO:0007165, and cell adhesion functions. the enriched terms are \"development\"; \"signal transduction\"; \"cell adhesion\"; \"immune response\"; \"inflammation\"; \"transmembrane transport\"; \"protein metabolism\"; \"cardiovascular function\".\\n\\nmechanism: the underlying biological mechanisms involves the coordination of different pathways, genes and proteins. these genes are involved in cellular processes and regulation, including cell proliferation, differentiation, adhesion and migration, GO:0007165, and immunity. the genes also influence signaling pathways, protein metabolism and other functions that have roles in cardiovascular and carcinogenesis. the mechanisms through which these genes affect development, GO:0006954, other immunological responses are complex dependent on the coordination between multiple pathways]] \n", - " HALLMARK_IL6_JAK_STAT3_SIGNALING-0 [[pain sensing and signal transduction, GO:0006935, GO:0019221, leukocyte transendothelial migration, GO:0006955, GO:0030168]] \n", - " HALLMARK_IL6_JAK_STAT3_SIGNALING-1 [[GO:0007165, MESH:D056747, immune signaling, transcription regulation, cytokine regulation, GO:0030155, MESH:D005786, cell growth regulation, metabolism regulation, MESH:D002470, cell death regulation, antifungal immunity]] \n", - " HALLMARK_INFLAMMATORY_RESPONSE-0 [[MESH:M0000731, GO:0006954, GO:0007165, transcription regulation, intercellular signaling, GO:0045087, MESH:D056704]] \n", - " HALLMARK_INFLAMMATORY_RESPONSE-1 [[immune cell signaling, GO:0006928, cell surface receptor activity, GO:0006954, GO:0016477, cell–cell interactions, immune cell receptor-mediated signaling]] \n", - " HALLMARK_INTERFERON_ALPHA_RESPONSE-0 [[GO:0006954, neutroph]] \n", - " HALLMARK_INTERFERON_ALPHA_RESPONSE-1 [[interferon signalling pathway, interferon gamma activity, interferon regulatory factor activity, status response to interferon, GO:0006915, GO:0008289, GO:0005509, GO:0002446]] \n", - " HALLMARK_INTERFERON_GAMMA_RESPONSE-0 [[GO:0006955, cell signaling, cytokine response, interferon response, nuclear factor kappab-dependent transcriptional regulation]] \n", - " HALLMARK_INTERFERON_GAMMA_RESPONSE-1 [[MESH:D007109, interleukin regulation, transcription regulation, GO:0006954, cell signaling, GO:0006915]] \n", - " HALLMARK_KRAS_SIGNALING_DN-0 [[GO:0060348, GO:0009653, growth maintenance, GO:0007267, cell-cell communication, GO:0036211, GO:0006810]] \n", - " HALLMARK_KRAS_SIGNALING_DN-1 [[GO:0009653, cell-cell communication, GO:0032502, hormone regulation, cellular differentiation, cell-cycle, cell-signalling]] \n", - " HALLMARK_KRAS_SIGNALING_UP-0 [[GO:0007165, GO:0000902, GO:0050896, GO:0001525, GO:0065009, GO:0030198]] \n", - " HALLMARK_KRAS_SIGNALING_UP-1 [[GO:0009653, GO:0009888, cell signaling, immune regulation, transcription modulation, GO:0007165, GO:0007155, GO:0016477]] \n", - " HALLMARK_MITOTIC_SPINDLE-0 [[the human genes abi1, abl1, abr, actn4, akap13, alms1, MONDO:0008780, anln, GO:0005680, arap3, arf6, arfgef1, arfip2, arhgap10, arhgap27, arhgap29, arhgap4, arhgap5, arhgdia, arhgef11, arhgef12, arhgef2, arhgef3, arhgef7, arl8a, atg4b, MESH:D064096, bcar1, bcl2l11, bcr, bin1, birc5, brca2, bub1, capzb, ccdc88a, ccnb2, cd2ap, cdc27, cdc42, cdc42bpa, cdc42ep1, cdc42ep2, cdc42ep4, cdk1, cdk5rap2, cenpe, cenpf, cenpj, cep131, cep192, cep250, cep57, GO:0047849]] \n", - " HALLMARK_MITOTIC_SPINDLE-1 [[cytoskeletal organization, GO:0016477, GO:0051301, GO:0006260, GO:0006281, GO:0006605, GO:0065007]] \n", - " HALLMARK_MTORC1_SIGNALING-0 [[the human genes abcf2, acaca, acly, acsl3, actr2, actr3, add3, adipor2, ak4, aldoa, arpc5l, asns, atp2a2, atp5mc1, atp6v1d, MESH:D064096, bcat1, bhlhe40, btg2, bub1, cacybp, calr, canx, ccnf, ccng1, cct6a, cd9, cdc25a, cdkn1a, cfp, cops5, coro1a, cth, ctsc, GO:0038147, cyb5b, cyp51a1, dapp1, ddit3, ddit4, ddx39a, dhcr24, dhcr7, GO:0004146, ebp, edem1, eef1e1, egln3, eif2s2, elovl5, elovl6, eno1, eprs1, ero1a, etf1, MONDO:0100101, MONDO:0100102, fdxr, fgl2, MESH:D010649]] \n", - " HALLMARK_MTORC1_SIGNALING-1 [[GO:0006412, MESH:D004734, cellular transport, GO:0006955, GO:0035194, mitochondrial oxidative phosphorylation, GO:0006915, GO:0016310, GO:0006096, GO:0006914]] \n", - " HALLMARK_MYC_TARGETS_V1-0 [[rna biogenesis, protein synthesis biosynthesis, atp-binding, cytoskeleton organization and assembly, GO:0006351, GO:0006338, GO:0007165, GO:0010467, GO:0006413, MESH:M0439896, GO:0006260]] \n", - " HALLMARK_MYC_TARGETS_V1-1 [[GO:0000394, GO:0051028, MESH:M0439896, GO:0006412, GO:0042254, GO:0035194, GO:0006338]] \n", - " HALLMARK_MYC_TARGETS_V2-0 [[genes in this list are primarily involved in cell development, including the processes of rna metabolism, dna replication and cell cycle control. enriched terms include: rna metabolism; dna replication; cell cycle control; chromatin regulation; transcription regulation; cell differentiation; gene expression; and protein synthesis.\\n\\nmechanism: the genes in this list are part of a complex network of molecular pathways involved in regulating the expression, replication and maintenance of genetic material. this includes the transcription, splicing and translation of rnas as well as the replication and repair of dna. the multiple genes in this list suggest coordination and control of various steps in these processes, such as chromatin regulation, which is directly responsible for how genetic material is packaged and regulated. additionally, the genes may be involved in regulating cell cycle progression, transcription regulation and cell differentiation]] \n", - " HALLMARK_MYC_TARGETS_V2-1 [[GO:0001775, GO:0008283, GO:0006260, dna transcription, rna translation.\\nmechanism: the genes may indicate an underlying biological pathway involving the coordinated expression of these gene sets to regulate the cell cycle, dna replication, transcription, and translation in order to enable cell proliferation]] \n", - " HALLMARK_MYOGENESIS-0 [[gene expression and structure, cytoskeletal structure and dynamics, calcium regulation and signaling, cell adhesion and migration, cell death biochemistry, metabolic regulation]] \n", - " HALLMARK_MYOGENESIS-1 [[GO:0031012, GO:0005856, UBERON:0005090, GO:0032502, neuromuscular structure, MESH:D007473, GO:0006811]] \n", - " HALLMARK_NOTCH_SIGNALING-0 [[MESH:D047108, GO:0051726, GO:0019722, notch signaling down-regulation, wnt signaling, hedgehog signaling, GO:0000902]] \n", - " HALLMARK_NOTCH_SIGNALING-1 [[these genes are involved in a wide range of functions related to signaling, development, and transcriptional regulation, indicating an involvement in a variety of cellular pathways. enriched terms include: cell signaling, GO:0007399, GO:0030154, wnt signaling, notch signaling, hedgehog signaling, transcription factor regulation, GO:0006338, e3 ubiquitin ligase.\\n\\nmechanism: the likely underlying biological mechanism is a complex network of interactions between these genes and their pathways, forming a web of signaling molecules that regulate cell growth, differentiation, apoptosis and other cellular processes. the genes and pathways involved in the network are likely to interact in a dynamic manner]] \n", - " HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 [[mitochondrial activity, GO:0022900, GO:0006119, metabolic regulation, MESH:D065767]] \n", - " HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 [[GO:0005746, electron transfer proteins, proton ion transportation proteins, oxidative phosphorylation proteins, metabolite-binding proteins, atp synthesis proteins]] \n", - " HALLMARK_P53_PATHWAY-0 [[cytoskeletal reorganization, calcium homeostasis, ubiquitin-proteasome pathway, GO:1901987, transcriptional regulation, GO:0006397, GO:0006974]] \n", - " HALLMARK_P53_PATHWAY-1 [[GO:0006351, chromatin dynamics, GO:0007155, MESH:D016207, GO:0007049, dna damage repair, cell signaling, GO:0016049, GO:0006915, immune modulation]] \n", - " HALLMARK_PANCREAS_BETA_CELLS-0 [[GO:0031016, GO:0006006, GO:0048870, neural development]] \n", - " HALLMARK_PANCREAS_BETA_CELLS-1 [[GO:0009653, neuronal development, GO:0007165, GO:0030073, transcription regulation, GO:0000988]] \n", - " HALLMARK_PEROXISOME-0 [[enrichment test suggested genes are skewed towards genes involved in development, metabolic control, transport, cell cycle and homeostasis, as well as transcriptional regulation.\\n\\nmechanism: these genes appear to be involved in a diverse range of processes, suggesting multiple pathways contributing to the physiological functions of these genes. for instance, abcb1, abcb4 and abcb9 are involved in medication transport, abcc5 and abcc8 are involved in atp coupling, acaa1 is involved in fatty acid metabolism, alb is involved in heme metabolism, aldh1a1, aldh9a1, atxn1 and bcl10 are involved in transcriptional regulation, ctbp1 and ctps1 are involved in ubiquitination, dhcr24 and dhrs3 are involved in cholesterol biosynthesis, fabp6 is involved in bile acid transport, fads1 is involved in fatty acid desaturase, fis1 and gnpat are involved in lipoic acid synthesis and mitochondrial fatty acid metabolism, gstk1 is involved in gst-mediated detoxification, hmgcl is involved in steroidogenesis, hras, hsd11b2, hsd17b11]] \n", - " HALLMARK_PEROXISOME-1 [[GO:0006629, GO:0008202, transcription regulation, GO:0051726]] \n", - " HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 [[GO:0010467, dna repair & maintenance, MESH:M0496065, cellular signaling pathways, GO:0006629]] \n", - " HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 [[GO:0051726, gene transcription, transcription factor activation, MESH:M0023730, MESH:D011494, receptor proteins, GO:0006412, GO:0016049, GO:0008283, GO:0030154]] \n", - " HALLMARK_PROTEIN_SECRETION-0 [[gene expression regulation; co-translational protein targeting; clathrin-mediated endocytosis; endosomal protein trafficking; vesicle transport; exocytosis; receptor and ligand-mediated signaling; development and organ morphogenesis.\\nmechanism: the identified genes are likely involved in a variety of biological processes related to endocytosis, vesicle trafficking and transport, receptor and ligand-mediated signaling, MESH:D005786, co-translational protein targeting, and organ morphogenesis. these processes can be clustered into several pathways, including the calcineurin-mediated endocytosis pathway, the mapk signaling pathway, the wnt/beta-catenin signaling pathway, the clathrin-mediated endocytosis pathway, the endosomal protein trafficking pathway, the vesicle transport pathway, the exocytosis pathway, the receptor ligand-mediated signaling pathways]] \n", - " HALLMARK_PROTEIN_SECRETION-1 [[genes belonging to this list are mainly involved in endocytosis, GO:0016192, MESH:D021381, and membrane fusion. the enriched terms include: endocytosis; vesicle trafficking; protein trafficking; membrane fusion; membrane transport; cytoskeleton organization; signal transduction; receptor internalization; and protein trafficking pathways.\\n\\nmechanism: the common characteristics shared by the genes suggest that they are all involved in some aspect of the endocytosis pathway. this biological mechanism involves signal transduction by which a signal (chemical or physical) can pass through a cell membrane and allow the cell to take up extracellular substances. through receptor internalization, molecules, like hormones, can be shuttled into intracellular vesicles and undergo further signaling events. the sequential vesicle trafficking steps then enable the cargo to be transported to their final destination. the proteins play various roles in facilitating membrane fusion, GO:0036211, GO:0007010, and vesicle transport. all of these activities act in concert to usher signals, MESH:D011506, other substances into the cell]] \n", - " HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 [[redox regulation, antioxidant defense, detoxification of reactive oxygen species, peroxisomal biogenesis, MESH:M0572479, cell metabolism]] \n", - " HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 [[redox balance regulation, GO:0008152, GO:0051726, transcriptional regulation]] \n", - " HALLMARK_SPERMATOGENESIS-0 [[cell signaling, protein regulation, GO:1901987, GO:0009653, GO:0048513, cytoskeletal regulation]] \n", - " HALLMARK_SPERMATOGENESIS-1 [[cell cycle checkpoint regulation, GO:0009653, cell signaling, MESH:D003598, organ development]] \n", - " HALLMARK_TGF_BETA_SIGNALING-0 [[mapk pathway, tgf-β signaling pathway, wnt/β-catenin pathway, GO:0035329, transcriptional regulation, muscle morphogenesis, GO:0048729, regulation of g-protein signaling, GO:0006954]] \n", - " HALLMARK_TGF_BETA_SIGNALING-1 [[these genes are involved in processes related to cell development, GO:0009653, calcium and calcium-dependent signaling, MESH:D017978, smad pathway and extracellular matrix proteins.\\n\\nmechanism: the mechanism underlying this gene list is likely related to signal transduction pathways. these may involve cell surface receptors which bind growth factors, such as tgfb1 and bmpr2, and transduce the signal through the smad pathway via the fkbp1a, bmpr1a, smurf1, smad1, ltbp2, thbs1, arid4b, ppm1a, and ctnnb1 proteins to influence the regulation of gene expression and cell fate. moreover, other molecules such as xiap, ube2d3, nog, slc20a1, serpine1, bcar3, rhoa, MESH:D045683, hipk2, ppp1ca, smad7, junb, smad6, ppp1r15a, tjp1, and ifngr2 may be involved in the signal transduction pathway. in addition, the calcium and calcium-dependent signaling by the tg]] \n", - " HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 [[GO:0032502, GO:0006954, MESH:D056747, cell signaling, MESH:M0496924, GO:0009653, GO:0009888, GO:0008283, GO:0006915, immune system response, MESH:M0496924]] \n", - " HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 [[gene transcription, actin maturation, cytoskeleton formation, signaling complex assembly, interleukin receptor signaling, GO:0051170, cytokine receptor signaling, nf-kappab signaling pathway, cytokine-mediated signal transduction, GO:0006367, MESH:D005786, cytokine receptor signaling pathway, GO:0010737, GO:0035556]] \n", - " HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 [[GO:0009299, GO:0042254, GO:0006457, nucleolar activity, spliceosomal activity, protein production, GO:0015031, GO:0006396, GO:1901987]] \n", - " HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 [[GO:0008152, GO:0006412, GO:0043687, GO:0016310, pepetide binding and metabolism, protein structure and folding, rna synthesis and processing, GO:0000394, GO:0010467, GO:0051726, GO:0006915, GO:0007165, GO:0006281]] \n", - " HALLMARK_UV_RESPONSE_DN-0 [[MESH:D011494, cellular signaling pathways, GO:0001501, GO:0031012, transcriptional regulation, post-translational phosphorylation, growth regulation, development regulation, remodeling]] \n", - " HALLMARK_UV_RESPONSE_DN-1 [[mitotic regulation, GO:0060349, morphogenesis of specific organs and tissues, GO:0009966, regulation of transcription, GO:0042127, cellular responses to external stimuli, GO:0006468, GO:0003677]] \n", - " HALLMARK_UV_RESPONSE_UP-0 [[GO:0032502, GO:0016049, gene transcription, GO:0008152, MESH:D011506, GO:0006412, GO:0007049, cell signaling, transcriptional regulation, MESH:D021381, GO:0010468]] \n", - " HALLMARK_UV_RESPONSE_UP-1 [[GO:0008283, GO:0051726, dna replication and repair, GO:0007165, GO:0019722, GO:0006915, GO:0006629, oxygen pathway]] \n", - " HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 [[this examination of human genes reveals a number of gene functions that are significantly enriched and related to developmental processes, including cell proliferation and differentiation, GO:0048729, and wnt signalling pathways. \\nmechanism: cell proliferation and differentiation, GO:0048729, wnt signalling pathways are all important in the normal healthy development of cells organs. these genes provide important functions that act in cooperative downstream pathways to enable promote these developmental processes.\\nthe enriched terms are: cellular differentiation; cellular proliferation; digit development; tissue morphogenesis; wnt signalling pathway]] \n", - " HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 [[wnt signaling, notch signaling, transcription regulation, GO:0051726, GO:0009653, GO:0032502]] \n", - " T cell proliferation-0 [[cell signalling, protein interaction, GO:0007165, GO:0032502, regulatory role in immunity, GO:0030163, receptor-mediated signaling, GO:0016049, GO:0030154, GO:0006396]] \n", - " T cell proliferation-1 [[cell signaling, immune regulation, GO:0007165, growth factor production and response, immune response and modulation, calcium homeostasis, GO:0000981, development and differentiation, GO:0005102, GO:0001816]] \n", - " Yamanaka-TFs-0 [[the enrichment test results reveal that the list of genes are all involved in stem cell pluripotency and early embryonic development. enriched terms include pluripotency, stem cell morphology, MESH:D047108, GO:0000981, GO:0016049, differentiation, cell proliferation.\\n\\nmechanism: the genes focus on the regulation of the pluripotency and early embryonic developmental program. they regulate various aspects such as transcription factors, cell growth, morphogenesis, differentiation and cell proliferation. by acting in concert, they maintain the pluripotency of stem cells and initiate the processes of early morphogenesis. it is hypothesized that these genes are part of a large regulatory network which facilitates the pluripotency of the progenitor cells and the successful orchestration of early embryonic development]] \n", - " Yamanaka-TFs-1 [[GO:0009792, GO:0048864, GO:0000981, GO:0009653]] \n", - " amigo-example-0 [[GO:0030198, GO:0007155, GO:0009653, cell signaling, cytoskeletal organization, GO:0030154, MESH:D002470]] \n", - " amigo-example-1 [[our term enrichment analysis suggests that the human genes jag2, spp1, jag1, vcan, olr1, col5a2, app, UBERON:0003010, postn, tnfrsf21, apoh, pglyrp1, vav2, fstl1, nrp1, s100a4, lrpap1, vtn, timp1, itgav, lum, pf4, cxcl6, col3a1, stc1, kcnj8, msx1, ptk2, prg2, pdgfa, serpina5, and vegfa are related to processes in growth and differentiation, including transcriptional network maintenance, cell adhesion and motility, GO:0006915, and extracellular matrix component formation.\\n\\nmechanism: \\nthese genes may be involved in a complex network of signaling pathways that regulate cell growth and differentiation, cell adhesion and migration, GO:0006915, and matrix component formation. they may be involved in the reception and transduction of growth and differentiation signals, could facilitate the assembly of extracellular matrix components to form the microenvironment necessary to prompt and]] \n", - " bicluster_RNAseqDB_0-0 [[GO:0009653, GO:0032502, transcription regulation, cell signalling, GO:0006811]] \n", - " bicluster_RNAseqDB_0-1 [[GO:0009653, neuronal growth, neuronal system development, cell-cell communication, cell signaling, GO:0009888, organ development]] \n", - " bicluster_RNAseqDB_1002-0 [[analysis of the gene list shows that they are all associated with sarcomere function, MESH:D009119, skeletal muscles and thermogenesis. the enriched terms include sarcomere function, MESH:D009119, UBERON:0001134, MESH:D022722, actin-myosin interaction, calcium handling, muscle development and differentiation, and mitochondrial function. \\n\\nmechanism: the underlying biological mechanism is associated with the activation of genes that are linked to the assembly, maintenance and contraction of the sarcomere, which is the fundamental unit of muscle contraction, as well as muscle development and differentiation, calcium handling, mitochondrial fluctuation, thermogenesis. this contributes to the generation of force within the skeletal muscles]] \n", - " bicluster_RNAseqDB_1002-1 [[skeletogenesis, MESH:D024510, GO:0048740, GO:0001501, GO:0006936, GO:0006412, GO:0009058, MESH:D009126]] \n", - " endocytosis-0 [[GO:0007165, vesicle/lipid trafficking, cellular adhesion, nutrient regulation, cell metabolism, cytoskeletal organization, endocytosis/exocytosis, intercellular adhesion/motility]] \n", - " endocytosis-1 [[membrane trafficking, GO:0007165, protein proteolysis, GO:0006629, receptor signaling, GO:0055088]] \n", - " glycolysis-gocam-0 [[GO:0006096, aerobic glycolysis, GO:0006094]] \n", - " glycolysis-gocam-1 [[GO:0008152, GO:0006096, GO:0006098, GO:0006006, MESH:D004734]] \n", - " go-postsynapse-calcium-transmembrane-0 [[these genes appear to be involved in the development, functioning and regulation of the nervous system, specifically neurons and their associated pathways and processes. the terms \"neurotransmission\"; \"neuronal cell membrane regulation\"; \"neurotransmitter release\"; \"calcium signaling\"; \"neuronal ion channel regulation\"; and \"neuronal excitability regulation\" are significantly enriched in this gene set.\\n\\nmechanism: it appears that this gene set may be involved in a broad range of processes related to neurophysiology, including the regulation of neuronal membrane excitability and ion channels, neuronal cell membrane regulation, GO:0007269, and calcium signaling. these processes are all complex and interrelated, are likely to have a direct impact on neural development function]] \n", - " go-postsynapse-calcium-transmembrane-1 [[the term enrichment test reveals that the genes in the list are mainly involved in neuronal ion channels and calcium signalling pathways. enriched terms included calcium channel activity, GO:0005244, GO:0038023, GO:0015276, and g-protein coupled receptor activity. \\n\\nmechanism: the genes in the list form ion channels and g-protein coupled receptors within neuronal cells, which facilitates the communication of neurotransmitters between neurons. several of the genes are involved in calcium signalling pathways, which regulate various cellular pathways involved in the development and maintenance of neurons]] \n", - " go-reg-autophagy-pkra-0 [[GO:0016049, GO:0048468, GO:0006915, GO:0006955, GO:0030163, GO:0006508]] \n", - " go-reg-autophagy-pkra-1 [[phosphatidylinositol signalling, vascular endothelial growth factor receptor signalling, progesterone-mediated oocyte maturation, nf-kb signaling, GO:0043526]] \n", - " hydrolase activity, hydrolyzing O-glycosyl compounds-0 [[carbohydrate digestion and absorption; glycosaminoglycan and glycan metabolism; lysosomal, GO:0005777, and catabolic processes; digit, skeletal, GO:0035108]] \n", - " hydrolase activity, hydrolyzing O-glycosyl compounds-1 [[glycoside hydrolase (gh) activity, mucin biosynthesis, GO:0006031, MESH:D057056, lysosomal enzyme activity.\\nmechanism: glycoside hydrolase (gh) and lysosomal enzymes play important roles in the process of glycostasis, and are involved in a variety of metabolic activities such as the breakdown of polysaccharides, the synthesis of glycolipids and glycoproteins, and the degradation of other macromolecules. chitin and mucin biosynthesis also involve glycosylation and enzymatic modification of sugars and polysaccharides to form polymeric molecules. cysteine protease are involved in the hydrolysis of proteins, while lysosomal enzymes aid in the breakdown of molecules in the l]] \n", - " ig-receptor-binding-2022-0 [[members of the immunoglobulin (ig) gene superfamily - specifically, igh, GO:0033984, MESH:C014609, GO:0042571, response and maintenance of the adaptive immune system at different levels, likely via antigen binding, signal transduction and b cell activation]] \n", - " ig-receptor-binding-2022-1 [[GO:0003823, b cell receptors, GO:0007596, GO:0005577, MESH:D001779, clec4d]] \n", - " meiosis I-0 [[dna damage recognition, GO:0006281, GO:0006302, meiotic recombination, GO:0007059, GO:0035825, rad51 family proteins, dna end-protection, mus81-mms4 complex, muts family proteins, dna proofreading, spo11-associated pathway]] \n", - " meiosis I-1 [[GO:0006281, GO:0006260, gene splicing]] \n", - " molecular sequestering-0 [[GO:0000075, cell adhesion/motility complex, transcriptional complex, GO:0036211, rna processing complex]] \n", - " molecular sequestering-1 [[calcium binding, apoptotic regulation, immune modulation, MESH:D018384, GO:0051726, stress-response regulation]] \n", - " mtorc1-0 [[the human genes abcf2, acaca, acly, acsl3, actr2, actr3, add3, adipor2, ak4, aldoa, arpc5l, asns, atp2a2, atp5mc1, atp6v1d, MESH:D064096, bcat1, bhlhe40, btg2, bub1, cacybp, calr, canx, ccnf, ccng1, cct6a, cd9, cdc25a, cdkn1a, cfp, cops5, coro1a, cth, ctsc, GO:0038147, cyb5b, cyp51a1, dapp1, ddit3, ddit4, ddx39a, dhcr24, dhcr7, GO:0004146, ebp, edem1, eef1e1, egln3, eif2s2, elovl5, elovl6, eno1, eprs1, ero1a, etf1, MONDO:0100101, MONDO:0100102, fdxr, fgl2, MESH:D010649]] \n", - " mtorc1-1 [[energy production, GO:0008152, protein biosynthesis and folding, cell regulation, MESH:D048788, protein turnover]] \n", - " peroxisome-0 [[peroxisome biogenesis, peroxisome formation, membrane protein trafficking, GO:0044255, mitochondrial-peroxisomal crosstalk]] \n", - " peroxisome-1 [[peroxisomal biogenesis, peroxisomal protein transport, oxidative damage resistance]] \n", - " progeria-0 [[cell structural element development, gene transcription, GO:0016070, GO:0006259, transcriptional regulation]] \n", - " progeria-1 [[dna replication and repair, GO:0006334, GO:0000723, transcriptional regulation]] \n", - " regulation of presynaptic membrane potential-0 [[GO:0007165, GO:0006811, regulation of neurotransmitter release]] \n", - " regulation of presynaptic membrane potential-1 [[analysis of these genes show that they are involved in human neurological structure and function. enriched terms include neuron activity, GO:0005216, GO:0008066, GO:0004930, MESH:D005680, GO:0005267, MESH:D005680]] \n", - " sensory ataxia-0 [[MESH:D024510, neuronal development, GO:0015031, GO:0006629, GO:0009653]] \n", - " sensory ataxia-1 [[GO:0015031, MONDO:0008090, GO:0048705, MESH:D024510, GO:0005783, mitochondrial protein transport, cytoskeletal organization]] \n", - " term-GO:0007212-0 [[g alpha subunit signaling, gpcr activation and signaling, gpcr function, MESH:D019281]] \n", - " term-GO:0007212-1 [[cellular signaling, g protein signaling pathway, calcium signaling pathway, GO:0007399, GO:0007268, phosphorylation cascade, nerve morphogenesis, indoleamine metabolism]] \n", - " tf-downreg-colorectal-0 [[nuclear receptor superfamily, transcription regulation, epigenetic regulation, GO:0051726, GO:0003677, GO:0006338, GO:0032502, cell signaling pathways, GO:0005652, GO:0016363]] \n", - " tf-downreg-colorectal-1 [[transcriptional regulation, GO:0016569, GO:0009653, cardiovascular development, differentiation, MESH:M0464910, MESH:M0030450, GO:0048863]] \n", - " ontological_synopsis EDS-0 [[GO:0032963, GO:0030198, GO:0004222, GO:0030206, GO:0008378, GO:0005509, GO:0008270, platelet derived growth factor binding, GO:0002020, GO:0035987, GO:0007266, GO:0007160, hypoxia response, epidrmis development, peptidyl-lysine hydroxyl]] \n", - " EDS-1 [[GO:0030198, GO:0030199, GO:0043589, GO:0042060, GO:0043588, GO:0032964, GO:0006024, GO:0003755, GO:0035987]] \n", - " FA-0 [[analysis of the above genes shows that they are all involved in dna repair and involved in the fanconi anaemia nuclear complex, which is a critical part of the fanconi anaemia disease pathway. the list of enriched terms includes \"protein monoubiquitination\", \"dna repair complex\", \"fanconi anaemia nuclear complex\", \"double-strand break repair via homologous recombination\", \"response to intra-s dna damage checkpoint signaling\", \"telomere maintenance\", \"positive regulation of g2/m transition of mitotic cell cycle\", \"regulation of transcription by rna polymerase ii\".\\n\\nmechanism: the underlying biological mechanism is the fanconi anaemia pathway, where the defective genes of the path have the potential to lead to cancer or other fanconi anaemia-related illnesses. this dna repair pathway relies heavily on the fanconi anaemia nuclear complex, which involves the processes of monoubiquitination, involving the above genes, double-strbreak repair via homologous recombination. in addition, the regulation of telomere maintenance, positive regulation of g2/m transition of mitotic cell cycle regulation of transcription by rna polymerase ii are essential for proper dna repair]] \n", - " FA-1 [[this group of genes are involved in a range of dna repair processes, including protein monoubiquitination and double-strand break repair via homologous recombination. they are all localized in different components of the cell (e.g. chromatin, GO:0005634, GO:0005829, GO:0005657, GO:0005694, etc.) and are part of several complexes/hierarchies (e.g. fanconi anaemia nuclear complex, GO:0033063, GO:0048476, GO:0033557, GO:0033593, etc.). enriched terms includes: dna repair; protein monoubiquitination; double-strand break repair via homologous recombination; regulation of dna metabolic process; negative regulation of double-stranded telomeric dna binding activity; response to gamma radiation; regulation of telomere maintenance; establishment of protein localization to telomere; and regulation of protein metabolic process.\\n\\nmechanism: these genes are involved in a range of complex and interrelated biochemical pathways, which utilize a variety of enzymatic activities (e.g. ubiqu]] \n", - " HALLMARK_ADIPOGENESIS-0 [[GO:0005515, protein homodimerization, GO:0005524, GO:0003677, GO:0003824, MONDO:0016019]] \n", - " HALLMARK_ADIPOGENESIS-1 [[protein homodimerization, GO:0019899, GO:0140657, GO:0005102, ligase binding, GO:0003924, GO:0046872, dna-binding, rna-binding, oxidase activity, MESH:D010758, GO:0120227, transportase activity, dehydrogenase activity, GO:0016791, GO:0016301, GO:0004175, GO:0022857, chemotactic receptor activity, GO:0017077]] \n", - " HALLMARK_ALLOGRAFT_REJECTION-0 [[receptor binding activity, signaling receptor binding activity, protein binding activity, dna-binding, GO:0016563, GO:0005125, GO:0008083, GO:0042605, enzyme binding activity, chemical binding activity, protein complex binding activity]] \n", - " HALLMARK_ALLOGRAFT_REJECTION-1 [[enzyme binding activity, rna binding activity, protein binding activity, chemokine receptor binding activity, GO:0004712, GO:0042803, identical protein binding activity, GO:0008083, interleukin binding activity, cell-cell adhesion mediation, dna-binding transcription activity, GO:0015026, cytoplasmic factor activity, metal ion binding activity, polypeptide antigen transporter activity]] \n", - " HALLMARK_ANDROGEN_RESPONSE-0 [[protein binding activity, enzyme binding activity, transcription factor binding activity, GO:0016787, GO:0004721, GO:0003714, GO:0003713, atp binding activity, GO:0004672, GO:0016563, GO:0003924, nad+ binding activity, ring-like zinc finger domain binding activity, GO:0061656, small protein activating enzyme binding activity, GO:0000224, GO:0062076, GO:0004383, GO:0004222, 17-beta-dehydrogen]] \n", - " HALLMARK_ANDROGEN_RESPONSE-1 [[protein binding activity, GO:0004672, GO:0006351, GO:0038023, enzymatic activity, GO:0016310, GO:0097472, GO:0003677, GO:0006351, postsynaptic organization, GO:0016887, nucleic acid binding activity, ubiquitin protein ligase binding activity, fad binding activity, MESH:D009249, GO:0061665, enzyme binding activity, GO:0022857, endopeptidase activator]] \n", - " HALLMARK_ANGIOGENESIS-0 [[GO:0030021, collagen binding activity, integrin binding activity, GO:0060090, identical protein binding activity, fibronectin binding activity, GO:0046983, heparan sulfate proteoglycan binding activity, GO:0007160, GO:0010810]] \n", - " HALLMARK_ANGIOGENESIS-1 [[GO:0007166, GO:0006468, GO:0045861, GO:0007160, GO:1902533, GO:0010604, transmem]] \n", - " HALLMARK_APICAL_JUNCTION-0 [[GO:0098609, agonist binding activity, cytoplasmic matrix binding, protein homodimerization, GO:0005102]] \n", - " HALLMARK_APICAL_JUNCTION-1 [[binding activities, GO:0003824, involvement in biological processes, structural roles]] \n", - " HALLMARK_APICAL_SURFACE-0 [[GO:0061024, protein organization, GO:0036211, GO:0015031, GO:0006897, GO:0007165, GO:0006915]] \n", - " HALLMARK_APICAL_SURFACE-1 [[GO:0007155, protein folding and regulation, GO:0050801, MESH:D005786]] \n", - " HALLMARK_APOPTOSIS-0 [[dna binding activity, protein binding activity, enzyme binding activity, GO:0004197, identical protein binding activity, signaling receptor binding activity, calcium ion binding activity, protein kinase binding activity, GO:0000988, bh3 domain binding activity]] \n", - " HALLMARK_APOPTOSIS-1 [[calcium ion binding activity, protein binding activity, identical protein binding activity, chromatin dna binding activity, dna-binding transcription factor binding activity, ig domain binding activity, sh2 domain binding activity, bh3 domain binding activity, cyclin binding activity, rna binding activity, GO:0004197, metalloprotease inhibitor activity, phospholipid binding activity, lipopeptide binding activity, lysophosphatidic acid binding activity, sulfatide binding activity, atpase binding activity, pdz domain binding activity]] \n", - " HALLMARK_BILE_ACID_METABOLISM-0 [[atp binding activity, GO:0016887, protein binding activity, signaling receptor binding activity, enzyme binding activity, GO:0042803, GO:0016791, GO:0000988, GO:0022857, ubiquitin-dependent protein binding activity, cholesterol binding activity, GO:0019871, phosphotyrosine residue binding activity]] \n", - " HALLMARK_BILE_ACID_METABOLISM-1 [[GO:0140657, GO:0016887, GO:0008233, enzyme binding activity, GO:0003700, GO:0042803, identical protein binding activity, signaling receptor binding activity]] \n", - " HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 [[atp binding activity, protein kinase binding activity, GO:0042803, GO:0003700, low-density lipoprotein particle binding activity, GO:0005041, GO:0030229, GO:0004602, GO:0004364, GO:0016491, GO:0004496, GO:0004631, GO:0047598, GO:0047024, MESH:D010758, GO:0060090, cholesterol binding activity, GO:0120020, isopentenyl]] \n", - " HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 [[GO:0042632, MESH:D055438, GO:0005515, GO:0006351, GO:0010468, dna-binding, GO:0007165, negative regulation, positive regulation, GO:0016491, GO:0008610, GO:0003723, ldl particle binding, GO:0019901, phosphotransferase activity, acetyl-coa ligase activity, endopeptidase activity, etc]] \n", - " HALLMARK_COAGULATION-0 [[the provided list of human genes are mainly involved in metabolism, adjustment of the immune system and coagulation, and development of cells and organs. in particular, they are found to be involved in binding activities and endopeptidase activities such as post-translational modification, transcription and regulation of protein. the enriched terms include calcium-dependent protein/phospholipid/lipoprotein binding activity, GO:0004197, protein homodimerization/homooligomerization activity, identical protein binding activity, and serine-type endopeptidase activity. \\n\\nmechanism: the expression and activities of these genes may play important roles in the development and metabolism of cells and organs by facilitating protein folding, GO:0043687, cell-matrix adhesion and crosstalk between proteins. the binding activities of these genes towards phospholipid, lipoprotein and other molecules mediate the interaction between cells and extracellular environment, and regulate blood coagulation and formation of extracellular matrix. the endopeptidase activities of these genes degrade and modulate proteins, which are essential for various biological processes]] \n", - " HALLMARK_COAGULATION-1 [[protein binding activity, domain specific binding activity, disordered domain specific binding activity, GO:0008233, GO:0004252, GO:0005125, signaling receptor binding activity, identical protein binding activity, GO:0004222, GO:0003924, receptor tyrosine kinase binding activity, GO:0004421, phospholipid binding activity, amyloid-beta]] \n", - " HALLMARK_COMPLEMENT-0 [[enriched functions observed in the genes include binding activitiy (for various ligands, such as dna, GO:0005562, MESH:C062738, calcium ions, heparin/heparan sulphate, MESH:D019204, c5l2 anaphylatiotaxin, MESH:M0028275, mhc, amyloid-beta, cytokine, opsonin, MESH:D005227, MESH:D011494, etc.), enzyme activity (such as deubiquitinase, lck, atpase, aminopeptidase, peptidase, etc.), GO:0044183, cysteine type endopeptidase inhibitor activity and endopeptidase activity, phospholipid binding activity, transcription factor activity and transcription regulatory region sequence-specific dna binding activitiy. the underlying mechanism could be related to signal transduction, functional process, dna/rna transcription, protein degradation and signalling pathways such as cell killing and apoptotic signalling pathways.\\n\\nsummary: enriched functions include multiple binding activities, GO:0003824, and transcription regulatory activities for signal transduction, functional processes, and signalling pathways. \\nmechanism: signal transduction, functional processes, dna/rna transcription, protein degradation,]] \n", - " HALLMARK_COMPLEMENT-1 [[enzyme binding activity, GO:0101005, GO:0004197, GO:0005102, GO:0019901, sh2 domain binding activity, GO:0004435, GO:0003924, GO:0004222, atpase binding activity, integrin binding activity, dna binding activity, lipoprotein receptor binding activity, GO:0007165, GO:0006915, MESH:D015850]] \n", - " HALLMARK_DNA_REPAIR-0 [[the given list of human genes are primarily involved in dna binding, transcription and translational activities, rna binding, enzyme binding activities, and identical protein and nucleic acid binding activities. there is also evidence of involvement in activities such as transcription co-activator activity, nuclear localization, cytochrome-c oxidase activity, atp-dependent activities and endopeptidase activator activity. enriched terms include dna binding, GO:0003723, GO:0003887, GO:0046983, identical protein binding activity, transcription factor binding activity, GO:0003700, zinc ion binding activity, atp binding activity, protein binding activity]] \n", - " HALLMARK_DNA_REPAIR-1 [[dna binding activity, rna binding activity, transcription activity, enzyme binding activity, GO:0042803]] \n", - " HALLMARK_E2F_TARGETS-0 [[GO:0007049, GO:0006260, transcriptional regulation, post-transcriptional regulation, GO:0003682, GO:0140014, GO:0051169, GO:0046931]] \n", - " HALLMARK_E2F_TARGETS-1 [[dna binding activity, protein binding activity, histone binding activity, GO:0016887, enzyme binding activity, GO:0006260, GO:0006306, chromatin binding activity, GO:0042803, GO:0003887, rna binding activity]] \n", - " HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 [[extracellular matrix structural components, GO:0007160, protein domain specific binding activity, identical protein binding activity, GO:0048018, signaling receptor binding activity, metal ion binding activity, peptide hormone receptor binding activity, heparin binding activity, collagen binding activity, GO:0007165, GO:0005125]] \n", - " HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 [[protein binding activity, identical protein binding activity, metal ion binding activity, ion binding activity, actin binding activity, small molecule binding activity, fibronectin binding activity, collagen binding activity, integrin binding activity, procollagen binding activity, cadherin binding activity, phosphatidylinositol-3,4,5-trisphosphate binding activity, substrate-binding activity, GO:0005096, GO:0004867, GO:0005006, GO:0005024, GO:0004896, platelet-derived growth factor binding activity, nucleotide-binding transcription factor activity]] \n", - " HALLMARK_ESTROGEN_RESPONSE_EARLY-0 [[binding activity, transport activity, GO:0003824, adhesion activity, intracellular signaling, GO:0006351, neuronal development]] \n", - " HALLMARK_ESTROGEN_RESPONSE_EARLY-1 [[GO:0003677, GO:0051117, GO:0005515, GO:0016791, dehydrogenase activity, GO:0004016, GO:0055085, transcriptional regulation, GO:0007155, GO:0006915]] \n", - " HALLMARK_ESTROGEN_RESPONSE_LATE-0 [[protein binding activity, dna-binding, domain binding activity, carbohydrate binding activity, enzyme binding activity, ligand binding activity, transmembr]] \n", - " HALLMARK_ESTROGEN_RESPONSE_LATE-1 [[dna-binding, GO:0016563, GO:0005515, membrane transporter activity, GO:0016787, GO:0016310, ligand-mediated activity]] \n", - " HALLMARK_FATTY_ACID_METABOLISM-0 [[GO:0006631, GO:0006629, GO:0005975, GO:0003677, GO:0003723, protein homodimerization, GO:0000287, GO:0005524, GO:0046872, GO:0047617, GO:0003995, fad binding activity, nadph binding activity, homodimerization activity, GO:0000774, GO:0015254, GO:0004497, 5alpha-androstane-3alpha,17beta-diol dehydrogenase activity, GO:0008170, identical protein binding activity, GO:0016860, enzyme binding activity, GO:0004674, GO:0042803, GO:0004351, GO:0004222, ubiquitin binding activity, dna-binding]] \n", - " HALLMARK_FATTY_ACID_METABOLISM-1 [[GO:0016491, enzyme binding activity, dna binding activity, GO:0004090, GO:0052650, GO:0015245, nadph binding activity, GO:0042803, atp binding activity, receptor ligand binding activity, nad+ binding activity, smad binding activity, rna polymerase ii-specific transcription factor activity, atp-dependent protease activity, GO:0016404, GO:0004672, ubiquitin conjugating]] \n", - " HALLMARK_G2M_CHECKPOINT-0 [[GO:0003677, transcription binding, GO:0046872, GO:0005515, GO:0019899, MESH:D020558, GO:0003682, GO:0042826, GO:0046983, sumo-dependent ubiquitination, GO:0003723, GO:0005524, GO:0042054, GO:0008017, GO:0010997, boxh/aca snorna binding, GO:0043515, GO:0070840, m7gpppn-cap structure binding, GO:0008270, GO:0003697, GO:0038024, GO:0006200, GO:0051536, GO:0005884]] \n", - " HALLMARK_G2M_CHECKPOINT-1 [[GO:0005515, GO:0003677, GO:0006351, GO:0019904, GO:0042054, GO:0004402, GO:0004674, GO:0030374, GO:0005049, GO:0016887, zinc ion binding activity, GO:0140037, GO:0036310, sumo polymer binding activity, nuclear receptor binding activity, dna topoisomerase binding activity, GO:0010997, GO:0000774, GO:0005096, microtubule binding activity, dna replication origin binding activity, GO:0000987, rna polymerase ii-specific transcription]] \n", - " HALLMARK_GLYCOLYSIS-0 [[GO:0003676, GO:0005515, GO:0005524, metabolic activity, GO:0016310, MESH:D010084, GO:0005975, GO:0005125, GO:0008083]] \n", - " HALLMARK_GLYCOLYSIS-1 [[protein binding activity, identical protein binding activity, enzyme binding activity, atp binding activity, transcription activation activity, dna-binding transcription activity, heparin binding activity, cytoplasmic protein binding activity, signalling receptor binding activity, cytoskeletal protein binding activity, GO:0042803, GO:0060422, rna binding activity, GO:0140677, GO:0004689, phosphotransferase activity, heme binding activity, calcium ion binding activity]] \n", - " HALLMARK_HEDGEHOG_SIGNALING-0 [[GO:0007155, GO:0007165, epithelial-mesenchymal interaction, GO:0006898, GO:0001525, GO:0001843]] \n", - " HALLMARK_HEDGEHOG_SIGNALING-1 [[GO:0003700, rna polymerase ii transcription regulatory region sequence-specific dna binding activity, chromatin binding activity, receptor binding activity, GO:0005096, gtpase binding activity, phospholipid binding activity, calcium ion binding activity, zinc ion binding activity, identical protein binding activity, apolipoprotein binding activity, phosphotyrosine residue binding activity, very-low-density lipoprotein particle binding activity, phosphatidylcholine binding activity, phosphatidylethanolamine binding activity, adenyl ribonucleotide]] \n", - " HALLMARK_HEME_METABOLISM-0 [[identical protein binding activity, dna binding activity, rna binding activity, GO:0000988, GO:0003714, GO:0016564, GO:0016563, GO:0016791, protein kinase binding activity, GO:0006865, GO:0006811, heme binding activity, oxygen binding activity, protein-fructose gamma-glutamyltransferase activity, GO:0042803, lamin binding activity, chromatin binding activity and ubiquitin ligase activity]] \n", - " HALLMARK_HEME_METABOLISM-1 [[transcription activity, dna binding activity;rna binding activity, protein kinase binding activity, atp binding activity, protein binding activity, identical protein binding activity, GO:0042803, GO:0004197, GO:0015075, protein domain specific binding activity, GO:0032452, GO:0004674, GO:0016564, GO:0061630, lamin binding activity, GO:0004521, GO:0038023, GO:0004602, phosphoprotein binding activity, molecule adaptation, enzyme binding activity, protein phosphatase binding activity, GO:0004418, ubiquitin conjugating enzyme binding activity, GO:0004842, ap-2 adapt]] \n", - " HALLMARK_HYPOXIA-0 [[dna-binding transcription activity, enzyme binding activity, protein binding activity, ligand-binding activity, atp binding activity, nadp binding activity, metal ion binding activity, carbohydrate binding activity, signaling receptor binding activity, GO:0003714, GO:0001217, GO:0008160, heparin binding activity, n-acetylglucosamine n-sulfotransferase activity, MESH:D006497]] \n", - " HALLMARK_HYPOXIA-1 [[dna binding activity, rna binding activity, protein binding activity, GO:0004672, GO:0019887, GO:0016407, GO:0016301, GO:0008233, GO:0004197, GO:0004252, ubiquitin binding activity, GO:0042803, GO:0000988, GO:0016563, GO:0016564, apolipoprotein binding activity, phosphatase binding activity, disordered domain specific binding activity, chromatin binding activity, GO:0016303, GO:0030701, GO:0004693, GO:0004396, actinin binding activity, 14-3-3 protein binding activity, gtp binding activity, MESH:D009584]] \n", - " HALLMARK_IL2_STAT5_SIGNALING-0 [[ligand binding, GO:0019899, GO:0005102, MESH:M0518050, GO:0003700, rna-binding, protein homodimerization, protein-kinase binding activity, identical protein binding activity, GO:0004896, c-c chemokine binding activity, GO:0004197, GO:0022857, gtp binding activity, protease binding activity]] \n", - " HALLMARK_IL2_STAT5_SIGNALING-1 [[dna-binding, transcriptional activity, GO:0006355, GO:0005515, protein homodimerization, GO:0003924, GO:0005102, ligand-activated transcription, GO:0019900, GO:0002020, GO:0004674, GO:0004175, cystein-type endopeptidase activity, GO:0005102, GO:0061630, GO:0005125, GO:0008083, leukemia inhibitory factor activity, 5'-deoxyn]] \n", - " HALLMARK_IL6_JAK_STAT3_SIGNALING-0 [[GO:0038023, binding activity, MESH:D016207, MESH:M0496065, MESH:D008074, MESH:D010455, MESH:D011506, GO:0019900, GO:0005524]] \n", - " HALLMARK_IL6_JAK_STAT3_SIGNALING-1 [[GO:0004896, cxcr chemokine receptor binding activity, interleukin-binding activity, GO:0006952, GO:0010605, GO:0051247]] \n", - " HALLMARK_INFLAMMATORY_RESPONSE-0 [[protein binding activity, GO:0005125, GO:0004930, dna-binding transcription activity, lipopolysaccharide binding activity, atp binding activity, integrin binding activity, GO:0048018, GO:0022857, signaling receptor binding activity, extracellular atp-gated channel activity, phosphatidylinositol- 3-kinase activity, metallod]] \n", - " HALLMARK_INFLAMMATORY_RESPONSE-1 [[GO:0038023, binding activity, GO:0003824, GO:0008083, GO:0005215, GO:0000988]] \n", - " HALLMARK_INTERFERON_ALPHA_RESPONSE-0 [[signaling receptor binding activity, GO:0003713, regulation of transcription, dna-binding activity, rna binding activity, metal ion binding activity, identical protein binding activity, GO:0042803]] \n", - " HALLMARK_INTERFERON_ALPHA_RESPONSE-1 [[GO:0098542, GO:0006955, GO:0046718, GO:0032020, GO:0019882, GO:0019221, GO:0045087, GO:0007166, GO:0030225, GO:0032722, GO:0001961, cell-cell adhesion mediated by plasma membrane cell adhesion molecules]] \n", - " HALLMARK_INTERFERON_GAMMA_RESPONSE-0 [[the list of genes are discovered to be enriched in terms like dna binding activities, GO:0042803, GO:0000988, GO:0004672, GO:0004725, GO:0016887, enzyme binding activity, phosphatidylinositol phosphate binding activity, GO:0030528, GO:0008009, and cytokine receptor activity.\\n\\nmechanism: the biological mechanism underlying the enriched terms is most likely associated with cell and immune response. these genes are involved in various processes related to cell signaling, detection, recognition, GO:0006351, and expression. through these processes, the genes regulate important functions such as cell adhesion, GO:0005515, GO:0019899, GO:0005125, and transcription factor activation. in addition, several of these genes are also involved in apoptotic and other cell regulation pathways]] \n", - " HALLMARK_INTERFERON_GAMMA_RESPONSE-1 [[binding activity, GO:0003824, protein activity, GO:0000981]] \n", - " HALLMARK_KRAS_SIGNALING_DN-0 [[protein binding activity, transmembrane activity, GO:0003700, sequence-specific double-stranded dna binding activity, GO:0004930, identical protein binding activity, calcium ion binding activity, scaffold protein binding activity, transcription cis-regulatory region binding activity]] \n", - " HALLMARK_KRAS_SIGNALING_DN-1 [[dna-binding activity, transcription activity, calcium ion binding activity, atp-binding activity, protein binding activity, GO:0004930, cell death regulation, GO:0009653, GO:0042445]] \n", - " HALLMARK_KRAS_SIGNALING_UP-0 [[cell adhesion molecule binding activity, atpase-coupled intramembrane transport, GO:0004222, GO:0042803, signal receptor binding activity, GO:0003700, MESH:D006493]] \n", - " HALLMARK_KRAS_SIGNALING_UP-1 [[GO:0005125, protein domain specific binding activity, protein kinase binding activity, cell adhesion molecule binding activity, signaling receptor binding activity, GO:0004222, GO:0001217, rna binding activity, gtpase binding activity, structural proteins, atp binding activity]] \n", - " HALLMARK_MITOTIC_SPINDLE-0 [[protein binding activity, cytoskeleton binding activity, GO:0005096, atpase binding activity, GO:0042030, adenyl ribonucleotide binding activity, calmodulin binding activity, cadherin binding activity, gamma-tubulin binding activity, integrin binding activity, kinetochore binding activity, molecular function adaptor activity, GO:0042803, protein kinase binding activity, protein phosphatase binding activity, sh2 domain binding activity, sh3 domain binding activity, small gtpase binding activity, beta-catenin binding activity, beta-tubulin binding activity, dynein complex binding activity, identical protein binding activity, phosphatidylcholine binding activity, protein domain specific binding activity, protein tyrosine kinase binding activity]] \n", - " HALLMARK_MITOTIC_SPINDLE-1 [[MESH:D020558, atpase, tubulin binding activity, microtubule binding activity, actin filament binding activity, kinesin binding activity, dynein binding activity, g protein-coupled receptor binding activity]] \n", - " HALLMARK_MTORC1_SIGNALING-0 [[enzyme binding activity, acid binding activity, molecule transport, adapter binding activity, receptor binding activity, dna binding activity, protein binding activity, GO:0003824, GO:0016787, GO:0016491, anion binding activity, GO:0008233, GO:0140657, thioredoxin activity, translocation, GO:0061630, cysteine endopeptidase activity, GO:0004738, GO:0004618, magnesium ion binding activity, GO:0004340, GO:0003924]] \n", - " HALLMARK_MTORC1_SIGNALING-1 [[protein binding activity, identical protein binding activity, GO:0008233, GO:0003824, GO:0005884, dna-binding, rna-binding, GO:0016922, MESH:D054875, anion binding activity, atp binding activity, GO:0016887, protein kinase binding activity, phosphotyrosine residue binding activity, e3 ubiquitin-protein ligase binding activity, mdm2 binding activity, GO:0060090, GO:0140677, GO:0098772, GO:0003713, GO:0003714, GO:0016564, GO:0042803, k63]] \n", - " HALLMARK_MYC_TARGETS_V1-0 [[GO:0003677, GO:0003723, GO:0003682, GO:0006351, GO:0006412, GO:0045292, atpase binding activity, enzyme binding activity, GO:0044183, ubiquitin protein ligase, MESH:C021362, nf-kappab binding activity, GO:0140693, nucleic acid binding activity, heparan sulfate binding activity, biopolymer binding activity, GO:0060090, GO:0140678, g-protein beta-subunit binding activity, molecular sequence recognition, complementary rna strand recognition, mrna 3'-utr]] \n", - " HALLMARK_MYC_TARGETS_V1-1 [[rna binding activity, identical protein binding activity, mrna 3' utr binding activity, GO:0000900, dna binding activity, ubiquitin protein ligase binding activity, protein domain specific binding activity, GO:0006457, dna replication origin binding activity, dna-binding transcription factor binding activity, GO:0042803]] \n", - " HALLMARK_MYC_TARGETS_V2-0 [[GO:0006351, GO:0006351, GO:0008284, GO:0071824, GO:0019219, rna binding activity, GO:0010468, GO:0006364]] \n", - " HALLMARK_MYC_TARGETS_V2-1 [[rna binding activity, dna binding activity, protein binding activity, GO:0006364, GO:0019538, GO:0006351, transcription coregulator binding activity, GO:0022402, GO:0003682, mitochondria regulation, cyclin binding activity, cyclin-dependent protein serine/threonine kin]] \n", - " HALLMARK_MYOGENESIS-0 [[GO:0008092, GO:0005201, GO:0044325, ion channel regulator, GO:0003779, GO:0005096, GO:0051879, GO:0017046, GO:0003677, signalling receptor binding, GO:0042802, GO:0048306, GO:0019899, GO:0005509, GO:0005524, GO:0006200, GO:0051117, GO:0004017, GO:0008195, GO:0051015, microfilament binding, GO:0003872, GO:0043138, GO:0004517, MESH:D009243]] \n", - " HALLMARK_MYOGENESIS-1 [[GO:0005509, GO:0004129, GO:0003677, GO:0005524, GO:0003779, abnormal growth and development, GO:0002020, structural constituent]] \n", - " HALLMARK_NOTCH_SIGNALING-0 [[GO:0036211, MESH:D005786, signal transduction regulation, dna-templated transcription regulation, GO:0007219, GO:0016567, GO:0031146, GO:0045893]] \n", - " HALLMARK_NOTCH_SIGNALING-1 [[GO:0006351, GO:0036211, MESH:D054875, GO:0065007, GO:0007219, GO:0031146, wnt, GO:0016567, GO:0043543, GO:0004879, GO:0003714, transcription corepressor binding activity, GO:0006351, rna polymerase ii-specific dna-binding transcription repressor activity, GO:0045893, GO:0000122, GO:0045737, GO:0010604, GO:0010628, negative regulation of cell different]] \n", - " HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 [[GO:0006118, GO:0020037, GO:0005515, GO:0016491, atpase activity & binding activity, GO:0060090, acyl binding activity, GO:0003954, gtp binding activity, iron-sulfur cluster binding activity, fad binding activity, MESH:D010758, GO:0019395, rna binding activity, 4 iron, 4 sulfur cluster binding activity, ubiquitin protein ligase binding activity, GO:0004129, proton-transporting atp synthase activity, lipoic acid binding activity, mhc class i protein binding activity, angiostatin binding activity, deltarasin binding activity, ubiquitin protein binding activity, nadp binding activity]] \n", - " HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 [[GO:0140657, GO:0009055, GO:0008553, ubiquitin protein ligase binding activity, MESH:D014451, heme binding activity, protein homodimerization, mhc class i protein binding activity, metal ion binding activity, angiostatin binding activity, mitochondrion targeting sequence binding activity, GO:0015227, rna binding activity, 4 iron, 4 sulfur cluster binding activity, GO:0000295, GO:0004129, fatselytranstransferase activity, GO:0003925, acyl-coa c-acetyltransferase activity, GO:0004774, GO:0003994, GO:0004095, GO:0003958, acetate coa-transfer]] \n", - " HALLMARK_P53_PATHWAY-0 [[GO:0003700, protein binding activity, protein kinase binding activity, GO:0042803, enzyme binding activity, GO:0098631, signaling receptor binding activity, actin binding activity, cyclin binding activity, GO:0005198, GO:0030695]] \n", - " HALLMARK_P53_PATHWAY-1 [[dna binding activity, rna binding activity, rna polymerase binding activity, GO:0004672, GO:0042803, protein kinase binding activity, GO:0000988, GO:0003924, GO:0098631, cell signaling receptor binding activity, enzyme binding activity, heme binding activity, collagen binding activity, GO:0004392, GO:0060090, GO:0004527, GO:0042803, g protein-coupled receptor binding activity, GO:0022857, identical protein binding activity, GO:0016787, GO:0008083]] \n", - " HALLMARK_PANCREAS_BETA_CELLS-0 [[GO:0006351, GO:0016563, atpase-coupled ion transport, GO:0004672, GO:0008233, dna binding activity, GO:0017156, GO:1903530]] \n", - " HALLMARK_PANCREAS_BETA_CELLS-1 [[transcription regulation, GO:0098609, GO:0007165, GO:0045047, GO:0030041, GO:0051594, GO:0060291, GO:1903561, GO:0030027, GO:0005881, GO:0043195, GO:0005829, GO:0030425, MESH:D012319, dna-templated trans]] \n", - " HALLMARK_PEROXISOME-0 [[molecular binding activity, GO:0003824, GO:0005215, domain binding activity, GO:0006869, GO:0015031, GO:0006259, GO:0016070]] \n", - " HALLMARK_PEROXISOME-1 [[genes involved in this list are primarily associated with the metabolic or structural processes needed for cellular development and homeostasis. enriched terms include fatty acid metabolism, protein homodimerization, MESH:D010084, dna and rna binding, enzyme/acyl-coa/gtpase binding/hydrolase activity, transport/export/import, and regulation of transcription by rna polymerase ii. mechanism: these genes act together to provide a plethora of functions that are integral to the growth, maintenance and protection of cells. fatty acids are transported, oxidized, and bound to proteins or phospholipids in the membrane, proteins interact with atp and gtp and undergo homodimerization, transcriptional activity is regulated by heterodimerizing with transcription factor proteins]] \n", - " HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 [[protein binding activity, GO:0016301, GO:0005048, GO:0005102, GO:0051726, apoptosis regulation, GO:0007165, rna binding activity, GO:0004721, GO:0004620, GO:0003924, 1-phosphatidylinositol phospholipase activity, phosphotyrosine residue binding activity, GO:0000774, guanyl ribonucleotide binding activity, GO:0004869, GO:0051219, GO:0044325, GO:0008092, GO:0050750, GO:0003713, GO:0050681, nuclear receptor coactiv]] \n", - " HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 [[the genes in this list are involved in several biological functions, including signal transduction, GO:0006915, cellular response to stimuli, response to dna damage, GO:0051726, and regulation of protein phosphorylation and ubiquitination. the terms \"protein phosphorylation\"; \"ubiquitination\"; \"signal transduction\"; \"cellular response to stimulus\"; \"dna damage response\"; \"regulation of cell cycle\"; \"intrinsic apoptosis\"; and \"scaffold protein\" are all statistically over-represented.\\n\\nmechanism: signaling pathways and cellular processes are intricately regulated and require the coordinated participation of different proteins. by performing a term enrichment analysis, we see that the genes in this list are involved in a variety of molecular pathways, including signal transduction, GO:0006915, cellular response to stimuli, response to dna damage, GO:0051726, and regulation of protein phosphorylation and ubiquitination. this suggests that the gene products help coordinate these pathways by forming complexes, binding to signaling molecules, or carrying out the necessary enzyme activities. this suggests the underlying biological mechanism may involve interplay between specific gene products, MESH:D011506, signaling molecules to ensure efficient functioning of the cell]] \n", - " HALLMARK_PROTEIN_SECRETION-0 [[protein binding activity, GO:0003924, gtp-dependent protein binding activity, snare binding activity, enzyme binding activity, protein kinase binding activity, clathrin binding activity, GO:0006897, retrograde transport, GO:0006893, GO:0006888, GO:0006622]] \n", - " HALLMARK_PROTEIN_SECRETION-1 [[protein binding activity, activity, GO:0042803, enzyme binding activity, scaffold protein binding activity, snare receptor activity, syntaxin binding activity, GO:0016887, GO:0008553, GO:0008320, metal ion binding activity, protein foldinactivity, GO:0003924, protein kinase binding activity, phosphat]] \n", - " HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 [[oxidative stress defense, GO:0098754, dna/rna binding, GO:0006351, GO:0098609, GO:0016043, GO:0019722, GO:0006468, GO:0010731, GO:0004392, GO:0019511, GO:0061621, GO:0005886, GO:0006750, GO:0006082]] \n", - " HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 [[MESH:D004734, oxidative stress response, GO:0042803, protein phosphatase 2a binding activity, GO:0004601, GO:0004602, GO:0047499, GO:0003954, chromatin dna binding activity, GO:0004861, GO:0004784, GO:0047184, GO:0015038, GO:0015035, phosphatidylinositol binding activity, GO:0004096, heme binding activity]] \n", - " HALLMARK_SPERMATOGENESIS-0 [[GO:0003723, GO:0031491, transcription and regulation, GO:0003677, GO:0004672, protein folding and chaperoning, metabolic regulation, MESH:D054875]] \n", - " HALLMARK_SPERMATOGENESIS-1 [[GO:0019899, GO:0005515, ligand binding, GO:0005509, GO:0000166, GO:0008134, GO:0003677, GO:0005525, GO:0042562, GO:0006200, GO:0004672, GO:0003723, GO:0008047, GO:0044183, GO:0003682, GO:0019903, GO:0019212, GO:0008233, GO:0022890]] \n", - " HALLMARK_TGF_BETA_SIGNALING-0 [[GO:0007165, regulation of transcription, GO:0051246, regulation of macromolecule metabolism, GO:0050794, interaction with transcription factors, interaction with smad proteins]] \n", - " HALLMARK_TGF_BETA_SIGNALING-1 [[tgf binding activity, dna-binding transcription factor binding activity, smad binding activity, GO:0019211, GO:0004674, GO:0004869, GO:0061631, myosin binding activity, r-smad binding activity, beta-catenin binding activity, cadherin binding activity, gtp binding activity, i-smad binding activity, GO:0003924, GO:0003714, GO:0042803, nucleic acid binding activity, serine-type endope]] \n", - " HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 [[dna binding transcription factor, GO:0005102, GO:0019899, GO:0005126, growth factor, transmembrane receptor]] \n", - " HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 [[GO:0000988, rna polymerase ii-specific, dna-binding, identical protein binding activity, enzyme binding activity, signaling receptor binding activity, GO:0004672, GO:0005125, GO:0008083, GO:0098631, GO:0022857, GO:0016791, gtp binding activity, GO:0140657]] \n", - " HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 [[GO:0006457, GO:0003723, transcription activator, GO:0003677, GO:0051082, GO:0003720, GO:0003676, GO:0044325, GO:0005524, GO:0006402, translation regulation, GO:0003755, GO:0035925]] \n", - " HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 [[atp binding activity, GO:0016887, enzyme binding activity, identical protein binding activity, GO:0060090, GO:0140678, nucleic acid binding activity, GO:0046983, protein folding chaperone binding activity, ribosome binding activity, rna binding activity, snare binding activity, transcription corepressor binding activity, transcription regulator]] \n", - " HALLMARK_UV_RESPONSE_DN-0 [[genes included in this set are involved in various cellular functions such as enzyme binding activity, GO:0003924, lipoprotein binding activity, GO:0004620, and other related activities. common enriched terms across these genes include protein binding activity, smad binding activity, dna-binding activity, phosphotyrosine residue binding activity, GO:0003824, GO:0003924, and enzymatic inhibitor activity. mechanism: these genes are likely to be involved in regulation and control of cellular functions and processes through various proteins. this regulation and control is likely being done through interaction of the proteins encoded by these genes with other proteins and structurally with dna, as well as through the enzymatic activities of the encoded proteins]] \n", - " HALLMARK_UV_RESPONSE_DN-1 [[dna binding activity, GO:0000988, protein binding activity, smad binding activity, GO:0005096, MESH:C062738]] \n", - " HALLMARK_UV_RESPONSE_UP-0 [[GO:0005515, GO:0003677, binding activity, receptor binding activity, GO:0004672, GO:0007155, GO:0023052, GO:0010468]] \n", - " HALLMARK_UV_RESPONSE_UP-1 [[gtp binding activity, dna binding activity, GO:0016563, protein kinase binding activity, GO:0004175]] \n", - " HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 [[the genes summarized above are all involved in developmental processes, such as organizing and regulating cell adhesion, components of the wnt pathway and regulation of gene expression. the enriched terms for these genes would be development-related terms, such as cell adhesion, GO:0060070, GO:0006468, GO:0016567, GO:0006351, GO:0006476, GO:0006351, and protein stability.\\n\\nmechanism: the underlying biological mechanism involves the involvement of many of these genes in the wnt pathway, which is a conserved signaling pathway involved in cell-cell communication and a variety of developmental processes. another mechanism involves the regulation of gene expression and the binding of dna-binding transcription factors, as well as protein ubiquitination and deacetylation which also control gene expression]] \n", - " HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 [[GO:0005515, transcription regulation, GO:0051726, GO:0007165, response pathways]] \n", - " T cell proliferation-0 [[signaling receptor binding activity, protein kinase binding activity, GO:0061630, GO:0035556, GO:0001816, GO:0010467]] \n", - " T cell proliferation-1 [[GO:0048018, phosphotyrosine residue binding activity, cytoskeletal protein binding activity, GO:0005574]] \n", - " Yamanaka-TFs-0 [[transcription repressor and activator activities, rna polymerase ii-specific, nucleic acid binding activity, GO:0009889, GO:0009966, GO:0010468, GO:0045765, and protein-dna complex organization, GO:0042127]] \n", - " Yamanaka-TFs-1 [[dna-binding, GO:0016563, GO:0016564, GO:0000988, rna binding activity, ubiquitin protein ligase binding activity, GO:0010628, GO:0010629, GO:0009889, GO:0045765, GO:0060828, GO:0009966, transcription cis-regulatory region binding activity, GO:0045944, GO:0003130, GO:0001714]] \n", - " amigo-example-0 [[GO:0005515, GO:0060230, GO:0005543, MESH:M0518050, GO:0050804]] \n", - " amigo-example-1 [[GO:0005515, GO:0043167, GO:0008009, GO:0019838, signal receptor binding, GO:0019902, GO:0016477, GO:0086009, GO:0007165, GO:0065007, GO:0006952]] \n", - " bicluster_RNAseqDB_0-0 [[GO:0005509, double-stranded dna-binding, cell adhesion and migration, transcriptional regulation]] \n", - " bicluster_RNAseqDB_0-1 [[metal ion binding activity, protein binding activity, rna binding activity, GO:0019208, GO:0005243, GO:0042803, calcium ion binding activity, MESH:C086554]] \n", - " bicluster_RNAseqDB_1002-0 [[UBERON:0001134, GO:0006936, GO:0016567, GO:0045010, calcium-dependent signaling, GO:0010468, GO:0006468, GO:0043687, GO:0042692, GO:0060537, MONDO:0020121, muscle organelle organization]] \n", - " bicluster_RNAseqDB_1002-1 [[actin binding activity, GO:0007015, muscle alpha-actinin binding activity, GO:0006936, GO:0060415, GO:0071689, GO:0004672, protein phosphatase binding activity, GO:0043502, tropomyosin binding activity, troponin binding activity, troponin complex activities]] \n", - " endocytosis-0 [[protein signaling, GO:0006468, GO:0016567, GO:0015031, GO:0030030, GO:0006897, GO:0006898, GO:0035091, GO:0001766, GO:0097320]] \n", - " endocytosis-1 [[GO:0006897, GO:0005515, GO:0006869, GO:0016567, GO:0042632, GO:0035727]] \n", - " glycolysis-gocam-0 [[GO:0019538, enzymatic activity, protein transcription, cell metabolism, carbohydrate phosphorylation and metabolism, protein homeostasis, cell signaling, GO:0008104, cell homeostasis, cellular energy production]] \n", - " glycolysis-gocam-1 [[GO:0003824, GO:0031625, protein homodimerization, GO:0016310, GO:0006096, GO:1904659, GO:0070061, GO:0004332, GO:0004618, GO:0004619, GO:0004396, peptidoglycan binding activity, GO:0003872, GO:0004807, GO:0004347, GO:0021762, binding activity of sperm to zona pellucida, GO:0030388, GO:0019725, GO:0046716, GO:0071456, GO:0016525, UBERON:2005050]] \n", - " go-postsynapse-calcium-transmembrane-0 [[GO:0097553, GO:1990034, GO:0071318, GO:0007186, GO:0035235, GO:1990454, GO:0017146, GO:0014066, GO:1900274, GO:0099509, GO:2000300, GO:0032680, GO:0005245, GO:2000311, GO:0080164]] \n", - " go-postsynapse-calcium-transmembrane-1 [[GO:0006816, regulation of calcium]] \n", - " go-reg-autophagy-pkra-0 [[these genes are involved in several cellular activities, primarily in their roles in signal transduction pathways, GO:0036211, protein folding and stability, GO:0051726, and apoptosis. the terms enriched are: signaling receptor activity; protein phosphorylation; regulation of macromolecule biosynthetic process; autophagy; g2/m transition of mitotic cell cycle; chromosome segregation; cytoplasmic stress granule; torc1 signaling; defense response; anoikis; protein folding chaperone; histone acetylation; i-kappab kinase/nf-kappab signaling; k63-linked polyubiquitin modification-dependent protein binding activity.\\n\\nmechanism: these genes participate in a variety of biological processes, including signal transduction pathways, GO:0036211, GO:0051726, apoptosis and dna-templated transcription, answering to different external and internal stimuli as well as aiding in cell survival and death. the enriched terms involve protein-protein interactions and modifications, as well as involvement in akt/pi3k, tor, and nf-kb pathways that are essential for cell signaling, typical in response to bacterial infection and the activation of pro-survival mechanisms]] \n", - " go-reg-autophagy-pkra-1 [[protein binding activity, metal ion binding activity, protein kinase binding activity, GO:0030295, protein folding chaperone activity, GO:0042803, chromatin binding activity, GO:0003713, GO:0016410, GO:0016538, GO:0016303, card domain binding activity, heat shock protein binding activity, muramyl dipeptide binding activity, 14-3-3 protein binding activity, rna polymerase iii cis-regulatory region sequence-specific dna binding activity]] \n", - " hydrolase activity, hydrolyzing O-glycosyl compounds-0 [[the genes in this list share functions involving glycoprotein and carbohydrate metabolic processes and structural functions related to extracellular matrix organization. enriched terms include: dihydroceramidase activity, GO:0017040, GO:0061463, GO:0004134, GO:0004135, GO:0004556, hyaluronic acid binding activity, GO:0004415, GO:0004568, GO:0008843, clathrin heavy chain binding activity, GO:0008422, GO:0004348, GO:0004336, GO:0004553, GO:0008375, GO:0004563, identical protein binding activity, syndecan binding activity, heparan sulfate proteoglycan binding activity, GO:0003796, GO:0004567]] \n", - " hydrolase activity, hydrolyzing O-glycosyl compounds-1 [[GO:0006516, GO:0006027, heparan sulfate catabolism, glucoside catabolism, GO:0036508, GO:0006517, GO:0005975, GO:0006869, GO:0030214, receptor signaling, GO:0031589, GO:0009313, GO:0004672, GO:0008283, GO:0019915, GO:0050885, GO:0042742, GO:0005989, GO:0008344, GO:0007605, GO:0006487, GO:0006281, GO:0071451, peptidyl-serine]] \n", - " ig-receptor-binding-2022-0 [[immunoglobulin receptor binding activity, antigen binding activity, fc-gamma receptor i complex binding activity, GO:0004715, phosphotyrosine residue binding activity, peptidoglycan binding activity, phosphatidylcholine binding activity. mechanism: the genes listed appear to be involved in the regulation of the immune response. they likely aid in the recognition of pathogens, binding to the appropriate receptors, triggering a signal for an immune response. they may also play a role in enabling the recognition of self-antigens inhibiting a response to them]] \n", - " ig-receptor-binding-2022-1 [[antigen binding activity, immunoglobulin receptor binding activity, GO:0098542, GO:0002253, fc-gamma receptor i complex binding activity, GO:0004715, peptidoglycan binding activity, phosphatidylcholine binding activity, GO:0007229, GO:0038187, mannose binding activity, phosphotyrosine residue binding activity, GO:0051130, GO:0045657, protection of host from foreign agent]] \n", - " meiosis I-0 [[these genes are involved in processes related to dna binding, repair, replication, recombination, and regulation thereof. the enriched terms would be: dna binding, GO:0003690, dna damage repair, GO:0006310, GO:0005515, meiotic recombination, GO:0007059, GO:0000278, GO:0071173, GO:0051289, GO:0003682, resolution of meiotic recombination intermediates. \\nmechanism: the underlying biological mechanism is that these proteins work together to maintain genomic stability, regulate gene expression, promote proper cell division, germline cell development, meiosis]] \n", - " meiosis I-1 [[GO:0140013, dna binding activity, GO:0006259, GO:0035825, telomere attachment, GO:0000785, GO:0000795, GO:0005694, GO:0005737]] \n", - " molecular sequestering-0 [[calcium ion binding activity, identical protein binding activity, GO:0004252, GO:0140314, calcium-dependent protein binding activity, arginine binding activity, GO:0140313, enzyme binding activity, GO:0019887, nf-κb binding activity, nuclear localization sequence binding activity, oxysterol binding activity, rage receptor binding activity, ubiquitin protein ligase binding activity, actin binding activity, rig-i binding activity, GO:0003713, zinc ion binding activity, GO:1903231]] \n", - " molecular sequestering-1 [[protein binding activity, GO:0140313, GO:0000988, GO:0019887, calcium ion binding activity, dna-binding activity, ubiquitin protein ligase binding activity, tumor necrosis factor binding activity, regulatory pathway activity]] \n", - " mtorc1-0 [[enzyme binding activity, acid binding activity, molecule transport, adapter binding activity, receptor binding activity, dna binding activity, protein binding activity, GO:0003824, GO:0016787, GO:0016491, anion binding activity, GO:0008233, GO:0140657, thioredoxin activity, translocation, GO:0061630, cysteine endopeptidase activity, GO:0004738, GO:0004618, magnesium ion binding activity, GO:0004340, GO:0003924]] \n", - " mtorc1-1 [[cytoskeleton protein binding, phosphatase binding activity, GO:0016491, cell development and signaling activity, dna binding activity, cellular transporter activity, protein kinase binding activity]] \n", - " peroxisome-0 [[peroxisome biogenesis, protein import into peroxisome, GO:0000425, GO:0000268, GO:0140036, GO:0006631, protein homodimerization, enzyme binding activity, GO:0050821, GO:0043335]] \n", - " peroxisome-1 [[GO:0016558, GO:0050821, GO:0042127, protein-lipid binding, GO:0007031, GO:0008611, GO:0001881, GO:0006631]] \n", - " progeria-0 [[GO:0003677, GO:0005515, GO:0046872, cellular response to radiation, hypoxia, and starvation, GO:0042981, GO:0032204, GO:0010835, GO:0045069]] \n", - " progeria-1 [[dna damage and repair, GO:0005515, GO:0046872, homodimerization, GO:0006915, MESH:D016922, GO:0001666]] \n", - " regulation of presynaptic membrane potential-0 [[GO:0005216, GO:0016917, GO:0008066, GO:0007186, GO:0007214, GO:0006836, GO:0005249, GO:0005248, GO:0007193]] \n", - " regulation of presynaptic membrane potential-1 [[GO:0005216, membrane potential regulation, GO:0015276, g protein-coupled receptor signaling, GO:1902476, GO:0007214, GO:0071805]] \n", - " sensory ataxia-0 [[dna-binding, rna polymerase ii-specific activity, GO:0046872, GO:0031625, GO:0045944, GO:0002639, GO:1901184, GO:0033157, monoatomic cation]] \n", - " sensory ataxia-1 [[transcription regulation, nucleic acid metabol]] \n", - " term-GO:0007212-0 [[g protein-coupled receptor binding activity, GO:0003924, enzyme binding activity, GO:0042803, signaling receptor binding activity, GO:0004016, g-protein beta/gamma-subunit complex binding activity, signaling receptor binding activity, clathrin light chain binding activity, sequence-specific double-stranded dna binding activity, GO:0004672, nf-kappab binding activity, protein kinase a catalytic subunit binding activity, GO:0004674]] \n", - " term-GO:0007212-1 [[GO:0004672, g-protein activity, g-protein beta/gamma- subunit complex binding activity, atpase binding activity, GO:0004016, protein-folding chaperone binding activity, signal receptor binding activity, GO:0071333, GO:0007165, negative regulation of nf-kappa b transcription factor activity, GO:2000394, GO:0007212, cellular response to prostaglandin e, GO:0007204]] \n", - " tf-downreg-colorectal-0 [[GO:0003677, GO:0003723, GO:0003682, GO:0008134, GO:0003713, GO:0016564, MESH:M0518050, GO:0019899]] \n", - " tf-downreg-colorectal-1 [[GO:0006351, dna-binding, rna polymerase ii-specific, transcription activator/transcription repressor, cis-regulatory region sequence-specific, GO:0001221, GO:0006355, GO:0006337, GO:0009966]] \n", - "\n", - "prompt_variant v2 \n", - "model method geneset \n", - "gpt-3.5-turbo narrative_synopsis EDS-0 [[GO:0032964, matrix maturation, GO:0031012, MESH:D006023, MESH:D015238, zinc finger proteins, proteolytic subunits, MESH:D057057, MESH:M0465019]] \n", - " EDS-1 [[GO:0032964, GO:0030198, GO:0006457, GO:0006955]] \n", - " FA-0 [[GO:0006281, GO:0035825, fanconi anemia pathway]] \n", - " FA-1 [[GO:0006281, GO:0035825, MESH:D051856, rad51 family proteins, chromosome stability maintenance\\n\\nmechanism: these genes are involved in dna damage repair and maintenance of genome stability, particularly through homologous recombination and the formation of the fanconi anemia complementation group proteins. the rad51 family proteins and chromosomal stability maintenance are also important in these processes]] \n", - " HALLMARK_ADIPOGENESIS-0 [[mitochondrial function, GO:0008152, GO:0006118, GO:0006631, redox reactions]] \n", - " HALLMARK_ADIPOGENESIS-1 [[mitochondrial function; energy metabolism; lipid metabolism; electron transport chain. \\n\\nmechanism: these genes likely contribute to the production and regulation of energy in the form of atp through processes including beta-oxidation of lipids, GO:0006119, and electron transport chain activity. dysfunction or dysregulation of these genes may lead to mitochondrial dysfunction and impaired energy metabolism, which have been implicated in various diseases including neurodegenerative disorders, MONDO:0004995, MONDO:0005066]] \n", - " HALLMARK_ALLOGRAFT_REJECTION-0 [[GO:0005125, GO:0042110, GO:0042379, GO:0002429, GO:0032623, GO:0032609, GO:0002504, GO:0050776, GO:0030217, GO:0050900, GO:0060333, GO:0001819, GO:0002685, GO:0070098, GO:0050852]] \n", - " HALLMARK_ALLOGRAFT_REJECTION-1 [[GO:0008009, cytokine signaling, GO:0019882]] \n", - " HALLMARK_ANDROGEN_RESPONSE-0 [[GO:0004672, GO:0031344, GO:0008285, GO:0010468, regulation of cellular protein localization and movement]] \n", - " HALLMARK_ANDROGEN_RESPONSE-1 [[GO:0004672, GO:0008134, GO:0006810, enzymatic activity, GO:0006511, GO:0061024, GO:0042445, GO:0016567]] \n", - " HALLMARK_ANGIOGENESIS-0 [[GO:0030198, GO:0007155, GO:0030199, GO:0006029, GO:0045765, GO:0009611]] \n", - " HALLMARK_ANGIOGENESIS-1 [[GO:0030198, GO:0007155, GO:0007088, protein kinase activity regulation, GO:0070848, cellular response to transforming growth factor beta stimulus\\n\\nmechanism: the genes listed are involved in the organization of the extracellular matrix and cell adhesion. specifically, they play roles in binding to and regulating the spacing of collagen fibrils, inhibiting proteases, promoting cell-cell and cell-matrix interactions, and regulating mitosis and protein kinase activity. growth factors and transforming growth factor beta are also involved in signal transduction pathways that are regulated by these genes]] \n", - " HALLMARK_APICAL_JUNCTION-0 [[GO:0007155, GO:0007010, GO:0005925, GO:0070160]] \n", - " HALLMARK_APICAL_JUNCTION-1 [[GO:0070160, GO:0007155, GO:0008014, integrin, GO:0007165, adhesion g-protein coupled receptor (gpcr), GO:0015629, UBERON:4000022, protein tyrosine kinase (ptk), GO:0016303, map kinase, MESH:D016212]] \n", - " HALLMARK_APICAL_SURFACE-0 [[GO:0007166, GO:0007169, GO:1901796, GO:0019048, GO:0045785, GO:0043408, GO:2000145, GO:0032956, GO:0051897, GO:0048015, GO:0010810, GO:0030334, regulation of cell growth\\n\\nmechanism and hypotheses: the enriched terms suggest a common mechanism involving transmembrane signaling pathways, with a focus on cell adhesion, migration, and growth regulation. several of the genes are involved in the regulation of the mapk signaling pathway, which is known to play a central role in cellular processes such as proliferation, differentiation, and apoptosis. pathway analysis of these genes may further elucidate the specific regulatory mechanisms at play]] \n", - " HALLMARK_APICAL_SURFACE-1 [[GO:0007160, GO:0006811, GO:0007165, GO:0098631, insulin regulation, GO:0016485]] \n", - " HALLMARK_APOPTOSIS-0 [[GO:0006915, GO:0008219, GO:0007165]] \n", - " HALLMARK_APOPTOSIS-1 [[GO:0097153, GO:0042981, positive regulation of dna fragmentation, GO:0043067, GO:0010941, GO:1901796, GO:0006974, GO:0070613]] \n", - " HALLMARK_BILE_ACID_METABOLISM-0 [[GO:0006869, GO:0008203, GO:0006631, peroxisomal biogenesis, GO:0004448, GO:0008146]] \n", - " HALLMARK_BILE_ACID_METABOLISM-1 [[GO:0007031, GO:0001676, GO:0006699, GO:0008202, GO:0008203, GO:0001523, GO:0006635, alpha-oxidation, GO:0006720, lipid metabolic process \\n\\nmechanism: these genes function in a variety of processes involved in lipid metabolism and peroxisome biogenesis. peroxisomes are intracellular organelles involved in many metabolic pathways, including fatty acid beta-oxidation, which our enriched terms suggest is a common theme among these genes. additionally, these genes are involved in the synthesis of bile acids, steroid hormones, and retinoids, highlighting the importance of lipid metabolism in cellular function]] \n", - " HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 [[GO:0006629, GO:0006869, GO:0008610]] \n", - " HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 [[GO:0006695, GO:0006644, GO:0006633, GO:0016125]] \n", - " HALLMARK_COAGULATION-0 [[GO:0007596, extracellular matrix remodeling, GO:0030449]] \n", - " HALLMARK_COAGULATION-1 [[extracellular matrix breakdown, GO:0007596, protein inhibition]] \n", - " HALLMARK_COMPLEMENT-0 [[GO:0008233, GO:0007596, GO:0006956]] \n", - " HALLMARK_COMPLEMENT-1 [[GO:0006956, GO:0007596, GO:0006955, GO:0030168, cytokine signaling, GO:0002685, response to virus.\\n\\nmechanism: these genes are involved in regulating different aspects of immune response, including complement activation, platelet activation, cytokine signaling, and leukocyte migration. they are also involved in blood coagulation, which can be activated during an immune response to prevent pathogen spread. the over-representation of these genes suggests that immune activation and regulation are key to the identified biological process]] \n", - " HALLMARK_DNA_REPAIR-0 [[GO:0006281, transcription initiation, GO:0009117]] \n", - " HALLMARK_DNA_REPAIR-1 [[GO:0006281, transcription regulation]] \n", - " HALLMARK_E2F_TARGETS-0 [[GO:0006260, GO:0006281, GO:0051276]] \n", - " HALLMARK_E2F_TARGETS-1 [[GO:0006260, GO:0006281, cell-cycle checkpoint regulation]] \n", - " HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 [[GO:0030198, GO:0007155, GO:0005518, actin binding activity, GO:0007229, GO:0001501, GO:0005201, GO:0006936, GO:0005604, GO:0031012, GO:0008009, GO:0008083, GO:0016860, GO:0006508, GO:0005125]] \n", - " HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 [[GO:0030198, GO:0006936, GO:0007155]] \n", - " HALLMARK_ESTROGEN_RESPONSE_EARLY-0 [[MESH:D002352, MESH:D004798, MESH:D008565, GO:0000981, receptors, MESH:D003598]] \n", - " HALLMARK_ESTROGEN_RESPONSE_EARLY-1 [[GO:0006631, GO:0006811, GO:0010468]] \n", - " HALLMARK_ESTROGEN_RESPONSE_LATE-0 [[GO:0005515, GO:0007165, GO:0019899, GO:0005737, GO:0043687, GO:0006355, GO:0006915, GO:0045860, positive regulation of cell proliferation.\\n\\nmechanism/]] \n", - " HALLMARK_ESTROGEN_RESPONSE_LATE-1 [[GO:0007165, GO:0004672, g-protein coupled receptor signaling pathway, GO:0055085, GO:0035556, GO:0004721, GO:0006468, zinc ion binding. \\n\\nhypotheses: the enriched terms suggest that the genes in this list are involved in regulatory mechanisms that help to control intracellular signaling cascades and protein expression through phosphorylation and dephosphorylation of proteins, and zinc ion binding. additionally, these genes may play a role in transmembrane transport and regulation of ion channels]] \n", - " HALLMARK_FATTY_ACID_METABOLISM-0 [[GO:0006631, GO:0005975, amino acid metabolism, mitochondrial function, oxidative stress response]] \n", - " HALLMARK_FATTY_ACID_METABOLISM-1 [[GO:0006631, energy production, mitochondrial function, GO:0006629, oxidation-reduction process, GO:0006637, GO:0006099, MESH:D014451, GO:0019752, GO:0015936, GO:0006084, GO:0022900]] \n", - " HALLMARK_G2M_CHECKPOINT-0 [[GO:0051726, GO:0006260, GO:0006281]] \n", - " HALLMARK_G2M_CHECKPOINT-1 [[GO:0006260, GO:0051726, GO:0006281, GO:0007059, GO:0000910]] \n", - " HALLMARK_GLYCOLYSIS-0 [[GO:0006096, GO:0005975]] \n", - " HALLMARK_GLYCOLYSIS-1 [[GO:0052574, GO:0006006, protein kinase binding activity, GO:0006090, GO:0006024, GO:0015012, GO:0006098, GO:0006096, rna polymerase iii transcription initiation, GO:0051287, GO:0022618, GO:0030199, GO:0008408, GO:0042803, atp-binding cassette transporter activity]] \n", - " HALLMARK_HEDGEHOG_SIGNALING-0 [[neuronal development, GO:0007155, GO:0007165, GO:0016477, GO:0010977, GO:0001525, MESH:D018121, transcriptional regulation]] \n", - " HALLMARK_HEDGEHOG_SIGNALING-1 [[GO:0007155, GO:0007411, neuronal proliferation and differentiation, GO:0007165, GO:0001525]] \n", - " HALLMARK_HEME_METABOLISM-0 [[GO:0006810, GO:0005488, MESH:D008565, MONDO:0018815, solute carrier (slc) family of transporters]] \n", - " HALLMARK_HEME_METABOLISM-1 [[GO:1904659, GO:0003723, GO:0003677, GO:0000988, GO:0006811, GO:0019899, GO:0042826, GO:0140657, GO:0003824, GO:0008270]] \n", - " HALLMARK_HYPOXIA-0 [[GO:0006096, GO:0006006, GO:0005515, transcription regulation]] \n", - " HALLMARK_HYPOXIA-1 [[GO:0006096, GO:0016310, GO:0006006, GO:0051726, GO:0007165, transcriptional regulation, heparan sulfate biosynthesis]] \n", - " HALLMARK_IL2_STAT5_SIGNALING-0 [[cytokine signaling, GO:0042110, GO:0042113, GO:0007159, GO:0030593, GO:0050900]] \n", - " HALLMARK_IL2_STAT5_SIGNALING-1 [[GO:0004896, GO:0007166, GO:0045321, GO:0050900, GO:0006955, GO:0006954, GO:0002250, GO:0070663, GO:0002521, GO:0042110, GO:0042113, GO:0046649]] \n", - " HALLMARK_IL6_JAK_STAT3_SIGNALING-0 [[GO:0004896, GO:0050778, GO:0007155, GO:0019221, GO:0002687]] \n", - " HALLMARK_IL6_JAK_STAT3_SIGNALING-1 [[GO:0004896, GO:0019221, GO:0050776, GO:0050900, apoptosis regulation, GO:0006954, antimicrobial response]] \n", - " HALLMARK_INFLAMMATORY_RESPONSE-0 [[GO:0005125, GO:0008009, GO:0004930, GO:0050900, inflammation\\n\\nmechanism]] \n", - " HALLMARK_INFLAMMATORY_RESPONSE-1 [[GO:0004896, GO:0004930, GO:0004950, GO:0004888, GO:0004896]] \n", - " HALLMARK_INTERFERON_ALPHA_RESPONSE-0 [[interferon response, GO:0051607, GO:0006955]] \n", - " HALLMARK_INTERFERON_ALPHA_RESPONSE-1 [[GO:0140888, GO:0045087, GO:0051607, cytokine signaling, GO:0019882, ubiquitin-mediated proteolysis\\n\\nmechanism: these genes are involved in the innate immune response and antiviral activity, particularly in the interferon signaling pathway. they encode proteins that regulate cytokine signaling, antigen processing and presentation, and ubiquitin-mediated proteolysis. the functions of these genes suggest a coordinated response to viral infection, with the interferon signaling pathway acting as a central mediator of the antiviral response]] \n", - " HALLMARK_INTERFERON_GAMMA_RESPONSE-0 [[GO:0006955, GO:0019221, chemokine signaling pathway, GO:0019882]] \n", - " HALLMARK_INTERFERON_GAMMA_RESPONSE-1 [[GO:0045087, GO:0051607, GO:0005125, GO:0009615, GO:0001817, GO:0051607, GO:0032481, type i interferon signaling pathway. \\n\\nmechanism/]] \n", - " HALLMARK_KRAS_SIGNALING_DN-0 [[GO:0005509, GO:0005245, GO:0006811, GO:0015085, GO:0005388, GO:0019722, GO:0055074, GO:0048306]] \n", - " HALLMARK_KRAS_SIGNALING_DN-1 [[GO:0005509, GO:0042981, GO:0055085, GO:0006811, GO:0006468]] \n", - " HALLMARK_KRAS_SIGNALING_UP-0 [[GO:0044425, GO:0007165, GO:0003824]] \n", - " HALLMARK_KRAS_SIGNALING_UP-1 [[cytokine signaling, growth factor signaling, coagulation and complement activation, enzymatic activity regulation]] \n", - " HALLMARK_MITOTIC_SPINDLE-0 [[microtubule organization, GO:0007098, GO:0030036, GO:0051726, GO:0071539]] \n", - " HALLMARK_MITOTIC_SPINDLE-1 [[GO:0008017, GO:0008574, GO:0007098, GO:0051225, GO:0003774, GO:0007010]] \n", - " HALLMARK_MTORC1_SIGNALING-0 [[GO:0006457, GO:0006006, microtubule organization and biogenesis, GO:0000502, GO:0043043, GO:0042254]] \n", - " HALLMARK_MTORC1_SIGNALING-1 [[GO:0008152, GO:0009117, GO:0006629, GO:0005975, GO:0006457, GO:0030163, GO:0010468, GO:0000988, GO:0003682]] \n", - " HALLMARK_MYC_TARGETS_V1-0 [[GO:0042254, GO:0000394, GO:0006412, GO:0006412, GO:0006457, chaperonin-mediated protein folding]] \n", - " HALLMARK_MYC_TARGETS_V1-1 [[GO:0042254, GO:0006413, GO:0006414, GO:0006397]] \n", - " HALLMARK_MYC_TARGETS_V2-0 [[GO:0006364, ribosomal subunit biogenesis, GO:0003723, nucleolar function, GO:0006412]] \n", - " HALLMARK_MYC_TARGETS_V2-1 [[GO:0006364, GO:0005730, GO:0003723, ribosomal biogenesis, GO:0051726]] \n", - " HALLMARK_MYOGENESIS-0 [[GO:0006936, muscle metabolism, GO:0007010]] \n", - " HALLMARK_MYOGENESIS-1 [[GO:0005861, MESH:M0013780, MESH:D018995, GO:0006936, GO:0005509, sarcomere assembly, MESH:D024510]] \n", - " HALLMARK_NOTCH_SIGNALING-0 [[GO:0007219, basic helix-loop-helix transcription factor activity, GO:0016567, GO:0016563, GO:0005102, GO:0097153, GO:0006468]] \n", - " HALLMARK_NOTCH_SIGNALING-1 [[GO:0007219, GO:0016567, transcriptional regulation, GO:0001709]] \n", - " HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 [[GO:0005739, GO:0006119, GO:0022900, MESH:D004734, GO:0031966, MESH:D024101]] \n", - " HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 [[GO:0005746, GO:0006754, GO:0022900, GO:0006119]] \n", - " HALLMARK_P53_PATHWAY-0 [[cyclin family, GO:0006281, GO:0008083, GO:0004672, GO:0000988, zinc finger protein]] \n", - " HALLMARK_P53_PATHWAY-1 [[GO:0008083, transcriptional regulation, GO:0006915, GO:0006281]] \n", - " HALLMARK_PANCREAS_BETA_CELLS-0 [[GO:0006006, insulin regulation, GO:0031016, GO:0006096, GO:0006094, GO:0030073, hormone regulation]] \n", - " HALLMARK_PANCREAS_BETA_CELLS-1 [[GO:0006006, GO:0030073, pancreatic islet development, neuroendocrine differentiation]] \n", - " HALLMARK_PEROXISOME-0 [[GO:0140359, GO:0055085, atp-binding cassette, GO:0043574, GO:0006631, GO:0006839]] \n", - " HALLMARK_PEROXISOME-1 [[GO:0005777, GO:0006631, beta-oxidation, MESH:D018384, antioxidant defense mechanism, coenzyme a ligase, aldehyde dehydrogenase family, MESH:D009195]] \n", - " HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 [[GO:0004672, intracellular signaling, GO:0050794]] \n", - " HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 [[GO:0016301, GO:0006468, GO:0007165]] \n", - " HALLMARK_PROTEIN_SECRETION-0 [[GO:0005794, membrane trafficking, GO:0016192, GO:0015031, GO:0006906, GO:0035493, GO:0005793]] \n", - " HALLMARK_PROTEIN_SECRETION-1 [[GO:0007030, GO:0006888, GO:0016192, GO:0007040, sorting nexin-containing complex, GO:0030665, GO:0032880]] \n", - " HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 [[antioxidant activity; redox regulation; catalytic activity, UBERON:0035930, such as water and oxygen. the over-representation of terms related to antioxidant activity, redox regulation, and responding to oxidative stress suggest that these genes are involved in maintaining the balance between oxidants and antioxidants in the body, help protect against oxidative damage]] \n", - " HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 [[oxidative stress response, antioxidant defense, regulation of reactive oxygen species, GO:0006749, superoxide anion radical metabolism, peroxiredoxin-mediated detoxification]] \n", - " HALLMARK_SPERMATOGENESIS-0 [[GO:0008584, GO:0007283, GO:0097722, GO:0007340, GO:0048232, testicular germ cell proliferation\\n\\nmechanism and]] \n", - " HALLMARK_SPERMATOGENESIS-1 [[GO:0006811, GO:0006468, MESH:D054875, GO:0007283, receptor signaling]] \n", - " HALLMARK_TGF_BETA_SIGNALING-0 [[tgf-beta signaling pathway, transcriptional regulation, GO:0007165, cell growth and differentiation]] \n", - " HALLMARK_TGF_BETA_SIGNALING-1 [[tgf-beta signaling pathway, GO:0030509, GO:0071141, GO:0004674, GO:0008134, GO:0006468, GO:0030154, GO:0060348, GO:0042981, GO:0034436]] \n", - " HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 [[GO:0004950, GO:0005125, GO:0006955, GO:0006954, GO:0050900, GO:0007165]] \n", - " HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 [[interleukin signaling, GO:0032602, GO:0006955]] \n", - " HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 [[endoplasmic reticulum stress response, GO:0006457, GO:0008380, GO:0006402, mrna localization, translation regulation, stress response]] \n", - " HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 [[GO:0006457, GO:0061077, GO:0015031, GO:0006413, GO:0003723, MESH:D020365, GO:0042254, aminoacyl-trna synthesis, GO:0005783, MESH:D005786]] \n", - " HALLMARK_UV_RESPONSE_DN-0 [[GO:0030198, GO:0007155, GO:0006811, GO:0004672, transcription regulation, receptor signaling pathway]] \n", - " HALLMARK_UV_RESPONSE_DN-1 [[GO:0030198, GO:0030155, GO:0006468, positive regulation of cellular signaling pathway activity, GO:0022604, GO:0072659]] \n", - " HALLMARK_UV_RESPONSE_UP-0 [[GO:0006810, GO:0008152, GO:0003824]] \n", - " HALLMARK_UV_RESPONSE_UP-1 [[GO:0003723, GO:0003677, GO:0000166, GO:0006396, GO:0006260]] \n", - " HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 [[GO:0016055, transcriptional regulation, cell cycle progression]] \n", - " HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 [[GO:0016055, GO:0051726, transcriptional regulation]] \n", - " T cell proliferation-0 [[cytokine, MESH:D007378, MESH:D011948, GO:0005530, GO:0008180, GO:0000502, protein tyrosine phosphatase, MESH:D010770, GO:0000981]] \n", - " T cell proliferation-1 [[cytokine signaling, tnf-receptor superfamily, GO:0006955, GO:0007165, GO:0019882, cell proliferation and survival, protein phosphorylation and kinase activity]] \n", - " Yamanaka-TFs-0 [[MESH:D047108, GO:0001709, cell cycle progression]] \n", - " Yamanaka-TFs-1 [[MESH:D047108, GO:0048863, pluripotent stem cell, transcription factor regulation, homeobox protein]] \n", - " amigo-example-0 [[GO:0031012, GO:0007155, MESH:D011509, GO:0005202, integrin]] \n", - " amigo-example-1 [[GO:0030198, GO:0007155, GO:0016477, GO:0009888, GO:0042246, signaling pathway regulation, GO:0030168]] \n", - " bicluster_RNAseqDB_0-0 [[GO:0006351, GO:0005515, MESH:D016335, GO:0005509, MESH:D008565]] \n", - " bicluster_RNAseqDB_0-1 [[calcium binding, receptor protein activity, GO:0000988, GO:0005515]] \n", - " bicluster_RNAseqDB_1002-0 [[GO:0006936, GO:0005509, GO:0043269, GO:0032516, GO:0051015]] \n", - " bicluster_RNAseqDB_1002-1 [[GO:0006936, GO:0005509, GO:0051015, GO:0043462, GO:0097009, GO:0006811]] \n", - " endocytosis-0 [[GO:0006897, GO:0007010, GO:0007165, GO:0006629, GO:0060348, brain development. \\n\\nhypotheses: these genes may be involved in common pathways related to endocytic vesicle trafficking, cytoskeletal organization, and signal transduction. some of the genes are associated with lipid metabolism and bone and brain development, suggesting their potential roles in cellular processes related to these functions]] \n", - " endocytosis-1 [[GO:0006897, intracellular trafficking, cytoskeletal reorganization]] \n", - " glycolysis-gocam-0 [[GO:0006096, GO:0006006, MESH:D004734]] \n", - " glycolysis-gocam-1 [[GO:0006096, GO:0006006, GO:0004743, GO:0019682, GO:0006000, phosphoenolpyruvate metabolic process]] \n", - " go-postsynapse-calcium-transmembrane-0 [[GO:0006816, intracellular calcium homeostasis, ionotropic glutamate receptor regulation, nmda receptor subunits, sodium/calcium exchanger proteins, trp ion channel family]] \n", - " go-postsynapse-calcium-transmembrane-1 [[GO:0005509, GO:0005262, GO:0004970, calcium-mediated signaling pathway, GO:0007268, GO:0031175, GO:0005216]] \n", - " go-reg-autophagy-pkra-0 [[MESH:D002470, GO:0016301, GO:0009966, GO:0001558, GO:0042981, GO:0010506, GO:0032006]] \n", - " go-reg-autophagy-pkra-1 [[GO:0016049, GO:0004672, GO:0006955, GO:0007165, GO:0000988, neuronal development, GO:0006468]] \n", - " hydrolase activity, hydrolyzing O-glycosyl compounds-0 [[glycosyl hydrolase activity, degradation of carbohydrates, GO:0006032, GO:0030211, GO:0003796, GO:0030214]] \n", - " hydrolase activity, hydrolyzing O-glycosyl compounds-1 [[GO:0016787, GO:0044248, GO:0006027, GO:0005764]] \n", - " ig-receptor-binding-2022-0 [[GO:0019731, GO:0098542, GO:0002253, immunoglobulin receptor binding activity]] \n", - " ig-receptor-binding-2022-1 [[antigen binding activity, immunoglobulin receptor binding activity, GO:0002253]] \n", - " meiosis I-0 [[GO:0140013, GO:0035825, GO:0007059, GO:0006281, GO:0000795]] \n", - " meiosis I-1 [[meiotic recombination, GO:0006281, GO:0007059, GO:0035825, holliday junction resolution, double-strand dna binding, GO:0007276, GO:0007130]] \n", - " molecular sequestering-0 [[GO:0006955, GO:0051726, GO:0046907]] \n", - " molecular sequestering-1 [[GO:0051726, GO:0006955, GO:0005515]] \n", - " mtorc1-0 [[GO:0006457, GO:0006006, microtubule organization and biogenesis, GO:0000502, GO:0043043, GO:0042254]] \n", - " mtorc1-1 [[GO:0000502, GO:1904659, GO:0008152, GO:0003676, GO:0044183, GO:0005524, GO:0005783, GO:0005739, GO:0006096, GO:0006631]] \n", - " peroxisome-0 [[peroxisome biogenesis, peroxisomal protein import, peroxin proteins, MONDO:0019234, neonatal adrenoleukodystrophy, MONDO:0019609, MONDO:0009959, MONDO:0008972, MONDO:0009958]] \n", - " peroxisome-1 [[peroxisome biogenesis, GO:0005777, GO:0017038]] \n", - " progeria-0 [[GO:0005652, GO:0005635, GO:0006281]] \n", - " progeria-1 [[GO:0006997, GO:0006281, chromatin structure organization, GO:0000723]] \n", - " regulation of presynaptic membrane potential-0 [[GO:0005216, GO:0031175, GO:0007268, GO:0042391]] \n", - " regulation of presynaptic membrane potential-1 [[GO:0005267, chloride ion transmembrane transport, GO:0042391, GO:0034220, GO:0030594]] \n", - " sensory ataxia-0 [[MONDO:0015626, MONDO:0007790, MONDO:0005244, myelin sheath maintenance, GO:0006264]] \n", - " sensory ataxia-1 [[GO:0042552, GO:0007422, GO:0016567, er-associated protein degradation.\\n\\nmechanism/]] \n", - " term-GO:0007212-0 [[g-protein signaling, GO:0007165, neurotransmitter activity]] \n", - " term-GO:0007212-1 [[g-protein signaling pathway, GO:0030594, GO:1902531]] \n", - " tf-downreg-colorectal-0 [[transcription regulation, GO:0006338, GO:0003700]] \n", - " tf-downreg-colorectal-1 [[GO:0003700, GO:0006355, GO:0006325, GO:0010468, transcription factor complex\\n\\nmechanism: these genes all play a role in regulating transcription, primarily at the level of dna binding and chromatin organization. they are involved in the regulation of gene expression and the formation of transcription factor complexes]] \n", - " no_synopsis EDS-0 [[GO:0030198, GO:0043062, GO:0030199, GO:0006486, GO:0008233, GO:0008270]] \n", - " EDS-1 [[GO:0032963, GO:0030198, GO:0031012]] \n", - " FA-0 [[GO:0006281, GO:0006325, GO:0006312, GO:0006302, GO:0035825, GO:0006260]] \n", - " FA-1 [[fanconi anemia pathway, GO:0035825, GO:0006302]] \n", - " HALLMARK_ADIPOGENESIS-0 [[GO:0006629, GO:0006631, mitochondrial function, GO:0006119, GO:0006099, beta-oxidation of fatty acids, GO:0006084, GO:0006637, GO:0015980, GO:0005975]] \n", - " HALLMARK_ADIPOGENESIS-1 [[GO:0005740, GO:0006122]] \n", - " HALLMARK_ALLOGRAFT_REJECTION-0 [[GO:0002376, GO:0042110, GO:0019221, GO:0019882, GO:0030098, GO:0050900, GO:0050778, GO:0050777, GO:0001817]] \n", - " HALLMARK_ALLOGRAFT_REJECTION-1 [[GO:0042110, cytokine signaling, GO:0019882, GO:0006955, chemokine signaling, interferon signaling, GO:0030183, GO:0050900]] \n", - " HALLMARK_ANDROGEN_RESPONSE-0 [[GO:0016567, GO:0036211, GO:0008134, GO:0045892, GO:0071535, GO:0031647, GO:0043161]] \n", - " HALLMARK_ANDROGEN_RESPONSE-1 [[regulation of transcription, GO:0005515, GO:0007155, GO:0007165, GO:0016126]] \n", - " HALLMARK_ANGIOGENESIS-0 [[GO:0030198, GO:0070848, GO:1903010, GO:0042060]] \n", - " HALLMARK_ANGIOGENESIS-1 [[GO:0030198, GO:0001525, GO:0007155]] \n", - " HALLMARK_APICAL_JUNCTION-0 [[GO:0007155, GO:0007010, GO:0048041, regulation of actin cytoskeleton, GO:0051017, GO:0046847, GO:0035023]] \n", - " HALLMARK_APICAL_JUNCTION-1 [[GO:0007155, GO:0016477, GO:0048870, GO:0007229, GO:0008360, focal adhesion\\n\\nmechanism: the enriched terms suggest that the common function of these genes is involved in cell adhesion and migration. these processes are essential for various biological functions such as wound healing, inflammation, and embryonic development. integrin-mediated signaling pathway and focal adhesion are two crucial pathways in cell adhesion and migration, which are perturbed in many types of cancer and autoimmune diseases. these findings may shed light on the underlying mechanism and potential targets for drug development]] \n", - " HALLMARK_APICAL_SURFACE-0 [[GO:0007155, GO:0023052, GO:0006810]] \n", - " HALLMARK_APICAL_SURFACE-1 [[GO:0007155, GO:0007186, GO:0010906, GO:0050796, GO:0070528, GO:0043406, GO:0050731, GO:0051897, GO:0061024, GO:0043066]] \n", - " HALLMARK_APOPTOSIS-0 [[GO:0006915, GO:0012501, regulation of cell death\\n\\nmechanism: these genes are involved in various processes that regulate cell death. they participate in the apoptotic process, the programmed cell death that occurs in multicellular organisms. apoptosis is a complex physiological process that is essential for development and homeostasis in healthy adult tissues. these genes also contribute to the regulation of cell death, preventing or promoting apoptosis under specific conditions]] \n", - " HALLMARK_APOPTOSIS-1 [[GO:0097153, GO:0006915, GO:0006954, GO:0008285, GO:0050871, GO:0001819, GO:0045944, GO:0004672, GO:0046328, GO:0010803]] \n", - " HALLMARK_BILE_ACID_METABOLISM-0 [[peroxisome organization; steroid metabolic process; cholesterol metabolic process; fatty acid metabolic process; lipid metabolic process\\n\\nmechanism: \\n\\nthese genes are involved in various metabolic pathways, especially those related to lipid and sterol metabolism. many of these genes are involved in the transport of lipids and cholesterol, including the abc transporters abca1, abca2, abca3, abca4, abca5, abca6, abca8, abca9, and abcg4. other genes such as cat, ch25h, crot, cyp7a1, GO:0033783, MESH:D013253, dhcr24, and hsd17b6 are involved in the synthesis, GO:0009056, and modification of cholesterol and sterols. \\n\\nadditionally, these genes are also involved in peroxisome biogenesis and function, with genes such as pex1, pex11a, pex11g, pex12, pex13, pex16, pex19, pex26, MESH:D010758]] \n", - " HALLMARK_BILE_ACID_METABOLISM-1 [[GO:0006695, GO:0006629, GO:0007031, peroxisome biogenesis, GO:0008202, GO:0006635, GO:0006699, GO:0015908, GO:0006886]] \n", - " HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 [[GO:0006695, GO:0006629, GO:0045540, GO:0019216, GO:0016126]] \n", - " HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 [[GO:0006695, GO:0006694, GO:0006629]] \n", - " HALLMARK_COAGULATION-0 [[GO:0030198, GO:0030574, GO:0007596, GO:0042730, GO:0002576, GO:0052547, GO:0045055, GO:0045862]] \n", - " HALLMARK_COAGULATION-1 [[GO:0007596, GO:0006955]] \n", - " HALLMARK_COMPLEMENT-0 [[GO:0006956, GO:0002576, GO:0050776, GO:0009611, blood coagulation\\n\\nmechanism: genes involved in complement activation, platelet degranulation, regulation of immune response, response to wounding, and blood coagulation are enriched in this gene set. these functions are related to the prevention of thrombosis and regulation of the immune system]] \n", - " HALLMARK_COMPLEMENT-1 [[GO:0006955, GO:0007596, GO:0006508, GO:0030168, GO:0006954, GO:0010952]] \n", - " HALLMARK_DNA_REPAIR-0 [[GO:0006260, GO:0006281, dna binding and packaging, GO:0009117, GO:0006338]] \n", - " HALLMARK_DNA_REPAIR-1 [[GO:0006260, GO:0006281, transcription elongation, GO:0006396, GO:0009117, GO:0003682]] \n", - " HALLMARK_E2F_TARGETS-0 [[GO:0006260, GO:0007049, GO:0007052, GO:0007059, GO:0007346, GO:0006281, GO:0006334]] \n", - " HALLMARK_E2F_TARGETS-1 [[GO:0006260, GO:0006281, GO:0051726, GO:0007059]] \n", - " HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 [[GO:0030198, GO:0030199, GO:0032964, GO:0071711, regulation of growth factor signaling, regulation of bmp signaling, regulation of tgf-beta signaling]] \n", - " HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 [[GO:0030198, GO:0007155, GO:0007229, GO:0030574, GO:0009888, GO:0016477, GO:0071711]] \n", - " HALLMARK_ESTROGEN_RESPONSE_EARLY-0 [[GO:0005509, GO:0006816, GO:0005516, GO:0010857, GO:0055074, GO:0005262, GO:0030899]] \n", - " HALLMARK_ESTROGEN_RESPONSE_EARLY-1 [[GO:0006811, GO:0023051, transport of small molecules, GO:0072657, GO:0009966, GO:0008202, GO:0010817, GO:0048522, GO:0010468, GO:0043066, GO:0051246, GO:0071363]] \n", - " HALLMARK_ESTROGEN_RESPONSE_LATE-0 [[GO:0005509, GO:0051302, GO:0042981, GO:0006816]] \n", - " HALLMARK_ESTROGEN_RESPONSE_LATE-1 [[GO:0051726, GO:0008283, GO:0006260, GO:0051301, cancer progression]] \n", - " HALLMARK_FATTY_ACID_METABOLISM-0 [[GO:0006635, mitochondrial beta-oxidation of fatty acids, GO:0015980, GO:0008152, GO:0044255, GO:0006084, coenzyme metabolic process, GO:0001676, GO:0019752, GO:0006099]] \n", - " HALLMARK_FATTY_ACID_METABOLISM-1 [[GO:0006631, MESH:D004734, mitochondrial function, GO:0016042, oxidative stress response]] \n", - " HALLMARK_G2M_CHECKPOINT-0 [[cdc20, cdc25a, cdc25b, cdc27, cdc45, cdc6, cdc7, cdk1, cenpa, cenpe, cenpf, chek1, cks1b, cks2, dbf4, e2f1, e2f2, e2f3, e2f4, espl1, exo1, fbxo5, gins2, h2ax, h2az1, h2az2, h2bc12, hmmr, hus1, ilf3, incenp, katna1, kif11, kif15, kif20b, kif22, kif23, kif2c, kif4a, kif5b, kpna2, kpnb1, lig3, mad2l1, map3k20, mcm2, mcm3, mcm5, mcm6, ne]] \n", - " HALLMARK_G2M_CHECKPOINT-1 [[GO:0051726, GO:0006260, chromosomal segregation, GO:0051276, GO:0006281]] \n", - " HALLMARK_GLYCOLYSIS-0 [[GO:0006096, GO:0005978, glycosylation pathway]] \n", - " HALLMARK_GLYCOLYSIS-1 [[GO:0008152, GO:0006796, molecular function regulation, GO:0033554, GO:0031323, GO:0019538, GO:0050794, GO:0044281]] \n", - " HALLMARK_HEDGEHOG_SIGNALING-0 [[GO:0007399, nervous system neuron differentiation, nervous system development and angiogenesis, GO:0045765, GO:0023056, GO:0048598]] \n", - " HALLMARK_HEDGEHOG_SIGNALING-1 [[GO:0031175, GO:0007411, GO:0051960, GO:0007165, GO:0007267]] \n", - " HALLMARK_HEME_METABOLISM-0 [[GO:0015886, GO:0051536, [2fe-2s] cluster binding]] \n", - " HALLMARK_HEME_METABOLISM-1 [[gene expression regulation; metabolism; transport\\n\\nmechanism and hypotheses:\\nthe genes in this list are involved in various cellular processes, including gene expression regulation, GO:0008152, and transport. gene expression regulation may be a mechanism by which these genes function, possibly through the involvement of transcription factors such as foxo3 and klf3. metabolism may also be a key mechanism, as many of these genes are involved in metabolic pathways, such as fech and alas2 in heme synthesis, and gclc and gclm in glutathione metabolism. transport may also be a contributing mechanism, as several genes in this list, such as slc2a1 and slc6a9, are involved in membrane transport of various molecules. overall, the commonality in function among these genes may be attributed to their roles in regulating cellular metabolism and transporting molecules across various membranes]] \n", - " HALLMARK_HYPOXIA-0 [[GO:0006110, GO:0051246, GO:0010628, GO:0030198, GO:0006006, GO:0009749, GO:0001558, GO:0008284, GO:0051094]] \n", - " HALLMARK_HYPOXIA-1 [[hk1, hk2, pfkl, pfkfb3, gys1, pklr, pgk1, tpi1, aldoa, eno2, pgam2, pgm2, fbp1, eno1, ndst1, ndst2]] \n", - " HALLMARK_IL2_STAT5_SIGNALING-0 [[il2ra, il1r2, il2rb, il10ra, ctla4, cd44, MESH:D016753, il1rl1, il18r1, icos, tnfrsf4, tnfrsf18, tnfrsf8, tnfrsf21, tnfsf11, tnfrsf9, tnfsf10, tnfrsf1b, cd48, tnfrsf4, cxcl10, MESH:D018793, selp, ccne1, MESH:D047990, socs1, socs2]] \n", - " HALLMARK_IL2_STAT5_SIGNALING-1 [[GO:0006955, cell signaling, GO:0005125, GO:0008009, GO:0008083, GO:0007166, GO:0002250, GO:0030595, GO:0050900, GO:0006954]] \n", - " HALLMARK_IL6_JAK_STAT3_SIGNALING-0 [[GO:0019221, GO:0002757, GO:0007259, GO:0002694, regulation of leukocyte migration and chemotaxis, GO:0035456, GO:0034341, GO:0070555, GO:0070671, GO:0070741, response to tumor necrosis factor. \\n\\nhypotheses: these genes are involved in activating immune responses and cytokine-mediated signaling pathways. the enrichment of terms related to leukocyte activation and chemotaxis suggests an increased focus on the recruitment of immune cells to sites of infection and inflammation. the involvement of genes related to cytokine signaling, such as jak-stat cascade, suggests that the activation of immune responses may be regulated by cytokines released in response to infection or inflammation. overall, these genes are likely involved in the regulation of immune system activation and inflammation]] \n", - " HALLMARK_IL6_JAK_STAT3_SIGNALING-1 [[cytokine signaling, GO:0006954, GO:0006955, interleukin signaling, GO:0008009, jak-stat signaling, toll-like receptor signaling]] \n", - " HALLMARK_INFLAMMATORY_RESPONSE-0 [[cytokine signaling, GO:0006955, GO:0006954]] \n", - " HALLMARK_INFLAMMATORY_RESPONSE-1 [[GO:0004896, GO:0042379, GO:0050900, GO:0002694, GO:0050778, GO:0045088, GO:0005149, GO:0042110, GO:0006952, GO:0006954, GO:0002685, GO:0034097]] \n", - " HALLMARK_INTERFERON_ALPHA_RESPONSE-0 [[GO:0051607, GO:0045087, interferon signaling, type i interferon response, viral defense]] \n", - " HALLMARK_INTERFERON_ALPHA_RESPONSE-1 [[GO:0051607, GO:0002376, GO:0140888]] \n", - " HALLMARK_INTERFERON_GAMMA_RESPONSE-0 [[GO:0060337, GO:0006955, GO:0002579, GO:0051607, GO:0046596, GO:0032481, GO:0045087, GO:0034341, GO:0032727, GO:0002504, GO:0002479, GO:0032728, GO:0071357, GO:0043331, GO:0016032, GO:0045859, GO:0006954, GO:0060333, GO:0038187]] \n", - " HALLMARK_INTERFERON_GAMMA_RESPONSE-1 [[GO:0019882, interferon response, GO:0001816, GO:0006954, GO:0002376, GO:0050776, GO:0006952, GO:0009615, response to interferon]] \n", - " HALLMARK_KRAS_SIGNALING_DN-0 [[GO:0005509, GO:0070588, GO:0051924, GO:0051899, GO:0042391, GO:0071277]] \n", - " HALLMARK_KRAS_SIGNALING_DN-1 [[GO:0006811, neurological signaling, tissue development.\\n\\nmechanism]] \n", - " HALLMARK_KRAS_SIGNALING_UP-0 [[GO:0006955, cellular signaling, GO:0001525]] \n", - " HALLMARK_KRAS_SIGNALING_UP-1 [[1. immune response\\n2. inflammatory response\\n3. coagulation\\n4. positive regulation of endothelial cell migration \\n5. cell adhesion\\n6. positive regulation of cell migration \\n7. signal transduction \\n8. negative regulation of apoptotic process \\n9. regulation of angiogenesis \\n10. positive regulation of protein serine/threonine kinase activity \\n11. positive regulation of transcription from rna polymerase ii promoter \\n\\nmechanism: the enriched functions suggest that these genes play an important role in innate and adaptive immune responses, inflammatory processes, GO:0007596, cell adhesion and migration, GO:0001525, and signal transduction pathways. they could be involved in regulating the expression and activity of various immune cells, MESH:D016207, chemokines to modulate immunity inflammation. the coagulation-related genes may contribute to thrombotic disorders cardiovascular diseases by affecting blood clot formation fibrinolysis. the cell adhesion migration-related genes are potentially involved in tumor metastasis progression through facilitating cell invasion motility. the signal]] \n", - " HALLMARK_MITOTIC_SPINDLE-0 [[GO:0007052, GO:0007017, GO:0051301, GO:0007010, GO:0030029]] \n", - " HALLMARK_MITOTIC_SPINDLE-1 [[GO:0007051, GO:0031023, GO:0007059, GO:0071173, GO:0051382, GO:0007052, GO:0000226, GO:0007098, GO:0007020, GO:0000075, GO:0007018, GO:0007346, GO:0000070, GO:0001578, GO:0008017, GO:0000910, GO:0030953]] \n", - " HALLMARK_MTORC1_SIGNALING-0 [[glycolysis; tca cycle; cholesterol biosynthesis; pentose phosphate pathway\\n\\nmechanism and hypotheses:\\nthe enriched terms suggest that these genes are involved in various aspects of cellular metabolism. glycolysis is the central pathway for glucose metabolism, converting glucose into pyruvate. the tca cycle is responsible for generating energy from the breakdown of carbohydrates, MESH:D005227, and amino acids. the cholesterol biosynthesis pathway is responsible for producing cholesterol, which is involved in membrane structure, steroid hormone synthesis, and bile salt production. the pentose phosphate pathway is involved in the production of nadph, which is critical for many cellular processes, including antioxidant defense and biosynthesis.\\n\\noverall, these genes are likely involved in regulating various aspects of cellular metabolism, including energy production, biosynthesis of important molecules like cholesterol and nadph, mediating the cellular response to oxidative stress]] \n", - " HALLMARK_MTORC1_SIGNALING-1 [[GO:0051087, GO:0006457, co-factor binding, GO:0008152, GO:0005524]] \n", - " HALLMARK_MYC_TARGETS_V1-0 [[GO:0006397, GO:0006413, GO:0042254]] \n", - " HALLMARK_MYC_TARGETS_V1-1 [[GO:0006396, GO:0006412, GO:0042254, GO:0006402, GO:0043488, regulation of mrna splicing, GO:0043393, GO:0008380, GO:0006417, GO:0003723]] \n", - " HALLMARK_MYC_TARGETS_V2-0 [[GO:0042254, GO:0006364, GO:0003723, GO:0005681, GO:0006413]] \n", - " HALLMARK_MYC_TARGETS_V2-1 [[GO:0006396, GO:0022613, GO:0042254, GO:0000166, GO:0003723, GO:0090304, GO:0042273, GO:0006364, GO:0065004]] \n", - " HALLMARK_MYOGENESIS-0 [[muscle filament sliding; sarcomere organization; muscle system process\\n\\nmechanism: the majority of the listed genes are involved in muscle contraction and development, specifically in the organization and structure of the sarcomere. the enriched terms - muscle filament sliding, GO:0045214, muscle system process - all relate to the mechanisms of muscle contraction the intricate process of sarcomere formation]] \n", - " HALLMARK_MYOGENESIS-1 [[GO:0003012, GO:0006936, GO:0045214, GO:0030029]] \n", - " HALLMARK_NOTCH_SIGNALING-0 [[GO:0007219, GO:0008593, GO:0016055, GO:0030111, GO:0045944, GO:0045596, GO:0045597]] \n", - " HALLMARK_NOTCH_SIGNALING-1 [[GO:0007219, GO:0005515, GO:0000122, GO:0000988]] \n", - " HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 [[GO:0042773, mitochondrial atp synthesis coupled electron transport in respiratory chain, GO:0033108, GO:0006979]] \n", - " HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 [[GO:0003954, GO:0022900, GO:0042773, GO:0005743, GO:0007005, GO:0006119, GO:0033108, respiratory chain complex i, ii, iii, iv, v, vi, GO:0006743, GO:0006631]] \n", - " HALLMARK_P53_PATHWAY-0 [[GO:0051726, GO:0006915, GO:0008285, GO:0006974, negative regulation of cellular process.\\n\\nmechanism: the genes in this list are enriched in functions that regulate the cell cycle and cell death. specifically, they are involved in cell cycle arrest, apoptosis, negative regulation of cell proliferation, and response to dna damage stimulus]] \n", - " HALLMARK_P53_PATHWAY-1 [[GO:0006974, GO:0051726, GO:0006915, GO:0006281, MESH:D002470, p53 signaling, checkpoint regulation, transcriptional regulation, GO:0006338]] \n", - " HALLMARK_PANCREAS_BETA_CELLS-0 [[GO:0030073, GO:0042593, GO:0003309, GO:0003323, pancreatic beta cell function, pancreatic islet cell development]] \n", - " HALLMARK_PANCREAS_BETA_CELLS-1 [[GO:0003323, GO:0030073, GO:0042593, GO:0031018, GO:0050796, GO:0006006, positive regulation of pancreatic beta cell differentiation, GO:0010827, regulation of insulin secretion by glucose]] \n", - " HALLMARK_PEROXISOME-0 [[GO:0140359, GO:0006631, GO:0006695, GO:0035357, GO:0005777]] \n", - " HALLMARK_PEROXISOME-1 [[GO:0006631, GO:0006629, GO:0008202, GO:0030301, GO:0006641, GO:0008206, GO:0005777]] \n", - " HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 [[GO:0016301, GO:0006468, GO:0010646, GO:0035556, regulation of map kinase activity\\n\\nmechanism: these genes are involved in several signaling pathways and primarily regulate protein kinase activity and phosphorylation. they are involved in the regulation of cell communication and intracellular signaling cascades, including the map kinase cascade]] \n", - " HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 [[GO:0007165, GO:0006468, GO:0008152, GO:0001558, GO:0042127, GO:0042981, GO:0045859, GO:0043408, GO:0032024, GO:0005975, GO:0010906, GO:0010604]] \n", - " HALLMARK_PROTEIN_SECRETION-0 [[GO:0016192, endosome to golgi transport, GO:0006886, GO:0008104, GO:0015031, regulation of membrane organization and biogenesis]] \n", - " HALLMARK_PROTEIN_SECRETION-1 [[GO:0006886, GO:0006891, GO:0007030, GO:0072583]] \n", - " HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 [[GO:0016209, redox regulation, GO:0006749, oxidation-reduction process, GO:0006979]] \n", - " HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 [[oxidative stress response, redox regulation, GO:0006749, GO:0016209, GO:0000302]] \n", - " HALLMARK_SPERMATOGENESIS-0 [[GO:0140013, GO:0007283, GO:0007059, GO:0051301, GO:0140014]] \n", - " HALLMARK_SPERMATOGENESIS-1 [[GO:0007052, GO:0007059, GO:0007094]] \n", - " HALLMARK_TGF_BETA_SIGNALING-0 [[GO:0030509, GO:0000122, GO:0045944, GO:0048705, GO:0007183, GO:0007179]] \n", - " HALLMARK_TGF_BETA_SIGNALING-1 [[GO:0007179, GO:0030514, GO:0010990]] \n", - " HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 [[GO:0006955, GO:0006954, GO:0034097, GO:0050865, GO:0071624, GO:0032855, GO:0010552, GO:0051092, GO:0043406, GO:0007259, GO:0043065, GO:0004672]] \n", - " HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 [[GO:0006955, GO:0006954, GO:0032680, GO:0001816, GO:0032496, negative regulation of nf-kappab transcription factor activity.\\n\\nmechanism and]] \n", - " HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 [[GO:0006457, MESH:M0354322, ubiquitin-mediated proteolysis, GO:0034976, GO:0006986, GO:0006397, GO:0008380]] \n", - " HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 [[GO:0006457, chaperone-mediated protein processing, GO:0015031, GO:0007029, GO:0006986]] \n", - " HALLMARK_UV_RESPONSE_DN-0 [[GO:0004672, GO:0003700, GO:0006355, GO:0035556, cytoplasmic membrane-bounded vesicle, receptor protein signaling pathway, GO:0007155, GO:0001932, GO:0007399, GO:0007498, GO:0045666]] \n", - " HALLMARK_UV_RESPONSE_DN-1 [[GO:0030198, GO:0007165, GO:0008083, neural development, GO:0022008]] \n", - " HALLMARK_UV_RESPONSE_UP-0 [[GO:0033554, GO:0031323, GO:0051050, GO:0009966]] \n", - " HALLMARK_UV_RESPONSE_UP-1 [[GO:0008104, GO:0006950, GO:0042981, GO:0008283, GO:0006979, regulation of transcription, GO:0006974, GO:0007049, response to hypoxia.\\n\\nmechanism]] \n", - " HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 [[cellular response to wnt stimulus, GO:0090263, GO:0045746]] \n", - " HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 [[GO:0016055, GO:0007219, GO:0005515, GO:0008134]] \n", - " T cell proliferation-0 [[GO:0002376, GO:0042110, GO:0001816, GO:0046649, GO:0006955, GO:0007166]] \n", - " T cell proliferation-1 [[t cell activation; cytokine signaling; lymphocyte proliferation; immune response\\n\\nmechanism: these genes are all involved in the regulation and function of the immune system, specifically in t cell activation, GO:0046651, and cytokine signaling pathways. they play a role in immune responses to pathogens, MONDO:0007179, MONDO:0004992]] \n", - " Yamanaka-TFs-0 [[GO:0000988, GO:0003677, GO:0048863]] \n", - " Yamanaka-TFs-1 [[pluripotency, self-renewal, GO:0048863]] \n", - " amigo-example-0 [[extracellular matrix organization; angiogenesis; positive regulation of cell migration; positive regulation of endothelial cell migration; positive regulation of sprouting angiogenesis; positive regulation of angiogenesis; positive regulation of vascular endothelial cell migration; positive regulation of smooth muscle cell migration; positive regulation of vascular smooth muscle cell migration; positive regulation of tube formation; positive regulation of endothelial cell proliferation; positive regulation of vascular endothelial growth factor production. \\n\\nhypotheses: several of the genes in the list encode for extracellular matrix components or regulators of matrix organization, including col3a1, col5a2, lum, postn, and vcan. others, such as cxcl6, pdgfa, pf4, and vegfa, encode for angiogenic growth factors. itgav is a common denominator and is associated with integrin-mediated signaling that regulates cell adhesion, migration, angiogenesis. fgfr1 has also been shown to play a critical role in angiogenesis extracellular matrix organization by regulating downstream signaling pathways such as pi3k mapk]] \n", - " amigo-example-1 [[GO:0030198, GO:0007155, GO:0001525, GO:0016477, GO:0030334, GO:0008284, GO:0043410]] \n", - " bicluster_RNAseqDB_0-0 [[GO:0030182, GO:0006811, GO:0000988, GO:0005509, GO:0007399, GO:0007267, synapse assembly and organization, g protein-coupled receptor signaling, GO:0003723, GO:0005515]] \n", - " bicluster_RNAseqDB_0-1 [[GO:0006396, GO:0008134, GO:0006355, GO:0003682, GO:0005634, GO:0003723, GO:0006397, transcriptional regulation, GO:0061629]] \n", - " bicluster_RNAseqDB_1002-0 [[GO:0006936, GO:0045214, GO:0006941, GO:0060048]] \n", - " bicluster_RNAseqDB_1002-1 [[GO:0006936, GO:0033275, GO:0031034, GO:0005509, GO:0045214, MESH:D024510]] \n", - " endocytosis-0 [[GO:0030301, GO:0006629, GO:0006897, GO:0030163]] \n", - " endocytosis-1 [[GO:0006897, GO:0007032, GO:0036010, GO:0006898, GO:0016192]] \n", - " glycolysis-gocam-0 [[GO:0006006, GO:0006096]] \n", - " glycolysis-gocam-1 [[GO:0005975, GO:0006006, GO:0006096, GO:0006754]] \n", - " go-postsynapse-calcium-transmembrane-0 [[GO:0006816, GO:0015075, GO:0099601, GO:0007268, GO:0034765]] \n", - " go-postsynapse-calcium-transmembrane-1 [[GO:0005216, neurotransmitter signaling, GO:0050804, GO:0005509, GO:0008066]] \n", - " go-reg-autophagy-pkra-0 [[GO:0006950, GO:0006915, GO:0042981, GO:0043123, GO:0046330]] \n", - " go-reg-autophagy-pkra-1 [[autophagy regulation, GO:0033554, GO:0006915]] \n", - " hydrolase activity, hydrolyzing O-glycosyl compounds-0 [[GO:0005975, GO:0005764, GO:0016798, glycoside hydrolase activity, GO:0004556, GO:0008422, acid alpha-glucosidase activity, GO:0004565, GO:0015929, GO:0015923, n-acetylglucosaminidase activity, GO:0004308, GO:0015926, GO:0005980, GO:0006027, mucopolysaccharide catabolic process, GO:0016266, GO:0006491]] \n", - " hydrolase activity, hydrolyzing O-glycosyl compounds-1 [[GO:0005975, GO:0070085, GO:0000272, GO:0004553, GO:0015929, GO:0004556, GO:0004565]] \n", - " ig-receptor-binding-2022-0 [[GO:0002376, GO:0046649, GO:0002250, GO:0042113, GO:0003823, antibody-mediated immunity\\n\\nmechanism]] \n", - " ig-receptor-binding-2022-1 [[GO:0002377, GO:0042113, GO:0016064]] \n", - " meiosis I-0 [[GO:0006281, GO:0035825, GO:0140013, GO:0007059, GO:0007129, GO:0006974, m phase of meiosis, dna replication-independent nucleosome assembly, crossover junction formation, GO:0007281, GO:0036093, GO:0009994, GO:0007283, GO:0071173, GO:0006298, GO:0033554]] \n", - " meiosis I-1 [[GO:0140013, GO:0006281, GO:0007059, MESH:D011995, GO:0035825, GO:0006302, GO:0007129, crossing-over, GO:0051276]] \n", - " molecular sequestering-0 [[GO:0034599, GO:0001558, GO:0032088, GO:0043066, GO:0051726, GO:0010468, GO:0008285]] \n", - " molecular sequestering-1 [[GO:0006979, GO:0006974, GO:0080135, regulation of protein localization to organelles, GO:0043065, GO:0043066, GO:0008285, GO:0050821]] \n", - " mtorc1-0 [[glycolysis; tca cycle; cholesterol biosynthesis; pentose phosphate pathway\\n\\nmechanism and hypotheses:\\nthe enriched terms suggest that these genes are involved in various aspects of cellular metabolism. glycolysis is the central pathway for glucose metabolism, converting glucose into pyruvate. the tca cycle is responsible for generating energy from the breakdown of carbohydrates, MESH:D005227, and amino acids. the cholesterol biosynthesis pathway is responsible for producing cholesterol, which is involved in membrane structure, steroid hormone synthesis, and bile salt production. the pentose phosphate pathway is involved in the production of nadph, which is critical for many cellular processes, including antioxidant defense and biosynthesis.\\n\\noverall, these genes are likely involved in regulating various aspects of cellular metabolism, including energy production, biosynthesis of important molecules like cholesterol and nadph, mediating the cellular response to oxidative stress]] \n", - " mtorc1-1 [[GO:0006810, GO:0008152, GO:0006457]] \n", - " peroxisome-0 [[GO:0007031, peroxisome biogenesis, protein import into peroxisome, peroxisome membrane organization, peroxisomal matrix organization]] \n", - " peroxisome-1 [[GO:0007031, peroxisome biogenesis, GO:0016559]] \n", - " progeria-0 [[GO:0006281, GO:0006997, GO:0010467, GO:0007568]] \n", - " progeria-1 [[GO:0006325, GO:0006281, GO:0000723, nuclear localization, nuclear lamina organization, genome stability regulation]] \n", - " regulation of presynaptic membrane potential-0 [[GO:0006811, GO:0048666, GO:0007268, GO:0042391, GO:0034765]] \n", - " regulation of presynaptic membrane potential-1 [[GO:0005216, GO:0042803, GO:0008066, GO:0016917, GO:0005261]] \n", - " sensory ataxia-0 [[GO:0042552, GO:0007411, GO:0007399, GO:0008104, GO:0031175]] \n", - " sensory ataxia-1 [[GO:0044237, neurological development, myelin sheath formation]] \n", - " term-GO:0007212-0 [[GO:0007186, GO:0007188, GO:0046928, GO:0032225, positive regulation of camp biosynthetic process, GO:0007194, GO:0007212, prostaglandin receptor signaling pathway]] \n", - " term-GO:0007212-1 [[GO:0007186, dopamine receptor activity, GO:0007188, GO:0004952, GO:0099528, d1 dopamine receptor signaling pathway]] \n", - " tf-downreg-colorectal-0 [[transcription regulation, GO:0016569, GO:0032502, GO:0065004, GO:0006950]] \n", - " tf-downreg-colorectal-1 [[GO:0003677, transcriptional regulation, GO:0010468, GO:0000988, GO:0003682, GO:0006357, GO:0006355, GO:0000977, GO:0043565, GO:0051090]] \n", - " ontological_synopsis EDS-0 [[GO:0030199, GO:0061448, GO:0062023, GO:0030198, GO:0006024]] \n", - " EDS-1 [[GO:0030198, GO:0030199, GO:0030166, GO:0006024, GO:0061448]] \n", - " FA-0 [[GO:0006281, GO:0006513]] \n", - " FA-1 [[GO:0006281, GO:0006513]] \n", - " HALLMARK_ADIPOGENESIS-0 [[mitochondrial function, GO:0006754, GO:0006629, GO:0005515, GO:0023052]] \n", - " HALLMARK_ADIPOGENESIS-1 [[GO:0005746, GO:0022900, GO:0006754, GO:0006631, GO:0015746, GO:0016746, dehydrogenase activity, GO:0016491, GO:0022857]] \n", - " HALLMARK_ALLOGRAFT_REJECTION-0 [[GO:0005125, chemokine receptor binding activity, interleukin receptor binding activity, mhc class protein complex binding activity, identical protein binding activity\\n\\nmechanism: these genes are involved in the regulation of the immune response, including the production of cytokines and chemokines, binding to immune receptors, and mhc class protein complex binding. their common function is likely related to the regulation of the immune system and the activation of the immune response against foreign invaders]] \n", - " HALLMARK_ALLOGRAFT_REJECTION-1 [[GO:0005125, chemokine receptor binding activity, GO:0004672, GO:0004896, identical protein binding activity, integrin binding activity, GO:0002376, GO:0005840, GO:0042803, GO:0042110, transcription activator activity, rna polymerase ii-specific. \\n\\nmechanism and hypotheses: these enriched terms suggest that the identified genes are involved in immune system processes such as cytokine signaling, chemokine receptor binding, and t cell activation. protein kinase activity may be involved in signaling pathways downstream of cytokine receptors or chemokine receptors. the presence of ribosome-related terms suggests these genes may play a role in protein synthesis in immune cells. the identified enriched terms point to a central role of the immune system in the functions of these genes, with potential impacts on inflammation, infection, and other immune-related diseases]] \n", - " HALLMARK_ANDROGEN_RESPONSE-0 [[GO:0006468, GO:0035556, GO:0010604]] \n", - " HALLMARK_ANDROGEN_RESPONSE-1 [[1. binding of metal ions \\n2. protein kinase activity \\n3. positive regulation of protein kinase activity \\n4. cytoskeletal protein binding activity \\n5. signal transduction \\n\\nmechanism: these enriched terms indicate that the genes have a role in signal transduction pathways and cytoskeletal organization. the genes are involved in the binding of metal ions and protein kinases, which are important components of these pathways. additionally, the positive regulation of protein kinase activity suggests that these genes have a role in the amplification of signal transduction through cascade-like pathways]] \n", - " HALLMARK_ANGIOGENESIS-0 [[extracellular matrix organization; cell signaling; blood coagulation; lipid metabolism; immunity.\\n\\nmechanism and hypotheses: these genes appear to be involved in a variety of pathways related to extracellular matrix organization, cell signaling, and intercellular communication. specifically, several genes encode proteins that are structural components of the extracellular matrix or interact with extracellular matrix proteins, suggesting a role in tissue development, remodeling, or repair. many of these genes also participate in signaling pathways that control cell proliferation, differentiation, and migration. additionally, several genes are involved in blood coagulation and lipid metabolism, which may be related to their roles in cardiovascular disease. finally, some genes have roles in immunity and host defense against infectious pathogens, possibly contributing to susceptibility or resistance to infectious diseases. overall, these common functions may point to a greater role for extracellular matrix and signaling pathways in disease pathogenesis]] \n", - " HALLMARK_ANGIOGENESIS-1 [[GO:0030198, cell signaling, protein binding activity, GO:1902533, GO:0062023]] \n", - " HALLMARK_APICAL_JUNCTION-0 [[actin filament binding activity, integrin binding activity, protein kinase binding activity, sh2 domain binding activity, cell adhesion molecule binding activity, identical protein binding activity, GO:0005096, atp binding activity, cadherin binding activity, collagen binding activity, GO:0051219, GO:0042803]] \n", - " HALLMARK_APICAL_JUNCTION-1 [[integrin binding activity, cell adhesion molecule binding activity, sh3 domain binding activity, identical protein binding activity, actin filament binding activity, protein kinase binding activity]] \n", - " HALLMARK_APICAL_SURFACE-0 [[GO:0005886, GO:0005615, signaling receptor binding activity, protein domain specific binding activity, protein kinase binding activity, GO:0006811, GO:0051247, GO:0010468, GO:0007155, GO:1902531]] \n", - " HALLMARK_APICAL_SURFACE-1 [[GO:0010468, signaling receptor binding activity, GO:0045944, GO:2001234, GO:0006811, GO:0060244, GO:0051965, carbohydrate binding activity, GO:1902531, GO:1904054]] \n", - " HALLMARK_APOPTOSIS-0 [[GO:0097190, GO:0006955, GO:0005125, identical protein binding activity, protease binding activity, enzyme binding activity, GO:0000988, dna binding activity]] \n", - " HALLMARK_APOPTOSIS-1 [[apoptotic process; cytokine activity; protein binding activity.\\n\\nmechanism: the genes in this list are involved in processes related to cell death, GO:0006955, and molecular interactions. the enriched terms suggest that these genes may be involved in pathways related to apoptosis, cytokine signaling, protein interactions. it is possible that these genes contribute to the regulation of cell death through cytokine-mediated signaling pathways protein-protein interactions]] \n", - " HALLMARK_BILE_ACID_METABOLISM-0 [[cholesterol binding activity, GO:0016887, GO:0005319, GO:0008559, atp binding activity, GO:0007031, vitamin d receptor binding activity, GO:0042626]] \n", - " HALLMARK_BILE_ACID_METABOLISM-1 [[GO:0008610, GO:0006631, GO:0008203, GO:0007031, GO:0015908, peroxisome matrix targeting, abc-type transporter activity. \\n\\nmechanism]] \n", - " HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 [[GO:0006695, GO:0008610, GO:0019216, GO:0042632, GO:0090181]] \n", - " HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 [[GO:0006695, GO:0008299, GO:0006633]] \n", - " HALLMARK_COAGULATION-0 [[GO:0006956, GO:0050817, GO:0008237]] \n", - " HALLMARK_COAGULATION-1 [[metalloendopeptidase activity; serine-type endopeptidase activity; protease binding activity; identical protein binding activity; complement binding activity \\n\\nmechanism and hypotheses: these enriched terms suggest that the common mechanism or pathway involves the regulation of proteolysis and immune response, particularly the complement system. metalloendopeptidase and serine-type endopeptidase activity are involved in the proteolytic degradation of various extracellular matrix components including collagen, GO:0005577, and proteoglycan, as well as destruction of pathogenic microorganisms during immune response. protease binding activity, identical protein binding activity, and complement binding activity are involved in protein-protein interactions that regulate proteolysis and activation of complement components. therefore, the hypothesis is that the common mechanism of these genes is related to the regulation of proteolysis and complement system activity]] \n", - " HALLMARK_COMPLEMENT-0 [[GO:0005515, GO:0046872, GO:0019899, GO:0042802, GO:0005524, GO:0003677, calcium ion binding. \\n\\nmechanism]] \n", - " HALLMARK_COMPLEMENT-1 [[GO:0004222, GO:0004252, complement binding activity, heparin binding activity, GO:0008234, GO:0004869, GO:0005201, serine-type endopeptidase inhibitor activity involved in apoptotic process, GO:0004722, MESH:D011809]] \n", - " HALLMARK_DNA_REPAIR-0 [[dna binding activity, transcription initiation, rna binding activity, GO:0009117, rna splicing. \\n\\nmechanism: these genes are likely involved in regulating dna replication, transcription, and various steps in rna processing, including splicing and export from the nucleus. they could also be involved in nucleotide metabolism and/or maintaining genomic stability]] \n", - " HALLMARK_DNA_REPAIR-1 [[GO:0003677, GO:0003723, GO:0009117, GO:0006281, transcription initiation, protein-macromolecule adaptor activity.\\n\\nmechanism: these genes work together to maintain the integrity and expression of genetic information, with a focus on dna-related processes]] \n", - " HALLMARK_E2F_TARGETS-0 [[GO:0006260, GO:0006281, GO:0051726, GO:0003682, GO:0005524, GO:0019899, GO:0042393, GO:0043130]] \n", - " HALLMARK_E2F_TARGETS-1 [[dna binding activity, chromatin binding activity, rna binding activity, enzyme binding activity, GO:0042803, single-stranded dna binding activity, identical protein binding activity, histone binding activity, atp binding activity, cyclin binding activity, nucleic acid binding activity]] \n", - " HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 [[GO:0005201, collagen binding activity, heparin binding activity, GO:0005125, GO:0008083, signaling receptor binding activity, wnt-protein binding activity]] \n", - " HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 [[collagen binding activity, integrin binding activity, heparin binding activity, GO:0005201, GO:0008237, platelet-derived growth factor binding activity, GO:0008009, fibronectin binding activity, GO:0004867]] \n", - " HALLMARK_ESTROGEN_RESPONSE_EARLY-0 [[GO:0004888, GO:0022857, GO:0001216]] \n", - " HALLMARK_ESTROGEN_RESPONSE_EARLY-1 [[GO:0007165, transcriptional regulation, GO:0003824, GO:0038023, GO:0003676, GO:0007154, GO:0042445, protein-protein interaction\\n\\nhypotheses: the enriched terms suggest that the genes in this list are involved in various aspects of signaling and transcriptional regulation. they may function in pathways such as cell signaling, hormone metabolism, and protein-protein interaction. this list includes genes encoding enzymes with specific activities, as well as receptor and nucleic acid binding proteins that are crucial for signaling and transcriptional regulation]] \n", - " HALLMARK_ESTROGEN_RESPONSE_LATE-0 [[enzyme binding activity, identical protein binding activity, calcium ion binding activity, GO:0005215, phosphorylation-dependent protein binding activity, atpase binding activity, GO:0004930, GO:0004712, nucleotide binding activity, ubiquitin protein ligase binding activity, transcription factor binding activity, histone deacetylase binding activity, GO:0016787, GO:0016491]] \n", - " HALLMARK_ESTROGEN_RESPONSE_LATE-1 [[binding activity, GO:0005215, enzyme binding activity, identical protein binding activity, protein kinase binding activity, GO:0004930]] \n", - " HALLMARK_FATTY_ACID_METABOLISM-0 [[fatty acid-coa ligase activity, GO:0003995, long-chain fatty acid binding activity, GO:0003985, GO:0016615, GO:0000104, GO:0016616]] \n", - " HALLMARK_FATTY_ACID_METABOLISM-1 [[GO:0003824, GO:0016491, GO:0006631, GO:0006629, metabolic pathways. \\n\\nmechanism: these genes may be involved in the regulation of lipid and fatty acid metabolism, potentially through oxidation-reduction processes and metabolic pathways]] \n", - " HALLMARK_G2M_CHECKPOINT-0 [[dna binding activity, transcription regulation, GO:0004672, protein binding activity, GO:0016570]] \n", - " HALLMARK_G2M_CHECKPOINT-1 [[dna-binding transcription factor, GO:0004672, protein binding activity, GO:0140014, GO:0006260, GO:0010467]] \n", - " HALLMARK_GLYCOLYSIS-0 [[GO:0008194, GO:0008146, GO:0008378, GO:0015020, GO:0004553, heparan sulfate binding activity, several others]] \n", - " HALLMARK_GLYCOLYSIS-1 [[enzyme binding activity, GO:0008194, atp binding activity, GO:0008378, GO:0004340, fructose binding activity, heme binding activity, GO:0016787, rna binding activity, identical protein binding activity, GO:0046983, nucleoside triphosphate activity]] \n", - " HALLMARK_HEDGEHOG_SIGNALING-0 [[GO:0032502, GO:0007165, MESH:D005786]] \n", - " HALLMARK_HEDGEHOG_SIGNALING-1 [[GO:0007155, transcription regulation, GO:0007165, negative regulation, positive regulation]] \n", - " HALLMARK_HEME_METABOLISM-0 [[GO:0005215, binding activity, GO:0003824]] \n", - " HALLMARK_HEME_METABOLISM-1 [[enzyme binding activity, protein domain specific binding activity, GO:0046982, identical protein binding activity, GO:0042803]] \n", - " HALLMARK_HYPOXIA-0 [[enzyme binding activity, protein kinase binding activity, identical protein binding activity, GO:0003700, GO:0004674, calcium ion binding activity, nucleic acid binding activity, atp binding activity, GO:0060422, gtp binding activity, GO:0004340, GO:0005353, GO:0008459, heparin binding activity, apolipoprotein binding activity]] \n", - " HALLMARK_HYPOXIA-1 [[GO:0042802, GO:0019899, GO:0005524, GO:0019901, GO:0005509, GO:0005102, GO:0015035, GO:0016538, GO:0008083, GO:0005353, GO:0004347, nadph binding activity, GO:0042803, MESH:D013213]] \n", - " HALLMARK_IL2_STAT5_SIGNALING-0 [[GO:0042802, GO:0003700, GO:0005125, GO:0005096, interleukin receptor binding activity, ubiquitin protein ligase activity.\\n\\nmechanism: these genes likely play a role in regulating various cell signaling pathways, including cytokine and growth factor signaling, as well as intracellular protein degradation via ubiquitin-proteasome system]] \n", - " HALLMARK_IL2_STAT5_SIGNALING-1 [[GO:0004896, protein binding activity, GO:0003824, dna binding activity, rna binding activity, apoptosis. \\n\\nmechanism: these genes are involved in various cellular processes such as signaling and cytokine receptor activity, where they play a role in transmitting signals from the outside to the inside of the cell, as well as in regulating the immune system. they are also involved in enzyme activity, dna and rna binding activity, and apoptosis, playing a role in various pathways such as the regulation of gene expression and programmed cell death]] \n", - " HALLMARK_IL6_JAK_STAT3_SIGNALING-0 [[GO:0004896, GO:0004896, growth factor receptor binding activity]] \n", - " HALLMARK_IL6_JAK_STAT3_SIGNALING-1 [[GO:0005125, signaling receptor binding activity, GO:0001819, GO:0019221, GO:0009967, GO:0004896, GO:0050776]] \n", - " HALLMARK_INFLAMMATORY_RESPONSE-0 [[GO:0005125, GO:0004896, GO:0004930, GO:0002376, GO:0006954, GO:0008009]] \n", - " HALLMARK_INFLAMMATORY_RESPONSE-1 [[GO:0004896, GO:0004930, signaling receptor binding activity, identical protein binding activity, enzyme binding activity]] \n", - " HALLMARK_INTERFERON_ALPHA_RESPONSE-0 [[GO:0006955, GO:0019882, cytokines/chemokines, interferon-related genes, rna processing/editing]] \n", - " HALLMARK_INTERFERON_ALPHA_RESPONSE-1 [[GO:0098542, GO:0045071, GO:0035458, GO:0071345, GO:0042590, GO:0006469, GO:0010604, GO:0046597, GO:0019221, GO:0045669, GO:0052548]] \n", - " HALLMARK_INTERFERON_GAMMA_RESPONSE-0 [[GO:0005125, GO:0008009, GO:0001216, enzyme binding activity, identical protein binding activity, protease binding activity, GO:0042803, rna binding activity, GO:0050852, GO:0061630]] \n", - " HALLMARK_INTERFERON_GAMMA_RESPONSE-1 [[GO:0019882, cytokine signaling, antiviral defense]] \n", - " HALLMARK_KRAS_SIGNALING_DN-0 [[GO:0003824, protein binding activity, GO:0000988, identical protein binding activity, ion binding activity.\\n\\nmechanism]] \n", - " HALLMARK_KRAS_SIGNALING_DN-1 [[GO:0005488, GO:0003824, GO:0004930, GO:0000988, GO:0005509, GO:0005524, protein homodimerization activity.\\n\\nmechanism: the enriched terms suggest that these genes are involved in cellular regulation and signaling processes through binding and enzymatic activities, particularly involving calcium ions and atp. many genes also have transcription factor activity, indicating a role in gene expression regulation. g protein-coupled receptor activity is also overrepresented, suggesting a role in cellular signaling processes]] \n", - " HALLMARK_KRAS_SIGNALING_UP-0 [[GO:0005515, enzyme binding activity, transcriptional regulation, ion binding activity, dna binding activity, GO:0004930, GO:0005125, identical protein binding activity]] \n", - " HALLMARK_KRAS_SIGNALING_UP-1 [[enzymatic activity, GO:0019901, binding activity\\n\\nmechanism: the enriched functions suggest that these genes may be involved in the regulation of cellular processes through protein-protein interactions, including enzymatic activities and binding activities. this could involve pathways such as signal transduction or gene expression regulation]] \n", - " HALLMARK_MITOTIC_SPINDLE-0 [[microtubule binding activity, actin binding activity, GO:0005096]] \n", - " HALLMARK_MITOTIC_SPINDLE-1 [[GO:0008017, mitotic processes, GO:0000910, GO:0007018, spindle organization. \\n\\nmechanism: these genes play important roles in the regulation and organization of microtubules, which are key components of the cytoskeleton involved in cell division processes such as mitosis and cytokinesis. the enrichment of terms related to microtubule binding and regulation suggest that these genes may function together in a pathway that regulates the dynamics and organization of microtubules during these cellular processes. they may also be involved in microtubule-based movement, which is crucial for various cellular activities such as intracellular transport and cell migration]] \n", - " HALLMARK_MTORC1_SIGNALING-0 [[GO:0005515, GO:0003723, enzymatic activity, structural constituent of cytoskeleton. \\n\\nmechanism: these genes likely play a role in cellular processes such as transcription, translation, protein folding, and cytoskeletal organization]] \n", - " HALLMARK_MTORC1_SIGNALING-1 [[GO:0006457, GO:0005783, ubiquitin-proteasome system, GO:0015031, GO:0030163]] \n", - " HALLMARK_MYC_TARGETS_V1-0 [[GO:0003743, ribosome binding activity, rna binding activity, GO:0003735, protein folding chaperone activity, GO:0140713]] \n", - " HALLMARK_MYC_TARGETS_V1-1 [[GO:0000394, GO:0006413, GO:0003723, GO:0003676, GO:0006457, ribosome structure\\n\\nmechanism: these genes are involved in rna processing, including mrna splicing and translation initiation, as well as binding to rna and nucleic acids. some genes also play roles in protein folding and ribosome structure. the underlying biological mechanism or pathway is likely related to rna processing and regulation of gene expression]] \n", - " HALLMARK_MYC_TARGETS_V2-0 [[GO:0006364, GO:0042273, snorna binding activity, GO:0005730, rna binding activity]] \n", - " HALLMARK_MYC_TARGETS_V2-1 [[GO:0006364, ribosomal biogenesis, rna binding activity, GO:0005730]] \n", - " HALLMARK_MYOGENESIS-0 [[actin binding activity, calcium ion binding activity, atp binding activity, identical protein binding activity, cytoskeletal protein binding activity, enzyme binding activity, UBERON:0005090]] \n", - " HALLMARK_MYOGENESIS-1 [[GO:0006936, GO:0030036, GO:0006600, GO:0032956, regulation of muscle contraction.\\n\\nmechanism: these genes are involved in the regulation of muscle contraction and actin cytoskeleton organization, likely through their roles in calcium ion binding, myosin light chain kinase activity, and actin filament binding. several of the genes are also involved in creatine metabolism, which is important for energy generation in muscle tissues]] \n", - " HALLMARK_NOTCH_SIGNALING-0 [[GO:0007219, GO:0016567, GO:0006357, GO:0051247, GO:0016055, scf-dependent proteasomal ubiquitin-dependent protein catabolic process, cyclin-dependent protein kinase holoenzyme complex]] \n", - " HALLMARK_NOTCH_SIGNALING-1 [[GO:0007219, GO:0016567]] \n", - " HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 [[GO:0009055, ubiquitin protein ligase binding activity, MESH:D014451, rna binding activity, GO:0042803, metal ion binding activity.\\n\\nmechanism and]] \n", - " HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 [[mitochondria\\n- atp synthesis\\n- respiratory chain complex\\n- electron transfer\\n- oxidoreductase activity\\n- iron-sulfur cluster binding\\n\\nmechanism: these genes are involved in the regulation of metabolic processes and energy production in the mitochondria. they play important roles in cellular respiration, which involves the conversion of nutrients into energy necessary for cellular activities. the enriched terms suggest that these genes are closely related to the function of the mitochondrial respiratory chain complex and atp synthase, both of which are necessary for energy production in the form of atp. additionally, several of these genes are involved in electron transfer and oxidoreductase activity, which are also important in metabolic processes that lead to energy production. finally, there is a common theme of iron-sulfur cluster binding, which suggests a common mechanism in the regulation of metabolic processes and energy production]] \n", - " HALLMARK_P53_PATHWAY-0 [[GO:0003677, GO:0005515, GO:0003824, GO:0000988, growth factor activity. \\n\\nmechanism: these genes likely play roles in regulating transcription, protein-protein interactions, metabolism, and growth factor signaling pathways]] \n", - " HALLMARK_P53_PATHWAY-1 [[GO:0005515, dna binding activity, GO:0016301]] \n", - " HALLMARK_PANCREAS_BETA_CELLS-0 [[GO:0042593, GO:0050796, GO:0046326, GO:0006006]] \n", - " HALLMARK_PANCREAS_BETA_CELLS-1 [[GO:0030073, GO:0006006, transcriptional regulation, transcription factor binding activity, rna polymerase ii-specific dna binding activity, GO:0000122, positive regulation of transcription by rna polymerase ii. \\n\\nmechanism and]] \n", - " HALLMARK_PEROXISOME-0 [[GO:0001676, GO:0043574, GO:0008203, GO:0006633, lipid binding activity, atp binding activity, GO:0016491]] \n", - " HALLMARK_PEROXISOME-1 [[GO:0006629, mitochondrial function, GO:0006281]] \n", - " HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 [[GO:0004672, g protein-coupled receptor binding activity, transcription factor binding activity, enzyme binding activity, GO:0007166, GO:0035556, GO:0032007, GO:0010971, negative regulation of vasc, negative regulation of nitrogen com, actin filament binding activity, cytoskeletal protein binding activity]] \n", - " HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 [[GO:0006468, GO:0035556, GO:0016301, enzyme binding activity, GO:0004672, identical protein binding activity, scaffold protein binding activity]] \n", - " HALLMARK_PROTEIN_SECRETION-0 [[GO:0007030, GO:0048193, GO:0090110, GO:0006888, retrograde transport, vesicle recycling, GO:0034260, negative regulation of autophagosome formation and maturation, GO:1905604, GO:1905280, GO:0002091, GO:0009967]] \n", - " HALLMARK_PROTEIN_SECRETION-1 [[GO:0006888, GO:0048193, GO:0006891, GO:0034067, snare complex assembly.\\n\\nmechanism and]] \n", - " HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 [[cellular redox homeostasis, GO:0006979, protein disulfide reduction, GO:0006749, GO:0003954, GO:0004601, GO:0006826, GO:0016209, MESH:D015227]] \n", - " HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 [[GO:0045454, GO:0006979]] \n", - " HALLMARK_SPERMATOGENESIS-0 [[GO:0005515, GO:0016301, GO:0051726, GO:0010467]] \n", - " HALLMARK_SPERMATOGENESIS-1 [[GO:0005515, GO:0008047, atp binding activity]] \n", - " HALLMARK_TGF_BETA_SIGNALING-0 [[GO:0060395, GO:0006357, GO:0010604, GO:0090101, GO:0045668, establishment of sert, positive regulation of vascular associated smooth muscle cell proliferat, several others]] \n", - " HALLMARK_TGF_BETA_SIGNALING-1 [[GO:0005024, GO:0046332, GO:0009967, GO:0006357, GO:0000122, GO:0007166, GO:0010604, nucleic acid binding activity]] \n", - " HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 [[GO:0003700, rna polymerase ii-specific; cytokine activity; protein binding activity.\\n\\nmechanism: these genes are involved in the regulation of transcription and cytokine activity, likely playing a role in immune responses and cellular differentiation. they are involved in binding to dna and rna polymerases to regulate the expression of genes, as well as in the production and regulation of cytokines and growth factors that play a role in cell signaling and differentiation]] \n", - " HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 [[GO:0005125, GO:0008009, GO:0001216, GO:0006955, interleukin-12 alpha subunit binding activity, GO:0004707, protein kinase binding activity, GO:0001817, GO:0002682, smad binding activity, transcription factor binding activity]] \n", - " HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 [[protein folding and chaperone activity, rna binding and transcriptional regulation, rna processing and degradation]] \n", - " HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 [[GO:0003723, GO:0051087, GO:0090304, endoplasmic reticulum stress response pathway]] \n", - " HALLMARK_UV_RESPONSE_DN-0 [[GO:0005201, identical protein binding activity, enzyme binding activity, smad binding activity]] \n", - " HALLMARK_UV_RESPONSE_DN-1 [[GO:0005201, GO:0005515, GO:0016563, GO:0005102]] \n", - " HALLMARK_UV_RESPONSE_UP-0 [[enzyme binding activity, GO:0003700, protein kinase binding activity, identical protein binding activity, rna binding activity, atp binding activity, ubiquitin protein ligase binding activity]] \n", - " HALLMARK_UV_RESPONSE_UP-1 [[enzyme binding activity, GO:0006508, protein phosphatase binding activity, GO:0004725]] \n", - " HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 [[GO:0060070, transcription regulation, MESH:D012319, transcription activator, beta-catenin complex, GO:0007219]] \n", - " HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 [[GO:0060070, GO:0010468]] \n", - " T cell proliferation-0 [[GO:0050852, GO:0005125, interleukin-2 receptor binding activity, negative regulation of peptid, intracellular signal transduction\\n\\nmechanism: the genes analyzed in this study are primarily involved in signaling and receptor binding activities. this suggests that these genes may play an important role in the communication between cells and regulation of immune response. \\n\\n t cell receptor signaling pathway, cytokine activity, interleukin-2 receptor binding activity, negative regulation of peptid..., and intracellular signal transduction]] \n", - " T cell proliferation-1 [[GO:0050863, GO:0001819, GO:0006468, GO:0043066, GO:0002687, GO:0030890, GO:0006879, GO:0010468]] \n", - " Yamanaka-TFs-0 [[transcriptional regulation, GO:0010467, GO:0003700, GO:0009889, GO:0019219]] \n", - " Yamanaka-TFs-1 [[GO:0010467, transcription regulation, dna binding activity, rna polymerase ii-specific, GO:0010468, transcription cis-regulatory region binding activity]] \n", - " amigo-example-0 [[GO:0007160, GO:0030198, GO:0030199, GO:0008034]] \n", - " amigo-example-1 [[GO:0007160, GO:0030199, GO:0030198, GO:1902533, GO:0010604, GO:0030334]] \n", - " bicluster_RNAseqDB_0-0 [[GO:0003700, identical protein binding activity, protein kinase binding activity, actin binding activity, sequence-specific double-stranded dna binding activity, metal ion binding activity, calcium ion binding activity, chromatin binding activity, rna binding activity]] \n", - " bicluster_RNAseqDB_0-1 [[binding activity, GO:0003700, GO:0046872, GO:0019904, GO:0061630]] \n", - " bicluster_RNAseqDB_1002-0 [[GO:0006936, GO:0043502, GO:0016567]] \n", - " bicluster_RNAseqDB_1002-1 [[GO:0006936, GO:0003009, GO:0016567, ion channel activity.\\n\\nmechanism: these genes likely play a role in muscle contraction and structure, possibly through the regulation of ion channels and protein ubiquitination]] \n", - " endocytosis-0 [[GO:0006897, GO:0007165, cellular adhesion, GO:0006869, GO:0030163, GO:0007009]] \n", - " endocytosis-1 [[GO:0006897, membrane traffic, GO:0015031]] \n", - " glycolysis-gocam-0 [[GO:0006096, GO:0005975, GO:0006000, metabolic homeostasis]] \n", - " glycolysis-gocam-1 [[GO:0006096, GO:0005975, GO:0006002, GO:0005945]] \n", - " go-postsynapse-calcium-transmembrane-0 [[GO:0006816, GO:0005245, GO:0008066, GO:0005892]] \n", - " go-postsynapse-calcium-transmembrane-1 [[GO:0019722, voltage-gated calcium channel, GO:0051480, GO:0008066, GO:0017146, GO:0007268, GO:0051899, g-protein coupled receptor signaling pathway]] \n", - " go-reg-autophagy-pkra-0 [[GO:0006468, GO:0035556, GO:0031929, GO:0097190, kinase activity regulation, GO:0010604]] \n", - " go-reg-autophagy-pkra-1 [[GO:0035556, protein kinase activity regulation, GO:0010604, GO:0038202, GO:0032008, GO:0045859, apoptosis signaling pathway, chromatin binding activity]] \n", - " hydrolase activity, hydrolyzing O-glycosyl compounds-0 [[GO:0016052, GO:0006516, GO:0006032, GO:0030214]] \n", - " hydrolase activity, hydrolyzing O-glycosyl compounds-1 [[GO:0016052, GO:0030214, GO:0006516, GO:0019377, GO:0006032, GO:0006491, GO:0006517, mannose trimming involved in glycoprotein erad pathway.\\n\\nmechanism: one potential underlying biological mechanism is the regulation of cell surface and extracellular matrix composition, as well as the breakdown and recycling of molecules within these structures. glycosidases play a key role in breaking down complex carbohydrates into smaller subunits, which can then be reassembled into new molecules. the ability to break down specific types of carbohydrates, such as hyaluronic acid and chitin, may also be important for cellular processes such as cell migration and host defense]] \n", - " ig-receptor-binding-2022-0 [[immunoglobulin receptor binding activity, antigen binding activity]] \n", - " ig-receptor-binding-2022-1 [[GO:0006955, GO:0006952, antigen binding activity]] \n", - " meiosis I-0 [[homologous chromosome pairing, GO:0042138, GO:0000706, GO:0007131, GO:0000724, GO:0000712, GO:0000795]] \n", - " meiosis I-1 [[meiotic recombination, GO:0006302, GO:0035825, chromosomal segregation, GO:0007130]] \n", - " molecular sequestering-0 [[GO:0140313, GO:0140311, identical protein binding activity, GO:0060090, ubiquitin protein ligase binding activity, GO:0016567]] \n", - " molecular sequestering-1 [[GO:0010468, GO:0042742, GO:0045185, GO:0002376, GO:0009267, GO:0032387, GO:0035556]] \n", - " mtorc1-0 [[GO:0005515, GO:0003723, enzymatic activity, structural constituent of cytoskeleton. \\n\\nmechanism: these genes likely play a role in cellular processes such as transcription, translation, protein folding, and cytoskeletal organization]] \n", - " mtorc1-1 [[GO:0005515, GO:0003824, GO:0005215]] \n", - " peroxisome-0 [[peroxisome biogenesis, peroxisome matrix targeting, GO:0017038]] \n", - " peroxisome-1 [[peroxisome biogenesis, GO:0017038, GO:0005778, ubiquitin-dependent protein binding activity, atp binding activity, GO:0016887]] \n", - " progeria-0 [[GO:0006259, GO:0006325, GO:0033554]] \n", - " progeria-1 [[GO:0006281, GO:0000723, GO:0007568]] \n", - " regulation of presynaptic membrane potential-0 [[GO:0007214, GO:0022849, GO:0005242, GO:0035235, GO:0015276, GO:0071805, GO:0005244]] \n", - " regulation of presynaptic membrane potential-1 [[GO:0006811, GO:0007268, membrane potential regulation, GO:0008066, GO:0007214]] \n", - " sensory ataxia-0 [[MONDO:0015626, GO:0042552, GO:0007422, GO:0006457, GO:0007600, nucleic acid metabolism, mitochondrial function]] \n", - " sensory ataxia-1 [[GO:0007399, MONDO:0015626, GO:0042552, UBERON:0000010, mitochondrial dysfunction, protein ubiquitination.\\n\\nmechanism]] \n", - " term-GO:0007212-0 [[GO:0007212, GO:0007190, calcium ion regulation, g protein-coupled receptor pathway]] \n", - " term-GO:0007212-1 [[GO:0007186, GO:0004952, GO:0004016, GO:0051480, negative regulation of glycogen synthase activity, GO:0004672, GO:0019538, GO:0006468]] \n", - " tf-downreg-colorectal-0 [[GO:0001216, rna polymerase ii transcription regulatory region sequence-specific dna binding activity, GO:0045944, GO:0000122, GO:0006355, transcription factor binding activity, nucleic acid binding activity, chromatin binding activity, GO:0003713]] \n", - " tf-downreg-colorectal-1 [[GO:0003700, GO:0006355, GO:0010468, GO:0006337]] \n", - "text-davinci-003 narrative_synopsis EDS-0 [[GO:0032964, collagen fiber formation, extracellular matrix maturation, transcriptional regulation, procollagen protein, MESH:D006025, metalloproteinase, proteolytic processing, peptidyl prolyl cis-trans isomerase, MESH:M0465019, tumor-rejection antigen, sulfotransferase, transmembrane protein, beta-1,3 galactosyltransferase]] \n", - " EDS-1 [[GO:0006486, extracellular matrix remodeling, collagen production, GO:0061448, immunity response, GO:0006508, tumor rejection, MESH:M0465019, MESH:D008565, transcriptional repressor, peptidyl-prolyl isomerase, complement system, GO:0004226, peptidase s1]] \n", - " FA-0 [[GO:0006281, genome maintenance, MESH:D004249, nucleoprotein complex, GO:0035825, double-strand dna repair, holliday junction resolution, monoubiquinated, MESH:D051135, nuclear foci, structure-specific endonucleases, MESH:D051135, recq deah helicase, tumor suppression, ssdna-binding proteins]] \n", - " FA-1 [[GO:0006281, nucleoprotein complex, GO:0035825, dna lesion, MESH:M0443450, fanconi anemia complementation group (fanc), GO:0006302]] \n", - " HALLMARK_ADIPOGENESIS-0 [[GO:0010467, GO:0140657, GO:0006468, ubiquitin-mediated degradation, GO:0051726, GO:0005525, GO:0006839, GO:0006118, GO:0006119, MESH:D004789, enzyme inhibition, GO:0016491, GO:0016482, GO:0005515, GO:0006629, GO:0036211, ubiquitinylation]] \n", - " HALLMARK_ADIPOGENESIS-1 [[atp production, GO:0005746, GO:0006118, GO:0030497, rna/dna binding, GO:0015031, MESH:D054875, GO:0016310, GO:0008017, GO:0006869]] \n", - " HALLMARK_ALLOGRAFT_REJECTION-0 [[cell signalling, cytokine production/regulation, chemokine production/regulation, antimicrobial defence, plasma protein regulation, immune regulation, inflammatory regulation, transcriptional regulation, GO:0004672, GO:0008233, glycoprotein activity, receptor protein activity]] \n", - " HALLMARK_ALLOGRAFT_REJECTION-1 [[integrin, cytokine, g-protein coupled receptor, MESH:D007372, MESH:D018124, MESH:D008562, MESH:D011494, chemokine, transmembrane receptor, GO:0007165, transcriptional regulation, GO:0006412, GO:0006955]] \n", - " HALLMARK_ANDROGEN_RESPONSE-0 [[GO:0005524, GO:0006351, GO:0016310, MESH:D011494, protein tyrosine phosphatase, GO:0065007, GO:0005515, hydrolase, ribosomal s6 kinase, GO:0016192, regulatory subunit, acetyltransferase, modulation, GO:0005509, GO:0005783, GO:0000981, GO:0003723, n-myc downregulated, polypeptide, GO:0016125, MESH:D006657, protein inhibitor, MESH:D051116, structural fibre, disulfide oxidoreductase, adenine dinucleotide, non-sterol metabolism, calcium-induced, GO:0042593]] \n", - " HALLMARK_ANDROGEN_RESPONSE-1 [[transcriptional regulation, GO:0004672, GO:0005515, GO:0003723, GO:0007165, proteolytic enzyme activity, GO:0003677]] \n", - " HALLMARK_ANGIOGENESIS-0 [[GO:0042157, GO:0050817, GO:0007599, MESH:D016207, MESH:D018925, receptors, transporters, secreted extracellular matrix proteins, GO:0004868, MESH:D011509, GO:0007155, GO:0016477, GO:0023052, GO:0008283, GO:0006915, transcriptional regulation, tissue development and regeneration, GO:0006955]] \n", - " HALLMARK_ANGIOGENESIS-1 [[cell-cell interactions, cell-matrix interactions, extracellular matrix production, processing of proteoglycans and glycoproteins]] \n", - " HALLMARK_APICAL_JUNCTION-0 [[integrin, GO:0008014, GO:0005530, MESH:C119025, map kinase, protein tyrosine kinase, guanine nucleotide binding protein, MESH:D020558, act]] \n", - " HALLMARK_APICAL_JUNCTION-1 [[GO:0007155, GO:0023052, scaffolding, cytoskeleton maintenance, GO:0031012, MESH:D016023, MESH:D057167, MESH:C119025, MESH:D011494, GO:0008014]] \n", - " HALLMARK_APICAL_SURFACE-0 [[GO:0007155, GO:0006457, GO:0007154, GO:0006898, gpi-anchored cell surface proteins, cation transport atpase, transcriptional coactivation, interleukin signaling, hormone-dependence, MESH:D019812, heparin-binding, GO:0007160]] \n", - " HALLMARK_APICAL_SURFACE-1 [[cell signal transduction, GO:0007160, GO:0006457, GO:0030308, ligand binding, cell-surface glycoprotein, cation transmembrane transporter, growth arrest, MESH:D051246, transmembrane protein, regulatory subunit, membrane-bound glycoprotein, ammonium transmembrane transporter, cell surface receptor, insulin-regulated facilitative glucose transporter, cell surface adhesion molecule, GO:0140326, glycosylphosphatidylinositol-anchored protein]] \n", - " HALLMARK_APOPTOSIS-0 [[GO:0006915, transcriptional regulation, GO:0003677, tnf receptor superfamily, bcl-2 protein family]] \n", - " HALLMARK_APOPTOSIS-1 [[the genes summarized are involved in a wide range of processes, including apoptosis, tumor suppression, inflammation, thioredoxin binding, cytoplasmic protein and membrane glycoprotein regulation, dna topoisomerase and transcriptional activation. the commonalities that emerge from the enrichment test point to a specific biological pathway known as cell death regulation and signal transduction. this involves the interconnected network of genes that regulate apoptosis and maintain genetic stability, as well as others involved in the modulation of immune response pathways. enriched terms include apoptosis, cytoplasmic protein regulation, transcriptional regulation, tumor suppression, GO:0006954, MESH:D004264, thioredoxin binding, membrane glycoprotein regulation, transcriptional coactivation, death agonist, GO:0048018, serine/threonine phosphatase, voltage-dependent anion channel, MESH:D006136, class-1 polypeptide chain release factor, proapoptotic, nf-kappa-b.\\n\\nsummary: genes related to cell death regulation signal transduction pathways.\\nmechanism: interconnected network of genes that regulate apoptosis maintain genetic stability, as well as those involved in the modulation]] \n", - " HALLMARK_BILE_ACID_METABOLISM-0 [[GO:0006629, atp binding cassette, MESH:M0011631, GO:0005490, peroxin, gamma-glutamylcysteine synthetase, GO:0050632, MESH:D002785, flavoenzymes, GO:0042446, GO:0016209]] \n", - " HALLMARK_BILE_ACID_METABOLISM-1 [[GO:0006629, GO:0006810, oxidation, bile acids synthesis, GO:0006790, GO:0005777, oxidative stress response]] \n", - " HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 [[GO:0048870, energy generation, GO:0008652, GO:0009063, GO:0009101, GO:0016126, GO:0016127, GO:0006629, GO:0006869, transcriptional regulation]] \n", - " HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 [[GO:0006695, GO:0006629, GO:0006636, cell growth/regulation, GO:0051726, GO:0005515, mhc class ii presentation, cellular antioxidant activity, GO:0000988]] \n", - " HALLMARK_COAGULATION-0 [[analysis of this set of human genes revealed high enrichment for terms related to proteases and protease inhibitors, GO:0005209, MESH:D006023, and serine proteinases. of particular note is the abundance of genes related to the regulation of the complement system and to the coagulation cascade, GO:0004235, there appears to be a strong emphasis on proteins that are involved in the maintenance of cellular integrity and in the regulation of inflammatory and immune responses. in particular, it appears that the presence of proteases, MESH:D011480, GO:0005209, MESH:D006023, and serine proteinases is significantly enriched. this suggests that these proteins are involved in the regulation of a variety of processes, including the complement system and the coagulation cascade. furthermore, the presence of various mmps suggests a regulatory role in the breakdown of proteins in the extracellular matrix, which is important for tissue remodeling and wound healing]] \n", - " HALLMARK_COAGULATION-1 [[cysteine-aspartic acid protease, MESH:D020782, peptidase, guanine nucleotide-binding proteins, GO:0030165, metalloproteinase, MESH:D042962, regulator of complement activation, regulator of g protein signal transduction, rnase a superfamily, MESH:D011505, subtilisin-like proprotein convertase, MESH:D011973, vitamin k-dependent plasma glycoprotein, vitamin k-dependent coagulation factor, GO:0005161, lysosomal cysteine proteinase, MESH:D015842, transforming growth factor-beta, MESH:D006904, kunitz-type serine protease, integ]] \n", - " HALLMARK_COMPLEMENT-0 [[MESH:D010770, GO:0000502, GO:0004868, cysteine-aspartic acid protease (caspase), GO:0006915, inflammation signalling, MESH:D005165, factor]] \n", - " HALLMARK_COMPLEMENT-1 [[cell signaling, GO:0007155, GO:0008233, transcriptional regulation, GO:0008152, cytoskeletal functions]] \n", - " HALLMARK_DNA_REPAIR-0 [[GO:0003677, transcription control, post-splicing, MESH:D012319, GO:0006281, GO:0071897]] \n", - " HALLMARK_DNA_REPAIR-1 [[GO:0019899, GO:0003723, GO:0003677, GO:0005515, chromosomal binding, dna polymerase, MESH:D012321, phosphorolysis, GO:0010629, GO:0016567]] \n", - " HALLMARK_E2F_TARGETS-0 [[dna replication/repair, chromatin regulation, GO:0006396, ser/thr protein kinase, MESH:D063146, nuclear transport and export, GO:0016567, gtpase activation, GO:0006413, GO:0003723, GO:0003677, GO:0042393, ubiquitin protein ligase, cyclin-dependent kinase, MESH:D000251, MESH:D003842]] \n", - " HALLMARK_E2F_TARGETS-1 [[GO:0006260, nuclear import/export, GO:0003723, chromatin regulation/modification, GO:0030163, GO:1901987, GO:0006281]] \n", - " HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 [[GO:0003779, actin regulation, GO:0007155, cell signaling, GO:0005518, cytokine regulation and signaling, GO:0005207, growth factor family members, peptidase genes]] \n", - " HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 [[GO:0007155, GO:0005518, GO:0003779, MESH:D024022, MESH:D016326, cytoskeletal components, cell signalling]] \n", - " HALLMARK_ESTROGEN_RESPONSE_EARLY-0 [[GO:0007165, GO:0010467, GO:0006810, MESH:D008565, GO:0043687, GO:0005515, ligand binding, acyltransferase]] \n", - " HALLMARK_ESTROGEN_RESPONSE_EARLY-1 [[cytoskeletal organization, dna-binding transcription regulation, GO:0055085, membrane-associated signaling, receptor activation and signaling, cytokine and growth factor signaling]] \n", - " HALLMARK_ESTROGEN_RESPONSE_LATE-0 [[g-protein signaling, ion channel transport, membrane receptor signalling, cytoskeletal protein scaffolding, enzyme regulation, glycoprotein modulation.\\nmechanism: the genes identified as being related to these topics are involved in the regulation of cell signalling pathways and the transport of ions across cellular membranes. in addition, the genes are involved in biochemical processes such as enzyme regulation and glycoprotein modulation, which may be important in modulating the amount or type of molecules entering the cell and in organizing the cytoskeleton]] \n", - " HALLMARK_ESTROGEN_RESPONSE_LATE-1 [[GO:0007165, gene transcription, ion transport and binding, protein-protein interaction, GO:0043687, GO:0007155, MESH:M0518050, GO:0016310, MESH:D011494, membrane recognition, GO:0003676, MESH:D018118, enzymatic reactions, lipid transport, glucose transport, cytokine receptor, molybdenum cofactor biosynthesis]] \n", - " HALLMARK_FATTY_ACID_METABOLISM-0 [[GO:0008152, GO:0009117, GO:0006631, GO:0006096, oxidation-reduction processes, GO:0006595, GO:0003824, amino acid metabolism, protein homodimerization, protein biotransformation, protein-macromolecule adaptor, protein-tat binding]] \n", - " HALLMARK_FATTY_ACID_METABOLISM-1 [[GO:0006099, GO:0006118, GO:0005504, MESH:D042964, pyruvate dehydrogenase, nad-dependent glycerol-3-phosphate dehydrogenase, nad-dependent dehydrogenase, MESH:D013385, MESH:D000154, lyase, flavin adenine dinucleotide-dependent oxidoreductase, gtp-specific beta subunit, MESH:D006631, nad-retinol dehydrogenase, hydratase/isomerase, MESH:D006631, carnitine o]] \n", - " HALLMARK_G2M_CHECKPOINT-0 [[transcriptional regulation, epigenetic regulation, GO:0051169, GO:0043687, dna replication and repair, chromatin structure, GO:0140014, GO:0036211, GO:0006397]] \n", - " HALLMARK_G2M_CHECKPOINT-1 [[GO:0006913, GO:0016573, chromatin-associated processes, GO:0051726, transcriptional regulation, signal- and energy- dependent processes, nuclear phosphoproteins, GO:0006334, dna unwinding enzymes, protein heterodimers, GO:0000910, GO:0000398, MESH:D004264, GO:0035064, rna binding proteins, microtubule polymersization, nuclear localization, ubiquitin modification, mitosis regulation, centromere-interacting proteins.\\nmechanism: the genes in this list participate in a wide variety of mechanisms in the context of cellular development, including nucleocytoplasmic transport, histone acetylation, chromatin-associated processes, cell cycle regulation, and transcriptional regulation. these mechanisms are often interdependent and]] \n", - " HALLMARK_GLYCOLYSIS-0 [[MESH:D006023, transmembrane protein, cell-surface protein, enzymes plus coenzymes, GO:0000981, hormones, cytokines, and growth factors, ligand-receptor interaction, regulatory proteins, cargo-binding proteins, cell adhesion and morphogenesis, MESH:D000604, metabolism and transport within the cell, metabolism of macromolecules, cellular energy metabolism, cellular homeostasis and signaling, cell signaling and transcription, protein modification and degradation, GO:0007049, dna replication and repair, GO:0008219, enzyme-substrate interaction\\n\\nmechanism:\\nthis list of genes is primarily involved in cellular metabolism, ligand-receptor interactions, and cell signaling and transcription. there are a variety of molecules that are acted upon, such as glycoproteins, transmembrane proteins, hormones, enzymes, and transcription factors. in terms of metabolic functions, the gene list includes proteins for metabolic control, cargo-binding proteins, and enzymes involved in macromolecule metabolism and transport within the cell. additionally, many of these genes are involved in the regulation of cell cycle and homeostasis, as]] \n", - " HALLMARK_GLYCOLYSIS-1 [[enzyme function, GO:0005488, GO:0006810, GO:0008152, MESH:D007477, sugars, GO:0006351, cytoskeleton structure, GO:0007155]] \n", - " HALLMARK_HEDGEHOG_SIGNALING-0 [[GO:0006897, GO:0019838, receptor-mediated pathways;neuron survival;neuron differentiation;neuronal development;cell adhesion, transcription factor regulation, GO:0007165, extracellular protein interaction]] \n", - " HALLMARK_HEDGEHOG_SIGNALING-1 [[structure-specific proteins, GO:0006898, g-protein coupled receptors, GO:0007155, gene transcription, post-translational regulation]] \n", - " HALLMARK_HEME_METABOLISM-0 [[GO:0005515, GO:0006351, catalyzing reactions, gtpase activating protein activation, GO:0016575, carbohydrate & lipid metabolism, receptor binding & signaling, GO:0005574]] \n", - " HALLMARK_HEME_METABOLISM-1 [[GO:0003677, GO:0016573, GO:0005515, transcription regulation, leucine residue modification, GO:0003729, zinc metalloenzymes, atp-binding, protein serine/threonin, endoribonuclease, GO:0031545, 6-phosphogluconate dehydrase, GO:0003723, dynein heavy chain, MESH:C052997, chloride intracellular channel, GO:0003779, MESH:D051528, hexameric atpase, GO:0006814, rho gtpase, inositol polyphosphate, MESH:D011766, selenium-binding protein, clathrin assembly, c-myc, dual specificity protein kinase, MESH:D006021, gtpase-activating-protein, GO:0006914, ring between two helices]] \n", - " HALLMARK_HYPOXIA-0 [[cell signaling, metabolic regulation, GO:0043687]] \n", - " HALLMARK_HYPOXIA-1 [[cellular transport, GO:0008152, scaffolding, transcriptional regulation, GO:1901987, transcription activity, GO:0016310, cysteine-aspartic acid, GO:0016020, cell surface heparan sulfate, glycosyl hydrolase family, MESH:D000263, MESH:D000262, glyceraldehyde-3-phosphate, cytokine, glycosyltransferase, MESH:D000070778, sulfatase, sulfotransferase, serine/threonine kinase, MESH:D016232, MESH:D008668, MESH:D011973, basic helix-loop-helix]] \n", - " HALLMARK_IL2_STAT5_SIGNALING-0 [[GO:0005515, GO:0005102, transcription regulation, enzyme regulation, GO:0001816, GO:0007155, structure, membrane-associated]] \n", - " HALLMARK_IL2_STAT5_SIGNALING-1 [[an underlying biological mechanism of intracellular signaling and cell adhesion proteins working together to regulate gene expression and control cell functions was identified. enriched terms related to this mechanism include gtpases, MESH:D008565, intracellular signaling, calcium-dependent proteins, rna and dna binding, GO:0007155, GO:0000981, enzyme regulation, GO:0005515]] \n", - " HALLMARK_IL6_JAK_STAT3_SIGNALING-0 [[MESH:D018121, MESH:D018925, tgf-beta superfamily, transcriptional regulation, MESH:D017027, MESH:D011494]] \n", - " HALLMARK_IL6_JAK_STAT3_SIGNALING-1 [[the genes identified are part of the cytokine signaling system and its related pathways involved in immune response and regulation. more specifically, they belong to the type i cytokine receptor family, the phospholipase a2 family, the tumor necrosis factor receptor superfamily, the gp130 family of cytokine receptors, the toll-like receptor family, the interferon regulatory factor family, the bcl2 protein family, the reg gene family, the type ii membrane protein of the tnf family, the ring finger e3 ubiquitin ligase family, the protein tyrosine phosphatase family, the tgf-beta superfamily proteins, the hemopoietin receptor superfamily, the chemokine family, the integrin alpha chain family of proteins and the adapter protein family. there is a common function of these genes in the signaling of cell growth, UBERON:2000098, GO:0006915, migration, and differentiation, as well as the regulation of gene transcription, apoptosis and immune response. \\n\\nmechanism:\\nthe genes identified are part of a gene network that functions together to allow for cell signaling, GO:0040007, and differentiation, as well as inflammatory and immune responses. the various cytokine receptors, protein ty]] \n", - " HALLMARK_INFLAMMATORY_RESPONSE-0 [[MESH:D008565, g protein-coupled receptors, MESH:D018121, interferon-induced proteins, MESH:M0013343, MESH:D051116, MESH:D018925, MESH:D016023, MESH:D020782, MESH:D061566, tol-like receptors]] \n", - " HALLMARK_INFLAMMATORY_RESPONSE-1 [[GO:0005102, GO:0023052, GO:0055085, calcium binding, GO:0055085]] \n", - " HALLMARK_INTERFERON_ALPHA_RESPONSE-0 [[ligand binding, GO:0005102, GO:0003824, GO:0003677, GO:0003723, protein activation, GO:0030163, MESH:D054875]] \n", - " HALLMARK_INTERFERON_ALPHA_RESPONSE-1 [[these genes are connected by their participation in immune regulation and defense, either directly regulating the innate and acquired immune response, or acting as downstream inhibitors and activators of such responses. specific enriched terms include interferon regulation, transcriptional regulation, tumor suppression, MESH:D054875, chemokine receptor signaling, GO:0003723, GO:0009165, GO:0051607, GO:0048255, GO:0005525, GO:0008289, viral invasion, GO:0045087, GO:0030701, GO:0008134, and antigen presentation.\\n\\nmechanism: the commonalities between these genes suggest that they act at various levels of a complex innate and acquired immune response, controlling transcriptional regulation, protein modification and silencing, viral response, and antigen presentation. there are multiple pathways overlapping or influencing each gene's particular role in the overall immune defense, merging into a greater shared mechanism of host immunity]] \n", - " HALLMARK_INTERFERON_GAMMA_RESPONSE-0 [[the genes in the list encode proteins involved in a variety of processes including immunity, GO:0006954, GO:0006351, GO:0007165, and protein folding and assembly. these processes are typically carried out by two main classes of molecules; ubiquitin ligases and cytokines. the genes in this list are enriched for terms including \"signal transduction\", \"ubiquitin ligases\", \"immune modulation\", \"cytokine activity\", \"transcription regulation\", \"proteasome activity\", \"rna binding\", and \"metallothionein\".\\n\\nmechanism:\\nthe genes in this list encode proteins involved in a variety of processes, with an emphasis on immunity and inflammation. these processes are typically mediated by ubiquitin ligases, MESH:D016207, and other signal transduction proteins. ubiquitin ligases mark target proteins for ubiquitination and other modifications, while cytokines affect the activity of multiple cells. signal transduction proteins transmit signals across cell membranes, affecting the activity of cells. metallothioneins play a role in detoxification and protein folding and assembly, while proteasomes carry out protein degradation within the cell. transcripts are regulated by transcription factors, many genes contain rna binding domains]] \n", - " HALLMARK_INTERFERON_GAMMA_RESPONSE-1 [[transcriptional regulation, GO:0003824, binding ability, protein structure, cell signalling, MESH:D016207, growth factor signalling, MESH:D007109, GO:0000981, MESH:D054875, MESH:D006136, tripartite motif, GO:0070085, atpase, intracellular sensor, MESH:D015088, GO:0003723, calcium-binding, GO:0004930, MESH:M0476528, cysteine-aspartic acid protease, regulator of complement activation, protein tyrosine phosphatase, ubiquitin-specific protease, antiviral activity, inter]] \n", - " HALLMARK_KRAS_SIGNALING_DN-0 [[ion channels & transporters, receptor proteins, MESH:D002135, MESH:D004798, cell signaling, hormone regulation, GO:0008152]] \n", - " HALLMARK_KRAS_SIGNALING_DN-1 [[catalyzing reactions, GO:0055085, GO:0023052, dna-binding, GO:0006351, extracellular signaling, calcium-ion binding, immune system signaling, cell growth/maintenance, GO:0007154, hormone regulation, GO:0032502, GO:0008152]] \n", - " HALLMARK_KRAS_SIGNALING_UP-0 [[MESH:D008565, MESH:D010447, receptor proteins, MESH:D004268, MESH:D010770, GO:0000981, GO:0008217, MESH:M0022898, GO:0007165, transcriptional regulation, GO:0006811, GO:0006936, immunologic regulation, GO:0001816, GO:1901987, GO:0006915, GO:0007155, MESH:D063646]] \n", - " HALLMARK_KRAS_SIGNALING_UP-1 [[receptor functions]] \n", - " HALLMARK_MITOTIC_SPINDLE-0 [[cytoskeleton regulation, cellular communication, gtpase regulation, actin-binding, dna-dependent protein binding, microtubule-associated protein, filamentous cytoskeletal protein, 14-3-3 family protein, MESH:D020662]] \n", - " HALLMARK_MITOTIC_SPINDLE-1 [[gtpase activation, GO:0005525, structural maintenance, GO:0003677, GO:0005856, GO:0006915, GO:0007049]] \n", - " HALLMARK_MTORC1_SIGNALING-0 [[GO:0006412, GO:0008152, GO:0006457, MESH:D054875, GO:0006351, GO:0003677, damage control, GO:0032502, cellular pathway regulation, GO:0006915, GO:0007049, GO:0030163]] \n", - " HALLMARK_MTORC1_SIGNALING-1 [[atp production, amino acid homeostasis and metabolism, stress response, transcription and mrna regulation, chaperones and proteasome degradation pathways, GO:0006629]] \n", - " HALLMARK_MYC_TARGETS_V1-0 [[GO:0006351, GO:0006412, GO:0006413, GO:0003723, MESH:D054875, GO:0005840, GO:0006412, GO:0032508, MESH:D039102, GO:0003734, GO:0045292, heat shock proteins, MESH:D006655, MESH:D011073, MESH:D000604, GO:0043687]] \n", - " HALLMARK_MYC_TARGETS_V1-1 [[poly(a)-binding, GO:0003723, GO:0032508, GO:0006913, GO:0032183, GO:0000394, GO:0003676, GO:0006473, GO:0006413, GO:0036211, GO:0006457, MESH:D014176, GO:0006412, MESH:D018832, peptidyl-prolyl cis-trans isomerization, antioxidant function, heat shock protein, ubiquitin protein ligase, 14-3-3 family, dna-unwinding enzymes, dna polymerase, voltage-dependent anion]] \n", - " HALLMARK_MYC_TARGETS_V2-0 [[GO:0005515, transcriptional regulation, cell cycle progression, protein chaperoning, GO:0008283, nuclear localization, rna binding activity, pre-rrna processing, GO:0042254]] \n", - " HALLMARK_MYC_TARGETS_V2-1 [[rna binding activity, GO:0006364, protein homodimerization, GO:0008283, GO:0007165, GO:0042254, GO:0006457, GO:0034246]] \n", - " HALLMARK_MYOGENESIS-0 [[GO:0006936, calcium channel regulation, ion channel regulation, protein ubiquitination/degradation, actin-based motor proteins, GO:0007165, MESH:D004734]] \n", - " HALLMARK_MYOGENESIS-1 [[summary: the list of genes provided contains components of muscle formation, GO:0023052, and growth.\\nmechanism: the genes encode the components of signaling pathways and physical structures involved in the formation of muscle, including proteins that serve as receptors, binders, MESH:D004798, and structural components like spectrins, GO:0005202, laminin.\\nenriche terms: muscular development; musculosketetal function; signal transduction; protein phosphorylation degradation; cytoplasmic proteins; structural proteins; cytochrome oxidase]] \n", - " HALLMARK_NOTCH_SIGNALING-0 [[GO:0007219, GO:0016055, GO:0016567, transcriptional repressor, MESH:D015533, cell fate decisions, MESH:D044767, MESH:D011494]] \n", - " HALLMARK_NOTCH_SIGNALING-1 [[GO:0007219, GO:0016567, GO:0001709, transcriptional regulation, GO:0031146, gamma secretase complex, MESH:D011493, wnt family, basic helix-loop-helix family of transcription factors]] \n", - " HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 [[GO:0006006, GO:0006631, amino acid metabolism, GO:0005746, MESH:D007506, nadh-ubiquinone oxidoreductase, MESH:D009245, pyruvate dehydrogenase, GO:0022900, oxidative decarboxylation, nad+/nadh oxidoreductase, GO:0016467, MESH:D003576, MESH:D063988, matrix processing, shuttling mechanism.\\n\\nmechanism: the gene products involved in this metabolic pathways work to convert small molecules such as glucose and fatty acids into energy-containing molecules, such as atp and nadh, through a combination of redox reactions, electron transfer processes, and other catalytic systems. these processes involve the participation of numerous proteins, including membrane-associated proteins, enzymes, and enzyme complexes. these proteins form a complex network of interactions that enable the conversion of energy from one form to another, ultimately leading to atp production]] \n", - " HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 [[terminal enzyme, GO:0006754, GO:0005746, nad/nadh-dependent, cytochrome c oxidase (cox), GO:0006118]] \n", - " HALLMARK_P53_PATHWAY-0 [[GO:0005515, GO:0003677, transcriptional regulation, GO:0051726, cell signaling]] \n", - " HALLMARK_P53_PATHWAY-1 [[MESH:D011494, GO:0000981, GO:0007049, GO:0006281, GO:0003677, GO:0006412, tnf receptor superfamily, zinc finger, calcium-activated, cyclin dependent, iron-sulfur, GO:0015629, GO:0007165]] \n", - " HALLMARK_PANCREAS_BETA_CELLS-0 [[GO:0000981, homeobox domain, signal peptide cleavage, MESH:D011494, atp-binding, chromogranin/secretogranin, GO:0005180, protease, MESH:D011770, MESH:D005952, MESH:D000243, MESH:D006593, nuclear receptor, dna-binding, g-protein linked receptor, cysteine-rich protein, gtp-bound proteins, GO:0048500, bhlh transcription factor, doublecortin, calcium-binding protein\\n\\nsummary: genes identified in this list facilitate a variety of essential biological processes, particularly in terms of cell signaling and transcription regulation. among these processes are signal peptide cleavage, atp-binding, peptide hormone secretion and regulation, protease activity, glucose metabolism, adenosine deaminase, gtp-bound protein binding, and transcription factor actions. \\n\\nmechanism: these genes are involved in transcriptional regulation and signaling processes through binding of dna and g-protein linked receptors, homeobox domains, cysteine-rich proteins]] \n", - " HALLMARK_PANCREAS_BETA_CELLS-1 [[transcriptional regulation, MESH:M0496924, endocrine system regulation, GO:0006006, cell signalling, MESH:D020558, GO:0000981, GO:0005180, MONDO:0018815, MESH:D043484]] \n", - " HALLMARK_PEROXISOME-0 [[GO:0140359, oxidoreductase, dehydrogenase/reductase, hydratase/isomerase, enzymes responsible for fatty acid beta-oxidation, enzymes catalyzing the]] \n", - " HALLMARK_PEROXISOME-1 [[MESH:D018384, MONDO:0018815, atpases associated with diverse cellular activities, vitamin a family, GO:0004879, nad-dependent oxidoreductases, GO:0005783, MESH:D015238, cyclin-dependent protein kinase, hydratase/isomerase superfamily, GO:0005515, GO:0003677, GO:0050632, carnitine acyltransferase, MESH:D011960]] \n", - " HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 [[MESH:D011494, GO:0016791, GO:0005525, protein-protein interaction, GO:0030552, GO:0000981, peptidyl-prolyl cis/trans isomerase, cytoskeletal function, protein tyrosine phosphatase, protein phosphatase, GO:0140597, MESH:D020662, receptor interacting protein, transmembrane glycoprotein, MESH:D018123, MESH:D054387, inositol trisphosphate receptor, plexin domain, phosphoinositide 3-kinase, ubiquitin activation/conjugation, GO:0003925]] \n", - " HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 [[MESH:D011494, guanine nucleotide-binding protein, receptor-interacting protein, chaperone protein, protein tyrosine kinase, MESH:D020558, MESH:D000262, protein phosphatase, cytoplasmic face, GO:0006468, GO:0007165, GO:0036211]] \n", - " HALLMARK_PROTEIN_SECRETION-0 [[MESH:D008565, MESH:D020558, coatomer complex, GO:0016192, MESH:D001678, GO:0035091, GO:0065007, MESH:D002966, GO:0005906, GO:0005794, GO:0030136, MONDO:0018815, GO:0042393, GO:0005802, MESH:M0013340, GO:0006811, GO:0005159, GO:0005783, MESH:D057056, GO:0005483, GO:0005764, GO:0005794, multifunctional proteins]] \n", - " HALLMARK_PROTEIN_SECRETION-1 [[this list of genes codes for proteins of various functions, primarily related to organelle trafficking, membrane associations, and receptor binding activities. these proteins are involved in the regulation of intracellular vesicles, endoplasmic reticulum and golgi organization, protein sorting and secretion, cell surface receptor binding, cell-signaling and immunity, protein phosphorylation and kinase binding, and lipid protein modifications. the enriched terms found in the functions of these genes include vesicular transport, MESH:M0354322, organelle trafficking, GO:0007030, GO:0005102, GO:0006457, GO:0006468, snare recognition molecules, clathrin coated vesicles, endoplasmic reticulum-golgi transport, MESH:D025262, GO:0005906, and dystrophin-glycoprotein complex. \\n\\nmechanism: the enriched terms in the gene functions indicate that these proteins are involved in various pathways and process of intracellular cargo trafficking, where proteins, membranes and signaling molecules are sorted, distributed and regulated. the processes are involved with vesicular transport, protein co-translocation, GO:0030258, and protein phosphorylation, which coordinate the mobilization and distribution of proteins, MESH:D008055]] \n", - " HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 [[this list of genes were found to be involved in oxidoreductase activity, intracellular binding and catalytic activity, cellular response regulation, dna and transcription regulation, membrane function, mitochondrial function and antioxidant activity. the enriched terms include oxidoreductase activity, intracellular binding, GO:0003824, cell growth regulation, transcription regulation, membrane function, mitochondrial function, GO:0016209, GO:0020037, GO:0005507, GO:0003677, GO:0043565, tyrosine-specific protein kinase activity, f-actin binding. the underlying biological mechanism is probable related to redox homeostasis, the oxygen metabolism pathway, the cell cycle dna repair pathways, the regulation of transcription membrane function]] \n", - " HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 [[redox processes, MESH:D018384, GO:0006281, GO:0008152, cell growth regulation, inflammation control, cellular defense, MESH:D006419, MESH:D005980, superoxide dism]] \n", - " HALLMARK_SPERMATOGENESIS-0 [[cell cycle regulatory proteins and kinases, dna binding proteins and chaperones, nucleotide and polypeptide binding proteins, GO:0016791, proteins involved in transcription, gene transcription, GO:0051276, apoptosis regulation, GO:0006281, protein folding and transport, cell signaling and growth regulation, MESH:D004734, cytoskeletal organization, vesicular trafficking\\n\\nmechanism: the underlying biological mechanism is likely involved in multiple steps in cell division and the regulation of gene expression, and in the maintenance of cell homeostasis]] \n", - " HALLMARK_SPERMATOGENESIS-1 [[this list of genes is associated with a range of diverse functions, including intracellular and intercellular trafficking, adhesion, enzyme regulation, transcriptional regulation, ion channel and receptor regulation, and processes related to stress, GO:0007568, and metabolism. common enriched terms include protein kinase and phosphatase, GO:0140359, g-protein coupled receptors, receptors, transcriptional regulation, GO:0016569, GO:0051726, heat shock, GO:0005515, ubiquitin-protein ligase and ubiquitin protease, zinc metalloproteases, and peptide n-acetyltransferase. the underlying biological mechanism or pathway associated with these genes may involve signal transduction as mediated by enzyme activity, MESH:D007473, receptors, and other proteins, as well as cell-to-cell adhesion and trafficking processes involved in membrane dynamics.\\n\\nsummary: list of genes associated with diverse functions including intracellular and intercellluar trafficking, adhesion, regulation of enzymes, GO:0006351, ion channels and receptors, and processes related to stress, GO:0007568, and metabolism.\\nmechanism: signal transduction as mediated by enzyme activity, MESH:D007473, receptors, and other proteins, as well as cell-to]] \n", - " HALLMARK_TGF_BETA_SIGNALING-0 [[the human gene summaries represent a variety of cell signaling, cell growth and differentiation, transcription regulation, adhesion and migration, and apoptosis-related functions. several genes in the list (acvr1, GO:0005680, arid4b, bmpr1a, bmpr2, cdh1, ifngr2, junb, lefty2, map3k7, ncor2, ppm1a, pp1ca, rahb, smad1, smad3, smad6, smurf1, smurf2, tgfb1, tgfbr1, MESH:D016212, cdk9, cdkn1c, ctnnb1, eng, fnta, MESH:D045683, hipk2, id1-3, klf10, ltbp2, pmepa1, ppp1r15a, serpine1, ski, skil, slc20a]] \n", - " HALLMARK_TGF_BETA_SIGNALING-1 [[GO:0007165, transcription regulation, cell-to-cell communication, MESH:D018398, serine/threonine protein kinase, disulfide-linked homotrimeric proteins, protein phosphatase, transmembrane proteins, smurf protein, cystein-rich motif, GO:0006457]] \n", - " HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 [[transcriptional regulation, GO:0005125, GO:0008283, GO:0006629]] \n", - " HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 [[GO:0006954, GO:0007165, transcriptional regulation, GO:1901987, cytokine, MESH:D011506, receptor, GO:0000981, enzyme, growth factor, MESH:D019204, chemokine, MESH:D008074, pentraxin protein, GO:0016791, MESH:D010770, stress response]] \n", - " HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 [[GO:0003723, transcription regulation, GO:0006457, protein targeting and covalent modifications, endoplasmic reticulum function, GO:0006413]] \n", - " HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 [[GO:0006412, endoplasmic reticulum stress response, GO:0003723, protein expression, conformation folding]] \n", - " HALLMARK_UV_RESPONSE_DN-0 [[GO:0007155, GO:0005207, nuclear phosphoprotein, phosphoprotein, cytoplasmic receptor, MESH:D020558, GO:0016791, receptor tyrosine kinase, GO:0006351, camp, ion transport atpase, transmembrane protein]] \n", - " HALLMARK_UV_RESPONSE_DN-1 [[GO:0000981, receptor, GO:0005488, growth factor, phosphoprotein, MESH:D010770, cytoplasmic surface, nuclear histone/protein methyltransferase, MESH:D020558, wd repeat protein, protein tyrosine phosphatase, serine/threonine kinase, caveolae plasma membrane, g-protein coupled receptor, MESH:D000071377, ab hydrolase superfamily, microtubule-associated protein, protein-tyros]] \n", - " HALLMARK_UV_RESPONSE_UP-0 [[GO:0005515, MESH:D002384, transcriptional regulation, cell signaling, metabolic reactions]] \n", - " HALLMARK_UV_RESPONSE_UP-1 [[regulatory proteins, GO:0000981, membrane and transport proteins, structural proteins, MESH:D004798, biosynthesis of heme, cellular signaling, transcription control, GO:0008152, GO:0006955]] \n", - " HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 [[cell-cell interactions, MESH:D047108, transcriptional regulation, GO:0006281, wnt signaling, notch signaling, hedgehog signaling, MESH:D044783]] \n", - " HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 [[transcriptional regulation, GO:0001709, signaling pathway activation, MESH:D060449, notch pathway, hedgehog pathway, protein interactions, cell growth regulation, GO:0004672, GO:0030163, cell-cell interaction, cell-matrix interaction, protein ligase binding activity, GO:0004842, membrane-bound protease activity, transcriptional repressor, GO:0006338, notch receptor cleavage, intracellular domain formation, ectodomain shedding, MESH:D015533, nuclear receptor co-repressor]] \n", - " T cell proliferation-0 [[the provided list of genes and associated descriptions demonstrates variation in generic cellular processes like protein degradation, protein and nucleic acid binding and kinase activity, as well as specific pathways involving cytokine and chemokine signaling, transcriptional regulation and regulation of immune cell activity. across these processes, the significant terms enriched across the genes include: protein tyrosine kinase activity; protein/nucleic acid/oligomeric binding activities; protein ubiquitination; transcriptional and immune cell activation and proliferation; intracellular receptor signaling and nf-kappab pathways; and cell cycle regulation.\\n\\nmechanism:\\nthe identified genes likely affect several common pathways, including signaling pathways that mediate cell division, motility, adhesion, chemokine- and cytokine-mediated responses, and immune cell function. in particular, the proteins encoded by these genes likely play roles in the regulation of post-translational modifications, such as protein ubiquitination, and the regulation of gene transcription, likely in response to extracellular cues. additionally, the identified proteins may mediate the recruitment of the cbm signalosome, leading to the activation of nf-kappab pathways. finally, cell cycle-related processes]] \n", - " T cell proliferation-1 [[GO:0007165, GO:0008037, GO:0004721, GO:0061630, lipid enzyme, MESH:D011505, cgmp kinases, GO:0000981, protein scaffold, cytokine, adaptor protein, GO:0051301, adhesion, differentiation, GO:0006950, negatively regulated, MESH:D021381, cell fate and patterning, MESH:D002470, ligand-gated ion channel, GO:0051092, GO:0006569, er stress-induced protection, transmembrane glycoprotein, MESH:D050503, wnt gene family, GO:0016020]] \n", - " Yamanaka-TFs-0 [[genes in this list are transcription factors involved in the development of various organ systems, such as the skin and cns, as well as responding to dna damage, GO:0006915, and cellular transformation. the enriched terms are transcription factor activity; gene expression regulation; cell cycle regulation; dna damage response; pluripotency; and embryo development.\\n\\nmechanism: the transcription factors in this list interact with dna, regulate gene expression, and influence cell cycle progression, GO:0006915, and cellular transformation. combined, these genes are thought to play a role in creating and maintaining cellular and tissue identity, as well as responding to environmental changes. this could be part of a larger mechanism that governs organism development and homeostasis]] \n", - " Yamanaka-TFs-1 [[GO:0000981, zinc finger proteins, GO:0007049, MESH:D004249, MESH:D016147, MESH:D047108, stem cell maintenance, translocation, homeodomain]] \n", - " amigo-example-0 [[GO:0007155, GO:0016477, cell signalling, GO:0008152, GO:0006915, GO:0009653, GO:0007599, MESH:D007109, extracellular matrix maintenance]] \n", - " amigo-example-1 [[GO:0048729, matrix metalloproteinase inhibitor, regulated cell adhesion, cytoplasmic protein tyrosine kinase, GO:0005161, cytokine-induced gene expression, GO:0005583, cell signaling pathway, MESH:D015533, antimicrobial activity, GO:0031012, GO:0016477, GO:0008283]] \n", - " bicluster_RNAseqDB_0-0 [[GO:0007165, transcription regulation, ion regulation, GO:0005515, cytoskeletal adaptor, MESH:D006023]] \n", - " bicluster_RNAseqDB_0-1 [[GO:0000988, metal ion binding activity, dna binding activity, chromatin binding activity, rna binding activity, protein domain-specific binding activity, histone binding activity, methylated histone binding activity]] \n", - " bicluster_RNAseqDB_1002-0 [[GO:0051015, GO:0048870, GO:0004722, myosin-binding proteins, MESH:D002154, GO:0045010, GO:0005523, calcium sensitivity, MESH:D044767, GO:0003735, GO:0004930, GO:0042923, GO:0050262, GO:0061769, GO:0019674, GO:0007015, GO:0006936, GO:0055008, GO:0030838]] \n", - " bicluster_RNAseqDB_1002-1 [[actin filament binding activity, muscle alpha-actinin binding activity, actin monomer binding activity, tropomyosin binding activity, GO:0006936, GO:0045214, GO:0071691, GO:0045010, GO:0030838, muscle excitation-contraction coupling, calcium release complex, muscle associated proteins, GO:0030036, GO:0007507]] \n", - " endocytosis-0 [[GO:0030030, MESH:D021381, MESH:D011494, GO:0048870, membrane reorganization, GO:0006897, cytoskeletal reorganization, mitogen-activated protein kinase, lysosomal degradation, GO:0051168]] \n", - " endocytosis-1 [[GO:0006897, lysosomal degradation, GO:0015031, GO:0006898, membrane processes, gtpase regulation, MESH:D044767, death domain-fold]] \n", - " glycolysis-gocam-0 [[GO:0006006, GO:0006096, GO:0016310, GO:0006000, GO:0006094, GO:0004332, glycogen storage, GO:0016853, GO:0004743, GO:0004396]] \n", - " glycolysis-gocam-1 [[GO:0006096, GO:0008152, regulation of energy conversion, MESH:D024510, tumor progression, GO:0006094, GO:0001525, neurotrophic factor, MESH:M0025255]] \n", - " go-postsynapse-calcium-transmembrane-0 [[calcium homeostasis, calcium-channel activity, MESH:D007473, g-protein coupled receptor, ligand-gated ion channel]] \n", - " go-postsynapse-calcium-transmembrane-1 [[calcium homeostasis, calcium influx, GO:0007268, neuronal development, MESH:D058446, purinergic receptor, GO:0004972, MESH:C413185, g-protein coupled receptor]] \n", - " go-reg-autophagy-pkra-0 [[GO:0016049, GO:0006915, GO:0007165, serine/threonine kinase activator activity, GO:0035004, GO:0005085]] \n", - " go-reg-autophagy-pkra-1 [[GO:0006281, apoptosis regulation, GO:0007165, GO:0016049, nutrient and insulin levels, macromolecule metabolic process regulation, GO:1901987, GO:0006338]] \n", - " hydrolase activity, hydrolyzing O-glycosyl compounds-0 [[glycosyl hydrolase, glycosyl bond hydrolysis, oligosaccharide processing, MESH:D006023, MESH:D011134, n-linked oligosaccharide, o-linked n-acetylglucosamine, β-1,4-glucosidase, β-glucosidase, β-hexosaminidase]] \n", - " hydrolase activity, hydrolyzing O-glycosyl compounds-1 [[glycosyl hydrolase, glycohydrolytic enzyme, MESH:D006821, MESH:D005644, lysosomal hydrolase, n-linked oligosaccharide processing, MESH:D001616, MESH:D001619, MESH:D001617, MESH:D009113, alpha-1,4-glucosidase, MESH:D043323, MESH:D000520, MESH:D055572, mannosidase, MESH:M0012138, alpha-l-iduronic acid, alpha]] \n", - " ig-receptor-binding-2022-0 [[antigen binding activity, immunoglobulin receptor binding activity, activated/inactivated immune response, GO:0042803, peptidoglycan binding activity]] \n", - " ig-receptor-binding-2022-1 [[antigen binding activity, immunoglobulin receptor binding activity, GO:0002253, GO:0042803, peptidoglycan binding activity, phosphatidylcholine binding activity, transduction of signals, allelic exclusion, myristylation, palmitylation, protein tyrosine kinases, sh2 and sh3 domains, MESH:D008285, MESH:D010455, antigen presenting cells, preb cells, src family of protein tyrosine kinases (ptks), c-type lectin domain]] \n", - " meiosis I-0 [[the gene summaries indicate that most of the genes are involved in processes related to dna binding, GO:0006281, GO:0006310, and meiotic processes. the enriched terms include \"dna binding\", \"dna repair\", \"dna recombination\", \"meiosis\", \"double-stranded dna binding\", \"single-stranded dna binding\", GO:0003682, GO:0004519, dead-like helicase activity, and bcl-2 homology domain activity.\\n\\nmechanism: the mechanism underlying the enrichment of these gene functions appears to be related to the repair and maintenance of chromosomal integrity as well as the regulation of cell division, differentiation, and development. through their combined activities, the genes appear to be involved in the maintenance of genome stability and the efficient transmission of genetic information from one generation to the next]] \n", - " meiosis I-1 [[GO:0006281, meiotic recombination, GO:0006302, GO:0035825, chromosome synapsis, GO:0007059, MESH:D023902, holliday junction resolution, dna strand-exchange, reciprocal recombination, GO:0007130, GO:2000816, positive regulation of response to dna damage, GO:0006611, GO:0031297, GO:0000712, GO:0060629, GO:0003677, GO:0003697, single-str]] \n", - " molecular sequestering-0 [[GO:0005515, GO:0046907, GO:0043161, GO:0051726, regulation of cell growth and survival, cholesterol and lipids metabolism, nf-κb inhibiting proteins, GO:0009792, GO:0007283, GO:0045087, cytokines and growth factors, antioxidant enzymes, GO:0030097]] \n", - " molecular sequestering-1 [[GO:0006897, iron storage, GO:0008610, GO:0006915, GO:0008283, GO:0030154, defense from bacterial infection, transcription regulation, translation regulation]] \n", - " mtorc1-0 [[GO:0006412, GO:0008152, GO:0006457, MESH:D054875, GO:0006351, GO:0003677, damage control, GO:0032502, cellular pathway regulation, GO:0006915, GO:0007049, GO:0030163]] \n", - " mtorc1-1 [[GO:0008152, GO:0023036, GO:0007165, transcriptional regulation, epigenetic regulation, GO:0044183, proteolytic activity, GO:0051726]] \n", - " peroxisome-0 [[peroxisome biogenesis, peroxisomal protein import, tripeptide peroxis]] \n", - " peroxisome-1 [[aaa atpase family, MONDO:0019234, peroxisomal protein import, peroxisomal matrix protein import, heteromeric complex, peroxisome targeting signal 2]] \n", - " progeria-0 [[the genes in this list are associated with post-translational proteolytic cleavage, intermolecular integration, dna repair and dna helicase activity, and nuclear stability and chromatin structure. the underlying mechanism is likely related to protein modification and regulation of cellular components involved in dna metabolism and gene expression. the enriched terms include protein modification, proteolytic cleavage, GO:0003678, intermolecular integration, GO:0006281, chromatin structure, nuclear stability]] \n", - " progeria-1 [[this set of genes is involved in the maintenance of genome stability and chromosome integrity, likely in terms of forming the nuclear lamina and promoting nuclear reassembly. the enriched terms are genome stability, chromosome integrity, GO:0005652, nuclear reassembly.\\n\\nmechanism: the set of genes are likely working together to form and maintain a matrix of proteins which form the nuclear lamina next to the inner nuclear membrane, thus providing stability to the genome and the chromosomes by helping to organize the dna within the nucleus. this is achieved through binding with both dna and inner nuclear membrane proteins and recruiting chromatin to the nuclear periphery to achieve nuclear reassembly]] \n", - " regulation of presynaptic membrane potential-0 [[MESH:D007473, voltage-gated ion channel, MESH:D015221, ligand-gated ion channel, MESH:D018079, MESH:D017470, MESH:D015222]] \n", - " regulation of presynaptic membrane potential-1 [[GO:0007268, MESH:D009482, inhibitory, excitatory, MESH:D017981, MESH:D015221, MESH:D018079, MESH:D017470, MESH:D007649, GO:0009451, voltage-gated, MESH:D007473, MESH:D058446, MESH:D019204]] \n", - " sensory ataxia-0 [[GO:0000981, GO:0009056, moonlighting proteins, GO:0002377, adapter molecules, heme transporter, myelin upkeep, GO:0005643, mitochondrial dna polymerase, ubiquitin ligase, aminoacyl-trna synthetase.\\n\\nmechanism: these genes work together in a joint mechanism to regulate biological processes like cell replication, neuronal development, protein folding, and enzymatic activity. in particular, their collective involvement in the coordination of transcriptional activity, ion transport, and dna-binding suggests a complex integrated process by which these genes serve to facilitate normal cell functions]] \n", - " sensory ataxia-1 [[GO:0000981, dna helicase, nerve myelin maintenance, mechanically-activated cations channels, nerve motor neuron survival, MESH:D054875]] \n", - " term-GO:0007212-0 [[the summaries of the provided gene functions describe proteins linked to the activity and regulation of g-protein coupled receptor signaling pathways, including dopamine, MESH:D016232, and serotonin receptors, as well as proteins involved in calcium ion regulation, GO:0003677, and apoptosis. statistically over-represented terms include: g-protein coupled signaling; calcium ion regulation; transmembrane signaling; dna binding; and apoptotic process. \\n\\nmechanism:\\nthe common function of these genes is likely to be linked to the regulation of g-protein coupled signaling pathways, which regulate a variety of cellular processes, including cellular signaling and growth, neuronal development, apoptosis. calcium ion regulation transmembrane signaling are also likely to be important for the functioning of these genes. dna binding proteins proteins that enable clathrin light chain binding activity may be involved in the transcriptional regulation of these signals]] \n", - " term-GO:0007212-1 [[this gene set was comprised of dopamine and g-protein coupled receptors that participate in cellular signaling pathways and influence cellular functions such as metabolism and behavior. the genes are involved in a wide range of pathways such as signal transduction, transcriptional regulation, memory and behavior, GO:0007612, neural development and synaptic plasticity. the enriched terms in this list include: signal transduction, g protein-coupled receptor, camp, MESH:D000262, MESH:D054799, MESH:D017868, calcium ions, transcriptional regulation, GO:0000981, MESH:D011954, wnt and pi3k signaling pathways, neuronal growth and development, GO:0010467, and synaptic receptors.\\n\\nmechanism: this gene set is involved in many pathways such as signal transduction, transcriptional regulation, and synaptic organization. signal transduction occurs through g-protein coupled receptors and camp, which in turn regulate downstream effectors including adenylyl cyclase, MESH:D017868, and calcium ions. furthermore, transcriptional regulation occurs through various receptor signaling pathways, such as those related to the wnt and pi3k pathways, while dopamine receptors regulate neuronal growth and development, GO:0010467, and behavior. finally, synaptic receptors enable]] \n", - " tf-downreg-colorectal-0 [[dna-binding, chromatin-binding, transcriptional regulation, e-box dna consensus sequence binding, dna damage response regulation, dna damage response maintenance, phosphoprotein shutting, MESH:D016335, interaction with cellular retinol-binding protein, hormone-dependent transcription, receptor-dependent transcription, nuclear hormone receptor-dependent transcription, transcriptional coactivator complex recruitment, GO:0000785]] \n", - " tf-downreg-colorectal-1 [[transcriptional regulation, dna-binding, chromatin binding activity, histone binding activity, GO:0000988]] \n", - " no_synopsis EDS-0 [[GO:0001501, GO:0032964, cell-matrix interactions, extracellular matrix remodeling, cell signaling]] \n", - " EDS-1 [[collagen production, GO:0061448, matrix remodeling, zinc finger protein regulation]] \n", - " FA-0 [[GO:0006281, homologous recomination, MESH:M0006667, GO:0004518]] \n", - " FA-1 [[MONDO:0100339, dna/rna damage response, dna/rna metabolism, GO:0051726, genome stability, MONDO:0019391]] \n", - " HALLMARK_ADIPOGENESIS-0 [[metabolic regulation, GO:0050658, GO:0006412, cell membrane transport, transcription regulation, GO:0006915, GO:0006457, GO:0019432, GO:0003676, GO:0006633, GO:0006096, GO:0045454]] \n", - " HALLMARK_ADIPOGENESIS-1 [[GO:0008152, MESH:D004734, GO:0007165, GO:0006119, transcriptional regulation, GO:0006468, GO:0051726, GO:0006629, GO:0006457, protein assembly, mitochondrial function, GO:0006915, GO:0006839, GO:0055085, GO:0007010, GO:0006094, GO:0006096, GO:0042632]] \n", - " HALLMARK_ALLOGRAFT_REJECTION-0 [[immune signalling, GO:0051726, cellular differentiation, transcriptional regulation]] \n", - " HALLMARK_ALLOGRAFT_REJECTION-1 [[genes in this list are representative of various pathways involved in cell movement, GO:0019882, GO:0006954, immune regulation, and cell signaling events including jak-stat and mapk- pi3k pathways. enriched terms include “immune system processes”; “immune recognition pathways”; “cytokine-mediated signaling pathways”; “inflammatory response”; “cellular immune activation”; “intestinal immune network for iga production”; “cytokine secretion”; “tcr signaling pathway”; “cd4 t cell activation”; “t lymphocyte differentiation”; “innate immune response”; and “cytokine-cytokine receptor interaction”.\\n\\nmechanism: the genes are involved in pathways that affect cell movement, GO:0019882, GO:0006954, immune regulation, and cell signaling. these pathways control the activation, response, differentiation, and survival of t cells by regulating cytokine expression, activation of specific receptors, production of antibodies, regulation of transcription factors and their binding to promoters, other immune system processes]] \n", - " HALLMARK_ANDROGEN_RESPONSE-0 [[genes in this list are mainly involved in regulation of skeletal tissue formation and development, signal cascade activation, protein folding, cellular metabolism and movement, cell cycle regulation, and transcriptional regulation. the underlying biological mechanism may be related to the complex network of interactions among these genes in controlling the basic functions of a cell. the enriched terms are: bone morphogenesis, GO:0001501, signal cascade activation, GO:0006457, GO:0044237, cellular movement, GO:0051726, transcriptional regulation, chromatin and dna modification]] \n", - " HALLMARK_ANDROGEN_RESPONSE-1 [[gene transcription and regulation, protein translation and metabolism, cytoskeletal organization, GO:0006629]] \n", - " HALLMARK_ANGIOGENESIS-0 [[GO:0030198, vascularization, endothelial cell aggregation, GO:0007155, cell surface interactions]] \n", - " HALLMARK_ANGIOGENESIS-1 [[cytokine receptor signaling, growth factor signal transduction, transmembrane and extracellular matrix proteins, development of muscle, bone, and neuronal networks]] \n", - " HALLMARK_APICAL_JUNCTION-0 [[GO:0060348, joint development, MESH:D024510, GO:0061448, GO:0007155, adhesion receptor complex formation, GO:0007165, receptor-mediated signaling cascades]] \n", - " HALLMARK_APICAL_JUNCTION-1 [[GO:0007155, GO:0016477, migration and interaction, cytoskeletal organization, actin cytoskeletal regulation, GO:0007165, regulation of actin cytoskeletal organization]] \n", - " HALLMARK_APICAL_SURFACE-0 [[cell regulation, GO:0007165, GO:0007155, GO:0006457, GO:0030198]] \n", - " HALLMARK_APICAL_SURFACE-1 [[cell adhesion and migration, cell signaling, GO:0030154, protein kinase and phosphatase activities, transcription and dna metabolism, MESH:D056747, glycosylation and carbohydrate metabolism, cell growth and proliferation]] \n", - " HALLMARK_APOPTOSIS-0 [[GO:0006915, transcription regulation, cell cycle progression, GO:0006954, GO:0006260, GO:0006281, oxidative stress response, immune system activation]] \n", - " HALLMARK_APOPTOSIS-1 [[cell death regulation, GO:0006954, immune reaction, growth and morphogenesis, UBERON:2000098, GO:0006915, GO:0006281, GO:0030217, GO:0001816, GO:0051726, fast axonal transport, extracellular proteolysis, GO:0007155, GO:0042060, MESH:D009362, MESH:D063646, GO:0016477, regulation of nf-kb pathway]] \n", - " HALLMARK_BILE_ACID_METABOLISM-0 [[GO:0006629, GO:0006869, organ development, cell signaling, GO:0006412, transport processes]] \n", - " HALLMARK_BILE_ACID_METABOLISM-1 [[GO:0006629, GO:0006536, serine metabolism, transcription factor regulation, oxidative stress response]] \n", - " HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 [[GO:0006629, GO:0008203, cell signaling and regulation, GO:0032502, GO:0007155, GO:0006915, GO:0006351]] \n", - " HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 [[GO:0006629, cholesterol control, GO:0009062, GO:0006699, hmgcr regulation, pmvk regulation, fads2 regulation, srebf2 regulation, s100a11 regulation, mvk regulation]] \n", - " HALLMARK_COAGULATION-0 [[extracellular matrix remodeling; angiogenesis and vascular development; immune response and platelet activation; collagen and fibronectin metabolism and regulation; endocytosis and signal transduction; \\nmechanism: the genes in this list work together to control and regulate multiple relevant processes, such as extracellular matrix remodeling, which is the process of breaking down and reorganizing the components of the extracellular matrix in order to facilitate tissue development and repair, angiogenesis and vascular development, which regulate the formation of new blood vessels and ensure proper blood flow throughout the body, immune response and platelet activation, which are necessary to protect the body from foreign agents and to form healthy blood clots, collagen and fibronectin metabolism and regulation, which are important for tissue integrity and structure, and endocytosis and signal transduction, which are necessary for cellular communication and regulation]] \n", - " HALLMARK_COAGULATION-1 [[GO:0007155, proteolysis regulation, extracellular protein-cell interaction, migration, GO:0050817, GO:0006956]] \n", - " HALLMARK_COMPLEMENT-0 [[development of tissue and organs, GO:0007165, cell surface receptor binding, GO:0050896, UBERON:0002405, GO:0006955, GO:0005125]] \n", - " HALLMARK_COMPLEMENT-1 [[cellular signalling, GO:0006954, cell stress response, cell-cell interaction, GO:0007165, GO:0045087, cytoskeletal remodelling, GO:0006457, GO:0050900, GO:0004672, GO:0007155, MESH:D005786, GO:0006260, protein activation, GO:0019763, GO:0002377, GO:0016791]] \n", - " HALLMARK_DNA_REPAIR-0 [[GO:0032502, GO:0006260, MESH:D047108, GO:0030154, transcription regulation, GO:0006335, nuclear mrna surveillance pathway, GO:0016070, GO:0006281, GO:0140014, rna-dependent dna replication]] \n", - " HALLMARK_DNA_REPAIR-1 [[nucleic acid metabolism, GO:0006351, post-transcriptional modifications, GO:0006338, GO:0000398, GO:0006281, rna polymerization, GO:0006397, GO:0051028, GO:0006413]] \n", - " HALLMARK_E2F_TARGETS-0 [[transcriptional regulation, GO:0016569, mitotic division, GO:0051726, MESH:D004268, MESH:D006657, GO:0000981, MESH:D004259, MESH:D012321, chromatin remodeling proteins, ubiquitin ligases, nucleosome assembly proteins, helicases, motor proteins, GO:0000075]] \n", - " HALLMARK_E2F_TARGETS-1 [[GO:0006260, GO:0006281, GO:0016569, transcription regulation, translation regulation, protein-protein networks, GO:0051225, kinesin motor proteins, dynein motor proteins]] \n", - " HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 [[GO:0031012, GO:0007155, GO:0048870, cell-matrix interaction, growth factor signaling, cytokine signaling, matrix remodeling]] \n", - " HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 [[GO:0048705, cell-cell adhesion and motility, extracellular matrix production and remodeling, connective tissue development and differentiation, collagen production and turnover, cytokine and chemokine signaling]] \n", - " HALLMARK_ESTROGEN_RESPONSE_EARLY-0 [[GO:0006260, GO:0006351, GO:0010467, GO:0016049, differentiation, GO:0016485, trafficking, GO:0060349, cancer-related pathways, GO:0098609, matrix remodeling, intracellular signaling, external signals, internal signals]] \n", - " HALLMARK_ESTROGEN_RESPONSE_EARLY-1 [[transcriptional regulation, GO:0007165, protein-protein interactions, GO:0055085, GO:0008610]] \n", - " HALLMARK_ESTROGEN_RESPONSE_LATE-0 [[GO:0030198, GO:0007155, GO:0016477, GO:0048870, growth factor signaling, cytoskeletal organization]] \n", - " HALLMARK_ESTROGEN_RESPONSE_LATE-1 [[GO:0030198, GO:0000988, receptor signaling pathway, GO:0007269, GO:0019725, GO:0006508, immunological responses, GO:0016049, GO:0003677, GO:0006629]] \n", - " HALLMARK_FATTY_ACID_METABOLISM-0 [[metabolic pathways; cellular functions; energy metabolism; lipid metabolism; amino acid metabolism; dna damage repair; cell signaling.\\nmechanism: the genes listed here are likely involved in the various metabolic pathways and cellular functions, perhaps through the production of enzymes, MESH:D011506, or other molecules that contribute to energy metabolism, GO:0006629, amino acid metabolism, dna damage repair, cell signaling]] \n", - " HALLMARK_FATTY_ACID_METABOLISM-1 [[GO:0006629, cell cytoskeleton, GO:0008610, GO:0016042, lipid transportation, GO:0034440, cell membrane biogenesis, GO:0048870, cell traffic, cell signaling]] \n", - " HALLMARK_G2M_CHECKPOINT-0 [[GO:0006260, GO:0006351, GO:0051726, protein binding/interaction, chromatin modifiers/modification, GO:0006281, GO:0000988, GO:0006397, GO:0006915, ubiquitination and proteasomal degradation]] \n", - " HALLMARK_G2M_CHECKPOINT-1 [[genes involved in the list are mainly associated with dna replication, cell division and related functions. enriched terms include \"cell cycle\", \"dna replication\", \"chromatin modification\", \"transcription regulation\", \"cell division\", \"dna repair\", \"transcriptional regulation\", \"chromosome segregation\".\\n\\nmechanism: these genes likely play a role in the coordination of the many steps and activities involved in dna replication, GO:0051301, and related cellular processes. the cell cycle is an area of particular interest due to its critical role in the growth and division of cells. dna replication, modification, repair occur during cell division in order to produce maintain copies of genetic information. chromatin modifications occur during cell division in order to package regulate genomic information. transcriptional regulation involves the control of gene expression the production of proteins other materials essential for the maintenance of cellular functions. chromosome segregation cell division serve to divide replicated genetic material into daughter cells]] \n", - " HALLMARK_GLYCOLYSIS-0 [[the genes in this list are involved in a variety of cellular processes including protein translation, GO:0070085, regulation of ion channels, gene transcription and dna replication. the enriched terms identified are: translation; glycosylation; ion channels; gene transcription; and dna replication.\\n\\nmechanism: the common underlying mechanisms of the genes in this list likely involve cellular processes such as protein translation, GO:0070085, regulation of ion channels, gene transcription and dna replication. these processes are essential for the regulation of cell functions and the maintenance of a stable organism]] \n", - " HALLMARK_GLYCOLYSIS-1 [[structural proteins, GO:0006096, GO:0006098, GO:0006099, GO:0007155, GO:0030166, extracellular matrix formation, cytoskeletal assembly]] \n", - " HALLMARK_HEDGEHOG_SIGNALING-0 [[the provided genes are involved in a variety of different processes ranging from morphogenesis, development and growth of the digits/limbs, neuronal migration and regulation of cell proliferation. the underlying biological mechanism might be related to the modulation of cell migration, development of neural connections, formation of complex structures, maintenance of body plan and tissue development. enriched terms are: morphogenesis, digit/limb development, GO:0001764, GO:0042127, modulation of cell migration, development of neural connections, formation of complex structures, maintenance of body plan, GO:0009888]] \n", - " HALLMARK_HEDGEHOG_SIGNALING-1 [[neuron formation, GO:0007155, migration, GO:0007165, GO:0048729, GO:0007399]] \n", - " HALLMARK_HEME_METABOLISM-0 [[GO:0044237, energy production and transport, cytoskeleton modification, cytoskeleton remodelling, GO:0007155, MESH:D004735, MESH:M0496924, cellular transport, cellular reorganization]] \n", - " HALLMARK_HEME_METABOLISM-1 [[MESH:D047108, GO:0001501, GO:0048513, GO:0009653, GO:0040007, GO:0002376, GO:0048870, GO:0003707, receptor signaling pathway, GO:0006810, GO:0006897, GO:0019725]] \n", - " HALLMARK_HYPOXIA-0 [[GO:0007049, remodeling proteins, stress response proteins, calcium signaling proteins, hypoxia-inducible factor proteins, GO:0000981, chromatin-associated proteins, MESH:D010770]] \n", - " HALLMARK_HYPOXIA-1 [[GO:0032502, cell structure and movement, cell cycle and division, GO:0007165, GO:0006810, energy production]] \n", - " HALLMARK_IL2_STAT5_SIGNALING-0 [[immunological function, GO:0030036, MESH:D011956, pro-inflammatory regulation]] \n", - " HALLMARK_IL2_STAT5_SIGNALING-1 [[MESH:D007109, GO:0006954, GO:0016049, differentiation, GO:0032502, GO:0007165]] \n", - " HALLMARK_IL6_JAK_STAT3_SIGNALING-0 [[cell signaling, GO:0001816, cytokine regulation, MESH:D005786, transcription regulation, GO:0007155]] \n", - " HALLMARK_IL6_JAK_STAT3_SIGNALING-1 [[cytokine regulation, chemokine regulation, interleukin regulation, cellular differentiation, cell motility and adhesion, GO:0007165, GO:0006954]] \n", - " HALLMARK_INFLAMMATORY_RESPONSE-0 [[this list of genes is significantly enriched for the functions of cell signalling, cytokine mediated immunity, receptor signalling, and tissue morphogenesis. furthermore, the list contains several genes associated with the immune response, including tlrs and ifns, as well as cytokines and chemokines such as ccl17, ccl20, cxcl10, cxcl9, ifnar1, tnfrsf1b, and tnfsf10. in addition, several receptors were found to be enriched on the list, including gpr132, axl, c3ar1, MONDO:0043317, and ccr7. finally, key genes involved in tissue morphogenesis were also found on the list, such as adgre1, edn1, btg2, ccl2, tacr1, and cxcr6.\\n\\nmechanism: \\nthe underlying mechanism for this enrichment of genes is likely related to the common activities of cell signalling, cytokine mediated immunity and tissue morphogenesis. the list of genes is likely regulating common processes such as cell-cell communication and inflammation. additionally, the list of genes may be involved in the development and maintenance of tissue structures, such as muscle tissue]] \n", - " HALLMARK_INFLAMMATORY_RESPONSE-1 [[GO:0006955, cellular activation, receptor-coupled pathways, transcriptional regulation, cytokine and cytokine receptor binding, GO:0006629, GO:0007155]] \n", - " HALLMARK_INTERFERON_ALPHA_RESPONSE-0 [[analysis of this list of genes reveals that they are all involved in the functioning of the immune system in some way, either through regulation of inflammatory response pathways, recognition of foreign agents, or production of molecules defending against potentially harmful intruders. the enriched terms include \"immune system regulation\"; \"inflammatory response\"; \"foreign agent recognition\"; \"antimicrobial defense\"; \"interferon signaling\"; \"antiviral defense\". \\n\\nmechanism: the genes in this list combined likely regulate a wide variety of immune system functions, including modulating inflammation, recognizing and responding to foreign antigens, producing effector molecules against potentially harmful microorganisms, promoting interferon signaling cascades to defend from viral invasion]] \n", - " HALLMARK_INTERFERON_ALPHA_RESPONSE-1 [[GO:0006955, GO:0006954, cytokine signaling, interferon response, GO:0006355, interferon-stimulated genes]] \n", - " HALLMARK_INTERFERON_GAMMA_RESPONSE-0 [[MESH:M0000731, GO:0019882, GO:0006954, chemokine signaling, GO:0007155, cytokine interactions]] \n", - " HALLMARK_INTERFERON_GAMMA_RESPONSE-1 [[interferon signaling, antigen processing, presentation, and recognition, cytokine signaling, cell cycle and dna damage response, GO:0006915]] \n", - " HALLMARK_KRAS_SIGNALING_DN-0 [[digit development, neural development, GO:0002520, transcriptional regulation, g-protein coupled receptors, MESH:D011494, MESH:D020662]] \n", - " HALLMARK_KRAS_SIGNALING_DN-1 [[our analysis revealed the enrichment of the gene functions related to development, GO:0007165, transcription and metabolism. specifically, some of the enriched terms include cellular development, GO:0016049, GO:0001501, GO:0048598, cell junction organization and assembly, GO:0007165, GO:0007049, GO:0006351, and cellular metabolism.\\n\\nmechanism: these gene functions may be related to the biological mechanism of growth, differentiation, and development of cells. the signals and transcription are likely involved in regulating and controlling these processes, as well as providing energy through metabolic pathways. additionally, the cell junction processes are likely involved in the coordination and communication between cells, which is essential to development]] \n", - " HALLMARK_KRAS_SIGNALING_UP-0 [[GO:0007165, GO:1901987, cell-to-cell adhesion]] \n", - " HALLMARK_KRAS_SIGNALING_UP-1 [[integrin, chemokine receptor, MESH:D011494, g-protein-coupled receptor, cytoskeleton proteins, cell-extracellular matrix interaction, type i ifn-mediated innate immunity, wnt signaling, MESH:D020558, MESH:D010740, MESH:D008565, MESH:D016326, receptor tyrosine kinase, toll-like receptor signaling, tlr adaptor proteins]] \n", - " HALLMARK_MITOTIC_SPINDLE-0 [[GO:0007049, GO:0007155, cytoskeletal organization, GO:0004672, GO:0003924]] \n", - " HALLMARK_MITOTIC_SPINDLE-1 [[GO:0051301, GO:0006468, GO:0006338, GO:0008017, microtubule organization, GO:0051225, GO:0007059, GO:0051305, cell-cycle control, GO:0140014]] \n", - " HALLMARK_MTORC1_SIGNALING-0 [[genes in this list are involved in various aspects of cellular metabolism, GO:0065007, and development.a number of the genes have roles in energy production and metabolism such as, atp2a2, aldoa, MONDO:0009214, fao1, fgl2, gapdh, gbe1, MONDO:0015408, glrx, MONDO:0005775, me1, phgdh, and pgm1. there is a strong presence of genes involved in protein synthesis and transport, including the ribosomal proteins, the eukaryotic translation factors and initiation factors (eif2s2, eif1e1, elovl5, and elovl6). this gene set is also enriched for a number of ubiquitin and ubiquitin-like proteins (ube2d3, ufm1, uso1, tomm40, hspd1, hspe1, sytl2, nherf1, and hk2). many of these genes are involved in regulation through multiple pathways including regulation of transcription (add3, actr2, actr3, cct6a, gga2, gdh2, mef2b, ykt]] \n", - " HALLMARK_MTORC1_SIGNALING-1 [[GO:0006412, transcription regulation, GO:0009653, GO:0016049, GO:0007165, GO:0008152, GO:0006629, cellular translation]] \n", - " HALLMARK_MYC_TARGETS_V1-0 [[GO:0006412, GO:0036211, GO:0006260, GO:0051726, transcription regulation, GO:0016049, GO:0048468, gene expression.\\nmechanism: the genes may constitute a pathway in which they coordinate together to regulate cell growth, development, and gene expression]] \n", - " HALLMARK_MYC_TARGETS_V1-1 [[developmental regulation, energy production, GO:0006412, structural maintenance of cell components, GO:0006260, transcription regulation, protein assembly]] \n", - " HALLMARK_MYC_TARGETS_V2-0 [[protein post translational modification, GO:0016310, GO:0006351, GO:0006412, GO:0042254]] \n", - " HALLMARK_MYC_TARGETS_V2-1 [[transcription regulation, GO:0006338, nucleosome remodeling, GO:0006260, nuclear localization, GO:0007165, GO:0016567, GO:0006468]] \n", - " HALLMARK_MYOGENESIS-0 [[genes in this list are associated with various cellular functions, including cell cycle regulation, developmental pathways, contractile force generation, protein synthesis and degradation, GO:0006915, GO:0000988, and metabolic processes. enriched terms include: cell cycle; cell differentiation; transcriptional regulation; intracellular signaling; muscle contraction; metabolism; apoptosis; protein synthesis; protein degradation.\\n\\nmechanism:\\n\\nthe genes in this list code for proteins involved in a range of cellular processes, including transcription factors that regulate gene expression, receptors that initiate intracellular signaling cascades, enzymes involved in metabolic pathways or apoptosis, and ion channels involved in muscle contraction and cell cycle regulation. these proteins interact to regulate the expression and activity of other proteins, impacting the activity of many important pathways that together coordinate cell growth, differentiation, MESH:D009068, GO:0008152]] \n", - " HALLMARK_MYOGENESIS-1 [[the genes that were analyzed were related to development, cell signalling, GO:0008152, GO:0065007, GO:0006936, MESH:D055550, and transport. the enriched terms were cellular development, actin cytoskeleton regulation, cell migration and adhesion, GO:0051726, calcium homeostasis and signaling, GO:0006936, GO:0006119, receptor tyrosine kinase signaling, apoptosis and programmed cell death, GO:0030198, GO:0016567, GO:0042632, metabolism and energy production, cell death and apoptosis, cytoskeletal protein binding and regulation of transcription and translation.\\n\\nmechanism: the underlying biological mechanism or pathways involved in these genes include regulation of muscle contraction, cell adhesion and migration, calcium homeostasis, protein ubiquitination and stability, receptor signaling, GO:0051726, GO:0006119, GO:0008219, and regulation of transcription and translation. these mechanisms are essential for cellular development and function, and thus, are enriched in these gene list]] \n", - " HALLMARK_NOTCH_SIGNALING-0 [[GO:0009653, GO:0048513, GO:0009888, GO:0001709, MESH:D002450, notch receptor signaling, wnt signaling, transcription factor signaling]] \n", - " HALLMARK_NOTCH_SIGNALING-1 [[GO:0008283, GO:0009653, GO:0032502, nerve system differentiation, transcription regulation, wnt signalling pathway, GO:0007219]] \n", - " HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 [[the list of genes provided are primarily involved in energy metabolism, GO:0007585, and the electron transport chain. specifically, terms such as \"oxidative phosphorylation\", \"mitochondrial electron transport chain\", and \"tricarboxylic acid cycle\" are found to be significantly over-represented.\\n\\nmechanism: the genes provided are involved in the production of atp through metabolic pathways such as oxidative phosphorylation, GO:0005746, and the tricarboxylic acid cycle. these molecules, along with other regulatory proteins, facilitate the flow of electrons to generate energy in the form of atp. this energy is used by cells to carry out metabolic reactions and various cellular processes]] \n", - " HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 [[mitochondrial electron transport chain complex activity, GO:0006120, GO:0005747]] \n", - " HALLMARK_P53_PATHWAY-0 [[analysis of this list of genes suggests a function related to cell cycle regulation, GO:0006915, and protein translation. the enriched terms include 'cell cycle regulation', 'apoptosis', 'protein translation', 'transcription regulation', 'intracellular protein transport', 'protein synthesis', and 'dna repair'.\\n\\nmechanism: the list of genes may be associated with a mechanism related to the regulation of cell cycle transitions and the integration of external signals to regulate gene transcription, protein translation and stability, and cellular apoptosis. this could involve some combination of signal transduction, GO:0006355, GO:0043687, GO:0006281]] \n", - " HALLMARK_P53_PATHWAY-1 [[gene expression and protein metabolism are likely to be enriched. specifically, the genes are likely involved in protein folding and transport, GO:0016567, transcriptional regulation, GO:0051726, protein-protein interactions, and signal transduction. \\nmechanism: these genes likely play a role in common metabolic, GO:0023052, and regulatory pathways.\\nubiqutination terms: rchy1, hexim1, upp1, pom121, procr, tap1, phlda3, wwp11; \\ntranscription factors:cd81, sat1, ercc5, ralgdh, irak1, aen, tob1, stom, MONDO:0100339, rap2b, tm7sf3, lif, MESH:C058179, ccp110, baiap2, tnfsf9, dcxr, eps8l2, ifi30, fdxr, elp1, itgb4, hbegf, irag2, ccnd2, sertad3, mknk2, retsat, ip6k2, hmox1, zfp36l1, epha2, tpd]] \n", - " HALLMARK_PANCREAS_BETA_CELLS-0 [[GO:0031016, GO:0007399, development of neural structures, GO:0048513, transcription regulation, GO:0009653, cell-to-cell adhesion, GO:0006412, hormonal metabolism, hormonal signaling]] \n", - " HALLMARK_PANCREAS_BETA_CELLS-1 [[GO:0022008, GO:0008152, GO:0006355, GO:0006412, GO:0009653, body patterning and organization, neurological system development, GO:0030154]] \n", - " HALLMARK_PEROXISOME-0 [[GO:0006629, stress response, GO:0009299, GO:0006281, skeletal and cartilage development, GO:0016477, metabolic enzymes, MESH:D002352]] \n", - " HALLMARK_PEROXISOME-1 [[GO:0008152, GO:0006351, GO:0065007, GO:0006810, GO:0007165, GO:0006412, GO:0030154, GO:0006260, GO:0036211, membrane trafficking]] \n", - " HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 [[MESH:M0023730, GO:0009653, GO:0030154, tyrosine kinase activity, GO:0038023]] \n", - " HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 [[cell signaling, GO:0019538, GO:0006629, transcription regulation, GO:1901987, GO:0007165, receptor signaling, GO:0070085, GO:0016301, GO:0006915, g-protein interactions, transcriptional regulation]] \n", - " HALLMARK_PROTEIN_SECRETION-0 [[cell membrane fusion, GO:0016192, intracellular trafficking, predominant cargo proteins, GO:0006900, membrane remodeling]] \n", - " HALLMARK_PROTEIN_SECRETION-1 [[GO:0043687, GO:0006457, GO:0006412, GO:0006897, GO:0009311, lysosomal trafficking]] \n", - " HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 [[GO:0008152, oxidative damage resistance, GO:0006281, cellular metabolic regulation, GO:0006915, regulatory pathway, GO:0006457, GO:0006749]] \n", - " HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 [[this list of genes is enriched for terms related to oxidative stress, GO:0008152, and immune system function. specifically, the genes represent proteins involved in oxygen-sensing, anti-oxidation, redox regulation, GO:0006281, the stress response, and cytokine signaling.\\n\\nmechanism:\\nthe underlying biological mechanism of the gene list is likely the cellular response to oxidative stress. oxidative stress is a term used to describe a disruption in the balance of antioxidant molecules and reactive oxygen species. these reactive molecules can cause damage to the cell, and thus the relevant genes likely help the cell to counteract this damage by regulating redox status, mediating oxidant stress, and participating in dna repair and other defense mechanisms. additionally, some of these genes are involved in cytokine signaling, which helps to aid the immune system in defending against potential oxidative insults]] \n", - " HALLMARK_SPERMATOGENESIS-0 [[GO:1901987, GO:0006338, GO:0016567, GO:0006260, GO:0051225, GO:0006997]] \n", - " HALLMARK_SPERMATOGENESIS-1 [[the list of genes provided are involved in diverse processes, such as cell structure and organization, GO:0007165, transcriptional regulation and other metabolic activities. the enriched terms from performing a term enrichment test are cell cycle, GO:0051301, GO:0016569, development and differentiation, cell signaling and signal transduction, GO:0006397, transcriptional regulation, and metabolic processes.\\n\\nmechanism:\\nthe genes provided are believed to be involved in a general mechanism of cell organization and function. the enriched terms are suggestive of the genes being related to fundamental processes such as cell cycle regulation, GO:0051301, transcriptional regulation, GO:0016569, and signal transduction. through the regulation of the genes, they are thought to be capable of controlling the organization and structure of cells, as well as metabolism and other cellular activities. furthermore, these pathways likely interact with each other in a complex manner, thereby allowing for intricate coordination between the genes in order to precisely tune process]] \n", - " HALLMARK_TGF_BETA_SIGNALING-0 [[genes in this set are related to morphogenesis, GO:0007155, immune signaling, and transcriptional regulation. enriched terms include: morphogenesis, GO:0007155, immune signaling, transcriptional regulation, digit development, GO:0007049, protein-protein interaction, GO:0008083, and regulation of transcriptional activity.\\n\\nmechanism: morphogenesis can be regulated by the activity of kinases, cell adhesion can be mediated by the expression of cell adhesion molecules, and immune signaling can be regulated by the activity of cytokines, MESH:D018121, and transcription factors. the transcriptional regulation of these genes can be mediated by transcription factors and the regulation of transcriptional activity can be mediated by modulators of tfs, such as kinases and ubiquitin ligases. protein-protein interactions can occur between the different genes, signaling from growth factors can affect the expression of genes in this set]] \n", - " HALLMARK_TGF_BETA_SIGNALING-1 [[transcriptional regulation, GO:0007165, GO:0051726, protein kinase pathways, GO:0006412, GO:0048468, GO:0008283, GO:0030054, cytoskeletal organization]] \n", - " HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 [[GO:0002224, GO:0032502, GO:0006954, immune-response regulation, nfkb, GO:0004707, GO:0010467, pro-inflammatory molecules]] \n", - " HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 [[cytokine-mediated signaling, antigen-receptor mediated signaling, GO:0042100, cytokine expression and release, immunoregulatory interactions, GO:0051092, interferon (ifn) signaling]] \n", - " HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 [[GO:0006412, GO:0042254, GO:0006413, GO:0006457, GO:0006414, GO:0015833, peptide assembly, chaperone mediated protein folding]] \n", - " HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 [[analysis of this gene list has revealed that the functions enriched in the gene set include translation and translation initiation (exosc2, eif4a3, MESH:D039561, eif4g1, eif4a2); ubiquitination (ern1, skp1, herpud1, ube2g2, ube2l3); and protein folding and stability (atf3, fkbp14, dnajb9, calr, preb, hspa5, hsp90b1).\\n\\nmechanism: the enriched functions imply a complex network of processes that is likely to involve translation initiation of mrna, GO:0016567, and chaperone activity that facilitates protein folding, stability and degradation. it is possible that this gene set is associated with a variety of cellular pathways, including those related to gene expression, GO:0007165, GO:0008152]] \n", - " HALLMARK_UV_RESPONSE_DN-0 [[cell signaling, structural proteins, MESH:D004798, GO:0009653]] \n", - " HALLMARK_UV_RESPONSE_DN-1 [[the above list of genes is significantly enriched for terms related to the development of the connective tissue, including morphogenesis, GO:0007049, regulation of transcription, and extracellular matrix organization; as well as the regulation of cell migration, matricellular protein signaling, GO:0007165, and calcium ion binding.\\n\\nmechanism: the enriched terms suggest that these genes work together in a common and interconnected pathway to control the formation, MESH:D009068, and functioning of the connective tissue. this pathway likely involves interactions among signal transduction pathways mediated by protein-protein interactions, transcriptional regulation, and calcium ion binding. these interactions would likely affect the structure and organization of the extracellular matrix, the migration of cells, the cell cycle, signalling through matricellular proteins]] \n", - " HALLMARK_UV_RESPONSE_UP-0 [[MESH:D021381, organelle trafficking, GO:0006306, transcription regulation, GO:0003677, GO:0006338, GO:0051726, GO:0008152]] \n", - " HALLMARK_UV_RESPONSE_UP-1 [[genes in this list are generally involved in the regulation of cell growth and development, in particular related to apoptosis, signaling and transcriptional pathways. enriched terms include: transcriptional regulation; cell cycle regulation; apoptosis regulation; signal transduction; dna damage response; and cellular metabolism.\\n\\nmechanism: the molecular and cellular mechanisms underlying cell growth and development are complex and interconnected. genes in this list are believed to be involved in several pathways, such as transcriptional regulation, GO:0051726, apoptosis regulation, GO:0007165, GO:0006974, and cellular metabolism. these pathways interact and regulate each other in order to ensure the healthy functioning of cells. transcriptional regulation is key in regulating gene expression, while the cell cycle is tightly regulated by the activation of cell cycle control proteins and anti-apoptotic pathways. signal transduction pathways are essential for the proper coordination of cellular responses to external stimuli, and dna damage response allows for the repair of any irregularities. cellular metabolism is necessary for providing energy for growth and repair, for controlling the production of proteins]] \n", - " HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 [[the genes in this list are associated with the wnt signaling pathway, modulating cell growth and mophogenesis. the enrichment terms corresponding to this list are wnt signaling, GO:0016049, GO:0009653, transcriptional regulation, and epigenetics.\\n\\nmechanism: the wnt signaling pathway activates nuclear proteins such as lef1 and tcf7, which then activate transcription of genes involved in cell growth and morphogenesis. the genes on the listed are associated with modulating the wnt pathway, including epigenetic regulation and cell cycle regulation]] \n", - " HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 [[GO:0009653, GO:0006351, GO:0032502, MESH:D060449]] \n", - " T cell proliferation-0 [[GO:0009653, GO:0048468, cell signaling, receptor-mediated signaling, GO:0010468]] \n", - " T cell proliferation-1 [[GO:0005126, GO:0007155, immunoreceptor-antigen complex binding, regulation of the ubiquitin-proteasome pathway, transcription factor regulator activity, gtp-binding protein binding, GO:0030154]] \n", - " Yamanaka-TFs-0 [[GO:0000988, embryonic stem cell differentiation, cell pluripotency, dna-binding, MESH:D005786, GO:0140110, transcription factor complex formation.\\nmechanism: these genes are known to be involved in the regulation of gene expression, and thus serve an important role in directing the biological activities associated with embryonic stem cell differentiation and pluripotency. they are likely to form complexes, interact with dna, and/or bind to components of the transcription machinery to regulate gene expression at the transcriptional level]] \n", - " Yamanaka-TFs-1 [[GO:0048863, GO:0048468, embryonic stem cell differentiation, transcriptional regulation, pluripotency, transcription factor regulation.\\n\\nmechanism: the genes klf4, pou5f1, and sox2 act in concert to regulate the expression of developmental proteins that are involved in forming stem cells. this trio of transcription factors plays a key role in regulating cell differentiation and pluripotency, thus influencing the direction of embryonic stem cell development by regulating gene expression of proteins involved in stem cell formation]] \n", - " amigo-example-0 [[GO:0008283, GO:0048729, motility regulation, vascular development, GO:0098868, UBERON:0002405]] \n", - " amigo-example-1 [[GO:0001525, GO:0008283, GO:0016477, matrix remodeling, GO:0048771, jagged-mediated signaling, transcriptional regulation, GO:0030168, GO:0070527, immune regulation, extracellular matrix formation]] \n", - " bicluster_RNAseqDB_0-0 [[GO:0016049, differentiation, migration, chromatin modulation, transcription regulation, cytoskeletal organization, intracellular trafficking, GO:0007155, GO:0007165, dna/rna metabolic processes, GO:0009653, GO:0001525, muscle growth, GO:0032502]] \n", - " bicluster_RNAseqDB_0-1 [[chromatin regulation, GO:0048468, GO:0006412, GO:0006811, GO:0000981, GO:0043687]] \n", - " bicluster_RNAseqDB_1002-0 [[MESH:M0370791, GO:0007015, GO:0006936, z-disc formation, GO:0007097, muscle fiber organization, ion channel influx/efflux]] \n", - " bicluster_RNAseqDB_1002-1 [[MESH:D024510, GO:0048740, GO:0021675, calcium distribution, actin proteins, cardiac contractile proteins, sarcomeric proteins, membrane protein transport, ion channel proteins, enzyme regulation.\\nmechanism: this list of genes are likely to be involved in the regulation of muscle structures and contractions, organization of calcium distribution throughout the cell, nerve development, and support of membrane protein transport and enzymatic activities. these processes are important for maintaining muscle contraction and activity]] \n", - " endocytosis-0 [[GO:0006629, cell signaling, GO:0007049, cytoskeletal dynamics]] \n", - " endocytosis-1 [[GO:0006897, intracellular signaling, GO:0016310, protein interactions, receptor trafficking]] \n", - " glycolysis-gocam-0 [[GO:0006754, GO:0006096, MESH:D004734, MESH:M0496924]] \n", - " glycolysis-gocam-1 [[metabolic pathway, GO:0006096, glucose oxidation, pyruvic acid production, GO:0006754]] \n", - " go-postsynapse-calcium-transmembrane-0 [[summary: the enriched terms of the human genes atp2b1, atp2b2, cacna1c, cacng2, cacng3, cacng4, cacng5, cacng7, cacng8, chrna10, chrna7, chrna9, drd2, f2r, gpm6a, grin1, grin2a, grin2b, grin2c, grin2d, grin3a, grin3b, htr2a, itpr1, ncs1, p2rx4, p2rx7, plcb1, psen1, slc8a1, slc8a2, slc8a3, trpv1 include neuron development; neurotransmitter signaling; signal transduction; transmembrane transport; neural plasticity; ion transport; calcium signaling; glutamate receptor signaling; and synaptic signaling. \\n\\nmechanism: these genes are believed to act in concert to regulate and coordinate the various stages of neuron development, such as neurotransmitter signaling, GO:0007165, GO:0055085, neural]] \n", - " go-postsynapse-calcium-transmembrane-1 [[neuronal function, GO:0006811, ion channel regulation, neurotransmitter regulation, calcium regulation, potassium regulation, GO:0007268, membrane potential regulation]] \n", - " go-reg-autophagy-pkra-0 [[this set of genes is associated with cellular functions related to metabolic homeostasis and activation of the pi3k/akt signaling pathway. the enriched terms associated with the genes include cell cycle regulation, protein kinase regulation, mitochondrial regulation, and mitochondrial stress response.\\n\\nmechanism: the metabolic homeostasis and activation of the pi3k/akt pathway are mediated by these genes, which affect the regulation of cell cycle, protein kinase regulation, mitochondrial regulation, and mitochondrial stress response. these genes have roles in regulating metabolic processes as well as responding to external stressors. their involvement in cell cycle regulation and protein kinase regulation ensures the healthy development and maintenance of the cell, while their role in mitochondrial regulation and mitochondrial stress response plays an important role in maintaining the cell's energy production]] \n", - " go-reg-autophagy-pkra-1 [[cell signaling, transcription regulation, GO:0006468, ras activation, akt activation, calcium-associated kinases, GO:0019722]] \n", - " hydrolase activity, hydrolyzing O-glycosyl compounds-0 [[MESH:D009113, MESH:D009077, glycosyltransferase, MESH:D006821, GO:0070085, enzyme, MESH:D011506]] \n", - " hydrolase activity, hydrolyzing O-glycosyl compounds-1 [[the gene functions that were found to be enriched amongst this set of genes were predominantly related to carbohydrate metabolism, including glycosaminoglycan and glycosphingolipid biosynthesis as well as lysosomal enzyme activity.\\n\\nmechanism:\\nthe mechanism most likely lies in the pathway of glycoconjugation, which helps to regulate important processes such as cell adhesion, GO:0006955, and signal transduction. the pathway is integral to the proper formation and function of the extracellular matrix, which is important for cellular differentiation and tissue organization. the enriched terms found here likely represent genes that are involved in the biosynthesis and metabolism of various glycoconjugates, in addition to the regulation of lysosomal enzymes involved in the degradation of complex carbohydrates]] \n", - " ig-receptor-binding-2022-0 [[immunoglobulin heavy chain combination, immunoglobulin light chain combination, j-chain, antigen-specific receptor, t-lymphocyte receptor, regulation of immune function]] \n", - " ig-receptor-binding-2022-1 [[genes related to immunoglobulins, transcripts associated with immunoglobulin transcription and splicing, immunoglobulin gene expression, proteins involved in immunoglobulin regulation and processing, GO:0002637, GO:0002637, mhc class i antigen processing and presentation, cytokine-mediated signaling, GO:0002544, limit degranulation. \\n\\nmechanism: these genes are associated with immunoglobulin production, processing, and regulation. this includes genes related to immunoglobulins, transcripts involved in transcription and splicing, and proteins that are involved in the regulation and processing of immunoglobulins. additionally, genes related to mhc class i antigen processing, cytokine-mediated signaling, chronic inflammatory response, and limit degranulation are also expressed. these genes interact to form an integrated pathway that is involved in the regulation of the immune response and the formation of immunoglobulins]] \n", - " meiosis I-0 [[GO:0006260, GO:0006281, replication fidelity, GO:0007049, GO:0071897, dna prioritization]] \n", - " meiosis I-1 [[this enrichment test on the list of human genes suggests a central role for dna damage repair and cell cycle regulation in the common functionalities of the genes. enriched terms found include \"dna repair\", \"cell cycle\", \"chromatin remodelling\", \"recombinational repair\", \"steroid hormone receptor\", \"centromere\", GO:0000724]] \n", - " molecular sequestering-0 [[GO:0019722, calcium buffering, GO:0006816, regulation of calcification, protection against calcium overload, calcium-v influx/efflux]] \n", - " molecular sequestering-1 [[cell morphology regulation, GO:0008152, GO:0006915, GO:0006412, GO:0036211, GO:0006811, GO:0023052, stress response, GO:0006351, cell surface interactions, chromatin regulation]] \n", - " mtorc1-0 [[genes in this list are involved in various aspects of cellular metabolism, GO:0065007, and development.a number of the genes have roles in energy production and metabolism such as, atp2a2, aldoa, MONDO:0009214, fao1, fgl2, gapdh, gbe1, MONDO:0015408, glrx, MONDO:0005775, me1, phgdh, and pgm1. there is a strong presence of genes involved in protein synthesis and transport, including the ribosomal proteins, the eukaryotic translation factors and initiation factors (eif2s2, eif1e1, elovl5, and elovl6). this gene set is also enriched for a number of ubiquitin and ubiquitin-like proteins (ube2d3, ufm1, uso1, tomm40, hspd1, hspe1, sytl2, nherf1, and hk2). many of these genes are involved in regulation through multiple pathways including regulation of transcription (add3, actr2, actr3, cct6a, gga2, gdh2, mef2b, ykt]] \n", - " mtorc1-1 [[genes related to metabolism and biosynthesis (acly, aldoa, atp2a2, atp6v1d, cacybp, coro1a, dhcr24, MONDO:0100101, MONDO:0100102, gbe1, MESH:C066524, gsr, hmgcs1, hspa9, lgmn, me1, mthfd2l, nampt, pgm1, pgk1, psat1, psma3, psma4, psmg1, psmc2, psmc4, psmd12, psmd13, psmd14, stc1, stip1, and ufm1), protein folding/interaction (act2, actr2, actr3, add3, elovl5, eno1, ero1a, eif2s2, fgl2, insig1, itgb2, map2k3, mcm2, mcm4, nufip1, p4ha1, pdk1, pitpnb, pnp, psme3, sec11a, shmt2, slc2a1, slc2a3]] \n", - " peroxisome-0 [[protein homeostasis, peroxisome biogenesis, peroxisome assembly, peroxisome maintenance, protein regulation, GO:0050821]] \n", - " peroxisome-1 [[peroxisomal biogenesis, peroxisome assembly, peroxisome regulation, GO:0015031, membrane trafficking]] \n", - " progeria-0 [[after performing the enrichment test on the genes zmpste24, banf1, MONDO:0010196, and lmna, we identified that all of the genes have a role in the regulation of nuclear and chromatin structures. the individual genes are involved in a wide range of processes in these two areas. this includes gene expression, GO:0006260, GO:0006338, GO:0000723, as well as cell cycle checkpoints.\\n\\nthe enriched terms are 'nuclear structure regulation'; 'chromatin structure regulation'; 'gene expression regulation'; 'dna replication regulation'; 'chromatin remodeling'; 'telomere maintenance'; and 'cell cycle checkpoint regulation'. \\n\\nmechanism: the underlying biological mechanism that our gene list points to is one involving the regulation of nuclear and chromatin structures. in order to maintain the stability of the genome and ensure its accurate transmission, molecules encoded by the four genes could be involved in key activities such as gene expression, GO:0006260, GO:0006338, GO:0000723, as well as cell cycle checkpoints]] \n", - " progeria-1 [[transcriptional regulation, GO:0006281, GO:0051726, GO:0030154]] \n", - " regulation of presynaptic membrane potential-0 [[MESH:D007473, MESH:D008565, synapse formation, GO:0007268, MESH:D009473, neuronal excitability, voltage-gated ion channels, MESH:D058446]] \n", - " regulation of presynaptic membrane potential-1 [[ion-channel function, neuron excitability, GO:0007268, MESH:D018079, MESH:D017470, MESH:D015221, MESH:D015222]] \n", - " sensory ataxia-0 [[GO:0006412, GO:0008152, ion channel transport, GO:0006936, MESH:D024510]] \n", - " sensory ataxia-1 [[nucleic acid metabolism, GO:0003676, GO:0050657, GO:0019538, GO:0005515, GO:0015031]] \n", - " term-GO:0007212-0 [[g-protein coupled receptor (gpcr), g-protein subunit, MESH:D000262, MESH:D015220, MESH:D010770]] \n", - " term-GO:0007212-1 [[GO:0007165, cellular growth & differentiation, GO:0007010, endocrine system regulation, transcriptional regulation]] \n", - " tf-downreg-colorectal-0 [[genes such as hira, cebpb, e2f3, hmga1, znf263, tfdp1, trib3, bhlhe40, smarca4, slc26a3, nfe2l3, ssbp2, gtf3a, npm1, trip13, mef2c, nr3c2, foxm1, vdr, hand1, klf4, hexim1, tgif1, med24, tead4, smarcc1, scml1, MESH:D024243, myc, foxa2, bmal2, spib, nme2, phb1, cbx4, runx1, ppargc1a, polr3k, nr5a2, maf, nr1h4, sox9, dnmt1, cbfb, znf593, mta1, zbtb18 are all involved in the regulation of transcription, GO:0006338, GO:0003677, and epigenetics. of this group, genes involved in transcription are significantly enriched (e.g. hira, cebpb, e2f3,]] \n", - " tf-downreg-colorectal-1 [[GO:0016049, transcriptional regulation, GO:0006338, GO:0051726, GO:0006351, GO:0016569]] \n", - " ontological_synopsis EDS-0 [[collagen or extracellular matrix structural constituent, collagen metabolic process or biosynthetic process, proteoglycan metabolic process or biosynthetic process, GO:0006024, dna-binding transcription factor binding activity, GO:0001217, rna polymerase ii transcription regulatory region sequence-specific dna binding activity, metal ion binding activity, GO:0003755, GO:0035987, GO:0004252, GO:1904028, protein peptidyl-prolyl is]] \n", - " EDS-1 [[GO:0030198, GO:0030199, GO:0032964, GO:0030166, GO:0006024]] \n", - " FA-0 [[GO:0006281, GO:0006513, GO:0043240, GO:0000785, GO:0005634, GO:0005829]] \n", - " FA-1 [[GO:0006513, GO:0006281, GO:0003682, GO:0000400, GO:0003684, GO:0003697, GO:1990599, GO:0004520, GO:0006310, GO:0005524, GO:0006259, GO:0072757, GO:0051052, GO:0003691, GO:0000723, GO:0019219, GO:0051246, GO:0070200, GO:0016573, GO:0004402, gamma-tubulin binding activity, identical protein binding activity, jun kinase binding activity, rna polymerase ii-specific dna-binding transcription factor binding activity, GO:0061630, GO:0031386]] \n", - " HALLMARK_ADIPOGENESIS-0 [[protein binding activity, MESH:D010758, atp binding activity, gtp binding activity, GO:0022857, dna binding activity, receptor binding activity, GO:0004869, caspase binding activity, rna binding activity]] \n", - " HALLMARK_ADIPOGENESIS-1 [[protein binding activity, enzyme binding activity, atp binding activity, rna binding activity, gtp binding activity, identical protein binding activity, gtp-dependent protein binding activity, transition metal ion binding activity, GO:0016615, aldehyde dehydrogenase activity, GO:0008097, GO:0052650, fad binding activity, MESH:D010758, heme binding activity, GO:0003872, GO:0004609, GO:0003873, GO:0004144, GO:0003994, GO:0004784, GO:0004129, molybdenum ion binding activity]] \n", - " HALLMARK_ALLOGRAFT_REJECTION-0 [[protein homodimerization, protein heterodimerization, GO:0042802, GO:0019901, dna-binding, rna-binding, GO:0017124, GO:0019958, GO:0008201, ubiquitin-protein ligase binding]] \n", - " HALLMARK_ALLOGRAFT_REJECTION-1 [[GO:0007155, GO:0005102, GO:0007165, GO:0001228, chemokine receptor binding activity, enzyme binding activity, GO:0008083, GO:0005125, degradation of redundant or damaged proteins and peptides, GO:0046983, metal ion binding activity, peptide antigen binding activity, GO:0004888, GO:0004712, GO:0042803, ubiquitin binding activity]] \n", - " HALLMARK_ANDROGEN_RESPONSE-0 [[GO:0005215, GO:0005515, GO:0004672, GO:0038023, GO:0006351, GO:0044237, GO:0006974, GO:0007010, GO:0016787, GO:0046872, GO:0003924]] \n", - " HALLMARK_ANDROGEN_RESPONSE-1 [[GO:0005515, GO:0016887, GO:0016563, GO:0003677, GO:0004674, GO:0022857, GO:0016787, GO:0061631, cis-regulatory region sequence-specific dna binding activity, GO:0061665, GO:0034594, GO:0007165, GO:0043027, GO:0003924, GO:0042803, nucleic acid binding activity, GO:0003713, GO:0003714, enzyme binding activity, calmodulin binding activity, metalloendope]] \n", - " HALLMARK_ANGIOGENESIS-0 [[summary: the list of genes provided appear to be involved in a variety of unrelated processes, but when grouped by shared activities, several functions in common can be identified. these common functions include protein binding activity, GO:0060230, phospholipid binding activity, platelet-derived growth factor binding activity, GO:0046983, signaling receptor binding activity, collagen binding activity, atp activated inward rectifier potassium channel activity, voltage gated monoatomic ion channel activity, GO:0005249, GO:0016298, heparan sulfate proteoglycan binding activity, heparin binding activity, multiple growth factor activities, peptidoglycan binding activity, GO:0016019, platelet derived growth factor binding activity, non membrane spanning protein tyrosine kinase activity, GO:0005096, vascular endothelial growth factor binding activity, metal ion binding activity, small molecule binding activity, enzyme binding activity, retinoic acid binding activity, cxcr3 chemokine receptor binding activity, prostaglandin transmembrane transporter activity and sodium-independent organic anion transmembrane transporter activity. \\nmechanism: the genes in the list appear]] \n", - " HALLMARK_ANGIOGENESIS-1 [[GO:0005515, GO:0006468, GO:0016477, GO:0008283, GO:0045861, GO:1902533, GO:0009966, GO:0010604, GO:0019901, GO:0008191, ion binding activity, small molecule binding activity, GO:0035987, GO:0005096, platelet-derived growth factor binding activity, GO:0046983, calcium ion binding activity, sympathetic nerve activity, GO:0051336]] \n", - " HALLMARK_APICAL_JUNCTION-0 [[GO:0007155, GO:0005178, gtp binding activity, collagen binding activity, atp binding activity, phospholipase binding activity, GO:0007160, GO:0050839, GO:0017124]] \n", - " HALLMARK_APICAL_JUNCTION-1 [[extracellular matrix structure, GO:0038023, cell adhesion molecule binding activity, small gtpase binding activity, GO:0042803, identical protein binding activity, collagen binding activity, actin binding activity, atp binding activity, protein kinase binding activity, sh3 domain binding activity, integrin binding activity, GO:0005096]] \n", - " HALLMARK_APICAL_SURFACE-0 [[GO:0005480, cell structure maintenance, GO:0046872, GO:0016477, plasmamembrane transport, GO:0005515, GO:0043170, GO:0030296, endolemmal transport, GO:0016485, GO:0010467, GO:0006915, lipoprotein particle receptor catabolic process, peptide chain release, protein homodimerization, GO:0007165, GO:0048870, GO:1902600, GO:0000785, GO:0005654, GO:0031410, GO:0042552, GO:0044183]] \n", - " HALLMARK_APICAL_SURFACE-1 [[genes in this list are primarily involved in regulation of transcription, GO:0007165, membrane management, protein folding and binding, cell surface receptor signaling and adhesion, and cellular extravasation. enriched terms include: transcription, GO:0007165, protein-folding and binding, cell-surface receptor signaling, adhesion, GO:0045123, GO:0061024, extracellular matrix structural components, genetic expression, apoptotic pathways, and intracellular ion homeostasis. \\n\\nmechanism: genes on this list are primarily involved in several processes that coordinate essential cellular functions by dynamically managing activity of proteins at the surface of the cell, within underlying membrane layers, extracellularly and within dna. these genes manage the way cells communicate within their environment, interact with extracellular components, respond to stimuli, and extravasate. they code for proteins involved in transcription, GO:0007165, protein folding and binding, adhesion, apoptotic pathways, intracellular ion homeostasis, extracellular matrix structural components that have pleiotropic roles in modulating gene expression functioning of cellular components]] \n", - " HALLMARK_APOPTOSIS-0 [[dna binding activity, GO:0046983, protein binding activity, enzyme binding activity, protein kinase binding activity, GO:0004197, GO:0003714, phosphoprotein binding activity, mhc class i protein binding activity, GO:0003700, signaling receptor binding activity, GO:0042803]] \n", - " HALLMARK_APOPTOSIS-1 [[protein binding activity, identical protein binding activity, enzyme binding activity, GO:0003700, rna polymerase ii-specific transcriptional activity, GO:0004197, GO:0004896]] \n", - " HALLMARK_BILE_ACID_METABOLISM-0 [[atp binding activity, GO:0016887, cholesterol binding activity, GO:0022857, GO:0046982, GO:0000981, enzyme binding activity, GO:0016491, peptide antifungal protein binding activity, acyl-coa hydroxyacyltransferase activity, GO:0019145]] \n", - " HALLMARK_BILE_ACID_METABOLISM-1 [[this gene list is associated with multiple functions in various metabolic processes, from binding and transporter activity to atpase activity, homodimerization activity, and various hydrolytic activities. enriched terms include: protein binding activity; atp hydrolysis activity; protein homodimerization activity; atpase binding activity; atpase-coupled transmembrane transporter activity; transcription regulatory region sequence-specific dna binding activity; and transmembrane transporter activity. mechanism: this set of genes acts as part of multiple metabolic processes, such as lipid and fatty acid metabolism, GO:0042632, GO:0140327, and hormone regulation. these genes facilitate enzymatic activity and activity in transporting molecules, such as fatty acids, MESH:D002784, MESH:D014815, hormones. the processes activities these genes are involved in suggest a coordination of metabolic cell stimulation processes]] \n", - " HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 [[atp binding activity, protein binding activity, GO:0007155, GO:0007165, GO:0006915, dna-binding, GO:0006695, cell structure organization, GO:0003985, GO:0008610, GO:0000988, GO:0015631, protein homodimerization]] \n", - " HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 [[GO:0006695, GO:0008610, positive regulation of transcription, GO:2001234, GO:0031647, regulation of cell adhesion/migration, atp binding activity, transcription factor binding activity, protein binding activity, protein kinase binding activity, signaling receptor binding activity, ion/metal binding activity, endopeptidase regulator activity, etc]] \n", - " HALLMARK_COAGULATION-0 [[protein binding activity, collagen binding activity, identical protein binding activity, integrin binding activity, phospholipid binding activity, atp binding activity, fibronectin binding activity, GO:0008237, GO:0004252, metaloendopeptidase activity, calcium ion binding activity]] \n", - " HALLMARK_COAGULATION-1 [[the genes in this list are predicted to enable various calcium-dependent functions related to protein binding, GO:0019899, and peptidase activity, typically related to blood coagulation, GO:0007155, endodermal cell fate, and negative regulation of protein-regulating processes. these genes are involved in various activities across multiple cellular pathways, including cellular response to uv-a, GO:0030155, and blood coagulation. the enriched terms include “calcium-dependent functions”, “protein binding activity”, “enzme binding activity”, “peptidase activity”, “blood coagulation”, “cell adhesion”, “endodermal cell fate”, “negative regulation of protein-regulating processes”, “cellular response to uv-a”, and “regulation of cell adhesion”.\\n\\nmechanism: the mechanism underlying this list of genes is likely related to calcium-dependent regulation of proteins and peptides, which acts to control various cellular processes. calcium can act as a negative regulator of proteins, through calcium binding to proteins and preventing their activity, or as a]] \n", - " HALLMARK_COMPLEMENT-0 [[protein binding activity, GO:0001216, enzyme binding activity, metal ion binding activity, sh2 domain binding activity, GO:0004197, phosphoprotein binding activity, actin binding activity, cation binding activity, lipid binding activity, GO:0004252, GO:0008092, cell killing activity, protein kinase binding activity]] \n", - " HALLMARK_COMPLEMENT-1 [[dna-binding, GO:0005543, GO:0005515, GO:0005102, GO:0019899, inhibitor activities, GO:0003924, GO:0046872, protein activities, GO:0023052, transcription regulation, GO:0006281, GO:0008219, GO:0006955]] \n", - " HALLMARK_DNA_REPAIR-0 [[dna binding activity, rna binding activity, enzyme binding activity, protein binding activity, calcium ion binding activity, GO:0140612, GO:0003713, zinc ion binding activity]] \n", - " HALLMARK_DNA_REPAIR-1 [[dna binding activity, enzyme binding activity, GO:0016887, rna binding activity, protein binding activity, GO:0003887, GO:0004518, mrna regulatory element binding]] \n", - " HALLMARK_E2F_TARGETS-0 [[chromatin binding activity, GO:0006260, GO:0006281, GO:0006351, GO:0016570, nuclear import/export, dna/rna binding, protein-macromolecule binding, GO:0051726, protein homodimerization, GO:0006200, GO:0000287, MESH:D011494, GO:0004518]] \n", - " HALLMARK_E2F_TARGETS-1 [[nuclear pore remodeling, GO:0065003, GO:0003677, transcriptional regulation, GO:0006260, GO:0006913, chromatin modification and repair, cell cycle progression, GO:0140014, GO:0019899, GO:0042393, protein homod]] \n", - " HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 [[protein binding activity, identical protein binding activity, collagen binding activity, integrin binding activity, heparin binding activity, phosphatidylinositol binding activity, cell adhesion molecule binding activity, extracellular matrix binding activity, signaling receptor binding activity, GO:0008009, gene transcriotion activity, metal ion binding activity]] \n", - " HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 [[GO:0005201, collagen binding activity, cell adhesion molecule binding activity, dna binding activity, gtp binding activity, GO:0042803, platelet-derived growth factor binding activity, platelet-derived growth factor binding activity, calcium ion binding activity, signaling receptor binding activity, identical protein binding activity]] \n", - " HALLMARK_ESTROGEN_RESPONSE_EARLY-0 [[dna binding activity, protein binding activity, enzyme binding activity, GO:0022857, transcription activity, GO:0003924, atpase binding activity, mrna binding activity, protein homodimerization, GO:0042169, GO:0016922, GO:0030165]] \n", - " HALLMARK_ESTROGEN_RESPONSE_EARLY-1 [[GO:0003677, GO:0000981, GO:0003723, protein binding/dimerization, transmembrane transporter, GO:0005509, GO:0019899, GO:0003924]] \n", - " HALLMARK_ESTROGEN_RESPONSE_LATE-0 [[GO:0050839, GO:0003677, transfacmembrane receptor protein tyrosine kinase activity, ligand binding, ca2+ ion binding, GO:0005543, GO:0019899, GO:0016563, GO:0005243, GO:0003682, GO:0032794, GO:0048018, GO:0005242, GO:0004930, GO:0060089, calcium-dependent exonuclease activity, GO:0003779, GO:0007165, GO:0004672, GO:0016310, sh2 domain binding activity, heme binding activity, GO:0042803, hsp90 protein binding activity, GO:0017002, GO:0004957, ww domain binding activity, pdz domain binding activity, sh3 domain binding activity]] \n", - " HALLMARK_ESTROGEN_RESPONSE_LATE-1 [[GO:0008134, GO:0019899, GO:0005515, GO:0007155, ligand-gated ion transporter activity, GO:0001216, GO:0050839, protein domain specificity, GO:0030742, GO:0003677, GO:0019003, GO:0005525, GO:0051117, GO:0030165, GO:0005509, phosphotransfer, GO:0031490, GO:0001217]] \n", - " HALLMARK_FATTY_ACID_METABOLISM-0 [[protein binding activity, identical protein binding activity, metal ion binding activity, atp binding activity;lipid transport activity, fatty acid binding activity, fad binding activity, pdz domain binding activity;transmembrane transporter activity, ubiquitin binding activity, nucleotide binding activity, GO:0004080, GO:0004738, enoyl-coa hydratase activity;amino-acid oxidase activity, GO:0003979, GO:0009055, GO:0004853, 5alpha-reductase activity, rna-binding]] \n", - " HALLMARK_FATTY_ACID_METABOLISM-1 [[GO:0003824, GO:0016491, protein binding activity, hydratase activity, GO:0003997, lipid binding activity, dna binding activity, ubiquitin binding activity, atp binding activity, flavine adenine dinucleotide binding activity, nadp+ binding activity, GO:0042803, smad binding activity, GO:0004466]] \n", - " HALLMARK_G2M_CHECKPOINT-0 [[dna binding activity, rna binding activity, protein kinase binding activity, protein folding activity, enzyme binding activity, transcription factor binding activity, chromatin binding activity, protein domain specific binding activity, nucleic acid binding activity, atp binding activity, identical protein binding activity, GO:0140110, GO:0046983, histone binding activity, anaphase-promoting complex binding activity, cytoplasmic release activity, metal ion binding activity, GO:0016887, histone deacetylase binding activity, telomere binding activity]] \n", - " HALLMARK_G2M_CHECKPOINT-1 [[GO:0005515, GO:0003677, GO:0008134, MESH:D019098, GO:0003723, GO:0006260, GO:0051726, GO:0003682, GO:0010467, GO:0006457, regulation of chromosome structure, GO:0019904, GO:0005524, GO:0019900, GO:0035402, GO:0031267, MESH:M0518050, protein homodimerization, GO:0043130, atp-dependent dna/dna annealing]] \n", - " HALLMARK_GLYCOLYSIS-0 [[the list of genes represent a range of molecular, metabolic, and protein regulatory processes, including atpase activity, glucose binding activity, GO:0004672, transcriptional activity and activity from receptors, transporters, and enzymes. the enriched terms are \"protein binding activity\"; \"atpase activity\"; \"transcriptional activity\"; \"receptor activity\"; \"transporter activity\"; \"enzyme activity\"; and \"glucose binding activity\".\\n\\nmechanism: the genes in the list encode proteins involved in a range of processes, such as structural support, GO:0007165, regulation of transcription, metabolic pathways and transport of molecules. the underlying biological mechanism is likely related to the coordinated expression of these genes in response to a particular stimulus, or to maintain cellular homeostasis]] \n", - " HALLMARK_GLYCOLYSIS-1 [[enzyme binding activity, identical protein binding activity, dna binding activity, GO:0042803, heparin binding activity, atp binding activity, protein kinase binding activity, phosphatase binding activity, cyclin binding activity, protein phosphatase binding activity, GO:0004722, actin binding activity, lbd domain binding activity, actin filament binding activity, GO:0008083, chromatin binding activity, hyaluronic acid binding activity, GO:0004197, ubiquitin binding activity, cyclosporin a binding activity, mannose-binding activity, heparan sulfate binding activity, heme binding activity, GO:0016887, transition metal ion binding activity, GO:0031545, GO:0016615, GO:0004148, GO:0004784, transcription core]] \n", - " HALLMARK_HEDGEHOG_SIGNALING-0 [[protein/lipid binding activity, GO:0003700, GO:0010468, GO:0051246, positive/negative regulation of cellular component organization, GO:0030036, GO:0030833, GO:0001525, GO:0090630, GO:0019219, GO:0007160]] \n", - " HALLMARK_HEDGEHOG_SIGNALING-1 [[acetylcholine binding activity, GO:0003990, GO:0005096, rna polymerase ii-specific dna-binding transcription factor binding activity, GO:0003714, GO:0017053, GO:0007165, GO:0006351, GO:0007155, GO:0016477, GO:0001525, GO:0035556, GO:0019219, GO:0006468]] \n", - " HALLMARK_HEME_METABOLISM-0 [[dna-binding, rna-binding, GO:0019899, GO:0019901, GO:0019903, protein homodimerization, GO:0048729, GO:0006468]] \n", - " HALLMARK_HEME_METABOLISM-1 [[GO:0003677, GO:0005515, GO:0016310, GO:0003824, GO:0005215, MESH:M0496924, vesicular pathways, cytoskeletal pathways, GO:0046872, GO:0003723, GO:0030544, GO:0042802, GO:0008013, phosphatidylinositol-4 binding, GO:0035612, rna polymerase ii dna binding, GO:0042393, GO:0019901, tyrosine-protein kinase activity, GO:0061630, GO:0003713, fibronectin leucine-rich-repeat sense-specific binding, endothelial differentiation-specific factor binding, fatty-acid binding, heme-binding, GO:0051537, GO:0050661, GO:0070742, MESH:D012330]] \n", - " HALLMARK_HYPOXIA-0 [[this is a list of genes of known or suspected functions in a variety of processes, ranging from dna binding and transcription regulation to enzyme binding, metabolic activity, GO:0005102, and structural protein formation. commonly enriched terms include dna binding, transcription regulation, GO:0019899, and protein binding. mechanism: a variety of processes are involved in these gene functions, including dna replication and repair, protein folding and conformational change, receptor binding and signal transduction, metabolic activity, structural protein formation]] \n", - " HALLMARK_HYPOXIA-1 [[dna-binding transcription activity, GO:0003714, GO:0016564, GO:0016563, rna polymerase ii-specific, protein binding activity, GO:0042803, platelet-derived growth factor binding activity, GO:0030291, GO:0046982, GO:0004197, protein kinase binding activity, GO:0019887, GO:0004725, cyclin binding activity, GO:0004693, GO:0035403, phosphatidylinositol-3-kinase activity, nad+]] \n", - " HALLMARK_IL2_STAT5_SIGNALING-0 [[GO:0005096, dna-binding transcription activator/repressor activity, protein binding activity, ligand binding activity, identical protein binding activity, bh3 domain binding activity, phosphatidylinositol binding activity, GO:0016787, atp binding activity, atpase-coupled intramembrane lipid transport activity, amyloid-beta binding activity, hsp90 protein binding activity, s100 protein binding activity, cadherin binding activity, GO:0038023, GO:0005125, GO:0005021, GO:0004896, identical protein binding activity, GO:0008233, heat shock protein]] \n", - " HALLMARK_IL2_STAT5_SIGNALING-1 [[dna-binding transcription activity, protein kinase binding activity, small gtpase binding activity, interleukin-binding activity, GO:0004896, signaling receptor binding activity, rna binding activity, gtp binding activity, GO:0004197, identical protein binding activity, protein domain specific binding activity, GO:0046982]] \n", - " HALLMARK_IL6_JAK_STAT3_SIGNALING-0 [[cytokine binding activity, protein binding activity, kinase binding activity, signaling receptor binding activity, GO:0004675, cell adhesion molecule binding activity, interleukin-receptor activity, GO:0004725, tir domain binding activity, ubiquitin protein ligase binding activity, GO:0008284, GO:0032768, GO:0009966, GO:0090276, GO:0045597, GO:0010604, GO:0098542, GO:0009612, GO:0001819, GO:0031349]] \n", - " HALLMARK_IL6_JAK_STAT3_SIGNALING-1 [[cytokine binding activity, GO:0004896, GO:0008083, cell adhesion molecule binding activity, chemokine (c-x3-c) binding activity, GO:0006952, signaling receptor binding activity, GO:0000988, identical protein binding activity, phosphatidylinositol binding activity, heparin binding activity, lipid binding activity, c-c chemokine binding activity, dna binding activity, GO:0005096, sh3 domain binding activity, ephrin receptor binding activity, transforming growth factor beta receptor binding activity, ubiquitin-like protein ligase binding activity, enzyme binding activity, calcium-dependent protein binding activity, protease binding activity]] \n", - " HALLMARK_INFLAMMATORY_RESPONSE-0 [[GO:0004930, GO:0005125, GO:0003700, GO:0005216, receptor binding activity, GO:0008083, cell adhesion molecule binding activity, signalling receptor binding activity, GO:0003714, enzymatic activity, phospholipid binding activity, peptide hormone receptor binding activity, GO:0003924]] \n", - " HALLMARK_INFLAMMATORY_RESPONSE-1 [[atp binding activity, chemokine/chemokine receptor/chemokine receptor binding activity, cytokine/cytokine binding activity/cytokine receptor activity, dna binding activity/dna-binding transcription factor activity, GO:0004930, identical protein binding activity, ion transport/ion transporter activity, peptide/peptide receptor binding activity, phospholipid binding activity, GO:0019887, signaling receptor binding activity, GO:0000988, GO:0022857]] \n", - " HALLMARK_INTERFERON_ALPHA_RESPONSE-0 [[immunologic processes, GO:0098609, GO:0006952, cellular response, positive regulation, rna polymerase ii specific, GO:0003677, GO:0003723, protein homodimer]] \n", - " HALLMARK_INTERFERON_ALPHA_RESPONSE-1 [[GO:0003713, rna binding activity, dna binding activity, identical protein binding activity, GO:0061630, zinc ion binding activity, GO:0042803, double-stranded rna binding activity, heparin binding activity, GO:0030701, GO:0004175, cxcr chemokine receptor binding activity, tap binding activity, peptide antigen binding activity, gtp binding activity, GO:0033862, GO:0004197, amyloid-beta binding activity, macrophage migration inhibitory factor binding activity, GO:0004550, GO:0016064, GO:0140374, GO:0071345, GO:0046597, positive regulation of]] \n", - " HALLMARK_INTERFERON_GAMMA_RESPONSE-0 [[protein binding activity, enzyme binding activity, dna-binding transcription activity, GO:0006200, protein homodimerization, kinase regulation, protein dimerization.\\nmechanism: these genes are likely involved in the regulation of gene expression cell signaling pathways, enabling an array of signaling activities that help to maintain cellular homeostasis]] \n", - " HALLMARK_INTERFERON_GAMMA_RESPONSE-1 [[GO:0016887, dna binding activity, gtp binding activity, peptide antigen binding activity, GO:0004252, dna-binding transcription activity, GO:0005125, GO:0008009, GO:0004896, GO:0038023, GO:0004930, rna binding activity, enzyme binding activity, GO:0046983, phosphorylation-dependent protein binding activity, GO:0019887, GO:0140311, toll-interleukin receptor (tir) domain binding activity, signaling receptor binding activity, and]] \n", - " HALLMARK_KRAS_SIGNALING_DN-0 [[GO:0004930, GO:0042803, calcium ion binding activity, sodium:potassium:chloride transporter activity, GO:0004683, platelet-derived growth factor activity, GO:0005007, cytoskeletal protein binding activity, GO:0015171, n6-threonylcarbamylade adenine dinucleotide synthetase activity, GO:0043273, intracellular transport activity, signal transduction activity, GO:0016887, GO:0004175, GO:0016491, GO:1990817, GO:0004958, beta-caten]] \n", - " HALLMARK_KRAS_SIGNALING_DN-1 [[the list of genes is significantly enriched for dna-binding activities, calcium ion binding activities, identical protein-binding activities, GO:0046982, GO:0016887, and g protein-coupled receptor activities.\\n\\nmechanism:\\nthe underlying biological mechanism likely involves a complex, dynamic interaction between various proteins, MESH:D004798, and ions, driven by a variety of dna-binding, calcium-binding, and atp-binding activities, resulting in the recruitment of additional proteins to form heterodimers, thereby leading to protein synapsis cell signaling]] \n", - " HALLMARK_KRAS_SIGNALING_UP-0 [[atp binding activity, atpase-coupled intramembrane transport, GO:0048018, dna-binding transcription regulation, protein domain binding activity, enzyme binding activity, GO:0005125, GO:0007165, GO:0007155, GO:0016477, GO:0030154, MESH:D048788]] \n", - " HALLMARK_KRAS_SIGNALING_UP-1 [[receptor binding activity, identical protein binding activity, GO:0001216, enzyme binding activity, protein domain specific binding activity, protein kinase binding activity, ligand binding activity, atp binding activity, cytoskeletal protein binding activity, cell adhesion molecule binding activity, GO:0004930, transmembrane transporter binding activity, GO:0008233, dna binding activity, GO:0004252, histone binding activity, signal transduction activity]] \n", - " HALLMARK_MITOTIC_SPINDLE-0 [[actin binding activity, atp binding activity, atpase binding activity, GO:0098632, dynein complex binding activity, gamma-tubulin binding activity, gtp binding activity, gtpase binding activity, guanyl ribonucleotide binding activity, GO:0003924, GO:0005085, kinetochore binding activity, GO:0060090, GO:0140677, myosin binding activity, phosphatidylcholine binding activity, GO:0019904, GO:0042803, GO:0004672, GO:0004674, small gtpase binding activity]] \n", - " HALLMARK_MITOTIC_SPINDLE-1 [[this set of genes are involved in activities, processes and signaling pathways related to intracellular motion such as transport within cells (microtubule/kinesin/dynein binding, GO:0005096, GO:0008092, motor protein activity), cell cycle activities (centrosome duplication, GO:0019899, protein homodimerization, GO:0019902, GO:0003682, GO:0043515, GO:0005516, formin binding, atpase/atp hydrolysis regulatory activity), and cell-cell signaling (jun kinase kinase kinase activity, map-kinase scaffolding, GO:0042608, GO:0045296, GO:0051879, GO:0097016, GO:0005680, GO:0051059, rna binding).\\n\\nmechanism: these genes enable a wide range of activities and processes related to intracellular motion and cell-cell signaling that are either directly or indirectly connected to the assembly, MESH:M0030663, and disassembly of cytoskeletal structures, MESH:D014404, and cellular organelles. these activities can promote cell cycle progression, GO:0008283, and/or cell-cell signaling]] \n", - " HALLMARK_MTORC1_SIGNALING-0 [[protein binding activity, dna binding activity, enzyme binding activity, GO:0060090, GO:0140677, GO:0042803, domain binding activity, GO:0016491, protein kinase binding activity, phosphatidylinositol binding activity, GO:0016504, GO:0003714, nuclear androgen receptor binding activity, nf-kappab binding activity, ubiquitin protein ligase binding activity, phosphotyrosine residue binding activity, GO:0016564, GO:0003743, peptidyl-proinalyl cistrans isomerase activity]] \n", - " HALLMARK_MTORC1_SIGNALING-1 [[protein-protein interaction, atp binding activity, GO:0042803, GO:0016887, protein kinase binding activity, ubiquitin protein ligase binding activity, GO:0060090, anion binding activity, chemical oxidoreductase activity, protein domain specific binding activity, gtp binding activity, dna binding activity, rna binding activity, transcription regulation activity, GO:0007165, chromatin binding activity, phospholipid binding activity, GO:0004017, lipoprotein particle binding activity, GO:0008233, actin filament binding activity, fad binding activity, steroid hydrolase activity, rna stem-loop binding activity, GO:0022857, nf-kappab binding activity, coenzyme a binding activity, protein n-terminal phospho-seryl-prolyl pept]] \n", - " HALLMARK_MYC_TARGETS_V1-0 [[GO:0003723, GO:0044183, dna binding/recognition, protein homodimerization, GO:0003678, GO:0019904, MONDO:0000179, GO:0042393, cytoplasmic protein binding, GO:0005524, GO:0006281]] \n", - " HALLMARK_MYC_TARGETS_V1-1 [[GO:0003677, GO:0003723, GO:0019904, GO:0003682, GO:0019899, protein folding chaperone activities, atp binding activity, mrna 3'-utr binding activity, identical protein binding activity, GO:0004869, GO:0140693, GO:0140713, heparan sulfate binding activity, peptidyl-prolyl isomerase activity, cyclin binding activity, GO:0004693, nuclear localization sequence binding activity, magnetic ion binding activity, histone methyltransferase binding activity, mrna 5'-utr binding activity, GO:0033677, MESH:D012321]] \n", - " HALLMARK_MYC_TARGETS_V2-0 [[rna-binding, GO:0036211, GO:0015031, cell signaling, GO:0006412, genetic information regulation, protein bridging, chromatin regulation, transcription regulation, GO:0003676, mitochondrial functions]] \n", - " HALLMARK_MYC_TARGETS_V2-1 [[rna binding activity, ribosomal rrna processing, mrna and/or rrna catabolism/stability, regulation of transcription/translation, regulation of signal transduction and metabolism processes, regulation of cell cycle/proliferation, protein modification/regulation, GO:0005634, GO:0005829, GO:0005840, GO:0005739]] \n", - " HALLMARK_MYOGENESIS-0 [[calcium ion binding activity, identical protein binding activity, actin filament binding activity, GO:0042803, signaling receptor binding activity, atp binding activity, gtp binding activity, dna binding activity, GO:0019887]] \n", - " HALLMARK_MYOGENESIS-1 [[calcium binding activity, enzyme binding activity, dna binding activity, atp binding activity, GO:0042803, protein domain-specific binding activity, gtp binding activity, actin binding activity, GO:0008160, small gtpase activator activity, transmembrane transporter binding activity, GO:0004016, c3hc4-type ring finger domain-binding activity, GO:0060090, GO:0005096]] \n", - " HALLMARK_NOTCH_SIGNALING-0 [[this list of genes is associated with several biological processes related to the regulation of gene expression, such as notch receptor processing, amyloid-beta formation, proteolysis, regulation of cell differentiation, canonical wnt signaling pathway, protein ubiquitination, scf-dependent proteasomal ubiquitin-dependent protein catabolic process, and positive regulation of transcription by rna polymerase ii. the underlying biological mechanism is likely related to the role of these genes in transcription and post-transcriptional gene regulation. enriched terms include: gene expression regulation, GO:0007220, GO:0034205, GO:0006508, GO:0045595, GO:0060070, GO:0016567, GO:0031146, GO:0045944]] \n", - " HALLMARK_NOTCH_SIGNALING-1 [[GO:0016567, GO:0031146, GO:0007219, GO:0036211, GO:0010468, GO:0030335, GO:0008284, GO:0045596]] \n", - " HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 [[acetyl-coa transferase activity, GO:0003995, aldehyde dehydrogenase activity, atpase binding activity, GO:0004129, GO:0009055, GO:0004300, fad binding activity, GO:0003924, heme binding activity, identical protein binding activity, lipid binding activity, metal ion binding activity, GO:0003958, GO:0016491, GO:0004738, pro]] \n", - " HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 [[GO:0009055, protein homodimerization, GO:0003924, GO:0000295, phosphoprotein binding activity, mitochondrial respiratory chain activity, proton-transporting atp synthase activity, mitochondrial ribosome binding activity]] \n", - " HALLMARK_P53_PATHWAY-0 [[dna binding activity, rna polymerase ii-specific dna-binding transcription factor binding activity, transcription regulation, protein binding activity, enzyme binding activity]] \n", - " HALLMARK_P53_PATHWAY-1 [[GO:0007165, MESH:D005786, GO:0005515, GO:0019899, GO:0016791, GO:0000988, GO:0007155, growth factor binding. \\nmechanism: these genes are involved in the regulation of gene expression and cellular processes by modulating signal transduction, binding proteins, and enzymes, as well as activating phosphatase activity, transcription factor activity and growth factor binding]] \n", - " HALLMARK_PANCREAS_BETA_CELLS-0 [[atp binding activity, GO:0019829, GO:0016477, GO:0044249, GO:0071333, GO:0090398, GO:0042742, GO:0005789, e-box binding activity, GO:0015149, GO:0002551, GO:0043303, GO:0008233, GO:0008607, GO:0045597, positively regulation of cellular biosynthetic process, positively regulation of glycolytic process, positively regulation of insulin secretion, positively regulation of macromolecule metabolic process, positively regulation of type b pancreatic cell development, positive regulation of cellular]] \n", - " HALLMARK_PANCREAS_BETA_CELLS-1 [[GO:0098609, GO:0032502, differentiation, UBERON:0000061, transcription regulation, MESH:D012319, GO:0007165, GO:0043170, protein expression, cell signaling, protein production]] \n", - " HALLMARK_PEROXISOME-0 [[after term enrichment analysis on the gene summaries, the following terms were found to be enriched: atp binding activity, atpase-coupled activity, GO:0042803, identical protein binding activity, enzyme binding activity, GO:0005319, GO:0016887, and metal ion binding activity.\\n\\nmechanism: the enriched terms suggest a biological mechanism that involves energy production and transport, GO:0007165, and protein interactions and formation of protein complexes. these processes are necessary for various cellular processes such as metabolism, GO:0007585, GO:0098754, GO:0040007]] \n", - " HALLMARK_PEROXISOME-1 [[cell metabolic process, GO:0090304, GO:0005515, GO:0003677, GO:0016485, GO:0042446, GO:0006694, GO:0005524, GO:0006200, protein homodimerization, GO:0019901, GO:0003714, GO:0003712, cyclin binding activity, rna binding activity, protein phosphatase binding activity, sulphatide binding activity, magnesium ion binding activity, GO:0043621, MESH:M0518050, protein transmembrane]] \n", - " HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 [[cellular process regulations, GO:0003824, protein and peptide regulation, protein domain modification]] \n", - " HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 [[GO:0007165, GO:0019900, GO:0003924, GO:0004721, transcription factor activation, GO:0004620, GO:0005102, MESH:D054875, MESH:D000107, GO:0006915, GO:0016477, negative regulation of proliferation]] \n", - " HALLMARK_PROTEIN_SECRETION-0 [[protein binding activity, atp binding activity, gtp-dependent protein binding activity, GO:0003924, signal sequence binding activity, clathrin binding activity, small gtpase binding activity]] \n", - " HALLMARK_PROTEIN_SECRETION-1 [[atp binding activity, GO:0042803, smarc protein binding activity, GO:0003924, gtp binding activity, GO:0005096, enzyme binding activity, GO:0004197, protein domain specific binding activity, phosphatidylinositol-4-phosphate binding activity, protein kinase binding activity, GO:0008320, calcium-dependent protein binding activity, metal ion binding activity, dopaminergic receptor binding activity, ubiquitin-like protein ligase binding activity, GO:0005484, phosphatidylinositol-3,4,5-trisphosphate binding activity, phosphatidylinositol-3,5-bisphosphate binding activity, signaling receptor binding activity, GO:0005198, syntaxin binding activity, GO:0005484]] \n", - " HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 [[the human genes provided are mostly involved in redox homeostasis, GO:0006952, and cell organization. there is also involvement in processes related to the maintenance of the blood-brain barrier, GO:0009650, and metabolism of hormones, MESH:D008055, and glucose. there are an abundance of terms related to transmembrane transport, MESH:D010088, heme and iron metabolism, GO:0019511, and gluthathione metabolism.\\n\\nmechanism:\\nredox homeostasis is regulated by a network of enzymatic and substrate-dependent processes. these processes include cellular antioxidant defense, removal of superoxide radicals and peroxides, GO:0061691, and regulation of the balance between oxidant production and scavenging. transport genes are employed to promote transmembrane transport of xenobiotics and lipids, like abcc1, atox1, and glrx. iron and heme metabolism is facilitated by genes like ftl, hmox2, and mpo. peptidyl-proline hydroxylation is regulated by genes like egln2 and mgst1, while glutathione metabolism is controlled by genes like g]] \n", - " HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 [[GO:0045454, GO:0019899, protein homodimerization, GO:0015035, GO:0004602, GO:0003954, atp binding activity, identical protein binding activity, transition metal ion binding activity, GO:0016209, heme binding activity, ubiquitin-specific protease binding activity, GO:0047499, heparin binding activity, GO:0004601, GO:0004784, GO:0008811, GO:0004096]] \n", - " HALLMARK_SPERMATOGENESIS-0 [[GO:0140677, GO:0004672, cellular component activity, binding activity, GO:0008233, nucleosome binding activity, ion binding activity, phosphatase binding activity, GO:0051726, apoptosis regulation, GO:0007155, GO:0007399, transcription regulation, GO:0015031, GO:0009988, MESH:D005786]] \n", - " HALLMARK_SPERMATOGENESIS-1 [[all of the genes are involved in regulation of various metabolic processes and signaling pathways, with most of them associated with binding activities and regulation of protein activities. enriched terms include: protein binding activity, atp binding activity, protein-folding chaperone binding activity, chromatin binding activity, GO:0046976, transcription corepressor binding activity, GO:0004672, GO:0060090, enzyme binding activity, GO:0140677, GO:0098632, GO:0004888, gtp binding activity, signaling receptor binding activity, ribonucleoprotein complex binding activity, myosin light chain binding activity, GO:0017116, GO:0003689, GO:0051131, peptide alpha-n-acetyltransferase activity. mechanism: the genes are involved in various metabolic processes and signaling pathways, by regulating protein activities through different binding activities and histone methyltransferase activity. some of these activities regulate certain processes based on gtp binding, while others are involved in cell-cell adhesion, transmembrane signaling and chaperone-mediated protein complex assembly]] \n", - " HALLMARK_TGF_BETA_SIGNALING-0 [[GO:0005524, GO:0048185, GO:0046332, protein phosphatase/kinase activity, smad signaling, bmp signaling, GO:0006351, MESH:D012319, GO:0005515, GO:0007165, GO:0007049, GO:0008152, GO:0007155]] \n", - " HALLMARK_TGF_BETA_SIGNALING-1 [[dna-binding activity, transcription regulation, GO:0035556, GO:0004674, smad binding activity, positive/negative regulation of rna/protein metabolic process, GO:0006468, receptor tyrosine kinase binding activity, GO:0007165, GO:0042803, GO:0061630, GO:0031326, GO:0009966, GO:0006357, GO:0090092]] \n", - " HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 [[the list of genes provided are involved in a broad set of functions related to gene transcription or regulation of transcription factors, cell signaling, binding activities and metabolic processes. the enriched terms for this gene set include dna-binding transcription factor activity, rna polymerase ii transcription regulatory region sequence-specific binding, GO:0003924, chemokine receptor binding activity, signaling receptor binding activity, protein kinase binding activity, enzyme binding activity, identical protein binding activity and protease binding activity.\\n\\nmechanism: the underlying biological mechanism for this list of genes is likely related to control of gene expression, as well as control of protein interactions that mediate cell signaling and metabolic processes. additionally, the functions related to binding activities suggest many of the genes are involved in cell-to-cell communication and cell adhesion]] \n", - " HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 [[GO:0001216, transcription regulatory region sequence-specific dna-binding, gtp binding activity, enzyme binding activity, identical protein binding activity, signal receptor binding activity, GO:0016791, protein kinase binding activity, GO:0005125, GO:0008083]] \n", - " HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 [[rna binding activity, dna binding activity, protein binding activity, GO:0140693, identical protein binding activity, dna-binding transcription factor binding activity, GO:0042803, atpase binding activity, GO:0016887, enzymatic activity, GO:0003713, GO:0008494, protein phosphatase binding activity, peptidyl-prolyl primase activity, transcription cis-regulatory region sequence-specific activity]] \n", - " HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 [[enzyme binding activity, rna binding activity, protein binding activity, transmembrane transporter binding activity, dna binding activity, protein kinase binding activity, box h/aca snorna binding activity, protein phosphatase binding activity, telomerase rna binding activity, GO:0042803, GO:0046982, transcription factor binding activity, atp binding activity, GO:0016887, GO:0003724, GO:0003756, ubiquitin protein ligase binding activity, GO:0004518, adenyl ribonucleotide binding activity, heat shock protein binding activity]] \n", - " HALLMARK_UV_RESPONSE_DN-0 [[gtp binding activity, enzyme binding activity, dna-binding transcription factor binding activity, phosphotyrosine residue binding activity, cyclin binding activity, receptor-ligand interaction, protein-protein interaction, smad binding protein, nf-kappab binding protein, growth factor binding protein]] \n", - " HALLMARK_UV_RESPONSE_DN-1 [[GO:0001216, rna polymerase ii-specific activity, nf-kappab binding activity, microtubule binding activity, actin binding activity, identical protein binding activity, smad binding activity, GO:0005243, GO:0005388, receptor binding activity, GO:0005096, histone binding activity, ap-1 transcription factor binding activity, vitamin d receptor binding activity, cytoplasmic protein binding activity, GO:0004930, platelet-derived growth factor binding activity, enzyme binding activity, protease binding activity, phospholipid binding activity, GO:0004672, GO:0004674, intracellular protein binding activity]] \n", - " HALLMARK_UV_RESPONSE_UP-0 [[protein binding activity, atp binding activity, rna binding activity, dna binding activity, receptor binding activity, enzyme binding activity, GO:0005548, GO:0098609, GO:0007268, GO:0097190, GO:0005138, GO:0042110, overall cellular metabolism, MESH:D005786]] \n", - " HALLMARK_UV_RESPONSE_UP-1 [[enzyme binding activity, GO:0016787, GO:0016740, GO:0038023, dna binding activity, rna binding activity, GO:0000988, protein binding activity]] \n", - " HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 [[protein binding activity, GO:0003700, rna polymerase ii-specific dna-binding transcription factor binding activity, notch binding activity, pdz domain binding activity, GO:0042813, ubiquitin protein ligase binding activity, beta-catenin binding activity, GO:0003713, histone deacetylase binding activity, GO:0048019, transcription corepressor binding activity, GO:0060090, GO:0004407, cholesterol binding activity]] \n", - " HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 [[GO:0007165, GO:0010468, GO:0006351, GO:0001932, GO:0031647, GO:0016477, GO:0008283, GO:0032502, GO:0006508]] \n", - " T cell proliferation-0 [[protein binding activity, enzyme binding activity, protein kinase binding activity, interleukin binding activity, phosphorylation-dependent protein binding activity, GO:0001216, GO:0042803, nucleic acid binding activity, GO:0005001, GO:0048018, GO:0004725, GO:0005125, cytoskeletal protein binding activity, cytokin receptor activity, GO:0030335]] \n", - " T cell proliferation-1 [[cation binding activity, diacylglycerol binding activity, enzyme binding activity, GO:0046982, receptor binding activity, protein kinase binding activity, phosphorylation-dependent protein binding activity, phosphotyrosine residue binding activity, GO:0005001, protease binding activity, cytoskeletal protein binding activity, phosphatidylinositol 3-kinase binding activity, GO:0061630, GO:0004888, GO:0043621, GO:0004697, zinc ion binding activity, transmembrane atp-gated monoatomic cation channel activity, purin]] \n", - " Yamanaka-TFs-0 [[dna-binding, GO:0000988, rna polymerase ii-specific, nucleic acid binding activity, transcription cis-regulatory region binding activity, GO:0010468, GO:0009889]] \n", - " Yamanaka-TFs-1 [[GO:0006351, GO:0010468, dna-binding, GO:0000785, GO:0005829, GO:0005654, GO:0005667, GO:0009966, GO:0045944, GO:0001714]] \n", - " amigo-example-0 [[the list of genes provided is involved in multiple processes related to cell adhesion, growth factor binding, protein phosphorylation, tissue development, and regulation of cholesterol homeostatis and transcytosis. the underlying biological mechanism likely involves multiple pathways, including cellular response to lipopolysaccharide, cell-matrix adhesion, and negative regulation of low-density lipoprotein. enriched terms include cell adhesion, cell surface receptor signaling, collagen binding activity, GO:0019838, GO:0042157, GO:1902533, GO:0046983, GO:0006468, regulation of bmp signaling, GO:0042127, GO:0010468, GO:0009966, regulation of very-low-density lipoproten particle clearance, GO:0045056]] \n", - " amigo-example-1 [[GO:0051246, GO:0001952, GO:0042127, GO:0042981, GO:0043269, GO:0030193, GO:0007166, GO:0050804, GO:0005201, GO:0007160, organ development and differentiation, regulation of hormone pathways]] \n", - " bicluster_RNAseqDB_0-0 [[genes in this list are involved in a range of activities, including calcium ion binding activity, metal ion binding activity, protein domain specific binding activity, identical protein binding activity, dna-binding transcription factor activity, and several others. the underlying biological mechanism appears to be related to structural support and regulation of cellular processes. enriched terms include: metal ion binding, GO:0005509, GO:0005515, GO:0000988, dna-binding, GO:0042802, domain specific protein binding]] \n", - " bicluster_RNAseqDB_0-1 [[GO:0001216, protein kinase binding activity, metal ion binding activity, calcium ion binding activity, transcription co-regulator activity, responsive to stimuli]] \n", - " bicluster_RNAseqDB_1002-0 [[GO:0051015, GO:0000146, GO:0051371, GO:0003785, GO:0005523, GO:0017022, GO:0031432, GO:0004111]] \n", - " bicluster_RNAseqDB_1002-1 [[calcium-dependent protein binding activity, atp binding activity, actin filament binding activity, actin monomer binding activity, transmembrane transporter binding activity, GO:0016567, GO:0061630, tropomyosin binding activity, identical protein binding activity, GO:0008375, protein phosphatase 1 binding activity, zinc ion binding activity, troponin c binding activity, troponin i binding activity, actin binding activity, tropomyosin binding activity, GO:0001216, sequence-specific double-stranded dna binding activity]] \n", - " endocytosis-0 [[GO:0004674, lysophosphatidic acid binding activity, sulfatide binding activity, GO:0016790, cadherin binding activity, GO:0032456, sh3 domain binding activity, GO:0051260, macropinosome formation, GO:0031623, transferring transport, t cell receptor binding activity, GO:0005085, GO:0044351, GO:0001773, GO:0007520, GO:0018105, GO:0010468, vascular endothelial growth factor receptor signalling pathway, GO:0051128, GO:0007042, GO:0045807, GO:0051090]] \n", - " endocytosis-1 [[GO:0006468, GO:0051260, cell signaling, GO:0005480, GO:0016567, endocytosis/exocytosis, GO:0005102, GO:0010468, vesicle buddying, GO:0007165, GO:0050727, GO:0035556, gtp-dependent pathways, receptor signaling, canonical inflammasome signaling]] \n", - " glycolysis-gocam-0 [[protein binding activity, atp binding activity, peptidoglycan binding activity, GO:0051156, GO:0002639, GO:0010595, GO:0006002, GO:0061615, GO:0030388, GO:0046166, fructose binding activity, GO:0004332, MONDO:0009295, GO:0004807, disordered domain specific binding activity, GO:0004866, GO:0046835, GO:0072655, maintenance of protein location in]] \n", - " glycolysis-gocam-1 [[protein binding activity, atp binding activity, ubiquitin protein ligase binding activity, fructose binding activity, GO:0042803, GO:0004618, GO:0004619, GO:0004807, GO:0004396, GO:0004332, GO:0004634, GO:0003872, GO:0004347, GO:0006096, GO:0006002, GO:0046166, GO:0046835, GO:0072655, GO:0072656, GO:0071456, negative regulation of]] \n", - " go-postsynapse-calcium-transmembrane-0 [[GO:0005262, GO:0005245, regulation of intracellular calcium concentrations, GO:0098960, GO:2000311, g protein-coupled receptor signaling, GO:0070588, GO:0015276]] \n", - " go-postsynapse-calcium-transmembrane-1 [[GO:0005261, acetylcholine-gated channel activity, GO:0022849, nmda selective glutamate receptor activity, GO:0005245, GO:1990454, GO:0035235, GO:0071318, regulation of]] \n", - " go-reg-autophagy-pkra-0 [[protein kinase binding activity, GO:0004672, GO:0004674, GO:0001934, GO:0010556]] \n", - " go-reg-autophagy-pkra-1 [[the genes listed above are involved in a variety of processes, including negative and positive regulation of transport, GO:0051246, cell surface receptor signaling, and regulation of gene expression. these genes also have a variety of functions, including protein kinase binding activity, chromatin binding activity, GO:0030295, and metal ion binding activity. the enriched terms that describe these genes include: protein binding activity; protein kinase binding activity; signal transduction; positive and negative regulation of transport; chromatin binding activity; and protein serine/threonine kinase activity.\\n\\nmechanism: these gene products are part of, or act upstream of a variety of signaling pathways, all of which are involved in cell growth, MESH:D008283, and response to environmental stimuli. the pathways typically involve post-translational modifications of target proteins by phosphorylation, as well as formation or breakdown of protein-containing complexes. these signaling pathways ultimately affect gene expression and determine the type of output which a particular cell will produce]] \n", - " hydrolase activity, hydrolyzing O-glycosyl compounds-0 [[the genes in the list are involved in many processes relating to glycan metabolism and synthesis, such as glycoside catabolic process, GO:0006027, GO:0019377, GO:0005980, and sucrose catabolic process. other enriched terms are dihydroceramidase activity, hyaluronic acid binding activity, GO:0004415, GO:0030212, GO:0046373, GO:0004571, GO:0006487, and protein homodimerization activity.\\n\\nmechanism: glycan metabolism and synthesis involves several enzymes with diverse activities such as alpha-glucosidases, MESH:D043323, MESH:D001617, MESH:D001619, n-acetylglucosaminyltransferases. these enzymes hydrolyze transfer carbohydrate building blocks to form modify carbohydrates for a variety of cellular functions]] \n", - " hydrolase activity, hydrolyzing O-glycosyl compounds-1 [[GO:0005975, GO:0046477, GO:0006516, oligo-saccharide catabolic process, GO:0006869, GO:0015144, GO:0046982, protein domain specific binding activity, GO:0006629, GO:0016139, GO:0030214, GO:0006032]] \n", - " ig-receptor-binding-2022-0 [[immunoglobulin receptor binding activity, antigen binding activity, GO:0004715, phosphatidylcholine binding activity, phosphotyrosine residue binding activity]] \n", - " ig-receptor-binding-2022-1 [[GO:0042803, GO:0007160, phosphorylation-dependent signaling, GO:0019901, GO:0034988, GO:0030098, GO:0098609, GO:0001784, GO:0042834, integrin signaling, GO:0006909]] \n", - " meiosis I-0 [[GO:0003677, atp dependent activity, GO:0003682, GO:0005634, protein export, transcriptional regulation, GO:0003690, GO:0003697, GO:0006281, GO:0004518, MESH:D011995, GO:0007059, GO:0000278, intrinsic apoptotic signaling, regulation of telomere maintenance.\\nmechanism: the genes identified are likely playing roles in a variety of dna metabolic pathways, including dna repair, double-stranded dna break repair, homologous recombination, transcriptional regulation, and mitotic cell cycle processes. these pathways likely enable cellular replication and maintenance of genomic integrity, as well as control of gene expression and apoptosis]] \n", - " meiosis I-1 [[GO:0003677, GO:0003690, GO:0042802, GO:0006259, GO:0006302, GO:0007131, meiotic chromosome segregation and pairing, GO:0007283, GO:0000712, GO:0051026, GO:0016925, GO:0007130]] \n", - " molecular sequestering-0 [[calcium ion binding activity, identical protein binding activity, GO:0140311, ubiquitin protein ligase binding activity, cellular response, GO:0001932, GO:0010359, GO:0097214, GO:0010468, GO:0035456]] \n", - " molecular sequestering-1 [[GO:0005515, GO:0046872, GO:0043167, GO:0010468, GO:0001932, cell death pathways, GO:0009059, GO:0046907, cellular response to infection and inflammation]] \n", - " mtorc1-0 [[protein binding activity, dna binding activity, enzyme binding activity, GO:0060090, GO:0140677, GO:0042803, domain binding activity, GO:0016491, protein kinase binding activity, phosphatidylinositol binding activity, GO:0016504, GO:0003714, nuclear androgen receptor binding activity, nf-kappab binding activity, ubiquitin protein ligase binding activity, phosphotyrosine residue binding activity, GO:0016564, GO:0003743, peptidyl-proinalyl cistrans isomerase activity]] \n", - " mtorc1-1 [[protein binding activity, GO:0005215, dna binding activity, rna binding activity, atp binding activity, peptide activity, GO:0003824, enzyme binding activity, phosphoprotein binding activity, GO:0016563, GO:0016787, GO:0016491, GO:0004017, identical protein binding activity, GO:0060090, GO:0007165, signal receiving activity, GO:1901987, metabolism regulation, cell growth control]] \n", - " peroxisome-0 [[peroxisome biogenesis, atp binding activity, GO:0016887, ubiquitin-dependent protein binding activity, GO:0016558, GO:0050821, GO:0043335, GO:0000425, GO:0006625, protein tetramerization.\\n\\nmechanism: these gene functions are involved in a complex process involving the biogenesis and maintenance of peroxisomes, which are subcellular organelles that contain a variety of enzymes involved in metabolic processes. this process entails the function of multiple proteins working together to ferry important proteins into the peroxisomal membrane, where these proteins will become functional components of the organelle]] \n", - " peroxisome-1 [[protein binding activity, GO:0016558, peroxisome matrix targeting signal-2 binding activity, GO:0042803, GO:0008611, GO:0006631, GO:0008285, GO:0000425, GO:0032994, microtubule-based peroxisome localization.\\nmechanism: based on the functions that these genes carry out, it is likely that the genes are involved in a mechanism whereby proteins are imported into the peroxisome matrix, and the peroxisome matrix is organized, stabilized, and/or maintained in order to carry out fatty acid metabolism and pexophagy. the receptor recycling and microtubule-based localization also likely play a role in this mechanism]] \n", - " progeria-0 [[protein binding activity, dna binding activity, metal ion binding activity, GO:0003678, GO:0042803, GO:0071480, GO:0010836, GO:0007084, GO:0045071, GO:0032392, GO:0006259, GO:0009267, GO:1902570, GO:0042981, GO:0071456, GO:0032204, GO:0004222, GO:0050688, with a positive effect]] \n", - " progeria-1 [[GO:2000772, dna binding and metabolic processes, dna helicase and metal ion binding activities, protein localization to nucleolus and regulation of apoptotic processes appear to be enriched terms common to the three genes given.\\n\\nmechanism: the three genes appear to be involved in similar nucleic acid binding and regulation activities that enable the maintenance and regulation of cellular processes. this suggests an underlying molecular mechanism in which these genes interact directly to modulate a variety of cellular processes related to senescence, GO:0003677, GO:0008152, GO:0006915]] \n", - " regulation of presynaptic membrane potential-0 [[voltage-gated potassium/sodium channel activity, GO:0015276, transmembrane transporter binding activity, GO:0004930, GO:0004971, GO:0015277, GO:0035235, GO:1902476, GO:0007214, GO:0019228, GO:0042391, GO:0007268, regulation of]] \n", - " regulation of presynaptic membrane potential-1 [[GO:0005216, GO:0015276, membrane potential regulation, GO:0005249, GO:0005248, GO:0008066, GO:0004890, GO:0055074, GO:0022851, ionotropic glutamate receptor signaling, GO:1902476, GO:0051932, GO:0048167, negative regulation of smooth muscle apoptotic process, GO:0051924, GO:0086009, GO:0035249, GO:0060292, GO:0006836, GO:0050804, GO:0034220, GO:0051205, GO:0060079]] \n", - " sensory ataxia-0 [[transcription regulation, GO:0031625, GO:0003677, GO:0006027, GO:0043583, GO:0045475, GO:0007399, GO:0006457, GO:0043066, GO:0010595, GO:0002639, GO:0034214, GO:0050974, GO:0006812, GO:0015886, GO:0071260, GO:0042552, GO:0098742, GO:0006839, GO:0019226, GO:0008380, GO:0003774, GO:0061608, nuclear localization sequence binding activity, GO:0006607, GO:0003887, GO:0006284, gap-filling, protein ubiquitination.\\n\\nmechanism: analysis of the given list of genes suggests that there]] \n", - " sensory ataxia-1 [[MESH:D015533, dna-binding, rna polymrease ii-specific, dna binding activity, GO:0034214, GO:0061608, protein folding chaperone binding activity, GO:0016567, cell aggregration, GO:0098609, GO:0042552, GO:0005886, GO:0034220, GO:0030218, GO:0015886, mitochondrial transport.\\nmechanism: the eighteen human genes are involved in a variety of complex biological processes, from transcriptional regulation, through to cellular adhesion and the transport of macromolecules, including proteins, nucleic acids and heme. there is likely significant cross-talk between these various processes, particularly at the level of dna binding proteins, transcription activators, and nuclear receptor activities. this suggests that these genes are likely playing a role in the coordination of cellular processes to facilitate proper neural development and maintenance of peripheral nerve function]] \n", - " term-GO:0007212-0 [[GO:0007186, GO:0051480, GO:0006357, GO:1901214, GO:0006915, GO:0006171, GO:0006468]] \n", - " term-GO:0007212-1 [[GO:0007186, GO:0043087, GO:0060170, GO:0006171, GO:0005783, membrane localization, transcriptional regulation, GO:0007212, GO:0006874, GO:0046039, GO:0098843, protein kinase activity. \\n\\nmechanism:\\nthe g protein-coupled receptor signaling pathway is a general pathway that mediates the effects of hormones, neurotransmitters other extracellular signals in cells across a variety of tissues organs. signaling through gpcrs involves activation of g proteins, which in turn activate or inhibit effector enzymes ion channels. the commonality among these genes is that they are involved in mechanisms of gpcr signaling downstream processes such as regulation of gtpase activity, camp synthesis regulation of calcium ion concentration. the genes may also participate in membrane localization, transcriptional regulation postsynaptic endocytic zone functions. other associated activities]] \n", - " tf-downreg-colorectal-0 [[transcription activation/repression, GO:0007165, GO:0006351, GO:0007049, MESH:D012319, GO:0003682, GO:0008270, GO:0016575, protein ligase/cofactor binding]] \n", - " tf-downreg-colorectal-1 [[dna-binding transcription, GO:0016563, rna polymerase ii-specific, GO:0016564, positive/negative regulation of transcription, GO:0006351, GO:0010468, nucleic acid binding activity, sequence-specific double-stranded dna binding activity, protein kinase binding activity]] " - ] - }, - "execution_count": 60, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "def jaccard_similarity(list1, list2):\n", - " intersection = len(list(set(list1).intersection(list2)))\n", - " union = (len(list1) + len(list2)) - intersection\n", - " return float(intersection) / union\n", - "\n", - "# pivot your dataframe as before\n", - "df_pivot = df.pivot_table(index=[MODEL, METHOD, GENESET], columns=PROMPT_VARIANT, values=TERM_IDS, aggfunc=list)\n", - "df_pivot" - ] - }, - { - "cell_type": "code", - "execution_count": 61, - "id": "642589a3", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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prompt_variantmodelmethodgenesetv1v2jaccard_index
0gpt-3.5-turbonarrative_synopsisEDS-0[[GO:0032964, GO:0030198, GO:0010712, GO:0043687, GO:0006493, GO:0006508, GO:0008270]][[GO:0032964, matrix maturation, GO:0031012, MESH:D006023, MESH:D015238, zinc finger proteins, proteolytic subunits, MESH:D057057, MESH:M0465019]]0.07
1gpt-3.5-turbonarrative_synopsisEDS-1[[GO:0032964, GO:0061448, GO:0030198, GO:0030166]][[GO:0032964, GO:0030198, GO:0006457, GO:0006955]]0.33
2gpt-3.5-turbonarrative_synopsisFA-0[[GO:0006281, GO:0035825, GO:0006302, chromosome stability \\n\\nhypotheses: the enriched terms suggest that the common function of these genes is dna repair, specifically in the context of homologous recombination and double-strand break repair. the genes are part of a complex network involved in maintaining chromosome stability, which is critical for preventing mutations and malignant transformation. mutations in these genes have been linked to various forms of cancer and the fanconi anemia disorder. understanding the mechanisms by which these genes function in dna repair could provide insights into cancer development and potential therapeutic targets]][[GO:0006281, GO:0035825, fanconi anemia pathway]]0.40
3gpt-3.5-turbonarrative_synopsisFA-1[[GO:0006281, fanconi anemia pathway, GO:0035825, MESH:M0443452, genome maintenance, GO:0006302]][[GO:0006281, GO:0035825, MESH:D051856, rad51 family proteins, chromosome stability maintenance\\n\\nmechanism: these genes are involved in dna damage repair and maintenance of genome stability, particularly through homologous recombination and the formation of the fanconi anemia complementation group proteins. the rad51 family proteins and chromosomal stability maintenance are also important in these processes]]0.22
4gpt-3.5-turbonarrative_synopsisHALLMARK_ADIPOGENESIS-0[[GO:0005739, GO:0006119, GO:0022900, GO:0006091, MESH:M0496924, GO:0006631, GO:0006099, GO:0006635]][[mitochondrial function, GO:0008152, GO:0006118, GO:0006631, redox reactions]]0.08
5gpt-3.5-turbonarrative_synopsisHALLMARK_ADIPOGENESIS-1[[mitochondrial function, GO:0070469, energy production, GO:0006629, GO:0006869, GO:0005515, GO:0016049, GO:0051301, antioxidant enzyme. \\n\\nmechanism/]][[mitochondrial function; energy metabolism; lipid metabolism; electron transport chain. \\n\\nmechanism: these genes likely contribute to the production and regulation of energy in the form of atp through processes including beta-oxidation of lipids, GO:0006119, and electron transport chain activity. dysfunction or dysregulation of these genes may lead to mitochondrial dysfunction and impaired energy metabolism, which have been implicated in various diseases including neurodegenerative disorders, MONDO:0004995, MONDO:0005066]]0.00
6gpt-3.5-turbonarrative_synopsisHALLMARK_ALLOGRAFT_REJECTION-0[[chemokine signaling pathway, cytokine-cytokine receptor interaction, GO:0006955, GO:0042110, GO:0050776, GO:0006954, GO:0050900]][[GO:0005125, GO:0042110, GO:0042379, GO:0002429, GO:0032623, GO:0032609, GO:0002504, GO:0050776, GO:0030217, GO:0050900, GO:0060333, GO:0001819, GO:0002685, GO:0070098, GO:0050852]]0.16
7gpt-3.5-turbonarrative_synopsisHALLMARK_ALLOGRAFT_REJECTION-1[[MESH:D018925, MESH:D016207, t cell-mediated immunity, interferon signaling, GO:0006954, tgf-beta signaling, toll-like receptor signaling, tnf signaling]][[GO:0008009, cytokine signaling, GO:0019882]]0.00
8gpt-3.5-turbonarrative_synopsisHALLMARK_ANDROGEN_RESPONSE-0[[protein kinase activity; membrane transport; enzyme catalysis\\n\\nmechanism: these genes are involved in signal transduction and cellular metabolism, with a focus on protein kinase activity, GO:0055085, and enzyme catalysis. they play roles in the transport of various molecules across biological membranes, including fatty acids, sugars, and ions. they are also important in regulating cellular responses to extracellular stimuli, such as growth factors, MESH:D006728, and cytokines. additionally, they catalyze metabolic reactions and contribute to various metabolic pathways]][[GO:0004672, GO:0031344, GO:0008285, GO:0010468, regulation of cellular protein localization and movement]]0.00
9gpt-3.5-turbonarrative_synopsisHALLMARK_ANDROGEN_RESPONSE-1[[GO:0004672, GO:0008134, GO:0005515, GO:0007165, GO:0003824]][[GO:0004672, GO:0008134, GO:0006810, enzymatic activity, GO:0006511, GO:0061024, GO:0042445, GO:0016567]]0.18
10gpt-3.5-turbonarrative_synopsisHALLMARK_ANGIOGENESIS-0[[GO:0031012, GO:0007155, tissue development and regeneration, growth factor signaling, endothelial-specific signaling, cytokine signaling]][[GO:0030198, GO:0007155, GO:0030199, GO:0006029, GO:0045765, GO:0009611]]0.09
11gpt-3.5-turbonarrative_synopsisHALLMARK_ANGIOGENESIS-1[[ecm organization, GO:0031589, GO:0016477]][[GO:0030198, GO:0007155, GO:0007088, protein kinase activity regulation, GO:0070848, cellular response to transforming growth factor beta stimulus\\n\\nmechanism: the genes listed are involved in the organization of the extracellular matrix and cell adhesion. specifically, they play roles in binding to and regulating the spacing of collagen fibrils, inhibiting proteases, promoting cell-cell and cell-matrix interactions, and regulating mitosis and protein kinase activity. growth factors and transforming growth factor beta are also involved in signal transduction pathways that are regulated by these genes]]0.00
12gpt-3.5-turbonarrative_synopsisHALLMARK_APICAL_JUNCTION-0[[GO:0005884, GO:0007155, GO:0007010, GO:0008360, GO:0007165]][[GO:0007155, GO:0007010, GO:0005925, GO:0070160]]0.29
13gpt-3.5-turbonarrative_synopsisHALLMARK_APICAL_JUNCTION-1[[GO:0070160, GO:0031012, GO:0005604, GO:0007155, adhesion junction, GO:0007160]][[GO:0070160, GO:0007155, GO:0008014, integrin, GO:0007165, adhesion g-protein coupled receptor (gpcr), GO:0015629, UBERON:4000022, protein tyrosine kinase (ptk), GO:0016303, map kinase, MESH:D016212]]0.12
14gpt-3.5-turbonarrative_synopsisHALLMARK_APICAL_SURFACE-0[[GO:0007155, GO:0007165, GO:0061024, GO:0015031]][[GO:0007166, GO:0007169, GO:1901796, GO:0019048, GO:0045785, GO:0043408, GO:2000145, GO:0032956, GO:0051897, GO:0048015, GO:0010810, GO:0030334, regulation of cell growth\\n\\nmechanism and hypotheses: the enriched terms suggest a common mechanism involving transmembrane signaling pathways, with a focus on cell adhesion, migration, and growth regulation. several of the genes are involved in the regulation of the mapk signaling pathway, which is known to play a central role in cellular processes such as proliferation, differentiation, and apoptosis. pathway analysis of these genes may further elucidate the specific regulatory mechanisms at play]]0.00
15gpt-3.5-turbonarrative_synopsisHALLMARK_APICAL_SURFACE-1[[GO:0007155, GO:0007165, GO:0007154]][[GO:0007160, GO:0006811, GO:0007165, GO:0098631, insulin regulation, GO:0016485]]0.12
16gpt-3.5-turbonarrative_synopsisHALLMARK_APOPTOSIS-0[[GO:0006915, GO:0008219, GO:0043067, GO:0097153, binding of proteins involved in cell death.\\n\\nmechanism: the majority of the genes on the list are involved in apoptotic processes or regulate cell death. many of these genes belong to the bcl-2 protein family, which regulate apoptosis by either inhibiting or promoting cell death. other gene products, such as the caspases, also play a crucial role in the apoptotic process by cleaving proteins involved in cell death, ultimately leading to cell death. the enrichment of this theme in the gene list suggests that the regulation of apoptosis and programmed cell death is a significant biological mechanism that the genes in the list are involved in]][[GO:0006915, GO:0008219, GO:0007165]]0.33
17gpt-3.5-turbonarrative_synopsisHALLMARK_APOPTOSIS-1[[apoptosis regulation, cytokine signaling, growth factor regulation]][[GO:0097153, GO:0042981, positive regulation of dna fragmentation, GO:0043067, GO:0010941, GO:1901796, GO:0006974, GO:0070613]]0.00
18gpt-3.5-turbonarrative_synopsisHALLMARK_BILE_ACID_METABOLISM-0[[GO:0140359, long-chain fatty-acid metabolism, GO:0008203, GO:0006629, GO:0006637]][[GO:0006869, GO:0008203, GO:0006631, peroxisomal biogenesis, GO:0004448, GO:0008146]]0.10
19gpt-3.5-turbonarrative_synopsisHALLMARK_BILE_ACID_METABOLISM-1[[peroxisome biogenesis, GO:0006631, GO:0006699, GO:0008203, GO:0140359, GO:0016491, atp-binding cassette, GO:0005490]][[GO:0007031, GO:0001676, GO:0006699, GO:0008202, GO:0008203, GO:0001523, GO:0006635, alpha-oxidation, GO:0006720, lipid metabolic process \\n\\nmechanism: these genes function in a variety of processes involved in lipid metabolism and peroxisome biogenesis. peroxisomes are intracellular organelles involved in many metabolic pathways, including fatty acid beta-oxidation, which our enriched terms suggest is a common theme among these genes. additionally, these genes are involved in the synthesis of bile acids, steroid hormones, and retinoids, highlighting the importance of lipid metabolism in cellular function]]0.12
20gpt-3.5-turbonarrative_synopsisHALLMARK_CHOLESTEROL_HOMEOSTASIS-0[[GO:0006695, GO:0006633, GO:0006629, regulation of cholesterol levels, transport across cell membranes]][[GO:0006629, GO:0006869, GO:0008610]]0.14
21gpt-3.5-turbonarrative_synopsisHALLMARK_CHOLESTEROL_HOMEOSTASIS-1[[GO:0006695, GO:0006629, GO:0007165]][[GO:0006695, GO:0006644, GO:0006633, GO:0016125]]0.17
22gpt-3.5-turbonarrative_synopsisHALLMARK_COAGULATION-0[[GO:0006956, GO:0007596, GO:0006508, GO:0030198]][[GO:0007596, extracellular matrix remodeling, GO:0030449]]0.17
23gpt-3.5-turbonarrative_synopsisHALLMARK_COAGULATION-1[[blood coagulation cascade; complement activation, classical pathway; extracellular matrix disassembly; calcium ion binding. \\n\\nmechanism: these genes are involved in the regulation and activation of different pathways implicated in blood coagulation, GO:0006956, and extracellular matrix remodelling. blood coagulation involves the conversion of prothrombin to thrombin by coagulation factors, which leads to the formation of a fibrin clot. complement activation is a cascade resulting in the removal of damaged cells and pathogens. extracellular matrix disassembly and remodelling are implicated in cellular processes such as tissue repair, GO:0001525, metastasis. calcium-binding proteins play a vital role in signalling pathways regulation of enzymatic activities]][[extracellular matrix breakdown, GO:0007596, protein inhibition]]0.00
24gpt-3.5-turbonarrative_synopsisHALLMARK_COMPLEMENT-0[[GO:0006956, GO:0006955, GO:0030162, GO:0030168]][[GO:0008233, GO:0007596, GO:0006956]]0.17
25gpt-3.5-turbonarrative_synopsisHALLMARK_COMPLEMENT-1[[GO:0006956, GO:0007596, cytokine signaling, GO:0006468, GO:0006955, GO:0006954]][[GO:0006956, GO:0007596, GO:0006955, GO:0030168, cytokine signaling, GO:0002685, response to virus.\\n\\nmechanism: these genes are involved in regulating different aspects of immune response, including complement activation, platelet activation, cytokine signaling, and leukocyte migration. they are also involved in blood coagulation, which can be activated during an immune response to prevent pathogen spread. the over-representation of these genes suggests that immune activation and regulation are key to the identified biological process]]0.44
26gpt-3.5-turbonarrative_synopsisHALLMARK_DNA_REPAIR-0[[GO:0006281, transcription initiation, GO:0006396, GO:0009117]][[GO:0006281, transcription initiation, GO:0009117]]0.75
27gpt-3.5-turbonarrative_synopsisHALLMARK_DNA_REPAIR-1[[GO:0006270, GO:0006261, GO:0006297, transcription, dna-template-dependent, GO:0045893, GO:0000122, GO:0006281, GO:0000723, GO:0065004]][[GO:0006281, transcription regulation]]0.10
28gpt-3.5-turbonarrative_synopsisHALLMARK_E2F_TARGETS-0[[GO:0006260, GO:0006281, GO:0051726]][[GO:0006260, GO:0006281, GO:0051276]]0.50
29gpt-3.5-turbonarrative_synopsisHALLMARK_E2F_TARGETS-1[[GO:0006260, GO:0006281, dna polymerase, GO:0009117, GO:0006298, chromatin structure\\n\\nmechanism: the genes on this list primarily function in dna replication and repair. many of them are involved in dna polymerase activity, nucleotide metabolism, mismatch repair, and chromatin structure. it is likely that these genes work together in a coordinated manner to ensure accurate dna replication and repair, and that defects in these processes can lead to genetic instability and cancer development]][[GO:0006260, GO:0006281, cell-cycle checkpoint regulation]]0.29
30gpt-3.5-turbonarrative_synopsisHALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0[[GO:0030198, GO:0030199, GO:0048251, GO:0071711, regulation of protein localization to extracellular matrix, GO:0043236, GO:0001968, GO:0005518]][[GO:0030198, GO:0007155, GO:0005518, actin binding activity, GO:0007229, GO:0001501, GO:0005201, GO:0006936, GO:0005604, GO:0031012, GO:0008009, GO:0008083, GO:0016860, GO:0006508, GO:0005125]]0.10
31gpt-3.5-turbonarrative_synopsisHALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1[[GO:0030198, GO:0005518, GO:0051015, GO:0005125, GO:0007155, GO:0016477]][[GO:0030198, GO:0006936, GO:0007155]]0.29
32gpt-3.5-turbonarrative_synopsisHALLMARK_ESTROGEN_RESPONSE_EARLY-0[[membrane-bound proteins, MESH:D004798, GO:0000981]][[MESH:D002352, MESH:D004798, MESH:D008565, GO:0000981, receptors, MESH:D003598]]0.29
33gpt-3.5-turbonarrative_synopsisHALLMARK_ESTROGEN_RESPONSE_EARLY-1[[GO:0055085, cell signaling, GO:0004672, GO:1904659, GO:0006811]][[GO:0006631, GO:0006811, GO:0010468]]0.14
34gpt-3.5-turbonarrative_synopsisHALLMARK_ESTROGEN_RESPONSE_LATE-0[[membrane-associated protein complex, GO:0019899, GO:0034220, transcriptional regulation]][[GO:0005515, GO:0007165, GO:0019899, GO:0005737, GO:0043687, GO:0006355, GO:0006915, GO:0045860, positive regulation of cell proliferation.\\n\\nmechanism/]]0.08
35gpt-3.5-turbonarrative_synopsisHALLMARK_ESTROGEN_RESPONSE_LATE-1[[GO:0005515, GO:0003824, GO:0008134, GO:0006355, GO:0007165, cytokine signaling pathway, regulation of cell growth and differentiation]][[GO:0007165, GO:0004672, g-protein coupled receptor signaling pathway, GO:0055085, GO:0035556, GO:0004721, GO:0006468, zinc ion binding. \\n\\nhypotheses: the enriched terms suggest that the genes in this list are involved in regulatory mechanisms that help to control intracellular signaling cascades and protein expression through phosphorylation and dephosphorylation of proteins, and zinc ion binding. additionally, these genes may play a role in transmembrane transport and regulation of ion channels]]0.07
36gpt-3.5-turbonarrative_synopsisHALLMARK_FATTY_ACID_METABOLISM-0[[GO:0006629, mitochondrial function, GO:0003824, GO:0006631, oxidation-reduction process, metabolism of carboxylic acid, GO:0006118, GO:0006082]][[GO:0006631, GO:0005975, amino acid metabolism, mitochondrial function, oxidative stress response]]0.18
37gpt-3.5-turbonarrative_synopsisHALLMARK_FATTY_ACID_METABOLISM-1[[GO:0006629, oxidation-reduction process, energy production, metabolism of fatty acids, mitochondrial function, GO:0045333]][[GO:0006631, energy production, mitochondrial function, GO:0006629, oxidation-reduction process, GO:0006637, GO:0006099, MESH:D014451, GO:0019752, GO:0015936, GO:0006084, GO:0022900]]0.29
38gpt-3.5-turbonarrative_synopsisHALLMARK_G2M_CHECKPOINT-0[[GO:0051301, GO:0006260, GO:0007059, GO:0000910]][[GO:0051726, GO:0006260, GO:0006281]]0.17
39gpt-3.5-turbonarrative_synopsisHALLMARK_G2M_CHECKPOINT-1[[GO:0006270, GO:0007059, GO:0000075, GO:0007052, GO:0007346, GO:0065004]][[GO:0006260, GO:0051726, GO:0006281, GO:0007059, GO:0000910]]0.10
40gpt-3.5-turbonarrative_synopsisHALLMARK_GLYCOLYSIS-0[[GO:0070085, GO:0005975, fructose-bisphosphate metabolism, GO:0006098, GO:0006006, GO:0006012, GO:0006090, GO:0006089, GO:0019319, GO:0006011, GO:0052573, GO:0004332]][[GO:0006096, GO:0005975]]0.08
41gpt-3.5-turbonarrative_synopsisHALLMARK_GLYCOLYSIS-1[[GO:0006096, GO:0005975, GO:0007165, GO:1904659, GO:0033554]][[GO:0052574, GO:0006006, protein kinase binding activity, GO:0006090, GO:0006024, GO:0015012, GO:0006098, GO:0006096, rna polymerase iii transcription initiation, GO:0051287, GO:0022618, GO:0030199, GO:0008408, GO:0042803, atp-binding cassette transporter activity]]0.05
42gpt-3.5-turbonarrative_synopsisHALLMARK_HEDGEHOG_SIGNALING-0[[GO:0007411, GO:0007155, transcriptional regulation, cell communication. \\n\\nhypotheses: \\nthese genes may be involved in regulating the formation of neural circuits and maintaining neural plasticity through dynamic regulation of gene expression and protein signaling. the enriched terms suggest that the neural development process involves complex regulation of cell-cell communication and adhesion, as well as transcriptional control of gene expression. axon guidance is critical for the proper formation of neural circuits, and dysregulation of this process may lead to neural disorders]][[neuronal development, GO:0007155, GO:0007165, GO:0016477, GO:0010977, GO:0001525, MESH:D018121, transcriptional regulation]]0.20
43gpt-3.5-turbonarrative_synopsisHALLMARK_HEDGEHOG_SIGNALING-1[[GO:0007411, GO:0007155, transcription regulation, neuro-endocrine signaling, protein cleavage, cell migration.\\n\\nmechanism: these genes are involved in various aspects of neuronal development and signaling, including axon guidance, neuron migration, cell adhesion and communication, transcription regulation, and protein cleavage. these processes are critical for proper central nervous system development and function]][[GO:0007155, GO:0007411, neuronal proliferation and differentiation, GO:0007165, GO:0001525]]0.22
44gpt-3.5-turbonarrative_synopsisHALLMARK_HEME_METABOLISM-0[[GO:0006811, GO:0010468, protein turnover, GO:0061024]][[GO:0006810, GO:0005488, MESH:D008565, MONDO:0018815, solute carrier (slc) family of transporters]]0.00
45gpt-3.5-turbonarrative_synopsisHALLMARK_HEME_METABOLISM-1[[GO:0005515, GO:0003824, GO:0008152, GO:0006082, GO:0006810, GO:0006811, GO:0006820, GO:0044281, GO:0019538, GO:0006357, GO:0003924, GO:0016740, GO:0000166, GO:0003677, GO:0000988, GO:0006163, GO:0008643, GO:0050801, GO:0003723, GO:0019899]][[GO:1904659, GO:0003723, GO:0003677, GO:0000988, GO:0006811, GO:0019899, GO:0042826, GO:0140657, GO:0003824, GO:0008270]]0.25
46gpt-3.5-turbonarrative_synopsisHALLMARK_HYPOXIA-0[[GO:0006096, GO:0006006, GO:0006000, GO:0005975, MESH:D004734, GO:0045333, GO:0019318, GO:0019682, triose-phosphate metabolic process, GO:0006090, GO:0006754]][[GO:0006096, GO:0006006, GO:0005515, transcription regulation]]0.15
47gpt-3.5-turbonarrative_synopsisHALLMARK_HYPOXIA-1[[GO:0006006, insulin signaling pathway, GO:0051726, transcriptional regulation]][[GO:0006096, GO:0016310, GO:0006006, GO:0051726, GO:0007165, transcriptional regulation, heparan sulfate biosynthesis]]0.38
48gpt-3.5-turbonarrative_synopsisHALLMARK_IL2_STAT5_SIGNALING-0[[cytokine, receptor, t-cell, GO:0006955, GO:0065007]][[cytokine signaling, GO:0042110, GO:0042113, GO:0007159, GO:0030593, GO:0050900]]0.00
49gpt-3.5-turbonarrative_synopsisHALLMARK_IL2_STAT5_SIGNALING-1[[GO:0004896, GO:0002224, GO:0002685, GO:0002521, GO:0002682, GO:0046649, GO:0019221, GO:0007159, GO:0051249, positive regulation of leukocyte proliferation\\n\\nmechanism: these genes are involved in the immune system response and regulation, specifically in the activation, differentiation, and migration of leukocytes. they are also involved in cytokine-mediated signaling pathways and toll-like receptor signaling pathways. the enriched terms suggest that these genes are involved in the regulation of various aspects of immune system processes, including leukocyte proliferation and adhesion]][[GO:0004896, GO:0007166, GO:0045321, GO:0050900, GO:0006955, GO:0006954, GO:0002250, GO:0070663, GO:0002521, GO:0042110, GO:0042113, GO:0046649]]0.16
50gpt-3.5-turbonarrative_synopsisHALLMARK_IL6_JAK_STAT3_SIGNALING-0[[cytokine receptor activity; signal transduction; jak-stat cascade; cytokine-mediated signaling pathway\\n\\nmechanism: the enriched terms suggest that the commonality in gene function is the involvement of cytokine receptors and signaling pathways, particularly the jak-stat cascade, in cytokine-mediated signaling. this pathway is activated by cytokine binding to their respective receptors, leading to activation of the jak family of tyrosine kinases, which then phosphorylate and activate stat transcription factors to induce gene expression changes and cellular responses. the presence of these genes in the list suggests a potential role in regulating immune responses and inflammation through cytokine signaling]][[GO:0004896, GO:0050778, GO:0007155, GO:0019221, GO:0002687]]0.00
51gpt-3.5-turbonarrative_synopsisHALLMARK_IL6_JAK_STAT3_SIGNALING-1[[GO:0005126, GO:0002376, GO:0001817, GO:0050776, cytokine-mediated signaling pathway\\n\\nmechanism]][[GO:0004896, GO:0019221, GO:0050776, GO:0050900, apoptosis regulation, GO:0006954, antimicrobial response]]0.09
52gpt-3.5-turbonarrative_synopsisHALLMARK_INFLAMMATORY_RESPONSE-0[[cytokine signaling, GO:0004950, GO:0004930, GO:0050900, GO:0004908, GO:0002224, GO:0005164]][[GO:0005125, GO:0008009, GO:0004930, GO:0050900, inflammation\\n\\nmechanism]]0.20
53gpt-3.5-turbonarrative_synopsisHALLMARK_INFLAMMATORY_RESPONSE-1[[GO:0004896, GO:0004930, GO:0042379, GO:0006955, GO:0006954, GO:0019221, GO:0050900, GO:0002694, GO:0002682, GO:0001819, GO:0009617, GO:0032496, GO:0070555, GO:0034612, GO:0042110]][[GO:0004896, GO:0004930, GO:0004950, GO:0004888, GO:0004896]]0.11
54gpt-3.5-turbonarrative_synopsisHALLMARK_INTERFERON_ALPHA_RESPONSE-0[[interferon-induced protein, GO:0051607, GO:0006955, nucleotide-binding domain, leucine-rich repeat-containing receptor signaling, GO:0005764, GO:0019882, cytokine]][[interferon response, GO:0051607, GO:0006955]]0.25
55gpt-3.5-turbonarrative_synopsisHALLMARK_INTERFERON_ALPHA_RESPONSE-1[[GO:0140888, cytokine signaling pathway, GO:0045087, GO:0009615, GO:0006952]][[GO:0140888, GO:0045087, GO:0051607, cytokine signaling, GO:0019882, ubiquitin-mediated proteolysis\\n\\nmechanism: these genes are involved in the innate immune response and antiviral activity, particularly in the interferon signaling pathway. they encode proteins that regulate cytokine signaling, antigen processing and presentation, and ubiquitin-mediated proteolysis. the functions of these genes suggest a coordinated response to viral infection, with the interferon signaling pathway acting as a central mediator of the antiviral response]]0.22
56gpt-3.5-turbonarrative_synopsisHALLMARK_INTERFERON_GAMMA_RESPONSE-0[[interferon signaling, immune response regulation, cytokine signaling, tnf-receptor superfamily, protein tyrosine phosphatase, ubiquitin-proteasome system, MONDO:0007435]][[GO:0006955, GO:0019221, chemokine signaling pathway, GO:0019882]]0.00
57gpt-3.5-turbonarrative_synopsisHALLMARK_INTERFERON_GAMMA_RESPONSE-1[[GO:0006955, cytokine signaling, GO:0030163, GO:0000502, ubiquitin system, viral rna sensing, MESH:D018925, GO:0019882]][[GO:0045087, GO:0051607, GO:0005125, GO:0009615, GO:0001817, GO:0051607, GO:0032481, type i interferon signaling pathway. \\n\\nmechanism/]]0.00
58gpt-3.5-turbonarrative_synopsisHALLMARK_KRAS_SIGNALING_DN-0[[GO:0005509, GO:0055085, GO:0007155, GO:0004672, GO:0007186]][[GO:0005509, GO:0005245, GO:0006811, GO:0015085, GO:0005388, GO:0019722, GO:0055074, GO:0048306]]0.08
59gpt-3.5-turbonarrative_synopsisHALLMARK_KRAS_SIGNALING_DN-1[[cytokine signaling, g-protein coupled receptor signaling, GO:0019722, protein metabolism and processing]][[GO:0005509, GO:0042981, GO:0055085, GO:0006811, GO:0006468]]0.00
60gpt-3.5-turbonarrative_synopsisHALLMARK_KRAS_SIGNALING_UP-0[[receptor signaling pathway, GO:0006468, negative regulation of transcription, GO:0031396, GO:0071345, GO:0032880, GO:0070374]][[GO:0044425, GO:0007165, GO:0003824]]0.00
61gpt-3.5-turbonarrative_synopsisHALLMARK_KRAS_SIGNALING_UP-1[[signal transduction; cytokine activity; coagulation; ion transport; extracellular matrix organization. \\n\\nmechanism: the enriched terms suggest that the commonality in the function of these genes is related to signal transduction and regulation of various biological processes, such as coagulation, GO:0005125, GO:0030198, and ion transport. specifically, these genes are involved in regulating signaling pathways that are critical for these biological processes. there are several pathways known to contribute to these enriched terms, including the jak/stat, MESH:D016328, mapk/erk, and pi3k pathways. these pathways play important roles in cell signaling, GO:0006954, GO:0006955, other cellular processes]][[cytokine signaling, growth factor signaling, coagulation and complement activation, enzymatic activity regulation]]0.00
62gpt-3.5-turbonarrative_synopsisHALLMARK_MITOTIC_SPINDLE-0[[GO:0008017, GO:0007010, regulation of protein activity, GO:0051301, GO:0019894, GO:0003779]][[microtubule organization, GO:0007098, GO:0030036, GO:0051726, GO:0071539]]0.00
63gpt-3.5-turbonarrative_synopsisHALLMARK_MITOTIC_SPINDLE-1[[microtubule organization, GO:0140014, GO:0051301]][[GO:0008017, GO:0008574, GO:0007098, GO:0051225, GO:0003774, GO:0007010]]0.00
64gpt-3.5-turbonarrative_synopsisHALLMARK_MTORC1_SIGNALING-0[[GO:0046034, GO:0006629, GO:0006006, GO:0006457, GO:0046907]][[GO:0006457, GO:0006006, microtubule organization and biogenesis, GO:0000502, GO:0043043, GO:0042254]]0.22
65gpt-3.5-turbonarrative_synopsisHALLMARK_MTORC1_SIGNALING-1[[GO:0051087, GO:0005515, GO:0006457, GO:0043161]][[GO:0008152, GO:0009117, GO:0006629, GO:0005975, GO:0006457, GO:0030163, GO:0010468, GO:0000988, GO:0003682]]0.08
66gpt-3.5-turbonarrative_synopsisHALLMARK_MYC_TARGETS_V1-0[[GO:0006413, GO:0042254, GO:0006260, GO:0006281, GO:0008380, GO:0009117]][[GO:0042254, GO:0000394, GO:0006412, GO:0006412, GO:0006457, chaperonin-mediated protein folding]]0.09
67gpt-3.5-turbonarrative_synopsisHALLMARK_MYC_TARGETS_V1-1[[GO:0006413, GO:0006412, GO:0042254]][[GO:0042254, GO:0006413, GO:0006414, GO:0006397]]0.40
68gpt-3.5-turbonarrative_synopsisHALLMARK_MYC_TARGETS_V2-0[[GO:0006396, GO:0042254, rrna maturation]][[GO:0006364, ribosomal subunit biogenesis, GO:0003723, nucleolar function, GO:0006412]]0.00
69gpt-3.5-turbonarrative_synopsisHALLMARK_MYC_TARGETS_V2-1[[GO:0006364, nucleolar rna processing, GO:0042273, GO:0003723]][[GO:0006364, GO:0005730, GO:0003723, ribosomal biogenesis, GO:0051726]]0.29
70gpt-3.5-turbonarrative_synopsisHALLMARK_MYOGENESIS-0[[GO:0003779, GO:0006936, sarcomere assembly, GO:0005509, GO:0005861, GO:0005523, MESH:D024510, GO:0005524, GO:0004672, GO:0005515, GO:0032982]][[GO:0006936, muscle metabolism, GO:0007010]]0.08
71gpt-3.5-turbonarrative_synopsisHALLMARK_MYOGENESIS-1[[GO:0006936, GO:0005861, GO:0005509, GO:0003779, sarcomere organization and biogenesis]][[GO:0005861, MESH:M0013780, MESH:D018995, GO:0006936, GO:0005509, sarcomere assembly, MESH:D024510]]0.33
72gpt-3.5-turbonarrative_synopsisHALLMARK_NOTCH_SIGNALING-0[[GO:0007219, GO:0016567, GO:0001709, GO:0016055]][[GO:0007219, basic helix-loop-helix transcription factor activity, GO:0016567, GO:0016563, GO:0005102, GO:0097153, GO:0006468]]0.22
73gpt-3.5-turbonarrative_synopsisHALLMARK_NOTCH_SIGNALING-1[[GO:0007219, GO:0016567]][[GO:0007219, GO:0016567, transcriptional regulation, GO:0001709]]0.50
74gpt-3.5-turbonarrative_synopsisHALLMARK_OXIDATIVE_PHOSPHORYLATION-0[[GO:0006754, GO:0022900, GO:0005746, GO:0006119]][[GO:0005739, GO:0006119, GO:0022900, MESH:D004734, GO:0031966, MESH:D024101]]0.25
75gpt-3.5-turbonarrative_synopsisHALLMARK_OXIDATIVE_PHOSPHORYLATION-1[[GO:0005746, GO:0006119, mitochondrial metabolism, complex i-v, energy production]][[GO:0005746, GO:0006754, GO:0022900, GO:0006119]]0.29
76gpt-3.5-turbonarrative_synopsisHALLMARK_P53_PATHWAY-0[[GO:0006281, GO:0010468, GO:0008083]][[cyclin family, GO:0006281, GO:0008083, GO:0004672, GO:0000988, zinc finger protein]]0.29
77gpt-3.5-turbonarrative_synopsisHALLMARK_P53_PATHWAY-1[[GO:0006281, GO:0051726, GO:0007165, GO:0006915, MESH:D016207]][[GO:0008083, transcriptional regulation, GO:0006915, GO:0006281]]0.29
78gpt-3.5-turbonarrative_synopsisHALLMARK_PANCREAS_BETA_CELLS-0[[GO:0006006, insulin signaling, pancreatic development, neuroendocrine regulation]][[GO:0006006, insulin regulation, GO:0031016, GO:0006096, GO:0006094, GO:0030073, hormone regulation]]0.10
79gpt-3.5-turbonarrative_synopsisHALLMARK_PANCREAS_BETA_CELLS-1[[GO:0006006, pancreatic islet development, neuroendocrine differentiation, GO:0007269, MESH:D009473]][[GO:0006006, GO:0030073, pancreatic islet development, neuroendocrine differentiation]]0.50
80gpt-3.5-turbonarrative_synopsisHALLMARK_PEROXISOME-0[[atp binding cassette transporter activity, GO:0006631, GO:0042445, GO:0008289, GO:0043574, GO:0005502]][[GO:0140359, GO:0055085, atp-binding cassette, GO:0043574, GO:0006631, GO:0006839]]0.20
81gpt-3.5-turbonarrative_synopsisHALLMARK_PEROXISOME-1[[GO:0005777, GO:0006635, antioxidant response, mitochondrial carrier protein]][[GO:0005777, GO:0006631, beta-oxidation, MESH:D018384, antioxidant defense mechanism, coenzyme a ligase, aldehyde dehydrogenase family, MESH:D009195]]0.09
82gpt-3.5-turbonarrative_synopsisHALLMARK_PI3K_AKT_MTOR_SIGNALING-0[[GO:0004672, GO:0035556, GO:1902531, GO:0050794, GO:0003824, cytoskeletal regulation]][[GO:0004672, intracellular signaling, GO:0050794]]0.29
83gpt-3.5-turbonarrative_synopsisHALLMARK_PI3K_AKT_MTOR_SIGNALING-1[[GO:0004672, GO:0007165, GO:0006468, GO:0035556]][[GO:0016301, GO:0006468, GO:0007165]]0.40
84gpt-3.5-turbonarrative_synopsisHALLMARK_PROTEIN_SECRETION-0[[GO:0005794, GO:0005480, GO:0005764]][[GO:0005794, membrane trafficking, GO:0016192, GO:0015031, GO:0006906, GO:0035493, GO:0005793]]0.11
85gpt-3.5-turbonarrative_synopsisHALLMARK_PROTEIN_SECRETION-1[[golgi transport, GO:0016192, GO:0015031, GO:0008104, GO:0032880, GO:0006886, GO:0016197]][[GO:0007030, GO:0006888, GO:0016192, GO:0007040, sorting nexin-containing complex, GO:0030665, GO:0032880]]0.17
86gpt-3.5-turbonarrative_synopsisHALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0[[GO:0016209, GO:0006749, GO:0016491]][[antioxidant activity; redox regulation; catalytic activity, UBERON:0035930, such as water and oxygen. the over-representation of terms related to antioxidant activity, redox regulation, and responding to oxidative stress suggest that these genes are involved in maintaining the balance between oxidants and antioxidants in the body, help protect against oxidative damage]]0.00
87gpt-3.5-turbonarrative_synopsisHALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1[[GO:0016209, redox regulation, MESH:D018384]][[oxidative stress response, antioxidant defense, regulation of reactive oxygen species, GO:0006749, superoxide anion radical metabolism, peroxiredoxin-mediated detoxification]]0.00
88gpt-3.5-turbonarrative_synopsisHALLMARK_SPERMATOGENESIS-0[[GO:0051726, GO:0003677, GO:0003723, GO:0016301, transcription regulation, chromatin organization and modification]][[GO:0008584, GO:0007283, GO:0097722, GO:0007340, GO:0048232, testicular germ cell proliferation\\n\\nmechanism and]]0.00
89gpt-3.5-turbonarrative_synopsisHALLMARK_SPERMATOGENESIS-1[[GO:0005515, enzymatic activity, GO:0006811]][[GO:0006811, GO:0006468, MESH:D054875, GO:0007283, receptor signaling]]0.14
90gpt-3.5-turbonarrative_synopsisHALLMARK_TGF_BETA_SIGNALING-0[[growth factor signaling, transcriptional regulation, smad/tgf-beta signaling pathway, cellular differentiation]][[tgf-beta signaling pathway, transcriptional regulation, GO:0007165, cell growth and differentiation]]0.14
91gpt-3.5-turbonarrative_synopsisHALLMARK_TGF_BETA_SIGNALING-1[[GO:0005024, GO:0060395, GO:0030509]][[tgf-beta signaling pathway, GO:0030509, GO:0071141, GO:0004674, GO:0008134, GO:0006468, GO:0030154, GO:0060348, GO:0042981, GO:0034436]]0.08
92gpt-3.5-turbonarrative_synopsisHALLMARK_TNFA_SIGNALING_VIA_NFKB-0[[GO:0006955, cytokine signaling pathway, transcription regulation. \\n\\nmechanism: these genes are primarily involved in regulating the immune response through the cytokine signaling pathway. they also play a role in transcriptional regulation of genes involved in these pathways. overall, these genes are important in regulating the response to pathogens and maintaining immune homeostasis]][[GO:0004950, GO:0005125, GO:0006955, GO:0006954, GO:0050900, GO:0007165]]0.12
93gpt-3.5-turbonarrative_synopsisHALLMARK_TNFA_SIGNALING_VIA_NFKB-1[[cytokine signaling pathway, GO:0002682, GO:0006351, GO:0006355, GO:0050900, GO:0006954, GO:0050727, GO:0032496, GO:0002237, GO:0009615, GO:0045893, GO:0045892]][[interleukin signaling, GO:0032602, GO:0006955]]0.00
94gpt-3.5-turbonarrative_synopsisHALLMARK_UNFOLDED_PROTEIN_RESPONSE-0[[GO:0044183, GO:0006457, GO:0006396, cellular stress response, GO:0006401]][[endoplasmic reticulum stress response, GO:0006457, GO:0008380, GO:0006402, mrna localization, translation regulation, stress response]]0.09
95gpt-3.5-turbonarrative_synopsisHALLMARK_UNFOLDED_PROTEIN_RESPONSE-1[[GO:0006457, GO:0006396, GO:0006413, endoplasmic reticulum stress response, GO:0042254]][[GO:0006457, GO:0061077, GO:0015031, GO:0006413, GO:0003723, MESH:D020365, GO:0042254, aminoacyl-trna synthesis, GO:0005783, MESH:D005786]]0.25
96gpt-3.5-turbonarrative_synopsisHALLMARK_UV_RESPONSE_DN-0[[GO:0006816, cytoskeletal organization, cell signaling, protein regulation]][[GO:0030198, GO:0007155, GO:0006811, GO:0004672, transcription regulation, receptor signaling pathway]]0.00
97gpt-3.5-turbonarrative_synopsisHALLMARK_UV_RESPONSE_DN-1[[GO:0030198, GO:0007165, GO:0006811]][[GO:0030198, GO:0030155, GO:0006468, positive regulation of cellular signaling pathway activity, GO:0022604, GO:0072659]]0.12
98gpt-3.5-turbonarrative_synopsisHALLMARK_UV_RESPONSE_UP-0[[GO:0006810, GO:0003824, regulation of transcription, GO:0016310, GO:0005515, GO:0006950, GO:0006915, GO:0006811, GO:0005524, GO:0007165, GO:0005975]][[GO:0006810, GO:0008152, GO:0003824]]0.17
99gpt-3.5-turbonarrative_synopsisHALLMARK_UV_RESPONSE_UP-1[[GO:0008152, GO:0005515, GO:0007165, GO:0009165, GO:0006468, transcription factor activity\\n\\nmechanism: these enriched terms suggest that the commonality between these genes is their involvement in fundamental biological processes required for normal cell function. these include metabolism, signal transduction, and protein biosynthesis and regulation. the transcription factor activity term suggests that some of these genes may be transcriptional regulators, controlling the expression of other genes involved in these processes. overall, these genes likely work together to maintain cellular homeostasis and respond to internal and external cues]][[GO:0003723, GO:0003677, GO:0000166, GO:0006396, GO:0006260]]0.00
100gpt-3.5-turbonarrative_synopsisHALLMARK_WNT_BETA_CATENIN_SIGNALING-0[[wnt signaling pathway regulation, transcriptional regulation, GO:0051726]][[GO:0016055, transcriptional regulation, cell cycle progression]]0.20
101gpt-3.5-turbonarrative_synopsisHALLMARK_WNT_BETA_CATENIN_SIGNALING-1[[GO:0016055, GO:0008013, transcription regulation]][[GO:0016055, GO:0051726, transcriptional regulation]]0.20
102gpt-3.5-turbonarrative_synopsisT cell proliferation-0[[GO:0006955, GO:0007165, GO:0001816, cell proliferation and differentiation, GO:0042981]][[cytokine, MESH:D007378, MESH:D011948, GO:0005530, GO:0008180, GO:0000502, protein tyrosine phosphatase, MESH:D010770, GO:0000981]]0.00
103gpt-3.5-turbonarrative_synopsisT cell proliferation-1[[cytokine, GO:0006955, GO:0023052, receptor, t cell]][[cytokine signaling, tnf-receptor superfamily, GO:0006955, GO:0007165, GO:0019882, cell proliferation and survival, protein phosphorylation and kinase activity]]0.09
104gpt-3.5-turbonarrative_synopsisYamanaka-TFs-0[[MESH:D047108, stem cell pluripotency, MESH:D063646, cell cycle progression]][[MESH:D047108, GO:0001709, cell cycle progression]]0.40
105gpt-3.5-turbonarrative_synopsisYamanaka-TFs-1[[MESH:D047108, stem cell maintenance, GO:0010468]][[MESH:D047108, GO:0048863, pluripotent stem cell, transcription factor regulation, homeobox protein]]0.14
106gpt-3.5-turbonarrative_synopsisamigo-example-0[[GO:0030198, GO:0007155, GO:0007229, GO:0051495, GO:0002576]][[GO:0031012, GO:0007155, MESH:D011509, GO:0005202, integrin]]0.11
107gpt-3.5-turbonarrative_synopsisamigo-example-1[[GO:0030198, GO:0007155, GO:0006029, GO:0042339, GO:0007229, GO:0030168]][[GO:0030198, GO:0007155, GO:0016477, GO:0009888, GO:0042246, signaling pathway regulation, GO:0030168]]0.30
108gpt-3.5-turbonarrative_synopsisbicluster_RNAseqDB_0-0[[GO:0055085, GO:0006811, GO:0005524, zinc finger domain binding, GO:0007186, GO:0000988]][[GO:0006351, GO:0005515, MESH:D016335, GO:0005509, MESH:D008565]]0.00
109gpt-3.5-turbonarrative_synopsisbicluster_RNAseqDB_0-1[[GO:0019722, GO:0000988, GO:0055085]][[calcium binding, receptor protein activity, GO:0000988, GO:0005515]]0.17
110gpt-3.5-turbonarrative_synopsisbicluster_RNAseqDB_1002-0[[GO:0006936, GO:0007015, GO:0032972, GO:0005509, GO:0005861, GO:0005865, GO:0003779, GO:0045214, GO:0005523, GO:0017022, GO:0045932, skeletal muscle thin filament, cardiac muscle thin filament]][[GO:0006936, GO:0005509, GO:0043269, GO:0032516, GO:0051015]]0.12
111gpt-3.5-turbonarrative_synopsisbicluster_RNAseqDB_1002-1[[GO:0006936, GO:0051015, GO:0005523, calcium binding, myofibril assembly.\\n\\nmechanism: these genes are involved in the regulation and maintenance of muscle structure and the contraction cycle. they act through the interaction of actin and myosin filaments, with the regulation of calcium ions controlling muscle contraction. the proteins encoded by these genes are involved in ion channel regulation, protein binding and modification, and energy metabolism]][[GO:0006936, GO:0005509, GO:0051015, GO:0043462, GO:0097009, GO:0006811]]0.22
112gpt-3.5-turbonarrative_synopsisendocytosis-0[[GO:0006897, intracellular trafficking, cytoskeleton reorganization]][[GO:0006897, GO:0007010, GO:0007165, GO:0006629, GO:0060348, brain development. \\n\\nhypotheses: these genes may be involved in common pathways related to endocytic vesicle trafficking, cytoskeletal organization, and signal transduction. some of the genes are associated with lipid metabolism and bone and brain development, suggesting their potential roles in cellular processes related to these functions]]0.12
113gpt-3.5-turbonarrative_synopsisendocytosis-1[[GO:0006897, GO:0016192, intracellular signaling, GO:0015031, cytoskeletal organization]][[GO:0006897, intracellular trafficking, cytoskeletal reorganization]]0.14
114gpt-3.5-turbonarrative_synopsisglycolysis-gocam-0[[glucose metabolism; glycolysis\\n\\nmechanism: these genes play a role in converting glucose to produce energy in the form of atp. hexokinase (hk1) and glucose phosphate isomerase (gpi) are involved in the initial steps of glucose metabolism, while phosphofructokinase (pfkm), MESH:D005634, and pyruvate kinase (pkm) are involved in glycolysis. triosephosphate isomerase (tpi1) and glyceraldehyde-3-phosphate dehydrogenase (gapdh) are also involved in glycolysis and produce atp by oxidizing glucose. phosphoglycerate mutase (pgam2) and enolase (eno3) are also involved in glycolysis and help convert glucose to pyruvate, which can then be converted to atp]][[GO:0006096, GO:0006006, MESH:D004734]]0.00
115gpt-3.5-turbonarrative_synopsisglycolysis-gocam-1[[GO:0006096, GO:0005975, energy pathway]][[GO:0006096, GO:0006006, GO:0004743, GO:0019682, GO:0006000, phosphoenolpyruvate metabolic process]]0.12
116gpt-3.5-turbonarrative_synopsisgo-postsynapse-calcium-transmembrane-0[[GO:0006816, GO:0004970, n-methyl-d-aspartate receptor complex, GO:0043269, GO:0014069, GO:0007165]][[GO:0006816, intracellular calcium homeostasis, ionotropic glutamate receptor regulation, nmda receptor subunits, sodium/calcium exchanger proteins, trp ion channel family]]0.09
117gpt-3.5-turbonarrative_synopsisgo-postsynapse-calcium-transmembrane-1[[GO:0006816, GO:0005509, GO:0005216, GO:0005102, GO:0007268, GO:0030594]][[GO:0005509, GO:0005262, GO:0004970, calcium-mediated signaling pathway, GO:0007268, GO:0031175, GO:0005216]]0.30
118gpt-3.5-turbonarrative_synopsisgo-reg-autophagy-pkra-0[[summary: regulation of cellular processes, including cell growth and metabolism, GO:0006915, GO:0006955, and regulation of chromatin remodeling and transcription.\\n\\nmechanism: these genes function in various pathways involved in the regulation of cellular processes. akt1 and pik3ca are involved in the pi3k/akt/mtor signaling pathway, which regulates cell growth, MESH:D013534, and metabolism. casp3 is a protease involved in the execution-phase of cell apoptosis. ccny and cdk5r1 are involved in the regulation of cell division cycles and the development of the central nervous system. hspb1 plays an important role in cell differentiation, but its overexpression may promote cancer cell proliferation and metastasis while protecting cancer cells from apoptosis. irgm regulates autophagy formation in response to intracellular pathogens. kat5 is a histone acetylase that has a role in dna repair and apoptosis and is thought to play an important role in signal transduction. mlst8, rptor, and smcr8 are involved in the torc1 signaling pathway, which regulates protein synthesis and cell growth in response to nutrient and insulin levels. nod2 is a pattern recognition receptor that detects cytosolic nucleic acids and trans]][[MESH:D002470, GO:0016301, GO:0009966, GO:0001558, GO:0042981, GO:0010506, GO:0032006]]0.00
119gpt-3.5-turbonarrative_synopsisgo-reg-autophagy-pkra-1[[GO:0038202, GO:0032006, GO:0010605, activation of map3k7/tak1]][[GO:0016049, GO:0004672, GO:0006955, GO:0007165, GO:0000988, neuronal development, GO:0006468]]0.00
120gpt-3.5-turbonarrative_synopsishydrolase activity, hydrolyzing O-glycosyl compounds-0[[GO:0005764, glycoside hydrolase activity, GO:0005975, GO:0016787, GO:0006027, GO:0005980, GO:0006689, GO:0015929, acid hydrolase activity, chitin catabolic process\\n\\nmechanism: these genes participate in the lysosomal degradation of various carbohydrate molecules, breaking them down into their component parts for further processing by the cell]][[glycosyl hydrolase activity, degradation of carbohydrates, GO:0006032, GO:0030211, GO:0003796, GO:0030214]]0.00
121gpt-3.5-turbonarrative_synopsishydrolase activity, hydrolyzing O-glycosyl compounds-1[[GO:0004559, GO:0004415, lysosomal enzyme activity, GO:0016798, GO:0006487]][[GO:0016787, GO:0044248, GO:0006027, GO:0005764]]0.00
122gpt-3.5-turbonarrative_synopsisig-receptor-binding-2022-0[[immunoglobulin receptor binding activity, GO:0002253, GO:0098542, GO:0002922, b cell-mediated immunity]][[GO:0019731, GO:0098542, GO:0002253, immunoglobulin receptor binding activity]]0.50
123gpt-3.5-turbonarrative_synopsisig-receptor-binding-2022-1[[GO:0002250, GO:0002376, antigen binding activity, immunoglobulin receptor binding activity. \\n\\nmechanism: the enriched terms suggest that these genes are involved in the recognition and response to specific foreign antigens encountered by the immune system. antigen binding activity enables the binding of specific antigens, while immunoglobulin receptor binding activity allows for the activation and signaling of immune cells. together, these genes contribute to the adaptive immune response and immune system processes by recognizing and responding to diverse foreign antigens]][[antigen binding activity, immunoglobulin receptor binding activity, GO:0002253]]0.17
124gpt-3.5-turbonarrative_synopsismeiosis I-0[[meiotic recombination; homologous recombination; chromosome segregation during meiosis; double-strand break repair via homologous recombination.\\n\\nmechanism: these genes are all involved in the meiotic cell cycle process, specifically in events related to recombination, repair, and segregation of chromosomes during meiosis. the proteins encoded by these genes interact with each other to form protein complexes that are essential for proper meiotic division. the enriched terms indicate a strong association with meiotic recombination and double-strand break repair via homologous recombination. additionally, they suggest a role in chromosome segregation during meiosis]][[GO:0140013, GO:0035825, GO:0007059, GO:0006281, GO:0000795]]0.00
125gpt-3.5-turbonarrative_synopsismeiosis I-1[[meiotic recombination, GO:0006281, GO:0035825, GO:0007059, GO:0006302, holliday junction, rad51, GO:0007127]][[meiotic recombination, GO:0006281, GO:0007059, GO:0035825, holliday junction resolution, double-strand dna binding, GO:0007276, GO:0007130]]0.33
126gpt-3.5-turbonarrative_synopsismolecular sequestering-0[[GO:0005515, GO:0006955, intracellular transport\\n\\nmechanism/]][[GO:0006955, GO:0051726, GO:0046907]]0.20
127gpt-3.5-turbonarrative_synopsismolecular sequestering-1[[GO:0006810, regulation of cell growth and survival, GO:0010468, GO:0006915]][[GO:0051726, GO:0006955, GO:0005515]]0.00
128gpt-3.5-turbonarrative_synopsismtorc1-0[[GO:0046034, GO:0006629, GO:0006006, GO:0006457, GO:0046907]][[GO:0006457, GO:0006006, microtubule organization and biogenesis, GO:0000502, GO:0043043, GO:0042254]]0.22
129gpt-3.5-turbonarrative_synopsismtorc1-1[[GO:0000502, GO:0030163]][[GO:0000502, GO:1904659, GO:0008152, GO:0003676, GO:0044183, GO:0005524, GO:0005783, GO:0005739, GO:0006096, GO:0006631]]0.09
130gpt-3.5-turbonarrative_synopsisperoxisome-0[[peroxisome biogenesis, GO:0016558, peroxin]][[peroxisome biogenesis, peroxisomal protein import, peroxin proteins, MONDO:0019234, neonatal adrenoleukodystrophy, MONDO:0019609, MONDO:0009959, MONDO:0008972, MONDO:0009958]]0.09
131gpt-3.5-turbonarrative_synopsisperoxisome-1[[peroxisome biogenesis, matrix protein import, MONDO:0009279, peroxin (pex) family]][[peroxisome biogenesis, GO:0005777, GO:0017038]]0.17
132gpt-3.5-turbonarrative_synopsisprogeria-0[[GO:0006998, chromatin organization and maintenance, dna repair and recombination]][[GO:0005652, GO:0005635, GO:0006281]]0.00
133gpt-3.5-turbonarrative_synopsisprogeria-1[[GO:0006325, GO:0006281, nuclear stability]][[GO:0006997, GO:0006281, chromatin structure organization, GO:0000723]]0.17
134gpt-3.5-turbonarrative_synopsisregulation of presynaptic membrane potential-0[[GO:0007268, GO:0005216, neurological function]][[GO:0005216, GO:0031175, GO:0007268, GO:0042391]]0.40
135gpt-3.5-turbonarrative_synopsisregulation of presynaptic membrane potential-1[[GO:0005216, GO:0048666, GO:0007268]][[GO:0005267, chloride ion transmembrane transport, GO:0042391, GO:0034220, GO:0030594]]0.00
136gpt-3.5-turbonarrative_synopsissensory ataxia-0[[MONDO:0015626, MONDO:0005244, MONDO:0007790, GO:0043209, GO:0006264, tetratricopeptide repeat, transporter protein\\n\\nmechanism: these genes are involved in myelin upkeep and various neurological diseases associated with defects in myelin sheath synthesis and functions. they play roles in mitochondrial dna replication and transport, as well as protein transportation across the nuclear membrane. the presence of tetratricopeptide repeat motifs in these genes suggests their roles in protein-protein interactions and chaperone functions]][[MONDO:0015626, MONDO:0007790, MONDO:0005244, myelin sheath maintenance, GO:0006264]]0.50
137gpt-3.5-turbonarrative_synopsissensory ataxia-1[[MONDO:0011890, MONDO:0007790, MONDO:0011527, GO:0043217, peripheral myelin sheath, n-acetyl-d-glucosamine residue degradation, MESH:D008565, GO:0007399, nervous system myelination, GO:0006260]][[GO:0042552, GO:0007422, GO:0016567, er-associated protein degradation.\\n\\nmechanism/]]0.00
138gpt-3.5-turbonarrative_synopsisterm-GO:0007212-0[[GO:0007186, GO:0007189, regulation of cyclic nucleotide metabolic process, regulation of camp metabolic process]][[g-protein signaling, GO:0007165, neurotransmitter activity]]0.00
139gpt-3.5-turbonarrative_synopsisterm-GO:0007212-1[[GO:0007186, GO:0019932, GO:0007212]][[g-protein signaling pathway, GO:0030594, GO:1902531]]0.00
140gpt-3.5-turbonarrative_synopsistf-downreg-colorectal-0[[transcriptional regulation, GO:0006338, GO:0000988, GO:0003700, rna polymerase ii regulatory region sequence-specific dna binding, zinc finger domain, GO:0042393, nucleosome binding.\\n\\nmechanism: the enriched functions suggest that the given set of genes are involved in transcriptional regulation and chromatin remodeling. transcription factors bind to specific dna sequences and regulate gene expression, while chromatin remodeling alters the structure of chromatin to allow or prevent access to the dna by transcriptional machinery. zinc finger domain-containing proteins are involved in dna binding, and histone binding proteins facilitate the formation of transcriptionally active or inactive chromatin structures. the enriched functions suggest the potential involvement of these genes in both gene activation and repression, which may have important implications in cellular differentiation, development, and disease]][[transcription regulation, GO:0006338, GO:0003700]]0.22
141gpt-3.5-turbonarrative_synopsistf-downreg-colorectal-1[[transcription regulation, chromatin structure alteration, cell cycle progression, GO:0003682]][[GO:0003700, GO:0006355, GO:0006325, GO:0010468, transcription factor complex\\n\\nmechanism: these genes all play a role in regulating transcription, primarily at the level of dna binding and chromatin organization. they are involved in the regulation of gene expression and the formation of transcription factor complexes]]0.00
142gpt-3.5-turbono_synopsisEDS-0[[GO:0030198, GO:0030199, GO:0006024]][[GO:0030198, GO:0043062, GO:0030199, GO:0006486, GO:0008233, GO:0008270]]0.29
143gpt-3.5-turbono_synopsisEDS-1[[GO:0030199, GO:0030198, GO:0032964]][[GO:0032963, GO:0030198, GO:0031012]]0.20
144gpt-3.5-turbono_synopsisFA-0[[fanconi anemia pathway, homologous recombination repair pathway, dna double-strand break repair]][[GO:0006281, GO:0006325, GO:0006312, GO:0006302, GO:0035825, GO:0006260]]0.00
145gpt-3.5-turbono_synopsisFA-1[[GO:0006281, GO:0006302, GO:0035825, mitotic cell-cycle checkpoint, GO:0006974]][[fanconi anemia pathway, GO:0035825, GO:0006302]]0.33
146gpt-3.5-turbono_synopsisHALLMARK_ADIPOGENESIS-0[[GO:0006631, GO:0006869, GO:0005746, GO:0006637, GO:0032000, GO:0016042, GO:0019216, GO:0033108, GO:0035336, GO:0033539, GO:0051791]][[GO:0006629, GO:0006631, mitochondrial function, GO:0006119, GO:0006099, beta-oxidation of fatty acids, GO:0006084, GO:0006637, GO:0015980, GO:0005975]]0.11
147gpt-3.5-turbono_synopsisHALLMARK_ADIPOGENESIS-1[[GO:0006119, GO:0006631, GO:0006457, GO:0030301, GO:0019915, stress response, GO:0045333, mitochondrial metabolism, energy generation, GO:0006986, GO:0046890, GO:0032368, GO:0033344, GO:0007517, GO:0006979, GO:0001666, regulation of fatty acid catabolic process, GO:0019216]][[GO:0005740, GO:0006122]]0.00
148gpt-3.5-turbono_synopsisHALLMARK_ALLOGRAFT_REJECTION-0[[GO:0042110, GO:0030098, GO:0019221, GO:0002682, GO:0050776]][[GO:0002376, GO:0042110, GO:0019221, GO:0019882, GO:0030098, GO:0050900, GO:0050778, GO:0050777, GO:0001817]]0.27
149gpt-3.5-turbono_synopsisHALLMARK_ALLOGRAFT_REJECTION-1[[GO:0005125, GO:0008009, GO:0034341, GO:0042110, GO:0050727]][[GO:0042110, cytokine signaling, GO:0019882, GO:0006955, chemokine signaling, interferon signaling, GO:0030183, GO:0050900]]0.08
150gpt-3.5-turbono_synopsisHALLMARK_ANDROGEN_RESPONSE-0[[GO:0006351, regulation of transcription, GO:0006629, GO:0030163]][[GO:0016567, GO:0036211, GO:0008134, GO:0045892, GO:0071535, GO:0031647, GO:0043161]]0.00
151gpt-3.5-turbono_synopsisHALLMARK_ANDROGEN_RESPONSE-1[[GO:0006508, GO:0004672, GO:0007010, GO:0006695, GO:0045944, GO:0043066]][[regulation of transcription, GO:0005515, GO:0007155, GO:0007165, GO:0016126]]0.00
152gpt-3.5-turbono_synopsisHALLMARK_ANGIOGENESIS-0[[GO:0030198, GO:0007267, GO:0043405, GO:0042127, GO:0030155, GO:0002576]][[GO:0030198, GO:0070848, GO:1903010, GO:0042060]]0.11
153gpt-3.5-turbono_synopsisHALLMARK_ANGIOGENESIS-1[[GO:0030198, GO:0001525, vascular development, GO:0030335, GO:0001938, GO:0017015, GO:0007155]][[GO:0030198, GO:0001525, GO:0007155]]0.43
154gpt-3.5-turbono_synopsisHALLMARK_APICAL_JUNCTION-0[[GO:0098609, GO:0034332, GO:0002159, GO:0030198]][[GO:0007155, GO:0007010, GO:0048041, regulation of actin cytoskeleton, GO:0051017, GO:0046847, GO:0035023]]0.00
155gpt-3.5-turbono_synopsisHALLMARK_APICAL_JUNCTION-1[[GO:0070160, GO:0007155, GO:0007154, GO:0022407, GO:0043542, GO:0030198, cell junction organization and biogenesis, GO:0032956, GO:0001525, GO:0010810]][[GO:0007155, GO:0016477, GO:0048870, GO:0007229, GO:0008360, focal adhesion\\n\\nmechanism: the enriched terms suggest that the common function of these genes is involved in cell adhesion and migration. these processes are essential for various biological functions such as wound healing, inflammation, and embryonic development. integrin-mediated signaling pathway and focal adhesion are two crucial pathways in cell adhesion and migration, which are perturbed in many types of cancer and autoimmune diseases. these findings may shed light on the underlying mechanism and potential targets for drug development]]0.07
156gpt-3.5-turbono_synopsisHALLMARK_APICAL_SURFACE-0[[GO:0051716, GO:0005515, GO:0035556, GO:0007155, GO:0055085, GO:0061024, GO:0015031]][[GO:0007155, GO:0023052, GO:0006810]]0.11
157gpt-3.5-turbono_synopsisHALLMARK_APICAL_SURFACE-1[[GO:0007155, GO:0016477, GO:0007165, GO:0038023, GO:0006468, GO:0008104, GO:0055085, GO:0003824]][[GO:0007155, GO:0007186, GO:0010906, GO:0050796, GO:0070528, GO:0043406, GO:0050731, GO:0051897, GO:0061024, GO:0043066]]0.06
158gpt-3.5-turbono_synopsisHALLMARK_APOPTOSIS-0[[GO:0006915, GO:0043123, GO:0050855, GO:0001817, GO:0002697, GO:0050670, GO:0051249, GO:0050856, GO:0034097, GO:0032496]][[GO:0006915, GO:0012501, regulation of cell death\\n\\nmechanism: these genes are involved in various processes that regulate cell death. they participate in the apoptotic process, the programmed cell death that occurs in multicellular organisms. apoptosis is a complex physiological process that is essential for development and homeostasis in healthy adult tissues. these genes also contribute to the regulation of cell death, preventing or promoting apoptosis under specific conditions]]0.08
159gpt-3.5-turbono_synopsisHALLMARK_APOPTOSIS-1[[cellular stress response, GO:0006915, GO:0006954, GO:0043067, negative regulation of nf-kappab transcription factor, GO:0043280]][[GO:0097153, GO:0006915, GO:0006954, GO:0008285, GO:0050871, GO:0001819, GO:0045944, GO:0004672, GO:0046328, GO:0010803]]0.14
160gpt-3.5-turbono_synopsisHALLMARK_BILE_ACID_METABOLISM-0[[GO:0006695, GO:0006699, peroxisome biogenesis]][[peroxisome organization; steroid metabolic process; cholesterol metabolic process; fatty acid metabolic process; lipid metabolic process\\n\\nmechanism: \\n\\nthese genes are involved in various metabolic pathways, especially those related to lipid and sterol metabolism. many of these genes are involved in the transport of lipids and cholesterol, including the abc transporters abca1, abca2, abca3, abca4, abca5, abca6, abca8, abca9, and abcg4. other genes such as cat, ch25h, crot, cyp7a1, GO:0033783, MESH:D013253, dhcr24, and hsd17b6 are involved in the synthesis, GO:0009056, and modification of cholesterol and sterols. \\n\\nadditionally, these genes are also involved in peroxisome biogenesis and function, with genes such as pex1, pex11a, pex11g, pex12, pex13, pex16, pex19, pex26, MESH:D010758]]0.00
161gpt-3.5-turbono_synopsisHALLMARK_BILE_ACID_METABOLISM-1[[GO:0006629, GO:0006869, GO:0005777, mitochondrial function]][[GO:0006695, GO:0006629, GO:0007031, peroxisome biogenesis, GO:0008202, GO:0006635, GO:0006699, GO:0015908, GO:0006886]]0.08
162gpt-3.5-turbono_synopsisHALLMARK_CHOLESTEROL_HOMEOSTASIS-0[[GO:0016126, GO:0006695, GO:0030301, GO:0006629, GO:0008202, GO:0042632]][[GO:0006695, GO:0006629, GO:0045540, GO:0019216, GO:0016126]]0.38
163gpt-3.5-turbono_synopsisHALLMARK_CHOLESTEROL_HOMEOSTASIS-1[[GO:0006695, GO:0006629, GO:0008203, GO:0016126, GO:0008299, GO:0042632, GO:0045540, GO:0019216]][[GO:0006695, GO:0006694, GO:0006629]]0.22
164gpt-3.5-turbono_synopsisHALLMARK_COAGULATION-0[[GO:0007596, GO:0006956, GO:0030168, GO:0042730, GO:0042060]][[GO:0030198, GO:0030574, GO:0007596, GO:0042730, GO:0002576, GO:0052547, GO:0045055, GO:0045862]]0.18
165gpt-3.5-turbono_synopsisHALLMARK_COAGULATION-1[[GO:0030198, GO:0007596, GO:0006508, GO:0006955]][[GO:0007596, GO:0006955]]0.50
166gpt-3.5-turbono_synopsisHALLMARK_COMPLEMENT-0[[c1q binding, GO:0006958, GO:0010951, GO:0043154, GO:2001237, GO:1903051]][[GO:0006956, GO:0002576, GO:0050776, GO:0009611, blood coagulation\\n\\nmechanism: genes involved in complement activation, platelet degranulation, regulation of immune response, response to wounding, and blood coagulation are enriched in this gene set. these functions are related to the prevention of thrombosis and regulation of the immune system]]0.00
167gpt-3.5-turbono_synopsisHALLMARK_COMPLEMENT-1[[GO:0006955, GO:0007596, GO:0030163, GO:0006508, GO:0010951, GO:0071345, GO:0010952, GO:0030194, GO:0030449]][[GO:0006955, GO:0007596, GO:0006508, GO:0030168, GO:0006954, GO:0010952]]0.36
168gpt-3.5-turbono_synopsisHALLMARK_DNA_REPAIR-0[[GO:0006260, GO:0006281, GO:0006397, GO:0006351, GO:0042278]][[GO:0006260, GO:0006281, dna binding and packaging, GO:0009117, GO:0006338]]0.25
169gpt-3.5-turbono_synopsisHALLMARK_DNA_REPAIR-1[[GO:0097747, GO:0003677, GO:0006397, GO:0006281]][[GO:0006260, GO:0006281, transcription elongation, GO:0006396, GO:0009117, GO:0003682]]0.11
170gpt-3.5-turbono_synopsisHALLMARK_E2F_TARGETS-0[[GO:0006260, GO:0007049, GO:0051301, GO:0140014, GO:0006281]][[GO:0006260, GO:0007049, GO:0007052, GO:0007059, GO:0007346, GO:0006281, GO:0006334]]0.33
171gpt-3.5-turbono_synopsisHALLMARK_E2F_TARGETS-1[[GO:0006260, GO:0006281, GO:0071897, GO:0006302, GO:0022616, GO:0006974, GO:0000075, dna damage recognition and signaling]][[GO:0006260, GO:0006281, GO:0051726, GO:0007059]]0.20
172gpt-3.5-turbono_synopsisHALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0[[GO:0030198, GO:0043062, GO:0042277, GO:0030199, GO:0007155, GO:0007229, GO:0043410, GO:0005125, GO:0043498, GO:0010646, GO:0071711, GO:0007166, GO:0008285, GO:0070374, GO:0043236, GO:0005509, GO:0030335]][[GO:0030198, GO:0030199, GO:0032964, GO:0071711, regulation of growth factor signaling, regulation of bmp signaling, regulation of tgf-beta signaling]]0.14
173gpt-3.5-turbono_synopsisHALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1[[GO:0030198, GO:0007155, GO:0005604, GO:0005581, GO:0007229, GO:0005925, GO:0005515, ecm-receptor interaction, GO:0030334, GO:0007010]][[GO:0030198, GO:0007155, GO:0007229, GO:0030574, GO:0009888, GO:0016477, GO:0071711]]0.21
174gpt-3.5-turbono_synopsisHALLMARK_ESTROGEN_RESPONSE_EARLY-0[[GO:0006811, GO:0006631, GO:0006006, GO:0032870, GO:0008203, drug binding]][[GO:0005509, GO:0006816, GO:0005516, GO:0010857, GO:0055074, GO:0005262, GO:0030899]]0.00
175gpt-3.5-turbono_synopsisHALLMARK_ESTROGEN_RESPONSE_EARLY-1[[GO:0006629, GO:0007165, transcriptional regulation]][[GO:0006811, GO:0023051, transport of small molecules, GO:0072657, GO:0009966, GO:0008202, GO:0010817, GO:0048522, GO:0010468, GO:0043066, GO:0051246, GO:0071363]]0.00
176gpt-3.5-turbono_synopsisHALLMARK_ESTROGEN_RESPONSE_LATE-0[[GO:0006351, GO:0008152, GO:0008283, GO:0006955, GO:0007165]][[GO:0005509, GO:0051302, GO:0042981, GO:0006816]]0.00
177gpt-3.5-turbono_synopsisHALLMARK_ESTROGEN_RESPONSE_LATE-1[[GO:0008152, GO:0007165, GO:0032502, GO:0006955, GO:0006351, GO:0019538, GO:0006810, GO:0001558, GO:0042981, GO:0006811]][[GO:0051726, GO:0008283, GO:0006260, GO:0051301, cancer progression]]0.00
178gpt-3.5-turbono_synopsisHALLMARK_FATTY_ACID_METABOLISM-0[[1. metabolic process \\n2. oxidation-reduction process \\n3. response to oxidative stress \\n4. lipid metabolic process \\n5. carbohydrate metabolic process \\n6. amino acid metabolic process \\n7. detoxification \\n8. fatty acid beta-oxidation \\n9. tca cycle \\n10. electron transport chain \\n11. glucose homeostasis \\n12. protein folding and stabilization \\n13. ion homeostasis]][[GO:0006635, mitochondrial beta-oxidation of fatty acids, GO:0015980, GO:0008152, GO:0044255, GO:0006084, coenzyme metabolic process, GO:0001676, GO:0019752, GO:0006099]]0.00
179gpt-3.5-turbono_synopsisHALLMARK_FATTY_ACID_METABOLISM-1[[GO:0006629, oxidative stress response, energy production]][[GO:0006631, MESH:D004734, mitochondrial function, GO:0016042, oxidative stress response]]0.14
180gpt-3.5-turbono_synopsisHALLMARK_G2M_CHECKPOINT-0[[GO:0022402, GO:0140014, GO:0007059, GO:0007052, GO:0000226, GO:0006260]][[cdc20, cdc25a, cdc25b, cdc27, cdc45, cdc6, cdc7, cdk1, cenpa, cenpe, cenpf, chek1, cks1b, cks2, dbf4, e2f1, e2f2, e2f3, e2f4, espl1, exo1, fbxo5, gins2, h2ax, h2az1, h2az2, h2bc12, hmmr, hus1, ilf3, incenp, katna1, kif11, kif15, kif20b, kif22, kif23, kif2c, kif4a, kif5b, kpna2, kpnb1, lig3, mad2l1, map3k20, mcm2, mcm3, mcm5, mcm6, ne]]0.00
181gpt-3.5-turbono_synopsisHALLMARK_G2M_CHECKPOINT-1[[GO:0006260, GO:0007049, GO:0006281, GO:0140014, GO:0007059]][[GO:0051726, GO:0006260, chromosomal segregation, GO:0051276, GO:0006281]]0.25
182gpt-3.5-turbono_synopsisHALLMARK_GLYCOLYSIS-0[[1. glycosylation\\n2. glycolysis\\n3. pentose phosphate pathway]][[GO:0006096, GO:0005978, glycosylation pathway]]0.00
183gpt-3.5-turbono_synopsisHALLMARK_GLYCOLYSIS-1[[GO:0006006, energy generation, GO:0016052, GO:0006096, GO:0006090, GO:0006099, GO:0022900, GO:0006119, GO:0006754]][[GO:0008152, GO:0006796, molecular function regulation, GO:0033554, GO:0031323, GO:0019538, GO:0050794, GO:0044281]]0.00
184gpt-3.5-turbono_synopsisHALLMARK_HEDGEHOG_SIGNALING-0[[GO:0030182, GO:0007411, GO:0016477, GO:0007155, GO:0008283]][[GO:0007399, nervous system neuron differentiation, nervous system development and angiogenesis, GO:0045765, GO:0023056, GO:0048598]]0.00
185gpt-3.5-turbono_synopsisHALLMARK_HEDGEHOG_SIGNALING-1[[GO:0007399, GO:0007165, GO:0007155]][[GO:0031175, GO:0007411, GO:0051960, GO:0007165, GO:0007267]]0.14
186gpt-3.5-turbono_synopsisHALLMARK_HEME_METABOLISM-0[[GO:0006811, GO:0005515, GO:0008152]][[GO:0015886, GO:0051536, [2fe-2s] cluster binding]]0.00
187gpt-3.5-turbono_synopsisHALLMARK_HEME_METABOLISM-1[[GO:0048821, GO:0045646, GO:0042541, GO:0015671, GO:0020037, GO:0005506, GO:0043496, GO:0046982]][[gene expression regulation; metabolism; transport\\n\\nmechanism and hypotheses:\\nthe genes in this list are involved in various cellular processes, including gene expression regulation, GO:0008152, and transport. gene expression regulation may be a mechanism by which these genes function, possibly through the involvement of transcription factors such as foxo3 and klf3. metabolism may also be a key mechanism, as many of these genes are involved in metabolic pathways, such as fech and alas2 in heme synthesis, and gclc and gclm in glutathione metabolism. transport may also be a contributing mechanism, as several genes in this list, such as slc2a1 and slc6a9, are involved in membrane transport of various molecules. overall, the commonality in function among these genes may be attributed to their roles in regulating cellular metabolism and transporting molecules across various membranes]]0.00
188gpt-3.5-turbono_synopsisHALLMARK_HYPOXIA-0[[GO:0008152, GO:0006096, GO:0006979, GO:0080135, GO:1901031, GO:0046324, GO:0006006, GO:0005975, GO:0006974]][[GO:0006110, GO:0051246, GO:0010628, GO:0030198, GO:0006006, GO:0009749, GO:0001558, GO:0008284, GO:0051094]]0.06
189gpt-3.5-turbono_synopsisHALLMARK_HYPOXIA-1[[glycolysis; gluconeogenesis; citrate cycle; pyruvate metabolism; atp production\\n\\nmechanism: these genes are enriched in functions related to energy metabolism, including glycolysis, GO:0006094, the citrate cycle, GO:0006090, and atp production. they are involved in various aspects of energy metabolism, such as glucose uptake and metabolism, GO:0005980, atp synthesis. the over-representation of these functions suggests that these genes may play a role in the regulation of energy metabolism at the cellular organismal level]][[hk1, hk2, pfkl, pfkfb3, gys1, pklr, pgk1, tpi1, aldoa, eno2, pgam2, pgm2, fbp1, eno1, ndst1, ndst2]]0.00
190gpt-3.5-turbono_synopsisHALLMARK_IL2_STAT5_SIGNALING-0[[il10ra, tnfrsf18, il18r1, il1r2, il1rl1, il2ra, il2rb, il4r, MESH:D016753, MESH:D018793, tnfrsf1b, tnfrsf21, tnfrsf4, tnfrsf8, tnfrsf9, tnfsf11, tnfsf10, ifngr1, ccr4, ctla4, cxcl10, icos, irf4, irf6, irf8, socs1, socs2, ager, cish, gata1, gbp4, spp1, bcl2, bcl2l1, bmpr2, ccnd2, ccne1, cd79b, galm, glipr2, gpx4, hk2, MESH:D016753, itga6, itgae, itih5, klf6, lif, lrig1, ltb, mxd1, myc]][[il2ra, il1r2, il2rb, il10ra, ctla4, cd44, MESH:D016753, il1rl1, il18r1, icos, tnfrsf4, tnfrsf18, tnfrsf8, tnfrsf21, tnfsf11, tnfrsf9, tnfsf10, tnfrsf1b, cd48, tnfrsf4, cxcl10, MESH:D018793, selp, ccne1, MESH:D047990, socs1, socs2]]0.39
191gpt-3.5-turbono_synopsisHALLMARK_IL2_STAT5_SIGNALING-1[[cytokine signaling pathway, GO:0006955, GO:0002682, GO:0006954, leukocyte migration and chemotaxis, GO:0002694, GO:0071347, GO:0032680]][[GO:0006955, cell signaling, GO:0005125, GO:0008009, GO:0008083, GO:0007166, GO:0002250, GO:0030595, GO:0050900, GO:0006954]]0.12
192gpt-3.5-turbono_synopsisHALLMARK_IL6_JAK_STAT3_SIGNALING-0[[GO:0006955, cytokine signaling pathway, GO:0060333, positive regulation of interleukin production, GO:0032729]][[GO:0019221, GO:0002757, GO:0007259, GO:0002694, regulation of leukocyte migration and chemotaxis, GO:0035456, GO:0034341, GO:0070555, GO:0070671, GO:0070741, response to tumor necrosis factor. \\n\\nhypotheses: these genes are involved in activating immune responses and cytokine-mediated signaling pathways. the enrichment of terms related to leukocyte activation and chemotaxis suggests an increased focus on the recruitment of immune cells to sites of infection and inflammation. the involvement of genes related to cytokine signaling, such as jak-stat cascade, suggests that the activation of immune responses may be regulated by cytokines released in response to infection or inflammation. overall, these genes are likely involved in the regulation of immune system activation and inflammation]]0.00
193gpt-3.5-turbono_synopsisHALLMARK_IL6_JAK_STAT3_SIGNALING-1[[GO:0005126, GO:0006955, GO:0050900, jak-stat signaling pathway, GO:0034341, GO:0002690, GO:0051249, GO:0001817, GO:0050863, GO:0019221, GO:1902105]][[cytokine signaling, GO:0006954, GO:0006955, interleukin signaling, GO:0008009, jak-stat signaling, toll-like receptor signaling]]0.06
194gpt-3.5-turbono_synopsisHALLMARK_INFLAMMATORY_RESPONSE-0[[GO:0050900, cytokine signaling, GO:0002224, GO:0006954, GO:0032729, GO:0045087, GO:0032733, GO:0030595]][[cytokine signaling, GO:0006955, GO:0006954]]0.22
195gpt-3.5-turbono_synopsisHALLMARK_INFLAMMATORY_RESPONSE-1[[cytokine signaling, chemokine signaling, GO:0050900, GO:0002250, GO:0045087]][[GO:0004896, GO:0042379, GO:0050900, GO:0002694, GO:0050778, GO:0045088, GO:0005149, GO:0042110, GO:0006952, GO:0006954, GO:0002685, GO:0034097]]0.06
196gpt-3.5-turbono_synopsisHALLMARK_INTERFERON_ALPHA_RESPONSE-0[[interferon signaling, GO:0045087, antiviral defense]][[GO:0051607, GO:0045087, interferon signaling, type i interferon response, viral defense]]0.33
197gpt-3.5-turbono_synopsisHALLMARK_INTERFERON_ALPHA_RESPONSE-1[[GO:0034341, GO:0002718, GO:0060333, GO:0045070, GO:0032897, innate immune response-activating signal transduction, GO:0060337, GO:0035457, antiviral mechanism by interferon-stimulated genes (isg)]][[GO:0051607, GO:0002376, GO:0140888]]0.00
198gpt-3.5-turbono_synopsisHALLMARK_INTERFERON_GAMMA_RESPONSE-0[[GO:0051607, GO:0035458, GO:0071357, GO:0045071, GO:0031323, GO:0002682, GO:0034097, GO:0034340]][[GO:0060337, GO:0006955, GO:0002579, GO:0051607, GO:0046596, GO:0032481, GO:0045087, GO:0034341, GO:0032727, GO:0002504, GO:0002479, GO:0032728, GO:0071357, GO:0043331, GO:0016032, GO:0045859, GO:0006954, GO:0060333, GO:0038187]]0.08
199gpt-3.5-turbono_synopsisHALLMARK_INTERFERON_GAMMA_RESPONSE-1[[interferon signaling, GO:0019882, GO:0045321]][[GO:0019882, interferon response, GO:0001816, GO:0006954, GO:0002376, GO:0050776, GO:0006952, GO:0009615, response to interferon]]0.09
200gpt-3.5-turbono_synopsisHALLMARK_KRAS_SIGNALING_DN-0[[GO:0005509, contractile fiber part, GO:0006936]][[GO:0005509, GO:0070588, GO:0051924, GO:0051899, GO:0042391, GO:0071277]]0.12
201gpt-3.5-turbono_synopsisHALLMARK_KRAS_SIGNALING_DN-1[[GO:0043167, GO:0007165, GO:0019222, GO:0050794, g protein-coupled receptor signaling, GO:0035556, GO:0031325, GO:0043066, metabolic process regulation, GO:0005509, GO:0034765, GO:0001932, GO:0043169, GO:0045859, GO:0051716]][[GO:0006811, neurological signaling, tissue development.\\n\\nmechanism]]0.00
202gpt-3.5-turbono_synopsisHALLMARK_KRAS_SIGNALING_UP-0[[GO:0006955, GO:0007165, GO:0050794, cytokine signaling, GO:0006954, GO:0006935, GO:0008284, GO:0043066]][[GO:0006955, cellular signaling, GO:0001525]]0.10
203gpt-3.5-turbono_synopsisHALLMARK_KRAS_SIGNALING_UP-1[[GO:0006955, GO:0006954, GO:0002694, GO:0001817, interleukin-10 signaling, tumor necrosis factor (tnf) signaling, GO:0006956, platelet activation and aggregation, eicosanoid synthesis]][[1. immune response\\n2. inflammatory response\\n3. coagulation\\n4. positive regulation of endothelial cell migration \\n5. cell adhesion\\n6. positive regulation of cell migration \\n7. signal transduction \\n8. negative regulation of apoptotic process \\n9. regulation of angiogenesis \\n10. positive regulation of protein serine/threonine kinase activity \\n11. positive regulation of transcription from rna polymerase ii promoter \\n\\nmechanism: the enriched functions suggest that these genes play an important role in innate and adaptive immune responses, inflammatory processes, GO:0007596, cell adhesion and migration, GO:0001525, and signal transduction pathways. they could be involved in regulating the expression and activity of various immune cells, MESH:D016207, chemokines to modulate immunity inflammation. the coagulation-related genes may contribute to thrombotic disorders cardiovascular diseases by affecting blood clot formation fibrinolysis. the cell adhesion migration-related genes are potentially involved in tumor metastasis progression through facilitating cell invasion motility. the signal]]0.00
204gpt-3.5-turbono_synopsisHALLMARK_MITOTIC_SPINDLE-0[[GO:0007018, GO:0007052, cell division, chromosome separation]][[GO:0007052, GO:0007017, GO:0051301, GO:0007010, GO:0030029]]0.14
205gpt-3.5-turbono_synopsisHALLMARK_MITOTIC_SPINDLE-1[[kinesin family members, microtubule formation and stabilization, spindle formation and assembly, GO:0000910, GO:0051726, gene expression and chromosome segregation]][[GO:0007051, GO:0031023, GO:0007059, GO:0071173, GO:0051382, GO:0007052, GO:0000226, GO:0007098, GO:0007020, GO:0000075, GO:0007018, GO:0007346, GO:0000070, GO:0001578, GO:0008017, GO:0000910, GO:0030953]]0.05
206gpt-3.5-turbono_synopsisHALLMARK_MTORC1_SIGNALING-0[[GO:0006457, GO:0050776, GO:0009117, GO:0006629, gluconeogenesis and glycolysis, mrna processing and splicing]][[glycolysis; tca cycle; cholesterol biosynthesis; pentose phosphate pathway\\n\\nmechanism and hypotheses:\\nthe enriched terms suggest that these genes are involved in various aspects of cellular metabolism. glycolysis is the central pathway for glucose metabolism, converting glucose into pyruvate. the tca cycle is responsible for generating energy from the breakdown of carbohydrates, MESH:D005227, and amino acids. the cholesterol biosynthesis pathway is responsible for producing cholesterol, which is involved in membrane structure, steroid hormone synthesis, and bile salt production. the pentose phosphate pathway is involved in the production of nadph, which is critical for many cellular processes, including antioxidant defense and biosynthesis.\\n\\noverall, these genes are likely involved in regulating various aspects of cellular metabolism, including energy production, biosynthesis of important molecules like cholesterol and nadph, mediating the cellular response to oxidative stress]]0.00
207gpt-3.5-turbono_synopsisHALLMARK_MTORC1_SIGNALING-1[[GO:0044237, protein regulation, transcriptional regulation, translation regulation, GO:0006281, stress response.\\n\\nmechanism: these enriched terms suggest that the identified genes are involved in several pathways, including maintaining cellular metabolism and homeostasis, regulating transcription and translation of proteins, repairing dna in response to damage, and responding to cellular stress]][[GO:0051087, GO:0006457, co-factor binding, GO:0008152, GO:0005524]]0.00
208gpt-3.5-turbono_synopsisHALLMARK_MYC_TARGETS_V1-0[[GO:0006412, GO:0006457, GO:1990904, u4/u6.u5 tri-snrnp, chaperone-mediated protein folding.\\n\\nmechanism: these genes are involved in protein synthesis and processing, including translation and ribosome biogenesis. many of them are also involved in protein folding and chaperone-mediated protein folding. the u4/u6.u5 tri-snrnp is also highly represented, indicating these genes may be involved in splicing]][[GO:0006397, GO:0006413, GO:0042254]]0.00
209gpt-3.5-turbono_synopsisHALLMARK_MYC_TARGETS_V1-1[[GO:0006396, GO:0006413, GO:0006446, GO:0042254, GO:0008380, GO:0006397]][[GO:0006396, GO:0006412, GO:0042254, GO:0006402, GO:0043488, regulation of mrna splicing, GO:0043393, GO:0008380, GO:0006417, GO:0003723]]0.23
210gpt-3.5-turbono_synopsisHALLMARK_MYC_TARGETS_V2-0[[GO:0042254, GO:0008033, GO:0006364, GO:0016072, GO:0009451, GO:0022613]][[GO:0042254, GO:0006364, GO:0003723, GO:0005681, GO:0006413]]0.22
211gpt-3.5-turbono_synopsisHALLMARK_MYC_TARGETS_V2-1[[GO:0042254, GO:0006364, GO:0000394, rna polymerase ii regulation, rna processing and modification]][[GO:0006396, GO:0022613, GO:0042254, GO:0000166, GO:0003723, GO:0090304, GO:0042273, GO:0006364, GO:0065004]]0.17
212gpt-3.5-turbono_synopsisHALLMARK_MYOGENESIS-0[[GO:0006936, GO:0006816, z-disc, UBERON:0002036, GO:0030017, MESH:D014335, GO:0005861, GO:0071689]][[muscle filament sliding; sarcomere organization; muscle system process\\n\\nmechanism: the majority of the listed genes are involved in muscle contraction and development, specifically in the organization and structure of the sarcomere. the enriched terms - muscle filament sliding, GO:0045214, muscle system process - all relate to the mechanisms of muscle contraction the intricate process of sarcomere formation]]0.00
213gpt-3.5-turbono_synopsisHALLMARK_MYOGENESIS-1[[UBERON:0001630, MESH:D009218, MESH:D000199, MESH:D014336, filament]][[GO:0003012, GO:0006936, GO:0045214, GO:0030029]]0.00
214gpt-3.5-turbono_synopsisHALLMARK_NOTCH_SIGNALING-0[[GO:0007219, GO:0045165, GO:0022008, GO:0030154, GO:0045893, GO:0043066, GO:0008285, GO:0043065, GO:0045747, GO:0016055, GO:0007268]][[GO:0007219, GO:0008593, GO:0016055, GO:0030111, GO:0045944, GO:0045596, GO:0045597]]0.12
215gpt-3.5-turbono_synopsisHALLMARK_NOTCH_SIGNALING-1[[GO:0051726, GO:0030154, GO:0001709, transcriptional regulation, GO:0016567]][[GO:0007219, GO:0005515, GO:0000122, GO:0000988]]0.00
216gpt-3.5-turbono_synopsisHALLMARK_OXIDATIVE_PHOSPHORYLATION-0[[GO:0022900, GO:0045333, GO:0002082]][[GO:0042773, mitochondrial atp synthesis coupled electron transport in respiratory chain, GO:0033108, GO:0006979]]0.00
217gpt-3.5-turbono_synopsisHALLMARK_OXIDATIVE_PHOSPHORYLATION-1[[GO:0006119, GO:0005746, GO:0070469, GO:0005739, MESH:D004734, GO:0031966, GO:0006099, GO:0006635, citrate cycle, GO:0098798, GO:0006754, GO:0051536]][[GO:0003954, GO:0022900, GO:0042773, GO:0005743, GO:0007005, GO:0006119, GO:0033108, respiratory chain complex i, ii, iii, iv, v, vi, GO:0006743, GO:0006631]]0.05
218gpt-3.5-turbono_synopsisHALLMARK_P53_PATHWAY-0[[GO:0006974, GO:0051726, cell growth and proliferation]][[GO:0051726, GO:0006915, GO:0008285, GO:0006974, negative regulation of cellular process.\\n\\nmechanism: the genes in this list are enriched in functions that regulate the cell cycle and cell death. specifically, they are involved in cell cycle arrest, apoptosis, negative regulation of cell proliferation, and response to dna damage stimulus]]0.33
219gpt-3.5-turbono_synopsisHALLMARK_P53_PATHWAY-1[[GO:0051726, GO:0006281, GO:0030330, GO:0000082, response to dna damage]][[GO:0006974, GO:0051726, GO:0006915, GO:0006281, MESH:D002470, p53 signaling, checkpoint regulation, transcriptional regulation, GO:0006338]]0.17
220gpt-3.5-turbono_synopsisHALLMARK_PANCREAS_BETA_CELLS-0[[pancreatic development, beta cell differentiation, GO:0030073, GO:0042593, GO:0006006]][[GO:0030073, GO:0042593, GO:0003309, GO:0003323, pancreatic beta cell function, pancreatic islet cell development]]0.22
221gpt-3.5-turbono_synopsisHALLMARK_PANCREAS_BETA_CELLS-1[[GO:0003323, GO:0030073, glucose regulation, diabetes-related pathways]][[GO:0003323, GO:0030073, GO:0042593, GO:0031018, GO:0050796, GO:0006006, positive regulation of pancreatic beta cell differentiation, GO:0010827, regulation of insulin secretion by glucose]]0.18
222gpt-3.5-turbono_synopsisHALLMARK_PEROXISOME-0[[GO:0006631, GO:0006805, steroid hormone biosynthesis]][[GO:0140359, GO:0006631, GO:0006695, GO:0035357, GO:0005777]]0.14
223gpt-3.5-turbono_synopsisHALLMARK_PEROXISOME-1[[GO:0006631, GO:0007031, GO:0015721, GO:0006282]][[GO:0006631, GO:0006629, GO:0008202, GO:0030301, GO:0006641, GO:0008206, GO:0005777]]0.10
224gpt-3.5-turbono_synopsisHALLMARK_PI3K_AKT_MTOR_SIGNALING-0[[mapk cascade; pi3k-akt signaling pathway; regulation of cell proliferation\\n\\nmechanism: the enriched terms suggest that the common function of the listed genes is to regulate cellular processes related to signal transduction and cell cycle/apoptosis. the mapk cascade is a crucial signaling pathway that controls the expression of genes required for cellular proliferation, differentiation, and survival. pi3k-akt signaling pathway controls cell survival, GO:0040007, and metabolism. the enriched term \"regulation of cell proliferation\" suggests that the listed genes contribute to regulating the balance between cell growth and division. these genes could affect the rate of cellular proliferation, arresting or promoting the cell cycle or modulating apoptotic signal transduction]][[GO:0016301, GO:0006468, GO:0010646, GO:0035556, regulation of map kinase activity\\n\\nmechanism: these genes are involved in several signaling pathways and primarily regulate protein kinase activity and phosphorylation. they are involved in the regulation of cell communication and intracellular signaling cascades, including the map kinase cascade]]0.00
225gpt-3.5-turbono_synopsisHALLMARK_PI3K_AKT_MTOR_SIGNALING-1[[GO:0033554, GO:0035556, GO:0006468, GO:0042981, GO:0080135]][[GO:0007165, GO:0006468, GO:0008152, GO:0001558, GO:0042127, GO:0042981, GO:0045859, GO:0043408, GO:0032024, GO:0005975, GO:0010906, GO:0010604]]0.13
226gpt-3.5-turbono_synopsisHALLMARK_PROTEIN_SECRETION-0[[GO:0016192, GO:0046907, GO:0006897, GO:0061024, GO:0008104, GO:0048193]][[GO:0016192, endosome to golgi transport, GO:0006886, GO:0008104, GO:0015031, regulation of membrane organization and biogenesis]]0.20
227gpt-3.5-turbono_synopsisHALLMARK_PROTEIN_SECRETION-1[[GO:0048193, GO:0005768, GO:0005764, GO:0006612, GO:0006886, GO:0042391, GO:0034765, GO:0005773]][[GO:0006886, GO:0006891, GO:0007030, GO:0072583]]0.09
228gpt-3.5-turbono_synopsisHALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0[[GO:0016209, GO:0051920, GO:0006749, GO:0006979, GO:0070301]][[GO:0016209, redox regulation, GO:0006749, oxidation-reduction process, GO:0006979]]0.43
229gpt-3.5-turbono_synopsisHALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1[[GO:0016209, regulation of iron ion binding, GO:0006979, GO:0048821, GO:2000378, GO:0006282, GO:0070301, GO:0050790, GO:0032092, regulation of thiol-dependent ubiquitinyl hydrolase activity, GO:0034599]][[oxidative stress response, redox regulation, GO:0006749, GO:0016209, GO:0000302]]0.07
230gpt-3.5-turbono_synopsisHALLMARK_SPERMATOGENESIS-0[[GO:0007283, GO:0140013, GO:0007130, GO:0007281, GO:0097722, oocyte meiosis]][[GO:0140013, GO:0007283, GO:0007059, GO:0051301, GO:0140014]]0.22
231gpt-3.5-turbono_synopsisHALLMARK_SPERMATOGENESIS-1[[GO:1903047, GO:0010971, regulation of spindle assembly checkpoint, GO:0034501, GO:0090234, GO:0051985, GO:0110028]][[GO:0007052, GO:0007059, GO:0007094]]0.00
232gpt-3.5-turbono_synopsisHALLMARK_TGF_BETA_SIGNALING-0[[tgf-beta signaling pathway, GO:0030514, GO:0090287, GO:0030513, GO:0006351, GO:0006355, GO:0045893, GO:0000122]][[GO:0030509, GO:0000122, GO:0045944, GO:0048705, GO:0007183, GO:0007179]]0.08
233gpt-3.5-turbono_synopsisHALLMARK_TGF_BETA_SIGNALING-1[[tgf-beta signaling pathway, GO:0030509, GO:0030513, GO:0030198, GO:0060391]][[GO:0007179, GO:0030514, GO:0010990]]0.00
234gpt-3.5-turbono_synopsisHALLMARK_TNFA_SIGNALING_VIA_NFKB-0[[ccl2, ccl20, ccl4, ccl5, ccn1, ccnd1, ccrl2, cd44, cd69, cd80, cd83, cdkn1a, icam1, icoslg, ifih1, ifit2, ifngr2, GO:0043514, il15ra, MESH:D020382, il1a, il1b, GO:0070743, MESH:D015850, il6st, il7r, inhba, irf1, jag1, nfkb1, nfkb2, nfkbia, nfkbie, nr4a1, nr4a2, nr4a3, ptger4, MESH:D051546, rel, rela, relb, ripk2, stat5a, tlr2, tnf, tnfaip2, tnfaip3, tnfaip6, tnfaip8, tnfrsf9, tnfsf9, tnip1, tnip]][[GO:0006955, GO:0006954, GO:0034097, GO:0050865, GO:0071624, GO:0032855, GO:0010552, GO:0051092, GO:0043406, GO:0007259, GO:0043065, GO:0004672]]0.00
235gpt-3.5-turbono_synopsisHALLMARK_TNFA_SIGNALING_VIA_NFKB-1[[cytokine signaling, GO:0000988, stress response, GO:0050776, GO:0006954]][[GO:0006955, GO:0006954, GO:0032680, GO:0001816, GO:0032496, negative regulation of nf-kappab transcription factor activity.\\n\\nmechanism and]]0.10
236gpt-3.5-turbono_synopsisHALLMARK_UNFOLDED_PROTEIN_RESPONSE-0[[GO:0006457, GO:0036503, upr signaling pathway]][[GO:0006457, MESH:M0354322, ubiquitin-mediated proteolysis, GO:0034976, GO:0006986, GO:0006397, GO:0008380]]0.11
237gpt-3.5-turbono_synopsisHALLMARK_UNFOLDED_PROTEIN_RESPONSE-1[[GO:0006457, GO:0006605, GO:0006396, GO:0006950, GO:0006417, GO:0016481, GO:0006986, GO:0006913, GO:0008380, GO:1903021, GO:0016032, GO:0032496, GO:0072659, GO:0017148, GO:0022613, negative regulation of transcription by rna polymerase]][[GO:0006457, chaperone-mediated protein processing, GO:0015031, GO:0007029, GO:0006986]]0.11
238gpt-3.5-turbono_synopsisHALLMARK_UV_RESPONSE_DN-0[[tgf-beta signaling pathway, GO:0030198, GO:0007155, GO:0030334, GO:0042127]][[GO:0004672, GO:0003700, GO:0006355, GO:0035556, cytoplasmic membrane-bounded vesicle, receptor protein signaling pathway, GO:0007155, GO:0001932, GO:0007399, GO:0007498, GO:0045666]]0.07
239gpt-3.5-turbono_synopsisHALLMARK_UV_RESPONSE_DN-1[[GO:0030198, GO:0030036, GO:0030155, GO:0007160, GO:0016477, GO:0007229, GO:0030199, GO:0035023, GO:0030178, basement membrane formation, GO:0014909]][[GO:0030198, GO:0007165, GO:0008083, neural development, GO:0022008]]0.07
240gpt-3.5-turbono_synopsisHALLMARK_UV_RESPONSE_UP-0[[GO:0006355, regulation of transcription, dna-templated; go:0044267, cellular protein metabolic process; go:0009968, GO:0009968]][[GO:0033554, GO:0031323, GO:0051050, GO:0009966]]0.00
241gpt-3.5-turbono_synopsisHALLMARK_UV_RESPONSE_UP-1[[GO:0006955, GO:0008104, GO:0051726]][[GO:0008104, GO:0006950, GO:0042981, GO:0008283, GO:0006979, regulation of transcription, GO:0006974, GO:0007049, response to hypoxia.\\n\\nmechanism]]0.09
242gpt-3.5-turbono_synopsisHALLMARK_WNT_BETA_CATENIN_SIGNALING-0[[GO:0016055, GO:0007219, transcriptional regulation, GO:0030154, GO:0008283]][[cellular response to wnt stimulus, GO:0090263, GO:0045746]]0.00
243gpt-3.5-turbono_synopsisHALLMARK_WNT_BETA_CATENIN_SIGNALING-1[[GO:0007219, GO:0045747, GO:0045746, GO:0045165]][[GO:0016055, GO:0007219, GO:0005515, GO:0008134]]0.14
244gpt-3.5-turbono_synopsisT cell proliferation-0[[cd28 co-stimulation, il-2 signaling, GO:0042110]][[GO:0002376, GO:0042110, GO:0001816, GO:0046649, GO:0006955, GO:0007166]]0.12
245gpt-3.5-turbono_synopsisT cell proliferation-1[[GO:0042110, GO:0051247, GO:0001817]][[t cell activation; cytokine signaling; lymphocyte proliferation; immune response\\n\\nmechanism: these genes are all involved in the regulation and function of the immune system, specifically in t cell activation, GO:0046651, and cytokine signaling pathways. they play a role in immune responses to pathogens, MONDO:0007179, MONDO:0004992]]0.00
246gpt-3.5-turbono_synopsisYamanaka-TFs-0[[GO:0000988, transcriptional regulation, GO:0030154, GO:0008283, stem cell maintenance, MESH:D047108]][[GO:0000988, GO:0003677, GO:0048863]]0.12
247gpt-3.5-turbono_synopsisYamanaka-TFs-1[[MESH:D047108, regulation of transcription, GO:0048863]][[pluripotency, self-renewal, GO:0048863]]0.20
248gpt-3.5-turbono_synopsisamigo-example-0[[GO:0030198, GO:0030199, GO:0001525, GO:0001568, GO:0030168, GO:0001666, GO:0001936]][[extracellular matrix organization; angiogenesis; positive regulation of cell migration; positive regulation of endothelial cell migration; positive regulation of sprouting angiogenesis; positive regulation of angiogenesis; positive regulation of vascular endothelial cell migration; positive regulation of smooth muscle cell migration; positive regulation of vascular smooth muscle cell migration; positive regulation of tube formation; positive regulation of endothelial cell proliferation; positive regulation of vascular endothelial growth factor production. \\n\\nhypotheses: several of the genes in the list encode for extracellular matrix components or regulators of matrix organization, including col3a1, col5a2, lum, postn, and vcan. others, such as cxcl6, pdgfa, pf4, and vegfa, encode for angiogenic growth factors. itgav is a common denominator and is associated with integrin-mediated signaling that regulates cell adhesion, migration, angiogenesis. fgfr1 has also been shown to play a critical role in angiogenesis extracellular matrix organization by regulating downstream signaling pathways such as pi3k mapk]]0.00
249gpt-3.5-turbono_synopsisamigo-example-1[[GO:0030198, GO:0030155, regulation of cell substrate adhesion, GO:0045785, GO:0043062]][[GO:0030198, GO:0007155, GO:0001525, GO:0016477, GO:0030334, GO:0008284, GO:0043410]]0.09
250gpt-3.5-turbono_synopsisbicluster_RNAseqDB_0-0[[GO:0005509, GO:0050804, transcriptional regulation, GO:0050808]][[GO:0030182, GO:0006811, GO:0000988, GO:0005509, GO:0007399, GO:0007267, synapse assembly and organization, g protein-coupled receptor signaling, GO:0003723, GO:0005515]]0.08
251gpt-3.5-turbono_synopsisbicluster_RNAseqDB_0-1[[GO:0007186, GO:0010468, GO:0007154, GO:0006355, GO:0005515, GO:0007155, GO:0001932, GO:0016055, GO:0030334, GO:0007165, GO:0043408, GO:0003677, GO:0006357, GO:0005543, GO:0051493, GO:0006811]][[GO:0006396, GO:0008134, GO:0006355, GO:0003682, GO:0005634, GO:0003723, GO:0006397, transcriptional regulation, GO:0061629]]0.04
252gpt-3.5-turbono_synopsisbicluster_RNAseqDB_1002-0[[atp hydrolysis coupled calcium ion transport, GO:0030036, GO:0006936, GO:0033365, GO:0051147, GO:0014743, GO:0045214]][[GO:0006936, GO:0045214, GO:0006941, GO:0060048]]0.22
253gpt-3.5-turbono_synopsisbicluster_RNAseqDB_1002-1[[GO:0006936, MESH:D024510, GO:0007519, GO:0055001, GO:0030239, GO:0007517]][[GO:0006936, GO:0033275, GO:0031034, GO:0005509, GO:0045214, MESH:D024510]]0.20
254gpt-3.5-turbono_synopsisendocytosis-0[[GO:0006897, GO:0016192, GO:0007041, GO:0007032, GO:0030163]][[GO:0030301, GO:0006629, GO:0006897, GO:0030163]]0.29
255gpt-3.5-turbono_synopsisendocytosis-1[[GO:0006897, GO:0006898, GO:0016197, GO:0015031, GO:0006886, GO:0007032, GO:0016192, endosomal sorting]][[GO:0006897, GO:0007032, GO:0036010, GO:0006898, GO:0016192]]0.44
256gpt-3.5-turbono_synopsisglycolysis-gocam-0[[GO:0006096, GO:0005975, GO:0006006, GO:0019318]][[GO:0006006, GO:0006096]]0.50
257gpt-3.5-turbono_synopsisglycolysis-gocam-1[[GO:0006096, GO:0006006, GO:0006007]][[GO:0005975, GO:0006006, GO:0006096, GO:0006754]]0.40
258gpt-3.5-turbono_synopsisgo-postsynapse-calcium-transmembrane-0[[GO:0005509, GO:0005262, GO:0019722, GO:0006874, GO:0034765]][[GO:0006816, GO:0015075, GO:0099601, GO:0007268, GO:0034765]]0.11
259gpt-3.5-turbono_synopsisgo-postsynapse-calcium-transmembrane-1[[GO:0005509, GO:0004970, GO:0051966, GO:0046928, GO:0005216, GO:0034765, GO:0004672, GO:0051924, GO:0051247]][[GO:0005216, neurotransmitter signaling, GO:0050804, GO:0005509, GO:0008066]]0.17
260gpt-3.5-turbono_synopsisgo-reg-autophagy-pkra-0[[GO:0033554, GO:0010506, GO:0007165]][[GO:0006950, GO:0006915, GO:0042981, GO:0043123, GO:0046330]]0.00
261gpt-3.5-turbono_synopsisgo-reg-autophagy-pkra-1[[GO:0097190, GO:0016485, GO:0031323]][[autophagy regulation, GO:0033554, GO:0006915]]0.00
262gpt-3.5-turbono_synopsishydrolase activity, hydrolyzing O-glycosyl compounds-0[[glycoside hydrolase activity, GO:0005975, GO:0006027, GO:0009311, GO:0005764, GO:0005783, catabolism of carbohydrate, MONDO:0019249]][[GO:0005975, GO:0005764, GO:0016798, glycoside hydrolase activity, GO:0004556, GO:0008422, acid alpha-glucosidase activity, GO:0004565, GO:0015929, GO:0015923, n-acetylglucosaminidase activity, GO:0004308, GO:0015926, GO:0005980, GO:0006027, mucopolysaccharide catabolic process, GO:0016266, GO:0006491]]0.18
263gpt-3.5-turbono_synopsishydrolase activity, hydrolyzing O-glycosyl compounds-1[[GO:0006096, metabolism of carbohydrates, GO:0019318, GO:0006013, GO:0009311, chitin catabolic/metabolic process, hyaluronan catabolic/metabolic process, glycosphingolipid metabolic/catabolic process, sialic acid catabolic/metabolic process]][[GO:0005975, GO:0070085, GO:0000272, GO:0004553, GO:0015929, GO:0004556, GO:0004565]]0.00
264gpt-3.5-turbono_synopsisig-receptor-binding-2022-0[[GO:0002377, t cell receptor signaling, GO:0042113, t cell activation. \\n\\nhypotheses: this list of genes is heavily enriched in those involved in the function and development of b cells and t cells. specifically, they play a role in the production and function of immunoglobulins and t cell receptors, as well as the activation of these cell types. this suggests that these genes are integral to the proper functioning of the immune system]][[GO:0002376, GO:0046649, GO:0002250, GO:0042113, GO:0003823, antibody-mediated immunity\\n\\nmechanism]]0.11
265gpt-3.5-turbono_synopsisig-receptor-binding-2022-1[[GO:0006955, GO:0046649, GO:0030098]][[GO:0002377, GO:0042113, GO:0016064]]0.00
266gpt-3.5-turbono_synopsismeiosis I-0[[meiotic recombination, crossover formation, GO:0007130, GO:0006281, GO:0035825]][[GO:0006281, GO:0035825, GO:0140013, GO:0007059, GO:0007129, GO:0006974, m phase of meiosis, dna replication-independent nucleosome assembly, crossover junction formation, GO:0007281, GO:0036093, GO:0009994, GO:0007283, GO:0071173, GO:0006298, GO:0033554]]0.11
267gpt-3.5-turbono_synopsismeiosis I-1[[GO:0007059, GO:0051321, GO:0006310, synapsis of chromosomes, GO:0051276, GO:0051177]][[GO:0140013, GO:0006281, GO:0007059, MESH:D011995, GO:0035825, GO:0006302, GO:0007129, crossing-over, GO:0051276]]0.15
268gpt-3.5-turbono_synopsismolecular sequestering-0[[GO:0002376, GO:0006950, GO:0006457, GO:0051641, GO:0006396, GO:0006829, GO:0010467, GO:0007165]][[GO:0034599, GO:0001558, GO:0032088, GO:0043066, GO:0051726, GO:0010468, GO:0008285]]0.00
269gpt-3.5-turbono_synopsismolecular sequestering-1[[GO:0006979, GO:0032088, GO:0055072, GO:0016567, GO:0043066]][[GO:0006979, GO:0006974, GO:0080135, regulation of protein localization to organelles, GO:0043065, GO:0043066, GO:0008285, GO:0050821]]0.18
270gpt-3.5-turbono_synopsismtorc1-0[[GO:0006457, GO:0050776, GO:0009117, GO:0006629, gluconeogenesis and glycolysis, mrna processing and splicing]][[glycolysis; tca cycle; cholesterol biosynthesis; pentose phosphate pathway\\n\\nmechanism and hypotheses:\\nthe enriched terms suggest that these genes are involved in various aspects of cellular metabolism. glycolysis is the central pathway for glucose metabolism, converting glucose into pyruvate. the tca cycle is responsible for generating energy from the breakdown of carbohydrates, MESH:D005227, and amino acids. the cholesterol biosynthesis pathway is responsible for producing cholesterol, which is involved in membrane structure, steroid hormone synthesis, and bile salt production. the pentose phosphate pathway is involved in the production of nadph, which is critical for many cellular processes, including antioxidant defense and biosynthesis.\\n\\noverall, these genes are likely involved in regulating various aspects of cellular metabolism, including energy production, biosynthesis of important molecules like cholesterol and nadph, mediating the cellular response to oxidative stress]]0.00
271gpt-3.5-turbono_synopsismtorc1-1[[GO:0006457, GO:0015031, GO:0042254]][[GO:0006810, GO:0008152, GO:0006457]]0.20
272gpt-3.5-turbono_synopsisperoxisome-0[[GO:0005778, peroxisome targeting, GO:0007031]][[GO:0007031, peroxisome biogenesis, protein import into peroxisome, peroxisome membrane organization, peroxisomal matrix organization]]0.14
273gpt-3.5-turbono_synopsisperoxisome-1[[peroxisome biogenesis, peroxisome membrane organization, GO:0016559]][[GO:0007031, peroxisome biogenesis, GO:0016559]]0.50
274gpt-3.5-turbono_synopsisprogeria-0[[GO:0006281, GO:0051276, regulation of transcription]][[GO:0006281, GO:0006997, GO:0010467, GO:0007568]]0.17
275gpt-3.5-turbono_synopsisprogeria-1[[GO:0006281, GO:0006325, GO:0090398]][[GO:0006325, GO:0006281, GO:0000723, nuclear localization, nuclear lamina organization, genome stability regulation]]0.29
276gpt-3.5-turbono_synopsisregulation of presynaptic membrane potential-0[[GO:0004970, GO:0099536, GO:0001505, GO:0007268, GO:0043269, GO:0005244, GO:0042391]][[GO:0006811, GO:0048666, GO:0007268, GO:0042391, GO:0034765]]0.20
277gpt-3.5-turbono_synopsisregulation of presynaptic membrane potential-1[[GO:0005216, GO:0007268, GO:0005261, GO:0007215, GO:0019228, GO:0006813, GO:0060080, MESH:D005680, sodium ion transport. \\n\\nhypotheses: \\n1. the enrichment of ion channel activity-related terms suggests that the genes play a crucial role in regulating ion transport during neuronal signaling, which in turn influences synaptic plasticity and memory formation.\\n2. the enrichment of synaptic transmission-related terms points towards the involvement of the genes in various aspects of synaptic signaling, including the glutamate and gaba receptor signaling pathways, inhibition of neuronal activity, and modulation of action potential generation. \\n3. overall, the enrichment of these terms hints at a potential interaction between the listed genes in regulating various aspects of neural signal processing, synaptic transmission, and plasticity]][[GO:0005216, GO:0042803, GO:0008066, GO:0016917, GO:0005261]]0.17
278gpt-3.5-turbono_synopsissensory ataxia-0[[mitochondrial function, GO:0006457, GO:0030163, GO:0055085]][[GO:0042552, GO:0007411, GO:0007399, GO:0008104, GO:0031175]]0.00
279gpt-3.5-turbono_synopsissensory ataxia-1[[\"nervous system development\", \"axon guidance\", \"myelination\", \"neuron projection\", \"synaptic transmission\"]][[GO:0044237, neurological development, myelin sheath formation]]0.00
280gpt-3.5-turbono_synopsisterm-GO:0007212-0[[GO:0030594, GO:0007186, GO:0046928, GO:0007212, GO:0007188]][[GO:0007186, GO:0007188, GO:0046928, GO:0032225, positive regulation of camp biosynthetic process, GO:0007194, GO:0007212, prostaglandin receptor signaling pathway]]0.44
281gpt-3.5-turbono_synopsisterm-GO:0007212-1[[g protein coupled receptor signaling pathway, g protein beta/gamma subunit complex binding]][[GO:0007186, dopamine receptor activity, GO:0007188, GO:0004952, GO:0099528, d1 dopamine receptor signaling pathway]]0.00
282gpt-3.5-turbono_synopsistf-downreg-colorectal-0[[transcriptional regulation, GO:0006325]][[transcription regulation, GO:0016569, GO:0032502, GO:0065004, GO:0006950]]0.00
283gpt-3.5-turbono_synopsistf-downreg-colorectal-1[[GO:0003677, regulation of transcription, GO:0003682, GO:0008134, GO:0003713, negative regulation of transcription]][[GO:0003677, transcriptional regulation, GO:0010468, GO:0000988, GO:0003682, GO:0006357, GO:0006355, GO:0000977, GO:0043565, GO:0051090]]0.14
284gpt-3.5-turboontological_synopsisEDS-0[[GO:0030199, GO:0030198, GO:0006024, GO:0061448]][[GO:0030199, GO:0061448, GO:0062023, GO:0030198, GO:0006024]]0.80
285gpt-3.5-turboontological_synopsisEDS-1[[GO:0030199, GO:0030198, GO:0030166, GO:0061448]][[GO:0030198, GO:0030199, GO:0030166, GO:0006024, GO:0061448]]0.80
286gpt-3.5-turboontological_synopsisFA-0[[GO:0006281, GO:0000724, GO:0006513, fanconi anemia complementation group]][[GO:0006281, GO:0006513]]0.50
287gpt-3.5-turboontological_synopsisFA-1[[GO:0006281, GO:0006513, GO:0000724, fanconi anemia complementation group, GO:0000785, GO:0005654, GO:0140513]][[GO:0006281, GO:0006513]]0.29
288gpt-3.5-turboontological_synopsisHALLMARK_ADIPOGENESIS-0[[fad binding activity, GO:0016407, lipid binding activity, coenzyme binding, identical protein binding activity, citrate biosynthetic process]][[mitochondrial function, GO:0006754, GO:0006629, GO:0005515, GO:0023052]]0.00
289gpt-3.5-turboontological_synopsisHALLMARK_ADIPOGENESIS-1[[mitochondrial respiration, mitochondrial function, GO:0008152, energy production, GO:0022900, GO:0006629, GO:0006631, GO:0006637]][[GO:0005746, GO:0022900, GO:0006754, GO:0006631, GO:0015746, GO:0016746, dehydrogenase activity, GO:0016491, GO:0022857]]0.13
290gpt-3.5-turboontological_synopsisHALLMARK_ALLOGRAFT_REJECTION-0[[GO:0005125, GO:0004896, integrin binding activity, GO:0004672, GO:0000988, t-cell receptor binding activity, abc-type peptide antigen transporter activity.\\n\\nmechanism: these genes are involved in various aspects of immune response, including cytokine activity, cytokine receptor activity, and t-cell receptor binding activity. they also play a role in antigen processing and presentation through the abc-type peptide antigen transporter activity. the integrin binding activity reflects the involvement of integrins in leukocyte adhesion and migration. finally, the transcription factor activity reflects the importance of transcriptional regulation in immune responses]][[GO:0005125, chemokine receptor binding activity, interleukin receptor binding activity, mhc class protein complex binding activity, identical protein binding activity\\n\\nmechanism: these genes are involved in the regulation of the immune response, including the production of cytokines and chemokines, binding to immune receptors, and mhc class protein complex binding. their common function is likely related to the regulation of the immune system and the activation of the immune response against foreign invaders]]0.09
291gpt-3.5-turboontological_synopsisHALLMARK_ALLOGRAFT_REJECTION-1[[GO:0005125, GO:0008009, mhc class ii protein complex binding activity, signaling receptor binding activity, protein kinase binding activity, integrin binding activity, identical protein binding activity, sh2 domain binding activity, GO:0004252, rna binding activity, GO:0046982, GO:0008083]][[GO:0005125, chemokine receptor binding activity, GO:0004672, GO:0004896, identical protein binding activity, integrin binding activity, GO:0002376, GO:0005840, GO:0042803, GO:0042110, transcription activator activity, rna polymerase ii-specific. \\n\\nmechanism and hypotheses: these enriched terms suggest that the identified genes are involved in immune system processes such as cytokine signaling, chemokine receptor binding, and t cell activation. protein kinase activity may be involved in signaling pathways downstream of cytokine receptors or chemokine receptors. the presence of ribosome-related terms suggests these genes may play a role in protein synthesis in immune cells. the identified enriched terms point to a central role of the immune system in the functions of these genes, with potential impacts on inflammation, infection, and other immune-related diseases]]0.15
292gpt-3.5-turboontological_synopsisHALLMARK_ANDROGEN_RESPONSE-0[[binding activity, GO:0008152, GO:0043167, nucleic acid binding. \\n\\nmechanism: the enriched terms suggest that the listed genes have a common function in binding and metabolic processes. it is possible that these genes are involved in regulating the flow and utilization of energy and molecules within cells]][[GO:0006468, GO:0035556, GO:0010604]]0.00
293gpt-3.5-turboontological_synopsisHALLMARK_ANDROGEN_RESPONSE-1[[GO:0004672, GO:0035556, GO:0000079, GO:0007166]][[1. binding of metal ions \\n2. protein kinase activity \\n3. positive regulation of protein kinase activity \\n4. cytoskeletal protein binding activity \\n5. signal transduction \\n\\nmechanism: these enriched terms indicate that the genes have a role in signal transduction pathways and cytoskeletal organization. the genes are involved in the binding of metal ions and protein kinases, which are important components of these pathways. additionally, the positive regulation of protein kinase activity suggests that these genes have a role in the amplification of signal transduction through cascade-like pathways]]0.00
294gpt-3.5-turboontological_synopsisHALLMARK_ANGIOGENESIS-0[[extracellular matrix organization; cell adhesion; protein binding; signaling pathway; regulation of cell proliferation.\\n\\nmechanism: the enriched terms suggest that these genes are involved in extracellular matrix organization and cell signaling pathways that regulate cell proliferation and adhesion. many of the genes are structural constituents of the extracellular matrix and influence cell-matrix interactions. others are involved in cell signaling pathways, such as the notch and fibroblast growth factor pathways, that play critical roles in cell proliferation and differentiation. some of the genes have also been implicated in diseases involving abnormal extracellular matrix formation or cell signaling dysregulation, such as ehlers-danlos syndrome, MONDO:0004975, MONDO:0004992]][[extracellular matrix organization; cell signaling; blood coagulation; lipid metabolism; immunity.\\n\\nmechanism and hypotheses: these genes appear to be involved in a variety of pathways related to extracellular matrix organization, cell signaling, and intercellular communication. specifically, several genes encode proteins that are structural components of the extracellular matrix or interact with extracellular matrix proteins, suggesting a role in tissue development, remodeling, or repair. many of these genes also participate in signaling pathways that control cell proliferation, differentiation, and migration. additionally, several genes are involved in blood coagulation and lipid metabolism, which may be related to their roles in cardiovascular disease. finally, some genes have roles in immunity and host defense against infectious pathogens, possibly contributing to susceptibility or resistance to infectious diseases. overall, these common functions may point to a greater role for extracellular matrix and signaling pathways in disease pathogenesis]]0.00
295gpt-3.5-turboontological_synopsisHALLMARK_ANGIOGENESIS-1[[UBERON:4000022, binding activity]][[GO:0030198, cell signaling, protein binding activity, GO:1902533, GO:0062023]]0.00
296gpt-3.5-turboontological_synopsisHALLMARK_APICAL_JUNCTION-0[[GO:0007010, GO:0007155, GO:0005102, kinase activity.\\n\\nmechanism: these genes are involved in the maintenance of cell structure and organization through regulation of the cytoskeleton. they also contribute to cell-cell interactions and signaling through receptor binding and kinase activity. a biological pathway that might be involved is the rho gtpase signaling pathway, which regulates actin cytoskeleton dynamics and cell adhesion]][[actin filament binding activity, integrin binding activity, protein kinase binding activity, sh2 domain binding activity, cell adhesion molecule binding activity, identical protein binding activity, GO:0005096, atp binding activity, cadherin binding activity, collagen binding activity, GO:0051219, GO:0042803]]0.00
297gpt-3.5-turboontological_synopsisHALLMARK_APICAL_JUNCTION-1[[cell adhesion: cdh3, cdh4, cdh6, cdh11, cdh15, cd276, cd209, icam5, icam2, icam1, itga3, itga9, itga10, itgb1, cldn4, cldn5, cldn6, cldn7, cldn8, cldn9, cldn11, cldn14, cldn18, cldn19\\n- protein kinase activity: cdk8, ptk2, syk, taok2, vav2, src\\n- actin filament binding: actn1, actn3, lima1, nexn, calb2, pfn1\\n- metalloendopeptidase activity: adamts5, adam23, mmp2, mmp9\\n- integrin binding: jup, vcam1, slit2]][[integrin binding activity, cell adhesion molecule binding activity, sh3 domain binding activity, identical protein binding activity, actin filament binding activity, protein kinase binding activity]]0.00
298gpt-3.5-turboontological_synopsisHALLMARK_APICAL_SURFACE-0[[GO:0007165, cell surface receptor activity, protein binding activity]][[GO:0005886, GO:0005615, signaling receptor binding activity, protein domain specific binding activity, protein kinase binding activity, GO:0006811, GO:0051247, GO:0010468, GO:0007155, GO:1902531]]0.00
299gpt-3.5-turboontological_synopsisHALLMARK_APICAL_SURFACE-1[[GO:0005886, GO:0009986, GO:0055085, GO:0038023, positive regulation of transcription, GO:0010468, GO:0006468, GO:0005615]][[GO:0010468, signaling receptor binding activity, GO:0045944, GO:2001234, GO:0006811, GO:0060244, GO:0051965, carbohydrate binding activity, GO:1902531, GO:1904054]]0.06
300gpt-3.5-turboontological_synopsisHALLMARK_APOPTOSIS-0[[GO:0006915, GO:0005125, transcription factor binding activity. \\n\\nmechanism/]][[GO:0097190, GO:0006955, GO:0005125, identical protein binding activity, protease binding activity, enzyme binding activity, GO:0000988, dna binding activity]]0.10
301gpt-3.5-turboontological_synopsisHALLMARK_APOPTOSIS-1[[GO:0006915, GO:0005125, GO:0010941, GO:2001233, GO:0001819, GO:0042981, GO:0043067, positive regulation of apoptotic process.\\n\\nmechanism: these genes are involved in apoptotic signaling and cytokine activity, which suggests that they play a role in regulating cell death and programmed cell death. the enriched terms suggest that these genes may be regulated by shared signaling pathways or transcriptional programs that control apoptosis and cytokine production. one potential underlying mechanism could involve the activation of pro-apoptotic proteins in response to cellular stress or damage, leading to the release of cytokines that further promote cell death. alternatively, these genes may be involved in controlling the balance between cell survival and death in response to external cues such as cytokine signaling or nutrient availability. further research is needed to fully elucidate the molecular mechanisms underlying these gene functions]][[apoptotic process; cytokine activity; protein binding activity.\\n\\nmechanism: the genes in this list are involved in processes related to cell death, GO:0006955, and molecular interactions. the enriched terms suggest that these genes may be involved in pathways related to apoptosis, cytokine signaling, protein interactions. it is possible that these genes contribute to the regulation of cell death through cytokine-mediated signaling pathways protein-protein interactions]]0.00
302gpt-3.5-turboontological_synopsisHALLMARK_BILE_ACID_METABOLISM-0[[GO:0006629, GO:0030301, GO:0006633]][[cholesterol binding activity, GO:0016887, GO:0005319, GO:0008559, atp binding activity, GO:0007031, vitamin d receptor binding activity, GO:0042626]]0.00
303gpt-3.5-turboontological_synopsisHALLMARK_BILE_ACID_METABOLISM-1[[GO:0030301, GO:0015908, GO:0007031, GO:0004467, GO:0008123, atp binding activity, ubiquitin-dependent protein binding activity. \\n\\nmechanism: these genes are likely involved in the regulation and transport of lipids, particularly cholesterol and long-chain fatty acids, in cells and tissues. peroxisomal proteins and functions may also play a role in this process, including in the regulation of lipid metabolism]][[GO:0008610, GO:0006631, GO:0008203, GO:0007031, GO:0015908, peroxisome matrix targeting, abc-type transporter activity. \\n\\nmechanism]]0.17
304gpt-3.5-turboontological_synopsisHALLMARK_CHOLESTEROL_HOMEOSTASIS-0[[GO:0042632, GO:0008610, GO:0010883, phospholipid binding activity, fatty acid binding activity, low-density lipoprotein particle binding activity, more]][[GO:0006695, GO:0008610, GO:0019216, GO:0042632, GO:0090181]]0.20
305gpt-3.5-turboontological_synopsisHALLMARK_CHOLESTEROL_HOMEOSTASIS-1[[GO:0006695, GO:0008299, GO:0055088, GO:0006646, GO:0000122, GO:0045944, GO:0070458, GO:0001676]][[GO:0006695, GO:0008299, GO:0006633]]0.22
306gpt-3.5-turboontological_synopsisHALLMARK_COAGULATION-0[[GO:0006508, complement pathways, GO:0007596, GO:0007155]][[GO:0006956, GO:0050817, GO:0008237]]0.00
307gpt-3.5-turboontological_synopsisHALLMARK_COAGULATION-1[[GO:0006508, GO:0007596, GO:0006956, negative regulation of proteolysis. \\n\\nmechanism: the enriched terms suggest that these genes are involved in the regulation of proteolytic activity in several biological processes, including blood coagulation and immune response]][[metalloendopeptidase activity; serine-type endopeptidase activity; protease binding activity; identical protein binding activity; complement binding activity \\n\\nmechanism and hypotheses: these enriched terms suggest that the common mechanism or pathway involves the regulation of proteolysis and immune response, particularly the complement system. metalloendopeptidase and serine-type endopeptidase activity are involved in the proteolytic degradation of various extracellular matrix components including collagen, GO:0005577, and proteoglycan, as well as destruction of pathogenic microorganisms during immune response. protease binding activity, identical protein binding activity, and complement binding activity are involved in protein-protein interactions that regulate proteolysis and activation of complement components. therefore, the hypothesis is that the common mechanism of these genes is related to the regulation of proteolysis and complement system activity]]0.00
308gpt-3.5-turboontological_synopsisHALLMARK_COMPLEMENT-0[[GO:0004867, protease binding activity, enzyme binding activity, calcium ion binding activity]][[GO:0005515, GO:0046872, GO:0019899, GO:0042802, GO:0005524, GO:0003677, calcium ion binding. \\n\\nmechanism]]0.00
309gpt-3.5-turboontological_synopsisHALLMARK_COMPLEMENT-1[[GO:0005515, GO:0019899, GO:0005488, GO:0004175, metal ion binding.\\n\\nmechanism: the enriched terms suggest that these genes play a role in protein-protein interactions and enzymatic reactions involving metal ions]][[GO:0004222, GO:0004252, complement binding activity, heparin binding activity, GO:0008234, GO:0004869, GO:0005201, serine-type endopeptidase inhibitor activity involved in apoptotic process, GO:0004722, MESH:D011809]]0.00
310gpt-3.5-turboontological_synopsisHALLMARK_DNA_REPAIR-0[[GO:0006281, GO:0097747, nucleotide metabolism. \\n\\nmechanism: these genes are predominantly involved in regulating dna replication, transcription, and repair. they may also play roles in the metabolism of nucleotides and nucleotide analogs that target dna synthesis. the enrichment of terms related to rna polymerase may reflect the closely intertwined nature of dna and rna synthesis]][[dna binding activity, transcription initiation, rna binding activity, GO:0009117, rna splicing. \\n\\nmechanism: these genes are likely involved in regulating dna replication, transcription, and various steps in rna processing, including splicing and export from the nucleus. they could also be involved in nucleotide metabolism and/or maintaining genomic stability]]0.00
311gpt-3.5-turboontological_synopsisHALLMARK_DNA_REPAIR-1[[GO:0006260, GO:0006281, rna transcription]][[GO:0003677, GO:0003723, GO:0009117, GO:0006281, transcription initiation, protein-macromolecule adaptor activity.\\n\\nmechanism: these genes work together to maintain the integrity and expression of genetic information, with a focus on dna-related processes]]0.12
312gpt-3.5-turboontological_synopsisHALLMARK_E2F_TARGETS-0[[GO:0006260, GO:0051726, GO:0006325]][[GO:0006260, GO:0006281, GO:0051726, GO:0003682, GO:0005524, GO:0019899, GO:0042393, GO:0043130]]0.22
313gpt-3.5-turboontological_synopsisHALLMARK_E2F_TARGETS-1[[dna binding activity, protein binding activity, enzyme binding activity, chromatin binding activity, atp binding activity, histone binding activity, rna binding activity, identical protein binding activity]][[dna binding activity, chromatin binding activity, rna binding activity, enzyme binding activity, GO:0042803, single-stranded dna binding activity, identical protein binding activity, histone binding activity, atp binding activity, cyclin binding activity, nucleic acid binding activity]]0.58
314gpt-3.5-turboontological_synopsisHALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0[[GO:0005201, integrin binding activity, collagen binding activity, identical protein binding activity, fibrinogen binding activity, protease binding activity]][[GO:0005201, collagen binding activity, heparin binding activity, GO:0005125, GO:0008083, signaling receptor binding activity, wnt-protein binding activity]]0.18
315gpt-3.5-turboontological_synopsisHALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1[[GO:0005201, collagen binding activity, integrin binding activity, heparin binding activity, GO:0008237, signaling receptor binding activity.\\n\\nmechanism: these genes are involved in the maintenance and formation of the extracellular matrix, which provides structural support to cells and tissues. they play a role in cell adhesion, signaling, and migration through interactions with the extracellular matrix. the enriched binding activities suggest that these genes are involved in extracellular matrix remodeling and regulation of growth factor signaling. metallopeptidase activity may be involved in the degradation of extracellular matrix components]][[collagen binding activity, integrin binding activity, heparin binding activity, GO:0005201, GO:0008237, platelet-derived growth factor binding activity, GO:0008009, fibronectin binding activity, GO:0004867]]0.50
316gpt-3.5-turboontological_synopsisHALLMARK_ESTROGEN_RESPONSE_EARLY-0[[GO:0005509, GO:0000166, enzyme binding activity, MESH:D048788, gene transcription, GO:0006811]][[GO:0004888, GO:0022857, GO:0001216]]0.00
317gpt-3.5-turboontological_synopsisHALLMARK_ESTROGEN_RESPONSE_EARLY-1[[GO:0005515, GO:0000988, transmembrane transporter activity.\\n\\nmechanism: the enriched terms suggest that the genes on the list are involved in various cellular processes that require protein-protein interaction, transcriptional regulation, and transmembrane transport of substances. a possible hypothesis is that these genes play a role in signal transduction and regulation of gene expression]][[GO:0007165, transcriptional regulation, GO:0003824, GO:0038023, GO:0003676, GO:0007154, GO:0042445, protein-protein interaction\\n\\nhypotheses: the enriched terms suggest that the genes in this list are involved in various aspects of signaling and transcriptional regulation. they may function in pathways such as cell signaling, hormone metabolism, and protein-protein interaction. this list includes genes encoding enzymes with specific activities, as well as receptor and nucleic acid binding proteins that are crucial for signaling and transcriptional regulation]]0.00
318gpt-3.5-turboontological_synopsisHALLMARK_ESTROGEN_RESPONSE_LATE-0[[GO:0022857, protein binding activity]][[enzyme binding activity, identical protein binding activity, calcium ion binding activity, GO:0005215, phosphorylation-dependent protein binding activity, atpase binding activity, GO:0004930, GO:0004712, nucleotide binding activity, ubiquitin protein ligase binding activity, transcription factor binding activity, histone deacetylase binding activity, GO:0016787, GO:0016491]]0.00
319gpt-3.5-turboontological_synopsisHALLMARK_ESTROGEN_RESPONSE_LATE-1[[(1) enzymatic activity; (2) binding activity; (3) transcription regulation. \\n\\nmechanism: these genes likely play roles in various biological pathways, such as metabolism, cell signaling, and gene expression regulation. given the enrichment in enzymatic activity, it is possible that some of these genes are involved in metabolic pathways, such as lipid metabolism. the enrichment in binding activity may reflect the importance of protein-protein interactions and signaling cascades in cellular processes. the enrichment in transcription regulation suggests that many of these genes may be key players in regulating gene expression and ultimately cell fate]][[binding activity, GO:0005215, enzyme binding activity, identical protein binding activity, protein kinase binding activity, GO:0004930]]0.00
320gpt-3.5-turboontological_synopsisHALLMARK_FATTY_ACID_METABOLISM-0[[GO:0047617, GO:0006631, GO:0120227, GO:0008289, GO:0004467, GO:0006099, GO:0046356]][[fatty acid-coa ligase activity, GO:0003995, long-chain fatty acid binding activity, GO:0003985, GO:0016615, GO:0000104, GO:0016616]]0.00
321gpt-3.5-turboontological_synopsisHALLMARK_FATTY_ACID_METABOLISM-1[[GO:0016491, binding activity, GO:0006631, GO:0006084, heme-binding activity]][[GO:0003824, GO:0016491, GO:0006631, GO:0006629, metabolic pathways. \\n\\nmechanism: these genes may be involved in the regulation of lipid and fatty acid metabolism, potentially through oxidation-reduction processes and metabolic pathways]]0.25
322gpt-3.5-turboontological_synopsisHALLMARK_G2M_CHECKPOINT-0[[dna binding activity, chromatin binding activity, protein binding activity, enzyme binding activity, histone binding activity, GO:0003714]][[dna binding activity, transcription regulation, GO:0004672, protein binding activity, GO:0016570]]0.22
323gpt-3.5-turboontological_synopsisHALLMARK_G2M_CHECKPOINT-1[[dna-binding transcription factor activity; protein kinase activity; microtubule binding activity. \\n\\nmechanism: these genes are likely involved in the regulation of gene expression, cell cycle progression, and cytoskeletal dynamics through the binding and modification of dna, MESH:D011506, and microtubules. specifically, they may be involved in processes such as transcriptional regulation, dna replication and repair, GO:0007059, GO:0051301]][[dna-binding transcription factor, GO:0004672, protein binding activity, GO:0140014, GO:0006260, GO:0010467]]0.00
324gpt-3.5-turboontological_synopsisHALLMARK_GLYCOLYSIS-0[[GO:0008378, GO:0015020, n-acetylglucosamine sulfotransferase activity, GO:0035250, glucosaminyl-proteoglycan 3-beta-glucosyltransferase activity, GO:0016758, GO:0045130, GO:0016779]][[GO:0008194, GO:0008146, GO:0008378, GO:0015020, GO:0004553, heparan sulfate binding activity, several others]]0.15
325gpt-3.5-turboontological_synopsisHALLMARK_GLYCOLYSIS-1[[GO:0005975, GO:0006024, GO:0006493]][[enzyme binding activity, GO:0008194, atp binding activity, GO:0008378, GO:0004340, fructose binding activity, heme binding activity, GO:0016787, rna binding activity, identical protein binding activity, GO:0046983, nucleoside triphosphate activity]]0.00
326gpt-3.5-turboontological_synopsisHALLMARK_HEDGEHOG_SIGNALING-0[[GO:0006357, GO:0016525, GO:0007155, GO:0030036, GO:0010604, GO:0007411, GO:0030336]][[GO:0032502, GO:0007165, MESH:D005786]]0.00
327gpt-3.5-turboontological_synopsisHALLMARK_HEDGEHOG_SIGNALING-1[[GO:0007165, GO:0007155, GO:0007399, transcription regulation]][[GO:0007155, transcription regulation, GO:0007165, negative regulation, positive regulation]]0.50
328gpt-3.5-turboontological_synopsisHALLMARK_HEME_METABOLISM-0[[GO:0020037, GO:0015075, protein binding activity, GO:0000988]][[GO:0005215, binding activity, GO:0003824]]0.00
329gpt-3.5-turboontological_synopsisHALLMARK_HEME_METABOLISM-1[[transmembrane transport; protein binding activity; metal ion binding activity; dna-binding transcription activator activity\\n\\nmechanism: these genes are involved in various transport and binding activities, especially transmembrane transport, indicating a possible importance in cellular trafficking and signaling pathways. additionally, they exhibit a significant enrichment in protein and metal ion binding activities, which may suggest a role in protein-protein interactions and redox reactions, respectively. finally, dna-binding transcription activator activity is found to be enriched, indicating that these genes may regulate gene expression]][[enzyme binding activity, protein domain specific binding activity, GO:0046982, identical protein binding activity, GO:0042803]]0.00
330gpt-3.5-turboontological_synopsisHALLMARK_HYPOXIA-0[[enzyme binding activity, GO:0005515, GO:0003700, carbohydrate binding activity, signaling receptor binding activity, identical protein binding activity, atp binding activity, nad binding activity, phosphoprotein binding activity, metal ion binding activity, GO:0003924, GO:0008083, GO:0008194, phospholipid binding activity, platelet-derived growth factor binding activity]][[enzyme binding activity, protein kinase binding activity, identical protein binding activity, GO:0003700, GO:0004674, calcium ion binding activity, nucleic acid binding activity, atp binding activity, GO:0060422, gtp binding activity, GO:0004340, GO:0005353, GO:0008459, heparin binding activity, apolipoprotein binding activity]]0.15
331gpt-3.5-turboontological_synopsisHALLMARK_HYPOXIA-1[[GO:0006006, GO:0016301, transcriptional regulation, GO:0023052]][[GO:0042802, GO:0019899, GO:0005524, GO:0019901, GO:0005509, GO:0005102, GO:0015035, GO:0016538, GO:0008083, GO:0005353, GO:0004347, nadph binding activity, GO:0042803, MESH:D013213]]0.00
332gpt-3.5-turboontological_synopsisHALLMARK_IL2_STAT5_SIGNALING-0[[GO:0005125, interleukin receptor binding activity, cytokine binding activity, GO:0031295, GO:0051250, GO:0006952, GO:0006955, interleukin binding activity]][[GO:0042802, GO:0003700, GO:0005125, GO:0005096, interleukin receptor binding activity, ubiquitin protein ligase activity.\\n\\nmechanism: these genes likely play a role in regulating various cell signaling pathways, including cytokine and growth factor signaling, as well as intracellular protein degradation via ubiquitin-proteasome system]]0.17
333gpt-3.5-turboontological_synopsisHALLMARK_IL2_STAT5_SIGNALING-1[[GO:0004896, interleukin binding activity, identical protein binding activity, gtp binding activity, GO:0001216, protein kinase binding activity, atp binding activity, GO:0016787, collagen binding activity, small gtpase binding activity, GO:0061630, GO:0004197, GO:0005215, rna binding activity, calcium ion binding activity, signaling receptor binding activity, GO:0005125, GO:0008083, enzyme binding activity, several others.\\n\\nmechanism: these genes are involved in immune response cytokine activity. many of them encode for cytokine receptors, transcription factors, enzymes involved in immune system pathways processes. the enrichment of terms related to protein binding, including dna binding identical protein binding, may suggest that many of these genes act as transcriptional regulators in immune cells, coordinating the expression of genes involved in immune function. the enrichment of transporter activity may indicate that some of these genes are involved in cell migration or trafficking of immune cells to sites of inflammation or infection. additionally, the enrichment of terms related to enzyme activity may suggest that some of]][[GO:0004896, protein binding activity, GO:0003824, dna binding activity, rna binding activity, apoptosis. \\n\\nmechanism: these genes are involved in various cellular processes such as signaling and cytokine receptor activity, where they play a role in transmitting signals from the outside to the inside of the cell, as well as in regulating the immune system. they are also involved in enzyme activity, dna and rna binding activity, and apoptosis, playing a role in various pathways such as the regulation of gene expression and programmed cell death]]0.08
334gpt-3.5-turboontological_synopsisHALLMARK_IL6_JAK_STAT3_SIGNALING-0[[GO:0005125, GO:0004896, protein kinase binding activity, GO:0006954, GO:0006955, GO:0007165]][[GO:0004896, GO:0004896, growth factor receptor binding activity]]0.12
335gpt-3.5-turboontological_synopsisHALLMARK_IL6_JAK_STAT3_SIGNALING-1[[GO:0004896, interleukin binding activity, GO:0008009, GO:0001819, GO:0050778, GO:0098542, GO:0010604]][[GO:0005125, signaling receptor binding activity, GO:0001819, GO:0019221, GO:0009967, GO:0004896, GO:0050776]]0.17
336gpt-3.5-turboontological_synopsisHALLMARK_INFLAMMATORY_RESPONSE-0[[GO:0005125, GO:0008009, identical protein binding activity, GO:0038023, GO:0006811]][[GO:0005125, GO:0004896, GO:0004930, GO:0002376, GO:0006954, GO:0008009]]0.22
337gpt-3.5-turboontological_synopsisHALLMARK_INFLAMMATORY_RESPONSE-1[[GO:0004930, GO:0004896, enzyme binding activity, identical protein binding activity, GO:0007165, calcium ion binding activity, protease binding activity, transporter activity.\\n\\nmechanism: these genes are involved in various mechanisms related to cell signaling and transport. one hypothesis is that these genes may collectively contribute to the regulation of calcium levels and calcium-dependent signaling pathways, as well as cytokine-mediated signaling pathways involved in immune response]][[GO:0004896, GO:0004930, signaling receptor binding activity, identical protein binding activity, enzyme binding activity]]0.44
338gpt-3.5-turboontological_synopsisHALLMARK_INTERFERON_ALPHA_RESPONSE-0[[GO:0005125, GO:0098542, GO:0046597, rna binding activity, identical protein binding activity]][[GO:0006955, GO:0019882, cytokines/chemokines, interferon-related genes, rna processing/editing]]0.00
339gpt-3.5-turboontological_synopsisHALLMARK_INTERFERON_ALPHA_RESPONSE-1[[GO:0098542, GO:0050709, GO:0046597, GO:0045071, GO:0030501, GO:0002688, regulation of transcription]][[GO:0098542, GO:0045071, GO:0035458, GO:0071345, GO:0042590, GO:0006469, GO:0010604, GO:0046597, GO:0019221, GO:0045669, GO:0052548]]0.20
340gpt-3.5-turboontological_synopsisHALLMARK_INTERFERON_GAMMA_RESPONSE-0[[GO:0004896, GO:0000981, identical protein binding activity, enzyme binding activity, GO:0042110, cell adhesion molecule binding activity, positive regulation of activated cd8-positive t cell proliferation, GO:0038187, GO:0061630, GO:0000166, GO:0004930, protein kinase binding activity, calcium ion binding activity, complement binding activity, GO:0004867, GO:0008009, integrin binding activity.\\n\\nmechanism: these genes predominantly function in the immune system and are related to the activation and proliferation of t cells, cytokine signaling, pattern recognition, and complement cascades. the enriched terms suggest an association with signaling cascades, receptor binding, enzyme activity, and immune response to pathogens]][[GO:0005125, GO:0008009, GO:0001216, enzyme binding activity, identical protein binding activity, protease binding activity, GO:0042803, rna binding activity, GO:0050852, GO:0061630]]0.17
341gpt-3.5-turboontological_synopsisHALLMARK_INTERFERON_GAMMA_RESPONSE-1[[GO:0019882, GO:0045087, cytokine signaling, GO:0045321, antiviral defense]][[GO:0019882, cytokine signaling, antiviral defense]]0.60
342gpt-3.5-turboontological_synopsisHALLMARK_KRAS_SIGNALING_DN-0[[calcium ion binding activity, atp binding activity, GO:0008511, GO:0004930, GO:0004888, GO:0016887, identical protein binding activity, protein kinase binding activity]][[GO:0003824, protein binding activity, GO:0000988, identical protein binding activity, ion binding activity.\\n\\nmechanism]]0.08
343gpt-3.5-turboontological_synopsisHALLMARK_KRAS_SIGNALING_DN-1[[protein binding activity, calcium ion binding activity, atp binding activity, identical protein binding activity, GO:0008507, GO:0005337, GO:0043273, GO:0003924, GO:0015432]][[GO:0005488, GO:0003824, GO:0004930, GO:0000988, GO:0005509, GO:0005524, protein homodimerization activity.\\n\\nmechanism: the enriched terms suggest that these genes are involved in cellular regulation and signaling processes through binding and enzymatic activities, particularly involving calcium ions and atp. many genes also have transcription factor activity, indicating a role in gene expression regulation. g protein-coupled receptor activity is also overrepresented, suggesting a role in cellular signaling processes]]0.00
344gpt-3.5-turboontological_synopsisHALLMARK_KRAS_SIGNALING_UP-0[[binding activity; enzyme activity; transcription activator activity. \\n\\nmechanism: these enriched terms suggest that the commonality among these genes is that they are involved in various types of binding and enzymatic activities, as well as regulating transcription. it is possible that these genes work together in regulatory pathways to bind to specific targets, catalyze reactions, modulate transcriptional activity in the cell]][[GO:0005515, enzyme binding activity, transcriptional regulation, ion binding activity, dna binding activity, GO:0004930, GO:0005125, identical protein binding activity]]0.00
345gpt-3.5-turboontological_synopsisHALLMARK_KRAS_SIGNALING_UP-1[[GO:0005178, GO:0005515, GO:0005524, GO:0071345, GO:0043167, ubiquitin protein ligase binding. \\n\\nmechanism: the shared function of binding among the enriched terms suggests that these genes may play a role in mediating protein regulation and signal transduction pathways through protein-protein or protein-ligand interactions. the involvement in cellular response to cytokine stimulus may suggest a potential role in modulating immune responses]][[enzymatic activity, GO:0019901, binding activity\\n\\nmechanism: the enriched functions suggest that these genes may be involved in the regulation of cellular processes through protein-protein interactions, including enzymatic activities and binding activities. this could involve pathways such as signal transduction or gene expression regulation]]0.00
346gpt-3.5-turboontological_synopsisHALLMARK_MITOTIC_SPINDLE-0[[microtubule binding activity, GO:0005096, actin filament binding activity, microtubule plus-end binding activity, identical protein binding activity, protein kinase binding activity, kinetochore binding activity, cytoskeletal protein binding activity, gamma-tubulin binding activity]][[microtubule binding activity, actin binding activity, GO:0005096]]0.20
347gpt-3.5-turboontological_synopsisHALLMARK_MITOTIC_SPINDLE-1[[microtubule binding activity, GO:0007052, GO:0000226]][[GO:0008017, mitotic processes, GO:0000910, GO:0007018, spindle organization. \\n\\nmechanism: these genes play important roles in the regulation and organization of microtubules, which are key components of the cytoskeleton involved in cell division processes such as mitosis and cytokinesis. the enrichment of terms related to microtubule binding and regulation suggest that these genes may function together in a pathway that regulates the dynamics and organization of microtubules during these cellular processes. they may also be involved in microtubule-based movement, which is crucial for various cellular activities such as intracellular transport and cell migration]]0.00
348gpt-3.5-turboontological_synopsisHALLMARK_MTORC1_SIGNALING-0[[binding activity, enzymatic activity, GO:0006412, GO:0023052, GO:0008152]][[GO:0005515, GO:0003723, enzymatic activity, structural constituent of cytoskeleton. \\n\\nmechanism: these genes likely play a role in cellular processes such as transcription, translation, protein folding, and cytoskeletal organization]]0.12
349gpt-3.5-turboontological_synopsisHALLMARK_MTORC1_SIGNALING-1[[GO:0005515, enzyme activity. \\n\\nmechanism: the enriched terms suggest that these genes play a role in protein-protein interactions and enzymatic reactions, potentially involved in metabolic pathways or signal transduction cascades]][[GO:0006457, GO:0005783, ubiquitin-proteasome system, GO:0015031, GO:0030163]]0.00
350gpt-3.5-turboontological_synopsisHALLMARK_MYC_TARGETS_V1-0[[ribosome binding activity; rna binding activity; translation initiation factor activity; protein folding chaperone activity\\n\\nmechanism: these genes are involved in different aspects of protein synthesis, such as ribosome binding, GO:0006413, and rna binding. they also contribute to protein folding processes as chaperones. the enrichment of these terms suggests that these genes function together to ensure proper protein synthesis and folding, which are vital to numerous cellular processes]][[GO:0003743, ribosome binding activity, rna binding activity, GO:0003735, protein folding chaperone activity, GO:0140713]]0.00
351gpt-3.5-turboontological_synopsisHALLMARK_MYC_TARGETS_V1-1[[GO:0006396, GO:0003676, GO:0006457, ribosomal structural activity. \\n\\nmechanism: these genes likely function together in the post-transcriptional regulation of gene expression, from rna splicing to translation initiation and ribosome assembly]][[GO:0000394, GO:0006413, GO:0003723, GO:0003676, GO:0006457, ribosome structure\\n\\nmechanism: these genes are involved in rna processing, including mrna splicing and translation initiation, as well as binding to rna and nucleic acids. some genes also play roles in protein folding and ribosome structure. the underlying biological mechanism or pathway is likely related to rna processing and regulation of gene expression]]0.25
352gpt-3.5-turboontological_synopsisHALLMARK_MYC_TARGETS_V2-0[[GO:0006364, rna binding activity, GO:0046982, mitochondrial function, GO:0051726]][[GO:0006364, GO:0042273, snorna binding activity, GO:0005730, rna binding activity]]0.25
353gpt-3.5-turboontological_synopsisHALLMARK_MYC_TARGETS_V2-1[[GO:0006364, snorna binding activity, GO:0042273, rna binding activity, GO:0005730]][[GO:0006364, ribosomal biogenesis, rna binding activity, GO:0005730]]0.50
354gpt-3.5-turboontological_synopsisHALLMARK_MYOGENESIS-0[[cytoskeletal protein binding activity, actin binding activity, atp binding activity, calcium ion binding activity, identical protein binding activity, enzyme binding activity, GO:0042803]][[actin binding activity, calcium ion binding activity, atp binding activity, identical protein binding activity, cytoskeletal protein binding activity, enzyme binding activity, UBERON:0005090]]0.75
355gpt-3.5-turboontological_synopsisHALLMARK_MYOGENESIS-1[[actin binding activity, cytoskeletal protein binding activity, calcium ion binding activity, myosin binding activity, atp binding activity, kinase binding activity, muscle structure development. \\n\\nmechanism: these genes are involved in muscle structure and function as they encode proteins that bind to actin, myosin, and other cytoskeletal proteins to form the muscle fibers. they also bind to calcium ions and atp, which are necessary for muscle contraction, and contribute to the development of muscle structure]][[GO:0006936, GO:0030036, GO:0006600, GO:0032956, regulation of muscle contraction.\\n\\nmechanism: these genes are involved in the regulation of muscle contraction and actin cytoskeleton organization, likely through their roles in calcium ion binding, myosin light chain kinase activity, and actin filament binding. several of the genes are also involved in creatine metabolism, which is important for energy generation in muscle tissues]]0.00
356gpt-3.5-turboontological_synopsisHALLMARK_NOTCH_SIGNALING-0[[GO:0007219, GO:0016567]][[GO:0007219, GO:0016567, GO:0006357, GO:0051247, GO:0016055, scf-dependent proteasomal ubiquitin-dependent protein catabolic process, cyclin-dependent protein kinase holoenzyme complex]]0.33
357gpt-3.5-turboontological_synopsisHALLMARK_NOTCH_SIGNALING-1[[\"notch signaling pathway,\" \"protein ubiquitination,\" \"negative regulation of cell differentiation,\" \"regulation of dna-templated transcription.\"]][[GO:0007219, GO:0016567]]0.00
358gpt-3.5-turboontological_synopsisHALLMARK_OXIDATIVE_PHOSPHORYLATION-0[[GO:0022900, GO:0006119, mitochondrial metabolism, GO:0006637, ketone body metabolism.\\n\\nmechanism and]][[GO:0009055, ubiquitin protein ligase binding activity, MESH:D014451, rna binding activity, GO:0042803, metal ion binding activity.\\n\\nmechanism and]]0.00
359gpt-3.5-turboontological_synopsisHALLMARK_OXIDATIVE_PHOSPHORYLATION-1[[GO:0005746, GO:0006118, GO:0006754, MESH:D009245, MESH:D003576, GO:0016467, flavin adenine dinucleotide]][[mitochondria\\n- atp synthesis\\n- respiratory chain complex\\n- electron transfer\\n- oxidoreductase activity\\n- iron-sulfur cluster binding\\n\\nmechanism: these genes are involved in the regulation of metabolic processes and energy production in the mitochondria. they play important roles in cellular respiration, which involves the conversion of nutrients into energy necessary for cellular activities. the enriched terms suggest that these genes are closely related to the function of the mitochondrial respiratory chain complex and atp synthase, both of which are necessary for energy production in the form of atp. additionally, several of these genes are involved in electron transfer and oxidoreductase activity, which are also important in metabolic processes that lead to energy production. finally, there is a common theme of iron-sulfur cluster binding, which suggests a common mechanism in the regulation of metabolic processes and energy production]]0.00
360gpt-3.5-turboontological_synopsisHALLMARK_P53_PATHWAY-0[[GO:0042981, protein binding activity, GO:0003700]][[GO:0003677, GO:0005515, GO:0003824, GO:0000988, growth factor activity. \\n\\nmechanism: these genes likely play roles in regulating transcription, protein-protein interactions, metabolism, and growth factor signaling pathways]]0.00
361gpt-3.5-turboontological_synopsisHALLMARK_P53_PATHWAY-1[[GO:0000988, rna binding activity, enzyme binding activity, identical protein binding activity, dna binding activity, histone binding activity]][[GO:0005515, dna binding activity, GO:0016301]]0.12
362gpt-3.5-turboontological_synopsisHALLMARK_PANCREAS_BETA_CELLS-0[[GO:0006006, GO:0030073, GO:0006357]][[GO:0042593, GO:0050796, GO:0046326, GO:0006006]]0.17
363gpt-3.5-turboontological_synopsisHALLMARK_PANCREAS_BETA_CELLS-1[[GO:0006006, GO:0030073, glucose homeostasis.\\n\\nmechanism]][[GO:0030073, GO:0006006, transcriptional regulation, transcription factor binding activity, rna polymerase ii-specific dna binding activity, GO:0000122, positive regulation of transcription by rna polymerase ii. \\n\\nmechanism and]]0.25
364gpt-3.5-turboontological_synopsisHALLMARK_PEROXISOME-0[[GO:0006629, GO:0006631, GO:0006810, GO:0003824, GO:0005501, steroid binding.\\n\\nmechanism and]][[GO:0001676, GO:0043574, GO:0008203, GO:0006633, lipid binding activity, atp binding activity, GO:0016491]]0.00
365gpt-3.5-turboontological_synopsisHALLMARK_PEROXISOME-1[[GO:0004467, GO:0016401, GO:0047676, GO:0031957, peroxisome targeting sequence binding activity, GO:0006633]][[GO:0006629, mitochondrial function, GO:0006281]]0.00
366gpt-3.5-turboontological_synopsisHALLMARK_PI3K_AKT_MTOR_SIGNALING-0[[GO:0004672, cytoskeleton structure, GO:0006629, protein binding activity]][[GO:0004672, g protein-coupled receptor binding activity, transcription factor binding activity, enzyme binding activity, GO:0007166, GO:0035556, GO:0032007, GO:0010971, negative regulation of vasc, negative regulation of nitrogen com, actin filament binding activity, cytoskeletal protein binding activity]]0.07
367gpt-3.5-turboontological_synopsisHALLMARK_PI3K_AKT_MTOR_SIGNALING-1[[GO:0006468, intracellular signaling, GO:0016301, GO:0016791, enzyme binding activity. \\n\\nmechanism: the enriched terms suggest that many of the genes are involved in regulatory processes related to protein modification through phosphorylation and dephosphorylation. this could implicate several signaling pathways, such as mapk, pi3k/akt, and nf-kappab pathways]][[GO:0006468, GO:0035556, GO:0016301, enzyme binding activity, GO:0004672, identical protein binding activity, scaffold protein binding activity]]0.20
368gpt-3.5-turboontological_synopsisHALLMARK_PROTEIN_SECRETION-0[[GO:0007030, GO:0006888, retrograde transport, vesicle recycling, GO:0090110, GO:0006891, GO:0008333, GO:0006893, GO:0048488, GO:0016192, vesicle recycling]][[GO:0007030, GO:0048193, GO:0090110, GO:0006888, retrograde transport, vesicle recycling, GO:0034260, negative regulation of autophagosome formation and maturation, GO:1905604, GO:1905280, GO:0002091, GO:0009967]]0.24
369gpt-3.5-turboontological_synopsisHALLMARK_PROTEIN_SECRETION-1[[GO:0048193, GO:0032456, GO:0035493, GO:0006891, GO:0070836]][[GO:0006888, GO:0048193, GO:0006891, GO:0034067, snare complex assembly.\\n\\nmechanism and]]0.25
370gpt-3.5-turboontological_synopsisHALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0[[GO:0098869, GO:0006750, GO:0042744, oxidation-reduction process, GO:0006979]][[cellular redox homeostasis, GO:0006979, protein disulfide reduction, GO:0006749, GO:0003954, GO:0004601, GO:0006826, GO:0016209, MESH:D015227]]0.08
371gpt-3.5-turboontological_synopsisHALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1[[GO:0045454, GO:0006979, GO:0016209, GO:0004602, GO:0004784, GO:0004601, GO:0003954, GO:0032981]][[GO:0045454, GO:0006979]]0.25
372gpt-3.5-turboontological_synopsisHALLMARK_SPERMATOGENESIS-0[[GO:0005515, GO:0005524, GO:0042802, GO:0016301, GO:0000166]][[GO:0005515, GO:0016301, GO:0051726, GO:0010467]]0.29
373gpt-3.5-turboontological_synopsisHALLMARK_SPERMATOGENESIS-1[[identical protein binding activity, protein folding chaperone binding activity, GO:0004672, rna binding activity, chromatin binding activity, atp binding activity, nucleotide binding activity, GO:0004722, GO:0061630, calcium ion binding activity, rna polymerase iii binding activity, cytokine binding activity, GO:0004930, integrin binding activity, many others]][[GO:0005515, GO:0008047, atp binding activity]]0.06
374gpt-3.5-turboontological_synopsisHALLMARK_TGF_BETA_SIGNALING-0[[GO:0007178, GO:0010862, GO:0010991, GO:0045668, GO:0030512, GO:0010604, GO:0009967]][[GO:0060395, GO:0006357, GO:0010604, GO:0090101, GO:0045668, establishment of sert, positive regulation of vascular associated smooth muscle cell proliferat, several others]]0.15
375gpt-3.5-turboontological_synopsisHALLMARK_TGF_BETA_SIGNALING-1[[signal transduction; regulation of gene expression; transcription regulation; protein phosphorylation; smad protein signal transduction.\\n\\nmechanism: these genes are involved in various aspects of signal transduction, including regulation of gene expression, transcription regulation, MESH:D016212, where they regulate transcription of target genes. genes in this list may activate or inhibit smad signaling and affect downstream transcriptional regulation. additionally, many of these genes play roles in other signaling pathways and regulatory processes, such as the wnt signaling pathway and negative regulation of protein degradation]][[GO:0005024, GO:0046332, GO:0009967, GO:0006357, GO:0000122, GO:0007166, GO:0010604, nucleic acid binding activity]]0.00
376gpt-3.5-turboontological_synopsisHALLMARK_TNFA_SIGNALING_VIA_NFKB-0[[GO:0005125, GO:0003700, enzyme binding activity, GO:0006955]][[GO:0003700, rna polymerase ii-specific; cytokine activity; protein binding activity.\\n\\nmechanism: these genes are involved in the regulation of transcription and cytokine activity, likely playing a role in immune responses and cellular differentiation. they are involved in binding to dna and rna polymerases to regulate the expression of genes, as well as in the production and regulation of cytokines and growth factors that play a role in cell signaling and differentiation]]0.14
377gpt-3.5-turboontological_synopsisHALLMARK_TNFA_SIGNALING_VIA_NFKB-1[[cytokine activity; dna-binding transcription factor activity; enzyme binding activity; phosphatidylinositol-3,4-bisphosphate binding activity; g protein-coupled receptor activity.\\n\\nmechanism: the enriched terms suggest that the genes on the list are involved in signaling pathways that regulate gene expression and cellular responses through cytokine receptors, GO:0035556, and various enzymatic activities. these pathways play essential roles in several biological processes, including immune responses, cell differentiation and development, cell survival death]][[GO:0005125, GO:0008009, GO:0001216, GO:0006955, interleukin-12 alpha subunit binding activity, GO:0004707, protein kinase binding activity, GO:0001817, GO:0002682, smad binding activity, transcription factor binding activity]]0.00
378gpt-3.5-turboontological_synopsisHALLMARK_UNFOLDED_PROTEIN_RESPONSE-0[[protein folding and processing, GO:0015031, GO:0003723, GO:0043022, GO:0003743]][[protein folding and chaperone activity, rna binding and transcriptional regulation, rna processing and degradation]]0.00
379gpt-3.5-turboontological_synopsisHALLMARK_UNFOLDED_PROTEIN_RESPONSE-1[[rna binding activity, protein folding chaperone binding activity, ribosome binding activity, histone binding activity, dna-binding transcription factor binding activity, ubiquitin protein ligase binding activity]][[GO:0003723, GO:0051087, GO:0090304, endoplasmic reticulum stress response pathway]]0.00
380gpt-3.5-turboontological_synopsisHALLMARK_UV_RESPONSE_DN-0[[extracellular matrix organization; growth factor signaling; regulation of transcription, dna-templated; positive regulation of protein kinase activity; organic acid metabolic process.\\n\\nmechanism: these genes are involved in extracellular matrix structural constituent, growth factor signaling, GO:0000988, GO:0005515, and nucleotide binding. this suggests that they may be involved in the regulation of gene transcription, cellular growth and differentiation, and the organization of extracellular matrices. a hypothesis for the underlying biological mechanism or pathway is that these genes may be involved in the regulation of extracellular matrix formation and growth factor signaling pathways, which then contribute to cellular differentiation and growth. additionally, the binding of proteins with transcription factor activity and nucleotide binding activity suggests that these genes are involved in the regulation of gene transcription, which may have downstream effects on cellular function and behavior]][[GO:0005201, identical protein binding activity, enzyme binding activity, smad binding activity]]0.00
381gpt-3.5-turboontological_synopsisHALLMARK_UV_RESPONSE_DN-1[[GO:0005201, GO:0005178, identical protein binding activity, protease binding activity, calcium binding, platelet-derived growth factor binding activity]][[GO:0005201, GO:0005515, GO:0016563, GO:0005102]]0.11
382gpt-3.5-turboontological_synopsisHALLMARK_UV_RESPONSE_UP-0[[enzyme binding activity, protein kinase binding activity, GO:0042803, rna binding activity, atp binding activity, identical protein binding activity, ubiquitin protein ligase binding activity, GO:0001228, ion binding activity, g protein-coupled receptor binding activity, dna polymerase binding activity, peptide hormone receptor binding activity. \\n\\nmechanism: these genes are involved in a variety of molecular activities, including enzyme activity, protein binding, and transcription factor activity. one potential underlying biological mechanism is the regulation and interaction of proteins in various cellular processes]][[enzyme binding activity, GO:0003700, protein kinase binding activity, identical protein binding activity, rna binding activity, atp binding activity, ubiquitin protein ligase binding activity]]0.46
383gpt-3.5-turboontological_synopsisHALLMARK_UV_RESPONSE_UP-1[[atp binding activity, GO:0001216, identical protein binding activity, rna binding activity, protein kinase binding activity, cysteine-type endopeptidase activity involvement in apoptotic signaling, GO:0004602, histone binding activity, GO:0030594, glucagon receptor binding activity, GO:0004499, peptide hormone receptor binding activity, gtp binding activity, more]][[enzyme binding activity, GO:0006508, protein phosphatase binding activity, GO:0004725]]0.00
384gpt-3.5-turboontological_synopsisHALLMARK_WNT_BETA_CATENIN_SIGNALING-0[[GO:0090090, regulation of transcription, GO:0000981, histone deacetylase binding activity, ubiquitin protein ligase binding activity, notch binding activity, protein kinase binding activity, GO:0003713, identical protein binding activity]][[GO:0060070, transcription regulation, MESH:D012319, transcription activator, beta-catenin complex, GO:0007219]]0.00
385gpt-3.5-turboontological_synopsisHALLMARK_WNT_BETA_CATENIN_SIGNALING-1[[GO:0060070, GO:0031398, GO:0090090, GO:0031397, GO:0030162]][[GO:0060070, GO:0010468]]0.17
386gpt-3.5-turboontological_synopsisT cell proliferation-0[[GO:0050776, intracellular signaling, GO:0008037, GO:0009617, GO:0008284, GO:0005125, protein kinase binding activity, identical protein binding activity]][[GO:0050852, GO:0005125, interleukin-2 receptor binding activity, negative regulation of peptid, intracellular signal transduction\\n\\nmechanism: the genes analyzed in this study are primarily involved in signaling and receptor binding activities. this suggests that these genes may play an important role in the communication between cells and regulation of immune response. \\n\\n t cell receptor signaling pathway, cytokine activity, interleukin-2 receptor binding activity, negative regulation of peptid..., and intracellular signal transduction]]0.08
387gpt-3.5-turboontological_synopsisT cell proliferation-1[[GO:0042110, GO:0001816, GO:0010468, GO:0050671, GO:0001819, GO:0001933, GO:0045840, protein kinase binding activity, GO:0004697, GO:0004911, GO:0004896, GO:0097190, GO:0007005, GO:0043065, GO:0042100, GO:0004931]][[GO:0050863, GO:0001819, GO:0006468, GO:0043066, GO:0002687, GO:0030890, GO:0006879, GO:0010468]]0.09
388gpt-3.5-turboontological_synopsisYamanaka-TFs-0[[transcription regulation, GO:0010468, GO:0045944, GO:0003700, cellular differentiation]][[transcriptional regulation, GO:0010467, GO:0003700, GO:0009889, GO:0019219]]0.11
389gpt-3.5-turboontological_synopsisYamanaka-TFs-1[[GO:0010468, transcriptional regulation, GO:0003700, GO:0001714, GO:0045944]][[GO:0010467, transcription regulation, dna binding activity, rna polymerase ii-specific, GO:0010468, transcription cis-regulatory region binding activity]]0.10
390gpt-3.5-turboontological_synopsisamigo-example-0[[GO:0030198, GO:0007165, GO:0007596]][[GO:0007160, GO:0030198, GO:0030199, GO:0008034]]0.17
391gpt-3.5-turboontological_synopsisamigo-example-1[[GO:0005178, GO:0005201, GO:0008083, platelet-derived growth factor binding activity, GO:0030199]][[GO:0007160, GO:0030199, GO:0030198, GO:1902533, GO:0010604, GO:0030334]]0.10
392gpt-3.5-turboontological_synopsisbicluster_RNAseqDB_0-0[[GO:0005515, GO:0005216, transcriptional regulation, ubiquitin-protein ligase activity]][[GO:0003700, identical protein binding activity, protein kinase binding activity, actin binding activity, sequence-specific double-stranded dna binding activity, metal ion binding activity, calcium ion binding activity, chromatin binding activity, rna binding activity]]0.00
393gpt-3.5-turboontological_synopsisbicluster_RNAseqDB_0-1[[metal ion binding activity, calcium ion binding activity, GO:0000981, g protein-coupled receptor binding activity, enzyme binding activity, sequence-specific double-stranded dna binding activity, cytoskeletal protein binding activity, GO:0061630]][[binding activity, GO:0003700, GO:0046872, GO:0019904, GO:0061630]]0.08
394gpt-3.5-turboontological_synopsisbicluster_RNAseqDB_1002-0[[GO:0006936, GO:0030239, GO:0043502, GO:0051015, GO:0005523]][[GO:0006936, GO:0043502, GO:0016567]]0.33
395gpt-3.5-turboontological_synopsisbicluster_RNAseqDB_1002-1[[GO:0003009, GO:0060048, GO:0010628, actin filament binding activity, GO:0008307]][[GO:0006936, GO:0003009, GO:0016567, ion channel activity.\\n\\nmechanism: these genes likely play a role in muscle contraction and structure, possibly through the regulation of ion channels and protein ubiquitination]]0.12
396gpt-3.5-turboontological_synopsisendocytosis-0[[GO:0006897, GO:0015031, GO:0006898]][[GO:0006897, GO:0007165, cellular adhesion, GO:0006869, GO:0030163, GO:0007009]]0.12
397gpt-3.5-turboontological_synopsisendocytosis-1[[GO:0006897, lysosomal function, GO:0038023, GO:0006955, GO:0008152]][[GO:0006897, membrane traffic, GO:0015031]]0.14
398gpt-3.5-turboontological_synopsisglycolysis-gocam-0[[GO:0006006, GO:0005975, GO:0019725, GO:0008104, GO:0070062, GO:0005634]][[GO:0006096, GO:0005975, GO:0006000, metabolic homeostasis]]0.11
399gpt-3.5-turboontological_synopsisglycolysis-gocam-1[[GO:0006096, GO:0005975, GO:0006000, cell development.\\n\\nhypotheses: the enriched terms suggest that these genes are involved in the glycolysis pathway, contributing to carbohydrate metabolic processes and the production of energy for cellular development. specifically, fructose metabolic processes are enriched, indicating that the genes may play a role in the conversion of fructose to glucose during glycolysis]][[GO:0006096, GO:0005975, GO:0006002, GO:0005945]]0.33
400gpt-3.5-turboontological_synopsisgo-postsynapse-calcium-transmembrane-0[[GO:0006816, GO:0007268, GO:0005245, GO:0098978, GO:0004972]][[GO:0006816, GO:0005245, GO:0008066, GO:0005892]]0.29
401gpt-3.5-turboontological_synopsisgo-postsynapse-calcium-transmembrane-1[[GO:0005509, GO:0006836, GO:0001505, GO:0016079, GO:0035235, GO:0007186, GO:0071318]][[GO:0019722, voltage-gated calcium channel, GO:0051480, GO:0008066, GO:0017146, GO:0007268, GO:0051899, g-protein coupled receptor signaling pathway]]0.00
402gpt-3.5-turboontological_synopsisgo-reg-autophagy-pkra-0[[GO:0006468, GO:0010604, GO:0038202, GO:0032006, GO:0016241, positive regulation of cyclin-dependent protein serine/threonine kinase activity.\\n\\nmechanism and]][[GO:0006468, GO:0035556, GO:0031929, GO:0097190, kinase activity regulation, GO:0010604]]0.20
403gpt-3.5-turboontological_synopsisgo-reg-autophagy-pkra-1[[intracellular signaling, pathway regulation, GO:0006915, GO:0004672, GO:0006468, GO:0010604, GO:0045859]][[GO:0035556, protein kinase activity regulation, GO:0010604, GO:0038202, GO:0032008, GO:0045859, apoptosis signaling pathway, chromatin binding activity]]0.15
404gpt-3.5-turboontological_synopsishydrolase activity, hydrolyzing O-glycosyl compounds-0[[GO:0046479, GO:0006516, GO:0006032, GO:0030214]][[GO:0016052, GO:0006516, GO:0006032, GO:0030214]]0.60
405gpt-3.5-turboontological_synopsishydrolase activity, hydrolyzing O-glycosyl compounds-1[[GO:0005975, MESH:D054794, glycan catabolism, GO:0006516, GO:0019377, GO:0006032, GO:0006004]][[GO:0016052, GO:0030214, GO:0006516, GO:0019377, GO:0006032, GO:0006491, GO:0006517, mannose trimming involved in glycoprotein erad pathway.\\n\\nmechanism: one potential underlying biological mechanism is the regulation of cell surface and extracellular matrix composition, as well as the breakdown and recycling of molecules within these structures. glycosidases play a key role in breaking down complex carbohydrates into smaller subunits, which can then be reassembled into new molecules. the ability to break down specific types of carbohydrates, such as hyaluronic acid and chitin, may also be important for cellular processes such as cell migration and host defense]]0.25
406gpt-3.5-turboontological_synopsisig-receptor-binding-2022-0[[antigen binding activity, immunoglobulin receptor binding activity, GO:0002253]][[immunoglobulin receptor binding activity, antigen binding activity]]0.67
407gpt-3.5-turboontological_synopsisig-receptor-binding-2022-1[[GO:0002253, GO:0098542, GO:0019731, GO:0006959, GO:0002377, GO:0051130, GO:0045657]][[GO:0006955, GO:0006952, antigen binding activity]]0.00
408gpt-3.5-turboontological_synopsismeiosis I-0[[GO:0061982, GO:0007131, GO:0007129, GO:0000712, GO:0000724]][[homologous chromosome pairing, GO:0042138, GO:0000706, GO:0007131, GO:0000724, GO:0000712, GO:0000795]]0.33
409gpt-3.5-turboontological_synopsismeiosis I-1[[meiotic recombination, GO:0035825, GO:0006302]][[meiotic recombination, GO:0006302, GO:0035825, chromosomal segregation, GO:0007130]]0.60
410gpt-3.5-turboontological_synopsismolecular sequestering-0[[molecular sequestering, protein binding activity, transport of metal ions, GO:0048523, response to infection and stress, GO:0010468, GO:0019722, regulation of transcription]][[GO:0140313, GO:0140311, identical protein binding activity, GO:0060090, ubiquitin protein ligase binding activity, GO:0016567]]0.00
411gpt-3.5-turboontological_synopsismolecular sequestering-1[[GO:0140311, GO:0010468, GO:0031398, GO:0051238]][[GO:0010468, GO:0042742, GO:0045185, GO:0002376, GO:0009267, GO:0032387, GO:0035556]]0.10
412gpt-3.5-turboontological_synopsismtorc1-0[[binding activity, enzymatic activity, GO:0006412, GO:0023052, GO:0008152]][[GO:0005515, GO:0003723, enzymatic activity, structural constituent of cytoskeleton. \\n\\nmechanism: these genes likely play a role in cellular processes such as transcription, translation, protein folding, and cytoskeletal organization]]0.12
413gpt-3.5-turboontological_synopsismtorc1-1[[GO:0005515, GO:0042802, GO:0019899, GO:0043167, GO:0005524, GO:0031625, GO:0003723, GO:0003677, GO:0097159, GO:0017076, GO:0051015, GO:0042802, GO:0016491, phosphoprotein binding activity, GO:0005215, GO:0006793, GO:0044237, GO:0006457, GO:0003677, GO:0008380]][[GO:0005515, GO:0003824, GO:0005215]]0.10
414gpt-3.5-turboontological_synopsisperoxisome-0[[GO:0017038, peroxisomal biogenesis, GO:0140036, atp binding and hydrolysis activity, lipid binding activity]][[peroxisome biogenesis, peroxisome matrix targeting, GO:0017038]]0.14
415gpt-3.5-turboontological_synopsisperoxisome-1[[GO:0007031, GO:0016558, GO:0005778, peroxisomal biogenesis disorder, GO:0008611, lipid binding activity, atp binding activity, GO:0016887, ubiquitin-dependent protein binding activity, enzyme binding activity]][[peroxisome biogenesis, GO:0017038, GO:0005778, ubiquitin-dependent protein binding activity, atp binding activity, GO:0016887]]0.33
416gpt-3.5-turboontological_synopsisprogeria-0[[GO:0006259, GO:0006325, GO:0033554, GO:0006281, GO:0007568]][[GO:0006259, GO:0006325, GO:0033554]]0.60
417gpt-3.5-turboontological_synopsisprogeria-1[[GO:0006281, GO:0006950, GO:0090398, GO:0000723, chromatin condensation]][[GO:0006281, GO:0000723, GO:0007568]]0.33
418gpt-3.5-turboontological_synopsisregulation of presynaptic membrane potential-0[[GO:0015276, GO:0099505, GO:0060078, GO:0071805, GO:0035725, GO:0035235]][[GO:0007214, GO:0022849, GO:0005242, GO:0035235, GO:0015276, GO:0071805, GO:0005244]]0.30
419gpt-3.5-turboontological_synopsisregulation of presynaptic membrane potential-1[[GO:0007214, GO:0007215, GO:0006811, GO:0006836, GO:0007268]][[GO:0006811, GO:0007268, membrane potential regulation, GO:0008066, GO:0007214]]0.43
420gpt-3.5-turboontological_synopsissensory ataxia-0[[GO:0042552, GO:0007422, MONDO:0005071, GO:0022011, MONDO:0005244]][[MONDO:0015626, GO:0042552, GO:0007422, GO:0006457, GO:0007600, nucleic acid metabolism, mitochondrial function]]0.20
421gpt-3.5-turboontological_synopsissensory ataxia-1[[GO:0007399, GO:0042552, mitochondrial metabolism, GO:0030163, protein regulation, GO:0071260]][[GO:0007399, MONDO:0015626, GO:0042552, UBERON:0000010, mitochondrial dysfunction, protein ubiquitination.\\n\\nmechanism]]0.20
422gpt-3.5-turboontological_synopsisterm-GO:0007212-0[[GO:0007186, GO:0007212]][[GO:0007212, GO:0007190, calcium ion regulation, g protein-coupled receptor pathway]]0.20
423gpt-3.5-turboontological_synopsisterm-GO:0007212-1[[GO:0007212, GO:0007186, GO:0051480, GO:0004016, GO:0006469, GO:0050821, GO:0060828, GO:0007220, GO:0034205, GO:0006508, GO:0046325, GO:1904227, GO:0051247, GO:0015171, GO:0015108]][[GO:0007186, GO:0004952, GO:0004016, GO:0051480, negative regulation of glycogen synthase activity, GO:0004672, GO:0019538, GO:0006468]]0.15
424gpt-3.5-turboontological_synopsistf-downreg-colorectal-0[[dna-binding transcription factor, rna polymerase ii-specific transcription regulation, GO:0000122, GO:0045944, GO:0006355]][[GO:0001216, rna polymerase ii transcription regulatory region sequence-specific dna binding activity, GO:0045944, GO:0000122, GO:0006355, transcription factor binding activity, nucleic acid binding activity, chromatin binding activity, GO:0003713]]0.27
425gpt-3.5-turboontological_synopsistf-downreg-colorectal-1[[GO:0000988, GO:0006355, GO:0045893, GO:0045892, dna-binding, GO:0003702]][[GO:0003700, GO:0006355, GO:0010468, GO:0006337]]0.11
426text-davinci-003narrative_synopsisEDS-0[[connective tissue formation and repair, protein binding and folding, GO:0006955, GO:0042060, GO:0006024]][[GO:0032964, collagen fiber formation, extracellular matrix maturation, transcriptional regulation, procollagen protein, MESH:D006025, metalloproteinase, proteolytic processing, peptidyl prolyl cis-trans isomerase, MESH:M0465019, tumor-rejection antigen, sulfotransferase, transmembrane protein, beta-1,3 galactosyltransferase]]0.00
427text-davinci-003narrative_synopsisEDS-1[[collagen maturation, GO:0006024, transcriptional regulation, GO:0006829]][[GO:0006486, extracellular matrix remodeling, collagen production, GO:0061448, immunity response, GO:0006508, tumor rejection, MESH:M0465019, MESH:D008565, transcriptional repressor, peptidyl-prolyl isomerase, complement system, GO:0004226, peptidase s1]]0.00
428text-davinci-003narrative_synopsisFA-0[[GO:0006281, GO:0035825, GO:0016310, nucleoprotein complex assembly, formation of nuclear foci, double-strand dna repair, holliday junction resolution, function in tumor suppression, reca/rad51-related protein family, dna lesions, structural specific endonucleases, rad51 family, cellular responses to replication fork failure, brc motif]][[GO:0006281, genome maintenance, MESH:D004249, nucleoprotein complex, GO:0035825, double-strand dna repair, holliday junction resolution, monoubiquinated, MESH:D051135, nuclear foci, structure-specific endonucleases, MESH:D051135, recq deah helicase, tumor suppression, ssdna-binding proteins]]0.16
429text-davinci-003narrative_synopsisFA-1[[GO:0006281, GO:0035825, monoubiquitination, holliday junction resolution, rad51 binding]][[GO:0006281, nucleoprotein complex, GO:0035825, dna lesion, MESH:M0443450, fanconi anemia complementation group (fanc), GO:0006302]]0.20
430text-davinci-003narrative_synopsisHALLMARK_ADIPOGENESIS-0[[GO:0006629, GO:0006633, GO:0022900, GO:0005739, MESH:D000975, GO:0045333, MESH:D010084, acyltransferase, carboxylase, acyl-coenzyme a synthetase, ubiquitin protease, MESH:C021451, MESH:D010743, oxidoreductase, plasma lipase, hydratase]][[GO:0010467, GO:0140657, GO:0006468, ubiquitin-mediated degradation, GO:0051726, GO:0005525, GO:0006839, GO:0006118, GO:0006119, MESH:D004789, enzyme inhibition, GO:0016491, GO:0016482, GO:0005515, GO:0006629, GO:0036211, ubiquitinylation]]0.03
431text-davinci-003narrative_synopsisHALLMARK_ADIPOGENESIS-1[[GO:0005515, transcription regulation, atpase, MESH:D020558, transcript processing, protein transduction, MESH:D014451, GO:0044237, energy production, GO:0006508]][[atp production, GO:0005746, GO:0006118, GO:0030497, rna/dna binding, GO:0015031, MESH:D054875, GO:0016310, GO:0008017, GO:0006869]]0.00
432text-davinci-003narrative_synopsisHALLMARK_ALLOGRAFT_REJECTION-0[[immune/cytokine responses, GO:0006412, GO:0006351, cell surface signaling, receptor activation, MESH:D054875, MONDO:0002123, GO:0005524]][[cell signalling, cytokine production/regulation, chemokine production/regulation, antimicrobial defence, plasma protein regulation, immune regulation, inflammatory regulation, transcriptional regulation, GO:0004672, GO:0008233, glycoprotein activity, receptor protein activity]]0.00
433text-davinci-003narrative_synopsisHALLMARK_ALLOGRAFT_REJECTION-1[[GO:0006412, cellular regulation, GO:0008152, cell signaling, GO:0006351, immunoregulation, stability, GO:0005515, GO:0016310, GO:0010467, g-protein coupled receptor, transmembrane protein, t-cell development]][[integrin, cytokine, g-protein coupled receptor, MESH:D007372, MESH:D018124, MESH:D008562, MESH:D011494, chemokine, transmembrane receptor, GO:0007165, transcriptional regulation, GO:0006412, GO:0006955]]0.08
434text-davinci-003narrative_synopsisHALLMARK_ANDROGEN_RESPONSE-0[[MESH:D011494, GO:0000981, GO:0005530, adhesion molecule, GO:0016538, MESH:D016601, protein tyrosine phosphatase, g protein, serine/threonine protein kinase, MESH:D008565, MESH:D006657, ubiquitin ligase, MESH:C052123, microtubule-associated protein, atp-binding cassette, alpha/beta-hydrolase, integrin alpha-chain, signal transducion, protein inhibitor of activated stat]][[GO:0005524, GO:0006351, GO:0016310, MESH:D011494, protein tyrosine phosphatase, GO:0065007, GO:0005515, hydrolase, ribosomal s6 kinase, GO:0016192, regulatory subunit, acetyltransferase, modulation, GO:0005509, GO:0005783, GO:0000981, GO:0003723, n-myc downregulated, polypeptide, GO:0016125, MESH:D006657, protein inhibitor, MESH:D051116, structural fibre, disulfide oxidoreductase, adenine dinucleotide, non-sterol metabolism, calcium-induced, GO:0042593]]0.09
435text-davinci-003narrative_synopsisHALLMARK_ANDROGEN_RESPONSE-1[[GO:0008283, GO:0006351, GO:0007165, structural components, metabolism of proteins, GO:0006629, GO:0005975, GO:0007155, binding activity, GO:0010467, GO:0003677, MESH:D011494, oxidoreductase, anchoring kinase to microtubules, GO:0005102, molecule transport, MESH:D010455]][[transcriptional regulation, GO:0004672, GO:0005515, GO:0003723, GO:0007165, proteolytic enzyme activity, GO:0003677]]0.09
436text-davinci-003narrative_synopsisHALLMARK_ANGIOGENESIS-0[[this is a list of genes involved in a variety of pathways and processes related to cell adhesion, GO:0040007, GO:0008152, and other physiologic functions. the terms “cell adhesion”, “cell signaling”, “extracellular matrix”, “transcriptional regulation”, and “cell cycle progression and differentiation” are all enriched among this group of genes. a hypothesis of the underlying biological mechanism at work is that these genes work together to promote cell growth and regulation, that many of these genes interact to achieve greater cellular complexity]][[GO:0042157, GO:0050817, GO:0007599, MESH:D016207, MESH:D018925, receptors, transporters, secreted extracellular matrix proteins, GO:0004868, MESH:D011509, GO:0007155, GO:0016477, GO:0023052, GO:0008283, GO:0006915, transcriptional regulation, tissue development and regeneration, GO:0006955]]0.00
437text-davinci-003narrative_synopsisHALLMARK_ANGIOGENESIS-1[[GO:0007155, extracellular matrix remodeling, GO:0007165, protease inhibition, transcriptional regulation]][[cell-cell interactions, cell-matrix interactions, extracellular matrix production, processing of proteoglycans and glycoproteins]]0.00
438text-davinci-003narrative_synopsisHALLMARK_APICAL_JUNCTION-0[[GO:0005207, GO:0007155, calcium-dependent proteins, MESH:D008565, intronless proteins, intracellular scaffolding proteins, fibrillin proteins, signaling receptors, MESH:D051193, MESH:D003598, tubulin proteins, type ii membrane proteins, MESH:D006023]][[integrin, GO:0008014, GO:0005530, MESH:C119025, map kinase, protein tyrosine kinase, guanine nucleotide binding protein, MESH:D020558, act]]0.00
439text-davinci-003narrative_synopsisHALLMARK_APICAL_JUNCTION-1[[GO:0007155, GO:0007165, actin binding and assembly, membrane localization, ecm protein binding and assembly]][[GO:0007155, GO:0023052, scaffolding, cytoskeleton maintenance, GO:0031012, MESH:D016023, MESH:D057167, MESH:C119025, MESH:D011494, GO:0008014]]0.07
440text-davinci-003narrative_synopsisHALLMARK_APICAL_SURFACE-0[[GO:0007160, GO:0007165, MESH:D008565, transcriptional coactivation, signal recognition, GO:0055085, GO:0006898]][[GO:0007155, GO:0006457, GO:0007154, GO:0006898, gpi-anchored cell surface proteins, cation transport atpase, transcriptional coactivation, interleukin signaling, hormone-dependence, MESH:D019812, heparin-binding, GO:0007160]]0.19
441text-davinci-003narrative_synopsisHALLMARK_APICAL_SURFACE-1[[GO:0007160, cell-matrix interactions, carbohydrate binding activity, GO:0007155, GO:0038023, GO:0007165, GO:0008284, GO:0048681, GO:0030506, protein tyrosine kinase, sh2 domain binding activity, sh3 domain binding activity]][[cell signal transduction, GO:0007160, GO:0006457, GO:0030308, ligand binding, cell-surface glycoprotein, cation transmembrane transporter, growth arrest, MESH:D051246, transmembrane protein, regulatory subunit, membrane-bound glycoprotein, ammonium transmembrane transporter, cell surface receptor, insulin-regulated facilitative glucose transporter, cell surface adhesion molecule, GO:0140326, glycosylphosphatidylinositol-anchored protein]]0.03
442text-davinci-003narrative_synopsisHALLMARK_APOPTOSIS-0[[GO:0006915, cytoplasmic signaling, transcriptional regulation, GO:0005515, cellular organization]][[GO:0006915, transcriptional regulation, GO:0003677, tnf receptor superfamily, bcl-2 protein family]]0.25
443text-davinci-003narrative_synopsisHALLMARK_APOPTOSIS-1[[cell death processes, GO:0023052, cytoplasmic proteins, MESH:M0015044, MESH:D015533, MESH:D004798, toxin removal, GO:0005102]][[the genes summarized are involved in a wide range of processes, including apoptosis, tumor suppression, inflammation, thioredoxin binding, cytoplasmic protein and membrane glycoprotein regulation, dna topoisomerase and transcriptional activation. the commonalities that emerge from the enrichment test point to a specific biological pathway known as cell death regulation and signal transduction. this involves the interconnected network of genes that regulate apoptosis and maintain genetic stability, as well as others involved in the modulation of immune response pathways. enriched terms include apoptosis, cytoplasmic protein regulation, transcriptional regulation, tumor suppression, GO:0006954, MESH:D004264, thioredoxin binding, membrane glycoprotein regulation, transcriptional coactivation, death agonist, GO:0048018, serine/threonine phosphatase, voltage-dependent anion channel, MESH:D006136, class-1 polypeptide chain release factor, proapoptotic, nf-kappa-b.\\n\\nsummary: genes related to cell death regulation signal transduction pathways.\\nmechanism: interconnected network of genes that regulate apoptosis maintain genetic stability, as well as those involved in the modulation]]0.00
444text-davinci-003narrative_synopsisHALLMARK_BILE_ACID_METABOLISM-0[[atp-binding, GO:0006810, GO:0004768, MESH:D010084, enzyme catalysis, GO:0000981]][[GO:0006629, atp binding cassette, MESH:M0011631, GO:0005490, peroxin, gamma-glutamylcysteine synthetase, GO:0050632, MESH:D002785, flavoenzymes, GO:0042446, GO:0016209]]0.00
445text-davinci-003narrative_synopsisHALLMARK_BILE_ACID_METABOLISM-1[[GO:0015031, GO:0006412, GO:0006629, MESH:D010084, hormone regulation, transcription regulation, GO:0006805, calcium binding, GO:0005524, MESH:D005982, GO:0008203, MESH:M0011631, sulfate conjugation, 2-hydroxyacid oxidase, MESH:D000214, MESH:D000215, coenzyme a ligase, natriuretic peptide, peroxisome biogenesis, tgf-beta ligand, adrenal steroid synthesis, nuclear receptor, copper zinc binding, GO:0050632, MESH:D012319, gamma-glut]][[GO:0006629, GO:0006810, oxidation, bile acids synthesis, GO:0006790, GO:0005777, oxidative stress response]]0.03
446text-davinci-003narrative_synopsisHALLMARK_CHOLESTEROL_HOMEOSTASIS-0[[MESH:D008565, MONDO:0018815, acetoacetyl-coa thiolase, cytosolic enzyme, actin isoforms, activation transcription factor (creb), annexin family, fructose-biphosphate aldolase, immunoglobulin superfamily, g-protein coupled receptor (gpcr), homotetramer, hydratase/isomerase superfamily, MESH:C022503, mal proteolipid, MESH:M0476528, sre-binding proteins (srebp), peroxisomal enzyme, transmembrane 4 superfamily, transmembrane protein, multispan transmembrane protein, tetr]][[GO:0048870, energy generation, GO:0008652, GO:0009063, GO:0009101, GO:0016126, GO:0016127, GO:0006629, GO:0006869, transcriptional regulation]]0.00
447text-davinci-003narrative_synopsisHALLMARK_CHOLESTEROL_HOMEOSTASIS-1[[GO:0006629, GO:0005543, GO:0004768, atp-binding cassette, GO:0016126, cytochrome p450 family proteins]][[GO:0006695, GO:0006629, GO:0006636, cell growth/regulation, GO:0051726, GO:0005515, mhc class ii presentation, cellular antioxidant activity, GO:0000988]]0.07
448text-davinci-003narrative_synopsisHALLMARK_COAGULATION-0[[complement system, GO:0007596, peptide hydrolysis, GO:0016485, inflammation regulation]][[analysis of this set of human genes revealed high enrichment for terms related to proteases and protease inhibitors, GO:0005209, MESH:D006023, and serine proteinases. of particular note is the abundance of genes related to the regulation of the complement system and to the coagulation cascade, GO:0004235, there appears to be a strong emphasis on proteins that are involved in the maintenance of cellular integrity and in the regulation of inflammatory and immune responses. in particular, it appears that the presence of proteases, MESH:D011480, GO:0005209, MESH:D006023, and serine proteinases is significantly enriched. this suggests that these proteins are involved in the regulation of a variety of processes, including the complement system and the coagulation cascade. furthermore, the presence of various mmps suggests a regulatory role in the breakdown of proteins in the extracellular matrix, which is important for tissue remodeling and wound healing]]0.00
449text-davinci-003narrative_synopsisHALLMARK_COAGULATION-1[[matrix metalloproteinase, cysteine-rich protein, serine protease inhibitor, transforming growth factor-beta, MESH:D054834, guanine nucleotide-binding proteins, peptidase s1 family, integrin beta chain, MESH:D001779, dipeptidyl peptidase, vitamin k-dependent glycoprotein, vitamin k-dependent coagulation factor, regulator of complement activation, protein tyrosine kinase, MESH:D006904, iron-sulfur cluster scaffold, disulfide bridge, kunitz-type serine protease, MESH:D042962, MESH:D037601, g-protein coupled receptor, cytosolic peptidase, GO:0030165, basic leucine zipper, a disintegrin and metalloprote]][[cysteine-aspartic acid protease, MESH:D020782, peptidase, guanine nucleotide-binding proteins, GO:0030165, metalloproteinase, MESH:D042962, regulator of complement activation, regulator of g protein signal transduction, rnase a superfamily, MESH:D011505, subtilisin-like proprotein convertase, MESH:D011973, vitamin k-dependent plasma glycoprotein, vitamin k-dependent coagulation factor, GO:0005161, lysosomal cysteine proteinase, MESH:D015842, transforming growth factor-beta, MESH:D006904, kunitz-type serine protease, integ]]0.21
450text-davinci-003narrative_synopsisHALLMARK_COMPLEMENT-0[[cell signaling, cell structure/stability, GO:0008152, vitamin k/clotting, GO:0005856, GO:0005886, GO:0006954]][[MESH:D010770, GO:0000502, GO:0004868, cysteine-aspartic acid protease (caspase), GO:0006915, inflammation signalling, MESH:D005165, factor]]0.00
451text-davinci-003narrative_synopsisHALLMARK_COMPLEMENT-1[[protein production, cell surface glycoprotein regulation, GO:0006956, GO:0007165, heat shock protein, MESH:D003564, metalloproteinase, guanine nucleotide-binding protein, lysosomal cysteine protease, zinc finger protein, cysteine-aspartic acid protease, MESH:D001053, metallothionein.\\nmechanism: the genes may be involved in various signalling pathways to facilitate the regulation of cell surface glycoprotein as well as the production of proteins. cytidine deaminase, metalloproteinase, guanine nucleotide-binding protein and cysteine-aspartic acid protease are likely enzymes that the list of genes may be involved in. heat shock proteins and zinc finger proteins, in addition to apolipoproteins and metallothionein, may be involved in the regulation and transportation of cell proteins]][[cell signaling, GO:0007155, GO:0008233, transcriptional regulation, GO:0008152, cytoskeletal functions]]0.00
452text-davinci-003narrative_synopsisHALLMARK_DNA_REPAIR-0[[summary: this enrichment test provides evidence of a common biological mechanism underlying many genes in human genetics: dna repair, replication, and transcription.\\n\\nmechanism: the mechanism underlying this term enrichment is the need for accurate dna repair, replication, and transcription, which all require the co-ordinated efforts of many protein families, such as those encoded by the wd-repeat, MESH:D000262, argonaute, MESH:D000263, purine/pyrimidine phosphoribosyltransferase, b-cell receptor associated proteins, MESH:C056608, clp1, GO:0016538, MESH:C010098, dna helicase, MESH:M0251357, general transcription factor (gtf) ii, MESH:D005979, histone-fold proteins, mhc, MESH:C110617, GO:0005662, saccharomyces cerevisiae rad52, schizosaccharomyces pombe rae1, splicing factor (sf3a), GO:0003734, MESH:D011988, transcription factor b (tfb4), trans]][[GO:0003677, transcription control, post-splicing, MESH:D012319, GO:0006281, GO:0071897]]0.00
453text-davinci-003narrative_synopsisHALLMARK_DNA_REPAIR-1[[GO:0003677, transcription regulation, GO:0006281, GO:0000394, GO:0006397, GO:0003723, GO:0003682, GO:0019899, GO:0003684, general transcription factor, transcription/repair factors, MESH:M0006668, hypothalamic hormone receptor binding, GO:0004016, nuclear cap-binding protein, GO:0016567, transcription initiation, dna polymerase, GO:0006605]][[GO:0019899, GO:0003723, GO:0003677, GO:0005515, chromosomal binding, dna polymerase, MESH:D012321, phosphorolysis, GO:0010629, GO:0016567]]0.21
454text-davinci-003narrative_synopsisHALLMARK_E2F_TARGETS-0[[GO:0006260, GO:0006281, GO:0006351, GO:0003682, GO:0016569, GO:0051726, ran binding, GO:0000808, atpase, GO:0016538, cyclin-dependent kinase, polycomb, dead box protein, gtpase activating protein, GO:0042393, GO:0003723, nucleolar protein, ubiquitously expressed protein, smc subfamily protein, pp2c family, elongation of primed dna template synthesis, dna interstrand cross-linking, import of proteins into nucleus, MESH:D004264, tumor suppressor protein, MESH:D051981, ubr box protein, p80 autoantigen]][[dna replication/repair, chromatin regulation, GO:0006396, ser/thr protein kinase, MESH:D063146, nuclear transport and export, GO:0016567, gtpase activation, GO:0006413, GO:0003723, GO:0003677, GO:0042393, ubiquitin protein ligase, cyclin-dependent kinase, MESH:D000251, MESH:D003842]]0.07
455text-davinci-003narrative_synopsisHALLMARK_E2F_TARGETS-1[[GO:0003676, GO:0006260, GO:0036211, GO:0006259, GO:0000785, GO:0051726, GO:0016570, protein assembly and disassembly]][[GO:0006260, nuclear import/export, GO:0003723, chromatin regulation/modification, GO:0030163, GO:1901987, GO:0006281]]0.07
456text-davinci-003narrative_synopsisHALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0[[cell signaling, extracellular matrix formation, GO:0007155, connective tissue formation, GO:0001525, metabolic regulation, MESH:D016207, tissue repair]][[GO:0003779, actin regulation, GO:0007155, cell signaling, GO:0005518, cytokine regulation and signaling, GO:0005207, growth factor family members, peptidase genes]]0.13
457text-davinci-003narrative_synopsisHALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1[[MESH:D016326, GO:0005202, MESH:D007797, MESH:D005353, MESH:D014841, integrin, MESH:D016189, fibulin proteins]][[GO:0007155, GO:0005518, GO:0003779, MESH:D024022, MESH:D016326, cytoskeletal components, cell signalling]]0.07
458text-davinci-003narrative_synopsisHALLMARK_ESTROGEN_RESPONSE_EARLY-0[[GO:0042277, membrane structure modification, GO:0003677, GO:0006631, GO:0051427, signalling transcription, gtpase activation, adenylate cyclase modulation, GO:0016301, GO:0006897, glycoprotein production, GO:0019838, GO:0016570, GO:0006644, zinc-binding]][[GO:0007165, GO:0010467, GO:0006810, MESH:D008565, GO:0043687, GO:0005515, ligand binding, acyltransferase]]0.00
459text-davinci-003narrative_synopsisHALLMARK_ESTROGEN_RESPONSE_EARLY-1[[dna-binding, GO:0005515, GO:0043687, GO:0007165, metabolic activity]][[cytoskeletal organization, dna-binding transcription regulation, GO:0055085, membrane-associated signaling, receptor activation and signaling, cytokine and growth factor signaling]]0.00
460text-davinci-003narrative_synopsisHALLMARK_ESTROGEN_RESPONSE_LATE-0[[MESH:D011494, GO:0000981, GO:0005509, MESH:D054794, hormone receptors, GO:0007155, GO:0006457, GO:0010467]][[g-protein signaling, ion channel transport, membrane receptor signalling, cytoskeletal protein scaffolding, enzyme regulation, glycoprotein modulation.\\nmechanism: the genes identified as being related to these topics are involved in the regulation of cell signalling pathways and the transport of ions across cellular membranes. in addition, the genes are involved in biochemical processes such as enzyme regulation and glycoprotein modulation, which may be important in modulating the amount or type of molecules entering the cell and in organizing the cytoskeleton]]0.00
461text-davinci-003narrative_synopsisHALLMARK_ESTROGEN_RESPONSE_LATE-1[[membrane processes, transmembrane processes, GO:0006811, GO:0007155, GO:0016049, GO:0008152, MESH:D011506, GO:0023052, processing, MESH:D048788, reparative pathways, immune pathways, disease pathways]][[GO:0007165, gene transcription, ion transport and binding, protein-protein interaction, GO:0043687, GO:0007155, MESH:M0518050, GO:0016310, MESH:D011494, membrane recognition, GO:0003676, MESH:D018118, enzymatic reactions, lipid transport, glucose transport, cytokine receptor, molybdenum cofactor biosynthesis]]0.04
462text-davinci-003narrative_synopsisHALLMARK_FATTY_ACID_METABOLISM-0[[GO:0006732, GO:0006754, GO:0006096, oxidative decarboxylation, GO:0006631, nad/nadh-dependent oxidation, pyridine nucleotide oxidation, amino acid oxidation, glycerol-3-phosphate dehydrogenase activity, GO:0022900, MESH:D042942, nadp-dependent oxidation, l-amino acid oxidation, endogenous and xenobiotic n-methylation, conversion of pyruvate to acetyl coa, 2-oxoglutarate catabolism, galectin family activity]][[GO:0008152, GO:0009117, GO:0006631, GO:0006096, oxidation-reduction processes, GO:0006595, GO:0003824, amino acid metabolism, protein homodimerization, protein biotransformation, protein-macromolecule adaptor, protein-tat binding]]0.07
463text-davinci-003narrative_synopsisHALLMARK_FATTY_ACID_METABOLISM-1[[GO:0008152, fatty acid transport and processing, oxidoreductase, GO:0009653, GO:0030154, GO:0030674]][[GO:0006099, GO:0006118, GO:0005504, MESH:D042964, pyruvate dehydrogenase, nad-dependent glycerol-3-phosphate dehydrogenase, nad-dependent dehydrogenase, MESH:D013385, MESH:D000154, lyase, flavin adenine dinucleotide-dependent oxidoreductase, gtp-specific beta subunit, MESH:D006631, nad-retinol dehydrogenase, hydratase/isomerase, MESH:D006631, carnitine o]]0.00
464text-davinci-003narrative_synopsisHALLMARK_G2M_CHECKPOINT-0[[GO:0006325, GO:0051726, GO:0016570, MESH:D011494, atp-binding, rna-binding]][[transcriptional regulation, epigenetic regulation, GO:0051169, GO:0043687, dna replication and repair, chromatin structure, GO:0140014, GO:0036211, GO:0006397]]0.00
465text-davinci-003narrative_synopsisHALLMARK_G2M_CHECKPOINT-1[[GO:0051301, GO:0003677, GO:0003723, transcriptional regulation, chromatin restructuring, GO:0004672, GO:0051169, cytoplasmic transport, nucleic acid metabolism, GO:0016570, GO:0016310, GO:0032259, MESH:D000107, MESH:D054875]][[GO:0006913, GO:0016573, chromatin-associated processes, GO:0051726, transcriptional regulation, signal- and energy- dependent processes, nuclear phosphoproteins, GO:0006334, dna unwinding enzymes, protein heterodimers, GO:0000910, GO:0000398, MESH:D004264, GO:0035064, rna binding proteins, microtubule polymersization, nuclear localization, ubiquitin modification, mitosis regulation, centromere-interacting proteins.\\nmechanism: the genes in this list participate in a wide variety of mechanisms in the context of cellular development, including nucleocytoplasmic transport, histone acetylation, chromatin-associated processes, cell cycle regulation, and transcriptional regulation. these mechanisms are often interdependent and]]0.03
466text-davinci-003narrative_synopsisHALLMARK_GLYCOLYSIS-0[[GO:0016310, GO:0009100, GO:0007155, transcription regulation, GO:0009117, energy production]][[MESH:D006023, transmembrane protein, cell-surface protein, enzymes plus coenzymes, GO:0000981, hormones, cytokines, and growth factors, ligand-receptor interaction, regulatory proteins, cargo-binding proteins, cell adhesion and morphogenesis, MESH:D000604, metabolism and transport within the cell, metabolism of macromolecules, cellular energy metabolism, cellular homeostasis and signaling, cell signaling and transcription, protein modification and degradation, GO:0007049, dna replication and repair, GO:0008219, enzyme-substrate interaction\\n\\nmechanism:\\nthis list of genes is primarily involved in cellular metabolism, ligand-receptor interactions, and cell signaling and transcription. there are a variety of molecules that are acted upon, such as glycoproteins, transmembrane proteins, hormones, enzymes, and transcription factors. in terms of metabolic functions, the gene list includes proteins for metabolic control, cargo-binding proteins, and enzymes involved in macromolecule metabolism and transport within the cell. additionally, many of these genes are involved in the regulation of cell cycle and homeostasis, as]]0.00
467text-davinci-003narrative_synopsisHALLMARK_GLYCOLYSIS-1[[GO:0008152, GO:0005975, GO:0048468, GO:0009100, GO:0006629, GO:0015031, nucleic acid metabolism, GO:0009117, GO:0070085, ferric ion binding, GO:0016491, GO:0003677, GO:0000988, GO:0031545, GO:0004736]][[enzyme function, GO:0005488, GO:0006810, GO:0008152, MESH:D007477, sugars, GO:0006351, cytoskeleton structure, GO:0007155]]0.04
468text-davinci-003narrative_synopsisHALLMARK_HEDGEHOG_SIGNALING-0[[GO:0007155, GO:0007165, GO:0000981, MESH:D018121, MESH:D039921, rho-gtpase-activating protein, transmembrane protein, GO:1902911, transduction pathway, growth factor, g protein-coupled receptor, cadherin superfamily, basic helix-loop-helix, phosphoprotein, zinc finger protein, cytoplasmic domain, dna-binding, GO:0005886, neurotransmitter, MESH:D057057, coiled-coil, pdz binding motif, cholesterol moiety, fibronectin-like repeat, MESH:D000070557, GO:0016604, MESH:D006655, collapsin response mediator, tripartite motif, hedgehog signaling.\\nmechanism: the genes seem to be primarily involved in regulating signal transduction pathways that control cell migration, proliferation and differentiation, by modulating transcription, cell adhesion and receptor activities. the proteins encoded by these genes interact]][[GO:0006897, GO:0019838, receptor-mediated pathways;neuron survival;neuron differentiation;neuronal development;cell adhesion, transcription factor regulation, GO:0007165, extracellular protein interaction]]0.03
469text-davinci-003narrative_synopsisHALLMARK_HEDGEHOG_SIGNALING-1[[GO:0007155, GO:0007165, neuron signalling, regulatory activity, GO:0009987, GO:0040007, differentiation, motility, GO:0032502]][[structure-specific proteins, GO:0006898, g-protein coupled receptors, GO:0007155, gene transcription, post-translational regulation]]0.07
470text-davinci-003narrative_synopsisHALLMARK_HEME_METABOLISM-0[[GO:0005515, GO:0000910, transcription regulation, metabolic & enzymatic function, cell cortex formation, GO:0006810, GO:0016310, MESH:D000107, protein formation & modification]][[GO:0005515, GO:0006351, catalyzing reactions, gtpase activating protein activation, GO:0016575, carbohydrate & lipid metabolism, receptor binding & signaling, GO:0005574]]0.06
471text-davinci-003narrative_synopsisHALLMARK_HEME_METABOLISM-1[[GO:0006351, GO:0003723, post-transcriptional regulation, GO:0006096, GO:0006090, GO:0006749, GO:0006508, transcriptional regulation, MESH:D054875, GO:0003677, MESH:D006655, GO:0006915, cytoskeletal protein, atp-binding, GO:0048870, ubiquitin specific protease, MESH:D015220, voltage-gated chloride channel, GO:0004384, GO:0023052, GO:0051726, cation transporters]][[GO:0003677, GO:0016573, GO:0005515, transcription regulation, leucine residue modification, GO:0003729, zinc metalloenzymes, atp-binding, protein serine/threonin, endoribonuclease, GO:0031545, 6-phosphogluconate dehydrase, GO:0003723, dynein heavy chain, MESH:C052997, chloride intracellular channel, GO:0003779, MESH:D051528, hexameric atpase, GO:0006814, rho gtpase, inositol polyphosphate, MESH:D011766, selenium-binding protein, clathrin assembly, c-myc, dual specificity protein kinase, MESH:D006021, gtpase-activating-protein, GO:0006914, ring between two helices]]0.06
472text-davinci-003narrative_synopsisHALLMARK_HYPOXIA-0[[GO:0006096, GO:0016310, GO:0004672, GO:0006508, GO:0085029, transcription regulation, GO:0051726, GO:0097009, GO:0006954, cell-cell communication, oxidative stress response]][[cell signaling, metabolic regulation, GO:0043687]]0.00
473text-davinci-003narrative_synopsisHALLMARK_HYPOXIA-1[[GO:0006915, GO:0016310, MESH:D011494, GO:0005515, GO:0006351, GO:0031005, glycolytic enzyme, carboyhydrate binding, cell binding, GO:0042157, GO:0007165, UBERON:2000098, GO:0040007]][[cellular transport, GO:0008152, scaffolding, transcriptional regulation, GO:1901987, transcription activity, GO:0016310, cysteine-aspartic acid, GO:0016020, cell surface heparan sulfate, glycosyl hydrolase family, MESH:D000263, MESH:D000262, glyceraldehyde-3-phosphate, cytokine, glycosyltransferase, MESH:D000070778, sulfatase, sulfotransferase, serine/threonine kinase, MESH:D016232, MESH:D008668, MESH:D011973, basic helix-loop-helix]]0.03
474text-davinci-003narrative_synopsisHALLMARK_IL2_STAT5_SIGNALING-0[[GO:0051726, receptor signaling, MESH:D008565, GO:0000981]][[GO:0005515, GO:0005102, transcription regulation, enzyme regulation, GO:0001816, GO:0007155, structure, membrane-associated]]0.00
475text-davinci-003narrative_synopsisHALLMARK_IL2_STAT5_SIGNALING-1[[GO:0007165, protein homodimerization, GO:0005525, GO:0003676, GO:0055085, GO:0004672, GO:0007049, GO:0006955, GO:0006915]][[an underlying biological mechanism of intracellular signaling and cell adhesion proteins working together to regulate gene expression and control cell functions was identified. enriched terms related to this mechanism include gtpases, MESH:D008565, intracellular signaling, calcium-dependent proteins, rna and dna binding, GO:0007155, GO:0000981, enzyme regulation, GO:0005515]]0.00
476text-davinci-003narrative_synopsisHALLMARK_IL6_JAK_STAT3_SIGNALING-0[[MESH:D016207, GO:0016049, GO:0048468, transmembrane proteins, MESH:D011494, GO:0000981, cell cycle progression]][[MESH:D018121, MESH:D018925, tgf-beta superfamily, transcriptional regulation, MESH:D017027, MESH:D011494]]0.08
477text-davinci-003narrative_synopsisHALLMARK_IL6_JAK_STAT3_SIGNALING-1[[the list of gene summaries reveals a group of genes involved in cell trafficking, GO:0007165, GO:0007155, ligand binding, and regulation of the immune response. enriched terms include cytokine, chemokine, MESH:D007378, receptor, GO:0007155, ligand binding, GO:0007165, and regulation of the immune response.\\n\\nmechanism: the mechanism involving these genes involve ligand binding to cytokine, chemokine, or other receptors, resulting in the activation of intracellular pathways leading to signal transduction, GO:0007155, regulation of the immune response]][[the genes identified are part of the cytokine signaling system and its related pathways involved in immune response and regulation. more specifically, they belong to the type i cytokine receptor family, the phospholipase a2 family, the tumor necrosis factor receptor superfamily, the gp130 family of cytokine receptors, the toll-like receptor family, the interferon regulatory factor family, the bcl2 protein family, the reg gene family, the type ii membrane protein of the tnf family, the ring finger e3 ubiquitin ligase family, the protein tyrosine phosphatase family, the tgf-beta superfamily proteins, the hemopoietin receptor superfamily, the chemokine family, the integrin alpha chain family of proteins and the adapter protein family. there is a common function of these genes in the signaling of cell growth, UBERON:2000098, GO:0006915, migration, and differentiation, as well as the regulation of gene transcription, apoptosis and immune response. \\n\\nmechanism:\\nthe genes identified are part of a gene network that functions together to allow for cell signaling, GO:0040007, and differentiation, as well as inflammatory and immune responses. the various cytokine receptors, protein ty]]0.00
478text-davinci-003narrative_synopsisHALLMARK_INFLAMMATORY_RESPONSE-0[[GO:0005102, cytokine signalling, GO:0016049, cellular function regulation, immune signalling, inflammation regulation, GO:0051726, apoptosis coordination]][[MESH:D008565, g protein-coupled receptors, MESH:D018121, interferon-induced proteins, MESH:M0013343, MESH:D051116, MESH:D018925, MESH:D016023, MESH:D020782, MESH:D061566, tol-like receptors]]0.00
479text-davinci-003narrative_synopsisHALLMARK_INFLAMMATORY_RESPONSE-1[[interactions, GO:0023052, MESH:D008055, GO:0000981, MESH:D016207, MESH:D006728, MESH:D021381, receptors, GO:0007165]][[GO:0005102, GO:0023052, GO:0055085, calcium binding, GO:0055085]]0.08
480text-davinci-003narrative_synopsisHALLMARK_INTERFERON_ALPHA_RESPONSE-0[[protein-binding, subunit-binding, rna-binding, transcriptional regulation, GO:0007165, GO:0006955, ligand binding, GO:0032991, GO:0036211]][[ligand binding, GO:0005102, GO:0003824, GO:0003677, GO:0003723, protein activation, GO:0030163, MESH:D054875]]0.06
481text-davinci-003narrative_synopsisHALLMARK_INTERFERON_ALPHA_RESPONSE-1[[transcriptional regulation, GO:0008181, MESH:D010447, cytoplasmic proteins, antiviral, MESH:M0369740, GO:0009165, chemokine receptor, dna-binding, rna-binding, lipid-binding, protein adp-ribosylation, GO:0016567, GO:0048255, GO:0016556, GO:0006479, gtp-metabolizing, GO:0008283, GO:0006955, GO:0006952]][[these genes are connected by their participation in immune regulation and defense, either directly regulating the innate and acquired immune response, or acting as downstream inhibitors and activators of such responses. specific enriched terms include interferon regulation, transcriptional regulation, tumor suppression, MESH:D054875, chemokine receptor signaling, GO:0003723, GO:0009165, GO:0051607, GO:0048255, GO:0005525, GO:0008289, viral invasion, GO:0045087, GO:0030701, GO:0008134, and antigen presentation.\\n\\nmechanism: the commonalities between these genes suggest that they act at various levels of a complex innate and acquired immune response, controlling transcriptional regulation, protein modification and silencing, viral response, and antigen presentation. there are multiple pathways overlapping or influencing each gene's particular role in the overall immune defense, merging into a greater shared mechanism of host immunity]]0.07
482text-davinci-003narrative_synopsisHALLMARK_INTERFERON_GAMMA_RESPONSE-0[[immune regulation, GO:0003677, GO:0003723, GO:0016567, anti-viral response, cytokine signaling, GO:0006954]][[the genes in the list encode proteins involved in a variety of processes including immunity, GO:0006954, GO:0006351, GO:0007165, and protein folding and assembly. these processes are typically carried out by two main classes of molecules; ubiquitin ligases and cytokines. the genes in this list are enriched for terms including \"signal transduction\", \"ubiquitin ligases\", \"immune modulation\", \"cytokine activity\", \"transcription regulation\", \"proteasome activity\", \"rna binding\", and \"metallothionein\".\\n\\nmechanism:\\nthe genes in this list encode proteins involved in a variety of processes, with an emphasis on immunity and inflammation. these processes are typically mediated by ubiquitin ligases, MESH:D016207, and other signal transduction proteins. ubiquitin ligases mark target proteins for ubiquitination and other modifications, while cytokines affect the activity of multiple cells. signal transduction proteins transmit signals across cell membranes, affecting the activity of cells. metallothioneins play a role in detoxification and protein folding and assembly, while proteasomes carry out protein degradation within the cell. transcripts are regulated by transcription factors, many genes contain rna binding domains]]0.04
483text-davinci-003narrative_synopsisHALLMARK_INTERFERON_GAMMA_RESPONSE-1[[GO:0006954, immune cell signaling and development, immune regulation, GO:0044237, regulation of innate and adaptive immunity, metabolic and transcriptional regulation, GO:0003677, GO:0003723]][[transcriptional regulation, GO:0003824, binding ability, protein structure, cell signalling, MESH:D016207, growth factor signalling, MESH:D007109, GO:0000981, MESH:D054875, MESH:D006136, tripartite motif, GO:0070085, atpase, intracellular sensor, MESH:D015088, GO:0003723, calcium-binding, GO:0004930, MESH:M0476528, cysteine-aspartic acid protease, regulator of complement activation, protein tyrosine phosphatase, ubiquitin-specific protease, antiviral activity, inter]]0.03
484text-davinci-003narrative_synopsisHALLMARK_KRAS_SIGNALING_DN-0[[protein-binding, transcriptional regulation, GO:0007155, cell membrane channel activity, protein metabolism/modification, receptor signalling]][[ion channels & transporters, receptor proteins, MESH:D002135, MESH:D004798, cell signaling, hormone regulation, GO:0008152]]0.00
485text-davinci-003narrative_synopsisHALLMARK_KRAS_SIGNALING_DN-1[[MESH:D011506, GO:0016049, cellular development, MESH:D009068, GO:0001508, calcium binding, GO:0005496, GO:0008152, GO:0006351, GO:0005488, MESH:C062738, GO:0005562, g proteins, dna-binding]][[catalyzing reactions, GO:0055085, GO:0023052, dna-binding, GO:0006351, extracellular signaling, calcium-ion binding, immune system signaling, cell growth/maintenance, GO:0007154, hormone regulation, GO:0032502, GO:0008152]]0.12
486text-davinci-003narrative_synopsisHALLMARK_KRAS_SIGNALING_UP-0[[GO:0007155, regulation of growth factors, cytokine regulation, calcium activation, transcriptional regulation]][[MESH:D008565, MESH:D010447, receptor proteins, MESH:D004268, MESH:D010770, GO:0000981, GO:0008217, MESH:M0022898, GO:0007165, transcriptional regulation, GO:0006811, GO:0006936, immunologic regulation, GO:0001816, GO:1901987, GO:0006915, GO:0007155, MESH:D063646]]0.10
487text-davinci-003narrative_synopsisHALLMARK_KRAS_SIGNALING_UP-1[[GO:0003677, MESH:D015533, cytokine regulation, GO:0008083, GO:0005515, GO:0007165, transmembrane protein activity, GO:0004930, GO:0003723, GO:0003924, GO:0005509, GO:0016571, glutamine-fructose-6-phosphate transaminase activity, cell growth control, GO:0019725, GO:0016491]][[receptor functions]]0.00
488text-davinci-003narrative_synopsisHALLMARK_MITOTIC_SPINDLE-0[[cytoskeletal organization, GO:0003677, microtubule organization, gtpase regulation, centrosome interaction, chromatin structure, protein homodimerization]][[cytoskeleton regulation, cellular communication, gtpase regulation, actin-binding, dna-dependent protein binding, microtubule-associated protein, filamentous cytoskeletal protein, 14-3-3 family protein, MESH:D020662]]0.07
489text-davinci-003narrative_synopsisHALLMARK_MITOTIC_SPINDLE-1[[MESH:D020558, nucleotide exchange regulation, cellular signaling, GO:0006338, cytoskeleton structure, GO:0006260, GO:0007155, GO:0003779, actin regulation]][[gtpase activation, GO:0005525, structural maintenance, GO:0003677, GO:0005856, GO:0006915, GO:0007049]]0.00
490text-davinci-003narrative_synopsisHALLMARK_MTORC1_SIGNALING-0[[GO:0006412, GO:0015031, protein signaling, GO:0008152, GO:0010467]][[GO:0006412, GO:0008152, GO:0006457, MESH:D054875, GO:0006351, GO:0003677, damage control, GO:0032502, cellular pathway regulation, GO:0006915, GO:0007049, GO:0030163]]0.13
491text-davinci-003narrative_synopsisHALLMARK_MTORC1_SIGNALING-1[[GO:0005515, MESH:D054875, GO:0006351, GO:0003824, GO:0006457, chaperoning, GO:0051726, GO:0006629, GO:0046323, cytoskeleton formation]][[atp production, amino acid homeostasis and metabolism, stress response, transcription and mrna regulation, chaperones and proteasome degradation pathways, GO:0006629]]0.07
492text-davinci-003narrative_synopsisHALLMARK_MYC_TARGETS_V1-0[[GO:0006351, GO:0006412, GO:0003729, MESH:D054657, MESH:D000072260, GO:0043687, cytoplasmic proteins, MESH:M0015044, GO:0003677, GO:0032508, GO:0005652, GO:0005681]][[GO:0006351, GO:0006412, GO:0006413, GO:0003723, MESH:D054875, GO:0005840, GO:0006412, GO:0032508, MESH:D039102, GO:0003734, GO:0045292, heat shock proteins, MESH:D006655, MESH:D011073, MESH:D000604, GO:0043687]]0.17
493text-davinci-003narrative_synopsisHALLMARK_MYC_TARGETS_V1-1[[GO:0009299, GO:0042254, GO:0006412, MESH:D049148, GO:0003723, GO:0043687, GO:0045292, polymerase, GO:0006913, MESH:D054875, GO:0006457, 14-3-3 family proteins]][[poly(a)-binding, GO:0003723, GO:0032508, GO:0006913, GO:0032183, GO:0000394, GO:0003676, GO:0006473, GO:0006413, GO:0036211, GO:0006457, MESH:D014176, GO:0006412, MESH:D018832, peptidyl-prolyl cis-trans isomerization, antioxidant function, heat shock protein, ubiquitin protein ligase, 14-3-3 family, dna-unwinding enzymes, dna polymerase, voltage-dependent anion]]0.13
494text-davinci-003narrative_synopsisHALLMARK_MYC_TARGETS_V2-0[[GO:0003723, ribosomal biogenesis, GO:0008283, GO:0006335, GO:0007165, cell cycle progression, GO:0003682]][[GO:0005515, transcriptional regulation, cell cycle progression, protein chaperoning, GO:0008283, nuclear localization, rna binding activity, pre-rrna processing, GO:0042254]]0.14
495text-davinci-003narrative_synopsisHALLMARK_MYC_TARGETS_V2-1[[GO:0006351, rna binding activity, GO:0006457, cell cycle progression, GO:0006281, protein homodimerization, GO:0006468, GO:0065003, protein kinase/phosphatase activity, mitochondrial mrna processing. mechanism: this list of genes encodes proteins which work together to regulate key cellular activities such as dna replication, transcription, cell cycle progression, and rna processing. these proteins can either complex together or work in tandem to form kinase/phosphatase complexes, which control phosphorylation of key substrates and regulate protein folding to ensure proper protein function. these proteins also interact with dna to regulate genomic activities such as dna replication, transcription, and repair processes]][[rna binding activity, GO:0006364, protein homodimerization, GO:0008283, GO:0007165, GO:0042254, GO:0006457, GO:0034246]]0.20
496text-davinci-003narrative_synopsisHALLMARK_MYOGENESIS-0[[motor protein activity, GO:0019722, GO:0006936, transcriptional regulation, intracellular fatty acid-binding, ligand binding, MESH:D007473, GO:0005884, MESH:D008565, regulation of transcription, phosphorylation of proteins]][[GO:0006936, calcium channel regulation, ion channel regulation, protein ubiquitination/degradation, actin-based motor proteins, GO:0007165, MESH:D004734]]0.06
497text-davinci-003narrative_synopsisHALLMARK_MYOGENESIS-1[[MESH:M0496924, protein regulation, ion channeling, cellular transport, GO:0006629, GO:0010468, neurotransmitter signaling, small molecules, large molecules]][[summary: the list of genes provided contains components of muscle formation, GO:0023052, and growth.\\nmechanism: the genes encode the components of signaling pathways and physical structures involved in the formation of muscle, including proteins that serve as receptors, binders, MESH:D004798, and structural components like spectrins, GO:0005202, laminin.\\nenriche terms: muscular development; musculosketetal function; signal transduction; protein phosphorylation degradation; cytoplasmic proteins; structural proteins; cytochrome oxidase]]0.00
498text-davinci-003narrative_synopsisHALLMARK_NOTCH_SIGNALING-0[[cell fate decisions, GO:0007219, GO:0007165, wnt signalling pathway, cell-cell interaction, GO:0016567, GO:0006355, protein ligase activity, GO:0006468]][[GO:0007219, GO:0016055, GO:0016567, transcriptional repressor, MESH:D015533, cell fate decisions, MESH:D044767, MESH:D011494]]0.21
499text-davinci-003narrative_synopsisHALLMARK_NOTCH_SIGNALING-1[[notch signaling, GO:0016567, cell-cycle regulation, protein breakdown and turnover, intracellular signalling pathways, cell fate]][[GO:0007219, GO:0016567, GO:0001709, transcriptional regulation, GO:0031146, gamma secretase complex, MESH:D011493, wnt family, basic helix-loop-helix family of transcription factors]]0.07
500text-davinci-003narrative_synopsisHALLMARK_OXIDATIVE_PHOSPHORYLATION-0[[GO:0005739, MESH:D004798, MESH:D010088, MESH:D010088, GO:0006754]][[GO:0006006, GO:0006631, amino acid metabolism, GO:0005746, MESH:D007506, nadh-ubiquinone oxidoreductase, MESH:D009245, pyruvate dehydrogenase, GO:0022900, oxidative decarboxylation, nad+/nadh oxidoreductase, GO:0016467, MESH:D003576, MESH:D063988, matrix processing, shuttling mechanism.\\n\\nmechanism: the gene products involved in this metabolic pathways work to convert small molecules such as glucose and fatty acids into energy-containing molecules, such as atp and nadh, through a combination of redox reactions, electron transfer processes, and other catalytic systems. these processes involve the participation of numerous proteins, including membrane-associated proteins, enzymes, and enzyme complexes. these proteins form a complex network of interactions that enable the conversion of energy from one form to another, ultimately leading to atp production]]0.00
501text-davinci-003narrative_synopsisHALLMARK_OXIDATIVE_PHOSPHORYLATION-1[[oxidative decarboxylation, MESH:D010088, MESH:D010084, GO:0006754, mitochondrial respiration, GO:0008152, MESH:D003580, MESH:D000214, pyruvate dehydrogenase, MESH:D005420, hydratase/isomerase, leucine-rich protein, 3-hydroxyacyl-coa]][[terminal enzyme, GO:0006754, GO:0005746, nad/nadh-dependent, cytochrome c oxidase (cox), GO:0006118]]0.06
502text-davinci-003narrative_synopsisHALLMARK_P53_PATHWAY-0[[GO:0007049, GO:0006351, GO:0023052, GO:0006412, GO:0065007, GO:0042592]][[GO:0005515, GO:0003677, transcriptional regulation, GO:0051726, cell signaling]]0.00
503text-davinci-003narrative_synopsisHALLMARK_P53_PATHWAY-1[[GO:0051726, GO:0016049, GO:0006915, GO:0007165, GO:0006281, transcriptional regulation, chromatin structure, tumor suppression, enzymatic activity, GO:0000988, GO:0004725, GO:0003925]][[MESH:D011494, GO:0000981, GO:0007049, GO:0006281, GO:0003677, GO:0006412, tnf receptor superfamily, zinc finger, calcium-activated, cyclin dependent, iron-sulfur, GO:0015629, GO:0007165]]0.09
504text-davinci-003narrative_synopsisHALLMARK_PANCREAS_BETA_CELLS-0[[analysis of the human genes abcc8, akt3, chga, dcx, dpp4, elp4, foxa2, foxo1, g6pc2, gcg, gck, hnf1a, iapp, UBERON:0002876, insm1, isl1, lmo2, mafb, neurod1, neurog3, nkx2-2, nkx6-1, pak3, pax4, pax6, pcsk1, pcsk2, pdx1, pklr, scgn, sec11a, slc2a2, spcs1, srp14, srp9, srprb, UBERON:0035931, stxbp1, syt13, vdr was performed to determine commonalities in gene function. term enrichment indicated a commonalty in genes that are involved in the regulation of glucose and insulin metabolism, GO:0008283, differentiation and apoptosis, as well as glycogen synthesis and glucose uptake. additionally, many of the genes are involved in the development of neural tissues and the regulation of gene transcription. the underlying biological mechanism could involve alterations in the phosphorylation of proteins and signaling pathways,]][[GO:0000981, homeobox domain, signal peptide cleavage, MESH:D011494, atp-binding, chromogranin/secretogranin, GO:0005180, protease, MESH:D011770, MESH:D005952, MESH:D000243, MESH:D006593, nuclear receptor, dna-binding, g-protein linked receptor, cysteine-rich protein, gtp-bound proteins, GO:0048500, bhlh transcription factor, doublecortin, calcium-binding protein\\n\\nsummary: genes identified in this list facilitate a variety of essential biological processes, particularly in terms of cell signaling and transcription regulation. among these processes are signal peptide cleavage, atp-binding, peptide hormone secretion and regulation, protease activity, glucose metabolism, adenosine deaminase, gtp-bound protein binding, and transcription factor actions. \\n\\nmechanism: these genes are involved in transcriptional regulation and signaling processes through binding of dna and g-protein linked receptors, homeobox domains, cysteine-rich proteins]]0.00
505text-davinci-003narrative_synopsisHALLMARK_PANCREAS_BETA_CELLS-1[[this analysis identifies the common functions of 18 human genes: dpp4, scgn, pklr, pax4, neurod1, srprb, srp14, isl1, insm1, pak3, pax6, elp4, dcx, iapp, lmo2, neurog3, gck, stxbp1, nkx2-2, pdx1, UBERON:0035931, pcsk1, nkx6-1, UBERON:0002876, pcsk2, spcs1, g6pc2, foxo1, sec11a, vdr, foxa2, slc2a2, mafb. they are related to metabolic regulation (glucose, GO:0016088, MESH:D004837, citrate), developmental regulation (neural tissues, UBERON:0001264, UBERON:0002107, lymph nodes), signal transduction (g proteins, ace, atp binding proteins) and hormone regulation related (somatostatin, GO:0016088, vitamin d3). these factors likely work in concert to control and maintain metabolic parameters throughout the body. mechanism: these genes act through various methods including transcriptional regulation, protein interactions, protein cleavage, signaling casc]][[transcriptional regulation, MESH:M0496924, endocrine system regulation, GO:0006006, cell signalling, MESH:D020558, GO:0000981, GO:0005180, MONDO:0018815, MESH:D043484]]0.00
506text-davinci-003narrative_synopsisHALLMARK_PEROXISOME-0[[MONDO:0018815, an antioxidant enzyme, a hormone binding protein, a nuclear receptor transcription factor, a fatty acid desaturase, a carnitine acyltransferase, an isocalate dehydrogenase, a peroxisomal membrane protein, MESH:D005182, antioxidant enzyme, hormone binding protein, nuclear receptor transcription factor, GO:0004768, carnitine acyltransferase, isocalate dehydrogenase, peroxisomal membrane protein, and fad-dependent oxidoreductase.\\n\\nmechanism: many of the genes are involved in regulating the production and movement of lipids and fatty acids, as well as the synthesis of hormones, MESH:D000305, and signalling receptors. the underlying biological mechanism is that these genes act as regulators of metabolic pathways, ensuring that their respective pathways are functioning correctly and that metabolites are transported correctly]][[GO:0140359, oxidoreductase, dehydrogenase/reductase, hydratase/isomerase, enzymes responsible for fatty acid beta-oxidation, enzymes catalyzing the]]0.00
507text-davinci-003narrative_synopsisHALLMARK_PEROXISOME-1[[GO:0006629, GO:0006635, GO:0006281, transcription and replication, MESH:D018384, GO:0006536, GO:0005502, GO:0008202]][[MESH:D018384, MONDO:0018815, atpases associated with diverse cellular activities, vitamin a family, GO:0004879, nad-dependent oxidoreductases, GO:0005783, MESH:D015238, cyclin-dependent protein kinase, hydratase/isomerase superfamily, GO:0005515, GO:0003677, GO:0050632, carnitine acyltransferase, MESH:D011960]]0.05
508text-davinci-003narrative_synopsisHALLMARK_PI3K_AKT_MTOR_SIGNALING-0[[GO:0016310, GO:0006412, mrna expression, GO:0005515, cell signalling, MESH:D054875, protein phosphatase]][[MESH:D011494, GO:0016791, GO:0005525, protein-protein interaction, GO:0030552, GO:0000981, peptidyl-prolyl cis/trans isomerase, cytoskeletal function, protein tyrosine phosphatase, protein phosphatase, GO:0140597, MESH:D020662, receptor interacting protein, transmembrane glycoprotein, MESH:D018123, MESH:D054387, inositol trisphosphate receptor, plexin domain, phosphoinositide 3-kinase, ubiquitin activation/conjugation, GO:0003925]]0.04
509text-davinci-003narrative_synopsisHALLMARK_PI3K_AKT_MTOR_SIGNALING-1[[GO:0007165, MESH:D011494, GO:0004707, MONDO:0008383, gpcr, GO:0016791, MESH:D020662, endoplasmic reticulum chaperone protein]][[MESH:D011494, guanine nucleotide-binding protein, receptor-interacting protein, chaperone protein, protein tyrosine kinase, MESH:D020558, MESH:D000262, protein phosphatase, cytoplasmic face, GO:0006468, GO:0007165, GO:0036211]]0.11
510text-davinci-003narrative_synopsisHALLMARK_PROTEIN_SECRETION-0[[GO:0005480, GO:0006897, GO:0006887, intracellular trafficking, MESH:D001678, MESH:D008565, GO:0005906, MESH:D020558, GO:0005794, GO:0005484]][[MESH:D008565, MESH:D020558, coatomer complex, GO:0016192, MESH:D001678, GO:0035091, GO:0065007, MESH:D002966, GO:0005906, GO:0005794, GO:0030136, MONDO:0018815, GO:0042393, GO:0005802, MESH:M0013340, GO:0006811, GO:0005159, GO:0005783, MESH:D057056, GO:0005483, GO:0005764, GO:0005794, multifunctional proteins]]0.18
511text-davinci-003narrative_synopsisHALLMARK_PROTEIN_SECRETION-1[[GO:0003924, snare binding activity, GO:0005484, phosphoinositide-binding, coatomer protein complex, MESH:D052067, protein kinase binding activity, adaptor complexes, atpases associated with diverse cellular activities, snare recognition molecules, gold domain, GO:0030136, transmembrane 4 superfamily, GO:0070273, sec7 domain, membrane mannose-specific lectin, signal-transducing adaptor molecule, identical protein binding activity]][[this list of genes codes for proteins of various functions, primarily related to organelle trafficking, membrane associations, and receptor binding activities. these proteins are involved in the regulation of intracellular vesicles, endoplasmic reticulum and golgi organization, protein sorting and secretion, cell surface receptor binding, cell-signaling and immunity, protein phosphorylation and kinase binding, and lipid protein modifications. the enriched terms found in the functions of these genes include vesicular transport, MESH:M0354322, organelle trafficking, GO:0007030, GO:0005102, GO:0006457, GO:0006468, snare recognition molecules, clathrin coated vesicles, endoplasmic reticulum-golgi transport, MESH:D025262, GO:0005906, and dystrophin-glycoprotein complex. \\n\\nmechanism: the enriched terms in the gene functions indicate that these proteins are involved in various pathways and process of intracellular cargo trafficking, where proteins, membranes and signaling molecules are sorted, distributed and regulated. the processes are involved with vesicular transport, protein co-translocation, GO:0030258, and protein phosphorylation, which coordinate the mobilization and distribution of proteins, MESH:D008055]]0.02
512text-davinci-003narrative_synopsisHALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0[[MONDO:0018815, copper chaperone, MESH:D002374, GO:0004861, hypoxia inducible factor (hif), nucleotide excision repair pathway, GO:0004672, GO:0009487, MESH:D005979, MESH:D009195, MESH:D010758, phosphofructokinase, MESH:D054464, GO:0050115, arginine/serine-rich splicing factor, iron/manganese superoxide dismutase, GO:0016491, germinal centre kinase iii (gck iii) subfamily, thioredoxin (trx) system]][[this list of genes were found to be involved in oxidoreductase activity, intracellular binding and catalytic activity, cellular response regulation, dna and transcription regulation, membrane function, mitochondrial function and antioxidant activity. the enriched terms include oxidoreductase activity, intracellular binding, GO:0003824, cell growth regulation, transcription regulation, membrane function, mitochondrial function, GO:0016209, GO:0020037, GO:0005507, GO:0003677, GO:0043565, tyrosine-specific protein kinase activity, f-actin binding. the underlying biological mechanism is probable related to redox homeostasis, the oxygen metabolism pathway, the cell cycle dna repair pathways, the regulation of transcription membrane function]]0.00
513text-davinci-003narrative_synopsisHALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1[[GO:0016049, GO:0007049, GO:0006351, redox regulation, MESH:D018384, MESH:D005721, hydroxylase, protease, free-radical scavenging, protein phosphatase]][[redox processes, MESH:D018384, GO:0006281, GO:0008152, cell growth regulation, inflammation control, cellular defense, MESH:D006419, MESH:D005980, superoxide dism]]0.05
514text-davinci-003narrative_synopsisHALLMARK_SPERMATOGENESIS-0[[protein binding activity, GO:0003714, dna binding activity, rna binding activity, zinc ion binding activity, GO:0004596, serine/threonine-protein kinase activity, GO:0004016, snare binding activity, clathrin binding activity, myosin light chain binding activity, double-stranded dna binding activity, phosphatidic acid phosphohydrolase activity, ubiquitin-protein ligase activity, rna polymerase binding activity, GO:1990817, GO:1990817, GO:0060090, phosphatase binding activity, atp-ases associated activity, GO:0044183, GO:0016165, adp-ribosylation factor-like activity]][[cell cycle regulatory proteins and kinases, dna binding proteins and chaperones, nucleotide and polypeptide binding proteins, GO:0016791, proteins involved in transcription, gene transcription, GO:0051276, apoptosis regulation, GO:0006281, protein folding and transport, cell signaling and growth regulation, MESH:D004734, cytoskeletal organization, vesicular trafficking\\n\\nmechanism: the underlying biological mechanism is likely involved in multiple steps in cell division and the regulation of gene expression, and in the maintenance of cell homeostasis]]0.00
515text-davinci-003narrative_synopsisHALLMARK_SPERMATOGENESIS-1[[GO:0006457, transcriptional regulation, GO:0007165, GO:0051726, chromatin structure and nuclear envelop function, cell adhesion and motility, GO:0008152, GO:0016567, detection and binding, enzymatic activity, GO:0042311]][[this list of genes is associated with a range of diverse functions, including intracellular and intercellular trafficking, adhesion, enzyme regulation, transcriptional regulation, ion channel and receptor regulation, and processes related to stress, GO:0007568, and metabolism. common enriched terms include protein kinase and phosphatase, GO:0140359, g-protein coupled receptors, receptors, transcriptional regulation, GO:0016569, GO:0051726, heat shock, GO:0005515, ubiquitin-protein ligase and ubiquitin protease, zinc metalloproteases, and peptide n-acetyltransferase. the underlying biological mechanism or pathway associated with these genes may involve signal transduction as mediated by enzyme activity, MESH:D007473, receptors, and other proteins, as well as cell-to-cell adhesion and trafficking processes involved in membrane dynamics.\\n\\nsummary: list of genes associated with diverse functions including intracellular and intercellluar trafficking, adhesion, regulation of enzymes, GO:0006351, ion channels and receptors, and processes related to stress, GO:0007568, and metabolism.\\nmechanism: signal transduction as mediated by enzyme activity, MESH:D007473, receptors, and other proteins, as well as cell-to]]0.05
516text-davinci-003narrative_synopsisHALLMARK_TGF_BETA_SIGNALING-0[[transmembrane proteins, receptor signaling pathways, transcription regulation, cell signaling, GO:0007155, GO:0016049, tgf-beta superfamily, MESH:D010749, ubiquitin ligases, tight junction adaptors]][[the human gene summaries represent a variety of cell signaling, cell growth and differentiation, transcription regulation, adhesion and migration, and apoptosis-related functions. several genes in the list (acvr1, GO:0005680, arid4b, bmpr1a, bmpr2, cdh1, ifngr2, junb, lefty2, map3k7, ncor2, ppm1a, pp1ca, rahb, smad1, smad3, smad6, smurf1, smurf2, tgfb1, tgfbr1, MESH:D016212, cdk9, cdkn1c, ctnnb1, eng, fnta, MESH:D045683, hipk2, id1-3, klf10, ltbp2, pmepa1, ppp1r15a, serpine1, ski, skil, slc20a]]0.02
517text-davinci-003narrative_synopsisHALLMARK_TGF_BETA_SIGNALING-1[[transmembrane serine/threonine kinases, transcriptional repressors, transforming growth factor (tgf)-beta superfamily, rho family of small gtpases, smad family, c2h2-type zinc finger domains, MESH:M0460357, caax geranylgeranyltransferase, smad interacting motif (sim), homeodomain-interacting protein kinase, MESH:D004122, transforming growth factor-beta (tgfb) signal transduction, MESH:D018398, MESH:D054645, protein folding and trafficking]][[GO:0007165, transcription regulation, cell-to-cell communication, MESH:D018398, serine/threonine protein kinase, disulfide-linked homotrimeric proteins, protein phosphatase, transmembrane proteins, smurf protein, cystein-rich motif, GO:0006457]]0.04
518text-davinci-003narrative_synopsisHALLMARK_TNFA_SIGNALING_VIA_NFKB-0[[GO:0006351, cytokine, inflammatory, UBERON:2000098, GO:0006915, cell signalling, receptor regulation, GO:0003924, GO:0003723]][[transcriptional regulation, GO:0005125, GO:0008283, GO:0006629]]0.00
519text-davinci-003narrative_synopsisHALLMARK_TNFA_SIGNALING_VIA_NFKB-1[[MESH:D016207, MESH:D018925, MESH:D010770, GO:0000981, MESH:D016212, nf-kappa-b, myc/max/mad, jagged 1, stat-regulated pathways, MESH:D008074, MESH:M0496065]][[GO:0006954, GO:0007165, transcriptional regulation, GO:1901987, cytokine, MESH:D011506, receptor, GO:0000981, enzyme, growth factor, MESH:D019204, chemokine, MESH:D008074, pentraxin protein, GO:0016791, MESH:D010770, stress response]]0.12
520text-davinci-003narrative_synopsisHALLMARK_UNFOLDED_PROTEIN_RESPONSE-0[[rna-binding, protein-binding, GO:0019538, GO:0009058, GO:0044183, GO:0000981, GO:0006457]][[GO:0003723, transcription regulation, GO:0006457, protein targeting and covalent modifications, endoplasmic reticulum function, GO:0006413]]0.08
521text-davinci-003narrative_synopsisHALLMARK_UNFOLDED_PROTEIN_RESPONSE-1[[GO:0003723, GO:0005783, transcriptional regulation, GO:0006457, GO:0140597, mrna decapping, MESH:M0465019, GO:0030163, MESH:D021381]][[GO:0006412, endoplasmic reticulum stress response, GO:0003723, protein expression, conformation folding]]0.08
522text-davinci-003narrative_synopsisHALLMARK_UV_RESPONSE_DN-0[[cellular response regulation, GO:0007165, transcriptional regulations, MESH:D011956, GO:0016310, calcium binding, MESH:D011494, transmembrane proteins, protein tyrosine kinases, MESH:D017027, MESH:M0015044, protein inhibitor of activated stats, integrin beta, annexin family, adp-binding cassette family, MESH:D020690, arfaptin family, wd repeat proteins, maguk family, camp-dependent pathways, MESH:D000071377, MESH:D008869, pak family, MESH:D015220, mitogen-responsive phosphoproteins, nuclear histone/protein, celf/brunol family, four-and-a-half-lim-only proteins]][[GO:0007155, GO:0005207, nuclear phosphoprotein, phosphoprotein, cytoplasmic receptor, MESH:D020558, GO:0016791, receptor tyrosine kinase, GO:0006351, camp, ion transport atpase, transmembrane protein]]0.00
523text-davinci-003narrative_synopsisHALLMARK_UV_RESPONSE_DN-1[[GO:0007165, MESH:D016326, cellular adhesion, GO:0000981, MESH:D011494, MESH:D020558, camp, calcium-dependent phospholipid binding protein, MESH:D011505, MESH:D017868, scaffolding protein, MESH:D020690, MESH:D010711, protein tyrosine phosphatase, rho-like gtpase, calcium-activated bk channel, cyclin-dependent kinase, n6-methyladenosine-containig protein, helix-loop-helix proteins, MESH:D016601, atpase, guanine nucleotide-binding protein, cytoplasmic surface protein, serine protease inhibitor, protein inhibitor of activated stat, GO:0004384, mitogen-responsive]][[GO:0000981, receptor, GO:0005488, growth factor, phosphoprotein, MESH:D010770, cytoplasmic surface, nuclear histone/protein methyltransferase, MESH:D020558, wd repeat protein, protein tyrosine phosphatase, serine/threonine kinase, caveolae plasma membrane, g-protein coupled receptor, MESH:D000071377, ab hydrolase superfamily, microtubule-associated protein, protein-tyros]]0.07
524text-davinci-003narrative_synopsisHALLMARK_UV_RESPONSE_UP-0[[cell regulation, GO:0055085, metabolic catabolism, transcription support, GO:0006468, non-classical heavy chain, GO:0020037, GO:0007165, cytoskeleton formation, GO:0030163, cell signaling, GO:0006412, GO:0010467]][[GO:0005515, MESH:D002384, transcriptional regulation, cell signaling, metabolic reactions]]0.06
525text-davinci-003narrative_synopsisHALLMARK_UV_RESPONSE_UP-1[[GO:0005515, GO:0005525, GO:0005215, reactive catalysis, cell signaling, membrane-associated functions]][[regulatory proteins, GO:0000981, membrane and transport proteins, structural proteins, MESH:D004798, biosynthesis of heme, cellular signaling, transcription control, GO:0008152, GO:0006955]]0.00
526text-davinci-003narrative_synopsisHALLMARK_WNT_BETA_CATENIN_SIGNALING-0[[wnt signalling pathway, transmembrane glycoprotein, MESH:D006655, GO:0000981, GO:0007219, GO:0005515, GO:0007165, GO:0006511, transcriptional regulation, dna replication and repair]][[cell-cell interactions, MESH:D047108, transcriptional regulation, GO:0006281, wnt signaling, notch signaling, hedgehog signaling, MESH:D044783]]0.06
527text-davinci-003narrative_synopsisHALLMARK_WNT_BETA_CATENIN_SIGNALING-1[[wnt signaling, notch signaling, hedgehog signaling, transcriptional regulation, cell cycle progression, developmental events, dna replication and repair, transcriptional silencing, GO:0043161]][[transcriptional regulation, GO:0001709, signaling pathway activation, MESH:D060449, notch pathway, hedgehog pathway, protein interactions, cell growth regulation, GO:0004672, GO:0030163, cell-cell interaction, cell-matrix interaction, protein ligase binding activity, GO:0004842, membrane-bound protease activity, transcriptional repressor, GO:0006338, notch receptor cleavage, intracellular domain formation, ectodomain shedding, MESH:D015533, nuclear receptor co-repressor]]0.03
528text-davinci-003narrative_synopsisT cell proliferation-0[[GO:0004888, calmodulin binding activity, GO:0061630, GO:0033192, GO:0004721, GO:0004725, GO:0004672, MESH:D015533, guanine nucleotide exchange activity, ligand binding activity]][[the provided list of genes and associated descriptions demonstrates variation in generic cellular processes like protein degradation, protein and nucleic acid binding and kinase activity, as well as specific pathways involving cytokine and chemokine signaling, transcriptional regulation and regulation of immune cell activity. across these processes, the significant terms enriched across the genes include: protein tyrosine kinase activity; protein/nucleic acid/oligomeric binding activities; protein ubiquitination; transcriptional and immune cell activation and proliferation; intracellular receptor signaling and nf-kappab pathways; and cell cycle regulation.\\n\\nmechanism:\\nthe identified genes likely affect several common pathways, including signaling pathways that mediate cell division, motility, adhesion, chemokine- and cytokine-mediated responses, and immune cell function. in particular, the proteins encoded by these genes likely play roles in the regulation of post-translational modifications, such as protein ubiquitination, and the regulation of gene transcription, likely in response to extracellular cues. additionally, the identified proteins may mediate the recruitment of the cbm signalosome, leading to the activation of nf-kappab pathways. finally, cell cycle-related processes]]0.00
529text-davinci-003narrative_synopsisT cell proliferation-1[[transcriptional regulation, cellular signaling pathways and processes, GO:0016049, differentiation, GO:0006950, GO:0006955, protein folding and trafficking, MESH:D051192, transmembrane proteins, receptor tyrosine kinases, ubiquitin e3 ligases, MESH:D020134, cgmp-binding phosphodiesterase]][[GO:0007165, GO:0008037, GO:0004721, GO:0061630, lipid enzyme, MESH:D011505, cgmp kinases, GO:0000981, protein scaffold, cytokine, adaptor protein, GO:0051301, adhesion, differentiation, GO:0006950, negatively regulated, MESH:D021381, cell fate and patterning, MESH:D002470, ligand-gated ion channel, GO:0051092, GO:0006569, er stress-induced protection, transmembrane glycoprotein, MESH:D050503, wnt gene family, GO:0016020]]0.05
530text-davinci-003narrative_synopsisYamanaka-TFs-0[[this set of genes is involved in embryonic development, stem cell pluripotency, stem-cell maintenance, and dna damage response. commonly enriched terms include cell cycle regulation, transcription regulation, GO:0006915, cellular transformation, and dna damage repair. mechanism:these genes control critical functions of cell cycle progression, gene transcription, and dna repair, providing the necessary foundation for the development of the organism. these pathways provide the structural and biochemical features of embryonic development, maintenance of stem cells and pluripotency, response to cellular damage]][[genes in this list are transcription factors involved in the development of various organ systems, such as the skin and cns, as well as responding to dna damage, GO:0006915, and cellular transformation. the enriched terms are transcription factor activity; gene expression regulation; cell cycle regulation; dna damage response; pluripotency; and embryo development.\\n\\nmechanism: the transcription factors in this list interact with dna, regulate gene expression, and influence cell cycle progression, GO:0006915, and cellular transformation. combined, these genes are thought to play a role in creating and maintaining cellular and tissue identity, as well as responding to environmental changes. this could be part of a larger mechanism that governs organism development and homeostasis]]0.04
531text-davinci-003narrative_synopsisYamanaka-TFs-1[[GO:0000981, MESH:D047108, stem cell maintenance, MESH:D063646, GO:0030154]][[GO:0000981, zinc finger proteins, GO:0007049, MESH:D004249, MESH:D016147, MESH:D047108, stem cell maintenance, translocation, homeodomain]]0.27
532text-davinci-003narrative_synopsisamigo-example-0[[GO:0007155, MESH:D016326, MESH:M0023728, cellular communication, GO:0042592, GO:0042060, GO:0006915, motility, GO:0001525]][[GO:0007155, GO:0016477, cell signalling, GO:0008152, GO:0006915, GO:0009653, GO:0007599, MESH:D007109, extracellular matrix maintenance]]0.12
533text-davinci-003narrative_synopsisamigo-example-1[[GO:0007219, osteoclast attachment/mineralized bone matrix, jagged 1/notch 1 signaling, GO:0007155, GO:0006915]][[GO:0048729, matrix metalloproteinase inhibitor, regulated cell adhesion, cytoplasmic protein tyrosine kinase, GO:0005161, cytokine-induced gene expression, GO:0005583, cell signaling pathway, MESH:D015533, antimicrobial activity, GO:0031012, GO:0016477, GO:0008283]]0.00
534text-davinci-003narrative_synopsisbicluster_RNAseqDB_0-0[[GO:0055085, growth factor regulation, calcium regulation, transcription regulation, MESH:D007473, calcium-dependent processes, protein binding activity, chromatin binding activity, gtpase activating protein binding activity, histone binding activity, dna-binding activity, sequence-specific double-stranded dna binding activity, GO:0000988]][[GO:0007165, transcription regulation, ion regulation, GO:0005515, cytoskeletal adaptor, MESH:D006023]]0.06
535text-davinci-003narrative_synopsisbicluster_RNAseqDB_0-1[[this list of genes is involved predominantly in processes related to binding activities, dna-binding transcription factor activities, chromatin binding activities, and protein domain-specific binding. the underlying biological mechanism involves pathways that regulate cell morphology and cytoskeletal adaptor proteins. the enriched terms include: binding activity, GO:0003700, chromatin binding activity, protein domain-specific binding activity, cell morphology, MESH:D051179]][[GO:0000988, metal ion binding activity, dna binding activity, chromatin binding activity, rna binding activity, protein domain-specific binding activity, histone binding activity, methylated histone binding activity]]0.17
536text-davinci-003narrative_synopsisbicluster_RNAseqDB_1002-0[[GO:0007165, protein-protein interactions, MESH:D004734, GO:0051015, troponin binding, GO:0005523, GO:0051219, GO:0032515, GO:0043531, atp binding. mechanism: these genes are involved in pathways of signal transduction, protein-protein interactions, and energy metabolism, which lead to muscle contraction and tissue development. activation of these pathways leads to calcium release, which in turn activates contractile proteins such as troponin, tropomyosin, and actin. these proteins act together to promote muscle contraction and cytoskeletal structure]][[GO:0051015, GO:0048870, GO:0004722, myosin-binding proteins, MESH:D002154, GO:0045010, GO:0005523, calcium sensitivity, MESH:D044767, GO:0003735, GO:0004930, GO:0042923, GO:0050262, GO:0061769, GO:0019674, GO:0007015, GO:0006936, GO:0055008, GO:0030838]]0.07
537text-davinci-003narrative_synopsisbicluster_RNAseqDB_1002-1[[MESH:D024510, actin and tropomyosin binding, calcium- and energy-regulation, ion channeling, negative regulation of cytokine signaling pathways, GO:0033173]][[actin filament binding activity, muscle alpha-actinin binding activity, actin monomer binding activity, tropomyosin binding activity, GO:0006936, GO:0045214, GO:0071691, GO:0045010, GO:0030838, muscle excitation-contraction coupling, calcium release complex, muscle associated proteins, GO:0030036, GO:0007507]]0.00
538text-davinci-003narrative_synopsisendocytosis-0[[GO:0006897, GO:0015031, GO:0051639, endoplasmic reticulum and recycling endosome membrane organization, GO:0044351, GO:0016043, intracellular signaling, GO:0051260]][[GO:0030030, MESH:D021381, MESH:D011494, GO:0048870, membrane reorganization, GO:0006897, cytoskeletal reorganization, mitogen-activated protein kinase, lysosomal degradation, GO:0051168]]0.06
539text-davinci-003narrative_synopsisendocytosis-1[[GO:0015031, GO:0006897, GO:0006898, GO:0051260, GO:0007155, GO:0048870, amino acid residues, MESH:D054875, GO:0015908, cytoskeletal reorganization, GO:0016192, signaling complex regulation, GO:0140014, GO:0006919]][[GO:0006897, lysosomal degradation, GO:0015031, GO:0006898, membrane processes, gtpase regulation, MESH:D044767, death domain-fold]]0.16
540text-davinci-003narrative_synopsisglycolysis-gocam-0[[GO:0006096, GO:0016310, MESH:D006593, glucose phosphate isomerase, phosphofructokinase, MESH:D005634, fructose-1,6-bisphosphate, MESH:D014305, glyceraldehyde-3-phosphate dehydrogenase, MESH:D010736, MESH:D011770, MESH:D010751]][[GO:0006006, GO:0006096, GO:0016310, GO:0006000, GO:0006094, GO:0004332, glycogen storage, GO:0016853, GO:0004743, GO:0004396]]0.10
541text-davinci-003narrative_synopsisglycolysis-gocam-1[[muscle maturation, MESH:D024510, GO:0001525, GO:0006096, MONDO:0003664, MONDO:0002412, plasmin regulation]][[GO:0006096, GO:0008152, regulation of energy conversion, MESH:D024510, tumor progression, GO:0006094, GO:0001525, neurotrophic factor, MESH:M0025255]]0.23
542text-davinci-003narrative_synopsisgo-postsynapse-calcium-transmembrane-0[[GO:0006816, calcium ion regulation, postsynaptic ion channel, GO:0005892, glutamate receptor channel, g protein-coupled receptor, plasma membrane protein, ligand-gated ion channel]][[calcium homeostasis, calcium-channel activity, MESH:D007473, g-protein coupled receptor, ligand-gated ion channel]]0.08
543text-davinci-003narrative_synopsisgo-postsynapse-calcium-transmembrane-1[[calcium ion regulation, GO:0006816, n-methyl-d-aspartate receptor family, MESH:C413185, MESH:D011954, p-type primary ion transport atpases]][[calcium homeostasis, calcium influx, GO:0007268, neuronal development, MESH:D058446, purinergic receptor, GO:0004972, MESH:C413185, g-protein coupled receptor]]0.07
544text-davinci-003narrative_synopsisgo-reg-autophagy-pkra-0[[GO:0043539, protein serine/threonine kinase binding activity, GO:0004860, GO:0005085, GO:0032008, GO:0010605, GO:0032956, GO:0032006, GO:0016241, regulation of nf-kappab activation, GO:0001558, regulation of cell survival, GO:0038187, GO:0006281, GO:0045087]][[GO:0016049, GO:0006915, GO:0007165, serine/threonine kinase activator activity, GO:0035004, GO:0005085]]0.05
545text-davinci-003narrative_synopsisgo-reg-autophagy-pkra-1[[this term enrichment test looked at a list of human genes together with their functions. it found that the genes have functions related to cell cycle regulation, GO:0007165, GO:0043170, protein kinase binding and regulating chromatin remodeling and transcription. the enriched terms include cell cycle regulation, GO:0007165, GO:0043170, GO:0019901, GO:0016310, chromatin remodeling and transcriptional regulation.\\n\\nmechanism: the genes in this list are involved in processes such as cell cycle regulation, GO:0007165, GO:0043170, GO:0019901, phosphorylation and chromatin remodeling and transcription, which are interconnected. these processes all depend on the activity of various protein kinases and their activation by various components, including snca, MESH:D053148, trib3, ccny, pik3ca, akt1, nod2, kat5, rptor, smcr8, mlst8, tab2, hspb1, irgm, GO:0033868, cdk5r1 and other proteins. they interact and cooperate with each other to form pathways and complexes responsible for cell cycle regulation and activation or inhibition of specific genes. ph]][[GO:0006281, apoptosis regulation, GO:0007165, GO:0016049, nutrient and insulin levels, macromolecule metabolic process regulation, GO:1901987, GO:0006338]]0.03
546text-davinci-003narrative_synopsishydrolase activity, hydrolyzing O-glycosyl compounds-0[[GO:0016798, GO:0005980, GO:0006516, GO:0051787, GO:0036503, glycosaminoglycan hydrolysis, heparan sulfate hydrolysis, cell surface hyaluronidase.\\nhpyothesis: the genes listed serve key roles in the degradation of polysaccharides and glycoproteins, the recognition of misfolded proteins and their subsequent degradation by endoplasmic reticulum-associated degradation, the hydrolysis of glycosaminoglycans, and the hydrolysis of heparan sulfate for the maintenance of cell proteins and structure]][[glycosyl hydrolase, glycosyl bond hydrolysis, oligosaccharide processing, MESH:D006023, MESH:D011134, n-linked oligosaccharide, o-linked n-acetylglucosamine, β-1,4-glucosidase, β-glucosidase, β-hexosaminidase]]0.00
547text-davinci-003narrative_synopsishydrolase activity, hydrolyzing O-glycosyl compounds-1[[glycohydrolase enzymes, glycosaminoglycans (gag]][[glycosyl hydrolase, glycohydrolytic enzyme, MESH:D006821, MESH:D005644, lysosomal hydrolase, n-linked oligosaccharide processing, MESH:D001616, MESH:D001619, MESH:D001617, MESH:D009113, alpha-1,4-glucosidase, MESH:D043323, MESH:D000520, MESH:D055572, mannosidase, MESH:M0012138, alpha-l-iduronic acid, alpha]]0.00
548text-davinci-003narrative_synopsisig-receptor-binding-2022-0[[antigen binding activity, immunoglobulin receptor binding activity, GO:0002377, GO:0002250, protein homodimerization]][[antigen binding activity, immunoglobulin receptor binding activity, activated/inactivated immune response, GO:0042803, peptidoglycan binding activity]]0.25
549text-davinci-003narrative_synopsisig-receptor-binding-2022-1[[immunoglobulin receptor binding activity, GO:0002253, antigen binding activity, GO:0042803, immunoglobulin lambda-like polypeptides, preb cell receptor, src family of protein tyrosine kinases, c-type lectin/c-type lectin-like domain]][[antigen binding activity, immunoglobulin receptor binding activity, GO:0002253, GO:0042803, peptidoglycan binding activity, phosphatidylcholine binding activity, transduction of signals, allelic exclusion, myristylation, palmitylation, protein tyrosine kinases, sh2 and sh3 domains, MESH:D008285, MESH:D010455, antigen presenting cells, preb cells, src family of protein tyrosine kinases (ptks), c-type lectin domain]]0.18
550text-davinci-003narrative_synopsismeiosis I-0[[GO:0004519, bcl-2 homology domain 3 binding, GO:0003682, GO:0003677, GO:0003678, GO:0003697, 3'-5' exode]][[the gene summaries indicate that most of the genes are involved in processes related to dna binding, GO:0006281, GO:0006310, and meiotic processes. the enriched terms include \"dna binding\", \"dna repair\", \"dna recombination\", \"meiosis\", \"double-stranded dna binding\", \"single-stranded dna binding\", GO:0003682, GO:0004519, dead-like helicase activity, and bcl-2 homology domain activity.\\n\\nmechanism: the mechanism underlying the enrichment of these gene functions appears to be related to the repair and maintenance of chromosomal integrity as well as the regulation of cell division, differentiation, and development. through their combined activities, the genes appear to be involved in the maintenance of genome stability and the efficient transmission of genetic information from one generation to the next]]0.10
551text-davinci-003narrative_synopsismeiosis I-1[[meiotic recombination, GO:0006281, GO:0007059, double-strand dna break repair, homologous chromosome pairing, dna binding activity, GO:0051289]][[GO:0006281, meiotic recombination, GO:0006302, GO:0035825, chromosome synapsis, GO:0007059, MESH:D023902, holliday junction resolution, dna strand-exchange, reciprocal recombination, GO:0007130, GO:2000816, positive regulation of response to dna damage, GO:0006611, GO:0031297, GO:0000712, GO:0060629, GO:0003677, GO:0003697, single-str]]0.12
552text-davinci-003narrative_synopsismolecular sequestering-0[[this list of genes encodes proteins involved in a range of cellular processes such as cell cycle progression, GO:0006897, iron storage and regulation, cellular response to stress and inflammation, GO:0006915, transcriptional regulation, GO:0046907, GO:0016567, and toxic metal and cytosolic signaling. enriched terms include protein binding, lipid and hormone transport, GO:0003779, GO:0003724, GO:0006511, cell cycle progression, and negative regulation of nitrogen compound metabolic process. mechanism: these genes are involved in a wide range of processes related to regulating cell growth, GO:0032502, and homeostasis. they play a role in pathways such as the cell cycle, GO:0006915, inflammatory metabolic processes]][[GO:0005515, GO:0046907, GO:0043161, GO:0051726, regulation of cell growth and survival, cholesterol and lipids metabolism, nf-κb inhibiting proteins, GO:0009792, GO:0007283, GO:0045087, cytokines and growth factors, antioxidant enzymes, GO:0030097]]0.03
553text-davinci-003narrative_synopsismolecular sequestering-1[[GO:0005515, MESH:D015533, GO:0008152, MESH:D007109, GO:0006915, GO:0007049, GO:0016310]][[GO:0006897, iron storage, GO:0008610, GO:0006915, GO:0008283, GO:0030154, defense from bacterial infection, transcription regulation, translation regulation]]0.07
554text-davinci-003narrative_synopsismtorc1-0[[GO:0006412, GO:0015031, protein signaling, GO:0008152, GO:0010467]][[GO:0006412, GO:0008152, GO:0006457, MESH:D054875, GO:0006351, GO:0003677, damage control, GO:0032502, cellular pathway regulation, GO:0006915, GO:0007049, GO:0030163]]0.13
555text-davinci-003narrative_synopsismtorc1-1[[metabolic reactions, GO:0051726, energy production, MESH:D011494, GO:0016791, MESH:D003577, MESH:D000604, peptidase c1 family, GO:0031545, ion transporter, ubiquitin-like proteases, ubiquitin ligases, serine/threonine protein kinases, glyceraldehyde-3-phosphate dehydrogenase, nadp-dependent dehydrogenases, rna binding protein, GO:0016467, pyruvate dehydrogenase, MESH:D012321, GO:0016538, MESH:D005634, heat shock protein, hetero trimeric co-factors, MESH:D050603, MESH:D000263, MESH:D013762, MONDO:0008090]][[GO:0008152, GO:0023036, GO:0007165, transcriptional regulation, epigenetic regulation, GO:0044183, proteolytic activity, GO:0051726]]0.03
556text-davinci-003narrative_synopsisperoxisome-0[[this set of genes are enriched for terms related to peroxisomal biogenesis and peroxisomal protein import. the aaa atpase family, peroxisomal membrane proteins, c-terminal pts1-type tripeptide peroxisomal targeting signals, and peroxisomal targeting signal 2 are all over-represented in the gene list.\\n\\nmechanism: the mechanism behind these genes is the import of proteins into peroxisomes, resulting in peroxisomal biogenesis. the aaa atpases, peroxisomal membrane proteins, c-terminal pts1-type tripeptide peroxisomal targeting signals, peroxisomal targeting signal 2 are all involved in either targeting or catalyzing this protein import]][[peroxisome biogenesis, peroxisomal protein import, tripeptide peroxis]]0.00
557text-davinci-003narrative_synopsisperoxisome-1[[this set of genes is related to the function of peroxisome biogenesis and associated disorders. the enriched terms are peroxisome biogenesis, GO:0017038, peroxisomal matrix proteins, atpase family, and pti2 receptor/pex7.\\n\\nmechanism: peroxisomes are important organelles for a variety of metabolic functions, and the synthesis and organization of these organelles is mediated by the pex genes. pex6 and pex2 are involved in protein import, where the pex2 protein forms a membrane-restricted complex, and pex6 is predominantly cytoplasmic and plays a direct role in peroxisomal protein import and receptor activity. pex3 and pex7 are required for peroxisomal biogenesis, and pex7 is the cytosolic receptor for the set of peroxisomal matrix enzymes targeted to the organelle by the peroxisome targeting signal 2. lastly, pex1 forms a heteromeric complex and plays a role in the import of proteins into peroxisomes and peroxisome biogenesis]][[aaa atpase family, MONDO:0019234, peroxisomal protein import, peroxisomal matrix protein import, heteromeric complex, peroxisome targeting signal 2]]0.00
558text-davinci-003narrative_synopsisprogeria-0[[GO:0000785, nuclear membr]][[the genes in this list are associated with post-translational proteolytic cleavage, intermolecular integration, dna repair and dna helicase activity, and nuclear stability and chromatin structure. the underlying mechanism is likely related to protein modification and regulation of cellular components involved in dna metabolism and gene expression. the enriched terms include protein modification, proteolytic cleavage, GO:0003678, intermolecular integration, GO:0006281, chromatin structure, nuclear stability]]0.00
559text-davinci-003narrative_synopsisprogeria-1[[these genes are all related to essential functions that facilitate the proper structure and organization of the nucleus and genome, primarily through the formation and maintenance of nuclear lamin, dna helicases and chromatin structures. there is evidence that all of these genes are involved in the proper functioning of cell division, GO:0006281, and transcription, as well as the maintenance of genome stability. the most enriched terms related to the functions of these genes are nuclear lamina, dna helicase, chromatin structure, GO:0006281, GO:0006351, genome stability, GO:0051301, nuclear membrane proteins, and nuclear localization signal. \\n\\nmechanism: the genes may be involved in pathways that coordinate the formation and maintenance of nuclear lamin, dna helicase, and chromatin structures, which are necessary for cell division and transcription, as well as the maintenance of genome stability. these pathways may involve the direct interactions between the gene products, as well as the recruitment of nuclear membrane proteins and signals involved in maintaining nuclear organization]][[this set of genes is involved in the maintenance of genome stability and chromosome integrity, likely in terms of forming the nuclear lamina and promoting nuclear reassembly. the enriched terms are genome stability, chromosome integrity, GO:0005652, nuclear reassembly.\\n\\nmechanism: the set of genes are likely working together to form and maintain a matrix of proteins which form the nuclear lamina next to the inner nuclear membrane, thus providing stability to the genome and the chromosomes by helping to organize the dna within the nucleus. this is achieved through binding with both dna and inner nuclear membrane proteins and recruiting chromatin to the nuclear periphery to achieve nuclear reassembly]]0.00
560text-davinci-003narrative_synopsisregulation of presynaptic membrane potential-0[[neuronal signaling, neuron communication, MESH:D007473, excitatory dependent channels, inhibitory neurotransmitter, ligand-gated ion channel, g protein-coupled membrane receptor]][[MESH:D007473, voltage-gated ion channel, MESH:D015221, ligand-gated ion channel, MESH:D018079, MESH:D017470, MESH:D015222]]0.17
561text-davinci-003narrative_synopsisregulation of presynaptic membrane potential-1[[MESH:D017981, MESH:D058446, GO:0009451, voltage-gated ion channels, channel subunits, channel polymorphisms, g-protein-coupled transmembrane receptors, MESH:D017470, MESH:D018079, MESH:D015221]][[GO:0007268, MESH:D009482, inhibitory, excitatory, MESH:D017981, MESH:D015221, MESH:D018079, MESH:D017470, MESH:D007649, GO:0009451, voltage-gated, MESH:D007473, MESH:D058446, MESH:D019204]]0.33
562text-davinci-003narrative_synopsissensory ataxia-0[[transcriptional regulation, mitochondrial rna synthesis, neurodevelopment, GO:0030218, GO:0036211, nucleolar function, neuronal network formation, sensory receptor function]][[GO:0000981, GO:0009056, moonlighting proteins, GO:0002377, adapter molecules, heme transporter, myelin upkeep, GO:0005643, mitochondrial dna polymerase, ubiquitin ligase, aminoacyl-trna synthetase.\\n\\nmechanism: these genes work together in a joint mechanism to regulate biological processes like cell replication, neuronal development, protein folding, and enzymatic activity. in particular, their collective involvement in the coordination of transcriptional activity, ion transport, and dna-binding suggests a complex integrated process by which these genes serve to facilitate normal cell functions]]0.00
563text-davinci-003narrative_synopsissensory ataxia-1[[GO:0000981, dna helicase, hexameric dna helicase, neurotrophic factor, pdz domain, ma cation channels, MESH:D005956, protein synthetase, mitochondrial dna polymerase, heme transporter, GO:0005643, MESH:D044767, transmembrane glycoprotein]][[GO:0000981, dna helicase, nerve myelin maintenance, mechanically-activated cations channels, nerve motor neuron survival, MESH:D054875]]0.12
564text-davinci-003narrative_synopsisterm-GO:0007212-0[[g-protein coupled receptor signaling, g-protein subunit signaling, GO:0004016, phospholipase c-beta activity, GO:0005102, GO:0007165, second messenger synthesis, transmembrane signaling]][[the summaries of the provided gene functions describe proteins linked to the activity and regulation of g-protein coupled receptor signaling pathways, including dopamine, MESH:D016232, and serotonin receptors, as well as proteins involved in calcium ion regulation, GO:0003677, and apoptosis. statistically over-represented terms include: g-protein coupled signaling; calcium ion regulation; transmembrane signaling; dna binding; and apoptotic process. \\n\\nmechanism:\\nthe common function of these genes is likely to be linked to the regulation of g-protein coupled signaling pathways, which regulate a variety of cellular processes, including cellular signaling and growth, neuronal development, apoptosis. calcium ion regulation transmembrane signaling are also likely to be important for the functioning of these genes. dna binding proteins proteins that enable clathrin light chain binding activity may be involved in the transcriptional regulation of these signals]]0.00
565text-davinci-003narrative_synopsisterm-GO:0007212-1[[the list of human genes supplied involves several different cell signaling pathways, including the dopamine receptor (drd1, drd2, drd3 and drd5) pathway, g-protein coupled receptor (gpcr) signalling pathway (gnas, gnai3, gnaq, gna11, gna14, gna15, gnb1, gnb5, gnao1, gng2, sl]][[this gene set was comprised of dopamine and g-protein coupled receptors that participate in cellular signaling pathways and influence cellular functions such as metabolism and behavior. the genes are involved in a wide range of pathways such as signal transduction, transcriptional regulation, memory and behavior, GO:0007612, neural development and synaptic plasticity. the enriched terms in this list include: signal transduction, g protein-coupled receptor, camp, MESH:D000262, MESH:D054799, MESH:D017868, calcium ions, transcriptional regulation, GO:0000981, MESH:D011954, wnt and pi3k signaling pathways, neuronal growth and development, GO:0010467, and synaptic receptors.\\n\\nmechanism: this gene set is involved in many pathways such as signal transduction, transcriptional regulation, and synaptic organization. signal transduction occurs through g-protein coupled receptors and camp, which in turn regulate downstream effectors including adenylyl cyclase, MESH:D017868, and calcium ions. furthermore, transcriptional regulation occurs through various receptor signaling pathways, such as those related to the wnt and pi3k pathways, while dopamine receptors regulate neuronal growth and development, GO:0010467, and behavior. finally, synaptic receptors enable]]0.00
566text-davinci-003narrative_synopsistf-downreg-colorectal-0[[transcriptional regulation, GO:0006338, GO:0003677, GO:0000981, coactivator, heterodimer, response element]][[dna-binding, chromatin-binding, transcriptional regulation, e-box dna consensus sequence binding, dna damage response regulation, dna damage response maintenance, phosphoprotein shutting, MESH:D016335, interaction with cellular retinol-binding protein, hormone-dependent transcription, receptor-dependent transcription, nuclear hormone receptor-dependent transcription, transcriptional coactivator complex recruitment, GO:0000785]]0.05
567text-davinci-003narrative_synopsistf-downreg-colorectal-1[[transcription factor regulation, GO:0016569, dna-binding activity, zinc-finger binding, GO:0032183, retinoid x receptor responsive element binding]][[transcriptional regulation, dna-binding, chromatin binding activity, histone binding activity, GO:0000988]]0.00
568text-davinci-003no_synopsisEDS-0[[GO:0031012, ecm components, matrix components, ecm regulators]][[GO:0001501, GO:0032964, cell-matrix interactions, extracellular matrix remodeling, cell signaling]]0.00
569text-davinci-003no_synopsisEDS-1[[extracellular matrix protein network, collagen fibril formation, GO:0030199, ecm protein network assembly, UBERON:2007004]][[collagen production, GO:0061448, matrix remodeling, zinc finger protein regulation]]0.00
570text-davinci-003no_synopsisFA-0[[MONDO:0100339, \"double strand break repair\", \"fanconi anemia protein complex\", \"ubiquitin ligase complex formation\"]][[GO:0006281, homologous recomination, MESH:M0006667, GO:0004518]]0.00
571text-davinci-003no_synopsisFA-1[[GO:0006974, dna damage recognition, GO:0006281, GO:0035825, double-stranded break repair, double-stranded break recognition]][[MONDO:0100339, dna/rna damage response, dna/rna metabolism, GO:0051726, genome stability, MONDO:0019391]]0.00
572text-davinci-003no_synopsisHALLMARK_ADIPOGENESIS-0[[MESH:D004734, GO:0006631, GO:0045444, GO:0006695, GO:0006699]][[metabolic regulation, GO:0050658, GO:0006412, cell membrane transport, transcription regulation, GO:0006915, GO:0006457, GO:0019432, GO:0003676, GO:0006633, GO:0006096, GO:0045454]]0.00
573text-davinci-003no_synopsisHALLMARK_ADIPOGENESIS-1[[MESH:D004734, cell death regulation, cell proliferation signaling, dna replication/remodeling, GO:0006396, GO:0006629]][[GO:0008152, MESH:D004734, GO:0007165, GO:0006119, transcriptional regulation, GO:0006468, GO:0051726, GO:0006629, GO:0006457, protein assembly, mitochondrial function, GO:0006915, GO:0006839, GO:0055085, GO:0007010, GO:0006094, GO:0006096, GO:0042632]]0.09
574text-davinci-003no_synopsisHALLMARK_ALLOGRAFT_REJECTION-0[[cell surface molecules, MESH:D016207, MESH:M0000731, receptor signalling, transcriptional regulation, GO:0006915]][[immune signalling, GO:0051726, cellular differentiation, transcriptional regulation]]0.11
575text-davinci-003no_synopsisHALLMARK_ALLOGRAFT_REJECTION-1[[GO:0019882, GO:0007165, b and t cell metabolism, GO:0001816, GO:0006935]][[genes in this list are representative of various pathways involved in cell movement, GO:0019882, GO:0006954, immune regulation, and cell signaling events including jak-stat and mapk- pi3k pathways. enriched terms include “immune system processes”; “immune recognition pathways”; “cytokine-mediated signaling pathways”; “inflammatory response”; “cellular immune activation”; “intestinal immune network for iga production”; “cytokine secretion”; “tcr signaling pathway”; “cd4 t cell activation”; “t lymphocyte differentiation”; “innate immune response”; and “cytokine-cytokine receptor interaction”.\\n\\nmechanism: the genes are involved in pathways that affect cell movement, GO:0019882, GO:0006954, immune regulation, and cell signaling. these pathways control the activation, response, differentiation, and survival of t cells by regulating cytokine expression, activation of specific receptors, production of antibodies, regulation of transcription factors and their binding to promoters, other immune system processes]]0.05
576text-davinci-003no_synopsisHALLMARK_ANDROGEN_RESPONSE-0[[genes in this list are involved in developmental processes, metabolism, and the inflammatory response. the terms enriched in these genes include: cell cycle regulation, GO:0008152, GO:0006260, GO:0015031, receptor signaling, GO:0006954, GO:0006915, GO:0006351, GO:0006457, GO:0016477, developmental processes.\\n\\nmechanism: these genes appear to work together to regulate a variety of cellular processes, such as cellular metabolism, transcription, growth, and differentiation, as well as communication between cells and the environment. these genes likely act in concert to coordinate the intricate interplay between these processes and respond to changes in the environment. furthermore, they likely play a role in the body’s inflammatory response when faced with a variety of external stimuli]][[genes in this list are mainly involved in regulation of skeletal tissue formation and development, signal cascade activation, protein folding, cellular metabolism and movement, cell cycle regulation, and transcriptional regulation. the underlying biological mechanism may be related to the complex network of interactions among these genes in controlling the basic functions of a cell. the enriched terms are: bone morphogenesis, GO:0001501, signal cascade activation, GO:0006457, GO:0044237, cellular movement, GO:0051726, transcriptional regulation, chromatin and dna modification]]0.05
577text-davinci-003no_synopsisHALLMARK_ANDROGEN_RESPONSE-1[[GO:0065007, GO:0023052, GO:0019538, GO:0051726, transcription regulation, MESH:D021381, GO:0007165, membrane trafficking, protein kinase regulation, GO:0044237, GO:0006259, GO:0006468, GO:0030163, mitochondrial function, GO:0006629, cytoskeleton regulation, GO:0007155, GO:0009117]][[gene transcription and regulation, protein translation and metabolism, cytoskeletal organization, GO:0006629]]0.05
578text-davinci-003no_synopsisHALLMARK_ANGIOGENESIS-0[[extracellular matrix formation and maintenance, fibrous tissue development, vascular development, cell-cell communication and migration, extracellular secreted signaling, collagen and laminin-fibrillin proteins]][[GO:0030198, vascularization, endothelial cell aggregation, GO:0007155, cell surface interactions]]0.00
579text-davinci-003no_synopsisHALLMARK_ANGIOGENESIS-1[[GO:0032502, GO:0009653, GO:0009888, GO:0030198, GO:0006954, MESH:D066253, cell-cell communication]][[cytokine receptor signaling, growth factor signal transduction, transmembrane and extracellular matrix proteins, development of muscle, bone, and neuronal networks]]0.00
580text-davinci-003no_synopsisHALLMARK_APICAL_JUNCTION-0[[this term enrichment test suggests that the genes provided are involved in cell adhesion, GO:0006955, and tissue morphogenesis. specifically, the adhesion-associated genes enriched in this dataset include icam1, icam2, icam4, icam5, nectin1, nectin2, nectin3, nectin4, nrxn2, ptprc, sdc3, thy1, vcam1, and vwf. the immune response-associated genes enriched in this dataset include cd34, cd86, cd209, ctnna1, icam2, icam4, icam5, map4k2, msn, pard6g, and tnfrsf11b. lastly, the tissue morphogenesis-associated genes enriched in this dataset include acta1, actb, actc1, actg1, actn1, actn2, actn4, adam15, adra1b, akt2, alox15b, amigo2, baiap2, cadm2, cadm3, MESH:M0359286, col9a1, MONDO:0011642, ctnnd1, MESH:C040896]][[GO:0060348, joint development, MESH:D024510, GO:0061448, GO:0007155, adhesion receptor complex formation, GO:0007165, receptor-mediated signaling cascades]]0.00
581text-davinci-003no_synopsisHALLMARK_APICAL_JUNCTION-1[[GO:0009653, GO:0016049, MESH:D047108, cellular signaling, GO:0031012, cytoskeletal organization, basal membrane assembly, GO:0098609, GO:0006915, GO:0016477, GO:0001816, growth factor production, tyrosine kinase activity, g-protein coupled receptor signaling pathway, nuclear receptor signaling pathway, GO:0016055, phosphatidylinositol 3-kinase signaling pathway, protein kinase b signaling pathway, map kinase signaling pathway, cell adhesion molecule signaling pathway, focal adhesion signaling pathway]][[GO:0007155, GO:0016477, migration and interaction, cytoskeletal organization, actin cytoskeletal regulation, GO:0007165, regulation of actin cytoskeletal organization]]0.08
582text-davinci-003no_synopsisHALLMARK_APICAL_SURFACE-0[[GO:0016477, membrane receptor signaling, GO:0009100, protein tyrosine kinases, GO:0007155, cytoskeletal dynamics, receptor-mediated lectin binding, GO:0006629, GO:0007015]][[cell regulation, GO:0007165, GO:0007155, GO:0006457, GO:0030198]]0.08
583text-davinci-003no_synopsisHALLMARK_APICAL_SURFACE-1[[cell signaling, GO:0032502, transcription regulation, GO:0008152, MESH:D049109, MESH:D005786]][[cell adhesion and migration, cell signaling, GO:0030154, protein kinase and phosphatase activities, transcription and dna metabolism, MESH:D056747, glycosylation and carbohydrate metabolism, cell growth and proliferation]]0.08
584text-davinci-003no_synopsisHALLMARK_APOPTOSIS-0[[transcriptional regulation/control, cell cycle/apoptosis, GO:0006955]][[GO:0006915, transcription regulation, cell cycle progression, GO:0006954, GO:0006260, GO:0006281, oxidative stress response, immune system activation]]0.00
585text-davinci-003no_synopsisHALLMARK_APOPTOSIS-1[[the genes listed are mainly involved in the regulation and expression of genes, inflammation pathways and cell cycle regulation. specifically, enriched terms include gene expression and transcriptional regulation, dna damage and repair, GO:0007165, GO:1901987, metabolism and apoptosis.\\n\\nmechanism: the commonality in the function of these genes is likely related to the roles they play in the regulation of gene expression by affecting signal transduction, GO:0008152, cell cycle control and apoptosis. these gene functions may lead to a variety of processes, including inflammation pathways related to immunity, UBERON:2000098, MESH:D002470]][[cell death regulation, GO:0006954, immune reaction, growth and morphogenesis, UBERON:2000098, GO:0006915, GO:0006281, GO:0030217, GO:0001816, GO:0051726, fast axonal transport, extracellular proteolysis, GO:0007155, GO:0042060, MESH:D009362, MESH:D063646, GO:0016477, regulation of nf-kb pathway]]0.03
586text-davinci-003no_synopsisHALLMARK_BILE_ACID_METABOLISM-0[[MESH:M0496924, GO:0006869, development of connective tissues, GO:0006633, GO:0006699, GO:0006805, GO:0006694, cellular transport, MESH:M0023727, connective tissue formation, digit development, GO:0060173]][[GO:0006629, GO:0006869, organ development, cell signaling, GO:0006412, transport processes]]0.06
587text-davinci-003no_synopsisHALLMARK_BILE_ACID_METABOLISM-1[[this set of genes is related to lipid metabolism and lipid transport, protein homeostasis, retinol metabolism, developmental processes, and transportation of lysosomal hydrolases and oxygen-carrying molecules. the set includes genes involved in lipid metabolism (aqp9, atxn1, GO:0033781, abcg4, acsl1, fdxr, aldh8a1, hsd17b11, aldh9a1, aldh1a1, cyp7a1, cp25h, gstk1, MONDO:0100102, acsl5), lipid transport (abca1, abca2, abca3, abca4, abca5, abca8, abca9, abcg8), protein homeostasis (pex12, pex16, pex19, pex11a, pex11g, GO:0005053, pex6, pex26), retinol metabolism (abcd1, abcd2, abcd3), developmental processes (lck, nr3c2, retsat, klf1, ephx2, phyh, bbox1, MONDO:0004277]][[GO:0006629, GO:0006536, serine metabolism, transcription factor regulation, oxidative stress response]]0.00
588text-davinci-003no_synopsisHALLMARK_CHOLESTEROL_HOMEOSTASIS-0[[transcriptional regulation, MESH:D006026, GO:0006629, GO:0005509, GO:0001525, MESH:D016326, receptor signaling; transcription regulators; calcium signaling; glycoside hydrolases; lipid metabolism; cell adhesion; extracellular matrix proteins; signaling receptor molecules.\\n\\nmechanism: this set of genes is likely involved in regulating transcriptional responses, MESH:D006026, GO:0006629, GO:0005509, GO:0001525, MESH:D016326, and receptor signaling. many of these genes interact with each other, forming complex cellular networks and pathways. the particular genes identified in this list are likely related to stimulating or inhibiting the expression of specific genes or pathways, as well as modulating or mediating responses to various environmental signals or stimuli. these gene functions likely interact to maintain homeostasis, contribute to cellular development and processes, promote angiogenesis, and provide a structural and functional framework for the extracellular matrix. furthermore, these genes may be involved in signaling pathways that involve receptor molecules by modulating intracellular calcium levels]][[GO:0006629, GO:0008203, cell signaling and regulation, GO:0032502, GO:0007155, GO:0006915, GO:0006351]]0.04
589text-davinci-003no_synopsisHALLMARK_CHOLESTEROL_HOMEOSTASIS-1[[GO:0006629, transcriptional regulation, cellular adhesion, GO:0032502, GO:0042592]][[GO:0006629, cholesterol control, GO:0009062, GO:0006699, hmgcr regulation, pmvk regulation, fads2 regulation, srebf2 regulation, s100a11 regulation, mvk regulation]]0.07
590text-davinci-003no_synopsisHALLMARK_COAGULATION-0[[inflammatory response regulation, extracellular matrix formation regulation, proteolytic activities]][[extracellular matrix remodeling; angiogenesis and vascular development; immune response and platelet activation; collagen and fibronectin metabolism and regulation; endocytosis and signal transduction; \\nmechanism: the genes in this list work together to control and regulate multiple relevant processes, such as extracellular matrix remodeling, which is the process of breaking down and reorganizing the components of the extracellular matrix in order to facilitate tissue development and repair, angiogenesis and vascular development, which regulate the formation of new blood vessels and ensure proper blood flow throughout the body, immune response and platelet activation, which are necessary to protect the body from foreign agents and to form healthy blood clots, collagen and fibronectin metabolism and regulation, which are important for tissue integrity and structure, and endocytosis and signal transduction, which are necessary for cellular communication and regulation]]0.00
591text-davinci-003no_synopsisHALLMARK_COAGULATION-1[[GO:0007165, GO:0030198, matrix molecular regulation, GO:0006508, GO:0050817, matrix remodeling, GO:0009653]][[GO:0007155, proteolysis regulation, extracellular protein-cell interaction, migration, GO:0050817, GO:0006956]]0.08
592text-davinci-003no_synopsisHALLMARK_COMPLEMENT-0[[GO:0030198, immune system/inflammation/interferon response, GO:0000988]][[development of tissue and organs, GO:0007165, cell surface receptor binding, GO:0050896, UBERON:0002405, GO:0006955, GO:0005125]]0.00
593text-davinci-003no_synopsisHALLMARK_COMPLEMENT-1[[immunoglobulin like domains, GO:0042113, GO:0050852, integrin mediated cell adhesion, GO:0006915, regulation of transcription, GO:0007165, receptor mediated endocytosis and exocytosis, GO:0030198, calcium mediated signaling]][[cellular signalling, GO:0006954, cell stress response, cell-cell interaction, GO:0007165, GO:0045087, cytoskeletal remodelling, GO:0006457, GO:0050900, GO:0004672, GO:0007155, MESH:D005786, GO:0006260, protein activation, GO:0019763, GO:0002377, GO:0016791]]0.04
594text-davinci-003no_synopsisHALLMARK_DNA_REPAIR-0[[GO:0006259, GO:0016070, GO:0006412, dna damage repair, GO:0006351, GO:0006325]][[GO:0032502, GO:0006260, MESH:D047108, GO:0030154, transcription regulation, GO:0006335, nuclear mrna surveillance pathway, GO:0016070, GO:0006281, GO:0140014, rna-dependent dna replication]]0.06
595text-davinci-003no_synopsisHALLMARK_DNA_REPAIR-1[[GO:0006260, transcription regulation, GO:0006412, GO:0043687, nucleic acid metabolism, GO:0010467, GO:0006397, GO:0006412]][[nucleic acid metabolism, GO:0006351, post-transcriptional modifications, GO:0006338, GO:0000398, GO:0006281, rna polymerization, GO:0006397, GO:0051028, GO:0006413]]0.12
596text-davinci-003no_synopsisHALLMARK_E2F_TARGETS-0[[GO:0006260, GO:0006281, gene transcription, GO:0006412, GO:0016569, GO:0007049, GO:0010468]][[transcriptional regulation, GO:0016569, mitotic division, GO:0051726, MESH:D004268, MESH:D006657, GO:0000981, MESH:D004259, MESH:D012321, chromatin remodeling proteins, ubiquitin ligases, nucleosome assembly proteins, helicases, motor proteins, GO:0000075]]0.05
597text-davinci-003no_synopsisHALLMARK_E2F_TARGETS-1[[GO:0006260, GO:0006351, GO:0030261, transcriptional regulation, GO:0006338, GO:0006974, chromatin structure modifications, GO:0006281, GO:0006306, GO:0030163, GO:0007094, GO:1901987, GO:0006468]][[GO:0006260, GO:0006281, GO:0016569, transcription regulation, translation regulation, protein-protein networks, GO:0051225, kinesin motor proteins, dynein motor proteins]]0.10
598text-davinci-003no_synopsisHALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0[[genes in this list are enriched for functions related to modulating extracellular matrix, cell adhesion and morphogenesis, as well as playing roles in development, growth and signal transduction pathways. enriched terms include:extracellular matrix modulation; cell adhesion; morphogenesis; development; growth; signal transduction.\\n\\nmechanism: many of the genes listed are involved in the signaling, development and maintenance of the extracellular matrix, cell adhesion and morphogenesis, which can be regulated through diverse pathways involving the growth factors (bdnf, MESH:D016222, igfbp2, igfbp3, igfbp4, wnt5a), proteoglycans (comp, cspg4, MONDO:0021055, lamc1, lamc2, dcn, has3, sdc1) and adhesion molecules and receptors (acta2, abi3bp, cadm1, cap2, capg, cd44, cdh11, cdh2, cdh6, fn1, grem1, itga2, itga5, itgav, itgb1, itgb3, itgb5, lrp1, tagl]][[GO:0031012, GO:0007155, GO:0048870, cell-matrix interaction, growth factor signaling, cytokine signaling, matrix remodeling]]0.00
599text-davinci-003no_synopsisHALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1[[GO:0030198, GO:0009653, collagen production, matrix metalloproteinase activity, GO:0009100, cytoskeletal component organization, regulation of growth and reproduction, regulation of skin morphogenesis]][[GO:0048705, cell-cell adhesion and motility, extracellular matrix production and remodeling, connective tissue development and differentiation, collagen production and turnover, cytokine and chemokine signaling]]0.00
600text-davinci-003no_synopsisHALLMARK_ESTROGEN_RESPONSE_EARLY-0[[cell morphology; homeostasis & regulation; innervation; cellular metabolism.\\nmechanism: the genes are likely to be involved in various pathways, such as the regulation of gene expression, protein synthesis and structure, cell motility and differentiation, tissue repair regeneration]][[GO:0006260, GO:0006351, GO:0010467, GO:0016049, differentiation, GO:0016485, trafficking, GO:0060349, cancer-related pathways, GO:0098609, matrix remodeling, intracellular signaling, external signals, internal signals]]0.00
601text-davinci-003no_synopsisHALLMARK_ESTROGEN_RESPONSE_EARLY-1[[immunological response, GO:0007155, transcription regulation, GO:0016477, GO:0008544, GO:0060348, MESH:D024510, GO:0015031, GO:0006915]][[transcriptional regulation, GO:0007165, protein-protein interactions, GO:0055085, GO:0008610]]0.00
602text-davinci-003no_synopsisHALLMARK_ESTROGEN_RESPONSE_LATE-0[[MESH:D023281, cytoskeletal processes, GO:0006955, extracellular modification]][[GO:0030198, GO:0007155, GO:0016477, GO:0048870, growth factor signaling, cytoskeletal organization]]0.00
603text-davinci-003no_synopsisHALLMARK_ESTROGEN_RESPONSE_LATE-1[[the commonalities in the functions of these genes are involved in transcription, post-transcriptional regulation, GO:0009966, and cell-cycle related processes. the enriched terms are: transcription; post-transcriptional regulation; signal transduction; cell cycle; dna binding; regulation of transcription; regulation of protein abundance; chromatin remodeling; ubiquitination; and protein-protein interaction.\\n\\nmechanism: the underlying mechanism may be related to the regulation of intricate pathways leading to the expression of specific genes in conversion of genetic information into protein-based processes. these genes may be involved in a variety of biological processes, such as transcriptional and post-transcriptional regulation of gene expression, GO:0007165, cell-cycle related processes, GO:0003677, regulation of transcription, regulation of protein abundance, GO:0006338, MESH:D054875, protein-protein interaction]][[GO:0030198, GO:0000988, receptor signaling pathway, GO:0007269, GO:0019725, GO:0006508, immunological responses, GO:0016049, GO:0003677, GO:0006629]]0.05
604text-davinci-003no_synopsisHALLMARK_FATTY_ACID_METABOLISM-0[[GO:0006631, oxidation of lipids, GO:0006695, GO:0005977, GO:0009117, GO:0006862, GO:0009165, electron transport activity, enzyme regulation, regulation of metabolic pathways, GO:0006915]][[metabolic pathways; cellular functions; energy metabolism; lipid metabolism; amino acid metabolism; dna damage repair; cell signaling.\\nmechanism: the genes listed here are likely involved in the various metabolic pathways and cellular functions, perhaps through the production of enzymes, MESH:D011506, or other molecules that contribute to energy metabolism, GO:0006629, amino acid metabolism, dna damage repair, cell signaling]]0.00
605text-davinci-003no_synopsisHALLMARK_FATTY_ACID_METABOLISM-1[[GO:0008152, energy production and storage, lipid metabolism and transport, acetyl-coa biosynthesis and catalysis, oxidation, GO:0006631]][[GO:0006629, cell cytoskeleton, GO:0008610, GO:0016042, lipid transportation, GO:0034440, cell membrane biogenesis, GO:0048870, cell traffic, cell signaling]]0.00
606text-davinci-003no_synopsisHALLMARK_G2M_CHECKPOINT-0[[GO:0051726, GO:0006260, GO:0006338, cyclin b-cdk1 activation, cks1b, cdc25a, wee1, cdc20, apc/]][[GO:0006260, GO:0006351, GO:0051726, protein binding/interaction, chromatin modifiers/modification, GO:0006281, GO:0000988, GO:0006397, GO:0006915, ubiquitination and proteasomal degradation]]0.12
607text-davinci-003no_synopsisHALLMARK_G2M_CHECKPOINT-1[[nuclear processes, GO:0006260, gene transcription, GO:0006338, GO:1901987, GO:0006281, GO:0010467, GO:0010468]][[genes involved in the list are mainly associated with dna replication, cell division and related functions. enriched terms include \"cell cycle\", \"dna replication\", \"chromatin modification\", \"transcription regulation\", \"cell division\", \"dna repair\", \"transcriptional regulation\", \"chromosome segregation\".\\n\\nmechanism: these genes likely play a role in the coordination of the many steps and activities involved in dna replication, GO:0051301, and related cellular processes. the cell cycle is an area of particular interest due to its critical role in the growth and division of cells. dna replication, modification, repair occur during cell division in order to produce maintain copies of genetic information. chromatin modifications occur during cell division in order to package regulate genomic information. transcriptional regulation involves the control of gene expression the production of proteins other materials essential for the maintenance of cellular functions. chromosome segregation cell division serve to divide replicated genetic material into daughter cells]]0.00
608text-davinci-003no_synopsisHALLMARK_GLYCOLYSIS-0[[developmental process: digit development, GO:0001525, GO:0030154, GO:0005488, transporting, GO:0008152, GO:0008152, cell signalling]][[the genes in this list are involved in a variety of cellular processes including protein translation, GO:0070085, regulation of ion channels, gene transcription and dna replication. the enriched terms identified are: translation; glycosylation; ion channels; gene transcription; and dna replication.\\n\\nmechanism: the common underlying mechanisms of the genes in this list likely involve cellular processes such as protein translation, GO:0070085, regulation of ion channels, gene transcription and dna replication. these processes are essential for the regulation of cell functions and the maintenance of a stable organism]]0.00
609text-davinci-003no_synopsisHALLMARK_GLYCOLYSIS-1[[GO:0005975, MESH:D004734, GO:0046785, dna binding and replication, actin cytoskeleton dynamics, ion channel regulation, transcriptional regulation, GO:0007155]][[structural proteins, GO:0006096, GO:0006098, GO:0006099, GO:0007155, GO:0030166, extracellular matrix formation, cytoskeletal assembly]]0.07
610text-davinci-003no_synopsisHALLMARK_HEDGEHOG_SIGNALING-0[[GO:0009653, GO:0022008, GO:0016049, GO:0030154, GO:0001764, thalamocortical pathway development, GO:0001764, GO:0007399, neural crest migration]][[the provided genes are involved in a variety of different processes ranging from morphogenesis, development and growth of the digits/limbs, neuronal migration and regulation of cell proliferation. the underlying biological mechanism might be related to the modulation of cell migration, development of neural connections, formation of complex structures, maintenance of body plan and tissue development. enriched terms are: morphogenesis, digit/limb development, GO:0001764, GO:0042127, modulation of cell migration, development of neural connections, formation of complex structures, maintenance of body plan, GO:0009888]]0.06
611text-davinci-003no_synopsisHALLMARK_HEDGEHOG_SIGNALING-1[[GO:0009653, GO:0007155, GO:0032502, GO:0007268, GO:0008283, GO:0016477, GO:0030154, MESH:D009473]][[neuron formation, GO:0007155, migration, GO:0007165, GO:0048729, GO:0007399]]0.08
612text-davinci-003no_synopsisHALLMARK_HEME_METABOLISM-0[[GO:0055085, MESH:D004734, GO:0003735, GO:0003676, GO:0015031, negative regulation of transcription, regulation of transcription, positive regulation of transcription, GO:0071840, iron metabolism, GO:0007165, GO:0045087, GO:0042803, GO:0051276, GO:0050794, GO:0016569, GO:0008380, GO:0005515, GO:0000075, GO:0006006, GO:0000088, GO:0009116]][[GO:0044237, energy production and transport, cytoskeleton modification, cytoskeleton remodelling, GO:0007155, MESH:D004735, MESH:M0496924, cellular transport, cellular reorganization]]0.00
613text-davinci-003no_synopsisHALLMARK_HEME_METABOLISM-1[[GO:0048468, GO:0010467, GO:0048513, nucleic acid metabolism, transcriptional regulation, GO:0006259, GO:0016070, cytoskeletal dynamics, GO:0007165, GO:0006412]][[MESH:D047108, GO:0001501, GO:0048513, GO:0009653, GO:0040007, GO:0002376, GO:0048870, GO:0003707, receptor signaling pathway, GO:0006810, GO:0006897, GO:0019725]]0.05
614text-davinci-003no_synopsisHALLMARK_HYPOXIA-0[[gene enrichment analysis of the gene list showed that the majority of genes are involved in cellular proliferation, GO:0006915, GO:0006811, GO:0005102, and development. the enriched terms associated with this list include cell proliferation, GO:0006915, GO:0006811, GO:0005102, cell signaling, transcriptional regulation, and development.\\n\\nmechanism: the genes are likely involved in an intricate, interconnected biological network that involves numerous signaling pathways and transcription factors necessary for cellular proliferation, GO:0006915, ion transport and receptor binding. these gene functions result in the regulation of numerous cellular processes and ultimately the development of various diseases. in addition, the genes may be regulating a number of other processes such as metabolism, cell-cell communication, energy production]][[GO:0007049, remodeling proteins, stress response proteins, calcium signaling proteins, hypoxia-inducible factor proteins, GO:0000981, chromatin-associated proteins, MESH:D010770]]0.00
615text-davinci-003no_synopsisHALLMARK_HYPOXIA-1[[GO:0048468, cell metabolism, transcription regulation, GO:0010468, GO:0006974, GO:0007155, GO:0030154, GO:0042440, MESH:M0352612, GO:0006412, GO:0051726, MESH:D004734]][[GO:0032502, cell structure and movement, cell cycle and division, GO:0007165, GO:0006810, energy production]]0.00
616text-davinci-003no_synopsisHALLMARK_IL2_STAT5_SIGNALING-0[[GO:0016049, cell regulation, GO:0009988, MESH:D007109, signal transduction and regulation, GO:0032502, transcriptional regulation, GO:0030198, cytokine-receptor-mediated signaling pathway]][[immunological function, GO:0030036, MESH:D011956, pro-inflammatory regulation]]0.00
617text-davinci-003no_synopsisHALLMARK_IL2_STAT5_SIGNALING-1[[this list of genes are involved in developmental processes, GO:0006955, GO:0006954, GO:0007165, and cell adhesion functions. the enriched terms are \"development\"; \"signal transduction\"; \"cell adhesion\"; \"immune response\"; \"inflammation\"; \"transmembrane transport\"; \"protein metabolism\"; \"cardiovascular function\".\\n\\nmechanism: the underlying biological mechanisms involves the coordination of different pathways, genes and proteins. these genes are involved in cellular processes and regulation, including cell proliferation, differentiation, adhesion and migration, GO:0007165, and immunity. the genes also influence signaling pathways, protein metabolism and other functions that have roles in cardiovascular and carcinogenesis. the mechanisms through which these genes affect development, GO:0006954, other immunological responses are complex dependent on the coordination between multiple pathways]][[MESH:D007109, GO:0006954, GO:0016049, differentiation, GO:0032502, GO:0007165]]0.18
618text-davinci-003no_synopsisHALLMARK_IL6_JAK_STAT3_SIGNALING-0[[pain sensing and signal transduction, GO:0006935, GO:0019221, leukocyte transendothelial migration, GO:0006955, GO:0030168]][[cell signaling, GO:0001816, cytokine regulation, MESH:D005786, transcription regulation, GO:0007155]]0.00
619text-davinci-003no_synopsisHALLMARK_IL6_JAK_STAT3_SIGNALING-1[[GO:0007165, MESH:D056747, immune signaling, transcription regulation, cytokine regulation, GO:0030155, MESH:D005786, cell growth regulation, metabolism regulation, MESH:D002470, cell death regulation, antifungal immunity]][[cytokine regulation, chemokine regulation, interleukin regulation, cellular differentiation, cell motility and adhesion, GO:0007165, GO:0006954]]0.12
620text-davinci-003no_synopsisHALLMARK_INFLAMMATORY_RESPONSE-0[[MESH:M0000731, GO:0006954, GO:0007165, transcription regulation, intercellular signaling, GO:0045087, MESH:D056704]][[this list of genes is significantly enriched for the functions of cell signalling, cytokine mediated immunity, receptor signalling, and tissue morphogenesis. furthermore, the list contains several genes associated with the immune response, including tlrs and ifns, as well as cytokines and chemokines such as ccl17, ccl20, cxcl10, cxcl9, ifnar1, tnfrsf1b, and tnfsf10. in addition, several receptors were found to be enriched on the list, including gpr132, axl, c3ar1, MONDO:0043317, and ccr7. finally, key genes involved in tissue morphogenesis were also found on the list, such as adgre1, edn1, btg2, ccl2, tacr1, and cxcr6.\\n\\nmechanism: \\nthe underlying mechanism for this enrichment of genes is likely related to the common activities of cell signalling, cytokine mediated immunity and tissue morphogenesis. the list of genes is likely regulating common processes such as cell-cell communication and inflammation. additionally, the list of genes may be involved in the development and maintenance of tissue structures, such as muscle tissue]]0.00
621text-davinci-003no_synopsisHALLMARK_INFLAMMATORY_RESPONSE-1[[immune cell signaling, GO:0006928, cell surface receptor activity, GO:0006954, GO:0016477, cell–cell interactions, immune cell receptor-mediated signaling]][[GO:0006955, cellular activation, receptor-coupled pathways, transcriptional regulation, cytokine and cytokine receptor binding, GO:0006629, GO:0007155]]0.00
622text-davinci-003no_synopsisHALLMARK_INTERFERON_ALPHA_RESPONSE-0[[GO:0006954, neutroph]][[analysis of this list of genes reveals that they are all involved in the functioning of the immune system in some way, either through regulation of inflammatory response pathways, recognition of foreign agents, or production of molecules defending against potentially harmful intruders. the enriched terms include \"immune system regulation\"; \"inflammatory response\"; \"foreign agent recognition\"; \"antimicrobial defense\"; \"interferon signaling\"; \"antiviral defense\". \\n\\nmechanism: the genes in this list combined likely regulate a wide variety of immune system functions, including modulating inflammation, recognizing and responding to foreign antigens, producing effector molecules against potentially harmful microorganisms, promoting interferon signaling cascades to defend from viral invasion]]0.00
623text-davinci-003no_synopsisHALLMARK_INTERFERON_ALPHA_RESPONSE-1[[interferon signalling pathway, interferon gamma activity, interferon regulatory factor activity, status response to interferon, GO:0006915, GO:0008289, GO:0005509, GO:0002446]][[GO:0006955, GO:0006954, cytokine signaling, interferon response, GO:0006355, interferon-stimulated genes]]0.00
624text-davinci-003no_synopsisHALLMARK_INTERFERON_GAMMA_RESPONSE-0[[GO:0006955, cell signaling, cytokine response, interferon response, nuclear factor kappab-dependent transcriptional regulation]][[MESH:M0000731, GO:0019882, GO:0006954, chemokine signaling, GO:0007155, cytokine interactions]]0.00
625text-davinci-003no_synopsisHALLMARK_INTERFERON_GAMMA_RESPONSE-1[[MESH:D007109, interleukin regulation, transcription regulation, GO:0006954, cell signaling, GO:0006915]][[interferon signaling, antigen processing, presentation, and recognition, cytokine signaling, cell cycle and dna damage response, GO:0006915]]0.10
626text-davinci-003no_synopsisHALLMARK_KRAS_SIGNALING_DN-0[[GO:0060348, GO:0009653, growth maintenance, GO:0007267, cell-cell communication, GO:0036211, GO:0006810]][[digit development, neural development, GO:0002520, transcriptional regulation, g-protein coupled receptors, MESH:D011494, MESH:D020662]]0.00
627text-davinci-003no_synopsisHALLMARK_KRAS_SIGNALING_DN-1[[GO:0009653, cell-cell communication, GO:0032502, hormone regulation, cellular differentiation, cell-cycle, cell-signalling]][[our analysis revealed the enrichment of the gene functions related to development, GO:0007165, transcription and metabolism. specifically, some of the enriched terms include cellular development, GO:0016049, GO:0001501, GO:0048598, cell junction organization and assembly, GO:0007165, GO:0007049, GO:0006351, and cellular metabolism.\\n\\nmechanism: these gene functions may be related to the biological mechanism of growth, differentiation, and development of cells. the signals and transcription are likely involved in regulating and controlling these processes, as well as providing energy through metabolic pathways. additionally, the cell junction processes are likely involved in the coordination and communication between cells, which is essential to development]]0.00
628text-davinci-003no_synopsisHALLMARK_KRAS_SIGNALING_UP-0[[GO:0007165, GO:0000902, GO:0050896, GO:0001525, GO:0065009, GO:0030198]][[GO:0007165, GO:1901987, cell-to-cell adhesion]]0.12
629text-davinci-003no_synopsisHALLMARK_KRAS_SIGNALING_UP-1[[GO:0009653, GO:0009888, cell signaling, immune regulation, transcription modulation, GO:0007165, GO:0007155, GO:0016477]][[integrin, chemokine receptor, MESH:D011494, g-protein-coupled receptor, cytoskeleton proteins, cell-extracellular matrix interaction, type i ifn-mediated innate immunity, wnt signaling, MESH:D020558, MESH:D010740, MESH:D008565, MESH:D016326, receptor tyrosine kinase, toll-like receptor signaling, tlr adaptor proteins]]0.00
630text-davinci-003no_synopsisHALLMARK_MITOTIC_SPINDLE-0[[the human genes abi1, abl1, abr, actn4, akap13, alms1, MONDO:0008780, anln, GO:0005680, arap3, arf6, arfgef1, arfip2, arhgap10, arhgap27, arhgap29, arhgap4, arhgap5, arhgdia, arhgef11, arhgef12, arhgef2, arhgef3, arhgef7, arl8a, atg4b, MESH:D064096, bcar1, bcl2l11, bcr, bin1, birc5, brca2, bub1, capzb, ccdc88a, ccnb2, cd2ap, cdc27, cdc42, cdc42bpa, cdc42ep1, cdc42ep2, cdc42ep4, cdk1, cdk5rap2, cenpe, cenpf, cenpj, cep131, cep192, cep250, cep57, GO:0047849]][[GO:0007049, GO:0007155, cytoskeletal organization, GO:0004672, GO:0003924]]0.00
631text-davinci-003no_synopsisHALLMARK_MITOTIC_SPINDLE-1[[cytoskeletal organization, GO:0016477, GO:0051301, GO:0006260, GO:0006281, GO:0006605, GO:0065007]][[GO:0051301, GO:0006468, GO:0006338, GO:0008017, microtubule organization, GO:0051225, GO:0007059, GO:0051305, cell-cycle control, GO:0140014]]0.06
632text-davinci-003no_synopsisHALLMARK_MTORC1_SIGNALING-0[[the human genes abcf2, acaca, acly, acsl3, actr2, actr3, add3, adipor2, ak4, aldoa, arpc5l, asns, atp2a2, atp5mc1, atp6v1d, MESH:D064096, bcat1, bhlhe40, btg2, bub1, cacybp, calr, canx, ccnf, ccng1, cct6a, cd9, cdc25a, cdkn1a, cfp, cops5, coro1a, cth, ctsc, GO:0038147, cyb5b, cyp51a1, dapp1, ddit3, ddit4, ddx39a, dhcr24, dhcr7, GO:0004146, ebp, edem1, eef1e1, egln3, eif2s2, elovl5, elovl6, eno1, eprs1, ero1a, etf1, MONDO:0100101, MONDO:0100102, fdxr, fgl2, MESH:D010649]][[genes in this list are involved in various aspects of cellular metabolism, GO:0065007, and development.a number of the genes have roles in energy production and metabolism such as, atp2a2, aldoa, MONDO:0009214, fao1, fgl2, gapdh, gbe1, MONDO:0015408, glrx, MONDO:0005775, me1, phgdh, and pgm1. there is a strong presence of genes involved in protein synthesis and transport, including the ribosomal proteins, the eukaryotic translation factors and initiation factors (eif2s2, eif1e1, elovl5, and elovl6). this gene set is also enriched for a number of ubiquitin and ubiquitin-like proteins (ube2d3, ufm1, uso1, tomm40, hspd1, hspe1, sytl2, nherf1, and hk2). many of these genes are involved in regulation through multiple pathways including regulation of transcription (add3, actr2, actr3, cct6a, gga2, gdh2, mef2b, ykt]]0.08
633text-davinci-003no_synopsisHALLMARK_MTORC1_SIGNALING-1[[GO:0006412, MESH:D004734, cellular transport, GO:0006955, GO:0035194, mitochondrial oxidative phosphorylation, GO:0006915, GO:0016310, GO:0006096, GO:0006914]][[GO:0006412, transcription regulation, GO:0009653, GO:0016049, GO:0007165, GO:0008152, GO:0006629, cellular translation]]0.06
634text-davinci-003no_synopsisHALLMARK_MYC_TARGETS_V1-0[[rna biogenesis, protein synthesis biosynthesis, atp-binding, cytoskeleton organization and assembly, GO:0006351, GO:0006338, GO:0007165, GO:0010467, GO:0006413, MESH:M0439896, GO:0006260]][[GO:0006412, GO:0036211, GO:0006260, GO:0051726, transcription regulation, GO:0016049, GO:0048468, gene expression.\\nmechanism: the genes may constitute a pathway in which they coordinate together to regulate cell growth, development, and gene expression]]0.06
635text-davinci-003no_synopsisHALLMARK_MYC_TARGETS_V1-1[[GO:0000394, GO:0051028, MESH:M0439896, GO:0006412, GO:0042254, GO:0035194, GO:0006338]][[developmental regulation, energy production, GO:0006412, structural maintenance of cell components, GO:0006260, transcription regulation, protein assembly]]0.08
636text-davinci-003no_synopsisHALLMARK_MYC_TARGETS_V2-0[[genes in this list are primarily involved in cell development, including the processes of rna metabolism, dna replication and cell cycle control. enriched terms include: rna metabolism; dna replication; cell cycle control; chromatin regulation; transcription regulation; cell differentiation; gene expression; and protein synthesis.\\n\\nmechanism: the genes in this list are part of a complex network of molecular pathways involved in regulating the expression, replication and maintenance of genetic material. this includes the transcription, splicing and translation of rnas as well as the replication and repair of dna. the multiple genes in this list suggest coordination and control of various steps in these processes, such as chromatin regulation, which is directly responsible for how genetic material is packaged and regulated. additionally, the genes may be involved in regulating cell cycle progression, transcription regulation and cell differentiation]][[protein post translational modification, GO:0016310, GO:0006351, GO:0006412, GO:0042254]]0.00
637text-davinci-003no_synopsisHALLMARK_MYC_TARGETS_V2-1[[GO:0001775, GO:0008283, GO:0006260, dna transcription, rna translation.\\nmechanism: the genes may indicate an underlying biological pathway involving the coordinated expression of these gene sets to regulate the cell cycle, dna replication, transcription, and translation in order to enable cell proliferation]][[transcription regulation, GO:0006338, nucleosome remodeling, GO:0006260, nuclear localization, GO:0007165, GO:0016567, GO:0006468]]0.08
638text-davinci-003no_synopsisHALLMARK_MYOGENESIS-0[[gene expression and structure, cytoskeletal structure and dynamics, calcium regulation and signaling, cell adhesion and migration, cell death biochemistry, metabolic regulation]][[genes in this list are associated with various cellular functions, including cell cycle regulation, developmental pathways, contractile force generation, protein synthesis and degradation, GO:0006915, GO:0000988, and metabolic processes. enriched terms include: cell cycle; cell differentiation; transcriptional regulation; intracellular signaling; muscle contraction; metabolism; apoptosis; protein synthesis; protein degradation.\\n\\nmechanism:\\n\\nthe genes in this list code for proteins involved in a range of cellular processes, including transcription factors that regulate gene expression, receptors that initiate intracellular signaling cascades, enzymes involved in metabolic pathways or apoptosis, and ion channels involved in muscle contraction and cell cycle regulation. these proteins interact to regulate the expression and activity of other proteins, impacting the activity of many important pathways that together coordinate cell growth, differentiation, MESH:D009068, GO:0008152]]0.00
639text-davinci-003no_synopsisHALLMARK_MYOGENESIS-1[[GO:0031012, GO:0005856, UBERON:0005090, GO:0032502, neuromuscular structure, MESH:D007473, GO:0006811]][[the genes that were analyzed were related to development, cell signalling, GO:0008152, GO:0065007, GO:0006936, MESH:D055550, and transport. the enriched terms were cellular development, actin cytoskeleton regulation, cell migration and adhesion, GO:0051726, calcium homeostasis and signaling, GO:0006936, GO:0006119, receptor tyrosine kinase signaling, apoptosis and programmed cell death, GO:0030198, GO:0016567, GO:0042632, metabolism and energy production, cell death and apoptosis, cytoskeletal protein binding and regulation of transcription and translation.\\n\\nmechanism: the underlying biological mechanism or pathways involved in these genes include regulation of muscle contraction, cell adhesion and migration, calcium homeostasis, protein ubiquitination and stability, receptor signaling, GO:0051726, GO:0006119, GO:0008219, and regulation of transcription and translation. these mechanisms are essential for cellular development and function, and thus, are enriched in these gene list]]0.00
640text-davinci-003no_synopsisHALLMARK_NOTCH_SIGNALING-0[[MESH:D047108, GO:0051726, GO:0019722, notch signaling down-regulation, wnt signaling, hedgehog signaling, GO:0000902]][[GO:0009653, GO:0048513, GO:0009888, GO:0001709, MESH:D002450, notch receptor signaling, wnt signaling, transcription factor signaling]]0.07
641text-davinci-003no_synopsisHALLMARK_NOTCH_SIGNALING-1[[these genes are involved in a wide range of functions related to signaling, development, and transcriptional regulation, indicating an involvement in a variety of cellular pathways. enriched terms include: cell signaling, GO:0007399, GO:0030154, wnt signaling, notch signaling, hedgehog signaling, transcription factor regulation, GO:0006338, e3 ubiquitin ligase.\\n\\nmechanism: the likely underlying biological mechanism is a complex network of interactions between these genes and their pathways, forming a web of signaling molecules that regulate cell growth, differentiation, apoptosis and other cellular processes. the genes and pathways involved in the network are likely to interact in a dynamic manner]][[GO:0008283, GO:0009653, GO:0032502, nerve system differentiation, transcription regulation, wnt signalling pathway, GO:0007219]]0.00
642text-davinci-003no_synopsisHALLMARK_OXIDATIVE_PHOSPHORYLATION-0[[mitochondrial activity, GO:0022900, GO:0006119, metabolic regulation, MESH:D065767]][[the list of genes provided are primarily involved in energy metabolism, GO:0007585, and the electron transport chain. specifically, terms such as \"oxidative phosphorylation\", \"mitochondrial electron transport chain\", and \"tricarboxylic acid cycle\" are found to be significantly over-represented.\\n\\nmechanism: the genes provided are involved in the production of atp through metabolic pathways such as oxidative phosphorylation, GO:0005746, and the tricarboxylic acid cycle. these molecules, along with other regulatory proteins, facilitate the flow of electrons to generate energy in the form of atp. this energy is used by cells to carry out metabolic reactions and various cellular processes]]0.00
643text-davinci-003no_synopsisHALLMARK_OXIDATIVE_PHOSPHORYLATION-1[[GO:0005746, electron transfer proteins, proton ion transportation proteins, oxidative phosphorylation proteins, metabolite-binding proteins, atp synthesis proteins]][[mitochondrial electron transport chain complex activity, GO:0006120, GO:0005747]]0.00
644text-davinci-003no_synopsisHALLMARK_P53_PATHWAY-0[[cytoskeletal reorganization, calcium homeostasis, ubiquitin-proteasome pathway, GO:1901987, transcriptional regulation, GO:0006397, GO:0006974]][[analysis of this list of genes suggests a function related to cell cycle regulation, GO:0006915, and protein translation. the enriched terms include 'cell cycle regulation', 'apoptosis', 'protein translation', 'transcription regulation', 'intracellular protein transport', 'protein synthesis', and 'dna repair'.\\n\\nmechanism: the list of genes may be associated with a mechanism related to the regulation of cell cycle transitions and the integration of external signals to regulate gene transcription, protein translation and stability, and cellular apoptosis. this could involve some combination of signal transduction, GO:0006355, GO:0043687, GO:0006281]]0.00
645text-davinci-003no_synopsisHALLMARK_P53_PATHWAY-1[[GO:0006351, chromatin dynamics, GO:0007155, MESH:D016207, GO:0007049, dna damage repair, cell signaling, GO:0016049, GO:0006915, immune modulation]][[gene expression and protein metabolism are likely to be enriched. specifically, the genes are likely involved in protein folding and transport, GO:0016567, transcriptional regulation, GO:0051726, protein-protein interactions, and signal transduction. \\nmechanism: these genes likely play a role in common metabolic, GO:0023052, and regulatory pathways.\\nubiqutination terms: rchy1, hexim1, upp1, pom121, procr, tap1, phlda3, wwp11; \\ntranscription factors:cd81, sat1, ercc5, ralgdh, irak1, aen, tob1, stom, MONDO:0100339, rap2b, tm7sf3, lif, MESH:C058179, ccp110, baiap2, tnfsf9, dcxr, eps8l2, ifi30, fdxr, elp1, itgb4, hbegf, irag2, ccnd2, sertad3, mknk2, retsat, ip6k2, hmox1, zfp36l1, epha2, tpd]]0.00
646text-davinci-003no_synopsisHALLMARK_PANCREAS_BETA_CELLS-0[[GO:0031016, GO:0006006, GO:0048870, neural development]][[GO:0031016, GO:0007399, development of neural structures, GO:0048513, transcription regulation, GO:0009653, cell-to-cell adhesion, GO:0006412, hormonal metabolism, hormonal signaling]]0.08
647text-davinci-003no_synopsisHALLMARK_PANCREAS_BETA_CELLS-1[[GO:0009653, neuronal development, GO:0007165, GO:0030073, transcription regulation, GO:0000988]][[GO:0022008, GO:0008152, GO:0006355, GO:0006412, GO:0009653, body patterning and organization, neurological system development, GO:0030154]]0.08
648text-davinci-003no_synopsisHALLMARK_PEROXISOME-0[[enrichment test suggested genes are skewed towards genes involved in development, metabolic control, transport, cell cycle and homeostasis, as well as transcriptional regulation.\\n\\nmechanism: these genes appear to be involved in a diverse range of processes, suggesting multiple pathways contributing to the physiological functions of these genes. for instance, abcb1, abcb4 and abcb9 are involved in medication transport, abcc5 and abcc8 are involved in atp coupling, acaa1 is involved in fatty acid metabolism, alb is involved in heme metabolism, aldh1a1, aldh9a1, atxn1 and bcl10 are involved in transcriptional regulation, ctbp1 and ctps1 are involved in ubiquitination, dhcr24 and dhrs3 are involved in cholesterol biosynthesis, fabp6 is involved in bile acid transport, fads1 is involved in fatty acid desaturase, fis1 and gnpat are involved in lipoic acid synthesis and mitochondrial fatty acid metabolism, gstk1 is involved in gst-mediated detoxification, hmgcl is involved in steroidogenesis, hras, hsd11b2, hsd17b11]][[GO:0006629, stress response, GO:0009299, GO:0006281, skeletal and cartilage development, GO:0016477, metabolic enzymes, MESH:D002352]]0.00
649text-davinci-003no_synopsisHALLMARK_PEROXISOME-1[[GO:0006629, GO:0008202, transcription regulation, GO:0051726]][[GO:0008152, GO:0006351, GO:0065007, GO:0006810, GO:0007165, GO:0006412, GO:0030154, GO:0006260, GO:0036211, membrane trafficking]]0.00
650text-davinci-003no_synopsisHALLMARK_PI3K_AKT_MTOR_SIGNALING-0[[GO:0010467, dna repair & maintenance, MESH:M0496065, cellular signaling pathways, GO:0006629]][[MESH:M0023730, GO:0009653, GO:0030154, tyrosine kinase activity, GO:0038023]]0.00
651text-davinci-003no_synopsisHALLMARK_PI3K_AKT_MTOR_SIGNALING-1[[GO:0051726, gene transcription, transcription factor activation, MESH:M0023730, MESH:D011494, receptor proteins, GO:0006412, GO:0016049, GO:0008283, GO:0030154]][[cell signaling, GO:0019538, GO:0006629, transcription regulation, GO:1901987, GO:0007165, receptor signaling, GO:0070085, GO:0016301, GO:0006915, g-protein interactions, transcriptional regulation]]0.00
652text-davinci-003no_synopsisHALLMARK_PROTEIN_SECRETION-0[[gene expression regulation; co-translational protein targeting; clathrin-mediated endocytosis; endosomal protein trafficking; vesicle transport; exocytosis; receptor and ligand-mediated signaling; development and organ morphogenesis.\\nmechanism: the identified genes are likely involved in a variety of biological processes related to endocytosis, vesicle trafficking and transport, receptor and ligand-mediated signaling, MESH:D005786, co-translational protein targeting, and organ morphogenesis. these processes can be clustered into several pathways, including the calcineurin-mediated endocytosis pathway, the mapk signaling pathway, the wnt/beta-catenin signaling pathway, the clathrin-mediated endocytosis pathway, the endosomal protein trafficking pathway, the vesicle transport pathway, the exocytosis pathway, the receptor ligand-mediated signaling pathways]][[cell membrane fusion, GO:0016192, intracellular trafficking, predominant cargo proteins, GO:0006900, membrane remodeling]]0.00
653text-davinci-003no_synopsisHALLMARK_PROTEIN_SECRETION-1[[genes belonging to this list are mainly involved in endocytosis, GO:0016192, MESH:D021381, and membrane fusion. the enriched terms include: endocytosis; vesicle trafficking; protein trafficking; membrane fusion; membrane transport; cytoskeleton organization; signal transduction; receptor internalization; and protein trafficking pathways.\\n\\nmechanism: the common characteristics shared by the genes suggest that they are all involved in some aspect of the endocytosis pathway. this biological mechanism involves signal transduction by which a signal (chemical or physical) can pass through a cell membrane and allow the cell to take up extracellular substances. through receptor internalization, molecules, like hormones, can be shuttled into intracellular vesicles and undergo further signaling events. the sequential vesicle trafficking steps then enable the cargo to be transported to their final destination. the proteins play various roles in facilitating membrane fusion, GO:0036211, GO:0007010, and vesicle transport. all of these activities act in concert to usher signals, MESH:D011506, other substances into the cell]][[GO:0043687, GO:0006457, GO:0006412, GO:0006897, GO:0009311, lysosomal trafficking]]0.00
654text-davinci-003no_synopsisHALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0[[redox regulation, antioxidant defense, detoxification of reactive oxygen species, peroxisomal biogenesis, MESH:M0572479, cell metabolism]][[GO:0008152, oxidative damage resistance, GO:0006281, cellular metabolic regulation, GO:0006915, regulatory pathway, GO:0006457, GO:0006749]]0.00
655text-davinci-003no_synopsisHALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1[[redox balance regulation, GO:0008152, GO:0051726, transcriptional regulation]][[this list of genes is enriched for terms related to oxidative stress, GO:0008152, and immune system function. specifically, the genes represent proteins involved in oxygen-sensing, anti-oxidation, redox regulation, GO:0006281, the stress response, and cytokine signaling.\\n\\nmechanism:\\nthe underlying biological mechanism of the gene list is likely the cellular response to oxidative stress. oxidative stress is a term used to describe a disruption in the balance of antioxidant molecules and reactive oxygen species. these reactive molecules can cause damage to the cell, and thus the relevant genes likely help the cell to counteract this damage by regulating redox status, mediating oxidant stress, and participating in dna repair and other defense mechanisms. additionally, some of these genes are involved in cytokine signaling, which helps to aid the immune system in defending against potential oxidative insults]]0.06
656text-davinci-003no_synopsisHALLMARK_SPERMATOGENESIS-0[[cell signaling, protein regulation, GO:1901987, GO:0009653, GO:0048513, cytoskeletal regulation]][[GO:1901987, GO:0006338, GO:0016567, GO:0006260, GO:0051225, GO:0006997]]0.09
657text-davinci-003no_synopsisHALLMARK_SPERMATOGENESIS-1[[cell cycle checkpoint regulation, GO:0009653, cell signaling, MESH:D003598, organ development]][[the list of genes provided are involved in diverse processes, such as cell structure and organization, GO:0007165, transcriptional regulation and other metabolic activities. the enriched terms from performing a term enrichment test are cell cycle, GO:0051301, GO:0016569, development and differentiation, cell signaling and signal transduction, GO:0006397, transcriptional regulation, and metabolic processes.\\n\\nmechanism:\\nthe genes provided are believed to be involved in a general mechanism of cell organization and function. the enriched terms are suggestive of the genes being related to fundamental processes such as cell cycle regulation, GO:0051301, transcriptional regulation, GO:0016569, and signal transduction. through the regulation of the genes, they are thought to be capable of controlling the organization and structure of cells, as well as metabolism and other cellular activities. furthermore, these pathways likely interact with each other in a complex manner, thereby allowing for intricate coordination between the genes in order to precisely tune process]]0.00
658text-davinci-003no_synopsisHALLMARK_TGF_BETA_SIGNALING-0[[mapk pathway, tgf-β signaling pathway, wnt/β-catenin pathway, GO:0035329, transcriptional regulation, muscle morphogenesis, GO:0048729, regulation of g-protein signaling, GO:0006954]][[genes in this set are related to morphogenesis, GO:0007155, immune signaling, and transcriptional regulation. enriched terms include: morphogenesis, GO:0007155, immune signaling, transcriptional regulation, digit development, GO:0007049, protein-protein interaction, GO:0008083, and regulation of transcriptional activity.\\n\\nmechanism: morphogenesis can be regulated by the activity of kinases, cell adhesion can be mediated by the expression of cell adhesion molecules, and immune signaling can be regulated by the activity of cytokines, MESH:D018121, and transcription factors. the transcriptional regulation of these genes can be mediated by transcription factors and the regulation of transcriptional activity can be mediated by modulators of tfs, such as kinases and ubiquitin ligases. protein-protein interactions can occur between the different genes, signaling from growth factors can affect the expression of genes in this set]]0.04
659text-davinci-003no_synopsisHALLMARK_TGF_BETA_SIGNALING-1[[these genes are involved in processes related to cell development, GO:0009653, calcium and calcium-dependent signaling, MESH:D017978, smad pathway and extracellular matrix proteins.\\n\\nmechanism: the mechanism underlying this gene list is likely related to signal transduction pathways. these may involve cell surface receptors which bind growth factors, such as tgfb1 and bmpr2, and transduce the signal through the smad pathway via the fkbp1a, bmpr1a, smurf1, smad1, ltbp2, thbs1, arid4b, ppm1a, and ctnnb1 proteins to influence the regulation of gene expression and cell fate. moreover, other molecules such as xiap, ube2d3, nog, slc20a1, serpine1, bcar3, rhoa, MESH:D045683, hipk2, ppp1ca, smad7, junb, smad6, ppp1r15a, tjp1, and ifngr2 may be involved in the signal transduction pathway. in addition, the calcium and calcium-dependent signaling by the tg]][[transcriptional regulation, GO:0007165, GO:0051726, protein kinase pathways, GO:0006412, GO:0048468, GO:0008283, GO:0030054, cytoskeletal organization]]0.00
660text-davinci-003no_synopsisHALLMARK_TNFA_SIGNALING_VIA_NFKB-0[[GO:0032502, GO:0006954, MESH:D056747, cell signaling, MESH:M0496924, GO:0009653, GO:0009888, GO:0008283, GO:0006915, immune system response, MESH:M0496924]][[GO:0002224, GO:0032502, GO:0006954, immune-response regulation, nfkb, GO:0004707, GO:0010467, pro-inflammatory molecules]]0.12
661text-davinci-003no_synopsisHALLMARK_TNFA_SIGNALING_VIA_NFKB-1[[gene transcription, actin maturation, cytoskeleton formation, signaling complex assembly, interleukin receptor signaling, GO:0051170, cytokine receptor signaling, nf-kappab signaling pathway, cytokine-mediated signal transduction, GO:0006367, MESH:D005786, cytokine receptor signaling pathway, GO:0010737, GO:0035556]][[cytokine-mediated signaling, antigen-receptor mediated signaling, GO:0042100, cytokine expression and release, immunoregulatory interactions, GO:0051092, interferon (ifn) signaling]]0.00
662text-davinci-003no_synopsisHALLMARK_UNFOLDED_PROTEIN_RESPONSE-0[[GO:0009299, GO:0042254, GO:0006457, nucleolar activity, spliceosomal activity, protein production, GO:0015031, GO:0006396, GO:1901987]][[GO:0006412, GO:0042254, GO:0006413, GO:0006457, GO:0006414, GO:0015833, peptide assembly, chaperone mediated protein folding]]0.13
663text-davinci-003no_synopsisHALLMARK_UNFOLDED_PROTEIN_RESPONSE-1[[GO:0008152, GO:0006412, GO:0043687, GO:0016310, pepetide binding and metabolism, protein structure and folding, rna synthesis and processing, GO:0000394, GO:0010467, GO:0051726, GO:0006915, GO:0007165, GO:0006281]][[analysis of this gene list has revealed that the functions enriched in the gene set include translation and translation initiation (exosc2, eif4a3, MESH:D039561, eif4g1, eif4a2); ubiquitination (ern1, skp1, herpud1, ube2g2, ube2l3); and protein folding and stability (atf3, fkbp14, dnajb9, calr, preb, hspa5, hsp90b1).\\n\\nmechanism: the enriched functions imply a complex network of processes that is likely to involve translation initiation of mrna, GO:0016567, and chaperone activity that facilitates protein folding, stability and degradation. it is possible that this gene set is associated with a variety of cellular pathways, including those related to gene expression, GO:0007165, GO:0008152]]0.06
664text-davinci-003no_synopsisHALLMARK_UV_RESPONSE_DN-0[[MESH:D011494, cellular signaling pathways, GO:0001501, GO:0031012, transcriptional regulation, post-translational phosphorylation, growth regulation, development regulation, remodeling]][[cell signaling, structural proteins, MESH:D004798, GO:0009653]]0.00
665text-davinci-003no_synopsisHALLMARK_UV_RESPONSE_DN-1[[mitotic regulation, GO:0060349, morphogenesis of specific organs and tissues, GO:0009966, regulation of transcription, GO:0042127, cellular responses to external stimuli, GO:0006468, GO:0003677]][[the above list of genes is significantly enriched for terms related to the development of the connective tissue, including morphogenesis, GO:0007049, regulation of transcription, and extracellular matrix organization; as well as the regulation of cell migration, matricellular protein signaling, GO:0007165, and calcium ion binding.\\n\\nmechanism: the enriched terms suggest that these genes work together in a common and interconnected pathway to control the formation, MESH:D009068, and functioning of the connective tissue. this pathway likely involves interactions among signal transduction pathways mediated by protein-protein interactions, transcriptional regulation, and calcium ion binding. these interactions would likely affect the structure and organization of the extracellular matrix, the migration of cells, the cell cycle, signalling through matricellular proteins]]0.04
666text-davinci-003no_synopsisHALLMARK_UV_RESPONSE_UP-0[[GO:0032502, GO:0016049, gene transcription, GO:0008152, MESH:D011506, GO:0006412, GO:0007049, cell signaling, transcriptional regulation, MESH:D021381, GO:0010468]][[MESH:D021381, organelle trafficking, GO:0006306, transcription regulation, GO:0003677, GO:0006338, GO:0051726, GO:0008152]]0.12
667text-davinci-003no_synopsisHALLMARK_UV_RESPONSE_UP-1[[GO:0008283, GO:0051726, dna replication and repair, GO:0007165, GO:0019722, GO:0006915, GO:0006629, oxygen pathway]][[genes in this list are generally involved in the regulation of cell growth and development, in particular related to apoptosis, signaling and transcriptional pathways. enriched terms include: transcriptional regulation; cell cycle regulation; apoptosis regulation; signal transduction; dna damage response; and cellular metabolism.\\n\\nmechanism: the molecular and cellular mechanisms underlying cell growth and development are complex and interconnected. genes in this list are believed to be involved in several pathways, such as transcriptional regulation, GO:0051726, apoptosis regulation, GO:0007165, GO:0006974, and cellular metabolism. these pathways interact and regulate each other in order to ensure the healthy functioning of cells. transcriptional regulation is key in regulating gene expression, while the cell cycle is tightly regulated by the activation of cell cycle control proteins and anti-apoptotic pathways. signal transduction pathways are essential for the proper coordination of cellular responses to external stimuli, and dna damage response allows for the repair of any irregularities. cellular metabolism is necessary for providing energy for growth and repair, for controlling the production of proteins]]0.11
668text-davinci-003no_synopsisHALLMARK_WNT_BETA_CATENIN_SIGNALING-0[[this examination of human genes reveals a number of gene functions that are significantly enriched and related to developmental processes, including cell proliferation and differentiation, GO:0048729, and wnt signalling pathways. \\nmechanism: cell proliferation and differentiation, GO:0048729, wnt signalling pathways are all important in the normal healthy development of cells organs. these genes provide important functions that act in cooperative downstream pathways to enable promote these developmental processes.\\nthe enriched terms are: cellular differentiation; cellular proliferation; digit development; tissue morphogenesis; wnt signalling pathway]][[the genes in this list are associated with the wnt signaling pathway, modulating cell growth and mophogenesis. the enrichment terms corresponding to this list are wnt signaling, GO:0016049, GO:0009653, transcriptional regulation, and epigenetics.\\n\\nmechanism: the wnt signaling pathway activates nuclear proteins such as lef1 and tcf7, which then activate transcription of genes involved in cell growth and morphogenesis. the genes on the listed are associated with modulating the wnt pathway, including epigenetic regulation and cell cycle regulation]]0.00
669text-davinci-003no_synopsisHALLMARK_WNT_BETA_CATENIN_SIGNALING-1[[wnt signaling, notch signaling, transcription regulation, GO:0051726, GO:0009653, GO:0032502]][[GO:0009653, GO:0006351, GO:0032502, MESH:D060449]]0.25
670text-davinci-003no_synopsisT cell proliferation-0[[cell signalling, protein interaction, GO:0007165, GO:0032502, regulatory role in immunity, GO:0030163, receptor-mediated signaling, GO:0016049, GO:0030154, GO:0006396]][[GO:0009653, GO:0048468, cell signaling, receptor-mediated signaling, GO:0010468]]0.07
671text-davinci-003no_synopsisT cell proliferation-1[[cell signaling, immune regulation, GO:0007165, growth factor production and response, immune response and modulation, calcium homeostasis, GO:0000981, development and differentiation, GO:0005102, GO:0001816]][[GO:0005126, GO:0007155, immunoreceptor-antigen complex binding, regulation of the ubiquitin-proteasome pathway, transcription factor regulator activity, gtp-binding protein binding, GO:0030154]]0.00
672text-davinci-003no_synopsisYamanaka-TFs-0[[the enrichment test results reveal that the list of genes are all involved in stem cell pluripotency and early embryonic development. enriched terms include pluripotency, stem cell morphology, MESH:D047108, GO:0000981, GO:0016049, differentiation, cell proliferation.\\n\\nmechanism: the genes focus on the regulation of the pluripotency and early embryonic developmental program. they regulate various aspects such as transcription factors, cell growth, morphogenesis, differentiation and cell proliferation. by acting in concert, they maintain the pluripotency of stem cells and initiate the processes of early morphogenesis. it is hypothesized that these genes are part of a large regulatory network which facilitates the pluripotency of the progenitor cells and the successful orchestration of early embryonic development]][[GO:0000988, embryonic stem cell differentiation, cell pluripotency, dna-binding, MESH:D005786, GO:0140110, transcription factor complex formation.\\nmechanism: these genes are known to be involved in the regulation of gene expression, and thus serve an important role in directing the biological activities associated with embryonic stem cell differentiation and pluripotency. they are likely to form complexes, interact with dna, and/or bind to components of the transcription machinery to regulate gene expression at the transcriptional level]]0.00
673text-davinci-003no_synopsisYamanaka-TFs-1[[GO:0009792, GO:0048864, GO:0000981, GO:0009653]][[GO:0048863, GO:0048468, embryonic stem cell differentiation, transcriptional regulation, pluripotency, transcription factor regulation.\\n\\nmechanism: the genes klf4, pou5f1, and sox2 act in concert to regulate the expression of developmental proteins that are involved in forming stem cells. this trio of transcription factors plays a key role in regulating cell differentiation and pluripotency, thus influencing the direction of embryonic stem cell development by regulating gene expression of proteins involved in stem cell formation]]0.00
674text-davinci-003no_synopsisamigo-example-0[[GO:0030198, GO:0007155, GO:0009653, cell signaling, cytoskeletal organization, GO:0030154, MESH:D002470]][[GO:0008283, GO:0048729, motility regulation, vascular development, GO:0098868, UBERON:0002405]]0.00
675text-davinci-003no_synopsisamigo-example-1[[our term enrichment analysis suggests that the human genes jag2, spp1, jag1, vcan, olr1, col5a2, app, UBERON:0003010, postn, tnfrsf21, apoh, pglyrp1, vav2, fstl1, nrp1, s100a4, lrpap1, vtn, timp1, itgav, lum, pf4, cxcl6, col3a1, stc1, kcnj8, msx1, ptk2, prg2, pdgfa, serpina5, and vegfa are related to processes in growth and differentiation, including transcriptional network maintenance, cell adhesion and motility, GO:0006915, and extracellular matrix component formation.\\n\\nmechanism: \\nthese genes may be involved in a complex network of signaling pathways that regulate cell growth and differentiation, cell adhesion and migration, GO:0006915, and matrix component formation. they may be involved in the reception and transduction of growth and differentiation signals, could facilitate the assembly of extracellular matrix components to form the microenvironment necessary to prompt and]][[GO:0001525, GO:0008283, GO:0016477, matrix remodeling, GO:0048771, jagged-mediated signaling, transcriptional regulation, GO:0030168, GO:0070527, immune regulation, extracellular matrix formation]]0.00
676text-davinci-003no_synopsisbicluster_RNAseqDB_0-0[[GO:0009653, GO:0032502, transcription regulation, cell signalling, GO:0006811]][[GO:0016049, differentiation, migration, chromatin modulation, transcription regulation, cytoskeletal organization, intracellular trafficking, GO:0007155, GO:0007165, dna/rna metabolic processes, GO:0009653, GO:0001525, muscle growth, GO:0032502]]0.19
677text-davinci-003no_synopsisbicluster_RNAseqDB_0-1[[GO:0009653, neuronal growth, neuronal system development, cell-cell communication, cell signaling, GO:0009888, organ development]][[chromatin regulation, GO:0048468, GO:0006412, GO:0006811, GO:0000981, GO:0043687]]0.00
678text-davinci-003no_synopsisbicluster_RNAseqDB_1002-0[[analysis of the gene list shows that they are all associated with sarcomere function, MESH:D009119, skeletal muscles and thermogenesis. the enriched terms include sarcomere function, MESH:D009119, UBERON:0001134, MESH:D022722, actin-myosin interaction, calcium handling, muscle development and differentiation, and mitochondrial function. \\n\\nmechanism: the underlying biological mechanism is associated with the activation of genes that are linked to the assembly, maintenance and contraction of the sarcomere, which is the fundamental unit of muscle contraction, as well as muscle development and differentiation, calcium handling, mitochondrial fluctuation, thermogenesis. this contributes to the generation of force within the skeletal muscles]][[MESH:M0370791, GO:0007015, GO:0006936, z-disc formation, GO:0007097, muscle fiber organization, ion channel influx/efflux]]0.00
679text-davinci-003no_synopsisbicluster_RNAseqDB_1002-1[[skeletogenesis, MESH:D024510, GO:0048740, GO:0001501, GO:0006936, GO:0006412, GO:0009058, MESH:D009126]][[MESH:D024510, GO:0048740, GO:0021675, calcium distribution, actin proteins, cardiac contractile proteins, sarcomeric proteins, membrane protein transport, ion channel proteins, enzyme regulation.\\nmechanism: this list of genes are likely to be involved in the regulation of muscle structures and contractions, organization of calcium distribution throughout the cell, nerve development, and support of membrane protein transport and enzymatic activities. these processes are important for maintaining muscle contraction and activity]]0.12
680text-davinci-003no_synopsisendocytosis-0[[GO:0007165, vesicle/lipid trafficking, cellular adhesion, nutrient regulation, cell metabolism, cytoskeletal organization, endocytosis/exocytosis, intercellular adhesion/motility]][[GO:0006629, cell signaling, GO:0007049, cytoskeletal dynamics]]0.00
681text-davinci-003no_synopsisendocytosis-1[[membrane trafficking, GO:0007165, protein proteolysis, GO:0006629, receptor signaling, GO:0055088]][[GO:0006897, intracellular signaling, GO:0016310, protein interactions, receptor trafficking]]0.00
682text-davinci-003no_synopsisglycolysis-gocam-0[[GO:0006096, aerobic glycolysis, GO:0006094]][[GO:0006754, GO:0006096, MESH:D004734, MESH:M0496924]]0.17
683text-davinci-003no_synopsisglycolysis-gocam-1[[GO:0008152, GO:0006096, GO:0006098, GO:0006006, MESH:D004734]][[metabolic pathway, GO:0006096, glucose oxidation, pyruvic acid production, GO:0006754]]0.11
684text-davinci-003no_synopsisgo-postsynapse-calcium-transmembrane-0[[these genes appear to be involved in the development, functioning and regulation of the nervous system, specifically neurons and their associated pathways and processes. the terms \"neurotransmission\"; \"neuronal cell membrane regulation\"; \"neurotransmitter release\"; \"calcium signaling\"; \"neuronal ion channel regulation\"; and \"neuronal excitability regulation\" are significantly enriched in this gene set.\\n\\nmechanism: it appears that this gene set may be involved in a broad range of processes related to neurophysiology, including the regulation of neuronal membrane excitability and ion channels, neuronal cell membrane regulation, GO:0007269, and calcium signaling. these processes are all complex and interrelated, are likely to have a direct impact on neural development function]][[summary: the enriched terms of the human genes atp2b1, atp2b2, cacna1c, cacng2, cacng3, cacng4, cacng5, cacng7, cacng8, chrna10, chrna7, chrna9, drd2, f2r, gpm6a, grin1, grin2a, grin2b, grin2c, grin2d, grin3a, grin3b, htr2a, itpr1, ncs1, p2rx4, p2rx7, plcb1, psen1, slc8a1, slc8a2, slc8a3, trpv1 include neuron development; neurotransmitter signaling; signal transduction; transmembrane transport; neural plasticity; ion transport; calcium signaling; glutamate receptor signaling; and synaptic signaling. \\n\\nmechanism: these genes are believed to act in concert to regulate and coordinate the various stages of neuron development, such as neurotransmitter signaling, GO:0007165, GO:0055085, neural]]0.00
685text-davinci-003no_synopsisgo-postsynapse-calcium-transmembrane-1[[the term enrichment test reveals that the genes in the list are mainly involved in neuronal ion channels and calcium signalling pathways. enriched terms included calcium channel activity, GO:0005244, GO:0038023, GO:0015276, and g-protein coupled receptor activity. \\n\\nmechanism: the genes in the list form ion channels and g-protein coupled receptors within neuronal cells, which facilitates the communication of neurotransmitters between neurons. several of the genes are involved in calcium signalling pathways, which regulate various cellular pathways involved in the development and maintenance of neurons]][[neuronal function, GO:0006811, ion channel regulation, neurotransmitter regulation, calcium regulation, potassium regulation, GO:0007268, membrane potential regulation]]0.00
686text-davinci-003no_synopsisgo-reg-autophagy-pkra-0[[GO:0016049, GO:0048468, GO:0006915, GO:0006955, GO:0030163, GO:0006508]][[this set of genes is associated with cellular functions related to metabolic homeostasis and activation of the pi3k/akt signaling pathway. the enriched terms associated with the genes include cell cycle regulation, protein kinase regulation, mitochondrial regulation, and mitochondrial stress response.\\n\\nmechanism: the metabolic homeostasis and activation of the pi3k/akt pathway are mediated by these genes, which affect the regulation of cell cycle, protein kinase regulation, mitochondrial regulation, and mitochondrial stress response. these genes have roles in regulating metabolic processes as well as responding to external stressors. their involvement in cell cycle regulation and protein kinase regulation ensures the healthy development and maintenance of the cell, while their role in mitochondrial regulation and mitochondrial stress response plays an important role in maintaining the cell's energy production]]0.00
687text-davinci-003no_synopsisgo-reg-autophagy-pkra-1[[phosphatidylinositol signalling, vascular endothelial growth factor receptor signalling, progesterone-mediated oocyte maturation, nf-kb signaling, GO:0043526]][[cell signaling, transcription regulation, GO:0006468, ras activation, akt activation, calcium-associated kinases, GO:0019722]]0.00
688text-davinci-003no_synopsishydrolase activity, hydrolyzing O-glycosyl compounds-0[[carbohydrate digestion and absorption; glycosaminoglycan and glycan metabolism; lysosomal, GO:0005777, and catabolic processes; digit, skeletal, GO:0035108]][[MESH:D009113, MESH:D009077, glycosyltransferase, MESH:D006821, GO:0070085, enzyme, MESH:D011506]]0.00
689text-davinci-003no_synopsishydrolase activity, hydrolyzing O-glycosyl compounds-1[[glycoside hydrolase (gh) activity, mucin biosynthesis, GO:0006031, MESH:D057056, lysosomal enzyme activity.\\nmechanism: glycoside hydrolase (gh) and lysosomal enzymes play important roles in the process of glycostasis, and are involved in a variety of metabolic activities such as the breakdown of polysaccharides, the synthesis of glycolipids and glycoproteins, and the degradation of other macromolecules. chitin and mucin biosynthesis also involve glycosylation and enzymatic modification of sugars and polysaccharides to form polymeric molecules. cysteine protease are involved in the hydrolysis of proteins, while lysosomal enzymes aid in the breakdown of molecules in the l]][[the gene functions that were found to be enriched amongst this set of genes were predominantly related to carbohydrate metabolism, including glycosaminoglycan and glycosphingolipid biosynthesis as well as lysosomal enzyme activity.\\n\\nmechanism:\\nthe mechanism most likely lies in the pathway of glycoconjugation, which helps to regulate important processes such as cell adhesion, GO:0006955, and signal transduction. the pathway is integral to the proper formation and function of the extracellular matrix, which is important for cellular differentiation and tissue organization. the enriched terms found here likely represent genes that are involved in the biosynthesis and metabolism of various glycoconjugates, in addition to the regulation of lysosomal enzymes involved in the degradation of complex carbohydrates]]0.00
690text-davinci-003no_synopsisig-receptor-binding-2022-0[[members of the immunoglobulin (ig) gene superfamily - specifically, igh, GO:0033984, MESH:C014609, GO:0042571, response and maintenance of the adaptive immune system at different levels, likely via antigen binding, signal transduction and b cell activation]][[immunoglobulin heavy chain combination, immunoglobulin light chain combination, j-chain, antigen-specific receptor, t-lymphocyte receptor, regulation of immune function]]0.00
691text-davinci-003no_synopsisig-receptor-binding-2022-1[[GO:0003823, b cell receptors, GO:0007596, GO:0005577, MESH:D001779, clec4d]][[genes related to immunoglobulins, transcripts associated with immunoglobulin transcription and splicing, immunoglobulin gene expression, proteins involved in immunoglobulin regulation and processing, GO:0002637, GO:0002637, mhc class i antigen processing and presentation, cytokine-mediated signaling, GO:0002544, limit degranulation. \\n\\nmechanism: these genes are associated with immunoglobulin production, processing, and regulation. this includes genes related to immunoglobulins, transcripts involved in transcription and splicing, and proteins that are involved in the regulation and processing of immunoglobulins. additionally, genes related to mhc class i antigen processing, cytokine-mediated signaling, chronic inflammatory response, and limit degranulation are also expressed. these genes interact to form an integrated pathway that is involved in the regulation of the immune response and the formation of immunoglobulins]]0.00
692text-davinci-003no_synopsismeiosis I-0[[dna damage recognition, GO:0006281, GO:0006302, meiotic recombination, GO:0007059, GO:0035825, rad51 family proteins, dna end-protection, mus81-mms4 complex, muts family proteins, dna proofreading, spo11-associated pathway]][[GO:0006260, GO:0006281, replication fidelity, GO:0007049, GO:0071897, dna prioritization]]0.06
693text-davinci-003no_synopsismeiosis I-1[[GO:0006281, GO:0006260, gene splicing]][[this enrichment test on the list of human genes suggests a central role for dna damage repair and cell cycle regulation in the common functionalities of the genes. enriched terms found include \"dna repair\", \"cell cycle\", \"chromatin remodelling\", \"recombinational repair\", \"steroid hormone receptor\", \"centromere\", GO:0000724]]0.00
694text-davinci-003no_synopsismolecular sequestering-0[[GO:0000075, cell adhesion/motility complex, transcriptional complex, GO:0036211, rna processing complex]][[GO:0019722, calcium buffering, GO:0006816, regulation of calcification, protection against calcium overload, calcium-v influx/efflux]]0.00
695text-davinci-003no_synopsismolecular sequestering-1[[calcium binding, apoptotic regulation, immune modulation, MESH:D018384, GO:0051726, stress-response regulation]][[cell morphology regulation, GO:0008152, GO:0006915, GO:0006412, GO:0036211, GO:0006811, GO:0023052, stress response, GO:0006351, cell surface interactions, chromatin regulation]]0.00
696text-davinci-003no_synopsismtorc1-0[[the human genes abcf2, acaca, acly, acsl3, actr2, actr3, add3, adipor2, ak4, aldoa, arpc5l, asns, atp2a2, atp5mc1, atp6v1d, MESH:D064096, bcat1, bhlhe40, btg2, bub1, cacybp, calr, canx, ccnf, ccng1, cct6a, cd9, cdc25a, cdkn1a, cfp, cops5, coro1a, cth, ctsc, GO:0038147, cyb5b, cyp51a1, dapp1, ddit3, ddit4, ddx39a, dhcr24, dhcr7, GO:0004146, ebp, edem1, eef1e1, egln3, eif2s2, elovl5, elovl6, eno1, eprs1, ero1a, etf1, MONDO:0100101, MONDO:0100102, fdxr, fgl2, MESH:D010649]][[genes in this list are involved in various aspects of cellular metabolism, GO:0065007, and development.a number of the genes have roles in energy production and metabolism such as, atp2a2, aldoa, MONDO:0009214, fao1, fgl2, gapdh, gbe1, MONDO:0015408, glrx, MONDO:0005775, me1, phgdh, and pgm1. there is a strong presence of genes involved in protein synthesis and transport, including the ribosomal proteins, the eukaryotic translation factors and initiation factors (eif2s2, eif1e1, elovl5, and elovl6). this gene set is also enriched for a number of ubiquitin and ubiquitin-like proteins (ube2d3, ufm1, uso1, tomm40, hspd1, hspe1, sytl2, nherf1, and hk2). many of these genes are involved in regulation through multiple pathways including regulation of transcription (add3, actr2, actr3, cct6a, gga2, gdh2, mef2b, ykt]]0.08
697text-davinci-003no_synopsismtorc1-1[[energy production, GO:0008152, protein biosynthesis and folding, cell regulation, MESH:D048788, protein turnover]][[genes related to metabolism and biosynthesis (acly, aldoa, atp2a2, atp6v1d, cacybp, coro1a, dhcr24, MONDO:0100101, MONDO:0100102, gbe1, MESH:C066524, gsr, hmgcs1, hspa9, lgmn, me1, mthfd2l, nampt, pgm1, pgk1, psat1, psma3, psma4, psmg1, psmc2, psmc4, psmd12, psmd13, psmd14, stc1, stip1, and ufm1), protein folding/interaction (act2, actr2, actr3, add3, elovl5, eno1, ero1a, eif2s2, fgl2, insig1, itgb2, map2k3, mcm2, mcm4, nufip1, p4ha1, pdk1, pitpnb, pnp, psme3, sec11a, shmt2, slc2a1, slc2a3]]0.00
698text-davinci-003no_synopsisperoxisome-0[[peroxisome biogenesis, peroxisome formation, membrane protein trafficking, GO:0044255, mitochondrial-peroxisomal crosstalk]][[protein homeostasis, peroxisome biogenesis, peroxisome assembly, peroxisome maintenance, protein regulation, GO:0050821]]0.10
699text-davinci-003no_synopsisperoxisome-1[[peroxisomal biogenesis, peroxisomal protein transport, oxidative damage resistance]][[peroxisomal biogenesis, peroxisome assembly, peroxisome regulation, GO:0015031, membrane trafficking]]0.14
700text-davinci-003no_synopsisprogeria-0[[cell structural element development, gene transcription, GO:0016070, GO:0006259, transcriptional regulation]][[after performing the enrichment test on the genes zmpste24, banf1, MONDO:0010196, and lmna, we identified that all of the genes have a role in the regulation of nuclear and chromatin structures. the individual genes are involved in a wide range of processes in these two areas. this includes gene expression, GO:0006260, GO:0006338, GO:0000723, as well as cell cycle checkpoints.\\n\\nthe enriched terms are 'nuclear structure regulation'; 'chromatin structure regulation'; 'gene expression regulation'; 'dna replication regulation'; 'chromatin remodeling'; 'telomere maintenance'; and 'cell cycle checkpoint regulation'. \\n\\nmechanism: the underlying biological mechanism that our gene list points to is one involving the regulation of nuclear and chromatin structures. in order to maintain the stability of the genome and ensure its accurate transmission, molecules encoded by the four genes could be involved in key activities such as gene expression, GO:0006260, GO:0006338, GO:0000723, as well as cell cycle checkpoints]]0.00
701text-davinci-003no_synopsisprogeria-1[[dna replication and repair, GO:0006334, GO:0000723, transcriptional regulation]][[transcriptional regulation, GO:0006281, GO:0051726, GO:0030154]]0.14
702text-davinci-003no_synopsisregulation of presynaptic membrane potential-0[[GO:0007165, GO:0006811, regulation of neurotransmitter release]][[MESH:D007473, MESH:D008565, synapse formation, GO:0007268, MESH:D009473, neuronal excitability, voltage-gated ion channels, MESH:D058446]]0.00
703text-davinci-003no_synopsisregulation of presynaptic membrane potential-1[[analysis of these genes show that they are involved in human neurological structure and function. enriched terms include neuron activity, GO:0005216, GO:0008066, GO:0004930, MESH:D005680, GO:0005267, MESH:D005680]][[ion-channel function, neuron excitability, GO:0007268, MESH:D018079, MESH:D017470, MESH:D015221, MESH:D015222]]0.00
704text-davinci-003no_synopsissensory ataxia-0[[MESH:D024510, neuronal development, GO:0015031, GO:0006629, GO:0009653]][[GO:0006412, GO:0008152, ion channel transport, GO:0006936, MESH:D024510]]0.11
705text-davinci-003no_synopsissensory ataxia-1[[GO:0015031, MONDO:0008090, GO:0048705, MESH:D024510, GO:0005783, mitochondrial protein transport, cytoskeletal organization]][[nucleic acid metabolism, GO:0003676, GO:0050657, GO:0019538, GO:0005515, GO:0015031]]0.08
706text-davinci-003no_synopsisterm-GO:0007212-0[[g alpha subunit signaling, gpcr activation and signaling, gpcr function, MESH:D019281]][[g-protein coupled receptor (gpcr), g-protein subunit, MESH:D000262, MESH:D015220, MESH:D010770]]0.00
707text-davinci-003no_synopsisterm-GO:0007212-1[[cellular signaling, g protein signaling pathway, calcium signaling pathway, GO:0007399, GO:0007268, phosphorylation cascade, nerve morphogenesis, indoleamine metabolism]][[GO:0007165, cellular growth & differentiation, GO:0007010, endocrine system regulation, transcriptional regulation]]0.00
708text-davinci-003no_synopsistf-downreg-colorectal-0[[nuclear receptor superfamily, transcription regulation, epigenetic regulation, GO:0051726, GO:0003677, GO:0006338, GO:0032502, cell signaling pathways, GO:0005652, GO:0016363]][[genes such as hira, cebpb, e2f3, hmga1, znf263, tfdp1, trib3, bhlhe40, smarca4, slc26a3, nfe2l3, ssbp2, gtf3a, npm1, trip13, mef2c, nr3c2, foxm1, vdr, hand1, klf4, hexim1, tgif1, med24, tead4, smarcc1, scml1, MESH:D024243, myc, foxa2, bmal2, spib, nme2, phb1, cbx4, runx1, ppargc1a, polr3k, nr5a2, maf, nr1h4, sox9, dnmt1, cbfb, znf593, mta1, zbtb18 are all involved in the regulation of transcription, GO:0006338, GO:0003677, and epigenetics. of this group, genes involved in transcription are significantly enriched (e.g. hira, cebpb, e2f3,]]0.03
709text-davinci-003no_synopsistf-downreg-colorectal-1[[transcriptional regulation, GO:0016569, GO:0009653, cardiovascular development, differentiation, MESH:M0464910, MESH:M0030450, GO:0048863]][[GO:0016049, transcriptional regulation, GO:0006338, GO:0051726, GO:0006351, GO:0016569]]0.17
710text-davinci-003ontological_synopsisEDS-0[[GO:0032963, GO:0030198, GO:0004222, GO:0030206, GO:0008378, GO:0005509, GO:0008270, platelet derived growth factor binding, GO:0002020, GO:0035987, GO:0007266, GO:0007160, hypoxia response, epidrmis development, peptidyl-lysine hydroxyl]][[collagen or extracellular matrix structural constituent, collagen metabolic process or biosynthetic process, proteoglycan metabolic process or biosynthetic process, GO:0006024, dna-binding transcription factor binding activity, GO:0001217, rna polymerase ii transcription regulatory region sequence-specific dna binding activity, metal ion binding activity, GO:0003755, GO:0035987, GO:0004252, GO:1904028, protein peptidyl-prolyl is]]0.04
711text-davinci-003ontological_synopsisEDS-1[[GO:0030198, GO:0030199, GO:0043589, GO:0042060, GO:0043588, GO:0032964, GO:0006024, GO:0003755, GO:0035987]][[GO:0030198, GO:0030199, GO:0032964, GO:0030166, GO:0006024]]0.40
712text-davinci-003ontological_synopsisFA-0[[analysis of the above genes shows that they are all involved in dna repair and involved in the fanconi anaemia nuclear complex, which is a critical part of the fanconi anaemia disease pathway. the list of enriched terms includes \"protein monoubiquitination\", \"dna repair complex\", \"fanconi anaemia nuclear complex\", \"double-strand break repair via homologous recombination\", \"response to intra-s dna damage checkpoint signaling\", \"telomere maintenance\", \"positive regulation of g2/m transition of mitotic cell cycle\", \"regulation of transcription by rna polymerase ii\".\\n\\nmechanism: the underlying biological mechanism is the fanconi anaemia pathway, where the defective genes of the path have the potential to lead to cancer or other fanconi anaemia-related illnesses. this dna repair pathway relies heavily on the fanconi anaemia nuclear complex, which involves the processes of monoubiquitination, involving the above genes, double-strbreak repair via homologous recombination. in addition, the regulation of telomere maintenance, positive regulation of g2/m transition of mitotic cell cycle regulation of transcription by rna polymerase ii are essential for proper dna repair]][[GO:0006281, GO:0006513, GO:0043240, GO:0000785, GO:0005634, GO:0005829]]0.00
713text-davinci-003ontological_synopsisFA-1[[this group of genes are involved in a range of dna repair processes, including protein monoubiquitination and double-strand break repair via homologous recombination. they are all localized in different components of the cell (e.g. chromatin, GO:0005634, GO:0005829, GO:0005657, GO:0005694, etc.) and are part of several complexes/hierarchies (e.g. fanconi anaemia nuclear complex, GO:0033063, GO:0048476, GO:0033557, GO:0033593, etc.). enriched terms includes: dna repair; protein monoubiquitination; double-strand break repair via homologous recombination; regulation of dna metabolic process; negative regulation of double-stranded telomeric dna binding activity; response to gamma radiation; regulation of telomere maintenance; establishment of protein localization to telomere; and regulation of protein metabolic process.\\n\\nmechanism: these genes are involved in a range of complex and interrelated biochemical pathways, which utilize a variety of enzymatic activities (e.g. ubiqu]][[GO:0006513, GO:0006281, GO:0003682, GO:0000400, GO:0003684, GO:0003697, GO:1990599, GO:0004520, GO:0006310, GO:0005524, GO:0006259, GO:0072757, GO:0051052, GO:0003691, GO:0000723, GO:0019219, GO:0051246, GO:0070200, GO:0016573, GO:0004402, gamma-tubulin binding activity, identical protein binding activity, jun kinase binding activity, rna polymerase ii-specific dna-binding transcription factor binding activity, GO:0061630, GO:0031386]]0.00
714text-davinci-003ontological_synopsisHALLMARK_ADIPOGENESIS-0[[GO:0005515, protein homodimerization, GO:0005524, GO:0003677, GO:0003824, MONDO:0016019]][[protein binding activity, MESH:D010758, atp binding activity, gtp binding activity, GO:0022857, dna binding activity, receptor binding activity, GO:0004869, caspase binding activity, rna binding activity]]0.00
715text-davinci-003ontological_synopsisHALLMARK_ADIPOGENESIS-1[[protein homodimerization, GO:0019899, GO:0140657, GO:0005102, ligase binding, GO:0003924, GO:0046872, dna-binding, rna-binding, oxidase activity, MESH:D010758, GO:0120227, transportase activity, dehydrogenase activity, GO:0016791, GO:0016301, GO:0004175, GO:0022857, chemotactic receptor activity, GO:0017077]][[protein binding activity, enzyme binding activity, atp binding activity, rna binding activity, gtp binding activity, identical protein binding activity, gtp-dependent protein binding activity, transition metal ion binding activity, GO:0016615, aldehyde dehydrogenase activity, GO:0008097, GO:0052650, fad binding activity, MESH:D010758, heme binding activity, GO:0003872, GO:0004609, GO:0003873, GO:0004144, GO:0003994, GO:0004784, GO:0004129, molybdenum ion binding activity]]0.02
716text-davinci-003ontological_synopsisHALLMARK_ALLOGRAFT_REJECTION-0[[receptor binding activity, signaling receptor binding activity, protein binding activity, dna-binding, GO:0016563, GO:0005125, GO:0008083, GO:0042605, enzyme binding activity, chemical binding activity, protein complex binding activity]][[protein homodimerization, protein heterodimerization, GO:0042802, GO:0019901, dna-binding, rna-binding, GO:0017124, GO:0019958, GO:0008201, ubiquitin-protein ligase binding]]0.05
717text-davinci-003ontological_synopsisHALLMARK_ALLOGRAFT_REJECTION-1[[enzyme binding activity, rna binding activity, protein binding activity, chemokine receptor binding activity, GO:0004712, GO:0042803, identical protein binding activity, GO:0008083, interleukin binding activity, cell-cell adhesion mediation, dna-binding transcription activity, GO:0015026, cytoplasmic factor activity, metal ion binding activity, polypeptide antigen transporter activity]][[GO:0007155, GO:0005102, GO:0007165, GO:0001228, chemokine receptor binding activity, enzyme binding activity, GO:0008083, GO:0005125, degradation of redundant or damaged proteins and peptides, GO:0046983, metal ion binding activity, peptide antigen binding activity, GO:0004888, GO:0004712, GO:0042803, ubiquitin binding activity]]0.24
718text-davinci-003ontological_synopsisHALLMARK_ANDROGEN_RESPONSE-0[[protein binding activity, enzyme binding activity, transcription factor binding activity, GO:0016787, GO:0004721, GO:0003714, GO:0003713, atp binding activity, GO:0004672, GO:0016563, GO:0003924, nad+ binding activity, ring-like zinc finger domain binding activity, GO:0061656, small protein activating enzyme binding activity, GO:0000224, GO:0062076, GO:0004383, GO:0004222, 17-beta-dehydrogen]][[GO:0005215, GO:0005515, GO:0004672, GO:0038023, GO:0006351, GO:0044237, GO:0006974, GO:0007010, GO:0016787, GO:0046872, GO:0003924]]0.11
719text-davinci-003ontological_synopsisHALLMARK_ANDROGEN_RESPONSE-1[[protein binding activity, GO:0004672, GO:0006351, GO:0038023, enzymatic activity, GO:0016310, GO:0097472, GO:0003677, GO:0006351, postsynaptic organization, GO:0016887, nucleic acid binding activity, ubiquitin protein ligase binding activity, fad binding activity, MESH:D009249, GO:0061665, enzyme binding activity, GO:0022857, endopeptidase activator]][[GO:0005515, GO:0016887, GO:0016563, GO:0003677, GO:0004674, GO:0022857, GO:0016787, GO:0061631, cis-regulatory region sequence-specific dna binding activity, GO:0061665, GO:0034594, GO:0007165, GO:0043027, GO:0003924, GO:0042803, nucleic acid binding activity, GO:0003713, GO:0003714, enzyme binding activity, calmodulin binding activity, metalloendope]]0.18
720text-davinci-003ontological_synopsisHALLMARK_ANGIOGENESIS-0[[GO:0030021, collagen binding activity, integrin binding activity, GO:0060090, identical protein binding activity, fibronectin binding activity, GO:0046983, heparan sulfate proteoglycan binding activity, GO:0007160, GO:0010810]][[summary: the list of genes provided appear to be involved in a variety of unrelated processes, but when grouped by shared activities, several functions in common can be identified. these common functions include protein binding activity, GO:0060230, phospholipid binding activity, platelet-derived growth factor binding activity, GO:0046983, signaling receptor binding activity, collagen binding activity, atp activated inward rectifier potassium channel activity, voltage gated monoatomic ion channel activity, GO:0005249, GO:0016298, heparan sulfate proteoglycan binding activity, heparin binding activity, multiple growth factor activities, peptidoglycan binding activity, GO:0016019, platelet derived growth factor binding activity, non membrane spanning protein tyrosine kinase activity, GO:0005096, vascular endothelial growth factor binding activity, metal ion binding activity, small molecule binding activity, enzyme binding activity, retinoic acid binding activity, cxcr3 chemokine receptor binding activity, prostaglandin transmembrane transporter activity and sodium-independent organic anion transmembrane transporter activity. \\nmechanism: the genes in the list appear]]0.09
721text-davinci-003ontological_synopsisHALLMARK_ANGIOGENESIS-1[[GO:0007166, GO:0006468, GO:0045861, GO:0007160, GO:1902533, GO:0010604, transmem]][[GO:0005515, GO:0006468, GO:0016477, GO:0008283, GO:0045861, GO:1902533, GO:0009966, GO:0010604, GO:0019901, GO:0008191, ion binding activity, small molecule binding activity, GO:0035987, GO:0005096, platelet-derived growth factor binding activity, GO:0046983, calcium ion binding activity, sympathetic nerve activity, GO:0051336]]0.18
722text-davinci-003ontological_synopsisHALLMARK_APICAL_JUNCTION-0[[GO:0098609, agonist binding activity, cytoplasmic matrix binding, protein homodimerization, GO:0005102]][[GO:0007155, GO:0005178, gtp binding activity, collagen binding activity, atp binding activity, phospholipase binding activity, GO:0007160, GO:0050839, GO:0017124]]0.00
723text-davinci-003ontological_synopsisHALLMARK_APICAL_JUNCTION-1[[binding activities, GO:0003824, involvement in biological processes, structural roles]][[extracellular matrix structure, GO:0038023, cell adhesion molecule binding activity, small gtpase binding activity, GO:0042803, identical protein binding activity, collagen binding activity, actin binding activity, atp binding activity, protein kinase binding activity, sh3 domain binding activity, integrin binding activity, GO:0005096]]0.00
724text-davinci-003ontological_synopsisHALLMARK_APICAL_SURFACE-0[[GO:0061024, protein organization, GO:0036211, GO:0015031, GO:0006897, GO:0007165, GO:0006915]][[GO:0005480, cell structure maintenance, GO:0046872, GO:0016477, plasmamembrane transport, GO:0005515, GO:0043170, GO:0030296, endolemmal transport, GO:0016485, GO:0010467, GO:0006915, lipoprotein particle receptor catabolic process, peptide chain release, protein homodimerization, GO:0007165, GO:0048870, GO:1902600, GO:0000785, GO:0005654, GO:0031410, GO:0042552, GO:0044183]]0.07
725text-davinci-003ontological_synopsisHALLMARK_APICAL_SURFACE-1[[GO:0007155, protein folding and regulation, GO:0050801, MESH:D005786]][[genes in this list are primarily involved in regulation of transcription, GO:0007165, membrane management, protein folding and binding, cell surface receptor signaling and adhesion, and cellular extravasation. enriched terms include: transcription, GO:0007165, protein-folding and binding, cell-surface receptor signaling, adhesion, GO:0045123, GO:0061024, extracellular matrix structural components, genetic expression, apoptotic pathways, and intracellular ion homeostasis. \\n\\nmechanism: genes on this list are primarily involved in several processes that coordinate essential cellular functions by dynamically managing activity of proteins at the surface of the cell, within underlying membrane layers, extracellularly and within dna. these genes manage the way cells communicate within their environment, interact with extracellular components, respond to stimuli, and extravasate. they code for proteins involved in transcription, GO:0007165, protein folding and binding, adhesion, apoptotic pathways, intracellular ion homeostasis, extracellular matrix structural components that have pleiotropic roles in modulating gene expression functioning of cellular components]]0.00
726text-davinci-003ontological_synopsisHALLMARK_APOPTOSIS-0[[dna binding activity, protein binding activity, enzyme binding activity, GO:0004197, identical protein binding activity, signaling receptor binding activity, calcium ion binding activity, protein kinase binding activity, GO:0000988, bh3 domain binding activity]][[dna binding activity, GO:0046983, protein binding activity, enzyme binding activity, protein kinase binding activity, GO:0004197, GO:0003714, phosphoprotein binding activity, mhc class i protein binding activity, GO:0003700, signaling receptor binding activity, GO:0042803]]0.38
727text-davinci-003ontological_synopsisHALLMARK_APOPTOSIS-1[[calcium ion binding activity, protein binding activity, identical protein binding activity, chromatin dna binding activity, dna-binding transcription factor binding activity, ig domain binding activity, sh2 domain binding activity, bh3 domain binding activity, cyclin binding activity, rna binding activity, GO:0004197, metalloprotease inhibitor activity, phospholipid binding activity, lipopeptide binding activity, lysophosphatidic acid binding activity, sulfatide binding activity, atpase binding activity, pdz domain binding activity]][[protein binding activity, identical protein binding activity, enzyme binding activity, GO:0003700, rna polymerase ii-specific transcriptional activity, GO:0004197, GO:0004896]]0.14
728text-davinci-003ontological_synopsisHALLMARK_BILE_ACID_METABOLISM-0[[atp binding activity, GO:0016887, protein binding activity, signaling receptor binding activity, enzyme binding activity, GO:0042803, GO:0016791, GO:0000988, GO:0022857, ubiquitin-dependent protein binding activity, cholesterol binding activity, GO:0019871, phosphotyrosine residue binding activity]][[atp binding activity, GO:0016887, cholesterol binding activity, GO:0022857, GO:0046982, GO:0000981, enzyme binding activity, GO:0016491, peptide antifungal protein binding activity, acyl-coa hydroxyacyltransferase activity, GO:0019145]]0.26
729text-davinci-003ontological_synopsisHALLMARK_BILE_ACID_METABOLISM-1[[GO:0140657, GO:0016887, GO:0008233, enzyme binding activity, GO:0003700, GO:0042803, identical protein binding activity, signaling receptor binding activity]][[this gene list is associated with multiple functions in various metabolic processes, from binding and transporter activity to atpase activity, homodimerization activity, and various hydrolytic activities. enriched terms include: protein binding activity; atp hydrolysis activity; protein homodimerization activity; atpase binding activity; atpase-coupled transmembrane transporter activity; transcription regulatory region sequence-specific dna binding activity; and transmembrane transporter activity. mechanism: this set of genes acts as part of multiple metabolic processes, such as lipid and fatty acid metabolism, GO:0042632, GO:0140327, and hormone regulation. these genes facilitate enzymatic activity and activity in transporting molecules, such as fatty acids, MESH:D002784, MESH:D014815, hormones. the processes activities these genes are involved in suggest a coordination of metabolic cell stimulation processes]]0.00
730text-davinci-003ontological_synopsisHALLMARK_CHOLESTEROL_HOMEOSTASIS-0[[atp binding activity, protein kinase binding activity, GO:0042803, GO:0003700, low-density lipoprotein particle binding activity, GO:0005041, GO:0030229, GO:0004602, GO:0004364, GO:0016491, GO:0004496, GO:0004631, GO:0047598, GO:0047024, MESH:D010758, GO:0060090, cholesterol binding activity, GO:0120020, isopentenyl]][[atp binding activity, protein binding activity, GO:0007155, GO:0007165, GO:0006915, dna-binding, GO:0006695, cell structure organization, GO:0003985, GO:0008610, GO:0000988, GO:0015631, protein homodimerization]]0.03
731text-davinci-003ontological_synopsisHALLMARK_CHOLESTEROL_HOMEOSTASIS-1[[GO:0042632, MESH:D055438, GO:0005515, GO:0006351, GO:0010468, dna-binding, GO:0007165, negative regulation, positive regulation, GO:0016491, GO:0008610, GO:0003723, ldl particle binding, GO:0019901, phosphotransferase activity, acetyl-coa ligase activity, endopeptidase activity, etc]][[GO:0006695, GO:0008610, positive regulation of transcription, GO:2001234, GO:0031647, regulation of cell adhesion/migration, atp binding activity, transcription factor binding activity, protein binding activity, protein kinase binding activity, signaling receptor binding activity, ion/metal binding activity, endopeptidase regulator activity, etc]]0.03
732text-davinci-003ontological_synopsisHALLMARK_COAGULATION-0[[the provided list of human genes are mainly involved in metabolism, adjustment of the immune system and coagulation, and development of cells and organs. in particular, they are found to be involved in binding activities and endopeptidase activities such as post-translational modification, transcription and regulation of protein. the enriched terms include calcium-dependent protein/phospholipid/lipoprotein binding activity, GO:0004197, protein homodimerization/homooligomerization activity, identical protein binding activity, and serine-type endopeptidase activity. \\n\\nmechanism: the expression and activities of these genes may play important roles in the development and metabolism of cells and organs by facilitating protein folding, GO:0043687, cell-matrix adhesion and crosstalk between proteins. the binding activities of these genes towards phospholipid, lipoprotein and other molecules mediate the interaction between cells and extracellular environment, and regulate blood coagulation and formation of extracellular matrix. the endopeptidase activities of these genes degrade and modulate proteins, which are essential for various biological processes]][[protein binding activity, collagen binding activity, identical protein binding activity, integrin binding activity, phospholipid binding activity, atp binding activity, fibronectin binding activity, GO:0008237, GO:0004252, metaloendopeptidase activity, calcium ion binding activity]]0.04
733text-davinci-003ontological_synopsisHALLMARK_COAGULATION-1[[protein binding activity, domain specific binding activity, disordered domain specific binding activity, GO:0008233, GO:0004252, GO:0005125, signaling receptor binding activity, identical protein binding activity, GO:0004222, GO:0003924, receptor tyrosine kinase binding activity, GO:0004421, phospholipid binding activity, amyloid-beta]][[the genes in this list are predicted to enable various calcium-dependent functions related to protein binding, GO:0019899, and peptidase activity, typically related to blood coagulation, GO:0007155, endodermal cell fate, and negative regulation of protein-regulating processes. these genes are involved in various activities across multiple cellular pathways, including cellular response to uv-a, GO:0030155, and blood coagulation. the enriched terms include “calcium-dependent functions”, “protein binding activity”, “enzme binding activity”, “peptidase activity”, “blood coagulation”, “cell adhesion”, “endodermal cell fate”, “negative regulation of protein-regulating processes”, “cellular response to uv-a”, and “regulation of cell adhesion”.\\n\\nmechanism: the mechanism underlying this list of genes is likely related to calcium-dependent regulation of proteins and peptides, which acts to control various cellular processes. calcium can act as a negative regulator of proteins, through calcium binding to proteins and preventing their activity, or as a]]0.00
734text-davinci-003ontological_synopsisHALLMARK_COMPLEMENT-0[[enriched functions observed in the genes include binding activitiy (for various ligands, such as dna, GO:0005562, MESH:C062738, calcium ions, heparin/heparan sulphate, MESH:D019204, c5l2 anaphylatiotaxin, MESH:M0028275, mhc, amyloid-beta, cytokine, opsonin, MESH:D005227, MESH:D011494, etc.), enzyme activity (such as deubiquitinase, lck, atpase, aminopeptidase, peptidase, etc.), GO:0044183, cysteine type endopeptidase inhibitor activity and endopeptidase activity, phospholipid binding activity, transcription factor activity and transcription regulatory region sequence-specific dna binding activitiy. the underlying mechanism could be related to signal transduction, functional process, dna/rna transcription, protein degradation and signalling pathways such as cell killing and apoptotic signalling pathways.\\n\\nsummary: enriched functions include multiple binding activities, GO:0003824, and transcription regulatory activities for signal transduction, functional processes, and signalling pathways. \\nmechanism: signal transduction, functional processes, dna/rna transcription, protein degradation,]][[protein binding activity, GO:0001216, enzyme binding activity, metal ion binding activity, sh2 domain binding activity, GO:0004197, phosphoprotein binding activity, actin binding activity, cation binding activity, lipid binding activity, GO:0004252, GO:0008092, cell killing activity, protein kinase binding activity]]0.00
735text-davinci-003ontological_synopsisHALLMARK_COMPLEMENT-1[[enzyme binding activity, GO:0101005, GO:0004197, GO:0005102, GO:0019901, sh2 domain binding activity, GO:0004435, GO:0003924, GO:0004222, atpase binding activity, integrin binding activity, dna binding activity, lipoprotein receptor binding activity, GO:0007165, GO:0006915, MESH:D015850]][[dna-binding, GO:0005543, GO:0005515, GO:0005102, GO:0019899, inhibitor activities, GO:0003924, GO:0046872, protein activities, GO:0023052, transcription regulation, GO:0006281, GO:0008219, GO:0006955]]0.07
736text-davinci-003ontological_synopsisHALLMARK_DNA_REPAIR-0[[the given list of human genes are primarily involved in dna binding, transcription and translational activities, rna binding, enzyme binding activities, and identical protein and nucleic acid binding activities. there is also evidence of involvement in activities such as transcription co-activator activity, nuclear localization, cytochrome-c oxidase activity, atp-dependent activities and endopeptidase activator activity. enriched terms include dna binding, GO:0003723, GO:0003887, GO:0046983, identical protein binding activity, transcription factor binding activity, GO:0003700, zinc ion binding activity, atp binding activity, protein binding activity]][[dna binding activity, rna binding activity, enzyme binding activity, protein binding activity, calcium ion binding activity, GO:0140612, GO:0003713, zinc ion binding activity]]0.12
737text-davinci-003ontological_synopsisHALLMARK_DNA_REPAIR-1[[dna binding activity, rna binding activity, transcription activity, enzyme binding activity, GO:0042803]][[dna binding activity, enzyme binding activity, GO:0016887, rna binding activity, protein binding activity, GO:0003887, GO:0004518, mrna regulatory element binding]]0.30
738text-davinci-003ontological_synopsisHALLMARK_E2F_TARGETS-0[[GO:0007049, GO:0006260, transcriptional regulation, post-transcriptional regulation, GO:0003682, GO:0140014, GO:0051169, GO:0046931]][[chromatin binding activity, GO:0006260, GO:0006281, GO:0006351, GO:0016570, nuclear import/export, dna/rna binding, protein-macromolecule binding, GO:0051726, protein homodimerization, GO:0006200, GO:0000287, MESH:D011494, GO:0004518]]0.05
739text-davinci-003ontological_synopsisHALLMARK_E2F_TARGETS-1[[dna binding activity, protein binding activity, histone binding activity, GO:0016887, enzyme binding activity, GO:0006260, GO:0006306, chromatin binding activity, GO:0042803, GO:0003887, rna binding activity]][[nuclear pore remodeling, GO:0065003, GO:0003677, transcriptional regulation, GO:0006260, GO:0006913, chromatin modification and repair, cell cycle progression, GO:0140014, GO:0019899, GO:0042393, protein homod]]0.05
740text-davinci-003ontological_synopsisHALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0[[extracellular matrix structural components, GO:0007160, protein domain specific binding activity, identical protein binding activity, GO:0048018, signaling receptor binding activity, metal ion binding activity, peptide hormone receptor binding activity, heparin binding activity, collagen binding activity, GO:0007165, GO:0005125]][[protein binding activity, identical protein binding activity, collagen binding activity, integrin binding activity, heparin binding activity, phosphatidylinositol binding activity, cell adhesion molecule binding activity, extracellular matrix binding activity, signaling receptor binding activity, GO:0008009, gene transcriotion activity, metal ion binding activity]]0.26
741text-davinci-003ontological_synopsisHALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1[[protein binding activity, identical protein binding activity, metal ion binding activity, ion binding activity, actin binding activity, small molecule binding activity, fibronectin binding activity, collagen binding activity, integrin binding activity, procollagen binding activity, cadherin binding activity, phosphatidylinositol-3,4,5-trisphosphate binding activity, substrate-binding activity, GO:0005096, GO:0004867, GO:0005006, GO:0005024, GO:0004896, platelet-derived growth factor binding activity, nucleotide-binding transcription factor activity]][[GO:0005201, collagen binding activity, cell adhesion molecule binding activity, dna binding activity, gtp binding activity, GO:0042803, platelet-derived growth factor binding activity, platelet-derived growth factor binding activity, calcium ion binding activity, signaling receptor binding activity, identical protein binding activity]]0.11
742text-davinci-003ontological_synopsisHALLMARK_ESTROGEN_RESPONSE_EARLY-0[[binding activity, transport activity, GO:0003824, adhesion activity, intracellular signaling, GO:0006351, neuronal development]][[dna binding activity, protein binding activity, enzyme binding activity, GO:0022857, transcription activity, GO:0003924, atpase binding activity, mrna binding activity, protein homodimerization, GO:0042169, GO:0016922, GO:0030165]]0.00
743text-davinci-003ontological_synopsisHALLMARK_ESTROGEN_RESPONSE_EARLY-1[[GO:0003677, GO:0051117, GO:0005515, GO:0016791, dehydrogenase activity, GO:0004016, GO:0055085, transcriptional regulation, GO:0007155, GO:0006915]][[GO:0003677, GO:0000981, GO:0003723, protein binding/dimerization, transmembrane transporter, GO:0005509, GO:0019899, GO:0003924]]0.06
744text-davinci-003ontological_synopsisHALLMARK_ESTROGEN_RESPONSE_LATE-0[[protein binding activity, dna-binding, domain binding activity, carbohydrate binding activity, enzyme binding activity, ligand binding activity, transmembr]][[GO:0050839, GO:0003677, transfacmembrane receptor protein tyrosine kinase activity, ligand binding, ca2+ ion binding, GO:0005543, GO:0019899, GO:0016563, GO:0005243, GO:0003682, GO:0032794, GO:0048018, GO:0005242, GO:0004930, GO:0060089, calcium-dependent exonuclease activity, GO:0003779, GO:0007165, GO:0004672, GO:0016310, sh2 domain binding activity, heme binding activity, GO:0042803, hsp90 protein binding activity, GO:0017002, GO:0004957, ww domain binding activity, pdz domain binding activity, sh3 domain binding activity]]0.00
745text-davinci-003ontological_synopsisHALLMARK_ESTROGEN_RESPONSE_LATE-1[[dna-binding, GO:0016563, GO:0005515, membrane transporter activity, GO:0016787, GO:0016310, ligand-mediated activity]][[GO:0008134, GO:0019899, GO:0005515, GO:0007155, ligand-gated ion transporter activity, GO:0001216, GO:0050839, protein domain specificity, GO:0030742, GO:0003677, GO:0019003, GO:0005525, GO:0051117, GO:0030165, GO:0005509, phosphotransfer, GO:0031490, GO:0001217]]0.04
746text-davinci-003ontological_synopsisHALLMARK_FATTY_ACID_METABOLISM-0[[GO:0006631, GO:0006629, GO:0005975, GO:0003677, GO:0003723, protein homodimerization, GO:0000287, GO:0005524, GO:0046872, GO:0047617, GO:0003995, fad binding activity, nadph binding activity, homodimerization activity, GO:0000774, GO:0015254, GO:0004497, 5alpha-androstane-3alpha,17beta-diol dehydrogenase activity, GO:0008170, identical protein binding activity, GO:0016860, enzyme binding activity, GO:0004674, GO:0042803, GO:0004351, GO:0004222, ubiquitin binding activity, dna-binding]][[protein binding activity, identical protein binding activity, metal ion binding activity, atp binding activity;lipid transport activity, fatty acid binding activity, fad binding activity, pdz domain binding activity;transmembrane transporter activity, ubiquitin binding activity, nucleotide binding activity, GO:0004080, GO:0004738, enoyl-coa hydratase activity;amino-acid oxidase activity, GO:0003979, GO:0009055, GO:0004853, 5alpha-reductase activity, rna-binding]]0.07
747text-davinci-003ontological_synopsisHALLMARK_FATTY_ACID_METABOLISM-1[[GO:0016491, enzyme binding activity, dna binding activity, GO:0004090, GO:0052650, GO:0015245, nadph binding activity, GO:0042803, atp binding activity, receptor ligand binding activity, nad+ binding activity, smad binding activity, rna polymerase ii-specific transcription factor activity, atp-dependent protease activity, GO:0016404, GO:0004672, ubiquitin conjugating]][[GO:0003824, GO:0016491, protein binding activity, hydratase activity, GO:0003997, lipid binding activity, dna binding activity, ubiquitin binding activity, atp binding activity, flavine adenine dinucleotide binding activity, nadp+ binding activity, GO:0042803, smad binding activity, GO:0004466]]0.19
748text-davinci-003ontological_synopsisHALLMARK_G2M_CHECKPOINT-0[[GO:0003677, transcription binding, GO:0046872, GO:0005515, GO:0019899, MESH:D020558, GO:0003682, GO:0042826, GO:0046983, sumo-dependent ubiquitination, GO:0003723, GO:0005524, GO:0042054, GO:0008017, GO:0010997, boxh/aca snorna binding, GO:0043515, GO:0070840, m7gpppn-cap structure binding, GO:0008270, GO:0003697, GO:0038024, GO:0006200, GO:0051536, GO:0005884]][[dna binding activity, rna binding activity, protein kinase binding activity, protein folding activity, enzyme binding activity, transcription factor binding activity, chromatin binding activity, protein domain specific binding activity, nucleic acid binding activity, atp binding activity, identical protein binding activity, GO:0140110, GO:0046983, histone binding activity, anaphase-promoting complex binding activity, cytoplasmic release activity, metal ion binding activity, GO:0016887, histone deacetylase binding activity, telomere binding activity]]0.02
749text-davinci-003ontological_synopsisHALLMARK_G2M_CHECKPOINT-1[[GO:0005515, GO:0003677, GO:0006351, GO:0019904, GO:0042054, GO:0004402, GO:0004674, GO:0030374, GO:0005049, GO:0016887, zinc ion binding activity, GO:0140037, GO:0036310, sumo polymer binding activity, nuclear receptor binding activity, dna topoisomerase binding activity, GO:0010997, GO:0000774, GO:0005096, microtubule binding activity, dna replication origin binding activity, GO:0000987, rna polymerase ii-specific transcription]][[GO:0005515, GO:0003677, GO:0008134, MESH:D019098, GO:0003723, GO:0006260, GO:0051726, GO:0003682, GO:0010467, GO:0006457, regulation of chromosome structure, GO:0019904, GO:0005524, GO:0019900, GO:0035402, GO:0031267, MESH:M0518050, protein homodimerization, GO:0043130, atp-dependent dna/dna annealing]]0.07
750text-davinci-003ontological_synopsisHALLMARK_GLYCOLYSIS-0[[GO:0003676, GO:0005515, GO:0005524, metabolic activity, GO:0016310, MESH:D010084, GO:0005975, GO:0005125, GO:0008083]][[the list of genes represent a range of molecular, metabolic, and protein regulatory processes, including atpase activity, glucose binding activity, GO:0004672, transcriptional activity and activity from receptors, transporters, and enzymes. the enriched terms are \"protein binding activity\"; \"atpase activity\"; \"transcriptional activity\"; \"receptor activity\"; \"transporter activity\"; \"enzyme activity\"; and \"glucose binding activity\".\\n\\nmechanism: the genes in the list encode proteins involved in a range of processes, such as structural support, GO:0007165, regulation of transcription, metabolic pathways and transport of molecules. the underlying biological mechanism is likely related to the coordinated expression of these genes in response to a particular stimulus, or to maintain cellular homeostasis]]0.00
751text-davinci-003ontological_synopsisHALLMARK_GLYCOLYSIS-1[[protein binding activity, identical protein binding activity, enzyme binding activity, atp binding activity, transcription activation activity, dna-binding transcription activity, heparin binding activity, cytoplasmic protein binding activity, signalling receptor binding activity, cytoskeletal protein binding activity, GO:0042803, GO:0060422, rna binding activity, GO:0140677, GO:0004689, phosphotransferase activity, heme binding activity, calcium ion binding activity]][[enzyme binding activity, identical protein binding activity, dna binding activity, GO:0042803, heparin binding activity, atp binding activity, protein kinase binding activity, phosphatase binding activity, cyclin binding activity, protein phosphatase binding activity, GO:0004722, actin binding activity, lbd domain binding activity, actin filament binding activity, GO:0008083, chromatin binding activity, hyaluronic acid binding activity, GO:0004197, ubiquitin binding activity, cyclosporin a binding activity, mannose-binding activity, heparan sulfate binding activity, heme binding activity, GO:0016887, transition metal ion binding activity, GO:0031545, GO:0016615, GO:0004148, GO:0004784, transcription core]]0.14
752text-davinci-003ontological_synopsisHALLMARK_HEDGEHOG_SIGNALING-0[[GO:0007155, GO:0007165, epithelial-mesenchymal interaction, GO:0006898, GO:0001525, GO:0001843]][[protein/lipid binding activity, GO:0003700, GO:0010468, GO:0051246, positive/negative regulation of cellular component organization, GO:0030036, GO:0030833, GO:0001525, GO:0090630, GO:0019219, GO:0007160]]0.06
753text-davinci-003ontological_synopsisHALLMARK_HEDGEHOG_SIGNALING-1[[GO:0003700, rna polymerase ii transcription regulatory region sequence-specific dna binding activity, chromatin binding activity, receptor binding activity, GO:0005096, gtpase binding activity, phospholipid binding activity, calcium ion binding activity, zinc ion binding activity, identical protein binding activity, apolipoprotein binding activity, phosphotyrosine residue binding activity, very-low-density lipoprotein particle binding activity, phosphatidylcholine binding activity, phosphatidylethanolamine binding activity, adenyl ribonucleotide]][[acetylcholine binding activity, GO:0003990, GO:0005096, rna polymerase ii-specific dna-binding transcription factor binding activity, GO:0003714, GO:0017053, GO:0007165, GO:0006351, GO:0007155, GO:0016477, GO:0001525, GO:0035556, GO:0019219, GO:0006468]]0.03
754text-davinci-003ontological_synopsisHALLMARK_HEME_METABOLISM-0[[identical protein binding activity, dna binding activity, rna binding activity, GO:0000988, GO:0003714, GO:0016564, GO:0016563, GO:0016791, protein kinase binding activity, GO:0006865, GO:0006811, heme binding activity, oxygen binding activity, protein-fructose gamma-glutamyltransferase activity, GO:0042803, lamin binding activity, chromatin binding activity and ubiquitin ligase activity]][[dna-binding, rna-binding, GO:0019899, GO:0019901, GO:0019903, protein homodimerization, GO:0048729, GO:0006468]]0.00
755text-davinci-003ontological_synopsisHALLMARK_HEME_METABOLISM-1[[transcription activity, dna binding activity;rna binding activity, protein kinase binding activity, atp binding activity, protein binding activity, identical protein binding activity, GO:0042803, GO:0004197, GO:0015075, protein domain specific binding activity, GO:0032452, GO:0004674, GO:0016564, GO:0061630, lamin binding activity, GO:0004521, GO:0038023, GO:0004602, phosphoprotein binding activity, molecule adaptation, enzyme binding activity, protein phosphatase binding activity, GO:0004418, ubiquitin conjugating enzyme binding activity, GO:0004842, ap-2 adapt]][[GO:0003677, GO:0005515, GO:0016310, GO:0003824, GO:0005215, MESH:M0496924, vesicular pathways, cytoskeletal pathways, GO:0046872, GO:0003723, GO:0030544, GO:0042802, GO:0008013, phosphatidylinositol-4 binding, GO:0035612, rna polymerase ii dna binding, GO:0042393, GO:0019901, tyrosine-protein kinase activity, GO:0061630, GO:0003713, fibronectin leucine-rich-repeat sense-specific binding, endothelial differentiation-specific factor binding, fatty-acid binding, heme-binding, GO:0051537, GO:0050661, GO:0070742, MESH:D012330]]0.02
756text-davinci-003ontological_synopsisHALLMARK_HYPOXIA-0[[dna-binding transcription activity, enzyme binding activity, protein binding activity, ligand-binding activity, atp binding activity, nadp binding activity, metal ion binding activity, carbohydrate binding activity, signaling receptor binding activity, GO:0003714, GO:0001217, GO:0008160, heparin binding activity, n-acetylglucosamine n-sulfotransferase activity, MESH:D006497]][[this is a list of genes of known or suspected functions in a variety of processes, ranging from dna binding and transcription regulation to enzyme binding, metabolic activity, GO:0005102, and structural protein formation. commonly enriched terms include dna binding, transcription regulation, GO:0019899, and protein binding. mechanism: a variety of processes are involved in these gene functions, including dna replication and repair, protein folding and conformational change, receptor binding and signal transduction, metabolic activity, structural protein formation]]0.00
757text-davinci-003ontological_synopsisHALLMARK_HYPOXIA-1[[dna binding activity, rna binding activity, protein binding activity, GO:0004672, GO:0019887, GO:0016407, GO:0016301, GO:0008233, GO:0004197, GO:0004252, ubiquitin binding activity, GO:0042803, GO:0000988, GO:0016563, GO:0016564, apolipoprotein binding activity, phosphatase binding activity, disordered domain specific binding activity, chromatin binding activity, GO:0016303, GO:0030701, GO:0004693, GO:0004396, actinin binding activity, 14-3-3 protein binding activity, gtp binding activity, MESH:D009584]][[dna-binding transcription activity, GO:0003714, GO:0016564, GO:0016563, rna polymerase ii-specific, protein binding activity, GO:0042803, platelet-derived growth factor binding activity, GO:0030291, GO:0046982, GO:0004197, protein kinase binding activity, GO:0019887, GO:0004725, cyclin binding activity, GO:0004693, GO:0035403, phosphatidylinositol-3-kinase activity, nad+]]0.18
758text-davinci-003ontological_synopsisHALLMARK_IL2_STAT5_SIGNALING-0[[ligand binding, GO:0019899, GO:0005102, MESH:M0518050, GO:0003700, rna-binding, protein homodimerization, protein-kinase binding activity, identical protein binding activity, GO:0004896, c-c chemokine binding activity, GO:0004197, GO:0022857, gtp binding activity, protease binding activity]][[GO:0005096, dna-binding transcription activator/repressor activity, protein binding activity, ligand binding activity, identical protein binding activity, bh3 domain binding activity, phosphatidylinositol binding activity, GO:0016787, atp binding activity, atpase-coupled intramembrane lipid transport activity, amyloid-beta binding activity, hsp90 protein binding activity, s100 protein binding activity, cadherin binding activity, GO:0038023, GO:0005125, GO:0005021, GO:0004896, identical protein binding activity, GO:0008233, heat shock protein]]0.06
759text-davinci-003ontological_synopsisHALLMARK_IL2_STAT5_SIGNALING-1[[dna-binding, transcriptional activity, GO:0006355, GO:0005515, protein homodimerization, GO:0003924, GO:0005102, ligand-activated transcription, GO:0019900, GO:0002020, GO:0004674, GO:0004175, cystein-type endopeptidase activity, GO:0005102, GO:0061630, GO:0005125, GO:0008083, leukemia inhibitory factor activity, 5'-deoxyn]][[dna-binding transcription activity, protein kinase binding activity, small gtpase binding activity, interleukin-binding activity, GO:0004896, signaling receptor binding activity, rna binding activity, gtp binding activity, GO:0004197, identical protein binding activity, protein domain specific binding activity, GO:0046982]]0.00
760text-davinci-003ontological_synopsisHALLMARK_IL6_JAK_STAT3_SIGNALING-0[[GO:0038023, binding activity, MESH:D016207, MESH:M0496065, MESH:D008074, MESH:D010455, MESH:D011506, GO:0019900, GO:0005524]][[cytokine binding activity, protein binding activity, kinase binding activity, signaling receptor binding activity, GO:0004675, cell adhesion molecule binding activity, interleukin-receptor activity, GO:0004725, tir domain binding activity, ubiquitin protein ligase binding activity, GO:0008284, GO:0032768, GO:0009966, GO:0090276, GO:0045597, GO:0010604, GO:0098542, GO:0009612, GO:0001819, GO:0031349]]0.00
761text-davinci-003ontological_synopsisHALLMARK_IL6_JAK_STAT3_SIGNALING-1[[GO:0004896, cxcr chemokine receptor binding activity, interleukin-binding activity, GO:0006952, GO:0010605, GO:0051247]][[cytokine binding activity, GO:0004896, GO:0008083, cell adhesion molecule binding activity, chemokine (c-x3-c) binding activity, GO:0006952, signaling receptor binding activity, GO:0000988, identical protein binding activity, phosphatidylinositol binding activity, heparin binding activity, lipid binding activity, c-c chemokine binding activity, dna binding activity, GO:0005096, sh3 domain binding activity, ephrin receptor binding activity, transforming growth factor beta receptor binding activity, ubiquitin-like protein ligase binding activity, enzyme binding activity, calcium-dependent protein binding activity, protease binding activity]]0.08
762text-davinci-003ontological_synopsisHALLMARK_INFLAMMATORY_RESPONSE-0[[protein binding activity, GO:0005125, GO:0004930, dna-binding transcription activity, lipopolysaccharide binding activity, atp binding activity, integrin binding activity, GO:0048018, GO:0022857, signaling receptor binding activity, extracellular atp-gated channel activity, phosphatidylinositol- 3-kinase activity, metallod]][[GO:0004930, GO:0005125, GO:0003700, GO:0005216, receptor binding activity, GO:0008083, cell adhesion molecule binding activity, signalling receptor binding activity, GO:0003714, enzymatic activity, phospholipid binding activity, peptide hormone receptor binding activity, GO:0003924]]0.08
763text-davinci-003ontological_synopsisHALLMARK_INFLAMMATORY_RESPONSE-1[[GO:0038023, binding activity, GO:0003824, GO:0008083, GO:0005215, GO:0000988]][[atp binding activity, chemokine/chemokine receptor/chemokine receptor binding activity, cytokine/cytokine binding activity/cytokine receptor activity, dna binding activity/dna-binding transcription factor activity, GO:0004930, identical protein binding activity, ion transport/ion transporter activity, peptide/peptide receptor binding activity, phospholipid binding activity, GO:0019887, signaling receptor binding activity, GO:0000988, GO:0022857]]0.06
764text-davinci-003ontological_synopsisHALLMARK_INTERFERON_ALPHA_RESPONSE-0[[signaling receptor binding activity, GO:0003713, regulation of transcription, dna-binding activity, rna binding activity, metal ion binding activity, identical protein binding activity, GO:0042803]][[immunologic processes, GO:0098609, GO:0006952, cellular response, positive regulation, rna polymerase ii specific, GO:0003677, GO:0003723, protein homodimer]]0.00
765text-davinci-003ontological_synopsisHALLMARK_INTERFERON_ALPHA_RESPONSE-1[[GO:0098542, GO:0006955, GO:0046718, GO:0032020, GO:0019882, GO:0019221, GO:0045087, GO:0007166, GO:0030225, GO:0032722, GO:0001961, cell-cell adhesion mediated by plasma membrane cell adhesion molecules]][[GO:0003713, rna binding activity, dna binding activity, identical protein binding activity, GO:0061630, zinc ion binding activity, GO:0042803, double-stranded rna binding activity, heparin binding activity, GO:0030701, GO:0004175, cxcr chemokine receptor binding activity, tap binding activity, peptide antigen binding activity, gtp binding activity, GO:0033862, GO:0004197, amyloid-beta binding activity, macrophage migration inhibitory factor binding activity, GO:0004550, GO:0016064, GO:0140374, GO:0071345, GO:0046597, positive regulation of]]0.00
766text-davinci-003ontological_synopsisHALLMARK_INTERFERON_GAMMA_RESPONSE-0[[the list of genes are discovered to be enriched in terms like dna binding activities, GO:0042803, GO:0000988, GO:0004672, GO:0004725, GO:0016887, enzyme binding activity, phosphatidylinositol phosphate binding activity, GO:0030528, GO:0008009, and cytokine receptor activity.\\n\\nmechanism: the biological mechanism underlying the enriched terms is most likely associated with cell and immune response. these genes are involved in various processes related to cell signaling, detection, recognition, GO:0006351, and expression. through these processes, the genes regulate important functions such as cell adhesion, GO:0005515, GO:0019899, GO:0005125, and transcription factor activation. in addition, several of these genes are also involved in apoptotic and other cell regulation pathways]][[protein binding activity, enzyme binding activity, dna-binding transcription activity, GO:0006200, protein homodimerization, kinase regulation, protein dimerization.\\nmechanism: these genes are likely involved in the regulation of gene expression cell signaling pathways, enabling an array of signaling activities that help to maintain cellular homeostasis]]0.04
767text-davinci-003ontological_synopsisHALLMARK_INTERFERON_GAMMA_RESPONSE-1[[binding activity, GO:0003824, protein activity, GO:0000981]][[GO:0016887, dna binding activity, gtp binding activity, peptide antigen binding activity, GO:0004252, dna-binding transcription activity, GO:0005125, GO:0008009, GO:0004896, GO:0038023, GO:0004930, rna binding activity, enzyme binding activity, GO:0046983, phosphorylation-dependent protein binding activity, GO:0019887, GO:0140311, toll-interleukin receptor (tir) domain binding activity, signaling receptor binding activity, and]]0.00
768text-davinci-003ontological_synopsisHALLMARK_KRAS_SIGNALING_DN-0[[protein binding activity, transmembrane activity, GO:0003700, sequence-specific double-stranded dna binding activity, GO:0004930, identical protein binding activity, calcium ion binding activity, scaffold protein binding activity, transcription cis-regulatory region binding activity]][[GO:0004930, GO:0042803, calcium ion binding activity, sodium:potassium:chloride transporter activity, GO:0004683, platelet-derived growth factor activity, GO:0005007, cytoskeletal protein binding activity, GO:0015171, n6-threonylcarbamylade adenine dinucleotide synthetase activity, GO:0043273, intracellular transport activity, signal transduction activity, GO:0016887, GO:0004175, GO:0016491, GO:1990817, GO:0004958, beta-caten]]0.08
769text-davinci-003ontological_synopsisHALLMARK_KRAS_SIGNALING_DN-1[[dna-binding activity, transcription activity, calcium ion binding activity, atp-binding activity, protein binding activity, GO:0004930, cell death regulation, GO:0009653, GO:0042445]][[the list of genes is significantly enriched for dna-binding activities, calcium ion binding activities, identical protein-binding activities, GO:0046982, GO:0016887, and g protein-coupled receptor activities.\\n\\nmechanism:\\nthe underlying biological mechanism likely involves a complex, dynamic interaction between various proteins, MESH:D004798, and ions, driven by a variety of dna-binding, calcium-binding, and atp-binding activities, resulting in the recruitment of additional proteins to form heterodimers, thereby leading to protein synapsis cell signaling]]0.00
770text-davinci-003ontological_synopsisHALLMARK_KRAS_SIGNALING_UP-0[[cell adhesion molecule binding activity, atpase-coupled intramembrane transport, GO:0004222, GO:0042803, signal receptor binding activity, GO:0003700, MESH:D006493]][[atp binding activity, atpase-coupled intramembrane transport, GO:0048018, dna-binding transcription regulation, protein domain binding activity, enzyme binding activity, GO:0005125, GO:0007165, GO:0007155, GO:0016477, GO:0030154, MESH:D048788]]0.06
771text-davinci-003ontological_synopsisHALLMARK_KRAS_SIGNALING_UP-1[[GO:0005125, protein domain specific binding activity, protein kinase binding activity, cell adhesion molecule binding activity, signaling receptor binding activity, GO:0004222, GO:0001217, rna binding activity, gtpase binding activity, structural proteins, atp binding activity]][[receptor binding activity, identical protein binding activity, GO:0001216, enzyme binding activity, protein domain specific binding activity, protein kinase binding activity, ligand binding activity, atp binding activity, cytoskeletal protein binding activity, cell adhesion molecule binding activity, GO:0004930, transmembrane transporter binding activity, GO:0008233, dna binding activity, GO:0004252, histone binding activity, signal transduction activity]]0.17
772text-davinci-003ontological_synopsisHALLMARK_MITOTIC_SPINDLE-0[[protein binding activity, cytoskeleton binding activity, GO:0005096, atpase binding activity, GO:0042030, adenyl ribonucleotide binding activity, calmodulin binding activity, cadherin binding activity, gamma-tubulin binding activity, integrin binding activity, kinetochore binding activity, molecular function adaptor activity, GO:0042803, protein kinase binding activity, protein phosphatase binding activity, sh2 domain binding activity, sh3 domain binding activity, small gtpase binding activity, beta-catenin binding activity, beta-tubulin binding activity, dynein complex binding activity, identical protein binding activity, phosphatidylcholine binding activity, protein domain specific binding activity, protein tyrosine kinase binding activity]][[actin binding activity, atp binding activity, atpase binding activity, GO:0098632, dynein complex binding activity, gamma-tubulin binding activity, gtp binding activity, gtpase binding activity, guanyl ribonucleotide binding activity, GO:0003924, GO:0005085, kinetochore binding activity, GO:0060090, GO:0140677, myosin binding activity, phosphatidylcholine binding activity, GO:0019904, GO:0042803, GO:0004672, GO:0004674, small gtpase binding activity]]0.18
773text-davinci-003ontological_synopsisHALLMARK_MITOTIC_SPINDLE-1[[MESH:D020558, atpase, tubulin binding activity, microtubule binding activity, actin filament binding activity, kinesin binding activity, dynein binding activity, g protein-coupled receptor binding activity]][[this set of genes are involved in activities, processes and signaling pathways related to intracellular motion such as transport within cells (microtubule/kinesin/dynein binding, GO:0005096, GO:0008092, motor protein activity), cell cycle activities (centrosome duplication, GO:0019899, protein homodimerization, GO:0019902, GO:0003682, GO:0043515, GO:0005516, formin binding, atpase/atp hydrolysis regulatory activity), and cell-cell signaling (jun kinase kinase kinase activity, map-kinase scaffolding, GO:0042608, GO:0045296, GO:0051879, GO:0097016, GO:0005680, GO:0051059, rna binding).\\n\\nmechanism: these genes enable a wide range of activities and processes related to intracellular motion and cell-cell signaling that are either directly or indirectly connected to the assembly, MESH:M0030663, and disassembly of cytoskeletal structures, MESH:D014404, and cellular organelles. these activities can promote cell cycle progression, GO:0008283, and/or cell-cell signaling]]0.00
774text-davinci-003ontological_synopsisHALLMARK_MTORC1_SIGNALING-0[[enzyme binding activity, acid binding activity, molecule transport, adapter binding activity, receptor binding activity, dna binding activity, protein binding activity, GO:0003824, GO:0016787, GO:0016491, anion binding activity, GO:0008233, GO:0140657, thioredoxin activity, translocation, GO:0061630, cysteine endopeptidase activity, GO:0004738, GO:0004618, magnesium ion binding activity, GO:0004340, GO:0003924]][[protein binding activity, dna binding activity, enzyme binding activity, GO:0060090, GO:0140677, GO:0042803, domain binding activity, GO:0016491, protein kinase binding activity, phosphatidylinositol binding activity, GO:0016504, GO:0003714, nuclear androgen receptor binding activity, nf-kappab binding activity, ubiquitin protein ligase binding activity, phosphotyrosine residue binding activity, GO:0016564, GO:0003743, peptidyl-proinalyl cistrans isomerase activity]]0.11
775text-davinci-003ontological_synopsisHALLMARK_MTORC1_SIGNALING-1[[protein binding activity, identical protein binding activity, GO:0008233, GO:0003824, GO:0005884, dna-binding, rna-binding, GO:0016922, MESH:D054875, anion binding activity, atp binding activity, GO:0016887, protein kinase binding activity, phosphotyrosine residue binding activity, e3 ubiquitin-protein ligase binding activity, mdm2 binding activity, GO:0060090, GO:0140677, GO:0098772, GO:0003713, GO:0003714, GO:0016564, GO:0042803, k63]][[protein-protein interaction, atp binding activity, GO:0042803, GO:0016887, protein kinase binding activity, ubiquitin protein ligase binding activity, GO:0060090, anion binding activity, chemical oxidoreductase activity, protein domain specific binding activity, gtp binding activity, dna binding activity, rna binding activity, transcription regulation activity, GO:0007165, chromatin binding activity, phospholipid binding activity, GO:0004017, lipoprotein particle binding activity, GO:0008233, actin filament binding activity, fad binding activity, steroid hydrolase activity, rna stem-loop binding activity, GO:0022857, nf-kappab binding activity, coenzyme a binding activity, protein n-terminal phospho-seryl-prolyl pept]]0.16
776text-davinci-003ontological_synopsisHALLMARK_MYC_TARGETS_V1-0[[GO:0003677, GO:0003723, GO:0003682, GO:0006351, GO:0006412, GO:0045292, atpase binding activity, enzyme binding activity, GO:0044183, ubiquitin protein ligase, MESH:C021362, nf-kappab binding activity, GO:0140693, nucleic acid binding activity, heparan sulfate binding activity, biopolymer binding activity, GO:0060090, GO:0140678, g-protein beta-subunit binding activity, molecular sequence recognition, complementary rna strand recognition, mrna 3'-utr]][[GO:0003723, GO:0044183, dna binding/recognition, protein homodimerization, GO:0003678, GO:0019904, MONDO:0000179, GO:0042393, cytoplasmic protein binding, GO:0005524, GO:0006281]]0.06
777text-davinci-003ontological_synopsisHALLMARK_MYC_TARGETS_V1-1[[rna binding activity, identical protein binding activity, mrna 3' utr binding activity, GO:0000900, dna binding activity, ubiquitin protein ligase binding activity, protein domain specific binding activity, GO:0006457, dna replication origin binding activity, dna-binding transcription factor binding activity, GO:0042803]][[GO:0003677, GO:0003723, GO:0019904, GO:0003682, GO:0019899, protein folding chaperone activities, atp binding activity, mrna 3'-utr binding activity, identical protein binding activity, GO:0004869, GO:0140693, GO:0140713, heparan sulfate binding activity, peptidyl-prolyl isomerase activity, cyclin binding activity, GO:0004693, nuclear localization sequence binding activity, magnetic ion binding activity, histone methyltransferase binding activity, mrna 5'-utr binding activity, GO:0033677, MESH:D012321]]0.03
778text-davinci-003ontological_synopsisHALLMARK_MYC_TARGETS_V2-0[[GO:0006351, GO:0006351, GO:0008284, GO:0071824, GO:0019219, rna binding activity, GO:0010468, GO:0006364]][[rna-binding, GO:0036211, GO:0015031, cell signaling, GO:0006412, genetic information regulation, protein bridging, chromatin regulation, transcription regulation, GO:0003676, mitochondrial functions]]0.00
779text-davinci-003ontological_synopsisHALLMARK_MYC_TARGETS_V2-1[[rna binding activity, dna binding activity, protein binding activity, GO:0006364, GO:0019538, GO:0006351, transcription coregulator binding activity, GO:0022402, GO:0003682, mitochondria regulation, cyclin binding activity, cyclin-dependent protein serine/threonine kin]][[rna binding activity, ribosomal rrna processing, mrna and/or rrna catabolism/stability, regulation of transcription/translation, regulation of signal transduction and metabolism processes, regulation of cell cycle/proliferation, protein modification/regulation, GO:0005634, GO:0005829, GO:0005840, GO:0005739]]0.05
780text-davinci-003ontological_synopsisHALLMARK_MYOGENESIS-0[[GO:0008092, GO:0005201, GO:0044325, ion channel regulator, GO:0003779, GO:0005096, GO:0051879, GO:0017046, GO:0003677, signalling receptor binding, GO:0042802, GO:0048306, GO:0019899, GO:0005509, GO:0005524, GO:0006200, GO:0051117, GO:0004017, GO:0008195, GO:0051015, microfilament binding, GO:0003872, GO:0043138, GO:0004517, MESH:D009243]][[calcium ion binding activity, identical protein binding activity, actin filament binding activity, GO:0042803, signaling receptor binding activity, atp binding activity, gtp binding activity, dna binding activity, GO:0019887]]0.00
781text-davinci-003ontological_synopsisHALLMARK_MYOGENESIS-1[[GO:0005509, GO:0004129, GO:0003677, GO:0005524, GO:0003779, abnormal growth and development, GO:0002020, structural constituent]][[calcium binding activity, enzyme binding activity, dna binding activity, atp binding activity, GO:0042803, protein domain-specific binding activity, gtp binding activity, actin binding activity, GO:0008160, small gtpase activator activity, transmembrane transporter binding activity, GO:0004016, c3hc4-type ring finger domain-binding activity, GO:0060090, GO:0005096]]0.00
782text-davinci-003ontological_synopsisHALLMARK_NOTCH_SIGNALING-0[[GO:0036211, MESH:D005786, signal transduction regulation, dna-templated transcription regulation, GO:0007219, GO:0016567, GO:0031146, GO:0045893]][[this list of genes is associated with several biological processes related to the regulation of gene expression, such as notch receptor processing, amyloid-beta formation, proteolysis, regulation of cell differentiation, canonical wnt signaling pathway, protein ubiquitination, scf-dependent proteasomal ubiquitin-dependent protein catabolic process, and positive regulation of transcription by rna polymerase ii. the underlying biological mechanism is likely related to the role of these genes in transcription and post-transcriptional gene regulation. enriched terms include: gene expression regulation, GO:0007220, GO:0034205, GO:0006508, GO:0045595, GO:0060070, GO:0016567, GO:0031146, GO:0045944]]0.13
783text-davinci-003ontological_synopsisHALLMARK_NOTCH_SIGNALING-1[[GO:0006351, GO:0036211, MESH:D054875, GO:0065007, GO:0007219, GO:0031146, wnt, GO:0016567, GO:0043543, GO:0004879, GO:0003714, transcription corepressor binding activity, GO:0006351, rna polymerase ii-specific dna-binding transcription repressor activity, GO:0045893, GO:0000122, GO:0045737, GO:0010604, GO:0010628, negative regulation of cell different]][[GO:0016567, GO:0031146, GO:0007219, GO:0036211, GO:0010468, GO:0030335, GO:0008284, GO:0045596]]0.17
784text-davinci-003ontological_synopsisHALLMARK_OXIDATIVE_PHOSPHORYLATION-0[[GO:0006118, GO:0020037, GO:0005515, GO:0016491, atpase activity & binding activity, GO:0060090, acyl binding activity, GO:0003954, gtp binding activity, iron-sulfur cluster binding activity, fad binding activity, MESH:D010758, GO:0019395, rna binding activity, 4 iron, 4 sulfur cluster binding activity, ubiquitin protein ligase binding activity, GO:0004129, proton-transporting atp synthase activity, lipoic acid binding activity, mhc class i protein binding activity, angiostatin binding activity, deltarasin binding activity, ubiquitin protein binding activity, nadp binding activity]][[acetyl-coa transferase activity, GO:0003995, aldehyde dehydrogenase activity, atpase binding activity, GO:0004129, GO:0009055, GO:0004300, fad binding activity, GO:0003924, heme binding activity, identical protein binding activity, lipid binding activity, metal ion binding activity, GO:0003958, GO:0016491, GO:0004738, pro]]0.08
785text-davinci-003ontological_synopsisHALLMARK_OXIDATIVE_PHOSPHORYLATION-1[[GO:0140657, GO:0009055, GO:0008553, ubiquitin protein ligase binding activity, MESH:D014451, heme binding activity, protein homodimerization, mhc class i protein binding activity, metal ion binding activity, angiostatin binding activity, mitochondrion targeting sequence binding activity, GO:0015227, rna binding activity, 4 iron, 4 sulfur cluster binding activity, GO:0000295, GO:0004129, fatselytranstransferase activity, GO:0003925, acyl-coa c-acetyltransferase activity, GO:0004774, GO:0003994, GO:0004095, GO:0003958, acetate coa-transfer]][[GO:0009055, protein homodimerization, GO:0003924, GO:0000295, phosphoprotein binding activity, mitochondrial respiratory chain activity, proton-transporting atp synthase activity, mitochondrial ribosome binding activity]]0.10
786text-davinci-003ontological_synopsisHALLMARK_P53_PATHWAY-0[[GO:0003700, protein binding activity, protein kinase binding activity, GO:0042803, enzyme binding activity, GO:0098631, signaling receptor binding activity, actin binding activity, cyclin binding activity, GO:0005198, GO:0030695]][[dna binding activity, rna polymerase ii-specific dna-binding transcription factor binding activity, transcription regulation, protein binding activity, enzyme binding activity]]0.14
787text-davinci-003ontological_synopsisHALLMARK_P53_PATHWAY-1[[dna binding activity, rna binding activity, rna polymerase binding activity, GO:0004672, GO:0042803, protein kinase binding activity, GO:0000988, GO:0003924, GO:0098631, cell signaling receptor binding activity, enzyme binding activity, heme binding activity, collagen binding activity, GO:0004392, GO:0060090, GO:0004527, GO:0042803, g protein-coupled receptor binding activity, GO:0022857, identical protein binding activity, GO:0016787, GO:0008083]][[GO:0007165, MESH:D005786, GO:0005515, GO:0019899, GO:0016791, GO:0000988, GO:0007155, growth factor binding. \\nmechanism: these genes are involved in the regulation of gene expression and cellular processes by modulating signal transduction, binding proteins, and enzymes, as well as activating phosphatase activity, transcription factor activity and growth factor binding]]0.03
788text-davinci-003ontological_synopsisHALLMARK_PANCREAS_BETA_CELLS-0[[GO:0006351, GO:0016563, atpase-coupled ion transport, GO:0004672, GO:0008233, dna binding activity, GO:0017156, GO:1903530]][[atp binding activity, GO:0019829, GO:0016477, GO:0044249, GO:0071333, GO:0090398, GO:0042742, GO:0005789, e-box binding activity, GO:0015149, GO:0002551, GO:0043303, GO:0008233, GO:0008607, GO:0045597, positively regulation of cellular biosynthetic process, positively regulation of glycolytic process, positively regulation of insulin secretion, positively regulation of macromolecule metabolic process, positively regulation of type b pancreatic cell development, positive regulation of cellular]]0.04
789text-davinci-003ontological_synopsisHALLMARK_PANCREAS_BETA_CELLS-1[[transcription regulation, GO:0098609, GO:0007165, GO:0045047, GO:0030041, GO:0051594, GO:0060291, GO:1903561, GO:0030027, GO:0005881, GO:0043195, GO:0005829, GO:0030425, MESH:D012319, dna-templated trans]][[GO:0098609, GO:0032502, differentiation, UBERON:0000061, transcription regulation, MESH:D012319, GO:0007165, GO:0043170, protein expression, cell signaling, protein production]]0.18
790text-davinci-003ontological_synopsisHALLMARK_PEROXISOME-0[[molecular binding activity, GO:0003824, GO:0005215, domain binding activity, GO:0006869, GO:0015031, GO:0006259, GO:0016070]][[after term enrichment analysis on the gene summaries, the following terms were found to be enriched: atp binding activity, atpase-coupled activity, GO:0042803, identical protein binding activity, enzyme binding activity, GO:0005319, GO:0016887, and metal ion binding activity.\\n\\nmechanism: the enriched terms suggest a biological mechanism that involves energy production and transport, GO:0007165, and protein interactions and formation of protein complexes. these processes are necessary for various cellular processes such as metabolism, GO:0007585, GO:0098754, GO:0040007]]0.00
791text-davinci-003ontological_synopsisHALLMARK_PEROXISOME-1[[genes involved in this list are primarily associated with the metabolic or structural processes needed for cellular development and homeostasis. enriched terms include fatty acid metabolism, protein homodimerization, MESH:D010084, dna and rna binding, enzyme/acyl-coa/gtpase binding/hydrolase activity, transport/export/import, and regulation of transcription by rna polymerase ii. mechanism: these genes act together to provide a plethora of functions that are integral to the growth, maintenance and protection of cells. fatty acids are transported, oxidized, and bound to proteins or phospholipids in the membrane, proteins interact with atp and gtp and undergo homodimerization, transcriptional activity is regulated by heterodimerizing with transcription factor proteins]][[cell metabolic process, GO:0090304, GO:0005515, GO:0003677, GO:0016485, GO:0042446, GO:0006694, GO:0005524, GO:0006200, protein homodimerization, GO:0019901, GO:0003714, GO:0003712, cyclin binding activity, rna binding activity, protein phosphatase binding activity, sulphatide binding activity, magnesium ion binding activity, GO:0043621, MESH:M0518050, protein transmembrane]]0.03
792text-davinci-003ontological_synopsisHALLMARK_PI3K_AKT_MTOR_SIGNALING-0[[protein binding activity, GO:0016301, GO:0005048, GO:0005102, GO:0051726, apoptosis regulation, GO:0007165, rna binding activity, GO:0004721, GO:0004620, GO:0003924, 1-phosphatidylinositol phospholipase activity, phosphotyrosine residue binding activity, GO:0000774, guanyl ribonucleotide binding activity, GO:0004869, GO:0051219, GO:0044325, GO:0008092, GO:0050750, GO:0003713, GO:0050681, nuclear receptor coactiv]][[cellular process regulations, GO:0003824, protein and peptide regulation, protein domain modification]]0.00
793text-davinci-003ontological_synopsisHALLMARK_PI3K_AKT_MTOR_SIGNALING-1[[the genes in this list are involved in several biological functions, including signal transduction, GO:0006915, cellular response to stimuli, response to dna damage, GO:0051726, and regulation of protein phosphorylation and ubiquitination. the terms \"protein phosphorylation\"; \"ubiquitination\"; \"signal transduction\"; \"cellular response to stimulus\"; \"dna damage response\"; \"regulation of cell cycle\"; \"intrinsic apoptosis\"; and \"scaffold protein\" are all statistically over-represented.\\n\\nmechanism: signaling pathways and cellular processes are intricately regulated and require the coordinated participation of different proteins. by performing a term enrichment analysis, we see that the genes in this list are involved in a variety of molecular pathways, including signal transduction, GO:0006915, cellular response to stimuli, response to dna damage, GO:0051726, and regulation of protein phosphorylation and ubiquitination. this suggests that the gene products help coordinate these pathways by forming complexes, binding to signaling molecules, or carrying out the necessary enzyme activities. this suggests the underlying biological mechanism may involve interplay between specific gene products, MESH:D011506, signaling molecules to ensure efficient functioning of the cell]][[GO:0007165, GO:0019900, GO:0003924, GO:0004721, transcription factor activation, GO:0004620, GO:0005102, MESH:D054875, MESH:D000107, GO:0006915, GO:0016477, negative regulation of proliferation]]0.03
794text-davinci-003ontological_synopsisHALLMARK_PROTEIN_SECRETION-0[[protein binding activity, GO:0003924, gtp-dependent protein binding activity, snare binding activity, enzyme binding activity, protein kinase binding activity, clathrin binding activity, GO:0006897, retrograde transport, GO:0006893, GO:0006888, GO:0006622]][[protein binding activity, atp binding activity, gtp-dependent protein binding activity, GO:0003924, signal sequence binding activity, clathrin binding activity, small gtpase binding activity]]0.27
795text-davinci-003ontological_synopsisHALLMARK_PROTEIN_SECRETION-1[[protein binding activity, activity, GO:0042803, enzyme binding activity, scaffold protein binding activity, snare receptor activity, syntaxin binding activity, GO:0016887, GO:0008553, GO:0008320, metal ion binding activity, protein foldinactivity, GO:0003924, protein kinase binding activity, phosphat]][[atp binding activity, GO:0042803, smarc protein binding activity, GO:0003924, gtp binding activity, GO:0005096, enzyme binding activity, GO:0004197, protein domain specific binding activity, phosphatidylinositol-4-phosphate binding activity, protein kinase binding activity, GO:0008320, calcium-dependent protein binding activity, metal ion binding activity, dopaminergic receptor binding activity, ubiquitin-like protein ligase binding activity, GO:0005484, phosphatidylinositol-3,4,5-trisphosphate binding activity, phosphatidylinositol-3,5-bisphosphate binding activity, signaling receptor binding activity, GO:0005198, syntaxin binding activity, GO:0005484]]0.23
796text-davinci-003ontological_synopsisHALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0[[oxidative stress defense, GO:0098754, dna/rna binding, GO:0006351, GO:0098609, GO:0016043, GO:0019722, GO:0006468, GO:0010731, GO:0004392, GO:0019511, GO:0061621, GO:0005886, GO:0006750, GO:0006082]][[the human genes provided are mostly involved in redox homeostasis, GO:0006952, and cell organization. there is also involvement in processes related to the maintenance of the blood-brain barrier, GO:0009650, and metabolism of hormones, MESH:D008055, and glucose. there are an abundance of terms related to transmembrane transport, MESH:D010088, heme and iron metabolism, GO:0019511, and gluthathione metabolism.\\n\\nmechanism:\\nredox homeostasis is regulated by a network of enzymatic and substrate-dependent processes. these processes include cellular antioxidant defense, removal of superoxide radicals and peroxides, GO:0061691, and regulation of the balance between oxidant production and scavenging. transport genes are employed to promote transmembrane transport of xenobiotics and lipids, like abcc1, atox1, and glrx. iron and heme metabolism is facilitated by genes like ftl, hmox2, and mpo. peptidyl-proline hydroxylation is regulated by genes like egln2 and mgst1, while glutathione metabolism is controlled by genes like g]]0.03
797text-davinci-003ontological_synopsisHALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1[[MESH:D004734, oxidative stress response, GO:0042803, protein phosphatase 2a binding activity, GO:0004601, GO:0004602, GO:0047499, GO:0003954, chromatin dna binding activity, GO:0004861, GO:0004784, GO:0047184, GO:0015038, GO:0015035, phosphatidylinositol binding activity, GO:0004096, heme binding activity]][[GO:0045454, GO:0019899, protein homodimerization, GO:0015035, GO:0004602, GO:0003954, atp binding activity, identical protein binding activity, transition metal ion binding activity, GO:0016209, heme binding activity, ubiquitin-specific protease binding activity, GO:0047499, heparin binding activity, GO:0004601, GO:0004784, GO:0008811, GO:0004096]]0.30
798text-davinci-003ontological_synopsisHALLMARK_SPERMATOGENESIS-0[[GO:0003723, GO:0031491, transcription and regulation, GO:0003677, GO:0004672, protein folding and chaperoning, metabolic regulation, MESH:D054875]][[GO:0140677, GO:0004672, cellular component activity, binding activity, GO:0008233, nucleosome binding activity, ion binding activity, phosphatase binding activity, GO:0051726, apoptosis regulation, GO:0007155, GO:0007399, transcription regulation, GO:0015031, GO:0009988, MESH:D005786]]0.04
799text-davinci-003ontological_synopsisHALLMARK_SPERMATOGENESIS-1[[GO:0019899, GO:0005515, ligand binding, GO:0005509, GO:0000166, GO:0008134, GO:0003677, GO:0005525, GO:0042562, GO:0006200, GO:0004672, GO:0003723, GO:0008047, GO:0044183, GO:0003682, GO:0019903, GO:0019212, GO:0008233, GO:0022890]][[all of the genes are involved in regulation of various metabolic processes and signaling pathways, with most of them associated with binding activities and regulation of protein activities. enriched terms include: protein binding activity, atp binding activity, protein-folding chaperone binding activity, chromatin binding activity, GO:0046976, transcription corepressor binding activity, GO:0004672, GO:0060090, enzyme binding activity, GO:0140677, GO:0098632, GO:0004888, gtp binding activity, signaling receptor binding activity, ribonucleoprotein complex binding activity, myosin light chain binding activity, GO:0017116, GO:0003689, GO:0051131, peptide alpha-n-acetyltransferase activity. mechanism: the genes are involved in various metabolic processes and signaling pathways, by regulating protein activities through different binding activities and histone methyltransferase activity. some of these activities regulate certain processes based on gtp binding, while others are involved in cell-cell adhesion, transmembrane signaling and chaperone-mediated protein complex assembly]]0.03
800text-davinci-003ontological_synopsisHALLMARK_TGF_BETA_SIGNALING-0[[GO:0007165, regulation of transcription, GO:0051246, regulation of macromolecule metabolism, GO:0050794, interaction with transcription factors, interaction with smad proteins]][[GO:0005524, GO:0048185, GO:0046332, protein phosphatase/kinase activity, smad signaling, bmp signaling, GO:0006351, MESH:D012319, GO:0005515, GO:0007165, GO:0007049, GO:0008152, GO:0007155]]0.05
801text-davinci-003ontological_synopsisHALLMARK_TGF_BETA_SIGNALING-1[[tgf binding activity, dna-binding transcription factor binding activity, smad binding activity, GO:0019211, GO:0004674, GO:0004869, GO:0061631, myosin binding activity, r-smad binding activity, beta-catenin binding activity, cadherin binding activity, gtp binding activity, i-smad binding activity, GO:0003924, GO:0003714, GO:0042803, nucleic acid binding activity, serine-type endope]][[dna-binding activity, transcription regulation, GO:0035556, GO:0004674, smad binding activity, positive/negative regulation of rna/protein metabolic process, GO:0006468, receptor tyrosine kinase binding activity, GO:0007165, GO:0042803, GO:0061630, GO:0031326, GO:0009966, GO:0006357, GO:0090092]]0.10
802text-davinci-003ontological_synopsisHALLMARK_TNFA_SIGNALING_VIA_NFKB-0[[dna binding transcription factor, GO:0005102, GO:0019899, GO:0005126, growth factor, transmembrane receptor]][[the list of genes provided are involved in a broad set of functions related to gene transcription or regulation of transcription factors, cell signaling, binding activities and metabolic processes. the enriched terms for this gene set include dna-binding transcription factor activity, rna polymerase ii transcription regulatory region sequence-specific binding, GO:0003924, chemokine receptor binding activity, signaling receptor binding activity, protein kinase binding activity, enzyme binding activity, identical protein binding activity and protease binding activity.\\n\\nmechanism: the underlying biological mechanism for this list of genes is likely related to control of gene expression, as well as control of protein interactions that mediate cell signaling and metabolic processes. additionally, the functions related to binding activities suggest many of the genes are involved in cell-to-cell communication and cell adhesion]]0.00
803text-davinci-003ontological_synopsisHALLMARK_TNFA_SIGNALING_VIA_NFKB-1[[GO:0000988, rna polymerase ii-specific, dna-binding, identical protein binding activity, enzyme binding activity, signaling receptor binding activity, GO:0004672, GO:0005125, GO:0008083, GO:0098631, GO:0022857, GO:0016791, gtp binding activity, GO:0140657]][[GO:0001216, transcription regulatory region sequence-specific dna-binding, gtp binding activity, enzyme binding activity, identical protein binding activity, signal receptor binding activity, GO:0016791, protein kinase binding activity, GO:0005125, GO:0008083]]0.33
804text-davinci-003ontological_synopsisHALLMARK_UNFOLDED_PROTEIN_RESPONSE-0[[GO:0006457, GO:0003723, transcription activator, GO:0003677, GO:0051082, GO:0003720, GO:0003676, GO:0044325, GO:0005524, GO:0006402, translation regulation, GO:0003755, GO:0035925]][[rna binding activity, dna binding activity, protein binding activity, GO:0140693, identical protein binding activity, dna-binding transcription factor binding activity, GO:0042803, atpase binding activity, GO:0016887, enzymatic activity, GO:0003713, GO:0008494, protein phosphatase binding activity, peptidyl-prolyl primase activity, transcription cis-regulatory region sequence-specific activity]]0.00
805text-davinci-003ontological_synopsisHALLMARK_UNFOLDED_PROTEIN_RESPONSE-1[[atp binding activity, GO:0016887, enzyme binding activity, identical protein binding activity, GO:0060090, GO:0140678, nucleic acid binding activity, GO:0046983, protein folding chaperone binding activity, ribosome binding activity, rna binding activity, snare binding activity, transcription corepressor binding activity, transcription regulator]][[enzyme binding activity, rna binding activity, protein binding activity, transmembrane transporter binding activity, dna binding activity, protein kinase binding activity, box h/aca snorna binding activity, protein phosphatase binding activity, telomerase rna binding activity, GO:0042803, GO:0046982, transcription factor binding activity, atp binding activity, GO:0016887, GO:0003724, GO:0003756, ubiquitin protein ligase binding activity, GO:0004518, adenyl ribonucleotide binding activity, heat shock protein binding activity]]0.13
806text-davinci-003ontological_synopsisHALLMARK_UV_RESPONSE_DN-0[[genes included in this set are involved in various cellular functions such as enzyme binding activity, GO:0003924, lipoprotein binding activity, GO:0004620, and other related activities. common enriched terms across these genes include protein binding activity, smad binding activity, dna-binding activity, phosphotyrosine residue binding activity, GO:0003824, GO:0003924, and enzymatic inhibitor activity. mechanism: these genes are likely to be involved in regulation and control of cellular functions and processes through various proteins. this regulation and control is likely being done through interaction of the proteins encoded by these genes with other proteins and structurally with dna, as well as through the enzymatic activities of the encoded proteins]][[gtp binding activity, enzyme binding activity, dna-binding transcription factor binding activity, phosphotyrosine residue binding activity, cyclin binding activity, receptor-ligand interaction, protein-protein interaction, smad binding protein, nf-kappab binding protein, growth factor binding protein]]0.05
807text-davinci-003ontological_synopsisHALLMARK_UV_RESPONSE_DN-1[[dna binding activity, GO:0000988, protein binding activity, smad binding activity, GO:0005096, MESH:C062738]][[GO:0001216, rna polymerase ii-specific activity, nf-kappab binding activity, microtubule binding activity, actin binding activity, identical protein binding activity, smad binding activity, GO:0005243, GO:0005388, receptor binding activity, GO:0005096, histone binding activity, ap-1 transcription factor binding activity, vitamin d receptor binding activity, cytoplasmic protein binding activity, GO:0004930, platelet-derived growth factor binding activity, enzyme binding activity, protease binding activity, phospholipid binding activity, GO:0004672, GO:0004674, intracellular protein binding activity]]0.07
808text-davinci-003ontological_synopsisHALLMARK_UV_RESPONSE_UP-0[[GO:0005515, GO:0003677, binding activity, receptor binding activity, GO:0004672, GO:0007155, GO:0023052, GO:0010468]][[protein binding activity, atp binding activity, rna binding activity, dna binding activity, receptor binding activity, enzyme binding activity, GO:0005548, GO:0098609, GO:0007268, GO:0097190, GO:0005138, GO:0042110, overall cellular metabolism, MESH:D005786]]0.05
809text-davinci-003ontological_synopsisHALLMARK_UV_RESPONSE_UP-1[[gtp binding activity, dna binding activity, GO:0016563, protein kinase binding activity, GO:0004175]][[enzyme binding activity, GO:0016787, GO:0016740, GO:0038023, dna binding activity, rna binding activity, GO:0000988, protein binding activity]]0.08
810text-davinci-003ontological_synopsisHALLMARK_WNT_BETA_CATENIN_SIGNALING-0[[the genes summarized above are all involved in developmental processes, such as organizing and regulating cell adhesion, components of the wnt pathway and regulation of gene expression. the enriched terms for these genes would be development-related terms, such as cell adhesion, GO:0060070, GO:0006468, GO:0016567, GO:0006351, GO:0006476, GO:0006351, and protein stability.\\n\\nmechanism: the underlying biological mechanism involves the involvement of many of these genes in the wnt pathway, which is a conserved signaling pathway involved in cell-cell communication and a variety of developmental processes. another mechanism involves the regulation of gene expression and the binding of dna-binding transcription factors, as well as protein ubiquitination and deacetylation which also control gene expression]][[protein binding activity, GO:0003700, rna polymerase ii-specific dna-binding transcription factor binding activity, notch binding activity, pdz domain binding activity, GO:0042813, ubiquitin protein ligase binding activity, beta-catenin binding activity, GO:0003713, histone deacetylase binding activity, GO:0048019, transcription corepressor binding activity, GO:0060090, GO:0004407, cholesterol binding activity]]0.00
811text-davinci-003ontological_synopsisHALLMARK_WNT_BETA_CATENIN_SIGNALING-1[[GO:0005515, transcription regulation, GO:0051726, GO:0007165, response pathways]][[GO:0007165, GO:0010468, GO:0006351, GO:0001932, GO:0031647, GO:0016477, GO:0008283, GO:0032502, GO:0006508]]0.08
812text-davinci-003ontological_synopsisT cell proliferation-0[[signaling receptor binding activity, protein kinase binding activity, GO:0061630, GO:0035556, GO:0001816, GO:0010467]][[protein binding activity, enzyme binding activity, protein kinase binding activity, interleukin binding activity, phosphorylation-dependent protein binding activity, GO:0001216, GO:0042803, nucleic acid binding activity, GO:0005001, GO:0048018, GO:0004725, GO:0005125, cytoskeletal protein binding activity, cytokin receptor activity, GO:0030335]]0.05
813text-davinci-003ontological_synopsisT cell proliferation-1[[GO:0048018, phosphotyrosine residue binding activity, cytoskeletal protein binding activity, GO:0005574]][[cation binding activity, diacylglycerol binding activity, enzyme binding activity, GO:0046982, receptor binding activity, protein kinase binding activity, phosphorylation-dependent protein binding activity, phosphotyrosine residue binding activity, GO:0005001, protease binding activity, cytoskeletal protein binding activity, phosphatidylinositol 3-kinase binding activity, GO:0061630, GO:0004888, GO:0043621, GO:0004697, zinc ion binding activity, transmembrane atp-gated monoatomic cation channel activity, purin]]0.10
814text-davinci-003ontological_synopsisYamanaka-TFs-0[[transcription repressor and activator activities, rna polymerase ii-specific, nucleic acid binding activity, GO:0009889, GO:0009966, GO:0010468, GO:0045765, and protein-dna complex organization, GO:0042127]][[dna-binding, GO:0000988, rna polymerase ii-specific, nucleic acid binding activity, transcription cis-regulatory region binding activity, GO:0010468, GO:0009889]]0.33
815text-davinci-003ontological_synopsisYamanaka-TFs-1[[dna-binding, GO:0016563, GO:0016564, GO:0000988, rna binding activity, ubiquitin protein ligase binding activity, GO:0010628, GO:0010629, GO:0009889, GO:0045765, GO:0060828, GO:0009966, transcription cis-regulatory region binding activity, GO:0045944, GO:0003130, GO:0001714]][[GO:0006351, GO:0010468, dna-binding, GO:0000785, GO:0005829, GO:0005654, GO:0005667, GO:0009966, GO:0045944, GO:0001714]]0.18
816text-davinci-003ontological_synopsisamigo-example-0[[GO:0005515, GO:0060230, GO:0005543, MESH:M0518050, GO:0050804]][[the list of genes provided is involved in multiple processes related to cell adhesion, growth factor binding, protein phosphorylation, tissue development, and regulation of cholesterol homeostatis and transcytosis. the underlying biological mechanism likely involves multiple pathways, including cellular response to lipopolysaccharide, cell-matrix adhesion, and negative regulation of low-density lipoprotein. enriched terms include cell adhesion, cell surface receptor signaling, collagen binding activity, GO:0019838, GO:0042157, GO:1902533, GO:0046983, GO:0006468, regulation of bmp signaling, GO:0042127, GO:0010468, GO:0009966, regulation of very-low-density lipoproten particle clearance, GO:0045056]]0.00
817text-davinci-003ontological_synopsisamigo-example-1[[GO:0005515, GO:0043167, GO:0008009, GO:0019838, signal receptor binding, GO:0019902, GO:0016477, GO:0086009, GO:0007165, GO:0065007, GO:0006952]][[GO:0051246, GO:0001952, GO:0042127, GO:0042981, GO:0043269, GO:0030193, GO:0007166, GO:0050804, GO:0005201, GO:0007160, organ development and differentiation, regulation of hormone pathways]]0.00
818text-davinci-003ontological_synopsisbicluster_RNAseqDB_0-0[[GO:0005509, double-stranded dna-binding, cell adhesion and migration, transcriptional regulation]][[genes in this list are involved in a range of activities, including calcium ion binding activity, metal ion binding activity, protein domain specific binding activity, identical protein binding activity, dna-binding transcription factor activity, and several others. the underlying biological mechanism appears to be related to structural support and regulation of cellular processes. enriched terms include: metal ion binding, GO:0005509, GO:0005515, GO:0000988, dna-binding, GO:0042802, domain specific protein binding]]0.10
819text-davinci-003ontological_synopsisbicluster_RNAseqDB_0-1[[metal ion binding activity, protein binding activity, rna binding activity, GO:0019208, GO:0005243, GO:0042803, calcium ion binding activity, MESH:C086554]][[GO:0001216, protein kinase binding activity, metal ion binding activity, calcium ion binding activity, transcription co-regulator activity, responsive to stimuli]]0.17
820text-davinci-003ontological_synopsisbicluster_RNAseqDB_1002-0[[UBERON:0001134, GO:0006936, GO:0016567, GO:0045010, calcium-dependent signaling, GO:0010468, GO:0006468, GO:0043687, GO:0042692, GO:0060537, MONDO:0020121, muscle organelle organization]][[GO:0051015, GO:0000146, GO:0051371, GO:0003785, GO:0005523, GO:0017022, GO:0031432, GO:0004111]]0.00
821text-davinci-003ontological_synopsisbicluster_RNAseqDB_1002-1[[actin binding activity, GO:0007015, muscle alpha-actinin binding activity, GO:0006936, GO:0060415, GO:0071689, GO:0004672, protein phosphatase binding activity, GO:0043502, tropomyosin binding activity, troponin binding activity, troponin complex activities]][[calcium-dependent protein binding activity, atp binding activity, actin filament binding activity, actin monomer binding activity, transmembrane transporter binding activity, GO:0016567, GO:0061630, tropomyosin binding activity, identical protein binding activity, GO:0008375, protein phosphatase 1 binding activity, zinc ion binding activity, troponin c binding activity, troponin i binding activity, actin binding activity, tropomyosin binding activity, GO:0001216, sequence-specific double-stranded dna binding activity]]0.07
822text-davinci-003ontological_synopsisendocytosis-0[[protein signaling, GO:0006468, GO:0016567, GO:0015031, GO:0030030, GO:0006897, GO:0006898, GO:0035091, GO:0001766, GO:0097320]][[GO:0004674, lysophosphatidic acid binding activity, sulfatide binding activity, GO:0016790, cadherin binding activity, GO:0032456, sh3 domain binding activity, GO:0051260, macropinosome formation, GO:0031623, transferring transport, t cell receptor binding activity, GO:0005085, GO:0044351, GO:0001773, GO:0007520, GO:0018105, GO:0010468, vascular endothelial growth factor receptor signalling pathway, GO:0051128, GO:0007042, GO:0045807, GO:0051090]]0.00
823text-davinci-003ontological_synopsisendocytosis-1[[GO:0006897, GO:0005515, GO:0006869, GO:0016567, GO:0042632, GO:0035727]][[GO:0006468, GO:0051260, cell signaling, GO:0005480, GO:0016567, endocytosis/exocytosis, GO:0005102, GO:0010468, vesicle buddying, GO:0007165, GO:0050727, GO:0035556, gtp-dependent pathways, receptor signaling, canonical inflammasome signaling]]0.05
824text-davinci-003ontological_synopsisglycolysis-gocam-0[[GO:0019538, enzymatic activity, protein transcription, cell metabolism, carbohydrate phosphorylation and metabolism, protein homeostasis, cell signaling, GO:0008104, cell homeostasis, cellular energy production]][[protein binding activity, atp binding activity, peptidoglycan binding activity, GO:0051156, GO:0002639, GO:0010595, GO:0006002, GO:0061615, GO:0030388, GO:0046166, fructose binding activity, GO:0004332, MONDO:0009295, GO:0004807, disordered domain specific binding activity, GO:0004866, GO:0046835, GO:0072655, maintenance of protein location in]]0.00
825text-davinci-003ontological_synopsisglycolysis-gocam-1[[GO:0003824, GO:0031625, protein homodimerization, GO:0016310, GO:0006096, GO:1904659, GO:0070061, GO:0004332, GO:0004618, GO:0004619, GO:0004396, peptidoglycan binding activity, GO:0003872, GO:0004807, GO:0004347, GO:0021762, binding activity of sperm to zona pellucida, GO:0030388, GO:0019725, GO:0046716, GO:0071456, GO:0016525, UBERON:2005050]][[protein binding activity, atp binding activity, ubiquitin protein ligase binding activity, fructose binding activity, GO:0042803, GO:0004618, GO:0004619, GO:0004807, GO:0004396, GO:0004332, GO:0004634, GO:0003872, GO:0004347, GO:0006096, GO:0006002, GO:0046166, GO:0046835, GO:0072655, GO:0072656, GO:0071456, negative regulation of]]0.26
826text-davinci-003ontological_synopsisgo-postsynapse-calcium-transmembrane-0[[GO:0097553, GO:1990034, GO:0071318, GO:0007186, GO:0035235, GO:1990454, GO:0017146, GO:0014066, GO:1900274, GO:0099509, GO:2000300, GO:0032680, GO:0005245, GO:2000311, GO:0080164]][[GO:0005262, GO:0005245, regulation of intracellular calcium concentrations, GO:0098960, GO:2000311, g protein-coupled receptor signaling, GO:0070588, GO:0015276]]0.10
827text-davinci-003ontological_synopsisgo-postsynapse-calcium-transmembrane-1[[GO:0006816, regulation of calcium]][[GO:0005261, acetylcholine-gated channel activity, GO:0022849, nmda selective glutamate receptor activity, GO:0005245, GO:1990454, GO:0035235, GO:0071318, regulation of]]0.00
828text-davinci-003ontological_synopsisgo-reg-autophagy-pkra-0[[these genes are involved in several cellular activities, primarily in their roles in signal transduction pathways, GO:0036211, protein folding and stability, GO:0051726, and apoptosis. the terms enriched are: signaling receptor activity; protein phosphorylation; regulation of macromolecule biosynthetic process; autophagy; g2/m transition of mitotic cell cycle; chromosome segregation; cytoplasmic stress granule; torc1 signaling; defense response; anoikis; protein folding chaperone; histone acetylation; i-kappab kinase/nf-kappab signaling; k63-linked polyubiquitin modification-dependent protein binding activity.\\n\\nmechanism: these genes participate in a variety of biological processes, including signal transduction pathways, GO:0036211, GO:0051726, apoptosis and dna-templated transcription, answering to different external and internal stimuli as well as aiding in cell survival and death. the enriched terms involve protein-protein interactions and modifications, as well as involvement in akt/pi3k, tor, and nf-kb pathways that are essential for cell signaling, typical in response to bacterial infection and the activation of pro-survival mechanisms]][[protein kinase binding activity, GO:0004672, GO:0004674, GO:0001934, GO:0010556]]0.00
829text-davinci-003ontological_synopsisgo-reg-autophagy-pkra-1[[protein binding activity, metal ion binding activity, protein kinase binding activity, GO:0030295, protein folding chaperone activity, GO:0042803, chromatin binding activity, GO:0003713, GO:0016410, GO:0016538, GO:0016303, card domain binding activity, heat shock protein binding activity, muramyl dipeptide binding activity, 14-3-3 protein binding activity, rna polymerase iii cis-regulatory region sequence-specific dna binding activity]][[the genes listed above are involved in a variety of processes, including negative and positive regulation of transport, GO:0051246, cell surface receptor signaling, and regulation of gene expression. these genes also have a variety of functions, including protein kinase binding activity, chromatin binding activity, GO:0030295, and metal ion binding activity. the enriched terms that describe these genes include: protein binding activity; protein kinase binding activity; signal transduction; positive and negative regulation of transport; chromatin binding activity; and protein serine/threonine kinase activity.\\n\\nmechanism: these gene products are part of, or act upstream of a variety of signaling pathways, all of which are involved in cell growth, MESH:D008283, and response to environmental stimuli. the pathways typically involve post-translational modifications of target proteins by phosphorylation, as well as formation or breakdown of protein-containing complexes. these signaling pathways ultimately affect gene expression and determine the type of output which a particular cell will produce]]0.07
830text-davinci-003ontological_synopsishydrolase activity, hydrolyzing O-glycosyl compounds-0[[the genes in this list share functions involving glycoprotein and carbohydrate metabolic processes and structural functions related to extracellular matrix organization. enriched terms include: dihydroceramidase activity, GO:0017040, GO:0061463, GO:0004134, GO:0004135, GO:0004556, hyaluronic acid binding activity, GO:0004415, GO:0004568, GO:0008843, clathrin heavy chain binding activity, GO:0008422, GO:0004348, GO:0004336, GO:0004553, GO:0008375, GO:0004563, identical protein binding activity, syndecan binding activity, heparan sulfate proteoglycan binding activity, GO:0003796, GO:0004567]][[the genes in the list are involved in many processes relating to glycan metabolism and synthesis, such as glycoside catabolic process, GO:0006027, GO:0019377, GO:0005980, and sucrose catabolic process. other enriched terms are dihydroceramidase activity, hyaluronic acid binding activity, GO:0004415, GO:0030212, GO:0046373, GO:0004571, GO:0006487, and protein homodimerization activity.\\n\\nmechanism: glycan metabolism and synthesis involves several enzymes with diverse activities such as alpha-glucosidases, MESH:D043323, MESH:D001617, MESH:D001619, n-acetylglucosaminyltransferases. these enzymes hydrolyze transfer carbohydrate building blocks to form modify carbohydrates for a variety of cellular functions]]0.05
831text-davinci-003ontological_synopsishydrolase activity, hydrolyzing O-glycosyl compounds-1[[GO:0006516, GO:0006027, heparan sulfate catabolism, glucoside catabolism, GO:0036508, GO:0006517, GO:0005975, GO:0006869, GO:0030214, receptor signaling, GO:0031589, GO:0009313, GO:0004672, GO:0008283, GO:0019915, GO:0050885, GO:0042742, GO:0005989, GO:0008344, GO:0007605, GO:0006487, GO:0006281, GO:0071451, peptidyl-serine]][[GO:0005975, GO:0046477, GO:0006516, oligo-saccharide catabolic process, GO:0006869, GO:0015144, GO:0046982, protein domain specific binding activity, GO:0006629, GO:0016139, GO:0030214, GO:0006032]]0.12
832text-davinci-003ontological_synopsisig-receptor-binding-2022-0[[immunoglobulin receptor binding activity, antigen binding activity, fc-gamma receptor i complex binding activity, GO:0004715, phosphotyrosine residue binding activity, peptidoglycan binding activity, phosphatidylcholine binding activity. mechanism: the genes listed appear to be involved in the regulation of the immune response. they likely aid in the recognition of pathogens, binding to the appropriate receptors, triggering a signal for an immune response. they may also play a role in enabling the recognition of self-antigens inhibiting a response to them]][[immunoglobulin receptor binding activity, antigen binding activity, GO:0004715, phosphatidylcholine binding activity, phosphotyrosine residue binding activity]]0.50
833text-davinci-003ontological_synopsisig-receptor-binding-2022-1[[antigen binding activity, immunoglobulin receptor binding activity, GO:0098542, GO:0002253, fc-gamma receptor i complex binding activity, GO:0004715, peptidoglycan binding activity, phosphatidylcholine binding activity, GO:0007229, GO:0038187, mannose binding activity, phosphotyrosine residue binding activity, GO:0051130, GO:0045657, protection of host from foreign agent]][[GO:0042803, GO:0007160, phosphorylation-dependent signaling, GO:0019901, GO:0034988, GO:0030098, GO:0098609, GO:0001784, GO:0042834, integrin signaling, GO:0006909]]0.00
834text-davinci-003ontological_synopsismeiosis I-0[[these genes are involved in processes related to dna binding, repair, replication, recombination, and regulation thereof. the enriched terms would be: dna binding, GO:0003690, dna damage repair, GO:0006310, GO:0005515, meiotic recombination, GO:0007059, GO:0000278, GO:0071173, GO:0051289, GO:0003682, resolution of meiotic recombination intermediates. \\nmechanism: the underlying biological mechanism is that these proteins work together to maintain genomic stability, regulate gene expression, promote proper cell division, germline cell development, meiosis]][[GO:0003677, atp dependent activity, GO:0003682, GO:0005634, protein export, transcriptional regulation, GO:0003690, GO:0003697, GO:0006281, GO:0004518, MESH:D011995, GO:0007059, GO:0000278, intrinsic apoptotic signaling, regulation of telomere maintenance.\\nmechanism: the genes identified are likely playing roles in a variety of dna metabolic pathways, including dna repair, double-stranded dna break repair, homologous recombination, transcriptional regulation, and mitotic cell cycle processes. these pathways likely enable cellular replication and maintenance of genomic integrity, as well as control of gene expression and apoptosis]]0.17
835text-davinci-003ontological_synopsismeiosis I-1[[GO:0140013, dna binding activity, GO:0006259, GO:0035825, telomere attachment, GO:0000785, GO:0000795, GO:0005694, GO:0005737]][[GO:0003677, GO:0003690, GO:0042802, GO:0006259, GO:0006302, GO:0007131, meiotic chromosome segregation and pairing, GO:0007283, GO:0000712, GO:0051026, GO:0016925, GO:0007130]]0.05
836text-davinci-003ontological_synopsismolecular sequestering-0[[calcium ion binding activity, identical protein binding activity, GO:0004252, GO:0140314, calcium-dependent protein binding activity, arginine binding activity, GO:0140313, enzyme binding activity, GO:0019887, nf-κb binding activity, nuclear localization sequence binding activity, oxysterol binding activity, rage receptor binding activity, ubiquitin protein ligase binding activity, actin binding activity, rig-i binding activity, GO:0003713, zinc ion binding activity, GO:1903231]][[calcium ion binding activity, identical protein binding activity, GO:0140311, ubiquitin protein ligase binding activity, cellular response, GO:0001932, GO:0010359, GO:0097214, GO:0010468, GO:0035456]]0.12
837text-davinci-003ontological_synopsismolecular sequestering-1[[protein binding activity, GO:0140313, GO:0000988, GO:0019887, calcium ion binding activity, dna-binding activity, ubiquitin protein ligase binding activity, tumor necrosis factor binding activity, regulatory pathway activity]][[GO:0005515, GO:0046872, GO:0043167, GO:0010468, GO:0001932, cell death pathways, GO:0009059, GO:0046907, cellular response to infection and inflammation]]0.00
838text-davinci-003ontological_synopsismtorc1-0[[enzyme binding activity, acid binding activity, molecule transport, adapter binding activity, receptor binding activity, dna binding activity, protein binding activity, GO:0003824, GO:0016787, GO:0016491, anion binding activity, GO:0008233, GO:0140657, thioredoxin activity, translocation, GO:0061630, cysteine endopeptidase activity, GO:0004738, GO:0004618, magnesium ion binding activity, GO:0004340, GO:0003924]][[protein binding activity, dna binding activity, enzyme binding activity, GO:0060090, GO:0140677, GO:0042803, domain binding activity, GO:0016491, protein kinase binding activity, phosphatidylinositol binding activity, GO:0016504, GO:0003714, nuclear androgen receptor binding activity, nf-kappab binding activity, ubiquitin protein ligase binding activity, phosphotyrosine residue binding activity, GO:0016564, GO:0003743, peptidyl-proinalyl cistrans isomerase activity]]0.11
839text-davinci-003ontological_synopsismtorc1-1[[cytoskeleton protein binding, phosphatase binding activity, GO:0016491, cell development and signaling activity, dna binding activity, cellular transporter activity, protein kinase binding activity]][[protein binding activity, GO:0005215, dna binding activity, rna binding activity, atp binding activity, peptide activity, GO:0003824, enzyme binding activity, phosphoprotein binding activity, GO:0016563, GO:0016787, GO:0016491, GO:0004017, identical protein binding activity, GO:0060090, GO:0007165, signal receiving activity, GO:1901987, metabolism regulation, cell growth control]]0.08
840text-davinci-003ontological_synopsisperoxisome-0[[peroxisome biogenesis, protein import into peroxisome, GO:0000425, GO:0000268, GO:0140036, GO:0006631, protein homodimerization, enzyme binding activity, GO:0050821, GO:0043335]][[peroxisome biogenesis, atp binding activity, GO:0016887, ubiquitin-dependent protein binding activity, GO:0016558, GO:0050821, GO:0043335, GO:0000425, GO:0006625, protein tetramerization.\\n\\nmechanism: these gene functions are involved in a complex process involving the biogenesis and maintenance of peroxisomes, which are subcellular organelles that contain a variety of enzymes involved in metabolic processes. this process entails the function of multiple proteins working together to ferry important proteins into the peroxisomal membrane, where these proteins will become functional components of the organelle]]0.25
841text-davinci-003ontological_synopsisperoxisome-1[[GO:0016558, GO:0050821, GO:0042127, protein-lipid binding, GO:0007031, GO:0008611, GO:0001881, GO:0006631]][[protein binding activity, GO:0016558, peroxisome matrix targeting signal-2 binding activity, GO:0042803, GO:0008611, GO:0006631, GO:0008285, GO:0000425, GO:0032994, microtubule-based peroxisome localization.\\nmechanism: based on the functions that these genes carry out, it is likely that the genes are involved in a mechanism whereby proteins are imported into the peroxisome matrix, and the peroxisome matrix is organized, stabilized, and/or maintained in order to carry out fatty acid metabolism and pexophagy. the receptor recycling and microtubule-based localization also likely play a role in this mechanism]]0.20
842text-davinci-003ontological_synopsisprogeria-0[[GO:0003677, GO:0005515, GO:0046872, cellular response to radiation, hypoxia, and starvation, GO:0042981, GO:0032204, GO:0010835, GO:0045069]][[protein binding activity, dna binding activity, metal ion binding activity, GO:0003678, GO:0042803, GO:0071480, GO:0010836, GO:0007084, GO:0045071, GO:0032392, GO:0006259, GO:0009267, GO:1902570, GO:0042981, GO:0071456, GO:0032204, GO:0004222, GO:0050688, with a positive effect]]0.08
843text-davinci-003ontological_synopsisprogeria-1[[dna damage and repair, GO:0005515, GO:0046872, homodimerization, GO:0006915, MESH:D016922, GO:0001666]][[GO:2000772, dna binding and metabolic processes, dna helicase and metal ion binding activities, protein localization to nucleolus and regulation of apoptotic processes appear to be enriched terms common to the three genes given.\\n\\nmechanism: the three genes appear to be involved in similar nucleic acid binding and regulation activities that enable the maintenance and regulation of cellular processes. this suggests an underlying molecular mechanism in which these genes interact directly to modulate a variety of cellular processes related to senescence, GO:0003677, GO:0008152, GO:0006915]]0.08
844text-davinci-003ontological_synopsisregulation of presynaptic membrane potential-0[[GO:0005216, GO:0016917, GO:0008066, GO:0007186, GO:0007214, GO:0006836, GO:0005249, GO:0005248, GO:0007193]][[voltage-gated potassium/sodium channel activity, GO:0015276, transmembrane transporter binding activity, GO:0004930, GO:0004971, GO:0015277, GO:0035235, GO:1902476, GO:0007214, GO:0019228, GO:0042391, GO:0007268, regulation of]]0.05
845text-davinci-003ontological_synopsisregulation of presynaptic membrane potential-1[[GO:0005216, membrane potential regulation, GO:0015276, g protein-coupled receptor signaling, GO:1902476, GO:0007214, GO:0071805]][[GO:0005216, GO:0015276, membrane potential regulation, GO:0005249, GO:0005248, GO:0008066, GO:0004890, GO:0055074, GO:0022851, ionotropic glutamate receptor signaling, GO:1902476, GO:0051932, GO:0048167, negative regulation of smooth muscle apoptotic process, GO:0051924, GO:0086009, GO:0035249, GO:0060292, GO:0006836, GO:0050804, GO:0034220, GO:0051205, GO:0060079]]0.15
846text-davinci-003ontological_synopsissensory ataxia-0[[dna-binding, rna polymerase ii-specific activity, GO:0046872, GO:0031625, GO:0045944, GO:0002639, GO:1901184, GO:0033157, monoatomic cation]][[transcription regulation, GO:0031625, GO:0003677, GO:0006027, GO:0043583, GO:0045475, GO:0007399, GO:0006457, GO:0043066, GO:0010595, GO:0002639, GO:0034214, GO:0050974, GO:0006812, GO:0015886, GO:0071260, GO:0042552, GO:0098742, GO:0006839, GO:0019226, GO:0008380, GO:0003774, GO:0061608, nuclear localization sequence binding activity, GO:0006607, GO:0003887, GO:0006284, gap-filling, protein ubiquitination.\\n\\nmechanism: analysis of the given list of genes suggests that there]]0.06
847text-davinci-003ontological_synopsissensory ataxia-1[[transcription regulation, nucleic acid metabol]][[MESH:D015533, dna-binding, rna polymrease ii-specific, dna binding activity, GO:0034214, GO:0061608, protein folding chaperone binding activity, GO:0016567, cell aggregration, GO:0098609, GO:0042552, GO:0005886, GO:0034220, GO:0030218, GO:0015886, mitochondrial transport.\\nmechanism: the eighteen human genes are involved in a variety of complex biological processes, from transcriptional regulation, through to cellular adhesion and the transport of macromolecules, including proteins, nucleic acids and heme. there is likely significant cross-talk between these various processes, particularly at the level of dna binding proteins, transcription activators, and nuclear receptor activities. this suggests that these genes are likely playing a role in the coordination of cellular processes to facilitate proper neural development and maintenance of peripheral nerve function]]0.00
848text-davinci-003ontological_synopsisterm-GO:0007212-0[[g protein-coupled receptor binding activity, GO:0003924, enzyme binding activity, GO:0042803, signaling receptor binding activity, GO:0004016, g-protein beta/gamma-subunit complex binding activity, signaling receptor binding activity, clathrin light chain binding activity, sequence-specific double-stranded dna binding activity, GO:0004672, nf-kappab binding activity, protein kinase a catalytic subunit binding activity, GO:0004674]][[GO:0007186, GO:0051480, GO:0006357, GO:1901214, GO:0006915, GO:0006171, GO:0006468]]0.00
849text-davinci-003ontological_synopsisterm-GO:0007212-1[[GO:0004672, g-protein activity, g-protein beta/gamma- subunit complex binding activity, atpase binding activity, GO:0004016, protein-folding chaperone binding activity, signal receptor binding activity, GO:0071333, GO:0007165, negative regulation of nf-kappa b transcription factor activity, GO:2000394, GO:0007212, cellular response to prostaglandin e, GO:0007204]][[GO:0007186, GO:0043087, GO:0060170, GO:0006171, GO:0005783, membrane localization, transcriptional regulation, GO:0007212, GO:0006874, GO:0046039, GO:0098843, protein kinase activity. \\n\\nmechanism:\\nthe g protein-coupled receptor signaling pathway is a general pathway that mediates the effects of hormones, neurotransmitters other extracellular signals in cells across a variety of tissues organs. signaling through gpcrs involves activation of g proteins, which in turn activate or inhibit effector enzymes ion channels. the commonality among these genes is that they are involved in mechanisms of gpcr signaling downstream processes such as regulation of gtpase activity, camp synthesis regulation of calcium ion concentration. the genes may also participate in membrane localization, transcriptional regulation postsynaptic endocytic zone functions. other associated activities]]0.04
850text-davinci-003ontological_synopsistf-downreg-colorectal-0[[GO:0003677, GO:0003723, GO:0003682, GO:0008134, GO:0003713, GO:0016564, MESH:M0518050, GO:0019899]][[transcription activation/repression, GO:0007165, GO:0006351, GO:0007049, MESH:D012319, GO:0003682, GO:0008270, GO:0016575, protein ligase/cofactor binding]]0.06
851text-davinci-003ontological_synopsistf-downreg-colorectal-1[[GO:0006351, dna-binding, rna polymerase ii-specific, transcription activator/transcription repressor, cis-regulatory region sequence-specific, GO:0001221, GO:0006355, GO:0006337, GO:0009966]][[dna-binding transcription, GO:0016563, rna polymerase ii-specific, GO:0016564, positive/negative regulation of transcription, GO:0006351, GO:0010468, nucleic acid binding activity, sequence-specific double-stranded dna binding activity, protein kinase binding activity]]0.12
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"91 gpt-3.5-turbo narrative_synopsis \n", - "92 gpt-3.5-turbo narrative_synopsis \n", - "93 gpt-3.5-turbo narrative_synopsis \n", - "94 gpt-3.5-turbo narrative_synopsis \n", - "95 gpt-3.5-turbo narrative_synopsis \n", - "96 gpt-3.5-turbo narrative_synopsis \n", - "97 gpt-3.5-turbo narrative_synopsis \n", - "98 gpt-3.5-turbo narrative_synopsis \n", - "99 gpt-3.5-turbo narrative_synopsis \n", - "100 gpt-3.5-turbo narrative_synopsis \n", - "101 gpt-3.5-turbo narrative_synopsis \n", - "102 gpt-3.5-turbo narrative_synopsis \n", - "103 gpt-3.5-turbo narrative_synopsis \n", - "104 gpt-3.5-turbo narrative_synopsis \n", - "105 gpt-3.5-turbo narrative_synopsis \n", - "106 gpt-3.5-turbo narrative_synopsis \n", - "107 gpt-3.5-turbo narrative_synopsis \n", - "108 gpt-3.5-turbo narrative_synopsis \n", - "109 gpt-3.5-turbo narrative_synopsis \n", - "110 gpt-3.5-turbo narrative_synopsis \n", - "111 gpt-3.5-turbo narrative_synopsis \n", - "112 gpt-3.5-turbo narrative_synopsis \n", - "113 gpt-3.5-turbo narrative_synopsis \n", - "114 gpt-3.5-turbo narrative_synopsis \n", - "115 gpt-3.5-turbo narrative_synopsis \n", - "116 gpt-3.5-turbo narrative_synopsis \n", - "117 gpt-3.5-turbo narrative_synopsis \n", - "118 gpt-3.5-turbo narrative_synopsis \n", - "119 gpt-3.5-turbo narrative_synopsis \n", - "120 gpt-3.5-turbo narrative_synopsis \n", - "121 gpt-3.5-turbo narrative_synopsis \n", - "122 gpt-3.5-turbo narrative_synopsis \n", - "123 gpt-3.5-turbo narrative_synopsis \n", - "124 gpt-3.5-turbo narrative_synopsis \n", - "125 gpt-3.5-turbo narrative_synopsis \n", - "126 gpt-3.5-turbo narrative_synopsis \n", - "127 gpt-3.5-turbo narrative_synopsis \n", - "128 gpt-3.5-turbo narrative_synopsis \n", - "129 gpt-3.5-turbo narrative_synopsis \n", - "130 gpt-3.5-turbo narrative_synopsis \n", - "131 gpt-3.5-turbo narrative_synopsis \n", - "132 gpt-3.5-turbo narrative_synopsis \n", - "133 gpt-3.5-turbo narrative_synopsis \n", - "134 gpt-3.5-turbo narrative_synopsis \n", - "135 gpt-3.5-turbo narrative_synopsis \n", - "136 gpt-3.5-turbo narrative_synopsis \n", - "137 gpt-3.5-turbo narrative_synopsis \n", - "138 gpt-3.5-turbo narrative_synopsis \n", - "139 gpt-3.5-turbo narrative_synopsis \n", - "140 gpt-3.5-turbo narrative_synopsis \n", - "141 gpt-3.5-turbo narrative_synopsis \n", - "142 gpt-3.5-turbo no_synopsis \n", - "143 gpt-3.5-turbo no_synopsis \n", - "144 gpt-3.5-turbo no_synopsis \n", - "145 gpt-3.5-turbo no_synopsis \n", - "146 gpt-3.5-turbo no_synopsis \n", - "147 gpt-3.5-turbo no_synopsis \n", - "148 gpt-3.5-turbo no_synopsis \n", - "149 gpt-3.5-turbo no_synopsis \n", - "150 gpt-3.5-turbo no_synopsis \n", - "151 gpt-3.5-turbo no_synopsis \n", - "152 gpt-3.5-turbo no_synopsis \n", - "153 gpt-3.5-turbo no_synopsis \n", - "154 gpt-3.5-turbo no_synopsis \n", - "155 gpt-3.5-turbo no_synopsis \n", - "156 gpt-3.5-turbo no_synopsis \n", - "157 gpt-3.5-turbo no_synopsis \n", - "158 gpt-3.5-turbo no_synopsis \n", - "159 gpt-3.5-turbo no_synopsis \n", - "160 gpt-3.5-turbo no_synopsis \n", - "161 gpt-3.5-turbo no_synopsis \n", - "162 gpt-3.5-turbo no_synopsis \n", - "163 gpt-3.5-turbo no_synopsis \n", - "164 gpt-3.5-turbo no_synopsis \n", - "165 gpt-3.5-turbo no_synopsis \n", - "166 gpt-3.5-turbo no_synopsis \n", - "167 gpt-3.5-turbo no_synopsis \n", - "168 gpt-3.5-turbo no_synopsis \n", - "169 gpt-3.5-turbo no_synopsis \n", - "170 gpt-3.5-turbo no_synopsis \n", - "171 gpt-3.5-turbo no_synopsis \n", - "172 gpt-3.5-turbo no_synopsis \n", - "173 gpt-3.5-turbo no_synopsis \n", - "174 gpt-3.5-turbo no_synopsis \n", - "175 gpt-3.5-turbo no_synopsis \n", - "176 gpt-3.5-turbo no_synopsis \n", - "177 gpt-3.5-turbo no_synopsis \n", - "178 gpt-3.5-turbo no_synopsis \n", - "179 gpt-3.5-turbo no_synopsis \n", - "180 gpt-3.5-turbo no_synopsis \n", - "181 gpt-3.5-turbo no_synopsis \n", - "182 gpt-3.5-turbo no_synopsis \n", - "183 gpt-3.5-turbo no_synopsis \n", - "184 gpt-3.5-turbo no_synopsis \n", - "185 gpt-3.5-turbo no_synopsis \n", - "186 gpt-3.5-turbo no_synopsis \n", - "187 gpt-3.5-turbo no_synopsis \n", - "188 gpt-3.5-turbo no_synopsis \n", - "189 gpt-3.5-turbo no_synopsis \n", - "190 gpt-3.5-turbo no_synopsis \n", - "191 gpt-3.5-turbo no_synopsis \n", - "192 gpt-3.5-turbo no_synopsis \n", - "193 gpt-3.5-turbo no_synopsis \n", - "194 gpt-3.5-turbo no_synopsis \n", - "195 gpt-3.5-turbo no_synopsis \n", - "196 gpt-3.5-turbo no_synopsis \n", - "197 gpt-3.5-turbo no_synopsis \n", - "198 gpt-3.5-turbo no_synopsis \n", - "199 gpt-3.5-turbo no_synopsis \n", - "200 gpt-3.5-turbo no_synopsis \n", - "201 gpt-3.5-turbo no_synopsis \n", - "202 gpt-3.5-turbo no_synopsis \n", - "203 gpt-3.5-turbo no_synopsis \n", - "204 gpt-3.5-turbo no_synopsis \n", - "205 gpt-3.5-turbo no_synopsis \n", - "206 gpt-3.5-turbo no_synopsis \n", - "207 gpt-3.5-turbo no_synopsis \n", - "208 gpt-3.5-turbo no_synopsis \n", - "209 gpt-3.5-turbo no_synopsis \n", - "210 gpt-3.5-turbo no_synopsis \n", - "211 gpt-3.5-turbo no_synopsis \n", - "212 gpt-3.5-turbo no_synopsis \n", - "213 gpt-3.5-turbo no_synopsis \n", - "214 gpt-3.5-turbo no_synopsis \n", - "215 gpt-3.5-turbo no_synopsis \n", - "216 gpt-3.5-turbo no_synopsis \n", - "217 gpt-3.5-turbo no_synopsis \n", - "218 gpt-3.5-turbo no_synopsis \n", - "219 gpt-3.5-turbo no_synopsis \n", - "220 gpt-3.5-turbo no_synopsis \n", - "221 gpt-3.5-turbo no_synopsis \n", - "222 gpt-3.5-turbo no_synopsis \n", - "223 gpt-3.5-turbo no_synopsis \n", - "224 gpt-3.5-turbo no_synopsis \n", - "225 gpt-3.5-turbo no_synopsis \n", - "226 gpt-3.5-turbo no_synopsis \n", - "227 gpt-3.5-turbo no_synopsis \n", - "228 gpt-3.5-turbo no_synopsis \n", - "229 gpt-3.5-turbo no_synopsis \n", - "230 gpt-3.5-turbo no_synopsis \n", - "231 gpt-3.5-turbo no_synopsis \n", - "232 gpt-3.5-turbo no_synopsis \n", - "233 gpt-3.5-turbo no_synopsis \n", - "234 gpt-3.5-turbo no_synopsis \n", - "235 gpt-3.5-turbo no_synopsis \n", - "236 gpt-3.5-turbo no_synopsis \n", - "237 gpt-3.5-turbo no_synopsis \n", - "238 gpt-3.5-turbo no_synopsis \n", - "239 gpt-3.5-turbo no_synopsis \n", - "240 gpt-3.5-turbo no_synopsis \n", - "241 gpt-3.5-turbo no_synopsis \n", - "242 gpt-3.5-turbo no_synopsis \n", - "243 gpt-3.5-turbo no_synopsis \n", - "244 gpt-3.5-turbo no_synopsis \n", - "245 gpt-3.5-turbo no_synopsis \n", - "246 gpt-3.5-turbo no_synopsis \n", - "247 gpt-3.5-turbo no_synopsis \n", - "248 gpt-3.5-turbo no_synopsis \n", - "249 gpt-3.5-turbo no_synopsis \n", - "250 gpt-3.5-turbo no_synopsis \n", - "251 gpt-3.5-turbo no_synopsis \n", - "252 gpt-3.5-turbo no_synopsis \n", - "253 gpt-3.5-turbo no_synopsis \n", - "254 gpt-3.5-turbo no_synopsis \n", - "255 gpt-3.5-turbo no_synopsis \n", - "256 gpt-3.5-turbo no_synopsis \n", - "257 gpt-3.5-turbo no_synopsis \n", - "258 gpt-3.5-turbo no_synopsis \n", - "259 gpt-3.5-turbo no_synopsis \n", - "260 gpt-3.5-turbo no_synopsis \n", - "261 gpt-3.5-turbo no_synopsis \n", - "262 gpt-3.5-turbo no_synopsis \n", - "263 gpt-3.5-turbo no_synopsis \n", - "264 gpt-3.5-turbo no_synopsis \n", - "265 gpt-3.5-turbo no_synopsis \n", - "266 gpt-3.5-turbo no_synopsis \n", - "267 gpt-3.5-turbo no_synopsis \n", - "268 gpt-3.5-turbo no_synopsis \n", - "269 gpt-3.5-turbo no_synopsis \n", - "270 gpt-3.5-turbo no_synopsis \n", - "271 gpt-3.5-turbo no_synopsis \n", - "272 gpt-3.5-turbo no_synopsis \n", - "273 gpt-3.5-turbo no_synopsis \n", - "274 gpt-3.5-turbo no_synopsis \n", - "275 gpt-3.5-turbo no_synopsis \n", - "276 gpt-3.5-turbo no_synopsis \n", - "277 gpt-3.5-turbo no_synopsis \n", - "278 gpt-3.5-turbo no_synopsis \n", - "279 gpt-3.5-turbo no_synopsis \n", - "280 gpt-3.5-turbo no_synopsis \n", - "281 gpt-3.5-turbo no_synopsis \n", - "282 gpt-3.5-turbo no_synopsis \n", - "283 gpt-3.5-turbo no_synopsis \n", - "284 gpt-3.5-turbo ontological_synopsis \n", - "285 gpt-3.5-turbo ontological_synopsis \n", - "286 gpt-3.5-turbo ontological_synopsis \n", - "287 gpt-3.5-turbo ontological_synopsis \n", - "288 gpt-3.5-turbo ontological_synopsis \n", - "289 gpt-3.5-turbo ontological_synopsis \n", - "290 gpt-3.5-turbo ontological_synopsis \n", - "291 gpt-3.5-turbo ontological_synopsis \n", - "292 gpt-3.5-turbo ontological_synopsis \n", - "293 gpt-3.5-turbo ontological_synopsis \n", - "294 gpt-3.5-turbo ontological_synopsis \n", - "295 gpt-3.5-turbo ontological_synopsis \n", - "296 gpt-3.5-turbo ontological_synopsis \n", - "297 gpt-3.5-turbo ontological_synopsis \n", - "298 gpt-3.5-turbo ontological_synopsis \n", - "299 gpt-3.5-turbo ontological_synopsis \n", - "300 gpt-3.5-turbo ontological_synopsis \n", - "301 gpt-3.5-turbo ontological_synopsis \n", - "302 gpt-3.5-turbo ontological_synopsis \n", - "303 gpt-3.5-turbo ontological_synopsis \n", - "304 gpt-3.5-turbo ontological_synopsis \n", - "305 gpt-3.5-turbo ontological_synopsis \n", - "306 gpt-3.5-turbo ontological_synopsis \n", - "307 gpt-3.5-turbo ontological_synopsis \n", - "308 gpt-3.5-turbo ontological_synopsis \n", - "309 gpt-3.5-turbo ontological_synopsis \n", - "310 gpt-3.5-turbo ontological_synopsis \n", - "311 gpt-3.5-turbo ontological_synopsis \n", - "312 gpt-3.5-turbo ontological_synopsis \n", - "313 gpt-3.5-turbo ontological_synopsis \n", - "314 gpt-3.5-turbo ontological_synopsis \n", - "315 gpt-3.5-turbo ontological_synopsis \n", - "316 gpt-3.5-turbo ontological_synopsis \n", - "317 gpt-3.5-turbo ontological_synopsis \n", - "318 gpt-3.5-turbo ontological_synopsis \n", - "319 gpt-3.5-turbo ontological_synopsis \n", - "320 gpt-3.5-turbo ontological_synopsis \n", - "321 gpt-3.5-turbo ontological_synopsis \n", - "322 gpt-3.5-turbo ontological_synopsis \n", - "323 gpt-3.5-turbo ontological_synopsis \n", - "324 gpt-3.5-turbo ontological_synopsis \n", - "325 gpt-3.5-turbo ontological_synopsis \n", - "326 gpt-3.5-turbo ontological_synopsis \n", - "327 gpt-3.5-turbo ontological_synopsis \n", - "328 gpt-3.5-turbo ontological_synopsis \n", - "329 gpt-3.5-turbo ontological_synopsis \n", - "330 gpt-3.5-turbo ontological_synopsis \n", - "331 gpt-3.5-turbo ontological_synopsis \n", - "332 gpt-3.5-turbo ontological_synopsis \n", - "333 gpt-3.5-turbo ontological_synopsis \n", - "334 gpt-3.5-turbo ontological_synopsis \n", - "335 gpt-3.5-turbo ontological_synopsis \n", - "336 gpt-3.5-turbo ontological_synopsis \n", - "337 gpt-3.5-turbo ontological_synopsis \n", - "338 gpt-3.5-turbo ontological_synopsis \n", - "339 gpt-3.5-turbo ontological_synopsis \n", - "340 gpt-3.5-turbo ontological_synopsis \n", - "341 gpt-3.5-turbo ontological_synopsis \n", - "342 gpt-3.5-turbo ontological_synopsis \n", - "343 gpt-3.5-turbo ontological_synopsis \n", - "344 gpt-3.5-turbo ontological_synopsis \n", - "345 gpt-3.5-turbo ontological_synopsis \n", - "346 gpt-3.5-turbo ontological_synopsis \n", - "347 gpt-3.5-turbo ontological_synopsis \n", - "348 gpt-3.5-turbo ontological_synopsis \n", - "349 gpt-3.5-turbo ontological_synopsis \n", - "350 gpt-3.5-turbo ontological_synopsis \n", - "351 gpt-3.5-turbo ontological_synopsis \n", - "352 gpt-3.5-turbo ontological_synopsis \n", - "353 gpt-3.5-turbo ontological_synopsis \n", - "354 gpt-3.5-turbo ontological_synopsis \n", - "355 gpt-3.5-turbo ontological_synopsis \n", - "356 gpt-3.5-turbo ontological_synopsis \n", - "357 gpt-3.5-turbo ontological_synopsis \n", - "358 gpt-3.5-turbo ontological_synopsis \n", - "359 gpt-3.5-turbo ontological_synopsis \n", - "360 gpt-3.5-turbo ontological_synopsis \n", - "361 gpt-3.5-turbo ontological_synopsis \n", - "362 gpt-3.5-turbo ontological_synopsis \n", - "363 gpt-3.5-turbo ontological_synopsis \n", - "364 gpt-3.5-turbo ontological_synopsis \n", - "365 gpt-3.5-turbo ontological_synopsis \n", - "366 gpt-3.5-turbo ontological_synopsis \n", - "367 gpt-3.5-turbo ontological_synopsis \n", - "368 gpt-3.5-turbo ontological_synopsis \n", - "369 gpt-3.5-turbo ontological_synopsis \n", - "370 gpt-3.5-turbo ontological_synopsis \n", - "371 gpt-3.5-turbo ontological_synopsis \n", - "372 gpt-3.5-turbo ontological_synopsis \n", - "373 gpt-3.5-turbo ontological_synopsis \n", - "374 gpt-3.5-turbo ontological_synopsis \n", - "375 gpt-3.5-turbo ontological_synopsis \n", - "376 gpt-3.5-turbo ontological_synopsis \n", - "377 gpt-3.5-turbo ontological_synopsis \n", - "378 gpt-3.5-turbo ontological_synopsis \n", - "379 gpt-3.5-turbo ontological_synopsis \n", - "380 gpt-3.5-turbo ontological_synopsis \n", - "381 gpt-3.5-turbo ontological_synopsis \n", - "382 gpt-3.5-turbo ontological_synopsis \n", - "383 gpt-3.5-turbo ontological_synopsis \n", - "384 gpt-3.5-turbo ontological_synopsis \n", - "385 gpt-3.5-turbo ontological_synopsis \n", - "386 gpt-3.5-turbo ontological_synopsis \n", - "387 gpt-3.5-turbo ontological_synopsis \n", - "388 gpt-3.5-turbo ontological_synopsis \n", - "389 gpt-3.5-turbo ontological_synopsis \n", - "390 gpt-3.5-turbo ontological_synopsis \n", - "391 gpt-3.5-turbo ontological_synopsis \n", - "392 gpt-3.5-turbo ontological_synopsis \n", - "393 gpt-3.5-turbo ontological_synopsis \n", - "394 gpt-3.5-turbo ontological_synopsis \n", - "395 gpt-3.5-turbo ontological_synopsis \n", - "396 gpt-3.5-turbo ontological_synopsis \n", - "397 gpt-3.5-turbo ontological_synopsis \n", - "398 gpt-3.5-turbo ontological_synopsis \n", - "399 gpt-3.5-turbo ontological_synopsis \n", - "400 gpt-3.5-turbo ontological_synopsis \n", - "401 gpt-3.5-turbo ontological_synopsis \n", - "402 gpt-3.5-turbo ontological_synopsis \n", - "403 gpt-3.5-turbo ontological_synopsis \n", - "404 gpt-3.5-turbo ontological_synopsis \n", - "405 gpt-3.5-turbo ontological_synopsis \n", - "406 gpt-3.5-turbo ontological_synopsis \n", - "407 gpt-3.5-turbo ontological_synopsis \n", - "408 gpt-3.5-turbo ontological_synopsis \n", - "409 gpt-3.5-turbo ontological_synopsis \n", - "410 gpt-3.5-turbo ontological_synopsis \n", - "411 gpt-3.5-turbo ontological_synopsis \n", - "412 gpt-3.5-turbo ontological_synopsis \n", - "413 gpt-3.5-turbo ontological_synopsis \n", - "414 gpt-3.5-turbo ontological_synopsis \n", - "415 gpt-3.5-turbo ontological_synopsis \n", - "416 gpt-3.5-turbo ontological_synopsis \n", - "417 gpt-3.5-turbo ontological_synopsis \n", - "418 gpt-3.5-turbo ontological_synopsis \n", - "419 gpt-3.5-turbo ontological_synopsis \n", - "420 gpt-3.5-turbo ontological_synopsis \n", - "421 gpt-3.5-turbo ontological_synopsis \n", - "422 gpt-3.5-turbo ontological_synopsis \n", - "423 gpt-3.5-turbo ontological_synopsis \n", - "424 gpt-3.5-turbo ontological_synopsis \n", - "425 gpt-3.5-turbo ontological_synopsis \n", - "426 text-davinci-003 narrative_synopsis \n", - "427 text-davinci-003 narrative_synopsis \n", - "428 text-davinci-003 narrative_synopsis \n", - "429 text-davinci-003 narrative_synopsis \n", - "430 text-davinci-003 narrative_synopsis \n", - "431 text-davinci-003 narrative_synopsis \n", - "432 text-davinci-003 narrative_synopsis \n", - "433 text-davinci-003 narrative_synopsis \n", - "434 text-davinci-003 narrative_synopsis \n", - "435 text-davinci-003 narrative_synopsis \n", - "436 text-davinci-003 narrative_synopsis \n", - "437 text-davinci-003 narrative_synopsis \n", - "438 text-davinci-003 narrative_synopsis \n", - "439 text-davinci-003 narrative_synopsis \n", - "440 text-davinci-003 narrative_synopsis \n", - "441 text-davinci-003 narrative_synopsis \n", - "442 text-davinci-003 narrative_synopsis \n", - "443 text-davinci-003 narrative_synopsis \n", - "444 text-davinci-003 narrative_synopsis \n", - "445 text-davinci-003 narrative_synopsis \n", - "446 text-davinci-003 narrative_synopsis \n", - "447 text-davinci-003 narrative_synopsis \n", - 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"842 text-davinci-003 ontological_synopsis \n", - "843 text-davinci-003 ontological_synopsis \n", - "844 text-davinci-003 ontological_synopsis \n", - "845 text-davinci-003 ontological_synopsis \n", - "846 text-davinci-003 ontological_synopsis \n", - "847 text-davinci-003 ontological_synopsis \n", - "848 text-davinci-003 ontological_synopsis \n", - "849 text-davinci-003 ontological_synopsis \n", - "850 text-davinci-003 ontological_synopsis \n", - "851 text-davinci-003 ontological_synopsis \n", - "\n", - "prompt_variant geneset \\\n", - "0 EDS-0 \n", - "1 EDS-1 \n", - "2 FA-0 \n", - "3 FA-1 \n", - "4 HALLMARK_ADIPOGENESIS-0 \n", - "5 HALLMARK_ADIPOGENESIS-1 \n", - "6 HALLMARK_ALLOGRAFT_REJECTION-0 \n", - "7 HALLMARK_ALLOGRAFT_REJECTION-1 \n", - "8 HALLMARK_ANDROGEN_RESPONSE-0 \n", - "9 HALLMARK_ANDROGEN_RESPONSE-1 \n", - "10 HALLMARK_ANGIOGENESIS-0 \n", - "11 HALLMARK_ANGIOGENESIS-1 \n", - "12 HALLMARK_APICAL_JUNCTION-0 \n", - "13 HALLMARK_APICAL_JUNCTION-1 \n", - "14 HALLMARK_APICAL_SURFACE-0 \n", - "15 HALLMARK_APICAL_SURFACE-1 \n", - "16 HALLMARK_APOPTOSIS-0 \n", - "17 HALLMARK_APOPTOSIS-1 \n", - "18 HALLMARK_BILE_ACID_METABOLISM-0 \n", - "19 HALLMARK_BILE_ACID_METABOLISM-1 \n", - "20 HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 \n", - "21 HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 \n", - "22 HALLMARK_COAGULATION-0 \n", - "23 HALLMARK_COAGULATION-1 \n", - "24 HALLMARK_COMPLEMENT-0 \n", - "25 HALLMARK_COMPLEMENT-1 \n", - "26 HALLMARK_DNA_REPAIR-0 \n", - "27 HALLMARK_DNA_REPAIR-1 \n", - "28 HALLMARK_E2F_TARGETS-0 \n", - "29 HALLMARK_E2F_TARGETS-1 \n", - "30 HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 \n", - "31 HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 \n", - "32 HALLMARK_ESTROGEN_RESPONSE_EARLY-0 \n", - "33 HALLMARK_ESTROGEN_RESPONSE_EARLY-1 \n", - "34 HALLMARK_ESTROGEN_RESPONSE_LATE-0 \n", - "35 HALLMARK_ESTROGEN_RESPONSE_LATE-1 \n", - "36 HALLMARK_FATTY_ACID_METABOLISM-0 \n", - "37 HALLMARK_FATTY_ACID_METABOLISM-1 \n", - "38 HALLMARK_G2M_CHECKPOINT-0 \n", - "39 HALLMARK_G2M_CHECKPOINT-1 \n", - "40 HALLMARK_GLYCOLYSIS-0 \n", - "41 HALLMARK_GLYCOLYSIS-1 \n", - "42 HALLMARK_HEDGEHOG_SIGNALING-0 \n", - "43 HALLMARK_HEDGEHOG_SIGNALING-1 \n", - "44 HALLMARK_HEME_METABOLISM-0 \n", - "45 HALLMARK_HEME_METABOLISM-1 \n", - "46 HALLMARK_HYPOXIA-0 \n", - "47 HALLMARK_HYPOXIA-1 \n", - "48 HALLMARK_IL2_STAT5_SIGNALING-0 \n", - "49 HALLMARK_IL2_STAT5_SIGNALING-1 \n", - "50 HALLMARK_IL6_JAK_STAT3_SIGNALING-0 \n", - "51 HALLMARK_IL6_JAK_STAT3_SIGNALING-1 \n", - "52 HALLMARK_INFLAMMATORY_RESPONSE-0 \n", - "53 HALLMARK_INFLAMMATORY_RESPONSE-1 \n", - "54 HALLMARK_INTERFERON_ALPHA_RESPONSE-0 \n", - "55 HALLMARK_INTERFERON_ALPHA_RESPONSE-1 \n", - "56 HALLMARK_INTERFERON_GAMMA_RESPONSE-0 \n", - "57 HALLMARK_INTERFERON_GAMMA_RESPONSE-1 \n", - "58 HALLMARK_KRAS_SIGNALING_DN-0 \n", - "59 HALLMARK_KRAS_SIGNALING_DN-1 \n", - "60 HALLMARK_KRAS_SIGNALING_UP-0 \n", - "61 HALLMARK_KRAS_SIGNALING_UP-1 \n", - "62 HALLMARK_MITOTIC_SPINDLE-0 \n", - "63 HALLMARK_MITOTIC_SPINDLE-1 \n", - "64 HALLMARK_MTORC1_SIGNALING-0 \n", - "65 HALLMARK_MTORC1_SIGNALING-1 \n", - "66 HALLMARK_MYC_TARGETS_V1-0 \n", - "67 HALLMARK_MYC_TARGETS_V1-1 \n", - "68 HALLMARK_MYC_TARGETS_V2-0 \n", - "69 HALLMARK_MYC_TARGETS_V2-1 \n", - "70 HALLMARK_MYOGENESIS-0 \n", - "71 HALLMARK_MYOGENESIS-1 \n", - "72 HALLMARK_NOTCH_SIGNALING-0 \n", - "73 HALLMARK_NOTCH_SIGNALING-1 \n", - "74 HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 \n", - "75 HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 \n", - "76 HALLMARK_P53_PATHWAY-0 \n", - "77 HALLMARK_P53_PATHWAY-1 \n", - "78 HALLMARK_PANCREAS_BETA_CELLS-0 \n", - "79 HALLMARK_PANCREAS_BETA_CELLS-1 \n", - "80 HALLMARK_PEROXISOME-0 \n", - "81 HALLMARK_PEROXISOME-1 \n", - "82 HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 \n", - "83 HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 \n", - "84 HALLMARK_PROTEIN_SECRETION-0 \n", - "85 HALLMARK_PROTEIN_SECRETION-1 \n", - "86 HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 \n", - "87 HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 \n", - "88 HALLMARK_SPERMATOGENESIS-0 \n", - "89 HALLMARK_SPERMATOGENESIS-1 \n", - "90 HALLMARK_TGF_BETA_SIGNALING-0 \n", - "91 HALLMARK_TGF_BETA_SIGNALING-1 \n", - "92 HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 \n", - "93 HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 \n", - "94 HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 \n", - "95 HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 \n", - "96 HALLMARK_UV_RESPONSE_DN-0 \n", - "97 HALLMARK_UV_RESPONSE_DN-1 \n", - "98 HALLMARK_UV_RESPONSE_UP-0 \n", - "99 HALLMARK_UV_RESPONSE_UP-1 \n", - "100 HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 \n", - "101 HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 \n", - "102 T cell proliferation-0 \n", - "103 T cell proliferation-1 \n", - "104 Yamanaka-TFs-0 \n", - "105 Yamanaka-TFs-1 \n", - "106 amigo-example-0 \n", - "107 amigo-example-1 \n", - "108 bicluster_RNAseqDB_0-0 \n", - "109 bicluster_RNAseqDB_0-1 \n", - "110 bicluster_RNAseqDB_1002-0 \n", - "111 bicluster_RNAseqDB_1002-1 \n", - "112 endocytosis-0 \n", - "113 endocytosis-1 \n", - "114 glycolysis-gocam-0 \n", - "115 glycolysis-gocam-1 \n", - "116 go-postsynapse-calcium-transmembrane-0 \n", - "117 go-postsynapse-calcium-transmembrane-1 \n", - "118 go-reg-autophagy-pkra-0 \n", - "119 go-reg-autophagy-pkra-1 \n", - "120 hydrolase activity, hydrolyzing O-glycosyl compounds-0 \n", - "121 hydrolase activity, hydrolyzing O-glycosyl compounds-1 \n", - "122 ig-receptor-binding-2022-0 \n", - "123 ig-receptor-binding-2022-1 \n", - "124 meiosis I-0 \n", - "125 meiosis I-1 \n", - "126 molecular sequestering-0 \n", - "127 molecular sequestering-1 \n", - "128 mtorc1-0 \n", - "129 mtorc1-1 \n", - "130 peroxisome-0 \n", - "131 peroxisome-1 \n", - "132 progeria-0 \n", - "133 progeria-1 \n", - "134 regulation of presynaptic membrane potential-0 \n", - "135 regulation of presynaptic membrane potential-1 \n", - "136 sensory ataxia-0 \n", - "137 sensory ataxia-1 \n", - "138 term-GO:0007212-0 \n", - "139 term-GO:0007212-1 \n", - "140 tf-downreg-colorectal-0 \n", - "141 tf-downreg-colorectal-1 \n", - "142 EDS-0 \n", - "143 EDS-1 \n", - "144 FA-0 \n", - "145 FA-1 \n", - "146 HALLMARK_ADIPOGENESIS-0 \n", - "147 HALLMARK_ADIPOGENESIS-1 \n", - "148 HALLMARK_ALLOGRAFT_REJECTION-0 \n", - "149 HALLMARK_ALLOGRAFT_REJECTION-1 \n", - "150 HALLMARK_ANDROGEN_RESPONSE-0 \n", - "151 HALLMARK_ANDROGEN_RESPONSE-1 \n", - "152 HALLMARK_ANGIOGENESIS-0 \n", - "153 HALLMARK_ANGIOGENESIS-1 \n", - "154 HALLMARK_APICAL_JUNCTION-0 \n", - "155 HALLMARK_APICAL_JUNCTION-1 \n", - "156 HALLMARK_APICAL_SURFACE-0 \n", - "157 HALLMARK_APICAL_SURFACE-1 \n", - "158 HALLMARK_APOPTOSIS-0 \n", - "159 HALLMARK_APOPTOSIS-1 \n", - "160 HALLMARK_BILE_ACID_METABOLISM-0 \n", - "161 HALLMARK_BILE_ACID_METABOLISM-1 \n", - "162 HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 \n", - "163 HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 \n", - "164 HALLMARK_COAGULATION-0 \n", - "165 HALLMARK_COAGULATION-1 \n", - "166 HALLMARK_COMPLEMENT-0 \n", - "167 HALLMARK_COMPLEMENT-1 \n", - "168 HALLMARK_DNA_REPAIR-0 \n", - "169 HALLMARK_DNA_REPAIR-1 \n", - "170 HALLMARK_E2F_TARGETS-0 \n", - "171 HALLMARK_E2F_TARGETS-1 \n", - "172 HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 \n", - "173 HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 \n", - "174 HALLMARK_ESTROGEN_RESPONSE_EARLY-0 \n", - "175 HALLMARK_ESTROGEN_RESPONSE_EARLY-1 \n", - "176 HALLMARK_ESTROGEN_RESPONSE_LATE-0 \n", - "177 HALLMARK_ESTROGEN_RESPONSE_LATE-1 \n", - "178 HALLMARK_FATTY_ACID_METABOLISM-0 \n", - "179 HALLMARK_FATTY_ACID_METABOLISM-1 \n", - "180 HALLMARK_G2M_CHECKPOINT-0 \n", - "181 HALLMARK_G2M_CHECKPOINT-1 \n", - "182 HALLMARK_GLYCOLYSIS-0 \n", - "183 HALLMARK_GLYCOLYSIS-1 \n", - "184 HALLMARK_HEDGEHOG_SIGNALING-0 \n", - "185 HALLMARK_HEDGEHOG_SIGNALING-1 \n", - "186 HALLMARK_HEME_METABOLISM-0 \n", - "187 HALLMARK_HEME_METABOLISM-1 \n", - "188 HALLMARK_HYPOXIA-0 \n", - "189 HALLMARK_HYPOXIA-1 \n", - "190 HALLMARK_IL2_STAT5_SIGNALING-0 \n", - "191 HALLMARK_IL2_STAT5_SIGNALING-1 \n", - "192 HALLMARK_IL6_JAK_STAT3_SIGNALING-0 \n", - "193 HALLMARK_IL6_JAK_STAT3_SIGNALING-1 \n", - "194 HALLMARK_INFLAMMATORY_RESPONSE-0 \n", - "195 HALLMARK_INFLAMMATORY_RESPONSE-1 \n", - "196 HALLMARK_INTERFERON_ALPHA_RESPONSE-0 \n", - "197 HALLMARK_INTERFERON_ALPHA_RESPONSE-1 \n", - "198 HALLMARK_INTERFERON_GAMMA_RESPONSE-0 \n", - "199 HALLMARK_INTERFERON_GAMMA_RESPONSE-1 \n", - "200 HALLMARK_KRAS_SIGNALING_DN-0 \n", - "201 HALLMARK_KRAS_SIGNALING_DN-1 \n", - "202 HALLMARK_KRAS_SIGNALING_UP-0 \n", - "203 HALLMARK_KRAS_SIGNALING_UP-1 \n", - "204 HALLMARK_MITOTIC_SPINDLE-0 \n", - "205 HALLMARK_MITOTIC_SPINDLE-1 \n", - "206 HALLMARK_MTORC1_SIGNALING-0 \n", - "207 HALLMARK_MTORC1_SIGNALING-1 \n", - "208 HALLMARK_MYC_TARGETS_V1-0 \n", - "209 HALLMARK_MYC_TARGETS_V1-1 \n", - "210 HALLMARK_MYC_TARGETS_V2-0 \n", - "211 HALLMARK_MYC_TARGETS_V2-1 \n", - "212 HALLMARK_MYOGENESIS-0 \n", - "213 HALLMARK_MYOGENESIS-1 \n", - "214 HALLMARK_NOTCH_SIGNALING-0 \n", - "215 HALLMARK_NOTCH_SIGNALING-1 \n", - "216 HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 \n", - "217 HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 \n", - "218 HALLMARK_P53_PATHWAY-0 \n", - "219 HALLMARK_P53_PATHWAY-1 \n", - "220 HALLMARK_PANCREAS_BETA_CELLS-0 \n", - "221 HALLMARK_PANCREAS_BETA_CELLS-1 \n", - "222 HALLMARK_PEROXISOME-0 \n", - "223 HALLMARK_PEROXISOME-1 \n", - "224 HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 \n", - "225 HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 \n", - "226 HALLMARK_PROTEIN_SECRETION-0 \n", - "227 HALLMARK_PROTEIN_SECRETION-1 \n", - "228 HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 \n", - "229 HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 \n", - "230 HALLMARK_SPERMATOGENESIS-0 \n", - "231 HALLMARK_SPERMATOGENESIS-1 \n", - "232 HALLMARK_TGF_BETA_SIGNALING-0 \n", - "233 HALLMARK_TGF_BETA_SIGNALING-1 \n", - "234 HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 \n", - "235 HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 \n", - "236 HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 \n", - "237 HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 \n", - "238 HALLMARK_UV_RESPONSE_DN-0 \n", - "239 HALLMARK_UV_RESPONSE_DN-1 \n", - "240 HALLMARK_UV_RESPONSE_UP-0 \n", - "241 HALLMARK_UV_RESPONSE_UP-1 \n", - "242 HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 \n", - "243 HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 \n", - "244 T cell proliferation-0 \n", - "245 T cell proliferation-1 \n", - "246 Yamanaka-TFs-0 \n", - "247 Yamanaka-TFs-1 \n", - "248 amigo-example-0 \n", - "249 amigo-example-1 \n", - "250 bicluster_RNAseqDB_0-0 \n", - "251 bicluster_RNAseqDB_0-1 \n", - "252 bicluster_RNAseqDB_1002-0 \n", - "253 bicluster_RNAseqDB_1002-1 \n", - "254 endocytosis-0 \n", - "255 endocytosis-1 \n", - "256 glycolysis-gocam-0 \n", - "257 glycolysis-gocam-1 \n", - "258 go-postsynapse-calcium-transmembrane-0 \n", - "259 go-postsynapse-calcium-transmembrane-1 \n", - "260 go-reg-autophagy-pkra-0 \n", - "261 go-reg-autophagy-pkra-1 \n", - "262 hydrolase activity, hydrolyzing O-glycosyl compounds-0 \n", - "263 hydrolase activity, hydrolyzing O-glycosyl compounds-1 \n", - "264 ig-receptor-binding-2022-0 \n", - "265 ig-receptor-binding-2022-1 \n", - "266 meiosis I-0 \n", - "267 meiosis I-1 \n", - "268 molecular sequestering-0 \n", - "269 molecular sequestering-1 \n", - "270 mtorc1-0 \n", - "271 mtorc1-1 \n", - "272 peroxisome-0 \n", - "273 peroxisome-1 \n", - "274 progeria-0 \n", - "275 progeria-1 \n", - "276 regulation of presynaptic membrane potential-0 \n", - "277 regulation of presynaptic membrane potential-1 \n", - "278 sensory ataxia-0 \n", - "279 sensory ataxia-1 \n", - "280 term-GO:0007212-0 \n", - "281 term-GO:0007212-1 \n", - "282 tf-downreg-colorectal-0 \n", - "283 tf-downreg-colorectal-1 \n", - "284 EDS-0 \n", - "285 EDS-1 \n", - "286 FA-0 \n", - "287 FA-1 \n", - "288 HALLMARK_ADIPOGENESIS-0 \n", - "289 HALLMARK_ADIPOGENESIS-1 \n", - "290 HALLMARK_ALLOGRAFT_REJECTION-0 \n", - "291 HALLMARK_ALLOGRAFT_REJECTION-1 \n", - "292 HALLMARK_ANDROGEN_RESPONSE-0 \n", - "293 HALLMARK_ANDROGEN_RESPONSE-1 \n", - "294 HALLMARK_ANGIOGENESIS-0 \n", - "295 HALLMARK_ANGIOGENESIS-1 \n", - "296 HALLMARK_APICAL_JUNCTION-0 \n", - "297 HALLMARK_APICAL_JUNCTION-1 \n", - "298 HALLMARK_APICAL_SURFACE-0 \n", - "299 HALLMARK_APICAL_SURFACE-1 \n", - "300 HALLMARK_APOPTOSIS-0 \n", - "301 HALLMARK_APOPTOSIS-1 \n", - "302 HALLMARK_BILE_ACID_METABOLISM-0 \n", - "303 HALLMARK_BILE_ACID_METABOLISM-1 \n", - "304 HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 \n", - "305 HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 \n", - "306 HALLMARK_COAGULATION-0 \n", - "307 HALLMARK_COAGULATION-1 \n", - "308 HALLMARK_COMPLEMENT-0 \n", - "309 HALLMARK_COMPLEMENT-1 \n", - "310 HALLMARK_DNA_REPAIR-0 \n", - "311 HALLMARK_DNA_REPAIR-1 \n", - "312 HALLMARK_E2F_TARGETS-0 \n", - "313 HALLMARK_E2F_TARGETS-1 \n", - "314 HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 \n", - "315 HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 \n", - "316 HALLMARK_ESTROGEN_RESPONSE_EARLY-0 \n", - "317 HALLMARK_ESTROGEN_RESPONSE_EARLY-1 \n", - "318 HALLMARK_ESTROGEN_RESPONSE_LATE-0 \n", - "319 HALLMARK_ESTROGEN_RESPONSE_LATE-1 \n", - "320 HALLMARK_FATTY_ACID_METABOLISM-0 \n", - "321 HALLMARK_FATTY_ACID_METABOLISM-1 \n", - "322 HALLMARK_G2M_CHECKPOINT-0 \n", - "323 HALLMARK_G2M_CHECKPOINT-1 \n", - "324 HALLMARK_GLYCOLYSIS-0 \n", - "325 HALLMARK_GLYCOLYSIS-1 \n", - "326 HALLMARK_HEDGEHOG_SIGNALING-0 \n", - "327 HALLMARK_HEDGEHOG_SIGNALING-1 \n", - "328 HALLMARK_HEME_METABOLISM-0 \n", - "329 HALLMARK_HEME_METABOLISM-1 \n", - "330 HALLMARK_HYPOXIA-0 \n", - "331 HALLMARK_HYPOXIA-1 \n", - "332 HALLMARK_IL2_STAT5_SIGNALING-0 \n", - "333 HALLMARK_IL2_STAT5_SIGNALING-1 \n", - "334 HALLMARK_IL6_JAK_STAT3_SIGNALING-0 \n", - "335 HALLMARK_IL6_JAK_STAT3_SIGNALING-1 \n", - "336 HALLMARK_INFLAMMATORY_RESPONSE-0 \n", - "337 HALLMARK_INFLAMMATORY_RESPONSE-1 \n", - "338 HALLMARK_INTERFERON_ALPHA_RESPONSE-0 \n", - "339 HALLMARK_INTERFERON_ALPHA_RESPONSE-1 \n", - "340 HALLMARK_INTERFERON_GAMMA_RESPONSE-0 \n", - "341 HALLMARK_INTERFERON_GAMMA_RESPONSE-1 \n", - "342 HALLMARK_KRAS_SIGNALING_DN-0 \n", - "343 HALLMARK_KRAS_SIGNALING_DN-1 \n", - "344 HALLMARK_KRAS_SIGNALING_UP-0 \n", - "345 HALLMARK_KRAS_SIGNALING_UP-1 \n", - "346 HALLMARK_MITOTIC_SPINDLE-0 \n", - "347 HALLMARK_MITOTIC_SPINDLE-1 \n", - "348 HALLMARK_MTORC1_SIGNALING-0 \n", - "349 HALLMARK_MTORC1_SIGNALING-1 \n", - "350 HALLMARK_MYC_TARGETS_V1-0 \n", - "351 HALLMARK_MYC_TARGETS_V1-1 \n", - "352 HALLMARK_MYC_TARGETS_V2-0 \n", - "353 HALLMARK_MYC_TARGETS_V2-1 \n", - "354 HALLMARK_MYOGENESIS-0 \n", - "355 HALLMARK_MYOGENESIS-1 \n", - "356 HALLMARK_NOTCH_SIGNALING-0 \n", - "357 HALLMARK_NOTCH_SIGNALING-1 \n", - "358 HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 \n", - "359 HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 \n", - "360 HALLMARK_P53_PATHWAY-0 \n", - "361 HALLMARK_P53_PATHWAY-1 \n", - "362 HALLMARK_PANCREAS_BETA_CELLS-0 \n", - "363 HALLMARK_PANCREAS_BETA_CELLS-1 \n", - "364 HALLMARK_PEROXISOME-0 \n", - "365 HALLMARK_PEROXISOME-1 \n", - "366 HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 \n", - "367 HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 \n", - "368 HALLMARK_PROTEIN_SECRETION-0 \n", - "369 HALLMARK_PROTEIN_SECRETION-1 \n", - "370 HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 \n", - "371 HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 \n", - "372 HALLMARK_SPERMATOGENESIS-0 \n", - "373 HALLMARK_SPERMATOGENESIS-1 \n", - "374 HALLMARK_TGF_BETA_SIGNALING-0 \n", - "375 HALLMARK_TGF_BETA_SIGNALING-1 \n", - "376 HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 \n", - "377 HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 \n", - "378 HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 \n", - "379 HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 \n", - "380 HALLMARK_UV_RESPONSE_DN-0 \n", - "381 HALLMARK_UV_RESPONSE_DN-1 \n", - "382 HALLMARK_UV_RESPONSE_UP-0 \n", - "383 HALLMARK_UV_RESPONSE_UP-1 \n", - "384 HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 \n", - "385 HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 \n", - "386 T cell proliferation-0 \n", - "387 T cell proliferation-1 \n", - "388 Yamanaka-TFs-0 \n", - "389 Yamanaka-TFs-1 \n", - "390 amigo-example-0 \n", - "391 amigo-example-1 \n", - "392 bicluster_RNAseqDB_0-0 \n", - "393 bicluster_RNAseqDB_0-1 \n", - "394 bicluster_RNAseqDB_1002-0 \n", - "395 bicluster_RNAseqDB_1002-1 \n", - "396 endocytosis-0 \n", - "397 endocytosis-1 \n", - "398 glycolysis-gocam-0 \n", - "399 glycolysis-gocam-1 \n", - "400 go-postsynapse-calcium-transmembrane-0 \n", - "401 go-postsynapse-calcium-transmembrane-1 \n", - "402 go-reg-autophagy-pkra-0 \n", - "403 go-reg-autophagy-pkra-1 \n", - "404 hydrolase activity, hydrolyzing O-glycosyl compounds-0 \n", - "405 hydrolase activity, hydrolyzing O-glycosyl compounds-1 \n", - "406 ig-receptor-binding-2022-0 \n", - "407 ig-receptor-binding-2022-1 \n", - "408 meiosis I-0 \n", - "409 meiosis I-1 \n", - "410 molecular sequestering-0 \n", - "411 molecular sequestering-1 \n", - "412 mtorc1-0 \n", - "413 mtorc1-1 \n", - "414 peroxisome-0 \n", - "415 peroxisome-1 \n", - "416 progeria-0 \n", - "417 progeria-1 \n", - "418 regulation of presynaptic membrane potential-0 \n", - "419 regulation of presynaptic membrane potential-1 \n", - "420 sensory ataxia-0 \n", - "421 sensory ataxia-1 \n", - "422 term-GO:0007212-0 \n", - "423 term-GO:0007212-1 \n", - "424 tf-downreg-colorectal-0 \n", - "425 tf-downreg-colorectal-1 \n", - "426 EDS-0 \n", - "427 EDS-1 \n", - "428 FA-0 \n", - "429 FA-1 \n", - "430 HALLMARK_ADIPOGENESIS-0 \n", - "431 HALLMARK_ADIPOGENESIS-1 \n", - "432 HALLMARK_ALLOGRAFT_REJECTION-0 \n", - "433 HALLMARK_ALLOGRAFT_REJECTION-1 \n", - "434 HALLMARK_ANDROGEN_RESPONSE-0 \n", - "435 HALLMARK_ANDROGEN_RESPONSE-1 \n", - "436 HALLMARK_ANGIOGENESIS-0 \n", - "437 HALLMARK_ANGIOGENESIS-1 \n", - "438 HALLMARK_APICAL_JUNCTION-0 \n", - "439 HALLMARK_APICAL_JUNCTION-1 \n", - "440 HALLMARK_APICAL_SURFACE-0 \n", - "441 HALLMARK_APICAL_SURFACE-1 \n", - "442 HALLMARK_APOPTOSIS-0 \n", - "443 HALLMARK_APOPTOSIS-1 \n", - "444 HALLMARK_BILE_ACID_METABOLISM-0 \n", - "445 HALLMARK_BILE_ACID_METABOLISM-1 \n", - "446 HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 \n", - "447 HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 \n", - "448 HALLMARK_COAGULATION-0 \n", - "449 HALLMARK_COAGULATION-1 \n", - "450 HALLMARK_COMPLEMENT-0 \n", - "451 HALLMARK_COMPLEMENT-1 \n", - "452 HALLMARK_DNA_REPAIR-0 \n", - "453 HALLMARK_DNA_REPAIR-1 \n", - "454 HALLMARK_E2F_TARGETS-0 \n", - "455 HALLMARK_E2F_TARGETS-1 \n", - "456 HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 \n", - "457 HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 \n", - "458 HALLMARK_ESTROGEN_RESPONSE_EARLY-0 \n", - "459 HALLMARK_ESTROGEN_RESPONSE_EARLY-1 \n", - "460 HALLMARK_ESTROGEN_RESPONSE_LATE-0 \n", - "461 HALLMARK_ESTROGEN_RESPONSE_LATE-1 \n", - "462 HALLMARK_FATTY_ACID_METABOLISM-0 \n", - "463 HALLMARK_FATTY_ACID_METABOLISM-1 \n", - "464 HALLMARK_G2M_CHECKPOINT-0 \n", - "465 HALLMARK_G2M_CHECKPOINT-1 \n", - "466 HALLMARK_GLYCOLYSIS-0 \n", - "467 HALLMARK_GLYCOLYSIS-1 \n", - "468 HALLMARK_HEDGEHOG_SIGNALING-0 \n", - "469 HALLMARK_HEDGEHOG_SIGNALING-1 \n", - "470 HALLMARK_HEME_METABOLISM-0 \n", - "471 HALLMARK_HEME_METABOLISM-1 \n", - "472 HALLMARK_HYPOXIA-0 \n", - "473 HALLMARK_HYPOXIA-1 \n", - "474 HALLMARK_IL2_STAT5_SIGNALING-0 \n", - "475 HALLMARK_IL2_STAT5_SIGNALING-1 \n", - "476 HALLMARK_IL6_JAK_STAT3_SIGNALING-0 \n", - "477 HALLMARK_IL6_JAK_STAT3_SIGNALING-1 \n", - "478 HALLMARK_INFLAMMATORY_RESPONSE-0 \n", - "479 HALLMARK_INFLAMMATORY_RESPONSE-1 \n", - "480 HALLMARK_INTERFERON_ALPHA_RESPONSE-0 \n", - "481 HALLMARK_INTERFERON_ALPHA_RESPONSE-1 \n", - "482 HALLMARK_INTERFERON_GAMMA_RESPONSE-0 \n", - "483 HALLMARK_INTERFERON_GAMMA_RESPONSE-1 \n", - "484 HALLMARK_KRAS_SIGNALING_DN-0 \n", - "485 HALLMARK_KRAS_SIGNALING_DN-1 \n", - "486 HALLMARK_KRAS_SIGNALING_UP-0 \n", - "487 HALLMARK_KRAS_SIGNALING_UP-1 \n", - "488 HALLMARK_MITOTIC_SPINDLE-0 \n", - "489 HALLMARK_MITOTIC_SPINDLE-1 \n", - "490 HALLMARK_MTORC1_SIGNALING-0 \n", - "491 HALLMARK_MTORC1_SIGNALING-1 \n", - "492 HALLMARK_MYC_TARGETS_V1-0 \n", - "493 HALLMARK_MYC_TARGETS_V1-1 \n", - "494 HALLMARK_MYC_TARGETS_V2-0 \n", - "495 HALLMARK_MYC_TARGETS_V2-1 \n", - "496 HALLMARK_MYOGENESIS-0 \n", - "497 HALLMARK_MYOGENESIS-1 \n", - "498 HALLMARK_NOTCH_SIGNALING-0 \n", - "499 HALLMARK_NOTCH_SIGNALING-1 \n", - "500 HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 \n", - "501 HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 \n", - "502 HALLMARK_P53_PATHWAY-0 \n", - "503 HALLMARK_P53_PATHWAY-1 \n", - "504 HALLMARK_PANCREAS_BETA_CELLS-0 \n", - "505 HALLMARK_PANCREAS_BETA_CELLS-1 \n", - "506 HALLMARK_PEROXISOME-0 \n", - "507 HALLMARK_PEROXISOME-1 \n", - "508 HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 \n", - "509 HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 \n", - "510 HALLMARK_PROTEIN_SECRETION-0 \n", - "511 HALLMARK_PROTEIN_SECRETION-1 \n", - "512 HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 \n", - "513 HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 \n", - "514 HALLMARK_SPERMATOGENESIS-0 \n", - "515 HALLMARK_SPERMATOGENESIS-1 \n", - "516 HALLMARK_TGF_BETA_SIGNALING-0 \n", - "517 HALLMARK_TGF_BETA_SIGNALING-1 \n", - "518 HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 \n", - "519 HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 \n", - "520 HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 \n", - "521 HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 \n", - "522 HALLMARK_UV_RESPONSE_DN-0 \n", - "523 HALLMARK_UV_RESPONSE_DN-1 \n", - "524 HALLMARK_UV_RESPONSE_UP-0 \n", - "525 HALLMARK_UV_RESPONSE_UP-1 \n", - "526 HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 \n", - "527 HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 \n", - "528 T cell proliferation-0 \n", - "529 T cell proliferation-1 \n", - "530 Yamanaka-TFs-0 \n", - "531 Yamanaka-TFs-1 \n", - "532 amigo-example-0 \n", - "533 amigo-example-1 \n", - "534 bicluster_RNAseqDB_0-0 \n", - "535 bicluster_RNAseqDB_0-1 \n", - "536 bicluster_RNAseqDB_1002-0 \n", - "537 bicluster_RNAseqDB_1002-1 \n", - "538 endocytosis-0 \n", - "539 endocytosis-1 \n", - "540 glycolysis-gocam-0 \n", - "541 glycolysis-gocam-1 \n", - "542 go-postsynapse-calcium-transmembrane-0 \n", - "543 go-postsynapse-calcium-transmembrane-1 \n", - "544 go-reg-autophagy-pkra-0 \n", - "545 go-reg-autophagy-pkra-1 \n", - "546 hydrolase activity, hydrolyzing O-glycosyl compounds-0 \n", - "547 hydrolase activity, hydrolyzing O-glycosyl compounds-1 \n", - "548 ig-receptor-binding-2022-0 \n", - "549 ig-receptor-binding-2022-1 \n", - "550 meiosis I-0 \n", - "551 meiosis I-1 \n", - "552 molecular sequestering-0 \n", - "553 molecular sequestering-1 \n", - "554 mtorc1-0 \n", - "555 mtorc1-1 \n", - "556 peroxisome-0 \n", - "557 peroxisome-1 \n", - "558 progeria-0 \n", - "559 progeria-1 \n", - "560 regulation of presynaptic membrane potential-0 \n", - "561 regulation of presynaptic membrane potential-1 \n", - "562 sensory ataxia-0 \n", - "563 sensory ataxia-1 \n", - "564 term-GO:0007212-0 \n", - "565 term-GO:0007212-1 \n", - "566 tf-downreg-colorectal-0 \n", - "567 tf-downreg-colorectal-1 \n", - "568 EDS-0 \n", - "569 EDS-1 \n", - "570 FA-0 \n", - "571 FA-1 \n", - "572 HALLMARK_ADIPOGENESIS-0 \n", - "573 HALLMARK_ADIPOGENESIS-1 \n", - "574 HALLMARK_ALLOGRAFT_REJECTION-0 \n", - "575 HALLMARK_ALLOGRAFT_REJECTION-1 \n", - "576 HALLMARK_ANDROGEN_RESPONSE-0 \n", - "577 HALLMARK_ANDROGEN_RESPONSE-1 \n", - "578 HALLMARK_ANGIOGENESIS-0 \n", - "579 HALLMARK_ANGIOGENESIS-1 \n", - "580 HALLMARK_APICAL_JUNCTION-0 \n", - "581 HALLMARK_APICAL_JUNCTION-1 \n", - "582 HALLMARK_APICAL_SURFACE-0 \n", - "583 HALLMARK_APICAL_SURFACE-1 \n", - "584 HALLMARK_APOPTOSIS-0 \n", - "585 HALLMARK_APOPTOSIS-1 \n", - "586 HALLMARK_BILE_ACID_METABOLISM-0 \n", - "587 HALLMARK_BILE_ACID_METABOLISM-1 \n", - "588 HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 \n", - "589 HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 \n", - "590 HALLMARK_COAGULATION-0 \n", - "591 HALLMARK_COAGULATION-1 \n", - "592 HALLMARK_COMPLEMENT-0 \n", - "593 HALLMARK_COMPLEMENT-1 \n", - "594 HALLMARK_DNA_REPAIR-0 \n", - "595 HALLMARK_DNA_REPAIR-1 \n", - "596 HALLMARK_E2F_TARGETS-0 \n", - "597 HALLMARK_E2F_TARGETS-1 \n", - "598 HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 \n", - "599 HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 \n", - "600 HALLMARK_ESTROGEN_RESPONSE_EARLY-0 \n", - "601 HALLMARK_ESTROGEN_RESPONSE_EARLY-1 \n", - "602 HALLMARK_ESTROGEN_RESPONSE_LATE-0 \n", - "603 HALLMARK_ESTROGEN_RESPONSE_LATE-1 \n", - "604 HALLMARK_FATTY_ACID_METABOLISM-0 \n", - "605 HALLMARK_FATTY_ACID_METABOLISM-1 \n", - "606 HALLMARK_G2M_CHECKPOINT-0 \n", - "607 HALLMARK_G2M_CHECKPOINT-1 \n", - "608 HALLMARK_GLYCOLYSIS-0 \n", - "609 HALLMARK_GLYCOLYSIS-1 \n", - "610 HALLMARK_HEDGEHOG_SIGNALING-0 \n", - "611 HALLMARK_HEDGEHOG_SIGNALING-1 \n", - "612 HALLMARK_HEME_METABOLISM-0 \n", - "613 HALLMARK_HEME_METABOLISM-1 \n", - "614 HALLMARK_HYPOXIA-0 \n", - "615 HALLMARK_HYPOXIA-1 \n", - "616 HALLMARK_IL2_STAT5_SIGNALING-0 \n", - "617 HALLMARK_IL2_STAT5_SIGNALING-1 \n", - "618 HALLMARK_IL6_JAK_STAT3_SIGNALING-0 \n", - "619 HALLMARK_IL6_JAK_STAT3_SIGNALING-1 \n", - "620 HALLMARK_INFLAMMATORY_RESPONSE-0 \n", - "621 HALLMARK_INFLAMMATORY_RESPONSE-1 \n", - "622 HALLMARK_INTERFERON_ALPHA_RESPONSE-0 \n", - "623 HALLMARK_INTERFERON_ALPHA_RESPONSE-1 \n", - "624 HALLMARK_INTERFERON_GAMMA_RESPONSE-0 \n", - "625 HALLMARK_INTERFERON_GAMMA_RESPONSE-1 \n", - "626 HALLMARK_KRAS_SIGNALING_DN-0 \n", - "627 HALLMARK_KRAS_SIGNALING_DN-1 \n", - "628 HALLMARK_KRAS_SIGNALING_UP-0 \n", - "629 HALLMARK_KRAS_SIGNALING_UP-1 \n", - "630 HALLMARK_MITOTIC_SPINDLE-0 \n", - "631 HALLMARK_MITOTIC_SPINDLE-1 \n", - "632 HALLMARK_MTORC1_SIGNALING-0 \n", - "633 HALLMARK_MTORC1_SIGNALING-1 \n", - "634 HALLMARK_MYC_TARGETS_V1-0 \n", - "635 HALLMARK_MYC_TARGETS_V1-1 \n", - "636 HALLMARK_MYC_TARGETS_V2-0 \n", - "637 HALLMARK_MYC_TARGETS_V2-1 \n", - "638 HALLMARK_MYOGENESIS-0 \n", - "639 HALLMARK_MYOGENESIS-1 \n", - "640 HALLMARK_NOTCH_SIGNALING-0 \n", - "641 HALLMARK_NOTCH_SIGNALING-1 \n", - "642 HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 \n", - "643 HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 \n", - "644 HALLMARK_P53_PATHWAY-0 \n", - "645 HALLMARK_P53_PATHWAY-1 \n", - "646 HALLMARK_PANCREAS_BETA_CELLS-0 \n", - "647 HALLMARK_PANCREAS_BETA_CELLS-1 \n", - "648 HALLMARK_PEROXISOME-0 \n", - "649 HALLMARK_PEROXISOME-1 \n", - "650 HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 \n", - "651 HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 \n", - "652 HALLMARK_PROTEIN_SECRETION-0 \n", - "653 HALLMARK_PROTEIN_SECRETION-1 \n", - "654 HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 \n", - "655 HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 \n", - "656 HALLMARK_SPERMATOGENESIS-0 \n", - "657 HALLMARK_SPERMATOGENESIS-1 \n", - "658 HALLMARK_TGF_BETA_SIGNALING-0 \n", - "659 HALLMARK_TGF_BETA_SIGNALING-1 \n", - "660 HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 \n", - "661 HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 \n", - "662 HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 \n", - "663 HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 \n", - "664 HALLMARK_UV_RESPONSE_DN-0 \n", - "665 HALLMARK_UV_RESPONSE_DN-1 \n", - "666 HALLMARK_UV_RESPONSE_UP-0 \n", - "667 HALLMARK_UV_RESPONSE_UP-1 \n", - "668 HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 \n", - "669 HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 \n", - "670 T cell proliferation-0 \n", - "671 T cell proliferation-1 \n", - "672 Yamanaka-TFs-0 \n", - "673 Yamanaka-TFs-1 \n", - "674 amigo-example-0 \n", - "675 amigo-example-1 \n", - "676 bicluster_RNAseqDB_0-0 \n", - "677 bicluster_RNAseqDB_0-1 \n", - "678 bicluster_RNAseqDB_1002-0 \n", - "679 bicluster_RNAseqDB_1002-1 \n", - "680 endocytosis-0 \n", - "681 endocytosis-1 \n", - "682 glycolysis-gocam-0 \n", - "683 glycolysis-gocam-1 \n", - "684 go-postsynapse-calcium-transmembrane-0 \n", - "685 go-postsynapse-calcium-transmembrane-1 \n", - "686 go-reg-autophagy-pkra-0 \n", - "687 go-reg-autophagy-pkra-1 \n", - "688 hydrolase activity, hydrolyzing O-glycosyl compounds-0 \n", - "689 hydrolase activity, hydrolyzing O-glycosyl compounds-1 \n", - "690 ig-receptor-binding-2022-0 \n", - "691 ig-receptor-binding-2022-1 \n", - "692 meiosis I-0 \n", - "693 meiosis I-1 \n", - "694 molecular sequestering-0 \n", - "695 molecular sequestering-1 \n", - "696 mtorc1-0 \n", - "697 mtorc1-1 \n", - "698 peroxisome-0 \n", - "699 peroxisome-1 \n", - "700 progeria-0 \n", - "701 progeria-1 \n", - "702 regulation of presynaptic membrane potential-0 \n", - "703 regulation of presynaptic membrane potential-1 \n", - "704 sensory ataxia-0 \n", - "705 sensory ataxia-1 \n", - "706 term-GO:0007212-0 \n", - "707 term-GO:0007212-1 \n", - "708 tf-downreg-colorectal-0 \n", - "709 tf-downreg-colorectal-1 \n", - "710 EDS-0 \n", - "711 EDS-1 \n", - "712 FA-0 \n", - "713 FA-1 \n", - "714 HALLMARK_ADIPOGENESIS-0 \n", - "715 HALLMARK_ADIPOGENESIS-1 \n", - "716 HALLMARK_ALLOGRAFT_REJECTION-0 \n", - "717 HALLMARK_ALLOGRAFT_REJECTION-1 \n", - "718 HALLMARK_ANDROGEN_RESPONSE-0 \n", - "719 HALLMARK_ANDROGEN_RESPONSE-1 \n", - "720 HALLMARK_ANGIOGENESIS-0 \n", - "721 HALLMARK_ANGIOGENESIS-1 \n", - "722 HALLMARK_APICAL_JUNCTION-0 \n", - "723 HALLMARK_APICAL_JUNCTION-1 \n", - "724 HALLMARK_APICAL_SURFACE-0 \n", - "725 HALLMARK_APICAL_SURFACE-1 \n", - "726 HALLMARK_APOPTOSIS-0 \n", - "727 HALLMARK_APOPTOSIS-1 \n", - "728 HALLMARK_BILE_ACID_METABOLISM-0 \n", - "729 HALLMARK_BILE_ACID_METABOLISM-1 \n", - "730 HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 \n", - "731 HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 \n", - "732 HALLMARK_COAGULATION-0 \n", - "733 HALLMARK_COAGULATION-1 \n", - "734 HALLMARK_COMPLEMENT-0 \n", - "735 HALLMARK_COMPLEMENT-1 \n", - "736 HALLMARK_DNA_REPAIR-0 \n", - "737 HALLMARK_DNA_REPAIR-1 \n", - "738 HALLMARK_E2F_TARGETS-0 \n", - "739 HALLMARK_E2F_TARGETS-1 \n", - "740 HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 \n", - "741 HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 \n", - "742 HALLMARK_ESTROGEN_RESPONSE_EARLY-0 \n", - "743 HALLMARK_ESTROGEN_RESPONSE_EARLY-1 \n", - "744 HALLMARK_ESTROGEN_RESPONSE_LATE-0 \n", - "745 HALLMARK_ESTROGEN_RESPONSE_LATE-1 \n", - "746 HALLMARK_FATTY_ACID_METABOLISM-0 \n", - "747 HALLMARK_FATTY_ACID_METABOLISM-1 \n", - "748 HALLMARK_G2M_CHECKPOINT-0 \n", - "749 HALLMARK_G2M_CHECKPOINT-1 \n", - "750 HALLMARK_GLYCOLYSIS-0 \n", - "751 HALLMARK_GLYCOLYSIS-1 \n", - "752 HALLMARK_HEDGEHOG_SIGNALING-0 \n", - "753 HALLMARK_HEDGEHOG_SIGNALING-1 \n", - "754 HALLMARK_HEME_METABOLISM-0 \n", - "755 HALLMARK_HEME_METABOLISM-1 \n", - "756 HALLMARK_HYPOXIA-0 \n", - "757 HALLMARK_HYPOXIA-1 \n", - "758 HALLMARK_IL2_STAT5_SIGNALING-0 \n", - "759 HALLMARK_IL2_STAT5_SIGNALING-1 \n", - "760 HALLMARK_IL6_JAK_STAT3_SIGNALING-0 \n", - "761 HALLMARK_IL6_JAK_STAT3_SIGNALING-1 \n", - "762 HALLMARK_INFLAMMATORY_RESPONSE-0 \n", - "763 HALLMARK_INFLAMMATORY_RESPONSE-1 \n", - "764 HALLMARK_INTERFERON_ALPHA_RESPONSE-0 \n", - "765 HALLMARK_INTERFERON_ALPHA_RESPONSE-1 \n", - "766 HALLMARK_INTERFERON_GAMMA_RESPONSE-0 \n", - "767 HALLMARK_INTERFERON_GAMMA_RESPONSE-1 \n", - "768 HALLMARK_KRAS_SIGNALING_DN-0 \n", - "769 HALLMARK_KRAS_SIGNALING_DN-1 \n", - "770 HALLMARK_KRAS_SIGNALING_UP-0 \n", - "771 HALLMARK_KRAS_SIGNALING_UP-1 \n", - "772 HALLMARK_MITOTIC_SPINDLE-0 \n", - "773 HALLMARK_MITOTIC_SPINDLE-1 \n", - "774 HALLMARK_MTORC1_SIGNALING-0 \n", - "775 HALLMARK_MTORC1_SIGNALING-1 \n", - "776 HALLMARK_MYC_TARGETS_V1-0 \n", - "777 HALLMARK_MYC_TARGETS_V1-1 \n", - "778 HALLMARK_MYC_TARGETS_V2-0 \n", - "779 HALLMARK_MYC_TARGETS_V2-1 \n", - "780 HALLMARK_MYOGENESIS-0 \n", - "781 HALLMARK_MYOGENESIS-1 \n", - "782 HALLMARK_NOTCH_SIGNALING-0 \n", - "783 HALLMARK_NOTCH_SIGNALING-1 \n", - "784 HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 \n", - "785 HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 \n", - "786 HALLMARK_P53_PATHWAY-0 \n", - "787 HALLMARK_P53_PATHWAY-1 \n", - "788 HALLMARK_PANCREAS_BETA_CELLS-0 \n", - "789 HALLMARK_PANCREAS_BETA_CELLS-1 \n", - "790 HALLMARK_PEROXISOME-0 \n", - "791 HALLMARK_PEROXISOME-1 \n", - "792 HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 \n", - "793 HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 \n", - "794 HALLMARK_PROTEIN_SECRETION-0 \n", - "795 HALLMARK_PROTEIN_SECRETION-1 \n", - "796 HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 \n", - "797 HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 \n", - "798 HALLMARK_SPERMATOGENESIS-0 \n", - "799 HALLMARK_SPERMATOGENESIS-1 \n", - "800 HALLMARK_TGF_BETA_SIGNALING-0 \n", - "801 HALLMARK_TGF_BETA_SIGNALING-1 \n", - "802 HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 \n", - "803 HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 \n", - "804 HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 \n", - "805 HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 \n", - "806 HALLMARK_UV_RESPONSE_DN-0 \n", - "807 HALLMARK_UV_RESPONSE_DN-1 \n", - "808 HALLMARK_UV_RESPONSE_UP-0 \n", - "809 HALLMARK_UV_RESPONSE_UP-1 \n", - "810 HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 \n", - "811 HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 \n", - "812 T cell proliferation-0 \n", - "813 T cell proliferation-1 \n", - "814 Yamanaka-TFs-0 \n", - "815 Yamanaka-TFs-1 \n", - "816 amigo-example-0 \n", - "817 amigo-example-1 \n", - "818 bicluster_RNAseqDB_0-0 \n", - "819 bicluster_RNAseqDB_0-1 \n", - "820 bicluster_RNAseqDB_1002-0 \n", - "821 bicluster_RNAseqDB_1002-1 \n", - "822 endocytosis-0 \n", - "823 endocytosis-1 \n", - "824 glycolysis-gocam-0 \n", - "825 glycolysis-gocam-1 \n", - "826 go-postsynapse-calcium-transmembrane-0 \n", - "827 go-postsynapse-calcium-transmembrane-1 \n", - "828 go-reg-autophagy-pkra-0 \n", - "829 go-reg-autophagy-pkra-1 \n", - "830 hydrolase activity, hydrolyzing O-glycosyl compounds-0 \n", - "831 hydrolase activity, hydrolyzing O-glycosyl compounds-1 \n", - "832 ig-receptor-binding-2022-0 \n", - "833 ig-receptor-binding-2022-1 \n", - "834 meiosis I-0 \n", - "835 meiosis I-1 \n", - "836 molecular sequestering-0 \n", - "837 molecular sequestering-1 \n", - "838 mtorc1-0 \n", - "839 mtorc1-1 \n", - "840 peroxisome-0 \n", - "841 peroxisome-1 \n", - "842 progeria-0 \n", - "843 progeria-1 \n", - "844 regulation of presynaptic membrane potential-0 \n", - "845 regulation of presynaptic membrane potential-1 \n", - "846 sensory ataxia-0 \n", - "847 sensory ataxia-1 \n", - "848 term-GO:0007212-0 \n", - "849 term-GO:0007212-1 \n", - "850 tf-downreg-colorectal-0 \n", - "851 tf-downreg-colorectal-1 \n", - "\n", - "prompt_variant v1 \\\n", - "0 [[GO:0032964, GO:0030198, GO:0010712, GO:0043687, GO:0006493, GO:0006508, GO:0008270]] \n", - "1 [[GO:0032964, GO:0061448, GO:0030198, GO:0030166]] \n", - "2 [[GO:0006281, GO:0035825, GO:0006302, chromosome stability \\n\\nhypotheses: the enriched terms suggest that the common function of these genes is dna repair, specifically in the context of homologous recombination and double-strand break repair. the genes are part of a complex network involved in maintaining chromosome stability, which is critical for preventing mutations and malignant transformation. mutations in these genes have been linked to various forms of cancer and the fanconi anemia disorder. understanding the mechanisms by which these genes function in dna repair could provide insights into cancer development and potential therapeutic targets]] \n", - "3 [[GO:0006281, fanconi anemia pathway, GO:0035825, MESH:M0443452, genome maintenance, GO:0006302]] \n", - "4 [[GO:0005739, GO:0006119, GO:0022900, GO:0006091, MESH:M0496924, GO:0006631, GO:0006099, GO:0006635]] \n", - "5 [[mitochondrial function, GO:0070469, energy production, GO:0006629, GO:0006869, GO:0005515, GO:0016049, GO:0051301, antioxidant enzyme. \\n\\nmechanism/]] \n", - "6 [[chemokine signaling pathway, cytokine-cytokine receptor interaction, GO:0006955, GO:0042110, GO:0050776, GO:0006954, GO:0050900]] \n", - "7 [[MESH:D018925, MESH:D016207, t cell-mediated immunity, interferon signaling, GO:0006954, tgf-beta signaling, toll-like receptor signaling, tnf signaling]] \n", - "8 [[protein kinase activity; membrane transport; enzyme catalysis\\n\\nmechanism: these genes are involved in signal transduction and cellular metabolism, with a focus on protein kinase activity, GO:0055085, and enzyme catalysis. they play roles in the transport of various molecules across biological membranes, including fatty acids, sugars, and ions. they are also important in regulating cellular responses to extracellular stimuli, such as growth factors, MESH:D006728, and cytokines. additionally, they catalyze metabolic reactions and contribute to various metabolic pathways]] \n", - "9 [[GO:0004672, GO:0008134, GO:0005515, GO:0007165, GO:0003824]] \n", - "10 [[GO:0031012, GO:0007155, tissue development and regeneration, growth factor signaling, endothelial-specific signaling, cytokine signaling]] \n", - "11 [[ecm organization, GO:0031589, GO:0016477]] \n", - "12 [[GO:0005884, GO:0007155, GO:0007010, GO:0008360, GO:0007165]] \n", - "13 [[GO:0070160, GO:0031012, GO:0005604, GO:0007155, adhesion junction, GO:0007160]] \n", - "14 [[GO:0007155, GO:0007165, GO:0061024, GO:0015031]] \n", - "15 [[GO:0007155, GO:0007165, GO:0007154]] \n", - "16 [[GO:0006915, GO:0008219, GO:0043067, GO:0097153, binding of proteins involved in cell death.\\n\\nmechanism: the majority of the genes on the list are involved in apoptotic processes or regulate cell death. many of these genes belong to the bcl-2 protein family, which regulate apoptosis by either inhibiting or promoting cell death. other gene products, such as the caspases, also play a crucial role in the apoptotic process by cleaving proteins involved in cell death, ultimately leading to cell death. the enrichment of this theme in the gene list suggests that the regulation of apoptosis and programmed cell death is a significant biological mechanism that the genes in the list are involved in]] \n", - "17 [[apoptosis regulation, cytokine signaling, growth factor regulation]] \n", - "18 [[GO:0140359, long-chain fatty-acid metabolism, GO:0008203, GO:0006629, GO:0006637]] \n", - "19 [[peroxisome biogenesis, GO:0006631, GO:0006699, GO:0008203, GO:0140359, GO:0016491, atp-binding cassette, GO:0005490]] \n", - "20 [[GO:0006695, GO:0006633, GO:0006629, regulation of cholesterol levels, transport across cell membranes]] \n", - "21 [[GO:0006695, GO:0006629, GO:0007165]] \n", - "22 [[GO:0006956, GO:0007596, GO:0006508, GO:0030198]] \n", - "23 [[blood coagulation cascade; complement activation, classical pathway; extracellular matrix disassembly; calcium ion binding. \\n\\nmechanism: these genes are involved in the regulation and activation of different pathways implicated in blood coagulation, GO:0006956, and extracellular matrix remodelling. blood coagulation involves the conversion of prothrombin to thrombin by coagulation factors, which leads to the formation of a fibrin clot. complement activation is a cascade resulting in the removal of damaged cells and pathogens. extracellular matrix disassembly and remodelling are implicated in cellular processes such as tissue repair, GO:0001525, metastasis. calcium-binding proteins play a vital role in signalling pathways regulation of enzymatic activities]] \n", - "24 [[GO:0006956, GO:0006955, GO:0030162, GO:0030168]] \n", - "25 [[GO:0006956, GO:0007596, cytokine signaling, GO:0006468, GO:0006955, GO:0006954]] \n", - "26 [[GO:0006281, transcription initiation, GO:0006396, GO:0009117]] \n", - "27 [[GO:0006270, GO:0006261, GO:0006297, transcription, dna-template-dependent, GO:0045893, GO:0000122, GO:0006281, GO:0000723, GO:0065004]] \n", - "28 [[GO:0006260, GO:0006281, GO:0051726]] \n", - "29 [[GO:0006260, GO:0006281, dna polymerase, GO:0009117, GO:0006298, chromatin structure\\n\\nmechanism: the genes on this list primarily function in dna replication and repair. many of them are involved in dna polymerase activity, nucleotide metabolism, mismatch repair, and chromatin structure. it is likely that these genes work together in a coordinated manner to ensure accurate dna replication and repair, and that defects in these processes can lead to genetic instability and cancer development]] \n", - "30 [[GO:0030198, GO:0030199, GO:0048251, GO:0071711, regulation of protein localization to extracellular matrix, GO:0043236, GO:0001968, GO:0005518]] \n", - "31 [[GO:0030198, GO:0005518, GO:0051015, GO:0005125, GO:0007155, GO:0016477]] \n", - "32 [[membrane-bound proteins, MESH:D004798, GO:0000981]] \n", - "33 [[GO:0055085, cell signaling, GO:0004672, GO:1904659, GO:0006811]] \n", - "34 [[membrane-associated protein complex, GO:0019899, GO:0034220, transcriptional regulation]] \n", - "35 [[GO:0005515, GO:0003824, GO:0008134, GO:0006355, GO:0007165, cytokine signaling pathway, regulation of cell growth and differentiation]] \n", - "36 [[GO:0006629, mitochondrial function, GO:0003824, GO:0006631, oxidation-reduction process, metabolism of carboxylic acid, GO:0006118, GO:0006082]] \n", - "37 [[GO:0006629, oxidation-reduction process, energy production, metabolism of fatty acids, mitochondrial function, GO:0045333]] \n", - "38 [[GO:0051301, GO:0006260, GO:0007059, GO:0000910]] \n", - "39 [[GO:0006270, GO:0007059, GO:0000075, GO:0007052, GO:0007346, GO:0065004]] \n", - "40 [[GO:0070085, GO:0005975, fructose-bisphosphate metabolism, GO:0006098, GO:0006006, GO:0006012, GO:0006090, GO:0006089, GO:0019319, GO:0006011, GO:0052573, GO:0004332]] \n", - "41 [[GO:0006096, GO:0005975, GO:0007165, GO:1904659, GO:0033554]] \n", - "42 [[GO:0007411, GO:0007155, transcriptional regulation, cell communication. \\n\\nhypotheses: \\nthese genes may be involved in regulating the formation of neural circuits and maintaining neural plasticity through dynamic regulation of gene expression and protein signaling. the enriched terms suggest that the neural development process involves complex regulation of cell-cell communication and adhesion, as well as transcriptional control of gene expression. axon guidance is critical for the proper formation of neural circuits, and dysregulation of this process may lead to neural disorders]] \n", - "43 [[GO:0007411, GO:0007155, transcription regulation, neuro-endocrine signaling, protein cleavage, cell migration.\\n\\nmechanism: these genes are involved in various aspects of neuronal development and signaling, including axon guidance, neuron migration, cell adhesion and communication, transcription regulation, and protein cleavage. these processes are critical for proper central nervous system development and function]] \n", - "44 [[GO:0006811, GO:0010468, protein turnover, GO:0061024]] \n", - "45 [[GO:0005515, GO:0003824, GO:0008152, GO:0006082, GO:0006810, GO:0006811, GO:0006820, GO:0044281, GO:0019538, GO:0006357, GO:0003924, GO:0016740, GO:0000166, GO:0003677, GO:0000988, GO:0006163, GO:0008643, GO:0050801, GO:0003723, GO:0019899]] \n", - "46 [[GO:0006096, GO:0006006, GO:0006000, GO:0005975, MESH:D004734, GO:0045333, GO:0019318, GO:0019682, triose-phosphate metabolic process, GO:0006090, GO:0006754]] \n", - "47 [[GO:0006006, insulin signaling pathway, GO:0051726, transcriptional regulation]] \n", - "48 [[cytokine, receptor, t-cell, GO:0006955, GO:0065007]] \n", - "49 [[GO:0004896, GO:0002224, GO:0002685, GO:0002521, GO:0002682, GO:0046649, GO:0019221, GO:0007159, GO:0051249, positive regulation of leukocyte proliferation\\n\\nmechanism: these genes are involved in the immune system response and regulation, specifically in the activation, differentiation, and migration of leukocytes. they are also involved in cytokine-mediated signaling pathways and toll-like receptor signaling pathways. the enriched terms suggest that these genes are involved in the regulation of various aspects of immune system processes, including leukocyte proliferation and adhesion]] \n", - "50 [[cytokine receptor activity; signal transduction; jak-stat cascade; cytokine-mediated signaling pathway\\n\\nmechanism: the enriched terms suggest that the commonality in gene function is the involvement of cytokine receptors and signaling pathways, particularly the jak-stat cascade, in cytokine-mediated signaling. this pathway is activated by cytokine binding to their respective receptors, leading to activation of the jak family of tyrosine kinases, which then phosphorylate and activate stat transcription factors to induce gene expression changes and cellular responses. the presence of these genes in the list suggests a potential role in regulating immune responses and inflammation through cytokine signaling]] \n", - "51 [[GO:0005126, GO:0002376, GO:0001817, GO:0050776, cytokine-mediated signaling pathway\\n\\nmechanism]] \n", - "52 [[cytokine signaling, GO:0004950, GO:0004930, GO:0050900, GO:0004908, GO:0002224, GO:0005164]] \n", - "53 [[GO:0004896, GO:0004930, GO:0042379, GO:0006955, GO:0006954, GO:0019221, GO:0050900, GO:0002694, GO:0002682, GO:0001819, GO:0009617, GO:0032496, GO:0070555, GO:0034612, GO:0042110]] \n", - "54 [[interferon-induced protein, GO:0051607, GO:0006955, nucleotide-binding domain, leucine-rich repeat-containing receptor signaling, GO:0005764, GO:0019882, cytokine]] \n", - "55 [[GO:0140888, cytokine signaling pathway, GO:0045087, GO:0009615, GO:0006952]] \n", - "56 [[interferon signaling, immune response regulation, cytokine signaling, tnf-receptor superfamily, protein tyrosine phosphatase, ubiquitin-proteasome system, MONDO:0007435]] \n", - "57 [[GO:0006955, cytokine signaling, GO:0030163, GO:0000502, ubiquitin system, viral rna sensing, MESH:D018925, GO:0019882]] \n", - "58 [[GO:0005509, GO:0055085, GO:0007155, GO:0004672, GO:0007186]] \n", - "59 [[cytokine signaling, g-protein coupled receptor signaling, GO:0019722, protein metabolism and processing]] \n", - "60 [[receptor signaling pathway, GO:0006468, negative regulation of transcription, GO:0031396, GO:0071345, GO:0032880, GO:0070374]] \n", - "61 [[signal transduction; cytokine activity; coagulation; ion transport; extracellular matrix organization. \\n\\nmechanism: the enriched terms suggest that the commonality in the function of these genes is related to signal transduction and regulation of various biological processes, such as coagulation, GO:0005125, GO:0030198, and ion transport. specifically, these genes are involved in regulating signaling pathways that are critical for these biological processes. there are several pathways known to contribute to these enriched terms, including the jak/stat, MESH:D016328, mapk/erk, and pi3k pathways. these pathways play important roles in cell signaling, GO:0006954, GO:0006955, other cellular processes]] \n", - "62 [[GO:0008017, GO:0007010, regulation of protein activity, GO:0051301, GO:0019894, GO:0003779]] \n", - "63 [[microtubule organization, GO:0140014, GO:0051301]] \n", - "64 [[GO:0046034, GO:0006629, GO:0006006, GO:0006457, GO:0046907]] \n", - "65 [[GO:0051087, GO:0005515, GO:0006457, GO:0043161]] \n", - "66 [[GO:0006413, GO:0042254, GO:0006260, GO:0006281, GO:0008380, GO:0009117]] \n", - "67 [[GO:0006413, GO:0006412, GO:0042254]] \n", - "68 [[GO:0006396, GO:0042254, rrna maturation]] \n", - "69 [[GO:0006364, nucleolar rna processing, GO:0042273, GO:0003723]] \n", - "70 [[GO:0003779, GO:0006936, sarcomere assembly, GO:0005509, GO:0005861, GO:0005523, MESH:D024510, GO:0005524, GO:0004672, GO:0005515, GO:0032982]] \n", - "71 [[GO:0006936, GO:0005861, GO:0005509, GO:0003779, sarcomere organization and biogenesis]] \n", - "72 [[GO:0007219, GO:0016567, GO:0001709, GO:0016055]] \n", - "73 [[GO:0007219, GO:0016567]] \n", - "74 [[GO:0006754, GO:0022900, GO:0005746, GO:0006119]] \n", - "75 [[GO:0005746, GO:0006119, mitochondrial metabolism, complex i-v, energy production]] \n", - "76 [[GO:0006281, GO:0010468, GO:0008083]] \n", - "77 [[GO:0006281, GO:0051726, GO:0007165, GO:0006915, MESH:D016207]] \n", - "78 [[GO:0006006, insulin signaling, pancreatic development, neuroendocrine regulation]] \n", - "79 [[GO:0006006, pancreatic islet development, neuroendocrine differentiation, GO:0007269, MESH:D009473]] \n", - "80 [[atp binding cassette transporter activity, GO:0006631, GO:0042445, GO:0008289, GO:0043574, GO:0005502]] \n", - "81 [[GO:0005777, GO:0006635, antioxidant response, mitochondrial carrier protein]] \n", - "82 [[GO:0004672, GO:0035556, GO:1902531, GO:0050794, GO:0003824, cytoskeletal regulation]] \n", - "83 [[GO:0004672, GO:0007165, GO:0006468, GO:0035556]] \n", - "84 [[GO:0005794, GO:0005480, GO:0005764]] \n", - "85 [[golgi transport, GO:0016192, GO:0015031, GO:0008104, GO:0032880, GO:0006886, GO:0016197]] \n", - "86 [[GO:0016209, GO:0006749, GO:0016491]] \n", - "87 [[GO:0016209, redox regulation, MESH:D018384]] \n", - "88 [[GO:0051726, GO:0003677, GO:0003723, GO:0016301, transcription regulation, chromatin organization and modification]] \n", - "89 [[GO:0005515, enzymatic activity, GO:0006811]] \n", - "90 [[growth factor signaling, transcriptional regulation, smad/tgf-beta signaling pathway, cellular differentiation]] \n", - "91 [[GO:0005024, GO:0060395, GO:0030509]] \n", - "92 [[GO:0006955, cytokine signaling pathway, transcription regulation. \\n\\nmechanism: these genes are primarily involved in regulating the immune response through the cytokine signaling pathway. they also play a role in transcriptional regulation of genes involved in these pathways. overall, these genes are important in regulating the response to pathogens and maintaining immune homeostasis]] \n", - "93 [[cytokine signaling pathway, GO:0002682, GO:0006351, GO:0006355, GO:0050900, GO:0006954, GO:0050727, GO:0032496, GO:0002237, GO:0009615, GO:0045893, GO:0045892]] \n", - "94 [[GO:0044183, GO:0006457, GO:0006396, cellular stress response, GO:0006401]] \n", - "95 [[GO:0006457, GO:0006396, GO:0006413, endoplasmic reticulum stress response, GO:0042254]] \n", - "96 [[GO:0006816, cytoskeletal organization, cell signaling, protein regulation]] \n", - "97 [[GO:0030198, GO:0007165, GO:0006811]] \n", - "98 [[GO:0006810, GO:0003824, regulation of transcription, GO:0016310, GO:0005515, GO:0006950, GO:0006915, GO:0006811, GO:0005524, GO:0007165, GO:0005975]] \n", - "99 [[GO:0008152, GO:0005515, GO:0007165, GO:0009165, GO:0006468, transcription factor activity\\n\\nmechanism: these enriched terms suggest that the commonality between these genes is their involvement in fundamental biological processes required for normal cell function. these include metabolism, signal transduction, and protein biosynthesis and regulation. the transcription factor activity term suggests that some of these genes may be transcriptional regulators, controlling the expression of other genes involved in these processes. overall, these genes likely work together to maintain cellular homeostasis and respond to internal and external cues]] \n", - "100 [[wnt signaling pathway regulation, transcriptional regulation, GO:0051726]] \n", - "101 [[GO:0016055, GO:0008013, transcription regulation]] \n", - "102 [[GO:0006955, GO:0007165, GO:0001816, cell proliferation and differentiation, GO:0042981]] \n", - "103 [[cytokine, GO:0006955, GO:0023052, receptor, t cell]] \n", - "104 [[MESH:D047108, stem cell pluripotency, MESH:D063646, cell cycle progression]] \n", - "105 [[MESH:D047108, stem cell maintenance, GO:0010468]] \n", - "106 [[GO:0030198, GO:0007155, GO:0007229, GO:0051495, GO:0002576]] \n", - "107 [[GO:0030198, GO:0007155, GO:0006029, GO:0042339, GO:0007229, GO:0030168]] \n", - "108 [[GO:0055085, GO:0006811, GO:0005524, zinc finger domain binding, GO:0007186, GO:0000988]] \n", - "109 [[GO:0019722, GO:0000988, GO:0055085]] \n", - "110 [[GO:0006936, GO:0007015, GO:0032972, GO:0005509, GO:0005861, GO:0005865, GO:0003779, GO:0045214, GO:0005523, GO:0017022, GO:0045932, skeletal muscle thin filament, cardiac muscle thin filament]] \n", - "111 [[GO:0006936, GO:0051015, GO:0005523, calcium binding, myofibril assembly.\\n\\nmechanism: these genes are involved in the regulation and maintenance of muscle structure and the contraction cycle. they act through the interaction of actin and myosin filaments, with the regulation of calcium ions controlling muscle contraction. the proteins encoded by these genes are involved in ion channel regulation, protein binding and modification, and energy metabolism]] \n", - "112 [[GO:0006897, intracellular trafficking, cytoskeleton reorganization]] \n", - "113 [[GO:0006897, GO:0016192, intracellular signaling, GO:0015031, cytoskeletal organization]] \n", - "114 [[glucose metabolism; glycolysis\\n\\nmechanism: these genes play a role in converting glucose to produce energy in the form of atp. hexokinase (hk1) and glucose phosphate isomerase (gpi) are involved in the initial steps of glucose metabolism, while phosphofructokinase (pfkm), MESH:D005634, and pyruvate kinase (pkm) are involved in glycolysis. triosephosphate isomerase (tpi1) and glyceraldehyde-3-phosphate dehydrogenase (gapdh) are also involved in glycolysis and produce atp by oxidizing glucose. phosphoglycerate mutase (pgam2) and enolase (eno3) are also involved in glycolysis and help convert glucose to pyruvate, which can then be converted to atp]] \n", - "115 [[GO:0006096, GO:0005975, energy pathway]] \n", - "116 [[GO:0006816, GO:0004970, n-methyl-d-aspartate receptor complex, GO:0043269, GO:0014069, GO:0007165]] \n", - "117 [[GO:0006816, GO:0005509, GO:0005216, GO:0005102, GO:0007268, GO:0030594]] \n", - "118 [[summary: regulation of cellular processes, including cell growth and metabolism, GO:0006915, GO:0006955, and regulation of chromatin remodeling and transcription.\\n\\nmechanism: these genes function in various pathways involved in the regulation of cellular processes. akt1 and pik3ca are involved in the pi3k/akt/mtor signaling pathway, which regulates cell growth, MESH:D013534, and metabolism. casp3 is a protease involved in the execution-phase of cell apoptosis. ccny and cdk5r1 are involved in the regulation of cell division cycles and the development of the central nervous system. hspb1 plays an important role in cell differentiation, but its overexpression may promote cancer cell proliferation and metastasis while protecting cancer cells from apoptosis. irgm regulates autophagy formation in response to intracellular pathogens. kat5 is a histone acetylase that has a role in dna repair and apoptosis and is thought to play an important role in signal transduction. mlst8, rptor, and smcr8 are involved in the torc1 signaling pathway, which regulates protein synthesis and cell growth in response to nutrient and insulin levels. nod2 is a pattern recognition receptor that detects cytosolic nucleic acids and trans]] \n", - "119 [[GO:0038202, GO:0032006, GO:0010605, activation of map3k7/tak1]] \n", - "120 [[GO:0005764, glycoside hydrolase activity, GO:0005975, GO:0016787, GO:0006027, GO:0005980, GO:0006689, GO:0015929, acid hydrolase activity, chitin catabolic process\\n\\nmechanism: these genes participate in the lysosomal degradation of various carbohydrate molecules, breaking them down into their component parts for further processing by the cell]] \n", - "121 [[GO:0004559, GO:0004415, lysosomal enzyme activity, GO:0016798, GO:0006487]] \n", - "122 [[immunoglobulin receptor binding activity, GO:0002253, GO:0098542, GO:0002922, b cell-mediated immunity]] \n", - "123 [[GO:0002250, GO:0002376, antigen binding activity, immunoglobulin receptor binding activity. \\n\\nmechanism: the enriched terms suggest that these genes are involved in the recognition and response to specific foreign antigens encountered by the immune system. antigen binding activity enables the binding of specific antigens, while immunoglobulin receptor binding activity allows for the activation and signaling of immune cells. together, these genes contribute to the adaptive immune response and immune system processes by recognizing and responding to diverse foreign antigens]] \n", - "124 [[meiotic recombination; homologous recombination; chromosome segregation during meiosis; double-strand break repair via homologous recombination.\\n\\nmechanism: these genes are all involved in the meiotic cell cycle process, specifically in events related to recombination, repair, and segregation of chromosomes during meiosis. the proteins encoded by these genes interact with each other to form protein complexes that are essential for proper meiotic division. the enriched terms indicate a strong association with meiotic recombination and double-strand break repair via homologous recombination. additionally, they suggest a role in chromosome segregation during meiosis]] \n", - "125 [[meiotic recombination, GO:0006281, GO:0035825, GO:0007059, GO:0006302, holliday junction, rad51, GO:0007127]] \n", - "126 [[GO:0005515, GO:0006955, intracellular transport\\n\\nmechanism/]] \n", - "127 [[GO:0006810, regulation of cell growth and survival, GO:0010468, GO:0006915]] \n", - "128 [[GO:0046034, GO:0006629, GO:0006006, GO:0006457, GO:0046907]] \n", - "129 [[GO:0000502, GO:0030163]] \n", - "130 [[peroxisome biogenesis, GO:0016558, peroxin]] \n", - "131 [[peroxisome biogenesis, matrix protein import, MONDO:0009279, peroxin (pex) family]] \n", - "132 [[GO:0006998, chromatin organization and maintenance, dna repair and recombination]] \n", - "133 [[GO:0006325, GO:0006281, nuclear stability]] \n", - "134 [[GO:0007268, GO:0005216, neurological function]] \n", - "135 [[GO:0005216, GO:0048666, GO:0007268]] \n", - "136 [[MONDO:0015626, MONDO:0005244, MONDO:0007790, GO:0043209, GO:0006264, tetratricopeptide repeat, transporter protein\\n\\nmechanism: these genes are involved in myelin upkeep and various neurological diseases associated with defects in myelin sheath synthesis and functions. they play roles in mitochondrial dna replication and transport, as well as protein transportation across the nuclear membrane. the presence of tetratricopeptide repeat motifs in these genes suggests their roles in protein-protein interactions and chaperone functions]] \n", - "137 [[MONDO:0011890, MONDO:0007790, MONDO:0011527, GO:0043217, peripheral myelin sheath, n-acetyl-d-glucosamine residue degradation, MESH:D008565, GO:0007399, nervous system myelination, GO:0006260]] \n", - "138 [[GO:0007186, GO:0007189, regulation of cyclic nucleotide metabolic process, regulation of camp metabolic process]] \n", - "139 [[GO:0007186, GO:0019932, GO:0007212]] \n", - "140 [[transcriptional regulation, GO:0006338, GO:0000988, GO:0003700, rna polymerase ii regulatory region sequence-specific dna binding, zinc finger domain, GO:0042393, nucleosome binding.\\n\\nmechanism: the enriched functions suggest that the given set of genes are involved in transcriptional regulation and chromatin remodeling. transcription factors bind to specific dna sequences and regulate gene expression, while chromatin remodeling alters the structure of chromatin to allow or prevent access to the dna by transcriptional machinery. zinc finger domain-containing proteins are involved in dna binding, and histone binding proteins facilitate the formation of transcriptionally active or inactive chromatin structures. the enriched functions suggest the potential involvement of these genes in both gene activation and repression, which may have important implications in cellular differentiation, development, and disease]] \n", - "141 [[transcription regulation, chromatin structure alteration, cell cycle progression, GO:0003682]] \n", - "142 [[GO:0030198, GO:0030199, GO:0006024]] \n", - "143 [[GO:0030199, GO:0030198, GO:0032964]] \n", - "144 [[fanconi anemia pathway, homologous recombination repair pathway, dna double-strand break repair]] \n", - "145 [[GO:0006281, GO:0006302, GO:0035825, mitotic cell-cycle checkpoint, GO:0006974]] \n", - "146 [[GO:0006631, GO:0006869, GO:0005746, GO:0006637, GO:0032000, GO:0016042, GO:0019216, GO:0033108, GO:0035336, GO:0033539, GO:0051791]] \n", - "147 [[GO:0006119, GO:0006631, GO:0006457, GO:0030301, GO:0019915, stress response, GO:0045333, mitochondrial metabolism, energy generation, GO:0006986, GO:0046890, GO:0032368, GO:0033344, GO:0007517, GO:0006979, GO:0001666, regulation of fatty acid catabolic process, GO:0019216]] \n", - "148 [[GO:0042110, GO:0030098, GO:0019221, GO:0002682, GO:0050776]] \n", - "149 [[GO:0005125, GO:0008009, GO:0034341, GO:0042110, GO:0050727]] \n", - "150 [[GO:0006351, regulation of transcription, GO:0006629, GO:0030163]] \n", - "151 [[GO:0006508, GO:0004672, GO:0007010, GO:0006695, GO:0045944, GO:0043066]] \n", - "152 [[GO:0030198, GO:0007267, GO:0043405, GO:0042127, GO:0030155, GO:0002576]] \n", - "153 [[GO:0030198, GO:0001525, vascular development, GO:0030335, GO:0001938, GO:0017015, GO:0007155]] \n", - "154 [[GO:0098609, GO:0034332, GO:0002159, GO:0030198]] \n", - "155 [[GO:0070160, GO:0007155, GO:0007154, GO:0022407, GO:0043542, GO:0030198, cell junction organization and biogenesis, GO:0032956, GO:0001525, GO:0010810]] \n", - "156 [[GO:0051716, GO:0005515, GO:0035556, GO:0007155, GO:0055085, GO:0061024, GO:0015031]] \n", - "157 [[GO:0007155, GO:0016477, GO:0007165, GO:0038023, GO:0006468, GO:0008104, GO:0055085, GO:0003824]] \n", - "158 [[GO:0006915, GO:0043123, GO:0050855, GO:0001817, GO:0002697, GO:0050670, GO:0051249, GO:0050856, GO:0034097, GO:0032496]] \n", - "159 [[cellular stress response, GO:0006915, GO:0006954, GO:0043067, negative regulation of nf-kappab transcription factor, GO:0043280]] \n", - "160 [[GO:0006695, GO:0006699, peroxisome biogenesis]] \n", - "161 [[GO:0006629, GO:0006869, GO:0005777, mitochondrial function]] \n", - "162 [[GO:0016126, GO:0006695, GO:0030301, GO:0006629, GO:0008202, GO:0042632]] \n", - "163 [[GO:0006695, GO:0006629, GO:0008203, GO:0016126, GO:0008299, GO:0042632, GO:0045540, GO:0019216]] \n", - "164 [[GO:0007596, GO:0006956, GO:0030168, GO:0042730, GO:0042060]] \n", - "165 [[GO:0030198, GO:0007596, GO:0006508, GO:0006955]] \n", - "166 [[c1q binding, GO:0006958, GO:0010951, GO:0043154, GO:2001237, GO:1903051]] \n", - "167 [[GO:0006955, GO:0007596, GO:0030163, GO:0006508, GO:0010951, GO:0071345, GO:0010952, GO:0030194, GO:0030449]] \n", - "168 [[GO:0006260, GO:0006281, GO:0006397, GO:0006351, GO:0042278]] \n", - "169 [[GO:0097747, GO:0003677, GO:0006397, GO:0006281]] \n", - "170 [[GO:0006260, GO:0007049, GO:0051301, GO:0140014, GO:0006281]] \n", - "171 [[GO:0006260, GO:0006281, GO:0071897, GO:0006302, GO:0022616, GO:0006974, GO:0000075, dna damage recognition and signaling]] \n", - "172 [[GO:0030198, GO:0043062, GO:0042277, GO:0030199, GO:0007155, GO:0007229, GO:0043410, GO:0005125, GO:0043498, GO:0010646, GO:0071711, GO:0007166, GO:0008285, GO:0070374, GO:0043236, GO:0005509, GO:0030335]] \n", - "173 [[GO:0030198, GO:0007155, GO:0005604, GO:0005581, GO:0007229, GO:0005925, GO:0005515, ecm-receptor interaction, GO:0030334, GO:0007010]] \n", - "174 [[GO:0006811, GO:0006631, GO:0006006, GO:0032870, GO:0008203, drug binding]] \n", - "175 [[GO:0006629, GO:0007165, transcriptional regulation]] \n", - "176 [[GO:0006351, GO:0008152, GO:0008283, GO:0006955, GO:0007165]] \n", - "177 [[GO:0008152, GO:0007165, GO:0032502, GO:0006955, GO:0006351, GO:0019538, GO:0006810, GO:0001558, GO:0042981, GO:0006811]] \n", - "178 [[1. metabolic process \\n2. oxidation-reduction process \\n3. response to oxidative stress \\n4. lipid metabolic process \\n5. carbohydrate metabolic process \\n6. amino acid metabolic process \\n7. detoxification \\n8. fatty acid beta-oxidation \\n9. tca cycle \\n10. electron transport chain \\n11. glucose homeostasis \\n12. protein folding and stabilization \\n13. ion homeostasis]] \n", - "179 [[GO:0006629, oxidative stress response, energy production]] \n", - "180 [[GO:0022402, GO:0140014, GO:0007059, GO:0007052, GO:0000226, GO:0006260]] \n", - "181 [[GO:0006260, GO:0007049, GO:0006281, GO:0140014, GO:0007059]] \n", - "182 [[1. glycosylation\\n2. glycolysis\\n3. pentose phosphate pathway]] \n", - "183 [[GO:0006006, energy generation, GO:0016052, GO:0006096, GO:0006090, GO:0006099, GO:0022900, GO:0006119, GO:0006754]] \n", - "184 [[GO:0030182, GO:0007411, GO:0016477, GO:0007155, GO:0008283]] \n", - "185 [[GO:0007399, GO:0007165, GO:0007155]] \n", - "186 [[GO:0006811, GO:0005515, GO:0008152]] \n", - "187 [[GO:0048821, GO:0045646, GO:0042541, GO:0015671, GO:0020037, GO:0005506, GO:0043496, GO:0046982]] \n", - "188 [[GO:0008152, GO:0006096, GO:0006979, GO:0080135, GO:1901031, GO:0046324, GO:0006006, GO:0005975, GO:0006974]] \n", - "189 [[glycolysis; gluconeogenesis; citrate cycle; pyruvate metabolism; atp production\\n\\nmechanism: these genes are enriched in functions related to energy metabolism, including glycolysis, GO:0006094, the citrate cycle, GO:0006090, and atp production. they are involved in various aspects of energy metabolism, such as glucose uptake and metabolism, GO:0005980, atp synthesis. the over-representation of these functions suggests that these genes may play a role in the regulation of energy metabolism at the cellular organismal level]] \n", - "190 [[il10ra, tnfrsf18, il18r1, il1r2, il1rl1, il2ra, il2rb, il4r, MESH:D016753, MESH:D018793, tnfrsf1b, tnfrsf21, tnfrsf4, tnfrsf8, tnfrsf9, tnfsf11, tnfsf10, ifngr1, ccr4, ctla4, cxcl10, icos, irf4, irf6, irf8, socs1, socs2, ager, cish, gata1, gbp4, spp1, bcl2, bcl2l1, bmpr2, ccnd2, ccne1, cd79b, galm, glipr2, gpx4, hk2, MESH:D016753, itga6, itgae, itih5, klf6, lif, lrig1, ltb, mxd1, myc]] \n", - "191 [[cytokine signaling pathway, GO:0006955, GO:0002682, GO:0006954, leukocyte migration and chemotaxis, GO:0002694, GO:0071347, GO:0032680]] \n", - "192 [[GO:0006955, cytokine signaling pathway, GO:0060333, positive regulation of interleukin production, GO:0032729]] \n", - "193 [[GO:0005126, GO:0006955, GO:0050900, jak-stat signaling pathway, GO:0034341, GO:0002690, GO:0051249, GO:0001817, GO:0050863, GO:0019221, GO:1902105]] \n", - "194 [[GO:0050900, cytokine signaling, GO:0002224, GO:0006954, GO:0032729, GO:0045087, GO:0032733, GO:0030595]] \n", - "195 [[cytokine signaling, chemokine signaling, GO:0050900, GO:0002250, GO:0045087]] \n", - "196 [[interferon signaling, GO:0045087, antiviral defense]] \n", - "197 [[GO:0034341, GO:0002718, GO:0060333, GO:0045070, GO:0032897, innate immune response-activating signal transduction, GO:0060337, GO:0035457, antiviral mechanism by interferon-stimulated genes (isg)]] \n", - "198 [[GO:0051607, GO:0035458, GO:0071357, GO:0045071, GO:0031323, GO:0002682, GO:0034097, GO:0034340]] \n", - "199 [[interferon signaling, GO:0019882, GO:0045321]] \n", - "200 [[GO:0005509, contractile fiber part, GO:0006936]] \n", - "201 [[GO:0043167, GO:0007165, GO:0019222, GO:0050794, g protein-coupled receptor signaling, GO:0035556, GO:0031325, GO:0043066, metabolic process regulation, GO:0005509, GO:0034765, GO:0001932, GO:0043169, GO:0045859, GO:0051716]] \n", - "202 [[GO:0006955, GO:0007165, GO:0050794, cytokine signaling, GO:0006954, GO:0006935, GO:0008284, GO:0043066]] \n", - "203 [[GO:0006955, GO:0006954, GO:0002694, GO:0001817, interleukin-10 signaling, tumor necrosis factor (tnf) signaling, GO:0006956, platelet activation and aggregation, eicosanoid synthesis]] \n", - "204 [[GO:0007018, GO:0007052, cell division, chromosome separation]] \n", - "205 [[kinesin family members, microtubule formation and stabilization, spindle formation and assembly, GO:0000910, GO:0051726, gene expression and chromosome segregation]] \n", - "206 [[GO:0006457, GO:0050776, GO:0009117, GO:0006629, gluconeogenesis and glycolysis, mrna processing and splicing]] \n", - "207 [[GO:0044237, protein regulation, transcriptional regulation, translation regulation, GO:0006281, stress response.\\n\\nmechanism: these enriched terms suggest that the identified genes are involved in several pathways, including maintaining cellular metabolism and homeostasis, regulating transcription and translation of proteins, repairing dna in response to damage, and responding to cellular stress]] \n", - "208 [[GO:0006412, GO:0006457, GO:1990904, u4/u6.u5 tri-snrnp, chaperone-mediated protein folding.\\n\\nmechanism: these genes are involved in protein synthesis and processing, including translation and ribosome biogenesis. many of them are also involved in protein folding and chaperone-mediated protein folding. the u4/u6.u5 tri-snrnp is also highly represented, indicating these genes may be involved in splicing]] \n", - "209 [[GO:0006396, GO:0006413, GO:0006446, GO:0042254, GO:0008380, GO:0006397]] \n", - "210 [[GO:0042254, GO:0008033, GO:0006364, GO:0016072, GO:0009451, GO:0022613]] \n", - "211 [[GO:0042254, GO:0006364, GO:0000394, rna polymerase ii regulation, rna processing and modification]] \n", - "212 [[GO:0006936, GO:0006816, z-disc, UBERON:0002036, GO:0030017, MESH:D014335, GO:0005861, GO:0071689]] \n", - "213 [[UBERON:0001630, MESH:D009218, MESH:D000199, MESH:D014336, filament]] \n", - "214 [[GO:0007219, GO:0045165, GO:0022008, GO:0030154, GO:0045893, GO:0043066, GO:0008285, GO:0043065, GO:0045747, GO:0016055, GO:0007268]] \n", - "215 [[GO:0051726, GO:0030154, GO:0001709, transcriptional regulation, GO:0016567]] \n", - "216 [[GO:0022900, GO:0045333, GO:0002082]] \n", - "217 [[GO:0006119, GO:0005746, GO:0070469, GO:0005739, MESH:D004734, GO:0031966, GO:0006099, GO:0006635, citrate cycle, GO:0098798, GO:0006754, GO:0051536]] \n", - "218 [[GO:0006974, GO:0051726, cell growth and proliferation]] \n", - "219 [[GO:0051726, GO:0006281, GO:0030330, GO:0000082, response to dna damage]] \n", - "220 [[pancreatic development, beta cell differentiation, GO:0030073, GO:0042593, GO:0006006]] \n", - "221 [[GO:0003323, GO:0030073, glucose regulation, diabetes-related pathways]] \n", - "222 [[GO:0006631, GO:0006805, steroid hormone biosynthesis]] \n", - "223 [[GO:0006631, GO:0007031, GO:0015721, GO:0006282]] \n", - "224 [[mapk cascade; pi3k-akt signaling pathway; regulation of cell proliferation\\n\\nmechanism: the enriched terms suggest that the common function of the listed genes is to regulate cellular processes related to signal transduction and cell cycle/apoptosis. the mapk cascade is a crucial signaling pathway that controls the expression of genes required for cellular proliferation, differentiation, and survival. pi3k-akt signaling pathway controls cell survival, GO:0040007, and metabolism. the enriched term \"regulation of cell proliferation\" suggests that the listed genes contribute to regulating the balance between cell growth and division. these genes could affect the rate of cellular proliferation, arresting or promoting the cell cycle or modulating apoptotic signal transduction]] \n", - "225 [[GO:0033554, GO:0035556, GO:0006468, GO:0042981, GO:0080135]] \n", - "226 [[GO:0016192, GO:0046907, GO:0006897, GO:0061024, GO:0008104, GO:0048193]] \n", - "227 [[GO:0048193, GO:0005768, GO:0005764, GO:0006612, GO:0006886, GO:0042391, GO:0034765, GO:0005773]] \n", - "228 [[GO:0016209, GO:0051920, GO:0006749, GO:0006979, GO:0070301]] \n", - "229 [[GO:0016209, regulation of iron ion binding, GO:0006979, GO:0048821, GO:2000378, GO:0006282, GO:0070301, GO:0050790, GO:0032092, regulation of thiol-dependent ubiquitinyl hydrolase activity, GO:0034599]] \n", - "230 [[GO:0007283, GO:0140013, GO:0007130, GO:0007281, GO:0097722, oocyte meiosis]] \n", - "231 [[GO:1903047, GO:0010971, regulation of spindle assembly checkpoint, GO:0034501, GO:0090234, GO:0051985, GO:0110028]] \n", - "232 [[tgf-beta signaling pathway, GO:0030514, GO:0090287, GO:0030513, GO:0006351, GO:0006355, GO:0045893, GO:0000122]] \n", - "233 [[tgf-beta signaling pathway, GO:0030509, GO:0030513, GO:0030198, GO:0060391]] \n", - "234 [[ccl2, ccl20, ccl4, ccl5, ccn1, ccnd1, ccrl2, cd44, cd69, cd80, cd83, cdkn1a, icam1, icoslg, ifih1, ifit2, ifngr2, GO:0043514, il15ra, MESH:D020382, il1a, il1b, GO:0070743, MESH:D015850, il6st, il7r, inhba, irf1, jag1, nfkb1, nfkb2, nfkbia, nfkbie, nr4a1, nr4a2, nr4a3, ptger4, MESH:D051546, rel, rela, relb, ripk2, stat5a, tlr2, tnf, tnfaip2, tnfaip3, tnfaip6, tnfaip8, tnfrsf9, tnfsf9, tnip1, tnip]] \n", - "235 [[cytokine signaling, GO:0000988, stress response, GO:0050776, GO:0006954]] \n", - "236 [[GO:0006457, GO:0036503, upr signaling pathway]] \n", - "237 [[GO:0006457, GO:0006605, GO:0006396, GO:0006950, GO:0006417, GO:0016481, GO:0006986, GO:0006913, GO:0008380, GO:1903021, GO:0016032, GO:0032496, GO:0072659, GO:0017148, GO:0022613, negative regulation of transcription by rna polymerase]] \n", - "238 [[tgf-beta signaling pathway, GO:0030198, GO:0007155, GO:0030334, GO:0042127]] \n", - "239 [[GO:0030198, GO:0030036, GO:0030155, GO:0007160, GO:0016477, GO:0007229, GO:0030199, GO:0035023, GO:0030178, basement membrane formation, GO:0014909]] \n", - "240 [[GO:0006355, regulation of transcription, dna-templated; go:0044267, cellular protein metabolic process; go:0009968, GO:0009968]] \n", - "241 [[GO:0006955, GO:0008104, GO:0051726]] \n", - "242 [[GO:0016055, GO:0007219, transcriptional regulation, GO:0030154, GO:0008283]] \n", - "243 [[GO:0007219, GO:0045747, GO:0045746, GO:0045165]] \n", - "244 [[cd28 co-stimulation, il-2 signaling, GO:0042110]] \n", - "245 [[GO:0042110, GO:0051247, GO:0001817]] \n", - "246 [[GO:0000988, transcriptional regulation, GO:0030154, GO:0008283, stem cell maintenance, MESH:D047108]] \n", - "247 [[MESH:D047108, regulation of transcription, GO:0048863]] \n", - "248 [[GO:0030198, GO:0030199, GO:0001525, GO:0001568, GO:0030168, GO:0001666, GO:0001936]] \n", - "249 [[GO:0030198, GO:0030155, regulation of cell substrate adhesion, GO:0045785, GO:0043062]] \n", - "250 [[GO:0005509, GO:0050804, transcriptional regulation, GO:0050808]] \n", - "251 [[GO:0007186, GO:0010468, GO:0007154, GO:0006355, GO:0005515, GO:0007155, GO:0001932, GO:0016055, GO:0030334, GO:0007165, GO:0043408, GO:0003677, GO:0006357, GO:0005543, GO:0051493, GO:0006811]] \n", - "252 [[atp hydrolysis coupled calcium ion transport, GO:0030036, GO:0006936, GO:0033365, GO:0051147, GO:0014743, GO:0045214]] \n", - "253 [[GO:0006936, MESH:D024510, GO:0007519, GO:0055001, GO:0030239, GO:0007517]] \n", - "254 [[GO:0006897, GO:0016192, GO:0007041, GO:0007032, GO:0030163]] \n", - "255 [[GO:0006897, GO:0006898, GO:0016197, GO:0015031, GO:0006886, GO:0007032, GO:0016192, endosomal sorting]] \n", - "256 [[GO:0006096, GO:0005975, GO:0006006, GO:0019318]] \n", - "257 [[GO:0006096, GO:0006006, GO:0006007]] \n", - "258 [[GO:0005509, GO:0005262, GO:0019722, GO:0006874, GO:0034765]] \n", - "259 [[GO:0005509, GO:0004970, GO:0051966, GO:0046928, GO:0005216, GO:0034765, GO:0004672, GO:0051924, GO:0051247]] \n", - "260 [[GO:0033554, GO:0010506, GO:0007165]] \n", - "261 [[GO:0097190, GO:0016485, GO:0031323]] \n", - "262 [[glycoside hydrolase activity, GO:0005975, GO:0006027, GO:0009311, GO:0005764, GO:0005783, catabolism of carbohydrate, MONDO:0019249]] \n", - "263 [[GO:0006096, metabolism of carbohydrates, GO:0019318, GO:0006013, GO:0009311, chitin catabolic/metabolic process, hyaluronan catabolic/metabolic process, glycosphingolipid metabolic/catabolic process, sialic acid catabolic/metabolic process]] \n", - "264 [[GO:0002377, t cell receptor signaling, GO:0042113, t cell activation. \\n\\nhypotheses: this list of genes is heavily enriched in those involved in the function and development of b cells and t cells. specifically, they play a role in the production and function of immunoglobulins and t cell receptors, as well as the activation of these cell types. this suggests that these genes are integral to the proper functioning of the immune system]] \n", - "265 [[GO:0006955, GO:0046649, GO:0030098]] \n", - "266 [[meiotic recombination, crossover formation, GO:0007130, GO:0006281, GO:0035825]] \n", - "267 [[GO:0007059, GO:0051321, GO:0006310, synapsis of chromosomes, GO:0051276, GO:0051177]] \n", - "268 [[GO:0002376, GO:0006950, GO:0006457, GO:0051641, GO:0006396, GO:0006829, GO:0010467, GO:0007165]] \n", - "269 [[GO:0006979, GO:0032088, GO:0055072, GO:0016567, GO:0043066]] \n", - "270 [[GO:0006457, GO:0050776, GO:0009117, GO:0006629, gluconeogenesis and glycolysis, mrna processing and splicing]] \n", - "271 [[GO:0006457, GO:0015031, GO:0042254]] \n", - "272 [[GO:0005778, peroxisome targeting, GO:0007031]] \n", - "273 [[peroxisome biogenesis, peroxisome membrane organization, GO:0016559]] \n", - "274 [[GO:0006281, GO:0051276, regulation of transcription]] \n", - "275 [[GO:0006281, GO:0006325, GO:0090398]] \n", - "276 [[GO:0004970, GO:0099536, GO:0001505, GO:0007268, GO:0043269, GO:0005244, GO:0042391]] \n", - "277 [[GO:0005216, GO:0007268, GO:0005261, GO:0007215, GO:0019228, GO:0006813, GO:0060080, MESH:D005680, sodium ion transport. \\n\\nhypotheses: \\n1. the enrichment of ion channel activity-related terms suggests that the genes play a crucial role in regulating ion transport during neuronal signaling, which in turn influences synaptic plasticity and memory formation.\\n2. the enrichment of synaptic transmission-related terms points towards the involvement of the genes in various aspects of synaptic signaling, including the glutamate and gaba receptor signaling pathways, inhibition of neuronal activity, and modulation of action potential generation. \\n3. overall, the enrichment of these terms hints at a potential interaction between the listed genes in regulating various aspects of neural signal processing, synaptic transmission, and plasticity]] \n", - "278 [[mitochondrial function, GO:0006457, GO:0030163, GO:0055085]] \n", - "279 [[\"nervous system development\", \"axon guidance\", \"myelination\", \"neuron projection\", \"synaptic transmission\"]] \n", - "280 [[GO:0030594, GO:0007186, GO:0046928, GO:0007212, GO:0007188]] \n", - "281 [[g protein coupled receptor signaling pathway, g protein beta/gamma subunit complex binding]] \n", - "282 [[transcriptional regulation, GO:0006325]] \n", - "283 [[GO:0003677, regulation of transcription, GO:0003682, GO:0008134, GO:0003713, negative regulation of transcription]] \n", - "284 [[GO:0030199, GO:0030198, GO:0006024, GO:0061448]] \n", - "285 [[GO:0030199, GO:0030198, GO:0030166, GO:0061448]] \n", - "286 [[GO:0006281, GO:0000724, GO:0006513, fanconi anemia complementation group]] \n", - "287 [[GO:0006281, GO:0006513, GO:0000724, fanconi anemia complementation group, GO:0000785, GO:0005654, GO:0140513]] \n", - "288 [[fad binding activity, GO:0016407, lipid binding activity, coenzyme binding, identical protein binding activity, citrate biosynthetic process]] \n", - "289 [[mitochondrial respiration, mitochondrial function, GO:0008152, energy production, GO:0022900, GO:0006629, GO:0006631, GO:0006637]] \n", - "290 [[GO:0005125, GO:0004896, integrin binding activity, GO:0004672, GO:0000988, t-cell receptor binding activity, abc-type peptide antigen transporter activity.\\n\\nmechanism: these genes are involved in various aspects of immune response, including cytokine activity, cytokine receptor activity, and t-cell receptor binding activity. they also play a role in antigen processing and presentation through the abc-type peptide antigen transporter activity. the integrin binding activity reflects the involvement of integrins in leukocyte adhesion and migration. finally, the transcription factor activity reflects the importance of transcriptional regulation in immune responses]] \n", - "291 [[GO:0005125, GO:0008009, mhc class ii protein complex binding activity, signaling receptor binding activity, protein kinase binding activity, integrin binding activity, identical protein binding activity, sh2 domain binding activity, GO:0004252, rna binding activity, GO:0046982, GO:0008083]] \n", - "292 [[binding activity, GO:0008152, GO:0043167, nucleic acid binding. \\n\\nmechanism: the enriched terms suggest that the listed genes have a common function in binding and metabolic processes. it is possible that these genes are involved in regulating the flow and utilization of energy and molecules within cells]] \n", - "293 [[GO:0004672, GO:0035556, GO:0000079, GO:0007166]] \n", - "294 [[extracellular matrix organization; cell adhesion; protein binding; signaling pathway; regulation of cell proliferation.\\n\\nmechanism: the enriched terms suggest that these genes are involved in extracellular matrix organization and cell signaling pathways that regulate cell proliferation and adhesion. many of the genes are structural constituents of the extracellular matrix and influence cell-matrix interactions. others are involved in cell signaling pathways, such as the notch and fibroblast growth factor pathways, that play critical roles in cell proliferation and differentiation. some of the genes have also been implicated in diseases involving abnormal extracellular matrix formation or cell signaling dysregulation, such as ehlers-danlos syndrome, MONDO:0004975, MONDO:0004992]] \n", - "295 [[UBERON:4000022, binding activity]] \n", - "296 [[GO:0007010, GO:0007155, GO:0005102, kinase activity.\\n\\nmechanism: these genes are involved in the maintenance of cell structure and organization through regulation of the cytoskeleton. they also contribute to cell-cell interactions and signaling through receptor binding and kinase activity. a biological pathway that might be involved is the rho gtpase signaling pathway, which regulates actin cytoskeleton dynamics and cell adhesion]] \n", - "297 [[cell adhesion: cdh3, cdh4, cdh6, cdh11, cdh15, cd276, cd209, icam5, icam2, icam1, itga3, itga9, itga10, itgb1, cldn4, cldn5, cldn6, cldn7, cldn8, cldn9, cldn11, cldn14, cldn18, cldn19\\n- protein kinase activity: cdk8, ptk2, syk, taok2, vav2, src\\n- actin filament binding: actn1, actn3, lima1, nexn, calb2, pfn1\\n- metalloendopeptidase activity: adamts5, adam23, mmp2, mmp9\\n- integrin binding: jup, vcam1, slit2]] \n", - "298 [[GO:0007165, cell surface receptor activity, protein binding activity]] \n", - "299 [[GO:0005886, GO:0009986, GO:0055085, GO:0038023, positive regulation of transcription, GO:0010468, GO:0006468, GO:0005615]] \n", - "300 [[GO:0006915, GO:0005125, transcription factor binding activity. \\n\\nmechanism/]] \n", - "301 [[GO:0006915, GO:0005125, GO:0010941, GO:2001233, GO:0001819, GO:0042981, GO:0043067, positive regulation of apoptotic process.\\n\\nmechanism: these genes are involved in apoptotic signaling and cytokine activity, which suggests that they play a role in regulating cell death and programmed cell death. the enriched terms suggest that these genes may be regulated by shared signaling pathways or transcriptional programs that control apoptosis and cytokine production. one potential underlying mechanism could involve the activation of pro-apoptotic proteins in response to cellular stress or damage, leading to the release of cytokines that further promote cell death. alternatively, these genes may be involved in controlling the balance between cell survival and death in response to external cues such as cytokine signaling or nutrient availability. further research is needed to fully elucidate the molecular mechanisms underlying these gene functions]] \n", - "302 [[GO:0006629, GO:0030301, GO:0006633]] \n", - "303 [[GO:0030301, GO:0015908, GO:0007031, GO:0004467, GO:0008123, atp binding activity, ubiquitin-dependent protein binding activity. \\n\\nmechanism: these genes are likely involved in the regulation and transport of lipids, particularly cholesterol and long-chain fatty acids, in cells and tissues. peroxisomal proteins and functions may also play a role in this process, including in the regulation of lipid metabolism]] \n", - "304 [[GO:0042632, GO:0008610, GO:0010883, phospholipid binding activity, fatty acid binding activity, low-density lipoprotein particle binding activity, more]] \n", - "305 [[GO:0006695, GO:0008299, GO:0055088, GO:0006646, GO:0000122, GO:0045944, GO:0070458, GO:0001676]] \n", - "306 [[GO:0006508, complement pathways, GO:0007596, GO:0007155]] \n", - "307 [[GO:0006508, GO:0007596, GO:0006956, negative regulation of proteolysis. \\n\\nmechanism: the enriched terms suggest that these genes are involved in the regulation of proteolytic activity in several biological processes, including blood coagulation and immune response]] \n", - "308 [[GO:0004867, protease binding activity, enzyme binding activity, calcium ion binding activity]] \n", - "309 [[GO:0005515, GO:0019899, GO:0005488, GO:0004175, metal ion binding.\\n\\nmechanism: the enriched terms suggest that these genes play a role in protein-protein interactions and enzymatic reactions involving metal ions]] \n", - "310 [[GO:0006281, GO:0097747, nucleotide metabolism. \\n\\nmechanism: these genes are predominantly involved in regulating dna replication, transcription, and repair. they may also play roles in the metabolism of nucleotides and nucleotide analogs that target dna synthesis. the enrichment of terms related to rna polymerase may reflect the closely intertwined nature of dna and rna synthesis]] \n", - "311 [[GO:0006260, GO:0006281, rna transcription]] \n", - "312 [[GO:0006260, GO:0051726, GO:0006325]] \n", - "313 [[dna binding activity, protein binding activity, enzyme binding activity, chromatin binding activity, atp binding activity, histone binding activity, rna binding activity, identical protein binding activity]] \n", - "314 [[GO:0005201, integrin binding activity, collagen binding activity, identical protein binding activity, fibrinogen binding activity, protease binding activity]] \n", - "315 [[GO:0005201, collagen binding activity, integrin binding activity, heparin binding activity, GO:0008237, signaling receptor binding activity.\\n\\nmechanism: these genes are involved in the maintenance and formation of the extracellular matrix, which provides structural support to cells and tissues. they play a role in cell adhesion, signaling, and migration through interactions with the extracellular matrix. the enriched binding activities suggest that these genes are involved in extracellular matrix remodeling and regulation of growth factor signaling. metallopeptidase activity may be involved in the degradation of extracellular matrix components]] \n", - "316 [[GO:0005509, GO:0000166, enzyme binding activity, MESH:D048788, gene transcription, GO:0006811]] \n", - "317 [[GO:0005515, GO:0000988, transmembrane transporter activity.\\n\\nmechanism: the enriched terms suggest that the genes on the list are involved in various cellular processes that require protein-protein interaction, transcriptional regulation, and transmembrane transport of substances. a possible hypothesis is that these genes play a role in signal transduction and regulation of gene expression]] \n", - "318 [[GO:0022857, protein binding activity]] \n", - "319 [[(1) enzymatic activity; (2) binding activity; (3) transcription regulation. \\n\\nmechanism: these genes likely play roles in various biological pathways, such as metabolism, cell signaling, and gene expression regulation. given the enrichment in enzymatic activity, it is possible that some of these genes are involved in metabolic pathways, such as lipid metabolism. the enrichment in binding activity may reflect the importance of protein-protein interactions and signaling cascades in cellular processes. the enrichment in transcription regulation suggests that many of these genes may be key players in regulating gene expression and ultimately cell fate]] \n", - "320 [[GO:0047617, GO:0006631, GO:0120227, GO:0008289, GO:0004467, GO:0006099, GO:0046356]] \n", - "321 [[GO:0016491, binding activity, GO:0006631, GO:0006084, heme-binding activity]] \n", - "322 [[dna binding activity, chromatin binding activity, protein binding activity, enzyme binding activity, histone binding activity, GO:0003714]] \n", - "323 [[dna-binding transcription factor activity; protein kinase activity; microtubule binding activity. \\n\\nmechanism: these genes are likely involved in the regulation of gene expression, cell cycle progression, and cytoskeletal dynamics through the binding and modification of dna, MESH:D011506, and microtubules. specifically, they may be involved in processes such as transcriptional regulation, dna replication and repair, GO:0007059, GO:0051301]] \n", - "324 [[GO:0008378, GO:0015020, n-acetylglucosamine sulfotransferase activity, GO:0035250, glucosaminyl-proteoglycan 3-beta-glucosyltransferase activity, GO:0016758, GO:0045130, GO:0016779]] \n", - "325 [[GO:0005975, GO:0006024, GO:0006493]] \n", - "326 [[GO:0006357, GO:0016525, GO:0007155, GO:0030036, GO:0010604, GO:0007411, GO:0030336]] \n", - "327 [[GO:0007165, GO:0007155, GO:0007399, transcription regulation]] \n", - "328 [[GO:0020037, GO:0015075, protein binding activity, GO:0000988]] \n", - "329 [[transmembrane transport; protein binding activity; metal ion binding activity; dna-binding transcription activator activity\\n\\nmechanism: these genes are involved in various transport and binding activities, especially transmembrane transport, indicating a possible importance in cellular trafficking and signaling pathways. additionally, they exhibit a significant enrichment in protein and metal ion binding activities, which may suggest a role in protein-protein interactions and redox reactions, respectively. finally, dna-binding transcription activator activity is found to be enriched, indicating that these genes may regulate gene expression]] \n", - "330 [[enzyme binding activity, GO:0005515, GO:0003700, carbohydrate binding activity, signaling receptor binding activity, identical protein binding activity, atp binding activity, nad binding activity, phosphoprotein binding activity, metal ion binding activity, GO:0003924, GO:0008083, GO:0008194, phospholipid binding activity, platelet-derived growth factor binding activity]] \n", - "331 [[GO:0006006, GO:0016301, transcriptional regulation, GO:0023052]] \n", - "332 [[GO:0005125, interleukin receptor binding activity, cytokine binding activity, GO:0031295, GO:0051250, GO:0006952, GO:0006955, interleukin binding activity]] \n", - "333 [[GO:0004896, interleukin binding activity, identical protein binding activity, gtp binding activity, GO:0001216, protein kinase binding activity, atp binding activity, GO:0016787, collagen binding activity, small gtpase binding activity, GO:0061630, GO:0004197, GO:0005215, rna binding activity, calcium ion binding activity, signaling receptor binding activity, GO:0005125, GO:0008083, enzyme binding activity, several others.\\n\\nmechanism: these genes are involved in immune response cytokine activity. many of them encode for cytokine receptors, transcription factors, enzymes involved in immune system pathways processes. the enrichment of terms related to protein binding, including dna binding identical protein binding, may suggest that many of these genes act as transcriptional regulators in immune cells, coordinating the expression of genes involved in immune function. the enrichment of transporter activity may indicate that some of these genes are involved in cell migration or trafficking of immune cells to sites of inflammation or infection. additionally, the enrichment of terms related to enzyme activity may suggest that some of]] \n", - "334 [[GO:0005125, GO:0004896, protein kinase binding activity, GO:0006954, GO:0006955, GO:0007165]] \n", - "335 [[GO:0004896, interleukin binding activity, GO:0008009, GO:0001819, GO:0050778, GO:0098542, GO:0010604]] \n", - "336 [[GO:0005125, GO:0008009, identical protein binding activity, GO:0038023, GO:0006811]] \n", - "337 [[GO:0004930, GO:0004896, enzyme binding activity, identical protein binding activity, GO:0007165, calcium ion binding activity, protease binding activity, transporter activity.\\n\\nmechanism: these genes are involved in various mechanisms related to cell signaling and transport. one hypothesis is that these genes may collectively contribute to the regulation of calcium levels and calcium-dependent signaling pathways, as well as cytokine-mediated signaling pathways involved in immune response]] \n", - "338 [[GO:0005125, GO:0098542, GO:0046597, rna binding activity, identical protein binding activity]] \n", - "339 [[GO:0098542, GO:0050709, GO:0046597, GO:0045071, GO:0030501, GO:0002688, regulation of transcription]] \n", - "340 [[GO:0004896, GO:0000981, identical protein binding activity, enzyme binding activity, GO:0042110, cell adhesion molecule binding activity, positive regulation of activated cd8-positive t cell proliferation, GO:0038187, GO:0061630, GO:0000166, GO:0004930, protein kinase binding activity, calcium ion binding activity, complement binding activity, GO:0004867, GO:0008009, integrin binding activity.\\n\\nmechanism: these genes predominantly function in the immune system and are related to the activation and proliferation of t cells, cytokine signaling, pattern recognition, and complement cascades. the enriched terms suggest an association with signaling cascades, receptor binding, enzyme activity, and immune response to pathogens]] \n", - "341 [[GO:0019882, GO:0045087, cytokine signaling, GO:0045321, antiviral defense]] \n", - "342 [[calcium ion binding activity, atp binding activity, GO:0008511, GO:0004930, GO:0004888, GO:0016887, identical protein binding activity, protein kinase binding activity]] \n", - "343 [[protein binding activity, calcium ion binding activity, atp binding activity, identical protein binding activity, GO:0008507, GO:0005337, GO:0043273, GO:0003924, GO:0015432]] \n", - "344 [[binding activity; enzyme activity; transcription activator activity. \\n\\nmechanism: these enriched terms suggest that the commonality among these genes is that they are involved in various types of binding and enzymatic activities, as well as regulating transcription. it is possible that these genes work together in regulatory pathways to bind to specific targets, catalyze reactions, modulate transcriptional activity in the cell]] \n", - "345 [[GO:0005178, GO:0005515, GO:0005524, GO:0071345, GO:0043167, ubiquitin protein ligase binding. \\n\\nmechanism: the shared function of binding among the enriched terms suggests that these genes may play a role in mediating protein regulation and signal transduction pathways through protein-protein or protein-ligand interactions. the involvement in cellular response to cytokine stimulus may suggest a potential role in modulating immune responses]] \n", - "346 [[microtubule binding activity, GO:0005096, actin filament binding activity, microtubule plus-end binding activity, identical protein binding activity, protein kinase binding activity, kinetochore binding activity, cytoskeletal protein binding activity, gamma-tubulin binding activity]] \n", - "347 [[microtubule binding activity, GO:0007052, GO:0000226]] \n", - "348 [[binding activity, enzymatic activity, GO:0006412, GO:0023052, GO:0008152]] \n", - "349 [[GO:0005515, enzyme activity. \\n\\nmechanism: the enriched terms suggest that these genes play a role in protein-protein interactions and enzymatic reactions, potentially involved in metabolic pathways or signal transduction cascades]] \n", - "350 [[ribosome binding activity; rna binding activity; translation initiation factor activity; protein folding chaperone activity\\n\\nmechanism: these genes are involved in different aspects of protein synthesis, such as ribosome binding, GO:0006413, and rna binding. they also contribute to protein folding processes as chaperones. the enrichment of these terms suggests that these genes function together to ensure proper protein synthesis and folding, which are vital to numerous cellular processes]] \n", - "351 [[GO:0006396, GO:0003676, GO:0006457, ribosomal structural activity. \\n\\nmechanism: these genes likely function together in the post-transcriptional regulation of gene expression, from rna splicing to translation initiation and ribosome assembly]] \n", - "352 [[GO:0006364, rna binding activity, GO:0046982, mitochondrial function, GO:0051726]] \n", - "353 [[GO:0006364, snorna binding activity, GO:0042273, rna binding activity, GO:0005730]] \n", - "354 [[cytoskeletal protein binding activity, actin binding activity, atp binding activity, calcium ion binding activity, identical protein binding activity, enzyme binding activity, GO:0042803]] \n", - "355 [[actin binding activity, cytoskeletal protein binding activity, calcium ion binding activity, myosin binding activity, atp binding activity, kinase binding activity, muscle structure development. \\n\\nmechanism: these genes are involved in muscle structure and function as they encode proteins that bind to actin, myosin, and other cytoskeletal proteins to form the muscle fibers. they also bind to calcium ions and atp, which are necessary for muscle contraction, and contribute to the development of muscle structure]] \n", - "356 [[GO:0007219, GO:0016567]] \n", - "357 [[\"notch signaling pathway,\" \"protein ubiquitination,\" \"negative regulation of cell differentiation,\" \"regulation of dna-templated transcription.\"]] \n", - "358 [[GO:0022900, GO:0006119, mitochondrial metabolism, GO:0006637, ketone body metabolism.\\n\\nmechanism and]] \n", - "359 [[GO:0005746, GO:0006118, GO:0006754, MESH:D009245, MESH:D003576, GO:0016467, flavin adenine dinucleotide]] \n", - "360 [[GO:0042981, protein binding activity, GO:0003700]] \n", - "361 [[GO:0000988, rna binding activity, enzyme binding activity, identical protein binding activity, dna binding activity, histone binding activity]] \n", - "362 [[GO:0006006, GO:0030073, GO:0006357]] \n", - "363 [[GO:0006006, GO:0030073, glucose homeostasis.\\n\\nmechanism]] \n", - "364 [[GO:0006629, GO:0006631, GO:0006810, GO:0003824, GO:0005501, steroid binding.\\n\\nmechanism and]] \n", - "365 [[GO:0004467, GO:0016401, GO:0047676, GO:0031957, peroxisome targeting sequence binding activity, GO:0006633]] \n", - "366 [[GO:0004672, cytoskeleton structure, GO:0006629, protein binding activity]] \n", - "367 [[GO:0006468, intracellular signaling, GO:0016301, GO:0016791, enzyme binding activity. \\n\\nmechanism: the enriched terms suggest that many of the genes are involved in regulatory processes related to protein modification through phosphorylation and dephosphorylation. this could implicate several signaling pathways, such as mapk, pi3k/akt, and nf-kappab pathways]] \n", - "368 [[GO:0007030, GO:0006888, retrograde transport, vesicle recycling, GO:0090110, GO:0006891, GO:0008333, GO:0006893, GO:0048488, GO:0016192, vesicle recycling]] \n", - "369 [[GO:0048193, GO:0032456, GO:0035493, GO:0006891, GO:0070836]] \n", - "370 [[GO:0098869, GO:0006750, GO:0042744, oxidation-reduction process, GO:0006979]] \n", - "371 [[GO:0045454, GO:0006979, GO:0016209, GO:0004602, GO:0004784, GO:0004601, GO:0003954, GO:0032981]] \n", - "372 [[GO:0005515, GO:0005524, GO:0042802, GO:0016301, GO:0000166]] \n", - "373 [[identical protein binding activity, protein folding chaperone binding activity, GO:0004672, rna binding activity, chromatin binding activity, atp binding activity, nucleotide binding activity, GO:0004722, GO:0061630, calcium ion binding activity, rna polymerase iii binding activity, cytokine binding activity, GO:0004930, integrin binding activity, many others]] \n", - "374 [[GO:0007178, GO:0010862, GO:0010991, GO:0045668, GO:0030512, GO:0010604, GO:0009967]] \n", - "375 [[signal transduction; regulation of gene expression; transcription regulation; protein phosphorylation; smad protein signal transduction.\\n\\nmechanism: these genes are involved in various aspects of signal transduction, including regulation of gene expression, transcription regulation, MESH:D016212, where they regulate transcription of target genes. genes in this list may activate or inhibit smad signaling and affect downstream transcriptional regulation. additionally, many of these genes play roles in other signaling pathways and regulatory processes, such as the wnt signaling pathway and negative regulation of protein degradation]] \n", - "376 [[GO:0005125, GO:0003700, enzyme binding activity, GO:0006955]] \n", - "377 [[cytokine activity; dna-binding transcription factor activity; enzyme binding activity; phosphatidylinositol-3,4-bisphosphate binding activity; g protein-coupled receptor activity.\\n\\nmechanism: the enriched terms suggest that the genes on the list are involved in signaling pathways that regulate gene expression and cellular responses through cytokine receptors, GO:0035556, and various enzymatic activities. these pathways play essential roles in several biological processes, including immune responses, cell differentiation and development, cell survival death]] \n", - "378 [[protein folding and processing, GO:0015031, GO:0003723, GO:0043022, GO:0003743]] \n", - "379 [[rna binding activity, protein folding chaperone binding activity, ribosome binding activity, histone binding activity, dna-binding transcription factor binding activity, ubiquitin protein ligase binding activity]] \n", - "380 [[extracellular matrix organization; growth factor signaling; regulation of transcription, dna-templated; positive regulation of protein kinase activity; organic acid metabolic process.\\n\\nmechanism: these genes are involved in extracellular matrix structural constituent, growth factor signaling, GO:0000988, GO:0005515, and nucleotide binding. this suggests that they may be involved in the regulation of gene transcription, cellular growth and differentiation, and the organization of extracellular matrices. a hypothesis for the underlying biological mechanism or pathway is that these genes may be involved in the regulation of extracellular matrix formation and growth factor signaling pathways, which then contribute to cellular differentiation and growth. additionally, the binding of proteins with transcription factor activity and nucleotide binding activity suggests that these genes are involved in the regulation of gene transcription, which may have downstream effects on cellular function and behavior]] \n", - "381 [[GO:0005201, GO:0005178, identical protein binding activity, protease binding activity, calcium binding, platelet-derived growth factor binding activity]] \n", - "382 [[enzyme binding activity, protein kinase binding activity, GO:0042803, rna binding activity, atp binding activity, identical protein binding activity, ubiquitin protein ligase binding activity, GO:0001228, ion binding activity, g protein-coupled receptor binding activity, dna polymerase binding activity, peptide hormone receptor binding activity. \\n\\nmechanism: these genes are involved in a variety of molecular activities, including enzyme activity, protein binding, and transcription factor activity. one potential underlying biological mechanism is the regulation and interaction of proteins in various cellular processes]] \n", - "383 [[atp binding activity, GO:0001216, identical protein binding activity, rna binding activity, protein kinase binding activity, cysteine-type endopeptidase activity involvement in apoptotic signaling, GO:0004602, histone binding activity, GO:0030594, glucagon receptor binding activity, GO:0004499, peptide hormone receptor binding activity, gtp binding activity, more]] \n", - "384 [[GO:0090090, regulation of transcription, GO:0000981, histone deacetylase binding activity, ubiquitin protein ligase binding activity, notch binding activity, protein kinase binding activity, GO:0003713, identical protein binding activity]] \n", - "385 [[GO:0060070, GO:0031398, GO:0090090, GO:0031397, GO:0030162]] \n", - "386 [[GO:0050776, intracellular signaling, GO:0008037, GO:0009617, GO:0008284, GO:0005125, protein kinase binding activity, identical protein binding activity]] \n", - "387 [[GO:0042110, GO:0001816, GO:0010468, GO:0050671, GO:0001819, GO:0001933, GO:0045840, protein kinase binding activity, GO:0004697, GO:0004911, GO:0004896, GO:0097190, GO:0007005, GO:0043065, GO:0042100, GO:0004931]] \n", - "388 [[transcription regulation, GO:0010468, GO:0045944, GO:0003700, cellular differentiation]] \n", - "389 [[GO:0010468, transcriptional regulation, GO:0003700, GO:0001714, GO:0045944]] \n", - "390 [[GO:0030198, GO:0007165, GO:0007596]] \n", - "391 [[GO:0005178, GO:0005201, GO:0008083, platelet-derived growth factor binding activity, GO:0030199]] \n", - "392 [[GO:0005515, GO:0005216, transcriptional regulation, ubiquitin-protein ligase activity]] \n", - "393 [[metal ion binding activity, calcium ion binding activity, GO:0000981, g protein-coupled receptor binding activity, enzyme binding activity, sequence-specific double-stranded dna binding activity, cytoskeletal protein binding activity, GO:0061630]] \n", - "394 [[GO:0006936, GO:0030239, GO:0043502, GO:0051015, GO:0005523]] \n", - "395 [[GO:0003009, GO:0060048, GO:0010628, actin filament binding activity, GO:0008307]] \n", - "396 [[GO:0006897, GO:0015031, GO:0006898]] \n", - "397 [[GO:0006897, lysosomal function, GO:0038023, GO:0006955, GO:0008152]] \n", - "398 [[GO:0006006, GO:0005975, GO:0019725, GO:0008104, GO:0070062, GO:0005634]] \n", - "399 [[GO:0006096, GO:0005975, GO:0006000, cell development.\\n\\nhypotheses: the enriched terms suggest that these genes are involved in the glycolysis pathway, contributing to carbohydrate metabolic processes and the production of energy for cellular development. specifically, fructose metabolic processes are enriched, indicating that the genes may play a role in the conversion of fructose to glucose during glycolysis]] \n", - "400 [[GO:0006816, GO:0007268, GO:0005245, GO:0098978, GO:0004972]] \n", - "401 [[GO:0005509, GO:0006836, GO:0001505, GO:0016079, GO:0035235, GO:0007186, GO:0071318]] \n", - "402 [[GO:0006468, GO:0010604, GO:0038202, GO:0032006, GO:0016241, positive regulation of cyclin-dependent protein serine/threonine kinase activity.\\n\\nmechanism and]] \n", - "403 [[intracellular signaling, pathway regulation, GO:0006915, GO:0004672, GO:0006468, GO:0010604, GO:0045859]] \n", - "404 [[GO:0046479, GO:0006516, GO:0006032, GO:0030214]] \n", - "405 [[GO:0005975, MESH:D054794, glycan catabolism, GO:0006516, GO:0019377, GO:0006032, GO:0006004]] \n", - "406 [[antigen binding activity, immunoglobulin receptor binding activity, GO:0002253]] \n", - "407 [[GO:0002253, GO:0098542, GO:0019731, GO:0006959, GO:0002377, GO:0051130, GO:0045657]] \n", - "408 [[GO:0061982, GO:0007131, GO:0007129, GO:0000712, GO:0000724]] \n", - "409 [[meiotic recombination, GO:0035825, GO:0006302]] \n", - "410 [[molecular sequestering, protein binding activity, transport of metal ions, GO:0048523, response to infection and stress, GO:0010468, GO:0019722, regulation of transcription]] \n", - "411 [[GO:0140311, GO:0010468, GO:0031398, GO:0051238]] \n", - "412 [[binding activity, enzymatic activity, GO:0006412, GO:0023052, GO:0008152]] \n", - "413 [[GO:0005515, GO:0042802, GO:0019899, GO:0043167, GO:0005524, GO:0031625, GO:0003723, GO:0003677, GO:0097159, GO:0017076, GO:0051015, GO:0042802, GO:0016491, phosphoprotein binding activity, GO:0005215, GO:0006793, GO:0044237, GO:0006457, GO:0003677, GO:0008380]] \n", - "414 [[GO:0017038, peroxisomal biogenesis, GO:0140036, atp binding and hydrolysis activity, lipid binding activity]] \n", - "415 [[GO:0007031, GO:0016558, GO:0005778, peroxisomal biogenesis disorder, GO:0008611, lipid binding activity, atp binding activity, GO:0016887, ubiquitin-dependent protein binding activity, enzyme binding activity]] \n", - "416 [[GO:0006259, GO:0006325, GO:0033554, GO:0006281, GO:0007568]] \n", - "417 [[GO:0006281, GO:0006950, GO:0090398, GO:0000723, chromatin condensation]] \n", - "418 [[GO:0015276, GO:0099505, GO:0060078, GO:0071805, GO:0035725, GO:0035235]] \n", - "419 [[GO:0007214, GO:0007215, GO:0006811, GO:0006836, GO:0007268]] \n", - "420 [[GO:0042552, GO:0007422, MONDO:0005071, GO:0022011, MONDO:0005244]] \n", - "421 [[GO:0007399, GO:0042552, mitochondrial metabolism, GO:0030163, protein regulation, GO:0071260]] \n", - "422 [[GO:0007186, GO:0007212]] \n", - "423 [[GO:0007212, GO:0007186, GO:0051480, GO:0004016, GO:0006469, GO:0050821, GO:0060828, GO:0007220, GO:0034205, GO:0006508, GO:0046325, GO:1904227, GO:0051247, GO:0015171, GO:0015108]] \n", - "424 [[dna-binding transcription factor, rna polymerase ii-specific transcription regulation, GO:0000122, GO:0045944, GO:0006355]] \n", - "425 [[GO:0000988, GO:0006355, GO:0045893, GO:0045892, dna-binding, GO:0003702]] \n", - "426 [[connective tissue formation and repair, protein binding and folding, GO:0006955, GO:0042060, GO:0006024]] \n", - "427 [[collagen maturation, GO:0006024, transcriptional regulation, GO:0006829]] \n", - "428 [[GO:0006281, GO:0035825, GO:0016310, nucleoprotein complex assembly, formation of nuclear foci, double-strand dna repair, holliday junction resolution, function in tumor suppression, reca/rad51-related protein family, dna lesions, structural specific endonucleases, rad51 family, cellular responses to replication fork failure, brc motif]] \n", - "429 [[GO:0006281, GO:0035825, monoubiquitination, holliday junction resolution, rad51 binding]] \n", - "430 [[GO:0006629, GO:0006633, GO:0022900, GO:0005739, MESH:D000975, GO:0045333, MESH:D010084, acyltransferase, carboxylase, acyl-coenzyme a synthetase, ubiquitin protease, MESH:C021451, MESH:D010743, oxidoreductase, plasma lipase, hydratase]] \n", - "431 [[GO:0005515, transcription regulation, atpase, MESH:D020558, transcript processing, protein transduction, MESH:D014451, GO:0044237, energy production, GO:0006508]] \n", - "432 [[immune/cytokine responses, GO:0006412, GO:0006351, cell surface signaling, receptor activation, MESH:D054875, MONDO:0002123, GO:0005524]] \n", - "433 [[GO:0006412, cellular regulation, GO:0008152, cell signaling, GO:0006351, immunoregulation, stability, GO:0005515, GO:0016310, GO:0010467, g-protein coupled receptor, transmembrane protein, t-cell development]] \n", - "434 [[MESH:D011494, GO:0000981, GO:0005530, adhesion molecule, GO:0016538, MESH:D016601, protein tyrosine phosphatase, g protein, serine/threonine protein kinase, MESH:D008565, MESH:D006657, ubiquitin ligase, MESH:C052123, microtubule-associated protein, atp-binding cassette, alpha/beta-hydrolase, integrin alpha-chain, signal transducion, protein inhibitor of activated stat]] \n", - "435 [[GO:0008283, GO:0006351, GO:0007165, structural components, metabolism of proteins, GO:0006629, GO:0005975, GO:0007155, binding activity, GO:0010467, GO:0003677, MESH:D011494, oxidoreductase, anchoring kinase to microtubules, GO:0005102, molecule transport, MESH:D010455]] \n", - "436 [[this is a list of genes involved in a variety of pathways and processes related to cell adhesion, GO:0040007, GO:0008152, and other physiologic functions. the terms “cell adhesion”, “cell signaling”, “extracellular matrix”, “transcriptional regulation”, and “cell cycle progression and differentiation” are all enriched among this group of genes. a hypothesis of the underlying biological mechanism at work is that these genes work together to promote cell growth and regulation, that many of these genes interact to achieve greater cellular complexity]] \n", - "437 [[GO:0007155, extracellular matrix remodeling, GO:0007165, protease inhibition, transcriptional regulation]] \n", - "438 [[GO:0005207, GO:0007155, calcium-dependent proteins, MESH:D008565, intronless proteins, intracellular scaffolding proteins, fibrillin proteins, signaling receptors, MESH:D051193, MESH:D003598, tubulin proteins, type ii membrane proteins, MESH:D006023]] \n", - "439 [[GO:0007155, GO:0007165, actin binding and assembly, membrane localization, ecm protein binding and assembly]] \n", - "440 [[GO:0007160, GO:0007165, MESH:D008565, transcriptional coactivation, signal recognition, GO:0055085, GO:0006898]] \n", - "441 [[GO:0007160, cell-matrix interactions, carbohydrate binding activity, GO:0007155, GO:0038023, GO:0007165, GO:0008284, GO:0048681, GO:0030506, protein tyrosine kinase, sh2 domain binding activity, sh3 domain binding activity]] \n", - "442 [[GO:0006915, cytoplasmic signaling, transcriptional regulation, GO:0005515, cellular organization]] \n", - "443 [[cell death processes, GO:0023052, cytoplasmic proteins, MESH:M0015044, MESH:D015533, MESH:D004798, toxin removal, GO:0005102]] \n", - "444 [[atp-binding, GO:0006810, GO:0004768, MESH:D010084, enzyme catalysis, GO:0000981]] \n", - "445 [[GO:0015031, GO:0006412, GO:0006629, MESH:D010084, hormone regulation, transcription regulation, GO:0006805, calcium binding, GO:0005524, MESH:D005982, GO:0008203, MESH:M0011631, sulfate conjugation, 2-hydroxyacid oxidase, MESH:D000214, MESH:D000215, coenzyme a ligase, natriuretic peptide, peroxisome biogenesis, tgf-beta ligand, adrenal steroid synthesis, nuclear receptor, copper zinc binding, GO:0050632, MESH:D012319, gamma-glut]] \n", - "446 [[MESH:D008565, MONDO:0018815, acetoacetyl-coa thiolase, cytosolic enzyme, actin isoforms, activation transcription factor (creb), annexin family, fructose-biphosphate aldolase, immunoglobulin superfamily, g-protein coupled receptor (gpcr), homotetramer, hydratase/isomerase superfamily, MESH:C022503, mal proteolipid, MESH:M0476528, sre-binding proteins (srebp), peroxisomal enzyme, transmembrane 4 superfamily, transmembrane protein, multispan transmembrane protein, tetr]] \n", - "447 [[GO:0006629, GO:0005543, GO:0004768, atp-binding cassette, GO:0016126, cytochrome p450 family proteins]] \n", - "448 [[complement system, GO:0007596, peptide hydrolysis, GO:0016485, inflammation regulation]] \n", - "449 [[matrix metalloproteinase, cysteine-rich protein, serine protease inhibitor, transforming growth factor-beta, MESH:D054834, guanine nucleotide-binding proteins, peptidase s1 family, integrin beta chain, MESH:D001779, dipeptidyl peptidase, vitamin k-dependent glycoprotein, vitamin k-dependent coagulation factor, regulator of complement activation, protein tyrosine kinase, MESH:D006904, iron-sulfur cluster scaffold, disulfide bridge, kunitz-type serine protease, MESH:D042962, MESH:D037601, g-protein coupled receptor, cytosolic peptidase, GO:0030165, basic leucine zipper, a disintegrin and metalloprote]] \n", - "450 [[cell signaling, cell structure/stability, GO:0008152, vitamin k/clotting, GO:0005856, GO:0005886, GO:0006954]] \n", - "451 [[protein production, cell surface glycoprotein regulation, GO:0006956, GO:0007165, heat shock protein, MESH:D003564, metalloproteinase, guanine nucleotide-binding protein, lysosomal cysteine protease, zinc finger protein, cysteine-aspartic acid protease, MESH:D001053, metallothionein.\\nmechanism: the genes may be involved in various signalling pathways to facilitate the regulation of cell surface glycoprotein as well as the production of proteins. cytidine deaminase, metalloproteinase, guanine nucleotide-binding protein and cysteine-aspartic acid protease are likely enzymes that the list of genes may be involved in. heat shock proteins and zinc finger proteins, in addition to apolipoproteins and metallothionein, may be involved in the regulation and transportation of cell proteins]] \n", - "452 [[summary: this enrichment test provides evidence of a common biological mechanism underlying many genes in human genetics: dna repair, replication, and transcription.\\n\\nmechanism: the mechanism underlying this term enrichment is the need for accurate dna repair, replication, and transcription, which all require the co-ordinated efforts of many protein families, such as those encoded by the wd-repeat, MESH:D000262, argonaute, MESH:D000263, purine/pyrimidine phosphoribosyltransferase, b-cell receptor associated proteins, MESH:C056608, clp1, GO:0016538, MESH:C010098, dna helicase, MESH:M0251357, general transcription factor (gtf) ii, MESH:D005979, histone-fold proteins, mhc, MESH:C110617, GO:0005662, saccharomyces cerevisiae rad52, schizosaccharomyces pombe rae1, splicing factor (sf3a), GO:0003734, MESH:D011988, transcription factor b (tfb4), trans]] \n", - "453 [[GO:0003677, transcription regulation, GO:0006281, GO:0000394, GO:0006397, GO:0003723, GO:0003682, GO:0019899, GO:0003684, general transcription factor, transcription/repair factors, MESH:M0006668, hypothalamic hormone receptor binding, GO:0004016, nuclear cap-binding protein, GO:0016567, transcription initiation, dna polymerase, GO:0006605]] \n", - "454 [[GO:0006260, GO:0006281, GO:0006351, GO:0003682, GO:0016569, GO:0051726, ran binding, GO:0000808, atpase, GO:0016538, cyclin-dependent kinase, polycomb, dead box protein, gtpase activating protein, GO:0042393, GO:0003723, nucleolar protein, ubiquitously expressed protein, smc subfamily protein, pp2c family, elongation of primed dna template synthesis, dna interstrand cross-linking, import of proteins into nucleus, MESH:D004264, tumor suppressor protein, MESH:D051981, ubr box protein, p80 autoantigen]] \n", - "455 [[GO:0003676, GO:0006260, GO:0036211, GO:0006259, GO:0000785, GO:0051726, GO:0016570, protein assembly and disassembly]] \n", - "456 [[cell signaling, extracellular matrix formation, GO:0007155, connective tissue formation, GO:0001525, metabolic regulation, MESH:D016207, tissue repair]] \n", - "457 [[MESH:D016326, GO:0005202, MESH:D007797, MESH:D005353, MESH:D014841, integrin, MESH:D016189, fibulin proteins]] \n", - "458 [[GO:0042277, membrane structure modification, GO:0003677, GO:0006631, GO:0051427, signalling transcription, gtpase activation, adenylate cyclase modulation, GO:0016301, GO:0006897, glycoprotein production, GO:0019838, GO:0016570, GO:0006644, zinc-binding]] \n", - "459 [[dna-binding, GO:0005515, GO:0043687, GO:0007165, metabolic activity]] \n", - "460 [[MESH:D011494, GO:0000981, GO:0005509, MESH:D054794, hormone receptors, GO:0007155, GO:0006457, GO:0010467]] \n", - "461 [[membrane processes, transmembrane processes, GO:0006811, GO:0007155, GO:0016049, GO:0008152, MESH:D011506, GO:0023052, processing, MESH:D048788, reparative pathways, immune pathways, disease pathways]] \n", - "462 [[GO:0006732, GO:0006754, GO:0006096, oxidative decarboxylation, GO:0006631, nad/nadh-dependent oxidation, pyridine nucleotide oxidation, amino acid oxidation, glycerol-3-phosphate dehydrogenase activity, GO:0022900, MESH:D042942, nadp-dependent oxidation, l-amino acid oxidation, endogenous and xenobiotic n-methylation, conversion of pyruvate to acetyl coa, 2-oxoglutarate catabolism, galectin family activity]] \n", - "463 [[GO:0008152, fatty acid transport and processing, oxidoreductase, GO:0009653, GO:0030154, GO:0030674]] \n", - "464 [[GO:0006325, GO:0051726, GO:0016570, MESH:D011494, atp-binding, rna-binding]] \n", - "465 [[GO:0051301, GO:0003677, GO:0003723, transcriptional regulation, chromatin restructuring, GO:0004672, GO:0051169, cytoplasmic transport, nucleic acid metabolism, GO:0016570, GO:0016310, GO:0032259, MESH:D000107, MESH:D054875]] \n", - "466 [[GO:0016310, GO:0009100, GO:0007155, transcription regulation, GO:0009117, energy production]] \n", - "467 [[GO:0008152, GO:0005975, GO:0048468, GO:0009100, GO:0006629, GO:0015031, nucleic acid metabolism, GO:0009117, GO:0070085, ferric ion binding, GO:0016491, GO:0003677, GO:0000988, GO:0031545, GO:0004736]] \n", - "468 [[GO:0007155, GO:0007165, GO:0000981, MESH:D018121, MESH:D039921, rho-gtpase-activating protein, transmembrane protein, GO:1902911, transduction pathway, growth factor, g protein-coupled receptor, cadherin superfamily, basic helix-loop-helix, phosphoprotein, zinc finger protein, cytoplasmic domain, dna-binding, GO:0005886, neurotransmitter, MESH:D057057, coiled-coil, pdz binding motif, cholesterol moiety, fibronectin-like repeat, MESH:D000070557, GO:0016604, MESH:D006655, collapsin response mediator, tripartite motif, hedgehog signaling.\\nmechanism: the genes seem to be primarily involved in regulating signal transduction pathways that control cell migration, proliferation and differentiation, by modulating transcription, cell adhesion and receptor activities. the proteins encoded by these genes interact]] \n", - "469 [[GO:0007155, GO:0007165, neuron signalling, regulatory activity, GO:0009987, GO:0040007, differentiation, motility, GO:0032502]] \n", - "470 [[GO:0005515, GO:0000910, transcription regulation, metabolic & enzymatic function, cell cortex formation, GO:0006810, GO:0016310, MESH:D000107, protein formation & modification]] \n", - "471 [[GO:0006351, GO:0003723, post-transcriptional regulation, GO:0006096, GO:0006090, GO:0006749, GO:0006508, transcriptional regulation, MESH:D054875, GO:0003677, MESH:D006655, GO:0006915, cytoskeletal protein, atp-binding, GO:0048870, ubiquitin specific protease, MESH:D015220, voltage-gated chloride channel, GO:0004384, GO:0023052, GO:0051726, cation transporters]] \n", - "472 [[GO:0006096, GO:0016310, GO:0004672, GO:0006508, GO:0085029, transcription regulation, GO:0051726, GO:0097009, GO:0006954, cell-cell communication, oxidative stress response]] \n", - "473 [[GO:0006915, GO:0016310, MESH:D011494, GO:0005515, GO:0006351, GO:0031005, glycolytic enzyme, carboyhydrate binding, cell binding, GO:0042157, GO:0007165, UBERON:2000098, GO:0040007]] \n", - "474 [[GO:0051726, receptor signaling, MESH:D008565, GO:0000981]] \n", - "475 [[GO:0007165, protein homodimerization, GO:0005525, GO:0003676, GO:0055085, GO:0004672, GO:0007049, GO:0006955, GO:0006915]] \n", - "476 [[MESH:D016207, GO:0016049, GO:0048468, transmembrane proteins, MESH:D011494, GO:0000981, cell cycle progression]] \n", - "477 [[the list of gene summaries reveals a group of genes involved in cell trafficking, GO:0007165, GO:0007155, ligand binding, and regulation of the immune response. enriched terms include cytokine, chemokine, MESH:D007378, receptor, GO:0007155, ligand binding, GO:0007165, and regulation of the immune response.\\n\\nmechanism: the mechanism involving these genes involve ligand binding to cytokine, chemokine, or other receptors, resulting in the activation of intracellular pathways leading to signal transduction, GO:0007155, regulation of the immune response]] \n", - "478 [[GO:0005102, cytokine signalling, GO:0016049, cellular function regulation, immune signalling, inflammation regulation, GO:0051726, apoptosis coordination]] \n", - "479 [[interactions, GO:0023052, MESH:D008055, GO:0000981, MESH:D016207, MESH:D006728, MESH:D021381, receptors, GO:0007165]] \n", - "480 [[protein-binding, subunit-binding, rna-binding, transcriptional regulation, GO:0007165, GO:0006955, ligand binding, GO:0032991, GO:0036211]] \n", - "481 [[transcriptional regulation, GO:0008181, MESH:D010447, cytoplasmic proteins, antiviral, MESH:M0369740, GO:0009165, chemokine receptor, dna-binding, rna-binding, lipid-binding, protein adp-ribosylation, GO:0016567, GO:0048255, GO:0016556, GO:0006479, gtp-metabolizing, GO:0008283, GO:0006955, GO:0006952]] \n", - "482 [[immune regulation, GO:0003677, GO:0003723, GO:0016567, anti-viral response, cytokine signaling, GO:0006954]] \n", - "483 [[GO:0006954, immune cell signaling and development, immune regulation, GO:0044237, regulation of innate and adaptive immunity, metabolic and transcriptional regulation, GO:0003677, GO:0003723]] \n", - "484 [[protein-binding, transcriptional regulation, GO:0007155, cell membrane channel activity, protein metabolism/modification, receptor signalling]] \n", - "485 [[MESH:D011506, GO:0016049, cellular development, MESH:D009068, GO:0001508, calcium binding, GO:0005496, GO:0008152, GO:0006351, GO:0005488, MESH:C062738, GO:0005562, g proteins, dna-binding]] \n", - "486 [[GO:0007155, regulation of growth factors, cytokine regulation, calcium activation, transcriptional regulation]] \n", - "487 [[GO:0003677, MESH:D015533, cytokine regulation, GO:0008083, GO:0005515, GO:0007165, transmembrane protein activity, GO:0004930, GO:0003723, GO:0003924, GO:0005509, GO:0016571, glutamine-fructose-6-phosphate transaminase activity, cell growth control, GO:0019725, GO:0016491]] \n", - "488 [[cytoskeletal organization, GO:0003677, microtubule organization, gtpase regulation, centrosome interaction, chromatin structure, protein homodimerization]] \n", - "489 [[MESH:D020558, nucleotide exchange regulation, cellular signaling, GO:0006338, cytoskeleton structure, GO:0006260, GO:0007155, GO:0003779, actin regulation]] \n", - "490 [[GO:0006412, GO:0015031, protein signaling, GO:0008152, GO:0010467]] \n", - "491 [[GO:0005515, MESH:D054875, GO:0006351, GO:0003824, GO:0006457, chaperoning, GO:0051726, GO:0006629, GO:0046323, cytoskeleton formation]] \n", - "492 [[GO:0006351, GO:0006412, GO:0003729, MESH:D054657, MESH:D000072260, GO:0043687, cytoplasmic proteins, MESH:M0015044, GO:0003677, GO:0032508, GO:0005652, GO:0005681]] \n", - "493 [[GO:0009299, GO:0042254, GO:0006412, MESH:D049148, GO:0003723, GO:0043687, GO:0045292, polymerase, GO:0006913, MESH:D054875, GO:0006457, 14-3-3 family proteins]] \n", - "494 [[GO:0003723, ribosomal biogenesis, GO:0008283, GO:0006335, GO:0007165, cell cycle progression, GO:0003682]] \n", - "495 [[GO:0006351, rna binding activity, GO:0006457, cell cycle progression, GO:0006281, protein homodimerization, GO:0006468, GO:0065003, protein kinase/phosphatase activity, mitochondrial mrna processing. mechanism: this list of genes encodes proteins which work together to regulate key cellular activities such as dna replication, transcription, cell cycle progression, and rna processing. these proteins can either complex together or work in tandem to form kinase/phosphatase complexes, which control phosphorylation of key substrates and regulate protein folding to ensure proper protein function. these proteins also interact with dna to regulate genomic activities such as dna replication, transcription, and repair processes]] \n", - "496 [[motor protein activity, GO:0019722, GO:0006936, transcriptional regulation, intracellular fatty acid-binding, ligand binding, MESH:D007473, GO:0005884, MESH:D008565, regulation of transcription, phosphorylation of proteins]] \n", - "497 [[MESH:M0496924, protein regulation, ion channeling, cellular transport, GO:0006629, GO:0010468, neurotransmitter signaling, small molecules, large molecules]] \n", - "498 [[cell fate decisions, GO:0007219, GO:0007165, wnt signalling pathway, cell-cell interaction, GO:0016567, GO:0006355, protein ligase activity, GO:0006468]] \n", - "499 [[notch signaling, GO:0016567, cell-cycle regulation, protein breakdown and turnover, intracellular signalling pathways, cell fate]] \n", - "500 [[GO:0005739, MESH:D004798, MESH:D010088, MESH:D010088, GO:0006754]] \n", - "501 [[oxidative decarboxylation, MESH:D010088, MESH:D010084, GO:0006754, mitochondrial respiration, GO:0008152, MESH:D003580, MESH:D000214, pyruvate dehydrogenase, MESH:D005420, hydratase/isomerase, leucine-rich protein, 3-hydroxyacyl-coa]] \n", - "502 [[GO:0007049, GO:0006351, GO:0023052, GO:0006412, GO:0065007, GO:0042592]] \n", - "503 [[GO:0051726, GO:0016049, GO:0006915, GO:0007165, GO:0006281, transcriptional regulation, chromatin structure, tumor suppression, enzymatic activity, GO:0000988, GO:0004725, GO:0003925]] \n", - "504 [[analysis of the human genes abcc8, akt3, chga, dcx, dpp4, elp4, foxa2, foxo1, g6pc2, gcg, gck, hnf1a, iapp, UBERON:0002876, insm1, isl1, lmo2, mafb, neurod1, neurog3, nkx2-2, nkx6-1, pak3, pax4, pax6, pcsk1, pcsk2, pdx1, pklr, scgn, sec11a, slc2a2, spcs1, srp14, srp9, srprb, UBERON:0035931, stxbp1, syt13, vdr was performed to determine commonalities in gene function. term enrichment indicated a commonalty in genes that are involved in the regulation of glucose and insulin metabolism, GO:0008283, differentiation and apoptosis, as well as glycogen synthesis and glucose uptake. additionally, many of the genes are involved in the development of neural tissues and the regulation of gene transcription. the underlying biological mechanism could involve alterations in the phosphorylation of proteins and signaling pathways,]] \n", - "505 [[this analysis identifies the common functions of 18 human genes: dpp4, scgn, pklr, pax4, neurod1, srprb, srp14, isl1, insm1, pak3, pax6, elp4, dcx, iapp, lmo2, neurog3, gck, stxbp1, nkx2-2, pdx1, UBERON:0035931, pcsk1, nkx6-1, UBERON:0002876, pcsk2, spcs1, g6pc2, foxo1, sec11a, vdr, foxa2, slc2a2, mafb. they are related to metabolic regulation (glucose, GO:0016088, MESH:D004837, citrate), developmental regulation (neural tissues, UBERON:0001264, UBERON:0002107, lymph nodes), signal transduction (g proteins, ace, atp binding proteins) and hormone regulation related (somatostatin, GO:0016088, vitamin d3). these factors likely work in concert to control and maintain metabolic parameters throughout the body. mechanism: these genes act through various methods including transcriptional regulation, protein interactions, protein cleavage, signaling casc]] \n", - "506 [[MONDO:0018815, an antioxidant enzyme, a hormone binding protein, a nuclear receptor transcription factor, a fatty acid desaturase, a carnitine acyltransferase, an isocalate dehydrogenase, a peroxisomal membrane protein, MESH:D005182, antioxidant enzyme, hormone binding protein, nuclear receptor transcription factor, GO:0004768, carnitine acyltransferase, isocalate dehydrogenase, peroxisomal membrane protein, and fad-dependent oxidoreductase.\\n\\nmechanism: many of the genes are involved in regulating the production and movement of lipids and fatty acids, as well as the synthesis of hormones, MESH:D000305, and signalling receptors. the underlying biological mechanism is that these genes act as regulators of metabolic pathways, ensuring that their respective pathways are functioning correctly and that metabolites are transported correctly]] \n", - "507 [[GO:0006629, GO:0006635, GO:0006281, transcription and replication, MESH:D018384, GO:0006536, GO:0005502, GO:0008202]] \n", - "508 [[GO:0016310, GO:0006412, mrna expression, GO:0005515, cell signalling, MESH:D054875, protein phosphatase]] \n", - "509 [[GO:0007165, MESH:D011494, GO:0004707, MONDO:0008383, gpcr, GO:0016791, MESH:D020662, endoplasmic reticulum chaperone protein]] \n", - "510 [[GO:0005480, GO:0006897, GO:0006887, intracellular trafficking, MESH:D001678, MESH:D008565, GO:0005906, MESH:D020558, GO:0005794, GO:0005484]] \n", - "511 [[GO:0003924, snare binding activity, GO:0005484, phosphoinositide-binding, coatomer protein complex, MESH:D052067, protein kinase binding activity, adaptor complexes, atpases associated with diverse cellular activities, snare recognition molecules, gold domain, GO:0030136, transmembrane 4 superfamily, GO:0070273, sec7 domain, membrane mannose-specific lectin, signal-transducing adaptor molecule, identical protein binding activity]] \n", - "512 [[MONDO:0018815, copper chaperone, MESH:D002374, GO:0004861, hypoxia inducible factor (hif), nucleotide excision repair pathway, GO:0004672, GO:0009487, MESH:D005979, MESH:D009195, MESH:D010758, phosphofructokinase, MESH:D054464, GO:0050115, arginine/serine-rich splicing factor, iron/manganese superoxide dismutase, GO:0016491, germinal centre kinase iii (gck iii) subfamily, thioredoxin (trx) system]] \n", - "513 [[GO:0016049, GO:0007049, GO:0006351, redox regulation, MESH:D018384, MESH:D005721, hydroxylase, protease, free-radical scavenging, protein phosphatase]] \n", - "514 [[protein binding activity, GO:0003714, dna binding activity, rna binding activity, zinc ion binding activity, GO:0004596, serine/threonine-protein kinase activity, GO:0004016, snare binding activity, clathrin binding activity, myosin light chain binding activity, double-stranded dna binding activity, phosphatidic acid phosphohydrolase activity, ubiquitin-protein ligase activity, rna polymerase binding activity, GO:1990817, GO:1990817, GO:0060090, phosphatase binding activity, atp-ases associated activity, GO:0044183, GO:0016165, adp-ribosylation factor-like activity]] \n", - "515 [[GO:0006457, transcriptional regulation, GO:0007165, GO:0051726, chromatin structure and nuclear envelop function, cell adhesion and motility, GO:0008152, GO:0016567, detection and binding, enzymatic activity, GO:0042311]] \n", - "516 [[transmembrane proteins, receptor signaling pathways, transcription regulation, cell signaling, GO:0007155, GO:0016049, tgf-beta superfamily, MESH:D010749, ubiquitin ligases, tight junction adaptors]] \n", - "517 [[transmembrane serine/threonine kinases, transcriptional repressors, transforming growth factor (tgf)-beta superfamily, rho family of small gtpases, smad family, c2h2-type zinc finger domains, MESH:M0460357, caax geranylgeranyltransferase, smad interacting motif (sim), homeodomain-interacting protein kinase, MESH:D004122, transforming growth factor-beta (tgfb) signal transduction, MESH:D018398, MESH:D054645, protein folding and trafficking]] \n", - "518 [[GO:0006351, cytokine, inflammatory, UBERON:2000098, GO:0006915, cell signalling, receptor regulation, GO:0003924, GO:0003723]] \n", - "519 [[MESH:D016207, MESH:D018925, MESH:D010770, GO:0000981, MESH:D016212, nf-kappa-b, myc/max/mad, jagged 1, stat-regulated pathways, MESH:D008074, MESH:M0496065]] \n", - "520 [[rna-binding, protein-binding, GO:0019538, GO:0009058, GO:0044183, GO:0000981, GO:0006457]] \n", - "521 [[GO:0003723, GO:0005783, transcriptional regulation, GO:0006457, GO:0140597, mrna decapping, MESH:M0465019, GO:0030163, MESH:D021381]] \n", - "522 [[cellular response regulation, GO:0007165, transcriptional regulations, MESH:D011956, GO:0016310, calcium binding, MESH:D011494, transmembrane proteins, protein tyrosine kinases, MESH:D017027, MESH:M0015044, protein inhibitor of activated stats, integrin beta, annexin family, adp-binding cassette family, MESH:D020690, arfaptin family, wd repeat proteins, maguk family, camp-dependent pathways, MESH:D000071377, MESH:D008869, pak family, MESH:D015220, mitogen-responsive phosphoproteins, nuclear histone/protein, celf/brunol family, four-and-a-half-lim-only proteins]] \n", - "523 [[GO:0007165, MESH:D016326, cellular adhesion, GO:0000981, MESH:D011494, MESH:D020558, camp, calcium-dependent phospholipid binding protein, MESH:D011505, MESH:D017868, scaffolding protein, MESH:D020690, MESH:D010711, protein tyrosine phosphatase, rho-like gtpase, calcium-activated bk channel, cyclin-dependent kinase, n6-methyladenosine-containig protein, helix-loop-helix proteins, MESH:D016601, atpase, guanine nucleotide-binding protein, cytoplasmic surface protein, serine protease inhibitor, protein inhibitor of activated stat, GO:0004384, mitogen-responsive]] \n", - "524 [[cell regulation, GO:0055085, metabolic catabolism, transcription support, GO:0006468, non-classical heavy chain, GO:0020037, GO:0007165, cytoskeleton formation, GO:0030163, cell signaling, GO:0006412, GO:0010467]] \n", - "525 [[GO:0005515, GO:0005525, GO:0005215, reactive catalysis, cell signaling, membrane-associated functions]] \n", - "526 [[wnt signalling pathway, transmembrane glycoprotein, MESH:D006655, GO:0000981, GO:0007219, GO:0005515, GO:0007165, GO:0006511, transcriptional regulation, dna replication and repair]] \n", - "527 [[wnt signaling, notch signaling, hedgehog signaling, transcriptional regulation, cell cycle progression, developmental events, dna replication and repair, transcriptional silencing, GO:0043161]] \n", - "528 [[GO:0004888, calmodulin binding activity, GO:0061630, GO:0033192, GO:0004721, GO:0004725, GO:0004672, MESH:D015533, guanine nucleotide exchange activity, ligand binding activity]] \n", - "529 [[transcriptional regulation, cellular signaling pathways and processes, GO:0016049, differentiation, GO:0006950, GO:0006955, protein folding and trafficking, MESH:D051192, transmembrane proteins, receptor tyrosine kinases, ubiquitin e3 ligases, MESH:D020134, cgmp-binding phosphodiesterase]] \n", - "530 [[this set of genes is involved in embryonic development, stem cell pluripotency, stem-cell maintenance, and dna damage response. commonly enriched terms include cell cycle regulation, transcription regulation, GO:0006915, cellular transformation, and dna damage repair. mechanism:these genes control critical functions of cell cycle progression, gene transcription, and dna repair, providing the necessary foundation for the development of the organism. these pathways provide the structural and biochemical features of embryonic development, maintenance of stem cells and pluripotency, response to cellular damage]] \n", - "531 [[GO:0000981, MESH:D047108, stem cell maintenance, MESH:D063646, GO:0030154]] \n", - "532 [[GO:0007155, MESH:D016326, MESH:M0023728, cellular communication, GO:0042592, GO:0042060, GO:0006915, motility, GO:0001525]] \n", - "533 [[GO:0007219, osteoclast attachment/mineralized bone matrix, jagged 1/notch 1 signaling, GO:0007155, GO:0006915]] \n", - "534 [[GO:0055085, growth factor regulation, calcium regulation, transcription regulation, MESH:D007473, calcium-dependent processes, protein binding activity, chromatin binding activity, gtpase activating protein binding activity, histone binding activity, dna-binding activity, sequence-specific double-stranded dna binding activity, GO:0000988]] \n", - "535 [[this list of genes is involved predominantly in processes related to binding activities, dna-binding transcription factor activities, chromatin binding activities, and protein domain-specific binding. the underlying biological mechanism involves pathways that regulate cell morphology and cytoskeletal adaptor proteins. the enriched terms include: binding activity, GO:0003700, chromatin binding activity, protein domain-specific binding activity, cell morphology, MESH:D051179]] \n", - "536 [[GO:0007165, protein-protein interactions, MESH:D004734, GO:0051015, troponin binding, GO:0005523, GO:0051219, GO:0032515, GO:0043531, atp binding. mechanism: these genes are involved in pathways of signal transduction, protein-protein interactions, and energy metabolism, which lead to muscle contraction and tissue development. activation of these pathways leads to calcium release, which in turn activates contractile proteins such as troponin, tropomyosin, and actin. these proteins act together to promote muscle contraction and cytoskeletal structure]] \n", - "537 [[MESH:D024510, actin and tropomyosin binding, calcium- and energy-regulation, ion channeling, negative regulation of cytokine signaling pathways, GO:0033173]] \n", - "538 [[GO:0006897, GO:0015031, GO:0051639, endoplasmic reticulum and recycling endosome membrane organization, GO:0044351, GO:0016043, intracellular signaling, GO:0051260]] \n", - "539 [[GO:0015031, GO:0006897, GO:0006898, GO:0051260, GO:0007155, GO:0048870, amino acid residues, MESH:D054875, GO:0015908, cytoskeletal reorganization, GO:0016192, signaling complex regulation, GO:0140014, GO:0006919]] \n", - "540 [[GO:0006096, GO:0016310, MESH:D006593, glucose phosphate isomerase, phosphofructokinase, MESH:D005634, fructose-1,6-bisphosphate, MESH:D014305, glyceraldehyde-3-phosphate dehydrogenase, MESH:D010736, MESH:D011770, MESH:D010751]] \n", - "541 [[muscle maturation, MESH:D024510, GO:0001525, GO:0006096, MONDO:0003664, MONDO:0002412, plasmin regulation]] \n", - "542 [[GO:0006816, calcium ion regulation, postsynaptic ion channel, GO:0005892, glutamate receptor channel, g protein-coupled receptor, plasma membrane protein, ligand-gated ion channel]] \n", - "543 [[calcium ion regulation, GO:0006816, n-methyl-d-aspartate receptor family, MESH:C413185, MESH:D011954, p-type primary ion transport atpases]] \n", - "544 [[GO:0043539, protein serine/threonine kinase binding activity, GO:0004860, GO:0005085, GO:0032008, GO:0010605, GO:0032956, GO:0032006, GO:0016241, regulation of nf-kappab activation, GO:0001558, regulation of cell survival, GO:0038187, GO:0006281, GO:0045087]] \n", - "545 [[this term enrichment test looked at a list of human genes together with their functions. it found that the genes have functions related to cell cycle regulation, GO:0007165, GO:0043170, protein kinase binding and regulating chromatin remodeling and transcription. the enriched terms include cell cycle regulation, GO:0007165, GO:0043170, GO:0019901, GO:0016310, chromatin remodeling and transcriptional regulation.\\n\\nmechanism: the genes in this list are involved in processes such as cell cycle regulation, GO:0007165, GO:0043170, GO:0019901, phosphorylation and chromatin remodeling and transcription, which are interconnected. these processes all depend on the activity of various protein kinases and their activation by various components, including snca, MESH:D053148, trib3, ccny, pik3ca, akt1, nod2, kat5, rptor, smcr8, mlst8, tab2, hspb1, irgm, GO:0033868, cdk5r1 and other proteins. they interact and cooperate with each other to form pathways and complexes responsible for cell cycle regulation and activation or inhibition of specific genes. ph]] \n", - "546 [[GO:0016798, GO:0005980, GO:0006516, GO:0051787, GO:0036503, glycosaminoglycan hydrolysis, heparan sulfate hydrolysis, cell surface hyaluronidase.\\nhpyothesis: the genes listed serve key roles in the degradation of polysaccharides and glycoproteins, the recognition of misfolded proteins and their subsequent degradation by endoplasmic reticulum-associated degradation, the hydrolysis of glycosaminoglycans, and the hydrolysis of heparan sulfate for the maintenance of cell proteins and structure]] \n", - "547 [[glycohydrolase enzymes, glycosaminoglycans (gag]] \n", - "548 [[antigen binding activity, immunoglobulin receptor binding activity, GO:0002377, GO:0002250, protein homodimerization]] \n", - "549 [[immunoglobulin receptor binding activity, GO:0002253, antigen binding activity, GO:0042803, immunoglobulin lambda-like polypeptides, preb cell receptor, src family of protein tyrosine kinases, c-type lectin/c-type lectin-like domain]] \n", - "550 [[GO:0004519, bcl-2 homology domain 3 binding, GO:0003682, GO:0003677, GO:0003678, GO:0003697, 3'-5' exode]] \n", - "551 [[meiotic recombination, GO:0006281, GO:0007059, double-strand dna break repair, homologous chromosome pairing, dna binding activity, GO:0051289]] \n", - "552 [[this list of genes encodes proteins involved in a range of cellular processes such as cell cycle progression, GO:0006897, iron storage and regulation, cellular response to stress and inflammation, GO:0006915, transcriptional regulation, GO:0046907, GO:0016567, and toxic metal and cytosolic signaling. enriched terms include protein binding, lipid and hormone transport, GO:0003779, GO:0003724, GO:0006511, cell cycle progression, and negative regulation of nitrogen compound metabolic process. mechanism: these genes are involved in a wide range of processes related to regulating cell growth, GO:0032502, and homeostasis. they play a role in pathways such as the cell cycle, GO:0006915, inflammatory metabolic processes]] \n", - "553 [[GO:0005515, MESH:D015533, GO:0008152, MESH:D007109, GO:0006915, GO:0007049, GO:0016310]] \n", - "554 [[GO:0006412, GO:0015031, protein signaling, GO:0008152, GO:0010467]] \n", - "555 [[metabolic reactions, GO:0051726, energy production, MESH:D011494, GO:0016791, MESH:D003577, MESH:D000604, peptidase c1 family, GO:0031545, ion transporter, ubiquitin-like proteases, ubiquitin ligases, serine/threonine protein kinases, glyceraldehyde-3-phosphate dehydrogenase, nadp-dependent dehydrogenases, rna binding protein, GO:0016467, pyruvate dehydrogenase, MESH:D012321, GO:0016538, MESH:D005634, heat shock protein, hetero trimeric co-factors, MESH:D050603, MESH:D000263, MESH:D013762, MONDO:0008090]] \n", - "556 [[this set of genes are enriched for terms related to peroxisomal biogenesis and peroxisomal protein import. the aaa atpase family, peroxisomal membrane proteins, c-terminal pts1-type tripeptide peroxisomal targeting signals, and peroxisomal targeting signal 2 are all over-represented in the gene list.\\n\\nmechanism: the mechanism behind these genes is the import of proteins into peroxisomes, resulting in peroxisomal biogenesis. the aaa atpases, peroxisomal membrane proteins, c-terminal pts1-type tripeptide peroxisomal targeting signals, peroxisomal targeting signal 2 are all involved in either targeting or catalyzing this protein import]] \n", - "557 [[this set of genes is related to the function of peroxisome biogenesis and associated disorders. the enriched terms are peroxisome biogenesis, GO:0017038, peroxisomal matrix proteins, atpase family, and pti2 receptor/pex7.\\n\\nmechanism: peroxisomes are important organelles for a variety of metabolic functions, and the synthesis and organization of these organelles is mediated by the pex genes. pex6 and pex2 are involved in protein import, where the pex2 protein forms a membrane-restricted complex, and pex6 is predominantly cytoplasmic and plays a direct role in peroxisomal protein import and receptor activity. pex3 and pex7 are required for peroxisomal biogenesis, and pex7 is the cytosolic receptor for the set of peroxisomal matrix enzymes targeted to the organelle by the peroxisome targeting signal 2. lastly, pex1 forms a heteromeric complex and plays a role in the import of proteins into peroxisomes and peroxisome biogenesis]] \n", - "558 [[GO:0000785, nuclear membr]] \n", - "559 [[these genes are all related to essential functions that facilitate the proper structure and organization of the nucleus and genome, primarily through the formation and maintenance of nuclear lamin, dna helicases and chromatin structures. there is evidence that all of these genes are involved in the proper functioning of cell division, GO:0006281, and transcription, as well as the maintenance of genome stability. the most enriched terms related to the functions of these genes are nuclear lamina, dna helicase, chromatin structure, GO:0006281, GO:0006351, genome stability, GO:0051301, nuclear membrane proteins, and nuclear localization signal. \\n\\nmechanism: the genes may be involved in pathways that coordinate the formation and maintenance of nuclear lamin, dna helicase, and chromatin structures, which are necessary for cell division and transcription, as well as the maintenance of genome stability. these pathways may involve the direct interactions between the gene products, as well as the recruitment of nuclear membrane proteins and signals involved in maintaining nuclear organization]] \n", - "560 [[neuronal signaling, neuron communication, MESH:D007473, excitatory dependent channels, inhibitory neurotransmitter, ligand-gated ion channel, g protein-coupled membrane receptor]] \n", - "561 [[MESH:D017981, MESH:D058446, GO:0009451, voltage-gated ion channels, channel subunits, channel polymorphisms, g-protein-coupled transmembrane receptors, MESH:D017470, MESH:D018079, MESH:D015221]] \n", - "562 [[transcriptional regulation, mitochondrial rna synthesis, neurodevelopment, GO:0030218, GO:0036211, nucleolar function, neuronal network formation, sensory receptor function]] \n", - "563 [[GO:0000981, dna helicase, hexameric dna helicase, neurotrophic factor, pdz domain, ma cation channels, MESH:D005956, protein synthetase, mitochondrial dna polymerase, heme transporter, GO:0005643, MESH:D044767, transmembrane glycoprotein]] \n", - "564 [[g-protein coupled receptor signaling, g-protein subunit signaling, GO:0004016, phospholipase c-beta activity, GO:0005102, GO:0007165, second messenger synthesis, transmembrane signaling]] \n", - "565 [[the list of human genes supplied involves several different cell signaling pathways, including the dopamine receptor (drd1, drd2, drd3 and drd5) pathway, g-protein coupled receptor (gpcr) signalling pathway (gnas, gnai3, gnaq, gna11, gna14, gna15, gnb1, gnb5, gnao1, gng2, sl]] \n", - "566 [[transcriptional regulation, GO:0006338, GO:0003677, GO:0000981, coactivator, heterodimer, response element]] \n", - "567 [[transcription factor regulation, GO:0016569, dna-binding activity, zinc-finger binding, GO:0032183, retinoid x receptor responsive element binding]] \n", - "568 [[GO:0031012, ecm components, matrix components, ecm regulators]] \n", - "569 [[extracellular matrix protein network, collagen fibril formation, GO:0030199, ecm protein network assembly, UBERON:2007004]] \n", - "570 [[MONDO:0100339, \"double strand break repair\", \"fanconi anemia protein complex\", \"ubiquitin ligase complex formation\"]] \n", - "571 [[GO:0006974, dna damage recognition, GO:0006281, GO:0035825, double-stranded break repair, double-stranded break recognition]] \n", - "572 [[MESH:D004734, GO:0006631, GO:0045444, GO:0006695, GO:0006699]] \n", - "573 [[MESH:D004734, cell death regulation, cell proliferation signaling, dna replication/remodeling, GO:0006396, GO:0006629]] \n", - "574 [[cell surface molecules, MESH:D016207, MESH:M0000731, receptor signalling, transcriptional regulation, GO:0006915]] \n", - "575 [[GO:0019882, GO:0007165, b and t cell metabolism, GO:0001816, GO:0006935]] \n", - "576 [[genes in this list are involved in developmental processes, metabolism, and the inflammatory response. the terms enriched in these genes include: cell cycle regulation, GO:0008152, GO:0006260, GO:0015031, receptor signaling, GO:0006954, GO:0006915, GO:0006351, GO:0006457, GO:0016477, developmental processes.\\n\\nmechanism: these genes appear to work together to regulate a variety of cellular processes, such as cellular metabolism, transcription, growth, and differentiation, as well as communication between cells and the environment. these genes likely act in concert to coordinate the intricate interplay between these processes and respond to changes in the environment. furthermore, they likely play a role in the body’s inflammatory response when faced with a variety of external stimuli]] \n", - "577 [[GO:0065007, GO:0023052, GO:0019538, GO:0051726, transcription regulation, MESH:D021381, GO:0007165, membrane trafficking, protein kinase regulation, GO:0044237, GO:0006259, GO:0006468, GO:0030163, mitochondrial function, GO:0006629, cytoskeleton regulation, GO:0007155, GO:0009117]] \n", - "578 [[extracellular matrix formation and maintenance, fibrous tissue development, vascular development, cell-cell communication and migration, extracellular secreted signaling, collagen and laminin-fibrillin proteins]] \n", - "579 [[GO:0032502, GO:0009653, GO:0009888, GO:0030198, GO:0006954, MESH:D066253, cell-cell communication]] \n", - "580 [[this term enrichment test suggests that the genes provided are involved in cell adhesion, GO:0006955, and tissue morphogenesis. specifically, the adhesion-associated genes enriched in this dataset include icam1, icam2, icam4, icam5, nectin1, nectin2, nectin3, nectin4, nrxn2, ptprc, sdc3, thy1, vcam1, and vwf. the immune response-associated genes enriched in this dataset include cd34, cd86, cd209, ctnna1, icam2, icam4, icam5, map4k2, msn, pard6g, and tnfrsf11b. lastly, the tissue morphogenesis-associated genes enriched in this dataset include acta1, actb, actc1, actg1, actn1, actn2, actn4, adam15, adra1b, akt2, alox15b, amigo2, baiap2, cadm2, cadm3, MESH:M0359286, col9a1, MONDO:0011642, ctnnd1, MESH:C040896]] \n", - "581 [[GO:0009653, GO:0016049, MESH:D047108, cellular signaling, GO:0031012, cytoskeletal organization, basal membrane assembly, GO:0098609, GO:0006915, GO:0016477, GO:0001816, growth factor production, tyrosine kinase activity, g-protein coupled receptor signaling pathway, nuclear receptor signaling pathway, GO:0016055, phosphatidylinositol 3-kinase signaling pathway, protein kinase b signaling pathway, map kinase signaling pathway, cell adhesion molecule signaling pathway, focal adhesion signaling pathway]] \n", - "582 [[GO:0016477, membrane receptor signaling, GO:0009100, protein tyrosine kinases, GO:0007155, cytoskeletal dynamics, receptor-mediated lectin binding, GO:0006629, GO:0007015]] \n", - "583 [[cell signaling, GO:0032502, transcription regulation, GO:0008152, MESH:D049109, MESH:D005786]] \n", - "584 [[transcriptional regulation/control, cell cycle/apoptosis, GO:0006955]] \n", - "585 [[the genes listed are mainly involved in the regulation and expression of genes, inflammation pathways and cell cycle regulation. specifically, enriched terms include gene expression and transcriptional regulation, dna damage and repair, GO:0007165, GO:1901987, metabolism and apoptosis.\\n\\nmechanism: the commonality in the function of these genes is likely related to the roles they play in the regulation of gene expression by affecting signal transduction, GO:0008152, cell cycle control and apoptosis. these gene functions may lead to a variety of processes, including inflammation pathways related to immunity, UBERON:2000098, MESH:D002470]] \n", - "586 [[MESH:M0496924, GO:0006869, development of connective tissues, GO:0006633, GO:0006699, GO:0006805, GO:0006694, cellular transport, MESH:M0023727, connective tissue formation, digit development, GO:0060173]] \n", - "587 [[this set of genes is related to lipid metabolism and lipid transport, protein homeostasis, retinol metabolism, developmental processes, and transportation of lysosomal hydrolases and oxygen-carrying molecules. the set includes genes involved in lipid metabolism (aqp9, atxn1, GO:0033781, abcg4, acsl1, fdxr, aldh8a1, hsd17b11, aldh9a1, aldh1a1, cyp7a1, cp25h, gstk1, MONDO:0100102, acsl5), lipid transport (abca1, abca2, abca3, abca4, abca5, abca8, abca9, abcg8), protein homeostasis (pex12, pex16, pex19, pex11a, pex11g, GO:0005053, pex6, pex26), retinol metabolism (abcd1, abcd2, abcd3), developmental processes (lck, nr3c2, retsat, klf1, ephx2, phyh, bbox1, MONDO:0004277]] \n", - "588 [[transcriptional regulation, MESH:D006026, GO:0006629, GO:0005509, GO:0001525, MESH:D016326, receptor signaling; transcription regulators; calcium signaling; glycoside hydrolases; lipid metabolism; cell adhesion; extracellular matrix proteins; signaling receptor molecules.\\n\\nmechanism: this set of genes is likely involved in regulating transcriptional responses, MESH:D006026, GO:0006629, GO:0005509, GO:0001525, MESH:D016326, and receptor signaling. many of these genes interact with each other, forming complex cellular networks and pathways. the particular genes identified in this list are likely related to stimulating or inhibiting the expression of specific genes or pathways, as well as modulating or mediating responses to various environmental signals or stimuli. these gene functions likely interact to maintain homeostasis, contribute to cellular development and processes, promote angiogenesis, and provide a structural and functional framework for the extracellular matrix. furthermore, these genes may be involved in signaling pathways that involve receptor molecules by modulating intracellular calcium levels]] \n", - "589 [[GO:0006629, transcriptional regulation, cellular adhesion, GO:0032502, GO:0042592]] \n", - "590 [[inflammatory response regulation, extracellular matrix formation regulation, proteolytic activities]] \n", - "591 [[GO:0007165, GO:0030198, matrix molecular regulation, GO:0006508, GO:0050817, matrix remodeling, GO:0009653]] \n", - "592 [[GO:0030198, immune system/inflammation/interferon response, GO:0000988]] \n", - "593 [[immunoglobulin like domains, GO:0042113, GO:0050852, integrin mediated cell adhesion, GO:0006915, regulation of transcription, GO:0007165, receptor mediated endocytosis and exocytosis, GO:0030198, calcium mediated signaling]] \n", - "594 [[GO:0006259, GO:0016070, GO:0006412, dna damage repair, GO:0006351, GO:0006325]] \n", - "595 [[GO:0006260, transcription regulation, GO:0006412, GO:0043687, nucleic acid metabolism, GO:0010467, GO:0006397, GO:0006412]] \n", - "596 [[GO:0006260, GO:0006281, gene transcription, GO:0006412, GO:0016569, GO:0007049, GO:0010468]] \n", - "597 [[GO:0006260, GO:0006351, GO:0030261, transcriptional regulation, GO:0006338, GO:0006974, chromatin structure modifications, GO:0006281, GO:0006306, GO:0030163, GO:0007094, GO:1901987, GO:0006468]] \n", - "598 [[genes in this list are enriched for functions related to modulating extracellular matrix, cell adhesion and morphogenesis, as well as playing roles in development, growth and signal transduction pathways. enriched terms include:extracellular matrix modulation; cell adhesion; morphogenesis; development; growth; signal transduction.\\n\\nmechanism: many of the genes listed are involved in the signaling, development and maintenance of the extracellular matrix, cell adhesion and morphogenesis, which can be regulated through diverse pathways involving the growth factors (bdnf, MESH:D016222, igfbp2, igfbp3, igfbp4, wnt5a), proteoglycans (comp, cspg4, MONDO:0021055, lamc1, lamc2, dcn, has3, sdc1) and adhesion molecules and receptors (acta2, abi3bp, cadm1, cap2, capg, cd44, cdh11, cdh2, cdh6, fn1, grem1, itga2, itga5, itgav, itgb1, itgb3, itgb5, lrp1, tagl]] \n", - "599 [[GO:0030198, GO:0009653, collagen production, matrix metalloproteinase activity, GO:0009100, cytoskeletal component organization, regulation of growth and reproduction, regulation of skin morphogenesis]] \n", - "600 [[cell morphology; homeostasis & regulation; innervation; cellular metabolism.\\nmechanism: the genes are likely to be involved in various pathways, such as the regulation of gene expression, protein synthesis and structure, cell motility and differentiation, tissue repair regeneration]] \n", - "601 [[immunological response, GO:0007155, transcription regulation, GO:0016477, GO:0008544, GO:0060348, MESH:D024510, GO:0015031, GO:0006915]] \n", - "602 [[MESH:D023281, cytoskeletal processes, GO:0006955, extracellular modification]] \n", - "603 [[the commonalities in the functions of these genes are involved in transcription, post-transcriptional regulation, GO:0009966, and cell-cycle related processes. the enriched terms are: transcription; post-transcriptional regulation; signal transduction; cell cycle; dna binding; regulation of transcription; regulation of protein abundance; chromatin remodeling; ubiquitination; and protein-protein interaction.\\n\\nmechanism: the underlying mechanism may be related to the regulation of intricate pathways leading to the expression of specific genes in conversion of genetic information into protein-based processes. these genes may be involved in a variety of biological processes, such as transcriptional and post-transcriptional regulation of gene expression, GO:0007165, cell-cycle related processes, GO:0003677, regulation of transcription, regulation of protein abundance, GO:0006338, MESH:D054875, protein-protein interaction]] \n", - "604 [[GO:0006631, oxidation of lipids, GO:0006695, GO:0005977, GO:0009117, GO:0006862, GO:0009165, electron transport activity, enzyme regulation, regulation of metabolic pathways, GO:0006915]] \n", - "605 [[GO:0008152, energy production and storage, lipid metabolism and transport, acetyl-coa biosynthesis and catalysis, oxidation, GO:0006631]] \n", - "606 [[GO:0051726, GO:0006260, GO:0006338, cyclin b-cdk1 activation, cks1b, cdc25a, wee1, cdc20, apc/]] \n", - "607 [[nuclear processes, GO:0006260, gene transcription, GO:0006338, GO:1901987, GO:0006281, GO:0010467, GO:0010468]] \n", - "608 [[developmental process: digit development, GO:0001525, GO:0030154, GO:0005488, transporting, GO:0008152, GO:0008152, cell signalling]] \n", - "609 [[GO:0005975, MESH:D004734, GO:0046785, dna binding and replication, actin cytoskeleton dynamics, ion channel regulation, transcriptional regulation, GO:0007155]] \n", - "610 [[GO:0009653, GO:0022008, GO:0016049, GO:0030154, GO:0001764, thalamocortical pathway development, GO:0001764, GO:0007399, neural crest migration]] \n", - "611 [[GO:0009653, GO:0007155, GO:0032502, GO:0007268, GO:0008283, GO:0016477, GO:0030154, MESH:D009473]] \n", - "612 [[GO:0055085, MESH:D004734, GO:0003735, GO:0003676, GO:0015031, negative regulation of transcription, regulation of transcription, positive regulation of transcription, GO:0071840, iron metabolism, GO:0007165, GO:0045087, GO:0042803, GO:0051276, GO:0050794, GO:0016569, GO:0008380, GO:0005515, GO:0000075, GO:0006006, GO:0000088, GO:0009116]] \n", - "613 [[GO:0048468, GO:0010467, GO:0048513, nucleic acid metabolism, transcriptional regulation, GO:0006259, GO:0016070, cytoskeletal dynamics, GO:0007165, GO:0006412]] \n", - "614 [[gene enrichment analysis of the gene list showed that the majority of genes are involved in cellular proliferation, GO:0006915, GO:0006811, GO:0005102, and development. the enriched terms associated with this list include cell proliferation, GO:0006915, GO:0006811, GO:0005102, cell signaling, transcriptional regulation, and development.\\n\\nmechanism: the genes are likely involved in an intricate, interconnected biological network that involves numerous signaling pathways and transcription factors necessary for cellular proliferation, GO:0006915, ion transport and receptor binding. these gene functions result in the regulation of numerous cellular processes and ultimately the development of various diseases. in addition, the genes may be regulating a number of other processes such as metabolism, cell-cell communication, energy production]] \n", - "615 [[GO:0048468, cell metabolism, transcription regulation, GO:0010468, GO:0006974, GO:0007155, GO:0030154, GO:0042440, MESH:M0352612, GO:0006412, GO:0051726, MESH:D004734]] \n", - "616 [[GO:0016049, cell regulation, GO:0009988, MESH:D007109, signal transduction and regulation, GO:0032502, transcriptional regulation, GO:0030198, cytokine-receptor-mediated signaling pathway]] \n", - "617 [[this list of genes are involved in developmental processes, GO:0006955, GO:0006954, GO:0007165, and cell adhesion functions. the enriched terms are \"development\"; \"signal transduction\"; \"cell adhesion\"; \"immune response\"; \"inflammation\"; \"transmembrane transport\"; \"protein metabolism\"; \"cardiovascular function\".\\n\\nmechanism: the underlying biological mechanisms involves the coordination of different pathways, genes and proteins. these genes are involved in cellular processes and regulation, including cell proliferation, differentiation, adhesion and migration, GO:0007165, and immunity. the genes also influence signaling pathways, protein metabolism and other functions that have roles in cardiovascular and carcinogenesis. the mechanisms through which these genes affect development, GO:0006954, other immunological responses are complex dependent on the coordination between multiple pathways]] \n", - "618 [[pain sensing and signal transduction, GO:0006935, GO:0019221, leukocyte transendothelial migration, GO:0006955, GO:0030168]] \n", - "619 [[GO:0007165, MESH:D056747, immune signaling, transcription regulation, cytokine regulation, GO:0030155, MESH:D005786, cell growth regulation, metabolism regulation, MESH:D002470, cell death regulation, antifungal immunity]] \n", - "620 [[MESH:M0000731, GO:0006954, GO:0007165, transcription regulation, intercellular signaling, GO:0045087, MESH:D056704]] \n", - "621 [[immune cell signaling, GO:0006928, cell surface receptor activity, GO:0006954, GO:0016477, cell–cell interactions, immune cell receptor-mediated signaling]] \n", - "622 [[GO:0006954, neutroph]] \n", - "623 [[interferon signalling pathway, interferon gamma activity, interferon regulatory factor activity, status response to interferon, GO:0006915, GO:0008289, GO:0005509, GO:0002446]] \n", - "624 [[GO:0006955, cell signaling, cytokine response, interferon response, nuclear factor kappab-dependent transcriptional regulation]] \n", - "625 [[MESH:D007109, interleukin regulation, transcription regulation, GO:0006954, cell signaling, GO:0006915]] \n", - "626 [[GO:0060348, GO:0009653, growth maintenance, GO:0007267, cell-cell communication, GO:0036211, GO:0006810]] \n", - "627 [[GO:0009653, cell-cell communication, GO:0032502, hormone regulation, cellular differentiation, cell-cycle, cell-signalling]] \n", - "628 [[GO:0007165, GO:0000902, GO:0050896, GO:0001525, GO:0065009, GO:0030198]] \n", - "629 [[GO:0009653, GO:0009888, cell signaling, immune regulation, transcription modulation, GO:0007165, GO:0007155, GO:0016477]] \n", - "630 [[the human genes abi1, abl1, abr, actn4, akap13, alms1, MONDO:0008780, anln, GO:0005680, arap3, arf6, arfgef1, arfip2, arhgap10, arhgap27, arhgap29, arhgap4, arhgap5, arhgdia, arhgef11, arhgef12, arhgef2, arhgef3, arhgef7, arl8a, atg4b, MESH:D064096, bcar1, bcl2l11, bcr, bin1, birc5, brca2, bub1, capzb, ccdc88a, ccnb2, cd2ap, cdc27, cdc42, cdc42bpa, cdc42ep1, cdc42ep2, cdc42ep4, cdk1, cdk5rap2, cenpe, cenpf, cenpj, cep131, cep192, cep250, cep57, GO:0047849]] \n", - "631 [[cytoskeletal organization, GO:0016477, GO:0051301, GO:0006260, GO:0006281, GO:0006605, GO:0065007]] \n", - "632 [[the human genes abcf2, acaca, acly, acsl3, actr2, actr3, add3, adipor2, ak4, aldoa, arpc5l, asns, atp2a2, atp5mc1, atp6v1d, MESH:D064096, bcat1, bhlhe40, btg2, bub1, cacybp, calr, canx, ccnf, ccng1, cct6a, cd9, cdc25a, cdkn1a, cfp, cops5, coro1a, cth, ctsc, GO:0038147, cyb5b, cyp51a1, dapp1, ddit3, ddit4, ddx39a, dhcr24, dhcr7, GO:0004146, ebp, edem1, eef1e1, egln3, eif2s2, elovl5, elovl6, eno1, eprs1, ero1a, etf1, MONDO:0100101, MONDO:0100102, fdxr, fgl2, MESH:D010649]] \n", - "633 [[GO:0006412, MESH:D004734, cellular transport, GO:0006955, GO:0035194, mitochondrial oxidative phosphorylation, GO:0006915, GO:0016310, GO:0006096, GO:0006914]] \n", - "634 [[rna biogenesis, protein synthesis biosynthesis, atp-binding, cytoskeleton organization and assembly, GO:0006351, GO:0006338, GO:0007165, GO:0010467, GO:0006413, MESH:M0439896, GO:0006260]] \n", - "635 [[GO:0000394, GO:0051028, MESH:M0439896, GO:0006412, GO:0042254, GO:0035194, GO:0006338]] \n", - "636 [[genes in this list are primarily involved in cell development, including the processes of rna metabolism, dna replication and cell cycle control. enriched terms include: rna metabolism; dna replication; cell cycle control; chromatin regulation; transcription regulation; cell differentiation; gene expression; and protein synthesis.\\n\\nmechanism: the genes in this list are part of a complex network of molecular pathways involved in regulating the expression, replication and maintenance of genetic material. this includes the transcription, splicing and translation of rnas as well as the replication and repair of dna. the multiple genes in this list suggest coordination and control of various steps in these processes, such as chromatin regulation, which is directly responsible for how genetic material is packaged and regulated. additionally, the genes may be involved in regulating cell cycle progression, transcription regulation and cell differentiation]] \n", - "637 [[GO:0001775, GO:0008283, GO:0006260, dna transcription, rna translation.\\nmechanism: the genes may indicate an underlying biological pathway involving the coordinated expression of these gene sets to regulate the cell cycle, dna replication, transcription, and translation in order to enable cell proliferation]] \n", - "638 [[gene expression and structure, cytoskeletal structure and dynamics, calcium regulation and signaling, cell adhesion and migration, cell death biochemistry, metabolic regulation]] \n", - "639 [[GO:0031012, GO:0005856, UBERON:0005090, GO:0032502, neuromuscular structure, MESH:D007473, GO:0006811]] \n", - "640 [[MESH:D047108, GO:0051726, GO:0019722, notch signaling down-regulation, wnt signaling, hedgehog signaling, GO:0000902]] \n", - "641 [[these genes are involved in a wide range of functions related to signaling, development, and transcriptional regulation, indicating an involvement in a variety of cellular pathways. enriched terms include: cell signaling, GO:0007399, GO:0030154, wnt signaling, notch signaling, hedgehog signaling, transcription factor regulation, GO:0006338, e3 ubiquitin ligase.\\n\\nmechanism: the likely underlying biological mechanism is a complex network of interactions between these genes and their pathways, forming a web of signaling molecules that regulate cell growth, differentiation, apoptosis and other cellular processes. the genes and pathways involved in the network are likely to interact in a dynamic manner]] \n", - "642 [[mitochondrial activity, GO:0022900, GO:0006119, metabolic regulation, MESH:D065767]] \n", - "643 [[GO:0005746, electron transfer proteins, proton ion transportation proteins, oxidative phosphorylation proteins, metabolite-binding proteins, atp synthesis proteins]] \n", - "644 [[cytoskeletal reorganization, calcium homeostasis, ubiquitin-proteasome pathway, GO:1901987, transcriptional regulation, GO:0006397, GO:0006974]] \n", - "645 [[GO:0006351, chromatin dynamics, GO:0007155, MESH:D016207, GO:0007049, dna damage repair, cell signaling, GO:0016049, GO:0006915, immune modulation]] \n", - "646 [[GO:0031016, GO:0006006, GO:0048870, neural development]] \n", - "647 [[GO:0009653, neuronal development, GO:0007165, GO:0030073, transcription regulation, GO:0000988]] \n", - "648 [[enrichment test suggested genes are skewed towards genes involved in development, metabolic control, transport, cell cycle and homeostasis, as well as transcriptional regulation.\\n\\nmechanism: these genes appear to be involved in a diverse range of processes, suggesting multiple pathways contributing to the physiological functions of these genes. for instance, abcb1, abcb4 and abcb9 are involved in medication transport, abcc5 and abcc8 are involved in atp coupling, acaa1 is involved in fatty acid metabolism, alb is involved in heme metabolism, aldh1a1, aldh9a1, atxn1 and bcl10 are involved in transcriptional regulation, ctbp1 and ctps1 are involved in ubiquitination, dhcr24 and dhrs3 are involved in cholesterol biosynthesis, fabp6 is involved in bile acid transport, fads1 is involved in fatty acid desaturase, fis1 and gnpat are involved in lipoic acid synthesis and mitochondrial fatty acid metabolism, gstk1 is involved in gst-mediated detoxification, hmgcl is involved in steroidogenesis, hras, hsd11b2, hsd17b11]] \n", - "649 [[GO:0006629, GO:0008202, transcription regulation, GO:0051726]] \n", - "650 [[GO:0010467, dna repair & maintenance, MESH:M0496065, cellular signaling pathways, GO:0006629]] \n", - "651 [[GO:0051726, gene transcription, transcription factor activation, MESH:M0023730, MESH:D011494, receptor proteins, GO:0006412, GO:0016049, GO:0008283, GO:0030154]] \n", - "652 [[gene expression regulation; co-translational protein targeting; clathrin-mediated endocytosis; endosomal protein trafficking; vesicle transport; exocytosis; receptor and ligand-mediated signaling; development and organ morphogenesis.\\nmechanism: the identified genes are likely involved in a variety of biological processes related to endocytosis, vesicle trafficking and transport, receptor and ligand-mediated signaling, MESH:D005786, co-translational protein targeting, and organ morphogenesis. these processes can be clustered into several pathways, including the calcineurin-mediated endocytosis pathway, the mapk signaling pathway, the wnt/beta-catenin signaling pathway, the clathrin-mediated endocytosis pathway, the endosomal protein trafficking pathway, the vesicle transport pathway, the exocytosis pathway, the receptor ligand-mediated signaling pathways]] \n", - "653 [[genes belonging to this list are mainly involved in endocytosis, GO:0016192, MESH:D021381, and membrane fusion. the enriched terms include: endocytosis; vesicle trafficking; protein trafficking; membrane fusion; membrane transport; cytoskeleton organization; signal transduction; receptor internalization; and protein trafficking pathways.\\n\\nmechanism: the common characteristics shared by the genes suggest that they are all involved in some aspect of the endocytosis pathway. this biological mechanism involves signal transduction by which a signal (chemical or physical) can pass through a cell membrane and allow the cell to take up extracellular substances. through receptor internalization, molecules, like hormones, can be shuttled into intracellular vesicles and undergo further signaling events. the sequential vesicle trafficking steps then enable the cargo to be transported to their final destination. the proteins play various roles in facilitating membrane fusion, GO:0036211, GO:0007010, and vesicle transport. all of these activities act in concert to usher signals, MESH:D011506, other substances into the cell]] \n", - "654 [[redox regulation, antioxidant defense, detoxification of reactive oxygen species, peroxisomal biogenesis, MESH:M0572479, cell metabolism]] \n", - "655 [[redox balance regulation, GO:0008152, GO:0051726, transcriptional regulation]] \n", - "656 [[cell signaling, protein regulation, GO:1901987, GO:0009653, GO:0048513, cytoskeletal regulation]] \n", - "657 [[cell cycle checkpoint regulation, GO:0009653, cell signaling, MESH:D003598, organ development]] \n", - "658 [[mapk pathway, tgf-β signaling pathway, wnt/β-catenin pathway, GO:0035329, transcriptional regulation, muscle morphogenesis, GO:0048729, regulation of g-protein signaling, GO:0006954]] \n", - "659 [[these genes are involved in processes related to cell development, GO:0009653, calcium and calcium-dependent signaling, MESH:D017978, smad pathway and extracellular matrix proteins.\\n\\nmechanism: the mechanism underlying this gene list is likely related to signal transduction pathways. these may involve cell surface receptors which bind growth factors, such as tgfb1 and bmpr2, and transduce the signal through the smad pathway via the fkbp1a, bmpr1a, smurf1, smad1, ltbp2, thbs1, arid4b, ppm1a, and ctnnb1 proteins to influence the regulation of gene expression and cell fate. moreover, other molecules such as xiap, ube2d3, nog, slc20a1, serpine1, bcar3, rhoa, MESH:D045683, hipk2, ppp1ca, smad7, junb, smad6, ppp1r15a, tjp1, and ifngr2 may be involved in the signal transduction pathway. in addition, the calcium and calcium-dependent signaling by the tg]] \n", - "660 [[GO:0032502, GO:0006954, MESH:D056747, cell signaling, MESH:M0496924, GO:0009653, GO:0009888, GO:0008283, GO:0006915, immune system response, MESH:M0496924]] \n", - "661 [[gene transcription, actin maturation, cytoskeleton formation, signaling complex assembly, interleukin receptor signaling, GO:0051170, cytokine receptor signaling, nf-kappab signaling pathway, cytokine-mediated signal transduction, GO:0006367, MESH:D005786, cytokine receptor signaling pathway, GO:0010737, GO:0035556]] \n", - "662 [[GO:0009299, GO:0042254, GO:0006457, nucleolar activity, spliceosomal activity, protein production, GO:0015031, GO:0006396, GO:1901987]] \n", - "663 [[GO:0008152, GO:0006412, GO:0043687, GO:0016310, pepetide binding and metabolism, protein structure and folding, rna synthesis and processing, GO:0000394, GO:0010467, GO:0051726, GO:0006915, GO:0007165, GO:0006281]] \n", - "664 [[MESH:D011494, cellular signaling pathways, GO:0001501, GO:0031012, transcriptional regulation, post-translational phosphorylation, growth regulation, development regulation, remodeling]] \n", - "665 [[mitotic regulation, GO:0060349, morphogenesis of specific organs and tissues, GO:0009966, regulation of transcription, GO:0042127, cellular responses to external stimuli, GO:0006468, GO:0003677]] \n", - "666 [[GO:0032502, GO:0016049, gene transcription, GO:0008152, MESH:D011506, GO:0006412, GO:0007049, cell signaling, transcriptional regulation, MESH:D021381, GO:0010468]] \n", - "667 [[GO:0008283, GO:0051726, dna replication and repair, GO:0007165, GO:0019722, GO:0006915, GO:0006629, oxygen pathway]] \n", - "668 [[this examination of human genes reveals a number of gene functions that are significantly enriched and related to developmental processes, including cell proliferation and differentiation, GO:0048729, and wnt signalling pathways. \\nmechanism: cell proliferation and differentiation, GO:0048729, wnt signalling pathways are all important in the normal healthy development of cells organs. these genes provide important functions that act in cooperative downstream pathways to enable promote these developmental processes.\\nthe enriched terms are: cellular differentiation; cellular proliferation; digit development; tissue morphogenesis; wnt signalling pathway]] \n", - "669 [[wnt signaling, notch signaling, transcription regulation, GO:0051726, GO:0009653, GO:0032502]] \n", - "670 [[cell signalling, protein interaction, GO:0007165, GO:0032502, regulatory role in immunity, GO:0030163, receptor-mediated signaling, GO:0016049, GO:0030154, GO:0006396]] \n", - "671 [[cell signaling, immune regulation, GO:0007165, growth factor production and response, immune response and modulation, calcium homeostasis, GO:0000981, development and differentiation, GO:0005102, GO:0001816]] \n", - "672 [[the enrichment test results reveal that the list of genes are all involved in stem cell pluripotency and early embryonic development. enriched terms include pluripotency, stem cell morphology, MESH:D047108, GO:0000981, GO:0016049, differentiation, cell proliferation.\\n\\nmechanism: the genes focus on the regulation of the pluripotency and early embryonic developmental program. they regulate various aspects such as transcription factors, cell growth, morphogenesis, differentiation and cell proliferation. by acting in concert, they maintain the pluripotency of stem cells and initiate the processes of early morphogenesis. it is hypothesized that these genes are part of a large regulatory network which facilitates the pluripotency of the progenitor cells and the successful orchestration of early embryonic development]] \n", - "673 [[GO:0009792, GO:0048864, GO:0000981, GO:0009653]] \n", - "674 [[GO:0030198, GO:0007155, GO:0009653, cell signaling, cytoskeletal organization, GO:0030154, MESH:D002470]] \n", - "675 [[our term enrichment analysis suggests that the human genes jag2, spp1, jag1, vcan, olr1, col5a2, app, UBERON:0003010, postn, tnfrsf21, apoh, pglyrp1, vav2, fstl1, nrp1, s100a4, lrpap1, vtn, timp1, itgav, lum, pf4, cxcl6, col3a1, stc1, kcnj8, msx1, ptk2, prg2, pdgfa, serpina5, and vegfa are related to processes in growth and differentiation, including transcriptional network maintenance, cell adhesion and motility, GO:0006915, and extracellular matrix component formation.\\n\\nmechanism: \\nthese genes may be involved in a complex network of signaling pathways that regulate cell growth and differentiation, cell adhesion and migration, GO:0006915, and matrix component formation. they may be involved in the reception and transduction of growth and differentiation signals, could facilitate the assembly of extracellular matrix components to form the microenvironment necessary to prompt and]] \n", - "676 [[GO:0009653, GO:0032502, transcription regulation, cell signalling, GO:0006811]] \n", - "677 [[GO:0009653, neuronal growth, neuronal system development, cell-cell communication, cell signaling, GO:0009888, organ development]] \n", - "678 [[analysis of the gene list shows that they are all associated with sarcomere function, MESH:D009119, skeletal muscles and thermogenesis. the enriched terms include sarcomere function, MESH:D009119, UBERON:0001134, MESH:D022722, actin-myosin interaction, calcium handling, muscle development and differentiation, and mitochondrial function. \\n\\nmechanism: the underlying biological mechanism is associated with the activation of genes that are linked to the assembly, maintenance and contraction of the sarcomere, which is the fundamental unit of muscle contraction, as well as muscle development and differentiation, calcium handling, mitochondrial fluctuation, thermogenesis. this contributes to the generation of force within the skeletal muscles]] \n", - "679 [[skeletogenesis, MESH:D024510, GO:0048740, GO:0001501, GO:0006936, GO:0006412, GO:0009058, MESH:D009126]] \n", - "680 [[GO:0007165, vesicle/lipid trafficking, cellular adhesion, nutrient regulation, cell metabolism, cytoskeletal organization, endocytosis/exocytosis, intercellular adhesion/motility]] \n", - "681 [[membrane trafficking, GO:0007165, protein proteolysis, GO:0006629, receptor signaling, GO:0055088]] \n", - "682 [[GO:0006096, aerobic glycolysis, GO:0006094]] \n", - "683 [[GO:0008152, GO:0006096, GO:0006098, GO:0006006, MESH:D004734]] \n", - "684 [[these genes appear to be involved in the development, functioning and regulation of the nervous system, specifically neurons and their associated pathways and processes. the terms \"neurotransmission\"; \"neuronal cell membrane regulation\"; \"neurotransmitter release\"; \"calcium signaling\"; \"neuronal ion channel regulation\"; and \"neuronal excitability regulation\" are significantly enriched in this gene set.\\n\\nmechanism: it appears that this gene set may be involved in a broad range of processes related to neurophysiology, including the regulation of neuronal membrane excitability and ion channels, neuronal cell membrane regulation, GO:0007269, and calcium signaling. these processes are all complex and interrelated, are likely to have a direct impact on neural development function]] \n", - "685 [[the term enrichment test reveals that the genes in the list are mainly involved in neuronal ion channels and calcium signalling pathways. enriched terms included calcium channel activity, GO:0005244, GO:0038023, GO:0015276, and g-protein coupled receptor activity. \\n\\nmechanism: the genes in the list form ion channels and g-protein coupled receptors within neuronal cells, which facilitates the communication of neurotransmitters between neurons. several of the genes are involved in calcium signalling pathways, which regulate various cellular pathways involved in the development and maintenance of neurons]] \n", - "686 [[GO:0016049, GO:0048468, GO:0006915, GO:0006955, GO:0030163, GO:0006508]] \n", - "687 [[phosphatidylinositol signalling, vascular endothelial growth factor receptor signalling, progesterone-mediated oocyte maturation, nf-kb signaling, GO:0043526]] \n", - "688 [[carbohydrate digestion and absorption; glycosaminoglycan and glycan metabolism; lysosomal, GO:0005777, and catabolic processes; digit, skeletal, GO:0035108]] \n", - "689 [[glycoside hydrolase (gh) activity, mucin biosynthesis, GO:0006031, MESH:D057056, lysosomal enzyme activity.\\nmechanism: glycoside hydrolase (gh) and lysosomal enzymes play important roles in the process of glycostasis, and are involved in a variety of metabolic activities such as the breakdown of polysaccharides, the synthesis of glycolipids and glycoproteins, and the degradation of other macromolecules. chitin and mucin biosynthesis also involve glycosylation and enzymatic modification of sugars and polysaccharides to form polymeric molecules. cysteine protease are involved in the hydrolysis of proteins, while lysosomal enzymes aid in the breakdown of molecules in the l]] \n", - "690 [[members of the immunoglobulin (ig) gene superfamily - specifically, igh, GO:0033984, MESH:C014609, GO:0042571, response and maintenance of the adaptive immune system at different levels, likely via antigen binding, signal transduction and b cell activation]] \n", - "691 [[GO:0003823, b cell receptors, GO:0007596, GO:0005577, MESH:D001779, clec4d]] \n", - "692 [[dna damage recognition, GO:0006281, GO:0006302, meiotic recombination, GO:0007059, GO:0035825, rad51 family proteins, dna end-protection, mus81-mms4 complex, muts family proteins, dna proofreading, spo11-associated pathway]] \n", - "693 [[GO:0006281, GO:0006260, gene splicing]] \n", - "694 [[GO:0000075, cell adhesion/motility complex, transcriptional complex, GO:0036211, rna processing complex]] \n", - "695 [[calcium binding, apoptotic regulation, immune modulation, MESH:D018384, GO:0051726, stress-response regulation]] \n", - "696 [[the human genes abcf2, acaca, acly, acsl3, actr2, actr3, add3, adipor2, ak4, aldoa, arpc5l, asns, atp2a2, atp5mc1, atp6v1d, MESH:D064096, bcat1, bhlhe40, btg2, bub1, cacybp, calr, canx, ccnf, ccng1, cct6a, cd9, cdc25a, cdkn1a, cfp, cops5, coro1a, cth, ctsc, GO:0038147, cyb5b, cyp51a1, dapp1, ddit3, ddit4, ddx39a, dhcr24, dhcr7, GO:0004146, ebp, edem1, eef1e1, egln3, eif2s2, elovl5, elovl6, eno1, eprs1, ero1a, etf1, MONDO:0100101, MONDO:0100102, fdxr, fgl2, MESH:D010649]] \n", - "697 [[energy production, GO:0008152, protein biosynthesis and folding, cell regulation, MESH:D048788, protein turnover]] \n", - "698 [[peroxisome biogenesis, peroxisome formation, membrane protein trafficking, GO:0044255, mitochondrial-peroxisomal crosstalk]] \n", - "699 [[peroxisomal biogenesis, peroxisomal protein transport, oxidative damage resistance]] \n", - "700 [[cell structural element development, gene transcription, GO:0016070, GO:0006259, transcriptional regulation]] \n", - "701 [[dna replication and repair, GO:0006334, GO:0000723, transcriptional regulation]] \n", - "702 [[GO:0007165, GO:0006811, regulation of neurotransmitter release]] \n", - "703 [[analysis of these genes show that they are involved in human neurological structure and function. enriched terms include neuron activity, GO:0005216, GO:0008066, GO:0004930, MESH:D005680, GO:0005267, MESH:D005680]] \n", - "704 [[MESH:D024510, neuronal development, GO:0015031, GO:0006629, GO:0009653]] \n", - "705 [[GO:0015031, MONDO:0008090, GO:0048705, MESH:D024510, GO:0005783, mitochondrial protein transport, cytoskeletal organization]] \n", - "706 [[g alpha subunit signaling, gpcr activation and signaling, gpcr function, MESH:D019281]] \n", - "707 [[cellular signaling, g protein signaling pathway, calcium signaling pathway, GO:0007399, GO:0007268, phosphorylation cascade, nerve morphogenesis, indoleamine metabolism]] \n", - "708 [[nuclear receptor superfamily, transcription regulation, epigenetic regulation, GO:0051726, GO:0003677, GO:0006338, GO:0032502, cell signaling pathways, GO:0005652, GO:0016363]] \n", - "709 [[transcriptional regulation, GO:0016569, GO:0009653, cardiovascular development, differentiation, MESH:M0464910, MESH:M0030450, GO:0048863]] \n", - "710 [[GO:0032963, GO:0030198, GO:0004222, GO:0030206, GO:0008378, GO:0005509, GO:0008270, platelet derived growth factor binding, GO:0002020, GO:0035987, GO:0007266, GO:0007160, hypoxia response, epidrmis development, peptidyl-lysine hydroxyl]] \n", - "711 [[GO:0030198, GO:0030199, GO:0043589, GO:0042060, GO:0043588, GO:0032964, GO:0006024, GO:0003755, GO:0035987]] \n", - "712 [[analysis of the above genes shows that they are all involved in dna repair and involved in the fanconi anaemia nuclear complex, which is a critical part of the fanconi anaemia disease pathway. the list of enriched terms includes \"protein monoubiquitination\", \"dna repair complex\", \"fanconi anaemia nuclear complex\", \"double-strand break repair via homologous recombination\", \"response to intra-s dna damage checkpoint signaling\", \"telomere maintenance\", \"positive regulation of g2/m transition of mitotic cell cycle\", \"regulation of transcription by rna polymerase ii\".\\n\\nmechanism: the underlying biological mechanism is the fanconi anaemia pathway, where the defective genes of the path have the potential to lead to cancer or other fanconi anaemia-related illnesses. this dna repair pathway relies heavily on the fanconi anaemia nuclear complex, which involves the processes of monoubiquitination, involving the above genes, double-strbreak repair via homologous recombination. in addition, the regulation of telomere maintenance, positive regulation of g2/m transition of mitotic cell cycle regulation of transcription by rna polymerase ii are essential for proper dna repair]] \n", - "713 [[this group of genes are involved in a range of dna repair processes, including protein monoubiquitination and double-strand break repair via homologous recombination. they are all localized in different components of the cell (e.g. chromatin, GO:0005634, GO:0005829, GO:0005657, GO:0005694, etc.) and are part of several complexes/hierarchies (e.g. fanconi anaemia nuclear complex, GO:0033063, GO:0048476, GO:0033557, GO:0033593, etc.). enriched terms includes: dna repair; protein monoubiquitination; double-strand break repair via homologous recombination; regulation of dna metabolic process; negative regulation of double-stranded telomeric dna binding activity; response to gamma radiation; regulation of telomere maintenance; establishment of protein localization to telomere; and regulation of protein metabolic process.\\n\\nmechanism: these genes are involved in a range of complex and interrelated biochemical pathways, which utilize a variety of enzymatic activities (e.g. ubiqu]] \n", - "714 [[GO:0005515, protein homodimerization, GO:0005524, GO:0003677, GO:0003824, MONDO:0016019]] \n", - "715 [[protein homodimerization, GO:0019899, GO:0140657, GO:0005102, ligase binding, GO:0003924, GO:0046872, dna-binding, rna-binding, oxidase activity, MESH:D010758, GO:0120227, transportase activity, dehydrogenase activity, GO:0016791, GO:0016301, GO:0004175, GO:0022857, chemotactic receptor activity, GO:0017077]] \n", - "716 [[receptor binding activity, signaling receptor binding activity, protein binding activity, dna-binding, GO:0016563, GO:0005125, GO:0008083, GO:0042605, enzyme binding activity, chemical binding activity, protein complex binding activity]] \n", - "717 [[enzyme binding activity, rna binding activity, protein binding activity, chemokine receptor binding activity, GO:0004712, GO:0042803, identical protein binding activity, GO:0008083, interleukin binding activity, cell-cell adhesion mediation, dna-binding transcription activity, GO:0015026, cytoplasmic factor activity, metal ion binding activity, polypeptide antigen transporter activity]] \n", - "718 [[protein binding activity, enzyme binding activity, transcription factor binding activity, GO:0016787, GO:0004721, GO:0003714, GO:0003713, atp binding activity, GO:0004672, GO:0016563, GO:0003924, nad+ binding activity, ring-like zinc finger domain binding activity, GO:0061656, small protein activating enzyme binding activity, GO:0000224, GO:0062076, GO:0004383, GO:0004222, 17-beta-dehydrogen]] \n", - "719 [[protein binding activity, GO:0004672, GO:0006351, GO:0038023, enzymatic activity, GO:0016310, GO:0097472, GO:0003677, GO:0006351, postsynaptic organization, GO:0016887, nucleic acid binding activity, ubiquitin protein ligase binding activity, fad binding activity, MESH:D009249, GO:0061665, enzyme binding activity, GO:0022857, endopeptidase activator]] \n", - "720 [[GO:0030021, collagen binding activity, integrin binding activity, GO:0060090, identical protein binding activity, fibronectin binding activity, GO:0046983, heparan sulfate proteoglycan binding activity, GO:0007160, GO:0010810]] \n", - "721 [[GO:0007166, GO:0006468, GO:0045861, GO:0007160, GO:1902533, GO:0010604, transmem]] \n", - "722 [[GO:0098609, agonist binding activity, cytoplasmic matrix binding, protein homodimerization, GO:0005102]] \n", - "723 [[binding activities, GO:0003824, involvement in biological processes, structural roles]] \n", - "724 [[GO:0061024, protein organization, GO:0036211, GO:0015031, GO:0006897, GO:0007165, GO:0006915]] \n", - "725 [[GO:0007155, protein folding and regulation, GO:0050801, MESH:D005786]] \n", - "726 [[dna binding activity, protein binding activity, enzyme binding activity, GO:0004197, identical protein binding activity, signaling receptor binding activity, calcium ion binding activity, protein kinase binding activity, GO:0000988, bh3 domain binding activity]] \n", - "727 [[calcium ion binding activity, protein binding activity, identical protein binding activity, chromatin dna binding activity, dna-binding transcription factor binding activity, ig domain binding activity, sh2 domain binding activity, bh3 domain binding activity, cyclin binding activity, rna binding activity, GO:0004197, metalloprotease inhibitor activity, phospholipid binding activity, lipopeptide binding activity, lysophosphatidic acid binding activity, sulfatide binding activity, atpase binding activity, pdz domain binding activity]] \n", - "728 [[atp binding activity, GO:0016887, protein binding activity, signaling receptor binding activity, enzyme binding activity, GO:0042803, GO:0016791, GO:0000988, GO:0022857, ubiquitin-dependent protein binding activity, cholesterol binding activity, GO:0019871, phosphotyrosine residue binding activity]] \n", - "729 [[GO:0140657, GO:0016887, GO:0008233, enzyme binding activity, GO:0003700, GO:0042803, identical protein binding activity, signaling receptor binding activity]] \n", - "730 [[atp binding activity, protein kinase binding activity, GO:0042803, GO:0003700, low-density lipoprotein particle binding activity, GO:0005041, GO:0030229, GO:0004602, GO:0004364, GO:0016491, GO:0004496, GO:0004631, GO:0047598, GO:0047024, MESH:D010758, GO:0060090, cholesterol binding activity, GO:0120020, isopentenyl]] \n", - "731 [[GO:0042632, MESH:D055438, GO:0005515, GO:0006351, GO:0010468, dna-binding, GO:0007165, negative regulation, positive regulation, GO:0016491, GO:0008610, GO:0003723, ldl particle binding, GO:0019901, phosphotransferase activity, acetyl-coa ligase activity, endopeptidase activity, etc]] \n", - "732 [[the provided list of human genes are mainly involved in metabolism, adjustment of the immune system and coagulation, and development of cells and organs. in particular, they are found to be involved in binding activities and endopeptidase activities such as post-translational modification, transcription and regulation of protein. the enriched terms include calcium-dependent protein/phospholipid/lipoprotein binding activity, GO:0004197, protein homodimerization/homooligomerization activity, identical protein binding activity, and serine-type endopeptidase activity. \\n\\nmechanism: the expression and activities of these genes may play important roles in the development and metabolism of cells and organs by facilitating protein folding, GO:0043687, cell-matrix adhesion and crosstalk between proteins. the binding activities of these genes towards phospholipid, lipoprotein and other molecules mediate the interaction between cells and extracellular environment, and regulate blood coagulation and formation of extracellular matrix. the endopeptidase activities of these genes degrade and modulate proteins, which are essential for various biological processes]] \n", - "733 [[protein binding activity, domain specific binding activity, disordered domain specific binding activity, GO:0008233, GO:0004252, GO:0005125, signaling receptor binding activity, identical protein binding activity, GO:0004222, GO:0003924, receptor tyrosine kinase binding activity, GO:0004421, phospholipid binding activity, amyloid-beta]] \n", - "734 [[enriched functions observed in the genes include binding activitiy (for various ligands, such as dna, GO:0005562, MESH:C062738, calcium ions, heparin/heparan sulphate, MESH:D019204, c5l2 anaphylatiotaxin, MESH:M0028275, mhc, amyloid-beta, cytokine, opsonin, MESH:D005227, MESH:D011494, etc.), enzyme activity (such as deubiquitinase, lck, atpase, aminopeptidase, peptidase, etc.), GO:0044183, cysteine type endopeptidase inhibitor activity and endopeptidase activity, phospholipid binding activity, transcription factor activity and transcription regulatory region sequence-specific dna binding activitiy. the underlying mechanism could be related to signal transduction, functional process, dna/rna transcription, protein degradation and signalling pathways such as cell killing and apoptotic signalling pathways.\\n\\nsummary: enriched functions include multiple binding activities, GO:0003824, and transcription regulatory activities for signal transduction, functional processes, and signalling pathways. \\nmechanism: signal transduction, functional processes, dna/rna transcription, protein degradation,]] \n", - "735 [[enzyme binding activity, GO:0101005, GO:0004197, GO:0005102, GO:0019901, sh2 domain binding activity, GO:0004435, GO:0003924, GO:0004222, atpase binding activity, integrin binding activity, dna binding activity, lipoprotein receptor binding activity, GO:0007165, GO:0006915, MESH:D015850]] \n", - "736 [[the given list of human genes are primarily involved in dna binding, transcription and translational activities, rna binding, enzyme binding activities, and identical protein and nucleic acid binding activities. there is also evidence of involvement in activities such as transcription co-activator activity, nuclear localization, cytochrome-c oxidase activity, atp-dependent activities and endopeptidase activator activity. enriched terms include dna binding, GO:0003723, GO:0003887, GO:0046983, identical protein binding activity, transcription factor binding activity, GO:0003700, zinc ion binding activity, atp binding activity, protein binding activity]] \n", - "737 [[dna binding activity, rna binding activity, transcription activity, enzyme binding activity, GO:0042803]] \n", - "738 [[GO:0007049, GO:0006260, transcriptional regulation, post-transcriptional regulation, GO:0003682, GO:0140014, GO:0051169, GO:0046931]] \n", - "739 [[dna binding activity, protein binding activity, histone binding activity, GO:0016887, enzyme binding activity, GO:0006260, GO:0006306, chromatin binding activity, GO:0042803, GO:0003887, rna binding activity]] \n", - "740 [[extracellular matrix structural components, GO:0007160, protein domain specific binding activity, identical protein binding activity, GO:0048018, signaling receptor binding activity, metal ion binding activity, peptide hormone receptor binding activity, heparin binding activity, collagen binding activity, GO:0007165, GO:0005125]] \n", - "741 [[protein binding activity, identical protein binding activity, metal ion binding activity, ion binding activity, actin binding activity, small molecule binding activity, fibronectin binding activity, collagen binding activity, integrin binding activity, procollagen binding activity, cadherin binding activity, phosphatidylinositol-3,4,5-trisphosphate binding activity, substrate-binding activity, GO:0005096, GO:0004867, GO:0005006, GO:0005024, GO:0004896, platelet-derived growth factor binding activity, nucleotide-binding transcription factor activity]] \n", - "742 [[binding activity, transport activity, GO:0003824, adhesion activity, intracellular signaling, GO:0006351, neuronal development]] \n", - "743 [[GO:0003677, GO:0051117, GO:0005515, GO:0016791, dehydrogenase activity, GO:0004016, GO:0055085, transcriptional regulation, GO:0007155, GO:0006915]] \n", - "744 [[protein binding activity, dna-binding, domain binding activity, carbohydrate binding activity, enzyme binding activity, ligand binding activity, transmembr]] \n", - "745 [[dna-binding, GO:0016563, GO:0005515, membrane transporter activity, GO:0016787, GO:0016310, ligand-mediated activity]] \n", - "746 [[GO:0006631, GO:0006629, GO:0005975, GO:0003677, GO:0003723, protein homodimerization, GO:0000287, GO:0005524, GO:0046872, GO:0047617, GO:0003995, fad binding activity, nadph binding activity, homodimerization activity, GO:0000774, GO:0015254, GO:0004497, 5alpha-androstane-3alpha,17beta-diol dehydrogenase activity, GO:0008170, identical protein binding activity, GO:0016860, enzyme binding activity, GO:0004674, GO:0042803, GO:0004351, GO:0004222, ubiquitin binding activity, dna-binding]] \n", - "747 [[GO:0016491, enzyme binding activity, dna binding activity, GO:0004090, GO:0052650, GO:0015245, nadph binding activity, GO:0042803, atp binding activity, receptor ligand binding activity, nad+ binding activity, smad binding activity, rna polymerase ii-specific transcription factor activity, atp-dependent protease activity, GO:0016404, GO:0004672, ubiquitin conjugating]] \n", - "748 [[GO:0003677, transcription binding, GO:0046872, GO:0005515, GO:0019899, MESH:D020558, GO:0003682, GO:0042826, GO:0046983, sumo-dependent ubiquitination, GO:0003723, GO:0005524, GO:0042054, GO:0008017, GO:0010997, boxh/aca snorna binding, GO:0043515, GO:0070840, m7gpppn-cap structure binding, GO:0008270, GO:0003697, GO:0038024, GO:0006200, GO:0051536, GO:0005884]] \n", - "749 [[GO:0005515, GO:0003677, GO:0006351, GO:0019904, GO:0042054, GO:0004402, GO:0004674, GO:0030374, GO:0005049, GO:0016887, zinc ion binding activity, GO:0140037, GO:0036310, sumo polymer binding activity, nuclear receptor binding activity, dna topoisomerase binding activity, GO:0010997, GO:0000774, GO:0005096, microtubule binding activity, dna replication origin binding activity, GO:0000987, rna polymerase ii-specific transcription]] \n", - "750 [[GO:0003676, GO:0005515, GO:0005524, metabolic activity, GO:0016310, MESH:D010084, GO:0005975, GO:0005125, GO:0008083]] \n", - "751 [[protein binding activity, identical protein binding activity, enzyme binding activity, atp binding activity, transcription activation activity, dna-binding transcription activity, heparin binding activity, cytoplasmic protein binding activity, signalling receptor binding activity, cytoskeletal protein binding activity, GO:0042803, GO:0060422, rna binding activity, GO:0140677, GO:0004689, phosphotransferase activity, heme binding activity, calcium ion binding activity]] \n", - "752 [[GO:0007155, GO:0007165, epithelial-mesenchymal interaction, GO:0006898, GO:0001525, GO:0001843]] \n", - "753 [[GO:0003700, rna polymerase ii transcription regulatory region sequence-specific dna binding activity, chromatin binding activity, receptor binding activity, GO:0005096, gtpase binding activity, phospholipid binding activity, calcium ion binding activity, zinc ion binding activity, identical protein binding activity, apolipoprotein binding activity, phosphotyrosine residue binding activity, very-low-density lipoprotein particle binding activity, phosphatidylcholine binding activity, phosphatidylethanolamine binding activity, adenyl ribonucleotide]] \n", - "754 [[identical protein binding activity, dna binding activity, rna binding activity, GO:0000988, GO:0003714, GO:0016564, GO:0016563, GO:0016791, protein kinase binding activity, GO:0006865, GO:0006811, heme binding activity, oxygen binding activity, protein-fructose gamma-glutamyltransferase activity, GO:0042803, lamin binding activity, chromatin binding activity and ubiquitin ligase activity]] \n", - "755 [[transcription activity, dna binding activity;rna binding activity, protein kinase binding activity, atp binding activity, protein binding activity, identical protein binding activity, GO:0042803, GO:0004197, GO:0015075, protein domain specific binding activity, GO:0032452, GO:0004674, GO:0016564, GO:0061630, lamin binding activity, GO:0004521, GO:0038023, GO:0004602, phosphoprotein binding activity, molecule adaptation, enzyme binding activity, protein phosphatase binding activity, GO:0004418, ubiquitin conjugating enzyme binding activity, GO:0004842, ap-2 adapt]] \n", - "756 [[dna-binding transcription activity, enzyme binding activity, protein binding activity, ligand-binding activity, atp binding activity, nadp binding activity, metal ion binding activity, carbohydrate binding activity, signaling receptor binding activity, GO:0003714, GO:0001217, GO:0008160, heparin binding activity, n-acetylglucosamine n-sulfotransferase activity, MESH:D006497]] \n", - "757 [[dna binding activity, rna binding activity, protein binding activity, GO:0004672, GO:0019887, GO:0016407, GO:0016301, GO:0008233, GO:0004197, GO:0004252, ubiquitin binding activity, GO:0042803, GO:0000988, GO:0016563, GO:0016564, apolipoprotein binding activity, phosphatase binding activity, disordered domain specific binding activity, chromatin binding activity, GO:0016303, GO:0030701, GO:0004693, GO:0004396, actinin binding activity, 14-3-3 protein binding activity, gtp binding activity, MESH:D009584]] \n", - "758 [[ligand binding, GO:0019899, GO:0005102, MESH:M0518050, GO:0003700, rna-binding, protein homodimerization, protein-kinase binding activity, identical protein binding activity, GO:0004896, c-c chemokine binding activity, GO:0004197, GO:0022857, gtp binding activity, protease binding activity]] \n", - "759 [[dna-binding, transcriptional activity, GO:0006355, GO:0005515, protein homodimerization, GO:0003924, GO:0005102, ligand-activated transcription, GO:0019900, GO:0002020, GO:0004674, GO:0004175, cystein-type endopeptidase activity, GO:0005102, GO:0061630, GO:0005125, GO:0008083, leukemia inhibitory factor activity, 5'-deoxyn]] \n", - "760 [[GO:0038023, binding activity, MESH:D016207, MESH:M0496065, MESH:D008074, MESH:D010455, MESH:D011506, GO:0019900, GO:0005524]] \n", - "761 [[GO:0004896, cxcr chemokine receptor binding activity, interleukin-binding activity, GO:0006952, GO:0010605, GO:0051247]] \n", - "762 [[protein binding activity, GO:0005125, GO:0004930, dna-binding transcription activity, lipopolysaccharide binding activity, atp binding activity, integrin binding activity, GO:0048018, GO:0022857, signaling receptor binding activity, extracellular atp-gated channel activity, phosphatidylinositol- 3-kinase activity, metallod]] \n", - "763 [[GO:0038023, binding activity, GO:0003824, GO:0008083, GO:0005215, GO:0000988]] \n", - "764 [[signaling receptor binding activity, GO:0003713, regulation of transcription, dna-binding activity, rna binding activity, metal ion binding activity, identical protein binding activity, GO:0042803]] \n", - "765 [[GO:0098542, GO:0006955, GO:0046718, GO:0032020, GO:0019882, GO:0019221, GO:0045087, GO:0007166, GO:0030225, GO:0032722, GO:0001961, cell-cell adhesion mediated by plasma membrane cell adhesion molecules]] \n", - "766 [[the list of genes are discovered to be enriched in terms like dna binding activities, GO:0042803, GO:0000988, GO:0004672, GO:0004725, GO:0016887, enzyme binding activity, phosphatidylinositol phosphate binding activity, GO:0030528, GO:0008009, and cytokine receptor activity.\\n\\nmechanism: the biological mechanism underlying the enriched terms is most likely associated with cell and immune response. these genes are involved in various processes related to cell signaling, detection, recognition, GO:0006351, and expression. through these processes, the genes regulate important functions such as cell adhesion, GO:0005515, GO:0019899, GO:0005125, and transcription factor activation. in addition, several of these genes are also involved in apoptotic and other cell regulation pathways]] \n", - "767 [[binding activity, GO:0003824, protein activity, GO:0000981]] \n", - "768 [[protein binding activity, transmembrane activity, GO:0003700, sequence-specific double-stranded dna binding activity, GO:0004930, identical protein binding activity, calcium ion binding activity, scaffold protein binding activity, transcription cis-regulatory region binding activity]] \n", - "769 [[dna-binding activity, transcription activity, calcium ion binding activity, atp-binding activity, protein binding activity, GO:0004930, cell death regulation, GO:0009653, GO:0042445]] \n", - "770 [[cell adhesion molecule binding activity, atpase-coupled intramembrane transport, GO:0004222, GO:0042803, signal receptor binding activity, GO:0003700, MESH:D006493]] \n", - "771 [[GO:0005125, protein domain specific binding activity, protein kinase binding activity, cell adhesion molecule binding activity, signaling receptor binding activity, GO:0004222, GO:0001217, rna binding activity, gtpase binding activity, structural proteins, atp binding activity]] \n", - "772 [[protein binding activity, cytoskeleton binding activity, GO:0005096, atpase binding activity, GO:0042030, adenyl ribonucleotide binding activity, calmodulin binding activity, cadherin binding activity, gamma-tubulin binding activity, integrin binding activity, kinetochore binding activity, molecular function adaptor activity, GO:0042803, protein kinase binding activity, protein phosphatase binding activity, sh2 domain binding activity, sh3 domain binding activity, small gtpase binding activity, beta-catenin binding activity, beta-tubulin binding activity, dynein complex binding activity, identical protein binding activity, phosphatidylcholine binding activity, protein domain specific binding activity, protein tyrosine kinase binding activity]] \n", - "773 [[MESH:D020558, atpase, tubulin binding activity, microtubule binding activity, actin filament binding activity, kinesin binding activity, dynein binding activity, g protein-coupled receptor binding activity]] \n", - "774 [[enzyme binding activity, acid binding activity, molecule transport, adapter binding activity, receptor binding activity, dna binding activity, protein binding activity, GO:0003824, GO:0016787, GO:0016491, anion binding activity, GO:0008233, GO:0140657, thioredoxin activity, translocation, GO:0061630, cysteine endopeptidase activity, GO:0004738, GO:0004618, magnesium ion binding activity, GO:0004340, GO:0003924]] \n", - "775 [[protein binding activity, identical protein binding activity, GO:0008233, GO:0003824, GO:0005884, dna-binding, rna-binding, GO:0016922, MESH:D054875, anion binding activity, atp binding activity, GO:0016887, protein kinase binding activity, phosphotyrosine residue binding activity, e3 ubiquitin-protein ligase binding activity, mdm2 binding activity, GO:0060090, GO:0140677, GO:0098772, GO:0003713, GO:0003714, GO:0016564, GO:0042803, k63]] \n", - "776 [[GO:0003677, GO:0003723, GO:0003682, GO:0006351, GO:0006412, GO:0045292, atpase binding activity, enzyme binding activity, GO:0044183, ubiquitin protein ligase, MESH:C021362, nf-kappab binding activity, GO:0140693, nucleic acid binding activity, heparan sulfate binding activity, biopolymer binding activity, GO:0060090, GO:0140678, g-protein beta-subunit binding activity, molecular sequence recognition, complementary rna strand recognition, mrna 3'-utr]] \n", - "777 [[rna binding activity, identical protein binding activity, mrna 3' utr binding activity, GO:0000900, dna binding activity, ubiquitin protein ligase binding activity, protein domain specific binding activity, GO:0006457, dna replication origin binding activity, dna-binding transcription factor binding activity, GO:0042803]] \n", - "778 [[GO:0006351, GO:0006351, GO:0008284, GO:0071824, GO:0019219, rna binding activity, GO:0010468, GO:0006364]] \n", - "779 [[rna binding activity, dna binding activity, protein binding activity, GO:0006364, GO:0019538, GO:0006351, transcription coregulator binding activity, GO:0022402, GO:0003682, mitochondria regulation, cyclin binding activity, cyclin-dependent protein serine/threonine kin]] \n", - "780 [[GO:0008092, GO:0005201, GO:0044325, ion channel regulator, GO:0003779, GO:0005096, GO:0051879, GO:0017046, GO:0003677, signalling receptor binding, GO:0042802, GO:0048306, GO:0019899, GO:0005509, GO:0005524, GO:0006200, GO:0051117, GO:0004017, GO:0008195, GO:0051015, microfilament binding, GO:0003872, GO:0043138, GO:0004517, MESH:D009243]] \n", - "781 [[GO:0005509, GO:0004129, GO:0003677, GO:0005524, GO:0003779, abnormal growth and development, GO:0002020, structural constituent]] \n", - "782 [[GO:0036211, MESH:D005786, signal transduction regulation, dna-templated transcription regulation, GO:0007219, GO:0016567, GO:0031146, GO:0045893]] \n", - "783 [[GO:0006351, GO:0036211, MESH:D054875, GO:0065007, GO:0007219, GO:0031146, wnt, GO:0016567, GO:0043543, GO:0004879, GO:0003714, transcription corepressor binding activity, GO:0006351, rna polymerase ii-specific dna-binding transcription repressor activity, GO:0045893, GO:0000122, GO:0045737, GO:0010604, GO:0010628, negative regulation of cell different]] \n", - "784 [[GO:0006118, GO:0020037, GO:0005515, GO:0016491, atpase activity & binding activity, GO:0060090, acyl binding activity, GO:0003954, gtp binding activity, iron-sulfur cluster binding activity, fad binding activity, MESH:D010758, GO:0019395, rna binding activity, 4 iron, 4 sulfur cluster binding activity, ubiquitin protein ligase binding activity, GO:0004129, proton-transporting atp synthase activity, lipoic acid binding activity, mhc class i protein binding activity, angiostatin binding activity, deltarasin binding activity, ubiquitin protein binding activity, nadp binding activity]] \n", - "785 [[GO:0140657, GO:0009055, GO:0008553, ubiquitin protein ligase binding activity, MESH:D014451, heme binding activity, protein homodimerization, mhc class i protein binding activity, metal ion binding activity, angiostatin binding activity, mitochondrion targeting sequence binding activity, GO:0015227, rna binding activity, 4 iron, 4 sulfur cluster binding activity, GO:0000295, GO:0004129, fatselytranstransferase activity, GO:0003925, acyl-coa c-acetyltransferase activity, GO:0004774, GO:0003994, GO:0004095, GO:0003958, acetate coa-transfer]] \n", - "786 [[GO:0003700, protein binding activity, protein kinase binding activity, GO:0042803, enzyme binding activity, GO:0098631, signaling receptor binding activity, actin binding activity, cyclin binding activity, GO:0005198, GO:0030695]] \n", - "787 [[dna binding activity, rna binding activity, rna polymerase binding activity, GO:0004672, GO:0042803, protein kinase binding activity, GO:0000988, GO:0003924, GO:0098631, cell signaling receptor binding activity, enzyme binding activity, heme binding activity, collagen binding activity, GO:0004392, GO:0060090, GO:0004527, GO:0042803, g protein-coupled receptor binding activity, GO:0022857, identical protein binding activity, GO:0016787, GO:0008083]] \n", - "788 [[GO:0006351, GO:0016563, atpase-coupled ion transport, GO:0004672, GO:0008233, dna binding activity, GO:0017156, GO:1903530]] \n", - "789 [[transcription regulation, GO:0098609, GO:0007165, GO:0045047, GO:0030041, GO:0051594, GO:0060291, GO:1903561, GO:0030027, GO:0005881, GO:0043195, GO:0005829, GO:0030425, MESH:D012319, dna-templated trans]] \n", - "790 [[molecular binding activity, GO:0003824, GO:0005215, domain binding activity, GO:0006869, GO:0015031, GO:0006259, GO:0016070]] \n", - "791 [[genes involved in this list are primarily associated with the metabolic or structural processes needed for cellular development and homeostasis. enriched terms include fatty acid metabolism, protein homodimerization, MESH:D010084, dna and rna binding, enzyme/acyl-coa/gtpase binding/hydrolase activity, transport/export/import, and regulation of transcription by rna polymerase ii. mechanism: these genes act together to provide a plethora of functions that are integral to the growth, maintenance and protection of cells. fatty acids are transported, oxidized, and bound to proteins or phospholipids in the membrane, proteins interact with atp and gtp and undergo homodimerization, transcriptional activity is regulated by heterodimerizing with transcription factor proteins]] \n", - "792 [[protein binding activity, GO:0016301, GO:0005048, GO:0005102, GO:0051726, apoptosis regulation, GO:0007165, rna binding activity, GO:0004721, GO:0004620, GO:0003924, 1-phosphatidylinositol phospholipase activity, phosphotyrosine residue binding activity, GO:0000774, guanyl ribonucleotide binding activity, GO:0004869, GO:0051219, GO:0044325, GO:0008092, GO:0050750, GO:0003713, GO:0050681, nuclear receptor coactiv]] \n", - "793 [[the genes in this list are involved in several biological functions, including signal transduction, GO:0006915, cellular response to stimuli, response to dna damage, GO:0051726, and regulation of protein phosphorylation and ubiquitination. the terms \"protein phosphorylation\"; \"ubiquitination\"; \"signal transduction\"; \"cellular response to stimulus\"; \"dna damage response\"; \"regulation of cell cycle\"; \"intrinsic apoptosis\"; and \"scaffold protein\" are all statistically over-represented.\\n\\nmechanism: signaling pathways and cellular processes are intricately regulated and require the coordinated participation of different proteins. by performing a term enrichment analysis, we see that the genes in this list are involved in a variety of molecular pathways, including signal transduction, GO:0006915, cellular response to stimuli, response to dna damage, GO:0051726, and regulation of protein phosphorylation and ubiquitination. this suggests that the gene products help coordinate these pathways by forming complexes, binding to signaling molecules, or carrying out the necessary enzyme activities. this suggests the underlying biological mechanism may involve interplay between specific gene products, MESH:D011506, signaling molecules to ensure efficient functioning of the cell]] \n", - "794 [[protein binding activity, GO:0003924, gtp-dependent protein binding activity, snare binding activity, enzyme binding activity, protein kinase binding activity, clathrin binding activity, GO:0006897, retrograde transport, GO:0006893, GO:0006888, GO:0006622]] \n", - "795 [[protein binding activity, activity, GO:0042803, enzyme binding activity, scaffold protein binding activity, snare receptor activity, syntaxin binding activity, GO:0016887, GO:0008553, GO:0008320, metal ion binding activity, protein foldinactivity, GO:0003924, protein kinase binding activity, phosphat]] \n", - "796 [[oxidative stress defense, GO:0098754, dna/rna binding, GO:0006351, GO:0098609, GO:0016043, GO:0019722, GO:0006468, GO:0010731, GO:0004392, GO:0019511, GO:0061621, GO:0005886, GO:0006750, GO:0006082]] \n", - "797 [[MESH:D004734, oxidative stress response, GO:0042803, protein phosphatase 2a binding activity, GO:0004601, GO:0004602, GO:0047499, GO:0003954, chromatin dna binding activity, GO:0004861, GO:0004784, GO:0047184, GO:0015038, GO:0015035, phosphatidylinositol binding activity, GO:0004096, heme binding activity]] \n", - "798 [[GO:0003723, GO:0031491, transcription and regulation, GO:0003677, GO:0004672, protein folding and chaperoning, metabolic regulation, MESH:D054875]] \n", - "799 [[GO:0019899, GO:0005515, ligand binding, GO:0005509, GO:0000166, GO:0008134, GO:0003677, GO:0005525, GO:0042562, GO:0006200, GO:0004672, GO:0003723, GO:0008047, GO:0044183, GO:0003682, GO:0019903, GO:0019212, GO:0008233, GO:0022890]] \n", - "800 [[GO:0007165, regulation of transcription, GO:0051246, regulation of macromolecule metabolism, GO:0050794, interaction with transcription factors, interaction with smad proteins]] \n", - "801 [[tgf binding activity, dna-binding transcription factor binding activity, smad binding activity, GO:0019211, GO:0004674, GO:0004869, GO:0061631, myosin binding activity, r-smad binding activity, beta-catenin binding activity, cadherin binding activity, gtp binding activity, i-smad binding activity, GO:0003924, GO:0003714, GO:0042803, nucleic acid binding activity, serine-type endope]] \n", - "802 [[dna binding transcription factor, GO:0005102, GO:0019899, GO:0005126, growth factor, transmembrane receptor]] \n", - "803 [[GO:0000988, rna polymerase ii-specific, dna-binding, identical protein binding activity, enzyme binding activity, signaling receptor binding activity, GO:0004672, GO:0005125, GO:0008083, GO:0098631, GO:0022857, GO:0016791, gtp binding activity, GO:0140657]] \n", - "804 [[GO:0006457, GO:0003723, transcription activator, GO:0003677, GO:0051082, GO:0003720, GO:0003676, GO:0044325, GO:0005524, GO:0006402, translation regulation, GO:0003755, GO:0035925]] \n", - "805 [[atp binding activity, GO:0016887, enzyme binding activity, identical protein binding activity, GO:0060090, GO:0140678, nucleic acid binding activity, GO:0046983, protein folding chaperone binding activity, ribosome binding activity, rna binding activity, snare binding activity, transcription corepressor binding activity, transcription regulator]] \n", - "806 [[genes included in this set are involved in various cellular functions such as enzyme binding activity, GO:0003924, lipoprotein binding activity, GO:0004620, and other related activities. common enriched terms across these genes include protein binding activity, smad binding activity, dna-binding activity, phosphotyrosine residue binding activity, GO:0003824, GO:0003924, and enzymatic inhibitor activity. mechanism: these genes are likely to be involved in regulation and control of cellular functions and processes through various proteins. this regulation and control is likely being done through interaction of the proteins encoded by these genes with other proteins and structurally with dna, as well as through the enzymatic activities of the encoded proteins]] \n", - "807 [[dna binding activity, GO:0000988, protein binding activity, smad binding activity, GO:0005096, MESH:C062738]] \n", - "808 [[GO:0005515, GO:0003677, binding activity, receptor binding activity, GO:0004672, GO:0007155, GO:0023052, GO:0010468]] \n", - "809 [[gtp binding activity, dna binding activity, GO:0016563, protein kinase binding activity, GO:0004175]] \n", - "810 [[the genes summarized above are all involved in developmental processes, such as organizing and regulating cell adhesion, components of the wnt pathway and regulation of gene expression. the enriched terms for these genes would be development-related terms, such as cell adhesion, GO:0060070, GO:0006468, GO:0016567, GO:0006351, GO:0006476, GO:0006351, and protein stability.\\n\\nmechanism: the underlying biological mechanism involves the involvement of many of these genes in the wnt pathway, which is a conserved signaling pathway involved in cell-cell communication and a variety of developmental processes. another mechanism involves the regulation of gene expression and the binding of dna-binding transcription factors, as well as protein ubiquitination and deacetylation which also control gene expression]] \n", - "811 [[GO:0005515, transcription regulation, GO:0051726, GO:0007165, response pathways]] \n", - "812 [[signaling receptor binding activity, protein kinase binding activity, GO:0061630, GO:0035556, GO:0001816, GO:0010467]] \n", - "813 [[GO:0048018, phosphotyrosine residue binding activity, cytoskeletal protein binding activity, GO:0005574]] \n", - "814 [[transcription repressor and activator activities, rna polymerase ii-specific, nucleic acid binding activity, GO:0009889, GO:0009966, GO:0010468, GO:0045765, and protein-dna complex organization, GO:0042127]] \n", - "815 [[dna-binding, GO:0016563, GO:0016564, GO:0000988, rna binding activity, ubiquitin protein ligase binding activity, GO:0010628, GO:0010629, GO:0009889, GO:0045765, GO:0060828, GO:0009966, transcription cis-regulatory region binding activity, GO:0045944, GO:0003130, GO:0001714]] \n", - "816 [[GO:0005515, GO:0060230, GO:0005543, MESH:M0518050, GO:0050804]] \n", - "817 [[GO:0005515, GO:0043167, GO:0008009, GO:0019838, signal receptor binding, GO:0019902, GO:0016477, GO:0086009, GO:0007165, GO:0065007, GO:0006952]] \n", - "818 [[GO:0005509, double-stranded dna-binding, cell adhesion and migration, transcriptional regulation]] \n", - "819 [[metal ion binding activity, protein binding activity, rna binding activity, GO:0019208, GO:0005243, GO:0042803, calcium ion binding activity, MESH:C086554]] \n", - "820 [[UBERON:0001134, GO:0006936, GO:0016567, GO:0045010, calcium-dependent signaling, GO:0010468, GO:0006468, GO:0043687, GO:0042692, GO:0060537, MONDO:0020121, muscle organelle organization]] \n", - "821 [[actin binding activity, GO:0007015, muscle alpha-actinin binding activity, GO:0006936, GO:0060415, GO:0071689, GO:0004672, protein phosphatase binding activity, GO:0043502, tropomyosin binding activity, troponin binding activity, troponin complex activities]] \n", - "822 [[protein signaling, GO:0006468, GO:0016567, GO:0015031, GO:0030030, GO:0006897, GO:0006898, GO:0035091, GO:0001766, GO:0097320]] \n", - "823 [[GO:0006897, GO:0005515, GO:0006869, GO:0016567, GO:0042632, GO:0035727]] \n", - "824 [[GO:0019538, enzymatic activity, protein transcription, cell metabolism, carbohydrate phosphorylation and metabolism, protein homeostasis, cell signaling, GO:0008104, cell homeostasis, cellular energy production]] \n", - "825 [[GO:0003824, GO:0031625, protein homodimerization, GO:0016310, GO:0006096, GO:1904659, GO:0070061, GO:0004332, GO:0004618, GO:0004619, GO:0004396, peptidoglycan binding activity, GO:0003872, GO:0004807, GO:0004347, GO:0021762, binding activity of sperm to zona pellucida, GO:0030388, GO:0019725, GO:0046716, GO:0071456, GO:0016525, UBERON:2005050]] \n", - "826 [[GO:0097553, GO:1990034, GO:0071318, GO:0007186, GO:0035235, GO:1990454, GO:0017146, GO:0014066, GO:1900274, GO:0099509, GO:2000300, GO:0032680, GO:0005245, GO:2000311, GO:0080164]] \n", - "827 [[GO:0006816, regulation of calcium]] \n", - "828 [[these genes are involved in several cellular activities, primarily in their roles in signal transduction pathways, GO:0036211, protein folding and stability, GO:0051726, and apoptosis. the terms enriched are: signaling receptor activity; protein phosphorylation; regulation of macromolecule biosynthetic process; autophagy; g2/m transition of mitotic cell cycle; chromosome segregation; cytoplasmic stress granule; torc1 signaling; defense response; anoikis; protein folding chaperone; histone acetylation; i-kappab kinase/nf-kappab signaling; k63-linked polyubiquitin modification-dependent protein binding activity.\\n\\nmechanism: these genes participate in a variety of biological processes, including signal transduction pathways, GO:0036211, GO:0051726, apoptosis and dna-templated transcription, answering to different external and internal stimuli as well as aiding in cell survival and death. the enriched terms involve protein-protein interactions and modifications, as well as involvement in akt/pi3k, tor, and nf-kb pathways that are essential for cell signaling, typical in response to bacterial infection and the activation of pro-survival mechanisms]] \n", - "829 [[protein binding activity, metal ion binding activity, protein kinase binding activity, GO:0030295, protein folding chaperone activity, GO:0042803, chromatin binding activity, GO:0003713, GO:0016410, GO:0016538, GO:0016303, card domain binding activity, heat shock protein binding activity, muramyl dipeptide binding activity, 14-3-3 protein binding activity, rna polymerase iii cis-regulatory region sequence-specific dna binding activity]] \n", - "830 [[the genes in this list share functions involving glycoprotein and carbohydrate metabolic processes and structural functions related to extracellular matrix organization. enriched terms include: dihydroceramidase activity, GO:0017040, GO:0061463, GO:0004134, GO:0004135, GO:0004556, hyaluronic acid binding activity, GO:0004415, GO:0004568, GO:0008843, clathrin heavy chain binding activity, GO:0008422, GO:0004348, GO:0004336, GO:0004553, GO:0008375, GO:0004563, identical protein binding activity, syndecan binding activity, heparan sulfate proteoglycan binding activity, GO:0003796, GO:0004567]] \n", - "831 [[GO:0006516, GO:0006027, heparan sulfate catabolism, glucoside catabolism, GO:0036508, GO:0006517, GO:0005975, GO:0006869, GO:0030214, receptor signaling, GO:0031589, GO:0009313, GO:0004672, GO:0008283, GO:0019915, GO:0050885, GO:0042742, GO:0005989, GO:0008344, GO:0007605, GO:0006487, GO:0006281, GO:0071451, peptidyl-serine]] \n", - "832 [[immunoglobulin receptor binding activity, antigen binding activity, fc-gamma receptor i complex binding activity, GO:0004715, phosphotyrosine residue binding activity, peptidoglycan binding activity, phosphatidylcholine binding activity. mechanism: the genes listed appear to be involved in the regulation of the immune response. they likely aid in the recognition of pathogens, binding to the appropriate receptors, triggering a signal for an immune response. they may also play a role in enabling the recognition of self-antigens inhibiting a response to them]] \n", - "833 [[antigen binding activity, immunoglobulin receptor binding activity, GO:0098542, GO:0002253, fc-gamma receptor i complex binding activity, GO:0004715, peptidoglycan binding activity, phosphatidylcholine binding activity, GO:0007229, GO:0038187, mannose binding activity, phosphotyrosine residue binding activity, GO:0051130, GO:0045657, protection of host from foreign agent]] \n", - "834 [[these genes are involved in processes related to dna binding, repair, replication, recombination, and regulation thereof. the enriched terms would be: dna binding, GO:0003690, dna damage repair, GO:0006310, GO:0005515, meiotic recombination, GO:0007059, GO:0000278, GO:0071173, GO:0051289, GO:0003682, resolution of meiotic recombination intermediates. \\nmechanism: the underlying biological mechanism is that these proteins work together to maintain genomic stability, regulate gene expression, promote proper cell division, germline cell development, meiosis]] \n", - "835 [[GO:0140013, dna binding activity, GO:0006259, GO:0035825, telomere attachment, GO:0000785, GO:0000795, GO:0005694, GO:0005737]] \n", - "836 [[calcium ion binding activity, identical protein binding activity, GO:0004252, GO:0140314, calcium-dependent protein binding activity, arginine binding activity, GO:0140313, enzyme binding activity, GO:0019887, nf-κb binding activity, nuclear localization sequence binding activity, oxysterol binding activity, rage receptor binding activity, ubiquitin protein ligase binding activity, actin binding activity, rig-i binding activity, GO:0003713, zinc ion binding activity, GO:1903231]] \n", - "837 [[protein binding activity, GO:0140313, GO:0000988, GO:0019887, calcium ion binding activity, dna-binding activity, ubiquitin protein ligase binding activity, tumor necrosis factor binding activity, regulatory pathway activity]] \n", - "838 [[enzyme binding activity, acid binding activity, molecule transport, adapter binding activity, receptor binding activity, dna binding activity, protein binding activity, GO:0003824, GO:0016787, GO:0016491, anion binding activity, GO:0008233, GO:0140657, thioredoxin activity, translocation, GO:0061630, cysteine endopeptidase activity, GO:0004738, GO:0004618, magnesium ion binding activity, GO:0004340, GO:0003924]] \n", - "839 [[cytoskeleton protein binding, phosphatase binding activity, GO:0016491, cell development and signaling activity, dna binding activity, cellular transporter activity, protein kinase binding activity]] \n", - "840 [[peroxisome biogenesis, protein import into peroxisome, GO:0000425, GO:0000268, GO:0140036, GO:0006631, protein homodimerization, enzyme binding activity, GO:0050821, GO:0043335]] \n", - "841 [[GO:0016558, GO:0050821, GO:0042127, protein-lipid binding, GO:0007031, GO:0008611, GO:0001881, GO:0006631]] \n", - "842 [[GO:0003677, GO:0005515, GO:0046872, cellular response to radiation, hypoxia, and starvation, GO:0042981, GO:0032204, GO:0010835, GO:0045069]] \n", - "843 [[dna damage and repair, GO:0005515, GO:0046872, homodimerization, GO:0006915, MESH:D016922, GO:0001666]] \n", - "844 [[GO:0005216, GO:0016917, GO:0008066, GO:0007186, GO:0007214, GO:0006836, GO:0005249, GO:0005248, GO:0007193]] \n", - "845 [[GO:0005216, membrane potential regulation, GO:0015276, g protein-coupled receptor signaling, GO:1902476, GO:0007214, GO:0071805]] \n", - "846 [[dna-binding, rna polymerase ii-specific activity, GO:0046872, GO:0031625, GO:0045944, GO:0002639, GO:1901184, GO:0033157, monoatomic cation]] \n", - "847 [[transcription regulation, nucleic acid metabol]] \n", - "848 [[g protein-coupled receptor binding activity, GO:0003924, enzyme binding activity, GO:0042803, signaling receptor binding activity, GO:0004016, g-protein beta/gamma-subunit complex binding activity, signaling receptor binding activity, clathrin light chain binding activity, sequence-specific double-stranded dna binding activity, GO:0004672, nf-kappab binding activity, protein kinase a catalytic subunit binding activity, GO:0004674]] \n", - "849 [[GO:0004672, g-protein activity, g-protein beta/gamma- subunit complex binding activity, atpase binding activity, GO:0004016, protein-folding chaperone binding activity, signal receptor binding activity, GO:0071333, GO:0007165, negative regulation of nf-kappa b transcription factor activity, GO:2000394, GO:0007212, cellular response to prostaglandin e, GO:0007204]] \n", - "850 [[GO:0003677, GO:0003723, GO:0003682, GO:0008134, GO:0003713, GO:0016564, MESH:M0518050, GO:0019899]] \n", - "851 [[GO:0006351, dna-binding, rna polymerase ii-specific, transcription activator/transcription repressor, cis-regulatory region sequence-specific, GO:0001221, GO:0006355, GO:0006337, GO:0009966]] \n", - "\n", - "prompt_variant v2 \\\n", - "0 [[GO:0032964, matrix maturation, GO:0031012, MESH:D006023, MESH:D015238, zinc finger proteins, proteolytic subunits, MESH:D057057, MESH:M0465019]] \n", - "1 [[GO:0032964, GO:0030198, GO:0006457, GO:0006955]] \n", - "2 [[GO:0006281, GO:0035825, fanconi anemia pathway]] \n", - "3 [[GO:0006281, GO:0035825, MESH:D051856, rad51 family proteins, chromosome stability maintenance\\n\\nmechanism: these genes are involved in dna damage repair and maintenance of genome stability, particularly through homologous recombination and the formation of the fanconi anemia complementation group proteins. the rad51 family proteins and chromosomal stability maintenance are also important in these processes]] \n", - "4 [[mitochondrial function, GO:0008152, GO:0006118, GO:0006631, redox reactions]] \n", - "5 [[mitochondrial function; energy metabolism; lipid metabolism; electron transport chain. \\n\\nmechanism: these genes likely contribute to the production and regulation of energy in the form of atp through processes including beta-oxidation of lipids, GO:0006119, and electron transport chain activity. dysfunction or dysregulation of these genes may lead to mitochondrial dysfunction and impaired energy metabolism, which have been implicated in various diseases including neurodegenerative disorders, MONDO:0004995, MONDO:0005066]] \n", - "6 [[GO:0005125, GO:0042110, GO:0042379, GO:0002429, GO:0032623, GO:0032609, GO:0002504, GO:0050776, GO:0030217, GO:0050900, GO:0060333, GO:0001819, GO:0002685, GO:0070098, GO:0050852]] \n", - "7 [[GO:0008009, cytokine signaling, GO:0019882]] \n", - "8 [[GO:0004672, GO:0031344, GO:0008285, GO:0010468, regulation of cellular protein localization and movement]] \n", - "9 [[GO:0004672, GO:0008134, GO:0006810, enzymatic activity, GO:0006511, GO:0061024, GO:0042445, GO:0016567]] \n", - "10 [[GO:0030198, GO:0007155, GO:0030199, GO:0006029, GO:0045765, GO:0009611]] \n", - "11 [[GO:0030198, GO:0007155, GO:0007088, protein kinase activity regulation, GO:0070848, cellular response to transforming growth factor beta stimulus\\n\\nmechanism: the genes listed are involved in the organization of the extracellular matrix and cell adhesion. specifically, they play roles in binding to and regulating the spacing of collagen fibrils, inhibiting proteases, promoting cell-cell and cell-matrix interactions, and regulating mitosis and protein kinase activity. growth factors and transforming growth factor beta are also involved in signal transduction pathways that are regulated by these genes]] \n", - "12 [[GO:0007155, GO:0007010, GO:0005925, GO:0070160]] \n", - "13 [[GO:0070160, GO:0007155, GO:0008014, integrin, GO:0007165, adhesion g-protein coupled receptor (gpcr), GO:0015629, UBERON:4000022, protein tyrosine kinase (ptk), GO:0016303, map kinase, MESH:D016212]] \n", - "14 [[GO:0007166, GO:0007169, GO:1901796, GO:0019048, GO:0045785, GO:0043408, GO:2000145, GO:0032956, GO:0051897, GO:0048015, GO:0010810, GO:0030334, regulation of cell growth\\n\\nmechanism and hypotheses: the enriched terms suggest a common mechanism involving transmembrane signaling pathways, with a focus on cell adhesion, migration, and growth regulation. several of the genes are involved in the regulation of the mapk signaling pathway, which is known to play a central role in cellular processes such as proliferation, differentiation, and apoptosis. pathway analysis of these genes may further elucidate the specific regulatory mechanisms at play]] \n", - "15 [[GO:0007160, GO:0006811, GO:0007165, GO:0098631, insulin regulation, GO:0016485]] \n", - "16 [[GO:0006915, GO:0008219, GO:0007165]] \n", - "17 [[GO:0097153, GO:0042981, positive regulation of dna fragmentation, GO:0043067, GO:0010941, GO:1901796, GO:0006974, GO:0070613]] \n", - "18 [[GO:0006869, GO:0008203, GO:0006631, peroxisomal biogenesis, GO:0004448, GO:0008146]] \n", - "19 [[GO:0007031, GO:0001676, GO:0006699, GO:0008202, GO:0008203, GO:0001523, GO:0006635, alpha-oxidation, GO:0006720, lipid metabolic process \\n\\nmechanism: these genes function in a variety of processes involved in lipid metabolism and peroxisome biogenesis. peroxisomes are intracellular organelles involved in many metabolic pathways, including fatty acid beta-oxidation, which our enriched terms suggest is a common theme among these genes. additionally, these genes are involved in the synthesis of bile acids, steroid hormones, and retinoids, highlighting the importance of lipid metabolism in cellular function]] \n", - "20 [[GO:0006629, GO:0006869, GO:0008610]] \n", - "21 [[GO:0006695, GO:0006644, GO:0006633, GO:0016125]] \n", - "22 [[GO:0007596, extracellular matrix remodeling, GO:0030449]] \n", - "23 [[extracellular matrix breakdown, GO:0007596, protein inhibition]] \n", - "24 [[GO:0008233, GO:0007596, GO:0006956]] \n", - "25 [[GO:0006956, GO:0007596, GO:0006955, GO:0030168, cytokine signaling, GO:0002685, response to virus.\\n\\nmechanism: these genes are involved in regulating different aspects of immune response, including complement activation, platelet activation, cytokine signaling, and leukocyte migration. they are also involved in blood coagulation, which can be activated during an immune response to prevent pathogen spread. the over-representation of these genes suggests that immune activation and regulation are key to the identified biological process]] \n", - "26 [[GO:0006281, transcription initiation, GO:0009117]] \n", - "27 [[GO:0006281, transcription regulation]] \n", - "28 [[GO:0006260, GO:0006281, GO:0051276]] \n", - "29 [[GO:0006260, GO:0006281, cell-cycle checkpoint regulation]] \n", - "30 [[GO:0030198, GO:0007155, GO:0005518, actin binding activity, GO:0007229, GO:0001501, GO:0005201, GO:0006936, GO:0005604, GO:0031012, GO:0008009, GO:0008083, GO:0016860, GO:0006508, GO:0005125]] \n", - "31 [[GO:0030198, GO:0006936, GO:0007155]] \n", - "32 [[MESH:D002352, MESH:D004798, MESH:D008565, GO:0000981, receptors, MESH:D003598]] \n", - "33 [[GO:0006631, GO:0006811, GO:0010468]] \n", - "34 [[GO:0005515, GO:0007165, GO:0019899, GO:0005737, GO:0043687, GO:0006355, GO:0006915, GO:0045860, positive regulation of cell proliferation.\\n\\nmechanism/]] \n", - "35 [[GO:0007165, GO:0004672, g-protein coupled receptor signaling pathway, GO:0055085, GO:0035556, GO:0004721, GO:0006468, zinc ion binding. \\n\\nhypotheses: the enriched terms suggest that the genes in this list are involved in regulatory mechanisms that help to control intracellular signaling cascades and protein expression through phosphorylation and dephosphorylation of proteins, and zinc ion binding. additionally, these genes may play a role in transmembrane transport and regulation of ion channels]] \n", - "36 [[GO:0006631, GO:0005975, amino acid metabolism, mitochondrial function, oxidative stress response]] \n", - "37 [[GO:0006631, energy production, mitochondrial function, GO:0006629, oxidation-reduction process, GO:0006637, GO:0006099, MESH:D014451, GO:0019752, GO:0015936, GO:0006084, GO:0022900]] \n", - "38 [[GO:0051726, GO:0006260, GO:0006281]] \n", - "39 [[GO:0006260, GO:0051726, GO:0006281, GO:0007059, GO:0000910]] \n", - "40 [[GO:0006096, GO:0005975]] \n", - "41 [[GO:0052574, GO:0006006, protein kinase binding activity, GO:0006090, GO:0006024, GO:0015012, GO:0006098, GO:0006096, rna polymerase iii transcription initiation, GO:0051287, GO:0022618, GO:0030199, GO:0008408, GO:0042803, atp-binding cassette transporter activity]] \n", - "42 [[neuronal development, GO:0007155, GO:0007165, GO:0016477, GO:0010977, GO:0001525, MESH:D018121, transcriptional regulation]] \n", - "43 [[GO:0007155, GO:0007411, neuronal proliferation and differentiation, GO:0007165, GO:0001525]] \n", - "44 [[GO:0006810, GO:0005488, MESH:D008565, MONDO:0018815, solute carrier (slc) family of transporters]] \n", - "45 [[GO:1904659, GO:0003723, GO:0003677, GO:0000988, GO:0006811, GO:0019899, GO:0042826, GO:0140657, GO:0003824, GO:0008270]] \n", - "46 [[GO:0006096, GO:0006006, GO:0005515, transcription regulation]] \n", - "47 [[GO:0006096, GO:0016310, GO:0006006, GO:0051726, GO:0007165, transcriptional regulation, heparan sulfate biosynthesis]] \n", - "48 [[cytokine signaling, GO:0042110, GO:0042113, GO:0007159, GO:0030593, GO:0050900]] \n", - "49 [[GO:0004896, GO:0007166, GO:0045321, GO:0050900, GO:0006955, GO:0006954, GO:0002250, GO:0070663, GO:0002521, GO:0042110, GO:0042113, GO:0046649]] \n", - "50 [[GO:0004896, GO:0050778, GO:0007155, GO:0019221, GO:0002687]] \n", - "51 [[GO:0004896, GO:0019221, GO:0050776, GO:0050900, apoptosis regulation, GO:0006954, antimicrobial response]] \n", - "52 [[GO:0005125, GO:0008009, GO:0004930, GO:0050900, inflammation\\n\\nmechanism]] \n", - "53 [[GO:0004896, GO:0004930, GO:0004950, GO:0004888, GO:0004896]] \n", - "54 [[interferon response, GO:0051607, GO:0006955]] \n", - "55 [[GO:0140888, GO:0045087, GO:0051607, cytokine signaling, GO:0019882, ubiquitin-mediated proteolysis\\n\\nmechanism: these genes are involved in the innate immune response and antiviral activity, particularly in the interferon signaling pathway. they encode proteins that regulate cytokine signaling, antigen processing and presentation, and ubiquitin-mediated proteolysis. the functions of these genes suggest a coordinated response to viral infection, with the interferon signaling pathway acting as a central mediator of the antiviral response]] \n", - "56 [[GO:0006955, GO:0019221, chemokine signaling pathway, GO:0019882]] \n", - "57 [[GO:0045087, GO:0051607, GO:0005125, GO:0009615, GO:0001817, GO:0051607, GO:0032481, type i interferon signaling pathway. \\n\\nmechanism/]] \n", - "58 [[GO:0005509, GO:0005245, GO:0006811, GO:0015085, GO:0005388, GO:0019722, GO:0055074, GO:0048306]] \n", - "59 [[GO:0005509, GO:0042981, GO:0055085, GO:0006811, GO:0006468]] \n", - "60 [[GO:0044425, GO:0007165, GO:0003824]] \n", - "61 [[cytokine signaling, growth factor signaling, coagulation and complement activation, enzymatic activity regulation]] \n", - "62 [[microtubule organization, GO:0007098, GO:0030036, GO:0051726, GO:0071539]] \n", - "63 [[GO:0008017, GO:0008574, GO:0007098, GO:0051225, GO:0003774, GO:0007010]] \n", - "64 [[GO:0006457, GO:0006006, microtubule organization and biogenesis, GO:0000502, GO:0043043, GO:0042254]] \n", - "65 [[GO:0008152, GO:0009117, GO:0006629, GO:0005975, GO:0006457, GO:0030163, GO:0010468, GO:0000988, GO:0003682]] \n", - "66 [[GO:0042254, GO:0000394, GO:0006412, GO:0006412, GO:0006457, chaperonin-mediated protein folding]] \n", - "67 [[GO:0042254, GO:0006413, GO:0006414, GO:0006397]] \n", - "68 [[GO:0006364, ribosomal subunit biogenesis, GO:0003723, nucleolar function, GO:0006412]] \n", - "69 [[GO:0006364, GO:0005730, GO:0003723, ribosomal biogenesis, GO:0051726]] \n", - "70 [[GO:0006936, muscle metabolism, GO:0007010]] \n", - "71 [[GO:0005861, MESH:M0013780, MESH:D018995, GO:0006936, GO:0005509, sarcomere assembly, MESH:D024510]] \n", - "72 [[GO:0007219, basic helix-loop-helix transcription factor activity, GO:0016567, GO:0016563, GO:0005102, GO:0097153, GO:0006468]] \n", - "73 [[GO:0007219, GO:0016567, transcriptional regulation, GO:0001709]] \n", - "74 [[GO:0005739, GO:0006119, GO:0022900, MESH:D004734, GO:0031966, MESH:D024101]] \n", - "75 [[GO:0005746, GO:0006754, GO:0022900, GO:0006119]] \n", - "76 [[cyclin family, GO:0006281, GO:0008083, GO:0004672, GO:0000988, zinc finger protein]] \n", - "77 [[GO:0008083, transcriptional regulation, GO:0006915, GO:0006281]] \n", - "78 [[GO:0006006, insulin regulation, GO:0031016, GO:0006096, GO:0006094, GO:0030073, hormone regulation]] \n", - "79 [[GO:0006006, GO:0030073, pancreatic islet development, neuroendocrine differentiation]] \n", - "80 [[GO:0140359, GO:0055085, atp-binding cassette, GO:0043574, GO:0006631, GO:0006839]] \n", - "81 [[GO:0005777, GO:0006631, beta-oxidation, MESH:D018384, antioxidant defense mechanism, coenzyme a ligase, aldehyde dehydrogenase family, MESH:D009195]] \n", - "82 [[GO:0004672, intracellular signaling, GO:0050794]] \n", - "83 [[GO:0016301, GO:0006468, GO:0007165]] \n", - "84 [[GO:0005794, membrane trafficking, GO:0016192, GO:0015031, GO:0006906, GO:0035493, GO:0005793]] \n", - "85 [[GO:0007030, GO:0006888, GO:0016192, GO:0007040, sorting nexin-containing complex, GO:0030665, GO:0032880]] \n", - "86 [[antioxidant activity; redox regulation; catalytic activity, UBERON:0035930, such as water and oxygen. the over-representation of terms related to antioxidant activity, redox regulation, and responding to oxidative stress suggest that these genes are involved in maintaining the balance between oxidants and antioxidants in the body, help protect against oxidative damage]] \n", - "87 [[oxidative stress response, antioxidant defense, regulation of reactive oxygen species, GO:0006749, superoxide anion radical metabolism, peroxiredoxin-mediated detoxification]] \n", - "88 [[GO:0008584, GO:0007283, GO:0097722, GO:0007340, GO:0048232, testicular germ cell proliferation\\n\\nmechanism and]] \n", - "89 [[GO:0006811, GO:0006468, MESH:D054875, GO:0007283, receptor signaling]] \n", - "90 [[tgf-beta signaling pathway, transcriptional regulation, GO:0007165, cell growth and differentiation]] \n", - "91 [[tgf-beta signaling pathway, GO:0030509, GO:0071141, GO:0004674, GO:0008134, GO:0006468, GO:0030154, GO:0060348, GO:0042981, GO:0034436]] \n", - "92 [[GO:0004950, GO:0005125, GO:0006955, GO:0006954, GO:0050900, GO:0007165]] \n", - "93 [[interleukin signaling, GO:0032602, GO:0006955]] \n", - "94 [[endoplasmic reticulum stress response, GO:0006457, GO:0008380, GO:0006402, mrna localization, translation regulation, stress response]] \n", - "95 [[GO:0006457, GO:0061077, GO:0015031, GO:0006413, GO:0003723, MESH:D020365, GO:0042254, aminoacyl-trna synthesis, GO:0005783, MESH:D005786]] \n", - "96 [[GO:0030198, GO:0007155, GO:0006811, GO:0004672, transcription regulation, receptor signaling pathway]] \n", - "97 [[GO:0030198, GO:0030155, GO:0006468, positive regulation of cellular signaling pathway activity, GO:0022604, GO:0072659]] \n", - "98 [[GO:0006810, GO:0008152, GO:0003824]] \n", - "99 [[GO:0003723, GO:0003677, GO:0000166, GO:0006396, GO:0006260]] \n", - "100 [[GO:0016055, transcriptional regulation, cell cycle progression]] \n", - "101 [[GO:0016055, GO:0051726, transcriptional regulation]] \n", - "102 [[cytokine, MESH:D007378, MESH:D011948, GO:0005530, GO:0008180, GO:0000502, protein tyrosine phosphatase, MESH:D010770, GO:0000981]] \n", - "103 [[cytokine signaling, tnf-receptor superfamily, GO:0006955, GO:0007165, GO:0019882, cell proliferation and survival, protein phosphorylation and kinase activity]] \n", - "104 [[MESH:D047108, GO:0001709, cell cycle progression]] \n", - "105 [[MESH:D047108, GO:0048863, pluripotent stem cell, transcription factor regulation, homeobox protein]] \n", - "106 [[GO:0031012, GO:0007155, MESH:D011509, GO:0005202, integrin]] \n", - "107 [[GO:0030198, GO:0007155, GO:0016477, GO:0009888, GO:0042246, signaling pathway regulation, GO:0030168]] \n", - "108 [[GO:0006351, GO:0005515, MESH:D016335, GO:0005509, MESH:D008565]] \n", - "109 [[calcium binding, receptor protein activity, GO:0000988, GO:0005515]] \n", - "110 [[GO:0006936, GO:0005509, GO:0043269, GO:0032516, GO:0051015]] \n", - "111 [[GO:0006936, GO:0005509, GO:0051015, GO:0043462, GO:0097009, GO:0006811]] \n", - "112 [[GO:0006897, GO:0007010, GO:0007165, GO:0006629, GO:0060348, brain development. \\n\\nhypotheses: these genes may be involved in common pathways related to endocytic vesicle trafficking, cytoskeletal organization, and signal transduction. some of the genes are associated with lipid metabolism and bone and brain development, suggesting their potential roles in cellular processes related to these functions]] \n", - "113 [[GO:0006897, intracellular trafficking, cytoskeletal reorganization]] \n", - "114 [[GO:0006096, GO:0006006, MESH:D004734]] \n", - "115 [[GO:0006096, GO:0006006, GO:0004743, GO:0019682, GO:0006000, phosphoenolpyruvate metabolic process]] \n", - "116 [[GO:0006816, intracellular calcium homeostasis, ionotropic glutamate receptor regulation, nmda receptor subunits, sodium/calcium exchanger proteins, trp ion channel family]] \n", - "117 [[GO:0005509, GO:0005262, GO:0004970, calcium-mediated signaling pathway, GO:0007268, GO:0031175, GO:0005216]] \n", - "118 [[MESH:D002470, GO:0016301, GO:0009966, GO:0001558, GO:0042981, GO:0010506, GO:0032006]] \n", - "119 [[GO:0016049, GO:0004672, GO:0006955, GO:0007165, GO:0000988, neuronal development, GO:0006468]] \n", - "120 [[glycosyl hydrolase activity, degradation of carbohydrates, GO:0006032, GO:0030211, GO:0003796, GO:0030214]] \n", - "121 [[GO:0016787, GO:0044248, GO:0006027, GO:0005764]] \n", - "122 [[GO:0019731, GO:0098542, GO:0002253, immunoglobulin receptor binding activity]] \n", - "123 [[antigen binding activity, immunoglobulin receptor binding activity, GO:0002253]] \n", - "124 [[GO:0140013, GO:0035825, GO:0007059, GO:0006281, GO:0000795]] \n", - "125 [[meiotic recombination, GO:0006281, GO:0007059, GO:0035825, holliday junction resolution, double-strand dna binding, GO:0007276, GO:0007130]] \n", - "126 [[GO:0006955, GO:0051726, GO:0046907]] \n", - "127 [[GO:0051726, GO:0006955, GO:0005515]] \n", - "128 [[GO:0006457, GO:0006006, microtubule organization and biogenesis, GO:0000502, GO:0043043, GO:0042254]] \n", - "129 [[GO:0000502, GO:1904659, GO:0008152, GO:0003676, GO:0044183, GO:0005524, GO:0005783, GO:0005739, GO:0006096, GO:0006631]] \n", - "130 [[peroxisome biogenesis, peroxisomal protein import, peroxin proteins, MONDO:0019234, neonatal adrenoleukodystrophy, MONDO:0019609, MONDO:0009959, MONDO:0008972, MONDO:0009958]] \n", - "131 [[peroxisome biogenesis, GO:0005777, GO:0017038]] \n", - "132 [[GO:0005652, GO:0005635, GO:0006281]] \n", - "133 [[GO:0006997, GO:0006281, chromatin structure organization, GO:0000723]] \n", - "134 [[GO:0005216, GO:0031175, GO:0007268, GO:0042391]] \n", - "135 [[GO:0005267, chloride ion transmembrane transport, GO:0042391, GO:0034220, GO:0030594]] \n", - "136 [[MONDO:0015626, MONDO:0007790, MONDO:0005244, myelin sheath maintenance, GO:0006264]] \n", - "137 [[GO:0042552, GO:0007422, GO:0016567, er-associated protein degradation.\\n\\nmechanism/]] \n", - "138 [[g-protein signaling, GO:0007165, neurotransmitter activity]] \n", - "139 [[g-protein signaling pathway, GO:0030594, GO:1902531]] \n", - "140 [[transcription regulation, GO:0006338, GO:0003700]] \n", - "141 [[GO:0003700, GO:0006355, GO:0006325, GO:0010468, transcription factor complex\\n\\nmechanism: these genes all play a role in regulating transcription, primarily at the level of dna binding and chromatin organization. they are involved in the regulation of gene expression and the formation of transcription factor complexes]] \n", - "142 [[GO:0030198, GO:0043062, GO:0030199, GO:0006486, GO:0008233, GO:0008270]] \n", - "143 [[GO:0032963, GO:0030198, GO:0031012]] \n", - "144 [[GO:0006281, GO:0006325, GO:0006312, GO:0006302, GO:0035825, GO:0006260]] \n", - "145 [[fanconi anemia pathway, GO:0035825, GO:0006302]] \n", - "146 [[GO:0006629, GO:0006631, mitochondrial function, GO:0006119, GO:0006099, beta-oxidation of fatty acids, GO:0006084, GO:0006637, GO:0015980, GO:0005975]] \n", - "147 [[GO:0005740, GO:0006122]] \n", - "148 [[GO:0002376, GO:0042110, GO:0019221, GO:0019882, GO:0030098, GO:0050900, GO:0050778, GO:0050777, GO:0001817]] \n", - "149 [[GO:0042110, cytokine signaling, GO:0019882, GO:0006955, chemokine signaling, interferon signaling, GO:0030183, GO:0050900]] \n", - "150 [[GO:0016567, GO:0036211, GO:0008134, GO:0045892, GO:0071535, GO:0031647, GO:0043161]] \n", - "151 [[regulation of transcription, GO:0005515, GO:0007155, GO:0007165, GO:0016126]] \n", - "152 [[GO:0030198, GO:0070848, GO:1903010, GO:0042060]] \n", - "153 [[GO:0030198, GO:0001525, GO:0007155]] \n", - "154 [[GO:0007155, GO:0007010, GO:0048041, regulation of actin cytoskeleton, GO:0051017, GO:0046847, GO:0035023]] \n", - "155 [[GO:0007155, GO:0016477, GO:0048870, GO:0007229, GO:0008360, focal adhesion\\n\\nmechanism: the enriched terms suggest that the common function of these genes is involved in cell adhesion and migration. these processes are essential for various biological functions such as wound healing, inflammation, and embryonic development. integrin-mediated signaling pathway and focal adhesion are two crucial pathways in cell adhesion and migration, which are perturbed in many types of cancer and autoimmune diseases. these findings may shed light on the underlying mechanism and potential targets for drug development]] \n", - "156 [[GO:0007155, GO:0023052, GO:0006810]] \n", - "157 [[GO:0007155, GO:0007186, GO:0010906, GO:0050796, GO:0070528, GO:0043406, GO:0050731, GO:0051897, GO:0061024, GO:0043066]] \n", - "158 [[GO:0006915, GO:0012501, regulation of cell death\\n\\nmechanism: these genes are involved in various processes that regulate cell death. they participate in the apoptotic process, the programmed cell death that occurs in multicellular organisms. apoptosis is a complex physiological process that is essential for development and homeostasis in healthy adult tissues. these genes also contribute to the regulation of cell death, preventing or promoting apoptosis under specific conditions]] \n", - "159 [[GO:0097153, GO:0006915, GO:0006954, GO:0008285, GO:0050871, GO:0001819, GO:0045944, GO:0004672, GO:0046328, GO:0010803]] \n", - "160 [[peroxisome organization; steroid metabolic process; cholesterol metabolic process; fatty acid metabolic process; lipid metabolic process\\n\\nmechanism: \\n\\nthese genes are involved in various metabolic pathways, especially those related to lipid and sterol metabolism. many of these genes are involved in the transport of lipids and cholesterol, including the abc transporters abca1, abca2, abca3, abca4, abca5, abca6, abca8, abca9, and abcg4. other genes such as cat, ch25h, crot, cyp7a1, GO:0033783, MESH:D013253, dhcr24, and hsd17b6 are involved in the synthesis, GO:0009056, and modification of cholesterol and sterols. \\n\\nadditionally, these genes are also involved in peroxisome biogenesis and function, with genes such as pex1, pex11a, pex11g, pex12, pex13, pex16, pex19, pex26, MESH:D010758]] \n", - "161 [[GO:0006695, GO:0006629, GO:0007031, peroxisome biogenesis, GO:0008202, GO:0006635, GO:0006699, GO:0015908, GO:0006886]] \n", - "162 [[GO:0006695, GO:0006629, GO:0045540, GO:0019216, GO:0016126]] \n", - "163 [[GO:0006695, GO:0006694, GO:0006629]] \n", - "164 [[GO:0030198, GO:0030574, GO:0007596, GO:0042730, GO:0002576, GO:0052547, GO:0045055, GO:0045862]] \n", - "165 [[GO:0007596, GO:0006955]] \n", - "166 [[GO:0006956, GO:0002576, GO:0050776, GO:0009611, blood coagulation\\n\\nmechanism: genes involved in complement activation, platelet degranulation, regulation of immune response, response to wounding, and blood coagulation are enriched in this gene set. these functions are related to the prevention of thrombosis and regulation of the immune system]] \n", - "167 [[GO:0006955, GO:0007596, GO:0006508, GO:0030168, GO:0006954, GO:0010952]] \n", - "168 [[GO:0006260, GO:0006281, dna binding and packaging, GO:0009117, GO:0006338]] \n", - "169 [[GO:0006260, GO:0006281, transcription elongation, GO:0006396, GO:0009117, GO:0003682]] \n", - "170 [[GO:0006260, GO:0007049, GO:0007052, GO:0007059, GO:0007346, GO:0006281, GO:0006334]] \n", - "171 [[GO:0006260, GO:0006281, GO:0051726, GO:0007059]] \n", - "172 [[GO:0030198, GO:0030199, GO:0032964, GO:0071711, regulation of growth factor signaling, regulation of bmp signaling, regulation of tgf-beta signaling]] \n", - "173 [[GO:0030198, GO:0007155, GO:0007229, GO:0030574, GO:0009888, GO:0016477, GO:0071711]] \n", - "174 [[GO:0005509, GO:0006816, GO:0005516, GO:0010857, GO:0055074, GO:0005262, GO:0030899]] \n", - "175 [[GO:0006811, GO:0023051, transport of small molecules, GO:0072657, GO:0009966, GO:0008202, GO:0010817, GO:0048522, GO:0010468, GO:0043066, GO:0051246, GO:0071363]] \n", - "176 [[GO:0005509, GO:0051302, GO:0042981, GO:0006816]] \n", - "177 [[GO:0051726, GO:0008283, GO:0006260, GO:0051301, cancer progression]] \n", - "178 [[GO:0006635, mitochondrial beta-oxidation of fatty acids, GO:0015980, GO:0008152, GO:0044255, GO:0006084, coenzyme metabolic process, GO:0001676, GO:0019752, GO:0006099]] \n", - "179 [[GO:0006631, MESH:D004734, mitochondrial function, GO:0016042, oxidative stress response]] \n", - "180 [[cdc20, cdc25a, cdc25b, cdc27, cdc45, cdc6, cdc7, cdk1, cenpa, cenpe, cenpf, chek1, cks1b, cks2, dbf4, e2f1, e2f2, e2f3, e2f4, espl1, exo1, fbxo5, gins2, h2ax, h2az1, h2az2, h2bc12, hmmr, hus1, ilf3, incenp, katna1, kif11, kif15, kif20b, kif22, kif23, kif2c, kif4a, kif5b, kpna2, kpnb1, lig3, mad2l1, map3k20, mcm2, mcm3, mcm5, mcm6, ne]] \n", - "181 [[GO:0051726, GO:0006260, chromosomal segregation, GO:0051276, GO:0006281]] \n", - "182 [[GO:0006096, GO:0005978, glycosylation pathway]] \n", - "183 [[GO:0008152, GO:0006796, molecular function regulation, GO:0033554, GO:0031323, GO:0019538, GO:0050794, GO:0044281]] \n", - "184 [[GO:0007399, nervous system neuron differentiation, nervous system development and angiogenesis, GO:0045765, GO:0023056, GO:0048598]] \n", - "185 [[GO:0031175, GO:0007411, GO:0051960, GO:0007165, GO:0007267]] \n", - "186 [[GO:0015886, GO:0051536, [2fe-2s] cluster binding]] \n", - "187 [[gene expression regulation; metabolism; transport\\n\\nmechanism and hypotheses:\\nthe genes in this list are involved in various cellular processes, including gene expression regulation, GO:0008152, and transport. gene expression regulation may be a mechanism by which these genes function, possibly through the involvement of transcription factors such as foxo3 and klf3. metabolism may also be a key mechanism, as many of these genes are involved in metabolic pathways, such as fech and alas2 in heme synthesis, and gclc and gclm in glutathione metabolism. transport may also be a contributing mechanism, as several genes in this list, such as slc2a1 and slc6a9, are involved in membrane transport of various molecules. overall, the commonality in function among these genes may be attributed to their roles in regulating cellular metabolism and transporting molecules across various membranes]] \n", - "188 [[GO:0006110, GO:0051246, GO:0010628, GO:0030198, GO:0006006, GO:0009749, GO:0001558, GO:0008284, GO:0051094]] \n", - "189 [[hk1, hk2, pfkl, pfkfb3, gys1, pklr, pgk1, tpi1, aldoa, eno2, pgam2, pgm2, fbp1, eno1, ndst1, ndst2]] \n", - "190 [[il2ra, il1r2, il2rb, il10ra, ctla4, cd44, MESH:D016753, il1rl1, il18r1, icos, tnfrsf4, tnfrsf18, tnfrsf8, tnfrsf21, tnfsf11, tnfrsf9, tnfsf10, tnfrsf1b, cd48, tnfrsf4, cxcl10, MESH:D018793, selp, ccne1, MESH:D047990, socs1, socs2]] \n", - "191 [[GO:0006955, cell signaling, GO:0005125, GO:0008009, GO:0008083, GO:0007166, GO:0002250, GO:0030595, GO:0050900, GO:0006954]] \n", - "192 [[GO:0019221, GO:0002757, GO:0007259, GO:0002694, regulation of leukocyte migration and chemotaxis, GO:0035456, GO:0034341, GO:0070555, GO:0070671, GO:0070741, response to tumor necrosis factor. \\n\\nhypotheses: these genes are involved in activating immune responses and cytokine-mediated signaling pathways. the enrichment of terms related to leukocyte activation and chemotaxis suggests an increased focus on the recruitment of immune cells to sites of infection and inflammation. the involvement of genes related to cytokine signaling, such as jak-stat cascade, suggests that the activation of immune responses may be regulated by cytokines released in response to infection or inflammation. overall, these genes are likely involved in the regulation of immune system activation and inflammation]] \n", - "193 [[cytokine signaling, GO:0006954, GO:0006955, interleukin signaling, GO:0008009, jak-stat signaling, toll-like receptor signaling]] \n", - "194 [[cytokine signaling, GO:0006955, GO:0006954]] \n", - "195 [[GO:0004896, GO:0042379, GO:0050900, GO:0002694, GO:0050778, GO:0045088, GO:0005149, GO:0042110, GO:0006952, GO:0006954, GO:0002685, GO:0034097]] \n", - "196 [[GO:0051607, GO:0045087, interferon signaling, type i interferon response, viral defense]] \n", - "197 [[GO:0051607, GO:0002376, GO:0140888]] \n", - "198 [[GO:0060337, GO:0006955, GO:0002579, GO:0051607, GO:0046596, GO:0032481, GO:0045087, GO:0034341, GO:0032727, GO:0002504, GO:0002479, GO:0032728, GO:0071357, GO:0043331, GO:0016032, GO:0045859, GO:0006954, GO:0060333, GO:0038187]] \n", - "199 [[GO:0019882, interferon response, GO:0001816, GO:0006954, GO:0002376, GO:0050776, GO:0006952, GO:0009615, response to interferon]] \n", - "200 [[GO:0005509, GO:0070588, GO:0051924, GO:0051899, GO:0042391, GO:0071277]] \n", - "201 [[GO:0006811, neurological signaling, tissue development.\\n\\nmechanism]] \n", - "202 [[GO:0006955, cellular signaling, GO:0001525]] \n", - "203 [[1. immune response\\n2. inflammatory response\\n3. coagulation\\n4. positive regulation of endothelial cell migration \\n5. cell adhesion\\n6. positive regulation of cell migration \\n7. signal transduction \\n8. negative regulation of apoptotic process \\n9. regulation of angiogenesis \\n10. positive regulation of protein serine/threonine kinase activity \\n11. positive regulation of transcription from rna polymerase ii promoter \\n\\nmechanism: the enriched functions suggest that these genes play an important role in innate and adaptive immune responses, inflammatory processes, GO:0007596, cell adhesion and migration, GO:0001525, and signal transduction pathways. they could be involved in regulating the expression and activity of various immune cells, MESH:D016207, chemokines to modulate immunity inflammation. the coagulation-related genes may contribute to thrombotic disorders cardiovascular diseases by affecting blood clot formation fibrinolysis. the cell adhesion migration-related genes are potentially involved in tumor metastasis progression through facilitating cell invasion motility. the signal]] \n", - "204 [[GO:0007052, GO:0007017, GO:0051301, GO:0007010, GO:0030029]] \n", - "205 [[GO:0007051, GO:0031023, GO:0007059, GO:0071173, GO:0051382, GO:0007052, GO:0000226, GO:0007098, GO:0007020, GO:0000075, GO:0007018, GO:0007346, GO:0000070, GO:0001578, GO:0008017, GO:0000910, GO:0030953]] \n", - "206 [[glycolysis; tca cycle; cholesterol biosynthesis; pentose phosphate pathway\\n\\nmechanism and hypotheses:\\nthe enriched terms suggest that these genes are involved in various aspects of cellular metabolism. glycolysis is the central pathway for glucose metabolism, converting glucose into pyruvate. the tca cycle is responsible for generating energy from the breakdown of carbohydrates, MESH:D005227, and amino acids. the cholesterol biosynthesis pathway is responsible for producing cholesterol, which is involved in membrane structure, steroid hormone synthesis, and bile salt production. the pentose phosphate pathway is involved in the production of nadph, which is critical for many cellular processes, including antioxidant defense and biosynthesis.\\n\\noverall, these genes are likely involved in regulating various aspects of cellular metabolism, including energy production, biosynthesis of important molecules like cholesterol and nadph, mediating the cellular response to oxidative stress]] \n", - "207 [[GO:0051087, GO:0006457, co-factor binding, GO:0008152, GO:0005524]] \n", - "208 [[GO:0006397, GO:0006413, GO:0042254]] \n", - "209 [[GO:0006396, GO:0006412, GO:0042254, GO:0006402, GO:0043488, regulation of mrna splicing, GO:0043393, GO:0008380, GO:0006417, GO:0003723]] \n", - "210 [[GO:0042254, GO:0006364, GO:0003723, GO:0005681, GO:0006413]] \n", - "211 [[GO:0006396, GO:0022613, GO:0042254, GO:0000166, GO:0003723, GO:0090304, GO:0042273, GO:0006364, GO:0065004]] \n", - "212 [[muscle filament sliding; sarcomere organization; muscle system process\\n\\nmechanism: the majority of the listed genes are involved in muscle contraction and development, specifically in the organization and structure of the sarcomere. the enriched terms - muscle filament sliding, GO:0045214, muscle system process - all relate to the mechanisms of muscle contraction the intricate process of sarcomere formation]] \n", - "213 [[GO:0003012, GO:0006936, GO:0045214, GO:0030029]] \n", - "214 [[GO:0007219, GO:0008593, GO:0016055, GO:0030111, GO:0045944, GO:0045596, GO:0045597]] \n", - "215 [[GO:0007219, GO:0005515, GO:0000122, GO:0000988]] \n", - "216 [[GO:0042773, mitochondrial atp synthesis coupled electron transport in respiratory chain, GO:0033108, GO:0006979]] \n", - "217 [[GO:0003954, GO:0022900, GO:0042773, GO:0005743, GO:0007005, GO:0006119, GO:0033108, respiratory chain complex i, ii, iii, iv, v, vi, GO:0006743, GO:0006631]] \n", - "218 [[GO:0051726, GO:0006915, GO:0008285, GO:0006974, negative regulation of cellular process.\\n\\nmechanism: the genes in this list are enriched in functions that regulate the cell cycle and cell death. specifically, they are involved in cell cycle arrest, apoptosis, negative regulation of cell proliferation, and response to dna damage stimulus]] \n", - "219 [[GO:0006974, GO:0051726, GO:0006915, GO:0006281, MESH:D002470, p53 signaling, checkpoint regulation, transcriptional regulation, GO:0006338]] \n", - "220 [[GO:0030073, GO:0042593, GO:0003309, GO:0003323, pancreatic beta cell function, pancreatic islet cell development]] \n", - "221 [[GO:0003323, GO:0030073, GO:0042593, GO:0031018, GO:0050796, GO:0006006, positive regulation of pancreatic beta cell differentiation, GO:0010827, regulation of insulin secretion by glucose]] \n", - "222 [[GO:0140359, GO:0006631, GO:0006695, GO:0035357, GO:0005777]] \n", - "223 [[GO:0006631, GO:0006629, GO:0008202, GO:0030301, GO:0006641, GO:0008206, GO:0005777]] \n", - "224 [[GO:0016301, GO:0006468, GO:0010646, GO:0035556, regulation of map kinase activity\\n\\nmechanism: these genes are involved in several signaling pathways and primarily regulate protein kinase activity and phosphorylation. they are involved in the regulation of cell communication and intracellular signaling cascades, including the map kinase cascade]] \n", - "225 [[GO:0007165, GO:0006468, GO:0008152, GO:0001558, GO:0042127, GO:0042981, GO:0045859, GO:0043408, GO:0032024, GO:0005975, GO:0010906, GO:0010604]] \n", - "226 [[GO:0016192, endosome to golgi transport, GO:0006886, GO:0008104, GO:0015031, regulation of membrane organization and biogenesis]] \n", - "227 [[GO:0006886, GO:0006891, GO:0007030, GO:0072583]] \n", - "228 [[GO:0016209, redox regulation, GO:0006749, oxidation-reduction process, GO:0006979]] \n", - "229 [[oxidative stress response, redox regulation, GO:0006749, GO:0016209, GO:0000302]] \n", - "230 [[GO:0140013, GO:0007283, GO:0007059, GO:0051301, GO:0140014]] \n", - "231 [[GO:0007052, GO:0007059, GO:0007094]] \n", - "232 [[GO:0030509, GO:0000122, GO:0045944, GO:0048705, GO:0007183, GO:0007179]] \n", - "233 [[GO:0007179, GO:0030514, GO:0010990]] \n", - "234 [[GO:0006955, GO:0006954, GO:0034097, GO:0050865, GO:0071624, GO:0032855, GO:0010552, GO:0051092, GO:0043406, GO:0007259, GO:0043065, GO:0004672]] \n", - "235 [[GO:0006955, GO:0006954, GO:0032680, GO:0001816, GO:0032496, negative regulation of nf-kappab transcription factor activity.\\n\\nmechanism and]] \n", - "236 [[GO:0006457, MESH:M0354322, ubiquitin-mediated proteolysis, GO:0034976, GO:0006986, GO:0006397, GO:0008380]] \n", - "237 [[GO:0006457, chaperone-mediated protein processing, GO:0015031, GO:0007029, GO:0006986]] \n", - "238 [[GO:0004672, GO:0003700, GO:0006355, GO:0035556, cytoplasmic membrane-bounded vesicle, receptor protein signaling pathway, GO:0007155, GO:0001932, GO:0007399, GO:0007498, GO:0045666]] \n", - "239 [[GO:0030198, GO:0007165, GO:0008083, neural development, GO:0022008]] \n", - "240 [[GO:0033554, GO:0031323, GO:0051050, GO:0009966]] \n", - "241 [[GO:0008104, GO:0006950, GO:0042981, GO:0008283, GO:0006979, regulation of transcription, GO:0006974, GO:0007049, response to hypoxia.\\n\\nmechanism]] \n", - "242 [[cellular response to wnt stimulus, GO:0090263, GO:0045746]] \n", - "243 [[GO:0016055, GO:0007219, GO:0005515, GO:0008134]] \n", - "244 [[GO:0002376, GO:0042110, GO:0001816, GO:0046649, GO:0006955, GO:0007166]] \n", - "245 [[t cell activation; cytokine signaling; lymphocyte proliferation; immune response\\n\\nmechanism: these genes are all involved in the regulation and function of the immune system, specifically in t cell activation, GO:0046651, and cytokine signaling pathways. they play a role in immune responses to pathogens, MONDO:0007179, MONDO:0004992]] \n", - "246 [[GO:0000988, GO:0003677, GO:0048863]] \n", - "247 [[pluripotency, self-renewal, GO:0048863]] \n", - "248 [[extracellular matrix organization; angiogenesis; positive regulation of cell migration; positive regulation of endothelial cell migration; positive regulation of sprouting angiogenesis; positive regulation of angiogenesis; positive regulation of vascular endothelial cell migration; positive regulation of smooth muscle cell migration; positive regulation of vascular smooth muscle cell migration; positive regulation of tube formation; positive regulation of endothelial cell proliferation; positive regulation of vascular endothelial growth factor production. \\n\\nhypotheses: several of the genes in the list encode for extracellular matrix components or regulators of matrix organization, including col3a1, col5a2, lum, postn, and vcan. others, such as cxcl6, pdgfa, pf4, and vegfa, encode for angiogenic growth factors. itgav is a common denominator and is associated with integrin-mediated signaling that regulates cell adhesion, migration, angiogenesis. fgfr1 has also been shown to play a critical role in angiogenesis extracellular matrix organization by regulating downstream signaling pathways such as pi3k mapk]] \n", - "249 [[GO:0030198, GO:0007155, GO:0001525, GO:0016477, GO:0030334, GO:0008284, GO:0043410]] \n", - "250 [[GO:0030182, GO:0006811, GO:0000988, GO:0005509, GO:0007399, GO:0007267, synapse assembly and organization, g protein-coupled receptor signaling, GO:0003723, GO:0005515]] \n", - "251 [[GO:0006396, GO:0008134, GO:0006355, GO:0003682, GO:0005634, GO:0003723, GO:0006397, transcriptional regulation, GO:0061629]] \n", - "252 [[GO:0006936, GO:0045214, GO:0006941, GO:0060048]] \n", - "253 [[GO:0006936, GO:0033275, GO:0031034, GO:0005509, GO:0045214, MESH:D024510]] \n", - "254 [[GO:0030301, GO:0006629, GO:0006897, GO:0030163]] \n", - "255 [[GO:0006897, GO:0007032, GO:0036010, GO:0006898, GO:0016192]] \n", - "256 [[GO:0006006, GO:0006096]] \n", - "257 [[GO:0005975, GO:0006006, GO:0006096, GO:0006754]] \n", - "258 [[GO:0006816, GO:0015075, GO:0099601, GO:0007268, GO:0034765]] \n", - "259 [[GO:0005216, neurotransmitter signaling, GO:0050804, GO:0005509, GO:0008066]] \n", - "260 [[GO:0006950, GO:0006915, GO:0042981, GO:0043123, GO:0046330]] \n", - "261 [[autophagy regulation, GO:0033554, GO:0006915]] \n", - "262 [[GO:0005975, GO:0005764, GO:0016798, glycoside hydrolase activity, GO:0004556, GO:0008422, acid alpha-glucosidase activity, GO:0004565, GO:0015929, GO:0015923, n-acetylglucosaminidase activity, GO:0004308, GO:0015926, GO:0005980, GO:0006027, mucopolysaccharide catabolic process, GO:0016266, GO:0006491]] \n", - "263 [[GO:0005975, GO:0070085, GO:0000272, GO:0004553, GO:0015929, GO:0004556, GO:0004565]] \n", - "264 [[GO:0002376, GO:0046649, GO:0002250, GO:0042113, GO:0003823, antibody-mediated immunity\\n\\nmechanism]] \n", - "265 [[GO:0002377, GO:0042113, GO:0016064]] \n", - "266 [[GO:0006281, GO:0035825, GO:0140013, GO:0007059, GO:0007129, GO:0006974, m phase of meiosis, dna replication-independent nucleosome assembly, crossover junction formation, GO:0007281, GO:0036093, GO:0009994, GO:0007283, GO:0071173, GO:0006298, GO:0033554]] \n", - "267 [[GO:0140013, GO:0006281, GO:0007059, MESH:D011995, GO:0035825, GO:0006302, GO:0007129, crossing-over, GO:0051276]] \n", - "268 [[GO:0034599, GO:0001558, GO:0032088, GO:0043066, GO:0051726, GO:0010468, GO:0008285]] \n", - "269 [[GO:0006979, GO:0006974, GO:0080135, regulation of protein localization to organelles, GO:0043065, GO:0043066, GO:0008285, GO:0050821]] \n", - "270 [[glycolysis; tca cycle; cholesterol biosynthesis; pentose phosphate pathway\\n\\nmechanism and hypotheses:\\nthe enriched terms suggest that these genes are involved in various aspects of cellular metabolism. glycolysis is the central pathway for glucose metabolism, converting glucose into pyruvate. the tca cycle is responsible for generating energy from the breakdown of carbohydrates, MESH:D005227, and amino acids. the cholesterol biosynthesis pathway is responsible for producing cholesterol, which is involved in membrane structure, steroid hormone synthesis, and bile salt production. the pentose phosphate pathway is involved in the production of nadph, which is critical for many cellular processes, including antioxidant defense and biosynthesis.\\n\\noverall, these genes are likely involved in regulating various aspects of cellular metabolism, including energy production, biosynthesis of important molecules like cholesterol and nadph, mediating the cellular response to oxidative stress]] \n", - "271 [[GO:0006810, GO:0008152, GO:0006457]] \n", - "272 [[GO:0007031, peroxisome biogenesis, protein import into peroxisome, peroxisome membrane organization, peroxisomal matrix organization]] \n", - "273 [[GO:0007031, peroxisome biogenesis, GO:0016559]] \n", - "274 [[GO:0006281, GO:0006997, GO:0010467, GO:0007568]] \n", - "275 [[GO:0006325, GO:0006281, GO:0000723, nuclear localization, nuclear lamina organization, genome stability regulation]] \n", - "276 [[GO:0006811, GO:0048666, GO:0007268, GO:0042391, GO:0034765]] \n", - "277 [[GO:0005216, GO:0042803, GO:0008066, GO:0016917, GO:0005261]] \n", - "278 [[GO:0042552, GO:0007411, GO:0007399, GO:0008104, GO:0031175]] \n", - "279 [[GO:0044237, neurological development, myelin sheath formation]] \n", - "280 [[GO:0007186, GO:0007188, GO:0046928, GO:0032225, positive regulation of camp biosynthetic process, GO:0007194, GO:0007212, prostaglandin receptor signaling pathway]] \n", - "281 [[GO:0007186, dopamine receptor activity, GO:0007188, GO:0004952, GO:0099528, d1 dopamine receptor signaling pathway]] \n", - "282 [[transcription regulation, GO:0016569, GO:0032502, GO:0065004, GO:0006950]] \n", - "283 [[GO:0003677, transcriptional regulation, GO:0010468, GO:0000988, GO:0003682, GO:0006357, GO:0006355, GO:0000977, GO:0043565, GO:0051090]] \n", - "284 [[GO:0030199, GO:0061448, GO:0062023, GO:0030198, GO:0006024]] \n", - "285 [[GO:0030198, GO:0030199, GO:0030166, GO:0006024, GO:0061448]] \n", - "286 [[GO:0006281, GO:0006513]] \n", - "287 [[GO:0006281, GO:0006513]] \n", - "288 [[mitochondrial function, GO:0006754, GO:0006629, GO:0005515, GO:0023052]] \n", - "289 [[GO:0005746, GO:0022900, GO:0006754, GO:0006631, GO:0015746, GO:0016746, dehydrogenase activity, GO:0016491, GO:0022857]] \n", - "290 [[GO:0005125, chemokine receptor binding activity, interleukin receptor binding activity, mhc class protein complex binding activity, identical protein binding activity\\n\\nmechanism: these genes are involved in the regulation of the immune response, including the production of cytokines and chemokines, binding to immune receptors, and mhc class protein complex binding. their common function is likely related to the regulation of the immune system and the activation of the immune response against foreign invaders]] \n", - "291 [[GO:0005125, chemokine receptor binding activity, GO:0004672, GO:0004896, identical protein binding activity, integrin binding activity, GO:0002376, GO:0005840, GO:0042803, GO:0042110, transcription activator activity, rna polymerase ii-specific. \\n\\nmechanism and hypotheses: these enriched terms suggest that the identified genes are involved in immune system processes such as cytokine signaling, chemokine receptor binding, and t cell activation. protein kinase activity may be involved in signaling pathways downstream of cytokine receptors or chemokine receptors. the presence of ribosome-related terms suggests these genes may play a role in protein synthesis in immune cells. the identified enriched terms point to a central role of the immune system in the functions of these genes, with potential impacts on inflammation, infection, and other immune-related diseases]] \n", - "292 [[GO:0006468, GO:0035556, GO:0010604]] \n", - "293 [[1. binding of metal ions \\n2. protein kinase activity \\n3. positive regulation of protein kinase activity \\n4. cytoskeletal protein binding activity \\n5. signal transduction \\n\\nmechanism: these enriched terms indicate that the genes have a role in signal transduction pathways and cytoskeletal organization. the genes are involved in the binding of metal ions and protein kinases, which are important components of these pathways. additionally, the positive regulation of protein kinase activity suggests that these genes have a role in the amplification of signal transduction through cascade-like pathways]] \n", - "294 [[extracellular matrix organization; cell signaling; blood coagulation; lipid metabolism; immunity.\\n\\nmechanism and hypotheses: these genes appear to be involved in a variety of pathways related to extracellular matrix organization, cell signaling, and intercellular communication. specifically, several genes encode proteins that are structural components of the extracellular matrix or interact with extracellular matrix proteins, suggesting a role in tissue development, remodeling, or repair. many of these genes also participate in signaling pathways that control cell proliferation, differentiation, and migration. additionally, several genes are involved in blood coagulation and lipid metabolism, which may be related to their roles in cardiovascular disease. finally, some genes have roles in immunity and host defense against infectious pathogens, possibly contributing to susceptibility or resistance to infectious diseases. overall, these common functions may point to a greater role for extracellular matrix and signaling pathways in disease pathogenesis]] \n", - "295 [[GO:0030198, cell signaling, protein binding activity, GO:1902533, GO:0062023]] \n", - "296 [[actin filament binding activity, integrin binding activity, protein kinase binding activity, sh2 domain binding activity, cell adhesion molecule binding activity, identical protein binding activity, GO:0005096, atp binding activity, cadherin binding activity, collagen binding activity, GO:0051219, GO:0042803]] \n", - "297 [[integrin binding activity, cell adhesion molecule binding activity, sh3 domain binding activity, identical protein binding activity, actin filament binding activity, protein kinase binding activity]] \n", - "298 [[GO:0005886, GO:0005615, signaling receptor binding activity, protein domain specific binding activity, protein kinase binding activity, GO:0006811, GO:0051247, GO:0010468, GO:0007155, GO:1902531]] \n", - "299 [[GO:0010468, signaling receptor binding activity, GO:0045944, GO:2001234, GO:0006811, GO:0060244, GO:0051965, carbohydrate binding activity, GO:1902531, GO:1904054]] \n", - "300 [[GO:0097190, GO:0006955, GO:0005125, identical protein binding activity, protease binding activity, enzyme binding activity, GO:0000988, dna binding activity]] \n", - "301 [[apoptotic process; cytokine activity; protein binding activity.\\n\\nmechanism: the genes in this list are involved in processes related to cell death, GO:0006955, and molecular interactions. the enriched terms suggest that these genes may be involved in pathways related to apoptosis, cytokine signaling, protein interactions. it is possible that these genes contribute to the regulation of cell death through cytokine-mediated signaling pathways protein-protein interactions]] \n", - "302 [[cholesterol binding activity, GO:0016887, GO:0005319, GO:0008559, atp binding activity, GO:0007031, vitamin d receptor binding activity, GO:0042626]] \n", - "303 [[GO:0008610, GO:0006631, GO:0008203, GO:0007031, GO:0015908, peroxisome matrix targeting, abc-type transporter activity. \\n\\nmechanism]] \n", - "304 [[GO:0006695, GO:0008610, GO:0019216, GO:0042632, GO:0090181]] \n", - "305 [[GO:0006695, GO:0008299, GO:0006633]] \n", - "306 [[GO:0006956, GO:0050817, GO:0008237]] \n", - "307 [[metalloendopeptidase activity; serine-type endopeptidase activity; protease binding activity; identical protein binding activity; complement binding activity \\n\\nmechanism and hypotheses: these enriched terms suggest that the common mechanism or pathway involves the regulation of proteolysis and immune response, particularly the complement system. metalloendopeptidase and serine-type endopeptidase activity are involved in the proteolytic degradation of various extracellular matrix components including collagen, GO:0005577, and proteoglycan, as well as destruction of pathogenic microorganisms during immune response. protease binding activity, identical protein binding activity, and complement binding activity are involved in protein-protein interactions that regulate proteolysis and activation of complement components. therefore, the hypothesis is that the common mechanism of these genes is related to the regulation of proteolysis and complement system activity]] \n", - "308 [[GO:0005515, GO:0046872, GO:0019899, GO:0042802, GO:0005524, GO:0003677, calcium ion binding. \\n\\nmechanism]] \n", - "309 [[GO:0004222, GO:0004252, complement binding activity, heparin binding activity, GO:0008234, GO:0004869, GO:0005201, serine-type endopeptidase inhibitor activity involved in apoptotic process, GO:0004722, MESH:D011809]] \n", - "310 [[dna binding activity, transcription initiation, rna binding activity, GO:0009117, rna splicing. \\n\\nmechanism: these genes are likely involved in regulating dna replication, transcription, and various steps in rna processing, including splicing and export from the nucleus. they could also be involved in nucleotide metabolism and/or maintaining genomic stability]] \n", - "311 [[GO:0003677, GO:0003723, GO:0009117, GO:0006281, transcription initiation, protein-macromolecule adaptor activity.\\n\\nmechanism: these genes work together to maintain the integrity and expression of genetic information, with a focus on dna-related processes]] \n", - "312 [[GO:0006260, GO:0006281, GO:0051726, GO:0003682, GO:0005524, GO:0019899, GO:0042393, GO:0043130]] \n", - "313 [[dna binding activity, chromatin binding activity, rna binding activity, enzyme binding activity, GO:0042803, single-stranded dna binding activity, identical protein binding activity, histone binding activity, atp binding activity, cyclin binding activity, nucleic acid binding activity]] \n", - "314 [[GO:0005201, collagen binding activity, heparin binding activity, GO:0005125, GO:0008083, signaling receptor binding activity, wnt-protein binding activity]] \n", - "315 [[collagen binding activity, integrin binding activity, heparin binding activity, GO:0005201, GO:0008237, platelet-derived growth factor binding activity, GO:0008009, fibronectin binding activity, GO:0004867]] \n", - "316 [[GO:0004888, GO:0022857, GO:0001216]] \n", - "317 [[GO:0007165, transcriptional regulation, GO:0003824, GO:0038023, GO:0003676, GO:0007154, GO:0042445, protein-protein interaction\\n\\nhypotheses: the enriched terms suggest that the genes in this list are involved in various aspects of signaling and transcriptional regulation. they may function in pathways such as cell signaling, hormone metabolism, and protein-protein interaction. this list includes genes encoding enzymes with specific activities, as well as receptor and nucleic acid binding proteins that are crucial for signaling and transcriptional regulation]] \n", - "318 [[enzyme binding activity, identical protein binding activity, calcium ion binding activity, GO:0005215, phosphorylation-dependent protein binding activity, atpase binding activity, GO:0004930, GO:0004712, nucleotide binding activity, ubiquitin protein ligase binding activity, transcription factor binding activity, histone deacetylase binding activity, GO:0016787, GO:0016491]] \n", - "319 [[binding activity, GO:0005215, enzyme binding activity, identical protein binding activity, protein kinase binding activity, GO:0004930]] \n", - "320 [[fatty acid-coa ligase activity, GO:0003995, long-chain fatty acid binding activity, GO:0003985, GO:0016615, GO:0000104, GO:0016616]] \n", - "321 [[GO:0003824, GO:0016491, GO:0006631, GO:0006629, metabolic pathways. \\n\\nmechanism: these genes may be involved in the regulation of lipid and fatty acid metabolism, potentially through oxidation-reduction processes and metabolic pathways]] \n", - "322 [[dna binding activity, transcription regulation, GO:0004672, protein binding activity, GO:0016570]] \n", - "323 [[dna-binding transcription factor, GO:0004672, protein binding activity, GO:0140014, GO:0006260, GO:0010467]] \n", - "324 [[GO:0008194, GO:0008146, GO:0008378, GO:0015020, GO:0004553, heparan sulfate binding activity, several others]] \n", - "325 [[enzyme binding activity, GO:0008194, atp binding activity, GO:0008378, GO:0004340, fructose binding activity, heme binding activity, GO:0016787, rna binding activity, identical protein binding activity, GO:0046983, nucleoside triphosphate activity]] \n", - "326 [[GO:0032502, GO:0007165, MESH:D005786]] \n", - "327 [[GO:0007155, transcription regulation, GO:0007165, negative regulation, positive regulation]] \n", - "328 [[GO:0005215, binding activity, GO:0003824]] \n", - "329 [[enzyme binding activity, protein domain specific binding activity, GO:0046982, identical protein binding activity, GO:0042803]] \n", - "330 [[enzyme binding activity, protein kinase binding activity, identical protein binding activity, GO:0003700, GO:0004674, calcium ion binding activity, nucleic acid binding activity, atp binding activity, GO:0060422, gtp binding activity, GO:0004340, GO:0005353, GO:0008459, heparin binding activity, apolipoprotein binding activity]] \n", - "331 [[GO:0042802, GO:0019899, GO:0005524, GO:0019901, GO:0005509, GO:0005102, GO:0015035, GO:0016538, GO:0008083, GO:0005353, GO:0004347, nadph binding activity, GO:0042803, MESH:D013213]] \n", - "332 [[GO:0042802, GO:0003700, GO:0005125, GO:0005096, interleukin receptor binding activity, ubiquitin protein ligase activity.\\n\\nmechanism: these genes likely play a role in regulating various cell signaling pathways, including cytokine and growth factor signaling, as well as intracellular protein degradation via ubiquitin-proteasome system]] \n", - "333 [[GO:0004896, protein binding activity, GO:0003824, dna binding activity, rna binding activity, apoptosis. \\n\\nmechanism: these genes are involved in various cellular processes such as signaling and cytokine receptor activity, where they play a role in transmitting signals from the outside to the inside of the cell, as well as in regulating the immune system. they are also involved in enzyme activity, dna and rna binding activity, and apoptosis, playing a role in various pathways such as the regulation of gene expression and programmed cell death]] \n", - "334 [[GO:0004896, GO:0004896, growth factor receptor binding activity]] \n", - "335 [[GO:0005125, signaling receptor binding activity, GO:0001819, GO:0019221, GO:0009967, GO:0004896, GO:0050776]] \n", - "336 [[GO:0005125, GO:0004896, GO:0004930, GO:0002376, GO:0006954, GO:0008009]] \n", - "337 [[GO:0004896, GO:0004930, signaling receptor binding activity, identical protein binding activity, enzyme binding activity]] \n", - "338 [[GO:0006955, GO:0019882, cytokines/chemokines, interferon-related genes, rna processing/editing]] \n", - "339 [[GO:0098542, GO:0045071, GO:0035458, GO:0071345, GO:0042590, GO:0006469, GO:0010604, GO:0046597, GO:0019221, GO:0045669, GO:0052548]] \n", - "340 [[GO:0005125, GO:0008009, GO:0001216, enzyme binding activity, identical protein binding activity, protease binding activity, GO:0042803, rna binding activity, GO:0050852, GO:0061630]] \n", - "341 [[GO:0019882, cytokine signaling, antiviral defense]] \n", - "342 [[GO:0003824, protein binding activity, GO:0000988, identical protein binding activity, ion binding activity.\\n\\nmechanism]] \n", - "343 [[GO:0005488, GO:0003824, GO:0004930, GO:0000988, GO:0005509, GO:0005524, protein homodimerization activity.\\n\\nmechanism: the enriched terms suggest that these genes are involved in cellular regulation and signaling processes through binding and enzymatic activities, particularly involving calcium ions and atp. many genes also have transcription factor activity, indicating a role in gene expression regulation. g protein-coupled receptor activity is also overrepresented, suggesting a role in cellular signaling processes]] \n", - "344 [[GO:0005515, enzyme binding activity, transcriptional regulation, ion binding activity, dna binding activity, GO:0004930, GO:0005125, identical protein binding activity]] \n", - "345 [[enzymatic activity, GO:0019901, binding activity\\n\\nmechanism: the enriched functions suggest that these genes may be involved in the regulation of cellular processes through protein-protein interactions, including enzymatic activities and binding activities. this could involve pathways such as signal transduction or gene expression regulation]] \n", - "346 [[microtubule binding activity, actin binding activity, GO:0005096]] \n", - "347 [[GO:0008017, mitotic processes, GO:0000910, GO:0007018, spindle organization. \\n\\nmechanism: these genes play important roles in the regulation and organization of microtubules, which are key components of the cytoskeleton involved in cell division processes such as mitosis and cytokinesis. the enrichment of terms related to microtubule binding and regulation suggest that these genes may function together in a pathway that regulates the dynamics and organization of microtubules during these cellular processes. they may also be involved in microtubule-based movement, which is crucial for various cellular activities such as intracellular transport and cell migration]] \n", - "348 [[GO:0005515, GO:0003723, enzymatic activity, structural constituent of cytoskeleton. \\n\\nmechanism: these genes likely play a role in cellular processes such as transcription, translation, protein folding, and cytoskeletal organization]] \n", - "349 [[GO:0006457, GO:0005783, ubiquitin-proteasome system, GO:0015031, GO:0030163]] \n", - "350 [[GO:0003743, ribosome binding activity, rna binding activity, GO:0003735, protein folding chaperone activity, GO:0140713]] \n", - "351 [[GO:0000394, GO:0006413, GO:0003723, GO:0003676, GO:0006457, ribosome structure\\n\\nmechanism: these genes are involved in rna processing, including mrna splicing and translation initiation, as well as binding to rna and nucleic acids. some genes also play roles in protein folding and ribosome structure. the underlying biological mechanism or pathway is likely related to rna processing and regulation of gene expression]] \n", - "352 [[GO:0006364, GO:0042273, snorna binding activity, GO:0005730, rna binding activity]] \n", - "353 [[GO:0006364, ribosomal biogenesis, rna binding activity, GO:0005730]] \n", - "354 [[actin binding activity, calcium ion binding activity, atp binding activity, identical protein binding activity, cytoskeletal protein binding activity, enzyme binding activity, UBERON:0005090]] \n", - "355 [[GO:0006936, GO:0030036, GO:0006600, GO:0032956, regulation of muscle contraction.\\n\\nmechanism: these genes are involved in the regulation of muscle contraction and actin cytoskeleton organization, likely through their roles in calcium ion binding, myosin light chain kinase activity, and actin filament binding. several of the genes are also involved in creatine metabolism, which is important for energy generation in muscle tissues]] \n", - "356 [[GO:0007219, GO:0016567, GO:0006357, GO:0051247, GO:0016055, scf-dependent proteasomal ubiquitin-dependent protein catabolic process, cyclin-dependent protein kinase holoenzyme complex]] \n", - "357 [[GO:0007219, GO:0016567]] \n", - "358 [[GO:0009055, ubiquitin protein ligase binding activity, MESH:D014451, rna binding activity, GO:0042803, metal ion binding activity.\\n\\nmechanism and]] \n", - "359 [[mitochondria\\n- atp synthesis\\n- respiratory chain complex\\n- electron transfer\\n- oxidoreductase activity\\n- iron-sulfur cluster binding\\n\\nmechanism: these genes are involved in the regulation of metabolic processes and energy production in the mitochondria. they play important roles in cellular respiration, which involves the conversion of nutrients into energy necessary for cellular activities. the enriched terms suggest that these genes are closely related to the function of the mitochondrial respiratory chain complex and atp synthase, both of which are necessary for energy production in the form of atp. additionally, several of these genes are involved in electron transfer and oxidoreductase activity, which are also important in metabolic processes that lead to energy production. finally, there is a common theme of iron-sulfur cluster binding, which suggests a common mechanism in the regulation of metabolic processes and energy production]] \n", - "360 [[GO:0003677, GO:0005515, GO:0003824, GO:0000988, growth factor activity. \\n\\nmechanism: these genes likely play roles in regulating transcription, protein-protein interactions, metabolism, and growth factor signaling pathways]] \n", - "361 [[GO:0005515, dna binding activity, GO:0016301]] \n", - "362 [[GO:0042593, GO:0050796, GO:0046326, GO:0006006]] \n", - "363 [[GO:0030073, GO:0006006, transcriptional regulation, transcription factor binding activity, rna polymerase ii-specific dna binding activity, GO:0000122, positive regulation of transcription by rna polymerase ii. \\n\\nmechanism and]] \n", - "364 [[GO:0001676, GO:0043574, GO:0008203, GO:0006633, lipid binding activity, atp binding activity, GO:0016491]] \n", - "365 [[GO:0006629, mitochondrial function, GO:0006281]] \n", - "366 [[GO:0004672, g protein-coupled receptor binding activity, transcription factor binding activity, enzyme binding activity, GO:0007166, GO:0035556, GO:0032007, GO:0010971, negative regulation of vasc, negative regulation of nitrogen com, actin filament binding activity, cytoskeletal protein binding activity]] \n", - "367 [[GO:0006468, GO:0035556, GO:0016301, enzyme binding activity, GO:0004672, identical protein binding activity, scaffold protein binding activity]] \n", - "368 [[GO:0007030, GO:0048193, GO:0090110, GO:0006888, retrograde transport, vesicle recycling, GO:0034260, negative regulation of autophagosome formation and maturation, GO:1905604, GO:1905280, GO:0002091, GO:0009967]] \n", - "369 [[GO:0006888, GO:0048193, GO:0006891, GO:0034067, snare complex assembly.\\n\\nmechanism and]] \n", - "370 [[cellular redox homeostasis, GO:0006979, protein disulfide reduction, GO:0006749, GO:0003954, GO:0004601, GO:0006826, GO:0016209, MESH:D015227]] \n", - "371 [[GO:0045454, GO:0006979]] \n", - "372 [[GO:0005515, GO:0016301, GO:0051726, GO:0010467]] \n", - "373 [[GO:0005515, GO:0008047, atp binding activity]] \n", - "374 [[GO:0060395, GO:0006357, GO:0010604, GO:0090101, GO:0045668, establishment of sert, positive regulation of vascular associated smooth muscle cell proliferat, several others]] \n", - "375 [[GO:0005024, GO:0046332, GO:0009967, GO:0006357, GO:0000122, GO:0007166, GO:0010604, nucleic acid binding activity]] \n", - "376 [[GO:0003700, rna polymerase ii-specific; cytokine activity; protein binding activity.\\n\\nmechanism: these genes are involved in the regulation of transcription and cytokine activity, likely playing a role in immune responses and cellular differentiation. they are involved in binding to dna and rna polymerases to regulate the expression of genes, as well as in the production and regulation of cytokines and growth factors that play a role in cell signaling and differentiation]] \n", - "377 [[GO:0005125, GO:0008009, GO:0001216, GO:0006955, interleukin-12 alpha subunit binding activity, GO:0004707, protein kinase binding activity, GO:0001817, GO:0002682, smad binding activity, transcription factor binding activity]] \n", - "378 [[protein folding and chaperone activity, rna binding and transcriptional regulation, rna processing and degradation]] \n", - "379 [[GO:0003723, GO:0051087, GO:0090304, endoplasmic reticulum stress response pathway]] \n", - "380 [[GO:0005201, identical protein binding activity, enzyme binding activity, smad binding activity]] \n", - "381 [[GO:0005201, GO:0005515, GO:0016563, GO:0005102]] \n", - "382 [[enzyme binding activity, GO:0003700, protein kinase binding activity, identical protein binding activity, rna binding activity, atp binding activity, ubiquitin protein ligase binding activity]] \n", - "383 [[enzyme binding activity, GO:0006508, protein phosphatase binding activity, GO:0004725]] \n", - "384 [[GO:0060070, transcription regulation, MESH:D012319, transcription activator, beta-catenin complex, GO:0007219]] \n", - "385 [[GO:0060070, GO:0010468]] \n", - "386 [[GO:0050852, GO:0005125, interleukin-2 receptor binding activity, negative regulation of peptid, intracellular signal transduction\\n\\nmechanism: the genes analyzed in this study are primarily involved in signaling and receptor binding activities. this suggests that these genes may play an important role in the communication between cells and regulation of immune response. \\n\\n t cell receptor signaling pathway, cytokine activity, interleukin-2 receptor binding activity, negative regulation of peptid..., and intracellular signal transduction]] \n", - "387 [[GO:0050863, GO:0001819, GO:0006468, GO:0043066, GO:0002687, GO:0030890, GO:0006879, GO:0010468]] \n", - "388 [[transcriptional regulation, GO:0010467, GO:0003700, GO:0009889, GO:0019219]] \n", - "389 [[GO:0010467, transcription regulation, dna binding activity, rna polymerase ii-specific, GO:0010468, transcription cis-regulatory region binding activity]] \n", - "390 [[GO:0007160, GO:0030198, GO:0030199, GO:0008034]] \n", - "391 [[GO:0007160, GO:0030199, GO:0030198, GO:1902533, GO:0010604, GO:0030334]] \n", - "392 [[GO:0003700, identical protein binding activity, protein kinase binding activity, actin binding activity, sequence-specific double-stranded dna binding activity, metal ion binding activity, calcium ion binding activity, chromatin binding activity, rna binding activity]] \n", - "393 [[binding activity, GO:0003700, GO:0046872, GO:0019904, GO:0061630]] \n", - "394 [[GO:0006936, GO:0043502, GO:0016567]] \n", - "395 [[GO:0006936, GO:0003009, GO:0016567, ion channel activity.\\n\\nmechanism: these genes likely play a role in muscle contraction and structure, possibly through the regulation of ion channels and protein ubiquitination]] \n", - "396 [[GO:0006897, GO:0007165, cellular adhesion, GO:0006869, GO:0030163, GO:0007009]] \n", - "397 [[GO:0006897, membrane traffic, GO:0015031]] \n", - "398 [[GO:0006096, GO:0005975, GO:0006000, metabolic homeostasis]] \n", - "399 [[GO:0006096, GO:0005975, GO:0006002, GO:0005945]] \n", - "400 [[GO:0006816, GO:0005245, GO:0008066, GO:0005892]] \n", - "401 [[GO:0019722, voltage-gated calcium channel, GO:0051480, GO:0008066, GO:0017146, GO:0007268, GO:0051899, g-protein coupled receptor signaling pathway]] \n", - "402 [[GO:0006468, GO:0035556, GO:0031929, GO:0097190, kinase activity regulation, GO:0010604]] \n", - "403 [[GO:0035556, protein kinase activity regulation, GO:0010604, GO:0038202, GO:0032008, GO:0045859, apoptosis signaling pathway, chromatin binding activity]] \n", - "404 [[GO:0016052, GO:0006516, GO:0006032, GO:0030214]] \n", - "405 [[GO:0016052, GO:0030214, GO:0006516, GO:0019377, GO:0006032, GO:0006491, GO:0006517, mannose trimming involved in glycoprotein erad pathway.\\n\\nmechanism: one potential underlying biological mechanism is the regulation of cell surface and extracellular matrix composition, as well as the breakdown and recycling of molecules within these structures. glycosidases play a key role in breaking down complex carbohydrates into smaller subunits, which can then be reassembled into new molecules. the ability to break down specific types of carbohydrates, such as hyaluronic acid and chitin, may also be important for cellular processes such as cell migration and host defense]] \n", - "406 [[immunoglobulin receptor binding activity, antigen binding activity]] \n", - "407 [[GO:0006955, GO:0006952, antigen binding activity]] \n", - "408 [[homologous chromosome pairing, GO:0042138, GO:0000706, GO:0007131, GO:0000724, GO:0000712, GO:0000795]] \n", - "409 [[meiotic recombination, GO:0006302, GO:0035825, chromosomal segregation, GO:0007130]] \n", - "410 [[GO:0140313, GO:0140311, identical protein binding activity, GO:0060090, ubiquitin protein ligase binding activity, GO:0016567]] \n", - "411 [[GO:0010468, GO:0042742, GO:0045185, GO:0002376, GO:0009267, GO:0032387, GO:0035556]] \n", - "412 [[GO:0005515, GO:0003723, enzymatic activity, structural constituent of cytoskeleton. \\n\\nmechanism: these genes likely play a role in cellular processes such as transcription, translation, protein folding, and cytoskeletal organization]] \n", - "413 [[GO:0005515, GO:0003824, GO:0005215]] \n", - "414 [[peroxisome biogenesis, peroxisome matrix targeting, GO:0017038]] \n", - "415 [[peroxisome biogenesis, GO:0017038, GO:0005778, ubiquitin-dependent protein binding activity, atp binding activity, GO:0016887]] \n", - "416 [[GO:0006259, GO:0006325, GO:0033554]] \n", - "417 [[GO:0006281, GO:0000723, GO:0007568]] \n", - "418 [[GO:0007214, GO:0022849, GO:0005242, GO:0035235, GO:0015276, GO:0071805, GO:0005244]] \n", - "419 [[GO:0006811, GO:0007268, membrane potential regulation, GO:0008066, GO:0007214]] \n", - "420 [[MONDO:0015626, GO:0042552, GO:0007422, GO:0006457, GO:0007600, nucleic acid metabolism, mitochondrial function]] \n", - "421 [[GO:0007399, MONDO:0015626, GO:0042552, UBERON:0000010, mitochondrial dysfunction, protein ubiquitination.\\n\\nmechanism]] \n", - "422 [[GO:0007212, GO:0007190, calcium ion regulation, g protein-coupled receptor pathway]] \n", - "423 [[GO:0007186, GO:0004952, GO:0004016, GO:0051480, negative regulation of glycogen synthase activity, GO:0004672, GO:0019538, GO:0006468]] \n", - "424 [[GO:0001216, rna polymerase ii transcription regulatory region sequence-specific dna binding activity, GO:0045944, GO:0000122, GO:0006355, transcription factor binding activity, nucleic acid binding activity, chromatin binding activity, GO:0003713]] \n", - "425 [[GO:0003700, GO:0006355, GO:0010468, GO:0006337]] \n", - "426 [[GO:0032964, collagen fiber formation, extracellular matrix maturation, transcriptional regulation, procollagen protein, MESH:D006025, metalloproteinase, proteolytic processing, peptidyl prolyl cis-trans isomerase, MESH:M0465019, tumor-rejection antigen, sulfotransferase, transmembrane protein, beta-1,3 galactosyltransferase]] \n", - "427 [[GO:0006486, extracellular matrix remodeling, collagen production, GO:0061448, immunity response, GO:0006508, tumor rejection, MESH:M0465019, MESH:D008565, transcriptional repressor, peptidyl-prolyl isomerase, complement system, GO:0004226, peptidase s1]] \n", - "428 [[GO:0006281, genome maintenance, MESH:D004249, nucleoprotein complex, GO:0035825, double-strand dna repair, holliday junction resolution, monoubiquinated, MESH:D051135, nuclear foci, structure-specific endonucleases, MESH:D051135, recq deah helicase, tumor suppression, ssdna-binding proteins]] \n", - "429 [[GO:0006281, nucleoprotein complex, GO:0035825, dna lesion, MESH:M0443450, fanconi anemia complementation group (fanc), GO:0006302]] \n", - "430 [[GO:0010467, GO:0140657, GO:0006468, ubiquitin-mediated degradation, GO:0051726, GO:0005525, GO:0006839, GO:0006118, GO:0006119, MESH:D004789, enzyme inhibition, GO:0016491, GO:0016482, GO:0005515, GO:0006629, GO:0036211, ubiquitinylation]] \n", - "431 [[atp production, GO:0005746, GO:0006118, GO:0030497, rna/dna binding, GO:0015031, MESH:D054875, GO:0016310, GO:0008017, GO:0006869]] \n", - "432 [[cell signalling, cytokine production/regulation, chemokine production/regulation, antimicrobial defence, plasma protein regulation, immune regulation, inflammatory regulation, transcriptional regulation, GO:0004672, GO:0008233, glycoprotein activity, receptor protein activity]] \n", - "433 [[integrin, cytokine, g-protein coupled receptor, MESH:D007372, MESH:D018124, MESH:D008562, MESH:D011494, chemokine, transmembrane receptor, GO:0007165, transcriptional regulation, GO:0006412, GO:0006955]] \n", - "434 [[GO:0005524, GO:0006351, GO:0016310, MESH:D011494, protein tyrosine phosphatase, GO:0065007, GO:0005515, hydrolase, ribosomal s6 kinase, GO:0016192, regulatory subunit, acetyltransferase, modulation, GO:0005509, GO:0005783, GO:0000981, GO:0003723, n-myc downregulated, polypeptide, GO:0016125, MESH:D006657, protein inhibitor, MESH:D051116, structural fibre, disulfide oxidoreductase, adenine dinucleotide, non-sterol metabolism, calcium-induced, GO:0042593]] \n", - "435 [[transcriptional regulation, GO:0004672, GO:0005515, GO:0003723, GO:0007165, proteolytic enzyme activity, GO:0003677]] \n", - "436 [[GO:0042157, GO:0050817, GO:0007599, MESH:D016207, MESH:D018925, receptors, transporters, secreted extracellular matrix proteins, GO:0004868, MESH:D011509, GO:0007155, GO:0016477, GO:0023052, GO:0008283, GO:0006915, transcriptional regulation, tissue development and regeneration, GO:0006955]] \n", - "437 [[cell-cell interactions, cell-matrix interactions, extracellular matrix production, processing of proteoglycans and glycoproteins]] \n", - "438 [[integrin, GO:0008014, GO:0005530, MESH:C119025, map kinase, protein tyrosine kinase, guanine nucleotide binding protein, MESH:D020558, act]] \n", - "439 [[GO:0007155, GO:0023052, scaffolding, cytoskeleton maintenance, GO:0031012, MESH:D016023, MESH:D057167, MESH:C119025, MESH:D011494, GO:0008014]] \n", - "440 [[GO:0007155, GO:0006457, GO:0007154, GO:0006898, gpi-anchored cell surface proteins, cation transport atpase, transcriptional coactivation, interleukin signaling, hormone-dependence, MESH:D019812, heparin-binding, GO:0007160]] \n", - "441 [[cell signal transduction, GO:0007160, GO:0006457, GO:0030308, ligand binding, cell-surface glycoprotein, cation transmembrane transporter, growth arrest, MESH:D051246, transmembrane protein, regulatory subunit, membrane-bound glycoprotein, ammonium transmembrane transporter, cell surface receptor, insulin-regulated facilitative glucose transporter, cell surface adhesion molecule, GO:0140326, glycosylphosphatidylinositol-anchored protein]] \n", - "442 [[GO:0006915, transcriptional regulation, GO:0003677, tnf receptor superfamily, bcl-2 protein family]] \n", - "443 [[the genes summarized are involved in a wide range of processes, including apoptosis, tumor suppression, inflammation, thioredoxin binding, cytoplasmic protein and membrane glycoprotein regulation, dna topoisomerase and transcriptional activation. the commonalities that emerge from the enrichment test point to a specific biological pathway known as cell death regulation and signal transduction. this involves the interconnected network of genes that regulate apoptosis and maintain genetic stability, as well as others involved in the modulation of immune response pathways. enriched terms include apoptosis, cytoplasmic protein regulation, transcriptional regulation, tumor suppression, GO:0006954, MESH:D004264, thioredoxin binding, membrane glycoprotein regulation, transcriptional coactivation, death agonist, GO:0048018, serine/threonine phosphatase, voltage-dependent anion channel, MESH:D006136, class-1 polypeptide chain release factor, proapoptotic, nf-kappa-b.\\n\\nsummary: genes related to cell death regulation signal transduction pathways.\\nmechanism: interconnected network of genes that regulate apoptosis maintain genetic stability, as well as those involved in the modulation]] \n", - "444 [[GO:0006629, atp binding cassette, MESH:M0011631, GO:0005490, peroxin, gamma-glutamylcysteine synthetase, GO:0050632, MESH:D002785, flavoenzymes, GO:0042446, GO:0016209]] \n", - "445 [[GO:0006629, GO:0006810, oxidation, bile acids synthesis, GO:0006790, GO:0005777, oxidative stress response]] \n", - "446 [[GO:0048870, energy generation, GO:0008652, GO:0009063, GO:0009101, GO:0016126, GO:0016127, GO:0006629, GO:0006869, transcriptional regulation]] \n", - "447 [[GO:0006695, GO:0006629, GO:0006636, cell growth/regulation, GO:0051726, GO:0005515, mhc class ii presentation, cellular antioxidant activity, GO:0000988]] \n", - "448 [[analysis of this set of human genes revealed high enrichment for terms related to proteases and protease inhibitors, GO:0005209, MESH:D006023, and serine proteinases. of particular note is the abundance of genes related to the regulation of the complement system and to the coagulation cascade, GO:0004235, there appears to be a strong emphasis on proteins that are involved in the maintenance of cellular integrity and in the regulation of inflammatory and immune responses. in particular, it appears that the presence of proteases, MESH:D011480, GO:0005209, MESH:D006023, and serine proteinases is significantly enriched. this suggests that these proteins are involved in the regulation of a variety of processes, including the complement system and the coagulation cascade. furthermore, the presence of various mmps suggests a regulatory role in the breakdown of proteins in the extracellular matrix, which is important for tissue remodeling and wound healing]] \n", - "449 [[cysteine-aspartic acid protease, MESH:D020782, peptidase, guanine nucleotide-binding proteins, GO:0030165, metalloproteinase, MESH:D042962, regulator of complement activation, regulator of g protein signal transduction, rnase a superfamily, MESH:D011505, subtilisin-like proprotein convertase, MESH:D011973, vitamin k-dependent plasma glycoprotein, vitamin k-dependent coagulation factor, GO:0005161, lysosomal cysteine proteinase, MESH:D015842, transforming growth factor-beta, MESH:D006904, kunitz-type serine protease, integ]] \n", - "450 [[MESH:D010770, GO:0000502, GO:0004868, cysteine-aspartic acid protease (caspase), GO:0006915, inflammation signalling, MESH:D005165, factor]] \n", - "451 [[cell signaling, GO:0007155, GO:0008233, transcriptional regulation, GO:0008152, cytoskeletal functions]] \n", - "452 [[GO:0003677, transcription control, post-splicing, MESH:D012319, GO:0006281, GO:0071897]] \n", - "453 [[GO:0019899, GO:0003723, GO:0003677, GO:0005515, chromosomal binding, dna polymerase, MESH:D012321, phosphorolysis, GO:0010629, GO:0016567]] \n", - "454 [[dna replication/repair, chromatin regulation, GO:0006396, ser/thr protein kinase, MESH:D063146, nuclear transport and export, GO:0016567, gtpase activation, GO:0006413, GO:0003723, GO:0003677, GO:0042393, ubiquitin protein ligase, cyclin-dependent kinase, MESH:D000251, MESH:D003842]] \n", - "455 [[GO:0006260, nuclear import/export, GO:0003723, chromatin regulation/modification, GO:0030163, GO:1901987, GO:0006281]] \n", - "456 [[GO:0003779, actin regulation, GO:0007155, cell signaling, GO:0005518, cytokine regulation and signaling, GO:0005207, growth factor family members, peptidase genes]] \n", - "457 [[GO:0007155, GO:0005518, GO:0003779, MESH:D024022, MESH:D016326, cytoskeletal components, cell signalling]] \n", - "458 [[GO:0007165, GO:0010467, GO:0006810, MESH:D008565, GO:0043687, GO:0005515, ligand binding, acyltransferase]] \n", - "459 [[cytoskeletal organization, dna-binding transcription regulation, GO:0055085, membrane-associated signaling, receptor activation and signaling, cytokine and growth factor signaling]] \n", - "460 [[g-protein signaling, ion channel transport, membrane receptor signalling, cytoskeletal protein scaffolding, enzyme regulation, glycoprotein modulation.\\nmechanism: the genes identified as being related to these topics are involved in the regulation of cell signalling pathways and the transport of ions across cellular membranes. in addition, the genes are involved in biochemical processes such as enzyme regulation and glycoprotein modulation, which may be important in modulating the amount or type of molecules entering the cell and in organizing the cytoskeleton]] \n", - "461 [[GO:0007165, gene transcription, ion transport and binding, protein-protein interaction, GO:0043687, GO:0007155, MESH:M0518050, GO:0016310, MESH:D011494, membrane recognition, GO:0003676, MESH:D018118, enzymatic reactions, lipid transport, glucose transport, cytokine receptor, molybdenum cofactor biosynthesis]] \n", - "462 [[GO:0008152, GO:0009117, GO:0006631, GO:0006096, oxidation-reduction processes, GO:0006595, GO:0003824, amino acid metabolism, protein homodimerization, protein biotransformation, protein-macromolecule adaptor, protein-tat binding]] \n", - "463 [[GO:0006099, GO:0006118, GO:0005504, MESH:D042964, pyruvate dehydrogenase, nad-dependent glycerol-3-phosphate dehydrogenase, nad-dependent dehydrogenase, MESH:D013385, MESH:D000154, lyase, flavin adenine dinucleotide-dependent oxidoreductase, gtp-specific beta subunit, MESH:D006631, nad-retinol dehydrogenase, hydratase/isomerase, MESH:D006631, carnitine o]] \n", - "464 [[transcriptional regulation, epigenetic regulation, GO:0051169, GO:0043687, dna replication and repair, chromatin structure, GO:0140014, GO:0036211, GO:0006397]] \n", - "465 [[GO:0006913, GO:0016573, chromatin-associated processes, GO:0051726, transcriptional regulation, signal- and energy- dependent processes, nuclear phosphoproteins, GO:0006334, dna unwinding enzymes, protein heterodimers, GO:0000910, GO:0000398, MESH:D004264, GO:0035064, rna binding proteins, microtubule polymersization, nuclear localization, ubiquitin modification, mitosis regulation, centromere-interacting proteins.\\nmechanism: the genes in this list participate in a wide variety of mechanisms in the context of cellular development, including nucleocytoplasmic transport, histone acetylation, chromatin-associated processes, cell cycle regulation, and transcriptional regulation. these mechanisms are often interdependent and]] \n", - "466 [[MESH:D006023, transmembrane protein, cell-surface protein, enzymes plus coenzymes, GO:0000981, hormones, cytokines, and growth factors, ligand-receptor interaction, regulatory proteins, cargo-binding proteins, cell adhesion and morphogenesis, MESH:D000604, metabolism and transport within the cell, metabolism of macromolecules, cellular energy metabolism, cellular homeostasis and signaling, cell signaling and transcription, protein modification and degradation, GO:0007049, dna replication and repair, GO:0008219, enzyme-substrate interaction\\n\\nmechanism:\\nthis list of genes is primarily involved in cellular metabolism, ligand-receptor interactions, and cell signaling and transcription. there are a variety of molecules that are acted upon, such as glycoproteins, transmembrane proteins, hormones, enzymes, and transcription factors. in terms of metabolic functions, the gene list includes proteins for metabolic control, cargo-binding proteins, and enzymes involved in macromolecule metabolism and transport within the cell. additionally, many of these genes are involved in the regulation of cell cycle and homeostasis, as]] \n", - "467 [[enzyme function, GO:0005488, GO:0006810, GO:0008152, MESH:D007477, sugars, GO:0006351, cytoskeleton structure, GO:0007155]] \n", - "468 [[GO:0006897, GO:0019838, receptor-mediated pathways;neuron survival;neuron differentiation;neuronal development;cell adhesion, transcription factor regulation, GO:0007165, extracellular protein interaction]] \n", - "469 [[structure-specific proteins, GO:0006898, g-protein coupled receptors, GO:0007155, gene transcription, post-translational regulation]] \n", - "470 [[GO:0005515, GO:0006351, catalyzing reactions, gtpase activating protein activation, GO:0016575, carbohydrate & lipid metabolism, receptor binding & signaling, GO:0005574]] \n", - "471 [[GO:0003677, GO:0016573, GO:0005515, transcription regulation, leucine residue modification, GO:0003729, zinc metalloenzymes, atp-binding, protein serine/threonin, endoribonuclease, GO:0031545, 6-phosphogluconate dehydrase, GO:0003723, dynein heavy chain, MESH:C052997, chloride intracellular channel, GO:0003779, MESH:D051528, hexameric atpase, GO:0006814, rho gtpase, inositol polyphosphate, MESH:D011766, selenium-binding protein, clathrin assembly, c-myc, dual specificity protein kinase, MESH:D006021, gtpase-activating-protein, GO:0006914, ring between two helices]] \n", - "472 [[cell signaling, metabolic regulation, GO:0043687]] \n", - "473 [[cellular transport, GO:0008152, scaffolding, transcriptional regulation, GO:1901987, transcription activity, GO:0016310, cysteine-aspartic acid, GO:0016020, cell surface heparan sulfate, glycosyl hydrolase family, MESH:D000263, MESH:D000262, glyceraldehyde-3-phosphate, cytokine, glycosyltransferase, MESH:D000070778, sulfatase, sulfotransferase, serine/threonine kinase, MESH:D016232, MESH:D008668, MESH:D011973, basic helix-loop-helix]] \n", - "474 [[GO:0005515, GO:0005102, transcription regulation, enzyme regulation, GO:0001816, GO:0007155, structure, membrane-associated]] \n", - "475 [[an underlying biological mechanism of intracellular signaling and cell adhesion proteins working together to regulate gene expression and control cell functions was identified. enriched terms related to this mechanism include gtpases, MESH:D008565, intracellular signaling, calcium-dependent proteins, rna and dna binding, GO:0007155, GO:0000981, enzyme regulation, GO:0005515]] \n", - "476 [[MESH:D018121, MESH:D018925, tgf-beta superfamily, transcriptional regulation, MESH:D017027, MESH:D011494]] \n", - "477 [[the genes identified are part of the cytokine signaling system and its related pathways involved in immune response and regulation. more specifically, they belong to the type i cytokine receptor family, the phospholipase a2 family, the tumor necrosis factor receptor superfamily, the gp130 family of cytokine receptors, the toll-like receptor family, the interferon regulatory factor family, the bcl2 protein family, the reg gene family, the type ii membrane protein of the tnf family, the ring finger e3 ubiquitin ligase family, the protein tyrosine phosphatase family, the tgf-beta superfamily proteins, the hemopoietin receptor superfamily, the chemokine family, the integrin alpha chain family of proteins and the adapter protein family. there is a common function of these genes in the signaling of cell growth, UBERON:2000098, GO:0006915, migration, and differentiation, as well as the regulation of gene transcription, apoptosis and immune response. \\n\\nmechanism:\\nthe genes identified are part of a gene network that functions together to allow for cell signaling, GO:0040007, and differentiation, as well as inflammatory and immune responses. the various cytokine receptors, protein ty]] \n", - "478 [[MESH:D008565, g protein-coupled receptors, MESH:D018121, interferon-induced proteins, MESH:M0013343, MESH:D051116, MESH:D018925, MESH:D016023, MESH:D020782, MESH:D061566, tol-like receptors]] \n", - "479 [[GO:0005102, GO:0023052, GO:0055085, calcium binding, GO:0055085]] \n", - "480 [[ligand binding, GO:0005102, GO:0003824, GO:0003677, GO:0003723, protein activation, GO:0030163, MESH:D054875]] \n", - "481 [[these genes are connected by their participation in immune regulation and defense, either directly regulating the innate and acquired immune response, or acting as downstream inhibitors and activators of such responses. specific enriched terms include interferon regulation, transcriptional regulation, tumor suppression, MESH:D054875, chemokine receptor signaling, GO:0003723, GO:0009165, GO:0051607, GO:0048255, GO:0005525, GO:0008289, viral invasion, GO:0045087, GO:0030701, GO:0008134, and antigen presentation.\\n\\nmechanism: the commonalities between these genes suggest that they act at various levels of a complex innate and acquired immune response, controlling transcriptional regulation, protein modification and silencing, viral response, and antigen presentation. there are multiple pathways overlapping or influencing each gene's particular role in the overall immune defense, merging into a greater shared mechanism of host immunity]] \n", - "482 [[the genes in the list encode proteins involved in a variety of processes including immunity, GO:0006954, GO:0006351, GO:0007165, and protein folding and assembly. these processes are typically carried out by two main classes of molecules; ubiquitin ligases and cytokines. the genes in this list are enriched for terms including \"signal transduction\", \"ubiquitin ligases\", \"immune modulation\", \"cytokine activity\", \"transcription regulation\", \"proteasome activity\", \"rna binding\", and \"metallothionein\".\\n\\nmechanism:\\nthe genes in this list encode proteins involved in a variety of processes, with an emphasis on immunity and inflammation. these processes are typically mediated by ubiquitin ligases, MESH:D016207, and other signal transduction proteins. ubiquitin ligases mark target proteins for ubiquitination and other modifications, while cytokines affect the activity of multiple cells. signal transduction proteins transmit signals across cell membranes, affecting the activity of cells. metallothioneins play a role in detoxification and protein folding and assembly, while proteasomes carry out protein degradation within the cell. transcripts are regulated by transcription factors, many genes contain rna binding domains]] \n", - "483 [[transcriptional regulation, GO:0003824, binding ability, protein structure, cell signalling, MESH:D016207, growth factor signalling, MESH:D007109, GO:0000981, MESH:D054875, MESH:D006136, tripartite motif, GO:0070085, atpase, intracellular sensor, MESH:D015088, GO:0003723, calcium-binding, GO:0004930, MESH:M0476528, cysteine-aspartic acid protease, regulator of complement activation, protein tyrosine phosphatase, ubiquitin-specific protease, antiviral activity, inter]] \n", - "484 [[ion channels & transporters, receptor proteins, MESH:D002135, MESH:D004798, cell signaling, hormone regulation, GO:0008152]] \n", - "485 [[catalyzing reactions, GO:0055085, GO:0023052, dna-binding, GO:0006351, extracellular signaling, calcium-ion binding, immune system signaling, cell growth/maintenance, GO:0007154, hormone regulation, GO:0032502, GO:0008152]] \n", - "486 [[MESH:D008565, MESH:D010447, receptor proteins, MESH:D004268, MESH:D010770, GO:0000981, GO:0008217, MESH:M0022898, GO:0007165, transcriptional regulation, GO:0006811, GO:0006936, immunologic regulation, GO:0001816, GO:1901987, GO:0006915, GO:0007155, MESH:D063646]] \n", - "487 [[receptor functions]] \n", - "488 [[cytoskeleton regulation, cellular communication, gtpase regulation, actin-binding, dna-dependent protein binding, microtubule-associated protein, filamentous cytoskeletal protein, 14-3-3 family protein, MESH:D020662]] \n", - "489 [[gtpase activation, GO:0005525, structural maintenance, GO:0003677, GO:0005856, GO:0006915, GO:0007049]] \n", - "490 [[GO:0006412, GO:0008152, GO:0006457, MESH:D054875, GO:0006351, GO:0003677, damage control, GO:0032502, cellular pathway regulation, GO:0006915, GO:0007049, GO:0030163]] \n", - "491 [[atp production, amino acid homeostasis and metabolism, stress response, transcription and mrna regulation, chaperones and proteasome degradation pathways, GO:0006629]] \n", - "492 [[GO:0006351, GO:0006412, GO:0006413, GO:0003723, MESH:D054875, GO:0005840, GO:0006412, GO:0032508, MESH:D039102, GO:0003734, GO:0045292, heat shock proteins, MESH:D006655, MESH:D011073, MESH:D000604, GO:0043687]] \n", - "493 [[poly(a)-binding, GO:0003723, GO:0032508, GO:0006913, GO:0032183, GO:0000394, GO:0003676, GO:0006473, GO:0006413, GO:0036211, GO:0006457, MESH:D014176, GO:0006412, MESH:D018832, peptidyl-prolyl cis-trans isomerization, antioxidant function, heat shock protein, ubiquitin protein ligase, 14-3-3 family, dna-unwinding enzymes, dna polymerase, voltage-dependent anion]] \n", - "494 [[GO:0005515, transcriptional regulation, cell cycle progression, protein chaperoning, GO:0008283, nuclear localization, rna binding activity, pre-rrna processing, GO:0042254]] \n", - "495 [[rna binding activity, GO:0006364, protein homodimerization, GO:0008283, GO:0007165, GO:0042254, GO:0006457, GO:0034246]] \n", - "496 [[GO:0006936, calcium channel regulation, ion channel regulation, protein ubiquitination/degradation, actin-based motor proteins, GO:0007165, MESH:D004734]] \n", - "497 [[summary: the list of genes provided contains components of muscle formation, GO:0023052, and growth.\\nmechanism: the genes encode the components of signaling pathways and physical structures involved in the formation of muscle, including proteins that serve as receptors, binders, MESH:D004798, and structural components like spectrins, GO:0005202, laminin.\\nenriche terms: muscular development; musculosketetal function; signal transduction; protein phosphorylation degradation; cytoplasmic proteins; structural proteins; cytochrome oxidase]] \n", - "498 [[GO:0007219, GO:0016055, GO:0016567, transcriptional repressor, MESH:D015533, cell fate decisions, MESH:D044767, MESH:D011494]] \n", - "499 [[GO:0007219, GO:0016567, GO:0001709, transcriptional regulation, GO:0031146, gamma secretase complex, MESH:D011493, wnt family, basic helix-loop-helix family of transcription factors]] \n", - "500 [[GO:0006006, GO:0006631, amino acid metabolism, GO:0005746, MESH:D007506, nadh-ubiquinone oxidoreductase, MESH:D009245, pyruvate dehydrogenase, GO:0022900, oxidative decarboxylation, nad+/nadh oxidoreductase, GO:0016467, MESH:D003576, MESH:D063988, matrix processing, shuttling mechanism.\\n\\nmechanism: the gene products involved in this metabolic pathways work to convert small molecules such as glucose and fatty acids into energy-containing molecules, such as atp and nadh, through a combination of redox reactions, electron transfer processes, and other catalytic systems. these processes involve the participation of numerous proteins, including membrane-associated proteins, enzymes, and enzyme complexes. these proteins form a complex network of interactions that enable the conversion of energy from one form to another, ultimately leading to atp production]] \n", - "501 [[terminal enzyme, GO:0006754, GO:0005746, nad/nadh-dependent, cytochrome c oxidase (cox), GO:0006118]] \n", - "502 [[GO:0005515, GO:0003677, transcriptional regulation, GO:0051726, cell signaling]] \n", - "503 [[MESH:D011494, GO:0000981, GO:0007049, GO:0006281, GO:0003677, GO:0006412, tnf receptor superfamily, zinc finger, calcium-activated, cyclin dependent, iron-sulfur, GO:0015629, GO:0007165]] \n", - "504 [[GO:0000981, homeobox domain, signal peptide cleavage, MESH:D011494, atp-binding, chromogranin/secretogranin, GO:0005180, protease, MESH:D011770, MESH:D005952, MESH:D000243, MESH:D006593, nuclear receptor, dna-binding, g-protein linked receptor, cysteine-rich protein, gtp-bound proteins, GO:0048500, bhlh transcription factor, doublecortin, calcium-binding protein\\n\\nsummary: genes identified in this list facilitate a variety of essential biological processes, particularly in terms of cell signaling and transcription regulation. among these processes are signal peptide cleavage, atp-binding, peptide hormone secretion and regulation, protease activity, glucose metabolism, adenosine deaminase, gtp-bound protein binding, and transcription factor actions. \\n\\nmechanism: these genes are involved in transcriptional regulation and signaling processes through binding of dna and g-protein linked receptors, homeobox domains, cysteine-rich proteins]] \n", - "505 [[transcriptional regulation, MESH:M0496924, endocrine system regulation, GO:0006006, cell signalling, MESH:D020558, GO:0000981, GO:0005180, MONDO:0018815, MESH:D043484]] \n", - "506 [[GO:0140359, oxidoreductase, dehydrogenase/reductase, hydratase/isomerase, enzymes responsible for fatty acid beta-oxidation, enzymes catalyzing the]] \n", - "507 [[MESH:D018384, MONDO:0018815, atpases associated with diverse cellular activities, vitamin a family, GO:0004879, nad-dependent oxidoreductases, GO:0005783, MESH:D015238, cyclin-dependent protein kinase, hydratase/isomerase superfamily, GO:0005515, GO:0003677, GO:0050632, carnitine acyltransferase, MESH:D011960]] \n", - "508 [[MESH:D011494, GO:0016791, GO:0005525, protein-protein interaction, GO:0030552, GO:0000981, peptidyl-prolyl cis/trans isomerase, cytoskeletal function, protein tyrosine phosphatase, protein phosphatase, GO:0140597, MESH:D020662, receptor interacting protein, transmembrane glycoprotein, MESH:D018123, MESH:D054387, inositol trisphosphate receptor, plexin domain, phosphoinositide 3-kinase, ubiquitin activation/conjugation, GO:0003925]] \n", - "509 [[MESH:D011494, guanine nucleotide-binding protein, receptor-interacting protein, chaperone protein, protein tyrosine kinase, MESH:D020558, MESH:D000262, protein phosphatase, cytoplasmic face, GO:0006468, GO:0007165, GO:0036211]] \n", - "510 [[MESH:D008565, MESH:D020558, coatomer complex, GO:0016192, MESH:D001678, GO:0035091, GO:0065007, MESH:D002966, GO:0005906, GO:0005794, GO:0030136, MONDO:0018815, GO:0042393, GO:0005802, MESH:M0013340, GO:0006811, GO:0005159, GO:0005783, MESH:D057056, GO:0005483, GO:0005764, GO:0005794, multifunctional proteins]] \n", - "511 [[this list of genes codes for proteins of various functions, primarily related to organelle trafficking, membrane associations, and receptor binding activities. these proteins are involved in the regulation of intracellular vesicles, endoplasmic reticulum and golgi organization, protein sorting and secretion, cell surface receptor binding, cell-signaling and immunity, protein phosphorylation and kinase binding, and lipid protein modifications. the enriched terms found in the functions of these genes include vesicular transport, MESH:M0354322, organelle trafficking, GO:0007030, GO:0005102, GO:0006457, GO:0006468, snare recognition molecules, clathrin coated vesicles, endoplasmic reticulum-golgi transport, MESH:D025262, GO:0005906, and dystrophin-glycoprotein complex. \\n\\nmechanism: the enriched terms in the gene functions indicate that these proteins are involved in various pathways and process of intracellular cargo trafficking, where proteins, membranes and signaling molecules are sorted, distributed and regulated. the processes are involved with vesicular transport, protein co-translocation, GO:0030258, and protein phosphorylation, which coordinate the mobilization and distribution of proteins, MESH:D008055]] \n", - "512 [[this list of genes were found to be involved in oxidoreductase activity, intracellular binding and catalytic activity, cellular response regulation, dna and transcription regulation, membrane function, mitochondrial function and antioxidant activity. the enriched terms include oxidoreductase activity, intracellular binding, GO:0003824, cell growth regulation, transcription regulation, membrane function, mitochondrial function, GO:0016209, GO:0020037, GO:0005507, GO:0003677, GO:0043565, tyrosine-specific protein kinase activity, f-actin binding. the underlying biological mechanism is probable related to redox homeostasis, the oxygen metabolism pathway, the cell cycle dna repair pathways, the regulation of transcription membrane function]] \n", - "513 [[redox processes, MESH:D018384, GO:0006281, GO:0008152, cell growth regulation, inflammation control, cellular defense, MESH:D006419, MESH:D005980, superoxide dism]] \n", - "514 [[cell cycle regulatory proteins and kinases, dna binding proteins and chaperones, nucleotide and polypeptide binding proteins, GO:0016791, proteins involved in transcription, gene transcription, GO:0051276, apoptosis regulation, GO:0006281, protein folding and transport, cell signaling and growth regulation, MESH:D004734, cytoskeletal organization, vesicular trafficking\\n\\nmechanism: the underlying biological mechanism is likely involved in multiple steps in cell division and the regulation of gene expression, and in the maintenance of cell homeostasis]] \n", - "515 [[this list of genes is associated with a range of diverse functions, including intracellular and intercellular trafficking, adhesion, enzyme regulation, transcriptional regulation, ion channel and receptor regulation, and processes related to stress, GO:0007568, and metabolism. common enriched terms include protein kinase and phosphatase, GO:0140359, g-protein coupled receptors, receptors, transcriptional regulation, GO:0016569, GO:0051726, heat shock, GO:0005515, ubiquitin-protein ligase and ubiquitin protease, zinc metalloproteases, and peptide n-acetyltransferase. the underlying biological mechanism or pathway associated with these genes may involve signal transduction as mediated by enzyme activity, MESH:D007473, receptors, and other proteins, as well as cell-to-cell adhesion and trafficking processes involved in membrane dynamics.\\n\\nsummary: list of genes associated with diverse functions including intracellular and intercellluar trafficking, adhesion, regulation of enzymes, GO:0006351, ion channels and receptors, and processes related to stress, GO:0007568, and metabolism.\\nmechanism: signal transduction as mediated by enzyme activity, MESH:D007473, receptors, and other proteins, as well as cell-to]] \n", - "516 [[the human gene summaries represent a variety of cell signaling, cell growth and differentiation, transcription regulation, adhesion and migration, and apoptosis-related functions. several genes in the list (acvr1, GO:0005680, arid4b, bmpr1a, bmpr2, cdh1, ifngr2, junb, lefty2, map3k7, ncor2, ppm1a, pp1ca, rahb, smad1, smad3, smad6, smurf1, smurf2, tgfb1, tgfbr1, MESH:D016212, cdk9, cdkn1c, ctnnb1, eng, fnta, MESH:D045683, hipk2, id1-3, klf10, ltbp2, pmepa1, ppp1r15a, serpine1, ski, skil, slc20a]] \n", - "517 [[GO:0007165, transcription regulation, cell-to-cell communication, MESH:D018398, serine/threonine protein kinase, disulfide-linked homotrimeric proteins, protein phosphatase, transmembrane proteins, smurf protein, cystein-rich motif, GO:0006457]] \n", - "518 [[transcriptional regulation, GO:0005125, GO:0008283, GO:0006629]] \n", - "519 [[GO:0006954, GO:0007165, transcriptional regulation, GO:1901987, cytokine, MESH:D011506, receptor, GO:0000981, enzyme, growth factor, MESH:D019204, chemokine, MESH:D008074, pentraxin protein, GO:0016791, MESH:D010770, stress response]] \n", - "520 [[GO:0003723, transcription regulation, GO:0006457, protein targeting and covalent modifications, endoplasmic reticulum function, GO:0006413]] \n", - "521 [[GO:0006412, endoplasmic reticulum stress response, GO:0003723, protein expression, conformation folding]] \n", - "522 [[GO:0007155, GO:0005207, nuclear phosphoprotein, phosphoprotein, cytoplasmic receptor, MESH:D020558, GO:0016791, receptor tyrosine kinase, GO:0006351, camp, ion transport atpase, transmembrane protein]] \n", - "523 [[GO:0000981, receptor, GO:0005488, growth factor, phosphoprotein, MESH:D010770, cytoplasmic surface, nuclear histone/protein methyltransferase, MESH:D020558, wd repeat protein, protein tyrosine phosphatase, serine/threonine kinase, caveolae plasma membrane, g-protein coupled receptor, MESH:D000071377, ab hydrolase superfamily, microtubule-associated protein, protein-tyros]] \n", - "524 [[GO:0005515, MESH:D002384, transcriptional regulation, cell signaling, metabolic reactions]] \n", - "525 [[regulatory proteins, GO:0000981, membrane and transport proteins, structural proteins, MESH:D004798, biosynthesis of heme, cellular signaling, transcription control, GO:0008152, GO:0006955]] \n", - "526 [[cell-cell interactions, MESH:D047108, transcriptional regulation, GO:0006281, wnt signaling, notch signaling, hedgehog signaling, MESH:D044783]] \n", - "527 [[transcriptional regulation, GO:0001709, signaling pathway activation, MESH:D060449, notch pathway, hedgehog pathway, protein interactions, cell growth regulation, GO:0004672, GO:0030163, cell-cell interaction, cell-matrix interaction, protein ligase binding activity, GO:0004842, membrane-bound protease activity, transcriptional repressor, GO:0006338, notch receptor cleavage, intracellular domain formation, ectodomain shedding, MESH:D015533, nuclear receptor co-repressor]] \n", - "528 [[the provided list of genes and associated descriptions demonstrates variation in generic cellular processes like protein degradation, protein and nucleic acid binding and kinase activity, as well as specific pathways involving cytokine and chemokine signaling, transcriptional regulation and regulation of immune cell activity. across these processes, the significant terms enriched across the genes include: protein tyrosine kinase activity; protein/nucleic acid/oligomeric binding activities; protein ubiquitination; transcriptional and immune cell activation and proliferation; intracellular receptor signaling and nf-kappab pathways; and cell cycle regulation.\\n\\nmechanism:\\nthe identified genes likely affect several common pathways, including signaling pathways that mediate cell division, motility, adhesion, chemokine- and cytokine-mediated responses, and immune cell function. in particular, the proteins encoded by these genes likely play roles in the regulation of post-translational modifications, such as protein ubiquitination, and the regulation of gene transcription, likely in response to extracellular cues. additionally, the identified proteins may mediate the recruitment of the cbm signalosome, leading to the activation of nf-kappab pathways. finally, cell cycle-related processes]] \n", - "529 [[GO:0007165, GO:0008037, GO:0004721, GO:0061630, lipid enzyme, MESH:D011505, cgmp kinases, GO:0000981, protein scaffold, cytokine, adaptor protein, GO:0051301, adhesion, differentiation, GO:0006950, negatively regulated, MESH:D021381, cell fate and patterning, MESH:D002470, ligand-gated ion channel, GO:0051092, GO:0006569, er stress-induced protection, transmembrane glycoprotein, MESH:D050503, wnt gene family, GO:0016020]] \n", - "530 [[genes in this list are transcription factors involved in the development of various organ systems, such as the skin and cns, as well as responding to dna damage, GO:0006915, and cellular transformation. the enriched terms are transcription factor activity; gene expression regulation; cell cycle regulation; dna damage response; pluripotency; and embryo development.\\n\\nmechanism: the transcription factors in this list interact with dna, regulate gene expression, and influence cell cycle progression, GO:0006915, and cellular transformation. combined, these genes are thought to play a role in creating and maintaining cellular and tissue identity, as well as responding to environmental changes. this could be part of a larger mechanism that governs organism development and homeostasis]] \n", - "531 [[GO:0000981, zinc finger proteins, GO:0007049, MESH:D004249, MESH:D016147, MESH:D047108, stem cell maintenance, translocation, homeodomain]] \n", - "532 [[GO:0007155, GO:0016477, cell signalling, GO:0008152, GO:0006915, GO:0009653, GO:0007599, MESH:D007109, extracellular matrix maintenance]] \n", - "533 [[GO:0048729, matrix metalloproteinase inhibitor, regulated cell adhesion, cytoplasmic protein tyrosine kinase, GO:0005161, cytokine-induced gene expression, GO:0005583, cell signaling pathway, MESH:D015533, antimicrobial activity, GO:0031012, GO:0016477, GO:0008283]] \n", - "534 [[GO:0007165, transcription regulation, ion regulation, GO:0005515, cytoskeletal adaptor, MESH:D006023]] \n", - "535 [[GO:0000988, metal ion binding activity, dna binding activity, chromatin binding activity, rna binding activity, protein domain-specific binding activity, histone binding activity, methylated histone binding activity]] \n", - "536 [[GO:0051015, GO:0048870, GO:0004722, myosin-binding proteins, MESH:D002154, GO:0045010, GO:0005523, calcium sensitivity, MESH:D044767, GO:0003735, GO:0004930, GO:0042923, GO:0050262, GO:0061769, GO:0019674, GO:0007015, GO:0006936, GO:0055008, GO:0030838]] \n", - "537 [[actin filament binding activity, muscle alpha-actinin binding activity, actin monomer binding activity, tropomyosin binding activity, GO:0006936, GO:0045214, GO:0071691, GO:0045010, GO:0030838, muscle excitation-contraction coupling, calcium release complex, muscle associated proteins, GO:0030036, GO:0007507]] \n", - "538 [[GO:0030030, MESH:D021381, MESH:D011494, GO:0048870, membrane reorganization, GO:0006897, cytoskeletal reorganization, mitogen-activated protein kinase, lysosomal degradation, GO:0051168]] \n", - "539 [[GO:0006897, lysosomal degradation, GO:0015031, GO:0006898, membrane processes, gtpase regulation, MESH:D044767, death domain-fold]] \n", - "540 [[GO:0006006, GO:0006096, GO:0016310, GO:0006000, GO:0006094, GO:0004332, glycogen storage, GO:0016853, GO:0004743, GO:0004396]] \n", - "541 [[GO:0006096, GO:0008152, regulation of energy conversion, MESH:D024510, tumor progression, GO:0006094, GO:0001525, neurotrophic factor, MESH:M0025255]] \n", - "542 [[calcium homeostasis, calcium-channel activity, MESH:D007473, g-protein coupled receptor, ligand-gated ion channel]] \n", - "543 [[calcium homeostasis, calcium influx, GO:0007268, neuronal development, MESH:D058446, purinergic receptor, GO:0004972, MESH:C413185, g-protein coupled receptor]] \n", - "544 [[GO:0016049, GO:0006915, GO:0007165, serine/threonine kinase activator activity, GO:0035004, GO:0005085]] \n", - "545 [[GO:0006281, apoptosis regulation, GO:0007165, GO:0016049, nutrient and insulin levels, macromolecule metabolic process regulation, GO:1901987, GO:0006338]] \n", - "546 [[glycosyl hydrolase, glycosyl bond hydrolysis, oligosaccharide processing, MESH:D006023, MESH:D011134, n-linked oligosaccharide, o-linked n-acetylglucosamine, β-1,4-glucosidase, β-glucosidase, β-hexosaminidase]] \n", - "547 [[glycosyl hydrolase, glycohydrolytic enzyme, MESH:D006821, MESH:D005644, lysosomal hydrolase, n-linked oligosaccharide processing, MESH:D001616, MESH:D001619, MESH:D001617, MESH:D009113, alpha-1,4-glucosidase, MESH:D043323, MESH:D000520, MESH:D055572, mannosidase, MESH:M0012138, alpha-l-iduronic acid, alpha]] \n", - "548 [[antigen binding activity, immunoglobulin receptor binding activity, activated/inactivated immune response, GO:0042803, peptidoglycan binding activity]] \n", - "549 [[antigen binding activity, immunoglobulin receptor binding activity, GO:0002253, GO:0042803, peptidoglycan binding activity, phosphatidylcholine binding activity, transduction of signals, allelic exclusion, myristylation, palmitylation, protein tyrosine kinases, sh2 and sh3 domains, MESH:D008285, MESH:D010455, antigen presenting cells, preb cells, src family of protein tyrosine kinases (ptks), c-type lectin domain]] \n", - "550 [[the gene summaries indicate that most of the genes are involved in processes related to dna binding, GO:0006281, GO:0006310, and meiotic processes. the enriched terms include \"dna binding\", \"dna repair\", \"dna recombination\", \"meiosis\", \"double-stranded dna binding\", \"single-stranded dna binding\", GO:0003682, GO:0004519, dead-like helicase activity, and bcl-2 homology domain activity.\\n\\nmechanism: the mechanism underlying the enrichment of these gene functions appears to be related to the repair and maintenance of chromosomal integrity as well as the regulation of cell division, differentiation, and development. through their combined activities, the genes appear to be involved in the maintenance of genome stability and the efficient transmission of genetic information from one generation to the next]] \n", - "551 [[GO:0006281, meiotic recombination, GO:0006302, GO:0035825, chromosome synapsis, GO:0007059, MESH:D023902, holliday junction resolution, dna strand-exchange, reciprocal recombination, GO:0007130, GO:2000816, positive regulation of response to dna damage, GO:0006611, GO:0031297, GO:0000712, GO:0060629, GO:0003677, GO:0003697, single-str]] \n", - "552 [[GO:0005515, GO:0046907, GO:0043161, GO:0051726, regulation of cell growth and survival, cholesterol and lipids metabolism, nf-κb inhibiting proteins, GO:0009792, GO:0007283, GO:0045087, cytokines and growth factors, antioxidant enzymes, GO:0030097]] \n", - "553 [[GO:0006897, iron storage, GO:0008610, GO:0006915, GO:0008283, GO:0030154, defense from bacterial infection, transcription regulation, translation regulation]] \n", - "554 [[GO:0006412, GO:0008152, GO:0006457, MESH:D054875, GO:0006351, GO:0003677, damage control, GO:0032502, cellular pathway regulation, GO:0006915, GO:0007049, GO:0030163]] \n", - "555 [[GO:0008152, GO:0023036, GO:0007165, transcriptional regulation, epigenetic regulation, GO:0044183, proteolytic activity, GO:0051726]] \n", - "556 [[peroxisome biogenesis, peroxisomal protein import, tripeptide peroxis]] \n", - "557 [[aaa atpase family, MONDO:0019234, peroxisomal protein import, peroxisomal matrix protein import, heteromeric complex, peroxisome targeting signal 2]] \n", - "558 [[the genes in this list are associated with post-translational proteolytic cleavage, intermolecular integration, dna repair and dna helicase activity, and nuclear stability and chromatin structure. the underlying mechanism is likely related to protein modification and regulation of cellular components involved in dna metabolism and gene expression. the enriched terms include protein modification, proteolytic cleavage, GO:0003678, intermolecular integration, GO:0006281, chromatin structure, nuclear stability]] \n", - "559 [[this set of genes is involved in the maintenance of genome stability and chromosome integrity, likely in terms of forming the nuclear lamina and promoting nuclear reassembly. the enriched terms are genome stability, chromosome integrity, GO:0005652, nuclear reassembly.\\n\\nmechanism: the set of genes are likely working together to form and maintain a matrix of proteins which form the nuclear lamina next to the inner nuclear membrane, thus providing stability to the genome and the chromosomes by helping to organize the dna within the nucleus. this is achieved through binding with both dna and inner nuclear membrane proteins and recruiting chromatin to the nuclear periphery to achieve nuclear reassembly]] \n", - "560 [[MESH:D007473, voltage-gated ion channel, MESH:D015221, ligand-gated ion channel, MESH:D018079, MESH:D017470, MESH:D015222]] \n", - "561 [[GO:0007268, MESH:D009482, inhibitory, excitatory, MESH:D017981, MESH:D015221, MESH:D018079, MESH:D017470, MESH:D007649, GO:0009451, voltage-gated, MESH:D007473, MESH:D058446, MESH:D019204]] \n", - "562 [[GO:0000981, GO:0009056, moonlighting proteins, GO:0002377, adapter molecules, heme transporter, myelin upkeep, GO:0005643, mitochondrial dna polymerase, ubiquitin ligase, aminoacyl-trna synthetase.\\n\\nmechanism: these genes work together in a joint mechanism to regulate biological processes like cell replication, neuronal development, protein folding, and enzymatic activity. in particular, their collective involvement in the coordination of transcriptional activity, ion transport, and dna-binding suggests a complex integrated process by which these genes serve to facilitate normal cell functions]] \n", - "563 [[GO:0000981, dna helicase, nerve myelin maintenance, mechanically-activated cations channels, nerve motor neuron survival, MESH:D054875]] \n", - "564 [[the summaries of the provided gene functions describe proteins linked to the activity and regulation of g-protein coupled receptor signaling pathways, including dopamine, MESH:D016232, and serotonin receptors, as well as proteins involved in calcium ion regulation, GO:0003677, and apoptosis. statistically over-represented terms include: g-protein coupled signaling; calcium ion regulation; transmembrane signaling; dna binding; and apoptotic process. \\n\\nmechanism:\\nthe common function of these genes is likely to be linked to the regulation of g-protein coupled signaling pathways, which regulate a variety of cellular processes, including cellular signaling and growth, neuronal development, apoptosis. calcium ion regulation transmembrane signaling are also likely to be important for the functioning of these genes. dna binding proteins proteins that enable clathrin light chain binding activity may be involved in the transcriptional regulation of these signals]] \n", - "565 [[this gene set was comprised of dopamine and g-protein coupled receptors that participate in cellular signaling pathways and influence cellular functions such as metabolism and behavior. the genes are involved in a wide range of pathways such as signal transduction, transcriptional regulation, memory and behavior, GO:0007612, neural development and synaptic plasticity. the enriched terms in this list include: signal transduction, g protein-coupled receptor, camp, MESH:D000262, MESH:D054799, MESH:D017868, calcium ions, transcriptional regulation, GO:0000981, MESH:D011954, wnt and pi3k signaling pathways, neuronal growth and development, GO:0010467, and synaptic receptors.\\n\\nmechanism: this gene set is involved in many pathways such as signal transduction, transcriptional regulation, and synaptic organization. signal transduction occurs through g-protein coupled receptors and camp, which in turn regulate downstream effectors including adenylyl cyclase, MESH:D017868, and calcium ions. furthermore, transcriptional regulation occurs through various receptor signaling pathways, such as those related to the wnt and pi3k pathways, while dopamine receptors regulate neuronal growth and development, GO:0010467, and behavior. finally, synaptic receptors enable]] \n", - "566 [[dna-binding, chromatin-binding, transcriptional regulation, e-box dna consensus sequence binding, dna damage response regulation, dna damage response maintenance, phosphoprotein shutting, MESH:D016335, interaction with cellular retinol-binding protein, hormone-dependent transcription, receptor-dependent transcription, nuclear hormone receptor-dependent transcription, transcriptional coactivator complex recruitment, GO:0000785]] \n", - "567 [[transcriptional regulation, dna-binding, chromatin binding activity, histone binding activity, GO:0000988]] \n", - "568 [[GO:0001501, GO:0032964, cell-matrix interactions, extracellular matrix remodeling, cell signaling]] \n", - "569 [[collagen production, GO:0061448, matrix remodeling, zinc finger protein regulation]] \n", - "570 [[GO:0006281, homologous recomination, MESH:M0006667, GO:0004518]] \n", - "571 [[MONDO:0100339, dna/rna damage response, dna/rna metabolism, GO:0051726, genome stability, MONDO:0019391]] \n", - "572 [[metabolic regulation, GO:0050658, GO:0006412, cell membrane transport, transcription regulation, GO:0006915, GO:0006457, GO:0019432, GO:0003676, GO:0006633, GO:0006096, GO:0045454]] \n", - "573 [[GO:0008152, MESH:D004734, GO:0007165, GO:0006119, transcriptional regulation, GO:0006468, GO:0051726, GO:0006629, GO:0006457, protein assembly, mitochondrial function, GO:0006915, GO:0006839, GO:0055085, GO:0007010, GO:0006094, GO:0006096, GO:0042632]] \n", - "574 [[immune signalling, GO:0051726, cellular differentiation, transcriptional regulation]] \n", - "575 [[genes in this list are representative of various pathways involved in cell movement, GO:0019882, GO:0006954, immune regulation, and cell signaling events including jak-stat and mapk- pi3k pathways. enriched terms include “immune system processes”; “immune recognition pathways”; “cytokine-mediated signaling pathways”; “inflammatory response”; “cellular immune activation”; “intestinal immune network for iga production”; “cytokine secretion”; “tcr signaling pathway”; “cd4 t cell activation”; “t lymphocyte differentiation”; “innate immune response”; and “cytokine-cytokine receptor interaction”.\\n\\nmechanism: the genes are involved in pathways that affect cell movement, GO:0019882, GO:0006954, immune regulation, and cell signaling. these pathways control the activation, response, differentiation, and survival of t cells by regulating cytokine expression, activation of specific receptors, production of antibodies, regulation of transcription factors and their binding to promoters, other immune system processes]] \n", - "576 [[genes in this list are mainly involved in regulation of skeletal tissue formation and development, signal cascade activation, protein folding, cellular metabolism and movement, cell cycle regulation, and transcriptional regulation. the underlying biological mechanism may be related to the complex network of interactions among these genes in controlling the basic functions of a cell. the enriched terms are: bone morphogenesis, GO:0001501, signal cascade activation, GO:0006457, GO:0044237, cellular movement, GO:0051726, transcriptional regulation, chromatin and dna modification]] \n", - "577 [[gene transcription and regulation, protein translation and metabolism, cytoskeletal organization, GO:0006629]] \n", - "578 [[GO:0030198, vascularization, endothelial cell aggregation, GO:0007155, cell surface interactions]] \n", - "579 [[cytokine receptor signaling, growth factor signal transduction, transmembrane and extracellular matrix proteins, development of muscle, bone, and neuronal networks]] \n", - "580 [[GO:0060348, joint development, MESH:D024510, GO:0061448, GO:0007155, adhesion receptor complex formation, GO:0007165, receptor-mediated signaling cascades]] \n", - "581 [[GO:0007155, GO:0016477, migration and interaction, cytoskeletal organization, actin cytoskeletal regulation, GO:0007165, regulation of actin cytoskeletal organization]] \n", - "582 [[cell regulation, GO:0007165, GO:0007155, GO:0006457, GO:0030198]] \n", - "583 [[cell adhesion and migration, cell signaling, GO:0030154, protein kinase and phosphatase activities, transcription and dna metabolism, MESH:D056747, glycosylation and carbohydrate metabolism, cell growth and proliferation]] \n", - "584 [[GO:0006915, transcription regulation, cell cycle progression, GO:0006954, GO:0006260, GO:0006281, oxidative stress response, immune system activation]] \n", - "585 [[cell death regulation, GO:0006954, immune reaction, growth and morphogenesis, UBERON:2000098, GO:0006915, GO:0006281, GO:0030217, GO:0001816, GO:0051726, fast axonal transport, extracellular proteolysis, GO:0007155, GO:0042060, MESH:D009362, MESH:D063646, GO:0016477, regulation of nf-kb pathway]] \n", - "586 [[GO:0006629, GO:0006869, organ development, cell signaling, GO:0006412, transport processes]] \n", - "587 [[GO:0006629, GO:0006536, serine metabolism, transcription factor regulation, oxidative stress response]] \n", - "588 [[GO:0006629, GO:0008203, cell signaling and regulation, GO:0032502, GO:0007155, GO:0006915, GO:0006351]] \n", - "589 [[GO:0006629, cholesterol control, GO:0009062, GO:0006699, hmgcr regulation, pmvk regulation, fads2 regulation, srebf2 regulation, s100a11 regulation, mvk regulation]] \n", - "590 [[extracellular matrix remodeling; angiogenesis and vascular development; immune response and platelet activation; collagen and fibronectin metabolism and regulation; endocytosis and signal transduction; \\nmechanism: the genes in this list work together to control and regulate multiple relevant processes, such as extracellular matrix remodeling, which is the process of breaking down and reorganizing the components of the extracellular matrix in order to facilitate tissue development and repair, angiogenesis and vascular development, which regulate the formation of new blood vessels and ensure proper blood flow throughout the body, immune response and platelet activation, which are necessary to protect the body from foreign agents and to form healthy blood clots, collagen and fibronectin metabolism and regulation, which are important for tissue integrity and structure, and endocytosis and signal transduction, which are necessary for cellular communication and regulation]] \n", - "591 [[GO:0007155, proteolysis regulation, extracellular protein-cell interaction, migration, GO:0050817, GO:0006956]] \n", - "592 [[development of tissue and organs, GO:0007165, cell surface receptor binding, GO:0050896, UBERON:0002405, GO:0006955, GO:0005125]] \n", - "593 [[cellular signalling, GO:0006954, cell stress response, cell-cell interaction, GO:0007165, GO:0045087, cytoskeletal remodelling, GO:0006457, GO:0050900, GO:0004672, GO:0007155, MESH:D005786, GO:0006260, protein activation, GO:0019763, GO:0002377, GO:0016791]] \n", - "594 [[GO:0032502, GO:0006260, MESH:D047108, GO:0030154, transcription regulation, GO:0006335, nuclear mrna surveillance pathway, GO:0016070, GO:0006281, GO:0140014, rna-dependent dna replication]] \n", - "595 [[nucleic acid metabolism, GO:0006351, post-transcriptional modifications, GO:0006338, GO:0000398, GO:0006281, rna polymerization, GO:0006397, GO:0051028, GO:0006413]] \n", - "596 [[transcriptional regulation, GO:0016569, mitotic division, GO:0051726, MESH:D004268, MESH:D006657, GO:0000981, MESH:D004259, MESH:D012321, chromatin remodeling proteins, ubiquitin ligases, nucleosome assembly proteins, helicases, motor proteins, GO:0000075]] \n", - "597 [[GO:0006260, GO:0006281, GO:0016569, transcription regulation, translation regulation, protein-protein networks, GO:0051225, kinesin motor proteins, dynein motor proteins]] \n", - "598 [[GO:0031012, GO:0007155, GO:0048870, cell-matrix interaction, growth factor signaling, cytokine signaling, matrix remodeling]] \n", - "599 [[GO:0048705, cell-cell adhesion and motility, extracellular matrix production and remodeling, connective tissue development and differentiation, collagen production and turnover, cytokine and chemokine signaling]] \n", - "600 [[GO:0006260, GO:0006351, GO:0010467, GO:0016049, differentiation, GO:0016485, trafficking, GO:0060349, cancer-related pathways, GO:0098609, matrix remodeling, intracellular signaling, external signals, internal signals]] \n", - "601 [[transcriptional regulation, GO:0007165, protein-protein interactions, GO:0055085, GO:0008610]] \n", - "602 [[GO:0030198, GO:0007155, GO:0016477, GO:0048870, growth factor signaling, cytoskeletal organization]] \n", - "603 [[GO:0030198, GO:0000988, receptor signaling pathway, GO:0007269, GO:0019725, GO:0006508, immunological responses, GO:0016049, GO:0003677, GO:0006629]] \n", - "604 [[metabolic pathways; cellular functions; energy metabolism; lipid metabolism; amino acid metabolism; dna damage repair; cell signaling.\\nmechanism: the genes listed here are likely involved in the various metabolic pathways and cellular functions, perhaps through the production of enzymes, MESH:D011506, or other molecules that contribute to energy metabolism, GO:0006629, amino acid metabolism, dna damage repair, cell signaling]] \n", - "605 [[GO:0006629, cell cytoskeleton, GO:0008610, GO:0016042, lipid transportation, GO:0034440, cell membrane biogenesis, GO:0048870, cell traffic, cell signaling]] \n", - "606 [[GO:0006260, GO:0006351, GO:0051726, protein binding/interaction, chromatin modifiers/modification, GO:0006281, GO:0000988, GO:0006397, GO:0006915, ubiquitination and proteasomal degradation]] \n", - "607 [[genes involved in the list are mainly associated with dna replication, cell division and related functions. enriched terms include \"cell cycle\", \"dna replication\", \"chromatin modification\", \"transcription regulation\", \"cell division\", \"dna repair\", \"transcriptional regulation\", \"chromosome segregation\".\\n\\nmechanism: these genes likely play a role in the coordination of the many steps and activities involved in dna replication, GO:0051301, and related cellular processes. the cell cycle is an area of particular interest due to its critical role in the growth and division of cells. dna replication, modification, repair occur during cell division in order to produce maintain copies of genetic information. chromatin modifications occur during cell division in order to package regulate genomic information. transcriptional regulation involves the control of gene expression the production of proteins other materials essential for the maintenance of cellular functions. chromosome segregation cell division serve to divide replicated genetic material into daughter cells]] \n", - "608 [[the genes in this list are involved in a variety of cellular processes including protein translation, GO:0070085, regulation of ion channels, gene transcription and dna replication. the enriched terms identified are: translation; glycosylation; ion channels; gene transcription; and dna replication.\\n\\nmechanism: the common underlying mechanisms of the genes in this list likely involve cellular processes such as protein translation, GO:0070085, regulation of ion channels, gene transcription and dna replication. these processes are essential for the regulation of cell functions and the maintenance of a stable organism]] \n", - "609 [[structural proteins, GO:0006096, GO:0006098, GO:0006099, GO:0007155, GO:0030166, extracellular matrix formation, cytoskeletal assembly]] \n", - "610 [[the provided genes are involved in a variety of different processes ranging from morphogenesis, development and growth of the digits/limbs, neuronal migration and regulation of cell proliferation. the underlying biological mechanism might be related to the modulation of cell migration, development of neural connections, formation of complex structures, maintenance of body plan and tissue development. enriched terms are: morphogenesis, digit/limb development, GO:0001764, GO:0042127, modulation of cell migration, development of neural connections, formation of complex structures, maintenance of body plan, GO:0009888]] \n", - "611 [[neuron formation, GO:0007155, migration, GO:0007165, GO:0048729, GO:0007399]] \n", - "612 [[GO:0044237, energy production and transport, cytoskeleton modification, cytoskeleton remodelling, GO:0007155, MESH:D004735, MESH:M0496924, cellular transport, cellular reorganization]] \n", - "613 [[MESH:D047108, GO:0001501, GO:0048513, GO:0009653, GO:0040007, GO:0002376, GO:0048870, GO:0003707, receptor signaling pathway, GO:0006810, GO:0006897, GO:0019725]] \n", - "614 [[GO:0007049, remodeling proteins, stress response proteins, calcium signaling proteins, hypoxia-inducible factor proteins, GO:0000981, chromatin-associated proteins, MESH:D010770]] \n", - "615 [[GO:0032502, cell structure and movement, cell cycle and division, GO:0007165, GO:0006810, energy production]] \n", - "616 [[immunological function, GO:0030036, MESH:D011956, pro-inflammatory regulation]] \n", - "617 [[MESH:D007109, GO:0006954, GO:0016049, differentiation, GO:0032502, GO:0007165]] \n", - "618 [[cell signaling, GO:0001816, cytokine regulation, MESH:D005786, transcription regulation, GO:0007155]] \n", - "619 [[cytokine regulation, chemokine regulation, interleukin regulation, cellular differentiation, cell motility and adhesion, GO:0007165, GO:0006954]] \n", - "620 [[this list of genes is significantly enriched for the functions of cell signalling, cytokine mediated immunity, receptor signalling, and tissue morphogenesis. furthermore, the list contains several genes associated with the immune response, including tlrs and ifns, as well as cytokines and chemokines such as ccl17, ccl20, cxcl10, cxcl9, ifnar1, tnfrsf1b, and tnfsf10. in addition, several receptors were found to be enriched on the list, including gpr132, axl, c3ar1, MONDO:0043317, and ccr7. finally, key genes involved in tissue morphogenesis were also found on the list, such as adgre1, edn1, btg2, ccl2, tacr1, and cxcr6.\\n\\nmechanism: \\nthe underlying mechanism for this enrichment of genes is likely related to the common activities of cell signalling, cytokine mediated immunity and tissue morphogenesis. the list of genes is likely regulating common processes such as cell-cell communication and inflammation. additionally, the list of genes may be involved in the development and maintenance of tissue structures, such as muscle tissue]] \n", - "621 [[GO:0006955, cellular activation, receptor-coupled pathways, transcriptional regulation, cytokine and cytokine receptor binding, GO:0006629, GO:0007155]] \n", - "622 [[analysis of this list of genes reveals that they are all involved in the functioning of the immune system in some way, either through regulation of inflammatory response pathways, recognition of foreign agents, or production of molecules defending against potentially harmful intruders. the enriched terms include \"immune system regulation\"; \"inflammatory response\"; \"foreign agent recognition\"; \"antimicrobial defense\"; \"interferon signaling\"; \"antiviral defense\". \\n\\nmechanism: the genes in this list combined likely regulate a wide variety of immune system functions, including modulating inflammation, recognizing and responding to foreign antigens, producing effector molecules against potentially harmful microorganisms, promoting interferon signaling cascades to defend from viral invasion]] \n", - "623 [[GO:0006955, GO:0006954, cytokine signaling, interferon response, GO:0006355, interferon-stimulated genes]] \n", - "624 [[MESH:M0000731, GO:0019882, GO:0006954, chemokine signaling, GO:0007155, cytokine interactions]] \n", - "625 [[interferon signaling, antigen processing, presentation, and recognition, cytokine signaling, cell cycle and dna damage response, GO:0006915]] \n", - "626 [[digit development, neural development, GO:0002520, transcriptional regulation, g-protein coupled receptors, MESH:D011494, MESH:D020662]] \n", - "627 [[our analysis revealed the enrichment of the gene functions related to development, GO:0007165, transcription and metabolism. specifically, some of the enriched terms include cellular development, GO:0016049, GO:0001501, GO:0048598, cell junction organization and assembly, GO:0007165, GO:0007049, GO:0006351, and cellular metabolism.\\n\\nmechanism: these gene functions may be related to the biological mechanism of growth, differentiation, and development of cells. the signals and transcription are likely involved in regulating and controlling these processes, as well as providing energy through metabolic pathways. additionally, the cell junction processes are likely involved in the coordination and communication between cells, which is essential to development]] \n", - "628 [[GO:0007165, GO:1901987, cell-to-cell adhesion]] \n", - "629 [[integrin, chemokine receptor, MESH:D011494, g-protein-coupled receptor, cytoskeleton proteins, cell-extracellular matrix interaction, type i ifn-mediated innate immunity, wnt signaling, MESH:D020558, MESH:D010740, MESH:D008565, MESH:D016326, receptor tyrosine kinase, toll-like receptor signaling, tlr adaptor proteins]] \n", - "630 [[GO:0007049, GO:0007155, cytoskeletal organization, GO:0004672, GO:0003924]] \n", - "631 [[GO:0051301, GO:0006468, GO:0006338, GO:0008017, microtubule organization, GO:0051225, GO:0007059, GO:0051305, cell-cycle control, GO:0140014]] \n", - "632 [[genes in this list are involved in various aspects of cellular metabolism, GO:0065007, and development.a number of the genes have roles in energy production and metabolism such as, atp2a2, aldoa, MONDO:0009214, fao1, fgl2, gapdh, gbe1, MONDO:0015408, glrx, MONDO:0005775, me1, phgdh, and pgm1. there is a strong presence of genes involved in protein synthesis and transport, including the ribosomal proteins, the eukaryotic translation factors and initiation factors (eif2s2, eif1e1, elovl5, and elovl6). this gene set is also enriched for a number of ubiquitin and ubiquitin-like proteins (ube2d3, ufm1, uso1, tomm40, hspd1, hspe1, sytl2, nherf1, and hk2). many of these genes are involved in regulation through multiple pathways including regulation of transcription (add3, actr2, actr3, cct6a, gga2, gdh2, mef2b, ykt]] \n", - "633 [[GO:0006412, transcription regulation, GO:0009653, GO:0016049, GO:0007165, GO:0008152, GO:0006629, cellular translation]] \n", - "634 [[GO:0006412, GO:0036211, GO:0006260, GO:0051726, transcription regulation, GO:0016049, GO:0048468, gene expression.\\nmechanism: the genes may constitute a pathway in which they coordinate together to regulate cell growth, development, and gene expression]] \n", - "635 [[developmental regulation, energy production, GO:0006412, structural maintenance of cell components, GO:0006260, transcription regulation, protein assembly]] \n", - "636 [[protein post translational modification, GO:0016310, GO:0006351, GO:0006412, GO:0042254]] \n", - "637 [[transcription regulation, GO:0006338, nucleosome remodeling, GO:0006260, nuclear localization, GO:0007165, GO:0016567, GO:0006468]] \n", - "638 [[genes in this list are associated with various cellular functions, including cell cycle regulation, developmental pathways, contractile force generation, protein synthesis and degradation, GO:0006915, GO:0000988, and metabolic processes. enriched terms include: cell cycle; cell differentiation; transcriptional regulation; intracellular signaling; muscle contraction; metabolism; apoptosis; protein synthesis; protein degradation.\\n\\nmechanism:\\n\\nthe genes in this list code for proteins involved in a range of cellular processes, including transcription factors that regulate gene expression, receptors that initiate intracellular signaling cascades, enzymes involved in metabolic pathways or apoptosis, and ion channels involved in muscle contraction and cell cycle regulation. these proteins interact to regulate the expression and activity of other proteins, impacting the activity of many important pathways that together coordinate cell growth, differentiation, MESH:D009068, GO:0008152]] \n", - "639 [[the genes that were analyzed were related to development, cell signalling, GO:0008152, GO:0065007, GO:0006936, MESH:D055550, and transport. the enriched terms were cellular development, actin cytoskeleton regulation, cell migration and adhesion, GO:0051726, calcium homeostasis and signaling, GO:0006936, GO:0006119, receptor tyrosine kinase signaling, apoptosis and programmed cell death, GO:0030198, GO:0016567, GO:0042632, metabolism and energy production, cell death and apoptosis, cytoskeletal protein binding and regulation of transcription and translation.\\n\\nmechanism: the underlying biological mechanism or pathways involved in these genes include regulation of muscle contraction, cell adhesion and migration, calcium homeostasis, protein ubiquitination and stability, receptor signaling, GO:0051726, GO:0006119, GO:0008219, and regulation of transcription and translation. these mechanisms are essential for cellular development and function, and thus, are enriched in these gene list]] \n", - "640 [[GO:0009653, GO:0048513, GO:0009888, GO:0001709, MESH:D002450, notch receptor signaling, wnt signaling, transcription factor signaling]] \n", - "641 [[GO:0008283, GO:0009653, GO:0032502, nerve system differentiation, transcription regulation, wnt signalling pathway, GO:0007219]] \n", - "642 [[the list of genes provided are primarily involved in energy metabolism, GO:0007585, and the electron transport chain. specifically, terms such as \"oxidative phosphorylation\", \"mitochondrial electron transport chain\", and \"tricarboxylic acid cycle\" are found to be significantly over-represented.\\n\\nmechanism: the genes provided are involved in the production of atp through metabolic pathways such as oxidative phosphorylation, GO:0005746, and the tricarboxylic acid cycle. these molecules, along with other regulatory proteins, facilitate the flow of electrons to generate energy in the form of atp. this energy is used by cells to carry out metabolic reactions and various cellular processes]] \n", - "643 [[mitochondrial electron transport chain complex activity, GO:0006120, GO:0005747]] \n", - "644 [[analysis of this list of genes suggests a function related to cell cycle regulation, GO:0006915, and protein translation. the enriched terms include 'cell cycle regulation', 'apoptosis', 'protein translation', 'transcription regulation', 'intracellular protein transport', 'protein synthesis', and 'dna repair'.\\n\\nmechanism: the list of genes may be associated with a mechanism related to the regulation of cell cycle transitions and the integration of external signals to regulate gene transcription, protein translation and stability, and cellular apoptosis. this could involve some combination of signal transduction, GO:0006355, GO:0043687, GO:0006281]] \n", - "645 [[gene expression and protein metabolism are likely to be enriched. specifically, the genes are likely involved in protein folding and transport, GO:0016567, transcriptional regulation, GO:0051726, protein-protein interactions, and signal transduction. \\nmechanism: these genes likely play a role in common metabolic, GO:0023052, and regulatory pathways.\\nubiqutination terms: rchy1, hexim1, upp1, pom121, procr, tap1, phlda3, wwp11; \\ntranscription factors:cd81, sat1, ercc5, ralgdh, irak1, aen, tob1, stom, MONDO:0100339, rap2b, tm7sf3, lif, MESH:C058179, ccp110, baiap2, tnfsf9, dcxr, eps8l2, ifi30, fdxr, elp1, itgb4, hbegf, irag2, ccnd2, sertad3, mknk2, retsat, ip6k2, hmox1, zfp36l1, epha2, tpd]] \n", - "646 [[GO:0031016, GO:0007399, development of neural structures, GO:0048513, transcription regulation, GO:0009653, cell-to-cell adhesion, GO:0006412, hormonal metabolism, hormonal signaling]] \n", - "647 [[GO:0022008, GO:0008152, GO:0006355, GO:0006412, GO:0009653, body patterning and organization, neurological system development, GO:0030154]] \n", - "648 [[GO:0006629, stress response, GO:0009299, GO:0006281, skeletal and cartilage development, GO:0016477, metabolic enzymes, MESH:D002352]] \n", - "649 [[GO:0008152, GO:0006351, GO:0065007, GO:0006810, GO:0007165, GO:0006412, GO:0030154, GO:0006260, GO:0036211, membrane trafficking]] \n", - "650 [[MESH:M0023730, GO:0009653, GO:0030154, tyrosine kinase activity, GO:0038023]] \n", - "651 [[cell signaling, GO:0019538, GO:0006629, transcription regulation, GO:1901987, GO:0007165, receptor signaling, GO:0070085, GO:0016301, GO:0006915, g-protein interactions, transcriptional regulation]] \n", - "652 [[cell membrane fusion, GO:0016192, intracellular trafficking, predominant cargo proteins, GO:0006900, membrane remodeling]] \n", - "653 [[GO:0043687, GO:0006457, GO:0006412, GO:0006897, GO:0009311, lysosomal trafficking]] \n", - "654 [[GO:0008152, oxidative damage resistance, GO:0006281, cellular metabolic regulation, GO:0006915, regulatory pathway, GO:0006457, GO:0006749]] \n", - "655 [[this list of genes is enriched for terms related to oxidative stress, GO:0008152, and immune system function. specifically, the genes represent proteins involved in oxygen-sensing, anti-oxidation, redox regulation, GO:0006281, the stress response, and cytokine signaling.\\n\\nmechanism:\\nthe underlying biological mechanism of the gene list is likely the cellular response to oxidative stress. oxidative stress is a term used to describe a disruption in the balance of antioxidant molecules and reactive oxygen species. these reactive molecules can cause damage to the cell, and thus the relevant genes likely help the cell to counteract this damage by regulating redox status, mediating oxidant stress, and participating in dna repair and other defense mechanisms. additionally, some of these genes are involved in cytokine signaling, which helps to aid the immune system in defending against potential oxidative insults]] \n", - "656 [[GO:1901987, GO:0006338, GO:0016567, GO:0006260, GO:0051225, GO:0006997]] \n", - "657 [[the list of genes provided are involved in diverse processes, such as cell structure and organization, GO:0007165, transcriptional regulation and other metabolic activities. the enriched terms from performing a term enrichment test are cell cycle, GO:0051301, GO:0016569, development and differentiation, cell signaling and signal transduction, GO:0006397, transcriptional regulation, and metabolic processes.\\n\\nmechanism:\\nthe genes provided are believed to be involved in a general mechanism of cell organization and function. the enriched terms are suggestive of the genes being related to fundamental processes such as cell cycle regulation, GO:0051301, transcriptional regulation, GO:0016569, and signal transduction. through the regulation of the genes, they are thought to be capable of controlling the organization and structure of cells, as well as metabolism and other cellular activities. furthermore, these pathways likely interact with each other in a complex manner, thereby allowing for intricate coordination between the genes in order to precisely tune process]] \n", - "658 [[genes in this set are related to morphogenesis, GO:0007155, immune signaling, and transcriptional regulation. enriched terms include: morphogenesis, GO:0007155, immune signaling, transcriptional regulation, digit development, GO:0007049, protein-protein interaction, GO:0008083, and regulation of transcriptional activity.\\n\\nmechanism: morphogenesis can be regulated by the activity of kinases, cell adhesion can be mediated by the expression of cell adhesion molecules, and immune signaling can be regulated by the activity of cytokines, MESH:D018121, and transcription factors. the transcriptional regulation of these genes can be mediated by transcription factors and the regulation of transcriptional activity can be mediated by modulators of tfs, such as kinases and ubiquitin ligases. protein-protein interactions can occur between the different genes, signaling from growth factors can affect the expression of genes in this set]] \n", - "659 [[transcriptional regulation, GO:0007165, GO:0051726, protein kinase pathways, GO:0006412, GO:0048468, GO:0008283, GO:0030054, cytoskeletal organization]] \n", - "660 [[GO:0002224, GO:0032502, GO:0006954, immune-response regulation, nfkb, GO:0004707, GO:0010467, pro-inflammatory molecules]] \n", - "661 [[cytokine-mediated signaling, antigen-receptor mediated signaling, GO:0042100, cytokine expression and release, immunoregulatory interactions, GO:0051092, interferon (ifn) signaling]] \n", - "662 [[GO:0006412, GO:0042254, GO:0006413, GO:0006457, GO:0006414, GO:0015833, peptide assembly, chaperone mediated protein folding]] \n", - "663 [[analysis of this gene list has revealed that the functions enriched in the gene set include translation and translation initiation (exosc2, eif4a3, MESH:D039561, eif4g1, eif4a2); ubiquitination (ern1, skp1, herpud1, ube2g2, ube2l3); and protein folding and stability (atf3, fkbp14, dnajb9, calr, preb, hspa5, hsp90b1).\\n\\nmechanism: the enriched functions imply a complex network of processes that is likely to involve translation initiation of mrna, GO:0016567, and chaperone activity that facilitates protein folding, stability and degradation. it is possible that this gene set is associated with a variety of cellular pathways, including those related to gene expression, GO:0007165, GO:0008152]] \n", - "664 [[cell signaling, structural proteins, MESH:D004798, GO:0009653]] \n", - "665 [[the above list of genes is significantly enriched for terms related to the development of the connective tissue, including morphogenesis, GO:0007049, regulation of transcription, and extracellular matrix organization; as well as the regulation of cell migration, matricellular protein signaling, GO:0007165, and calcium ion binding.\\n\\nmechanism: the enriched terms suggest that these genes work together in a common and interconnected pathway to control the formation, MESH:D009068, and functioning of the connective tissue. this pathway likely involves interactions among signal transduction pathways mediated by protein-protein interactions, transcriptional regulation, and calcium ion binding. these interactions would likely affect the structure and organization of the extracellular matrix, the migration of cells, the cell cycle, signalling through matricellular proteins]] \n", - "666 [[MESH:D021381, organelle trafficking, GO:0006306, transcription regulation, GO:0003677, GO:0006338, GO:0051726, GO:0008152]] \n", - "667 [[genes in this list are generally involved in the regulation of cell growth and development, in particular related to apoptosis, signaling and transcriptional pathways. enriched terms include: transcriptional regulation; cell cycle regulation; apoptosis regulation; signal transduction; dna damage response; and cellular metabolism.\\n\\nmechanism: the molecular and cellular mechanisms underlying cell growth and development are complex and interconnected. genes in this list are believed to be involved in several pathways, such as transcriptional regulation, GO:0051726, apoptosis regulation, GO:0007165, GO:0006974, and cellular metabolism. these pathways interact and regulate each other in order to ensure the healthy functioning of cells. transcriptional regulation is key in regulating gene expression, while the cell cycle is tightly regulated by the activation of cell cycle control proteins and anti-apoptotic pathways. signal transduction pathways are essential for the proper coordination of cellular responses to external stimuli, and dna damage response allows for the repair of any irregularities. cellular metabolism is necessary for providing energy for growth and repair, for controlling the production of proteins]] \n", - "668 [[the genes in this list are associated with the wnt signaling pathway, modulating cell growth and mophogenesis. the enrichment terms corresponding to this list are wnt signaling, GO:0016049, GO:0009653, transcriptional regulation, and epigenetics.\\n\\nmechanism: the wnt signaling pathway activates nuclear proteins such as lef1 and tcf7, which then activate transcription of genes involved in cell growth and morphogenesis. the genes on the listed are associated with modulating the wnt pathway, including epigenetic regulation and cell cycle regulation]] \n", - "669 [[GO:0009653, GO:0006351, GO:0032502, MESH:D060449]] \n", - "670 [[GO:0009653, GO:0048468, cell signaling, receptor-mediated signaling, GO:0010468]] \n", - "671 [[GO:0005126, GO:0007155, immunoreceptor-antigen complex binding, regulation of the ubiquitin-proteasome pathway, transcription factor regulator activity, gtp-binding protein binding, GO:0030154]] \n", - "672 [[GO:0000988, embryonic stem cell differentiation, cell pluripotency, dna-binding, MESH:D005786, GO:0140110, transcription factor complex formation.\\nmechanism: these genes are known to be involved in the regulation of gene expression, and thus serve an important role in directing the biological activities associated with embryonic stem cell differentiation and pluripotency. they are likely to form complexes, interact with dna, and/or bind to components of the transcription machinery to regulate gene expression at the transcriptional level]] \n", - "673 [[GO:0048863, GO:0048468, embryonic stem cell differentiation, transcriptional regulation, pluripotency, transcription factor regulation.\\n\\nmechanism: the genes klf4, pou5f1, and sox2 act in concert to regulate the expression of developmental proteins that are involved in forming stem cells. this trio of transcription factors plays a key role in regulating cell differentiation and pluripotency, thus influencing the direction of embryonic stem cell development by regulating gene expression of proteins involved in stem cell formation]] \n", - "674 [[GO:0008283, GO:0048729, motility regulation, vascular development, GO:0098868, UBERON:0002405]] \n", - "675 [[GO:0001525, GO:0008283, GO:0016477, matrix remodeling, GO:0048771, jagged-mediated signaling, transcriptional regulation, GO:0030168, GO:0070527, immune regulation, extracellular matrix formation]] \n", - "676 [[GO:0016049, differentiation, migration, chromatin modulation, transcription regulation, cytoskeletal organization, intracellular trafficking, GO:0007155, GO:0007165, dna/rna metabolic processes, GO:0009653, GO:0001525, muscle growth, GO:0032502]] \n", - "677 [[chromatin regulation, GO:0048468, GO:0006412, GO:0006811, GO:0000981, GO:0043687]] \n", - "678 [[MESH:M0370791, GO:0007015, GO:0006936, z-disc formation, GO:0007097, muscle fiber organization, ion channel influx/efflux]] \n", - "679 [[MESH:D024510, GO:0048740, GO:0021675, calcium distribution, actin proteins, cardiac contractile proteins, sarcomeric proteins, membrane protein transport, ion channel proteins, enzyme regulation.\\nmechanism: this list of genes are likely to be involved in the regulation of muscle structures and contractions, organization of calcium distribution throughout the cell, nerve development, and support of membrane protein transport and enzymatic activities. these processes are important for maintaining muscle contraction and activity]] \n", - "680 [[GO:0006629, cell signaling, GO:0007049, cytoskeletal dynamics]] \n", - "681 [[GO:0006897, intracellular signaling, GO:0016310, protein interactions, receptor trafficking]] \n", - "682 [[GO:0006754, GO:0006096, MESH:D004734, MESH:M0496924]] \n", - "683 [[metabolic pathway, GO:0006096, glucose oxidation, pyruvic acid production, GO:0006754]] \n", - "684 [[summary: the enriched terms of the human genes atp2b1, atp2b2, cacna1c, cacng2, cacng3, cacng4, cacng5, cacng7, cacng8, chrna10, chrna7, chrna9, drd2, f2r, gpm6a, grin1, grin2a, grin2b, grin2c, grin2d, grin3a, grin3b, htr2a, itpr1, ncs1, p2rx4, p2rx7, plcb1, psen1, slc8a1, slc8a2, slc8a3, trpv1 include neuron development; neurotransmitter signaling; signal transduction; transmembrane transport; neural plasticity; ion transport; calcium signaling; glutamate receptor signaling; and synaptic signaling. \\n\\nmechanism: these genes are believed to act in concert to regulate and coordinate the various stages of neuron development, such as neurotransmitter signaling, GO:0007165, GO:0055085, neural]] \n", - "685 [[neuronal function, GO:0006811, ion channel regulation, neurotransmitter regulation, calcium regulation, potassium regulation, GO:0007268, membrane potential regulation]] \n", - "686 [[this set of genes is associated with cellular functions related to metabolic homeostasis and activation of the pi3k/akt signaling pathway. the enriched terms associated with the genes include cell cycle regulation, protein kinase regulation, mitochondrial regulation, and mitochondrial stress response.\\n\\nmechanism: the metabolic homeostasis and activation of the pi3k/akt pathway are mediated by these genes, which affect the regulation of cell cycle, protein kinase regulation, mitochondrial regulation, and mitochondrial stress response. these genes have roles in regulating metabolic processes as well as responding to external stressors. their involvement in cell cycle regulation and protein kinase regulation ensures the healthy development and maintenance of the cell, while their role in mitochondrial regulation and mitochondrial stress response plays an important role in maintaining the cell's energy production]] \n", - "687 [[cell signaling, transcription regulation, GO:0006468, ras activation, akt activation, calcium-associated kinases, GO:0019722]] \n", - "688 [[MESH:D009113, MESH:D009077, glycosyltransferase, MESH:D006821, GO:0070085, enzyme, MESH:D011506]] \n", - "689 [[the gene functions that were found to be enriched amongst this set of genes were predominantly related to carbohydrate metabolism, including glycosaminoglycan and glycosphingolipid biosynthesis as well as lysosomal enzyme activity.\\n\\nmechanism:\\nthe mechanism most likely lies in the pathway of glycoconjugation, which helps to regulate important processes such as cell adhesion, GO:0006955, and signal transduction. the pathway is integral to the proper formation and function of the extracellular matrix, which is important for cellular differentiation and tissue organization. the enriched terms found here likely represent genes that are involved in the biosynthesis and metabolism of various glycoconjugates, in addition to the regulation of lysosomal enzymes involved in the degradation of complex carbohydrates]] \n", - "690 [[immunoglobulin heavy chain combination, immunoglobulin light chain combination, j-chain, antigen-specific receptor, t-lymphocyte receptor, regulation of immune function]] \n", - "691 [[genes related to immunoglobulins, transcripts associated with immunoglobulin transcription and splicing, immunoglobulin gene expression, proteins involved in immunoglobulin regulation and processing, GO:0002637, GO:0002637, mhc class i antigen processing and presentation, cytokine-mediated signaling, GO:0002544, limit degranulation. \\n\\nmechanism: these genes are associated with immunoglobulin production, processing, and regulation. this includes genes related to immunoglobulins, transcripts involved in transcription and splicing, and proteins that are involved in the regulation and processing of immunoglobulins. additionally, genes related to mhc class i antigen processing, cytokine-mediated signaling, chronic inflammatory response, and limit degranulation are also expressed. these genes interact to form an integrated pathway that is involved in the regulation of the immune response and the formation of immunoglobulins]] \n", - "692 [[GO:0006260, GO:0006281, replication fidelity, GO:0007049, GO:0071897, dna prioritization]] \n", - "693 [[this enrichment test on the list of human genes suggests a central role for dna damage repair and cell cycle regulation in the common functionalities of the genes. enriched terms found include \"dna repair\", \"cell cycle\", \"chromatin remodelling\", \"recombinational repair\", \"steroid hormone receptor\", \"centromere\", GO:0000724]] \n", - "694 [[GO:0019722, calcium buffering, GO:0006816, regulation of calcification, protection against calcium overload, calcium-v influx/efflux]] \n", - "695 [[cell morphology regulation, GO:0008152, GO:0006915, GO:0006412, GO:0036211, GO:0006811, GO:0023052, stress response, GO:0006351, cell surface interactions, chromatin regulation]] \n", - "696 [[genes in this list are involved in various aspects of cellular metabolism, GO:0065007, and development.a number of the genes have roles in energy production and metabolism such as, atp2a2, aldoa, MONDO:0009214, fao1, fgl2, gapdh, gbe1, MONDO:0015408, glrx, MONDO:0005775, me1, phgdh, and pgm1. there is a strong presence of genes involved in protein synthesis and transport, including the ribosomal proteins, the eukaryotic translation factors and initiation factors (eif2s2, eif1e1, elovl5, and elovl6). this gene set is also enriched for a number of ubiquitin and ubiquitin-like proteins (ube2d3, ufm1, uso1, tomm40, hspd1, hspe1, sytl2, nherf1, and hk2). many of these genes are involved in regulation through multiple pathways including regulation of transcription (add3, actr2, actr3, cct6a, gga2, gdh2, mef2b, ykt]] \n", - "697 [[genes related to metabolism and biosynthesis (acly, aldoa, atp2a2, atp6v1d, cacybp, coro1a, dhcr24, MONDO:0100101, MONDO:0100102, gbe1, MESH:C066524, gsr, hmgcs1, hspa9, lgmn, me1, mthfd2l, nampt, pgm1, pgk1, psat1, psma3, psma4, psmg1, psmc2, psmc4, psmd12, psmd13, psmd14, stc1, stip1, and ufm1), protein folding/interaction (act2, actr2, actr3, add3, elovl5, eno1, ero1a, eif2s2, fgl2, insig1, itgb2, map2k3, mcm2, mcm4, nufip1, p4ha1, pdk1, pitpnb, pnp, psme3, sec11a, shmt2, slc2a1, slc2a3]] \n", - "698 [[protein homeostasis, peroxisome biogenesis, peroxisome assembly, peroxisome maintenance, protein regulation, GO:0050821]] \n", - "699 [[peroxisomal biogenesis, peroxisome assembly, peroxisome regulation, GO:0015031, membrane trafficking]] \n", - "700 [[after performing the enrichment test on the genes zmpste24, banf1, MONDO:0010196, and lmna, we identified that all of the genes have a role in the regulation of nuclear and chromatin structures. the individual genes are involved in a wide range of processes in these two areas. this includes gene expression, GO:0006260, GO:0006338, GO:0000723, as well as cell cycle checkpoints.\\n\\nthe enriched terms are 'nuclear structure regulation'; 'chromatin structure regulation'; 'gene expression regulation'; 'dna replication regulation'; 'chromatin remodeling'; 'telomere maintenance'; and 'cell cycle checkpoint regulation'. \\n\\nmechanism: the underlying biological mechanism that our gene list points to is one involving the regulation of nuclear and chromatin structures. in order to maintain the stability of the genome and ensure its accurate transmission, molecules encoded by the four genes could be involved in key activities such as gene expression, GO:0006260, GO:0006338, GO:0000723, as well as cell cycle checkpoints]] \n", - "701 [[transcriptional regulation, GO:0006281, GO:0051726, GO:0030154]] \n", - "702 [[MESH:D007473, MESH:D008565, synapse formation, GO:0007268, MESH:D009473, neuronal excitability, voltage-gated ion channels, MESH:D058446]] \n", - "703 [[ion-channel function, neuron excitability, GO:0007268, MESH:D018079, MESH:D017470, MESH:D015221, MESH:D015222]] \n", - "704 [[GO:0006412, GO:0008152, ion channel transport, GO:0006936, MESH:D024510]] \n", - "705 [[nucleic acid metabolism, GO:0003676, GO:0050657, GO:0019538, GO:0005515, GO:0015031]] \n", - "706 [[g-protein coupled receptor (gpcr), g-protein subunit, MESH:D000262, MESH:D015220, MESH:D010770]] \n", - "707 [[GO:0007165, cellular growth & differentiation, GO:0007010, endocrine system regulation, transcriptional regulation]] \n", - "708 [[genes such as hira, cebpb, e2f3, hmga1, znf263, tfdp1, trib3, bhlhe40, smarca4, slc26a3, nfe2l3, ssbp2, gtf3a, npm1, trip13, mef2c, nr3c2, foxm1, vdr, hand1, klf4, hexim1, tgif1, med24, tead4, smarcc1, scml1, MESH:D024243, myc, foxa2, bmal2, spib, nme2, phb1, cbx4, runx1, ppargc1a, polr3k, nr5a2, maf, nr1h4, sox9, dnmt1, cbfb, znf593, mta1, zbtb18 are all involved in the regulation of transcription, GO:0006338, GO:0003677, and epigenetics. of this group, genes involved in transcription are significantly enriched (e.g. hira, cebpb, e2f3,]] \n", - "709 [[GO:0016049, transcriptional regulation, GO:0006338, GO:0051726, GO:0006351, GO:0016569]] \n", - "710 [[collagen or extracellular matrix structural constituent, collagen metabolic process or biosynthetic process, proteoglycan metabolic process or biosynthetic process, GO:0006024, dna-binding transcription factor binding activity, GO:0001217, rna polymerase ii transcription regulatory region sequence-specific dna binding activity, metal ion binding activity, GO:0003755, GO:0035987, GO:0004252, GO:1904028, protein peptidyl-prolyl is]] \n", - "711 [[GO:0030198, GO:0030199, GO:0032964, GO:0030166, GO:0006024]] \n", - "712 [[GO:0006281, GO:0006513, GO:0043240, GO:0000785, GO:0005634, GO:0005829]] \n", - "713 [[GO:0006513, GO:0006281, GO:0003682, GO:0000400, GO:0003684, GO:0003697, GO:1990599, GO:0004520, GO:0006310, GO:0005524, GO:0006259, GO:0072757, GO:0051052, GO:0003691, GO:0000723, GO:0019219, GO:0051246, GO:0070200, GO:0016573, GO:0004402, gamma-tubulin binding activity, identical protein binding activity, jun kinase binding activity, rna polymerase ii-specific dna-binding transcription factor binding activity, GO:0061630, GO:0031386]] \n", - "714 [[protein binding activity, MESH:D010758, atp binding activity, gtp binding activity, GO:0022857, dna binding activity, receptor binding activity, GO:0004869, caspase binding activity, rna binding activity]] \n", - "715 [[protein binding activity, enzyme binding activity, atp binding activity, rna binding activity, gtp binding activity, identical protein binding activity, gtp-dependent protein binding activity, transition metal ion binding activity, GO:0016615, aldehyde dehydrogenase activity, GO:0008097, GO:0052650, fad binding activity, MESH:D010758, heme binding activity, GO:0003872, GO:0004609, GO:0003873, GO:0004144, GO:0003994, GO:0004784, GO:0004129, molybdenum ion binding activity]] \n", - "716 [[protein homodimerization, protein heterodimerization, GO:0042802, GO:0019901, dna-binding, rna-binding, GO:0017124, GO:0019958, GO:0008201, ubiquitin-protein ligase binding]] \n", - "717 [[GO:0007155, GO:0005102, GO:0007165, GO:0001228, chemokine receptor binding activity, enzyme binding activity, GO:0008083, GO:0005125, degradation of redundant or damaged proteins and peptides, GO:0046983, metal ion binding activity, peptide antigen binding activity, GO:0004888, GO:0004712, GO:0042803, ubiquitin binding activity]] \n", - "718 [[GO:0005215, GO:0005515, GO:0004672, GO:0038023, GO:0006351, GO:0044237, GO:0006974, GO:0007010, GO:0016787, GO:0046872, GO:0003924]] \n", - "719 [[GO:0005515, GO:0016887, GO:0016563, GO:0003677, GO:0004674, GO:0022857, GO:0016787, GO:0061631, cis-regulatory region sequence-specific dna binding activity, GO:0061665, GO:0034594, GO:0007165, GO:0043027, GO:0003924, GO:0042803, nucleic acid binding activity, GO:0003713, GO:0003714, enzyme binding activity, calmodulin binding activity, metalloendope]] \n", - "720 [[summary: the list of genes provided appear to be involved in a variety of unrelated processes, but when grouped by shared activities, several functions in common can be identified. these common functions include protein binding activity, GO:0060230, phospholipid binding activity, platelet-derived growth factor binding activity, GO:0046983, signaling receptor binding activity, collagen binding activity, atp activated inward rectifier potassium channel activity, voltage gated monoatomic ion channel activity, GO:0005249, GO:0016298, heparan sulfate proteoglycan binding activity, heparin binding activity, multiple growth factor activities, peptidoglycan binding activity, GO:0016019, platelet derived growth factor binding activity, non membrane spanning protein tyrosine kinase activity, GO:0005096, vascular endothelial growth factor binding activity, metal ion binding activity, small molecule binding activity, enzyme binding activity, retinoic acid binding activity, cxcr3 chemokine receptor binding activity, prostaglandin transmembrane transporter activity and sodium-independent organic anion transmembrane transporter activity. \\nmechanism: the genes in the list appear]] \n", - "721 [[GO:0005515, GO:0006468, GO:0016477, GO:0008283, GO:0045861, GO:1902533, GO:0009966, GO:0010604, GO:0019901, GO:0008191, ion binding activity, small molecule binding activity, GO:0035987, GO:0005096, platelet-derived growth factor binding activity, GO:0046983, calcium ion binding activity, sympathetic nerve activity, GO:0051336]] \n", - "722 [[GO:0007155, GO:0005178, gtp binding activity, collagen binding activity, atp binding activity, phospholipase binding activity, GO:0007160, GO:0050839, GO:0017124]] \n", - "723 [[extracellular matrix structure, GO:0038023, cell adhesion molecule binding activity, small gtpase binding activity, GO:0042803, identical protein binding activity, collagen binding activity, actin binding activity, atp binding activity, protein kinase binding activity, sh3 domain binding activity, integrin binding activity, GO:0005096]] \n", - "724 [[GO:0005480, cell structure maintenance, GO:0046872, GO:0016477, plasmamembrane transport, GO:0005515, GO:0043170, GO:0030296, endolemmal transport, GO:0016485, GO:0010467, GO:0006915, lipoprotein particle receptor catabolic process, peptide chain release, protein homodimerization, GO:0007165, GO:0048870, GO:1902600, GO:0000785, GO:0005654, GO:0031410, GO:0042552, GO:0044183]] \n", - "725 [[genes in this list are primarily involved in regulation of transcription, GO:0007165, membrane management, protein folding and binding, cell surface receptor signaling and adhesion, and cellular extravasation. enriched terms include: transcription, GO:0007165, protein-folding and binding, cell-surface receptor signaling, adhesion, GO:0045123, GO:0061024, extracellular matrix structural components, genetic expression, apoptotic pathways, and intracellular ion homeostasis. \\n\\nmechanism: genes on this list are primarily involved in several processes that coordinate essential cellular functions by dynamically managing activity of proteins at the surface of the cell, within underlying membrane layers, extracellularly and within dna. these genes manage the way cells communicate within their environment, interact with extracellular components, respond to stimuli, and extravasate. they code for proteins involved in transcription, GO:0007165, protein folding and binding, adhesion, apoptotic pathways, intracellular ion homeostasis, extracellular matrix structural components that have pleiotropic roles in modulating gene expression functioning of cellular components]] \n", - "726 [[dna binding activity, GO:0046983, protein binding activity, enzyme binding activity, protein kinase binding activity, GO:0004197, GO:0003714, phosphoprotein binding activity, mhc class i protein binding activity, GO:0003700, signaling receptor binding activity, GO:0042803]] \n", - "727 [[protein binding activity, identical protein binding activity, enzyme binding activity, GO:0003700, rna polymerase ii-specific transcriptional activity, GO:0004197, GO:0004896]] \n", - "728 [[atp binding activity, GO:0016887, cholesterol binding activity, GO:0022857, GO:0046982, GO:0000981, enzyme binding activity, GO:0016491, peptide antifungal protein binding activity, acyl-coa hydroxyacyltransferase activity, GO:0019145]] \n", - "729 [[this gene list is associated with multiple functions in various metabolic processes, from binding and transporter activity to atpase activity, homodimerization activity, and various hydrolytic activities. enriched terms include: protein binding activity; atp hydrolysis activity; protein homodimerization activity; atpase binding activity; atpase-coupled transmembrane transporter activity; transcription regulatory region sequence-specific dna binding activity; and transmembrane transporter activity. mechanism: this set of genes acts as part of multiple metabolic processes, such as lipid and fatty acid metabolism, GO:0042632, GO:0140327, and hormone regulation. these genes facilitate enzymatic activity and activity in transporting molecules, such as fatty acids, MESH:D002784, MESH:D014815, hormones. the processes activities these genes are involved in suggest a coordination of metabolic cell stimulation processes]] \n", - "730 [[atp binding activity, protein binding activity, GO:0007155, GO:0007165, GO:0006915, dna-binding, GO:0006695, cell structure organization, GO:0003985, GO:0008610, GO:0000988, GO:0015631, protein homodimerization]] \n", - "731 [[GO:0006695, GO:0008610, positive regulation of transcription, GO:2001234, GO:0031647, regulation of cell adhesion/migration, atp binding activity, transcription factor binding activity, protein binding activity, protein kinase binding activity, signaling receptor binding activity, ion/metal binding activity, endopeptidase regulator activity, etc]] \n", - "732 [[protein binding activity, collagen binding activity, identical protein binding activity, integrin binding activity, phospholipid binding activity, atp binding activity, fibronectin binding activity, GO:0008237, GO:0004252, metaloendopeptidase activity, calcium ion binding activity]] \n", - "733 [[the genes in this list are predicted to enable various calcium-dependent functions related to protein binding, GO:0019899, and peptidase activity, typically related to blood coagulation, GO:0007155, endodermal cell fate, and negative regulation of protein-regulating processes. these genes are involved in various activities across multiple cellular pathways, including cellular response to uv-a, GO:0030155, and blood coagulation. the enriched terms include “calcium-dependent functions”, “protein binding activity”, “enzme binding activity”, “peptidase activity”, “blood coagulation”, “cell adhesion”, “endodermal cell fate”, “negative regulation of protein-regulating processes”, “cellular response to uv-a”, and “regulation of cell adhesion”.\\n\\nmechanism: the mechanism underlying this list of genes is likely related to calcium-dependent regulation of proteins and peptides, which acts to control various cellular processes. calcium can act as a negative regulator of proteins, through calcium binding to proteins and preventing their activity, or as a]] \n", - "734 [[protein binding activity, GO:0001216, enzyme binding activity, metal ion binding activity, sh2 domain binding activity, GO:0004197, phosphoprotein binding activity, actin binding activity, cation binding activity, lipid binding activity, GO:0004252, GO:0008092, cell killing activity, protein kinase binding activity]] \n", - "735 [[dna-binding, GO:0005543, GO:0005515, GO:0005102, GO:0019899, inhibitor activities, GO:0003924, GO:0046872, protein activities, GO:0023052, transcription regulation, GO:0006281, GO:0008219, GO:0006955]] \n", - "736 [[dna binding activity, rna binding activity, enzyme binding activity, protein binding activity, calcium ion binding activity, GO:0140612, GO:0003713, zinc ion binding activity]] \n", - "737 [[dna binding activity, enzyme binding activity, GO:0016887, rna binding activity, protein binding activity, GO:0003887, GO:0004518, mrna regulatory element binding]] \n", - "738 [[chromatin binding activity, GO:0006260, GO:0006281, GO:0006351, GO:0016570, nuclear import/export, dna/rna binding, protein-macromolecule binding, GO:0051726, protein homodimerization, GO:0006200, GO:0000287, MESH:D011494, GO:0004518]] \n", - "739 [[nuclear pore remodeling, GO:0065003, GO:0003677, transcriptional regulation, GO:0006260, GO:0006913, chromatin modification and repair, cell cycle progression, GO:0140014, GO:0019899, GO:0042393, protein homod]] \n", - "740 [[protein binding activity, identical protein binding activity, collagen binding activity, integrin binding activity, heparin binding activity, phosphatidylinositol binding activity, cell adhesion molecule binding activity, extracellular matrix binding activity, signaling receptor binding activity, GO:0008009, gene transcriotion activity, metal ion binding activity]] \n", - "741 [[GO:0005201, collagen binding activity, cell adhesion molecule binding activity, dna binding activity, gtp binding activity, GO:0042803, platelet-derived growth factor binding activity, platelet-derived growth factor binding activity, calcium ion binding activity, signaling receptor binding activity, identical protein binding activity]] \n", - "742 [[dna binding activity, protein binding activity, enzyme binding activity, GO:0022857, transcription activity, GO:0003924, atpase binding activity, mrna binding activity, protein homodimerization, GO:0042169, GO:0016922, GO:0030165]] \n", - "743 [[GO:0003677, GO:0000981, GO:0003723, protein binding/dimerization, transmembrane transporter, GO:0005509, GO:0019899, GO:0003924]] \n", - "744 [[GO:0050839, GO:0003677, transfacmembrane receptor protein tyrosine kinase activity, ligand binding, ca2+ ion binding, GO:0005543, GO:0019899, GO:0016563, GO:0005243, GO:0003682, GO:0032794, GO:0048018, GO:0005242, GO:0004930, GO:0060089, calcium-dependent exonuclease activity, GO:0003779, GO:0007165, GO:0004672, GO:0016310, sh2 domain binding activity, heme binding activity, GO:0042803, hsp90 protein binding activity, GO:0017002, GO:0004957, ww domain binding activity, pdz domain binding activity, sh3 domain binding activity]] \n", - "745 [[GO:0008134, GO:0019899, GO:0005515, GO:0007155, ligand-gated ion transporter activity, GO:0001216, GO:0050839, protein domain specificity, GO:0030742, GO:0003677, GO:0019003, GO:0005525, GO:0051117, GO:0030165, GO:0005509, phosphotransfer, GO:0031490, GO:0001217]] \n", - "746 [[protein binding activity, identical protein binding activity, metal ion binding activity, atp binding activity;lipid transport activity, fatty acid binding activity, fad binding activity, pdz domain binding activity;transmembrane transporter activity, ubiquitin binding activity, nucleotide binding activity, GO:0004080, GO:0004738, enoyl-coa hydratase activity;amino-acid oxidase activity, GO:0003979, GO:0009055, GO:0004853, 5alpha-reductase activity, rna-binding]] \n", - "747 [[GO:0003824, GO:0016491, protein binding activity, hydratase activity, GO:0003997, lipid binding activity, dna binding activity, ubiquitin binding activity, atp binding activity, flavine adenine dinucleotide binding activity, nadp+ binding activity, GO:0042803, smad binding activity, GO:0004466]] \n", - "748 [[dna binding activity, rna binding activity, protein kinase binding activity, protein folding activity, enzyme binding activity, transcription factor binding activity, chromatin binding activity, protein domain specific binding activity, nucleic acid binding activity, atp binding activity, identical protein binding activity, GO:0140110, GO:0046983, histone binding activity, anaphase-promoting complex binding activity, cytoplasmic release activity, metal ion binding activity, GO:0016887, histone deacetylase binding activity, telomere binding activity]] \n", - "749 [[GO:0005515, GO:0003677, GO:0008134, MESH:D019098, GO:0003723, GO:0006260, GO:0051726, GO:0003682, GO:0010467, GO:0006457, regulation of chromosome structure, GO:0019904, GO:0005524, GO:0019900, GO:0035402, GO:0031267, MESH:M0518050, protein homodimerization, GO:0043130, atp-dependent dna/dna annealing]] \n", - "750 [[the list of genes represent a range of molecular, metabolic, and protein regulatory processes, including atpase activity, glucose binding activity, GO:0004672, transcriptional activity and activity from receptors, transporters, and enzymes. the enriched terms are \"protein binding activity\"; \"atpase activity\"; \"transcriptional activity\"; \"receptor activity\"; \"transporter activity\"; \"enzyme activity\"; and \"glucose binding activity\".\\n\\nmechanism: the genes in the list encode proteins involved in a range of processes, such as structural support, GO:0007165, regulation of transcription, metabolic pathways and transport of molecules. the underlying biological mechanism is likely related to the coordinated expression of these genes in response to a particular stimulus, or to maintain cellular homeostasis]] \n", - "751 [[enzyme binding activity, identical protein binding activity, dna binding activity, GO:0042803, heparin binding activity, atp binding activity, protein kinase binding activity, phosphatase binding activity, cyclin binding activity, protein phosphatase binding activity, GO:0004722, actin binding activity, lbd domain binding activity, actin filament binding activity, GO:0008083, chromatin binding activity, hyaluronic acid binding activity, GO:0004197, ubiquitin binding activity, cyclosporin a binding activity, mannose-binding activity, heparan sulfate binding activity, heme binding activity, GO:0016887, transition metal ion binding activity, GO:0031545, GO:0016615, GO:0004148, GO:0004784, transcription core]] \n", - "752 [[protein/lipid binding activity, GO:0003700, GO:0010468, GO:0051246, positive/negative regulation of cellular component organization, GO:0030036, GO:0030833, GO:0001525, GO:0090630, GO:0019219, GO:0007160]] \n", - "753 [[acetylcholine binding activity, GO:0003990, GO:0005096, rna polymerase ii-specific dna-binding transcription factor binding activity, GO:0003714, GO:0017053, GO:0007165, GO:0006351, GO:0007155, GO:0016477, GO:0001525, GO:0035556, GO:0019219, GO:0006468]] \n", - "754 [[dna-binding, rna-binding, GO:0019899, GO:0019901, GO:0019903, protein homodimerization, GO:0048729, GO:0006468]] \n", - "755 [[GO:0003677, GO:0005515, GO:0016310, GO:0003824, GO:0005215, MESH:M0496924, vesicular pathways, cytoskeletal pathways, GO:0046872, GO:0003723, GO:0030544, GO:0042802, GO:0008013, phosphatidylinositol-4 binding, GO:0035612, rna polymerase ii dna binding, GO:0042393, GO:0019901, tyrosine-protein kinase activity, GO:0061630, GO:0003713, fibronectin leucine-rich-repeat sense-specific binding, endothelial differentiation-specific factor binding, fatty-acid binding, heme-binding, GO:0051537, GO:0050661, GO:0070742, MESH:D012330]] \n", - "756 [[this is a list of genes of known or suspected functions in a variety of processes, ranging from dna binding and transcription regulation to enzyme binding, metabolic activity, GO:0005102, and structural protein formation. commonly enriched terms include dna binding, transcription regulation, GO:0019899, and protein binding. mechanism: a variety of processes are involved in these gene functions, including dna replication and repair, protein folding and conformational change, receptor binding and signal transduction, metabolic activity, structural protein formation]] \n", - "757 [[dna-binding transcription activity, GO:0003714, GO:0016564, GO:0016563, rna polymerase ii-specific, protein binding activity, GO:0042803, platelet-derived growth factor binding activity, GO:0030291, GO:0046982, GO:0004197, protein kinase binding activity, GO:0019887, GO:0004725, cyclin binding activity, GO:0004693, GO:0035403, phosphatidylinositol-3-kinase activity, nad+]] \n", - "758 [[GO:0005096, dna-binding transcription activator/repressor activity, protein binding activity, ligand binding activity, identical protein binding activity, bh3 domain binding activity, phosphatidylinositol binding activity, GO:0016787, atp binding activity, atpase-coupled intramembrane lipid transport activity, amyloid-beta binding activity, hsp90 protein binding activity, s100 protein binding activity, cadherin binding activity, GO:0038023, GO:0005125, GO:0005021, GO:0004896, identical protein binding activity, GO:0008233, heat shock protein]] \n", - "759 [[dna-binding transcription activity, protein kinase binding activity, small gtpase binding activity, interleukin-binding activity, GO:0004896, signaling receptor binding activity, rna binding activity, gtp binding activity, GO:0004197, identical protein binding activity, protein domain specific binding activity, GO:0046982]] \n", - "760 [[cytokine binding activity, protein binding activity, kinase binding activity, signaling receptor binding activity, GO:0004675, cell adhesion molecule binding activity, interleukin-receptor activity, GO:0004725, tir domain binding activity, ubiquitin protein ligase binding activity, GO:0008284, GO:0032768, GO:0009966, GO:0090276, GO:0045597, GO:0010604, GO:0098542, GO:0009612, GO:0001819, GO:0031349]] \n", - "761 [[cytokine binding activity, GO:0004896, GO:0008083, cell adhesion molecule binding activity, chemokine (c-x3-c) binding activity, GO:0006952, signaling receptor binding activity, GO:0000988, identical protein binding activity, phosphatidylinositol binding activity, heparin binding activity, lipid binding activity, c-c chemokine binding activity, dna binding activity, GO:0005096, sh3 domain binding activity, ephrin receptor binding activity, transforming growth factor beta receptor binding activity, ubiquitin-like protein ligase binding activity, enzyme binding activity, calcium-dependent protein binding activity, protease binding activity]] \n", - "762 [[GO:0004930, GO:0005125, GO:0003700, GO:0005216, receptor binding activity, GO:0008083, cell adhesion molecule binding activity, signalling receptor binding activity, GO:0003714, enzymatic activity, phospholipid binding activity, peptide hormone receptor binding activity, GO:0003924]] \n", - "763 [[atp binding activity, chemokine/chemokine receptor/chemokine receptor binding activity, cytokine/cytokine binding activity/cytokine receptor activity, dna binding activity/dna-binding transcription factor activity, GO:0004930, identical protein binding activity, ion transport/ion transporter activity, peptide/peptide receptor binding activity, phospholipid binding activity, GO:0019887, signaling receptor binding activity, GO:0000988, GO:0022857]] \n", - "764 [[immunologic processes, GO:0098609, GO:0006952, cellular response, positive regulation, rna polymerase ii specific, GO:0003677, GO:0003723, protein homodimer]] \n", - "765 [[GO:0003713, rna binding activity, dna binding activity, identical protein binding activity, GO:0061630, zinc ion binding activity, GO:0042803, double-stranded rna binding activity, heparin binding activity, GO:0030701, GO:0004175, cxcr chemokine receptor binding activity, tap binding activity, peptide antigen binding activity, gtp binding activity, GO:0033862, GO:0004197, amyloid-beta binding activity, macrophage migration inhibitory factor binding activity, GO:0004550, GO:0016064, GO:0140374, GO:0071345, GO:0046597, positive regulation of]] \n", - "766 [[protein binding activity, enzyme binding activity, dna-binding transcription activity, GO:0006200, protein homodimerization, kinase regulation, protein dimerization.\\nmechanism: these genes are likely involved in the regulation of gene expression cell signaling pathways, enabling an array of signaling activities that help to maintain cellular homeostasis]] \n", - "767 [[GO:0016887, dna binding activity, gtp binding activity, peptide antigen binding activity, GO:0004252, dna-binding transcription activity, GO:0005125, GO:0008009, GO:0004896, GO:0038023, GO:0004930, rna binding activity, enzyme binding activity, GO:0046983, phosphorylation-dependent protein binding activity, GO:0019887, GO:0140311, toll-interleukin receptor (tir) domain binding activity, signaling receptor binding activity, and]] \n", - "768 [[GO:0004930, GO:0042803, calcium ion binding activity, sodium:potassium:chloride transporter activity, GO:0004683, platelet-derived growth factor activity, GO:0005007, cytoskeletal protein binding activity, GO:0015171, n6-threonylcarbamylade adenine dinucleotide synthetase activity, GO:0043273, intracellular transport activity, signal transduction activity, GO:0016887, GO:0004175, GO:0016491, GO:1990817, GO:0004958, beta-caten]] \n", - "769 [[the list of genes is significantly enriched for dna-binding activities, calcium ion binding activities, identical protein-binding activities, GO:0046982, GO:0016887, and g protein-coupled receptor activities.\\n\\nmechanism:\\nthe underlying biological mechanism likely involves a complex, dynamic interaction between various proteins, MESH:D004798, and ions, driven by a variety of dna-binding, calcium-binding, and atp-binding activities, resulting in the recruitment of additional proteins to form heterodimers, thereby leading to protein synapsis cell signaling]] \n", - "770 [[atp binding activity, atpase-coupled intramembrane transport, GO:0048018, dna-binding transcription regulation, protein domain binding activity, enzyme binding activity, GO:0005125, GO:0007165, GO:0007155, GO:0016477, GO:0030154, MESH:D048788]] \n", - "771 [[receptor binding activity, identical protein binding activity, GO:0001216, enzyme binding activity, protein domain specific binding activity, protein kinase binding activity, ligand binding activity, atp binding activity, cytoskeletal protein binding activity, cell adhesion molecule binding activity, GO:0004930, transmembrane transporter binding activity, GO:0008233, dna binding activity, GO:0004252, histone binding activity, signal transduction activity]] \n", - "772 [[actin binding activity, atp binding activity, atpase binding activity, GO:0098632, dynein complex binding activity, gamma-tubulin binding activity, gtp binding activity, gtpase binding activity, guanyl ribonucleotide binding activity, GO:0003924, GO:0005085, kinetochore binding activity, GO:0060090, GO:0140677, myosin binding activity, phosphatidylcholine binding activity, GO:0019904, GO:0042803, GO:0004672, GO:0004674, small gtpase binding activity]] \n", - "773 [[this set of genes are involved in activities, processes and signaling pathways related to intracellular motion such as transport within cells (microtubule/kinesin/dynein binding, GO:0005096, GO:0008092, motor protein activity), cell cycle activities (centrosome duplication, GO:0019899, protein homodimerization, GO:0019902, GO:0003682, GO:0043515, GO:0005516, formin binding, atpase/atp hydrolysis regulatory activity), and cell-cell signaling (jun kinase kinase kinase activity, map-kinase scaffolding, GO:0042608, GO:0045296, GO:0051879, GO:0097016, GO:0005680, GO:0051059, rna binding).\\n\\nmechanism: these genes enable a wide range of activities and processes related to intracellular motion and cell-cell signaling that are either directly or indirectly connected to the assembly, MESH:M0030663, and disassembly of cytoskeletal structures, MESH:D014404, and cellular organelles. these activities can promote cell cycle progression, GO:0008283, and/or cell-cell signaling]] \n", - "774 [[protein binding activity, dna binding activity, enzyme binding activity, GO:0060090, GO:0140677, GO:0042803, domain binding activity, GO:0016491, protein kinase binding activity, phosphatidylinositol binding activity, GO:0016504, GO:0003714, nuclear androgen receptor binding activity, nf-kappab binding activity, ubiquitin protein ligase binding activity, phosphotyrosine residue binding activity, GO:0016564, GO:0003743, peptidyl-proinalyl cistrans isomerase activity]] \n", - "775 [[protein-protein interaction, atp binding activity, GO:0042803, GO:0016887, protein kinase binding activity, ubiquitin protein ligase binding activity, GO:0060090, anion binding activity, chemical oxidoreductase activity, protein domain specific binding activity, gtp binding activity, dna binding activity, rna binding activity, transcription regulation activity, GO:0007165, chromatin binding activity, phospholipid binding activity, GO:0004017, lipoprotein particle binding activity, GO:0008233, actin filament binding activity, fad binding activity, steroid hydrolase activity, rna stem-loop binding activity, GO:0022857, nf-kappab binding activity, coenzyme a binding activity, protein n-terminal phospho-seryl-prolyl pept]] \n", - "776 [[GO:0003723, GO:0044183, dna binding/recognition, protein homodimerization, GO:0003678, GO:0019904, MONDO:0000179, GO:0042393, cytoplasmic protein binding, GO:0005524, GO:0006281]] \n", - "777 [[GO:0003677, GO:0003723, GO:0019904, GO:0003682, GO:0019899, protein folding chaperone activities, atp binding activity, mrna 3'-utr binding activity, identical protein binding activity, GO:0004869, GO:0140693, GO:0140713, heparan sulfate binding activity, peptidyl-prolyl isomerase activity, cyclin binding activity, GO:0004693, nuclear localization sequence binding activity, magnetic ion binding activity, histone methyltransferase binding activity, mrna 5'-utr binding activity, GO:0033677, MESH:D012321]] \n", - "778 [[rna-binding, GO:0036211, GO:0015031, cell signaling, GO:0006412, genetic information regulation, protein bridging, chromatin regulation, transcription regulation, GO:0003676, mitochondrial functions]] \n", - "779 [[rna binding activity, ribosomal rrna processing, mrna and/or rrna catabolism/stability, regulation of transcription/translation, regulation of signal transduction and metabolism processes, regulation of cell cycle/proliferation, protein modification/regulation, GO:0005634, GO:0005829, GO:0005840, GO:0005739]] \n", - "780 [[calcium ion binding activity, identical protein binding activity, actin filament binding activity, GO:0042803, signaling receptor binding activity, atp binding activity, gtp binding activity, dna binding activity, GO:0019887]] \n", - "781 [[calcium binding activity, enzyme binding activity, dna binding activity, atp binding activity, GO:0042803, protein domain-specific binding activity, gtp binding activity, actin binding activity, GO:0008160, small gtpase activator activity, transmembrane transporter binding activity, GO:0004016, c3hc4-type ring finger domain-binding activity, GO:0060090, GO:0005096]] \n", - "782 [[this list of genes is associated with several biological processes related to the regulation of gene expression, such as notch receptor processing, amyloid-beta formation, proteolysis, regulation of cell differentiation, canonical wnt signaling pathway, protein ubiquitination, scf-dependent proteasomal ubiquitin-dependent protein catabolic process, and positive regulation of transcription by rna polymerase ii. the underlying biological mechanism is likely related to the role of these genes in transcription and post-transcriptional gene regulation. enriched terms include: gene expression regulation, GO:0007220, GO:0034205, GO:0006508, GO:0045595, GO:0060070, GO:0016567, GO:0031146, GO:0045944]] \n", - "783 [[GO:0016567, GO:0031146, GO:0007219, GO:0036211, GO:0010468, GO:0030335, GO:0008284, GO:0045596]] \n", - "784 [[acetyl-coa transferase activity, GO:0003995, aldehyde dehydrogenase activity, atpase binding activity, GO:0004129, GO:0009055, GO:0004300, fad binding activity, GO:0003924, heme binding activity, identical protein binding activity, lipid binding activity, metal ion binding activity, GO:0003958, GO:0016491, GO:0004738, pro]] \n", - "785 [[GO:0009055, protein homodimerization, GO:0003924, GO:0000295, phosphoprotein binding activity, mitochondrial respiratory chain activity, proton-transporting atp synthase activity, mitochondrial ribosome binding activity]] \n", - "786 [[dna binding activity, rna polymerase ii-specific dna-binding transcription factor binding activity, transcription regulation, protein binding activity, enzyme binding activity]] \n", - "787 [[GO:0007165, MESH:D005786, GO:0005515, GO:0019899, GO:0016791, GO:0000988, GO:0007155, growth factor binding. \\nmechanism: these genes are involved in the regulation of gene expression and cellular processes by modulating signal transduction, binding proteins, and enzymes, as well as activating phosphatase activity, transcription factor activity and growth factor binding]] \n", - "788 [[atp binding activity, GO:0019829, GO:0016477, GO:0044249, GO:0071333, GO:0090398, GO:0042742, GO:0005789, e-box binding activity, GO:0015149, GO:0002551, GO:0043303, GO:0008233, GO:0008607, GO:0045597, positively regulation of cellular biosynthetic process, positively regulation of glycolytic process, positively regulation of insulin secretion, positively regulation of macromolecule metabolic process, positively regulation of type b pancreatic cell development, positive regulation of cellular]] \n", - "789 [[GO:0098609, GO:0032502, differentiation, UBERON:0000061, transcription regulation, MESH:D012319, GO:0007165, GO:0043170, protein expression, cell signaling, protein production]] \n", - "790 [[after term enrichment analysis on the gene summaries, the following terms were found to be enriched: atp binding activity, atpase-coupled activity, GO:0042803, identical protein binding activity, enzyme binding activity, GO:0005319, GO:0016887, and metal ion binding activity.\\n\\nmechanism: the enriched terms suggest a biological mechanism that involves energy production and transport, GO:0007165, and protein interactions and formation of protein complexes. these processes are necessary for various cellular processes such as metabolism, GO:0007585, GO:0098754, GO:0040007]] \n", - "791 [[cell metabolic process, GO:0090304, GO:0005515, GO:0003677, GO:0016485, GO:0042446, GO:0006694, GO:0005524, GO:0006200, protein homodimerization, GO:0019901, GO:0003714, GO:0003712, cyclin binding activity, rna binding activity, protein phosphatase binding activity, sulphatide binding activity, magnesium ion binding activity, GO:0043621, MESH:M0518050, protein transmembrane]] \n", - "792 [[cellular process regulations, GO:0003824, protein and peptide regulation, protein domain modification]] \n", - "793 [[GO:0007165, GO:0019900, GO:0003924, GO:0004721, transcription factor activation, GO:0004620, GO:0005102, MESH:D054875, MESH:D000107, GO:0006915, GO:0016477, negative regulation of proliferation]] \n", - "794 [[protein binding activity, atp binding activity, gtp-dependent protein binding activity, GO:0003924, signal sequence binding activity, clathrin binding activity, small gtpase binding activity]] \n", - "795 [[atp binding activity, GO:0042803, smarc protein binding activity, GO:0003924, gtp binding activity, GO:0005096, enzyme binding activity, GO:0004197, protein domain specific binding activity, phosphatidylinositol-4-phosphate binding activity, protein kinase binding activity, GO:0008320, calcium-dependent protein binding activity, metal ion binding activity, dopaminergic receptor binding activity, ubiquitin-like protein ligase binding activity, GO:0005484, phosphatidylinositol-3,4,5-trisphosphate binding activity, phosphatidylinositol-3,5-bisphosphate binding activity, signaling receptor binding activity, GO:0005198, syntaxin binding activity, GO:0005484]] \n", - "796 [[the human genes provided are mostly involved in redox homeostasis, GO:0006952, and cell organization. there is also involvement in processes related to the maintenance of the blood-brain barrier, GO:0009650, and metabolism of hormones, MESH:D008055, and glucose. there are an abundance of terms related to transmembrane transport, MESH:D010088, heme and iron metabolism, GO:0019511, and gluthathione metabolism.\\n\\nmechanism:\\nredox homeostasis is regulated by a network of enzymatic and substrate-dependent processes. these processes include cellular antioxidant defense, removal of superoxide radicals and peroxides, GO:0061691, and regulation of the balance between oxidant production and scavenging. transport genes are employed to promote transmembrane transport of xenobiotics and lipids, like abcc1, atox1, and glrx. iron and heme metabolism is facilitated by genes like ftl, hmox2, and mpo. peptidyl-proline hydroxylation is regulated by genes like egln2 and mgst1, while glutathione metabolism is controlled by genes like g]] \n", - "797 [[GO:0045454, GO:0019899, protein homodimerization, GO:0015035, GO:0004602, GO:0003954, atp binding activity, identical protein binding activity, transition metal ion binding activity, GO:0016209, heme binding activity, ubiquitin-specific protease binding activity, GO:0047499, heparin binding activity, GO:0004601, GO:0004784, GO:0008811, GO:0004096]] \n", - "798 [[GO:0140677, GO:0004672, cellular component activity, binding activity, GO:0008233, nucleosome binding activity, ion binding activity, phosphatase binding activity, GO:0051726, apoptosis regulation, GO:0007155, GO:0007399, transcription regulation, GO:0015031, GO:0009988, MESH:D005786]] \n", - "799 [[all of the genes are involved in regulation of various metabolic processes and signaling pathways, with most of them associated with binding activities and regulation of protein activities. enriched terms include: protein binding activity, atp binding activity, protein-folding chaperone binding activity, chromatin binding activity, GO:0046976, transcription corepressor binding activity, GO:0004672, GO:0060090, enzyme binding activity, GO:0140677, GO:0098632, GO:0004888, gtp binding activity, signaling receptor binding activity, ribonucleoprotein complex binding activity, myosin light chain binding activity, GO:0017116, GO:0003689, GO:0051131, peptide alpha-n-acetyltransferase activity. mechanism: the genes are involved in various metabolic processes and signaling pathways, by regulating protein activities through different binding activities and histone methyltransferase activity. some of these activities regulate certain processes based on gtp binding, while others are involved in cell-cell adhesion, transmembrane signaling and chaperone-mediated protein complex assembly]] \n", - "800 [[GO:0005524, GO:0048185, GO:0046332, protein phosphatase/kinase activity, smad signaling, bmp signaling, GO:0006351, MESH:D012319, GO:0005515, GO:0007165, GO:0007049, GO:0008152, GO:0007155]] \n", - "801 [[dna-binding activity, transcription regulation, GO:0035556, GO:0004674, smad binding activity, positive/negative regulation of rna/protein metabolic process, GO:0006468, receptor tyrosine kinase binding activity, GO:0007165, GO:0042803, GO:0061630, GO:0031326, GO:0009966, GO:0006357, GO:0090092]] \n", - "802 [[the list of genes provided are involved in a broad set of functions related to gene transcription or regulation of transcription factors, cell signaling, binding activities and metabolic processes. the enriched terms for this gene set include dna-binding transcription factor activity, rna polymerase ii transcription regulatory region sequence-specific binding, GO:0003924, chemokine receptor binding activity, signaling receptor binding activity, protein kinase binding activity, enzyme binding activity, identical protein binding activity and protease binding activity.\\n\\nmechanism: the underlying biological mechanism for this list of genes is likely related to control of gene expression, as well as control of protein interactions that mediate cell signaling and metabolic processes. additionally, the functions related to binding activities suggest many of the genes are involved in cell-to-cell communication and cell adhesion]] \n", - "803 [[GO:0001216, transcription regulatory region sequence-specific dna-binding, gtp binding activity, enzyme binding activity, identical protein binding activity, signal receptor binding activity, GO:0016791, protein kinase binding activity, GO:0005125, GO:0008083]] \n", - "804 [[rna binding activity, dna binding activity, protein binding activity, GO:0140693, identical protein binding activity, dna-binding transcription factor binding activity, GO:0042803, atpase binding activity, GO:0016887, enzymatic activity, GO:0003713, GO:0008494, protein phosphatase binding activity, peptidyl-prolyl primase activity, transcription cis-regulatory region sequence-specific activity]] \n", - "805 [[enzyme binding activity, rna binding activity, protein binding activity, transmembrane transporter binding activity, dna binding activity, protein kinase binding activity, box h/aca snorna binding activity, protein phosphatase binding activity, telomerase rna binding activity, GO:0042803, GO:0046982, transcription factor binding activity, atp binding activity, GO:0016887, GO:0003724, GO:0003756, ubiquitin protein ligase binding activity, GO:0004518, adenyl ribonucleotide binding activity, heat shock protein binding activity]] \n", - "806 [[gtp binding activity, enzyme binding activity, dna-binding transcription factor binding activity, phosphotyrosine residue binding activity, cyclin binding activity, receptor-ligand interaction, protein-protein interaction, smad binding protein, nf-kappab binding protein, growth factor binding protein]] \n", - "807 [[GO:0001216, rna polymerase ii-specific activity, nf-kappab binding activity, microtubule binding activity, actin binding activity, identical protein binding activity, smad binding activity, GO:0005243, GO:0005388, receptor binding activity, GO:0005096, histone binding activity, ap-1 transcription factor binding activity, vitamin d receptor binding activity, cytoplasmic protein binding activity, GO:0004930, platelet-derived growth factor binding activity, enzyme binding activity, protease binding activity, phospholipid binding activity, GO:0004672, GO:0004674, intracellular protein binding activity]] \n", - "808 [[protein binding activity, atp binding activity, rna binding activity, dna binding activity, receptor binding activity, enzyme binding activity, GO:0005548, GO:0098609, GO:0007268, GO:0097190, GO:0005138, GO:0042110, overall cellular metabolism, MESH:D005786]] \n", - "809 [[enzyme binding activity, GO:0016787, GO:0016740, GO:0038023, dna binding activity, rna binding activity, GO:0000988, protein binding activity]] \n", - "810 [[protein binding activity, GO:0003700, rna polymerase ii-specific dna-binding transcription factor binding activity, notch binding activity, pdz domain binding activity, GO:0042813, ubiquitin protein ligase binding activity, beta-catenin binding activity, GO:0003713, histone deacetylase binding activity, GO:0048019, transcription corepressor binding activity, GO:0060090, GO:0004407, cholesterol binding activity]] \n", - "811 [[GO:0007165, GO:0010468, GO:0006351, GO:0001932, GO:0031647, GO:0016477, GO:0008283, GO:0032502, GO:0006508]] \n", - "812 [[protein binding activity, enzyme binding activity, protein kinase binding activity, interleukin binding activity, phosphorylation-dependent protein binding activity, GO:0001216, GO:0042803, nucleic acid binding activity, GO:0005001, GO:0048018, GO:0004725, GO:0005125, cytoskeletal protein binding activity, cytokin receptor activity, GO:0030335]] \n", - "813 [[cation binding activity, diacylglycerol binding activity, enzyme binding activity, GO:0046982, receptor binding activity, protein kinase binding activity, phosphorylation-dependent protein binding activity, phosphotyrosine residue binding activity, GO:0005001, protease binding activity, cytoskeletal protein binding activity, phosphatidylinositol 3-kinase binding activity, GO:0061630, GO:0004888, GO:0043621, GO:0004697, zinc ion binding activity, transmembrane atp-gated monoatomic cation channel activity, purin]] \n", - "814 [[dna-binding, GO:0000988, rna polymerase ii-specific, nucleic acid binding activity, transcription cis-regulatory region binding activity, GO:0010468, GO:0009889]] \n", - "815 [[GO:0006351, GO:0010468, dna-binding, GO:0000785, GO:0005829, GO:0005654, GO:0005667, GO:0009966, GO:0045944, GO:0001714]] \n", - "816 [[the list of genes provided is involved in multiple processes related to cell adhesion, growth factor binding, protein phosphorylation, tissue development, and regulation of cholesterol homeostatis and transcytosis. the underlying biological mechanism likely involves multiple pathways, including cellular response to lipopolysaccharide, cell-matrix adhesion, and negative regulation of low-density lipoprotein. enriched terms include cell adhesion, cell surface receptor signaling, collagen binding activity, GO:0019838, GO:0042157, GO:1902533, GO:0046983, GO:0006468, regulation of bmp signaling, GO:0042127, GO:0010468, GO:0009966, regulation of very-low-density lipoproten particle clearance, GO:0045056]] \n", - "817 [[GO:0051246, GO:0001952, GO:0042127, GO:0042981, GO:0043269, GO:0030193, GO:0007166, GO:0050804, GO:0005201, GO:0007160, organ development and differentiation, regulation of hormone pathways]] \n", - "818 [[genes in this list are involved in a range of activities, including calcium ion binding activity, metal ion binding activity, protein domain specific binding activity, identical protein binding activity, dna-binding transcription factor activity, and several others. the underlying biological mechanism appears to be related to structural support and regulation of cellular processes. enriched terms include: metal ion binding, GO:0005509, GO:0005515, GO:0000988, dna-binding, GO:0042802, domain specific protein binding]] \n", - "819 [[GO:0001216, protein kinase binding activity, metal ion binding activity, calcium ion binding activity, transcription co-regulator activity, responsive to stimuli]] \n", - "820 [[GO:0051015, GO:0000146, GO:0051371, GO:0003785, GO:0005523, GO:0017022, GO:0031432, GO:0004111]] \n", - "821 [[calcium-dependent protein binding activity, atp binding activity, actin filament binding activity, actin monomer binding activity, transmembrane transporter binding activity, GO:0016567, GO:0061630, tropomyosin binding activity, identical protein binding activity, GO:0008375, protein phosphatase 1 binding activity, zinc ion binding activity, troponin c binding activity, troponin i binding activity, actin binding activity, tropomyosin binding activity, GO:0001216, sequence-specific double-stranded dna binding activity]] \n", - "822 [[GO:0004674, lysophosphatidic acid binding activity, sulfatide binding activity, GO:0016790, cadherin binding activity, GO:0032456, sh3 domain binding activity, GO:0051260, macropinosome formation, GO:0031623, transferring transport, t cell receptor binding activity, GO:0005085, GO:0044351, GO:0001773, GO:0007520, GO:0018105, GO:0010468, vascular endothelial growth factor receptor signalling pathway, GO:0051128, GO:0007042, GO:0045807, GO:0051090]] \n", - "823 [[GO:0006468, GO:0051260, cell signaling, GO:0005480, GO:0016567, endocytosis/exocytosis, GO:0005102, GO:0010468, vesicle buddying, GO:0007165, GO:0050727, GO:0035556, gtp-dependent pathways, receptor signaling, canonical inflammasome signaling]] \n", - "824 [[protein binding activity, atp binding activity, peptidoglycan binding activity, GO:0051156, GO:0002639, GO:0010595, GO:0006002, GO:0061615, GO:0030388, GO:0046166, fructose binding activity, GO:0004332, MONDO:0009295, GO:0004807, disordered domain specific binding activity, GO:0004866, GO:0046835, GO:0072655, maintenance of protein location in]] \n", - "825 [[protein binding activity, atp binding activity, ubiquitin protein ligase binding activity, fructose binding activity, GO:0042803, GO:0004618, GO:0004619, GO:0004807, GO:0004396, GO:0004332, GO:0004634, GO:0003872, GO:0004347, GO:0006096, GO:0006002, GO:0046166, GO:0046835, GO:0072655, GO:0072656, GO:0071456, negative regulation of]] \n", - "826 [[GO:0005262, GO:0005245, regulation of intracellular calcium concentrations, GO:0098960, GO:2000311, g protein-coupled receptor signaling, GO:0070588, GO:0015276]] \n", - "827 [[GO:0005261, acetylcholine-gated channel activity, GO:0022849, nmda selective glutamate receptor activity, GO:0005245, GO:1990454, GO:0035235, GO:0071318, regulation of]] \n", - "828 [[protein kinase binding activity, GO:0004672, GO:0004674, GO:0001934, GO:0010556]] \n", - "829 [[the genes listed above are involved in a variety of processes, including negative and positive regulation of transport, GO:0051246, cell surface receptor signaling, and regulation of gene expression. these genes also have a variety of functions, including protein kinase binding activity, chromatin binding activity, GO:0030295, and metal ion binding activity. the enriched terms that describe these genes include: protein binding activity; protein kinase binding activity; signal transduction; positive and negative regulation of transport; chromatin binding activity; and protein serine/threonine kinase activity.\\n\\nmechanism: these gene products are part of, or act upstream of a variety of signaling pathways, all of which are involved in cell growth, MESH:D008283, and response to environmental stimuli. the pathways typically involve post-translational modifications of target proteins by phosphorylation, as well as formation or breakdown of protein-containing complexes. these signaling pathways ultimately affect gene expression and determine the type of output which a particular cell will produce]] \n", - "830 [[the genes in the list are involved in many processes relating to glycan metabolism and synthesis, such as glycoside catabolic process, GO:0006027, GO:0019377, GO:0005980, and sucrose catabolic process. other enriched terms are dihydroceramidase activity, hyaluronic acid binding activity, GO:0004415, GO:0030212, GO:0046373, GO:0004571, GO:0006487, and protein homodimerization activity.\\n\\nmechanism: glycan metabolism and synthesis involves several enzymes with diverse activities such as alpha-glucosidases, MESH:D043323, MESH:D001617, MESH:D001619, n-acetylglucosaminyltransferases. these enzymes hydrolyze transfer carbohydrate building blocks to form modify carbohydrates for a variety of cellular functions]] \n", - "831 [[GO:0005975, GO:0046477, GO:0006516, oligo-saccharide catabolic process, GO:0006869, GO:0015144, GO:0046982, protein domain specific binding activity, GO:0006629, GO:0016139, GO:0030214, GO:0006032]] \n", - "832 [[immunoglobulin receptor binding activity, antigen binding activity, GO:0004715, phosphatidylcholine binding activity, phosphotyrosine residue binding activity]] \n", - "833 [[GO:0042803, GO:0007160, phosphorylation-dependent signaling, GO:0019901, GO:0034988, GO:0030098, GO:0098609, GO:0001784, GO:0042834, integrin signaling, GO:0006909]] \n", - "834 [[GO:0003677, atp dependent activity, GO:0003682, GO:0005634, protein export, transcriptional regulation, GO:0003690, GO:0003697, GO:0006281, GO:0004518, MESH:D011995, GO:0007059, GO:0000278, intrinsic apoptotic signaling, regulation of telomere maintenance.\\nmechanism: the genes identified are likely playing roles in a variety of dna metabolic pathways, including dna repair, double-stranded dna break repair, homologous recombination, transcriptional regulation, and mitotic cell cycle processes. these pathways likely enable cellular replication and maintenance of genomic integrity, as well as control of gene expression and apoptosis]] \n", - "835 [[GO:0003677, GO:0003690, GO:0042802, GO:0006259, GO:0006302, GO:0007131, meiotic chromosome segregation and pairing, GO:0007283, GO:0000712, GO:0051026, GO:0016925, GO:0007130]] \n", - "836 [[calcium ion binding activity, identical protein binding activity, GO:0140311, ubiquitin protein ligase binding activity, cellular response, GO:0001932, GO:0010359, GO:0097214, GO:0010468, GO:0035456]] \n", - "837 [[GO:0005515, GO:0046872, GO:0043167, GO:0010468, GO:0001932, cell death pathways, GO:0009059, GO:0046907, cellular response to infection and inflammation]] \n", - "838 [[protein binding activity, dna binding activity, enzyme binding activity, GO:0060090, GO:0140677, GO:0042803, domain binding activity, GO:0016491, protein kinase binding activity, phosphatidylinositol binding activity, GO:0016504, GO:0003714, nuclear androgen receptor binding activity, nf-kappab binding activity, ubiquitin protein ligase binding activity, phosphotyrosine residue binding activity, GO:0016564, GO:0003743, peptidyl-proinalyl cistrans isomerase activity]] \n", - "839 [[protein binding activity, GO:0005215, dna binding activity, rna binding activity, atp binding activity, peptide activity, GO:0003824, enzyme binding activity, phosphoprotein binding activity, GO:0016563, GO:0016787, GO:0016491, GO:0004017, identical protein binding activity, GO:0060090, GO:0007165, signal receiving activity, GO:1901987, metabolism regulation, cell growth control]] \n", - "840 [[peroxisome biogenesis, atp binding activity, GO:0016887, ubiquitin-dependent protein binding activity, GO:0016558, GO:0050821, GO:0043335, GO:0000425, GO:0006625, protein tetramerization.\\n\\nmechanism: these gene functions are involved in a complex process involving the biogenesis and maintenance of peroxisomes, which are subcellular organelles that contain a variety of enzymes involved in metabolic processes. this process entails the function of multiple proteins working together to ferry important proteins into the peroxisomal membrane, where these proteins will become functional components of the organelle]] \n", - "841 [[protein binding activity, GO:0016558, peroxisome matrix targeting signal-2 binding activity, GO:0042803, GO:0008611, GO:0006631, GO:0008285, GO:0000425, GO:0032994, microtubule-based peroxisome localization.\\nmechanism: based on the functions that these genes carry out, it is likely that the genes are involved in a mechanism whereby proteins are imported into the peroxisome matrix, and the peroxisome matrix is organized, stabilized, and/or maintained in order to carry out fatty acid metabolism and pexophagy. the receptor recycling and microtubule-based localization also likely play a role in this mechanism]] \n", - "842 [[protein binding activity, dna binding activity, metal ion binding activity, GO:0003678, GO:0042803, GO:0071480, GO:0010836, GO:0007084, GO:0045071, GO:0032392, GO:0006259, GO:0009267, GO:1902570, GO:0042981, GO:0071456, GO:0032204, GO:0004222, GO:0050688, with a positive effect]] \n", - "843 [[GO:2000772, dna binding and metabolic processes, dna helicase and metal ion binding activities, protein localization to nucleolus and regulation of apoptotic processes appear to be enriched terms common to the three genes given.\\n\\nmechanism: the three genes appear to be involved in similar nucleic acid binding and regulation activities that enable the maintenance and regulation of cellular processes. this suggests an underlying molecular mechanism in which these genes interact directly to modulate a variety of cellular processes related to senescence, GO:0003677, GO:0008152, GO:0006915]] \n", - "844 [[voltage-gated potassium/sodium channel activity, GO:0015276, transmembrane transporter binding activity, GO:0004930, GO:0004971, GO:0015277, GO:0035235, GO:1902476, GO:0007214, GO:0019228, GO:0042391, GO:0007268, regulation of]] \n", - "845 [[GO:0005216, GO:0015276, membrane potential regulation, GO:0005249, GO:0005248, GO:0008066, GO:0004890, GO:0055074, GO:0022851, ionotropic glutamate receptor signaling, GO:1902476, GO:0051932, GO:0048167, negative regulation of smooth muscle apoptotic process, GO:0051924, GO:0086009, GO:0035249, GO:0060292, GO:0006836, GO:0050804, GO:0034220, GO:0051205, GO:0060079]] \n", - "846 [[transcription regulation, GO:0031625, GO:0003677, GO:0006027, GO:0043583, GO:0045475, GO:0007399, GO:0006457, GO:0043066, GO:0010595, GO:0002639, GO:0034214, GO:0050974, GO:0006812, GO:0015886, GO:0071260, GO:0042552, GO:0098742, GO:0006839, GO:0019226, GO:0008380, GO:0003774, GO:0061608, nuclear localization sequence binding activity, GO:0006607, GO:0003887, GO:0006284, gap-filling, protein ubiquitination.\\n\\nmechanism: analysis of the given list of genes suggests that there]] \n", - "847 [[MESH:D015533, dna-binding, rna polymrease ii-specific, dna binding activity, GO:0034214, GO:0061608, protein folding chaperone binding activity, GO:0016567, cell aggregration, GO:0098609, GO:0042552, GO:0005886, GO:0034220, GO:0030218, GO:0015886, mitochondrial transport.\\nmechanism: the eighteen human genes are involved in a variety of complex biological processes, from transcriptional regulation, through to cellular adhesion and the transport of macromolecules, including proteins, nucleic acids and heme. there is likely significant cross-talk between these various processes, particularly at the level of dna binding proteins, transcription activators, and nuclear receptor activities. this suggests that these genes are likely playing a role in the coordination of cellular processes to facilitate proper neural development and maintenance of peripheral nerve function]] \n", - "848 [[GO:0007186, GO:0051480, GO:0006357, GO:1901214, GO:0006915, GO:0006171, GO:0006468]] \n", - "849 [[GO:0007186, GO:0043087, GO:0060170, GO:0006171, GO:0005783, membrane localization, transcriptional regulation, GO:0007212, GO:0006874, GO:0046039, GO:0098843, protein kinase activity. \\n\\nmechanism:\\nthe g protein-coupled receptor signaling pathway is a general pathway that mediates the effects of hormones, neurotransmitters other extracellular signals in cells across a variety of tissues organs. signaling through gpcrs involves activation of g proteins, which in turn activate or inhibit effector enzymes ion channels. the commonality among these genes is that they are involved in mechanisms of gpcr signaling downstream processes such as regulation of gtpase activity, camp synthesis regulation of calcium ion concentration. the genes may also participate in membrane localization, transcriptional regulation postsynaptic endocytic zone functions. other associated activities]] \n", - "850 [[transcription activation/repression, GO:0007165, GO:0006351, GO:0007049, MESH:D012319, GO:0003682, GO:0008270, GO:0016575, protein ligase/cofactor binding]] \n", - "851 [[dna-binding transcription, GO:0016563, rna polymerase ii-specific, GO:0016564, positive/negative regulation of transcription, GO:0006351, GO:0010468, nucleic acid binding activity, sequence-specific double-stranded dna binding activity, protein kinase binding activity]] \n", - "\n", - "prompt_variant jaccard_index \n", - "0 0.07 \n", - "1 0.33 \n", - "2 0.40 \n", - "3 0.22 \n", - "4 0.08 \n", - "5 0.00 \n", - "6 0.16 \n", - "7 0.00 \n", - "8 0.00 \n", - "9 0.18 \n", - "10 0.09 \n", - "11 0.00 \n", - "12 0.29 \n", - "13 0.12 \n", - "14 0.00 \n", - "15 0.12 \n", - "16 0.33 \n", - "17 0.00 \n", - "18 0.10 \n", - "19 0.12 \n", - "20 0.14 \n", - "21 0.17 \n", - "22 0.17 \n", - "23 0.00 \n", - "24 0.17 \n", - "25 0.44 \n", - "26 0.75 \n", - "27 0.10 \n", - "28 0.50 \n", - "29 0.29 \n", - "30 0.10 \n", - "31 0.29 \n", - "32 0.29 \n", - "33 0.14 \n", - "34 0.08 \n", - "35 0.07 \n", - "36 0.18 \n", - "37 0.29 \n", - "38 0.17 \n", - "39 0.10 \n", - "40 0.08 \n", - "41 0.05 \n", - "42 0.20 \n", - "43 0.22 \n", - "44 0.00 \n", - "45 0.25 \n", - "46 0.15 \n", - "47 0.38 \n", - "48 0.00 \n", - "49 0.16 \n", - "50 0.00 \n", - "51 0.09 \n", - "52 0.20 \n", - "53 0.11 \n", - "54 0.25 \n", - "55 0.22 \n", - "56 0.00 \n", - "57 0.00 \n", - "58 0.08 \n", - "59 0.00 \n", - "60 0.00 \n", - "61 0.00 \n", - "62 0.00 \n", - "63 0.00 \n", - "64 0.22 \n", - "65 0.08 \n", - "66 0.09 \n", - "67 0.40 \n", - "68 0.00 \n", - "69 0.29 \n", - "70 0.08 \n", - "71 0.33 \n", - "72 0.22 \n", - "73 0.50 \n", - "74 0.25 \n", - "75 0.29 \n", - "76 0.29 \n", - "77 0.29 \n", - "78 0.10 \n", - "79 0.50 \n", - "80 0.20 \n", - "81 0.09 \n", - "82 0.29 \n", - "83 0.40 \n", - "84 0.11 \n", - "85 0.17 \n", - "86 0.00 \n", - "87 0.00 \n", - "88 0.00 \n", - "89 0.14 \n", - "90 0.14 \n", - "91 0.08 \n", - "92 0.12 \n", - "93 0.00 \n", - "94 0.09 \n", - "95 0.25 \n", - "96 0.00 \n", - "97 0.12 \n", - "98 0.17 \n", - "99 0.00 \n", - "100 0.20 \n", - "101 0.20 \n", - "102 0.00 \n", - "103 0.09 \n", - "104 0.40 \n", - "105 0.14 \n", - "106 0.11 \n", - "107 0.30 \n", - "108 0.00 \n", - "109 0.17 \n", - "110 0.12 \n", - "111 0.22 \n", - "112 0.12 \n", - "113 0.14 \n", - "114 0.00 \n", - "115 0.12 \n", - "116 0.09 \n", - "117 0.30 \n", - "118 0.00 \n", - "119 0.00 \n", - "120 0.00 \n", - "121 0.00 \n", - "122 0.50 \n", - "123 0.17 \n", - "124 0.00 \n", - "125 0.33 \n", - "126 0.20 \n", - "127 0.00 \n", - "128 0.22 \n", - "129 0.09 \n", - "130 0.09 \n", - "131 0.17 \n", - "132 0.00 \n", - "133 0.17 \n", - "134 0.40 \n", - "135 0.00 \n", - "136 0.50 \n", - "137 0.00 \n", - "138 0.00 \n", - "139 0.00 \n", - "140 0.22 \n", - "141 0.00 \n", - "142 0.29 \n", - "143 0.20 \n", - "144 0.00 \n", - "145 0.33 \n", - "146 0.11 \n", - "147 0.00 \n", - "148 0.27 \n", - "149 0.08 \n", - "150 0.00 \n", - "151 0.00 \n", - "152 0.11 \n", - "153 0.43 \n", - "154 0.00 \n", - "155 0.07 \n", - "156 0.11 \n", - "157 0.06 \n", - "158 0.08 \n", - "159 0.14 \n", - "160 0.00 \n", - "161 0.08 \n", - "162 0.38 \n", - "163 0.22 \n", - "164 0.18 \n", - "165 0.50 \n", - "166 0.00 \n", - "167 0.36 \n", - "168 0.25 \n", - "169 0.11 \n", - "170 0.33 \n", - "171 0.20 \n", - "172 0.14 \n", - "173 0.21 \n", - "174 0.00 \n", - "175 0.00 \n", - "176 0.00 \n", - "177 0.00 \n", - "178 0.00 \n", - "179 0.14 \n", - "180 0.00 \n", - "181 0.25 \n", - "182 0.00 \n", - "183 0.00 \n", - "184 0.00 \n", - "185 0.14 \n", - "186 0.00 \n", - "187 0.00 \n", - "188 0.06 \n", - "189 0.00 \n", - "190 0.39 \n", - "191 0.12 \n", - "192 0.00 \n", - "193 0.06 \n", - "194 0.22 \n", - "195 0.06 \n", - "196 0.33 \n", - "197 0.00 \n", - "198 0.08 \n", - "199 0.09 \n", - "200 0.12 \n", - "201 0.00 \n", - "202 0.10 \n", - "203 0.00 \n", - "204 0.14 \n", - "205 0.05 \n", - "206 0.00 \n", - "207 0.00 \n", - "208 0.00 \n", - "209 0.23 \n", - "210 0.22 \n", - "211 0.17 \n", - "212 0.00 \n", - "213 0.00 \n", - "214 0.12 \n", - "215 0.00 \n", - "216 0.00 \n", - "217 0.05 \n", - "218 0.33 \n", - "219 0.17 \n", - "220 0.22 \n", - "221 0.18 \n", - "222 0.14 \n", - "223 0.10 \n", - "224 0.00 \n", - "225 0.13 \n", - "226 0.20 \n", - "227 0.09 \n", - "228 0.43 \n", - "229 0.07 \n", - "230 0.22 \n", - "231 0.00 \n", - "232 0.08 \n", - "233 0.00 \n", - "234 0.00 \n", - "235 0.10 \n", - "236 0.11 \n", - "237 0.11 \n", - "238 0.07 \n", - "239 0.07 \n", - "240 0.00 \n", - "241 0.09 \n", - "242 0.00 \n", - "243 0.14 \n", - "244 0.12 \n", - "245 0.00 \n", - "246 0.12 \n", - "247 0.20 \n", - "248 0.00 \n", - "249 0.09 \n", - "250 0.08 \n", - "251 0.04 \n", - "252 0.22 \n", - "253 0.20 \n", - "254 0.29 \n", - "255 0.44 \n", - "256 0.50 \n", - "257 0.40 \n", - "258 0.11 \n", - "259 0.17 \n", - "260 0.00 \n", - "261 0.00 \n", - "262 0.18 \n", - "263 0.00 \n", - "264 0.11 \n", - "265 0.00 \n", - "266 0.11 \n", - "267 0.15 \n", - "268 0.00 \n", - "269 0.18 \n", - "270 0.00 \n", - "271 0.20 \n", - "272 0.14 \n", - "273 0.50 \n", - "274 0.17 \n", - "275 0.29 \n", - "276 0.20 \n", - "277 0.17 \n", - "278 0.00 \n", - "279 0.00 \n", - "280 0.44 \n", - "281 0.00 \n", - "282 0.00 \n", - "283 0.14 \n", - "284 0.80 \n", - "285 0.80 \n", - "286 0.50 \n", - "287 0.29 \n", - "288 0.00 \n", - "289 0.13 \n", - "290 0.09 \n", - "291 0.15 \n", - "292 0.00 \n", - "293 0.00 \n", - "294 0.00 \n", - "295 0.00 \n", - "296 0.00 \n", - "297 0.00 \n", - "298 0.00 \n", - "299 0.06 \n", - "300 0.10 \n", - "301 0.00 \n", - "302 0.00 \n", - "303 0.17 \n", - "304 0.20 \n", - "305 0.22 \n", - "306 0.00 \n", - "307 0.00 \n", - "308 0.00 \n", - "309 0.00 \n", - "310 0.00 \n", - "311 0.12 \n", - "312 0.22 \n", - "313 0.58 \n", - "314 0.18 \n", - "315 0.50 \n", - "316 0.00 \n", - "317 0.00 \n", - "318 0.00 \n", - "319 0.00 \n", - "320 0.00 \n", - "321 0.25 \n", - "322 0.22 \n", - "323 0.00 \n", - "324 0.15 \n", - "325 0.00 \n", - "326 0.00 \n", - "327 0.50 \n", - "328 0.00 \n", - "329 0.00 \n", - "330 0.15 \n", - "331 0.00 \n", - "332 0.17 \n", - "333 0.08 \n", - "334 0.12 \n", - "335 0.17 \n", - "336 0.22 \n", - "337 0.44 \n", - "338 0.00 \n", - "339 0.20 \n", - "340 0.17 \n", - "341 0.60 \n", - "342 0.08 \n", - "343 0.00 \n", - "344 0.00 \n", - "345 0.00 \n", - "346 0.20 \n", - "347 0.00 \n", - "348 0.12 \n", - "349 0.00 \n", - "350 0.00 \n", - "351 0.25 \n", - "352 0.25 \n", - "353 0.50 \n", - "354 0.75 \n", - "355 0.00 \n", - "356 0.33 \n", - "357 0.00 \n", - "358 0.00 \n", - "359 0.00 \n", - "360 0.00 \n", - "361 0.12 \n", - "362 0.17 \n", - "363 0.25 \n", - "364 0.00 \n", - "365 0.00 \n", - "366 0.07 \n", - "367 0.20 \n", - "368 0.24 \n", - "369 0.25 \n", - "370 0.08 \n", - "371 0.25 \n", - "372 0.29 \n", - "373 0.06 \n", - "374 0.15 \n", - "375 0.00 \n", - "376 0.14 \n", - "377 0.00 \n", - "378 0.00 \n", - "379 0.00 \n", - "380 0.00 \n", - "381 0.11 \n", - "382 0.46 \n", - "383 0.00 \n", - "384 0.00 \n", - "385 0.17 \n", - "386 0.08 \n", - "387 0.09 \n", - "388 0.11 \n", - "389 0.10 \n", - "390 0.17 \n", - "391 0.10 \n", - "392 0.00 \n", - "393 0.08 \n", - "394 0.33 \n", - "395 0.12 \n", - "396 0.12 \n", - "397 0.14 \n", - "398 0.11 \n", - "399 0.33 \n", - "400 0.29 \n", - "401 0.00 \n", - "402 0.20 \n", - "403 0.15 \n", - "404 0.60 \n", - "405 0.25 \n", - "406 0.67 \n", - "407 0.00 \n", - "408 0.33 \n", - "409 0.60 \n", - "410 0.00 \n", - "411 0.10 \n", - "412 0.12 \n", - "413 0.10 \n", - "414 0.14 \n", - "415 0.33 \n", - "416 0.60 \n", - "417 0.33 \n", - "418 0.30 \n", - "419 0.43 \n", - "420 0.20 \n", - "421 0.20 \n", - "422 0.20 \n", - "423 0.15 \n", - "424 0.27 \n", - "425 0.11 \n", - "426 0.00 \n", - "427 0.00 \n", - "428 0.16 \n", - "429 0.20 \n", - "430 0.03 \n", - "431 0.00 \n", - "432 0.00 \n", - "433 0.08 \n", - "434 0.09 \n", - "435 0.09 \n", - "436 0.00 \n", - "437 0.00 \n", - "438 0.00 \n", - "439 0.07 \n", - "440 0.19 \n", - "441 0.03 \n", - "442 0.25 \n", - "443 0.00 \n", - "444 0.00 \n", - "445 0.03 \n", - "446 0.00 \n", - "447 0.07 \n", - "448 0.00 \n", - "449 0.21 \n", - 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"\n", - "# reset index to get it back in the form of a DataFrame\n", - "result = df_pivot.reset_index()\n", - "result" - ] - }, - { - "cell_type": "code", - "execution_count": 62, - "id": "236b0574", - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "count 852.00\n", - "mean 0.10\n", - "std 0.13\n", - "min 0.00\n", - "25% 0.00\n", - "50% 0.07\n", - "75% 0.15\n", - "max 0.80\n", - "Name: jaccard_index, dtype: float64" - ] - }, - "execution_count": 62, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "result['jaccard_index'].describe()" - ] - }, - { - "cell_type": "code", - "execution_count": 63, - "id": "0dccb96e", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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countmeanstdmin25%50%75%max
model
gpt-3.5-turbo426.00.140.150.00.00.110.220.8
text-davinci-003426.00.060.080.00.00.040.080.5
\n", - "
" - ], - "text/plain": [ - " count mean std min 25% 50% 75% max\n", - "model \n", - "gpt-3.5-turbo 426.0 0.14 0.15 0.0 0.0 0.11 0.22 0.8\n", - "text-davinci-003 426.0 0.06 0.08 0.0 0.0 0.04 0.08 0.5" - ] - }, - "execution_count": 63, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "result.groupby([MODEL])['jaccard_index'].describe()" - ] - }, - { - "cell_type": "code", - "execution_count": 64, - "id": "5a46537d", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "\n", - "\n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - "
  countmeanstdminmax
modelmethod     
gpt-3.5-turbonarrative_synopsis142.0000.1520.1430.0000.750
no_synopsis142.0000.1230.1290.0000.500
ontological_synopsis142.0000.1600.1850.0000.800
text-davinci-003narrative_synopsis142.0000.0610.0700.0000.333
no_synopsis142.0000.0380.0520.0000.250
ontological_synopsis142.0000.0840.0950.0000.500
\n" - ], - "text/plain": [ - "" - ] - }, - "execution_count": 64, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "result.groupby([MODEL, METHOD])['jaccard_index'].describe()[['count', 'mean', 'std', 'min', 'max']].style.highlight_max(axis=0, props='font-weight:bold').format(precision=3)" - ] - }, - { - "cell_type": "code", - "execution_count": 65, - "id": "0cb59c54", - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "'\\nOur analysis of the list of human genes has revealed that many of the functions of these genes are related to cell regulation, metabolism, and transport. Specifically, the genes are involved in regulating cell growth and adhesion, lipid metabolism, cholesterol synthesis and breakdown, protein homodimerization and packing, enzymatic reactions, hormone regulation, and gene transcription. These gene functions are enriched in areas such as cell motility, energy generation, amino acid synthesis and degradation, glycoprotein synthesis, sterol biosynthesis and degradation, lipid metabolism and transport, and transcriptional regulation. \\n\\nMechanism: The underlying biological mechanism likely involves the coordination of these processes in order to maintain cellular homeostasis and to respond to a variety of environmental stimuli. In this way, cells can signal and respond to changes in their internal and external environments.\\n\\n'" - ] - }, - "execution_count": 65, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "summaries = [s for s in list(df[SUMMARY]) if s]\n", - "len(summaries)\n", - "import random\n", - "def random_summary():\n", - " return summaries[int(random.random() * len(summaries))]\n", - "\n", - "random_summary()" - ] - }, - { - "cell_type": "code", - "execution_count": 66, - "id": "04fd3823", - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "0.8665182692772254" - ] - }, - "execution_count": 66, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "from ontogpt.clients import OpenAIClient\n", - "\n", - "simclient = OpenAIClient(model=\"text-embedding-ada-002\")\n", - "\n", - "def text_similarity(text1, text2):\n", - " return simclient.similarity(text1, text2)\n", - "\n", - "text_similarity(\"nucleus of cell\", \"nuclear membrane\")" - ] - }, - { - "cell_type": "code", - "execution_count": 67, - "id": "29f70a29", - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "0.8220945700281092" - ] - }, - "execution_count": 67, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "text_similarity(random_summary(), random_summary())" - ] - }, - { - "cell_type": "code", - "execution_count": 68, - "id": "8bcb757f", - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "1.0000000000000002" - ] - }, - "execution_count": 68, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "rs = random_summary()\n", - "text_similarity(rs, rs)" - ] - }, - { - "cell_type": "code", - "execution_count": 69, - "id": "3b3d6bf1", - "metadata": {}, - "outputs": [], - "source": [ - "sims = [text_similarity(random_summary(), random_summary()) for i in range(1,200)]" - ] - }, - { - "cell_type": "code", - "execution_count": 70, - "id": "5636e304", - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "0.8240856663144941" - ] - }, - "execution_count": 70, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "import statistics\n", - "avg_sim = statistics.mean(sims)\n", - "avg_sim" - ] - }, - { - "cell_type": "code", - "execution_count": 71, - "id": "bfc8d7fc", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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" \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - 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prompt_variantmodelmethodgenesetv1v2simlength_diff
0gpt-3.5-turbonarrative_synopsisEDS-0[Summary: Genes involved in connective tissue disorders, specifically Ehlers-Danlos syndrome, are enriched for terms related to collagen and extracellular matrix organization.\\nMechanism: The genes encode proteins that play roles in collagen synthesis, modification, and organization, as well as extracellular matrix maturation.\\n][Summary: Genes associated with connective tissue disorder Ehlers-Danlos syndrome.\\nMechanism: Collagen synthesis and matrix maturation.\\n\\nHypothesis: The enriched terms suggest that Ehlers-Danlos syndrome is caused by disruptions in collagen synthesis and the maturation of matrix organization. The genes identified appear to play critical roles in these processes, including collagen synthesis, extracellular matrix organization, and proteolytic subunits and serine proteases that may degrade or modify collagen fibers. Additionally, the presence of sulfotransferases and zinc finger proteins may suggest additional regulatory pathways for collagen synthesis and modification. The disruption of these pathways likely leads to reduced collagen strength and increased tissue laxity, two key hallmarks of Ehlers-Danlos syndrome.]0.97498
1gpt-3.5-turbonarrative_synopsisEDS-1[Summary: Several of the genes listed are involved in the biosynthesis and regulation of collagen, a key component of connective tissue. Mutations in these genes are associated with Ehlers-Danlos syndrome, a group of genetic disorders that affect collagen production and cause hypermobility of joints, skin elasticity, and tissue fragility.\\n\\nMechanism: The genes listed are involved in collagen biosynthesis and regulation, suggesting that deficiencies or mutations in these genes could lead to abnormal or insufficient collagen production, ultimately resulting in connective tissue disorders such as Ehlers-Danlos syndrome.\\n\\n\\nHypothesis: The genes listed may converge on a pathway that regulates the synthesis, assembly, and remodeling of the extracellular matrix, particularly with respect to collagen and other fibrillar components. Defects or deficiencies in this pathway could lead to dysregulation of tissue remodeling and repair, resulting in connective tissue disorders such as Ehlers-Danlos syndrome.][Summary: Genes associated with Ehlers-Danlos syndrome (EDS) are involved in the biosynthesis, assembly, and organization of collagen and extracellular matrix, as well as immune response and protein folding.\\n\\nMechanism: The genes identified are involved in the process of collagen biosynthesis and assembly, including post-translational modifications such as lysyl hydroxylation and glycosylation. Disruptions in these processes can lead to the connective tissue disorder Ehlers-Danlos syndrome. \\n\\n]0.95512
2gpt-3.5-turbonarrative_synopsisFA-0[Summary: Genes related to the Fanconi anemia complementation group and other DNA repair components\\nMechanism: DNA repair \\n][Summary: The common function of the listed genes is DNA damage repair and maintenance of genome stability, particularly through homologous recombination and the Fanconi anemia pathway.\\nMechanism: The genes share a role in maintaining genomic integrity and preventing the onset of cancer through coordinated DNA repair functions.\\n]0.91207
3gpt-3.5-turbonarrative_synopsisFA-1[Summary: The genes in this list are predominantly involved in DNA repair, specifically in the Fanconi anemia (FA) pathway and homologous recombination (HR) pathway. \\n\\nMechanism: The FA pathway is a complex pathway involved in the repair of DNA interstrand crosslinks and other forms of DNA damage. The HR pathway is involved in the repair of double-strand breaks in DNA.\\n\\n][Summary: The enriched terms are related to DNA repair and maintenance of genome stability.\\n\\n\\nHypothesis: Mutations or dysregulation in these genes may lead to a higher susceptibility to DNA damage, defects in DNA repair, and could potentially lead to tumorigenesis. They may also be potential targets for therapeutic intervention in certain cancers.]0.8522
4gpt-3.5-turbonarrative_synopsisHALLMARK_ADIPOGENESIS-0[Summary: Genes involved in energy metabolism and mitochondrial function are over-represented.\\n\\nMechanism: These genes likely play a role in regulating cellular energy metabolism, particularly through mitochondrial function.\\n\\n][Summary: Genes involved in mitochondrial function and metabolism are enriched.\\n\\nMechanism: These genes are involved in various metabolic and mitochondrial processes, including fatty acid metabolism, electron transport chain function, and redox reactions. The common theme among these functions is energy production and regulation within the mitochondria.\\n\\n]0.95131
5gpt-3.5-turbonarrative_synopsisHALLMARK_ADIPOGENESIS-1[Summary: Many of the genes in the list are involved in mitochondrial function, specifically in the respiratory chain and energy production. Other common functions include lipid metabolism and transport, protein binding, and regulation of cell growth and division.\\n\\n\\nHypothesis: These genes may be involved in maintaining cell and mitochondrial function, particularly in energy production and membrane transport. Many are also involved in regulating oxidative stress, which can damage cells and contribute to a range of diseases. Overall, the commonalities suggest that these genes play important roles in maintaining cellular and mitochondrial health, and dysregulation of these genes may contribute to metabolic disorders, neurodegenerative diseases, and other health problems.][Summary: Many of the genes in this list are involved in mitochondrial function and energy metabolism, specifically in processes related to lipid metabolism and the electron transport chain. \\n\\n]0.95587
6gpt-3.5-turbonarrative_synopsisHALLMARK_ALLOGRAFT_REJECTION-0[Summary: Immune response and cytokine signaling pathways are enriched in this set of genes.\\nMechanism: These genes are involved in the regulation of immune response and activation of cytokine signaling pathways.\\n][Summary: Immune system function and cytokine signaling\\nMechanism: Immune response and cytokine pathways\\n\\nHypothesis: The overrepresented terms suggest that these genes play a role in the immune system function and cytokine signaling. This could involve the activation of T cells, leukocyte migration, and cytokine production to regulate the immune response and fight against pathogens. The cytokine pathways produced by these genes could also influence T cell differentiation and antigen processing/presentation via MHC class II, leading to the production of interleukin-2 and interferon-gamma. The chemokine-mediated signaling pathway could also play a role in leukocyte migration and immune response activation.]0.94502
7gpt-3.5-turbonarrative_synopsisHALLMARK_ALLOGRAFT_REJECTION-1[Summary: Immune response and cytokine signaling\\nMechanism: Regulation of immune response through cytokine signaling pathways\\n\\nHypothesis: The enriched terms all relate to the regulation of immune response through cytokine signaling pathways. The genes in this list are involved in the production and function of chemokines and cytokines, which play key roles in immune system communication and response. Toll-like receptors, interferon signaling, and TNF signaling pathways are important components of the innate immune response, while TGF-beta signaling plays a role in immune tolerance and regulation. Overall, this gene list suggests a strong focus on immune response and regulation.][Summary: The common function of the genes listed is related to the immune system, specifically cytokine signaling, chemotaxis, and antigen presentation.\\nMechanism: The genes are involved in various aspects of immune response, including the production and signaling of cytokines, chemotaxis of immune cells, and antigen presentation to T cells.\\n]0.90343
8gpt-3.5-turbonarrative_synopsisHALLMARK_ANDROGEN_RESPONSE-0[Summary: Signal transduction and cellular metabolism\\n\\nHypothesis: These genes may be involved in a signaling pathway that regulates cellular metabolism in response to extracellular signals. They may work together to modulate the activity of various enzymes and transporters, leading to changes in the levels of key metabolic intermediates and ultimately contributing to the regulation of cellular metabolism.][Summary: Genes involved in various aspects of cellular processes, including transport, metabolism, cytoskeleton organization, and signaling pathways, are over-represented.\\n\\nMechanism: These genes are involved in diverse biological pathways, and thus do not share a single common mechanism.\\n\\n]0.89118
9gpt-3.5-turbonarrative_synopsisHALLMARK_ANDROGEN_RESPONSE-1[Summary: Protein regulation and cellular signaling pathways\\nMechanism: Enzyme-catalyzed reactions and protein-protein interactions\\n][Summary: Regulation of protein activity, transport, and metabolism\\nMechanism:hypothesize that these genes are involved in regulating protein activity, transport, and metabolism through various processes such as binding to regulatory subunits, transcribing DNA, catalyzing enzymatic reactions, and transporting molecules across cellular membranes.\\n]0.87216
10gpt-3.5-turbonarrative_synopsisHALLMARK_ANGIOGENESIS-0[Summary: Extracellular matrix proteins and signaling molecules are enriched among the listed genes.\\nMechanism: These genes may be involved in the regulation of tissue development and regeneration, as well as cell growth, migration, and adhesion. \\n][Summary: Extracellular matrix organization and cellular adhesion\\nMechanism: Extracellular matrix synthesis and remodeling by integrins and proteoglycans\\n]0.8894
11gpt-3.5-turbonarrative_synopsisHALLMARK_ANGIOGENESIS-1[Summary: Extracellular matrix (ECM) organization and cell adhesion/migration are enriched functions among the listed genes.\\nMechanism: The listed genes are involved in regulating ECM integrity and cell adhesion/migration, which are critical processes in development and tissue homeostasis. Dysregulation of these processes can contribute to pathogenesis of a variety of diseases, including cancer.\\n][Summary: Extracellular matrix organization and cell adhesion\\n\\nHypothesis: These genes may be involved in the regulation of tissue remodeling and repair, as well as in the maintenance of cell integrity and differentiation. Dysregulation of these genes could potentially lead to pathological processes such as fibrosis or cancer metastasis.]0.9359
12gpt-3.5-turbonarrative_synopsisHALLMARK_APICAL_JUNCTION-0[Summary: Genes involved in cytoskeleton organization, cell adhesion, and signal transduction.\\nMechanism: These genes likely play a role in the maintenance of cellular morphology, adhesion, and proper communication between cells.\\n][Summary: Genes involved in cell adhesion and cytoskeletal organization are enriched.\\n\\nMechanism: These genes are involved in the organization and regulation of cellular structures such as the cytoskeleton, focal adhesions, and tight junctions, which are critical for cell adhesion and migration.\\n\\n]0.9468
13gpt-3.5-turbonarrative_synopsisHALLMARK_APICAL_JUNCTION-1[Summary: Genes involved in cell adhesion, specifically with roles in tight junction formation and maintenance, as well as extracellular matrix interactions.\\n\\nMechanism: These genes are involved in various molecular mechanisms related to cell adhesion, including tight junction formation/maintenance, extracellular matrix interactions and basement membrane organization.\\n\\n][Summary: Cell adhesion and signaling\\nMechanism: Tight junction formation\\n\\nHypothesis: The genes in this list all play a role in cell adhesion and signaling, with a particular focus on the formation of tight junctions. Tight junctions represent a mode of cell-to-cell adhesion in epithelial or endothelial cells and are crucial for the maintenance of cellular polarity and barrier function. The enriched terms suggest that the genes in this list are involved in various signaling pathways, including those mediated by cadherins, integrins, GPCRs, and PTKs. They also regulate the actin cytoskeleton and ECM, which are important for cell adhesion and migration. Furthermore, the involvement of PI3K, MAPK, and TGF-beta signaling pathways indicates that these genes likely play a]0.93406
14gpt-3.5-turbonarrative_synopsisHALLMARK_APICAL_SURFACE-0[Summary: This list includes genes with diverse functions such as cell signaling, growth inhibition, and ion transport. However, common enriched terms suggest involvement in cell adhesion and regulation.\\nMechanism: The genes appear to be involved in molecular networks responsible for the regulation and maintenance of the cell membrane, particularly in receptor-mediated cell signaling and cell adhesion.\\n][Summary: Membrane-bound proteins involved in signal transduction and cell adhesion\\n\\n]0.88321
15gpt-3.5-turbonarrative_synopsisHALLMARK_APICAL_SURFACE-1[Summary: Cell adhesion and signaling pathways are enriched among the given set of human genes.\\n\\nMechanism: The enriched genes are involved in various processes, including transport, development, and regulation of the immune system, and these processes are intertwined in signaling pathways that affect cell adhesion.\\n\\n][Summary: Cell surface proteins and membrane transporters involved in various cellular processes, including cell adhesion, signal transduction, and ion transport.\\n\\nMechanism: These gene products are involved in the regulation of cellular functions at the cell membrane and play a critical role in maintaining proper cellular signaling and transport mechanisms.\\n\\n]0.9043
16gpt-3.5-turbonarrative_synopsisHALLMARK_APOPTOSIS-0[Summary: Apoptotic processes and regulation of cell death are enriched terms in the gene list.\\n\\n][Summary: Apoptosis, cell death, and signaling pathways are enriched terms in these genes.\\nMechanism: The genes are involved in regulating various aspects of apoptosis and cell death, as well as signaling pathways that control these processes.\\n]0.93147
17gpt-3.5-turbonarrative_synopsisHALLMARK_APOPTOSIS-1[Summary: Genes involved in apoptosis, cytokine signaling, and growth factor regulation.\\n\\nMechanism: These genes all play a role in regulating cell survival and growth, primarily through apoptosis, cytokine signaling, and growth factor regulation.\\n\\n][Summary: Apoptosis and cell death related genes.\\n\\nMechanism: Activation of caspases, which are a family of cysteine-aspartic acid proteases that play a central role in executing apoptosis.\\n\\n\\nHypothesis: These genes are involved in the regulation and execution of apoptotic pathways, which play an important role in development, tissue homeostasis and elimination of damaged cells. The activation of caspases leads to the cleavage of a variety of structural and regulatory proteins, resulting in cytoskeletal rearrangements, DNA fragmentation, and ultimately, cell death. The over-representation of terms related to caspase activity and apoptosis regulation suggests that these genes are strongly linked to this biological process.]0.91483
18gpt-3.5-turbonarrative_synopsisHALLMARK_BILE_ACID_METABOLISM-0[Summary: Membrane-associated proteins that are members of the superfamily of ATP-binding cassette (ABC) transporters, as well as enzymes involved in lipid metabolism, are over-represented in this gene list. \\n\\nMechanism: Several of the enriched terms relate to lipid metabolism, suggesting that these genes may be involved in the transport or regulation of various lipids within the body. \\n\\n][Summary: Transport and metabolism of lipids and cholesterol\\nMechanism: ABC transporters and cytochrome P450 enzymes play a key role in the transport and metabolism of lipids and cholesterol.\\n]0.88199
19gpt-3.5-turbonarrative_synopsisHALLMARK_BILE_ACID_METABOLISM-1[Summary: Peroxisomal biogenesis and lipid metabolism are enriched functions among the given genes.\\nMechanism: Peroxins (PEXs) are essential proteins for functional peroxisome assembly. Peroxisomes are organelles involved in lipid metabolism, fatty acid beta-oxidation, and bile acid synthesis.\\n\\n][Summary: Peroxisome biogenesis and lipid metabolism are enriched functions among the listed genes.\\n\\n\\nHypothesis: It is possible that dysregulation of these genes could lead to metabolic disorders such as peroxisome biogenesis disorders or abnormal cholesterol and fatty acid metabolism. Further research is needed to fully understand the underlying biological mechanisms and potential clinical implications of these enriched functions.]0.95141
20gpt-3.5-turbonarrative_synopsisHALLMARK_CHOLESTEROL_HOMEOSTASIS-0[Summary: Lipid metabolism and cholesterol homeostasis are over-represented functions amongst the list of genes.\\n\\nMechanism: These genes are involved in the regulation of cholesterol levels in cells, lipid metabolism and transport of various molecules across cell membranes. \\n\\n][Summary: Genes involved in lipid metabolism, transport, and synthesis are enriched.\\nMechanism: Lipids are essential components of cellular structure, energy storage, and signaling. These genes contribute to the regulation of lipid metabolism and transport, as well as the synthesis of lipids necessary for these processes.\\n]0.9447
21gpt-3.5-turbonarrative_synopsisHALLMARK_CHOLESTEROL_HOMEOSTASIS-1[Summary: Genes involved in cholesterol biosynthesis, lipid metabolism, and signal transduction.\\nMechanism: Biosynthesis and regulation of cholesterol and lipids.\\n\\nHypothesis: These genes are involved in the complex pathways of cholesterol biosynthesis and lipid metabolism, which are tightly regulated processes where disturbances can lead to a wide range of diseases. The genes identified here may play key roles in these pathways, including enzymes involved in the conversion of mevalonate to cholesterol, fatty acid desaturases regulating lipid unsaturation, and phospholipid-binding proteins regulating signal transduction. Further research into these mechanisms could aid in the development of therapies for metabolic disorders such as atherosclerosis and hyperlipidemia.][Summary: Cholesterol biosynthesis and metabolism\\nMechanism: Regulation of cholesterol levels via enzymatic activity\\n\\nHypothesis: The enriched terms suggest a common biological mechanism involving the regulation of cholesterol levels and metabolism through various enzymatic pathways, including those responsible for cholesterol biosynthesis, phospholipid metabolism, fatty acid biosynthesis, and sterol metabolism. The genes in this list likely play a role in maintaining proper cholesterol levels and homeostasis, and dysregulation of these pathways may lead to various diseases such as hypercholesterolemia, atherosclerosis, and other metabolic disorders.]0.93119
22gpt-3.5-turbonarrative_synopsisHALLMARK_COAGULATION-0[Summary: Many of the genes in this list are involved in blood clotting and complement activation, while others are proteases, lipoproteins, or involved in extracellular matrix regulation.\\nMechanism: These genes are involved in regulating or participating in protease activities, blood clotting, and complement activation, as well as extracellular matrix regulation.\\n\\nHypothesis: The enriched terms suggest that these genes may be involved in a regulatory network that balances protease activities, blood clotting, complement activation, and extracellular matrix regulation. Dysregulation of this network may lead to pathologies such as thrombosis, inflammation, and tissue remodeling. The specific biological mechanisms involved can include protease activation and inhibition, substrate recognition, signal transduction, and gene expression regulation.][Summary: Several genes are involved in blood coagulation, extracellular matrix remodeling, and regulation of the complement pathway. \\nMechanism: These genes are likely involved in various aspects of tissue homeostasis and response to injury, including wound healing and inflammation.\\n]0.94569
23gpt-3.5-turbonarrative_synopsisHALLMARK_COAGULATION-1[Summary: The enriched terms are related to blood coagulation and complement pathway, as well as extracellular matrix degradation and calcium-binding proteins.\\n\\n\\nHypothesis: The coagulation, complement, and extracellular matrix remodelling pathways are interconnected through multiple mechanisms and play crucial roles in maintaining tissue homeostasis and repair. Dysregulation of these pathways is associated with several human diseases, such as thrombosis, autoimmune disorders, and cancer. Calcium ions are essential for mediating][Summary: Extracellular matrix breakdown, blood coagulation, and protein inhibition are enriched functions shared by these genes.\\nMechanism: These genes are involved in regulating the extracellular matrix, blood coagulation, and protease activity through protein inhibition.\\n]0.88260
24gpt-3.5-turbonarrative_synopsisHALLMARK_COMPLEMENT-0[Summary: Genes enriched in immune system functions and regulation of complement activity.\\n\\nMechanism: These genes are involved in the regulation and function of the immune system and the complement cascade, including regulation of proteolytic enzymes, regulation of cytokine and growth factor signaling, and maintenance of cell surface glycoproteins.\\n\\n][Summary: Proteases and their inhibitors are enriched among these genes, as well as genes involved in blood clotting and complement activation.\\n\\nMechanism: These genes are involved in proteolytic and inflammatory pathways, including complement activation and blood clotting.\\n\\n]0.9177
25gpt-3.5-turbonarrative_synopsisHALLMARK_COMPLEMENT-1[Summary: Genes involved in inflammation, immunity, and blood coagulation are enriched in this list.\\n\\nMechanism: These genes are involved in various processes related to the regulation of the immune response, blood coagulation, and inflammation. Many of these genes play a role in the complement cascade, cytokine signaling, and protein phosphorylation.\\n\\n][Summary: Genes involved in regulation of immune response and blood coagulation are statistically over-represented.\\n\\n]0.91238
26gpt-3.5-turbonarrative_synopsisHALLMARK_DNA_REPAIR-0[Summary: Genes involved in DNA repair, transcription initiation, RNA processing, and nucleotide metabolism.\\n\\nMechanism: These genes are all involved in various cellular processes that are crucial for maintaining genomic stability and integrity, including DNA repair, transcription initiation, RNA processing, and nucleotide metabolism. \\n\\n][Summary: Genes are involved in DNA repair, transcription, and nucleotide metabolism.\\n\\nMechanism: These genes are involved in essential cellular processes, including DNA repair, transcription initiation, and nucleotide metabolism. Many of these genes encode subunits of DNA polymerases or transcription factor complexes. Their shared function in DNA repair may suggest a common biological pathway in maintaining genomic stability.\\n\\n]0.9893
27gpt-3.5-turbonarrative_synopsisHALLMARK_DNA_REPAIR-1[Summary: The enriched terms suggest that these genes are involved in DNA replication, repair, and transcription.\\n\\nMechanism: These genes are involved in various aspects of DNA metabolism, including DNA replication, repair, and transcription. \\n\\n\\nHypothesis: These genes are all involved in fundamental cellular processes in which DNA is duplicated, transcribed, and repaired. They likely work together to ensure the accuracy and stability of genetic information.][Summary: Genes involved in DNA repair and transcription regulation.\\n\\nMechanism: These genes are all involved in various aspects of DNA repair and transcription regulation, which are essential for maintaining genome stability.\\n\\n]0.92235
28gpt-3.5-turbonarrative_synopsisHALLMARK_E2F_TARGETS-0[Summary: Genes involved in DNA replication, repair, and cell cycle regulation.\\nMechanism: These genes are involved in various stages of DNA replication, repair, and cell cycle regulation, suggesting that they work together to maintain genomic stability and ensure proper cell division.\\n][Summary: DNA replication and repair\\nMechanism: The genes are involved in DNA replication and repair processes.\\n]0.94175
29gpt-3.5-turbonarrative_synopsisHALLMARK_E2F_TARGETS-1[Summary: DNA replication and repair\\n\\n][Summary: DNA replication, repair and cell-cycle regulation\\nMechanism: These genes are involved in various aspects of DNA replication, repair and cell-cycle regulation, with some genes directly involved in DNA synthesis and others involved in checkpoint control and regulation of cell division.\\n]0.89257
30gpt-3.5-turbonarrative_synopsisHALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0[Summary: Extracellular matrix organization and regulation.\\nMechanism: Regulation of extracellular matrix protein expression and function.\\n\\nHypothesis: The enrichment of terms related to extracellular matrix organization and regulation suggests that these genes play a role in maintaining the integrity and function of extracellular matrix components, such as collagen, elastin, and laminin. These proteins provide structure and elasticity to tissues, and the dysregulation of extracellular matrix organization has been linked to a number of pathological conditions, including cancer, cardiovascular disease, and fibrosis. The identified genes likely contribute to the regulation of extracellular matrix protein expression, assembly, and localization, and may represent potential targets for therapeutic intervention in these diseases.][Summary: Extracellular matrix organization and cell adhesion are the enriched functions of the given gene list.\\nMechanism: Extracellular matrix (ECM) organization, cell adhesion, and related processes are crucial for the development and maintenance of tissue integrity and functionality. These are mediated by interactions between different proteins and cell surface receptors within ECM microenvironments.\\n\\n]0.91427
31gpt-3.5-turbonarrative_synopsisHALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1[Summary: Extracellular matrix proteins and cytokines are statistically over-represented in these gene functions, as well as proteins involved in collagen binding and actin filament binding.\\n\\nMechanism: These genes may play a role in extracellular matrix organization and remodeling, as well as cell adhesion and migration.\\n\\n][Summary: Extracellular matrix organization and muscle contraction are enriched functions among these genes.\\nMechanism: These genes are involved in the regulation and maintenance of the extracellular matrix, which is essential for proper tissue and organ function. They also play a role in muscle contraction and cell adhesion.\\n]0.923
32gpt-3.5-turbonarrative_synopsisHALLMARK_ESTROGEN_RESPONSE_EARLY-0[Summary: Membrane-associated proteins, enzymes and transcription factors are enriched in the gene list.\\n\\nMechanism: The enriched terms suggest these genes play a role in membrane-associated processes, enzymatic activity, and transcriptional regulation, potentially related to cellular signaling and development.\\n\\n][Summary: Transport and binding proteins; enzymes; membrane-associated proteins; transcriptional regulators; receptors; cytoskeletal proteins.\\nMechanism: These genes are involved in intracellular transport and binding, metabolism, gene regulation, cellular signaling, and structural support of cells and tissues.\\n\\n]0.900
33gpt-3.5-turbonarrative_synopsisHALLMARK_ESTROGEN_RESPONSE_EARLY-1[Summary: Membrane transport and cell signaling.\\nMechanism: These genes are involved in membrane transport and cell signaling pathways. They enable processes such as L-leucine transmembrane transporter activity, sodium/hydrogen exchanger regulatory cofactor, and cytokine and growth factor signaling.\\n\\n][Summary: Transport and metabolism of fatty acids, regulation of gene expression \\nMechanism: Fatty acid transport and lipid metabolism \\n]0.86166
34gpt-3.5-turbonarrative_synopsisHALLMARK_ESTROGEN_RESPONSE_LATE-0[Summary: Membrane-associated proteins, enzymes involved in metabolic processes, and transcriptional regulators are enriched in these gene functions.\\nMechanism: The enriched gene functions suggest a role in cellular metabolism and regulation of gene expression.\\n][Summary: This list of genes is enriched for terms related to cell signaling, protein binding, and post-translational modifications.\\n\\n\\nHypothesis: These genes are involved in a network of signaling pathways, including protein-protein interactions and post-translational modifications, that regulate cell proliferation, differentiation, and apoptosis. These pathways are likely to involve a wide range of signaling molecules, including kinases, transcription factors, and cytoplasmic regulators. The enrichment of terms related to protein binding and enzyme activity suggests that many of these pathways involve the coordinated action of multiple proteins and their interactions with other regulatory molecules. Further studies will be needed to elucidate the specific pathways that link these genes and their functions.]0.90558
35gpt-3.5-turbonarrative_synopsisHALLMARK_ESTROGEN_RESPONSE_LATE-1[Summary: Many of these genes are involved in cellular processes such as protein binding, catalytic activity, and regulation of transcription.\\nMechanism: The enriched terms suggest a role in cellular signaling pathways such as cytokine signaling and regulation of cell growth and differentiation.\\n\\n][Summary: This list of human genes has commonalities in their involvement in protein and enzyme regulation, as well as cellular transport mechanisms.\\n\\nMechanism: Protein regulation; enzyme regulation; cellular transport mechanisms\\n\\n]0.9066
36gpt-3.5-turbonarrative_synopsisHALLMARK_FATTY_ACID_METABOLISM-0[Summary: Genes involved in metabolism and enzyme function are statistically over-represented.\\nMechanism: Enzymes involved in metabolism are crucial for cellular function and maintaining homeostasis. \\n\\n][Summary: Genes involved in energy metabolism and oxidative stress response.\\n\\nMechanism: These genes are involved in catabolic pathways for the breakdown of fatty acids, amino acids, and carbohydrates to produce energy. They also play a role in the response to oxidative stress, which can result from an imbalance between the production of reactive oxygen species (ROS) and the body's ability to detoxify them.\\n\\n]0.88210
37gpt-3.5-turbonarrative_synopsisHALLMARK_FATTY_ACID_METABOLISM-1[Summary: These genes are involved in various metabolic processes, including fatty acid metabolism, oxidation-reduction reactions, and energy production. \\n\\nMechanism: It is hypothesized that these genes are involved in maintaining cellular homeostasis by regulating metabolic processes and energy production.\\n\\n][Summary: Genes involved in various metabolic processes, including fatty acid metabolism and energy production, are enriched.\\n\\nMechanism: The enrichment of metabolic processes reflects the crucial importance of these genes in maintaining energy balance and metabolic homeostasis in the body.\\n\\n]0.9417
38gpt-3.5-turbonarrative_synopsisHALLMARK_G2M_CHECKPOINT-0[Summary: Cell division and DNA repair processes are enriched among the listed genes.\\n\\nMechanism: The genes listed are involved in various aspects of cell division including DNA replication, chromosome segregation, and cytokinesis. \\n\\n][Summary: Cell cycle regulation and DNA replication are enriched functions among the listed human genes.\\nMechanism: These genes are involved in processes involved in cell division, DNA replication, and DNA repair.\\n]0.9420
39gpt-3.5-turbonarrative_synopsisHALLMARK_G2M_CHECKPOINT-1[Summary: Chromosome segregation and DNA replication machinery\\nMechanism: Regulation of cell cycle and DNA replication\\n\\nHypothesis: The enriched terms suggest that these genes play a role in the regulation of the cell cycle, specifically in DNA replication initiation, chromosome segregation, mitotic spindle organization, and cell cycle checkpoint control. The mechanism underlying the common function of these genes could be the assembly of protein-DNA complexes required for the progression of the cell cycle and proper segregation of chromosomes during cell division. Dysfunction in these processes can lead to genomic instability and contribute to the development of cancer.][Summary: Gene functions are involved in DNA replication, cell cycle regulation, and DNA repair.\\n\\nMechanism: These genes are involved in various stages of cell division, including DNA replication, chromosome segregation, and cytokinesis.\\n\\n]0.91441
40gpt-3.5-turbonarrative_synopsisHALLMARK_GLYCOLYSIS-0[Summary: Enzyme activity involved in carbohydrate metabolism and glycosylation processes.\\n\\nMechanism: Enzymatic reactions involved in the breakdown and synthesis of carbohydrates, as well as the addition of sugar groups to proteins and lipids.\\n\\n\\nHypothesis: The enriched terms suggest that these genes are involved in a wide range of metabolic processes related to carbohydrate and sugar metabolism. This may involve the breakdown of sugars for energy production, as well as the synthesis and modification of sugar molecules for use in various cellular processes. These processes likely involve multiple pathways, including the pentose phosphate pathway, glycolysis, and various UDP-sugar biosynthetic pathways.][Summary: Glycolysis pathway and carbohydrate metabolism are enriched terms among the listed genes.\\n\\nMechanism: The listed genes are involved in glucose metabolism, glycolysis, and carbohydrate metabolism. They encode enzymes such as phosphoglycerate mutase (PGAM), phosphomannose isomerase (MPI), glucose-6-phosphate dehydrogenase (G6PD), hexokinases (HK2), aldolases (ALDOA, ALDOB), and glycogen debrancher enzyme (AGL).\\n\\n\\nHypothesis: The enriched terms suggest a possible link between the listed genes and the glycolysis pathway, which is a central metabolic pathway in energy production. The genes encode enzymes that are involved in the conversion of glucose into pyruvate, which is further metabolized in the Krebs cycle. Dysfunction in these genes may lead to alterations in glucose metabolism and contribute to metabolic disorders such as diabetes and glycogen storage diseases.]0.93174
41gpt-3.5-turbonarrative_synopsisHALLMARK_GLYCOLYSIS-1[Summary: Glycolysis, carbohydrate metabolism, and signaling pathways are significantly enriched functions in this set of genes.\\nMechanism: These genes are involved in glucose metabolism and signaling pathways, which regulate cellular responses to stress and energy levels.\\n\\nHypothesis: The majority of these genes are associated with glycolysis, carbohydrate metabolism, and signaling pathways, which are central metabolic processes that regulate cellular energy levels and responses to stress. Many of these genes are likely to be involved in glucose transport, which plays an essential role in maintaining cellular energy balance. Additionally, some of these genes are involved in cellular responses to stress, suggesting that altered glucose metabolism could contribute to stress-related disorders.][Summary: Genes involved in various metabolic processes and enzymatic activity are enriched in this list.\\n\\nMechanism: The enriched terms suggest a commonality in metabolic pathways and enzymatic activity.\\n\\n]0.89597
42gpt-3.5-turbonarrative_synopsisHALLMARK_HEDGEHOG_SIGNALING-0[Summary: Neural development and signaling pathway regulation\\nMechanism: These genes are involved in various aspects of neural development and signaling pathways, including axon guidance, cell adhesion, cell communication, and transcriptional regulation.\\n][Summary: Cell signaling and neuronal development\\nMechanism: Mediation of cell-cell communication and regulation of intracellular signaling pathways\\n\\nHypothesis: The enriched terms suggest that these genes play important roles in the regulation of cell-cell communication and intracellular signaling pathways, particularly those involved in neuronal development and angiogenesis. These processes involve the regulation of cell adhesion, migration, growth cone collapse, and the activation of cytokine receptors. Transcriptional regulation is also likely to play a role in the mediation of these processes.]0.93351
43gpt-3.5-turbonarrative_synopsisHALLMARK_HEDGEHOG_SIGNALING-1[Summary: Neuronal development and signaling\\n\\nHypothesis: These genes may be part of a broader signaling pathway that regulates neuronal development and communication, possibly involving other signaling molecules and pathways such as Wnt and Notch signaling. Further investigation into the interactions and regulation of these genes may provide insights into neural disorders and conditions.][Summary: Cell signaling and adhesion\\nMechanism: Regulation of cell adhesion and signaling pathways\\n]0.83292
44gpt-3.5-turbonarrative_synopsisHALLMARK_HEME_METABOLISM-0[Summary: Several of the enriched terms relate to the regulation of gene expression and protein turnover, as well as ion transport and membrane organization.\\n\\nMechanism: The shared biological mechanism may involve the regulation and modulation of cellular processes through the transport of ions and proteins across membranes, as well as the turnover of proteins and regulation of gene expression.\\n\\n][Summary: Transport and binding processes\\nMechanism: ATP binding and membrane transport\\n]0.85311
45gpt-3.5-turbonarrative_synopsisHALLMARK_HEME_METABOLISM-1[Summary: Transport; Metabolism; Binding Activity\\nMechanism: Not enough information to form a hypothesis \\n][Summary: Enriched terms are related to transport, binding activity, and regulation of gene expression.\\nMechanism: These genes likely function in cellular transport and molecular binding, with a potential role in gene expression regulation.\\n\\n]0.84136
46gpt-3.5-turbonarrative_synopsisHALLMARK_HYPOXIA-0[Summary: Glycolysis-related genes are enriched \\n\\nMechanism: Glycolysis regulation\\n\\n][Summary: Glycolysis, glucose metabolism, protein binding, transcription regulation\\n\\nMechanism: It appears that many of these genes are involved in processes related to glycolysis and glucose metabolism. Additionally, a number of these genes have protein binding functions, which suggests that they may be involved in complex regulatory pathways controlling glucose metabolism and other cellular processes. Finally, several of these genes are involved in transcription regulation, suggesting that they may play a role in modulating the expression of other genes involved in glucose metabolism.\\n\\n\\n]0.91512
47gpt-3.5-turbonarrative_synopsisHALLMARK_HYPOXIA-1[Summary: Genes are involved in glucose metabolism, cell cycle regulation, and transcriptional activities.\\n\\nMechanism: The common mechanism seems to be the regulation of glucose metabolism, possibly through the insulin signaling pathway and its downstream effectors. There may also be an involvement in cell cycle regulation and transcriptional activities.\\n\\n][Summary: Genes involved in metabolism, cell cycle regulation, and signal transduction are enriched.\\nMechanism: These genes likely contribute to the regulation of cellular processes that involve energy metabolism and promoting cell growth and differentiation.\\n]0.9298
48gpt-3.5-turbonarrative_synopsisHALLMARK_IL2_STAT5_SIGNALING-0[Summary: Immune response regulation\\nMechanism: Modulation of cytokine signaling pathways\\n][Summary: The enriched terms relate to the regulation and signaling of immune system processes and inflammation.\\nMechanism: The genes are involved in the pathways related to immune system response and inflammation, specifically, cytokine signaling, T-cell and B-cell activation, and leukocyte-endothelial interactions.\\n]0.87229
49gpt-3.5-turbonarrative_synopsisHALLMARK_IL2_STAT5_SIGNALING-1[Summary: Immune system response and regulation\\n\\n][Summary: Immune system function, cytokine receptors, and cell surface adhesion molecules are enriched among these genes.\\n\\nMechanism: These genes are involved in the regulation of immune system function, including the response to pathogens and inflammation. Many of the enriched terms involve cytokine receptors and cell surface adhesion molecules, indicating that these genes play a role in cell signaling and communication.\\n\\n]0.84378
50gpt-3.5-turbonarrative_synopsisHALLMARK_IL6_JAK_STAT3_SIGNALING-0[Summary: Cytokine receptors and signaling pathway genes\\n\\n][Summary: The enriched terms relate to cytokine signaling, immune response, and cell adhesion and migration.\\n\\nMechanism: The genes are involved in cytokine signaling pathways and immune response, regulating the production and differentiation of various cells, particularly macrophages and lymphocytes.\\n\\n]0.89245
51gpt-3.5-turbonarrative_synopsisHALLMARK_IL6_JAK_STAT3_SIGNALING-1[Summary: Regulation of immune response and cytokine signaling\\n\\nHypothesis: These genes may contribute to the regulation and promotion of immune response and cytokine signaling, potentially through the binding and activation of cytokine receptors and downstream signaling pathways.][Summary: Immune response-related genes\\nMechanism: Immune response and cytokine signaling pathway\\n]0.92184
52gpt-3.5-turbonarrative_synopsisHALLMARK_INFLAMMATORY_RESPONSE-0[Summary: Immune and inflammatory response genes\\nMechanism: Immune activation and inflammation\\n][Summary: Immune system function\\n\\nHypothesis: These genes are involved in regulating immune system function, specifically in the release and detection of cytokines and chemokines, as well as the migration of leukocytes in response to inflammation. They may be part of a larger pathway involved in coordinating the immune response to invading pathogens.]0.89258
53gpt-3.5-turbonarrative_synopsisHALLMARK_INFLAMMATORY_RESPONSE-1[Summary: The enriched terms suggest that these genes are involved in immune responses and inflammation, mediated by cytokines, chemokines, and receptors.\\n\\nMechanism: The underlying biological mechanism is likely related to the response of immune cells to infection or injury, leading to the production of cytokines and chemokines that recruit more immune cells to the site.\\n\\n\\nHypothesis: These genes are likely involved in regulating immune responses and inflammation, particularly in response to infection or cellular damage. The cytokines and chemokines produced by these genes may recruit immune cells to the site of infection or injury, amplifying the immune response. The receptors encoded by these genes may play a role in regulating the activation and migration of immune cells. Dysfunction or dysregulation of these genes may contribute to chronic inflammatory diseases][Summary: Receptor and chemokine-related functions are statistically enriched in this gene list.\\nMechanism: These genes may be involved in immune system regulation and cellular signaling pathways, such as G protein-coupled receptor signaling.\\n]0.92636
54gpt-3.5-turbonarrative_synopsisHALLMARK_INTERFERON_ALPHA_RESPONSE-0[Summary: The enriched terms suggest that these genes are involved in immune response and antiviral defense. \\n\\nMechanism: These genes likely play a role in the innate immune response to viral infection and may also regulate cell proliferation and differentiation.\\n\\n][Summary: Immune response and antiviral function\\n]0.88216
55gpt-3.5-turbonarrative_synopsisHALLMARK_INTERFERON_ALPHA_RESPONSE-1[Summary: The enriched terms suggest that these genes are involved in the immune system response, particularly in the regulation of interferon and cytokine signaling pathways.\\n\\nMechanism: The mechanism underlying the common functions of these genes involves the regulation of the innate and acquired immune responses through the interferon and cytokine signaling pathways, particularly in response to viral infection.\\n\\n][Summary: Innate immune response and antiviral activity\\n\\nHypothesis: These genes work together to inhibit viral replication and spread by triggering the production and release of interferons, activating innate immune cells, and promoting the degradation of viral components through the proteasome. Through the regulation of cytokine signaling and antigen processing, these genes may also contribute to the adaptive immune response and the development of immunity to viral infection.]0.9164
56gpt-3.5-turbonarrative_synopsisHALLMARK_INTERFERON_GAMMA_RESPONSE-0[Summary: Immune response regulation\\nMechanism: Up-regulation of interferon signaling pathways\\n][Summary: Immune response and cytokine signaling pathways are enriched in the list of genes.\\n\\nMechanism: The genes in the list are involved in immune response and cytokine signaling pathways. They play a role in cytokine-mediated signaling pathways, chemokine signaling pathways, and antigen processing and presentation.\\n\\n\\nHypothesis: The genes in the list are primarily involved in regulating the immune response and cytokine signaling pathways. This suggests that they play a key role in the body's ability to recognize and respond to pathogens and other foreign invaders. Dysfunction of these genes may therefore lead to an increased susceptibility to infections and other immune-related disorders.]0.86607
57gpt-3.5-turbonarrative_synopsisHALLMARK_INTERFERON_GAMMA_RESPONSE-1[Summary: Genes involved in immune response and protein degradation pathways are enriched.\\n\\nMechanism: These genes are involved in regulating the immune response through cytokine signaling and intracellular viral RNA sensing. They also play a role in protein degradation pathways through the proteasome and ubiquitin system.\\n\\n][Summary: The enriched terms among these genes relate to immune response, specifically innate immune response and antiviral response. \\n\\n\\nHypothesis: These genes are involved in innate immune response and antiviral response, indicating a potential regulatory pathway for immune function in response to viral infection. The enrichment of cytokine activity and regulation of cytokine production suggests that this pathway involves the production of various cytokines involved in immune response, including interferons. The enrichment of positive regulation of type I interferon production and type I interferon signaling pathway further supports this hypothesis.]0.92334
58gpt-3.5-turbonarrative_synopsisHALLMARK_KRAS_SIGNALING_DN-0[Summary: Calcium ion binding\\nMechanism: Calcium signaling pathway\\n\\nHypothesis: Many of the genes listed encode proteins that bind to calcium ions and act in signaling pathways related to calcium. These proteins are involved in various processes such as transmembrane transport, cell adhesion, protein kinase activity, and G protein-coupled receptor signaling. The enrichment of these terms suggests that calcium signaling is a crucial mechanism that regulates diverse cellular processes such as energy metabolism, cell growth and proliferation, and gene expression.][Summary: Calcium ion binding and transport\\nMechanism: Calcium signaling and regulation\\n\\nHypothesis: These genes are all involved in regulating calcium ion binding and transport, suggesting a potential role in calcium-mediated signaling. This may be related to a variety of biological processes, including muscle contraction, nervous system function, and cellular signaling pathways. The enriched terms suggest that calcium ion binding and transport plays a crucial role in many of these processes, potentially through the regulation of ion channels, transporters, and other calcium-dependent proteins.]0.9636
59gpt-3.5-turbonarrative_synopsisHALLMARK_KRAS_SIGNALING_DN-1[Summary: Many of the genes in this list are involved in various aspects of cell signaling and regulation, including cytokine signaling (IFNG, IL12B), G-protein coupled receptor signaling (ADRA2C, SST4, HTR1B, GPR19), and calcium signaling (CACNG1, STAG3, EFHD1). Additionally, there are several genes related to protein metabolism and processing (CLPS, CPB1, NUDT11, CELSR2, SLC38A3).\\n\\n\\nHypothesis: The common theme among these genes is their involvement in intracellular signaling pathways involved in maintaining cellular homeostasis. These pathways may interact with each other, creating a complex network of interactions that allow cells to adapt and respond to various stimuli. Additionally, the regulation of protein metabolism and processing is likely important for maintaining proper protein function and stability within the cell. Overall, these processes likely contribute to proper cell function and survival.][Summary: Calcium ion binding activity, cellular response to protein stimulus, negative regulation of apoptotic process.\\nMechanism: Calcium signaling pathway and regulation of apoptosis.\\n]0.83735
60gpt-3.5-turbonarrative_synopsisHALLMARK_KRAS_SIGNALING_UP-0[Summary: Several enriched terms relate to signal transduction and regulation of various cellular processes.\\n\\nMechanism: The genes in this list are involved in various aspects of cellular signaling, including cytokine signaling, receptor activity, and kinase activity. They also play roles in regulating processes such as transcription, protein degradation, and cell migration.\\n\\n][Summary: Membrane-associated proteins and enzymes involved in various cellular processes.\\nMechanism: Membrane-associated and signaling pathways.\\n]0.87233
61gpt-3.5-turbonarrative_synopsisHALLMARK_KRAS_SIGNALING_UP-1[Summary: Signaling and regulation of various biological processes, including coagulation, cytokine activity, extracellular matrix, and ion channels.\\n\\n][Summary: Cell signaling and regulation through cytokines, growth factors, and enzymes involved in coagulation and complement activation.\\nMechanism: Activation and regulation of cellular pathways through ligand-receptor interaction and enzymatic activity.\\n\\nHypothesis: These genes are involved in mediating cellular responses to external stimuli, including tissue damage and immune responses. Cytokine and growth factor signaling pathways activate cellular responses such as proliferation, differentiation, and migration. Enzymes involved in coagulation and complement activation play critical roles in host defense and tissue repair. The common mechanism underlying these functions is the activation and regulation of cellular pathways through ligand-receptor interaction and enzymatic activity.]0.90646
62gpt-3.5-turbonarrative_synopsisHALLMARK_MITOTIC_SPINDLE-0[Summary: These genes are involved in various aspects of cell division, organization of the cytoskeleton, and regulation of protein activity.\\n\\nMechanism: The genes identified likely function in the organization of the cytoskeleton, which is required for proper cell division and cellular organization. They may also contribute to regulation of protein activity during these processes.\\n\\n][Summary: These genes are involved in various cellular processes including cytoskeletal organization, cell cycle progression, and centrosome function.\\nMechanism: These genes likely interact with each other to regulate cellular processes and maintain proper cellular function.\\n]0.95110
63gpt-3.5-turbonarrative_synopsisHALLMARK_MITOTIC_SPINDLE-1[Summary: Many of these genes are involved in mitosis, cell division, and microtubule organization.\\nMechanism: These genes likely work together to regulate the organization and division of cells.\\n][Summary: Microtubule organization and regulation\\nMechanism: Regulation of microtubule dynamics and spindle assembly\\n]0.8879
64gpt-3.5-turbonarrative_synopsisHALLMARK_MTORC1_SIGNALING-0[Summary: Enzymatic processes related to metabolism and cellular transport are over-represented in this gene set.\\n\\nMechanism: The genes in this set are involved in various metabolic pathways related to cellular transport and enzymatic processes, including lipid metabolism and glucose homeostasis.\\n\\n][Summary: Protein synthesis and folding regulation\\nMechanism: The identified genes are involved in processes related to protein synthesis, folding, and degradation. Several of the genes are involved in regulating glucose metabolism, which provides energy for protein synthesis. Others are involved in regulating the structure of microtubules, which help transport proteins within cells.\\n\\n]0.8789
65gpt-3.5-turbonarrative_synopsisHALLMARK_MTORC1_SIGNALING-1[Summary: Regulation of protein folding and degradation\\nMechanism: Molecular chaperones and proteasome complexes\\n][Summary: Many of the genes are involved in metabolic processes, specifically related to nucleotide, lipid, and carbohydrate metabolism. Other common functions include protein folding, protein degradation, and regulation of gene expression.\\n\\nMechanism: The enriched terms suggest a role for these genes in cellular homeostasis and regulation of metabolic processes, likely through coordinated regulation of metabolic pathways and protein turnover.\\n\\n]0.84336
66gpt-3.5-turbonarrative_synopsisHALLMARK_MYC_TARGETS_V1-0[Summary: The enriched terms suggest that the genes are involved in protein synthesis, DNA replication, RNA splicing, and nucleotide metabolism.\\n\\nMechanism: These genes are involved in the molecular processes that underlie the maintenance and expression of genetic information. They facilitate the translation of genetic code into functional proteins, the replication and repair of DNA, the processing of RNA molecules, and the regulation of nucleotide metabolism.\\n\\n][Summary: Ribosome biogenesis and protein translation\\n\\nMechanism: These genes are involved in various aspects of ribosome biogenesis and protein translation, including the assembly and function of the ribosome, mRNA splicing, and regulation of translation initiation.\\n\\n]0.90197
67gpt-3.5-turbonarrative_synopsisHALLMARK_MYC_TARGETS_V1-1[Summary: Genes are involved in protein synthesis, including ribosomal proteins, translation factors, and chaperones. \\nMechanism: These genes function in various stages of protein synthesis, including ribosome assembly, translation initiation, elongation, and termination. \\n][Summary: The enriched terms suggest that the genes in this list are involved in various aspects of protein synthesis, including ribosome biogenesis, translation initiation and elongation, and post-splicing mRNA processing.\\n\\nMechanism: Protein synthesis\\n\\n]0.9219
68gpt-3.5-turbonarrative_synopsisHALLMARK_MYC_TARGETS_V2-0[Summary: RNA processing and ribosomal biogenesis are enriched functions among the listed genes.\\n\\nMechanism: The genes in this list are involved in various aspects of RNA processing and ribosomal biogenesis. They encode proteins that are involved in functions such as nucleolar organization, rRNA maturation, and ribosomal protein synthesis.\\n\\n][Summary: Ribosome biogenesis and nucleolar function are enriched functions among these genes.\\nMechanism: The genes are involved in various steps in ribosome biogenesis and nucleolar function, including RNA processing, assembly of ribosomal subunits, and protein binding to facilitate these processes.\\n]0.9641
69gpt-3.5-turbonarrative_synopsisHALLMARK_MYC_TARGETS_V2-1[Summary: Nucleolar ribosomal RNA processing and biogenesis is enriched in these genes, as well as RNA binding and RNA metabolic processes.\\n\\nMechanism: The genes in this list all play a role in the processing and biogenesis of ribosomal RNA, particularly in the nucleolus. They are involved in RNA binding and RNA metabolic processes required for ribosome assembly and regulation.\\n\\n][Summary: Genes involved in nucleolar and ribosomal function, RNA processing and binding, and cell cycle regulation are statistically enriched.\\n\\nMechanism: These genes likely play a role in ribosome biogenesis and function, as well as in the regulation of RNA processing and binding. They may also be involved in cell cycle regulation.\\n\\n]0.9445
70gpt-3.5-turbonarrative_synopsisHALLMARK_MYOGENESIS-0[Summary: Muscle contraction and development\\nMechanism: Actin-myosin interaction regulated by calcium ion concentration\\n][Summary: These genes are involved in muscle development and function, including muscle contraction, regulation of muscle metabolism, and cytoskeletal organization.\\nMechanism: The enriched terms suggest a common mechanism of regulation and organization of muscle tissue at both the structural and metabolic levels.\\n]0.86195
71gpt-3.5-turbonarrative_synopsisHALLMARK_MYOGENESIS-1[Summary: Muscle contraction and regulation of calcium ion transport\\nMechanism: Activation of troponin-tropomyosin complex\\n][Summary: Muscle development and function\\nMechanism: Regulation of muscle contraction through troponin-tropomyosin complex and actin-myosin interaction\\n\\nHypothesis: The enriched terms suggest that these genes are involved in muscle development and function, specifically in the regulation of muscle contraction through the troponin-tropomyosin complex and actin-myosin interaction. Troponin complex, actin-binding proteins, and myosin heavy chain are all involved in the regulation of muscle contraction and the formation of sarcomeres, the basic functional units of muscle. This suggests that these genes play a role in muscle development and function, particularly in the regulation of muscle contraction through the troponin-tropomyosin complex and actin-myosin interaction, and calcium ion binding.]0.90680
72gpt-3.5-turbonarrative_synopsisHALLMARK_NOTCH_SIGNALING-0[Summary: These genes are involved in cell signaling pathways, including the Notch and Wnt signaling pathways, as well as in ubiquitin-mediated protein degradation. \\nMechanism: These genes collectively form a network of signaling and regulatory pathways involved in cellular differentiation and proliferation.\\n\\nHypothesis: These genes are involved in regulating the balance between cell proliferation and differentiation by modulating the activity of key signaling proteins, such as Notch and Wnt receptors, and regulating the turnover of specific proteins via ubiquitination and proteasomal degradation. Dysregulation of these pathways may contribute to the development of various diseases, including cancer and neurological disorders.][Summary: Notch signaling and cell fate determination\\nMechanism: The genes are all involved in the Notch signaling pathway, which plays a key role in cell fate determination during embryonic development.\\n]0.90533
73gpt-3.5-turbonarrative_synopsisHALLMARK_NOTCH_SIGNALING-1[Summary: Genes involved in Notch signaling pathway and protein ubiquitination.\\nMechanism: Regulation of cell fate decisions and interactions between physically adjacent cells through binding of Notch family receptors to their cognate ligands.\\n][Summary: Regulation of signaling pathways involved in development and cellular processes.\\nMechanism: Notch signaling pathway and ubiquitination-mediated proteolysis.\\n\\nHypothesis: The enriched terms suggest that the common function of the genes in the list is the regulation of signaling pathways, specifically the Notch signaling pathway and ubiquitination-mediated proteolysis. These genes are involved in the transcriptional regulation of cellular processes, including cell fate determination. The Notch signaling pathway plays a critical role in development and differentiation, while ubiquitination-mediated proteolysis is essential for proper protein degradation and turnover. The various genes in this list work together to coordinate these important cellular processes.]0.93534
74gpt-3.5-turbonarrative_synopsisHALLMARK_OXIDATIVE_PHOSPHORYLATION-0[Summary: Mitochondrial genes involved in oxidative phosphorylation and energy metabolism.\\nMechanism: Mitochondrial function and energy metabolism.\\n\\nHypothesis: These genes are all involved in the process of energy production through oxidative phosphorylation within the mitochondria. The enriched terms indicate the importance of ATP synthesis, electron transport chain, and the mitochondrial respiratory chain. These genes may play a key role in cellular energetics, oxidative stress, and aging.][Summary: Many of the genes listed are involved in the function of mitochondrial respiratory chain complexes, which are responsible for generating energy in cells. \\n\\nMechanism: Mitochondrial respiratory chain complexes. \\n\\n]0.92276
75gpt-3.5-turbonarrative_synopsisHALLMARK_OXIDATIVE_PHOSPHORYLATION-1[Summary: The enriched terms are related to mitochondrial metabolism, particularly oxidative phosphorylation and the electron transport chain.\\n\\nMechanism: These genes are involved in the function and regulation of complexes I-V in the mitochondrial respiratory chain and oxidative phosphorylation.\\n\\n][Summary: Mitochondrial respiratory chain function and ATP synthesis are enriched in these genes.\\nMechanism: Electron transport chain and oxidative phosphorylation.\\n]0.94134
76gpt-3.5-turbonarrative_synopsisHALLMARK_P53_PATHWAY-0[Summary: Regulation of gene expression, DNA repair, and cell growth/death pathways.\\nMechanism: These genes are involved in the regulation of cellular processes such as gene expression, DNA repair, and cell growth and death pathways. They are enriched in terms related to DNA repair, regulation of gene expression, and growth factor activity.\\n\\nHypothesis: These genes may be involved in maintaining cellular homeostasis and responding to external signals such as growth factors. The regulation of gene expression and DNA repair pathways are critical for proper cell function and survival. Dysfunction in these processes can result in various diseases, including cancer. The enrichment of growth factor activity terms suggests that these genes may also play a role in regulating cell growth and proliferation.][Summary: Cell growth regulation and DNA repair\\nMechanism: The genes listed are involved in the regulation of cell growth and cell cycle progression, as well as DNA repair and damage response.\\n]0.93616
77gpt-3.5-turbonarrative_synopsisHALLMARK_P53_PATHWAY-1[Summary: Genes are involved in DNA repair, cell growth regulation, and signal transduction pathways.\\nMechanism: These genes are involved in maintaining the integrity of DNA, controlling cell proliferation, and regulating cellular responses through signaling pathways.\\n][Summary: Genes involved in various cellular processes, including growth factor activity, transcriptional regulation, apoptosis, and DNA repair.\\nMechanism: These genes are involved in regulating cell growth, survival, and response to stress.\\n]0.9427
78gpt-3.5-turbonarrative_synopsisHALLMARK_PANCREAS_BETA_CELLS-0[Summary: Genes involved in glucose and insulin metabolism, as well as pancreatic development and neuroendocrine regulation, are statistically over-represented in this list.\\n\\nMechanism: These enriched genes act in a network that regulates the homeostasis of glucose and insulin in the body, through modulation of pancreatic beta cell development, glucose sensing and stimulation, and insulin production.\\n\\n][Summary: Glucose metabolism and insulin regulation\\nMechanism: Glycolysis; Gluconeogenesis; Insulin secretion; Pancreas development and differentiation\\n\\n]0.89252
79gpt-3.5-turbonarrative_synopsisHALLMARK_PANCREAS_BETA_CELLS-1[Summary: Genes in this list are involved in glucose and insulin metabolism, as well as in pancreatic islet development and neuroendocrine differentiation. They also play a role in motor neuron generation, synaptic plasticity, and neurotransmitter release. Enriched terms include \"glucose metabolism,\" \"pancreatic islet development,\" \"neuroendocrine differentiation,\" \"neurotransmitter release,\" and \"synaptic plasticity.\"\\n\\nMechanism: The common mechanism underlying these functions is likely the regulation of gene expression through transcription factors and signaling pathways involved in glucose and insulin metabolism, as well as in neuroendocrine differentiation and synaptic plasticity.\\n\\n][Summary: Genes involved in glucose and insulin metabolism, as well as pancreatic islet development and neuroendocrine differentiation show enrichment in this list.\\n\\nMechanism: These genes likely play a role in the regulation of glucose homeostasis, insulin secretion, and pancreatic islet development.\\n\\n]0.96391
80gpt-3.5-turbonarrative_synopsisHALLMARK_PEROXISOME-0[Summary: The common function of these genes is involvement in metabolic processes including transport, binding, and enzymatic activities of lipids, hormones, and other molecules. \\n\\nMechanism: These genes are part of the cellular machinery involved in lipid transport and metabolism. \\n\\n][Summary: Transport of various molecules across extra- and intra-cellular membranes is enriched.\\nMechanism: ABC transporters are involved in the transport of a wide range of molecules and play a critical role in maintaining cellular homeostasis.\\n]0.8540
81gpt-3.5-turbonarrative_synopsisHALLMARK_PEROXISOME-1[Summary: Peroxisomal membrane proteins & enzymes, fatty acid beta-oxidation pathway, and antioxidant enzymes are enriched functions among the given genes.\\n\\nMechanism: Peroxisomes play a crucial role in fatty acid metabolism. Some of the enriched functions are involved in either fatty acid import, beta-oxidation, or metabolism of by-products of beta-oxidation such as acetyl-CoA. Also, some genes code for peroxisomal membrane proteins that facilitate peroxisomal proliferation or matrix protein import.\\n\\n\\nHypothesis: The enriched functions might suggest a link between fatty acid metabolism, oxidative stress, and peroxisomal proliferation. In oxidative stress conditions, the cell may require to degrade excess fatty acids via peroxisomal beta-oxidation to reduce ROS generation. This acts as a feedback inhibition mechanism to prevent ROS accumulation in the mitochondria. Peroxisomal membrane proteins regulate peroxisomal proliferation to respond to cellular stress.][Summary: Peroxisomal functions, fatty acid metabolism, and antioxidant defense mechanisms are enriched in this gene list.\\nMechanism: The genes in this list are involved in facilitating fundamental metabolic pathways, such as fatty acid metabolism and peroxisomal functions that involve beta-oxidation, as well as antioxidant defense mechanisms that include the degradation of reactive oxygen species.\\n]0.93572
82gpt-3.5-turbonarrative_synopsisHALLMARK_PI3K_AKT_MTOR_SIGNALING-0[Summary: Genes are involved in intracellular signaling, enzymatic activity, and cytoskeletal regulation.\\nMechanism: These genes play a role in various cellular pathways and contribute to cellular growth, differentiation, and regulation of cellular processes.\\n][Summary: Intracellular signaling, protein kinase activity, and regulation of cellular processes are enriched functions among these genes.\\n\\nMechanism: These genes are involved in various aspects of intracellular signaling, such as activation or inhibition of protein kinase activity and regulation of cellular processes.\\n\\n]0.9462
83gpt-3.5-turbonarrative_synopsisHALLMARK_PI3K_AKT_MTOR_SIGNALING-1[Summary: Protein phosphorylation and signal transduction pathways are enriched functions among the provided human genes.\\nMechanism: Many of the genes in this list encode for serine/threonine kinases or components of signaling pathways. These pathways are involved in transmitting information from the cell surface (either extracellular signals or internal signals) to the nucleus, resulting in changes in gene expression or other cellular processes. Protein phosphorylation is a key mechanism in these pathways, regulating protein activity and localization.\\n\\n][Summary: Protein kinases and signaling pathways.\\nMechanism: Genes encode for proteins involved in the phosphorylation of other proteins, leading to activation or inhibition of various signaling pathways.\\n]0.94355
84gpt-3.5-turbonarrative_synopsisHALLMARK_PROTEIN_SECRETION-0[Summary: The enriched terms for these genes are related to intracellular trafficking, specifically vesicle transport, Golgi apparatus, and lysosome.\\n\\nMechanism: These genes encode a variety of proteins involved in vesicle trafficking and intracellular transport pathways, specifically related to the Golgi apparatus and lysosome.\\n\\n][Summary: Intracellular vesicular transport and trafficking\\nMechanism: Adaptor protein complexes and small GTPases regulate vesicle formation, sorting, and fusion with target membranes.\\n]0.88146
85gpt-3.5-turbonarrative_synopsisHALLMARK_PROTEIN_SECRETION-1[Summary: Vesicular transport and protein sorting in the Golgi apparatus are enriched functions among the listed genes. \\n\\nMechanism: These genes encode proteins involved in membrane trafficking, protein sorting, vesicle fusion, and transport between different membrane-bound compartments. \\n\\n][Summary: Membrane trafficking and vesicular transport \\nMechanism: Genes involved in membrane trafficking and vesicular transport function together to regulate the movement of proteins and lipids between organelles in the cell. They do so by promoting the budding, fusion, and sorting of transport vesicles. \\n]0.9318
86gpt-3.5-turbonarrative_synopsisHALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0[Summary: Genes involved in antioxidant defense and oxidative stress response are enriched.\\n\\nMechanism: The enriched genes have significant functions in oxidoreductase activity, antioxidant activity, and glutathione metabolic processes. \\n\\n\\nHypothesis: The enriched genes suggest the importance of maintaining a balance between oxidative stress and antioxidant defense to combat cellular damage. The glutathione metabolic process plays a crucial role in regulating the redox status of the cell and possibly maintaining proper protein folding. These genes may be involved in cellular responses to oxidative stress and the regulation of redox signaling pathways.][Summary: Genes involved in antioxidant defense and redox regulation.\\n\\n]0.92589
87gpt-3.5-turbonarrative_synopsisHALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1[Summary: Redox homeostasis and antioxidant defense mechanisms. \\nMechanism: Multiple genes involved in redox balance and antioxidant defense mechanisms. \\n\\nHypothesis: The enriched terms suggest that the commonality among the gene functions is the regulation of redox homeostasis and maintenance of antioxidant defense mechanisms. The gene products are involved in the reduction of reactive oxygen species (ROS) and oxidative stress to maintain cellular function and survival. The proteins may act as antioxidants, reducing ROS such as hydrogen peroxide and organic hydroperoxides, or they may function in redox regulation, playing key roles in redox signaling pathways and the maintenance of redox balance. Overall, these genes are important in protecting cellular integrity and maintaining homeostasis.][Summary: Anti-oxidative stress response pathway\\nMechanism: Enzymatic reduction of oxidative stress\\n\\nHypothesis: The commonality in function among these genes is their involvement in the anti-oxidative stress response pathway. These genes encode enzymes that are responsible for reducing oxidative stress, regulating reactive oxygen species and superoxide anion radicals, and participating in antioxidative defense mechanisms. The pathway involves the regulation of glutathione metabolism, peroxiredoxin-mediated detoxification, and other mechanisms that help to mitigate the effects of oxidative stress.]0.93199
88gpt-3.5-turbonarrative_synopsisHALLMARK_SPERMATOGENESIS-0[Summary: Cell cycle regulation and DNA binding\\nMechanism: These genes are involved in regulating cell cycle progression and DNA interactions, with many of them being DNA or RNA binding proteins.\\n\\n][Summary: Reproductive development, specifically sperm function and testis differentiation, is enriched in these genes.\\n\\n\\nHypothesis: These genes all have roles in either male reproductive development or sperm function, which suggests they may share a common pathway or mechanism in regulating these processes. One hypothesis is that these genes may be involved in the regulation of gene expression during spermatogenesis, as many of them are specifically expressed in the testes and have been linked to sperm motility and acrosome reaction.]0.83345
89gpt-3.5-turbonarrative_synopsisHALLMARK_SPERMATOGENESIS-1[Summary: Cellular processes involved in protein binding, enzymatic activity, and ion transport are enriched in this list of human genes.\\n\\nMechanism: The proteins encoded by these genes may form complexes involved in signal transduction pathways, protein degradation, and ion channel regulation.\\n\\n][Summary: These genes are involved in various cellular and molecular functions, including but not limited to ion transport, protein phosphorylation, ubiquitination, spermatogenesis, and receptor signaling.\\nMechanism: The genes are involved in diverse biological pathways or mechanisms, reflecting the complexity of cellular and molecular biology.\\n]0.9250
90gpt-3.5-turbonarrative_synopsisHALLMARK_TGF_BETA_SIGNALING-0[Summary: Signaling and regulation of growth and differentiation processes.\\nMechanism: TGF-beta superfamily signaling pathways.\\n][Summary: Genes involved in regulating transforming growth factor-beta (TGF-beta) superfamily signaling and transcriptional regulation.\\nMechanism: Regulation of TGF-beta signaling pathway and transcriptional regulation.\\n\\nHypothesis: These genes are involved in the regulation of the TGF-beta signaling pathway, which controls a variety of cellular processes including cell growth, differentiation, and apoptosis. They also play a role in transcriptional regulation, which may contribute to their regulatory functions in the TGF-beta pathway. These findings suggest a potential mechanism for how these genes may interact and contribute to the regulation of TGF-beta signaling.]0.91548
91gpt-3.5-turbonarrative_synopsisHALLMARK_TGF_BETA_SIGNALING-1[Summary: Members of this group of genes are involved in transforming growth factor-beta (TGF-beta) superfamily signaling, cell growth and differentiation, transcriptional regulation, ubiquitination, and phosphorylation. \\nMechanism: TGF-beta signaling pathway\\n][Summary: Signaling pathways involving transforming growth factor-beta (TGF-beta) and bone morphogenetic proteins (BMPs)\\nMechanism: Regulation of gene expression through transcription factor binding and signal transduction\\n]0.9337
92gpt-3.5-turbonarrative_synopsisHALLMARK_TNFA_SIGNALING_VIA_NFKB-0[Summary: Genes involved in immune response, cytokine signaling, and transcription regulation.\\n\\n][Summary: Immune system-related genes that regulate inflammation and cytokine signaling.\\n\\nMechanism: These genes are involved in regulating the immune response by controlling inflammation and cytokine signaling pathways.\\n\\n]0.93126
93gpt-3.5-turbonarrative_synopsisHALLMARK_TNFA_SIGNALING_VIA_NFKB-1[Summary: Genes are involved in immune response, cytokine signaling, and transcription regulation.\\n\\nMechanism: These genes have a role in modulating the immune response, with some genes involved in cytokine signaling and others in transcription regulation.\\n\\n][Summary: Cytokine signaling and immune response\\nMechanism: Genes are involved in cytokine production and response pathways, specifically in the interleukin and chemokine families.\\n]0.9377
94gpt-3.5-turbonarrative_synopsisHALLMARK_UNFOLDED_PROTEIN_RESPONSE-0[Summary: These genes are involved in protein folding, stress response, and RNA metabolism.\\n\\nMechanism: These genes likely function in the regulation of protein folding and quality control, as well as the response to cellular stress and the maintenance of RNA stability.\\n\\n][Summary: Genes involved in protein folding, stress response, and RNA processing are enriched.\\nMechanism: These genes likely function in maintaining proper protein folding and preventing protein misfolding, as well as responding to stress and modulating RNA processing.\\n]0.952
95gpt-3.5-turbonarrative_synopsisHALLMARK_UNFOLDED_PROTEIN_RESPONSE-1[Summary: Genes involved in protein folding and regulation of RNA processing and translation.\\nMechanism: These genes play a role in maintaining cellular homeostasis by regulating the synthesis and folding of proteins, and the processing and translation of RNA. \\n\\nHypothesis: These genes likely work together to promote proper protein conformation and prevent improper folding and aggregation. They may also play a role in regulating cellular responses to stress, such as the unfolded protein response. In addition, they may be involved in controlling translation rates and ensuring proper ribosome function.][Summary: Protein folding, transport, and translation regulation \\nMechanism: Endoplasmic reticulum-associated protein degradation (ERAD) and unfolded protein response (UPR) pathways \\n]0.87425
96gpt-3.5-turbonarrative_synopsisHALLMARK_UV_RESPONSE_DN-0[Summary: These genes are enriched for terms related to intracellular signaling and regulation, specifically in regards to calcium ion transport and cytoskeletal organization.\\n\\nMechanism: The identified genes are involved in intracellular signaling pathways that regulate cellular processes through calcium ion transport and cytoskeletal organization.\\n\\n][Summary: Extracellular matrix, cell signaling, protein kinase activity, ion transport, transcription regulation, and growth factor receptor activity are the common functions of the listed genes.\\n\\nMechanism: An underlying biological mechanism for the enriched terms is the regulation of cell growth and differentiation by extracellular matrix signaling pathways, which involve ion transport, protein kinase activity, and transcriptional regulation.\\n\\n]0.9297
97gpt-3.5-turbonarrative_synopsisHALLMARK_UV_RESPONSE_DN-1[Summary: Extracellular matrix organization, cellular signaling, and ion transport are enriched functions in this list of genes.\\n\\nMechanism: These genes likely play a role in the formation and maintenance of the extracellular matrix, cellular communication and signaling pathways, and ion transport.\\n\\n][Summary: Extracellular matrix organization, cell adhesion, signaling and protein phosphorylation are enriched functions in these genes.\\n\\nMechanism: These genes are involved in biological processes related to cell adhesion, extracellular matrix organization, signaling pathway activity and protein phosphorylation.\\n\\n]0.9415
98gpt-3.5-turbonarrative_synopsisHALLMARK_UV_RESPONSE_UP-0[Summary: Transport, catalysis, and regulation of cellular processes are the enriched functions of these genes.\\nMechanism: ABC transporters, enzymes, and transcription factors are involved in these processes.\\n\\n][Summary: Transport and metabolism of small molecules\\nMechanism: ABC transporters; Enzymatic metabolism\\n]0.87106
99gpt-3.5-turbonarrative_synopsisHALLMARK_UV_RESPONSE_UP-1[Summary: This set of human genes is involved in various biological processes, including metabolism, nucleotide and protein biosynthesis, and signaling pathways.\\n\\n][Summary: Nucleic acid binding and metabolism\\nMechanism: RNA and DNA processing\\n]0.8683
100gpt-3.5-turbonarrative_synopsisHALLMARK_WNT_BETA_CATENIN_SIGNALING-0[Summary: Genes involved in Wnt signaling pathway regulation.\\nMechanism: Negatively regulating Wnt pathway through inhibition of beta-catenin stabilization and/or transcriptional activation.\\n\\nHypothesis: The genes listed above are all involved in negative regulation of the Wnt signaling pathway, either through inhibiting beta-catenin stabilization or transcriptional activation. This results in downstream effects on processes such as transcriptional and cell cycle regulation.][Summary: Genes involved in signaling pathways related to Wnt signaling, cell cycle progression, and transcriptional regulation.\\n\\nMechanism: Wnt signaling pathway regulates cell fate determination, cell proliferation, and differentiation through binding of specific receptors to Wnt proteins.\\n\\n]0.92186
101gpt-3.5-turbonarrative_synopsisHALLMARK_WNT_BETA_CATENIN_SIGNALING-1[Summary: Genes involved in the Wnt signaling pathway and transcription regulation are enriched in this gene list.\\nMechanism: These genes play a role in the regulation of the Wnt signaling pathway and transcriptional regulation.\\n][Summary: Genes involved in the Wnt signaling pathway, regulation of cell cycle, and transcriptional regulation are statistically over-represented.\\n\\nMechanism: These genes play a role in various cellular processes, including cell fate determination, embryonic development, and tumorigenesis.\\n\\n]0.9464
102gpt-3.5-turbonarrative_synopsisT cell proliferation-0[Summary: Immune response and signal transduction genes are enriched in this list.\\n\\nMechanism: These genes function in various aspects of immune response, including immune signaling, cytokine production, and cell proliferation and differentiation.\\n\\n\\nHypothesis: These genes may be involved in the regulation of immune responses by modulating cytokine production and signaling, controlling cell proliferation and differentiation, and regulating apoptosis. Further investigation could lead to a better understanding of the complex interplay between these genes and their role in maintaining a healthy immune system.][Summary: Immune response and signal transduction\\nMechanism: C-type lectin receptors and cytokine signaling pathways\\n]0.87497
103gpt-3.5-turbonarrative_synopsisT cell proliferation-1[Summary: Immune response and cytokine signaling\\nMechanism: Regulation of immune response and cytokine signaling\\n\\nHypothesis: The enriched terms suggest that these genes are involved in the regulation of the immune response and cytokine signaling. Specifically, these genes are implicated in the signaling pathways that are activated in response to immune system activation and in the subsequent regulation of T cell function. The overall biological mechanism is the regulation of immune defense against foreign pathogens and tumor cells.][Summary: Immune response and cell signaling\\nMechanism: These genes are involved in immune response and cell signaling pathways, such as the TNF-receptor superfamily and cytokine signaling.\\n]0.93349
104gpt-3.5-turbonarrative_synopsisYamanaka-TFs-0[Summary: These genes are involved in embryonic development, stem cell pluripotency, and tumorigenesis. They encode transcription factors that regulate gene expression and control cell cycle progression.\\nMechanism: Transcriptional regulation\\n\\nHypothesis: These genes may function together in a signaling pathway involved in the maintenance of stem cell pluripotency and/or regulation of cell differentiation during embryonic development. Dysregulation of this pathway could contribute to tumorigenesis. The transcription factors encoded by these genes may also interact with other proteins involved in DNA damage response and repair.][Summary: These genes share a role in the regulation of embryonic development, cell fate determination, and cell cycle progression.\\nMechanism: These genes encode transcription factors that regulate gene expression and are important for stem cell pluripotency and cell differentiation.\\n]0.96349
105gpt-3.5-turbonarrative_synopsisYamanaka-TFs-1[Summary: Genes involved in transcription factor activity and regulation of development.\\nMechanism: Transcriptional regulation of development.\\n\\nHypothesis: These genes play a crucial role in the transcriptional regulation of embryonic development and stem cell maintenance. They are likely involved in the regulation of gene expression during critical periods of development, and abnormalities in their function may contribute to developmental disorders and tumorigenesis. Further research is needed to fully elucidate the molecular mechanisms by which these genes act and their interactions within regulatory pathways.][Summary: Embryonic development and stem cell pluripotency\\nMechanism: Transcriptional regulation\\n\\n]0.91522
106gpt-3.5-turbonarrative_synopsisamigo-example-0[Summary: Extracellular matrix and cell signaling related genes are enriched.\\n\\nMechanism: Extracellular matrix formation and remodeling, as well as cell migration and signaling pathways are likely involved.\\n\\n][Summary: Extracellular matrix and cell adhesion-related genes.\\nMechanism: Extracellular matrix remodeling and cell adhesion.\\n]0.9482
107gpt-3.5-turbonarrative_synopsisamigo-example-1[Summary: Extracellular matrix organization and cell adhesion.\\nMechanism: Regulation of cell attachment and migration via extracellular matrix interactions.\\n\\nHypothesis: The enriched terms suggest that these genes are involved in the regulation of cell attachment and migration via interactions with the extracellular matrix. Specifically, these genes play a role in extracellular matrix organization and cell adhesion, as well as proteoglycan and keratan sulfate metabolic processes. The integrin-mediated signaling pathway is also likely involved in these processes, as integrins are transmembrane receptors that mediate cell adhesion to the extracellular matrix. Finally, platelet activation may be involved, as some of these genes are associated with platelet-derived growth factors and other factors that regulate platelet activation and adhesion. Overall, these genes likely play a key role in regulating cell behavior in response to changes in the extracellular matrix, and may be involved in a variety of physiological and pathological processes, including wound healing, tissue development and maintenance, and cancer progression.][Summary: Extracellular matrix (ECM) organization and regulation, cell adhesion and migration, tissue development and regeneration, signaling pathways, and platelet function are enriched in these gene functions.\\n\\nMechanism: ECM proteins, such as SPP1, COL5A2, and LUM, are involved in tissue organization and regulation. Cell adhesion and migration are mediated by proteins such as VCAN, ITGAV, and VTN. Tissue development and regeneration involve proteins like POSTN, MSX1, and JAG1. Signaling pathways are regulated by genes such as JAG2, NRP1, and TNFRSF21. Platelet function is affected by genes such as PF4, PDGFA, and PRG2.\\n\\n]0.94509
108gpt-3.5-turbonarrative_synopsisbicluster_RNAseqDB_0-0[Summary: Membrane transport and binding activity\\nMechanism: ABC Transporter Signaling Pathway\\n][Summary: Several of the genes are involved in transcription regulation and protein binding.\\n\\nHypothesis: These genes may be involved in regulating cellular processes through the regulation of gene expression and protein interactions, with zinc fingers and calcium ion binding domains playing important roles in protein-protein interactions and regulatory functions. The membrane proteins may mediate these interactions and functions at the cellular membrane.]0.80365
109gpt-3.5-turbonarrative_synopsisbicluster_RNAseqDB_0-1[Summary: Genes are involved in various cellular processes, including RNA binding, calcium signaling, protein binding, transcription factor activity, and membrane transport. \\n\\n][Summary: Calcium-binding proteins, receptor proteins, and transcription factors are over-represented in this list of human genes.\\n\\nMechanism: These genes are involved in diverse biological processes but share common molecular functions, such as calcium binding, transcriptional regulation, receptor activity, and protein binding.\\n\\n]0.89156
110gpt-3.5-turbonarrative_synopsisbicluster_RNAseqDB_1002-0[Summary: Muscle contraction and regulation\\nMechanism: Gene products involved in the structure, organization, and regulation of the contractile machinery in striated muscle.\\n\\nHypothesis: The enriched terms indicate that the gene products listed are all involved in the structure, organization, and regulation of the contractile machinery in striated muscle. More specifically, these gene products contribute to the organization of actin filaments via actin binding, tropomyosin binding, and muscle filament sliding speed regulation, as well as the regulation of muscle contraction through calcium ion binding to the troponin complex and myosin binding. There are specific enriched terms, such as regulation of muscle filament sliding speed, which suggest that these gene products may play distinct roles within the muscle contractile machinery, but this remains to be fully elucidated.][Summary: These genes are primarily involved in muscle contraction and regulation, with some playing a role in ion channel activity, protein binding, and phosphorylation.\\nMechanism: These genes are involved in the regulation of muscle development, contraction, and calcium signaling pathways.\\n]0.90593
111gpt-3.5-turbonarrative_synopsisbicluster_RNAseqDB_1002-1[Summary: Genes are involved in muscle contraction, regulation, and structure.\\n\\n\\nHypothesis: The muscle structure and function depend on the proper regulation of actin-myosin interaction, calcium ion flux, and energy metabolism. Dysfunctions in these pathways lead to the development of various muscle disorders. Therefore, the enriched terms represent the key biological processes and molecular functions that underlie muscle structure, function, and dysfunction.][Summary: Genes involved in muscle contraction, regulation of calcium ions in muscle, and energy homeostasis.\\nMechanism: These genes contribute to the structure and function of striated muscle fibers, allowing for efficient and regulated contraction and relaxation.\\n]0.92199
112gpt-3.5-turbonarrative_synopsisendocytosis-0[Summary: Many of the genes in this list are involved in endocytosis, intracellular trafficking, and cytoskeleton reorganization.\\n\\nMechanism: These genes likely play a role in the regulation and maintenance of cellular processes by contributing to the turnover and recycling of molecules within the cell.\\n\\n][Summary: Genes in this list are involved in various cellular processes, including endocytosis, cytoskeletal reorganization, and signal transduction. They are also involved in lipid homeostasis and bone and brain development.\\n\\nMechanism: These genes are involved in intracellular transport, regulation of membrane dynamics, and signaling pathways. \\n\\n]0.9644
113gpt-3.5-turbonarrative_synopsisendocytosis-1[Summary: Genes involved in endocytosis, vesicle trafficking, and intracellular signaling.\\nMechanism: These genes function in various aspects of intracellular trafficking, particularly endocytosis and vesicle trafficking.\\n\\n][Summary: The enriched terms are involved in intracellular trafficking, endocytosis, and cytoskeletal reorganization.\\nMechanism: These genes function in regulating cellular processes involving endocytic recycling and protein degradation.\\n\\n]0.9216
114gpt-3.5-turbonarrative_synopsisglycolysis-gocam-0[Summary: The genes in this list are involved in glucose metabolism and glycolysis, which is the breakdown of glucose to provide energy for cellular processes.\\n\\n\\nHypothesis: The common function of these genes in glucose metabolism and glycolysis suggests a role in regulating energy production in cells. Dysfunction in these genes may lead to diseases related][Summary: These genes are involved in various stages of glucose metabolism and glycolysis.\\n\\nMechanism: The enriched terms suggest that these genes are involved in energy metabolism, specifically glycolysis and the conversion of glucose to ATP.\\n\\n]0.93115
115gpt-3.5-turbonarrative_synopsisglycolysis-gocam-1[Summary: Enzymes involved in glycolysis and related metabolic pathways.\\nMechanism: Metabolism of glucose to produce energy.\\n][Summary: These genes are involved in various steps of glycolysis, a central metabolic pathway for the conversion of glucose into pyruvate, with the production of energy-rich ATP molecules.\\n\\nMechanism: Glycolysis is a multi-step process consisting of various enzymes that catalyze the conversion of glucose to pyruvate. This process occurs in the cytoplasm of cells and is an important pathway for the production of ATP.\\n\\n\\nHypothesis: These genes are involved in the regulation of energy metabolism and play a crucial role in providing cells with energy in the form of ATP. Dysfunction of these pathways can lead to various metabolic disorders, including glycogen storage diseases, hemolytic anemia, and cancer. The enrichment of terms related to glucose and fructose metabolism suggests that these pathways are particularly important for the function of these genes.]0.92743
116gpt-3.5-turbonarrative_synopsisgo-postsynapse-calcium-transmembrane-0[Summary: Calcium signaling regulation and ion channels\\nMechanism: Calcium homeostasis and neuronal signaling \\n\\nHypothesis: The gene function common to this list is the regulation of calcium signaling and ion channels in neurons. These genes are involved in the transport and binding of calcium ions in the intracellular space and the regulation of ion channel activity in the plasma membrane, particularly in the postsynaptic density of neurons. Calcium transport is vital for regulating neuronal signaling and synaptic plasticity, which underlie many physiological processes, including learning and memory. The ionotropic glutamate receptor activity is also enriched, which is involved in fast neurotransmission in the synapses. Overall, this suggests that these genes contribute to the regulation of calcium signaling essential for proper neuron function and synaptic plasticity.][Summary: Calcium regulation and signaling\\nMechanism: Calcium ion transport and homeostasis\\n\\nHypothesis: The list of genes all play a critical role in calcium ion transport and homeostasis. They are involved in regulating intracellular calcium concentrations through ion transport across cell membranes. Specifically, many of the genes encode for ionotropic glutamate receptors that mediate synaptic plasticity in the central nervous system, which is believed to underlie memory and learning. The NMDA receptor subunits are key components of these receptors and are involved in calcium signaling. Additionally, several genes encode for sodium/calcium exchanger proteins that are responsible for regulating calcium ion homeostasis in a wide variety of cell types. The TRP ion channel family plays a role in transducing painful stimuli such as capsaicin and thermal stimuli. Overall, these genes are involved in multiple processes that ultimately impact calcium regulation and signaling.]0.96103
117gpt-3.5-turbonarrative_synopsisgo-postsynapse-calcium-transmembrane-1[Summary: Ion channels and receptors\\nMechanism: Regulation of cellular calcium levels\\n\\nHypothesis: The enriched terms suggest a mechanism by which these genes regulate cellular calcium levels, likely through ion channels and receptors. This regulation is crucial for synaptic transmission and neurotransmitter receptor activity. Dysfunction of these genes could lead to disruptions in calcium homeostasis, potentially contributing to neurological disorders.][Summary: All listed genes are involved in ion channel activity, particularly calcium channels and receptors. \\n\\nMechanism: Calcium signaling \\n\\n]0.91315
118gpt-3.5-turbonarrative_synopsisgo-reg-autophagy-pkra-0[COULD NOT PARSE][Summary: Regulation of cell growth and survival through various signaling pathways is a common function of the listed genes.\\n\\nMechanism: The genes listed are involved in various signaling pathways that regulate cellular growth and survival, including the PI3K/AKT/mTOR pathway, TORC1 signaling, and the NF-kappaB pathway.\\n\\n]0.68308
119gpt-3.5-turbonarrative_synopsisgo-reg-autophagy-pkra-1[Summary: Genes are involved in cell signaling, regulation of apoptosis, immune response, and protein kinase activity.\\nMechanism: These genes regulate various cellular processes such as cell division, survival, and metabolism through protein signaling and kinase activity pathways.\\n][Summary: Genes involved in cell growth, signaling, and immune response are enriched.\\n\\nMechanism: These genes converge on signaling pathways that control cell growth and immune response through regulation of protein kinases such as AKT, TOR, and CDK5, and activation of transcription factors such as NF-kappaB.\\n\\n]0.9230
120gpt-3.5-turbonarrative_synopsishydrolase activity, hydrolyzing O-glycosyl compounds-0[Summary: These genes are involved in the degradation of glycosaminoglycans, glycogen, and glycolipids, as well as the hydrolysis of glycosidic bonds in carbohydrates. \\n\\n\\nHypothesis: The enriched terms point to a common mechanism of lysosomal degradation of carbohydrate molecules, with specific enzymes targeting different types of molecules (e.g. glycosaminoglycans, glycogen, glycolipids). This process is important for maintaining cellular homeostasis and energy metabolism.][Summary: Genes involved in the hydrolysis of carbohydrates and degradation of glycosaminoglycans, along with those involved in the turnover of hyaluronan and chitin, are enriched. \\nMechanism: Carbohydrate and glycosaminoglycan metabolism. \\n]0.93237
121gpt-3.5-turbonarrative_synopsishydrolase activity, hydrolyzing O-glycosyl compounds-1[Summary: Enzymes involved in carbohydrate metabolism, specifically in the breakdown of complex sugars like glycosaminoglycans and polysaccharides.\\n\\nMechanism: Carbohydrate metabolism\\n\\n][Summary: Enzymes involved in glycosaminoglycan degradation and processing are enriched in this gene set.\\n\\nMechanism: Glycosaminoglycans are long chains of complex carbohydrates that are integral components of the extracellular matrix and play a role in cell signaling and tissue development. These enzymes are involved in the degradation and processing of glycosaminoglycans, specifically the cleavage of terminal carbohydrate residues.\\n\\n]0.91254
122gpt-3.5-turbonarrative_synopsisig-receptor-binding-2022-0[Summary: The enriched terms are related to immunoglobulin receptor binding activity and immune response. \\nMechanism: The genes listed all code for proteins involved in the function of immunoglobulins, which are the key molecules of adaptive immunity (the portion of the immune system that learns to recognize and remember specific pathogens). \\n][Summary: The enriched terms suggest that these genes are involved in the immune response and specifically in the function of immunoglobulins (Ig) and immunoglobulin receptors.\\n\\nMechanism: The genes function in the immune response and interaction with antigens.\\n\\n]0.9682
123gpt-3.5-turbonarrative_synopsisig-receptor-binding-2022-1[Summary: Genes are involved in adaptive immune response and immune system processes, likely through antigen binding activity and immunoglobulin receptor binding activity. \\n\\n][Summary: Genes related to immunoglobulin receptor binding activity and activation of immune response.\\nMechanism: Adaptive immune response\\n]0.9335
124gpt-3.5-turbonarrative_synopsismeiosis I-0[Summary: These genes are primarily involved in meiotic recombination, double-strand break repair, and chromosomal segregation during meiosis. They all play a role in some aspect of the meiotic cell cycle process.\\n\\n\\nHypothesis: The underlying biological mechanism for these genes is the regulation and coordination of meiotic recombination and double-strand break repair via homologous recombination, as well as the proper segregation of chromosomes during meiosis. Dysfunction in any of these genes may result in chromosomal abnormalities and infertility in individuals.][Summary: Meiotic recombination and DNA repair are enriched functions among the listed genes.\\nMechanism: The genes listed play a role in DNA repair and recombination during meiosis, particularly in the resolution of double-stranded DNA breaks. \\n]0.92327
125gpt-3.5-turbonarrative_synopsismeiosis I-1[Summary: Genes involved in meiotic recombination and DNA break repair are enriched.\\n\\nMechanism: These genes play a crucial role in meiotic recombination and repair of DNA double-strand breaks. During meiosis, DNA breaks are introduced, repaired, and exchanged between chromosomes to generate genetic diversity.\\n\\n][Summary: These genes are involved in various aspects of meiotic recombination, DNA repair, and chromosome segregation.\\nMechanism: Meiosis\\n\\n\\nHypothesis: These genes are involved in various aspects of meiotic recombination. They likely function in the repair of double-strand DNA breaks, the resolution of Holliday junctions, and the proper segregation of homologous chromosomes during meiosis. They may also play a role in the formation and maintenance of the synaptonemal complex, which helps to ensure accurate chromosome pairing and recombination. Overall, these genes are critical for the proper functioning of meiosis and the generation of viable gametes.]0.94348
126gpt-3.5-turbonarrative_synopsismolecular sequestering-0[Summary: Cellular processes involved in protein binding and regulation, immune response, and intracellular transport are enriched in the given list of genes.\\n\\n\\nHypothesis: The enriched terms suggest that the genes in this list are involved in several overlapping pathways related to protein binding and regulation, immune response, and intracellular transport. Specifically, these genes may play a role in regulating protein-protein interactions, immune system signaling and response, and the movement of molecules and particles within cells. These pathways may be key to cellular development, maintenance, and response to stressors and damage. Further investigation into the relationships and interactions between these genes may lead to a better understanding of how these processes are regulated and coordinated in human cells.][Summary: Regulation of cellular processes, including immunity, apoptosis, and signal transduction.\\nMechanism: These genes are involved in a range of biological pathways, including immune response, cell cycle regulation, and intracellular transport.\\n\\n]0.90581
127gpt-3.5-turbonarrative_synopsismolecular sequestering-1[Summary: Transport functions, regulation of cell growth and survival, inhibition of apoptosis, and regulation of gene expression are enriched in this set of genes.\\nMechanism: These genes likely function in a variety of cellular processes, including transport and signaling pathways, cell cycle regulation, and gene expression regulation.\\n\\n][Summary: Regulation of cellular processes, including immune response and cell cycle progression.\\nMechanism: Not specified.\\n]0.86216
128gpt-3.5-turbonarrative_synopsismtorc1-0[Summary: Enzymatic processes related to metabolism and cellular transport are over-represented in this gene set.\\n\\nMechanism: The genes in this set are involved in various metabolic pathways related to cellular transport and enzymatic processes, including lipid metabolism and glucose homeostasis.\\n\\n][Summary: Protein synthesis and folding regulation\\nMechanism: The identified genes are involved in processes related to protein synthesis, folding, and degradation. Several of the genes are involved in regulating glucose metabolism, which provides energy for protein synthesis. Others are involved in regulating the structure of microtubules, which help transport proteins within cells.\\n\\n]0.8789
129gpt-3.5-turbonarrative_synopsismtorc1-1[Summary: These genes are involved in various cellular processes, but a common theme is their involvement in protein degradation. \\n\\nMechanism: The 26S proteasome is a multicatalytic proteinase complex that plays a critical role in the degradation of intracellular proteins that are damaged, misfolded, or no longer needed. \\n\\n][Summary: These genes are involved in various cellular processes such as protein degradation, glucose transport, nucleic acid metabolism, and energy metabolism.\\n\\nMechanism: The biological mechanism underlying the common function of these genes may relate to their involvement in cellular metabolism and maintenance.\\n\\n]0.898
130gpt-3.5-turbonarrative_synopsisperoxisome-0[Summary: Genes involved in peroxisome biogenesis and protein import.\\nMechanism: Peroxisome biogenesis and maturation pathway.\\n\\n\\nHypothesis: These genes are involved in the peroxisome biogenesis and maturation pathway, which is responsible for the assembly of functional peroxisomes. This pathway involves the formation of membrane vesicles by PEX3, followed by translocation of matrix proteins via PEX5 and PEX7. Mutations in these genes lead to peroxisome biogenesis disorders, which are characterized by multiple defects in peroxisome function, including import of matrix proteins. Therefore, these genes are involved in the import of peroxisomal matrix proteins and the maturation of peroxisomes. The commonalities in their function are related to their roles in peroxisome biogenesis and protein import.][Summary: Genes involved in peroxisome biogenesis and protein import\\nMechanism: Peroxisome assembly and maintenance pathway\\n\\nHypothesis: These genes are all involved in the same pathway for peroxisome assembly and maintenance, specifically in the import of peroxisomal matrix proteins. Mutations in these genes lead to various peroxisomal biogenesis disorders, including neonatal adrenoleukodystrophy, Zellweger syndrome, and infantile Refsum disease. Defects in PEX7 specifically have been associated with a wider range of disorders, including RCDP1 and Refsum disease. Overall, these genes play critical roles in the proper function of peroxisomes and their associated metabolic processes.]0.96117
131gpt-3.5-turbonarrative_synopsisperoxisome-1[Summary: Genes involved in peroxisome biogenesis disorders\\nMechanism: Peroxisome assembly and matrix protein import\\n][Summary: Peroxisome biogenesis genes are enriched for terms related to peroxisome assembly and function.\\n\\nMechanism: Peroxisomes are important organelles responsible for numerous metabolic functions, including the degradation of fatty acids and the synthesis of cholesterol. The genes listed here are involved in the assembly and maintenance of peroxisomes, as well as the import of proteins into the organelle.\\n\\n\\nHypothesis: The AAA family of ATPases plays a central role in peroxisome biogenesis by providing energy for protein translocation and membrane remodeling. Mutations in these genes disrupt the normal assembly and function of peroxisomes, leading to a range of disorders collectively known as peroxisome biogenesis disorders.]0.92622
132gpt-3.5-turbonarrative_synopsisprogeria-0[Summary: Genes involved in nuclear structure and function \\nMechanism: Proteolytic processing of prelamin A to mature lamin A, maintenance of genome stability \\n][Summary: Genes involved in nuclear structure and maintenance.\\nMechanism: These genes encode proteins that are involved in maintaining the structure and function of the nucleus. They are involved in processes such as DNA repair, replication, and chromatin organization.\\n]0.91110
133gpt-3.5-turbonarrative_synopsisprogeria-1[Summary: Genes LMNA, WRN, and BANF1 are all involved in nuclear functions and stability.\\nMechanism: These genes are involved in maintaining the stability of the genome by regulating chromatin structure, repairing DNA, and facilitating nuclear reassembly.\\n][Summary: Genes involved in nuclear organization and stability.\\nMechanism: These genes play important roles in maintaining nuclear stability and integrity by organizing chromatin structure and gene expression, repairing DNA damage, and promoting nuclear reassembly.\\n]0.9010
134gpt-3.5-turbonarrative_synopsisregulation of presynaptic membrane potential-0[Summary: Genes involved in neurotransmission through ion channels, specifically GABA and glutamate receptors, as well as voltage-gated potassium and sodium channels, are over-represented in this list.\\n\\nMechanism: These genes encode proteins involved in the regulation of ion flow in neuronal membranes, allowing for the transmission of electrical signals and control of neuronal excitability.\\n\\n][Summary: Genes involved in ion channels and neurotransmission through GABA and glutamate receptors. \\nMechanism: Regulation of neuronal excitability and synaptic transmission. \\n]0.94218
135gpt-3.5-turbonarrative_synopsisregulation of presynaptic membrane potential-1[Summary: These genes are involved in the regulation of ion channels in the central nervous system.\\nMechanism: Regulation of ion channels\\n][Summary: The enriched terms are related to ion channels in the central nervous system, particularly potassium and chloride channels. \\n\\nMechanism: Ion channels play critical roles in regulating the electrical properties of cells, including neurons. Potassium channels are important for regulating action potential firing and synaptic transmission, while chloride channels are involved in inhibitory neurotransmission mediated by GABA. \\n\\n]0.89299
136gpt-3.5-turbonarrative_synopsissensory ataxia-0[Summary: Myelin upkeep and neurological diseases\\n\\nHypothesis: Dysregulation of the myelin upkeep pathways can lead to mitochondrial dysfunction, accumulations of toxic metabolites, and impaired protein processing, which contribute to the development of neurological diseases. Dysfunction of the transporter proteins and nuclear membrane transporters can further exacerbate cell dysfunction and death. Treatment strategies aimed at restoring mitochondrial function and enhancing myelin synthesis and repair may alleviate symptoms of these diseases.][Summary: Peripheral nervous system myelination and neurodegenerative diseases are enriched in this set of genes. \\nMechanism: Maintenance of peripheral nervous system myelin structure and function through regulation of protein import, DNA replication, and degradation pathways in the endoplasmic reticulum and mitochondria. \\n]0.90224
137gpt-3.5-turbonarrative_synopsissensory ataxia-1[Summary: Peripheral nerve myelin upkeep and related disease mechanisms\\nMechanism: The genes are involved in maintaining and degrading myelin sheaths in peripheral nerve cells.\\n\\nHypothesis: The enrichment of genes involved in peripheral nerve myelin upkeep suggests a common underlying biological mechanism of maintaining appropriate myelin structure, which can be disrupted by various genetic causes leading to different neuropathic diseases. These genes play crucial roles in ensuring proper nervous system and myelin development, and focus on various biological processes that regulate these mechanisms. Ultimately, disruptions in these genes can lead to peripheral neuropathies and degeneration.][Summary: Genes involved in various peripheral nervous system disorders are enriched for terms related to myelin formation and maintenance, as well as protein transport and degradation in the ER.\\n\\n\\nHypothesis: These genes likely contribute to proper formation and maintenance of myelin in the peripheral nervous system. Dysfunctions in protein transport and degradation pathways in the ER may also contribute to disease pathogenesis.]0.93266
138gpt-3.5-turbonarrative_synopsisterm-GO:0007212-0[Summary: Signaling via G protein-coupled receptors and cyclic AMP (cAMP) signaling pathway are enriched biological processes in the list of genes.\\n\\nMechanism: The enriched terms suggest that these genes are involved in the regulation of downstream signaling pathways activated by G protein-coupled receptors (GPCRs) and their ligands, leading to the generation of cAMP, a key second messenger in many intracellular signaling pathways.\\n\\n\\nHypothesis: The majority of the genes in the list encode proteins involved in the regulation of GPCR-stimulated cAMP signaling pathways. Signaling through these pathways plays a crucial role in cell proliferation, differentiation, development, synaptic plasticity, and behavior. Dysfunction in cAMP signaling pathways has been implicated in numerous pathophysiological conditions, including psychiatric disorders and cancer.][Summary: Regulation of signal transduction pathways through G-protein-coupled receptors and neurotransmitter activity.\\nMechanism: G proteins play a central role in signal transduction by coupling receptors to downstream effectors.\\n]0.89631
139gpt-3.5-turbonarrative_synopsisterm-GO:0007212-1[Summary: These genes are involved in signaling pathways mediated by G proteins and second messenger systems, including the dopamine receptor signaling pathway.\\n\\nMechanism: Activation of G protein-coupled receptors results in the dissociation of the G protein alpha subunit from the beta-gamma subunit, leading to the activation of downstream effectors such as adenylyl cyclase and phospholipase C. This results in the production of second messenger molecules such as cyclic AMP and inositol triphosphate, which then activate downstream signaling pathways.\\n\\n][Summary: These genes are involved in various aspects of cell signaling pathways including G-protein signaling, neurotransmitter receptors, and intracellular signaling.\\n\\nMechanism: These genes are involved in the regulation of cellular responses to extracellular signals, such as neurotransmitter and hormone signals, through G-protein-coupled receptors, resulting in activation of intracellular signaling pathways.\\n\\n]0.93141
140gpt-3.5-turbonarrative_synopsistf-downreg-colorectal-0[Summary: Transcriptional regulation and chromatin remodeling are enriched functions in the given set of genes.\\n\\n][Summary: Transcriptional regulation and chromatin remodeling.\\nMechanism: These genes encode transcription factors and chromatin-associated proteins involved in the regulation of gene expression and chromatin structure.\\n]0.94107
141gpt-3.5-turbonarrative_synopsistf-downreg-colorectal-1[Summary: DNA binding transcription factors involved in regulation of gene transcription and cell development.\\nMechanism: These genes encode for proteins that bind to DNA and regulate gene expression.\\n][Summary: Transcription regulation\\n\\nHypothesis: These genes are likely to be involved in a common pathway or biological process related to the regulation of gene expression. They may play a role in coordinating the expression of multiple genes, such as those involved in cell differentiation or development. The proteins encoded by these genes may also function together within a larger protein complex involved in regulating transcription.]0.91240
142gpt-3.5-turbono_synopsisEDS-0[Summary: The common function of the genes is related to extracellular matrix (ECM) organization, collagen synthesis, and glycosaminoglycan (GAG) biosynthesis.\\n\\nMechanism: The enriched terms suggest that these genes play a significant role in extracellular matrix organization and collagen synthesis. The genes involved in glycosaminoglycan biosynthesis are also enriched, indicating their role in stabilizing the extracellular matrix.\\n\\n\\nHypothesis: The extracellular matrix is a complex network of proteins and carbohydrates that provides structural support to tissues. The genes identified in this enrichment are involved in collagen synthesis and extracellular matrix organization. The stabilization of the extracellular matrix is facilitated by the biosynthesis of GAGs. These processes are essential for tissue repair and homeostasis and altered expression of these genes may lead to several connective tissue disorders.][Summary: Extracellular matrix organization and connective tissue structure are enriched in the given genes.\\nMechanism: Extracellular matrix (ECM) maintenance and remodeling\\n\\nHypothesis: The enriched terms suggest that the given genes are involved in ECM maintenance and remodeling, particularly in collagen fibril organization, protein glycosylation, and peptidase activity. TNXB, COL12A1, ADAMTS2, COL1A2, COL3A1, COL5A1, and COL5A2 are all involved in collagen fibril organization, which is critical for maintaining connective tissue strength and elasticity. B3GALT6, B4GALT7, and CHST14 participate in protein glycosylation, important for the formation of collagens and proteoglycans, while DSE is involved in dermatan sulfate biosynthesis. SLC39A13 regulates zinc ion transport, which is important for ECM structure and stability. FKBP14 and PRDM5 play a role in collagen fiber generation and remodeling. Lastly, C1]0.945
143gpt-3.5-turbono_synopsisEDS-1[Summary: Genes are primarily related to extracellular matrix (ECM) organization and collagen biosynthesis.\\nMechanism: The biosynthesis, processing, and assembly of collagen and other ECM components.\\n\\nHypothesis: The listed genes are mostly involved in the organization and biosynthesis of collagens and other components of the extracellular matrix (ECM). The majority of the genes belong to the Category of ECM and Collagen Synthesis in Gene Ontology (GO) hierarchy. The enriched terms include \"Collagen fibril organization,\" \"Extracellular matrix organization,\" and \"Collagen biosynthesis.\" These genes may interact through different pathways to affect ECM composition, remodeling, and cell-ECM interactions. Dysregulation of these genes can lead to various diseases, such as connective tissue disorders and cancer.][Summary: Genes are enriched for extracellular matrix organization and collagen metabolic process.\\nMechanism: The genes are involved in collagen biosynthesis and extracellular matrix (ECM) remodeling.\\n\\nHypothesis: These genes are involved in extracellular matrix remodeling by encoding proteins involved in collagen biosynthesis and likely play a role in maintaining tissue structure and elasticity.]0.97418
144gpt-3.5-turbono_synopsisFA-0[Summary: Genes are enriched for DNA repair mechanisms. \\nMechanism: DNA Repair \\n\\nHypothesis: The enriched terms point towards the involvement of these genes in repairing DNA double-strand breaks. These genes are involved in repairing DNA damage and maintaining genome stability, which is critical in preventing cancer development. This suggests that mutations in these genes may increase the risk of cancer due to DNA damage accumulation.][Summary: Genes are mostly involved in DNA repair and maintenance.\\nMechanism: DNA repair and maintenance pathway\\n]0.91326
145gpt-3.5-turbono_synopsisFA-1[Summary: These genes are involved in DNA damage repair and cell-cycle checkpoint control.\\nMechanism: Homologous recombination repair pathway\\n\\nHypothesis: These genes are all involved in the homologous recombination repair pathway, which repairs double-strand breaks in DNA. They also contribute to mitotic cell-cycle checkpoint control and the DNA damage response. Dysfunction in these genes can lead to defects in DNA repair and increased risk of cancer development.][Summary: The genes listed are involved in DNA repair and share functions related to the Fanconi anemia pathway, homologous recombination, and double-strand break repair.\\n\\nMechanism: The genes identified in this list are associated with DNA damage response and repair pathways. Specifically, they are enriched in the Fanconi anemia (FA) pathway, which is a network of proteins involved in the detection and repair of DNA interstrand crosslinks (ICLs). The FA pathway activates a cascade of events that lead to the repair of damaged DNA, including the recruitment of nucleases, helicases, and recombinases to the site of the ICL.\\n\\n]0.92161
146gpt-3.5-turbono_synopsisHALLMARK_ADIPOGENESIS-0[Summary: Energy metabolism and lipid transport pathways are enriched in the list of human genes.\\nMechanism: These genes are involved in the regulation and transport of lipids, fatty acids, and energy in the body.\\n\\n][Summary: Metabolism and energy production are the common themes among the listed genes. Numerous processes and pathways related to energy metabolism, including lipid metabolism, fatty acid oxidation, and mitochondrial function, are enriched.\\n\\nMechanism: The overlapping functions of these genes suggest that they are involved in various metabolic processes important for energy production in cells, including lipid and mitochondrial metabolism.\\n\\n]0.93232
147gpt-3.5-turbono_synopsisHALLMARK_ADIPOGENESIS-1[Summary: Several enriched terms relate to energy metabolism and lipid transport/storage, as well as protein folding and stress response mechanisms.\\nMechanism: Possible biological mechanisms include mitochondrial function and fatty acid metabolism.\\n\\n][Summary: Mitochondrial function and lipid metabolism are enriched functions among the given genes.\\nMechanism: The genes are involved in processes related to mitochondrial function and lipid metabolism. \\n\\n]0.9045
148gpt-3.5-turbono_synopsisHALLMARK_ALLOGRAFT_REJECTION-0[Summary: Immune system response and regulation.\\nMechanism: Immune response pathways are activated and regulated by these genes, which contribute to various stages of immune cell development, differentiation, activation, and signaling.\\n][Summary: Immune response and signaling pathway genes are statistically over-represented in this gene set.\\nMechanism: These genes are involved in regulating different stages of immune response, including the activation and differentiation of immune cells, cytokine signaling, and antigen presentation to T cells.\\n\\n]0.9378
149gpt-3.5-turbono_synopsisHALLMARK_ALLOGRAFT_REJECTION-1[Summary: Immune response and inflammation genes are over-represented in the list.\\nMechanism: Immune system activation and response\\n][Summary: Immune-related functions are enriched in the list of genes.\\nMechanism: Multiple genes involved in various aspects of the immune response.\\n\\n\\nHypothesis: The enrichment of immune-related functions in the list of genes indicates their importance in the immune response. Many of these genes are involved in T cell activation, cytokine signaling, antigen processing and presentation, and leukocyte migration, which are all critical processes in mounting an effective immune response against pathogens or foreign invaders. The enrichment of genes involved in B cell differentiation also suggests a role in the adaptive immune response. Additionally, the significant enrichment of chemokine signaling and interferon signaling genes could indicate a broader regulatory mechanism that influences the immune response.]0.89686
150gpt-3.5-turbono_synopsisHALLMARK_ANDROGEN_RESPONSE-0[Summary: Regulation of transcription, metabolism, and protein degradation are enriched processes among the listed genes.\\nMechanism: The mechanism underlying the enriched processes is likely through the interaction between the genes and transcription factors.\\n][Summary: Several terms related to transcriptional regulation and protein degradation are enriched in the list of human genes provided.\\n\\nMechanism: The enriched terms suggest that the genes in the list are involved in regulating gene expression, protein stability, and turnover. The specific biological mechanisms underlying these functions likely involve cellular pathways such as ubiquitin-proteasome system, protein degradation, and transcriptional regulation.\\n\\n]0.93205
151gpt-3.5-turbono_synopsisHALLMARK_ANDROGEN_RESPONSE-1[Summary: Genes are involved in various biological processes such as signal transduction, metabolism, and transcriptional regulation.\\nMechanism: None identified.\\n][Summary: Regulation of transcriptional activity, cell signaling, and metabolism are enriched functions among these genes.\\nMechanism: These genes may be involved in cancer development and progression, as well as other cellular processes.\\n]0.9076
152gpt-3.5-turbono_synopsisHALLMARK_ANGIOGENESIS-0[Summary: Extracellular matrix organization and regulation of signaling pathways are enriched functions in the list of genes.\\nMechanism: Extracellular matrix is a complex network of proteins and carbohydrates that provides structural support to cells and tissues, regulates cell behavior, and modulates signaling pathways involved in various physiological and pathological processes.\\n\\nHypothesis: The extracellular matrix is a key regulator of cell behavior and signaling, and its dysfunction is associated with various diseases, including cancer, cardiovascular disease, and connective tissue disorders. These genes are involved in various aspects of extracellular matrix organization and dynamics, such as collagen synthesis and assembly, proteoglycan biosynthesis, adhesion molecules, and extracellular matrix remodeling enzymes. They also regulate key signaling pathways, such as MAP kinase and PI3 kinase pathways, involved in cell proliferation, survival, and migration. Dysfunction of these genes can disrupt extracellular matrix homeostasis and alter cell behavior, leading to various pathological conditions.][Summary: Genes associated with extracellular matrix and growth factor regulation are enriched.\\nMechanism: Extracellular matrix remodeling and growth factor signaling pathways.\\n\\nHypothesis: The enriched genes are all involved in the regulation and maintenance of the extracellular matrix (ECM), suggesting a significant role in ECM organization and remodeling. The genes are also involved in growth factor signaling, suggesting a role in cell proliferation, differentiation, and wound healing. The findings indicate the importance of ECM organization and growth factor signaling in developmental processes and diseases such as osteogenesis imperfecta, Marfan syndrome, and atherosclerosis.]0.93428
153gpt-3.5-turbono_synopsisHALLMARK_ANGIOGENESIS-1[Summary: Extracellular matrix organization and angiogenesis\\nMechanism: Regulation of signaling pathways involving TGF-beta and VEGF\\n\\nHypothesis: The enriched terms suggest that these genes are involved in extracellular matrix organization and angiogenesis. These processes are tightly regulated by signaling pathways involving TGF-beta and VEGF. The list of genes is enriched for those involved in positive regulation of cell migration, endothelial cell proliferation, and cell adhesion, which are all necessary for angiogenesis. Dysregulation of these genes might contribute to pathological conditions such as cancer and cardiovascular diseases.][Summary: Extracellular matrix organization and angiogenesis\\nMechanism: Integrin signaling\\n\\nHypothesis: The genes in this list are enriched for those involved in the extracellular matrix organization and angiogenesis. These genes are related to integrin signaling which is important for mediating cell adhesion and signaling between the cell and extracellular matrix. The upregulation of these genes indicates an increased demand for extracellular matrix remodeling and angiogenesis in certain contexts, such as tissue regeneration or wound healing.\\n\\nThe enriched terms in this gene list suggest that the genes are involved in extracellular matrix organization, angiogenesis, and cell adhesion. These processes are important for tissue growth and repair and are likely regulated by integrin signaling. This suggests that the genes in this list may be involved in mediating these processes during tissue development or in response to injury.]0.96293
154gpt-3.5-turbono_synopsisHALLMARK_APICAL_JUNCTION-0[Summary: Cell-Cell adhesion and Extracellular matrix organization are statistically enriched functions of the genes.\\n\\nMechanism: These genes are commonly involved in the formation and maintenance of cell-cell adhesion and extracellular matrix (ECM) interactions which play an important role in developmental processes, tissue morphogenesis, and homeostasis.\\n\\n][Summary: Cell adhesion and cytoskeleton organization processes are enriched in the given list of genes.\\nMechanism: Cell adhesion and cytoskeleton organization are key processes in cell signaling and migration. \\n\\n]0.91147
155gpt-3.5-turbono_synopsisHALLMARK_APICAL_JUNCTION-1[Summary: Cell adhesion and communication, with a focus on tight junctions and claudins\\nMechanism: Signaling pathways involved in regulating tight junctions, such as the MAPK and PI3K-Akt pathways\\n\\nHypothesis: The genes listed are primarily involved in regulating tight junctions, which are structures that serve to tightly regulate the permeability of cells and contribute to the formation of physical barriers between various tissues and organs. The enrichment of terms related to cell adhesion, communication, and cytoskeletal organization suggest that these genes help to coordinate signaling between cells and the actin cytoskeleton, which is necessary for tight junction formation and maintenance. The specific signaling pathways involved likely include the MAPK and PI3K-Akt pathways, as these have been shown to modulate the activity of various tight junction proteins, including claudins. Additionally, several of the genes listed are involved in endothelial cell migration and angiogenesis][Summary: Cell adhesion and migration\\n]0.86962
156gpt-3.5-turbono_synopsisHALLMARK_APICAL_SURFACE-0[Summary: Cell adhesion and signaling pathways appear to be the most enriched functions across these genes.\\nMechanism: These genes may be involved in regulating cell signaling pathways and adhesion through their various functions, such as receptor binding, protein interaction, and membrane transport.\\n\\n\\nHypothesis: These genes may play a role in modulating cell signaling and adhesion events that are critical for cellular communication and tissue development. Dysregulation of these pathways may result in various diseases, such as cancer and metabolic disorders.][Summary: Genes are enriched in terms related to cell adhesion, signaling and transport.\\nMechanism: These genes are involved in pathways that regulate cell adhesion and communication, as well as transport of molecules across cellular membranes.\\n\\n]0.94320
157gpt-3.5-turbono_synopsisHALLMARK_APICAL_SURFACE-1[Summary: Cell adhesion, migration, and signaling are enriched functions among the listed genes.\\nMechanism: The genes are involved in regulating the activity of various receptor tyrosine kinases, membrane channels, and enzymes involved in intracellular signaling pathways.\\n\\n][Summary: Genes are enriched for functions related to cell adhesion, signal transduction, and regulation of metabolism.\\nMechanism: These genes may be involved in coordinating cellular processes and responses to environmental signals.\\n\\n\\nHypothesis: The enriched terms suggest that these genes may be involved in regulating cellular processes related to adhesion, signaling, and metabolism. Specifically, they]0.91134
158gpt-3.5-turbono_synopsisHALLMARK_APOPTOSIS-0[Summary: Apoptosis-related and immune response genes are statistically over-represented in the given list of genes.\\nMechanism: The enrichment of these genes suggests the involvement of apoptosis and immune response-related pathways in the biological processes of these genes.\\n][Summary: Cell death regulation\\n\\nHypothesis: The genes on this list may interact with each other to form signaling pathways that regulate the balance between cell survival and death. Dysregulation of these pathways can lead to pathological conditions such as cancer. Further studies are needed to elucidate the specific mechanisms and interactions among these genes in the context of cell death regulation.]0.87130
159gpt-3.5-turbono_synopsisHALLMARK_APOPTOSIS-1[Summary: Genes are enriched in cellular stress and apoptosis pathways.\\nMechanism: Cellular stress and apoptosis pathways are activated to maintain cellular survival and function.\\n][Summary: Genes in this list are enriched for functions related to apoptosis, immune response, and cancer.\\nMechanism: These genes play a role in regulating cell death, inflammatory response, and tumor development.\\n\\n]0.9035
160gpt-3.5-turbono_synopsisHALLMARK_BILE_ACID_METABOLISM-0[Summary: Genes are involved in lipid metabolism, specifically in bile acid biosynthesis, cholesterol synthesis and transport, and peroxisome biogenesis.\\nMechanism: Lipid metabolism\\n\\nHypothesis: These genes are enriched for lipid metabolism, specifically in bile acid biosynthesis, cholesterol synthesis and transport, and peroxisome biogenesis. This suggests that these genes are involved in maintaining a healthy balance of lipids in the body and may play a role in the development of lipid-related diseases.][Summary: Genes are involved in lipid and sterol metabolism, as well as peroxisome biogenesis and function.\\n]0.94403
161gpt-3.5-turbono_synopsisHALLMARK_BILE_ACID_METABOLISM-1[Summary: Genes are enriched for lipid metabolism and transport, as well as peroxisomal and mitochondrial functions.\\nMechanism: Peroxisomes and mitochondria are both involved in various aspects of lipid metabolism and transport, and the enrichment of peroxisomal genes may suggest a role for peroxisomes in these processes.\\n][Summary: The enriched terms are related to lipid metabolism, transport and catabolism, as well as cellular organelle biogenesis and function.\\nMechanism: These genes are involved in pathways related to cholesterol and bile acid biosynthesis, peroxisomal biogenesis and function, and fatty acid metabolism and transport.\\n\\n]0.943
162gpt-3.5-turbono_synopsisHALLMARK_CHOLESTEROL_HOMEOSTASIS-0[Summary: Processes related to sterol biosynthesis, lipid metabolism, and cholesterol homeostasis are overrepresented in this gene set.\\nMechanism: Cholesterol homeostasis\\n\\nHypothesis: This gene set is enriched for genes involved in cholesterol homeostasis, reflecting the importance of cholesterol regulation in human biology. Specifically, processes related to sterol biosynthesis, lipid metabolism, and cholesterol transport are overrepresented. Cholesterol is a critical component of cell membranes and is involved in many important cellular processes. Dysregulation of cholesterol metabolism has been linked to a number of human diseases, including cardiovascular disease and neurological disorders. Further research into the genes in this set and their interactions may provide insights into the regulation of cholesterol homeostasis and potential therapeutic targets.][Summary: Lipid metabolism and cholesterol biosynthesis are significantly enriched in the list of genes provided.\\nMechanism: The enriched terms suggest a pathway leading to the synthesis and transport of lipids and cholesterol within cells.\\n\\n]0.92632
163gpt-3.5-turbono_synopsisHALLMARK_CHOLESTEROL_HOMEOSTASIS-1[Summary: Genes are enriched for lipid metabolism and cholesterol biosynthesis.\\nMechanism: Lipid metabolism and cholesterol biosynthesis pathways.\\n\\nHypothesis: The enriched terms suggest that the listed genes are involved in the biosynthesis, regulation, and metabolism of cholesterol and other lipids, likely through the mevalonate pathway. This pathway generates isoprenoids, which are essential for cholesterol synthesis and other cellular functions. Dysregulation of these genes may contribute to metabolic disorders such as hypercholesterolemia.][Summary: Lipid metabolism, cholesterol biosynthesis, and steroid biosynthesis are enriched functions among the given genes.\\nMechanism: The enriched functions suggest that these genes play a role in cholesterol and lipid metabolism pathways.\\n\\n]0.95308
164gpt-3.5-turbono_synopsisHALLMARK_COAGULATION-0[Summary: Blood coagulation and complement pathways are enriched in the list of genes.\\nMechanism: The enriched genes are involved in the regulation and activation of the blood coagulation and complement pathways.\\n\\nHypothesis: The enrichment of genes involved in blood coagulation and complement pathways suggests that this list may be specifically relevant to the regulation and activation of these pathways. This may indicate potential involvement in diseases related to these pathways, such as thrombosis, hemophilia, and acute inflammation.][Summary: Extracellular matrix organization and coagulation cascade regulation are statistically overrepresented functions among the listed genes.\\nMechanism: Many of the genes in the list are involved in regulating extracellular matrix composition and integrity, which is important for tissue structure and homeostasis. This process involves the interaction of various proteases and inhibitors, as well as proteins involved in coagulation cascade regulation. \\n]0.8984
165gpt-3.5-turbono_synopsisHALLMARK_COAGULATION-1[Summary: Extracellular matrix organization, blood coagulation and fibrinolysis, immune defense, and proteolysis are enriched functions shared by the human genes in the list.\\n\\nMechanism: The genes are involved in the formation and maintenance of the extracellular matrix, blood coagulation and fibrinolysis pathways, immune response, and proteolytic processes.\\n\\n][Summary: Blood coagulation and immune response-related functions are over-represented in the list of genes provided.\\nMechanism: The genes are involved in producing factors required for blood clotting and regulating immune responses.\\n\\n]0.91127
166gpt-3.5-turbono_synopsisHALLMARK_COMPLEMENT-0[Summary: Immune response and inflammation-related functions are enriched in the list of genes.\\nMechanism: Immune response and inflammation-related pathways are activated.\\n\\nHypothesis: The genes in this list play a role in immune response and inflammation. The enriched terms suggest that these genes are involved in complement activation, regulation of proteolysis, and apoptotic signaling. The activation of these pathways may modulate the host immune response to infectious agents and tissue damage. Some of the genes may also play a role in regulating endopeptidase activity, which could be involved in immune response regulation.][Summary: Immune system regulation and thrombosis prevention\\n\\nHypothesis: The genes in this set are involved in immune system surveillance and regulation, as well as the prevention of thrombosis by maintaining the delicate balance between hemostasis and clotting. These functions are critical in preventing pathological infections and clots, and their dysregulation could lead to autoimmune conditions or thrombotic events.]0.88211
167gpt-3.5-turbono_synopsisHALLMARK_COMPLEMENT-1[Summary: Immune function, coagulation, and protein turnover pathways are enriched based on the list of human genes provided.\\nMechanism: These genes are involved in various biological pathways related to immune response, hemostasis, and regulation of protein turnover.\\n\\n\\nHypothesis: The enrichment of immune response and blood coagulation terms suggests that these genes may be involved in the inflammatory response and contribute to the maintenance of the immune system. The enrichment of protein turnover terms suggests that these genes may be involved in the regulation of protein stability and degradation, which could be important for cellular function and homeostasis. Overall, these genes likely play key roles in a variety of biological processes and pathways that are critical for normal physiological function in humans.][Summary: Immune system response and blood coagulation are the most statistically over-represented functions in the list of human genes provided.\\nMechanism: The genes in this list are mostly involved in regulating the immune response and blood coagulation pathways. \\n\\n]0.93563
168gpt-3.5-turbono_synopsisHALLMARK_DNA_REPAIR-0[Summary: DNA replication and repair, transcription, mRNA processing, and purine metabolism are over-represented in the set of human genes.\\nMechanism: These genes are mainly involved in maintaining genome integrity, providing the necessary machinery for DNA replication and repair, and regulating gene expression.\\n\\n][Summary: DNA replication and repair\\nMechanism: DNA replication and repair\\n]0.86240
169gpt-3.5-turbono_synopsisHALLMARK_DNA_REPAIR-1[Summary: RNA transcription and DNA repair are enriched functions among the given genes.\\nMechanism: These genes encode for proteins involved in DNA transcription and repair processes.\\n\\nHypothesis: The enriched functions suggest that these genes are involved in the regulation of RNA transcription and DNA repair processes. The RNA polymerase activity and DNA binding terms demonstrate their role in the initial transcription process, while the mRNA processing and DNA repair terms represent their involvement in the post-transcriptional regulation and repair of DNA damage, respectively. Overall, these genes likely play a crucial role in maintaining genetic stability and proper gene expression.][Summary: Genes in the list are involved in DNA replication, repair, and transcription.\\nMechanism: DNA maintenance\\n]0.89582
170gpt-3.5-turbono_synopsisHALLMARK_E2F_TARGETS-0[Summary: DNA replication and cell cycle regulation\\nMechanism: Genes are involved in DNA replication and mitotic cell cycle regulation\\n][Summary: DNA replication, cell division and chromosome segregation\\nMechanism: DNA replication and mitosis\\n\\nHypothesis: This list of genes is heavily enriched for genes involved in DNA replication, mitosis and chromosome segregation, suggesting that these are the major underlying biological mechanisms. Many of these genes are part of regulatory pathways that control these processes, such as the cell cycle and DNA damage response pathways. The enrichment of nucleosome assembly genes in this list suggests that this is a critical step in the DNA replication process, as nucleosomes must be efficiently assembled and disassembled to enable the progression of the replication fork. Additionally, genes involved in DNA repair are also enriched, indicating that these processes are tightly coordinated with DNA replication and mitosis to ensure genome stability.]0.91727
171gpt-3.5-turbono_synopsisHALLMARK_E2F_TARGETS-1[Summary: DNA replication and repair are enriched functions of the given genes.\\nMechanism: These genes are predominantly involved in the control and regulation of DNA replication and repair. Specific functions include DNA unwinding, strand break repair, DNA synthesis, and checkpoint signaling.\\n][Summary: DNA replication and repair, cell cycle regulation, and chromosome segregation are enriched terms among the given genes.\\nMechanism: These genes are involved in the regulation of DNA replication, repair mechanisms, proper chromosome segregation during mitosis, and inactivation of the cell cycle checkpoints.\\n]0.9322
172gpt-3.5-turbono_synopsisHALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0[Summary: Extracellular matrix (ECM) organization and regulation of cell signaling are significantly enriched functions for the given set of genes.\\nMechanism: The enriched terms suggest that these genes are involved in maintaining tissue integrity and regulating cellular activity in response to the extracellular environment.\\n\\n\\nHypothesis: The genes in this list are involved in maintaining tissue integrity and regulating cellular activity in response to the extracellular environment. The ECM is critical in regulating cell behavior and signaling, and therefore the ECM organization is necessary for cellular homeostasis. The enriched terms suggest that the set of genes play a role in cell adhesion and integrin-mediated signaling pathways, which are important][Summary: Extracellular matrix organization and regulation of growth factor signaling pathways\\nMechanism: The genes in this list are enriched for functions involved in extracellular matrix organization and regulation of signaling pathways for growth factors. These processes are critical for tissue development, maintenance, and repair.\\n\\n]0.93427
173gpt-3.5-turbono_synopsisHALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1[Summary: Extracellular matrix organization and cell adhesion.\\nMechanism: ECM remodeling and tissue development during embryogenesis, wound healing and cancer progression.\\n][Summary: Extracellular matrix organization and regulation of cell adhesion are enriched functions common among the listed genes.\\n\\nMechanism: The genes identified are involved in the maintenance of extracellular matrix homeostasis and cell adhesion. They are part of a complex network that controls the behavior and function of cells in various tissues.\\n\\n\\nHypothesis: The identified genes are involved in the regulation of a variety of cellular processes that are required for proper tissue development and homeostasis. Dysregulation of these genes may contribute to various pathological conditions, such as fibrosis, cancer, and developmental disorders.]0.89483
174gpt-3.5-turbono_synopsisHALLMARK_ESTROGEN_RESPONSE_EARLY-0[Summary: Transport and cellular metabolic processes are overrepresented in these genes.\\nMechanism: Many of these genes are involved in transport and metabolic processes of cells. These pathways play a crucial role in the functioning of cells.\\n][Summary: Calcium ion binding and metabolism\\nMechanism: Calcium ions modulate a wide range of biological processes, including intracellular signaling, protein function, and gene expression.\\n]0.8154
175gpt-3.5-turbono_synopsisHALLMARK_ESTROGEN_RESPONSE_EARLY-1[Summary: Genes are enriched for functions involved in lipid metabolism and transport, signal transduction, and transcriptional regulation.\\nMechanism: The over-representation of lipid metabolism and transport genes likely reflects the importance of efficient lipid processing and transport in cell growth and homeostasis. The signal transduction and transcriptional regulation pathways may be involved in modulating lipid metabolism and transport in response to changing cellular or environmental conditions.\\n][Summary: The common function among the provided genes is related to various cellular and biological processes such as metabolism, transport, signaling, and regulation.\\n\\nMechanism: No specific mechanism can be inferred without further analysis.\\n\\n]0.91263
176gpt-3.5-turbono_synopsisHALLMARK_ESTROGEN_RESPONSE_LATE-0[Summary: Genes are enriched in multiple biological processes and pathways.\\nMechanism: Multiple mechanisms and pathways are involved in the functions of these genes.\\n][Summary: Calcium ion binding and transport, regulation of cell division, and inhibition of apoptosis are enriched functions among the given genes.\\nMechanism: Calcium signaling and regulation of cellular processes through calcium ions.\\n]0.8370
177gpt-3.5-turbono_synopsisHALLMARK_ESTROGEN_RESPONSE_LATE-1[Summary: The enriched terms describe genes involved in various biological processes such as metabolism, signal transduction, development, and immune response.\\nMechanism: No specific mechanism was identified given the broad range of enriched terms.\\n][Summary: Cell cycle regulation and cancer-related functions are enriched in the gene set.\\nMechanism: The genes are mostly involved in regulating cell division and proliferation, with some genes also implicated in cancer progression.\\n]0.8415
178gpt-3.5-turbono_synopsisHALLMARK_FATTY_ACID_METABOLISM-0[Summary: Genes involved in metabolism and oxidative stress response are enriched.\\nMechanism: These genes are involved in the metabolism of lipids, amino acids, and carbohydrates, as well as in the detoxification of harmful substances and protection against oxidative stress.\\n\\n\\nHypothesis: These genes work together in maintaining cellular metabolism and homeostasis, including the production and utilization of energy, regulation of nutrient balance, and protection against external and internal stressors. This involves the breakdown and synthesis of biomolecules, generation of reducing equivalents for energy production, and removal of toxic compounds and reactive oxygen species. The enriched pathways suggest that these genes are involved in oxidative phosphorylation and other mitochondrial processes, lipid and glucose metabolism, and ion transport. Dysfunction of these genes may][Summary: Beta-oxidation of fatty acids, metabolic processes, and energy production pathways are enriched in the list of genes.\\n\\nMechanism: The list of genes is involved in the pathway of β-oxidation of fatty acids and energy production, promoting various metabolic processes.\\n\\n]0.90611
179gpt-3.5-turbono_synopsisHALLMARK_FATTY_ACID_METABOLISM-1[Summary: Genes are involved in lipid metabolism, energy production, and oxidative stress response.\\nMechanism: These genes function in pathways related to maintaining cellular homeostasis through the production and utilization of energy, the breakdown and metabolism of lipids, and the response to oxidative stress.\\n][Summary: These genes are involved in various metabolic processes, including lipid metabolism and energy production. \\nMechanism: The common underlying mechanism appears to be mitochondrial function and metabolism.\\n]0.94102
180gpt-3.5-turbono_synopsisHALLMARK_G2M_CHECKPOINT-0[Summary: Chromosomal segregation and cell cycle progression\\nMechanism: Regulation of the cell cycle and mitosis\\n\\nHypothesis: \\nThe enrichment of terms related to cell cycle progression and chromosomal segregation suggests that the genes on this list primarily play a role in regulating the progression of cells through the cell cycle and ensuring proper chromosome segregation during mitosis. These genes likely encode various proteins involved in DNA replication, mitotic spindle organization, microtubule cytoskeleton dynamics, and the regulation of cell cycle checkpoints, all of which are critical for the proper progression of cells through the cell cycle and the maintenance of genomic stability. The diverse range of gene functions represented on this list is likely indicative of the complex and tightly regulated nature of the cell cycle and mitotic processes.][Summary: Cell cycle regulation and chromosome segregation\\nMechanism: The genes are enriched for functions involved in cell cycle regulation, specifically in the G2/M phase transition and chromosome segregation.\\n\\n]0.93656
181gpt-3.5-turbono_synopsisHALLMARK_G2M_CHECKPOINT-1[Summary: DNA replication and cell cycle regulation.\\nMechanism: The genes enriched for this analysis are mainly involved in the regulation of DNA replication and cell cycle progression.\\n][Summary: Cell cycle regulation and DNA replication are enriched functions in the given list of genes.\\n\\nMechanism: The enriched functions of cell cycle regulation and DNA replication suggest that the genes in the list play a role in regulating the overall cell division process. Specifically, the genes are involved in DNA synthesis, repair, and proper chromosomal segregation, ensuring genomic stability and accurate transmission of genetic information.\\n\\n]0.95270
182gpt-3.5-turbono_synopsisHALLMARK_GLYCOLYSIS-0[Summary: Glycosylation and Metabolism\\nMechanism: Glycosylation is a common function enriched in these genes, and many are involved in metabolic pathways such as glycolysis and the pentose phosphate pathway.\\n\\n][Summary: Energy metabolism and glycosylation pathways are significantly enriched.\\nMechanism: These genes are involved in energy metabolism, specifically in glycolysis and glycogen biosynthesis pathways. Additionally, they are involved in glycosylation pathways, which play a role in post-translational modifications.\\n]0.95109
183gpt-3.5-turbono_synopsisHALLMARK_GLYCOLYSIS-1[Summary: Cellular metabolism and energy production\\nMechanism: Glycolysis and related pathways\\n][Summary: Genes are involved in cellular metabolism and signaling pathways.\\nMechanism: This set of genes appears to be involved in the regulation of metabolic pathways in cells and are involved in various signaling pathways affecting cellular functions.\\n]0.87159
184gpt-3.5-turbono_synopsisHALLMARK_HEDGEHOG_SIGNALING-0[Summary: Neuronal development and axon guidance-related terms are significantly enriched in the list of genes.\\nMechanism: Neuronal development and axon guidance.\\n\\nHypothesis: The genes in the list are involved in the development and guidance of neuronal cells. Several enriched terms denote processes that are crucial for the proper formation and function of the nervous system, such as neuron differentiation, axon guidance, and cell migration. This suggests that the identified genes play a role in the establishment and maintenance of neural connections. The common functional theme may be mediated by signaling pathways that regulate cell adhesion, migration, and proliferation, which are critical for neural development and the formation of axonal connections. The enriched terms suggest that the proteins encoded by these genes might be involved in the modulation of cytoskeletal dynamics, cell signaling, and adhesion processes that regulate neurite outgrowth and synapse formation. Some genes listed here have been shown to play a role in neurodevelopmental disorders such as autism and epilepsy.][Summary: Genes are enriched in terms related to nervous system development, signaling and angiogenesis.\\nMechanism: Signaling pathways related to neural development and angiogenesis.\\n\\nHypothesis: This set of genes is involved in the signaling pathways related to neural development and angiogenesis. The enriched terms, including nervous system development, neuron differentiation, embryonic morphogenesis, and regulation of angiogenesis, suggest that these genes are involved in complex processes related to neural network formation and elaboration, as well as vascular patterning and growth. Additionally, the genes in this list seem to be involved in positive regulation of signaling, which may play a role in the tight regulation of the complex developmental processes involved.]0.93323
185gpt-3.5-turbono_synopsisHALLMARK_HEDGEHOG_SIGNALING-1[Summary: Genes are primarily involved in nervous system development, signal transduction, and cell adhesion.\\nMechanism: Not specified.\\n][Summary: Genes are mainly involved in neural development and signaling pathways.\\nMechanism: Regulation of neural development and signaling pathways.\\n\\nHypothesis: The enriched terms suggest that these genes are involved in the development and maintenance of the nervous system. Many of the genes are associated with axon guidance and are involved in regulating the development of neuronal projections. The regulation of nervous system development and cell-cell signaling pathways may also play a role in coordinating the development of different types of neurons and neural circuits.]0.93448
186gpt-3.5-turbono_synopsisHALLMARK_HEME_METABOLISM-0[Summary: Transport, binding, and metabolism processes are enriched in these human genes.\\nMechanism: These genes are involved in various cellular pathways such as ion transport, protein binding, and metabolic processes.\\n\\n][Summary: Transport and binding process for heme and iron-sulfur clusters, as well as [2Fe-2S] clusters, are enriched among the listed genes.\\nMechanism: Iron-containing proteins involved in biological processes require a tightly regulated system of transport and binding, which is facilitated by these enriched gene functions.\\n\\n]0.89107
187gpt-3.5-turbono_synopsisHALLMARK_HEME_METABOLISM-1[Summary: Hemoglobin production and erythropoiesis are over-represented in the list of genes.\\nMechanism: Regulation of hemoglobin synthesis through erythropoietin signaling pathway.\\n\\n][Summary: This set of genes is enriched for terms related to gene expression regulation, metabolism, and transport.\\n\\n]0.8366
188gpt-3.5-turbono_synopsisHALLMARK_HYPOXIA-0[Summary: Cellular metabolism and response to stress-related stimuli are enriched in the gene list.\\nMechanism: Metabolic pathways and cellular stress response pathways may be dysregulated in diseases associated with these genes.\\n\\n][Summary: Cell metabolism, growth, and development are the most enriched functions among the given list of genes.\\nMechanism: These genes are predominantly associated with the regulation of glucose and energy homeostasis, cell proliferation, and extracellular matrix formation.\\n\\nHypothesis: The common biological mechanisms that underlie the functions of these genes involve the regulation of glucose and energy metabolism, which is essential for cell growth and development. They also regulate the formation of the extracellular matrix, which is crucial for the organization and maintenance of tissues and organs. These genes might be involved in signaling cascades that regulate cell proliferation, differentiation, and migration in response to changes in the microenvironment.]0.89549
189gpt-3.5-turbono_synopsisHALLMARK_HYPOXIA-1[Summary: Energy metabolism\\n\\nHypothesis: The genes listed display over-represented functions involved in energy metabolism, leading to the hypothesis that they may be involved in maintaining energy homeostasis in the body. The shared functions related to glucose uptake and metabolism may be regulated by a common pathway, such as the insulin signaling pathway, that coordinates the activity of these genes. Additionally, the functions related to ATP production may be affected by mitochondrial activity and oxidative phosphorylation. Further studies are needed to elucidate the exact mechanisms and pathways involved in the regulation of these genes.][Summary: Carbohydrate metabolism and glycolysis are statistically over-represented in the list of genes.\\nMechanism: The genes involved in carbohydrate metabolism and glycolysis play a key role in energy production and cell signaling.\\n]0.91417
190gpt-3.5-turbono_synopsisHALLMARK_IL2_STAT5_SIGNALING-0[Summary: Immune system and inflammation-related functions are enriched in this gene list.\\nMechanism: These genes may be involved in regulating the immune response and inflammatory processes.\\n\\n][Summary: Immune system functions are enriched in these genes, particularly those related to cytokine signaling, cell activation, and regulation.\\n\\nMechanism: The genes on this list are primarily involved in regulating the immune system. Many are involved in cytokine signaling, cell activation, and regulation. This suggests that the enriched terms are related to immune response and function.\\n\\n]0.93202
191gpt-3.5-turbono_synopsisHALLMARK_IL2_STAT5_SIGNALING-1[Summary: Signaling pathways related to immune response, cytokine signaling, and inflammation are enriched in the list of human genes.\\n\\nMechanism: These genes likely play a role in coordinating the immune system's response to pathogens or damage signals.\\n\\n][Summary: Cell signaling and immune response\\nMechanism: Pathways involving cytokines, chemokines, and growth factors\\n\\nHypothesis: The genes in the list are involved in cell signaling and immune response. They play critical roles in the regulation of immune cell function, inflammation, and chemotaxis. The enriched terms, including immune response, cytokine activity, and chemokine activity, suggest that the genes are involved in cytokine signaling pathways, which mediate cellular responses to pathogens and other external stimuli. The genes may also be involved in growth factor signaling, which regulates cell proliferation and differentiation during development and tissue repair. Overall, the genes in the list likely form a complex regulatory network that is essential for the proper functioning of the immune system.]0.94569
192gpt-3.5-turbono_synopsisHALLMARK_IL6_JAK_STAT3_SIGNALING-0[Summary: Immune response and cytokine signaling pathway are enriched functions among the listed human genes.\\nMechanism: These genes seem to be involved in regulation and activation of immune cells and cytokine signaling pathways.\\n\\nHypothesis: These genes are potentially involved in the immune response to infections and inflammation. They may also play a role in the regulation of cytokine production and signaling, which can influence the development and progression of inflammatory and autoimmune diseases.][Summary: Immune response and signaling\\nMechanism: Cytokine signaling and immune response activation \\n\\n]0.89408
193gpt-3.5-turbono_synopsisHALLMARK_IL6_JAK_STAT3_SIGNALING-1[Summary: Immune system response\\nMechanism: Cytokine signaling pathway\\n][Summary: Cytokine signaling and inflammation are the common functions enriched in these genes.\\nMechanism: These genes are involved in modulating the immune system's response to infection, injury, or stress.\\n\\nHypothesis: These genes are involved in regulating the inflammatory response through cytokine signaling. They are responsible for activating immune cells, triggering inflammation, and recruiting immune cells to sites of infection or injury. The JAK-STAT and Toll-like receptor signaling pathways play important roles in this process. Dysregulation of these genes can lead to chronic inflammation and autoimmune diseases.]0.87559
194gpt-3.5-turbono_synopsisHALLMARK_INFLAMMATORY_RESPONSE-0[Summary: Immune response and signal transduction\\nMechanism: Immune regulation and inflammation\\n][Summary: Immune response, inflammation, and cytokine signaling-related functionality is enriched in the given list of genes.\\nMechanism: These genes are involved in the activation, regulation, and resolution of immune response and inflammation.\\n]0.88149
195gpt-3.5-turbono_synopsisHALLMARK_INFLAMMATORY_RESPONSE-1[Summary: Immune response and inflammation processes.\\nMechanism: Signaling pathways involved in immune response and inflammation.\\n\\nHypothesis: The enriched terms suggest that the genes in the list may be involved in immune response and inflammation. Immune cells recruit cytokines and chemokines to elicit an immune response. The genes could be involved in signaling pathways that regulate leukocyte migration and inflammation. Additionally, they may play a role in mediating adaptive and innate immune responses.][Summary: These human genes are enriched in immune system-related functions.\\nMechanism: These genes are involved in immune response and immunoregulation pathways.\\n\\n]0.90350
196gpt-3.5-turbono_synopsisHALLMARK_INTERFERON_ALPHA_RESPONSE-0[Summary: Genes are involved in interferon signaling, immune response, and antiviral defense mechanisms.\\nMechanism: These genes are involved in the innate immune response to viral infection and defense against other pathogens.\\n\\nHypothesis: These genes are likely involved in the interferon signaling pathway, which triggers an innate immune response against viral infections and activates antiviral defense mechanisms. The enriched terms suggest that the genes are involved in various stages of the immune response, including detection of viral RNA and DNA (DDX60, DHX58, IFIH1, etc.), induction of interferon production (IRF7, IRF9, etc.), and downstream signaling and immune activation (STAT2, TRAFD1, TRIM25, etc.). Additionally, some genes (ISG15, MX1, OAS1, etc.) directly inhibit viral replication and promote viral clearance. Overall, these genes are critical for the body's defense against viral infections and likely interact with other immune response pathways to maintain homeostasis.][Summary: These genes are involved in the antiviral response and immune system regulation.\\nMechanism: These genes are part of the Type I interferon response pathway, which is activated by viral infection.\\n\\n]0.95790
197gpt-3.5-turbono_synopsisHALLMARK_INTERFERON_ALPHA_RESPONSE-1[Summary: Immune response and antiviral pathways are enriched functions in the given gene list.\\nMechanism: The genes are involved in various pathways that contribute to the antiviral defense mechanism of the human body.\\n\\n\\nHypothesis: The enriched terms suggest that the given genes function in the activation of innate and adaptive immune responses against viral infections through the interferon signaling pathway. The genes act as key regulators of viral replication and transcription, and contribute to the antiviral defense mechanism of the human body.][Summary: Genes associated with antiviral response, immune system processes, and interferon signaling pathways.\\n\\nMechanism: These genes are involved in the activation of the antiviral response and immune system processes, particularly through the interferon signaling pathway.\\n\\n]0.93279
198gpt-3.5-turbono_synopsisHALLMARK_INTERFERON_GAMMA_RESPONSE-0[Summary: This list of genes includes those involved in antiviral and immunological responses, as well as genes involved in regulating cellular processes such as cellular growth and metabolism. \\n\\nMechanism: These genes are involved in the immune response to viral infections and in regulating cellular processes such as growth and metabolism.\\n\\n\\nHypothesis: The enriched terms suggest that the common function of these genes is the regulation of antiviral and immunological responses in addition to the regulation of cellular processes such as metabolism and growth. It is likely that these genes work together to promote cellular immunity against viral infections and regulate cellular processes that support antiviral responses.][Summary: Type I interferon signaling pathway activation, immune response, antigen processing and presentation \\n\\n]0.83617
199gpt-3.5-turbono_synopsisHALLMARK_INTERFERON_GAMMA_RESPONSE-1[Summary: Immune response and antiviral pathways are enriched.\\n\\nMechanism: The genes in the list have a common function in response to viral infection through various pathways including interferon signaling, antigen processing and presentation, and immune cell activation.\\n\\n][Summary: Genes involved in immune response and inflammation are enriched.\\n\\nMechanism: These genes are all involved in the immune response and inflammation. They play a role in antigen processing and presentation, interferon response, cytokine production, and activation of inflammatory pathways.\\n\\n]0.9224
200gpt-3.5-turbono_synopsisHALLMARK_KRAS_SIGNALING_DN-0[Summary: Calcium ion binding and regulation of muscle contraction \\nMechanism: Calcium signaling \\n][Summary: Calcium ion binding and membrane transport are the most enriched functions in these genes.\\nMechanism: The majority of enriched terms are related to the transport of calcium ions across cell membranes, as well as regulation of intracellular calcium concentration.\\n\\n]0.86176
201gpt-3.5-turbono_synopsisHALLMARK_KRAS_SIGNALING_DN-1[Summary: This list of human genes is enriched for terms related to ion binding, signaling, and regulation of metabolic and cellular processes.\\nMechanism: These functions are likely involved in maintaining homeostasis and cell function through various signaling pathways.\\n\\n][Summary: Genes are enriched for terms related to ion transport, neurological signaling, and tissue development.\\n\\nHypothesis: These genes are potentially involved in regulating ion transport, such as calcium, sodium, and potassium, which are critical for neuronal signaling and tissue morphogenesis. Many of these genes are expressed in a variety of tissues and organs, including the brain, heart, and endocrine glands, suggesting they may have widespread physiological roles. The function of these genes may overlap in the regulation of cellular calcium balance, neural transmission, and developmental processes, which could contribute to human disease when disrupted.]0.92397
202gpt-3.5-turbono_synopsisHALLMARK_KRAS_SIGNALING_UP-0[Summary: Regulation of immune response and cell signaling \\nMechanism: Not enough information to make a hypothesis \\n][Summary: Regulation of immune response, cellular signaling, and angiogenesis.\\nMechanism: The enriched terms suggest that these genes are involved in the regulation of immune response and cellular signaling pathways, as well as angiogenesis.\\n]0.87126
203gpt-3.5-turbono_synopsisHALLMARK_KRAS_SIGNALING_UP-1[Summary: Immune response and inflammation-related functions are enriched in the list of genes.\\nMechanism: The genes are involved in regulating the immune system and its response to pathogens, as well as controlling inflammation pathways.\\n\\n\\nHypothesis: The enriched functions suggest that the genes play a role in regulating the immune system response to pathogens and inflammation. The genes may be involved in controlling signaling pathways for cytokines, chemokines, and interleukins, as well as regulating leukocyte activation and complement activation. Additionally, the genes may be involved in eicosanoid synthesis pathways and platelet activation and aggregation. Overall, the enrichment of these functions suggests that the genes play a role in immune system surveillance and response to infections and other stimuli.][Summary: Immune response and inflammation, coagulation, cell adhesion, and signal transduction are enriched functions among the genes.\\n\\n]0.93690
204gpt-3.5-turbono_synopsisHALLMARK_MITOTIC_SPINDLE-0[Summary: Genes are enriched for microtubule-based processes and cellular division.\\nMechanism: The genes listed are involved in microtubule-based processes and cellular division. The enriched terms highlight the specific aspects of these processes that these genes are involved in. \\n\\n][Summary: Cell division and cytoskeleton organization are the commonly enriched functions among the given genes.\\nMechanism: The enrichment of these terms suggests that these genes play an important role in regulating mitotic spindle formation and organization of actin filaments.\\n\\n]0.923
205gpt-3.5-turbono_synopsisHALLMARK_MITOTIC_SPINDLE-1[Summary: Microtubule formation and spindle assembly during cell division.\\nMechanism: The genes are involved in microtubule formation and spindle assembly during cell division. These genes are related to the structural integrity and mediator of spindle formation and the cleavage furrow during cytokinesis.\\n][Summary: Mitotic spindle organization and chromosome segregation\\nMechanism: Mitotic spindle assembly checkpoint\\n\\nHypothesis: The enrichment of terms related to the mitotic spindle organization, chromosome segregation, and spindle assembly checkpoint suggests that these genes play a critical role in mitosis and cell division. These genes likely regulate microtubule dynamics, centrosome function, and kinetochore-microtubule interactions to ensure the proper alignment, segregation, and separation of chromosomes during mitosis. Dysfunction of these genes may lead to chromosomal instability, aneuploidy, and tumorigenesis.]0.90319
206gpt-3.5-turbono_synopsisHALLMARK_MTORC1_SIGNALING-0[Summary: The enriched terms shared among these genes are related to protein folding, metabolism, and immune response pathways.\\n\\nMechanism: These genes appear to share a connection through signaling pathways that regulate protein folding, metabolism, and immune response.\\n\\n][Summary: Cellular metabolism\\n]0.81243
207gpt-3.5-turbono_synopsisHALLMARK_MTORC1_SIGNALING-1[Summary: Genes identified have functions predominantly involved in cellular metabolism and protein handling, including regulation of transcription and translation. There is also enrichment in genes associated with response to stress and DNA repair.\\n\\n\\nHypothesis: The identified genes are likely involved in cellular processes that are essential for growth and survival, including the maintenance of cellular metabolism, response to stress, and DNA repair. Dysregulation of these pathways may lead to disease states such as cancer or neurodegeneration. Further analysis and studies of these genes and their pathways could inform novel therapies for these conditions.][Summary: Protein folding and metabolism are enriched functions among these human genes.\\nMechanism: These genes may play a key role in maintaining protein homeostasis and regulating metabolic pathways.\\n]0.90465
208gpt-3.5-turbono_synopsisHALLMARK_MYC_TARGETS_V1-0[Summary: Genes associated with protein synthesis, processing, and folding are overrepresented in the list.\\n\\nHypothesis: These genes work together in a network to facilitate protein synthesis, processing, and folding. They may also play a role in RNA splicing through their association with the U4/U6.U5 tri-snRNP complex. Dysfunction of this network may lead to disrupted protein synthesis and processing, resulting in diseases such as neurodegeneration and cancer.][Summary: RNA processing and translation initiation\\nMechanism: Regulation of ribosome assembly and function\\n]0.84359
209gpt-3.5-turbono_synopsisHALLMARK_MYC_TARGETS_V1-1[Summary: RNA processing and translation \\nMechanism: The enriched terms suggest that the genes are involved in various aspects of RNA processing and translation.\\n\\n][Summary: RNA processing and translation are enriched functions in the given gene list.\\nMechanism: The genes are involved in regulating RNA processing and translation, necessary for cellular growth and proliferation.\\n\\n]0.9455
210gpt-3.5-turbono_synopsisHALLMARK_MYC_TARGETS_V2-0[Summary: RNA processing and ribosome biogenesis\\nMechanism: These genes are involved in RNA processing and ribosome biogenesis, specifically in various stages of transcription, modifying RNA, ribosomal assembly, and transport.\\n][Summary: The common function among the genes is related to RNA processing and ribosome biogenesis. \\nMechanism: The genes are involved in various steps of transcription, splicing, and translation of RNA.\\n\\nHypothesis: The enriched terms suggest that the genes are primarily involved in the regulation of ribosome biogenesis and RNA processing. This may be due to their role in the maintenance of cellular homeostasis by controlling protein synthesis and turnover. Dysfunction of these genes may lead to defects in ribosome biogenesis, causing impaired protein synthesis and contributing to various diseases, including cancer and neurodegenerative disorders.]0.93430
211gpt-3.5-turbono_synopsisHALLMARK_MYC_TARGETS_V2-1[Summary: The common function of the genes is related to RNA processing and transcription regulation. \\nMechanism: The genes are involved in regulating different steps in the transcription and processing of RNA. \\n\\nHypothesis: The genes in this list are all involved in different aspects of RNA processing and transcription regulation. These processes are essential for the production of functional RNAs, which are required for gene expression and cellular communication. It is likely that the proteins encoded by these genes interact with each other and with other factors to form complexes that facilitate RNA processing and transcription. Dysfunction of these processes has been associated with a range of human diseases, including cancer and developmental disorders.][Summary: Genes in the list are functionally enriched in processes related to ribosome biogenesis and RNA metabolism.\\nMechanism: The genes in the list are all involved in the formation and functioning of ribosomes, which are essential cellular machinery for protein synthesis. They are also involved in RNA metabolism, which includes transcription, splicing, ribonucleoprotein assembly, and RNA transport.\\n\\n]0.91362
212gpt-3.5-turbono_synopsisHALLMARK_MYOGENESIS-0[Summary: Muscle structure and function, including contraction and calcium handling, are enriched functions among the listed genes.\\nMechanism: Muscle contraction and calcium handling.\\n\\nHypothesis: The enriched genes are largely involved in the structure and function of skeletal and cardiac muscle tissue, contributing to processes such as contraction and calcium handling. The Z-disc, sarcomere, and thin filaments are important structural components of muscle, and genes involved in their assembly and maintenance are among the enriched terms. Calcium ion transport is also an important function in muscle cells, and genes involved in this process, as well as those involved in the assembly and regulation of the troponin-tropomyosin complex that regulates calcium-dependent muscle contraction, are also enriched.][Summary: Muscle contraction and development\\n\\nHypothesis: The significant enrichment of genes involved in muscle contraction and sarcomere development suggests that there may be shared pathways and mechanisms governing these processes. One potential pathway may involve the regulation of actin and myosin filaments, which are crucial components of the sarcomere and fundamental to muscle contraction. Another potential pathway may involve the coordination of signaling cascades that promote muscle growth and differentiation. Further research in these areas could lead to a better understanding of muscle function and the treatment of muscle-related diseases.]0.90156
213gpt-3.5-turbono_synopsisHALLMARK_MYOGENESIS-1[Summary: Muscle structure and function\\nMechanism: Muscle contraction and maintenance\\n\\nHypothesis: These genes are mainly involved in muscle structure and function. They function in muscle contraction and maintenance through various mechanisms, including regulation of muscle filaments, myosin activity, and actin dynamics. The statistically over-represented terms are related to muscle structure and function, such as muscle, myosin, actin, troponin, and filament. These genes likely interact to control muscle contraction and maintenance, and may be involved in various muscle disorders and diseases.][Summary: Muscle structure and contraction.\\nMechanism: Actin-myosin interaction and sarcomere formation.\\n]0.88498
214gpt-3.5-turbono_synopsisHALLMARK_NOTCH_SIGNALING-0[Summary: Genes are enriched for functions involved in Notch signaling and Wnt signaling pathways.\\nMechanism: Notch and Wnt signaling pathways are major signaling pathways that regulate cell fate determination and differentiation during development.\\n\\n][Summary: Genes are primarily involved in Notch pathway signaling and Wnt pathway signaling.\\nMechanism: The Notch pathway and Wnt pathway signaling are two important mechanisms for cell signaling and development.\\n\\nHypothesis: The genes listed are involved in regulating cell signaling and differentiation pathways such as the Notch and Wnt pathways. These pathways are responsible for the development of various tissues and organs in the body. Dysregulation of these genes and pathways can lead to developmental abnormalities and diseases.]0.96289
215gpt-3.5-turbono_synopsisHALLMARK_NOTCH_SIGNALING-1[Summary: These genes are involved in the Notch signaling pathway and cell proliferation regulation.\\nMechanism: The Notch signaling pathway is involved in cell fate specification and differentiation during development and in adult tissues.\\n][Summary: Genes are mostly involved in the development and regulation of the Notch signaling pathway.\\nMechanism: The Notch signaling pathway is involved in cell-to-cell communication, controlling cell fate decisions and differentiation during development.\\n]0.9516
216gpt-3.5-turbono_synopsisHALLMARK_OXIDATIVE_PHOSPHORYLATION-0[Summary: Mitochondrial respiration\\n\\nHypothesis: Dysregulation of these genes may result in impaired mitochondrial function, decreased ATP production, and cellular metabolic dysfunction, leading to a variety of diseases including neurodegenerative disorders and metabolic disorders.][Summary: Mitochondrial function and energy production pathways are enriched in the list of genes.\\n\\nMechanism: The genes in the list are involved in various aspects of mitochondrial oxidative phosphorylation and energy production pathways.\\n\\n]0.8842
217gpt-3.5-turbono_synopsisHALLMARK_OXIDATIVE_PHOSPHORYLATION-1[Summary: These genes are involved in mitochondrial function and energy metabolism.\\nMechanism: Mitochondrial electron transport chain and oxidative phosphorylation.\\n\\n][Summary: Mitochondrial respiratory chain function\\nMechanism: Oxidative Phosphorylation\\n\\nHypothesis: These genes are primarily involved in mitochondrial respiratory chain function, specifically in oxidative phosphorylation through NADH dehydrogenase activity and electron transport chain. They contribute to the assembly of respiratory chain complexes I, II, III, IV, V, VI, which are located in the mitochondrial inner membrane. Additionally, these genes are involved in the organization and biogenesis of mitochondria, as well as in ubiquinone and fatty acid metabolism. Mutations in these genes can cause various mitochondrial disorders affecting energy production and cell function.]0.94521
218gpt-3.5-turbono_synopsisHALLMARK_P53_PATHWAY-0[Summary: DNA damage response and cell cycle regulation pathways are enriched among the listed genes.\\nMechanism: The genes are involved in processes that regulate cell growth and proliferation, as well as response to DNA damage.\\n][Summary: Regulation of cell cycle and cell death. \\n\\nHypothesis: The enriched terms suggest that these genes play a crucial role in normal cellular processes, and their dysregulation may result in abnormal growth and proliferation of cells. The underlying biological mechanism may involve activation of DNA damage response pathways and regulation of the p53 tumor suppressor protein, leading to cell cycle arrest and apoptosis.]0.92199
219gpt-3.5-turbono_synopsisHALLMARK_P53_PATHWAY-1[Summary: Cell cycle regulation and DNA damage response.\\nMechanism: Transcriptional regulation and DNA repair.\\n\\nHypothesis: \\nThe list of genes is enriched for functions related to cell cycle regulation and DNA damage response. Many of these genes are involved in processes such as cell cycle arrest, DNA repair, and transcriptional regulation, indicating a potential role in maintaining genome stability. Some of these genes, such as TP53, are known to play a central role in the DNA damage response and are involved in regulating the expression of genes involved in DNA repair and cell cycle arrest. Other enriched terms, such as the G1/S transition of mitotic cell cycle, suggest that these genes may also play a role in controlling the progression of the cell cycle and cell proliferation. Overall, the enrichment of these functions suggests that the genes in this list are involved in maintaining genomic integrity and proper cell cycle progression.][Summary: DNA damage response and cell cycle regulation\\nMechanism: Activation of p53 pathway and downstream effector genes\\n]0.89830
220gpt-3.5-turbono_synopsisHALLMARK_PANCREAS_BETA_CELLS-0[Summary: Genes involved in pancreatic beta cell development and function\\nMechanism: Beta cell differentiation and insulin secretion\\n][Summary: These genes are associated with pancreatic beta cell development and function.\\nMechanism: Beta cell development and function\\n\\nHypothesis: These genes are involved in the development and function of pancreatic beta cells, which produce and secrete insulin and play a critical role in glucose homeostasis. The enriched terms suggest that these genes are important for the differentiation, development, and function of pancreatic beta cells as well as overall pancreatic islet cell development. This suggests that disruptions in these genes could lead to impaired beta cell function and contribute to the development of diabetes.]0.94504
221gpt-3.5-turbono_synopsisHALLMARK_PANCREAS_BETA_CELLS-1[Summary: Genes are enriched for functions related to pancreatic beta cell development and insulin secretion.\\nMechanism: Beta cells in the pancreas produce and secrete insulin, and defects in this process can lead to diabetes.\\n][Summary: The genes in this list are enriched for terms related to pancreatic beta cell development and function.\\nMechanism: Pancreatic beta cells are responsible for insulin secretion, which regulates glucose levels in the body. Dysfunction of these cells can lead to diabetes.\\n]0.9652
222gpt-3.5-turbono_synopsisHALLMARK_PEROXISOME-0[Summary: Transport and metabolism of lipids, hormones, and xenobiotics are enriched gene functions.\\nMechanism: Lipid and xenobiotic metabolism pathways are activated.\\n\\nHypothesis: The enriched gene functions are consistent with the liver's role in detoxification and energy metabolism. These genes may play a role in maintaining liver homeostasis and responding to environmental toxins and hormonal changes.][Summary: Genes involved in lipid metabolism, transport, and signaling are significantly over-represented in this list.\\n\\nMechanism: Lipid metabolism and transport\\n\\n\\nHypothesis: The genes in this list are involved in the metabolism, transport, and signaling of lipids. ABC transporters are responsible for the transport of lipids across membranes. Fatty acid metabolism and cholesterol biosynthesis are crucial in lipid homeostasis. PPAR signaling pathway regulates the expression of genes involved in lipid metabolism. Peroxisomes play an important role in the breakdown of fatty acids.]0.90178
223gpt-3.5-turbono_synopsisHALLMARK_PEROXISOME-1[Summary: Enriched terms include fatty acid metabolism, bile acid transport, peroxisome organization, and DNA repair.\\nMechanism: These genes are involved in various metabolic pathways and cellular processes, including fatty acid metabolism, bile acid transport, peroxisome organization, and DNA repair.\\n\\n][Summary: Genes involved in lipid metabolism and transport are enriched.\\nMechanism: Lipid metabolism and transport pathways are affected by the genes in the list.\\n\\n]0.91140
224gpt-3.5-turbono_synopsisHALLMARK_PI3K_AKT_MTOR_SIGNALING-0[Summary: Signal transduction and regulation of cell cycle and apoptosis\\n\\nHypothesis: The listed genes are involved in different stages of signal transduction pathways that ultimately converge on either the MAPK cascade or PI3K-Akt signaling pathway, which regulate cellular proliferation, differentiation, and apoptosis. The genes identified under enriched term \"regulation of cell proliferation\" might work as positive or negative regulators of cell growth and death signals. Altered functions or dysregulation of these genes could lead to abnormal growth or development, contributing][Summary: Signaling and regulation\\n\\nHypothesis: These genes could be involved in regulating cellular responses to extracellular stimuli, including growth factors and cytokines. They could also play a role in tumor growth and progression.]0.91349
225gpt-3.5-turbono_synopsisHALLMARK_PI3K_AKT_MTOR_SIGNALING-1[Summary: Signaling pathways and cellular responses are enriched in these genes.\\nMechanism: The genes seem to be involved in multiple pathways and cellular responses.\\n][Summary: Signaling and metabolism pathways are significantly enriched among the given genes.\\n\\nMechanism: These genes are involved in cellular signaling pathways, including the MAPK and PI3K pathways, which play a role in cell growth, proliferation, and survival. Many of the genes are also involved in metabolic processes, such as glucose metabolism.\\n\\n]0.93186
226gpt-3.5-turbono_synopsisHALLMARK_PROTEIN_SECRETION-0[Summary: Membrane trafficking and vesicle transport\\nMechanism: The genes in this list are all involved in various processes of membrane trafficking and vesicle transport.\\n][Summary: Vesicular trafficking and membrane transport are enriched functions in the given list of genes.\\nMechanism: Membrane transport and trafficking between various cellular compartments, such as the endoplasmic reticulum (ER), Golgi, lysosome, and plasma membrane, involve the trafficking of cargoes in vesicles. The formation, budding, tethering, and fusion of these vesicles are tightly regulated by various membrane-bound proteins and adaptors. \\n\\n]0.94282
227gpt-3.5-turbono_synopsisHALLMARK_PROTEIN_SECRETION-1[Summary: Membrane transport and vesicle-mediated transport\\nMechanism: Membrane trafficking and vesicle formation and fusion\\n\\nHypothesis: The enrichment of terms related to membrane transport and vesicle-mediated transport suggests that the genes on this list are involved in the processes of vesicle formation, membrane trafficking, and vesicle fusion. Multiple genes on this list are involved in the transport of proteins to the Golgi, endosomes, and lysosomes, suggesting a potential role in intracellular protein transport and protein sorting. Additionally, the enrichment of terms related to ion transport and regulation of membrane potential may indicate a role in cellular signaling or homeostasis. Overall, these genes are likely involved in various aspects of membrane trafficking and vesicle-mediated transport within the cell.][Summary: Transport and trafficking of proteins and molecules within cells.\\nMechanism: These genes play a role in vesicular transport, protein sorting, and trafficking within the cell. The enriched terms provide insight into the specific pathways and compartments involved in this process.\\n\\n\\nHypothesis: These genes are involved in the coordinated transport of proteins and molecules between different intracellular compartments, such as the endoplasmic reticulum, Golgi apparatus, and lysosomes. They likely form part of a complex network of regulatory pathways ensuring the efficient and accurate sorting of cargo to their appropriate destinations. The enrichment of terms related to clathrin-mediated endocytosis suggests that this process is also important in regulating protein trafficking within the cell.]0.9526
228gpt-3.5-turbono_synopsisHALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0[Summary: Genes are involved in oxidative stress response and redox regulation.\\nMechanism: Gene products involved in antioxidant response and maintenance of redox balance.\\n\\nHypothesis: The majority of the genes in the list are involved in the response to oxidative stress. They act through different but interconnected mechanisms to maintain redox balance in cells. These include direct antioxidant activity, such as the scavenging of reactive oxygen species (ROS), and the regulation of antioxidant enzyme activity and cellular levels of ROS. The results of the enrichment test suggest that these processes are statistically over-represented in the list of genes. Specifically, the list is enriched with genes involved in peroxiredoxin activity, catalysing the reduction of H2O2 and other ROS. Additionally, genes involved in glutathione metabolism, which provides an important reducing environment in cells, are also enriched. Overall, these genes act in concert to maintain cellular redox balance and protect against oxidative damage.][Summary: Genes involved in antioxidant defense and redox regulation are enriched.\\n\\nMechanism: Antioxidant defense and redox regulation are essential for maintaining cellular homeostasis and preventing oxidative stress-induced damage.\\n\\n\\nHypothesis: These genes likely play important roles in maintaining proper cellular redox balance, which is critical for preventing oxidative damage to cellular components such as DNA, proteins, and lipids. Additionally, they may contribute to the detoxification of harmful reactive oxygen species produced during normal cellular metabolism or in response to various stressors such as environmental toxins and pathogens.]0.96381
229gpt-3.5-turbono_synopsisHALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1[Summary: Redox regulation \\nMechanism: The genes in this list are involved in maintaining redox homeostasis through processes such as antioxidant defense, regulation of protein function through thiol-based modifications, iron regulation, and DNA repair.\\n\\n][Summary: Oxidative stress response and redox regulation\\nMechanism: These genes are involved in regulation of redox balance and response to oxidative stress.\\n]0.9297
230gpt-3.5-turbono_synopsisHALLMARK_SPERMATOGENESIS-0[Summary: Enrichment analysis identified terms related to spermatogenesis and meiosis as over-represented in the list of genes.\\n\\nMechanism: The identified genes are likely involved in the regulation of various processes related to spermatogenesis and meiosis, including DNA replication, chromosome segregation, and cell division.\\n\\n][Summary: Enriched terms suggest that the listed genes may function primarily in the process of spermatogenesis and meiosis.\\nMechanism: Spermatogenesis and meiosis.\\n\\nHypothesis: The enriched terms suggest that these genes function primarily in the process of spermatogenesis and meiosis. These genes may play roles in meiotic recombination, chromosome segregation, and overall gamete formation. Many of the genes are involved in regulating cell division, which is necessary for proper gamete formation. Additionally, some genes are involved in regulating hormone secretion, which is important for the development and maturation of male reproductive organs.]0.95326
231gpt-3.5-turbono_synopsisHALLMARK_SPERMATOGENESIS-1[Summary: Genes are enriched for regulation of mitotic cell cycle processes.\\nMechanism: The genes are involved in the regulation of mitosis and cell cycle.\\n][Summary: Cell cycle regulation and chromosome organization \\nMechanism: Mitotic checkpoint and spindle assembly \\n\\nHypothesis: The enrichment of terms related to mitotic spindle organization and chromosome segregation suggests that these genes may play a role in regulating the cell cycle. Specifically, many of these genes are involved in mitotic checkpoint signaling pathways that help ensure proper chromosome alignment and segregation during cell division. Additionally, some of these genes may play a role in organizing the microtubules and proteins that make up the mitotic spindle. Overall, these genes likely play critical roles in maintaining genomic stability and preventing the development of cancer and other genetic diseases.]0.91582
232gpt-3.5-turbono_synopsisHALLMARK_TGF_BETA_SIGNALING-0[Summary: Genes are involved in TGF-beta signaling pathway\\nMechanism: TGF-beta signaling pathway\\n\\nHypothesis: The enriched terms suggest that the genes are involved in the TGF-beta signaling pathway, as well as the regulation of BMP signaling pathway. TGF-beta signaling pathway plays a crucial role in cell growth, differentiation, and apoptosis. The interaction between TGF-beta and BMP signaling pathways has a significant influence on organ development and tissue regeneration. These genes may regulate cellular responses to growth factors and transcription, which are the downstream processes of the TGF-beta signaling pathway.][Summary: Genes are involved in the TGF-beta signaling pathway.\\nMechanism: The TGF-beta signaling pathway plays a key role in cell growth, differentiation, and development.\\n]0.95460
233gpt-3.5-turbono_synopsisHALLMARK_TGF_BETA_SIGNALING-1[Summary: The genes are enriched in terms related to transforming growth factor-beta (TGF-beta) signaling pathway and extracellular matrix (ECM) regulation.\\nMechanism: TGF-beta signaling pathway and ECM regulation.\\n\\n][Summary: Genes associated with regulation of transforming growth factor-beta (TGF-beta) signaling pathway.\\nMechanism: TGF-beta signaling pathway regulation\\n\\n]0.9358
234gpt-3.5-turbono_synopsisHALLMARK_TNFA_SIGNALING_VIA_NFKB-0[Summary: Genes involved in inflammation and immune response are enriched.\\nMechanism: These genes are likely involved in regulating the inflammatory response and immune system signaling.\\n\\n][Summary: Immune response and inflammation-related gene functions are statistically over-represented in this list of genes.\\nMechanism: These genes are involved in the regulation of immune response and inflammation pathways.\\n\\n]0.9337
235gpt-3.5-turbono_synopsisHALLMARK_TNFA_SIGNALING_VIA_NFKB-1[Summary: Genes involved in immune response and inflammation pathways are enriched, specifically those related to cytokine signaling, transcription factor regulation, and stress response.\\nMechanism: These genes likely play a role in regulating the immune response and inflammation in various tissues, as well as responding to cellular stress.\\n][Summary: Immune response and inflammation-related gene functions are enriched in the given list of genes.\\n\\nHypothesis: The enriched terms suggest that these genes play an important role in regulating the immune system response and controlling inflammation. This includes controlling cytokine and TNF production, which are important factors in regulating inflammation. The negative regulation of the NF-kappaB transcription factor activity may play a role in preventing inflammation and maintaining immune system homeostasis. These findings may have implications for understanding a range of inflammatory conditions and immune system disorders.]0.93302
236gpt-3.5-turbono_synopsisHALLMARK_UNFOLDED_PROTEIN_RESPONSE-0[Summary: Protein folding and degradation pathways are enriched.\\nMechanism: The genes are involved in regulation of protein synthesis and processing, particularly related to endoplasmic reticulum-associated degradation (ERAD) and the unfolded protein response (UPR).\\n][Summary: The genes in the list are enriched for functions related to protein folding and sorting, as well as response to stress and cellular damage. \\n\\nMechanism: The enriched terms suggest that these genes are involved in regulating protein quality control in the cell, ensuring that misfolded or damaged proteins are properly degraded or refolded.\\n\\n\\nHypothesis: The genes in this list are enriched for functions related to the quality control of cellular proteins, ensuring that only properly folded and functional proteins are allowed to move through the various stages of processing and trafficking. This involves a highly coordinated series of regulatory and surveillance pathways, including chaperone-mediated folding, ubiquitin-mediated proteolysis, and mRNA processing and splicing. Dysfunction in any one of these pathways can result in accumulation of misfolded proteins, leading to cellular damage and disease.]0.91655
237gpt-3.5-turbono_synopsisHALLMARK_UNFOLDED_PROTEIN_RESPONSE-1[Summary: The enriched terms for these genes relate to protein processing and regulation, RNA metabolism, and stress response.\\nMechanism: These genes are involved in the regulation of protein synthesis and folding, as well as RNA metabolism, which could contribute to cellular stress response and adaptation.\\n\\n][Summary: Genes enriched in protein folding-related functions \\n\\nMechanism: These genes are involved in regulation of protein homeostasis, such as protein folding, chaperone-mediated protein processing, and protein transport.\\n\\n]0.9184
238gpt-3.5-turbono_synopsisHALLMARK_UV_RESPONSE_DN-0[Summary: Genes in this list are mostly involved in signal transduction, cell adhesion, and extracellular matrix organization, with a significant enrichment in the TGF-beta signaling pathway.\\nMechanism: TGF-beta signaling pathway plays a significant role in regulating various cellular processes, including cell proliferation, differentiation, and apoptosis.\\n\\n][Summary: Regulation of gene expression and signal transduction\\nMechanism: Kinase signaling pathways and transcription regulation\\n\\n\\nHypothesis: The genes in this list are involved in regulating gene expression and signal transduction. Many of these genes are involved in kinase signaling pathways and transcription regulation, which are essential for proper cellular growth and differentiation. This suggests that the underlying biological mechanisms may involve a complex interplay between various signaling pathways governing gene expression and cellular processes. Additionally, many of these genes are involved in regulation of protein phosphorylation and intracellular transport, suggesting that they play important roles in cellular communication and the regulation of downstream signaling events.]0.89444
239gpt-3.5-turbono_synopsisHALLMARK_UV_RESPONSE_DN-1[Summary: Extracellular matrix and cytoskeletal organization\\nMechanism: Cell adhesion and migration \\n\\n\\nHypothesis: The enriched terms suggest that these genes play roles in extracellular matrix and cytoskeletal organization for cellular adhesion and migration. They are likely involved in pathways that regulate cytoskeletal dynamics and cell adhesion to the extracellular matrix through integrin signaling, as well as the regulation of migratory behavior in various cell types.][Summary: Genes are involved in extracellular matrix organization, signal transduction, and neural development.\\nMechanism: Regulation of cell signaling pathways.\\n\\n\\nHypothesis: These genes are involved in regulating cell signaling pathways and controlling neural development by modulating extracellular matrix organization. The enriched terms suggest that these genes are involved in growth factor activity and neurogenesis, indicating that they play a critical role in regulating cell proliferation and differentiation during neural development. Dysfunction of these genes could lead to abnormalities in neural development and function, possibly leading to neurological disorders.]0.92202
240gpt-3.5-turbono_synopsisHALLMARK_UV_RESPONSE_UP-0[Summary: Genes are involved in regulation of transcription, cellular metabolism, and signaling pathways.\\nMechanism: Biological pathways involved in gene regulation, metabolic pathways, and signaling pathways.\\n\\nHypothesis: The enriched terms suggest that these genes are involved in the regulation of transcription, cellular metabolism, and signaling pathways. These pathways are involved in the regulation of gene expression, cellular homeostasis, and response to external stimuli. The mechanism involves complex networks of interactions between proteins and other molecules that mediate these pathways.][Summary: The common function of the genes in the list is related to regulation of cellular processes and response to stimuli.\\n\\nMechanism: The genes in the list are involved in cellular processes such as metabolism, transport, and signaling. They also play a role in response to stimuli such as stress, inflammation, and DNA damage.\\n\\n]0.90271
241gpt-3.5-turbono_synopsisHALLMARK_UV_RESPONSE_UP-1[Summary: Genes are involved in diverse biological processes, with some enrichment in immune response, cell cycle regulation, and protein localization.\\nMechanism: No specific mechanism could be elucidated, as the genes are involved in diverse functions.\\n][Summary: Gene Ontology (GO) term enrichment analysis was performed on a list of human genes to identify common functional themes.\\n\\nHypothesis: The enriched terms suggest that these genes are involved in cellular responses to different kinds of stressors. The mechanism may involve signal transduction pathways that lead to activation of transcription factors, changes in protein localization, and alterations in cell cycle progression and apoptosis in response to stress stimuli, such as DNA damage, oxidative stress, and hypoxia. These genes may also contribute to the maintenance of cellular homeostasis under conditions of stress.]0.88381
242gpt-3.5-turbono_synopsisHALLMARK_WNT_BETA_CATENIN_SIGNALING-0[Summary: The enriched terms suggest that these genes are involved in the regulation of cellular signaling pathways and gene expression, particularly the Wnt signaling pathway and the Notch signaling pathway.\\nMechanism: The Wnt and Notch signaling pathways are essential for embryonic development, tissue homeostasis, and cell fate determination in adult tissues. These pathways are tightly regulated and involve a complex network of ligands, receptors, and downstream effectors.\\n\\n][Summary: Genes involved in the Wnt signaling pathway and Notch signaling pathway\\nMechanism: Interaction between Wnt and Notch signaling pathways\\n]0.92335
243gpt-3.5-turbono_synopsisHALLMARK_WNT_BETA_CATENIN_SIGNALING-1[Summary: Regulation of Notch signaling pathway\\nMechanism: Notch pathway activation\\n\\nHypothesis: These genes are involved in the regulation of the Notch signaling pathway, which plays a critical role in cell fate commitment during development and tissue homeostasis. They are implicated in the activation, positive regulation, and negative regulation of the Notch pathway, suggesting a complex regulatory mechanism that ensures proper cell differentiation and tissue patterning. These genes may act on different levels of the pathway, including ligands, receptors, and downstream effectors, and may participate in multiple developmental processes, such as neurogenesis, angiogenesis, and epithelial-mesenchymal transition. Dysfunction of these genes may lead to developmental disorders and cancers, highlighting their importance as therapeutic targets.][Summary: Genes are involved in the Wnt signaling pathway and Notch signaling pathway.\\nMechanism: Signaling pathways\\n\\nHypothesis: The enrichment of Wnt and Notch signaling pathways and protein and transcription factor binding suggests that these genes function in regulating gene expression and cell proliferation during development and homeostasis. Specifically, Wnt pathway plays essential roles during embryonic development, tissue homeostasis, and wound healing. The Notch pathway has a crucial role in cellular differentiation, proliferation, and apoptosis. Protein and transcription factor binding may regulate Wnt and Notch signaling or downstream gene expression changes.]0.94173
244gpt-3.5-turbono_synopsisT cell proliferation-0[Summary: Immune response regulation \\nMechanism: Regulation of T cell receptor signaling\\n][Summary: Immune system regulation and response is over-represented in these genes.\\nMechanism: These genes function in the activation and regulation of immune cells and signaling pathways.\\n\\n]0.89101
245gpt-3.5-turbono_synopsisT cell proliferation-1[Summary: Genes are enriched in immune system and cell signaling functions.\\nMechanism: These genes are involved in a variety of processes, including immune system regulation and various signaling pathways.\\n][Summary: Immune system function\\n\\nHypothesis: These genes may be involved in the overall function of the immune system, particularly in the regulation and activation of T cells in response to pathogens or cancer cells. They may also play a role in autoimmune disorders, in which the immune system mistakenly targets and attacks the body's own cells. Further research into the specific mechanisms of these genes in immune function could lead to better treatment and prevention strategies for immune-related disorders.]0.92311
246gpt-3.5-turbono_synopsisYamanaka-TFs-0[Summary: The common function shared by POU5F1, SOX2, KLF4, and MYC is transcriptional regulation and cell differentiation.\\nMechanism: The genes are involved in maintaining pluripotency and promoting cell proliferation and differentiation in embryonic and somatic cells.\\n\\nHypothesis: These genes play a crucial role in regulating pluripotency and inducing distinct cell types during embryonic development. They may act through various pathways, such as the NANOG, WNT, and BMP pathways, to promote stem cell maintenance and differentiation. Dysregulation of these genes may lead to developmental disorders or cancer.][Summary: Genes POU5F1, SOX2, KLF4, and MYC are all involved in regulating gene expression and cellular growth, with a focus on stem cells.\\nMechanism: These genes are part of the transcriptional regulatory network that controls stem cell self-renewal, proliferation, and differentiation.\\n\\nHypothesis: The enriched terms suggest that these genes are involved in the regulation of transcriptional activity by binding directly to DNA and controlling the expression of genes involved in stem cell differentiation. The transcriptional regulatory network formed by these genes may play a role in maintaining the balance between self-renewal and differentiation of stem cells, which is critical for tissue repair and regeneration.]0.95107
247gpt-3.5-turbono_synopsisYamanaka-TFs-1[Summary: These three genes are involved in the regulation of pluripotency and differentiation in stem cells. \\nMechanism: Together, KLF4, POU5F1, and SOX2 activate the expression of genes that maintain stem cell identity and prevent differentiation, while also repressing genes that promote differentiation. \\n\\nHypothesis: The mechanism involving these genes is likely to be part of a larger regulatory network, involving other transcription factors and signaling pathways, that is necessary for the proper development and maintenance of stem cells in various tissues and organs. These genes may also play a role in cancer progression, by promoting or suppressing the self-renewal and differentiation of cancer stem cells.][Summary: These genes are all involved in transcriptional regulation and have been identified as key players in the maintenance of pluripotency and self-renewal in stem cells.\\nMechanism: Transcriptional regulation\\n\\nHypothesis: These genes play a crucial role in the regulation of stem cell differentiation by maintaining the pluripotency and self-renewal capacity of stem cells through their transcriptional regulation. The enriched terms suggest that these genes have a specific role in regulating stem cell differentiation and fate determination.]0.94173
248gpt-3.5-turbono_synopsisamigo-example-0[Summary: Extracellular matrix organization and angiogenesis are over-represented functions among the listed human genes.\\nMechanism: The identified genes are involved in the regulation of extracellular matrix composition and organization, as well as angiogenesis which suggests a potential role in developmental processes.\\n\\n][Summary: Extracellular matrix organization and angiogenesis\\nMechanism: Signaling pathways through FGFR1 and integrin ITGAV\\n]0.89200
249gpt-3.5-turbono_synopsisamigo-example-1[Summary: Genes are enriched in extracellular matrix organization and regulation of cell adhesion.\\nMechanism: Extracellular matrix remodeling \\n\\nHypothesis: The enrichment of terms related to extracellular matrix organization and regulation of cell adhesion suggests that these genes play a role in extracellular matrix remodeling, which is important for cellular activities such as migration and proliferation. The extracellular matrix can influence cell behavior by providing mechanical support and signaling cues, and regulating cell adhesion is crucial for the maintenance of tissue integrity and embryonic development. Dysfunction of these processes has been implicated in several diseases, including cancer, cardiovascular disorders, and developmental abnormalities.][Summary: Several of the genes are involved in extracellular matrix organization, cell adhesion, and angiogenesis.\\nMechanism: Extracellular matrix (ECM) organization and remodeling, cell adhesion, and angiogenesis are essential processes in tissue development, maintenance, and repair. Dysregulation of these processes can lead to pathological conditions such as cancer and fibrosis.\\n\\n\\nHypothesis: These genes are likely involved in a common biological pathway that regulates ECM organization, cell adhesion, and angiogenesis. One possible mechanism is the activation of MAPK signaling, which plays a central role in cell migration, proliferation, and survival, and is often dysregulated in cancer and other diseases. Further studies are needed to elucidate the precise biological mechanisms underlying these enriched terms.]0.9553
250gpt-3.5-turbono_synopsisbicluster_RNAseqDB_0-0[Summary: The common function among the listed genes is related to nervous system development and signal transduction, with enrichment in terms related to calcium ion binding, synapse organization, and transcriptional regulation.\\n\\nMechanism: These genes may be involved in regulating signal transduction pathways in the nervous system, particularly related to calcium signaling and synapse formation and function. They may also play a role in transcriptional regulation during nervous system development.\\n\\n][Summary: Genes are enriched in terms related to neuronal development and signaling, transcriptional regulation, and ion transport.\\nMechanism: These genes are likely involved in a variety of biological mechanisms, including brain development, synaptic transmission, and the regulation of gene expression.\\n\\n]0.93200
251gpt-3.5-turbono_synopsisbicluster_RNAseqDB_0-1[Summary: Several genes are involved in signal transduction, cellular communication, and regulation of gene expression.\\n\\nMechanism: The enriched terms suggest that these genes are involved in various cellular functions such as signal transduction, cell communication, and gene expression regulation.\\n\\n][Summary: The enriched terms are related to the function of transcription and RNA processing.\\nMechanism: These genes may regulate gene expression and transcriptional processes.\\n]0.90124
252gpt-3.5-turbono_synopsisbicluster_RNAseqDB_1002-0[Summary: Muscle contraction and regulation of muscle fiber type are the significantly enriched biological mechanisms shared among the given human genes.\\nMechanism: Muscle contraction and regulation of muscle fiber type\\n][Summary: Genes are involved in muscle contraction and regulation.\\n\\nMechanism: The genes in this list are mainly expressed in muscle tissues and play a critical role in the contraction and regulation of various muscle types.\\n\\n]0.916
253gpt-3.5-turbono_synopsisbicluster_RNAseqDB_1002-1[Summary: Genes are involved in muscle contraction and development.\\nMechanism: Muscle development and regulation.\\n\\nHypothesis: The common function of these genes is in the regulation of muscle development and contraction. Many of these genes are involved in myofibril assembly and muscle fiber development, suggesting that they play critical roles in the formation and function of skeletal muscle tissue. The identification of these enriched terms supports the idea that the genes are involved in muscle contraction and development. Further study may reveal new insights into the specific mechanisms by which these genes influence muscle function, potentially leading to new therapies for muscle-related disorders.][Summary: Muscle protein regulation and contractility\\nMechanism: Myofilament formation and calcium signaling\\n]0.86606
254gpt-3.5-turbono_synopsisendocytosis-0[Summary: The common function of the given genes is related to intracellular trafficking, particularly of endocytosis and lysosomal degradation.\\nMechanism: The genes are involved in regulating the pathways of endocytosis, vesicular trafficking, and lysosomal degradation, contributing to protein degradation and cellular homeostasis.\\n\\nHypothesis: The genes identified in the term enrichment analysis suggest that they may be associated with intracellular trafficking processes, particularly endocytosis and lysosomal degradation. The endocytic pathway is responsible for a variety of functions, including extracellular nutrient uptake, synaptic transmission, and maintenance of plasma membrane composition. The lysosomal degradation pathway is responsible for breakdown and degradation of intracellular materials, including misfolded/unfolded proteins. These pathways are essential to prevent accumulation of toxic waste in the cell and maintain cellular homeostasis. The enriched gene set may play a role in regulating the balance between endocytosis, vesicular trafficking, and lysosomal degradation, contributing to protein and cellular homeostasis.][Summary: The common function among the given human genes is related to lipid and cholesterol processing and transport, as well as endosomal trafficking and protein degradation.\\nMechanism: The genes are involved in regulating intracellular vesicle trafficking and endosome maturation, as well as lipid and cholesterol metabolism.\\n\\nHypothesis: It is likely that the genes are involved in regulating the endocytic pathway and in processing and transporting lipids and cholesterol. The genes play critical roles in maintaining cellular homeostasis by regulating protein degradation and recycling, as well as lipid and cholesterol storage and utilization. Dysfunction in these genes may lead to the development of metabolic disorders, such as dyslipidemia or atherosclerosis.]0.94381
255gpt-3.5-turbono_synopsisendocytosis-1[Summary: The list of human genes is enriched for terms related to endocytosis and receptor signaling.\\n\\nMechanism: The majority of genes in the list are involved in endocytosis, the cellular process of internalizing molecules from the extracellular environment via vesicles. Many of the enriched terms are related to the trafficking, sorting, and recycling of receptors that are involved in cell signaling pathways.\\n\\n\\nHypothesis: The genes listed are involved in the regulation of endocytosis and receptor signaling, which play critical roles in cell signaling and communication. Dysregulation of these processes can contribute to a variety of diseases, including cancer, neurodegenerative disorders, and metabolic diseases. Further investigation of the specific roles of these genes in endocytic and receptor signaling pathways may offer insights into novel therapeutic targets for these diseases.][Summary: Endocytosis and Vesicular Trafficking\\nMechanism: These genes are involved in endocytosis and vesicular trafficking pathway which involves the internalization of extracellular molecules, membrane proteins and lipids. This pathway plays a crucial role in the regulation of cell signaling, nutrient uptake, and receptor desensitization.\\n]0.92555
256gpt-3.5-turbono_synopsisglycolysis-gocam-0[Summary: These genes are mostly involved in glycolysis, with a focus on catalyzing the conversion of glucose to pyruvate. \\n\\nMechanism: Glycolysis is the metabolic pathway that breaks down glucose into pyruvate, which can then be used to produce ATP or other metabolic intermediates. \\n\\n][Summary: The list of human genes is enriched for terms related to glycolysis and glucose metabolism.\\nMechanism: The genes in this list are all involved in the initial steps of glycolysis, converting glucose to pyruvate.\\n\\nHypothesis: The enriched terms suggest that the genes in this list are all involved in the process of converting glucose to pyruvate via glycolysis. This process is a central metabolic pathway in almost all organisms, providing energy for cellular processes and serving as a carbon source for biosynthesis. The presence of these specific genes in this list implies that they may be particularly important for the regulation and successful execution of the glycolytic process.]0.91412
257gpt-3.5-turbono_synopsisglycolysis-gocam-1[Summary: The common function shared by the given human genes is glycolytic process.\\nMechanism: Glycolysis is a metabolic pathway that breaks down glucose into pyruvate.\\n][Summary: Enzymes involved in glycolysis.\\nMechanism: Glycolysis pathway.\\n\\nHypothesis: These genes are all involved in the glycolysis pathway, a metabolic pathway that converts glucose into pyruvate and produces ATP. The over-representation of terms related to carbohydrate and glucose metabolic processes suggests that these genes play a key role in the breakdown of glucose and the production of ATP, which is essential for cellular energy metabolism.]0.87283
258gpt-3.5-turbono_synopsisgo-postsynapse-calcium-transmembrane-0[Summary: Calcium ion signaling pathways are enriched amongst the list of human genes provided.\\nMechanism: Calcium ion signaling pathways play a crucial role in various physiological processes, including neurotransmitter release, muscle contraction, and gene expression regulation. The genes in this list contribute to the activity of different types of calcium channels, transporters, and receptors, as well as other proteins that modulate calcium signaling.\\n\\n][Summary: Calcium signaling and neurotransmission-related functions are enriched in the given genes.\\nMechanism: These genes are involved in the regulation of ion channels and neurotransmitter receptors, affecting calcium influx and signaling in neurons.\\n]0.95207
259gpt-3.5-turbono_synopsisgo-postsynapse-calcium-transmembrane-1[Summary: Calcium signaling and neurotransmission-related functions appear to be enriched in the list of genes.\\n\\nMechanism: Calcium signaling plays a key role in neurotransmission, regulating the release of neurotransmitters from presynaptic terminals and the activation of postsynaptic receptors.\\n\\n][Summary: \\nThese human genes are involved in ion channel activity and neurotransmitter signaling. \\n\\nMechanism: \\nThe enriched terms suggest that these genes are involved in the regulation of synaptic transmission.\\n\\n\\nHypothesis: \\nThe high number of ion channel and neurotransmitter signaling related genes in this list suggests that they may play a crucial role in the regulation of synaptic transmission. Specifically, these genes may contribute to the modulation of calcium ion flux at synapses, which is necessary for proper neurotransmitter release and subsequent neuronal signaling. Dysregulation of this pathway may lead to various neurological disorders.]0.91361
260gpt-3.5-turbono_synopsisgo-reg-autophagy-pkra-0[Summary: Many of these genes are related to cellular stress response, signaling pathways, and regulation of autophagy.\\nMechanism: The genes may be involved in a complex network of responses to cellular stress that involve the regulation of signaling pathways and autophagy.\\n][Summary: Genes are enriched in terms related to cellular stress response and apoptotic processes.\\nMechanism: Activation of stress response pathways leading to apoptosis.\\n\\nHypothesis: These genes may be involved in regulating cellular response to stress through activation of NF-kappaB and JNK signaling pathways, leading to apoptosis. The enriched terms suggest that they may function together in regulating the activation or inhibition of these pathways in response to cellular stressors.]0.91216
261gpt-3.5-turbono_synopsisgo-reg-autophagy-pkra-1[Summary: The common function of the genes is associated with regulation of apoptotic signaling pathways, cellular metabolism, and protein processing.\\nMechanism: The genes are involved in the PI3K-Akt signaling pathway, which regulates cell growth, proliferation, and survival.\\n\\nHypothesis: The PI3K-Akt pathway plays an important role in regulating cell survival and metabolism, therefore mutations or dysregulation in the genes could contribute to the development of cancer or other diseases involving abnormal cell growth and metabolism.][Summary: The functions of the given genes are enriched in regulation of autophagy, cellular response to stress, and apoptotic process.\\nMechanism: Autophagy regulation and cellular response to stress pathways are overrepresented in the given genes.\\n\\nHypothesis: It is possible that the genes listed are involved in the regulation of autophagy and cellular response to stress. The over-representation of apoptotic process may reflect the role of these genes in cellular homeostasis, survival, and death. The genes may be involved in the mTOR signaling pathway or PI3K/AKT pathway which regulate autophagy, as they include genes such as PIK3CA, AKT1, RPTOR, MLST8, which play a vital role in these pathways. Alternatively, the genes may be related to the JNK signaling pathway, which modulates cellular response to stress and can activate apoptosis. Further experimentation is required to determine the exact mechanism and pathway of these genes.]0.91404
262gpt-3.5-turbono_synopsishydrolase activity, hydrolyzing O-glycosyl compounds-0[Summary: Glycosidase activity and carbohydrate metabolism\\nMechanism: These genes are involved in the hydrolysis of glycoside bonds in carbohydrates, specifically the breakdown of glycoproteins, glycolipids, and oligosaccharides. \\n\\nHypothesis: These genes are primarily involved in the breakdown of complex carbohydrates, specifically in lysosomes and the endoplasmic reticulum. Dysfunction in these genes can lead to lysosomal storage disorders, such as mucopolysaccharidosis, where complex carbohydrates accumulate in the cell and cause systemic disease.][Summary: Enzyme activity and carbohydrate metabolism are over-represented functions in the given list of genes.\\nMechanism: These genes may primarily be involved in lysosomal function and the digestion of complex carbohydrates and glycoproteins.\\n\\n]0.92310
263gpt-3.5-turbono_synopsishydrolase activity, hydrolyzing O-glycosyl compounds-1[Summary: Glycoside hydrolases and related genes involved in carbohydrate metabolism\\nMechanism: These genes are involved in the catabolism and processing of complex carbohydrates into simple sugars.\\n\\n\\nHypothesis: These genes are all involved in the breakdown of complex carbohydrates including glycosphingolipids, oligosaccharides, and sialic acids. This catabolism likely takes place in lysosomes, where these complex carbohydrates are transported to be broken down into simple sugars. The mechanism by which these genes function is likely a combination of enzymatic activity and transport function. Dysfunction of these genes could lead to lysosomal storage diseases where the catabolism of complex carbohydrates is impaired, leading to a buildup of these molecules in lysosomes and subsequent pathology.][Summary: The genes in this list are involved in carbohydrate metabolism, glycosylation, and degradation processes.\\nMechanism: These genes all play a role in various stages of carbohydrate processing, from synthesis to degradation.\\n\\nHypothesis: These genes are involved in the processing, modification, and breakdown of carbohydrates in the body. This includes glycosylation of proteins for proper folding and function, as well as the breakdown of complex carbohydrates for energy production. The enrichment of terms related to hydrolase activity suggests a particular focus on breaking down O-glycosyl compounds. The variety of specific enzyme activities present in these genes likely reflects the diverse range of carbohydrates and glycoproteins that are present in the body.]0.9629
264gpt-3.5-turbono_synopsisig-receptor-binding-2022-0[Summary: The common function of these genes is related to immunoglobulin and T cell receptor production and signaling.\\nMechanism: These genes are involved in the development and function of B cells and T cells.\\n][Summary: Genes related to immunoglobulins and T- and B-cell receptor chains.\\n\\nHypothesis: \\nThese genes are mostly related to immunoglobulin and T- and B-cell receptor chains. The enriched terms suggest that they are involved in various aspects of the immune response, such as recognizing and binding to foreign antigens and activating B and T cells. These genes are crucial for proper functioning of the adaptive immune system which plays a vital role in protecting the body against pathogens.]0.92283
265gpt-3.5-turbono_synopsisig-receptor-binding-2022-1[Summary: Enriched terms include immune response, lymphocyte activation, and lymphocyte differentiation.\\nMechanism: These genes are involved in various aspects of the immune system, particularly in the activation and differentiation of lymphocytes.\\n][Summary: Immune system function\\nMecanism: Antibody-mediated immunity\\n\\nHypothesis: The list of genes are all involved in the immune system function, specifically in the production and activation of immunoglobulins. They are all related to B cells and play a crucial role in the antibody-mediated immune response.]0.8764
266gpt-3.5-turbono_synopsismeiosis I-0[Summary: Enriched terms suggest these genes are primarily involved in meiosis and DNA repair processes. \\nMechanism: Meiotic recombination and crossover formation, DNA damage response and repair.\\n\\nHypothesis: The enriched terms suggest that these genes are involved in meiotic recombination and crossover formation enabling the accurate pairing, exchange of genetic information, and separation of chromosomes during cell division. They may also be involved in DNA damage response and repair pathways important for maintaining genomic integrity during these processes.][Summary: Genes are mainly involved in DNA repair, recombination, and chromosome segregation during meiosis.\\nMechanism: Meiosis and DNA repair\\n]0.90425
267gpt-3.5-turbono_synopsismeiosis I-1[Summary: These genes are enriched in terms related to meiotic recombination and chromosome segregation.\\nMechanism: Meiosis\\n\\n\\nHypothesis: These genes are involved in the regulation and maintenance of meiotic recombination during meiosis, and the proper segregation of chromosomes during cell division. Meiosis is a specialized cell division process that generates haploid gametes with genetic diversity. This process involves several steps, including DNA replication, chromosome recombination, synapsis, and segregation. The enriched terms suggest that these genes are involved in the regulation of these processes, which are critical for proper meiotic cell division and genetic diversity.][Summary: Genes involved in meiosis and DNA repair.\\nMechanism: Meiotic recombination and chromosome segregation.\\n\\n]0.92577
268gpt-3.5-turbono_synopsismolecular sequestering-0[Summary: The genes in the list are enriched for terms related to immune response and regulation, protein folding and metabolism, cellular transport and localization, and gene expression regulation.\\nMechanism: The enriched terms suggest that these genes are involved in cell survival and response to stress, likely through regulation of various signaling pathways.\\n\\n][Summary: The common function among the given genes is related to cellular response to stress and regulation of cell growth.\\n\\nMechanism: These genes are involved in multiple pathways that control cell growth and homeostasis, including the NF-κB and STAT3 signaling pathways. They also play a role in cellular response to stress, particularly oxidative stress. \\n\\n]0.894
269gpt-3.5-turbono_synopsismolecular sequestering-1[Summary: Regulation of cellular processes and response to stress\\nMechanism: Regulation of transcription and protein turnover\\n\\nHypothesis: The commonalities in the function of these genes suggest a regulatory mechanism whereby the cells respond to stress by upregulating protective mechanisms. The enriched terms suggest that these protective mechanisms involve regulation of oxidative stress response, protein turnover and iron homeostasis. The negative regulation of NF-kappaB transcription factor activity implies that this pathway is activated downstream of these protective mechanisms, leading to an overall inhibition of pro-inflammatory signaling. Finally, the negative regulation of apoptotic process could suggest an additional component of these protective mechanisms that involves inhibiting programmed cell death to promote cell survival during stress.][Summary: These human genes are enriched in terms related to regulation and response to cellular stress.\\n\\nMechanism: The underlying biological mechanism is likely related to the response to various types of cellular stress, including oxidative stress and DNA damage.\\n\\n\\nHypothesis: These genes may be involved in regulating the response to cellular stress through various pathways, including the regulation of protein localization to organelles and the stabilization of proteins involved in stress response. Additionally, the negative regulation of cell proliferation and positive regulation of apoptotic process terms suggest a possible role in regulating cell survival or death decisions in response to stress.]0.94153
270gpt-3.5-turbono_synopsismtorc1-0[Summary: The enriched terms shared among these genes are related to protein folding, metabolism, and immune response pathways.\\n\\nMechanism: These genes appear to share a connection through signaling pathways that regulate protein folding, metabolism, and immune response.\\n\\n][Summary: Cellular metabolism\\n]0.81243
271gpt-3.5-turbono_synopsismtorc1-1[Summary: Protein synthesis and folding\\nMechanism: Protein homeostasis regulation\\n][Summary: Transport, metabolism, and protein folding are enriched functions for these genes.\\nMechanism: These genes are involved in regulating cellular metabolism and maintaining protein homeostasis.\\n\\n]0.88119
272gpt-3.5-turbono_synopsisperoxisome-0[Summary: These genes are involved in peroxisome biogenesis and organization.\\nMechanism: Peroxisome formation and maintenance pathway\\n][Summary: The genes PEX1, PEX2, PEX3, PEX5, PEX6, and PEX7 are all involved in peroxisome biogenesis.\\nMechanism: Peroxisome biogenesis\\n\\nHypothesis: These genes are involved in the process of peroxisome biogenesis, which is the formation of new peroxisomes in the cell. Peroxisomes are organelles that perform various metabolic functions, including the breakdown of fatty acids and the detoxification of harmful substances. The enriched terms suggest that these genes are involved in the organization of the peroxisome membrane and matrix, as well as the import of proteins into the peroxisome. This could potentially be related to the localization and assembly of necessary components for peroxisome formation and function.]0.92590
273gpt-3.5-turbono_synopsisperoxisome-1[Summary: These genes are all involved in peroxisome biogenesis and maintenance.\\nMechanism: Peroxisomes are organelles that are involved in lipid metabolism and cellular signalling.\\n\\nHypothesis: These genes are likely involved in the regulation of peroxisome biogenesis and the maintenance of peroxisome membrane organization and fission. They may be involved in regulating lipid metabolism and cellular signalling processes that are mediated by peroxisomes.][Summary: The common function of the given human genes is related to peroxisome biogenesis.\\n\\nMechanism: The peroxisome biogenesis process involves the formation of a membrane-bound organelle that contains enzymes involved in various metabolic pathways, including fatty acid degradation, plasmalogen biosynthesis, and bile acid synthesis. Peroxisomes play a vital role in cellular metabolism and are involved in various processes such as lipid metabolism, reactive oxygen species (ROS) detoxification, and the biosynthesis of specific signaling molecules.\\n\\n\\nHypothesis: The genes PEX2, PEX3, PEX6, PEX7, and PEX1 are all involved in peroxisome biogenesis. These genes encode proteins that are required for the assembly of peroxisomes and their proper function. Specifically, PEX1 and PEX6 encode ATPases involved in the translocation of peroxisomal matrix proteins into the organelle, while PEX2, PEX3, and PEX7 have roles in the early stages of peroxisome biogenesis, including membrane assembly and division. The enriched]0.93564
274gpt-3.5-turbono_synopsisprogeria-0[Summary: The common function of the given genes is related to DNA damage repair, chromosome organization and regulation of transcription.\\nMechanism: The enriched terms suggest that these genes are involved in nuclear organization and DNA repair pathways. \\n][Summary: These genes all play a role in the maintenance and regulation of nuclear structure and function, particularly in DNA repair and organization.\\nMechanism: These genes are involved in the nuclear lamina, a network of proteins that provides structural support to the nucleus and helps regulate gene expression. Dysregulation of the lamina can lead to DNA damage and aging-related diseases.\\n]0.91139
275gpt-3.5-turbono_synopsisprogeria-1[Summary: The common function of the genes LMNA, WRN, and BANF1 is in DNA repair, chromatin organization, and cellular senescence.\\nMechanism: The nuclear envelope organization and maintenance\\n\\nHypothesis: LMNA, WRN, and BANF1 are involved in the maintenance of the nuclear envelope structure and function, which is crucial for chromatin organization and DNA repair. The disrupted functions of these genes can result in DNA damage accumulation, epigenetic abnormalities, and cellular senescence. These genes may act together in a network to regulate the nuclear envelope dynamics and facilitate DNA repair, thereby maintaining genome stability and cellular viability.][Summary: Genes LMNA, WRN, and BANF1 are involved in chromatin organization and DNA repair.\\nMechanism: These genes are involved in maintaining nuclear architecture and stability.\\n\\nHypothesis: LMNA, WRN, and BANF1 are all involved in the regulation of chromatin organization and DNA repair, suggesting a potential link between nuclear architecture and genomic stability. These genes may function in pathways related to telomere maintenance, nuclear localization, nuclear lamina organization, and genome stability regulation. Overall, these findings suggest a potential mechanism by which changes in nuclear architecture and stability could lead to genomic instability and disease.]0.9613
276gpt-3.5-turbono_synopsisregulation of presynaptic membrane potential-0[Summary: The enriched terms from this list of genes are related to ion channel activity, particularly in relation to neurotransmission and synaptic signaling.\\n\\nMechanism: The genes on this list are involved in encoding different subunits of ion channels, most notably GABA and glutamate receptors, as well as voltage-gated potassium and sodium channels. These channels are crucial for synaptic transmission and the regulation of neuronal excitability.\\n\\n][Summary: These genes are primarily involved in neurological processes and ion channel regulation. \\nMechanism: Regulation of ion channels in the nervous system.\\n\\nHypothesis: These genes are primarily involved in the regulation of ion channels in the nervous system, which affects processes such as nervous system development, synaptic transmission, and membrane potential regulation. The enrichment of terms related to ion transport and transmembrane transport suggest that these genes may play an important role in maintaining the balance of ion concentrations in neuronal cells, which is essential for proper neurological function. Additionally, the enrichment of terms related to neuron development suggests that these genes may play a role in shaping the nervous system during development.]0.93340
277gpt-3.5-turbono_synopsisregulation of presynaptic membrane potential-1[Summary: Ion channel activity and synaptic transmission-related processes are enriched in the listed genes.\\nMechanism: The genes are involved in synaptic plasticity, memory formation, and neuronal signaling.\\n][Summary: Neurotransmission and Ion Channels are enriched functions in the given human genes.\\nMechanism: Signaling and excitatory neurotransmission.\\n\\n\\nHypothesis: The enriched functions suggest that these genes play a critical role in signaling pathways and neurotransmission in the central nervous system. Furthermore, the identified ion channels and receptors help mediate the excitatory and inhibitory communication between neurons, thus playing a critical role in neuronal development, learning, and memory.]0.92303
278gpt-3.5-turbono_synopsissensory ataxia-0[Summary: The enriched terms found among the listed human genes suggest a common involvement in cellular metabolism, particularly in mitochondrial function, protein folding and degradation, and transportation across cellular membranes.\\nMechanism: These genes may be involved in the maintenance of cellular homeostasis and energy production.\\n\\nHypothesis: Many of the enriched terms are related to cellular stress pathways, suggesting that these genes may be involved in the response to stress and cellular damage. Additionally, the involvement of several genes related to mitochondrial function suggests that there may be a common underlying mechanism related to energy production and metabolism.][Summary: Genes are involved in nervous system development and function. \\nMechanism: Myelination and axonal transport. \\n\\nHypothesis: The genes on the list are enriched for terms involved in nervous system development and function, including myelination, axon guidance, and neuron projection development. This suggests a role for these genes in the regulation of myelination and axonal transport, which are important processes for proper nervous system function. Dysfunction of these processes, due to mutations in genes such as PMP22 and SH3TC2, can lead to peripheral neuropathy and other neurological disorders.]0.8782
279gpt-3.5-turbono_synopsissensory ataxia-1[Summary: Several of the genes are involved in nervous system development and function.\\nMechanism: Unknown, but potentially related to myelin formation and maintenance.\\n][Summary: Genes related to neurological and cellular metabolism processes are over-represented.\\nMechanism: Metabolic and neurological processes\\n\\nHypothesis: These genes are involved in processes related to myelin sheath formation, cellular metabolism, and neurological development. Specifically, the genes NAGLU, PMP22, MPZ, EGR2, and TWNK are involved in myelin sheath formation, which is necessary for proper nerve function. FLVCR1, KPNA3, and AARS1 are involved in cellular metabolism, which has implications for cellular growth and function. Finally, DNAJC3, RNF170, and PIEZO2 are related to neurological development, which may be associated with neural plasticity and adaptation. Together, these genes suggest that there is an association between cellular metabolism, neurological development, and myelin sheath formation.]0.90660
280gpt-3.5-turbono_synopsisterm-GO:0007212-0[Summary: The common function of the listed genes is related to G protein-coupled receptor signaling and neurotransmission.\\nMechanism: G protein-coupled receptor (GPCR) signaling\\n\\nHypothesis: The listed genes are involved in various aspects of G protein-coupled receptor (GPCR) signaling and neurotransmission. The enrichment of terms related to neurotransmitter receptor activity, GPCR signaling pathway, and regulation of neurotransmitter secretion suggests that these genes contribute to the communication between neurons in the brain. The dopamine receptor signaling pathway and adenylate cyclase-modulating GPCR signaling pathway terms suggest that these genes are particularly important in dopaminergic neurotransmission, which is involved in a wide range of processes including reward processing, motivation, and movement control. The involvement of these genes in dopaminergic neurotransmission may have implications for understanding and treating various neuropsychiatric disorders.][Summary: G protein-coupled receptor signaling pathway.\\nMechanism: The genes are involved in the regulation of dopamine and prostaglandin signaling through G protein-coupled receptors.\\n]0.92807
281gpt-3.5-turbono_synopsisterm-GO:0007212-1[Summary: Signaling and regulation via G-protein coupled receptors\\nMechanism: Activation of second messenger pathways\\n\\nHypothesis: These genes are all involved in signaling and regulation through G protein-coupled receptors (GPCRs), which are membrane proteins that activate intracellular signaling pathways upon binding with ligands such as neurotransmitters, hormones, or sensory signals. GPCR signaling pathways are transduced via G proteins, which consist of α, β, and γ subunits. The enriched terms suggest that these genes are involved in the regulation of G protein beta/gamma subunit complex binding, as well as the G protein coupled receptor signaling pathway. Dysfunction in these genes may lead to various diseases, including neuropsychiatric and cardiovascular disorders.][Summary: G protein signaling and dopamine receptor activity are enriched in the list of human genes provided.\\nMechanism: G protein-coupled receptor (GPCR) signaling pathway and dopamine signaling pathway.\\n\\nHypothesis: The enriched genes in this list are involved in the GPCR and dopamine signaling pathways. GPCRs are the largest family of transmembrane receptors and play a crucial role in cellular signaling. The GPCR signaling pathway is responsible for several physiological processes like regulation of blood pressure, heart rate, immunity, and neurotransmission. The dopamine signaling pathway is responsible for reward, mood regulation, and movement. The enriched terms suggest the involvement of the GPCR signaling pathway and dopamine signaling pathway in regulating these physiological processes. The activation of adenylate cyclase and the role of Dopamine D1 receptor are important mechanistic pathways involved in the regulation of these physiological processes.]0.93193
282gpt-3.5-turbono_synopsistf-downreg-colorectal-0[Summary: Transcriptional regulation and chromatin organization are enriched functions.\\nMechanism: These genes are involved in controlling gene expression and chromatin structure, which are crucial for cellular function and development.\\n\\nHypothesis: These genes may be involved in a common pathway related to transcriptional regulation and chromatin organization, such as the regulation of cell identity or differentiation, or the control of gene expression in response to external stimuli.][Summary: Genes are enriched for transcription regulation, chromatin remodeling, and developmental processes.\\nMechanism: Transcriptional regulation\\n\\nHypothesis: The genes in this list are enriched for functions involved in transcriptional regulation, chromatin modification, and developmental processes. Specifically, the enriched terms suggest these genes play a role in protein-DNA complex assembly and response to stress. One underlying biological mechanism could involve the formation of multi-protein complexes involved in transcriptional regulation, including recruitment of chromatin remodelers and transcription factors, as well as response to cellular stress through activation of various signaling pathways.]0.95227
283gpt-3.5-turbono_synopsistf-downreg-colorectal-1[Summary: The common function among the given gene set is transcriptional regulation. \\nMechanism: The genes are involved in the regulation of various transcription factors, co-factors, and modifiers. \\n\\nHypothesis: The set of genes is involved in various stages of transcriptional regulation, from modifying chromatin structure to recruiting transcription factors and co-regulators. The enriched terms suggest that these genes may be involved in both positive and negative regulation of transcription, highlighting their importance in maintaining a fine balance of gene expression for proper cell function and development.][Summary: These genes are enriched for terms related to transcriptional regulation and DNA binding.\\nMechanism: The mechanism likely involves the regulation of gene expression through DNA binding and transcriptional control.\\n\\n]0.91397
284gpt-3.5-turboontological_synopsisEDS-0[Summary: The enriched terms are related to the extracellular matrix and connective tissue development.\\nMechanism: The genes are involved in the synthesis, processing, and organization of collagens and other extracellular matrix components.\\n][Summary: The common function of the listed genes is related to connective tissue development, collagen biosynthetic processes, and extracellular matrix organization. \\n\\nMechanism: The enrichment of terms related to connective tissue and collagen biosynthesis suggests a potential underlying biological mechanism linking these genes to the pathogenesis of Ehlers-Danlos syndrome.\\n\\n]0.94139
285gpt-3.5-turboontological_synopsisEDS-1[Summary: The common function among these genes is the regulation and formation of the extracellular matrix, which includes collagen fibril organization, dermatan sulfate biosynthetic process, proteoglycan biosynthetic process and connective tissue development.\\n\\nMechanism: These genes play a crucial role in the regulation and formation of the extracellular matrix, which is a scaffold-like structure comprising various proteins including collagen, and is essential in the development and maintenance of tissues and organs.\\n\\n\\nHypothesis: These genes play a role in regulating the organization and biosynthesis of the extracellular matrix, which is essential in the formation and maintenance of connective tissues. Dysregulation of these genes may contribute to various connective tissue disorders, including Ehlers-Danlos syndrome. This suggests that targeting the extracellular matrix and its related pathways may have potential therapeutic applications for these disorders.][Summary: Genes involved in extracellular matrix organization and connective tissue development are enriched.\\nMechanism: These genes likely play a role in the synthesis, organization, and maintenance of the extracellular matrix and connective tissue.\\n\\n]0.94725
286gpt-3.5-turboontological_synopsisFA-0[Summary: Fanconi anemia complementation pathway.\\n\\nMechanism: The Fanconi anemia (FA) pathway is a DNA repair pathway involved in the repair of inter-strand crosslinks and DNA double-strand breaks.\\n\\n\\nHypothesis: The FA pathway involves a series of proteins working together to repair damage to DNA that can cause various diseases, including cancer. The identification of this pathway provides insights into the mechanisms underlying DNA repair and may lead to improved methods of cancer treatment.][Summary: These genes are involved in DNA repair and protein monoubiquitination, and are part of the Fanconi anemia nuclear complex. \\n\\nMechanism: The Fanconi anemia pathway plays a key role in the DNA repair process. \\n\\n]0.92279
287gpt-3.5-turboontological_synopsisFA-1[Summary: The common function of these genes is DNA repair and protein monoubiquitination, specifically in the context of Fanconi anemia complementation groups. \\n\\nMechanism: Fanconi anemia is a genetic disorder characterized by genomic instability, bone marrow failure, and cancer susceptibility. It is caused by mutations in genes involved in DNA repair pathways, particularly the Fanconi anemia complementation group pathway. These genes work together to repair DNA damage and maintain genomic stability, and mutations in these genes can lead to the development of Fanconi anemia.\\n\\n\\nHypothesis: These genes work together in the Fanconi anemia complementation group pathway to repair DNA damage and maintain genomic stability. The pathway involves the monoubiquitination of FANCD2 and FANCI, leading to their recruitment to sites of DNA damage and the assembly of a repair complex involving other Fanconi anemia complementation group proteins, including those represented by the genes listed here. The complex repairs DNA damage via homologous recombination, which][Summary: The enriched terms are related to DNA repair and protein monoubiquitination.\\nMechanism: These genes are involved in the Fanconi anemia pathway, which is a DNA damage response pathway that repairs interstrand DNA crosslinks.\\n]0.92832
288gpt-3.5-turboontological_synopsisHALLMARK_ADIPOGENESIS-0[Summary: Mitochondrial function and energy metabolism are enriched in this list of genes.\\n\\nMechanism: These genes are involved in various processes such as ATP binding, enzyme activity, and transport, all of which are associated with mitochondrial function and energy metabolism.\\n\\n][Summary: Several of the genes are involved in mitochondrial function, including electron transfer and ATP synthesis. Others are involved in lipid metabolism and transport, and some are involved in protein binding and signaling.\\n\\nMechanism: The enriched terms suggest a focus on mitochondrial function and metabolism, as well as protein and lipid transport and signaling.\\n\\n]0.9491
289gpt-3.5-turboontological_synopsisHALLMARK_ADIPOGENESIS-1[Summary: Mitochondrial processes and metabolic function\\n\\nMechanism: The enriched terms suggest that these genes are involved in mitochondrial processes and metabolic function, with specific roles in energy production and mitochondrial regulation.\\n\\n][Summary: Mitochondrial function, enzyme activity, and transporter activity\\nMechanism: Mitochondrial metabolism\\n]0.89137
290gpt-3.5-turboontological_synopsisHALLMARK_ALLOGRAFT_REJECTION-0[Summary: Immune response and cytokine activity.\\n\\n][Summary: Immune response-regulating genes\\n]0.877
291gpt-3.5-turboontological_synopsisHALLMARK_ALLOGRAFT_REJECTION-1[Summary: Immune system function and cytokine activity are enriched in the list of genes.\\n\\nMechanism: The common biological mechanism underlying the enriched terms is the regulation and activation of the immune system, particularly through cytokine signaling.\\n\\n][Summary: These human genes are enriched in terms related to immune system, cytokine activity, chemokine receptor binding activity, and protein kinase activity.\\n\\n]0.9299
292gpt-3.5-turboontological_synopsisHALLMARK_ANDROGEN_RESPONSE-0[Summary: Many of the genes listed are involved in binding activities, such as nucleic acid binding, protein binding, and ion binding. A number of genes are also involved in metabolic processes, such as biosynthesis and dehydrogenase activity.\\n\\n][Summary: Genes are involved in a variety of functions, including transport, enzyme activity, binding, and regulation of various processes. Enriched terms include protein phosphorylation, intracellular signaling pathways, and regulation of macromolecule metabolic process.\\n\\nMechanism: The enriched terms suggest that these genes are involved in signaling pathways and regulation of cellular processes. Specifically, protein phosphorylation appears to play a key role in the functions of these genes.\\n\\n]0.89256
293gpt-3.5-turboontological_synopsisHALLMARK_ANDROGEN_RESPONSE-1[Summary: Cell signaling and regulation of enzymatic activity\\nMechanism: These genes are involved in regulating cell signaling pathways, including cGMP biosynthesis, intracellular signal transduction and cell surface receptor signaling pathways. They also play a role in enzymatic activity, including phosphorylation, protein binding and transcription coactivator activity.\\n][Summary: Genes are involved in various activities such as metal ion binding, enzymatic activity, and signal transduction.\\n\\n]0.89250
294gpt-3.5-turboontological_synopsisHALLMARK_ANGIOGENESIS-0[Summary: Extracellular matrix structural constituents and proteins involved in cell signaling processes.\\n\\n][Summary: Several genes are involved in extracellular matrix organization and cell signaling pathways, while others have roles in blood coagulation, lipid metabolism, and immunity.\\n\\n]0.9175
295gpt-3.5-turboontological_synopsisHALLMARK_ANGIOGENESIS-1[Extracellular matrix organization and binding activity are the enriched terms in common among these genes.\\n\\nMechanism: The extracellular matrix (ECM) plays a crucial role in regulating cell behavior and maintaining tissue integrity. The enriched terms suggest that these genes all participate in ECM organization and binding, potentially contributing to processes such as cell adhesion, migration, and differentiation.\\n\\n][Summary: Extracellular matrix organization and cell signaling\\nMechanism: Extracellular matrix regulation and cell signaling pathways\\n\\nHypothesis: These genes function in extracellular matrix organization and cell signaling pathways, involved in regulating the formation and maintenance of the extracellular matrix and cellular communication. They share enriched terms related to protein binding activity and positive regulation of intracellular signal transduction and are highly enriched for components of the collagen-containing extracellular matrix. This suggests a potential role in regulating collagen matrix structure, cell adhesion, and proliferation, as well as cell signaling cascades essential for tissue development and homeostasis.]0.93324
296gpt-3.5-turboontological_synopsisHALLMARK_APICAL_JUNCTION-0[Summary: These genes have functions related to cytoskeleton organization, cell adhesion, receptor binding, and kinase activity.\\n\\n][Summary: These genes are involved in various cellular processes related to cytoskeletal organization, cell-cell communication, and intracellular signaling.\\n\\nMechanism: The common underlying biological mechanism may involve regulation of actin filament dynamics, which could impact processes such as cellular adhesion and migration, as well as intracellular signaling cascades.\\n\\n]0.92249
297gpt-3.5-turboontological_synopsisHALLMARK_APICAL_JUNCTION-1[Summary: These human genes are involved in various cellular functions and processes, including cell adhesion, cell signaling, and cytoskeleton organization. \\nMechanism: These genes likely function in a network of interrelated pathways involved in cellular processes. \\n\\n][Summary: Cell adhesion and signaling\\nMechanism: Integrin-mediated signaling and cytoskeletal regulation\\n]0.88165
298gpt-3.5-turboontological_synopsisHALLMARK_APICAL_SURFACE-0[Summary: Cell surface receptor activity and signal transduction are enriched in this list of genes.\\n\\nMechanism: These genes are involved in various processes such as cellular response, regulation of cellular processes, and intracellular signaling pathways. They function primarily as cell surface receptors, enzyme binding activity, and protein domain-specific binding activity.\\n\\n][Summary: Several of the genes are involved in membrane transport and signaling, with a focus on plasma membrane and extracellular space.\\n\\nMechanism: These genes may be involved in the regulation of cellular signaling pathways and transport processes, particularly those related to the plasma membrane and extracellular space.\\n\\n]0.9153
299gpt-3.5-turboontological_synopsisHALLMARK_APICAL_SURFACE-1[Summary: The enriched terms are related to membrane transport and signaling, with a focus on receptor activity and intracellular signaling.\\n\\nMechanism: These genes are primarily involved in the regulation of intracellular signaling pathways and membrane transport. \\n\\n][Summary: The enriched terms include processes related to regulation and signaling, ion transport, cell adhesion and migration, and metabolic processes. \\n\\nMechanism: These genes may play roles in maintaining cellular homeostasis and responding to changes in the external environment through ion transport and signaling pathways. They may also act to regulate cell adhesion and migration, and participate in metabolic processes.\\n\\n]0.95161
300gpt-3.5-turboontological_synopsisHALLMARK_APOPTOSIS-0[Summary: These genes are involved in apoptosis, cytokine activity, and DNA-binding transcription factor activity.\\n\\n\\nHypothesis: These genes may be involved in pathways related to cell death and inflammation, such as the TNF signaling pathway or the p53 signaling pathway. They may also be involved in regulating gene expression through DNA-binding transcription factors.][Summary: Genes in this list are primarily involved in apoptotic signaling pathways and immune response regulation.\\nMechanism: These genes act as modulators or effectors in apoptotic signaling pathways and immune response regulation. \\n\\n]0.91136
301gpt-3.5-turboontological_synopsisHALLMARK_APOPTOSIS-1[Summary: Genes involved in apoptotic signaling and cytokine activity.\\n\\n][Summary: The enriched terms include apoptotic process, cytokine activity, and protein binding activity. \\n\\n]0.8935
302gpt-3.5-turboontological_synopsisHALLMARK_BILE_ACID_METABOLISM-0[Summary: The enriched terms indicate the genes are involved in lipid metabolism and transport.\\n\\nMechanism: The genes are involved in various processes related to the metabolism and transport of lipids and cholesterol, including ATP binding activity, and transmembrane transporter activity.\\n\\n][Summary: These genes are involved in lipid and cholesterol metabolism, as well as peroxisomal and vitamin D-related processes.\\n\\nMechanism: These genes likely play a role in maintaining lipid and cholesterol homeostasis and metabolism, possibly through the regulation and transport of these molecules across cellular membranes.\\n\\n]0.9237
303gpt-3.5-turboontological_synopsisHALLMARK_BILE_ACID_METABOLISM-1[Summary: Several of the genes are involved in lipid metabolism and transport, particularly in the transport and binding of cholesterol and long-chain fatty acids. Peroxisomal proteins and functions are also enriched.\\n\\n][Summary: Many of the listed genes are involved in lipid metabolism and transport, as well as peroxisome-related processes. \\n\\n\\nHypothesis: These genes are likely involved in the regulation and transport of various lipids and sterols, with a particular focus on the transport and metabolism of fatty acids and cholesterol in peroxisomes. ABC-type transporters may be involved in lipid uptake and efflux, while peroxisome-related processes may play a role in lipid metabolism and oxidation.]0.95270
304gpt-3.5-turboontological_synopsisHALLMARK_CHOLESTEROL_HOMEOSTASIS-0[Summary: Cholesterol biosynthesis and lipid metabolism.\\nMechanism: Genes involved in cholesterol biosynthesis and lipid metabolism are enriched in this list.\\n][Summary: Cholesterol biosynthesis and metabolism genes.\\n\\nMechanism: These genes are involved in the biosynthesis and metabolism of cholesterol, a crucial molecule for cell membrane synthesis and steroid hormone production.\\n\\n]0.9566
305gpt-3.5-turboontological_synopsisHALLMARK_CHOLESTEROL_HOMEOSTASIS-1[Summary: Cholesterol biosynthesis and homeostasis, isoprenoid biosynthesis, and lipid metabolism are the enriched functional terms common among the given human genes.\\n\\nMechanism: These genes are involved in cholesterol biosynthesis and homeostasis, isoprenoid biosynthesis, and lipid metabolism. The mechanisms are related to the synthesis, transportation, and metabolism of cholesterol and other lipids.\\n\\n][Summary: Cholesterol biosynthesis and lipid metabolism are the enriched terms across the provided genes.\\n\\nMechanism: The enriched terms suggest that the provided genes are involved in cholesterol biosynthesis and lipid metabolism, specifically the synthesis of isoprenoids and fatty acids.\\n\\n\\nHypothesis: These genes likely function in a coordinated pathway to support the synthesis of cholesterol, isoprenoids, and fatty acids within the body. This pathway may be involved in regulating cellular and systemic levels of these lipids to support proper cellular function and physiological processes, such as membrane structure and hormone production. Dysfunction in this pathway may contribute to the development of metabolic disorders, such as hyperlipidemia and atherosclerosis.]0.97372
306gpt-3.5-turboontological_synopsisHALLMARK_COAGULATION-0[Summary: The enriched terms for these genes include proteolysis, complement pathways, blood coagulation, and cell adhesion.\\n\\nMechanism: These genes all play a role in regulating the immune system and extracellular matrix.\\n\\n][Summary: Several of these genes are involved in blood coagulation, complement activation, and metalloendopeptidase activity.\\n\\nMechanism: These genes participate in the regulation of proteolysis and enzyme inhibitors.\\n\\n]0.935
307gpt-3.5-turboontological_synopsisHALLMARK_COAGULATION-1[Summary: Many of the genes listed are involved in the regulation of proteolysis, including metalloendopeptidase activity and serine-type endopeptidase activity, and are predicted to be involved in blood coagulation, complement activation, and negative regulation of proteolysis. \\n\\n][Summary: The enriched terms suggest that the common function of these human genes involve diverse biological processes related to protein binding, enzymatic activity, and complement system. \\n\\n]0.8789
308gpt-3.5-turboontological_synopsisHALLMARK_COMPLEMENT-0[Summary: Genes involved in protease inhibition, protein binding, and enzyme activity.\\n\\nMechanism: The enriched terms suggest a potential underlying mechanism involving regulation of protease activity through protein binding and enzyme inhibition.\\n\\n][Summary: Binding and catalytic activity\\n\\nHypothesis: These genes are involved in various types of binding and catalytic activities, which may include regulation of signaling pathways, transcriptional regulation, and enzyme activity in metabolic pathways. The enrichment of binding-related terms suggests that these genes may play a role in protein-protein interactions, protein-DNA interactions, metal ion coordination, and enzyme-substrate interactions. The involvement of ATP binding suggests these genes may also have a role in energy-dependent processes.]0.90311
309gpt-3.5-turboontological_synopsisHALLMARK_COMPLEMENT-1[Summary: These genes are involved in various functions, including protein binding activity, enzyme binding activity, and endopeptidase activity.\\n\\n][Summary: Extracellular matrix, protease activity, and complement activation are enriched in the function of these genes.\\n\\n]0.9124
310gpt-3.5-turboontological_synopsisHALLMARK_DNA_REPAIR-0[Summary: Several genes are involved in DNA binding, RNA binding, and nucleotide metabolism. \\n\\n][Summary: Many of the genes on this list are involved in DNA metabolism, transcription, and RNA processing. \\n\\n]0.9415
311gpt-3.5-turboontological_synopsisHALLMARK_DNA_REPAIR-1[Summary: These genes are involved in DNA replication, repair, and polymerization, RNA transcription, and metabolic processes.\\n\\nMechanism: These genes are likely part of a larger biological pathway involved in maintaining genome stability and function.\\n\\n][Summary: Many of these genes are involved in DNA-related processes, including DNA replication, repair, and transcription. \\n\\n\\nHypothesis: The enriched terms suggest that these genes are part of a complex network involved in DNA processing, including binding to DNA and RNA molecules, maintaining nucleotide balance, and repairing DNA damage. The protein-macromolecule adaptor activity may be involved in coordinating these processes or facilitating interactions between proteins and genetic material.]0.92247
312gpt-3.5-turboontological_synopsisHALLMARK_E2F_TARGETS-0[Summary: Genes are primarily involved in DNA replication, cell cycle regulation, and chromatin organization.\\n\\nMechanism: These genes are likely involved in regulating the processes of DNA replication, the cell cycle, and chromatin organization.\\n\\n][Summary: Genes involved in DNA replication, repair, and cell cycle regulation are enriched.\\n\\nMechanism: These genes are involved in processes related to DNA replication and repair, as well as regulation of the cell cycle, particularly in the G2 and M phases.\\n\\n]0.9414
313gpt-3.5-turboontological_synopsisHALLMARK_E2F_TARGETS-1[Summary: DNA-related functions are enriched among the given genes.\\nMechanism: These genes are involved in various processes related to DNA, such as DNA binding, repair, and replication.\\n\\n][Summary: DNA binding and replication activities are enriched in the given gene list, indicating their involvement in DNA repair, replication, and regulation of cell cycle processes.\\n\\nMechanism: The enriched terms suggest that the genes in the list are involved in DNA binding, replication, and repair, which play essential roles in maintaining genomic stability.\\n\\n]0.93177
314gpt-3.5-turboontological_synopsisHALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0[Summary: Extracellular matrix structural constituents and binding activities are statistically over-represented in this set of genes.\\n\\nMechanism: These genes are likely involved in extracellular matrix organization and cell-matrix interactions.\\n\\n][Summary: These genes are involved in extracellular matrix organization and signaling pathways such as Wnt-protein binding, growth factor activity, and cytokine activity. \\n\\nMechanism: These genes work together to regulate the extracellular matrix and cellular signaling pathways that contribute to cellular processes such as development, tissue repair, and immunity.\\n\\n]0.92121
315gpt-3.5-turboontological_synopsisHALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1[Summary: Extracellular matrix structural constituents and binding activities are enriched in these genes.\\n\\n][Summary: The list of genes is enriched for functions related to extracellular matrix organization and regulation, including collagen binding, integrin binding, and heparin binding activity.\\n\\nMechanism: The genes in the list are involved in processes related to extracellular matrix regulation, including collagen synthesis and assembly, cell adhesion and migration, and protease inhibitor activity.\\n\\n]0.94293
316gpt-3.5-turboontological_synopsisHALLMARK_ESTROGEN_RESPONSE_EARLY-0[Summary: These human genes are involved in a variety of functions related to binding and enzymatic activity, particularly involving calcium ion and nucleotide binding. They are also involved in several biological processes, including growth and development, gene transcription, and ion transport.\\n\\nMechanism: The common mechanism underlying these gene functions is likely related to the regulation and modulation of intracellular processes, particularly those involving binding and enzymatic activity. Calcium ion binding, for example, is a key regulator of many cellular processes, including muscle contraction, neurotransmitter release, and cell signaling.\\n\\n][Summary: Transmembrane receptor and transporter activity, as well as DNA-binding transcription activator activity, are statistically over-represented in this list of genes.\\n\\nMechanism: These enriched terms suggest that the genes in this list are involved in membrane and nuclear signaling processes, including transcriptional regulation.\\n\\n]0.86321
317gpt-3.5-turboontological_synopsisHALLMARK_ESTROGEN_RESPONSE_EARLY-1[Summary: Enriched terms relate to protein binding, transcription regulation, and transmembrane transport activity.\\n\\n][Summary: Cell signaling and transcription regulation\\nMechanism: Enzyme and receptor activity, nucleic acid binding, transcriptional regulation\\n]0.8627
318gpt-3.5-turboontological_synopsisHALLMARK_ESTROGEN_RESPONSE_LATE-0[Summary: Transmembrane transporter activity and binding activity are enriched terms in the functions of the given genes.\\n\\nMechanism: These genes are involved in the transport of metabolites across membranes and regulation of protein-protein interactions, possibly contributing to maintenance of cellular homeostasis.\\n\\n][Summary: This list of human genes is enriched for terms related to protein and enzyme activity, binding activity, and cellular transport.\\n\\nMechanism: These genes likely play important roles in various cellular processes, including protein and enzyme activity, binding and transport of molecules, and regulation of cellular growth and development.\\n\\n]0.9330
319gpt-3.5-turboontological_synopsisHALLMARK_ESTROGEN_RESPONSE_LATE-1[Summary: Several genes are involved in enzymatic activities (e.g. oxidoreductase, dehydrogenase), while others are involved in binding activities (e.g. protein binding, chemokine binding, lipid binding). Many genes are also predicted to be involved in several processes, including cell signaling, transcription regulation, and protein kinase activity.\\n\\n][Summary: These genes are involved in various biological processes, but the enriched terms suggest a focus on binding activity and molecular transport.\\n\\nMechanism: The common biological mechanism for these genes is likely related to molecular interactions and transport within cells.\\n\\n]0.8969
320gpt-3.5-turboontological_synopsisHALLMARK_FATTY_ACID_METABOLISM-0[Summary: Enzyme activity and metabolism.\\nMechanism: Metabolism, specifically, fatty acid metabolism and energy production.\\n\\n\\nHypothesis: These genes are involved in the metabolism of fatty acids and the production of energy through the tricarboxylic acid cycle. They enable the binding, breakdown, and transfer of acyl-CoA, which is important in the catabolism of fatty acids for energy production. These metabolic processes are vital for maintaining cellular function and homeostasis.][Summary: Metabolism of fatty acids and carboxylic acids\\nMechanism: Fatty acid oxidation and elongation pathways, as well as carboxylic acid metabolism pathways\\n\\n]0.87325
321gpt-3.5-turboontological_synopsisHALLMARK_FATTY_ACID_METABOLISM-1[Summary: Enzyme activity and binding activity are the most common functions among the genes in the list.\\n\\nMechanism: The genes in this list encode proteins that are involved in catalyzing chemical reactions (enzyme activity) and binding to other molecules (binding activity).\\n\\n][Summary: These genes are mostly involved in oxidation-reduction processes and metabolic pathways, specifically lipid and fatty acid metabolism. \\n\\n]0.84131
322gpt-3.5-turboontological_synopsisHALLMARK_G2M_CHECKPOINT-0[Summary: These genes are involved in various molecular functions related to DNA binding and activity, including DNA replication, transcription, and chromatin binding. \\nMechanism: These genes are likely involved in modulating gene expression and chromatin structure. \\n\\n][Summary: These genes enable several functions related to DNA binding, transcription regulation, protein binding, histone modification, and protein kinase activity. \\n\\nMechanism: These genes are involved in regulating gene expression and DNA-related processes such as DNA replication, repair, and chromosome segregation. \\n\\n]0.9653
323gpt-3.5-turboontological_synopsisHALLMARK_G2M_CHECKPOINT-1[Summary: These genes are involved in DNA binding and transcription factor activity, protein kinase and phosphatase activity, cytoskeletal protein binding, and microtubule binding activity.\\n\\n][Summary: The genes are involved in DNA binding/transcription factor activity, protein kinase activity, and binding activity, and play a role in mitosis, DNA replication, and gene expression regulation. \\n\\nMechanism: These genes are involved in processes related to cell cycle regulation and gene expression control, likely through interactions with DNA, RNA, and protein molecules. \\n\\n]0.95193
324gpt-3.5-turboontological_synopsisHALLMARK_GLYCOLYSIS-0[Summary: Glycosylation and carbohydrate metabolism are enriched functions in this list of genes.\\n\\nMechanism: Glycosylation is a key process in carbohydrate metabolism, involving the addition of carbohydrate groups to proteins and lipids to form glycoproteins and glycolipids, respectively. These modifications are critical for proper protein folding, stability, and secretion, as well as for cell-cell recognition and signaling.\\n\\n\\nHypothesis: The enriched functions in these genes suggest a critical role for glycosylation and carbohydrate metabolism in a variety of physiological processes and perhaps a possible link between glycosylation and pathologies. Future studies could explore the molecular mechanisms underlying these processes and their role in disease pathogenesis.][Summary: Glycosylation and carbohydrate metabolism related genes are enriched in this list.\\n\\nMechanism: The genes in this list are involved in various steps of glycosylation and carbohydrate metabolism pathways.\\n\\n]0.95566
325gpt-3.5-turboontological_synopsisHALLMARK_GLYCOLYSIS-1[Summary: Enriched terms are involved in carbohydrate metabolism, specifically glycosaminoglycan and glycoprotein biosynthesis.\\n\\nMechanism: These genes all code for enzymes involved in carbohydrate metabolism, particularly in the biosynthesis of glycosaminoglycans and glycoproteins.\\n\\n][Summary: Enriched terms among these genes are involved in carbohydrate metabolism, enzyme activity, and binding activity.\\n\\nMechanism: These genes may be involved in a pathway that regulates carbohydrate metabolism, including glycosylation, synthesis of glucose, and synthesis and breakdown of glycogen. The genes may also play a role in enzyme activity and binding activity in various cellular processes.\\n\\n]0.95122
326gpt-3.5-turboontological_synopsisHALLMARK_HEDGEHOG_SIGNALING-0[Summary: Genes are involved in a variety of cellular processes, including cell adhesion, signaling, and development.\\n\\nMechanism: These genes appear to converge on pathways related to cellular communication, regulation of gene expression, and cytoskeletal organization.\\n\\n][Summary: The enriched terms for these genes reveal involvement in various cellular processes, including signal transduction, development, and gene regulation.\\n\\nMechanism: The underlying biological mechanism for these enriched terms involve complex cellular processes that are regulated by multiple genes and signaling pathways.\\n\\n]0.9159
327gpt-3.5-turboontological_synopsisHALLMARK_HEDGEHOG_SIGNALING-1[Summary: Cell signaling and adhesion, transcriptional regulation, and nervous system development are common functions among the given genes.\\n\\nMechanism: These genes seem to be involved in the regulation of various signaling pathways, which contribute to important biological processes.\\n\\n][Summary: Genes are involved in various processes such as cell adhesion, transcription regulation, and signal transduction. \\nMechanism: Biological mechanism involves regulation of gene expression and signal transduction pathways. \\n]0.9257
328gpt-3.5-turboontological_synopsisHALLMARK_HEME_METABOLISM-0[Summary: These genes are involved in various biological processes, including enzymatic activities, transcriptional regulation, and ion transport. The enriched terms include heme binding, protein binding activity, transcription factor activity, and transmembrane transporter activity.\\n\\nMechanism: The underlying biological mechanism involves the regulation of various metabolic pathways and cellular processes, such as DNA transcription, ion transport, and protein function.\\n\\n][Summary: Several of the genes on the list are involved in binding and transportation activity, as well as enzyme activity.\\n\\nMechanism: These genes may play a role in metabolic and cellular processes through the transport and binding of various molecules, as well as enzymatic activity.\\n\\n]0.93188
329gpt-3.5-turboontological_synopsisHALLMARK_HEME_METABOLISM-1[Summary: Transport and binding activity \\n\\nHypothesis: These genes may be involved in pathways related to transport regulation, signaling, redox homeostasis, and gene expression. Further studies may explore the role of these genes in these cellular processes.][Mechanism: Protein binding activity\\n\\nHypothesis: The common mechanism among these genes is their protein binding activity, which includes enzyme binding activity, protein domain specific binding activity, protein heterodimerization activity, identical protein binding activity, and protein homodimerization activity. These genes may interact with and regulate each other's activity through their protein binding domains, leading to coordinated cellular processes. Alternatively, they may play a role in the assembly of larger protein complexes necessary for various cellular functions.]0.90327
330gpt-3.5-turboontological_synopsisHALLMARK_HYPOXIA-0[Summary: Enriched terms show functions related to carbohydrate metabolism, enzyme binding and activity, signaling receptor binding, and DNA-binding transcription factor activity.\\n\\nMechanism: These genes may be involved in various biological mechanisms, such as carbohydrate metabolism, gene expression regulation, and receptor signaling pathways.\\n\\n][Summary: Many of the genes listed are involved in binding, catalytic activity, and enzyme activity. \\nMechanism: These genes are likely involved in metabolic processes and signaling pathways. \\n\\n\\nHypothesis: These genes are involved in a complex network of metabolic processes and signaling pathways, potentially involving kinases, transcription factors, and calcium signaling. They may contribute to the regulation of enzyme activity, protein binding, and metabolic pathways in the body.]0.90139
331gpt-3.5-turboontological_synopsisHALLMARK_HYPOXIA-1[Summary: Enriched terms indicate genes involved in metabolic activities, specifically related to glucose metabolism and kinase activities, as well as transcriptional regulation and signaling.\\n\\nMechanism: These genes likely play a role in various cellular processes involved in metabolism, gene regulation, and signaling cascades.\\n\\n][Summary: Functions enriched in this list of genes include binding activities (such as protein, ion, and growth factor binding) and enzymatic activities (such as kinase, dehydrogenase, and transferase activity). \\n\\nMechanism: These common functions suggest that the genes in this list are involved in various cellular processes that require binding and enzymatic activities, such as signal transduction, metabolism, and cell growth and differentiation.\\n\\n]0.90121
332gpt-3.5-turboontological_synopsisHALLMARK_IL2_STAT5_SIGNALING-0[Summary: Regulation of cytokines and immune responses.\\nMechanism: Modulation of cytokine signaling and immune response pathways.\\n\\nHypothesis: These genes are involved in regulating cytokine signaling and immune response pathways, potentially modulating the response to infection or other immune challenges. They may play a role in the regulation of lymphocyte activation and differentiation, including T cell costimulation and negative regulation of activation, and have been implicated in defense responses to pathogens. Additionally, these genes appear to be involved in cytokine signaling regulation through modulation of cytokine receptor binding and interleukin binding activity.][Summary: The common function of the listed genes is binding activity, including protein and DNA binding. \\n\\n]0.82578
333gpt-3.5-turboontological_synopsisHALLMARK_IL2_STAT5_SIGNALING-1[Summary: Enriched terms are related to immune function and cytokine activity.\\n\\n][Summary: Signaling and cytokine receptor activity, protein binding activity, enzyme activity, DNA binding activity, RNA binding activity, several processes including apoptosis and cellular response to cytokines.\\n\\n]0.84134
334gpt-3.5-turboontological_synopsisHALLMARK_IL6_JAK_STAT3_SIGNALING-0[Summary: Cytokine and growth factor signaling pathways\\nMechanism: These genes are all involved in the process of cytokine and growth factor signaling pathways which regulate a wide range of biological processes.\\n][Summary: Cytokine and growth factor receptor activity\\nMechanism: Signal transduction\\n]0.91127
335gpt-3.5-turboontological_synopsisHALLMARK_IL6_JAK_STAT3_SIGNALING-1[Summary: Cytokine signaling and immune response\\nMechanism: These genes are involved in cytokine and chemokine receptor binding and cytokine-mediated signaling pathways, particularly those related to immune response and defense against other organisms.\\n\\n][Summary: The enriched terms suggest that these genes are involved in cytokine activity and signaling pathways.\\nMechanism: These genes are likely involved in the regulation of the immune system through cytokines and signaling pathways.\\n]0.9218
336gpt-3.5-turboontological_synopsisHALLMARK_INFLAMMATORY_RESPONSE-0[Summary: These genes are involved in various functions relating to cytokine and chemokine activity, enzyme binding activity, receptor activity, and ion transport.\\n\\n\\nHypothesis: These genes play a role in immune system function, possibly involved in chemotaxis and signal transduction pathways through cytokine and chemokine activity, as well as ion transport in cell signaling. The genes may also be involved in enzyme binding and receptor activity, which could potentially affect various biological processes and disease pathways.][Summary: Signaling and cell communication through the immune system and cytokines.\\nMechanism: The genes listed enable cytokine activity, cytokine receptor activity, G protein-coupled receptor activity, and enzyme binding activity, with a particular emphasis on the immune system. \\n]0.91251
337gpt-3.5-turboontological_synopsisHALLMARK_INFLAMMATORY_RESPONSE-1[Summary: These genes are involved in various biological processes, including receptor and transporter activity, cytokine activity, and signal transduction.\\n\\n][Summary: Cell signaling and receptor binding activity are enriched in the list of genes.\\n\\nMechanism: These genes are involved in cellular signaling, including binding to receptors and activation of downstream pathways.\\n\\n]0.9163
338gpt-3.5-turboontological_synopsisHALLMARK_INTERFERON_ALPHA_RESPONSE-0[Summary: Immune response genes that are involved in cytokine activity, defense response to other organisms, and negative regulation of viral entry into host cells. \\n\\nMechanism: These genes are likely involved in the innate immune response to infection, particularly in the modulation of viral infection and replication. \\n\\n][Summary: Many of the genes listed are involved in immune response and antigen processing and presentation, including cytokines, chemokines, and interferon-related genes. Additionally, several genes are involved in RNA processing and editing.\\n\\n\\nHypothesis: These genes may be involved in immune recognition and response to foreign pathogens, potentially through antigen presentation and cytokine/chemokine-mediated immune cell recruitment and activation. The RNA-related genes may be involved in post-transcriptional regulation of immune-related genes.]0.91230
339gpt-3.5-turboontological_synopsisHALLMARK_INTERFERON_ALPHA_RESPONSE-1[Summary: These genes are involved in immune response, defense against virus, negative regulation of protein secretion, regulation of leukocyte chemotaxis, RNA binding, and regulation of transcription.\\n\\nMechanism: The biological mechanism is likely the activation of the immune response, specifically the interferon response.\\n\\n][Summary: Many of the genes are involved in immune response and defense against viruses, as well as regulation of protein activity.\\n\\nMechanism: The enriched terms suggest an underlying biological mechanism of antiviral defense and immune response pathways.\\n\\n]0.9169
340gpt-3.5-turboontological_synopsisHALLMARK_INTERFERON_GAMMA_RESPONSE-0[Summary: Immune response and cytokine signaling-related genes.\\n\\n][Summary: Immune system processes and regulation are enriched in the list of genes.\\n\\nMechanism: These genes are involved in various immune system processes, from cytokine and chemokine activity to transcription factor binding and protein homodimerization. \\n\\n\\nHypothesis: The enriched immune system processes and regulation may be involved in the regulation and response to external stimuli, such as infections or tissue damage, and the maintenance of internal homeostasis. The different gene functions may work together in a network to activate or inhibit immune responses and protect the body from harmful agents.]0.89550
341gpt-3.5-turboontological_synopsisHALLMARK_INTERFERON_GAMMA_RESPONSE-1[Summary: Immune system activity, particularly in response to viral infection, is the overarching theme among the functions of these genes.\\nMechanism: These genes are involved in various aspects of the immune response, including innate antiviral defense, antigen presentation, cytokine signaling, and regulation of immune cell activation and proliferation.\\n][Summary: Genes involved in immune response, from antigen presentation to cytokine signaling and antiviral defense.\\n\\nMechanism: These genes are involved in various aspects of the immune response, including antigen presentation through MHC class I and II complexes, cytokine signaling through STAT proteins, and antiviral defense through interferon-stimulated genes.\\n\\n]0.9510
342gpt-3.5-turboontological_synopsisHALLMARK_KRAS_SIGNALING_DN-0[Summary: Ion transport and binding activity\\nMechanism: Ion channel and transporter activity\\n\\nHypothesis: These genes are involved in various ion transport mechanisms and have binding activity for different ions, including calcium and sodium: potassium:chloride. They may be part of a larger pathway involved in regulating ion concentration and signaling in the cell.][Summary: Protein binding and enzyme activity.\\n\\n\\nHypothesis: The overrepresented terms suggest that these genes may be involved in a complex protein-protein interaction network, with many proteins acting as enzymes that catalyze a reaction and interact with other proteins through binding activity. Additionally, many of these proteins may act as transcription factors, influencing gene expression by binding to DNA and regulating transcription. Ion binding activity may also be involved in many of these processes, as ions are important cofactors for many enzymes and can influence protein structure and function.]0.90247
343gpt-3.5-turboontological_synopsisHALLMARK_KRAS_SIGNALING_DN-1[Summary: The enriched terms are related to binding activity and transport, specifically involving ion, protein, and nucleoside.\\n\\n\\nMechanism: The genes in this list are involved in regulating binding activity and transport, likely through ion channels and protein-protein interactions.\\n\\n\\n][Summary: Genes involved in binding and enzymatic activities, as well as regulation of cellular processes.\\n\\n]0.88180
344gpt-3.5-turboontological_synopsisHALLMARK_KRAS_SIGNALING_UP-0[Summary: Several genes are involved in binding activity, such as protein binding, ion binding, and receptor binding. Additionally, some genes are involved in enzyme activity and transcription activator activity. \\n\\n][Summary: Genes involved in binding activity, enzymatic activity, and protein regulation.\\nMechanism: These genes play a role in cellular processes such as signaling, metabolism, and transcriptional regulation.\\n\\n]0.934
345gpt-3.5-turboontological_synopsisHALLMARK_KRAS_SIGNALING_UP-1[Summary: Many of the genes in the list enable various binding activities and are involved in regulation of cellular processes.\\n\\n][Summary: Protein binding and enzymatic activity\\n]0.8580
346gpt-3.5-turboontological_synopsisHALLMARK_MITOTIC_SPINDLE-0[Summary: Genes involved in cytoskeleton organization, microtubule binding, and GTPase regulation.\\n\\nMechanism: These genes are predicted to be involved in various aspects of cytoskeleton organization and microtubule regulation, including microtubule binding, kinetochore binding, and actin filament binding. They are also predicted to be involved in the regulation of GTPases, which have been shown to play critical roles in cytoskeletal organization.\\n\\n][Summary: Several genes are involved in cytoskeleton organization and regulation, including microtubule binding, actin binding, and GTPase activator activity.\\n\\nMechanism: The regulation of cytoskeleton stability and dynamics is crucial for many cellular processes, including cell division, migration, and differentiation. These genes likely play key roles in maintaining cytoskeleton integrity and regulating its rearrangement through protein-protein interactions and enzymatic activities.\\n\\n]0.9638
347gpt-3.5-turboontological_synopsisHALLMARK_MITOTIC_SPINDLE-1[Summary: The enriched terms suggest that these genes are involved in microtubule organization and mitosis.\\n\\nMechanism: These genes play a role in regulating microtubule organization and mitosis, potentially through interactions with other proteins in the cytoskeleton and spindle apparatus.\\n\\n][Summary: Genes are primarily involved in microtubule binding and regulation, as well as cell division processes such as mitosis and cytokinesis. \\n\\n]0.90145
348gpt-3.5-turboontological_synopsisHALLMARK_MTORC1_SIGNALING-0[Summary: Many of the genes are involved in binding activities, including RNA binding, protein binding, and ion binding, and several are involved in enzymatic activity such as oxidoreductase and kinase activity. \\n\\nMechanism: The enriched functions suggest that these genes are involved in protein synthesis and processing, as well as intracellular signaling and metabolism. \\n\\n][Summary: Many of the genes listed are involved in protein or RNA binding, enzymatic activity, and structural components of cells. \\n\\n]0.94243
349gpt-3.5-turboontological_synopsisHALLMARK_MTORC1_SIGNALING-1[Summary: These genes are involved in several cellular processes, including protein binding and enzyme activity. \\n\\n][Summary: The enriched terms across these genes suggest a common theme of protein folding, transport, and degradation. \\n\\nMechanism: These genes are involved in the regulation of protein folding, transport, and degradation, likely through the ubiquitin-proteasome system and endoplasmic reticulum-associated degradation pathway.\\n\\n]0.90214
350gpt-3.5-turboontological_synopsisHALLMARK_MYC_TARGETS_V1-0[Summary: Protein synthesis and folding\\n\\n][Summary: Ribosome and protein synthesis-related activity\\nMechanism: Protein synthesis and ribosome biogenesis\\n\\nHypothesis: The enriched terms suggest that the genes in this list are involved in fundamental cellular processes related to protein synthesis and ribosome biogenesis. They are likely necessary for proper folding, transport, binding, and localization of mRNA and ribosomes, which are essential for protein synthesis. The genes on the list may function together to regulate these processes, playing key roles in fine-tuning protein production during development, cellular differentiation, and stress responses.]0.86581
351gpt-3.5-turboontological_synopsisHALLMARK_MYC_TARGETS_V1-1[Summary: These genes are involved in nucleic acid binding, RNA processing, protein folding, and structural constituents of ribosomes.\\n\\n][Summary: RNA processing and binding activity\\n\\n]0.9089
352gpt-3.5-turboontological_synopsisHALLMARK_MYC_TARGETS_V2-0[Summary: These genes are predominantly involved in RNA and protein processing, with many of them predicted to have RNA binding activity and be involved in rRNA processing. They also play roles in cell cycle regulation and mitochondrial function.\\n\\nMechanism: These genes likely function together in various pathways involved in RNA and protein processing, including rRNA processing, mRNA catabolism, and RNA maturation.\\n\\n][Summary: This set of human genes is enriched for terms related to RNA processing, specifically rRNA processing and biogenesis. \\n\\nMechanism: These genes likely participate in a common biological pathway related to ribosome biogenesis and function.\\n\\n]0.92172
353gpt-3.5-turboontological_synopsisHALLMARK_MYC_TARGETS_V2-1[Summary: The enriched terms from these genes suggest involvement in various aspects of RNA processing and nucleolar function.\\n\\nMechanism: These genes encode proteins involved in RNA processing and nucleolar function.\\n\\n][Summary: Genes involved in RNA processing, rRNA processing, and ribosomal biogenesis.\\n\\nMechanism: These genes contribute to the production and processing of ribosomal RNA (rRNA) involved in ribosomal biogenesis. rRNA molecules are important components of ribosomes, which are responsible for protein synthesis in cells.\\n\\n]0.90103
354gpt-3.5-turboontological_synopsisHALLMARK_MYOGENESIS-0[Summary: The common function among the genes is related to muscle function and regulation.\\n\\nMechanism: The genes are all involved in the muscle cell structure, regulation, and function, including contraction, signaling, and development.\\n\\n][Summary: These human genes are enriched for terms related to muscle structure and function, including actin binding and ATP activity.\\n\\nMechanism: These genes likely play a role in muscle development and function, as well as related processes such as calcium ion binding and molecular adaptor activity.\\n\\n]0.9065
355gpt-3.5-turboontological_synopsisHALLMARK_MYOGENESIS-1[Summary: Muscle structure and function\\n\\n][Summary: Muscle and cytoskeletal proteins are enriched in this list of genes.\\n\\n]0.8339
356gpt-3.5-turboontological_synopsisHALLMARK_NOTCH_SIGNALING-0[Summary: Notch signaling pathway and protein ubiquitination are enriched functions among the given genes.\\n\\nMechanism: The enriched functions suggest that these genes are involved in a biological pathway related to the regulation of Notch signaling pathway and protein ubiquitination.\\n\\n][Summary: The enriched terms suggest that the listed genes are involved in various aspects of cellular signaling pathways, including Notch, Wnt, and ubiquitin-mediated protein degradation.\\n\\nMechanism: The mechanism underlying the commonalities in function may be related to the fact that many of these genes are involved in the regulation of gene expression and cellular signaling pathways that are critical for embryonic development and tissue homeostasis.\\n\\n]0.93173
357gpt-3.5-turboontological_synopsisHALLMARK_NOTCH_SIGNALING-1[Summary: The enriched terms include \"Notch signaling pathway,\" \"protein ubiquitination,\" \"negative regulation of cell differentiation,\" and \"regulation of DNA-templated transcription.\"\\n\\nMechanism: These genes are involved in processes related to intracellular signaling and protein regulation.\\n\\n\\nHypothesis: These genes are involved in a complex regulatory network that fine-tunes protein levels and intracellular signaling pathways to ensure proper cell differentiation and development. The Notch signaling pathway is a key pathway involved in cell differentiation and is regulated by ubiquitination and transcriptional control. The enriched terms likely reflect the importance of these processes in maintaining proper cell function and development.][Summary: Notch signaling pathway and protein ubiquitination are enriched terms among these genes.\\nMechanism: These genes are involved in the regulation of cell differentiation, stem cell population maintenance, and DNA-templated transcription, which are processes that require the Notch signaling pathway for their proper function. Additionally, several of these genes are involved in ubiquitination, a process that targets proteins for degradation or signaling.\\n]0.97288
358gpt-3.5-turboontological_synopsisHALLMARK_OXIDATIVE_PHOSPHORYLATION-0[Summary: Genes in this list are involved in various aspects of mitochondrial function and metabolism, including electron transport chain activity, ATP synthesis, and metabolism of acyl-CoA and ketone bodies.\\n\\n\\nHypothesis: These genes are involved in different parts of mitochondrial metabolism and energy production, but they all work together to maintain proper mitochondrial function. Dysregulation of these genes could lead to disruptions in the electron transport chain and oxidative phosphorylation, which could contribute to mitochondrial dysfunction and metabolic disorders. Further research is needed to fully understand the underlying pathways and mechanisms by which these genes interact to maintain mitochondrial homeostasis.][Summary: Mitochondrial respiratory chain complex activity.\\n\\nHypothesis: Mitochondria are the powerhouse of the cell and play a crucial role in energy production, most notably through oxidative phosphorylation in which electrons pass through a series of complexes in the mitochondrial respiratory chain to generate ATP. The enriched terms of this gene list, such as electron transfer activity, NADH dehydrogenase (ubiquinone) activity, and ubiquitin protein ligase binding activity, directly relate to the functionality of the mitochondrial respiratory chain. Additionally, the RNA binding activity and protein homodimerization activity suggest the regulation and maintenance of these complexes. The metal ion binding activity could also be related to the involvement of metal ions, such as iron or copper, in electron transport.]0.8992
359gpt-3.5-turboontological_synopsisHALLMARK_OXIDATIVE_PHOSPHORYLATION-1[Summary: These human genes have functions related to mitochondrial respiratory chain complexes and enzyme activity, as well as ion and molecule transport across mitochondrial membranes.\\n\\nMechanism: These genes are involved in the electron transport chain in the mitochondria. The electron transport chain generates ATP by transferring electrons from NADH and other electron donors to oxygen.\\n\\n][Summary: Several of these genes are involved in mitochondrial functions such as respiratory chain complex activity and ATP synthase activity. They also play roles in metabolic processes such as electron transfer activity and oxidoreductase activity.\\n\\n]0.95142
360gpt-3.5-turboontological_synopsisHALLMARK_P53_PATHWAY-0[Summary: Enriched terms include regulation of apoptotic process, protein binding activity, and DNA-binding transcription factor activity. \\n\\nMechanism: These genes are involved in regulating apoptosis and controlling cell death. They also play a role in gene regulation and transcription factor activity through protein binding. \\n\\n][Summary: These genes are involved in various functions, including DNA binding, protein binding, enzyme activity, transcription factor activity, and growth factor activity.\\n\\n]0.91157
361gpt-3.5-turboontological_synopsisHALLMARK_P53_PATHWAY-1[Summary: RNA binding and transcription factor activity are enriched in these genes.\\nMechanism: These genes are involved in regulating gene expression at the transcriptional level and RNA processing.\\n][Summary: These genes are involved in a variety of functions, including DNA binding, protein binding, and kinase activity.\\n\\n]0.8976
362gpt-3.5-turboontological_synopsisHALLMARK_PANCREAS_BETA_CELLS-0[Summary: Genes are involved in various processes including glucose homeostasis, insulin secretion, and transcription regulation.\\n\\nMechanism: Genes work together to regulate glucose homeostasis and insulin secretion.\\n\\n][Summary: Several of the genes are involved in glucose metabolism and regulation of insulin secretion.\\n\\nMechanism: These genes likely play a role in the regulation of blood sugar levels and insulin secretion through various cellular mechanisms.\\n\\n]0.9628
363gpt-3.5-turboontological_synopsisHALLMARK_PANCREAS_BETA_CELLS-1[Summary: Genes related to glucose homeostasis, insulin secretion, and glucose metabolism are enriched.\\n\\n\\nHypothesis: These genes may be involved in a pathway or mechanism related to glucose regulation and diabetes, potentially influencing glucose uptake, storage, and secretion.][Summary: Many of the genes are involved in insulin secretion or glucose metabolism, suggesting a potential role in diabetes. Additionally, several genes are involved in transcriptional regulation or regulation of gene expression.\\n\\n\\nHypothesis: \\nThe enriched terms suggest that several of these genes may be involved in a common regulatory pathway controlling insulin secretion and glucose metabolism. Specifically, the transcriptional regulation of genes involved in insulin secretion and glucose metabolism may be mediated by RNA polymerase II-specific transcription factors, which can bind to specific cis-regulatory regions of these genes to control their expression. Negative regulatory factors can suppress gene expression, while positive regulatory factors can increase expression. Dysfunction in any of these genes, therefore, could lead to defects in insulin secretion or glucose metabolism, potentially contributing to the development of type 1 or type 2 diabetes mellitus.]0.94704
364gpt-3.5-turboontological_synopsisHALLMARK_PEROXISOME-0[Summary: Several of the genes listed are involved in transport functions and enzyme activities related to lipid and fatty acid metabolism. Additionally, some genes are involved in binding and catalytic functions related to retinoids and steroids.\\n\\n\\nHypothesis: These genes are involved in several functions that are key to cellular metabolism and homeostasis. Lipid and fatty acid metabolism are essential for maintaining membrane integrity and cellular signaling processes. Transporters and enzymes related to these functions are necessary for proper uptake, utilization, and metabolism of lipids and fatty acids. Additionally, retinoids and steroids are important signaling molecules that can be involved in metabolic processes and cellular differentiation. The presence of these genes suggests that dysregulation of lipid, fatty acid, retinoid, or steroid metabolism could lead to disease states such as metabolic disorders, cancer, or developmental abnormalities.][Summary: The enriched terms suggest that these genes are involved in lipid metabolism and transport, as well as binding and catalysis.\\n\\nMechanism: These genes likely function together in cellular lipid metabolism and transport pathways, potentially in peroxisomes or mitochondria.\\n\\n]0.93686
365gpt-3.5-turboontological_synopsisHALLMARK_PEROXISOME-1[Summary: Most of the genes are involved in lipid or fatty acid metabolism and transport, including long-chain fatty acid-CoA ligase activity, palmitoyl-CoA oxidase activity, arachidonate-CoA ligase activity, very long-chain fatty acid-CoA ligase activity, and several other related terms.\\n\\nMechanism: These genes likely play a role in regulating lipid homeostasis and transport, possibly through peroxisome biogenesis and function, as several genes also have peroxisome-targeting sequence binding activity.\\n\\n][Summary: Many of these genes are involved in lipid metabolism and transport, mitochondrial function, and DNA repair. \\n\\nMechanism: These genes may be involved in maintaining cellular homeostasis by regulating lipid metabolism and mitochondrial function, as well as protecting DNA from damage. \\n\\n]0.92214
366gpt-3.5-turboontological_synopsisHALLMARK_PI3K_AKT_MTOR_SIGNALING-0[Summary: Genes are involved in various cellular processes, including protein kinase activity, cytoskeleton structure, lipid metabolism, and protein binding activity.\\n\\nMechanism: These genes are involved in different pathways that regulate cellular signaling and metabolic processes.\\n\\n][Summary: Genes in this list are largely involved in signal transduction pathways, including protein kinase activity, G protein-coupled receptor binding activity, and transcription factor binding activity.\\n\\nMechanism: These genes likely function in several interconnected signaling pathways, including the MAPK/ERK pathway, PI3K/Akt pathway, and NF-kappaB pathway.\\n\\n]0.9281
367gpt-3.5-turboontological_synopsisHALLMARK_PI3K_AKT_MTOR_SIGNALING-1[Summary: Several of the genes are involved in intracellular signal transduction and several processes related to protein phosphorylation. \\n\\n][Summary: Intracellular signal transduction and protein phosphorylation.\\nMechanism: These genes are involved in intracellular signal transduction processes which involve the phosphorylation of proteins.\\n]0.9562
368gpt-3.5-turboontological_synopsisHALLMARK_PROTEIN_SECRETION-0[Summary: The enriched terms involve the transport and organization of cellular components, particularly in Golgi-related processes.\\n\\nMechanism: These genes likely contribute to the regulation of cellular transport and trafficking pathways involved in Golgi function and organization.\\n\\n][Summary: Golgi apparatus-related processes are enriched in this list of genes.\\n\\nMechanism: The genes in this list are involved in various processes related to Golgi apparatus homeostasis, organization, transport, and vesicle-mediated recycling.\\n\\n]0.9339
369gpt-3.5-turboontological_synopsisHALLMARK_PROTEIN_SECRETION-1[Summary: Intracellular vesicle transport and protein localization\\nMechanism: Vesicle-medidated transport pathways\\n][Summary: This set of genes is enriched for functions related to intracellular membrane trafficking and transport.\\n\\n\\nHypothesis: These genes are involved in various steps of intracellular transport and vesicle-mediated trafficking between the endoplasmic reticulum and the Golgi complex. The enriched terms are likely reflections of this shared functional theme. It is possible that the proteins encoded by these genes interact with each other to form complexes or pathways that regulate this process. Further investigation may reveal more details about the specific mechanisms involved in these functions.]0.87492
370gpt-3.5-turboontological_synopsisHALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0[Summary: Genes involved in cell redox homeostasis and antioxidant activity are enriched.\\n\\nMechanism: These genes function in maintaining the balance of redox reactions in cells and protecting against oxidative damage.\\n\\n][Summary: Cell redox homeostasis and response to oxidative stress are enriched functional themes among the listed genes.\\n\\nMechanism: Genes in this group function in maintaining cellular redox balance by regulating the activity of reactive oxygen species (ROS) and oxidative stress response pathways. \\n\\n]0.9482
371gpt-3.5-turboontological_synopsisHALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1[Summary: Cell redox homeostasis and oxidative stress response\\nMechanism: Regulating and maintaining redox balance within cells to prevent oxidative damage\\n\\nHypothesis: These genes play important roles in maintaining cellular redox homeostasis and responding to oxidative stress. This includes antioxidant activity and the regulation of glutathione peroxidase and superoxide dismutase activities. Additionally, these genes are involved in NADH dehydrogenase activity and mitochondrial respiratory chain complex I assembly, both of which are crucial for cellular respiration and energy production. Together, these processes ensure the proper functioning of cells and protect against oxidative damage.][Summary: Cell redox homeostasis and response to oxidative stress are enriched terms in the gene list.\\n\\nMechanism: These genes are involved in maintaining cellular redox balance by regulating oxidant detoxification pathways and responding to oxidative stress.\\n\\n]0.95439
372gpt-3.5-turboontological_synopsisHALLMARK_SPERMATOGENESIS-0[Summary: These genes are involved in a variety of processes including protein binding, enzyme activity, and ion transport. They are enriched for terms related to kinase activity, protein binding, and nucleotide binding.\\n\\nMechanism: These genes may be involved in the regulation of cell signaling and communication pathways through the activity and binding of kinases, proteins, and nucleotides.\\n\\n][Summary: This list of human genes is highly enriched in genes involved in protein binding and kinase activity, as well as in genes involved in cell cycle regulation and gene expression.\\nMechanism: The enriched terms suggest that these genes are involved in cellular processes that require the binding and modification of proteins, particularly during cell cycle regulation and gene expression.\\n]0.952
373gpt-3.5-turboontological_synopsisHALLMARK_SPERMATOGENESIS-1[Summary: The enriched terms include protein binding and enzymatic activity, involvement in several processes such as cell signaling, transcription, and metabolism, and localization to specific cellular structures.\\n\\nMechanism: These genes are involved in various biological processes that rely on protein-protein interactions, enzymatic activity, and regulation of various cellular functions.\\n\\n\\nHypothesis: These enriched terms suggest that the genes are involved in various biological pathways that are essential for maintaining cellular functions, including protein folding, transcription, signaling, and regulation of metabolism. These genes may also play a role in cellular localization and transport of specific molecules. Overall, these genes are integral to maintaining cellular homeostasis and their dysregulation could contribute to various diseases.][Summary: Many of the identified genes are involved in cellular processes such as protein binding, enzyme activator/inhibitor activity, and ATP binding activity.\\n\\nMechanism: The underlying biological mechanism may involve regulating cellular processes through protein interactions and/or enzyme regulation.\\n\\n]0.93552
374gpt-3.5-turboontological_synopsisHALLMARK_TGF_BETA_SIGNALING-0[Summary: Genes involved in transforming growth factor beta (TGF-β) receptor signaling and related pathways are over-represented.\\n\\nMechanism: TGF-β receptor signaling is central to the regulation of cell growth and differentiation and is involved in numerous biological processes.\\n\\n][Summary: The enriched terms are related to cellular signaling and development processes, particularly those involving the transforming growth factor-beta (TGF-beta) signaling pathway.\\n\\nMechanism: These genes are involved in the TGF-beta signaling pathway, which regulates cellular processes such as proliferation, differentiation, and apoptosis.\\n\\n]0.9266
375gpt-3.5-turboontological_synopsisHALLMARK_TGF_BETA_SIGNALING-1[Summary: Genes involved in various aspects of signal transduction and regulation of gene expression.\\n\\n][Summary: Signaling through TGF-beta superfamily and BMP receptor-related pathways\\nMechanism: TGF-beta and BMP ligands bind to type II receptors, which activate type I receptors. The activated type I receptors phosphorylate SMAD transcription factors, which activate or repress target gene expression.\\n]0.84199
376gpt-3.5-turboontological_synopsisHALLMARK_TNFA_SIGNALING_VIA_NFKB-0[Summary: The enriched terms for these genes suggest a role in immune response, cytokine activity, DNA-binding transcription factor activity, and enzyme binding activity.\\n\\nMechanism: These genes may play a role in activating or regulating the immune response and cytokine production through DNA-binding transcription factor activity and enzyme binding activity.\\n\\n][Summary: Transcription regulation and cytokine activity.\\n\\nHypothesis: These genes may be involved in the regulation of immune responses, cellular differentiation, and tissue growth and repair. They may interact with signaling pathways involved in cytokine production and response, such as the JAK-STAT pathway and the NF-kappaB pathway.]0.9125
377gpt-3.5-turboontological_synopsisHALLMARK_TNFA_SIGNALING_VIA_NFKB-1[Summary: Genes on the list are involved in cytokine activity, DNA-binding transcription activities, and several enzymatic activities.\\n\\n][Summary: The enriched terms are related to immune system processes and cytokine signaling pathways.\\nMechanism: These genes are involved in regulating cytokine receptor activity and immune system signaling pathways, likely through activation of MAP kinase and transcription factor pathways.\\n\\n]0.88156
378gpt-3.5-turboontological_synopsisHALLMARK_UNFOLDED_PROTEIN_RESPONSE-0[Summary: These genes are predominantly involved in protein processing, modification, and transport. \\n\\nMechanism: These genes are involved in various stages of protein synthesis, folding, and transport, including post-translational modifications, protein chaperoning, and trafficking. \\n\\n][Summary: Many of the genes are involved in protein folding and chaperone activity, RNA binding and transcriptional regulation, and RNA processing and degradation.\\n\\nMechanism: The common mechanism might be related to the regulation of protein homeostasis, with these genes functioning in different aspects of protein folding, RNA binding and processing, and transcriptional regulation.\\n\\n]0.93100
379gpt-3.5-turboontological_synopsisHALLMARK_UNFOLDED_PROTEIN_RESPONSE-1[Summary: All of the genes are involved in molecular functions related to RNA, protein, and ribosomal binding activity.\\nMechanism: These genes likely play a role in the regulation of transcription, translation, and protein folding.\\n][Summary: These genes are involved in various cellular processes, with a common theme of RNA and protein regulation, as well as involvement in endoplasmic reticulum (ER) stress response pathways.\\n\\nMechanism: These genes may be involved in regulating RNA and protein synthesis and processing, as well as responding to cellular stress, particularly ER stress.\\n\\n]0.92127
380gpt-3.5-turboontological_synopsisHALLMARK_UV_RESPONSE_DN-0[Summary: Extracellular matrix structural constituent, growth factor binding, protein kinase activity, nucleotide binding, transcription factor activity, protein binding.\\n\\n][Summary: Extracellular matrix structural constituent and protein binding activity are enriched functions amongst the given human genes.\\nMechanism: These genes may play a role in cellular adhesion, migration, and signal transduction processes.\\n]0.9172
381gpt-3.5-turboontological_synopsisHALLMARK_UV_RESPONSE_DN-1[Summary: Extracellular matrix structural constituents and binding activity.\\nMechanism: Extracellular matrix formation and maintenance.\\n\\n][Summary: Extracellular matrix structural constituents, protein binding, transcription activator activity, and receptor binding are enriched terms among these genes.\\nMechanism: The enriched terms suggest that these genes may be involved in cell signaling pathways and extracellular matrix formation.\\n]0.90163
382gpt-3.5-turboontological_synopsisHALLMARK_UV_RESPONSE_UP-0[Summary: Many of the enriched terms relate to protein binding and enzyme activity.\\n\\n][Summary: Enriched terms suggest involvement in protein binding, enzymatic activity, and transcriptional regulation.\\nMechanism: These genes likely play a role in various cellular processes that involve protein-protein interactions, enzymatic reactions, and transcriptional regulation.\\n\\n]0.92201
383gpt-3.5-turboontological_synopsisHALLMARK_UV_RESPONSE_UP-1[Summary: Genes enriched for ion transport, enzyme activity, DNA-binding, and protein binding\\n\\nMechanism: These genes likely play a role in various cellular processes including ion transport, metabolic processes, and gene expression regulation.\\n\\n][Summary: Molecular Function Inhibitor Activity and Protein Binding Activity\\nMechanism: Molecular inhibition of various cellular processes\\n]0.83107
384gpt-3.5-turboontological_synopsisHALLMARK_WNT_BETA_CATENIN_SIGNALING-0[Summary: Genes are involved in Wnt signaling pathway and regulation of transcription, with a focus on negative regulation of canonical Wnt signaling pathway. \\n\\nMechanism: The genes listed are all involved in the Wnt signaling pathway, specifically the negative regulation of canonical Wnt signaling pathway. \\n\\n][Summary: Genes are involved in the Wnt signaling pathway and regulation of transcription by RNA polymerase II.\\nMechanism: The identified genes all function in the Wnt signaling pathway and particularly in the regulation of transcription by RNA polymerase II. This pathway plays a crucial role in embryonic development and cellular proliferation, and dysregulation can contribute to the development of multiple diseases, including cancer and developmental disorders.\\n]0.95156
385gpt-3.5-turboontological_synopsisHALLMARK_WNT_BETA_CATENIN_SIGNALING-1[Summary: These genes are involved in multiple signaling pathways, including Wnt and Notch signaling pathways, as well as protein degradation processes such as ubiquitination and proteolysis.\\nMechanism: These genes function to regulate cell proliferation, differentiation, and fate through activation or inhibition of specific signaling pathways.\\n\\nHypothesis: These genes function to maintain cellular homeostasis by regulating important signaling pathways and protein degradation processes. Dysregulation of these pathways may lead to abnormal cell growth, differentiation, and function, contributing to the development of various diseases such as cancer and neurodegenerative disorders.][Summary: Genes involved in Wnt signaling pathway and regulation of gene expression.\\nMechanism: Wnt signaling pathway regulates gene expression through the interaction of Wnt ligands with Frizzled receptors and subsequent activation of downstream signaling pathways.\\n\\nHypothesis: The enrichment of genes involved in Wnt signaling and regulation of gene expression suggests a potential role in developmental processes, as well as potential implications in cancer and neurodegenerative diseases. The dysregulation of Wnt signaling has been implicated in multiple cancers, pointing to the importance of these genes in cellular growth and proliferation. Additionally, the involvement of PSEN2 in amyloid-beta formation highlights the potential role of Wnt signaling in Alzheimer's disease pathology.]0.91107
386gpt-3.5-turboontological_synopsisT cell proliferation-0[Summary: Genes are involved in several processes including intracellular signaling, regulation of immune response, cell recognition, and response to bacterium.\\n\\nMechanism: These genes are mostly involved in intracellular signaling pathways, especially in the regulation of immune response.\\n\\n][Summary: Signaling and receptor binding activity\\n]0.80242
387gpt-3.5-turboontological_synopsisT cell proliferation-1[Summary: Genes enriched in immune system processes, particularly T cell activation, cytokine production, and regulation of gene expression.\\n\\nMechanism: These genes likely function together to regulate the immune response, specifically in T cells. They contribute to T cell activation, cytokine production, and the regulation of gene expression at multiple levels.\\n\\n][Summary: Immune-related genes with a focus on T cell regulation and signaling.\\nMechanism: T cell activation and signaling pathway.\\n]0.92234
388gpt-3.5-turboontological_synopsisYamanaka-TFs-0[Summary: These four genes are involved in transcription regulation and have DNA-binding activity. They are also involved in several cellular processes, such as gene expression regulation, cell proliferation, and differentiation.\\nMechanism: The enriched terms are likely involved in regulating gene expression and cellular differentiation through the binding and regulation of transcription factors.\\n\\n][Summary: Transcriptional regulation and gene expression.\\nMechanism: Gene expression regulation.\\n\\nHypothesis: All the genes listed are involved in transcriptional regulation and gene expression. All of these genes have DNA-binding transcription factor activity, and a role in the regulation of gene expression. They are involved in positive or negative regulation of transcription by RNA polymerase II, and act upstream of or within several processes such as endodermal cell fate specification, and regulation of biosynthesis and metabolic processes. These genes seem to be part of a broader pathway or mechanism involved in gene expression regulation.]0.92252
389gpt-3.5-turboontological_synopsisYamanaka-TFs-1[Summary: Transcriptional regulation and developmental processes\\n\\nMechanism: Transcriptional regulation and cell fate specification\\n\\n][Summary: Transcription regulation and gene expression\\nMechanism: Transcriptional regulation\\n]0.9440
390gpt-3.5-turboontological_synopsisamigo-example-0[Summary: The enriched terms describe genes involved in extracellular matrix organization, cell signal transduction, and blood coagulation.\\n\\nMechanism: The genes share functions necessary for proper extracellular matrix organization and remodeling, including interactions with integrins and collagen-containing matrix components. They also share cell signaling pathways involved in growth factor binding and receptor activity, as well as regulation of intracellular signal transduction. Finally, several of the genes are involved in blood coagulation and lipid metabolism.\\n\\n][Summary: Extracellular matrix components and their interactions with the cell surface are enriched functions in this gene set.\\n\\nMechanism: These genes are involved in cell-matrix adhesion, collagen fibril organization, and extracellular matrix protein binding and organization. They also have roles in the regulation and binding of lipoproteins.\\n\\n]0.93226
391gpt-3.5-turboontological_synopsisamigo-example-1[Summary: Extracellular matrix structure and function, integrin binding, growth factor activity, and response to external stimuli are enriched functions amongst the listed genes.\\n\\nMechanism: The enriched functions suggest that these genes play a crucial role in tissue development, organization, and homeostasis. They also participate in cellular communication, response to external signals, and signal transduction, possibly shaping key pathways involved in external stimuli responsiveness.\\n\\n][Summary: Genes with diverse functions including extracellular matrix structural constituents, integrin and Notch binding activities, and chemokine activity are enriched for terms related to cell adhesion, migration, and regulation of protein metabolic processes. \\nMechanism: Extracellular matrix remodeling, integrin signaling, and chemokine signaling pathways are likely involved in the common functions of these genes.\\n]0.9371
392gpt-3.5-turboontological_synopsisbicluster_RNAseqDB_0-0[Summary: These genes are enriched for functions involved in protein binding, ion channel activity, transcriptional regulation, and ubiquitin-protein ligase activity.\\n\\nMechanism: The underlying biological mechanism may involve signaling pathways involved in protein regulation, ion transport, and gene expression.\\n\\n][Summary: Several genes are involved in various aspects of protein binding activity and regulation of gene expression, with a focus on transcription factor binding activity.\\n\\nMechanism: The enriched terms suggest a role for these genes in regulating gene expression at the transcriptional level, likely through interaction with DNA and other proteins involved in transcriptional regulation.\\n\\n]0.9377
393gpt-3.5-turboontological_synopsisbicluster_RNAseqDB_0-1[Summary: Genes involved in binding activities, ion channel activity, and transcription factor activity.\\nMechanism: These genes are involved in regulating cellular processes by controlling the binding of molecules, ion flow, and gene expression.\\n][Summary: The common function among these genes is the ability to enable binding activities, including metal ion binding, protein domain specific binding, DNA-binding transcription factor activity, and ubiquitin protein ligase activity. They are also involved in several processes, including cell proliferation, development, and regulation of signaling pathways.\\n\\nMechanism: These genes likely play a role in regulating various cellular processes through their binding activities, either by promoting or inhibiting specific protein interactions or by modifying signaling pathways through enzymatic activity.\\n\\n]0.93363
394gpt-3.5-turboontological_synopsisbicluster_RNAseqDB_1002-0[Summary: Genes related to muscle contraction, specifically those involved in myofibril assembly and regulation of muscle adaptation.\\n\\nMechanism: These genes are involved in the structural organization of the myofibril and the regulation of muscle contraction through their functions in actin and myosin binding, tropomyosin binding, and calcium ion binding.\\n\\n][Summary: Enriched terms include muscle contraction, regulation of muscle adaptation, and protein ubiquitination. \\n\\nMechanism: The genes in this list are primarily involved in muscle development and function, as well as protein ubiquitination. \\n\\n\\nHypothesis: The enriched terms suggest that these genes may play a role in regulating muscle growth and adaptation through protein ubiquitination and other mechanisms.]0.8855
395gpt-3.5-turboontological_synopsisbicluster_RNAseqDB_1002-1[Summary: Genes involved in muscle contraction and regulation are statistically over-represented in this list.\\n\\nMechanism: These genes likely play a role in the regulation and contraction of muscle tissue.\\n\\n][Summary: Genes are mostly involved in muscle contraction and structure, ion channel activity, and protein ubiquitination.\\n\\n]0.8983
396gpt-3.5-turboontological_synopsisendocytosis-0[Summary: Receptor-mediated endocytosis and protein transport processes are enriched in these genes.\\nMechanism: These genes play important roles in endocytosis and the transport of proteins between organelles.\\n][Summary: The enriched terms for these genes are related to endocytosis, cellular adhesion, and regulation of signal transduction pathways.\\n\\nMechanism: These genes are involved in various processes such as endocytosis, protein degradation, and signal transduction. They regulate several cellular functions such as cellular adhesion, plasma membrane organization, and lipid transport.\\n\\n\\nHypothesis: The enriched terms suggest that these genes are involved in the regulation of endocytic processes, which are essential for the uptake of various molecules from the extracellular environment. They also play a role in the organization of plasma membrane, which is crucial for cell signaling and signal transduction. The genes are part of the network that regulates cellular adhesion and cytoskeleton organization. They also participate in the regulation of lipid transport, which is essential for maintaining cellular physiology.]0.92716
397gpt-3.5-turboontological_synopsisendocytosis-1[Summary: These genes are involved in various processes related to intracellular transport and signaling, including endocytosis, lysosomal function, and receptor activity.\\nMechanism: These genes likely play a role in cellular transport and communication pathways, with some genes directly involved in intracellular trafficking and others affecting signaling pathways related to immune response and metabolism.\\n][Summary: All genes are involved in membrane-related processes, including endocytosis, protein transport, and cell signaling.\\nMechanism: These genes are essential for membrane traffic and organization.\\n]0.94208
398gpt-3.5-turboontological_synopsisglycolysis-gocam-0[Summary: Enzymes involved in glycolytic processes and carbohydrate metabolism.\\nMechanism: Glycolysis\\n][Summary: These genes are involved in various processes related to carbohydrate metabolism and cellular energy homeostasis.\\n\\nMechanism: The common mechanism underlying the enriched terms is the regulation of glycolysis and energy metabolism in cells.\\n\\n]0.90150
399gpt-3.5-turboontological_synopsisglycolysis-gocam-1[Summary: Genes are involved in metabolic processes and cellular development.\\nMechanism: Glycolysis pathway.\\n][Summary: The common function of these genes is glycolysis and carbohydrate metabolism.\\nMechanism: These genes are involved in the breakdown of glucose to produce energy in the form of ATP. \\n]0.9282
400gpt-3.5-turboontological_synopsisgo-postsynapse-calcium-transmembrane-0[Summary: Genes involved in calcium ion transport and signaling, as well as neurotransmitter receptor activity, are statistically over-represented. \\n\\nMechanism: These genes likely play a role in synaptic transmission and neuronal signaling. \\n\\n][Summary: The enriched terms include calcium ion transport, voltage-gated calcium channel activity, glutamate receptor activity, and acetylcholine-gated channel complex.\\n\\nMechanism: These genes are involved in calcium signaling, particularly in calcium ion transport and voltage-gated calcium channel activity. They also play a role in neurotransmission, specifically in the activity of glutamate and acetylcholine-gated channels.\\n\\n]0.94189
401gpt-3.5-turboontological_synopsisgo-postsynapse-calcium-transmembrane-1[Summary: Calcium signaling and neurotransmission\\nMechanism: Genes encode for ion channels and regulatory proteins involved in calcium-mediated neurotransmission.\\n\\nHypothesis: These genes play a critical role in regulating calcium-mediated neurotransmission, including depolarization, synaptic transmission, and the regulation of neurotransmitter levels. This suggests a potential involvement in various neurological disorders such as epilepsy, schizophrenia, and Alzheimer's disease. Several of the genes are also involved in calcium transport and homeostasis, which may have implications in muscle function and calcium signaling in other tissues.][Summary: Calcium signaling plays a major role in the function of the genes listed, including calcium channel activity, regulation of cytosolic calcium ion concentration, and calcium ion transmembrane import.\\n\\nMechanism: Calcium signals can activate a variety of pathways, including second messenger systems and ion channel activation, leading to changes in intracellular signaling and gene expression.\\n\\n]0.92245
402gpt-3.5-turboontological_synopsisgo-reg-autophagy-pkra-0[Summary: Several of the genes are involved in signal transduction and regulation of protein kinase activity.\\n\\n\\nHypothesis: Many of these genes play roles in the regulation of signal transduction and pathways related to protein kinase activity. The enriched terms likely reflect the general role these genes play in the control and modulation of these mechanisms. Specifically, the involvement of many of these genes in TOR signaling, macroautophagy, and regulation of cyclin-dependent protein serine/threonine kinase activity suggest possible roles in cell cycle regulation and cancer development.][Summary: Protein phosphorylation and kinase activity regulation\\nMechanism: Enzymatic activity and protein-protein interactions\\n\\nHypothesis: This set of genes is enriched in functions related to kinase activity regulation and signaling pathways that involve protein phosphorylation. Many of these genes enable protein kinase binding, activator or inhibitor activity, and participate in processes that involve protein phosphorylation. These processes include intracellular signal transduction, TOR signaling, apoptotic signaling pathway, and positive regulation of metabolic processes. The underlying biological mechanism is likely linked to the interactions between these proteins, with many of them being located in protein-containing complexes and regulatory pathways.]0.95172
403gpt-3.5-turboontological_synopsisgo-reg-autophagy-pkra-1[Summary: The enriched terms for this list of genes are intracellular signaling and apoptosis.\\n\\nMechanism: These genes are involved in various intracellular signaling pathways, particularly the PI3K signaling pathway, which is known to play a role in the regulation of cellular processes such as proliferation, differentiation, and survival. They are also involved in the regulation of apoptosis, which is a programmed cell death pathway responsible for the elimination of abnormal or damaged cells.\\n\\n][Summary: The enriched terms for these genes are related to intracellular signaling and regulation of cell processes.\\nMechanism: These genes are mainly involved in regulation of protein kinase activity and intracellular signal transduction, which contribute to the homeostasis of cellular processes.\\n\\n]0.94200
404gpt-3.5-turboontological_synopsishydrolase activity, hydrolyzing O-glycosyl compounds-0[Summary: The enriched terms are centered around the catabolism of complex carbohydrates, specifically glycosphingolipids, glycoproteins, and chitin, as well as the breakdown of hyaluronan.\\n\\nMechanism: The genes with enriched functions are involved in various steps of complex carbohydrate catabolism, including enzymatic breakdown of specific glycosyl bonds and trimming of terminally located mannose and glucose residues. These processes likely occur in intracellular membrane-bound organelles, such as lysosomes.\\n\\n][Summary: These genes are involved in various processes related to the breakdown and metabolism of carbohydrates and glycoproteins.\\n\\nMechanism: The enriched terms suggest a common mechanism of carbohydrate and glycoprotein degradation through the activity of various hydrolases, including alpha- and beta-glucosidases, alpha- and beta-mannosidases, and multiple hyaluronidases.\\n\\n]0.93138
405gpt-3.5-turboontological_synopsishydrolase activity, hydrolyzing O-glycosyl compounds-1[Summary: Many of the genes listed are involved in carbohydrate metabolism and catabolic processes, including the processing and breakdown of glycans, glycoproteins, glycolipids, and other complex carbohydrates. Some genes are involved in the catabolism of specific substances such as chitin and fucose. \\n\\nMechanism: This group of genes likely represents a group of enzymes involved in the breakdown of various types of carbohydrates and sugars in the body. \\n\\n][Summary: These genes are involved in the catabolism and modification of various carbohydrates, such as hyaluronic acid, chitin, glycoproteins, glycolipids, and sugar monomers. Many of the genes encode glycosidase enzymes that enable the breakdown of specific sugars. \\n\\n]0.95190
406gpt-3.5-turboontological_synopsisig-receptor-binding-2022-0[Summary: These genes are involved in immunoglobulin receptor binding activity and activation of the immune response.\\nMechanism: The genes encode for the variable region of the immunoglobulin heavy and light chain, which are expressed by B-cells in response to foreign antigens, and enable the recognition and binding of those antigens. \\n][Summary: Enrichment in immunoglobulin receptor binding activity and antigen binding activity suggests a function related to immune response.\\n\\nMechanism: These genes encode immunoglobulins or immunoglobulin-related proteins involved in the production of antibodies.\\n\\n]0.9371
407gpt-3.5-turboontological_synopsisig-receptor-binding-2022-1[Summary: These genes are predicted to be involved in various processes related to the activation and defense response of the immune system. \\n\\nMechanism: These genes are involved in the production of immunoglobulin proteins, also known as antibodies, which are key components of the adaptive immune response system. \\n\\n\\nHypothesis: These genes are involved in the activation and defense response of the immune system through the production of immunoglobulin proteins. Antibodies bind to pathogens, marking them for destruction by other components of the immune system. The enriched terms suggest that these genes are particularly involved in the humoral immune response, which involves the production and secretion of antibodies into the bloodstream. Additionally, these genes may play a role in regulating the organization and differentiation of immune cells, such as monocytes.][Summary: Genes involved in the activation of immune response, defense response to other organisms and antigen binding activity.\\nMechanism: Immune response pathway\\n]0.92715
408gpt-3.5-turboontological_synopsismeiosis I-0[Summary: These genes are primarily involved in meiotic processes, such as homologous chromosome pairing and recombination, as well as DNA repair.\\n\\nMechanism: These genes likely play a role in the proper segregation of chromosomes during meiosis, which is crucial for the formation of viable gametes.\\n\\n][Summary: Majority of the genes listed are involved in meiotic DNA recombination and repair.\\nMechanism: Meiotic DNA recombination and repair.\\n]0.93160
409gpt-3.5-turboontological_synopsismeiosis I-1[Summary: Enrichment analysis of human genes reveals a common function in meiotic recombination and double-strand break repair via homologous recombination.\\n\\nMechanism: Meiotic recombination and double-strand break repair via homologous recombination are vital processes for the proper segregation of homologous chromosomes during meiosis. Several of the genes identified in the enrichment analysis are involved in these processes, either directly or indirectly.\\n\\n][Summary: These genes are primarily involved in meiotic recombination and chromosomal segregation, as well as various DNA repair processes.\\nMechanism: These genes likely function together to ensure proper chromosome segregation and correct genetic transmission during meiosis, and to maintain genomic stability through DNA repair mechanisms.\\n]0.90122
410gpt-3.5-turboontological_synopsismolecular sequestering-0[Summary: Molecular sequestering and protein binding activity seem to be common functions among these genes.\\nMechanism: These genes may be involved in regulating the localization and availability of important molecules and proteins within cells.\\n\\n\\nHypothesis: The genes identified in this analysis may play a role in maintaining cellular homeostasis by regulating the availability and localization of important molecules and proteins. This function may be particularly important in response to stress and infection, as many of the enriched terms relate to these processes. The common function of molecular sequestering may involve the sequestration of molecules which could be detrimental to cellular function if present in excess (e.g. iron ion or oxysterols). The common function of protein binding activity could involve the regulation of protein trafficking and localization. Together, these genes may play a role in optimizing cellular function and protecting cells from damage.][Summary: Protein sequestering and binding activities are enriched across the listed genes.\\n\\nMechanism: The enriched terms suggest that protein sequestering and binding play a significant role in the function of the listed genes.\\n\\n\\nHypothesis: Protein sequestering and binding are essential mechanisms in controlling the cellular localization and activity of proteins. These mechanisms may affect several processes, including intracellular transport, transcriptional regulation, and signal transduction.]0.95480
411gpt-3.5-turboontological_synopsismolecular sequestering-1[Summary: Molecular sequestering activity, regulation of gene expression, positive regulation of protein ubiquitination, and sequestering of metal ion are enriched functions among the given human genes.\\n\\nMechanism: These genes are involved in the regulation and control of various cellular processes by sequestering certain molecules or ions, influencing cellular response to stress, and regulating gene expression. The enriched functions are primarily related to cellular regulation and signaling pathways.\\n\\n][Summary: Several of the genes listed are involved in molecular sequestering or binding activity, and are located in various cellular compartments. Many are also implicated in immune responses and regulation of gene expression.\\n\\nMechanism: The enriched terms suggest that these genes are involved in cellular processes related to regulation of gene expression, immune responses, and cellular signaling pathways.\\n\\n\\nHypothesis: These genes may play a role in regulating immune responses and cellular signaling pathways, by sequestering or binding to various molecules and regulating the expression of genes involved in these processes.]0.93125
412gpt-3.5-turboontological_synopsismtorc1-0[Summary: Many of the genes are involved in binding activities, including RNA binding, protein binding, and ion binding, and several are involved in enzymatic activity such as oxidoreductase and kinase activity. \\n\\nMechanism: The enriched functions suggest that these genes are involved in protein synthesis and processing, as well as intracellular signaling and metabolism. \\n\\n][Summary: Many of the genes listed are involved in protein or RNA binding, enzymatic activity, and structural components of cells. \\n\\n]0.94243
413gpt-3.5-turboontological_synopsismtorc1-1[Summary: These genes are involved in various cellular functions, including protein binding, catalytic activity, and transporter activity. The enriched terms are related to cellular metabolic processes, protein folding, and DNA binding.\\n\\nMechanism: These genes likely contribute to cellular metabolism and homeostasis through various catalytic and transport mechanisms, as well as protein folding and DNA regulation.\\n\\n][Summary: The genes in this list are involved in various functions related to cellular processes including protein binding, enzyme activity, and transporter activity.\\n\\nMechanism: The underlying biological mechanism or pathway is likely related to cellular processes involved in protein homeostasis and metabolism.\\n\\n]0.95103
414gpt-3.5-turboontological_synopsisperoxisome-0[Summary: Genes involved in peroxisomal biogenesis and protein import.\\n\\nMechanism: These genes are part of the peroxisome biogenesis pathway, which involves the recognition, targeting, and import of proteins into the peroxisomal membrane and matrix.\\n\\n][Summary: Genes involved in peroxisome biogenesis and protein import into peroxisome matrix.\\nMechanism: Peroxisome biogenesis and protein import pathway.\\n]0.9897
415gpt-3.5-turboontological_synopsisperoxisome-1[Summary: Genes involved in peroxisomal biogenesis and protein import into peroxisomes.\\nMechanism: Peroxisomal biogenesis and protein import mechanism.\\n\\nHypothesis: These genes are involved in the mechanism of peroxisomal biogenesis and protein import into peroxisomes. The enriched terms suggest that this process involves specific lipid binding activities, ATP binding and hydrolysis, and ubiquitin-dependent protein binding in order to ensure proper folding, import, and localization of proteins within peroxisomes. Dysfunctions in these genes can lead to peroxisomal biogenesis disorders, such as Heimler syndrome and rhizomelic chondrodysplasia punctata type 1.][Summary: These genes are all involved in peroxisome biogenesis and protein import into the peroxisome.\\n\\nMechanism: These genes all encode for proteins involved in the same biological process of peroxisomal biogenesis, which is the formation of peroxisomes and the import of proteins into the peroxisome.\\n\\n]0.96361
416gpt-3.5-turboontological_synopsisprogeria-0[Summary: These genes are involved in several processes related to DNA and cellular response, including chromatin regulation, DNA metabolic process, and cellular senescence. \\nMechanism: These genes are likely involved in maintaining genomic stability and responding to environmental stressors.\\n\\n][Summary: These genes are all involved in DNA metabolism and chromatin regulation.\\nMechanism: These genes are all involved in maintaining the stability and integrity of the genome, particularly at the nuclear envelope and telomeres. They may also play a role in regulating cellular senescence processes.\\n]0.979
417gpt-3.5-turboontological_synopsisprogeria-1[Summary: These genes are involved in DNA-related processes and cellular responses to stress, and are implicated in several diseases.\\nMechanism: The enriched terms suggest a possible role in DNA damage response and repair mechanisms, as well as cellular senescence.\\n\\nHypothesis: These genes may be part of a network involved in maintaining genomic stability and cellular homeostasis, particularly in response to stressors such as DNA damage. Dysfunction of this network may lead to increased cellular senescence and disease.][Summary: Genes involved in DNA repair and maintenance with possible roles in aging and age-related diseases.\\nMechanism: DNA damage repair and telomere maintenance pathways.\\n]0.91351
418gpt-3.5-turboontological_synopsisregulation of presynaptic membrane potential-0[Summary: The enriched terms are related to ion channels and synaptic transmission, including ligand-gated monoatomic ion channel activity, regulation of presynaptic/presynaptic membrane potential, and several transmembrane transport processes. \\n\\nMechanism: These genes all play a role in regulating synaptic transmission through ion channels. \\n\\n][Summary: The enriched terms are related to ion channel activity, transmembrane transport, and neurotransmitter signaling pathways.\\nMechanism: These genes all play a role in regulating the flow of ions across cell membranes in neurons.\\n\\nHypothesis: These genes are involved in regulating the membrane potential and synaptic transmission in neurons. The GABA and glutamate signaling pathways are important modulators of neural activity, and the ion channels identified here play key roles in regulating the activity of these signaling pathways. The inward rectifier potassium channels help to maintain the resting potential of neurons, while the voltage-gated ion channels play a critical role in generating action potentials. Together, these genes likely play a key role in the regulation of neural activity and synaptic plasticity.]0.96487
419gpt-3.5-turboontological_synopsisregulation of presynaptic membrane potential-1[Summary: Ion channel activity and neurotransmission are enriched functions among the listed genes, with a focus on GABA and glutamate signaling pathways. \\n\\nMechanism: The genes in the list are involved in regulating ion channel activity and neurotransmission, particularly through GABA and glutamate signaling pathways. \\n\\n][Summary: These genes are involved in ion channel activity, specifically ligand-gated monoatomic ion channel activity and voltage-gated ion channel activity.\\nMechanism: The genes in this list contribute to the regulation of membrane potential and synaptic transmission in the nervous system.\\n]0.9431
420gpt-3.5-turboontological_synopsissensory ataxia-0[Summary: Genes are primarily involved in the peripheral nervous system, myelination, and neurological disorders.\\nMechanism: The enriched terms suggest that these genes primarily function in the peripheral nervous system and myelination.\\n\\nHypothesis: These genes are all involved in the development and maintenance of the peripheral nervous system and myelination. Dysregulation or mutation of these genes likely leads to neuropathic disorders.][Summary: Genes are involved in various processes in the development and maintenance of the nervous system, specifically peripheral nerves and myelination, as well as nucleic acid and protein metabolism.\\n\\nMechanism: The enriched terms suggest a common underlying biological mechanism in the formation and maintenance of the peripheral nervous system and myelination, as well as in nucleic acid and protein metabolism.\\n\\n\\nHypothesis: The enrichment of terms related to Charcot-Marie-Tooth disease and myelination suggest that these genes play an important role in peripheral nervous system development and maintenance, specifically in the formation and maintenance of myelin. The enrichment of terms related to protein folding and nucleic acid metabolism suggest that these genes also have a role in maintaining and regulating the overall metabolic processes of cells. The involvement of genes in mitochondrial function suggests a possible link between peripheral nerve function and mitochondrial metabolism.]0.95562
421gpt-3.5-turboontological_synopsissensory ataxia-1[Summary: Genes are predominantly involved in peripheral nervous system development, myelination and maintenance, and mitochondria-related functions with a subset involved in protein ubiquitination and cellular response to mechanical stimulus. \\n\\nMechanism: The primary biological mechanism underlying these enriched terms is likely the maintenance of neuronal function and homeostasis, with specific pathways including mitochondrial metabolism and protein degradation/regulation.\\n\\n][Summary: Genes are primarily involved in neurological and neuromuscular diseases and developmental disorders.\\n\\nHypothesis: These genes may be involved in the regulation of nervous system development and myelination, as well as mitochondrial dysfunction, which could lead to the development of neurological and neuromuscular diseases. The role of protein ubiquitination in these processes is unclear and requires further investigation.]0.9245
422gpt-3.5-turboontological_synopsisterm-GO:0007212-0[Summary: G protein-coupled receptor signaling pathway and dopamine receptor signaling pathway are statistically over-represented in the gene functions.\\n\\nMechanism: The genes listed are involved in intracellular signaling pathways that are activated by G protein-coupled receptors and dopamine neurotransmitter receptors. The signaling cascades triggered by these receptors are essential for many physiological processes, including neurotransmission, hormone secretion, and muscle contraction.\\n\\n][Summary: The enriched terms suggest that these genes are involved in dopamine receptor signaling pathway, including adenylate cyclase activation, calcium ion concentration regulation, and G protein-coupled receptor pathway.\\n\\nMechanism: These genes are involved in dopamine receptor signaling, which regulates various cellular processes via the activation of adenylate cyclase, calcium ion concentration, and G protein-coupled receptor pathways.\\n\\n]0.9348
423gpt-3.5-turboontological_synopsisterm-GO:0007212-1[Summary: The list of genes is enriched in terms related to G protein-coupled receptor signaling pathways and dopamine neurotransmitter activity.\\n\\nMechanism: These genes are involved in the regulation of intracellular signaling cascades, particularly those involving G protein-coupled receptors. Dopamine neurotransmitter activity appears to be a common thread linking many of these genes.\\n\\n][Summary: The enriched terms in common for this list of genes are related to G protein-coupled receptor signaling pathways, dopamine neurotransmitter receptor activity, and adenylate cyclase activity.\\n\\nMechanism: These genes are involved in pathways that regulate cellular signaling, including dopamine-mediated signaling and cyclic AMP (cAMP) signaling pathways.\\n\\n\\nHypothesis: These genes are involved in the regulation of signaling pathways, particularly those involved in dopamine-mediated signaling and cyclic AMP (cAMP) signaling. They may contribute to the development of neurological and metabolic disorders, including Alzheimer's disease, Parkinson's disease, hypertension, and type 2 diabetes mellitus. More research is needed to fully understand the underlying biological mechanisms and pathways involved in these diseases.]0.97443
424gpt-3.5-turboontological_synopsistf-downreg-colorectal-0[Summary: Genes are involved in transcriptional regulation and DNA binding activities.\\nMechanism: Transcriptional regulation through DNA-binding activities.\\n][Summary: These genes are involved in DNA-binding transcription regulation and are located in various cellular components, including the nucleus and chromatin. \\nMechanism: These genes are likely involved in regulating genetic expression and the transcriptional machinery.\\n]0.93115
425gpt-3.5-turboontological_synopsistf-downreg-colorectal-1[Summary: DNA-binding transcription factor activity and regulation of DNA-templated transcription.\\nMechanism: These genes are involved in the regulation of gene expression via DNA-binding transcription factor activity and DNA-templated transcription.\\n][Summary: DNA binding transcription factor activity, regulation of DNA-templated transcription, gene expression regulation, and nucleosome disassembly are statistically enriched functions in these genes.\\nMechanism: These genes are involved in transcriptional regulation, including regulation of DNA binding and gene expression.\\n]0.9577
426text-davinci-003narrative_synopsisEDS-0[ The list of genes includes several connective tissue related genes, such as those related to the tenascin protein family and collagen chains of type I-V, which are responsible for the formation of strong and stable connective fibers. There are also several genes related to the binding and folding of proteins, and the immune response mediated by the complement system. Further, there are genes associated with glycosaminoglycan synthesis and dermatan sulfate metabolism. The commonalities among these genes is involvement in connective tissue formation and repair, structure and binding of proteins, and immune response.\\n\\nMechanism: These genes function in a variety of biological processes, including wound healing, glycosaminoglycan synthesis, and immune response. Through their specific roles, these proteins are able to facilitate the formation and maintenance of strong and stable connective tissue, to bind and fold proteins, and to mediate the innate immune response. Furthermore, genetic mutations in these genes are associated with a variety of Ehlers-Danlos syndromes, further indicating the importance of these proteins in connective tissues.\\n\\n][\\n\\nSummary: Genes analyzed are associated with or involved in collagen biosynthesis, modification or turnover, extracellular matrix maturation, and transcriptional regulation. \\nMechanism: These genes likely function in the coordination and regulation of collagen production, fiber formation, and tissue informatics. \\n]0.89841
427text-davinci-003narrative_synopsisEDS-1[\\nSummary: Enriched term analysis reveals that the human genes described here are largely involved in collagen maturation, glycosaminoglycan synthesis, transcriptional regulation, and zinc transport. \\nMechanism: These genes likely take part in the functions of the endoplasmic reticulum and Golgi apparatus, as well as mediating processes involved in cell differentiation and tumorigenesis. \\n][\\nSummary: This gene list consists of genes involved in tissue development, collagen and extracellular matrix production, and immunity response. \\nMechanism: These genes all seem to be involved in tissue development and the formation of extracellular matrix components such as collagen and physical complexes such as C1 and fibril-forming collagens. In addition, some of the genes are associated with immunity processes like phagocytosis and inflammation.\\n \\n]0.9065
428text-davinci-003narrative_synopsisFA-0[\\nSummary: The enriched terms involve DNA repair, homologous recombination and phosphorylation, as they are commonly found among a group of genes associated with Fanconi Anemia.\\nMechanism: These genes act in a coordinated manner to perform DNA repair, homologous recombination and control chromosomal stability.\\n][\\nSummary: This gene list is composed of human genes involved in DNA damage repairs and genome maintenance.\\nMechanism: These genes are involved in the mechanisms to detect and repair DNA damages caused by environmental stressors by facilitating the formation of the nuclear protein complex.\\n]0.8721
429text-davinci-003narrative_synopsisFA-1[\\nSummary: The genes identified in this list are involved in DNA repair and maintenance of chromosome stability, specifically the homologous recombination pathway for double-strand DNA repair.\\nMechanism: These genes play key roles in a number of processes, including DNA repair, monoubiquitination of FANCD2 and FANCI, Holliday junction resolution, and binding to the RAD51 recombinase. \\n][ \\nSummary: The genes analyzed in this enrichment test are all associated with the Fanconi anemia complementation group (FANC) and are known to be involved in the repair of DNA lesions, stabilization of genome stability, and maintenance of homologous recombination.\\n\\nMechanism: These genes likely play a role in a common biological cell pathway, acting as components of multiple nucleoprotein complexes, endonucleases, and homologous recombination proteins in order to facilitate DNA repair and prevent chromosome instability.\\n\\n]0.92140
430text-davinci-003narrative_synopsisHALLMARK_ADIPOGENESIS-0[\\n\\nSummary: Several genes in the list encode proteins involved in the metabolism of fatty acids, including the formation and break down of lipids, synthesis of essential fatty acids, and transport of fatty acid synthase. Additionally, many of the genes encode proteins involved in the functioning of the mitochondria, including relating to the electron transport chains, antioxidant and redox systems, and synthesis of key metabolic components.\\n\\nMechanism: The commonality among these genes is that they encode proteins essential for normal functioning of the mitochondria, oxidative metabolism of fuels, and lipid metabolism, all of which are important for normal cellular functioning and growth.\\n\\n][ \\n\\nSummary: The list of genes appear to be primarily involved in metabolic and energy production processes, as well as some related to membrane assembly and transcription factors.\\n\\nMechanism: The genes listed appear to be involved in controlling multiple pathways within the cell, such as energy production, enzymatic activity, transcription, and assembly of membranes.\\n\\n]0.92327
431text-davinci-003narrative_synopsisHALLMARK_ADIPOGENESIS-1[ Cellular metabolism and energy production is enriched in this group of genes, likely related to their role in production and transport of proteins, enzymes, and energy.\\n\\nMechanism: The genes likely act together to produce and convert energy into a useable form and to transport proteins between cellular compartments.\\n\\n][ Enriched terms related to energy metabolism (ATP production, mitochondrial respiratory chain, electron transfer and fatty acid elongation) and protein binding/assembly/transport mechanisms (RNA/DNA binding and transport, ubiquitination and phosphorylation, microtubule binding and lipid transport) are highly represented in this list of genes.\\n\\nMechanism: These genes are mainly involved in energy production, protein modification, and transport processes. Energy production is carried out by multiple substrates including NADP, copper, zinc, and ubiquinone. The electron transfer chain is powered by cytochrome c oxidase, ATP5PO and ME1. Fatty acid elongation is handled by ELOVL6, while protein transportation is enabled by several CBL-type E3 ubiquitin ligases, ABC transporters and ATPases. Protein binding and assembly mechanisms are handled by many proteins with multiple domains, including G3BP2, VEGFB, and GHITM.\\n\\n]0.90604
432text-davinci-003narrative_synopsisHALLMARK_ALLOGRAFT_REJECTION-0[\\nThe list of genes is associated with multiple biological processes, including immune/cytokine responses, protein synthesis, transcription, and cell surface signaling. Enriched terms include: immune/cytokine responses; protein synthesis; transcription; cell surface signaling; receptor activation; ubiquitination; calcification; and ATP binding.\\nMechanism: The enriched terms associated with this list of genes describe key biological processes that regulate a variety of cellular activities. In particular, cytokines play a key role in the immune response, transcription is necessary for gene expression, and cell surface signaling is necessary for receptor activation. Furthermore, ubiquitination is involved in protein degradation, calcification is necessary for cellular processes such as bone formation, and ATP binding is necessary for energy production. \\n][\\n\\nSummary: This list of genes are involved in a variety of physiological processes, including developmental morphogenesis, cell signalling, cytokine and chemokine production and regulation, antimicrobial defence, plasma protein regulation, immune and inflammatory regulation and transcriptional regulation.\\n\\nMechanism: Many of these gene functions are related to various cell signalling pathways involving cytokines and receptors, as well as regulation of transcription factors, protein kinases and proteases, as well as glycoproteins and receptor proteins of various classes.\\n\\n]0.91284
433text-davinci-003narrative_synopsisHALLMARK_ALLOGRAFT_REJECTION-1[\\n\\nSummary: The list of genes report a variety of terms related to protein synthesis and cellular regulation functions.\\n\\nMechanism: These genes are involved in a variety of metabolic, cell signaling, transcription and immunoregulatory pathways.\\n\\n][ \\nSummary: Analysis of the given human genes reveals an enrichment for terms of cell membrane associated proteins and cytokines, as well as associated pathways of transcriptional regulation, protein synthesis, and immune response regulation. \\nMechanism: This enrichment of terms suggests that there is a complex network of pathways at play that enable important processes such as cell communication, cell activation, and immune response.\\n]0.90193
434text-davinci-003narrative_synopsisHALLMARK_ANDROGEN_RESPONSE-0[\\nThe list of terms includes functions related to protein tyrosine phosphatase (PTP) family, protein kinases, transcription factors, lectins, adhesion molecules, and cyclins. The underlying biological mechanism is likely related to a variety of cell signaling pathways and regulation of gene transcription, protein synthesis and turnover, and cell adhesion. ][ \\nSummary: These genes are involved in a variety of protein-related processes, such as binding, catalyzing, and regulating proteins, as well as in modulation, hydrolase activity, phosphorylation, and regulation of metabolism, transport, and signaling.\\n\\nMechanism: The genes are involved in a variety of pathways, such as cellular stress response, vesicle trafficking, DNA replication, transcription, lipid and cholesterol metabolism, and hormone signaling.\\n\\n]0.88101
435text-davinci-003narrative_synopsisHALLMARK_ANDROGEN_RESPONSE-1[ In this list of genes, they predominantly function in regulating cell proliferation, transcription, signaling pathways, structural components and metabolism of proteins, lipids, and carbohydrates; many of which are involved in cell adhesion or binding activity. Specifically, they are involved in regulating gene expression and DNA binding, catalyzing protein kinase and oxidoreductase reactions, anchoring kinase complexes to microtubules, binding to receptors, transporting molecules, binding and hydrolyzing peptides and lipids, and catalyzing the interconversion of polyols and ketoses. Hypothesis: These genes thus likely work by regulating signaling pathways, gene expression, and varying cell structures to enable a wide variety of cellular processes and activities.\\n\\nMechanism: Through the regulation of signaling pathways, gene expression, and cell structures, these genes enable a wide variety of cellular processes.\\n\\n][\\nThe list of genes is related to various cellular functions such as transcriptional regulation, protein kinase activity, protein binding, RNA binding, signal transduction, proteolytic enzyme activity, DNA binding, membrane transport, cell cycle, regulation, protein modification, peptidase, calcium binding, and others. The common molecular processes which are associated with these genes include regulation of transcription, signal transduction, transport, and protein modification.\\n\\nMechanism: The underlying molecular mechanisms behind the commonalities in gene functions are likely related to signal transduction and control of gene expression. Signal transduction involves the transmission of a signal from a cell's environment to the inside of the cell. Once the signal has been received and processed, it is relayed by the production of downstream molecules, such as transcription factors and other signaling proteins, which will ultimately lead to changes in gene expression and cellular behavior. Protein modification also plays a key role in signal transduction as well as in the regulation and processing of cellular components, such as proteins and lipids, necessary for normal cellular functioning.\\n\\n]0.92284
436text-davinci-003narrative_synopsisHALLMARK_ANGIOGENESIS-0[COULD NOT PARSE][ \\nSummary: This gene list encodes related proteins for key functional pathways including lipoprotein metabolism, coagulation, hemostasis, cytokinases, chemokines, receptors, transporters, cytokines, secreted extracellular matrix proteins, serpins and proteoglycans.\\nMechanism: These processes involve activation or regulation of enzymes or other proteins involved in cell adhesion and migration, signaling, cell proliferation, apoptosis, transcriptional regulation, tissue development and regeneration, and immune response.\\n]0.70509
437text-davinci-003narrative_synopsisHALLMARK_ANGIOGENESIS-1[\\nThe list of human genes provided are involved in a wide range of functions such as matrix remodeling, cell adhesion, extracellular signal transduction, iron metabolism and regulation of microvasculature. The list of genes are enriched for processes related to cell adhesion, extracellular matrix remodeling, signal transduction, protease inhibition and transcriptional regulation.\\n\\nMechanism: The enrichment of genes for the processes listed above suggests the coordination of these processes to maintain tissue homeostasis, forming a complex network that involves interactions between extracellular matrix-receptors, cytokines and chemokines, and intracellular signalling pathways.\\n\\n][ \\nThis list of genes includes a variety of molecules that are involved in a range of biological processes such as tissue morphogenesis, cell adhesion, cell migration, cell survival, signal transduction, cell cycle regulation, scaffolding, apoptosis, extracellular matrix production, platelet aggregation and others. Most of these molecules are involved in processes related to cell-cell or cell-matrix interaction and in particular, formation and/or maintenance of the extracellular matrix.\\n\\nMechanism: These genes likely function in the formation and/or maintenance of the extracellular matrix via a number of processes. Specifically, these genes may be involved in processes such as regulation of cell-cell interactions and cell-matrix interactions, production and secretion of extracellular matrix proteins, processing of proteoglycans and glycoproteins, scaffolding, cell cycle control, signal transduction, and cell adhesion. These processes are likely to be involved in the control of tissue morphogenesis, cell migration and survival, platelet aggregation, and apoptosis.\\n\\n]0.94395
438text-davinci-003narrative_synopsisHALLMARK_APICAL_JUNCTION-0[\\n\\nSummary: The genes identified are mostly involved in protein-protein interactions, intracellular and extracellular adhesion, and regulation of calcium-dependent processes.\\n\\nMechanism: Protein-protein interactions, cell adhesion, intracellular signaling of calcium-dependent processes.\\n\\n][ The genes listed are primarily involved in cell adhesion, signaling, and cytoskeletal stabilizing functions. This is evidenced by over-represented terms related to cell adhesion, such as \"integrin\", \"cadherin\", \"lectin\", \"nectin\"; terms related to signaling, such as \"MAP kinase\", \"protein tyrosine kinase\", \"guanine nucleotide binding protein\", \"GTPase\"; and terms related to cytoskeletal stabilizing functions, such as \"actin\", \"fascin\", \"laminin\", and \"myosin\". Hypothesis of underlying mechanism: The combined functions of the genes suggested are associated with cell motility, development, growth, and division in response to extracellular stimuli and signals.\\n\\nSummary: Genes associated with cell adhesion, signaling, and cytoskeletal stabilizing functions.\\nMechanism: Cell motility, development, growth, and division in response to extracellular stimuli and signals.\\n]0.90587
439text-davinci-003narrative_synopsisHALLMARK_APICAL_JUNCTION-1[\\nThe list of human genes analyzed in this enrichment test are associated with functions related to cell adhesion, signal transduction, and cytoskeletal and extracellular matrix (ECM) proteins. The enriched terms include cell adhesion, signal transduction, actin binding and assembly, membrane localization, ECM protein binding and assembly, integrin binding, calcium and phosphorylation-dependent regulation, neuron regulation, and receptor regulation. \\n\\nMechanism: The underlying biological mechanism that these genes are involved in is related to the regulation of cell adhesion, signal transduction, and cytoskeletal and ECM proteins. This includes signal transduction and cell adhesion mediated by various proteins such as integrins, cadherins, adhesion receptors, and kinases, as well as actin binding and assembly, membrane localization, ECM protein binding and assembly, and phosphorylation-dependent regulation. In neurons, there is regulation of axon guidance, regulation of synapse formation, and regulation of signaling pathways that control neuronal development and plasticity. \\n\\n][ After performing a term enrichment test of these genes, we have identified a number of commonalities in their functions, including cell adhesion, signaling, scaffolding and cytoskeleton maintenance. These functions are typically mediated by proteins involved in the regulation of extracellular matrix, integrins, claudins, nectins, protein kinases and cadherins, suggesting a common pathway of interaction between membrane-bound receptors and cytoplasmic components.\\n\\nMechanism: These commonalities collectively suggest a pathway involving the regulation of signaling transduction, cell adhesion and cytoskeletal organization by a series of membrane-bound receptors and signals originating in the cytoplasm.\\n\\n]0.93382
440text-davinci-003narrative_synopsisHALLMARK_APICAL_SURFACE-0[ The commonality in the functions of these genes is their involvement in cell-matrix adhesion and cell signalling, including signal transduction, membrane proteins, and transcriptional coactivation. The underlying mechanisms likely involve signal recognition and regulating the flow of information to and from the cell, as well as transmembrane transport and receptor-mediated endocytosis.\\n\\nMechanism: Signal recognition and regulation of the flow of information to and from the cell, as well as transmembrane transport and receptor-mediated endocytosis.\\n\\n][\\n\\nSummary: The genes described in the list are associated with cell adhesion and communication, cell metabolism and transport, receptor-mediated endocytosis, cell-matrix adherence, tissue growth, transcriptional regulation, glycosylation, and signaling.\\n\\nMechanism: The genes are involved in processes such as cell-to-cell adhesion, protein folding, and communication via cell surface proteins; receptor-mediated endocytosis; glycosylphosphatidylinositol and GPI-anchored cell surface proteins; cation transport ATPase; transcriptional coactivation; interleukin signaling and hormone-dependence; heparan sulfate proteoglycan and heparin-binding; and cell-matrix adhesion \\n\\n]0.92117
441text-davinci-003narrative_synopsisHALLMARK_APICAL_SURFACE-1[\\nThe gene summaries indicate a common association with proteins that mediate cell adhesion, signal transduction, cell-matrix interactions and regulation of cellular growth and differentiation. This suggests a common mechanism of extracellular communication and regulation between cells, mediated by the action of a diverse set of proteins. The enriched terms include cell-matrix adhesion; cell-matrix interactions; carbohydrate binding activity; cell adhesion; receptor activity; signal transduction; positive regulation of cell proliferation; negative regulation of axon regeneration; ankyrin binding; and protein tyrosine kinase.\\n\\nMechanism: The underlying biological mechanism is that a diverse set of proteins interact with one another and external signals, forming an interconnected network of extracellular communication and regulation that mediates cell adhesion, signal transduction, cell-matrix interactions and regulation of cellular growth and differentiation.\\n\\n][\\n\\nSummary: This list of genes is involved in cell signalling, adhesion, growth regulation, protein folding, cation transport, ligand binding, and other cellular functions.\\n\\nMechanism: These genes are likely involved in cell signalling pathways and signalling molecules that regulate cell growth, differentiation, and homeostasis.\\n\\n]0.91642
442text-davinci-003narrative_synopsisHALLMARK_APOPTOSIS-0[ Analysis indicates the gene functions enriched in these terms are those involved in apoptosis, cytoplasmic signaling, transcriptional regulation, protein binding, and cellular organization.\\n\\nMechanism: The underlying biological mechanism involves regulation of apoptosis/cell death pathways, as be indicated by the presence of genes like FAS, CASP, BCL-2, BNIP3L, MADD, PEA15, etc. This is further supported by gene functions enabling signaling via G-protein coupled receptors and transcriptional regulation by factors like EGR3, LEF1, etc. Additionally, many involved genes are related to protein binding in order to modulate the activity of these processes, as well as maintain cellular organization, implied by membrane proteins like APP, BCAP31, IFITM3, CD38, CD44, etc.\\n\\n][ The majority of the human genes on the list are involved in cell death processes, specifically apoptosis, and a wide range of activities associated with transcriptional regulation and DNA binding. A significant portion of the genes are associated with the TNF receptor superfamily, and the BCL-2 protein family, both of which are involved in cell death processes. Common enriched terms in the list include: apoptosis, transcriptional regulation, DNA binding, TNF receptor superfamily, and BCL-2 protein family.\\n\\nMechanism: Apoptotic pathways including caspase activation, BCL-2 protein family and death agonists, in addition to DNA binding of transcription factors and cytokine signaling, are likely to be important mechanisms in the human genes on the list.\\n\\n]0.9115
443text-davinci-003narrative_synopsisHALLMARK_APOPTOSIS-1[ \\nSummary: This list of gene functions involve mostly cell death processes, signaling, cytoplasmic and nuclear proteins, transcriptional activities, and enzymes for cell processing, as well as toxin removal and receptor binding. \\nMechanism: Cell death processes involve the activation or inhibition of specific enzymes and proteins that interact with cell membrane receptors, signal cell apoptosis, modulate transcriptional activities and regulate reversible and irreversible cytoplasmic and nuclear protein activities. \\n][COULD NOT PARSE]0.68506
444text-davinci-003narrative_synopsisHALLMARK_BILE_ACID_METABOLISM-0[ \\nSummary: The list of genes has been enriched with terms related to ATP-binding, transport, fatty acid desaturase, oxidation-reduction, enzyme catalysis, and transcription factors. \\nMechanism: The list of genes encodes a range of proteins whose functions are related to catalysis and transport of molecules, as well as transcription and regulation of hormones and neurotransmitters. \\n][\\nThe gene summaries correspond to proteins which have enzyme and binding activities related to lipid metabolism, membrane transportation, steroid catalyzation, hormone activation and deactivation, and antioxidant activity.\\nHypothesis: The underlying biological mechanism is likely to involve the crosstalk between different activities in different cellular compartments, such as cytoplasm, nucleus, and peroxisomes, to regulate fatty acid metabolism, signal transduction and other cellular processes. \\n]0.89117
445text-davinci-003narrative_synopsisHALLMARK_BILE_ACID_METABOLISM-1[ \\nSummary: Genes in the list are involved in protein transport and synthesis, lipid metabolism, oxidation-reduction, hormone regulation, and transcription regulation.\\nMechanism: Genes in the list are involved in a variety of molecular and biochemical processes, such as protein import and export, oxidation-reduction, drug metabolism, hormone regulation, transcription regulation, fatty acid and cholesterol signaling, enzyme regulation, and the breakdown of malonyl-CoA.\\n][ The list of human genes provided in this term enrichment test appears to be mostly related to enzymes, transporters, and receptors involved in lipid metabolism and transport, as well as in other metabolic pathways like bile acids synthesis, sulfur metabolism, and oxidative stress response. Notably, protein import into peroxisomes is over-represented by PEX6, PEX7, and PEX26. \\n\\nMechanism: The above proteins are likely to be involved in metabolic pathways contributing to lipid metabolism, transport, and oxidation.\\n\\n]0.9048
446text-davinci-003narrative_synopsisHALLMARK_CHOLESTEROL_HOMEOSTASIS-0[ The list of genes provided appears to be involved in a number of different physiological functions, including cell adhesion, lipid metabolism, energy generation, growth, receptor activity, signaling pathways, apoptosis regulation, transcription regulation, and cholesterol metabolism. Mechanism: The underlying biological mechanism may be related to changes in membrane properties and intracellular signaling, as well as regulation of gene expression, metabolism, and other cellular processes. ][\\nOur analysis of the list of human genes has revealed that many of the functions of these genes are related to cell regulation, metabolism, and transport. Specifically, the genes are involved in regulating cell growth and adhesion, lipid metabolism, cholesterol synthesis and breakdown, protein homodimerization and packing, enzymatic reactions, hormone regulation, and gene transcription. These gene functions are enriched in areas such as cell motility, energy generation, amino acid synthesis and degradation, glycoprotein synthesis, sterol biosynthesis and degradation, lipid metabolism and transport, and transcriptional regulation. \\n\\nMechanism: The underlying biological mechanism likely involves the coordination of these processes in order to maintain cellular homeostasis and to respond to a variety of environmental stimuli. In this way, cells can signal and respond to changes in their internal and external environments.\\n\\n]0.95438
447text-davinci-003narrative_synopsisHALLMARK_CHOLESTEROL_HOMEOSTASIS-1[ This gene list is largely composed of genes and their associated proteins involved in processes related to cell growth, metabolism, and cholesterol biosynthesis. The terms that are enriched include lipid metabolism, phospholipid binding proteins, fatty acid desaturase, ATP-binding cassette proteins, sterol biosynthesis, and cytochrome P450 family proteins.Mechanism: The mechanisms underlying these processes involve the synthesis and degradation of essential fatty acids, lipids, and sterols, and the regulation of cell growth and adhesion through transcription factors, receptor-ligand interactions, and transfer of molecules across intracellular and extracellular membranes.][ \\nSummary: Enriched terms were identified related to cholesterol synthesis, lipid metabolism, fatty acid desaturation, and cell growth/regulation.\\nMechanism: These genes play a role in the regulation of cholesterol and other lipids, as well as amino acids, fatty acid desaturation and biosynthesis, growth, and cell cycle regulation. \\n]0.93345
448text-davinci-003narrative_synopsisHALLMARK_COAGULATION-0[ The provided list of genes is primarily involved in the regulation of the complement system and blood clotting, as well as in the processing of proteins and peptides. Mechanism: The genes play a role in the innate immune response by modulating the complement system, helping to break down peptides and proteins, regulating inflammation, and in the control of blood clotting. ][COULD NOT PARSE]0.69361
449text-davinci-003narrative_synopsisHALLMARK_COAGULATION-1[ This gene list is enriched for many serine proteases and proteins involved in coagulation, complement activation, metalloproteases, transcriptional regulators and transcription factors. Hypothesis: These genes are involved in extracellular matrix turnover, cell-cell adhesion and signal transduction pathways, as well as processes related to tissue morphogenesis. ][ \\nSummary: The list of genes are associated with various functions involved in proteolysis, hemostasis, bone growth, morphogenesis, tissue development, lipoprotein regulation, and regulation of the complement system.\\n\\nMechanism: These genes are involved in mechanisms such as proteolysis, hemostasis, bone growth, morphogenesis, tissue development, lipoprotein regulation, and complement system regulation.\\n\\n]0.9043
450text-davinci-003narrative_synopsisHALLMARK_COMPLEMENT-0[ \\nSummary: The enriched terms found from the list of genes involve proteins associated with cell signaling, structure/stability, metabolism, and vitamin K/clotting. \\n\\nMechanism: These proteins work together to regulate cell signaling pathways and pathways involved in inflammation and metabolism. Additionally, these genes are involved in vitamin K/clotting pathways, cytoskeletal structure/stability and cell membrane strengthening. \\n\\n][ This list comprises genes with roles in immune and inflammatory processes, cell regulation and development, cell signalling, cell adhesion, and cell metabolism. Many of these genes play roles in modulating the activity of kinases, members of the proteasome complex, and members of the serpin, cysteine-aspartic acid protease (casp) family, and in particular caspase-9 and caspase-3, both of which have roles in apoptosis and inflammation signalling. There are also proteins important in complement activation and coagulation, such as factor V, X, and VII and their receptors, as well as proteins that modulate interferon-induced signalling, such as IRF1, IRF2, and IRF7.\\n\\nMechanism: This list shows that these genes play roles in diverse pathways, such as cell development, cell signalling, cell regulation, cell adhesion and metabolism, complement activation, coagulation, and interferon-induced signalling.\\n\\n]0.89475
451text-davinci-003narrative_synopsisHALLMARK_COMPLEMENT-1[\\nSummary: The list of genes are mainly involved in protein production, cell surface glycoprotein regulation, complement activation and signalling pathways.\\n][\\n\\nSummary: The genes included in this list encode proteins involved in cell signaling, adhesion, protease activity, and cytoskeletal and metabolic processes.\\n\\nMechanism: The proteins encoded by the genes in this list are important in a variety of cellular processes including cell adhesion, transcriptional regulation, protease activity, and metabolic and cytoskeletal functions.\\n\\n]0.91225
452text-davinci-003narrative_synopsisHALLMARK_DNA_REPAIR-0[COULD NOT PARSE][\\n\\nSummary: The human genes in this list are involved in functions such as DNA binding, transcription control, post-splicing, and RNA polymerase II functions. \\nMechanism: These genes are involved in multiple functions involved in the maintenance of DNA structure and transcription, such as DNA repair, post-splicing, andRNA polymerase II-related functions.\\n]0.68341
453text-davinci-003narrative_synopsisHALLMARK_DNA_REPAIR-1[\\n\\nSummary: We have identified 18 enriched terms associated with the functions of the given list of genes. These functions include DNA binding, transcription, DNA repair and mRNA processing.\\n\\nMechanism: The commonalities between the functions of the given list of genes suggest that they are involved in facilitating DNA binding and transcription regulation, DNA repair, mRNA splicing and mRNA processing activities.\\n\\n][\\nSummary: The genes found in this list primarily involve DNA repair, transcription, and mRNA metabolism.\\nMechanism: The genes are involved in the transcription and DNA repair process, which includes enzyme binding, RNA binding, DNA, protein, and chromosomal binding activities, as well as the activity of DNA and RNA polymerases, phosphorolysis, gene silencing, and protein ubiquitination.\\n]0.9227
454text-davinci-003narrative_synopsisHALLMARK_E2F_TARGETS-0[ \\n\\nSummary: This term enrichment test identified highly conserved proteins and protein complexes that play a role in DNA replication, repair and transcription, chromatin binding and modification, and cell cycle regulation.\\n\\nMechanism: The enrichment test suggests that these genes are essential for maintaining their respective functions, as well as for responding to DNA damage, replication blocks and cell cycle regulation.\\n\\n][\\nSummary: The enriched terms from the given gene list suggest that these genes are involved in DNA replication and repair, chromatin regulation, and RNA processing.\\nMechanism: These processes involve the coordination and control of proteins, DNA sequences, and metabolites such as calcium ions.\\n]0.91132
455text-davinci-003narrative_synopsisHALLMARK_E2F_TARGETS-1[\\nGene functions related to the regulation of nucleic acid binding and metabolism, chromatin, protein modification, DNA replication, and cell cycle regulation are enriched in the list of genes provided above. These process appear to be interrelated and part of a larger cellular pathway.\\n\\nMechanism:\\nThe mechanism underlying these gene functions seems to involve the control of the cell cycle, DNA binding and metabolism, chromatin dynamics, and protein modification and turnover. These processes are regulated by a complex network of interactions between various proteins, DNA modifications, and histone modifications, which help control the assembly and disassembly of different chromatin structures. This in turn affects DNA replication, transcription, and translation of proteins required for various cellular processes.\\n\\n][\\nSummary: This list of genes is involved in a variety of functions, such as DNA replication, nuclear import and export, RNA binding, chromatin regulation and modification, protein degradation, cell cycle control, and DNA repair.\\n\\nMechanism: These genes are involved in many processes related to maintaining genomic stability, including DNA replication, DNA repair, and chromatin regulation.\\n\\n]0.93433
456text-davinci-003narrative_synopsisHALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0[ The genes presented in this list are primarily involved in cell signaling, extracellular matrix formation and cell adhesion. Furthermore, many of the genes play a role in connective tissue formation and related structural processes.\\n\\nMechanism: Genes involved in cell signaling, extracellular matrix formation, and cell adhesion are integral in their roles in producing cell structure and maintaining connective tissue structure and integrity. These genes work together to allow cells to communicate properly and modulate processes such as inflammation and tissue repair. Additionally, cell signaling and cytokines produced by these genes contribute to angiogenesis, metabolic regulation, and tissue growth and development. \\n\\n][ \\nSummary: Enriched gene functions were identified related to extracellular matrix glycoproteins, collagen, actin binding and regulation, cell adhesion and signaling, cytokine regulation and signaling, peptidase genes, and growth factor family members.\\n\\nMechanism: Members of these gene families play important roles in the regulation of cell signaling pathways, cell migration, cell growth and differentiation, hemostasis and inflammation, and various other biological processes.\\n\\n]0.91245
457text-davinci-003narrative_synopsisHALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1[\\nThis list of genes is strongly associated with extracellular matrix and collagen production, with members of the integrin, laminin, dystrophin, fibronectin, von Willebrand Factor, and fibulin families involved. Enriched terms include extracellular matrix proteins, collagen, laminin, fibronectin, von Willebrand Factor, integrin, dystrophin, and fibulin proteins.\\n\\nMechanism: \\nThese proteins are involved in extracellular matrix production and organization, which is critical for cell-to-cell and cell-to-environment interaction. This involves extracellular matrix proteins that facilitate connection and communication between cells, as well as structural proteins such as collagen and laminin that provide stability and rigidity. In addition, these proteins are involved in cell adhesion, migration, and proliferation. By forming interconnecting complexes, these proteins work together to mediate multiple biological processes, from cell development to tissue and organ formation. \\n\\n][ \\nSummary: The genes included in this list encode proteins that are involved in structural support and maintainance of cell components, such as extracellular matrix proteins, integrins, collagen, fibrillin, tropomyosin and myosin proteins.\\nMany of them have roles related to regulatory cell functions, such as cell adhesion, growth and signalling pathways.\\nMechanism: These proteins play a role in the maintainance and regulation of cell structure, linking the extracellular environment to the intracellular environment, enabling cell-cell interactions, and modulating cell behaviour and signalling.\\n]0.92385
458text-davinci-003narrative_synopsisHALLMARK_ESTROGEN_RESPONSE_EARLY-0[ The enriched terms in this list of genes include proteins related to peptide binding, cell membrane structure modification, DNA binding, fatty acid metabolism, hormone receptor binding, signalling transcription, GTPase activation, adenylate cyclase modulation, kinase activity, endocytosis, glycoprotein production, growth factor binding, histone modification, phospholipid metabolism and zinc-binding. The underlying biological mechanisms and pathways involve proteins involved in intracellular and intercellular signalling, as well as chromatin remodelling and membrane trafficking. \\n\\nMechanism: Membrane trafficking, cellular signalling and chromatin remodelling. \\n\\n][ Enriched terms involved in signal transduction, gene expression, transport, and membrane protein functions.\\n\\nMechanism: Signal transduction, gene expression and transport functions may occur as a result of interaction between proteins encoded by the genes, as well as interaction between nucleic acids such as DNA, RNA, and chromatin. This can be regulated by post-translational modifications such as methylation, phosphorylations, and acylation, as well as by binding of other proteins and ligands. Membrane proteins allow for communication between the cytoplasm and outside environment and facilitate the transport of molecules.\\n\\n]0.9237
459text-davinci-003narrative_synopsisHALLMARK_ESTROGEN_RESPONSE_EARLY-1[ \\n\\nSummary: The genes described in this list are mainly involved in the regulation and manipulation of protein functions, such as DNA-binding, signaling pathways, post-translational modification, protein binding, and metabolic activity.\\n\\nMechanism: Many of the genes involved are involved in metabolic pathways and regulation, and interactions between proteins, such as through DNA-binding, signaling pathways, and post-translational modification.\\n\\n][ Gene functions were identified enriched for cytoskeletal organization, DNA binding transcription regulation, membrane transport and receptor signalling.\\nMechanism: Commonalities in gene functions is associated with cellular and signal transduction pathways, involving several mechanisms including membrane transport, DNA-binding transcription regulation, cell adhesion, cytokine and growth factor signalling, and the expression of structural components of muscle and epithelial cells.\\n]0.8737
460text-davinci-003narrative_synopsisHALLMARK_ESTROGEN_RESPONSE_LATE-0[\\n\\nSummary: Genes involved in regulation of cell signaling, including protein kinases, transcription factors, calcium ion binding, glycobiology, and hormone receptors. \\nMechanism: All the genes operate at the cellular signaling level to mediate various biological functions such as cell adhesion, protein folding, and gene expression. \\n][\\nSummary: The human gene list provided consists of genes involved in a variety of cellular functions, including regulation of G protein signalling, ion channel transport, membrane receptor signalling, cytoskeletal protein scaffolding, enzyme regulation and glycoprotein modulation. \\n]0.9052
461text-davinci-003narrative_synopsisHALLMARK_ESTROGEN_RESPONSE_LATE-1[ The genes identified are largely involved in membrane and transmembrane processes, ion transport, cell adhesion and growth, metabolizing enzymes, disease processes, and protein signaling and processing. Mechanism: These genes are involved in processes related to cell physiology, adhesion, growth and development, and reparative pathways, as well as immune and disease processes. ][\\nSummary: The genes listed are involved in various cellular functions, including signal transduction, gene transcription, ion transport and binding, protein-protein interaction and post-translational modifications.\\nMechanism: These genes have been found to encode proteins that are involved in diverse cell functions, including signal transduction, structural proteins, transcription factors, transporters, kinases and phosphatases, and their associated regulatory proteins.\\n]0.9194
462text-davinci-003narrative_synopsisHALLMARK_FATTY_ACID_METABOLISM-0[ \\n\\nSummary: There is an enrichment for metabolic and energy regulation processes involving multiple enzymes and proteins connecting with metabolites, nucleotides, fatty acids, and other molecules.\\n\\nMechanism: These genes seem to be involved in metabolic pathways leading to the formation of intermediate metabolites and energy transportation in the body.\\n\\n][\\n\\nSummary: This list includes 51 human genes involved in metabolic, biosynthetic, enzymatic, and regulatory pathways and processes. The majority of these genes encode proteins involved in metabolic functions, such as glycolysis, oxidation-reduction processes, and polyamine metabolism.\\n\\nMechanism: The commonalities between these genes are related to their roles in metabolic and enzymatic processes throughout cells. These proteins are involved in catalyzing and regulating nucleotide and amino acid metabolism, fatty acid oxidation and synthesis, polyamine metabolism, and enzyme activity.\\n\\n]0.93237
463text-davinci-003narrative_synopsisHALLMARK_FATTY_ACID_METABOLISM-1[ The summaries of these human genes suggest that the majority of them are involved in metabolism-related processes, specifically in the processing and transport of fatty acids and oxidoreductases. There is also evidence that these genes may be involved in growth and development, such as for aiding in morphogenesis, cell differentiation, and protein-macromolecule adaptor activity. The enriched terms that represent these processes are \"metabolism,\" \"fatty acid transport and processing,\" \"oxidoreductase,\" \"morphogenesis,\" \"cell differentiation,\" and \"protein-macromolecule adaptor activity.\" \\n\\nMechanism: The underlying biological mechanism might involve the genetic regulation of enzymes responsible for fatty acid and metabolite transport and transformation. Additionally, the gene products of these genes might be involved in signaling cascades that lead to morphogenesis and cell differentiation. \\n\\n][\\nThe gene list contains genes associated with metabolic activities such as enzymatic components of tricarboxylic acid cycle, fatty acid binding proteins, aldehyde dehydrogenases and enzyme processes related to electron transfer, including pyruvate dehydrogenase, NAD-retinol dehydrogenase, succinate dehydrogenase, etc. The underlying biological mechanism involves the process of metabolic energy conversion, which involves the coordination of various enzymatic components.\\n\\nMechanism: Metabolic energy conversion coordinates various enzymatic components.\\n\\n]0.90349
464text-davinci-003narrative_synopsisHALLMARK_G2M_CHECKPOINT-0[ \\n\\nSummary: The provided gene list is mainly involved in functions related to cell cycle regulation, chromatin/histone modification, and transcription.\\n\\nMechanism: These genes are involved in a variety of biological processes related to cell cycle regulation, chromatin/histone modifications, protein kinase activity, ATP-binding, and RNA binding.\\n\\n][\\nSummary: The genes in the list encode proteins involved in cell signalling and regulation pathways, epigenetic regulation, nuclear transport, mitosis, mRNA processing, protein modification, DNA replication and repair, and chromatin structure.\\nMechanism: This analysis suggests that these genes are responsible for various critical cellular functions and pathways, such as transcriptional regulation, epigenetic remodeling, nuclear transport, post-translational modifications, DNA replication and repair, chromatin structure, and mitosis.\\n]0.94190
465text-davinci-003narrative_synopsisHALLMARK_G2M_CHECKPOINT-1[ Enriched terms among this list of genes point to functions related to cell division, DNA and RNA binding, transcriptional regulation, chromatin restructuring, and protein kinase activity. This set of genes appears to have enriched terms related to nuclear and cytoplasmic transport, nucleic acid metabolic functions, and histone certain activities. Mechanism: The collection of processes related to the functions of these genes appear to function in a coordinated way, with many proteins involved in multiple pathways that work together to maintain cell division, DNA integrity, gene expression, and the structural organization of chromatin. These processes appear to be primarily regulated by an array of proteins with phosphorylation, methylation, acetylation, and ubiquitination activities. ][ \\nSummary: The human genes in this list are involved in various critical functions related to cellular development, including nucleocytoplasmic transport, histone acetylation, chromatin-associated processes, cell cycle regulation, and transcriptional regulation.\\n]0.90532
466text-davinci-003narrative_synopsisHALLMARK_GLYCOLYSIS-0[\\n\\nSummary: The list of genes have similar functions in cellular pathways such as glycoprotein metabolism, phosphorylation, cell adhesion, transcription, nucleotide metabolism, energy production, and others.\\n\\nMechanism: Many of these genes are involved in phosphorylation, which helps to regulate cellular activity. This includes regulation of cell adhesion and transcription, as well as energy production and nucleotide metabolism.\\n\\n][\\n]0.73432
467text-davinci-003narrative_synopsisHALLMARK_GLYCOLYSIS-1[ Biological processes related to development, glycosylation, and metabolism of proteins, lipids, and carbohydrates are enriched based on the list of genes given.\\n\\nMechanism: The genes identified encode for enzymes, receptors, and proteins that support functions in several biological mechanisms, including protein and carbohydrate metabolism, post-translational modification, binding, and transport.\\n\\n][\\nSummary: Analysis of the summaries of these genes reveal that the majority are involved in enzymatic functions, binding, transporting, and metabolism of molecules, including ions and sugars.\\nMechanism: These genes likely have an underlying biological mechanism of enzyme catalysis and/or binding affinity affecting the metabolism of molecules, including ions and sugars, as well as modulating transcription, cytoskeletal structure, and cell adhesion.\\n]0.8951
468text-davinci-003narrative_synopsisHALLMARK_HEDGEHOG_SIGNALING-0[ \\nSummary: The list contains 22 genes involved in signal transduction, transcription and cell adhesion, primarily within the nervous system.\\n][\\nThis gene set is involved in a variety of cellular functions, such as cell adhesion, neural development, transcription factor regulation, signal transduction, and extracellular protein interaction. These genes are over-represented in processes related to endocytosis, growth factor binding, and receptor-mediated pathways. The hypothesis is that these genes are involved in pathways associated with the regulation of neuron survival, differentiation, and youthfulness.\\n\\nMechanism: This gene set is hypothesised to be involved in signalling pathways related to neuron survival, differentiation, and development. These pathways are probable mediated by endocytosis, growth factor binding, and receptors.\\n\\n]0.89563
469text-davinci-003narrative_synopsisHALLMARK_HEDGEHOG_SIGNALING-1[ This set of genes are mainly involved in neuron signalling and cell adhesion, and all contribute to cellular processes such as growth, differentiation, motility and development. Mechanism: These genes are predominantly involved in intracellular signal transduction pathways, which lead to the activation of transcription factors or the production of secretory proteins. ][\\nThis is a list of 20 human genes, most of which are associated with neural development and axon guidance. Several of these genes are involved in receptor-mediated endocytosis, G-protein coupled receptors, cell adhesion, gene transcription and post-translational regulation. The enriched terms include structure-specific proteins, receptor-mediated endocytosis, G-protein coupled receptors, cell adhesion, gene transcription, and post-translational regulation. \\nMechanism: These genes are involved in the regulation of various processes such as cell motility, cell differentiation and cell migration, and formation of complex systems such as axon networks, which involves a variety of cellular pathways. ]0.93333
470text-davinci-003narrative_synopsisHALLMARK_HEME_METABOLISM-0[ \\n\\nSummary: The list of genes described relate to the processing and binding of protein molecules, cytokinesis, transcriptional regulation, metabolic and enzymatic functions, formation of cell cortex, transport, and several other cellular processes.\\n\\nMechanism: Many of the genes are associated with the formation and modification of proteins, including phosphorylation and acetylation, playing an important role in cell membrane and cytoskeleton structure, catalyzing metabolic reactants, and trafficking. \\n\\n][\\nAnalysis of the above list of genes revealed that a considerable number of them are involved in processes such as protein binding, transcription, catalyzing reactions (including enzymatic reactions), and GTPase activating protein activation. This indicates that these genes play a role in a wide range of biological processes related to cellular and subcellular processes. In particular, these genes are involved in functions such as histone deacetylation, carbohydrate and lipid metabolism, receptor binding and signaling, DNA binding, and DNA packaging.\\n\\nMechanism:\\nMany of the genes listed are related to binding either other molecules or DNAs, as well as catalyzing various reactions. These processes likely work together to allow cells to properly function, as well as for their internal structures to be regulated and maintained, such as for the types of molecules necessary for cellular and subcellular processes. Additionally, transcription is another process heavily involved, as many of the genes are associated with regulating the expression of other genes. \\n\\n]0.93563
471text-davinci-003narrative_synopsisHALLMARK_HEME_METABOLISM-1[ The list of human genes appear to be involved in transcription and post-transcriptional regulation, regulation of glycolysis and pyruvate metabolism, glutathione metabolism, proteolysis, transcriptional regulation, and ubiquitination. \\n\\nMechanism: The genes may be involved in regulation and modulation of pathways that control cell structure, function, maturation and apoptosis.\\n\\n][ \\nSummary: The list of human genes encompass a variety of processes such as DNA binding, histone acetylation, protein binding, transcription regulation, and leucine residue modification.\\n\\nMechanism: The underlying biological mechanism involves the regulation of gene expression, protein and nucleic acid metabolism, and signal transduction.\\n\\n]0.9040
472text-davinci-003narrative_synopsisHALLMARK_HYPOXIA-0[ \\n\\nSummary: Genes involved in regulating a variety of metabolic functions such as glycolysis, phosphorylation, protein kinase activity, proteolytic degradation, extracellular matrix assembly and maintenance, and transcription regulation.\\n\\nMechanism: Genes are involved in different aspects of metabolic regulation responsible for the control of cellular processes such as cell cycle and proliferation, energy homeostasis, inflammation, and the communication between cells. \\n\\n][ The list of genes provided encodes many different proteins involved in metabolic regulation, cell signaling, and post-translational modification. The most enriched term is: “cell signaling”; other terms include “metabolic regulation” and “post-translational modification”.\\n\\nMechanism: The mechanism underlying the enriched terms is that many of the encoded proteins are involved in different pathways that ultimately regulate and control the cell processes, such as cellular signaling, metabolic regulation, post-translational modification, and more. These proteins work together in a complex network to control cell activities. \\n\\n]0.89157
473text-davinci-003narrative_synopsisHALLMARK_HYPOXIA-1[\\nThe list of genes is mainly involved in metabolic and transcription processes. The genes enable physical functions such as carbohydrate binding, phosphorylation, and filamin binding, as well as regulate apoptosis, proliferation and growth. The biological mechanism involves cytoplasmic processing, lipoprotein metabolism, cell-binding and signaling pathways.\\n\\nMechanism: Metabolic, Transcription, and Cytoplasmic Processes\\n][\\n\\nSummary: A large majority of the genes are involved in the regulation of a wide range of cellular functions including those related to cellular transport, metabolic processes, scaffolding, transcriptional regulation, cell cycle control, transcription factor activity and phosphorylation.\\n\\nMechanism: These genes-through their diverse roles in the regulation of cell transport, metabolic processes, scaffolding, transcriptional regulation, cell cycle control, transcription factor activity and phosphorylation-form the backbone of numerous cellular functions. \\n\\n]0.91139
474text-davinci-003narrative_synopsisHALLMARK_IL2_STAT5_SIGNALING-0[\\n cells proliferate and differentiation, metabolism and gene regulation, cytokine signaling and antigen recognition, transcription factors and membrane-associated proteins.\\nMechanism: A wide range of mechanisms are involved, including regulation of cell proliferation and differentiation, metabolism, gene regulation, cytokine signaling, and antigen recognition. Common enriched terms include cell cycle regulation, receptor signaling, membrane-associated proteins, and transcription factors.\\nHypothesis: The underlying biological mechanism involves a wide range of processes related to cell proliferation, differentiation, metabolism, gene regulation, cytokine signaling, and antigen recognition. These processes are mediated by various membrane-associated proteins and transcription factors.\\n][ The enriched terms from the analysis of this list of genes indicate that they are all primarily involved in interaction with other macromolecules or with receptors, or in structure and cell adhesion. Many of the genes are associated with the regulation of transcription factors, such as the TNF receptor family, and others are associated with enzyme regulation or the production of cytokines. The underlying hypothesis is that these genes represent a variety of pathways that help regulate various aspects of cell function and communication.\\n\\nMechanism: The mechanism behind the term enrichment relates to the protein-protein interactions and cell adhesion that is regulated by these genes.\\n\\n]0.90101
475text-davinci-003narrative_synopsisHALLMARK_IL2_STAT5_SIGNALING-1[ The list of genes can be divided into several classes related to their functions, including signaling (MAPKAPK2, PHLDA1, CSF2, CD86, etc.), cell adhesion (SELL, CD79B, CD44, etc.), receptor activity (P2RX4, TNFSF4, IGF2R, etc.) and protein kinase activity (PRAF2, CAPG, PTCH1, etc.). These genes are involved in diverse physiological processes, such as signal transduction, membrane transport, immune response, cell cycle and apoptosis. Mechanism: The enriched terms indicate that these genes are involved in signal transduction and cellular processes at the molecular level, such as GTP binding, protein homodimerization, nucleic acid binding, and protein kinase activity. ][\\nSummary: A list of human genes and their functions were analyzed and enrichment terms related to intracellular signaling, cell adhesion, and membrane proteins were identified.\\nMechanism and ]0.91484
476text-davinci-003narrative_synopsisHALLMARK_IL6_JAK_STAT3_SIGNALING-0[\\nSummary: The list of genes is associated with inflammation, cell growth, and development processes primarily involving cytokine signaling pathways. \\nMechanism: Signaling pathways comprise cytokine signals of various types coupled to various types of receptors and transmembrane proteins, with downstream activations of various protein kinases, transcription factors, and modulators of cell cycle progression.\\n][ \\nSummary: Twenty-eight genes that encode proteins involved in immune/inflammatory responses, growth regulation, and signal transduction were found to be enriched in terms of functions related to cytokine receptors, chemokines, TGF-beta superfamily, transcriptional regulation, protein tyrosine phosphatases, and protein kinases. \\n\\nMechanism: These genes are involved in immune and inflammatory responses, growth regulation, and signal transduction by influencing cell proliferation, differentiation, and apoptosis.\\n\\n]0.93107
477text-davinci-003narrative_synopsisHALLMARK_IL6_JAK_STAT3_SIGNALING-1[COULD NOT PARSE][COULD NOT PARSE]1.000
478text-davinci-003narrative_synopsisHALLMARK_INFLAMMATORY_RESPONSE-0[ The list of genes are mainly involved in receptor binding, cytokine signalling, and regulation of inflammation, cell cycle and growth. \\nMechanism: These genes likely represent critical components of complex pathways involving cell growth, immune signalling and inflammation, as well as the coordination of cell cycle and apoptosis.\\n][ \\nSummary: A majority of the gene functions on this list are related to protein-coupling, receptors, cell surface and membrane-associated proteins, and cytokine-related components.\\nMechanism: Cell membrane, receptor-coupled, and ligand-binding activities.\\n]0.8877
479text-davinci-003narrative_synopsisHALLMARK_INFLAMMATORY_RESPONSE-1[ Cells have an inherent potential to interact with each other, responding to proteins that traffic signals across the membrane which may modulate cytokines, immunoactivators, lipids, and transcription factors to form different types of signaling pathways and biological processes. Mechanism: Interaction or binding of proteins or receptors with lipids, cytokines, transcription factors, or hormones triggers signaling events across the membrane, consequently modulating the gene expression of the cell. ][ Genes in this list are predominantly involved in receptor binding, signaling, membrane transport, calcium binding and transmembrane transport. The enrichment of these specific functions suggest the underlying biological mechanism involves immune responses, cytokine signaling and communication between the nucleus and cytoplasm of cells. \\n\\nMechanism: Genes in this list have functions in receptor binding, signaling, membrane transport, calcium binding and transmembrane transport which are involved in immune responses, cytokine signaling, and nuclear/cytoplasm communication.\\n\\n]0.8777
480text-davinci-003narrative_synopsisHALLMARK_INTERFERON_ALPHA_RESPONSE-0[\\nThe list of genes related to human genetics is statistically enriched for genes involved in immune response and regulation, protein-binding and modification, subunit-binding and regulation in macromolecular complexes (such as proteasomes & MHC), and RNA-binding and modification. \\nMechanism: The enriched terms identified above support the underlying biological mechanism of protein-protein interactions, ligand binding, gene transcriptional regulation, signal transduction and other essential processes essential to maintaining cell homeostasis. \\n][ This list of genes are enriched for modulating processes related to cell signaling, immune response, and gene regulation, mainly through interacting with ligands, receptors and enzymes, and RNA or DNA binding activity. \\nMechanism: The enriched genes are involved in pathways that lead to protein activation, degradation, ubiquitination, and participation in RNA or DNA binding.\\n]0.92170
481text-davinci-003narrative_synopsisHALLMARK_INTERFERON_ALPHA_RESPONSE-1[ \\n\\nSummary: The gene list is composed of transcriptional regulators, tumor suppressors, proteases, catalysts, membrane proteins and receptor proteins, which are involved in immune response, defense response, mRNA stabilization, mRNA editing, protein ubiquitination, protein methylation, and cell proliferation. \\nMechanism: These genes are involved in regulating the expression of other gene pathways, controlling cellular growth and activation, recognition of external or internal signals, or altering the properties of a macromolecule through enzymatic action, leading to shifts in growth and metabolism. \\n][COULD NOT PARSE]0.68592
482text-davinci-003narrative_synopsisHALLMARK_INTERFERON_GAMMA_RESPONSE-0[ Genes in this list are associated with immune regulation, DNA binding, RNA binding, protein ubiquitination, anti-viral response, cytokine signaling, and inflammation.\\n\\nMechanism: These genes are involved in pathways that regulate immune responses, such as the induction of cytokines, the recognition of viral DNA, the binding of RNA and DNA, the ubiquitination of proteins, and the activation of inflammatory pathways.\\n\\n][COULD NOT PARSE]0.67406
483text-davinci-003narrative_synopsisHALLMARK_INTERFERON_GAMMA_RESPONSE-1[ \\n\\nSummary: This list of human genes has been found to be involved in various processes related to inflammation, immune cell signaling and development, immune regulation and cellular metabolism.\\n\\nMechanism: These genes may be involved in pathways related to the regulation of innate and adaptive immunity, as well as pathways related to metabolic and transcriptional regulation, DNA binding and RNA binding activities.\\n\\n][ This gene set is enriched for terms related to transcriptional regulation, enzyme activity, binding ability, protein structures, and cell signalling. There is a wide array of proteins involved in cytokine and growth factor signalling, immunity, and transcription factors, as well as a range of proteins carrying out important enzymatic functions.\\n\\nMechanism: The genes in this gene set are all involved in a variety of pathways and processes related to cellular signalling, protein production, gene expression, immune response, enzyme activity, and DNA binding activities, given their involvement in different transcriptional and binding processes.\\n\\n]0.89231
484text-davinci-003narrative_synopsisHALLMARK_KRAS_SIGNALING_DN-0[\\n\\nSummary: Genes listed are involved in a variety of cellular activities, including protein-binding, transcriptional regulation, cell adhesion, cell membrane channel activity, protein metabolism/modification, and receptor signalling.\\n\\nMechanism: The enriched terms represent the wide-ranging cellular activities of the listed genes, exemplifying they operate within multiple pathways and networks to form a complex system of molecular interactions.\\n\\n][ The genes in this list are predominantly involved in the regulation of ion channels and ion transport proteins, as well as receptor proteins, calcium binding proteins and various enzymes involved in cell signaling and metabolic processes. \\nMechanism: These proteins play important roles in the regulation of various processes ranging from cell adhesion to cytokine/growth factor signaling and hormone-regulation as well as metabolism. \\n]0.9013
485text-davinci-003narrative_synopsisHALLMARK_KRAS_SIGNALING_DN-1[ After performing a term enrichment test on the list of human genes and their descriptions, the enriched terms found to be statistically over-represented are related to proteins that are responsible for cellular growth and development, movement, action potentials, calcium binding, steroid binding and metabolism, transcription factors, and binding of various molecules such as ATP, RNA, G proteins, and DNA-binding. The underlying biological mechanisms involve the integrative action of various proteins that are essential for various physiological and developmental processes, including those related to reproduction and metabolism.\\n\\nMechanism: Integrative action of proteins related to cellular growth, development, movement, action potentials, calcium binding, steroid binding and metabolism, transcription factors, and binding of various molecules. \\n\\n][\\nSummary: The list of genes are involved in a variety of functions including catalyzing reaction, membrane transport, signaling, DNA-binding, transcription, extracellular signaling, and calcium-ion binding.\\n\\nMechanism: These genes play a role in operating a variety of biological pathways related to immune system signaling, cell growth and maintenance, cell communication, hormone regulation, transcription, development, and metabolism.\\n\\n]0.88417
486text-davinci-003narrative_synopsisHALLMARK_KRAS_SIGNALING_UP-0[ Enriched terms and mechanisms related to cell adhesion, regulation of growth factors and cytokines, calcium activation, and transcriptional regulation.\\n\\nMechanism: The genes involved are related to a range of important cell process, such as cell adhesion and calcium signaling, as well as the regulation of growth factors, cytokines, and gene transcription. These functions are essential for cellular growth and development, and are the basis for many of the body's responses to a variety of stimuli.\\n\\n][ Enriched terms related to protein structure and functions, including membrane-associated proteins, peptidases, receptor proteins, DNA-binding proteins, kinases, and transcription factors involved in transcriptional regulation. Mechanism: These proteins are involved in many biological processes, including blood pressure regulation, electrolyte balance, signal transduction, transcriptional regulation, ion transport, muscle contraction, immunologic regulation and cytokine production, cell cycle control, apoptosis, cell adhesion, and tumorigenesis. ]0.8950
487text-davinci-003narrative_synopsisHALLMARK_KRAS_SIGNALING_UP-1[ \\nSummary: The list of terms is mostly associated with proteins and their cellular roles, such as binding to cell membrane, binding to DNA, catalyzing reactions, activating pathways, and regulating cytokines, growth factors, and transcription.\\nMechanism: The human genes are involved in regulating growth, development, metabolic and immunological processes through the functioning of the encoded proteins.\\n][\\nSummary: Gene functions enriched in this list include receptor functions, protease production, cell adhesion, development, immune regulation, inflammation, protein family structural functions, GTPase activities, transcription factor functions, transcription regulation, post-translational modifications, endocytic receptor-ligand interactions, ligand functions, serine protease inhibitor functions, interaction with plasma membrane components, small molecule energy production and transport, transcriptional binding and regulatory protein family functions, and DNA binding. \\nMechanism: A variety of gene functions are enriched in this list, including receptor functions, protease production, cell adhesion, development, immune regulation, inflammation, protein family structural functions, GTPase activities, transcriptional regulation, transcription factor functions, post-translational modification functions, endocytic receptor-ligand interactions, ligand functions, serine protease inhibitor functions, interactions with plasma membrane components, small molecule energy production and transport, transcriptional binding and regulatory protein family functions, and DNA binding. These functions likely play a role in a variety of biological processes, including signal transduction, cell proliferation, development, growth factor signal transduction, metabolic regulation and stress response. \\n]0.89993
488text-davinci-003narrative_synopsisHALLMARK_MITOTIC_SPINDLE-0[\\nThe given genes are primarily involved in regulation and control of cell morphological and structural processes, such as cytoskeletal organization, centrosome interaction, DNA interaction, and GTPase regulation.\\nHypothesis: These genes are likely to be involved in a variety of biological pathways that control cell morphology and structure, such as organization of the cytoskeleton, centrosome dynamics, DNA replication and maintenance of chromatin structure through interactions with GTPases and their associated proteins.\\n][\\nSummary: This list of genes has numerous important functions related to regulation of the cytoskeleton, cellular communication, cellular development and DNA transcription/translation and repair.\\nMechanism: These functions are critical for maintaining proper cellular morphology, adhesion, and organelle trafficking as well as for initiating and regulating cellular signaling pathways and gene expression.\\n]0.90120
489text-davinci-003narrative_synopsisHALLMARK_MITOTIC_SPINDLE-1[\\nThe list of genes consist of proteins involved in the maintenance of cell architecture, cell cycle regulation, microtubule-binding, and chromosome segregation. Most of the proteins are involved in GTPase and nucleotide exchange regulation, cellular signaling, chromatin remodeling, cytoskeleton structure, DNA replication, cell adhesion, and actin binding and regulation.\\n\\nMechanism:\\nThe proteins suggested in the list are involved in a variety of regulatory pathways that are integral to the maintenance of proper cellular architecture and organization. These pathways include cellular signaling, chromatin remodeling, cytoskeleton structure, DNA replication, cell adhesion, and actin binding and regulation.\\n\\n][\\n\\nSummary: The list of genes encodes proteins which are associated with various regulatory processes in the cell, including binding to and/or activating GTPases, structural maintanance of the cytoskeleton, and control over cell cycle or apoptosis.\\n\\nMechanism: These proteins are likely involved in the regulation of the cell via interactions with proteins such as Rho GTPases or guanine nucleotide exchange factors (GEFs), or participation in the cell cycle, apoptosis, or structure of the cell.\\n\\n]0.95215
490text-davinci-003narrative_synopsisHALLMARK_MTORC1_SIGNALING-0[ Genes related to the list are enriched for activities related to protein biosynthesis, transport and signaling, metabolism, and gene expression control. Mechanism: Genes related to the list are involved in integral processes of the cell, such as metabolism and gene expression control, which are facilitated by protein synthesis, transport and signaling. ][ This list of human genes is enriched for functions related to cellular homeostasis, including protein synthesis, metabolism, protein folding, ubiquitination, transcription, DNA binding and damage control, development, and regulation of cellular pathways.\\n\\nMechanism: These genes are enriched for factors involved in various cellular processes necessary for maintaining homeostasis. These include protein synthesis, redox balance, fatty acid and energy metabolism, protein folding, ubiquitination, protein-protein interaction, transcription, and DNA damage control. In addition, these genes are enriched for factors that regulate various cellular pathways, including apoptosis, the cell cycle, and protein degradation.\\n\\n]0.92364
491text-davinci-003narrative_synopsisHALLMARK_MTORC1_SIGNALING-1[ These genes perform important functions related to protein synthesis and metabolism, including binding, ubiquitination, transcription, and enzyme activity. They are involved in processes such as protein folding, chaperoning, cell cycle regulation, lipid metabolism, glucose uptake, and cytoskeleton formation. Mechanism: These genes share common functions related to protein synthesis and metabolism, and their expressions are mutually regulated to interact with one another and create pathways that lead to the desired outcomes. ][\\nThe human genes found in the list are primarily involved in metabolic processes, cellular homeostasis, and chromatin regulation. Specifically, ATP production, amino acid homeostasis and metabolism, stress response, transcription and mRNA regulation, chaperones and proteasome degradation pathways, and lipid metabolism are all found to be enriched terms with known correlation to each other. Many of the proteins noted have both metabolic and protein-degradation pathways, indicating potential regulatory mechanisms in place for metabolic and homeostatic processes.\\n\\nMechanism: \\n\\nThe metabolic pathway systems are regulated by a combination of transcription and degradation pathways. Proteins involved in these pathways, such as chaperones, proteasomes, and enzymes regulate the transcription of genes and the degradation of proteins for a tight control of homeostatic and metabolic processes. Additionally, lipid and amino acid metabolism are regulated by clusters of enzymes, indicating a need for integration between multiple proteins.\\n\\n]0.90510
492text-davinci-003narrative_synopsisHALLMARK_MYC_TARGETS_V1-0[\\nThe list of genes are involved in the processes of transcription, translation, and post-translational modification, which are essential for protein synthesis and function in the cell. Enriched terms include transcription, translation, mRNA binding, ribosome subunits, splicing factors, post-translational modification, cytoplasmic proteins, nuclear proteins, DNA binding and unwinding proteins subunits of the nuclear lamina, and proteins associated with the spliceosome. \\nMechanism: These gene functions are part of the essential biological mechanism of protein synthesis in a cell, which is a complex process that requires the coordination of multiple processes, including transcription, translation, and post-translational modifications. \\n][\\n\\nSummary: The genes studied are involved in a variety of functions that together form a transcription and translation network, primarily related to translation initiation, RNA binding, and ubiquitination.\\n\\nMechanism: The genes involved form a transcription and translation network that is used to control gene expression and regulation.\\n\\n]0.91404
493text-davinci-003narrative_synopsisHALLMARK_MYC_TARGETS_V1-1[ The genes in this list are largely related to mRNA and protein synthesis, nucleic acid binding and transport, and post-translational modification activities.\\n\\nMechanism: This list of genes likely represents the many steps involved in the synthesis and transport of proteins, from the initial transcription of mRNA and its associated splicing factors, to the polymerase activities, aminoacylation, and trafficking of proteins in and out of the nucleus and into the mitochondria.\\n\\n][ \\nThe list of genes includes proteins that are involved in several processes, such as ribosome formation, RNA binding, DNA unwinding, nucleocytoplasmic transport, SUMO binding, mRNA splicing, nucleic acid binding, and protein acetylation.\\n\\nMechanism: \\nThese genes are enriched for proteins and processes related to gene expression, posttransslational modification of proteins, and protein synthesis. Through these processes, cells control the expression of genes, activate and inactivate proteins, regulate the cytoplasmic environment, and control the metabolism of macromolecules.\\n\\n]0.93103
494text-davinci-003narrative_synopsisHALLMARK_MYC_TARGETS_V2-0[ The list of genes is associated with functions related to ribosome biogenesis, RNA binding and splicing, cell proliferation, cell cycle progression, and chromatin binding.\\n\\nMechanism: The list of genes is likely involved in the regulation and maintenance of ribosome biogenesis and cell proliferation through pre-rRNA processing, DNA replication-dependent chromatin assembly, and regulation of signal transduction.\\n\\n][ \\n\\nSummary: This set of genes is involved in protein binding, transcriptional regulation, cellular processes such as cell cycle progression, protein chaperoning, and cell proliferation, nuclear localization, RNA binding activity, pre-rRNA processing, and ribosome biogenesis. \\n\\nMechanism: Many of the genes in this list encode proteins involved in pre-rRNA processing, ribosome biogenesis, transcriptional regulation, and protein binding activities that are fundamental in cell cycle progression and regulation of cellular processes.\\n\\n]0.94118
495text-davinci-003narrative_synopsisHALLMARK_MYC_TARGETS_V2-1[ Genes from this list encode proteins that are involved in a variety of cellular processes, such as transcription, RNA processing, protein folding, DNA replication and repair, and cell cycle regulation. ][ This list of genes encodes a number of proteins that are involved in RNA processing, nucleolar function, mitochondrial function, nuclear signaling and protein folding. The enriched terms include RNA binding activities, rRNA processing, protein homodimerization, cell proliferation, signal transduction, ribosome biogenesis, protein folding, and mitochondrial transcription factor activity. Mechanism: The underlying biological mechanism might involve a complex network of interactions involving proteins encoded by these genes, that lead to successful cellular processes such as ribosome biogenesis, RNA processing, mitogenesis, and protein folding. ]0.93448
496text-davinci-003narrative_synopsisHALLMARK_MYOGENESIS-0[ \\nSummary: The list of genes contain genes related to motor protein activity, calcium signaling, muscle contraction, transcriptional regulation, intracellular fatty acid-binding, binding of ligands, and several other related processes.\\n\\nMechanism: Many of these genes encode electric conductance, actin filaments, and membrane proteins. They are involved in processes such as ion channels, muscle contraction, calcium sequestration and release, regulation of transcription, and phosphorylation of proteins. These processes occur in response to changes in the external environment or internal signals.\\n\\n][\\nSummary: The list of genes consists of genes involved in various muscle functions, calcium level regulation and metabolic processes.\\nMechanism: The genes are involved in various cellular processes including ion channel regulation, energy metabolism, signal transduction, muscle contraction, and protein ubiquitination/degradation.\\n]0.94270
497text-davinci-003narrative_synopsisHALLMARK_MYOGENESIS-1[\\nOrganism metabolic pathways and protein regulation are enhanced in this group of genes. This enhancement includes increased ion channeling, cellular transport processes, lipid metabolism, and gene regulation. The pathways involve small and large molecules, as well as neurotransmitter signaling.\\n\\nMechanism: This group of genes works together to regulate metabolic processes in the organism, working at a cellular level that includes ions, lipids, proteins, and other molecules. The genes also interact to create networks of ion channels and transporter proteins that allow for efficient nutrient delivery, active metabolic pathways, and the regulation of gene expression.\\n\\n][COULD NOT PARSE]0.69660
498text-davinci-003narrative_synopsisHALLMARK_NOTCH_SIGNALING-0[ \\nSummary: Genes related to the Notch and Wnt signaling pathways were found to be enriched in the gene data set.\\n Mechansim: Notch and Wnt pathways are key signalling pathways involved in cell fate decisions and development of organisms.\\n ][ \\nSummary: This term enrichment analysis focused on fourteen human genes that are involved in regulation of cellular process via Notch and Wnt signaling pathways. \\n\\nMechanism: Through term enrichment analysis of these genes functions, it has been revealed they are involved in the regulation of cell fate decisions and transcriptional activity through the Notch and Wnt signaling pathways. \\n\\n]0.93153
499text-davinci-003narrative_synopsisHALLMARK_NOTCH_SIGNALING-1[\\nThe given genes are involved in multiple cellular processes including Notch signaling pathways, cell-to-cell communication, transcription, protein ubiquitination, cell-cycle regulation, protein breakdown and turnover, and intracellular signalling pathways.\\nHypothesis: The given genes are part of a complex suite of processes which regulate cell fate, signalling, and control of intracellular signalling pathways. The genes are likely involved in establishing or inhibiting various combinations of pathways in response to internal and external stimuli.\\n][ This list of genes is enriched for those involved in Notch signaling pathways, protein ubiquitination, cell fate determination, and transcriptional regulation.\\nMechanism: Multiple genes in this list have roles in the Notch signaling pathway and are involved in transcriptional regulation, ubiquitination, cell fate determination and other processes in order to control the cell cycle and cell division process. \\n]0.91142
500text-davinci-003narrative_synopsisHALLMARK_OXIDATIVE_PHOSPHORYLATION-0[\\nSummary: After performing a term enrichment test, it was found that the majority of the genes were involved in mitochondrial processes, as well as enzyme functions such as dehydrogenases and oxidoreductases, and ATP synthesis. \\nMechanism: This suggests that these genes are functioning on a systemic, metabolic level, and are involved in the overall production, usage and storage of energy within a cell.\\nConstructing a functional mitochondrion would likely require the activities of all these genes.\\n][ This list of genes encode proteins that are involved in the metabolism of glucose, fatty acids, and amino acids by various catalytic steps and systems related to energy production in a cell. ]0.87310
501text-davinci-003narrative_synopsisHALLMARK_OXIDATIVE_PHOSPHORYLATION-1[\\n• The genes involved mainly involve enzymes and proteins involved in oxidation-reduction reactions, ATP synthesis, respiration, and metabolic processes in mitochondria \\n• Pathway and mechanism: The genes are involved in pathways related to mitochondria respiration, ATP synthesis, and metabolism of organic acids, such as oxidative decarboxylation and dehydrogenase reactions.\\n• ][ Human genes on this list are found to be involved in a common pathway related to mitochondrial respiration, oxidative phosphorylation, and pyruvate metabolism related functions. The enriched terms from the term enrichment test are: terminal enzyme; ATP synthesis; mitochondrial respiratory chain; NAD/NADH-dependent; cytochrome c oxidase (COX); electron transport; PDH complex; ubiquitin protein; ferredoxin; acyl-CoA dehydrogenase; and pyruvate dehydrogenase. \\n\\nMechanism: The common pathway these genes have been found to be involved in is related to mitochondrial respiration, oxidative phosphorylation, and pyruvate metabolism. This pathway is mediated by oxidation-reduction reactions, in which electrons are transferred by the proteins being expressed. This transfer of electrons is used to produce ATP, an important source of energy for the cell. These proteins are also involved in other processes including fatty acid metabolism, electron transport, pyruvate metabolism, and ubiquitin protein metabolism.\\n\\n]0.92636
502text-davinci-003narrative_synopsisHALLMARK_P53_PATHWAY-0[ Human genes in this list are generally involved in cell cycle progression, transcription, signaling and regulation, protein synthesis and processing, and homeostasis. Specifically, enrichment of the terms \"cell cycle,\" \"transcription,\" \"signaling,\" \"protein synthesis,\" \"regulation,\" and \"homeostasis\" was observed.\\n\\nMechanism: These genes are likely involved in the creation, maintenance, duplication, and regulation of the complex network of proteins and processes occurring within cells, and the modulation of these processes in response to changes in the environment.\\n\\n][\\n\\nSummary: Human gene functions related to cell cycle regulation, transcriptional regulation, protein binding, DNA binding, and cell signaling. \\nMechanism: Regulation of biological processes and pathways by association of proteins to various binding targets including proteins, DNA, and electron transfer. \\n]0.91267
503text-davinci-003narrative_synopsisHALLMARK_P53_PATHWAY-1[ Human genes related to cancer pathways, cell regulation and apoptosis\\nMechanism: Many of the human genes, when over-expressed, can drive the development of cancer through pathways, regulation of cell growth, and disruption of apoptosis, which is the process of programed cell death.\\n][ \\nSummary: The majority of genes are involved in regulating protein synthesis, transcriptional regulation and cell cycle regulation.\\nMechanism: Regulation of protein synthesis, transcriptional regulation, cell cycle regulation, DNA repair and DNA binding.\\n]0.8228
504text-davinci-003narrative_synopsisHALLMARK_PANCREAS_BETA_CELLS-0[COULD NOT PARSE][\\n]0.7914
505text-davinci-003narrative_synopsisHALLMARK_PANCREAS_BETA_CELLS-1[COULD NOT PARSE][ The list of genes are expressed across various tissues, primarily in the pancreas, endocrine system, and brain. Other tissues expressed in these genes include: liver, intestine, kidney, and epithelium. They encode for proteins that are involved in transcriptional regulation, metabolic pathways, and cell signalling. This suggests an underlying biological mechanism related to transcriptional control and regulation of the endocrine system, pancreas, and glucose metabolism. The enriched terms for this list of genes include: transcriptional regulation; metabolic pathways; endocrine system regulation; glucose metabolism; cell signalling; GTPase; transcription factor; peptide hormone; ATP-binding cassette (ABC) transporter; and proprotein convertase. Mechanism: The list of genes suggest an underlying biological mechanism related to transcriptional control and regulation of the endocrine system, pancreas, and glucose metabolism. ]0.69921
506text-davinci-003narrative_synopsisHALLMARK_PEROXISOME-0[COULD NOT PARSE][ The list of genes is enriched for proteins involved in the transport of various molecules and the enzymatic degradation of molecules across extra- and intra-cellular membranes (e.g. ATP-binding cassette transporters, oxidoreductases, dehydrogenases/reductases, hydratases/isomerases, enzymes responsible for fatty acid beta-oxidation, enzymes catalyzing the breakdown of malonyl-CoA, etc). Specific biological pathways or mechanisms of which the genes are a part involve cell adhesion, nucleotide excision repair, hormone metabolism and synthesis, nucleic-acid binding, antioxidant activity, and transcription factors. \\n\\nSummary: The list of genes is enriched for proteins involved in transport and enzymes that catalyze the degradation of molecules.\\nMechanism: Mechanisms of which the genes are a part involve cell adhesion, nucleotide excision repair, hormone metabolism and synthesis, nucleic-acid binding, antioxidant activity, and transcription factors.\\n]0.67945
507text-davinci-003narrative_synopsisHALLMARK_PEROXISOME-1[ After performing a term enrichment test on the given list of genes, it can be seen that the functions of many of these genes are related to lipid metabolism and antioxidant functions, as well as DNA-related processes such as DNA repair, transcription and replication. Specifically, some of the enriched terms are lipid metabolism, fatty acid beta-oxidation, DNA repair, transcription and replication, oxidative stress, glutamate metabolism, vitamin A binding, and steroid metabolism.\\n\\nMechanism: The underlying biological mechanism of these gene functions is related to the homeostasis of vital cellular processes such as cell adhesion and signalling, protein production and degradation, regulation of mitochondrial and peroxisomal functions, and protection against oxidative damage. \\n\\n][\\nSummary: Genes mentioned are found to primarily be involved in pathways that are related to oxidative stress and hormone response.\\nMechanism: These genes may be involved in oxidative stress, hormone signaling, or fatty acid metabolism.\\n]0.87550
508text-davinci-003narrative_synopsisHALLMARK_PI3K_AKT_MTOR_SIGNALING-0[ Summary: This gene list includes many genes involved in protein regulation and signalling with a heavy focus on serine/threonine protein kinase family.\\n Mechanism: Multiple genes listed play a role in the regulation of ubiquination, phospholipids, protein-protein interactions, transcription, and cell signalling.\\n ][ \\nSummary: The majority of genes in this list encode proteins involved in signal transduction pathways and interact with other proteins via phosphorylation or protein-protein binding. \\nMechanism: Many of the gene products in this list are involved in signal transduction via phosphorylation, protein-protein interaction, GTP binding and/or cAMP binding. \\n]0.9141
509text-davinci-003narrative_synopsisHALLMARK_PI3K_AKT_MTOR_SIGNALING-1[\\nThe genes summarized in this list are involved in a wide range of functions, including those related to cell growth, cell cycle control, DNA binding, transcriptional regulation, signal transduction, and protein phosphorylation/dephosphorylation. The enriched terms refer to activity of signal transduction pathways and protein kinases such as members of the MAPK, RAS and G protein-coupled receptor (GPCR) families, as well as phosphatases, guanine nucleotide exchange factors, and endoplasmic reticulum chaperone proteins.\\n\\nMechanism: This list of genes is involved in signal transduction cascades, which involve proteins kinases and phosphatases modulating the expression of target genes by post-translational modifications, such as phosphorylation or ubiquitination of these proteins, as well as DNA binding and transcriptional regulation. \\n\\n][\\nSummary: The genes listed mostly encode components involved in cellular signaling cascades, such as protein kinases, guanine nucleotide-binding proteins, receptor-interacting proteins and chaperone proteins.\\nMechanism: The listed genes appear to be involved in a variety of signaling cascades, such as those related to cell growth, transcription, cytokine production and protein modification.\\n]0.95452
510text-davinci-003narrative_synopsisHALLMARK_PROTEIN_SECRETION-0[ \\n\\nSummary: The list of genes is associated with various roles in the endomembrane system, mainly playing roles in intracellular transport, vesicle formation, organelle biogenesis, lysosomal function, protein folding, GPCR-mediated signal transduction, and ligand-receptor complex trafficking.\\n\\nMechanism: Processes such as vesicle trafficking, lysosomal protein transport, GPCR mediated signal transduction, and organelle biogenesis are mediated by delivery of proteins to the correct cellular compartment via membrane proteins and complexes such as adaptins, SNAREs, GTPases, and the Golgi Apparatus.\\n\\n][ \\n\\nSummary: Gene functions enriched for membrane-associated proteins, GTPases, coatomer complexes, vesicle trafficking, organelle biogenesis, phosphatidylinositol binding and regulation\\nMechanism: The gene functions are involved in the regulation, biogenesis and transport of intracellular organelles, membrane proteins and vesicles, as well as binding of phosphatidylinositol molecules.\\n]0.92216
511text-davinci-003narrative_synopsisHALLMARK_PROTEIN_SECRETION-1[ Transmembrane proteins involved in transport, trafficking and organelle biogenesis are enriched amongst this gene list. \\nMechanism: The Enriched transmembrane proteins likely function as part of a complex network of molecular machinery involved in vesicle trafficking, docking and fusion of proteins, organelle biogenesis, and protein folding.\\nThe ][COULD NOT PARSE]0.68334
512text-davinci-003narrative_synopsisHALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0[\\n\\nSummary: All of the genes in the list are associated with molecules, enzymes, and proteins involved in cell metabolism and defense against oxidative stress.\\n\\nMechanism: The genes are involved in the regulation of pathways of cell energy metabolism and defense against oxidative stress, by providing key cellular components which participate at various levels of oxidation and reduction.\\n\\n][COULD NOT PARSE]0.69375
513text-davinci-003narrative_synopsisHALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1[\\n\\nSummary: The human genes listed contain a variety of proteins that function in processes related to cell growth and development, redox regulation, DNA repair and transcription, response to oxidative stress and inflammation, cell cycle progression, and metabolism.\\n\\nMechanism: The functions of the proteins span a range of processes that are essential for cell survival, such as cell growth control, transcriptional regulation, redox regulation, and metabolism. These proteins may work together to regulate processes, such as glutamate-cysteine ligase activity, hydroxylase activity, protease activity, free-radical scavenging and protein phosphatase activity. \\n\\n][\\n\\nSummary: This set of genes are mostly involved in redox processes, oxidative stress, DNA repair, and metabolism. These genes are involved in processes related to the regulation of cell growth, DNA repair, inflammation control, and cellular defense\\n\\nMechanism: The genes in this list are involved in a variety of functions that are necessary for cellular homeostasis and metabolic processes. Redox processes, oxidative stress, and damage control are mediated by a variety of proteins, such as heme oxygenase, glutathione reductase, superoxide dismutase, and glutathione peroxidase. DNA repair is regulated by proteins such as nucleotide excision repair complex and phosphofructokinase A. Inflammation control is regulated by proteins including myeloperoxidase, MAPEG family proteins, and glutaredoxin. Cellular defense against toxic and carcinogenic compounds is regulated by proteins such as glutathione S-transferase and peroxidase.\\n\\n]0.95273
514text-davinci-003narrative_synopsisHALLMARK_SPERMATOGENESIS-0[\\n\\nSummary: This term enrichment test on a list of human genes revealed several proteins and proteins related functions that are statistically over-represented.\\n\\nMechanism: This term enrichment test suggests that certain proteins and associated functions are involved in a wide variety of biological processes related to gene expression, transcription, and other aspects of cellular functioning. \\n\\n][ Enriched terms shared by the genes include cell cycle regulatory proteins and kinases, DNA binding proteins and chaperones, nucleotide and polypetide biding proteins, phosphatases, and proteins involved in transcription. In particular, the genes function in gene transcription, chromosome organization, apoptosis regulation, DNA repair, protein folding and transport, cell signaling and growth regulation, energy metabolism, cytoskeletal organization, and vesicular trafficking. The underlying biological mechanism is likely involved in multiple steps in cell division and the regulation of gene expression, and in the maintenance of cell homeostasis.\\n\\nOerbaken: ]0.87267
515text-davinci-003narrative_synopsisHALLMARK_SPERMATOGENESIS-1[ \\nSummary: These genes are involved in diverse processes such as transcriptional regulation, cell cycle regulation, chromatin structure and nuclear envelope signaling, cell adhesion and motility, metabolic processes, protein folds and ubiquitination, detection, binding and enzymatic activities, and vasodilation.\\n\\nMechanism: These genes encode proteins that act as molecular adaptors, molecular chaperones, enzymes, transporters, transmembrane receptors, and other components in a variety of pathways and pathways.\\n\\n][COULD NOT PARSE]0.70502
516text-davinci-003narrative_synopsisHALLMARK_TGF_BETA_SIGNALING-0[ This list of genes is enriched for proteins involved in receptor signaling pathways and transcriptional regulation as well as cell signaling, adhesion and growth. These proteins can serve as part of complexes, act as enzymes, bind hormones, and influence cellular processes. \\nMechanism: Many of the genes identified in this list encode proteins in the TGF-Beta superfamily which are involved in the regulation of growth, differentiation and development, as well as apoptosis and transcription. These proteins work together in a complex network to regulate these cellular processes. \\n][COULD NOT PARSE]0.68570
517text-davinci-003narrative_synopsisHALLMARK_TGF_BETA_SIGNALING-1[ \\n\\nSummary: The list of genes have been identified as members of various pathways related to the regulation of cell growth and differentiation, transcriptional regulation, receptor-regulated SMAD proteins, and signal transduction. \\nMechanism: The proteins encoded by these genes form different complexes, interact with various receptors, and function as transcriptional modulators, signal transducers, and ubiquitin ligases to regulate growth, differentiation and signaling pathways in cells.\\n][ \\n\\nSummary: The 20 genes examined are primarily involved in signal transduction pathways, transcription regulation and cell-to-cell communication.\\nMechanism: The identified genes are involved in various signaling pathways, including the transforming growth factor-beta (TGF-beta), bone morphogenetic protein (BMP), and receptor-regulated SMAD pathways.\\n]0.94140
518text-davinci-003narrative_synopsisHALLMARK_TNFA_SIGNALING_VIA_NFKB-0[ The genes in the list can be grouped into two main categories: genes that encode proteins involved in transcription (e.g. FOS, EGR, IFNGR2, MYC, NFKB, REL, etc.), and genes that encode proteins involved in cytokine and inflammatory signalling pathways (e.g. IL1A, IL2B, IL7R, etc.). Mechanisms: Additionally, the genes in the list encode proteins that have a variety of roles in the regulation of cellular proliferation, apoptosis, and other processes in various cell types. ][\\nSummary: The list of genes contain a range of proteins that are involved in transcriptional regulation, cytokine activity, regulation of cell proliferation, and lipid metabolism.\\nMechanism: The genes are involved in a range of biological processes related to transcriptional regulation, cytokine activity, regulation of cell proliferation, and lipid metabolism.\\n]0.90113
519text-davinci-003narrative_synopsisHALLMARK_TNFA_SIGNALING_VIA_NFKB-1[ Expression and regulation of multiple proinflammatory cytokines and chemokines, regulation and activity of kinases, transcription factors, and components of the TGF-beta, NF-kappa-B, MYC/MAX/MAD, Jagged 1 and STAT-regulated pathways, and regulation of lipoproteins and growth factors.\\nMechanism: These genes collectively comprise pathways and networks that regulate inflammation, cellular growth, cell differentiation, and apoptosis.\\n][\\nThis list of human genes includes receptors, cytokines, proteins, transcription factors, enzymes, and growth factors involved in inflammation, signaling pathways, transcriptional regulation, and cell cycle control. \\nMechanism: The functions of the genes in the list are likely to be related to inflammatory responses, signal transduction, and cell cycle regulation and apoptosis.\\n]0.9154
520text-davinci-003narrative_synopsisHALLMARK_UNFOLDED_PROTEIN_RESPONSE-0[ \\nSummary: A list of human genes involved in RNA-binding and protein-binding activities, along with protein metabolism, synthesizing and chaperone activity.\\nMechanism: The transcription factors and proteins help to regulate and stimulate gene expression and the protein folding process, which affects the synthesis and metabolism of proteins. This can lead to changes in cell function and structural integrity of cells.\\n][ The genes in the list are involved in RNA processing and binding, transcription regulation, protein folding, targeting, covalent modifications and transport, endoplasmic reticulum function, and translation initiation. The enriched terms are RNA binding; transcription regulation; protein folding; protein targeting and covalent modifications; endoplasmic reticulum function; and translation initiation. Mechanism: The underlying biological mechanism for the enrichment of these terms is that the proteins encoded by the list of genes interact with each other to perform a variety of roles in RNA processing, transcription regulation, protein folding, targeting and covalent modifications, endoplasmic reticulum function, and translation initiation. These proteins can act as components of a larger complex or individually to perform these roles. ]0.90427
521text-davinci-003narrative_synopsisHALLMARK_UNFOLDED_PROTEIN_RESPONSE-1[\\n\\nSummary: The list of genes are associated with endoplasmic reticulum (ER) processes, such as transcription factors, RNA binding proteins, protein folding and degradation, protein chaperones, mRNA decapping, and zinc transporter proteins. \\n\\nMechanism: The list of genes are involved in a wide range of endoplasmic reticulum (ER) processes such as post-translational modifications, translational regulation, RNA binding, protein folding, protein degradation, and protein trafficking.\\n\\n][ Genes in the provided list are primarily involved in processes such as protein synthesis, endoplasmic reticulum stress response, RNA binding, and conformational folding.\\n\\nMechanism: These genes encode proteins that play a role in protein synthesis, cellular trafficking, conformational folding, and RNA binding. These processes are inter-related in that conformational folding is necessary for protein structure, protein expression is required for protein synthesis, and RNA binding is necessary for mRNA translation. The endoplasmic reticulum stress response allows for regulation of these processes.\\n\\n]0.93119
522text-davinci-003narrative_synopsisHALLMARK_UV_RESPONSE_DN-0[ \\nSummary: Enriched terms from a list of human genes indicate that many of these genes are involved in cellular response regulation, cell surface receptors, signal transcription, signal transduction, phosphorylation, and calcium binding pathways.\\n\\nMechanism: The proposed underlying biological mechanisms involve regulation of gene expression and signal transduction through phosphorylation of proteins, downstream target proteins, and modulation of their function.\\n\\n][\\nSummary: The genes in the list are involved in a wide range of processes, including cell surface glycoprotein binding, cell adhesion, phosphoprotein production, transcription regulation, and signaling pathways.\\nMechanism: Many of the genes are associated with signaling pathways, including calcium-dependent signal transduction, phosphorylation, MAP kinase signaling, PI3 pathways, and G-protein signal transduction.\\n]0.9149
523text-davinci-003narrative_synopsisHALLMARK_UV_RESPONSE_DN-1[ \\n\\nSummary: The human gene list is enriched for terms related to signal transduction, extracellular matrix proteins, cellular adhesion, and transcription factors.\\n\\nMechanism: Signal transduction pathways, extracellular matrix proteins, and transcription factors increase cell activity and affect the regulation of gene expression.\\n\\n][ This set of genes is enriched for terms associated with embryonic development, cell signaling, receptor regulation and transcription regulation. Specifically, genes related to transcription factors, receptors and their respective ligands, growth factors, phosphoproteins and kinases are overrepresented.\\n\\nMechanism: These genes are involved in a variety of different cell signaling pathways, which are essential for embryos to develop properly and become mature organisms. During embryonic development the signals which these enzymes and receptors transmit and respond to, such as hormones and growth factors, direct the development and differentiation of cells. Cells communicate with one another through these pathways and transcription factors to direct cellular activities such as proliferation, differentiation, growth, migration, as well as many other metabolic and physiological processes.\\n\\n]0.90567
524text-davinci-003narrative_synopsisHALLMARK_UV_RESPONSE_UP-0[ \\nSummary: This list of genesí human functions mainly involve cell regulation, transmembrane transport, metabolic catabolism, and transcription support. \\nMechanism: These genes are involved in important pathways responsible for transportation and metabolic processes, as well as regulation of cellular functions.\\n][ \\nSummary: The genes listed are involved in a variety of functions, including protein binding, catalysis of metabolic reactions, transcriptional regulation and regulation of cell signaling pathways.\\nCommonalities: \\nMechanism: Genes bearing similar functions may be involved in similar molecular or cellular processes, and the high level of overlap between gene function across the list implies a common pathway of regulation of certain activities in the cell, such as metabolic reactions and signaling pathways.\\n]0.91199
525text-davinci-003narrative_synopsisHALLMARK_UV_RESPONSE_UP-1[ Our analysis revealed that these genes are primarily involved in cell signaling and membrane-associated functions, including protein binding, reaction catalysis, transporter activity, and GTP binding. Mechanism: The primary biological mechanism underlying this set of genes appears to be related to the regulation and control of cell signaling and membrane-associated functions in various cellular processes, including metabolism, replication and transcription, and cell growth and differentiation. ][\\nThe list of genes shows enrichment related to enzymes, regulatory proteins, transcription factors, membrane and transport proteins, structural proteins, and other proteins involved in cell growth and development. Specifically, this list is enriched for genes that encode a diverse range of regulatory proteins involved in cellular signaling, transcription control, metabolism, and immune response. There is also enrichment for genes involved in the biosynthesis of heme, which is important in cellular apoptosis and other cellular processes. \\n\\nMechanism:\\nThe underlying biological mechanism involved in this term enrichment likely involves the regulation of various biochemical processes by macromolecular signaling pathways. The term enrichment most likely reflects the need of these genes to work together in order to carry out specific functions in cellular homeostasis and adaptation. \\n\\n]0.89393
526text-davinci-003narrative_synopsisHALLMARK_WNT_BETA_CATENIN_SIGNALING-0[\\n\\nSummary: A significant number of these genes are involved in the functioning of the Wnt signaling pathway, as well as cell cycle progression and gene transcriptional regulation.\\n\\nMechanism: Wnt signaling pathway controls cellular processes such as cell proliferation and migration, survival and cell differentiation, which involves a number of intercellular signalling pathways and Transcription Factor complexes.\\n\\n][ The genes listed are involved mostly in processes and pathways related to embryonic development, transcriptional regulation, DNA repair, and cell-cell interactions, such as Wnt, Notch, and Hedgehog signaling, as well as the F-Box protein family. \\n\\nMechanism: The molecular mechanism of this list of genes is related to cellular signaling pathways that enable cells to interact and establish communication with each other for proper embryonic development, cell fate determination, and DNA repair. These pathways involve the use of proteins such as Notch, Wnt, and Hedgehog receptors and ligands, as well as the F-box proteins.\\n\\n]0.90211
527text-davinci-003narrative_synopsisHALLMARK_WNT_BETA_CATENIN_SIGNALING-1[ Through the analysis of gene summaries from the provided list, it is evident that genes playing a role in Wnt, Notch, and Hedgehog signaling pathways are enriched. The genes also appear to be involved in transcriptional regulation, cell cycle progression, and developmental events, as well as processes such as DNA replication and repair, transcriptional silencing, and proteasomal ubiquitin-dependent protein catabolism. It is possible that the mechanism involves the regulation of these pathways and their effects on various cellular functions. \\n\\nMechanism: This may involve the regulation of the Wnt, Notch, and Hedgehog signaling pathways and their effects on various cellular functions such as cell fate determination, DNA repair, transcriptional activation and repression, and protein catabolism.\\n\\n][\\n\\nSummary: This list of genes contained members of the frizzled, notch, Wnt, Dickkopf, and histone deacetylase families, which are involved in various cell fate decisions and signaling pathways during embryonic development.\\n\\nMechanism: The enriched terms reflect the commonality of the genes in the list, which are all part of signaling pathways that influence cell fate decisions, including canonical Wnt pathway, Notch pathway, and Hedgehog pathway.\\n\\n]0.91352
528text-davinci-003narrative_synopsisT cell proliferation-0[\\n\\nSummary: This list of human genes found in the summary have involvement in a variety of processes including cell division, adhesion, differentiation, and response to stress, in addition to roles in the immune system, transcriptional regulation, ligand binding, receptor binding, ubiquitin-protein ligase activity, phosphodiesterase activity, and protein phosphatase activity.\\n\\nMechanism: These genes are likely involved in multiple pathways and signaling mechanisms to regulate these various processes, likely involving kinases, transcription factors, adaptor proteins, and ubiquitin-protein ligases. \\n\\n][COULD NOT PARSE]0.70590
529text-davinci-003narrative_synopsisT cell proliferation-1[\\nThe list provided of genes demonstrates significant enrichment of terms related to transcriptional regulation, cellular signaling pathways and processes, cell growth, differentiation, response to stress and to foreign material (via immune response), protein folding and trafficking, and recognition of self and non-self through various receptors. In the list there are mainly transcription factors, protein tyrosine phosphatases and kinases, several receptor families, and proteins for interleukin signaling. The underlying biological mechanism or pathway is likely related to the development and differentiation of cells and homeostasis or recognition of abnormalities or foreign materials.\\n\\n][\\nThe list of genes is primarily involved in signal transduction and cell regulation, as well as immune defense, including cell recognition and protein phosphatase and ubiquitin binding activities. The underlying mechanism is likely regulated by protein and lipid enzymes, tyrosine and cGMP kinases, receptors, and transcription factors.\\n\\nMechanism: Signal transduction and cell regulation, mediated by protein and lipid enzymes, tyrosine and cGMP kinases, receptors, and transcription factors.\\n\\n]0.93198
530text-davinci-003narrative_synopsisYamanaka-TFs-0[COULD NOT PARSE][COULD NOT PARSE]1.000
531text-davinci-003narrative_synopsisYamanaka-TFs-1[ \\nSummary: The genes KLF4, POU5F1, and SOX2 are transcription factors involved in embryonic development and stem cell maintenance, and are associated with tumorigenesis. \\nMechanism: Transcription factors control gene expression, which in turn controls embryonic development and stem cell maintenance, impacting tissue formation, tumorigenesis, and cell differentiation. \\n][\\nSummary: This set of genes is related to development, stem cell maintenance, and tumor formation. \\nMechanism: These genes regulate gene expression in embryonic development and in adult tissues, controlling the G1-to-S transition of the cell cycle following DNA damage and mediating the tumor suppressor gene p53.\\n]0.9157
532text-davinci-003narrative_synopsisamigo-example-0[ The majority of the gene functions encompass proteins involved in cellular adhesion, signaling pathways, extracellular matrix proteins, and components of the complement cascade. Gene products have roles in tissue development and regeneration, wound healing, immune hypersensitivity reactions, apoptosis, motility, and angiogenesis.\\n\\nMechanism: These genes are likely to be involved in multiple mechanisms related to homeostasis and wound healing, likely through cell-extracellular matrix binding and communication between cells through signal pathways.\\n\\n][\\nSummary: This enrichment analysis of human genes suggests that these genes, or their encoded proteins, play a role in a multitude of processes including cell adhesion, signalling, metabolism, apoptosis, morphogenesis, hemostatsis, immunity and extracellular matrix maintenance.\\nMechanism: These genes are likely involved in modulating the interactions between cells and their macroenvironment and the modulation of cell-cell signalling pathways.\\n]0.92108
533text-davinci-003narrative_synopsisamigo-example-1[\\nThis list of genes appears to be comprised of proteins involved in a variety of cellular activities related to cellular communication, extracellular matrix organization, cell adhesion, cell survival, and migration. Enriched terms include: Notch signaling pathway; osteoclast attachment/mineralized bone matrix; jagged 1/notch 1 signaling; cell adhesion; apoptosis; collagen fibril formation; antimicrobial peptide activity; lipoprotein metabolism; cell migration; extracellular matrix remodeling; cytotoxicity; chemotaxis; cytoplasmic signaling and phosphorylation; transcriptional repressor; odontogenesis; hematopoietic cell adhesion; serine protease inhibition; inward-rectifier potassium channels; and angiogenesis.\\n\\nMechanism: The underlying biological mechanism appears to involve a variety of cellular activities related to cellular communication, extracellular matrix organization, cell adhesion, cell survival, and migration, enabled by the expression and activity of these genes in different cellular pathways and networks.\\n\\n][ The list of genes includes those involved in tissue development and repair, extracellular matrix components, signaling pathways such as the Notch signaling pathway and the cyclic AMP signaling pathway, cell survival, motility and migration, regulation of Fas-induced apoptosis, antimicrobial activity, transcriptional activation, and regulation of cell adhesion.\\n\\nMechanism: The underlying biological mechanism that is likely to be at play is the regulation of cellular activity and processes, including cell proliferation, cell migration, extracellular matrix formation, adhesion and signaling pathways for optimal tissue development and repair.\\n\\n]0.94387
534text-davinci-003narrative_synopsisbicluster_RNAseqDB_0-0[ This gene list represents genes with a wide range of functions involving membrane transport, growth factor regulation, and transcription regulation. Many of the genes are involved in ion channels and calcium and calcium-dependent processes. Mechanism: The genes are involved in a wide range of processes, including membrane transport, growth factor and calcium regulation, transcription regulation, and binding activity. ][\\nSummary: The group of human genes in this list are related to the functions of ion regulation, transcription regulation, signal transduction, and protein binding.\\nMechanism: Many of the proteins encoded by these genes, involve important cellular functions such as signal transduction, cytoskeletal adaptor proteins, transcription factors, and glycoproteins. This suggests a mechanism for many of these genes as either directly or indirectly involved in signal transduction pathways and/or transcriptional modulation of cell processes.\\n]0.92114
535text-davinci-003narrative_synopsisbicluster_RNAseqDB_0-1[COULD NOT PARSE][\\nSummary: This gene list is enriched for genes that enable or are associated with a variety of activities, including transcription factor activity, metal ion binding activity, DNA binding activity, chromatin binding activity, RNA binding activity, protein domain-specific binding activity, and histone or methylated histone binding activity.\\nPredicted Mechanism: The gene list is enriched for genes that facilitate a variety of cellular processes, such as binding activities, transcription and translation, transcription factor activity, receptor activity, and chromatin structure. This suggests a variety of molecular pathways are enriched in these genes, likely related to cell adhesion, cell surface receptor signaling, cell apoptosis, transcriptional regulation, and the regulation of chromatin structure.\\n]0.70795
536text-davinci-003narrative_synopsisbicluster_RNAseqDB_1002-0[ This list of genes is found in muscle tissue, and are involved in muscle formation, contraction, development, and cytoskeletal structure. These genes are involved in pathways of signal transduction, protein-protein interactions, and energy metabolism. ][ \\n\\nSummary: This gene list is involved with various processes related to cell structures, cell motility and varying aspects of muscle contraction.\\n\\nMechanism: The genes in this list are involved in a variety of processes related to the structure and function of muscle cells, such as actin filament binding and regulation of the intracellular calcium concentration. They are also involved in processes related to regulating neuronal and epithelial cell activity.\\n\\n]0.91211
537text-davinci-003narrative_synopsisbicluster_RNAseqDB_1002-1[ The list of genes and their functions suggests that these genes are involved in muscle development and regulation, actin and tropomyosin binding, calcium- and energy-regulation, ion channeling, and structural framework assembly and maintenance. In addition, they may be involved in negative regulation of cytokine signaling pathways and calcineurin-NFAT signaling cascade. The enriched terms include muscle development, actin and tropomyosin binding, calcium- and energy-regulation, ion channeling, negative regulation of cytokine signaling pathways, and calcineurin-NFAT signaling cascade.\\n\\nMechanism: These genes likely work together to ensure proper muscle development and maintenance by regulating calcium levels, energy homeostasis, and structural abundance of actin and other proteins in the muscle cells. The negative regulation of cytokine signaling pathways and calcineurin-NFAT signaling cascades could play a role in controlling the expression of these genes, allowing for the precise control of muscle development.\\n\\n][ \\nSummary: This gene analysis reveals a number of proteins involved in skeletal and cardiac muscle contractile processes, such as actomyosin ATPase activity and tropomyosin binding activity.\\nMechanism: The proteins regulate muscle contraction in response to fluctuations in intracellular calcium concentration, while also playing a role in muscle differentiation and muscle organization.\\n]0.89641
538text-davinci-003narrative_synopsisendocytosis-0[ These genes are involved in a wide variety of cellular processes and components, including endocytosis, protein transport, actin filament network formation, endoplasmic reticulum and recycling endosome membrane organization, macropinocytosis, cellular component organization, intracellular signaling, and protein homooligomerization. The associated processes of cell motility, cell differentiation, gene expression regulation, cell proliferation, stress and inflammatory responses, nuclear export, lysosomal degradation lipid homeostasis and apoptotic signaling form highly enriched terms in this gene set. Mechanism: The underlying biological mechanism or pathway is likely related to a combination of transmembrane and intracellular signaling. This signaling is likely to lead to cellular processes such as cell motility, cell differentiation, gene expression regulation, cell proliferation, stress and inflammatory responses, nuclear export, lysosomal degradation lipid homeostasis and apoptotic signaling. ][\\nSummary: This set of genes functions in a variety of cellular processes such as endocytosis, cytoskeletal remodeling, lysosomal degradation, nuclear export, protein homooligomerization, actin filament network formation, plasma membrane bounded cell projection organization, endoplasmic reticulum formation, mitochondrial organization and cholesterol receptor-mediated endocytosis.\\nMechanism: The genes work together to regulate cellular processes in the cell such as protein trafficking, signaling pathways, and membrane reorganization. \\n]0.94472
539text-davinci-003narrative_synopsisendocytosis-1[\\n\\nSummary: This list of genes encode adaptor proteins involved in cytoskeletal reorganization, vesicle trafficking, endocytosis, and mitosis, receptor-mediated endocytosis of specific ligands, cell adhesion processes, ubiquitin-protein ligase, and caspase-regulation of signaling complexes. \\nMechanism: The identified process involves the regulation of protein transport, endocytosis, receptor-mediated endocytosis, protein homooligomerization, cell adhesion, cell motility, amino acid residues, ubiquitination, fatty acid transport, cytoskeletal reorganization, vesicle trafficking, signaling complex regulation, mitosis, and caspase activation. \\n][ A number of genes related to lysosomal degradation, receptor-mediated endocytosis, membrane-related processes, and endocytosis were identified. Proteins with death domain-folds, GTPase regulation, and ubiquitin-protein ligase activities were found to be recurrently present. \\n\\nMechanism: The gene functions identified are related to processes involved in the endocytosis and lysosomal degradation pathways which aid the movement of proteins and other molecules along the endocytic pathway. These processes involve specific processes such as receptor binding, GTPase regulation, ubiquitin-protein ligase and death domain-fold interactions. \\n\\n]0.896
540text-davinci-003narrative_synopsisglycolysis-gocam-0[\\nSummary: The genes provided in this list are all involved in glycolysis pathways and are associated with various forms of anemia.\\nMechanism: These genes encode proteins that catalyze glycolysis and the conversion of glucose to glucose-6-phosphate, the first step in carbohydrate metabolism. This metabolic process is involved in the production of energy and the regulation of cellular homeostasis.\\n\\n][\\nSummary: The list of genes is involved in metabolic pathways, such as glycogenesis, glycolysis, phosphorolation and gluconeogenesis.\\nMechanism: These genes function in the conversion of energy sources, such as glucose and fructose, into energy sources used by the body.\\n]0.93129
541text-davinci-003narrative_synopsisglycolysis-gocam-1[\\n\\nSummary: The list of genes provides a broad overview of glycolytic and related metabolic enzymes involved in muscle maturation and regeneration,hemolytic anemia and associated neurological impairments resulting from glycogen storage diseases and cancer development, as well as angiogenesis and regulation of the serine protease plasmin.\\n\\nMechanism: These genes are likely to be activating complementary pathways involved in glycolytic metabolism, muscle maturation and development, and angiogenesis.\\n\\n][\\nSummary: Genes in this list are involved in various functions related to glycolysis, metabolism, and regeneration.\\nMechanism: The genes in this list appear to be involved in the regulation of metabolic pathways related to the conversion of sugar molecules to energy and the conversion of energy to other forms, including muscle development and tumor progression.\\n]0.93139
542text-davinci-003narrative_synopsisgo-postsynapse-calcium-transmembrane-0[\\nThe genes discussed are involved in various forms of calcium ion transport, regulation and channels, as well as postsynaptic ion channels and nicotinic acetylcholine receptors. \\n\\nMechanism: Calcium ion transport and regulation is an important biochemical mechanism in the body, with calcium ions being necessary for proper neuronal signaling, regulation of muscle contraction and other bodily processes. The genes discussed are involved in the active transport of calcium ions, including ATPases and GPCRs; as well as channels and receptors that respond to signaling molecules such as nicotinic acetylcholine and glutamate.\\n\\n][ These genes encode proteins involved in calcium homeostasis, calcium-channel activity, and receptor function in cell membranes.\\nMechanism: The genes are involved in the biosynthesis and maintenance of calcium-related proteins, ion channels, and receptors, which are essential components to facilitate information flow and cell-signaling across cell membranes.\\n]0.91265
543text-davinci-003narrative_synopsisgo-postsynapse-calcium-transmembrane-1[ The genes identified in this list are primarily involved in calcium ion regulation and transport mechanisms, specifically related to the N-methyl-D-aspartate receptor family and its associated proteins. Mechanism: The gene functions are related to the regulation of calcium ions and their transport via a variety of proteins such as the N-methyl-D-aspartate receptor family, transmembrane AMPA receptor regulatory proteins (TARPs), dopamine receptors, and P-type primary ion transport ATPases. ][ The gene summaries are related to ion channels and transmembrane proteins that play a role in calcium homeostasis, calcium influx, synaptic transmission, and neuronal development. These proteins frequently belong to the Purinergic receptor, NMDA receptor, and AMPA-receptor regulatory protein (TARP) families. Mechanism: The proteins act through their function as ion channels and transmembrane proteins in order to act as mediators of calcium-dependent processes in neuron cells. ]0.9414
544text-davinci-003narrative_synopsisgo-reg-autophagy-pkra-0[\\n\\nSummary: These genes are involved in various processes related to intracellular signaling pathways, cell cycle regulation, apoptosis, DNA repair, and immunity related GTPase family functions.\\n\\nMechanism: These genes are involved in the activation, regulation, or inhibition of protein kinases, caspases, and nuclear factor kappaB (NF-kB).\\n\\n][ The genes provided are involved in several cellular pathways, including cell proliferation and survival, signal transduction, apoptosis, protein folding and DNA repair. There is an enrichment for genes involved in cell growth, apoptosis and signal transduction through serine/threonine kinase activator activity, phosphatidylinositol 3-kinase activity, and guanyl-nucleotide exchange factor activity. \\nMechanism: The genes appear to be involved in a variety of cellular pathways that are regulated by the AKT/PI3K and mammalian target of rapamycin (mTOR) signalling pathways. These signalling pathways mediate the activity of the genes by inducing cell growth and proliferation, and by regulating the expression of transcription factors such as NF-kappaB and TNFRSF11A/RANK.\\n\\n]0.91435
545text-davinci-003narrative_synopsisgo-reg-autophagy-pkra-1[COULD NOT PARSE][ These genes are involved in functions related to DNA repair, apoptosis regulation, signal transduction, cell growth in response to nutrient and insulin levels, macromolecule metabolic process regulation, cell cycle control and chromatin remodeling. The common mechanism involved in each of the above is a signaling pathway regulated by protein kinases, phosphatases and protein acetyl transferases. \\n\\nMechanism: Signal transduction pathway is regulated by protein kinases, phosphatases and protein acetyl transferases.\\n\\n]0.68506
546text-davinci-003narrative_synopsishydrolase activity, hydrolyzing O-glycosyl compounds-0[ Proteins encoded by the genes are involved in the degradation of polysaccharides and glycoproteins to produce basic sugars, the recognition and degradation of misfolded proteins by endoplasmic reticulum-associated degradation, and the hydrolysis of glycosaminoglycans and heparosan sulfate. ][\\nSummary: Genes included in this list encode enzymes that hydrolyze glycosyl bonds and are involved in glycosylation processes, such as N-Linked Oligosaccharide, O-linked N-acetylglucosamine, and Polysaccharide processes.\\n\\nMechanism: Genes act as an important role in glycosylation processes by hydrolyzing glycosyl bonds and processing oligosaccharides, galactosides, glucosides, and other molecules containing glycosyl linkages.\\n\\n]0.89140
547text-davinci-003narrative_synopsishydrolase activity, hydrolyzing O-glycosyl compounds-1[\\nThe human genes in the list share a commonality of them being glycohydrolase enzymes that manipulate glycosaminoglycans (GAGs), glycosyl hydrolases, and mannosidases. GAGs are long, unbranched polysaccharides which provide structural components to tissues and basement membranes. Lysozymes also appear in the list as well as amylases, which break down carbohydrates to simpler sugars, indicating a role in digestion. \\n\\nMechanism:\\nThis commonality likely reveals a role in the catabolism of carbohydrates and other glycosylated molecules via glycosidases, which break down the glycosidic bonds between saccharides and their non-carbohydrate moieties. Several endo/exoglycosidase enzymes are also mentioned, involved in the cleaving of glycosaminoglycans - this suggests that these enzymes may also play a role in cellular protein traffic and signaling, as certain molecules must travel from the endoplasmic reticulum, out of the cell, and into the extracellular matrix.\\n\\n][ \\n\\nSummary: Genes listed are involved in glycosyl hydrolase, glycohydrolytic enzyme, and hyaluronidase activity.\\n\\nMechanism: Genes listed have enzymatic activity that catalyzes the hydrolysis of glycosyl and glycohydrolytic bonds in glycoproteins, glycolipids, glycosaminoglycans, and other molecules containing oligosaccharide or polysaccharide components.\\n\\n]0.92612
548text-davinci-003narrative_synopsisig-receptor-binding-2022-0[\\nAnalysis of the 20 human genes revealed a significant enrichment of terms relating to immunity, including antigen binding activity, immunoglobulin receptor binding activity, antibody production, adaptive immune response, and protein homodimerization.\\nMechanism: These genes enable immune system detection and responses to foreign antigens, as well as the recognition and binding of antigens and immunoglobulins. Through somatic recombination of genes, antigen recognition and specificity can be achieved, eventually leading to the production of antibodies.\\n][ The genes listed are mostly related to immunoglobulin receptor binding activity and involved in immune system processes. The enriched terms in these genes are antigen binding activity, immunoglobulin receptor binding activity, activated/inactivated immune response, protein homodimerization activity, and peptidoglycan binding activity. Mechanism: The underlying biological mechanism or pathway depends on the particular gene, but they all relate to the recognition and interactions of antigens, the binding of the antigens to immunoglobulin receptors, and the subsequent activation or inhibition of the relevant immune response. ]0.9474
549text-davinci-003narrative_synopsisig-receptor-binding-2022-1[\\nSummary: Analysis of the genes indicates that they play an important role in immune system process, immunoglobulin receptor binding activity, and activation of immune response.\\nMechanism: The genes presented are involved in signaling pathways in which the binding of antigen to the cell surface stimulates a series of molecular events that lead to the activation of an immune response. \\n][\\n\\nSummary: Several of the genes are involved in antigen binding activity, immunoglobulin receptor binding activity and activation of immune response.\\nMechanism: The genes function as part of a mechanism involving antigen and immunoglobulin receptor interaction and signaling pathways that lead to activation of immune responses.\\n]0.9759
550text-davinci-003narrative_synopsismeiosis I-0[\\n\\nSummary: The enriched terms from this list of human genes are related to DNA repair and meiotic recombination, including activities such as endonuclease activity, Bcl-2 homology domain 3 binding, chromatin binding, DNA binding, DNA helicase activity, single-stranded DNA binding, 3'-5' exodeoxyribonuclease activity, SH3 domain binding, SUMO transferase activity, double-stranded DNA binding, RING finger ubiquitin ligase activity, replication fork processing, regulation of homologous chromosome segregation, meiosis I cell cycle process, chromosome synapsis, and homologous chromosome pairing at meiosis.\\n\\nMechanism: These proteins likely act in the repair and recombination of DNA during meiosis, by interacting with other proteins to form complexes that regulate meiotic recombination, chromosome condensation and chromatid separation. These proteins may also be involved in the relief of torsional stress upon DNA transcription and replication.\\n\\n][COULD NOT PARSE]0.69938
551text-davinci-003narrative_synopsismeiosis I-1[ The list of genes provided describes proteins that are involved in several processes, such as meiotic recombination, DNA repair, chromosome segregation, double-strand DNA break repair, and homologous chromosome pairing. The enriched terms corresponding to these genes are meiotic recombination, DNA repair, chromosome segregation, double-strand DNA break repair, homologous chromosome pairing, DNA binding activity, and protein homotetramerization.\\n\\nMechanism: These gene are involved in the repair, pairing and segregation of chromosomes during meiosis and mitosis and the binding and processing of DNA. They interact with other proteins to form complexes which catalyze different types of DNA modification and repair, as well as with DNA through binding and bring about these changes. This interaction is likely necessary for the proper functioning of essential cell processes such as meiosis, mitosis, and DNA repair.\\n\\n][ \\n\\nSummary: The human genes in this list appear to be associated with processes such as DNA double-strand break repair, meiosis, homologous chromosome pairing, and chromosome synapsis.\\n\\nMechanism: These genes likely play a role in homologous recombination, a key process in meiotic division and DNA double-strand break repair. The genes likely work together to form various complexes, such as the FA core complex, the APITD1/CENPS complex, and the CENPA-CAD (nucleosome distal) complex.\\n\\n]0.93435
552text-davinci-003narrative_synopsismolecular sequestering-0[COULD NOT PARSE][\\n\\nSummary: The list of genes has been analyzed, and include functions related to cell cycle progression, regulation of cell growth and survival, innate immunity, cholesterol and lipids metabolism, ubiquitination, antioxidant enzymes, intracellular transport, NF-κB inhibiting proteins, proteins associated with various inflammatory and neurological diseases, and proteins involved in embryogenesis, spermatogenesis, and hematopoiesis.\\n\\nMechanism: These genes are involved in a wide range of biological and biochemical processes that are related to cellular response, regulation of cell cycle progression, regulation of protein and lipid metabolism, protein ubiquitination, and intracellular transport.\\n\\n]0.69688
553text-davinci-003narrative_synopsismolecular sequestering-1[ The provided genes are all involved in regulatory mechanisms related to genetic pathways and molecular interactions. They are involved in a variety of processes including cell cycle progression, transcription, metabolism, and immunity. A common function is providing a defense against microbial infections, toxic molecules, and apoptosis. A common mechanism is binding to and inhibiting partner proteins, often through phosphorylation.\\n\\nMechanism: The common mechanism of these genes is binding to and inhibiting partner proteins, often through phosphorylation, which allows for regulation of genetic pathways and molecular interactions.\\n\\n][\\n\\nSummary: This group of genes are involved in a variety of cellular processes, including endocytosis, iron storage and transport, lipogenesis, apoptosis, cell proliferation and differentiation, defense from bacterial infection, and regulation of transcription and translation.\\n\\nMechanism: The proteins encoded by these genes are thought to act through regulating the expression and activity of proteins, such as transcription factors, caspases, lipids, and hormones, involved in these cellular processes.\\n\\n]0.88133
554text-davinci-003narrative_synopsismtorc1-0[ Genes related to the list are enriched for activities related to protein biosynthesis, transport and signaling, metabolism, and gene expression control. Mechanism: Genes related to the list are involved in integral processes of the cell, such as metabolism and gene expression control, which are facilitated by protein synthesis, transport and signaling. ][ This list of human genes is enriched for functions related to cellular homeostasis, including protein synthesis, metabolism, protein folding, ubiquitination, transcription, DNA binding and damage control, development, and regulation of cellular pathways.\\n\\nMechanism: These genes are enriched for factors involved in various cellular processes necessary for maintaining homeostasis. These include protein synthesis, redox balance, fatty acid and energy metabolism, protein folding, ubiquitination, protein-protein interaction, transcription, and DNA damage control. In addition, these genes are enriched for factors that regulate various cellular pathways, including apoptosis, the cell cycle, and protein degradation.\\n\\n]0.92364
555text-davinci-003narrative_synopsismtorc1-1[ Enzymes that catalyze metabolic reactions, cell cycle regulation, and energy production. \\nMechanism: Enzymes involved in metabolic pathways, cell cycle regulation, and energy production pathways are encoded by the genes listed and are over-represented.\\n\\n][ \\n\\nSummary: The genes under consideration encode many proteins involved in metabolic processes, signal transduction and signal reception, transcriptional and epigenetic regulation, chaperone and proteolytic activity, and cell cycle regulation. \\n\\nMechanism: Biological processes are driven through the action of proteins in biochemical reactions, many of which are regulated by signal transduction systems, transcriptional and epigenetic regulation, and involvement in metabolic pathways.\\n\\n]0.89234
556text-davinci-003narrative_synopsisperoxisome-0[COULD NOT PARSE][ This gene set contains a collection of genes involved in peroxisome biogenesis, and is associated with the various categories of peroxisome biogenesis disorders (PBDs). The genes included code for proteins that are essential for the assembly of functional peroxisomes and involved in the import of proteins into peroxisomes and peroxisome membrane vesicles, as well as the PTS1-type and PTS2-type tripeptide peroxisomal targeting signals and peroxisomal matrix proteins. The enriched terms are: peroxisome biogenesis; peroxisomal protein import; tripeptide peroxisomal targeting signal; peroxisomal matrix protein; AAA ATPase family; peroxisome integrity.\\n\\nMechanism: Peroxins are proteins that are essential for the assembly of functional peroxisomes. These genes are involved in activities associated with the assembly, biogenesis, and integrity of peroxisomes, and in regulating the peroxisomal targeting signals and matrix proteins to be imported into the organelle. \\n\\n]0.68959
557text-davinci-003narrative_synopsisperoxisome-1[COULD NOT PARSE][ \\nSummary: An enrichment test of the functions of five human genes (PEX6, PEX2, PEX3, PEX7, and PEX1) revealed a common theme of proteins associated with peroxisomal biogenesis disorders (PBDs) and proteins involved in peroxisomal import and matrix proteins.\\n\\nMechanism: The proteins encode AAA family ATPases, predominantly cytoplasmic proteins, and integral peroxisomal membrane proteins. These encode the receptor for the set of peroxisomal matrix enzymes targeted to the organelle by the peroxisome targeting signal 2 (PTS2). The proteins play a role in the import of proteins into peroxisomes, where they form a heteromeric complex, and also in peroxisome biogenesis.\\n\\n]0.71659
558text-davinci-003narrative_synopsisprogeria-0[ The list of human genes provided have a significant overlap between the proteins they encode and their effects on the maintenance of genome stability, DNA repair, replication, transcription, prelamin A proteolytic cleavage, DNA integration to the host cell genome, nuclear reassembly, and chromatin structure and gene expression. These involve mainly functions related to the nuclear membrane, chromatin, DNA and biogenesis, interaction and metabolism, as well as cellular processes involved in genetic architecture and gene expression. Furthermore, commonalities were identified between the associated diseases and characteristics, such as Werner Syndrome and mandibuloacral Dysplasia, Emery-Dreifuss muscular dystrophy, familial partial lipodystrophy, limb girdle muscular dystrophy, dilated cardiomyopathy, and Hutchinson-Gilford progeria syndrome.\\n\\nMechanism: The function of these genes and the diseases they affect involve a wide variety of cellular processes related to storage and identification of genetic information, stability and rearrangements of the nuclear architecture, gene expression and turnover, and production of specialized proteins. These involve complex interactions between various components of the nucleus and between other parts of the cell.\\n\\n][COULD NOT PARSE]0.691257
559text-davinci-003narrative_synopsisprogeria-1[COULD NOT PARSE][COULD NOT PARSE]1.000
560text-davinci-003narrative_synopsisregulation of presynaptic membrane potential-0[ Our gene summary comes from a group of genes involved in a variety of neuronal functions including GABA, glutamate, and potassium receptor-related activities as well as ion channel function. This suggests that these genes are involved in a variety of roles related to neural communication and signaling. The common enriched terms from this gene set include \"neuronal signaling,\" \"neuron communication,\" \"ion channel,\" \"excitatory dependent channels,\" \"inhibitory neurotransmitter,\" \"ligand-gated ion channel,\" and \"G protein-coupled membrane receptor.\" Mechanism: The underlying biological mechanism relates to the role of the genes in providing the necessary components for neuronal signaling and information transfer. This includes roles in the formation of ligand-gated ion channels and G protein-coupled membrane receptors as well as the regulation of neurotransmitter release and excitability. ][\\nSummary: The list of genes is related to ion channel gated ion channels and various neurotransmitters.\\nMechanism: The genes encode proteins responsible for mediating electrical signaling and transmitters of signals like glutamate, GABA, and potassium.\\n]0.93647
561text-davinci-003narrative_synopsisregulation of presynaptic membrane potential-1[\\nThe genes in this list are involved in glutamate, GABA, and potassium channel related pathways found in the mammalian brain. Enriched terms include: neurotransmitter receptors (e.g. glutamate receptors, GABA receptors, potassium channels); ligand-gated ion channels; RNA editing; voltage-gated ion channels; channel subunits; channel polymorphisms; G-protein-coupled transmembrane receptors, etc.\\n\\nMechanism: Several of these genes encode for subunits of neurotransmitter receptor complexes, which suggest a mechanism for the modulation of synaptic transmission through the binding of agonists and antagonists that modulate the activity of the channels and facilitate the transport of ions across membranes. Additionally, some of the genes in this list play a role in the control of G-proteins and the regulation of heartbeat, suggesting that they may also be involved in regulating cell signalling pathways.\\n\\n][\\nSummary: These genes are associated with a variety of neurological functions, including glutamate and GABA receptor activity, potassium channel activity, and N-methyl-D-aspartate (NMDA) receptor activity. \\nMechanism: The genes encode proteins involved in a variety of neurological functions, including ligand-gated ion channels, receptor ligands, and glutamate-gated ionic channels. \\n]0.95526
562text-davinci-003narrative_synopsissensory ataxia-0[\\nSummary: These genes are associated with functions related to development and maintenance of the nervous system, sensory systems, and erythropoiesis, as well as mitochodnrial mRNA synthesis and transcriptional regulation. \\n\\nMechanism: These genes regulate post-translational processes including ubiquitination and processing, protein synthesis, transcription and activity of transcription factors, and organization of the cytoskeleton and nucleus.\\n\\n][\\n\\nSummary: List of genes are involved in transcription factors, degradation heparan sulfate, moonlighting proteins, immunoglobulin secretion, adapter or docking molecule, heme transporter, myelin upkeep, nuclear pore complex, mitochondrial DNA polymerase, ubiquitin ligase, and aminoacyl-tRNA synthetase.\\n\\n]0.87144
563text-davinci-003narrative_synopsissensory ataxia-1[ Genes in this list are involved in transcriptional, structural and signaling pathways that are related to maintaining the structure and function of peripheral nerve cells, including Schwann cells and myelin sheath maintenance.\\n\\nMechanism: Transcriptional, structural, and signaling pathways in peripheral neurons play a key role in maintaining nerve cell health and homeostasis.\\n\\n][ The analyzed gene summaries demonstrate enrichment of terms related to peripheral nerve and muscle function. Specifically, these include terms such as transcription factor, DNA helicase, nerve myelin maintenance, mechanically-activated cations channels, nerve motor neuron survival, and ubiquitination. \\n\\nMechanism: These genes appear to work together in a variety of ways to regulate transcription and the structural integrity of proteins in the peripheral nervous system, as well as regulate motor neuron and myelin maintenance, which contribute to nerve impulse transmission. \\n\\n]0.92201
564text-davinci-003narrative_synopsisterm-GO:0007212-0[ This gene set encodes many G-protein coupled receptors involved in signal transduction from extracellular signals to intracellular responses. Mechanism: G-protein coupled receptor signaling pathways initiate transmembrane signal transduction in response to hormones, neurotransmitters, and sensory signals by regulating adenylyl cyclase, phospholipase C-beta, and other downstream effectors. ][COULD NOT PARSE]0.69378
565text-davinci-003narrative_synopsisterm-GO:0007212-1[COULD NOT PARSE][COULD NOT PARSE]1.000
566text-davinci-003narrative_synopsistf-downreg-colorectal-0[ The list of human genes includes proteins that play a role in transcriptional regulation, chromatin remodeling, and DNA binding. The mechanism likely involves transcriptional coactivators and transcription factors forming heterodimers to bind to enhancers and promoters at specific response elements. ][ This list of genes is enriched in terms related to transcription regulation, cellular organization and tissue development. Specifically, genes are enriched for functions related to DNA-binding, chromatin-binding, transcriptional regulation, bind to E-box DNA consensus sequence, regulation of DNA damage response, DNA damage response maintenance, phosphoprotein shuttling, zinc finger motifs, interaction with cellular retinol-binding proteins, hormone-dependent transcription, receptor-dependent transcription, nuclear hormone receptor-dependent transcription, transcriptional coactivator complex recruitment, chromatin remodeling complex formation, and transcriptional activator complex formation. The mechanism likely involves the formation of heterodimers, protein complexes, and chromatin regulators.\\n\\n]0.93506
567text-davinci-003narrative_synopsistf-downreg-colorectal-1[\\nThe human genes analyzed in this term enrichment test were associated with functions such as transcriptional regulation, chromatin remodeling, DNA-binding, and zinc-finger binding. These genes were found to be enriched for terms related to transcription factor regulation of gene expression, chromatin modification, and DNA-binding activity.\\n\\nMechanism: These genes are a part of pathways responsible for the regulation of gene expression. The encoded proteins function as transcription factors, ligands, and chromatin remodelers which bind to DNA, interact with other transcription factors, and promote or inhibit the transcription of genomic regions. Zinc-finger binding, SUMO binding, and retinoid X receptor responsive element binding are also important regulators of gene expression and are involved in this term enrichment test.\\n\\n][\\nThis list of human genes is mainly related to transcriptional regulation, chromatin remodeling, and DNA-binding activities. Enriched terms include transcriptional regulation, DNA-binding, chromatin binding activity, histone binding activity, and transcription factor activity. These genes are associated with various cellular processes including cell cycle progression, apoptosis, gene transcription, transcriptional activator/repressor activity, protein chaperoning, cell differentiation, DNA damage response, and transcriptional enhancement. The underlying biological mechanism of these genes is related to the regulation of gene expression as well as its downstream gene expression, which is further regulated by transcription factor signaling pathways, chromatin remodeling, and post-translational modification activities.\\n\\nSummary: This list of human genes is mainly related to transcriptional regulation, chromatin remodeling, and DNA-binding.\\nMechanism: These genes are associated with various cellular processes and are regulated by transcription factor signaling pathways, chromatin remodeling, and post-translational modification activities.\\n]0.94316
568text-davinci-003no_synopsisEDS-0[ The nine genes are associated with extracellular matrix (ECM) components and their regulators. Mechanism: The proteins coded by these genes could be involved in the regulation of the expression of ECM components, which can contribute to the formation of the physical integrity of the ECM and its interaction with the cellular environment. ][\\n\\nSummary: The genes in the list are associated with a broad range of functions involved in skeletal development, collagen production and other extracellular matrix processes.\\n\\nMechanism: The mechanism appears to involve different genes acting on multiple pathways related to the synthesis, remodeling, and maintenance of extracellular matrix components.\\n\\n]0.9016
569text-davinci-003no_synopsisEDS-1[ This list of genes is enriched in proteins involved in the Extracellular Matrix (ECM) protein network, which is a component of the larger Cell Adhesion and Morphogenesis (CAM) pathway. Specifically, the genetic list is enriched for components involved in the processes of collagen fibril formation, collagen fibril organization, extracellular matrix (ECM) protein network assembly, ECM protein network stabilization, epidermal cell fate commitment, epithelial tube growth and branching morphogenesis, collagen modification and deposition, and zinc-finger protein motif binding.\\n\\nMechanism: The ECM protein network mediates cell-cell and cell-matrix interactions in order to regulate the adhesive, motile, and proliferative states of cells. It consists of a variety of molecules, including ECM proteins, which serve as substrates to guide cell migration, growth and differentiation. ECM proteins are those that contain one or more structural domains capable of interacting with the ECM components, such as extracellular domains, as well as those containing adhesive domains. \\n\\n][ The genes listed above are associated with various development processes and tissue formation, such as collagen production, connective tissue development, matrix remodeling, and zinc finger protein regulation.\\nMechanism: The underlying known mechanism is the combination of transcriptional regulation and post-translational modification of the proteins encoded by these genes.\\n]0.89699
570text-davinci-003no_synopsisFA-0[COULD NOT PARSE\\nHypothesis: The genes in this list are likely involved in the regulated repair of DNA double strand breaks due to replication-mediated damage, with the coordinated action of the Fanconi Anemia protein complex and the shared components of the ubiquitin ligase complex.][ The list of genes is significantly and specifically associated with homologous recombination and DNA repair, as evidenced by an enrichment in terms related to these processes, such as \"dna repair\", \"homologous recombination\", \"excision repair\", and \"nuclease activity\".\\n\\nMechanism: The genes in this list are involved in a variety of DNA repair activities, such as excision repair and homologous recombination. These processes are important for maintaining the correct sequence of DNA and avoiding mutations that can lead to disease. \\n\\n]0.85253
571text-davinci-003no_synopsisFA-1[ Several genes involved in DNA repair and homologous recombination processes, such as FANCL, RAD51C, FANCE, MAD2L2, ERCC4, FANCA, BRCA2, FANCF, XRCC2, BRIP1, FANCD2, SLX4, FANCB, FANCG, UBE2T, RAD51, PALB2, and FANCC, were observed to be statistically enriched for terms related to DNA damage recognition and repair, DNA damage response, and homologous recombination processes.\\n\\nMechanism: These genes enable the cellular response to double-stranded breaks (DSBs) by providing components of the DNA damage recognition and repair variety. They also function in the homologous recombination pathway for DNA repair, which is used for error-free repair of damaged DNA strands. \\n\\n][COULD NOT PARSE]0.69660
572text-davinci-003no_synopsisHALLMARK_ADIPOGENESIS-0[ Enrichment analysis of this list has revealed that many of the genes are involved in energy metabolism and fatty acid metabolism, such as ATP1B3, ACOX1, ACADM, SLC19A1, SLC25A10, PGM1, UCP2, GPX3 and GPX4. They are also related to adipogenesis, with genes such as ADIPOR2, APLP2, LEP, ADIG and ADIPOQ. Lastly, several of the genes are involved in cholesterol and bile acid synthesis, such as DHCR7, DHRS7, CYP4B1 and HMGCR.\\n\\nMechanism: The genes identified as being involved in energy metabolism and fatty acid metabolism appear to share a common mechanism in which these molecules are generated from multiple sources to form energy. The genes involved in adipogenesis appear to be related to the regulation and development of fat cells and adipose tissue. Similarly, the genes involved in cholesterol and bile acid synthesis appear to be related to the synthesis of these molecules from multiple sources.\\n\\n][ \\nSummary: A term enrichment test on the above list of genes based on biological classification hierarchies has identified terms related to metabolic and cellular functions that are statistically over-represented.\\nMechanism: These commonalities likely indicate a shared pathway, mechanism or process as related to metabolic and cell regulation functions.\\n]0.85553
573text-davinci-003no_synopsisHALLMARK_ADIPOGENESIS-1[ This term enrichment test revealed a group of genes associated with energy metabolism, regulation of cell death, cell proliferation and signaling, DNA replication/remodeling, RNA processing, and lipid metabolism.\\nMechanism: This group of genes may be involved in binding, regulating, or expressing other proteins in order to influence the cell's metabolic and signaling status. \\n][\\nSummary: This list of genes are mainly involved in energy metabolism and signal transduction. \\nMechanism: The genes in this list form a biochemical pathway responsible for the production of energy and for the detection and execution of cellular signals.\\n]0.90125
574text-davinci-003no_synopsisHALLMARK_ALLOGRAFT_REJECTION-0[ This enrichment test examines a list of 73 human genes and reveals enrichments for the functions related to cell surface molecules, cytokines, immunology, receptor signalling, transcriptional regulation and apoptosis.\\n\\nMechanism: These genes are involved in a variety of pathways that include cytokine signaling, cell surface molecules, transcriptional regulation, apoptosis, and receptor signaling.\\n\\n][ Genes related to the list are largely enriched for immune signalling/activation, regulation of cell cycle and differentiation, and transcriptional regulation.\\nMechanism: This likely indicates involvement of these genes in the processes of immune signalling, development or tissue remodelling, and metabolic regulation.\\n]0.8882
575text-davinci-003no_synopsisHALLMARK_ALLOGRAFT_REJECTION-1[ This analysis results in the enrichment of genes functions related to immune system regulation, including antigen presentation, signaling, B and T cell metabolism, cytokine production and chemotaxis. Mechanism: The genes identified in this list are involved in controlling a range of processes that are necessary for proper immune system functioning, such as antigen presentation, signaling pathways, metabolizing T and B cells, production and secretion of cytokines, and chemotaxis of immune cells. These functions are necessary for the body to defend itself against pathogens. ][COULD NOT PARSE\\nHypothesis: It is likely]0.72539
576text-davinci-003no_synopsisHALLMARK_ANDROGEN_RESPONSE-0[COULD NOT PARSE][COULD NOT PARSE]1.000
577text-davinci-003no_synopsisHALLMARK_ANDROGEN_RESPONSE-1[ \\nSummary: The genes are enriched in terms related to regulation, signaling, and metabolism.\\nMechanism: The genes are likely to be involved in molecular mechanisms governing cellular activities and pathways, with signaling pathways such as Wnt, MAPK, and PKA pathways playing an important role. \\n][ \\nThe genes provided are significantly enriched in terms related to gene transcription and regulation, protein translation and metabolism, cytoskeletal organization, and lipid metabolism.\\nMechanism: These genes are likely to be involved in the regulation of genetic expression, transcriptional regulation, protein translation and metabolism, improvement of cell structure, and lipid metabolism. \\n]0.93100
578text-davinci-003no_synopsisHALLMARK_ANGIOGENESIS-0[ \\n\\nSummary: A set of 34 genes related to extracellular matrix formation and maintenance, fibrous tissue development, vascular development, and extracellular secreted signaling. \\n\\nMechanism: Together, these genes encode proteins involved in multiple signaling pathways to regulate the development, maintenance and repair of the extracellular matrix (ECM), including fibrous, collagen, and laminin-fibrillin proteins, along with proteins involved in vascular regulation, cell-cell communication and migration, and extracellular secreted signaling molecules. \\n\\n][ The list of gene terms are involved primarily in cell communication processes like extracellular matrix organization, adhesion, and cell surface interactions. Specifically, they encode proteins involved in the aggregation of endothelial cells and vascularization processes. Mechanism: The proteins encoded by the genes in the list are likely involved in regulating the growth, development, extracellular environment, and adhesiveness of cells. ]0.89113
579text-davinci-003no_synopsisHALLMARK_ANGIOGENESIS-1[ Genes in this list are primarily associated with development, vascular remodeling and cell-cell communication.\\nMechanism: These genes likely play a role in various aspects of development, including morphogenesis, tissue development, extracellular matrix organization, inflammation, vascular remodeling and cell-cell communication.\\n][ \\n\\nSummary: This list of genes appears to be involved in growth and morphogenesis of cells, including development of muscle, bone, and neuronal networks. \\nMechanism: Growth appears to be mediated by signals from cytokines and hormones, most notably VEGFA and PDGF, and mediated by transmembrane and extracellular matrix proteins, including LUM, VTN, and S100A4.\\n]0.8930
580text-davinci-003no_synopsisHALLMARK_APICAL_JUNCTION-0[COULD NOT PARSE][\\nThis list of genes is related to development, tissue morphogenesis, contractile organs, extracellular matrix and cytoskeletal proteins. Enriched terms include bone, joint, muscle and connective tissue development; cell adhesion; adhesion receptor complex formation; signal transduction; and receptor-mediated signaling cascades.\\n\\nMechanism:\\nThese genes likely act together to facilitate the intricate networks of molecular and cellular pathways involved in development, homeostasis, and tissue repair. These include extracellular matrix formation and remodeling; cell adhesion; and signaling pathways associated with cell migration, proliferation, differentiation, and growth. The genes may work in tandem to promote changes in gene expression, stability, and intercellular communication involved in development and tissue repair processes.\\n\\n]0.69829
581text-davinci-003no_synopsisHALLMARK_APICAL_JUNCTION-1[\\nSummary: The genes in this list are involved in a wide variety of processes, including development, growth, morphology, and molecular signaling.\\nMechanism: These genes appear to be involved in the regulation of cellular processes by mediating signals that modulate development, growth and morphology.\\n][ Our term enrichment analysis of the list of genes provided revealed statistically over-represented terms in gene function associated with cell adhesion, cell migration, migration and interaction, cytoskeletal organization, actin cytoskeletal regulation, signaling pathways, and regulation of the actin cytoskeletal organization. \\nMechanism: These results suggest that the underlying biological mechanism likely involves cytoplasmic signaling and regulation of the cytoskeletal organization, which would provide mechanical integrity to the cells, their adhesion to neighboring cells, and their migratory ability. This is supported by the evidence that many of the enriched terms relate to cell adhesion, migration and interaction, and cytoskeletal organization.\\n]0.84460
582text-davinci-003no_synopsisHALLMARK_APICAL_SURFACE-0[\\nSummary: The list of genes provided is enriched for terms relating to cell migration, membrane receptor signaling, and glycoprotein metabolism.\\nMechanism: These gene functions serve to coordinate cell migration and receptor-mediated signaling, as well as metabolism. \\n][ The list of genes is enriched for terms related to cell regulation, signal transduction, cell adhesion, protein folding, extracellular matrix organization.\\nMechanism: The list of genes are likely involved in a variety of cell regulation mechanisms such as activating responses to extracellular signals, influencing protein folding and assembly, regulating cell adhesion, and mediating phosphorylation cascades. \\n]0.91144
583text-davinci-003no_synopsisHALLMARK_APICAL_SURFACE-1[\\nSummary: The genes provided are involved in diverse biological pathways related to cell signaling, development, transcription, and metabolism.\\nMechanism: The genes likely represent an underlying biological mechanism that is involved in cellular proliferation and the regulation of gene expression.\\n][ This list of genes appears to be involved in the development and maintenance of various organs, tissues and cellular processes. Specifically, enriched terms for this gene list include cell adhesion and migration; cell signaling; cell differentiation; protein kinase and phosphatase activities; transcription and DNA metabolism; immunomodulation; glycosylation and carbohydrate metabolism; and cell growth and proliferation. \\n\\nMechanism: The genes in this list play a role in a variety of molecular mechanisms that are important for normal development and tissue homeostasis. On the molecular level, these genes are involved in cell-cell adhesion, translation and translation regulation, signal transduction, and other processes. Moreover, the genes in this list regulate the expression of various cellular receptor, kinase, and phosphatase pathways, which may lead to downstream changes in cell growth, proliferation, and differentiation. \\n\\n]0.91643
584text-davinci-003no_synopsisHALLMARK_APOPTOSIS-0[ The list of human genes given is statistically significantly enriched for the gene functions of transcriptional regulation/control, cell-cycle/apoptosis, and immune responses.\\nMechanism: The genes listed encode proteins involved in transcriptional regulation through control pathways such as the activation of caspases, the inhibition of cyclin-dependent kinase activity, and the upregulation of apoptosis-related proteins. They also encode molecules involved in immune-related processes such as the binding and activation of proinflammatory cytokines, the formation of interferon gamma receptor complexes, and the regulation of major histocompatibility complex class I molecules. \\n][\\n\\nSummary: The human genes provided in this list are mainly related to apoptosis, transcription, cell cycle progression, and inflammation.\\nMechanism: These genes likely act together to execute pathways related to the regulation of cell growth and maintenance, DNA replication and repair, oxidative stress response, and immune system activation.\\n]0.94338
585text-davinci-003no_synopsisHALLMARK_APOPTOSIS-1[COULD NOT PARSE][ This list of genes is enriched for terms related to cell death regulation, inflammation, immune reaction, and growth and morphogenesis, which is a mechanism indicative of homeostasis in several biological functions.\\t\\n\\nMechanism: Expression of these genes contributes to cell survival by regulating the balance between cell death and survival, restraint of pro-inflammatory responses and activation of pro-inflammatory responses, promoting expression of genes involved in innate and adaptive immune responses and playing a part in promoting tissue growth, remodeling and morphogenesis. \\n\\n]0.68573
586text-davinci-003no_synopsisHALLMARK_BILE_ACID_METABOLISM-0[\\nSummary: The genes listed are enriched in terms related to metabolic pathways, lipid transport, and development of connective tissues.\\nMechanism: The functions of the genes appear to involve a number of metabolic pathways, such as fatty acid and bile acid synthesis, xenobiotic metabolism, and steroidogenesis, as well as pathways related to cellular transport and signaling, including those related to lipid transport and receptor-mediated signal transduction.\\nIn addition, several of the genes are involved in connective tissue formation, as well as development of digits and limbs.\\n][ This list of genes is enriched for functions related to lipid metabolism and transport, development of vital organs, and cell signaling pathways.\\nMechanism: The enrichment of these genes suggests roles in cellular metabolic processes such as breakdown, transport, and synthesis of lipids, as well as cell-signaling pathways involved in development of vital organs such as liver, heart, and brain. \\n]0.95187
587text-davinci-003no_synopsisHALLMARK_BILE_ACID_METABOLISM-1[COULD NOT PARSE][ A large proportion of the genes provided are involved in lipid and fatty acid metabolism, including the movement and processing of lipids, such as through cytochrome P450 superfamily enzymes, hydroxyacyl-CoA dehydrogenases, SLCO1A2, FADS2 and SLC27A2. As well as lipid metabolism, genes are also enriched for other metabolic processes, such as glutamate metabolism (IDH1, 2, HSD17B6) and serine metabolism (SERPINA6 and PIPOX). In addition, there are genes associated with the regulation of transcription factors, including RXRA, LCK, and optineurin, as well as those involved in oxidative stress (SOD1, CTH, PNPLA8).\\n\\nMechanism: The enriched terms implicate a cross-regulatory and potentially inter-linked metabolic network involving lipid, fatty acid and disulphide bridge metabolism, with potential connections to oxidative stress response and gene expression regulatory mechanisms. \\n\\n]0.69874
588text-davinci-003no_synopsisHALLMARK_CHOLESTEROL_HOMEOSTASIS-0[COULD NOT PARSE][\\nSummary: A number of genes involved in lipid and cholesterol metabolism, cell signaling and regulation, development, cell adhesion, apoptosis and transcription have been identified.\\nMechanism: Genes associated with lipid and cholesterol metabolism are involved in regulating the synthesis, degradation and transport of lipids, while genes associated with cell signaling and regulation are involved in regulating cell growth, differentiation and apoptosis. Additionally, genes related to development, apoptosis, and transcription act in the regulation of cell adhesion, differentiation and development.\\n]0.67588
589text-davinci-003no_synopsisHALLMARK_CHOLESTEROL_HOMEOSTASIS-1[\\nSummary: The genes populated are predominantly involved in lipid metabolism (eg. HMGCR, PMVK, FDPS), transcription regulation (eg. ACTG1, NRAF), cellular adhesion (eg. CD9, ANXA13, COUNTY), and other development related processes (eg. S100A11, MVD, IDI1).\\nMechanism: The genes are associated with a number of different functions but are likely involved in maintaining cellular homeostasis, regulating transcription, and participating in development processes.\\n][ Proteins involved in lipid and lipid metabolism pathways, related to cholesterol control.\\nMechanism: Proteins involved in cholesterol regulation, such as HMGCR, PMVK, FADS2, SREBF2, S100A11, and MVK are likely to be involved in the upregulation and modulation of cholesterol levels. These proteins regulate the breakdown of fatty acids and also mediate the synthesis of bile acids, both of which are important in cholesterol metabolism. ]0.8923
590text-davinci-003no_synopsisHALLMARK_COAGULATION-0[\\nSummary: Several of the human genes on this list play a role in extracellular matrix formation, inflammatory response, and proteolytic activities.\\nMechanism: The common functional mechanisms included in this term enrichment test are the regulation of the inflammatory response, regulation of extracellular matrix formation, and proteolytic activities.\\n][ Genes in this list represent functions related to extracellular matrix remodeling, angiogenesis and vascular development, immune response and platelet activation, collagen and fibronectin metabolism and regulation, and endocytosis and signal transduction.\\n]0.8996
591text-davinci-003no_synopsisHALLMARK_COAGULATION-1[\\nSummary: The genes identified are predominantly involved in matrix molecular regulation, pathways related to proteolysis and coagulation, signal transduction, and extracellular matrix organization.\\nMechanism: The genes act as regulators of specific molecular functions and as mediators of signal transduction pathways. The identified genes are likely involved in the processing and remodeling of the extracellular matrix because of their relation to proteolysis and other matrix-related functions.\\n][ The term enrichment test suggests that proteins involved in cell adhesion, proteolysis regulation, and interactions between extracellular proteins and cells are significantly enriched in this gene list. \\n\\nMechanism: These proteins likely act together in a coordinated manner to modulate cell adhesion, proteinase activity, and communication between cells. \\n\\n]0.86141
592text-davinci-003no_synopsisHALLMARK_COMPLEMENT-0[\\nSummary: These genes are enriched in functions related to extracellular matrix organization, immune system/inflammation/interferon response, and transcription factor activity.\\nMechanism: These genes could be involved in a pathway that is responsible for coordinating and controlling aspects of extracellular matrix organization, immune system/inflammation/interferon response and the activity of transcription factors.\\n][ Our term enrichment test suggests that the commonalities in function of these genes are related to the regulation of cell growth and development, signal transduction pathways, and immunity. Specifically enriched terms include development of tissue and organs; signal transduction; cell surface receptor binding; response to stimulus; immune system; immune response; and cytokine activities.\\n\\nMechanism: These functions likely occur through a combined mechanism of modulating transcription factors, receptor-ligand binding, cytokine release and signaling, and a balance of intracellular concentrations of proteins and lipids.\\n\\n]0.89207
593text-davinci-003no_synopsisHALLMARK_COMPLEMENT-1[ This enrichment test revealed several terms related to immune system functioning, cell adhesion and regulation, and extracellular matrix organization, which are likely the underlying mechanisms behind the commonalities among the listed genes. Enriched terms include: immunoglobulin like domains; B cell activation; T cell receptor signaling pathway; integrin mediated cell adhesion; apoptosis; regulation of transcription; signal transduction; receptor mediated endocytosis and exocytosis; extracellular matrix organization; and calcium mediated signaling. \\n\\nMechanism: These findings suggest that the genes involved in this test collectively contribute to a range of processes related to immune system functioning, cell adhesion, extracellular matrix organization, and intracellular communication. \\n\\n][\\nThe list of genes provided is heavily enriched for functions related to cellular signalling, inflammatory responses, and cellular stress response.\\nMechanism: These genes are typically involved in regulating and mediating signalling pathways, activating and responding to the inflammatory response, activating and functioning in the cell stress response, and facilitating cell-cell interactions.\\n]0.87406
594text-davinci-003no_synopsisHALLMARK_DNA_REPAIR-0[ Gene functions related to DNA and RNA metabolism, protein synthesis, DNA damage repair, transcription, and chromatin organization are significantly over-represented.\\nMechanism: It is likely that many of these genes are involved in the same pathway related to the fundamental processes of DNA replication, transcription, and protein synthesis.\\n][ The common functions for the human genes are involved in various developmental processes and DNA replication, with enrichment of terms such as \"developmental process\" and \"DNA replication\". \\n\\nMechanism: The genes act together to facilitate a variety of molecular processes in the cellular pathways to support embryonic and post-natal development, as well as DNA replication, transcription, and translation.\\n\\n]0.8765
595text-davinci-003no_synopsisHALLMARK_DNA_REPAIR-1[ \\nSummary: These genes are enriched for roles in DNA replication, transcription, translation and post-translational modifications.\\nMechanism: These genes are involved in various biological processes, including DNA replication, transcriptional regulation, translation, and post-translational modifications involved in gene expression. \\n][\\nSummary: Our genes are primarily involved in nucleic acid metabolism, transcription, and post-transcriptional modifications.\\nMechanism: The proteins encoded by the genes in our list likely play roles in the various biochemical steps involved in transcription, such as chromatin remodelling, pre-mRNA splicing, DNA repair, RNA polymerization, mRNA processing, mRNA transport, and translation initiation.\\n]0.9269
596text-davinci-003no_synopsisHALLMARK_E2F_TARGETS-0[ Genes on the list are primarily involved in DNA cell cycle and replication, gene regulation, transcription and translation, chromatin modification, and DNA repair. \\n\\nMechanism: The genes are involved in the regulation of DNA replication and transcription, chromatin modification, and DNA repair processes during cell cycle progression. \\n\\n][ The provided gene list is over-represented for transcriptional regulation, chromatin modification and mitotic division/cell cycle components.\\nMechanism: The underlying mechanism of this gene set is that the enrichments are involved in the regulation of transcription for gene expression, maintenance of chromatin and DNA structure and function, and regulation of mitotic division and cell cycle checkpoints.\\n]0.8970
597text-davinci-003no_synopsisHALLMARK_E2F_TARGETS-1[\\nSummary: The genes in the list are involved in diverse functions related to DNA replication, transcription, chromosome condensation and transcriptional regulation.\\nMechanism: These functions are likely related to canonical pathways and processes involved in coordinating and regulating DNA replication, the transcription of genetic information into proteins, and maintaining appropriate chromosome condensation states.\\n][ This list of genes is enriched for functions related to DNA replication and repair, chromatin modification, transcriptional and translational regulation, network formation, spindle formation and kinesin and dynein motor proteins. Mechanism: These genes are likely to function as part of an interconnected cellular pathway and/or network that allows for the generation of daughter cells and the coordination of transcriptional activity and post-translational modifications. ]0.9354
598text-davinci-003no_synopsisHALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0[COULD NOT PARSE][ The list of genes provided show enrichment for terms relevant to extracellular matrix composition, cell adhesion and motility, cell-matrix interactions, growth factor and cytokine signaling, and matrix remodeling. \\n\\nMechanism: The mechanisms underlying the enrichment of these terms likely involve cell-matrix interactions, growth factor and cytokine signaling, and matrix remodeling.\\n\\n]0.67372
599text-davinci-003no_synopsisHALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1[ Our enrichment test uncovered several terms related to extracellular matrix function, morphogenesis, and reproduction/growth. These terms include extracellular matrix organization; morphogenesis; collagen production; matrix metalloproteinase activity; glycoprotein metabolism; cytoskeletal component organization; regulation of growth and reproduction; and regulation of skin morphogenesis. Mechanism: The underlying biological mechanisms related to these genes likely involve the extracellular matrix (ECM), which provides structural and biochemical support to the cells and tissues. ECM components, such as collagen, can regulate activities such as cell signaling, structure formation and growth, and gene expression. Morphogenesis is likely modulated by ECM components, as well as by signaling pathways. ][ The identified genes are enriched for terms related to skeletal morphogenesis, cell-cell adhesion and motility, extracellular matrix production and remodeling, development and differentiation of connective tissue, collagen production and turnover, and cytokine and chemokine signaling. \\n\\nMechanism: It is likely that these genes are involved in mechanisms that coordinate protein interactions during skeletal development and morphogenesis, cell adhesion and migration, and the maintenance of a healthy extracellular matrix. In addition, these genes likely contribute to the production and turnover of extracellular matrix components such as collagens and chemokines and cytokines involved in development and differentiation of connective tissue. \\n\\n]0.9160
600text-davinci-003no_synopsisHALLMARK_ESTROGEN_RESPONSE_EARLY-0[\\nSummary: The list of genes identified are associated with cell morphology, homeostasis and regulation, innervation, and cellular metabolism.\\n][\\nThis list of human genes was analysed in a term enrichment test. The test revealed that many of these genes were involved in a common pathway which supports normal cellular processes including DNA replication, transcription and gene expression, cell growth and differentiation, protein processing and trafficking. Furthermore, many of these genes were involved in bone morphogenesis and cancer-related pathways.\\n\\nMechanism:\\nThe underlying biological mechanism likely involves a number of distinct pathways, each with its own mechanism of action. Common processes shared by many of these genes include DNA replication, translation, and post-translational modification. Additionally, several of these genes are involved in cell-cell adhesion and the control of cellular migration and matrix remodeling, indicating roles in tissue morphogenesis. Furthermore, many of these genes are involved in intracellular signaling and signaling pathways that are essential for the processing and coordination of external and internal signals, which can ultimately result in cell growth, differentiation, and apoptosis.\\n\\n]0.87964
601text-davinci-003no_synopsisHALLMARK_ESTROGEN_RESPONSE_EARLY-1[ Our analysis of the 34 human genes suggests an enrichment of gene functions related to cell signaling, regulation and morphology, including: immunological response; cell adhesion; transcription regulation; cell migration; development of epidermis, bones and muscle; transport of proteins between cellular compartments; and apoptosis. \\n\\nMechanism: These gene functions are likely related to the regulation of diverse mechanisms within the cell, such as protein-protein interactions, transcription signaling, and intracellular trafficking. \\n\\n][ \\nSummary: The gene list includes genes involved in transcriptional regulation, signal transduction, membrane transport and lipid biosynthesis.\\nMechanism: The genes exhibit common patterns of transcriptional regulation and signal transduction, with a focus on protein-protein interactions and membrane transport.\\n]0.88228
602text-davinci-003no_synopsisHALLMARK_ESTROGEN_RESPONSE_LATE-0[\\nThe genes in the list are enriched for functions in the genomics and cytoskeletal processes, as well as immune response and extracellular modification.\\n\\nMechanism:\\nThe gene functions are implicated in various biological processes that are orchestrated by genetic control and/or regulation pathways. These pathways typically involve protein interactions and cellular processes. Additionally, these pathways often correlate to extracellular modification, immune response, and/or modulation of receptor signaling.\\n\\n][ Genes related to extracellular matrix organization, cellular adhesion and migration, cell mobility and growth factor-mediated signaling pathways;\\nMechanism: This gene list suggests that extracellular matrix organization, adhesion and migration, cell motility, and growth factor signaling pathways are involved in gene expression in these genes. \\n]0.88166
603text-davinci-003no_synopsisHALLMARK_ESTROGEN_RESPONSE_LATE-1[COULD NOT PARSE][ The genes are enriched for terms related to the structural organization of cells, transcriptional regulation, signal transduction, and immune responses.\\n\\nMechanism: These genes likely comprise a network that influences the physical and biochemical properties of the cell, including its membrane integrity, signal transduction pathways, gene expression, and immunomodulatory functions. \\n\\n]0.67373
604text-davinci-003no_synopsisHALLMARK_FATTY_ACID_METABOLISM-0[ This list of genes is highly enriched for metabolic processes such as fatty acid metabolism and oxidation, cholesterol biosynthesis, glycogen metabolism, nucleotide metabolism and transport, and electron transport activity. This suggests that the list reflects a highly coordinated and interconnected network of metabolic processes to maintain the homeostasis of the cell. Enriched terms include: fatty acid metabolism; oxidation of lipids; cholesterol biosynthesis; glycogen metabolism; nucleotide metabolism; nucleotide transport; nucleotide biosynthesis; electron transport activity; enzyme regulation and regulation of metabolic pathways; and apoptosis. \\nMechanism: This set of genes likely acts through a number of interconnected pathways to maintain cellular homeostasis. Lipid metabolism is known to be important in cellular signaling, while other metabolic pathways interact with each other through enzyme regulation and regulation of metabolic pathways. Additionally, many of the genes are associated with cell death pathways, suggesting that these can also act in a coordinated way to respond to stress and maintain cellular homeostasis. \\n][\\nSummary: The genes shown here are involved in a wide range of metabolic pathways and cellular functions, such as energy metabolism, lipid metabolism, amino acid metabolism, DNA damage repair, and cell signaling.\\n]0.91937
605text-davinci-003no_synopsisHALLMARK_FATTY_ACID_METABOLISM-1[\\n\\nSummary: There is a strong enrichment of genes involved in metabolic processes, energy production and storage, lipid metabolism and transport, as well as acetyl-CoA biosynthesis and catalysis.\\n\\nMechanism: The identified genes likely influence the metabolic processes, energy production and storage, lipid metabolism and transport, as well as acetyl-CoA biosynthesis and catalysis by modulating cellular processes, protein and enzyme production, and functional metabolic pathways, such as oxidation and fatty acid metabolism.\\n\\n][ Genes are enriched in roles associated with lipid metabolism and the cell cytoskeleton. Both pathways involve important signaling and metabolic roles. Mechanism: Lipid metabolism pathways involve synthesizing and degrading lipids, transporting lipids, and their oxidation. The cell cytoskeleton is involved in a variety of functions, including building of cell membranes, cell motility and traffic. ]0.90128
606text-davinci-003no_synopsisHALLMARK_G2M_CHECKPOINT-0[\\nGene functions involved in cell cycle regulation, DNA replication, and chromatin remodeling are enriched among the provided list of genes. This could reflect a core pathway of regulation that has been conserved across multiple species.\\n\\nMechanism:\\nThe enriched terms suggest that this gene list could be involved in the G1/S transition of the cell cycle, DNA replication, and chromatin remodeling or modification. Specifically, cell cycle progression and DNA replication is likely driven by cyclin B-CDK1 activation, which is facilitated by Cks1b and Cdc25A mediated activation and either Wee1 or Cdc20-anaphase promoting complex-cyclosome (APC/C)-mediated inhibition. Chromatin modification is likely driven by histone H2A and H2B acetylation and lysine methylation, which involve various proteins, such as Hmga1, Hmgn2, H2az1, H2bc12, and Myc.\\n\\n][ \\nSummary: This list of human genes are enriched for functions related to cell cycle and/or development, such as DNA replication and transcription, and may be involved in a variety of pathways and processes.\\nMechanism: These genes may be involved in pathways related to DNA replication, transcription and expression, and cell cycle regulation.\\n]0.92504
607text-davinci-003no_synopsisHALLMARK_G2M_CHECKPOINT-1[ \\nSummary: This list of human genes are primarily involved in nuclear processes such as DNA replication, gene transcription, chromatin remodelling and cell cycle control.\\nMechanism: The genes may be involved in the regulation of a number of biological processes such as DNA repair, cell cycle regulation, gene expression, and gene regulation.\\n][COULD NOT PARSE]0.68328
608text-davinci-003no_synopsisHALLMARK_GLYCOLYSIS-0[\\nSummary: Our term enrichment test shows that many of the genes on this list are involved in various aspects of developmental and morphogenic processes, including digit development, cell differentiation, angiogenesis, and metabolism.\\nMechanism: These genes are likely to be involved in biological pathways involving the development and maintenance of cellular structure, binding and transporting of molecules, energy metabolism and other metabolic processes, and cell signaling.\\n][COULD NOT PARSE]0.71464
609text-davinci-003no_synopsisHALLMARK_GLYCOLYSIS-1[ The list of genes are primarily involved in essential metabolic functions in the cell. Specifically, they are involved in carbohydrate and energy metabolism, microtubule assembly, DNA binding and replication, actin cytoskeleton dynamics, ion channel regulation, transcriptional regulation, and cell adhesion. The mechanism is likely related to the coordination of these processes in order to maintain homeostasis and proper cell functioning.\\n\\nSummary: Genes mainly involved in metabolic processes. \\n\\nMechanism: Coordination of these processes to maintain cellular homeostasis.\\n\\n][ \\nThis gene list is enriched for proteins involved in structural development and energy metabolism, such as structural proteins and enzymes of glycolysis, the pentose phosphate pathway, and the tricarboxylic acid (TCA) cycle. These terms are supported by evidence from gene ontologies (GO) assigned to the genes in the list.\\n\\nMechanism: \\nThe list of genes is involved in pathways which facilitate the efficient production and utilization of energy, such as glycolysis, the pentose phosphate pathway, and the tricarboxylic acid (TCA) cycle. They are also involved in the dynamic assembly of integral structures, such as the cytoskeleton, cell adhesion serve, proteoglycan synthesis, and extracellular matrix formation.\\n\\n]0.89140
610text-davinci-003no_synopsisHALLMARK_HEDGEHOG_SIGNALING-0[\\nSummary: Many of the genes listed are involved in the development and morphogenesis of neurons and other cells. \\nMechanism: These genes are likely to work together to regulate cell and tissue shaping and differentiation, providing for the formation of specialized neuron structures and neural pathways. \\n][COULD NOT PARSE]0.68290
611text-davinci-003no_synopsisHALLMARK_HEDGEHOG_SIGNALING-1[\\n\\nSummary: This group of genes is commonly associated with morphogenesis, cell adhesion, development, and neuronal signaling\\nMechanism: The underlying biological mechanism is likely related to the regulation of cell proliferation, migration, differentiation, and neural plasticity during development. \\n][ The genes appear to be involved in the development of various cell types, organs, and other growth processes, including neuron formation, cell adhesion and migration, signal transduction, tissue morphogenesis, and development of the nervous system. \\nMechanism: These genes likely act in a number of ways to promote and coordinate these processes, including recognizing and binding signaling molecules, relaying signals to other molecules, and affecting transcription of target genes. \\n]0.92184
612text-davinci-003no_synopsisHALLMARK_HEME_METABOLISM-0[\\nSummary: The genes in this list are highly enriched for functions related to membrane transport, energy metabolism, ribosomal proteins, and nucleic acid binding.\\nMechanism: The underlying biological mechanism or pathway may involve regulation and control of cellular functions and transcription activity, with multiple proteins interacting to ensure proper functioning of a variety of cellular pathways.\\n][ The list of genes has a statistically significant enrichment of terms related to cellular metabolism, energy production and transport, cytoskeleton modification and remodelling, and cell adhesion. \\nMechanism: The molecular mechanisms involve the transfer of energy, metabolic pathways, and the coordination of cellular transport and reorganization.\\n\\n]0.9154
613text-davinci-003no_synopsisHALLMARK_HEME_METABOLISM-1[\\n\\nSummary: The human genes identified in this list are predominantly involved in cell development, gene expression, organogenesis and nucleic acid metabolism.\\n\\nMechanism: The human genes identified in this list are likely to be involved in processes that regulate cell development, including transcriptional regulation and organogenesis, as well as nucleic acid metabolism. \\n\\n][ The enriched terms for this list of human genes suggest a common functional theme in organ development, morphogenesis and growth, immune system function, and transport processes. Enriched terms include: embryonic development; skeletal system development; organogenesis; morphogenesis; growth; immune system process; cell motility; steroid hormone receptor activity; receptor signaling pathway; transport; endocytosis; and cellular homeostasis.\\n\\nMechanism: The underlying biological mechanism suggested by the enriched gene functions is that these genes are involved in various organ and skeletal system development processes, in particular morphogenesis and growth, as well as immune system and transport processes. Specifically, these genes are involved in organogenesis, morphogenesis, growth, and cell motility through receptor signaling pathways, endocytosis, transport processes, and cellular homeostasis. Additionally, the genes are involved in steroid hormone receptor activity, further contributing to organ and skeletal system development.\\n\\n]0.88675
614text-davinci-003no_synopsisHALLMARK_HYPOXIA-0[COULD NOT PARSE][ The list of genes is involved in a variety of pathways and functions related to cell differentiation, metabolism, protein processing, and the regulation of gene expression. Specifically, this list was enriched for terms related to cell cycle, remodeling proteins, stress response proteins, calcium signaling proteins, hypoxia-inducible factor proteins, transcription factors, chromatin-associated proteins, and kinases.\\n\\nMechanism: The overall mechanism of action of the genes appears to be related to the regulation of cellular processes via the modulation of expression of target genes, primarily through the regulation of epigenetic and transcriptional factors, in order to enable proper differentiation, metabolism, and protein processing. This is further supported by the enrichment of terms related to stress response proteins, calcium signaling proteins, hypoxia-inducible factor proteins, transcription factors, chromatin-associated proteins, and kinases.\\n\\n]0.68951
615text-davinci-003no_synopsisHALLMARK_HYPOXIA-1[ \\nSummary: Genes related to cell development, cell metabolism, transcription, and regulation are enriched in this set.\\nMechanism: These genes regulate a variety of cellular processes such as cell cycle regulation, transcriptional regulation, and energy metabolism.\\n][ Genes identified in this set are associated with several DNA/RNA binding and regulatory processes, including transcription and epigenetic modification. Statistically over-represented functions in these genes include development, cell structure and movement, cell cycle and division, signal transduction, transport, and energy production; proteins involved in these processes include transcription factors, kinases, histones, and other enzymes. Mechanism: This enrichment likely reflects the underlying biological pathways governing various aspects of gene expression and regulation. ]0.92319
616text-davinci-003no_synopsisHALLMARK_IL2_STAT5_SIGNALING-0[ The gene set is enriched for genes involved in cell growth, cell detection/regulation, and immunity. Mechanism: These genes are likely involved in a number of pathways that contribute to cell and tissue development, growth, and regulation, as well as regulation of the immune system. ][\\nSummary: These genes are predominantly related to immunological functions, actin cytoskeleton organization, cell surface receptors, and pro-inflammatory regulation.\\nMechanism: The genes listed appear to be involved in the immune response, actin cytoskeleton organization, cell surface receptor-mediated signaling, and pro-inflammatory regulation.\\n]0.8863
617text-davinci-003no_synopsisHALLMARK_IL2_STAT5_SIGNALING-1[COULD NOT PARSE][ The list of human genes provided are enriched for terms related to immunity, inflammatory response, cell growth, differentiation and development, and signaling pathways.\\n\\nMechanism: This underlying biological mechanism could involve proteins interacting with each other and coordinating pathways to govern immune response, inflammatory response, cell growth, differentiation, and development, as well as other cellular processes.\\n\\n]0.69417
618text-davinci-003no_synopsisHALLMARK_IL6_JAK_STAT3_SIGNALING-0[ Genes in the list are enriched for the Cellular Processes of Pain Sensing and Signal Transduction; Chemotaxis; Cytokine-mediated Signaling Pathway; Leukocyte Transendothelial Migration; Immune Response; and Platelet Activation. There is a potential mechanism for the underlying biological pathway whereby these genes interact in signal transduction to facilitate pain sensing and immune response, including ligand-receptor interactions, signal transduction of cytokines, and the actions of transcription factors, such as those encoded by JUN, REG1A, STAT1, STAT2, STAT3 and TLR2.\\n\\n][ This list of genes is enriched in terms related to cell signaling, cytokine production and regulation, regulation of gene expression and transcription, and cell adhesion.\\nMechanism: This list of genes promotes the core pathways of cell signaling, cytokine production and regulation, regulation of gene expression and transcription, and cell adhesion. This enables the body to respond to a variety of external signals, to recognize and respond to inflammation and stress, to produce the necessary molecules for the body to function correctly, and to hold the cell together so that it may adhere to corresponding cells and fulfill its role within the network of cells.\\n]0.9086
619text-davinci-003no_synopsisHALLMARK_IL6_JAK_STAT3_SIGNALING-1[\\nSummary: The list of genes are significantly enriched for functions of immunity, signaling, and transcription regulation\\nMechanism: These genes are likely involved in the coordination of immune responses and the regulation of pathways for signal transduction and transcription.\\n][ Increased expression of cytokines, chemokines, and interleukins; increased expression of developmental, signal transduction, and immune system pathways involved in cellular differentiation, cell motility and adhesion, signal transduction, and inflammation. \\nMechanism: The genes listed all appear to be involved in immune system, signal transduction and intercellular communication pathways. Through the identification of commonalities between the gene functions, inference can be made that these genes are involved in up-regulation of cytokines, chemokines, and interleukins involved in cellular differentiation, cell motility, adhesion, signal transduction and inflammation. \\n]0.89400
620text-davinci-003no_synopsisHALLMARK_INFLAMMATORY_RESPONSE-0[ Genes associated with human immunity, inflammation and signalling pathways are enriched.\\n\\nMechanism: These genes are likely involved in pathways related to human immunity, inflammation and signalling, either directly or through regulation of transcription and translation activity.\\n\\n][COULD NOT PARSE]0.67269
621text-davinci-003no_synopsisHALLMARK_INFLAMMATORY_RESPONSE-1[ The list of genes is significantly enriched for terms related to immune cell signaling, cell movement, and cell surface receptor activity. \\nMechanism: These genes are likely involved in the regulation of pathways involved in initiating and responding to inflammation, cell migration, cell–cell interactions, and immune cell receptor-mediated signaling.\\n][ The list of genes is enriched in functions related to the immune system, especially mediation of inflammatory response and cytokine production and signalling.\\nMechanism: The genes are involved in a variety of functions related to immune cell activation and cellular signaling, including cell adhesion, G-protein and receptor-coupled pathways, transcriptional regulation, cytokine and cytokine receptor binding, and lipid metabolism. \\n]0.9381
622text-davinci-003no_synopsisHALLMARK_INTERFERON_ALPHA_RESPONSE-0[ Our analysis of the list of human genes have revealed a set of enriched terms related to the activation and inhibition of immune signaling pathways, and their functions in regulating inflammation. Specifically, we observed an increased prevalence of molecules and proteins involved in mechanism activating or inhibiting the Nuclear Factor Kappa B (NF-κB), Interferon Regulatory Factor (IRF) as well as JAK-STAT pathways. Terms such as \"inflammatory response\", \"neutrophilic activation and degranulation\", \"T-Cell receptor signaling pathway\", \"Toll-Like Receptor Cascade\", \"Type I Interferon Signaling\", and \"Inflammatory Regulation\" were enriched in this gene set.\\n\\nMechanism: The genes in this list are involved in multiple pathways that are related to the modulation of inflammatory responses and can be broadly summarized as either regulating cytokine production or modulating the inflammatory response by inhibiting the NF-κB, IRF and JAK-STAT pathways. While there is significant overlap of these genes with the NF-κB pathway, the IRF and JAK-STAT pathways are also significant contributors, as evidenced by the enriched terms. \\n\\n][COULD NOT PARSE]0.701122
623text-davinci-003no_synopsisHALLMARK_INTERFERON_ALPHA_RESPONSE-1[ This group of genes is significantly enriched for functions related to immune system regulation, interferon response, apoptosis, and cell membrane regulation.\\n\\nMechanism: This list of genes is likely involved in both innate and adaptive immune responses, functioning to modulate the level of inflammation and cytokine production, as well as to induce cell death and regulate cell membrane composition. Specific terms enriched that pertain to these functions include interferon signalling pathways, interferon gamma activity, interferon regulatory factor activity, status response to interferon, apoptosis, lipid binding, calcium ion binding, and neutrophil mediated immunity. \\n\\n][ Genes listed appear to be primarily involved in the regulation of interferon response pathways and the transcriptional control of interferon-stimulated genes. The genes appear enriched for the cellular pathways of immune response, inflammation, and cytokine signaling.\\n \\nMechanisms: The interferon response pathways activated in this population of genes modulate the expression of cytokines, chemokines, and antimicrobial and antiviral proteins, in order to activate an innate immune response to virus and bacteria. \\n\\n]0.93160
624text-davinci-003no_synopsisHALLMARK_INTERFERON_GAMMA_RESPONSE-0[\\nSummary: A majority of the genes were found to be involved in important immune response and cell signaling pathways.\\nMechanism: The immune response and cell signaling pathways are likely to be regulated by cytokines and transcription factors such as those related to interferon responses and nuclear factor kappaB-dependent transcriptional regulation.\\n][ In this gene set, there are multiple genes that are enriched for functions related to immunology, such as antigen presentation, inflammatory responses, chemokine signaling, cell adhesion, and cytokine interactions. \\nMechanism: One hypothesis is that these genes are involved in an immune-mediated response related to their roles in antigen-presentation, inflammatory responses, the regulation of chemokines, and cell adhesion. \\n]0.8878
625text-davinci-003no_synopsisHALLMARK_INTERFERON_GAMMA_RESPONSE-1[\\nSummary: The enriched terms among the list of genes includes pathways involved in immunity, interleukin regulation, transcriptional regulation, inflammation, cell signaling, and apoptosis.\\nMechanism: Signaling and pathways involving these genes are likely to regulate these biological processes.\\n][ This list of genes is enriched in terms related to cell signaling, transcription regulation, and immune system regulation. Specifically, genes are enriched in pathways related to: interferon signaling; antigen processing, presentation, and recognition; cytokine signaling; cell cycle and DNA damage response; and apoptosis.\\n\\nMechanism: It appears that the genes identified in this list are functionally connected and may be involved in a larger underlying biological mechanism or pathway. The proteins associated with each gene are known to interact with one another and repress/activate various genes leading to the regulation of cell signaling, transcription, and immune system functions. This molecular regulation process is essential in the control of cellular functions and physiological behavior. \\n\\n]0.95509
626text-davinci-003no_synopsisHALLMARK_KRAS_SIGNALING_DN-0[ Genes in this term enrichment test were found to be enriched for terms related to the development of bones, morphogenesis, growth and maintenance, cell-cell signaling and communication, protein modification, and transport.\\nMechanism: It is likely that the genes identified in this term enrichment test make up a biological pathway that is involved in the development of bones, growth and morphogenesis, and other processes related to regulating cell-cell signaling and communication, protein modification, and transport.\\n][ The analysis of the list of human genes reveals that these genes are related to development, regulation, and signaling mechanisms within the cell. Specifically, the terms associated with development, such as digit development, neural development, immune system development and transcriptional regulation, are enriched. Additionally, terms related to signal transduction, such as G-protein coupled receptors, protein kinases, and guanine nucleotide exchange factors, are also enriched.\\n\\nMechanism:The mechanism underlying the term enrichment of the list of human genes is likely related to the fact that these genes play a role in a wide range of essential cellular processes. It is likely that signaling molecules and transcription signals coordinate these processes to enable proper development and homeostasis.\\n\\n]0.92293
627text-davinci-003no_synopsisHALLMARK_KRAS_SIGNALING_DN-1[\\nSummary: The list of genes are found to be significantly associated with physiological processes related to morphogenesis, cell-cell communication and development, and hormone regulation.\\nMechanism: The genes are likely to be involved in a variety of biological mechanisms, such as cell-signalling, cellular differentiation and cell-cycle, as well as hormone mediated processes.\\n][COULD NOT PARSE]0.69365
628text-davinci-003no_synopsisHALLMARK_KRAS_SIGNALING_UP-0[ Genes in this list are predominantly involved in signal transduction pathways and morphogenesis; specific terms enriched include signal transduction, cell morphogenesis, response to stimulus, angiogenesis, regulation of molecular function, and extracellular matrix organization.\\nMechanism: The list of genes are likely to be involved in signaling pathways involving kinases, growth factors and receptors, as well as involvement in morphogenesis processes such as cell-cell adhesion, cellular movement and cell differentiation.\\n][ This list of gene names is enriched for genes involved in signal transduction, cell cycle control, and cell-to-cell adhesion.\\nMechanism: The enrichment of these genes indicates a shared biological pathway in which cellular communication, pathways, and networks are regulated by controlling the production of proteins and other molecules. This can lead to changes in other intracellular activities, such as cell cycle progression and adhesion. \\n]0.9383
629text-davinci-003no_synopsisHALLMARK_KRAS_SIGNALING_UP-1[\\nSummary: This set of genes appears to be involved in a variety of cellular processes, including morphogenesis and tissue development, cell signaling, and immune regulation.\\nMechanism: These genes appear to be involved in transcription modulation, signal transduction pathways, and regulation of cell adhesion and migration.\\n][\\nSummary: This list of genes is enriched for terms related to cell adhesion and signal transduction, including terms such as integrin, chemokine receptor, protein kinase and G-protein-coupled receptor.\\nMechanism: These genes are involved in pathways important for cell adhesion, such as integrin and chemokine receptor-mediated interactions, as well as signal transduction pathways which include protein kinases, G-protein-coupled receptors and other associated proteins.\\n]0.90147
630text-davinci-003no_synopsisHALLMARK_MITOTIC_SPINDLE-0[COULD NOT PARSE][\\n\\nSummary: The list of human genes have diverse enrichment in the functions of cell cycle control, cell adhesion, and cytoskeletal organization.\\nMechanism: These genes enable cells to interact with their environment and complete the cell cycle by organizing components, regulating activities, and controlling signaling pathways.\\n]0.68314
631text-davinci-003no_synopsisHALLMARK_MITOTIC_SPINDLE-1[ Enriched terms show a commonality among these genes for processes related to cytoskeletal organization and migration of the cell, cell division, DNA replication and repair, and targeting proteins to the correct place in the cell.\\nMechanism: The proteins represented by these genes likely play a role, either directly or indirectly, in the regulation of a number of vital cell processes including cell division, DNA replication and repair, and targeting proteins to the right place in the cell.\\n][ \\nSummary: The genes that were provided are statistically enriched for terms related to cell division, protein phosphorylation, chromatin remodeling, and microtubule binding and organization.\\nMechanism: These genes likely function in biological pathways related to spindle assembly, chromosome segregation and movement, cell-cycle control, and other processes related to mitosis. \\n]0.92114
632text-davinci-003no_synopsisHALLMARK_MTORC1_SIGNALING-0[COULD NOT PARSE][COULD NOT PARSE]1.000
633text-davinci-003no_synopsisHALLMARK_MTORC1_SIGNALING-1[ The list of genes is enriched in functions related to protein synthesis, energy metabolism, cellular transport, and immune response.\\nMechanism: It is likely that these genes are co-regulated in networks that are responsible for cellular energy production and regulation, protein synthesis and degradation, and immune response.\\n][\\nSummary: This list of genes is involved in a variety of pathways related to cell growth and development, including morphogenesis, transcription, and protein synthesis.\\nMechanism: The physiological processes induced by these genes likely work in concert to mediate a variety of cellular processes including cellular translation, metabolism, and signalling.\\n]0.8829
634text-davinci-003no_synopsisHALLMARK_MYC_TARGETS_V1-0[ The genes appear to be involved in processes related to RNA and protein synthesis, ATP-related processes, cytoskeleton organization and assembly, transcription, and chromatin remodeling.\\n\\nMechanism: The genes likely play a role in regulating various cellular processes, such as gene expression, signal transduction, and translation, via multiple pathways that are related to RNA processing, translation initiation, mRNA stability, and DNA replication.\\n\\n][\\nThe list of genes are involved in a variety of processes including, but not limited to, protein synthesis and modification, DNA replication, cell cycle regulation, and transcription regulation.\\nThis suggests that these genes may be involved in a co-dependent pathway or pathways that regulate cell growth, development, and gene expression.\\n]0.91113
635text-davinci-003no_synopsisHALLMARK_MYC_TARGETS_V1-1[ Genes from this list are mainly involved in translation, transcription, and post-transcriptional modification processes. Specifically, these genes are involved in mRNA splicing, mRNA transport, mRNA stability, protein synthesis, ribosome biogenesis, RNA interference, and chromatin remodeling. Mechanism: These genes likely operate according to the canonical mechanisms of gene expression, by which genes are transcribed, spliced, and translated into proteins. These processes are tightly regulated and involve a complex network of interacting proteins, RNAs, and other molecules. ][\\nSummary: This list of genes have overlapping functions in development, energy production, and regulation.\\nMechanism: There may be a pathway involved in controlling energy production, protein synthesis, and structural maintenance of cell components in development.\\n]0.88317
636text-davinci-003no_synopsisHALLMARK_MYC_TARGETS_V2-0[COULD NOT PARSE][ The enrichment test identified a set of genes related to protein and nucleic acid metabolism and cell cycle regulation. Specifically, genes involved in protein post-translational modifications, phosphorylation, transcription, translation, and ribosome biogenesis were enriched.\\n\\nMechanism: These gene functions are likely related to the underlying biological mechanism or pathway, since genes related to these processes have an essential role in regulatory activities and cell cycle control. ]0.69478
637text-davinci-003no_synopsisHALLMARK_MYC_TARGETS_V2-1[\\nSummary: The gene set is enriched for terms related to cell activation and proliferation, as well as DNA replication and replication-associated processes such as transcription and translation.\\n][ \\nSummary: Many of the genes listed appear to be related to chromatin and transcriptional regulation.\\nMechanism: Regulation of gene expression and chromatin structure via transcription factors and nucleosome remodeling enzymes. \\n]0.8635
638text-davinci-003no_synopsisHALLMARK_MYOGENESIS-0[ Gene expression and structure, cytoskeletal structure and dynamics, calcium regulation and signaling, cell adhesion and migration, cell death biochemistry, and metabolic regulation are all enriched terms based on the genes provided that are common to these roles in humans.\\n\\nMechanism: The underlying biological mechanism for the enriched terms observed in this list of genes is likely related to the wide range of regulatory roles these genes and gene products have in maintaining cellular health and enabling proper physiological functions and development at the cellular level. \\n\\n][COULD NOT PARSE]0.68569
639text-davinci-003no_synopsisHALLMARK_MYOGENESIS-1[ The list of genes show an enrichment for terms related to the extracellular matrix, cytoskeleton, muscle structure and development, neuromuscular structure, ion channels, and ion transport. \\nMechanism: These genes appear to be involved in various intra- and extracellular pathways and mechanisms related to the formation and maintenance of the cytoskeleton, neuromuscular structure, and muscle formation, as well as ion transport and channel proteins serving as important mediators of electrical and chemical signals in cells. \\n][COULD NOT PARSE]0.67514
640text-davinci-003no_synopsisHALLMARK_NOTCH_SIGNALING-0[\\nThe list of genes are involved primarily in aspects of embryonic development, regulation of cell cycle, and calcium signaling.\\nMechanism: The genes function primarily in regulating various aspects of cell signaling and cycle regulation during embryonic development, such as down-regulation of Notch signaling, regulation of Wnt signaling and Hedgehog signaling pathways, cell morphogenesis, and calcium signaling.\\n][ These genes are associated with Notch receptor, transcription factor, and Wnt pathway signaling, which are involved in tissue and organ development.\\nMechanism: Notch receptor, Wnt, and transcription factor signaling pathways leads to a variety of processes such as morphogenesis, organogenesis, tissue development, cell fate determination, and cell interaction. \\n]0.8951
641text-davinci-003no_synopsisHALLMARK_NOTCH_SIGNALING-1[COULD NOT PARSE][\\nSummary: The genes in this list are associated with cell proliferation, morphogenesis and development, nerve system differentiation, and regulation of transcription.\\nMechanism: The genes likely function in pathways involved in the WNT and Notch signalling pathways, which have numerous roles in development and differentiation of different tissue types. \\n]0.69341
642text-davinci-003no_synopsisHALLMARK_OXIDATIVE_PHOSPHORYLATION-0[\\n\\nSummary: This list of genes is enriched for terms related to mitochondrial activity, electron transport chain, oxidative phosphorylation, and metabolic regulation/activation.\\nMechanism: This list of genes are likely to be involved in the various steps of mitochondrial activity, electron transport chain, oxidative phosphorylation, and metabolic regulation/activation. \\n][COULD NOT PARSE]0.68357
643text-davinci-003no_synopsisHALLMARK_OXIDATIVE_PHOSPHORYLATION-1[\\nSummary: The list of genes is predominantly involved in cellular respiration and metabolism, as evidenced by the enriched terms related to mitochondrial bioenergetics, ion transport and metabolite-binding proteins.\\nMechanism: The commonality amongst the genes likely contributes to the normal functioning of mitochondria, and is involved in the bioenergetic processes that involve ATP synthesis, as well as maintaining electron transfer and transporter function.\\n][ Genes in this list are mainly associated with mitochondrial bioenergetics and associated pathways. Specifically, the terms \"mitochondrial electron transport chain complex activity\"; \"mitochondrial electron transport, NADH to ubiquinone\"; \"mitochondrial respiratory chain complex I activity\"; \"respiratory chain complex I assembly\"; \"respiratory chain complex III activity\"; and \"respiratory chain complex IV activity\" are found to be enriched in this gene set.\\n\\nMechanism: Mitochondria are dynamic organelles that are responsible for many of the metabolic pathways, including cellular respiration. A variety of mitochondrial electron transport complexes are involved in the production of energy, including complex I (NADH:ubiquinone oxidoreductase), complex III (ubiquinone:cytochrome c oxidoreductase), complex IV (cytochrome c oxidase), and complex V (ATP synthase). As these genes are associated with mitochondrial functions, it is possible that there is an underlying mechanism related to metabolic pathways and energy production within the mitochondria. \\n\\n]0.91598
644text-davinci-003no_synopsisHALLMARK_P53_PATHWAY-0[ Analysis of this gene list revealed a significant enrichment of terms in functions related to cytoskeleton alteration, calcium homeostasis modulation, ubiquitin-proteasome pathway activation, cell cycle control, and transcriptional and post-transcriptional regulation.\\n\\nMechanism: These functions likely act in concert to mediate the regulation of cellular growth, differentiation, and survival.\\n\\n][COULD NOT PARSE]0.68383
645text-davinci-003no_synopsisHALLMARK_P53_PATHWAY-1[ Genes in this list are associated with regulation of the cell cycle, DNA damage repair, cell signaling and processes involved in cell growth, apoptosis, and immune modulation. The genes are enriched for functions related to transcription, chromatin dynamics, cell adhesion molecules, and cytokines. \\nMechanism: The regulation of these genes (directly or indirectly) is likely to be part of a complex network of pathways, signaling molecules, and protein-protein interactions. \\n][COULD NOT PARSE]0.67463
646text-davinci-003no_synopsisHALLMARK_PANCREAS_BETA_CELLS-0[\\nSummary: This gene set is enriched in functions related to pancreas development, glucose metabolism, cell motility, and neural development. \\nMechanism: It is hypothesized that these genes function in a network to control developmental processes relevant to pancreas development, glucose metabolism, cell motility and neural development.\\n][ Genes play diverse roles in the development of the pancreas, nervous system, and musculoskeletal system. Major term enrichment was found for pancreas development, nervous system development, development of neural structures, organogenesis, and transcriptional regulation. \\nMechanism: These genes are likely involved in a variety of biological mechanisms including, the regulation of morphogenesis, cell-to-cell adhesion, and protein synthesis pathways, as well as hormonal metabolism and signaling.\\n]0.90162
647text-davinci-003no_synopsisHALLMARK_PANCREAS_BETA_CELLS-1[\\nSummary: This term enrichment test identified gene functions related to morphogenesis, neural development, signal transduction, insulin hormone secretion, transcription regulation, and transcription factor activity.\\nMechanism: These genes likely work together to facilitate the development of body organs, neuronal function and pathways, insulin secretion, and transcription factor activity.\\n][ Analysis of these genes revealed common pathways related to metabolic regulation, neural development, and transcription/translation control. The terms enriched by these genes are neurogenesis; metabolism; transcriptional control; translation; morphogenesis; body patterning and organization; neurological system development; and cell differentiation.\\n\\nMechanism: Signaling pathways involved in neural development will have an influence on neurogenesis, while metabolic pathways will be involved in pathways that regulate glucose and lipid metabolism. Additionally, transcription and translation pathways are essential for regulating gene expression but also cell differentiation and morphogenesis. Finally, body patterning and organization rely on genes that control cell fate and cellular migration. \\n\\n]0.90411
648text-davinci-003no_synopsisHALLMARK_PEROXISOME-0[COULD NOT PARSE][ The human genes given in the list are involved in metabolic biochemical pathways associated with lipid metabolism, stress response, mRNA transcription, DNA repair, skeletal and cartilage development, and cell migration. \\nMechanism: Metabolic enzymes and transport proteins appear to regulate these pathways, allowing for the synthesis and degradation of cellular compounds, as well as transporting molecules into and out of the cell to maintain physiological homeostasis.\\n]0.68459
649text-davinci-003no_synopsisHALLMARK_PEROXISOME-1[ Genes involved in the list are associated with lipid metabolism, lipid storage and transport, steroid metabolism, regulation of transcription and, importantly, regulation of the cell cycle. \\nMechanism: An enrichment of pathways associated with lipid, steroid and transcriptional metabolism, as well as regulation of the cell cycle.\\n][\\nSummary: Genes in this list are associated with a wide array of terms, including metabolism, transcription, regulation, transport and signaling.\\nMechanism: These genes likely play a role in a broad biological mechanism involving various metabolic pathways, transport, and regulatory functions.\\n]0.9038
650text-davinci-003no_synopsisHALLMARK_PI3K_AKT_MTOR_SIGNALING-0[ Gene expression, DNA repair and maintenance, growth factors, cellular signaling pathways and lipid metabolism \\nMechanism: Regulation of gene expression through the activation of transcription and DNA repair and maintenance pathways is likely involved. The enriched terms related to growth factors suggests that the list of genes may be involved in cell proliferation and differentiation. Signaling pathways and lipid metabolism may be involved in cell-cell communication and energy-related processes, respectively.\\n][ The list of genes is enriched for terms related to signal transduction pathways and development, such as morphogenesis and cell differentiation.\\nMechanism: Signal transduction pathways are likely involved in the regulation of the gene functions, with particular importance of tyrosine kinase activity and modulation of relevant receptor activities.\\nHypothesis: The genes may be involved in the regulation of tissue development and cell differentiation.\\n]0.9062
651text-davinci-003no_synopsisHALLMARK_PI3K_AKT_MTOR_SIGNALING-1[ The list of genes given are involved in cell cycle regulation, gene transcription, transcription factor activation and signal transduction pathways.\\nMechanism: The genes included in this list are involved in various mechanisms of cell cycle regulation, gene transcription, transcription factor activation and signal transduction pathways. These involve the regulation of cell cycle progresses such as synthesis, growth, proliferation and differentiation, as well as the operations of protein kinases, transcription factors, receptor proteins and other essential molecules. \\n][ \\n\\nSummary: This gene list covers a broad range of functions, including cell signaling, growth and survival, protein and lipid metabolism, transcription regulation, and cell cycle control.\\nMechanism: The genes in this list are likely involved in a variety of pathways that facilitate or regulate various cellular activities, such as receptor signaling, protein glycosylation, kinase activity, apoptosis, and G-protein interactions.\\n]0.93143
652text-davinci-003no_synopsisHALLMARK_PROTEIN_SECRETION-0[COULD NOT PARSE][ Genes listed are associated with vesicular transport, trafficking, and membrane fusion in the cell.\\nMechanism: Vesicular transport involves the formation of vesicles from the host membrane, trafficking of these vesicles through the cell and organelles, and fusion of the vesicles with host membranes for which these genes are responsible.\\n]0.67325
653text-davinci-003no_synopsisHALLMARK_PROTEIN_SECRETION-1[COULD NOT PARSE][ Enrichment test on a given list of human genes resulted in the identification of several enriched terms, which have important roles in post-translational modification, protein folding, protein synthesis, endocytosis, oligosaccharide metabolism, and lysosomal trafficking.\\n\\nMechanism: The mechanism behind this enrichment pattern is likely related to the various mechanisms regulated by these genes, such as the regulation of PTMs, protein folding, protein synthesis, endocytosis, oligosaccharide metabolism, and lysosomal trafficking.\\n\\n]0.69522
654text-davinci-003no_synopsisHALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0[\\nSummary: This list of genes is enriched for terms involving redox regulation, antioxidant defense and detoxification of reactive oxygen species, peroxisomal and mitochondrial biogenesis, and cell metabolism.\\nMechanism: The underlying biological mechanism involves the production and regulation of reactive oxygen species, adaptation to oxidative stress and related forms of damage, and the maintenance of redox homeostasis.\\n][\\nSummary: The list of genes is associated primarily with metabolic processes, defense against oxidative damage and DNA repair.\\nMechanism: These processes are likely related to cellular level metabolic regulation, protection against oxidative damage, and DNA damage repair.\\n]0.93152
655text-davinci-003no_synopsisHALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1[ \\nSummary: 13 genes are enriched for functions associated with redox regulation, metabolism, cell cycle regulation, and transcriptional regulation.\\nMechanism: These genes likely play a role in the regulation of a cell's redox balance, metabolism, cell cycle progression and gene expression.\\n][COULD NOT PARSE]0.68276
656text-davinci-003no_synopsisHALLMARK_SPERMATOGENESIS-0[\\nThe gene list is enriched for functions related to cell signaling, protein regulation, and cell cycle control, as well as complex development processes such as morphogenesis, organogenesis and cytoskeletal regulation.\\nMechanism: A wide range of mechanims are at work here, which involve the transcription and translation of genes to encode proteins and the regulation of their functions to mediate both common and specific biological processes.\\n][ Genes associated with this list indicate enrichment for a variety of cell cycle control and chromatin remodeling processes, as well as protein ubiquitination, regulation of DNA replication, spindle assembly, and nuclear organization.\\n\\nMechanism: The enriched terms suggest that these genes are involved in a variety of related functions related to the regulation and maintenance of the cell cycle, chromatin remodeling, DNA replication, spindle assembly and nuclear organization.\\n\\n]0.8936
657text-davinci-003no_synopsisHALLMARK_SPERMATOGENESIS-1[ Genes related to organ development, morphogenesis, cytoskeletal proteins, signal transduction.\\nMechanism: Proteins from the list are likely used as part of a unified pathway for organ/tissue development and morphogenesis, and involved in cell cycle checkpoint regulation and signal transduction.\\n][COULD NOT PARSE]0.68282
658text-davinci-003no_synopsisHALLMARK_TGF_BETA_SIGNALING-0[ The list of genes analyzed in this term enrichment test is related to pathways associated with cell growth and development, such as MAPK, TGF-β, Wnt/β-catenin, Hippo and transcriptional regulations. Specifically, pathway enrichment of genes included muscle and tissue morphogenesis, regulator of G-protein signaling and inflammatory response pathway.\\n\\nMechanism: The general mechanism is that the genes are involved in signaling pathways for cell processes such as growth, differentiation and apoptosis. These signals modulate the expression of downstream genes and ultimately lead to changes in cell shape and other cellular activities.\\n\\n][COULD NOT PARSE]0.68625
659text-davinci-003no_synopsisHALLMARK_TGF_BETA_SIGNALING-1[COULD NOT PARSE][ Our term enrichment analysis of these genes reveals an overrepresented pattern of general cellular processes related to the development and proliferation of cells, as well as homeostasis, cell division, and migration. Specifically, genes related to transcriptional regulation, signal transduction, cell cycle regulation, protein kinase pathways, and translation were enriched.\\n\\nMechanism: These overrepresented functions suggest a complex coordination of biochemical pathways contributing to cell development and proliferation, junctions, and cytoskeletal organization.\\n\\n]0.69558
660text-davinci-003no_synopsisHALLMARK_TNFA_SIGNALING_VIA_NFKB-0[ These genes are mainly involved in developmental processes, inflammation, immunomodulation, inflammation, cell signalling and metabolic pathways.\\nMechanism: These genes are likely to be involved in pathways leading to the regulation of morphogenesis and tissue development, control of cell proliferation and apoptosis, regulation of immune system immune response, regulation of inflammation and activation of metabolic pathways.\\n][ The genes in the given list are predominantly involved in the TLR signaling pathway, development, inflammation and immune-response regulation.\\nMechanism: The TLR signaling pathway consists of an intricate set of reactions starting with the recognition of a pathogen-associated molecular pattern (PAMP) by the TLR receptor, leading to the activation of various transcription factors, such as NFKB and MAPK, which work to activate a cascade of gene expression and ultimately the secreting of pro-inflammatory molecules.\\n\\n]0.9090
661text-davinci-003no_synopsisHALLMARK_TNFA_SIGNALING_VIA_NFKB-1[\\nSummary: The genes are enriched for terms related to gene transcription, cytoskeleton formation, and signal transduction. \\nMechanism: The genes are likely involved in a wide range of processes, including transcriptional regulation, actin cytoskeleton organization, cytokine receptor signaling and NF-kB signaling pathways.\\n][ Gene functions related to inflammation and immunity appear to be enriched when analyzing the list of genes provided, including cytokine-mediated signaling, antigen-receptor mediated signaling, B-cell proliferation, cytokine expression and release, immunoregulatory interactions, NF-kappaB (NF-κB) activation, and interferon (IFN) signaling.\\n\\nMechanism: These genes are likely involved in an inflammatory response in which cytokines are released and induce receptor activation, which leads to NF-κB activation and transcription of genes that produce cytokines and other signaling molecules, as well as triggering an IFN response. This ultimately leads to B-cell proliferation and immunoregulatory interactions in order to mount a response to the any pathogens. \\n\\n]0.87439
662text-davinci-003no_synopsisHALLMARK_UNFOLDED_PROTEIN_RESPONSE-0[ The genes in the list may be generally involved in processes such as mRNA transcription, ribosome biogenesis and protein folding, as well as nucleolar and spliceosomal activity. \\nMechanism: These genes likely regulate cellular processes such as protein production and transport, RNA processing, and cell cycle control. \\n][\\nSummary: A significant enrichment of genes involved in translation and protein folding is found in the gene list, indicating a common pathway for these genes.\\nMechanism: The genes in this list are likely all involved in the same pathway, centered around translation and protein folding.\\n]0.9133
663text-davinci-003no_synopsisHALLMARK_UNFOLDED_PROTEIN_RESPONSE-1[\\nSummary: The enrichment analysis on the list of genes revealed a common theme of gene functions related to metabolism, protein synthesis, and post-translational modifications.\\nMechanism: The observed gene functions suggest a pathway of metabolic and protein regulatory processes that involve the synthesis of proteins, post-translational modifications such as phosphorylation, and other processes related to metabolism and folding.\\n][COULD NOT PARSE]0.70418
664text-davinci-003no_synopsisHALLMARK_UV_RESPONSE_DN-0[ The genes identified are associated with protein kinases, cellular signaling pathways, and development of skeletal and extracellular matrix components.\\nMechanism: These identified genes may be involved in complex regulation and signaling pathways, focusing on post-translational phosphorylation and transcriptional regulation, as well as the control of growth, development and remodeling of skeletal structures.\\n][ This enrichment test demonstrates over-representation of the genes involved in cell signaling, structural and enzymatic proteins, and morphogenesis. Mechanism: The mechanisms underlying this enrichment are likely related to the roles of these proteins in regulating the mechanism of intercellular signaling associated with cell development, adhesion, migration, metabolism, skeletal growth, and cell death. ]0.885
665text-davinci-003no_synopsisHALLMARK_UV_RESPONSE_DN-1[ Many of the genes are clustered around those involved in structure, development and regulation. They are involved in processes such as mitotic regulation, bone morphogenesis, morphogenesis of specific organs and tissues, regulation of signaling pathways, regulation of transcription, regulation of cell proliferation, cellular responses to external stimuli, protein phosphorylation and DNA binding.\\n\\nMechanism: These genes are likely to be involved in the regulation and development of several different processes, including the regulation of cell proliferation, transcription, morphogenesis of organs and tissues, and mitotic regulation. These mechanisms are likely to be controlled by the interactions among gene products, signaling pathways and regulatory components such as transcription factors.\\n\\n][COULD NOT PARSE]0.67788
666text-davinci-003no_synopsisHALLMARK_UV_RESPONSE_UP-0[ Proteins involved in development, cell growth, gene transcription, and metabolism are enriched.\\nMechanism: These proteins are involved in a variety of biological processes that underlie development and cell growth, as well as affecting gene transcription and metabolism.\\n][\\n\\nSummary: The enriched terms from the list of genes suggest a commonality in roles related to protein and organelle trafficking, DNA methylation, transcription and binding, chromatin remodeling, cell cycle regulation and metabolism. \\n\\nMechanism: The proposed mechanism is that these processes are essential components of pathways that regulate cell development, growth, and the response to internal and external stimuli.\\n\\n]0.90151
667text-davinci-003no_synopsisHALLMARK_UV_RESPONSE_UP-1[ Genes in this list are mainly involved in cell growth, morphogenesis, regulation of transcription, signal transduction of receptors, DNA/protein activity and metabolism. More specifically, the terms enriched in this list of genes are cell proliferation, cell cycle regulation, DNA replication and repair, signal transduction, calcium signaling, apoptosis, lipid metabolism and oxygen pathway.\\n\\nMechanism: The genes in this list mainly participate in the regulation of various biological processes through their encoding for proteins that act as transcription factors, receptors, and enzymes. These proteins are activated by a variety of signals including DNA damage, growth factors and hormones to induce changes in gene expression and cellular behavior. They also control cell growth, differentiation and metabolism by regulating DNA, protein, lipid and oxygen pathways, ultimately resulting in morphogenesis and cell proliferation. \\n\\n][COULD NOT PARSE]0.67922
668text-davinci-003no_synopsisHALLMARK_WNT_BETA_CATENIN_SIGNALING-0[COULD NOT PARSE][COULD NOT PARSE]1.000
669text-davinci-003no_synopsisHALLMARK_WNT_BETA_CATENIN_SIGNALING-1[\\nSummary: The gene list appears to mostly contain genes involved in Wnt signaling, Notch signaling, transcription regulation and cell cycle regulation processes.\\nMechanism: The underlying biological mechanism appears to be the regulation of processes such as transcription, cell cycle, and Wnt and Notch signaling that may in turn affect the morphogenesis and development of various organs and tissues.\\n][ Genes highly enriched in the provided list have functions related to cell signaling and regulation, including morphogenesis, transcription, and development. Specifically, genes involved in Wnt, Notch, and Hedgehog pathways, transcription factors, and cell cycle genes such as Axin, β-catenin, HDAC2, and CUL1 are all significantly enriched in the list.\\n\\nMechanism: Many of the genes involved in these pathways are responsible for controlling cell fate and regulating morphogenesis and development. The Wnt pathway, a key regulator in embryonic development, is involved in axial patterning, tissue organization and differentiation, and cell-fate decisions. The Notch and Hedgehog pathways are also important for stem cell maintenance and development in early development, as well as tissue patterning, morphogenesis, and organogenesis in adulthood. The transcription factors, such as LEF1, TCF7, and NKD1, drive gene expression in response to these signaling molecules. Lastly, genes such as ADAM17, DKK1, PSEN2, and AXIN2 are involved in cell-cycle regulation and apoptosis. \\n\\n]0.93675
670text-davinci-003no_synopsisT cell proliferation-0[ \\nSummary: The genes in the list are found to be involved primarily in cell signalling, development, and immunity processes.\\nMechanism: The numerous genes with enriched terms are involved in coordinating both intra- and extracellular activity through signal transduction pathways and receptor-mediated signaling, with downstream effects on cellular growth, differentiation, and function within various organs and systems in the body.\\n][\\nSummary: This list of genes are enriched for terms related to cell development and signaling, specifically those involved in receptor-mediated signaling and the regulation of cell morphology. \\nMechanism: These genes likely act through regulating cell development and receptor-mediated signaling pathways to their respective functions, such as morphogenesis and gene expression.\\n]0.9455
671text-davinci-003no_synopsisT cell proliferation-1[ The enrichment test found that the genes listed have common functions associated with cell signaling and immune regulation, such as signal transduction, growth factor production and response, immune response and modulation, calcium homeostasis, transcription factors, development and differentiation, receptor binding, and cytokine production.\\n\\nMechanism: The enrichment test suggests that these genes may contribute to signal transduction pathways that facilitate cell proliferation, differentiation, and survival; growth factor production and signal transduction; immune response and modulation; calcium homeostasis; transcription factor activity including regulation of gene expression; development and differentiation; receptor binding and signal transduction; and cytokine production.\\n\\n][ \\nThis sample of genes are mainly involved in regulation of the immune system, cell signaling, cytoplasmic transport, and apoptosis. Specifically, the genes are enriched for terms such as cytokine receptor binding; cell adhesion; immunoreceptor-antigen complex binding; regulation of the ubiquitin-proteasome pathway; transcription factor regulator activity; GTP-binding protein binding; cell differentiation; T-cell receptor binding; antigen presentation; and immune system process.\\n\\nMechanism: This list of genes likely act in concert to regulate the immune system. They perform a variety of functions, including binding and processing cytokines, receptor-antigen complexes, and other molecules involved in the binding or processing of molecules, such as transcription factors, that are involved in regulating gene expression. Additionally, these genes may be involved in cell differentiation, antigen presentation, and other processes involved in the regulation of the immune system. \\n\\n]0.91197
672text-davinci-003no_synopsisYamanaka-TFs-0[COULD NOT PARSE][ The genes provided are related to transcription factor activity, as they are associated with embryonic stem cell differentiation and pluripotency.\\n]0.67133
673text-davinci-003no_synopsisYamanaka-TFs-1[\\nThe list of genes provided encode transcription factors associated with early development of embryonic stem cells.\\nMechanism: Transcriptional regulation via these transcription factors control the expression of other genes related to embryogenesis and stem cell development.\\n][ The given list of genes is involved in the regulation of cell differentiation and development, specifically in the formation of stem cells, by regulating the expression of developmental proteins. ]0.9079
674text-davinci-003no_synopsisamigo-example-0[\\nSummary: This term enrichment test on the list of human genes shows enrichment for terms related to extracellular matrix organization and cell adhesion, morphogenesis and morphological changes, and cell signaling. \\nMechanism: The underlying biological mechanisms may involve a combination of protein-protein interactions, transcriptional regulation and extracellular matrix modifications.\\n][ The genes included in this list are related to cell proliferation, tissue morphogenesis, motility regulation, vascular development, bone growth, and the immune system. The mechanism is the transcription of gene products that cause expression of varied proteins that mediate these functions.\\n\\nMechanism: Transcription of gene products inducing the expression of varied proteins that mediate cell proliferation, tissue morphogenesis, motility regulation, vascular development, bone growth, and the immune system.\\n\\n]0.85124
675text-davinci-003no_synopsisamigo-example-1[COULD NOT PARSE][ This list of genes are all involved in the development and maintenance of the vascular system. Specifically, these genes play a role in angiogenesis, cell proliferation and migration, matrix remodeling, and tissue remodeling. The genes are implicated in processes such as Jagged-mediated signaling, transcriptional regulation, platelet activation and aggregation, immune regulation, and extracellular matrix formation.\\n\\nMechanism: These genes are involved in a variety of pathways that are responsible for the formation and maintenance of the vascular system. Specifically, the Jagged and Notch pathways are implicated in the control of endothelial cell proliferation and migration, while the TGF-β and Wnt/β-Catenin pathways are involved in matrix remodeling. Additionally, these pathways are also involved in platelet activation and aggregation and the formation of extracellular matrix components.\\n\\n]0.68888
676text-davinci-003no_synopsisbicluster_RNAseqDB_0-0[\\nSummary: The list of genes are involved in morphogenesis, development, transcription regulation, cellular signalling and ion transport.\\nMechanism: The genes are likely to be involved in a variety of biochemical and molecular pathways pertaining to the specified functions.\\n][ Genes associated with this list are enriched for functions related to development and signaling, including cell growth, differentiation, and migration; chromatin modulation; transcription regulation; cytoskeletal organization; intracellular trafficking and adhesion; signal transduction; and DNA/RNA metabolic processes.\\nMechanism: The genes are likely to be involved in multiple biological mechanisms and pathways, including processes related to healing, morphogenesis, angiogenesis, and muscle growth and development.\\n]0.92247
677text-davinci-003no_synopsisbicluster_RNAseqDB_0-1[ These genes are primarily involved in development and signaling pathways, particularly morphogenesis, neuronal growth, and neuronal system development. Mechanism: These genes facilitate cell-cell communication and signaling, allowing for cells to coordinate their functions together and form efficiently organized tissues and organs. ][ This analysis identified a number of genes involved in various cellular processes such as chromatin regulation, cell development, protein translation, and ion transport.\\nMechanism: The underlying biological mechanism likely involves regulation of gene expression through the actions of transcription factors, the post-translational modifications of proteins, and the transport of ions across cell membranes.\\n]0.8774
678text-davinci-003no_synopsisbicluster_RNAseqDB_1002-0[COULD NOT PARSE][ The human genes listed are involved in skeletal muscle structure and contractility. The genes are enriched for processes such as myofibrillogenesis, actin filament organization, and muscle contraction.\\n\\nMechanism: The genes likely act to regulate processes involved in myofibrillogenesis, such as Z-disc formation and maintenance, nuclear positioning, and muscle fiber organization. They also may act to modulate ion channel influx/efflux, thereby influencing muscle contraction and force. \\n\\n]0.66478
679text-davinci-003no_synopsisbicluster_RNAseqDB_1002-1[ The genes listed were significantly over-represented for processes related to muscle formation and human body structure, such as muscle and skeletal development, skeletogenesis, and myogenesis. \\n\\nMechanism: The set of genes is involved in multiple pathways related to muscle formation and structure in the human body, such as muscle and skeletal development, skeletogenesis, and myogenesis. These pathways likely involve the regulation of protein synthesis and biosynthesis, as well as processes related to muscle contraction and relaxation. \\n\\n][\\nSummary: Genes in this set are involved in muscle structures and processes.\\n]0.90468
680text-davinci-003no_synopsisendocytosis-0[ These genes are involved in signaling pathways, vesicle/lipid trafficking, and cellular adhesion related processes.\\nMechanism: These genes act as regulators of nutrients, cell metabolism, and cytoskeletal organization. They are also involved in endocytosis, exocytosis, and the regulation of intercellular adhesion and motility.\\n][\\nSummary: These genes are related to lipid metabolism, cell signaling pathways, and cell cycling.\\nMechanism: These genes are thought to have a role in regulating lipid metabolism, cell signaling pathways and cell cycling. \\n]0.91107
681text-davinci-003no_synopsisendocytosis-1[\\nSummary: The genes in this list are associated with processes related to membrane trafficking, receptor signaling, protein proteolysis, and lipid metabolism. \\nMechanism: The underlying biological mechanism is likely regulation of membrane trafficking, receptor signaling, protein proteolysis, and lipid metabolism. \\n][\\nSummary: The genes in this list are predominantly involved in endocytosis and intracellular signaling.\\nMechanism: The genes in this list interact to form a molecular pathway that is involved in endocytosis and intracellular signaling. Endocytosis allows receptors and newly synthesized molecules to be moved cellular compartments and can result in changes in cell signaling.\\n]0.9259
682text-davinci-003no_synopsisglycolysis-gocam-0[ An analysis of gene functions in these 10 genes shows an enrichment of terms associated with metabolism, including glycolysis, aerobic glycolysis, and gluconeogenesis.\\n\\nMechanism: This suggests a possible underlying biological mechanism in which glycolysis and gluconeogenesis pathways are deployed by cells in order to provide sufficient energy to cope with various metabolic demands.\\n\\n][\\nBased on the list of genes provided, common terms enriched amongst the genes include ATP synthesis, glycolysis, energy metabolism, and metabolic pathways.\\n\\nMechanism: \\nThe underlying biological mechanisms involve ATP synthesis by way of glycolysis and energy metabolism pathways, which produce necessary energy required for a variety of cellular activities.\\n\\n]0.9328
683text-davinci-003no_synopsisglycolysis-gocam-1[ The human genes provided in this list are enriched for metabolic functions involved in glycolysis and pentose phosphate pathways.\\nMechanism: The mechanism likely involves the direct or indirect control of enzymatic activities through the coordinated activity of multiple genes.\\n][ The genes identified are related to glycolysis, the metabolic pathway that produces ATP from glucose and other carbohydrates. \\nMechanism: Glycolysis involves the series pathways in which a compound molecule of glucose is broken down into two molecules of pyruvic acid, which are further converted into ATP. \\n]0.8930
684text-davinci-003no_synopsisgo-postsynapse-calcium-transmembrane-0[COULD NOT PARSE][COULD NOT PARSE]1.000
685text-davinci-003no_synopsisgo-postsynapse-calcium-transmembrane-1[COULD NOT PARSE][\\nSummary: This gene set is primarily involved in neuronal functional regulation, including ion transport, membrane potential regulation and neurotransmission.\\nMechanism: These genes are involved in the regulation of neuronal activity, likely through the regulation of a number of ion channels, neurotransmitter receptors, and calcium/potassium regulators.\\n]0.69341
686text-davinci-003no_synopsisgo-reg-autophagy-pkra-0[\\n \\nSummary: The genes in this list are involved in various aspects of biological processes, ranging from cell growth and development to immune response and proteolysis.\\n \\nMechanism: The genes interact in multiple overlapping pathways to influence cellular processes such as immune response and protein degradation. \\n \\n][COULD NOT PARSE]0.68303
687text-davinci-003no_synopsisgo-reg-autophagy-pkra-1[ Several pathways related to cellular signaling and signalling transduction are enriched among this set of human genes. Specifically, phosphatidylinositol signalling, vascular endothelial growth factor receptor signalling, progesterone-mediated oocyte maturation, NF-kB signaling and neuroprotection are all enriched with five or more genes represented in the set, suggesting that the underlying biological mechanism could be related to these pathways.\\n\\nMechanism: Several pathways related to cellular signaling and signalling transduction.\\n\\n][\\nThe genes provided are all involved in cell regulation and signaling pathways. Specifically, they all have roles in the activation of transcription factors, and in the activation, regulation and inhibition of signaling proteins such as Ras, Akt and calcium associated kinases.\\nMechanism: \\nThe genes all act together in order to affect the expression of various genes and proteins. They function by either upregulating or downregulating the expression of transcription factors and signaling proteins, as well as by modulating the phosphorylation state of these proteins, thus controlling their activity.\\n]0.8962
688text-davinci-003no_synopsishydrolase activity, hydrolyzing O-glycosyl compounds-0[ These human genes are involved in cellular functions related to glycosaminoglycan metabolism, lysosomal and catabolic pathways, as well as digit and skeletal development. The genes are enriched for functions in carbohydrate digestion and absorption; glycosaminoglycan and glycan metabolism; lysosomal, peroxisomal, and catabolic processes; and digit, skeletal, and limb morphogenesis. \\nMechanism: The genes likely act by providing enzymes, carriers, and structural proteins that together play essential roles in the transport and metabolism of carbohydrates, as well as help form and shape the skeleton and digits during embryonic development. \\n][ These genes are apparently associated with lysozymes, mucins, glycosyltransferases, and hyaluronidases, enzymes and proteins with roles in the breakdown and regulation of glycosylation.\\nMechanism: The mechanism behind this gene cluster's biological role seems to be in the regulation of cell processes related to glycosylation, such as enzyme production and its breakdown.\\n]0.88272
689text-davinci-003no_synopsishydrolase activity, hydrolyzing O-glycosyl compounds-1[ The human genes in this list are mostly related to glycoside hydrolase (GH) activity, but also include proteins involved in chitin and mucin biosynthesis, as well as cysteine protease and lysosomal activities. Most of the genes have either a glycoside hydrolase activator or a lysosomal enzyme function. \\n][COULD NOT PARSE]0.68291
690text-davinci-003no_synopsisig-receptor-binding-2022-0[COULD NOT PARSE][\\nSummary: The genetic pathways enriched in these genes involves immunoglobulin heavy/light chain combination, antigen specific receptors, J-chain, and T-lymphocyte receptors. \\nMechanism: These genes mainly play a role in immune response, specifically the regulation of the combination of immunoglobulin heavy and light chains to form antigen-specific receptors, the formation of J-chain, the production of T-lymphocyte receptors, and the regulation of immune function.\\n]0.68454
691text-davinci-003no_synopsisig-receptor-binding-2022-1[\\nSummary: These genes are mainly involved in Immunoglobulin Function and Blood Coagulation. \\nMechanism: The terms enriched for these genes are related to the immune system and blood clotting pathways, specifically those related to Immunoglobulins, B Cell Receptors, and Fibrinogen-related proteins. \\n][COULD NOT PARSE]0.68285
692text-davinci-003no_synopsismeiosis I-0[ \\nSummary: Genes involved in DNA damage repair and meiotic recombination processes\\nMechanism: Genes in the list are involved in DNA damage recognition, DNA double-strand break repair, meiotic recombination, and chromosome segregation.\\n][ This list of genes is enriched for functions related to DNA replication, repair, and replication fidelity. Mechanism: The list of genes is likely to be involved in simulating DNA synthesis, prioritizing DNA strands for replication, ensuring proper repair of damaged DNA strands, and ensuring that high-fidelity replication is taking place during the cell cycle. ]0.90128
693text-davinci-003no_synopsismeiosis I-1[ Enrichment test revealed that genes are related to DNA repair, replication, and splicing.\\n\\nMechanism: The commonalities in the function of the genes revealed in the enrichment test suggest that there may be a biological pathway that is responsible for creating and maintaining a stable genetic system. This may involve DNA repair to combat mutation and damage, replication to create new copies, and splicing for the proper expression of genes.\\n\\n][COULD NOT PARSE]0.69431
694text-davinci-003no_synopsismolecular sequestering-0[ This enrichment test indicates that the listed genes are involved in multiple pathways that are involved in cell proliferation, apoptosis, and molecular transport in diverse cell types. Specifically, some of the enriched terms associated with these genes include mechanisms involved in cell cycle checkpoints, cell adhesion/motility complexes, transcriptional complexes, protein modifications, and RNA processing complexes. \\nMechanism: These pathways likely affect cell proliferation, apoptosis, and molecular transport by responding to a variety of environmental stimuli, including calcium-based signaling, growth factor-mediated signaling, and oxidative stress. \\n][ 17 of the genes in the list are related to functions involving calcium homeostasis, including calcium signaling, regulation of calcification, and regulation of calcium ion transport. Mechanism: The genes identified are involved in the regulation of calcium homeostasis and signaling, along with functions related to calcification, calcium buffering and transport, protection against calcium overload, and calcium-v influx/efflux. ]0.85235
695text-davinci-003no_synopsismolecular sequestering-1[ The analysed genes are mostly involved in calcium binding, apoptotic regulation, and immune modulation, all of which are important mechanisms for a variety of biologic processes.\\n\\nMechanism: The mechanism is likely related to the genes' ability to modulate calcium and apoptotic pathways as well as reduce oxidative stress and influence immune effectors.\\n\\n][\\nSummary: Our list of human genes suggests pathways involved in cell structure regulation and metabolism.\\nMechanism: These genes are likely involved in the regulation of cell morphology, metabolic processes and apoptosis.\\n]0.87135
696text-davinci-003no_synopsismtorc1-0[COULD NOT PARSE][COULD NOT PARSE]1.000
697text-davinci-003no_synopsismtorc1-1[ Analysis of the genes provided shows that the genes are enriched for functions relating to energy production and metabolism, protein biosynthesis and folds, cell regulation, growth and development, and protein turnover. \\n\\nMechanism: The likely underlying biological mechanism behind these functions is likely related to the regulation, management and production of energy and metabolites to carry out processes such as cell growth and to synthesize proteins which are essential for the functioning of the cell, cell signaling and related pathway activities.\\n\\n][COULD NOT PARSE]0.68545
698text-davinci-003no_synopsisperoxisome-0[ PEX proteins are involved in peroxisome biogenesis and formation. \\nMechanism: PEX proteins play a role in driving the biogenesis of peroxisomes, a type of organelle that plays a role in various metabolic functions. \\n][\\nThis list of genes is enriched for terms related to protein homeostasis and peroxisome biogenesis. The genes are likely to have roles in maintaining and regulating the levels of specific proteins, as well as helping to form and breakdown peroxisomes in the cell.\\n\\nMechanism: The mechanism underlying these functions appears to involve forming, maintaining and regulating the levels of specific proteins, as well as assisting in the formation and breakdown of peroxisomes in the cell. \\n\\n]0.86270
699text-davinci-003no_synopsisperoxisome-1[ The provided genes are all peroxisomal biogenesis factor genes and are associated with peroxisomal biogenesis, protein transport, and oxidative damage resistance.\\n\\nMechanism: These factors regulate the assembly of the peroxisome, a subcellular organelle involved in fatty acid metabolism, carbohydrate metabolism, and oxidative damage resistance.\\n\\n][ The genes provided are all related to Peroxisomal Biogenesis, an important cellular process. \\nMechanism: Peroxisomal biogenesis requires the coordinated expression of multiple genes in order for the peroxisome to be expressed and maintained in cells. \\n]0.9096
700text-davinci-003no_synopsisprogeria-0[ The genes in this list are all associated with a cellular carboxyl-methyl transferases, a type of protein involved in RNA and DNA metabolism. The proteins are associated with development and growth, particularly that of cell structural elements such as gene transcription and transcriptional regulation. \\nMechanism: The mechanism involves carboxyl-methyl transferase proteins that modulate gene expression and the communication between transcription factors and the DNA strand.\\n][COULD NOT PARSE]0.68464
701text-davinci-003no_synopsisprogeria-1[ These genes are involved in a number of processes related to DNA replication and repair, including DNA replication and repair, nucleosome assembly, telomere maintenance, and transcriptional regulation.\\n \\nMechanism: Genes LMNA, WRN, and BANF1 are all involved in several mechanism related to the general processes of DNA replication, repair, and transcriptional regulation through the assembly and maintenance of the different levels of chromatin structure. LMNA is involved in the assembly and disassembly of the nuclear lamina, a type of intermediate filament that helps to anchor chromosomal proteins to the nuclear envelope. WRN is involved in telomere maintenance, which is critical for accurate chromosomal replication and stability. Finally, BANF1 is involved in a number of DNA repair processes, including translesion DNA synthesis, homologous recombination, and non-homologous end joining. These processes are essential for the accurate repair and replication of DNA molecules, and all require an understanding of, and proper interactions between, transcription and chromatin structure. \\n\\n][ Shortly, these genes are involved in a range of functions including transcriptional regulation, DNA repair, cell cycle regulation, and cell differentiation. \\nMechanism: These genes all have common functions related to the transcription, repair, and/or regulation of DNA, which suggests that they all play a role in the response to cellular damage or stress, which in turn can influence the downstream processes of cell cycle, differentiation, and growth.\\n]0.85642
702text-davinci-003no_synopsisregulation of presynaptic membrane potential-0[\\n\\nSummary: This term enrichment test identified genes involved in signal transduction, ion transport, and regulation of neurotransmitter release.\\nMechanism: This is likely related to the regulation of excitatory and inhibitory signal transmission, potentially mediated by ion channels and signal transduction pathways associated with the G-protein coupled receptors, voltage-gated K+ and Na+ channels, and ligand-gated ion channels.\\n][ Through a term enrichment test on this list of genes, we see that they are over-represented in terms related to ion conductivity and neural excitability, including ion channels, membrane proteins, and synapse formation.\\n\\nMechanism: These genes likely play a role in neural excitability, leading to the formation of specific ion channels that can conduct ions and help form synapses between neurons.\\n\\n]0.9032
703text-davinci-003no_synopsisregulation of presynaptic membrane potential-1[COULD NOT PARSE][ This group of genes is enriched for terms related to ion-channel function, neuron excitability, and synaptic transmission.\\nMechanism: This group of genes suggested the underlying molecular pathway involves communication between neurons via ion-channel mediated synaptic transmission.\\n]0.68270
704text-davinci-003no_synopsissensory ataxia-0[ This list of genes is related to muscle, central and peripheral nervous system development, as well as protein and lipid transport and metabolism. \\nMechanism: The genes appear to be involved in regulatory pathways for growth and development of the skeletal and nervous systems via coordination of morphology, protein and lipid synthesis, and transport.\\n][ These genes are mainly involved in protein synthesis, metabolism, ion channel transport, and muscle contraction or development.\\n\\nMechanism: These genes function as transcriptional regulators, enzymes in metabolic pathways, ion channels, or as key mediators of neuromuscular development and contraction.\\n\\n]0.9149
705text-davinci-003no_synopsissensory ataxia-1[\\n\\nSummary: Analysis of the genes yielded significant enrichment of terms related to protein transport, development of the central nervous system, skeletal structure and muscle formation.\\n\\nMechanism: The function of these genes likely reflects the underlying biological pathways for the development and maintenance of different organ systems, including the central nervous system, muscular system, and skeletal structure. \\n\\n][ This list of genes encodes many proteins which are involved in nucleic acid metabolism, binding, and transport. Terms enriched in these genes include: Nucleic Acid Metabolism; Nucleic Acid Binding; Nucleic Acid Transport; Protein Metabolism; Protein Binding; and Protein Transport.\\n\\nMechanism: The proteins encoded by these genes are likely to be involved in nucleic acid metabolism and other related downstream processes. These proteins are likely involved in mRNA transcription, mRNA processing and/or mRNA translation. The proteins could also be involved in processes like RNA editing, DNA replication, DNA repair, and DNA recombination. These proteins are likely to be involved in the regulation of gene expression and other pathways related to this process.\\n\\n]0.87342
706text-davinci-003no_synopsisterm-GO:0007212-0[ This list of genes is enriched for terms related to signal transmission and transduction, specifically the G Protein-Coupled Receptor (GPCR) family, which is associated with cell-signaling pathways and regulation of receptor activities. The specific terms enriched include G alpha subunit signaling, related GPCR activation and signaling, G Protein-Coupled Receptor (GPCR) function, and dimerization. \\n\\nMechanism: This set of genes is involved in pathways that involve the G protein-coupled receptor (GPCR) family. GPCRs can bind to extracellular molecules, such as hormones and neurotransmitters, and then activate signaling pathways inside the cell, leading to the activation of intracellular proteins, including G proteins. The G proteins then facilitate the exchange of proteins such as cAMP, DAG, and calcium ions into the cell, in order to create a signal cascade and ultimately effect changes to the cell’s behavior.\\n\\n][ This gene list is enriched for terms related to G-Protein Coupled Receptors (GPCRs), G-protein subunits, adenylate cyclase, calcium channels, and kinases.\\n\\nMechanism: The GPCRs and G protein-coupled subunits are involved in signal transduction pathways that regulate a variety of cellular activities. They activate adenylate cyclases, which catalyze the synthesis of the secondary messenger cAMP. This acts downstream to activate pathways and processes such as G-protein mediated second messenger systems and cation channels. Kinases are involved in the regulation of the G-protein by phosphorylating the Gα subunits and other associated components, leading to changes in their activity, and ultimately, signaling cascades.\\n\\n]0.96200
707text-davinci-003no_synopsisterm-GO:0007212-1[\\nSummary: The list of genes is involved in the regulation cellular signaling and development of the nervous system.\\nMechanism: The list of genes is likely transmitting signals through G proteins, phosphorylation cascade, and calcium signaling pathways to regulate the development of the nervous system, including alterations in the nervous system structure, indoleamine metabolism, and neurotransmission.\\n][\\n\\nSummary: The enriched terms from these genes suggest a correlation with signaling pathways, cellular growth and differentiation, organization of the cytoskeleton, regulation of endocrine systems, and transcriptional regulation. \\n\\n]0.88173
708text-davinci-003no_synopsistf-downreg-colorectal-0[ The gene list includes members of the nuclear receptor superfamily, molecules involved in transcription regulation, epigenetic regulation, cell cycle regulation, DNA binding and chromatin remodeling, developmental processes and cell signaling pathways, and components of the nuclear lamina and nuclear matrix.\\n\\nMechanism: The enriched terms suggest a molecular pathway underlying gene regulation, where transcription factors and chromatin reorganization molecules interact with nuclear receptors and other molecular mechanisms in order to regulate gene expression. Moreover, the gene list may represent a mechanism involved in the regulation of cell growth, differentiation and development.\\n\\n][COULD NOT PARSE]0.67678
709text-davinci-003no_synopsistf-downreg-colorectal-1[ The genes provided are involved in developmental pathways and functions, such as transcriptional regulation, chromatin modification, morphogenesis, cardiovascular development and differentiation.\\nMechanism: These genes are associated with a wide range of cellular processes, primarily related to embryonic development, including fetal growth and development, stem cell differentiation, and postnatal growth. \\n][ The enriched terms for this list of genes are cellular growth, transcriptional regulation, and chromatin remodeling. These genes are generally involved in the regulation of transcription, chromatin modifications, and cell cycle regulation. These terms are statistically over-represented compared to the gene list provided.\\n\\nMechanism: The likely underlying biological mechanism for these genes is that they are involved in multiple pathways like transcription, chromatin modifications, and cell cycle regulation. These pathways control essential processes such as cell growth and differentiation in the body. Through these mechanisms, the genes may help to regulate embryonic development and maintain tissue homeostasis in adults. \\n\\n]0.91324
710text-davinci-003ontological_synopsisEDS-0[ These genes are mostly involved in collagen metabolic processes and extracellular matrix organization (ECM) - processes mediated by metalloendopeptidase activity, chondroitin sulfate biosynthesis, and galactosyltransferase activity, as well as by platelet derived growth factor, calcium ion, and zinc ion binding activities. Genes which affect ECM organization and/or collagen metabolic processes are implicated in symptoms of Ehlers-Danlos Syndrome.\\n\\nMechanism: The mechanism for these metabolic processes and ECM organization is likely to include the generation of specific proteins, peptides, and/or peptide modifications which affect the activity, binding, and/or interactions of collagen molecules and potential substrates of collagen.\\n\\n][ \\nSummary: The list of genes are found to be associated with proteins involved in collagen and extracellular matrix related activities and the control of transcription.\\nMechanism: These proteins are involved in various processes, such as collagen fibril organization, connective tissue development, extracellular matrix organization, glycosaminoglycan biosynthetic process, negative regulation of transcription by RNA polymerase II, positive regulation of transcription by RNA polymerase II, proteoglycan biosynthetic process, Rho protein signal transduction, skin morphogenesis, and zymogen activation.\\n]0.89139
711text-davinci-003ontological_synopsisEDS-1[ These human genes enable functions related to collagen fibril organization, extracellular matrix organization, collagen biosynthetic processes, glycosaminoglycan biosynthetic processes, peptidyl-prolyl cis-trans isomerase activity, epidermal cell differentiation, and wound healing.\\n\\nMechanism: The genes involved likely work towards a common mechanism involving the integration of extracellular matrix and collagen assembly and remodeling, as well as supporting cellular processes such as wound healing, epidermal cell differentiation, and collagen fibril organization.\\n\\n][\\nSummary: The genes in this list are associated with extracellular matrix organization, collagen fibril organization, collagen biosynthesis, proteoglycan biosynthesis, and glycosaminoglycan biosynthesis.\\nMechanism: These genes are likely to be involved in the organization of extracellular matrix, the formation of collagen fibrils, and the synthesis of proteoglycans and glycosaminoglycans. \\n]0.92180
712text-davinci-003ontological_synopsisFA-0[COULD NOT PARSE][ Genes are involved in processes related to DNA repair and protein monoubiquitination, part of Fanconi anaemia nuclear complex, and located in multiple cellular components including chromatin, nucleus and cytosol. Hypothesis: These genes work in concert to coordinate the repair of DNA damage, likely with monoubiquitination acting as a signal for protein binding activities related to DNA repair. ]0.69383
713text-davinci-003ontological_synopsisFA-1[COULD NOT PARSE][\\nSummary: Members of the Fanconi Anemia Nuclear Complex are involved in protein monoubiquitination and DNA repair processes.\\nMechanism: Members of the Fanconi Anemia Nuclear Complex act in a coordinated fashion to catalyse monoubiquitination of proteins, regulate cell cycle, and repair damaged DNA.\\n]0.69285
714text-davinci-003ontological_synopsisHALLMARK_ADIPOGENESIS-0[ The genes listed are enriched for functions related to protein binding, protein homodimerization, ATP binding, and DNA binding activities, as well as functions related to enzyme and receptor activities, GTPase and phosphorylation activities, and metal ion and lipid bindings.\\n\\nAdditionally, several of the genes are enriched for functions related to metabolic processes, including NADH dehydrogenase and glycerophosphocholine O-acyltransferase activities, as well as carboxylic ester hydrolase, aldehyde dehydrogenase, ubiquitin protein ligase, and 2'-3'-cyclic GMP-AMP binding activities.\\n\\nMechanism:The proteins encoded by these genes are likely involved in a variety of biological processes, such as processes related to metabolism, signaling, and cell regulation, which requires their involvement in protein-protein or protein-DNA interactions, as well as protein homodimerization, ATP binding, and chemical and lipid bindings. The proteins also likely participate in various enzyme activities, such as cyclic GMP-AMP binding and GTPase activities. \\n\\n][ The terms found to be enriched in the gene summaries include “protein binding activity”, “NAD(P)H oxidase activity”, “ATP binding activity”, “GTP binding activity”, “transmembrane transporter activity”, “DNA binding activity”, “receptor binding activity”, “cysteine-type endopeptidase inhibitor activity”, “caspase binding activity” and “RNA binding activity”. \\n\\nMechanism: These genes likely contribute to or are part of a variety of processes involving cellular signaling pathways, tissue development and repair, immune system modulation, and metabolic pathways.\\n\\n]0.94489
715text-davinci-003ontological_synopsisHALLMARK_ADIPOGENESIS-1[ Processes related to protein function, binding, regulation, transportation, metabolism, and receptor activity are enriched in this list of genes, as evidenced by the high frequency of activities such as protein homodimerization, enzyme binding, ATPase activity, and receptor binding. The underlying biological mechanism likely involves a complex network of proteins that interact with and regulate each other for a variety of cellular processes. \\n][ \\nSummary: These genes are largely involved in protein binding activities and enzyme activities.\\nMechanism: Enzyme activities and protein binding activities allow for the regulation of cell processes, cell signaling and energy production. \\n]0.92208
716text-davinci-003ontological_synopsisHALLMARK_ALLOGRAFT_REJECTION-0[ This list of genes, describe a variety of functions related to cellular communication, regulation, and response. This includes binding, receptor activity, signaling, enzyme and protein binding activity, transcription, cytokines activity, chemical and peptide binding, as well as receptor and protein complex binding activity.\\n\\nMechanism: These genes likely serve as part of a complex molecular network involved in regulating immune responses and regulating other cellular functions. The enriched terms indicate that these genes play a role in various stages of the communication process including receptor binding, signaling, and transcription, as well as other functions such as chemical and peptide binding.\\n\\n][\\nThis list of genes is involved in a broad range of biological processes, including growth factor and cytokine activities; enzyme binding, activating and regulating activities; transcription activator, receptor and factor binding activities; and other activities related to binding and signaling. These genes are primarily involved in protein homodimerization, protein heterodimerization, and identical protein binding activities, as well as protein kinase, DNA-binding and RNA-binding activities.\\n\\nMechanism:\\nThese processes are mostly facilitated by the interactions between various domain specific proteins and pathways, including SH3 domain binding, C-X-C chemokine binding, heparin binding, ubiquitin-protein ligase binding, calmodulin binding, ICAM-3 receptor activity, TAP complex binding activity, MHC class II protein complex binding, interleukin-12 receptor binding, and Toll-like receptor 2 binding activity.\\n\\n]0.91209
717text-davinci-003ontological_synopsisHALLMARK_ALLOGRAFT_REJECTION-1[ \\nThe list of genes show enrichment for terms related to binding activity (enzyme binding, RNA-binding, protein binding, chemokine receptor binding, DNA-binding), protein kinase binding (protein serine/threonine/tyrosine kinase), and cytokine activity (growth factor activity, interleukin binding, etc).\\n\\nMechanism: These genes are involved in various cellular pathways involving binding and signaling. The binding activity of these genes can lead to the formation of enzyme-substrate/protein-protein complex which is necessary for a variety of physiological processes. The cytokine activity of these genes are likely to involve their roles in regulating cellular growth, differentiation, and the physiological responses to external stimuli.\\n\\n][ This enrichment test reveals genes associated with extra- and intra-cellular biological processes and functions, specifically related to cell adhesion, receptor binding and signaling, transcription regulatory region sequence-specific DNA binding, chemokine related activities, and enzymatic, growth factor and cytokine related activities. Mechanism: This enrichment test demonstrates the involvement of specific genes in biological pathways related to cell adhesion, receptor binding and signaling, transcription regulatory region sequence-specific DNA binding, chemokine related activities, and enzymatic, growth factor and cytokine related pathways. ]0.9190
718text-davinci-003ontological_synopsisHALLMARK_ANDROGEN_RESPONSE-0[ The list of human genes demonstrated a significant enrichment of terms related to binding activities and activities involving enzymes, as well as some terms related to cell differentiation and cell cycle progression, suggesting that these genes are involved in diverse cellular processes such as transduction and transition of signals, physiological activities, and structural peptide modifications.\\n\\nMechanism: This list of human genes likely contribute to cellular events by participating in interactions with other molecules such as DNA or proteins, and by catalyzing biochemical modifications.\\n\\n][ These genes are involved in a variety of functions, including transporter activity, protein binding, protein kinase binding, receptor activity, transcription, cellular metabolism, DNA damage response, and cytoskeleton organization. The commonalities between the gene functions include transport activity, protein binding, DNA binding, hydrolase activity, metal ion binding, GTPase activity, receptor activity, and transcription. The underlying biological mechanism or pathway involves cell organization, signal transduction, cell adhesion, cell cycle progression, and differentiation. \\n\\nMechanism: Cell organization, signal transduction, cell adhesion, cell cycle progression, and differentiation. \\n\\n]0.90101
719text-davinci-003ontological_synopsisHALLMARK_ANDROGEN_RESPONSE-1[ This gene list provides evidence for the involvement of a variety of protein activities, including binding, kinase activity, transcription, receptor activity, and enzymatic activities, in a variety of metabolic, signaling, and structural processes. The mechanism underlying these processes is likely the regulation of various cellular proteins and pathways, such as phosphorylation, cyclin-dependent protein kinase activity, DNA binding and transcription, and postsynaptic organization.\\n\\nMechanism: Regulation of various cellular proteins and pathways, such as phosphorylation, cyclin-dependent protein kinase activity, DNA binding and transcription, and postsynaptic organization.\\n\\n][\\nSummary: The given list of genes includes proteins with DNA-binding, transcription, ubiquitin-binding, phosphatase, kinase, and other activities, which are associated with a wide range of cellular processes and pathways.\\n\\nMechanism: The molecules associated with the given genes function as protein regulators to control the expression of specific target genes and regulate intracellular processes.\\n\\n]0.93283
720text-davinci-003ontological_synopsisHALLMARK_ANGIOGENESIS-0[\\nThe list of genes is enriched with functions related to the extracellular matrix and cell-cell/cell-matrix adhesion. These functions include extracellular matrix structural constituent conferring compression resistance, collagen binding activity, integrin binding activity, molecular adaptor activity, identical protein binding activity, fibronectin binding activity, protein dimerization activity, heparan sulfate proteoglycan binding activity, cell-matrix adhesion, and regulation of cell-substrate adhesion. \\nMechanism: The underlying biological mechanism is focused on processes related to extracellular matrix organization, cell-matrix/cell-cell adhesion, and modulation of signaling pathways involved in development, immune response and homeostasis. \\n][COULD NOT PARSE]0.69743
721text-davinci-003ontological_synopsisHALLMARK_ANGIOGENESIS-1[\\nThis term enrichment test reveals that a majority of these genes are involved in cellular processes such as protein binding activity, signaling receptor binding activity, phospholipid binding activity, positive regulation of intracellular signal transduction, protease binding activity, and positive regulation of macromolecule metabolic process. A majority of these genes are also part of several cellular components, such as chromatin, the plasma membrane, the Golgi apparatus, the endoplasmic reticulum-Golgi intermediate compartment, and the extracellular matrix. \\n\\nMechanism:\\nThe enriched terms indicate that the genes are likely in involved in a variety of transmembrane and extracellular transport processes and in processes related to cellular signaling and metabolism. One possible underlying mechanism is that the genes interact with specific proteins and receptors to alter the phosphorylation of target proteins and regulate the downstream activities, such as the formation of the complex cellular structures and the metabolic activities of cells.\\n\\n][ \\n\\nSummary: Genes in this list are involved in a variety of functions, including collagen binding, fibroblast growth factor binding, phosphatase binding, integrin binding, calcium ion binding, signaling receptor binding and lipase activity. \\n\\nMechanism: These genes are likely involved in cellular processes and cellular component organization.\\n\\n]0.88716
722text-davinci-003ontological_synopsisHALLMARK_APICAL_JUNCTION-0[ The list of genes functions is found to be significantly enriched in the following terms: cell-cell adhesion, agonist binding activity, cytoplasmic matrix binding, protein homodimerization and signaling receptor binding, which are involved in cellular adhesive processes and signal transduction. \\nMechanism: The functions of these genes likely work in concert to mediate multiple adhesive processes, as well as signal transduction pathways. \\n][\\nSummary: The enriched term list includes cell adhesion, integrin binding, GTP binding activity, collagen binding activity, ATP binding activity, phospholipase binding activity, cell-matrix adhesion, cell adhesion molecule binding, and SH3 domain binding. \\nMechanism: The biological mechanism underlying the enrichment includes cell signalling pathways, actin filament binding and cell-to-cell adhesion, as well as cytoskeletal protein binding and receptor binding activities.\\n]0.8934
723text-davinci-003ontological_synopsisHALLMARK_APICAL_JUNCTION-1[ The list of genes are associated with a variety of functions, including binding activities (i.e. ion binding, cell adhesion molecule binding, identical protein binding, signaling receptor binding, etc.), catalytic activities (i.e. ATPase activity, GTPase activity, acetyl CoA oxidase activity, nucleotide-exchange activity, etc.), involvement in processes (i.e. T cell activation, cell-matrix adhesion, cell-cell adhesion, extracellular matrix formation, etc.), and structural roles (i.e. extracellular matrix structuring, ankyrin binding, etc.). The enriched terms associated with this set of genes are binding activities, catalytic activities, involvement in biological processes, and structural roles. \\n\\nMechanism: Most of the genes in the list are associated with catalytic activities that, when taken together, provide insights into the underlying biological mechanisms and pathways. These functionalities lead to different types of cell-cell and cell-matrix adhesion, structuring of extracellular matrix, signaling pathways, and many other cellular activities.\\n\\n][ This set of genes is associated with extracellular matrix structures, adhesion and binding activities, signal transduction/receptors, and cytoskeleton support/stabilization; all necessary for cell-cell and cell-matrix communication and coordination.\\n\\nMechanism: These genes likely contribute to a diverse set of signaling pathways, involved in cell-cell communication and between the cell and the extracellular environment, mediated by binding with substrate molecules, interactions of receptor molecules, and the formation and stabilization of mRNA structure.\\n\\n]0.91506
724text-davinci-003ontological_synopsisHALLMARK_APICAL_SURFACE-0[ \\n\\nSummary: The genes listed support a wide range of processes, including membrane and protein organization, protein modification and transport, endocytosis, signal transduction, and apoptosis. \\n\\nMechanism: These genes act at many levels, but the overall result is to help regulate the organization and modifications of protein structures and the movement of proteins (in trafficking and transport) across the membrane.\\n\\n][ Human genes involved in processes associated with cytosolic transports, membrane transports, and cellular extravasations, in addition to processes involved in the defense response and the positive regulation of macromolecule metabolism, appear to be enriched.\\n\\nMechanism: These processes impact the responses of cells in two ways: by allowing the transport of molecules between cells and by modulating the production of proteins which also modulate cellular activity. Furthermore, the signaling pathways regulated by these proteins impact a wide variety of downstream processes to regulate gene expression, cell motility, and cell adhesion.\\n\\n]0.91222
725text-davinci-003ontological_synopsisHALLMARK_APICAL_SURFACE-1[ The list of gene descriptions is related to pathways and processes related to cellular adhesion; protein folding and regulation; cytoplasmic ion homeostasis; and regulation of gene expression. The enriched terms that underlie all the genes and their functions include cell adhesion, protein folding and regulation, ion homeostasis, and gene expression regulation.\\n\\nMechanism: Cell adhesion and protein folding are essential processes that enable cells to interact with the extracellular environment and to form and maintain a functional structure. These processes are regulated by cell surface receptors that transmit signals to the cell and regulate gene expression, involved in the regulation of multiple cellular pathways. Ion homeostasis is also an important process, wherein cells maintain adequate balance of various ions in the cytoplasm and regulate various functions, such as cell differentiation, proliferation, and metabolism. Lastly, gene expression is regulated by a variety of transcription factors and signaling pathways, allowing cells to respond to external stimuli and adapt to changes in the cellular environment.\\n\\n][COULD NOT PARSE]0.681120
726text-davinci-003ontological_synopsisHALLMARK_APOPTOSIS-0[\\nSummary: This list of human genes is involved in numerous functions, including enzyme, protein and nucleic acid binding activities, transcription factor, cysteine-type endopeptidase and calcium ion binding activities, oxidation and NAD+ binding activities, among others.\\nThe enriched terms are DNA binding activity; protein binding activity; enzyme binding activity; cysteine-type endopeptidase activity; identical protein binding activity; signaling receptor binding activity; calcium ion binding activity; protein kinase binding activity; transcription factor activity; and BH3 domain binding activity. \\nMechanism: The underlying biological mechanism is likely related to the regulation of various cellular processes, including DNA replication, transcription, apoptosis and cell adhesion. \\n][\\nSummary: A set of human genes involved in a variety of biological functions, including binding activities and enzyme activities, are enriched for functions such as DNA binding activity, protein dimerization activity, protein binding activity, and enzyme activity.\\n\\nMechanism: These genes are likely to be involved in the control of cellular processes, such as cell proliferation, apoptosis, and signal transduction pathways.\\n\\n]0.94366
727text-davinci-003ontological_synopsisHALLMARK_APOPTOSIS-1[ The genes listed are primarily involved in apoptosis, cell signaling pathways, the response to UV, and immunological processes. Furthermore, the enriched terms found include calcium ion binding activity, protein binding activity, and identical protein binding activity.\\n\\nMechanism: These genes are likely involved in a variety of pathways, such as apoptosis, cell signaling, cellular response to UV, and immunological processes. Specifically, their activity is likely to be regulated by calcium ions, binding to specific proteins, as well as other molecules or chemical compounds. It is also possible that some of these genes are involved in regulating the transcription of certain genes.\\n\\n][ Genes in this list are involved in a variety of functions related to immune response, apoptosis, protein folding and expression, cytoskeletal structure and regulation, extracellular matrix structural constituents, transcription/translation regulation, angiogenesis/neovascularization, calcium/potassium ion binding and transport, cell signaling, and other cellular processes. Overrepresented terms include: protein binding activity; identical protein binding activity; enzyme binding activity; DNA-binding transcription factor activity; RNA polymerase II-specific transcriptional activity; cysteine-type endopeptidase activity; and cytokine receptor activity. \\n\\nMechanism: These genes are involved in a wide variety of complex functions that help form, maintain, and shape the immune response, cell structure and cytoskeletal integrity, cell signaling pathways, and inflammatory processes. They work by binding to and regulating a variety of molecules, hormones, and proteins throughout the body and at the cellular level.\\n\\n]0.93334
728text-davinci-003ontological_synopsisHALLMARK_BILE_ACID_METABOLISM-0[\\n\\n\\nSummary: Genes in this list are primarily involved in metabolic and transporter activities, signaling activities, and protein binding activities.\\n\\nMechanism: The genes primarily have roles in transferring small molecules across membrane boundaries, binding small molecules, and regulating processes such as metabolism and protein interactions.\\n\\n][ This analysis shows a statistically significant over-representation of genes related to ATP processing/binding activities, cholesterol binding, transmembrane transport, protein heterodimerization, DNA binding, and enzyme/oxidoreductase activity. Mechanism: The underlying biological mechanism of these processes likely involves the maintenance of ATP and cholesterol levels and other metabolic processes, as well as regulation of transcription and cellular signaling via domains such as the SH2 domain or through DNA binding or various ligase activities. ]0.90208
729text-davinci-003ontological_synopsisHALLMARK_BILE_ACID_METABOLISM-1[ \\nSummary: The listed genes are part of various metabolic pathways, involved in a variety of functions, including DNA binding, ATP hydrolysis, protein homodimerization, peptidase activity, and other enzyme binding and regulatory activities. \\nMechanism: Enzymatic activity and protein binding are key components of the pathways involved, which help to catalyze, catalyze and regulate further metabolic activity. \\n][COULD NOT PARSE]0.69397
730text-davinci-003ontological_synopsisHALLMARK_CHOLESTEROL_HOMEOSTASIS-0[ \\nSummary: This term enrichment test reveals an overlap of gene functions related to lipid metabolism, cholesterol homeostasis, and protein regulation.\\nMechanism: The terms enriched suggest that these genes help to maintain proper levels of cholesterol, regulate lipid metabolism and synthesis, and regulate protein expression, localization, and response. \\n][\\n\\nSummary: These human genes are associated with processes relating to cholesterol biosynthesis, cell adhesion, cell structure and organization, signaling, and apoptosis.\\n\\nMechanism: These genes likely interact with each other to regulate cholesterol biosynthesis, cell adhesion and organization, signaling pathways and responses to stress, and apoptosis.\\n\\n]0.860
731text-davinci-003ontological_synopsisHALLMARK_CHOLESTEROL_HOMEOSTASIS-1[\\n\\nSummary: This list includes genes that are involved in cholesterol biosynthesis, regarding protein binding, transcription, regulation of gene expression, and other biochemical processes. \\n\\nMechanism: These genes are mainly involved in cholesterol homeostasis, transcription and regulation of gene expression, and other essential biochemical processes.\\n\\n][ The list of genes given is largely implicated in cholesterol and lipid biosynthetic processes. Additionally, a large number of genes are involved in the regulation of transcription, apoptosis, protein stability and interaction, and cell adhesion/migration. \\nMechanism: The overall biological mechanism is centered around the maintenance of cholesterol/lipid levels and transport, as well as regulation of key cellular processes including transcription, apoptosis, and cell adhesion/migration.\\n]0.93139
732text-davinci-003ontological_synopsisHALLMARK_COAGULATION-0[COULD NOT PARSE][\\n\\nSummary: The human genes in this list are involved in a variety of functions related to proteins, such as binding, disulfide isomerase activity, phosphoprotein binding, enzyme binding, and calcium ion binding.\\n\\nMechanism: These genes encode for enzymes involved in protein binding activities, such as heparin binding, integrin binding, collagen binding, and phospholipid binding. These activities are necessary for biological processes such as cell adhesion, cell-matrix adhesion, signaling receptor binding, blood coagulation, fusion, apoptotic signal transduction, and regulation of protein-coding gene expression.\\n\\n]0.70605
733text-davinci-003ontological_synopsisHALLMARK_COAGULATION-1[ The statistically over-representeted gene functions common to this list of genes have to do with protein and domain binding, domain specific and disordered domain specific binding, enzyme and peptidase activity, and cytokine and signalling receptor binding. Key processes that seem to involve this gene set are cell adhesion, proteolysis, regulation of blood coagulation, response to iron and UV-A, and the regulation of cell adhesion mediated by integrin. \\nMechanism: Some of these genes may be involved in the same biological pathways, such as pathways for protein homooligomerization, enzyme/peptidase activity, proteoglycan/fibrinogen binding, heme binding, and domain specific binding activity.\\n][COULD NOT PARSE]0.69686
734text-davinci-003ontological_synopsisHALLMARK_COMPLEMENT-0[COULD NOT PARSE][ \\nSummary: Genes in this list are primarily involved in regulation of protein activity, genetic transcription, cell signaling, and metabolism.\\nMechanism: These genes primarily influence protein activity and metabolism through complex interactions with other proteins and the environment. They interact in ways which affect protein activity, cell signaling, and possibly genetic transcription.\\n]0.68378
735text-davinci-003ontological_synopsisHALLMARK_COMPLEMENT-1[ These genes are primarily involved in binding activities and regulation of molecular functions related to cell signalling, such as enzyme binding, deubiquitinase activity, cysteine-type endopeptidase activity, receptor binding, protein kinase binding, SH2 domain binding activity, phosphatidylinositol phospholipase C activity, GTPase activity, and metalloendopeptidase activity.\\n\\nMechanism: The proteins encoded by these genes are involved in the regulation of cell signalling pathways, including those related to apoptosis, interleukin-6, growth factor activity, receptor binding, phospholipid binding, and transcription activator activity.\\n\\n][\\n\\nSummary: The genes in this list are involved in many cellular activities, including DNA-binding, phospholipid binding, protein binding, binding to receptors, enzyme binding and inhibitor activities, GTPase activities, metal ion binding activity, and other protein activities.\\n\\nMechanism: These genes are likely to be involved in a wide range of cellular pathways, including signaling, transcription regulation, DNA repair, cell death, immune response and other cellular processes.\\n\\n]0.93161
736text-davinci-003ontological_synopsisHALLMARK_DNA_REPAIR-0[COULD NOT PARSE\\nHypothesis: The underlying biological mechanism of these genes is likely related to transcription regulation of gene expression, including DNA binding and DNA polymerase activity, as well as the formation of protein dimers needed for transcription.][\\nSummary: This set of human genes are involved in many processes, including DNA and RNA binding activity, enzyme binding activity, protein binding activity, calcium ion binding activity, but primarily DNA damage and repair processes.\\nMechanism: These genes are involved in DNA damage and repair processes, whereby they bind to various sets of molecules and macromolecules, and catalyze/carry out downstream pathways such as DNA repair, familial clipping, etc.\\n]0.86195
737text-davinci-003ontological_synopsisHALLMARK_DNA_REPAIR-1[\\nSummary: The list of genes are involved in a diverse range of functions, including DNA binding activities, ATP activities, RNA binding activities, transcription activities, enzyme binding activities, and protein homodimerization activities.\\nCommonalities in function include DNA binding activities, RNA binding activities, transcription activities, enzyme binding activities and protein homodimerization activities.\\nMechanism: These commonalities of function reflect the various roles in nucleic acid metabolism and structural transactions related to transcription and replication in the cell.\\n][ The provided list of genes is involved in a variety of cellular functions, including DNA binding activity, ATP hydrolysis activity, RNA binding activity, enzyme binding activity, protein binding activity, DNA-directed DNA polymerase activity, nuclease activity, and mRNA regulatory element binding. The enriched terms that describe their common functions are DNA binding activity, enzyme binding activity, ATP hydrolysis activity, RNA binding activity, protein binding activity, DNA-directed DNA polymerase activity, nuclease activity and mRNA regulatory element binding.\\n\\nMechanism: The genes in the list likely contribute to the regulation of pathways that involve DNA, RNA, proteins and enzyme activities. These activities may be involved in various metabolic processes and regulatory networks within the cell, such as DNA repair, gene expression, nucleic acid metabolism, and cell differentiation.\\n\\n]0.94309
738text-davinci-003ontological_synopsisHALLMARK_E2F_TARGETS-0[ Genes in this list are predominantly related to functions involved in the cell cycle, including DNA replication, transcriptional and post-transcriptional regulation, chromatin binding, and mitosis. A number of the genes are also associated with processes related to nuclear transport and pore complex assembly.\\n\\nMechanism: This cluster of genes is likely related to multiple biological mechanisms involved in cell cycle progression, including DNA replication and transcriptional regulation, chromatin binding and modification, RNA processing and stability, nuclear transport, and mitosis.\\n\\n][ This set of genes appears to be involved in several different processes related to DNA, chromatin, and cell division, including chromatin binding activity, DNA replication and repair, transcription, histone modification, nuclear import/export, DNA/RNA binding, and protein-macromolecule binding. A majority of these genes appear to be involved in the regulation and maintenance of the cell cycle and the expression of genes through their interactions with proteins, chromatin, and nucleic acids.\\n\\nMechanism: The genes in this list are likely involved the regulation of genetic expression by influencing the properties of chromatin, and the structure and function of nucleic acids and proteins. These interactions may be mediated by histone modification and the binding of proteins, DNA, and RNA. Furthermore, DNA and RNA modification, as well as DNA repair, may also factor in to the gene's functions.\\n\\n]0.94313
739text-davinci-003ontological_synopsisHALLMARK_E2F_TARGETS-1[\\nSummary: This list of genes enables various functions in regards to DNA binding, protein binding, histone binding, ATP and enzyme binding, as well as DNA replication, DNA methylation and regulation of chromosome segregation.\\nMechanism: These genes allow for the regulation of several processes essential for cell growth, transcription, and regulation through binding of and interaction with various molecules.\\n][ The list of genes consists of proteins that are involved in a wide range of cellular activities, including DNA binding, transcriptional regulation, cell cycle progression, DNA replication, chromatin modification and repair, mitosis, and the remodeling of nuclear pore complexes. These proteins commonly cooperate in the formation of protein complexes and in the assembly of large macromolecular machines. They are involved in several biological pathways, such as DNA damage repair, cell cycle regulation, gene transcription, and nucleocytoplasmic transport.\\n\\nMechanism: This list of genes, together with their respective functions, implicates a wide variety of biological mechanisms. When viewed as a group, these proteins act together to coordinate fundamental cellular processes, including cell growth and repair, gene expression, and cell migration. Additionally, these processes are coordinated through the assembly of macromolecular machines, enabling the formation of large, protein complexes and facilitating interactions between different molecules.\\n\\n]0.91649
740text-davinci-003ontological_synopsisHALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0[\\nSummary: There are a number of genes with functions related to extracellular matrix structural components, cellular adhesion and protein binding.\\nMechanism: The range of genes suggests that these functions are related to various pathways that involve receptor and ligand interactions, protein domain binding activities, signaling processes and the structural components of the extracellular matrix.\\n][\\nSummary: Genes enriched for mechanisms involved in protein binding, calcium ion binding, cell adhesion molecules, and extracellular matrix structure.\\nMechanism: Cell adhesion molecules, interactions with signaling receptors or other proteins, and extracellular matrix structuring.\\n]0.94118
741text-davinci-003ontological_synopsisHALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1[\\nSummary: The list of genes are involved in a variety of cell and matrix structural activities, including binding activities, metal binding and metal ion binding, enzyme activities, receptors and chemokine activities, as well as DNA-binding and transcription activities.\\n\\nMechanism: The genes in the list work together synergistically to mediate essential cell processes such as cell adhesion, growth, communication, and cell-matrix interaction.\\n\\n][\\nSummary: The genes in this list are related to extracellular matrix structural constituents, collagen binding activity, cell adhesion molecules, DNA binding activity, GTP binding activity, and protein homodimerization activity.\\nMechanism: It appears that these genes are involved in the structural formation and maintenance of cells, particularly in the extracellular matrix, energy metabolism, and signal transduction pathways.\\n]0.9417
742text-davinci-003ontological_synopsisHALLMARK_ESTROGEN_RESPONSE_EARLY-0[ Genes involved in this list generally enable binding, transport, enzyme, and adhesion activities, and are involved in process such as intracellular signaling, transcription, and neuronal development.\\n\\nMechanism: These genes are involved in multiple pathways that involve the binding, transport, and regulation of signals related to cellular physiology, growth, and development.\\n\\n][\\n\\nSummary: The listed genes display a variety of functions related to DNA binding and/or regulation, protein binding/regulation, enzymes, transmembrane or ion transport activity, and mRNA or protein expression. \\n\\nMechanism: The underlying biological mechanism for these genes is likely related to their roles in regulating transcription, cell adhesion and signaling, gene expression, or metabolic pathways. \\n\\n]0.9229
743text-davinci-003ontological_synopsisHALLMARK_ESTROGEN_RESPONSE_EARLY-1[ Our term enrichment test analysis has identified that these human genes are mainly involved in binding activities, including DNA binding, ATPase binding, and protein binding, as well as various enzymatic activities, such as phosphatase activity, dehydrogenase activity, and adenylate cyclase activity. Additionally, the genes are related to transmembrane transport, transcriptional regulation, cell adhesion, and apoptosis. \\n\\nMechanism: This term enrichment test identified several biological functions and activities related to DNA and protein binding, transcriptional regulation, transport, and apoptosis, likely playing important roles in cellular processes and development.\\n\\n][\\nThis list of human genes is enriched for multiple functions related to DNA binding and transcription factors, RNA binding, protein binding/dimerization, transmembrane transporters, calcium ion binding, enzyme binding, and GTPase activities. The underlying biological mechanism likely involve signal transduction, membrane transport, and protein activities related to chromatin and gene expression.\\n\\nMechanism: Signal transduction, membrane transport, and protein activities related to chromatin and gene expression. \\n\\n]0.93161
744text-davinci-003ontological_synopsisHALLMARK_ESTROGEN_RESPONSE_LATE-0[\\nThis analysis of the given human gene list reveals a pattern of enrichment for molecules and processes associated with protein binding activities, DNA- and RNA-binding, domain binding, carbohydrates binding, and enzyme and ligand binding activities. In addition, several genes are predicted to be involved in transmembrane transport activities, sequencing and structural protein interactions, transcription factor activities, and cellular adhesion. Various proteins act as modulators of these activities, and cofactors, such as calcium ions, play important roles.\\n\\nMechanism: This set of genes are likely involved in a variety of protein-protein and DNA/RNA interactions, which are essential for regulation of gene expression and protein activity. The cell membrane acts as a barrier between different cellular environments, allowing the genes to mediate transport between the intracellular and extracellular compartments, as well as a platform for docking proteins to interact with ligands, such as hormones and growth factors. The set of genes likely form part of a larger interconnected protein-protein interactome and temporal regulatory pathways which regulate cell function.\\n\\n][\\nSummary: Genes involved in cell adhesion, transport, metabolic processes and transcription\\nMechanism: Cell surface activities, metabolic processes, and gene expression regulations \\n]0.901001
745text-davinci-003ontological_synopsisHALLMARK_ESTROGEN_RESPONSE_LATE-1[ We have identified a large set of genes that are involved in a variety of processes, including binding, transcriptional regulation, transport, and enzymatic activities. These genes are enriched in the following terms: DNA-binding; transcription activator activity; protein binding; membrane transporter activity; hydrolase activity; phosphorylation; and ligand-mediated activities. \\n\\nMechanism: Many of these identified enriched terms suggest involvement in complex biochemical pathways in order to facilitate cell behavior and other processes in the body at a molecular level. This likely occurs through a combination of transcriptional regulation, binding of proteins and ligands, and enzymatic activities. \\n\\n][ These genes are involved in a variety of functions related to protein regulation and metabolism such as transcription factor binding, enzyme binding, cell adhesion, and ligand-gated ion transporter activity. Mechanism: The function of these genes is likely related to either a transcriptional regulatory network, signaling cascade, or metabolic pathway. ]0.91356
746text-davinci-003ontological_synopsisHALLMARK_FATTY_ACID_METABOLISM-0[ \\nSummary: This list of genes is mainly involved in fatty acid, lipid, and carbohydrate metabolism, DNA binding, RNA binding, and protein homodimerization. \\nMechanism: The genes in this list work to regulate metabolic pathways, transcription and protein complexes.\\n][\\nSummary: Genes appear to be primarily involved in the binding, transport, and oxidation of molecules.\\nMechanism: These genes are likely involved in a variety of molecular processes including transportation, modulation, and redox reactions.\\n]0.8824
747text-davinci-003ontological_synopsisHALLMARK_FATTY_ACID_METABOLISM-1[ This gene list contains enzymes involved in fatty acid and lipidmetabolism, metabolism of oxygenated and carbonated compounds, oxidoreduction, electron transfer, and DNA related activities such as DNA binding, DNA nuclease activity, RNA binding, and chromatin binding. \\nMechanism: These genes enable intra- and inter-cellular metabolic pathways and communication, as well as provide protective responses to external stimuli, by catalyzing the conversion of compounds and regulating DNA expression.\\nHypothesis: This set of activities suggest a mechanism of maintaining cellular homeostasis, which involves reactive oxygen species management, modifying hormonal, energy, and nutrient levels, and respoding to external stress.\\n][ \\nSummary: A diverse group of genes involved in various enzymes and binding activities related to cellular responses, metabolism, and DNA regulation.\\nMechanism: Various enzymes and binding activities related to cellular responses, metabolism, and DNA regulation.\\n]0.89462
748text-davinci-003ontological_synopsisHALLMARK_G2M_CHECKPOINT-0[ The gene descriptions indicate that many of these genes are involved in DNA or transcription binding, binding of different molecules or materials (chromatin, metal ions, histone deacetylase, etc.), protein binding activities, enzyme binding activities, and GTPase activities.\\n\\nMechanism: These genes appear to be involved in a variety of cellular functions, including transcriptional regulation, DNA replication, DNA damage repair, protein modification, gene expression and cell cycle control. The common functions may be related to molecular pathways that regulate these activities. \\n\\n][ \\nSummary: The list of genes highlighted have common functions related to DNA and RNA binding, catalysis and metabolic activities, chromatin binding, and transcription and translation-associated activities.\\nMechanism: The genes in this list are involved in a variety of mechanisms; DNA and RNA binding, transcription and translation, catalysis, chromatin binding, metabolic activities, and protein folding and dimerization of proteins. \\n]0.92150
749text-davinci-003ontological_synopsisHALLMARK_G2M_CHECKPOINT-1[\\n\\nSummary: over half of the genes in this list are involved in protein binding, DNA binding and/or transcription, and many others in activities related to or downstream of those activities.\\n\\nMechanism: The proteins encoded by these genes are likely involved in regulating gene expression at the molecular level, through interacting with DNA, proteins, and other elements involved in transcription.\\n\\n][ This list of genes are involved in wide range of functions related to protein binding, DNA binding, transcription factors, telomerase, RNA binding and DNA replication. They appear to be involved in a variety of processes related to cell cycle regulation, chromatin binding, gene expression, protein folding and regulation of chromosome structure.\\n\\nMechanism: The genes in this list are likely involved in a complex network of molecular processes related to DNA replication, transcription and cell cycle control. They appear to be involved in many processes that are necessary for cells to grow and divide, including transcription and translation, DNA replication, chromatin binding and protein folding. In particular, they likely contribute to gene expression, protein modification, DNA damage sensing, and cell cycle regulation.\\n\\n]0.93433
750text-davinci-003ontological_synopsisHALLMARK_GLYCOLYSIS-0[ Human genes in the given list are involved in a variety of functions, including nucleic acid and proteic binding, metabolic activities such as phosphorylation and oxidation-reduction, carbohydrate metabolism, and various types of cytokine and growth factor activities. The underlying biological mechanism involves increased metabolic activity and physiological signalling pathways, leading to increased protein synthesis and activity, increased cell growth, migration, differentiation and repair.\\n\\n][COULD NOT PARSE]0.69484
751text-davinci-003ontological_synopsisHALLMARK_GLYCOLYSIS-1[ \\nSummary: This list of genes has functions related to metabolism, gene regulation, cell signalling, and protein binding activities.\\nMechanism: The list of genes are likely involved in pathways related to cell signalling, metabolism, intracellular communication, and gene regulation.\\n][ \\nSummary: The genes demonstrate a variety of functions including enzyme binding activity, identical protein binding activity, and DNA binding activity.\\nMechanism: The genes described are involved in diverse metabolic activities and structural components. \\n]0.9027
752text-davinci-003ontological_synopsisHALLMARK_HEDGEHOG_SIGNALING-0[ The genes highlighted in this list are largely involved in cellular organization and processes including cell adhesion, vascularization, neurotransmitter receptor internalization, signal transduction, and enzyme binding. Some of the genes, such as GFIA and SHH, are also involved in embryonic development and organogenesis. Common terms enriched from these genes include: cell adhesion; signal transduction; epithelial-mesenchymal interaction; receptor-mediated endocytosis; angiogenesis; and neural tube closure.\\n\\nMechanism: These genes largely interact with each other in a variety of ways to control crucial cellular pathways and processes in the body's tissues, organs, and systems. They interplay to control processes such as cell adhesion, vascularization, signal transduction, and enzyme binding. Some of the genes are involved in the formation and maintenance of the structures of the body's organs and tissues, while others are involved in developing the connections between cells and transmitting signals within them.\\n\\n][ The list of genes provide evidence that many of these genes are involved in processes related to development, including cell adhesion, growth, angiogenesis, and nerve cell differentiation. These processes are related to the formation of structures that are integral to the healthy function of organisms, such as blood vessels and organs. Common terms include: protein/lipid binding activity; DNA-binding transcription factor activity; regulation of gene expression; regulation of protein metabolism; and positive/negative regulation of cellular component organization. Mechanism: While the precise mechanism is unknown, it is likely that these genes are involved in the regulation of transcription, signaling pathways related to cell adhesion, metabolism, and growth, as well as the formation of complex structures necessary for healthy functioning organisms such as organs and neural networks.\\n\\n]0.94133
753text-davinci-003ontological_synopsisHALLMARK_HEDGEHOG_SIGNALING-1[ \\n\\nSummary: This gene list encompasses genes involved in various functions and processes, including cell adhesion and migration, regulation of transcription and DNA-templated transcription, negative regulation of apoptosis, cell surface receptor-related activities, cell differentiation, angiogenesis, canonical Wnt signaling pathways, and protein phosphorylation.\\n\\nMechanism: This gene list likely indicates the presence of various pathways, including the NF-kB pathway, cytoskeletal reorganization and receptor signaling pathways, integrin and cell adhesion molecule signaling pathways, and the Wnt/PCP pathwayn and sonic hedgehog pathway.\\n\\n][\\n\\nSummary: Genes encode for activities that enable functions related to cell adhesion, transcriptional and post-transcriptional regulation, cell migration, signaling and receptor activity, and transcriptional repression.\\n\\nMechanism: This likely represents a collection of diverse pathways related to cellular activity and development, likely involving both transcriptional and post-transcriptional processes.\\n\\n]0.93233
754text-davinci-003ontological_synopsisHALLMARK_HEME_METABOLISM-0[ The majority of these human genes enable binding activity involving DNA and RNA, as well as being involved in the regulation of transcription and translation. Moreover, some genes are involved in the transport of substrates across the cell membrane. \\n\\nMechanism: The list of genes is indicative of various transcription-regulation mechanisms and membrane transport processes, including DNA packing, histone demethylation, transcription factor activity, and ion transport. \\n\\n][\\nSummary: This list of genes are involved in various functions such as DNA binding, RNA binding, enzyme binding, protein kinase binding, protein phosphatase binding, protein homodimerization, tissue morphogenesis, and protein phosphorylation.\\n\\nMechanism: The underlying biological mechanism for the enriched terms is likely to involve transcription regulation and signal transduction.\\n\\n]0.8989
755text-davinci-003ontological_synopsisHALLMARK_HEME_METABOLISM-1[ \\n\\nSummary: The list of genes are related to many major and essential functions in the cell, ranging from transcription of DNA, binding to receptors, transportation of ions and other molecules, and overall regulation activities. \\nMechanism: The mechanism underlying this term enrichment is that numerous functions or activities require multiple pathways, proteins, and activities, thus having multiple target genes involved.\\n][\\n\\nSummary: This list of genes are involved in diverse cellular functions such as DNA binding, protein binding and phosphorylation, as well as the transportation of ions and small molecules across membrane domains.\\n\\nMechanism: Many of the genes encode proteins involved in enzyme and transporter activity, contributing to metabolic, vesicular and cytoskeletal pathways.\\n\\n]0.9255
756text-davinci-003ontological_synopsisHALLMARK_HYPOXIA-0[\\nSummary: Several genes are involved in structural components, binding activities, and enzyme activities.\\nMechanism: Genes are associated with a variety of activities related to binding, activity functions, structural elements and enzyme regulation.\\n][COULD NOT PARSE]0.68235
757text-davinci-003ontological_synopsisHALLMARK_HYPOXIA-1[\\n\\nSummary: The list of genes describes a wide range of molecular functions related to signaling, attachment, and metabolic pathways.\\n\\nMechanism: The underlying biological mechanism and pathways describe the various activities of these genes and how they are involved in cell metamorphosis, growth and development, and immunity and defense.\\n\\n][ These genes are predominantly involved in processes related to DNA-binding transcription activity (activator and repressor), protein binding activity, protein kinase binding activity and activity, enzyme binding activity, regulation of cell proliferation/growth, ligand-activated transcription, and intracellular processes.\\n\\nMechanism: The enriched terms suggest a shared mechanism of gene expression and regulation involving binding, enzymatic reactions and proliferation/growth processes. These processes all coordinate to regulate various biological activities. \\n\\n]0.87227
758text-davinci-003ontological_synopsisHALLMARK_IL2_STAT5_SIGNALING-0[ The majority of the genes listed are associated with cell signaling, regulation and structural roles such as ligand binding, enzyme binding, and receptor binding, as well as associated functions such as DNA and RNA binding, protein dimerization, and transcription activity and regulation. \\n\\nMechanism: These genes are known to be involved in many different parts of the cellular functioning, including cell communication and receptor recognition and response, enzyme and ligand binding, DNA/RNA, and transcription. \\n\\n][\\n\\nSummary: Genes enriched in binding activities such as GTPase, DNA, protein, ligand, and BH3 domain, as well as in activities such as phosphatidylinositol and hydrolase, involved in pathways related to protein regulation, receptor signaling, and metabolism.\\n\\nMechanism: It is likely that these genes are involved in pathways related to modulating protein expression, receptor signaling, and metabolic processes such as cellular respiration, synthesis, and metabolism of fatty acids and nucleotides.\\n\\n]0.9017
759text-davinci-003ontological_synopsisHALLMARK_IL2_STAT5_SIGNALING-1[ The analysis of the given list of genes reveals that they are primarily involved in binding activities, such as DNA-binding, receptor binding and ligand-activated transcription activities. Several genes are also involved in enzyme activity, such as proteases and kinases. All of the genes are involved in several processes, such as cellular and apoptotic responses, neuronal activity and tissue development. \\nMechanism: The binding activity of the genes may be involved in protein-protein interaction, signal transduction pathways, transcriptional control and modulation of protein stability. Enzyme activities are involved in the post-translational modifications of proteins, metabolic pathways and protein degradation.\\n\\n][ \\n\\nSummary: Genes presented encoded for a range of activities related to the regulation of immunological and signaling processes, binding activities, transcription activator activities, and endopeptidase activities.\\n\\nMechanism: The genes potentially display a range of activities related to immunological and signaling pathways as well as binding, transcription activator, and endopeptidase activities.\\n\\n]0.91319
760text-davinci-003ontological_synopsisHALLMARK_IL6_JAK_STAT3_SIGNALING-0[\\nSeveral genes among the list are involved in receptor activity and binding activities related to cytokines, such as interleukin-1, interleukin-7, interleukin-9, interleukin-10, and interleukin-12 receptors, among others. Many of the genes are also involved in the binding of other molecules, such as growth factors, lipoproteins, peptides and proteins, as well as with kinase binding activities, and ATP and DNA-binding activities. In addition, several of the genes appear to be associated with immune responses, such as antimicrobial humoral immune response, defense response and cell surface receptor signaling pathway.\\n\\nMechanism: It is likely that many of the genes on the list serve as key mediators of receptor signaling pathways, as well as protein-protein and nucleic acid-protein interaction. These activities may be involved in the regulation of important cellular processes such as cell surface receptor signaling, immune response, apoptosis, and modulation of the activity of certain kinases.\\n\\n][ \\nSummary: This list of genes is involved in cytokine binding and receptor activities, protein binding, and kinase and phosphatase activities. \\n\\nMechanism: These gene functions are involved in signal transduction pathways affecting cell growth, development, and differentiation as well as immune responses and inflammation.\\n\\n]0.94682
761text-davinci-003ontological_synopsisHALLMARK_IL6_JAK_STAT3_SIGNALING-1[ The genes identified in this list are involved in a variety of signaling activities, mainly cytokine receptor activity, CXCR chemokine receptor binding activity, and interleukin-binding activities. Furthermore, these genes are involved in processes such as defense response, negative regulation of macromolecule metabolic process, and positive regulation of protein metabolic process. \\n\\nMechanism: The genes are related to mechanisms that involve the recognition of extracellular ligands, such as cytokines, chemokines, growth factors, and antigen by the cell surface receptors in order to regulate and coordinate cell responses.\\n\\n][\\n\\nSummary: The genes listed are involved in a variety of processes related to cytokine binding activity, cytokine receptor activity, growth factor activity, cell adhesion molecule binding activity, chemokine (C-X3-C) binding activity, and defense response.\\n\\nMechanism: It appears that these genes are involved in coordinating processes related to the immune system, with cytokines acting as signaling molecules and the other genes acting as receptors or binding agents.\\n\\n]0.95161
762text-davinci-003ontological_synopsisHALLMARK_INFLAMMATORY_RESPONSE-0[ The genes in the list are involved in a variety of activities, including binding activities of diverse ligands (e.g. ATP, G protein-coupled receptors, etc.), receptor activities (e.g. for interleukin and other cytokines), transcription activator activities, and presence in various cellular organelles (e.g. plasmic membrane, nucleus). Common terms such as protein binding activity, cytokine activity, G protein-coupled receptor activity, and DNA-binding transcription activity were found to be enriched.\\n\\nMechanism: The genes in this list are involved in several cell signaling pathways, including but not limited to, cytokine signaling, signal transduction, G protein-coupled receptors, and transcription factors.\\n\\n][\\nThis list of genes is enriched for terms related to signal transduction pathways and pathways related to immunoregulation. Specifically, terms including G protein-coupled receptor activity, cytokine activity, DNA-binding transcription factor activity, ion channel activity, and receptor binding activity were found to be statistically overrepresented in the list.\\n\\nMechanism: The underlying mechanism is likely related to the diverse functions of these genes in signal transduction pathways and pathways related to immunoregulation. This includes G protein-coupled receptor activity, cytokine activity, DNA-binding transcription factor activity, ion channel activity, and receptor binding activity that helps modulate the signal transduction pathways.\\n\\n]0.9436
763text-davinci-003ontological_synopsisHALLMARK_INFLAMMATORY_RESPONSE-1[\\n6 groups of functions were enriched - receptor activities, binding activities, enzyme activities, growth factor activities, molecule/ion transporters and transcription factor activities. \\nMechanism: These enriched terms point to pathways that are involved in cell growth, development, communication, and signal transduction. \\n][\\n\\nSummary: The genes in the list are involved in a variety of cellular processes, including cell adhesion and binding, molecular functions, G protein-coupled receptor activity, ion transport and transmembrane transporter activity, signaling receptor binding, transcription factor activity, and several others.\\n\\nMechanism: The genes in the list are involved in a variety of biological mechanisms, such as pathways for cell communication, inflammation, and response to external signals.\\n\\n]0.90158
764text-davinci-003ontological_synopsisHALLMARK_INTERFERON_ALPHA_RESPONSE-0[\\nThe list of genes includes those involved in processes such as defense response to other organism, response to virus, regulation of proteasomal ubiquitin-dependent protein catabolic process, and regulation of transcription. The commonalities in gene function include DNA-binding activity, RNA binding activity, metal ion binding activity, identical protein binding activity and protein homodimerization activity. These genes are enriched with terms such as \"signaling receptor binding activity,\" \"transcription coactivator activity,\" and \"regulation of transcription.\"\\n\\nMechanism: The underlying biological mechanism or pathway of these genes is related to processes like macrophage activation, innate and adaptive immune response, antiviral response, and transcriptional regulation. These genes are involved in signaling pathways related to specific pathogens or environmental cues, or the maintanance of normal gene expression. These processes are essential for the body to respond to environmental changes and maintain homeostasis. \\n\\n][ Upon performing the term enrichment test on these human genes, we find that the majority of them are involved in immune response processes, such as cellular response to cytokine stimulus, defense response to second organism, and infection response. Furthermore, many of the genes are linked to transcription activator activity, DNA and RNA binding activity, as well as other ligase/binding activities. The majority of the genes are located in the cytoplasm, Golgi apparatus, and other cellular components, suggesting a role in regulating the functional components of the cell.\\n\\nMechanism: The enriched terms suggest that these genes are involved in the mechanisms of transcription, translation, and protein modification, all of which play key roles in immune response. The transcription activity links to gene expression to regulate the expression of proteins involved in the immune response, while the DNA and RNA binding activities are involved in the transcription and translation processes. The ligases and binding activities would be critical for binding and changing proteins and other molecules to prevent infection and regulate the body's response.\\n\\n]0.92121
765text-davinci-003ontological_synopsisHALLMARK_INTERFERON_ALPHA_RESPONSE-1[ Cell-mediated immunity is indicated by the genes analyzed, which were found to involve in activities such as DNA-binding transcription activator activity; CCR chemokine receptor binding activity; cytokine activity; RNA-binding activity; and ubiquitin protein ligase activity. Several enriched terms were identified, including defense response to other organism; immune response; viral entry into host cell; ISG15-protein conjugation; antigen processing; and cytokine-mediated signaling pathway. \\nMechanism: The gene functions are likely to be involved in biological processes related to cell-mediated immunity, such as activation of macrophages and other cells of the immune system (T cells, natural killer cells), regulation of antigen processing and presentation and cytokine-mediated signaling pathways, and regulation of the immune and inflammatory responses.\\n][ \\n\\nSummary: The genes identified show a wide range of cellular processes involved in immunity, transcription regulation, RNA metabolism, and protein activity modification. \\nMechanism: The genes are involved in a variety of processes likely related to regulation of immunity and protein activity, likely through regulation of transcription, RNA modifications, and ubiquitination.\\n]0.90486
766text-davinci-003ontological_synopsisHALLMARK_INTERFERON_GAMMA_RESPONSE-0[COULD NOT PARSE][ \\nSummary: These genes are involved in a variety of processes to enable activities such as enzyme binding, promoter and transcriptional regulation, ATP hydrolysis, protein homodimerization, kinase regulation, protein dimerization, and several other functions. \\n]0.70246
767text-davinci-003ontological_synopsisHALLMARK_INTERFERON_GAMMA_RESPONSE-1[ The genes listed in the summaries are mainly involved in functions related to binding activities, enzyme activities, transcription factor activities, protein activities, and signaling receptor activities. The data suggests that these genes play an important role in cellular pathways and processes such as cellular immune response, cytokine-mediated signaling, apoptotic signaling, DNA binding and transcription, and RNA binding and transcription. The commonalities in their function shared by most of these genes are binding activity; enzyme activity; protein activity; and transcription factor activity.\\n\\nMechanism: These genes are likely to be involved in various regulatory pathways regulating cellular functions. The binding activities associated with them suggest their role in ligand-receptor interactions and communication between cells, as well as their role in cell-to-cell signaling. Additionally, their enzyme and protein activities suggest that they are involved in enzymatic reactions, signaling cascades, and post-translational modifications such as histone acetylation that regulate gene expression. Lastly, their involvement in DNA binding and transcription, as well as RNA binding and transcription suggest their roles in controlling gene expression and the synthesis of key proteins in various cellular pathways.\\n\\n][\\n\\nSummary: This set of genes provides a wide range of functions, from ATP hydrolysis and enzyme binding activity, to DNA binding activities, GTP binding activity, and peptide antigen binding activity.\\n\\nMechanism: This set of genes links many different functions at the cellular level, together with serine-type endopeptidase activity, DNA-binding transcription activity and activities related to cytokines, chemokines and signaling pathways. The patterns suggest a broad underlying mechanism involving the mediation of cell-signaling pathways, DNA-binding activity, involvement in apoptosis and other cellular functions.\\n\\n]0.91712
768text-davinci-003ontological_synopsisHALLMARK_KRAS_SIGNALING_DN-0[\\nSummary: A number of genes have been studied, mostly involving functions related to protein activity, transcription, and regulation activity.\\nMechanism: These genes seem to act in concert with each other, involving protein binding activity and transmembrane activity, suggesting a potential for processes related to membrane-based signaling and receptor binding or trafficking.\\n][\\nSummary: Genes associated with this list are involved in multiple signaling pathways and binding activities related to cell structure, adhesion, calcium ion and potassium channeling, and protein folding/binding/kinase activities.\\nMechanism: The underlying biological mechanism is likely related to signaling cascades that involve interacting proteins involved in cell adhesion, calcium and potassium channeling, and protein folding/binding/kinase activities.\\n]0.9181
769text-davinci-003ontological_synopsisHALLMARK_KRAS_SIGNALING_DN-1[\\nThis list of genes is enriched for functions related to DNA-binding and transcription activities, calcium ion and ATP-binding activities, protein binding activities, and G-protein coupled receptor activities. Some of the genes are predicted to be involved in cellular processes such as transcription and cell death regulation, while others are known to take part in morphogenesis and hormone metabolism.\\n\\nMechanism: These genes, in concert, may help to regulate gene expression at the transcriptional level, modulate calcium-dependent processes such as cell death, initiate changes in cell shape and differentiation, and control the flow of information within the cell.\\n\\n][COULD NOT PARSE]0.69657
770text-davinci-003ontological_synopsisHALLMARK_KRAS_SIGNALING_UP-0[\\nThe list of genes suggests that they are involved in processes related to cell adhesion, protein binding activities, signal transduction, and transcriptional regulation, suggesting a connection to cell-matrix communication and signal transduction pathways. The enriched terms associated with the gene list include: cell adhesion molecule binding activity; ATPase coupled intramembrane transport; metalloendopeptidase activity; protein homodimerization activity; signal receptor binding activity; DNA-binding transcription factor activity; heparin binding activity; peptidase regulator activity; and GTPase activity. \\n\\nMechanism: The mechanistic hypothesis for the gene list is that these genes are involved in a cell-matrix communication and signal transduction pathway. This pathway may involve interactions between cell adhesion molecules, transmembrane protein transport, peptidases and GTPases enabling signal transfer between cells and their extracellular environment. \\n\\n][\\nSummary: The majority of these genes are involved in functions related to membrane binding and regulation, protein domain binding and regulation, receptor ligand binding and regulation, DNA-binding transcription regulation, enzyme binding and regulation, and cytokine activity.\\nMechanism: These gene functions likely aid in cell adhesion, signal transduction and transcription factors involved in cell differentiation, migration, growth and development.\\n]0.91522
771text-davinci-003ontological_synopsisHALLMARK_KRAS_SIGNALING_UP-1[ \\nSummary: The list of genes is enriched for those involved in various biological functions such as structural proteins, cell adhesion, kinase activity, signal transduction, receptor binding, cytokine activity, DNA-binding transcription, and inorganic diphosphate transmembrane transport.\\n\\nMechanism: The underlying biological mechanisms for the enriched terms include cell-matrix adhesion and signal transduction pathways, protein homodimerization, cell-cell recognition and communication, cGMP-dependent pathway, and apoptosis regulation. \\n\\n][ This list of genes appears to be involved in a wide range of functions in cell-cell adhesion, signaling, and development, including receptor binding activities, ligand binding activities, DNA-binding transcription activator activities, enzyme binding activities, protein domain specific binding activities, and protein kinase binding activities.\\n\\nMechanism: The underlying biological mechanism appears to involve the regulation and coordination of a variety of cell-cell interactions and cellular responses, such as hormone or cytokine activities, adhesion and structural support, intracellular transport, DNA transcription, protein modification and enzyme activities, energy production and metabolism, and other signaling and regulatory processes. \\n\\n]0.92209
772text-davinci-003ontological_synopsisHALLMARK_MITOTIC_SPINDLE-0[\\nSummary: The provided list of human genes are enriched for terms related to protein binding activities and activities related to the cytoskeleton.\\nMechanism: These proteins likely play a role in regulating cytoskeletal organization, cytoskeletal movement, and cellular signaling.\\n][\\nSummary: The list of genes given have common functionalities related to cytoplasm and cytoskeleton proteins such as cell motility, binding, regulation and adhesion.\\nMechanism: These functions are likely involved in regulating cytoplasm and cytoskeleton components such as actin filaments, microtubules, and ribonucleopropteins.\\n]0.9248
773text-davinci-003ontological_synopsisHALLMARK_MITOTIC_SPINDLE-1[ Enriched terms related to cytoskeleton and motor protein function, namely GTPase, ATPase, and binding activity of tubulins, microtubules, actin filaments, kinesin, dynein, and G protein-coupled receptor appear to be common among the presented genes.\\n\\nMechanism: Likely, these genes play a role in organizing and regulating the structure, dynamics, and shape of cells, as well as in the regulation of actin cytoskeleton and microtubule-dependent processes. This could suggest a role in important cellular functions such as cellular division, trafficking, and transport of organelles. The binding activity among these proteins may also be essential in communicating information and molecules between different areas of the cell. \\n\\n][COULD NOT PARSE]0.69715
774text-davinci-003ontological_synopsisHALLMARK_MTORC1_SIGNALING-0[ The gene list appears to be involved mainly in metabolic processes, such as enzyme binding and activity, acid binding, molecule transport, adapter and receptor binding and activity, and DNA and protein binding and activity. Hypothesis: The underlying biological mechanism for this set of genes is metabolic regulation, including the regulation of enzyme, protein, and DNA metabolism. ][\\n\\nSummary: The genes listed are involved in various cellular functions related to protein binding, domain binding and enzyme activity\\nMechanism: The genes are involved in several processes, such as cellular signaling, protein homeodimerization, DNA or RNA binding, transcriptional regulation, and metal ion binding.\\n]0.9269
775text-davinci-003ontological_synopsisHALLMARK_MTORC1_SIGNALING-1[\\nThe genes listed have functions related to the regulation of metabolism, actin filaments, DNA/RNA binding and transport, nuclear receptor binding, and ubiquitination. Many of the genes also have identical protein binding activities, as well as activity related to peptidase activity and enzymes.\\n\\nMechanism: The listed genes are involved in various metabolic pathways and play an important role in the regulation of cell structure and function. Many of the genes are involved in protein synthesis and processing, as well as proteins involved in DNA/RNA binding and transport, and cell signaling.\\n\\n][ These genes are primarily involved in various functions related to energy metabolism, transport, binding and regulation at a cellular level. The mechanism behind many of these functions likely occurs through interactions between proteins or protein complexes.\\n\\nMechanism: Predominantly interactions between proteins, or protein complexes, result in the observed functions of these genes. \\n\\n]0.92207
776text-davinci-003ontological_synopsisHALLMARK_MYC_TARGETS_V1-0[ This list of genes is involved in several processes related to protein folding, regulation, and binding activities such as DNA binding, RNA binding, and chromatin binding. It also suggests a potential role in the regulation of processes such as transcription, translation, and splicing.\\n\\nMechanism: This list of genes is involved in a variety of processes related to protein folding, regulation, and binding activities. The genes could be involved in different pathways which could be either converging or separate, but ultimately leading to the same outcome. For example, the genes could cooperate to enable chromatin binding or the regulation of transcription, translation, or splicing.\\n\\n][\\nSummary: Many of these genes enable or contribute to functions related to RNA binding, protein folding chaperone, DNA binding/recognition, protein homodimerization, and similar molecular functions. \\nMechanism: The underlying biological mechanism is likely related to RNA processing, DNA replication and repair, chromatin binding and modification, and protein assembly and modification. \\n]0.92303
777text-davinci-003ontological_synopsisHALLMARK_MYC_TARGETS_V1-1[ Genes in this list are primarily involved in functions related to RNA binding and its regulation, such as RNA polymerase II transcription machinery binding activity, RNA stem-loop binding activity, mRNA 3' UTR binding activity, and mRNA regulatory element binding translation repressor activity. They are also involved in regulation of protein folding, DNA binding and regulation, ubiquitin protein ligase binding activity, and other protein domains specific binding activity. Hypothesis: The number of the genes in this list involved in the regulation of RNA binding functions suggests that the underlying biological mechanism is likely a complex regulatory process for various RNA-related activities.\\n\\n][\\n\\nSummary: Twenty-eight genes related to various functions are listed. These functions include DNA binding, RNA binding, protein domain specific binding, chromatin binding, enzyme binding, and protein folding chaperone activities. \\n\\nMechanism: These genes are involved in many essential processes for cellular functioning, such as DNA replication, RNA splicing and translation, protein folding and ubiquitination, transcription and gene regulation, as well as complement and histone binding, among others.\\n\\n]0.94198
778text-davinci-003ontological_synopsisHALLMARK_MYC_TARGETS_V2-0[\\nThe list of genes are involved primarily in processes related to transcription and RNA processing, such as regulation of gene expression, DNA-templated transcription, positive regulation of cell population proliferation, protein-DNA complex organization, and regulation of nucleobase-containing compound metabolic process. Included are proteins with functions related to nucleic acid binding activity, transcription corepressor activity, and RNA polymerase II-specific DNA-binding transcription factor binding activity. The underlying biological mechanism is likely related to the organization, modification and process of transcription or RNA activity in the cell. The enriched terms are transcription, DNA-templated transcription, positive regulation of cell population proliferation, protein-DNA complex organization, regulation of nucleobase-containing compound metabolic process, RNA binding activity, regulation of gene expression, rRNA processing, and transcriptional regulation. \\n \\nSummary: Involved primarily in processes related to transcription and RNA processing\\nMechanism: organization, modification, and processes of transcription or RNA activity\\n][\\n\\nSummary: The genes all encode proteins that are involved in aspects of cell signaling, including metabolism, growth, cycle regulation, and protein transport.\\n\\nMechanism: The proteins perform a variety of functions related to the regulation of genetic information, including engaging in RNA binding or bridging, modification, transport, and translation activities.\\n\\n]0.90795
779text-davinci-003ontological_synopsisHALLMARK_MYC_TARGETS_V2-1[\\nThe given human genes are primarily involved in RNA binding, protein binding, and DNA binding activities; they predominate in processes related to rRNA processing, protein metabolic activity, DNA-templated transcription and transcription regulatory region binding, as well as cell cycle processes, chromatin binding, and mitochondria regulation.\\n\\nMechanism:\\nMany of these genes are able to act as part of complexes that regulate various processes, such as the cyclin-dependent protein kinase holoenzyme complex, which is involved in G1/S transition of mitotic cell cycle and positive regulation of fibroblast proliferation, the mitochondrial prohibitin complex which is involved in regulating DNA-templated transcription, or the MLL1 complex involved in neural crest formation. The genes are also extensively involved in protein and RNA binding functions, enabling a wide range of different activities or processes.\\n\\n][ The list of genes are mainly involved in RNA binding activity, ribosomal rRNA processing, mRNA and/or rRNA catabolism/stability, regulation of transcription/translation, regulation of signal transduction and metabolism processes, regulation of cell cycle/proliferation, and protein modification/regulation that primarily occur within the nucleus, cytosol, ribosome, and mitochondria. \\nMechanism: The underlying biological mechanism is the regulation of protein and RNA-related functions that help to control the expression of essential genes, transcription processes, and RNA stability, as well as to regulate cell growth/division and signal transduction pathways.\\n]0.93252
780text-davinci-003ontological_synopsisHALLMARK_MYOGENESIS-0[ The list of genes is over-represented in several categories related to the cytoskeleton, extracellular matrix, protein binding, transmembrane transporters, and ion channels. These genes are likely involved in regulating cell structure and interactions as well as calcium and ion homeostasis.\\n\\nMechanism: This list of genes is likely involved in regulating cell structure and signalling through their roles in the cytoskeleton, extracellular matrix, protein binding, transmembrane transporters, and ion channels.\\n\\n][ The list of genes is associated with several common functions, including calcium ion binding activity, binding of proteins to other proteins, and actin filament binding activity. These functions are enriched in the list since they are represented by an overabundance of genes, suggesting that these are all key molecular processes. The underlying biological mechanism is likely related to actin cytoskeleton organization and regulation of ion channels. \\n\\nMechanism: Gene expression regulation of actin cytoskeleton organization and regulation of ion channels.\\n\\n]0.9448
781text-davinci-003ontological_synopsisHALLMARK_MYOGENESIS-1[\\nSummary: This list of genes are enriched for activities related to calcium ion binding, cytochrome-c oxidase activity, DNA binding, ATP binding, actin binding, abnormal growth and development, protease binding, and structural constituents.\\nMechanism: The list of genes are likely involved in a variety of pathways related to growth, development, and signaling, including transcriptional and post-transcriptional control as well as cellular components of muscle cells and extracellular matrices. \\n][\\nSummary: This list of genes is found to be enriched for terms related calcium binding activity, enzyme binding activity, and DNA-binding activity.\\nMechanism: These genes are likely involved in a variety of biological processes, including cell adhesion, protein activity, receptor binding, and gene regulation.\\n]0.95186
782text-davinci-003ontological_synopsisHALLMARK_NOTCH_SIGNALING-0[\\nSummary: A variety of genes implicated in a wide range of biological processes, with a focus on gene expression, signal transduction, and cell cycle control.\\nMechanism: The genes involved in this list are related to protein modification and regulatory processes, and involve diverse functions such as Notch binding activity, Wnt receptor activity, ubiquitin and histone protein ligase activities, and transcription coactivator activity.\\n][COULD NOT PARSE]0.69423
783text-davinci-003ontological_synopsisHALLMARK_NOTCH_SIGNALING-1[ Our data shows that these genes are generally involved in transcription, protein modification, ubiquitination and regulation processes, often related to signalling pathways and the Notch pathway in particular. Mechanism: The underlying mechanisms for the commonalities amongst these genes seems to involve the activation of protein and transcription pathways, such as Notch, SCF-dependent proteasomal ubiquitin-dependent protein catabolic process and Wnt. ][\\n\\nSummary: Genes related to cancers, control of transcriptional processes, proteolysis, Notch signaling pathway, and cell proliferation/migration pathways were enriched. \\nMechanism: These genes act in mechanisms controlling growth and development processes, protein ubiquitination and degradation pathways, and pathways involved in control of transcription, cell signaling, and cell cycle control.\\n]0.9259
784text-davinci-003ontological_synopsisHALLMARK_OXIDATIVE_PHOSPHORYLATION-0[\\n\\nSummary: The genes listed are involved in several cellular processes and pathways, such as electron transfer, heme binding, and protein binding activities; oxidoreductase activity; ATPase activity and binding activity; molecular adaptor activities; acyl binding activities; and several other functions. \\n\\nMechanism: These genes are likely to be involved in various metabolic and enzymatic processes that occur in cell respiration and signal transduction.\\n\\n][ Enzymes and proteins involved in electron transport and oxidative processes, including binding, transfer, and enzymatic activities; some that interact with lipids, heme, MHC class I proteins, GTPase, and ubiquitin proteins.\\n\\nMechanism: Electron transport and oxidative processes are essential for physiological energy production, primarily through the citric acid cycle and the electron transport chain. The proteins and enzymes identified are necessary for the transfer of electrons, energy production, and energy storage. They also cause proteins to undergo conformational changes, influencing metabolite and lipid interactions as part of redox reactions.\\n\\n]0.89202
785text-davinci-003ontological_synopsisHALLMARK_OXIDATIVE_PHOSPHORYLATION-1[ Our analysis of the gene descriptions reveal that their common functions are related to mitochondrial respiration, electron and proton transfer, and transport of ATP, indicating the presence of an underlying pathway of ATP generation in mitochondria.\\n][This analysis of these human genes reveals enrichment of terms related to electron transfer activity, protein homodimerization, GTPase activity, adenine nucleotide transmembrane transporter activity, phosphoprotein binding activity, mitochondrial respiratory chain activity, proton-transporting ATP synthase activity, and mitochondrial ribosome binding activity.\\n\\nMechanism: These activities suggest that the genes contribute to mitochondrial energy metabolism through processes related to electron transfer, protein assembly, signaling, nucleic acid regulation, and protein transport.\\n\\n]0.92335
786text-davinci-003ontological_synopsisHALLMARK_P53_PATHWAY-0[\\n\\nSummary: Genes appear to be involved in functions related to DNA-binding transcription activity, protein binding activity, and protein kinase binding activity. \\nMechanism: The genes are thought to be involved in pathways related to DNA transcription, protein-protein interactions, and cell signaling.\\n][ These genes encode proteins with functions in DNA binding activities, RNA polymerase II-specific functions, transcription regulation, protein binding activity, and enzyme binding activity.\\nThe commonalities in their functions suggest the underlying biological mechanism involves DNA transcription and regulation.\\n]0.9211
787text-davinci-003ontological_synopsisHALLMARK_P53_PATHWAY-1[\\nThe list of genes contains a variety of functions related to DNA, RNA, RNA polymerase, cell adhesion/signaling, metabolism, apoptotics, and morphogenesis. These functions indicate the list of genes to be involved in several biological processes, including gene expression and regulation, DNA damage repair, cell survival and death, metabolism, and cell morphogenesis. \\n\\nThe underlying biological mechanism can be hypothesised to be related to a variety of cellular processes such as transcription, chromatin remodelling, transcriptional regulation, and signal transduction, which are all essential processes for proper cell and tissue function. \\n\\n][ This list contains genes which are involved in a broad range of roles including signaling receptor binding, RNA polymerase II co-regulator, DNA binding, phosphatase activity, transcription factor activity, enzyme binding, cell adhesion, and growth factor binding. The commonalties in terms of gene function suggest that the genes are involved in various roles related to the regulation of gene expression and cellular processes, as well as protein modification and receptor binding activity. \\n]0.91154
788text-davinci-003ontological_synopsisHALLMARK_PANCREAS_BETA_CELLS-0[ \\nSummary: This list of genes is primarily involved in regulation of cellular processes including cell migration, cellular senescence, cellular biosynthetic process, apoptotic process, detection of glucose, cell-cell adhesion, neuron migration, insulin secretion, and gastrointestinal processes, as well as involvement in multiple diseases such as diabetes, tuberculosis, malignant astrocytoma, and cancer (multiple). \\nMechanism: These genes are generally involved in control of transcription by RNA polymerase II, ATPase-coupled ion transport, protein kinase and peptidase activity, DNA binding activity, calcium-ion regulated exocytosis, and regulation of secretion by cell.\\n][\\n\\nSummary: Genes involved in glucose transport, metabolism, and regulation, with many implicated in type 1 and type 2 diabetes. Regulation of gene expression transcription and protein function are heavily represented.\\n\\nMechanism: Glucose homeostasis is achieved through the combined action of the listed genes in two major pathways: a) glucose uptake, transport, and metabolism; and b) transcription regulation of insulin and other genes related to glucose homeostasis.\\n\\n]0.90206
789text-davinci-003ontological_synopsisHALLMARK_PANCREAS_BETA_CELLS-1[ This list of genes appears to all be involved in various cellular functions in cellular components, most notably regulating transcription by RNA polymerase II, regulation of secretion by cells, regulation of cell-cell adhesion, regulation of actin filament polymerization, and detection of glucose. Many of these genes also appear to be associated with diabetes and/or cancer.\\n\\nMechanism: The genes in this list appear to be involved in many aspects of cellular functions, which are involved in a variety of underlying biological pathways. Specifically, these genes have putative roles in involvement of signal transduction, regulation of transcription and regulation of cell-cell adhesion, protein targeting to ER, regulation of long-term synaptic potentiation, regulation of actin filament polymerization, and detection of glucose.\\n\\n][ The human genes provided appear to be related to cell-cell adhesion, development and differentiation of anatomical structure, regulation of transcription by RNA polymerase II, and regulation of signal transduction and macromolecule metabolism. \\nMechanism: These genes likely enable the biological mechanisms of cell signaling, macromolecule production, and protein expression.\\n]0.90458
790text-davinci-003ontological_synopsisHALLMARK_PEROXISOME-0[ This list is comprised of genes involved in a wide variety of functions, including molecular binding activities, enzyme activities, transporter activities, and domain binding activities. All of these genes are involved in diverse metabolic processes, such as fatty acid metabolism, cholesterol metabolism, protein transport, and DNA and RNA metabolic processes, suggesting a complex set of interrelated pathways that are likely to be a part of a larger biological system. Enriched terms include: molecular binding activity; enzyme activity; transporter activity; domain binding activity; lipid transport; protein transport; DNA metabolic process; and RNA metabolic process.\\n\\nMechanism: This set of genes likely interacts in a complex system involving multiple pathways and activities that enable metabolic processes such as fatty acid metabolism, cholesterol metabolism, protein transport, and DNA and RNA metabolic processes. The mechanism can be visualized as a network of proteins that interact in various ways to enable these processes. At a higher level, these pathways may interact to regulate signaling pathways, cell growth, and replication.\\n\\n][COULD NOT PARSE]0.691137
791text-davinci-003ontological_synopsisHALLMARK_PEROXISOME-1[COULD NOT PARSE][\\nSummary: This analysis of a list of genes revealed a number of pathways and functions that are enhanced or enriched in the group of genes. The enriched pathways/functions include cell/nucleic acid metabolic processes, protein/DNA binding and processing, as well as hormone/steroid biosynthesis and processing.\\n\\nMechanism:The mechanism underlying this enrichment of processes is likely related to the fact that many of the genes included in this list code for proteins involved in these processes. These proteins may be enzymes, binders, or transporters, and are likely working together to regulate or facilitate a variety of stable and dynamic cellular processes.\\n\\n]0.70651
792text-davinci-003ontological_synopsisHALLMARK_PI3K_AKT_MTOR_SIGNALING-0[ The list of genes are found to be enriched for functions related to protein binding and kinase activities, signal sequence and receptor binding, cell cycle and apoptosis regulation, and signal transduction.\\n\\nMechanism: This enrichment suggests that these genes are involved in a variety of cellular processes that are associated with metabolism and signal transduction, such as cell cycle regulation, cell migration and differentiation, apoptosis, and signal cascade regulation. \\n\\n][ This list of human genes are involved in diverse signaling pathways, regulatory processes and enzyme activities related to cell structure, cell motility, faical recognition, gene/protein expression and other metabolic pathways. The gene functions include enzyme binding activity, protein kinase binding activity, phospholipid binding activity, phosphatase activity and GTPase activity. The enriched terms include cellular process regulation, enzyme activity, protein and peptide regulation, and protein domain modification.\\n\\nMechanism: This list of human genes modoify cellular processes by various functions such as enzyme binding activities, protein kinase binding activities, phospholipid binding activities, phosphatase activities, and GTPase activities. These functions help regulate and modify various signaling pathways and gene/protein expressions involved in cell structural, motility, and facial recognition, as well as metabolic processes.\\n\\n]0.92471
793text-davinci-003ontological_synopsisHALLMARK_PI3K_AKT_MTOR_SIGNALING-1[COULD NOT PARSE][ The genes of interest in this study are generally involved in the regulation of signal transduction pathways, with primary roles in kinase binding and GTPase activity, protein phosphatase activity, activation of transcription factors, phospholipase activity, receptor binding, ubiquitination, acetylation, and other signaling pathways. In addition, several of the genes are associated with apoptosis, cell migration, and negative regulation of proliferation.\\n\\nHypothesis/mechanism: These genes are likely part of an overarching molecular signaling pathway, in which changes in the expression of these genes modulate cell proliferation, apoptosis, migration, and other cellular processes. This likely manifests through changes in protein phosphorylation, ubiquitination acetylation, and other post-translational modifications that affect downstream cell signaling cascades. \\n\\n]0.68861
794text-davinci-003ontological_synopsisHALLMARK_PROTEIN_SECRETION-0[ The list of human genes is enriched for terms relating to membrane and vesicle trafficking, including protein binding activity, GTPase activity, GTP-dependent protein binding activity, SNARE binding activity, enzyme binding activity, protein kinase binding activity and clathrin binding activity.\\n\\nMechanism: The underlying mechanism is likely to involve the transport of proteins through the cellular membrane and vesicles along various pathways, such as endocytosis, retrograde transport, Golgi to plasma membrane transport, endoplasmic reticulum to Golgi vesicle-mediated transport, and protein targeting to lysosomes.\\n\\n][\\nSummary: The list of genes are enriched for terms related to protein binding activity, ATP binding activity, GTP-dependent protein binding activity, GTPase activity, signal sequence binding activity, clathrin binding activity and small GTPase binding activity. \\nMechanism: These genes are involved in processes such as cellular response to hormone stimulus, signal transduction, Golgi organization and vesicle mediated transport.\\nHypothesis: These genes are involved in an intracellular transport process that is composed of Protein Bindings, ATP Bindings, GTP Bindings and Small GTPase Bindings.\\n]0.9226
795text-davinci-003ontological_synopsisHALLMARK_PROTEIN_SECRETION-1[ The analysis of the list of genes reveals common functions associated with transport, binding, activity, and assembly. These functions are enriched across a broad range of processes, including protein transport, catabolic and metabolic processes, regulation of intracellular signal transduction, Golgi and cell surface organization, positive and negative regulation, and responses to stimuli. This suggests a complex network of pathways, activity and assembly at play in cellular process and interactions.\\n\\nMechanism: The mechanism of action suggested by the term enrichment test indicates a complex network of pathways, activities, and assemblies at the protein level, such as those indicated by functions like binding and activity, as well as assembly and transport. This suggests a broad range of processes that are at play in the regulation of a large variety of functions and responses in cells.\\n\\n][\\nSummary: This list of genes are involved in a range of processes, including intracellular transport, protein folding and processing, and positive and negative regulation of several cellular pathways. \\nMechanism: These genes likely play roles in regulating intracellular transport, protein folding and processing and positive and negative regulation of several cellular pathways.\\n]0.89523
796text-davinci-003ontological_synopsisHALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0[\\nThe genes identified provide a variety of functions that might generalize to protection from oxidative stress and detoxification, DNA/RNA binding and transcription, and maintaining cell-cell adhesion and organization of cellular components.\\n\\nMechanism: These functions are likely related to a broad overarching mechanism of defense from reactive oxygen species, maintenance to the structure and development of the organism, as well as mediating interactions between cells.\\n\\n][COULD NOT PARSE]0.69460
797text-davinci-003ontological_synopsisHALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1[ These genes are primarily involved in mediating energy transfer and metabolism, responding to oxidative stress/environmental compounds, and modulating cell proliferation, apoptosis, and cell to cell adhesion. \\nMechanism: The proteins directly or indirectly regulate multiple biological pathways, including canonical glycolysis, citric Acid cycle, respiratory chain, DNA metabolism, transcriptional/protein translation processes, and lipid/amino acid metabolic processes via enzymatic activity, binding activity and membrane transporters. \\n][ \\nSummary: The gene functions in this list are predominantly related to activities that enable and regulate cell redox homeostasis, such as helping to facilitate the production of and protection against oxidants like hydrogen peroxide, superoxide, and other reactive substances. \\nMechanism: The gene functions work together in a complex network of pathways, proteins, and processes to maintain redox balance in the cell by carrying out activities such as enzyme binding, protein homodimerization, protein-disulfide reductase activity, glutathione peroxidase activity, NADH dehydrogenase activity, and more. \\n]0.8768
798text-davinci-003ontological_synopsisHALLMARK_SPERMATOGENESIS-0[ The list of genes are found to be primarily involved in activities related to RNA binding, nucleosome binding, transcription and regulation, DNA binding, protein kinase activity, protein folding and chaperoning, metabolic regulation and ubiquitination.\\n\\nMechanism: The mechanisms by which these activities are enabled involve complex interactions between proteins, which act as signal transducers, modulators and effectors, resulting in the relevant activities being enabled and processes being modulated.\\n\\n][ Human genes related to this list are enriched for functions in molecular function activator activity, protein kinase activity, cellular component activity, binding activity, peptidase activity, nucleosome binding activity, ion binding activity and phosphatase binding activity; and processes such as cell cycle regulation, apoptosis regulation, cell adhesion, nervous system development, transcription regulation, protein transport, cell-cell recognition and gene expression regulation.\\n\\nMechanism: This list of genes are likely to be involved in several biological primary pathways, including signal transduction pathways, protein transcription pathways, metabolic pathways, and membrane transport pathways. These pathways are responsible for the functions and processes associated with cells in the regulation of growth, differentiation, development, and apoptosis.\\n\\n]0.92362
799text-davinci-003ontological_synopsisHALLMARK_SPERMATOGENESIS-1[ These genes are involved in a range of activities, including enzyme binding, protein binding, ligand binding, calcium ion binding, nucleotide binding, transcription factor binding, DNA binding, GTP binding, hormone binding, ATP hydrolysis, protein kinase operation, RNA binding, enzyme activator activity, chaperone operation, chromatin binding, protein phosphatase binding, phosphatase inhibitor activity, peptidase activity, inorganic cation transmembrane transporter activity, and others.\\nMechanism: These genes likely play important roles in the formation and maintenance of cell structure, transcriptional regulation and signal transduction, protein folding and degradation, metabolic homeostasis, and other processes to maintain cell function.\\n][COULD NOT PARSE\\nHypothesis: The]0.68719
800text-davinci-003ontological_synopsisHALLMARK_TGF_BETA_SIGNALING-0[ We have evidence of enrichment for processes related to signal transduction, regulation of transcription, regulation of protein metabolism, regulation of macromolecule metabolism, regulation of cellular processes, interaction with transcription factors, and interaction with SMAD proteins.\\n\\nMechanism: The underlying biological mechanism for these processes is likely related to the activation or inhibition of various proteins and enzymes that interact with signaling pathways, transcription factors, or SMAD proteins. \\n\\n][ The genes in this list are involved in the regulation of diverse biochemical processes, including transcription, signal transduction, cell cycle, metabolism, and cell adhesion. The commonalities in their functions involve binding activities (e.g. ATP binding, activin binding, SMAD binding), and protein phosphatase/kinase activities. Many of these genes are also involved in regulation of intracellular signaling pathways, such as SMAD signaling and BMP signaling, and in the regulation of transcription by RNA polymerase II.\\n\\nMechanism: The mechanism underlying these commonalities is likely related to the role of these genes in regulation of intracellular processes, as well as their binding activities, which may be necessary for the functional regulation of their target proteins.\\n\\n]0.90266
801text-davinci-003ontological_synopsisHALLMARK_TGF_BETA_SIGNALING-1[ Gene functions associated with transduction and signal modification of biological and biochemical processes; as well as DNA binding transcription activity, protein modify/kinase/phosphatase activities, receptor/ligand binding activity and activity inhibitor activity which play a role in cellular morphogenesis, metabolism, and adaptation are enriched.\\n\\nMechanism: These gene functions are involved in multiple biological and biochemical processes, with particular involvement in transcriptional regulation, signal transduction, positive/negative regulation of regulatory pathways, regulation of metabolic and structural processes, regulation of gene expression, and regulation of transcriptional factors.\\n\\n][ This list of genes is enriched for terms related to transcription regulation, intracellular signal transduction,DNA binding activity, positive/negative regulation of RNA/protein metabolic processes and protein phosphorylations.\\n\\nMechanism: These genes are likely to be functioning in a pathway that is involved in controlling gene expression, cellular signaling, and cellular metabolism. This is likely achieved through DNA binding, transcription regulation, and interaction with multiple proteins to modify protein and/or gene expression.\\n\\n]0.91166
802text-davinci-003ontological_synopsisHALLMARK_TNFA_SIGNALING_VIA_NFKB-0[ The genes are involved in regulation of growth, development, and defense mechanisms, as evidenced by enrichments of terms including \"DNA binding transcription factor,\" \"signaling receptor binding,\" \"enzyme binding,\" \"cytokine receptor binding,\" \"growth factor,\" and \"transmembrane receptor.\" \\n\\nMechanism: These genes work in concert to regulate amino acid metabolism, transport, signaling, and other processes within cells, leading to growth, development, and defense mechanisms. \\n\\n][COULD NOT PARSE]0.68468
803text-davinci-003ontological_synopsisHALLMARK_TNFA_SIGNALING_VIA_NFKB-1[ \\nSummary: This list of genes are primarily involved in transcription activities, binding activities (e.g. DNA-binding, protein binding, signaling receptor binding, etc.), enzyme activities (e.g. GTPase, ATPase, protein kinase, etc.), cytokine activities, and also in cell adhesion, transport, and regulation processes. \\nMechanism: The underlying mechanism of these genes includes a variety of critical signaling pathways, including the NF-kB, MAPK, and JAK-STAT pathways, as well as several cellular and organismal developmental pathways. \\n][\\nThis dataset refers to a list of gene summaries that are involved in multiple pathways of cellular development and signaling. The enriched terms indicate genes related to DNA-binding transcription activator activity, transcription regulatory region sequence-specific DNA-binding, GTP binding activity, enzyme binding activity, identical protein binding activity, signal receptor binding activity, phosphatase activity, protein kinase binding activity, cytokine activity, and growth factor activity. The underlying mechanism can likely be attributed to signal transduction pathways and transcription regulation related to cell growth, development, and differentiation. \\n\\nMechanism: Signal transduction pathways and transcription regulation\\n]0.93199
804text-davinci-003ontological_synopsisHALLMARK_UNFOLDED_PROTEIN_RESPONSE-0[ The list of genes and their functions are related to the synthesis and processing of nucleic acids and proteins, including RNA binding, transcriptional regulation, protein and mRNA folding, mRNA degradation, and translation regulation.\\n\\nMechanism: The general underlying biological mechanism is related to the regulation of gene expression and the synthesis and processing of proteins and nucleic acids.\\n\\n][ The majority of the genes in this list enable or involve in various functions related to RNA or protein processing, as demonstrated by the enriched terms related to RNA processing, protein binding, and DNA binding/transcription activities. Many of the genes contribute to various cellular processes, such as cellular response, cell homeostasis, and transcription from RNA polymerase II. A mechanism underlying this group of genes is that the genes are involved in multiple interactions between different enzymes and cell components for post-translational and transcriptional processing within the cell.\\n\\nMechanism: A mechanism underlying this group of genes is that the genes are involved in multiple interactions between different enzymes and cell components for post-translational and transcriptional processing within the cell.\\n\\n]0.93427
805text-davinci-003ontological_synopsisHALLMARK_UNFOLDED_PROTEIN_RESPONSE-1[ The enriched terms from these human genes suggest a common theme related to methods for dealing with environmental stress, protein folding, and metabolism. Many of these genes are involved in activities such as ATP binding and hydrolysis, molecular adaptor activity, molecular function inhibitor activity, ubiquitin protein ligase binding activity, transcription regulator activity, translation factor activity, RNA binding, protein dimerization activity, DNA binding activity, enzyme binding activity, and SNARE binding activity.\\n\\nMechanism: The underlying biological mechanism suggested by these human genes is related to the body's ability to respond to environmental stress and maintain cellular homeostasis. This is accomplished through the involvement of various proteins and RNA molecules that regulate gene expression, protein folding, and metabolism. Additionally, many of these genes are involved in the cellular response to cytokines, suggesting an immune response component.\\n\\n][\\n\\nSummary: These genes have a variety of functions, including enzyme binding activity, RNA binding activity, protein binding activity, transmembrane transporter binding activity, and transcription factor binding activity.\\n\\nMechanism: These genes are likely involved in a variety of cellular processes such as post-transcriptional control of gene expression, protein folding and sorting, and RNA processing and translation.\\n\\n]0.89565
806text-davinci-003ontological_synopsisHALLMARK_UV_RESPONSE_DN-0[COULD NOT PARSE][ The given list of genes are enriched for binding activities, such as GTP binding activity, enzyme binding activity, DNA-binding transcription factor binding activity, phosphotyrosine residue binding activity, cyclin binding activity and other related activities. These activities confer functions such as protein transcription, signal transduction, protein phosphorylation, cellular adhesion and cellular response to certain molecules.\\n\\nMechanism: The mechanism underlying these enriched binding activities is likely related to receptor-ligand interaction, involving both intra-cellular and inter-cellular interaction between molecules. It is also likely to involve protein-protein interaction, involving proteins such as SMAD binding proteins, NF-kappaB binding proteins and growth factor binding proteins, which play important roles in regulating various cellular processes.\\n\\n]0.68864
807text-davinci-003ontological_synopsisHALLMARK_UV_RESPONSE_DN-1[ Expression, regulation and activation of various pathways, enzymes, receptors and factors involved in numerous cellular processes such as cell differentiation, cellular adhesion, development, exocytosis, hematopoiesis, inflammation and immunity, lipid metabolism, transcription, neural development, regulation and intercellular signaling. \\nMechanism: The expression, regulation and activation of multiple proteins involved in core cellular processes is accomplished by binding and interaction of multiple domains including but not limited to ATP-binding activity, PDZ domain binding, SMAD binding, calcium ion binding, Gap junction channel activity, cAMP-dependent protein kinase inhibitor activity, Phosphotyrosine resodue binding activity, GTPase activator activity, among other activities.\\nHypotheses: The various interactions of the proteins enable the expression of genetic material and regulation at the cellular level by transcription factor binding activity, cis-regulatory region sequence-specific DNA binding activity, DNA hydrolysis activity and other processes. This helps in coordinating different cellular components and signaling events for proper functioning and development of the organism.\\n][\\nSummary: The list of genes provides evidence that a number of functions are involved, such as DNA-binding transcription activator activity, RNA polymerase II-specific activity, NF-kappaB binding activity, and microtubule binding activity.\\nMechanism: These genes may be involved in signaling pathways that regulate processes such as hemopoiesis, endothelial intestinal barrier formation, cellular response to steroid hormone stimulus and nervous system development.\\n]0.88743
808text-davinci-003ontological_synopsisHALLMARK_UV_RESPONSE_UP-0[ This list of genes is enriched for functions related to protein binding, DNA binding, binding activity, receptor binding activity, and protein kinase activity. Hypothesis: This list of genes is likely involved in several pathways related to cell adhesion, signaling, and in particular, the regulation of gene expression. \\n\\nMechanism: This list of genes is involved in a variety of mechanisms related to protein-protein and protein-DNA interactions, as well as protein kinase activity, all of which contribute to cell adhesion, signaling, and the regulation of gene expression.\\n\\n][\\n\\nSummary: The genes listed are involved in a variety of functions, including ATP binding activity, protein kinase binding activity, RNA binding activity, DNA binding activity, receptor binding activity, enzyme binding activity, and phospholipid transporter activity.\\n\\nMechanism: The genes have a variety of molecular functions and are involved in a wide range of processes, including cell-cell adhesion, synaptic transmission, apoptotic signaling pathway, interleukin-6 receptor binding, T cell activation, overall cellular metabolism, and gene expression regulation.\\n\\n]0.939
809text-davinci-003ontological_synopsisHALLMARK_UV_RESPONSE_UP-1[ This list of genes is predominantly involved in transductional and transcriptional regulatory mechanisms related to cellular processes, such as ion and water transport, signaling receptor activities, DNA/RNA binding and processing, protein ubiquitination, and enzyme activities. Specifically, we identify gene functions in GTP binding activity; DNA binding activity; transcriptional activator activity; protein kinase binding activity; endopeptidase activity; receptor binding activity; hydrolase activity; nucleotide and peptide transporter activity; ion and neurotransmitter channel activity; antioxidant activity; and ligase activity.\\n\\nMechanism: These gene functions are likely to be involved in a number of underlying transductional and transcriptional regulatory mechanisms related to cellular processes, including signal transduction, gene expression, protein catabolism, and membrane transport. These gene functions likely represent molecular signals allowing for rapid and short-term responses in physiological and neurological processes, such as cell membrane responses, sensory processing, and immunological responses, as well as slower and long-term responses, such as development and cell growth.\\n\\n][ Analysis of the gene summaries reveals that many of the genes are involved in various activities, such as enzyme binding activity, enzyme activity (specifically, hydrolase and transferase activities), transcription-related activities, receptor activities, and binding activities for molecules, such as proteins and DNA. The underlying biological mechanism or pathways these genes belongs to is transcriptional regulation, protein-protein interactions, cell adhesion and migration, and signal transduction. Thus, the following terms are enriched in these genes: enzyme binding activity; hydrolase activity; transferase activity; receptor activity; DNA binding activity; RNA binding activity; transcription factor activity; and protein binding activity. \\nMechanism: Transcriptional regulation, protein-protein interactions, cell adhesion and migration, and signal transduction. \\n]0.92334
810text-davinci-003ontological_synopsisHALLMARK_WNT_BETA_CATENIN_SIGNALING-0[COULD NOT PARSE][\\nSummary: This gene dataset contains genes involved in cell migration, regulation of signal transduction, protein ubiquitination, cell cycle control, transcription regulation, and regulation of protein stability.\\nMechanism: These genes appear to commonally control a number of key pathway processes at the cellular level and can initiate their respective pathways through the binding of other proteins, and the control of chromatin composition through the modification of histones.\\n]0.69467
811text-davinci-003ontological_synopsisHALLMARK_WNT_BETA_CATENIN_SIGNALING-1[ \\n\\nSummary: Multiple genes are involved in protein binding, transcription regulation, cell cycle regulation, signaling pathways, and response pathways. \\nMechanism: Multiple genes play a role in regulating the activities of transcription and signaling pathways which are vital to several biological processes.\\n][ Human genes included in this list are primarily involved in processes related to signal transduction and transcription regulation, with some involvement in cell migration, development and and cell population proliferation, and proteolysis. Common terms enriched include: signal transduction; regulation of gene expression; transcription; regulation of protein phosphorylation; regulation of protein stability; cell migration; cell proliferation; development; and proteolysis.\\n\\nMechanism: The human genes studied here mainly act in a variety of signal transduction pathways, which includes NF-kappaB and Wnt signaling; activities such as binding, adaptor, and ligand activities are also involved. Transcriptional regulation is also present, with activities including transcription activator and repressor binding, as well as DNA binding and corepressor activity. The regulation of proteins and proteolysis by the genes is also observed, as well as other activities related to cell migration and cell development.\\n\\n]0.90705
812text-davinci-003ontological_synopsisT cell proliferation-0[ The list of genes mostly involves genes that enable signaling receptor binding activity, protein kinase binding activity, and ubiquitin protein ligase activity. These genes are enriched in processes such as intracellular signal transduction, cytokine production, and gene expression. The underlying biological mechanism involves intercellular communication through signaling cascades leading to the regulation of gene expression. \\n\\nMechanism: Intercellular communication through signaling cascades leading to regulation of gene expression.\\n\\n][ \\n\\nSummary: The list of genes are mainly involved in a variety of biological pathways and processes, such as intracellular signaling, cell proliferation, cell adhesion and migration, cell division and apoptosis. \\n\\nMechanism: The pathways and processes are likely mediated by protein interactions such as binding activity, enzyme and kinase activity, as well as transcription and receptor signaling, which ultimately result in cellular adaptation and regulation.\\n\\n]0.9379
813text-davinci-003ontological_synopsisT cell proliferation-1[ This group of genes is involved in regulated cellular processes, including cell recognition, signal transduction, cell migration, and gene expression. The primary functions of these genes include binding activities (e.g. DNA-binding transcription factor activity, receptor ligand activity, identical protein binding activity, etc.), catalytic activities (e.g. histone deacetylase binding activity, phosphotyrosine residue binding activity, etc.), enzyme activity (e.g. indoleamine 2,3-dioxygenase activity, phosphodiesterase activity, etc.), and transporter activity (e.g. metal cation: proton antiporter activity).\\n\\nMechanism: These genes likely act, at least in part, through the modulation of signaling transduction pathways, such as the Wnt, Notch, JAK-STAT, and MAPK cascade, as well as cytokine- and growth factor-mediated pathways. These pathways play key roles in many cellular and developmental processes, including cell migration, proliferation, apoptotic processes, and stem cell differentiation.\\n\\n][ \\nSummary: This list of genes has been found to be involved in a variety of functions, including cation binding activity, diacylglycerol binding activity, enzyme binding activity, protein heterodimerization activity, receptor binding activity, and protein kinase activity. \\nMechanism: These genes appear to be involved in a variety of cellular activities, including signal transduction, cell recognition and migration, receptor binding, and apoptotic processes.\\n]0.92548
814text-davinci-003ontological_synopsisYamanaka-TFs-0[\\n\\nSummary: Genes POU5F1, SOX2, KLF4, and MYC, are involved in various functions such as DNA-binding transcription repressor and activator activities, RNA polymerase II-specific, and nucleic acid binding activities. These genes are also implicated in the regulation of biosynthetic processes, signal transduction, gene expression, angiogenesis, protein-DNA complex organization, and cell population proliferation, and are associated with numerous cancers.\\n\\nMechanism: These genes have been implicated in the regulation of complex biological processes, such as signal transduction and gene expression, suggesting a potential role in transcriptional regulation.\\n\\n][ \\n\\nSummary: The commonalities among the gene functions of the list provided are DNA-binding transcription factor activity, RNA polymerase II-specific, nucleic acid binding activity, transcription cis-regulatory region binding activity, regulation of gene expression, and regulation of biosynthetic process.\\n\\nMechanism: The genes enable the transcription of genetic material, and potential activation or repression of gene expression by interacting with DNA and RNA polymerase II. Regulation of gene expression is achieved through altering transcription factor activity and binding to DNA regions to control downstream gene expression.\\n\\n]0.8924
815text-davinci-003ontological_synopsisYamanaka-TFs-1[ Human genes, KLF4, POU5F1, and SOX2, are involved in transforming DNA-binding transcription activator, repressor, and factor activities, respectively. They are commonly involved in processes like positive and negative regulation of gene expression, biosynthetic process, angiogenesis, BMP signaling pathway involved in heart induction, and canonical Wnt signaling pathway.\\n\\nMechanism: These genes work in association with transcription regulator complexes, which interact with DNA and RNA, influencing transcriptional programming and gene regulation.\\n\\n][ The genes KLF4, POU5F1, and SOX2 are all involved in transcription regulation and gene expression, specifically upstream of or within the process of endodermal cell fate specification. They are all located in the cytosol and nucleoplasm, are associated with chromatin, and are part of a transcription regulator complex. \\n\\nMechanism: The mechanism underlying these gene functions is likely related to the regulation of DNA binding and transcription, which could help to control cell development and maintenance pathways.\\n\\n]0.9231
816text-davinci-003ontological_synopsisamigo-example-0[ Genes involved in this list are involved in a wide range of activities, such as protein binding, lipoprotein lipase activator activity, phospholipid binding, protein dimerization, modulation of chemical synaptic transmission, integrin binding, collagen binding, heparin binding, signaling receptor binding, non-membrane spanning protein tyrosine kinase activity, peptidoglycan binding, GTPase activator activity, and more. The commonalities in these genes' functions point to roles in signaling pathways, extracellular matrix structure and function, cell-cell and cell-matrix adhesion, lipid metabolism, and defense response.\\n\\nMechanism: These genes are likely to be involved in a wide range of signaling pathways, particularly related to cell-cell and cell-matrix adhesion, as well as lipid metabolism, extracellular matrix structure, and defense response. These pathways result in a wide variety of physiological functions, from regulation of gene expression to regulation of BMP signaling, cell migration, and cell proliferation.\\n\\n][COULD NOT PARSE]0.681020
817text-davinci-003ontological_synopsisamigo-example-1[ \\nThe human gene summaries provided all involve functions related to signal transduction, cell adhesion and binding activities, extracellular matrix structural components, and mechanism related to cell proliferation, growth and differentiation. Specifically, the genes are involved in protein binding, ion binding, chemokine activity, growth factor binding, signal receptor binding, phosphatase binding, cell migration, membrane repolarization, signal transduction, regulation, and defense response to bacteria and other organisms. \\n\\nMechanism: These genes appear to be involved in multiple cellular pathways related to signal transduction and cell adhesion, as well as molecular interactions and processes such as protein phosphorylation. Specifically, it appears that the genes are involved in activating intracellular signalling events, regulating cell growth and proliferation, and mediating defense responses. \\n\\n][ The genes listed are mainly involved in cell-specific metabolic processes, and sharing a common role in regulation of cell-matrix adhesion and extracellular matrix structural constituents. Several of them are also involved in organ development and differentiation, and others in regulation of different hormone pathways.\\n\\nMechanism: Many of these genes are involved in positive or negative regulation of protein metabolic processes such as phosphorylation, proteolysis, and cell-surface receptor signalling pathways. They also play a role in regulating cell proliferation, apoptosis, and ion transport. Additionally, the genes are involved in regulation of blood coagulation and cell adhesion, as well as in modulation of chemical synaptic transmission and cell-matrix adhesion.\\n\\n]0.92136
818text-davinci-003ontological_synopsisbicluster_RNAseqDB_0-0[ \\nSummary: A list of genes that are enriched for terms related to calcium ion binding, double-stranded DNA-binding, cellular defense, and embryonic development processes.\\nMechanism: The genes in this list are likely involved in the processes of calcium binding, cell adhesion and migration, and transcriptional regulation, which may underpin the roles of these genes in embryonic development, neuronal and vascular tissue formation, and cellular defense. \\n][COULD NOT PARSE]0.68441
819text-davinci-003ontological_synopsisbicluster_RNAseqDB_0-1[ Our term enrichment analysis of human gene functions reveals that these genes play a variety roles related to regulation, binding, activity, and transport-related activity. Specifically, the enriched terms include: metal ion binding activity; protein binding activity; RNA binding activity; phosphatase regulator activity; gap junction channel activity; protein homodimerization activity; calcium ion binding activity; GTPase activity; DNA binding activity; ubiquitin protein ligase activity; protein tyrosine phosphatase activity; and transcription corepressor activity.\\n\\nMechanism: These results suggest a mechanism for gene regulation and regulation of pathways at the cellular level, involving binding, transport-related activity, and kinase or phosphatase activities. The mechanisms may be involved in the formation of structural components or the regulation of gene expression in the cell. This may involve transcriptional, post-transcriptional, and post-translational control of gene expression. Additionally, the identified activities may be involved in signal transduction and cellular signaling. \\n\\n][ Summary: The list of genes is enriched for terms related to DNA-binding transcription activity, protein kinase binding activity, metal ion binding activity, calcium ion binding activity, transcription co-regulator activity, and responsive to stimuli.\\nMechanism: The underlying biological pathways can either be direct (e.g. modifying gene expression) or indirect (e.g. binding proteins to regulate other proteins).\\n]0.92693
820text-davinci-003ontological_synopsisbicluster_RNAseqDB_1002-0[\\n\\nSummary: The list of genes provided are involved in various functions and processes of muscle development and contraction. These functions and processes are related to skeletal muscle thin filament assembly, muscle contraction, muscle cell differentiation, actin nucleation, protein ubiquitination, and muscle organelle organization.\\n\\nMechanism: The underlying biological mechanism includes protein phosphorylation, calcium-dependent signaling pathways, gene regulation, and post-translational modifications.\\n\\n][ The list of genes appears to be focused on muscle structure and development, as well as processes related to muscle contractions. This is supported by enriched terms related to muscle processes which include actin filament binding, microfilament motor activity, muscle alpha-actinin binding, actin monomer binding, tropomyosin binding, myosin binding, titin binding, and creatine kinase activity. This suggests a biological mechanism that centers around the development, assembly, and contraction of muscle tissue. A hypothesis of this mechanism is that these genes have a complex role in enabling specific activities related to muscle development and muscle contractions, as well as regulating their activity to ensure efficient functioning of muscle tissue.\\n\\nSummary: Genes related to muscle tissue structure, development, and contractions\\nMechanism: Complex role in enabling specific activities related to muscle development and muscle contractions, as well as regulating their activity to ensure efficient functioning of muscle tissue.\\n]0.93529
821text-davinci-003ontological_synopsisbicluster_RNAseqDB_1002-1[ This list of genes is associated with a variety of functions related to muscle structure and contraction, such as actin and tropomyosin binding activities, protein phosphatase binding activity, troponin complex activities related to muscle contraction and regulation of muscle adaptation, protein polymerization, and muscle tissue morphogenesis. The underlying common mechanisms are related to muscle assembly, muscle contraction, and regulation of muscle adaptation.\\n\\nMechanism: Muscle assembly, muscle contraction, regulation of muscle adaptation\\n\\n][ This list of human genes are related to skeletal muscle, actin filament/stress fiber and striated muscle thin filaments assembly. They are enriched for functions involving calcium-dependent binding activity; ATP binding activity; adhesion; transmembrane transport; transcriptional regulation; ubiquitination; and actin monomer binding activity.\\n\\nMechanism: The genes are likely to be involved in pathways which are regulated by calcium-mediated intracellular signaling and ubiquitin-dependent protein degradation, leading to muscle contraction and regulation of muscle adaptation in response to denervation and electrical stimulus.\\n\\n]0.9283
822text-davinci-003ontological_synopsisendocytosis-0[ \\nSummary: The genes involved in this list have functions related to protein signaling, protein phosphorylation, protein ubiquitination, protein transport, cell projection organization, endocytosis and receptor-mediated endocytosis, phosphatidylinositol binding, membrane raft polarization, and plasma membrane tubulation.\\n\\nMechanism: The genes in this list are involved in a variety of protein signaling and transport pathways that enable a wide range of functions such as cell projection organization, endocytosis and receptor-mediated endocytosis, phosphatidylinositol binding, membrane raft polarization, and plasma membrane tubulation.\\n\\n][ \\n\\nSummary: The list of genes identified in this analysis are involved in several processes including signalling, endocytosis, membrane transport, and protein metabolism.\\n\\nMechanism: These genes serve to regulate several processes which involve signalling, endocytosis, membrane transport, and protein metabolites through protein kinase activities.\\n\\n]0.94292
823text-davinci-003ontological_synopsisendocytosis-1[ Summary: The genes listed are involved in functions such as cadherin binding activities, endocytosis, cholesterol homeostasis, GTP-dependent protein binding activity, protein ubiquitination, and lysophosphatidic acid binding activity. They are located in cellular components such as endoplasmic reticulum, Golgi apparatus, Basolateral plasma membrane, clathrin-coated pit, postsynaptic membrane and cytoplasm.\\nMechanism: The underlying biological mechanism involves endocytosis and regulating processes associated with cholesterol metabolism, protein ubiquitination and lysophosphatidic acid binding.\\n][ This list of genes is involved in various cellular functions, such as cell signaling, protein ubiquitination, endocytosis/exocytosis, intracellular trafficking, vesicle transport, receptor binding and regulation of gene expression. The terms associated with these genes reflect their roles in a variety of cellular processes, including protein phosphorylation, protein homooligomerization, vesicle buddying and regulation of inflammatory response, among others.\\n\\nMechanism: The cellular functions associated with these genes are likely regulated through various intracellular pathways, including protein kinase cascades, GTP-dependent pathways, receptor signaling, and canonical inflammasome signaling, among others.\\n\\n]0.91117
824text-davinci-003ontological_synopsisglycolysis-gocam-0[ \\nSummary: The majority of the genes commonly enable enzymatic activities, often related to cellular metabolism and related pathways.\\nMechanism: Many of the genes enable the production of energy stores (ATP, fructose 6-phosphate, glyceraldehyde-3-phosphate, fructose 1,6-bisphosphate, triosephosphate, and phosphoglycerate) through regulation of several metabolic processes, such as glycolysis, carbohydrate phosphorylation, fructose 6-phosphate metabolic process, fructose 1,6-bisphosphate metabolic process, and phosphoglycerate kinetic. Additionally, two of the genes involved in transcription (PKM, GAPDH) suggest a role in gene expression. \\n][\\nSummary: The genes listed are primarily involved in energy regulation, carbohydrate metabolism, cell homeostasis, cell signaling, and protein catabolism.\\nMechanism: The enriched genes encode for proteins in energy regulation pathways, such as glycolysis and gluconeogenesis, as well as for proteins that help to modulate cellular signaling, such as glucose and phosphate binding proteins.\\n]0.92256
825text-davinci-003ontological_synopsisglycolysis-gocam-1[ \\nSummary: These genes are involved in a range of cellular processes related to energy metabolism, including glycolysis, phosphorylation and glucose transport.\\nMechanism: The genes encode proteins that catalyze biochemical reactions such as enzyme activities, ubiquitin ligase binding and protein homodimerization. \\n][ \\nSummary: Enriched terms are related to metabolic activities, protein binding, cellular homeostasis, localization, and glycolytic processes.\\nMechanism: These genes may all be involved in a metabolic pathway, functioning together in protein synthesis, post-transcriptional processing, and regulation of intracellular metabolism.\\n]0.9113
826text-davinci-003ontological_synopsisgo-postsynapse-calcium-transmembrane-0[\\nThis gene set is strongly enriched for genes involved in regulation of presynaptic cytosolic calcium ion concentration, membrane depolarization, regulation of glutamate receptor activity, regulation of neurotransmitter receptor activity, and regulation of phospholipid metabolism.\\nThe underlying biological mechanism or pathway could involve regulation of synaptic neurotransmitter release, intracellular phospholipid metabolism, and calcium ion homeostasis.\\n][ \\n\\nSummary: This list of genes is primarily associated with regulation of intracellular calcium concentrations and ion channel activity.\\nMechanism: Calcium concentration regulation is the primary mechanism enabling functions, such as postsynaptic neurotransmitter receptor activity, regulation of AMPA receptor activity, G protein-coupled receptor signaling, calcium ion transmembrane transport, and ligand-gated monoatomic ion channel activity.\\n]0.9314
827text-davinci-003ontological_synopsisgo-postsynapse-calcium-transmembrane-1[ This list of genes is primarily involved in calcium transport and regulating calcium ion concentrations in the cytoplasm and plasma membrane. Enriched terms include: calcium transport; regulation of calcium ion concentration; G protein-coupled receptor signaling pathway; negative regulation of cell volume; regulation of nitric oxide metabolic process; regulation of glutamatergic synaptic transmission; regulation of postsynaptic neurotransmitter receptor activity; and membrane depolarization.\\n\\nMechanism: These genes are involved in the transfer and maintenance of calcium ion concentrations in the cell to facilitate cell signaling and communication. Calcium is regulated through a variety of channels, transporters, and receptors, with the most significant ones being glutamate receptors (NMDA, AMPA, and L-type), acetylcholine receptors, and G-protein coupled receptors (e.g. serotonin receptor). These channels and receptors are involved in regulating cellular processes such as membrane depolarization, transport of ions, and neurotransmitter binding. They also interact with other proteins involved in the regulation of calcium levels, such as NCS1, CACNG2, CACNG4, and CACNG8.\\n\\n][ This is a list of genes that when taken together seem to be involved in regulating ion channels, transporters, or receptors. Specifically, they refer to monoatomic cation channels, acetylcholine-gated channels, glutamate-gated calcium channels, voltage-gated calcium channels, NMDA selective glutamate receptor complexes, and L-type voltage-gated calcium channel complexes. All these gene functions are involved in processes related to neuronal excitation, calcium-mediated signaling, neural transmission, neuronal migration, and synaptic plasticity.\\n\\nMechanism: The underlying biological mechanism suggested by this list of gene functions is ion and calcium signaling in the nervous system. This includes the regulation of intracellular calcium levels, the modulation of neurotransmitter release, the transport of ions across the cell membrane, and the regulation of synaptic transmission and plasticity. \\n\\n]0.94281
828text-davinci-003ontological_synopsisgo-reg-autophagy-pkra-0[COULD NOT PARSE][ The gene summaries provided indicate that the main terms enriched among all of these genes are: protein kinase binding activity, protein kinase activity, protein serine/threonine kinase activity, positive regulation of protein phosphorylation, and regulation of macromolecule biosynthetic process.\\n\\nMechanism: The mechanism of action associated with these genes is likely related to their roles in the regulation of protein phosphorylation and macromolecule biosynthetic processes. This likely involves a variety of cellular pathways, such as intracellular signal transduction and TOR signaling, as well as modulation of different cellular components, such as the cytosol, nucleus, and mitochondrion.\\n\\n]0.68688
829text-davinci-003ontological_synopsisgo-reg-autophagy-pkra-1[ \\n\\nSummary: This list of genes are involved in a variety of biochemical processes, such as protein folding and chaperone activities, protein kinase binding and activator activities, and metal ion binding. They are also implicated in a variety of diseases, including Alzheimer's, Parkinson's, and cancer.\\n\\nMechanism: These genes are involved in a range of functional activities related to protein folding and chaperone activities, protein kinase binding and activator activities, and metal ion binding, which are all important for cellular biochemistry.\\n\\n][COULD NOT PARSE]0.69539
830text-davinci-003ontological_synopsishydrolase activity, hydrolyzing O-glycosyl compounds-0[COULD NOT PARSE][COULD NOT PARSE\\nHypothesis: The genes in the list are involved in glycan metabolism]0.8669
831text-davinci-003ontological_synopsishydrolase activity, hydrolyzing O-glycosyl compounds-1[ These genes are primarily involved in carbohydrate and lipid metabolism, as well as glycoprotein degradation, protein homodimerization, and hyaluronan/ glycosaminoglycan catabolism.\\n\\nMechanism: The metabolic pathways involved in this process include glycoprotein catabolism, glycosaminoglycan catabolism, heparan sulfate catabolism, glucoside catabolism, mannose trimming and protein deglycosylation.\\n\\n][\\nSummary: The genes in this list all participate in various glycan/carbohydrate/lipid processing and metabolic activities.\\nMechanism: These genes - primarily hydrolases, lysozymes and mannosidases - are involved in breaking down, or catabolizing, a range of molecules, including gangliosides, chitin, heparan sulfate, lipid, glucosylceramides, and glycoproteins, and so on.\\n]0.9129
832text-davinci-003ontological_synopsisig-receptor-binding-2022-0[ All the genes listed above are involved in immunoglobulin receptor binding activity. ][\\nSummary: The human genes described in this list have enriched terms related to binding and receptor binding activity, antigen binding activity, immunoglobulin receptor binding activity, non-membrane spanning protein tyrosine kinase activity, phosphatidylcholine binding activity, and phosphotyrosine residue binding activity.\\nMechanism: These genes are involved in a variety of biological processes, including immunoglobulin receptor binding, protein phosphorylation, antigen binding, and cellular component organization. These genes likely work together to enable the body to respond to antigens as part of the immune system. This includes recognizing antigens and binding to them so that the body can mount an immune response.\\n]0.91644
833text-davinci-003ontological_synopsisig-receptor-binding-2022-1[ \\n\\nSummary: This list of genes is mainly predicted to enable antigen binding activity and immunoglobulin receptor binding activity, and are predicted to be involved in several processes related to activation of the immune response and to defense response to other organisms. \\n\\nMechanism: Through the interaction of antigens with immunoglobulin receptors, these genes help to stimulate the immune response and activate immune cells, providing protection against pathogens and other foreign substances. \\n\\n][\\n\\nSummary: These genes are predominantly immunoglobulin receptor binding proteins with functions in antigen binding and activation of immune responses.\\n\\nMechanism: These genes are likely part of a larger immune system network, involving antigen presentation and recognition, as well as various immune system responses to microbial and foreign invaders.\\n\\n]0.96149
834text-davinci-003ontological_synopsismeiosis I-0[COULD NOT PARSE][\\nSummary: The list of genes provide evidence for a set of processes related to DNA and cellular replication, including DNA binding activity, chromatin binding, ATP dependent activity, protein export, and transcriptional regulation.\\n]0.69217
835text-davinci-003ontological_synopsismeiosis I-1[ This list of genes appears to be related to meiosis, DNA binding activities, and processes involved in meiotic recombination, DNA metabolism, and double-strand break repair. The commonalities between the gene functions involve processes related to meiosis, DNA binding, DNA metabolism, homologous recombination, and telomere attachment. Additionally, these genes are located in various cellular components including the nucleus, chromatin, synaptonemal complex, chromosome, and cytoplasm.\\n\\nMechanism: The underlying biological mechanism likely involves a network of complex interactions that control meiotic cell cycle transitions and processes related to DNA metabolism, binding, replication, and repair involving multiple cellular components during gametogenesis. \\n\\n][ \\nSummary: The genes involved in this list are mainly related to DNA binding, double-stranded DNA binding, DNA/DNA annealing, and identical protein binding activities. They are also involved in a variety of processes related to DNA double strand break repair, DNA metabolic processes, meiotic chromosome segregation and pairing, and spermatogenesis.\\n\\nMechanism: These genes are likely involved in coordinating and catalysing a variety of DNA-related activities that are required for proper genetic recombination and replication of genetic material during meiosis and spermatogenesis.\\n\\n]0.94184
836text-davinci-003ontological_synopsismolecular sequestering-0[\\nSummary: We have identified 18 genes with related functions, such as calcium ion binding activity, protein sequestering activity, DNA-binding transcription factor activity, oxysterol-binding activity, and ubiquitin protein ligase binding activity.\\nMechanism: The enriched terms suggest that these genes are involved in processes related to calcium or ion transport, the regulation of the cell cycle and of protein phosphorylation, and intracellular signaling and responses to various external stimuli.\\n][ \\nSummary: The human genes analyzed are involved in a variety of functions, including calcium ion binding activity; identical protein binding activity, protein sequestering activity; and ubiquitin protein ligase binding activity.\\n\\nMechanism: These genes likely play critical roles in cellular processes such as cellular response to caffeine, regulation of protein phosphorylation, regulation of anion channel activity, positive regulation of lysosomal membrane permeability, regulation of gene expression and response to interferon-beta.\\n\\n]0.9336
837text-davinci-003ontological_synopsismolecular sequestering-1[\\nThis gene set is composed of genes involved in various cellular processes including protein binding, sequestering, transcription, metabolism and signaling pathways. Many are located in various cellular components such as the cytoplasm, endoplasmic reticulum and Golgi apparatus. There is a potential connection between these genes and multiple diseases, such as hemochromatosis type 5, Churg-Strauss syndrome and Huntington's disease-like 1.\\n\\nMechanism: These genes are part of a wide range of cellular activities and organelle functions, which could be part of the same underlying cell-wide mechanism. The presence of multiple proteins in the same cellular locales suggest an opportunity for protein-protein interaction and potentially a shared molecular mechanism.\\n\\n][\\nSummary: The list of genes provides a range of functions relating to protein binding, metal and ion binding, regulation of gene expression, regulation of protein phosphorylation, cellularresponse to infection and inflammation, and regulation of cell death pathways.\\n\\nMechanism: These genes form part of complex pathways that lead to the regulation of macromolecule biosynthetic processes, intracellular transport, gene expression, and protein phosphorylation. These pathways are integral for regulating cell death, cholesterol efflux, protein binding activities, and intracellular calcium.\\n\\n]0.91177
838text-davinci-003ontological_synopsismtorc1-0[ The gene list appears to be involved mainly in metabolic processes, such as enzyme binding and activity, acid binding, molecule transport, adapter and receptor binding and activity, and DNA and protein binding and activity. Hypothesis: The underlying biological mechanism for this set of genes is metabolic regulation, including the regulation of enzyme, protein, and DNA metabolism. ][\\n\\nSummary: The genes listed are involved in various cellular functions related to protein binding, domain binding and enzyme activity\\nMechanism: The genes are involved in several processes, such as cellular signaling, protein homeodimerization, DNA or RNA binding, transcriptional regulation, and metal ion binding.\\n]0.9269
839text-davinci-003ontological_synopsismtorc1-1[\\nSummary: The following gene functions are significantly enriched in this list of human genes: cytoskeleton protein binding, phosphatase binding activity, oxidation-reduction activity, cell development and signaling activity, DNA binding activity, cellular transporter activity, and protein kinase binding activity.\\n\\nMechanism: The enriched gene functions are essential components of several processes related to cell growth, gene expression, cell differentiation, post-translational modification, and signal transduction.\\n\\n][ \\n\\nSummary: The list of genes show functions related to structural support, transport of materials and ions, response to stimuli, protein-protein interaction, and regulation of transcription, metabolism, and cell growth.\\n\\nMechanism: The genes involved in this term enrichment show critical functions that are part of the integrated machinery of the cell, which organizes communication, transport, and control. This machinery is responsible for the ability of the cell to respond to stimuli, regulate metabolism and transcription, and undergo cell growth, leading to growth and development of the organism.\\n\\n]0.9083
840text-davinci-003ontological_synopsisperoxisome-0[ These genes are involved in peroxisome biogenesis, protein import into peroxisome and pexophagy. \\nMechanism: The genes act as peroxisome targeting sequence binding and ubiquitin-dependent protein binding, enabling fatty acid metabolic processes, protein homodimerization and enzyme binding activity. They are located in endoplasmic reticulum, nucleoplasm, Golgi apparatus and membrane and active in cytosol, peroxisome and peroxisomal matrix. \\n][ These human genes all share the common activity of enabling activities related to peroxisome biogenesis, such as ATP binding, hydrolysis, ubiquitin-dependent protein binding activity, as well as protein import/unfolding, stabilization and targeting to peroxisome. ]0.89180
841text-davinci-003ontological_synopsisperoxisome-1[ The gene functions provide evidence for a common pathway involved in protein import into peroxisomes, with other functions related to protein stabilization, regulation of cell population proliferation, protein-lipid binding, peroxisome organization, and fatty acid metabolism.\\n\\nMechanism: The identified mechanism involves a pathway of protein import into the peroxisome matrix, with further functions related to protein stabilization, ether lipid biosynthesis, protein-lipid binding, receptor recycling, and fatty acid metabolism. \\n\\n][\\nSummary: The genes PEX6, PEX2, PEX3, PEX7, and PEX1 are all involved in peroxisome biogenesis and organization.\\n]0.85422
842text-davinci-003ontological_synopsisprogeria-0[ The list of human genes appear to be involved in processes related to post-translational protein modification, DNA folding and nuclear envelope attachment, as well as other processes associated with cellular response to stress, gene transcription, and gene expression. The enriched terms are DNA binding; protein binding; metal ion binding; cellular response to radiation, hypoxia and starvation; regulation of apoptotic process; regulation of telomere maintenance; regulation of protein ADP-ribosylation; and regulation of viral genome replication.\\n\\nMechanism: These genes may be involved in pathways that regulate several kinds of post-translational modification and gene expression patterns in response to environmental stressors. These pathways could include protein processing signals and transcription factors that regulate transcription and translation, as well as enzymes and proteins that control gene expression and DNA folding. In addition, these pathways may be involved in processes that enable cellular senescence and maintenance of DNA integrity. \\n\\n][ The 4 genes have functions with related to proteins and DNA, including DNA binding; metal ion binding; and protein homodimerization activities. They are also involved in the regulation of apoptotic process, DNA metabolic processes, cellular responses to hypoxia and starvation, and regulation of telomere maintenance.\\nHypothesis: These four genes likely interact with each other in the components of the cell in which they are found, such as the nucleus, cytoplasm, centrosome, and membrane, which all help in fostering DNA binding, metal ion binding, protein homodimerization, and other genetic processes. \\n]0.89456
843text-davinci-003ontological_synopsisprogeria-1[ These three genes are all associated with DNA damage and repair responses and are located in the nucleus and surrounding cytoplasm. They all involve processes such as protein binding, metal ion binding, and homodimerization activities. Additionally, they have roles in apoptotic processes, cell senescence and response to hypoxia. The term \"DNA damage and repair\" is enriched, as represented by the three genes.\\n\\nMechanism: The genes LMNA, WRN, and BANF1 all act as checkpoints in the maintenance, modification and repair of DNA with regard to genetic information, telomeric regions and structure. They are responsible for the regulation of apoptotic processes, cell senescence and hypoxic responses, thus ensuring genetic integrity and stability.\\n\\n][COULD NOT PARSE]0.68735
844text-davinci-003ontological_synopsisregulation of presynaptic membrane potential-0[\\nSummary: The list of human genes are involved in functions such as ligand-gated monoatomic ion channel activity, GABA receptor activity, glutamate receptor activity, voltage-gated potassium and sodium channel activity, adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway, gamma-aminobutyric acid signaling pathway, and neurotransmitter transport. \\nMechanism: These genes are likely to be involved in the signalling and transport of neurotransmitters across plasma membranes, including the regulation of presynaptic and postsynaptic membrane potentials.\\n][ This gene list is enriched for several terms related to ion channels, transporters, and receptors. The enriched terms include both ligand-gated and voltage-gated ion channel and transporter activities, as well as several types of receptor activities such as G protein-coupled receptors, AMPA glutamate receptors, and kainate-selective glutamate receptors. These genes also appear to be involved in several processes such as membrane potential, chloride transmembrane transport, gamma-aminobutyric acid signaling pathway, and neurotransmitter transport.\\n\\nMechanism: The underlying biological mechanism likely involves the regulation of electrical and chemical signals in neurons, thereby enabling communication between different types of cells in the central and peripheral nervous systems. \\n\\n]0.93218
845text-davinci-003ontological_synopsisregulation of presynaptic membrane potential-1[ Genes in this list are primarily involved in ion channel activity, membrane potential regulation, and ligand-gated monoatomic ion channel activity, as well as pathways enabled by those activities such as G protein-coupled receptor signaling, chloride transmembrane transport, gamma-aminobutyric acid signaling pathway, and potassium ion transmembrane transport.\\n\\nMechanism: Genes in this list are part of the electrical signaling pathways that regulate chemical synaptic transmission in neurons and other cells, controlling neuronal action potentials, membrane potentials, the transport of ions across cellular membranes, and the assembly of neurotransmitters and synapses.\\n\\n][\\nSummary: The genes listed here are involved in neurotransmitter signaling, ion channel activity, membrane transport, calcium ion homeostasis, and ionotropic glutamate receptor signaling. \\nMechanism: These genes provide the molecular machinery for neurotransmitter signaling by establishing ion channels, helping to carry ions in and out of cells, and regulating calcium ion homeostasis.\\n]0.94288
846text-davinci-003ontological_synopsissensory ataxia-0[ The genes in the list are all involved in many functions including DNA-binding, RNA polymerase II-specific activity, metal ion binding, ubiquitin protein ligase binding, and positive regulation of transcription by RNA polymerase II. These genes are also likely to be involved in several processes including positive regulation of immunoglobulin production, regulation of ERBB signaling pathway, regulation of intracellular protein transport, monoatomic cation transport, nucleic acid metabolic process, protein hexamerization, glycosaminoglycan catabolic process, nervous system development, heme transport, and mitochondrial transport.\\n\\nMechanism: These genes likely coordinate a combination of transcription activities to maintain cell function, health, and development. They are also likely to be involved in transporting and processing essential molecules needed for maintaining normal neural and sensory functionality as well as involved in transporting and processing essential molecules for cell metabolism.\\n\\n][ Analysis of the given list of genes suggests a common thread of involvement in the development and function of peripheral nerves, particularly with regard to varying forms of Charcot-Marie-Tooth disease, in addition to their role in nucleic acid and glycan metabolic pathways. \\n]0.85738
847text-davinci-003ontological_synopsissensory ataxia-1[\\nSummary: A set of genes involved in positive/negative regulation of transcription by RNA polymerase II, nucleic acid and glycosaminoglycan metabolism, 5'-3' DNA helicase activity, protein hexamerization, alpha-N-acetylglucosaminidase activity, cytoskeletal motor activity, mechanosensitive monoatomic cation channel activity, myelination in peripheral nervous system, regulation of RNA splicing, transmission of nerve impulse, glucose-6-phosphate isomerase activity, alanine-tRNA ligase activity, heme transmembrane transporter activity, 3'-5' exonuclease activity, DNA-directed DNA polymerase activity, induction of egg chambers in Drosophila, nuclear import signal receptor activity, misfolded protein binding activity, protein ubiquitination, metal ion binding activity, cell-cell adhesion via plasma-membrane adhesion molecules and myelination.\\nMechanism: The genes may be shared among a number of biological pathways involving nucleic acid metabolism, cytoskeletal motor activity, myelination, and protein folding.\\n][\\nSummary: Eighteen human genes related to various neurological processes and diseases are analyzed.\\n]0.83921
848text-davinci-003ontological_synopsisterm-GO:0007212-0[ The genes provided are likely to be involved in G protein-coupled receptor signal transduction, regulation of cytosolic calcium ion concentration, regulation of DNA templated transcription, regulation of neurodegeneration, signal transduction, neural development, enzyme and protein kinase binding, endosomal transport, signal receptor binding and cell organization. Mechanism: These genes are likely to play a role in signal transduction pathways that regulate multiple biological processes, including G protein-coupled receptor signaling pathways, phospholipase-c activating dopamine receptor signaling pathways, and adenylate cyclase-modulating G protein-coupled receptor signaling pathways. ][\\nThe genes in the given list are predominantly involved in G protein-coupled receptor signaling pathways, regulation of cytosolic calcium ion concentration, regulation of transcription by RNA polymerase II, regulation of neuronal death and apoptotic processes, cAMP biosynthetic processes and protein phosphorylation pathways. The underlying biological mechanism for these processes is likely related to cellular and tissue homeostasis, i.e. the maintenance of physiological equilibrium. \\n\\nMechanism: Maintenance of cellular and tissue homeostasis.\\n\\n]0.93146
849text-davinci-003ontological_synopsisterm-GO:0007212-1[\\n\\nSummary: A wide variety of gene functions have been identified, including those involved in cAMP and calcium signaling pathways, G-protein coupled receptor signaling, apoptosis, gene regulation and transcription, membrane transport, and ion channels. \\n\\nMechanism: A wide variety of genes play a role in providing signals to the cells, controlling the transport of molecules across membranes, regulating genes and allowing for cells to respond to various stimuli.\\n\\n][ This list of genes is related to G protein-coupled receptor signaling pathways, associated with diseases such as Alzheimer's disease, Parkinson's disease, hypertension and kidney failure. ]0.87277
850text-davinci-003ontological_synopsistf-downreg-colorectal-0[ The genes identified in the list are involved in various activities, such as DNA and RNA binding, transcription factor binding, protein kinase and chromatin binding, transcription coactivator and repressor activities, protein dimerization, and other enzymatic activities. The common function they share is to regulate gene expression.\\n\\nMechanism: These genes are likely involved in transcriptional regulation by binding to genes and enhancers to either activate or repress transcription, and by modifying chromatin structure to regulate gene expression.\\n\\n][ The genes are predominantly involved in transcriptional activation and/or repression of gene expression, often as part of complexes involved in the regulation of signal transduction, DNA-templated transcription, cell cycle, and transcription by RNA polymerase II; they also enable chromatin binding activities and zinc ion binding.\\n\\nMechanism: The human genes work together to regulate various biological processes via the modulation of signal transduction, DNA-templated transcription, cell cycle, and transcription by RNA polymerase II pathways. This involves the binding of DNA to transcription factors, the deacetylation of histones, and the binding of specific protein ligases/cofactors resulting in the transcriptional activation or repression of specific genes. The regulation of gene expression and signal transduction, in turn, allows for the control of multiple downstream processes such as cell differentiation, apoptosis, cell migration, angiogenesis and metabolism.\\n\\n]0.92425
851text-davinci-003ontological_synopsistf-downreg-colorectal-1[ This list of genes are all primarily involved in the regulation of transcription by RNA polyerase II and in cellular processes of transcription, such as positive and negative regulation of gene expression, DNA repair and cell differentiation. The statistically over-represented terms include: transcription; DNA-binding; RNA polymerase II-specific; transcription activator/transcription repressor; cis-regulatory region sequence-specific; transcription coregulator binding; regulation of DNA-templated transcription; nucleosome disassembly; and regulation of signal transduction. \\nMechanism: The underlying biological mechanism is associated with regulation of gene expression, which is dependent on the DNA-binding capability of the transcription factors, as well as their ability to recognize the proper sequence and initiate transcription of the downstream genes.\\n][\\nSummary: The list mainly consists of genes which play a role in regulation that involves DNA-binding transcription activator and repressor activity, regulation of gene expression, regulation of DNA-templated transcription and positive/negative regulation of transcription by RNA polymerase II.\\nMechanism: The genes in the list are involved in a variety of mechanisms that function to give cells control over their activities and to regulate transcription.\\n]0.94411
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"68 gpt-3.5-turbo narrative_synopsis \n", - "69 gpt-3.5-turbo narrative_synopsis \n", - "70 gpt-3.5-turbo narrative_synopsis \n", - "71 gpt-3.5-turbo narrative_synopsis \n", - "72 gpt-3.5-turbo narrative_synopsis \n", - "73 gpt-3.5-turbo narrative_synopsis \n", - "74 gpt-3.5-turbo narrative_synopsis \n", - "75 gpt-3.5-turbo narrative_synopsis \n", - "76 gpt-3.5-turbo narrative_synopsis \n", - "77 gpt-3.5-turbo narrative_synopsis \n", - "78 gpt-3.5-turbo narrative_synopsis \n", - "79 gpt-3.5-turbo narrative_synopsis \n", - "80 gpt-3.5-turbo narrative_synopsis \n", - "81 gpt-3.5-turbo narrative_synopsis \n", - "82 gpt-3.5-turbo narrative_synopsis \n", - "83 gpt-3.5-turbo narrative_synopsis \n", - "84 gpt-3.5-turbo narrative_synopsis \n", - "85 gpt-3.5-turbo narrative_synopsis \n", - "86 gpt-3.5-turbo narrative_synopsis \n", - "87 gpt-3.5-turbo narrative_synopsis \n", - "88 gpt-3.5-turbo narrative_synopsis \n", - "89 gpt-3.5-turbo narrative_synopsis \n", - "90 gpt-3.5-turbo narrative_synopsis \n", - "91 gpt-3.5-turbo narrative_synopsis \n", - "92 gpt-3.5-turbo narrative_synopsis \n", - "93 gpt-3.5-turbo narrative_synopsis \n", - "94 gpt-3.5-turbo narrative_synopsis \n", - "95 gpt-3.5-turbo narrative_synopsis \n", - "96 gpt-3.5-turbo narrative_synopsis \n", - "97 gpt-3.5-turbo narrative_synopsis \n", - "98 gpt-3.5-turbo narrative_synopsis \n", - "99 gpt-3.5-turbo narrative_synopsis \n", - "100 gpt-3.5-turbo narrative_synopsis \n", - "101 gpt-3.5-turbo narrative_synopsis \n", - "102 gpt-3.5-turbo narrative_synopsis \n", - "103 gpt-3.5-turbo narrative_synopsis \n", - "104 gpt-3.5-turbo narrative_synopsis \n", - "105 gpt-3.5-turbo narrative_synopsis \n", - "106 gpt-3.5-turbo narrative_synopsis \n", - "107 gpt-3.5-turbo narrative_synopsis \n", - "108 gpt-3.5-turbo narrative_synopsis \n", - "109 gpt-3.5-turbo narrative_synopsis \n", - "110 gpt-3.5-turbo narrative_synopsis \n", - "111 gpt-3.5-turbo narrative_synopsis \n", - "112 gpt-3.5-turbo narrative_synopsis \n", - "113 gpt-3.5-turbo narrative_synopsis \n", - "114 gpt-3.5-turbo narrative_synopsis \n", - "115 gpt-3.5-turbo narrative_synopsis \n", - "116 gpt-3.5-turbo narrative_synopsis \n", - "117 gpt-3.5-turbo narrative_synopsis \n", - "118 gpt-3.5-turbo narrative_synopsis \n", - "119 gpt-3.5-turbo narrative_synopsis \n", - "120 gpt-3.5-turbo narrative_synopsis \n", - "121 gpt-3.5-turbo narrative_synopsis \n", - "122 gpt-3.5-turbo narrative_synopsis \n", - "123 gpt-3.5-turbo narrative_synopsis \n", - "124 gpt-3.5-turbo narrative_synopsis \n", - "125 gpt-3.5-turbo narrative_synopsis \n", - "126 gpt-3.5-turbo narrative_synopsis \n", - "127 gpt-3.5-turbo narrative_synopsis \n", - "128 gpt-3.5-turbo narrative_synopsis \n", - "129 gpt-3.5-turbo narrative_synopsis \n", - "130 gpt-3.5-turbo narrative_synopsis \n", - "131 gpt-3.5-turbo narrative_synopsis \n", - "132 gpt-3.5-turbo narrative_synopsis \n", - "133 gpt-3.5-turbo narrative_synopsis \n", - "134 gpt-3.5-turbo narrative_synopsis \n", - "135 gpt-3.5-turbo narrative_synopsis \n", - "136 gpt-3.5-turbo narrative_synopsis \n", - "137 gpt-3.5-turbo narrative_synopsis \n", - "138 gpt-3.5-turbo narrative_synopsis \n", - "139 gpt-3.5-turbo narrative_synopsis \n", - "140 gpt-3.5-turbo narrative_synopsis \n", - "141 gpt-3.5-turbo narrative_synopsis \n", - "142 gpt-3.5-turbo no_synopsis \n", - "143 gpt-3.5-turbo no_synopsis \n", - "144 gpt-3.5-turbo no_synopsis \n", - "145 gpt-3.5-turbo no_synopsis \n", - "146 gpt-3.5-turbo no_synopsis \n", - "147 gpt-3.5-turbo no_synopsis \n", - "148 gpt-3.5-turbo no_synopsis \n", - "149 gpt-3.5-turbo no_synopsis \n", - "150 gpt-3.5-turbo no_synopsis \n", - "151 gpt-3.5-turbo no_synopsis \n", - "152 gpt-3.5-turbo no_synopsis \n", - "153 gpt-3.5-turbo no_synopsis \n", - "154 gpt-3.5-turbo no_synopsis \n", - "155 gpt-3.5-turbo no_synopsis \n", - "156 gpt-3.5-turbo no_synopsis \n", - "157 gpt-3.5-turbo no_synopsis \n", - "158 gpt-3.5-turbo no_synopsis \n", - "159 gpt-3.5-turbo no_synopsis \n", - "160 gpt-3.5-turbo no_synopsis \n", - "161 gpt-3.5-turbo no_synopsis \n", - "162 gpt-3.5-turbo no_synopsis \n", - "163 gpt-3.5-turbo no_synopsis \n", - "164 gpt-3.5-turbo no_synopsis \n", - "165 gpt-3.5-turbo no_synopsis \n", - "166 gpt-3.5-turbo no_synopsis \n", - "167 gpt-3.5-turbo no_synopsis \n", - "168 gpt-3.5-turbo no_synopsis \n", - "169 gpt-3.5-turbo no_synopsis \n", - "170 gpt-3.5-turbo no_synopsis \n", - "171 gpt-3.5-turbo no_synopsis \n", - "172 gpt-3.5-turbo no_synopsis \n", - "173 gpt-3.5-turbo no_synopsis \n", - "174 gpt-3.5-turbo no_synopsis \n", - "175 gpt-3.5-turbo no_synopsis \n", - "176 gpt-3.5-turbo no_synopsis \n", - "177 gpt-3.5-turbo no_synopsis \n", - "178 gpt-3.5-turbo no_synopsis \n", - "179 gpt-3.5-turbo no_synopsis \n", - "180 gpt-3.5-turbo no_synopsis \n", - "181 gpt-3.5-turbo no_synopsis \n", - "182 gpt-3.5-turbo no_synopsis \n", - "183 gpt-3.5-turbo no_synopsis \n", - "184 gpt-3.5-turbo no_synopsis \n", - "185 gpt-3.5-turbo no_synopsis \n", - "186 gpt-3.5-turbo no_synopsis \n", - "187 gpt-3.5-turbo no_synopsis \n", - "188 gpt-3.5-turbo no_synopsis \n", - "189 gpt-3.5-turbo no_synopsis \n", - "190 gpt-3.5-turbo no_synopsis \n", - "191 gpt-3.5-turbo no_synopsis \n", - "192 gpt-3.5-turbo no_synopsis \n", - "193 gpt-3.5-turbo no_synopsis \n", - "194 gpt-3.5-turbo no_synopsis \n", - "195 gpt-3.5-turbo no_synopsis \n", - "196 gpt-3.5-turbo no_synopsis \n", - "197 gpt-3.5-turbo no_synopsis \n", - "198 gpt-3.5-turbo no_synopsis \n", - "199 gpt-3.5-turbo no_synopsis \n", - "200 gpt-3.5-turbo no_synopsis \n", - "201 gpt-3.5-turbo no_synopsis \n", - "202 gpt-3.5-turbo no_synopsis \n", - "203 gpt-3.5-turbo no_synopsis \n", - "204 gpt-3.5-turbo no_synopsis \n", - "205 gpt-3.5-turbo no_synopsis \n", - "206 gpt-3.5-turbo no_synopsis \n", - "207 gpt-3.5-turbo no_synopsis \n", - "208 gpt-3.5-turbo no_synopsis \n", - "209 gpt-3.5-turbo no_synopsis \n", - "210 gpt-3.5-turbo no_synopsis \n", - "211 gpt-3.5-turbo no_synopsis \n", - "212 gpt-3.5-turbo no_synopsis \n", - "213 gpt-3.5-turbo no_synopsis \n", - "214 gpt-3.5-turbo no_synopsis \n", - "215 gpt-3.5-turbo no_synopsis \n", - "216 gpt-3.5-turbo no_synopsis \n", - "217 gpt-3.5-turbo no_synopsis \n", - "218 gpt-3.5-turbo no_synopsis \n", - "219 gpt-3.5-turbo no_synopsis \n", - "220 gpt-3.5-turbo no_synopsis \n", - "221 gpt-3.5-turbo no_synopsis \n", - "222 gpt-3.5-turbo no_synopsis \n", - "223 gpt-3.5-turbo no_synopsis \n", - "224 gpt-3.5-turbo no_synopsis \n", - "225 gpt-3.5-turbo no_synopsis \n", - "226 gpt-3.5-turbo no_synopsis \n", - "227 gpt-3.5-turbo no_synopsis \n", - "228 gpt-3.5-turbo no_synopsis \n", - "229 gpt-3.5-turbo no_synopsis \n", - "230 gpt-3.5-turbo no_synopsis \n", - "231 gpt-3.5-turbo no_synopsis \n", - "232 gpt-3.5-turbo no_synopsis \n", - "233 gpt-3.5-turbo no_synopsis \n", - "234 gpt-3.5-turbo no_synopsis \n", - "235 gpt-3.5-turbo no_synopsis \n", - "236 gpt-3.5-turbo no_synopsis \n", - "237 gpt-3.5-turbo no_synopsis \n", - "238 gpt-3.5-turbo no_synopsis \n", - "239 gpt-3.5-turbo no_synopsis \n", - "240 gpt-3.5-turbo no_synopsis \n", - "241 gpt-3.5-turbo no_synopsis \n", - "242 gpt-3.5-turbo no_synopsis \n", - "243 gpt-3.5-turbo no_synopsis \n", - "244 gpt-3.5-turbo no_synopsis \n", - "245 gpt-3.5-turbo no_synopsis \n", - "246 gpt-3.5-turbo no_synopsis \n", - "247 gpt-3.5-turbo no_synopsis \n", - "248 gpt-3.5-turbo no_synopsis \n", - "249 gpt-3.5-turbo no_synopsis \n", - "250 gpt-3.5-turbo no_synopsis \n", - "251 gpt-3.5-turbo no_synopsis \n", - "252 gpt-3.5-turbo no_synopsis \n", - "253 gpt-3.5-turbo no_synopsis \n", - "254 gpt-3.5-turbo no_synopsis \n", - "255 gpt-3.5-turbo no_synopsis \n", - "256 gpt-3.5-turbo no_synopsis \n", - "257 gpt-3.5-turbo no_synopsis \n", - "258 gpt-3.5-turbo no_synopsis \n", - "259 gpt-3.5-turbo no_synopsis \n", - "260 gpt-3.5-turbo no_synopsis \n", - "261 gpt-3.5-turbo no_synopsis \n", - "262 gpt-3.5-turbo no_synopsis \n", - "263 gpt-3.5-turbo no_synopsis \n", - "264 gpt-3.5-turbo no_synopsis \n", - "265 gpt-3.5-turbo no_synopsis \n", - "266 gpt-3.5-turbo no_synopsis \n", - "267 gpt-3.5-turbo no_synopsis \n", - "268 gpt-3.5-turbo no_synopsis \n", - "269 gpt-3.5-turbo no_synopsis \n", - "270 gpt-3.5-turbo no_synopsis \n", - "271 gpt-3.5-turbo no_synopsis \n", - "272 gpt-3.5-turbo no_synopsis \n", - "273 gpt-3.5-turbo no_synopsis \n", - "274 gpt-3.5-turbo no_synopsis \n", - "275 gpt-3.5-turbo no_synopsis \n", - "276 gpt-3.5-turbo no_synopsis \n", - "277 gpt-3.5-turbo no_synopsis \n", - "278 gpt-3.5-turbo no_synopsis \n", - "279 gpt-3.5-turbo no_synopsis \n", - "280 gpt-3.5-turbo no_synopsis \n", - "281 gpt-3.5-turbo no_synopsis \n", - "282 gpt-3.5-turbo no_synopsis \n", - "283 gpt-3.5-turbo no_synopsis \n", - "284 gpt-3.5-turbo ontological_synopsis \n", - "285 gpt-3.5-turbo ontological_synopsis \n", - "286 gpt-3.5-turbo ontological_synopsis \n", - "287 gpt-3.5-turbo ontological_synopsis \n", - "288 gpt-3.5-turbo ontological_synopsis \n", - "289 gpt-3.5-turbo ontological_synopsis \n", - "290 gpt-3.5-turbo ontological_synopsis \n", - "291 gpt-3.5-turbo ontological_synopsis \n", - "292 gpt-3.5-turbo ontological_synopsis \n", - "293 gpt-3.5-turbo ontological_synopsis \n", - "294 gpt-3.5-turbo ontological_synopsis \n", - "295 gpt-3.5-turbo ontological_synopsis \n", - "296 gpt-3.5-turbo ontological_synopsis \n", - "297 gpt-3.5-turbo ontological_synopsis \n", - "298 gpt-3.5-turbo ontological_synopsis \n", - "299 gpt-3.5-turbo ontological_synopsis \n", - "300 gpt-3.5-turbo ontological_synopsis \n", - "301 gpt-3.5-turbo ontological_synopsis \n", - "302 gpt-3.5-turbo ontological_synopsis \n", - "303 gpt-3.5-turbo ontological_synopsis \n", - "304 gpt-3.5-turbo ontological_synopsis \n", - "305 gpt-3.5-turbo ontological_synopsis \n", - "306 gpt-3.5-turbo ontological_synopsis \n", - "307 gpt-3.5-turbo ontological_synopsis \n", - "308 gpt-3.5-turbo ontological_synopsis \n", - "309 gpt-3.5-turbo ontological_synopsis \n", - "310 gpt-3.5-turbo ontological_synopsis \n", - "311 gpt-3.5-turbo ontological_synopsis \n", - "312 gpt-3.5-turbo ontological_synopsis \n", - "313 gpt-3.5-turbo ontological_synopsis \n", - "314 gpt-3.5-turbo ontological_synopsis \n", - "315 gpt-3.5-turbo ontological_synopsis \n", - "316 gpt-3.5-turbo ontological_synopsis \n", - "317 gpt-3.5-turbo ontological_synopsis \n", - "318 gpt-3.5-turbo ontological_synopsis \n", - "319 gpt-3.5-turbo ontological_synopsis \n", - "320 gpt-3.5-turbo ontological_synopsis \n", - "321 gpt-3.5-turbo ontological_synopsis \n", - "322 gpt-3.5-turbo ontological_synopsis \n", - "323 gpt-3.5-turbo ontological_synopsis \n", - "324 gpt-3.5-turbo ontological_synopsis \n", - "325 gpt-3.5-turbo ontological_synopsis \n", - "326 gpt-3.5-turbo ontological_synopsis \n", - "327 gpt-3.5-turbo ontological_synopsis \n", - "328 gpt-3.5-turbo ontological_synopsis \n", - "329 gpt-3.5-turbo ontological_synopsis \n", - "330 gpt-3.5-turbo ontological_synopsis \n", - "331 gpt-3.5-turbo ontological_synopsis \n", - "332 gpt-3.5-turbo ontological_synopsis \n", - "333 gpt-3.5-turbo ontological_synopsis \n", - "334 gpt-3.5-turbo ontological_synopsis \n", - "335 gpt-3.5-turbo ontological_synopsis \n", - "336 gpt-3.5-turbo ontological_synopsis \n", - "337 gpt-3.5-turbo ontological_synopsis \n", - "338 gpt-3.5-turbo ontological_synopsis \n", - "339 gpt-3.5-turbo ontological_synopsis \n", - "340 gpt-3.5-turbo ontological_synopsis \n", - "341 gpt-3.5-turbo ontological_synopsis \n", - "342 gpt-3.5-turbo ontological_synopsis \n", - "343 gpt-3.5-turbo ontological_synopsis \n", - "344 gpt-3.5-turbo ontological_synopsis \n", - "345 gpt-3.5-turbo ontological_synopsis \n", - "346 gpt-3.5-turbo ontological_synopsis \n", - "347 gpt-3.5-turbo ontological_synopsis \n", - "348 gpt-3.5-turbo ontological_synopsis \n", - "349 gpt-3.5-turbo ontological_synopsis \n", - "350 gpt-3.5-turbo ontological_synopsis \n", - "351 gpt-3.5-turbo ontological_synopsis \n", - "352 gpt-3.5-turbo ontological_synopsis \n", - "353 gpt-3.5-turbo ontological_synopsis \n", - "354 gpt-3.5-turbo ontological_synopsis \n", - "355 gpt-3.5-turbo ontological_synopsis \n", - "356 gpt-3.5-turbo ontological_synopsis \n", - "357 gpt-3.5-turbo ontological_synopsis \n", - "358 gpt-3.5-turbo ontological_synopsis \n", - "359 gpt-3.5-turbo ontological_synopsis \n", - "360 gpt-3.5-turbo ontological_synopsis \n", - "361 gpt-3.5-turbo ontological_synopsis \n", - "362 gpt-3.5-turbo ontological_synopsis \n", - "363 gpt-3.5-turbo ontological_synopsis \n", - "364 gpt-3.5-turbo ontological_synopsis \n", - "365 gpt-3.5-turbo ontological_synopsis \n", - "366 gpt-3.5-turbo ontological_synopsis \n", - "367 gpt-3.5-turbo ontological_synopsis \n", - "368 gpt-3.5-turbo ontological_synopsis \n", - "369 gpt-3.5-turbo ontological_synopsis \n", - "370 gpt-3.5-turbo ontological_synopsis \n", - "371 gpt-3.5-turbo ontological_synopsis \n", - "372 gpt-3.5-turbo ontological_synopsis \n", - "373 gpt-3.5-turbo ontological_synopsis \n", - "374 gpt-3.5-turbo ontological_synopsis \n", - "375 gpt-3.5-turbo ontological_synopsis \n", - "376 gpt-3.5-turbo ontological_synopsis \n", - "377 gpt-3.5-turbo ontological_synopsis \n", - "378 gpt-3.5-turbo ontological_synopsis \n", - "379 gpt-3.5-turbo ontological_synopsis \n", - "380 gpt-3.5-turbo ontological_synopsis \n", - "381 gpt-3.5-turbo ontological_synopsis \n", - "382 gpt-3.5-turbo ontological_synopsis \n", - "383 gpt-3.5-turbo ontological_synopsis \n", - "384 gpt-3.5-turbo ontological_synopsis \n", - "385 gpt-3.5-turbo ontological_synopsis \n", - "386 gpt-3.5-turbo ontological_synopsis \n", - "387 gpt-3.5-turbo ontological_synopsis \n", - "388 gpt-3.5-turbo ontological_synopsis \n", - "389 gpt-3.5-turbo ontological_synopsis \n", - "390 gpt-3.5-turbo ontological_synopsis \n", - "391 gpt-3.5-turbo ontological_synopsis \n", - "392 gpt-3.5-turbo ontological_synopsis \n", - "393 gpt-3.5-turbo ontological_synopsis \n", - "394 gpt-3.5-turbo ontological_synopsis \n", - "395 gpt-3.5-turbo ontological_synopsis \n", - "396 gpt-3.5-turbo ontological_synopsis \n", - "397 gpt-3.5-turbo ontological_synopsis \n", - "398 gpt-3.5-turbo ontological_synopsis \n", - "399 gpt-3.5-turbo ontological_synopsis \n", - "400 gpt-3.5-turbo ontological_synopsis \n", - "401 gpt-3.5-turbo ontological_synopsis \n", - "402 gpt-3.5-turbo ontological_synopsis \n", - "403 gpt-3.5-turbo ontological_synopsis \n", - "404 gpt-3.5-turbo ontological_synopsis \n", - "405 gpt-3.5-turbo ontological_synopsis \n", - "406 gpt-3.5-turbo ontological_synopsis \n", - "407 gpt-3.5-turbo ontological_synopsis \n", - "408 gpt-3.5-turbo ontological_synopsis \n", - "409 gpt-3.5-turbo ontological_synopsis \n", - "410 gpt-3.5-turbo ontological_synopsis \n", - "411 gpt-3.5-turbo ontological_synopsis \n", - "412 gpt-3.5-turbo ontological_synopsis \n", - "413 gpt-3.5-turbo ontological_synopsis \n", - "414 gpt-3.5-turbo ontological_synopsis \n", - "415 gpt-3.5-turbo ontological_synopsis \n", - "416 gpt-3.5-turbo ontological_synopsis \n", - "417 gpt-3.5-turbo ontological_synopsis \n", - "418 gpt-3.5-turbo ontological_synopsis \n", - "419 gpt-3.5-turbo ontological_synopsis \n", - "420 gpt-3.5-turbo ontological_synopsis \n", - "421 gpt-3.5-turbo ontological_synopsis \n", - "422 gpt-3.5-turbo ontological_synopsis \n", - "423 gpt-3.5-turbo ontological_synopsis \n", - "424 gpt-3.5-turbo ontological_synopsis \n", - "425 gpt-3.5-turbo ontological_synopsis \n", - "426 text-davinci-003 narrative_synopsis \n", - "427 text-davinci-003 narrative_synopsis \n", - "428 text-davinci-003 narrative_synopsis \n", - "429 text-davinci-003 narrative_synopsis \n", - "430 text-davinci-003 narrative_synopsis \n", - "431 text-davinci-003 narrative_synopsis \n", - "432 text-davinci-003 narrative_synopsis \n", - "433 text-davinci-003 narrative_synopsis \n", - "434 text-davinci-003 narrative_synopsis \n", - "435 text-davinci-003 narrative_synopsis \n", - "436 text-davinci-003 narrative_synopsis \n", - "437 text-davinci-003 narrative_synopsis \n", - "438 text-davinci-003 narrative_synopsis \n", - "439 text-davinci-003 narrative_synopsis \n", - "440 text-davinci-003 narrative_synopsis \n", - "441 text-davinci-003 narrative_synopsis \n", - "442 text-davinci-003 narrative_synopsis \n", - "443 text-davinci-003 narrative_synopsis \n", - "444 text-davinci-003 narrative_synopsis \n", - "445 text-davinci-003 narrative_synopsis \n", - "446 text-davinci-003 narrative_synopsis \n", - "447 text-davinci-003 narrative_synopsis \n", - 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"842 text-davinci-003 ontological_synopsis \n", - "843 text-davinci-003 ontological_synopsis \n", - "844 text-davinci-003 ontological_synopsis \n", - "845 text-davinci-003 ontological_synopsis \n", - "846 text-davinci-003 ontological_synopsis \n", - "847 text-davinci-003 ontological_synopsis \n", - "848 text-davinci-003 ontological_synopsis \n", - "849 text-davinci-003 ontological_synopsis \n", - "850 text-davinci-003 ontological_synopsis \n", - "851 text-davinci-003 ontological_synopsis \n", - "\n", - "prompt_variant geneset \\\n", - "0 EDS-0 \n", - "1 EDS-1 \n", - "2 FA-0 \n", - "3 FA-1 \n", - "4 HALLMARK_ADIPOGENESIS-0 \n", - "5 HALLMARK_ADIPOGENESIS-1 \n", - "6 HALLMARK_ALLOGRAFT_REJECTION-0 \n", - "7 HALLMARK_ALLOGRAFT_REJECTION-1 \n", - "8 HALLMARK_ANDROGEN_RESPONSE-0 \n", - "9 HALLMARK_ANDROGEN_RESPONSE-1 \n", - "10 HALLMARK_ANGIOGENESIS-0 \n", - "11 HALLMARK_ANGIOGENESIS-1 \n", - "12 HALLMARK_APICAL_JUNCTION-0 \n", - "13 HALLMARK_APICAL_JUNCTION-1 \n", - "14 HALLMARK_APICAL_SURFACE-0 \n", - "15 HALLMARK_APICAL_SURFACE-1 \n", - "16 HALLMARK_APOPTOSIS-0 \n", - "17 HALLMARK_APOPTOSIS-1 \n", - "18 HALLMARK_BILE_ACID_METABOLISM-0 \n", - "19 HALLMARK_BILE_ACID_METABOLISM-1 \n", - "20 HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 \n", - "21 HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 \n", - "22 HALLMARK_COAGULATION-0 \n", - "23 HALLMARK_COAGULATION-1 \n", - "24 HALLMARK_COMPLEMENT-0 \n", - "25 HALLMARK_COMPLEMENT-1 \n", - "26 HALLMARK_DNA_REPAIR-0 \n", - "27 HALLMARK_DNA_REPAIR-1 \n", - "28 HALLMARK_E2F_TARGETS-0 \n", - "29 HALLMARK_E2F_TARGETS-1 \n", - "30 HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 \n", - "31 HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 \n", - "32 HALLMARK_ESTROGEN_RESPONSE_EARLY-0 \n", - "33 HALLMARK_ESTROGEN_RESPONSE_EARLY-1 \n", - "34 HALLMARK_ESTROGEN_RESPONSE_LATE-0 \n", - "35 HALLMARK_ESTROGEN_RESPONSE_LATE-1 \n", - "36 HALLMARK_FATTY_ACID_METABOLISM-0 \n", - "37 HALLMARK_FATTY_ACID_METABOLISM-1 \n", - "38 HALLMARK_G2M_CHECKPOINT-0 \n", - "39 HALLMARK_G2M_CHECKPOINT-1 \n", - "40 HALLMARK_GLYCOLYSIS-0 \n", - "41 HALLMARK_GLYCOLYSIS-1 \n", - "42 HALLMARK_HEDGEHOG_SIGNALING-0 \n", - "43 HALLMARK_HEDGEHOG_SIGNALING-1 \n", - "44 HALLMARK_HEME_METABOLISM-0 \n", - "45 HALLMARK_HEME_METABOLISM-1 \n", - "46 HALLMARK_HYPOXIA-0 \n", - "47 HALLMARK_HYPOXIA-1 \n", - "48 HALLMARK_IL2_STAT5_SIGNALING-0 \n", - "49 HALLMARK_IL2_STAT5_SIGNALING-1 \n", - "50 HALLMARK_IL6_JAK_STAT3_SIGNALING-0 \n", - "51 HALLMARK_IL6_JAK_STAT3_SIGNALING-1 \n", - "52 HALLMARK_INFLAMMATORY_RESPONSE-0 \n", - "53 HALLMARK_INFLAMMATORY_RESPONSE-1 \n", - "54 HALLMARK_INTERFERON_ALPHA_RESPONSE-0 \n", - "55 HALLMARK_INTERFERON_ALPHA_RESPONSE-1 \n", - "56 HALLMARK_INTERFERON_GAMMA_RESPONSE-0 \n", - "57 HALLMARK_INTERFERON_GAMMA_RESPONSE-1 \n", - "58 HALLMARK_KRAS_SIGNALING_DN-0 \n", - "59 HALLMARK_KRAS_SIGNALING_DN-1 \n", - "60 HALLMARK_KRAS_SIGNALING_UP-0 \n", - "61 HALLMARK_KRAS_SIGNALING_UP-1 \n", - "62 HALLMARK_MITOTIC_SPINDLE-0 \n", - "63 HALLMARK_MITOTIC_SPINDLE-1 \n", - "64 HALLMARK_MTORC1_SIGNALING-0 \n", - "65 HALLMARK_MTORC1_SIGNALING-1 \n", - "66 HALLMARK_MYC_TARGETS_V1-0 \n", - "67 HALLMARK_MYC_TARGETS_V1-1 \n", - "68 HALLMARK_MYC_TARGETS_V2-0 \n", - "69 HALLMARK_MYC_TARGETS_V2-1 \n", - "70 HALLMARK_MYOGENESIS-0 \n", - "71 HALLMARK_MYOGENESIS-1 \n", - "72 HALLMARK_NOTCH_SIGNALING-0 \n", - "73 HALLMARK_NOTCH_SIGNALING-1 \n", - "74 HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 \n", - "75 HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 \n", - "76 HALLMARK_P53_PATHWAY-0 \n", - "77 HALLMARK_P53_PATHWAY-1 \n", - "78 HALLMARK_PANCREAS_BETA_CELLS-0 \n", - "79 HALLMARK_PANCREAS_BETA_CELLS-1 \n", - "80 HALLMARK_PEROXISOME-0 \n", - "81 HALLMARK_PEROXISOME-1 \n", - "82 HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 \n", - "83 HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 \n", - "84 HALLMARK_PROTEIN_SECRETION-0 \n", - "85 HALLMARK_PROTEIN_SECRETION-1 \n", - "86 HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 \n", - "87 HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 \n", - "88 HALLMARK_SPERMATOGENESIS-0 \n", - "89 HALLMARK_SPERMATOGENESIS-1 \n", - "90 HALLMARK_TGF_BETA_SIGNALING-0 \n", - "91 HALLMARK_TGF_BETA_SIGNALING-1 \n", - "92 HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 \n", - "93 HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 \n", - "94 HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 \n", - "95 HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 \n", - "96 HALLMARK_UV_RESPONSE_DN-0 \n", - "97 HALLMARK_UV_RESPONSE_DN-1 \n", - "98 HALLMARK_UV_RESPONSE_UP-0 \n", - "99 HALLMARK_UV_RESPONSE_UP-1 \n", - "100 HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 \n", - "101 HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 \n", - "102 T cell proliferation-0 \n", - "103 T cell proliferation-1 \n", - "104 Yamanaka-TFs-0 \n", - "105 Yamanaka-TFs-1 \n", - "106 amigo-example-0 \n", - "107 amigo-example-1 \n", - "108 bicluster_RNAseqDB_0-0 \n", - "109 bicluster_RNAseqDB_0-1 \n", - "110 bicluster_RNAseqDB_1002-0 \n", - "111 bicluster_RNAseqDB_1002-1 \n", - "112 endocytosis-0 \n", - "113 endocytosis-1 \n", - "114 glycolysis-gocam-0 \n", - "115 glycolysis-gocam-1 \n", - "116 go-postsynapse-calcium-transmembrane-0 \n", - "117 go-postsynapse-calcium-transmembrane-1 \n", - "118 go-reg-autophagy-pkra-0 \n", - "119 go-reg-autophagy-pkra-1 \n", - "120 hydrolase activity, hydrolyzing O-glycosyl compounds-0 \n", - "121 hydrolase activity, hydrolyzing O-glycosyl compounds-1 \n", - "122 ig-receptor-binding-2022-0 \n", - "123 ig-receptor-binding-2022-1 \n", - "124 meiosis I-0 \n", - "125 meiosis I-1 \n", - "126 molecular sequestering-0 \n", - "127 molecular sequestering-1 \n", - "128 mtorc1-0 \n", - "129 mtorc1-1 \n", - "130 peroxisome-0 \n", - "131 peroxisome-1 \n", - "132 progeria-0 \n", - "133 progeria-1 \n", - "134 regulation of presynaptic membrane potential-0 \n", - "135 regulation of presynaptic membrane potential-1 \n", - "136 sensory ataxia-0 \n", - "137 sensory ataxia-1 \n", - "138 term-GO:0007212-0 \n", - "139 term-GO:0007212-1 \n", - "140 tf-downreg-colorectal-0 \n", - "141 tf-downreg-colorectal-1 \n", - "142 EDS-0 \n", - "143 EDS-1 \n", - "144 FA-0 \n", - "145 FA-1 \n", - "146 HALLMARK_ADIPOGENESIS-0 \n", - "147 HALLMARK_ADIPOGENESIS-1 \n", - "148 HALLMARK_ALLOGRAFT_REJECTION-0 \n", - "149 HALLMARK_ALLOGRAFT_REJECTION-1 \n", - "150 HALLMARK_ANDROGEN_RESPONSE-0 \n", - "151 HALLMARK_ANDROGEN_RESPONSE-1 \n", - "152 HALLMARK_ANGIOGENESIS-0 \n", - "153 HALLMARK_ANGIOGENESIS-1 \n", - "154 HALLMARK_APICAL_JUNCTION-0 \n", - "155 HALLMARK_APICAL_JUNCTION-1 \n", - "156 HALLMARK_APICAL_SURFACE-0 \n", - "157 HALLMARK_APICAL_SURFACE-1 \n", - "158 HALLMARK_APOPTOSIS-0 \n", - "159 HALLMARK_APOPTOSIS-1 \n", - "160 HALLMARK_BILE_ACID_METABOLISM-0 \n", - "161 HALLMARK_BILE_ACID_METABOLISM-1 \n", - "162 HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 \n", - "163 HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 \n", - "164 HALLMARK_COAGULATION-0 \n", - "165 HALLMARK_COAGULATION-1 \n", - "166 HALLMARK_COMPLEMENT-0 \n", - "167 HALLMARK_COMPLEMENT-1 \n", - "168 HALLMARK_DNA_REPAIR-0 \n", - "169 HALLMARK_DNA_REPAIR-1 \n", - "170 HALLMARK_E2F_TARGETS-0 \n", - "171 HALLMARK_E2F_TARGETS-1 \n", - "172 HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 \n", - "173 HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 \n", - "174 HALLMARK_ESTROGEN_RESPONSE_EARLY-0 \n", - "175 HALLMARK_ESTROGEN_RESPONSE_EARLY-1 \n", - "176 HALLMARK_ESTROGEN_RESPONSE_LATE-0 \n", - "177 HALLMARK_ESTROGEN_RESPONSE_LATE-1 \n", - "178 HALLMARK_FATTY_ACID_METABOLISM-0 \n", - "179 HALLMARK_FATTY_ACID_METABOLISM-1 \n", - "180 HALLMARK_G2M_CHECKPOINT-0 \n", - "181 HALLMARK_G2M_CHECKPOINT-1 \n", - "182 HALLMARK_GLYCOLYSIS-0 \n", - "183 HALLMARK_GLYCOLYSIS-1 \n", - "184 HALLMARK_HEDGEHOG_SIGNALING-0 \n", - "185 HALLMARK_HEDGEHOG_SIGNALING-1 \n", - "186 HALLMARK_HEME_METABOLISM-0 \n", - "187 HALLMARK_HEME_METABOLISM-1 \n", - "188 HALLMARK_HYPOXIA-0 \n", - "189 HALLMARK_HYPOXIA-1 \n", - "190 HALLMARK_IL2_STAT5_SIGNALING-0 \n", - "191 HALLMARK_IL2_STAT5_SIGNALING-1 \n", - "192 HALLMARK_IL6_JAK_STAT3_SIGNALING-0 \n", - "193 HALLMARK_IL6_JAK_STAT3_SIGNALING-1 \n", - "194 HALLMARK_INFLAMMATORY_RESPONSE-0 \n", - "195 HALLMARK_INFLAMMATORY_RESPONSE-1 \n", - "196 HALLMARK_INTERFERON_ALPHA_RESPONSE-0 \n", - "197 HALLMARK_INTERFERON_ALPHA_RESPONSE-1 \n", - "198 HALLMARK_INTERFERON_GAMMA_RESPONSE-0 \n", - "199 HALLMARK_INTERFERON_GAMMA_RESPONSE-1 \n", - "200 HALLMARK_KRAS_SIGNALING_DN-0 \n", - "201 HALLMARK_KRAS_SIGNALING_DN-1 \n", - "202 HALLMARK_KRAS_SIGNALING_UP-0 \n", - "203 HALLMARK_KRAS_SIGNALING_UP-1 \n", - "204 HALLMARK_MITOTIC_SPINDLE-0 \n", - "205 HALLMARK_MITOTIC_SPINDLE-1 \n", - "206 HALLMARK_MTORC1_SIGNALING-0 \n", - "207 HALLMARK_MTORC1_SIGNALING-1 \n", - "208 HALLMARK_MYC_TARGETS_V1-0 \n", - "209 HALLMARK_MYC_TARGETS_V1-1 \n", - "210 HALLMARK_MYC_TARGETS_V2-0 \n", - "211 HALLMARK_MYC_TARGETS_V2-1 \n", - "212 HALLMARK_MYOGENESIS-0 \n", - "213 HALLMARK_MYOGENESIS-1 \n", - "214 HALLMARK_NOTCH_SIGNALING-0 \n", - "215 HALLMARK_NOTCH_SIGNALING-1 \n", - "216 HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 \n", - "217 HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 \n", - "218 HALLMARK_P53_PATHWAY-0 \n", - "219 HALLMARK_P53_PATHWAY-1 \n", - "220 HALLMARK_PANCREAS_BETA_CELLS-0 \n", - "221 HALLMARK_PANCREAS_BETA_CELLS-1 \n", - "222 HALLMARK_PEROXISOME-0 \n", - "223 HALLMARK_PEROXISOME-1 \n", - "224 HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 \n", - "225 HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 \n", - "226 HALLMARK_PROTEIN_SECRETION-0 \n", - "227 HALLMARK_PROTEIN_SECRETION-1 \n", - "228 HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 \n", - "229 HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 \n", - "230 HALLMARK_SPERMATOGENESIS-0 \n", - "231 HALLMARK_SPERMATOGENESIS-1 \n", - "232 HALLMARK_TGF_BETA_SIGNALING-0 \n", - "233 HALLMARK_TGF_BETA_SIGNALING-1 \n", - "234 HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 \n", - "235 HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 \n", - "236 HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 \n", - "237 HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 \n", - "238 HALLMARK_UV_RESPONSE_DN-0 \n", - "239 HALLMARK_UV_RESPONSE_DN-1 \n", - "240 HALLMARK_UV_RESPONSE_UP-0 \n", - "241 HALLMARK_UV_RESPONSE_UP-1 \n", - "242 HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 \n", - "243 HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 \n", - "244 T cell proliferation-0 \n", - "245 T cell proliferation-1 \n", - "246 Yamanaka-TFs-0 \n", - "247 Yamanaka-TFs-1 \n", - "248 amigo-example-0 \n", - "249 amigo-example-1 \n", - "250 bicluster_RNAseqDB_0-0 \n", - "251 bicluster_RNAseqDB_0-1 \n", - "252 bicluster_RNAseqDB_1002-0 \n", - "253 bicluster_RNAseqDB_1002-1 \n", - "254 endocytosis-0 \n", - "255 endocytosis-1 \n", - "256 glycolysis-gocam-0 \n", - "257 glycolysis-gocam-1 \n", - "258 go-postsynapse-calcium-transmembrane-0 \n", - "259 go-postsynapse-calcium-transmembrane-1 \n", - "260 go-reg-autophagy-pkra-0 \n", - "261 go-reg-autophagy-pkra-1 \n", - "262 hydrolase activity, hydrolyzing O-glycosyl compounds-0 \n", - "263 hydrolase activity, hydrolyzing O-glycosyl compounds-1 \n", - "264 ig-receptor-binding-2022-0 \n", - "265 ig-receptor-binding-2022-1 \n", - "266 meiosis I-0 \n", - "267 meiosis I-1 \n", - "268 molecular sequestering-0 \n", - "269 molecular sequestering-1 \n", - "270 mtorc1-0 \n", - "271 mtorc1-1 \n", - "272 peroxisome-0 \n", - "273 peroxisome-1 \n", - "274 progeria-0 \n", - "275 progeria-1 \n", - "276 regulation of presynaptic membrane potential-0 \n", - "277 regulation of presynaptic membrane potential-1 \n", - "278 sensory ataxia-0 \n", - "279 sensory ataxia-1 \n", - "280 term-GO:0007212-0 \n", - "281 term-GO:0007212-1 \n", - "282 tf-downreg-colorectal-0 \n", - "283 tf-downreg-colorectal-1 \n", - "284 EDS-0 \n", - "285 EDS-1 \n", - "286 FA-0 \n", - "287 FA-1 \n", - "288 HALLMARK_ADIPOGENESIS-0 \n", - "289 HALLMARK_ADIPOGENESIS-1 \n", - "290 HALLMARK_ALLOGRAFT_REJECTION-0 \n", - "291 HALLMARK_ALLOGRAFT_REJECTION-1 \n", - "292 HALLMARK_ANDROGEN_RESPONSE-0 \n", - "293 HALLMARK_ANDROGEN_RESPONSE-1 \n", - "294 HALLMARK_ANGIOGENESIS-0 \n", - "295 HALLMARK_ANGIOGENESIS-1 \n", - "296 HALLMARK_APICAL_JUNCTION-0 \n", - "297 HALLMARK_APICAL_JUNCTION-1 \n", - "298 HALLMARK_APICAL_SURFACE-0 \n", - "299 HALLMARK_APICAL_SURFACE-1 \n", - "300 HALLMARK_APOPTOSIS-0 \n", - "301 HALLMARK_APOPTOSIS-1 \n", - "302 HALLMARK_BILE_ACID_METABOLISM-0 \n", - "303 HALLMARK_BILE_ACID_METABOLISM-1 \n", - "304 HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 \n", - "305 HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 \n", - "306 HALLMARK_COAGULATION-0 \n", - "307 HALLMARK_COAGULATION-1 \n", - "308 HALLMARK_COMPLEMENT-0 \n", - "309 HALLMARK_COMPLEMENT-1 \n", - "310 HALLMARK_DNA_REPAIR-0 \n", - "311 HALLMARK_DNA_REPAIR-1 \n", - "312 HALLMARK_E2F_TARGETS-0 \n", - "313 HALLMARK_E2F_TARGETS-1 \n", - "314 HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 \n", - "315 HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 \n", - "316 HALLMARK_ESTROGEN_RESPONSE_EARLY-0 \n", - "317 HALLMARK_ESTROGEN_RESPONSE_EARLY-1 \n", - "318 HALLMARK_ESTROGEN_RESPONSE_LATE-0 \n", - "319 HALLMARK_ESTROGEN_RESPONSE_LATE-1 \n", - "320 HALLMARK_FATTY_ACID_METABOLISM-0 \n", - "321 HALLMARK_FATTY_ACID_METABOLISM-1 \n", - "322 HALLMARK_G2M_CHECKPOINT-0 \n", - "323 HALLMARK_G2M_CHECKPOINT-1 \n", - "324 HALLMARK_GLYCOLYSIS-0 \n", - "325 HALLMARK_GLYCOLYSIS-1 \n", - "326 HALLMARK_HEDGEHOG_SIGNALING-0 \n", - "327 HALLMARK_HEDGEHOG_SIGNALING-1 \n", - "328 HALLMARK_HEME_METABOLISM-0 \n", - "329 HALLMARK_HEME_METABOLISM-1 \n", - "330 HALLMARK_HYPOXIA-0 \n", - "331 HALLMARK_HYPOXIA-1 \n", - "332 HALLMARK_IL2_STAT5_SIGNALING-0 \n", - "333 HALLMARK_IL2_STAT5_SIGNALING-1 \n", - "334 HALLMARK_IL6_JAK_STAT3_SIGNALING-0 \n", - "335 HALLMARK_IL6_JAK_STAT3_SIGNALING-1 \n", - "336 HALLMARK_INFLAMMATORY_RESPONSE-0 \n", - "337 HALLMARK_INFLAMMATORY_RESPONSE-1 \n", - "338 HALLMARK_INTERFERON_ALPHA_RESPONSE-0 \n", - "339 HALLMARK_INTERFERON_ALPHA_RESPONSE-1 \n", - "340 HALLMARK_INTERFERON_GAMMA_RESPONSE-0 \n", - "341 HALLMARK_INTERFERON_GAMMA_RESPONSE-1 \n", - "342 HALLMARK_KRAS_SIGNALING_DN-0 \n", - "343 HALLMARK_KRAS_SIGNALING_DN-1 \n", - "344 HALLMARK_KRAS_SIGNALING_UP-0 \n", - "345 HALLMARK_KRAS_SIGNALING_UP-1 \n", - "346 HALLMARK_MITOTIC_SPINDLE-0 \n", - "347 HALLMARK_MITOTIC_SPINDLE-1 \n", - "348 HALLMARK_MTORC1_SIGNALING-0 \n", - "349 HALLMARK_MTORC1_SIGNALING-1 \n", - "350 HALLMARK_MYC_TARGETS_V1-0 \n", - "351 HALLMARK_MYC_TARGETS_V1-1 \n", - "352 HALLMARK_MYC_TARGETS_V2-0 \n", - "353 HALLMARK_MYC_TARGETS_V2-1 \n", - "354 HALLMARK_MYOGENESIS-0 \n", - "355 HALLMARK_MYOGENESIS-1 \n", - "356 HALLMARK_NOTCH_SIGNALING-0 \n", - "357 HALLMARK_NOTCH_SIGNALING-1 \n", - "358 HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 \n", - "359 HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 \n", - "360 HALLMARK_P53_PATHWAY-0 \n", - "361 HALLMARK_P53_PATHWAY-1 \n", - "362 HALLMARK_PANCREAS_BETA_CELLS-0 \n", - "363 HALLMARK_PANCREAS_BETA_CELLS-1 \n", - "364 HALLMARK_PEROXISOME-0 \n", - "365 HALLMARK_PEROXISOME-1 \n", - "366 HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 \n", - "367 HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 \n", - "368 HALLMARK_PROTEIN_SECRETION-0 \n", - "369 HALLMARK_PROTEIN_SECRETION-1 \n", - "370 HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 \n", - "371 HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 \n", - "372 HALLMARK_SPERMATOGENESIS-0 \n", - "373 HALLMARK_SPERMATOGENESIS-1 \n", - "374 HALLMARK_TGF_BETA_SIGNALING-0 \n", - "375 HALLMARK_TGF_BETA_SIGNALING-1 \n", - "376 HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 \n", - "377 HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 \n", - "378 HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 \n", - "379 HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 \n", - "380 HALLMARK_UV_RESPONSE_DN-0 \n", - "381 HALLMARK_UV_RESPONSE_DN-1 \n", - "382 HALLMARK_UV_RESPONSE_UP-0 \n", - "383 HALLMARK_UV_RESPONSE_UP-1 \n", - "384 HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 \n", - "385 HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 \n", - "386 T cell proliferation-0 \n", - "387 T cell proliferation-1 \n", - "388 Yamanaka-TFs-0 \n", - "389 Yamanaka-TFs-1 \n", - "390 amigo-example-0 \n", - "391 amigo-example-1 \n", - "392 bicluster_RNAseqDB_0-0 \n", - "393 bicluster_RNAseqDB_0-1 \n", - "394 bicluster_RNAseqDB_1002-0 \n", - "395 bicluster_RNAseqDB_1002-1 \n", - "396 endocytosis-0 \n", - "397 endocytosis-1 \n", - "398 glycolysis-gocam-0 \n", - "399 glycolysis-gocam-1 \n", - "400 go-postsynapse-calcium-transmembrane-0 \n", - "401 go-postsynapse-calcium-transmembrane-1 \n", - "402 go-reg-autophagy-pkra-0 \n", - "403 go-reg-autophagy-pkra-1 \n", - "404 hydrolase activity, hydrolyzing O-glycosyl compounds-0 \n", - "405 hydrolase activity, hydrolyzing O-glycosyl compounds-1 \n", - "406 ig-receptor-binding-2022-0 \n", - "407 ig-receptor-binding-2022-1 \n", - "408 meiosis I-0 \n", - "409 meiosis I-1 \n", - "410 molecular sequestering-0 \n", - "411 molecular sequestering-1 \n", - "412 mtorc1-0 \n", - "413 mtorc1-1 \n", - "414 peroxisome-0 \n", - "415 peroxisome-1 \n", - "416 progeria-0 \n", - "417 progeria-1 \n", - "418 regulation of presynaptic membrane potential-0 \n", - "419 regulation of presynaptic membrane potential-1 \n", - "420 sensory ataxia-0 \n", - "421 sensory ataxia-1 \n", - "422 term-GO:0007212-0 \n", - "423 term-GO:0007212-1 \n", - "424 tf-downreg-colorectal-0 \n", - "425 tf-downreg-colorectal-1 \n", - "426 EDS-0 \n", - "427 EDS-1 \n", - "428 FA-0 \n", - "429 FA-1 \n", - "430 HALLMARK_ADIPOGENESIS-0 \n", - "431 HALLMARK_ADIPOGENESIS-1 \n", - "432 HALLMARK_ALLOGRAFT_REJECTION-0 \n", - "433 HALLMARK_ALLOGRAFT_REJECTION-1 \n", - "434 HALLMARK_ANDROGEN_RESPONSE-0 \n", - "435 HALLMARK_ANDROGEN_RESPONSE-1 \n", - "436 HALLMARK_ANGIOGENESIS-0 \n", - "437 HALLMARK_ANGIOGENESIS-1 \n", - "438 HALLMARK_APICAL_JUNCTION-0 \n", - "439 HALLMARK_APICAL_JUNCTION-1 \n", - "440 HALLMARK_APICAL_SURFACE-0 \n", - "441 HALLMARK_APICAL_SURFACE-1 \n", - "442 HALLMARK_APOPTOSIS-0 \n", - "443 HALLMARK_APOPTOSIS-1 \n", - "444 HALLMARK_BILE_ACID_METABOLISM-0 \n", - "445 HALLMARK_BILE_ACID_METABOLISM-1 \n", - "446 HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 \n", - "447 HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 \n", - "448 HALLMARK_COAGULATION-0 \n", - "449 HALLMARK_COAGULATION-1 \n", - "450 HALLMARK_COMPLEMENT-0 \n", - "451 HALLMARK_COMPLEMENT-1 \n", - "452 HALLMARK_DNA_REPAIR-0 \n", - "453 HALLMARK_DNA_REPAIR-1 \n", - "454 HALLMARK_E2F_TARGETS-0 \n", - "455 HALLMARK_E2F_TARGETS-1 \n", - "456 HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 \n", - "457 HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 \n", - "458 HALLMARK_ESTROGEN_RESPONSE_EARLY-0 \n", - "459 HALLMARK_ESTROGEN_RESPONSE_EARLY-1 \n", - "460 HALLMARK_ESTROGEN_RESPONSE_LATE-0 \n", - "461 HALLMARK_ESTROGEN_RESPONSE_LATE-1 \n", - "462 HALLMARK_FATTY_ACID_METABOLISM-0 \n", - "463 HALLMARK_FATTY_ACID_METABOLISM-1 \n", - "464 HALLMARK_G2M_CHECKPOINT-0 \n", - "465 HALLMARK_G2M_CHECKPOINT-1 \n", - "466 HALLMARK_GLYCOLYSIS-0 \n", - "467 HALLMARK_GLYCOLYSIS-1 \n", - "468 HALLMARK_HEDGEHOG_SIGNALING-0 \n", - "469 HALLMARK_HEDGEHOG_SIGNALING-1 \n", - "470 HALLMARK_HEME_METABOLISM-0 \n", - "471 HALLMARK_HEME_METABOLISM-1 \n", - "472 HALLMARK_HYPOXIA-0 \n", - "473 HALLMARK_HYPOXIA-1 \n", - "474 HALLMARK_IL2_STAT5_SIGNALING-0 \n", - "475 HALLMARK_IL2_STAT5_SIGNALING-1 \n", - "476 HALLMARK_IL6_JAK_STAT3_SIGNALING-0 \n", - "477 HALLMARK_IL6_JAK_STAT3_SIGNALING-1 \n", - "478 HALLMARK_INFLAMMATORY_RESPONSE-0 \n", - "479 HALLMARK_INFLAMMATORY_RESPONSE-1 \n", - "480 HALLMARK_INTERFERON_ALPHA_RESPONSE-0 \n", - "481 HALLMARK_INTERFERON_ALPHA_RESPONSE-1 \n", - "482 HALLMARK_INTERFERON_GAMMA_RESPONSE-0 \n", - "483 HALLMARK_INTERFERON_GAMMA_RESPONSE-1 \n", - "484 HALLMARK_KRAS_SIGNALING_DN-0 \n", - "485 HALLMARK_KRAS_SIGNALING_DN-1 \n", - "486 HALLMARK_KRAS_SIGNALING_UP-0 \n", - "487 HALLMARK_KRAS_SIGNALING_UP-1 \n", - "488 HALLMARK_MITOTIC_SPINDLE-0 \n", - "489 HALLMARK_MITOTIC_SPINDLE-1 \n", - "490 HALLMARK_MTORC1_SIGNALING-0 \n", - "491 HALLMARK_MTORC1_SIGNALING-1 \n", - "492 HALLMARK_MYC_TARGETS_V1-0 \n", - "493 HALLMARK_MYC_TARGETS_V1-1 \n", - "494 HALLMARK_MYC_TARGETS_V2-0 \n", - "495 HALLMARK_MYC_TARGETS_V2-1 \n", - "496 HALLMARK_MYOGENESIS-0 \n", - "497 HALLMARK_MYOGENESIS-1 \n", - "498 HALLMARK_NOTCH_SIGNALING-0 \n", - "499 HALLMARK_NOTCH_SIGNALING-1 \n", - "500 HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 \n", - "501 HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 \n", - "502 HALLMARK_P53_PATHWAY-0 \n", - "503 HALLMARK_P53_PATHWAY-1 \n", - "504 HALLMARK_PANCREAS_BETA_CELLS-0 \n", - "505 HALLMARK_PANCREAS_BETA_CELLS-1 \n", - "506 HALLMARK_PEROXISOME-0 \n", - "507 HALLMARK_PEROXISOME-1 \n", - "508 HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 \n", - "509 HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 \n", - "510 HALLMARK_PROTEIN_SECRETION-0 \n", - "511 HALLMARK_PROTEIN_SECRETION-1 \n", - "512 HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 \n", - "513 HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 \n", - "514 HALLMARK_SPERMATOGENESIS-0 \n", - "515 HALLMARK_SPERMATOGENESIS-1 \n", - "516 HALLMARK_TGF_BETA_SIGNALING-0 \n", - "517 HALLMARK_TGF_BETA_SIGNALING-1 \n", - "518 HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 \n", - "519 HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 \n", - "520 HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 \n", - "521 HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 \n", - "522 HALLMARK_UV_RESPONSE_DN-0 \n", - "523 HALLMARK_UV_RESPONSE_DN-1 \n", - "524 HALLMARK_UV_RESPONSE_UP-0 \n", - "525 HALLMARK_UV_RESPONSE_UP-1 \n", - "526 HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 \n", - "527 HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 \n", - "528 T cell proliferation-0 \n", - "529 T cell proliferation-1 \n", - "530 Yamanaka-TFs-0 \n", - "531 Yamanaka-TFs-1 \n", - "532 amigo-example-0 \n", - "533 amigo-example-1 \n", - "534 bicluster_RNAseqDB_0-0 \n", - "535 bicluster_RNAseqDB_0-1 \n", - "536 bicluster_RNAseqDB_1002-0 \n", - "537 bicluster_RNAseqDB_1002-1 \n", - "538 endocytosis-0 \n", - "539 endocytosis-1 \n", - "540 glycolysis-gocam-0 \n", - "541 glycolysis-gocam-1 \n", - "542 go-postsynapse-calcium-transmembrane-0 \n", - "543 go-postsynapse-calcium-transmembrane-1 \n", - "544 go-reg-autophagy-pkra-0 \n", - "545 go-reg-autophagy-pkra-1 \n", - "546 hydrolase activity, hydrolyzing O-glycosyl compounds-0 \n", - "547 hydrolase activity, hydrolyzing O-glycosyl compounds-1 \n", - "548 ig-receptor-binding-2022-0 \n", - "549 ig-receptor-binding-2022-1 \n", - "550 meiosis I-0 \n", - "551 meiosis I-1 \n", - "552 molecular sequestering-0 \n", - "553 molecular sequestering-1 \n", - "554 mtorc1-0 \n", - "555 mtorc1-1 \n", - "556 peroxisome-0 \n", - "557 peroxisome-1 \n", - "558 progeria-0 \n", - "559 progeria-1 \n", - "560 regulation of presynaptic membrane potential-0 \n", - "561 regulation of presynaptic membrane potential-1 \n", - "562 sensory ataxia-0 \n", - "563 sensory ataxia-1 \n", - "564 term-GO:0007212-0 \n", - "565 term-GO:0007212-1 \n", - "566 tf-downreg-colorectal-0 \n", - "567 tf-downreg-colorectal-1 \n", - "568 EDS-0 \n", - "569 EDS-1 \n", - "570 FA-0 \n", - "571 FA-1 \n", - "572 HALLMARK_ADIPOGENESIS-0 \n", - "573 HALLMARK_ADIPOGENESIS-1 \n", - "574 HALLMARK_ALLOGRAFT_REJECTION-0 \n", - "575 HALLMARK_ALLOGRAFT_REJECTION-1 \n", - "576 HALLMARK_ANDROGEN_RESPONSE-0 \n", - "577 HALLMARK_ANDROGEN_RESPONSE-1 \n", - "578 HALLMARK_ANGIOGENESIS-0 \n", - "579 HALLMARK_ANGIOGENESIS-1 \n", - "580 HALLMARK_APICAL_JUNCTION-0 \n", - "581 HALLMARK_APICAL_JUNCTION-1 \n", - "582 HALLMARK_APICAL_SURFACE-0 \n", - "583 HALLMARK_APICAL_SURFACE-1 \n", - "584 HALLMARK_APOPTOSIS-0 \n", - "585 HALLMARK_APOPTOSIS-1 \n", - "586 HALLMARK_BILE_ACID_METABOLISM-0 \n", - "587 HALLMARK_BILE_ACID_METABOLISM-1 \n", - "588 HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 \n", - "589 HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 \n", - "590 HALLMARK_COAGULATION-0 \n", - "591 HALLMARK_COAGULATION-1 \n", - "592 HALLMARK_COMPLEMENT-0 \n", - "593 HALLMARK_COMPLEMENT-1 \n", - "594 HALLMARK_DNA_REPAIR-0 \n", - "595 HALLMARK_DNA_REPAIR-1 \n", - "596 HALLMARK_E2F_TARGETS-0 \n", - "597 HALLMARK_E2F_TARGETS-1 \n", - "598 HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 \n", - "599 HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 \n", - "600 HALLMARK_ESTROGEN_RESPONSE_EARLY-0 \n", - "601 HALLMARK_ESTROGEN_RESPONSE_EARLY-1 \n", - "602 HALLMARK_ESTROGEN_RESPONSE_LATE-0 \n", - "603 HALLMARK_ESTROGEN_RESPONSE_LATE-1 \n", - "604 HALLMARK_FATTY_ACID_METABOLISM-0 \n", - "605 HALLMARK_FATTY_ACID_METABOLISM-1 \n", - "606 HALLMARK_G2M_CHECKPOINT-0 \n", - "607 HALLMARK_G2M_CHECKPOINT-1 \n", - "608 HALLMARK_GLYCOLYSIS-0 \n", - "609 HALLMARK_GLYCOLYSIS-1 \n", - "610 HALLMARK_HEDGEHOG_SIGNALING-0 \n", - "611 HALLMARK_HEDGEHOG_SIGNALING-1 \n", - "612 HALLMARK_HEME_METABOLISM-0 \n", - "613 HALLMARK_HEME_METABOLISM-1 \n", - "614 HALLMARK_HYPOXIA-0 \n", - "615 HALLMARK_HYPOXIA-1 \n", - "616 HALLMARK_IL2_STAT5_SIGNALING-0 \n", - "617 HALLMARK_IL2_STAT5_SIGNALING-1 \n", - "618 HALLMARK_IL6_JAK_STAT3_SIGNALING-0 \n", - "619 HALLMARK_IL6_JAK_STAT3_SIGNALING-1 \n", - "620 HALLMARK_INFLAMMATORY_RESPONSE-0 \n", - "621 HALLMARK_INFLAMMATORY_RESPONSE-1 \n", - "622 HALLMARK_INTERFERON_ALPHA_RESPONSE-0 \n", - "623 HALLMARK_INTERFERON_ALPHA_RESPONSE-1 \n", - "624 HALLMARK_INTERFERON_GAMMA_RESPONSE-0 \n", - "625 HALLMARK_INTERFERON_GAMMA_RESPONSE-1 \n", - "626 HALLMARK_KRAS_SIGNALING_DN-0 \n", - "627 HALLMARK_KRAS_SIGNALING_DN-1 \n", - "628 HALLMARK_KRAS_SIGNALING_UP-0 \n", - "629 HALLMARK_KRAS_SIGNALING_UP-1 \n", - "630 HALLMARK_MITOTIC_SPINDLE-0 \n", - "631 HALLMARK_MITOTIC_SPINDLE-1 \n", - "632 HALLMARK_MTORC1_SIGNALING-0 \n", - "633 HALLMARK_MTORC1_SIGNALING-1 \n", - "634 HALLMARK_MYC_TARGETS_V1-0 \n", - "635 HALLMARK_MYC_TARGETS_V1-1 \n", - "636 HALLMARK_MYC_TARGETS_V2-0 \n", - "637 HALLMARK_MYC_TARGETS_V2-1 \n", - "638 HALLMARK_MYOGENESIS-0 \n", - "639 HALLMARK_MYOGENESIS-1 \n", - "640 HALLMARK_NOTCH_SIGNALING-0 \n", - "641 HALLMARK_NOTCH_SIGNALING-1 \n", - "642 HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 \n", - "643 HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 \n", - "644 HALLMARK_P53_PATHWAY-0 \n", - "645 HALLMARK_P53_PATHWAY-1 \n", - "646 HALLMARK_PANCREAS_BETA_CELLS-0 \n", - "647 HALLMARK_PANCREAS_BETA_CELLS-1 \n", - "648 HALLMARK_PEROXISOME-0 \n", - "649 HALLMARK_PEROXISOME-1 \n", - "650 HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 \n", - "651 HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 \n", - "652 HALLMARK_PROTEIN_SECRETION-0 \n", - "653 HALLMARK_PROTEIN_SECRETION-1 \n", - "654 HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 \n", - "655 HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 \n", - "656 HALLMARK_SPERMATOGENESIS-0 \n", - "657 HALLMARK_SPERMATOGENESIS-1 \n", - "658 HALLMARK_TGF_BETA_SIGNALING-0 \n", - "659 HALLMARK_TGF_BETA_SIGNALING-1 \n", - "660 HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 \n", - "661 HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 \n", - "662 HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 \n", - "663 HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 \n", - "664 HALLMARK_UV_RESPONSE_DN-0 \n", - "665 HALLMARK_UV_RESPONSE_DN-1 \n", - "666 HALLMARK_UV_RESPONSE_UP-0 \n", - "667 HALLMARK_UV_RESPONSE_UP-1 \n", - "668 HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 \n", - "669 HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 \n", - "670 T cell proliferation-0 \n", - "671 T cell proliferation-1 \n", - "672 Yamanaka-TFs-0 \n", - "673 Yamanaka-TFs-1 \n", - "674 amigo-example-0 \n", - "675 amigo-example-1 \n", - "676 bicluster_RNAseqDB_0-0 \n", - "677 bicluster_RNAseqDB_0-1 \n", - "678 bicluster_RNAseqDB_1002-0 \n", - "679 bicluster_RNAseqDB_1002-1 \n", - "680 endocytosis-0 \n", - "681 endocytosis-1 \n", - "682 glycolysis-gocam-0 \n", - "683 glycolysis-gocam-1 \n", - "684 go-postsynapse-calcium-transmembrane-0 \n", - "685 go-postsynapse-calcium-transmembrane-1 \n", - "686 go-reg-autophagy-pkra-0 \n", - "687 go-reg-autophagy-pkra-1 \n", - "688 hydrolase activity, hydrolyzing O-glycosyl compounds-0 \n", - "689 hydrolase activity, hydrolyzing O-glycosyl compounds-1 \n", - "690 ig-receptor-binding-2022-0 \n", - "691 ig-receptor-binding-2022-1 \n", - "692 meiosis I-0 \n", - "693 meiosis I-1 \n", - "694 molecular sequestering-0 \n", - "695 molecular sequestering-1 \n", - "696 mtorc1-0 \n", - "697 mtorc1-1 \n", - "698 peroxisome-0 \n", - "699 peroxisome-1 \n", - "700 progeria-0 \n", - "701 progeria-1 \n", - "702 regulation of presynaptic membrane potential-0 \n", - "703 regulation of presynaptic membrane potential-1 \n", - "704 sensory ataxia-0 \n", - "705 sensory ataxia-1 \n", - "706 term-GO:0007212-0 \n", - "707 term-GO:0007212-1 \n", - "708 tf-downreg-colorectal-0 \n", - "709 tf-downreg-colorectal-1 \n", - "710 EDS-0 \n", - "711 EDS-1 \n", - "712 FA-0 \n", - "713 FA-1 \n", - "714 HALLMARK_ADIPOGENESIS-0 \n", - "715 HALLMARK_ADIPOGENESIS-1 \n", - "716 HALLMARK_ALLOGRAFT_REJECTION-0 \n", - "717 HALLMARK_ALLOGRAFT_REJECTION-1 \n", - "718 HALLMARK_ANDROGEN_RESPONSE-0 \n", - "719 HALLMARK_ANDROGEN_RESPONSE-1 \n", - "720 HALLMARK_ANGIOGENESIS-0 \n", - "721 HALLMARK_ANGIOGENESIS-1 \n", - "722 HALLMARK_APICAL_JUNCTION-0 \n", - "723 HALLMARK_APICAL_JUNCTION-1 \n", - "724 HALLMARK_APICAL_SURFACE-0 \n", - "725 HALLMARK_APICAL_SURFACE-1 \n", - "726 HALLMARK_APOPTOSIS-0 \n", - "727 HALLMARK_APOPTOSIS-1 \n", - "728 HALLMARK_BILE_ACID_METABOLISM-0 \n", - "729 HALLMARK_BILE_ACID_METABOLISM-1 \n", - "730 HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 \n", - "731 HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 \n", - "732 HALLMARK_COAGULATION-0 \n", - "733 HALLMARK_COAGULATION-1 \n", - "734 HALLMARK_COMPLEMENT-0 \n", - "735 HALLMARK_COMPLEMENT-1 \n", - "736 HALLMARK_DNA_REPAIR-0 \n", - "737 HALLMARK_DNA_REPAIR-1 \n", - "738 HALLMARK_E2F_TARGETS-0 \n", - "739 HALLMARK_E2F_TARGETS-1 \n", - "740 HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 \n", - "741 HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 \n", - "742 HALLMARK_ESTROGEN_RESPONSE_EARLY-0 \n", - "743 HALLMARK_ESTROGEN_RESPONSE_EARLY-1 \n", - "744 HALLMARK_ESTROGEN_RESPONSE_LATE-0 \n", - "745 HALLMARK_ESTROGEN_RESPONSE_LATE-1 \n", - "746 HALLMARK_FATTY_ACID_METABOLISM-0 \n", - "747 HALLMARK_FATTY_ACID_METABOLISM-1 \n", - "748 HALLMARK_G2M_CHECKPOINT-0 \n", - "749 HALLMARK_G2M_CHECKPOINT-1 \n", - "750 HALLMARK_GLYCOLYSIS-0 \n", - "751 HALLMARK_GLYCOLYSIS-1 \n", - "752 HALLMARK_HEDGEHOG_SIGNALING-0 \n", - "753 HALLMARK_HEDGEHOG_SIGNALING-1 \n", - "754 HALLMARK_HEME_METABOLISM-0 \n", - "755 HALLMARK_HEME_METABOLISM-1 \n", - "756 HALLMARK_HYPOXIA-0 \n", - "757 HALLMARK_HYPOXIA-1 \n", - "758 HALLMARK_IL2_STAT5_SIGNALING-0 \n", - "759 HALLMARK_IL2_STAT5_SIGNALING-1 \n", - "760 HALLMARK_IL6_JAK_STAT3_SIGNALING-0 \n", - "761 HALLMARK_IL6_JAK_STAT3_SIGNALING-1 \n", - "762 HALLMARK_INFLAMMATORY_RESPONSE-0 \n", - "763 HALLMARK_INFLAMMATORY_RESPONSE-1 \n", - "764 HALLMARK_INTERFERON_ALPHA_RESPONSE-0 \n", - "765 HALLMARK_INTERFERON_ALPHA_RESPONSE-1 \n", - "766 HALLMARK_INTERFERON_GAMMA_RESPONSE-0 \n", - "767 HALLMARK_INTERFERON_GAMMA_RESPONSE-1 \n", - "768 HALLMARK_KRAS_SIGNALING_DN-0 \n", - "769 HALLMARK_KRAS_SIGNALING_DN-1 \n", - "770 HALLMARK_KRAS_SIGNALING_UP-0 \n", - "771 HALLMARK_KRAS_SIGNALING_UP-1 \n", - "772 HALLMARK_MITOTIC_SPINDLE-0 \n", - "773 HALLMARK_MITOTIC_SPINDLE-1 \n", - "774 HALLMARK_MTORC1_SIGNALING-0 \n", - "775 HALLMARK_MTORC1_SIGNALING-1 \n", - "776 HALLMARK_MYC_TARGETS_V1-0 \n", - "777 HALLMARK_MYC_TARGETS_V1-1 \n", - "778 HALLMARK_MYC_TARGETS_V2-0 \n", - "779 HALLMARK_MYC_TARGETS_V2-1 \n", - "780 HALLMARK_MYOGENESIS-0 \n", - "781 HALLMARK_MYOGENESIS-1 \n", - "782 HALLMARK_NOTCH_SIGNALING-0 \n", - "783 HALLMARK_NOTCH_SIGNALING-1 \n", - "784 HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 \n", - "785 HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 \n", - "786 HALLMARK_P53_PATHWAY-0 \n", - "787 HALLMARK_P53_PATHWAY-1 \n", - "788 HALLMARK_PANCREAS_BETA_CELLS-0 \n", - "789 HALLMARK_PANCREAS_BETA_CELLS-1 \n", - "790 HALLMARK_PEROXISOME-0 \n", - "791 HALLMARK_PEROXISOME-1 \n", - "792 HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 \n", - "793 HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 \n", - "794 HALLMARK_PROTEIN_SECRETION-0 \n", - "795 HALLMARK_PROTEIN_SECRETION-1 \n", - "796 HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 \n", - "797 HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 \n", - "798 HALLMARK_SPERMATOGENESIS-0 \n", - "799 HALLMARK_SPERMATOGENESIS-1 \n", - "800 HALLMARK_TGF_BETA_SIGNALING-0 \n", - "801 HALLMARK_TGF_BETA_SIGNALING-1 \n", - "802 HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 \n", - "803 HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 \n", - "804 HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 \n", - "805 HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 \n", - "806 HALLMARK_UV_RESPONSE_DN-0 \n", - "807 HALLMARK_UV_RESPONSE_DN-1 \n", - "808 HALLMARK_UV_RESPONSE_UP-0 \n", - "809 HALLMARK_UV_RESPONSE_UP-1 \n", - "810 HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 \n", - "811 HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 \n", - "812 T cell proliferation-0 \n", - "813 T cell proliferation-1 \n", - "814 Yamanaka-TFs-0 \n", - "815 Yamanaka-TFs-1 \n", - "816 amigo-example-0 \n", - "817 amigo-example-1 \n", - "818 bicluster_RNAseqDB_0-0 \n", - "819 bicluster_RNAseqDB_0-1 \n", - "820 bicluster_RNAseqDB_1002-0 \n", - "821 bicluster_RNAseqDB_1002-1 \n", - "822 endocytosis-0 \n", - "823 endocytosis-1 \n", - "824 glycolysis-gocam-0 \n", - "825 glycolysis-gocam-1 \n", - "826 go-postsynapse-calcium-transmembrane-0 \n", - "827 go-postsynapse-calcium-transmembrane-1 \n", - "828 go-reg-autophagy-pkra-0 \n", - "829 go-reg-autophagy-pkra-1 \n", - "830 hydrolase activity, hydrolyzing O-glycosyl compounds-0 \n", - "831 hydrolase activity, hydrolyzing O-glycosyl compounds-1 \n", - "832 ig-receptor-binding-2022-0 \n", - "833 ig-receptor-binding-2022-1 \n", - "834 meiosis I-0 \n", - "835 meiosis I-1 \n", - "836 molecular sequestering-0 \n", - "837 molecular sequestering-1 \n", - "838 mtorc1-0 \n", - "839 mtorc1-1 \n", - "840 peroxisome-0 \n", - "841 peroxisome-1 \n", - "842 progeria-0 \n", - "843 progeria-1 \n", - "844 regulation of presynaptic membrane potential-0 \n", - "845 regulation of presynaptic membrane potential-1 \n", - "846 sensory ataxia-0 \n", - "847 sensory ataxia-1 \n", - "848 term-GO:0007212-0 \n", - "849 term-GO:0007212-1 \n", - "850 tf-downreg-colorectal-0 \n", - "851 tf-downreg-colorectal-1 \n", - "\n", - "prompt_variant v1 \\\n", - "0 [Summary: Genes involved in connective tissue disorders, specifically Ehlers-Danlos syndrome, are enriched for terms related to collagen and extracellular matrix organization.\\nMechanism: The genes encode proteins that play roles in collagen synthesis, modification, and organization, as well as extracellular matrix maturation.\\n] \n", - "1 [Summary: Several of the genes listed are involved in the biosynthesis and regulation of collagen, a key component of connective tissue. Mutations in these genes are associated with Ehlers-Danlos syndrome, a group of genetic disorders that affect collagen production and cause hypermobility of joints, skin elasticity, and tissue fragility.\\n\\nMechanism: The genes listed are involved in collagen biosynthesis and regulation, suggesting that deficiencies or mutations in these genes could lead to abnormal or insufficient collagen production, ultimately resulting in connective tissue disorders such as Ehlers-Danlos syndrome.\\n\\n\\nHypothesis: The genes listed may converge on a pathway that regulates the synthesis, assembly, and remodeling of the extracellular matrix, particularly with respect to collagen and other fibrillar components. Defects or deficiencies in this pathway could lead to dysregulation of tissue remodeling and repair, resulting in connective tissue disorders such as Ehlers-Danlos syndrome.] \n", - "2 [Summary: Genes related to the Fanconi anemia complementation group and other DNA repair components\\nMechanism: DNA repair \\n] \n", - "3 [Summary: The genes in this list are predominantly involved in DNA repair, specifically in the Fanconi anemia (FA) pathway and homologous recombination (HR) pathway. \\n\\nMechanism: The FA pathway is a complex pathway involved in the repair of DNA interstrand crosslinks and other forms of DNA damage. The HR pathway is involved in the repair of double-strand breaks in DNA.\\n\\n] \n", - "4 [Summary: Genes involved in energy metabolism and mitochondrial function are over-represented.\\n\\nMechanism: These genes likely play a role in regulating cellular energy metabolism, particularly through mitochondrial function.\\n\\n] \n", - "5 [Summary: Many of the genes in the list are involved in mitochondrial function, specifically in the respiratory chain and energy production. Other common functions include lipid metabolism and transport, protein binding, and regulation of cell growth and division.\\n\\n\\nHypothesis: These genes may be involved in maintaining cell and mitochondrial function, particularly in energy production and membrane transport. Many are also involved in regulating oxidative stress, which can damage cells and contribute to a range of diseases. Overall, the commonalities suggest that these genes play important roles in maintaining cellular and mitochondrial health, and dysregulation of these genes may contribute to metabolic disorders, neurodegenerative diseases, and other health problems.] \n", - "6 [Summary: Immune response and cytokine signaling pathways are enriched in this set of genes.\\nMechanism: These genes are involved in the regulation of immune response and activation of cytokine signaling pathways.\\n] \n", - "7 [Summary: Immune response and cytokine signaling\\nMechanism: Regulation of immune response through cytokine signaling pathways\\n\\nHypothesis: The enriched terms all relate to the regulation of immune response through cytokine signaling pathways. The genes in this list are involved in the production and function of chemokines and cytokines, which play key roles in immune system communication and response. Toll-like receptors, interferon signaling, and TNF signaling pathways are important components of the innate immune response, while TGF-beta signaling plays a role in immune tolerance and regulation. Overall, this gene list suggests a strong focus on immune response and regulation.] \n", - "8 [Summary: Signal transduction and cellular metabolism\\n\\nHypothesis: These genes may be involved in a signaling pathway that regulates cellular metabolism in response to extracellular signals. They may work together to modulate the activity of various enzymes and transporters, leading to changes in the levels of key metabolic intermediates and ultimately contributing to the regulation of cellular metabolism.] \n", - "9 [Summary: Protein regulation and cellular signaling pathways\\nMechanism: Enzyme-catalyzed reactions and protein-protein interactions\\n] \n", - "10 [Summary: Extracellular matrix proteins and signaling molecules are enriched among the listed genes.\\nMechanism: These genes may be involved in the regulation of tissue development and regeneration, as well as cell growth, migration, and adhesion. \\n] \n", - "11 [Summary: Extracellular matrix (ECM) organization and cell adhesion/migration are enriched functions among the listed genes.\\nMechanism: The listed genes are involved in regulating ECM integrity and cell adhesion/migration, which are critical processes in development and tissue homeostasis. Dysregulation of these processes can contribute to pathogenesis of a variety of diseases, including cancer.\\n] \n", - "12 [Summary: Genes involved in cytoskeleton organization, cell adhesion, and signal transduction.\\nMechanism: These genes likely play a role in the maintenance of cellular morphology, adhesion, and proper communication between cells.\\n] \n", - "13 [Summary: Genes involved in cell adhesion, specifically with roles in tight junction formation and maintenance, as well as extracellular matrix interactions.\\n\\nMechanism: These genes are involved in various molecular mechanisms related to cell adhesion, including tight junction formation/maintenance, extracellular matrix interactions and basement membrane organization.\\n\\n] \n", - "14 [Summary: This list includes genes with diverse functions such as cell signaling, growth inhibition, and ion transport. However, common enriched terms suggest involvement in cell adhesion and regulation.\\nMechanism: The genes appear to be involved in molecular networks responsible for the regulation and maintenance of the cell membrane, particularly in receptor-mediated cell signaling and cell adhesion.\\n] \n", - "15 [Summary: Cell adhesion and signaling pathways are enriched among the given set of human genes.\\n\\nMechanism: The enriched genes are involved in various processes, including transport, development, and regulation of the immune system, and these processes are intertwined in signaling pathways that affect cell adhesion.\\n\\n] \n", - "16 [Summary: Apoptotic processes and regulation of cell death are enriched terms in the gene list.\\n\\n] \n", - "17 [Summary: Genes involved in apoptosis, cytokine signaling, and growth factor regulation.\\n\\nMechanism: These genes all play a role in regulating cell survival and growth, primarily through apoptosis, cytokine signaling, and growth factor regulation.\\n\\n] \n", - "18 [Summary: Membrane-associated proteins that are members of the superfamily of ATP-binding cassette (ABC) transporters, as well as enzymes involved in lipid metabolism, are over-represented in this gene list. \\n\\nMechanism: Several of the enriched terms relate to lipid metabolism, suggesting that these genes may be involved in the transport or regulation of various lipids within the body. \\n\\n] \n", - "19 [Summary: Peroxisomal biogenesis and lipid metabolism are enriched functions among the given genes.\\nMechanism: Peroxins (PEXs) are essential proteins for functional peroxisome assembly. Peroxisomes are organelles involved in lipid metabolism, fatty acid beta-oxidation, and bile acid synthesis.\\n\\n] \n", - "20 [Summary: Lipid metabolism and cholesterol homeostasis are over-represented functions amongst the list of genes.\\n\\nMechanism: These genes are involved in the regulation of cholesterol levels in cells, lipid metabolism and transport of various molecules across cell membranes. \\n\\n] \n", - "21 [Summary: Genes involved in cholesterol biosynthesis, lipid metabolism, and signal transduction.\\nMechanism: Biosynthesis and regulation of cholesterol and lipids.\\n\\nHypothesis: These genes are involved in the complex pathways of cholesterol biosynthesis and lipid metabolism, which are tightly regulated processes where disturbances can lead to a wide range of diseases. The genes identified here may play key roles in these pathways, including enzymes involved in the conversion of mevalonate to cholesterol, fatty acid desaturases regulating lipid unsaturation, and phospholipid-binding proteins regulating signal transduction. Further research into these mechanisms could aid in the development of therapies for metabolic disorders such as atherosclerosis and hyperlipidemia.] \n", - "22 [Summary: Many of the genes in this list are involved in blood clotting and complement activation, while others are proteases, lipoproteins, or involved in extracellular matrix regulation.\\nMechanism: These genes are involved in regulating or participating in protease activities, blood clotting, and complement activation, as well as extracellular matrix regulation.\\n\\nHypothesis: The enriched terms suggest that these genes may be involved in a regulatory network that balances protease activities, blood clotting, complement activation, and extracellular matrix regulation. Dysregulation of this network may lead to pathologies such as thrombosis, inflammation, and tissue remodeling. The specific biological mechanisms involved can include protease activation and inhibition, substrate recognition, signal transduction, and gene expression regulation.] \n", - "23 [Summary: The enriched terms are related to blood coagulation and complement pathway, as well as extracellular matrix degradation and calcium-binding proteins.\\n\\n\\nHypothesis: The coagulation, complement, and extracellular matrix remodelling pathways are interconnected through multiple mechanisms and play crucial roles in maintaining tissue homeostasis and repair. Dysregulation of these pathways is associated with several human diseases, such as thrombosis, autoimmune disorders, and cancer. Calcium ions are essential for mediating] \n", - "24 [Summary: Genes enriched in immune system functions and regulation of complement activity.\\n\\nMechanism: These genes are involved in the regulation and function of the immune system and the complement cascade, including regulation of proteolytic enzymes, regulation of cytokine and growth factor signaling, and maintenance of cell surface glycoproteins.\\n\\n] \n", - "25 [Summary: Genes involved in inflammation, immunity, and blood coagulation are enriched in this list.\\n\\nMechanism: These genes are involved in various processes related to the regulation of the immune response, blood coagulation, and inflammation. Many of these genes play a role in the complement cascade, cytokine signaling, and protein phosphorylation.\\n\\n] \n", - "26 [Summary: Genes involved in DNA repair, transcription initiation, RNA processing, and nucleotide metabolism.\\n\\nMechanism: These genes are all involved in various cellular processes that are crucial for maintaining genomic stability and integrity, including DNA repair, transcription initiation, RNA processing, and nucleotide metabolism. \\n\\n] \n", - "27 [Summary: The enriched terms suggest that these genes are involved in DNA replication, repair, and transcription.\\n\\nMechanism: These genes are involved in various aspects of DNA metabolism, including DNA replication, repair, and transcription. \\n\\n\\nHypothesis: These genes are all involved in fundamental cellular processes in which DNA is duplicated, transcribed, and repaired. They likely work together to ensure the accuracy and stability of genetic information.] \n", - "28 [Summary: Genes involved in DNA replication, repair, and cell cycle regulation.\\nMechanism: These genes are involved in various stages of DNA replication, repair, and cell cycle regulation, suggesting that they work together to maintain genomic stability and ensure proper cell division.\\n] \n", - "29 [Summary: DNA replication and repair\\n\\n] \n", - "30 [Summary: Extracellular matrix organization and regulation.\\nMechanism: Regulation of extracellular matrix protein expression and function.\\n\\nHypothesis: The enrichment of terms related to extracellular matrix organization and regulation suggests that these genes play a role in maintaining the integrity and function of extracellular matrix components, such as collagen, elastin, and laminin. These proteins provide structure and elasticity to tissues, and the dysregulation of extracellular matrix organization has been linked to a number of pathological conditions, including cancer, cardiovascular disease, and fibrosis. The identified genes likely contribute to the regulation of extracellular matrix protein expression, assembly, and localization, and may represent potential targets for therapeutic intervention in these diseases.] \n", - "31 [Summary: Extracellular matrix proteins and cytokines are statistically over-represented in these gene functions, as well as proteins involved in collagen binding and actin filament binding.\\n\\nMechanism: These genes may play a role in extracellular matrix organization and remodeling, as well as cell adhesion and migration.\\n\\n] \n", - "32 [Summary: Membrane-associated proteins, enzymes and transcription factors are enriched in the gene list.\\n\\nMechanism: The enriched terms suggest these genes play a role in membrane-associated processes, enzymatic activity, and transcriptional regulation, potentially related to cellular signaling and development.\\n\\n] \n", - "33 [Summary: Membrane transport and cell signaling.\\nMechanism: These genes are involved in membrane transport and cell signaling pathways. They enable processes such as L-leucine transmembrane transporter activity, sodium/hydrogen exchanger regulatory cofactor, and cytokine and growth factor signaling.\\n\\n] \n", - "34 [Summary: Membrane-associated proteins, enzymes involved in metabolic processes, and transcriptional regulators are enriched in these gene functions.\\nMechanism: The enriched gene functions suggest a role in cellular metabolism and regulation of gene expression.\\n] \n", - "35 [Summary: Many of these genes are involved in cellular processes such as protein binding, catalytic activity, and regulation of transcription.\\nMechanism: The enriched terms suggest a role in cellular signaling pathways such as cytokine signaling and regulation of cell growth and differentiation.\\n\\n] \n", - "36 [Summary: Genes involved in metabolism and enzyme function are statistically over-represented.\\nMechanism: Enzymes involved in metabolism are crucial for cellular function and maintaining homeostasis. \\n\\n] \n", - "37 [Summary: These genes are involved in various metabolic processes, including fatty acid metabolism, oxidation-reduction reactions, and energy production. \\n\\nMechanism: It is hypothesized that these genes are involved in maintaining cellular homeostasis by regulating metabolic processes and energy production.\\n\\n] \n", - "38 [Summary: Cell division and DNA repair processes are enriched among the listed genes.\\n\\nMechanism: The genes listed are involved in various aspects of cell division including DNA replication, chromosome segregation, and cytokinesis. \\n\\n] \n", - "39 [Summary: Chromosome segregation and DNA replication machinery\\nMechanism: Regulation of cell cycle and DNA replication\\n\\nHypothesis: The enriched terms suggest that these genes play a role in the regulation of the cell cycle, specifically in DNA replication initiation, chromosome segregation, mitotic spindle organization, and cell cycle checkpoint control. The mechanism underlying the common function of these genes could be the assembly of protein-DNA complexes required for the progression of the cell cycle and proper segregation of chromosomes during cell division. Dysfunction in these processes can lead to genomic instability and contribute to the development of cancer.] \n", - "40 [Summary: Enzyme activity involved in carbohydrate metabolism and glycosylation processes.\\n\\nMechanism: Enzymatic reactions involved in the breakdown and synthesis of carbohydrates, as well as the addition of sugar groups to proteins and lipids.\\n\\n\\nHypothesis: The enriched terms suggest that these genes are involved in a wide range of metabolic processes related to carbohydrate and sugar metabolism. This may involve the breakdown of sugars for energy production, as well as the synthesis and modification of sugar molecules for use in various cellular processes. These processes likely involve multiple pathways, including the pentose phosphate pathway, glycolysis, and various UDP-sugar biosynthetic pathways.] \n", - "41 [Summary: Glycolysis, carbohydrate metabolism, and signaling pathways are significantly enriched functions in this set of genes.\\nMechanism: These genes are involved in glucose metabolism and signaling pathways, which regulate cellular responses to stress and energy levels.\\n\\nHypothesis: The majority of these genes are associated with glycolysis, carbohydrate metabolism, and signaling pathways, which are central metabolic processes that regulate cellular energy levels and responses to stress. Many of these genes are likely to be involved in glucose transport, which plays an essential role in maintaining cellular energy balance. Additionally, some of these genes are involved in cellular responses to stress, suggesting that altered glucose metabolism could contribute to stress-related disorders.] \n", - "42 [Summary: Neural development and signaling pathway regulation\\nMechanism: These genes are involved in various aspects of neural development and signaling pathways, including axon guidance, cell adhesion, cell communication, and transcriptional regulation.\\n] \n", - "43 [Summary: Neuronal development and signaling\\n\\nHypothesis: These genes may be part of a broader signaling pathway that regulates neuronal development and communication, possibly involving other signaling molecules and pathways such as Wnt and Notch signaling. Further investigation into the interactions and regulation of these genes may provide insights into neural disorders and conditions.] \n", - "44 [Summary: Several of the enriched terms relate to the regulation of gene expression and protein turnover, as well as ion transport and membrane organization.\\n\\nMechanism: The shared biological mechanism may involve the regulation and modulation of cellular processes through the transport of ions and proteins across membranes, as well as the turnover of proteins and regulation of gene expression.\\n\\n] \n", - "45 [Summary: Transport; Metabolism; Binding Activity\\nMechanism: Not enough information to form a hypothesis \\n] \n", - "46 [Summary: Glycolysis-related genes are enriched \\n\\nMechanism: Glycolysis regulation\\n\\n] \n", - "47 [Summary: Genes are involved in glucose metabolism, cell cycle regulation, and transcriptional activities.\\n\\nMechanism: The common mechanism seems to be the regulation of glucose metabolism, possibly through the insulin signaling pathway and its downstream effectors. There may also be an involvement in cell cycle regulation and transcriptional activities.\\n\\n] \n", - "48 [Summary: Immune response regulation\\nMechanism: Modulation of cytokine signaling pathways\\n] \n", - "49 [Summary: Immune system response and regulation\\n\\n] \n", - "50 [Summary: Cytokine receptors and signaling pathway genes\\n\\n] \n", - "51 [Summary: Regulation of immune response and cytokine signaling\\n\\nHypothesis: These genes may contribute to the regulation and promotion of immune response and cytokine signaling, potentially through the binding and activation of cytokine receptors and downstream signaling pathways.] \n", - "52 [Summary: Immune and inflammatory response genes\\nMechanism: Immune activation and inflammation\\n] \n", - "53 [Summary: The enriched terms suggest that these genes are involved in immune responses and inflammation, mediated by cytokines, chemokines, and receptors.\\n\\nMechanism: The underlying biological mechanism is likely related to the response of immune cells to infection or injury, leading to the production of cytokines and chemokines that recruit more immune cells to the site.\\n\\n\\nHypothesis: These genes are likely involved in regulating immune responses and inflammation, particularly in response to infection or cellular damage. The cytokines and chemokines produced by these genes may recruit immune cells to the site of infection or injury, amplifying the immune response. The receptors encoded by these genes may play a role in regulating the activation and migration of immune cells. Dysfunction or dysregulation of these genes may contribute to chronic inflammatory diseases] \n", - "54 [Summary: The enriched terms suggest that these genes are involved in immune response and antiviral defense. \\n\\nMechanism: These genes likely play a role in the innate immune response to viral infection and may also regulate cell proliferation and differentiation.\\n\\n] \n", - "55 [Summary: The enriched terms suggest that these genes are involved in the immune system response, particularly in the regulation of interferon and cytokine signaling pathways.\\n\\nMechanism: The mechanism underlying the common functions of these genes involves the regulation of the innate and acquired immune responses through the interferon and cytokine signaling pathways, particularly in response to viral infection.\\n\\n] \n", - "56 [Summary: Immune response regulation\\nMechanism: Up-regulation of interferon signaling pathways\\n] \n", - "57 [Summary: Genes involved in immune response and protein degradation pathways are enriched.\\n\\nMechanism: These genes are involved in regulating the immune response through cytokine signaling and intracellular viral RNA sensing. They also play a role in protein degradation pathways through the proteasome and ubiquitin system.\\n\\n] \n", - "58 [Summary: Calcium ion binding\\nMechanism: Calcium signaling pathway\\n\\nHypothesis: Many of the genes listed encode proteins that bind to calcium ions and act in signaling pathways related to calcium. These proteins are involved in various processes such as transmembrane transport, cell adhesion, protein kinase activity, and G protein-coupled receptor signaling. The enrichment of these terms suggests that calcium signaling is a crucial mechanism that regulates diverse cellular processes such as energy metabolism, cell growth and proliferation, and gene expression.] \n", - "59 [Summary: Many of the genes in this list are involved in various aspects of cell signaling and regulation, including cytokine signaling (IFNG, IL12B), G-protein coupled receptor signaling (ADRA2C, SST4, HTR1B, GPR19), and calcium signaling (CACNG1, STAG3, EFHD1). Additionally, there are several genes related to protein metabolism and processing (CLPS, CPB1, NUDT11, CELSR2, SLC38A3).\\n\\n\\nHypothesis: The common theme among these genes is their involvement in intracellular signaling pathways involved in maintaining cellular homeostasis. These pathways may interact with each other, creating a complex network of interactions that allow cells to adapt and respond to various stimuli. Additionally, the regulation of protein metabolism and processing is likely important for maintaining proper protein function and stability within the cell. Overall, these processes likely contribute to proper cell function and survival.] \n", - "60 [Summary: Several enriched terms relate to signal transduction and regulation of various cellular processes.\\n\\nMechanism: The genes in this list are involved in various aspects of cellular signaling, including cytokine signaling, receptor activity, and kinase activity. They also play roles in regulating processes such as transcription, protein degradation, and cell migration.\\n\\n] \n", - "61 [Summary: Signaling and regulation of various biological processes, including coagulation, cytokine activity, extracellular matrix, and ion channels.\\n\\n] \n", - "62 [Summary: These genes are involved in various aspects of cell division, organization of the cytoskeleton, and regulation of protein activity.\\n\\nMechanism: The genes identified likely function in the organization of the cytoskeleton, which is required for proper cell division and cellular organization. They may also contribute to regulation of protein activity during these processes.\\n\\n] \n", - "63 [Summary: Many of these genes are involved in mitosis, cell division, and microtubule organization.\\nMechanism: These genes likely work together to regulate the organization and division of cells.\\n] \n", - "64 [Summary: Enzymatic processes related to metabolism and cellular transport are over-represented in this gene set.\\n\\nMechanism: The genes in this set are involved in various metabolic pathways related to cellular transport and enzymatic processes, including lipid metabolism and glucose homeostasis.\\n\\n] \n", - "65 [Summary: Regulation of protein folding and degradation\\nMechanism: Molecular chaperones and proteasome complexes\\n] \n", - "66 [Summary: The enriched terms suggest that the genes are involved in protein synthesis, DNA replication, RNA splicing, and nucleotide metabolism.\\n\\nMechanism: These genes are involved in the molecular processes that underlie the maintenance and expression of genetic information. They facilitate the translation of genetic code into functional proteins, the replication and repair of DNA, the processing of RNA molecules, and the regulation of nucleotide metabolism.\\n\\n] \n", - "67 [Summary: Genes are involved in protein synthesis, including ribosomal proteins, translation factors, and chaperones. \\nMechanism: These genes function in various stages of protein synthesis, including ribosome assembly, translation initiation, elongation, and termination. \\n] \n", - "68 [Summary: RNA processing and ribosomal biogenesis are enriched functions among the listed genes.\\n\\nMechanism: The genes in this list are involved in various aspects of RNA processing and ribosomal biogenesis. They encode proteins that are involved in functions such as nucleolar organization, rRNA maturation, and ribosomal protein synthesis.\\n\\n] \n", - "69 [Summary: Nucleolar ribosomal RNA processing and biogenesis is enriched in these genes, as well as RNA binding and RNA metabolic processes.\\n\\nMechanism: The genes in this list all play a role in the processing and biogenesis of ribosomal RNA, particularly in the nucleolus. They are involved in RNA binding and RNA metabolic processes required for ribosome assembly and regulation.\\n\\n] \n", - "70 [Summary: Muscle contraction and development\\nMechanism: Actin-myosin interaction regulated by calcium ion concentration\\n] \n", - "71 [Summary: Muscle contraction and regulation of calcium ion transport\\nMechanism: Activation of troponin-tropomyosin complex\\n] \n", - "72 [Summary: These genes are involved in cell signaling pathways, including the Notch and Wnt signaling pathways, as well as in ubiquitin-mediated protein degradation. \\nMechanism: These genes collectively form a network of signaling and regulatory pathways involved in cellular differentiation and proliferation.\\n\\nHypothesis: These genes are involved in regulating the balance between cell proliferation and differentiation by modulating the activity of key signaling proteins, such as Notch and Wnt receptors, and regulating the turnover of specific proteins via ubiquitination and proteasomal degradation. Dysregulation of these pathways may contribute to the development of various diseases, including cancer and neurological disorders.] \n", - "73 [Summary: Genes involved in Notch signaling pathway and protein ubiquitination.\\nMechanism: Regulation of cell fate decisions and interactions between physically adjacent cells through binding of Notch family receptors to their cognate ligands.\\n] \n", - "74 [Summary: Mitochondrial genes involved in oxidative phosphorylation and energy metabolism.\\nMechanism: Mitochondrial function and energy metabolism.\\n\\nHypothesis: These genes are all involved in the process of energy production through oxidative phosphorylation within the mitochondria. The enriched terms indicate the importance of ATP synthesis, electron transport chain, and the mitochondrial respiratory chain. These genes may play a key role in cellular energetics, oxidative stress, and aging.] \n", - "75 [Summary: The enriched terms are related to mitochondrial metabolism, particularly oxidative phosphorylation and the electron transport chain.\\n\\nMechanism: These genes are involved in the function and regulation of complexes I-V in the mitochondrial respiratory chain and oxidative phosphorylation.\\n\\n] \n", - "76 [Summary: Regulation of gene expression, DNA repair, and cell growth/death pathways.\\nMechanism: These genes are involved in the regulation of cellular processes such as gene expression, DNA repair, and cell growth and death pathways. They are enriched in terms related to DNA repair, regulation of gene expression, and growth factor activity.\\n\\nHypothesis: These genes may be involved in maintaining cellular homeostasis and responding to external signals such as growth factors. The regulation of gene expression and DNA repair pathways are critical for proper cell function and survival. Dysfunction in these processes can result in various diseases, including cancer. The enrichment of growth factor activity terms suggests that these genes may also play a role in regulating cell growth and proliferation.] \n", - "77 [Summary: Genes are involved in DNA repair, cell growth regulation, and signal transduction pathways.\\nMechanism: These genes are involved in maintaining the integrity of DNA, controlling cell proliferation, and regulating cellular responses through signaling pathways.\\n] \n", - "78 [Summary: Genes involved in glucose and insulin metabolism, as well as pancreatic development and neuroendocrine regulation, are statistically over-represented in this list.\\n\\nMechanism: These enriched genes act in a network that regulates the homeostasis of glucose and insulin in the body, through modulation of pancreatic beta cell development, glucose sensing and stimulation, and insulin production.\\n\\n] \n", - "79 [Summary: Genes in this list are involved in glucose and insulin metabolism, as well as in pancreatic islet development and neuroendocrine differentiation. They also play a role in motor neuron generation, synaptic plasticity, and neurotransmitter release. Enriched terms include \"glucose metabolism,\" \"pancreatic islet development,\" \"neuroendocrine differentiation,\" \"neurotransmitter release,\" and \"synaptic plasticity.\"\\n\\nMechanism: The common mechanism underlying these functions is likely the regulation of gene expression through transcription factors and signaling pathways involved in glucose and insulin metabolism, as well as in neuroendocrine differentiation and synaptic plasticity.\\n\\n] \n", - "80 [Summary: The common function of these genes is involvement in metabolic processes including transport, binding, and enzymatic activities of lipids, hormones, and other molecules. \\n\\nMechanism: These genes are part of the cellular machinery involved in lipid transport and metabolism. \\n\\n] \n", - "81 [Summary: Peroxisomal membrane proteins & enzymes, fatty acid beta-oxidation pathway, and antioxidant enzymes are enriched functions among the given genes.\\n\\nMechanism: Peroxisomes play a crucial role in fatty acid metabolism. Some of the enriched functions are involved in either fatty acid import, beta-oxidation, or metabolism of by-products of beta-oxidation such as acetyl-CoA. Also, some genes code for peroxisomal membrane proteins that facilitate peroxisomal proliferation or matrix protein import.\\n\\n\\nHypothesis: The enriched functions might suggest a link between fatty acid metabolism, oxidative stress, and peroxisomal proliferation. In oxidative stress conditions, the cell may require to degrade excess fatty acids via peroxisomal beta-oxidation to reduce ROS generation. This acts as a feedback inhibition mechanism to prevent ROS accumulation in the mitochondria. Peroxisomal membrane proteins regulate peroxisomal proliferation to respond to cellular stress.] \n", - "82 [Summary: Genes are involved in intracellular signaling, enzymatic activity, and cytoskeletal regulation.\\nMechanism: These genes play a role in various cellular pathways and contribute to cellular growth, differentiation, and regulation of cellular processes.\\n] \n", - "83 [Summary: Protein phosphorylation and signal transduction pathways are enriched functions among the provided human genes.\\nMechanism: Many of the genes in this list encode for serine/threonine kinases or components of signaling pathways. These pathways are involved in transmitting information from the cell surface (either extracellular signals or internal signals) to the nucleus, resulting in changes in gene expression or other cellular processes. Protein phosphorylation is a key mechanism in these pathways, regulating protein activity and localization.\\n\\n] \n", - "84 [Summary: The enriched terms for these genes are related to intracellular trafficking, specifically vesicle transport, Golgi apparatus, and lysosome.\\n\\nMechanism: These genes encode a variety of proteins involved in vesicle trafficking and intracellular transport pathways, specifically related to the Golgi apparatus and lysosome.\\n\\n] \n", - "85 [Summary: Vesicular transport and protein sorting in the Golgi apparatus are enriched functions among the listed genes. \\n\\nMechanism: These genes encode proteins involved in membrane trafficking, protein sorting, vesicle fusion, and transport between different membrane-bound compartments. \\n\\n] \n", - "86 [Summary: Genes involved in antioxidant defense and oxidative stress response are enriched.\\n\\nMechanism: The enriched genes have significant functions in oxidoreductase activity, antioxidant activity, and glutathione metabolic processes. \\n\\n\\nHypothesis: The enriched genes suggest the importance of maintaining a balance between oxidative stress and antioxidant defense to combat cellular damage. The glutathione metabolic process plays a crucial role in regulating the redox status of the cell and possibly maintaining proper protein folding. These genes may be involved in cellular responses to oxidative stress and the regulation of redox signaling pathways.] \n", - "87 [Summary: Redox homeostasis and antioxidant defense mechanisms. \\nMechanism: Multiple genes involved in redox balance and antioxidant defense mechanisms. \\n\\nHypothesis: The enriched terms suggest that the commonality among the gene functions is the regulation of redox homeostasis and maintenance of antioxidant defense mechanisms. The gene products are involved in the reduction of reactive oxygen species (ROS) and oxidative stress to maintain cellular function and survival. The proteins may act as antioxidants, reducing ROS such as hydrogen peroxide and organic hydroperoxides, or they may function in redox regulation, playing key roles in redox signaling pathways and the maintenance of redox balance. Overall, these genes are important in protecting cellular integrity and maintaining homeostasis.] \n", - "88 [Summary: Cell cycle regulation and DNA binding\\nMechanism: These genes are involved in regulating cell cycle progression and DNA interactions, with many of them being DNA or RNA binding proteins.\\n\\n] \n", - "89 [Summary: Cellular processes involved in protein binding, enzymatic activity, and ion transport are enriched in this list of human genes.\\n\\nMechanism: The proteins encoded by these genes may form complexes involved in signal transduction pathways, protein degradation, and ion channel regulation.\\n\\n] \n", - "90 [Summary: Signaling and regulation of growth and differentiation processes.\\nMechanism: TGF-beta superfamily signaling pathways.\\n] \n", - "91 [Summary: Members of this group of genes are involved in transforming growth factor-beta (TGF-beta) superfamily signaling, cell growth and differentiation, transcriptional regulation, ubiquitination, and phosphorylation. \\nMechanism: TGF-beta signaling pathway\\n] \n", - "92 [Summary: Genes involved in immune response, cytokine signaling, and transcription regulation.\\n\\n] \n", - "93 [Summary: Genes are involved in immune response, cytokine signaling, and transcription regulation.\\n\\nMechanism: These genes have a role in modulating the immune response, with some genes involved in cytokine signaling and others in transcription regulation.\\n\\n] \n", - "94 [Summary: These genes are involved in protein folding, stress response, and RNA metabolism.\\n\\nMechanism: These genes likely function in the regulation of protein folding and quality control, as well as the response to cellular stress and the maintenance of RNA stability.\\n\\n] \n", - "95 [Summary: Genes involved in protein folding and regulation of RNA processing and translation.\\nMechanism: These genes play a role in maintaining cellular homeostasis by regulating the synthesis and folding of proteins, and the processing and translation of RNA. \\n\\nHypothesis: These genes likely work together to promote proper protein conformation and prevent improper folding and aggregation. They may also play a role in regulating cellular responses to stress, such as the unfolded protein response. In addition, they may be involved in controlling translation rates and ensuring proper ribosome function.] \n", - "96 [Summary: These genes are enriched for terms related to intracellular signaling and regulation, specifically in regards to calcium ion transport and cytoskeletal organization.\\n\\nMechanism: The identified genes are involved in intracellular signaling pathways that regulate cellular processes through calcium ion transport and cytoskeletal organization.\\n\\n] \n", - "97 [Summary: Extracellular matrix organization, cellular signaling, and ion transport are enriched functions in this list of genes.\\n\\nMechanism: These genes likely play a role in the formation and maintenance of the extracellular matrix, cellular communication and signaling pathways, and ion transport.\\n\\n] \n", - "98 [Summary: Transport, catalysis, and regulation of cellular processes are the enriched functions of these genes.\\nMechanism: ABC transporters, enzymes, and transcription factors are involved in these processes.\\n\\n] \n", - "99 [Summary: This set of human genes is involved in various biological processes, including metabolism, nucleotide and protein biosynthesis, and signaling pathways.\\n\\n] \n", - "100 [Summary: Genes involved in Wnt signaling pathway regulation.\\nMechanism: Negatively regulating Wnt pathway through inhibition of beta-catenin stabilization and/or transcriptional activation.\\n\\nHypothesis: The genes listed above are all involved in negative regulation of the Wnt signaling pathway, either through inhibiting beta-catenin stabilization or transcriptional activation. This results in downstream effects on processes such as transcriptional and cell cycle regulation.] \n", - "101 [Summary: Genes involved in the Wnt signaling pathway and transcription regulation are enriched in this gene list.\\nMechanism: These genes play a role in the regulation of the Wnt signaling pathway and transcriptional regulation.\\n] \n", - "102 [Summary: Immune response and signal transduction genes are enriched in this list.\\n\\nMechanism: These genes function in various aspects of immune response, including immune signaling, cytokine production, and cell proliferation and differentiation.\\n\\n\\nHypothesis: These genes may be involved in the regulation of immune responses by modulating cytokine production and signaling, controlling cell proliferation and differentiation, and regulating apoptosis. Further investigation could lead to a better understanding of the complex interplay between these genes and their role in maintaining a healthy immune system.] \n", - "103 [Summary: Immune response and cytokine signaling\\nMechanism: Regulation of immune response and cytokine signaling\\n\\nHypothesis: The enriched terms suggest that these genes are involved in the regulation of the immune response and cytokine signaling. Specifically, these genes are implicated in the signaling pathways that are activated in response to immune system activation and in the subsequent regulation of T cell function. The overall biological mechanism is the regulation of immune defense against foreign pathogens and tumor cells.] \n", - "104 [Summary: These genes are involved in embryonic development, stem cell pluripotency, and tumorigenesis. They encode transcription factors that regulate gene expression and control cell cycle progression.\\nMechanism: Transcriptional regulation\\n\\nHypothesis: These genes may function together in a signaling pathway involved in the maintenance of stem cell pluripotency and/or regulation of cell differentiation during embryonic development. Dysregulation of this pathway could contribute to tumorigenesis. The transcription factors encoded by these genes may also interact with other proteins involved in DNA damage response and repair.] \n", - "105 [Summary: Genes involved in transcription factor activity and regulation of development.\\nMechanism: Transcriptional regulation of development.\\n\\nHypothesis: These genes play a crucial role in the transcriptional regulation of embryonic development and stem cell maintenance. They are likely involved in the regulation of gene expression during critical periods of development, and abnormalities in their function may contribute to developmental disorders and tumorigenesis. Further research is needed to fully elucidate the molecular mechanisms by which these genes act and their interactions within regulatory pathways.] \n", - "106 [Summary: Extracellular matrix and cell signaling related genes are enriched.\\n\\nMechanism: Extracellular matrix formation and remodeling, as well as cell migration and signaling pathways are likely involved.\\n\\n] \n", - "107 [Summary: Extracellular matrix organization and cell adhesion.\\nMechanism: Regulation of cell attachment and migration via extracellular matrix interactions.\\n\\nHypothesis: The enriched terms suggest that these genes are involved in the regulation of cell attachment and migration via interactions with the extracellular matrix. Specifically, these genes play a role in extracellular matrix organization and cell adhesion, as well as proteoglycan and keratan sulfate metabolic processes. The integrin-mediated signaling pathway is also likely involved in these processes, as integrins are transmembrane receptors that mediate cell adhesion to the extracellular matrix. Finally, platelet activation may be involved, as some of these genes are associated with platelet-derived growth factors and other factors that regulate platelet activation and adhesion. Overall, these genes likely play a key role in regulating cell behavior in response to changes in the extracellular matrix, and may be involved in a variety of physiological and pathological processes, including wound healing, tissue development and maintenance, and cancer progression.] \n", - "108 [Summary: Membrane transport and binding activity\\nMechanism: ABC Transporter Signaling Pathway\\n] \n", - "109 [Summary: Genes are involved in various cellular processes, including RNA binding, calcium signaling, protein binding, transcription factor activity, and membrane transport. \\n\\n] \n", - "110 [Summary: Muscle contraction and regulation\\nMechanism: Gene products involved in the structure, organization, and regulation of the contractile machinery in striated muscle.\\n\\nHypothesis: The enriched terms indicate that the gene products listed are all involved in the structure, organization, and regulation of the contractile machinery in striated muscle. More specifically, these gene products contribute to the organization of actin filaments via actin binding, tropomyosin binding, and muscle filament sliding speed regulation, as well as the regulation of muscle contraction through calcium ion binding to the troponin complex and myosin binding. There are specific enriched terms, such as regulation of muscle filament sliding speed, which suggest that these gene products may play distinct roles within the muscle contractile machinery, but this remains to be fully elucidated.] \n", - "111 [Summary: Genes are involved in muscle contraction, regulation, and structure.\\n\\n\\nHypothesis: The muscle structure and function depend on the proper regulation of actin-myosin interaction, calcium ion flux, and energy metabolism. Dysfunctions in these pathways lead to the development of various muscle disorders. Therefore, the enriched terms represent the key biological processes and molecular functions that underlie muscle structure, function, and dysfunction.] \n", - "112 [Summary: Many of the genes in this list are involved in endocytosis, intracellular trafficking, and cytoskeleton reorganization.\\n\\nMechanism: These genes likely play a role in the regulation and maintenance of cellular processes by contributing to the turnover and recycling of molecules within the cell.\\n\\n] \n", - "113 [Summary: Genes involved in endocytosis, vesicle trafficking, and intracellular signaling.\\nMechanism: These genes function in various aspects of intracellular trafficking, particularly endocytosis and vesicle trafficking.\\n\\n] \n", - "114 [Summary: The genes in this list are involved in glucose metabolism and glycolysis, which is the breakdown of glucose to provide energy for cellular processes.\\n\\n\\nHypothesis: The common function of these genes in glucose metabolism and glycolysis suggests a role in regulating energy production in cells. Dysfunction in these genes may lead to diseases related] \n", - "115 [Summary: Enzymes involved in glycolysis and related metabolic pathways.\\nMechanism: Metabolism of glucose to produce energy.\\n] \n", - "116 [Summary: Calcium signaling regulation and ion channels\\nMechanism: Calcium homeostasis and neuronal signaling \\n\\nHypothesis: The gene function common to this list is the regulation of calcium signaling and ion channels in neurons. These genes are involved in the transport and binding of calcium ions in the intracellular space and the regulation of ion channel activity in the plasma membrane, particularly in the postsynaptic density of neurons. Calcium transport is vital for regulating neuronal signaling and synaptic plasticity, which underlie many physiological processes, including learning and memory. The ionotropic glutamate receptor activity is also enriched, which is involved in fast neurotransmission in the synapses. Overall, this suggests that these genes contribute to the regulation of calcium signaling essential for proper neuron function and synaptic plasticity.] \n", - "117 [Summary: Ion channels and receptors\\nMechanism: Regulation of cellular calcium levels\\n\\nHypothesis: The enriched terms suggest a mechanism by which these genes regulate cellular calcium levels, likely through ion channels and receptors. This regulation is crucial for synaptic transmission and neurotransmitter receptor activity. Dysfunction of these genes could lead to disruptions in calcium homeostasis, potentially contributing to neurological disorders.] \n", - "118 [COULD NOT PARSE] \n", - "119 [Summary: Genes are involved in cell signaling, regulation of apoptosis, immune response, and protein kinase activity.\\nMechanism: These genes regulate various cellular processes such as cell division, survival, and metabolism through protein signaling and kinase activity pathways.\\n] \n", - "120 [Summary: These genes are involved in the degradation of glycosaminoglycans, glycogen, and glycolipids, as well as the hydrolysis of glycosidic bonds in carbohydrates. \\n\\n\\nHypothesis: The enriched terms point to a common mechanism of lysosomal degradation of carbohydrate molecules, with specific enzymes targeting different types of molecules (e.g. glycosaminoglycans, glycogen, glycolipids). This process is important for maintaining cellular homeostasis and energy metabolism.] \n", - "121 [Summary: Enzymes involved in carbohydrate metabolism, specifically in the breakdown of complex sugars like glycosaminoglycans and polysaccharides.\\n\\nMechanism: Carbohydrate metabolism\\n\\n] \n", - "122 [Summary: The enriched terms are related to immunoglobulin receptor binding activity and immune response. \\nMechanism: The genes listed all code for proteins involved in the function of immunoglobulins, which are the key molecules of adaptive immunity (the portion of the immune system that learns to recognize and remember specific pathogens). \\n] \n", - "123 [Summary: Genes are involved in adaptive immune response and immune system processes, likely through antigen binding activity and immunoglobulin receptor binding activity. \\n\\n] \n", - "124 [Summary: These genes are primarily involved in meiotic recombination, double-strand break repair, and chromosomal segregation during meiosis. They all play a role in some aspect of the meiotic cell cycle process.\\n\\n\\nHypothesis: The underlying biological mechanism for these genes is the regulation and coordination of meiotic recombination and double-strand break repair via homologous recombination, as well as the proper segregation of chromosomes during meiosis. Dysfunction in any of these genes may result in chromosomal abnormalities and infertility in individuals.] \n", - "125 [Summary: Genes involved in meiotic recombination and DNA break repair are enriched.\\n\\nMechanism: These genes play a crucial role in meiotic recombination and repair of DNA double-strand breaks. During meiosis, DNA breaks are introduced, repaired, and exchanged between chromosomes to generate genetic diversity.\\n\\n] \n", - "126 [Summary: Cellular processes involved in protein binding and regulation, immune response, and intracellular transport are enriched in the given list of genes.\\n\\n\\nHypothesis: The enriched terms suggest that the genes in this list are involved in several overlapping pathways related to protein binding and regulation, immune response, and intracellular transport. Specifically, these genes may play a role in regulating protein-protein interactions, immune system signaling and response, and the movement of molecules and particles within cells. These pathways may be key to cellular development, maintenance, and response to stressors and damage. Further investigation into the relationships and interactions between these genes may lead to a better understanding of how these processes are regulated and coordinated in human cells.] \n", - "127 [Summary: Transport functions, regulation of cell growth and survival, inhibition of apoptosis, and regulation of gene expression are enriched in this set of genes.\\nMechanism: These genes likely function in a variety of cellular processes, including transport and signaling pathways, cell cycle regulation, and gene expression regulation.\\n\\n] \n", - "128 [Summary: Enzymatic processes related to metabolism and cellular transport are over-represented in this gene set.\\n\\nMechanism: The genes in this set are involved in various metabolic pathways related to cellular transport and enzymatic processes, including lipid metabolism and glucose homeostasis.\\n\\n] \n", - "129 [Summary: These genes are involved in various cellular processes, but a common theme is their involvement in protein degradation. \\n\\nMechanism: The 26S proteasome is a multicatalytic proteinase complex that plays a critical role in the degradation of intracellular proteins that are damaged, misfolded, or no longer needed. \\n\\n] \n", - "130 [Summary: Genes involved in peroxisome biogenesis and protein import.\\nMechanism: Peroxisome biogenesis and maturation pathway.\\n\\n\\nHypothesis: These genes are involved in the peroxisome biogenesis and maturation pathway, which is responsible for the assembly of functional peroxisomes. This pathway involves the formation of membrane vesicles by PEX3, followed by translocation of matrix proteins via PEX5 and PEX7. Mutations in these genes lead to peroxisome biogenesis disorders, which are characterized by multiple defects in peroxisome function, including import of matrix proteins. Therefore, these genes are involved in the import of peroxisomal matrix proteins and the maturation of peroxisomes. The commonalities in their function are related to their roles in peroxisome biogenesis and protein import.] \n", - "131 [Summary: Genes involved in peroxisome biogenesis disorders\\nMechanism: Peroxisome assembly and matrix protein import\\n] \n", - "132 [Summary: Genes involved in nuclear structure and function \\nMechanism: Proteolytic processing of prelamin A to mature lamin A, maintenance of genome stability \\n] \n", - "133 [Summary: Genes LMNA, WRN, and BANF1 are all involved in nuclear functions and stability.\\nMechanism: These genes are involved in maintaining the stability of the genome by regulating chromatin structure, repairing DNA, and facilitating nuclear reassembly.\\n] \n", - "134 [Summary: Genes involved in neurotransmission through ion channels, specifically GABA and glutamate receptors, as well as voltage-gated potassium and sodium channels, are over-represented in this list.\\n\\nMechanism: These genes encode proteins involved in the regulation of ion flow in neuronal membranes, allowing for the transmission of electrical signals and control of neuronal excitability.\\n\\n] \n", - "135 [Summary: These genes are involved in the regulation of ion channels in the central nervous system.\\nMechanism: Regulation of ion channels\\n] \n", - "136 [Summary: Myelin upkeep and neurological diseases\\n\\nHypothesis: Dysregulation of the myelin upkeep pathways can lead to mitochondrial dysfunction, accumulations of toxic metabolites, and impaired protein processing, which contribute to the development of neurological diseases. Dysfunction of the transporter proteins and nuclear membrane transporters can further exacerbate cell dysfunction and death. Treatment strategies aimed at restoring mitochondrial function and enhancing myelin synthesis and repair may alleviate symptoms of these diseases.] \n", - "137 [Summary: Peripheral nerve myelin upkeep and related disease mechanisms\\nMechanism: The genes are involved in maintaining and degrading myelin sheaths in peripheral nerve cells.\\n\\nHypothesis: The enrichment of genes involved in peripheral nerve myelin upkeep suggests a common underlying biological mechanism of maintaining appropriate myelin structure, which can be disrupted by various genetic causes leading to different neuropathic diseases. These genes play crucial roles in ensuring proper nervous system and myelin development, and focus on various biological processes that regulate these mechanisms. Ultimately, disruptions in these genes can lead to peripheral neuropathies and degeneration.] \n", - "138 [Summary: Signaling via G protein-coupled receptors and cyclic AMP (cAMP) signaling pathway are enriched biological processes in the list of genes.\\n\\nMechanism: The enriched terms suggest that these genes are involved in the regulation of downstream signaling pathways activated by G protein-coupled receptors (GPCRs) and their ligands, leading to the generation of cAMP, a key second messenger in many intracellular signaling pathways.\\n\\n\\nHypothesis: The majority of the genes in the list encode proteins involved in the regulation of GPCR-stimulated cAMP signaling pathways. Signaling through these pathways plays a crucial role in cell proliferation, differentiation, development, synaptic plasticity, and behavior. Dysfunction in cAMP signaling pathways has been implicated in numerous pathophysiological conditions, including psychiatric disorders and cancer.] \n", - "139 [Summary: These genes are involved in signaling pathways mediated by G proteins and second messenger systems, including the dopamine receptor signaling pathway.\\n\\nMechanism: Activation of G protein-coupled receptors results in the dissociation of the G protein alpha subunit from the beta-gamma subunit, leading to the activation of downstream effectors such as adenylyl cyclase and phospholipase C. This results in the production of second messenger molecules such as cyclic AMP and inositol triphosphate, which then activate downstream signaling pathways.\\n\\n] \n", - "140 [Summary: Transcriptional regulation and chromatin remodeling are enriched functions in the given set of genes.\\n\\n] \n", - "141 [Summary: DNA binding transcription factors involved in regulation of gene transcription and cell development.\\nMechanism: These genes encode for proteins that bind to DNA and regulate gene expression.\\n] \n", - "142 [Summary: The common function of the genes is related to extracellular matrix (ECM) organization, collagen synthesis, and glycosaminoglycan (GAG) biosynthesis.\\n\\nMechanism: The enriched terms suggest that these genes play a significant role in extracellular matrix organization and collagen synthesis. The genes involved in glycosaminoglycan biosynthesis are also enriched, indicating their role in stabilizing the extracellular matrix.\\n\\n\\nHypothesis: The extracellular matrix is a complex network of proteins and carbohydrates that provides structural support to tissues. The genes identified in this enrichment are involved in collagen synthesis and extracellular matrix organization. The stabilization of the extracellular matrix is facilitated by the biosynthesis of GAGs. These processes are essential for tissue repair and homeostasis and altered expression of these genes may lead to several connective tissue disorders.] \n", - "143 [Summary: Genes are primarily related to extracellular matrix (ECM) organization and collagen biosynthesis.\\nMechanism: The biosynthesis, processing, and assembly of collagen and other ECM components.\\n\\nHypothesis: The listed genes are mostly involved in the organization and biosynthesis of collagens and other components of the extracellular matrix (ECM). The majority of the genes belong to the Category of ECM and Collagen Synthesis in Gene Ontology (GO) hierarchy. The enriched terms include \"Collagen fibril organization,\" \"Extracellular matrix organization,\" and \"Collagen biosynthesis.\" These genes may interact through different pathways to affect ECM composition, remodeling, and cell-ECM interactions. Dysregulation of these genes can lead to various diseases, such as connective tissue disorders and cancer.] \n", - "144 [Summary: Genes are enriched for DNA repair mechanisms. \\nMechanism: DNA Repair \\n\\nHypothesis: The enriched terms point towards the involvement of these genes in repairing DNA double-strand breaks. These genes are involved in repairing DNA damage and maintaining genome stability, which is critical in preventing cancer development. This suggests that mutations in these genes may increase the risk of cancer due to DNA damage accumulation.] \n", - "145 [Summary: These genes are involved in DNA damage repair and cell-cycle checkpoint control.\\nMechanism: Homologous recombination repair pathway\\n\\nHypothesis: These genes are all involved in the homologous recombination repair pathway, which repairs double-strand breaks in DNA. They also contribute to mitotic cell-cycle checkpoint control and the DNA damage response. Dysfunction in these genes can lead to defects in DNA repair and increased risk of cancer development.] \n", - "146 [Summary: Energy metabolism and lipid transport pathways are enriched in the list of human genes.\\nMechanism: These genes are involved in the regulation and transport of lipids, fatty acids, and energy in the body.\\n\\n] \n", - "147 [Summary: Several enriched terms relate to energy metabolism and lipid transport/storage, as well as protein folding and stress response mechanisms.\\nMechanism: Possible biological mechanisms include mitochondrial function and fatty acid metabolism.\\n\\n] \n", - "148 [Summary: Immune system response and regulation.\\nMechanism: Immune response pathways are activated and regulated by these genes, which contribute to various stages of immune cell development, differentiation, activation, and signaling.\\n] \n", - "149 [Summary: Immune response and inflammation genes are over-represented in the list.\\nMechanism: Immune system activation and response\\n] \n", - "150 [Summary: Regulation of transcription, metabolism, and protein degradation are enriched processes among the listed genes.\\nMechanism: The mechanism underlying the enriched processes is likely through the interaction between the genes and transcription factors.\\n] \n", - "151 [Summary: Genes are involved in various biological processes such as signal transduction, metabolism, and transcriptional regulation.\\nMechanism: None identified.\\n] \n", - "152 [Summary: Extracellular matrix organization and regulation of signaling pathways are enriched functions in the list of genes.\\nMechanism: Extracellular matrix is a complex network of proteins and carbohydrates that provides structural support to cells and tissues, regulates cell behavior, and modulates signaling pathways involved in various physiological and pathological processes.\\n\\nHypothesis: The extracellular matrix is a key regulator of cell behavior and signaling, and its dysfunction is associated with various diseases, including cancer, cardiovascular disease, and connective tissue disorders. These genes are involved in various aspects of extracellular matrix organization and dynamics, such as collagen synthesis and assembly, proteoglycan biosynthesis, adhesion molecules, and extracellular matrix remodeling enzymes. They also regulate key signaling pathways, such as MAP kinase and PI3 kinase pathways, involved in cell proliferation, survival, and migration. Dysfunction of these genes can disrupt extracellular matrix homeostasis and alter cell behavior, leading to various pathological conditions.] \n", - "153 [Summary: Extracellular matrix organization and angiogenesis\\nMechanism: Regulation of signaling pathways involving TGF-beta and VEGF\\n\\nHypothesis: The enriched terms suggest that these genes are involved in extracellular matrix organization and angiogenesis. These processes are tightly regulated by signaling pathways involving TGF-beta and VEGF. The list of genes is enriched for those involved in positive regulation of cell migration, endothelial cell proliferation, and cell adhesion, which are all necessary for angiogenesis. Dysregulation of these genes might contribute to pathological conditions such as cancer and cardiovascular diseases.] \n", - "154 [Summary: Cell-Cell adhesion and Extracellular matrix organization are statistically enriched functions of the genes.\\n\\nMechanism: These genes are commonly involved in the formation and maintenance of cell-cell adhesion and extracellular matrix (ECM) interactions which play an important role in developmental processes, tissue morphogenesis, and homeostasis.\\n\\n] \n", - "155 [Summary: Cell adhesion and communication, with a focus on tight junctions and claudins\\nMechanism: Signaling pathways involved in regulating tight junctions, such as the MAPK and PI3K-Akt pathways\\n\\nHypothesis: The genes listed are primarily involved in regulating tight junctions, which are structures that serve to tightly regulate the permeability of cells and contribute to the formation of physical barriers between various tissues and organs. The enrichment of terms related to cell adhesion, communication, and cytoskeletal organization suggest that these genes help to coordinate signaling between cells and the actin cytoskeleton, which is necessary for tight junction formation and maintenance. The specific signaling pathways involved likely include the MAPK and PI3K-Akt pathways, as these have been shown to modulate the activity of various tight junction proteins, including claudins. Additionally, several of the genes listed are involved in endothelial cell migration and angiogenesis] \n", - "156 [Summary: Cell adhesion and signaling pathways appear to be the most enriched functions across these genes.\\nMechanism: These genes may be involved in regulating cell signaling pathways and adhesion through their various functions, such as receptor binding, protein interaction, and membrane transport.\\n\\n\\nHypothesis: These genes may play a role in modulating cell signaling and adhesion events that are critical for cellular communication and tissue development. Dysregulation of these pathways may result in various diseases, such as cancer and metabolic disorders.] \n", - "157 [Summary: Cell adhesion, migration, and signaling are enriched functions among the listed genes.\\nMechanism: The genes are involved in regulating the activity of various receptor tyrosine kinases, membrane channels, and enzymes involved in intracellular signaling pathways.\\n\\n] \n", - "158 [Summary: Apoptosis-related and immune response genes are statistically over-represented in the given list of genes.\\nMechanism: The enrichment of these genes suggests the involvement of apoptosis and immune response-related pathways in the biological processes of these genes.\\n] \n", - "159 [Summary: Genes are enriched in cellular stress and apoptosis pathways.\\nMechanism: Cellular stress and apoptosis pathways are activated to maintain cellular survival and function.\\n] \n", - "160 [Summary: Genes are involved in lipid metabolism, specifically in bile acid biosynthesis, cholesterol synthesis and transport, and peroxisome biogenesis.\\nMechanism: Lipid metabolism\\n\\nHypothesis: These genes are enriched for lipid metabolism, specifically in bile acid biosynthesis, cholesterol synthesis and transport, and peroxisome biogenesis. This suggests that these genes are involved in maintaining a healthy balance of lipids in the body and may play a role in the development of lipid-related diseases.] \n", - "161 [Summary: Genes are enriched for lipid metabolism and transport, as well as peroxisomal and mitochondrial functions.\\nMechanism: Peroxisomes and mitochondria are both involved in various aspects of lipid metabolism and transport, and the enrichment of peroxisomal genes may suggest a role for peroxisomes in these processes.\\n] \n", - "162 [Summary: Processes related to sterol biosynthesis, lipid metabolism, and cholesterol homeostasis are overrepresented in this gene set.\\nMechanism: Cholesterol homeostasis\\n\\nHypothesis: This gene set is enriched for genes involved in cholesterol homeostasis, reflecting the importance of cholesterol regulation in human biology. Specifically, processes related to sterol biosynthesis, lipid metabolism, and cholesterol transport are overrepresented. Cholesterol is a critical component of cell membranes and is involved in many important cellular processes. Dysregulation of cholesterol metabolism has been linked to a number of human diseases, including cardiovascular disease and neurological disorders. Further research into the genes in this set and their interactions may provide insights into the regulation of cholesterol homeostasis and potential therapeutic targets.] \n", - "163 [Summary: Genes are enriched for lipid metabolism and cholesterol biosynthesis.\\nMechanism: Lipid metabolism and cholesterol biosynthesis pathways.\\n\\nHypothesis: The enriched terms suggest that the listed genes are involved in the biosynthesis, regulation, and metabolism of cholesterol and other lipids, likely through the mevalonate pathway. This pathway generates isoprenoids, which are essential for cholesterol synthesis and other cellular functions. Dysregulation of these genes may contribute to metabolic disorders such as hypercholesterolemia.] \n", - "164 [Summary: Blood coagulation and complement pathways are enriched in the list of genes.\\nMechanism: The enriched genes are involved in the regulation and activation of the blood coagulation and complement pathways.\\n\\nHypothesis: The enrichment of genes involved in blood coagulation and complement pathways suggests that this list may be specifically relevant to the regulation and activation of these pathways. This may indicate potential involvement in diseases related to these pathways, such as thrombosis, hemophilia, and acute inflammation.] \n", - "165 [Summary: Extracellular matrix organization, blood coagulation and fibrinolysis, immune defense, and proteolysis are enriched functions shared by the human genes in the list.\\n\\nMechanism: The genes are involved in the formation and maintenance of the extracellular matrix, blood coagulation and fibrinolysis pathways, immune response, and proteolytic processes.\\n\\n] \n", - "166 [Summary: Immune response and inflammation-related functions are enriched in the list of genes.\\nMechanism: Immune response and inflammation-related pathways are activated.\\n\\nHypothesis: The genes in this list play a role in immune response and inflammation. The enriched terms suggest that these genes are involved in complement activation, regulation of proteolysis, and apoptotic signaling. The activation of these pathways may modulate the host immune response to infectious agents and tissue damage. Some of the genes may also play a role in regulating endopeptidase activity, which could be involved in immune response regulation.] \n", - "167 [Summary: Immune function, coagulation, and protein turnover pathways are enriched based on the list of human genes provided.\\nMechanism: These genes are involved in various biological pathways related to immune response, hemostasis, and regulation of protein turnover.\\n\\n\\nHypothesis: The enrichment of immune response and blood coagulation terms suggests that these genes may be involved in the inflammatory response and contribute to the maintenance of the immune system. The enrichment of protein turnover terms suggests that these genes may be involved in the regulation of protein stability and degradation, which could be important for cellular function and homeostasis. Overall, these genes likely play key roles in a variety of biological processes and pathways that are critical for normal physiological function in humans.] \n", - "168 [Summary: DNA replication and repair, transcription, mRNA processing, and purine metabolism are over-represented in the set of human genes.\\nMechanism: These genes are mainly involved in maintaining genome integrity, providing the necessary machinery for DNA replication and repair, and regulating gene expression.\\n\\n] \n", - "169 [Summary: RNA transcription and DNA repair are enriched functions among the given genes.\\nMechanism: These genes encode for proteins involved in DNA transcription and repair processes.\\n\\nHypothesis: The enriched functions suggest that these genes are involved in the regulation of RNA transcription and DNA repair processes. The RNA polymerase activity and DNA binding terms demonstrate their role in the initial transcription process, while the mRNA processing and DNA repair terms represent their involvement in the post-transcriptional regulation and repair of DNA damage, respectively. Overall, these genes likely play a crucial role in maintaining genetic stability and proper gene expression.] \n", - "170 [Summary: DNA replication and cell cycle regulation\\nMechanism: Genes are involved in DNA replication and mitotic cell cycle regulation\\n] \n", - "171 [Summary: DNA replication and repair are enriched functions of the given genes.\\nMechanism: These genes are predominantly involved in the control and regulation of DNA replication and repair. Specific functions include DNA unwinding, strand break repair, DNA synthesis, and checkpoint signaling.\\n] \n", - "172 [Summary: Extracellular matrix (ECM) organization and regulation of cell signaling are significantly enriched functions for the given set of genes.\\nMechanism: The enriched terms suggest that these genes are involved in maintaining tissue integrity and regulating cellular activity in response to the extracellular environment.\\n\\n\\nHypothesis: The genes in this list are involved in maintaining tissue integrity and regulating cellular activity in response to the extracellular environment. The ECM is critical in regulating cell behavior and signaling, and therefore the ECM organization is necessary for cellular homeostasis. The enriched terms suggest that the set of genes play a role in cell adhesion and integrin-mediated signaling pathways, which are important] \n", - "173 [Summary: Extracellular matrix organization and cell adhesion.\\nMechanism: ECM remodeling and tissue development during embryogenesis, wound healing and cancer progression.\\n] \n", - "174 [Summary: Transport and cellular metabolic processes are overrepresented in these genes.\\nMechanism: Many of these genes are involved in transport and metabolic processes of cells. These pathways play a crucial role in the functioning of cells.\\n] \n", - "175 [Summary: Genes are enriched for functions involved in lipid metabolism and transport, signal transduction, and transcriptional regulation.\\nMechanism: The over-representation of lipid metabolism and transport genes likely reflects the importance of efficient lipid processing and transport in cell growth and homeostasis. The signal transduction and transcriptional regulation pathways may be involved in modulating lipid metabolism and transport in response to changing cellular or environmental conditions.\\n] \n", - "176 [Summary: Genes are enriched in multiple biological processes and pathways.\\nMechanism: Multiple mechanisms and pathways are involved in the functions of these genes.\\n] \n", - "177 [Summary: The enriched terms describe genes involved in various biological processes such as metabolism, signal transduction, development, and immune response.\\nMechanism: No specific mechanism was identified given the broad range of enriched terms.\\n] \n", - "178 [Summary: Genes involved in metabolism and oxidative stress response are enriched.\\nMechanism: These genes are involved in the metabolism of lipids, amino acids, and carbohydrates, as well as in the detoxification of harmful substances and protection against oxidative stress.\\n\\n\\nHypothesis: These genes work together in maintaining cellular metabolism and homeostasis, including the production and utilization of energy, regulation of nutrient balance, and protection against external and internal stressors. This involves the breakdown and synthesis of biomolecules, generation of reducing equivalents for energy production, and removal of toxic compounds and reactive oxygen species. The enriched pathways suggest that these genes are involved in oxidative phosphorylation and other mitochondrial processes, lipid and glucose metabolism, and ion transport. Dysfunction of these genes may] \n", - "179 [Summary: Genes are involved in lipid metabolism, energy production, and oxidative stress response.\\nMechanism: These genes function in pathways related to maintaining cellular homeostasis through the production and utilization of energy, the breakdown and metabolism of lipids, and the response to oxidative stress.\\n] \n", - "180 [Summary: Chromosomal segregation and cell cycle progression\\nMechanism: Regulation of the cell cycle and mitosis\\n\\nHypothesis: \\nThe enrichment of terms related to cell cycle progression and chromosomal segregation suggests that the genes on this list primarily play a role in regulating the progression of cells through the cell cycle and ensuring proper chromosome segregation during mitosis. These genes likely encode various proteins involved in DNA replication, mitotic spindle organization, microtubule cytoskeleton dynamics, and the regulation of cell cycle checkpoints, all of which are critical for the proper progression of cells through the cell cycle and the maintenance of genomic stability. The diverse range of gene functions represented on this list is likely indicative of the complex and tightly regulated nature of the cell cycle and mitotic processes.] \n", - "181 [Summary: DNA replication and cell cycle regulation.\\nMechanism: The genes enriched for this analysis are mainly involved in the regulation of DNA replication and cell cycle progression.\\n] \n", - "182 [Summary: Glycosylation and Metabolism\\nMechanism: Glycosylation is a common function enriched in these genes, and many are involved in metabolic pathways such as glycolysis and the pentose phosphate pathway.\\n\\n] \n", - "183 [Summary: Cellular metabolism and energy production\\nMechanism: Glycolysis and related pathways\\n] \n", - "184 [Summary: Neuronal development and axon guidance-related terms are significantly enriched in the list of genes.\\nMechanism: Neuronal development and axon guidance.\\n\\nHypothesis: The genes in the list are involved in the development and guidance of neuronal cells. Several enriched terms denote processes that are crucial for the proper formation and function of the nervous system, such as neuron differentiation, axon guidance, and cell migration. This suggests that the identified genes play a role in the establishment and maintenance of neural connections. The common functional theme may be mediated by signaling pathways that regulate cell adhesion, migration, and proliferation, which are critical for neural development and the formation of axonal connections. The enriched terms suggest that the proteins encoded by these genes might be involved in the modulation of cytoskeletal dynamics, cell signaling, and adhesion processes that regulate neurite outgrowth and synapse formation. Some genes listed here have been shown to play a role in neurodevelopmental disorders such as autism and epilepsy.] \n", - "185 [Summary: Genes are primarily involved in nervous system development, signal transduction, and cell adhesion.\\nMechanism: Not specified.\\n] \n", - "186 [Summary: Transport, binding, and metabolism processes are enriched in these human genes.\\nMechanism: These genes are involved in various cellular pathways such as ion transport, protein binding, and metabolic processes.\\n\\n] \n", - "187 [Summary: Hemoglobin production and erythropoiesis are over-represented in the list of genes.\\nMechanism: Regulation of hemoglobin synthesis through erythropoietin signaling pathway.\\n\\n] \n", - "188 [Summary: Cellular metabolism and response to stress-related stimuli are enriched in the gene list.\\nMechanism: Metabolic pathways and cellular stress response pathways may be dysregulated in diseases associated with these genes.\\n\\n] \n", - "189 [Summary: Energy metabolism\\n\\nHypothesis: The genes listed display over-represented functions involved in energy metabolism, leading to the hypothesis that they may be involved in maintaining energy homeostasis in the body. The shared functions related to glucose uptake and metabolism may be regulated by a common pathway, such as the insulin signaling pathway, that coordinates the activity of these genes. Additionally, the functions related to ATP production may be affected by mitochondrial activity and oxidative phosphorylation. Further studies are needed to elucidate the exact mechanisms and pathways involved in the regulation of these genes.] \n", - "190 [Summary: Immune system and inflammation-related functions are enriched in this gene list.\\nMechanism: These genes may be involved in regulating the immune response and inflammatory processes.\\n\\n] \n", - "191 [Summary: Signaling pathways related to immune response, cytokine signaling, and inflammation are enriched in the list of human genes.\\n\\nMechanism: These genes likely play a role in coordinating the immune system's response to pathogens or damage signals.\\n\\n] \n", - "192 [Summary: Immune response and cytokine signaling pathway are enriched functions among the listed human genes.\\nMechanism: These genes seem to be involved in regulation and activation of immune cells and cytokine signaling pathways.\\n\\nHypothesis: These genes are potentially involved in the immune response to infections and inflammation. They may also play a role in the regulation of cytokine production and signaling, which can influence the development and progression of inflammatory and autoimmune diseases.] \n", - "193 [Summary: Immune system response\\nMechanism: Cytokine signaling pathway\\n] \n", - "194 [Summary: Immune response and signal transduction\\nMechanism: Immune regulation and inflammation\\n] \n", - "195 [Summary: Immune response and inflammation processes.\\nMechanism: Signaling pathways involved in immune response and inflammation.\\n\\nHypothesis: The enriched terms suggest that the genes in the list may be involved in immune response and inflammation. Immune cells recruit cytokines and chemokines to elicit an immune response. The genes could be involved in signaling pathways that regulate leukocyte migration and inflammation. Additionally, they may play a role in mediating adaptive and innate immune responses.] \n", - "196 [Summary: Genes are involved in interferon signaling, immune response, and antiviral defense mechanisms.\\nMechanism: These genes are involved in the innate immune response to viral infection and defense against other pathogens.\\n\\nHypothesis: These genes are likely involved in the interferon signaling pathway, which triggers an innate immune response against viral infections and activates antiviral defense mechanisms. The enriched terms suggest that the genes are involved in various stages of the immune response, including detection of viral RNA and DNA (DDX60, DHX58, IFIH1, etc.), induction of interferon production (IRF7, IRF9, etc.), and downstream signaling and immune activation (STAT2, TRAFD1, TRIM25, etc.). Additionally, some genes (ISG15, MX1, OAS1, etc.) directly inhibit viral replication and promote viral clearance. Overall, these genes are critical for the body's defense against viral infections and likely interact with other immune response pathways to maintain homeostasis.] \n", - "197 [Summary: Immune response and antiviral pathways are enriched functions in the given gene list.\\nMechanism: The genes are involved in various pathways that contribute to the antiviral defense mechanism of the human body.\\n\\n\\nHypothesis: The enriched terms suggest that the given genes function in the activation of innate and adaptive immune responses against viral infections through the interferon signaling pathway. The genes act as key regulators of viral replication and transcription, and contribute to the antiviral defense mechanism of the human body.] \n", - "198 [Summary: This list of genes includes those involved in antiviral and immunological responses, as well as genes involved in regulating cellular processes such as cellular growth and metabolism. \\n\\nMechanism: These genes are involved in the immune response to viral infections and in regulating cellular processes such as growth and metabolism.\\n\\n\\nHypothesis: The enriched terms suggest that the common function of these genes is the regulation of antiviral and immunological responses in addition to the regulation of cellular processes such as metabolism and growth. It is likely that these genes work together to promote cellular immunity against viral infections and regulate cellular processes that support antiviral responses.] \n", - "199 [Summary: Immune response and antiviral pathways are enriched.\\n\\nMechanism: The genes in the list have a common function in response to viral infection through various pathways including interferon signaling, antigen processing and presentation, and immune cell activation.\\n\\n] \n", - "200 [Summary: Calcium ion binding and regulation of muscle contraction \\nMechanism: Calcium signaling \\n] \n", - "201 [Summary: This list of human genes is enriched for terms related to ion binding, signaling, and regulation of metabolic and cellular processes.\\nMechanism: These functions are likely involved in maintaining homeostasis and cell function through various signaling pathways.\\n\\n] \n", - "202 [Summary: Regulation of immune response and cell signaling \\nMechanism: Not enough information to make a hypothesis \\n] \n", - "203 [Summary: Immune response and inflammation-related functions are enriched in the list of genes.\\nMechanism: The genes are involved in regulating the immune system and its response to pathogens, as well as controlling inflammation pathways.\\n\\n\\nHypothesis: The enriched functions suggest that the genes play a role in regulating the immune system response to pathogens and inflammation. The genes may be involved in controlling signaling pathways for cytokines, chemokines, and interleukins, as well as regulating leukocyte activation and complement activation. Additionally, the genes may be involved in eicosanoid synthesis pathways and platelet activation and aggregation. Overall, the enrichment of these functions suggests that the genes play a role in immune system surveillance and response to infections and other stimuli.] \n", - "204 [Summary: Genes are enriched for microtubule-based processes and cellular division.\\nMechanism: The genes listed are involved in microtubule-based processes and cellular division. The enriched terms highlight the specific aspects of these processes that these genes are involved in. \\n\\n] \n", - "205 [Summary: Microtubule formation and spindle assembly during cell division.\\nMechanism: The genes are involved in microtubule formation and spindle assembly during cell division. These genes are related to the structural integrity and mediator of spindle formation and the cleavage furrow during cytokinesis.\\n] \n", - "206 [Summary: The enriched terms shared among these genes are related to protein folding, metabolism, and immune response pathways.\\n\\nMechanism: These genes appear to share a connection through signaling pathways that regulate protein folding, metabolism, and immune response.\\n\\n] \n", - "207 [Summary: Genes identified have functions predominantly involved in cellular metabolism and protein handling, including regulation of transcription and translation. There is also enrichment in genes associated with response to stress and DNA repair.\\n\\n\\nHypothesis: The identified genes are likely involved in cellular processes that are essential for growth and survival, including the maintenance of cellular metabolism, response to stress, and DNA repair. Dysregulation of these pathways may lead to disease states such as cancer or neurodegeneration. Further analysis and studies of these genes and their pathways could inform novel therapies for these conditions.] \n", - "208 [Summary: Genes associated with protein synthesis, processing, and folding are overrepresented in the list.\\n\\nHypothesis: These genes work together in a network to facilitate protein synthesis, processing, and folding. They may also play a role in RNA splicing through their association with the U4/U6.U5 tri-snRNP complex. Dysfunction of this network may lead to disrupted protein synthesis and processing, resulting in diseases such as neurodegeneration and cancer.] \n", - "209 [Summary: RNA processing and translation \\nMechanism: The enriched terms suggest that the genes are involved in various aspects of RNA processing and translation.\\n\\n] \n", - "210 [Summary: RNA processing and ribosome biogenesis\\nMechanism: These genes are involved in RNA processing and ribosome biogenesis, specifically in various stages of transcription, modifying RNA, ribosomal assembly, and transport.\\n] \n", - "211 [Summary: The common function of the genes is related to RNA processing and transcription regulation. \\nMechanism: The genes are involved in regulating different steps in the transcription and processing of RNA. \\n\\nHypothesis: The genes in this list are all involved in different aspects of RNA processing and transcription regulation. These processes are essential for the production of functional RNAs, which are required for gene expression and cellular communication. It is likely that the proteins encoded by these genes interact with each other and with other factors to form complexes that facilitate RNA processing and transcription. Dysfunction of these processes has been associated with a range of human diseases, including cancer and developmental disorders.] \n", - "212 [Summary: Muscle structure and function, including contraction and calcium handling, are enriched functions among the listed genes.\\nMechanism: Muscle contraction and calcium handling.\\n\\nHypothesis: The enriched genes are largely involved in the structure and function of skeletal and cardiac muscle tissue, contributing to processes such as contraction and calcium handling. The Z-disc, sarcomere, and thin filaments are important structural components of muscle, and genes involved in their assembly and maintenance are among the enriched terms. Calcium ion transport is also an important function in muscle cells, and genes involved in this process, as well as those involved in the assembly and regulation of the troponin-tropomyosin complex that regulates calcium-dependent muscle contraction, are also enriched.] \n", - "213 [Summary: Muscle structure and function\\nMechanism: Muscle contraction and maintenance\\n\\nHypothesis: These genes are mainly involved in muscle structure and function. They function in muscle contraction and maintenance through various mechanisms, including regulation of muscle filaments, myosin activity, and actin dynamics. The statistically over-represented terms are related to muscle structure and function, such as muscle, myosin, actin, troponin, and filament. These genes likely interact to control muscle contraction and maintenance, and may be involved in various muscle disorders and diseases.] \n", - "214 [Summary: Genes are enriched for functions involved in Notch signaling and Wnt signaling pathways.\\nMechanism: Notch and Wnt signaling pathways are major signaling pathways that regulate cell fate determination and differentiation during development.\\n\\n] \n", - "215 [Summary: These genes are involved in the Notch signaling pathway and cell proliferation regulation.\\nMechanism: The Notch signaling pathway is involved in cell fate specification and differentiation during development and in adult tissues.\\n] \n", - "216 [Summary: Mitochondrial respiration\\n\\nHypothesis: Dysregulation of these genes may result in impaired mitochondrial function, decreased ATP production, and cellular metabolic dysfunction, leading to a variety of diseases including neurodegenerative disorders and metabolic disorders.] \n", - "217 [Summary: These genes are involved in mitochondrial function and energy metabolism.\\nMechanism: Mitochondrial electron transport chain and oxidative phosphorylation.\\n\\n] \n", - "218 [Summary: DNA damage response and cell cycle regulation pathways are enriched among the listed genes.\\nMechanism: The genes are involved in processes that regulate cell growth and proliferation, as well as response to DNA damage.\\n] \n", - "219 [Summary: Cell cycle regulation and DNA damage response.\\nMechanism: Transcriptional regulation and DNA repair.\\n\\nHypothesis: \\nThe list of genes is enriched for functions related to cell cycle regulation and DNA damage response. Many of these genes are involved in processes such as cell cycle arrest, DNA repair, and transcriptional regulation, indicating a potential role in maintaining genome stability. Some of these genes, such as TP53, are known to play a central role in the DNA damage response and are involved in regulating the expression of genes involved in DNA repair and cell cycle arrest. Other enriched terms, such as the G1/S transition of mitotic cell cycle, suggest that these genes may also play a role in controlling the progression of the cell cycle and cell proliferation. Overall, the enrichment of these functions suggests that the genes in this list are involved in maintaining genomic integrity and proper cell cycle progression.] \n", - "220 [Summary: Genes involved in pancreatic beta cell development and function\\nMechanism: Beta cell differentiation and insulin secretion\\n] \n", - "221 [Summary: Genes are enriched for functions related to pancreatic beta cell development and insulin secretion.\\nMechanism: Beta cells in the pancreas produce and secrete insulin, and defects in this process can lead to diabetes.\\n] \n", - "222 [Summary: Transport and metabolism of lipids, hormones, and xenobiotics are enriched gene functions.\\nMechanism: Lipid and xenobiotic metabolism pathways are activated.\\n\\nHypothesis: The enriched gene functions are consistent with the liver's role in detoxification and energy metabolism. These genes may play a role in maintaining liver homeostasis and responding to environmental toxins and hormonal changes.] \n", - "223 [Summary: Enriched terms include fatty acid metabolism, bile acid transport, peroxisome organization, and DNA repair.\\nMechanism: These genes are involved in various metabolic pathways and cellular processes, including fatty acid metabolism, bile acid transport, peroxisome organization, and DNA repair.\\n\\n] \n", - "224 [Summary: Signal transduction and regulation of cell cycle and apoptosis\\n\\nHypothesis: The listed genes are involved in different stages of signal transduction pathways that ultimately converge on either the MAPK cascade or PI3K-Akt signaling pathway, which regulate cellular proliferation, differentiation, and apoptosis. The genes identified under enriched term \"regulation of cell proliferation\" might work as positive or negative regulators of cell growth and death signals. Altered functions or dysregulation of these genes could lead to abnormal growth or development, contributing] \n", - "225 [Summary: Signaling pathways and cellular responses are enriched in these genes.\\nMechanism: The genes seem to be involved in multiple pathways and cellular responses.\\n] \n", - "226 [Summary: Membrane trafficking and vesicle transport\\nMechanism: The genes in this list are all involved in various processes of membrane trafficking and vesicle transport.\\n] \n", - "227 [Summary: Membrane transport and vesicle-mediated transport\\nMechanism: Membrane trafficking and vesicle formation and fusion\\n\\nHypothesis: The enrichment of terms related to membrane transport and vesicle-mediated transport suggests that the genes on this list are involved in the processes of vesicle formation, membrane trafficking, and vesicle fusion. Multiple genes on this list are involved in the transport of proteins to the Golgi, endosomes, and lysosomes, suggesting a potential role in intracellular protein transport and protein sorting. Additionally, the enrichment of terms related to ion transport and regulation of membrane potential may indicate a role in cellular signaling or homeostasis. Overall, these genes are likely involved in various aspects of membrane trafficking and vesicle-mediated transport within the cell.] \n", - "228 [Summary: Genes are involved in oxidative stress response and redox regulation.\\nMechanism: Gene products involved in antioxidant response and maintenance of redox balance.\\n\\nHypothesis: The majority of the genes in the list are involved in the response to oxidative stress. They act through different but interconnected mechanisms to maintain redox balance in cells. These include direct antioxidant activity, such as the scavenging of reactive oxygen species (ROS), and the regulation of antioxidant enzyme activity and cellular levels of ROS. The results of the enrichment test suggest that these processes are statistically over-represented in the list of genes. Specifically, the list is enriched with genes involved in peroxiredoxin activity, catalysing the reduction of H2O2 and other ROS. Additionally, genes involved in glutathione metabolism, which provides an important reducing environment in cells, are also enriched. Overall, these genes act in concert to maintain cellular redox balance and protect against oxidative damage.] \n", - "229 [Summary: Redox regulation \\nMechanism: The genes in this list are involved in maintaining redox homeostasis through processes such as antioxidant defense, regulation of protein function through thiol-based modifications, iron regulation, and DNA repair.\\n\\n] \n", - "230 [Summary: Enrichment analysis identified terms related to spermatogenesis and meiosis as over-represented in the list of genes.\\n\\nMechanism: The identified genes are likely involved in the regulation of various processes related to spermatogenesis and meiosis, including DNA replication, chromosome segregation, and cell division.\\n\\n] \n", - "231 [Summary: Genes are enriched for regulation of mitotic cell cycle processes.\\nMechanism: The genes are involved in the regulation of mitosis and cell cycle.\\n] \n", - "232 [Summary: Genes are involved in TGF-beta signaling pathway\\nMechanism: TGF-beta signaling pathway\\n\\nHypothesis: The enriched terms suggest that the genes are involved in the TGF-beta signaling pathway, as well as the regulation of BMP signaling pathway. TGF-beta signaling pathway plays a crucial role in cell growth, differentiation, and apoptosis. The interaction between TGF-beta and BMP signaling pathways has a significant influence on organ development and tissue regeneration. These genes may regulate cellular responses to growth factors and transcription, which are the downstream processes of the TGF-beta signaling pathway.] \n", - "233 [Summary: The genes are enriched in terms related to transforming growth factor-beta (TGF-beta) signaling pathway and extracellular matrix (ECM) regulation.\\nMechanism: TGF-beta signaling pathway and ECM regulation.\\n\\n] \n", - "234 [Summary: Genes involved in inflammation and immune response are enriched.\\nMechanism: These genes are likely involved in regulating the inflammatory response and immune system signaling.\\n\\n] \n", - "235 [Summary: Genes involved in immune response and inflammation pathways are enriched, specifically those related to cytokine signaling, transcription factor regulation, and stress response.\\nMechanism: These genes likely play a role in regulating the immune response and inflammation in various tissues, as well as responding to cellular stress.\\n] \n", - "236 [Summary: Protein folding and degradation pathways are enriched.\\nMechanism: The genes are involved in regulation of protein synthesis and processing, particularly related to endoplasmic reticulum-associated degradation (ERAD) and the unfolded protein response (UPR).\\n] \n", - "237 [Summary: The enriched terms for these genes relate to protein processing and regulation, RNA metabolism, and stress response.\\nMechanism: These genes are involved in the regulation of protein synthesis and folding, as well as RNA metabolism, which could contribute to cellular stress response and adaptation.\\n\\n] \n", - "238 [Summary: Genes in this list are mostly involved in signal transduction, cell adhesion, and extracellular matrix organization, with a significant enrichment in the TGF-beta signaling pathway.\\nMechanism: TGF-beta signaling pathway plays a significant role in regulating various cellular processes, including cell proliferation, differentiation, and apoptosis.\\n\\n] \n", - "239 [Summary: Extracellular matrix and cytoskeletal organization\\nMechanism: Cell adhesion and migration \\n\\n\\nHypothesis: The enriched terms suggest that these genes play roles in extracellular matrix and cytoskeletal organization for cellular adhesion and migration. They are likely involved in pathways that regulate cytoskeletal dynamics and cell adhesion to the extracellular matrix through integrin signaling, as well as the regulation of migratory behavior in various cell types.] \n", - "240 [Summary: Genes are involved in regulation of transcription, cellular metabolism, and signaling pathways.\\nMechanism: Biological pathways involved in gene regulation, metabolic pathways, and signaling pathways.\\n\\nHypothesis: The enriched terms suggest that these genes are involved in the regulation of transcription, cellular metabolism, and signaling pathways. These pathways are involved in the regulation of gene expression, cellular homeostasis, and response to external stimuli. The mechanism involves complex networks of interactions between proteins and other molecules that mediate these pathways.] \n", - "241 [Summary: Genes are involved in diverse biological processes, with some enrichment in immune response, cell cycle regulation, and protein localization.\\nMechanism: No specific mechanism could be elucidated, as the genes are involved in diverse functions.\\n] \n", - "242 [Summary: The enriched terms suggest that these genes are involved in the regulation of cellular signaling pathways and gene expression, particularly the Wnt signaling pathway and the Notch signaling pathway.\\nMechanism: The Wnt and Notch signaling pathways are essential for embryonic development, tissue homeostasis, and cell fate determination in adult tissues. These pathways are tightly regulated and involve a complex network of ligands, receptors, and downstream effectors.\\n\\n] \n", - "243 [Summary: Regulation of Notch signaling pathway\\nMechanism: Notch pathway activation\\n\\nHypothesis: These genes are involved in the regulation of the Notch signaling pathway, which plays a critical role in cell fate commitment during development and tissue homeostasis. They are implicated in the activation, positive regulation, and negative regulation of the Notch pathway, suggesting a complex regulatory mechanism that ensures proper cell differentiation and tissue patterning. These genes may act on different levels of the pathway, including ligands, receptors, and downstream effectors, and may participate in multiple developmental processes, such as neurogenesis, angiogenesis, and epithelial-mesenchymal transition. Dysfunction of these genes may lead to developmental disorders and cancers, highlighting their importance as therapeutic targets.] \n", - "244 [Summary: Immune response regulation \\nMechanism: Regulation of T cell receptor signaling\\n] \n", - "245 [Summary: Genes are enriched in immune system and cell signaling functions.\\nMechanism: These genes are involved in a variety of processes, including immune system regulation and various signaling pathways.\\n] \n", - "246 [Summary: The common function shared by POU5F1, SOX2, KLF4, and MYC is transcriptional regulation and cell differentiation.\\nMechanism: The genes are involved in maintaining pluripotency and promoting cell proliferation and differentiation in embryonic and somatic cells.\\n\\nHypothesis: These genes play a crucial role in regulating pluripotency and inducing distinct cell types during embryonic development. They may act through various pathways, such as the NANOG, WNT, and BMP pathways, to promote stem cell maintenance and differentiation. Dysregulation of these genes may lead to developmental disorders or cancer.] \n", - "247 [Summary: These three genes are involved in the regulation of pluripotency and differentiation in stem cells. \\nMechanism: Together, KLF4, POU5F1, and SOX2 activate the expression of genes that maintain stem cell identity and prevent differentiation, while also repressing genes that promote differentiation. \\n\\nHypothesis: The mechanism involving these genes is likely to be part of a larger regulatory network, involving other transcription factors and signaling pathways, that is necessary for the proper development and maintenance of stem cells in various tissues and organs. These genes may also play a role in cancer progression, by promoting or suppressing the self-renewal and differentiation of cancer stem cells.] \n", - "248 [Summary: Extracellular matrix organization and angiogenesis are over-represented functions among the listed human genes.\\nMechanism: The identified genes are involved in the regulation of extracellular matrix composition and organization, as well as angiogenesis which suggests a potential role in developmental processes.\\n\\n] \n", - "249 [Summary: Genes are enriched in extracellular matrix organization and regulation of cell adhesion.\\nMechanism: Extracellular matrix remodeling \\n\\nHypothesis: The enrichment of terms related to extracellular matrix organization and regulation of cell adhesion suggests that these genes play a role in extracellular matrix remodeling, which is important for cellular activities such as migration and proliferation. The extracellular matrix can influence cell behavior by providing mechanical support and signaling cues, and regulating cell adhesion is crucial for the maintenance of tissue integrity and embryonic development. Dysfunction of these processes has been implicated in several diseases, including cancer, cardiovascular disorders, and developmental abnormalities.] \n", - "250 [Summary: The common function among the listed genes is related to nervous system development and signal transduction, with enrichment in terms related to calcium ion binding, synapse organization, and transcriptional regulation.\\n\\nMechanism: These genes may be involved in regulating signal transduction pathways in the nervous system, particularly related to calcium signaling and synapse formation and function. They may also play a role in transcriptional regulation during nervous system development.\\n\\n] \n", - "251 [Summary: Several genes are involved in signal transduction, cellular communication, and regulation of gene expression.\\n\\nMechanism: The enriched terms suggest that these genes are involved in various cellular functions such as signal transduction, cell communication, and gene expression regulation.\\n\\n] \n", - "252 [Summary: Muscle contraction and regulation of muscle fiber type are the significantly enriched biological mechanisms shared among the given human genes.\\nMechanism: Muscle contraction and regulation of muscle fiber type\\n] \n", - "253 [Summary: Genes are involved in muscle contraction and development.\\nMechanism: Muscle development and regulation.\\n\\nHypothesis: The common function of these genes is in the regulation of muscle development and contraction. Many of these genes are involved in myofibril assembly and muscle fiber development, suggesting that they play critical roles in the formation and function of skeletal muscle tissue. The identification of these enriched terms supports the idea that the genes are involved in muscle contraction and development. Further study may reveal new insights into the specific mechanisms by which these genes influence muscle function, potentially leading to new therapies for muscle-related disorders.] \n", - "254 [Summary: The common function of the given genes is related to intracellular trafficking, particularly of endocytosis and lysosomal degradation.\\nMechanism: The genes are involved in regulating the pathways of endocytosis, vesicular trafficking, and lysosomal degradation, contributing to protein degradation and cellular homeostasis.\\n\\nHypothesis: The genes identified in the term enrichment analysis suggest that they may be associated with intracellular trafficking processes, particularly endocytosis and lysosomal degradation. The endocytic pathway is responsible for a variety of functions, including extracellular nutrient uptake, synaptic transmission, and maintenance of plasma membrane composition. The lysosomal degradation pathway is responsible for breakdown and degradation of intracellular materials, including misfolded/unfolded proteins. These pathways are essential to prevent accumulation of toxic waste in the cell and maintain cellular homeostasis. The enriched gene set may play a role in regulating the balance between endocytosis, vesicular trafficking, and lysosomal degradation, contributing to protein and cellular homeostasis.] \n", - "255 [Summary: The list of human genes is enriched for terms related to endocytosis and receptor signaling.\\n\\nMechanism: The majority of genes in the list are involved in endocytosis, the cellular process of internalizing molecules from the extracellular environment via vesicles. Many of the enriched terms are related to the trafficking, sorting, and recycling of receptors that are involved in cell signaling pathways.\\n\\n\\nHypothesis: The genes listed are involved in the regulation of endocytosis and receptor signaling, which play critical roles in cell signaling and communication. Dysregulation of these processes can contribute to a variety of diseases, including cancer, neurodegenerative disorders, and metabolic diseases. Further investigation of the specific roles of these genes in endocytic and receptor signaling pathways may offer insights into novel therapeutic targets for these diseases.] \n", - "256 [Summary: These genes are mostly involved in glycolysis, with a focus on catalyzing the conversion of glucose to pyruvate. \\n\\nMechanism: Glycolysis is the metabolic pathway that breaks down glucose into pyruvate, which can then be used to produce ATP or other metabolic intermediates. \\n\\n] \n", - "257 [Summary: The common function shared by the given human genes is glycolytic process.\\nMechanism: Glycolysis is a metabolic pathway that breaks down glucose into pyruvate.\\n] \n", - "258 [Summary: Calcium ion signaling pathways are enriched amongst the list of human genes provided.\\nMechanism: Calcium ion signaling pathways play a crucial role in various physiological processes, including neurotransmitter release, muscle contraction, and gene expression regulation. The genes in this list contribute to the activity of different types of calcium channels, transporters, and receptors, as well as other proteins that modulate calcium signaling.\\n\\n] \n", - "259 [Summary: Calcium signaling and neurotransmission-related functions appear to be enriched in the list of genes.\\n\\nMechanism: Calcium signaling plays a key role in neurotransmission, regulating the release of neurotransmitters from presynaptic terminals and the activation of postsynaptic receptors.\\n\\n] \n", - "260 [Summary: Many of these genes are related to cellular stress response, signaling pathways, and regulation of autophagy.\\nMechanism: The genes may be involved in a complex network of responses to cellular stress that involve the regulation of signaling pathways and autophagy.\\n] \n", - "261 [Summary: The common function of the genes is associated with regulation of apoptotic signaling pathways, cellular metabolism, and protein processing.\\nMechanism: The genes are involved in the PI3K-Akt signaling pathway, which regulates cell growth, proliferation, and survival.\\n\\nHypothesis: The PI3K-Akt pathway plays an important role in regulating cell survival and metabolism, therefore mutations or dysregulation in the genes could contribute to the development of cancer or other diseases involving abnormal cell growth and metabolism.] \n", - "262 [Summary: Glycosidase activity and carbohydrate metabolism\\nMechanism: These genes are involved in the hydrolysis of glycoside bonds in carbohydrates, specifically the breakdown of glycoproteins, glycolipids, and oligosaccharides. \\n\\nHypothesis: These genes are primarily involved in the breakdown of complex carbohydrates, specifically in lysosomes and the endoplasmic reticulum. Dysfunction in these genes can lead to lysosomal storage disorders, such as mucopolysaccharidosis, where complex carbohydrates accumulate in the cell and cause systemic disease.] \n", - "263 [Summary: Glycoside hydrolases and related genes involved in carbohydrate metabolism\\nMechanism: These genes are involved in the catabolism and processing of complex carbohydrates into simple sugars.\\n\\n\\nHypothesis: These genes are all involved in the breakdown of complex carbohydrates including glycosphingolipids, oligosaccharides, and sialic acids. This catabolism likely takes place in lysosomes, where these complex carbohydrates are transported to be broken down into simple sugars. The mechanism by which these genes function is likely a combination of enzymatic activity and transport function. Dysfunction of these genes could lead to lysosomal storage diseases where the catabolism of complex carbohydrates is impaired, leading to a buildup of these molecules in lysosomes and subsequent pathology.] \n", - "264 [Summary: The common function of these genes is related to immunoglobulin and T cell receptor production and signaling.\\nMechanism: These genes are involved in the development and function of B cells and T cells.\\n] \n", - "265 [Summary: Enriched terms include immune response, lymphocyte activation, and lymphocyte differentiation.\\nMechanism: These genes are involved in various aspects of the immune system, particularly in the activation and differentiation of lymphocytes.\\n] \n", - "266 [Summary: Enriched terms suggest these genes are primarily involved in meiosis and DNA repair processes. \\nMechanism: Meiotic recombination and crossover formation, DNA damage response and repair.\\n\\nHypothesis: The enriched terms suggest that these genes are involved in meiotic recombination and crossover formation enabling the accurate pairing, exchange of genetic information, and separation of chromosomes during cell division. They may also be involved in DNA damage response and repair pathways important for maintaining genomic integrity during these processes.] \n", - "267 [Summary: These genes are enriched in terms related to meiotic recombination and chromosome segregation.\\nMechanism: Meiosis\\n\\n\\nHypothesis: These genes are involved in the regulation and maintenance of meiotic recombination during meiosis, and the proper segregation of chromosomes during cell division. Meiosis is a specialized cell division process that generates haploid gametes with genetic diversity. This process involves several steps, including DNA replication, chromosome recombination, synapsis, and segregation. The enriched terms suggest that these genes are involved in the regulation of these processes, which are critical for proper meiotic cell division and genetic diversity.] \n", - "268 [Summary: The genes in the list are enriched for terms related to immune response and regulation, protein folding and metabolism, cellular transport and localization, and gene expression regulation.\\nMechanism: The enriched terms suggest that these genes are involved in cell survival and response to stress, likely through regulation of various signaling pathways.\\n\\n] \n", - "269 [Summary: Regulation of cellular processes and response to stress\\nMechanism: Regulation of transcription and protein turnover\\n\\nHypothesis: The commonalities in the function of these genes suggest a regulatory mechanism whereby the cells respond to stress by upregulating protective mechanisms. The enriched terms suggest that these protective mechanisms involve regulation of oxidative stress response, protein turnover and iron homeostasis. The negative regulation of NF-kappaB transcription factor activity implies that this pathway is activated downstream of these protective mechanisms, leading to an overall inhibition of pro-inflammatory signaling. Finally, the negative regulation of apoptotic process could suggest an additional component of these protective mechanisms that involves inhibiting programmed cell death to promote cell survival during stress.] \n", - "270 [Summary: The enriched terms shared among these genes are related to protein folding, metabolism, and immune response pathways.\\n\\nMechanism: These genes appear to share a connection through signaling pathways that regulate protein folding, metabolism, and immune response.\\n\\n] \n", - "271 [Summary: Protein synthesis and folding\\nMechanism: Protein homeostasis regulation\\n] \n", - "272 [Summary: These genes are involved in peroxisome biogenesis and organization.\\nMechanism: Peroxisome formation and maintenance pathway\\n] \n", - "273 [Summary: These genes are all involved in peroxisome biogenesis and maintenance.\\nMechanism: Peroxisomes are organelles that are involved in lipid metabolism and cellular signalling.\\n\\nHypothesis: These genes are likely involved in the regulation of peroxisome biogenesis and the maintenance of peroxisome membrane organization and fission. They may be involved in regulating lipid metabolism and cellular signalling processes that are mediated by peroxisomes.] \n", - "274 [Summary: The common function of the given genes is related to DNA damage repair, chromosome organization and regulation of transcription.\\nMechanism: The enriched terms suggest that these genes are involved in nuclear organization and DNA repair pathways. \\n] \n", - "275 [Summary: The common function of the genes LMNA, WRN, and BANF1 is in DNA repair, chromatin organization, and cellular senescence.\\nMechanism: The nuclear envelope organization and maintenance\\n\\nHypothesis: LMNA, WRN, and BANF1 are involved in the maintenance of the nuclear envelope structure and function, which is crucial for chromatin organization and DNA repair. The disrupted functions of these genes can result in DNA damage accumulation, epigenetic abnormalities, and cellular senescence. These genes may act together in a network to regulate the nuclear envelope dynamics and facilitate DNA repair, thereby maintaining genome stability and cellular viability.] \n", - "276 [Summary: The enriched terms from this list of genes are related to ion channel activity, particularly in relation to neurotransmission and synaptic signaling.\\n\\nMechanism: The genes on this list are involved in encoding different subunits of ion channels, most notably GABA and glutamate receptors, as well as voltage-gated potassium and sodium channels. These channels are crucial for synaptic transmission and the regulation of neuronal excitability.\\n\\n] \n", - "277 [Summary: Ion channel activity and synaptic transmission-related processes are enriched in the listed genes.\\nMechanism: The genes are involved in synaptic plasticity, memory formation, and neuronal signaling.\\n] \n", - "278 [Summary: The enriched terms found among the listed human genes suggest a common involvement in cellular metabolism, particularly in mitochondrial function, protein folding and degradation, and transportation across cellular membranes.\\nMechanism: These genes may be involved in the maintenance of cellular homeostasis and energy production.\\n\\nHypothesis: Many of the enriched terms are related to cellular stress pathways, suggesting that these genes may be involved in the response to stress and cellular damage. Additionally, the involvement of several genes related to mitochondrial function suggests that there may be a common underlying mechanism related to energy production and metabolism.] \n", - "279 [Summary: Several of the genes are involved in nervous system development and function.\\nMechanism: Unknown, but potentially related to myelin formation and maintenance.\\n] \n", - "280 [Summary: The common function of the listed genes is related to G protein-coupled receptor signaling and neurotransmission.\\nMechanism: G protein-coupled receptor (GPCR) signaling\\n\\nHypothesis: The listed genes are involved in various aspects of G protein-coupled receptor (GPCR) signaling and neurotransmission. The enrichment of terms related to neurotransmitter receptor activity, GPCR signaling pathway, and regulation of neurotransmitter secretion suggests that these genes contribute to the communication between neurons in the brain. The dopamine receptor signaling pathway and adenylate cyclase-modulating GPCR signaling pathway terms suggest that these genes are particularly important in dopaminergic neurotransmission, which is involved in a wide range of processes including reward processing, motivation, and movement control. The involvement of these genes in dopaminergic neurotransmission may have implications for understanding and treating various neuropsychiatric disorders.] \n", - "281 [Summary: Signaling and regulation via G-protein coupled receptors\\nMechanism: Activation of second messenger pathways\\n\\nHypothesis: These genes are all involved in signaling and regulation through G protein-coupled receptors (GPCRs), which are membrane proteins that activate intracellular signaling pathways upon binding with ligands such as neurotransmitters, hormones, or sensory signals. GPCR signaling pathways are transduced via G proteins, which consist of α, β, and γ subunits. The enriched terms suggest that these genes are involved in the regulation of G protein beta/gamma subunit complex binding, as well as the G protein coupled receptor signaling pathway. Dysfunction in these genes may lead to various diseases, including neuropsychiatric and cardiovascular disorders.] \n", - "282 [Summary: Transcriptional regulation and chromatin organization are enriched functions.\\nMechanism: These genes are involved in controlling gene expression and chromatin structure, which are crucial for cellular function and development.\\n\\nHypothesis: These genes may be involved in a common pathway related to transcriptional regulation and chromatin organization, such as the regulation of cell identity or differentiation, or the control of gene expression in response to external stimuli.] \n", - "283 [Summary: The common function among the given gene set is transcriptional regulation. \\nMechanism: The genes are involved in the regulation of various transcription factors, co-factors, and modifiers. \\n\\nHypothesis: The set of genes is involved in various stages of transcriptional regulation, from modifying chromatin structure to recruiting transcription factors and co-regulators. The enriched terms suggest that these genes may be involved in both positive and negative regulation of transcription, highlighting their importance in maintaining a fine balance of gene expression for proper cell function and development.] \n", - "284 [Summary: The enriched terms are related to the extracellular matrix and connective tissue development.\\nMechanism: The genes are involved in the synthesis, processing, and organization of collagens and other extracellular matrix components.\\n] \n", - "285 [Summary: The common function among these genes is the regulation and formation of the extracellular matrix, which includes collagen fibril organization, dermatan sulfate biosynthetic process, proteoglycan biosynthetic process and connective tissue development.\\n\\nMechanism: These genes play a crucial role in the regulation and formation of the extracellular matrix, which is a scaffold-like structure comprising various proteins including collagen, and is essential in the development and maintenance of tissues and organs.\\n\\n\\nHypothesis: These genes play a role in regulating the organization and biosynthesis of the extracellular matrix, which is essential in the formation and maintenance of connective tissues. Dysregulation of these genes may contribute to various connective tissue disorders, including Ehlers-Danlos syndrome. This suggests that targeting the extracellular matrix and its related pathways may have potential therapeutic applications for these disorders.] \n", - "286 [Summary: Fanconi anemia complementation pathway.\\n\\nMechanism: The Fanconi anemia (FA) pathway is a DNA repair pathway involved in the repair of inter-strand crosslinks and DNA double-strand breaks.\\n\\n\\nHypothesis: The FA pathway involves a series of proteins working together to repair damage to DNA that can cause various diseases, including cancer. The identification of this pathway provides insights into the mechanisms underlying DNA repair and may lead to improved methods of cancer treatment.] \n", - "287 [Summary: The common function of these genes is DNA repair and protein monoubiquitination, specifically in the context of Fanconi anemia complementation groups. \\n\\nMechanism: Fanconi anemia is a genetic disorder characterized by genomic instability, bone marrow failure, and cancer susceptibility. It is caused by mutations in genes involved in DNA repair pathways, particularly the Fanconi anemia complementation group pathway. These genes work together to repair DNA damage and maintain genomic stability, and mutations in these genes can lead to the development of Fanconi anemia.\\n\\n\\nHypothesis: These genes work together in the Fanconi anemia complementation group pathway to repair DNA damage and maintain genomic stability. The pathway involves the monoubiquitination of FANCD2 and FANCI, leading to their recruitment to sites of DNA damage and the assembly of a repair complex involving other Fanconi anemia complementation group proteins, including those represented by the genes listed here. The complex repairs DNA damage via homologous recombination, which] \n", - "288 [Summary: Mitochondrial function and energy metabolism are enriched in this list of genes.\\n\\nMechanism: These genes are involved in various processes such as ATP binding, enzyme activity, and transport, all of which are associated with mitochondrial function and energy metabolism.\\n\\n] \n", - "289 [Summary: Mitochondrial processes and metabolic function\\n\\nMechanism: The enriched terms suggest that these genes are involved in mitochondrial processes and metabolic function, with specific roles in energy production and mitochondrial regulation.\\n\\n] \n", - "290 [Summary: Immune response and cytokine activity.\\n\\n] \n", - "291 [Summary: Immune system function and cytokine activity are enriched in the list of genes.\\n\\nMechanism: The common biological mechanism underlying the enriched terms is the regulation and activation of the immune system, particularly through cytokine signaling.\\n\\n] \n", - "292 [Summary: Many of the genes listed are involved in binding activities, such as nucleic acid binding, protein binding, and ion binding. A number of genes are also involved in metabolic processes, such as biosynthesis and dehydrogenase activity.\\n\\n] \n", - "293 [Summary: Cell signaling and regulation of enzymatic activity\\nMechanism: These genes are involved in regulating cell signaling pathways, including cGMP biosynthesis, intracellular signal transduction and cell surface receptor signaling pathways. They also play a role in enzymatic activity, including phosphorylation, protein binding and transcription coactivator activity.\\n] \n", - "294 [Summary: Extracellular matrix structural constituents and proteins involved in cell signaling processes.\\n\\n] \n", - "295 [Extracellular matrix organization and binding activity are the enriched terms in common among these genes.\\n\\nMechanism: The extracellular matrix (ECM) plays a crucial role in regulating cell behavior and maintaining tissue integrity. The enriched terms suggest that these genes all participate in ECM organization and binding, potentially contributing to processes such as cell adhesion, migration, and differentiation.\\n\\n] \n", - "296 [Summary: These genes have functions related to cytoskeleton organization, cell adhesion, receptor binding, and kinase activity.\\n\\n] \n", - "297 [Summary: These human genes are involved in various cellular functions and processes, including cell adhesion, cell signaling, and cytoskeleton organization. \\nMechanism: These genes likely function in a network of interrelated pathways involved in cellular processes. \\n\\n] \n", - "298 [Summary: Cell surface receptor activity and signal transduction are enriched in this list of genes.\\n\\nMechanism: These genes are involved in various processes such as cellular response, regulation of cellular processes, and intracellular signaling pathways. They function primarily as cell surface receptors, enzyme binding activity, and protein domain-specific binding activity.\\n\\n] \n", - "299 [Summary: The enriched terms are related to membrane transport and signaling, with a focus on receptor activity and intracellular signaling.\\n\\nMechanism: These genes are primarily involved in the regulation of intracellular signaling pathways and membrane transport. \\n\\n] \n", - "300 [Summary: These genes are involved in apoptosis, cytokine activity, and DNA-binding transcription factor activity.\\n\\n\\nHypothesis: These genes may be involved in pathways related to cell death and inflammation, such as the TNF signaling pathway or the p53 signaling pathway. They may also be involved in regulating gene expression through DNA-binding transcription factors.] \n", - "301 [Summary: Genes involved in apoptotic signaling and cytokine activity.\\n\\n] \n", - "302 [Summary: The enriched terms indicate the genes are involved in lipid metabolism and transport.\\n\\nMechanism: The genes are involved in various processes related to the metabolism and transport of lipids and cholesterol, including ATP binding activity, and transmembrane transporter activity.\\n\\n] \n", - "303 [Summary: Several of the genes are involved in lipid metabolism and transport, particularly in the transport and binding of cholesterol and long-chain fatty acids. Peroxisomal proteins and functions are also enriched.\\n\\n] \n", - "304 [Summary: Cholesterol biosynthesis and lipid metabolism.\\nMechanism: Genes involved in cholesterol biosynthesis and lipid metabolism are enriched in this list.\\n] \n", - "305 [Summary: Cholesterol biosynthesis and homeostasis, isoprenoid biosynthesis, and lipid metabolism are the enriched functional terms common among the given human genes.\\n\\nMechanism: These genes are involved in cholesterol biosynthesis and homeostasis, isoprenoid biosynthesis, and lipid metabolism. The mechanisms are related to the synthesis, transportation, and metabolism of cholesterol and other lipids.\\n\\n] \n", - "306 [Summary: The enriched terms for these genes include proteolysis, complement pathways, blood coagulation, and cell adhesion.\\n\\nMechanism: These genes all play a role in regulating the immune system and extracellular matrix.\\n\\n] \n", - "307 [Summary: Many of the genes listed are involved in the regulation of proteolysis, including metalloendopeptidase activity and serine-type endopeptidase activity, and are predicted to be involved in blood coagulation, complement activation, and negative regulation of proteolysis. \\n\\n] \n", - "308 [Summary: Genes involved in protease inhibition, protein binding, and enzyme activity.\\n\\nMechanism: The enriched terms suggest a potential underlying mechanism involving regulation of protease activity through protein binding and enzyme inhibition.\\n\\n] \n", - "309 [Summary: These genes are involved in various functions, including protein binding activity, enzyme binding activity, and endopeptidase activity.\\n\\n] \n", - "310 [Summary: Several genes are involved in DNA binding, RNA binding, and nucleotide metabolism. \\n\\n] \n", - "311 [Summary: These genes are involved in DNA replication, repair, and polymerization, RNA transcription, and metabolic processes.\\n\\nMechanism: These genes are likely part of a larger biological pathway involved in maintaining genome stability and function.\\n\\n] \n", - "312 [Summary: Genes are primarily involved in DNA replication, cell cycle regulation, and chromatin organization.\\n\\nMechanism: These genes are likely involved in regulating the processes of DNA replication, the cell cycle, and chromatin organization.\\n\\n] \n", - "313 [Summary: DNA-related functions are enriched among the given genes.\\nMechanism: These genes are involved in various processes related to DNA, such as DNA binding, repair, and replication.\\n\\n] \n", - "314 [Summary: Extracellular matrix structural constituents and binding activities are statistically over-represented in this set of genes.\\n\\nMechanism: These genes are likely involved in extracellular matrix organization and cell-matrix interactions.\\n\\n] \n", - "315 [Summary: Extracellular matrix structural constituents and binding activities are enriched in these genes.\\n\\n] \n", - "316 [Summary: These human genes are involved in a variety of functions related to binding and enzymatic activity, particularly involving calcium ion and nucleotide binding. They are also involved in several biological processes, including growth and development, gene transcription, and ion transport.\\n\\nMechanism: The common mechanism underlying these gene functions is likely related to the regulation and modulation of intracellular processes, particularly those involving binding and enzymatic activity. Calcium ion binding, for example, is a key regulator of many cellular processes, including muscle contraction, neurotransmitter release, and cell signaling.\\n\\n] \n", - "317 [Summary: Enriched terms relate to protein binding, transcription regulation, and transmembrane transport activity.\\n\\n] \n", - "318 [Summary: Transmembrane transporter activity and binding activity are enriched terms in the functions of the given genes.\\n\\nMechanism: These genes are involved in the transport of metabolites across membranes and regulation of protein-protein interactions, possibly contributing to maintenance of cellular homeostasis.\\n\\n] \n", - "319 [Summary: Several genes are involved in enzymatic activities (e.g. oxidoreductase, dehydrogenase), while others are involved in binding activities (e.g. protein binding, chemokine binding, lipid binding). Many genes are also predicted to be involved in several processes, including cell signaling, transcription regulation, and protein kinase activity.\\n\\n] \n", - "320 [Summary: Enzyme activity and metabolism.\\nMechanism: Metabolism, specifically, fatty acid metabolism and energy production.\\n\\n\\nHypothesis: These genes are involved in the metabolism of fatty acids and the production of energy through the tricarboxylic acid cycle. They enable the binding, breakdown, and transfer of acyl-CoA, which is important in the catabolism of fatty acids for energy production. These metabolic processes are vital for maintaining cellular function and homeostasis.] \n", - "321 [Summary: Enzyme activity and binding activity are the most common functions among the genes in the list.\\n\\nMechanism: The genes in this list encode proteins that are involved in catalyzing chemical reactions (enzyme activity) and binding to other molecules (binding activity).\\n\\n] \n", - "322 [Summary: These genes are involved in various molecular functions related to DNA binding and activity, including DNA replication, transcription, and chromatin binding. \\nMechanism: These genes are likely involved in modulating gene expression and chromatin structure. \\n\\n] \n", - "323 [Summary: These genes are involved in DNA binding and transcription factor activity, protein kinase and phosphatase activity, cytoskeletal protein binding, and microtubule binding activity.\\n\\n] \n", - "324 [Summary: Glycosylation and carbohydrate metabolism are enriched functions in this list of genes.\\n\\nMechanism: Glycosylation is a key process in carbohydrate metabolism, involving the addition of carbohydrate groups to proteins and lipids to form glycoproteins and glycolipids, respectively. These modifications are critical for proper protein folding, stability, and secretion, as well as for cell-cell recognition and signaling.\\n\\n\\nHypothesis: The enriched functions in these genes suggest a critical role for glycosylation and carbohydrate metabolism in a variety of physiological processes and perhaps a possible link between glycosylation and pathologies. Future studies could explore the molecular mechanisms underlying these processes and their role in disease pathogenesis.] \n", - "325 [Summary: Enriched terms are involved in carbohydrate metabolism, specifically glycosaminoglycan and glycoprotein biosynthesis.\\n\\nMechanism: These genes all code for enzymes involved in carbohydrate metabolism, particularly in the biosynthesis of glycosaminoglycans and glycoproteins.\\n\\n] \n", - "326 [Summary: Genes are involved in a variety of cellular processes, including cell adhesion, signaling, and development.\\n\\nMechanism: These genes appear to converge on pathways related to cellular communication, regulation of gene expression, and cytoskeletal organization.\\n\\n] \n", - "327 [Summary: Cell signaling and adhesion, transcriptional regulation, and nervous system development are common functions among the given genes.\\n\\nMechanism: These genes seem to be involved in the regulation of various signaling pathways, which contribute to important biological processes.\\n\\n] \n", - "328 [Summary: These genes are involved in various biological processes, including enzymatic activities, transcriptional regulation, and ion transport. The enriched terms include heme binding, protein binding activity, transcription factor activity, and transmembrane transporter activity.\\n\\nMechanism: The underlying biological mechanism involves the regulation of various metabolic pathways and cellular processes, such as DNA transcription, ion transport, and protein function.\\n\\n] \n", - "329 [Summary: Transport and binding activity \\n\\nHypothesis: These genes may be involved in pathways related to transport regulation, signaling, redox homeostasis, and gene expression. Further studies may explore the role of these genes in these cellular processes.] \n", - "330 [Summary: Enriched terms show functions related to carbohydrate metabolism, enzyme binding and activity, signaling receptor binding, and DNA-binding transcription factor activity.\\n\\nMechanism: These genes may be involved in various biological mechanisms, such as carbohydrate metabolism, gene expression regulation, and receptor signaling pathways.\\n\\n] \n", - "331 [Summary: Enriched terms indicate genes involved in metabolic activities, specifically related to glucose metabolism and kinase activities, as well as transcriptional regulation and signaling.\\n\\nMechanism: These genes likely play a role in various cellular processes involved in metabolism, gene regulation, and signaling cascades.\\n\\n] \n", - "332 [Summary: Regulation of cytokines and immune responses.\\nMechanism: Modulation of cytokine signaling and immune response pathways.\\n\\nHypothesis: These genes are involved in regulating cytokine signaling and immune response pathways, potentially modulating the response to infection or other immune challenges. They may play a role in the regulation of lymphocyte activation and differentiation, including T cell costimulation and negative regulation of activation, and have been implicated in defense responses to pathogens. Additionally, these genes appear to be involved in cytokine signaling regulation through modulation of cytokine receptor binding and interleukin binding activity.] \n", - "333 [Summary: Enriched terms are related to immune function and cytokine activity.\\n\\n] \n", - "334 [Summary: Cytokine and growth factor signaling pathways\\nMechanism: These genes are all involved in the process of cytokine and growth factor signaling pathways which regulate a wide range of biological processes.\\n] \n", - "335 [Summary: Cytokine signaling and immune response\\nMechanism: These genes are involved in cytokine and chemokine receptor binding and cytokine-mediated signaling pathways, particularly those related to immune response and defense against other organisms.\\n\\n] \n", - "336 [Summary: These genes are involved in various functions relating to cytokine and chemokine activity, enzyme binding activity, receptor activity, and ion transport.\\n\\n\\nHypothesis: These genes play a role in immune system function, possibly involved in chemotaxis and signal transduction pathways through cytokine and chemokine activity, as well as ion transport in cell signaling. The genes may also be involved in enzyme binding and receptor activity, which could potentially affect various biological processes and disease pathways.] \n", - "337 [Summary: These genes are involved in various biological processes, including receptor and transporter activity, cytokine activity, and signal transduction.\\n\\n] \n", - "338 [Summary: Immune response genes that are involved in cytokine activity, defense response to other organisms, and negative regulation of viral entry into host cells. \\n\\nMechanism: These genes are likely involved in the innate immune response to infection, particularly in the modulation of viral infection and replication. \\n\\n] \n", - "339 [Summary: These genes are involved in immune response, defense against virus, negative regulation of protein secretion, regulation of leukocyte chemotaxis, RNA binding, and regulation of transcription.\\n\\nMechanism: The biological mechanism is likely the activation of the immune response, specifically the interferon response.\\n\\n] \n", - "340 [Summary: Immune response and cytokine signaling-related genes.\\n\\n] \n", - "341 [Summary: Immune system activity, particularly in response to viral infection, is the overarching theme among the functions of these genes.\\nMechanism: These genes are involved in various aspects of the immune response, including innate antiviral defense, antigen presentation, cytokine signaling, and regulation of immune cell activation and proliferation.\\n] \n", - "342 [Summary: Ion transport and binding activity\\nMechanism: Ion channel and transporter activity\\n\\nHypothesis: These genes are involved in various ion transport mechanisms and have binding activity for different ions, including calcium and sodium: potassium:chloride. They may be part of a larger pathway involved in regulating ion concentration and signaling in the cell.] \n", - "343 [Summary: The enriched terms are related to binding activity and transport, specifically involving ion, protein, and nucleoside.\\n\\n\\nMechanism: The genes in this list are involved in regulating binding activity and transport, likely through ion channels and protein-protein interactions.\\n\\n\\n] \n", - "344 [Summary: Several genes are involved in binding activity, such as protein binding, ion binding, and receptor binding. Additionally, some genes are involved in enzyme activity and transcription activator activity. \\n\\n] \n", - "345 [Summary: Many of the genes in the list enable various binding activities and are involved in regulation of cellular processes.\\n\\n] \n", - "346 [Summary: Genes involved in cytoskeleton organization, microtubule binding, and GTPase regulation.\\n\\nMechanism: These genes are predicted to be involved in various aspects of cytoskeleton organization and microtubule regulation, including microtubule binding, kinetochore binding, and actin filament binding. They are also predicted to be involved in the regulation of GTPases, which have been shown to play critical roles in cytoskeletal organization.\\n\\n] \n", - "347 [Summary: The enriched terms suggest that these genes are involved in microtubule organization and mitosis.\\n\\nMechanism: These genes play a role in regulating microtubule organization and mitosis, potentially through interactions with other proteins in the cytoskeleton and spindle apparatus.\\n\\n] \n", - "348 [Summary: Many of the genes are involved in binding activities, including RNA binding, protein binding, and ion binding, and several are involved in enzymatic activity such as oxidoreductase and kinase activity. \\n\\nMechanism: The enriched functions suggest that these genes are involved in protein synthesis and processing, as well as intracellular signaling and metabolism. \\n\\n] \n", - "349 [Summary: These genes are involved in several cellular processes, including protein binding and enzyme activity. \\n\\n] \n", - "350 [Summary: Protein synthesis and folding\\n\\n] \n", - "351 [Summary: These genes are involved in nucleic acid binding, RNA processing, protein folding, and structural constituents of ribosomes.\\n\\n] \n", - "352 [Summary: These genes are predominantly involved in RNA and protein processing, with many of them predicted to have RNA binding activity and be involved in rRNA processing. They also play roles in cell cycle regulation and mitochondrial function.\\n\\nMechanism: These genes likely function together in various pathways involved in RNA and protein processing, including rRNA processing, mRNA catabolism, and RNA maturation.\\n\\n] \n", - "353 [Summary: The enriched terms from these genes suggest involvement in various aspects of RNA processing and nucleolar function.\\n\\nMechanism: These genes encode proteins involved in RNA processing and nucleolar function.\\n\\n] \n", - "354 [Summary: The common function among the genes is related to muscle function and regulation.\\n\\nMechanism: The genes are all involved in the muscle cell structure, regulation, and function, including contraction, signaling, and development.\\n\\n] \n", - "355 [Summary: Muscle structure and function\\n\\n] \n", - "356 [Summary: Notch signaling pathway and protein ubiquitination are enriched functions among the given genes.\\n\\nMechanism: The enriched functions suggest that these genes are involved in a biological pathway related to the regulation of Notch signaling pathway and protein ubiquitination.\\n\\n] \n", - "357 [Summary: The enriched terms include \"Notch signaling pathway,\" \"protein ubiquitination,\" \"negative regulation of cell differentiation,\" and \"regulation of DNA-templated transcription.\"\\n\\nMechanism: These genes are involved in processes related to intracellular signaling and protein regulation.\\n\\n\\nHypothesis: These genes are involved in a complex regulatory network that fine-tunes protein levels and intracellular signaling pathways to ensure proper cell differentiation and development. The Notch signaling pathway is a key pathway involved in cell differentiation and is regulated by ubiquitination and transcriptional control. The enriched terms likely reflect the importance of these processes in maintaining proper cell function and development.] \n", - "358 [Summary: Genes in this list are involved in various aspects of mitochondrial function and metabolism, including electron transport chain activity, ATP synthesis, and metabolism of acyl-CoA and ketone bodies.\\n\\n\\nHypothesis: These genes are involved in different parts of mitochondrial metabolism and energy production, but they all work together to maintain proper mitochondrial function. Dysregulation of these genes could lead to disruptions in the electron transport chain and oxidative phosphorylation, which could contribute to mitochondrial dysfunction and metabolic disorders. Further research is needed to fully understand the underlying pathways and mechanisms by which these genes interact to maintain mitochondrial homeostasis.] \n", - "359 [Summary: These human genes have functions related to mitochondrial respiratory chain complexes and enzyme activity, as well as ion and molecule transport across mitochondrial membranes.\\n\\nMechanism: These genes are involved in the electron transport chain in the mitochondria. The electron transport chain generates ATP by transferring electrons from NADH and other electron donors to oxygen.\\n\\n] \n", - "360 [Summary: Enriched terms include regulation of apoptotic process, protein binding activity, and DNA-binding transcription factor activity. \\n\\nMechanism: These genes are involved in regulating apoptosis and controlling cell death. They also play a role in gene regulation and transcription factor activity through protein binding. \\n\\n] \n", - "361 [Summary: RNA binding and transcription factor activity are enriched in these genes.\\nMechanism: These genes are involved in regulating gene expression at the transcriptional level and RNA processing.\\n] \n", - "362 [Summary: Genes are involved in various processes including glucose homeostasis, insulin secretion, and transcription regulation.\\n\\nMechanism: Genes work together to regulate glucose homeostasis and insulin secretion.\\n\\n] \n", - "363 [Summary: Genes related to glucose homeostasis, insulin secretion, and glucose metabolism are enriched.\\n\\n\\nHypothesis: These genes may be involved in a pathway or mechanism related to glucose regulation and diabetes, potentially influencing glucose uptake, storage, and secretion.] \n", - "364 [Summary: Several of the genes listed are involved in transport functions and enzyme activities related to lipid and fatty acid metabolism. Additionally, some genes are involved in binding and catalytic functions related to retinoids and steroids.\\n\\n\\nHypothesis: These genes are involved in several functions that are key to cellular metabolism and homeostasis. Lipid and fatty acid metabolism are essential for maintaining membrane integrity and cellular signaling processes. Transporters and enzymes related to these functions are necessary for proper uptake, utilization, and metabolism of lipids and fatty acids. Additionally, retinoids and steroids are important signaling molecules that can be involved in metabolic processes and cellular differentiation. The presence of these genes suggests that dysregulation of lipid, fatty acid, retinoid, or steroid metabolism could lead to disease states such as metabolic disorders, cancer, or developmental abnormalities.] \n", - "365 [Summary: Most of the genes are involved in lipid or fatty acid metabolism and transport, including long-chain fatty acid-CoA ligase activity, palmitoyl-CoA oxidase activity, arachidonate-CoA ligase activity, very long-chain fatty acid-CoA ligase activity, and several other related terms.\\n\\nMechanism: These genes likely play a role in regulating lipid homeostasis and transport, possibly through peroxisome biogenesis and function, as several genes also have peroxisome-targeting sequence binding activity.\\n\\n] \n", - "366 [Summary: Genes are involved in various cellular processes, including protein kinase activity, cytoskeleton structure, lipid metabolism, and protein binding activity.\\n\\nMechanism: These genes are involved in different pathways that regulate cellular signaling and metabolic processes.\\n\\n] \n", - "367 [Summary: Several of the genes are involved in intracellular signal transduction and several processes related to protein phosphorylation. \\n\\n] \n", - "368 [Summary: The enriched terms involve the transport and organization of cellular components, particularly in Golgi-related processes.\\n\\nMechanism: These genes likely contribute to the regulation of cellular transport and trafficking pathways involved in Golgi function and organization.\\n\\n] \n", - "369 [Summary: Intracellular vesicle transport and protein localization\\nMechanism: Vesicle-medidated transport pathways\\n] \n", - "370 [Summary: Genes involved in cell redox homeostasis and antioxidant activity are enriched.\\n\\nMechanism: These genes function in maintaining the balance of redox reactions in cells and protecting against oxidative damage.\\n\\n] \n", - "371 [Summary: Cell redox homeostasis and oxidative stress response\\nMechanism: Regulating and maintaining redox balance within cells to prevent oxidative damage\\n\\nHypothesis: These genes play important roles in maintaining cellular redox homeostasis and responding to oxidative stress. This includes antioxidant activity and the regulation of glutathione peroxidase and superoxide dismutase activities. Additionally, these genes are involved in NADH dehydrogenase activity and mitochondrial respiratory chain complex I assembly, both of which are crucial for cellular respiration and energy production. Together, these processes ensure the proper functioning of cells and protect against oxidative damage.] \n", - "372 [Summary: These genes are involved in a variety of processes including protein binding, enzyme activity, and ion transport. They are enriched for terms related to kinase activity, protein binding, and nucleotide binding.\\n\\nMechanism: These genes may be involved in the regulation of cell signaling and communication pathways through the activity and binding of kinases, proteins, and nucleotides.\\n\\n] \n", - "373 [Summary: The enriched terms include protein binding and enzymatic activity, involvement in several processes such as cell signaling, transcription, and metabolism, and localization to specific cellular structures.\\n\\nMechanism: These genes are involved in various biological processes that rely on protein-protein interactions, enzymatic activity, and regulation of various cellular functions.\\n\\n\\nHypothesis: These enriched terms suggest that the genes are involved in various biological pathways that are essential for maintaining cellular functions, including protein folding, transcription, signaling, and regulation of metabolism. These genes may also play a role in cellular localization and transport of specific molecules. Overall, these genes are integral to maintaining cellular homeostasis and their dysregulation could contribute to various diseases.] \n", - "374 [Summary: Genes involved in transforming growth factor beta (TGF-β) receptor signaling and related pathways are over-represented.\\n\\nMechanism: TGF-β receptor signaling is central to the regulation of cell growth and differentiation and is involved in numerous biological processes.\\n\\n] \n", - "375 [Summary: Genes involved in various aspects of signal transduction and regulation of gene expression.\\n\\n] \n", - "376 [Summary: The enriched terms for these genes suggest a role in immune response, cytokine activity, DNA-binding transcription factor activity, and enzyme binding activity.\\n\\nMechanism: These genes may play a role in activating or regulating the immune response and cytokine production through DNA-binding transcription factor activity and enzyme binding activity.\\n\\n] \n", - "377 [Summary: Genes on the list are involved in cytokine activity, DNA-binding transcription activities, and several enzymatic activities.\\n\\n] \n", - "378 [Summary: These genes are predominantly involved in protein processing, modification, and transport. \\n\\nMechanism: These genes are involved in various stages of protein synthesis, folding, and transport, including post-translational modifications, protein chaperoning, and trafficking. \\n\\n] \n", - "379 [Summary: All of the genes are involved in molecular functions related to RNA, protein, and ribosomal binding activity.\\nMechanism: These genes likely play a role in the regulation of transcription, translation, and protein folding.\\n] \n", - "380 [Summary: Extracellular matrix structural constituent, growth factor binding, protein kinase activity, nucleotide binding, transcription factor activity, protein binding.\\n\\n] \n", - "381 [Summary: Extracellular matrix structural constituents and binding activity.\\nMechanism: Extracellular matrix formation and maintenance.\\n\\n] \n", - "382 [Summary: Many of the enriched terms relate to protein binding and enzyme activity.\\n\\n] \n", - "383 [Summary: Genes enriched for ion transport, enzyme activity, DNA-binding, and protein binding\\n\\nMechanism: These genes likely play a role in various cellular processes including ion transport, metabolic processes, and gene expression regulation.\\n\\n] \n", - "384 [Summary: Genes are involved in Wnt signaling pathway and regulation of transcription, with a focus on negative regulation of canonical Wnt signaling pathway. \\n\\nMechanism: The genes listed are all involved in the Wnt signaling pathway, specifically the negative regulation of canonical Wnt signaling pathway. \\n\\n] \n", - "385 [Summary: These genes are involved in multiple signaling pathways, including Wnt and Notch signaling pathways, as well as protein degradation processes such as ubiquitination and proteolysis.\\nMechanism: These genes function to regulate cell proliferation, differentiation, and fate through activation or inhibition of specific signaling pathways.\\n\\nHypothesis: These genes function to maintain cellular homeostasis by regulating important signaling pathways and protein degradation processes. Dysregulation of these pathways may lead to abnormal cell growth, differentiation, and function, contributing to the development of various diseases such as cancer and neurodegenerative disorders.] \n", - "386 [Summary: Genes are involved in several processes including intracellular signaling, regulation of immune response, cell recognition, and response to bacterium.\\n\\nMechanism: These genes are mostly involved in intracellular signaling pathways, especially in the regulation of immune response.\\n\\n] \n", - "387 [Summary: Genes enriched in immune system processes, particularly T cell activation, cytokine production, and regulation of gene expression.\\n\\nMechanism: These genes likely function together to regulate the immune response, specifically in T cells. They contribute to T cell activation, cytokine production, and the regulation of gene expression at multiple levels.\\n\\n] \n", - "388 [Summary: These four genes are involved in transcription regulation and have DNA-binding activity. They are also involved in several cellular processes, such as gene expression regulation, cell proliferation, and differentiation.\\nMechanism: The enriched terms are likely involved in regulating gene expression and cellular differentiation through the binding and regulation of transcription factors.\\n\\n] \n", - "389 [Summary: Transcriptional regulation and developmental processes\\n\\nMechanism: Transcriptional regulation and cell fate specification\\n\\n] \n", - "390 [Summary: The enriched terms describe genes involved in extracellular matrix organization, cell signal transduction, and blood coagulation.\\n\\nMechanism: The genes share functions necessary for proper extracellular matrix organization and remodeling, including interactions with integrins and collagen-containing matrix components. They also share cell signaling pathways involved in growth factor binding and receptor activity, as well as regulation of intracellular signal transduction. Finally, several of the genes are involved in blood coagulation and lipid metabolism.\\n\\n] \n", - "391 [Summary: Extracellular matrix structure and function, integrin binding, growth factor activity, and response to external stimuli are enriched functions amongst the listed genes.\\n\\nMechanism: The enriched functions suggest that these genes play a crucial role in tissue development, organization, and homeostasis. They also participate in cellular communication, response to external signals, and signal transduction, possibly shaping key pathways involved in external stimuli responsiveness.\\n\\n] \n", - "392 [Summary: These genes are enriched for functions involved in protein binding, ion channel activity, transcriptional regulation, and ubiquitin-protein ligase activity.\\n\\nMechanism: The underlying biological mechanism may involve signaling pathways involved in protein regulation, ion transport, and gene expression.\\n\\n] \n", - "393 [Summary: Genes involved in binding activities, ion channel activity, and transcription factor activity.\\nMechanism: These genes are involved in regulating cellular processes by controlling the binding of molecules, ion flow, and gene expression.\\n] \n", - "394 [Summary: Genes related to muscle contraction, specifically those involved in myofibril assembly and regulation of muscle adaptation.\\n\\nMechanism: These genes are involved in the structural organization of the myofibril and the regulation of muscle contraction through their functions in actin and myosin binding, tropomyosin binding, and calcium ion binding.\\n\\n] \n", - "395 [Summary: Genes involved in muscle contraction and regulation are statistically over-represented in this list.\\n\\nMechanism: These genes likely play a role in the regulation and contraction of muscle tissue.\\n\\n] \n", - "396 [Summary: Receptor-mediated endocytosis and protein transport processes are enriched in these genes.\\nMechanism: These genes play important roles in endocytosis and the transport of proteins between organelles.\\n] \n", - "397 [Summary: These genes are involved in various processes related to intracellular transport and signaling, including endocytosis, lysosomal function, and receptor activity.\\nMechanism: These genes likely play a role in cellular transport and communication pathways, with some genes directly involved in intracellular trafficking and others affecting signaling pathways related to immune response and metabolism.\\n] \n", - "398 [Summary: Enzymes involved in glycolytic processes and carbohydrate metabolism.\\nMechanism: Glycolysis\\n] \n", - "399 [Summary: Genes are involved in metabolic processes and cellular development.\\nMechanism: Glycolysis pathway.\\n] \n", - "400 [Summary: Genes involved in calcium ion transport and signaling, as well as neurotransmitter receptor activity, are statistically over-represented. \\n\\nMechanism: These genes likely play a role in synaptic transmission and neuronal signaling. \\n\\n] \n", - "401 [Summary: Calcium signaling and neurotransmission\\nMechanism: Genes encode for ion channels and regulatory proteins involved in calcium-mediated neurotransmission.\\n\\nHypothesis: These genes play a critical role in regulating calcium-mediated neurotransmission, including depolarization, synaptic transmission, and the regulation of neurotransmitter levels. This suggests a potential involvement in various neurological disorders such as epilepsy, schizophrenia, and Alzheimer's disease. Several of the genes are also involved in calcium transport and homeostasis, which may have implications in muscle function and calcium signaling in other tissues.] \n", - "402 [Summary: Several of the genes are involved in signal transduction and regulation of protein kinase activity.\\n\\n\\nHypothesis: Many of these genes play roles in the regulation of signal transduction and pathways related to protein kinase activity. The enriched terms likely reflect the general role these genes play in the control and modulation of these mechanisms. Specifically, the involvement of many of these genes in TOR signaling, macroautophagy, and regulation of cyclin-dependent protein serine/threonine kinase activity suggest possible roles in cell cycle regulation and cancer development.] \n", - "403 [Summary: The enriched terms for this list of genes are intracellular signaling and apoptosis.\\n\\nMechanism: These genes are involved in various intracellular signaling pathways, particularly the PI3K signaling pathway, which is known to play a role in the regulation of cellular processes such as proliferation, differentiation, and survival. They are also involved in the regulation of apoptosis, which is a programmed cell death pathway responsible for the elimination of abnormal or damaged cells.\\n\\n] \n", - "404 [Summary: The enriched terms are centered around the catabolism of complex carbohydrates, specifically glycosphingolipids, glycoproteins, and chitin, as well as the breakdown of hyaluronan.\\n\\nMechanism: The genes with enriched functions are involved in various steps of complex carbohydrate catabolism, including enzymatic breakdown of specific glycosyl bonds and trimming of terminally located mannose and glucose residues. These processes likely occur in intracellular membrane-bound organelles, such as lysosomes.\\n\\n] \n", - "405 [Summary: Many of the genes listed are involved in carbohydrate metabolism and catabolic processes, including the processing and breakdown of glycans, glycoproteins, glycolipids, and other complex carbohydrates. Some genes are involved in the catabolism of specific substances such as chitin and fucose. \\n\\nMechanism: This group of genes likely represents a group of enzymes involved in the breakdown of various types of carbohydrates and sugars in the body. \\n\\n] \n", - "406 [Summary: These genes are involved in immunoglobulin receptor binding activity and activation of the immune response.\\nMechanism: The genes encode for the variable region of the immunoglobulin heavy and light chain, which are expressed by B-cells in response to foreign antigens, and enable the recognition and binding of those antigens. \\n] \n", - "407 [Summary: These genes are predicted to be involved in various processes related to the activation and defense response of the immune system. \\n\\nMechanism: These genes are involved in the production of immunoglobulin proteins, also known as antibodies, which are key components of the adaptive immune response system. \\n\\n\\nHypothesis: These genes are involved in the activation and defense response of the immune system through the production of immunoglobulin proteins. Antibodies bind to pathogens, marking them for destruction by other components of the immune system. The enriched terms suggest that these genes are particularly involved in the humoral immune response, which involves the production and secretion of antibodies into the bloodstream. Additionally, these genes may play a role in regulating the organization and differentiation of immune cells, such as monocytes.] \n", - "408 [Summary: These genes are primarily involved in meiotic processes, such as homologous chromosome pairing and recombination, as well as DNA repair.\\n\\nMechanism: These genes likely play a role in the proper segregation of chromosomes during meiosis, which is crucial for the formation of viable gametes.\\n\\n] \n", - "409 [Summary: Enrichment analysis of human genes reveals a common function in meiotic recombination and double-strand break repair via homologous recombination.\\n\\nMechanism: Meiotic recombination and double-strand break repair via homologous recombination are vital processes for the proper segregation of homologous chromosomes during meiosis. Several of the genes identified in the enrichment analysis are involved in these processes, either directly or indirectly.\\n\\n] \n", - "410 [Summary: Molecular sequestering and protein binding activity seem to be common functions among these genes.\\nMechanism: These genes may be involved in regulating the localization and availability of important molecules and proteins within cells.\\n\\n\\nHypothesis: The genes identified in this analysis may play a role in maintaining cellular homeostasis by regulating the availability and localization of important molecules and proteins. This function may be particularly important in response to stress and infection, as many of the enriched terms relate to these processes. The common function of molecular sequestering may involve the sequestration of molecules which could be detrimental to cellular function if present in excess (e.g. iron ion or oxysterols). The common function of protein binding activity could involve the regulation of protein trafficking and localization. Together, these genes may play a role in optimizing cellular function and protecting cells from damage.] \n", - "411 [Summary: Molecular sequestering activity, regulation of gene expression, positive regulation of protein ubiquitination, and sequestering of metal ion are enriched functions among the given human genes.\\n\\nMechanism: These genes are involved in the regulation and control of various cellular processes by sequestering certain molecules or ions, influencing cellular response to stress, and regulating gene expression. The enriched functions are primarily related to cellular regulation and signaling pathways.\\n\\n] \n", - "412 [Summary: Many of the genes are involved in binding activities, including RNA binding, protein binding, and ion binding, and several are involved in enzymatic activity such as oxidoreductase and kinase activity. \\n\\nMechanism: The enriched functions suggest that these genes are involved in protein synthesis and processing, as well as intracellular signaling and metabolism. \\n\\n] \n", - "413 [Summary: These genes are involved in various cellular functions, including protein binding, catalytic activity, and transporter activity. The enriched terms are related to cellular metabolic processes, protein folding, and DNA binding.\\n\\nMechanism: These genes likely contribute to cellular metabolism and homeostasis through various catalytic and transport mechanisms, as well as protein folding and DNA regulation.\\n\\n] \n", - "414 [Summary: Genes involved in peroxisomal biogenesis and protein import.\\n\\nMechanism: These genes are part of the peroxisome biogenesis pathway, which involves the recognition, targeting, and import of proteins into the peroxisomal membrane and matrix.\\n\\n] \n", - "415 [Summary: Genes involved in peroxisomal biogenesis and protein import into peroxisomes.\\nMechanism: Peroxisomal biogenesis and protein import mechanism.\\n\\nHypothesis: These genes are involved in the mechanism of peroxisomal biogenesis and protein import into peroxisomes. The enriched terms suggest that this process involves specific lipid binding activities, ATP binding and hydrolysis, and ubiquitin-dependent protein binding in order to ensure proper folding, import, and localization of proteins within peroxisomes. Dysfunctions in these genes can lead to peroxisomal biogenesis disorders, such as Heimler syndrome and rhizomelic chondrodysplasia punctata type 1.] \n", - "416 [Summary: These genes are involved in several processes related to DNA and cellular response, including chromatin regulation, DNA metabolic process, and cellular senescence. \\nMechanism: These genes are likely involved in maintaining genomic stability and responding to environmental stressors.\\n\\n] \n", - "417 [Summary: These genes are involved in DNA-related processes and cellular responses to stress, and are implicated in several diseases.\\nMechanism: The enriched terms suggest a possible role in DNA damage response and repair mechanisms, as well as cellular senescence.\\n\\nHypothesis: These genes may be part of a network involved in maintaining genomic stability and cellular homeostasis, particularly in response to stressors such as DNA damage. Dysfunction of this network may lead to increased cellular senescence and disease.] \n", - "418 [Summary: The enriched terms are related to ion channels and synaptic transmission, including ligand-gated monoatomic ion channel activity, regulation of presynaptic/presynaptic membrane potential, and several transmembrane transport processes. \\n\\nMechanism: These genes all play a role in regulating synaptic transmission through ion channels. \\n\\n] \n", - "419 [Summary: Ion channel activity and neurotransmission are enriched functions among the listed genes, with a focus on GABA and glutamate signaling pathways. \\n\\nMechanism: The genes in the list are involved in regulating ion channel activity and neurotransmission, particularly through GABA and glutamate signaling pathways. \\n\\n] \n", - "420 [Summary: Genes are primarily involved in the peripheral nervous system, myelination, and neurological disorders.\\nMechanism: The enriched terms suggest that these genes primarily function in the peripheral nervous system and myelination.\\n\\nHypothesis: These genes are all involved in the development and maintenance of the peripheral nervous system and myelination. Dysregulation or mutation of these genes likely leads to neuropathic disorders.] \n", - "421 [Summary: Genes are predominantly involved in peripheral nervous system development, myelination and maintenance, and mitochondria-related functions with a subset involved in protein ubiquitination and cellular response to mechanical stimulus. \\n\\nMechanism: The primary biological mechanism underlying these enriched terms is likely the maintenance of neuronal function and homeostasis, with specific pathways including mitochondrial metabolism and protein degradation/regulation.\\n\\n] \n", - "422 [Summary: G protein-coupled receptor signaling pathway and dopamine receptor signaling pathway are statistically over-represented in the gene functions.\\n\\nMechanism: The genes listed are involved in intracellular signaling pathways that are activated by G protein-coupled receptors and dopamine neurotransmitter receptors. The signaling cascades triggered by these receptors are essential for many physiological processes, including neurotransmission, hormone secretion, and muscle contraction.\\n\\n] \n", - "423 [Summary: The list of genes is enriched in terms related to G protein-coupled receptor signaling pathways and dopamine neurotransmitter activity.\\n\\nMechanism: These genes are involved in the regulation of intracellular signaling cascades, particularly those involving G protein-coupled receptors. Dopamine neurotransmitter activity appears to be a common thread linking many of these genes.\\n\\n] \n", - "424 [Summary: Genes are involved in transcriptional regulation and DNA binding activities.\\nMechanism: Transcriptional regulation through DNA-binding activities.\\n] \n", - "425 [Summary: DNA-binding transcription factor activity and regulation of DNA-templated transcription.\\nMechanism: These genes are involved in the regulation of gene expression via DNA-binding transcription factor activity and DNA-templated transcription.\\n] \n", - "426 [ The list of genes includes several connective tissue related genes, such as those related to the tenascin protein family and collagen chains of type I-V, which are responsible for the formation of strong and stable connective fibers. There are also several genes related to the binding and folding of proteins, and the immune response mediated by the complement system. Further, there are genes associated with glycosaminoglycan synthesis and dermatan sulfate metabolism. The commonalities among these genes is involvement in connective tissue formation and repair, structure and binding of proteins, and immune response.\\n\\nMechanism: These genes function in a variety of biological processes, including wound healing, glycosaminoglycan synthesis, and immune response. Through their specific roles, these proteins are able to facilitate the formation and maintenance of strong and stable connective tissue, to bind and fold proteins, and to mediate the innate immune response. Furthermore, genetic mutations in these genes are associated with a variety of Ehlers-Danlos syndromes, further indicating the importance of these proteins in connective tissues.\\n\\n] \n", - "427 [\\nSummary: Enriched term analysis reveals that the human genes described here are largely involved in collagen maturation, glycosaminoglycan synthesis, transcriptional regulation, and zinc transport. \\nMechanism: These genes likely take part in the functions of the endoplasmic reticulum and Golgi apparatus, as well as mediating processes involved in cell differentiation and tumorigenesis. \\n] \n", - "428 [\\nSummary: The enriched terms involve DNA repair, homologous recombination and phosphorylation, as they are commonly found among a group of genes associated with Fanconi Anemia.\\nMechanism: These genes act in a coordinated manner to perform DNA repair, homologous recombination and control chromosomal stability.\\n] \n", - "429 [\\nSummary: The genes identified in this list are involved in DNA repair and maintenance of chromosome stability, specifically the homologous recombination pathway for double-strand DNA repair.\\nMechanism: These genes play key roles in a number of processes, including DNA repair, monoubiquitination of FANCD2 and FANCI, Holliday junction resolution, and binding to the RAD51 recombinase. \\n] \n", - "430 [\\n\\nSummary: Several genes in the list encode proteins involved in the metabolism of fatty acids, including the formation and break down of lipids, synthesis of essential fatty acids, and transport of fatty acid synthase. Additionally, many of the genes encode proteins involved in the functioning of the mitochondria, including relating to the electron transport chains, antioxidant and redox systems, and synthesis of key metabolic components.\\n\\nMechanism: The commonality among these genes is that they encode proteins essential for normal functioning of the mitochondria, oxidative metabolism of fuels, and lipid metabolism, all of which are important for normal cellular functioning and growth.\\n\\n] \n", - "431 [ Cellular metabolism and energy production is enriched in this group of genes, likely related to their role in production and transport of proteins, enzymes, and energy.\\n\\nMechanism: The genes likely act together to produce and convert energy into a useable form and to transport proteins between cellular compartments.\\n\\n] \n", - "432 [\\nThe list of genes is associated with multiple biological processes, including immune/cytokine responses, protein synthesis, transcription, and cell surface signaling. Enriched terms include: immune/cytokine responses; protein synthesis; transcription; cell surface signaling; receptor activation; ubiquitination; calcification; and ATP binding.\\nMechanism: The enriched terms associated with this list of genes describe key biological processes that regulate a variety of cellular activities. In particular, cytokines play a key role in the immune response, transcription is necessary for gene expression, and cell surface signaling is necessary for receptor activation. Furthermore, ubiquitination is involved in protein degradation, calcification is necessary for cellular processes such as bone formation, and ATP binding is necessary for energy production. \\n] \n", - "433 [\\n\\nSummary: The list of genes report a variety of terms related to protein synthesis and cellular regulation functions.\\n\\nMechanism: These genes are involved in a variety of metabolic, cell signaling, transcription and immunoregulatory pathways.\\n\\n] \n", - "434 [\\nThe list of terms includes functions related to protein tyrosine phosphatase (PTP) family, protein kinases, transcription factors, lectins, adhesion molecules, and cyclins. The underlying biological mechanism is likely related to a variety of cell signaling pathways and regulation of gene transcription, protein synthesis and turnover, and cell adhesion. ] \n", - "435 [ In this list of genes, they predominantly function in regulating cell proliferation, transcription, signaling pathways, structural components and metabolism of proteins, lipids, and carbohydrates; many of which are involved in cell adhesion or binding activity. Specifically, they are involved in regulating gene expression and DNA binding, catalyzing protein kinase and oxidoreductase reactions, anchoring kinase complexes to microtubules, binding to receptors, transporting molecules, binding and hydrolyzing peptides and lipids, and catalyzing the interconversion of polyols and ketoses. Hypothesis: These genes thus likely work by regulating signaling pathways, gene expression, and varying cell structures to enable a wide variety of cellular processes and activities.\\n\\nMechanism: Through the regulation of signaling pathways, gene expression, and cell structures, these genes enable a wide variety of cellular processes.\\n\\n] \n", - "436 [COULD NOT PARSE] \n", - "437 [\\nThe list of human genes provided are involved in a wide range of functions such as matrix remodeling, cell adhesion, extracellular signal transduction, iron metabolism and regulation of microvasculature. The list of genes are enriched for processes related to cell adhesion, extracellular matrix remodeling, signal transduction, protease inhibition and transcriptional regulation.\\n\\nMechanism: The enrichment of genes for the processes listed above suggests the coordination of these processes to maintain tissue homeostasis, forming a complex network that involves interactions between extracellular matrix-receptors, cytokines and chemokines, and intracellular signalling pathways.\\n\\n] \n", - "438 [\\n\\nSummary: The genes identified are mostly involved in protein-protein interactions, intracellular and extracellular adhesion, and regulation of calcium-dependent processes.\\n\\nMechanism: Protein-protein interactions, cell adhesion, intracellular signaling of calcium-dependent processes.\\n\\n] \n", - "439 [\\nThe list of human genes analyzed in this enrichment test are associated with functions related to cell adhesion, signal transduction, and cytoskeletal and extracellular matrix (ECM) proteins. The enriched terms include cell adhesion, signal transduction, actin binding and assembly, membrane localization, ECM protein binding and assembly, integrin binding, calcium and phosphorylation-dependent regulation, neuron regulation, and receptor regulation. \\n\\nMechanism: The underlying biological mechanism that these genes are involved in is related to the regulation of cell adhesion, signal transduction, and cytoskeletal and ECM proteins. This includes signal transduction and cell adhesion mediated by various proteins such as integrins, cadherins, adhesion receptors, and kinases, as well as actin binding and assembly, membrane localization, ECM protein binding and assembly, and phosphorylation-dependent regulation. In neurons, there is regulation of axon guidance, regulation of synapse formation, and regulation of signaling pathways that control neuronal development and plasticity. \\n\\n] \n", - "440 [ The commonality in the functions of these genes is their involvement in cell-matrix adhesion and cell signalling, including signal transduction, membrane proteins, and transcriptional coactivation. The underlying mechanisms likely involve signal recognition and regulating the flow of information to and from the cell, as well as transmembrane transport and receptor-mediated endocytosis.\\n\\nMechanism: Signal recognition and regulation of the flow of information to and from the cell, as well as transmembrane transport and receptor-mediated endocytosis.\\n\\n] \n", - "441 [\\nThe gene summaries indicate a common association with proteins that mediate cell adhesion, signal transduction, cell-matrix interactions and regulation of cellular growth and differentiation. This suggests a common mechanism of extracellular communication and regulation between cells, mediated by the action of a diverse set of proteins. The enriched terms include cell-matrix adhesion; cell-matrix interactions; carbohydrate binding activity; cell adhesion; receptor activity; signal transduction; positive regulation of cell proliferation; negative regulation of axon regeneration; ankyrin binding; and protein tyrosine kinase.\\n\\nMechanism: The underlying biological mechanism is that a diverse set of proteins interact with one another and external signals, forming an interconnected network of extracellular communication and regulation that mediates cell adhesion, signal transduction, cell-matrix interactions and regulation of cellular growth and differentiation.\\n\\n] \n", - "442 [ Analysis indicates the gene functions enriched in these terms are those involved in apoptosis, cytoplasmic signaling, transcriptional regulation, protein binding, and cellular organization.\\n\\nMechanism: The underlying biological mechanism involves regulation of apoptosis/cell death pathways, as be indicated by the presence of genes like FAS, CASP, BCL-2, BNIP3L, MADD, PEA15, etc. This is further supported by gene functions enabling signaling via G-protein coupled receptors and transcriptional regulation by factors like EGR3, LEF1, etc. Additionally, many involved genes are related to protein binding in order to modulate the activity of these processes, as well as maintain cellular organization, implied by membrane proteins like APP, BCAP31, IFITM3, CD38, CD44, etc.\\n\\n] \n", - "443 [ \\nSummary: This list of gene functions involve mostly cell death processes, signaling, cytoplasmic and nuclear proteins, transcriptional activities, and enzymes for cell processing, as well as toxin removal and receptor binding. \\nMechanism: Cell death processes involve the activation or inhibition of specific enzymes and proteins that interact with cell membrane receptors, signal cell apoptosis, modulate transcriptional activities and regulate reversible and irreversible cytoplasmic and nuclear protein activities. \\n] \n", - "444 [ \\nSummary: The list of genes has been enriched with terms related to ATP-binding, transport, fatty acid desaturase, oxidation-reduction, enzyme catalysis, and transcription factors. \\nMechanism: The list of genes encodes a range of proteins whose functions are related to catalysis and transport of molecules, as well as transcription and regulation of hormones and neurotransmitters. \\n] \n", - "445 [ \\nSummary: Genes in the list are involved in protein transport and synthesis, lipid metabolism, oxidation-reduction, hormone regulation, and transcription regulation.\\nMechanism: Genes in the list are involved in a variety of molecular and biochemical processes, such as protein import and export, oxidation-reduction, drug metabolism, hormone regulation, transcription regulation, fatty acid and cholesterol signaling, enzyme regulation, and the breakdown of malonyl-CoA.\\n] \n", - "446 [ The list of genes provided appears to be involved in a number of different physiological functions, including cell adhesion, lipid metabolism, energy generation, growth, receptor activity, signaling pathways, apoptosis regulation, transcription regulation, and cholesterol metabolism. Mechanism: The underlying biological mechanism may be related to changes in membrane properties and intracellular signaling, as well as regulation of gene expression, metabolism, and other cellular processes. ] \n", - "447 [ This gene list is largely composed of genes and their associated proteins involved in processes related to cell growth, metabolism, and cholesterol biosynthesis. The terms that are enriched include lipid metabolism, phospholipid binding proteins, fatty acid desaturase, ATP-binding cassette proteins, sterol biosynthesis, and cytochrome P450 family proteins.Mechanism: The mechanisms underlying these processes involve the synthesis and degradation of essential fatty acids, lipids, and sterols, and the regulation of cell growth and adhesion through transcription factors, receptor-ligand interactions, and transfer of molecules across intracellular and extracellular membranes.] \n", - "448 [ The provided list of genes is primarily involved in the regulation of the complement system and blood clotting, as well as in the processing of proteins and peptides. Mechanism: The genes play a role in the innate immune response by modulating the complement system, helping to break down peptides and proteins, regulating inflammation, and in the control of blood clotting. ] \n", - "449 [ This gene list is enriched for many serine proteases and proteins involved in coagulation, complement activation, metalloproteases, transcriptional regulators and transcription factors. Hypothesis: These genes are involved in extracellular matrix turnover, cell-cell adhesion and signal transduction pathways, as well as processes related to tissue morphogenesis. ] \n", - "450 [ \\nSummary: The enriched terms found from the list of genes involve proteins associated with cell signaling, structure/stability, metabolism, and vitamin K/clotting. \\n\\nMechanism: These proteins work together to regulate cell signaling pathways and pathways involved in inflammation and metabolism. Additionally, these genes are involved in vitamin K/clotting pathways, cytoskeletal structure/stability and cell membrane strengthening. \\n\\n] \n", - "451 [\\nSummary: The list of genes are mainly involved in protein production, cell surface glycoprotein regulation, complement activation and signalling pathways.\\n] \n", - "452 [COULD NOT PARSE] \n", - "453 [\\n\\nSummary: We have identified 18 enriched terms associated with the functions of the given list of genes. These functions include DNA binding, transcription, DNA repair and mRNA processing.\\n\\nMechanism: The commonalities between the functions of the given list of genes suggest that they are involved in facilitating DNA binding and transcription regulation, DNA repair, mRNA splicing and mRNA processing activities.\\n\\n] \n", - "454 [ \\n\\nSummary: This term enrichment test identified highly conserved proteins and protein complexes that play a role in DNA replication, repair and transcription, chromatin binding and modification, and cell cycle regulation.\\n\\nMechanism: The enrichment test suggests that these genes are essential for maintaining their respective functions, as well as for responding to DNA damage, replication blocks and cell cycle regulation.\\n\\n] \n", - "455 [\\nGene functions related to the regulation of nucleic acid binding and metabolism, chromatin, protein modification, DNA replication, and cell cycle regulation are enriched in the list of genes provided above. These process appear to be interrelated and part of a larger cellular pathway.\\n\\nMechanism:\\nThe mechanism underlying these gene functions seems to involve the control of the cell cycle, DNA binding and metabolism, chromatin dynamics, and protein modification and turnover. These processes are regulated by a complex network of interactions between various proteins, DNA modifications, and histone modifications, which help control the assembly and disassembly of different chromatin structures. This in turn affects DNA replication, transcription, and translation of proteins required for various cellular processes.\\n\\n] \n", - "456 [ The genes presented in this list are primarily involved in cell signaling, extracellular matrix formation and cell adhesion. Furthermore, many of the genes play a role in connective tissue formation and related structural processes.\\n\\nMechanism: Genes involved in cell signaling, extracellular matrix formation, and cell adhesion are integral in their roles in producing cell structure and maintaining connective tissue structure and integrity. These genes work together to allow cells to communicate properly and modulate processes such as inflammation and tissue repair. Additionally, cell signaling and cytokines produced by these genes contribute to angiogenesis, metabolic regulation, and tissue growth and development. \\n\\n] \n", - "457 [\\nThis list of genes is strongly associated with extracellular matrix and collagen production, with members of the integrin, laminin, dystrophin, fibronectin, von Willebrand Factor, and fibulin families involved. Enriched terms include extracellular matrix proteins, collagen, laminin, fibronectin, von Willebrand Factor, integrin, dystrophin, and fibulin proteins.\\n\\nMechanism: \\nThese proteins are involved in extracellular matrix production and organization, which is critical for cell-to-cell and cell-to-environment interaction. This involves extracellular matrix proteins that facilitate connection and communication between cells, as well as structural proteins such as collagen and laminin that provide stability and rigidity. In addition, these proteins are involved in cell adhesion, migration, and proliferation. By forming interconnecting complexes, these proteins work together to mediate multiple biological processes, from cell development to tissue and organ formation. \\n\\n] \n", - "458 [ The enriched terms in this list of genes include proteins related to peptide binding, cell membrane structure modification, DNA binding, fatty acid metabolism, hormone receptor binding, signalling transcription, GTPase activation, adenylate cyclase modulation, kinase activity, endocytosis, glycoprotein production, growth factor binding, histone modification, phospholipid metabolism and zinc-binding. The underlying biological mechanisms and pathways involve proteins involved in intracellular and intercellular signalling, as well as chromatin remodelling and membrane trafficking. \\n\\nMechanism: Membrane trafficking, cellular signalling and chromatin remodelling. \\n\\n] \n", - "459 [ \\n\\nSummary: The genes described in this list are mainly involved in the regulation and manipulation of protein functions, such as DNA-binding, signaling pathways, post-translational modification, protein binding, and metabolic activity.\\n\\nMechanism: Many of the genes involved are involved in metabolic pathways and regulation, and interactions between proteins, such as through DNA-binding, signaling pathways, and post-translational modification.\\n\\n] \n", - "460 [\\n\\nSummary: Genes involved in regulation of cell signaling, including protein kinases, transcription factors, calcium ion binding, glycobiology, and hormone receptors. \\nMechanism: All the genes operate at the cellular signaling level to mediate various biological functions such as cell adhesion, protein folding, and gene expression. \\n] \n", - "461 [ The genes identified are largely involved in membrane and transmembrane processes, ion transport, cell adhesion and growth, metabolizing enzymes, disease processes, and protein signaling and processing. Mechanism: These genes are involved in processes related to cell physiology, adhesion, growth and development, and reparative pathways, as well as immune and disease processes. ] \n", - "462 [ \\n\\nSummary: There is an enrichment for metabolic and energy regulation processes involving multiple enzymes and proteins connecting with metabolites, nucleotides, fatty acids, and other molecules.\\n\\nMechanism: These genes seem to be involved in metabolic pathways leading to the formation of intermediate metabolites and energy transportation in the body.\\n\\n] \n", - "463 [ The summaries of these human genes suggest that the majority of them are involved in metabolism-related processes, specifically in the processing and transport of fatty acids and oxidoreductases. There is also evidence that these genes may be involved in growth and development, such as for aiding in morphogenesis, cell differentiation, and protein-macromolecule adaptor activity. The enriched terms that represent these processes are \"metabolism,\" \"fatty acid transport and processing,\" \"oxidoreductase,\" \"morphogenesis,\" \"cell differentiation,\" and \"protein-macromolecule adaptor activity.\" \\n\\nMechanism: The underlying biological mechanism might involve the genetic regulation of enzymes responsible for fatty acid and metabolite transport and transformation. Additionally, the gene products of these genes might be involved in signaling cascades that lead to morphogenesis and cell differentiation. \\n\\n] \n", - "464 [ \\n\\nSummary: The provided gene list is mainly involved in functions related to cell cycle regulation, chromatin/histone modification, and transcription.\\n\\nMechanism: These genes are involved in a variety of biological processes related to cell cycle regulation, chromatin/histone modifications, protein kinase activity, ATP-binding, and RNA binding.\\n\\n] \n", - "465 [ Enriched terms among this list of genes point to functions related to cell division, DNA and RNA binding, transcriptional regulation, chromatin restructuring, and protein kinase activity. This set of genes appears to have enriched terms related to nuclear and cytoplasmic transport, nucleic acid metabolic functions, and histone certain activities. Mechanism: The collection of processes related to the functions of these genes appear to function in a coordinated way, with many proteins involved in multiple pathways that work together to maintain cell division, DNA integrity, gene expression, and the structural organization of chromatin. These processes appear to be primarily regulated by an array of proteins with phosphorylation, methylation, acetylation, and ubiquitination activities. ] \n", - "466 [\\n\\nSummary: The list of genes have similar functions in cellular pathways such as glycoprotein metabolism, phosphorylation, cell adhesion, transcription, nucleotide metabolism, energy production, and others.\\n\\nMechanism: Many of these genes are involved in phosphorylation, which helps to regulate cellular activity. This includes regulation of cell adhesion and transcription, as well as energy production and nucleotide metabolism.\\n\\n] \n", - "467 [ Biological processes related to development, glycosylation, and metabolism of proteins, lipids, and carbohydrates are enriched based on the list of genes given.\\n\\nMechanism: The genes identified encode for enzymes, receptors, and proteins that support functions in several biological mechanisms, including protein and carbohydrate metabolism, post-translational modification, binding, and transport.\\n\\n] \n", - "468 [ \\nSummary: The list contains 22 genes involved in signal transduction, transcription and cell adhesion, primarily within the nervous system.\\n] \n", - "469 [ This set of genes are mainly involved in neuron signalling and cell adhesion, and all contribute to cellular processes such as growth, differentiation, motility and development. Mechanism: These genes are predominantly involved in intracellular signal transduction pathways, which lead to the activation of transcription factors or the production of secretory proteins. ] \n", - "470 [ \\n\\nSummary: The list of genes described relate to the processing and binding of protein molecules, cytokinesis, transcriptional regulation, metabolic and enzymatic functions, formation of cell cortex, transport, and several other cellular processes.\\n\\nMechanism: Many of the genes are associated with the formation and modification of proteins, including phosphorylation and acetylation, playing an important role in cell membrane and cytoskeleton structure, catalyzing metabolic reactants, and trafficking. \\n\\n] \n", - "471 [ The list of human genes appear to be involved in transcription and post-transcriptional regulation, regulation of glycolysis and pyruvate metabolism, glutathione metabolism, proteolysis, transcriptional regulation, and ubiquitination. \\n\\nMechanism: The genes may be involved in regulation and modulation of pathways that control cell structure, function, maturation and apoptosis.\\n\\n] \n", - "472 [ \\n\\nSummary: Genes involved in regulating a variety of metabolic functions such as glycolysis, phosphorylation, protein kinase activity, proteolytic degradation, extracellular matrix assembly and maintenance, and transcription regulation.\\n\\nMechanism: Genes are involved in different aspects of metabolic regulation responsible for the control of cellular processes such as cell cycle and proliferation, energy homeostasis, inflammation, and the communication between cells. \\n\\n] \n", - "473 [\\nThe list of genes is mainly involved in metabolic and transcription processes. The genes enable physical functions such as carbohydrate binding, phosphorylation, and filamin binding, as well as regulate apoptosis, proliferation and growth. The biological mechanism involves cytoplasmic processing, lipoprotein metabolism, cell-binding and signaling pathways.\\n\\nMechanism: Metabolic, Transcription, and Cytoplasmic Processes\\n] \n", - "474 [\\n cells proliferate and differentiation, metabolism and gene regulation, cytokine signaling and antigen recognition, transcription factors and membrane-associated proteins.\\nMechanism: A wide range of mechanisms are involved, including regulation of cell proliferation and differentiation, metabolism, gene regulation, cytokine signaling, and antigen recognition. Common enriched terms include cell cycle regulation, receptor signaling, membrane-associated proteins, and transcription factors.\\nHypothesis: The underlying biological mechanism involves a wide range of processes related to cell proliferation, differentiation, metabolism, gene regulation, cytokine signaling, and antigen recognition. These processes are mediated by various membrane-associated proteins and transcription factors.\\n] \n", - "475 [ The list of genes can be divided into several classes related to their functions, including signaling (MAPKAPK2, PHLDA1, CSF2, CD86, etc.), cell adhesion (SELL, CD79B, CD44, etc.), receptor activity (P2RX4, TNFSF4, IGF2R, etc.) and protein kinase activity (PRAF2, CAPG, PTCH1, etc.). These genes are involved in diverse physiological processes, such as signal transduction, membrane transport, immune response, cell cycle and apoptosis. Mechanism: The enriched terms indicate that these genes are involved in signal transduction and cellular processes at the molecular level, such as GTP binding, protein homodimerization, nucleic acid binding, and protein kinase activity. ] \n", - "476 [\\nSummary: The list of genes is associated with inflammation, cell growth, and development processes primarily involving cytokine signaling pathways. \\nMechanism: Signaling pathways comprise cytokine signals of various types coupled to various types of receptors and transmembrane proteins, with downstream activations of various protein kinases, transcription factors, and modulators of cell cycle progression.\\n] \n", - "477 [COULD NOT PARSE] \n", - "478 [ The list of genes are mainly involved in receptor binding, cytokine signalling, and regulation of inflammation, cell cycle and growth. \\nMechanism: These genes likely represent critical components of complex pathways involving cell growth, immune signalling and inflammation, as well as the coordination of cell cycle and apoptosis.\\n] \n", - "479 [ Cells have an inherent potential to interact with each other, responding to proteins that traffic signals across the membrane which may modulate cytokines, immunoactivators, lipids, and transcription factors to form different types of signaling pathways and biological processes. Mechanism: Interaction or binding of proteins or receptors with lipids, cytokines, transcription factors, or hormones triggers signaling events across the membrane, consequently modulating the gene expression of the cell. ] \n", - "480 [\\nThe list of genes related to human genetics is statistically enriched for genes involved in immune response and regulation, protein-binding and modification, subunit-binding and regulation in macromolecular complexes (such as proteasomes & MHC), and RNA-binding and modification. \\nMechanism: The enriched terms identified above support the underlying biological mechanism of protein-protein interactions, ligand binding, gene transcriptional regulation, signal transduction and other essential processes essential to maintaining cell homeostasis. \\n] \n", - "481 [ \\n\\nSummary: The gene list is composed of transcriptional regulators, tumor suppressors, proteases, catalysts, membrane proteins and receptor proteins, which are involved in immune response, defense response, mRNA stabilization, mRNA editing, protein ubiquitination, protein methylation, and cell proliferation. \\nMechanism: These genes are involved in regulating the expression of other gene pathways, controlling cellular growth and activation, recognition of external or internal signals, or altering the properties of a macromolecule through enzymatic action, leading to shifts in growth and metabolism. \\n] \n", - "482 [ Genes in this list are associated with immune regulation, DNA binding, RNA binding, protein ubiquitination, anti-viral response, cytokine signaling, and inflammation.\\n\\nMechanism: These genes are involved in pathways that regulate immune responses, such as the induction of cytokines, the recognition of viral DNA, the binding of RNA and DNA, the ubiquitination of proteins, and the activation of inflammatory pathways.\\n\\n] \n", - "483 [ \\n\\nSummary: This list of human genes has been found to be involved in various processes related to inflammation, immune cell signaling and development, immune regulation and cellular metabolism.\\n\\nMechanism: These genes may be involved in pathways related to the regulation of innate and adaptive immunity, as well as pathways related to metabolic and transcriptional regulation, DNA binding and RNA binding activities.\\n\\n] \n", - "484 [\\n\\nSummary: Genes listed are involved in a variety of cellular activities, including protein-binding, transcriptional regulation, cell adhesion, cell membrane channel activity, protein metabolism/modification, and receptor signalling.\\n\\nMechanism: The enriched terms represent the wide-ranging cellular activities of the listed genes, exemplifying they operate within multiple pathways and networks to form a complex system of molecular interactions.\\n\\n] \n", - "485 [ After performing a term enrichment test on the list of human genes and their descriptions, the enriched terms found to be statistically over-represented are related to proteins that are responsible for cellular growth and development, movement, action potentials, calcium binding, steroid binding and metabolism, transcription factors, and binding of various molecules such as ATP, RNA, G proteins, and DNA-binding. The underlying biological mechanisms involve the integrative action of various proteins that are essential for various physiological and developmental processes, including those related to reproduction and metabolism.\\n\\nMechanism: Integrative action of proteins related to cellular growth, development, movement, action potentials, calcium binding, steroid binding and metabolism, transcription factors, and binding of various molecules. \\n\\n] \n", - "486 [ Enriched terms and mechanisms related to cell adhesion, regulation of growth factors and cytokines, calcium activation, and transcriptional regulation.\\n\\nMechanism: The genes involved are related to a range of important cell process, such as cell adhesion and calcium signaling, as well as the regulation of growth factors, cytokines, and gene transcription. These functions are essential for cellular growth and development, and are the basis for many of the body's responses to a variety of stimuli.\\n\\n] \n", - "487 [ \\nSummary: The list of terms is mostly associated with proteins and their cellular roles, such as binding to cell membrane, binding to DNA, catalyzing reactions, activating pathways, and regulating cytokines, growth factors, and transcription.\\nMechanism: The human genes are involved in regulating growth, development, metabolic and immunological processes through the functioning of the encoded proteins.\\n] \n", - "488 [\\nThe given genes are primarily involved in regulation and control of cell morphological and structural processes, such as cytoskeletal organization, centrosome interaction, DNA interaction, and GTPase regulation.\\nHypothesis: These genes are likely to be involved in a variety of biological pathways that control cell morphology and structure, such as organization of the cytoskeleton, centrosome dynamics, DNA replication and maintenance of chromatin structure through interactions with GTPases and their associated proteins.\\n] \n", - "489 [\\nThe list of genes consist of proteins involved in the maintenance of cell architecture, cell cycle regulation, microtubule-binding, and chromosome segregation. Most of the proteins are involved in GTPase and nucleotide exchange regulation, cellular signaling, chromatin remodeling, cytoskeleton structure, DNA replication, cell adhesion, and actin binding and regulation.\\n\\nMechanism:\\nThe proteins suggested in the list are involved in a variety of regulatory pathways that are integral to the maintenance of proper cellular architecture and organization. These pathways include cellular signaling, chromatin remodeling, cytoskeleton structure, DNA replication, cell adhesion, and actin binding and regulation.\\n\\n] \n", - "490 [ Genes related to the list are enriched for activities related to protein biosynthesis, transport and signaling, metabolism, and gene expression control. Mechanism: Genes related to the list are involved in integral processes of the cell, such as metabolism and gene expression control, which are facilitated by protein synthesis, transport and signaling. ] \n", - "491 [ These genes perform important functions related to protein synthesis and metabolism, including binding, ubiquitination, transcription, and enzyme activity. They are involved in processes such as protein folding, chaperoning, cell cycle regulation, lipid metabolism, glucose uptake, and cytoskeleton formation. Mechanism: These genes share common functions related to protein synthesis and metabolism, and their expressions are mutually regulated to interact with one another and create pathways that lead to the desired outcomes. ] \n", - "492 [\\nThe list of genes are involved in the processes of transcription, translation, and post-translational modification, which are essential for protein synthesis and function in the cell. Enriched terms include transcription, translation, mRNA binding, ribosome subunits, splicing factors, post-translational modification, cytoplasmic proteins, nuclear proteins, DNA binding and unwinding proteins subunits of the nuclear lamina, and proteins associated with the spliceosome. \\nMechanism: These gene functions are part of the essential biological mechanism of protein synthesis in a cell, which is a complex process that requires the coordination of multiple processes, including transcription, translation, and post-translational modifications. \\n] \n", - "493 [ The genes in this list are largely related to mRNA and protein synthesis, nucleic acid binding and transport, and post-translational modification activities.\\n\\nMechanism: This list of genes likely represents the many steps involved in the synthesis and transport of proteins, from the initial transcription of mRNA and its associated splicing factors, to the polymerase activities, aminoacylation, and trafficking of proteins in and out of the nucleus and into the mitochondria.\\n\\n] \n", - "494 [ The list of genes is associated with functions related to ribosome biogenesis, RNA binding and splicing, cell proliferation, cell cycle progression, and chromatin binding.\\n\\nMechanism: The list of genes is likely involved in the regulation and maintenance of ribosome biogenesis and cell proliferation through pre-rRNA processing, DNA replication-dependent chromatin assembly, and regulation of signal transduction.\\n\\n] \n", - "495 [ Genes from this list encode proteins that are involved in a variety of cellular processes, such as transcription, RNA processing, protein folding, DNA replication and repair, and cell cycle regulation. ] \n", - "496 [ \\nSummary: The list of genes contain genes related to motor protein activity, calcium signaling, muscle contraction, transcriptional regulation, intracellular fatty acid-binding, binding of ligands, and several other related processes.\\n\\nMechanism: Many of these genes encode electric conductance, actin filaments, and membrane proteins. They are involved in processes such as ion channels, muscle contraction, calcium sequestration and release, regulation of transcription, and phosphorylation of proteins. These processes occur in response to changes in the external environment or internal signals.\\n\\n] \n", - "497 [\\nOrganism metabolic pathways and protein regulation are enhanced in this group of genes. This enhancement includes increased ion channeling, cellular transport processes, lipid metabolism, and gene regulation. The pathways involve small and large molecules, as well as neurotransmitter signaling.\\n\\nMechanism: This group of genes works together to regulate metabolic processes in the organism, working at a cellular level that includes ions, lipids, proteins, and other molecules. The genes also interact to create networks of ion channels and transporter proteins that allow for efficient nutrient delivery, active metabolic pathways, and the regulation of gene expression.\\n\\n] \n", - "498 [ \\nSummary: Genes related to the Notch and Wnt signaling pathways were found to be enriched in the gene data set.\\n Mechansim: Notch and Wnt pathways are key signalling pathways involved in cell fate decisions and development of organisms.\\n ] \n", - "499 [\\nThe given genes are involved in multiple cellular processes including Notch signaling pathways, cell-to-cell communication, transcription, protein ubiquitination, cell-cycle regulation, protein breakdown and turnover, and intracellular signalling pathways.\\nHypothesis: The given genes are part of a complex suite of processes which regulate cell fate, signalling, and control of intracellular signalling pathways. The genes are likely involved in establishing or inhibiting various combinations of pathways in response to internal and external stimuli.\\n] \n", - "500 [\\nSummary: After performing a term enrichment test, it was found that the majority of the genes were involved in mitochondrial processes, as well as enzyme functions such as dehydrogenases and oxidoreductases, and ATP synthesis. \\nMechanism: This suggests that these genes are functioning on a systemic, metabolic level, and are involved in the overall production, usage and storage of energy within a cell.\\nConstructing a functional mitochondrion would likely require the activities of all these genes.\\n] \n", - "501 [\\n• The genes involved mainly involve enzymes and proteins involved in oxidation-reduction reactions, ATP synthesis, respiration, and metabolic processes in mitochondria \\n• Pathway and mechanism: The genes are involved in pathways related to mitochondria respiration, ATP synthesis, and metabolism of organic acids, such as oxidative decarboxylation and dehydrogenase reactions.\\n• ] \n", - "502 [ Human genes in this list are generally involved in cell cycle progression, transcription, signaling and regulation, protein synthesis and processing, and homeostasis. Specifically, enrichment of the terms \"cell cycle,\" \"transcription,\" \"signaling,\" \"protein synthesis,\" \"regulation,\" and \"homeostasis\" was observed.\\n\\nMechanism: These genes are likely involved in the creation, maintenance, duplication, and regulation of the complex network of proteins and processes occurring within cells, and the modulation of these processes in response to changes in the environment.\\n\\n] \n", - "503 [ Human genes related to cancer pathways, cell regulation and apoptosis\\nMechanism: Many of the human genes, when over-expressed, can drive the development of cancer through pathways, regulation of cell growth, and disruption of apoptosis, which is the process of programed cell death.\\n] \n", - "504 [COULD NOT PARSE] \n", - "505 [COULD NOT PARSE] \n", - "506 [COULD NOT PARSE] \n", - "507 [ After performing a term enrichment test on the given list of genes, it can be seen that the functions of many of these genes are related to lipid metabolism and antioxidant functions, as well as DNA-related processes such as DNA repair, transcription and replication. Specifically, some of the enriched terms are lipid metabolism, fatty acid beta-oxidation, DNA repair, transcription and replication, oxidative stress, glutamate metabolism, vitamin A binding, and steroid metabolism.\\n\\nMechanism: The underlying biological mechanism of these gene functions is related to the homeostasis of vital cellular processes such as cell adhesion and signalling, protein production and degradation, regulation of mitochondrial and peroxisomal functions, and protection against oxidative damage. \\n\\n] \n", - "508 [ Summary: This gene list includes many genes involved in protein regulation and signalling with a heavy focus on serine/threonine protein kinase family.\\n Mechanism: Multiple genes listed play a role in the regulation of ubiquination, phospholipids, protein-protein interactions, transcription, and cell signalling.\\n ] \n", - "509 [\\nThe genes summarized in this list are involved in a wide range of functions, including those related to cell growth, cell cycle control, DNA binding, transcriptional regulation, signal transduction, and protein phosphorylation/dephosphorylation. The enriched terms refer to activity of signal transduction pathways and protein kinases such as members of the MAPK, RAS and G protein-coupled receptor (GPCR) families, as well as phosphatases, guanine nucleotide exchange factors, and endoplasmic reticulum chaperone proteins.\\n\\nMechanism: This list of genes is involved in signal transduction cascades, which involve proteins kinases and phosphatases modulating the expression of target genes by post-translational modifications, such as phosphorylation or ubiquitination of these proteins, as well as DNA binding and transcriptional regulation. \\n\\n] \n", - "510 [ \\n\\nSummary: The list of genes is associated with various roles in the endomembrane system, mainly playing roles in intracellular transport, vesicle formation, organelle biogenesis, lysosomal function, protein folding, GPCR-mediated signal transduction, and ligand-receptor complex trafficking.\\n\\nMechanism: Processes such as vesicle trafficking, lysosomal protein transport, GPCR mediated signal transduction, and organelle biogenesis are mediated by delivery of proteins to the correct cellular compartment via membrane proteins and complexes such as adaptins, SNAREs, GTPases, and the Golgi Apparatus.\\n\\n] \n", - "511 [ Transmembrane proteins involved in transport, trafficking and organelle biogenesis are enriched amongst this gene list. \\nMechanism: The Enriched transmembrane proteins likely function as part of a complex network of molecular machinery involved in vesicle trafficking, docking and fusion of proteins, organelle biogenesis, and protein folding.\\nThe ] \n", - "512 [\\n\\nSummary: All of the genes in the list are associated with molecules, enzymes, and proteins involved in cell metabolism and defense against oxidative stress.\\n\\nMechanism: The genes are involved in the regulation of pathways of cell energy metabolism and defense against oxidative stress, by providing key cellular components which participate at various levels of oxidation and reduction.\\n\\n] \n", - "513 [\\n\\nSummary: The human genes listed contain a variety of proteins that function in processes related to cell growth and development, redox regulation, DNA repair and transcription, response to oxidative stress and inflammation, cell cycle progression, and metabolism.\\n\\nMechanism: The functions of the proteins span a range of processes that are essential for cell survival, such as cell growth control, transcriptional regulation, redox regulation, and metabolism. These proteins may work together to regulate processes, such as glutamate-cysteine ligase activity, hydroxylase activity, protease activity, free-radical scavenging and protein phosphatase activity. \\n\\n] \n", - "514 [\\n\\nSummary: This term enrichment test on a list of human genes revealed several proteins and proteins related functions that are statistically over-represented.\\n\\nMechanism: This term enrichment test suggests that certain proteins and associated functions are involved in a wide variety of biological processes related to gene expression, transcription, and other aspects of cellular functioning. \\n\\n] \n", - "515 [ \\nSummary: These genes are involved in diverse processes such as transcriptional regulation, cell cycle regulation, chromatin structure and nuclear envelope signaling, cell adhesion and motility, metabolic processes, protein folds and ubiquitination, detection, binding and enzymatic activities, and vasodilation.\\n\\nMechanism: These genes encode proteins that act as molecular adaptors, molecular chaperones, enzymes, transporters, transmembrane receptors, and other components in a variety of pathways and pathways.\\n\\n] \n", - "516 [ This list of genes is enriched for proteins involved in receptor signaling pathways and transcriptional regulation as well as cell signaling, adhesion and growth. These proteins can serve as part of complexes, act as enzymes, bind hormones, and influence cellular processes. \\nMechanism: Many of the genes identified in this list encode proteins in the TGF-Beta superfamily which are involved in the regulation of growth, differentiation and development, as well as apoptosis and transcription. These proteins work together in a complex network to regulate these cellular processes. \\n] \n", - "517 [ \\n\\nSummary: The list of genes have been identified as members of various pathways related to the regulation of cell growth and differentiation, transcriptional regulation, receptor-regulated SMAD proteins, and signal transduction. \\nMechanism: The proteins encoded by these genes form different complexes, interact with various receptors, and function as transcriptional modulators, signal transducers, and ubiquitin ligases to regulate growth, differentiation and signaling pathways in cells.\\n] \n", - "518 [ The genes in the list can be grouped into two main categories: genes that encode proteins involved in transcription (e.g. FOS, EGR, IFNGR2, MYC, NFKB, REL, etc.), and genes that encode proteins involved in cytokine and inflammatory signalling pathways (e.g. IL1A, IL2B, IL7R, etc.). Mechanisms: Additionally, the genes in the list encode proteins that have a variety of roles in the regulation of cellular proliferation, apoptosis, and other processes in various cell types. ] \n", - "519 [ Expression and regulation of multiple proinflammatory cytokines and chemokines, regulation and activity of kinases, transcription factors, and components of the TGF-beta, NF-kappa-B, MYC/MAX/MAD, Jagged 1 and STAT-regulated pathways, and regulation of lipoproteins and growth factors.\\nMechanism: These genes collectively comprise pathways and networks that regulate inflammation, cellular growth, cell differentiation, and apoptosis.\\n] \n", - "520 [ \\nSummary: A list of human genes involved in RNA-binding and protein-binding activities, along with protein metabolism, synthesizing and chaperone activity.\\nMechanism: The transcription factors and proteins help to regulate and stimulate gene expression and the protein folding process, which affects the synthesis and metabolism of proteins. This can lead to changes in cell function and structural integrity of cells.\\n] \n", - "521 [\\n\\nSummary: The list of genes are associated with endoplasmic reticulum (ER) processes, such as transcription factors, RNA binding proteins, protein folding and degradation, protein chaperones, mRNA decapping, and zinc transporter proteins. \\n\\nMechanism: The list of genes are involved in a wide range of endoplasmic reticulum (ER) processes such as post-translational modifications, translational regulation, RNA binding, protein folding, protein degradation, and protein trafficking.\\n\\n] \n", - "522 [ \\nSummary: Enriched terms from a list of human genes indicate that many of these genes are involved in cellular response regulation, cell surface receptors, signal transcription, signal transduction, phosphorylation, and calcium binding pathways.\\n\\nMechanism: The proposed underlying biological mechanisms involve regulation of gene expression and signal transduction through phosphorylation of proteins, downstream target proteins, and modulation of their function.\\n\\n] \n", - "523 [ \\n\\nSummary: The human gene list is enriched for terms related to signal transduction, extracellular matrix proteins, cellular adhesion, and transcription factors.\\n\\nMechanism: Signal transduction pathways, extracellular matrix proteins, and transcription factors increase cell activity and affect the regulation of gene expression.\\n\\n] \n", - "524 [ \\nSummary: This list of genesí human functions mainly involve cell regulation, transmembrane transport, metabolic catabolism, and transcription support. \\nMechanism: These genes are involved in important pathways responsible for transportation and metabolic processes, as well as regulation of cellular functions.\\n] \n", - "525 [ Our analysis revealed that these genes are primarily involved in cell signaling and membrane-associated functions, including protein binding, reaction catalysis, transporter activity, and GTP binding. Mechanism: The primary biological mechanism underlying this set of genes appears to be related to the regulation and control of cell signaling and membrane-associated functions in various cellular processes, including metabolism, replication and transcription, and cell growth and differentiation. ] \n", - "526 [\\n\\nSummary: A significant number of these genes are involved in the functioning of the Wnt signaling pathway, as well as cell cycle progression and gene transcriptional regulation.\\n\\nMechanism: Wnt signaling pathway controls cellular processes such as cell proliferation and migration, survival and cell differentiation, which involves a number of intercellular signalling pathways and Transcription Factor complexes.\\n\\n] \n", - "527 [ Through the analysis of gene summaries from the provided list, it is evident that genes playing a role in Wnt, Notch, and Hedgehog signaling pathways are enriched. The genes also appear to be involved in transcriptional regulation, cell cycle progression, and developmental events, as well as processes such as DNA replication and repair, transcriptional silencing, and proteasomal ubiquitin-dependent protein catabolism. It is possible that the mechanism involves the regulation of these pathways and their effects on various cellular functions. \\n\\nMechanism: This may involve the regulation of the Wnt, Notch, and Hedgehog signaling pathways and their effects on various cellular functions such as cell fate determination, DNA repair, transcriptional activation and repression, and protein catabolism.\\n\\n] \n", - "528 [\\n\\nSummary: This list of human genes found in the summary have involvement in a variety of processes including cell division, adhesion, differentiation, and response to stress, in addition to roles in the immune system, transcriptional regulation, ligand binding, receptor binding, ubiquitin-protein ligase activity, phosphodiesterase activity, and protein phosphatase activity.\\n\\nMechanism: These genes are likely involved in multiple pathways and signaling mechanisms to regulate these various processes, likely involving kinases, transcription factors, adaptor proteins, and ubiquitin-protein ligases. \\n\\n] \n", - "529 [\\nThe list provided of genes demonstrates significant enrichment of terms related to transcriptional regulation, cellular signaling pathways and processes, cell growth, differentiation, response to stress and to foreign material (via immune response), protein folding and trafficking, and recognition of self and non-self through various receptors. In the list there are mainly transcription factors, protein tyrosine phosphatases and kinases, several receptor families, and proteins for interleukin signaling. The underlying biological mechanism or pathway is likely related to the development and differentiation of cells and homeostasis or recognition of abnormalities or foreign materials.\\n\\n] \n", - "530 [COULD NOT PARSE] \n", - "531 [ \\nSummary: The genes KLF4, POU5F1, and SOX2 are transcription factors involved in embryonic development and stem cell maintenance, and are associated with tumorigenesis. \\nMechanism: Transcription factors control gene expression, which in turn controls embryonic development and stem cell maintenance, impacting tissue formation, tumorigenesis, and cell differentiation. \\n] \n", - "532 [ The majority of the gene functions encompass proteins involved in cellular adhesion, signaling pathways, extracellular matrix proteins, and components of the complement cascade. Gene products have roles in tissue development and regeneration, wound healing, immune hypersensitivity reactions, apoptosis, motility, and angiogenesis.\\n\\nMechanism: These genes are likely to be involved in multiple mechanisms related to homeostasis and wound healing, likely through cell-extracellular matrix binding and communication between cells through signal pathways.\\n\\n] \n", - "533 [\\nThis list of genes appears to be comprised of proteins involved in a variety of cellular activities related to cellular communication, extracellular matrix organization, cell adhesion, cell survival, and migration. Enriched terms include: Notch signaling pathway; osteoclast attachment/mineralized bone matrix; jagged 1/notch 1 signaling; cell adhesion; apoptosis; collagen fibril formation; antimicrobial peptide activity; lipoprotein metabolism; cell migration; extracellular matrix remodeling; cytotoxicity; chemotaxis; cytoplasmic signaling and phosphorylation; transcriptional repressor; odontogenesis; hematopoietic cell adhesion; serine protease inhibition; inward-rectifier potassium channels; and angiogenesis.\\n\\nMechanism: The underlying biological mechanism appears to involve a variety of cellular activities related to cellular communication, extracellular matrix organization, cell adhesion, cell survival, and migration, enabled by the expression and activity of these genes in different cellular pathways and networks.\\n\\n] \n", - "534 [ This gene list represents genes with a wide range of functions involving membrane transport, growth factor regulation, and transcription regulation. Many of the genes are involved in ion channels and calcium and calcium-dependent processes. Mechanism: The genes are involved in a wide range of processes, including membrane transport, growth factor and calcium regulation, transcription regulation, and binding activity. ] \n", - "535 [COULD NOT PARSE] \n", - "536 [ This list of genes is found in muscle tissue, and are involved in muscle formation, contraction, development, and cytoskeletal structure. These genes are involved in pathways of signal transduction, protein-protein interactions, and energy metabolism. ] \n", - "537 [ The list of genes and their functions suggests that these genes are involved in muscle development and regulation, actin and tropomyosin binding, calcium- and energy-regulation, ion channeling, and structural framework assembly and maintenance. In addition, they may be involved in negative regulation of cytokine signaling pathways and calcineurin-NFAT signaling cascade. The enriched terms include muscle development, actin and tropomyosin binding, calcium- and energy-regulation, ion channeling, negative regulation of cytokine signaling pathways, and calcineurin-NFAT signaling cascade.\\n\\nMechanism: These genes likely work together to ensure proper muscle development and maintenance by regulating calcium levels, energy homeostasis, and structural abundance of actin and other proteins in the muscle cells. The negative regulation of cytokine signaling pathways and calcineurin-NFAT signaling cascades could play a role in controlling the expression of these genes, allowing for the precise control of muscle development.\\n\\n] \n", - "538 [ These genes are involved in a wide variety of cellular processes and components, including endocytosis, protein transport, actin filament network formation, endoplasmic reticulum and recycling endosome membrane organization, macropinocytosis, cellular component organization, intracellular signaling, and protein homooligomerization. The associated processes of cell motility, cell differentiation, gene expression regulation, cell proliferation, stress and inflammatory responses, nuclear export, lysosomal degradation lipid homeostasis and apoptotic signaling form highly enriched terms in this gene set. Mechanism: The underlying biological mechanism or pathway is likely related to a combination of transmembrane and intracellular signaling. This signaling is likely to lead to cellular processes such as cell motility, cell differentiation, gene expression regulation, cell proliferation, stress and inflammatory responses, nuclear export, lysosomal degradation lipid homeostasis and apoptotic signaling. ] \n", - "539 [\\n\\nSummary: This list of genes encode adaptor proteins involved in cytoskeletal reorganization, vesicle trafficking, endocytosis, and mitosis, receptor-mediated endocytosis of specific ligands, cell adhesion processes, ubiquitin-protein ligase, and caspase-regulation of signaling complexes. \\nMechanism: The identified process involves the regulation of protein transport, endocytosis, receptor-mediated endocytosis, protein homooligomerization, cell adhesion, cell motility, amino acid residues, ubiquitination, fatty acid transport, cytoskeletal reorganization, vesicle trafficking, signaling complex regulation, mitosis, and caspase activation. \\n] \n", - "540 [\\nSummary: The genes provided in this list are all involved in glycolysis pathways and are associated with various forms of anemia.\\nMechanism: These genes encode proteins that catalyze glycolysis and the conversion of glucose to glucose-6-phosphate, the first step in carbohydrate metabolism. This metabolic process is involved in the production of energy and the regulation of cellular homeostasis.\\n\\n] \n", - "541 [\\n\\nSummary: The list of genes provides a broad overview of glycolytic and related metabolic enzymes involved in muscle maturation and regeneration,hemolytic anemia and associated neurological impairments resulting from glycogen storage diseases and cancer development, as well as angiogenesis and regulation of the serine protease plasmin.\\n\\nMechanism: These genes are likely to be activating complementary pathways involved in glycolytic metabolism, muscle maturation and development, and angiogenesis.\\n\\n] \n", - "542 [\\nThe genes discussed are involved in various forms of calcium ion transport, regulation and channels, as well as postsynaptic ion channels and nicotinic acetylcholine receptors. \\n\\nMechanism: Calcium ion transport and regulation is an important biochemical mechanism in the body, with calcium ions being necessary for proper neuronal signaling, regulation of muscle contraction and other bodily processes. The genes discussed are involved in the active transport of calcium ions, including ATPases and GPCRs; as well as channels and receptors that respond to signaling molecules such as nicotinic acetylcholine and glutamate.\\n\\n] \n", - "543 [ The genes identified in this list are primarily involved in calcium ion regulation and transport mechanisms, specifically related to the N-methyl-D-aspartate receptor family and its associated proteins. Mechanism: The gene functions are related to the regulation of calcium ions and their transport via a variety of proteins such as the N-methyl-D-aspartate receptor family, transmembrane AMPA receptor regulatory proteins (TARPs), dopamine receptors, and P-type primary ion transport ATPases. ] \n", - "544 [\\n\\nSummary: These genes are involved in various processes related to intracellular signaling pathways, cell cycle regulation, apoptosis, DNA repair, and immunity related GTPase family functions.\\n\\nMechanism: These genes are involved in the activation, regulation, or inhibition of protein kinases, caspases, and nuclear factor kappaB (NF-kB).\\n\\n] \n", - "545 [COULD NOT PARSE] \n", - "546 [ Proteins encoded by the genes are involved in the degradation of polysaccharides and glycoproteins to produce basic sugars, the recognition and degradation of misfolded proteins by endoplasmic reticulum-associated degradation, and the hydrolysis of glycosaminoglycans and heparosan sulfate. ] \n", - "547 [\\nThe human genes in the list share a commonality of them being glycohydrolase enzymes that manipulate glycosaminoglycans (GAGs), glycosyl hydrolases, and mannosidases. GAGs are long, unbranched polysaccharides which provide structural components to tissues and basement membranes. Lysozymes also appear in the list as well as amylases, which break down carbohydrates to simpler sugars, indicating a role in digestion. \\n\\nMechanism:\\nThis commonality likely reveals a role in the catabolism of carbohydrates and other glycosylated molecules via glycosidases, which break down the glycosidic bonds between saccharides and their non-carbohydrate moieties. Several endo/exoglycosidase enzymes are also mentioned, involved in the cleaving of glycosaminoglycans - this suggests that these enzymes may also play a role in cellular protein traffic and signaling, as certain molecules must travel from the endoplasmic reticulum, out of the cell, and into the extracellular matrix.\\n\\n] \n", - "548 [\\nAnalysis of the 20 human genes revealed a significant enrichment of terms relating to immunity, including antigen binding activity, immunoglobulin receptor binding activity, antibody production, adaptive immune response, and protein homodimerization.\\nMechanism: These genes enable immune system detection and responses to foreign antigens, as well as the recognition and binding of antigens and immunoglobulins. Through somatic recombination of genes, antigen recognition and specificity can be achieved, eventually leading to the production of antibodies.\\n] \n", - "549 [\\nSummary: Analysis of the genes indicates that they play an important role in immune system process, immunoglobulin receptor binding activity, and activation of immune response.\\nMechanism: The genes presented are involved in signaling pathways in which the binding of antigen to the cell surface stimulates a series of molecular events that lead to the activation of an immune response. \\n] \n", - "550 [\\n\\nSummary: The enriched terms from this list of human genes are related to DNA repair and meiotic recombination, including activities such as endonuclease activity, Bcl-2 homology domain 3 binding, chromatin binding, DNA binding, DNA helicase activity, single-stranded DNA binding, 3'-5' exodeoxyribonuclease activity, SH3 domain binding, SUMO transferase activity, double-stranded DNA binding, RING finger ubiquitin ligase activity, replication fork processing, regulation of homologous chromosome segregation, meiosis I cell cycle process, chromosome synapsis, and homologous chromosome pairing at meiosis.\\n\\nMechanism: These proteins likely act in the repair and recombination of DNA during meiosis, by interacting with other proteins to form complexes that regulate meiotic recombination, chromosome condensation and chromatid separation. These proteins may also be involved in the relief of torsional stress upon DNA transcription and replication.\\n\\n] \n", - "551 [ The list of genes provided describes proteins that are involved in several processes, such as meiotic recombination, DNA repair, chromosome segregation, double-strand DNA break repair, and homologous chromosome pairing. The enriched terms corresponding to these genes are meiotic recombination, DNA repair, chromosome segregation, double-strand DNA break repair, homologous chromosome pairing, DNA binding activity, and protein homotetramerization.\\n\\nMechanism: These gene are involved in the repair, pairing and segregation of chromosomes during meiosis and mitosis and the binding and processing of DNA. They interact with other proteins to form complexes which catalyze different types of DNA modification and repair, as well as with DNA through binding and bring about these changes. This interaction is likely necessary for the proper functioning of essential cell processes such as meiosis, mitosis, and DNA repair.\\n\\n] \n", - "552 [COULD NOT PARSE] \n", - "553 [ The provided genes are all involved in regulatory mechanisms related to genetic pathways and molecular interactions. They are involved in a variety of processes including cell cycle progression, transcription, metabolism, and immunity. A common function is providing a defense against microbial infections, toxic molecules, and apoptosis. A common mechanism is binding to and inhibiting partner proteins, often through phosphorylation.\\n\\nMechanism: The common mechanism of these genes is binding to and inhibiting partner proteins, often through phosphorylation, which allows for regulation of genetic pathways and molecular interactions.\\n\\n] \n", - "554 [ Genes related to the list are enriched for activities related to protein biosynthesis, transport and signaling, metabolism, and gene expression control. Mechanism: Genes related to the list are involved in integral processes of the cell, such as metabolism and gene expression control, which are facilitated by protein synthesis, transport and signaling. ] \n", - "555 [ Enzymes that catalyze metabolic reactions, cell cycle regulation, and energy production. \\nMechanism: Enzymes involved in metabolic pathways, cell cycle regulation, and energy production pathways are encoded by the genes listed and are over-represented.\\n\\n] \n", - "556 [COULD NOT PARSE] \n", - "557 [COULD NOT PARSE] \n", - "558 [ The list of human genes provided have a significant overlap between the proteins they encode and their effects on the maintenance of genome stability, DNA repair, replication, transcription, prelamin A proteolytic cleavage, DNA integration to the host cell genome, nuclear reassembly, and chromatin structure and gene expression. These involve mainly functions related to the nuclear membrane, chromatin, DNA and biogenesis, interaction and metabolism, as well as cellular processes involved in genetic architecture and gene expression. Furthermore, commonalities were identified between the associated diseases and characteristics, such as Werner Syndrome and mandibuloacral Dysplasia, Emery-Dreifuss muscular dystrophy, familial partial lipodystrophy, limb girdle muscular dystrophy, dilated cardiomyopathy, and Hutchinson-Gilford progeria syndrome.\\n\\nMechanism: The function of these genes and the diseases they affect involve a wide variety of cellular processes related to storage and identification of genetic information, stability and rearrangements of the nuclear architecture, gene expression and turnover, and production of specialized proteins. These involve complex interactions between various components of the nucleus and between other parts of the cell.\\n\\n] \n", - "559 [COULD NOT PARSE] \n", - "560 [ Our gene summary comes from a group of genes involved in a variety of neuronal functions including GABA, glutamate, and potassium receptor-related activities as well as ion channel function. This suggests that these genes are involved in a variety of roles related to neural communication and signaling. The common enriched terms from this gene set include \"neuronal signaling,\" \"neuron communication,\" \"ion channel,\" \"excitatory dependent channels,\" \"inhibitory neurotransmitter,\" \"ligand-gated ion channel,\" and \"G protein-coupled membrane receptor.\" Mechanism: The underlying biological mechanism relates to the role of the genes in providing the necessary components for neuronal signaling and information transfer. This includes roles in the formation of ligand-gated ion channels and G protein-coupled membrane receptors as well as the regulation of neurotransmitter release and excitability. ] \n", - "561 [\\nThe genes in this list are involved in glutamate, GABA, and potassium channel related pathways found in the mammalian brain. Enriched terms include: neurotransmitter receptors (e.g. glutamate receptors, GABA receptors, potassium channels); ligand-gated ion channels; RNA editing; voltage-gated ion channels; channel subunits; channel polymorphisms; G-protein-coupled transmembrane receptors, etc.\\n\\nMechanism: Several of these genes encode for subunits of neurotransmitter receptor complexes, which suggest a mechanism for the modulation of synaptic transmission through the binding of agonists and antagonists that modulate the activity of the channels and facilitate the transport of ions across membranes. Additionally, some of the genes in this list play a role in the control of G-proteins and the regulation of heartbeat, suggesting that they may also be involved in regulating cell signalling pathways.\\n\\n] \n", - "562 [\\nSummary: These genes are associated with functions related to development and maintenance of the nervous system, sensory systems, and erythropoiesis, as well as mitochodnrial mRNA synthesis and transcriptional regulation. \\n\\nMechanism: These genes regulate post-translational processes including ubiquitination and processing, protein synthesis, transcription and activity of transcription factors, and organization of the cytoskeleton and nucleus.\\n\\n] \n", - "563 [ Genes in this list are involved in transcriptional, structural and signaling pathways that are related to maintaining the structure and function of peripheral nerve cells, including Schwann cells and myelin sheath maintenance.\\n\\nMechanism: Transcriptional, structural, and signaling pathways in peripheral neurons play a key role in maintaining nerve cell health and homeostasis.\\n\\n] \n", - "564 [ This gene set encodes many G-protein coupled receptors involved in signal transduction from extracellular signals to intracellular responses. Mechanism: G-protein coupled receptor signaling pathways initiate transmembrane signal transduction in response to hormones, neurotransmitters, and sensory signals by regulating adenylyl cyclase, phospholipase C-beta, and other downstream effectors. ] \n", - "565 [COULD NOT PARSE] \n", - "566 [ The list of human genes includes proteins that play a role in transcriptional regulation, chromatin remodeling, and DNA binding. The mechanism likely involves transcriptional coactivators and transcription factors forming heterodimers to bind to enhancers and promoters at specific response elements. ] \n", - "567 [\\nThe human genes analyzed in this term enrichment test were associated with functions such as transcriptional regulation, chromatin remodeling, DNA-binding, and zinc-finger binding. These genes were found to be enriched for terms related to transcription factor regulation of gene expression, chromatin modification, and DNA-binding activity.\\n\\nMechanism: These genes are a part of pathways responsible for the regulation of gene expression. The encoded proteins function as transcription factors, ligands, and chromatin remodelers which bind to DNA, interact with other transcription factors, and promote or inhibit the transcription of genomic regions. Zinc-finger binding, SUMO binding, and retinoid X receptor responsive element binding are also important regulators of gene expression and are involved in this term enrichment test.\\n\\n] \n", - "568 [ The nine genes are associated with extracellular matrix (ECM) components and their regulators. Mechanism: The proteins coded by these genes could be involved in the regulation of the expression of ECM components, which can contribute to the formation of the physical integrity of the ECM and its interaction with the cellular environment. ] \n", - "569 [ This list of genes is enriched in proteins involved in the Extracellular Matrix (ECM) protein network, which is a component of the larger Cell Adhesion and Morphogenesis (CAM) pathway. Specifically, the genetic list is enriched for components involved in the processes of collagen fibril formation, collagen fibril organization, extracellular matrix (ECM) protein network assembly, ECM protein network stabilization, epidermal cell fate commitment, epithelial tube growth and branching morphogenesis, collagen modification and deposition, and zinc-finger protein motif binding.\\n\\nMechanism: The ECM protein network mediates cell-cell and cell-matrix interactions in order to regulate the adhesive, motile, and proliferative states of cells. It consists of a variety of molecules, including ECM proteins, which serve as substrates to guide cell migration, growth and differentiation. ECM proteins are those that contain one or more structural domains capable of interacting with the ECM components, such as extracellular domains, as well as those containing adhesive domains. \\n\\n] \n", - "570 [COULD NOT PARSE\\nHypothesis: The genes in this list are likely involved in the regulated repair of DNA double strand breaks due to replication-mediated damage, with the coordinated action of the Fanconi Anemia protein complex and the shared components of the ubiquitin ligase complex.] \n", - "571 [ Several genes involved in DNA repair and homologous recombination processes, such as FANCL, RAD51C, FANCE, MAD2L2, ERCC4, FANCA, BRCA2, FANCF, XRCC2, BRIP1, FANCD2, SLX4, FANCB, FANCG, UBE2T, RAD51, PALB2, and FANCC, were observed to be statistically enriched for terms related to DNA damage recognition and repair, DNA damage response, and homologous recombination processes.\\n\\nMechanism: These genes enable the cellular response to double-stranded breaks (DSBs) by providing components of the DNA damage recognition and repair variety. They also function in the homologous recombination pathway for DNA repair, which is used for error-free repair of damaged DNA strands. \\n\\n] \n", - "572 [ Enrichment analysis of this list has revealed that many of the genes are involved in energy metabolism and fatty acid metabolism, such as ATP1B3, ACOX1, ACADM, SLC19A1, SLC25A10, PGM1, UCP2, GPX3 and GPX4. They are also related to adipogenesis, with genes such as ADIPOR2, APLP2, LEP, ADIG and ADIPOQ. Lastly, several of the genes are involved in cholesterol and bile acid synthesis, such as DHCR7, DHRS7, CYP4B1 and HMGCR.\\n\\nMechanism: The genes identified as being involved in energy metabolism and fatty acid metabolism appear to share a common mechanism in which these molecules are generated from multiple sources to form energy. The genes involved in adipogenesis appear to be related to the regulation and development of fat cells and adipose tissue. Similarly, the genes involved in cholesterol and bile acid synthesis appear to be related to the synthesis of these molecules from multiple sources.\\n\\n] \n", - "573 [ This term enrichment test revealed a group of genes associated with energy metabolism, regulation of cell death, cell proliferation and signaling, DNA replication/remodeling, RNA processing, and lipid metabolism.\\nMechanism: This group of genes may be involved in binding, regulating, or expressing other proteins in order to influence the cell's metabolic and signaling status. \\n] \n", - "574 [ This enrichment test examines a list of 73 human genes and reveals enrichments for the functions related to cell surface molecules, cytokines, immunology, receptor signalling, transcriptional regulation and apoptosis.\\n\\nMechanism: These genes are involved in a variety of pathways that include cytokine signaling, cell surface molecules, transcriptional regulation, apoptosis, and receptor signaling.\\n\\n] \n", - "575 [ This analysis results in the enrichment of genes functions related to immune system regulation, including antigen presentation, signaling, B and T cell metabolism, cytokine production and chemotaxis. Mechanism: The genes identified in this list are involved in controlling a range of processes that are necessary for proper immune system functioning, such as antigen presentation, signaling pathways, metabolizing T and B cells, production and secretion of cytokines, and chemotaxis of immune cells. These functions are necessary for the body to defend itself against pathogens. ] \n", - "576 [COULD NOT PARSE] \n", - "577 [ \\nSummary: The genes are enriched in terms related to regulation, signaling, and metabolism.\\nMechanism: The genes are likely to be involved in molecular mechanisms governing cellular activities and pathways, with signaling pathways such as Wnt, MAPK, and PKA pathways playing an important role. \\n] \n", - "578 [ \\n\\nSummary: A set of 34 genes related to extracellular matrix formation and maintenance, fibrous tissue development, vascular development, and extracellular secreted signaling. \\n\\nMechanism: Together, these genes encode proteins involved in multiple signaling pathways to regulate the development, maintenance and repair of the extracellular matrix (ECM), including fibrous, collagen, and laminin-fibrillin proteins, along with proteins involved in vascular regulation, cell-cell communication and migration, and extracellular secreted signaling molecules. \\n\\n] \n", - "579 [ Genes in this list are primarily associated with development, vascular remodeling and cell-cell communication.\\nMechanism: These genes likely play a role in various aspects of development, including morphogenesis, tissue development, extracellular matrix organization, inflammation, vascular remodeling and cell-cell communication.\\n] \n", - "580 [COULD NOT PARSE] \n", - "581 [\\nSummary: The genes in this list are involved in a wide variety of processes, including development, growth, morphology, and molecular signaling.\\nMechanism: These genes appear to be involved in the regulation of cellular processes by mediating signals that modulate development, growth and morphology.\\n] \n", - "582 [\\nSummary: The list of genes provided is enriched for terms relating to cell migration, membrane receptor signaling, and glycoprotein metabolism.\\nMechanism: These gene functions serve to coordinate cell migration and receptor-mediated signaling, as well as metabolism. \\n] \n", - "583 [\\nSummary: The genes provided are involved in diverse biological pathways related to cell signaling, development, transcription, and metabolism.\\nMechanism: The genes likely represent an underlying biological mechanism that is involved in cellular proliferation and the regulation of gene expression.\\n] \n", - "584 [ The list of human genes given is statistically significantly enriched for the gene functions of transcriptional regulation/control, cell-cycle/apoptosis, and immune responses.\\nMechanism: The genes listed encode proteins involved in transcriptional regulation through control pathways such as the activation of caspases, the inhibition of cyclin-dependent kinase activity, and the upregulation of apoptosis-related proteins. They also encode molecules involved in immune-related processes such as the binding and activation of proinflammatory cytokines, the formation of interferon gamma receptor complexes, and the regulation of major histocompatibility complex class I molecules. \\n] \n", - "585 [COULD NOT PARSE] \n", - "586 [\\nSummary: The genes listed are enriched in terms related to metabolic pathways, lipid transport, and development of connective tissues.\\nMechanism: The functions of the genes appear to involve a number of metabolic pathways, such as fatty acid and bile acid synthesis, xenobiotic metabolism, and steroidogenesis, as well as pathways related to cellular transport and signaling, including those related to lipid transport and receptor-mediated signal transduction.\\nIn addition, several of the genes are involved in connective tissue formation, as well as development of digits and limbs.\\n] \n", - "587 [COULD NOT PARSE] \n", - "588 [COULD NOT PARSE] \n", - "589 [\\nSummary: The genes populated are predominantly involved in lipid metabolism (eg. HMGCR, PMVK, FDPS), transcription regulation (eg. ACTG1, NRAF), cellular adhesion (eg. CD9, ANXA13, COUNTY), and other development related processes (eg. S100A11, MVD, IDI1).\\nMechanism: The genes are associated with a number of different functions but are likely involved in maintaining cellular homeostasis, regulating transcription, and participating in development processes.\\n] \n", - "590 [\\nSummary: Several of the human genes on this list play a role in extracellular matrix formation, inflammatory response, and proteolytic activities.\\nMechanism: The common functional mechanisms included in this term enrichment test are the regulation of the inflammatory response, regulation of extracellular matrix formation, and proteolytic activities.\\n] \n", - "591 [\\nSummary: The genes identified are predominantly involved in matrix molecular regulation, pathways related to proteolysis and coagulation, signal transduction, and extracellular matrix organization.\\nMechanism: The genes act as regulators of specific molecular functions and as mediators of signal transduction pathways. The identified genes are likely involved in the processing and remodeling of the extracellular matrix because of their relation to proteolysis and other matrix-related functions.\\n] \n", - "592 [\\nSummary: These genes are enriched in functions related to extracellular matrix organization, immune system/inflammation/interferon response, and transcription factor activity.\\nMechanism: These genes could be involved in a pathway that is responsible for coordinating and controlling aspects of extracellular matrix organization, immune system/inflammation/interferon response and the activity of transcription factors.\\n] \n", - "593 [ This enrichment test revealed several terms related to immune system functioning, cell adhesion and regulation, and extracellular matrix organization, which are likely the underlying mechanisms behind the commonalities among the listed genes. Enriched terms include: immunoglobulin like domains; B cell activation; T cell receptor signaling pathway; integrin mediated cell adhesion; apoptosis; regulation of transcription; signal transduction; receptor mediated endocytosis and exocytosis; extracellular matrix organization; and calcium mediated signaling. \\n\\nMechanism: These findings suggest that the genes involved in this test collectively contribute to a range of processes related to immune system functioning, cell adhesion, extracellular matrix organization, and intracellular communication. \\n\\n] \n", - "594 [ Gene functions related to DNA and RNA metabolism, protein synthesis, DNA damage repair, transcription, and chromatin organization are significantly over-represented.\\nMechanism: It is likely that many of these genes are involved in the same pathway related to the fundamental processes of DNA replication, transcription, and protein synthesis.\\n] \n", - "595 [ \\nSummary: These genes are enriched for roles in DNA replication, transcription, translation and post-translational modifications.\\nMechanism: These genes are involved in various biological processes, including DNA replication, transcriptional regulation, translation, and post-translational modifications involved in gene expression. \\n] \n", - "596 [ Genes on the list are primarily involved in DNA cell cycle and replication, gene regulation, transcription and translation, chromatin modification, and DNA repair. \\n\\nMechanism: The genes are involved in the regulation of DNA replication and transcription, chromatin modification, and DNA repair processes during cell cycle progression. \\n\\n] \n", - "597 [\\nSummary: The genes in the list are involved in diverse functions related to DNA replication, transcription, chromosome condensation and transcriptional regulation.\\nMechanism: These functions are likely related to canonical pathways and processes involved in coordinating and regulating DNA replication, the transcription of genetic information into proteins, and maintaining appropriate chromosome condensation states.\\n] \n", - "598 [COULD NOT PARSE] \n", - "599 [ Our enrichment test uncovered several terms related to extracellular matrix function, morphogenesis, and reproduction/growth. These terms include extracellular matrix organization; morphogenesis; collagen production; matrix metalloproteinase activity; glycoprotein metabolism; cytoskeletal component organization; regulation of growth and reproduction; and regulation of skin morphogenesis. Mechanism: The underlying biological mechanisms related to these genes likely involve the extracellular matrix (ECM), which provides structural and biochemical support to the cells and tissues. ECM components, such as collagen, can regulate activities such as cell signaling, structure formation and growth, and gene expression. Morphogenesis is likely modulated by ECM components, as well as by signaling pathways. ] \n", - "600 [\\nSummary: The list of genes identified are associated with cell morphology, homeostasis and regulation, innervation, and cellular metabolism.\\n] \n", - "601 [ Our analysis of the 34 human genes suggests an enrichment of gene functions related to cell signaling, regulation and morphology, including: immunological response; cell adhesion; transcription regulation; cell migration; development of epidermis, bones and muscle; transport of proteins between cellular compartments; and apoptosis. \\n\\nMechanism: These gene functions are likely related to the regulation of diverse mechanisms within the cell, such as protein-protein interactions, transcription signaling, and intracellular trafficking. \\n\\n] \n", - "602 [\\nThe genes in the list are enriched for functions in the genomics and cytoskeletal processes, as well as immune response and extracellular modification.\\n\\nMechanism:\\nThe gene functions are implicated in various biological processes that are orchestrated by genetic control and/or regulation pathways. These pathways typically involve protein interactions and cellular processes. Additionally, these pathways often correlate to extracellular modification, immune response, and/or modulation of receptor signaling.\\n\\n] \n", - "603 [COULD NOT PARSE] \n", - "604 [ This list of genes is highly enriched for metabolic processes such as fatty acid metabolism and oxidation, cholesterol biosynthesis, glycogen metabolism, nucleotide metabolism and transport, and electron transport activity. This suggests that the list reflects a highly coordinated and interconnected network of metabolic processes to maintain the homeostasis of the cell. Enriched terms include: fatty acid metabolism; oxidation of lipids; cholesterol biosynthesis; glycogen metabolism; nucleotide metabolism; nucleotide transport; nucleotide biosynthesis; electron transport activity; enzyme regulation and regulation of metabolic pathways; and apoptosis. \\nMechanism: This set of genes likely acts through a number of interconnected pathways to maintain cellular homeostasis. Lipid metabolism is known to be important in cellular signaling, while other metabolic pathways interact with each other through enzyme regulation and regulation of metabolic pathways. Additionally, many of the genes are associated with cell death pathways, suggesting that these can also act in a coordinated way to respond to stress and maintain cellular homeostasis. \\n] \n", - "605 [\\n\\nSummary: There is a strong enrichment of genes involved in metabolic processes, energy production and storage, lipid metabolism and transport, as well as acetyl-CoA biosynthesis and catalysis.\\n\\nMechanism: The identified genes likely influence the metabolic processes, energy production and storage, lipid metabolism and transport, as well as acetyl-CoA biosynthesis and catalysis by modulating cellular processes, protein and enzyme production, and functional metabolic pathways, such as oxidation and fatty acid metabolism.\\n\\n] \n", - "606 [\\nGene functions involved in cell cycle regulation, DNA replication, and chromatin remodeling are enriched among the provided list of genes. This could reflect a core pathway of regulation that has been conserved across multiple species.\\n\\nMechanism:\\nThe enriched terms suggest that this gene list could be involved in the G1/S transition of the cell cycle, DNA replication, and chromatin remodeling or modification. Specifically, cell cycle progression and DNA replication is likely driven by cyclin B-CDK1 activation, which is facilitated by Cks1b and Cdc25A mediated activation and either Wee1 or Cdc20-anaphase promoting complex-cyclosome (APC/C)-mediated inhibition. Chromatin modification is likely driven by histone H2A and H2B acetylation and lysine methylation, which involve various proteins, such as Hmga1, Hmgn2, H2az1, H2bc12, and Myc.\\n\\n] \n", - "607 [ \\nSummary: This list of human genes are primarily involved in nuclear processes such as DNA replication, gene transcription, chromatin remodelling and cell cycle control.\\nMechanism: The genes may be involved in the regulation of a number of biological processes such as DNA repair, cell cycle regulation, gene expression, and gene regulation.\\n] \n", - "608 [\\nSummary: Our term enrichment test shows that many of the genes on this list are involved in various aspects of developmental and morphogenic processes, including digit development, cell differentiation, angiogenesis, and metabolism.\\nMechanism: These genes are likely to be involved in biological pathways involving the development and maintenance of cellular structure, binding and transporting of molecules, energy metabolism and other metabolic processes, and cell signaling.\\n] \n", - "609 [ The list of genes are primarily involved in essential metabolic functions in the cell. Specifically, they are involved in carbohydrate and energy metabolism, microtubule assembly, DNA binding and replication, actin cytoskeleton dynamics, ion channel regulation, transcriptional regulation, and cell adhesion. The mechanism is likely related to the coordination of these processes in order to maintain homeostasis and proper cell functioning.\\n\\nSummary: Genes mainly involved in metabolic processes. \\n\\nMechanism: Coordination of these processes to maintain cellular homeostasis.\\n\\n] \n", - "610 [\\nSummary: Many of the genes listed are involved in the development and morphogenesis of neurons and other cells. \\nMechanism: These genes are likely to work together to regulate cell and tissue shaping and differentiation, providing for the formation of specialized neuron structures and neural pathways. \\n] \n", - "611 [\\n\\nSummary: This group of genes is commonly associated with morphogenesis, cell adhesion, development, and neuronal signaling\\nMechanism: The underlying biological mechanism is likely related to the regulation of cell proliferation, migration, differentiation, and neural plasticity during development. \\n] \n", - "612 [\\nSummary: The genes in this list are highly enriched for functions related to membrane transport, energy metabolism, ribosomal proteins, and nucleic acid binding.\\nMechanism: The underlying biological mechanism or pathway may involve regulation and control of cellular functions and transcription activity, with multiple proteins interacting to ensure proper functioning of a variety of cellular pathways.\\n] \n", - "613 [\\n\\nSummary: The human genes identified in this list are predominantly involved in cell development, gene expression, organogenesis and nucleic acid metabolism.\\n\\nMechanism: The human genes identified in this list are likely to be involved in processes that regulate cell development, including transcriptional regulation and organogenesis, as well as nucleic acid metabolism. \\n\\n] \n", - "614 [COULD NOT PARSE] \n", - "615 [ \\nSummary: Genes related to cell development, cell metabolism, transcription, and regulation are enriched in this set.\\nMechanism: These genes regulate a variety of cellular processes such as cell cycle regulation, transcriptional regulation, and energy metabolism.\\n] \n", - "616 [ The gene set is enriched for genes involved in cell growth, cell detection/regulation, and immunity. Mechanism: These genes are likely involved in a number of pathways that contribute to cell and tissue development, growth, and regulation, as well as regulation of the immune system. ] \n", - "617 [COULD NOT PARSE] \n", - "618 [ Genes in the list are enriched for the Cellular Processes of Pain Sensing and Signal Transduction; Chemotaxis; Cytokine-mediated Signaling Pathway; Leukocyte Transendothelial Migration; Immune Response; and Platelet Activation. There is a potential mechanism for the underlying biological pathway whereby these genes interact in signal transduction to facilitate pain sensing and immune response, including ligand-receptor interactions, signal transduction of cytokines, and the actions of transcription factors, such as those encoded by JUN, REG1A, STAT1, STAT2, STAT3 and TLR2.\\n\\n] \n", - "619 [\\nSummary: The list of genes are significantly enriched for functions of immunity, signaling, and transcription regulation\\nMechanism: These genes are likely involved in the coordination of immune responses and the regulation of pathways for signal transduction and transcription.\\n] \n", - "620 [ Genes associated with human immunity, inflammation and signalling pathways are enriched.\\n\\nMechanism: These genes are likely involved in pathways related to human immunity, inflammation and signalling, either directly or through regulation of transcription and translation activity.\\n\\n] \n", - "621 [ The list of genes is significantly enriched for terms related to immune cell signaling, cell movement, and cell surface receptor activity. \\nMechanism: These genes are likely involved in the regulation of pathways involved in initiating and responding to inflammation, cell migration, cell–cell interactions, and immune cell receptor-mediated signaling.\\n] \n", - "622 [ Our analysis of the list of human genes have revealed a set of enriched terms related to the activation and inhibition of immune signaling pathways, and their functions in regulating inflammation. Specifically, we observed an increased prevalence of molecules and proteins involved in mechanism activating or inhibiting the Nuclear Factor Kappa B (NF-κB), Interferon Regulatory Factor (IRF) as well as JAK-STAT pathways. Terms such as \"inflammatory response\", \"neutrophilic activation and degranulation\", \"T-Cell receptor signaling pathway\", \"Toll-Like Receptor Cascade\", \"Type I Interferon Signaling\", and \"Inflammatory Regulation\" were enriched in this gene set.\\n\\nMechanism: The genes in this list are involved in multiple pathways that are related to the modulation of inflammatory responses and can be broadly summarized as either regulating cytokine production or modulating the inflammatory response by inhibiting the NF-κB, IRF and JAK-STAT pathways. While there is significant overlap of these genes with the NF-κB pathway, the IRF and JAK-STAT pathways are also significant contributors, as evidenced by the enriched terms. \\n\\n] \n", - "623 [ This group of genes is significantly enriched for functions related to immune system regulation, interferon response, apoptosis, and cell membrane regulation.\\n\\nMechanism: This list of genes is likely involved in both innate and adaptive immune responses, functioning to modulate the level of inflammation and cytokine production, as well as to induce cell death and regulate cell membrane composition. Specific terms enriched that pertain to these functions include interferon signalling pathways, interferon gamma activity, interferon regulatory factor activity, status response to interferon, apoptosis, lipid binding, calcium ion binding, and neutrophil mediated immunity. \\n\\n] \n", - "624 [\\nSummary: A majority of the genes were found to be involved in important immune response and cell signaling pathways.\\nMechanism: The immune response and cell signaling pathways are likely to be regulated by cytokines and transcription factors such as those related to interferon responses and nuclear factor kappaB-dependent transcriptional regulation.\\n] \n", - "625 [\\nSummary: The enriched terms among the list of genes includes pathways involved in immunity, interleukin regulation, transcriptional regulation, inflammation, cell signaling, and apoptosis.\\nMechanism: Signaling and pathways involving these genes are likely to regulate these biological processes.\\n] \n", - "626 [ Genes in this term enrichment test were found to be enriched for terms related to the development of bones, morphogenesis, growth and maintenance, cell-cell signaling and communication, protein modification, and transport.\\nMechanism: It is likely that the genes identified in this term enrichment test make up a biological pathway that is involved in the development of bones, growth and morphogenesis, and other processes related to regulating cell-cell signaling and communication, protein modification, and transport.\\n] \n", - "627 [\\nSummary: The list of genes are found to be significantly associated with physiological processes related to morphogenesis, cell-cell communication and development, and hormone regulation.\\nMechanism: The genes are likely to be involved in a variety of biological mechanisms, such as cell-signalling, cellular differentiation and cell-cycle, as well as hormone mediated processes.\\n] \n", - "628 [ Genes in this list are predominantly involved in signal transduction pathways and morphogenesis; specific terms enriched include signal transduction, cell morphogenesis, response to stimulus, angiogenesis, regulation of molecular function, and extracellular matrix organization.\\nMechanism: The list of genes are likely to be involved in signaling pathways involving kinases, growth factors and receptors, as well as involvement in morphogenesis processes such as cell-cell adhesion, cellular movement and cell differentiation.\\n] \n", - "629 [\\nSummary: This set of genes appears to be involved in a variety of cellular processes, including morphogenesis and tissue development, cell signaling, and immune regulation.\\nMechanism: These genes appear to be involved in transcription modulation, signal transduction pathways, and regulation of cell adhesion and migration.\\n] \n", - "630 [COULD NOT PARSE] \n", - "631 [ Enriched terms show a commonality among these genes for processes related to cytoskeletal organization and migration of the cell, cell division, DNA replication and repair, and targeting proteins to the correct place in the cell.\\nMechanism: The proteins represented by these genes likely play a role, either directly or indirectly, in the regulation of a number of vital cell processes including cell division, DNA replication and repair, and targeting proteins to the right place in the cell.\\n] \n", - "632 [COULD NOT PARSE] \n", - "633 [ The list of genes is enriched in functions related to protein synthesis, energy metabolism, cellular transport, and immune response.\\nMechanism: It is likely that these genes are co-regulated in networks that are responsible for cellular energy production and regulation, protein synthesis and degradation, and immune response.\\n] \n", - "634 [ The genes appear to be involved in processes related to RNA and protein synthesis, ATP-related processes, cytoskeleton organization and assembly, transcription, and chromatin remodeling.\\n\\nMechanism: The genes likely play a role in regulating various cellular processes, such as gene expression, signal transduction, and translation, via multiple pathways that are related to RNA processing, translation initiation, mRNA stability, and DNA replication.\\n\\n] \n", - "635 [ Genes from this list are mainly involved in translation, transcription, and post-transcriptional modification processes. Specifically, these genes are involved in mRNA splicing, mRNA transport, mRNA stability, protein synthesis, ribosome biogenesis, RNA interference, and chromatin remodeling. Mechanism: These genes likely operate according to the canonical mechanisms of gene expression, by which genes are transcribed, spliced, and translated into proteins. These processes are tightly regulated and involve a complex network of interacting proteins, RNAs, and other molecules. ] \n", - "636 [COULD NOT PARSE] \n", - "637 [\\nSummary: The gene set is enriched for terms related to cell activation and proliferation, as well as DNA replication and replication-associated processes such as transcription and translation.\\n] \n", - "638 [ Gene expression and structure, cytoskeletal structure and dynamics, calcium regulation and signaling, cell adhesion and migration, cell death biochemistry, and metabolic regulation are all enriched terms based on the genes provided that are common to these roles in humans.\\n\\nMechanism: The underlying biological mechanism for the enriched terms observed in this list of genes is likely related to the wide range of regulatory roles these genes and gene products have in maintaining cellular health and enabling proper physiological functions and development at the cellular level. \\n\\n] \n", - "639 [ The list of genes show an enrichment for terms related to the extracellular matrix, cytoskeleton, muscle structure and development, neuromuscular structure, ion channels, and ion transport. \\nMechanism: These genes appear to be involved in various intra- and extracellular pathways and mechanisms related to the formation and maintenance of the cytoskeleton, neuromuscular structure, and muscle formation, as well as ion transport and channel proteins serving as important mediators of electrical and chemical signals in cells. \\n] \n", - "640 [\\nThe list of genes are involved primarily in aspects of embryonic development, regulation of cell cycle, and calcium signaling.\\nMechanism: The genes function primarily in regulating various aspects of cell signaling and cycle regulation during embryonic development, such as down-regulation of Notch signaling, regulation of Wnt signaling and Hedgehog signaling pathways, cell morphogenesis, and calcium signaling.\\n] \n", - "641 [COULD NOT PARSE] \n", - "642 [\\n\\nSummary: This list of genes is enriched for terms related to mitochondrial activity, electron transport chain, oxidative phosphorylation, and metabolic regulation/activation.\\nMechanism: This list of genes are likely to be involved in the various steps of mitochondrial activity, electron transport chain, oxidative phosphorylation, and metabolic regulation/activation. \\n] \n", - "643 [\\nSummary: The list of genes is predominantly involved in cellular respiration and metabolism, as evidenced by the enriched terms related to mitochondrial bioenergetics, ion transport and metabolite-binding proteins.\\nMechanism: The commonality amongst the genes likely contributes to the normal functioning of mitochondria, and is involved in the bioenergetic processes that involve ATP synthesis, as well as maintaining electron transfer and transporter function.\\n] \n", - "644 [ Analysis of this gene list revealed a significant enrichment of terms in functions related to cytoskeleton alteration, calcium homeostasis modulation, ubiquitin-proteasome pathway activation, cell cycle control, and transcriptional and post-transcriptional regulation.\\n\\nMechanism: These functions likely act in concert to mediate the regulation of cellular growth, differentiation, and survival.\\n\\n] \n", - "645 [ Genes in this list are associated with regulation of the cell cycle, DNA damage repair, cell signaling and processes involved in cell growth, apoptosis, and immune modulation. The genes are enriched for functions related to transcription, chromatin dynamics, cell adhesion molecules, and cytokines. \\nMechanism: The regulation of these genes (directly or indirectly) is likely to be part of a complex network of pathways, signaling molecules, and protein-protein interactions. \\n] \n", - "646 [\\nSummary: This gene set is enriched in functions related to pancreas development, glucose metabolism, cell motility, and neural development. \\nMechanism: It is hypothesized that these genes function in a network to control developmental processes relevant to pancreas development, glucose metabolism, cell motility and neural development.\\n] \n", - "647 [\\nSummary: This term enrichment test identified gene functions related to morphogenesis, neural development, signal transduction, insulin hormone secretion, transcription regulation, and transcription factor activity.\\nMechanism: These genes likely work together to facilitate the development of body organs, neuronal function and pathways, insulin secretion, and transcription factor activity.\\n] \n", - "648 [COULD NOT PARSE] \n", - "649 [ Genes involved in the list are associated with lipid metabolism, lipid storage and transport, steroid metabolism, regulation of transcription and, importantly, regulation of the cell cycle. \\nMechanism: An enrichment of pathways associated with lipid, steroid and transcriptional metabolism, as well as regulation of the cell cycle.\\n] \n", - "650 [ Gene expression, DNA repair and maintenance, growth factors, cellular signaling pathways and lipid metabolism \\nMechanism: Regulation of gene expression through the activation of transcription and DNA repair and maintenance pathways is likely involved. The enriched terms related to growth factors suggests that the list of genes may be involved in cell proliferation and differentiation. Signaling pathways and lipid metabolism may be involved in cell-cell communication and energy-related processes, respectively.\\n] \n", - "651 [ The list of genes given are involved in cell cycle regulation, gene transcription, transcription factor activation and signal transduction pathways.\\nMechanism: The genes included in this list are involved in various mechanisms of cell cycle regulation, gene transcription, transcription factor activation and signal transduction pathways. These involve the regulation of cell cycle progresses such as synthesis, growth, proliferation and differentiation, as well as the operations of protein kinases, transcription factors, receptor proteins and other essential molecules. \\n] \n", - "652 [COULD NOT PARSE] \n", - "653 [COULD NOT PARSE] \n", - "654 [\\nSummary: This list of genes is enriched for terms involving redox regulation, antioxidant defense and detoxification of reactive oxygen species, peroxisomal and mitochondrial biogenesis, and cell metabolism.\\nMechanism: The underlying biological mechanism involves the production and regulation of reactive oxygen species, adaptation to oxidative stress and related forms of damage, and the maintenance of redox homeostasis.\\n] \n", - "655 [ \\nSummary: 13 genes are enriched for functions associated with redox regulation, metabolism, cell cycle regulation, and transcriptional regulation.\\nMechanism: These genes likely play a role in the regulation of a cell's redox balance, metabolism, cell cycle progression and gene expression.\\n] \n", - "656 [\\nThe gene list is enriched for functions related to cell signaling, protein regulation, and cell cycle control, as well as complex development processes such as morphogenesis, organogenesis and cytoskeletal regulation.\\nMechanism: A wide range of mechanims are at work here, which involve the transcription and translation of genes to encode proteins and the regulation of their functions to mediate both common and specific biological processes.\\n] \n", - "657 [ Genes related to organ development, morphogenesis, cytoskeletal proteins, signal transduction.\\nMechanism: Proteins from the list are likely used as part of a unified pathway for organ/tissue development and morphogenesis, and involved in cell cycle checkpoint regulation and signal transduction.\\n] \n", - "658 [ The list of genes analyzed in this term enrichment test is related to pathways associated with cell growth and development, such as MAPK, TGF-β, Wnt/β-catenin, Hippo and transcriptional regulations. Specifically, pathway enrichment of genes included muscle and tissue morphogenesis, regulator of G-protein signaling and inflammatory response pathway.\\n\\nMechanism: The general mechanism is that the genes are involved in signaling pathways for cell processes such as growth, differentiation and apoptosis. These signals modulate the expression of downstream genes and ultimately lead to changes in cell shape and other cellular activities.\\n\\n] \n", - "659 [COULD NOT PARSE] \n", - "660 [ These genes are mainly involved in developmental processes, inflammation, immunomodulation, inflammation, cell signalling and metabolic pathways.\\nMechanism: These genes are likely to be involved in pathways leading to the regulation of morphogenesis and tissue development, control of cell proliferation and apoptosis, regulation of immune system immune response, regulation of inflammation and activation of metabolic pathways.\\n] \n", - "661 [\\nSummary: The genes are enriched for terms related to gene transcription, cytoskeleton formation, and signal transduction. \\nMechanism: The genes are likely involved in a wide range of processes, including transcriptional regulation, actin cytoskeleton organization, cytokine receptor signaling and NF-kB signaling pathways.\\n] \n", - "662 [ The genes in the list may be generally involved in processes such as mRNA transcription, ribosome biogenesis and protein folding, as well as nucleolar and spliceosomal activity. \\nMechanism: These genes likely regulate cellular processes such as protein production and transport, RNA processing, and cell cycle control. \\n] \n", - "663 [\\nSummary: The enrichment analysis on the list of genes revealed a common theme of gene functions related to metabolism, protein synthesis, and post-translational modifications.\\nMechanism: The observed gene functions suggest a pathway of metabolic and protein regulatory processes that involve the synthesis of proteins, post-translational modifications such as phosphorylation, and other processes related to metabolism and folding.\\n] \n", - "664 [ The genes identified are associated with protein kinases, cellular signaling pathways, and development of skeletal and extracellular matrix components.\\nMechanism: These identified genes may be involved in complex regulation and signaling pathways, focusing on post-translational phosphorylation and transcriptional regulation, as well as the control of growth, development and remodeling of skeletal structures.\\n] \n", - "665 [ Many of the genes are clustered around those involved in structure, development and regulation. They are involved in processes such as mitotic regulation, bone morphogenesis, morphogenesis of specific organs and tissues, regulation of signaling pathways, regulation of transcription, regulation of cell proliferation, cellular responses to external stimuli, protein phosphorylation and DNA binding.\\n\\nMechanism: These genes are likely to be involved in the regulation and development of several different processes, including the regulation of cell proliferation, transcription, morphogenesis of organs and tissues, and mitotic regulation. These mechanisms are likely to be controlled by the interactions among gene products, signaling pathways and regulatory components such as transcription factors.\\n\\n] \n", - "666 [ Proteins involved in development, cell growth, gene transcription, and metabolism are enriched.\\nMechanism: These proteins are involved in a variety of biological processes that underlie development and cell growth, as well as affecting gene transcription and metabolism.\\n] \n", - "667 [ Genes in this list are mainly involved in cell growth, morphogenesis, regulation of transcription, signal transduction of receptors, DNA/protein activity and metabolism. More specifically, the terms enriched in this list of genes are cell proliferation, cell cycle regulation, DNA replication and repair, signal transduction, calcium signaling, apoptosis, lipid metabolism and oxygen pathway.\\n\\nMechanism: The genes in this list mainly participate in the regulation of various biological processes through their encoding for proteins that act as transcription factors, receptors, and enzymes. These proteins are activated by a variety of signals including DNA damage, growth factors and hormones to induce changes in gene expression and cellular behavior. They also control cell growth, differentiation and metabolism by regulating DNA, protein, lipid and oxygen pathways, ultimately resulting in morphogenesis and cell proliferation. \\n\\n] \n", - "668 [COULD NOT PARSE] \n", - "669 [\\nSummary: The gene list appears to mostly contain genes involved in Wnt signaling, Notch signaling, transcription regulation and cell cycle regulation processes.\\nMechanism: The underlying biological mechanism appears to be the regulation of processes such as transcription, cell cycle, and Wnt and Notch signaling that may in turn affect the morphogenesis and development of various organs and tissues.\\n] \n", - "670 [ \\nSummary: The genes in the list are found to be involved primarily in cell signalling, development, and immunity processes.\\nMechanism: The numerous genes with enriched terms are involved in coordinating both intra- and extracellular activity through signal transduction pathways and receptor-mediated signaling, with downstream effects on cellular growth, differentiation, and function within various organs and systems in the body.\\n] \n", - "671 [ The enrichment test found that the genes listed have common functions associated with cell signaling and immune regulation, such as signal transduction, growth factor production and response, immune response and modulation, calcium homeostasis, transcription factors, development and differentiation, receptor binding, and cytokine production.\\n\\nMechanism: The enrichment test suggests that these genes may contribute to signal transduction pathways that facilitate cell proliferation, differentiation, and survival; growth factor production and signal transduction; immune response and modulation; calcium homeostasis; transcription factor activity including regulation of gene expression; development and differentiation; receptor binding and signal transduction; and cytokine production.\\n\\n] \n", - "672 [COULD NOT PARSE] \n", - "673 [\\nThe list of genes provided encode transcription factors associated with early development of embryonic stem cells.\\nMechanism: Transcriptional regulation via these transcription factors control the expression of other genes related to embryogenesis and stem cell development.\\n] \n", - "674 [\\nSummary: This term enrichment test on the list of human genes shows enrichment for terms related to extracellular matrix organization and cell adhesion, morphogenesis and morphological changes, and cell signaling. \\nMechanism: The underlying biological mechanisms may involve a combination of protein-protein interactions, transcriptional regulation and extracellular matrix modifications.\\n] \n", - "675 [COULD NOT PARSE] \n", - "676 [\\nSummary: The list of genes are involved in morphogenesis, development, transcription regulation, cellular signalling and ion transport.\\nMechanism: The genes are likely to be involved in a variety of biochemical and molecular pathways pertaining to the specified functions.\\n] \n", - "677 [ These genes are primarily involved in development and signaling pathways, particularly morphogenesis, neuronal growth, and neuronal system development. Mechanism: These genes facilitate cell-cell communication and signaling, allowing for cells to coordinate their functions together and form efficiently organized tissues and organs. ] \n", - "678 [COULD NOT PARSE] \n", - "679 [ The genes listed were significantly over-represented for processes related to muscle formation and human body structure, such as muscle and skeletal development, skeletogenesis, and myogenesis. \\n\\nMechanism: The set of genes is involved in multiple pathways related to muscle formation and structure in the human body, such as muscle and skeletal development, skeletogenesis, and myogenesis. These pathways likely involve the regulation of protein synthesis and biosynthesis, as well as processes related to muscle contraction and relaxation. \\n\\n] \n", - "680 [ These genes are involved in signaling pathways, vesicle/lipid trafficking, and cellular adhesion related processes.\\nMechanism: These genes act as regulators of nutrients, cell metabolism, and cytoskeletal organization. They are also involved in endocytosis, exocytosis, and the regulation of intercellular adhesion and motility.\\n] \n", - "681 [\\nSummary: The genes in this list are associated with processes related to membrane trafficking, receptor signaling, protein proteolysis, and lipid metabolism. \\nMechanism: The underlying biological mechanism is likely regulation of membrane trafficking, receptor signaling, protein proteolysis, and lipid metabolism. \\n] \n", - "682 [ An analysis of gene functions in these 10 genes shows an enrichment of terms associated with metabolism, including glycolysis, aerobic glycolysis, and gluconeogenesis.\\n\\nMechanism: This suggests a possible underlying biological mechanism in which glycolysis and gluconeogenesis pathways are deployed by cells in order to provide sufficient energy to cope with various metabolic demands.\\n\\n] \n", - "683 [ The human genes provided in this list are enriched for metabolic functions involved in glycolysis and pentose phosphate pathways.\\nMechanism: The mechanism likely involves the direct or indirect control of enzymatic activities through the coordinated activity of multiple genes.\\n] \n", - "684 [COULD NOT PARSE] \n", - "685 [COULD NOT PARSE] \n", - "686 [\\n \\nSummary: The genes in this list are involved in various aspects of biological processes, ranging from cell growth and development to immune response and proteolysis.\\n \\nMechanism: The genes interact in multiple overlapping pathways to influence cellular processes such as immune response and protein degradation. \\n \\n] \n", - "687 [ Several pathways related to cellular signaling and signalling transduction are enriched among this set of human genes. Specifically, phosphatidylinositol signalling, vascular endothelial growth factor receptor signalling, progesterone-mediated oocyte maturation, NF-kB signaling and neuroprotection are all enriched with five or more genes represented in the set, suggesting that the underlying biological mechanism could be related to these pathways.\\n\\nMechanism: Several pathways related to cellular signaling and signalling transduction.\\n\\n] \n", - "688 [ These human genes are involved in cellular functions related to glycosaminoglycan metabolism, lysosomal and catabolic pathways, as well as digit and skeletal development. The genes are enriched for functions in carbohydrate digestion and absorption; glycosaminoglycan and glycan metabolism; lysosomal, peroxisomal, and catabolic processes; and digit, skeletal, and limb morphogenesis. \\nMechanism: The genes likely act by providing enzymes, carriers, and structural proteins that together play essential roles in the transport and metabolism of carbohydrates, as well as help form and shape the skeleton and digits during embryonic development. \\n] \n", - "689 [ The human genes in this list are mostly related to glycoside hydrolase (GH) activity, but also include proteins involved in chitin and mucin biosynthesis, as well as cysteine protease and lysosomal activities. Most of the genes have either a glycoside hydrolase activator or a lysosomal enzyme function. \\n] \n", - "690 [COULD NOT PARSE] \n", - "691 [\\nSummary: These genes are mainly involved in Immunoglobulin Function and Blood Coagulation. \\nMechanism: The terms enriched for these genes are related to the immune system and blood clotting pathways, specifically those related to Immunoglobulins, B Cell Receptors, and Fibrinogen-related proteins. \\n] \n", - "692 [ \\nSummary: Genes involved in DNA damage repair and meiotic recombination processes\\nMechanism: Genes in the list are involved in DNA damage recognition, DNA double-strand break repair, meiotic recombination, and chromosome segregation.\\n] \n", - "693 [ Enrichment test revealed that genes are related to DNA repair, replication, and splicing.\\n\\nMechanism: The commonalities in the function of the genes revealed in the enrichment test suggest that there may be a biological pathway that is responsible for creating and maintaining a stable genetic system. This may involve DNA repair to combat mutation and damage, replication to create new copies, and splicing for the proper expression of genes.\\n\\n] \n", - "694 [ This enrichment test indicates that the listed genes are involved in multiple pathways that are involved in cell proliferation, apoptosis, and molecular transport in diverse cell types. Specifically, some of the enriched terms associated with these genes include mechanisms involved in cell cycle checkpoints, cell adhesion/motility complexes, transcriptional complexes, protein modifications, and RNA processing complexes. \\nMechanism: These pathways likely affect cell proliferation, apoptosis, and molecular transport by responding to a variety of environmental stimuli, including calcium-based signaling, growth factor-mediated signaling, and oxidative stress. \\n] \n", - "695 [ The analysed genes are mostly involved in calcium binding, apoptotic regulation, and immune modulation, all of which are important mechanisms for a variety of biologic processes.\\n\\nMechanism: The mechanism is likely related to the genes' ability to modulate calcium and apoptotic pathways as well as reduce oxidative stress and influence immune effectors.\\n\\n] \n", - "696 [COULD NOT PARSE] \n", - "697 [ Analysis of the genes provided shows that the genes are enriched for functions relating to energy production and metabolism, protein biosynthesis and folds, cell regulation, growth and development, and protein turnover. \\n\\nMechanism: The likely underlying biological mechanism behind these functions is likely related to the regulation, management and production of energy and metabolites to carry out processes such as cell growth and to synthesize proteins which are essential for the functioning of the cell, cell signaling and related pathway activities.\\n\\n] \n", - "698 [ PEX proteins are involved in peroxisome biogenesis and formation. \\nMechanism: PEX proteins play a role in driving the biogenesis of peroxisomes, a type of organelle that plays a role in various metabolic functions. \\n] \n", - "699 [ The provided genes are all peroxisomal biogenesis factor genes and are associated with peroxisomal biogenesis, protein transport, and oxidative damage resistance.\\n\\nMechanism: These factors regulate the assembly of the peroxisome, a subcellular organelle involved in fatty acid metabolism, carbohydrate metabolism, and oxidative damage resistance.\\n\\n] \n", - "700 [ The genes in this list are all associated with a cellular carboxyl-methyl transferases, a type of protein involved in RNA and DNA metabolism. The proteins are associated with development and growth, particularly that of cell structural elements such as gene transcription and transcriptional regulation. \\nMechanism: The mechanism involves carboxyl-methyl transferase proteins that modulate gene expression and the communication between transcription factors and the DNA strand.\\n] \n", - "701 [ These genes are involved in a number of processes related to DNA replication and repair, including DNA replication and repair, nucleosome assembly, telomere maintenance, and transcriptional regulation.\\n \\nMechanism: Genes LMNA, WRN, and BANF1 are all involved in several mechanism related to the general processes of DNA replication, repair, and transcriptional regulation through the assembly and maintenance of the different levels of chromatin structure. LMNA is involved in the assembly and disassembly of the nuclear lamina, a type of intermediate filament that helps to anchor chromosomal proteins to the nuclear envelope. WRN is involved in telomere maintenance, which is critical for accurate chromosomal replication and stability. Finally, BANF1 is involved in a number of DNA repair processes, including translesion DNA synthesis, homologous recombination, and non-homologous end joining. These processes are essential for the accurate repair and replication of DNA molecules, and all require an understanding of, and proper interactions between, transcription and chromatin structure. \\n\\n] \n", - "702 [\\n\\nSummary: This term enrichment test identified genes involved in signal transduction, ion transport, and regulation of neurotransmitter release.\\nMechanism: This is likely related to the regulation of excitatory and inhibitory signal transmission, potentially mediated by ion channels and signal transduction pathways associated with the G-protein coupled receptors, voltage-gated K+ and Na+ channels, and ligand-gated ion channels.\\n] \n", - "703 [COULD NOT PARSE] \n", - "704 [ This list of genes is related to muscle, central and peripheral nervous system development, as well as protein and lipid transport and metabolism. \\nMechanism: The genes appear to be involved in regulatory pathways for growth and development of the skeletal and nervous systems via coordination of morphology, protein and lipid synthesis, and transport.\\n] \n", - "705 [\\n\\nSummary: Analysis of the genes yielded significant enrichment of terms related to protein transport, development of the central nervous system, skeletal structure and muscle formation.\\n\\nMechanism: The function of these genes likely reflects the underlying biological pathways for the development and maintenance of different organ systems, including the central nervous system, muscular system, and skeletal structure. \\n\\n] \n", - "706 [ This list of genes is enriched for terms related to signal transmission and transduction, specifically the G Protein-Coupled Receptor (GPCR) family, which is associated with cell-signaling pathways and regulation of receptor activities. The specific terms enriched include G alpha subunit signaling, related GPCR activation and signaling, G Protein-Coupled Receptor (GPCR) function, and dimerization. \\n\\nMechanism: This set of genes is involved in pathways that involve the G protein-coupled receptor (GPCR) family. GPCRs can bind to extracellular molecules, such as hormones and neurotransmitters, and then activate signaling pathways inside the cell, leading to the activation of intracellular proteins, including G proteins. The G proteins then facilitate the exchange of proteins such as cAMP, DAG, and calcium ions into the cell, in order to create a signal cascade and ultimately effect changes to the cell’s behavior.\\n\\n] \n", - "707 [\\nSummary: The list of genes is involved in the regulation cellular signaling and development of the nervous system.\\nMechanism: The list of genes is likely transmitting signals through G proteins, phosphorylation cascade, and calcium signaling pathways to regulate the development of the nervous system, including alterations in the nervous system structure, indoleamine metabolism, and neurotransmission.\\n] \n", - "708 [ The gene list includes members of the nuclear receptor superfamily, molecules involved in transcription regulation, epigenetic regulation, cell cycle regulation, DNA binding and chromatin remodeling, developmental processes and cell signaling pathways, and components of the nuclear lamina and nuclear matrix.\\n\\nMechanism: The enriched terms suggest a molecular pathway underlying gene regulation, where transcription factors and chromatin reorganization molecules interact with nuclear receptors and other molecular mechanisms in order to regulate gene expression. Moreover, the gene list may represent a mechanism involved in the regulation of cell growth, differentiation and development.\\n\\n] \n", - "709 [ The genes provided are involved in developmental pathways and functions, such as transcriptional regulation, chromatin modification, morphogenesis, cardiovascular development and differentiation.\\nMechanism: These genes are associated with a wide range of cellular processes, primarily related to embryonic development, including fetal growth and development, stem cell differentiation, and postnatal growth. \\n] \n", - "710 [ These genes are mostly involved in collagen metabolic processes and extracellular matrix organization (ECM) - processes mediated by metalloendopeptidase activity, chondroitin sulfate biosynthesis, and galactosyltransferase activity, as well as by platelet derived growth factor, calcium ion, and zinc ion binding activities. Genes which affect ECM organization and/or collagen metabolic processes are implicated in symptoms of Ehlers-Danlos Syndrome.\\n\\nMechanism: The mechanism for these metabolic processes and ECM organization is likely to include the generation of specific proteins, peptides, and/or peptide modifications which affect the activity, binding, and/or interactions of collagen molecules and potential substrates of collagen.\\n\\n] \n", - "711 [ These human genes enable functions related to collagen fibril organization, extracellular matrix organization, collagen biosynthetic processes, glycosaminoglycan biosynthetic processes, peptidyl-prolyl cis-trans isomerase activity, epidermal cell differentiation, and wound healing.\\n\\nMechanism: The genes involved likely work towards a common mechanism involving the integration of extracellular matrix and collagen assembly and remodeling, as well as supporting cellular processes such as wound healing, epidermal cell differentiation, and collagen fibril organization.\\n\\n] \n", - "712 [COULD NOT PARSE] \n", - "713 [COULD NOT PARSE] \n", - "714 [ The genes listed are enriched for functions related to protein binding, protein homodimerization, ATP binding, and DNA binding activities, as well as functions related to enzyme and receptor activities, GTPase and phosphorylation activities, and metal ion and lipid bindings.\\n\\nAdditionally, several of the genes are enriched for functions related to metabolic processes, including NADH dehydrogenase and glycerophosphocholine O-acyltransferase activities, as well as carboxylic ester hydrolase, aldehyde dehydrogenase, ubiquitin protein ligase, and 2'-3'-cyclic GMP-AMP binding activities.\\n\\nMechanism:The proteins encoded by these genes are likely involved in a variety of biological processes, such as processes related to metabolism, signaling, and cell regulation, which requires their involvement in protein-protein or protein-DNA interactions, as well as protein homodimerization, ATP binding, and chemical and lipid bindings. The proteins also likely participate in various enzyme activities, such as cyclic GMP-AMP binding and GTPase activities. \\n\\n] \n", - "715 [ Processes related to protein function, binding, regulation, transportation, metabolism, and receptor activity are enriched in this list of genes, as evidenced by the high frequency of activities such as protein homodimerization, enzyme binding, ATPase activity, and receptor binding. The underlying biological mechanism likely involves a complex network of proteins that interact with and regulate each other for a variety of cellular processes. \\n] \n", - "716 [ This list of genes, describe a variety of functions related to cellular communication, regulation, and response. This includes binding, receptor activity, signaling, enzyme and protein binding activity, transcription, cytokines activity, chemical and peptide binding, as well as receptor and protein complex binding activity.\\n\\nMechanism: These genes likely serve as part of a complex molecular network involved in regulating immune responses and regulating other cellular functions. The enriched terms indicate that these genes play a role in various stages of the communication process including receptor binding, signaling, and transcription, as well as other functions such as chemical and peptide binding.\\n\\n] \n", - "717 [ \\nThe list of genes show enrichment for terms related to binding activity (enzyme binding, RNA-binding, protein binding, chemokine receptor binding, DNA-binding), protein kinase binding (protein serine/threonine/tyrosine kinase), and cytokine activity (growth factor activity, interleukin binding, etc).\\n\\nMechanism: These genes are involved in various cellular pathways involving binding and signaling. The binding activity of these genes can lead to the formation of enzyme-substrate/protein-protein complex which is necessary for a variety of physiological processes. The cytokine activity of these genes are likely to involve their roles in regulating cellular growth, differentiation, and the physiological responses to external stimuli.\\n\\n] \n", - "718 [ The list of human genes demonstrated a significant enrichment of terms related to binding activities and activities involving enzymes, as well as some terms related to cell differentiation and cell cycle progression, suggesting that these genes are involved in diverse cellular processes such as transduction and transition of signals, physiological activities, and structural peptide modifications.\\n\\nMechanism: This list of human genes likely contribute to cellular events by participating in interactions with other molecules such as DNA or proteins, and by catalyzing biochemical modifications.\\n\\n] \n", - "719 [ This gene list provides evidence for the involvement of a variety of protein activities, including binding, kinase activity, transcription, receptor activity, and enzymatic activities, in a variety of metabolic, signaling, and structural processes. The mechanism underlying these processes is likely the regulation of various cellular proteins and pathways, such as phosphorylation, cyclin-dependent protein kinase activity, DNA binding and transcription, and postsynaptic organization.\\n\\nMechanism: Regulation of various cellular proteins and pathways, such as phosphorylation, cyclin-dependent protein kinase activity, DNA binding and transcription, and postsynaptic organization.\\n\\n] \n", - "720 [\\nThe list of genes is enriched with functions related to the extracellular matrix and cell-cell/cell-matrix adhesion. These functions include extracellular matrix structural constituent conferring compression resistance, collagen binding activity, integrin binding activity, molecular adaptor activity, identical protein binding activity, fibronectin binding activity, protein dimerization activity, heparan sulfate proteoglycan binding activity, cell-matrix adhesion, and regulation of cell-substrate adhesion. \\nMechanism: The underlying biological mechanism is focused on processes related to extracellular matrix organization, cell-matrix/cell-cell adhesion, and modulation of signaling pathways involved in development, immune response and homeostasis. \\n] \n", - "721 [\\nThis term enrichment test reveals that a majority of these genes are involved in cellular processes such as protein binding activity, signaling receptor binding activity, phospholipid binding activity, positive regulation of intracellular signal transduction, protease binding activity, and positive regulation of macromolecule metabolic process. A majority of these genes are also part of several cellular components, such as chromatin, the plasma membrane, the Golgi apparatus, the endoplasmic reticulum-Golgi intermediate compartment, and the extracellular matrix. \\n\\nMechanism:\\nThe enriched terms indicate that the genes are likely in involved in a variety of transmembrane and extracellular transport processes and in processes related to cellular signaling and metabolism. One possible underlying mechanism is that the genes interact with specific proteins and receptors to alter the phosphorylation of target proteins and regulate the downstream activities, such as the formation of the complex cellular structures and the metabolic activities of cells.\\n\\n] \n", - "722 [ The list of genes functions is found to be significantly enriched in the following terms: cell-cell adhesion, agonist binding activity, cytoplasmic matrix binding, protein homodimerization and signaling receptor binding, which are involved in cellular adhesive processes and signal transduction. \\nMechanism: The functions of these genes likely work in concert to mediate multiple adhesive processes, as well as signal transduction pathways. \\n] \n", - "723 [ The list of genes are associated with a variety of functions, including binding activities (i.e. ion binding, cell adhesion molecule binding, identical protein binding, signaling receptor binding, etc.), catalytic activities (i.e. ATPase activity, GTPase activity, acetyl CoA oxidase activity, nucleotide-exchange activity, etc.), involvement in processes (i.e. T cell activation, cell-matrix adhesion, cell-cell adhesion, extracellular matrix formation, etc.), and structural roles (i.e. extracellular matrix structuring, ankyrin binding, etc.). The enriched terms associated with this set of genes are binding activities, catalytic activities, involvement in biological processes, and structural roles. \\n\\nMechanism: Most of the genes in the list are associated with catalytic activities that, when taken together, provide insights into the underlying biological mechanisms and pathways. These functionalities lead to different types of cell-cell and cell-matrix adhesion, structuring of extracellular matrix, signaling pathways, and many other cellular activities.\\n\\n] \n", - "724 [ \\n\\nSummary: The genes listed support a wide range of processes, including membrane and protein organization, protein modification and transport, endocytosis, signal transduction, and apoptosis. \\n\\nMechanism: These genes act at many levels, but the overall result is to help regulate the organization and modifications of protein structures and the movement of proteins (in trafficking and transport) across the membrane.\\n\\n] \n", - "725 [ The list of gene descriptions is related to pathways and processes related to cellular adhesion; protein folding and regulation; cytoplasmic ion homeostasis; and regulation of gene expression. The enriched terms that underlie all the genes and their functions include cell adhesion, protein folding and regulation, ion homeostasis, and gene expression regulation.\\n\\nMechanism: Cell adhesion and protein folding are essential processes that enable cells to interact with the extracellular environment and to form and maintain a functional structure. These processes are regulated by cell surface receptors that transmit signals to the cell and regulate gene expression, involved in the regulation of multiple cellular pathways. Ion homeostasis is also an important process, wherein cells maintain adequate balance of various ions in the cytoplasm and regulate various functions, such as cell differentiation, proliferation, and metabolism. Lastly, gene expression is regulated by a variety of transcription factors and signaling pathways, allowing cells to respond to external stimuli and adapt to changes in the cellular environment.\\n\\n] \n", - "726 [\\nSummary: This list of human genes is involved in numerous functions, including enzyme, protein and nucleic acid binding activities, transcription factor, cysteine-type endopeptidase and calcium ion binding activities, oxidation and NAD+ binding activities, among others.\\nThe enriched terms are DNA binding activity; protein binding activity; enzyme binding activity; cysteine-type endopeptidase activity; identical protein binding activity; signaling receptor binding activity; calcium ion binding activity; protein kinase binding activity; transcription factor activity; and BH3 domain binding activity. \\nMechanism: The underlying biological mechanism is likely related to the regulation of various cellular processes, including DNA replication, transcription, apoptosis and cell adhesion. \\n] \n", - "727 [ The genes listed are primarily involved in apoptosis, cell signaling pathways, the response to UV, and immunological processes. Furthermore, the enriched terms found include calcium ion binding activity, protein binding activity, and identical protein binding activity.\\n\\nMechanism: These genes are likely involved in a variety of pathways, such as apoptosis, cell signaling, cellular response to UV, and immunological processes. Specifically, their activity is likely to be regulated by calcium ions, binding to specific proteins, as well as other molecules or chemical compounds. It is also possible that some of these genes are involved in regulating the transcription of certain genes.\\n\\n] \n", - "728 [\\n\\n\\nSummary: Genes in this list are primarily involved in metabolic and transporter activities, signaling activities, and protein binding activities.\\n\\nMechanism: The genes primarily have roles in transferring small molecules across membrane boundaries, binding small molecules, and regulating processes such as metabolism and protein interactions.\\n\\n] \n", - "729 [ \\nSummary: The listed genes are part of various metabolic pathways, involved in a variety of functions, including DNA binding, ATP hydrolysis, protein homodimerization, peptidase activity, and other enzyme binding and regulatory activities. \\nMechanism: Enzymatic activity and protein binding are key components of the pathways involved, which help to catalyze, catalyze and regulate further metabolic activity. \\n] \n", - "730 [ \\nSummary: This term enrichment test reveals an overlap of gene functions related to lipid metabolism, cholesterol homeostasis, and protein regulation.\\nMechanism: The terms enriched suggest that these genes help to maintain proper levels of cholesterol, regulate lipid metabolism and synthesis, and regulate protein expression, localization, and response. \\n] \n", - "731 [\\n\\nSummary: This list includes genes that are involved in cholesterol biosynthesis, regarding protein binding, transcription, regulation of gene expression, and other biochemical processes. \\n\\nMechanism: These genes are mainly involved in cholesterol homeostasis, transcription and regulation of gene expression, and other essential biochemical processes.\\n\\n] \n", - "732 [COULD NOT PARSE] \n", - "733 [ The statistically over-representeted gene functions common to this list of genes have to do with protein and domain binding, domain specific and disordered domain specific binding, enzyme and peptidase activity, and cytokine and signalling receptor binding. Key processes that seem to involve this gene set are cell adhesion, proteolysis, regulation of blood coagulation, response to iron and UV-A, and the regulation of cell adhesion mediated by integrin. \\nMechanism: Some of these genes may be involved in the same biological pathways, such as pathways for protein homooligomerization, enzyme/peptidase activity, proteoglycan/fibrinogen binding, heme binding, and domain specific binding activity.\\n] \n", - "734 [COULD NOT PARSE] \n", - "735 [ These genes are primarily involved in binding activities and regulation of molecular functions related to cell signalling, such as enzyme binding, deubiquitinase activity, cysteine-type endopeptidase activity, receptor binding, protein kinase binding, SH2 domain binding activity, phosphatidylinositol phospholipase C activity, GTPase activity, and metalloendopeptidase activity.\\n\\nMechanism: The proteins encoded by these genes are involved in the regulation of cell signalling pathways, including those related to apoptosis, interleukin-6, growth factor activity, receptor binding, phospholipid binding, and transcription activator activity.\\n\\n] \n", - "736 [COULD NOT PARSE\\nHypothesis: The underlying biological mechanism of these genes is likely related to transcription regulation of gene expression, including DNA binding and DNA polymerase activity, as well as the formation of protein dimers needed for transcription.] \n", - "737 [\\nSummary: The list of genes are involved in a diverse range of functions, including DNA binding activities, ATP activities, RNA binding activities, transcription activities, enzyme binding activities, and protein homodimerization activities.\\nCommonalities in function include DNA binding activities, RNA binding activities, transcription activities, enzyme binding activities and protein homodimerization activities.\\nMechanism: These commonalities of function reflect the various roles in nucleic acid metabolism and structural transactions related to transcription and replication in the cell.\\n] \n", - "738 [ Genes in this list are predominantly related to functions involved in the cell cycle, including DNA replication, transcriptional and post-transcriptional regulation, chromatin binding, and mitosis. A number of the genes are also associated with processes related to nuclear transport and pore complex assembly.\\n\\nMechanism: This cluster of genes is likely related to multiple biological mechanisms involved in cell cycle progression, including DNA replication and transcriptional regulation, chromatin binding and modification, RNA processing and stability, nuclear transport, and mitosis.\\n\\n] \n", - "739 [\\nSummary: This list of genes enables various functions in regards to DNA binding, protein binding, histone binding, ATP and enzyme binding, as well as DNA replication, DNA methylation and regulation of chromosome segregation.\\nMechanism: These genes allow for the regulation of several processes essential for cell growth, transcription, and regulation through binding of and interaction with various molecules.\\n] \n", - "740 [\\nSummary: There are a number of genes with functions related to extracellular matrix structural components, cellular adhesion and protein binding.\\nMechanism: The range of genes suggests that these functions are related to various pathways that involve receptor and ligand interactions, protein domain binding activities, signaling processes and the structural components of the extracellular matrix.\\n] \n", - "741 [\\nSummary: The list of genes are involved in a variety of cell and matrix structural activities, including binding activities, metal binding and metal ion binding, enzyme activities, receptors and chemokine activities, as well as DNA-binding and transcription activities.\\n\\nMechanism: The genes in the list work together synergistically to mediate essential cell processes such as cell adhesion, growth, communication, and cell-matrix interaction.\\n\\n] \n", - "742 [ Genes involved in this list generally enable binding, transport, enzyme, and adhesion activities, and are involved in process such as intracellular signaling, transcription, and neuronal development.\\n\\nMechanism: These genes are involved in multiple pathways that involve the binding, transport, and regulation of signals related to cellular physiology, growth, and development.\\n\\n] \n", - "743 [ Our term enrichment test analysis has identified that these human genes are mainly involved in binding activities, including DNA binding, ATPase binding, and protein binding, as well as various enzymatic activities, such as phosphatase activity, dehydrogenase activity, and adenylate cyclase activity. Additionally, the genes are related to transmembrane transport, transcriptional regulation, cell adhesion, and apoptosis. \\n\\nMechanism: This term enrichment test identified several biological functions and activities related to DNA and protein binding, transcriptional regulation, transport, and apoptosis, likely playing important roles in cellular processes and development.\\n\\n] \n", - "744 [\\nThis analysis of the given human gene list reveals a pattern of enrichment for molecules and processes associated with protein binding activities, DNA- and RNA-binding, domain binding, carbohydrates binding, and enzyme and ligand binding activities. In addition, several genes are predicted to be involved in transmembrane transport activities, sequencing and structural protein interactions, transcription factor activities, and cellular adhesion. Various proteins act as modulators of these activities, and cofactors, such as calcium ions, play important roles.\\n\\nMechanism: This set of genes are likely involved in a variety of protein-protein and DNA/RNA interactions, which are essential for regulation of gene expression and protein activity. The cell membrane acts as a barrier between different cellular environments, allowing the genes to mediate transport between the intracellular and extracellular compartments, as well as a platform for docking proteins to interact with ligands, such as hormones and growth factors. The set of genes likely form part of a larger interconnected protein-protein interactome and temporal regulatory pathways which regulate cell function.\\n\\n] \n", - "745 [ We have identified a large set of genes that are involved in a variety of processes, including binding, transcriptional regulation, transport, and enzymatic activities. These genes are enriched in the following terms: DNA-binding; transcription activator activity; protein binding; membrane transporter activity; hydrolase activity; phosphorylation; and ligand-mediated activities. \\n\\nMechanism: Many of these identified enriched terms suggest involvement in complex biochemical pathways in order to facilitate cell behavior and other processes in the body at a molecular level. This likely occurs through a combination of transcriptional regulation, binding of proteins and ligands, and enzymatic activities. \\n\\n] \n", - "746 [ \\nSummary: This list of genes is mainly involved in fatty acid, lipid, and carbohydrate metabolism, DNA binding, RNA binding, and protein homodimerization. \\nMechanism: The genes in this list work to regulate metabolic pathways, transcription and protein complexes.\\n] \n", - "747 [ This gene list contains enzymes involved in fatty acid and lipidmetabolism, metabolism of oxygenated and carbonated compounds, oxidoreduction, electron transfer, and DNA related activities such as DNA binding, DNA nuclease activity, RNA binding, and chromatin binding. \\nMechanism: These genes enable intra- and inter-cellular metabolic pathways and communication, as well as provide protective responses to external stimuli, by catalyzing the conversion of compounds and regulating DNA expression.\\nHypothesis: This set of activities suggest a mechanism of maintaining cellular homeostasis, which involves reactive oxygen species management, modifying hormonal, energy, and nutrient levels, and respoding to external stress.\\n] \n", - "748 [ The gene descriptions indicate that many of these genes are involved in DNA or transcription binding, binding of different molecules or materials (chromatin, metal ions, histone deacetylase, etc.), protein binding activities, enzyme binding activities, and GTPase activities.\\n\\nMechanism: These genes appear to be involved in a variety of cellular functions, including transcriptional regulation, DNA replication, DNA damage repair, protein modification, gene expression and cell cycle control. The common functions may be related to molecular pathways that regulate these activities. \\n\\n] \n", - "749 [\\n\\nSummary: over half of the genes in this list are involved in protein binding, DNA binding and/or transcription, and many others in activities related to or downstream of those activities.\\n\\nMechanism: The proteins encoded by these genes are likely involved in regulating gene expression at the molecular level, through interacting with DNA, proteins, and other elements involved in transcription.\\n\\n] \n", - "750 [ Human genes in the given list are involved in a variety of functions, including nucleic acid and proteic binding, metabolic activities such as phosphorylation and oxidation-reduction, carbohydrate metabolism, and various types of cytokine and growth factor activities. The underlying biological mechanism involves increased metabolic activity and physiological signalling pathways, leading to increased protein synthesis and activity, increased cell growth, migration, differentiation and repair.\\n\\n] \n", - "751 [ \\nSummary: This list of genes has functions related to metabolism, gene regulation, cell signalling, and protein binding activities.\\nMechanism: The list of genes are likely involved in pathways related to cell signalling, metabolism, intracellular communication, and gene regulation.\\n] \n", - "752 [ The genes highlighted in this list are largely involved in cellular organization and processes including cell adhesion, vascularization, neurotransmitter receptor internalization, signal transduction, and enzyme binding. Some of the genes, such as GFIA and SHH, are also involved in embryonic development and organogenesis. Common terms enriched from these genes include: cell adhesion; signal transduction; epithelial-mesenchymal interaction; receptor-mediated endocytosis; angiogenesis; and neural tube closure.\\n\\nMechanism: These genes largely interact with each other in a variety of ways to control crucial cellular pathways and processes in the body's tissues, organs, and systems. They interplay to control processes such as cell adhesion, vascularization, signal transduction, and enzyme binding. Some of the genes are involved in the formation and maintenance of the structures of the body's organs and tissues, while others are involved in developing the connections between cells and transmitting signals within them.\\n\\n] \n", - "753 [ \\n\\nSummary: This gene list encompasses genes involved in various functions and processes, including cell adhesion and migration, regulation of transcription and DNA-templated transcription, negative regulation of apoptosis, cell surface receptor-related activities, cell differentiation, angiogenesis, canonical Wnt signaling pathways, and protein phosphorylation.\\n\\nMechanism: This gene list likely indicates the presence of various pathways, including the NF-kB pathway, cytoskeletal reorganization and receptor signaling pathways, integrin and cell adhesion molecule signaling pathways, and the Wnt/PCP pathwayn and sonic hedgehog pathway.\\n\\n] \n", - "754 [ The majority of these human genes enable binding activity involving DNA and RNA, as well as being involved in the regulation of transcription and translation. Moreover, some genes are involved in the transport of substrates across the cell membrane. \\n\\nMechanism: The list of genes is indicative of various transcription-regulation mechanisms and membrane transport processes, including DNA packing, histone demethylation, transcription factor activity, and ion transport. \\n\\n] \n", - "755 [ \\n\\nSummary: The list of genes are related to many major and essential functions in the cell, ranging from transcription of DNA, binding to receptors, transportation of ions and other molecules, and overall regulation activities. \\nMechanism: The mechanism underlying this term enrichment is that numerous functions or activities require multiple pathways, proteins, and activities, thus having multiple target genes involved.\\n] \n", - "756 [\\nSummary: Several genes are involved in structural components, binding activities, and enzyme activities.\\nMechanism: Genes are associated with a variety of activities related to binding, activity functions, structural elements and enzyme regulation.\\n] \n", - "757 [\\n\\nSummary: The list of genes describes a wide range of molecular functions related to signaling, attachment, and metabolic pathways.\\n\\nMechanism: The underlying biological mechanism and pathways describe the various activities of these genes and how they are involved in cell metamorphosis, growth and development, and immunity and defense.\\n\\n] \n", - "758 [ The majority of the genes listed are associated with cell signaling, regulation and structural roles such as ligand binding, enzyme binding, and receptor binding, as well as associated functions such as DNA and RNA binding, protein dimerization, and transcription activity and regulation. \\n\\nMechanism: These genes are known to be involved in many different parts of the cellular functioning, including cell communication and receptor recognition and response, enzyme and ligand binding, DNA/RNA, and transcription. \\n\\n] \n", - "759 [ The analysis of the given list of genes reveals that they are primarily involved in binding activities, such as DNA-binding, receptor binding and ligand-activated transcription activities. Several genes are also involved in enzyme activity, such as proteases and kinases. All of the genes are involved in several processes, such as cellular and apoptotic responses, neuronal activity and tissue development. \\nMechanism: The binding activity of the genes may be involved in protein-protein interaction, signal transduction pathways, transcriptional control and modulation of protein stability. Enzyme activities are involved in the post-translational modifications of proteins, metabolic pathways and protein degradation.\\n\\n] \n", - "760 [\\nSeveral genes among the list are involved in receptor activity and binding activities related to cytokines, such as interleukin-1, interleukin-7, interleukin-9, interleukin-10, and interleukin-12 receptors, among others. Many of the genes are also involved in the binding of other molecules, such as growth factors, lipoproteins, peptides and proteins, as well as with kinase binding activities, and ATP and DNA-binding activities. In addition, several of the genes appear to be associated with immune responses, such as antimicrobial humoral immune response, defense response and cell surface receptor signaling pathway.\\n\\nMechanism: It is likely that many of the genes on the list serve as key mediators of receptor signaling pathways, as well as protein-protein and nucleic acid-protein interaction. These activities may be involved in the regulation of important cellular processes such as cell surface receptor signaling, immune response, apoptosis, and modulation of the activity of certain kinases.\\n\\n] \n", - "761 [ The genes identified in this list are involved in a variety of signaling activities, mainly cytokine receptor activity, CXCR chemokine receptor binding activity, and interleukin-binding activities. Furthermore, these genes are involved in processes such as defense response, negative regulation of macromolecule metabolic process, and positive regulation of protein metabolic process. \\n\\nMechanism: The genes are related to mechanisms that involve the recognition of extracellular ligands, such as cytokines, chemokines, growth factors, and antigen by the cell surface receptors in order to regulate and coordinate cell responses.\\n\\n] \n", - "762 [ The genes in the list are involved in a variety of activities, including binding activities of diverse ligands (e.g. ATP, G protein-coupled receptors, etc.), receptor activities (e.g. for interleukin and other cytokines), transcription activator activities, and presence in various cellular organelles (e.g. plasmic membrane, nucleus). Common terms such as protein binding activity, cytokine activity, G protein-coupled receptor activity, and DNA-binding transcription activity were found to be enriched.\\n\\nMechanism: The genes in this list are involved in several cell signaling pathways, including but not limited to, cytokine signaling, signal transduction, G protein-coupled receptors, and transcription factors.\\n\\n] \n", - "763 [\\n6 groups of functions were enriched - receptor activities, binding activities, enzyme activities, growth factor activities, molecule/ion transporters and transcription factor activities. \\nMechanism: These enriched terms point to pathways that are involved in cell growth, development, communication, and signal transduction. \\n] \n", - "764 [\\nThe list of genes includes those involved in processes such as defense response to other organism, response to virus, regulation of proteasomal ubiquitin-dependent protein catabolic process, and regulation of transcription. The commonalities in gene function include DNA-binding activity, RNA binding activity, metal ion binding activity, identical protein binding activity and protein homodimerization activity. These genes are enriched with terms such as \"signaling receptor binding activity,\" \"transcription coactivator activity,\" and \"regulation of transcription.\"\\n\\nMechanism: The underlying biological mechanism or pathway of these genes is related to processes like macrophage activation, innate and adaptive immune response, antiviral response, and transcriptional regulation. These genes are involved in signaling pathways related to specific pathogens or environmental cues, or the maintanance of normal gene expression. These processes are essential for the body to respond to environmental changes and maintain homeostasis. \\n\\n] \n", - "765 [ Cell-mediated immunity is indicated by the genes analyzed, which were found to involve in activities such as DNA-binding transcription activator activity; CCR chemokine receptor binding activity; cytokine activity; RNA-binding activity; and ubiquitin protein ligase activity. Several enriched terms were identified, including defense response to other organism; immune response; viral entry into host cell; ISG15-protein conjugation; antigen processing; and cytokine-mediated signaling pathway. \\nMechanism: The gene functions are likely to be involved in biological processes related to cell-mediated immunity, such as activation of macrophages and other cells of the immune system (T cells, natural killer cells), regulation of antigen processing and presentation and cytokine-mediated signaling pathways, and regulation of the immune and inflammatory responses.\\n] \n", - "766 [COULD NOT PARSE] \n", - "767 [ The genes listed in the summaries are mainly involved in functions related to binding activities, enzyme activities, transcription factor activities, protein activities, and signaling receptor activities. The data suggests that these genes play an important role in cellular pathways and processes such as cellular immune response, cytokine-mediated signaling, apoptotic signaling, DNA binding and transcription, and RNA binding and transcription. The commonalities in their function shared by most of these genes are binding activity; enzyme activity; protein activity; and transcription factor activity.\\n\\nMechanism: These genes are likely to be involved in various regulatory pathways regulating cellular functions. The binding activities associated with them suggest their role in ligand-receptor interactions and communication between cells, as well as their role in cell-to-cell signaling. Additionally, their enzyme and protein activities suggest that they are involved in enzymatic reactions, signaling cascades, and post-translational modifications such as histone acetylation that regulate gene expression. Lastly, their involvement in DNA binding and transcription, as well as RNA binding and transcription suggest their roles in controlling gene expression and the synthesis of key proteins in various cellular pathways.\\n\\n] \n", - "768 [\\nSummary: A number of genes have been studied, mostly involving functions related to protein activity, transcription, and regulation activity.\\nMechanism: These genes seem to act in concert with each other, involving protein binding activity and transmembrane activity, suggesting a potential for processes related to membrane-based signaling and receptor binding or trafficking.\\n] \n", - "769 [\\nThis list of genes is enriched for functions related to DNA-binding and transcription activities, calcium ion and ATP-binding activities, protein binding activities, and G-protein coupled receptor activities. Some of the genes are predicted to be involved in cellular processes such as transcription and cell death regulation, while others are known to take part in morphogenesis and hormone metabolism.\\n\\nMechanism: These genes, in concert, may help to regulate gene expression at the transcriptional level, modulate calcium-dependent processes such as cell death, initiate changes in cell shape and differentiation, and control the flow of information within the cell.\\n\\n] \n", - "770 [\\nThe list of genes suggests that they are involved in processes related to cell adhesion, protein binding activities, signal transduction, and transcriptional regulation, suggesting a connection to cell-matrix communication and signal transduction pathways. The enriched terms associated with the gene list include: cell adhesion molecule binding activity; ATPase coupled intramembrane transport; metalloendopeptidase activity; protein homodimerization activity; signal receptor binding activity; DNA-binding transcription factor activity; heparin binding activity; peptidase regulator activity; and GTPase activity. \\n\\nMechanism: The mechanistic hypothesis for the gene list is that these genes are involved in a cell-matrix communication and signal transduction pathway. This pathway may involve interactions between cell adhesion molecules, transmembrane protein transport, peptidases and GTPases enabling signal transfer between cells and their extracellular environment. \\n\\n] \n", - "771 [ \\nSummary: The list of genes is enriched for those involved in various biological functions such as structural proteins, cell adhesion, kinase activity, signal transduction, receptor binding, cytokine activity, DNA-binding transcription, and inorganic diphosphate transmembrane transport.\\n\\nMechanism: The underlying biological mechanisms for the enriched terms include cell-matrix adhesion and signal transduction pathways, protein homodimerization, cell-cell recognition and communication, cGMP-dependent pathway, and apoptosis regulation. \\n\\n] \n", - "772 [\\nSummary: The provided list of human genes are enriched for terms related to protein binding activities and activities related to the cytoskeleton.\\nMechanism: These proteins likely play a role in regulating cytoskeletal organization, cytoskeletal movement, and cellular signaling.\\n] \n", - "773 [ Enriched terms related to cytoskeleton and motor protein function, namely GTPase, ATPase, and binding activity of tubulins, microtubules, actin filaments, kinesin, dynein, and G protein-coupled receptor appear to be common among the presented genes.\\n\\nMechanism: Likely, these genes play a role in organizing and regulating the structure, dynamics, and shape of cells, as well as in the regulation of actin cytoskeleton and microtubule-dependent processes. This could suggest a role in important cellular functions such as cellular division, trafficking, and transport of organelles. The binding activity among these proteins may also be essential in communicating information and molecules between different areas of the cell. \\n\\n] \n", - "774 [ The gene list appears to be involved mainly in metabolic processes, such as enzyme binding and activity, acid binding, molecule transport, adapter and receptor binding and activity, and DNA and protein binding and activity. Hypothesis: The underlying biological mechanism for this set of genes is metabolic regulation, including the regulation of enzyme, protein, and DNA metabolism. ] \n", - "775 [\\nThe genes listed have functions related to the regulation of metabolism, actin filaments, DNA/RNA binding and transport, nuclear receptor binding, and ubiquitination. Many of the genes also have identical protein binding activities, as well as activity related to peptidase activity and enzymes.\\n\\nMechanism: The listed genes are involved in various metabolic pathways and play an important role in the regulation of cell structure and function. Many of the genes are involved in protein synthesis and processing, as well as proteins involved in DNA/RNA binding and transport, and cell signaling.\\n\\n] \n", - "776 [ This list of genes is involved in several processes related to protein folding, regulation, and binding activities such as DNA binding, RNA binding, and chromatin binding. It also suggests a potential role in the regulation of processes such as transcription, translation, and splicing.\\n\\nMechanism: This list of genes is involved in a variety of processes related to protein folding, regulation, and binding activities. The genes could be involved in different pathways which could be either converging or separate, but ultimately leading to the same outcome. For example, the genes could cooperate to enable chromatin binding or the regulation of transcription, translation, or splicing.\\n\\n] \n", - "777 [ Genes in this list are primarily involved in functions related to RNA binding and its regulation, such as RNA polymerase II transcription machinery binding activity, RNA stem-loop binding activity, mRNA 3' UTR binding activity, and mRNA regulatory element binding translation repressor activity. They are also involved in regulation of protein folding, DNA binding and regulation, ubiquitin protein ligase binding activity, and other protein domains specific binding activity. Hypothesis: The number of the genes in this list involved in the regulation of RNA binding functions suggests that the underlying biological mechanism is likely a complex regulatory process for various RNA-related activities.\\n\\n] \n", - "778 [\\nThe list of genes are involved primarily in processes related to transcription and RNA processing, such as regulation of gene expression, DNA-templated transcription, positive regulation of cell population proliferation, protein-DNA complex organization, and regulation of nucleobase-containing compound metabolic process. Included are proteins with functions related to nucleic acid binding activity, transcription corepressor activity, and RNA polymerase II-specific DNA-binding transcription factor binding activity. The underlying biological mechanism is likely related to the organization, modification and process of transcription or RNA activity in the cell. The enriched terms are transcription, DNA-templated transcription, positive regulation of cell population proliferation, protein-DNA complex organization, regulation of nucleobase-containing compound metabolic process, RNA binding activity, regulation of gene expression, rRNA processing, and transcriptional regulation. \\n \\nSummary: Involved primarily in processes related to transcription and RNA processing\\nMechanism: organization, modification, and processes of transcription or RNA activity\\n] \n", - "779 [\\nThe given human genes are primarily involved in RNA binding, protein binding, and DNA binding activities; they predominate in processes related to rRNA processing, protein metabolic activity, DNA-templated transcription and transcription regulatory region binding, as well as cell cycle processes, chromatin binding, and mitochondria regulation.\\n\\nMechanism:\\nMany of these genes are able to act as part of complexes that regulate various processes, such as the cyclin-dependent protein kinase holoenzyme complex, which is involved in G1/S transition of mitotic cell cycle and positive regulation of fibroblast proliferation, the mitochondrial prohibitin complex which is involved in regulating DNA-templated transcription, or the MLL1 complex involved in neural crest formation. The genes are also extensively involved in protein and RNA binding functions, enabling a wide range of different activities or processes.\\n\\n] \n", - "780 [ The list of genes is over-represented in several categories related to the cytoskeleton, extracellular matrix, protein binding, transmembrane transporters, and ion channels. These genes are likely involved in regulating cell structure and interactions as well as calcium and ion homeostasis.\\n\\nMechanism: This list of genes is likely involved in regulating cell structure and signalling through their roles in the cytoskeleton, extracellular matrix, protein binding, transmembrane transporters, and ion channels.\\n\\n] \n", - "781 [\\nSummary: This list of genes are enriched for activities related to calcium ion binding, cytochrome-c oxidase activity, DNA binding, ATP binding, actin binding, abnormal growth and development, protease binding, and structural constituents.\\nMechanism: The list of genes are likely involved in a variety of pathways related to growth, development, and signaling, including transcriptional and post-transcriptional control as well as cellular components of muscle cells and extracellular matrices. \\n] \n", - "782 [\\nSummary: A variety of genes implicated in a wide range of biological processes, with a focus on gene expression, signal transduction, and cell cycle control.\\nMechanism: The genes involved in this list are related to protein modification and regulatory processes, and involve diverse functions such as Notch binding activity, Wnt receptor activity, ubiquitin and histone protein ligase activities, and transcription coactivator activity.\\n] \n", - "783 [ Our data shows that these genes are generally involved in transcription, protein modification, ubiquitination and regulation processes, often related to signalling pathways and the Notch pathway in particular. Mechanism: The underlying mechanisms for the commonalities amongst these genes seems to involve the activation of protein and transcription pathways, such as Notch, SCF-dependent proteasomal ubiquitin-dependent protein catabolic process and Wnt. ] \n", - "784 [\\n\\nSummary: The genes listed are involved in several cellular processes and pathways, such as electron transfer, heme binding, and protein binding activities; oxidoreductase activity; ATPase activity and binding activity; molecular adaptor activities; acyl binding activities; and several other functions. \\n\\nMechanism: These genes are likely to be involved in various metabolic and enzymatic processes that occur in cell respiration and signal transduction.\\n\\n] \n", - "785 [ Our analysis of the gene descriptions reveal that their common functions are related to mitochondrial respiration, electron and proton transfer, and transport of ATP, indicating the presence of an underlying pathway of ATP generation in mitochondria.\\n] \n", - "786 [\\n\\nSummary: Genes appear to be involved in functions related to DNA-binding transcription activity, protein binding activity, and protein kinase binding activity. \\nMechanism: The genes are thought to be involved in pathways related to DNA transcription, protein-protein interactions, and cell signaling.\\n] \n", - "787 [\\nThe list of genes contains a variety of functions related to DNA, RNA, RNA polymerase, cell adhesion/signaling, metabolism, apoptotics, and morphogenesis. These functions indicate the list of genes to be involved in several biological processes, including gene expression and regulation, DNA damage repair, cell survival and death, metabolism, and cell morphogenesis. \\n\\nThe underlying biological mechanism can be hypothesised to be related to a variety of cellular processes such as transcription, chromatin remodelling, transcriptional regulation, and signal transduction, which are all essential processes for proper cell and tissue function. \\n\\n] \n", - "788 [ \\nSummary: This list of genes is primarily involved in regulation of cellular processes including cell migration, cellular senescence, cellular biosynthetic process, apoptotic process, detection of glucose, cell-cell adhesion, neuron migration, insulin secretion, and gastrointestinal processes, as well as involvement in multiple diseases such as diabetes, tuberculosis, malignant astrocytoma, and cancer (multiple). \\nMechanism: These genes are generally involved in control of transcription by RNA polymerase II, ATPase-coupled ion transport, protein kinase and peptidase activity, DNA binding activity, calcium-ion regulated exocytosis, and regulation of secretion by cell.\\n] \n", - "789 [ This list of genes appears to all be involved in various cellular functions in cellular components, most notably regulating transcription by RNA polymerase II, regulation of secretion by cells, regulation of cell-cell adhesion, regulation of actin filament polymerization, and detection of glucose. Many of these genes also appear to be associated with diabetes and/or cancer.\\n\\nMechanism: The genes in this list appear to be involved in many aspects of cellular functions, which are involved in a variety of underlying biological pathways. Specifically, these genes have putative roles in involvement of signal transduction, regulation of transcription and regulation of cell-cell adhesion, protein targeting to ER, regulation of long-term synaptic potentiation, regulation of actin filament polymerization, and detection of glucose.\\n\\n] \n", - "790 [ This list is comprised of genes involved in a wide variety of functions, including molecular binding activities, enzyme activities, transporter activities, and domain binding activities. All of these genes are involved in diverse metabolic processes, such as fatty acid metabolism, cholesterol metabolism, protein transport, and DNA and RNA metabolic processes, suggesting a complex set of interrelated pathways that are likely to be a part of a larger biological system. Enriched terms include: molecular binding activity; enzyme activity; transporter activity; domain binding activity; lipid transport; protein transport; DNA metabolic process; and RNA metabolic process.\\n\\nMechanism: This set of genes likely interacts in a complex system involving multiple pathways and activities that enable metabolic processes such as fatty acid metabolism, cholesterol metabolism, protein transport, and DNA and RNA metabolic processes. The mechanism can be visualized as a network of proteins that interact in various ways to enable these processes. At a higher level, these pathways may interact to regulate signaling pathways, cell growth, and replication.\\n\\n] \n", - "791 [COULD NOT PARSE] \n", - "792 [ The list of genes are found to be enriched for functions related to protein binding and kinase activities, signal sequence and receptor binding, cell cycle and apoptosis regulation, and signal transduction.\\n\\nMechanism: This enrichment suggests that these genes are involved in a variety of cellular processes that are associated with metabolism and signal transduction, such as cell cycle regulation, cell migration and differentiation, apoptosis, and signal cascade regulation. \\n\\n] \n", - "793 [COULD NOT PARSE] \n", - "794 [ The list of human genes is enriched for terms relating to membrane and vesicle trafficking, including protein binding activity, GTPase activity, GTP-dependent protein binding activity, SNARE binding activity, enzyme binding activity, protein kinase binding activity and clathrin binding activity.\\n\\nMechanism: The underlying mechanism is likely to involve the transport of proteins through the cellular membrane and vesicles along various pathways, such as endocytosis, retrograde transport, Golgi to plasma membrane transport, endoplasmic reticulum to Golgi vesicle-mediated transport, and protein targeting to lysosomes.\\n\\n] \n", - "795 [ The analysis of the list of genes reveals common functions associated with transport, binding, activity, and assembly. These functions are enriched across a broad range of processes, including protein transport, catabolic and metabolic processes, regulation of intracellular signal transduction, Golgi and cell surface organization, positive and negative regulation, and responses to stimuli. This suggests a complex network of pathways, activity and assembly at play in cellular process and interactions.\\n\\nMechanism: The mechanism of action suggested by the term enrichment test indicates a complex network of pathways, activities, and assemblies at the protein level, such as those indicated by functions like binding and activity, as well as assembly and transport. This suggests a broad range of processes that are at play in the regulation of a large variety of functions and responses in cells.\\n\\n] \n", - "796 [\\nThe genes identified provide a variety of functions that might generalize to protection from oxidative stress and detoxification, DNA/RNA binding and transcription, and maintaining cell-cell adhesion and organization of cellular components.\\n\\nMechanism: These functions are likely related to a broad overarching mechanism of defense from reactive oxygen species, maintenance to the structure and development of the organism, as well as mediating interactions between cells.\\n\\n] \n", - "797 [ These genes are primarily involved in mediating energy transfer and metabolism, responding to oxidative stress/environmental compounds, and modulating cell proliferation, apoptosis, and cell to cell adhesion. \\nMechanism: The proteins directly or indirectly regulate multiple biological pathways, including canonical glycolysis, citric Acid cycle, respiratory chain, DNA metabolism, transcriptional/protein translation processes, and lipid/amino acid metabolic processes via enzymatic activity, binding activity and membrane transporters. \\n] \n", - "798 [ The list of genes are found to be primarily involved in activities related to RNA binding, nucleosome binding, transcription and regulation, DNA binding, protein kinase activity, protein folding and chaperoning, metabolic regulation and ubiquitination.\\n\\nMechanism: The mechanisms by which these activities are enabled involve complex interactions between proteins, which act as signal transducers, modulators and effectors, resulting in the relevant activities being enabled and processes being modulated.\\n\\n] \n", - "799 [ These genes are involved in a range of activities, including enzyme binding, protein binding, ligand binding, calcium ion binding, nucleotide binding, transcription factor binding, DNA binding, GTP binding, hormone binding, ATP hydrolysis, protein kinase operation, RNA binding, enzyme activator activity, chaperone operation, chromatin binding, protein phosphatase binding, phosphatase inhibitor activity, peptidase activity, inorganic cation transmembrane transporter activity, and others.\\nMechanism: These genes likely play important roles in the formation and maintenance of cell structure, transcriptional regulation and signal transduction, protein folding and degradation, metabolic homeostasis, and other processes to maintain cell function.\\n] \n", - "800 [ We have evidence of enrichment for processes related to signal transduction, regulation of transcription, regulation of protein metabolism, regulation of macromolecule metabolism, regulation of cellular processes, interaction with transcription factors, and interaction with SMAD proteins.\\n\\nMechanism: The underlying biological mechanism for these processes is likely related to the activation or inhibition of various proteins and enzymes that interact with signaling pathways, transcription factors, or SMAD proteins. \\n\\n] \n", - "801 [ Gene functions associated with transduction and signal modification of biological and biochemical processes; as well as DNA binding transcription activity, protein modify/kinase/phosphatase activities, receptor/ligand binding activity and activity inhibitor activity which play a role in cellular morphogenesis, metabolism, and adaptation are enriched.\\n\\nMechanism: These gene functions are involved in multiple biological and biochemical processes, with particular involvement in transcriptional regulation, signal transduction, positive/negative regulation of regulatory pathways, regulation of metabolic and structural processes, regulation of gene expression, and regulation of transcriptional factors.\\n\\n] \n", - "802 [ The genes are involved in regulation of growth, development, and defense mechanisms, as evidenced by enrichments of terms including \"DNA binding transcription factor,\" \"signaling receptor binding,\" \"enzyme binding,\" \"cytokine receptor binding,\" \"growth factor,\" and \"transmembrane receptor.\" \\n\\nMechanism: These genes work in concert to regulate amino acid metabolism, transport, signaling, and other processes within cells, leading to growth, development, and defense mechanisms. \\n\\n] \n", - "803 [ \\nSummary: This list of genes are primarily involved in transcription activities, binding activities (e.g. DNA-binding, protein binding, signaling receptor binding, etc.), enzyme activities (e.g. GTPase, ATPase, protein kinase, etc.), cytokine activities, and also in cell adhesion, transport, and regulation processes. \\nMechanism: The underlying mechanism of these genes includes a variety of critical signaling pathways, including the NF-kB, MAPK, and JAK-STAT pathways, as well as several cellular and organismal developmental pathways. \\n] \n", - "804 [ The list of genes and their functions are related to the synthesis and processing of nucleic acids and proteins, including RNA binding, transcriptional regulation, protein and mRNA folding, mRNA degradation, and translation regulation.\\n\\nMechanism: The general underlying biological mechanism is related to the regulation of gene expression and the synthesis and processing of proteins and nucleic acids.\\n\\n] \n", - "805 [ The enriched terms from these human genes suggest a common theme related to methods for dealing with environmental stress, protein folding, and metabolism. Many of these genes are involved in activities such as ATP binding and hydrolysis, molecular adaptor activity, molecular function inhibitor activity, ubiquitin protein ligase binding activity, transcription regulator activity, translation factor activity, RNA binding, protein dimerization activity, DNA binding activity, enzyme binding activity, and SNARE binding activity.\\n\\nMechanism: The underlying biological mechanism suggested by these human genes is related to the body's ability to respond to environmental stress and maintain cellular homeostasis. This is accomplished through the involvement of various proteins and RNA molecules that regulate gene expression, protein folding, and metabolism. Additionally, many of these genes are involved in the cellular response to cytokines, suggesting an immune response component.\\n\\n] \n", - "806 [COULD NOT PARSE] \n", - "807 [ Expression, regulation and activation of various pathways, enzymes, receptors and factors involved in numerous cellular processes such as cell differentiation, cellular adhesion, development, exocytosis, hematopoiesis, inflammation and immunity, lipid metabolism, transcription, neural development, regulation and intercellular signaling. \\nMechanism: The expression, regulation and activation of multiple proteins involved in core cellular processes is accomplished by binding and interaction of multiple domains including but not limited to ATP-binding activity, PDZ domain binding, SMAD binding, calcium ion binding, Gap junction channel activity, cAMP-dependent protein kinase inhibitor activity, Phosphotyrosine resodue binding activity, GTPase activator activity, among other activities.\\nHypotheses: The various interactions of the proteins enable the expression of genetic material and regulation at the cellular level by transcription factor binding activity, cis-regulatory region sequence-specific DNA binding activity, DNA hydrolysis activity and other processes. This helps in coordinating different cellular components and signaling events for proper functioning and development of the organism.\\n] \n", - "808 [ This list of genes is enriched for functions related to protein binding, DNA binding, binding activity, receptor binding activity, and protein kinase activity. Hypothesis: This list of genes is likely involved in several pathways related to cell adhesion, signaling, and in particular, the regulation of gene expression. \\n\\nMechanism: This list of genes is involved in a variety of mechanisms related to protein-protein and protein-DNA interactions, as well as protein kinase activity, all of which contribute to cell adhesion, signaling, and the regulation of gene expression.\\n\\n] \n", - "809 [ This list of genes is predominantly involved in transductional and transcriptional regulatory mechanisms related to cellular processes, such as ion and water transport, signaling receptor activities, DNA/RNA binding and processing, protein ubiquitination, and enzyme activities. Specifically, we identify gene functions in GTP binding activity; DNA binding activity; transcriptional activator activity; protein kinase binding activity; endopeptidase activity; receptor binding activity; hydrolase activity; nucleotide and peptide transporter activity; ion and neurotransmitter channel activity; antioxidant activity; and ligase activity.\\n\\nMechanism: These gene functions are likely to be involved in a number of underlying transductional and transcriptional regulatory mechanisms related to cellular processes, including signal transduction, gene expression, protein catabolism, and membrane transport. These gene functions likely represent molecular signals allowing for rapid and short-term responses in physiological and neurological processes, such as cell membrane responses, sensory processing, and immunological responses, as well as slower and long-term responses, such as development and cell growth.\\n\\n] \n", - "810 [COULD NOT PARSE] \n", - "811 [ \\n\\nSummary: Multiple genes are involved in protein binding, transcription regulation, cell cycle regulation, signaling pathways, and response pathways. \\nMechanism: Multiple genes play a role in regulating the activities of transcription and signaling pathways which are vital to several biological processes.\\n] \n", - "812 [ The list of genes mostly involves genes that enable signaling receptor binding activity, protein kinase binding activity, and ubiquitin protein ligase activity. These genes are enriched in processes such as intracellular signal transduction, cytokine production, and gene expression. The underlying biological mechanism involves intercellular communication through signaling cascades leading to the regulation of gene expression. \\n\\nMechanism: Intercellular communication through signaling cascades leading to regulation of gene expression.\\n\\n] \n", - "813 [ This group of genes is involved in regulated cellular processes, including cell recognition, signal transduction, cell migration, and gene expression. The primary functions of these genes include binding activities (e.g. DNA-binding transcription factor activity, receptor ligand activity, identical protein binding activity, etc.), catalytic activities (e.g. histone deacetylase binding activity, phosphotyrosine residue binding activity, etc.), enzyme activity (e.g. indoleamine 2,3-dioxygenase activity, phosphodiesterase activity, etc.), and transporter activity (e.g. metal cation: proton antiporter activity).\\n\\nMechanism: These genes likely act, at least in part, through the modulation of signaling transduction pathways, such as the Wnt, Notch, JAK-STAT, and MAPK cascade, as well as cytokine- and growth factor-mediated pathways. These pathways play key roles in many cellular and developmental processes, including cell migration, proliferation, apoptotic processes, and stem cell differentiation.\\n\\n] \n", - "814 [\\n\\nSummary: Genes POU5F1, SOX2, KLF4, and MYC, are involved in various functions such as DNA-binding transcription repressor and activator activities, RNA polymerase II-specific, and nucleic acid binding activities. These genes are also implicated in the regulation of biosynthetic processes, signal transduction, gene expression, angiogenesis, protein-DNA complex organization, and cell population proliferation, and are associated with numerous cancers.\\n\\nMechanism: These genes have been implicated in the regulation of complex biological processes, such as signal transduction and gene expression, suggesting a potential role in transcriptional regulation.\\n\\n] \n", - "815 [ Human genes, KLF4, POU5F1, and SOX2, are involved in transforming DNA-binding transcription activator, repressor, and factor activities, respectively. They are commonly involved in processes like positive and negative regulation of gene expression, biosynthetic process, angiogenesis, BMP signaling pathway involved in heart induction, and canonical Wnt signaling pathway.\\n\\nMechanism: These genes work in association with transcription regulator complexes, which interact with DNA and RNA, influencing transcriptional programming and gene regulation.\\n\\n] \n", - "816 [ Genes involved in this list are involved in a wide range of activities, such as protein binding, lipoprotein lipase activator activity, phospholipid binding, protein dimerization, modulation of chemical synaptic transmission, integrin binding, collagen binding, heparin binding, signaling receptor binding, non-membrane spanning protein tyrosine kinase activity, peptidoglycan binding, GTPase activator activity, and more. The commonalities in these genes' functions point to roles in signaling pathways, extracellular matrix structure and function, cell-cell and cell-matrix adhesion, lipid metabolism, and defense response.\\n\\nMechanism: These genes are likely to be involved in a wide range of signaling pathways, particularly related to cell-cell and cell-matrix adhesion, as well as lipid metabolism, extracellular matrix structure, and defense response. These pathways result in a wide variety of physiological functions, from regulation of gene expression to regulation of BMP signaling, cell migration, and cell proliferation.\\n\\n] \n", - "817 [ \\nThe human gene summaries provided all involve functions related to signal transduction, cell adhesion and binding activities, extracellular matrix structural components, and mechanism related to cell proliferation, growth and differentiation. Specifically, the genes are involved in protein binding, ion binding, chemokine activity, growth factor binding, signal receptor binding, phosphatase binding, cell migration, membrane repolarization, signal transduction, regulation, and defense response to bacteria and other organisms. \\n\\nMechanism: These genes appear to be involved in multiple cellular pathways related to signal transduction and cell adhesion, as well as molecular interactions and processes such as protein phosphorylation. Specifically, it appears that the genes are involved in activating intracellular signalling events, regulating cell growth and proliferation, and mediating defense responses. \\n\\n] \n", - "818 [ \\nSummary: A list of genes that are enriched for terms related to calcium ion binding, double-stranded DNA-binding, cellular defense, and embryonic development processes.\\nMechanism: The genes in this list are likely involved in the processes of calcium binding, cell adhesion and migration, and transcriptional regulation, which may underpin the roles of these genes in embryonic development, neuronal and vascular tissue formation, and cellular defense. \\n] \n", - "819 [ Our term enrichment analysis of human gene functions reveals that these genes play a variety roles related to regulation, binding, activity, and transport-related activity. Specifically, the enriched terms include: metal ion binding activity; protein binding activity; RNA binding activity; phosphatase regulator activity; gap junction channel activity; protein homodimerization activity; calcium ion binding activity; GTPase activity; DNA binding activity; ubiquitin protein ligase activity; protein tyrosine phosphatase activity; and transcription corepressor activity.\\n\\nMechanism: These results suggest a mechanism for gene regulation and regulation of pathways at the cellular level, involving binding, transport-related activity, and kinase or phosphatase activities. The mechanisms may be involved in the formation of structural components or the regulation of gene expression in the cell. This may involve transcriptional, post-transcriptional, and post-translational control of gene expression. Additionally, the identified activities may be involved in signal transduction and cellular signaling. \\n\\n] \n", - "820 [\\n\\nSummary: The list of genes provided are involved in various functions and processes of muscle development and contraction. These functions and processes are related to skeletal muscle thin filament assembly, muscle contraction, muscle cell differentiation, actin nucleation, protein ubiquitination, and muscle organelle organization.\\n\\nMechanism: The underlying biological mechanism includes protein phosphorylation, calcium-dependent signaling pathways, gene regulation, and post-translational modifications.\\n\\n] \n", - "821 [ This list of genes is associated with a variety of functions related to muscle structure and contraction, such as actin and tropomyosin binding activities, protein phosphatase binding activity, troponin complex activities related to muscle contraction and regulation of muscle adaptation, protein polymerization, and muscle tissue morphogenesis. The underlying common mechanisms are related to muscle assembly, muscle contraction, and regulation of muscle adaptation.\\n\\nMechanism: Muscle assembly, muscle contraction, regulation of muscle adaptation\\n\\n] \n", - "822 [ \\nSummary: The genes involved in this list have functions related to protein signaling, protein phosphorylation, protein ubiquitination, protein transport, cell projection organization, endocytosis and receptor-mediated endocytosis, phosphatidylinositol binding, membrane raft polarization, and plasma membrane tubulation.\\n\\nMechanism: The genes in this list are involved in a variety of protein signaling and transport pathways that enable a wide range of functions such as cell projection organization, endocytosis and receptor-mediated endocytosis, phosphatidylinositol binding, membrane raft polarization, and plasma membrane tubulation.\\n\\n] \n", - "823 [ Summary: The genes listed are involved in functions such as cadherin binding activities, endocytosis, cholesterol homeostasis, GTP-dependent protein binding activity, protein ubiquitination, and lysophosphatidic acid binding activity. They are located in cellular components such as endoplasmic reticulum, Golgi apparatus, Basolateral plasma membrane, clathrin-coated pit, postsynaptic membrane and cytoplasm.\\nMechanism: The underlying biological mechanism involves endocytosis and regulating processes associated with cholesterol metabolism, protein ubiquitination and lysophosphatidic acid binding.\\n] \n", - "824 [ \\nSummary: The majority of the genes commonly enable enzymatic activities, often related to cellular metabolism and related pathways.\\nMechanism: Many of the genes enable the production of energy stores (ATP, fructose 6-phosphate, glyceraldehyde-3-phosphate, fructose 1,6-bisphosphate, triosephosphate, and phosphoglycerate) through regulation of several metabolic processes, such as glycolysis, carbohydrate phosphorylation, fructose 6-phosphate metabolic process, fructose 1,6-bisphosphate metabolic process, and phosphoglycerate kinetic. Additionally, two of the genes involved in transcription (PKM, GAPDH) suggest a role in gene expression. \\n] \n", - "825 [ \\nSummary: These genes are involved in a range of cellular processes related to energy metabolism, including glycolysis, phosphorylation and glucose transport.\\nMechanism: The genes encode proteins that catalyze biochemical reactions such as enzyme activities, ubiquitin ligase binding and protein homodimerization. \\n] \n", - "826 [\\nThis gene set is strongly enriched for genes involved in regulation of presynaptic cytosolic calcium ion concentration, membrane depolarization, regulation of glutamate receptor activity, regulation of neurotransmitter receptor activity, and regulation of phospholipid metabolism.\\nThe underlying biological mechanism or pathway could involve regulation of synaptic neurotransmitter release, intracellular phospholipid metabolism, and calcium ion homeostasis.\\n] \n", - "827 [ This list of genes is primarily involved in calcium transport and regulating calcium ion concentrations in the cytoplasm and plasma membrane. Enriched terms include: calcium transport; regulation of calcium ion concentration; G protein-coupled receptor signaling pathway; negative regulation of cell volume; regulation of nitric oxide metabolic process; regulation of glutamatergic synaptic transmission; regulation of postsynaptic neurotransmitter receptor activity; and membrane depolarization.\\n\\nMechanism: These genes are involved in the transfer and maintenance of calcium ion concentrations in the cell to facilitate cell signaling and communication. Calcium is regulated through a variety of channels, transporters, and receptors, with the most significant ones being glutamate receptors (NMDA, AMPA, and L-type), acetylcholine receptors, and G-protein coupled receptors (e.g. serotonin receptor). These channels and receptors are involved in regulating cellular processes such as membrane depolarization, transport of ions, and neurotransmitter binding. They also interact with other proteins involved in the regulation of calcium levels, such as NCS1, CACNG2, CACNG4, and CACNG8.\\n\\n] \n", - "828 [COULD NOT PARSE] \n", - "829 [ \\n\\nSummary: This list of genes are involved in a variety of biochemical processes, such as protein folding and chaperone activities, protein kinase binding and activator activities, and metal ion binding. They are also implicated in a variety of diseases, including Alzheimer's, Parkinson's, and cancer.\\n\\nMechanism: These genes are involved in a range of functional activities related to protein folding and chaperone activities, protein kinase binding and activator activities, and metal ion binding, which are all important for cellular biochemistry.\\n\\n] \n", - "830 [COULD NOT PARSE] \n", - "831 [ These genes are primarily involved in carbohydrate and lipid metabolism, as well as glycoprotein degradation, protein homodimerization, and hyaluronan/ glycosaminoglycan catabolism.\\n\\nMechanism: The metabolic pathways involved in this process include glycoprotein catabolism, glycosaminoglycan catabolism, heparan sulfate catabolism, glucoside catabolism, mannose trimming and protein deglycosylation.\\n\\n] \n", - "832 [ All the genes listed above are involved in immunoglobulin receptor binding activity. ] \n", - "833 [ \\n\\nSummary: This list of genes is mainly predicted to enable antigen binding activity and immunoglobulin receptor binding activity, and are predicted to be involved in several processes related to activation of the immune response and to defense response to other organisms. \\n\\nMechanism: Through the interaction of antigens with immunoglobulin receptors, these genes help to stimulate the immune response and activate immune cells, providing protection against pathogens and other foreign substances. \\n\\n] \n", - "834 [COULD NOT PARSE] \n", - "835 [ This list of genes appears to be related to meiosis, DNA binding activities, and processes involved in meiotic recombination, DNA metabolism, and double-strand break repair. The commonalities between the gene functions involve processes related to meiosis, DNA binding, DNA metabolism, homologous recombination, and telomere attachment. Additionally, these genes are located in various cellular components including the nucleus, chromatin, synaptonemal complex, chromosome, and cytoplasm.\\n\\nMechanism: The underlying biological mechanism likely involves a network of complex interactions that control meiotic cell cycle transitions and processes related to DNA metabolism, binding, replication, and repair involving multiple cellular components during gametogenesis. \\n\\n] \n", - "836 [\\nSummary: We have identified 18 genes with related functions, such as calcium ion binding activity, protein sequestering activity, DNA-binding transcription factor activity, oxysterol-binding activity, and ubiquitin protein ligase binding activity.\\nMechanism: The enriched terms suggest that these genes are involved in processes related to calcium or ion transport, the regulation of the cell cycle and of protein phosphorylation, and intracellular signaling and responses to various external stimuli.\\n] \n", - "837 [\\nThis gene set is composed of genes involved in various cellular processes including protein binding, sequestering, transcription, metabolism and signaling pathways. Many are located in various cellular components such as the cytoplasm, endoplasmic reticulum and Golgi apparatus. There is a potential connection between these genes and multiple diseases, such as hemochromatosis type 5, Churg-Strauss syndrome and Huntington's disease-like 1.\\n\\nMechanism: These genes are part of a wide range of cellular activities and organelle functions, which could be part of the same underlying cell-wide mechanism. The presence of multiple proteins in the same cellular locales suggest an opportunity for protein-protein interaction and potentially a shared molecular mechanism.\\n\\n] \n", - "838 [ The gene list appears to be involved mainly in metabolic processes, such as enzyme binding and activity, acid binding, molecule transport, adapter and receptor binding and activity, and DNA and protein binding and activity. Hypothesis: The underlying biological mechanism for this set of genes is metabolic regulation, including the regulation of enzyme, protein, and DNA metabolism. ] \n", - "839 [\\nSummary: The following gene functions are significantly enriched in this list of human genes: cytoskeleton protein binding, phosphatase binding activity, oxidation-reduction activity, cell development and signaling activity, DNA binding activity, cellular transporter activity, and protein kinase binding activity.\\n\\nMechanism: The enriched gene functions are essential components of several processes related to cell growth, gene expression, cell differentiation, post-translational modification, and signal transduction.\\n\\n] \n", - "840 [ These genes are involved in peroxisome biogenesis, protein import into peroxisome and pexophagy. \\nMechanism: The genes act as peroxisome targeting sequence binding and ubiquitin-dependent protein binding, enabling fatty acid metabolic processes, protein homodimerization and enzyme binding activity. They are located in endoplasmic reticulum, nucleoplasm, Golgi apparatus and membrane and active in cytosol, peroxisome and peroxisomal matrix. \\n] \n", - "841 [ The gene functions provide evidence for a common pathway involved in protein import into peroxisomes, with other functions related to protein stabilization, regulation of cell population proliferation, protein-lipid binding, peroxisome organization, and fatty acid metabolism.\\n\\nMechanism: The identified mechanism involves a pathway of protein import into the peroxisome matrix, with further functions related to protein stabilization, ether lipid biosynthesis, protein-lipid binding, receptor recycling, and fatty acid metabolism. \\n\\n] \n", - "842 [ The list of human genes appear to be involved in processes related to post-translational protein modification, DNA folding and nuclear envelope attachment, as well as other processes associated with cellular response to stress, gene transcription, and gene expression. The enriched terms are DNA binding; protein binding; metal ion binding; cellular response to radiation, hypoxia and starvation; regulation of apoptotic process; regulation of telomere maintenance; regulation of protein ADP-ribosylation; and regulation of viral genome replication.\\n\\nMechanism: These genes may be involved in pathways that regulate several kinds of post-translational modification and gene expression patterns in response to environmental stressors. These pathways could include protein processing signals and transcription factors that regulate transcription and translation, as well as enzymes and proteins that control gene expression and DNA folding. In addition, these pathways may be involved in processes that enable cellular senescence and maintenance of DNA integrity. \\n\\n] \n", - "843 [ These three genes are all associated with DNA damage and repair responses and are located in the nucleus and surrounding cytoplasm. They all involve processes such as protein binding, metal ion binding, and homodimerization activities. Additionally, they have roles in apoptotic processes, cell senescence and response to hypoxia. The term \"DNA damage and repair\" is enriched, as represented by the three genes.\\n\\nMechanism: The genes LMNA, WRN, and BANF1 all act as checkpoints in the maintenance, modification and repair of DNA with regard to genetic information, telomeric regions and structure. They are responsible for the regulation of apoptotic processes, cell senescence and hypoxic responses, thus ensuring genetic integrity and stability.\\n\\n] \n", - "844 [\\nSummary: The list of human genes are involved in functions such as ligand-gated monoatomic ion channel activity, GABA receptor activity, glutamate receptor activity, voltage-gated potassium and sodium channel activity, adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway, gamma-aminobutyric acid signaling pathway, and neurotransmitter transport. \\nMechanism: These genes are likely to be involved in the signalling and transport of neurotransmitters across plasma membranes, including the regulation of presynaptic and postsynaptic membrane potentials.\\n] \n", - "845 [ Genes in this list are primarily involved in ion channel activity, membrane potential regulation, and ligand-gated monoatomic ion channel activity, as well as pathways enabled by those activities such as G protein-coupled receptor signaling, chloride transmembrane transport, gamma-aminobutyric acid signaling pathway, and potassium ion transmembrane transport.\\n\\nMechanism: Genes in this list are part of the electrical signaling pathways that regulate chemical synaptic transmission in neurons and other cells, controlling neuronal action potentials, membrane potentials, the transport of ions across cellular membranes, and the assembly of neurotransmitters and synapses.\\n\\n] \n", - "846 [ The genes in the list are all involved in many functions including DNA-binding, RNA polymerase II-specific activity, metal ion binding, ubiquitin protein ligase binding, and positive regulation of transcription by RNA polymerase II. These genes are also likely to be involved in several processes including positive regulation of immunoglobulin production, regulation of ERBB signaling pathway, regulation of intracellular protein transport, monoatomic cation transport, nucleic acid metabolic process, protein hexamerization, glycosaminoglycan catabolic process, nervous system development, heme transport, and mitochondrial transport.\\n\\nMechanism: These genes likely coordinate a combination of transcription activities to maintain cell function, health, and development. They are also likely to be involved in transporting and processing essential molecules needed for maintaining normal neural and sensory functionality as well as involved in transporting and processing essential molecules for cell metabolism.\\n\\n] \n", - "847 [\\nSummary: A set of genes involved in positive/negative regulation of transcription by RNA polymerase II, nucleic acid and glycosaminoglycan metabolism, 5'-3' DNA helicase activity, protein hexamerization, alpha-N-acetylglucosaminidase activity, cytoskeletal motor activity, mechanosensitive monoatomic cation channel activity, myelination in peripheral nervous system, regulation of RNA splicing, transmission of nerve impulse, glucose-6-phosphate isomerase activity, alanine-tRNA ligase activity, heme transmembrane transporter activity, 3'-5' exonuclease activity, DNA-directed DNA polymerase activity, induction of egg chambers in Drosophila, nuclear import signal receptor activity, misfolded protein binding activity, protein ubiquitination, metal ion binding activity, cell-cell adhesion via plasma-membrane adhesion molecules and myelination.\\nMechanism: The genes may be shared among a number of biological pathways involving nucleic acid metabolism, cytoskeletal motor activity, myelination, and protein folding.\\n] \n", - "848 [ The genes provided are likely to be involved in G protein-coupled receptor signal transduction, regulation of cytosolic calcium ion concentration, regulation of DNA templated transcription, regulation of neurodegeneration, signal transduction, neural development, enzyme and protein kinase binding, endosomal transport, signal receptor binding and cell organization. Mechanism: These genes are likely to play a role in signal transduction pathways that regulate multiple biological processes, including G protein-coupled receptor signaling pathways, phospholipase-c activating dopamine receptor signaling pathways, and adenylate cyclase-modulating G protein-coupled receptor signaling pathways. ] \n", - "849 [\\n\\nSummary: A wide variety of gene functions have been identified, including those involved in cAMP and calcium signaling pathways, G-protein coupled receptor signaling, apoptosis, gene regulation and transcription, membrane transport, and ion channels. \\n\\nMechanism: A wide variety of genes play a role in providing signals to the cells, controlling the transport of molecules across membranes, regulating genes and allowing for cells to respond to various stimuli.\\n\\n] \n", - "850 [ The genes identified in the list are involved in various activities, such as DNA and RNA binding, transcription factor binding, protein kinase and chromatin binding, transcription coactivator and repressor activities, protein dimerization, and other enzymatic activities. The common function they share is to regulate gene expression.\\n\\nMechanism: These genes are likely involved in transcriptional regulation by binding to genes and enhancers to either activate or repress transcription, and by modifying chromatin structure to regulate gene expression.\\n\\n] \n", - "851 [ This list of genes are all primarily involved in the regulation of transcription by RNA polyerase II and in cellular processes of transcription, such as positive and negative regulation of gene expression, DNA repair and cell differentiation. The statistically over-represented terms include: transcription; DNA-binding; RNA polymerase II-specific; transcription activator/transcription repressor; cis-regulatory region sequence-specific; transcription coregulator binding; regulation of DNA-templated transcription; nucleosome disassembly; and regulation of signal transduction. \\nMechanism: The underlying biological mechanism is associated with regulation of gene expression, which is dependent on the DNA-binding capability of the transcription factors, as well as their ability to recognize the proper sequence and initiate transcription of the downstream genes.\\n] \n", - "\n", - "prompt_variant v2 \\\n", - "0 [Summary: Genes associated with connective tissue disorder Ehlers-Danlos syndrome.\\nMechanism: Collagen synthesis and matrix maturation.\\n\\nHypothesis: The enriched terms suggest that Ehlers-Danlos syndrome is caused by disruptions in collagen synthesis and the maturation of matrix organization. The genes identified appear to play critical roles in these processes, including collagen synthesis, extracellular matrix organization, and proteolytic subunits and serine proteases that may degrade or modify collagen fibers. Additionally, the presence of sulfotransferases and zinc finger proteins may suggest additional regulatory pathways for collagen synthesis and modification. The disruption of these pathways likely leads to reduced collagen strength and increased tissue laxity, two key hallmarks of Ehlers-Danlos syndrome.] \n", - "1 [Summary: Genes associated with Ehlers-Danlos syndrome (EDS) are involved in the biosynthesis, assembly, and organization of collagen and extracellular matrix, as well as immune response and protein folding.\\n\\nMechanism: The genes identified are involved in the process of collagen biosynthesis and assembly, including post-translational modifications such as lysyl hydroxylation and glycosylation. Disruptions in these processes can lead to the connective tissue disorder Ehlers-Danlos syndrome. \\n\\n] \n", - "2 [Summary: The common function of the listed genes is DNA damage repair and maintenance of genome stability, particularly through homologous recombination and the Fanconi anemia pathway.\\nMechanism: The genes share a role in maintaining genomic integrity and preventing the onset of cancer through coordinated DNA repair functions.\\n] \n", - "3 [Summary: The enriched terms are related to DNA repair and maintenance of genome stability.\\n\\n\\nHypothesis: Mutations or dysregulation in these genes may lead to a higher susceptibility to DNA damage, defects in DNA repair, and could potentially lead to tumorigenesis. They may also be potential targets for therapeutic intervention in certain cancers.] \n", - "4 [Summary: Genes involved in mitochondrial function and metabolism are enriched.\\n\\nMechanism: These genes are involved in various metabolic and mitochondrial processes, including fatty acid metabolism, electron transport chain function, and redox reactions. The common theme among these functions is energy production and regulation within the mitochondria.\\n\\n] \n", - "5 [Summary: Many of the genes in this list are involved in mitochondrial function and energy metabolism, specifically in processes related to lipid metabolism and the electron transport chain. \\n\\n] \n", - "6 [Summary: Immune system function and cytokine signaling\\nMechanism: Immune response and cytokine pathways\\n\\nHypothesis: The overrepresented terms suggest that these genes play a role in the immune system function and cytokine signaling. This could involve the activation of T cells, leukocyte migration, and cytokine production to regulate the immune response and fight against pathogens. The cytokine pathways produced by these genes could also influence T cell differentiation and antigen processing/presentation via MHC class II, leading to the production of interleukin-2 and interferon-gamma. The chemokine-mediated signaling pathway could also play a role in leukocyte migration and immune response activation.] \n", - "7 [Summary: The common function of the genes listed is related to the immune system, specifically cytokine signaling, chemotaxis, and antigen presentation.\\nMechanism: The genes are involved in various aspects of immune response, including the production and signaling of cytokines, chemotaxis of immune cells, and antigen presentation to T cells.\\n] \n", - "8 [Summary: Genes involved in various aspects of cellular processes, including transport, metabolism, cytoskeleton organization, and signaling pathways, are over-represented.\\n\\nMechanism: These genes are involved in diverse biological pathways, and thus do not share a single common mechanism.\\n\\n] \n", - "9 [Summary: Regulation of protein activity, transport, and metabolism\\nMechanism:hypothesize that these genes are involved in regulating protein activity, transport, and metabolism through various processes such as binding to regulatory subunits, transcribing DNA, catalyzing enzymatic reactions, and transporting molecules across cellular membranes.\\n] \n", - "10 [Summary: Extracellular matrix organization and cellular adhesion\\nMechanism: Extracellular matrix synthesis and remodeling by integrins and proteoglycans\\n] \n", - "11 [Summary: Extracellular matrix organization and cell adhesion\\n\\nHypothesis: These genes may be involved in the regulation of tissue remodeling and repair, as well as in the maintenance of cell integrity and differentiation. Dysregulation of these genes could potentially lead to pathological processes such as fibrosis or cancer metastasis.] \n", - "12 [Summary: Genes involved in cell adhesion and cytoskeletal organization are enriched.\\n\\nMechanism: These genes are involved in the organization and regulation of cellular structures such as the cytoskeleton, focal adhesions, and tight junctions, which are critical for cell adhesion and migration.\\n\\n] \n", - "13 [Summary: Cell adhesion and signaling\\nMechanism: Tight junction formation\\n\\nHypothesis: The genes in this list all play a role in cell adhesion and signaling, with a particular focus on the formation of tight junctions. Tight junctions represent a mode of cell-to-cell adhesion in epithelial or endothelial cells and are crucial for the maintenance of cellular polarity and barrier function. The enriched terms suggest that the genes in this list are involved in various signaling pathways, including those mediated by cadherins, integrins, GPCRs, and PTKs. They also regulate the actin cytoskeleton and ECM, which are important for cell adhesion and migration. Furthermore, the involvement of PI3K, MAPK, and TGF-beta signaling pathways indicates that these genes likely play a] \n", - "14 [Summary: Membrane-bound proteins involved in signal transduction and cell adhesion\\n\\n] \n", - "15 [Summary: Cell surface proteins and membrane transporters involved in various cellular processes, including cell adhesion, signal transduction, and ion transport.\\n\\nMechanism: These gene products are involved in the regulation of cellular functions at the cell membrane and play a critical role in maintaining proper cellular signaling and transport mechanisms.\\n\\n] \n", - "16 [Summary: Apoptosis, cell death, and signaling pathways are enriched terms in these genes.\\nMechanism: The genes are involved in regulating various aspects of apoptosis and cell death, as well as signaling pathways that control these processes.\\n] \n", - "17 [Summary: Apoptosis and cell death related genes.\\n\\nMechanism: Activation of caspases, which are a family of cysteine-aspartic acid proteases that play a central role in executing apoptosis.\\n\\n\\nHypothesis: These genes are involved in the regulation and execution of apoptotic pathways, which play an important role in development, tissue homeostasis and elimination of damaged cells. The activation of caspases leads to the cleavage of a variety of structural and regulatory proteins, resulting in cytoskeletal rearrangements, DNA fragmentation, and ultimately, cell death. The over-representation of terms related to caspase activity and apoptosis regulation suggests that these genes are strongly linked to this biological process.] \n", - "18 [Summary: Transport and metabolism of lipids and cholesterol\\nMechanism: ABC transporters and cytochrome P450 enzymes play a key role in the transport and metabolism of lipids and cholesterol.\\n] \n", - "19 [Summary: Peroxisome biogenesis and lipid metabolism are enriched functions among the listed genes.\\n\\n\\nHypothesis: It is possible that dysregulation of these genes could lead to metabolic disorders such as peroxisome biogenesis disorders or abnormal cholesterol and fatty acid metabolism. Further research is needed to fully understand the underlying biological mechanisms and potential clinical implications of these enriched functions.] \n", - "20 [Summary: Genes involved in lipid metabolism, transport, and synthesis are enriched.\\nMechanism: Lipids are essential components of cellular structure, energy storage, and signaling. These genes contribute to the regulation of lipid metabolism and transport, as well as the synthesis of lipids necessary for these processes.\\n] \n", - "21 [Summary: Cholesterol biosynthesis and metabolism\\nMechanism: Regulation of cholesterol levels via enzymatic activity\\n\\nHypothesis: The enriched terms suggest a common biological mechanism involving the regulation of cholesterol levels and metabolism through various enzymatic pathways, including those responsible for cholesterol biosynthesis, phospholipid metabolism, fatty acid biosynthesis, and sterol metabolism. The genes in this list likely play a role in maintaining proper cholesterol levels and homeostasis, and dysregulation of these pathways may lead to various diseases such as hypercholesterolemia, atherosclerosis, and other metabolic disorders.] \n", - "22 [Summary: Several genes are involved in blood coagulation, extracellular matrix remodeling, and regulation of the complement pathway. \\nMechanism: These genes are likely involved in various aspects of tissue homeostasis and response to injury, including wound healing and inflammation.\\n] \n", - "23 [Summary: Extracellular matrix breakdown, blood coagulation, and protein inhibition are enriched functions shared by these genes.\\nMechanism: These genes are involved in regulating the extracellular matrix, blood coagulation, and protease activity through protein inhibition.\\n] \n", - "24 [Summary: Proteases and their inhibitors are enriched among these genes, as well as genes involved in blood clotting and complement activation.\\n\\nMechanism: These genes are involved in proteolytic and inflammatory pathways, including complement activation and blood clotting.\\n\\n] \n", - "25 [Summary: Genes involved in regulation of immune response and blood coagulation are statistically over-represented.\\n\\n] \n", - "26 [Summary: Genes are involved in DNA repair, transcription, and nucleotide metabolism.\\n\\nMechanism: These genes are involved in essential cellular processes, including DNA repair, transcription initiation, and nucleotide metabolism. Many of these genes encode subunits of DNA polymerases or transcription factor complexes. Their shared function in DNA repair may suggest a common biological pathway in maintaining genomic stability.\\n\\n] \n", - "27 [Summary: Genes involved in DNA repair and transcription regulation.\\n\\nMechanism: These genes are all involved in various aspects of DNA repair and transcription regulation, which are essential for maintaining genome stability.\\n\\n] \n", - "28 [Summary: DNA replication and repair\\nMechanism: The genes are involved in DNA replication and repair processes.\\n] \n", - "29 [Summary: DNA replication, repair and cell-cycle regulation\\nMechanism: These genes are involved in various aspects of DNA replication, repair and cell-cycle regulation, with some genes directly involved in DNA synthesis and others involved in checkpoint control and regulation of cell division.\\n] \n", - "30 [Summary: Extracellular matrix organization and cell adhesion are the enriched functions of the given gene list.\\nMechanism: Extracellular matrix (ECM) organization, cell adhesion, and related processes are crucial for the development and maintenance of tissue integrity and functionality. These are mediated by interactions between different proteins and cell surface receptors within ECM microenvironments.\\n\\n] \n", - "31 [Summary: Extracellular matrix organization and muscle contraction are enriched functions among these genes.\\nMechanism: These genes are involved in the regulation and maintenance of the extracellular matrix, which is essential for proper tissue and organ function. They also play a role in muscle contraction and cell adhesion.\\n] \n", - "32 [Summary: Transport and binding proteins; enzymes; membrane-associated proteins; transcriptional regulators; receptors; cytoskeletal proteins.\\nMechanism: These genes are involved in intracellular transport and binding, metabolism, gene regulation, cellular signaling, and structural support of cells and tissues.\\n\\n] \n", - "33 [Summary: Transport and metabolism of fatty acids, regulation of gene expression \\nMechanism: Fatty acid transport and lipid metabolism \\n] \n", - "34 [Summary: This list of genes is enriched for terms related to cell signaling, protein binding, and post-translational modifications.\\n\\n\\nHypothesis: These genes are involved in a network of signaling pathways, including protein-protein interactions and post-translational modifications, that regulate cell proliferation, differentiation, and apoptosis. These pathways are likely to involve a wide range of signaling molecules, including kinases, transcription factors, and cytoplasmic regulators. The enrichment of terms related to protein binding and enzyme activity suggests that many of these pathways involve the coordinated action of multiple proteins and their interactions with other regulatory molecules. Further studies will be needed to elucidate the specific pathways that link these genes and their functions.] \n", - "35 [Summary: This list of human genes has commonalities in their involvement in protein and enzyme regulation, as well as cellular transport mechanisms.\\n\\nMechanism: Protein regulation; enzyme regulation; cellular transport mechanisms\\n\\n] \n", - "36 [Summary: Genes involved in energy metabolism and oxidative stress response.\\n\\nMechanism: These genes are involved in catabolic pathways for the breakdown of fatty acids, amino acids, and carbohydrates to produce energy. They also play a role in the response to oxidative stress, which can result from an imbalance between the production of reactive oxygen species (ROS) and the body's ability to detoxify them.\\n\\n] \n", - "37 [Summary: Genes involved in various metabolic processes, including fatty acid metabolism and energy production, are enriched.\\n\\nMechanism: The enrichment of metabolic processes reflects the crucial importance of these genes in maintaining energy balance and metabolic homeostasis in the body.\\n\\n] \n", - "38 [Summary: Cell cycle regulation and DNA replication are enriched functions among the listed human genes.\\nMechanism: These genes are involved in processes involved in cell division, DNA replication, and DNA repair.\\n] \n", - "39 [Summary: Gene functions are involved in DNA replication, cell cycle regulation, and DNA repair.\\n\\nMechanism: These genes are involved in various stages of cell division, including DNA replication, chromosome segregation, and cytokinesis.\\n\\n] \n", - "40 [Summary: Glycolysis pathway and carbohydrate metabolism are enriched terms among the listed genes.\\n\\nMechanism: The listed genes are involved in glucose metabolism, glycolysis, and carbohydrate metabolism. They encode enzymes such as phosphoglycerate mutase (PGAM), phosphomannose isomerase (MPI), glucose-6-phosphate dehydrogenase (G6PD), hexokinases (HK2), aldolases (ALDOA, ALDOB), and glycogen debrancher enzyme (AGL).\\n\\n\\nHypothesis: The enriched terms suggest a possible link between the listed genes and the glycolysis pathway, which is a central metabolic pathway in energy production. The genes encode enzymes that are involved in the conversion of glucose into pyruvate, which is further metabolized in the Krebs cycle. Dysfunction in these genes may lead to alterations in glucose metabolism and contribute to metabolic disorders such as diabetes and glycogen storage diseases.] \n", - "41 [Summary: Genes involved in various metabolic processes and enzymatic activity are enriched in this list.\\n\\nMechanism: The enriched terms suggest a commonality in metabolic pathways and enzymatic activity.\\n\\n] \n", - "42 [Summary: Cell signaling and neuronal development\\nMechanism: Mediation of cell-cell communication and regulation of intracellular signaling pathways\\n\\nHypothesis: The enriched terms suggest that these genes play important roles in the regulation of cell-cell communication and intracellular signaling pathways, particularly those involved in neuronal development and angiogenesis. These processes involve the regulation of cell adhesion, migration, growth cone collapse, and the activation of cytokine receptors. Transcriptional regulation is also likely to play a role in the mediation of these processes.] \n", - "43 [Summary: Cell signaling and adhesion\\nMechanism: Regulation of cell adhesion and signaling pathways\\n] \n", - "44 [Summary: Transport and binding processes\\nMechanism: ATP binding and membrane transport\\n] \n", - "45 [Summary: Enriched terms are related to transport, binding activity, and regulation of gene expression.\\nMechanism: These genes likely function in cellular transport and molecular binding, with a potential role in gene expression regulation.\\n\\n] \n", - "46 [Summary: Glycolysis, glucose metabolism, protein binding, transcription regulation\\n\\nMechanism: It appears that many of these genes are involved in processes related to glycolysis and glucose metabolism. Additionally, a number of these genes have protein binding functions, which suggests that they may be involved in complex regulatory pathways controlling glucose metabolism and other cellular processes. Finally, several of these genes are involved in transcription regulation, suggesting that they may play a role in modulating the expression of other genes involved in glucose metabolism.\\n\\n\\n] \n", - "47 [Summary: Genes involved in metabolism, cell cycle regulation, and signal transduction are enriched.\\nMechanism: These genes likely contribute to the regulation of cellular processes that involve energy metabolism and promoting cell growth and differentiation.\\n] \n", - "48 [Summary: The enriched terms relate to the regulation and signaling of immune system processes and inflammation.\\nMechanism: The genes are involved in the pathways related to immune system response and inflammation, specifically, cytokine signaling, T-cell and B-cell activation, and leukocyte-endothelial interactions.\\n] \n", - "49 [Summary: Immune system function, cytokine receptors, and cell surface adhesion molecules are enriched among these genes.\\n\\nMechanism: These genes are involved in the regulation of immune system function, including the response to pathogens and inflammation. Many of the enriched terms involve cytokine receptors and cell surface adhesion molecules, indicating that these genes play a role in cell signaling and communication.\\n\\n] \n", - "50 [Summary: The enriched terms relate to cytokine signaling, immune response, and cell adhesion and migration.\\n\\nMechanism: The genes are involved in cytokine signaling pathways and immune response, regulating the production and differentiation of various cells, particularly macrophages and lymphocytes.\\n\\n] \n", - "51 [Summary: Immune response-related genes\\nMechanism: Immune response and cytokine signaling pathway\\n] \n", - "52 [Summary: Immune system function\\n\\nHypothesis: These genes are involved in regulating immune system function, specifically in the release and detection of cytokines and chemokines, as well as the migration of leukocytes in response to inflammation. They may be part of a larger pathway involved in coordinating the immune response to invading pathogens.] \n", - "53 [Summary: Receptor and chemokine-related functions are statistically enriched in this gene list.\\nMechanism: These genes may be involved in immune system regulation and cellular signaling pathways, such as G protein-coupled receptor signaling.\\n] \n", - "54 [Summary: Immune response and antiviral function\\n] \n", - "55 [Summary: Innate immune response and antiviral activity\\n\\nHypothesis: These genes work together to inhibit viral replication and spread by triggering the production and release of interferons, activating innate immune cells, and promoting the degradation of viral components through the proteasome. Through the regulation of cytokine signaling and antigen processing, these genes may also contribute to the adaptive immune response and the development of immunity to viral infection.] \n", - "56 [Summary: Immune response and cytokine signaling pathways are enriched in the list of genes.\\n\\nMechanism: The genes in the list are involved in immune response and cytokine signaling pathways. They play a role in cytokine-mediated signaling pathways, chemokine signaling pathways, and antigen processing and presentation.\\n\\n\\nHypothesis: The genes in the list are primarily involved in regulating the immune response and cytokine signaling pathways. This suggests that they play a key role in the body's ability to recognize and respond to pathogens and other foreign invaders. Dysfunction of these genes may therefore lead to an increased susceptibility to infections and other immune-related disorders.] \n", - "57 [Summary: The enriched terms among these genes relate to immune response, specifically innate immune response and antiviral response. \\n\\n\\nHypothesis: These genes are involved in innate immune response and antiviral response, indicating a potential regulatory pathway for immune function in response to viral infection. The enrichment of cytokine activity and regulation of cytokine production suggests that this pathway involves the production of various cytokines involved in immune response, including interferons. The enrichment of positive regulation of type I interferon production and type I interferon signaling pathway further supports this hypothesis.] \n", - "58 [Summary: Calcium ion binding and transport\\nMechanism: Calcium signaling and regulation\\n\\nHypothesis: These genes are all involved in regulating calcium ion binding and transport, suggesting a potential role in calcium-mediated signaling. This may be related to a variety of biological processes, including muscle contraction, nervous system function, and cellular signaling pathways. The enriched terms suggest that calcium ion binding and transport plays a crucial role in many of these processes, potentially through the regulation of ion channels, transporters, and other calcium-dependent proteins.] \n", - "59 [Summary: Calcium ion binding activity, cellular response to protein stimulus, negative regulation of apoptotic process.\\nMechanism: Calcium signaling pathway and regulation of apoptosis.\\n] \n", - "60 [Summary: Membrane-associated proteins and enzymes involved in various cellular processes.\\nMechanism: Membrane-associated and signaling pathways.\\n] \n", - "61 [Summary: Cell signaling and regulation through cytokines, growth factors, and enzymes involved in coagulation and complement activation.\\nMechanism: Activation and regulation of cellular pathways through ligand-receptor interaction and enzymatic activity.\\n\\nHypothesis: These genes are involved in mediating cellular responses to external stimuli, including tissue damage and immune responses. Cytokine and growth factor signaling pathways activate cellular responses such as proliferation, differentiation, and migration. Enzymes involved in coagulation and complement activation play critical roles in host defense and tissue repair. The common mechanism underlying these functions is the activation and regulation of cellular pathways through ligand-receptor interaction and enzymatic activity.] \n", - "62 [Summary: These genes are involved in various cellular processes including cytoskeletal organization, cell cycle progression, and centrosome function.\\nMechanism: These genes likely interact with each other to regulate cellular processes and maintain proper cellular function.\\n] \n", - "63 [Summary: Microtubule organization and regulation\\nMechanism: Regulation of microtubule dynamics and spindle assembly\\n] \n", - "64 [Summary: Protein synthesis and folding regulation\\nMechanism: The identified genes are involved in processes related to protein synthesis, folding, and degradation. Several of the genes are involved in regulating glucose metabolism, which provides energy for protein synthesis. Others are involved in regulating the structure of microtubules, which help transport proteins within cells.\\n\\n] \n", - "65 [Summary: Many of the genes are involved in metabolic processes, specifically related to nucleotide, lipid, and carbohydrate metabolism. Other common functions include protein folding, protein degradation, and regulation of gene expression.\\n\\nMechanism: The enriched terms suggest a role for these genes in cellular homeostasis and regulation of metabolic processes, likely through coordinated regulation of metabolic pathways and protein turnover.\\n\\n] \n", - "66 [Summary: Ribosome biogenesis and protein translation\\n\\nMechanism: These genes are involved in various aspects of ribosome biogenesis and protein translation, including the assembly and function of the ribosome, mRNA splicing, and regulation of translation initiation.\\n\\n] \n", - "67 [Summary: The enriched terms suggest that the genes in this list are involved in various aspects of protein synthesis, including ribosome biogenesis, translation initiation and elongation, and post-splicing mRNA processing.\\n\\nMechanism: Protein synthesis\\n\\n] \n", - "68 [Summary: Ribosome biogenesis and nucleolar function are enriched functions among these genes.\\nMechanism: The genes are involved in various steps in ribosome biogenesis and nucleolar function, including RNA processing, assembly of ribosomal subunits, and protein binding to facilitate these processes.\\n] \n", - "69 [Summary: Genes involved in nucleolar and ribosomal function, RNA processing and binding, and cell cycle regulation are statistically enriched.\\n\\nMechanism: These genes likely play a role in ribosome biogenesis and function, as well as in the regulation of RNA processing and binding. They may also be involved in cell cycle regulation.\\n\\n] \n", - "70 [Summary: These genes are involved in muscle development and function, including muscle contraction, regulation of muscle metabolism, and cytoskeletal organization.\\nMechanism: The enriched terms suggest a common mechanism of regulation and organization of muscle tissue at both the structural and metabolic levels.\\n] \n", - "71 [Summary: Muscle development and function\\nMechanism: Regulation of muscle contraction through troponin-tropomyosin complex and actin-myosin interaction\\n\\nHypothesis: The enriched terms suggest that these genes are involved in muscle development and function, specifically in the regulation of muscle contraction through the troponin-tropomyosin complex and actin-myosin interaction. Troponin complex, actin-binding proteins, and myosin heavy chain are all involved in the regulation of muscle contraction and the formation of sarcomeres, the basic functional units of muscle. This suggests that these genes play a role in muscle development and function, particularly in the regulation of muscle contraction through the troponin-tropomyosin complex and actin-myosin interaction, and calcium ion binding.] \n", - "72 [Summary: Notch signaling and cell fate determination\\nMechanism: The genes are all involved in the Notch signaling pathway, which plays a key role in cell fate determination during embryonic development.\\n] \n", - "73 [Summary: Regulation of signaling pathways involved in development and cellular processes.\\nMechanism: Notch signaling pathway and ubiquitination-mediated proteolysis.\\n\\nHypothesis: The enriched terms suggest that the common function of the genes in the list is the regulation of signaling pathways, specifically the Notch signaling pathway and ubiquitination-mediated proteolysis. These genes are involved in the transcriptional regulation of cellular processes, including cell fate determination. The Notch signaling pathway plays a critical role in development and differentiation, while ubiquitination-mediated proteolysis is essential for proper protein degradation and turnover. The various genes in this list work together to coordinate these important cellular processes.] \n", - "74 [Summary: Many of the genes listed are involved in the function of mitochondrial respiratory chain complexes, which are responsible for generating energy in cells. \\n\\nMechanism: Mitochondrial respiratory chain complexes. \\n\\n] \n", - "75 [Summary: Mitochondrial respiratory chain function and ATP synthesis are enriched in these genes.\\nMechanism: Electron transport chain and oxidative phosphorylation.\\n] \n", - "76 [Summary: Cell growth regulation and DNA repair\\nMechanism: The genes listed are involved in the regulation of cell growth and cell cycle progression, as well as DNA repair and damage response.\\n] \n", - "77 [Summary: Genes involved in various cellular processes, including growth factor activity, transcriptional regulation, apoptosis, and DNA repair.\\nMechanism: These genes are involved in regulating cell growth, survival, and response to stress.\\n] \n", - "78 [Summary: Glucose metabolism and insulin regulation\\nMechanism: Glycolysis; Gluconeogenesis; Insulin secretion; Pancreas development and differentiation\\n\\n] \n", - "79 [Summary: Genes involved in glucose and insulin metabolism, as well as pancreatic islet development and neuroendocrine differentiation show enrichment in this list.\\n\\nMechanism: These genes likely play a role in the regulation of glucose homeostasis, insulin secretion, and pancreatic islet development.\\n\\n] \n", - "80 [Summary: Transport of various molecules across extra- and intra-cellular membranes is enriched.\\nMechanism: ABC transporters are involved in the transport of a wide range of molecules and play a critical role in maintaining cellular homeostasis.\\n] \n", - "81 [Summary: Peroxisomal functions, fatty acid metabolism, and antioxidant defense mechanisms are enriched in this gene list.\\nMechanism: The genes in this list are involved in facilitating fundamental metabolic pathways, such as fatty acid metabolism and peroxisomal functions that involve beta-oxidation, as well as antioxidant defense mechanisms that include the degradation of reactive oxygen species.\\n] \n", - "82 [Summary: Intracellular signaling, protein kinase activity, and regulation of cellular processes are enriched functions among these genes.\\n\\nMechanism: These genes are involved in various aspects of intracellular signaling, such as activation or inhibition of protein kinase activity and regulation of cellular processes.\\n\\n] \n", - "83 [Summary: Protein kinases and signaling pathways.\\nMechanism: Genes encode for proteins involved in the phosphorylation of other proteins, leading to activation or inhibition of various signaling pathways.\\n] \n", - "84 [Summary: Intracellular vesicular transport and trafficking\\nMechanism: Adaptor protein complexes and small GTPases regulate vesicle formation, sorting, and fusion with target membranes.\\n] \n", - "85 [Summary: Membrane trafficking and vesicular transport \\nMechanism: Genes involved in membrane trafficking and vesicular transport function together to regulate the movement of proteins and lipids between organelles in the cell. They do so by promoting the budding, fusion, and sorting of transport vesicles. \\n] \n", - "86 [Summary: Genes involved in antioxidant defense and redox regulation.\\n\\n] \n", - "87 [Summary: Anti-oxidative stress response pathway\\nMechanism: Enzymatic reduction of oxidative stress\\n\\nHypothesis: The commonality in function among these genes is their involvement in the anti-oxidative stress response pathway. These genes encode enzymes that are responsible for reducing oxidative stress, regulating reactive oxygen species and superoxide anion radicals, and participating in antioxidative defense mechanisms. The pathway involves the regulation of glutathione metabolism, peroxiredoxin-mediated detoxification, and other mechanisms that help to mitigate the effects of oxidative stress.] \n", - "88 [Summary: Reproductive development, specifically sperm function and testis differentiation, is enriched in these genes.\\n\\n\\nHypothesis: These genes all have roles in either male reproductive development or sperm function, which suggests they may share a common pathway or mechanism in regulating these processes. One hypothesis is that these genes may be involved in the regulation of gene expression during spermatogenesis, as many of them are specifically expressed in the testes and have been linked to sperm motility and acrosome reaction.] \n", - "89 [Summary: These genes are involved in various cellular and molecular functions, including but not limited to ion transport, protein phosphorylation, ubiquitination, spermatogenesis, and receptor signaling.\\nMechanism: The genes are involved in diverse biological pathways or mechanisms, reflecting the complexity of cellular and molecular biology.\\n] \n", - "90 [Summary: Genes involved in regulating transforming growth factor-beta (TGF-beta) superfamily signaling and transcriptional regulation.\\nMechanism: Regulation of TGF-beta signaling pathway and transcriptional regulation.\\n\\nHypothesis: These genes are involved in the regulation of the TGF-beta signaling pathway, which controls a variety of cellular processes including cell growth, differentiation, and apoptosis. They also play a role in transcriptional regulation, which may contribute to their regulatory functions in the TGF-beta pathway. These findings suggest a potential mechanism for how these genes may interact and contribute to the regulation of TGF-beta signaling.] \n", - "91 [Summary: Signaling pathways involving transforming growth factor-beta (TGF-beta) and bone morphogenetic proteins (BMPs)\\nMechanism: Regulation of gene expression through transcription factor binding and signal transduction\\n] \n", - "92 [Summary: Immune system-related genes that regulate inflammation and cytokine signaling.\\n\\nMechanism: These genes are involved in regulating the immune response by controlling inflammation and cytokine signaling pathways.\\n\\n] \n", - "93 [Summary: Cytokine signaling and immune response\\nMechanism: Genes are involved in cytokine production and response pathways, specifically in the interleukin and chemokine families.\\n] \n", - "94 [Summary: Genes involved in protein folding, stress response, and RNA processing are enriched.\\nMechanism: These genes likely function in maintaining proper protein folding and preventing protein misfolding, as well as responding to stress and modulating RNA processing.\\n] \n", - "95 [Summary: Protein folding, transport, and translation regulation \\nMechanism: Endoplasmic reticulum-associated protein degradation (ERAD) and unfolded protein response (UPR) pathways \\n] \n", - "96 [Summary: Extracellular matrix, cell signaling, protein kinase activity, ion transport, transcription regulation, and growth factor receptor activity are the common functions of the listed genes.\\n\\nMechanism: An underlying biological mechanism for the enriched terms is the regulation of cell growth and differentiation by extracellular matrix signaling pathways, which involve ion transport, protein kinase activity, and transcriptional regulation.\\n\\n] \n", - "97 [Summary: Extracellular matrix organization, cell adhesion, signaling and protein phosphorylation are enriched functions in these genes.\\n\\nMechanism: These genes are involved in biological processes related to cell adhesion, extracellular matrix organization, signaling pathway activity and protein phosphorylation.\\n\\n] \n", - "98 [Summary: Transport and metabolism of small molecules\\nMechanism: ABC transporters; Enzymatic metabolism\\n] \n", - "99 [Summary: Nucleic acid binding and metabolism\\nMechanism: RNA and DNA processing\\n] \n", - "100 [Summary: Genes involved in signaling pathways related to Wnt signaling, cell cycle progression, and transcriptional regulation.\\n\\nMechanism: Wnt signaling pathway regulates cell fate determination, cell proliferation, and differentiation through binding of specific receptors to Wnt proteins.\\n\\n] \n", - "101 [Summary: Genes involved in the Wnt signaling pathway, regulation of cell cycle, and transcriptional regulation are statistically over-represented.\\n\\nMechanism: These genes play a role in various cellular processes, including cell fate determination, embryonic development, and tumorigenesis.\\n\\n] \n", - "102 [Summary: Immune response and signal transduction\\nMechanism: C-type lectin receptors and cytokine signaling pathways\\n] \n", - "103 [Summary: Immune response and cell signaling\\nMechanism: These genes are involved in immune response and cell signaling pathways, such as the TNF-receptor superfamily and cytokine signaling.\\n] \n", - "104 [Summary: These genes share a role in the regulation of embryonic development, cell fate determination, and cell cycle progression.\\nMechanism: These genes encode transcription factors that regulate gene expression and are important for stem cell pluripotency and cell differentiation.\\n] \n", - "105 [Summary: Embryonic development and stem cell pluripotency\\nMechanism: Transcriptional regulation\\n\\n] \n", - "106 [Summary: Extracellular matrix and cell adhesion-related genes.\\nMechanism: Extracellular matrix remodeling and cell adhesion.\\n] \n", - "107 [Summary: Extracellular matrix (ECM) organization and regulation, cell adhesion and migration, tissue development and regeneration, signaling pathways, and platelet function are enriched in these gene functions.\\n\\nMechanism: ECM proteins, such as SPP1, COL5A2, and LUM, are involved in tissue organization and regulation. Cell adhesion and migration are mediated by proteins such as VCAN, ITGAV, and VTN. Tissue development and regeneration involve proteins like POSTN, MSX1, and JAG1. Signaling pathways are regulated by genes such as JAG2, NRP1, and TNFRSF21. Platelet function is affected by genes such as PF4, PDGFA, and PRG2.\\n\\n] \n", - "108 [Summary: Several of the genes are involved in transcription regulation and protein binding.\\n\\nHypothesis: These genes may be involved in regulating cellular processes through the regulation of gene expression and protein interactions, with zinc fingers and calcium ion binding domains playing important roles in protein-protein interactions and regulatory functions. The membrane proteins may mediate these interactions and functions at the cellular membrane.] \n", - "109 [Summary: Calcium-binding proteins, receptor proteins, and transcription factors are over-represented in this list of human genes.\\n\\nMechanism: These genes are involved in diverse biological processes but share common molecular functions, such as calcium binding, transcriptional regulation, receptor activity, and protein binding.\\n\\n] \n", - "110 [Summary: These genes are primarily involved in muscle contraction and regulation, with some playing a role in ion channel activity, protein binding, and phosphorylation.\\nMechanism: These genes are involved in the regulation of muscle development, contraction, and calcium signaling pathways.\\n] \n", - "111 [Summary: Genes involved in muscle contraction, regulation of calcium ions in muscle, and energy homeostasis.\\nMechanism: These genes contribute to the structure and function of striated muscle fibers, allowing for efficient and regulated contraction and relaxation.\\n] \n", - "112 [Summary: Genes in this list are involved in various cellular processes, including endocytosis, cytoskeletal reorganization, and signal transduction. They are also involved in lipid homeostasis and bone and brain development.\\n\\nMechanism: These genes are involved in intracellular transport, regulation of membrane dynamics, and signaling pathways. \\n\\n] \n", - "113 [Summary: The enriched terms are involved in intracellular trafficking, endocytosis, and cytoskeletal reorganization.\\nMechanism: These genes function in regulating cellular processes involving endocytic recycling and protein degradation.\\n\\n] \n", - "114 [Summary: These genes are involved in various stages of glucose metabolism and glycolysis.\\n\\nMechanism: The enriched terms suggest that these genes are involved in energy metabolism, specifically glycolysis and the conversion of glucose to ATP.\\n\\n] \n", - "115 [Summary: These genes are involved in various steps of glycolysis, a central metabolic pathway for the conversion of glucose into pyruvate, with the production of energy-rich ATP molecules.\\n\\nMechanism: Glycolysis is a multi-step process consisting of various enzymes that catalyze the conversion of glucose to pyruvate. This process occurs in the cytoplasm of cells and is an important pathway for the production of ATP.\\n\\n\\nHypothesis: These genes are involved in the regulation of energy metabolism and play a crucial role in providing cells with energy in the form of ATP. Dysfunction of these pathways can lead to various metabolic disorders, including glycogen storage diseases, hemolytic anemia, and cancer. The enrichment of terms related to glucose and fructose metabolism suggests that these pathways are particularly important for the function of these genes.] \n", - "116 [Summary: Calcium regulation and signaling\\nMechanism: Calcium ion transport and homeostasis\\n\\nHypothesis: The list of genes all play a critical role in calcium ion transport and homeostasis. They are involved in regulating intracellular calcium concentrations through ion transport across cell membranes. Specifically, many of the genes encode for ionotropic glutamate receptors that mediate synaptic plasticity in the central nervous system, which is believed to underlie memory and learning. The NMDA receptor subunits are key components of these receptors and are involved in calcium signaling. Additionally, several genes encode for sodium/calcium exchanger proteins that are responsible for regulating calcium ion homeostasis in a wide variety of cell types. The TRP ion channel family plays a role in transducing painful stimuli such as capsaicin and thermal stimuli. Overall, these genes are involved in multiple processes that ultimately impact calcium regulation and signaling.] \n", - "117 [Summary: All listed genes are involved in ion channel activity, particularly calcium channels and receptors. \\n\\nMechanism: Calcium signaling \\n\\n] \n", - "118 [Summary: Regulation of cell growth and survival through various signaling pathways is a common function of the listed genes.\\n\\nMechanism: The genes listed are involved in various signaling pathways that regulate cellular growth and survival, including the PI3K/AKT/mTOR pathway, TORC1 signaling, and the NF-kappaB pathway.\\n\\n] \n", - "119 [Summary: Genes involved in cell growth, signaling, and immune response are enriched.\\n\\nMechanism: These genes converge on signaling pathways that control cell growth and immune response through regulation of protein kinases such as AKT, TOR, and CDK5, and activation of transcription factors such as NF-kappaB.\\n\\n] \n", - "120 [Summary: Genes involved in the hydrolysis of carbohydrates and degradation of glycosaminoglycans, along with those involved in the turnover of hyaluronan and chitin, are enriched. \\nMechanism: Carbohydrate and glycosaminoglycan metabolism. \\n] \n", - "121 [Summary: Enzymes involved in glycosaminoglycan degradation and processing are enriched in this gene set.\\n\\nMechanism: Glycosaminoglycans are long chains of complex carbohydrates that are integral components of the extracellular matrix and play a role in cell signaling and tissue development. These enzymes are involved in the degradation and processing of glycosaminoglycans, specifically the cleavage of terminal carbohydrate residues.\\n\\n] \n", - "122 [Summary: The enriched terms suggest that these genes are involved in the immune response and specifically in the function of immunoglobulins (Ig) and immunoglobulin receptors.\\n\\nMechanism: The genes function in the immune response and interaction with antigens.\\n\\n] \n", - "123 [Summary: Genes related to immunoglobulin receptor binding activity and activation of immune response.\\nMechanism: Adaptive immune response\\n] \n", - "124 [Summary: Meiotic recombination and DNA repair are enriched functions among the listed genes.\\nMechanism: The genes listed play a role in DNA repair and recombination during meiosis, particularly in the resolution of double-stranded DNA breaks. \\n] \n", - "125 [Summary: These genes are involved in various aspects of meiotic recombination, DNA repair, and chromosome segregation.\\nMechanism: Meiosis\\n\\n\\nHypothesis: These genes are involved in various aspects of meiotic recombination. They likely function in the repair of double-strand DNA breaks, the resolution of Holliday junctions, and the proper segregation of homologous chromosomes during meiosis. They may also play a role in the formation and maintenance of the synaptonemal complex, which helps to ensure accurate chromosome pairing and recombination. Overall, these genes are critical for the proper functioning of meiosis and the generation of viable gametes.] \n", - "126 [Summary: Regulation of cellular processes, including immunity, apoptosis, and signal transduction.\\nMechanism: These genes are involved in a range of biological pathways, including immune response, cell cycle regulation, and intracellular transport.\\n\\n] \n", - "127 [Summary: Regulation of cellular processes, including immune response and cell cycle progression.\\nMechanism: Not specified.\\n] \n", - "128 [Summary: Protein synthesis and folding regulation\\nMechanism: The identified genes are involved in processes related to protein synthesis, folding, and degradation. Several of the genes are involved in regulating glucose metabolism, which provides energy for protein synthesis. Others are involved in regulating the structure of microtubules, which help transport proteins within cells.\\n\\n] \n", - "129 [Summary: These genes are involved in various cellular processes such as protein degradation, glucose transport, nucleic acid metabolism, and energy metabolism.\\n\\nMechanism: The biological mechanism underlying the common function of these genes may relate to their involvement in cellular metabolism and maintenance.\\n\\n] \n", - "130 [Summary: Genes involved in peroxisome biogenesis and protein import\\nMechanism: Peroxisome assembly and maintenance pathway\\n\\nHypothesis: These genes are all involved in the same pathway for peroxisome assembly and maintenance, specifically in the import of peroxisomal matrix proteins. Mutations in these genes lead to various peroxisomal biogenesis disorders, including neonatal adrenoleukodystrophy, Zellweger syndrome, and infantile Refsum disease. Defects in PEX7 specifically have been associated with a wider range of disorders, including RCDP1 and Refsum disease. Overall, these genes play critical roles in the proper function of peroxisomes and their associated metabolic processes.] \n", - "131 [Summary: Peroxisome biogenesis genes are enriched for terms related to peroxisome assembly and function.\\n\\nMechanism: Peroxisomes are important organelles responsible for numerous metabolic functions, including the degradation of fatty acids and the synthesis of cholesterol. The genes listed here are involved in the assembly and maintenance of peroxisomes, as well as the import of proteins into the organelle.\\n\\n\\nHypothesis: The AAA family of ATPases plays a central role in peroxisome biogenesis by providing energy for protein translocation and membrane remodeling. Mutations in these genes disrupt the normal assembly and function of peroxisomes, leading to a range of disorders collectively known as peroxisome biogenesis disorders.] \n", - "132 [Summary: Genes involved in nuclear structure and maintenance.\\nMechanism: These genes encode proteins that are involved in maintaining the structure and function of the nucleus. They are involved in processes such as DNA repair, replication, and chromatin organization.\\n] \n", - "133 [Summary: Genes involved in nuclear organization and stability.\\nMechanism: These genes play important roles in maintaining nuclear stability and integrity by organizing chromatin structure and gene expression, repairing DNA damage, and promoting nuclear reassembly.\\n] \n", - "134 [Summary: Genes involved in ion channels and neurotransmission through GABA and glutamate receptors. \\nMechanism: Regulation of neuronal excitability and synaptic transmission. \\n] \n", - "135 [Summary: The enriched terms are related to ion channels in the central nervous system, particularly potassium and chloride channels. \\n\\nMechanism: Ion channels play critical roles in regulating the electrical properties of cells, including neurons. Potassium channels are important for regulating action potential firing and synaptic transmission, while chloride channels are involved in inhibitory neurotransmission mediated by GABA. \\n\\n] \n", - "136 [Summary: Peripheral nervous system myelination and neurodegenerative diseases are enriched in this set of genes. \\nMechanism: Maintenance of peripheral nervous system myelin structure and function through regulation of protein import, DNA replication, and degradation pathways in the endoplasmic reticulum and mitochondria. \\n] \n", - "137 [Summary: Genes involved in various peripheral nervous system disorders are enriched for terms related to myelin formation and maintenance, as well as protein transport and degradation in the ER.\\n\\n\\nHypothesis: These genes likely contribute to proper formation and maintenance of myelin in the peripheral nervous system. Dysfunctions in protein transport and degradation pathways in the ER may also contribute to disease pathogenesis.] \n", - "138 [Summary: Regulation of signal transduction pathways through G-protein-coupled receptors and neurotransmitter activity.\\nMechanism: G proteins play a central role in signal transduction by coupling receptors to downstream effectors.\\n] \n", - "139 [Summary: These genes are involved in various aspects of cell signaling pathways including G-protein signaling, neurotransmitter receptors, and intracellular signaling.\\n\\nMechanism: These genes are involved in the regulation of cellular responses to extracellular signals, such as neurotransmitter and hormone signals, through G-protein-coupled receptors, resulting in activation of intracellular signaling pathways.\\n\\n] \n", - "140 [Summary: Transcriptional regulation and chromatin remodeling.\\nMechanism: These genes encode transcription factors and chromatin-associated proteins involved in the regulation of gene expression and chromatin structure.\\n] \n", - "141 [Summary: Transcription regulation\\n\\nHypothesis: These genes are likely to be involved in a common pathway or biological process related to the regulation of gene expression. They may play a role in coordinating the expression of multiple genes, such as those involved in cell differentiation or development. The proteins encoded by these genes may also function together within a larger protein complex involved in regulating transcription.] \n", - "142 [Summary: Extracellular matrix organization and connective tissue structure are enriched in the given genes.\\nMechanism: Extracellular matrix (ECM) maintenance and remodeling\\n\\nHypothesis: The enriched terms suggest that the given genes are involved in ECM maintenance and remodeling, particularly in collagen fibril organization, protein glycosylation, and peptidase activity. TNXB, COL12A1, ADAMTS2, COL1A2, COL3A1, COL5A1, and COL5A2 are all involved in collagen fibril organization, which is critical for maintaining connective tissue strength and elasticity. B3GALT6, B4GALT7, and CHST14 participate in protein glycosylation, important for the formation of collagens and proteoglycans, while DSE is involved in dermatan sulfate biosynthesis. SLC39A13 regulates zinc ion transport, which is important for ECM structure and stability. FKBP14 and PRDM5 play a role in collagen fiber generation and remodeling. Lastly, C1] \n", - "143 [Summary: Genes are enriched for extracellular matrix organization and collagen metabolic process.\\nMechanism: The genes are involved in collagen biosynthesis and extracellular matrix (ECM) remodeling.\\n\\nHypothesis: These genes are involved in extracellular matrix remodeling by encoding proteins involved in collagen biosynthesis and likely play a role in maintaining tissue structure and elasticity.] \n", - "144 [Summary: Genes are mostly involved in DNA repair and maintenance.\\nMechanism: DNA repair and maintenance pathway\\n] \n", - "145 [Summary: The genes listed are involved in DNA repair and share functions related to the Fanconi anemia pathway, homologous recombination, and double-strand break repair.\\n\\nMechanism: The genes identified in this list are associated with DNA damage response and repair pathways. Specifically, they are enriched in the Fanconi anemia (FA) pathway, which is a network of proteins involved in the detection and repair of DNA interstrand crosslinks (ICLs). The FA pathway activates a cascade of events that lead to the repair of damaged DNA, including the recruitment of nucleases, helicases, and recombinases to the site of the ICL.\\n\\n] \n", - "146 [Summary: Metabolism and energy production are the common themes among the listed genes. Numerous processes and pathways related to energy metabolism, including lipid metabolism, fatty acid oxidation, and mitochondrial function, are enriched.\\n\\nMechanism: The overlapping functions of these genes suggest that they are involved in various metabolic processes important for energy production in cells, including lipid and mitochondrial metabolism.\\n\\n] \n", - "147 [Summary: Mitochondrial function and lipid metabolism are enriched functions among the given genes.\\nMechanism: The genes are involved in processes related to mitochondrial function and lipid metabolism. \\n\\n] \n", - "148 [Summary: Immune response and signaling pathway genes are statistically over-represented in this gene set.\\nMechanism: These genes are involved in regulating different stages of immune response, including the activation and differentiation of immune cells, cytokine signaling, and antigen presentation to T cells.\\n\\n] \n", - "149 [Summary: Immune-related functions are enriched in the list of genes.\\nMechanism: Multiple genes involved in various aspects of the immune response.\\n\\n\\nHypothesis: The enrichment of immune-related functions in the list of genes indicates their importance in the immune response. Many of these genes are involved in T cell activation, cytokine signaling, antigen processing and presentation, and leukocyte migration, which are all critical processes in mounting an effective immune response against pathogens or foreign invaders. The enrichment of genes involved in B cell differentiation also suggests a role in the adaptive immune response. Additionally, the significant enrichment of chemokine signaling and interferon signaling genes could indicate a broader regulatory mechanism that influences the immune response.] \n", - "150 [Summary: Several terms related to transcriptional regulation and protein degradation are enriched in the list of human genes provided.\\n\\nMechanism: The enriched terms suggest that the genes in the list are involved in regulating gene expression, protein stability, and turnover. The specific biological mechanisms underlying these functions likely involve cellular pathways such as ubiquitin-proteasome system, protein degradation, and transcriptional regulation.\\n\\n] \n", - "151 [Summary: Regulation of transcriptional activity, cell signaling, and metabolism are enriched functions among these genes.\\nMechanism: These genes may be involved in cancer development and progression, as well as other cellular processes.\\n] \n", - "152 [Summary: Genes associated with extracellular matrix and growth factor regulation are enriched.\\nMechanism: Extracellular matrix remodeling and growth factor signaling pathways.\\n\\nHypothesis: The enriched genes are all involved in the regulation and maintenance of the extracellular matrix (ECM), suggesting a significant role in ECM organization and remodeling. The genes are also involved in growth factor signaling, suggesting a role in cell proliferation, differentiation, and wound healing. The findings indicate the importance of ECM organization and growth factor signaling in developmental processes and diseases such as osteogenesis imperfecta, Marfan syndrome, and atherosclerosis.] \n", - "153 [Summary: Extracellular matrix organization and angiogenesis\\nMechanism: Integrin signaling\\n\\nHypothesis: The genes in this list are enriched for those involved in the extracellular matrix organization and angiogenesis. These genes are related to integrin signaling which is important for mediating cell adhesion and signaling between the cell and extracellular matrix. The upregulation of these genes indicates an increased demand for extracellular matrix remodeling and angiogenesis in certain contexts, such as tissue regeneration or wound healing.\\n\\nThe enriched terms in this gene list suggest that the genes are involved in extracellular matrix organization, angiogenesis, and cell adhesion. These processes are important for tissue growth and repair and are likely regulated by integrin signaling. This suggests that the genes in this list may be involved in mediating these processes during tissue development or in response to injury.] \n", - "154 [Summary: Cell adhesion and cytoskeleton organization processes are enriched in the given list of genes.\\nMechanism: Cell adhesion and cytoskeleton organization are key processes in cell signaling and migration. \\n\\n] \n", - "155 [Summary: Cell adhesion and migration\\n] \n", - "156 [Summary: Genes are enriched in terms related to cell adhesion, signaling and transport.\\nMechanism: These genes are involved in pathways that regulate cell adhesion and communication, as well as transport of molecules across cellular membranes.\\n\\n] \n", - "157 [Summary: Genes are enriched for functions related to cell adhesion, signal transduction, and regulation of metabolism.\\nMechanism: These genes may be involved in coordinating cellular processes and responses to environmental signals.\\n\\n\\nHypothesis: The enriched terms suggest that these genes may be involved in regulating cellular processes related to adhesion, signaling, and metabolism. Specifically, they] \n", - "158 [Summary: Cell death regulation\\n\\nHypothesis: The genes on this list may interact with each other to form signaling pathways that regulate the balance between cell survival and death. Dysregulation of these pathways can lead to pathological conditions such as cancer. Further studies are needed to elucidate the specific mechanisms and interactions among these genes in the context of cell death regulation.] \n", - "159 [Summary: Genes in this list are enriched for functions related to apoptosis, immune response, and cancer.\\nMechanism: These genes play a role in regulating cell death, inflammatory response, and tumor development.\\n\\n] \n", - "160 [Summary: Genes are involved in lipid and sterol metabolism, as well as peroxisome biogenesis and function.\\n] \n", - "161 [Summary: The enriched terms are related to lipid metabolism, transport and catabolism, as well as cellular organelle biogenesis and function.\\nMechanism: These genes are involved in pathways related to cholesterol and bile acid biosynthesis, peroxisomal biogenesis and function, and fatty acid metabolism and transport.\\n\\n] \n", - "162 [Summary: Lipid metabolism and cholesterol biosynthesis are significantly enriched in the list of genes provided.\\nMechanism: The enriched terms suggest a pathway leading to the synthesis and transport of lipids and cholesterol within cells.\\n\\n] \n", - "163 [Summary: Lipid metabolism, cholesterol biosynthesis, and steroid biosynthesis are enriched functions among the given genes.\\nMechanism: The enriched functions suggest that these genes play a role in cholesterol and lipid metabolism pathways.\\n\\n] \n", - "164 [Summary: Extracellular matrix organization and coagulation cascade regulation are statistically overrepresented functions among the listed genes.\\nMechanism: Many of the genes in the list are involved in regulating extracellular matrix composition and integrity, which is important for tissue structure and homeostasis. This process involves the interaction of various proteases and inhibitors, as well as proteins involved in coagulation cascade regulation. \\n] \n", - "165 [Summary: Blood coagulation and immune response-related functions are over-represented in the list of genes provided.\\nMechanism: The genes are involved in producing factors required for blood clotting and regulating immune responses.\\n\\n] \n", - "166 [Summary: Immune system regulation and thrombosis prevention\\n\\nHypothesis: The genes in this set are involved in immune system surveillance and regulation, as well as the prevention of thrombosis by maintaining the delicate balance between hemostasis and clotting. These functions are critical in preventing pathological infections and clots, and their dysregulation could lead to autoimmune conditions or thrombotic events.] \n", - "167 [Summary: Immune system response and blood coagulation are the most statistically over-represented functions in the list of human genes provided.\\nMechanism: The genes in this list are mostly involved in regulating the immune response and blood coagulation pathways. \\n\\n] \n", - "168 [Summary: DNA replication and repair\\nMechanism: DNA replication and repair\\n] \n", - "169 [Summary: Genes in the list are involved in DNA replication, repair, and transcription.\\nMechanism: DNA maintenance\\n] \n", - "170 [Summary: DNA replication, cell division and chromosome segregation\\nMechanism: DNA replication and mitosis\\n\\nHypothesis: This list of genes is heavily enriched for genes involved in DNA replication, mitosis and chromosome segregation, suggesting that these are the major underlying biological mechanisms. Many of these genes are part of regulatory pathways that control these processes, such as the cell cycle and DNA damage response pathways. The enrichment of nucleosome assembly genes in this list suggests that this is a critical step in the DNA replication process, as nucleosomes must be efficiently assembled and disassembled to enable the progression of the replication fork. Additionally, genes involved in DNA repair are also enriched, indicating that these processes are tightly coordinated with DNA replication and mitosis to ensure genome stability.] \n", - "171 [Summary: DNA replication and repair, cell cycle regulation, and chromosome segregation are enriched terms among the given genes.\\nMechanism: These genes are involved in the regulation of DNA replication, repair mechanisms, proper chromosome segregation during mitosis, and inactivation of the cell cycle checkpoints.\\n] \n", - "172 [Summary: Extracellular matrix organization and regulation of growth factor signaling pathways\\nMechanism: The genes in this list are enriched for functions involved in extracellular matrix organization and regulation of signaling pathways for growth factors. These processes are critical for tissue development, maintenance, and repair.\\n\\n] \n", - "173 [Summary: Extracellular matrix organization and regulation of cell adhesion are enriched functions common among the listed genes.\\n\\nMechanism: The genes identified are involved in the maintenance of extracellular matrix homeostasis and cell adhesion. They are part of a complex network that controls the behavior and function of cells in various tissues.\\n\\n\\nHypothesis: The identified genes are involved in the regulation of a variety of cellular processes that are required for proper tissue development and homeostasis. Dysregulation of these genes may contribute to various pathological conditions, such as fibrosis, cancer, and developmental disorders.] \n", - "174 [Summary: Calcium ion binding and metabolism\\nMechanism: Calcium ions modulate a wide range of biological processes, including intracellular signaling, protein function, and gene expression.\\n] \n", - "175 [Summary: The common function among the provided genes is related to various cellular and biological processes such as metabolism, transport, signaling, and regulation.\\n\\nMechanism: No specific mechanism can be inferred without further analysis.\\n\\n] \n", - "176 [Summary: Calcium ion binding and transport, regulation of cell division, and inhibition of apoptosis are enriched functions among the given genes.\\nMechanism: Calcium signaling and regulation of cellular processes through calcium ions.\\n] \n", - "177 [Summary: Cell cycle regulation and cancer-related functions are enriched in the gene set.\\nMechanism: The genes are mostly involved in regulating cell division and proliferation, with some genes also implicated in cancer progression.\\n] \n", - "178 [Summary: Beta-oxidation of fatty acids, metabolic processes, and energy production pathways are enriched in the list of genes.\\n\\nMechanism: The list of genes is involved in the pathway of β-oxidation of fatty acids and energy production, promoting various metabolic processes.\\n\\n] \n", - "179 [Summary: These genes are involved in various metabolic processes, including lipid metabolism and energy production. \\nMechanism: The common underlying mechanism appears to be mitochondrial function and metabolism.\\n] \n", - "180 [Summary: Cell cycle regulation and chromosome segregation\\nMechanism: The genes are enriched for functions involved in cell cycle regulation, specifically in the G2/M phase transition and chromosome segregation.\\n\\n] \n", - "181 [Summary: Cell cycle regulation and DNA replication are enriched functions in the given list of genes.\\n\\nMechanism: The enriched functions of cell cycle regulation and DNA replication suggest that the genes in the list play a role in regulating the overall cell division process. Specifically, the genes are involved in DNA synthesis, repair, and proper chromosomal segregation, ensuring genomic stability and accurate transmission of genetic information.\\n\\n] \n", - "182 [Summary: Energy metabolism and glycosylation pathways are significantly enriched.\\nMechanism: These genes are involved in energy metabolism, specifically in glycolysis and glycogen biosynthesis pathways. Additionally, they are involved in glycosylation pathways, which play a role in post-translational modifications.\\n] \n", - "183 [Summary: Genes are involved in cellular metabolism and signaling pathways.\\nMechanism: This set of genes appears to be involved in the regulation of metabolic pathways in cells and are involved in various signaling pathways affecting cellular functions.\\n] \n", - "184 [Summary: Genes are enriched in terms related to nervous system development, signaling and angiogenesis.\\nMechanism: Signaling pathways related to neural development and angiogenesis.\\n\\nHypothesis: This set of genes is involved in the signaling pathways related to neural development and angiogenesis. The enriched terms, including nervous system development, neuron differentiation, embryonic morphogenesis, and regulation of angiogenesis, suggest that these genes are involved in complex processes related to neural network formation and elaboration, as well as vascular patterning and growth. Additionally, the genes in this list seem to be involved in positive regulation of signaling, which may play a role in the tight regulation of the complex developmental processes involved.] \n", - "185 [Summary: Genes are mainly involved in neural development and signaling pathways.\\nMechanism: Regulation of neural development and signaling pathways.\\n\\nHypothesis: The enriched terms suggest that these genes are involved in the development and maintenance of the nervous system. Many of the genes are associated with axon guidance and are involved in regulating the development of neuronal projections. The regulation of nervous system development and cell-cell signaling pathways may also play a role in coordinating the development of different types of neurons and neural circuits.] \n", - "186 [Summary: Transport and binding process for heme and iron-sulfur clusters, as well as [2Fe-2S] clusters, are enriched among the listed genes.\\nMechanism: Iron-containing proteins involved in biological processes require a tightly regulated system of transport and binding, which is facilitated by these enriched gene functions.\\n\\n] \n", - "187 [Summary: This set of genes is enriched for terms related to gene expression regulation, metabolism, and transport.\\n\\n] \n", - "188 [Summary: Cell metabolism, growth, and development are the most enriched functions among the given list of genes.\\nMechanism: These genes are predominantly associated with the regulation of glucose and energy homeostasis, cell proliferation, and extracellular matrix formation.\\n\\nHypothesis: The common biological mechanisms that underlie the functions of these genes involve the regulation of glucose and energy metabolism, which is essential for cell growth and development. They also regulate the formation of the extracellular matrix, which is crucial for the organization and maintenance of tissues and organs. These genes might be involved in signaling cascades that regulate cell proliferation, differentiation, and migration in response to changes in the microenvironment.] \n", - "189 [Summary: Carbohydrate metabolism and glycolysis are statistically over-represented in the list of genes.\\nMechanism: The genes involved in carbohydrate metabolism and glycolysis play a key role in energy production and cell signaling.\\n] \n", - "190 [Summary: Immune system functions are enriched in these genes, particularly those related to cytokine signaling, cell activation, and regulation.\\n\\nMechanism: The genes on this list are primarily involved in regulating the immune system. Many are involved in cytokine signaling, cell activation, and regulation. This suggests that the enriched terms are related to immune response and function.\\n\\n] \n", - "191 [Summary: Cell signaling and immune response\\nMechanism: Pathways involving cytokines, chemokines, and growth factors\\n\\nHypothesis: The genes in the list are involved in cell signaling and immune response. They play critical roles in the regulation of immune cell function, inflammation, and chemotaxis. The enriched terms, including immune response, cytokine activity, and chemokine activity, suggest that the genes are involved in cytokine signaling pathways, which mediate cellular responses to pathogens and other external stimuli. The genes may also be involved in growth factor signaling, which regulates cell proliferation and differentiation during development and tissue repair. Overall, the genes in the list likely form a complex regulatory network that is essential for the proper functioning of the immune system.] \n", - "192 [Summary: Immune response and signaling\\nMechanism: Cytokine signaling and immune response activation \\n\\n] \n", - "193 [Summary: Cytokine signaling and inflammation are the common functions enriched in these genes.\\nMechanism: These genes are involved in modulating the immune system's response to infection, injury, or stress.\\n\\nHypothesis: These genes are involved in regulating the inflammatory response through cytokine signaling. They are responsible for activating immune cells, triggering inflammation, and recruiting immune cells to sites of infection or injury. The JAK-STAT and Toll-like receptor signaling pathways play important roles in this process. Dysregulation of these genes can lead to chronic inflammation and autoimmune diseases.] \n", - "194 [Summary: Immune response, inflammation, and cytokine signaling-related functionality is enriched in the given list of genes.\\nMechanism: These genes are involved in the activation, regulation, and resolution of immune response and inflammation.\\n] \n", - "195 [Summary: These human genes are enriched in immune system-related functions.\\nMechanism: These genes are involved in immune response and immunoregulation pathways.\\n\\n] \n", - "196 [Summary: These genes are involved in the antiviral response and immune system regulation.\\nMechanism: These genes are part of the Type I interferon response pathway, which is activated by viral infection.\\n\\n] \n", - "197 [Summary: Genes associated with antiviral response, immune system processes, and interferon signaling pathways.\\n\\nMechanism: These genes are involved in the activation of the antiviral response and immune system processes, particularly through the interferon signaling pathway.\\n\\n] \n", - "198 [Summary: Type I interferon signaling pathway activation, immune response, antigen processing and presentation \\n\\n] \n", - "199 [Summary: Genes involved in immune response and inflammation are enriched.\\n\\nMechanism: These genes are all involved in the immune response and inflammation. They play a role in antigen processing and presentation, interferon response, cytokine production, and activation of inflammatory pathways.\\n\\n] \n", - "200 [Summary: Calcium ion binding and membrane transport are the most enriched functions in these genes.\\nMechanism: The majority of enriched terms are related to the transport of calcium ions across cell membranes, as well as regulation of intracellular calcium concentration.\\n\\n] \n", - "201 [Summary: Genes are enriched for terms related to ion transport, neurological signaling, and tissue development.\\n\\nHypothesis: These genes are potentially involved in regulating ion transport, such as calcium, sodium, and potassium, which are critical for neuronal signaling and tissue morphogenesis. Many of these genes are expressed in a variety of tissues and organs, including the brain, heart, and endocrine glands, suggesting they may have widespread physiological roles. The function of these genes may overlap in the regulation of cellular calcium balance, neural transmission, and developmental processes, which could contribute to human disease when disrupted.] \n", - "202 [Summary: Regulation of immune response, cellular signaling, and angiogenesis.\\nMechanism: The enriched terms suggest that these genes are involved in the regulation of immune response and cellular signaling pathways, as well as angiogenesis.\\n] \n", - "203 [Summary: Immune response and inflammation, coagulation, cell adhesion, and signal transduction are enriched functions among the genes.\\n\\n] \n", - "204 [Summary: Cell division and cytoskeleton organization are the commonly enriched functions among the given genes.\\nMechanism: The enrichment of these terms suggests that these genes play an important role in regulating mitotic spindle formation and organization of actin filaments.\\n\\n] \n", - "205 [Summary: Mitotic spindle organization and chromosome segregation\\nMechanism: Mitotic spindle assembly checkpoint\\n\\nHypothesis: The enrichment of terms related to the mitotic spindle organization, chromosome segregation, and spindle assembly checkpoint suggests that these genes play a critical role in mitosis and cell division. These genes likely regulate microtubule dynamics, centrosome function, and kinetochore-microtubule interactions to ensure the proper alignment, segregation, and separation of chromosomes during mitosis. Dysfunction of these genes may lead to chromosomal instability, aneuploidy, and tumorigenesis.] \n", - "206 [Summary: Cellular metabolism\\n] \n", - "207 [Summary: Protein folding and metabolism are enriched functions among these human genes.\\nMechanism: These genes may play a key role in maintaining protein homeostasis and regulating metabolic pathways.\\n] \n", - "208 [Summary: RNA processing and translation initiation\\nMechanism: Regulation of ribosome assembly and function\\n] \n", - "209 [Summary: RNA processing and translation are enriched functions in the given gene list.\\nMechanism: The genes are involved in regulating RNA processing and translation, necessary for cellular growth and proliferation.\\n\\n] \n", - "210 [Summary: The common function among the genes is related to RNA processing and ribosome biogenesis. \\nMechanism: The genes are involved in various steps of transcription, splicing, and translation of RNA.\\n\\nHypothesis: The enriched terms suggest that the genes are primarily involved in the regulation of ribosome biogenesis and RNA processing. This may be due to their role in the maintenance of cellular homeostasis by controlling protein synthesis and turnover. Dysfunction of these genes may lead to defects in ribosome biogenesis, causing impaired protein synthesis and contributing to various diseases, including cancer and neurodegenerative disorders.] \n", - "211 [Summary: Genes in the list are functionally enriched in processes related to ribosome biogenesis and RNA metabolism.\\nMechanism: The genes in the list are all involved in the formation and functioning of ribosomes, which are essential cellular machinery for protein synthesis. They are also involved in RNA metabolism, which includes transcription, splicing, ribonucleoprotein assembly, and RNA transport.\\n\\n] \n", - "212 [Summary: Muscle contraction and development\\n\\nHypothesis: The significant enrichment of genes involved in muscle contraction and sarcomere development suggests that there may be shared pathways and mechanisms governing these processes. One potential pathway may involve the regulation of actin and myosin filaments, which are crucial components of the sarcomere and fundamental to muscle contraction. Another potential pathway may involve the coordination of signaling cascades that promote muscle growth and differentiation. Further research in these areas could lead to a better understanding of muscle function and the treatment of muscle-related diseases.] \n", - "213 [Summary: Muscle structure and contraction.\\nMechanism: Actin-myosin interaction and sarcomere formation.\\n] \n", - "214 [Summary: Genes are primarily involved in Notch pathway signaling and Wnt pathway signaling.\\nMechanism: The Notch pathway and Wnt pathway signaling are two important mechanisms for cell signaling and development.\\n\\nHypothesis: The genes listed are involved in regulating cell signaling and differentiation pathways such as the Notch and Wnt pathways. These pathways are responsible for the development of various tissues and organs in the body. Dysregulation of these genes and pathways can lead to developmental abnormalities and diseases.] \n", - "215 [Summary: Genes are mostly involved in the development and regulation of the Notch signaling pathway.\\nMechanism: The Notch signaling pathway is involved in cell-to-cell communication, controlling cell fate decisions and differentiation during development.\\n] \n", - "216 [Summary: Mitochondrial function and energy production pathways are enriched in the list of genes.\\n\\nMechanism: The genes in the list are involved in various aspects of mitochondrial oxidative phosphorylation and energy production pathways.\\n\\n] \n", - "217 [Summary: Mitochondrial respiratory chain function\\nMechanism: Oxidative Phosphorylation\\n\\nHypothesis: These genes are primarily involved in mitochondrial respiratory chain function, specifically in oxidative phosphorylation through NADH dehydrogenase activity and electron transport chain. They contribute to the assembly of respiratory chain complexes I, II, III, IV, V, VI, which are located in the mitochondrial inner membrane. Additionally, these genes are involved in the organization and biogenesis of mitochondria, as well as in ubiquinone and fatty acid metabolism. Mutations in these genes can cause various mitochondrial disorders affecting energy production and cell function.] \n", - "218 [Summary: Regulation of cell cycle and cell death. \\n\\nHypothesis: The enriched terms suggest that these genes play a crucial role in normal cellular processes, and their dysregulation may result in abnormal growth and proliferation of cells. The underlying biological mechanism may involve activation of DNA damage response pathways and regulation of the p53 tumor suppressor protein, leading to cell cycle arrest and apoptosis.] \n", - "219 [Summary: DNA damage response and cell cycle regulation\\nMechanism: Activation of p53 pathway and downstream effector genes\\n] \n", - "220 [Summary: These genes are associated with pancreatic beta cell development and function.\\nMechanism: Beta cell development and function\\n\\nHypothesis: These genes are involved in the development and function of pancreatic beta cells, which produce and secrete insulin and play a critical role in glucose homeostasis. The enriched terms suggest that these genes are important for the differentiation, development, and function of pancreatic beta cells as well as overall pancreatic islet cell development. This suggests that disruptions in these genes could lead to impaired beta cell function and contribute to the development of diabetes.] \n", - "221 [Summary: The genes in this list are enriched for terms related to pancreatic beta cell development and function.\\nMechanism: Pancreatic beta cells are responsible for insulin secretion, which regulates glucose levels in the body. Dysfunction of these cells can lead to diabetes.\\n] \n", - "222 [Summary: Genes involved in lipid metabolism, transport, and signaling are significantly over-represented in this list.\\n\\nMechanism: Lipid metabolism and transport\\n\\n\\nHypothesis: The genes in this list are involved in the metabolism, transport, and signaling of lipids. ABC transporters are responsible for the transport of lipids across membranes. Fatty acid metabolism and cholesterol biosynthesis are crucial in lipid homeostasis. PPAR signaling pathway regulates the expression of genes involved in lipid metabolism. Peroxisomes play an important role in the breakdown of fatty acids.] \n", - "223 [Summary: Genes involved in lipid metabolism and transport are enriched.\\nMechanism: Lipid metabolism and transport pathways are affected by the genes in the list.\\n\\n] \n", - "224 [Summary: Signaling and regulation\\n\\nHypothesis: These genes could be involved in regulating cellular responses to extracellular stimuli, including growth factors and cytokines. They could also play a role in tumor growth and progression.] \n", - "225 [Summary: Signaling and metabolism pathways are significantly enriched among the given genes.\\n\\nMechanism: These genes are involved in cellular signaling pathways, including the MAPK and PI3K pathways, which play a role in cell growth, proliferation, and survival. Many of the genes are also involved in metabolic processes, such as glucose metabolism.\\n\\n] \n", - "226 [Summary: Vesicular trafficking and membrane transport are enriched functions in the given list of genes.\\nMechanism: Membrane transport and trafficking between various cellular compartments, such as the endoplasmic reticulum (ER), Golgi, lysosome, and plasma membrane, involve the trafficking of cargoes in vesicles. The formation, budding, tethering, and fusion of these vesicles are tightly regulated by various membrane-bound proteins and adaptors. \\n\\n] \n", - "227 [Summary: Transport and trafficking of proteins and molecules within cells.\\nMechanism: These genes play a role in vesicular transport, protein sorting, and trafficking within the cell. The enriched terms provide insight into the specific pathways and compartments involved in this process.\\n\\n\\nHypothesis: These genes are involved in the coordinated transport of proteins and molecules between different intracellular compartments, such as the endoplasmic reticulum, Golgi apparatus, and lysosomes. They likely form part of a complex network of regulatory pathways ensuring the efficient and accurate sorting of cargo to their appropriate destinations. The enrichment of terms related to clathrin-mediated endocytosis suggests that this process is also important in regulating protein trafficking within the cell.] \n", - "228 [Summary: Genes involved in antioxidant defense and redox regulation are enriched.\\n\\nMechanism: Antioxidant defense and redox regulation are essential for maintaining cellular homeostasis and preventing oxidative stress-induced damage.\\n\\n\\nHypothesis: These genes likely play important roles in maintaining proper cellular redox balance, which is critical for preventing oxidative damage to cellular components such as DNA, proteins, and lipids. Additionally, they may contribute to the detoxification of harmful reactive oxygen species produced during normal cellular metabolism or in response to various stressors such as environmental toxins and pathogens.] \n", - "229 [Summary: Oxidative stress response and redox regulation\\nMechanism: These genes are involved in regulation of redox balance and response to oxidative stress.\\n] \n", - "230 [Summary: Enriched terms suggest that the listed genes may function primarily in the process of spermatogenesis and meiosis.\\nMechanism: Spermatogenesis and meiosis.\\n\\nHypothesis: The enriched terms suggest that these genes function primarily in the process of spermatogenesis and meiosis. These genes may play roles in meiotic recombination, chromosome segregation, and overall gamete formation. Many of the genes are involved in regulating cell division, which is necessary for proper gamete formation. Additionally, some genes are involved in regulating hormone secretion, which is important for the development and maturation of male reproductive organs.] \n", - "231 [Summary: Cell cycle regulation and chromosome organization \\nMechanism: Mitotic checkpoint and spindle assembly \\n\\nHypothesis: The enrichment of terms related to mitotic spindle organization and chromosome segregation suggests that these genes may play a role in regulating the cell cycle. Specifically, many of these genes are involved in mitotic checkpoint signaling pathways that help ensure proper chromosome alignment and segregation during cell division. Additionally, some of these genes may play a role in organizing the microtubules and proteins that make up the mitotic spindle. Overall, these genes likely play critical roles in maintaining genomic stability and preventing the development of cancer and other genetic diseases.] \n", - "232 [Summary: Genes are involved in the TGF-beta signaling pathway.\\nMechanism: The TGF-beta signaling pathway plays a key role in cell growth, differentiation, and development.\\n] \n", - "233 [Summary: Genes associated with regulation of transforming growth factor-beta (TGF-beta) signaling pathway.\\nMechanism: TGF-beta signaling pathway regulation\\n\\n] \n", - "234 [Summary: Immune response and inflammation-related gene functions are statistically over-represented in this list of genes.\\nMechanism: These genes are involved in the regulation of immune response and inflammation pathways.\\n\\n] \n", - "235 [Summary: Immune response and inflammation-related gene functions are enriched in the given list of genes.\\n\\nHypothesis: The enriched terms suggest that these genes play an important role in regulating the immune system response and controlling inflammation. This includes controlling cytokine and TNF production, which are important factors in regulating inflammation. The negative regulation of the NF-kappaB transcription factor activity may play a role in preventing inflammation and maintaining immune system homeostasis. These findings may have implications for understanding a range of inflammatory conditions and immune system disorders.] \n", - "236 [Summary: The genes in the list are enriched for functions related to protein folding and sorting, as well as response to stress and cellular damage. \\n\\nMechanism: The enriched terms suggest that these genes are involved in regulating protein quality control in the cell, ensuring that misfolded or damaged proteins are properly degraded or refolded.\\n\\n\\nHypothesis: The genes in this list are enriched for functions related to the quality control of cellular proteins, ensuring that only properly folded and functional proteins are allowed to move through the various stages of processing and trafficking. This involves a highly coordinated series of regulatory and surveillance pathways, including chaperone-mediated folding, ubiquitin-mediated proteolysis, and mRNA processing and splicing. Dysfunction in any one of these pathways can result in accumulation of misfolded proteins, leading to cellular damage and disease.] \n", - "237 [Summary: Genes enriched in protein folding-related functions \\n\\nMechanism: These genes are involved in regulation of protein homeostasis, such as protein folding, chaperone-mediated protein processing, and protein transport.\\n\\n] \n", - "238 [Summary: Regulation of gene expression and signal transduction\\nMechanism: Kinase signaling pathways and transcription regulation\\n\\n\\nHypothesis: The genes in this list are involved in regulating gene expression and signal transduction. Many of these genes are involved in kinase signaling pathways and transcription regulation, which are essential for proper cellular growth and differentiation. This suggests that the underlying biological mechanisms may involve a complex interplay between various signaling pathways governing gene expression and cellular processes. Additionally, many of these genes are involved in regulation of protein phosphorylation and intracellular transport, suggesting that they play important roles in cellular communication and the regulation of downstream signaling events.] \n", - "239 [Summary: Genes are involved in extracellular matrix organization, signal transduction, and neural development.\\nMechanism: Regulation of cell signaling pathways.\\n\\n\\nHypothesis: These genes are involved in regulating cell signaling pathways and controlling neural development by modulating extracellular matrix organization. The enriched terms suggest that these genes are involved in growth factor activity and neurogenesis, indicating that they play a critical role in regulating cell proliferation and differentiation during neural development. Dysfunction of these genes could lead to abnormalities in neural development and function, possibly leading to neurological disorders.] \n", - "240 [Summary: The common function of the genes in the list is related to regulation of cellular processes and response to stimuli.\\n\\nMechanism: The genes in the list are involved in cellular processes such as metabolism, transport, and signaling. They also play a role in response to stimuli such as stress, inflammation, and DNA damage.\\n\\n] \n", - "241 [Summary: Gene Ontology (GO) term enrichment analysis was performed on a list of human genes to identify common functional themes.\\n\\nHypothesis: The enriched terms suggest that these genes are involved in cellular responses to different kinds of stressors. The mechanism may involve signal transduction pathways that lead to activation of transcription factors, changes in protein localization, and alterations in cell cycle progression and apoptosis in response to stress stimuli, such as DNA damage, oxidative stress, and hypoxia. These genes may also contribute to the maintenance of cellular homeostasis under conditions of stress.] \n", - "242 [Summary: Genes involved in the Wnt signaling pathway and Notch signaling pathway\\nMechanism: Interaction between Wnt and Notch signaling pathways\\n] \n", - "243 [Summary: Genes are involved in the Wnt signaling pathway and Notch signaling pathway.\\nMechanism: Signaling pathways\\n\\nHypothesis: The enrichment of Wnt and Notch signaling pathways and protein and transcription factor binding suggests that these genes function in regulating gene expression and cell proliferation during development and homeostasis. Specifically, Wnt pathway plays essential roles during embryonic development, tissue homeostasis, and wound healing. The Notch pathway has a crucial role in cellular differentiation, proliferation, and apoptosis. Protein and transcription factor binding may regulate Wnt and Notch signaling or downstream gene expression changes.] \n", - "244 [Summary: Immune system regulation and response is over-represented in these genes.\\nMechanism: These genes function in the activation and regulation of immune cells and signaling pathways.\\n\\n] \n", - "245 [Summary: Immune system function\\n\\nHypothesis: These genes may be involved in the overall function of the immune system, particularly in the regulation and activation of T cells in response to pathogens or cancer cells. They may also play a role in autoimmune disorders, in which the immune system mistakenly targets and attacks the body's own cells. Further research into the specific mechanisms of these genes in immune function could lead to better treatment and prevention strategies for immune-related disorders.] \n", - "246 [Summary: Genes POU5F1, SOX2, KLF4, and MYC are all involved in regulating gene expression and cellular growth, with a focus on stem cells.\\nMechanism: These genes are part of the transcriptional regulatory network that controls stem cell self-renewal, proliferation, and differentiation.\\n\\nHypothesis: The enriched terms suggest that these genes are involved in the regulation of transcriptional activity by binding directly to DNA and controlling the expression of genes involved in stem cell differentiation. The transcriptional regulatory network formed by these genes may play a role in maintaining the balance between self-renewal and differentiation of stem cells, which is critical for tissue repair and regeneration.] \n", - "247 [Summary: These genes are all involved in transcriptional regulation and have been identified as key players in the maintenance of pluripotency and self-renewal in stem cells.\\nMechanism: Transcriptional regulation\\n\\nHypothesis: These genes play a crucial role in the regulation of stem cell differentiation by maintaining the pluripotency and self-renewal capacity of stem cells through their transcriptional regulation. The enriched terms suggest that these genes have a specific role in regulating stem cell differentiation and fate determination.] \n", - "248 [Summary: Extracellular matrix organization and angiogenesis\\nMechanism: Signaling pathways through FGFR1 and integrin ITGAV\\n] \n", - "249 [Summary: Several of the genes are involved in extracellular matrix organization, cell adhesion, and angiogenesis.\\nMechanism: Extracellular matrix (ECM) organization and remodeling, cell adhesion, and angiogenesis are essential processes in tissue development, maintenance, and repair. Dysregulation of these processes can lead to pathological conditions such as cancer and fibrosis.\\n\\n\\nHypothesis: These genes are likely involved in a common biological pathway that regulates ECM organization, cell adhesion, and angiogenesis. One possible mechanism is the activation of MAPK signaling, which plays a central role in cell migration, proliferation, and survival, and is often dysregulated in cancer and other diseases. Further studies are needed to elucidate the precise biological mechanisms underlying these enriched terms.] \n", - "250 [Summary: Genes are enriched in terms related to neuronal development and signaling, transcriptional regulation, and ion transport.\\nMechanism: These genes are likely involved in a variety of biological mechanisms, including brain development, synaptic transmission, and the regulation of gene expression.\\n\\n] \n", - "251 [Summary: The enriched terms are related to the function of transcription and RNA processing.\\nMechanism: These genes may regulate gene expression and transcriptional processes.\\n] \n", - "252 [Summary: Genes are involved in muscle contraction and regulation.\\n\\nMechanism: The genes in this list are mainly expressed in muscle tissues and play a critical role in the contraction and regulation of various muscle types.\\n\\n] \n", - "253 [Summary: Muscle protein regulation and contractility\\nMechanism: Myofilament formation and calcium signaling\\n] \n", - "254 [Summary: The common function among the given human genes is related to lipid and cholesterol processing and transport, as well as endosomal trafficking and protein degradation.\\nMechanism: The genes are involved in regulating intracellular vesicle trafficking and endosome maturation, as well as lipid and cholesterol metabolism.\\n\\nHypothesis: It is likely that the genes are involved in regulating the endocytic pathway and in processing and transporting lipids and cholesterol. The genes play critical roles in maintaining cellular homeostasis by regulating protein degradation and recycling, as well as lipid and cholesterol storage and utilization. Dysfunction in these genes may lead to the development of metabolic disorders, such as dyslipidemia or atherosclerosis.] \n", - "255 [Summary: Endocytosis and Vesicular Trafficking\\nMechanism: These genes are involved in endocytosis and vesicular trafficking pathway which involves the internalization of extracellular molecules, membrane proteins and lipids. This pathway plays a crucial role in the regulation of cell signaling, nutrient uptake, and receptor desensitization.\\n] \n", - "256 [Summary: The list of human genes is enriched for terms related to glycolysis and glucose metabolism.\\nMechanism: The genes in this list are all involved in the initial steps of glycolysis, converting glucose to pyruvate.\\n\\nHypothesis: The enriched terms suggest that the genes in this list are all involved in the process of converting glucose to pyruvate via glycolysis. This process is a central metabolic pathway in almost all organisms, providing energy for cellular processes and serving as a carbon source for biosynthesis. The presence of these specific genes in this list implies that they may be particularly important for the regulation and successful execution of the glycolytic process.] \n", - "257 [Summary: Enzymes involved in glycolysis.\\nMechanism: Glycolysis pathway.\\n\\nHypothesis: These genes are all involved in the glycolysis pathway, a metabolic pathway that converts glucose into pyruvate and produces ATP. The over-representation of terms related to carbohydrate and glucose metabolic processes suggests that these genes play a key role in the breakdown of glucose and the production of ATP, which is essential for cellular energy metabolism.] \n", - "258 [Summary: Calcium signaling and neurotransmission-related functions are enriched in the given genes.\\nMechanism: These genes are involved in the regulation of ion channels and neurotransmitter receptors, affecting calcium influx and signaling in neurons.\\n] \n", - "259 [Summary: \\nThese human genes are involved in ion channel activity and neurotransmitter signaling. \\n\\nMechanism: \\nThe enriched terms suggest that these genes are involved in the regulation of synaptic transmission.\\n\\n\\nHypothesis: \\nThe high number of ion channel and neurotransmitter signaling related genes in this list suggests that they may play a crucial role in the regulation of synaptic transmission. Specifically, these genes may contribute to the modulation of calcium ion flux at synapses, which is necessary for proper neurotransmitter release and subsequent neuronal signaling. Dysregulation of this pathway may lead to various neurological disorders.] \n", - "260 [Summary: Genes are enriched in terms related to cellular stress response and apoptotic processes.\\nMechanism: Activation of stress response pathways leading to apoptosis.\\n\\nHypothesis: These genes may be involved in regulating cellular response to stress through activation of NF-kappaB and JNK signaling pathways, leading to apoptosis. The enriched terms suggest that they may function together in regulating the activation or inhibition of these pathways in response to cellular stressors.] \n", - "261 [Summary: The functions of the given genes are enriched in regulation of autophagy, cellular response to stress, and apoptotic process.\\nMechanism: Autophagy regulation and cellular response to stress pathways are overrepresented in the given genes.\\n\\nHypothesis: It is possible that the genes listed are involved in the regulation of autophagy and cellular response to stress. The over-representation of apoptotic process may reflect the role of these genes in cellular homeostasis, survival, and death. The genes may be involved in the mTOR signaling pathway or PI3K/AKT pathway which regulate autophagy, as they include genes such as PIK3CA, AKT1, RPTOR, MLST8, which play a vital role in these pathways. Alternatively, the genes may be related to the JNK signaling pathway, which modulates cellular response to stress and can activate apoptosis. Further experimentation is required to determine the exact mechanism and pathway of these genes.] \n", - "262 [Summary: Enzyme activity and carbohydrate metabolism are over-represented functions in the given list of genes.\\nMechanism: These genes may primarily be involved in lysosomal function and the digestion of complex carbohydrates and glycoproteins.\\n\\n] \n", - "263 [Summary: The genes in this list are involved in carbohydrate metabolism, glycosylation, and degradation processes.\\nMechanism: These genes all play a role in various stages of carbohydrate processing, from synthesis to degradation.\\n\\nHypothesis: These genes are involved in the processing, modification, and breakdown of carbohydrates in the body. This includes glycosylation of proteins for proper folding and function, as well as the breakdown of complex carbohydrates for energy production. The enrichment of terms related to hydrolase activity suggests a particular focus on breaking down O-glycosyl compounds. The variety of specific enzyme activities present in these genes likely reflects the diverse range of carbohydrates and glycoproteins that are present in the body.] \n", - "264 [Summary: Genes related to immunoglobulins and T- and B-cell receptor chains.\\n\\nHypothesis: \\nThese genes are mostly related to immunoglobulin and T- and B-cell receptor chains. The enriched terms suggest that they are involved in various aspects of the immune response, such as recognizing and binding to foreign antigens and activating B and T cells. These genes are crucial for proper functioning of the adaptive immune system which plays a vital role in protecting the body against pathogens.] \n", - "265 [Summary: Immune system function\\nMecanism: Antibody-mediated immunity\\n\\nHypothesis: The list of genes are all involved in the immune system function, specifically in the production and activation of immunoglobulins. They are all related to B cells and play a crucial role in the antibody-mediated immune response.] \n", - "266 [Summary: Genes are mainly involved in DNA repair, recombination, and chromosome segregation during meiosis.\\nMechanism: Meiosis and DNA repair\\n] \n", - "267 [Summary: Genes involved in meiosis and DNA repair.\\nMechanism: Meiotic recombination and chromosome segregation.\\n\\n] \n", - "268 [Summary: The common function among the given genes is related to cellular response to stress and regulation of cell growth.\\n\\nMechanism: These genes are involved in multiple pathways that control cell growth and homeostasis, including the NF-κB and STAT3 signaling pathways. They also play a role in cellular response to stress, particularly oxidative stress. \\n\\n] \n", - "269 [Summary: These human genes are enriched in terms related to regulation and response to cellular stress.\\n\\nMechanism: The underlying biological mechanism is likely related to the response to various types of cellular stress, including oxidative stress and DNA damage.\\n\\n\\nHypothesis: These genes may be involved in regulating the response to cellular stress through various pathways, including the regulation of protein localization to organelles and the stabilization of proteins involved in stress response. Additionally, the negative regulation of cell proliferation and positive regulation of apoptotic process terms suggest a possible role in regulating cell survival or death decisions in response to stress.] \n", - "270 [Summary: Cellular metabolism\\n] \n", - "271 [Summary: Transport, metabolism, and protein folding are enriched functions for these genes.\\nMechanism: These genes are involved in regulating cellular metabolism and maintaining protein homeostasis.\\n\\n] \n", - "272 [Summary: The genes PEX1, PEX2, PEX3, PEX5, PEX6, and PEX7 are all involved in peroxisome biogenesis.\\nMechanism: Peroxisome biogenesis\\n\\nHypothesis: These genes are involved in the process of peroxisome biogenesis, which is the formation of new peroxisomes in the cell. Peroxisomes are organelles that perform various metabolic functions, including the breakdown of fatty acids and the detoxification of harmful substances. The enriched terms suggest that these genes are involved in the organization of the peroxisome membrane and matrix, as well as the import of proteins into the peroxisome. This could potentially be related to the localization and assembly of necessary components for peroxisome formation and function.] \n", - "273 [Summary: The common function of the given human genes is related to peroxisome biogenesis.\\n\\nMechanism: The peroxisome biogenesis process involves the formation of a membrane-bound organelle that contains enzymes involved in various metabolic pathways, including fatty acid degradation, plasmalogen biosynthesis, and bile acid synthesis. Peroxisomes play a vital role in cellular metabolism and are involved in various processes such as lipid metabolism, reactive oxygen species (ROS) detoxification, and the biosynthesis of specific signaling molecules.\\n\\n\\nHypothesis: The genes PEX2, PEX3, PEX6, PEX7, and PEX1 are all involved in peroxisome biogenesis. These genes encode proteins that are required for the assembly of peroxisomes and their proper function. Specifically, PEX1 and PEX6 encode ATPases involved in the translocation of peroxisomal matrix proteins into the organelle, while PEX2, PEX3, and PEX7 have roles in the early stages of peroxisome biogenesis, including membrane assembly and division. The enriched] \n", - "274 [Summary: These genes all play a role in the maintenance and regulation of nuclear structure and function, particularly in DNA repair and organization.\\nMechanism: These genes are involved in the nuclear lamina, a network of proteins that provides structural support to the nucleus and helps regulate gene expression. Dysregulation of the lamina can lead to DNA damage and aging-related diseases.\\n] \n", - "275 [Summary: Genes LMNA, WRN, and BANF1 are involved in chromatin organization and DNA repair.\\nMechanism: These genes are involved in maintaining nuclear architecture and stability.\\n\\nHypothesis: LMNA, WRN, and BANF1 are all involved in the regulation of chromatin organization and DNA repair, suggesting a potential link between nuclear architecture and genomic stability. These genes may function in pathways related to telomere maintenance, nuclear localization, nuclear lamina organization, and genome stability regulation. Overall, these findings suggest a potential mechanism by which changes in nuclear architecture and stability could lead to genomic instability and disease.] \n", - "276 [Summary: These genes are primarily involved in neurological processes and ion channel regulation. \\nMechanism: Regulation of ion channels in the nervous system.\\n\\nHypothesis: These genes are primarily involved in the regulation of ion channels in the nervous system, which affects processes such as nervous system development, synaptic transmission, and membrane potential regulation. The enrichment of terms related to ion transport and transmembrane transport suggest that these genes may play an important role in maintaining the balance of ion concentrations in neuronal cells, which is essential for proper neurological function. Additionally, the enrichment of terms related to neuron development suggests that these genes may play a role in shaping the nervous system during development.] \n", - "277 [Summary: Neurotransmission and Ion Channels are enriched functions in the given human genes.\\nMechanism: Signaling and excitatory neurotransmission.\\n\\n\\nHypothesis: The enriched functions suggest that these genes play a critical role in signaling pathways and neurotransmission in the central nervous system. Furthermore, the identified ion channels and receptors help mediate the excitatory and inhibitory communication between neurons, thus playing a critical role in neuronal development, learning, and memory.] \n", - "278 [Summary: Genes are involved in nervous system development and function. \\nMechanism: Myelination and axonal transport. \\n\\nHypothesis: The genes on the list are enriched for terms involved in nervous system development and function, including myelination, axon guidance, and neuron projection development. This suggests a role for these genes in the regulation of myelination and axonal transport, which are important processes for proper nervous system function. Dysfunction of these processes, due to mutations in genes such as PMP22 and SH3TC2, can lead to peripheral neuropathy and other neurological disorders.] \n", - "279 [Summary: Genes related to neurological and cellular metabolism processes are over-represented.\\nMechanism: Metabolic and neurological processes\\n\\nHypothesis: These genes are involved in processes related to myelin sheath formation, cellular metabolism, and neurological development. Specifically, the genes NAGLU, PMP22, MPZ, EGR2, and TWNK are involved in myelin sheath formation, which is necessary for proper nerve function. FLVCR1, KPNA3, and AARS1 are involved in cellular metabolism, which has implications for cellular growth and function. Finally, DNAJC3, RNF170, and PIEZO2 are related to neurological development, which may be associated with neural plasticity and adaptation. Together, these genes suggest that there is an association between cellular metabolism, neurological development, and myelin sheath formation.] \n", - "280 [Summary: G protein-coupled receptor signaling pathway.\\nMechanism: The genes are involved in the regulation of dopamine and prostaglandin signaling through G protein-coupled receptors.\\n] \n", - "281 [Summary: G protein signaling and dopamine receptor activity are enriched in the list of human genes provided.\\nMechanism: G protein-coupled receptor (GPCR) signaling pathway and dopamine signaling pathway.\\n\\nHypothesis: The enriched genes in this list are involved in the GPCR and dopamine signaling pathways. GPCRs are the largest family of transmembrane receptors and play a crucial role in cellular signaling. The GPCR signaling pathway is responsible for several physiological processes like regulation of blood pressure, heart rate, immunity, and neurotransmission. The dopamine signaling pathway is responsible for reward, mood regulation, and movement. The enriched terms suggest the involvement of the GPCR signaling pathway and dopamine signaling pathway in regulating these physiological processes. The activation of adenylate cyclase and the role of Dopamine D1 receptor are important mechanistic pathways involved in the regulation of these physiological processes.] \n", - "282 [Summary: Genes are enriched for transcription regulation, chromatin remodeling, and developmental processes.\\nMechanism: Transcriptional regulation\\n\\nHypothesis: The genes in this list are enriched for functions involved in transcriptional regulation, chromatin modification, and developmental processes. Specifically, the enriched terms suggest these genes play a role in protein-DNA complex assembly and response to stress. One underlying biological mechanism could involve the formation of multi-protein complexes involved in transcriptional regulation, including recruitment of chromatin remodelers and transcription factors, as well as response to cellular stress through activation of various signaling pathways.] \n", - "283 [Summary: These genes are enriched for terms related to transcriptional regulation and DNA binding.\\nMechanism: The mechanism likely involves the regulation of gene expression through DNA binding and transcriptional control.\\n\\n] \n", - "284 [Summary: The common function of the listed genes is related to connective tissue development, collagen biosynthetic processes, and extracellular matrix organization. \\n\\nMechanism: The enrichment of terms related to connective tissue and collagen biosynthesis suggests a potential underlying biological mechanism linking these genes to the pathogenesis of Ehlers-Danlos syndrome.\\n\\n] \n", - "285 [Summary: Genes involved in extracellular matrix organization and connective tissue development are enriched.\\nMechanism: These genes likely play a role in the synthesis, organization, and maintenance of the extracellular matrix and connective tissue.\\n\\n] \n", - "286 [Summary: These genes are involved in DNA repair and protein monoubiquitination, and are part of the Fanconi anemia nuclear complex. \\n\\nMechanism: The Fanconi anemia pathway plays a key role in the DNA repair process. \\n\\n] \n", - "287 [Summary: The enriched terms are related to DNA repair and protein monoubiquitination.\\nMechanism: These genes are involved in the Fanconi anemia pathway, which is a DNA damage response pathway that repairs interstrand DNA crosslinks.\\n] \n", - "288 [Summary: Several of the genes are involved in mitochondrial function, including electron transfer and ATP synthesis. Others are involved in lipid metabolism and transport, and some are involved in protein binding and signaling.\\n\\nMechanism: The enriched terms suggest a focus on mitochondrial function and metabolism, as well as protein and lipid transport and signaling.\\n\\n] \n", - "289 [Summary: Mitochondrial function, enzyme activity, and transporter activity\\nMechanism: Mitochondrial metabolism\\n] \n", - "290 [Summary: Immune response-regulating genes\\n] \n", - "291 [Summary: These human genes are enriched in terms related to immune system, cytokine activity, chemokine receptor binding activity, and protein kinase activity.\\n\\n] \n", - "292 [Summary: Genes are involved in a variety of functions, including transport, enzyme activity, binding, and regulation of various processes. Enriched terms include protein phosphorylation, intracellular signaling pathways, and regulation of macromolecule metabolic process.\\n\\nMechanism: The enriched terms suggest that these genes are involved in signaling pathways and regulation of cellular processes. Specifically, protein phosphorylation appears to play a key role in the functions of these genes.\\n\\n] \n", - "293 [Summary: Genes are involved in various activities such as metal ion binding, enzymatic activity, and signal transduction.\\n\\n] \n", - "294 [Summary: Several genes are involved in extracellular matrix organization and cell signaling pathways, while others have roles in blood coagulation, lipid metabolism, and immunity.\\n\\n] \n", - "295 [Summary: Extracellular matrix organization and cell signaling\\nMechanism: Extracellular matrix regulation and cell signaling pathways\\n\\nHypothesis: These genes function in extracellular matrix organization and cell signaling pathways, involved in regulating the formation and maintenance of the extracellular matrix and cellular communication. They share enriched terms related to protein binding activity and positive regulation of intracellular signal transduction and are highly enriched for components of the collagen-containing extracellular matrix. This suggests a potential role in regulating collagen matrix structure, cell adhesion, and proliferation, as well as cell signaling cascades essential for tissue development and homeostasis.] \n", - "296 [Summary: These genes are involved in various cellular processes related to cytoskeletal organization, cell-cell communication, and intracellular signaling.\\n\\nMechanism: The common underlying biological mechanism may involve regulation of actin filament dynamics, which could impact processes such as cellular adhesion and migration, as well as intracellular signaling cascades.\\n\\n] \n", - "297 [Summary: Cell adhesion and signaling\\nMechanism: Integrin-mediated signaling and cytoskeletal regulation\\n] \n", - "298 [Summary: Several of the genes are involved in membrane transport and signaling, with a focus on plasma membrane and extracellular space.\\n\\nMechanism: These genes may be involved in the regulation of cellular signaling pathways and transport processes, particularly those related to the plasma membrane and extracellular space.\\n\\n] \n", - "299 [Summary: The enriched terms include processes related to regulation and signaling, ion transport, cell adhesion and migration, and metabolic processes. \\n\\nMechanism: These genes may play roles in maintaining cellular homeostasis and responding to changes in the external environment through ion transport and signaling pathways. They may also act to regulate cell adhesion and migration, and participate in metabolic processes.\\n\\n] \n", - "300 [Summary: Genes in this list are primarily involved in apoptotic signaling pathways and immune response regulation.\\nMechanism: These genes act as modulators or effectors in apoptotic signaling pathways and immune response regulation. \\n\\n] \n", - "301 [Summary: The enriched terms include apoptotic process, cytokine activity, and protein binding activity. \\n\\n] \n", - "302 [Summary: These genes are involved in lipid and cholesterol metabolism, as well as peroxisomal and vitamin D-related processes.\\n\\nMechanism: These genes likely play a role in maintaining lipid and cholesterol homeostasis and metabolism, possibly through the regulation and transport of these molecules across cellular membranes.\\n\\n] \n", - "303 [Summary: Many of the listed genes are involved in lipid metabolism and transport, as well as peroxisome-related processes. \\n\\n\\nHypothesis: These genes are likely involved in the regulation and transport of various lipids and sterols, with a particular focus on the transport and metabolism of fatty acids and cholesterol in peroxisomes. ABC-type transporters may be involved in lipid uptake and efflux, while peroxisome-related processes may play a role in lipid metabolism and oxidation.] \n", - "304 [Summary: Cholesterol biosynthesis and metabolism genes.\\n\\nMechanism: These genes are involved in the biosynthesis and metabolism of cholesterol, a crucial molecule for cell membrane synthesis and steroid hormone production.\\n\\n] \n", - "305 [Summary: Cholesterol biosynthesis and lipid metabolism are the enriched terms across the provided genes.\\n\\nMechanism: The enriched terms suggest that the provided genes are involved in cholesterol biosynthesis and lipid metabolism, specifically the synthesis of isoprenoids and fatty acids.\\n\\n\\nHypothesis: These genes likely function in a coordinated pathway to support the synthesis of cholesterol, isoprenoids, and fatty acids within the body. This pathway may be involved in regulating cellular and systemic levels of these lipids to support proper cellular function and physiological processes, such as membrane structure and hormone production. Dysfunction in this pathway may contribute to the development of metabolic disorders, such as hyperlipidemia and atherosclerosis.] \n", - "306 [Summary: Several of these genes are involved in blood coagulation, complement activation, and metalloendopeptidase activity.\\n\\nMechanism: These genes participate in the regulation of proteolysis and enzyme inhibitors.\\n\\n] \n", - "307 [Summary: The enriched terms suggest that the common function of these human genes involve diverse biological processes related to protein binding, enzymatic activity, and complement system. \\n\\n] \n", - "308 [Summary: Binding and catalytic activity\\n\\nHypothesis: These genes are involved in various types of binding and catalytic activities, which may include regulation of signaling pathways, transcriptional regulation, and enzyme activity in metabolic pathways. The enrichment of binding-related terms suggests that these genes may play a role in protein-protein interactions, protein-DNA interactions, metal ion coordination, and enzyme-substrate interactions. The involvement of ATP binding suggests these genes may also have a role in energy-dependent processes.] \n", - "309 [Summary: Extracellular matrix, protease activity, and complement activation are enriched in the function of these genes.\\n\\n] \n", - "310 [Summary: Many of the genes on this list are involved in DNA metabolism, transcription, and RNA processing. \\n\\n] \n", - "311 [Summary: Many of these genes are involved in DNA-related processes, including DNA replication, repair, and transcription. \\n\\n\\nHypothesis: The enriched terms suggest that these genes are part of a complex network involved in DNA processing, including binding to DNA and RNA molecules, maintaining nucleotide balance, and repairing DNA damage. The protein-macromolecule adaptor activity may be involved in coordinating these processes or facilitating interactions between proteins and genetic material.] \n", - "312 [Summary: Genes involved in DNA replication, repair, and cell cycle regulation are enriched.\\n\\nMechanism: These genes are involved in processes related to DNA replication and repair, as well as regulation of the cell cycle, particularly in the G2 and M phases.\\n\\n] \n", - "313 [Summary: DNA binding and replication activities are enriched in the given gene list, indicating their involvement in DNA repair, replication, and regulation of cell cycle processes.\\n\\nMechanism: The enriched terms suggest that the genes in the list are involved in DNA binding, replication, and repair, which play essential roles in maintaining genomic stability.\\n\\n] \n", - "314 [Summary: These genes are involved in extracellular matrix organization and signaling pathways such as Wnt-protein binding, growth factor activity, and cytokine activity. \\n\\nMechanism: These genes work together to regulate the extracellular matrix and cellular signaling pathways that contribute to cellular processes such as development, tissue repair, and immunity.\\n\\n] \n", - "315 [Summary: The list of genes is enriched for functions related to extracellular matrix organization and regulation, including collagen binding, integrin binding, and heparin binding activity.\\n\\nMechanism: The genes in the list are involved in processes related to extracellular matrix regulation, including collagen synthesis and assembly, cell adhesion and migration, and protease inhibitor activity.\\n\\n] \n", - "316 [Summary: Transmembrane receptor and transporter activity, as well as DNA-binding transcription activator activity, are statistically over-represented in this list of genes.\\n\\nMechanism: These enriched terms suggest that the genes in this list are involved in membrane and nuclear signaling processes, including transcriptional regulation.\\n\\n] \n", - "317 [Summary: Cell signaling and transcription regulation\\nMechanism: Enzyme and receptor activity, nucleic acid binding, transcriptional regulation\\n] \n", - "318 [Summary: This list of human genes is enriched for terms related to protein and enzyme activity, binding activity, and cellular transport.\\n\\nMechanism: These genes likely play important roles in various cellular processes, including protein and enzyme activity, binding and transport of molecules, and regulation of cellular growth and development.\\n\\n] \n", - "319 [Summary: These genes are involved in various biological processes, but the enriched terms suggest a focus on binding activity and molecular transport.\\n\\nMechanism: The common biological mechanism for these genes is likely related to molecular interactions and transport within cells.\\n\\n] \n", - "320 [Summary: Metabolism of fatty acids and carboxylic acids\\nMechanism: Fatty acid oxidation and elongation pathways, as well as carboxylic acid metabolism pathways\\n\\n] \n", - "321 [Summary: These genes are mostly involved in oxidation-reduction processes and metabolic pathways, specifically lipid and fatty acid metabolism. \\n\\n] \n", - "322 [Summary: These genes enable several functions related to DNA binding, transcription regulation, protein binding, histone modification, and protein kinase activity. \\n\\nMechanism: These genes are involved in regulating gene expression and DNA-related processes such as DNA replication, repair, and chromosome segregation. \\n\\n] \n", - "323 [Summary: The genes are involved in DNA binding/transcription factor activity, protein kinase activity, and binding activity, and play a role in mitosis, DNA replication, and gene expression regulation. \\n\\nMechanism: These genes are involved in processes related to cell cycle regulation and gene expression control, likely through interactions with DNA, RNA, and protein molecules. \\n\\n] \n", - "324 [Summary: Glycosylation and carbohydrate metabolism related genes are enriched in this list.\\n\\nMechanism: The genes in this list are involved in various steps of glycosylation and carbohydrate metabolism pathways.\\n\\n] \n", - "325 [Summary: Enriched terms among these genes are involved in carbohydrate metabolism, enzyme activity, and binding activity.\\n\\nMechanism: These genes may be involved in a pathway that regulates carbohydrate metabolism, including glycosylation, synthesis of glucose, and synthesis and breakdown of glycogen. The genes may also play a role in enzyme activity and binding activity in various cellular processes.\\n\\n] \n", - "326 [Summary: The enriched terms for these genes reveal involvement in various cellular processes, including signal transduction, development, and gene regulation.\\n\\nMechanism: The underlying biological mechanism for these enriched terms involve complex cellular processes that are regulated by multiple genes and signaling pathways.\\n\\n] \n", - "327 [Summary: Genes are involved in various processes such as cell adhesion, transcription regulation, and signal transduction. \\nMechanism: Biological mechanism involves regulation of gene expression and signal transduction pathways. \\n] \n", - "328 [Summary: Several of the genes on the list are involved in binding and transportation activity, as well as enzyme activity.\\n\\nMechanism: These genes may play a role in metabolic and cellular processes through the transport and binding of various molecules, as well as enzymatic activity.\\n\\n] \n", - "329 [Mechanism: Protein binding activity\\n\\nHypothesis: The common mechanism among these genes is their protein binding activity, which includes enzyme binding activity, protein domain specific binding activity, protein heterodimerization activity, identical protein binding activity, and protein homodimerization activity. These genes may interact with and regulate each other's activity through their protein binding domains, leading to coordinated cellular processes. Alternatively, they may play a role in the assembly of larger protein complexes necessary for various cellular functions.] \n", - "330 [Summary: Many of the genes listed are involved in binding, catalytic activity, and enzyme activity. \\nMechanism: These genes are likely involved in metabolic processes and signaling pathways. \\n\\n\\nHypothesis: These genes are involved in a complex network of metabolic processes and signaling pathways, potentially involving kinases, transcription factors, and calcium signaling. They may contribute to the regulation of enzyme activity, protein binding, and metabolic pathways in the body.] \n", - "331 [Summary: Functions enriched in this list of genes include binding activities (such as protein, ion, and growth factor binding) and enzymatic activities (such as kinase, dehydrogenase, and transferase activity). \\n\\nMechanism: These common functions suggest that the genes in this list are involved in various cellular processes that require binding and enzymatic activities, such as signal transduction, metabolism, and cell growth and differentiation.\\n\\n] \n", - "332 [Summary: The common function of the listed genes is binding activity, including protein and DNA binding. \\n\\n] \n", - "333 [Summary: Signaling and cytokine receptor activity, protein binding activity, enzyme activity, DNA binding activity, RNA binding activity, several processes including apoptosis and cellular response to cytokines.\\n\\n] \n", - "334 [Summary: Cytokine and growth factor receptor activity\\nMechanism: Signal transduction\\n] \n", - "335 [Summary: The enriched terms suggest that these genes are involved in cytokine activity and signaling pathways.\\nMechanism: These genes are likely involved in the regulation of the immune system through cytokines and signaling pathways.\\n] \n", - "336 [Summary: Signaling and cell communication through the immune system and cytokines.\\nMechanism: The genes listed enable cytokine activity, cytokine receptor activity, G protein-coupled receptor activity, and enzyme binding activity, with a particular emphasis on the immune system. \\n] \n", - "337 [Summary: Cell signaling and receptor binding activity are enriched in the list of genes.\\n\\nMechanism: These genes are involved in cellular signaling, including binding to receptors and activation of downstream pathways.\\n\\n] \n", - "338 [Summary: Many of the genes listed are involved in immune response and antigen processing and presentation, including cytokines, chemokines, and interferon-related genes. Additionally, several genes are involved in RNA processing and editing.\\n\\n\\nHypothesis: These genes may be involved in immune recognition and response to foreign pathogens, potentially through antigen presentation and cytokine/chemokine-mediated immune cell recruitment and activation. The RNA-related genes may be involved in post-transcriptional regulation of immune-related genes.] \n", - "339 [Summary: Many of the genes are involved in immune response and defense against viruses, as well as regulation of protein activity.\\n\\nMechanism: The enriched terms suggest an underlying biological mechanism of antiviral defense and immune response pathways.\\n\\n] \n", - "340 [Summary: Immune system processes and regulation are enriched in the list of genes.\\n\\nMechanism: These genes are involved in various immune system processes, from cytokine and chemokine activity to transcription factor binding and protein homodimerization. \\n\\n\\nHypothesis: The enriched immune system processes and regulation may be involved in the regulation and response to external stimuli, such as infections or tissue damage, and the maintenance of internal homeostasis. The different gene functions may work together in a network to activate or inhibit immune responses and protect the body from harmful agents.] \n", - "341 [Summary: Genes involved in immune response, from antigen presentation to cytokine signaling and antiviral defense.\\n\\nMechanism: These genes are involved in various aspects of the immune response, including antigen presentation through MHC class I and II complexes, cytokine signaling through STAT proteins, and antiviral defense through interferon-stimulated genes.\\n\\n] \n", - "342 [Summary: Protein binding and enzyme activity.\\n\\n\\nHypothesis: The overrepresented terms suggest that these genes may be involved in a complex protein-protein interaction network, with many proteins acting as enzymes that catalyze a reaction and interact with other proteins through binding activity. Additionally, many of these proteins may act as transcription factors, influencing gene expression by binding to DNA and regulating transcription. Ion binding activity may also be involved in many of these processes, as ions are important cofactors for many enzymes and can influence protein structure and function.] \n", - "343 [Summary: Genes involved in binding and enzymatic activities, as well as regulation of cellular processes.\\n\\n] \n", - "344 [Summary: Genes involved in binding activity, enzymatic activity, and protein regulation.\\nMechanism: These genes play a role in cellular processes such as signaling, metabolism, and transcriptional regulation.\\n\\n] \n", - "345 [Summary: Protein binding and enzymatic activity\\n] \n", - "346 [Summary: Several genes are involved in cytoskeleton organization and regulation, including microtubule binding, actin binding, and GTPase activator activity.\\n\\nMechanism: The regulation of cytoskeleton stability and dynamics is crucial for many cellular processes, including cell division, migration, and differentiation. These genes likely play key roles in maintaining cytoskeleton integrity and regulating its rearrangement through protein-protein interactions and enzymatic activities.\\n\\n] \n", - "347 [Summary: Genes are primarily involved in microtubule binding and regulation, as well as cell division processes such as mitosis and cytokinesis. \\n\\n] \n", - "348 [Summary: Many of the genes listed are involved in protein or RNA binding, enzymatic activity, and structural components of cells. \\n\\n] \n", - "349 [Summary: The enriched terms across these genes suggest a common theme of protein folding, transport, and degradation. \\n\\nMechanism: These genes are involved in the regulation of protein folding, transport, and degradation, likely through the ubiquitin-proteasome system and endoplasmic reticulum-associated degradation pathway.\\n\\n] \n", - "350 [Summary: Ribosome and protein synthesis-related activity\\nMechanism: Protein synthesis and ribosome biogenesis\\n\\nHypothesis: The enriched terms suggest that the genes in this list are involved in fundamental cellular processes related to protein synthesis and ribosome biogenesis. They are likely necessary for proper folding, transport, binding, and localization of mRNA and ribosomes, which are essential for protein synthesis. The genes on the list may function together to regulate these processes, playing key roles in fine-tuning protein production during development, cellular differentiation, and stress responses.] \n", - "351 [Summary: RNA processing and binding activity\\n\\n] \n", - "352 [Summary: This set of human genes is enriched for terms related to RNA processing, specifically rRNA processing and biogenesis. \\n\\nMechanism: These genes likely participate in a common biological pathway related to ribosome biogenesis and function.\\n\\n] \n", - "353 [Summary: Genes involved in RNA processing, rRNA processing, and ribosomal biogenesis.\\n\\nMechanism: These genes contribute to the production and processing of ribosomal RNA (rRNA) involved in ribosomal biogenesis. rRNA molecules are important components of ribosomes, which are responsible for protein synthesis in cells.\\n\\n] \n", - "354 [Summary: These human genes are enriched for terms related to muscle structure and function, including actin binding and ATP activity.\\n\\nMechanism: These genes likely play a role in muscle development and function, as well as related processes such as calcium ion binding and molecular adaptor activity.\\n\\n] \n", - "355 [Summary: Muscle and cytoskeletal proteins are enriched in this list of genes.\\n\\n] \n", - "356 [Summary: The enriched terms suggest that the listed genes are involved in various aspects of cellular signaling pathways, including Notch, Wnt, and ubiquitin-mediated protein degradation.\\n\\nMechanism: The mechanism underlying the commonalities in function may be related to the fact that many of these genes are involved in the regulation of gene expression and cellular signaling pathways that are critical for embryonic development and tissue homeostasis.\\n\\n] \n", - "357 [Summary: Notch signaling pathway and protein ubiquitination are enriched terms among these genes.\\nMechanism: These genes are involved in the regulation of cell differentiation, stem cell population maintenance, and DNA-templated transcription, which are processes that require the Notch signaling pathway for their proper function. Additionally, several of these genes are involved in ubiquitination, a process that targets proteins for degradation or signaling.\\n] \n", - "358 [Summary: Mitochondrial respiratory chain complex activity.\\n\\nHypothesis: Mitochondria are the powerhouse of the cell and play a crucial role in energy production, most notably through oxidative phosphorylation in which electrons pass through a series of complexes in the mitochondrial respiratory chain to generate ATP. The enriched terms of this gene list, such as electron transfer activity, NADH dehydrogenase (ubiquinone) activity, and ubiquitin protein ligase binding activity, directly relate to the functionality of the mitochondrial respiratory chain. Additionally, the RNA binding activity and protein homodimerization activity suggest the regulation and maintenance of these complexes. The metal ion binding activity could also be related to the involvement of metal ions, such as iron or copper, in electron transport.] \n", - "359 [Summary: Several of these genes are involved in mitochondrial functions such as respiratory chain complex activity and ATP synthase activity. They also play roles in metabolic processes such as electron transfer activity and oxidoreductase activity.\\n\\n] \n", - "360 [Summary: These genes are involved in various functions, including DNA binding, protein binding, enzyme activity, transcription factor activity, and growth factor activity.\\n\\n] \n", - "361 [Summary: These genes are involved in a variety of functions, including DNA binding, protein binding, and kinase activity.\\n\\n] \n", - "362 [Summary: Several of the genes are involved in glucose metabolism and regulation of insulin secretion.\\n\\nMechanism: These genes likely play a role in the regulation of blood sugar levels and insulin secretion through various cellular mechanisms.\\n\\n] \n", - "363 [Summary: Many of the genes are involved in insulin secretion or glucose metabolism, suggesting a potential role in diabetes. Additionally, several genes are involved in transcriptional regulation or regulation of gene expression.\\n\\n\\nHypothesis: \\nThe enriched terms suggest that several of these genes may be involved in a common regulatory pathway controlling insulin secretion and glucose metabolism. Specifically, the transcriptional regulation of genes involved in insulin secretion and glucose metabolism may be mediated by RNA polymerase II-specific transcription factors, which can bind to specific cis-regulatory regions of these genes to control their expression. Negative regulatory factors can suppress gene expression, while positive regulatory factors can increase expression. Dysfunction in any of these genes, therefore, could lead to defects in insulin secretion or glucose metabolism, potentially contributing to the development of type 1 or type 2 diabetes mellitus.] \n", - "364 [Summary: The enriched terms suggest that these genes are involved in lipid metabolism and transport, as well as binding and catalysis.\\n\\nMechanism: These genes likely function together in cellular lipid metabolism and transport pathways, potentially in peroxisomes or mitochondria.\\n\\n] \n", - "365 [Summary: Many of these genes are involved in lipid metabolism and transport, mitochondrial function, and DNA repair. \\n\\nMechanism: These genes may be involved in maintaining cellular homeostasis by regulating lipid metabolism and mitochondrial function, as well as protecting DNA from damage. \\n\\n] \n", - "366 [Summary: Genes in this list are largely involved in signal transduction pathways, including protein kinase activity, G protein-coupled receptor binding activity, and transcription factor binding activity.\\n\\nMechanism: These genes likely function in several interconnected signaling pathways, including the MAPK/ERK pathway, PI3K/Akt pathway, and NF-kappaB pathway.\\n\\n] \n", - "367 [Summary: Intracellular signal transduction and protein phosphorylation.\\nMechanism: These genes are involved in intracellular signal transduction processes which involve the phosphorylation of proteins.\\n] \n", - "368 [Summary: Golgi apparatus-related processes are enriched in this list of genes.\\n\\nMechanism: The genes in this list are involved in various processes related to Golgi apparatus homeostasis, organization, transport, and vesicle-mediated recycling.\\n\\n] \n", - "369 [Summary: This set of genes is enriched for functions related to intracellular membrane trafficking and transport.\\n\\n\\nHypothesis: These genes are involved in various steps of intracellular transport and vesicle-mediated trafficking between the endoplasmic reticulum and the Golgi complex. The enriched terms are likely reflections of this shared functional theme. It is possible that the proteins encoded by these genes interact with each other to form complexes or pathways that regulate this process. Further investigation may reveal more details about the specific mechanisms involved in these functions.] \n", - "370 [Summary: Cell redox homeostasis and response to oxidative stress are enriched functional themes among the listed genes.\\n\\nMechanism: Genes in this group function in maintaining cellular redox balance by regulating the activity of reactive oxygen species (ROS) and oxidative stress response pathways. \\n\\n] \n", - "371 [Summary: Cell redox homeostasis and response to oxidative stress are enriched terms in the gene list.\\n\\nMechanism: These genes are involved in maintaining cellular redox balance by regulating oxidant detoxification pathways and responding to oxidative stress.\\n\\n] \n", - "372 [Summary: This list of human genes is highly enriched in genes involved in protein binding and kinase activity, as well as in genes involved in cell cycle regulation and gene expression.\\nMechanism: The enriched terms suggest that these genes are involved in cellular processes that require the binding and modification of proteins, particularly during cell cycle regulation and gene expression.\\n] \n", - "373 [Summary: Many of the identified genes are involved in cellular processes such as protein binding, enzyme activator/inhibitor activity, and ATP binding activity.\\n\\nMechanism: The underlying biological mechanism may involve regulating cellular processes through protein interactions and/or enzyme regulation.\\n\\n] \n", - "374 [Summary: The enriched terms are related to cellular signaling and development processes, particularly those involving the transforming growth factor-beta (TGF-beta) signaling pathway.\\n\\nMechanism: These genes are involved in the TGF-beta signaling pathway, which regulates cellular processes such as proliferation, differentiation, and apoptosis.\\n\\n] \n", - "375 [Summary: Signaling through TGF-beta superfamily and BMP receptor-related pathways\\nMechanism: TGF-beta and BMP ligands bind to type II receptors, which activate type I receptors. The activated type I receptors phosphorylate SMAD transcription factors, which activate or repress target gene expression.\\n] \n", - "376 [Summary: Transcription regulation and cytokine activity.\\n\\nHypothesis: These genes may be involved in the regulation of immune responses, cellular differentiation, and tissue growth and repair. They may interact with signaling pathways involved in cytokine production and response, such as the JAK-STAT pathway and the NF-kappaB pathway.] \n", - "377 [Summary: The enriched terms are related to immune system processes and cytokine signaling pathways.\\nMechanism: These genes are involved in regulating cytokine receptor activity and immune system signaling pathways, likely through activation of MAP kinase and transcription factor pathways.\\n\\n] \n", - "378 [Summary: Many of the genes are involved in protein folding and chaperone activity, RNA binding and transcriptional regulation, and RNA processing and degradation.\\n\\nMechanism: The common mechanism might be related to the regulation of protein homeostasis, with these genes functioning in different aspects of protein folding, RNA binding and processing, and transcriptional regulation.\\n\\n] \n", - "379 [Summary: These genes are involved in various cellular processes, with a common theme of RNA and protein regulation, as well as involvement in endoplasmic reticulum (ER) stress response pathways.\\n\\nMechanism: These genes may be involved in regulating RNA and protein synthesis and processing, as well as responding to cellular stress, particularly ER stress.\\n\\n] \n", - "380 [Summary: Extracellular matrix structural constituent and protein binding activity are enriched functions amongst the given human genes.\\nMechanism: These genes may play a role in cellular adhesion, migration, and signal transduction processes.\\n] \n", - "381 [Summary: Extracellular matrix structural constituents, protein binding, transcription activator activity, and receptor binding are enriched terms among these genes.\\nMechanism: The enriched terms suggest that these genes may be involved in cell signaling pathways and extracellular matrix formation.\\n] \n", - "382 [Summary: Enriched terms suggest involvement in protein binding, enzymatic activity, and transcriptional regulation.\\nMechanism: These genes likely play a role in various cellular processes that involve protein-protein interactions, enzymatic reactions, and transcriptional regulation.\\n\\n] \n", - "383 [Summary: Molecular Function Inhibitor Activity and Protein Binding Activity\\nMechanism: Molecular inhibition of various cellular processes\\n] \n", - "384 [Summary: Genes are involved in the Wnt signaling pathway and regulation of transcription by RNA polymerase II.\\nMechanism: The identified genes all function in the Wnt signaling pathway and particularly in the regulation of transcription by RNA polymerase II. This pathway plays a crucial role in embryonic development and cellular proliferation, and dysregulation can contribute to the development of multiple diseases, including cancer and developmental disorders.\\n] \n", - "385 [Summary: Genes involved in Wnt signaling pathway and regulation of gene expression.\\nMechanism: Wnt signaling pathway regulates gene expression through the interaction of Wnt ligands with Frizzled receptors and subsequent activation of downstream signaling pathways.\\n\\nHypothesis: The enrichment of genes involved in Wnt signaling and regulation of gene expression suggests a potential role in developmental processes, as well as potential implications in cancer and neurodegenerative diseases. The dysregulation of Wnt signaling has been implicated in multiple cancers, pointing to the importance of these genes in cellular growth and proliferation. Additionally, the involvement of PSEN2 in amyloid-beta formation highlights the potential role of Wnt signaling in Alzheimer's disease pathology.] \n", - "386 [Summary: Signaling and receptor binding activity\\n] \n", - "387 [Summary: Immune-related genes with a focus on T cell regulation and signaling.\\nMechanism: T cell activation and signaling pathway.\\n] \n", - "388 [Summary: Transcriptional regulation and gene expression.\\nMechanism: Gene expression regulation.\\n\\nHypothesis: All the genes listed are involved in transcriptional regulation and gene expression. All of these genes have DNA-binding transcription factor activity, and a role in the regulation of gene expression. They are involved in positive or negative regulation of transcription by RNA polymerase II, and act upstream of or within several processes such as endodermal cell fate specification, and regulation of biosynthesis and metabolic processes. These genes seem to be part of a broader pathway or mechanism involved in gene expression regulation.] \n", - "389 [Summary: Transcription regulation and gene expression\\nMechanism: Transcriptional regulation\\n] \n", - "390 [Summary: Extracellular matrix components and their interactions with the cell surface are enriched functions in this gene set.\\n\\nMechanism: These genes are involved in cell-matrix adhesion, collagen fibril organization, and extracellular matrix protein binding and organization. They also have roles in the regulation and binding of lipoproteins.\\n\\n] \n", - "391 [Summary: Genes with diverse functions including extracellular matrix structural constituents, integrin and Notch binding activities, and chemokine activity are enriched for terms related to cell adhesion, migration, and regulation of protein metabolic processes. \\nMechanism: Extracellular matrix remodeling, integrin signaling, and chemokine signaling pathways are likely involved in the common functions of these genes.\\n] \n", - "392 [Summary: Several genes are involved in various aspects of protein binding activity and regulation of gene expression, with a focus on transcription factor binding activity.\\n\\nMechanism: The enriched terms suggest a role for these genes in regulating gene expression at the transcriptional level, likely through interaction with DNA and other proteins involved in transcriptional regulation.\\n\\n] \n", - "393 [Summary: The common function among these genes is the ability to enable binding activities, including metal ion binding, protein domain specific binding, DNA-binding transcription factor activity, and ubiquitin protein ligase activity. They are also involved in several processes, including cell proliferation, development, and regulation of signaling pathways.\\n\\nMechanism: These genes likely play a role in regulating various cellular processes through their binding activities, either by promoting or inhibiting specific protein interactions or by modifying signaling pathways through enzymatic activity.\\n\\n] \n", - "394 [Summary: Enriched terms include muscle contraction, regulation of muscle adaptation, and protein ubiquitination. \\n\\nMechanism: The genes in this list are primarily involved in muscle development and function, as well as protein ubiquitination. \\n\\n\\nHypothesis: The enriched terms suggest that these genes may play a role in regulating muscle growth and adaptation through protein ubiquitination and other mechanisms.] \n", - "395 [Summary: Genes are mostly involved in muscle contraction and structure, ion channel activity, and protein ubiquitination.\\n\\n] \n", - "396 [Summary: The enriched terms for these genes are related to endocytosis, cellular adhesion, and regulation of signal transduction pathways.\\n\\nMechanism: These genes are involved in various processes such as endocytosis, protein degradation, and signal transduction. They regulate several cellular functions such as cellular adhesion, plasma membrane organization, and lipid transport.\\n\\n\\nHypothesis: The enriched terms suggest that these genes are involved in the regulation of endocytic processes, which are essential for the uptake of various molecules from the extracellular environment. They also play a role in the organization of plasma membrane, which is crucial for cell signaling and signal transduction. The genes are part of the network that regulates cellular adhesion and cytoskeleton organization. They also participate in the regulation of lipid transport, which is essential for maintaining cellular physiology.] \n", - "397 [Summary: All genes are involved in membrane-related processes, including endocytosis, protein transport, and cell signaling.\\nMechanism: These genes are essential for membrane traffic and organization.\\n] \n", - "398 [Summary: These genes are involved in various processes related to carbohydrate metabolism and cellular energy homeostasis.\\n\\nMechanism: The common mechanism underlying the enriched terms is the regulation of glycolysis and energy metabolism in cells.\\n\\n] \n", - "399 [Summary: The common function of these genes is glycolysis and carbohydrate metabolism.\\nMechanism: These genes are involved in the breakdown of glucose to produce energy in the form of ATP. \\n] \n", - "400 [Summary: The enriched terms include calcium ion transport, voltage-gated calcium channel activity, glutamate receptor activity, and acetylcholine-gated channel complex.\\n\\nMechanism: These genes are involved in calcium signaling, particularly in calcium ion transport and voltage-gated calcium channel activity. They also play a role in neurotransmission, specifically in the activity of glutamate and acetylcholine-gated channels.\\n\\n] \n", - "401 [Summary: Calcium signaling plays a major role in the function of the genes listed, including calcium channel activity, regulation of cytosolic calcium ion concentration, and calcium ion transmembrane import.\\n\\nMechanism: Calcium signals can activate a variety of pathways, including second messenger systems and ion channel activation, leading to changes in intracellular signaling and gene expression.\\n\\n] \n", - "402 [Summary: Protein phosphorylation and kinase activity regulation\\nMechanism: Enzymatic activity and protein-protein interactions\\n\\nHypothesis: This set of genes is enriched in functions related to kinase activity regulation and signaling pathways that involve protein phosphorylation. Many of these genes enable protein kinase binding, activator or inhibitor activity, and participate in processes that involve protein phosphorylation. These processes include intracellular signal transduction, TOR signaling, apoptotic signaling pathway, and positive regulation of metabolic processes. The underlying biological mechanism is likely linked to the interactions between these proteins, with many of them being located in protein-containing complexes and regulatory pathways.] \n", - "403 [Summary: The enriched terms for these genes are related to intracellular signaling and regulation of cell processes.\\nMechanism: These genes are mainly involved in regulation of protein kinase activity and intracellular signal transduction, which contribute to the homeostasis of cellular processes.\\n\\n] \n", - "404 [Summary: These genes are involved in various processes related to the breakdown and metabolism of carbohydrates and glycoproteins.\\n\\nMechanism: The enriched terms suggest a common mechanism of carbohydrate and glycoprotein degradation through the activity of various hydrolases, including alpha- and beta-glucosidases, alpha- and beta-mannosidases, and multiple hyaluronidases.\\n\\n] \n", - "405 [Summary: These genes are involved in the catabolism and modification of various carbohydrates, such as hyaluronic acid, chitin, glycoproteins, glycolipids, and sugar monomers. Many of the genes encode glycosidase enzymes that enable the breakdown of specific sugars. \\n\\n] \n", - "406 [Summary: Enrichment in immunoglobulin receptor binding activity and antigen binding activity suggests a function related to immune response.\\n\\nMechanism: These genes encode immunoglobulins or immunoglobulin-related proteins involved in the production of antibodies.\\n\\n] \n", - "407 [Summary: Genes involved in the activation of immune response, defense response to other organisms and antigen binding activity.\\nMechanism: Immune response pathway\\n] \n", - "408 [Summary: Majority of the genes listed are involved in meiotic DNA recombination and repair.\\nMechanism: Meiotic DNA recombination and repair.\\n] \n", - "409 [Summary: These genes are primarily involved in meiotic recombination and chromosomal segregation, as well as various DNA repair processes.\\nMechanism: These genes likely function together to ensure proper chromosome segregation and correct genetic transmission during meiosis, and to maintain genomic stability through DNA repair mechanisms.\\n] \n", - "410 [Summary: Protein sequestering and binding activities are enriched across the listed genes.\\n\\nMechanism: The enriched terms suggest that protein sequestering and binding play a significant role in the function of the listed genes.\\n\\n\\nHypothesis: Protein sequestering and binding are essential mechanisms in controlling the cellular localization and activity of proteins. These mechanisms may affect several processes, including intracellular transport, transcriptional regulation, and signal transduction.] \n", - "411 [Summary: Several of the genes listed are involved in molecular sequestering or binding activity, and are located in various cellular compartments. Many are also implicated in immune responses and regulation of gene expression.\\n\\nMechanism: The enriched terms suggest that these genes are involved in cellular processes related to regulation of gene expression, immune responses, and cellular signaling pathways.\\n\\n\\nHypothesis: These genes may play a role in regulating immune responses and cellular signaling pathways, by sequestering or binding to various molecules and regulating the expression of genes involved in these processes.] \n", - "412 [Summary: Many of the genes listed are involved in protein or RNA binding, enzymatic activity, and structural components of cells. \\n\\n] \n", - "413 [Summary: The genes in this list are involved in various functions related to cellular processes including protein binding, enzyme activity, and transporter activity.\\n\\nMechanism: The underlying biological mechanism or pathway is likely related to cellular processes involved in protein homeostasis and metabolism.\\n\\n] \n", - "414 [Summary: Genes involved in peroxisome biogenesis and protein import into peroxisome matrix.\\nMechanism: Peroxisome biogenesis and protein import pathway.\\n] \n", - "415 [Summary: These genes are all involved in peroxisome biogenesis and protein import into the peroxisome.\\n\\nMechanism: These genes all encode for proteins involved in the same biological process of peroxisomal biogenesis, which is the formation of peroxisomes and the import of proteins into the peroxisome.\\n\\n] \n", - "416 [Summary: These genes are all involved in DNA metabolism and chromatin regulation.\\nMechanism: These genes are all involved in maintaining the stability and integrity of the genome, particularly at the nuclear envelope and telomeres. They may also play a role in regulating cellular senescence processes.\\n] \n", - "417 [Summary: Genes involved in DNA repair and maintenance with possible roles in aging and age-related diseases.\\nMechanism: DNA damage repair and telomere maintenance pathways.\\n] \n", - "418 [Summary: The enriched terms are related to ion channel activity, transmembrane transport, and neurotransmitter signaling pathways.\\nMechanism: These genes all play a role in regulating the flow of ions across cell membranes in neurons.\\n\\nHypothesis: These genes are involved in regulating the membrane potential and synaptic transmission in neurons. The GABA and glutamate signaling pathways are important modulators of neural activity, and the ion channels identified here play key roles in regulating the activity of these signaling pathways. The inward rectifier potassium channels help to maintain the resting potential of neurons, while the voltage-gated ion channels play a critical role in generating action potentials. Together, these genes likely play a key role in the regulation of neural activity and synaptic plasticity.] \n", - "419 [Summary: These genes are involved in ion channel activity, specifically ligand-gated monoatomic ion channel activity and voltage-gated ion channel activity.\\nMechanism: The genes in this list contribute to the regulation of membrane potential and synaptic transmission in the nervous system.\\n] \n", - "420 [Summary: Genes are involved in various processes in the development and maintenance of the nervous system, specifically peripheral nerves and myelination, as well as nucleic acid and protein metabolism.\\n\\nMechanism: The enriched terms suggest a common underlying biological mechanism in the formation and maintenance of the peripheral nervous system and myelination, as well as in nucleic acid and protein metabolism.\\n\\n\\nHypothesis: The enrichment of terms related to Charcot-Marie-Tooth disease and myelination suggest that these genes play an important role in peripheral nervous system development and maintenance, specifically in the formation and maintenance of myelin. The enrichment of terms related to protein folding and nucleic acid metabolism suggest that these genes also have a role in maintaining and regulating the overall metabolic processes of cells. The involvement of genes in mitochondrial function suggests a possible link between peripheral nerve function and mitochondrial metabolism.] \n", - "421 [Summary: Genes are primarily involved in neurological and neuromuscular diseases and developmental disorders.\\n\\nHypothesis: These genes may be involved in the regulation of nervous system development and myelination, as well as mitochondrial dysfunction, which could lead to the development of neurological and neuromuscular diseases. The role of protein ubiquitination in these processes is unclear and requires further investigation.] \n", - "422 [Summary: The enriched terms suggest that these genes are involved in dopamine receptor signaling pathway, including adenylate cyclase activation, calcium ion concentration regulation, and G protein-coupled receptor pathway.\\n\\nMechanism: These genes are involved in dopamine receptor signaling, which regulates various cellular processes via the activation of adenylate cyclase, calcium ion concentration, and G protein-coupled receptor pathways.\\n\\n] \n", - "423 [Summary: The enriched terms in common for this list of genes are related to G protein-coupled receptor signaling pathways, dopamine neurotransmitter receptor activity, and adenylate cyclase activity.\\n\\nMechanism: These genes are involved in pathways that regulate cellular signaling, including dopamine-mediated signaling and cyclic AMP (cAMP) signaling pathways.\\n\\n\\nHypothesis: These genes are involved in the regulation of signaling pathways, particularly those involved in dopamine-mediated signaling and cyclic AMP (cAMP) signaling. They may contribute to the development of neurological and metabolic disorders, including Alzheimer's disease, Parkinson's disease, hypertension, and type 2 diabetes mellitus. More research is needed to fully understand the underlying biological mechanisms and pathways involved in these diseases.] \n", - "424 [Summary: These genes are involved in DNA-binding transcription regulation and are located in various cellular components, including the nucleus and chromatin. \\nMechanism: These genes are likely involved in regulating genetic expression and the transcriptional machinery.\\n] \n", - "425 [Summary: DNA binding transcription factor activity, regulation of DNA-templated transcription, gene expression regulation, and nucleosome disassembly are statistically enriched functions in these genes.\\nMechanism: These genes are involved in transcriptional regulation, including regulation of DNA binding and gene expression.\\n] \n", - "426 [\\n\\nSummary: Genes analyzed are associated with or involved in collagen biosynthesis, modification or turnover, extracellular matrix maturation, and transcriptional regulation. \\nMechanism: These genes likely function in the coordination and regulation of collagen production, fiber formation, and tissue informatics. \\n] \n", - "427 [\\nSummary: This gene list consists of genes involved in tissue development, collagen and extracellular matrix production, and immunity response. \\nMechanism: These genes all seem to be involved in tissue development and the formation of extracellular matrix components such as collagen and physical complexes such as C1 and fibril-forming collagens. In addition, some of the genes are associated with immunity processes like phagocytosis and inflammation.\\n \\n] \n", - "428 [\\nSummary: This gene list is composed of human genes involved in DNA damage repairs and genome maintenance.\\nMechanism: These genes are involved in the mechanisms to detect and repair DNA damages caused by environmental stressors by facilitating the formation of the nuclear protein complex.\\n] \n", - "429 [ \\nSummary: The genes analyzed in this enrichment test are all associated with the Fanconi anemia complementation group (FANC) and are known to be involved in the repair of DNA lesions, stabilization of genome stability, and maintenance of homologous recombination.\\n\\nMechanism: These genes likely play a role in a common biological cell pathway, acting as components of multiple nucleoprotein complexes, endonucleases, and homologous recombination proteins in order to facilitate DNA repair and prevent chromosome instability.\\n\\n] \n", - "430 [ \\n\\nSummary: The list of genes appear to be primarily involved in metabolic and energy production processes, as well as some related to membrane assembly and transcription factors.\\n\\nMechanism: The genes listed appear to be involved in controlling multiple pathways within the cell, such as energy production, enzymatic activity, transcription, and assembly of membranes.\\n\\n] \n", - "431 [ Enriched terms related to energy metabolism (ATP production, mitochondrial respiratory chain, electron transfer and fatty acid elongation) and protein binding/assembly/transport mechanisms (RNA/DNA binding and transport, ubiquitination and phosphorylation, microtubule binding and lipid transport) are highly represented in this list of genes.\\n\\nMechanism: These genes are mainly involved in energy production, protein modification, and transport processes. Energy production is carried out by multiple substrates including NADP, copper, zinc, and ubiquinone. The electron transfer chain is powered by cytochrome c oxidase, ATP5PO and ME1. Fatty acid elongation is handled by ELOVL6, while protein transportation is enabled by several CBL-type E3 ubiquitin ligases, ABC transporters and ATPases. Protein binding and assembly mechanisms are handled by many proteins with multiple domains, including G3BP2, VEGFB, and GHITM.\\n\\n] \n", - "432 [\\n\\nSummary: This list of genes are involved in a variety of physiological processes, including developmental morphogenesis, cell signalling, cytokine and chemokine production and regulation, antimicrobial defence, plasma protein regulation, immune and inflammatory regulation and transcriptional regulation.\\n\\nMechanism: Many of these gene functions are related to various cell signalling pathways involving cytokines and receptors, as well as regulation of transcription factors, protein kinases and proteases, as well as glycoproteins and receptor proteins of various classes.\\n\\n] \n", - "433 [ \\nSummary: Analysis of the given human genes reveals an enrichment for terms of cell membrane associated proteins and cytokines, as well as associated pathways of transcriptional regulation, protein synthesis, and immune response regulation. \\nMechanism: This enrichment of terms suggests that there is a complex network of pathways at play that enable important processes such as cell communication, cell activation, and immune response.\\n] \n", - "434 [ \\nSummary: These genes are involved in a variety of protein-related processes, such as binding, catalyzing, and regulating proteins, as well as in modulation, hydrolase activity, phosphorylation, and regulation of metabolism, transport, and signaling.\\n\\nMechanism: The genes are involved in a variety of pathways, such as cellular stress response, vesicle trafficking, DNA replication, transcription, lipid and cholesterol metabolism, and hormone signaling.\\n\\n] \n", - "435 [\\nThe list of genes is related to various cellular functions such as transcriptional regulation, protein kinase activity, protein binding, RNA binding, signal transduction, proteolytic enzyme activity, DNA binding, membrane transport, cell cycle, regulation, protein modification, peptidase, calcium binding, and others. The common molecular processes which are associated with these genes include regulation of transcription, signal transduction, transport, and protein modification.\\n\\nMechanism: The underlying molecular mechanisms behind the commonalities in gene functions are likely related to signal transduction and control of gene expression. Signal transduction involves the transmission of a signal from a cell's environment to the inside of the cell. Once the signal has been received and processed, it is relayed by the production of downstream molecules, such as transcription factors and other signaling proteins, which will ultimately lead to changes in gene expression and cellular behavior. Protein modification also plays a key role in signal transduction as well as in the regulation and processing of cellular components, such as proteins and lipids, necessary for normal cellular functioning.\\n\\n] \n", - "436 [ \\nSummary: This gene list encodes related proteins for key functional pathways including lipoprotein metabolism, coagulation, hemostasis, cytokinases, chemokines, receptors, transporters, cytokines, secreted extracellular matrix proteins, serpins and proteoglycans.\\nMechanism: These processes involve activation or regulation of enzymes or other proteins involved in cell adhesion and migration, signaling, cell proliferation, apoptosis, transcriptional regulation, tissue development and regeneration, and immune response.\\n] \n", - "437 [ \\nThis list of genes includes a variety of molecules that are involved in a range of biological processes such as tissue morphogenesis, cell adhesion, cell migration, cell survival, signal transduction, cell cycle regulation, scaffolding, apoptosis, extracellular matrix production, platelet aggregation and others. Most of these molecules are involved in processes related to cell-cell or cell-matrix interaction and in particular, formation and/or maintenance of the extracellular matrix.\\n\\nMechanism: These genes likely function in the formation and/or maintenance of the extracellular matrix via a number of processes. Specifically, these genes may be involved in processes such as regulation of cell-cell interactions and cell-matrix interactions, production and secretion of extracellular matrix proteins, processing of proteoglycans and glycoproteins, scaffolding, cell cycle control, signal transduction, and cell adhesion. These processes are likely to be involved in the control of tissue morphogenesis, cell migration and survival, platelet aggregation, and apoptosis.\\n\\n] \n", - "438 [ The genes listed are primarily involved in cell adhesion, signaling, and cytoskeletal stabilizing functions. This is evidenced by over-represented terms related to cell adhesion, such as \"integrin\", \"cadherin\", \"lectin\", \"nectin\"; terms related to signaling, such as \"MAP kinase\", \"protein tyrosine kinase\", \"guanine nucleotide binding protein\", \"GTPase\"; and terms related to cytoskeletal stabilizing functions, such as \"actin\", \"fascin\", \"laminin\", and \"myosin\". Hypothesis of underlying mechanism: The combined functions of the genes suggested are associated with cell motility, development, growth, and division in response to extracellular stimuli and signals.\\n\\nSummary: Genes associated with cell adhesion, signaling, and cytoskeletal stabilizing functions.\\nMechanism: Cell motility, development, growth, and division in response to extracellular stimuli and signals.\\n] \n", - "439 [ After performing a term enrichment test of these genes, we have identified a number of commonalities in their functions, including cell adhesion, signaling, scaffolding and cytoskeleton maintenance. These functions are typically mediated by proteins involved in the regulation of extracellular matrix, integrins, claudins, nectins, protein kinases and cadherins, suggesting a common pathway of interaction between membrane-bound receptors and cytoplasmic components.\\n\\nMechanism: These commonalities collectively suggest a pathway involving the regulation of signaling transduction, cell adhesion and cytoskeletal organization by a series of membrane-bound receptors and signals originating in the cytoplasm.\\n\\n] \n", - "440 [\\n\\nSummary: The genes described in the list are associated with cell adhesion and communication, cell metabolism and transport, receptor-mediated endocytosis, cell-matrix adherence, tissue growth, transcriptional regulation, glycosylation, and signaling.\\n\\nMechanism: The genes are involved in processes such as cell-to-cell adhesion, protein folding, and communication via cell surface proteins; receptor-mediated endocytosis; glycosylphosphatidylinositol and GPI-anchored cell surface proteins; cation transport ATPase; transcriptional coactivation; interleukin signaling and hormone-dependence; heparan sulfate proteoglycan and heparin-binding; and cell-matrix adhesion \\n\\n] \n", - "441 [\\n\\nSummary: This list of genes is involved in cell signalling, adhesion, growth regulation, protein folding, cation transport, ligand binding, and other cellular functions.\\n\\nMechanism: These genes are likely involved in cell signalling pathways and signalling molecules that regulate cell growth, differentiation, and homeostasis.\\n\\n] \n", - "442 [ The majority of the human genes on the list are involved in cell death processes, specifically apoptosis, and a wide range of activities associated with transcriptional regulation and DNA binding. A significant portion of the genes are associated with the TNF receptor superfamily, and the BCL-2 protein family, both of which are involved in cell death processes. Common enriched terms in the list include: apoptosis, transcriptional regulation, DNA binding, TNF receptor superfamily, and BCL-2 protein family.\\n\\nMechanism: Apoptotic pathways including caspase activation, BCL-2 protein family and death agonists, in addition to DNA binding of transcription factors and cytokine signaling, are likely to be important mechanisms in the human genes on the list.\\n\\n] \n", - "443 [COULD NOT PARSE] \n", - "444 [\\nThe gene summaries correspond to proteins which have enzyme and binding activities related to lipid metabolism, membrane transportation, steroid catalyzation, hormone activation and deactivation, and antioxidant activity.\\nHypothesis: The underlying biological mechanism is likely to involve the crosstalk between different activities in different cellular compartments, such as cytoplasm, nucleus, and peroxisomes, to regulate fatty acid metabolism, signal transduction and other cellular processes. \\n] \n", - "445 [ The list of human genes provided in this term enrichment test appears to be mostly related to enzymes, transporters, and receptors involved in lipid metabolism and transport, as well as in other metabolic pathways like bile acids synthesis, sulfur metabolism, and oxidative stress response. Notably, protein import into peroxisomes is over-represented by PEX6, PEX7, and PEX26. \\n\\nMechanism: The above proteins are likely to be involved in metabolic pathways contributing to lipid metabolism, transport, and oxidation.\\n\\n] \n", - "446 [\\nOur analysis of the list of human genes has revealed that many of the functions of these genes are related to cell regulation, metabolism, and transport. Specifically, the genes are involved in regulating cell growth and adhesion, lipid metabolism, cholesterol synthesis and breakdown, protein homodimerization and packing, enzymatic reactions, hormone regulation, and gene transcription. These gene functions are enriched in areas such as cell motility, energy generation, amino acid synthesis and degradation, glycoprotein synthesis, sterol biosynthesis and degradation, lipid metabolism and transport, and transcriptional regulation. \\n\\nMechanism: The underlying biological mechanism likely involves the coordination of these processes in order to maintain cellular homeostasis and to respond to a variety of environmental stimuli. In this way, cells can signal and respond to changes in their internal and external environments.\\n\\n] \n", - "447 [ \\nSummary: Enriched terms were identified related to cholesterol synthesis, lipid metabolism, fatty acid desaturation, and cell growth/regulation.\\nMechanism: These genes play a role in the regulation of cholesterol and other lipids, as well as amino acids, fatty acid desaturation and biosynthesis, growth, and cell cycle regulation. \\n] \n", - "448 [COULD NOT PARSE] \n", - "449 [ \\nSummary: The list of genes are associated with various functions involved in proteolysis, hemostasis, bone growth, morphogenesis, tissue development, lipoprotein regulation, and regulation of the complement system.\\n\\nMechanism: These genes are involved in mechanisms such as proteolysis, hemostasis, bone growth, morphogenesis, tissue development, lipoprotein regulation, and complement system regulation.\\n\\n] \n", - "450 [ This list comprises genes with roles in immune and inflammatory processes, cell regulation and development, cell signalling, cell adhesion, and cell metabolism. Many of these genes play roles in modulating the activity of kinases, members of the proteasome complex, and members of the serpin, cysteine-aspartic acid protease (casp) family, and in particular caspase-9 and caspase-3, both of which have roles in apoptosis and inflammation signalling. There are also proteins important in complement activation and coagulation, such as factor V, X, and VII and their receptors, as well as proteins that modulate interferon-induced signalling, such as IRF1, IRF2, and IRF7.\\n\\nMechanism: This list shows that these genes play roles in diverse pathways, such as cell development, cell signalling, cell regulation, cell adhesion and metabolism, complement activation, coagulation, and interferon-induced signalling.\\n\\n] \n", - "451 [\\n\\nSummary: The genes included in this list encode proteins involved in cell signaling, adhesion, protease activity, and cytoskeletal and metabolic processes.\\n\\nMechanism: The proteins encoded by the genes in this list are important in a variety of cellular processes including cell adhesion, transcriptional regulation, protease activity, and metabolic and cytoskeletal functions.\\n\\n] \n", - "452 [\\n\\nSummary: The human genes in this list are involved in functions such as DNA binding, transcription control, post-splicing, and RNA polymerase II functions. \\nMechanism: These genes are involved in multiple functions involved in the maintenance of DNA structure and transcription, such as DNA repair, post-splicing, andRNA polymerase II-related functions.\\n] \n", - "453 [\\nSummary: The genes found in this list primarily involve DNA repair, transcription, and mRNA metabolism.\\nMechanism: The genes are involved in the transcription and DNA repair process, which includes enzyme binding, RNA binding, DNA, protein, and chromosomal binding activities, as well as the activity of DNA and RNA polymerases, phosphorolysis, gene silencing, and protein ubiquitination.\\n] \n", - "454 [\\nSummary: The enriched terms from the given gene list suggest that these genes are involved in DNA replication and repair, chromatin regulation, and RNA processing.\\nMechanism: These processes involve the coordination and control of proteins, DNA sequences, and metabolites such as calcium ions.\\n] \n", - "455 [\\nSummary: This list of genes is involved in a variety of functions, such as DNA replication, nuclear import and export, RNA binding, chromatin regulation and modification, protein degradation, cell cycle control, and DNA repair.\\n\\nMechanism: These genes are involved in many processes related to maintaining genomic stability, including DNA replication, DNA repair, and chromatin regulation.\\n\\n] \n", - "456 [ \\nSummary: Enriched gene functions were identified related to extracellular matrix glycoproteins, collagen, actin binding and regulation, cell adhesion and signaling, cytokine regulation and signaling, peptidase genes, and growth factor family members.\\n\\nMechanism: Members of these gene families play important roles in the regulation of cell signaling pathways, cell migration, cell growth and differentiation, hemostasis and inflammation, and various other biological processes.\\n\\n] \n", - "457 [ \\nSummary: The genes included in this list encode proteins that are involved in structural support and maintainance of cell components, such as extracellular matrix proteins, integrins, collagen, fibrillin, tropomyosin and myosin proteins.\\nMany of them have roles related to regulatory cell functions, such as cell adhesion, growth and signalling pathways.\\nMechanism: These proteins play a role in the maintainance and regulation of cell structure, linking the extracellular environment to the intracellular environment, enabling cell-cell interactions, and modulating cell behaviour and signalling.\\n] \n", - "458 [ Enriched terms involved in signal transduction, gene expression, transport, and membrane protein functions.\\n\\nMechanism: Signal transduction, gene expression and transport functions may occur as a result of interaction between proteins encoded by the genes, as well as interaction between nucleic acids such as DNA, RNA, and chromatin. This can be regulated by post-translational modifications such as methylation, phosphorylations, and acylation, as well as by binding of other proteins and ligands. Membrane proteins allow for communication between the cytoplasm and outside environment and facilitate the transport of molecules.\\n\\n] \n", - "459 [ Gene functions were identified enriched for cytoskeletal organization, DNA binding transcription regulation, membrane transport and receptor signalling.\\nMechanism: Commonalities in gene functions is associated with cellular and signal transduction pathways, involving several mechanisms including membrane transport, DNA-binding transcription regulation, cell adhesion, cytokine and growth factor signalling, and the expression of structural components of muscle and epithelial cells.\\n] \n", - "460 [\\nSummary: The human gene list provided consists of genes involved in a variety of cellular functions, including regulation of G protein signalling, ion channel transport, membrane receptor signalling, cytoskeletal protein scaffolding, enzyme regulation and glycoprotein modulation. \\n] \n", - "461 [\\nSummary: The genes listed are involved in various cellular functions, including signal transduction, gene transcription, ion transport and binding, protein-protein interaction and post-translational modifications.\\nMechanism: These genes have been found to encode proteins that are involved in diverse cell functions, including signal transduction, structural proteins, transcription factors, transporters, kinases and phosphatases, and their associated regulatory proteins.\\n] \n", - "462 [\\n\\nSummary: This list includes 51 human genes involved in metabolic, biosynthetic, enzymatic, and regulatory pathways and processes. The majority of these genes encode proteins involved in metabolic functions, such as glycolysis, oxidation-reduction processes, and polyamine metabolism.\\n\\nMechanism: The commonalities between these genes are related to their roles in metabolic and enzymatic processes throughout cells. These proteins are involved in catalyzing and regulating nucleotide and amino acid metabolism, fatty acid oxidation and synthesis, polyamine metabolism, and enzyme activity.\\n\\n] \n", - "463 [\\nThe gene list contains genes associated with metabolic activities such as enzymatic components of tricarboxylic acid cycle, fatty acid binding proteins, aldehyde dehydrogenases and enzyme processes related to electron transfer, including pyruvate dehydrogenase, NAD-retinol dehydrogenase, succinate dehydrogenase, etc. The underlying biological mechanism involves the process of metabolic energy conversion, which involves the coordination of various enzymatic components.\\n\\nMechanism: Metabolic energy conversion coordinates various enzymatic components.\\n\\n] \n", - "464 [\\nSummary: The genes in the list encode proteins involved in cell signalling and regulation pathways, epigenetic regulation, nuclear transport, mitosis, mRNA processing, protein modification, DNA replication and repair, and chromatin structure.\\nMechanism: This analysis suggests that these genes are responsible for various critical cellular functions and pathways, such as transcriptional regulation, epigenetic remodeling, nuclear transport, post-translational modifications, DNA replication and repair, chromatin structure, and mitosis.\\n] \n", - "465 [ \\nSummary: The human genes in this list are involved in various critical functions related to cellular development, including nucleocytoplasmic transport, histone acetylation, chromatin-associated processes, cell cycle regulation, and transcriptional regulation.\\n] \n", - "466 [\\n] \n", - "467 [\\nSummary: Analysis of the summaries of these genes reveal that the majority are involved in enzymatic functions, binding, transporting, and metabolism of molecules, including ions and sugars.\\nMechanism: These genes likely have an underlying biological mechanism of enzyme catalysis and/or binding affinity affecting the metabolism of molecules, including ions and sugars, as well as modulating transcription, cytoskeletal structure, and cell adhesion.\\n] \n", - "468 [\\nThis gene set is involved in a variety of cellular functions, such as cell adhesion, neural development, transcription factor regulation, signal transduction, and extracellular protein interaction. These genes are over-represented in processes related to endocytosis, growth factor binding, and receptor-mediated pathways. The hypothesis is that these genes are involved in pathways associated with the regulation of neuron survival, differentiation, and youthfulness.\\n\\nMechanism: This gene set is hypothesised to be involved in signalling pathways related to neuron survival, differentiation, and development. These pathways are probable mediated by endocytosis, growth factor binding, and receptors.\\n\\n] \n", - "469 [\\nThis is a list of 20 human genes, most of which are associated with neural development and axon guidance. Several of these genes are involved in receptor-mediated endocytosis, G-protein coupled receptors, cell adhesion, gene transcription and post-translational regulation. The enriched terms include structure-specific proteins, receptor-mediated endocytosis, G-protein coupled receptors, cell adhesion, gene transcription, and post-translational regulation. \\nMechanism: These genes are involved in the regulation of various processes such as cell motility, cell differentiation and cell migration, and formation of complex systems such as axon networks, which involves a variety of cellular pathways. ] \n", - "470 [\\nAnalysis of the above list of genes revealed that a considerable number of them are involved in processes such as protein binding, transcription, catalyzing reactions (including enzymatic reactions), and GTPase activating protein activation. This indicates that these genes play a role in a wide range of biological processes related to cellular and subcellular processes. In particular, these genes are involved in functions such as histone deacetylation, carbohydrate and lipid metabolism, receptor binding and signaling, DNA binding, and DNA packaging.\\n\\nMechanism:\\nMany of the genes listed are related to binding either other molecules or DNAs, as well as catalyzing various reactions. These processes likely work together to allow cells to properly function, as well as for their internal structures to be regulated and maintained, such as for the types of molecules necessary for cellular and subcellular processes. Additionally, transcription is another process heavily involved, as many of the genes are associated with regulating the expression of other genes. \\n\\n] \n", - "471 [ \\nSummary: The list of human genes encompass a variety of processes such as DNA binding, histone acetylation, protein binding, transcription regulation, and leucine residue modification.\\n\\nMechanism: The underlying biological mechanism involves the regulation of gene expression, protein and nucleic acid metabolism, and signal transduction.\\n\\n] \n", - "472 [ The list of genes provided encodes many different proteins involved in metabolic regulation, cell signaling, and post-translational modification. The most enriched term is: “cell signaling”; other terms include “metabolic regulation” and “post-translational modification”.\\n\\nMechanism: The mechanism underlying the enriched terms is that many of the encoded proteins are involved in different pathways that ultimately regulate and control the cell processes, such as cellular signaling, metabolic regulation, post-translational modification, and more. These proteins work together in a complex network to control cell activities. \\n\\n] \n", - "473 [\\n\\nSummary: A large majority of the genes are involved in the regulation of a wide range of cellular functions including those related to cellular transport, metabolic processes, scaffolding, transcriptional regulation, cell cycle control, transcription factor activity and phosphorylation.\\n\\nMechanism: These genes-through their diverse roles in the regulation of cell transport, metabolic processes, scaffolding, transcriptional regulation, cell cycle control, transcription factor activity and phosphorylation-form the backbone of numerous cellular functions. \\n\\n] \n", - "474 [ The enriched terms from the analysis of this list of genes indicate that they are all primarily involved in interaction with other macromolecules or with receptors, or in structure and cell adhesion. Many of the genes are associated with the regulation of transcription factors, such as the TNF receptor family, and others are associated with enzyme regulation or the production of cytokines. The underlying hypothesis is that these genes represent a variety of pathways that help regulate various aspects of cell function and communication.\\n\\nMechanism: The mechanism behind the term enrichment relates to the protein-protein interactions and cell adhesion that is regulated by these genes.\\n\\n] \n", - "475 [\\nSummary: A list of human genes and their functions were analyzed and enrichment terms related to intracellular signaling, cell adhesion, and membrane proteins were identified.\\nMechanism and ] \n", - "476 [ \\nSummary: Twenty-eight genes that encode proteins involved in immune/inflammatory responses, growth regulation, and signal transduction were found to be enriched in terms of functions related to cytokine receptors, chemokines, TGF-beta superfamily, transcriptional regulation, protein tyrosine phosphatases, and protein kinases. \\n\\nMechanism: These genes are involved in immune and inflammatory responses, growth regulation, and signal transduction by influencing cell proliferation, differentiation, and apoptosis.\\n\\n] \n", - "477 [COULD NOT PARSE] \n", - "478 [ \\nSummary: A majority of the gene functions on this list are related to protein-coupling, receptors, cell surface and membrane-associated proteins, and cytokine-related components.\\nMechanism: Cell membrane, receptor-coupled, and ligand-binding activities.\\n] \n", - "479 [ Genes in this list are predominantly involved in receptor binding, signaling, membrane transport, calcium binding and transmembrane transport. The enrichment of these specific functions suggest the underlying biological mechanism involves immune responses, cytokine signaling and communication between the nucleus and cytoplasm of cells. \\n\\nMechanism: Genes in this list have functions in receptor binding, signaling, membrane transport, calcium binding and transmembrane transport which are involved in immune responses, cytokine signaling, and nuclear/cytoplasm communication.\\n\\n] \n", - "480 [ This list of genes are enriched for modulating processes related to cell signaling, immune response, and gene regulation, mainly through interacting with ligands, receptors and enzymes, and RNA or DNA binding activity. \\nMechanism: The enriched genes are involved in pathways that lead to protein activation, degradation, ubiquitination, and participation in RNA or DNA binding.\\n] \n", - "481 [COULD NOT PARSE] \n", - "482 [COULD NOT PARSE] \n", - "483 [ This gene set is enriched for terms related to transcriptional regulation, enzyme activity, binding ability, protein structures, and cell signalling. There is a wide array of proteins involved in cytokine and growth factor signalling, immunity, and transcription factors, as well as a range of proteins carrying out important enzymatic functions.\\n\\nMechanism: The genes in this gene set are all involved in a variety of pathways and processes related to cellular signalling, protein production, gene expression, immune response, enzyme activity, and DNA binding activities, given their involvement in different transcriptional and binding processes.\\n\\n] \n", - "484 [ The genes in this list are predominantly involved in the regulation of ion channels and ion transport proteins, as well as receptor proteins, calcium binding proteins and various enzymes involved in cell signaling and metabolic processes. \\nMechanism: These proteins play important roles in the regulation of various processes ranging from cell adhesion to cytokine/growth factor signaling and hormone-regulation as well as metabolism. \\n] \n", - "485 [\\nSummary: The list of genes are involved in a variety of functions including catalyzing reaction, membrane transport, signaling, DNA-binding, transcription, extracellular signaling, and calcium-ion binding.\\n\\nMechanism: These genes play a role in operating a variety of biological pathways related to immune system signaling, cell growth and maintenance, cell communication, hormone regulation, transcription, development, and metabolism.\\n\\n] \n", - "486 [ Enriched terms related to protein structure and functions, including membrane-associated proteins, peptidases, receptor proteins, DNA-binding proteins, kinases, and transcription factors involved in transcriptional regulation. Mechanism: These proteins are involved in many biological processes, including blood pressure regulation, electrolyte balance, signal transduction, transcriptional regulation, ion transport, muscle contraction, immunologic regulation and cytokine production, cell cycle control, apoptosis, cell adhesion, and tumorigenesis. ] \n", - "487 [\\nSummary: Gene functions enriched in this list include receptor functions, protease production, cell adhesion, development, immune regulation, inflammation, protein family structural functions, GTPase activities, transcription factor functions, transcription regulation, post-translational modifications, endocytic receptor-ligand interactions, ligand functions, serine protease inhibitor functions, interaction with plasma membrane components, small molecule energy production and transport, transcriptional binding and regulatory protein family functions, and DNA binding. \\nMechanism: A variety of gene functions are enriched in this list, including receptor functions, protease production, cell adhesion, development, immune regulation, inflammation, protein family structural functions, GTPase activities, transcriptional regulation, transcription factor functions, post-translational modification functions, endocytic receptor-ligand interactions, ligand functions, serine protease inhibitor functions, interactions with plasma membrane components, small molecule energy production and transport, transcriptional binding and regulatory protein family functions, and DNA binding. These functions likely play a role in a variety of biological processes, including signal transduction, cell proliferation, development, growth factor signal transduction, metabolic regulation and stress response. \\n] \n", - "488 [\\nSummary: This list of genes has numerous important functions related to regulation of the cytoskeleton, cellular communication, cellular development and DNA transcription/translation and repair.\\nMechanism: These functions are critical for maintaining proper cellular morphology, adhesion, and organelle trafficking as well as for initiating and regulating cellular signaling pathways and gene expression.\\n] \n", - "489 [\\n\\nSummary: The list of genes encodes proteins which are associated with various regulatory processes in the cell, including binding to and/or activating GTPases, structural maintanance of the cytoskeleton, and control over cell cycle or apoptosis.\\n\\nMechanism: These proteins are likely involved in the regulation of the cell via interactions with proteins such as Rho GTPases or guanine nucleotide exchange factors (GEFs), or participation in the cell cycle, apoptosis, or structure of the cell.\\n\\n] \n", - "490 [ This list of human genes is enriched for functions related to cellular homeostasis, including protein synthesis, metabolism, protein folding, ubiquitination, transcription, DNA binding and damage control, development, and regulation of cellular pathways.\\n\\nMechanism: These genes are enriched for factors involved in various cellular processes necessary for maintaining homeostasis. These include protein synthesis, redox balance, fatty acid and energy metabolism, protein folding, ubiquitination, protein-protein interaction, transcription, and DNA damage control. In addition, these genes are enriched for factors that regulate various cellular pathways, including apoptosis, the cell cycle, and protein degradation.\\n\\n] \n", - "491 [\\nThe human genes found in the list are primarily involved in metabolic processes, cellular homeostasis, and chromatin regulation. Specifically, ATP production, amino acid homeostasis and metabolism, stress response, transcription and mRNA regulation, chaperones and proteasome degradation pathways, and lipid metabolism are all found to be enriched terms with known correlation to each other. Many of the proteins noted have both metabolic and protein-degradation pathways, indicating potential regulatory mechanisms in place for metabolic and homeostatic processes.\\n\\nMechanism: \\n\\nThe metabolic pathway systems are regulated by a combination of transcription and degradation pathways. Proteins involved in these pathways, such as chaperones, proteasomes, and enzymes regulate the transcription of genes and the degradation of proteins for a tight control of homeostatic and metabolic processes. Additionally, lipid and amino acid metabolism are regulated by clusters of enzymes, indicating a need for integration between multiple proteins.\\n\\n] \n", - "492 [\\n\\nSummary: The genes studied are involved in a variety of functions that together form a transcription and translation network, primarily related to translation initiation, RNA binding, and ubiquitination.\\n\\nMechanism: The genes involved form a transcription and translation network that is used to control gene expression and regulation.\\n\\n] \n", - "493 [ \\nThe list of genes includes proteins that are involved in several processes, such as ribosome formation, RNA binding, DNA unwinding, nucleocytoplasmic transport, SUMO binding, mRNA splicing, nucleic acid binding, and protein acetylation.\\n\\nMechanism: \\nThese genes are enriched for proteins and processes related to gene expression, posttransslational modification of proteins, and protein synthesis. Through these processes, cells control the expression of genes, activate and inactivate proteins, regulate the cytoplasmic environment, and control the metabolism of macromolecules.\\n\\n] \n", - "494 [ \\n\\nSummary: This set of genes is involved in protein binding, transcriptional regulation, cellular processes such as cell cycle progression, protein chaperoning, and cell proliferation, nuclear localization, RNA binding activity, pre-rRNA processing, and ribosome biogenesis. \\n\\nMechanism: Many of the genes in this list encode proteins involved in pre-rRNA processing, ribosome biogenesis, transcriptional regulation, and protein binding activities that are fundamental in cell cycle progression and regulation of cellular processes.\\n\\n] \n", - "495 [ This list of genes encodes a number of proteins that are involved in RNA processing, nucleolar function, mitochondrial function, nuclear signaling and protein folding. The enriched terms include RNA binding activities, rRNA processing, protein homodimerization, cell proliferation, signal transduction, ribosome biogenesis, protein folding, and mitochondrial transcription factor activity. Mechanism: The underlying biological mechanism might involve a complex network of interactions involving proteins encoded by these genes, that lead to successful cellular processes such as ribosome biogenesis, RNA processing, mitogenesis, and protein folding. ] \n", - "496 [\\nSummary: The list of genes consists of genes involved in various muscle functions, calcium level regulation and metabolic processes.\\nMechanism: The genes are involved in various cellular processes including ion channel regulation, energy metabolism, signal transduction, muscle contraction, and protein ubiquitination/degradation.\\n] \n", - "497 [COULD NOT PARSE] \n", - "498 [ \\nSummary: This term enrichment analysis focused on fourteen human genes that are involved in regulation of cellular process via Notch and Wnt signaling pathways. \\n\\nMechanism: Through term enrichment analysis of these genes functions, it has been revealed they are involved in the regulation of cell fate decisions and transcriptional activity through the Notch and Wnt signaling pathways. \\n\\n] \n", - "499 [ This list of genes is enriched for those involved in Notch signaling pathways, protein ubiquitination, cell fate determination, and transcriptional regulation.\\nMechanism: Multiple genes in this list have roles in the Notch signaling pathway and are involved in transcriptional regulation, ubiquitination, cell fate determination and other processes in order to control the cell cycle and cell division process. \\n] \n", - "500 [ This list of genes encode proteins that are involved in the metabolism of glucose, fatty acids, and amino acids by various catalytic steps and systems related to energy production in a cell. ] \n", - "501 [ Human genes on this list are found to be involved in a common pathway related to mitochondrial respiration, oxidative phosphorylation, and pyruvate metabolism related functions. The enriched terms from the term enrichment test are: terminal enzyme; ATP synthesis; mitochondrial respiratory chain; NAD/NADH-dependent; cytochrome c oxidase (COX); electron transport; PDH complex; ubiquitin protein; ferredoxin; acyl-CoA dehydrogenase; and pyruvate dehydrogenase. \\n\\nMechanism: The common pathway these genes have been found to be involved in is related to mitochondrial respiration, oxidative phosphorylation, and pyruvate metabolism. This pathway is mediated by oxidation-reduction reactions, in which electrons are transferred by the proteins being expressed. This transfer of electrons is used to produce ATP, an important source of energy for the cell. These proteins are also involved in other processes including fatty acid metabolism, electron transport, pyruvate metabolism, and ubiquitin protein metabolism.\\n\\n] \n", - "502 [\\n\\nSummary: Human gene functions related to cell cycle regulation, transcriptional regulation, protein binding, DNA binding, and cell signaling. \\nMechanism: Regulation of biological processes and pathways by association of proteins to various binding targets including proteins, DNA, and electron transfer. \\n] \n", - "503 [ \\nSummary: The majority of genes are involved in regulating protein synthesis, transcriptional regulation and cell cycle regulation.\\nMechanism: Regulation of protein synthesis, transcriptional regulation, cell cycle regulation, DNA repair and DNA binding.\\n] \n", - "504 [\\n] \n", - "505 [ The list of genes are expressed across various tissues, primarily in the pancreas, endocrine system, and brain. Other tissues expressed in these genes include: liver, intestine, kidney, and epithelium. They encode for proteins that are involved in transcriptional regulation, metabolic pathways, and cell signalling. This suggests an underlying biological mechanism related to transcriptional control and regulation of the endocrine system, pancreas, and glucose metabolism. The enriched terms for this list of genes include: transcriptional regulation; metabolic pathways; endocrine system regulation; glucose metabolism; cell signalling; GTPase; transcription factor; peptide hormone; ATP-binding cassette (ABC) transporter; and proprotein convertase. Mechanism: The list of genes suggest an underlying biological mechanism related to transcriptional control and regulation of the endocrine system, pancreas, and glucose metabolism. ] \n", - "506 [ The list of genes is enriched for proteins involved in the transport of various molecules and the enzymatic degradation of molecules across extra- and intra-cellular membranes (e.g. ATP-binding cassette transporters, oxidoreductases, dehydrogenases/reductases, hydratases/isomerases, enzymes responsible for fatty acid beta-oxidation, enzymes catalyzing the breakdown of malonyl-CoA, etc). Specific biological pathways or mechanisms of which the genes are a part involve cell adhesion, nucleotide excision repair, hormone metabolism and synthesis, nucleic-acid binding, antioxidant activity, and transcription factors. \\n\\nSummary: The list of genes is enriched for proteins involved in transport and enzymes that catalyze the degradation of molecules.\\nMechanism: Mechanisms of which the genes are a part involve cell adhesion, nucleotide excision repair, hormone metabolism and synthesis, nucleic-acid binding, antioxidant activity, and transcription factors.\\n] \n", - "507 [\\nSummary: Genes mentioned are found to primarily be involved in pathways that are related to oxidative stress and hormone response.\\nMechanism: These genes may be involved in oxidative stress, hormone signaling, or fatty acid metabolism.\\n] \n", - "508 [ \\nSummary: The majority of genes in this list encode proteins involved in signal transduction pathways and interact with other proteins via phosphorylation or protein-protein binding. \\nMechanism: Many of the gene products in this list are involved in signal transduction via phosphorylation, protein-protein interaction, GTP binding and/or cAMP binding. \\n] \n", - "509 [\\nSummary: The genes listed mostly encode components involved in cellular signaling cascades, such as protein kinases, guanine nucleotide-binding proteins, receptor-interacting proteins and chaperone proteins.\\nMechanism: The listed genes appear to be involved in a variety of signaling cascades, such as those related to cell growth, transcription, cytokine production and protein modification.\\n] \n", - "510 [ \\n\\nSummary: Gene functions enriched for membrane-associated proteins, GTPases, coatomer complexes, vesicle trafficking, organelle biogenesis, phosphatidylinositol binding and regulation\\nMechanism: The gene functions are involved in the regulation, biogenesis and transport of intracellular organelles, membrane proteins and vesicles, as well as binding of phosphatidylinositol molecules.\\n] \n", - "511 [COULD NOT PARSE] \n", - "512 [COULD NOT PARSE] \n", - "513 [\\n\\nSummary: This set of genes are mostly involved in redox processes, oxidative stress, DNA repair, and metabolism. These genes are involved in processes related to the regulation of cell growth, DNA repair, inflammation control, and cellular defense\\n\\nMechanism: The genes in this list are involved in a variety of functions that are necessary for cellular homeostasis and metabolic processes. Redox processes, oxidative stress, and damage control are mediated by a variety of proteins, such as heme oxygenase, glutathione reductase, superoxide dismutase, and glutathione peroxidase. DNA repair is regulated by proteins such as nucleotide excision repair complex and phosphofructokinase A. Inflammation control is regulated by proteins including myeloperoxidase, MAPEG family proteins, and glutaredoxin. Cellular defense against toxic and carcinogenic compounds is regulated by proteins such as glutathione S-transferase and peroxidase.\\n\\n] \n", - "514 [ Enriched terms shared by the genes include cell cycle regulatory proteins and kinases, DNA binding proteins and chaperones, nucleotide and polypetide biding proteins, phosphatases, and proteins involved in transcription. In particular, the genes function in gene transcription, chromosome organization, apoptosis regulation, DNA repair, protein folding and transport, cell signaling and growth regulation, energy metabolism, cytoskeletal organization, and vesicular trafficking. The underlying biological mechanism is likely involved in multiple steps in cell division and the regulation of gene expression, and in the maintenance of cell homeostasis.\\n\\nOerbaken: ] \n", - "515 [COULD NOT PARSE] \n", - "516 [COULD NOT PARSE] \n", - "517 [ \\n\\nSummary: The 20 genes examined are primarily involved in signal transduction pathways, transcription regulation and cell-to-cell communication.\\nMechanism: The identified genes are involved in various signaling pathways, including the transforming growth factor-beta (TGF-beta), bone morphogenetic protein (BMP), and receptor-regulated SMAD pathways.\\n] \n", - "518 [\\nSummary: The list of genes contain a range of proteins that are involved in transcriptional regulation, cytokine activity, regulation of cell proliferation, and lipid metabolism.\\nMechanism: The genes are involved in a range of biological processes related to transcriptional regulation, cytokine activity, regulation of cell proliferation, and lipid metabolism.\\n] \n", - "519 [\\nThis list of human genes includes receptors, cytokines, proteins, transcription factors, enzymes, and growth factors involved in inflammation, signaling pathways, transcriptional regulation, and cell cycle control. \\nMechanism: The functions of the genes in the list are likely to be related to inflammatory responses, signal transduction, and cell cycle regulation and apoptosis.\\n] \n", - "520 [ The genes in the list are involved in RNA processing and binding, transcription regulation, protein folding, targeting, covalent modifications and transport, endoplasmic reticulum function, and translation initiation. The enriched terms are RNA binding; transcription regulation; protein folding; protein targeting and covalent modifications; endoplasmic reticulum function; and translation initiation. Mechanism: The underlying biological mechanism for the enrichment of these terms is that the proteins encoded by the list of genes interact with each other to perform a variety of roles in RNA processing, transcription regulation, protein folding, targeting and covalent modifications, endoplasmic reticulum function, and translation initiation. These proteins can act as components of a larger complex or individually to perform these roles. ] \n", - "521 [ Genes in the provided list are primarily involved in processes such as protein synthesis, endoplasmic reticulum stress response, RNA binding, and conformational folding.\\n\\nMechanism: These genes encode proteins that play a role in protein synthesis, cellular trafficking, conformational folding, and RNA binding. These processes are inter-related in that conformational folding is necessary for protein structure, protein expression is required for protein synthesis, and RNA binding is necessary for mRNA translation. The endoplasmic reticulum stress response allows for regulation of these processes.\\n\\n] \n", - "522 [\\nSummary: The genes in the list are involved in a wide range of processes, including cell surface glycoprotein binding, cell adhesion, phosphoprotein production, transcription regulation, and signaling pathways.\\nMechanism: Many of the genes are associated with signaling pathways, including calcium-dependent signal transduction, phosphorylation, MAP kinase signaling, PI3 pathways, and G-protein signal transduction.\\n] \n", - "523 [ This set of genes is enriched for terms associated with embryonic development, cell signaling, receptor regulation and transcription regulation. Specifically, genes related to transcription factors, receptors and their respective ligands, growth factors, phosphoproteins and kinases are overrepresented.\\n\\nMechanism: These genes are involved in a variety of different cell signaling pathways, which are essential for embryos to develop properly and become mature organisms. During embryonic development the signals which these enzymes and receptors transmit and respond to, such as hormones and growth factors, direct the development and differentiation of cells. Cells communicate with one another through these pathways and transcription factors to direct cellular activities such as proliferation, differentiation, growth, migration, as well as many other metabolic and physiological processes.\\n\\n] \n", - "524 [ \\nSummary: The genes listed are involved in a variety of functions, including protein binding, catalysis of metabolic reactions, transcriptional regulation and regulation of cell signaling pathways.\\nCommonalities: \\nMechanism: Genes bearing similar functions may be involved in similar molecular or cellular processes, and the high level of overlap between gene function across the list implies a common pathway of regulation of certain activities in the cell, such as metabolic reactions and signaling pathways.\\n] \n", - "525 [\\nThe list of genes shows enrichment related to enzymes, regulatory proteins, transcription factors, membrane and transport proteins, structural proteins, and other proteins involved in cell growth and development. Specifically, this list is enriched for genes that encode a diverse range of regulatory proteins involved in cellular signaling, transcription control, metabolism, and immune response. There is also enrichment for genes involved in the biosynthesis of heme, which is important in cellular apoptosis and other cellular processes. \\n\\nMechanism:\\nThe underlying biological mechanism involved in this term enrichment likely involves the regulation of various biochemical processes by macromolecular signaling pathways. The term enrichment most likely reflects the need of these genes to work together in order to carry out specific functions in cellular homeostasis and adaptation. \\n\\n] \n", - "526 [ The genes listed are involved mostly in processes and pathways related to embryonic development, transcriptional regulation, DNA repair, and cell-cell interactions, such as Wnt, Notch, and Hedgehog signaling, as well as the F-Box protein family. \\n\\nMechanism: The molecular mechanism of this list of genes is related to cellular signaling pathways that enable cells to interact and establish communication with each other for proper embryonic development, cell fate determination, and DNA repair. These pathways involve the use of proteins such as Notch, Wnt, and Hedgehog receptors and ligands, as well as the F-box proteins.\\n\\n] \n", - "527 [\\n\\nSummary: This list of genes contained members of the frizzled, notch, Wnt, Dickkopf, and histone deacetylase families, which are involved in various cell fate decisions and signaling pathways during embryonic development.\\n\\nMechanism: The enriched terms reflect the commonality of the genes in the list, which are all part of signaling pathways that influence cell fate decisions, including canonical Wnt pathway, Notch pathway, and Hedgehog pathway.\\n\\n] \n", - "528 [COULD NOT PARSE] \n", - "529 [\\nThe list of genes is primarily involved in signal transduction and cell regulation, as well as immune defense, including cell recognition and protein phosphatase and ubiquitin binding activities. The underlying mechanism is likely regulated by protein and lipid enzymes, tyrosine and cGMP kinases, receptors, and transcription factors.\\n\\nMechanism: Signal transduction and cell regulation, mediated by protein and lipid enzymes, tyrosine and cGMP kinases, receptors, and transcription factors.\\n\\n] \n", - "530 [COULD NOT PARSE] \n", - "531 [\\nSummary: This set of genes is related to development, stem cell maintenance, and tumor formation. \\nMechanism: These genes regulate gene expression in embryonic development and in adult tissues, controlling the G1-to-S transition of the cell cycle following DNA damage and mediating the tumor suppressor gene p53.\\n] \n", - "532 [\\nSummary: This enrichment analysis of human genes suggests that these genes, or their encoded proteins, play a role in a multitude of processes including cell adhesion, signalling, metabolism, apoptosis, morphogenesis, hemostatsis, immunity and extracellular matrix maintenance.\\nMechanism: These genes are likely involved in modulating the interactions between cells and their macroenvironment and the modulation of cell-cell signalling pathways.\\n] \n", - "533 [ The list of genes includes those involved in tissue development and repair, extracellular matrix components, signaling pathways such as the Notch signaling pathway and the cyclic AMP signaling pathway, cell survival, motility and migration, regulation of Fas-induced apoptosis, antimicrobial activity, transcriptional activation, and regulation of cell adhesion.\\n\\nMechanism: The underlying biological mechanism that is likely to be at play is the regulation of cellular activity and processes, including cell proliferation, cell migration, extracellular matrix formation, adhesion and signaling pathways for optimal tissue development and repair.\\n\\n] \n", - "534 [\\nSummary: The group of human genes in this list are related to the functions of ion regulation, transcription regulation, signal transduction, and protein binding.\\nMechanism: Many of the proteins encoded by these genes, involve important cellular functions such as signal transduction, cytoskeletal adaptor proteins, transcription factors, and glycoproteins. This suggests a mechanism for many of these genes as either directly or indirectly involved in signal transduction pathways and/or transcriptional modulation of cell processes.\\n] \n", - "535 [\\nSummary: This gene list is enriched for genes that enable or are associated with a variety of activities, including transcription factor activity, metal ion binding activity, DNA binding activity, chromatin binding activity, RNA binding activity, protein domain-specific binding activity, and histone or methylated histone binding activity.\\nPredicted Mechanism: The gene list is enriched for genes that facilitate a variety of cellular processes, such as binding activities, transcription and translation, transcription factor activity, receptor activity, and chromatin structure. This suggests a variety of molecular pathways are enriched in these genes, likely related to cell adhesion, cell surface receptor signaling, cell apoptosis, transcriptional regulation, and the regulation of chromatin structure.\\n] \n", - "536 [ \\n\\nSummary: This gene list is involved with various processes related to cell structures, cell motility and varying aspects of muscle contraction.\\n\\nMechanism: The genes in this list are involved in a variety of processes related to the structure and function of muscle cells, such as actin filament binding and regulation of the intracellular calcium concentration. They are also involved in processes related to regulating neuronal and epithelial cell activity.\\n\\n] \n", - "537 [ \\nSummary: This gene analysis reveals a number of proteins involved in skeletal and cardiac muscle contractile processes, such as actomyosin ATPase activity and tropomyosin binding activity.\\nMechanism: The proteins regulate muscle contraction in response to fluctuations in intracellular calcium concentration, while also playing a role in muscle differentiation and muscle organization.\\n] \n", - "538 [\\nSummary: This set of genes functions in a variety of cellular processes such as endocytosis, cytoskeletal remodeling, lysosomal degradation, nuclear export, protein homooligomerization, actin filament network formation, plasma membrane bounded cell projection organization, endoplasmic reticulum formation, mitochondrial organization and cholesterol receptor-mediated endocytosis.\\nMechanism: The genes work together to regulate cellular processes in the cell such as protein trafficking, signaling pathways, and membrane reorganization. \\n] \n", - "539 [ A number of genes related to lysosomal degradation, receptor-mediated endocytosis, membrane-related processes, and endocytosis were identified. Proteins with death domain-folds, GTPase regulation, and ubiquitin-protein ligase activities were found to be recurrently present. \\n\\nMechanism: The gene functions identified are related to processes involved in the endocytosis and lysosomal degradation pathways which aid the movement of proteins and other molecules along the endocytic pathway. These processes involve specific processes such as receptor binding, GTPase regulation, ubiquitin-protein ligase and death domain-fold interactions. \\n\\n] \n", - "540 [\\nSummary: The list of genes is involved in metabolic pathways, such as glycogenesis, glycolysis, phosphorolation and gluconeogenesis.\\nMechanism: These genes function in the conversion of energy sources, such as glucose and fructose, into energy sources used by the body.\\n] \n", - "541 [\\nSummary: Genes in this list are involved in various functions related to glycolysis, metabolism, and regeneration.\\nMechanism: The genes in this list appear to be involved in the regulation of metabolic pathways related to the conversion of sugar molecules to energy and the conversion of energy to other forms, including muscle development and tumor progression.\\n] \n", - "542 [ These genes encode proteins involved in calcium homeostasis, calcium-channel activity, and receptor function in cell membranes.\\nMechanism: The genes are involved in the biosynthesis and maintenance of calcium-related proteins, ion channels, and receptors, which are essential components to facilitate information flow and cell-signaling across cell membranes.\\n] \n", - "543 [ The gene summaries are related to ion channels and transmembrane proteins that play a role in calcium homeostasis, calcium influx, synaptic transmission, and neuronal development. These proteins frequently belong to the Purinergic receptor, NMDA receptor, and AMPA-receptor regulatory protein (TARP) families. Mechanism: The proteins act through their function as ion channels and transmembrane proteins in order to act as mediators of calcium-dependent processes in neuron cells. ] \n", - "544 [ The genes provided are involved in several cellular pathways, including cell proliferation and survival, signal transduction, apoptosis, protein folding and DNA repair. There is an enrichment for genes involved in cell growth, apoptosis and signal transduction through serine/threonine kinase activator activity, phosphatidylinositol 3-kinase activity, and guanyl-nucleotide exchange factor activity. \\nMechanism: The genes appear to be involved in a variety of cellular pathways that are regulated by the AKT/PI3K and mammalian target of rapamycin (mTOR) signalling pathways. These signalling pathways mediate the activity of the genes by inducing cell growth and proliferation, and by regulating the expression of transcription factors such as NF-kappaB and TNFRSF11A/RANK.\\n\\n] \n", - "545 [ These genes are involved in functions related to DNA repair, apoptosis regulation, signal transduction, cell growth in response to nutrient and insulin levels, macromolecule metabolic process regulation, cell cycle control and chromatin remodeling. The common mechanism involved in each of the above is a signaling pathway regulated by protein kinases, phosphatases and protein acetyl transferases. \\n\\nMechanism: Signal transduction pathway is regulated by protein kinases, phosphatases and protein acetyl transferases.\\n\\n] \n", - "546 [\\nSummary: Genes included in this list encode enzymes that hydrolyze glycosyl bonds and are involved in glycosylation processes, such as N-Linked Oligosaccharide, O-linked N-acetylglucosamine, and Polysaccharide processes.\\n\\nMechanism: Genes act as an important role in glycosylation processes by hydrolyzing glycosyl bonds and processing oligosaccharides, galactosides, glucosides, and other molecules containing glycosyl linkages.\\n\\n] \n", - "547 [ \\n\\nSummary: Genes listed are involved in glycosyl hydrolase, glycohydrolytic enzyme, and hyaluronidase activity.\\n\\nMechanism: Genes listed have enzymatic activity that catalyzes the hydrolysis of glycosyl and glycohydrolytic bonds in glycoproteins, glycolipids, glycosaminoglycans, and other molecules containing oligosaccharide or polysaccharide components.\\n\\n] \n", - "548 [ The genes listed are mostly related to immunoglobulin receptor binding activity and involved in immune system processes. The enriched terms in these genes are antigen binding activity, immunoglobulin receptor binding activity, activated/inactivated immune response, protein homodimerization activity, and peptidoglycan binding activity. Mechanism: The underlying biological mechanism or pathway depends on the particular gene, but they all relate to the recognition and interactions of antigens, the binding of the antigens to immunoglobulin receptors, and the subsequent activation or inhibition of the relevant immune response. ] \n", - "549 [\\n\\nSummary: Several of the genes are involved in antigen binding activity, immunoglobulin receptor binding activity and activation of immune response.\\nMechanism: The genes function as part of a mechanism involving antigen and immunoglobulin receptor interaction and signaling pathways that lead to activation of immune responses.\\n] \n", - "550 [COULD NOT PARSE] \n", - "551 [ \\n\\nSummary: The human genes in this list appear to be associated with processes such as DNA double-strand break repair, meiosis, homologous chromosome pairing, and chromosome synapsis.\\n\\nMechanism: These genes likely play a role in homologous recombination, a key process in meiotic division and DNA double-strand break repair. The genes likely work together to form various complexes, such as the FA core complex, the APITD1/CENPS complex, and the CENPA-CAD (nucleosome distal) complex.\\n\\n] \n", - "552 [\\n\\nSummary: The list of genes has been analyzed, and include functions related to cell cycle progression, regulation of cell growth and survival, innate immunity, cholesterol and lipids metabolism, ubiquitination, antioxidant enzymes, intracellular transport, NF-κB inhibiting proteins, proteins associated with various inflammatory and neurological diseases, and proteins involved in embryogenesis, spermatogenesis, and hematopoiesis.\\n\\nMechanism: These genes are involved in a wide range of biological and biochemical processes that are related to cellular response, regulation of cell cycle progression, regulation of protein and lipid metabolism, protein ubiquitination, and intracellular transport.\\n\\n] \n", - "553 [\\n\\nSummary: This group of genes are involved in a variety of cellular processes, including endocytosis, iron storage and transport, lipogenesis, apoptosis, cell proliferation and differentiation, defense from bacterial infection, and regulation of transcription and translation.\\n\\nMechanism: The proteins encoded by these genes are thought to act through regulating the expression and activity of proteins, such as transcription factors, caspases, lipids, and hormones, involved in these cellular processes.\\n\\n] \n", - "554 [ This list of human genes is enriched for functions related to cellular homeostasis, including protein synthesis, metabolism, protein folding, ubiquitination, transcription, DNA binding and damage control, development, and regulation of cellular pathways.\\n\\nMechanism: These genes are enriched for factors involved in various cellular processes necessary for maintaining homeostasis. These include protein synthesis, redox balance, fatty acid and energy metabolism, protein folding, ubiquitination, protein-protein interaction, transcription, and DNA damage control. In addition, these genes are enriched for factors that regulate various cellular pathways, including apoptosis, the cell cycle, and protein degradation.\\n\\n] \n", - "555 [ \\n\\nSummary: The genes under consideration encode many proteins involved in metabolic processes, signal transduction and signal reception, transcriptional and epigenetic regulation, chaperone and proteolytic activity, and cell cycle regulation. \\n\\nMechanism: Biological processes are driven through the action of proteins in biochemical reactions, many of which are regulated by signal transduction systems, transcriptional and epigenetic regulation, and involvement in metabolic pathways.\\n\\n] \n", - "556 [ This gene set contains a collection of genes involved in peroxisome biogenesis, and is associated with the various categories of peroxisome biogenesis disorders (PBDs). The genes included code for proteins that are essential for the assembly of functional peroxisomes and involved in the import of proteins into peroxisomes and peroxisome membrane vesicles, as well as the PTS1-type and PTS2-type tripeptide peroxisomal targeting signals and peroxisomal matrix proteins. The enriched terms are: peroxisome biogenesis; peroxisomal protein import; tripeptide peroxisomal targeting signal; peroxisomal matrix protein; AAA ATPase family; peroxisome integrity.\\n\\nMechanism: Peroxins are proteins that are essential for the assembly of functional peroxisomes. These genes are involved in activities associated with the assembly, biogenesis, and integrity of peroxisomes, and in regulating the peroxisomal targeting signals and matrix proteins to be imported into the organelle. \\n\\n] \n", - "557 [ \\nSummary: An enrichment test of the functions of five human genes (PEX6, PEX2, PEX3, PEX7, and PEX1) revealed a common theme of proteins associated with peroxisomal biogenesis disorders (PBDs) and proteins involved in peroxisomal import and matrix proteins.\\n\\nMechanism: The proteins encode AAA family ATPases, predominantly cytoplasmic proteins, and integral peroxisomal membrane proteins. These encode the receptor for the set of peroxisomal matrix enzymes targeted to the organelle by the peroxisome targeting signal 2 (PTS2). The proteins play a role in the import of proteins into peroxisomes, where they form a heteromeric complex, and also in peroxisome biogenesis.\\n\\n] \n", - "558 [COULD NOT PARSE] \n", - "559 [COULD NOT PARSE] \n", - "560 [\\nSummary: The list of genes is related to ion channel gated ion channels and various neurotransmitters.\\nMechanism: The genes encode proteins responsible for mediating electrical signaling and transmitters of signals like glutamate, GABA, and potassium.\\n] \n", - "561 [\\nSummary: These genes are associated with a variety of neurological functions, including glutamate and GABA receptor activity, potassium channel activity, and N-methyl-D-aspartate (NMDA) receptor activity. \\nMechanism: The genes encode proteins involved in a variety of neurological functions, including ligand-gated ion channels, receptor ligands, and glutamate-gated ionic channels. \\n] \n", - "562 [\\n\\nSummary: List of genes are involved in transcription factors, degradation heparan sulfate, moonlighting proteins, immunoglobulin secretion, adapter or docking molecule, heme transporter, myelin upkeep, nuclear pore complex, mitochondrial DNA polymerase, ubiquitin ligase, and aminoacyl-tRNA synthetase.\\n\\n] \n", - "563 [ The analyzed gene summaries demonstrate enrichment of terms related to peripheral nerve and muscle function. Specifically, these include terms such as transcription factor, DNA helicase, nerve myelin maintenance, mechanically-activated cations channels, nerve motor neuron survival, and ubiquitination. \\n\\nMechanism: These genes appear to work together in a variety of ways to regulate transcription and the structural integrity of proteins in the peripheral nervous system, as well as regulate motor neuron and myelin maintenance, which contribute to nerve impulse transmission. \\n\\n] \n", - "564 [COULD NOT PARSE] \n", - "565 [COULD NOT PARSE] \n", - "566 [ This list of genes is enriched in terms related to transcription regulation, cellular organization and tissue development. Specifically, genes are enriched for functions related to DNA-binding, chromatin-binding, transcriptional regulation, bind to E-box DNA consensus sequence, regulation of DNA damage response, DNA damage response maintenance, phosphoprotein shuttling, zinc finger motifs, interaction with cellular retinol-binding proteins, hormone-dependent transcription, receptor-dependent transcription, nuclear hormone receptor-dependent transcription, transcriptional coactivator complex recruitment, chromatin remodeling complex formation, and transcriptional activator complex formation. The mechanism likely involves the formation of heterodimers, protein complexes, and chromatin regulators.\\n\\n] \n", - "567 [\\nThis list of human genes is mainly related to transcriptional regulation, chromatin remodeling, and DNA-binding activities. Enriched terms include transcriptional regulation, DNA-binding, chromatin binding activity, histone binding activity, and transcription factor activity. These genes are associated with various cellular processes including cell cycle progression, apoptosis, gene transcription, transcriptional activator/repressor activity, protein chaperoning, cell differentiation, DNA damage response, and transcriptional enhancement. The underlying biological mechanism of these genes is related to the regulation of gene expression as well as its downstream gene expression, which is further regulated by transcription factor signaling pathways, chromatin remodeling, and post-translational modification activities.\\n\\nSummary: This list of human genes is mainly related to transcriptional regulation, chromatin remodeling, and DNA-binding.\\nMechanism: These genes are associated with various cellular processes and are regulated by transcription factor signaling pathways, chromatin remodeling, and post-translational modification activities.\\n] \n", - "568 [\\n\\nSummary: The genes in the list are associated with a broad range of functions involved in skeletal development, collagen production and other extracellular matrix processes.\\n\\nMechanism: The mechanism appears to involve different genes acting on multiple pathways related to the synthesis, remodeling, and maintenance of extracellular matrix components.\\n\\n] \n", - "569 [ The genes listed above are associated with various development processes and tissue formation, such as collagen production, connective tissue development, matrix remodeling, and zinc finger protein regulation.\\nMechanism: The underlying known mechanism is the combination of transcriptional regulation and post-translational modification of the proteins encoded by these genes.\\n] \n", - "570 [ The list of genes is significantly and specifically associated with homologous recombination and DNA repair, as evidenced by an enrichment in terms related to these processes, such as \"dna repair\", \"homologous recombination\", \"excision repair\", and \"nuclease activity\".\\n\\nMechanism: The genes in this list are involved in a variety of DNA repair activities, such as excision repair and homologous recombination. These processes are important for maintaining the correct sequence of DNA and avoiding mutations that can lead to disease. \\n\\n] \n", - "571 [COULD NOT PARSE] \n", - "572 [ \\nSummary: A term enrichment test on the above list of genes based on biological classification hierarchies has identified terms related to metabolic and cellular functions that are statistically over-represented.\\nMechanism: These commonalities likely indicate a shared pathway, mechanism or process as related to metabolic and cell regulation functions.\\n] \n", - "573 [\\nSummary: This list of genes are mainly involved in energy metabolism and signal transduction. \\nMechanism: The genes in this list form a biochemical pathway responsible for the production of energy and for the detection and execution of cellular signals.\\n] \n", - "574 [ Genes related to the list are largely enriched for immune signalling/activation, regulation of cell cycle and differentiation, and transcriptional regulation.\\nMechanism: This likely indicates involvement of these genes in the processes of immune signalling, development or tissue remodelling, and metabolic regulation.\\n] \n", - "575 [COULD NOT PARSE\\nHypothesis: It is likely] \n", - "576 [COULD NOT PARSE] \n", - "577 [ \\nThe genes provided are significantly enriched in terms related to gene transcription and regulation, protein translation and metabolism, cytoskeletal organization, and lipid metabolism.\\nMechanism: These genes are likely to be involved in the regulation of genetic expression, transcriptional regulation, protein translation and metabolism, improvement of cell structure, and lipid metabolism. \\n] \n", - "578 [ The list of gene terms are involved primarily in cell communication processes like extracellular matrix organization, adhesion, and cell surface interactions. Specifically, they encode proteins involved in the aggregation of endothelial cells and vascularization processes. Mechanism: The proteins encoded by the genes in the list are likely involved in regulating the growth, development, extracellular environment, and adhesiveness of cells. ] \n", - "579 [ \\n\\nSummary: This list of genes appears to be involved in growth and morphogenesis of cells, including development of muscle, bone, and neuronal networks. \\nMechanism: Growth appears to be mediated by signals from cytokines and hormones, most notably VEGFA and PDGF, and mediated by transmembrane and extracellular matrix proteins, including LUM, VTN, and S100A4.\\n] \n", - "580 [\\nThis list of genes is related to development, tissue morphogenesis, contractile organs, extracellular matrix and cytoskeletal proteins. Enriched terms include bone, joint, muscle and connective tissue development; cell adhesion; adhesion receptor complex formation; signal transduction; and receptor-mediated signaling cascades.\\n\\nMechanism:\\nThese genes likely act together to facilitate the intricate networks of molecular and cellular pathways involved in development, homeostasis, and tissue repair. These include extracellular matrix formation and remodeling; cell adhesion; and signaling pathways associated with cell migration, proliferation, differentiation, and growth. The genes may work in tandem to promote changes in gene expression, stability, and intercellular communication involved in development and tissue repair processes.\\n\\n] \n", - "581 [ Our term enrichment analysis of the list of genes provided revealed statistically over-represented terms in gene function associated with cell adhesion, cell migration, migration and interaction, cytoskeletal organization, actin cytoskeletal regulation, signaling pathways, and regulation of the actin cytoskeletal organization. \\nMechanism: These results suggest that the underlying biological mechanism likely involves cytoplasmic signaling and regulation of the cytoskeletal organization, which would provide mechanical integrity to the cells, their adhesion to neighboring cells, and their migratory ability. This is supported by the evidence that many of the enriched terms relate to cell adhesion, migration and interaction, and cytoskeletal organization.\\n] \n", - "582 [ The list of genes is enriched for terms related to cell regulation, signal transduction, cell adhesion, protein folding, extracellular matrix organization.\\nMechanism: The list of genes are likely involved in a variety of cell regulation mechanisms such as activating responses to extracellular signals, influencing protein folding and assembly, regulating cell adhesion, and mediating phosphorylation cascades. \\n] \n", - "583 [ This list of genes appears to be involved in the development and maintenance of various organs, tissues and cellular processes. Specifically, enriched terms for this gene list include cell adhesion and migration; cell signaling; cell differentiation; protein kinase and phosphatase activities; transcription and DNA metabolism; immunomodulation; glycosylation and carbohydrate metabolism; and cell growth and proliferation. \\n\\nMechanism: The genes in this list play a role in a variety of molecular mechanisms that are important for normal development and tissue homeostasis. On the molecular level, these genes are involved in cell-cell adhesion, translation and translation regulation, signal transduction, and other processes. Moreover, the genes in this list regulate the expression of various cellular receptor, kinase, and phosphatase pathways, which may lead to downstream changes in cell growth, proliferation, and differentiation. \\n\\n] \n", - "584 [\\n\\nSummary: The human genes provided in this list are mainly related to apoptosis, transcription, cell cycle progression, and inflammation.\\nMechanism: These genes likely act together to execute pathways related to the regulation of cell growth and maintenance, DNA replication and repair, oxidative stress response, and immune system activation.\\n] \n", - "585 [ This list of genes is enriched for terms related to cell death regulation, inflammation, immune reaction, and growth and morphogenesis, which is a mechanism indicative of homeostasis in several biological functions.\\t\\n\\nMechanism: Expression of these genes contributes to cell survival by regulating the balance between cell death and survival, restraint of pro-inflammatory responses and activation of pro-inflammatory responses, promoting expression of genes involved in innate and adaptive immune responses and playing a part in promoting tissue growth, remodeling and morphogenesis. \\n\\n] \n", - "586 [ This list of genes is enriched for functions related to lipid metabolism and transport, development of vital organs, and cell signaling pathways.\\nMechanism: The enrichment of these genes suggests roles in cellular metabolic processes such as breakdown, transport, and synthesis of lipids, as well as cell-signaling pathways involved in development of vital organs such as liver, heart, and brain. \\n] \n", - "587 [ A large proportion of the genes provided are involved in lipid and fatty acid metabolism, including the movement and processing of lipids, such as through cytochrome P450 superfamily enzymes, hydroxyacyl-CoA dehydrogenases, SLCO1A2, FADS2 and SLC27A2. As well as lipid metabolism, genes are also enriched for other metabolic processes, such as glutamate metabolism (IDH1, 2, HSD17B6) and serine metabolism (SERPINA6 and PIPOX). In addition, there are genes associated with the regulation of transcription factors, including RXRA, LCK, and optineurin, as well as those involved in oxidative stress (SOD1, CTH, PNPLA8).\\n\\nMechanism: The enriched terms implicate a cross-regulatory and potentially inter-linked metabolic network involving lipid, fatty acid and disulphide bridge metabolism, with potential connections to oxidative stress response and gene expression regulatory mechanisms. \\n\\n] \n", - "588 [\\nSummary: A number of genes involved in lipid and cholesterol metabolism, cell signaling and regulation, development, cell adhesion, apoptosis and transcription have been identified.\\nMechanism: Genes associated with lipid and cholesterol metabolism are involved in regulating the synthesis, degradation and transport of lipids, while genes associated with cell signaling and regulation are involved in regulating cell growth, differentiation and apoptosis. Additionally, genes related to development, apoptosis, and transcription act in the regulation of cell adhesion, differentiation and development.\\n] \n", - "589 [ Proteins involved in lipid and lipid metabolism pathways, related to cholesterol control.\\nMechanism: Proteins involved in cholesterol regulation, such as HMGCR, PMVK, FADS2, SREBF2, S100A11, and MVK are likely to be involved in the upregulation and modulation of cholesterol levels. These proteins regulate the breakdown of fatty acids and also mediate the synthesis of bile acids, both of which are important in cholesterol metabolism. ] \n", - "590 [ Genes in this list represent functions related to extracellular matrix remodeling, angiogenesis and vascular development, immune response and platelet activation, collagen and fibronectin metabolism and regulation, and endocytosis and signal transduction.\\n] \n", - "591 [ The term enrichment test suggests that proteins involved in cell adhesion, proteolysis regulation, and interactions between extracellular proteins and cells are significantly enriched in this gene list. \\n\\nMechanism: These proteins likely act together in a coordinated manner to modulate cell adhesion, proteinase activity, and communication between cells. \\n\\n] \n", - "592 [ Our term enrichment test suggests that the commonalities in function of these genes are related to the regulation of cell growth and development, signal transduction pathways, and immunity. Specifically enriched terms include development of tissue and organs; signal transduction; cell surface receptor binding; response to stimulus; immune system; immune response; and cytokine activities.\\n\\nMechanism: These functions likely occur through a combined mechanism of modulating transcription factors, receptor-ligand binding, cytokine release and signaling, and a balance of intracellular concentrations of proteins and lipids.\\n\\n] \n", - "593 [\\nThe list of genes provided is heavily enriched for functions related to cellular signalling, inflammatory responses, and cellular stress response.\\nMechanism: These genes are typically involved in regulating and mediating signalling pathways, activating and responding to the inflammatory response, activating and functioning in the cell stress response, and facilitating cell-cell interactions.\\n] \n", - "594 [ The common functions for the human genes are involved in various developmental processes and DNA replication, with enrichment of terms such as \"developmental process\" and \"DNA replication\". \\n\\nMechanism: The genes act together to facilitate a variety of molecular processes in the cellular pathways to support embryonic and post-natal development, as well as DNA replication, transcription, and translation.\\n\\n] \n", - "595 [\\nSummary: Our genes are primarily involved in nucleic acid metabolism, transcription, and post-transcriptional modifications.\\nMechanism: The proteins encoded by the genes in our list likely play roles in the various biochemical steps involved in transcription, such as chromatin remodelling, pre-mRNA splicing, DNA repair, RNA polymerization, mRNA processing, mRNA transport, and translation initiation.\\n] \n", - "596 [ The provided gene list is over-represented for transcriptional regulation, chromatin modification and mitotic division/cell cycle components.\\nMechanism: The underlying mechanism of this gene set is that the enrichments are involved in the regulation of transcription for gene expression, maintenance of chromatin and DNA structure and function, and regulation of mitotic division and cell cycle checkpoints.\\n] \n", - "597 [ This list of genes is enriched for functions related to DNA replication and repair, chromatin modification, transcriptional and translational regulation, network formation, spindle formation and kinesin and dynein motor proteins. Mechanism: These genes are likely to function as part of an interconnected cellular pathway and/or network that allows for the generation of daughter cells and the coordination of transcriptional activity and post-translational modifications. ] \n", - "598 [ The list of genes provided show enrichment for terms relevant to extracellular matrix composition, cell adhesion and motility, cell-matrix interactions, growth factor and cytokine signaling, and matrix remodeling. \\n\\nMechanism: The mechanisms underlying the enrichment of these terms likely involve cell-matrix interactions, growth factor and cytokine signaling, and matrix remodeling.\\n\\n] \n", - "599 [ The identified genes are enriched for terms related to skeletal morphogenesis, cell-cell adhesion and motility, extracellular matrix production and remodeling, development and differentiation of connective tissue, collagen production and turnover, and cytokine and chemokine signaling. \\n\\nMechanism: It is likely that these genes are involved in mechanisms that coordinate protein interactions during skeletal development and morphogenesis, cell adhesion and migration, and the maintenance of a healthy extracellular matrix. In addition, these genes likely contribute to the production and turnover of extracellular matrix components such as collagens and chemokines and cytokines involved in development and differentiation of connective tissue. \\n\\n] \n", - "600 [\\nThis list of human genes was analysed in a term enrichment test. The test revealed that many of these genes were involved in a common pathway which supports normal cellular processes including DNA replication, transcription and gene expression, cell growth and differentiation, protein processing and trafficking. Furthermore, many of these genes were involved in bone morphogenesis and cancer-related pathways.\\n\\nMechanism:\\nThe underlying biological mechanism likely involves a number of distinct pathways, each with its own mechanism of action. Common processes shared by many of these genes include DNA replication, translation, and post-translational modification. Additionally, several of these genes are involved in cell-cell adhesion and the control of cellular migration and matrix remodeling, indicating roles in tissue morphogenesis. Furthermore, many of these genes are involved in intracellular signaling and signaling pathways that are essential for the processing and coordination of external and internal signals, which can ultimately result in cell growth, differentiation, and apoptosis.\\n\\n] \n", - "601 [ \\nSummary: The gene list includes genes involved in transcriptional regulation, signal transduction, membrane transport and lipid biosynthesis.\\nMechanism: The genes exhibit common patterns of transcriptional regulation and signal transduction, with a focus on protein-protein interactions and membrane transport.\\n] \n", - "602 [ Genes related to extracellular matrix organization, cellular adhesion and migration, cell mobility and growth factor-mediated signaling pathways;\\nMechanism: This gene list suggests that extracellular matrix organization, adhesion and migration, cell motility, and growth factor signaling pathways are involved in gene expression in these genes. \\n] \n", - "603 [ The genes are enriched for terms related to the structural organization of cells, transcriptional regulation, signal transduction, and immune responses.\\n\\nMechanism: These genes likely comprise a network that influences the physical and biochemical properties of the cell, including its membrane integrity, signal transduction pathways, gene expression, and immunomodulatory functions. \\n\\n] \n", - "604 [\\nSummary: The genes shown here are involved in a wide range of metabolic pathways and cellular functions, such as energy metabolism, lipid metabolism, amino acid metabolism, DNA damage repair, and cell signaling.\\n] \n", - "605 [ Genes are enriched in roles associated with lipid metabolism and the cell cytoskeleton. Both pathways involve important signaling and metabolic roles. Mechanism: Lipid metabolism pathways involve synthesizing and degrading lipids, transporting lipids, and their oxidation. The cell cytoskeleton is involved in a variety of functions, including building of cell membranes, cell motility and traffic. ] \n", - "606 [ \\nSummary: This list of human genes are enriched for functions related to cell cycle and/or development, such as DNA replication and transcription, and may be involved in a variety of pathways and processes.\\nMechanism: These genes may be involved in pathways related to DNA replication, transcription and expression, and cell cycle regulation.\\n] \n", - "607 [COULD NOT PARSE] \n", - "608 [COULD NOT PARSE] \n", - "609 [ \\nThis gene list is enriched for proteins involved in structural development and energy metabolism, such as structural proteins and enzymes of glycolysis, the pentose phosphate pathway, and the tricarboxylic acid (TCA) cycle. These terms are supported by evidence from gene ontologies (GO) assigned to the genes in the list.\\n\\nMechanism: \\nThe list of genes is involved in pathways which facilitate the efficient production and utilization of energy, such as glycolysis, the pentose phosphate pathway, and the tricarboxylic acid (TCA) cycle. They are also involved in the dynamic assembly of integral structures, such as the cytoskeleton, cell adhesion serve, proteoglycan synthesis, and extracellular matrix formation.\\n\\n] \n", - "610 [COULD NOT PARSE] \n", - "611 [ The genes appear to be involved in the development of various cell types, organs, and other growth processes, including neuron formation, cell adhesion and migration, signal transduction, tissue morphogenesis, and development of the nervous system. \\nMechanism: These genes likely act in a number of ways to promote and coordinate these processes, including recognizing and binding signaling molecules, relaying signals to other molecules, and affecting transcription of target genes. \\n] \n", - "612 [ The list of genes has a statistically significant enrichment of terms related to cellular metabolism, energy production and transport, cytoskeleton modification and remodelling, and cell adhesion. \\nMechanism: The molecular mechanisms involve the transfer of energy, metabolic pathways, and the coordination of cellular transport and reorganization.\\n\\n] \n", - "613 [ The enriched terms for this list of human genes suggest a common functional theme in organ development, morphogenesis and growth, immune system function, and transport processes. Enriched terms include: embryonic development; skeletal system development; organogenesis; morphogenesis; growth; immune system process; cell motility; steroid hormone receptor activity; receptor signaling pathway; transport; endocytosis; and cellular homeostasis.\\n\\nMechanism: The underlying biological mechanism suggested by the enriched gene functions is that these genes are involved in various organ and skeletal system development processes, in particular morphogenesis and growth, as well as immune system and transport processes. Specifically, these genes are involved in organogenesis, morphogenesis, growth, and cell motility through receptor signaling pathways, endocytosis, transport processes, and cellular homeostasis. Additionally, the genes are involved in steroid hormone receptor activity, further contributing to organ and skeletal system development.\\n\\n] \n", - "614 [ The list of genes is involved in a variety of pathways and functions related to cell differentiation, metabolism, protein processing, and the regulation of gene expression. Specifically, this list was enriched for terms related to cell cycle, remodeling proteins, stress response proteins, calcium signaling proteins, hypoxia-inducible factor proteins, transcription factors, chromatin-associated proteins, and kinases.\\n\\nMechanism: The overall mechanism of action of the genes appears to be related to the regulation of cellular processes via the modulation of expression of target genes, primarily through the regulation of epigenetic and transcriptional factors, in order to enable proper differentiation, metabolism, and protein processing. This is further supported by the enrichment of terms related to stress response proteins, calcium signaling proteins, hypoxia-inducible factor proteins, transcription factors, chromatin-associated proteins, and kinases.\\n\\n] \n", - "615 [ Genes identified in this set are associated with several DNA/RNA binding and regulatory processes, including transcription and epigenetic modification. Statistically over-represented functions in these genes include development, cell structure and movement, cell cycle and division, signal transduction, transport, and energy production; proteins involved in these processes include transcription factors, kinases, histones, and other enzymes. Mechanism: This enrichment likely reflects the underlying biological pathways governing various aspects of gene expression and regulation. ] \n", - "616 [\\nSummary: These genes are predominantly related to immunological functions, actin cytoskeleton organization, cell surface receptors, and pro-inflammatory regulation.\\nMechanism: The genes listed appear to be involved in the immune response, actin cytoskeleton organization, cell surface receptor-mediated signaling, and pro-inflammatory regulation.\\n] \n", - "617 [ The list of human genes provided are enriched for terms related to immunity, inflammatory response, cell growth, differentiation and development, and signaling pathways.\\n\\nMechanism: This underlying biological mechanism could involve proteins interacting with each other and coordinating pathways to govern immune response, inflammatory response, cell growth, differentiation, and development, as well as other cellular processes.\\n\\n] \n", - "618 [ This list of genes is enriched in terms related to cell signaling, cytokine production and regulation, regulation of gene expression and transcription, and cell adhesion.\\nMechanism: This list of genes promotes the core pathways of cell signaling, cytokine production and regulation, regulation of gene expression and transcription, and cell adhesion. This enables the body to respond to a variety of external signals, to recognize and respond to inflammation and stress, to produce the necessary molecules for the body to function correctly, and to hold the cell together so that it may adhere to corresponding cells and fulfill its role within the network of cells.\\n] \n", - "619 [ Increased expression of cytokines, chemokines, and interleukins; increased expression of developmental, signal transduction, and immune system pathways involved in cellular differentiation, cell motility and adhesion, signal transduction, and inflammation. \\nMechanism: The genes listed all appear to be involved in immune system, signal transduction and intercellular communication pathways. Through the identification of commonalities between the gene functions, inference can be made that these genes are involved in up-regulation of cytokines, chemokines, and interleukins involved in cellular differentiation, cell motility, adhesion, signal transduction and inflammation. \\n] \n", - "620 [COULD NOT PARSE] \n", - "621 [ The list of genes is enriched in functions related to the immune system, especially mediation of inflammatory response and cytokine production and signalling.\\nMechanism: The genes are involved in a variety of functions related to immune cell activation and cellular signaling, including cell adhesion, G-protein and receptor-coupled pathways, transcriptional regulation, cytokine and cytokine receptor binding, and lipid metabolism. \\n] \n", - "622 [COULD NOT PARSE] \n", - "623 [ Genes listed appear to be primarily involved in the regulation of interferon response pathways and the transcriptional control of interferon-stimulated genes. The genes appear enriched for the cellular pathways of immune response, inflammation, and cytokine signaling.\\n \\nMechanisms: The interferon response pathways activated in this population of genes modulate the expression of cytokines, chemokines, and antimicrobial and antiviral proteins, in order to activate an innate immune response to virus and bacteria. \\n\\n] \n", - "624 [ In this gene set, there are multiple genes that are enriched for functions related to immunology, such as antigen presentation, inflammatory responses, chemokine signaling, cell adhesion, and cytokine interactions. \\nMechanism: One hypothesis is that these genes are involved in an immune-mediated response related to their roles in antigen-presentation, inflammatory responses, the regulation of chemokines, and cell adhesion. \\n] \n", - "625 [ This list of genes is enriched in terms related to cell signaling, transcription regulation, and immune system regulation. Specifically, genes are enriched in pathways related to: interferon signaling; antigen processing, presentation, and recognition; cytokine signaling; cell cycle and DNA damage response; and apoptosis.\\n\\nMechanism: It appears that the genes identified in this list are functionally connected and may be involved in a larger underlying biological mechanism or pathway. The proteins associated with each gene are known to interact with one another and repress/activate various genes leading to the regulation of cell signaling, transcription, and immune system functions. This molecular regulation process is essential in the control of cellular functions and physiological behavior. \\n\\n] \n", - "626 [ The analysis of the list of human genes reveals that these genes are related to development, regulation, and signaling mechanisms within the cell. Specifically, the terms associated with development, such as digit development, neural development, immune system development and transcriptional regulation, are enriched. Additionally, terms related to signal transduction, such as G-protein coupled receptors, protein kinases, and guanine nucleotide exchange factors, are also enriched.\\n\\nMechanism:The mechanism underlying the term enrichment of the list of human genes is likely related to the fact that these genes play a role in a wide range of essential cellular processes. It is likely that signaling molecules and transcription signals coordinate these processes to enable proper development and homeostasis.\\n\\n] \n", - "627 [COULD NOT PARSE] \n", - "628 [ This list of gene names is enriched for genes involved in signal transduction, cell cycle control, and cell-to-cell adhesion.\\nMechanism: The enrichment of these genes indicates a shared biological pathway in which cellular communication, pathways, and networks are regulated by controlling the production of proteins and other molecules. This can lead to changes in other intracellular activities, such as cell cycle progression and adhesion. \\n] \n", - "629 [\\nSummary: This list of genes is enriched for terms related to cell adhesion and signal transduction, including terms such as integrin, chemokine receptor, protein kinase and G-protein-coupled receptor.\\nMechanism: These genes are involved in pathways important for cell adhesion, such as integrin and chemokine receptor-mediated interactions, as well as signal transduction pathways which include protein kinases, G-protein-coupled receptors and other associated proteins.\\n] \n", - "630 [\\n\\nSummary: The list of human genes have diverse enrichment in the functions of cell cycle control, cell adhesion, and cytoskeletal organization.\\nMechanism: These genes enable cells to interact with their environment and complete the cell cycle by organizing components, regulating activities, and controlling signaling pathways.\\n] \n", - "631 [ \\nSummary: The genes that were provided are statistically enriched for terms related to cell division, protein phosphorylation, chromatin remodeling, and microtubule binding and organization.\\nMechanism: These genes likely function in biological pathways related to spindle assembly, chromosome segregation and movement, cell-cycle control, and other processes related to mitosis. \\n] \n", - "632 [COULD NOT PARSE] \n", - "633 [\\nSummary: This list of genes is involved in a variety of pathways related to cell growth and development, including morphogenesis, transcription, and protein synthesis.\\nMechanism: The physiological processes induced by these genes likely work in concert to mediate a variety of cellular processes including cellular translation, metabolism, and signalling.\\n] \n", - "634 [\\nThe list of genes are involved in a variety of processes including, but not limited to, protein synthesis and modification, DNA replication, cell cycle regulation, and transcription regulation.\\nThis suggests that these genes may be involved in a co-dependent pathway or pathways that regulate cell growth, development, and gene expression.\\n] \n", - "635 [\\nSummary: This list of genes have overlapping functions in development, energy production, and regulation.\\nMechanism: There may be a pathway involved in controlling energy production, protein synthesis, and structural maintenance of cell components in development.\\n] \n", - "636 [ The enrichment test identified a set of genes related to protein and nucleic acid metabolism and cell cycle regulation. Specifically, genes involved in protein post-translational modifications, phosphorylation, transcription, translation, and ribosome biogenesis were enriched.\\n\\nMechanism: These gene functions are likely related to the underlying biological mechanism or pathway, since genes related to these processes have an essential role in regulatory activities and cell cycle control. ] \n", - "637 [ \\nSummary: Many of the genes listed appear to be related to chromatin and transcriptional regulation.\\nMechanism: Regulation of gene expression and chromatin structure via transcription factors and nucleosome remodeling enzymes. \\n] \n", - "638 [COULD NOT PARSE] \n", - "639 [COULD NOT PARSE] \n", - "640 [ These genes are associated with Notch receptor, transcription factor, and Wnt pathway signaling, which are involved in tissue and organ development.\\nMechanism: Notch receptor, Wnt, and transcription factor signaling pathways leads to a variety of processes such as morphogenesis, organogenesis, tissue development, cell fate determination, and cell interaction. \\n] \n", - "641 [\\nSummary: The genes in this list are associated with cell proliferation, morphogenesis and development, nerve system differentiation, and regulation of transcription.\\nMechanism: The genes likely function in pathways involved in the WNT and Notch signalling pathways, which have numerous roles in development and differentiation of different tissue types. \\n] \n", - "642 [COULD NOT PARSE] \n", - "643 [ Genes in this list are mainly associated with mitochondrial bioenergetics and associated pathways. Specifically, the terms \"mitochondrial electron transport chain complex activity\"; \"mitochondrial electron transport, NADH to ubiquinone\"; \"mitochondrial respiratory chain complex I activity\"; \"respiratory chain complex I assembly\"; \"respiratory chain complex III activity\"; and \"respiratory chain complex IV activity\" are found to be enriched in this gene set.\\n\\nMechanism: Mitochondria are dynamic organelles that are responsible for many of the metabolic pathways, including cellular respiration. A variety of mitochondrial electron transport complexes are involved in the production of energy, including complex I (NADH:ubiquinone oxidoreductase), complex III (ubiquinone:cytochrome c oxidoreductase), complex IV (cytochrome c oxidase), and complex V (ATP synthase). As these genes are associated with mitochondrial functions, it is possible that there is an underlying mechanism related to metabolic pathways and energy production within the mitochondria. \\n\\n] \n", - "644 [COULD NOT PARSE] \n", - "645 [COULD NOT PARSE] \n", - "646 [ Genes play diverse roles in the development of the pancreas, nervous system, and musculoskeletal system. Major term enrichment was found for pancreas development, nervous system development, development of neural structures, organogenesis, and transcriptional regulation. \\nMechanism: These genes are likely involved in a variety of biological mechanisms including, the regulation of morphogenesis, cell-to-cell adhesion, and protein synthesis pathways, as well as hormonal metabolism and signaling.\\n] \n", - "647 [ Analysis of these genes revealed common pathways related to metabolic regulation, neural development, and transcription/translation control. The terms enriched by these genes are neurogenesis; metabolism; transcriptional control; translation; morphogenesis; body patterning and organization; neurological system development; and cell differentiation.\\n\\nMechanism: Signaling pathways involved in neural development will have an influence on neurogenesis, while metabolic pathways will be involved in pathways that regulate glucose and lipid metabolism. Additionally, transcription and translation pathways are essential for regulating gene expression but also cell differentiation and morphogenesis. Finally, body patterning and organization rely on genes that control cell fate and cellular migration. \\n\\n] \n", - "648 [ The human genes given in the list are involved in metabolic biochemical pathways associated with lipid metabolism, stress response, mRNA transcription, DNA repair, skeletal and cartilage development, and cell migration. \\nMechanism: Metabolic enzymes and transport proteins appear to regulate these pathways, allowing for the synthesis and degradation of cellular compounds, as well as transporting molecules into and out of the cell to maintain physiological homeostasis.\\n] \n", - "649 [\\nSummary: Genes in this list are associated with a wide array of terms, including metabolism, transcription, regulation, transport and signaling.\\nMechanism: These genes likely play a role in a broad biological mechanism involving various metabolic pathways, transport, and regulatory functions.\\n] \n", - "650 [ The list of genes is enriched for terms related to signal transduction pathways and development, such as morphogenesis and cell differentiation.\\nMechanism: Signal transduction pathways are likely involved in the regulation of the gene functions, with particular importance of tyrosine kinase activity and modulation of relevant receptor activities.\\nHypothesis: The genes may be involved in the regulation of tissue development and cell differentiation.\\n] \n", - "651 [ \\n\\nSummary: This gene list covers a broad range of functions, including cell signaling, growth and survival, protein and lipid metabolism, transcription regulation, and cell cycle control.\\nMechanism: The genes in this list are likely involved in a variety of pathways that facilitate or regulate various cellular activities, such as receptor signaling, protein glycosylation, kinase activity, apoptosis, and G-protein interactions.\\n] \n", - "652 [ Genes listed are associated with vesicular transport, trafficking, and membrane fusion in the cell.\\nMechanism: Vesicular transport involves the formation of vesicles from the host membrane, trafficking of these vesicles through the cell and organelles, and fusion of the vesicles with host membranes for which these genes are responsible.\\n] \n", - "653 [ Enrichment test on a given list of human genes resulted in the identification of several enriched terms, which have important roles in post-translational modification, protein folding, protein synthesis, endocytosis, oligosaccharide metabolism, and lysosomal trafficking.\\n\\nMechanism: The mechanism behind this enrichment pattern is likely related to the various mechanisms regulated by these genes, such as the regulation of PTMs, protein folding, protein synthesis, endocytosis, oligosaccharide metabolism, and lysosomal trafficking.\\n\\n] \n", - "654 [\\nSummary: The list of genes is associated primarily with metabolic processes, defense against oxidative damage and DNA repair.\\nMechanism: These processes are likely related to cellular level metabolic regulation, protection against oxidative damage, and DNA damage repair.\\n] \n", - "655 [COULD NOT PARSE] \n", - "656 [ Genes associated with this list indicate enrichment for a variety of cell cycle control and chromatin remodeling processes, as well as protein ubiquitination, regulation of DNA replication, spindle assembly, and nuclear organization.\\n\\nMechanism: The enriched terms suggest that these genes are involved in a variety of related functions related to the regulation and maintenance of the cell cycle, chromatin remodeling, DNA replication, spindle assembly and nuclear organization.\\n\\n] \n", - "657 [COULD NOT PARSE] \n", - "658 [COULD NOT PARSE] \n", - "659 [ Our term enrichment analysis of these genes reveals an overrepresented pattern of general cellular processes related to the development and proliferation of cells, as well as homeostasis, cell division, and migration. Specifically, genes related to transcriptional regulation, signal transduction, cell cycle regulation, protein kinase pathways, and translation were enriched.\\n\\nMechanism: These overrepresented functions suggest a complex coordination of biochemical pathways contributing to cell development and proliferation, junctions, and cytoskeletal organization.\\n\\n] \n", - "660 [ The genes in the given list are predominantly involved in the TLR signaling pathway, development, inflammation and immune-response regulation.\\nMechanism: The TLR signaling pathway consists of an intricate set of reactions starting with the recognition of a pathogen-associated molecular pattern (PAMP) by the TLR receptor, leading to the activation of various transcription factors, such as NFKB and MAPK, which work to activate a cascade of gene expression and ultimately the secreting of pro-inflammatory molecules.\\n\\n] \n", - "661 [ Gene functions related to inflammation and immunity appear to be enriched when analyzing the list of genes provided, including cytokine-mediated signaling, antigen-receptor mediated signaling, B-cell proliferation, cytokine expression and release, immunoregulatory interactions, NF-kappaB (NF-κB) activation, and interferon (IFN) signaling.\\n\\nMechanism: These genes are likely involved in an inflammatory response in which cytokines are released and induce receptor activation, which leads to NF-κB activation and transcription of genes that produce cytokines and other signaling molecules, as well as triggering an IFN response. This ultimately leads to B-cell proliferation and immunoregulatory interactions in order to mount a response to the any pathogens. \\n\\n] \n", - "662 [\\nSummary: A significant enrichment of genes involved in translation and protein folding is found in the gene list, indicating a common pathway for these genes.\\nMechanism: The genes in this list are likely all involved in the same pathway, centered around translation and protein folding.\\n] \n", - "663 [COULD NOT PARSE] \n", - "664 [ This enrichment test demonstrates over-representation of the genes involved in cell signaling, structural and enzymatic proteins, and morphogenesis. Mechanism: The mechanisms underlying this enrichment are likely related to the roles of these proteins in regulating the mechanism of intercellular signaling associated with cell development, adhesion, migration, metabolism, skeletal growth, and cell death. ] \n", - "665 [COULD NOT PARSE] \n", - "666 [\\n\\nSummary: The enriched terms from the list of genes suggest a commonality in roles related to protein and organelle trafficking, DNA methylation, transcription and binding, chromatin remodeling, cell cycle regulation and metabolism. \\n\\nMechanism: The proposed mechanism is that these processes are essential components of pathways that regulate cell development, growth, and the response to internal and external stimuli.\\n\\n] \n", - "667 [COULD NOT PARSE] \n", - "668 [COULD NOT PARSE] \n", - "669 [ Genes highly enriched in the provided list have functions related to cell signaling and regulation, including morphogenesis, transcription, and development. Specifically, genes involved in Wnt, Notch, and Hedgehog pathways, transcription factors, and cell cycle genes such as Axin, β-catenin, HDAC2, and CUL1 are all significantly enriched in the list.\\n\\nMechanism: Many of the genes involved in these pathways are responsible for controlling cell fate and regulating morphogenesis and development. The Wnt pathway, a key regulator in embryonic development, is involved in axial patterning, tissue organization and differentiation, and cell-fate decisions. The Notch and Hedgehog pathways are also important for stem cell maintenance and development in early development, as well as tissue patterning, morphogenesis, and organogenesis in adulthood. The transcription factors, such as LEF1, TCF7, and NKD1, drive gene expression in response to these signaling molecules. Lastly, genes such as ADAM17, DKK1, PSEN2, and AXIN2 are involved in cell-cycle regulation and apoptosis. \\n\\n] \n", - "670 [\\nSummary: This list of genes are enriched for terms related to cell development and signaling, specifically those involved in receptor-mediated signaling and the regulation of cell morphology. \\nMechanism: These genes likely act through regulating cell development and receptor-mediated signaling pathways to their respective functions, such as morphogenesis and gene expression.\\n] \n", - "671 [ \\nThis sample of genes are mainly involved in regulation of the immune system, cell signaling, cytoplasmic transport, and apoptosis. Specifically, the genes are enriched for terms such as cytokine receptor binding; cell adhesion; immunoreceptor-antigen complex binding; regulation of the ubiquitin-proteasome pathway; transcription factor regulator activity; GTP-binding protein binding; cell differentiation; T-cell receptor binding; antigen presentation; and immune system process.\\n\\nMechanism: This list of genes likely act in concert to regulate the immune system. They perform a variety of functions, including binding and processing cytokines, receptor-antigen complexes, and other molecules involved in the binding or processing of molecules, such as transcription factors, that are involved in regulating gene expression. Additionally, these genes may be involved in cell differentiation, antigen presentation, and other processes involved in the regulation of the immune system. \\n\\n] \n", - "672 [ The genes provided are related to transcription factor activity, as they are associated with embryonic stem cell differentiation and pluripotency.\\n] \n", - "673 [ The given list of genes is involved in the regulation of cell differentiation and development, specifically in the formation of stem cells, by regulating the expression of developmental proteins. ] \n", - "674 [ The genes included in this list are related to cell proliferation, tissue morphogenesis, motility regulation, vascular development, bone growth, and the immune system. The mechanism is the transcription of gene products that cause expression of varied proteins that mediate these functions.\\n\\nMechanism: Transcription of gene products inducing the expression of varied proteins that mediate cell proliferation, tissue morphogenesis, motility regulation, vascular development, bone growth, and the immune system.\\n\\n] \n", - "675 [ This list of genes are all involved in the development and maintenance of the vascular system. Specifically, these genes play a role in angiogenesis, cell proliferation and migration, matrix remodeling, and tissue remodeling. The genes are implicated in processes such as Jagged-mediated signaling, transcriptional regulation, platelet activation and aggregation, immune regulation, and extracellular matrix formation.\\n\\nMechanism: These genes are involved in a variety of pathways that are responsible for the formation and maintenance of the vascular system. Specifically, the Jagged and Notch pathways are implicated in the control of endothelial cell proliferation and migration, while the TGF-β and Wnt/β-Catenin pathways are involved in matrix remodeling. Additionally, these pathways are also involved in platelet activation and aggregation and the formation of extracellular matrix components.\\n\\n] \n", - "676 [ Genes associated with this list are enriched for functions related to development and signaling, including cell growth, differentiation, and migration; chromatin modulation; transcription regulation; cytoskeletal organization; intracellular trafficking and adhesion; signal transduction; and DNA/RNA metabolic processes.\\nMechanism: The genes are likely to be involved in multiple biological mechanisms and pathways, including processes related to healing, morphogenesis, angiogenesis, and muscle growth and development.\\n] \n", - "677 [ This analysis identified a number of genes involved in various cellular processes such as chromatin regulation, cell development, protein translation, and ion transport.\\nMechanism: The underlying biological mechanism likely involves regulation of gene expression through the actions of transcription factors, the post-translational modifications of proteins, and the transport of ions across cell membranes.\\n] \n", - "678 [ The human genes listed are involved in skeletal muscle structure and contractility. The genes are enriched for processes such as myofibrillogenesis, actin filament organization, and muscle contraction.\\n\\nMechanism: The genes likely act to regulate processes involved in myofibrillogenesis, such as Z-disc formation and maintenance, nuclear positioning, and muscle fiber organization. They also may act to modulate ion channel influx/efflux, thereby influencing muscle contraction and force. \\n\\n] \n", - "679 [\\nSummary: Genes in this set are involved in muscle structures and processes.\\n] \n", - "680 [\\nSummary: These genes are related to lipid metabolism, cell signaling pathways, and cell cycling.\\nMechanism: These genes are thought to have a role in regulating lipid metabolism, cell signaling pathways and cell cycling. \\n] \n", - "681 [\\nSummary: The genes in this list are predominantly involved in endocytosis and intracellular signaling.\\nMechanism: The genes in this list interact to form a molecular pathway that is involved in endocytosis and intracellular signaling. Endocytosis allows receptors and newly synthesized molecules to be moved cellular compartments and can result in changes in cell signaling.\\n] \n", - "682 [\\nBased on the list of genes provided, common terms enriched amongst the genes include ATP synthesis, glycolysis, energy metabolism, and metabolic pathways.\\n\\nMechanism: \\nThe underlying biological mechanisms involve ATP synthesis by way of glycolysis and energy metabolism pathways, which produce necessary energy required for a variety of cellular activities.\\n\\n] \n", - "683 [ The genes identified are related to glycolysis, the metabolic pathway that produces ATP from glucose and other carbohydrates. \\nMechanism: Glycolysis involves the series pathways in which a compound molecule of glucose is broken down into two molecules of pyruvic acid, which are further converted into ATP. \\n] \n", - "684 [COULD NOT PARSE] \n", - "685 [\\nSummary: This gene set is primarily involved in neuronal functional regulation, including ion transport, membrane potential regulation and neurotransmission.\\nMechanism: These genes are involved in the regulation of neuronal activity, likely through the regulation of a number of ion channels, neurotransmitter receptors, and calcium/potassium regulators.\\n] \n", - "686 [COULD NOT PARSE] \n", - "687 [\\nThe genes provided are all involved in cell regulation and signaling pathways. Specifically, they all have roles in the activation of transcription factors, and in the activation, regulation and inhibition of signaling proteins such as Ras, Akt and calcium associated kinases.\\nMechanism: \\nThe genes all act together in order to affect the expression of various genes and proteins. They function by either upregulating or downregulating the expression of transcription factors and signaling proteins, as well as by modulating the phosphorylation state of these proteins, thus controlling their activity.\\n] \n", - "688 [ These genes are apparently associated with lysozymes, mucins, glycosyltransferases, and hyaluronidases, enzymes and proteins with roles in the breakdown and regulation of glycosylation.\\nMechanism: The mechanism behind this gene cluster's biological role seems to be in the regulation of cell processes related to glycosylation, such as enzyme production and its breakdown.\\n] \n", - "689 [COULD NOT PARSE] \n", - "690 [\\nSummary: The genetic pathways enriched in these genes involves immunoglobulin heavy/light chain combination, antigen specific receptors, J-chain, and T-lymphocyte receptors. \\nMechanism: These genes mainly play a role in immune response, specifically the regulation of the combination of immunoglobulin heavy and light chains to form antigen-specific receptors, the formation of J-chain, the production of T-lymphocyte receptors, and the regulation of immune function.\\n] \n", - "691 [COULD NOT PARSE] \n", - "692 [ This list of genes is enriched for functions related to DNA replication, repair, and replication fidelity. Mechanism: The list of genes is likely to be involved in simulating DNA synthesis, prioritizing DNA strands for replication, ensuring proper repair of damaged DNA strands, and ensuring that high-fidelity replication is taking place during the cell cycle. ] \n", - "693 [COULD NOT PARSE] \n", - "694 [ 17 of the genes in the list are related to functions involving calcium homeostasis, including calcium signaling, regulation of calcification, and regulation of calcium ion transport. Mechanism: The genes identified are involved in the regulation of calcium homeostasis and signaling, along with functions related to calcification, calcium buffering and transport, protection against calcium overload, and calcium-v influx/efflux. ] \n", - "695 [\\nSummary: Our list of human genes suggests pathways involved in cell structure regulation and metabolism.\\nMechanism: These genes are likely involved in the regulation of cell morphology, metabolic processes and apoptosis.\\n] \n", - "696 [COULD NOT PARSE] \n", - "697 [COULD NOT PARSE] \n", - "698 [\\nThis list of genes is enriched for terms related to protein homeostasis and peroxisome biogenesis. The genes are likely to have roles in maintaining and regulating the levels of specific proteins, as well as helping to form and breakdown peroxisomes in the cell.\\n\\nMechanism: The mechanism underlying these functions appears to involve forming, maintaining and regulating the levels of specific proteins, as well as assisting in the formation and breakdown of peroxisomes in the cell. \\n\\n] \n", - "699 [ The genes provided are all related to Peroxisomal Biogenesis, an important cellular process. \\nMechanism: Peroxisomal biogenesis requires the coordinated expression of multiple genes in order for the peroxisome to be expressed and maintained in cells. \\n] \n", - "700 [COULD NOT PARSE] \n", - "701 [ Shortly, these genes are involved in a range of functions including transcriptional regulation, DNA repair, cell cycle regulation, and cell differentiation. \\nMechanism: These genes all have common functions related to the transcription, repair, and/or regulation of DNA, which suggests that they all play a role in the response to cellular damage or stress, which in turn can influence the downstream processes of cell cycle, differentiation, and growth.\\n] \n", - "702 [ Through a term enrichment test on this list of genes, we see that they are over-represented in terms related to ion conductivity and neural excitability, including ion channels, membrane proteins, and synapse formation.\\n\\nMechanism: These genes likely play a role in neural excitability, leading to the formation of specific ion channels that can conduct ions and help form synapses between neurons.\\n\\n] \n", - "703 [ This group of genes is enriched for terms related to ion-channel function, neuron excitability, and synaptic transmission.\\nMechanism: This group of genes suggested the underlying molecular pathway involves communication between neurons via ion-channel mediated synaptic transmission.\\n] \n", - "704 [ These genes are mainly involved in protein synthesis, metabolism, ion channel transport, and muscle contraction or development.\\n\\nMechanism: These genes function as transcriptional regulators, enzymes in metabolic pathways, ion channels, or as key mediators of neuromuscular development and contraction.\\n\\n] \n", - "705 [ This list of genes encodes many proteins which are involved in nucleic acid metabolism, binding, and transport. Terms enriched in these genes include: Nucleic Acid Metabolism; Nucleic Acid Binding; Nucleic Acid Transport; Protein Metabolism; Protein Binding; and Protein Transport.\\n\\nMechanism: The proteins encoded by these genes are likely to be involved in nucleic acid metabolism and other related downstream processes. These proteins are likely involved in mRNA transcription, mRNA processing and/or mRNA translation. The proteins could also be involved in processes like RNA editing, DNA replication, DNA repair, and DNA recombination. These proteins are likely to be involved in the regulation of gene expression and other pathways related to this process.\\n\\n] \n", - "706 [ This gene list is enriched for terms related to G-Protein Coupled Receptors (GPCRs), G-protein subunits, adenylate cyclase, calcium channels, and kinases.\\n\\nMechanism: The GPCRs and G protein-coupled subunits are involved in signal transduction pathways that regulate a variety of cellular activities. They activate adenylate cyclases, which catalyze the synthesis of the secondary messenger cAMP. This acts downstream to activate pathways and processes such as G-protein mediated second messenger systems and cation channels. Kinases are involved in the regulation of the G-protein by phosphorylating the Gα subunits and other associated components, leading to changes in their activity, and ultimately, signaling cascades.\\n\\n] \n", - "707 [\\n\\nSummary: The enriched terms from these genes suggest a correlation with signaling pathways, cellular growth and differentiation, organization of the cytoskeleton, regulation of endocrine systems, and transcriptional regulation. \\n\\n] \n", - "708 [COULD NOT PARSE] \n", - "709 [ The enriched terms for this list of genes are cellular growth, transcriptional regulation, and chromatin remodeling. These genes are generally involved in the regulation of transcription, chromatin modifications, and cell cycle regulation. These terms are statistically over-represented compared to the gene list provided.\\n\\nMechanism: The likely underlying biological mechanism for these genes is that they are involved in multiple pathways like transcription, chromatin modifications, and cell cycle regulation. These pathways control essential processes such as cell growth and differentiation in the body. Through these mechanisms, the genes may help to regulate embryonic development and maintain tissue homeostasis in adults. \\n\\n] \n", - "710 [ \\nSummary: The list of genes are found to be associated with proteins involved in collagen and extracellular matrix related activities and the control of transcription.\\nMechanism: These proteins are involved in various processes, such as collagen fibril organization, connective tissue development, extracellular matrix organization, glycosaminoglycan biosynthetic process, negative regulation of transcription by RNA polymerase II, positive regulation of transcription by RNA polymerase II, proteoglycan biosynthetic process, Rho protein signal transduction, skin morphogenesis, and zymogen activation.\\n] \n", - "711 [\\nSummary: The genes in this list are associated with extracellular matrix organization, collagen fibril organization, collagen biosynthesis, proteoglycan biosynthesis, and glycosaminoglycan biosynthesis.\\nMechanism: These genes are likely to be involved in the organization of extracellular matrix, the formation of collagen fibrils, and the synthesis of proteoglycans and glycosaminoglycans. \\n] \n", - "712 [ Genes are involved in processes related to DNA repair and protein monoubiquitination, part of Fanconi anaemia nuclear complex, and located in multiple cellular components including chromatin, nucleus and cytosol. Hypothesis: These genes work in concert to coordinate the repair of DNA damage, likely with monoubiquitination acting as a signal for protein binding activities related to DNA repair. ] \n", - "713 [\\nSummary: Members of the Fanconi Anemia Nuclear Complex are involved in protein monoubiquitination and DNA repair processes.\\nMechanism: Members of the Fanconi Anemia Nuclear Complex act in a coordinated fashion to catalyse monoubiquitination of proteins, regulate cell cycle, and repair damaged DNA.\\n] \n", - "714 [ The terms found to be enriched in the gene summaries include “protein binding activity”, “NAD(P)H oxidase activity”, “ATP binding activity”, “GTP binding activity”, “transmembrane transporter activity”, “DNA binding activity”, “receptor binding activity”, “cysteine-type endopeptidase inhibitor activity”, “caspase binding activity” and “RNA binding activity”. \\n\\nMechanism: These genes likely contribute to or are part of a variety of processes involving cellular signaling pathways, tissue development and repair, immune system modulation, and metabolic pathways.\\n\\n] \n", - "715 [ \\nSummary: These genes are largely involved in protein binding activities and enzyme activities.\\nMechanism: Enzyme activities and protein binding activities allow for the regulation of cell processes, cell signaling and energy production. \\n] \n", - "716 [\\nThis list of genes is involved in a broad range of biological processes, including growth factor and cytokine activities; enzyme binding, activating and regulating activities; transcription activator, receptor and factor binding activities; and other activities related to binding and signaling. These genes are primarily involved in protein homodimerization, protein heterodimerization, and identical protein binding activities, as well as protein kinase, DNA-binding and RNA-binding activities.\\n\\nMechanism:\\nThese processes are mostly facilitated by the interactions between various domain specific proteins and pathways, including SH3 domain binding, C-X-C chemokine binding, heparin binding, ubiquitin-protein ligase binding, calmodulin binding, ICAM-3 receptor activity, TAP complex binding activity, MHC class II protein complex binding, interleukin-12 receptor binding, and Toll-like receptor 2 binding activity.\\n\\n] \n", - "717 [ This enrichment test reveals genes associated with extra- and intra-cellular biological processes and functions, specifically related to cell adhesion, receptor binding and signaling, transcription regulatory region sequence-specific DNA binding, chemokine related activities, and enzymatic, growth factor and cytokine related activities. Mechanism: This enrichment test demonstrates the involvement of specific genes in biological pathways related to cell adhesion, receptor binding and signaling, transcription regulatory region sequence-specific DNA binding, chemokine related activities, and enzymatic, growth factor and cytokine related pathways. ] \n", - "718 [ These genes are involved in a variety of functions, including transporter activity, protein binding, protein kinase binding, receptor activity, transcription, cellular metabolism, DNA damage response, and cytoskeleton organization. The commonalities between the gene functions include transport activity, protein binding, DNA binding, hydrolase activity, metal ion binding, GTPase activity, receptor activity, and transcription. The underlying biological mechanism or pathway involves cell organization, signal transduction, cell adhesion, cell cycle progression, and differentiation. \\n\\nMechanism: Cell organization, signal transduction, cell adhesion, cell cycle progression, and differentiation. \\n\\n] \n", - "719 [\\nSummary: The given list of genes includes proteins with DNA-binding, transcription, ubiquitin-binding, phosphatase, kinase, and other activities, which are associated with a wide range of cellular processes and pathways.\\n\\nMechanism: The molecules associated with the given genes function as protein regulators to control the expression of specific target genes and regulate intracellular processes.\\n\\n] \n", - "720 [COULD NOT PARSE] \n", - "721 [ \\n\\nSummary: Genes in this list are involved in a variety of functions, including collagen binding, fibroblast growth factor binding, phosphatase binding, integrin binding, calcium ion binding, signaling receptor binding and lipase activity. \\n\\nMechanism: These genes are likely involved in cellular processes and cellular component organization.\\n\\n] \n", - "722 [\\nSummary: The enriched term list includes cell adhesion, integrin binding, GTP binding activity, collagen binding activity, ATP binding activity, phospholipase binding activity, cell-matrix adhesion, cell adhesion molecule binding, and SH3 domain binding. \\nMechanism: The biological mechanism underlying the enrichment includes cell signalling pathways, actin filament binding and cell-to-cell adhesion, as well as cytoskeletal protein binding and receptor binding activities.\\n] \n", - "723 [ This set of genes is associated with extracellular matrix structures, adhesion and binding activities, signal transduction/receptors, and cytoskeleton support/stabilization; all necessary for cell-cell and cell-matrix communication and coordination.\\n\\nMechanism: These genes likely contribute to a diverse set of signaling pathways, involved in cell-cell communication and between the cell and the extracellular environment, mediated by binding with substrate molecules, interactions of receptor molecules, and the formation and stabilization of mRNA structure.\\n\\n] \n", - "724 [ Human genes involved in processes associated with cytosolic transports, membrane transports, and cellular extravasations, in addition to processes involved in the defense response and the positive regulation of macromolecule metabolism, appear to be enriched.\\n\\nMechanism: These processes impact the responses of cells in two ways: by allowing the transport of molecules between cells and by modulating the production of proteins which also modulate cellular activity. Furthermore, the signaling pathways regulated by these proteins impact a wide variety of downstream processes to regulate gene expression, cell motility, and cell adhesion.\\n\\n] \n", - "725 [COULD NOT PARSE] \n", - "726 [\\nSummary: A set of human genes involved in a variety of biological functions, including binding activities and enzyme activities, are enriched for functions such as DNA binding activity, protein dimerization activity, protein binding activity, and enzyme activity.\\n\\nMechanism: These genes are likely to be involved in the control of cellular processes, such as cell proliferation, apoptosis, and signal transduction pathways.\\n\\n] \n", - "727 [ Genes in this list are involved in a variety of functions related to immune response, apoptosis, protein folding and expression, cytoskeletal structure and regulation, extracellular matrix structural constituents, transcription/translation regulation, angiogenesis/neovascularization, calcium/potassium ion binding and transport, cell signaling, and other cellular processes. Overrepresented terms include: protein binding activity; identical protein binding activity; enzyme binding activity; DNA-binding transcription factor activity; RNA polymerase II-specific transcriptional activity; cysteine-type endopeptidase activity; and cytokine receptor activity. \\n\\nMechanism: These genes are involved in a wide variety of complex functions that help form, maintain, and shape the immune response, cell structure and cytoskeletal integrity, cell signaling pathways, and inflammatory processes. They work by binding to and regulating a variety of molecules, hormones, and proteins throughout the body and at the cellular level.\\n\\n] \n", - "728 [ This analysis shows a statistically significant over-representation of genes related to ATP processing/binding activities, cholesterol binding, transmembrane transport, protein heterodimerization, DNA binding, and enzyme/oxidoreductase activity. Mechanism: The underlying biological mechanism of these processes likely involves the maintenance of ATP and cholesterol levels and other metabolic processes, as well as regulation of transcription and cellular signaling via domains such as the SH2 domain or through DNA binding or various ligase activities. ] \n", - "729 [COULD NOT PARSE] \n", - "730 [\\n\\nSummary: These human genes are associated with processes relating to cholesterol biosynthesis, cell adhesion, cell structure and organization, signaling, and apoptosis.\\n\\nMechanism: These genes likely interact with each other to regulate cholesterol biosynthesis, cell adhesion and organization, signaling pathways and responses to stress, and apoptosis.\\n\\n] \n", - "731 [ The list of genes given is largely implicated in cholesterol and lipid biosynthetic processes. Additionally, a large number of genes are involved in the regulation of transcription, apoptosis, protein stability and interaction, and cell adhesion/migration. \\nMechanism: The overall biological mechanism is centered around the maintenance of cholesterol/lipid levels and transport, as well as regulation of key cellular processes including transcription, apoptosis, and cell adhesion/migration.\\n] \n", - "732 [\\n\\nSummary: The human genes in this list are involved in a variety of functions related to proteins, such as binding, disulfide isomerase activity, phosphoprotein binding, enzyme binding, and calcium ion binding.\\n\\nMechanism: These genes encode for enzymes involved in protein binding activities, such as heparin binding, integrin binding, collagen binding, and phospholipid binding. These activities are necessary for biological processes such as cell adhesion, cell-matrix adhesion, signaling receptor binding, blood coagulation, fusion, apoptotic signal transduction, and regulation of protein-coding gene expression.\\n\\n] \n", - "733 [COULD NOT PARSE] \n", - "734 [ \\nSummary: Genes in this list are primarily involved in regulation of protein activity, genetic transcription, cell signaling, and metabolism.\\nMechanism: These genes primarily influence protein activity and metabolism through complex interactions with other proteins and the environment. They interact in ways which affect protein activity, cell signaling, and possibly genetic transcription.\\n] \n", - "735 [\\n\\nSummary: The genes in this list are involved in many cellular activities, including DNA-binding, phospholipid binding, protein binding, binding to receptors, enzyme binding and inhibitor activities, GTPase activities, metal ion binding activity, and other protein activities.\\n\\nMechanism: These genes are likely to be involved in a wide range of cellular pathways, including signaling, transcription regulation, DNA repair, cell death, immune response and other cellular processes.\\n\\n] \n", - "736 [\\nSummary: This set of human genes are involved in many processes, including DNA and RNA binding activity, enzyme binding activity, protein binding activity, calcium ion binding activity, but primarily DNA damage and repair processes.\\nMechanism: These genes are involved in DNA damage and repair processes, whereby they bind to various sets of molecules and macromolecules, and catalyze/carry out downstream pathways such as DNA repair, familial clipping, etc.\\n] \n", - "737 [ The provided list of genes is involved in a variety of cellular functions, including DNA binding activity, ATP hydrolysis activity, RNA binding activity, enzyme binding activity, protein binding activity, DNA-directed DNA polymerase activity, nuclease activity, and mRNA regulatory element binding. The enriched terms that describe their common functions are DNA binding activity, enzyme binding activity, ATP hydrolysis activity, RNA binding activity, protein binding activity, DNA-directed DNA polymerase activity, nuclease activity and mRNA regulatory element binding.\\n\\nMechanism: The genes in the list likely contribute to the regulation of pathways that involve DNA, RNA, proteins and enzyme activities. These activities may be involved in various metabolic processes and regulatory networks within the cell, such as DNA repair, gene expression, nucleic acid metabolism, and cell differentiation.\\n\\n] \n", - "738 [ This set of genes appears to be involved in several different processes related to DNA, chromatin, and cell division, including chromatin binding activity, DNA replication and repair, transcription, histone modification, nuclear import/export, DNA/RNA binding, and protein-macromolecule binding. A majority of these genes appear to be involved in the regulation and maintenance of the cell cycle and the expression of genes through their interactions with proteins, chromatin, and nucleic acids.\\n\\nMechanism: The genes in this list are likely involved the regulation of genetic expression by influencing the properties of chromatin, and the structure and function of nucleic acids and proteins. These interactions may be mediated by histone modification and the binding of proteins, DNA, and RNA. Furthermore, DNA and RNA modification, as well as DNA repair, may also factor in to the gene's functions.\\n\\n] \n", - "739 [ The list of genes consists of proteins that are involved in a wide range of cellular activities, including DNA binding, transcriptional regulation, cell cycle progression, DNA replication, chromatin modification and repair, mitosis, and the remodeling of nuclear pore complexes. These proteins commonly cooperate in the formation of protein complexes and in the assembly of large macromolecular machines. They are involved in several biological pathways, such as DNA damage repair, cell cycle regulation, gene transcription, and nucleocytoplasmic transport.\\n\\nMechanism: This list of genes, together with their respective functions, implicates a wide variety of biological mechanisms. When viewed as a group, these proteins act together to coordinate fundamental cellular processes, including cell growth and repair, gene expression, and cell migration. Additionally, these processes are coordinated through the assembly of macromolecular machines, enabling the formation of large, protein complexes and facilitating interactions between different molecules.\\n\\n] \n", - "740 [\\nSummary: Genes enriched for mechanisms involved in protein binding, calcium ion binding, cell adhesion molecules, and extracellular matrix structure.\\nMechanism: Cell adhesion molecules, interactions with signaling receptors or other proteins, and extracellular matrix structuring.\\n] \n", - "741 [\\nSummary: The genes in this list are related to extracellular matrix structural constituents, collagen binding activity, cell adhesion molecules, DNA binding activity, GTP binding activity, and protein homodimerization activity.\\nMechanism: It appears that these genes are involved in the structural formation and maintenance of cells, particularly in the extracellular matrix, energy metabolism, and signal transduction pathways.\\n] \n", - "742 [\\n\\nSummary: The listed genes display a variety of functions related to DNA binding and/or regulation, protein binding/regulation, enzymes, transmembrane or ion transport activity, and mRNA or protein expression. \\n\\nMechanism: The underlying biological mechanism for these genes is likely related to their roles in regulating transcription, cell adhesion and signaling, gene expression, or metabolic pathways. \\n\\n] \n", - "743 [\\nThis list of human genes is enriched for multiple functions related to DNA binding and transcription factors, RNA binding, protein binding/dimerization, transmembrane transporters, calcium ion binding, enzyme binding, and GTPase activities. The underlying biological mechanism likely involve signal transduction, membrane transport, and protein activities related to chromatin and gene expression.\\n\\nMechanism: Signal transduction, membrane transport, and protein activities related to chromatin and gene expression. \\n\\n] \n", - "744 [\\nSummary: Genes involved in cell adhesion, transport, metabolic processes and transcription\\nMechanism: Cell surface activities, metabolic processes, and gene expression regulations \\n] \n", - "745 [ These genes are involved in a variety of functions related to protein regulation and metabolism such as transcription factor binding, enzyme binding, cell adhesion, and ligand-gated ion transporter activity. Mechanism: The function of these genes is likely related to either a transcriptional regulatory network, signaling cascade, or metabolic pathway. ] \n", - "746 [\\nSummary: Genes appear to be primarily involved in the binding, transport, and oxidation of molecules.\\nMechanism: These genes are likely involved in a variety of molecular processes including transportation, modulation, and redox reactions.\\n] \n", - "747 [ \\nSummary: A diverse group of genes involved in various enzymes and binding activities related to cellular responses, metabolism, and DNA regulation.\\nMechanism: Various enzymes and binding activities related to cellular responses, metabolism, and DNA regulation.\\n] \n", - "748 [ \\nSummary: The list of genes highlighted have common functions related to DNA and RNA binding, catalysis and metabolic activities, chromatin binding, and transcription and translation-associated activities.\\nMechanism: The genes in this list are involved in a variety of mechanisms; DNA and RNA binding, transcription and translation, catalysis, chromatin binding, metabolic activities, and protein folding and dimerization of proteins. \\n] \n", - "749 [ This list of genes are involved in wide range of functions related to protein binding, DNA binding, transcription factors, telomerase, RNA binding and DNA replication. They appear to be involved in a variety of processes related to cell cycle regulation, chromatin binding, gene expression, protein folding and regulation of chromosome structure.\\n\\nMechanism: The genes in this list are likely involved in a complex network of molecular processes related to DNA replication, transcription and cell cycle control. They appear to be involved in many processes that are necessary for cells to grow and divide, including transcription and translation, DNA replication, chromatin binding and protein folding. In particular, they likely contribute to gene expression, protein modification, DNA damage sensing, and cell cycle regulation.\\n\\n] \n", - "750 [COULD NOT PARSE] \n", - "751 [ \\nSummary: The genes demonstrate a variety of functions including enzyme binding activity, identical protein binding activity, and DNA binding activity.\\nMechanism: The genes described are involved in diverse metabolic activities and structural components. \\n] \n", - "752 [ The list of genes provide evidence that many of these genes are involved in processes related to development, including cell adhesion, growth, angiogenesis, and nerve cell differentiation. These processes are related to the formation of structures that are integral to the healthy function of organisms, such as blood vessels and organs. Common terms include: protein/lipid binding activity; DNA-binding transcription factor activity; regulation of gene expression; regulation of protein metabolism; and positive/negative regulation of cellular component organization. Mechanism: While the precise mechanism is unknown, it is likely that these genes are involved in the regulation of transcription, signaling pathways related to cell adhesion, metabolism, and growth, as well as the formation of complex structures necessary for healthy functioning organisms such as organs and neural networks.\\n\\n] \n", - "753 [\\n\\nSummary: Genes encode for activities that enable functions related to cell adhesion, transcriptional and post-transcriptional regulation, cell migration, signaling and receptor activity, and transcriptional repression.\\n\\nMechanism: This likely represents a collection of diverse pathways related to cellular activity and development, likely involving both transcriptional and post-transcriptional processes.\\n\\n] \n", - "754 [\\nSummary: This list of genes are involved in various functions such as DNA binding, RNA binding, enzyme binding, protein kinase binding, protein phosphatase binding, protein homodimerization, tissue morphogenesis, and protein phosphorylation.\\n\\nMechanism: The underlying biological mechanism for the enriched terms is likely to involve transcription regulation and signal transduction.\\n\\n] \n", - "755 [\\n\\nSummary: This list of genes are involved in diverse cellular functions such as DNA binding, protein binding and phosphorylation, as well as the transportation of ions and small molecules across membrane domains.\\n\\nMechanism: Many of the genes encode proteins involved in enzyme and transporter activity, contributing to metabolic, vesicular and cytoskeletal pathways.\\n\\n] \n", - "756 [COULD NOT PARSE] \n", - "757 [ These genes are predominantly involved in processes related to DNA-binding transcription activity (activator and repressor), protein binding activity, protein kinase binding activity and activity, enzyme binding activity, regulation of cell proliferation/growth, ligand-activated transcription, and intracellular processes.\\n\\nMechanism: The enriched terms suggest a shared mechanism of gene expression and regulation involving binding, enzymatic reactions and proliferation/growth processes. These processes all coordinate to regulate various biological activities. \\n\\n] \n", - "758 [\\n\\nSummary: Genes enriched in binding activities such as GTPase, DNA, protein, ligand, and BH3 domain, as well as in activities such as phosphatidylinositol and hydrolase, involved in pathways related to protein regulation, receptor signaling, and metabolism.\\n\\nMechanism: It is likely that these genes are involved in pathways related to modulating protein expression, receptor signaling, and metabolic processes such as cellular respiration, synthesis, and metabolism of fatty acids and nucleotides.\\n\\n] \n", - "759 [ \\n\\nSummary: Genes presented encoded for a range of activities related to the regulation of immunological and signaling processes, binding activities, transcription activator activities, and endopeptidase activities.\\n\\nMechanism: The genes potentially display a range of activities related to immunological and signaling pathways as well as binding, transcription activator, and endopeptidase activities.\\n\\n] \n", - "760 [ \\nSummary: This list of genes is involved in cytokine binding and receptor activities, protein binding, and kinase and phosphatase activities. \\n\\nMechanism: These gene functions are involved in signal transduction pathways affecting cell growth, development, and differentiation as well as immune responses and inflammation.\\n\\n] \n", - "761 [\\n\\nSummary: The genes listed are involved in a variety of processes related to cytokine binding activity, cytokine receptor activity, growth factor activity, cell adhesion molecule binding activity, chemokine (C-X3-C) binding activity, and defense response.\\n\\nMechanism: It appears that these genes are involved in coordinating processes related to the immune system, with cytokines acting as signaling molecules and the other genes acting as receptors or binding agents.\\n\\n] \n", - "762 [\\nThis list of genes is enriched for terms related to signal transduction pathways and pathways related to immunoregulation. Specifically, terms including G protein-coupled receptor activity, cytokine activity, DNA-binding transcription factor activity, ion channel activity, and receptor binding activity were found to be statistically overrepresented in the list.\\n\\nMechanism: The underlying mechanism is likely related to the diverse functions of these genes in signal transduction pathways and pathways related to immunoregulation. This includes G protein-coupled receptor activity, cytokine activity, DNA-binding transcription factor activity, ion channel activity, and receptor binding activity that helps modulate the signal transduction pathways.\\n\\n] \n", - "763 [\\n\\nSummary: The genes in the list are involved in a variety of cellular processes, including cell adhesion and binding, molecular functions, G protein-coupled receptor activity, ion transport and transmembrane transporter activity, signaling receptor binding, transcription factor activity, and several others.\\n\\nMechanism: The genes in the list are involved in a variety of biological mechanisms, such as pathways for cell communication, inflammation, and response to external signals.\\n\\n] \n", - "764 [ Upon performing the term enrichment test on these human genes, we find that the majority of them are involved in immune response processes, such as cellular response to cytokine stimulus, defense response to second organism, and infection response. Furthermore, many of the genes are linked to transcription activator activity, DNA and RNA binding activity, as well as other ligase/binding activities. The majority of the genes are located in the cytoplasm, Golgi apparatus, and other cellular components, suggesting a role in regulating the functional components of the cell.\\n\\nMechanism: The enriched terms suggest that these genes are involved in the mechanisms of transcription, translation, and protein modification, all of which play key roles in immune response. The transcription activity links to gene expression to regulate the expression of proteins involved in the immune response, while the DNA and RNA binding activities are involved in the transcription and translation processes. The ligases and binding activities would be critical for binding and changing proteins and other molecules to prevent infection and regulate the body's response.\\n\\n] \n", - "765 [ \\n\\nSummary: The genes identified show a wide range of cellular processes involved in immunity, transcription regulation, RNA metabolism, and protein activity modification. \\nMechanism: The genes are involved in a variety of processes likely related to regulation of immunity and protein activity, likely through regulation of transcription, RNA modifications, and ubiquitination.\\n] \n", - "766 [ \\nSummary: These genes are involved in a variety of processes to enable activities such as enzyme binding, promoter and transcriptional regulation, ATP hydrolysis, protein homodimerization, kinase regulation, protein dimerization, and several other functions. \\n] \n", - "767 [\\n\\nSummary: This set of genes provides a wide range of functions, from ATP hydrolysis and enzyme binding activity, to DNA binding activities, GTP binding activity, and peptide antigen binding activity.\\n\\nMechanism: This set of genes links many different functions at the cellular level, together with serine-type endopeptidase activity, DNA-binding transcription activity and activities related to cytokines, chemokines and signaling pathways. The patterns suggest a broad underlying mechanism involving the mediation of cell-signaling pathways, DNA-binding activity, involvement in apoptosis and other cellular functions.\\n\\n] \n", - "768 [\\nSummary: Genes associated with this list are involved in multiple signaling pathways and binding activities related to cell structure, adhesion, calcium ion and potassium channeling, and protein folding/binding/kinase activities.\\nMechanism: The underlying biological mechanism is likely related to signaling cascades that involve interacting proteins involved in cell adhesion, calcium and potassium channeling, and protein folding/binding/kinase activities.\\n] \n", - "769 [COULD NOT PARSE] \n", - "770 [\\nSummary: The majority of these genes are involved in functions related to membrane binding and regulation, protein domain binding and regulation, receptor ligand binding and regulation, DNA-binding transcription regulation, enzyme binding and regulation, and cytokine activity.\\nMechanism: These gene functions likely aid in cell adhesion, signal transduction and transcription factors involved in cell differentiation, migration, growth and development.\\n] \n", - "771 [ This list of genes appears to be involved in a wide range of functions in cell-cell adhesion, signaling, and development, including receptor binding activities, ligand binding activities, DNA-binding transcription activator activities, enzyme binding activities, protein domain specific binding activities, and protein kinase binding activities.\\n\\nMechanism: The underlying biological mechanism appears to involve the regulation and coordination of a variety of cell-cell interactions and cellular responses, such as hormone or cytokine activities, adhesion and structural support, intracellular transport, DNA transcription, protein modification and enzyme activities, energy production and metabolism, and other signaling and regulatory processes. \\n\\n] \n", - "772 [\\nSummary: The list of genes given have common functionalities related to cytoplasm and cytoskeleton proteins such as cell motility, binding, regulation and adhesion.\\nMechanism: These functions are likely involved in regulating cytoplasm and cytoskeleton components such as actin filaments, microtubules, and ribonucleopropteins.\\n] \n", - "773 [COULD NOT PARSE] \n", - "774 [\\n\\nSummary: The genes listed are involved in various cellular functions related to protein binding, domain binding and enzyme activity\\nMechanism: The genes are involved in several processes, such as cellular signaling, protein homeodimerization, DNA or RNA binding, transcriptional regulation, and metal ion binding.\\n] \n", - "775 [ These genes are primarily involved in various functions related to energy metabolism, transport, binding and regulation at a cellular level. The mechanism behind many of these functions likely occurs through interactions between proteins or protein complexes.\\n\\nMechanism: Predominantly interactions between proteins, or protein complexes, result in the observed functions of these genes. \\n\\n] \n", - "776 [\\nSummary: Many of these genes enable or contribute to functions related to RNA binding, protein folding chaperone, DNA binding/recognition, protein homodimerization, and similar molecular functions. \\nMechanism: The underlying biological mechanism is likely related to RNA processing, DNA replication and repair, chromatin binding and modification, and protein assembly and modification. \\n] \n", - "777 [\\n\\nSummary: Twenty-eight genes related to various functions are listed. These functions include DNA binding, RNA binding, protein domain specific binding, chromatin binding, enzyme binding, and protein folding chaperone activities. \\n\\nMechanism: These genes are involved in many essential processes for cellular functioning, such as DNA replication, RNA splicing and translation, protein folding and ubiquitination, transcription and gene regulation, as well as complement and histone binding, among others.\\n\\n] \n", - "778 [\\n\\nSummary: The genes all encode proteins that are involved in aspects of cell signaling, including metabolism, growth, cycle regulation, and protein transport.\\n\\nMechanism: The proteins perform a variety of functions related to the regulation of genetic information, including engaging in RNA binding or bridging, modification, transport, and translation activities.\\n\\n] \n", - "779 [ The list of genes are mainly involved in RNA binding activity, ribosomal rRNA processing, mRNA and/or rRNA catabolism/stability, regulation of transcription/translation, regulation of signal transduction and metabolism processes, regulation of cell cycle/proliferation, and protein modification/regulation that primarily occur within the nucleus, cytosol, ribosome, and mitochondria. \\nMechanism: The underlying biological mechanism is the regulation of protein and RNA-related functions that help to control the expression of essential genes, transcription processes, and RNA stability, as well as to regulate cell growth/division and signal transduction pathways.\\n] \n", - "780 [ The list of genes is associated with several common functions, including calcium ion binding activity, binding of proteins to other proteins, and actin filament binding activity. These functions are enriched in the list since they are represented by an overabundance of genes, suggesting that these are all key molecular processes. The underlying biological mechanism is likely related to actin cytoskeleton organization and regulation of ion channels. \\n\\nMechanism: Gene expression regulation of actin cytoskeleton organization and regulation of ion channels.\\n\\n] \n", - "781 [\\nSummary: This list of genes is found to be enriched for terms related calcium binding activity, enzyme binding activity, and DNA-binding activity.\\nMechanism: These genes are likely involved in a variety of biological processes, including cell adhesion, protein activity, receptor binding, and gene regulation.\\n] \n", - "782 [COULD NOT PARSE] \n", - "783 [\\n\\nSummary: Genes related to cancers, control of transcriptional processes, proteolysis, Notch signaling pathway, and cell proliferation/migration pathways were enriched. \\nMechanism: These genes act in mechanisms controlling growth and development processes, protein ubiquitination and degradation pathways, and pathways involved in control of transcription, cell signaling, and cell cycle control.\\n] \n", - "784 [ Enzymes and proteins involved in electron transport and oxidative processes, including binding, transfer, and enzymatic activities; some that interact with lipids, heme, MHC class I proteins, GTPase, and ubiquitin proteins.\\n\\nMechanism: Electron transport and oxidative processes are essential for physiological energy production, primarily through the citric acid cycle and the electron transport chain. The proteins and enzymes identified are necessary for the transfer of electrons, energy production, and energy storage. They also cause proteins to undergo conformational changes, influencing metabolite and lipid interactions as part of redox reactions.\\n\\n] \n", - "785 [This analysis of these human genes reveals enrichment of terms related to electron transfer activity, protein homodimerization, GTPase activity, adenine nucleotide transmembrane transporter activity, phosphoprotein binding activity, mitochondrial respiratory chain activity, proton-transporting ATP synthase activity, and mitochondrial ribosome binding activity.\\n\\nMechanism: These activities suggest that the genes contribute to mitochondrial energy metabolism through processes related to electron transfer, protein assembly, signaling, nucleic acid regulation, and protein transport.\\n\\n] \n", - "786 [ These genes encode proteins with functions in DNA binding activities, RNA polymerase II-specific functions, transcription regulation, protein binding activity, and enzyme binding activity.\\nThe commonalities in their functions suggest the underlying biological mechanism involves DNA transcription and regulation.\\n] \n", - "787 [ This list contains genes which are involved in a broad range of roles including signaling receptor binding, RNA polymerase II co-regulator, DNA binding, phosphatase activity, transcription factor activity, enzyme binding, cell adhesion, and growth factor binding. The commonalties in terms of gene function suggest that the genes are involved in various roles related to the regulation of gene expression and cellular processes, as well as protein modification and receptor binding activity. \\n] \n", - "788 [\\n\\nSummary: Genes involved in glucose transport, metabolism, and regulation, with many implicated in type 1 and type 2 diabetes. Regulation of gene expression transcription and protein function are heavily represented.\\n\\nMechanism: Glucose homeostasis is achieved through the combined action of the listed genes in two major pathways: a) glucose uptake, transport, and metabolism; and b) transcription regulation of insulin and other genes related to glucose homeostasis.\\n\\n] \n", - "789 [ The human genes provided appear to be related to cell-cell adhesion, development and differentiation of anatomical structure, regulation of transcription by RNA polymerase II, and regulation of signal transduction and macromolecule metabolism. \\nMechanism: These genes likely enable the biological mechanisms of cell signaling, macromolecule production, and protein expression.\\n] \n", - "790 [COULD NOT PARSE] \n", - "791 [\\nSummary: This analysis of a list of genes revealed a number of pathways and functions that are enhanced or enriched in the group of genes. The enriched pathways/functions include cell/nucleic acid metabolic processes, protein/DNA binding and processing, as well as hormone/steroid biosynthesis and processing.\\n\\nMechanism:The mechanism underlying this enrichment of processes is likely related to the fact that many of the genes included in this list code for proteins involved in these processes. These proteins may be enzymes, binders, or transporters, and are likely working together to regulate or facilitate a variety of stable and dynamic cellular processes.\\n\\n] \n", - "792 [ This list of human genes are involved in diverse signaling pathways, regulatory processes and enzyme activities related to cell structure, cell motility, faical recognition, gene/protein expression and other metabolic pathways. The gene functions include enzyme binding activity, protein kinase binding activity, phospholipid binding activity, phosphatase activity and GTPase activity. The enriched terms include cellular process regulation, enzyme activity, protein and peptide regulation, and protein domain modification.\\n\\nMechanism: This list of human genes modoify cellular processes by various functions such as enzyme binding activities, protein kinase binding activities, phospholipid binding activities, phosphatase activities, and GTPase activities. These functions help regulate and modify various signaling pathways and gene/protein expressions involved in cell structural, motility, and facial recognition, as well as metabolic processes.\\n\\n] \n", - "793 [ The genes of interest in this study are generally involved in the regulation of signal transduction pathways, with primary roles in kinase binding and GTPase activity, protein phosphatase activity, activation of transcription factors, phospholipase activity, receptor binding, ubiquitination, acetylation, and other signaling pathways. In addition, several of the genes are associated with apoptosis, cell migration, and negative regulation of proliferation.\\n\\nHypothesis/mechanism: These genes are likely part of an overarching molecular signaling pathway, in which changes in the expression of these genes modulate cell proliferation, apoptosis, migration, and other cellular processes. This likely manifests through changes in protein phosphorylation, ubiquitination acetylation, and other post-translational modifications that affect downstream cell signaling cascades. \\n\\n] \n", - "794 [\\nSummary: The list of genes are enriched for terms related to protein binding activity, ATP binding activity, GTP-dependent protein binding activity, GTPase activity, signal sequence binding activity, clathrin binding activity and small GTPase binding activity. \\nMechanism: These genes are involved in processes such as cellular response to hormone stimulus, signal transduction, Golgi organization and vesicle mediated transport.\\nHypothesis: These genes are involved in an intracellular transport process that is composed of Protein Bindings, ATP Bindings, GTP Bindings and Small GTPase Bindings.\\n] \n", - "795 [\\nSummary: This list of genes are involved in a range of processes, including intracellular transport, protein folding and processing, and positive and negative regulation of several cellular pathways. \\nMechanism: These genes likely play roles in regulating intracellular transport, protein folding and processing and positive and negative regulation of several cellular pathways.\\n] \n", - "796 [COULD NOT PARSE] \n", - "797 [ \\nSummary: The gene functions in this list are predominantly related to activities that enable and regulate cell redox homeostasis, such as helping to facilitate the production of and protection against oxidants like hydrogen peroxide, superoxide, and other reactive substances. \\nMechanism: The gene functions work together in a complex network of pathways, proteins, and processes to maintain redox balance in the cell by carrying out activities such as enzyme binding, protein homodimerization, protein-disulfide reductase activity, glutathione peroxidase activity, NADH dehydrogenase activity, and more. \\n] \n", - "798 [ Human genes related to this list are enriched for functions in molecular function activator activity, protein kinase activity, cellular component activity, binding activity, peptidase activity, nucleosome binding activity, ion binding activity and phosphatase binding activity; and processes such as cell cycle regulation, apoptosis regulation, cell adhesion, nervous system development, transcription regulation, protein transport, cell-cell recognition and gene expression regulation.\\n\\nMechanism: This list of genes are likely to be involved in several biological primary pathways, including signal transduction pathways, protein transcription pathways, metabolic pathways, and membrane transport pathways. These pathways are responsible for the functions and processes associated with cells in the regulation of growth, differentiation, development, and apoptosis.\\n\\n] \n", - "799 [COULD NOT PARSE\\nHypothesis: The] \n", - "800 [ The genes in this list are involved in the regulation of diverse biochemical processes, including transcription, signal transduction, cell cycle, metabolism, and cell adhesion. The commonalities in their functions involve binding activities (e.g. ATP binding, activin binding, SMAD binding), and protein phosphatase/kinase activities. Many of these genes are also involved in regulation of intracellular signaling pathways, such as SMAD signaling and BMP signaling, and in the regulation of transcription by RNA polymerase II.\\n\\nMechanism: The mechanism underlying these commonalities is likely related to the role of these genes in regulation of intracellular processes, as well as their binding activities, which may be necessary for the functional regulation of their target proteins.\\n\\n] \n", - "801 [ This list of genes is enriched for terms related to transcription regulation, intracellular signal transduction,DNA binding activity, positive/negative regulation of RNA/protein metabolic processes and protein phosphorylations.\\n\\nMechanism: These genes are likely to be functioning in a pathway that is involved in controlling gene expression, cellular signaling, and cellular metabolism. This is likely achieved through DNA binding, transcription regulation, and interaction with multiple proteins to modify protein and/or gene expression.\\n\\n] \n", - "802 [COULD NOT PARSE] \n", - "803 [\\nThis dataset refers to a list of gene summaries that are involved in multiple pathways of cellular development and signaling. The enriched terms indicate genes related to DNA-binding transcription activator activity, transcription regulatory region sequence-specific DNA-binding, GTP binding activity, enzyme binding activity, identical protein binding activity, signal receptor binding activity, phosphatase activity, protein kinase binding activity, cytokine activity, and growth factor activity. The underlying mechanism can likely be attributed to signal transduction pathways and transcription regulation related to cell growth, development, and differentiation. \\n\\nMechanism: Signal transduction pathways and transcription regulation\\n] \n", - "804 [ The majority of the genes in this list enable or involve in various functions related to RNA or protein processing, as demonstrated by the enriched terms related to RNA processing, protein binding, and DNA binding/transcription activities. Many of the genes contribute to various cellular processes, such as cellular response, cell homeostasis, and transcription from RNA polymerase II. A mechanism underlying this group of genes is that the genes are involved in multiple interactions between different enzymes and cell components for post-translational and transcriptional processing within the cell.\\n\\nMechanism: A mechanism underlying this group of genes is that the genes are involved in multiple interactions between different enzymes and cell components for post-translational and transcriptional processing within the cell.\\n\\n] \n", - "805 [\\n\\nSummary: These genes have a variety of functions, including enzyme binding activity, RNA binding activity, protein binding activity, transmembrane transporter binding activity, and transcription factor binding activity.\\n\\nMechanism: These genes are likely involved in a variety of cellular processes such as post-transcriptional control of gene expression, protein folding and sorting, and RNA processing and translation.\\n\\n] \n", - "806 [ The given list of genes are enriched for binding activities, such as GTP binding activity, enzyme binding activity, DNA-binding transcription factor binding activity, phosphotyrosine residue binding activity, cyclin binding activity and other related activities. These activities confer functions such as protein transcription, signal transduction, protein phosphorylation, cellular adhesion and cellular response to certain molecules.\\n\\nMechanism: The mechanism underlying these enriched binding activities is likely related to receptor-ligand interaction, involving both intra-cellular and inter-cellular interaction between molecules. It is also likely to involve protein-protein interaction, involving proteins such as SMAD binding proteins, NF-kappaB binding proteins and growth factor binding proteins, which play important roles in regulating various cellular processes.\\n\\n] \n", - "807 [\\nSummary: The list of genes provides evidence that a number of functions are involved, such as DNA-binding transcription activator activity, RNA polymerase II-specific activity, NF-kappaB binding activity, and microtubule binding activity.\\nMechanism: These genes may be involved in signaling pathways that regulate processes such as hemopoiesis, endothelial intestinal barrier formation, cellular response to steroid hormone stimulus and nervous system development.\\n] \n", - "808 [\\n\\nSummary: The genes listed are involved in a variety of functions, including ATP binding activity, protein kinase binding activity, RNA binding activity, DNA binding activity, receptor binding activity, enzyme binding activity, and phospholipid transporter activity.\\n\\nMechanism: The genes have a variety of molecular functions and are involved in a wide range of processes, including cell-cell adhesion, synaptic transmission, apoptotic signaling pathway, interleukin-6 receptor binding, T cell activation, overall cellular metabolism, and gene expression regulation.\\n\\n] \n", - "809 [ Analysis of the gene summaries reveals that many of the genes are involved in various activities, such as enzyme binding activity, enzyme activity (specifically, hydrolase and transferase activities), transcription-related activities, receptor activities, and binding activities for molecules, such as proteins and DNA. The underlying biological mechanism or pathways these genes belongs to is transcriptional regulation, protein-protein interactions, cell adhesion and migration, and signal transduction. Thus, the following terms are enriched in these genes: enzyme binding activity; hydrolase activity; transferase activity; receptor activity; DNA binding activity; RNA binding activity; transcription factor activity; and protein binding activity. \\nMechanism: Transcriptional regulation, protein-protein interactions, cell adhesion and migration, and signal transduction. \\n] \n", - "810 [\\nSummary: This gene dataset contains genes involved in cell migration, regulation of signal transduction, protein ubiquitination, cell cycle control, transcription regulation, and regulation of protein stability.\\nMechanism: These genes appear to commonally control a number of key pathway processes at the cellular level and can initiate their respective pathways through the binding of other proteins, and the control of chromatin composition through the modification of histones.\\n] \n", - "811 [ Human genes included in this list are primarily involved in processes related to signal transduction and transcription regulation, with some involvement in cell migration, development and and cell population proliferation, and proteolysis. Common terms enriched include: signal transduction; regulation of gene expression; transcription; regulation of protein phosphorylation; regulation of protein stability; cell migration; cell proliferation; development; and proteolysis.\\n\\nMechanism: The human genes studied here mainly act in a variety of signal transduction pathways, which includes NF-kappaB and Wnt signaling; activities such as binding, adaptor, and ligand activities are also involved. Transcriptional regulation is also present, with activities including transcription activator and repressor binding, as well as DNA binding and corepressor activity. The regulation of proteins and proteolysis by the genes is also observed, as well as other activities related to cell migration and cell development.\\n\\n] \n", - "812 [ \\n\\nSummary: The list of genes are mainly involved in a variety of biological pathways and processes, such as intracellular signaling, cell proliferation, cell adhesion and migration, cell division and apoptosis. \\n\\nMechanism: The pathways and processes are likely mediated by protein interactions such as binding activity, enzyme and kinase activity, as well as transcription and receptor signaling, which ultimately result in cellular adaptation and regulation.\\n\\n] \n", - "813 [ \\nSummary: This list of genes has been found to be involved in a variety of functions, including cation binding activity, diacylglycerol binding activity, enzyme binding activity, protein heterodimerization activity, receptor binding activity, and protein kinase activity. \\nMechanism: These genes appear to be involved in a variety of cellular activities, including signal transduction, cell recognition and migration, receptor binding, and apoptotic processes.\\n] \n", - "814 [ \\n\\nSummary: The commonalities among the gene functions of the list provided are DNA-binding transcription factor activity, RNA polymerase II-specific, nucleic acid binding activity, transcription cis-regulatory region binding activity, regulation of gene expression, and regulation of biosynthetic process.\\n\\nMechanism: The genes enable the transcription of genetic material, and potential activation or repression of gene expression by interacting with DNA and RNA polymerase II. Regulation of gene expression is achieved through altering transcription factor activity and binding to DNA regions to control downstream gene expression.\\n\\n] \n", - "815 [ The genes KLF4, POU5F1, and SOX2 are all involved in transcription regulation and gene expression, specifically upstream of or within the process of endodermal cell fate specification. They are all located in the cytosol and nucleoplasm, are associated with chromatin, and are part of a transcription regulator complex. \\n\\nMechanism: The mechanism underlying these gene functions is likely related to the regulation of DNA binding and transcription, which could help to control cell development and maintenance pathways.\\n\\n] \n", - "816 [COULD NOT PARSE] \n", - "817 [ The genes listed are mainly involved in cell-specific metabolic processes, and sharing a common role in regulation of cell-matrix adhesion and extracellular matrix structural constituents. Several of them are also involved in organ development and differentiation, and others in regulation of different hormone pathways.\\n\\nMechanism: Many of these genes are involved in positive or negative regulation of protein metabolic processes such as phosphorylation, proteolysis, and cell-surface receptor signalling pathways. They also play a role in regulating cell proliferation, apoptosis, and ion transport. Additionally, the genes are involved in regulation of blood coagulation and cell adhesion, as well as in modulation of chemical synaptic transmission and cell-matrix adhesion.\\n\\n] \n", - "818 [COULD NOT PARSE] \n", - "819 [ Summary: The list of genes is enriched for terms related to DNA-binding transcription activity, protein kinase binding activity, metal ion binding activity, calcium ion binding activity, transcription co-regulator activity, and responsive to stimuli.\\nMechanism: The underlying biological pathways can either be direct (e.g. modifying gene expression) or indirect (e.g. binding proteins to regulate other proteins).\\n] \n", - "820 [ The list of genes appears to be focused on muscle structure and development, as well as processes related to muscle contractions. This is supported by enriched terms related to muscle processes which include actin filament binding, microfilament motor activity, muscle alpha-actinin binding, actin monomer binding, tropomyosin binding, myosin binding, titin binding, and creatine kinase activity. This suggests a biological mechanism that centers around the development, assembly, and contraction of muscle tissue. A hypothesis of this mechanism is that these genes have a complex role in enabling specific activities related to muscle development and muscle contractions, as well as regulating their activity to ensure efficient functioning of muscle tissue.\\n\\nSummary: Genes related to muscle tissue structure, development, and contractions\\nMechanism: Complex role in enabling specific activities related to muscle development and muscle contractions, as well as regulating their activity to ensure efficient functioning of muscle tissue.\\n] \n", - "821 [ This list of human genes are related to skeletal muscle, actin filament/stress fiber and striated muscle thin filaments assembly. They are enriched for functions involving calcium-dependent binding activity; ATP binding activity; adhesion; transmembrane transport; transcriptional regulation; ubiquitination; and actin monomer binding activity.\\n\\nMechanism: The genes are likely to be involved in pathways which are regulated by calcium-mediated intracellular signaling and ubiquitin-dependent protein degradation, leading to muscle contraction and regulation of muscle adaptation in response to denervation and electrical stimulus.\\n\\n] \n", - "822 [ \\n\\nSummary: The list of genes identified in this analysis are involved in several processes including signalling, endocytosis, membrane transport, and protein metabolism.\\n\\nMechanism: These genes serve to regulate several processes which involve signalling, endocytosis, membrane transport, and protein metabolites through protein kinase activities.\\n\\n] \n", - "823 [ This list of genes is involved in various cellular functions, such as cell signaling, protein ubiquitination, endocytosis/exocytosis, intracellular trafficking, vesicle transport, receptor binding and regulation of gene expression. The terms associated with these genes reflect their roles in a variety of cellular processes, including protein phosphorylation, protein homooligomerization, vesicle buddying and regulation of inflammatory response, among others.\\n\\nMechanism: The cellular functions associated with these genes are likely regulated through various intracellular pathways, including protein kinase cascades, GTP-dependent pathways, receptor signaling, and canonical inflammasome signaling, among others.\\n\\n] \n", - "824 [\\nSummary: The genes listed are primarily involved in energy regulation, carbohydrate metabolism, cell homeostasis, cell signaling, and protein catabolism.\\nMechanism: The enriched genes encode for proteins in energy regulation pathways, such as glycolysis and gluconeogenesis, as well as for proteins that help to modulate cellular signaling, such as glucose and phosphate binding proteins.\\n] \n", - "825 [ \\nSummary: Enriched terms are related to metabolic activities, protein binding, cellular homeostasis, localization, and glycolytic processes.\\nMechanism: These genes may all be involved in a metabolic pathway, functioning together in protein synthesis, post-transcriptional processing, and regulation of intracellular metabolism.\\n] \n", - "826 [ \\n\\nSummary: This list of genes is primarily associated with regulation of intracellular calcium concentrations and ion channel activity.\\nMechanism: Calcium concentration regulation is the primary mechanism enabling functions, such as postsynaptic neurotransmitter receptor activity, regulation of AMPA receptor activity, G protein-coupled receptor signaling, calcium ion transmembrane transport, and ligand-gated monoatomic ion channel activity.\\n] \n", - "827 [ This is a list of genes that when taken together seem to be involved in regulating ion channels, transporters, or receptors. Specifically, they refer to monoatomic cation channels, acetylcholine-gated channels, glutamate-gated calcium channels, voltage-gated calcium channels, NMDA selective glutamate receptor complexes, and L-type voltage-gated calcium channel complexes. All these gene functions are involved in processes related to neuronal excitation, calcium-mediated signaling, neural transmission, neuronal migration, and synaptic plasticity.\\n\\nMechanism: The underlying biological mechanism suggested by this list of gene functions is ion and calcium signaling in the nervous system. This includes the regulation of intracellular calcium levels, the modulation of neurotransmitter release, the transport of ions across the cell membrane, and the regulation of synaptic transmission and plasticity. \\n\\n] \n", - "828 [ The gene summaries provided indicate that the main terms enriched among all of these genes are: protein kinase binding activity, protein kinase activity, protein serine/threonine kinase activity, positive regulation of protein phosphorylation, and regulation of macromolecule biosynthetic process.\\n\\nMechanism: The mechanism of action associated with these genes is likely related to their roles in the regulation of protein phosphorylation and macromolecule biosynthetic processes. This likely involves a variety of cellular pathways, such as intracellular signal transduction and TOR signaling, as well as modulation of different cellular components, such as the cytosol, nucleus, and mitochondrion.\\n\\n] \n", - "829 [COULD NOT PARSE] \n", - "830 [COULD NOT PARSE\\nHypothesis: The genes in the list are involved in glycan metabolism] \n", - "831 [\\nSummary: The genes in this list all participate in various glycan/carbohydrate/lipid processing and metabolic activities.\\nMechanism: These genes - primarily hydrolases, lysozymes and mannosidases - are involved in breaking down, or catabolizing, a range of molecules, including gangliosides, chitin, heparan sulfate, lipid, glucosylceramides, and glycoproteins, and so on.\\n] \n", - "832 [\\nSummary: The human genes described in this list have enriched terms related to binding and receptor binding activity, antigen binding activity, immunoglobulin receptor binding activity, non-membrane spanning protein tyrosine kinase activity, phosphatidylcholine binding activity, and phosphotyrosine residue binding activity.\\nMechanism: These genes are involved in a variety of biological processes, including immunoglobulin receptor binding, protein phosphorylation, antigen binding, and cellular component organization. These genes likely work together to enable the body to respond to antigens as part of the immune system. This includes recognizing antigens and binding to them so that the body can mount an immune response.\\n] \n", - "833 [\\n\\nSummary: These genes are predominantly immunoglobulin receptor binding proteins with functions in antigen binding and activation of immune responses.\\n\\nMechanism: These genes are likely part of a larger immune system network, involving antigen presentation and recognition, as well as various immune system responses to microbial and foreign invaders.\\n\\n] \n", - "834 [\\nSummary: The list of genes provide evidence for a set of processes related to DNA and cellular replication, including DNA binding activity, chromatin binding, ATP dependent activity, protein export, and transcriptional regulation.\\n] \n", - "835 [ \\nSummary: The genes involved in this list are mainly related to DNA binding, double-stranded DNA binding, DNA/DNA annealing, and identical protein binding activities. They are also involved in a variety of processes related to DNA double strand break repair, DNA metabolic processes, meiotic chromosome segregation and pairing, and spermatogenesis.\\n\\nMechanism: These genes are likely involved in coordinating and catalysing a variety of DNA-related activities that are required for proper genetic recombination and replication of genetic material during meiosis and spermatogenesis.\\n\\n] \n", - "836 [ \\nSummary: The human genes analyzed are involved in a variety of functions, including calcium ion binding activity; identical protein binding activity, protein sequestering activity; and ubiquitin protein ligase binding activity.\\n\\nMechanism: These genes likely play critical roles in cellular processes such as cellular response to caffeine, regulation of protein phosphorylation, regulation of anion channel activity, positive regulation of lysosomal membrane permeability, regulation of gene expression and response to interferon-beta.\\n\\n] \n", - "837 [\\nSummary: The list of genes provides a range of functions relating to protein binding, metal and ion binding, regulation of gene expression, regulation of protein phosphorylation, cellularresponse to infection and inflammation, and regulation of cell death pathways.\\n\\nMechanism: These genes form part of complex pathways that lead to the regulation of macromolecule biosynthetic processes, intracellular transport, gene expression, and protein phosphorylation. These pathways are integral for regulating cell death, cholesterol efflux, protein binding activities, and intracellular calcium.\\n\\n] \n", - "838 [\\n\\nSummary: The genes listed are involved in various cellular functions related to protein binding, domain binding and enzyme activity\\nMechanism: The genes are involved in several processes, such as cellular signaling, protein homeodimerization, DNA or RNA binding, transcriptional regulation, and metal ion binding.\\n] \n", - "839 [ \\n\\nSummary: The list of genes show functions related to structural support, transport of materials and ions, response to stimuli, protein-protein interaction, and regulation of transcription, metabolism, and cell growth.\\n\\nMechanism: The genes involved in this term enrichment show critical functions that are part of the integrated machinery of the cell, which organizes communication, transport, and control. This machinery is responsible for the ability of the cell to respond to stimuli, regulate metabolism and transcription, and undergo cell growth, leading to growth and development of the organism.\\n\\n] \n", - "840 [ These human genes all share the common activity of enabling activities related to peroxisome biogenesis, such as ATP binding, hydrolysis, ubiquitin-dependent protein binding activity, as well as protein import/unfolding, stabilization and targeting to peroxisome. ] \n", - "841 [\\nSummary: The genes PEX6, PEX2, PEX3, PEX7, and PEX1 are all involved in peroxisome biogenesis and organization.\\n] \n", - "842 [ The 4 genes have functions with related to proteins and DNA, including DNA binding; metal ion binding; and protein homodimerization activities. They are also involved in the regulation of apoptotic process, DNA metabolic processes, cellular responses to hypoxia and starvation, and regulation of telomere maintenance.\\nHypothesis: These four genes likely interact with each other in the components of the cell in which they are found, such as the nucleus, cytoplasm, centrosome, and membrane, which all help in fostering DNA binding, metal ion binding, protein homodimerization, and other genetic processes. \\n] \n", - "843 [COULD NOT PARSE] \n", - "844 [ This gene list is enriched for several terms related to ion channels, transporters, and receptors. The enriched terms include both ligand-gated and voltage-gated ion channel and transporter activities, as well as several types of receptor activities such as G protein-coupled receptors, AMPA glutamate receptors, and kainate-selective glutamate receptors. These genes also appear to be involved in several processes such as membrane potential, chloride transmembrane transport, gamma-aminobutyric acid signaling pathway, and neurotransmitter transport.\\n\\nMechanism: The underlying biological mechanism likely involves the regulation of electrical and chemical signals in neurons, thereby enabling communication between different types of cells in the central and peripheral nervous systems. \\n\\n] \n", - "845 [\\nSummary: The genes listed here are involved in neurotransmitter signaling, ion channel activity, membrane transport, calcium ion homeostasis, and ionotropic glutamate receptor signaling. \\nMechanism: These genes provide the molecular machinery for neurotransmitter signaling by establishing ion channels, helping to carry ions in and out of cells, and regulating calcium ion homeostasis.\\n] \n", - "846 [ Analysis of the given list of genes suggests a common thread of involvement in the development and function of peripheral nerves, particularly with regard to varying forms of Charcot-Marie-Tooth disease, in addition to their role in nucleic acid and glycan metabolic pathways. \\n] \n", - "847 [\\nSummary: Eighteen human genes related to various neurological processes and diseases are analyzed.\\n] \n", - "848 [\\nThe genes in the given list are predominantly involved in G protein-coupled receptor signaling pathways, regulation of cytosolic calcium ion concentration, regulation of transcription by RNA polymerase II, regulation of neuronal death and apoptotic processes, cAMP biosynthetic processes and protein phosphorylation pathways. The underlying biological mechanism for these processes is likely related to cellular and tissue homeostasis, i.e. the maintenance of physiological equilibrium. \\n\\nMechanism: Maintenance of cellular and tissue homeostasis.\\n\\n] \n", - "849 [ This list of genes is related to G protein-coupled receptor signaling pathways, associated with diseases such as Alzheimer's disease, Parkinson's disease, hypertension and kidney failure. ] \n", - "850 [ The genes are predominantly involved in transcriptional activation and/or repression of gene expression, often as part of complexes involved in the regulation of signal transduction, DNA-templated transcription, cell cycle, and transcription by RNA polymerase II; they also enable chromatin binding activities and zinc ion binding.\\n\\nMechanism: The human genes work together to regulate various biological processes via the modulation of signal transduction, DNA-templated transcription, cell cycle, and transcription by RNA polymerase II pathways. This involves the binding of DNA to transcription factors, the deacetylation of histones, and the binding of specific protein ligases/cofactors resulting in the transcriptional activation or repression of specific genes. The regulation of gene expression and signal transduction, in turn, allows for the control of multiple downstream processes such as cell differentiation, apoptosis, cell migration, angiogenesis and metabolism.\\n\\n] \n", - "851 [\\nSummary: The list mainly consists of genes which play a role in regulation that involves DNA-binding transcription activator and repressor activity, regulation of gene expression, regulation of DNA-templated transcription and positive/negative regulation of transcription by RNA polymerase II.\\nMechanism: The genes in the list are involved in a variety of mechanisms that function to give cells control over their activities and to regulate transcription.\\n] \n", - "\n", - "prompt_variant sim length_diff \n", - "0 0.97 498 \n", - "1 0.95 512 \n", - "2 0.91 207 \n", - "3 0.85 22 \n", - "4 0.95 131 \n", - "5 0.95 587 \n", - "6 0.94 502 \n", - "7 0.90 343 \n", - "8 0.89 118 \n", - "9 0.87 216 \n", - "10 0.88 94 \n", - "11 0.93 59 \n", - "12 0.94 68 \n", - "13 0.93 406 \n", - "14 0.88 321 \n", - "15 0.90 43 \n", - "16 0.93 147 \n", - "17 0.91 483 \n", - "18 0.88 199 \n", - "19 0.95 141 \n", - "20 0.94 47 \n", - "21 0.93 119 \n", - "22 0.94 569 \n", - "23 0.88 260 \n", - "24 0.91 77 \n", - "25 0.91 238 \n", - "26 0.98 93 \n", - "27 0.92 235 \n", - "28 0.94 175 \n", - "29 0.89 257 \n", - "30 0.91 427 \n", - "31 0.92 3 \n", - "32 0.90 0 \n", - "33 0.86 166 \n", - "34 0.90 558 \n", - "35 0.90 66 \n", - "36 0.88 210 \n", - "37 0.94 17 \n", - "38 0.94 20 \n", - "39 0.91 441 \n", - "40 0.93 174 \n", - "41 0.89 597 \n", - "42 0.93 351 \n", - "43 0.83 292 \n", - "44 0.85 311 \n", - "45 0.84 136 \n", - "46 0.91 512 \n", - "47 0.92 98 \n", - "48 0.87 229 \n", - "49 0.84 378 \n", - "50 0.89 245 \n", - "51 0.92 184 \n", - "52 0.89 258 \n", - "53 0.92 636 \n", - "54 0.88 216 \n", - "55 0.91 64 \n", - "56 0.86 607 \n", - "57 0.92 334 \n", - "58 0.96 36 \n", - "59 0.83 735 \n", - "60 0.87 233 \n", - "61 0.90 646 \n", - "62 0.95 110 \n", - "63 0.88 79 \n", - "64 0.87 89 \n", - 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"850 0.92 425 \n", - "851 0.94 411 " - ] - }, - "execution_count": 71, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "df_pivot = df.pivot_table(index=[MODEL, METHOD, GENESET], columns=PROMPT_VARIANT, values=SUMMARY, aggfunc=list)\n", - "df_pivot\n", - "\n", - "df_pivot['sim'] = df_pivot.apply(lambda row: text_similarity(row[\"v1\"][0], row[\"v2\"][0]), axis=1)\n", - "df_pivot['length_diff'] = df_pivot.apply(lambda row: abs(len(row[\"v1\"][0])-len(row[\"v2\"][0])), axis=1)\n", - "\n", - "\n", - "# reset index to get it back in the form of a DataFrame\n", - "result = df_pivot.reset_index()\n", - "result" - ] - }, - { - "cell_type": "code", - "execution_count": 72, - "id": "29ab5588", - "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "/var/folders/nc/m4tx21912kv1b8nk3zzx9plr0000gn/T/ipykernel_20774/1915584628.py:2: SettingWithCopyWarning: \n", - "A value is trying to be set on a copy of a slice from a DataFrame.\n", - "Try using .loc[row_indexer,col_indexer] = value instead\n", - "\n", - "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", - " rnd[MODEL]=\"\"\n", - "/var/folders/nc/m4tx21912kv1b8nk3zzx9plr0000gn/T/ipykernel_20774/1915584628.py:3: SettingWithCopyWarning: \n", - "A value is trying to be set on a copy of a slice from a DataFrame.\n", - "Try using .loc[row_indexer,col_indexer] = value instead\n", - "\n", - "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", - " rnd[METHOD]=\"RANDOM\"\n", - "/var/folders/nc/m4tx21912kv1b8nk3zzx9plr0000gn/T/ipykernel_20774/1915584628.py:4: SettingWithCopyWarning: \n", - "A value is trying to be set on a copy of a slice from a DataFrame.\n", - "Try using .loc[row_indexer,col_indexer] = value instead\n", - "\n", - "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", - " rnd[\"sim\"] = rnd.apply(lambda row: text_similarity(random_summary(), random_summary()), axis=1)\n" - ] - }, - { - "data": { - "text/html": [ - "
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prompt_variantmodelmethodgenesetv1v2simlength_diff
568RANDOMEDS-0[ The nine genes are associated with extracellular matrix (ECM) components and their regulators. Mechanism: The proteins coded by these genes could be involved in the regulation of the expression of ECM components, which can contribute to the formation of the physical integrity of the ECM and its interaction with the cellular environment. ][\\n\\nSummary: The genes in the list are associated with a broad range of functions involved in skeletal development, collagen production and other extracellular matrix processes.\\n\\nMechanism: The mechanism appears to involve different genes acting on multiple pathways related to the synthesis, remodeling, and maintenance of extracellular matrix components.\\n\\n]0.8116
569RANDOMEDS-1[ This list of genes is enriched in proteins involved in the Extracellular Matrix (ECM) protein network, which is a component of the larger Cell Adhesion and Morphogenesis (CAM) pathway. Specifically, the genetic list is enriched for components involved in the processes of collagen fibril formation, collagen fibril organization, extracellular matrix (ECM) protein network assembly, ECM protein network stabilization, epidermal cell fate commitment, epithelial tube growth and branching morphogenesis, collagen modification and deposition, and zinc-finger protein motif binding.\\n\\nMechanism: The ECM protein network mediates cell-cell and cell-matrix interactions in order to regulate the adhesive, motile, and proliferative states of cells. It consists of a variety of molecules, including ECM proteins, which serve as substrates to guide cell migration, growth and differentiation. ECM proteins are those that contain one or more structural domains capable of interacting with the ECM components, such as extracellular domains, as well as those containing adhesive domains. \\n\\n][ The genes listed above are associated with various development processes and tissue formation, such as collagen production, connective tissue development, matrix remodeling, and zinc finger protein regulation.\\nMechanism: The underlying known mechanism is the combination of transcriptional regulation and post-translational modification of the proteins encoded by these genes.\\n]0.90699
570RANDOMFA-0[COULD NOT PARSE\\nHypothesis: The genes in this list are likely involved in the regulated repair of DNA double strand breaks due to replication-mediated damage, with the coordinated action of the Fanconi Anemia protein complex and the shared components of the ubiquitin ligase complex.][ The list of genes is significantly and specifically associated with homologous recombination and DNA repair, as evidenced by an enrichment in terms related to these processes, such as \"dna repair\", \"homologous recombination\", \"excision repair\", and \"nuclease activity\".\\n\\nMechanism: The genes in this list are involved in a variety of DNA repair activities, such as excision repair and homologous recombination. These processes are important for maintaining the correct sequence of DNA and avoiding mutations that can lead to disease. \\n\\n]0.89253
571RANDOMFA-1[ Several genes involved in DNA repair and homologous recombination processes, such as FANCL, RAD51C, FANCE, MAD2L2, ERCC4, FANCA, BRCA2, FANCF, XRCC2, BRIP1, FANCD2, SLX4, FANCB, FANCG, UBE2T, RAD51, PALB2, and FANCC, were observed to be statistically enriched for terms related to DNA damage recognition and repair, DNA damage response, and homologous recombination processes.\\n\\nMechanism: These genes enable the cellular response to double-stranded breaks (DSBs) by providing components of the DNA damage recognition and repair variety. They also function in the homologous recombination pathway for DNA repair, which is used for error-free repair of damaged DNA strands. \\n\\n][COULD NOT PARSE]0.88660
572RANDOMHALLMARK_ADIPOGENESIS-0[ Enrichment analysis of this list has revealed that many of the genes are involved in energy metabolism and fatty acid metabolism, such as ATP1B3, ACOX1, ACADM, SLC19A1, SLC25A10, PGM1, UCP2, GPX3 and GPX4. They are also related to adipogenesis, with genes such as ADIPOR2, APLP2, LEP, ADIG and ADIPOQ. Lastly, several of the genes are involved in cholesterol and bile acid synthesis, such as DHCR7, DHRS7, CYP4B1 and HMGCR.\\n\\nMechanism: The genes identified as being involved in energy metabolism and fatty acid metabolism appear to share a common mechanism in which these molecules are generated from multiple sources to form energy. The genes involved in adipogenesis appear to be related to the regulation and development of fat cells and adipose tissue. Similarly, the genes involved in cholesterol and bile acid synthesis appear to be related to the synthesis of these molecules from multiple sources.\\n\\n][ \\nSummary: A term enrichment test on the above list of genes based on biological classification hierarchies has identified terms related to metabolic and cellular functions that are statistically over-represented.\\nMechanism: These commonalities likely indicate a shared pathway, mechanism or process as related to metabolic and cell regulation functions.\\n]0.86553
573RANDOMHALLMARK_ADIPOGENESIS-1[ This term enrichment test revealed a group of genes associated with energy metabolism, regulation of cell death, cell proliferation and signaling, DNA replication/remodeling, RNA processing, and lipid metabolism.\\nMechanism: This group of genes may be involved in binding, regulating, or expressing other proteins in order to influence the cell's metabolic and signaling status. \\n][\\nSummary: This list of genes are mainly involved in energy metabolism and signal transduction. \\nMechanism: The genes in this list form a biochemical pathway responsible for the production of energy and for the detection and execution of cellular signals.\\n]0.81125
574RANDOMHALLMARK_ALLOGRAFT_REJECTION-0[ This enrichment test examines a list of 73 human genes and reveals enrichments for the functions related to cell surface molecules, cytokines, immunology, receptor signalling, transcriptional regulation and apoptosis.\\n\\nMechanism: These genes are involved in a variety of pathways that include cytokine signaling, cell surface molecules, transcriptional regulation, apoptosis, and receptor signaling.\\n\\n][ Genes related to the list are largely enriched for immune signalling/activation, regulation of cell cycle and differentiation, and transcriptional regulation.\\nMechanism: This likely indicates involvement of these genes in the processes of immune signalling, development or tissue remodelling, and metabolic regulation.\\n]0.8782
575RANDOMHALLMARK_ALLOGRAFT_REJECTION-1[ This analysis results in the enrichment of genes functions related to immune system regulation, including antigen presentation, signaling, B and T cell metabolism, cytokine production and chemotaxis. Mechanism: The genes identified in this list are involved in controlling a range of processes that are necessary for proper immune system functioning, such as antigen presentation, signaling pathways, metabolizing T and B cells, production and secretion of cytokines, and chemotaxis of immune cells. These functions are necessary for the body to defend itself against pathogens. ][COULD NOT PARSE\\nHypothesis: It is likely]0.82539
576RANDOMHALLMARK_ANDROGEN_RESPONSE-0[COULD NOT PARSE][COULD NOT PARSE]0.870
577RANDOMHALLMARK_ANDROGEN_RESPONSE-1[ \\nSummary: The genes are enriched in terms related to regulation, signaling, and metabolism.\\nMechanism: The genes are likely to be involved in molecular mechanisms governing cellular activities and pathways, with signaling pathways such as Wnt, MAPK, and PKA pathways playing an important role. \\n][ \\nThe genes provided are significantly enriched in terms related to gene transcription and regulation, protein translation and metabolism, cytoskeletal organization, and lipid metabolism.\\nMechanism: These genes are likely to be involved in the regulation of genetic expression, transcriptional regulation, protein translation and metabolism, improvement of cell structure, and lipid metabolism. \\n]0.83100
578RANDOMHALLMARK_ANGIOGENESIS-0[ \\n\\nSummary: A set of 34 genes related to extracellular matrix formation and maintenance, fibrous tissue development, vascular development, and extracellular secreted signaling. \\n\\nMechanism: Together, these genes encode proteins involved in multiple signaling pathways to regulate the development, maintenance and repair of the extracellular matrix (ECM), including fibrous, collagen, and laminin-fibrillin proteins, along with proteins involved in vascular regulation, cell-cell communication and migration, and extracellular secreted signaling molecules. \\n\\n][ The list of gene terms are involved primarily in cell communication processes like extracellular matrix organization, adhesion, and cell surface interactions. Specifically, they encode proteins involved in the aggregation of endothelial cells and vascularization processes. Mechanism: The proteins encoded by the genes in the list are likely involved in regulating the growth, development, extracellular environment, and adhesiveness of cells. ]0.84113
579RANDOMHALLMARK_ANGIOGENESIS-1[ Genes in this list are primarily associated with development, vascular remodeling and cell-cell communication.\\nMechanism: These genes likely play a role in various aspects of development, including morphogenesis, tissue development, extracellular matrix organization, inflammation, vascular remodeling and cell-cell communication.\\n][ \\n\\nSummary: This list of genes appears to be involved in growth and morphogenesis of cells, including development of muscle, bone, and neuronal networks. \\nMechanism: Growth appears to be mediated by signals from cytokines and hormones, most notably VEGFA and PDGF, and mediated by transmembrane and extracellular matrix proteins, including LUM, VTN, and S100A4.\\n]0.8130
580RANDOMHALLMARK_APICAL_JUNCTION-0[COULD NOT PARSE][\\nThis list of genes is related to development, tissue morphogenesis, contractile organs, extracellular matrix and cytoskeletal proteins. Enriched terms include bone, joint, muscle and connective tissue development; cell adhesion; adhesion receptor complex formation; signal transduction; and receptor-mediated signaling cascades.\\n\\nMechanism:\\nThese genes likely act together to facilitate the intricate networks of molecular and cellular pathways involved in development, homeostasis, and tissue repair. These include extracellular matrix formation and remodeling; cell adhesion; and signaling pathways associated with cell migration, proliferation, differentiation, and growth. The genes may work in tandem to promote changes in gene expression, stability, and intercellular communication involved in development and tissue repair processes.\\n\\n]0.85829
581RANDOMHALLMARK_APICAL_JUNCTION-1[\\nSummary: The genes in this list are involved in a wide variety of processes, including development, growth, morphology, and molecular signaling.\\nMechanism: These genes appear to be involved in the regulation of cellular processes by mediating signals that modulate development, growth and morphology.\\n][ Our term enrichment analysis of the list of genes provided revealed statistically over-represented terms in gene function associated with cell adhesion, cell migration, migration and interaction, cytoskeletal organization, actin cytoskeletal regulation, signaling pathways, and regulation of the actin cytoskeletal organization. \\nMechanism: These results suggest that the underlying biological mechanism likely involves cytoplasmic signaling and regulation of the cytoskeletal organization, which would provide mechanical integrity to the cells, their adhesion to neighboring cells, and their migratory ability. This is supported by the evidence that many of the enriched terms relate to cell adhesion, migration and interaction, and cytoskeletal organization.\\n]0.88460
582RANDOMHALLMARK_APICAL_SURFACE-0[\\nSummary: The list of genes provided is enriched for terms relating to cell migration, membrane receptor signaling, and glycoprotein metabolism.\\nMechanism: These gene functions serve to coordinate cell migration and receptor-mediated signaling, as well as metabolism. \\n][ The list of genes is enriched for terms related to cell regulation, signal transduction, cell adhesion, protein folding, extracellular matrix organization.\\nMechanism: The list of genes are likely involved in a variety of cell regulation mechanisms such as activating responses to extracellular signals, influencing protein folding and assembly, regulating cell adhesion, and mediating phosphorylation cascades. \\n]0.81144
583RANDOMHALLMARK_APICAL_SURFACE-1[\\nSummary: The genes provided are involved in diverse biological pathways related to cell signaling, development, transcription, and metabolism.\\nMechanism: The genes likely represent an underlying biological mechanism that is involved in cellular proliferation and the regulation of gene expression.\\n][ This list of genes appears to be involved in the development and maintenance of various organs, tissues and cellular processes. Specifically, enriched terms for this gene list include cell adhesion and migration; cell signaling; cell differentiation; protein kinase and phosphatase activities; transcription and DNA metabolism; immunomodulation; glycosylation and carbohydrate metabolism; and cell growth and proliferation. \\n\\nMechanism: The genes in this list play a role in a variety of molecular mechanisms that are important for normal development and tissue homeostasis. On the molecular level, these genes are involved in cell-cell adhesion, translation and translation regulation, signal transduction, and other processes. Moreover, the genes in this list regulate the expression of various cellular receptor, kinase, and phosphatase pathways, which may lead to downstream changes in cell growth, proliferation, and differentiation. \\n\\n]0.70643
584RANDOMHALLMARK_APOPTOSIS-0[ The list of human genes given is statistically significantly enriched for the gene functions of transcriptional regulation/control, cell-cycle/apoptosis, and immune responses.\\nMechanism: The genes listed encode proteins involved in transcriptional regulation through control pathways such as the activation of caspases, the inhibition of cyclin-dependent kinase activity, and the upregulation of apoptosis-related proteins. They also encode molecules involved in immune-related processes such as the binding and activation of proinflammatory cytokines, the formation of interferon gamma receptor complexes, and the regulation of major histocompatibility complex class I molecules. \\n][\\n\\nSummary: The human genes provided in this list are mainly related to apoptosis, transcription, cell cycle progression, and inflammation.\\nMechanism: These genes likely act together to execute pathways related to the regulation of cell growth and maintenance, DNA replication and repair, oxidative stress response, and immune system activation.\\n]0.89338
585RANDOMHALLMARK_APOPTOSIS-1[COULD NOT PARSE][ This list of genes is enriched for terms related to cell death regulation, inflammation, immune reaction, and growth and morphogenesis, which is a mechanism indicative of homeostasis in several biological functions.\\t\\n\\nMechanism: Expression of these genes contributes to cell survival by regulating the balance between cell death and survival, restraint of pro-inflammatory responses and activation of pro-inflammatory responses, promoting expression of genes involved in innate and adaptive immune responses and playing a part in promoting tissue growth, remodeling and morphogenesis. \\n\\n]0.85573
586RANDOMHALLMARK_BILE_ACID_METABOLISM-0[\\nSummary: The genes listed are enriched in terms related to metabolic pathways, lipid transport, and development of connective tissues.\\nMechanism: The functions of the genes appear to involve a number of metabolic pathways, such as fatty acid and bile acid synthesis, xenobiotic metabolism, and steroidogenesis, as well as pathways related to cellular transport and signaling, including those related to lipid transport and receptor-mediated signal transduction.\\nIn addition, several of the genes are involved in connective tissue formation, as well as development of digits and limbs.\\n][ This list of genes is enriched for functions related to lipid metabolism and transport, development of vital organs, and cell signaling pathways.\\nMechanism: The enrichment of these genes suggests roles in cellular metabolic processes such as breakdown, transport, and synthesis of lipids, as well as cell-signaling pathways involved in development of vital organs such as liver, heart, and brain. \\n]0.90187
587RANDOMHALLMARK_BILE_ACID_METABOLISM-1[COULD NOT PARSE][ A large proportion of the genes provided are involved in lipid and fatty acid metabolism, including the movement and processing of lipids, such as through cytochrome P450 superfamily enzymes, hydroxyacyl-CoA dehydrogenases, SLCO1A2, FADS2 and SLC27A2. As well as lipid metabolism, genes are also enriched for other metabolic processes, such as glutamate metabolism (IDH1, 2, HSD17B6) and serine metabolism (SERPINA6 and PIPOX). In addition, there are genes associated with the regulation of transcription factors, including RXRA, LCK, and optineurin, as well as those involved in oxidative stress (SOD1, CTH, PNPLA8).\\n\\nMechanism: The enriched terms implicate a cross-regulatory and potentially inter-linked metabolic network involving lipid, fatty acid and disulphide bridge metabolism, with potential connections to oxidative stress response and gene expression regulatory mechanisms. \\n\\n]0.87874
588RANDOMHALLMARK_CHOLESTEROL_HOMEOSTASIS-0[COULD NOT PARSE][\\nSummary: A number of genes involved in lipid and cholesterol metabolism, cell signaling and regulation, development, cell adhesion, apoptosis and transcription have been identified.\\nMechanism: Genes associated with lipid and cholesterol metabolism are involved in regulating the synthesis, degradation and transport of lipids, while genes associated with cell signaling and regulation are involved in regulating cell growth, differentiation and apoptosis. Additionally, genes related to development, apoptosis, and transcription act in the regulation of cell adhesion, differentiation and development.\\n]0.71588
589RANDOMHALLMARK_CHOLESTEROL_HOMEOSTASIS-1[\\nSummary: The genes populated are predominantly involved in lipid metabolism (eg. HMGCR, PMVK, FDPS), transcription regulation (eg. ACTG1, NRAF), cellular adhesion (eg. CD9, ANXA13, COUNTY), and other development related processes (eg. S100A11, MVD, IDI1).\\nMechanism: The genes are associated with a number of different functions but are likely involved in maintaining cellular homeostasis, regulating transcription, and participating in development processes.\\n][ Proteins involved in lipid and lipid metabolism pathways, related to cholesterol control.\\nMechanism: Proteins involved in cholesterol regulation, such as HMGCR, PMVK, FADS2, SREBF2, S100A11, and MVK are likely to be involved in the upregulation and modulation of cholesterol levels. These proteins regulate the breakdown of fatty acids and also mediate the synthesis of bile acids, both of which are important in cholesterol metabolism. ]0.9023
590RANDOMHALLMARK_COAGULATION-0[\\nSummary: Several of the human genes on this list play a role in extracellular matrix formation, inflammatory response, and proteolytic activities.\\nMechanism: The common functional mechanisms included in this term enrichment test are the regulation of the inflammatory response, regulation of extracellular matrix formation, and proteolytic activities.\\n][ Genes in this list represent functions related to extracellular matrix remodeling, angiogenesis and vascular development, immune response and platelet activation, collagen and fibronectin metabolism and regulation, and endocytosis and signal transduction.\\n]0.7196
591RANDOMHALLMARK_COAGULATION-1[\\nSummary: The genes identified are predominantly involved in matrix molecular regulation, pathways related to proteolysis and coagulation, signal transduction, and extracellular matrix organization.\\nMechanism: The genes act as regulators of specific molecular functions and as mediators of signal transduction pathways. The identified genes are likely involved in the processing and remodeling of the extracellular matrix because of their relation to proteolysis and other matrix-related functions.\\n][ The term enrichment test suggests that proteins involved in cell adhesion, proteolysis regulation, and interactions between extracellular proteins and cells are significantly enriched in this gene list. \\n\\nMechanism: These proteins likely act together in a coordinated manner to modulate cell adhesion, proteinase activity, and communication between cells. \\n\\n]0.79141
592RANDOMHALLMARK_COMPLEMENT-0[\\nSummary: These genes are enriched in functions related to extracellular matrix organization, immune system/inflammation/interferon response, and transcription factor activity.\\nMechanism: These genes could be involved in a pathway that is responsible for coordinating and controlling aspects of extracellular matrix organization, immune system/inflammation/interferon response and the activity of transcription factors.\\n][ Our term enrichment test suggests that the commonalities in function of these genes are related to the regulation of cell growth and development, signal transduction pathways, and immunity. Specifically enriched terms include development of tissue and organs; signal transduction; cell surface receptor binding; response to stimulus; immune system; immune response; and cytokine activities.\\n\\nMechanism: These functions likely occur through a combined mechanism of modulating transcription factors, receptor-ligand binding, cytokine release and signaling, and a balance of intracellular concentrations of proteins and lipids.\\n\\n]0.80207
593RANDOMHALLMARK_COMPLEMENT-1[ This enrichment test revealed several terms related to immune system functioning, cell adhesion and regulation, and extracellular matrix organization, which are likely the underlying mechanisms behind the commonalities among the listed genes. Enriched terms include: immunoglobulin like domains; B cell activation; T cell receptor signaling pathway; integrin mediated cell adhesion; apoptosis; regulation of transcription; signal transduction; receptor mediated endocytosis and exocytosis; extracellular matrix organization; and calcium mediated signaling. \\n\\nMechanism: These findings suggest that the genes involved in this test collectively contribute to a range of processes related to immune system functioning, cell adhesion, extracellular matrix organization, and intracellular communication. \\n\\n][\\nThe list of genes provided is heavily enriched for functions related to cellular signalling, inflammatory responses, and cellular stress response.\\nMechanism: These genes are typically involved in regulating and mediating signalling pathways, activating and responding to the inflammatory response, activating and functioning in the cell stress response, and facilitating cell-cell interactions.\\n]0.83406
594RANDOMHALLMARK_DNA_REPAIR-0[ Gene functions related to DNA and RNA metabolism, protein synthesis, DNA damage repair, transcription, and chromatin organization are significantly over-represented.\\nMechanism: It is likely that many of these genes are involved in the same pathway related to the fundamental processes of DNA replication, transcription, and protein synthesis.\\n][ The common functions for the human genes are involved in various developmental processes and DNA replication, with enrichment of terms such as \"developmental process\" and \"DNA replication\". \\n\\nMechanism: The genes act together to facilitate a variety of molecular processes in the cellular pathways to support embryonic and post-natal development, as well as DNA replication, transcription, and translation.\\n\\n]0.9265
595RANDOMHALLMARK_DNA_REPAIR-1[ \\nSummary: These genes are enriched for roles in DNA replication, transcription, translation and post-translational modifications.\\nMechanism: These genes are involved in various biological processes, including DNA replication, transcriptional regulation, translation, and post-translational modifications involved in gene expression. \\n][\\nSummary: Our genes are primarily involved in nucleic acid metabolism, transcription, and post-transcriptional modifications.\\nMechanism: The proteins encoded by the genes in our list likely play roles in the various biochemical steps involved in transcription, such as chromatin remodelling, pre-mRNA splicing, DNA repair, RNA polymerization, mRNA processing, mRNA transport, and translation initiation.\\n]0.9069
596RANDOMHALLMARK_E2F_TARGETS-0[ Genes on the list are primarily involved in DNA cell cycle and replication, gene regulation, transcription and translation, chromatin modification, and DNA repair. \\n\\nMechanism: The genes are involved in the regulation of DNA replication and transcription, chromatin modification, and DNA repair processes during cell cycle progression. \\n\\n][ The provided gene list is over-represented for transcriptional regulation, chromatin modification and mitotic division/cell cycle components.\\nMechanism: The underlying mechanism of this gene set is that the enrichments are involved in the regulation of transcription for gene expression, maintenance of chromatin and DNA structure and function, and regulation of mitotic division and cell cycle checkpoints.\\n]0.8370
597RANDOMHALLMARK_E2F_TARGETS-1[\\nSummary: The genes in the list are involved in diverse functions related to DNA replication, transcription, chromosome condensation and transcriptional regulation.\\nMechanism: These functions are likely related to canonical pathways and processes involved in coordinating and regulating DNA replication, the transcription of genetic information into proteins, and maintaining appropriate chromosome condensation states.\\n][ This list of genes is enriched for functions related to DNA replication and repair, chromatin modification, transcriptional and translational regulation, network formation, spindle formation and kinesin and dynein motor proteins. Mechanism: These genes are likely to function as part of an interconnected cellular pathway and/or network that allows for the generation of daughter cells and the coordination of transcriptional activity and post-translational modifications. ]0.8454
598RANDOMHALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0[COULD NOT PARSE][ The list of genes provided show enrichment for terms relevant to extracellular matrix composition, cell adhesion and motility, cell-matrix interactions, growth factor and cytokine signaling, and matrix remodeling. \\n\\nMechanism: The mechanisms underlying the enrichment of these terms likely involve cell-matrix interactions, growth factor and cytokine signaling, and matrix remodeling.\\n\\n]0.75372
599RANDOMHALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1[ Our enrichment test uncovered several terms related to extracellular matrix function, morphogenesis, and reproduction/growth. These terms include extracellular matrix organization; morphogenesis; collagen production; matrix metalloproteinase activity; glycoprotein metabolism; cytoskeletal component organization; regulation of growth and reproduction; and regulation of skin morphogenesis. Mechanism: The underlying biological mechanisms related to these genes likely involve the extracellular matrix (ECM), which provides structural and biochemical support to the cells and tissues. ECM components, such as collagen, can regulate activities such as cell signaling, structure formation and growth, and gene expression. Morphogenesis is likely modulated by ECM components, as well as by signaling pathways. ][ The identified genes are enriched for terms related to skeletal morphogenesis, cell-cell adhesion and motility, extracellular matrix production and remodeling, development and differentiation of connective tissue, collagen production and turnover, and cytokine and chemokine signaling. \\n\\nMechanism: It is likely that these genes are involved in mechanisms that coordinate protein interactions during skeletal development and morphogenesis, cell adhesion and migration, and the maintenance of a healthy extracellular matrix. In addition, these genes likely contribute to the production and turnover of extracellular matrix components such as collagens and chemokines and cytokines involved in development and differentiation of connective tissue. \\n\\n]0.8960
600RANDOMHALLMARK_ESTROGEN_RESPONSE_EARLY-0[\\nSummary: The list of genes identified are associated with cell morphology, homeostasis and regulation, innervation, and cellular metabolism.\\n][\\nThis list of human genes was analysed in a term enrichment test. The test revealed that many of these genes were involved in a common pathway which supports normal cellular processes including DNA replication, transcription and gene expression, cell growth and differentiation, protein processing and trafficking. Furthermore, many of these genes were involved in bone morphogenesis and cancer-related pathways.\\n\\nMechanism:\\nThe underlying biological mechanism likely involves a number of distinct pathways, each with its own mechanism of action. Common processes shared by many of these genes include DNA replication, translation, and post-translational modification. Additionally, several of these genes are involved in cell-cell adhesion and the control of cellular migration and matrix remodeling, indicating roles in tissue morphogenesis. Furthermore, many of these genes are involved in intracellular signaling and signaling pathways that are essential for the processing and coordination of external and internal signals, which can ultimately result in cell growth, differentiation, and apoptosis.\\n\\n]0.78964
601RANDOMHALLMARK_ESTROGEN_RESPONSE_EARLY-1[ Our analysis of the 34 human genes suggests an enrichment of gene functions related to cell signaling, regulation and morphology, including: immunological response; cell adhesion; transcription regulation; cell migration; development of epidermis, bones and muscle; transport of proteins between cellular compartments; and apoptosis. \\n\\nMechanism: These gene functions are likely related to the regulation of diverse mechanisms within the cell, such as protein-protein interactions, transcription signaling, and intracellular trafficking. \\n\\n][ \\nSummary: The gene list includes genes involved in transcriptional regulation, signal transduction, membrane transport and lipid biosynthesis.\\nMechanism: The genes exhibit common patterns of transcriptional regulation and signal transduction, with a focus on protein-protein interactions and membrane transport.\\n]0.87228
602RANDOMHALLMARK_ESTROGEN_RESPONSE_LATE-0[\\nThe genes in the list are enriched for functions in the genomics and cytoskeletal processes, as well as immune response and extracellular modification.\\n\\nMechanism:\\nThe gene functions are implicated in various biological processes that are orchestrated by genetic control and/or regulation pathways. These pathways typically involve protein interactions and cellular processes. Additionally, these pathways often correlate to extracellular modification, immune response, and/or modulation of receptor signaling.\\n\\n][ Genes related to extracellular matrix organization, cellular adhesion and migration, cell mobility and growth factor-mediated signaling pathways;\\nMechanism: This gene list suggests that extracellular matrix organization, adhesion and migration, cell motility, and growth factor signaling pathways are involved in gene expression in these genes. \\n]0.83166
603RANDOMHALLMARK_ESTROGEN_RESPONSE_LATE-1[COULD NOT PARSE][ The genes are enriched for terms related to the structural organization of cells, transcriptional regulation, signal transduction, and immune responses.\\n\\nMechanism: These genes likely comprise a network that influences the physical and biochemical properties of the cell, including its membrane integrity, signal transduction pathways, gene expression, and immunomodulatory functions. \\n\\n]0.87373
604RANDOMHALLMARK_FATTY_ACID_METABOLISM-0[ This list of genes is highly enriched for metabolic processes such as fatty acid metabolism and oxidation, cholesterol biosynthesis, glycogen metabolism, nucleotide metabolism and transport, and electron transport activity. This suggests that the list reflects a highly coordinated and interconnected network of metabolic processes to maintain the homeostasis of the cell. Enriched terms include: fatty acid metabolism; oxidation of lipids; cholesterol biosynthesis; glycogen metabolism; nucleotide metabolism; nucleotide transport; nucleotide biosynthesis; electron transport activity; enzyme regulation and regulation of metabolic pathways; and apoptosis. \\nMechanism: This set of genes likely acts through a number of interconnected pathways to maintain cellular homeostasis. Lipid metabolism is known to be important in cellular signaling, while other metabolic pathways interact with each other through enzyme regulation and regulation of metabolic pathways. Additionally, many of the genes are associated with cell death pathways, suggesting that these can also act in a coordinated way to respond to stress and maintain cellular homeostasis. \\n][\\nSummary: The genes shown here are involved in a wide range of metabolic pathways and cellular functions, such as energy metabolism, lipid metabolism, amino acid metabolism, DNA damage repair, and cell signaling.\\n]0.81937
605RANDOMHALLMARK_FATTY_ACID_METABOLISM-1[\\n\\nSummary: There is a strong enrichment of genes involved in metabolic processes, energy production and storage, lipid metabolism and transport, as well as acetyl-CoA biosynthesis and catalysis.\\n\\nMechanism: The identified genes likely influence the metabolic processes, energy production and storage, lipid metabolism and transport, as well as acetyl-CoA biosynthesis and catalysis by modulating cellular processes, protein and enzyme production, and functional metabolic pathways, such as oxidation and fatty acid metabolism.\\n\\n][ Genes are enriched in roles associated with lipid metabolism and the cell cytoskeleton. Both pathways involve important signaling and metabolic roles. Mechanism: Lipid metabolism pathways involve synthesizing and degrading lipids, transporting lipids, and their oxidation. The cell cytoskeleton is involved in a variety of functions, including building of cell membranes, cell motility and traffic. ]0.82128
606RANDOMHALLMARK_G2M_CHECKPOINT-0[\\nGene functions involved in cell cycle regulation, DNA replication, and chromatin remodeling are enriched among the provided list of genes. This could reflect a core pathway of regulation that has been conserved across multiple species.\\n\\nMechanism:\\nThe enriched terms suggest that this gene list could be involved in the G1/S transition of the cell cycle, DNA replication, and chromatin remodeling or modification. Specifically, cell cycle progression and DNA replication is likely driven by cyclin B-CDK1 activation, which is facilitated by Cks1b and Cdc25A mediated activation and either Wee1 or Cdc20-anaphase promoting complex-cyclosome (APC/C)-mediated inhibition. Chromatin modification is likely driven by histone H2A and H2B acetylation and lysine methylation, which involve various proteins, such as Hmga1, Hmgn2, H2az1, H2bc12, and Myc.\\n\\n][ \\nSummary: This list of human genes are enriched for functions related to cell cycle and/or development, such as DNA replication and transcription, and may be involved in a variety of pathways and processes.\\nMechanism: These genes may be involved in pathways related to DNA replication, transcription and expression, and cell cycle regulation.\\n]0.81504
607RANDOMHALLMARK_G2M_CHECKPOINT-1[ \\nSummary: This list of human genes are primarily involved in nuclear processes such as DNA replication, gene transcription, chromatin remodelling and cell cycle control.\\nMechanism: The genes may be involved in the regulation of a number of biological processes such as DNA repair, cell cycle regulation, gene expression, and gene regulation.\\n][COULD NOT PARSE]0.84328
608RANDOMHALLMARK_GLYCOLYSIS-0[\\nSummary: Our term enrichment test shows that many of the genes on this list are involved in various aspects of developmental and morphogenic processes, including digit development, cell differentiation, angiogenesis, and metabolism.\\nMechanism: These genes are likely to be involved in biological pathways involving the development and maintenance of cellular structure, binding and transporting of molecules, energy metabolism and other metabolic processes, and cell signaling.\\n][COULD NOT PARSE]0.89464
609RANDOMHALLMARK_GLYCOLYSIS-1[ The list of genes are primarily involved in essential metabolic functions in the cell. Specifically, they are involved in carbohydrate and energy metabolism, microtubule assembly, DNA binding and replication, actin cytoskeleton dynamics, ion channel regulation, transcriptional regulation, and cell adhesion. The mechanism is likely related to the coordination of these processes in order to maintain homeostasis and proper cell functioning.\\n\\nSummary: Genes mainly involved in metabolic processes. \\n\\nMechanism: Coordination of these processes to maintain cellular homeostasis.\\n\\n][ \\nThis gene list is enriched for proteins involved in structural development and energy metabolism, such as structural proteins and enzymes of glycolysis, the pentose phosphate pathway, and the tricarboxylic acid (TCA) cycle. These terms are supported by evidence from gene ontologies (GO) assigned to the genes in the list.\\n\\nMechanism: \\nThe list of genes is involved in pathways which facilitate the efficient production and utilization of energy, such as glycolysis, the pentose phosphate pathway, and the tricarboxylic acid (TCA) cycle. They are also involved in the dynamic assembly of integral structures, such as the cytoskeleton, cell adhesion serve, proteoglycan synthesis, and extracellular matrix formation.\\n\\n]0.85140
610RANDOMHALLMARK_HEDGEHOG_SIGNALING-0[\\nSummary: Many of the genes listed are involved in the development and morphogenesis of neurons and other cells. \\nMechanism: These genes are likely to work together to regulate cell and tissue shaping and differentiation, providing for the formation of specialized neuron structures and neural pathways. \\n][COULD NOT PARSE]0.85290
611RANDOMHALLMARK_HEDGEHOG_SIGNALING-1[\\n\\nSummary: This group of genes is commonly associated with morphogenesis, cell adhesion, development, and neuronal signaling\\nMechanism: The underlying biological mechanism is likely related to the regulation of cell proliferation, migration, differentiation, and neural plasticity during development. \\n][ The genes appear to be involved in the development of various cell types, organs, and other growth processes, including neuron formation, cell adhesion and migration, signal transduction, tissue morphogenesis, and development of the nervous system. \\nMechanism: These genes likely act in a number of ways to promote and coordinate these processes, including recognizing and binding signaling molecules, relaying signals to other molecules, and affecting transcription of target genes. \\n]0.90184
612RANDOMHALLMARK_HEME_METABOLISM-0[\\nSummary: The genes in this list are highly enriched for functions related to membrane transport, energy metabolism, ribosomal proteins, and nucleic acid binding.\\nMechanism: The underlying biological mechanism or pathway may involve regulation and control of cellular functions and transcription activity, with multiple proteins interacting to ensure proper functioning of a variety of cellular pathways.\\n][ The list of genes has a statistically significant enrichment of terms related to cellular metabolism, energy production and transport, cytoskeleton modification and remodelling, and cell adhesion. \\nMechanism: The molecular mechanisms involve the transfer of energy, metabolic pathways, and the coordination of cellular transport and reorganization.\\n\\n]0.8754
613RANDOMHALLMARK_HEME_METABOLISM-1[\\n\\nSummary: The human genes identified in this list are predominantly involved in cell development, gene expression, organogenesis and nucleic acid metabolism.\\n\\nMechanism: The human genes identified in this list are likely to be involved in processes that regulate cell development, including transcriptional regulation and organogenesis, as well as nucleic acid metabolism. \\n\\n][ The enriched terms for this list of human genes suggest a common functional theme in organ development, morphogenesis and growth, immune system function, and transport processes. Enriched terms include: embryonic development; skeletal system development; organogenesis; morphogenesis; growth; immune system process; cell motility; steroid hormone receptor activity; receptor signaling pathway; transport; endocytosis; and cellular homeostasis.\\n\\nMechanism: The underlying biological mechanism suggested by the enriched gene functions is that these genes are involved in various organ and skeletal system development processes, in particular morphogenesis and growth, as well as immune system and transport processes. Specifically, these genes are involved in organogenesis, morphogenesis, growth, and cell motility through receptor signaling pathways, endocytosis, transport processes, and cellular homeostasis. Additionally, the genes are involved in steroid hormone receptor activity, further contributing to organ and skeletal system development.\\n\\n]0.80675
614RANDOMHALLMARK_HYPOXIA-0[COULD NOT PARSE][ The list of genes is involved in a variety of pathways and functions related to cell differentiation, metabolism, protein processing, and the regulation of gene expression. Specifically, this list was enriched for terms related to cell cycle, remodeling proteins, stress response proteins, calcium signaling proteins, hypoxia-inducible factor proteins, transcription factors, chromatin-associated proteins, and kinases.\\n\\nMechanism: The overall mechanism of action of the genes appears to be related to the regulation of cellular processes via the modulation of expression of target genes, primarily through the regulation of epigenetic and transcriptional factors, in order to enable proper differentiation, metabolism, and protein processing. This is further supported by the enrichment of terms related to stress response proteins, calcium signaling proteins, hypoxia-inducible factor proteins, transcription factors, chromatin-associated proteins, and kinases.\\n\\n]0.93951
615RANDOMHALLMARK_HYPOXIA-1[ \\nSummary: Genes related to cell development, cell metabolism, transcription, and regulation are enriched in this set.\\nMechanism: These genes regulate a variety of cellular processes such as cell cycle regulation, transcriptional regulation, and energy metabolism.\\n][ Genes identified in this set are associated with several DNA/RNA binding and regulatory processes, including transcription and epigenetic modification. Statistically over-represented functions in these genes include development, cell structure and movement, cell cycle and division, signal transduction, transport, and energy production; proteins involved in these processes include transcription factors, kinases, histones, and other enzymes. Mechanism: This enrichment likely reflects the underlying biological pathways governing various aspects of gene expression and regulation. ]0.82319
616RANDOMHALLMARK_IL2_STAT5_SIGNALING-0[ The gene set is enriched for genes involved in cell growth, cell detection/regulation, and immunity. Mechanism: These genes are likely involved in a number of pathways that contribute to cell and tissue development, growth, and regulation, as well as regulation of the immune system. ][\\nSummary: These genes are predominantly related to immunological functions, actin cytoskeleton organization, cell surface receptors, and pro-inflammatory regulation.\\nMechanism: The genes listed appear to be involved in the immune response, actin cytoskeleton organization, cell surface receptor-mediated signaling, and pro-inflammatory regulation.\\n]0.8763
617RANDOMHALLMARK_IL2_STAT5_SIGNALING-1[COULD NOT PARSE][ The list of human genes provided are enriched for terms related to immunity, inflammatory response, cell growth, differentiation and development, and signaling pathways.\\n\\nMechanism: This underlying biological mechanism could involve proteins interacting with each other and coordinating pathways to govern immune response, inflammatory response, cell growth, differentiation, and development, as well as other cellular processes.\\n\\n]0.68417
618RANDOMHALLMARK_IL6_JAK_STAT3_SIGNALING-0[ Genes in the list are enriched for the Cellular Processes of Pain Sensing and Signal Transduction; Chemotaxis; Cytokine-mediated Signaling Pathway; Leukocyte Transendothelial Migration; Immune Response; and Platelet Activation. There is a potential mechanism for the underlying biological pathway whereby these genes interact in signal transduction to facilitate pain sensing and immune response, including ligand-receptor interactions, signal transduction of cytokines, and the actions of transcription factors, such as those encoded by JUN, REG1A, STAT1, STAT2, STAT3 and TLR2.\\n\\n][ This list of genes is enriched in terms related to cell signaling, cytokine production and regulation, regulation of gene expression and transcription, and cell adhesion.\\nMechanism: This list of genes promotes the core pathways of cell signaling, cytokine production and regulation, regulation of gene expression and transcription, and cell adhesion. This enables the body to respond to a variety of external signals, to recognize and respond to inflammation and stress, to produce the necessary molecules for the body to function correctly, and to hold the cell together so that it may adhere to corresponding cells and fulfill its role within the network of cells.\\n]0.6986
619RANDOMHALLMARK_IL6_JAK_STAT3_SIGNALING-1[\\nSummary: The list of genes are significantly enriched for functions of immunity, signaling, and transcription regulation\\nMechanism: These genes are likely involved in the coordination of immune responses and the regulation of pathways for signal transduction and transcription.\\n][ Increased expression of cytokines, chemokines, and interleukins; increased expression of developmental, signal transduction, and immune system pathways involved in cellular differentiation, cell motility and adhesion, signal transduction, and inflammation. \\nMechanism: The genes listed all appear to be involved in immune system, signal transduction and intercellular communication pathways. Through the identification of commonalities between the gene functions, inference can be made that these genes are involved in up-regulation of cytokines, chemokines, and interleukins involved in cellular differentiation, cell motility, adhesion, signal transduction and inflammation. \\n]0.86400
620RANDOMHALLMARK_INFLAMMATORY_RESPONSE-0[ Genes associated with human immunity, inflammation and signalling pathways are enriched.\\n\\nMechanism: These genes are likely involved in pathways related to human immunity, inflammation and signalling, either directly or through regulation of transcription and translation activity.\\n\\n][COULD NOT PARSE]0.90269
621RANDOMHALLMARK_INFLAMMATORY_RESPONSE-1[ The list of genes is significantly enriched for terms related to immune cell signaling, cell movement, and cell surface receptor activity. \\nMechanism: These genes are likely involved in the regulation of pathways involved in initiating and responding to inflammation, cell migration, cell–cell interactions, and immune cell receptor-mediated signaling.\\n][ The list of genes is enriched in functions related to the immune system, especially mediation of inflammatory response and cytokine production and signalling.\\nMechanism: The genes are involved in a variety of functions related to immune cell activation and cellular signaling, including cell adhesion, G-protein and receptor-coupled pathways, transcriptional regulation, cytokine and cytokine receptor binding, and lipid metabolism. \\n]0.6981
622RANDOMHALLMARK_INTERFERON_ALPHA_RESPONSE-0[ Our analysis of the list of human genes have revealed a set of enriched terms related to the activation and inhibition of immune signaling pathways, and their functions in regulating inflammation. Specifically, we observed an increased prevalence of molecules and proteins involved in mechanism activating or inhibiting the Nuclear Factor Kappa B (NF-κB), Interferon Regulatory Factor (IRF) as well as JAK-STAT pathways. Terms such as \"inflammatory response\", \"neutrophilic activation and degranulation\", \"T-Cell receptor signaling pathway\", \"Toll-Like Receptor Cascade\", \"Type I Interferon Signaling\", and \"Inflammatory Regulation\" were enriched in this gene set.\\n\\nMechanism: The genes in this list are involved in multiple pathways that are related to the modulation of inflammatory responses and can be broadly summarized as either regulating cytokine production or modulating the inflammatory response by inhibiting the NF-κB, IRF and JAK-STAT pathways. While there is significant overlap of these genes with the NF-κB pathway, the IRF and JAK-STAT pathways are also significant contributors, as evidenced by the enriched terms. \\n\\n][COULD NOT PARSE]0.841122
623RANDOMHALLMARK_INTERFERON_ALPHA_RESPONSE-1[ This group of genes is significantly enriched for functions related to immune system regulation, interferon response, apoptosis, and cell membrane regulation.\\n\\nMechanism: This list of genes is likely involved in both innate and adaptive immune responses, functioning to modulate the level of inflammation and cytokine production, as well as to induce cell death and regulate cell membrane composition. Specific terms enriched that pertain to these functions include interferon signalling pathways, interferon gamma activity, interferon regulatory factor activity, status response to interferon, apoptosis, lipid binding, calcium ion binding, and neutrophil mediated immunity. \\n\\n][ Genes listed appear to be primarily involved in the regulation of interferon response pathways and the transcriptional control of interferon-stimulated genes. The genes appear enriched for the cellular pathways of immune response, inflammation, and cytokine signaling.\\n \\nMechanisms: The interferon response pathways activated in this population of genes modulate the expression of cytokines, chemokines, and antimicrobial and antiviral proteins, in order to activate an innate immune response to virus and bacteria. \\n\\n]0.75160
624RANDOMHALLMARK_INTERFERON_GAMMA_RESPONSE-0[\\nSummary: A majority of the genes were found to be involved in important immune response and cell signaling pathways.\\nMechanism: The immune response and cell signaling pathways are likely to be regulated by cytokines and transcription factors such as those related to interferon responses and nuclear factor kappaB-dependent transcriptional regulation.\\n][ In this gene set, there are multiple genes that are enriched for functions related to immunology, such as antigen presentation, inflammatory responses, chemokine signaling, cell adhesion, and cytokine interactions. \\nMechanism: One hypothesis is that these genes are involved in an immune-mediated response related to their roles in antigen-presentation, inflammatory responses, the regulation of chemokines, and cell adhesion. \\n]0.8378
625RANDOMHALLMARK_INTERFERON_GAMMA_RESPONSE-1[\\nSummary: The enriched terms among the list of genes includes pathways involved in immunity, interleukin regulation, transcriptional regulation, inflammation, cell signaling, and apoptosis.\\nMechanism: Signaling and pathways involving these genes are likely to regulate these biological processes.\\n][ This list of genes is enriched in terms related to cell signaling, transcription regulation, and immune system regulation. Specifically, genes are enriched in pathways related to: interferon signaling; antigen processing, presentation, and recognition; cytokine signaling; cell cycle and DNA damage response; and apoptosis.\\n\\nMechanism: It appears that the genes identified in this list are functionally connected and may be involved in a larger underlying biological mechanism or pathway. The proteins associated with each gene are known to interact with one another and repress/activate various genes leading to the regulation of cell signaling, transcription, and immune system functions. This molecular regulation process is essential in the control of cellular functions and physiological behavior. \\n\\n]0.69509
626RANDOMHALLMARK_KRAS_SIGNALING_DN-0[ Genes in this term enrichment test were found to be enriched for terms related to the development of bones, morphogenesis, growth and maintenance, cell-cell signaling and communication, protein modification, and transport.\\nMechanism: It is likely that the genes identified in this term enrichment test make up a biological pathway that is involved in the development of bones, growth and morphogenesis, and other processes related to regulating cell-cell signaling and communication, protein modification, and transport.\\n][ The analysis of the list of human genes reveals that these genes are related to development, regulation, and signaling mechanisms within the cell. Specifically, the terms associated with development, such as digit development, neural development, immune system development and transcriptional regulation, are enriched. Additionally, terms related to signal transduction, such as G-protein coupled receptors, protein kinases, and guanine nucleotide exchange factors, are also enriched.\\n\\nMechanism:The mechanism underlying the term enrichment of the list of human genes is likely related to the fact that these genes play a role in a wide range of essential cellular processes. It is likely that signaling molecules and transcription signals coordinate these processes to enable proper development and homeostasis.\\n\\n]0.77293
627RANDOMHALLMARK_KRAS_SIGNALING_DN-1[\\nSummary: The list of genes are found to be significantly associated with physiological processes related to morphogenesis, cell-cell communication and development, and hormone regulation.\\nMechanism: The genes are likely to be involved in a variety of biological mechanisms, such as cell-signalling, cellular differentiation and cell-cycle, as well as hormone mediated processes.\\n][COULD NOT PARSE]0.89365
628RANDOMHALLMARK_KRAS_SIGNALING_UP-0[ Genes in this list are predominantly involved in signal transduction pathways and morphogenesis; specific terms enriched include signal transduction, cell morphogenesis, response to stimulus, angiogenesis, regulation of molecular function, and extracellular matrix organization.\\nMechanism: The list of genes are likely to be involved in signaling pathways involving kinases, growth factors and receptors, as well as involvement in morphogenesis processes such as cell-cell adhesion, cellular movement and cell differentiation.\\n][ This list of gene names is enriched for genes involved in signal transduction, cell cycle control, and cell-to-cell adhesion.\\nMechanism: The enrichment of these genes indicates a shared biological pathway in which cellular communication, pathways, and networks are regulated by controlling the production of proteins and other molecules. This can lead to changes in other intracellular activities, such as cell cycle progression and adhesion. \\n]0.7583
629RANDOMHALLMARK_KRAS_SIGNALING_UP-1[\\nSummary: This set of genes appears to be involved in a variety of cellular processes, including morphogenesis and tissue development, cell signaling, and immune regulation.\\nMechanism: These genes appear to be involved in transcription modulation, signal transduction pathways, and regulation of cell adhesion and migration.\\n][\\nSummary: This list of genes is enriched for terms related to cell adhesion and signal transduction, including terms such as integrin, chemokine receptor, protein kinase and G-protein-coupled receptor.\\nMechanism: These genes are involved in pathways important for cell adhesion, such as integrin and chemokine receptor-mediated interactions, as well as signal transduction pathways which include protein kinases, G-protein-coupled receptors and other associated proteins.\\n]0.85147
630RANDOMHALLMARK_MITOTIC_SPINDLE-0[COULD NOT PARSE][\\n\\nSummary: The list of human genes have diverse enrichment in the functions of cell cycle control, cell adhesion, and cytoskeletal organization.\\nMechanism: These genes enable cells to interact with their environment and complete the cell cycle by organizing components, regulating activities, and controlling signaling pathways.\\n]0.81314
631RANDOMHALLMARK_MITOTIC_SPINDLE-1[ Enriched terms show a commonality among these genes for processes related to cytoskeletal organization and migration of the cell, cell division, DNA replication and repair, and targeting proteins to the correct place in the cell.\\nMechanism: The proteins represented by these genes likely play a role, either directly or indirectly, in the regulation of a number of vital cell processes including cell division, DNA replication and repair, and targeting proteins to the right place in the cell.\\n][ \\nSummary: The genes that were provided are statistically enriched for terms related to cell division, protein phosphorylation, chromatin remodeling, and microtubule binding and organization.\\nMechanism: These genes likely function in biological pathways related to spindle assembly, chromosome segregation and movement, cell-cycle control, and other processes related to mitosis. \\n]0.84114
632RANDOMHALLMARK_MTORC1_SIGNALING-0[COULD NOT PARSE][COULD NOT PARSE]0.840
633RANDOMHALLMARK_MTORC1_SIGNALING-1[ The list of genes is enriched in functions related to protein synthesis, energy metabolism, cellular transport, and immune response.\\nMechanism: It is likely that these genes are co-regulated in networks that are responsible for cellular energy production and regulation, protein synthesis and degradation, and immune response.\\n][\\nSummary: This list of genes is involved in a variety of pathways related to cell growth and development, including morphogenesis, transcription, and protein synthesis.\\nMechanism: The physiological processes induced by these genes likely work in concert to mediate a variety of cellular processes including cellular translation, metabolism, and signalling.\\n]0.8329
634RANDOMHALLMARK_MYC_TARGETS_V1-0[ The genes appear to be involved in processes related to RNA and protein synthesis, ATP-related processes, cytoskeleton organization and assembly, transcription, and chromatin remodeling.\\n\\nMechanism: The genes likely play a role in regulating various cellular processes, such as gene expression, signal transduction, and translation, via multiple pathways that are related to RNA processing, translation initiation, mRNA stability, and DNA replication.\\n\\n][\\nThe list of genes are involved in a variety of processes including, but not limited to, protein synthesis and modification, DNA replication, cell cycle regulation, and transcription regulation.\\nThis suggests that these genes may be involved in a co-dependent pathway or pathways that regulate cell growth, development, and gene expression.\\n]0.81113
635RANDOMHALLMARK_MYC_TARGETS_V1-1[ Genes from this list are mainly involved in translation, transcription, and post-transcriptional modification processes. Specifically, these genes are involved in mRNA splicing, mRNA transport, mRNA stability, protein synthesis, ribosome biogenesis, RNA interference, and chromatin remodeling. Mechanism: These genes likely operate according to the canonical mechanisms of gene expression, by which genes are transcribed, spliced, and translated into proteins. These processes are tightly regulated and involve a complex network of interacting proteins, RNAs, and other molecules. ][\\nSummary: This list of genes have overlapping functions in development, energy production, and regulation.\\nMechanism: There may be a pathway involved in controlling energy production, protein synthesis, and structural maintenance of cell components in development.\\n]0.78317
636RANDOMHALLMARK_MYC_TARGETS_V2-0[COULD NOT PARSE][ The enrichment test identified a set of genes related to protein and nucleic acid metabolism and cell cycle regulation. Specifically, genes involved in protein post-translational modifications, phosphorylation, transcription, translation, and ribosome biogenesis were enriched.\\n\\nMechanism: These gene functions are likely related to the underlying biological mechanism or pathway, since genes related to these processes have an essential role in regulatory activities and cell cycle control. ]0.86478
637RANDOMHALLMARK_MYC_TARGETS_V2-1[\\nSummary: The gene set is enriched for terms related to cell activation and proliferation, as well as DNA replication and replication-associated processes such as transcription and translation.\\n][ \\nSummary: Many of the genes listed appear to be related to chromatin and transcriptional regulation.\\nMechanism: Regulation of gene expression and chromatin structure via transcription factors and nucleosome remodeling enzymes. \\n]0.7735
638RANDOMHALLMARK_MYOGENESIS-0[ Gene expression and structure, cytoskeletal structure and dynamics, calcium regulation and signaling, cell adhesion and migration, cell death biochemistry, and metabolic regulation are all enriched terms based on the genes provided that are common to these roles in humans.\\n\\nMechanism: The underlying biological mechanism for the enriched terms observed in this list of genes is likely related to the wide range of regulatory roles these genes and gene products have in maintaining cellular health and enabling proper physiological functions and development at the cellular level. \\n\\n][COULD NOT PARSE]0.69569
639RANDOMHALLMARK_MYOGENESIS-1[ The list of genes show an enrichment for terms related to the extracellular matrix, cytoskeleton, muscle structure and development, neuromuscular structure, ion channels, and ion transport. \\nMechanism: These genes appear to be involved in various intra- and extracellular pathways and mechanisms related to the formation and maintenance of the cytoskeleton, neuromuscular structure, and muscle formation, as well as ion transport and channel proteins serving as important mediators of electrical and chemical signals in cells. \\n][COULD NOT PARSE]0.91514
640RANDOMHALLMARK_NOTCH_SIGNALING-0[\\nThe list of genes are involved primarily in aspects of embryonic development, regulation of cell cycle, and calcium signaling.\\nMechanism: The genes function primarily in regulating various aspects of cell signaling and cycle regulation during embryonic development, such as down-regulation of Notch signaling, regulation of Wnt signaling and Hedgehog signaling pathways, cell morphogenesis, and calcium signaling.\\n][ These genes are associated with Notch receptor, transcription factor, and Wnt pathway signaling, which are involved in tissue and organ development.\\nMechanism: Notch receptor, Wnt, and transcription factor signaling pathways leads to a variety of processes such as morphogenesis, organogenesis, tissue development, cell fate determination, and cell interaction. \\n]0.8251
641RANDOMHALLMARK_NOTCH_SIGNALING-1[COULD NOT PARSE][\\nSummary: The genes in this list are associated with cell proliferation, morphogenesis and development, nerve system differentiation, and regulation of transcription.\\nMechanism: The genes likely function in pathways involved in the WNT and Notch signalling pathways, which have numerous roles in development and differentiation of different tissue types. \\n]0.86341
642RANDOMHALLMARK_OXIDATIVE_PHOSPHORYLATION-0[\\n\\nSummary: This list of genes is enriched for terms related to mitochondrial activity, electron transport chain, oxidative phosphorylation, and metabolic regulation/activation.\\nMechanism: This list of genes are likely to be involved in the various steps of mitochondrial activity, electron transport chain, oxidative phosphorylation, and metabolic regulation/activation. \\n][COULD NOT PARSE]0.86357
643RANDOMHALLMARK_OXIDATIVE_PHOSPHORYLATION-1[\\nSummary: The list of genes is predominantly involved in cellular respiration and metabolism, as evidenced by the enriched terms related to mitochondrial bioenergetics, ion transport and metabolite-binding proteins.\\nMechanism: The commonality amongst the genes likely contributes to the normal functioning of mitochondria, and is involved in the bioenergetic processes that involve ATP synthesis, as well as maintaining electron transfer and transporter function.\\n][ Genes in this list are mainly associated with mitochondrial bioenergetics and associated pathways. Specifically, the terms \"mitochondrial electron transport chain complex activity\"; \"mitochondrial electron transport, NADH to ubiquinone\"; \"mitochondrial respiratory chain complex I activity\"; \"respiratory chain complex I assembly\"; \"respiratory chain complex III activity\"; and \"respiratory chain complex IV activity\" are found to be enriched in this gene set.\\n\\nMechanism: Mitochondria are dynamic organelles that are responsible for many of the metabolic pathways, including cellular respiration. A variety of mitochondrial electron transport complexes are involved in the production of energy, including complex I (NADH:ubiquinone oxidoreductase), complex III (ubiquinone:cytochrome c oxidoreductase), complex IV (cytochrome c oxidase), and complex V (ATP synthase). As these genes are associated with mitochondrial functions, it is possible that there is an underlying mechanism related to metabolic pathways and energy production within the mitochondria. \\n\\n]0.84598
644RANDOMHALLMARK_P53_PATHWAY-0[ Analysis of this gene list revealed a significant enrichment of terms in functions related to cytoskeleton alteration, calcium homeostasis modulation, ubiquitin-proteasome pathway activation, cell cycle control, and transcriptional and post-transcriptional regulation.\\n\\nMechanism: These functions likely act in concert to mediate the regulation of cellular growth, differentiation, and survival.\\n\\n][COULD NOT PARSE]0.70383
645RANDOMHALLMARK_P53_PATHWAY-1[ Genes in this list are associated with regulation of the cell cycle, DNA damage repair, cell signaling and processes involved in cell growth, apoptosis, and immune modulation. The genes are enriched for functions related to transcription, chromatin dynamics, cell adhesion molecules, and cytokines. \\nMechanism: The regulation of these genes (directly or indirectly) is likely to be part of a complex network of pathways, signaling molecules, and protein-protein interactions. \\n][COULD NOT PARSE]0.72463
646RANDOMHALLMARK_PANCREAS_BETA_CELLS-0[\\nSummary: This gene set is enriched in functions related to pancreas development, glucose metabolism, cell motility, and neural development. \\nMechanism: It is hypothesized that these genes function in a network to control developmental processes relevant to pancreas development, glucose metabolism, cell motility and neural development.\\n][ Genes play diverse roles in the development of the pancreas, nervous system, and musculoskeletal system. Major term enrichment was found for pancreas development, nervous system development, development of neural structures, organogenesis, and transcriptional regulation. \\nMechanism: These genes are likely involved in a variety of biological mechanisms including, the regulation of morphogenesis, cell-to-cell adhesion, and protein synthesis pathways, as well as hormonal metabolism and signaling.\\n]0.84162
647RANDOMHALLMARK_PANCREAS_BETA_CELLS-1[\\nSummary: This term enrichment test identified gene functions related to morphogenesis, neural development, signal transduction, insulin hormone secretion, transcription regulation, and transcription factor activity.\\nMechanism: These genes likely work together to facilitate the development of body organs, neuronal function and pathways, insulin secretion, and transcription factor activity.\\n][ Analysis of these genes revealed common pathways related to metabolic regulation, neural development, and transcription/translation control. The terms enriched by these genes are neurogenesis; metabolism; transcriptional control; translation; morphogenesis; body patterning and organization; neurological system development; and cell differentiation.\\n\\nMechanism: Signaling pathways involved in neural development will have an influence on neurogenesis, while metabolic pathways will be involved in pathways that regulate glucose and lipid metabolism. Additionally, transcription and translation pathways are essential for regulating gene expression but also cell differentiation and morphogenesis. Finally, body patterning and organization rely on genes that control cell fate and cellular migration. \\n\\n]0.71411
648RANDOMHALLMARK_PEROXISOME-0[COULD NOT PARSE][ The human genes given in the list are involved in metabolic biochemical pathways associated with lipid metabolism, stress response, mRNA transcription, DNA repair, skeletal and cartilage development, and cell migration. \\nMechanism: Metabolic enzymes and transport proteins appear to regulate these pathways, allowing for the synthesis and degradation of cellular compounds, as well as transporting molecules into and out of the cell to maintain physiological homeostasis.\\n]0.76459
649RANDOMHALLMARK_PEROXISOME-1[ Genes involved in the list are associated with lipid metabolism, lipid storage and transport, steroid metabolism, regulation of transcription and, importantly, regulation of the cell cycle. \\nMechanism: An enrichment of pathways associated with lipid, steroid and transcriptional metabolism, as well as regulation of the cell cycle.\\n][\\nSummary: Genes in this list are associated with a wide array of terms, including metabolism, transcription, regulation, transport and signaling.\\nMechanism: These genes likely play a role in a broad biological mechanism involving various metabolic pathways, transport, and regulatory functions.\\n]0.8338
650RANDOMHALLMARK_PI3K_AKT_MTOR_SIGNALING-0[ Gene expression, DNA repair and maintenance, growth factors, cellular signaling pathways and lipid metabolism \\nMechanism: Regulation of gene expression through the activation of transcription and DNA repair and maintenance pathways is likely involved. The enriched terms related to growth factors suggests that the list of genes may be involved in cell proliferation and differentiation. Signaling pathways and lipid metabolism may be involved in cell-cell communication and energy-related processes, respectively.\\n][ The list of genes is enriched for terms related to signal transduction pathways and development, such as morphogenesis and cell differentiation.\\nMechanism: Signal transduction pathways are likely involved in the regulation of the gene functions, with particular importance of tyrosine kinase activity and modulation of relevant receptor activities.\\nHypothesis: The genes may be involved in the regulation of tissue development and cell differentiation.\\n]0.7662
651RANDOMHALLMARK_PI3K_AKT_MTOR_SIGNALING-1[ The list of genes given are involved in cell cycle regulation, gene transcription, transcription factor activation and signal transduction pathways.\\nMechanism: The genes included in this list are involved in various mechanisms of cell cycle regulation, gene transcription, transcription factor activation and signal transduction pathways. These involve the regulation of cell cycle progresses such as synthesis, growth, proliferation and differentiation, as well as the operations of protein kinases, transcription factors, receptor proteins and other essential molecules. \\n][ \\n\\nSummary: This gene list covers a broad range of functions, including cell signaling, growth and survival, protein and lipid metabolism, transcription regulation, and cell cycle control.\\nMechanism: The genes in this list are likely involved in a variety of pathways that facilitate or regulate various cellular activities, such as receptor signaling, protein glycosylation, kinase activity, apoptosis, and G-protein interactions.\\n]0.88143
652RANDOMHALLMARK_PROTEIN_SECRETION-0[COULD NOT PARSE][ Genes listed are associated with vesicular transport, trafficking, and membrane fusion in the cell.\\nMechanism: Vesicular transport involves the formation of vesicles from the host membrane, trafficking of these vesicles through the cell and organelles, and fusion of the vesicles with host membranes for which these genes are responsible.\\n]0.68325
653RANDOMHALLMARK_PROTEIN_SECRETION-1[COULD NOT PARSE][ Enrichment test on a given list of human genes resulted in the identification of several enriched terms, which have important roles in post-translational modification, protein folding, protein synthesis, endocytosis, oligosaccharide metabolism, and lysosomal trafficking.\\n\\nMechanism: The mechanism behind this enrichment pattern is likely related to the various mechanisms regulated by these genes, such as the regulation of PTMs, protein folding, protein synthesis, endocytosis, oligosaccharide metabolism, and lysosomal trafficking.\\n\\n]0.86522
654RANDOMHALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0[\\nSummary: This list of genes is enriched for terms involving redox regulation, antioxidant defense and detoxification of reactive oxygen species, peroxisomal and mitochondrial biogenesis, and cell metabolism.\\nMechanism: The underlying biological mechanism involves the production and regulation of reactive oxygen species, adaptation to oxidative stress and related forms of damage, and the maintenance of redox homeostasis.\\n][\\nSummary: The list of genes is associated primarily with metabolic processes, defense against oxidative damage and DNA repair.\\nMechanism: These processes are likely related to cellular level metabolic regulation, protection against oxidative damage, and DNA damage repair.\\n]0.82152
655RANDOMHALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1[ \\nSummary: 13 genes are enriched for functions associated with redox regulation, metabolism, cell cycle regulation, and transcriptional regulation.\\nMechanism: These genes likely play a role in the regulation of a cell's redox balance, metabolism, cell cycle progression and gene expression.\\n][COULD NOT PARSE]0.86276
656RANDOMHALLMARK_SPERMATOGENESIS-0[\\nThe gene list is enriched for functions related to cell signaling, protein regulation, and cell cycle control, as well as complex development processes such as morphogenesis, organogenesis and cytoskeletal regulation.\\nMechanism: A wide range of mechanims are at work here, which involve the transcription and translation of genes to encode proteins and the regulation of their functions to mediate both common and specific biological processes.\\n][ Genes associated with this list indicate enrichment for a variety of cell cycle control and chromatin remodeling processes, as well as protein ubiquitination, regulation of DNA replication, spindle assembly, and nuclear organization.\\n\\nMechanism: The enriched terms suggest that these genes are involved in a variety of related functions related to the regulation and maintenance of the cell cycle, chromatin remodeling, DNA replication, spindle assembly and nuclear organization.\\n\\n]0.8236
657RANDOMHALLMARK_SPERMATOGENESIS-1[ Genes related to organ development, morphogenesis, cytoskeletal proteins, signal transduction.\\nMechanism: Proteins from the list are likely used as part of a unified pathway for organ/tissue development and morphogenesis, and involved in cell cycle checkpoint regulation and signal transduction.\\n][COULD NOT PARSE]0.90282
658RANDOMHALLMARK_TGF_BETA_SIGNALING-0[ The list of genes analyzed in this term enrichment test is related to pathways associated with cell growth and development, such as MAPK, TGF-β, Wnt/β-catenin, Hippo and transcriptional regulations. Specifically, pathway enrichment of genes included muscle and tissue morphogenesis, regulator of G-protein signaling and inflammatory response pathway.\\n\\nMechanism: The general mechanism is that the genes are involved in signaling pathways for cell processes such as growth, differentiation and apoptosis. These signals modulate the expression of downstream genes and ultimately lead to changes in cell shape and other cellular activities.\\n\\n][COULD NOT PARSE]0.80625
659RANDOMHALLMARK_TGF_BETA_SIGNALING-1[COULD NOT PARSE][ Our term enrichment analysis of these genes reveals an overrepresented pattern of general cellular processes related to the development and proliferation of cells, as well as homeostasis, cell division, and migration. Specifically, genes related to transcriptional regulation, signal transduction, cell cycle regulation, protein kinase pathways, and translation were enriched.\\n\\nMechanism: These overrepresented functions suggest a complex coordination of biochemical pathways contributing to cell development and proliferation, junctions, and cytoskeletal organization.\\n\\n]0.83558
660RANDOMHALLMARK_TNFA_SIGNALING_VIA_NFKB-0[ These genes are mainly involved in developmental processes, inflammation, immunomodulation, inflammation, cell signalling and metabolic pathways.\\nMechanism: These genes are likely to be involved in pathways leading to the regulation of morphogenesis and tissue development, control of cell proliferation and apoptosis, regulation of immune system immune response, regulation of inflammation and activation of metabolic pathways.\\n][ The genes in the given list are predominantly involved in the TLR signaling pathway, development, inflammation and immune-response regulation.\\nMechanism: The TLR signaling pathway consists of an intricate set of reactions starting with the recognition of a pathogen-associated molecular pattern (PAMP) by the TLR receptor, leading to the activation of various transcription factors, such as NFKB and MAPK, which work to activate a cascade of gene expression and ultimately the secreting of pro-inflammatory molecules.\\n\\n]0.8690
661RANDOMHALLMARK_TNFA_SIGNALING_VIA_NFKB-1[\\nSummary: The genes are enriched for terms related to gene transcription, cytoskeleton formation, and signal transduction. \\nMechanism: The genes are likely involved in a wide range of processes, including transcriptional regulation, actin cytoskeleton organization, cytokine receptor signaling and NF-kB signaling pathways.\\n][ Gene functions related to inflammation and immunity appear to be enriched when analyzing the list of genes provided, including cytokine-mediated signaling, antigen-receptor mediated signaling, B-cell proliferation, cytokine expression and release, immunoregulatory interactions, NF-kappaB (NF-κB) activation, and interferon (IFN) signaling.\\n\\nMechanism: These genes are likely involved in an inflammatory response in which cytokines are released and induce receptor activation, which leads to NF-κB activation and transcription of genes that produce cytokines and other signaling molecules, as well as triggering an IFN response. This ultimately leads to B-cell proliferation and immunoregulatory interactions in order to mount a response to the any pathogens. \\n\\n]0.86439
662RANDOMHALLMARK_UNFOLDED_PROTEIN_RESPONSE-0[ The genes in the list may be generally involved in processes such as mRNA transcription, ribosome biogenesis and protein folding, as well as nucleolar and spliceosomal activity. \\nMechanism: These genes likely regulate cellular processes such as protein production and transport, RNA processing, and cell cycle control. \\n][\\nSummary: A significant enrichment of genes involved in translation and protein folding is found in the gene list, indicating a common pathway for these genes.\\nMechanism: The genes in this list are likely all involved in the same pathway, centered around translation and protein folding.\\n]0.8733
663RANDOMHALLMARK_UNFOLDED_PROTEIN_RESPONSE-1[\\nSummary: The enrichment analysis on the list of genes revealed a common theme of gene functions related to metabolism, protein synthesis, and post-translational modifications.\\nMechanism: The observed gene functions suggest a pathway of metabolic and protein regulatory processes that involve the synthesis of proteins, post-translational modifications such as phosphorylation, and other processes related to metabolism and folding.\\n][COULD NOT PARSE]0.85418
664RANDOMHALLMARK_UV_RESPONSE_DN-0[ The genes identified are associated with protein kinases, cellular signaling pathways, and development of skeletal and extracellular matrix components.\\nMechanism: These identified genes may be involved in complex regulation and signaling pathways, focusing on post-translational phosphorylation and transcriptional regulation, as well as the control of growth, development and remodeling of skeletal structures.\\n][ This enrichment test demonstrates over-representation of the genes involved in cell signaling, structural and enzymatic proteins, and morphogenesis. Mechanism: The mechanisms underlying this enrichment are likely related to the roles of these proteins in regulating the mechanism of intercellular signaling associated with cell development, adhesion, migration, metabolism, skeletal growth, and cell death. ]0.815
665RANDOMHALLMARK_UV_RESPONSE_DN-1[ Many of the genes are clustered around those involved in structure, development and regulation. They are involved in processes such as mitotic regulation, bone morphogenesis, morphogenesis of specific organs and tissues, regulation of signaling pathways, regulation of transcription, regulation of cell proliferation, cellular responses to external stimuli, protein phosphorylation and DNA binding.\\n\\nMechanism: These genes are likely to be involved in the regulation and development of several different processes, including the regulation of cell proliferation, transcription, morphogenesis of organs and tissues, and mitotic regulation. These mechanisms are likely to be controlled by the interactions among gene products, signaling pathways and regulatory components such as transcription factors.\\n\\n][COULD NOT PARSE]0.79788
666RANDOMHALLMARK_UV_RESPONSE_UP-0[ Proteins involved in development, cell growth, gene transcription, and metabolism are enriched.\\nMechanism: These proteins are involved in a variety of biological processes that underlie development and cell growth, as well as affecting gene transcription and metabolism.\\n][\\n\\nSummary: The enriched terms from the list of genes suggest a commonality in roles related to protein and organelle trafficking, DNA methylation, transcription and binding, chromatin remodeling, cell cycle regulation and metabolism. \\n\\nMechanism: The proposed mechanism is that these processes are essential components of pathways that regulate cell development, growth, and the response to internal and external stimuli.\\n\\n]0.66151
667RANDOMHALLMARK_UV_RESPONSE_UP-1[ Genes in this list are mainly involved in cell growth, morphogenesis, regulation of transcription, signal transduction of receptors, DNA/protein activity and metabolism. More specifically, the terms enriched in this list of genes are cell proliferation, cell cycle regulation, DNA replication and repair, signal transduction, calcium signaling, apoptosis, lipid metabolism and oxygen pathway.\\n\\nMechanism: The genes in this list mainly participate in the regulation of various biological processes through their encoding for proteins that act as transcription factors, receptors, and enzymes. These proteins are activated by a variety of signals including DNA damage, growth factors and hormones to induce changes in gene expression and cellular behavior. They also control cell growth, differentiation and metabolism by regulating DNA, protein, lipid and oxygen pathways, ultimately resulting in morphogenesis and cell proliferation. \\n\\n][COULD NOT PARSE]0.82922
668RANDOMHALLMARK_WNT_BETA_CATENIN_SIGNALING-0[COULD NOT PARSE][COULD NOT PARSE]0.680
669RANDOMHALLMARK_WNT_BETA_CATENIN_SIGNALING-1[\\nSummary: The gene list appears to mostly contain genes involved in Wnt signaling, Notch signaling, transcription regulation and cell cycle regulation processes.\\nMechanism: The underlying biological mechanism appears to be the regulation of processes such as transcription, cell cycle, and Wnt and Notch signaling that may in turn affect the morphogenesis and development of various organs and tissues.\\n][ Genes highly enriched in the provided list have functions related to cell signaling and regulation, including morphogenesis, transcription, and development. Specifically, genes involved in Wnt, Notch, and Hedgehog pathways, transcription factors, and cell cycle genes such as Axin, β-catenin, HDAC2, and CUL1 are all significantly enriched in the list.\\n\\nMechanism: Many of the genes involved in these pathways are responsible for controlling cell fate and regulating morphogenesis and development. The Wnt pathway, a key regulator in embryonic development, is involved in axial patterning, tissue organization and differentiation, and cell-fate decisions. The Notch and Hedgehog pathways are also important for stem cell maintenance and development in early development, as well as tissue patterning, morphogenesis, and organogenesis in adulthood. The transcription factors, such as LEF1, TCF7, and NKD1, drive gene expression in response to these signaling molecules. Lastly, genes such as ADAM17, DKK1, PSEN2, and AXIN2 are involved in cell-cycle regulation and apoptosis. \\n\\n]0.92675
670RANDOMT cell proliferation-0[ \\nSummary: The genes in the list are found to be involved primarily in cell signalling, development, and immunity processes.\\nMechanism: The numerous genes with enriched terms are involved in coordinating both intra- and extracellular activity through signal transduction pathways and receptor-mediated signaling, with downstream effects on cellular growth, differentiation, and function within various organs and systems in the body.\\n][\\nSummary: This list of genes are enriched for terms related to cell development and signaling, specifically those involved in receptor-mediated signaling and the regulation of cell morphology. \\nMechanism: These genes likely act through regulating cell development and receptor-mediated signaling pathways to their respective functions, such as morphogenesis and gene expression.\\n]0.8255
671RANDOMT cell proliferation-1[ The enrichment test found that the genes listed have common functions associated with cell signaling and immune regulation, such as signal transduction, growth factor production and response, immune response and modulation, calcium homeostasis, transcription factors, development and differentiation, receptor binding, and cytokine production.\\n\\nMechanism: The enrichment test suggests that these genes may contribute to signal transduction pathways that facilitate cell proliferation, differentiation, and survival; growth factor production and signal transduction; immune response and modulation; calcium homeostasis; transcription factor activity including regulation of gene expression; development and differentiation; receptor binding and signal transduction; and cytokine production.\\n\\n][ \\nThis sample of genes are mainly involved in regulation of the immune system, cell signaling, cytoplasmic transport, and apoptosis. Specifically, the genes are enriched for terms such as cytokine receptor binding; cell adhesion; immunoreceptor-antigen complex binding; regulation of the ubiquitin-proteasome pathway; transcription factor regulator activity; GTP-binding protein binding; cell differentiation; T-cell receptor binding; antigen presentation; and immune system process.\\n\\nMechanism: This list of genes likely act in concert to regulate the immune system. They perform a variety of functions, including binding and processing cytokines, receptor-antigen complexes, and other molecules involved in the binding or processing of molecules, such as transcription factors, that are involved in regulating gene expression. Additionally, these genes may be involved in cell differentiation, antigen presentation, and other processes involved in the regulation of the immune system. \\n\\n]0.84197
672RANDOMYamanaka-TFs-0[COULD NOT PARSE][ The genes provided are related to transcription factor activity, as they are associated with embryonic stem cell differentiation and pluripotency.\\n]0.69133
673RANDOMYamanaka-TFs-1[\\nThe list of genes provided encode transcription factors associated with early development of embryonic stem cells.\\nMechanism: Transcriptional regulation via these transcription factors control the expression of other genes related to embryogenesis and stem cell development.\\n][ The given list of genes is involved in the regulation of cell differentiation and development, specifically in the formation of stem cells, by regulating the expression of developmental proteins. ]0.8879
674RANDOMamigo-example-0[\\nSummary: This term enrichment test on the list of human genes shows enrichment for terms related to extracellular matrix organization and cell adhesion, morphogenesis and morphological changes, and cell signaling. \\nMechanism: The underlying biological mechanisms may involve a combination of protein-protein interactions, transcriptional regulation and extracellular matrix modifications.\\n][ The genes included in this list are related to cell proliferation, tissue morphogenesis, motility regulation, vascular development, bone growth, and the immune system. The mechanism is the transcription of gene products that cause expression of varied proteins that mediate these functions.\\n\\nMechanism: Transcription of gene products inducing the expression of varied proteins that mediate cell proliferation, tissue morphogenesis, motility regulation, vascular development, bone growth, and the immune system.\\n\\n]0.90124
675RANDOMamigo-example-1[COULD NOT PARSE][ This list of genes are all involved in the development and maintenance of the vascular system. Specifically, these genes play a role in angiogenesis, cell proliferation and migration, matrix remodeling, and tissue remodeling. The genes are implicated in processes such as Jagged-mediated signaling, transcriptional regulation, platelet activation and aggregation, immune regulation, and extracellular matrix formation.\\n\\nMechanism: These genes are involved in a variety of pathways that are responsible for the formation and maintenance of the vascular system. Specifically, the Jagged and Notch pathways are implicated in the control of endothelial cell proliferation and migration, while the TGF-β and Wnt/β-Catenin pathways are involved in matrix remodeling. Additionally, these pathways are also involved in platelet activation and aggregation and the formation of extracellular matrix components.\\n\\n]0.68888
676RANDOMbicluster_RNAseqDB_0-0[\\nSummary: The list of genes are involved in morphogenesis, development, transcription regulation, cellular signalling and ion transport.\\nMechanism: The genes are likely to be involved in a variety of biochemical and molecular pathways pertaining to the specified functions.\\n][ Genes associated with this list are enriched for functions related to development and signaling, including cell growth, differentiation, and migration; chromatin modulation; transcription regulation; cytoskeletal organization; intracellular trafficking and adhesion; signal transduction; and DNA/RNA metabolic processes.\\nMechanism: The genes are likely to be involved in multiple biological mechanisms and pathways, including processes related to healing, morphogenesis, angiogenesis, and muscle growth and development.\\n]0.69247
677RANDOMbicluster_RNAseqDB_0-1[ These genes are primarily involved in development and signaling pathways, particularly morphogenesis, neuronal growth, and neuronal system development. Mechanism: These genes facilitate cell-cell communication and signaling, allowing for cells to coordinate their functions together and form efficiently organized tissues and organs. ][ This analysis identified a number of genes involved in various cellular processes such as chromatin regulation, cell development, protein translation, and ion transport.\\nMechanism: The underlying biological mechanism likely involves regulation of gene expression through the actions of transcription factors, the post-translational modifications of proteins, and the transport of ions across cell membranes.\\n]0.7374
678RANDOMbicluster_RNAseqDB_1002-0[COULD NOT PARSE][ The human genes listed are involved in skeletal muscle structure and contractility. The genes are enriched for processes such as myofibrillogenesis, actin filament organization, and muscle contraction.\\n\\nMechanism: The genes likely act to regulate processes involved in myofibrillogenesis, such as Z-disc formation and maintenance, nuclear positioning, and muscle fiber organization. They also may act to modulate ion channel influx/efflux, thereby influencing muscle contraction and force. \\n\\n]0.84478
679RANDOMbicluster_RNAseqDB_1002-1[ The genes listed were significantly over-represented for processes related to muscle formation and human body structure, such as muscle and skeletal development, skeletogenesis, and myogenesis. \\n\\nMechanism: The set of genes is involved in multiple pathways related to muscle formation and structure in the human body, such as muscle and skeletal development, skeletogenesis, and myogenesis. These pathways likely involve the regulation of protein synthesis and biosynthesis, as well as processes related to muscle contraction and relaxation. \\n\\n][\\nSummary: Genes in this set are involved in muscle structures and processes.\\n]0.67468
680RANDOMendocytosis-0[ These genes are involved in signaling pathways, vesicle/lipid trafficking, and cellular adhesion related processes.\\nMechanism: These genes act as regulators of nutrients, cell metabolism, and cytoskeletal organization. They are also involved in endocytosis, exocytosis, and the regulation of intercellular adhesion and motility.\\n][\\nSummary: These genes are related to lipid metabolism, cell signaling pathways, and cell cycling.\\nMechanism: These genes are thought to have a role in regulating lipid metabolism, cell signaling pathways and cell cycling. \\n]0.84107
681RANDOMendocytosis-1[\\nSummary: The genes in this list are associated with processes related to membrane trafficking, receptor signaling, protein proteolysis, and lipid metabolism. \\nMechanism: The underlying biological mechanism is likely regulation of membrane trafficking, receptor signaling, protein proteolysis, and lipid metabolism. \\n][\\nSummary: The genes in this list are predominantly involved in endocytosis and intracellular signaling.\\nMechanism: The genes in this list interact to form a molecular pathway that is involved in endocytosis and intracellular signaling. Endocytosis allows receptors and newly synthesized molecules to be moved cellular compartments and can result in changes in cell signaling.\\n]0.8959
682RANDOMglycolysis-gocam-0[ An analysis of gene functions in these 10 genes shows an enrichment of terms associated with metabolism, including glycolysis, aerobic glycolysis, and gluconeogenesis.\\n\\nMechanism: This suggests a possible underlying biological mechanism in which glycolysis and gluconeogenesis pathways are deployed by cells in order to provide sufficient energy to cope with various metabolic demands.\\n\\n][\\nBased on the list of genes provided, common terms enriched amongst the genes include ATP synthesis, glycolysis, energy metabolism, and metabolic pathways.\\n\\nMechanism: \\nThe underlying biological mechanisms involve ATP synthesis by way of glycolysis and energy metabolism pathways, which produce necessary energy required for a variety of cellular activities.\\n\\n]0.8528
683RANDOMglycolysis-gocam-1[ The human genes provided in this list are enriched for metabolic functions involved in glycolysis and pentose phosphate pathways.\\nMechanism: The mechanism likely involves the direct or indirect control of enzymatic activities through the coordinated activity of multiple genes.\\n][ The genes identified are related to glycolysis, the metabolic pathway that produces ATP from glucose and other carbohydrates. \\nMechanism: Glycolysis involves the series pathways in which a compound molecule of glucose is broken down into two molecules of pyruvic acid, which are further converted into ATP. \\n]0.8930
684RANDOMgo-postsynapse-calcium-transmembrane-0[COULD NOT PARSE][COULD NOT PARSE]0.890
685RANDOMgo-postsynapse-calcium-transmembrane-1[COULD NOT PARSE][\\nSummary: This gene set is primarily involved in neuronal functional regulation, including ion transport, membrane potential regulation and neurotransmission.\\nMechanism: These genes are involved in the regulation of neuronal activity, likely through the regulation of a number of ion channels, neurotransmitter receptors, and calcium/potassium regulators.\\n]0.83341
686RANDOMgo-reg-autophagy-pkra-0[\\n \\nSummary: The genes in this list are involved in various aspects of biological processes, ranging from cell growth and development to immune response and proteolysis.\\n \\nMechanism: The genes interact in multiple overlapping pathways to influence cellular processes such as immune response and protein degradation. \\n \\n][COULD NOT PARSE]0.82303
687RANDOMgo-reg-autophagy-pkra-1[ Several pathways related to cellular signaling and signalling transduction are enriched among this set of human genes. Specifically, phosphatidylinositol signalling, vascular endothelial growth factor receptor signalling, progesterone-mediated oocyte maturation, NF-kB signaling and neuroprotection are all enriched with five or more genes represented in the set, suggesting that the underlying biological mechanism could be related to these pathways.\\n\\nMechanism: Several pathways related to cellular signaling and signalling transduction.\\n\\n][\\nThe genes provided are all involved in cell regulation and signaling pathways. Specifically, they all have roles in the activation of transcription factors, and in the activation, regulation and inhibition of signaling proteins such as Ras, Akt and calcium associated kinases.\\nMechanism: \\nThe genes all act together in order to affect the expression of various genes and proteins. They function by either upregulating or downregulating the expression of transcription factors and signaling proteins, as well as by modulating the phosphorylation state of these proteins, thus controlling their activity.\\n]0.8562
688RANDOMhydrolase activity, hydrolyzing O-glycosyl compounds-0[ These human genes are involved in cellular functions related to glycosaminoglycan metabolism, lysosomal and catabolic pathways, as well as digit and skeletal development. The genes are enriched for functions in carbohydrate digestion and absorption; glycosaminoglycan and glycan metabolism; lysosomal, peroxisomal, and catabolic processes; and digit, skeletal, and limb morphogenesis. \\nMechanism: The genes likely act by providing enzymes, carriers, and structural proteins that together play essential roles in the transport and metabolism of carbohydrates, as well as help form and shape the skeleton and digits during embryonic development. \\n][ These genes are apparently associated with lysozymes, mucins, glycosyltransferases, and hyaluronidases, enzymes and proteins with roles in the breakdown and regulation of glycosylation.\\nMechanism: The mechanism behind this gene cluster's biological role seems to be in the regulation of cell processes related to glycosylation, such as enzyme production and its breakdown.\\n]0.88272
689RANDOMhydrolase activity, hydrolyzing O-glycosyl compounds-1[ The human genes in this list are mostly related to glycoside hydrolase (GH) activity, but also include proteins involved in chitin and mucin biosynthesis, as well as cysteine protease and lysosomal activities. Most of the genes have either a glycoside hydrolase activator or a lysosomal enzyme function. \\n][COULD NOT PARSE]0.83291
690RANDOMig-receptor-binding-2022-0[COULD NOT PARSE][\\nSummary: The genetic pathways enriched in these genes involves immunoglobulin heavy/light chain combination, antigen specific receptors, J-chain, and T-lymphocyte receptors. \\nMechanism: These genes mainly play a role in immune response, specifically the regulation of the combination of immunoglobulin heavy and light chains to form antigen-specific receptors, the formation of J-chain, the production of T-lymphocyte receptors, and the regulation of immune function.\\n]0.80454
691RANDOMig-receptor-binding-2022-1[\\nSummary: These genes are mainly involved in Immunoglobulin Function and Blood Coagulation. \\nMechanism: The terms enriched for these genes are related to the immune system and blood clotting pathways, specifically those related to Immunoglobulins, B Cell Receptors, and Fibrinogen-related proteins. \\n][COULD NOT PARSE]0.88285
692RANDOMmeiosis I-0[ \\nSummary: Genes involved in DNA damage repair and meiotic recombination processes\\nMechanism: Genes in the list are involved in DNA damage recognition, DNA double-strand break repair, meiotic recombination, and chromosome segregation.\\n][ This list of genes is enriched for functions related to DNA replication, repair, and replication fidelity. Mechanism: The list of genes is likely to be involved in simulating DNA synthesis, prioritizing DNA strands for replication, ensuring proper repair of damaged DNA strands, and ensuring that high-fidelity replication is taking place during the cell cycle. ]0.83128
693RANDOMmeiosis I-1[ Enrichment test revealed that genes are related to DNA repair, replication, and splicing.\\n\\nMechanism: The commonalities in the function of the genes revealed in the enrichment test suggest that there may be a biological pathway that is responsible for creating and maintaining a stable genetic system. This may involve DNA repair to combat mutation and damage, replication to create new copies, and splicing for the proper expression of genes.\\n\\n][COULD NOT PARSE]0.84431
694RANDOMmolecular sequestering-0[ This enrichment test indicates that the listed genes are involved in multiple pathways that are involved in cell proliferation, apoptosis, and molecular transport in diverse cell types. Specifically, some of the enriched terms associated with these genes include mechanisms involved in cell cycle checkpoints, cell adhesion/motility complexes, transcriptional complexes, protein modifications, and RNA processing complexes. \\nMechanism: These pathways likely affect cell proliferation, apoptosis, and molecular transport by responding to a variety of environmental stimuli, including calcium-based signaling, growth factor-mediated signaling, and oxidative stress. \\n][ 17 of the genes in the list are related to functions involving calcium homeostasis, including calcium signaling, regulation of calcification, and regulation of calcium ion transport. Mechanism: The genes identified are involved in the regulation of calcium homeostasis and signaling, along with functions related to calcification, calcium buffering and transport, protection against calcium overload, and calcium-v influx/efflux. ]0.79235
695RANDOMmolecular sequestering-1[ The analysed genes are mostly involved in calcium binding, apoptotic regulation, and immune modulation, all of which are important mechanisms for a variety of biologic processes.\\n\\nMechanism: The mechanism is likely related to the genes' ability to modulate calcium and apoptotic pathways as well as reduce oxidative stress and influence immune effectors.\\n\\n][\\nSummary: Our list of human genes suggests pathways involved in cell structure regulation and metabolism.\\nMechanism: These genes are likely involved in the regulation of cell morphology, metabolic processes and apoptosis.\\n]0.84135
696RANDOMmtorc1-0[COULD NOT PARSE][COULD NOT PARSE]0.850
697RANDOMmtorc1-1[ Analysis of the genes provided shows that the genes are enriched for functions relating to energy production and metabolism, protein biosynthesis and folds, cell regulation, growth and development, and protein turnover. \\n\\nMechanism: The likely underlying biological mechanism behind these functions is likely related to the regulation, management and production of energy and metabolites to carry out processes such as cell growth and to synthesize proteins which are essential for the functioning of the cell, cell signaling and related pathway activities.\\n\\n][COULD NOT PARSE]0.78545
698RANDOMperoxisome-0[ PEX proteins are involved in peroxisome biogenesis and formation. \\nMechanism: PEX proteins play a role in driving the biogenesis of peroxisomes, a type of organelle that plays a role in various metabolic functions. \\n][\\nThis list of genes is enriched for terms related to protein homeostasis and peroxisome biogenesis. The genes are likely to have roles in maintaining and regulating the levels of specific proteins, as well as helping to form and breakdown peroxisomes in the cell.\\n\\nMechanism: The mechanism underlying these functions appears to involve forming, maintaining and regulating the levels of specific proteins, as well as assisting in the formation and breakdown of peroxisomes in the cell. \\n\\n]0.87270
699RANDOMperoxisome-1[ The provided genes are all peroxisomal biogenesis factor genes and are associated with peroxisomal biogenesis, protein transport, and oxidative damage resistance.\\n\\nMechanism: These factors regulate the assembly of the peroxisome, a subcellular organelle involved in fatty acid metabolism, carbohydrate metabolism, and oxidative damage resistance.\\n\\n][ The genes provided are all related to Peroxisomal Biogenesis, an important cellular process. \\nMechanism: Peroxisomal biogenesis requires the coordinated expression of multiple genes in order for the peroxisome to be expressed and maintained in cells. \\n]0.8396
700RANDOMprogeria-0[ The genes in this list are all associated with a cellular carboxyl-methyl transferases, a type of protein involved in RNA and DNA metabolism. The proteins are associated with development and growth, particularly that of cell structural elements such as gene transcription and transcriptional regulation. \\nMechanism: The mechanism involves carboxyl-methyl transferase proteins that modulate gene expression and the communication between transcription factors and the DNA strand.\\n][COULD NOT PARSE]0.87464
701RANDOMprogeria-1[ These genes are involved in a number of processes related to DNA replication and repair, including DNA replication and repair, nucleosome assembly, telomere maintenance, and transcriptional regulation.\\n \\nMechanism: Genes LMNA, WRN, and BANF1 are all involved in several mechanism related to the general processes of DNA replication, repair, and transcriptional regulation through the assembly and maintenance of the different levels of chromatin structure. LMNA is involved in the assembly and disassembly of the nuclear lamina, a type of intermediate filament that helps to anchor chromosomal proteins to the nuclear envelope. WRN is involved in telomere maintenance, which is critical for accurate chromosomal replication and stability. Finally, BANF1 is involved in a number of DNA repair processes, including translesion DNA synthesis, homologous recombination, and non-homologous end joining. These processes are essential for the accurate repair and replication of DNA molecules, and all require an understanding of, and proper interactions between, transcription and chromatin structure. \\n\\n][ Shortly, these genes are involved in a range of functions including transcriptional regulation, DNA repair, cell cycle regulation, and cell differentiation. \\nMechanism: These genes all have common functions related to the transcription, repair, and/or regulation of DNA, which suggests that they all play a role in the response to cellular damage or stress, which in turn can influence the downstream processes of cell cycle, differentiation, and growth.\\n]0.78642
702RANDOMregulation of presynaptic membrane potential-0[\\n\\nSummary: This term enrichment test identified genes involved in signal transduction, ion transport, and regulation of neurotransmitter release.\\nMechanism: This is likely related to the regulation of excitatory and inhibitory signal transmission, potentially mediated by ion channels and signal transduction pathways associated with the G-protein coupled receptors, voltage-gated K+ and Na+ channels, and ligand-gated ion channels.\\n][ Through a term enrichment test on this list of genes, we see that they are over-represented in terms related to ion conductivity and neural excitability, including ion channels, membrane proteins, and synapse formation.\\n\\nMechanism: These genes likely play a role in neural excitability, leading to the formation of specific ion channels that can conduct ions and help form synapses between neurons.\\n\\n]0.8632
703RANDOMregulation of presynaptic membrane potential-1[COULD NOT PARSE][ This group of genes is enriched for terms related to ion-channel function, neuron excitability, and synaptic transmission.\\nMechanism: This group of genes suggested the underlying molecular pathway involves communication between neurons via ion-channel mediated synaptic transmission.\\n]0.88270
704RANDOMsensory ataxia-0[ This list of genes is related to muscle, central and peripheral nervous system development, as well as protein and lipid transport and metabolism. \\nMechanism: The genes appear to be involved in regulatory pathways for growth and development of the skeletal and nervous systems via coordination of morphology, protein and lipid synthesis, and transport.\\n][ These genes are mainly involved in protein synthesis, metabolism, ion channel transport, and muscle contraction or development.\\n\\nMechanism: These genes function as transcriptional regulators, enzymes in metabolic pathways, ion channels, or as key mediators of neuromuscular development and contraction.\\n\\n]0.8749
705RANDOMsensory ataxia-1[\\n\\nSummary: Analysis of the genes yielded significant enrichment of terms related to protein transport, development of the central nervous system, skeletal structure and muscle formation.\\n\\nMechanism: The function of these genes likely reflects the underlying biological pathways for the development and maintenance of different organ systems, including the central nervous system, muscular system, and skeletal structure. \\n\\n][ This list of genes encodes many proteins which are involved in nucleic acid metabolism, binding, and transport. Terms enriched in these genes include: Nucleic Acid Metabolism; Nucleic Acid Binding; Nucleic Acid Transport; Protein Metabolism; Protein Binding; and Protein Transport.\\n\\nMechanism: The proteins encoded by these genes are likely to be involved in nucleic acid metabolism and other related downstream processes. These proteins are likely involved in mRNA transcription, mRNA processing and/or mRNA translation. The proteins could also be involved in processes like RNA editing, DNA replication, DNA repair, and DNA recombination. These proteins are likely to be involved in the regulation of gene expression and other pathways related to this process.\\n\\n]0.84342
706RANDOMterm-GO:0007212-0[ This list of genes is enriched for terms related to signal transmission and transduction, specifically the G Protein-Coupled Receptor (GPCR) family, which is associated with cell-signaling pathways and regulation of receptor activities. The specific terms enriched include G alpha subunit signaling, related GPCR activation and signaling, G Protein-Coupled Receptor (GPCR) function, and dimerization. \\n\\nMechanism: This set of genes is involved in pathways that involve the G protein-coupled receptor (GPCR) family. GPCRs can bind to extracellular molecules, such as hormones and neurotransmitters, and then activate signaling pathways inside the cell, leading to the activation of intracellular proteins, including G proteins. The G proteins then facilitate the exchange of proteins such as cAMP, DAG, and calcium ions into the cell, in order to create a signal cascade and ultimately effect changes to the cell’s behavior.\\n\\n][ This gene list is enriched for terms related to G-Protein Coupled Receptors (GPCRs), G-protein subunits, adenylate cyclase, calcium channels, and kinases.\\n\\nMechanism: The GPCRs and G protein-coupled subunits are involved in signal transduction pathways that regulate a variety of cellular activities. They activate adenylate cyclases, which catalyze the synthesis of the secondary messenger cAMP. This acts downstream to activate pathways and processes such as G-protein mediated second messenger systems and cation channels. Kinases are involved in the regulation of the G-protein by phosphorylating the Gα subunits and other associated components, leading to changes in their activity, and ultimately, signaling cascades.\\n\\n]0.87200
707RANDOMterm-GO:0007212-1[\\nSummary: The list of genes is involved in the regulation cellular signaling and development of the nervous system.\\nMechanism: The list of genes is likely transmitting signals through G proteins, phosphorylation cascade, and calcium signaling pathways to regulate the development of the nervous system, including alterations in the nervous system structure, indoleamine metabolism, and neurotransmission.\\n][\\n\\nSummary: The enriched terms from these genes suggest a correlation with signaling pathways, cellular growth and differentiation, organization of the cytoskeleton, regulation of endocrine systems, and transcriptional regulation. \\n\\n]0.85173
708RANDOMtf-downreg-colorectal-0[ The gene list includes members of the nuclear receptor superfamily, molecules involved in transcription regulation, epigenetic regulation, cell cycle regulation, DNA binding and chromatin remodeling, developmental processes and cell signaling pathways, and components of the nuclear lamina and nuclear matrix.\\n\\nMechanism: The enriched terms suggest a molecular pathway underlying gene regulation, where transcription factors and chromatin reorganization molecules interact with nuclear receptors and other molecular mechanisms in order to regulate gene expression. Moreover, the gene list may represent a mechanism involved in the regulation of cell growth, differentiation and development.\\n\\n][COULD NOT PARSE]0.82678
709RANDOMtf-downreg-colorectal-1[ The genes provided are involved in developmental pathways and functions, such as transcriptional regulation, chromatin modification, morphogenesis, cardiovascular development and differentiation.\\nMechanism: These genes are associated with a wide range of cellular processes, primarily related to embryonic development, including fetal growth and development, stem cell differentiation, and postnatal growth. \\n][ The enriched terms for this list of genes are cellular growth, transcriptional regulation, and chromatin remodeling. These genes are generally involved in the regulation of transcription, chromatin modifications, and cell cycle regulation. These terms are statistically over-represented compared to the gene list provided.\\n\\nMechanism: The likely underlying biological mechanism for these genes is that they are involved in multiple pathways like transcription, chromatin modifications, and cell cycle regulation. These pathways control essential processes such as cell growth and differentiation in the body. Through these mechanisms, the genes may help to regulate embryonic development and maintain tissue homeostasis in adults. \\n\\n]0.92324
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"671 RANDOM \n", - "672 RANDOM \n", - "673 RANDOM \n", - "674 RANDOM \n", - "675 RANDOM \n", - "676 RANDOM \n", - "677 RANDOM \n", - "678 RANDOM \n", - "679 RANDOM \n", - "680 RANDOM \n", - "681 RANDOM \n", - "682 RANDOM \n", - "683 RANDOM \n", - "684 RANDOM \n", - "685 RANDOM \n", - "686 RANDOM \n", - "687 RANDOM \n", - "688 RANDOM \n", - "689 RANDOM \n", - "690 RANDOM \n", - "691 RANDOM \n", - "692 RANDOM \n", - "693 RANDOM \n", - "694 RANDOM \n", - "695 RANDOM \n", - "696 RANDOM \n", - "697 RANDOM \n", - "698 RANDOM \n", - "699 RANDOM \n", - "700 RANDOM \n", - "701 RANDOM \n", - "702 RANDOM \n", - "703 RANDOM \n", - "704 RANDOM \n", - "705 RANDOM \n", - "706 RANDOM \n", - "707 RANDOM \n", - "708 RANDOM \n", - "709 RANDOM \n", - "\n", - "prompt_variant geneset \\\n", - "568 EDS-0 \n", - "569 EDS-1 \n", - "570 FA-0 \n", - "571 FA-1 \n", - "572 HALLMARK_ADIPOGENESIS-0 \n", - "573 HALLMARK_ADIPOGENESIS-1 \n", - "574 HALLMARK_ALLOGRAFT_REJECTION-0 \n", - "575 HALLMARK_ALLOGRAFT_REJECTION-1 \n", - "576 HALLMARK_ANDROGEN_RESPONSE-0 \n", - "577 HALLMARK_ANDROGEN_RESPONSE-1 \n", - "578 HALLMARK_ANGIOGENESIS-0 \n", - "579 HALLMARK_ANGIOGENESIS-1 \n", - "580 HALLMARK_APICAL_JUNCTION-0 \n", - "581 HALLMARK_APICAL_JUNCTION-1 \n", - "582 HALLMARK_APICAL_SURFACE-0 \n", - "583 HALLMARK_APICAL_SURFACE-1 \n", - "584 HALLMARK_APOPTOSIS-0 \n", - "585 HALLMARK_APOPTOSIS-1 \n", - "586 HALLMARK_BILE_ACID_METABOLISM-0 \n", - "587 HALLMARK_BILE_ACID_METABOLISM-1 \n", - "588 HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 \n", - "589 HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 \n", - "590 HALLMARK_COAGULATION-0 \n", - "591 HALLMARK_COAGULATION-1 \n", - "592 HALLMARK_COMPLEMENT-0 \n", - "593 HALLMARK_COMPLEMENT-1 \n", - "594 HALLMARK_DNA_REPAIR-0 \n", - "595 HALLMARK_DNA_REPAIR-1 \n", - "596 HALLMARK_E2F_TARGETS-0 \n", - "597 HALLMARK_E2F_TARGETS-1 \n", - "598 HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 \n", - "599 HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 \n", - "600 HALLMARK_ESTROGEN_RESPONSE_EARLY-0 \n", - "601 HALLMARK_ESTROGEN_RESPONSE_EARLY-1 \n", - "602 HALLMARK_ESTROGEN_RESPONSE_LATE-0 \n", - "603 HALLMARK_ESTROGEN_RESPONSE_LATE-1 \n", - "604 HALLMARK_FATTY_ACID_METABOLISM-0 \n", - "605 HALLMARK_FATTY_ACID_METABOLISM-1 \n", - "606 HALLMARK_G2M_CHECKPOINT-0 \n", - "607 HALLMARK_G2M_CHECKPOINT-1 \n", - "608 HALLMARK_GLYCOLYSIS-0 \n", - "609 HALLMARK_GLYCOLYSIS-1 \n", - "610 HALLMARK_HEDGEHOG_SIGNALING-0 \n", - "611 HALLMARK_HEDGEHOG_SIGNALING-1 \n", - "612 HALLMARK_HEME_METABOLISM-0 \n", - "613 HALLMARK_HEME_METABOLISM-1 \n", - "614 HALLMARK_HYPOXIA-0 \n", - "615 HALLMARK_HYPOXIA-1 \n", - "616 HALLMARK_IL2_STAT5_SIGNALING-0 \n", - "617 HALLMARK_IL2_STAT5_SIGNALING-1 \n", - "618 HALLMARK_IL6_JAK_STAT3_SIGNALING-0 \n", - "619 HALLMARK_IL6_JAK_STAT3_SIGNALING-1 \n", - "620 HALLMARK_INFLAMMATORY_RESPONSE-0 \n", - "621 HALLMARK_INFLAMMATORY_RESPONSE-1 \n", - "622 HALLMARK_INTERFERON_ALPHA_RESPONSE-0 \n", - "623 HALLMARK_INTERFERON_ALPHA_RESPONSE-1 \n", - "624 HALLMARK_INTERFERON_GAMMA_RESPONSE-0 \n", - "625 HALLMARK_INTERFERON_GAMMA_RESPONSE-1 \n", - "626 HALLMARK_KRAS_SIGNALING_DN-0 \n", - "627 HALLMARK_KRAS_SIGNALING_DN-1 \n", - "628 HALLMARK_KRAS_SIGNALING_UP-0 \n", - "629 HALLMARK_KRAS_SIGNALING_UP-1 \n", - "630 HALLMARK_MITOTIC_SPINDLE-0 \n", - "631 HALLMARK_MITOTIC_SPINDLE-1 \n", - "632 HALLMARK_MTORC1_SIGNALING-0 \n", - "633 HALLMARK_MTORC1_SIGNALING-1 \n", - "634 HALLMARK_MYC_TARGETS_V1-0 \n", - "635 HALLMARK_MYC_TARGETS_V1-1 \n", - "636 HALLMARK_MYC_TARGETS_V2-0 \n", - "637 HALLMARK_MYC_TARGETS_V2-1 \n", - "638 HALLMARK_MYOGENESIS-0 \n", - "639 HALLMARK_MYOGENESIS-1 \n", - "640 HALLMARK_NOTCH_SIGNALING-0 \n", - "641 HALLMARK_NOTCH_SIGNALING-1 \n", - "642 HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 \n", - "643 HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 \n", - "644 HALLMARK_P53_PATHWAY-0 \n", - "645 HALLMARK_P53_PATHWAY-1 \n", - "646 HALLMARK_PANCREAS_BETA_CELLS-0 \n", - "647 HALLMARK_PANCREAS_BETA_CELLS-1 \n", - "648 HALLMARK_PEROXISOME-0 \n", - "649 HALLMARK_PEROXISOME-1 \n", - "650 HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 \n", - "651 HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 \n", - "652 HALLMARK_PROTEIN_SECRETION-0 \n", - "653 HALLMARK_PROTEIN_SECRETION-1 \n", - "654 HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 \n", - "655 HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 \n", - "656 HALLMARK_SPERMATOGENESIS-0 \n", - "657 HALLMARK_SPERMATOGENESIS-1 \n", - "658 HALLMARK_TGF_BETA_SIGNALING-0 \n", - "659 HALLMARK_TGF_BETA_SIGNALING-1 \n", - "660 HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 \n", - "661 HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 \n", - "662 HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 \n", - "663 HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 \n", - "664 HALLMARK_UV_RESPONSE_DN-0 \n", - "665 HALLMARK_UV_RESPONSE_DN-1 \n", - "666 HALLMARK_UV_RESPONSE_UP-0 \n", - "667 HALLMARK_UV_RESPONSE_UP-1 \n", - "668 HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 \n", - "669 HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 \n", - "670 T cell proliferation-0 \n", - "671 T cell proliferation-1 \n", - "672 Yamanaka-TFs-0 \n", - "673 Yamanaka-TFs-1 \n", - "674 amigo-example-0 \n", - "675 amigo-example-1 \n", - "676 bicluster_RNAseqDB_0-0 \n", - "677 bicluster_RNAseqDB_0-1 \n", - "678 bicluster_RNAseqDB_1002-0 \n", - "679 bicluster_RNAseqDB_1002-1 \n", - "680 endocytosis-0 \n", - "681 endocytosis-1 \n", - "682 glycolysis-gocam-0 \n", - "683 glycolysis-gocam-1 \n", - "684 go-postsynapse-calcium-transmembrane-0 \n", - "685 go-postsynapse-calcium-transmembrane-1 \n", - "686 go-reg-autophagy-pkra-0 \n", - "687 go-reg-autophagy-pkra-1 \n", - "688 hydrolase activity, hydrolyzing O-glycosyl compounds-0 \n", - "689 hydrolase activity, hydrolyzing O-glycosyl compounds-1 \n", - "690 ig-receptor-binding-2022-0 \n", - "691 ig-receptor-binding-2022-1 \n", - "692 meiosis I-0 \n", - "693 meiosis I-1 \n", - "694 molecular sequestering-0 \n", - "695 molecular sequestering-1 \n", - "696 mtorc1-0 \n", - "697 mtorc1-1 \n", - "698 peroxisome-0 \n", - "699 peroxisome-1 \n", - "700 progeria-0 \n", - "701 progeria-1 \n", - "702 regulation of presynaptic membrane potential-0 \n", - "703 regulation of presynaptic membrane potential-1 \n", - "704 sensory ataxia-0 \n", - "705 sensory ataxia-1 \n", - "706 term-GO:0007212-0 \n", - "707 term-GO:0007212-1 \n", - "708 tf-downreg-colorectal-0 \n", - "709 tf-downreg-colorectal-1 \n", - "\n", - "prompt_variant v1 \\\n", - "568 [ The nine genes are associated with extracellular matrix (ECM) components and their regulators. Mechanism: The proteins coded by these genes could be involved in the regulation of the expression of ECM components, which can contribute to the formation of the physical integrity of the ECM and its interaction with the cellular environment. ] \n", - "569 [ This list of genes is enriched in proteins involved in the Extracellular Matrix (ECM) protein network, which is a component of the larger Cell Adhesion and Morphogenesis (CAM) pathway. Specifically, the genetic list is enriched for components involved in the processes of collagen fibril formation, collagen fibril organization, extracellular matrix (ECM) protein network assembly, ECM protein network stabilization, epidermal cell fate commitment, epithelial tube growth and branching morphogenesis, collagen modification and deposition, and zinc-finger protein motif binding.\\n\\nMechanism: The ECM protein network mediates cell-cell and cell-matrix interactions in order to regulate the adhesive, motile, and proliferative states of cells. It consists of a variety of molecules, including ECM proteins, which serve as substrates to guide cell migration, growth and differentiation. ECM proteins are those that contain one or more structural domains capable of interacting with the ECM components, such as extracellular domains, as well as those containing adhesive domains. \\n\\n] \n", - "570 [COULD NOT PARSE\\nHypothesis: The genes in this list are likely involved in the regulated repair of DNA double strand breaks due to replication-mediated damage, with the coordinated action of the Fanconi Anemia protein complex and the shared components of the ubiquitin ligase complex.] \n", - "571 [ Several genes involved in DNA repair and homologous recombination processes, such as FANCL, RAD51C, FANCE, MAD2L2, ERCC4, FANCA, BRCA2, FANCF, XRCC2, BRIP1, FANCD2, SLX4, FANCB, FANCG, UBE2T, RAD51, PALB2, and FANCC, were observed to be statistically enriched for terms related to DNA damage recognition and repair, DNA damage response, and homologous recombination processes.\\n\\nMechanism: These genes enable the cellular response to double-stranded breaks (DSBs) by providing components of the DNA damage recognition and repair variety. They also function in the homologous recombination pathway for DNA repair, which is used for error-free repair of damaged DNA strands. \\n\\n] \n", - "572 [ Enrichment analysis of this list has revealed that many of the genes are involved in energy metabolism and fatty acid metabolism, such as ATP1B3, ACOX1, ACADM, SLC19A1, SLC25A10, PGM1, UCP2, GPX3 and GPX4. They are also related to adipogenesis, with genes such as ADIPOR2, APLP2, LEP, ADIG and ADIPOQ. Lastly, several of the genes are involved in cholesterol and bile acid synthesis, such as DHCR7, DHRS7, CYP4B1 and HMGCR.\\n\\nMechanism: The genes identified as being involved in energy metabolism and fatty acid metabolism appear to share a common mechanism in which these molecules are generated from multiple sources to form energy. The genes involved in adipogenesis appear to be related to the regulation and development of fat cells and adipose tissue. Similarly, the genes involved in cholesterol and bile acid synthesis appear to be related to the synthesis of these molecules from multiple sources.\\n\\n] \n", - "573 [ This term enrichment test revealed a group of genes associated with energy metabolism, regulation of cell death, cell proliferation and signaling, DNA replication/remodeling, RNA processing, and lipid metabolism.\\nMechanism: This group of genes may be involved in binding, regulating, or expressing other proteins in order to influence the cell's metabolic and signaling status. \\n] \n", - "574 [ This enrichment test examines a list of 73 human genes and reveals enrichments for the functions related to cell surface molecules, cytokines, immunology, receptor signalling, transcriptional regulation and apoptosis.\\n\\nMechanism: These genes are involved in a variety of pathways that include cytokine signaling, cell surface molecules, transcriptional regulation, apoptosis, and receptor signaling.\\n\\n] \n", - "575 [ This analysis results in the enrichment of genes functions related to immune system regulation, including antigen presentation, signaling, B and T cell metabolism, cytokine production and chemotaxis. Mechanism: The genes identified in this list are involved in controlling a range of processes that are necessary for proper immune system functioning, such as antigen presentation, signaling pathways, metabolizing T and B cells, production and secretion of cytokines, and chemotaxis of immune cells. These functions are necessary for the body to defend itself against pathogens. ] \n", - "576 [COULD NOT PARSE] \n", - "577 [ \\nSummary: The genes are enriched in terms related to regulation, signaling, and metabolism.\\nMechanism: The genes are likely to be involved in molecular mechanisms governing cellular activities and pathways, with signaling pathways such as Wnt, MAPK, and PKA pathways playing an important role. \\n] \n", - "578 [ \\n\\nSummary: A set of 34 genes related to extracellular matrix formation and maintenance, fibrous tissue development, vascular development, and extracellular secreted signaling. \\n\\nMechanism: Together, these genes encode proteins involved in multiple signaling pathways to regulate the development, maintenance and repair of the extracellular matrix (ECM), including fibrous, collagen, and laminin-fibrillin proteins, along with proteins involved in vascular regulation, cell-cell communication and migration, and extracellular secreted signaling molecules. \\n\\n] \n", - "579 [ Genes in this list are primarily associated with development, vascular remodeling and cell-cell communication.\\nMechanism: These genes likely play a role in various aspects of development, including morphogenesis, tissue development, extracellular matrix organization, inflammation, vascular remodeling and cell-cell communication.\\n] \n", - "580 [COULD NOT PARSE] \n", - "581 [\\nSummary: The genes in this list are involved in a wide variety of processes, including development, growth, morphology, and molecular signaling.\\nMechanism: These genes appear to be involved in the regulation of cellular processes by mediating signals that modulate development, growth and morphology.\\n] \n", - "582 [\\nSummary: The list of genes provided is enriched for terms relating to cell migration, membrane receptor signaling, and glycoprotein metabolism.\\nMechanism: These gene functions serve to coordinate cell migration and receptor-mediated signaling, as well as metabolism. \\n] \n", - "583 [\\nSummary: The genes provided are involved in diverse biological pathways related to cell signaling, development, transcription, and metabolism.\\nMechanism: The genes likely represent an underlying biological mechanism that is involved in cellular proliferation and the regulation of gene expression.\\n] \n", - "584 [ The list of human genes given is statistically significantly enriched for the gene functions of transcriptional regulation/control, cell-cycle/apoptosis, and immune responses.\\nMechanism: The genes listed encode proteins involved in transcriptional regulation through control pathways such as the activation of caspases, the inhibition of cyclin-dependent kinase activity, and the upregulation of apoptosis-related proteins. They also encode molecules involved in immune-related processes such as the binding and activation of proinflammatory cytokines, the formation of interferon gamma receptor complexes, and the regulation of major histocompatibility complex class I molecules. \\n] \n", - "585 [COULD NOT PARSE] \n", - "586 [\\nSummary: The genes listed are enriched in terms related to metabolic pathways, lipid transport, and development of connective tissues.\\nMechanism: The functions of the genes appear to involve a number of metabolic pathways, such as fatty acid and bile acid synthesis, xenobiotic metabolism, and steroidogenesis, as well as pathways related to cellular transport and signaling, including those related to lipid transport and receptor-mediated signal transduction.\\nIn addition, several of the genes are involved in connective tissue formation, as well as development of digits and limbs.\\n] \n", - "587 [COULD NOT PARSE] \n", - "588 [COULD NOT PARSE] \n", - "589 [\\nSummary: The genes populated are predominantly involved in lipid metabolism (eg. HMGCR, PMVK, FDPS), transcription regulation (eg. ACTG1, NRAF), cellular adhesion (eg. CD9, ANXA13, COUNTY), and other development related processes (eg. S100A11, MVD, IDI1).\\nMechanism: The genes are associated with a number of different functions but are likely involved in maintaining cellular homeostasis, regulating transcription, and participating in development processes.\\n] \n", - "590 [\\nSummary: Several of the human genes on this list play a role in extracellular matrix formation, inflammatory response, and proteolytic activities.\\nMechanism: The common functional mechanisms included in this term enrichment test are the regulation of the inflammatory response, regulation of extracellular matrix formation, and proteolytic activities.\\n] \n", - "591 [\\nSummary: The genes identified are predominantly involved in matrix molecular regulation, pathways related to proteolysis and coagulation, signal transduction, and extracellular matrix organization.\\nMechanism: The genes act as regulators of specific molecular functions and as mediators of signal transduction pathways. The identified genes are likely involved in the processing and remodeling of the extracellular matrix because of their relation to proteolysis and other matrix-related functions.\\n] \n", - "592 [\\nSummary: These genes are enriched in functions related to extracellular matrix organization, immune system/inflammation/interferon response, and transcription factor activity.\\nMechanism: These genes could be involved in a pathway that is responsible for coordinating and controlling aspects of extracellular matrix organization, immune system/inflammation/interferon response and the activity of transcription factors.\\n] \n", - "593 [ This enrichment test revealed several terms related to immune system functioning, cell adhesion and regulation, and extracellular matrix organization, which are likely the underlying mechanisms behind the commonalities among the listed genes. Enriched terms include: immunoglobulin like domains; B cell activation; T cell receptor signaling pathway; integrin mediated cell adhesion; apoptosis; regulation of transcription; signal transduction; receptor mediated endocytosis and exocytosis; extracellular matrix organization; and calcium mediated signaling. \\n\\nMechanism: These findings suggest that the genes involved in this test collectively contribute to a range of processes related to immune system functioning, cell adhesion, extracellular matrix organization, and intracellular communication. \\n\\n] \n", - "594 [ Gene functions related to DNA and RNA metabolism, protein synthesis, DNA damage repair, transcription, and chromatin organization are significantly over-represented.\\nMechanism: It is likely that many of these genes are involved in the same pathway related to the fundamental processes of DNA replication, transcription, and protein synthesis.\\n] \n", - "595 [ \\nSummary: These genes are enriched for roles in DNA replication, transcription, translation and post-translational modifications.\\nMechanism: These genes are involved in various biological processes, including DNA replication, transcriptional regulation, translation, and post-translational modifications involved in gene expression. \\n] \n", - "596 [ Genes on the list are primarily involved in DNA cell cycle and replication, gene regulation, transcription and translation, chromatin modification, and DNA repair. \\n\\nMechanism: The genes are involved in the regulation of DNA replication and transcription, chromatin modification, and DNA repair processes during cell cycle progression. \\n\\n] \n", - "597 [\\nSummary: The genes in the list are involved in diverse functions related to DNA replication, transcription, chromosome condensation and transcriptional regulation.\\nMechanism: These functions are likely related to canonical pathways and processes involved in coordinating and regulating DNA replication, the transcription of genetic information into proteins, and maintaining appropriate chromosome condensation states.\\n] \n", - "598 [COULD NOT PARSE] \n", - "599 [ Our enrichment test uncovered several terms related to extracellular matrix function, morphogenesis, and reproduction/growth. These terms include extracellular matrix organization; morphogenesis; collagen production; matrix metalloproteinase activity; glycoprotein metabolism; cytoskeletal component organization; regulation of growth and reproduction; and regulation of skin morphogenesis. Mechanism: The underlying biological mechanisms related to these genes likely involve the extracellular matrix (ECM), which provides structural and biochemical support to the cells and tissues. ECM components, such as collagen, can regulate activities such as cell signaling, structure formation and growth, and gene expression. Morphogenesis is likely modulated by ECM components, as well as by signaling pathways. ] \n", - "600 [\\nSummary: The list of genes identified are associated with cell morphology, homeostasis and regulation, innervation, and cellular metabolism.\\n] \n", - "601 [ Our analysis of the 34 human genes suggests an enrichment of gene functions related to cell signaling, regulation and morphology, including: immunological response; cell adhesion; transcription regulation; cell migration; development of epidermis, bones and muscle; transport of proteins between cellular compartments; and apoptosis. \\n\\nMechanism: These gene functions are likely related to the regulation of diverse mechanisms within the cell, such as protein-protein interactions, transcription signaling, and intracellular trafficking. \\n\\n] \n", - "602 [\\nThe genes in the list are enriched for functions in the genomics and cytoskeletal processes, as well as immune response and extracellular modification.\\n\\nMechanism:\\nThe gene functions are implicated in various biological processes that are orchestrated by genetic control and/or regulation pathways. These pathways typically involve protein interactions and cellular processes. Additionally, these pathways often correlate to extracellular modification, immune response, and/or modulation of receptor signaling.\\n\\n] \n", - "603 [COULD NOT PARSE] \n", - "604 [ This list of genes is highly enriched for metabolic processes such as fatty acid metabolism and oxidation, cholesterol biosynthesis, glycogen metabolism, nucleotide metabolism and transport, and electron transport activity. This suggests that the list reflects a highly coordinated and interconnected network of metabolic processes to maintain the homeostasis of the cell. Enriched terms include: fatty acid metabolism; oxidation of lipids; cholesterol biosynthesis; glycogen metabolism; nucleotide metabolism; nucleotide transport; nucleotide biosynthesis; electron transport activity; enzyme regulation and regulation of metabolic pathways; and apoptosis. \\nMechanism: This set of genes likely acts through a number of interconnected pathways to maintain cellular homeostasis. Lipid metabolism is known to be important in cellular signaling, while other metabolic pathways interact with each other through enzyme regulation and regulation of metabolic pathways. Additionally, many of the genes are associated with cell death pathways, suggesting that these can also act in a coordinated way to respond to stress and maintain cellular homeostasis. \\n] \n", - "605 [\\n\\nSummary: There is a strong enrichment of genes involved in metabolic processes, energy production and storage, lipid metabolism and transport, as well as acetyl-CoA biosynthesis and catalysis.\\n\\nMechanism: The identified genes likely influence the metabolic processes, energy production and storage, lipid metabolism and transport, as well as acetyl-CoA biosynthesis and catalysis by modulating cellular processes, protein and enzyme production, and functional metabolic pathways, such as oxidation and fatty acid metabolism.\\n\\n] \n", - "606 [\\nGene functions involved in cell cycle regulation, DNA replication, and chromatin remodeling are enriched among the provided list of genes. This could reflect a core pathway of regulation that has been conserved across multiple species.\\n\\nMechanism:\\nThe enriched terms suggest that this gene list could be involved in the G1/S transition of the cell cycle, DNA replication, and chromatin remodeling or modification. Specifically, cell cycle progression and DNA replication is likely driven by cyclin B-CDK1 activation, which is facilitated by Cks1b and Cdc25A mediated activation and either Wee1 or Cdc20-anaphase promoting complex-cyclosome (APC/C)-mediated inhibition. Chromatin modification is likely driven by histone H2A and H2B acetylation and lysine methylation, which involve various proteins, such as Hmga1, Hmgn2, H2az1, H2bc12, and Myc.\\n\\n] \n", - "607 [ \\nSummary: This list of human genes are primarily involved in nuclear processes such as DNA replication, gene transcription, chromatin remodelling and cell cycle control.\\nMechanism: The genes may be involved in the regulation of a number of biological processes such as DNA repair, cell cycle regulation, gene expression, and gene regulation.\\n] \n", - "608 [\\nSummary: Our term enrichment test shows that many of the genes on this list are involved in various aspects of developmental and morphogenic processes, including digit development, cell differentiation, angiogenesis, and metabolism.\\nMechanism: These genes are likely to be involved in biological pathways involving the development and maintenance of cellular structure, binding and transporting of molecules, energy metabolism and other metabolic processes, and cell signaling.\\n] \n", - "609 [ The list of genes are primarily involved in essential metabolic functions in the cell. Specifically, they are involved in carbohydrate and energy metabolism, microtubule assembly, DNA binding and replication, actin cytoskeleton dynamics, ion channel regulation, transcriptional regulation, and cell adhesion. The mechanism is likely related to the coordination of these processes in order to maintain homeostasis and proper cell functioning.\\n\\nSummary: Genes mainly involved in metabolic processes. \\n\\nMechanism: Coordination of these processes to maintain cellular homeostasis.\\n\\n] \n", - "610 [\\nSummary: Many of the genes listed are involved in the development and morphogenesis of neurons and other cells. \\nMechanism: These genes are likely to work together to regulate cell and tissue shaping and differentiation, providing for the formation of specialized neuron structures and neural pathways. \\n] \n", - "611 [\\n\\nSummary: This group of genes is commonly associated with morphogenesis, cell adhesion, development, and neuronal signaling\\nMechanism: The underlying biological mechanism is likely related to the regulation of cell proliferation, migration, differentiation, and neural plasticity during development. \\n] \n", - "612 [\\nSummary: The genes in this list are highly enriched for functions related to membrane transport, energy metabolism, ribosomal proteins, and nucleic acid binding.\\nMechanism: The underlying biological mechanism or pathway may involve regulation and control of cellular functions and transcription activity, with multiple proteins interacting to ensure proper functioning of a variety of cellular pathways.\\n] \n", - "613 [\\n\\nSummary: The human genes identified in this list are predominantly involved in cell development, gene expression, organogenesis and nucleic acid metabolism.\\n\\nMechanism: The human genes identified in this list are likely to be involved in processes that regulate cell development, including transcriptional regulation and organogenesis, as well as nucleic acid metabolism. \\n\\n] \n", - "614 [COULD NOT PARSE] \n", - "615 [ \\nSummary: Genes related to cell development, cell metabolism, transcription, and regulation are enriched in this set.\\nMechanism: These genes regulate a variety of cellular processes such as cell cycle regulation, transcriptional regulation, and energy metabolism.\\n] \n", - "616 [ The gene set is enriched for genes involved in cell growth, cell detection/regulation, and immunity. Mechanism: These genes are likely involved in a number of pathways that contribute to cell and tissue development, growth, and regulation, as well as regulation of the immune system. ] \n", - "617 [COULD NOT PARSE] \n", - "618 [ Genes in the list are enriched for the Cellular Processes of Pain Sensing and Signal Transduction; Chemotaxis; Cytokine-mediated Signaling Pathway; Leukocyte Transendothelial Migration; Immune Response; and Platelet Activation. There is a potential mechanism for the underlying biological pathway whereby these genes interact in signal transduction to facilitate pain sensing and immune response, including ligand-receptor interactions, signal transduction of cytokines, and the actions of transcription factors, such as those encoded by JUN, REG1A, STAT1, STAT2, STAT3 and TLR2.\\n\\n] \n", - "619 [\\nSummary: The list of genes are significantly enriched for functions of immunity, signaling, and transcription regulation\\nMechanism: These genes are likely involved in the coordination of immune responses and the regulation of pathways for signal transduction and transcription.\\n] \n", - "620 [ Genes associated with human immunity, inflammation and signalling pathways are enriched.\\n\\nMechanism: These genes are likely involved in pathways related to human immunity, inflammation and signalling, either directly or through regulation of transcription and translation activity.\\n\\n] \n", - "621 [ The list of genes is significantly enriched for terms related to immune cell signaling, cell movement, and cell surface receptor activity. \\nMechanism: These genes are likely involved in the regulation of pathways involved in initiating and responding to inflammation, cell migration, cell–cell interactions, and immune cell receptor-mediated signaling.\\n] \n", - "622 [ Our analysis of the list of human genes have revealed a set of enriched terms related to the activation and inhibition of immune signaling pathways, and their functions in regulating inflammation. Specifically, we observed an increased prevalence of molecules and proteins involved in mechanism activating or inhibiting the Nuclear Factor Kappa B (NF-κB), Interferon Regulatory Factor (IRF) as well as JAK-STAT pathways. Terms such as \"inflammatory response\", \"neutrophilic activation and degranulation\", \"T-Cell receptor signaling pathway\", \"Toll-Like Receptor Cascade\", \"Type I Interferon Signaling\", and \"Inflammatory Regulation\" were enriched in this gene set.\\n\\nMechanism: The genes in this list are involved in multiple pathways that are related to the modulation of inflammatory responses and can be broadly summarized as either regulating cytokine production or modulating the inflammatory response by inhibiting the NF-κB, IRF and JAK-STAT pathways. While there is significant overlap of these genes with the NF-κB pathway, the IRF and JAK-STAT pathways are also significant contributors, as evidenced by the enriched terms. \\n\\n] \n", - "623 [ This group of genes is significantly enriched for functions related to immune system regulation, interferon response, apoptosis, and cell membrane regulation.\\n\\nMechanism: This list of genes is likely involved in both innate and adaptive immune responses, functioning to modulate the level of inflammation and cytokine production, as well as to induce cell death and regulate cell membrane composition. Specific terms enriched that pertain to these functions include interferon signalling pathways, interferon gamma activity, interferon regulatory factor activity, status response to interferon, apoptosis, lipid binding, calcium ion binding, and neutrophil mediated immunity. \\n\\n] \n", - "624 [\\nSummary: A majority of the genes were found to be involved in important immune response and cell signaling pathways.\\nMechanism: The immune response and cell signaling pathways are likely to be regulated by cytokines and transcription factors such as those related to interferon responses and nuclear factor kappaB-dependent transcriptional regulation.\\n] \n", - "625 [\\nSummary: The enriched terms among the list of genes includes pathways involved in immunity, interleukin regulation, transcriptional regulation, inflammation, cell signaling, and apoptosis.\\nMechanism: Signaling and pathways involving these genes are likely to regulate these biological processes.\\n] \n", - "626 [ Genes in this term enrichment test were found to be enriched for terms related to the development of bones, morphogenesis, growth and maintenance, cell-cell signaling and communication, protein modification, and transport.\\nMechanism: It is likely that the genes identified in this term enrichment test make up a biological pathway that is involved in the development of bones, growth and morphogenesis, and other processes related to regulating cell-cell signaling and communication, protein modification, and transport.\\n] \n", - "627 [\\nSummary: The list of genes are found to be significantly associated with physiological processes related to morphogenesis, cell-cell communication and development, and hormone regulation.\\nMechanism: The genes are likely to be involved in a variety of biological mechanisms, such as cell-signalling, cellular differentiation and cell-cycle, as well as hormone mediated processes.\\n] \n", - "628 [ Genes in this list are predominantly involved in signal transduction pathways and morphogenesis; specific terms enriched include signal transduction, cell morphogenesis, response to stimulus, angiogenesis, regulation of molecular function, and extracellular matrix organization.\\nMechanism: The list of genes are likely to be involved in signaling pathways involving kinases, growth factors and receptors, as well as involvement in morphogenesis processes such as cell-cell adhesion, cellular movement and cell differentiation.\\n] \n", - "629 [\\nSummary: This set of genes appears to be involved in a variety of cellular processes, including morphogenesis and tissue development, cell signaling, and immune regulation.\\nMechanism: These genes appear to be involved in transcription modulation, signal transduction pathways, and regulation of cell adhesion and migration.\\n] \n", - "630 [COULD NOT PARSE] \n", - "631 [ Enriched terms show a commonality among these genes for processes related to cytoskeletal organization and migration of the cell, cell division, DNA replication and repair, and targeting proteins to the correct place in the cell.\\nMechanism: The proteins represented by these genes likely play a role, either directly or indirectly, in the regulation of a number of vital cell processes including cell division, DNA replication and repair, and targeting proteins to the right place in the cell.\\n] \n", - "632 [COULD NOT PARSE] \n", - "633 [ The list of genes is enriched in functions related to protein synthesis, energy metabolism, cellular transport, and immune response.\\nMechanism: It is likely that these genes are co-regulated in networks that are responsible for cellular energy production and regulation, protein synthesis and degradation, and immune response.\\n] \n", - "634 [ The genes appear to be involved in processes related to RNA and protein synthesis, ATP-related processes, cytoskeleton organization and assembly, transcription, and chromatin remodeling.\\n\\nMechanism: The genes likely play a role in regulating various cellular processes, such as gene expression, signal transduction, and translation, via multiple pathways that are related to RNA processing, translation initiation, mRNA stability, and DNA replication.\\n\\n] \n", - "635 [ Genes from this list are mainly involved in translation, transcription, and post-transcriptional modification processes. Specifically, these genes are involved in mRNA splicing, mRNA transport, mRNA stability, protein synthesis, ribosome biogenesis, RNA interference, and chromatin remodeling. Mechanism: These genes likely operate according to the canonical mechanisms of gene expression, by which genes are transcribed, spliced, and translated into proteins. These processes are tightly regulated and involve a complex network of interacting proteins, RNAs, and other molecules. ] \n", - "636 [COULD NOT PARSE] \n", - "637 [\\nSummary: The gene set is enriched for terms related to cell activation and proliferation, as well as DNA replication and replication-associated processes such as transcription and translation.\\n] \n", - "638 [ Gene expression and structure, cytoskeletal structure and dynamics, calcium regulation and signaling, cell adhesion and migration, cell death biochemistry, and metabolic regulation are all enriched terms based on the genes provided that are common to these roles in humans.\\n\\nMechanism: The underlying biological mechanism for the enriched terms observed in this list of genes is likely related to the wide range of regulatory roles these genes and gene products have in maintaining cellular health and enabling proper physiological functions and development at the cellular level. \\n\\n] \n", - "639 [ The list of genes show an enrichment for terms related to the extracellular matrix, cytoskeleton, muscle structure and development, neuromuscular structure, ion channels, and ion transport. \\nMechanism: These genes appear to be involved in various intra- and extracellular pathways and mechanisms related to the formation and maintenance of the cytoskeleton, neuromuscular structure, and muscle formation, as well as ion transport and channel proteins serving as important mediators of electrical and chemical signals in cells. \\n] \n", - "640 [\\nThe list of genes are involved primarily in aspects of embryonic development, regulation of cell cycle, and calcium signaling.\\nMechanism: The genes function primarily in regulating various aspects of cell signaling and cycle regulation during embryonic development, such as down-regulation of Notch signaling, regulation of Wnt signaling and Hedgehog signaling pathways, cell morphogenesis, and calcium signaling.\\n] \n", - "641 [COULD NOT PARSE] \n", - "642 [\\n\\nSummary: This list of genes is enriched for terms related to mitochondrial activity, electron transport chain, oxidative phosphorylation, and metabolic regulation/activation.\\nMechanism: This list of genes are likely to be involved in the various steps of mitochondrial activity, electron transport chain, oxidative phosphorylation, and metabolic regulation/activation. \\n] \n", - "643 [\\nSummary: The list of genes is predominantly involved in cellular respiration and metabolism, as evidenced by the enriched terms related to mitochondrial bioenergetics, ion transport and metabolite-binding proteins.\\nMechanism: The commonality amongst the genes likely contributes to the normal functioning of mitochondria, and is involved in the bioenergetic processes that involve ATP synthesis, as well as maintaining electron transfer and transporter function.\\n] \n", - "644 [ Analysis of this gene list revealed a significant enrichment of terms in functions related to cytoskeleton alteration, calcium homeostasis modulation, ubiquitin-proteasome pathway activation, cell cycle control, and transcriptional and post-transcriptional regulation.\\n\\nMechanism: These functions likely act in concert to mediate the regulation of cellular growth, differentiation, and survival.\\n\\n] \n", - "645 [ Genes in this list are associated with regulation of the cell cycle, DNA damage repair, cell signaling and processes involved in cell growth, apoptosis, and immune modulation. The genes are enriched for functions related to transcription, chromatin dynamics, cell adhesion molecules, and cytokines. \\nMechanism: The regulation of these genes (directly or indirectly) is likely to be part of a complex network of pathways, signaling molecules, and protein-protein interactions. \\n] \n", - "646 [\\nSummary: This gene set is enriched in functions related to pancreas development, glucose metabolism, cell motility, and neural development. \\nMechanism: It is hypothesized that these genes function in a network to control developmental processes relevant to pancreas development, glucose metabolism, cell motility and neural development.\\n] \n", - "647 [\\nSummary: This term enrichment test identified gene functions related to morphogenesis, neural development, signal transduction, insulin hormone secretion, transcription regulation, and transcription factor activity.\\nMechanism: These genes likely work together to facilitate the development of body organs, neuronal function and pathways, insulin secretion, and transcription factor activity.\\n] \n", - "648 [COULD NOT PARSE] \n", - "649 [ Genes involved in the list are associated with lipid metabolism, lipid storage and transport, steroid metabolism, regulation of transcription and, importantly, regulation of the cell cycle. \\nMechanism: An enrichment of pathways associated with lipid, steroid and transcriptional metabolism, as well as regulation of the cell cycle.\\n] \n", - "650 [ Gene expression, DNA repair and maintenance, growth factors, cellular signaling pathways and lipid metabolism \\nMechanism: Regulation of gene expression through the activation of transcription and DNA repair and maintenance pathways is likely involved. The enriched terms related to growth factors suggests that the list of genes may be involved in cell proliferation and differentiation. Signaling pathways and lipid metabolism may be involved in cell-cell communication and energy-related processes, respectively.\\n] \n", - "651 [ The list of genes given are involved in cell cycle regulation, gene transcription, transcription factor activation and signal transduction pathways.\\nMechanism: The genes included in this list are involved in various mechanisms of cell cycle regulation, gene transcription, transcription factor activation and signal transduction pathways. These involve the regulation of cell cycle progresses such as synthesis, growth, proliferation and differentiation, as well as the operations of protein kinases, transcription factors, receptor proteins and other essential molecules. \\n] \n", - "652 [COULD NOT PARSE] \n", - "653 [COULD NOT PARSE] \n", - "654 [\\nSummary: This list of genes is enriched for terms involving redox regulation, antioxidant defense and detoxification of reactive oxygen species, peroxisomal and mitochondrial biogenesis, and cell metabolism.\\nMechanism: The underlying biological mechanism involves the production and regulation of reactive oxygen species, adaptation to oxidative stress and related forms of damage, and the maintenance of redox homeostasis.\\n] \n", - "655 [ \\nSummary: 13 genes are enriched for functions associated with redox regulation, metabolism, cell cycle regulation, and transcriptional regulation.\\nMechanism: These genes likely play a role in the regulation of a cell's redox balance, metabolism, cell cycle progression and gene expression.\\n] \n", - "656 [\\nThe gene list is enriched for functions related to cell signaling, protein regulation, and cell cycle control, as well as complex development processes such as morphogenesis, organogenesis and cytoskeletal regulation.\\nMechanism: A wide range of mechanims are at work here, which involve the transcription and translation of genes to encode proteins and the regulation of their functions to mediate both common and specific biological processes.\\n] \n", - "657 [ Genes related to organ development, morphogenesis, cytoskeletal proteins, signal transduction.\\nMechanism: Proteins from the list are likely used as part of a unified pathway for organ/tissue development and morphogenesis, and involved in cell cycle checkpoint regulation and signal transduction.\\n] \n", - "658 [ The list of genes analyzed in this term enrichment test is related to pathways associated with cell growth and development, such as MAPK, TGF-β, Wnt/β-catenin, Hippo and transcriptional regulations. Specifically, pathway enrichment of genes included muscle and tissue morphogenesis, regulator of G-protein signaling and inflammatory response pathway.\\n\\nMechanism: The general mechanism is that the genes are involved in signaling pathways for cell processes such as growth, differentiation and apoptosis. These signals modulate the expression of downstream genes and ultimately lead to changes in cell shape and other cellular activities.\\n\\n] \n", - "659 [COULD NOT PARSE] \n", - "660 [ These genes are mainly involved in developmental processes, inflammation, immunomodulation, inflammation, cell signalling and metabolic pathways.\\nMechanism: These genes are likely to be involved in pathways leading to the regulation of morphogenesis and tissue development, control of cell proliferation and apoptosis, regulation of immune system immune response, regulation of inflammation and activation of metabolic pathways.\\n] \n", - "661 [\\nSummary: The genes are enriched for terms related to gene transcription, cytoskeleton formation, and signal transduction. \\nMechanism: The genes are likely involved in a wide range of processes, including transcriptional regulation, actin cytoskeleton organization, cytokine receptor signaling and NF-kB signaling pathways.\\n] \n", - "662 [ The genes in the list may be generally involved in processes such as mRNA transcription, ribosome biogenesis and protein folding, as well as nucleolar and spliceosomal activity. \\nMechanism: These genes likely regulate cellular processes such as protein production and transport, RNA processing, and cell cycle control. \\n] \n", - "663 [\\nSummary: The enrichment analysis on the list of genes revealed a common theme of gene functions related to metabolism, protein synthesis, and post-translational modifications.\\nMechanism: The observed gene functions suggest a pathway of metabolic and protein regulatory processes that involve the synthesis of proteins, post-translational modifications such as phosphorylation, and other processes related to metabolism and folding.\\n] \n", - "664 [ The genes identified are associated with protein kinases, cellular signaling pathways, and development of skeletal and extracellular matrix components.\\nMechanism: These identified genes may be involved in complex regulation and signaling pathways, focusing on post-translational phosphorylation and transcriptional regulation, as well as the control of growth, development and remodeling of skeletal structures.\\n] \n", - "665 [ Many of the genes are clustered around those involved in structure, development and regulation. They are involved in processes such as mitotic regulation, bone morphogenesis, morphogenesis of specific organs and tissues, regulation of signaling pathways, regulation of transcription, regulation of cell proliferation, cellular responses to external stimuli, protein phosphorylation and DNA binding.\\n\\nMechanism: These genes are likely to be involved in the regulation and development of several different processes, including the regulation of cell proliferation, transcription, morphogenesis of organs and tissues, and mitotic regulation. These mechanisms are likely to be controlled by the interactions among gene products, signaling pathways and regulatory components such as transcription factors.\\n\\n] \n", - "666 [ Proteins involved in development, cell growth, gene transcription, and metabolism are enriched.\\nMechanism: These proteins are involved in a variety of biological processes that underlie development and cell growth, as well as affecting gene transcription and metabolism.\\n] \n", - "667 [ Genes in this list are mainly involved in cell growth, morphogenesis, regulation of transcription, signal transduction of receptors, DNA/protein activity and metabolism. More specifically, the terms enriched in this list of genes are cell proliferation, cell cycle regulation, DNA replication and repair, signal transduction, calcium signaling, apoptosis, lipid metabolism and oxygen pathway.\\n\\nMechanism: The genes in this list mainly participate in the regulation of various biological processes through their encoding for proteins that act as transcription factors, receptors, and enzymes. These proteins are activated by a variety of signals including DNA damage, growth factors and hormones to induce changes in gene expression and cellular behavior. They also control cell growth, differentiation and metabolism by regulating DNA, protein, lipid and oxygen pathways, ultimately resulting in morphogenesis and cell proliferation. \\n\\n] \n", - "668 [COULD NOT PARSE] \n", - "669 [\\nSummary: The gene list appears to mostly contain genes involved in Wnt signaling, Notch signaling, transcription regulation and cell cycle regulation processes.\\nMechanism: The underlying biological mechanism appears to be the regulation of processes such as transcription, cell cycle, and Wnt and Notch signaling that may in turn affect the morphogenesis and development of various organs and tissues.\\n] \n", - "670 [ \\nSummary: The genes in the list are found to be involved primarily in cell signalling, development, and immunity processes.\\nMechanism: The numerous genes with enriched terms are involved in coordinating both intra- and extracellular activity through signal transduction pathways and receptor-mediated signaling, with downstream effects on cellular growth, differentiation, and function within various organs and systems in the body.\\n] \n", - "671 [ The enrichment test found that the genes listed have common functions associated with cell signaling and immune regulation, such as signal transduction, growth factor production and response, immune response and modulation, calcium homeostasis, transcription factors, development and differentiation, receptor binding, and cytokine production.\\n\\nMechanism: The enrichment test suggests that these genes may contribute to signal transduction pathways that facilitate cell proliferation, differentiation, and survival; growth factor production and signal transduction; immune response and modulation; calcium homeostasis; transcription factor activity including regulation of gene expression; development and differentiation; receptor binding and signal transduction; and cytokine production.\\n\\n] \n", - "672 [COULD NOT PARSE] \n", - "673 [\\nThe list of genes provided encode transcription factors associated with early development of embryonic stem cells.\\nMechanism: Transcriptional regulation via these transcription factors control the expression of other genes related to embryogenesis and stem cell development.\\n] \n", - "674 [\\nSummary: This term enrichment test on the list of human genes shows enrichment for terms related to extracellular matrix organization and cell adhesion, morphogenesis and morphological changes, and cell signaling. \\nMechanism: The underlying biological mechanisms may involve a combination of protein-protein interactions, transcriptional regulation and extracellular matrix modifications.\\n] \n", - "675 [COULD NOT PARSE] \n", - "676 [\\nSummary: The list of genes are involved in morphogenesis, development, transcription regulation, cellular signalling and ion transport.\\nMechanism: The genes are likely to be involved in a variety of biochemical and molecular pathways pertaining to the specified functions.\\n] \n", - "677 [ These genes are primarily involved in development and signaling pathways, particularly morphogenesis, neuronal growth, and neuronal system development. Mechanism: These genes facilitate cell-cell communication and signaling, allowing for cells to coordinate their functions together and form efficiently organized tissues and organs. ] \n", - "678 [COULD NOT PARSE] \n", - "679 [ The genes listed were significantly over-represented for processes related to muscle formation and human body structure, such as muscle and skeletal development, skeletogenesis, and myogenesis. \\n\\nMechanism: The set of genes is involved in multiple pathways related to muscle formation and structure in the human body, such as muscle and skeletal development, skeletogenesis, and myogenesis. These pathways likely involve the regulation of protein synthesis and biosynthesis, as well as processes related to muscle contraction and relaxation. \\n\\n] \n", - "680 [ These genes are involved in signaling pathways, vesicle/lipid trafficking, and cellular adhesion related processes.\\nMechanism: These genes act as regulators of nutrients, cell metabolism, and cytoskeletal organization. They are also involved in endocytosis, exocytosis, and the regulation of intercellular adhesion and motility.\\n] \n", - "681 [\\nSummary: The genes in this list are associated with processes related to membrane trafficking, receptor signaling, protein proteolysis, and lipid metabolism. \\nMechanism: The underlying biological mechanism is likely regulation of membrane trafficking, receptor signaling, protein proteolysis, and lipid metabolism. \\n] \n", - "682 [ An analysis of gene functions in these 10 genes shows an enrichment of terms associated with metabolism, including glycolysis, aerobic glycolysis, and gluconeogenesis.\\n\\nMechanism: This suggests a possible underlying biological mechanism in which glycolysis and gluconeogenesis pathways are deployed by cells in order to provide sufficient energy to cope with various metabolic demands.\\n\\n] \n", - "683 [ The human genes provided in this list are enriched for metabolic functions involved in glycolysis and pentose phosphate pathways.\\nMechanism: The mechanism likely involves the direct or indirect control of enzymatic activities through the coordinated activity of multiple genes.\\n] \n", - "684 [COULD NOT PARSE] \n", - "685 [COULD NOT PARSE] \n", - "686 [\\n \\nSummary: The genes in this list are involved in various aspects of biological processes, ranging from cell growth and development to immune response and proteolysis.\\n \\nMechanism: The genes interact in multiple overlapping pathways to influence cellular processes such as immune response and protein degradation. \\n \\n] \n", - "687 [ Several pathways related to cellular signaling and signalling transduction are enriched among this set of human genes. Specifically, phosphatidylinositol signalling, vascular endothelial growth factor receptor signalling, progesterone-mediated oocyte maturation, NF-kB signaling and neuroprotection are all enriched with five or more genes represented in the set, suggesting that the underlying biological mechanism could be related to these pathways.\\n\\nMechanism: Several pathways related to cellular signaling and signalling transduction.\\n\\n] \n", - "688 [ These human genes are involved in cellular functions related to glycosaminoglycan metabolism, lysosomal and catabolic pathways, as well as digit and skeletal development. The genes are enriched for functions in carbohydrate digestion and absorption; glycosaminoglycan and glycan metabolism; lysosomal, peroxisomal, and catabolic processes; and digit, skeletal, and limb morphogenesis. \\nMechanism: The genes likely act by providing enzymes, carriers, and structural proteins that together play essential roles in the transport and metabolism of carbohydrates, as well as help form and shape the skeleton and digits during embryonic development. \\n] \n", - "689 [ The human genes in this list are mostly related to glycoside hydrolase (GH) activity, but also include proteins involved in chitin and mucin biosynthesis, as well as cysteine protease and lysosomal activities. Most of the genes have either a glycoside hydrolase activator or a lysosomal enzyme function. \\n] \n", - "690 [COULD NOT PARSE] \n", - "691 [\\nSummary: These genes are mainly involved in Immunoglobulin Function and Blood Coagulation. \\nMechanism: The terms enriched for these genes are related to the immune system and blood clotting pathways, specifically those related to Immunoglobulins, B Cell Receptors, and Fibrinogen-related proteins. \\n] \n", - "692 [ \\nSummary: Genes involved in DNA damage repair and meiotic recombination processes\\nMechanism: Genes in the list are involved in DNA damage recognition, DNA double-strand break repair, meiotic recombination, and chromosome segregation.\\n] \n", - "693 [ Enrichment test revealed that genes are related to DNA repair, replication, and splicing.\\n\\nMechanism: The commonalities in the function of the genes revealed in the enrichment test suggest that there may be a biological pathway that is responsible for creating and maintaining a stable genetic system. This may involve DNA repair to combat mutation and damage, replication to create new copies, and splicing for the proper expression of genes.\\n\\n] \n", - "694 [ This enrichment test indicates that the listed genes are involved in multiple pathways that are involved in cell proliferation, apoptosis, and molecular transport in diverse cell types. Specifically, some of the enriched terms associated with these genes include mechanisms involved in cell cycle checkpoints, cell adhesion/motility complexes, transcriptional complexes, protein modifications, and RNA processing complexes. \\nMechanism: These pathways likely affect cell proliferation, apoptosis, and molecular transport by responding to a variety of environmental stimuli, including calcium-based signaling, growth factor-mediated signaling, and oxidative stress. \\n] \n", - "695 [ The analysed genes are mostly involved in calcium binding, apoptotic regulation, and immune modulation, all of which are important mechanisms for a variety of biologic processes.\\n\\nMechanism: The mechanism is likely related to the genes' ability to modulate calcium and apoptotic pathways as well as reduce oxidative stress and influence immune effectors.\\n\\n] \n", - "696 [COULD NOT PARSE] \n", - "697 [ Analysis of the genes provided shows that the genes are enriched for functions relating to energy production and metabolism, protein biosynthesis and folds, cell regulation, growth and development, and protein turnover. \\n\\nMechanism: The likely underlying biological mechanism behind these functions is likely related to the regulation, management and production of energy and metabolites to carry out processes such as cell growth and to synthesize proteins which are essential for the functioning of the cell, cell signaling and related pathway activities.\\n\\n] \n", - "698 [ PEX proteins are involved in peroxisome biogenesis and formation. \\nMechanism: PEX proteins play a role in driving the biogenesis of peroxisomes, a type of organelle that plays a role in various metabolic functions. \\n] \n", - "699 [ The provided genes are all peroxisomal biogenesis factor genes and are associated with peroxisomal biogenesis, protein transport, and oxidative damage resistance.\\n\\nMechanism: These factors regulate the assembly of the peroxisome, a subcellular organelle involved in fatty acid metabolism, carbohydrate metabolism, and oxidative damage resistance.\\n\\n] \n", - "700 [ The genes in this list are all associated with a cellular carboxyl-methyl transferases, a type of protein involved in RNA and DNA metabolism. The proteins are associated with development and growth, particularly that of cell structural elements such as gene transcription and transcriptional regulation. \\nMechanism: The mechanism involves carboxyl-methyl transferase proteins that modulate gene expression and the communication between transcription factors and the DNA strand.\\n] \n", - "701 [ These genes are involved in a number of processes related to DNA replication and repair, including DNA replication and repair, nucleosome assembly, telomere maintenance, and transcriptional regulation.\\n \\nMechanism: Genes LMNA, WRN, and BANF1 are all involved in several mechanism related to the general processes of DNA replication, repair, and transcriptional regulation through the assembly and maintenance of the different levels of chromatin structure. LMNA is involved in the assembly and disassembly of the nuclear lamina, a type of intermediate filament that helps to anchor chromosomal proteins to the nuclear envelope. WRN is involved in telomere maintenance, which is critical for accurate chromosomal replication and stability. Finally, BANF1 is involved in a number of DNA repair processes, including translesion DNA synthesis, homologous recombination, and non-homologous end joining. These processes are essential for the accurate repair and replication of DNA molecules, and all require an understanding of, and proper interactions between, transcription and chromatin structure. \\n\\n] \n", - "702 [\\n\\nSummary: This term enrichment test identified genes involved in signal transduction, ion transport, and regulation of neurotransmitter release.\\nMechanism: This is likely related to the regulation of excitatory and inhibitory signal transmission, potentially mediated by ion channels and signal transduction pathways associated with the G-protein coupled receptors, voltage-gated K+ and Na+ channels, and ligand-gated ion channels.\\n] \n", - "703 [COULD NOT PARSE] \n", - "704 [ This list of genes is related to muscle, central and peripheral nervous system development, as well as protein and lipid transport and metabolism. \\nMechanism: The genes appear to be involved in regulatory pathways for growth and development of the skeletal and nervous systems via coordination of morphology, protein and lipid synthesis, and transport.\\n] \n", - "705 [\\n\\nSummary: Analysis of the genes yielded significant enrichment of terms related to protein transport, development of the central nervous system, skeletal structure and muscle formation.\\n\\nMechanism: The function of these genes likely reflects the underlying biological pathways for the development and maintenance of different organ systems, including the central nervous system, muscular system, and skeletal structure. \\n\\n] \n", - "706 [ This list of genes is enriched for terms related to signal transmission and transduction, specifically the G Protein-Coupled Receptor (GPCR) family, which is associated with cell-signaling pathways and regulation of receptor activities. The specific terms enriched include G alpha subunit signaling, related GPCR activation and signaling, G Protein-Coupled Receptor (GPCR) function, and dimerization. \\n\\nMechanism: This set of genes is involved in pathways that involve the G protein-coupled receptor (GPCR) family. GPCRs can bind to extracellular molecules, such as hormones and neurotransmitters, and then activate signaling pathways inside the cell, leading to the activation of intracellular proteins, including G proteins. The G proteins then facilitate the exchange of proteins such as cAMP, DAG, and calcium ions into the cell, in order to create a signal cascade and ultimately effect changes to the cell’s behavior.\\n\\n] \n", - "707 [\\nSummary: The list of genes is involved in the regulation cellular signaling and development of the nervous system.\\nMechanism: The list of genes is likely transmitting signals through G proteins, phosphorylation cascade, and calcium signaling pathways to regulate the development of the nervous system, including alterations in the nervous system structure, indoleamine metabolism, and neurotransmission.\\n] \n", - "708 [ The gene list includes members of the nuclear receptor superfamily, molecules involved in transcription regulation, epigenetic regulation, cell cycle regulation, DNA binding and chromatin remodeling, developmental processes and cell signaling pathways, and components of the nuclear lamina and nuclear matrix.\\n\\nMechanism: The enriched terms suggest a molecular pathway underlying gene regulation, where transcription factors and chromatin reorganization molecules interact with nuclear receptors and other molecular mechanisms in order to regulate gene expression. Moreover, the gene list may represent a mechanism involved in the regulation of cell growth, differentiation and development.\\n\\n] \n", - "709 [ The genes provided are involved in developmental pathways and functions, such as transcriptional regulation, chromatin modification, morphogenesis, cardiovascular development and differentiation.\\nMechanism: These genes are associated with a wide range of cellular processes, primarily related to embryonic development, including fetal growth and development, stem cell differentiation, and postnatal growth. \\n] \n", - "\n", - "prompt_variant v2 \\\n", - "568 [\\n\\nSummary: The genes in the list are associated with a broad range of functions involved in skeletal development, collagen production and other extracellular matrix processes.\\n\\nMechanism: The mechanism appears to involve different genes acting on multiple pathways related to the synthesis, remodeling, and maintenance of extracellular matrix components.\\n\\n] \n", - "569 [ The genes listed above are associated with various development processes and tissue formation, such as collagen production, connective tissue development, matrix remodeling, and zinc finger protein regulation.\\nMechanism: The underlying known mechanism is the combination of transcriptional regulation and post-translational modification of the proteins encoded by these genes.\\n] \n", - "570 [ The list of genes is significantly and specifically associated with homologous recombination and DNA repair, as evidenced by an enrichment in terms related to these processes, such as \"dna repair\", \"homologous recombination\", \"excision repair\", and \"nuclease activity\".\\n\\nMechanism: The genes in this list are involved in a variety of DNA repair activities, such as excision repair and homologous recombination. These processes are important for maintaining the correct sequence of DNA and avoiding mutations that can lead to disease. \\n\\n] \n", - "571 [COULD NOT PARSE] \n", - "572 [ \\nSummary: A term enrichment test on the above list of genes based on biological classification hierarchies has identified terms related to metabolic and cellular functions that are statistically over-represented.\\nMechanism: These commonalities likely indicate a shared pathway, mechanism or process as related to metabolic and cell regulation functions.\\n] \n", - "573 [\\nSummary: This list of genes are mainly involved in energy metabolism and signal transduction. \\nMechanism: The genes in this list form a biochemical pathway responsible for the production of energy and for the detection and execution of cellular signals.\\n] \n", - "574 [ Genes related to the list are largely enriched for immune signalling/activation, regulation of cell cycle and differentiation, and transcriptional regulation.\\nMechanism: This likely indicates involvement of these genes in the processes of immune signalling, development or tissue remodelling, and metabolic regulation.\\n] \n", - "575 [COULD NOT PARSE\\nHypothesis: It is likely] \n", - "576 [COULD NOT PARSE] \n", - "577 [ \\nThe genes provided are significantly enriched in terms related to gene transcription and regulation, protein translation and metabolism, cytoskeletal organization, and lipid metabolism.\\nMechanism: These genes are likely to be involved in the regulation of genetic expression, transcriptional regulation, protein translation and metabolism, improvement of cell structure, and lipid metabolism. \\n] \n", - "578 [ The list of gene terms are involved primarily in cell communication processes like extracellular matrix organization, adhesion, and cell surface interactions. Specifically, they encode proteins involved in the aggregation of endothelial cells and vascularization processes. Mechanism: The proteins encoded by the genes in the list are likely involved in regulating the growth, development, extracellular environment, and adhesiveness of cells. ] \n", - "579 [ \\n\\nSummary: This list of genes appears to be involved in growth and morphogenesis of cells, including development of muscle, bone, and neuronal networks. \\nMechanism: Growth appears to be mediated by signals from cytokines and hormones, most notably VEGFA and PDGF, and mediated by transmembrane and extracellular matrix proteins, including LUM, VTN, and S100A4.\\n] \n", - "580 [\\nThis list of genes is related to development, tissue morphogenesis, contractile organs, extracellular matrix and cytoskeletal proteins. Enriched terms include bone, joint, muscle and connective tissue development; cell adhesion; adhesion receptor complex formation; signal transduction; and receptor-mediated signaling cascades.\\n\\nMechanism:\\nThese genes likely act together to facilitate the intricate networks of molecular and cellular pathways involved in development, homeostasis, and tissue repair. These include extracellular matrix formation and remodeling; cell adhesion; and signaling pathways associated with cell migration, proliferation, differentiation, and growth. The genes may work in tandem to promote changes in gene expression, stability, and intercellular communication involved in development and tissue repair processes.\\n\\n] \n", - "581 [ Our term enrichment analysis of the list of genes provided revealed statistically over-represented terms in gene function associated with cell adhesion, cell migration, migration and interaction, cytoskeletal organization, actin cytoskeletal regulation, signaling pathways, and regulation of the actin cytoskeletal organization. \\nMechanism: These results suggest that the underlying biological mechanism likely involves cytoplasmic signaling and regulation of the cytoskeletal organization, which would provide mechanical integrity to the cells, their adhesion to neighboring cells, and their migratory ability. This is supported by the evidence that many of the enriched terms relate to cell adhesion, migration and interaction, and cytoskeletal organization.\\n] \n", - "582 [ The list of genes is enriched for terms related to cell regulation, signal transduction, cell adhesion, protein folding, extracellular matrix organization.\\nMechanism: The list of genes are likely involved in a variety of cell regulation mechanisms such as activating responses to extracellular signals, influencing protein folding and assembly, regulating cell adhesion, and mediating phosphorylation cascades. \\n] \n", - "583 [ This list of genes appears to be involved in the development and maintenance of various organs, tissues and cellular processes. Specifically, enriched terms for this gene list include cell adhesion and migration; cell signaling; cell differentiation; protein kinase and phosphatase activities; transcription and DNA metabolism; immunomodulation; glycosylation and carbohydrate metabolism; and cell growth and proliferation. \\n\\nMechanism: The genes in this list play a role in a variety of molecular mechanisms that are important for normal development and tissue homeostasis. On the molecular level, these genes are involved in cell-cell adhesion, translation and translation regulation, signal transduction, and other processes. Moreover, the genes in this list regulate the expression of various cellular receptor, kinase, and phosphatase pathways, which may lead to downstream changes in cell growth, proliferation, and differentiation. \\n\\n] \n", - "584 [\\n\\nSummary: The human genes provided in this list are mainly related to apoptosis, transcription, cell cycle progression, and inflammation.\\nMechanism: These genes likely act together to execute pathways related to the regulation of cell growth and maintenance, DNA replication and repair, oxidative stress response, and immune system activation.\\n] \n", - "585 [ This list of genes is enriched for terms related to cell death regulation, inflammation, immune reaction, and growth and morphogenesis, which is a mechanism indicative of homeostasis in several biological functions.\\t\\n\\nMechanism: Expression of these genes contributes to cell survival by regulating the balance between cell death and survival, restraint of pro-inflammatory responses and activation of pro-inflammatory responses, promoting expression of genes involved in innate and adaptive immune responses and playing a part in promoting tissue growth, remodeling and morphogenesis. \\n\\n] \n", - "586 [ This list of genes is enriched for functions related to lipid metabolism and transport, development of vital organs, and cell signaling pathways.\\nMechanism: The enrichment of these genes suggests roles in cellular metabolic processes such as breakdown, transport, and synthesis of lipids, as well as cell-signaling pathways involved in development of vital organs such as liver, heart, and brain. \\n] \n", - "587 [ A large proportion of the genes provided are involved in lipid and fatty acid metabolism, including the movement and processing of lipids, such as through cytochrome P450 superfamily enzymes, hydroxyacyl-CoA dehydrogenases, SLCO1A2, FADS2 and SLC27A2. As well as lipid metabolism, genes are also enriched for other metabolic processes, such as glutamate metabolism (IDH1, 2, HSD17B6) and serine metabolism (SERPINA6 and PIPOX). In addition, there are genes associated with the regulation of transcription factors, including RXRA, LCK, and optineurin, as well as those involved in oxidative stress (SOD1, CTH, PNPLA8).\\n\\nMechanism: The enriched terms implicate a cross-regulatory and potentially inter-linked metabolic network involving lipid, fatty acid and disulphide bridge metabolism, with potential connections to oxidative stress response and gene expression regulatory mechanisms. \\n\\n] \n", - "588 [\\nSummary: A number of genes involved in lipid and cholesterol metabolism, cell signaling and regulation, development, cell adhesion, apoptosis and transcription have been identified.\\nMechanism: Genes associated with lipid and cholesterol metabolism are involved in regulating the synthesis, degradation and transport of lipids, while genes associated with cell signaling and regulation are involved in regulating cell growth, differentiation and apoptosis. Additionally, genes related to development, apoptosis, and transcription act in the regulation of cell adhesion, differentiation and development.\\n] \n", - "589 [ Proteins involved in lipid and lipid metabolism pathways, related to cholesterol control.\\nMechanism: Proteins involved in cholesterol regulation, such as HMGCR, PMVK, FADS2, SREBF2, S100A11, and MVK are likely to be involved in the upregulation and modulation of cholesterol levels. These proteins regulate the breakdown of fatty acids and also mediate the synthesis of bile acids, both of which are important in cholesterol metabolism. ] \n", - "590 [ Genes in this list represent functions related to extracellular matrix remodeling, angiogenesis and vascular development, immune response and platelet activation, collagen and fibronectin metabolism and regulation, and endocytosis and signal transduction.\\n] \n", - "591 [ The term enrichment test suggests that proteins involved in cell adhesion, proteolysis regulation, and interactions between extracellular proteins and cells are significantly enriched in this gene list. \\n\\nMechanism: These proteins likely act together in a coordinated manner to modulate cell adhesion, proteinase activity, and communication between cells. \\n\\n] \n", - "592 [ Our term enrichment test suggests that the commonalities in function of these genes are related to the regulation of cell growth and development, signal transduction pathways, and immunity. Specifically enriched terms include development of tissue and organs; signal transduction; cell surface receptor binding; response to stimulus; immune system; immune response; and cytokine activities.\\n\\nMechanism: These functions likely occur through a combined mechanism of modulating transcription factors, receptor-ligand binding, cytokine release and signaling, and a balance of intracellular concentrations of proteins and lipids.\\n\\n] \n", - "593 [\\nThe list of genes provided is heavily enriched for functions related to cellular signalling, inflammatory responses, and cellular stress response.\\nMechanism: These genes are typically involved in regulating and mediating signalling pathways, activating and responding to the inflammatory response, activating and functioning in the cell stress response, and facilitating cell-cell interactions.\\n] \n", - "594 [ The common functions for the human genes are involved in various developmental processes and DNA replication, with enrichment of terms such as \"developmental process\" and \"DNA replication\". \\n\\nMechanism: The genes act together to facilitate a variety of molecular processes in the cellular pathways to support embryonic and post-natal development, as well as DNA replication, transcription, and translation.\\n\\n] \n", - "595 [\\nSummary: Our genes are primarily involved in nucleic acid metabolism, transcription, and post-transcriptional modifications.\\nMechanism: The proteins encoded by the genes in our list likely play roles in the various biochemical steps involved in transcription, such as chromatin remodelling, pre-mRNA splicing, DNA repair, RNA polymerization, mRNA processing, mRNA transport, and translation initiation.\\n] \n", - "596 [ The provided gene list is over-represented for transcriptional regulation, chromatin modification and mitotic division/cell cycle components.\\nMechanism: The underlying mechanism of this gene set is that the enrichments are involved in the regulation of transcription for gene expression, maintenance of chromatin and DNA structure and function, and regulation of mitotic division and cell cycle checkpoints.\\n] \n", - "597 [ This list of genes is enriched for functions related to DNA replication and repair, chromatin modification, transcriptional and translational regulation, network formation, spindle formation and kinesin and dynein motor proteins. Mechanism: These genes are likely to function as part of an interconnected cellular pathway and/or network that allows for the generation of daughter cells and the coordination of transcriptional activity and post-translational modifications. ] \n", - "598 [ The list of genes provided show enrichment for terms relevant to extracellular matrix composition, cell adhesion and motility, cell-matrix interactions, growth factor and cytokine signaling, and matrix remodeling. \\n\\nMechanism: The mechanisms underlying the enrichment of these terms likely involve cell-matrix interactions, growth factor and cytokine signaling, and matrix remodeling.\\n\\n] \n", - "599 [ The identified genes are enriched for terms related to skeletal morphogenesis, cell-cell adhesion and motility, extracellular matrix production and remodeling, development and differentiation of connective tissue, collagen production and turnover, and cytokine and chemokine signaling. \\n\\nMechanism: It is likely that these genes are involved in mechanisms that coordinate protein interactions during skeletal development and morphogenesis, cell adhesion and migration, and the maintenance of a healthy extracellular matrix. In addition, these genes likely contribute to the production and turnover of extracellular matrix components such as collagens and chemokines and cytokines involved in development and differentiation of connective tissue. \\n\\n] \n", - "600 [\\nThis list of human genes was analysed in a term enrichment test. The test revealed that many of these genes were involved in a common pathway which supports normal cellular processes including DNA replication, transcription and gene expression, cell growth and differentiation, protein processing and trafficking. Furthermore, many of these genes were involved in bone morphogenesis and cancer-related pathways.\\n\\nMechanism:\\nThe underlying biological mechanism likely involves a number of distinct pathways, each with its own mechanism of action. Common processes shared by many of these genes include DNA replication, translation, and post-translational modification. Additionally, several of these genes are involved in cell-cell adhesion and the control of cellular migration and matrix remodeling, indicating roles in tissue morphogenesis. Furthermore, many of these genes are involved in intracellular signaling and signaling pathways that are essential for the processing and coordination of external and internal signals, which can ultimately result in cell growth, differentiation, and apoptosis.\\n\\n] \n", - "601 [ \\nSummary: The gene list includes genes involved in transcriptional regulation, signal transduction, membrane transport and lipid biosynthesis.\\nMechanism: The genes exhibit common patterns of transcriptional regulation and signal transduction, with a focus on protein-protein interactions and membrane transport.\\n] \n", - "602 [ Genes related to extracellular matrix organization, cellular adhesion and migration, cell mobility and growth factor-mediated signaling pathways;\\nMechanism: This gene list suggests that extracellular matrix organization, adhesion and migration, cell motility, and growth factor signaling pathways are involved in gene expression in these genes. \\n] \n", - "603 [ The genes are enriched for terms related to the structural organization of cells, transcriptional regulation, signal transduction, and immune responses.\\n\\nMechanism: These genes likely comprise a network that influences the physical and biochemical properties of the cell, including its membrane integrity, signal transduction pathways, gene expression, and immunomodulatory functions. \\n\\n] \n", - "604 [\\nSummary: The genes shown here are involved in a wide range of metabolic pathways and cellular functions, such as energy metabolism, lipid metabolism, amino acid metabolism, DNA damage repair, and cell signaling.\\n] \n", - "605 [ Genes are enriched in roles associated with lipid metabolism and the cell cytoskeleton. Both pathways involve important signaling and metabolic roles. Mechanism: Lipid metabolism pathways involve synthesizing and degrading lipids, transporting lipids, and their oxidation. The cell cytoskeleton is involved in a variety of functions, including building of cell membranes, cell motility and traffic. ] \n", - "606 [ \\nSummary: This list of human genes are enriched for functions related to cell cycle and/or development, such as DNA replication and transcription, and may be involved in a variety of pathways and processes.\\nMechanism: These genes may be involved in pathways related to DNA replication, transcription and expression, and cell cycle regulation.\\n] \n", - "607 [COULD NOT PARSE] \n", - "608 [COULD NOT PARSE] \n", - "609 [ \\nThis gene list is enriched for proteins involved in structural development and energy metabolism, such as structural proteins and enzymes of glycolysis, the pentose phosphate pathway, and the tricarboxylic acid (TCA) cycle. These terms are supported by evidence from gene ontologies (GO) assigned to the genes in the list.\\n\\nMechanism: \\nThe list of genes is involved in pathways which facilitate the efficient production and utilization of energy, such as glycolysis, the pentose phosphate pathway, and the tricarboxylic acid (TCA) cycle. They are also involved in the dynamic assembly of integral structures, such as the cytoskeleton, cell adhesion serve, proteoglycan synthesis, and extracellular matrix formation.\\n\\n] \n", - "610 [COULD NOT PARSE] \n", - "611 [ The genes appear to be involved in the development of various cell types, organs, and other growth processes, including neuron formation, cell adhesion and migration, signal transduction, tissue morphogenesis, and development of the nervous system. \\nMechanism: These genes likely act in a number of ways to promote and coordinate these processes, including recognizing and binding signaling molecules, relaying signals to other molecules, and affecting transcription of target genes. \\n] \n", - "612 [ The list of genes has a statistically significant enrichment of terms related to cellular metabolism, energy production and transport, cytoskeleton modification and remodelling, and cell adhesion. \\nMechanism: The molecular mechanisms involve the transfer of energy, metabolic pathways, and the coordination of cellular transport and reorganization.\\n\\n] \n", - "613 [ The enriched terms for this list of human genes suggest a common functional theme in organ development, morphogenesis and growth, immune system function, and transport processes. Enriched terms include: embryonic development; skeletal system development; organogenesis; morphogenesis; growth; immune system process; cell motility; steroid hormone receptor activity; receptor signaling pathway; transport; endocytosis; and cellular homeostasis.\\n\\nMechanism: The underlying biological mechanism suggested by the enriched gene functions is that these genes are involved in various organ and skeletal system development processes, in particular morphogenesis and growth, as well as immune system and transport processes. Specifically, these genes are involved in organogenesis, morphogenesis, growth, and cell motility through receptor signaling pathways, endocytosis, transport processes, and cellular homeostasis. Additionally, the genes are involved in steroid hormone receptor activity, further contributing to organ and skeletal system development.\\n\\n] \n", - "614 [ The list of genes is involved in a variety of pathways and functions related to cell differentiation, metabolism, protein processing, and the regulation of gene expression. Specifically, this list was enriched for terms related to cell cycle, remodeling proteins, stress response proteins, calcium signaling proteins, hypoxia-inducible factor proteins, transcription factors, chromatin-associated proteins, and kinases.\\n\\nMechanism: The overall mechanism of action of the genes appears to be related to the regulation of cellular processes via the modulation of expression of target genes, primarily through the regulation of epigenetic and transcriptional factors, in order to enable proper differentiation, metabolism, and protein processing. This is further supported by the enrichment of terms related to stress response proteins, calcium signaling proteins, hypoxia-inducible factor proteins, transcription factors, chromatin-associated proteins, and kinases.\\n\\n] \n", - "615 [ Genes identified in this set are associated with several DNA/RNA binding and regulatory processes, including transcription and epigenetic modification. Statistically over-represented functions in these genes include development, cell structure and movement, cell cycle and division, signal transduction, transport, and energy production; proteins involved in these processes include transcription factors, kinases, histones, and other enzymes. Mechanism: This enrichment likely reflects the underlying biological pathways governing various aspects of gene expression and regulation. ] \n", - "616 [\\nSummary: These genes are predominantly related to immunological functions, actin cytoskeleton organization, cell surface receptors, and pro-inflammatory regulation.\\nMechanism: The genes listed appear to be involved in the immune response, actin cytoskeleton organization, cell surface receptor-mediated signaling, and pro-inflammatory regulation.\\n] \n", - "617 [ The list of human genes provided are enriched for terms related to immunity, inflammatory response, cell growth, differentiation and development, and signaling pathways.\\n\\nMechanism: This underlying biological mechanism could involve proteins interacting with each other and coordinating pathways to govern immune response, inflammatory response, cell growth, differentiation, and development, as well as other cellular processes.\\n\\n] \n", - "618 [ This list of genes is enriched in terms related to cell signaling, cytokine production and regulation, regulation of gene expression and transcription, and cell adhesion.\\nMechanism: This list of genes promotes the core pathways of cell signaling, cytokine production and regulation, regulation of gene expression and transcription, and cell adhesion. This enables the body to respond to a variety of external signals, to recognize and respond to inflammation and stress, to produce the necessary molecules for the body to function correctly, and to hold the cell together so that it may adhere to corresponding cells and fulfill its role within the network of cells.\\n] \n", - "619 [ Increased expression of cytokines, chemokines, and interleukins; increased expression of developmental, signal transduction, and immune system pathways involved in cellular differentiation, cell motility and adhesion, signal transduction, and inflammation. \\nMechanism: The genes listed all appear to be involved in immune system, signal transduction and intercellular communication pathways. Through the identification of commonalities between the gene functions, inference can be made that these genes are involved in up-regulation of cytokines, chemokines, and interleukins involved in cellular differentiation, cell motility, adhesion, signal transduction and inflammation. \\n] \n", - "620 [COULD NOT PARSE] \n", - "621 [ The list of genes is enriched in functions related to the immune system, especially mediation of inflammatory response and cytokine production and signalling.\\nMechanism: The genes are involved in a variety of functions related to immune cell activation and cellular signaling, including cell adhesion, G-protein and receptor-coupled pathways, transcriptional regulation, cytokine and cytokine receptor binding, and lipid metabolism. \\n] \n", - "622 [COULD NOT PARSE] \n", - "623 [ Genes listed appear to be primarily involved in the regulation of interferon response pathways and the transcriptional control of interferon-stimulated genes. The genes appear enriched for the cellular pathways of immune response, inflammation, and cytokine signaling.\\n \\nMechanisms: The interferon response pathways activated in this population of genes modulate the expression of cytokines, chemokines, and antimicrobial and antiviral proteins, in order to activate an innate immune response to virus and bacteria. \\n\\n] \n", - "624 [ In this gene set, there are multiple genes that are enriched for functions related to immunology, such as antigen presentation, inflammatory responses, chemokine signaling, cell adhesion, and cytokine interactions. \\nMechanism: One hypothesis is that these genes are involved in an immune-mediated response related to their roles in antigen-presentation, inflammatory responses, the regulation of chemokines, and cell adhesion. \\n] \n", - "625 [ This list of genes is enriched in terms related to cell signaling, transcription regulation, and immune system regulation. Specifically, genes are enriched in pathways related to: interferon signaling; antigen processing, presentation, and recognition; cytokine signaling; cell cycle and DNA damage response; and apoptosis.\\n\\nMechanism: It appears that the genes identified in this list are functionally connected and may be involved in a larger underlying biological mechanism or pathway. The proteins associated with each gene are known to interact with one another and repress/activate various genes leading to the regulation of cell signaling, transcription, and immune system functions. This molecular regulation process is essential in the control of cellular functions and physiological behavior. \\n\\n] \n", - "626 [ The analysis of the list of human genes reveals that these genes are related to development, regulation, and signaling mechanisms within the cell. Specifically, the terms associated with development, such as digit development, neural development, immune system development and transcriptional regulation, are enriched. Additionally, terms related to signal transduction, such as G-protein coupled receptors, protein kinases, and guanine nucleotide exchange factors, are also enriched.\\n\\nMechanism:The mechanism underlying the term enrichment of the list of human genes is likely related to the fact that these genes play a role in a wide range of essential cellular processes. It is likely that signaling molecules and transcription signals coordinate these processes to enable proper development and homeostasis.\\n\\n] \n", - "627 [COULD NOT PARSE] \n", - "628 [ This list of gene names is enriched for genes involved in signal transduction, cell cycle control, and cell-to-cell adhesion.\\nMechanism: The enrichment of these genes indicates a shared biological pathway in which cellular communication, pathways, and networks are regulated by controlling the production of proteins and other molecules. This can lead to changes in other intracellular activities, such as cell cycle progression and adhesion. \\n] \n", - "629 [\\nSummary: This list of genes is enriched for terms related to cell adhesion and signal transduction, including terms such as integrin, chemokine receptor, protein kinase and G-protein-coupled receptor.\\nMechanism: These genes are involved in pathways important for cell adhesion, such as integrin and chemokine receptor-mediated interactions, as well as signal transduction pathways which include protein kinases, G-protein-coupled receptors and other associated proteins.\\n] \n", - "630 [\\n\\nSummary: The list of human genes have diverse enrichment in the functions of cell cycle control, cell adhesion, and cytoskeletal organization.\\nMechanism: These genes enable cells to interact with their environment and complete the cell cycle by organizing components, regulating activities, and controlling signaling pathways.\\n] \n", - "631 [ \\nSummary: The genes that were provided are statistically enriched for terms related to cell division, protein phosphorylation, chromatin remodeling, and microtubule binding and organization.\\nMechanism: These genes likely function in biological pathways related to spindle assembly, chromosome segregation and movement, cell-cycle control, and other processes related to mitosis. \\n] \n", - "632 [COULD NOT PARSE] \n", - "633 [\\nSummary: This list of genes is involved in a variety of pathways related to cell growth and development, including morphogenesis, transcription, and protein synthesis.\\nMechanism: The physiological processes induced by these genes likely work in concert to mediate a variety of cellular processes including cellular translation, metabolism, and signalling.\\n] \n", - "634 [\\nThe list of genes are involved in a variety of processes including, but not limited to, protein synthesis and modification, DNA replication, cell cycle regulation, and transcription regulation.\\nThis suggests that these genes may be involved in a co-dependent pathway or pathways that regulate cell growth, development, and gene expression.\\n] \n", - "635 [\\nSummary: This list of genes have overlapping functions in development, energy production, and regulation.\\nMechanism: There may be a pathway involved in controlling energy production, protein synthesis, and structural maintenance of cell components in development.\\n] \n", - "636 [ The enrichment test identified a set of genes related to protein and nucleic acid metabolism and cell cycle regulation. Specifically, genes involved in protein post-translational modifications, phosphorylation, transcription, translation, and ribosome biogenesis were enriched.\\n\\nMechanism: These gene functions are likely related to the underlying biological mechanism or pathway, since genes related to these processes have an essential role in regulatory activities and cell cycle control. ] \n", - "637 [ \\nSummary: Many of the genes listed appear to be related to chromatin and transcriptional regulation.\\nMechanism: Regulation of gene expression and chromatin structure via transcription factors and nucleosome remodeling enzymes. \\n] \n", - "638 [COULD NOT PARSE] \n", - "639 [COULD NOT PARSE] \n", - "640 [ These genes are associated with Notch receptor, transcription factor, and Wnt pathway signaling, which are involved in tissue and organ development.\\nMechanism: Notch receptor, Wnt, and transcription factor signaling pathways leads to a variety of processes such as morphogenesis, organogenesis, tissue development, cell fate determination, and cell interaction. \\n] \n", - "641 [\\nSummary: The genes in this list are associated with cell proliferation, morphogenesis and development, nerve system differentiation, and regulation of transcription.\\nMechanism: The genes likely function in pathways involved in the WNT and Notch signalling pathways, which have numerous roles in development and differentiation of different tissue types. \\n] \n", - "642 [COULD NOT PARSE] \n", - "643 [ Genes in this list are mainly associated with mitochondrial bioenergetics and associated pathways. Specifically, the terms \"mitochondrial electron transport chain complex activity\"; \"mitochondrial electron transport, NADH to ubiquinone\"; \"mitochondrial respiratory chain complex I activity\"; \"respiratory chain complex I assembly\"; \"respiratory chain complex III activity\"; and \"respiratory chain complex IV activity\" are found to be enriched in this gene set.\\n\\nMechanism: Mitochondria are dynamic organelles that are responsible for many of the metabolic pathways, including cellular respiration. A variety of mitochondrial electron transport complexes are involved in the production of energy, including complex I (NADH:ubiquinone oxidoreductase), complex III (ubiquinone:cytochrome c oxidoreductase), complex IV (cytochrome c oxidase), and complex V (ATP synthase). As these genes are associated with mitochondrial functions, it is possible that there is an underlying mechanism related to metabolic pathways and energy production within the mitochondria. \\n\\n] \n", - "644 [COULD NOT PARSE] \n", - "645 [COULD NOT PARSE] \n", - "646 [ Genes play diverse roles in the development of the pancreas, nervous system, and musculoskeletal system. Major term enrichment was found for pancreas development, nervous system development, development of neural structures, organogenesis, and transcriptional regulation. \\nMechanism: These genes are likely involved in a variety of biological mechanisms including, the regulation of morphogenesis, cell-to-cell adhesion, and protein synthesis pathways, as well as hormonal metabolism and signaling.\\n] \n", - "647 [ Analysis of these genes revealed common pathways related to metabolic regulation, neural development, and transcription/translation control. The terms enriched by these genes are neurogenesis; metabolism; transcriptional control; translation; morphogenesis; body patterning and organization; neurological system development; and cell differentiation.\\n\\nMechanism: Signaling pathways involved in neural development will have an influence on neurogenesis, while metabolic pathways will be involved in pathways that regulate glucose and lipid metabolism. Additionally, transcription and translation pathways are essential for regulating gene expression but also cell differentiation and morphogenesis. Finally, body patterning and organization rely on genes that control cell fate and cellular migration. \\n\\n] \n", - "648 [ The human genes given in the list are involved in metabolic biochemical pathways associated with lipid metabolism, stress response, mRNA transcription, DNA repair, skeletal and cartilage development, and cell migration. \\nMechanism: Metabolic enzymes and transport proteins appear to regulate these pathways, allowing for the synthesis and degradation of cellular compounds, as well as transporting molecules into and out of the cell to maintain physiological homeostasis.\\n] \n", - "649 [\\nSummary: Genes in this list are associated with a wide array of terms, including metabolism, transcription, regulation, transport and signaling.\\nMechanism: These genes likely play a role in a broad biological mechanism involving various metabolic pathways, transport, and regulatory functions.\\n] \n", - "650 [ The list of genes is enriched for terms related to signal transduction pathways and development, such as morphogenesis and cell differentiation.\\nMechanism: Signal transduction pathways are likely involved in the regulation of the gene functions, with particular importance of tyrosine kinase activity and modulation of relevant receptor activities.\\nHypothesis: The genes may be involved in the regulation of tissue development and cell differentiation.\\n] \n", - "651 [ \\n\\nSummary: This gene list covers a broad range of functions, including cell signaling, growth and survival, protein and lipid metabolism, transcription regulation, and cell cycle control.\\nMechanism: The genes in this list are likely involved in a variety of pathways that facilitate or regulate various cellular activities, such as receptor signaling, protein glycosylation, kinase activity, apoptosis, and G-protein interactions.\\n] \n", - "652 [ Genes listed are associated with vesicular transport, trafficking, and membrane fusion in the cell.\\nMechanism: Vesicular transport involves the formation of vesicles from the host membrane, trafficking of these vesicles through the cell and organelles, and fusion of the vesicles with host membranes for which these genes are responsible.\\n] \n", - "653 [ Enrichment test on a given list of human genes resulted in the identification of several enriched terms, which have important roles in post-translational modification, protein folding, protein synthesis, endocytosis, oligosaccharide metabolism, and lysosomal trafficking.\\n\\nMechanism: The mechanism behind this enrichment pattern is likely related to the various mechanisms regulated by these genes, such as the regulation of PTMs, protein folding, protein synthesis, endocytosis, oligosaccharide metabolism, and lysosomal trafficking.\\n\\n] \n", - "654 [\\nSummary: The list of genes is associated primarily with metabolic processes, defense against oxidative damage and DNA repair.\\nMechanism: These processes are likely related to cellular level metabolic regulation, protection against oxidative damage, and DNA damage repair.\\n] \n", - "655 [COULD NOT PARSE] \n", - "656 [ Genes associated with this list indicate enrichment for a variety of cell cycle control and chromatin remodeling processes, as well as protein ubiquitination, regulation of DNA replication, spindle assembly, and nuclear organization.\\n\\nMechanism: The enriched terms suggest that these genes are involved in a variety of related functions related to the regulation and maintenance of the cell cycle, chromatin remodeling, DNA replication, spindle assembly and nuclear organization.\\n\\n] \n", - "657 [COULD NOT PARSE] \n", - "658 [COULD NOT PARSE] \n", - "659 [ Our term enrichment analysis of these genes reveals an overrepresented pattern of general cellular processes related to the development and proliferation of cells, as well as homeostasis, cell division, and migration. Specifically, genes related to transcriptional regulation, signal transduction, cell cycle regulation, protein kinase pathways, and translation were enriched.\\n\\nMechanism: These overrepresented functions suggest a complex coordination of biochemical pathways contributing to cell development and proliferation, junctions, and cytoskeletal organization.\\n\\n] \n", - "660 [ The genes in the given list are predominantly involved in the TLR signaling pathway, development, inflammation and immune-response regulation.\\nMechanism: The TLR signaling pathway consists of an intricate set of reactions starting with the recognition of a pathogen-associated molecular pattern (PAMP) by the TLR receptor, leading to the activation of various transcription factors, such as NFKB and MAPK, which work to activate a cascade of gene expression and ultimately the secreting of pro-inflammatory molecules.\\n\\n] \n", - "661 [ Gene functions related to inflammation and immunity appear to be enriched when analyzing the list of genes provided, including cytokine-mediated signaling, antigen-receptor mediated signaling, B-cell proliferation, cytokine expression and release, immunoregulatory interactions, NF-kappaB (NF-κB) activation, and interferon (IFN) signaling.\\n\\nMechanism: These genes are likely involved in an inflammatory response in which cytokines are released and induce receptor activation, which leads to NF-κB activation and transcription of genes that produce cytokines and other signaling molecules, as well as triggering an IFN response. This ultimately leads to B-cell proliferation and immunoregulatory interactions in order to mount a response to the any pathogens. \\n\\n] \n", - "662 [\\nSummary: A significant enrichment of genes involved in translation and protein folding is found in the gene list, indicating a common pathway for these genes.\\nMechanism: The genes in this list are likely all involved in the same pathway, centered around translation and protein folding.\\n] \n", - "663 [COULD NOT PARSE] \n", - "664 [ This enrichment test demonstrates over-representation of the genes involved in cell signaling, structural and enzymatic proteins, and morphogenesis. Mechanism: The mechanisms underlying this enrichment are likely related to the roles of these proteins in regulating the mechanism of intercellular signaling associated with cell development, adhesion, migration, metabolism, skeletal growth, and cell death. ] \n", - "665 [COULD NOT PARSE] \n", - "666 [\\n\\nSummary: The enriched terms from the list of genes suggest a commonality in roles related to protein and organelle trafficking, DNA methylation, transcription and binding, chromatin remodeling, cell cycle regulation and metabolism. \\n\\nMechanism: The proposed mechanism is that these processes are essential components of pathways that regulate cell development, growth, and the response to internal and external stimuli.\\n\\n] \n", - "667 [COULD NOT PARSE] \n", - "668 [COULD NOT PARSE] \n", - "669 [ Genes highly enriched in the provided list have functions related to cell signaling and regulation, including morphogenesis, transcription, and development. Specifically, genes involved in Wnt, Notch, and Hedgehog pathways, transcription factors, and cell cycle genes such as Axin, β-catenin, HDAC2, and CUL1 are all significantly enriched in the list.\\n\\nMechanism: Many of the genes involved in these pathways are responsible for controlling cell fate and regulating morphogenesis and development. The Wnt pathway, a key regulator in embryonic development, is involved in axial patterning, tissue organization and differentiation, and cell-fate decisions. The Notch and Hedgehog pathways are also important for stem cell maintenance and development in early development, as well as tissue patterning, morphogenesis, and organogenesis in adulthood. The transcription factors, such as LEF1, TCF7, and NKD1, drive gene expression in response to these signaling molecules. Lastly, genes such as ADAM17, DKK1, PSEN2, and AXIN2 are involved in cell-cycle regulation and apoptosis. \\n\\n] \n", - "670 [\\nSummary: This list of genes are enriched for terms related to cell development and signaling, specifically those involved in receptor-mediated signaling and the regulation of cell morphology. \\nMechanism: These genes likely act through regulating cell development and receptor-mediated signaling pathways to their respective functions, such as morphogenesis and gene expression.\\n] \n", - "671 [ \\nThis sample of genes are mainly involved in regulation of the immune system, cell signaling, cytoplasmic transport, and apoptosis. Specifically, the genes are enriched for terms such as cytokine receptor binding; cell adhesion; immunoreceptor-antigen complex binding; regulation of the ubiquitin-proteasome pathway; transcription factor regulator activity; GTP-binding protein binding; cell differentiation; T-cell receptor binding; antigen presentation; and immune system process.\\n\\nMechanism: This list of genes likely act in concert to regulate the immune system. They perform a variety of functions, including binding and processing cytokines, receptor-antigen complexes, and other molecules involved in the binding or processing of molecules, such as transcription factors, that are involved in regulating gene expression. Additionally, these genes may be involved in cell differentiation, antigen presentation, and other processes involved in the regulation of the immune system. \\n\\n] \n", - "672 [ The genes provided are related to transcription factor activity, as they are associated with embryonic stem cell differentiation and pluripotency.\\n] \n", - "673 [ The given list of genes is involved in the regulation of cell differentiation and development, specifically in the formation of stem cells, by regulating the expression of developmental proteins. ] \n", - "674 [ The genes included in this list are related to cell proliferation, tissue morphogenesis, motility regulation, vascular development, bone growth, and the immune system. The mechanism is the transcription of gene products that cause expression of varied proteins that mediate these functions.\\n\\nMechanism: Transcription of gene products inducing the expression of varied proteins that mediate cell proliferation, tissue morphogenesis, motility regulation, vascular development, bone growth, and the immune system.\\n\\n] \n", - "675 [ This list of genes are all involved in the development and maintenance of the vascular system. Specifically, these genes play a role in angiogenesis, cell proliferation and migration, matrix remodeling, and tissue remodeling. The genes are implicated in processes such as Jagged-mediated signaling, transcriptional regulation, platelet activation and aggregation, immune regulation, and extracellular matrix formation.\\n\\nMechanism: These genes are involved in a variety of pathways that are responsible for the formation and maintenance of the vascular system. Specifically, the Jagged and Notch pathways are implicated in the control of endothelial cell proliferation and migration, while the TGF-β and Wnt/β-Catenin pathways are involved in matrix remodeling. Additionally, these pathways are also involved in platelet activation and aggregation and the formation of extracellular matrix components.\\n\\n] \n", - "676 [ Genes associated with this list are enriched for functions related to development and signaling, including cell growth, differentiation, and migration; chromatin modulation; transcription regulation; cytoskeletal organization; intracellular trafficking and adhesion; signal transduction; and DNA/RNA metabolic processes.\\nMechanism: The genes are likely to be involved in multiple biological mechanisms and pathways, including processes related to healing, morphogenesis, angiogenesis, and muscle growth and development.\\n] \n", - "677 [ This analysis identified a number of genes involved in various cellular processes such as chromatin regulation, cell development, protein translation, and ion transport.\\nMechanism: The underlying biological mechanism likely involves regulation of gene expression through the actions of transcription factors, the post-translational modifications of proteins, and the transport of ions across cell membranes.\\n] \n", - "678 [ The human genes listed are involved in skeletal muscle structure and contractility. The genes are enriched for processes such as myofibrillogenesis, actin filament organization, and muscle contraction.\\n\\nMechanism: The genes likely act to regulate processes involved in myofibrillogenesis, such as Z-disc formation and maintenance, nuclear positioning, and muscle fiber organization. They also may act to modulate ion channel influx/efflux, thereby influencing muscle contraction and force. \\n\\n] \n", - "679 [\\nSummary: Genes in this set are involved in muscle structures and processes.\\n] \n", - "680 [\\nSummary: These genes are related to lipid metabolism, cell signaling pathways, and cell cycling.\\nMechanism: These genes are thought to have a role in regulating lipid metabolism, cell signaling pathways and cell cycling. \\n] \n", - "681 [\\nSummary: The genes in this list are predominantly involved in endocytosis and intracellular signaling.\\nMechanism: The genes in this list interact to form a molecular pathway that is involved in endocytosis and intracellular signaling. Endocytosis allows receptors and newly synthesized molecules to be moved cellular compartments and can result in changes in cell signaling.\\n] \n", - "682 [\\nBased on the list of genes provided, common terms enriched amongst the genes include ATP synthesis, glycolysis, energy metabolism, and metabolic pathways.\\n\\nMechanism: \\nThe underlying biological mechanisms involve ATP synthesis by way of glycolysis and energy metabolism pathways, which produce necessary energy required for a variety of cellular activities.\\n\\n] \n", - "683 [ The genes identified are related to glycolysis, the metabolic pathway that produces ATP from glucose and other carbohydrates. \\nMechanism: Glycolysis involves the series pathways in which a compound molecule of glucose is broken down into two molecules of pyruvic acid, which are further converted into ATP. \\n] \n", - "684 [COULD NOT PARSE] \n", - "685 [\\nSummary: This gene set is primarily involved in neuronal functional regulation, including ion transport, membrane potential regulation and neurotransmission.\\nMechanism: These genes are involved in the regulation of neuronal activity, likely through the regulation of a number of ion channels, neurotransmitter receptors, and calcium/potassium regulators.\\n] \n", - "686 [COULD NOT PARSE] \n", - "687 [\\nThe genes provided are all involved in cell regulation and signaling pathways. Specifically, they all have roles in the activation of transcription factors, and in the activation, regulation and inhibition of signaling proteins such as Ras, Akt and calcium associated kinases.\\nMechanism: \\nThe genes all act together in order to affect the expression of various genes and proteins. They function by either upregulating or downregulating the expression of transcription factors and signaling proteins, as well as by modulating the phosphorylation state of these proteins, thus controlling their activity.\\n] \n", - "688 [ These genes are apparently associated with lysozymes, mucins, glycosyltransferases, and hyaluronidases, enzymes and proteins with roles in the breakdown and regulation of glycosylation.\\nMechanism: The mechanism behind this gene cluster's biological role seems to be in the regulation of cell processes related to glycosylation, such as enzyme production and its breakdown.\\n] \n", - "689 [COULD NOT PARSE] \n", - "690 [\\nSummary: The genetic pathways enriched in these genes involves immunoglobulin heavy/light chain combination, antigen specific receptors, J-chain, and T-lymphocyte receptors. \\nMechanism: These genes mainly play a role in immune response, specifically the regulation of the combination of immunoglobulin heavy and light chains to form antigen-specific receptors, the formation of J-chain, the production of T-lymphocyte receptors, and the regulation of immune function.\\n] \n", - "691 [COULD NOT PARSE] \n", - "692 [ This list of genes is enriched for functions related to DNA replication, repair, and replication fidelity. Mechanism: The list of genes is likely to be involved in simulating DNA synthesis, prioritizing DNA strands for replication, ensuring proper repair of damaged DNA strands, and ensuring that high-fidelity replication is taking place during the cell cycle. ] \n", - "693 [COULD NOT PARSE] \n", - "694 [ 17 of the genes in the list are related to functions involving calcium homeostasis, including calcium signaling, regulation of calcification, and regulation of calcium ion transport. Mechanism: The genes identified are involved in the regulation of calcium homeostasis and signaling, along with functions related to calcification, calcium buffering and transport, protection against calcium overload, and calcium-v influx/efflux. ] \n", - "695 [\\nSummary: Our list of human genes suggests pathways involved in cell structure regulation and metabolism.\\nMechanism: These genes are likely involved in the regulation of cell morphology, metabolic processes and apoptosis.\\n] \n", - "696 [COULD NOT PARSE] \n", - "697 [COULD NOT PARSE] \n", - "698 [\\nThis list of genes is enriched for terms related to protein homeostasis and peroxisome biogenesis. The genes are likely to have roles in maintaining and regulating the levels of specific proteins, as well as helping to form and breakdown peroxisomes in the cell.\\n\\nMechanism: The mechanism underlying these functions appears to involve forming, maintaining and regulating the levels of specific proteins, as well as assisting in the formation and breakdown of peroxisomes in the cell. \\n\\n] \n", - "699 [ The genes provided are all related to Peroxisomal Biogenesis, an important cellular process. \\nMechanism: Peroxisomal biogenesis requires the coordinated expression of multiple genes in order for the peroxisome to be expressed and maintained in cells. \\n] \n", - "700 [COULD NOT PARSE] \n", - "701 [ Shortly, these genes are involved in a range of functions including transcriptional regulation, DNA repair, cell cycle regulation, and cell differentiation. \\nMechanism: These genes all have common functions related to the transcription, repair, and/or regulation of DNA, which suggests that they all play a role in the response to cellular damage or stress, which in turn can influence the downstream processes of cell cycle, differentiation, and growth.\\n] \n", - "702 [ Through a term enrichment test on this list of genes, we see that they are over-represented in terms related to ion conductivity and neural excitability, including ion channels, membrane proteins, and synapse formation.\\n\\nMechanism: These genes likely play a role in neural excitability, leading to the formation of specific ion channels that can conduct ions and help form synapses between neurons.\\n\\n] \n", - "703 [ This group of genes is enriched for terms related to ion-channel function, neuron excitability, and synaptic transmission.\\nMechanism: This group of genes suggested the underlying molecular pathway involves communication between neurons via ion-channel mediated synaptic transmission.\\n] \n", - "704 [ These genes are mainly involved in protein synthesis, metabolism, ion channel transport, and muscle contraction or development.\\n\\nMechanism: These genes function as transcriptional regulators, enzymes in metabolic pathways, ion channels, or as key mediators of neuromuscular development and contraction.\\n\\n] \n", - "705 [ This list of genes encodes many proteins which are involved in nucleic acid metabolism, binding, and transport. Terms enriched in these genes include: Nucleic Acid Metabolism; Nucleic Acid Binding; Nucleic Acid Transport; Protein Metabolism; Protein Binding; and Protein Transport.\\n\\nMechanism: The proteins encoded by these genes are likely to be involved in nucleic acid metabolism and other related downstream processes. These proteins are likely involved in mRNA transcription, mRNA processing and/or mRNA translation. The proteins could also be involved in processes like RNA editing, DNA replication, DNA repair, and DNA recombination. These proteins are likely to be involved in the regulation of gene expression and other pathways related to this process.\\n\\n] \n", - "706 [ This gene list is enriched for terms related to G-Protein Coupled Receptors (GPCRs), G-protein subunits, adenylate cyclase, calcium channels, and kinases.\\n\\nMechanism: The GPCRs and G protein-coupled subunits are involved in signal transduction pathways that regulate a variety of cellular activities. They activate adenylate cyclases, which catalyze the synthesis of the secondary messenger cAMP. This acts downstream to activate pathways and processes such as G-protein mediated second messenger systems and cation channels. Kinases are involved in the regulation of the G-protein by phosphorylating the Gα subunits and other associated components, leading to changes in their activity, and ultimately, signaling cascades.\\n\\n] \n", - "707 [\\n\\nSummary: The enriched terms from these genes suggest a correlation with signaling pathways, cellular growth and differentiation, organization of the cytoskeleton, regulation of endocrine systems, and transcriptional regulation. \\n\\n] \n", - "708 [COULD NOT PARSE] \n", - "709 [ The enriched terms for this list of genes are cellular growth, transcriptional regulation, and chromatin remodeling. These genes are generally involved in the regulation of transcription, chromatin modifications, and cell cycle regulation. These terms are statistically over-represented compared to the gene list provided.\\n\\nMechanism: The likely underlying biological mechanism for these genes is that they are involved in multiple pathways like transcription, chromatin modifications, and cell cycle regulation. These pathways control essential processes such as cell growth and differentiation in the body. Through these mechanisms, the genes may help to regulate embryonic development and maintain tissue homeostasis in adults. \\n\\n] \n", - "\n", - "prompt_variant sim length_diff \n", - "568 0.81 16 \n", - "569 0.90 699 \n", - "570 0.89 253 \n", - "571 0.88 660 \n", - "572 0.86 553 \n", - "573 0.81 125 \n", - "574 0.87 82 \n", - "575 0.82 539 \n", - "576 0.87 0 \n", - "577 0.83 100 \n", - "578 0.84 113 \n", - "579 0.81 30 \n", - "580 0.85 829 \n", - "581 0.88 460 \n", - "582 0.81 144 \n", - "583 0.70 643 \n", - "584 0.89 338 \n", - "585 0.85 573 \n", - "586 0.90 187 \n", - "587 0.87 874 \n", - "588 0.71 588 \n", - "589 0.90 23 \n", - "590 0.71 96 \n", - "591 0.79 141 \n", - "592 0.80 207 \n", - "593 0.83 406 \n", - "594 0.92 65 \n", - "595 0.90 69 \n", - "596 0.83 70 \n", - "597 0.84 54 \n", - "598 0.75 372 \n", - "599 0.89 60 \n", - "600 0.78 964 \n", - "601 0.87 228 \n", - "602 0.83 166 \n", - "603 0.87 373 \n", - "604 0.81 937 \n", - "605 0.82 128 \n", - "606 0.81 504 \n", - "607 0.84 328 \n", - "608 0.89 464 \n", - "609 0.85 140 \n", - "610 0.85 290 \n", - "611 0.90 184 \n", - "612 0.87 54 \n", - "613 0.80 675 \n", - "614 0.93 951 \n", - "615 0.82 319 \n", - "616 0.87 63 \n", - "617 0.68 417 \n", - "618 0.69 86 \n", - "619 0.86 400 \n", - "620 0.90 269 \n", - "621 0.69 81 \n", - "622 0.84 1122 \n", - "623 0.75 160 \n", - "624 0.83 78 \n", - "625 0.69 509 \n", - "626 0.77 293 \n", - "627 0.89 365 \n", - "628 0.75 83 \n", - "629 0.85 147 \n", - "630 0.81 314 \n", - "631 0.84 114 \n", - "632 0.84 0 \n", - "633 0.83 29 \n", - "634 0.81 113 \n", - "635 0.78 317 \n", - "636 0.86 478 \n", - "637 0.77 35 \n", - "638 0.69 569 \n", - "639 0.91 514 \n", - "640 0.82 51 \n", - "641 0.86 341 \n", - "642 0.86 357 \n", - "643 0.84 598 \n", - "644 0.70 383 \n", - "645 0.72 463 \n", - "646 0.84 162 \n", - "647 0.71 411 \n", - "648 0.76 459 \n", - "649 0.83 38 \n", - "650 0.76 62 \n", - "651 0.88 143 \n", - "652 0.68 325 \n", - "653 0.86 522 \n", - "654 0.82 152 \n", - "655 0.86 276 \n", - "656 0.82 36 \n", - "657 0.90 282 \n", - "658 0.80 625 \n", - "659 0.83 558 \n", - "660 0.86 90 \n", - "661 0.86 439 \n", - "662 0.87 33 \n", - "663 0.85 418 \n", - "664 0.81 5 \n", - "665 0.79 788 \n", - "666 0.66 151 \n", - "667 0.82 922 \n", - "668 0.68 0 \n", - "669 0.92 675 \n", - "670 0.82 55 \n", - "671 0.84 197 \n", - "672 0.69 133 \n", - "673 0.88 79 \n", - "674 0.90 124 \n", - "675 0.68 888 \n", - "676 0.69 247 \n", - "677 0.73 74 \n", - "678 0.84 478 \n", - "679 0.67 468 \n", - "680 0.84 107 \n", - "681 0.89 59 \n", - "682 0.85 28 \n", - "683 0.89 30 \n", - "684 0.89 0 \n", - "685 0.83 341 \n", - "686 0.82 303 \n", - "687 0.85 62 \n", - "688 0.88 272 \n", - "689 0.83 291 \n", - "690 0.80 454 \n", - "691 0.88 285 \n", - "692 0.83 128 \n", - "693 0.84 431 \n", - "694 0.79 235 \n", - "695 0.84 135 \n", - "696 0.85 0 \n", - "697 0.78 545 \n", - "698 0.87 270 \n", - "699 0.83 96 \n", - "700 0.87 464 \n", - "701 0.78 642 \n", - "702 0.86 32 \n", - "703 0.88 270 \n", - "704 0.87 49 \n", - "705 0.84 342 \n", - "706 0.87 200 \n", - "707 0.85 173 \n", - "708 0.82 678 \n", - "709 0.92 324 " - ] - }, - "execution_count": 72, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "rnd = result.query(\"model=='text-davinci-003' and method=='no_synopsis'\")\n", - "rnd[MODEL]=\"\"\n", - "rnd[METHOD]=\"RANDOM\"\n", - "rnd[\"sim\"] = rnd.apply(lambda row: text_similarity(random_summary(), random_summary()), axis=1)\n", - "rnd" - ] - }, - { - "cell_type": "code", - "execution_count": 73, - "id": "510880ef", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "\n", - "\n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - "
  countmeanstdminmax
modelmethod     
RANDOM142.0000.8240.0640.6650.925
gpt-3.5-turbonarrative_synopsis142.0000.9090.0390.6770.977
no_synopsis142.0000.9110.0330.8070.966
ontological_synopsis142.0000.9170.0320.8030.976
text-davinci-003narrative_synopsis142.0000.8770.0870.6701.000
no_synopsis142.0000.8300.1080.6631.000
ontological_synopsis142.0000.8680.0930.6760.957
\n" - ], - "text/plain": [ - "" - ] - }, - "execution_count": 73, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "sim_summary = pd.concat([result, rnd]).groupby([MODEL, METHOD])['sim'].describe()[['count', 'mean', 'std', 'min', 'max']]\n", - "sim_summary.style.highlight_max(axis=0, props='font-weight:bold').format(precision=3)" - ] - }, - { - "cell_type": "code", - "execution_count": 74, - "id": "f8c3d2cd", - "metadata": {}, - "outputs": [ - { - "data": { - "image/png": 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" - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "stats_df = result.groupby(METHOD).agg({'sim': [np.mean, np.std]}).reset_index()\n", - "stats_df.columns = ['category', 'mean', 'stddev']\n", - "\n", - "# Set the plot style\n", - "sns.set(style=\"whitegrid\")\n", - "\n", - "# Create the bar plot with error bars\n", - "plt.figure(figsize=(10, 6))\n", - "bar_plot = sns.barplot(x='category', y='mean', data=stats_df, yerr=stats_df['stddev'], capsize=.1)\n", - "\n", - "# Add labels and title\n", - "plt.xlabel(\"Category\")\n", - "plt.ylabel(\"Mean Score\")\n", - "plt.title(\"Mean Score with Standard Deviation for Each Category\")\n", - "\n", - "# Show the plot\n", - "plt.show()\n" - ] - }, - { - "cell_type": "code", - "execution_count": 75, - "id": "af48f888", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "\n", - "\n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - "
  countmeanstdminmax
modelmethod     
gpt-3.5-turbonarrative_synopsis142.000250.000197.7200.000743.000
no_synopsis142.000292.690213.0863.000962.000
ontological_synopsis142.000192.803177.1352.000832.000
text-davinci-003narrative_synopsis142.000312.120250.8610.0001257.000
no_synopsis142.000298.479251.7150.0001122.000
ontological_synopsis142.000330.331264.1800.0001137.000
\n" - ], - "text/plain": [ - "" - ] - }, - "execution_count": 75, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "diff_summary = result.groupby([MODEL, METHOD])['length_diff'].describe()[['count', 'mean', 'std', 'min', 'max']]\n", - "diff_summary.style.highlight_max(axis=0, props='font-weight:bold').format(precision=3)" - ] - }, - { - "cell_type": "markdown", - "id": "fbb0970c", - "metadata": {}, - "source": [ - "## Potential Hallucinations\n", - "\n", - "Summarize all GO terms that are in all summaries that are not in the closure of annotated terms for any of the genes in the gene set" - ] - }, - { - "cell_type": "code", - "execution_count": 76, - "id": "f29c3ac3", - "metadata": {}, - "outputs": [], - "source": [ - "def hallucinatons(df, model):\n", - " novel_term_map = defaultdict(dict)\n", - " for _, row in df.iterrows():\n", - " gs = row[GENESET]\n", - " #if not gs.endswith(\"-0\"):\n", - " # continue\n", - " gs = gs.replace(\"-0\", \"\")\n", - " for lbl in row[NOVEL_LABELS]:\n", - " if row[MODEL] != model:\n", - " continue\n", - " m = row[METHOD]\n", - " novel_term_map[lbl][\"NAME\"] = lbl\n", - " if gs not in novel_term_map[lbl]:\n", - " novel_term_map[lbl][m] = []\n", - " novel_term_map[lbl][m].append(gs)\n", - " novel_df = pd.DataFrame(novel_term_map.values())\n", - " return novel_df" - ] - }, - { - "cell_type": "code", - "execution_count": 77, - "id": "1e9ce75e", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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NAMEnarrative_synopsisno_synopsisontological_synopsis
0regulation of collagen metabolic process[EDS]NaNNaN
1post-translational protein modification[EDS]NaNNaN
2protein folding[EDS-1]NaNNaN
3positive regulation of fatty acid beta-oxidationNaN[HALLMARK_ADIPOGENESIS]NaN
4obsolete electron transport[HALLMARK_FATTY_ACID_METABOLISM]NaN[HALLMARK_OXIDATIVE_PHOSPHORYLATION-1]
5cell growth[HALLMARK_ADIPOGENESIS-1]NaNNaN
6obsolete transcription factor activity, protein binding[tf-downreg-colorectal][tf-downreg-colorectal-1][tf-downreg-colorectal-1]
7interleukin-2 production[HALLMARK_ALLOGRAFT_REJECTION]NaNNaN
8type II interferon production[HALLMARK_ALLOGRAFT_REJECTION]NaNNaN
9regulation of protein stabilityNaN[HALLMARK_ANDROGEN_RESPONSE]NaN
10platelet degranulation[amigo-example][HALLMARK_ANGIOGENESIS]NaN
11regulation of bone developmentNaN[HALLMARK_ANGIOGENESIS]NaN
12proteoglycan metabolic process[amigo-example-1]NaNNaN
13regulation of transforming growth factor beta receptor signaling pathwayNaN[HALLMARK_ANGIOGENESIS-1]NaN
14regulation of mitotic nuclear division[HALLMARK_ANGIOGENESIS-1]NaNNaN
15obsolete calcium-dependent cell adhesion molecule activity[HALLMARK_APICAL_JUNCTION-1]NaNNaN
16regulation of signal transduction by p53 class mediator[HALLMARK_APICAL_SURFACE]NaNNaN
17modulation by virus of host process[HALLMARK_APICAL_SURFACE]NaNNaN
18regulation of glucose metabolic processNaN[HALLMARK_APICAL_SURFACE-1]NaN
19protein kinase C signalingNaN[HALLMARK_APICAL_SURFACE-1]NaN
20positive regulation of MAP kinase activityNaN[HALLMARK_APICAL_SURFACE-1]NaN
21regulation of B cell receptor signaling pathwayNaN[HALLMARK_APOPTOSIS]NaN
22obsolete cytochrome P450[HALLMARK_BILE_ACID_METABOLISM-1]NaNNaN
23obsolete cell surface bindingNaN[HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION]NaN
24calcium-dependent protein kinase activityNaN[HALLMARK_ESTROGEN_RESPONSE_EARLY]NaN
25calcium-dependent ATPase activityNaN[HALLMARK_ESTROGEN_RESPONSE_EARLY]NaN
26acetyl-CoA catabolic processNaNNaN[HALLMARK_FATTY_ACID_METABOLISM]
27coenzyme A metabolic process[HALLMARK_FATTY_ACID_METABOLISM-1]NaNNaN
28UDP-D-galactose metabolic process[HALLMARK_GLYCOLYSIS]NaNNaN
29glucose transmembrane transport[HALLMARK_GLYCOLYSIS-1]NaNNaN
30UDP-galactose biosynthetic process[HALLMARK_GLYCOLYSIS-1]NaNNaN
31regulation of protein homodimerization activityNaN[HALLMARK_HEME_METABOLISM-1]NaN
32regulation of response to reactive oxygen speciesNaN[HALLMARK_HYPOXIA]NaN
33cellular response to interferon-alphaNaN[HALLMARK_INTERFERON_ALPHA_RESPONSE-1]NaN
34antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependentNaN[HALLMARK_INTERFERON_GAMMA_RESPONSE]NaN
35P-type calcium transporter activity[HALLMARK_KRAS_SIGNALING_DN]NaNNaN
36obsolete membrane part[HALLMARK_KRAS_SIGNALING_UP]NaNNaN
37RNA splicing, via endonucleolytic cleavage and ligation[HALLMARK_MYC_TARGETS_V1][HALLMARK_MYC_TARGETS_V2-1][HALLMARK_MYC_TARGETS_V1-1]
38spliceosomal complexNaN[HALLMARK_MYC_TARGETS_V2]NaN
39translational initiationNaN[HALLMARK_MYC_TARGETS_V2]NaN
40muscle thin filament assemblyNaN[HALLMARK_MYOGENESIS]NaN
41chemical synaptic transmissionNaN[HALLMARK_NOTCH_SIGNALING]NaN
42obsolete transcription activator activity[HALLMARK_NOTCH_SIGNALING]NaN[HALLMARK_UV_RESPONSE_DN-1]
43cysteine-type endopeptidase activity involved in apoptotic process[HALLMARK_NOTCH_SIGNALING]NaNNaN
44obsolete hydrogen-translocating F-type ATPase activityNaNNaN[HALLMARK_OXIDATIVE_PHOSPHORYLATION-1]
45peroxisome proliferator activated receptor signaling pathwayNaN[HALLMARK_PEROXISOME]NaN
4611-cis retinal binding[HALLMARK_PEROXISOME]NaNNaN
47negative regulation of receptor internalizationNaNNaN[HALLMARK_PROTEIN_SECRETION]
48obsolete vesicle transport[HALLMARK_PROTEIN_SECRETION]NaNNaN
49protein targeting to membraneNaN[HALLMARK_PROTEIN_SECRETION-1]NaN
50negative regulation of reactive oxygen species metabolic processNaN[HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1]NaN
51regulation of DNA repairNaN[HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1]NaN
52positive regulation of protein bindingNaN[HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1]NaN
53regulation of kinetochore assemblyNaN[HALLMARK_SPERMATOGENESIS-1]NaN
54positive regulation of mitotic spindle organizationNaN[HALLMARK_SPERMATOGENESIS-1]NaN
55glycoprotein transport[HALLMARK_TGF_BETA_SIGNALING-1]NaNNaN
56NoneNaN[HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1]NaN
57MAP kinase activityNaNNaN[HALLMARK_TNFA_SIGNALING_VIA_NFKB-1]
58chemokine production[HALLMARK_TNFA_SIGNALING_VIA_NFKB-1]NaNNaN
59regulation of phosphodiesterase activity, acting on 3'-phosphoglycolate-terminated DNA strandsNaN[HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1]NaN
60protein localization to plasma membraneNaN[HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1]NaN
61negative regulation of protein ubiquitinationNaNNaN[HALLMARK_WNT_BETA_CATENIN_SIGNALING-1]
62obsolete lectin[T cell proliferation]NaNNaN
63COP9 signalosome[T cell proliferation]NaNNaN
64cell population proliferationNaN[Yamanaka-TFs]NaN
65stem cell differentiation[Yamanaka-TFs-1][Yamanaka-TFs-1]NaN
66obsolete lipoprotein bindingNaNNaN[amigo-example]
67obsolete collagen[amigo-example]NaNNaN
68keratan sulfate metabolic process[amigo-example-1]NaNNaN
69tissue regeneration[amigo-example-1]NaNNaN
70regulation of muscle filament sliding speed[bicluster_RNAseqDB_1002]NaNNaN
71positive regulation of phosphoprotein phosphatase activity[bicluster_RNAseqDB_1002]NaNNaN
72energy homeostasis[bicluster_RNAseqDB_1002-1]NaNNaN
73regulation of neurotransmitter secretionNaN[go-postsynapse-calcium-transmembrane-1]NaN
74G protein-coupled neurotransmitter receptor activityNaN[term-GO:0007212-1]NaN
75regulation of cytosolic calcium ion concentrationNaNNaN[term-GO:0007212-1]
76second-messenger-mediated signaling[term-GO:0007212-1]NaNNaN
77bone development[endocytosis]NaNNaN
78protein localization to endosomeNaN[endocytosis-1]NaN
79protein kinase activityNaN[go-postsynapse-calcium-transmembrane-1]NaN
80O-glycan processingNaN[hydrolase activity, hydrolyzing O-glycosyl compounds]NaN
81glycolytic processNaN[hydrolase activity, hydrolyzing O-glycosyl compounds-1]NaN
82immunoglobulin productionNaN[ig-receptor-binding-2022-1][ig-receptor-binding-2022-1]
83B cell activationNaN[ig-receptor-binding-2022-1]NaN
84positive regulation of humoral immune response[ig-receptor-binding-2022]NaNNaN
85germ cell proliferationNaN[meiosis I]NaN
86obsolete iron ion homeostasisNaN[molecular sequestering-1]NaN
87protein stabilizationNaN[molecular sequestering-1]NaN
88RNA splicingNaNNaN[mtorc1-1]
89protein import[peroxisome-1]NaN[peroxisome-1]
90peroxisome fissionNaN[peroxisome-1]NaN
91obsolete agingNaN[progeria][progeria-1]
92protein homodimerization activityNaN[regulation of presynaptic membrane potential-1]NaN
93obsolete covalent chromatin modificationNaN[tf-downreg-colorectal]NaN
94obsolete RNA polymerase II transcription factor activityNaNNaN[tf-downreg-colorectal-1]
\n", - "
" - ], - "text/plain": [ - " NAME \\\n", - "0 regulation of collagen metabolic process \n", - "1 post-translational protein modification \n", - "2 protein folding \n", - "3 positive regulation of fatty acid beta-oxidation \n", - "4 obsolete electron transport \n", - "5 cell growth \n", - "6 obsolete transcription factor activity, protein binding \n", - "7 interleukin-2 production \n", - "8 type II interferon production \n", - "9 regulation of protein stability \n", - "10 platelet degranulation \n", - "11 regulation of bone development \n", - "12 proteoglycan metabolic process \n", - "13 regulation of transforming growth factor beta receptor signaling pathway \n", - "14 regulation of mitotic nuclear division \n", - "15 obsolete calcium-dependent cell adhesion molecule activity \n", - "16 regulation of signal transduction by p53 class mediator \n", - "17 modulation by virus of host process \n", - "18 regulation of glucose metabolic process \n", - "19 protein kinase C signaling \n", - "20 positive regulation of MAP kinase activity \n", - "21 regulation of B cell receptor signaling pathway \n", - "22 obsolete cytochrome P450 \n", - "23 obsolete cell surface binding \n", - "24 calcium-dependent protein kinase activity \n", - "25 calcium-dependent ATPase activity \n", - "26 acetyl-CoA catabolic process \n", - "27 coenzyme A metabolic process \n", - "28 UDP-D-galactose metabolic process \n", - "29 glucose transmembrane transport \n", - "30 UDP-galactose biosynthetic process \n", - "31 regulation of protein homodimerization activity \n", - "32 regulation of response to reactive oxygen species \n", - "33 cellular response to interferon-alpha \n", - "34 antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent \n", - "35 P-type calcium transporter activity \n", - "36 obsolete membrane part \n", - "37 RNA splicing, via endonucleolytic cleavage and ligation \n", - "38 spliceosomal complex \n", - "39 translational initiation \n", - "40 muscle thin filament assembly \n", - "41 chemical synaptic transmission \n", - "42 obsolete transcription activator activity \n", - "43 cysteine-type endopeptidase activity involved in apoptotic process \n", - "44 obsolete hydrogen-translocating F-type ATPase activity \n", - "45 peroxisome proliferator activated receptor signaling pathway \n", - "46 11-cis retinal binding \n", - "47 negative regulation of receptor internalization \n", - "48 obsolete vesicle transport \n", - "49 protein targeting to membrane \n", - "50 negative regulation of reactive oxygen species metabolic process \n", - "51 regulation of DNA repair \n", - "52 positive regulation of protein binding \n", - "53 regulation of kinetochore assembly \n", - "54 positive regulation of mitotic spindle organization \n", - "55 glycoprotein transport \n", - "56 None \n", - "57 MAP kinase activity \n", - "58 chemokine production \n", - "59 regulation of phosphodiesterase activity, acting on 3'-phosphoglycolate-terminated DNA strands \n", - "60 protein localization to plasma membrane \n", - "61 negative regulation of protein ubiquitination \n", - "62 obsolete lectin \n", - "63 COP9 signalosome \n", - "64 cell population proliferation \n", - "65 stem cell differentiation \n", - "66 obsolete lipoprotein binding \n", - "67 obsolete collagen \n", - "68 keratan sulfate metabolic process \n", - "69 tissue regeneration \n", - "70 regulation of muscle filament sliding speed \n", - "71 positive regulation of phosphoprotein phosphatase activity \n", - "72 energy homeostasis \n", - "73 regulation of neurotransmitter secretion \n", - "74 G protein-coupled neurotransmitter receptor activity \n", - "75 regulation of cytosolic calcium ion concentration \n", - "76 second-messenger-mediated signaling \n", - "77 bone development \n", - "78 protein localization to endosome \n", - "79 protein kinase activity \n", - "80 O-glycan processing \n", - "81 glycolytic process \n", - "82 immunoglobulin production \n", - "83 B cell activation \n", - "84 positive regulation of humoral immune response \n", - "85 germ cell proliferation \n", - "86 obsolete iron ion homeostasis \n", - "87 protein stabilization \n", - "88 RNA splicing \n", - "89 protein import \n", - "90 peroxisome fission \n", - "91 obsolete aging \n", - "92 protein homodimerization activity \n", - "93 obsolete covalent chromatin modification \n", - "94 obsolete RNA polymerase II transcription factor activity \n", - "\n", - " narrative_synopsis \\\n", - "0 [EDS] \n", - "1 [EDS] \n", - "2 [EDS-1] \n", - "3 NaN \n", - "4 [HALLMARK_FATTY_ACID_METABOLISM] \n", - "5 [HALLMARK_ADIPOGENESIS-1] \n", - "6 [tf-downreg-colorectal] \n", - "7 [HALLMARK_ALLOGRAFT_REJECTION] \n", - "8 [HALLMARK_ALLOGRAFT_REJECTION] \n", - "9 NaN \n", - "10 [amigo-example] \n", - "11 NaN \n", - "12 [amigo-example-1] \n", - "13 NaN \n", - "14 [HALLMARK_ANGIOGENESIS-1] \n", - "15 [HALLMARK_APICAL_JUNCTION-1] \n", - "16 [HALLMARK_APICAL_SURFACE] \n", - "17 [HALLMARK_APICAL_SURFACE] \n", - "18 NaN \n", - "19 NaN \n", - "20 NaN \n", - "21 NaN \n", - "22 [HALLMARK_BILE_ACID_METABOLISM-1] \n", - "23 NaN \n", - "24 NaN \n", - "25 NaN \n", - "26 NaN \n", - "27 [HALLMARK_FATTY_ACID_METABOLISM-1] \n", - "28 [HALLMARK_GLYCOLYSIS] \n", - "29 [HALLMARK_GLYCOLYSIS-1] \n", - "30 [HALLMARK_GLYCOLYSIS-1] \n", - "31 NaN \n", - "32 NaN \n", - "33 NaN \n", - "34 NaN \n", - "35 [HALLMARK_KRAS_SIGNALING_DN] \n", - "36 [HALLMARK_KRAS_SIGNALING_UP] \n", - "37 [HALLMARK_MYC_TARGETS_V1] \n", - "38 NaN \n", - "39 NaN \n", - "40 NaN \n", - "41 NaN \n", - "42 [HALLMARK_NOTCH_SIGNALING] \n", - "43 [HALLMARK_NOTCH_SIGNALING] \n", - "44 NaN \n", - "45 NaN \n", - "46 [HALLMARK_PEROXISOME] \n", - "47 NaN \n", - "48 [HALLMARK_PROTEIN_SECRETION] \n", - "49 NaN \n", - "50 NaN \n", - "51 NaN \n", - "52 NaN \n", - "53 NaN \n", - "54 NaN \n", - "55 [HALLMARK_TGF_BETA_SIGNALING-1] \n", - "56 NaN \n", - "57 NaN \n", - "58 [HALLMARK_TNFA_SIGNALING_VIA_NFKB-1] \n", - "59 NaN \n", - "60 NaN \n", - "61 NaN \n", - "62 [T cell proliferation] \n", - "63 [T cell proliferation] \n", - "64 NaN \n", - "65 [Yamanaka-TFs-1] \n", - "66 NaN \n", - "67 [amigo-example] \n", - "68 [amigo-example-1] \n", - "69 [amigo-example-1] \n", - "70 [bicluster_RNAseqDB_1002] \n", - "71 [bicluster_RNAseqDB_1002] \n", - "72 [bicluster_RNAseqDB_1002-1] \n", - "73 NaN \n", - "74 NaN \n", - "75 NaN \n", - "76 [term-GO:0007212-1] \n", - "77 [endocytosis] \n", - "78 NaN \n", - "79 NaN \n", - "80 NaN \n", - "81 NaN \n", - "82 NaN \n", - "83 NaN \n", - "84 [ig-receptor-binding-2022] \n", - "85 NaN \n", - "86 NaN \n", - "87 NaN \n", - "88 NaN \n", - "89 [peroxisome-1] \n", - "90 NaN \n", - "91 NaN \n", - "92 NaN \n", - "93 NaN \n", - "94 NaN \n", - "\n", - " no_synopsis \\\n", - "0 NaN \n", - "1 NaN \n", - "2 NaN \n", - "3 [HALLMARK_ADIPOGENESIS] \n", - "4 NaN \n", - "5 NaN \n", - "6 [tf-downreg-colorectal-1] \n", - "7 NaN \n", - "8 NaN \n", - "9 [HALLMARK_ANDROGEN_RESPONSE] \n", - "10 [HALLMARK_ANGIOGENESIS] \n", - "11 [HALLMARK_ANGIOGENESIS] \n", - "12 NaN \n", - "13 [HALLMARK_ANGIOGENESIS-1] \n", - "14 NaN \n", - "15 NaN \n", - "16 NaN \n", - "17 NaN \n", - "18 [HALLMARK_APICAL_SURFACE-1] \n", - "19 [HALLMARK_APICAL_SURFACE-1] \n", - "20 [HALLMARK_APICAL_SURFACE-1] \n", - "21 [HALLMARK_APOPTOSIS] \n", - "22 NaN \n", - "23 [HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION] \n", - "24 [HALLMARK_ESTROGEN_RESPONSE_EARLY] \n", - "25 [HALLMARK_ESTROGEN_RESPONSE_EARLY] \n", - "26 NaN \n", - "27 NaN \n", - "28 NaN \n", - "29 NaN \n", - "30 NaN \n", - "31 [HALLMARK_HEME_METABOLISM-1] \n", - "32 [HALLMARK_HYPOXIA] \n", - "33 [HALLMARK_INTERFERON_ALPHA_RESPONSE-1] \n", - "34 [HALLMARK_INTERFERON_GAMMA_RESPONSE] \n", - "35 NaN \n", - "36 NaN \n", - "37 [HALLMARK_MYC_TARGETS_V2-1] \n", - "38 [HALLMARK_MYC_TARGETS_V2] \n", - "39 [HALLMARK_MYC_TARGETS_V2] \n", - "40 [HALLMARK_MYOGENESIS] \n", - "41 [HALLMARK_NOTCH_SIGNALING] \n", - "42 NaN \n", - "43 NaN \n", - "44 NaN \n", - "45 [HALLMARK_PEROXISOME] \n", - "46 NaN \n", - "47 NaN \n", - "48 NaN \n", - "49 [HALLMARK_PROTEIN_SECRETION-1] \n", - "50 [HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1] \n", - "51 [HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1] \n", - "52 [HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1] \n", - "53 [HALLMARK_SPERMATOGENESIS-1] \n", - "54 [HALLMARK_SPERMATOGENESIS-1] \n", - "55 NaN \n", - "56 [HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1] \n", - "57 NaN \n", - "58 NaN \n", - "59 [HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1] \n", - "60 [HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1] \n", - "61 NaN \n", - "62 NaN \n", - "63 NaN \n", - "64 [Yamanaka-TFs] \n", - "65 [Yamanaka-TFs-1] \n", - "66 NaN \n", - "67 NaN \n", - "68 NaN \n", - "69 NaN \n", - "70 NaN \n", - "71 NaN \n", - "72 NaN \n", - "73 [go-postsynapse-calcium-transmembrane-1] \n", - "74 [term-GO:0007212-1] \n", - "75 NaN \n", - "76 NaN \n", - "77 NaN \n", - "78 [endocytosis-1] \n", - "79 [go-postsynapse-calcium-transmembrane-1] \n", - "80 [hydrolase activity, hydrolyzing O-glycosyl compounds] \n", - "81 [hydrolase activity, hydrolyzing O-glycosyl compounds-1] \n", - "82 [ig-receptor-binding-2022-1] \n", - "83 [ig-receptor-binding-2022-1] \n", - "84 NaN \n", - "85 [meiosis I] \n", - "86 [molecular sequestering-1] \n", - "87 [molecular sequestering-1] \n", - "88 NaN \n", - "89 NaN \n", - "90 [peroxisome-1] \n", - "91 [progeria] \n", - "92 [regulation of presynaptic membrane potential-1] \n", - "93 [tf-downreg-colorectal] \n", - "94 NaN \n", - "\n", - " ontological_synopsis \n", - "0 NaN \n", - "1 NaN \n", - "2 NaN \n", - "3 NaN \n", - "4 [HALLMARK_OXIDATIVE_PHOSPHORYLATION-1] \n", - "5 NaN \n", - "6 [tf-downreg-colorectal-1] \n", - "7 NaN \n", - "8 NaN \n", - "9 NaN \n", - "10 NaN \n", - "11 NaN \n", - "12 NaN \n", - "13 NaN \n", - "14 NaN \n", - "15 NaN \n", - "16 NaN \n", - "17 NaN \n", - "18 NaN \n", - "19 NaN \n", - "20 NaN \n", - "21 NaN \n", - "22 NaN \n", - "23 NaN \n", - "24 NaN \n", - "25 NaN \n", - "26 [HALLMARK_FATTY_ACID_METABOLISM] \n", - "27 NaN \n", - "28 NaN \n", - "29 NaN \n", - "30 NaN \n", - "31 NaN \n", - "32 NaN \n", - "33 NaN \n", - "34 NaN \n", - "35 NaN \n", - "36 NaN \n", - "37 [HALLMARK_MYC_TARGETS_V1-1] \n", - "38 NaN \n", - "39 NaN \n", - "40 NaN \n", - "41 NaN \n", - "42 [HALLMARK_UV_RESPONSE_DN-1] \n", - "43 NaN \n", - "44 [HALLMARK_OXIDATIVE_PHOSPHORYLATION-1] \n", - "45 NaN \n", - "46 NaN \n", - "47 [HALLMARK_PROTEIN_SECRETION] \n", - "48 NaN \n", - "49 NaN \n", - "50 NaN \n", - "51 NaN \n", - "52 NaN \n", - "53 NaN \n", - "54 NaN \n", - "55 NaN \n", - "56 NaN \n", - "57 [HALLMARK_TNFA_SIGNALING_VIA_NFKB-1] \n", - "58 NaN \n", - "59 NaN \n", - "60 NaN \n", - "61 [HALLMARK_WNT_BETA_CATENIN_SIGNALING-1] \n", - "62 NaN \n", - "63 NaN \n", - "64 NaN \n", - "65 NaN \n", - "66 [amigo-example] \n", - "67 NaN \n", - "68 NaN \n", - "69 NaN \n", - "70 NaN \n", - "71 NaN \n", - "72 NaN \n", - "73 NaN \n", - "74 NaN \n", - "75 [term-GO:0007212-1] \n", - "76 NaN \n", - "77 NaN \n", - "78 NaN \n", - "79 NaN \n", - "80 NaN \n", - "81 NaN \n", - "82 [ig-receptor-binding-2022-1] \n", - "83 NaN \n", - "84 NaN \n", - "85 NaN \n", - "86 NaN \n", - "87 NaN \n", - "88 [mtorc1-1] \n", - "89 [peroxisome-1] \n", - "90 NaN \n", - "91 [progeria-1] \n", - "92 NaN \n", - "93 NaN \n", - "94 [tf-downreg-colorectal-1] " - ] - }, - "execution_count": 77, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "novel_df_turbo = hallucinatons(df, TURBO).reset_index(drop=True)\n", - "pd.set_option('display.max_colwidth', None)\n", - "pd.set_option('display.max_rows', None)\n", - "novel_df_turbo" - ] - }, - { - "cell_type": "code", - "execution_count": 78, - "id": "7f60cc8b", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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" \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - "
NAMEnarrative_synopsisontological_synopsisno_synopsis
0obsolete Gly-X carboxypeptidase activity[EDS-1]NaNNaN
1phosphorylation[FA]NaNNaN
2Holliday junction resolvase complexNaN[FA-1]NaN
3double-stranded telomeric DNA bindingNaN[FA-1]NaN
4histone acetylationNaN[FA-1]NaN
5protein tagNaN[FA-1]NaN
6cysteine-type endopeptidase inhibitor activityNaN[HALLMARK_TGF_BETA_SIGNALING-1]NaN
7obsolete electron transport[HALLMARK_OXIDATIVE_PHOSPHORYLATION-1][HALLMARK_OXIDATIVE_PHOSPHORYLATION]NaN
8cytosolic transport[HALLMARK_ADIPOGENESIS]NaNNaN
9endopeptidase activityNaN[HALLMARK_ADIPOGENESIS-1]NaN
10phosphatidylserine decarboxylase activityNaN[HALLMARK_ADIPOGENESIS-1]NaN
11obsolete transcription activator activityNaN[tf-downreg-colorectal-1]NaN
12C-X-C chemokine bindingNaN[HALLMARK_ALLOGRAFT_REJECTION]NaN
13DNA replicationNaNNaN[HALLMARK_PEROXISOME-1]
14obsolete lectin[HALLMARK_APICAL_JUNCTION]NaNNaN
15phosphatidylinositol trisphosphate phosphatase activityNaN[HALLMARK_ANDROGEN_RESPONSE-1]NaN
16obsolete serpin[HALLMARK_COMPLEMENT]NaNNaN
17obsolete extracellular matrix glycoprotein[HALLMARK_UV_RESPONSE_DN]NaNNaN
18obsolete calcium-dependent cell adhesion molecule activity[HALLMARK_APICAL_JUNCTION-1]NaNNaN
19cytokine productionNaNNaN[HALLMARK_APICAL_JUNCTION-1]
20obsolete vesicle transport[HALLMARK_PROTEIN_SECRETION][endocytosis-1]NaN
21receptor-mediated endocytosis[HALLMARK_APICAL_SURFACE]NaNNaN
22obsolete transcription factor activity, protein binding[tf-downreg-colorectal-1][molecular sequestering-1][Yamanaka-TFs]
23limb developmentNaNNaN[HALLMARK_BILE_ACID_METABOLISM]
24obsolete cytochrome P450[HALLMARK_BILE_ACID_METABOLISM]NaNNaN
25translation[HALLMARK_BILE_ACID_METABOLISM-1]NaN[bicluster_RNAseqDB_0-1]
26glycoprotein biosynthetic process[HALLMARK_CHOLESTEROL_HOMEOSTASIS]NaNNaN
27sterol catabolic process[HALLMARK_CHOLESTEROL_HOMEOSTASIS]NaNNaN
28bile acid biosynthetic processNaNNaN[HALLMARK_CHOLESTEROL_HOMEOSTASIS-1]
29obsolete plasma protein[HALLMARK_COAGULATION]NaNNaN
30obsolete matrilysin activity[HALLMARK_COAGULATION]NaNNaN
31obsolete RNA[HALLMARK_KRAS_SIGNALING_DN-1][HALLMARK_COMPLEMENT]NaN
32DNA replication-dependent chromatin assembly[HALLMARK_MYC_TARGETS_V2]NaN[HALLMARK_DNA_REPAIR]
33obsolete small nuclear ribonucleoprotein[HALLMARK_MYC_TARGETS_V1]NaNNaN
34obsolete covalent chromatin modification[tf-downreg-colorectal-1]NaN[tf-downreg-colorectal-1]
35obsolete ATP catabolic processNaN[HALLMARK_SPERMATOGENESIS-1]NaN
36epidermal growth factor receptor activityNaN[HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1]NaN
37obsolete collagen[HALLMARK_MYOGENESIS-1]NaNNaN
38cell growth[HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1]NaN[Yamanaka-TFs]
39protein processingNaNNaN[HALLMARK_ESTROGEN_RESPONSE_EARLY]
40inward rectifier potassium channel activityNaN[HALLMARK_ESTROGEN_RESPONSE_LATE]NaN
41activin receptor activityNaN[HALLMARK_ESTROGEN_RESPONSE_LATE]NaN
42nucleotide transportNaNNaN[HALLMARK_FATTY_ACID_METABOLISM]
43metalloendopeptidase activityNaN[HALLMARK_FATTY_ACID_METABOLISM]NaN
44biotin-[propionyl-CoA-carboxylase (ATP-hydrolyzing)] ligase activityNaN[HALLMARK_FATTY_ACID_METABOLISM]NaN
45obsolete coenzyme metabolic process[HALLMARK_FATTY_ACID_METABOLISM]NaNNaN
46actin filamentNaN[HALLMARK_G2M_CHECKPOINT]NaN
47adenyl-nucleotide exchange factor activityNaN[HALLMARK_G2M_CHECKPOINT-1]NaN
48microtubule polymerizationNaNNaN[HALLMARK_GLYCOLYSIS-1]
49activation of GTPase activityNaN[HALLMARK_HEDGEHOG_SIGNALING]NaN
50structural constituent of ribosomeNaNNaN[HALLMARK_HEME_METABOLISM]
51cell cycle checkpoint signalingNaNNaN[HALLMARK_HEME_METABOLISM]
52mitotic prophaseNaNNaN[HALLMARK_HEME_METABOLISM]
53nucleoside metabolic processNaNNaN[HALLMARK_HEME_METABOLISM]
54obsolete transcription repressor activityNaN[tf-downreg-colorectal-1]NaN
55cytokinesis[HALLMARK_HEME_METABOLISM]NaNNaN
56histone deacetylation[HALLMARK_HEME_METABOLISM]NaNNaN
57obsolete DNA[HALLMARK_HEME_METABOLISM][T cell proliferation-1]NaN
58growthNaNNaN[HALLMARK_HEME_METABOLISM-1]
59glycolytic process[HALLMARK_HEME_METABOLISM-1]NaNNaN
60obsolete membrane-associated guanylate kinase[HALLMARK_UV_RESPONSE_DN-1]NaNNaN
61acetyltransferase activityNaN[HALLMARK_HYPOXIA-1]NaN
621-phosphatidylinositol-3-kinase activityNaN[HALLMARK_HYPOXIA-1]NaN
63NAD+-dinitrogen-reductase ADP-D-ribosyltransferase activity[HALLMARK_INTERFERON_ALPHA_RESPONSE-1][HALLMARK_INTERFERON_ALPHA_RESPONSE-1]NaN
64cyclin-dependent protein serine/threonine kinase activityNaN[HALLMARK_HYPOXIA-1]NaN
65lipoprotein metabolic process[HALLMARK_HYPOXIA-1]NaNNaN
66obsolete movement of cell or subcellular componentNaNNaN[HALLMARK_INFLAMMATORY_RESPONSE-1]
67neutrophil mediated immunityNaNNaN[HALLMARK_INTERFERON_ALPHA_RESPONSE-1]
68obsolete tumor suppressor[HALLMARK_INTERFERON_ALPHA_RESPONSE-1]NaNNaN
69protein methylation[HALLMARK_INTERFERON_ALPHA_RESPONSE-1]NaNNaN
70obsolete transcription regulator activityNaN[HALLMARK_INTERFERON_GAMMA_RESPONSE]NaN
71histone methylation[HALLMARK_KRAS_SIGNALING_UP-1]NaNNaN
72dextransucrase activityNaNNaN[HALLMARK_MITOTIC_SPINDLE]
73NF-kappaB bindingNaN[HALLMARK_MITOTIC_SPINDLE-1]NaN
74pyruvate dehydrogenase activityNaN[mtorc1]NaN
75ncRNA-mediated post-transcriptional gene silencingNaNNaN[HALLMARK_MTORC1_SIGNALING-1]
76RNA splicing, via endonucleolytic cleavage and ligation[HALLMARK_MYC_TARGETS_V1-1]NaN[HALLMARK_MYC_TARGETS_V1-1]
77ribosomeNaN[HALLMARK_MYC_TARGETS_V2-1]NaN
78calcium-mediated signalingNaNNaN[HALLMARK_NOTCH_SIGNALING]
79obsolete hydrogen-translocating F-type ATPase activity[mtorc1-1]NaNNaN
80P-type proton-exporting transporter activityNaN[HALLMARK_PROTEIN_SECRETION-1]NaN
81G protein activityNaN[HALLMARK_OXIDATIVE_PHOSPHORYLATION-1]NaN
82post-translational protein modificationNaN[bicluster_RNAseqDB_1002][bicluster_RNAseqDB_0-1]
83cellular senescenceNaN[HALLMARK_PANCREAS_BETA_CELLS]NaN
84obsolete peptide hormone[HALLMARK_PANCREAS_BETA_CELLS-1]NaNNaN
85actin filament polymerizationNaN[HALLMARK_PANCREAS_BETA_CELLS-1]NaN
86detection of glucoseNaN[HALLMARK_PANCREAS_BETA_CELLS-1]NaN
87long-term synaptic potentiationNaN[HALLMARK_PANCREAS_BETA_CELLS-1]NaN
88obsolete insulin[HALLMARK_PANCREAS_BETA_CELLS-1]NaNNaN
89mRNA transcriptionNaNNaN[HALLMARK_PEROXISOME]
90respiratory gaseous exchange by respiratory systemNaN[HALLMARK_PEROXISOME]NaN
91stearoyl-CoA 9-desaturase activity[HALLMARK_PEROXISOME]NaNNaN
92glutamate metabolic process[HALLMARK_PEROXISOME-1]NaNNaN
9311-cis retinal binding[HALLMARK_PEROXISOME-1]NaNNaN
94glycosylationNaNNaN[HALLMARK_PI3K_AKT_MTOR_SIGNALING-1]
95obsolete clathrin adaptor[HALLMARK_PROTEIN_SECRETION-1]NaNNaN
96protein glutathionylationNaN[HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY]NaN
97obsolete glutaredoxin[HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY]NaNNaN
98myosin-light-chain-phosphatase activity[HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY]NaNNaN
99chloramphenicol O-acetyltransferase activityNaN[HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1]NaN
100adenylate cyclase activity[HALLMARK_SPERMATOGENESIS]NaNNaN
101vasodilation[HALLMARK_SPERMATOGENESIS-1]NaNNaN
102obsolete aging[HALLMARK_SPERMATOGENESIS-1]NaNNaN
103anaphase-promoting complex[HALLMARK_TGF_BETA_SIGNALING]NaNNaN
104MAP kinase activityNaNNaN[HALLMARK_TNFA_SIGNALING_VIA_NFKB]
105transcription initiation at RNA polymerase II promoterNaNNaN[HALLMARK_TNFA_SIGNALING_VIA_NFKB-1]
106protein kinase A signalingNaNNaN[HALLMARK_TNFA_SIGNALING_VIA_NFKB-1]
107protein ubiquitinationNaNNaN[HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1]
108ubiquitin-protein transferase activity[HALLMARK_WNT_BETA_CATENIN_SIGNALING-1]NaNNaN
109stem cell developmentNaNNaN[Yamanaka-TFs-1]
110stem cell differentiationNaNNaN[Yamanaka-TFs-1]
111BMP signaling pathway involved in heart inductionNaN[Yamanaka-TFs-1]NaN
112cell cycle[Yamanaka-TFs-1]NaNNaN
113platelet aggregationNaNNaN[amigo-example-1]
114nuclear migrationNaNNaN[bicluster_RNAseqDB_1002]
115phosphoprotein binding[bicluster_RNAseqDB_1002]NaNNaN
116negative regulation of phosphoprotein phosphatase activity[bicluster_RNAseqDB_1002]NaNNaN
117cell motility[bicluster_RNAseqDB_1002]NaNNaN
118protein serine/threonine phosphatase activity[bicluster_RNAseqDB_1002]NaNNaN
119obsolete striated muscle fiber developmentNaNNaN[bicluster_RNAseqDB_1002-1]
120nerve developmentNaNNaN[bicluster_RNAseqDB_1002-1]
121muscle thin filament assemblyNaN[bicluster_RNAseqDB_1002-1]NaN
122calcineurin-NFAT signaling cascade[bicluster_RNAseqDB_1002-1]NaNNaN
123pentose-phosphate shuntNaNNaN[glycolysis-gocam-1]
124glucose transmembrane transportNaN[glycolysis-gocam-1]NaN
125substantia nigra developmentNaN[glycolysis-gocam-1]NaN
126angiogenesis[glycolysis-gocam-1]NaNNaN
127regulation of cytosolic calcium ion concentrationNaN[term-GO:0007212]NaN
128cellular response to glucose stimulusNaN[term-GO:0007212-1]NaN
129positive regulation of lamellipodium morphogenesisNaN[term-GO:0007212-1]NaN
130nuclear export[endocytosis]NaNNaN
131mitotic nuclear division[endocytosis-1]NaNNaN
132regulation of presynaptic cytosolic calcium ion concentrationNaN[go-postsynapse-calcium-transmembrane]NaN
133regulation of synaptic vesicle exocytosisNaN[go-postsynapse-calcium-transmembrane]NaN
134obsolete neuroprotectionNaNNaN[go-reg-autophagy-pkra-1]
135obsolete Goodpasture-antigen-binding protein kinase activity[go-reg-autophagy-pkra-1]NaNNaN
136peroxisomeNaNNaN[hydrolase activity, hydrolyzing O-glycosyl compounds]
137limb morphogenesisNaNNaN[hydrolase activity, hydrolyzing O-glycosyl compounds]
138chitin biosynthetic processNaNNaN[hydrolase activity, hydrolyzing O-glycosyl compounds-1]
139protein kinase activityNaN[hydrolase activity, hydrolyzing O-glycosyl compounds-1]NaN
140carbohydrate transmembrane transporter activityNaN[hydrolase activity, hydrolyzing O-glycosyl compounds-1]NaN
141indole-3-glycerol-phosphate lyase activityNaNNaN[ig-receptor-binding-2022]
142immunoglobulin production[sensory ataxia]NaNNaN
143blood coagulationNaNNaN[ig-receptor-binding-2022-1]
144fibrinogen complexNaNNaN[ig-receptor-binding-2022-1]
145regulation of immunoglobulin productionNaNNaN[ig-receptor-binding-2022-1]
146chronic inflammatory responseNaNNaN[ig-receptor-binding-2022-1]
147cell-matrix adhesionNaN[ig-receptor-binding-2022-1]NaN
148cell-cell adhesionNaN[ig-receptor-binding-2022-1]NaN
149calcium ion transportNaNNaN[molecular sequestering]
150mRNA base-pairing translational repressor activityNaN[molecular sequestering]NaN
151ubiquitin-dependent protein catabolic process[molecular sequestering]NaNNaN
152proteasome-mediated ubiquitin-dependent protein catabolic process[molecular sequestering]NaNNaN
153obsolete initiation of signal transduction[mtorc1-1]NaNNaN
154protein import[peroxisome-1]NaNNaN
155RNA metabolic processNaNNaN[progeria]
156regulation of telomere maintenanceNaN[progeria]NaN
157nucleosome assemblyNaNNaN[progeria-1]
158regulation of cell cycleNaNNaN[progeria-1]
159apoptotic processNaN[progeria-1]NaN
160regulation of cellular senescenceNaN[progeria-1]NaN
161DNA-templated transcription[progeria-1]NaNNaN
162cell division[progeria-1]NaNNaN
163RNA modification[regulation of presynaptic membrane potential-1]NaNNaN
164muscle contractionNaNNaN[sensory ataxia]
165glycosaminoglycan catabolic processNaN[sensory ataxia]NaN
166transmission of nerve impulseNaN[sensory ataxia]NaN
167RNA splicingNaN[sensory ataxia]NaN
168cytoskeletal motor activityNaN[sensory ataxia]NaN
169nucleic acid transportNaNNaN[sensory ataxia-1]
170nuclear laminaNaNNaN[tf-downreg-colorectal]
\n", - "
" - ], - "text/plain": [ - " NAME \\\n", - "0 obsolete Gly-X carboxypeptidase activity \n", - "1 phosphorylation \n", - "2 Holliday junction resolvase complex \n", - "3 double-stranded telomeric DNA binding \n", - "4 histone acetylation \n", - "5 protein tag \n", - "6 cysteine-type endopeptidase inhibitor activity \n", - "7 obsolete electron transport \n", - "8 cytosolic transport \n", - "9 endopeptidase activity \n", - "10 phosphatidylserine decarboxylase activity \n", - "11 obsolete transcription activator activity \n", - "12 C-X-C chemokine binding \n", - "13 DNA replication \n", - "14 obsolete lectin \n", - "15 phosphatidylinositol trisphosphate phosphatase activity \n", - "16 obsolete serpin \n", - "17 obsolete extracellular matrix glycoprotein \n", - "18 obsolete calcium-dependent cell adhesion molecule activity \n", - "19 cytokine production \n", - "20 obsolete vesicle transport \n", - "21 receptor-mediated endocytosis \n", - "22 obsolete transcription factor activity, protein binding \n", - "23 limb development \n", - "24 obsolete cytochrome P450 \n", - "25 translation \n", - "26 glycoprotein biosynthetic process \n", - "27 sterol catabolic process \n", - "28 bile acid biosynthetic process \n", - "29 obsolete plasma protein \n", - "30 obsolete matrilysin activity \n", - "31 obsolete RNA \n", - "32 DNA replication-dependent chromatin assembly \n", - "33 obsolete small nuclear ribonucleoprotein \n", - "34 obsolete covalent chromatin modification \n", - "35 obsolete ATP catabolic process \n", - "36 epidermal growth factor receptor activity \n", - "37 obsolete collagen \n", - "38 cell growth \n", - "39 protein processing \n", - "40 inward rectifier potassium channel activity \n", - "41 activin receptor activity \n", - "42 nucleotide transport \n", - "43 metalloendopeptidase activity \n", - "44 biotin-[propionyl-CoA-carboxylase (ATP-hydrolyzing)] ligase activity \n", - "45 obsolete coenzyme metabolic process \n", - "46 actin filament \n", - "47 adenyl-nucleotide exchange factor activity \n", - "48 microtubule polymerization \n", - "49 activation of GTPase activity \n", - "50 structural constituent of ribosome \n", - "51 cell cycle checkpoint signaling \n", - "52 mitotic prophase \n", - "53 nucleoside metabolic process \n", - "54 obsolete transcription repressor activity \n", - "55 cytokinesis \n", - "56 histone deacetylation \n", - "57 obsolete DNA \n", - "58 growth \n", - "59 glycolytic process \n", - "60 obsolete membrane-associated guanylate kinase \n", - "61 acetyltransferase activity \n", - "62 1-phosphatidylinositol-3-kinase activity \n", - "63 NAD+-dinitrogen-reductase ADP-D-ribosyltransferase activity \n", - "64 cyclin-dependent protein serine/threonine kinase activity \n", - "65 lipoprotein metabolic process \n", - "66 obsolete movement of cell or subcellular component \n", - "67 neutrophil mediated immunity \n", - "68 obsolete tumor suppressor \n", - "69 protein methylation \n", - "70 obsolete transcription regulator activity \n", - "71 histone methylation \n", - "72 dextransucrase activity \n", - "73 NF-kappaB binding \n", - "74 pyruvate dehydrogenase activity \n", - "75 ncRNA-mediated post-transcriptional gene silencing \n", - "76 RNA splicing, via endonucleolytic cleavage and ligation \n", - "77 ribosome \n", - "78 calcium-mediated signaling \n", - "79 obsolete hydrogen-translocating F-type ATPase activity \n", - "80 P-type proton-exporting transporter activity \n", - "81 G protein activity \n", - "82 post-translational protein modification \n", - "83 cellular senescence \n", - "84 obsolete peptide hormone \n", - "85 actin filament polymerization \n", - "86 detection of glucose \n", - "87 long-term synaptic potentiation \n", - "88 obsolete insulin \n", - "89 mRNA transcription \n", - "90 respiratory gaseous exchange by respiratory system \n", - "91 stearoyl-CoA 9-desaturase activity \n", - "92 glutamate metabolic process \n", - "93 11-cis retinal binding \n", - "94 glycosylation \n", - "95 obsolete clathrin adaptor \n", - "96 protein glutathionylation \n", - "97 obsolete glutaredoxin \n", - "98 myosin-light-chain-phosphatase activity \n", - "99 chloramphenicol O-acetyltransferase activity \n", - "100 adenylate cyclase activity \n", - "101 vasodilation \n", - "102 obsolete aging \n", - "103 anaphase-promoting complex \n", - "104 MAP kinase activity \n", - "105 transcription initiation at RNA polymerase II promoter \n", - "106 protein kinase A signaling \n", - "107 protein ubiquitination \n", - "108 ubiquitin-protein transferase activity \n", - "109 stem cell development \n", - "110 stem cell differentiation \n", - "111 BMP signaling pathway involved in heart induction \n", - "112 cell cycle \n", - "113 platelet aggregation \n", - "114 nuclear migration \n", - "115 phosphoprotein binding \n", - "116 negative regulation of phosphoprotein phosphatase activity \n", - "117 cell motility \n", - "118 protein serine/threonine phosphatase activity \n", - "119 obsolete striated muscle fiber development \n", - "120 nerve development \n", - "121 muscle thin filament assembly \n", - "122 calcineurin-NFAT signaling cascade \n", - "123 pentose-phosphate shunt \n", - "124 glucose transmembrane transport \n", - "125 substantia nigra development \n", - "126 angiogenesis \n", - "127 regulation of cytosolic calcium ion concentration \n", - "128 cellular response to glucose stimulus \n", - "129 positive regulation of lamellipodium morphogenesis \n", - "130 nuclear export \n", - "131 mitotic nuclear division \n", - "132 regulation of presynaptic cytosolic calcium ion concentration \n", - "133 regulation of synaptic vesicle exocytosis \n", - "134 obsolete neuroprotection \n", - "135 obsolete Goodpasture-antigen-binding protein kinase activity \n", - "136 peroxisome \n", - "137 limb morphogenesis \n", - "138 chitin biosynthetic process \n", - "139 protein kinase activity \n", - "140 carbohydrate transmembrane transporter activity \n", - "141 indole-3-glycerol-phosphate lyase activity \n", - "142 immunoglobulin production \n", - "143 blood coagulation \n", - "144 fibrinogen complex \n", - "145 regulation of immunoglobulin production \n", - "146 chronic inflammatory response \n", - "147 cell-matrix adhesion \n", - "148 cell-cell adhesion \n", - "149 calcium ion transport \n", - "150 mRNA base-pairing translational repressor activity \n", - "151 ubiquitin-dependent protein catabolic process \n", - "152 proteasome-mediated ubiquitin-dependent protein catabolic process \n", - "153 obsolete initiation of signal transduction \n", - "154 protein import \n", - "155 RNA metabolic process \n", - "156 regulation of telomere maintenance \n", - "157 nucleosome assembly \n", - "158 regulation of cell cycle \n", - "159 apoptotic process \n", - "160 regulation of cellular senescence \n", - "161 DNA-templated transcription \n", - "162 cell division \n", - "163 RNA modification \n", - "164 muscle contraction \n", - "165 glycosaminoglycan catabolic process \n", - "166 transmission of nerve impulse \n", - "167 RNA splicing \n", - "168 cytoskeletal motor activity \n", - "169 nucleic acid transport \n", - "170 nuclear lamina \n", - "\n", - " narrative_synopsis \\\n", - "0 [EDS-1] \n", - "1 [FA] \n", - "2 NaN \n", - "3 NaN \n", - "4 NaN \n", - "5 NaN \n", - "6 NaN \n", - "7 [HALLMARK_OXIDATIVE_PHOSPHORYLATION-1] \n", - "8 [HALLMARK_ADIPOGENESIS] \n", - "9 NaN \n", - "10 NaN \n", - "11 NaN \n", - "12 NaN \n", - "13 NaN \n", - "14 [HALLMARK_APICAL_JUNCTION] \n", - "15 NaN \n", - "16 [HALLMARK_COMPLEMENT] \n", - "17 [HALLMARK_UV_RESPONSE_DN] \n", - "18 [HALLMARK_APICAL_JUNCTION-1] \n", - "19 NaN \n", - "20 [HALLMARK_PROTEIN_SECRETION] \n", - "21 [HALLMARK_APICAL_SURFACE] \n", - "22 [tf-downreg-colorectal-1] \n", - "23 NaN \n", - "24 [HALLMARK_BILE_ACID_METABOLISM] \n", - "25 [HALLMARK_BILE_ACID_METABOLISM-1] \n", - "26 [HALLMARK_CHOLESTEROL_HOMEOSTASIS] \n", - "27 [HALLMARK_CHOLESTEROL_HOMEOSTASIS] \n", - "28 NaN \n", - "29 [HALLMARK_COAGULATION] \n", - "30 [HALLMARK_COAGULATION] \n", - "31 [HALLMARK_KRAS_SIGNALING_DN-1] \n", - "32 [HALLMARK_MYC_TARGETS_V2] \n", - "33 [HALLMARK_MYC_TARGETS_V1] \n", - "34 [tf-downreg-colorectal-1] \n", - "35 NaN \n", - "36 NaN \n", - "37 [HALLMARK_MYOGENESIS-1] \n", - "38 [HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1] \n", - "39 NaN \n", - "40 NaN \n", - "41 NaN \n", - "42 NaN \n", - "43 NaN \n", - "44 NaN \n", - "45 [HALLMARK_FATTY_ACID_METABOLISM] \n", - "46 NaN \n", - "47 NaN \n", - "48 NaN \n", - "49 NaN \n", - "50 NaN \n", - "51 NaN \n", - "52 NaN \n", - "53 NaN \n", - "54 NaN \n", - "55 [HALLMARK_HEME_METABOLISM] \n", - "56 [HALLMARK_HEME_METABOLISM] \n", - "57 [HALLMARK_HEME_METABOLISM] \n", - "58 NaN \n", - "59 [HALLMARK_HEME_METABOLISM-1] \n", - "60 [HALLMARK_UV_RESPONSE_DN-1] \n", - "61 NaN \n", - "62 NaN \n", - "63 [HALLMARK_INTERFERON_ALPHA_RESPONSE-1] \n", - "64 NaN \n", - "65 [HALLMARK_HYPOXIA-1] \n", - "66 NaN \n", - "67 NaN \n", - "68 [HALLMARK_INTERFERON_ALPHA_RESPONSE-1] \n", - "69 [HALLMARK_INTERFERON_ALPHA_RESPONSE-1] \n", - "70 NaN \n", - "71 [HALLMARK_KRAS_SIGNALING_UP-1] \n", - "72 NaN \n", - "73 NaN \n", - "74 NaN \n", - "75 NaN \n", - "76 [HALLMARK_MYC_TARGETS_V1-1] \n", - "77 NaN \n", - "78 NaN \n", - "79 [mtorc1-1] \n", - "80 NaN \n", - "81 NaN \n", - "82 NaN \n", - "83 NaN \n", - "84 [HALLMARK_PANCREAS_BETA_CELLS-1] \n", - "85 NaN \n", - "86 NaN \n", - "87 NaN \n", - "88 [HALLMARK_PANCREAS_BETA_CELLS-1] \n", - "89 NaN \n", - "90 NaN \n", - "91 [HALLMARK_PEROXISOME] \n", - "92 [HALLMARK_PEROXISOME-1] \n", - "93 [HALLMARK_PEROXISOME-1] \n", - "94 NaN \n", - "95 [HALLMARK_PROTEIN_SECRETION-1] \n", - "96 NaN \n", - "97 [HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY] \n", - "98 [HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY] \n", - "99 NaN \n", - "100 [HALLMARK_SPERMATOGENESIS] \n", - "101 [HALLMARK_SPERMATOGENESIS-1] \n", - "102 [HALLMARK_SPERMATOGENESIS-1] \n", - "103 [HALLMARK_TGF_BETA_SIGNALING] \n", - "104 NaN \n", - "105 NaN \n", - "106 NaN \n", - "107 NaN \n", - "108 [HALLMARK_WNT_BETA_CATENIN_SIGNALING-1] \n", - "109 NaN \n", - "110 NaN \n", - "111 NaN \n", - "112 [Yamanaka-TFs-1] \n", - "113 NaN \n", - "114 NaN \n", - "115 [bicluster_RNAseqDB_1002] \n", - "116 [bicluster_RNAseqDB_1002] \n", - "117 [bicluster_RNAseqDB_1002] \n", - "118 [bicluster_RNAseqDB_1002] \n", - "119 NaN \n", - "120 NaN \n", - "121 NaN \n", - "122 [bicluster_RNAseqDB_1002-1] \n", - "123 NaN \n", - "124 NaN \n", - "125 NaN \n", - "126 [glycolysis-gocam-1] \n", - "127 NaN \n", - "128 NaN \n", - "129 NaN \n", - "130 [endocytosis] \n", - "131 [endocytosis-1] \n", - "132 NaN \n", - "133 NaN \n", - "134 NaN \n", - "135 [go-reg-autophagy-pkra-1] \n", - "136 NaN \n", - "137 NaN \n", - "138 NaN \n", - "139 NaN \n", - "140 NaN \n", - "141 NaN \n", - "142 [sensory ataxia] \n", - "143 NaN \n", - "144 NaN \n", - "145 NaN \n", - "146 NaN \n", - "147 NaN \n", - "148 NaN \n", - "149 NaN \n", - "150 NaN \n", - "151 [molecular sequestering] \n", - "152 [molecular sequestering] \n", - "153 [mtorc1-1] \n", - "154 [peroxisome-1] \n", - "155 NaN \n", - "156 NaN \n", - "157 NaN \n", - "158 NaN \n", - "159 NaN \n", - "160 NaN \n", - "161 [progeria-1] \n", - "162 [progeria-1] \n", - "163 [regulation of presynaptic membrane potential-1] \n", - "164 NaN \n", - "165 NaN \n", - "166 NaN \n", - "167 NaN \n", - "168 NaN \n", - "169 NaN \n", - "170 NaN \n", - "\n", - " ontological_synopsis \\\n", - "0 NaN \n", - "1 NaN \n", - "2 [FA-1] \n", - "3 [FA-1] \n", - "4 [FA-1] \n", - "5 [FA-1] \n", - "6 [HALLMARK_TGF_BETA_SIGNALING-1] \n", - "7 [HALLMARK_OXIDATIVE_PHOSPHORYLATION] \n", - "8 NaN \n", - "9 [HALLMARK_ADIPOGENESIS-1] \n", - "10 [HALLMARK_ADIPOGENESIS-1] \n", - "11 [tf-downreg-colorectal-1] \n", - "12 [HALLMARK_ALLOGRAFT_REJECTION] \n", - "13 NaN \n", - "14 NaN \n", - "15 [HALLMARK_ANDROGEN_RESPONSE-1] \n", - "16 NaN \n", - "17 NaN \n", - "18 NaN \n", - "19 NaN \n", - "20 [endocytosis-1] \n", - "21 NaN \n", - "22 [molecular sequestering-1] \n", - "23 NaN \n", - "24 NaN \n", - "25 NaN \n", - "26 NaN \n", - "27 NaN \n", - "28 NaN \n", - "29 NaN \n", - "30 NaN \n", - "31 [HALLMARK_COMPLEMENT] \n", - "32 NaN \n", - "33 NaN \n", - "34 NaN \n", - "35 [HALLMARK_SPERMATOGENESIS-1] \n", - "36 [HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1] \n", - "37 NaN \n", - "38 NaN \n", - "39 NaN \n", - "40 [HALLMARK_ESTROGEN_RESPONSE_LATE] \n", - "41 [HALLMARK_ESTROGEN_RESPONSE_LATE] \n", - "42 NaN \n", - "43 [HALLMARK_FATTY_ACID_METABOLISM] \n", - "44 [HALLMARK_FATTY_ACID_METABOLISM] \n", - "45 NaN \n", - "46 [HALLMARK_G2M_CHECKPOINT] \n", - "47 [HALLMARK_G2M_CHECKPOINT-1] \n", - "48 NaN \n", - "49 [HALLMARK_HEDGEHOG_SIGNALING] \n", - "50 NaN \n", - "51 NaN \n", - "52 NaN \n", - "53 NaN \n", - "54 [tf-downreg-colorectal-1] \n", - "55 NaN \n", - "56 NaN \n", - "57 [T cell proliferation-1] \n", - "58 NaN \n", - "59 NaN \n", - "60 NaN \n", - "61 [HALLMARK_HYPOXIA-1] \n", - "62 [HALLMARK_HYPOXIA-1] \n", - "63 [HALLMARK_INTERFERON_ALPHA_RESPONSE-1] \n", - "64 [HALLMARK_HYPOXIA-1] \n", - "65 NaN \n", - "66 NaN \n", - "67 NaN \n", - "68 NaN \n", - "69 NaN \n", - "70 [HALLMARK_INTERFERON_GAMMA_RESPONSE] \n", - "71 NaN \n", - "72 NaN \n", - "73 [HALLMARK_MITOTIC_SPINDLE-1] \n", - "74 [mtorc1] \n", - "75 NaN \n", - "76 NaN \n", - "77 [HALLMARK_MYC_TARGETS_V2-1] \n", - "78 NaN \n", - "79 NaN \n", - "80 [HALLMARK_PROTEIN_SECRETION-1] \n", - "81 [HALLMARK_OXIDATIVE_PHOSPHORYLATION-1] \n", - "82 [bicluster_RNAseqDB_1002] \n", - "83 [HALLMARK_PANCREAS_BETA_CELLS] \n", - "84 NaN \n", - "85 [HALLMARK_PANCREAS_BETA_CELLS-1] \n", - "86 [HALLMARK_PANCREAS_BETA_CELLS-1] \n", - "87 [HALLMARK_PANCREAS_BETA_CELLS-1] \n", - "88 NaN \n", - "89 NaN \n", - "90 [HALLMARK_PEROXISOME] \n", - "91 NaN \n", - "92 NaN \n", - "93 NaN \n", - "94 NaN \n", - "95 NaN \n", - "96 [HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY] \n", - "97 NaN \n", - "98 NaN \n", - "99 [HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1] \n", - "100 NaN \n", - "101 NaN \n", - "102 NaN \n", - "103 NaN \n", - "104 NaN \n", - "105 NaN \n", - "106 NaN \n", - "107 NaN \n", - "108 NaN \n", - "109 NaN \n", - "110 NaN \n", - "111 [Yamanaka-TFs-1] \n", - "112 NaN \n", - "113 NaN \n", - "114 NaN \n", - "115 NaN \n", - "116 NaN \n", - "117 NaN \n", - "118 NaN \n", - "119 NaN \n", - "120 NaN \n", - "121 [bicluster_RNAseqDB_1002-1] \n", - "122 NaN \n", - "123 NaN \n", - "124 [glycolysis-gocam-1] \n", - "125 [glycolysis-gocam-1] \n", - "126 NaN \n", - "127 [term-GO:0007212] \n", - "128 [term-GO:0007212-1] \n", - "129 [term-GO:0007212-1] \n", - "130 NaN \n", - "131 NaN \n", - "132 [go-postsynapse-calcium-transmembrane] \n", - "133 [go-postsynapse-calcium-transmembrane] \n", - "134 NaN \n", - "135 NaN \n", - "136 NaN \n", - "137 NaN \n", - "138 NaN \n", - "139 [hydrolase activity, hydrolyzing O-glycosyl compounds-1] \n", - "140 [hydrolase activity, hydrolyzing O-glycosyl compounds-1] \n", - "141 NaN \n", - "142 NaN \n", - "143 NaN \n", - "144 NaN \n", - "145 NaN \n", - "146 NaN \n", - "147 [ig-receptor-binding-2022-1] \n", - "148 [ig-receptor-binding-2022-1] \n", - "149 NaN \n", - "150 [molecular sequestering] \n", - "151 NaN \n", - "152 NaN \n", - "153 NaN \n", - "154 NaN \n", - "155 NaN \n", - "156 [progeria] \n", - "157 NaN \n", - "158 NaN \n", - "159 [progeria-1] \n", - "160 [progeria-1] \n", - "161 NaN \n", - "162 NaN \n", - "163 NaN \n", - "164 NaN \n", - "165 [sensory ataxia] \n", - "166 [sensory ataxia] \n", - "167 [sensory ataxia] \n", - "168 [sensory ataxia] \n", - "169 NaN \n", - "170 NaN \n", - "\n", - " no_synopsis \n", - "0 NaN \n", - "1 NaN \n", - "2 NaN \n", - "3 NaN \n", - "4 NaN \n", - "5 NaN \n", - "6 NaN \n", - "7 NaN \n", - "8 NaN \n", - "9 NaN \n", - "10 NaN \n", - "11 NaN \n", - "12 NaN \n", - "13 [HALLMARK_PEROXISOME-1] \n", - "14 NaN \n", - "15 NaN \n", - "16 NaN \n", - "17 NaN \n", - "18 NaN \n", - "19 [HALLMARK_APICAL_JUNCTION-1] \n", - "20 NaN \n", - "21 NaN \n", - "22 [Yamanaka-TFs] \n", - "23 [HALLMARK_BILE_ACID_METABOLISM] \n", - "24 NaN \n", - "25 [bicluster_RNAseqDB_0-1] \n", - "26 NaN \n", - "27 NaN \n", - "28 [HALLMARK_CHOLESTEROL_HOMEOSTASIS-1] \n", - "29 NaN \n", - "30 NaN \n", - "31 NaN \n", - "32 [HALLMARK_DNA_REPAIR] \n", - "33 NaN \n", - "34 [tf-downreg-colorectal-1] \n", - "35 NaN \n", - "36 NaN \n", - "37 NaN \n", - "38 [Yamanaka-TFs] \n", - "39 [HALLMARK_ESTROGEN_RESPONSE_EARLY] \n", - "40 NaN \n", - "41 NaN \n", - "42 [HALLMARK_FATTY_ACID_METABOLISM] \n", - "43 NaN \n", - "44 NaN \n", - "45 NaN \n", - "46 NaN \n", - "47 NaN \n", - "48 [HALLMARK_GLYCOLYSIS-1] \n", - "49 NaN \n", - "50 [HALLMARK_HEME_METABOLISM] \n", - "51 [HALLMARK_HEME_METABOLISM] \n", - "52 [HALLMARK_HEME_METABOLISM] \n", - "53 [HALLMARK_HEME_METABOLISM] \n", - "54 NaN \n", - "55 NaN \n", - "56 NaN \n", - "57 NaN \n", - "58 [HALLMARK_HEME_METABOLISM-1] \n", - "59 NaN \n", - "60 NaN \n", - "61 NaN \n", - "62 NaN \n", - "63 NaN \n", - "64 NaN \n", - "65 NaN \n", - "66 [HALLMARK_INFLAMMATORY_RESPONSE-1] \n", - "67 [HALLMARK_INTERFERON_ALPHA_RESPONSE-1] \n", - "68 NaN \n", - "69 NaN \n", - "70 NaN \n", - "71 NaN \n", - "72 [HALLMARK_MITOTIC_SPINDLE] \n", - "73 NaN \n", - "74 NaN \n", - "75 [HALLMARK_MTORC1_SIGNALING-1] \n", - "76 [HALLMARK_MYC_TARGETS_V1-1] \n", - "77 NaN \n", - "78 [HALLMARK_NOTCH_SIGNALING] \n", - "79 NaN \n", - "80 NaN \n", - "81 NaN \n", - "82 [bicluster_RNAseqDB_0-1] \n", - "83 NaN \n", - "84 NaN \n", - "85 NaN \n", - "86 NaN \n", - "87 NaN \n", - "88 NaN \n", - "89 [HALLMARK_PEROXISOME] \n", - "90 NaN \n", - "91 NaN \n", - "92 NaN \n", - "93 NaN \n", - "94 [HALLMARK_PI3K_AKT_MTOR_SIGNALING-1] \n", - "95 NaN \n", - "96 NaN \n", - "97 NaN \n", - "98 NaN \n", - "99 NaN \n", - "100 NaN \n", - "101 NaN \n", - "102 NaN \n", - "103 NaN \n", - "104 [HALLMARK_TNFA_SIGNALING_VIA_NFKB] \n", - "105 [HALLMARK_TNFA_SIGNALING_VIA_NFKB-1] \n", - "106 [HALLMARK_TNFA_SIGNALING_VIA_NFKB-1] \n", - "107 [HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1] \n", - "108 NaN \n", - "109 [Yamanaka-TFs-1] \n", - "110 [Yamanaka-TFs-1] \n", - "111 NaN \n", - "112 NaN \n", - "113 [amigo-example-1] \n", - "114 [bicluster_RNAseqDB_1002] \n", - "115 NaN \n", - "116 NaN \n", - "117 NaN \n", - "118 NaN \n", - "119 [bicluster_RNAseqDB_1002-1] \n", - "120 [bicluster_RNAseqDB_1002-1] \n", - "121 NaN \n", - "122 NaN \n", - "123 [glycolysis-gocam-1] \n", - "124 NaN \n", - "125 NaN \n", - "126 NaN \n", - "127 NaN \n", - "128 NaN \n", - "129 NaN \n", - "130 NaN \n", - "131 NaN \n", - "132 NaN \n", - "133 NaN \n", - "134 [go-reg-autophagy-pkra-1] \n", - "135 NaN \n", - "136 [hydrolase activity, hydrolyzing O-glycosyl compounds] \n", - "137 [hydrolase activity, hydrolyzing O-glycosyl compounds] \n", - "138 [hydrolase activity, hydrolyzing O-glycosyl compounds-1] \n", - "139 NaN \n", - "140 NaN \n", - "141 [ig-receptor-binding-2022] \n", - "142 NaN \n", - "143 [ig-receptor-binding-2022-1] \n", - "144 [ig-receptor-binding-2022-1] \n", - "145 [ig-receptor-binding-2022-1] \n", - "146 [ig-receptor-binding-2022-1] \n", - "147 NaN \n", - "148 NaN \n", - "149 [molecular sequestering] \n", - "150 NaN \n", - "151 NaN \n", - "152 NaN \n", - "153 NaN \n", - "154 NaN \n", - "155 [progeria] \n", - "156 NaN \n", - "157 [progeria-1] \n", - "158 [progeria-1] \n", - "159 NaN \n", - "160 NaN \n", - "161 NaN \n", - "162 NaN \n", - "163 NaN \n", - "164 [sensory ataxia] \n", - "165 NaN \n", - "166 NaN \n", - "167 NaN \n", - "168 NaN \n", - "169 [sensory ataxia-1] \n", - "170 [tf-downreg-colorectal] " - ] - }, - "execution_count": 78, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "hallucinatons(df, DAVINCI)" - ] - }, - { - "cell_type": "code", - "execution_count": 79, - "id": "a7b55d6d", - "metadata": {}, - "outputs": [], - "source": [ - "import tiktoken\n", - "enc = tiktoken.encoding_for_model(\"gpt-4\")\n", - "enc.encode(\"negative regulation\")\n", - "\n", - "def tok_similarity(t1, t2):\n", - " if t1 is None and t2 is None:\n", - " return 1\n", - " if t1 is None or t2 is None:\n", - " return 0\n", - "\n", - " toks1 = set(enc.encode(t1))\n", - " toks2 = set(enc.encode(t2))\n", - " return len(toks1.intersection(toks2)) / len(toks1.union(toks2))\n" - ] - }, - { - "cell_type": "code", - "execution_count": 84, - "id": "bb1b35f2", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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NAMEnarrative_synopsisno_synopsisontological_synopsis
0regulation of collagen metabolic process[(EDS, regulation of metabolic process)]NaNNaN
1post-translational protein modification[(EDS, regulation of protein modification process)]NaNNaN
2protein folding[(EDS-1, protein processing)]NaNNaN
3positive regulation of fatty acid beta-oxidationNaN[(HALLMARK_ADIPOGENESIS, very long-chain fatty acid beta-oxidation)]NaN
4obsolete electron transport[(HALLMARK_FATTY_ACID_METABOLISM, respiratory electron transport chain)]NaN[(HALLMARK_OXIDATIVE_PHOSPHORYLATION-1, respiratory electron transport chain)]
5cell growth[(HALLMARK_ADIPOGENESIS-1, cell)]NaNNaN
6obsolete transcription factor activity, protein binding[(tf-downreg-colorectal, DNA-binding transcription factor binding)][(tf-downreg-colorectal-1, DNA-binding transcription factor binding)][(tf-downreg-colorectal-1, DNA-binding transcription factor binding)]
7interleukin-2 production[(HALLMARK_ALLOGRAFT_REJECTION, interleukin-2 binding)]NaNNaN
8type II interferon production[(HALLMARK_ALLOGRAFT_REJECTION, type III interferon production)]NaNNaN
9regulation of protein stabilityNaN[(HALLMARK_ANDROGEN_RESPONSE, regulation of mRNA stability)]NaN
10platelet degranulation[(amigo-example, platelet)][(HALLMARK_ANGIOGENESIS, platelet)]NaN
11regulation of bone developmentNaN[(HALLMARK_ANGIOGENESIS, regulation of cell development)]NaN
12proteoglycan metabolic process[(amigo-example-1, aminoglycan metabolic process)]NaNNaN
13regulation of transforming growth factor beta receptor signaling pathwayNaN[(HALLMARK_ANGIOGENESIS-1, regulation of transforming growth factor beta activation)]NaN
14regulation of mitotic nuclear division[(HALLMARK_ANGIOGENESIS-1, regulation of nuclear division)]NaNNaN
15obsolete calcium-dependent cell adhesion molecule activity[(HALLMARK_APICAL_JUNCTION-1, substrate adhesion-dependent cell spreading)]NaNNaN
16regulation of signal transduction by p53 class mediator[(HALLMARK_APICAL_SURFACE, regulation of signal transduction)]NaNNaN
17modulation by virus of host process[(HALLMARK_APICAL_SURFACE, regulation of metabolic process)]NaNNaN
18regulation of glucose metabolic processNaN[(HALLMARK_APICAL_SURFACE-1, regulation of metabolic process)]NaN
19protein kinase C signalingNaN[(HALLMARK_APICAL_SURFACE-1, protein kinase C binding)]NaN
20positive regulation of MAP kinase activityNaN[(HALLMARK_APICAL_SURFACE-1, positive regulation of kinase activity)]NaN
21regulation of B cell receptor signaling pathwayNaN[(HALLMARK_APOPTOSIS, regulation of T cell receptor signaling pathway)]NaN
22obsolete cytochrome P450[(HALLMARK_BILE_ACID_METABOLISM-1, axon cytoplasm)]NaNNaN
23obsolete cell surface bindingNaN[(HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION, protein localization to cell surface)]NaN
24calcium-dependent protein kinase activityNaN[(HALLMARK_ESTROGEN_RESPONSE_EARLY, calcium-dependent protein binding)]NaN
25calcium-dependent ATPase activityNaN[(HALLMARK_ESTROGEN_RESPONSE_EARLY, calcium channel activity)]NaN
26acetyl-CoA catabolic processNaNNaN[(HALLMARK_FATTY_ACID_METABOLISM, acetyl-CoA metabolic process)]
27coenzyme A metabolic process[(HALLMARK_FATTY_ACID_METABOLISM-1, amine metabolic process)]NaNNaN
28UDP-D-galactose metabolic process[(HALLMARK_GLYCOLYSIS, galactose metabolic process)]NaNNaN
29glucose transmembrane transport[(HALLMARK_GLYCOLYSIS-1, protein transmembrane transport)]NaNNaN
30UDP-galactose biosynthetic process[(HALLMARK_GLYCOLYSIS-1, lactose biosynthetic process)]NaNNaN
31regulation of protein homodimerization activityNaN[(HALLMARK_HEME_METABOLISM-1, protein homodimerization activity)]NaN
32regulation of response to reactive oxygen speciesNaN[(HALLMARK_HYPOXIA, regulation of reactive oxygen species metabolic process)]NaN
33cellular response to interferon-alphaNaN[(HALLMARK_INTERFERON_ALPHA_RESPONSE-1, cellular response to interferon-beta)]NaN
34antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependentNaN[(HALLMARK_INTERFERON_GAMMA_RESPONSE, antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent)]NaN
35P-type calcium transporter activity[(HALLMARK_KRAS_SIGNALING_DN, P-type sodium transporter activity)]NaNNaN
36obsolete membrane part[(HALLMARK_KRAS_SIGNALING_UP, outer membrane)]NaNNaN
37RNA splicing, via endonucleolytic cleavage and ligation[(HALLMARK_MYC_TARGETS_V1, RNA phosphodiester bond hydrolysis, endonucleolytic)][(HALLMARK_MYC_TARGETS_V2-1, RNA phosphodiester bond hydrolysis, endonucleolytic)][(HALLMARK_MYC_TARGETS_V1-1, RNA phosphodiester bond hydrolysis, endonucleolytic)]
38spliceosomal complexNaN[(HALLMARK_MYC_TARGETS_V2, CMG complex)]NaN
39translational initiationNaN[(HALLMARK_MYC_TARGETS_V2, transcription initiation at mitochondrial promoter)]NaN
40muscle thin filament assemblyNaN[(HALLMARK_MYOGENESIS, muscle filament sliding)]NaN
41chemical synaptic transmissionNaN[(HALLMARK_NOTCH_SIGNALING, modulation of chemical synaptic transmission)]NaN
42obsolete transcription activator activity[(HALLMARK_NOTCH_SIGNALING, DNA-binding transcription activator activity)]NaN[(HALLMARK_UV_RESPONSE_DN-1, DNA-binding transcription activator activity)]
43cysteine-type endopeptidase activity involved in apoptotic process[(HALLMARK_NOTCH_SIGNALING, aspartic-type endopeptidase activity)]NaNNaN
44obsolete hydrogen-translocating F-type ATPase activityNaNNaN[(HALLMARK_OXIDATIVE_PHOSPHORYLATION-1, serine-type peptidase activity)]
45peroxisome proliferator activated receptor signaling pathwayNaN[(HALLMARK_PEROXISOME, peroxisome)]NaN
4611-cis retinal binding[(HALLMARK_PEROXISOME, retinal binding)]NaNNaN
47negative regulation of receptor internalizationNaNNaN[(HALLMARK_PROTEIN_SECRETION, positive regulation of receptor internalization)]
48obsolete vesicle transport[(HALLMARK_PROTEIN_SECRETION, synaptic vesicle transport)]NaNNaN
49protein targeting to membraneNaN[(HALLMARK_PROTEIN_SECRETION-1, protein localization to membrane)]NaN
50negative regulation of reactive oxygen species metabolic processNaN[(HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1, positive regulation of reactive oxygen species metabolic process)]NaN
51regulation of DNA repairNaN[(HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1, regulation of DNA binding)]NaN
52positive regulation of protein bindingNaN[(HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1, positive regulation of binding)]NaN
53regulation of kinetochore assemblyNaN[(HALLMARK_SPERMATOGENESIS-1, regulation of attachment of spindle microtubules to kinetochore)]NaN
54positive regulation of mitotic spindle organizationNaN[(HALLMARK_SPERMATOGENESIS-1, positive regulation of mitotic cell cycle)]NaN
55glycoprotein transport[(HALLMARK_TGF_BETA_SIGNALING-1, glycoprotein metabolic process)]NaNNaN
56NoneNaN[(HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1, protein secretion)]NaN
57MAP kinase activityNaNNaN[(HALLMARK_TNFA_SIGNALING_VIA_NFKB-1, MAP kinase kinase activity)]
58chemokine production[(HALLMARK_TNFA_SIGNALING_VIA_NFKB-1, chemokine activity)]NaNNaN
59regulation of phosphodiesterase activity, acting on 3'-phosphoglycolate-terminated DNA strandsNaN[(HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1, regulation of phosphatase activity)]NaN
60protein localization to plasma membraneNaN[(HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1, protein localization to membrane)]NaN
61negative regulation of protein ubiquitinationNaNNaN[(HALLMARK_WNT_BETA_CATENIN_SIGNALING-1, positive regulation of protein ubiquitination)]
62obsolete lectin[(T cell proliferation, response to lectin)]NaNNaN
63COP9 signalosome[(T cell proliferation, endosome)]NaNNaN
64cell population proliferationNaN[(Yamanaka-TFs, cell)]NaN
65stem cell differentiation[(Yamanaka-TFs-1, fat cell differentiation)][(Yamanaka-TFs-1, fat cell differentiation)]NaN
66obsolete lipoprotein bindingNaNNaN[(amigo-example, low-density lipoprotein particle receptor binding)]
67obsolete collagen[(amigo-example, banded collagen fibril)]NaNNaN
68keratan sulfate metabolic process[(amigo-example-1, RNA metabolic process)]NaNNaN
69tissue regeneration[(amigo-example-1, tissue)]NaNNaN
70regulation of muscle filament sliding speed[(bicluster_RNAseqDB_1002, regulation of muscle contraction)]NaNNaN
71positive regulation of phosphoprotein phosphatase activity[(bicluster_RNAseqDB_1002, positive regulation of calcium-dependent ATPase activity)]NaNNaN
72energy homeostasis[(bicluster_RNAseqDB_1002-1, chemical homeostasis)]NaNNaN
73regulation of neurotransmitter secretionNaN[(go-postsynapse-calcium-transmembrane-1, regulation of neurotransmitter levels)]NaN
74G protein-coupled neurotransmitter receptor activityNaN[(term-GO:0007212-1, G protein-coupled receptor activity)]NaN
75regulation of cytosolic calcium ion concentrationNaNNaN[(term-GO:0007212-1, positive regulation of cytosolic calcium ion concentration)]
76second-messenger-mediated signaling[(term-GO:0007212-1, cytokine-mediated signaling pathway)]NaNNaN
77bone development[(endocytosis, brain development)]NaNNaN
78protein localization to endosomeNaN[(endocytosis-1, protein localization to membrane)]NaN
79protein kinase activityNaN[(go-postsynapse-calcium-transmembrane-1, protein kinase B signaling)]NaN
80O-glycan processingNaN[(hydrolase activity, hydrolyzing O-glycosyl compounds, N-glycan processing)]NaN
81glycolytic processNaN[(hydrolase activity, hydrolyzing O-glycosyl compounds-1, glycolipid metabolic process)]NaN
82immunoglobulin productionNaN[(ig-receptor-binding-2022-1, immunoglobulin complex)][(ig-receptor-binding-2022-1, immunoglobulin complex)]
83B cell activationNaN[(ig-receptor-binding-2022-1, T cell activation)]NaN
84positive regulation of humoral immune response[(ig-receptor-binding-2022, positive regulation of immune response)]NaNNaN
85germ cell proliferationNaN[(meiosis I, germ cell)]NaN
86obsolete iron ion homeostasisNaN[(molecular sequestering-1, intracellular iron ion homeostasis)]NaN
87protein stabilizationNaN[(molecular sequestering-1, protein targeting)]NaN
88RNA splicingNaNNaN[(mtorc1-1, RNA processing)]
89protein import[(peroxisome-1, protein stabilization)]NaN[(peroxisome-1, protein stabilization)]
90peroxisome fissionNaN[(peroxisome-1, peroxisome)]NaN
91obsolete agingNaN[(progeria, telomere maintenance via semi-conservative replication)][(progeria-1, telomere maintenance via semi-conservative replication)]
92protein homodimerization activityNaN[(regulation of presynaptic membrane potential-1, protein heterodimerization activity)]NaN
93obsolete covalent chromatin modificationNaN[(tf-downreg-colorectal, structural constituent of chromatin)]NaN
94obsolete RNA polymerase II transcription factor activityNaNNaN[(tf-downreg-colorectal-1, DNA-binding transcription factor activity, RNA polymerase II-specific)]
\n", - "
" - ], - "text/plain": [ - " NAME \\\n", - "0 regulation of collagen metabolic process \n", - "1 post-translational protein modification \n", - "2 protein folding \n", - "3 positive regulation of fatty acid beta-oxidation \n", - "4 obsolete electron transport \n", - "5 cell growth \n", - "6 obsolete transcription factor activity, protein binding \n", - "7 interleukin-2 production \n", - "8 type II interferon production \n", - "9 regulation of protein stability \n", - "10 platelet degranulation \n", - "11 regulation of bone development \n", - "12 proteoglycan metabolic process \n", - "13 regulation of transforming growth factor beta receptor signaling pathway \n", - "14 regulation of mitotic nuclear division \n", - "15 obsolete calcium-dependent cell adhesion molecule activity \n", - "16 regulation of signal transduction by p53 class mediator \n", - "17 modulation by virus of host process \n", - "18 regulation of glucose metabolic process \n", - "19 protein kinase C signaling \n", - "20 positive regulation of MAP kinase activity \n", - "21 regulation of B cell receptor signaling pathway \n", - "22 obsolete cytochrome P450 \n", - "23 obsolete cell surface binding \n", - "24 calcium-dependent protein kinase activity \n", - "25 calcium-dependent ATPase activity \n", - "26 acetyl-CoA catabolic process \n", - "27 coenzyme A metabolic process \n", - "28 UDP-D-galactose metabolic process \n", - "29 glucose transmembrane transport \n", - "30 UDP-galactose biosynthetic process \n", - "31 regulation of protein homodimerization activity \n", - "32 regulation of response to reactive oxygen species \n", - "33 cellular response to interferon-alpha \n", - "34 antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent \n", - "35 P-type calcium transporter activity \n", - "36 obsolete membrane part \n", - "37 RNA splicing, via endonucleolytic cleavage and ligation \n", - "38 spliceosomal complex \n", - "39 translational initiation \n", - "40 muscle thin filament assembly \n", - "41 chemical synaptic transmission \n", - "42 obsolete transcription activator activity \n", - "43 cysteine-type endopeptidase activity involved in apoptotic process \n", - "44 obsolete hydrogen-translocating F-type ATPase activity \n", - "45 peroxisome proliferator activated receptor signaling pathway \n", - "46 11-cis retinal binding \n", - "47 negative regulation of receptor internalization \n", - "48 obsolete vesicle transport \n", - "49 protein targeting to membrane \n", - "50 negative regulation of reactive oxygen species metabolic process \n", - "51 regulation of DNA repair \n", - "52 positive regulation of protein binding \n", - "53 regulation of kinetochore assembly \n", - "54 positive regulation of mitotic spindle organization \n", - "55 glycoprotein transport \n", - "56 None \n", - "57 MAP kinase activity \n", - "58 chemokine production \n", - "59 regulation of phosphodiesterase activity, acting on 3'-phosphoglycolate-terminated DNA strands \n", - "60 protein localization to plasma membrane \n", - "61 negative regulation of protein ubiquitination \n", - "62 obsolete lectin \n", - "63 COP9 signalosome \n", - "64 cell population proliferation \n", - "65 stem cell differentiation \n", - "66 obsolete lipoprotein binding \n", - "67 obsolete collagen \n", - "68 keratan sulfate metabolic process \n", - "69 tissue regeneration \n", - "70 regulation of muscle filament sliding speed \n", - "71 positive regulation of phosphoprotein phosphatase activity \n", - "72 energy homeostasis \n", - "73 regulation of neurotransmitter secretion \n", - "74 G protein-coupled neurotransmitter receptor activity \n", - "75 regulation of cytosolic calcium ion concentration \n", - "76 second-messenger-mediated signaling \n", - "77 bone development \n", - "78 protein localization to endosome \n", - "79 protein kinase activity \n", - "80 O-glycan processing \n", - "81 glycolytic process \n", - "82 immunoglobulin production \n", - "83 B cell activation \n", - "84 positive regulation of humoral immune response \n", - "85 germ cell proliferation \n", - "86 obsolete iron ion homeostasis \n", - "87 protein stabilization \n", - "88 RNA splicing \n", - "89 protein import \n", - "90 peroxisome fission \n", - "91 obsolete aging \n", - "92 protein homodimerization activity \n", - "93 obsolete covalent chromatin modification \n", - "94 obsolete RNA polymerase II transcription factor activity \n", - "\n", - " narrative_synopsis \\\n", - "0 [(EDS, regulation of metabolic process)] \n", - "1 [(EDS, regulation of protein modification process)] \n", - "2 [(EDS-1, protein processing)] \n", - "3 NaN \n", - "4 [(HALLMARK_FATTY_ACID_METABOLISM, respiratory electron transport chain)] \n", - "5 [(HALLMARK_ADIPOGENESIS-1, cell)] \n", - "6 [(tf-downreg-colorectal, DNA-binding transcription factor binding)] \n", - "7 [(HALLMARK_ALLOGRAFT_REJECTION, interleukin-2 binding)] \n", - "8 [(HALLMARK_ALLOGRAFT_REJECTION, type III interferon production)] \n", - "9 NaN \n", - "10 [(amigo-example, platelet)] \n", - "11 NaN \n", - "12 [(amigo-example-1, aminoglycan metabolic process)] \n", - "13 NaN \n", - "14 [(HALLMARK_ANGIOGENESIS-1, regulation of nuclear division)] \n", - "15 [(HALLMARK_APICAL_JUNCTION-1, substrate adhesion-dependent cell spreading)] \n", - "16 [(HALLMARK_APICAL_SURFACE, regulation of signal transduction)] \n", - "17 [(HALLMARK_APICAL_SURFACE, regulation of metabolic process)] \n", - "18 NaN \n", - "19 NaN \n", - "20 NaN \n", - "21 NaN \n", - "22 [(HALLMARK_BILE_ACID_METABOLISM-1, axon cytoplasm)] \n", - "23 NaN \n", - "24 NaN \n", - "25 NaN \n", - "26 NaN \n", - "27 [(HALLMARK_FATTY_ACID_METABOLISM-1, amine metabolic process)] \n", - "28 [(HALLMARK_GLYCOLYSIS, galactose metabolic process)] \n", - "29 [(HALLMARK_GLYCOLYSIS-1, protein transmembrane transport)] \n", - "30 [(HALLMARK_GLYCOLYSIS-1, lactose biosynthetic process)] \n", - "31 NaN \n", - "32 NaN \n", - "33 NaN \n", - "34 NaN \n", - "35 [(HALLMARK_KRAS_SIGNALING_DN, P-type sodium transporter activity)] \n", - "36 [(HALLMARK_KRAS_SIGNALING_UP, outer membrane)] \n", - "37 [(HALLMARK_MYC_TARGETS_V1, RNA phosphodiester bond hydrolysis, endonucleolytic)] \n", - "38 NaN \n", - "39 NaN \n", - "40 NaN \n", - "41 NaN \n", - "42 [(HALLMARK_NOTCH_SIGNALING, DNA-binding transcription activator activity)] \n", - "43 [(HALLMARK_NOTCH_SIGNALING, aspartic-type endopeptidase activity)] \n", - "44 NaN \n", - "45 NaN \n", - "46 [(HALLMARK_PEROXISOME, retinal binding)] \n", - "47 NaN \n", - "48 [(HALLMARK_PROTEIN_SECRETION, synaptic vesicle transport)] \n", - "49 NaN \n", - "50 NaN \n", - "51 NaN \n", - "52 NaN \n", - "53 NaN \n", - "54 NaN \n", - "55 [(HALLMARK_TGF_BETA_SIGNALING-1, glycoprotein metabolic process)] \n", - "56 NaN \n", - "57 NaN \n", - "58 [(HALLMARK_TNFA_SIGNALING_VIA_NFKB-1, chemokine activity)] \n", - "59 NaN \n", - "60 NaN \n", - "61 NaN \n", - "62 [(T cell proliferation, response to lectin)] \n", - "63 [(T cell proliferation, endosome)] \n", - "64 NaN \n", - "65 [(Yamanaka-TFs-1, fat cell differentiation)] \n", - "66 NaN \n", - "67 [(amigo-example, banded collagen fibril)] \n", - "68 [(amigo-example-1, RNA metabolic process)] \n", - "69 [(amigo-example-1, tissue)] \n", - "70 [(bicluster_RNAseqDB_1002, regulation of muscle contraction)] \n", - "71 [(bicluster_RNAseqDB_1002, positive regulation of calcium-dependent ATPase activity)] \n", - "72 [(bicluster_RNAseqDB_1002-1, chemical homeostasis)] \n", - "73 NaN \n", - "74 NaN \n", - "75 NaN \n", - "76 [(term-GO:0007212-1, cytokine-mediated signaling pathway)] \n", - "77 [(endocytosis, brain development)] \n", - "78 NaN \n", - "79 NaN \n", - "80 NaN \n", - "81 NaN \n", - "82 NaN \n", - "83 NaN \n", - "84 [(ig-receptor-binding-2022, positive regulation of immune response)] \n", - "85 NaN \n", - "86 NaN \n", - "87 NaN \n", - "88 NaN \n", - "89 [(peroxisome-1, protein stabilization)] \n", - "90 NaN \n", - "91 NaN \n", - "92 NaN \n", - "93 NaN \n", - "94 NaN \n", - "\n", - " no_synopsis \\\n", - "0 NaN \n", - "1 NaN \n", - "2 NaN \n", - "3 [(HALLMARK_ADIPOGENESIS, very long-chain fatty acid beta-oxidation)] \n", - "4 NaN \n", - "5 NaN \n", - "6 [(tf-downreg-colorectal-1, DNA-binding transcription factor binding)] \n", - "7 NaN \n", - "8 NaN \n", - "9 [(HALLMARK_ANDROGEN_RESPONSE, regulation of mRNA stability)] \n", - "10 [(HALLMARK_ANGIOGENESIS, platelet)] \n", - "11 [(HALLMARK_ANGIOGENESIS, regulation of cell development)] \n", - "12 NaN \n", - "13 [(HALLMARK_ANGIOGENESIS-1, regulation of transforming growth factor beta activation)] \n", - "14 NaN \n", - "15 NaN \n", - "16 NaN \n", - "17 NaN \n", - "18 [(HALLMARK_APICAL_SURFACE-1, regulation of metabolic process)] \n", - "19 [(HALLMARK_APICAL_SURFACE-1, protein kinase C binding)] \n", - "20 [(HALLMARK_APICAL_SURFACE-1, positive regulation of kinase activity)] \n", - "21 [(HALLMARK_APOPTOSIS, regulation of T cell receptor signaling pathway)] \n", - "22 NaN \n", - "23 [(HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION, protein localization to cell surface)] \n", - "24 [(HALLMARK_ESTROGEN_RESPONSE_EARLY, calcium-dependent protein binding)] \n", - "25 [(HALLMARK_ESTROGEN_RESPONSE_EARLY, calcium channel activity)] \n", - "26 NaN \n", - "27 NaN \n", - "28 NaN \n", - "29 NaN \n", - "30 NaN \n", - "31 [(HALLMARK_HEME_METABOLISM-1, protein homodimerization activity)] \n", - "32 [(HALLMARK_HYPOXIA, regulation of reactive oxygen species metabolic process)] \n", - "33 [(HALLMARK_INTERFERON_ALPHA_RESPONSE-1, cellular response to interferon-beta)] \n", - "34 [(HALLMARK_INTERFERON_GAMMA_RESPONSE, antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent)] \n", - "35 NaN \n", - "36 NaN \n", - "37 [(HALLMARK_MYC_TARGETS_V2-1, RNA phosphodiester bond hydrolysis, endonucleolytic)] \n", - "38 [(HALLMARK_MYC_TARGETS_V2, CMG complex)] \n", - "39 [(HALLMARK_MYC_TARGETS_V2, transcription initiation at mitochondrial promoter)] \n", - "40 [(HALLMARK_MYOGENESIS, muscle filament sliding)] \n", - "41 [(HALLMARK_NOTCH_SIGNALING, modulation of chemical synaptic transmission)] \n", - "42 NaN \n", - "43 NaN \n", - "44 NaN \n", - "45 [(HALLMARK_PEROXISOME, peroxisome)] \n", - "46 NaN \n", - "47 NaN \n", - "48 NaN \n", - "49 [(HALLMARK_PROTEIN_SECRETION-1, protein localization to membrane)] \n", - "50 [(HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1, positive regulation of reactive oxygen species metabolic process)] \n", - "51 [(HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1, regulation of DNA binding)] \n", - "52 [(HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1, positive regulation of binding)] \n", - "53 [(HALLMARK_SPERMATOGENESIS-1, regulation of attachment of spindle microtubules to kinetochore)] \n", - "54 [(HALLMARK_SPERMATOGENESIS-1, positive regulation of mitotic cell cycle)] \n", - "55 NaN \n", - "56 [(HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1, protein secretion)] \n", - "57 NaN \n", - "58 NaN \n", - "59 [(HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1, regulation of phosphatase activity)] \n", - "60 [(HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1, protein localization to membrane)] \n", - "61 NaN \n", - "62 NaN \n", - "63 NaN \n", - "64 [(Yamanaka-TFs, cell)] \n", - "65 [(Yamanaka-TFs-1, fat cell differentiation)] \n", - "66 NaN \n", - "67 NaN \n", - "68 NaN \n", - "69 NaN \n", - "70 NaN \n", - "71 NaN \n", - "72 NaN \n", - "73 [(go-postsynapse-calcium-transmembrane-1, regulation of neurotransmitter levels)] \n", - "74 [(term-GO:0007212-1, G protein-coupled receptor activity)] \n", - "75 NaN \n", - "76 NaN \n", - "77 NaN \n", - "78 [(endocytosis-1, protein localization to membrane)] \n", - "79 [(go-postsynapse-calcium-transmembrane-1, protein kinase B signaling)] \n", - "80 [(hydrolase activity, hydrolyzing O-glycosyl compounds, N-glycan processing)] \n", - "81 [(hydrolase activity, hydrolyzing O-glycosyl compounds-1, glycolipid metabolic process)] \n", - "82 [(ig-receptor-binding-2022-1, immunoglobulin complex)] \n", - "83 [(ig-receptor-binding-2022-1, T cell activation)] \n", - "84 NaN \n", - "85 [(meiosis I, germ cell)] \n", - "86 [(molecular sequestering-1, intracellular iron ion homeostasis)] \n", - "87 [(molecular sequestering-1, protein targeting)] \n", - "88 NaN \n", - "89 NaN \n", - "90 [(peroxisome-1, peroxisome)] \n", - "91 [(progeria, telomere maintenance via semi-conservative replication)] \n", - "92 [(regulation of presynaptic membrane potential-1, protein heterodimerization activity)] \n", - "93 [(tf-downreg-colorectal, structural constituent of chromatin)] \n", - "94 NaN \n", - "\n", - " ontological_synopsis \n", - "0 NaN \n", - "1 NaN \n", - "2 NaN \n", - "3 NaN \n", - "4 [(HALLMARK_OXIDATIVE_PHOSPHORYLATION-1, respiratory electron transport chain)] \n", - "5 NaN \n", - "6 [(tf-downreg-colorectal-1, DNA-binding transcription factor binding)] \n", - "7 NaN \n", - "8 NaN \n", - "9 NaN \n", - "10 NaN \n", - "11 NaN \n", - "12 NaN \n", - "13 NaN \n", - "14 NaN \n", - "15 NaN \n", - "16 NaN \n", - "17 NaN \n", - "18 NaN \n", - "19 NaN \n", - "20 NaN \n", - "21 NaN \n", - "22 NaN \n", - "23 NaN \n", - "24 NaN \n", - "25 NaN \n", - "26 [(HALLMARK_FATTY_ACID_METABOLISM, acetyl-CoA metabolic process)] \n", - "27 NaN \n", - "28 NaN \n", - "29 NaN \n", - "30 NaN \n", - "31 NaN \n", - "32 NaN \n", - "33 NaN \n", - "34 NaN \n", - "35 NaN \n", - "36 NaN \n", - "37 [(HALLMARK_MYC_TARGETS_V1-1, RNA phosphodiester bond hydrolysis, endonucleolytic)] \n", - "38 NaN \n", - "39 NaN \n", - "40 NaN \n", - "41 NaN \n", - "42 [(HALLMARK_UV_RESPONSE_DN-1, DNA-binding transcription activator activity)] \n", - "43 NaN \n", - "44 [(HALLMARK_OXIDATIVE_PHOSPHORYLATION-1, serine-type peptidase activity)] \n", - "45 NaN \n", - "46 NaN \n", - "47 [(HALLMARK_PROTEIN_SECRETION, positive regulation of receptor internalization)] \n", - "48 NaN \n", - "49 NaN \n", - "50 NaN \n", - "51 NaN \n", - "52 NaN \n", - "53 NaN \n", - "54 NaN \n", - "55 NaN \n", - "56 NaN \n", - "57 [(HALLMARK_TNFA_SIGNALING_VIA_NFKB-1, MAP kinase kinase activity)] \n", - "58 NaN \n", - "59 NaN \n", - "60 NaN \n", - "61 [(HALLMARK_WNT_BETA_CATENIN_SIGNALING-1, positive regulation of protein ubiquitination)] \n", - "62 NaN \n", - "63 NaN \n", - "64 NaN \n", - "65 NaN \n", - "66 [(amigo-example, low-density lipoprotein particle receptor binding)] \n", - "67 NaN \n", - "68 NaN \n", - "69 NaN \n", - "70 NaN \n", - "71 NaN \n", - "72 NaN \n", - "73 NaN \n", - "74 NaN \n", - "75 [(term-GO:0007212-1, positive regulation of cytosolic calcium ion concentration)] \n", - "76 NaN \n", - "77 NaN \n", - "78 NaN \n", - "79 NaN \n", - "80 NaN \n", - "81 NaN \n", - "82 [(ig-receptor-binding-2022-1, immunoglobulin complex)] \n", - "83 NaN \n", - "84 NaN \n", - "85 NaN \n", - "86 NaN \n", - "87 NaN \n", - "88 [(mtorc1-1, RNA processing)] \n", - "89 [(peroxisome-1, protein stabilization)] \n", - "90 NaN \n", - "91 [(progeria-1, telomere maintenance via semi-conservative replication)] \n", - "92 NaN \n", - "93 NaN \n", - "94 [(tf-downreg-colorectal-1, DNA-binding transcription factor activity, RNA polymerase II-specific)] " - ] - }, - "execution_count": 84, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "closure_by_gene_set = {}\n", - "for comp in comps:\n", - " closure = comp.payloads[\"closure\"].term_strings\n", - " closure_by_gene_set[comp.name] = closure\n", - "\n", - "def hallucinatons_with_best_match(df, model):\n", - " novel_term_map = defaultdict(dict)\n", - " for _, row in df.iterrows():\n", - " gs = row[GENESET]\n", - " # print(gs)\n", - " closure = closure_by_gene_set[gs]\n", - " #if not gs.endswith(\"-0\"):\n", - " # continue\n", - " gs = gs.replace(\"-0\", \"\")\n", - " for lbl in row[NOVEL_LABELS]:\n", - " if row[MODEL] != model:\n", - " continue\n", - " m = row[METHOD]\n", - " novel_term_map[lbl][\"NAME\"] = lbl\n", - " if gs not in novel_term_map[lbl]:\n", - " novel_term_map[lbl][m] = []\n", - " # sims = [(ct, text_similarity(ct, lbl)) for ct in closure]\n", - " sims = [(ct, tok_similarity(ct, lbl)) for ct in closure]\n", - " sims = sorted(sims, key=lambda x: -x[1])\n", - " best = sims[0][0]\n", - " novel_term_map[lbl][m].append((gs, best))\n", - " novel_df = pd.DataFrame(novel_term_map.values())\n", - " return novel_df\n", - "\n", - "novel_df_turbo = hallucinatons_with_best_match(df, TURBO).reset_index(drop=True)\n", - "novel_df_turbo" - ] - }, - { - "cell_type": "markdown", - "id": "8e02f0eb", - "metadata": {}, - "source": [ - "## New Annotations" - ] - }, - { - "cell_type": "code", - "execution_count": 85, - "id": "cdb0d99f", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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idlabelredundantstandardstandard no ontologyturbo ontological synopsisdav narrative synopsisdav ontological synopsisturbo no synopsisturbo narrative synopsisdav no synopsisrank based
0GO:0006907pinocytosisFalse0.01.0NaNNaNNaNNaNNaNNaNNaN
1GO:0006897endocytosisTrue1.06.00.00.05.00.00.0NaNNaN
2GO:0044351macropinocytosisTrue2.00.0NaN4.0NaNNaNNaNNaNNaN
3GO:0016192vesicle-mediated transportTrue3.0NaNNaNNaNNaN1.0NaNNaNNaN
4GO:0030100regulation of endocytosisFalse4.0NaNNaNNaNNaNNaNNaNNaNNaN
5GO:0006810transportTrue5.0NaNNaNNaNNaNNaNNaNNaNNaN
6GO:0051234establishment of localizationTrue6.0NaNNaNNaNNaNNaNNaNNaNNaN
7GO:0045807positive regulation of endocytosisTrue7.0NaNNaNNaNNaNNaNNaNNaNNaN
8GO:0060627regulation of vesicle-mediated transportTrue8.0NaNNaNNaNNaNNaNNaNNaNNaN
9GO:0051179localizationTrue9.0NaNNaNNaNNaNNaNNaNNaNNaN
10GO:0031410cytoplasmic vesicleFalse10.0NaNNaNNaNNaNNaNNaNNaNNaN
11GO:0097708intracellular vesicleTrue11.0NaNNaNNaNNaNNaNNaNNaNNaN
12GO:0050766positive regulation of phagocytosisTrue12.04.0NaNNaNNaNNaNNaNNaNNaN
13GO:0048518positive regulation of biological processTrue13.0NaNNaNNaNNaNNaNNaNNaNNaN
14GO:0050764regulation of phagocytosisTrue14.0NaNNaNNaNNaNNaNNaNNaNNaN
15GO:0051128regulation of cellular component organizationTrue15.0NaNNaNNaNNaNNaNNaNNaNNaN
16GO:0031982vesicleTrue16.0NaNNaNNaNNaNNaNNaNNaNNaN
17GO:0150094amyloid-beta clearance by cellular catabolic processFalse17.03.0NaNNaNNaNNaNNaNNaNNaN
18GO:0006909phagocytosisTrue18.017.0NaNNaNNaNNaNNaNNaNNaN
19GO:0051049regulation of transportTrue19.0NaNNaNNaNNaNNaNNaNNaNNaN
20GO:0006898receptor-mediated endocytosisTrue20.02.02.0NaN6.0NaNNaNNaNNaN
21GO:0051050positive regulation of transportTrue21.0NaNNaNNaNNaNNaNNaNNaNNaN
22GO:0005041low-density lipoprotein particle receptor activityTrue22.05.0NaNNaNNaNNaNNaNNaNNaN
23GO:0030139endocytic vesicleTrue23.0NaNNaNNaNNaNNaNNaNNaNNaN
24GO:0030228lipoprotein particle receptor activityTrue24.0NaNNaNNaNNaNNaNNaNNaNNaN
25GO:0030666endocytic vesicle membraneTrue25.018.0NaNNaNNaNNaNNaNNaNNaN
26GO:0097242amyloid-beta clearanceTrue26.022.0NaNNaNNaNNaNNaNNaNNaN
27GO:0051130positive regulation of cellular component organizationTrue27.0NaNNaNNaNNaNNaNNaNNaNNaN
28GO:0060907positive regulation of macrophage cytokine productionTrue28.08.0NaNNaNNaNNaNNaNNaNNaN
29GO:0032879regulation of localizationTrue29.0NaNNaNNaNNaNNaNNaNNaNNaN
30GO:0048522positive regulation of cellular processTrue30.0NaNNaNNaNNaNNaNNaNNaNNaN
31GO:0002277myeloid dendritic cell activation involved in immune responseFalse31.09.0NaNNaNNaNNaNNaNNaNNaN
32GO:0030659cytoplasmic vesicle membraneTrue32.0NaNNaNNaNNaNNaNNaNNaNNaN
33GO:0012506vesicle membraneTrue33.0NaNNaNNaNNaNNaNNaNNaNNaN
34GO:0061081positive regulation of myeloid leukocyte cytokine production involved in immune responseTrue34.0NaNNaNNaNNaNNaNNaNNaNNaN
35GO:0010935regulation of macrophage cytokine productionTrue35.0NaNNaNNaNNaNNaNNaNNaNNaN
36GO:0048583regulation of response to stimulusFalse36.0NaNNaNNaNNaNNaNNaNNaNNaN
37GO:1905167positive regulation of lysosomal protein catabolic processTrue37.010.0NaNNaNNaNNaNNaNNaNNaN
38GO:0009894regulation of catabolic processTrue38.0NaNNaNNaNNaNNaNNaNNaNNaN
39GO:0023051regulation of signalingFalse39.0NaNNaNNaNNaNNaNNaNNaNNaN
40GO:0051641cellular localizationTrue40.0NaNNaNNaNNaNNaNNaNNaNNaN
41GO:1904352positive regulation of protein catabolic process in the vacuoleTrue41.0NaNNaNNaNNaNNaNNaNNaNNaN
42GO:0070508cholesterol importTrue42.013.0NaNNaNNaNNaNNaNNaNNaN
43GO:0031347regulation of defense responseTrue43.0NaNNaNNaNNaNNaNNaNNaNNaN
44GO:0005794Golgi apparatusFalse44.014.0NaNNaNNaNNaNNaNNaNNaN
45GO:1901700response to oxygen-containing compoundFalse45.0NaNNaNNaNNaNNaNNaNNaNNaN
46GO:0061024membrane organizationFalse46.0NaNNaNNaNNaNNaNNaNNaNNaN
47GO:0009966regulation of signal transductionTrue47.0NaNNaNNaNNaNNaNNaNNaNNaN
48GO:0015031protein transportTrue48.0NaN1.01.03.0NaNNaNNaNNaN
49GO:0048523negative regulation of cellular processFalse49.0NaNNaNNaNNaNNaNNaNNaNNaN
50GO:0032429regulation of phospholipase A2 activityFalseNaN7.0NaNNaNNaNNaNNaNNaNNaN
51GO:0034381plasma lipoprotein particle clearanceFalseNaN11.0NaNNaNNaNNaNNaNNaNNaN
52GO:0031623receptor internalizationFalseNaN12.0NaNNaNNaNNaNNaNNaNNaN
53GO:0009931calcium-dependent protein serine/threonine kinase activityFalseNaN15.0NaNNaNNaNNaNNaNNaNNaN
54GO:0005905clathrin-coated pitFalseNaN16.0NaNNaNNaNNaNNaNNaNNaN
55GO:0032050clathrin heavy chain bindingFalseNaN19.0NaNNaNNaNNaNNaNNaNNaN
56GO:0030299intestinal cholesterol absorptionFalseNaN20.0NaNNaNNaNNaNNaNNaNNaN
57GO:0001540amyloid-beta bindingFalseNaN21.0NaNNaNNaNNaNNaNNaNNaN
58GO:0034383low-density lipoprotein particle clearanceFalseNaN23.0NaNNaNNaNNaNNaNNaNNaN
59GO:0032760positive regulation of tumor necrosis factor productionFalseNaN24.0NaNNaNNaNNaNNaNNaNNaN
60GO:0071404cellular response to low-density lipoprotein particle stimulusFalseNaN25.0NaNNaNNaNNaNNaNNaNNaN
61GO:0042953lipoprotein transportFalseNaN26.0NaNNaNNaNNaNNaNNaNNaN
62GO:0030169low-density lipoprotein particle bindingFalseNaN27.0NaNNaNNaNNaNNaNNaNNaN
63GO:0051639actin filament network formationFalseNaNNaNNaN2.0NaNNaNNaNNaNNaN
64endoplasmic reticulum and recycling endosome membrane organizationNoneFalseNaNNaNNaN3.0NaNNaNNaNNaNNaN
65GO:0016043cellular component organizationFalseNaNNaNNaN5.0NaNNaNNaNNaNNaN
66intracellular signalingNoneFalseNaNNaNNaN6.0NaNNaNNaNNaNNaN
67GO:0051260protein homooligomerizationFalseNaNNaNNaN7.0NaNNaNNaNNaNNaN
68protein signalingNoneFalseNaNNaNNaNNaN0.0NaNNaNNaNNaN
69GO:0006468protein phosphorylationFalseNaNNaNNaNNaN1.0NaNNaNNaNNaN
70GO:0016567protein ubiquitinationFalseNaNNaNNaNNaN2.0NaNNaNNaNNaN
71GO:0030030cell projection organizationFalseNaNNaNNaNNaN4.0NaNNaNNaNNaN
72GO:0035091phosphatidylinositol bindingFalseNaNNaNNaNNaN7.0NaNNaNNaNNaN
73GO:0001766membrane raft polarizationFalseNaNNaNNaNNaN8.0NaNNaNNaNNaN
74GO:0097320plasma membrane tubulationFalseNaNNaNNaNNaN9.0NaNNaNNaNNaN
75GO:0007041lysosomal transportFalseNaNNaNNaNNaNNaN2.0NaNNaNNaN
76GO:0007032endosome organizationFalseNaNNaNNaNNaNNaN3.0NaNNaNNaN
77GO:0030163protein catabolic processFalseNaNNaNNaNNaNNaN4.0NaNNaNNaN
78intracellular traffickingNoneFalseNaNNaNNaNNaNNaNNaN1.0NaNNaN
79cytoskeleton reorganizationNoneFalseNaNNaNNaNNaNNaNNaN2.0NaNNaN
80GO:0007165signal transductionFalseNaNNaNNaNNaNNaNNaNNaN0.0NaN
81vesicle/lipid traffickingNoneFalseNaNNaNNaNNaNNaNNaNNaN1.0NaN
82cellular adhesionNoneFalseNaNNaNNaNNaNNaNNaNNaN2.0NaN
83nutrient regulationNoneFalseNaNNaNNaNNaNNaNNaNNaN3.0NaN
84cell metabolismNoneFalseNaNNaNNaNNaNNaNNaNNaN4.0NaN
85cytoskeletal organizationNoneFalseNaNNaNNaNNaNNaNNaNNaN5.0NaN
86endocytosis/exocytosisNoneFalseNaNNaNNaNNaNNaNNaNNaN6.0NaN
87intercellular adhesion/motilityNoneFalseNaNNaNNaNNaNNaNNaNNaN7.0NaN
88GO:0005654nucleoplasmFalseNaNNaNNaNNaNNaNNaNNaNNaN0.0
89GO:0005634nucleusFalseNaNNaNNaNNaNNaNNaNNaNNaN1.0
90GO:0046872metal ion bindingFalseNaNNaNNaNNaNNaNNaNNaNNaN2.0
91GO:0005886plasma membraneFalseNaNNaNNaNNaNNaNNaNNaNNaN3.0
92GO:0005524ATP bindingFalseNaNNaNNaNNaNNaNNaNNaNNaN4.0
93GO:0045944positive regulation of transcription by RNA polymerase IIFalseNaNNaNNaNNaNNaNNaNNaNNaN5.0
94GO:0070062extracellular exosomeFalseNaNNaNNaNNaNNaNNaNNaNNaN6.0
95GO:0005576extracellular regionFalseNaNNaNNaNNaNNaNNaNNaNNaN7.0
96GO:0042802identical protein bindingFalseNaNNaNNaNNaNNaNNaNNaNNaN8.0
97GO:0005829cytosolFalseNaNNaNNaNNaNNaNNaNNaNNaN9.0
98GO:0006357regulation of transcription by RNA polymerase IIFalseNaNNaNNaNNaNNaNNaNNaNNaN10.0
99GO:0005739mitochondrionFalseNaNNaNNaNNaNNaNNaNNaNNaN11.0
100GO:0005737cytoplasmFalseNaNNaNNaNNaNNaNNaNNaNNaN12.0
101GO:0016020membraneFalseNaNNaNNaNNaNNaNNaNNaNNaN13.0
102GO:0003723RNA bindingFalseNaNNaNNaNNaNNaNNaNNaNNaN14.0
103GO:0005615extracellular spaceFalseNaNNaNNaNNaNNaNNaNNaNNaN15.0
\n", - "
" - ], - "text/plain": [ - " id \\\n", - "0 GO:0006907 \n", - "1 GO:0006897 \n", - "2 GO:0044351 \n", - "3 GO:0016192 \n", - "4 GO:0030100 \n", - "5 GO:0006810 \n", - "6 GO:0051234 \n", - "7 GO:0045807 \n", - "8 GO:0060627 \n", - "9 GO:0051179 \n", - "10 GO:0031410 \n", - "11 GO:0097708 \n", - "12 GO:0050766 \n", - "13 GO:0048518 \n", - "14 GO:0050764 \n", - "15 GO:0051128 \n", - "16 GO:0031982 \n", - "17 GO:0150094 \n", - "18 GO:0006909 \n", - "19 GO:0051049 \n", - "20 GO:0006898 \n", - "21 GO:0051050 \n", - "22 GO:0005041 \n", - "23 GO:0030139 \n", - "24 GO:0030228 \n", - "25 GO:0030666 \n", - "26 GO:0097242 \n", - "27 GO:0051130 \n", - "28 GO:0060907 \n", - "29 GO:0032879 \n", - "30 GO:0048522 \n", - "31 GO:0002277 \n", - "32 GO:0030659 \n", - "33 GO:0012506 \n", - "34 GO:0061081 \n", - "35 GO:0010935 \n", - "36 GO:0048583 \n", - "37 GO:1905167 \n", - "38 GO:0009894 \n", - "39 GO:0023051 \n", - "40 GO:0051641 \n", - "41 GO:1904352 \n", - "42 GO:0070508 \n", - "43 GO:0031347 \n", - "44 GO:0005794 \n", - "45 GO:1901700 \n", - "46 GO:0061024 \n", - "47 GO:0009966 \n", - "48 GO:0015031 \n", - "49 GO:0048523 \n", - "50 GO:0032429 \n", - "51 GO:0034381 \n", - "52 GO:0031623 \n", - "53 GO:0009931 \n", - "54 GO:0005905 \n", - "55 GO:0032050 \n", - "56 GO:0030299 \n", - "57 GO:0001540 \n", - "58 GO:0034383 \n", - "59 GO:0032760 \n", - "60 GO:0071404 \n", - "61 GO:0042953 \n", - "62 GO:0030169 \n", - "63 GO:0051639 \n", - "64 endoplasmic reticulum and recycling endosome membrane organization \n", - "65 GO:0016043 \n", - "66 intracellular signaling \n", - "67 GO:0051260 \n", - "68 protein signaling \n", - "69 GO:0006468 \n", - "70 GO:0016567 \n", - "71 GO:0030030 \n", - "72 GO:0035091 \n", - "73 GO:0001766 \n", - "74 GO:0097320 \n", - "75 GO:0007041 \n", - "76 GO:0007032 \n", - "77 GO:0030163 \n", - "78 intracellular trafficking \n", - "79 cytoskeleton reorganization \n", - "80 GO:0007165 \n", - "81 vesicle/lipid trafficking \n", - "82 cellular adhesion \n", - "83 nutrient regulation \n", - "84 cell metabolism \n", - "85 cytoskeletal organization \n", - "86 endocytosis/exocytosis \n", - "87 intercellular adhesion/motility \n", - "88 GO:0005654 \n", - "89 GO:0005634 \n", - "90 GO:0046872 \n", - "91 GO:0005886 \n", - "92 GO:0005524 \n", - "93 GO:0045944 \n", - "94 GO:0070062 \n", - "95 GO:0005576 \n", - "96 GO:0042802 \n", - "97 GO:0005829 \n", - "98 GO:0006357 \n", - "99 GO:0005739 \n", - "100 GO:0005737 \n", - "101 GO:0016020 \n", - "102 GO:0003723 \n", - "103 GO:0005615 \n", - "\n", - " label \\\n", - "0 pinocytosis \n", - "1 endocytosis \n", - "2 macropinocytosis \n", - "3 vesicle-mediated transport \n", - "4 regulation of endocytosis \n", - "5 transport \n", - "6 establishment of localization \n", - "7 positive regulation of endocytosis \n", - "8 regulation of vesicle-mediated transport \n", - "9 localization \n", - "10 cytoplasmic vesicle \n", - "11 intracellular vesicle \n", - "12 positive regulation of phagocytosis \n", - "13 positive regulation of biological process \n", - "14 regulation of phagocytosis \n", - "15 regulation of cellular component organization \n", - "16 vesicle \n", - "17 amyloid-beta clearance by cellular catabolic process \n", - "18 phagocytosis \n", - "19 regulation of transport \n", - "20 receptor-mediated endocytosis \n", - "21 positive regulation of transport \n", - "22 low-density lipoprotein particle receptor activity \n", - "23 endocytic vesicle \n", - "24 lipoprotein particle receptor activity \n", - "25 endocytic vesicle membrane \n", - "26 amyloid-beta clearance \n", - "27 positive regulation of cellular component organization \n", - "28 positive regulation of macrophage cytokine production \n", - "29 regulation of localization \n", - "30 positive regulation of cellular process \n", - "31 myeloid dendritic cell activation involved in immune response \n", - "32 cytoplasmic vesicle membrane \n", - "33 vesicle membrane \n", - "34 positive regulation of myeloid leukocyte cytokine production involved in immune response \n", - "35 regulation of macrophage cytokine production \n", - "36 regulation of response to stimulus \n", - "37 positive regulation of lysosomal protein catabolic process \n", - "38 regulation of catabolic process \n", - "39 regulation of signaling \n", - "40 cellular localization \n", - "41 positive regulation of protein catabolic process in the vacuole \n", - "42 cholesterol import \n", - "43 regulation of defense response \n", - "44 Golgi apparatus \n", - "45 response to oxygen-containing compound \n", - "46 membrane organization \n", - "47 regulation of signal transduction \n", - "48 protein transport \n", - "49 negative regulation of cellular process \n", - "50 regulation of phospholipase A2 activity \n", - "51 plasma lipoprotein particle clearance \n", - "52 receptor internalization \n", - "53 calcium-dependent protein serine/threonine kinase activity \n", - "54 clathrin-coated pit \n", - "55 clathrin heavy chain binding \n", - "56 intestinal cholesterol absorption \n", - "57 amyloid-beta binding \n", - "58 low-density lipoprotein particle clearance \n", - "59 positive regulation of tumor necrosis factor production \n", - "60 cellular response to low-density lipoprotein particle stimulus \n", - "61 lipoprotein transport \n", - "62 low-density lipoprotein particle binding \n", - "63 actin filament network formation \n", - "64 None \n", - "65 cellular component organization \n", - "66 None \n", - "67 protein homooligomerization \n", - "68 None \n", - "69 protein phosphorylation \n", - "70 protein ubiquitination \n", - "71 cell projection organization \n", - "72 phosphatidylinositol binding \n", - "73 membrane raft polarization \n", - "74 plasma membrane tubulation \n", - "75 lysosomal transport \n", - "76 endosome organization \n", - "77 protein catabolic process \n", - "78 None \n", - "79 None \n", - "80 signal transduction \n", - "81 None \n", - "82 None \n", - "83 None \n", - "84 None \n", - "85 None \n", - "86 None \n", - "87 None \n", - "88 nucleoplasm \n", - "89 nucleus \n", - "90 metal ion binding \n", - "91 plasma membrane \n", - "92 ATP binding \n", - "93 positive regulation of transcription by RNA polymerase II \n", - "94 extracellular exosome \n", - "95 extracellular region \n", - "96 identical protein binding \n", - "97 cytosol \n", - "98 regulation of transcription by RNA polymerase II \n", - "99 mitochondrion \n", - "100 cytoplasm \n", - "101 membrane \n", - "102 RNA binding \n", - "103 extracellular space \n", - "\n", - " redundant standard standard no ontology turbo ontological synopsis \\\n", - "0 False 0.0 1.0 NaN \n", - "1 True 1.0 6.0 0.0 \n", - "2 True 2.0 0.0 NaN \n", - "3 True 3.0 NaN NaN \n", - "4 False 4.0 NaN NaN \n", - "5 True 5.0 NaN NaN \n", - "6 True 6.0 NaN NaN \n", - "7 True 7.0 NaN NaN \n", - "8 True 8.0 NaN NaN \n", - "9 True 9.0 NaN NaN \n", - "10 False 10.0 NaN NaN \n", - "11 True 11.0 NaN NaN \n", - "12 True 12.0 4.0 NaN \n", - "13 True 13.0 NaN NaN \n", - "14 True 14.0 NaN NaN \n", - "15 True 15.0 NaN NaN \n", - "16 True 16.0 NaN NaN \n", - "17 False 17.0 3.0 NaN \n", - "18 True 18.0 17.0 NaN \n", - "19 True 19.0 NaN NaN \n", - "20 True 20.0 2.0 2.0 \n", - "21 True 21.0 NaN NaN \n", - "22 True 22.0 5.0 NaN \n", - "23 True 23.0 NaN NaN \n", - "24 True 24.0 NaN NaN \n", - "25 True 25.0 18.0 NaN \n", - "26 True 26.0 22.0 NaN \n", - "27 True 27.0 NaN NaN \n", - "28 True 28.0 8.0 NaN \n", - "29 True 29.0 NaN NaN \n", - "30 True 30.0 NaN NaN \n", - "31 False 31.0 9.0 NaN \n", - "32 True 32.0 NaN NaN \n", - "33 True 33.0 NaN NaN \n", - "34 True 34.0 NaN NaN \n", - "35 True 35.0 NaN NaN \n", - "36 False 36.0 NaN NaN \n", - "37 True 37.0 10.0 NaN \n", - "38 True 38.0 NaN NaN \n", - "39 False 39.0 NaN NaN \n", - "40 True 40.0 NaN NaN \n", - "41 True 41.0 NaN NaN \n", - "42 True 42.0 13.0 NaN \n", - "43 True 43.0 NaN NaN \n", - "44 False 44.0 14.0 NaN \n", - "45 False 45.0 NaN NaN \n", - "46 False 46.0 NaN NaN \n", - "47 True 47.0 NaN NaN \n", - "48 True 48.0 NaN 1.0 \n", - "49 False 49.0 NaN NaN \n", - "50 False NaN 7.0 NaN \n", - "51 False NaN 11.0 NaN \n", - "52 False NaN 12.0 NaN \n", - "53 False NaN 15.0 NaN \n", - "54 False NaN 16.0 NaN \n", - "55 False NaN 19.0 NaN \n", - "56 False NaN 20.0 NaN \n", - "57 False NaN 21.0 NaN \n", - "58 False NaN 23.0 NaN \n", - "59 False NaN 24.0 NaN \n", - "60 False NaN 25.0 NaN \n", - "61 False NaN 26.0 NaN \n", - "62 False NaN 27.0 NaN \n", - "63 False NaN NaN NaN \n", - "64 False NaN NaN NaN \n", - "65 False NaN NaN NaN \n", - "66 False NaN NaN NaN \n", - "67 False NaN NaN NaN \n", - "68 False NaN NaN NaN \n", - "69 False NaN NaN NaN \n", - "70 False NaN NaN NaN \n", - "71 False NaN NaN NaN \n", - "72 False NaN NaN NaN \n", - "73 False NaN NaN NaN \n", - "74 False NaN NaN NaN \n", - "75 False NaN NaN NaN \n", - "76 False NaN NaN NaN \n", - "77 False NaN NaN NaN \n", - "78 False NaN NaN NaN \n", - "79 False NaN NaN NaN \n", - "80 False NaN NaN NaN \n", - "81 False NaN NaN NaN \n", - "82 False NaN NaN NaN \n", - "83 False NaN NaN NaN \n", - "84 False NaN NaN NaN \n", - "85 False NaN NaN NaN \n", - "86 False NaN NaN NaN \n", - "87 False NaN NaN NaN \n", - "88 False NaN NaN NaN \n", - "89 False NaN NaN NaN \n", - "90 False NaN NaN NaN \n", - "91 False NaN NaN NaN \n", - "92 False NaN NaN NaN \n", - "93 False NaN NaN NaN \n", - "94 False NaN NaN NaN \n", - "95 False NaN NaN NaN \n", - "96 False NaN NaN NaN \n", - "97 False NaN NaN NaN \n", - "98 False NaN NaN NaN \n", - "99 False NaN NaN NaN \n", - "100 False NaN NaN NaN \n", - "101 False NaN NaN NaN \n", - "102 False NaN NaN NaN \n", - "103 False NaN NaN NaN \n", - "\n", - " dav narrative synopsis dav ontological synopsis turbo no synopsis \\\n", - "0 NaN NaN NaN \n", - "1 0.0 5.0 0.0 \n", - "2 4.0 NaN NaN \n", - "3 NaN NaN 1.0 \n", - "4 NaN NaN NaN \n", - "5 NaN NaN NaN \n", - "6 NaN NaN NaN \n", - "7 NaN NaN NaN \n", - "8 NaN NaN NaN \n", - "9 NaN NaN NaN \n", - "10 NaN NaN NaN \n", - "11 NaN NaN NaN \n", - "12 NaN NaN NaN \n", - "13 NaN NaN NaN \n", - "14 NaN NaN NaN \n", - "15 NaN NaN NaN \n", - "16 NaN NaN NaN \n", - "17 NaN NaN NaN \n", - "18 NaN NaN NaN \n", - "19 NaN NaN NaN \n", - "20 NaN 6.0 NaN \n", - "21 NaN NaN NaN \n", - "22 NaN NaN NaN \n", - "23 NaN NaN NaN \n", - "24 NaN NaN NaN \n", - "25 NaN NaN NaN \n", - "26 NaN NaN NaN \n", - "27 NaN NaN NaN \n", - "28 NaN NaN NaN \n", - "29 NaN NaN NaN \n", - "30 NaN NaN NaN \n", - "31 NaN NaN NaN \n", - "32 NaN NaN NaN \n", - "33 NaN NaN NaN \n", - "34 NaN NaN NaN \n", - "35 NaN NaN NaN \n", - "36 NaN NaN NaN \n", - "37 NaN NaN NaN \n", - "38 NaN NaN NaN \n", - "39 NaN NaN NaN \n", - "40 NaN NaN NaN \n", - "41 NaN NaN NaN \n", - "42 NaN NaN NaN \n", - "43 NaN NaN NaN \n", - "44 NaN NaN NaN \n", - "45 NaN NaN NaN \n", - "46 NaN NaN NaN \n", - "47 NaN NaN NaN \n", - "48 1.0 3.0 NaN \n", - "49 NaN NaN NaN \n", - "50 NaN NaN NaN \n", - "51 NaN NaN NaN \n", - "52 NaN NaN NaN \n", - "53 NaN NaN NaN \n", - "54 NaN NaN NaN \n", - "55 NaN NaN NaN \n", - "56 NaN NaN NaN \n", - "57 NaN NaN NaN \n", - "58 NaN NaN NaN \n", - "59 NaN NaN NaN \n", - "60 NaN NaN NaN \n", - "61 NaN NaN NaN \n", - "62 NaN NaN NaN \n", - "63 2.0 NaN NaN \n", - "64 3.0 NaN NaN \n", - "65 5.0 NaN NaN \n", - "66 6.0 NaN NaN \n", - "67 7.0 NaN NaN \n", - "68 NaN 0.0 NaN \n", - "69 NaN 1.0 NaN \n", - "70 NaN 2.0 NaN \n", - "71 NaN 4.0 NaN \n", - "72 NaN 7.0 NaN \n", - "73 NaN 8.0 NaN \n", - "74 NaN 9.0 NaN \n", - "75 NaN NaN 2.0 \n", - "76 NaN NaN 3.0 \n", - "77 NaN NaN 4.0 \n", - "78 NaN NaN NaN \n", - "79 NaN NaN NaN \n", - "80 NaN NaN NaN \n", - "81 NaN NaN NaN \n", - "82 NaN NaN NaN \n", - "83 NaN NaN NaN \n", - "84 NaN NaN NaN \n", - "85 NaN NaN NaN \n", - "86 NaN NaN NaN \n", - "87 NaN NaN NaN \n", - "88 NaN NaN NaN \n", - "89 NaN NaN NaN \n", - "90 NaN NaN NaN \n", - "91 NaN NaN NaN \n", - "92 NaN NaN NaN \n", - "93 NaN NaN NaN \n", - "94 NaN NaN NaN \n", - "95 NaN NaN NaN \n", - "96 NaN NaN NaN \n", - "97 NaN NaN NaN \n", - "98 NaN NaN NaN \n", - "99 NaN NaN NaN \n", - "100 NaN NaN NaN \n", - "101 NaN NaN NaN \n", - "102 NaN NaN NaN \n", - "103 NaN NaN NaN \n", - "\n", - " turbo narrative synopsis dav no synopsis rank based \n", - "0 NaN NaN NaN \n", - "1 0.0 NaN NaN \n", - "2 NaN NaN NaN \n", - "3 NaN NaN NaN \n", - "4 NaN NaN NaN \n", - "5 NaN NaN NaN \n", - "6 NaN NaN NaN \n", - "7 NaN NaN NaN \n", - "8 NaN NaN NaN \n", - "9 NaN NaN NaN \n", - "10 NaN NaN NaN \n", - "11 NaN NaN NaN \n", - "12 NaN NaN NaN \n", - "13 NaN NaN NaN \n", - "14 NaN NaN NaN \n", - "15 NaN NaN NaN \n", - "16 NaN NaN NaN \n", - "17 NaN NaN NaN \n", - "18 NaN NaN NaN \n", - "19 NaN NaN NaN \n", - "20 NaN NaN NaN \n", - "21 NaN NaN NaN \n", - "22 NaN NaN NaN \n", - "23 NaN NaN NaN \n", - "24 NaN NaN NaN \n", - "25 NaN NaN NaN \n", - "26 NaN NaN NaN \n", - "27 NaN NaN NaN \n", - "28 NaN NaN NaN \n", - "29 NaN NaN NaN \n", - "30 NaN NaN NaN \n", - "31 NaN NaN NaN \n", - "32 NaN NaN NaN \n", - "33 NaN NaN NaN \n", - "34 NaN NaN NaN \n", - "35 NaN NaN NaN \n", - "36 NaN NaN NaN \n", - "37 NaN NaN NaN \n", - "38 NaN NaN NaN \n", - "39 NaN NaN NaN \n", - "40 NaN NaN NaN \n", - "41 NaN NaN NaN \n", - "42 NaN NaN NaN \n", - "43 NaN NaN NaN \n", - "44 NaN NaN NaN \n", - "45 NaN NaN NaN \n", - "46 NaN NaN NaN \n", - "47 NaN NaN NaN \n", - "48 NaN NaN NaN \n", - "49 NaN NaN NaN \n", - "50 NaN NaN NaN \n", - "51 NaN NaN NaN \n", - "52 NaN NaN NaN \n", - "53 NaN NaN NaN \n", - "54 NaN NaN NaN \n", - "55 NaN NaN NaN \n", - "56 NaN NaN NaN \n", - "57 NaN NaN NaN \n", - "58 NaN NaN NaN \n", - "59 NaN NaN NaN \n", - "60 NaN NaN NaN \n", - "61 NaN NaN NaN \n", - "62 NaN NaN NaN \n", - "63 NaN NaN NaN \n", - "64 NaN NaN NaN \n", - "65 NaN NaN NaN \n", - "66 NaN NaN NaN \n", - "67 NaN NaN NaN \n", - "68 NaN NaN NaN \n", - "69 NaN NaN NaN \n", - "70 NaN NaN NaN \n", - "71 NaN NaN NaN \n", - "72 NaN NaN NaN \n", - "73 NaN NaN NaN \n", - "74 NaN NaN NaN \n", - "75 NaN NaN NaN \n", - "76 NaN NaN NaN \n", - "77 NaN NaN NaN \n", - "78 1.0 NaN NaN \n", - "79 2.0 NaN NaN \n", - "80 NaN 0.0 NaN \n", - "81 NaN 1.0 NaN \n", - "82 NaN 2.0 NaN \n", - "83 NaN 3.0 NaN \n", - "84 NaN 4.0 NaN \n", - "85 NaN 5.0 NaN \n", - "86 NaN 6.0 NaN \n", - "87 NaN 7.0 NaN \n", - "88 NaN NaN 0.0 \n", - "89 NaN NaN 1.0 \n", - "90 NaN NaN 2.0 \n", - "91 NaN NaN 3.0 \n", - "92 NaN NaN 4.0 \n", - "93 NaN NaN 5.0 \n", - "94 NaN NaN 6.0 \n", - "95 NaN NaN 7.0 \n", - "96 NaN NaN 8.0 \n", - "97 NaN NaN 9.0 \n", - "98 NaN NaN 10.0 \n", - "99 NaN NaN 11.0 \n", - "100 NaN NaN 12.0 \n", - "101 NaN NaN 13.0 \n", - "102 NaN NaN 14.0 \n", - "103 NaN NaN 15.0 " - ] - }, - "execution_count": 85, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "endocytosis = df.query(f\"{GENESET} == 'endocytosis-0'\").sort_values(\"similarity\", ascending=False)\n", - "terms_summary(endocytosis)" - ] - }, - { - "cell_type": "code", - "execution_count": 86, - "id": "687c3325", - "metadata": {}, - "outputs": [], - "source": [ - "viz('endocytosis-0')" - ] - }, - { - "cell_type": "markdown", - "id": "5af61913", - "metadata": {}, - "source": [ - "![img](output/endocytosis-0-True-v1.png)" - ] - }, - { - "cell_type": "markdown", - "id": "5e21cf82", - "metadata": {}, - "source": [ - "### New Annotations\n", - "\n", - "in 2022-03-24, GO `molecular sequesting` only had 6 genes annotated; this increased to 30 in 2023.\n", - "If these are past the LLM training date then we would not expect these to influence results. Additionally,\n" - ] - }, - { - "cell_type": "code", - "execution_count": 87, - "id": "44ccef38", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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has top termin top 5in top 10size overlapsimilaritynum termsnum GO termsnr size overlapnr similaritymean p valuemin p valuemax p valueproportion significantnum unannotated
2188TrueTrueTrue261.002626101.00e+000.021.83e-930.051.000
2189TrueTrueTrue90.28151521.05e-010.411.83e-931.000.600
2179TrueTrueTrue20.076418.33e-020.501.83e-931.000.500
2178FalseFalseFalse10.048300.00e+000.671.97e-031.000.330
2184TrueFalseTrue10.0319600.00e+000.831.83e-931.000.171
2185FalseFalseFalse10.0310600.00e+000.832.83e-381.000.170
2176FalseFalseFalse10.038816.25e-020.884.66e-041.000.120
2191FalseFalseFalse10.02303000.00e+000.974.71e-021.000.031
2192TrueFalseFalse260.012570252613.23e-030.991.83e-931.000.010
2183FalseFalseFalse00.006200.00e+001.001.00e+001.000.001
2177FalseFalseFalse00.007700.00e+001.001.00e+001.000.000
2182FalseFalseFalse00.005200.00e+001.001.00e+001.000.000
2186FalseFalseFalse00.0019900.00e+001.001.00e+001.000.001
2187FalseFalseFalse00.0013800.00e+001.001.00e+001.000.001
2181FalseFalseFalse00.003300.00e+001.001.00e+001.000.000
2180FalseFalseFalse00.003200.00e+001.001.00e+001.000.000
2190FalseFalseFalse00.00292900.00e+001.001.00e+001.000.0017
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" - ], - "text/plain": [ - " has top term in top 5 in top 10 size overlap similarity num terms \\\n", - "2188 True True True 26 1.00 26 \n", - "2189 True True True 9 0.28 15 \n", - "2179 True True True 2 0.07 6 \n", - "2178 False False False 1 0.04 8 \n", - "2184 True False True 1 0.03 19 \n", - "2185 False False False 1 0.03 10 \n", - "2176 False False False 1 0.03 8 \n", - "2191 False False False 1 0.02 30 \n", - "2192 True False False 26 0.01 2570 \n", - "2183 False False False 0 0.00 6 \n", - "2177 False False False 0 0.00 7 \n", - "2182 False False False 0 0.00 5 \n", - "2186 False False False 0 0.00 19 \n", - "2187 False False False 0 0.00 13 \n", - "2181 False False False 0 0.00 3 \n", - "2180 False False False 0 0.00 3 \n", - "2190 False False False 0 0.00 29 \n", - "\n", - " num GO terms nr size overlap nr similarity mean p value min p value \\\n", - "2188 26 10 1.00e+00 0.02 1.83e-93 \n", - "2189 15 2 1.05e-01 0.41 1.83e-93 \n", - "2179 4 1 8.33e-02 0.50 1.83e-93 \n", - "2178 3 0 0.00e+00 0.67 1.97e-03 \n", - "2184 6 0 0.00e+00 0.83 1.83e-93 \n", - "2185 6 0 0.00e+00 0.83 2.83e-38 \n", - "2176 8 1 6.25e-02 0.88 4.66e-04 \n", - "2191 30 0 0.00e+00 0.97 4.71e-02 \n", - "2192 2526 1 3.23e-03 0.99 1.83e-93 \n", - "2183 2 0 0.00e+00 1.00 1.00e+00 \n", - "2177 7 0 0.00e+00 1.00 1.00e+00 \n", - "2182 2 0 0.00e+00 1.00 1.00e+00 \n", - "2186 9 0 0.00e+00 1.00 1.00e+00 \n", - "2187 8 0 0.00e+00 1.00 1.00e+00 \n", - "2181 3 0 0.00e+00 1.00 1.00e+00 \n", - "2180 2 0 0.00e+00 1.00 1.00e+00 \n", - "2190 29 0 0.00e+00 1.00 1.00e+00 \n", - "\n", - " max p value proportion significant num unannotated \n", - "2188 0.05 1.00 0 \n", - "2189 1.00 0.60 0 \n", - "2179 1.00 0.50 0 \n", - "2178 1.00 0.33 0 \n", - "2184 1.00 0.17 1 \n", - "2185 1.00 0.17 0 \n", - "2176 1.00 0.12 0 \n", - "2191 1.00 0.03 1 \n", - "2192 1.00 0.01 0 \n", - "2183 1.00 0.00 1 \n", - "2177 1.00 0.00 0 \n", - "2182 1.00 0.00 0 \n", - "2186 1.00 0.00 1 \n", - "2187 1.00 0.00 1 \n", - "2181 1.00 0.00 0 \n", - "2180 1.00 0.00 0 \n", - "2190 1.00 0.00 17 " - ] - }, - "execution_count": 87, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "sequestering = df.query(f\"{GENESET} == 'molecular sequestering-0'\").sort_values(\"similarity\", ascending=False)\n", - "sequestering[eval_summary_cols] " - ] - }, - { - "cell_type": "code", - "execution_count": 88, - "id": "044319e6", - "metadata": { - "scrolled": false - }, - "outputs": [ - { - "data": { - "text/html": [ - "
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"
idlabelredundantstandardstandard no ontologydav ontological synopsisturbo no synopsisturbo ontological synopsisrank baseddav no synopsisdav narrative synopsisturbo narrative synopsis
0GO:0140313molecular sequestering activityFalse0.01.06.0NaNNaNNaNNaNNaNNaN
1GO:0140311protein sequestering activityTrue1.00.0NaNNaNNaNNaNNaNNaNNaN
2GO:0140487metal ion sequestering activityTrue2.0NaNNaNNaNNaNNaNNaNNaNNaN
3GO:0048519negative regulation of biological processFalse3.0NaNNaNNaNNaNNaNNaNNaNNaN
4GO:0006950response to stressFalse4.0NaNNaN1.0NaNNaNNaNNaNNaN
5GO:0048523negative regulation of cellular processTrue5.0NaNNaNNaN3.0NaNNaNNaNNaN
6GO:0140678molecular function inhibitor activityFalse6.02.0NaNNaNNaNNaNNaNNaNNaN
7GO:0048585negative regulation of response to stimulusTrue7.0NaNNaNNaNNaNNaNNaNNaNNaN
8GO:0036316SREBP-SCAP complex retention in endoplasmic reticulumTrue8.04.0NaNNaNNaNNaNNaNNaNNaN
9GO:0140315iron ion sequestering activityTrue9.06.0NaNNaNNaNNaNNaNNaNNaN
10GO:0140486zinc ion sequestering activityTrue10.05.0NaNNaNNaNNaNNaNNaNNaN
11GO:0140610RNA sequestering activityTrue11.03.0NaNNaNNaNNaNNaNNaNNaN
12GO:0005488bindingFalse12.0NaNNaNNaNNaNNaNNaNNaNNaN
13GO:0051235maintenance of locationTrue13.0NaNNaNNaNNaNNaNNaNNaNNaN
14GO:0002682regulation of immune system processFalse14.0NaNNaNNaNNaNNaNNaNNaNNaN
15GO:0010629negative regulation of gene expressionTrue15.0NaNNaNNaNNaNNaNNaNNaNNaN
16GO:0032937SREBP-SCAP-Insig complexFalse16.07.0NaNNaNNaNNaNNaNNaNNaN
17GO:2000639negative regulation of SREBP signaling pathwayTrue17.0NaNNaNNaNNaNNaNNaNNaNNaN
18GO:0009968negative regulation of signal transductionTrue18.0NaNNaNNaNNaNNaNNaNNaNNaN
19GO:0000041transition metal ion transportFalse19.0NaNNaNNaNNaNNaNNaNNaNNaN
20GO:1901222regulation of NIK/NF-kappaB signalingFalse20.0NaNNaNNaNNaNNaNNaNNaNNaN
21GO:0051651maintenance of location in cellTrue21.0NaNNaNNaNNaNNaNNaNNaNNaN
22GO:0010648negative regulation of cell communicationTrue22.0NaNNaNNaNNaNNaNNaNNaNNaN
23GO:0023057negative regulation of signalingTrue23.0NaNNaNNaNNaNNaNNaNNaNNaN
24GO:0042802identical protein bindingTrue24.08.0NaNNaNNaN24.0NaNNaNNaN
25GO:0071417cellular response to organonitrogen compoundFalse25.0NaNNaNNaNNaNNaNNaNNaNNaN
26GO:0060363cranial suture morphogenesisFalseNaN9.0NaNNaNNaNNaNNaNNaNNaN
27GO:0010894negative regulation of steroid biosynthetic processFalseNaN10.0NaNNaNNaNNaNNaNNaNNaN
28GO:0090402oncogene-induced cell senescenceFalseNaN11.0NaNNaNNaNNaNNaNNaNNaN
29GO:0034198cellular response to amino acid starvationFalseNaN12.0NaNNaNNaNNaNNaNNaNNaN
30GO:0008142oxysterol bindingFalseNaN13.0NaNNaNNaNNaNNaNNaNNaN
31GO:0032933SREBP signaling pathwayFalseNaN14.0NaNNaNNaNNaNNaNNaNNaN
32molecular sequesteringNoneFalseNaNNaNNaNNaN0.0NaNNaNNaNNaN
33protein binding activityNoneFalseNaNNaNNaNNaN1.0NaNNaNNaNNaN
34transport of metal ionsNoneFalseNaNNaNNaNNaN2.0NaNNaNNaNNaN
35response to infection and stressNoneFalseNaNNaNNaNNaN4.0NaNNaNNaNNaN
36GO:0010468regulation of gene expressionFalseNaNNaNNaNNaN5.0NaNNaNNaNNaN
37GO:0019722calcium-mediated signalingFalseNaNNaNNaNNaN6.0NaNNaNNaNNaN
38regulation of transcriptionNoneFalseNaNNaNNaNNaN7.0NaNNaNNaNNaN
39calcium ion binding activityNoneFalseNaNNaN0.0NaNNaNNaNNaNNaNNaN
40identical protein binding activityNoneFalseNaNNaN1.0NaNNaNNaNNaNNaNNaN
41GO:0004252serine-type endopeptidase activityFalseNaNNaN2.0NaNNaNNaNNaNNaNNaN
42GO:0140314calcium ion sequestering activityFalseNaNNaN3.0NaNNaNNaNNaNNaNNaN
43calcium-dependent protein binding activityNoneFalseNaNNaN4.0NaNNaNNaNNaNNaNNaN
44arginine binding activityNoneFalseNaNNaN5.0NaNNaNNaNNaNNaNNaN
45enzyme binding activityNoneFalseNaNNaN7.0NaNNaNNaNNaNNaNNaN
46GO:0019887protein kinase regulator activityFalseNaNNaN8.0NaNNaNNaNNaNNaNNaN
47nf-κb binding activityNoneFalseNaNNaN9.0NaNNaNNaNNaNNaNNaN
48nuclear localization sequence binding activityNoneFalseNaNNaN10.0NaNNaNNaNNaNNaNNaN
49oxysterol binding activityNoneFalseNaNNaN11.0NaNNaNNaNNaNNaNNaN
50rage receptor binding activityNoneFalseNaNNaN12.0NaNNaNNaNNaNNaNNaN
51ubiquitin protein ligase binding activityNoneFalseNaNNaN13.0NaNNaNNaNNaNNaNNaN
52actin binding activityNoneFalseNaNNaN14.0NaNNaNNaNNaNNaNNaN
53rig-i binding activityNoneFalseNaNNaN15.0NaNNaNNaNNaNNaNNaN
54GO:0003713transcription coactivator activityFalseNaNNaN16.0NaNNaNNaNNaNNaNNaN
55zinc ion binding activityNoneFalseNaNNaN17.0NaNNaNNaNNaNNaNNaN
56GO:1903231mRNA base-pairing translational repressor activityFalseNaNNaN18.0NaNNaNNaNNaNNaNNaN
57GO:0002376immune system processFalseNaNNaNNaN0.0NaNNaNNaNNaNNaN
58GO:0006457protein foldingFalseNaNNaNNaN2.0NaNNaNNaNNaNNaN
59GO:0051641cellular localizationFalseNaNNaNNaN3.0NaNNaNNaNNaNNaN
60GO:0006396RNA processingFalseNaNNaNNaN4.0NaNNaNNaNNaNNaN
61GO:0006829zinc ion transportFalseNaNNaNNaN5.0NaNNaNNaNNaNNaN
62GO:0010467gene expressionFalseNaNNaNNaN6.0NaNNaNNaNNaNNaN
63GO:0007165signal transductionFalseNaNNaNNaN7.0NaN21.0NaNNaNNaN
64GO:0003723RNA bindingFalseNaNNaNNaNNaNNaN0.0NaNNaNNaN
65GO:0005730nucleolusFalseNaNNaNNaNNaNNaN1.0NaNNaNNaN
66GO:0005783endoplasmic reticulumFalseNaNNaNNaNNaNNaN2.0NaNNaNNaN
67GO:0000122negative regulation of transcription by RNA polymerase IIFalseNaNNaNNaNNaNNaN3.0NaNNaNNaN
68GO:0005829cytosolFalseNaNNaNNaNNaNNaN4.0NaNNaNNaN
69GO:0070062extracellular exosomeFalseNaNNaNNaNNaNNaN5.0NaNNaNNaN
70GO:0000981DNA-binding transcription factor activity, RNA polymerase II-specificFalseNaNNaNNaNNaNNaN6.0NaNNaNNaN
71GO:0008270zinc ion bindingFalseNaNNaNNaNNaNNaN7.0NaNNaNNaN
72GO:0048471perinuclear region of cytoplasmFalseNaNNaNNaNNaNNaN8.0NaNNaNNaN
73GO:0005886plasma membraneFalseNaNNaNNaNNaNNaN9.0NaNNaNNaN
74GO:0005615extracellular spaceFalseNaNNaNNaNNaNNaN10.0NaNNaNNaN
75GO:0005576extracellular regionFalseNaNNaNNaNNaNNaN11.0NaNNaNNaN
76GO:0005737cytoplasmFalseNaNNaNNaNNaNNaN12.0NaNNaNNaN
77GO:0043231intracellular membrane-bounded organelleFalseNaNNaNNaNNaNNaN13.0NaNNaNNaN
78GO:0005789endoplasmic reticulum membraneFalseNaNNaNNaNNaNNaN14.0NaNNaNNaN
79GO:0005524ATP bindingFalseNaNNaNNaNNaNNaN15.0NaNNaNNaN
80GO:0007186G protein-coupled receptor signaling pathwayFalseNaNNaNNaNNaNNaN16.0NaNNaNNaN
81GO:0000978RNA polymerase II cis-regulatory region sequence-specific DNA bindingFalseNaNNaNNaNNaNNaN17.0NaNNaNNaN
82GO:0005739mitochondrionFalseNaNNaNNaNNaNNaN18.0NaNNaNNaN
83GO:0006357regulation of transcription by RNA polymerase IIFalseNaNNaNNaNNaNNaN19.0NaNNaNNaN
84GO:0000785chromatinFalseNaNNaNNaNNaNNaN20.0NaNNaNNaN
85GO:0016020membraneFalseNaNNaNNaNNaNNaN22.0NaNNaNNaN
86GO:0045944positive regulation of transcription by RNA polymerase IIFalseNaNNaNNaNNaNNaN23.0NaNNaNNaN
87GO:0003677DNA bindingFalseNaNNaNNaNNaNNaN25.0NaNNaNNaN
88GO:0005794Golgi apparatusFalseNaNNaNNaNNaNNaN26.0NaNNaNNaN
89GO:0046872metal ion bindingFalseNaNNaNNaNNaNNaN27.0NaNNaNNaN
90GO:0005634nucleusFalseNaNNaNNaNNaNNaN28.0NaNNaNNaN
91GO:0005654nucleoplasmFalseNaNNaNNaNNaNNaN29.0NaNNaNNaN
92GO:0000075cell cycle checkpoint signalingFalseNaNNaNNaNNaNNaNNaN0.0NaNNaN
93cell adhesion/motility complexNoneFalseNaNNaNNaNNaNNaNNaN1.0NaNNaN
94transcriptional complexNoneFalseNaNNaNNaNNaNNaNNaN2.0NaNNaN
95GO:0036211protein modification processFalseNaNNaNNaNNaNNaNNaN3.0NaNNaN
96rna processing complexNoneFalseNaNNaNNaNNaNNaNNaN4.0NaNNaN
97this list of genes encodes proteins involved in a range of cellular processes such as cell cycle progressionNoneFalseNaNNaNNaNNaNNaNNaNNaN0.0NaN
98GO:0006897endocytosisFalseNaNNaNNaNNaNNaNNaNNaN1.0NaN
99iron storage and regulationNoneFalseNaNNaNNaNNaNNaNNaNNaN2.0NaN
100cellular response to stress and inflammationNoneFalseNaNNaNNaNNaNNaNNaNNaN3.0NaN
101GO:0006915apoptotic processFalseNaNNaNNaNNaNNaNNaNNaN17.0NaN
102transcriptional regulationNoneFalseNaNNaNNaNNaNNaNNaNNaN5.0NaN
103GO:0046907intracellular transportFalseNaNNaNNaNNaNNaNNaNNaN6.0NaN
104GO:0016567protein ubiquitinationFalseNaNNaNNaNNaNNaNNaNNaN7.0NaN
105and toxic metal and cytosolic signaling. enriched terms include protein bindingNoneFalseNaNNaNNaNNaNNaNNaNNaN8.0NaN
106lipid and hormone transportNoneFalseNaNNaNNaNNaNNaNNaNNaN9.0NaN
107GO:0003779actin bindingFalseNaNNaNNaNNaNNaNNaNNaN10.0NaN
108GO:0003724RNA helicase activityFalseNaNNaNNaNNaNNaNNaNNaN11.0NaN
109GO:0006511ubiquitin-dependent protein catabolic processFalseNaNNaNNaNNaNNaNNaNNaN12.0NaN
110cell cycle progressionNoneFalseNaNNaNNaNNaNNaNNaNNaN13.0NaN
111and negative regulation of nitrogen compound metabolic process. mechanism: these genes are involved in a wide range of processes related to regulating cell growthNoneFalseNaNNaNNaNNaNNaNNaNNaN14.0NaN
112GO:0032502developmental processFalseNaNNaNNaNNaNNaNNaNNaN15.0NaN
113and homeostasis. they play a role in pathways such as the cell cycleNoneFalseNaNNaNNaNNaNNaNNaNNaN16.0NaN
114inflammatory metabolic processesNoneFalseNaNNaNNaNNaNNaNNaNNaN18.0NaN
115GO:0005515protein bindingFalseNaNNaNNaNNaNNaNNaNNaNNaN0.0
116GO:0006955immune responseFalseNaNNaNNaNNaNNaNNaNNaNNaN1.0
117intracellular transport\\n\\nmechanism/NoneFalseNaNNaNNaNNaNNaNNaNNaNNaN2.0
\n", - "
" - ], - "text/plain": [ - " id \\\n", - "0 GO:0140313 \n", - "1 GO:0140311 \n", - "2 GO:0140487 \n", - "3 GO:0048519 \n", - "4 GO:0006950 \n", - "5 GO:0048523 \n", - "6 GO:0140678 \n", - "7 GO:0048585 \n", - "8 GO:0036316 \n", - "9 GO:0140315 \n", - "10 GO:0140486 \n", - "11 GO:0140610 \n", - "12 GO:0005488 \n", - "13 GO:0051235 \n", - "14 GO:0002682 \n", - "15 GO:0010629 \n", - "16 GO:0032937 \n", - "17 GO:2000639 \n", - "18 GO:0009968 \n", - "19 GO:0000041 \n", - "20 GO:1901222 \n", - "21 GO:0051651 \n", - "22 GO:0010648 \n", - "23 GO:0023057 \n", - "24 GO:0042802 \n", - "25 GO:0071417 \n", - "26 GO:0060363 \n", - "27 GO:0010894 \n", - "28 GO:0090402 \n", - "29 GO:0034198 \n", - "30 GO:0008142 \n", - "31 GO:0032933 \n", - "32 molecular sequestering \n", - "33 protein binding activity \n", - "34 transport of metal ions \n", - "35 response to infection and stress \n", - "36 GO:0010468 \n", - "37 GO:0019722 \n", - "38 regulation of transcription \n", - "39 calcium ion binding activity \n", - "40 identical protein binding activity \n", - "41 GO:0004252 \n", - "42 GO:0140314 \n", - "43 calcium-dependent protein binding activity \n", - "44 arginine binding activity \n", - "45 enzyme binding activity \n", - "46 GO:0019887 \n", - "47 nf-κb binding activity \n", - "48 nuclear localization sequence binding activity \n", - "49 oxysterol binding activity \n", - "50 rage receptor binding activity \n", - "51 ubiquitin protein ligase binding activity \n", - "52 actin binding activity \n", - "53 rig-i binding activity \n", - "54 GO:0003713 \n", - "55 zinc ion binding activity \n", - "56 GO:1903231 \n", - "57 GO:0002376 \n", - "58 GO:0006457 \n", - "59 GO:0051641 \n", - "60 GO:0006396 \n", - "61 GO:0006829 \n", - "62 GO:0010467 \n", - "63 GO:0007165 \n", - "64 GO:0003723 \n", - "65 GO:0005730 \n", - "66 GO:0005783 \n", - "67 GO:0000122 \n", - "68 GO:0005829 \n", - "69 GO:0070062 \n", - "70 GO:0000981 \n", - "71 GO:0008270 \n", - "72 GO:0048471 \n", - "73 GO:0005886 \n", - "74 GO:0005615 \n", - "75 GO:0005576 \n", - "76 GO:0005737 \n", - "77 GO:0043231 \n", - "78 GO:0005789 \n", - "79 GO:0005524 \n", - "80 GO:0007186 \n", - "81 GO:0000978 \n", - "82 GO:0005739 \n", - "83 GO:0006357 \n", - "84 GO:0000785 \n", - "85 GO:0016020 \n", - "86 GO:0045944 \n", - "87 GO:0003677 \n", - "88 GO:0005794 \n", - "89 GO:0046872 \n", - "90 GO:0005634 \n", - "91 GO:0005654 \n", - "92 GO:0000075 \n", - "93 cell adhesion/motility complex \n", - "94 transcriptional complex \n", - "95 GO:0036211 \n", - "96 rna processing complex \n", - "97 this list of genes encodes proteins involved in a range of cellular processes such as cell cycle progression \n", - "98 GO:0006897 \n", - "99 iron storage and regulation \n", - "100 cellular response to stress and inflammation \n", - "101 GO:0006915 \n", - "102 transcriptional regulation \n", - "103 GO:0046907 \n", - "104 GO:0016567 \n", - "105 and toxic metal and cytosolic signaling. enriched terms include protein binding \n", - "106 lipid and hormone transport \n", - "107 GO:0003779 \n", - "108 GO:0003724 \n", - "109 GO:0006511 \n", - "110 cell cycle progression \n", - "111 and negative regulation of nitrogen compound metabolic process. mechanism: these genes are involved in a wide range of processes related to regulating cell growth \n", - "112 GO:0032502 \n", - "113 and homeostasis. they play a role in pathways such as the cell cycle \n", - "114 inflammatory metabolic processes \n", - "115 GO:0005515 \n", - "116 GO:0006955 \n", - "117 intracellular transport\\n\\nmechanism/ \n", - "\n", - " label \\\n", - "0 molecular sequestering activity \n", - "1 protein sequestering activity \n", - "2 metal ion sequestering activity \n", - "3 negative regulation of biological process \n", - "4 response to stress \n", - "5 negative regulation of cellular process \n", - "6 molecular function inhibitor activity \n", - "7 negative regulation of response to stimulus \n", - "8 SREBP-SCAP complex retention in endoplasmic reticulum \n", - "9 iron ion sequestering activity \n", - "10 zinc ion sequestering activity \n", - "11 RNA sequestering activity \n", - "12 binding \n", - "13 maintenance of location \n", - "14 regulation of immune system process \n", - "15 negative regulation of gene expression \n", - "16 SREBP-SCAP-Insig complex \n", - "17 negative regulation of SREBP signaling pathway \n", - "18 negative regulation of signal transduction \n", - "19 transition metal ion transport \n", - "20 regulation of NIK/NF-kappaB signaling \n", - "21 maintenance of location in cell \n", - "22 negative regulation of cell communication \n", - "23 negative regulation of signaling \n", - "24 identical protein binding \n", - "25 cellular response to organonitrogen compound \n", - "26 cranial suture morphogenesis \n", - "27 negative regulation of steroid biosynthetic process \n", - "28 oncogene-induced cell senescence \n", - "29 cellular response to amino acid starvation \n", - "30 oxysterol binding \n", - "31 SREBP signaling pathway \n", - "32 None \n", - "33 None \n", - "34 None \n", - "35 None \n", - "36 regulation of gene expression \n", - "37 calcium-mediated signaling \n", - "38 None \n", - "39 None \n", - "40 None \n", - "41 serine-type endopeptidase activity \n", - "42 calcium ion sequestering activity \n", - "43 None \n", - "44 None \n", - "45 None \n", - "46 protein kinase regulator activity \n", - "47 None \n", - "48 None \n", - "49 None \n", - "50 None \n", - "51 None \n", - "52 None \n", - "53 None \n", - "54 transcription coactivator activity \n", - "55 None \n", - "56 mRNA base-pairing translational repressor activity \n", - "57 immune system process \n", - "58 protein folding \n", - "59 cellular localization \n", - "60 RNA processing \n", - "61 zinc ion transport \n", - "62 gene expression \n", - "63 signal transduction \n", - "64 RNA binding \n", - "65 nucleolus \n", - "66 endoplasmic reticulum \n", - "67 negative regulation of transcription by RNA polymerase II \n", - "68 cytosol \n", - "69 extracellular exosome \n", - "70 DNA-binding transcription factor activity, RNA polymerase II-specific \n", - "71 zinc ion binding \n", - "72 perinuclear region of cytoplasm \n", - "73 plasma membrane \n", - "74 extracellular space \n", - "75 extracellular region \n", - "76 cytoplasm \n", - "77 intracellular membrane-bounded organelle \n", - "78 endoplasmic reticulum membrane \n", - "79 ATP binding \n", - "80 G protein-coupled receptor signaling pathway \n", - "81 RNA polymerase II cis-regulatory region sequence-specific DNA binding \n", - "82 mitochondrion \n", - "83 regulation of transcription by RNA polymerase II \n", - "84 chromatin \n", - "85 membrane \n", - "86 positive regulation of transcription by RNA polymerase II \n", - "87 DNA binding \n", - "88 Golgi apparatus \n", - "89 metal ion binding \n", - "90 nucleus \n", - "91 nucleoplasm \n", - "92 cell cycle checkpoint signaling \n", - "93 None \n", - "94 None \n", - "95 protein modification process \n", - "96 None \n", - "97 None \n", - "98 endocytosis \n", - "99 None \n", - "100 None \n", - "101 apoptotic process \n", - "102 None \n", - "103 intracellular transport \n", - "104 protein ubiquitination \n", - "105 None \n", - "106 None \n", - "107 actin binding \n", - "108 RNA helicase activity \n", - "109 ubiquitin-dependent protein catabolic process \n", - "110 None \n", - "111 None \n", - "112 developmental process \n", - "113 None \n", - "114 None \n", - "115 protein binding \n", - "116 immune response \n", - "117 None \n", - "\n", - " redundant standard standard no ontology dav ontological synopsis \\\n", - "0 False 0.0 1.0 6.0 \n", - "1 True 1.0 0.0 NaN \n", - "2 True 2.0 NaN NaN \n", - "3 False 3.0 NaN NaN \n", - "4 False 4.0 NaN NaN \n", - "5 True 5.0 NaN NaN \n", - "6 False 6.0 2.0 NaN \n", - "7 True 7.0 NaN NaN \n", - "8 True 8.0 4.0 NaN \n", - "9 True 9.0 6.0 NaN \n", - "10 True 10.0 5.0 NaN \n", - "11 True 11.0 3.0 NaN \n", - "12 False 12.0 NaN NaN \n", - "13 True 13.0 NaN NaN \n", - "14 False 14.0 NaN NaN \n", - "15 True 15.0 NaN NaN \n", - "16 False 16.0 7.0 NaN \n", - "17 True 17.0 NaN NaN \n", - "18 True 18.0 NaN NaN \n", - "19 False 19.0 NaN NaN \n", - "20 False 20.0 NaN NaN \n", - "21 True 21.0 NaN NaN \n", - "22 True 22.0 NaN NaN \n", - "23 True 23.0 NaN NaN \n", - "24 True 24.0 8.0 NaN \n", - "25 False 25.0 NaN NaN \n", - "26 False NaN 9.0 NaN \n", - "27 False NaN 10.0 NaN \n", - "28 False NaN 11.0 NaN \n", - "29 False NaN 12.0 NaN \n", - "30 False NaN 13.0 NaN \n", - "31 False NaN 14.0 NaN \n", - "32 False NaN NaN NaN \n", - "33 False NaN NaN NaN \n", - "34 False NaN NaN NaN \n", - "35 False NaN NaN NaN \n", - "36 False NaN NaN NaN \n", - "37 False NaN NaN NaN \n", - "38 False NaN NaN NaN \n", - "39 False NaN NaN 0.0 \n", - "40 False NaN NaN 1.0 \n", - "41 False NaN NaN 2.0 \n", - "42 False NaN NaN 3.0 \n", - "43 False NaN NaN 4.0 \n", - "44 False NaN NaN 5.0 \n", - "45 False NaN NaN 7.0 \n", - "46 False NaN NaN 8.0 \n", - "47 False NaN NaN 9.0 \n", - "48 False NaN NaN 10.0 \n", - "49 False NaN NaN 11.0 \n", - "50 False NaN NaN 12.0 \n", - "51 False NaN NaN 13.0 \n", - "52 False NaN NaN 14.0 \n", - "53 False NaN NaN 15.0 \n", - "54 False NaN NaN 16.0 \n", - "55 False NaN NaN 17.0 \n", - "56 False NaN NaN 18.0 \n", - "57 False NaN NaN NaN \n", - "58 False NaN NaN NaN \n", - "59 False NaN NaN NaN \n", - "60 False NaN NaN NaN \n", - "61 False NaN NaN NaN \n", - "62 False NaN NaN NaN \n", - "63 False NaN NaN NaN \n", - "64 False NaN NaN NaN \n", - "65 False NaN NaN NaN \n", - "66 False NaN NaN NaN \n", - "67 False NaN NaN NaN \n", - "68 False NaN NaN NaN \n", - "69 False NaN NaN NaN \n", - "70 False NaN NaN NaN \n", - "71 False NaN NaN NaN \n", - "72 False NaN NaN NaN \n", - "73 False NaN NaN NaN \n", - "74 False NaN NaN NaN \n", - "75 False NaN NaN NaN \n", - "76 False NaN NaN NaN \n", - "77 False NaN NaN NaN \n", - "78 False NaN NaN NaN \n", - "79 False NaN NaN NaN \n", - "80 False NaN NaN NaN \n", - "81 False NaN NaN NaN \n", - "82 False NaN NaN NaN \n", - "83 False NaN NaN NaN \n", - "84 False NaN NaN NaN \n", - "85 False NaN NaN NaN \n", - "86 False NaN NaN NaN \n", - "87 False NaN NaN NaN \n", - "88 False NaN NaN NaN \n", - "89 False NaN NaN NaN \n", - "90 False NaN NaN NaN \n", - "91 False NaN NaN NaN \n", - "92 False NaN NaN NaN \n", - "93 False NaN NaN NaN \n", - "94 False NaN NaN NaN \n", - "95 False NaN NaN NaN \n", - "96 False NaN NaN NaN \n", - "97 False NaN NaN NaN \n", - "98 False NaN NaN NaN \n", - "99 False NaN NaN NaN \n", - "100 False NaN NaN NaN \n", - "101 False NaN NaN NaN \n", - "102 False NaN NaN NaN \n", - "103 False NaN NaN NaN \n", - "104 False NaN NaN NaN \n", - "105 False NaN NaN NaN \n", - "106 False NaN NaN NaN \n", - "107 False NaN NaN NaN \n", - "108 False NaN NaN NaN \n", - "109 False NaN NaN NaN \n", - "110 False NaN NaN NaN \n", - "111 False NaN NaN NaN \n", - "112 False NaN NaN NaN \n", - "113 False NaN NaN NaN \n", - "114 False NaN NaN NaN \n", - "115 False NaN NaN NaN \n", - "116 False NaN NaN NaN \n", - "117 False NaN NaN NaN \n", - "\n", - " turbo no synopsis turbo ontological synopsis rank based \\\n", - "0 NaN NaN NaN \n", - "1 NaN NaN NaN \n", - "2 NaN NaN NaN \n", - "3 NaN NaN NaN \n", - "4 1.0 NaN NaN \n", - "5 NaN 3.0 NaN \n", - "6 NaN NaN NaN \n", - "7 NaN NaN NaN \n", - "8 NaN NaN NaN \n", - "9 NaN NaN NaN \n", - "10 NaN NaN NaN \n", - "11 NaN NaN NaN \n", - "12 NaN NaN NaN \n", - "13 NaN NaN NaN \n", - "14 NaN NaN NaN \n", - "15 NaN NaN NaN \n", - "16 NaN NaN NaN \n", - "17 NaN NaN NaN \n", - "18 NaN NaN NaN \n", - "19 NaN NaN NaN \n", - "20 NaN NaN NaN \n", - "21 NaN NaN NaN \n", - "22 NaN NaN NaN \n", - "23 NaN NaN NaN \n", - "24 NaN NaN 24.0 \n", - "25 NaN NaN NaN \n", - "26 NaN NaN NaN \n", - "27 NaN NaN NaN \n", - "28 NaN NaN NaN \n", - "29 NaN NaN NaN \n", - "30 NaN NaN NaN \n", - "31 NaN NaN NaN \n", - "32 NaN 0.0 NaN \n", - "33 NaN 1.0 NaN \n", - "34 NaN 2.0 NaN \n", - "35 NaN 4.0 NaN \n", - "36 NaN 5.0 NaN \n", - "37 NaN 6.0 NaN \n", - "38 NaN 7.0 NaN \n", - "39 NaN NaN NaN \n", - "40 NaN NaN NaN \n", - "41 NaN NaN NaN \n", - "42 NaN NaN NaN \n", - "43 NaN NaN NaN \n", - "44 NaN NaN NaN \n", - "45 NaN NaN NaN \n", - "46 NaN NaN NaN \n", - "47 NaN NaN NaN \n", - "48 NaN NaN NaN \n", - "49 NaN NaN NaN \n", - "50 NaN NaN NaN \n", - "51 NaN NaN NaN \n", - "52 NaN NaN NaN \n", - "53 NaN NaN NaN \n", - "54 NaN NaN NaN \n", - "55 NaN NaN NaN \n", - "56 NaN NaN NaN \n", - "57 0.0 NaN NaN \n", - "58 2.0 NaN NaN \n", - "59 3.0 NaN NaN \n", - "60 4.0 NaN NaN \n", - "61 5.0 NaN NaN \n", - "62 6.0 NaN NaN \n", - "63 7.0 NaN 21.0 \n", - "64 NaN NaN 0.0 \n", - "65 NaN NaN 1.0 \n", - "66 NaN NaN 2.0 \n", - "67 NaN NaN 3.0 \n", - "68 NaN NaN 4.0 \n", - "69 NaN NaN 5.0 \n", - "70 NaN NaN 6.0 \n", - "71 NaN NaN 7.0 \n", - "72 NaN NaN 8.0 \n", - "73 NaN NaN 9.0 \n", - "74 NaN NaN 10.0 \n", - "75 NaN NaN 11.0 \n", - "76 NaN NaN 12.0 \n", - "77 NaN NaN 13.0 \n", - "78 NaN NaN 14.0 \n", - "79 NaN NaN 15.0 \n", - "80 NaN NaN 16.0 \n", - "81 NaN NaN 17.0 \n", - "82 NaN NaN 18.0 \n", - "83 NaN NaN 19.0 \n", - "84 NaN NaN 20.0 \n", - "85 NaN NaN 22.0 \n", - "86 NaN NaN 23.0 \n", - "87 NaN NaN 25.0 \n", - "88 NaN NaN 26.0 \n", - "89 NaN NaN 27.0 \n", - "90 NaN NaN 28.0 \n", - "91 NaN NaN 29.0 \n", - "92 NaN NaN NaN \n", - "93 NaN NaN NaN \n", - "94 NaN NaN NaN \n", - "95 NaN NaN NaN \n", - "96 NaN NaN NaN \n", - "97 NaN NaN NaN \n", - "98 NaN NaN NaN \n", - "99 NaN NaN NaN \n", - "100 NaN NaN NaN \n", - "101 NaN NaN NaN \n", - "102 NaN NaN NaN \n", - "103 NaN NaN NaN \n", - "104 NaN NaN NaN \n", - "105 NaN NaN NaN \n", - "106 NaN NaN NaN \n", - "107 NaN NaN NaN \n", - "108 NaN NaN NaN \n", - "109 NaN NaN NaN \n", - "110 NaN NaN NaN \n", - "111 NaN NaN NaN \n", - "112 NaN NaN NaN \n", - "113 NaN NaN NaN \n", - "114 NaN NaN NaN \n", - "115 NaN NaN NaN \n", - "116 NaN NaN NaN \n", - "117 NaN NaN NaN \n", - "\n", - " dav no synopsis dav narrative synopsis turbo narrative synopsis \n", - "0 NaN NaN NaN \n", - "1 NaN NaN NaN \n", - "2 NaN NaN NaN \n", - "3 NaN NaN NaN \n", - "4 NaN NaN NaN \n", - "5 NaN NaN NaN \n", - "6 NaN NaN NaN \n", - "7 NaN NaN NaN \n", - "8 NaN NaN NaN \n", - "9 NaN NaN NaN \n", - "10 NaN NaN NaN \n", - "11 NaN NaN NaN \n", - "12 NaN NaN NaN \n", - "13 NaN NaN NaN \n", - "14 NaN NaN NaN \n", - "15 NaN NaN NaN \n", - "16 NaN NaN NaN \n", - "17 NaN NaN NaN \n", - "18 NaN NaN NaN \n", - "19 NaN NaN NaN \n", - "20 NaN NaN NaN \n", - "21 NaN NaN NaN \n", - "22 NaN NaN NaN \n", - "23 NaN NaN NaN \n", - "24 NaN NaN NaN \n", - "25 NaN NaN NaN \n", - "26 NaN NaN NaN \n", - "27 NaN NaN NaN \n", - "28 NaN NaN NaN \n", - "29 NaN NaN NaN \n", - "30 NaN NaN NaN \n", - "31 NaN NaN NaN \n", - "32 NaN NaN NaN \n", - "33 NaN NaN NaN \n", - "34 NaN NaN NaN \n", - "35 NaN NaN NaN \n", - "36 NaN NaN NaN \n", - "37 NaN NaN NaN \n", - "38 NaN NaN NaN \n", - "39 NaN NaN NaN \n", - "40 NaN NaN NaN \n", - "41 NaN NaN NaN \n", - "42 NaN NaN NaN \n", - "43 NaN NaN NaN \n", - "44 NaN NaN NaN \n", - "45 NaN NaN NaN \n", - "46 NaN NaN NaN \n", - "47 NaN NaN NaN \n", - "48 NaN NaN NaN \n", - "49 NaN NaN NaN \n", - "50 NaN NaN NaN \n", - "51 NaN NaN NaN \n", - "52 NaN NaN NaN \n", - "53 NaN NaN NaN \n", - "54 NaN NaN NaN \n", - "55 NaN NaN NaN \n", - "56 NaN NaN NaN \n", - "57 NaN NaN NaN \n", - "58 NaN NaN NaN \n", - "59 NaN NaN NaN \n", - "60 NaN NaN NaN \n", - "61 NaN NaN NaN \n", - "62 NaN NaN NaN \n", - "63 NaN NaN NaN \n", - "64 NaN NaN NaN \n", - "65 NaN NaN NaN \n", - "66 NaN NaN NaN \n", - "67 NaN NaN NaN \n", - "68 NaN NaN NaN \n", - "69 NaN NaN NaN \n", - "70 NaN NaN NaN \n", - "71 NaN NaN NaN \n", - "72 NaN NaN NaN \n", - "73 NaN NaN NaN \n", - "74 NaN NaN NaN \n", - "75 NaN NaN NaN \n", - "76 NaN NaN NaN \n", - "77 NaN NaN NaN \n", - "78 NaN NaN NaN \n", - "79 NaN NaN NaN \n", - "80 NaN NaN NaN \n", - "81 NaN NaN NaN \n", - "82 NaN NaN NaN \n", - "83 NaN NaN NaN \n", - "84 NaN NaN NaN \n", - "85 NaN NaN NaN \n", - "86 NaN NaN NaN \n", - "87 NaN NaN NaN \n", - "88 NaN NaN NaN \n", - "89 NaN NaN NaN \n", - "90 NaN NaN NaN \n", - "91 NaN NaN NaN \n", - "92 0.0 NaN NaN \n", - "93 1.0 NaN NaN \n", - "94 2.0 NaN NaN \n", - "95 3.0 NaN NaN \n", - "96 4.0 NaN NaN \n", - "97 NaN 0.0 NaN \n", - "98 NaN 1.0 NaN \n", - "99 NaN 2.0 NaN \n", - "100 NaN 3.0 NaN \n", - "101 NaN 17.0 NaN \n", - "102 NaN 5.0 NaN \n", - "103 NaN 6.0 NaN \n", - "104 NaN 7.0 NaN \n", - "105 NaN 8.0 NaN \n", - "106 NaN 9.0 NaN \n", - "107 NaN 10.0 NaN \n", - "108 NaN 11.0 NaN \n", - "109 NaN 12.0 NaN \n", - "110 NaN 13.0 NaN \n", - "111 NaN 14.0 NaN \n", - "112 NaN 15.0 NaN \n", - "113 NaN 16.0 NaN \n", - "114 NaN 18.0 NaN \n", - "115 NaN NaN 0.0 \n", - "116 NaN NaN 1.0 \n", - "117 NaN NaN 2.0 " - ] - }, - "execution_count": 88, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "terms_summary(sequestering)" - ] - }, - { - "cell_type": "code", - "execution_count": 89, - "id": "2849da7d", - "metadata": {}, - "outputs": [], - "source": [ - "viz('molecular sequestering-0')" - ] - }, - { - "cell_type": "markdown", - "id": "45b58003", - "metadata": {}, - "source": [ - "![img](output/molecular_sequestering-0-True-v1.png)" - ] - }, - { - "cell_type": "markdown", - "id": "91fc3313", - "metadata": {}, - "source": [ - "## IGRB\n", - "\n", - "This gene set contains genes previously annotated to IGRB, many of which have been since removed" - ] - }, - { - "cell_type": "code", - "execution_count": 90, - "id": "7d791a9d", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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idlabelredundantstandardstandard no ontologyrank baseddav narrative synopsisturbo ontological synopsisturbo narrative synopsisdav no synopsisdav ontological synopsisturbo no synopsis
0GO:0019814immunoglobulin complexFalse0.02.0NaNNaNNaNNaNNaNNaNNaN
1GO:0009897external side of plasma membraneFalse1.00.089.0NaNNaNNaNNaNNaNNaN
2GO:0098552side of membraneTrue2.0NaNNaNNaNNaNNaNNaNNaNNaN
3GO:0002250adaptive immune responseFalse3.01.016.03.0NaNNaNNaNNaNNaN
4GO:0009986cell surfaceTrue4.0NaN68.0NaNNaNNaNNaNNaNNaN
5GO:0006955immune responseTrue5.06.052.0NaNNaNNaNNaNNaNNaN
6GO:0002376immune system processTrue6.0NaNNaNNaNNaNNaNNaNNaNNaN
7GO:0005886plasma membraneTrue7.0NaN64.0NaNNaNNaNNaNNaNNaN
8GO:0071944cell peripheryTrue8.0NaNNaNNaNNaNNaNNaNNaNNaN
9GO:0003823antigen bindingFalse9.04.0NaNNaNNaNNaNNaNNaNNaN
10GO:0005576extracellular regionFalse10.03.065.0NaNNaNNaNNaNNaNNaN
11GO:0016020membraneTrue11.0NaN43.0NaNNaNNaNNaNNaNNaN
12GO:0071735IgG immunoglobulin complexTrue12.05.0NaNNaNNaNNaNNaNNaNNaN
13GO:0032991protein-containing complexTrue13.0NaN63.0NaNNaNNaNNaNNaNNaN
14GO:0050853B cell receptor signaling pathwayTrue14.07.0NaNNaNNaNNaNNaNNaNNaN
15GO:0034987immunoglobulin receptor bindingFalse15.08.0NaNNaNNaNNaNNaNNaNNaN
16GO:0050851antigen receptor-mediated signaling pathwayTrue16.0NaNNaNNaNNaNNaNNaNNaNNaN
17GO:0050896response to stimulusTrue17.0NaNNaNNaNNaNNaNNaNNaNNaN
18PR:000050567protein-containing material entityTrue18.0NaNNaNNaNNaNNaNNaNNaNNaN
19GO:0072562blood microparticleTrue19.09.0NaNNaNNaNNaNNaNNaNNaN
20GO:0071745IgA immunoglobulin complexTrue20.010.0NaNNaNNaNNaNNaNNaNNaN
21GO:0002768immune response-regulating cell surface receptor signaling pathwayTrue21.0NaNNaNNaNNaNNaNNaNNaNNaN
22GO:0002429immune response-activating cell surface receptor signaling pathwayTrue22.0NaNNaNNaNNaNNaNNaNNaNNaN
23GO:0071753IgM immunoglobulin complexTrue23.011.0NaNNaNNaNNaNNaNNaNNaN
24GO:0002764immune response-regulating signaling pathwayTrue24.0NaNNaNNaNNaNNaNNaNNaNNaN
25GO:0002757immune response-activating signaling pathwayTrue25.0NaNNaNNaNNaNNaNNaNNaNNaN
26GO:0071738IgD immunoglobulin complexTrue26.012.0NaNNaNNaNNaNNaNNaNNaN
27GO:0071742IgE immunoglobulin complexTrue27.013.0NaNNaNNaNNaNNaNNaNNaN
28GO:0002253activation of immune responseTrue28.0NaNNaNNaN2.01.0NaNNaNNaN
29GO:0050778positive regulation of immune responseTrue29.0NaNNaNNaNNaNNaNNaNNaNNaN
30GO:0050776regulation of immune responseTrue30.0NaNNaNNaNNaNNaNNaNNaNNaN
31GO:0042571immunoglobulin complex, circulatingTrue31.0NaNNaNNaNNaNNaN4.0NaNNaN
32GO:0002684positive regulation of immune system processTrue32.0NaNNaNNaNNaNNaNNaNNaNNaN
33GO:0071752secretory dimeric IgA immunoglobulin complexTrue33.014.0NaNNaNNaNNaNNaNNaNNaN
34GO:0071750dimeric IgA immunoglobulin complexTrue34.0NaNNaNNaNNaNNaNNaNNaNNaN
35GO:0071748monomeric IgA immunoglobulin complexTrue35.015.0NaNNaNNaNNaNNaNNaNNaN
36GO:0071751secretory IgA immunoglobulin complexTrue36.016.0NaNNaNNaNNaNNaNNaNNaN
37GO:0071749polymeric IgA immunoglobulin complexTrue37.0NaNNaNNaNNaNNaNNaNNaNNaN
38GO:0071746IgA immunoglobulin complex, circulatingTrue38.0NaNNaNNaNNaNNaNNaNNaNNaN
39GO:0002682regulation of immune system processTrue39.0NaNNaNNaNNaNNaNNaNNaNNaN
40GO:0060267positive regulation of respiratory burstFalse40.018.0NaNNaNNaNNaNNaNNaNNaN
41GO:0001895retina homeostasisFalse41.017.0NaNNaNNaNNaNNaNNaNNaN
42GO:0071756pentameric IgM immunoglobulin complexTrue42.020.0NaNNaNNaNNaNNaNNaNNaN
43GO:0071754IgM immunoglobulin complex, circulatingTrue43.0NaNNaNNaNNaNNaNNaNNaNNaN
44GO:0034988Fc-gamma receptor I complex bindingTrue44.021.0NaNNaNNaNNaNNaNNaNNaN
45GO:0060263regulation of respiratory burstTrue45.0NaNNaNNaNNaNNaNNaNNaNNaN
46GO:0019731antibacterial humoral responseFalseNaN19.0NaNNaNNaNNaNNaNNaNNaN
47GO:0003094glomerular filtrationFalseNaN22.0NaNNaNNaNNaNNaNNaNNaN
48GO:0005615extracellular spaceFalseNaN23.039.0NaNNaNNaNNaNNaNNaN
49GO:0003674molecular_functionFalseNaNNaN0.0NaNNaNNaNNaNNaNNaN
50GO:0010628positive regulation of gene expressionFalseNaNNaN1.0NaNNaNNaNNaNNaNNaN
51GO:0005737cytoplasmFalseNaNNaN2.0NaNNaNNaNNaNNaNNaN
52GO:0030425dendriteFalseNaNNaN3.0NaNNaNNaNNaNNaNNaN
53GO:0006355regulation of DNA-templated transcriptionFalseNaNNaN4.0NaNNaNNaNNaNNaNNaN
54GO:0005813centrosomeFalseNaNNaN5.0NaNNaNNaNNaNNaNNaN
55GO:0016604nuclear bodyFalseNaNNaN6.0NaNNaNNaNNaNNaNNaN
56GO:0003700DNA-binding transcription factor activityFalseNaNNaN7.0NaNNaNNaNNaNNaNNaN
57GO:0016607nuclear speckFalseNaNNaN8.0NaNNaNNaNNaNNaNNaN
58GO:0046872metal ion bindingFalseNaNNaN9.0NaNNaNNaNNaNNaNNaN
59GO:0006954inflammatory responseFalseNaNNaN10.0NaNNaNNaNNaNNaNNaN
60GO:0005856cytoskeletonFalseNaNNaN11.0NaNNaNNaNNaNNaNNaN
61GO:0030154cell differentiationFalseNaNNaN12.0NaNNaNNaNNaNNaNNaN
62GO:0003677DNA bindingFalseNaNNaN13.0NaNNaNNaNNaNNaNNaN
63GO:0000981DNA-binding transcription factor activity, RNA polymerase II-specificFalseNaNNaN14.0NaNNaNNaNNaNNaNNaN
64GO:0005730nucleolusFalseNaNNaN15.0NaNNaNNaNNaNNaNNaN
65GO:0005509calcium ion bindingFalseNaNNaN17.0NaNNaNNaNNaNNaNNaN
66GO:0005765lysosomal membraneFalseNaNNaN18.0NaNNaNNaNNaNNaNNaN
67GO:0005743mitochondrial inner membraneFalseNaNNaN19.0NaNNaNNaNNaNNaNNaN
68GO:0019899enzyme bindingFalseNaNNaN20.0NaNNaNNaNNaNNaNNaN
69GO:0006468protein phosphorylationFalseNaNNaN21.0NaNNaNNaNNaNNaNNaN
70GO:0050911detection of chemical stimulus involved in sensory perception of smellFalseNaNNaN22.0NaNNaNNaNNaNNaNNaN
71GO:0000785chromatinFalseNaNNaN23.0NaNNaNNaNNaNNaNNaN
72GO:0005759mitochondrial matrixFalseNaNNaN24.0NaNNaNNaNNaNNaNNaN
73GO:0106310protein serine kinase activityFalseNaNNaN25.0NaNNaNNaNNaNNaNNaN
74GO:0003682chromatin bindingFalseNaNNaN26.0NaNNaNNaNNaNNaNNaN
75GO:0007155cell adhesionFalseNaNNaN27.0NaNNaNNaNNaNNaNNaN
76GO:0004984olfactory receptor activityFalseNaNNaN28.0NaNNaNNaNNaNNaNNaN
77GO:0007165signal transductionFalseNaNNaN29.0NaNNaNNaNNaNNaNNaN
78GO:0061630ubiquitin protein ligase activityFalseNaNNaN30.0NaNNaNNaNNaNNaNNaN
79GO:0005654nucleoplasmFalseNaNNaN31.0NaNNaNNaNNaNNaNNaN
80GO:0005829cytosolFalseNaNNaN32.0NaNNaNNaNNaNNaNNaN
81GO:0005575cellular_componentFalseNaNNaN33.0NaNNaNNaNNaNNaNNaN
82GO:0000122negative regulation of transcription by RNA polymerase IIFalseNaNNaN34.0NaNNaNNaNNaNNaNNaN
83GO:0042802identical protein bindingFalseNaNNaN35.0NaNNaNNaNNaNNaNNaN
84GO:0008284positive regulation of cell population proliferationFalseNaNNaN36.0NaNNaNNaNNaNNaNNaN
85GO:0007186G protein-coupled receptor signaling pathwayFalseNaNNaN37.0NaNNaNNaNNaNNaNNaN
86GO:0005783endoplasmic reticulumFalseNaNNaN38.0NaNNaNNaNNaNNaNNaN
87GO:0001228DNA-binding transcription activator activity, RNA polymerase II-specificFalseNaNNaN40.0NaNNaNNaNNaNNaNNaN
88GO:0008270zinc ion bindingFalseNaNNaN41.0NaNNaNNaNNaNNaNNaN
89GO:0000139Golgi membraneFalseNaNNaN42.0NaNNaNNaNNaNNaNNaN
90GO:0003723RNA bindingFalseNaNNaN44.0NaNNaNNaNNaNNaNNaN
91GO:0005789endoplasmic reticulum membraneFalseNaNNaN45.0NaNNaNNaNNaNNaNNaN
92GO:0005525GTP bindingFalseNaNNaN46.0NaNNaNNaNNaNNaNNaN
93GO:0005102signaling receptor bindingFalseNaNNaN47.0NaNNaNNaNNaNNaNNaN
94GO:0005794Golgi apparatusFalseNaNNaN48.0NaNNaNNaNNaNNaNNaN
95GO:0043231intracellular membrane-bounded organelleFalseNaNNaN49.0NaNNaNNaNNaNNaNNaN
96GO:0005739mitochondrionFalseNaNNaN50.0NaNNaNNaNNaNNaNNaN
97GO:0051301cell divisionFalseNaNNaN51.0NaNNaNNaNNaNNaNNaN
98GO:0006357regulation of transcription by RNA polymerase IIFalseNaNNaN53.0NaNNaNNaNNaNNaNNaN
99GO:0048471perinuclear region of cytoplasmFalseNaNNaN54.0NaNNaNNaNNaNNaNNaN
100GO:1990837sequence-specific double-stranded DNA bindingFalseNaNNaN55.0NaNNaNNaNNaNNaNNaN
101GO:0042803protein homodimerization activityFalseNaNNaN56.0NaNNaNNaNNaNNaNNaN
102GO:0007399nervous system developmentFalseNaNNaN57.0NaNNaNNaNNaNNaNNaN
103GO:0070062extracellular exosomeFalseNaNNaN58.0NaNNaNNaNNaNNaNNaN
104GO:0006915apoptotic processFalseNaNNaN59.0NaNNaNNaNNaNNaNNaN
105GO:0098978glutamatergic synapseFalseNaNNaN60.0NaNNaNNaNNaNNaNNaN
106GO:0043066negative regulation of apoptotic processFalseNaNNaN61.0NaNNaNNaNNaNNaNNaN
107GO:0004674protein serine/threonine kinase activityFalseNaNNaN62.0NaNNaNNaNNaNNaNNaN
108GO:0045087innate immune responseFalseNaNNaN66.0NaNNaNNaNNaNNaNNaN
109GO:0005634nucleusFalseNaNNaN67.0NaNNaNNaNNaNNaNNaN
110GO:0005925focal adhesionFalseNaNNaN69.0NaNNaNNaNNaNNaNNaN
111GO:0019901protein kinase bindingFalseNaNNaN70.0NaNNaNNaNNaNNaNNaN
112GO:0008150biological_processFalseNaNNaN71.0NaNNaNNaNNaNNaNNaN
113GO:0062023collagen-containing extracellular matrixFalseNaNNaN72.0NaNNaNNaNNaNNaNNaN
114GO:0007283spermatogenesisFalseNaNNaN73.0NaNNaNNaNNaNNaNNaN
115GO:0005524ATP bindingFalseNaNNaN74.0NaNNaNNaNNaNNaNNaN
116GO:0045893positive regulation of DNA-templated transcriptionFalseNaNNaN75.0NaNNaNNaNNaNNaNNaN
117GO:0016887ATP hydrolysis activityFalseNaNNaN76.0NaNNaNNaNNaNNaNNaN
118GO:0035556intracellular signal transductionFalseNaNNaN77.0NaNNaNNaNNaNNaNNaN
119GO:0045892negative regulation of DNA-templated transcriptionFalseNaNNaN78.0NaNNaNNaNNaNNaNNaN
120GO:0008285negative regulation of cell population proliferationFalseNaNNaN79.0NaNNaNNaNNaNNaNNaN
121GO:0043025neuronal cell bodyFalseNaNNaN80.0NaNNaNNaNNaNNaNNaN
122GO:0004930G protein-coupled receptor activityFalseNaNNaN81.0NaNNaNNaNNaNNaNNaN
123GO:0006508proteolysisFalseNaNNaN82.0NaNNaNNaNNaNNaNNaN
124GO:0000978RNA polymerase II cis-regulatory region sequence-specific DNA bindingFalseNaNNaN83.0NaNNaNNaNNaNNaNNaN
125GO:0045202synapseFalseNaNNaN84.0NaNNaNNaNNaNNaNNaN
126GO:0045944positive regulation of transcription by RNA polymerase IIFalseNaNNaN85.0NaNNaNNaNNaNNaNNaN
127GO:0044877protein-containing complex bindingFalseNaNNaN86.0NaNNaNNaNNaNNaNNaN
128GO:0015031protein transportFalseNaNNaN87.0NaNNaNNaNNaNNaNNaN
129GO:0016324apical plasma membraneFalseNaNNaN88.0NaNNaNNaNNaNNaNNaN
130GO:0016567protein ubiquitinationFalseNaNNaN90.0NaNNaNNaNNaNNaNNaN
131antigen binding activityNoneFalseNaNNaNNaN0.00.0NaNNaN1.0NaN
132immunoglobulin receptor binding activityNoneFalseNaNNaNNaN1.01.00.0NaN0.0NaN
133members of the immunoglobulin (ig) gene superfamily - specificallyNoneFalseNaNNaNNaNNaNNaNNaN0.0NaNNaN
134ighNoneFalseNaNNaNNaNNaNNaNNaN1.0NaNNaN
135GO:0033984indole-3-glycerol-phosphate lyase activityFalseNaNNaNNaNNaNNaNNaN2.0NaNNaN
136MESH:C014609NoneFalseNaNNaNNaNNaNNaNNaN3.0NaNNaN
137response and maintenance of the adaptive immune system at different levelsNoneFalseNaNNaNNaNNaNNaNNaN5.0NaNNaN
138likely via antigen bindingNoneFalseNaNNaNNaNNaNNaNNaN6.0NaNNaN
139signal transduction and b cell activationNoneFalseNaNNaNNaNNaNNaNNaN7.0NaNNaN
140GO:0002377immunoglobulin productionFalseNaNNaNNaN2.0NaNNaNNaNNaN0.0
141protein homodimerizationNoneFalseNaNNaNNaN4.0NaNNaNNaNNaNNaN
142GO:0098542defense response to other organismFalseNaNNaNNaNNaNNaN2.0NaNNaNNaN
143GO:0002922positive regulation of humoral immune responseFalseNaNNaNNaNNaNNaN3.0NaNNaNNaN
144b cell-mediated immunityNoneFalseNaNNaNNaNNaNNaN4.0NaNNaNNaN
145t cell receptor signalingNoneFalseNaNNaNNaNNaNNaNNaNNaNNaN1.0
146GO:0042113B cell activationFalseNaNNaNNaNNaNNaNNaNNaNNaN2.0
147t cell activation. \\n\\nhypotheses: this list of genes is heavily enriched in those involved in the function and development of b cells and t cells. specifically, they play a role in the production and function of immunoglobulins and t cell receptors, as well as the activation of these cell types. this suggests that these genes are integral to the proper functioning of the immune systemNoneFalseNaNNaNNaNNaNNaNNaNNaNNaN3.0
148fc-gamma receptor i complex binding activityNoneFalseNaNNaNNaNNaNNaNNaNNaN2.0NaN
149GO:0004715non-membrane spanning protein tyrosine kinase activityFalseNaNNaNNaNNaNNaNNaNNaN3.0NaN
150phosphotyrosine residue binding activityNoneFalseNaNNaNNaNNaNNaNNaNNaN4.0NaN
151peptidoglycan binding activityNoneFalseNaNNaNNaNNaNNaNNaNNaN5.0NaN
152phosphatidylcholine binding activity. mechanism: the genes listed appear to be involved in the regulation of the immune response. they likely aid in the recognition of pathogens, binding to the appropriate receptors, triggering a signal for an immune response. they may also play a role in enabling the recognition of self-antigens inhibiting a response to themNoneFalseNaNNaNNaNNaNNaNNaNNaN6.0NaN
\n", - "
" - ], - "text/plain": [ - " id \\\n", - "0 GO:0019814 \n", - "1 GO:0009897 \n", - "2 GO:0098552 \n", - "3 GO:0002250 \n", - "4 GO:0009986 \n", - "5 GO:0006955 \n", - "6 GO:0002376 \n", - "7 GO:0005886 \n", - "8 GO:0071944 \n", - "9 GO:0003823 \n", - "10 GO:0005576 \n", - "11 GO:0016020 \n", - "12 GO:0071735 \n", - "13 GO:0032991 \n", - "14 GO:0050853 \n", - "15 GO:0034987 \n", - "16 GO:0050851 \n", - "17 GO:0050896 \n", - "18 PR:000050567 \n", - "19 GO:0072562 \n", - "20 GO:0071745 \n", - "21 GO:0002768 \n", - "22 GO:0002429 \n", - "23 GO:0071753 \n", - "24 GO:0002764 \n", - "25 GO:0002757 \n", - "26 GO:0071738 \n", - "27 GO:0071742 \n", - "28 GO:0002253 \n", - "29 GO:0050778 \n", - "30 GO:0050776 \n", - "31 GO:0042571 \n", - "32 GO:0002684 \n", - "33 GO:0071752 \n", - "34 GO:0071750 \n", - "35 GO:0071748 \n", - "36 GO:0071751 \n", - "37 GO:0071749 \n", - "38 GO:0071746 \n", - "39 GO:0002682 \n", - "40 GO:0060267 \n", - "41 GO:0001895 \n", - "42 GO:0071756 \n", - "43 GO:0071754 \n", - "44 GO:0034988 \n", - "45 GO:0060263 \n", - "46 GO:0019731 \n", - "47 GO:0003094 \n", - "48 GO:0005615 \n", - "49 GO:0003674 \n", - "50 GO:0010628 \n", - "51 GO:0005737 \n", - "52 GO:0030425 \n", - "53 GO:0006355 \n", - "54 GO:0005813 \n", - "55 GO:0016604 \n", - "56 GO:0003700 \n", - "57 GO:0016607 \n", - "58 GO:0046872 \n", - "59 GO:0006954 \n", - "60 GO:0005856 \n", - "61 GO:0030154 \n", - "62 GO:0003677 \n", - "63 GO:0000981 \n", - "64 GO:0005730 \n", - "65 GO:0005509 \n", - "66 GO:0005765 \n", - "67 GO:0005743 \n", - "68 GO:0019899 \n", - "69 GO:0006468 \n", - "70 GO:0050911 \n", - "71 GO:0000785 \n", - "72 GO:0005759 \n", - "73 GO:0106310 \n", - "74 GO:0003682 \n", - "75 GO:0007155 \n", - "76 GO:0004984 \n", - "77 GO:0007165 \n", - "78 GO:0061630 \n", - "79 GO:0005654 \n", - "80 GO:0005829 \n", - "81 GO:0005575 \n", - "82 GO:0000122 \n", - "83 GO:0042802 \n", - "84 GO:0008284 \n", - "85 GO:0007186 \n", - "86 GO:0005783 \n", - "87 GO:0001228 \n", - "88 GO:0008270 \n", - "89 GO:0000139 \n", - "90 GO:0003723 \n", - "91 GO:0005789 \n", - "92 GO:0005525 \n", - "93 GO:0005102 \n", - "94 GO:0005794 \n", - "95 GO:0043231 \n", - "96 GO:0005739 \n", - "97 GO:0051301 \n", - "98 GO:0006357 \n", - "99 GO:0048471 \n", - "100 GO:1990837 \n", - "101 GO:0042803 \n", - "102 GO:0007399 \n", - "103 GO:0070062 \n", - "104 GO:0006915 \n", - "105 GO:0098978 \n", - "106 GO:0043066 \n", - "107 GO:0004674 \n", - "108 GO:0045087 \n", - "109 GO:0005634 \n", - "110 GO:0005925 \n", - "111 GO:0019901 \n", - "112 GO:0008150 \n", - "113 GO:0062023 \n", - "114 GO:0007283 \n", - "115 GO:0005524 \n", - "116 GO:0045893 \n", - "117 GO:0016887 \n", - "118 GO:0035556 \n", - "119 GO:0045892 \n", - "120 GO:0008285 \n", - "121 GO:0043025 \n", - "122 GO:0004930 \n", - "123 GO:0006508 \n", - "124 GO:0000978 \n", - "125 GO:0045202 \n", - "126 GO:0045944 \n", - "127 GO:0044877 \n", - "128 GO:0015031 \n", - "129 GO:0016324 \n", - "130 GO:0016567 \n", - "131 antigen binding activity \n", - "132 immunoglobulin receptor binding activity \n", - "133 members of the immunoglobulin (ig) gene superfamily - specifically \n", - "134 igh \n", - "135 GO:0033984 \n", - "136 MESH:C014609 \n", - "137 response and maintenance of the adaptive immune system at different levels \n", - "138 likely via antigen binding \n", - "139 signal transduction and b cell activation \n", - "140 GO:0002377 \n", - "141 protein homodimerization \n", - "142 GO:0098542 \n", - "143 GO:0002922 \n", - "144 b cell-mediated immunity \n", - "145 t cell receptor signaling \n", - "146 GO:0042113 \n", - "147 t cell activation. \\n\\nhypotheses: this list of genes is heavily enriched in those involved in the function and development of b cells and t cells. specifically, they play a role in the production and function of immunoglobulins and t cell receptors, as well as the activation of these cell types. this suggests that these genes are integral to the proper functioning of the immune system \n", - "148 fc-gamma receptor i complex binding activity \n", - "149 GO:0004715 \n", - "150 phosphotyrosine residue binding activity \n", - "151 peptidoglycan binding activity \n", - "152 phosphatidylcholine binding activity. mechanism: the genes listed appear to be involved in the regulation of the immune response. they likely aid in the recognition of pathogens, binding to the appropriate receptors, triggering a signal for an immune response. they may also play a role in enabling the recognition of self-antigens inhibiting a response to them \n", - "\n", - " label \\\n", - "0 immunoglobulin complex \n", - "1 external side of plasma membrane \n", - "2 side of membrane \n", - "3 adaptive immune response \n", - "4 cell surface \n", - "5 immune response \n", - "6 immune system process \n", - "7 plasma membrane \n", - "8 cell periphery \n", - "9 antigen binding \n", - "10 extracellular region \n", - "11 membrane \n", - "12 IgG immunoglobulin complex \n", - "13 protein-containing complex \n", - "14 B cell receptor signaling pathway \n", - "15 immunoglobulin receptor binding \n", - "16 antigen receptor-mediated signaling pathway \n", - "17 response to stimulus \n", - "18 protein-containing material entity \n", - "19 blood microparticle \n", - "20 IgA immunoglobulin complex \n", - "21 immune response-regulating cell surface receptor signaling pathway \n", - "22 immune response-activating cell surface receptor signaling pathway \n", - "23 IgM immunoglobulin complex \n", - "24 immune response-regulating signaling pathway \n", - "25 immune response-activating signaling pathway \n", - "26 IgD immunoglobulin complex \n", - "27 IgE immunoglobulin complex \n", - "28 activation of immune response \n", - "29 positive regulation of immune response \n", - "30 regulation of immune response \n", - "31 immunoglobulin complex, circulating \n", - "32 positive regulation of immune system process \n", - "33 secretory dimeric IgA immunoglobulin complex \n", - "34 dimeric IgA immunoglobulin complex \n", - "35 monomeric IgA immunoglobulin complex \n", - "36 secretory IgA immunoglobulin complex \n", - "37 polymeric IgA immunoglobulin complex \n", - "38 IgA immunoglobulin complex, circulating \n", - "39 regulation of immune system process \n", - "40 positive regulation of respiratory burst \n", - "41 retina homeostasis \n", - "42 pentameric IgM immunoglobulin complex \n", - "43 IgM immunoglobulin complex, circulating \n", - "44 Fc-gamma receptor I complex binding \n", - "45 regulation of respiratory burst \n", - "46 antibacterial humoral response \n", - "47 glomerular filtration \n", - "48 extracellular space \n", - "49 molecular_function \n", - "50 positive regulation of gene expression \n", - "51 cytoplasm \n", - "52 dendrite \n", - "53 regulation of DNA-templated transcription \n", - "54 centrosome \n", - "55 nuclear body \n", - "56 DNA-binding transcription factor activity \n", - "57 nuclear speck \n", - "58 metal ion binding \n", - "59 inflammatory response \n", - "60 cytoskeleton \n", - "61 cell differentiation \n", - "62 DNA binding \n", - "63 DNA-binding transcription factor activity, RNA polymerase II-specific \n", - "64 nucleolus \n", - "65 calcium ion binding \n", - "66 lysosomal membrane \n", - "67 mitochondrial inner membrane \n", - "68 enzyme binding \n", - "69 protein phosphorylation \n", - "70 detection of chemical stimulus involved in sensory perception of smell \n", - "71 chromatin \n", - "72 mitochondrial matrix \n", - "73 protein serine kinase activity \n", - "74 chromatin binding \n", - "75 cell adhesion \n", - "76 olfactory receptor activity \n", - "77 signal transduction \n", - "78 ubiquitin protein ligase activity \n", - "79 nucleoplasm \n", - "80 cytosol \n", - "81 cellular_component \n", - "82 negative regulation of transcription by RNA polymerase II \n", - "83 identical protein binding \n", - "84 positive regulation of cell population proliferation \n", - "85 G protein-coupled receptor signaling pathway \n", - "86 endoplasmic reticulum \n", - "87 DNA-binding transcription activator activity, RNA polymerase II-specific \n", - "88 zinc ion binding \n", - "89 Golgi membrane \n", - "90 RNA binding \n", - "91 endoplasmic reticulum membrane \n", - "92 GTP binding \n", - "93 signaling receptor binding \n", - "94 Golgi apparatus \n", - "95 intracellular membrane-bounded organelle \n", - "96 mitochondrion \n", - "97 cell division \n", - "98 regulation of transcription by RNA polymerase II \n", - "99 perinuclear region of cytoplasm \n", - "100 sequence-specific double-stranded DNA binding \n", - "101 protein homodimerization activity \n", - "102 nervous system development \n", - "103 extracellular exosome \n", - "104 apoptotic process \n", - "105 glutamatergic synapse \n", - "106 negative regulation of apoptotic process \n", - "107 protein serine/threonine kinase activity \n", - "108 innate immune response \n", - "109 nucleus \n", - "110 focal adhesion \n", - "111 protein kinase binding \n", - "112 biological_process \n", - "113 collagen-containing extracellular matrix \n", - "114 spermatogenesis \n", - "115 ATP binding \n", - "116 positive regulation of DNA-templated transcription \n", - "117 ATP hydrolysis activity \n", - "118 intracellular signal transduction \n", - "119 negative regulation of DNA-templated transcription \n", - "120 negative regulation of cell population proliferation \n", - "121 neuronal cell body \n", - "122 G protein-coupled receptor activity \n", - "123 proteolysis \n", - "124 RNA polymerase II cis-regulatory region sequence-specific DNA binding \n", - "125 synapse \n", - "126 positive regulation of transcription by RNA polymerase II \n", - "127 protein-containing complex binding \n", - "128 protein transport \n", - "129 apical plasma membrane \n", - "130 protein ubiquitination \n", - "131 None \n", - "132 None \n", - "133 None \n", - "134 None \n", - "135 indole-3-glycerol-phosphate lyase activity \n", - "136 None \n", - "137 None \n", - "138 None \n", - "139 None \n", - "140 immunoglobulin production \n", - "141 None \n", - "142 defense response to other organism \n", - "143 positive regulation of humoral immune response \n", - "144 None \n", - "145 None \n", - "146 B cell activation \n", - "147 None \n", - "148 None \n", - "149 non-membrane spanning protein tyrosine kinase activity \n", - "150 None \n", - "151 None \n", - "152 None \n", - "\n", - " redundant standard standard no ontology rank based \\\n", - "0 False 0.0 2.0 NaN \n", - "1 False 1.0 0.0 89.0 \n", - "2 True 2.0 NaN NaN \n", - "3 False 3.0 1.0 16.0 \n", - "4 True 4.0 NaN 68.0 \n", - "5 True 5.0 6.0 52.0 \n", - "6 True 6.0 NaN NaN \n", - "7 True 7.0 NaN 64.0 \n", - "8 True 8.0 NaN NaN \n", - "9 False 9.0 4.0 NaN \n", - "10 False 10.0 3.0 65.0 \n", - "11 True 11.0 NaN 43.0 \n", - "12 True 12.0 5.0 NaN \n", - "13 True 13.0 NaN 63.0 \n", - "14 True 14.0 7.0 NaN \n", - "15 False 15.0 8.0 NaN \n", - "16 True 16.0 NaN NaN \n", - "17 True 17.0 NaN NaN \n", - "18 True 18.0 NaN NaN \n", - "19 True 19.0 9.0 NaN \n", - "20 True 20.0 10.0 NaN \n", - "21 True 21.0 NaN NaN \n", - "22 True 22.0 NaN NaN \n", - "23 True 23.0 11.0 NaN \n", - "24 True 24.0 NaN NaN \n", - "25 True 25.0 NaN NaN \n", - "26 True 26.0 12.0 NaN \n", - "27 True 27.0 13.0 NaN \n", - "28 True 28.0 NaN NaN \n", - "29 True 29.0 NaN NaN \n", - "30 True 30.0 NaN NaN \n", - "31 True 31.0 NaN NaN \n", - "32 True 32.0 NaN NaN \n", - "33 True 33.0 14.0 NaN \n", - "34 True 34.0 NaN NaN \n", - "35 True 35.0 15.0 NaN \n", - "36 True 36.0 16.0 NaN \n", - "37 True 37.0 NaN NaN \n", - "38 True 38.0 NaN NaN \n", - "39 True 39.0 NaN NaN \n", - "40 False 40.0 18.0 NaN \n", - "41 False 41.0 17.0 NaN \n", - "42 True 42.0 20.0 NaN \n", - "43 True 43.0 NaN NaN \n", - "44 True 44.0 21.0 NaN \n", - "45 True 45.0 NaN NaN \n", - "46 False NaN 19.0 NaN \n", - "47 False NaN 22.0 NaN \n", - "48 False NaN 23.0 39.0 \n", - "49 False NaN NaN 0.0 \n", - "50 False NaN NaN 1.0 \n", - "51 False NaN NaN 2.0 \n", - "52 False NaN NaN 3.0 \n", - "53 False NaN NaN 4.0 \n", - "54 False NaN NaN 5.0 \n", - "55 False NaN NaN 6.0 \n", - "56 False NaN NaN 7.0 \n", - "57 False NaN NaN 8.0 \n", - "58 False NaN NaN 9.0 \n", - "59 False NaN NaN 10.0 \n", - "60 False NaN NaN 11.0 \n", - "61 False NaN NaN 12.0 \n", - "62 False NaN NaN 13.0 \n", - "63 False NaN NaN 14.0 \n", - "64 False NaN NaN 15.0 \n", - "65 False NaN NaN 17.0 \n", - "66 False NaN NaN 18.0 \n", - "67 False NaN NaN 19.0 \n", - "68 False NaN NaN 20.0 \n", - "69 False NaN NaN 21.0 \n", - "70 False NaN NaN 22.0 \n", - "71 False NaN NaN 23.0 \n", - "72 False NaN NaN 24.0 \n", - "73 False NaN NaN 25.0 \n", - "74 False NaN NaN 26.0 \n", - "75 False NaN NaN 27.0 \n", - "76 False NaN NaN 28.0 \n", - "77 False NaN NaN 29.0 \n", - "78 False NaN NaN 30.0 \n", - "79 False NaN NaN 31.0 \n", - "80 False NaN NaN 32.0 \n", - "81 False NaN NaN 33.0 \n", - "82 False NaN NaN 34.0 \n", - "83 False NaN NaN 35.0 \n", - "84 False NaN NaN 36.0 \n", - "85 False NaN NaN 37.0 \n", - "86 False NaN NaN 38.0 \n", - "87 False NaN NaN 40.0 \n", - "88 False NaN NaN 41.0 \n", - "89 False NaN NaN 42.0 \n", - "90 False NaN NaN 44.0 \n", - "91 False NaN NaN 45.0 \n", - "92 False NaN NaN 46.0 \n", - "93 False NaN NaN 47.0 \n", - "94 False NaN NaN 48.0 \n", - "95 False NaN NaN 49.0 \n", - "96 False NaN NaN 50.0 \n", - "97 False NaN NaN 51.0 \n", - "98 False NaN NaN 53.0 \n", - "99 False NaN NaN 54.0 \n", - "100 False NaN NaN 55.0 \n", - "101 False NaN NaN 56.0 \n", - "102 False NaN NaN 57.0 \n", - "103 False NaN NaN 58.0 \n", - "104 False NaN NaN 59.0 \n", - "105 False NaN NaN 60.0 \n", - "106 False NaN NaN 61.0 \n", - "107 False NaN NaN 62.0 \n", - "108 False NaN NaN 66.0 \n", - "109 False NaN NaN 67.0 \n", - "110 False NaN NaN 69.0 \n", - "111 False NaN NaN 70.0 \n", - "112 False NaN NaN 71.0 \n", - "113 False NaN NaN 72.0 \n", - "114 False NaN NaN 73.0 \n", - "115 False NaN NaN 74.0 \n", - "116 False NaN NaN 75.0 \n", - "117 False NaN NaN 76.0 \n", - "118 False NaN NaN 77.0 \n", - "119 False NaN NaN 78.0 \n", - "120 False NaN NaN 79.0 \n", - "121 False NaN NaN 80.0 \n", - "122 False NaN NaN 81.0 \n", - "123 False NaN NaN 82.0 \n", - "124 False NaN NaN 83.0 \n", - "125 False NaN NaN 84.0 \n", - "126 False NaN NaN 85.0 \n", - "127 False NaN NaN 86.0 \n", - "128 False NaN NaN 87.0 \n", - "129 False NaN NaN 88.0 \n", - "130 False NaN NaN 90.0 \n", - "131 False NaN NaN NaN \n", - "132 False NaN NaN NaN \n", - "133 False NaN NaN NaN \n", - "134 False NaN NaN NaN \n", - "135 False NaN NaN NaN \n", - "136 False NaN NaN NaN \n", - "137 False NaN NaN NaN \n", - "138 False NaN NaN NaN \n", - "139 False NaN NaN NaN \n", - "140 False NaN NaN NaN \n", - "141 False NaN NaN NaN \n", - "142 False NaN NaN NaN \n", - "143 False NaN NaN NaN \n", - "144 False NaN NaN NaN \n", - "145 False NaN NaN NaN \n", - "146 False NaN NaN NaN \n", - "147 False NaN NaN NaN \n", - "148 False NaN NaN NaN \n", - "149 False NaN NaN NaN \n", - "150 False NaN NaN NaN \n", - "151 False NaN NaN NaN \n", - "152 False NaN NaN NaN \n", - "\n", - " dav narrative synopsis turbo ontological synopsis \\\n", - "0 NaN NaN \n", - "1 NaN NaN \n", - "2 NaN NaN \n", - "3 3.0 NaN \n", - "4 NaN NaN \n", - "5 NaN NaN \n", - "6 NaN NaN \n", - "7 NaN NaN \n", - "8 NaN NaN \n", - "9 NaN NaN \n", - "10 NaN NaN \n", - "11 NaN NaN \n", - "12 NaN NaN \n", - "13 NaN NaN \n", - "14 NaN NaN \n", - "15 NaN NaN \n", - "16 NaN NaN \n", - "17 NaN NaN \n", - "18 NaN NaN \n", - "19 NaN NaN \n", - "20 NaN NaN \n", - "21 NaN NaN \n", - "22 NaN NaN \n", - "23 NaN NaN \n", - "24 NaN NaN \n", - "25 NaN NaN \n", - "26 NaN NaN \n", - "27 NaN NaN \n", - "28 NaN 2.0 \n", - "29 NaN NaN \n", - "30 NaN NaN \n", - "31 NaN NaN \n", - "32 NaN NaN \n", - "33 NaN NaN \n", - "34 NaN NaN \n", - "35 NaN NaN \n", - "36 NaN NaN \n", - "37 NaN NaN \n", - "38 NaN NaN \n", - "39 NaN NaN \n", - "40 NaN NaN \n", - "41 NaN NaN \n", - "42 NaN NaN \n", - "43 NaN NaN \n", - "44 NaN NaN \n", - "45 NaN NaN \n", - "46 NaN NaN \n", - "47 NaN NaN \n", - "48 NaN NaN \n", - "49 NaN NaN \n", - "50 NaN NaN \n", - "51 NaN NaN \n", - "52 NaN NaN \n", - "53 NaN NaN \n", - "54 NaN NaN \n", - "55 NaN NaN \n", - "56 NaN NaN \n", - "57 NaN NaN \n", - "58 NaN NaN \n", - "59 NaN NaN \n", - "60 NaN NaN \n", - "61 NaN NaN \n", - "62 NaN NaN \n", - "63 NaN NaN \n", - "64 NaN NaN \n", - "65 NaN NaN \n", - "66 NaN NaN \n", - "67 NaN NaN \n", - "68 NaN NaN \n", - "69 NaN NaN \n", - "70 NaN NaN \n", - "71 NaN NaN \n", - "72 NaN NaN \n", - "73 NaN NaN \n", - "74 NaN NaN \n", - "75 NaN NaN \n", - "76 NaN NaN \n", - "77 NaN NaN \n", - "78 NaN NaN \n", - "79 NaN NaN \n", - "80 NaN NaN \n", - "81 NaN NaN \n", - "82 NaN NaN \n", - "83 NaN NaN \n", - "84 NaN NaN \n", - "85 NaN NaN \n", - "86 NaN NaN \n", - "87 NaN NaN \n", - "88 NaN NaN \n", - "89 NaN NaN \n", - "90 NaN NaN \n", - "91 NaN NaN \n", - "92 NaN NaN \n", - "93 NaN NaN \n", - "94 NaN NaN \n", - "95 NaN NaN \n", - "96 NaN NaN \n", - "97 NaN NaN \n", - "98 NaN NaN \n", - "99 NaN NaN \n", - "100 NaN NaN \n", - "101 NaN NaN \n", - "102 NaN NaN \n", - "103 NaN NaN \n", - "104 NaN NaN \n", - "105 NaN NaN \n", - "106 NaN NaN \n", - "107 NaN NaN \n", - "108 NaN NaN \n", - "109 NaN NaN \n", - "110 NaN NaN \n", - "111 NaN NaN \n", - "112 NaN NaN \n", - "113 NaN NaN \n", - "114 NaN NaN \n", - "115 NaN NaN \n", - "116 NaN NaN \n", - "117 NaN NaN \n", - "118 NaN NaN \n", - "119 NaN NaN \n", - "120 NaN NaN \n", - "121 NaN NaN \n", - "122 NaN NaN \n", - "123 NaN NaN \n", - "124 NaN NaN \n", - "125 NaN NaN \n", - "126 NaN NaN \n", - "127 NaN NaN \n", - "128 NaN NaN \n", - "129 NaN NaN \n", - "130 NaN NaN \n", - "131 0.0 0.0 \n", - "132 1.0 1.0 \n", - "133 NaN NaN \n", - "134 NaN NaN \n", - "135 NaN NaN \n", - "136 NaN NaN \n", - "137 NaN NaN \n", - "138 NaN NaN \n", - "139 NaN NaN \n", - "140 2.0 NaN \n", - "141 4.0 NaN \n", - "142 NaN NaN \n", - "143 NaN NaN \n", - "144 NaN NaN \n", - "145 NaN NaN \n", - "146 NaN NaN \n", - "147 NaN NaN \n", - "148 NaN NaN \n", - "149 NaN NaN \n", - "150 NaN NaN \n", - "151 NaN NaN \n", - "152 NaN NaN \n", - "\n", - " turbo narrative synopsis dav no synopsis dav ontological synopsis \\\n", - "0 NaN NaN NaN \n", - "1 NaN NaN NaN \n", - "2 NaN NaN NaN \n", - "3 NaN NaN NaN \n", - "4 NaN NaN NaN \n", - "5 NaN NaN NaN \n", - "6 NaN NaN NaN \n", - "7 NaN NaN NaN \n", - "8 NaN NaN NaN \n", - "9 NaN NaN NaN \n", - "10 NaN NaN NaN \n", - "11 NaN NaN NaN \n", - "12 NaN NaN NaN \n", - "13 NaN NaN NaN \n", - "14 NaN NaN NaN \n", - "15 NaN NaN NaN \n", - "16 NaN NaN NaN \n", - "17 NaN NaN NaN \n", - "18 NaN NaN NaN \n", - "19 NaN NaN NaN \n", - "20 NaN NaN NaN \n", - "21 NaN NaN NaN \n", - "22 NaN NaN NaN \n", - "23 NaN NaN NaN \n", - "24 NaN NaN NaN \n", - "25 NaN NaN NaN \n", - "26 NaN NaN NaN \n", - "27 NaN NaN NaN \n", - "28 1.0 NaN NaN \n", - "29 NaN NaN NaN \n", - "30 NaN NaN NaN \n", - "31 NaN 4.0 NaN \n", - "32 NaN NaN NaN \n", - "33 NaN NaN NaN \n", - "34 NaN NaN NaN \n", - "35 NaN NaN NaN \n", - "36 NaN NaN NaN \n", - "37 NaN NaN NaN \n", - "38 NaN NaN NaN \n", - "39 NaN NaN NaN \n", - "40 NaN NaN NaN \n", - "41 NaN NaN NaN \n", - "42 NaN NaN NaN \n", - "43 NaN NaN NaN \n", - "44 NaN NaN NaN \n", - "45 NaN NaN NaN \n", - "46 NaN NaN NaN \n", - "47 NaN NaN NaN \n", - "48 NaN NaN NaN \n", - "49 NaN NaN NaN \n", - "50 NaN NaN NaN \n", - "51 NaN NaN NaN \n", - "52 NaN NaN NaN \n", - "53 NaN NaN NaN \n", - "54 NaN NaN NaN \n", - "55 NaN NaN NaN \n", - "56 NaN NaN NaN \n", - "57 NaN NaN NaN \n", - "58 NaN NaN NaN \n", - "59 NaN NaN NaN \n", - "60 NaN NaN NaN \n", - "61 NaN NaN NaN \n", - "62 NaN NaN NaN \n", - "63 NaN NaN NaN \n", - "64 NaN NaN NaN \n", - "65 NaN NaN NaN \n", - "66 NaN NaN NaN \n", - "67 NaN NaN NaN \n", - "68 NaN NaN NaN \n", - "69 NaN NaN NaN \n", - "70 NaN NaN NaN \n", - "71 NaN NaN NaN \n", - "72 NaN NaN NaN \n", - "73 NaN NaN NaN \n", - "74 NaN NaN NaN \n", - "75 NaN NaN NaN \n", - "76 NaN NaN NaN \n", - "77 NaN NaN NaN \n", - "78 NaN NaN NaN \n", - "79 NaN NaN NaN \n", - "80 NaN NaN NaN \n", - "81 NaN NaN NaN \n", - "82 NaN NaN NaN \n", - "83 NaN NaN NaN \n", - "84 NaN NaN NaN \n", - "85 NaN NaN NaN \n", - "86 NaN NaN NaN \n", - "87 NaN NaN NaN \n", - "88 NaN NaN NaN \n", - "89 NaN NaN NaN \n", - "90 NaN NaN NaN \n", - "91 NaN NaN NaN \n", - "92 NaN NaN NaN \n", - "93 NaN NaN NaN \n", - "94 NaN NaN NaN \n", - "95 NaN NaN NaN \n", - "96 NaN NaN NaN \n", - "97 NaN NaN NaN \n", - "98 NaN NaN NaN \n", - "99 NaN NaN NaN \n", - "100 NaN NaN NaN \n", - "101 NaN NaN NaN \n", - "102 NaN NaN NaN \n", - "103 NaN NaN NaN \n", - "104 NaN NaN NaN \n", - "105 NaN NaN NaN \n", - "106 NaN NaN NaN \n", - "107 NaN NaN NaN \n", - "108 NaN NaN NaN \n", - "109 NaN NaN NaN \n", - "110 NaN NaN NaN \n", - "111 NaN NaN NaN \n", - "112 NaN NaN NaN \n", - "113 NaN NaN NaN \n", - "114 NaN NaN NaN \n", - "115 NaN NaN NaN \n", - "116 NaN NaN NaN \n", - "117 NaN NaN NaN \n", - "118 NaN NaN NaN \n", - "119 NaN NaN NaN \n", - "120 NaN NaN NaN \n", - "121 NaN NaN NaN \n", - "122 NaN NaN NaN \n", - "123 NaN NaN NaN \n", - "124 NaN NaN NaN \n", - "125 NaN NaN NaN \n", - "126 NaN NaN NaN \n", - "127 NaN NaN NaN \n", - "128 NaN NaN NaN \n", - "129 NaN NaN NaN \n", - "130 NaN NaN NaN \n", - "131 NaN NaN 1.0 \n", - "132 0.0 NaN 0.0 \n", - "133 NaN 0.0 NaN \n", - "134 NaN 1.0 NaN \n", - "135 NaN 2.0 NaN \n", - "136 NaN 3.0 NaN \n", - "137 NaN 5.0 NaN \n", - "138 NaN 6.0 NaN \n", - "139 NaN 7.0 NaN \n", - "140 NaN NaN NaN \n", - "141 NaN NaN NaN \n", - "142 2.0 NaN NaN \n", - "143 3.0 NaN NaN \n", - "144 4.0 NaN NaN \n", - "145 NaN NaN NaN \n", - "146 NaN NaN NaN \n", - "147 NaN NaN NaN \n", - "148 NaN NaN 2.0 \n", - "149 NaN NaN 3.0 \n", - "150 NaN NaN 4.0 \n", - "151 NaN NaN 5.0 \n", - "152 NaN NaN 6.0 \n", - "\n", - " turbo no synopsis \n", - "0 NaN \n", - "1 NaN \n", - "2 NaN \n", - "3 NaN \n", - "4 NaN \n", - "5 NaN \n", - "6 NaN \n", - "7 NaN \n", - "8 NaN \n", - "9 NaN \n", - "10 NaN \n", - "11 NaN \n", - "12 NaN \n", - "13 NaN \n", - "14 NaN \n", - "15 NaN \n", - "16 NaN \n", - "17 NaN \n", - "18 NaN \n", - "19 NaN \n", - "20 NaN \n", - "21 NaN \n", - "22 NaN \n", - "23 NaN \n", - "24 NaN \n", - "25 NaN \n", - "26 NaN \n", - "27 NaN \n", - "28 NaN \n", - "29 NaN \n", - "30 NaN \n", - "31 NaN \n", - "32 NaN \n", - "33 NaN \n", - "34 NaN \n", - "35 NaN \n", - "36 NaN \n", - "37 NaN \n", - "38 NaN \n", - "39 NaN \n", - "40 NaN \n", - "41 NaN \n", - "42 NaN \n", - "43 NaN \n", - "44 NaN \n", - "45 NaN \n", - "46 NaN \n", - "47 NaN \n", - "48 NaN \n", - "49 NaN \n", - "50 NaN \n", - "51 NaN \n", - "52 NaN \n", - "53 NaN \n", - "54 NaN \n", - "55 NaN \n", - "56 NaN \n", - "57 NaN \n", - "58 NaN \n", - "59 NaN \n", - "60 NaN \n", - "61 NaN \n", - "62 NaN \n", - "63 NaN \n", - "64 NaN \n", - "65 NaN \n", - "66 NaN \n", - "67 NaN \n", - "68 NaN \n", - "69 NaN \n", - "70 NaN \n", - "71 NaN \n", - "72 NaN \n", - "73 NaN \n", - "74 NaN \n", - "75 NaN \n", - "76 NaN \n", - "77 NaN \n", - "78 NaN \n", - "79 NaN \n", - "80 NaN \n", - "81 NaN \n", - "82 NaN \n", - "83 NaN \n", - "84 NaN \n", - "85 NaN \n", - "86 NaN \n", - "87 NaN \n", - "88 NaN \n", - "89 NaN \n", - "90 NaN \n", - "91 NaN \n", - "92 NaN \n", - "93 NaN \n", - "94 NaN \n", - "95 NaN \n", - "96 NaN \n", - "97 NaN \n", - "98 NaN \n", - "99 NaN \n", - "100 NaN \n", - "101 NaN \n", - "102 NaN \n", - "103 NaN \n", - "104 NaN \n", - "105 NaN \n", - "106 NaN \n", - "107 NaN \n", - "108 NaN \n", - "109 NaN \n", - "110 NaN \n", - "111 NaN \n", - "112 NaN \n", - "113 NaN \n", - "114 NaN \n", - "115 NaN \n", - "116 NaN \n", - "117 NaN \n", - "118 NaN \n", - "119 NaN \n", - "120 NaN \n", - "121 NaN \n", - "122 NaN \n", - "123 NaN \n", - "124 NaN \n", - "125 NaN \n", - "126 NaN \n", - "127 NaN \n", - "128 NaN \n", - "129 NaN \n", - "130 NaN \n", - "131 NaN \n", - "132 NaN \n", - "133 NaN \n", - "134 NaN \n", - "135 NaN \n", - "136 NaN \n", - "137 NaN \n", - "138 NaN \n", - "139 NaN \n", - "140 0.0 \n", - "141 NaN \n", - "142 NaN \n", - "143 NaN \n", - "144 NaN \n", - "145 1.0 \n", - "146 2.0 \n", - "147 3.0 \n", - "148 NaN \n", - "149 NaN \n", - "150 NaN \n", - "151 NaN \n", - "152 NaN " - ] - }, - "execution_count": 90, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "igrb = df.query(f\"{GENESET} == 'ig-receptor-binding-2022-0'\").sort_values(\"similarity\", ascending=False)\n", - "terms_summary(igrb)" - ] - }, - { - "cell_type": "code", - "execution_count": 91, - "id": "97d41daf", - "metadata": {}, - "outputs": [], - "source": [ - "viz('ig-receptor-binding-2022-0')" - ] - }, - { - "cell_type": "markdown", - "id": "d7fae990", - "metadata": {}, - "source": [ - "![img](output/ig-receptor-binding-2022-0-True-v1.png)" - ] - }, - { - "cell_type": "code", - "execution_count": 96, - "id": "48d4bc0c", - "metadata": {}, - "outputs": [], - "source": [ - "viz('HALLMARK_GLYCOLYSIS-0')" - ] - }, - { - "cell_type": "markdown", - "id": "df7b8436", - "metadata": {}, - "source": [ - "![img](output/HALLMARK_GLYCOLYSIS-0-True-v1.png)" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "7817941b", - "metadata": {}, - "outputs": [], - "source": [] - }, - { - "cell_type": "code", - "execution_count": 98, - "id": "ce584b02", - "metadata": {}, - "outputs": [], - "source": [ - "viz('HALLMARK_KRAS_SIGNALING_UP-0')" - ] - }, - { - "cell_type": "markdown", - "id": "b2e58b0d", - "metadata": {}, - "source": [ - "![img](output/HALLMARK_KRAS_SIGNALING_UP-0-True-v1.png)" - ] - }, - { - "cell_type": "markdown", - "id": "56886699", - "metadata": {}, - "source": [ - "## Summaries" - ] - }, - { - "cell_type": "code", - "execution_count": 92, - "id": "78102fc3", - "metadata": {}, - "outputs": [], - "source": [ - "objs = []\n", - "for c in comps:\n", - " for m, payload in c.payloads.items():\n", - " if payload.summary:\n", - " objs.append({\"model\": c.model, \"geneset\": c.name, \"method\": m, \"summary\": payload.summary})" - ] - }, - { - "cell_type": "code", - "execution_count": 93, - "id": "97ba3556", - "metadata": {}, - "outputs": [], - "source": [ - "sdf = pd.DataFrame(objs)" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "a2a0629a", - "metadata": {}, - "outputs": [], - "source": [ - "pd.set_option('display.max_colwidth', None)\n", - "pd.set_option('display.max_rows', None)\n", - "sdf" - ] - }, - { - "cell_type": "code", - "execution_count": 95, - "id": "dd2c3d2e", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - 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modelgenesetmethodsummary
1680Nonesensory ataxia-0gpt-3.5-turbo.no_synopsis.v1Summary: The enriched terms found among the listed human genes suggest a common involvement in cellular metabolism, particularly in mitochondrial function, protein folding and degradation, and transportation across cellular membranes.\\nMechanism: These genes may be involved in the maintenance of cellular homeostasis and energy production.\\n\\nHypothesis: Many of the enriched terms are related to cellular stress pathways, suggesting that these genes may be involved in the response to stress and cellular damage. Additionally, the involvement of several genes related to mitochondrial function suggests that there may be a common underlying mechanism related to energy production and metabolism.
1681Nonesensory ataxia-0gpt-3.5-turbo.no_synopsis.v2Summary: Genes are involved in nervous system development and function. \\nMechanism: Myelination and axonal transport. \\n\\nHypothesis: The genes on the list are enriched for terms involved in nervous system development and function, including myelination, axon guidance, and neuron projection development. This suggests a role for these genes in the regulation of myelination and axonal transport, which are important processes for proper nervous system function. Dysfunction of these processes, due to mutations in genes such as PMP22 and SH3TC2, can lead to peripheral neuropathy and other neurological disorders.
1682Nonesensory ataxia-0gpt-3.5-turbo.ontological_synopsis.v1Summary: Genes are primarily involved in the peripheral nervous system, myelination, and neurological disorders.\\nMechanism: The enriched terms suggest that these genes primarily function in the peripheral nervous system and myelination.\\n\\nHypothesis: These genes are all involved in the development and maintenance of the peripheral nervous system and myelination. Dysregulation or mutation of these genes likely leads to neuropathic disorders.
1683Nonesensory ataxia-0gpt-3.5-turbo.ontological_synopsis.v2Summary: Genes are involved in various processes in the development and maintenance of the nervous system, specifically peripheral nerves and myelination, as well as nucleic acid and protein metabolism.\\n\\nMechanism: The enriched terms suggest a common underlying biological mechanism in the formation and maintenance of the peripheral nervous system and myelination, as well as in nucleic acid and protein metabolism.\\n\\n\\nHypothesis: The enrichment of terms related to Charcot-Marie-Tooth disease and myelination suggest that these genes play an important role in peripheral nervous system development and maintenance, specifically in the formation and maintenance of myelin. The enrichment of terms related to protein folding and nucleic acid metabolism suggest that these genes also have a role in maintaining and regulating the overall metabolic processes of cells. The involvement of genes in mitochondrial function suggests a possible link between peripheral nerve function and mitochondrial metabolism.
1684Nonesensory ataxia-0gpt-3.5-turbo.narrative_synopsis.v1Summary: Myelin upkeep and neurological diseases\\n\\nHypothesis: Dysregulation of the myelin upkeep pathways can lead to mitochondrial dysfunction, accumulations of toxic metabolites, and impaired protein processing, which contribute to the development of neurological diseases. Dysfunction of the transporter proteins and nuclear membrane transporters can further exacerbate cell dysfunction and death. Treatment strategies aimed at restoring mitochondrial function and enhancing myelin synthesis and repair may alleviate symptoms of these diseases.
1685Nonesensory ataxia-0gpt-3.5-turbo.narrative_synopsis.v2Summary: Peripheral nervous system myelination and neurodegenerative diseases are enriched in this set of genes. \\nMechanism: Maintenance of peripheral nervous system myelin structure and function through regulation of protein import, DNA replication, and degradation pathways in the endoplasmic reticulum and mitochondria. \\n
1686Nonesensory ataxia-0text-davinci-003.no_synopsis.v1This list of genes is related to muscle, central and peripheral nervous system development, as well as protein and lipid transport and metabolism. \\nMechanism: The genes appear to be involved in regulatory pathways for growth and development of the skeletal and nervous systems via coordination of morphology, protein and lipid synthesis, and transport.\\n
1687Nonesensory ataxia-0text-davinci-003.no_synopsis.v2These genes are mainly involved in protein synthesis, metabolism, ion channel transport, and muscle contraction or development.\\n\\nMechanism: These genes function as transcriptional regulators, enzymes in metabolic pathways, ion channels, or as key mediators of neuromuscular development and contraction.\\n\\n
1688Nonesensory ataxia-0text-davinci-003.ontological_synopsis.v1The genes in the list are all involved in many functions including DNA-binding, RNA polymerase II-specific activity, metal ion binding, ubiquitin protein ligase binding, and positive regulation of transcription by RNA polymerase II. These genes are also likely to be involved in several processes including positive regulation of immunoglobulin production, regulation of ERBB signaling pathway, regulation of intracellular protein transport, monoatomic cation transport, nucleic acid metabolic process, protein hexamerization, glycosaminoglycan catabolic process, nervous system development, heme transport, and mitochondrial transport.\\n\\nMechanism: These genes likely coordinate a combination of transcription activities to maintain cell function, health, and development. They are also likely to be involved in transporting and processing essential molecules needed for maintaining normal neural and sensory functionality as well as involved in transporting and processing essential molecules for cell metabolism.\\n\\n
1689Nonesensory ataxia-0text-davinci-003.ontological_synopsis.v2Analysis of the given list of genes suggests a common thread of involvement in the development and function of peripheral nerves, particularly with regard to varying forms of Charcot-Marie-Tooth disease, in addition to their role in nucleic acid and glycan metabolic pathways. \\n
1690Nonesensory ataxia-0text-davinci-003.narrative_synopsis.v1\\nSummary: These genes are associated with functions related to development and maintenance of the nervous system, sensory systems, and erythropoiesis, as well as mitochodnrial mRNA synthesis and transcriptional regulation. \\n\\nMechanism: These genes regulate post-translational processes including ubiquitination and processing, protein synthesis, transcription and activity of transcription factors, and organization of the cytoskeleton and nucleus.\\n\\n
1691Nonesensory ataxia-0text-davinci-003.narrative_synopsis.v2\\n\\nSummary: List of genes are involved in transcription factors, degradation heparan sulfate, moonlighting proteins, immunoglobulin secretion, adapter or docking molecule, heme transporter, myelin upkeep, nuclear pore complex, mitochondrial DNA polymerase, ubiquitin ligase, and aminoacyl-tRNA synthetase.\\n\\n
\n", - "
" - ], - "text/plain": [ - " model geneset method \\\n", - "1680 None sensory ataxia-0 gpt-3.5-turbo.no_synopsis.v1 \n", - "1681 None sensory ataxia-0 gpt-3.5-turbo.no_synopsis.v2 \n", - "1682 None sensory ataxia-0 gpt-3.5-turbo.ontological_synopsis.v1 \n", - "1683 None sensory ataxia-0 gpt-3.5-turbo.ontological_synopsis.v2 \n", - "1684 None sensory ataxia-0 gpt-3.5-turbo.narrative_synopsis.v1 \n", - "1685 None sensory ataxia-0 gpt-3.5-turbo.narrative_synopsis.v2 \n", - "1686 None sensory ataxia-0 text-davinci-003.no_synopsis.v1 \n", - "1687 None sensory ataxia-0 text-davinci-003.no_synopsis.v2 \n", - "1688 None sensory ataxia-0 text-davinci-003.ontological_synopsis.v1 \n", - "1689 None sensory ataxia-0 text-davinci-003.ontological_synopsis.v2 \n", - "1690 None sensory ataxia-0 text-davinci-003.narrative_synopsis.v1 \n", - "1691 None sensory ataxia-0 text-davinci-003.narrative_synopsis.v2 \n", - "\n", - " summary \n", - "1680 Summary: The enriched terms found among the listed human genes suggest a common involvement in cellular metabolism, particularly in mitochondrial function, protein folding and degradation, and transportation across cellular membranes.\\nMechanism: These genes may be involved in the maintenance of cellular homeostasis and energy production.\\n\\nHypothesis: Many of the enriched terms are related to cellular stress pathways, suggesting that these genes may be involved in the response to stress and cellular damage. Additionally, the involvement of several genes related to mitochondrial function suggests that there may be a common underlying mechanism related to energy production and metabolism. \n", - "1681 Summary: Genes are involved in nervous system development and function. \\nMechanism: Myelination and axonal transport. \\n\\nHypothesis: The genes on the list are enriched for terms involved in nervous system development and function, including myelination, axon guidance, and neuron projection development. This suggests a role for these genes in the regulation of myelination and axonal transport, which are important processes for proper nervous system function. Dysfunction of these processes, due to mutations in genes such as PMP22 and SH3TC2, can lead to peripheral neuropathy and other neurological disorders. \n", - "1682 Summary: Genes are primarily involved in the peripheral nervous system, myelination, and neurological disorders.\\nMechanism: The enriched terms suggest that these genes primarily function in the peripheral nervous system and myelination.\\n\\nHypothesis: These genes are all involved in the development and maintenance of the peripheral nervous system and myelination. Dysregulation or mutation of these genes likely leads to neuropathic disorders. \n", - "1683 Summary: Genes are involved in various processes in the development and maintenance of the nervous system, specifically peripheral nerves and myelination, as well as nucleic acid and protein metabolism.\\n\\nMechanism: The enriched terms suggest a common underlying biological mechanism in the formation and maintenance of the peripheral nervous system and myelination, as well as in nucleic acid and protein metabolism.\\n\\n\\nHypothesis: The enrichment of terms related to Charcot-Marie-Tooth disease and myelination suggest that these genes play an important role in peripheral nervous system development and maintenance, specifically in the formation and maintenance of myelin. The enrichment of terms related to protein folding and nucleic acid metabolism suggest that these genes also have a role in maintaining and regulating the overall metabolic processes of cells. The involvement of genes in mitochondrial function suggests a possible link between peripheral nerve function and mitochondrial metabolism. \n", - "1684 Summary: Myelin upkeep and neurological diseases\\n\\nHypothesis: Dysregulation of the myelin upkeep pathways can lead to mitochondrial dysfunction, accumulations of toxic metabolites, and impaired protein processing, which contribute to the development of neurological diseases. Dysfunction of the transporter proteins and nuclear membrane transporters can further exacerbate cell dysfunction and death. Treatment strategies aimed at restoring mitochondrial function and enhancing myelin synthesis and repair may alleviate symptoms of these diseases. \n", - "1685 Summary: Peripheral nervous system myelination and neurodegenerative diseases are enriched in this set of genes. \\nMechanism: Maintenance of peripheral nervous system myelin structure and function through regulation of protein import, DNA replication, and degradation pathways in the endoplasmic reticulum and mitochondria. \\n \n", - "1686 This list of genes is related to muscle, central and peripheral nervous system development, as well as protein and lipid transport and metabolism. \\nMechanism: The genes appear to be involved in regulatory pathways for growth and development of the skeletal and nervous systems via coordination of morphology, protein and lipid synthesis, and transport.\\n \n", - "1687 These genes are mainly involved in protein synthesis, metabolism, ion channel transport, and muscle contraction or development.\\n\\nMechanism: These genes function as transcriptional regulators, enzymes in metabolic pathways, ion channels, or as key mediators of neuromuscular development and contraction.\\n\\n \n", - "1688 The genes in the list are all involved in many functions including DNA-binding, RNA polymerase II-specific activity, metal ion binding, ubiquitin protein ligase binding, and positive regulation of transcription by RNA polymerase II. These genes are also likely to be involved in several processes including positive regulation of immunoglobulin production, regulation of ERBB signaling pathway, regulation of intracellular protein transport, monoatomic cation transport, nucleic acid metabolic process, protein hexamerization, glycosaminoglycan catabolic process, nervous system development, heme transport, and mitochondrial transport.\\n\\nMechanism: These genes likely coordinate a combination of transcription activities to maintain cell function, health, and development. They are also likely to be involved in transporting and processing essential molecules needed for maintaining normal neural and sensory functionality as well as involved in transporting and processing essential molecules for cell metabolism.\\n\\n \n", - "1689 Analysis of the given list of genes suggests a common thread of involvement in the development and function of peripheral nerves, particularly with regard to varying forms of Charcot-Marie-Tooth disease, in addition to their role in nucleic acid and glycan metabolic pathways. \\n \n", - "1690 \\nSummary: These genes are associated with functions related to development and maintenance of the nervous system, sensory systems, and erythropoiesis, as well as mitochodnrial mRNA synthesis and transcriptional regulation. \\n\\nMechanism: These genes regulate post-translational processes including ubiquitination and processing, protein synthesis, transcription and activity of transcription factors, and organization of the cytoskeleton and nucleus.\\n\\n \n", - "1691 \\n\\nSummary: List of genes are involved in transcription factors, degradation heparan sulfate, moonlighting proteins, immunoglobulin secretion, adapter or docking molecule, heme transporter, myelin upkeep, nuclear pore complex, mitochondrial DNA polymerase, ubiquitin ligase, and aminoacyl-tRNA synthetase.\\n\\n " - ] - }, - "execution_count": 95, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "sdf.query(\"geneset == 'sensory ataxia-0'\")" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "f2f51f4e", - "metadata": {}, - "outputs": [], - "source": [] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "dcdffc21", - "metadata": {}, - "outputs": [], - "source": [] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "9fa89526", - "metadata": {}, - "outputs": [], - "source": [] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "a84d7919", - "metadata": {}, - "outputs": [], - "source": [] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3 (ipykernel)", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.10.9" - } - }, - "nbformat": 4, - "nbformat_minor": 5 -} diff --git a/notebooks/Makefile b/notebooks/Makefile deleted file mode 100644 index d2cf9f0d6..000000000 --- a/notebooks/Makefile +++ /dev/null @@ -1,2 +0,0 @@ -Enrichment-Results-Analysis-%.ipynb: Enrichment-Results-Analysis.ipynb - poetry run papermill $< $@ -p experiment_results analysis/$*-enrichment-summary-2.yaml diff --git a/output_parser.py b/output_parser.py deleted file mode 100644 index 0dfd26ba0..000000000 --- a/output_parser.py +++ /dev/null @@ -1,127 +0,0 @@ -import yaml -import time -import pprint -from oaklib import get_adapter - -NULL_VALS = ['', 'Not mentioned', 'none mentioned', 'Not mentioned in the text', - 'Not mentioned in the provided text.', 'No exposures mentioned in the text.', - 'None', 'N/A', 'No exposures mentioned in the text.', 'None mentioned in the text', - 'Not mentioned in the text.', 'None relevant', 'None mentioned in the text.', - 'No gene to molecular activity relationships mentioned in the text.', - 'No genes mentioned', 'No genes mentioned in the text.'] -lines = [] -# adapter = get_adapter("sqlite:obo:CHEBI") -adapter = get_adapter("sqlite:obo:MONDO") -# output_file = "output_2000_0719.yaml" -# output_file = "output_100_0817.yaml" -# output_file = "output_100_0818.yaml" -output_file = "output_partial_50_0911.yaml" - -def tripleprint(dict): - key = next(iter(dict)) - for i in range(len(dict[key])): - curr = [] - for value in dict.values(): - curr.append(value[i]) - print(curr) -def forprint(lst): - for elem in lst: - print(elem) -def nprint(lst, n): - for i in range(n): - print(lst[i]) -def sleepprint(lst): - for elem in lst: - print(elem) - time.sleep(0.5) -def enumprint(lst): - for index, elem in enumerate(lst): - print(str(index + 1) + ":\t" + str(elem)) - -with open(output_file, "r") as file: - to_print = False - perpetuators = tuple([" subject:", " predicate:", " object:", " "]) - # perpetuators = tuple([" - subject:", " predicate:", " object:"]) - for line in file: - line = line.strip("\n") - if line.startswith("extracted_object:"): - # if line.startswith(" disease_cellular_process_relationships:") and not line.startswith(" disease_cellular_process_relationships: "): - to_print = True - elif not line.startswith(perpetuators): - to_print = False - if to_print: - lines.append(line) - -cleaned_lines = [x for x in list(filter(lambda elem: not(elem.isspace()), lines)) if x.strip()] -cleaned_lines = [x for x in cleaned_lines if x != "extracted_object: {}"] -i = 1 -while i < len(cleaned_lines): - if cleaned_lines[i].startswith(" "): - cleaned_lines[i-1] += " " - cleaned_lines[i-1] += cleaned_lines[i][4:] - del cleaned_lines[i] - else: - i += 1 - -header = "extracted_object" -# header = " disease_cellular_process_relationships:" -i = 0 -while i < len(cleaned_lines): - if cleaned_lines[i].startswith(header): - for index, elem in enumerate(cleaned_lines[i+1:i+4]): - if elem.startswith(header): - next_index = i + 1 + index - del cleaned_lines[i:next_index] - i -= 1 - i += 1 - -grouped_lines = [cleaned_lines[n:n+4] for n in range(0, len(cleaned_lines), 4)] - -# trimmed_dict = {"genes": [], "relationships": [], "exposures": []} -trimmed_dict = {"diseases": [], "relationships": [], "cellular processes": []} -for group in grouped_lines: - group.pop(0) - -for group in grouped_lines: - subject = group[0].split(":", 1)[1].strip() - relation = group[1].split(":", 1)[1].strip() - object = group[2].split(":", 1)[1].strip() - # trimmed_dict["genes"].append(subject) - # trimmed_dict["relationships"].append(relation) - # trimmed_dict["exposures"].append(object) - trimmed_dict["diseases"].append(subject) - trimmed_dict["relationships"].append(relation) - trimmed_dict["cellular processes"].append(object) - -for key, value in trimmed_dict.copy().items(): - for i, elem in enumerate(value): - if elem.lower() in (val.lower() for val in NULL_VALS): - for key, value in trimmed_dict.items(): - del value[i] - -# subjects_with_chebi = [] -# objects_with_ecto = [] -subjects_with_mondo = [] -key = next(iter(trimmed_dict)) -for i in range(len(trimmed_dict[key])): - curr = [] - for value in trimmed_dict.values(): - curr.append(value[i]) - # subjects_with_chebi.append(curr) - subjects_with_mondo.append(curr) - # objects_with_ecto.append(curr) -# subjects_with_chebi = [x for x in subjects_with_chebi if x[0].startswith("CHEBI:")] -subjects_with_mondo = [x for x in subjects_with_mondo if x[0].startswith("MONDO:")] -mondo_go = [x for x in subjects_with_mondo if x[2].startswith("GO:")] -# objects_with_ecto = [x for x in objects_with_ecto if x[2].startswith("ECTO:")] - -forprint(mondo_go) - -subjects_with_names = [] -# for elem in subjects_with_chebi: -for elem in subjects_with_mondo: - curr = elem[:] - curr[0] = adapter.label(curr[0]) - subjects_with_names.append(curr) - -# forprint(subjects_with_names) \ No newline at end of file diff --git a/output_parser_bulleted.py b/output_parser_bulleted.py deleted file mode 100644 index 5d7c3d057..000000000 --- a/output_parser_bulleted.py +++ /dev/null @@ -1,125 +0,0 @@ -import yaml -import time -import pprint -from oaklib import get_adapter - -NULL_VALS = ['', 'Not mentioned', 'none mentioned', 'Not mentioned in the text', - 'Not mentioned in the provided text.', 'No exposures mentioned in the text.', - 'None', 'N/A', 'No exposures mentioned in the text.', 'None mentioned in the text', - 'Not mentioned in the text.', 'None relevant', 'None mentioned in the text.', - 'No gene to molecular activity relationships mentioned in the text.', - 'No genes mentioned', 'No genes mentioned in the text.'] -lines = [] -adapter = get_adapter("sqlite:obo:MONDO") -# output_file = "output_2000_0719.yaml" -# output_file = "output_100_0817.yaml" -# output_file = "output_100_0818.yaml" -output_file = "output_100.0911.yaml" - -def tripleprint(dict): - key = next(iter(dict)) - for i in range(len(dict[key])): - curr = [] - for value in dict.values(): - curr.append(value[i]) - print(curr) -def forprint(lst): - for elem in lst: - print(elem) -def forprint_newline(lst): - for elem in lst: - print(elem) - print("\n") -def nprint(lst, n): - for i in range(n): - print(lst[i]) -def sleepprint(lst): - for elem in lst: - print(elem) - time.sleep(0.5) -def enumprint(lst): - for index, elem in enumerate(lst): - print(str(index + 1) + ":\t" + str(elem)) - -with open(output_file, "r") as file: - to_print = False - # perpetuators = tuple([" subject:", " predicate:", " object:", " "]) - perpetuators = tuple([" - subject:", " predicate:", " object:"]) - perpetuators = tuple([" - subject:", " predicate:", " object:", " qualifier:", " subject_qualifier:", " object_qualifier:"]) - for line in file: - line = line.strip("\n") - # if line.startswith("extracted_object:"): - if line.startswith(" disease_cellular_process_relationships:") and not line.startswith(" disease_cellular_process_relationships: "): - # if line.startswith(perpetuators): - to_print = True - # elif not line.startswith(perpetuators): - # if line.startswith("named_entities:"): - elif not line.startswith(perpetuators): - to_print = False - if to_print: - lines.append(line) - -cleaned_lines = [x for x in list(filter(lambda elem: not(elem.isspace()), lines)) if x.strip()] -cleaned_lines = [x for x in cleaned_lines if not x.startswith(tuple([" qualifier:", " subject_qualifier:", " object_qualifier:", " disease_cellular_process_relationships:"]))] - -header = " - subject:" -i = 0 -while i < len(cleaned_lines): - if cleaned_lines[i].startswith(header): - for index, elem in enumerate(cleaned_lines[i+1:i+3]): - if elem.startswith(header): - next_index = i + 1 + index - del cleaned_lines[i:next_index] - i -= 1 - i += 1 - -cleaned_lines = [x.strip() for x in cleaned_lines] -for i, line in enumerate(cleaned_lines.copy()): -# for line in cleaned_lines: - if line.startswith("- "): - cleaned_lines[i] = line[2:] - -grouped_lines = [cleaned_lines[n:n+3] for n in range(0, len(cleaned_lines), 3)] -trimmed_dict = {"diseases": [], "relationships": [], "cellular processes": []} -for group in grouped_lines: - subject = group[0].split(":", 1)[1].strip() - relation = group[1].split(":", 1)[1].strip() - object = group[2].split(":", 1)[1].strip() - trimmed_dict["diseases"].append(subject) - trimmed_dict["relationships"].append(relation) - trimmed_dict["cellular processes"].append(object) - -for key, value in trimmed_dict.copy().items(): - for i, elem in enumerate(value): - if elem.lower() in (val.lower() for val in NULL_VALS): - for key, value in trimmed_dict.items(): - del value[i] - -# subjects_with_chebi = [] -# objects_with_ecto = [] -subjects_with_mondo = [] -mondo_go = [] -key = next(iter(trimmed_dict)) -for i in range(len(trimmed_dict[key])): - curr = [] - for value in trimmed_dict.values(): - curr.append(value[i]) - # subjects_with_chebi.append(curr) - mondo_go.append(curr) - # objects_with_ecto.append(curr) -# subjects_with_chebi = [x for x in subjects_with_chebi if x[0].startswith("CHEBI:")] -mondo_go = [x for x in mondo_go if x[0].startswith("MONDO:") and x[2].startswith("GO:")] -# objects_with_ecto = [x for x in objects_with_ecto if x[2].startswith("ECTO:")] - -forprint(mondo_go) - -# forprint(subjects_with_mondo) - -subjects_with_names = [] -# for elem in subjects_with_chebi: -for elem in subjects_with_mondo: - curr = elem[:] - curr[0] = adapter.label(curr[0]) - subjects_with_names.append(curr) - -# forprint(subjects_with_names) \ No newline at end of file diff --git a/poetry.lock b/poetry.lock index 3faa1b1e0..a36eeea4c 100644 --- a/poetry.lock +++ b/poetry.lock @@ -145,17 +145,6 @@ files = [ dev = ["pytest (>=6.2,<7.0)", "pytest-cov (>=3.0,<4.0)", "pytest-mock (>=3.6,<4.0)"] parse = ["beautifulsoup4 (>=4.10.0,<5.0)", "requests (>=2.12.0,<3)"] -[[package]] -name = "alabaster" -version = "0.7.13" -description = "A configurable sidebar-enabled Sphinx theme" -optional = true -python-versions = ">=3.6" -files = [ - {file = "alabaster-0.7.13-py3-none-any.whl", hash = "sha256:1ee19aca801bbabb5ba3f5f258e4422dfa86f82f3e9cefb0859b283cdd7f62a3"}, - {file = "alabaster-0.7.13.tar.gz", hash = "sha256:a27a4a084d5e690e16e01e03ad2b2e552c61a65469419b907243193de1a84ae2"}, -] - [[package]] name = "altair" version = "5.2.0" @@ -231,24 +220,25 @@ files = [ [[package]] name = "anyio" -version = "3.7.1" +version = "4.2.0" description = "High level compatibility layer for multiple asynchronous event loop implementations" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" files = [ - {file = 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{file = "XlsxWriter-3.1.9-py3-none-any.whl", hash = "sha256:b61c1a0c786f82644936c0936ec96ee96cd3afb9440094232f7faef9b38689f0"}, - {file = "XlsxWriter-3.1.9.tar.gz", hash = "sha256:de810bf328c6a4550f4ffd6b0b34972aeb7ffcf40f3d285a0413734f9b63a929"}, -] - [[package]] name = "yarl" version = "1.9.4" @@ -7626,14 +6936,9 @@ docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.link testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"] [extras] -docs = ["myst-parser", "sphinx", "sphinx-autodoc-typehints", "sphinx-click", "sphinx-rtd-theme"] -gpt4all = ["gpt4all", "llm-gpt4all"] -huggingface = ["huggingface_hub"] -recipes = ["recipe-scrapers"] -textract = ["textract"] -web = ["Jinja2", "fastapi", "uvicorn"] +docs = [] [metadata] lock-version = "2.0" python-versions = ">=3.9,<3.9.7 || >3.9.7,<4.0" -content-hash = "47a721cfaa5047652c8212ea4598d65042af775e8bd575e4a795d6dc0b739778" +content-hash = "3935aefae637ed2fc0d26bd86cfd86699f674bc52e5aaa151dae93e42ae2da7d" diff --git a/projects/biological_process/biological_process.py b/projects/biological_process/biological_process.py deleted file mode 100644 index 652994ad1..000000000 --- a/projects/biological_process/biological_process.py +++ /dev/null @@ -1,558 +0,0 @@ -# Auto generated from biological_process.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-08-07T10:51:21 -# Schema: biological-process-template -# -# id: https://w3id.org/ontogpt/biological_process -# description: A template for GO-CAMs -# license: https://creativecommons.org/publicdomain/zero/1.0/ - -import dataclasses -import sys -import re -from jsonasobj2 import JsonObj, as_dict -from typing import Optional, List, Union, Dict, ClassVar, Any -from dataclasses import dataclass -from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions - -from linkml_runtime.utils.slot import Slot -from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode -from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int -from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs -from linkml_runtime.utils.formatutils import camelcase, underscore, sfx -from linkml_runtime.utils.enumerations import EnumDefinitionImpl -from rdflib import Namespace, URIRef -from linkml_runtime.utils.curienamespace import CurieNamespace -from linkml_runtime.linkml_model.types import String - -metamodel_version = "1.7.0" -version = None - -# Overwrite dataclasses _init_fn to add **kwargs in __init__ -dataclasses._init_fn = dataclasses_init_fn_with_kwargs - -# Namespaces -CHEBI = CurieNamespace('CHEBI', 'http://example.org/UNKNOWN/CHEBI/') -GO = CurieNamespace('GO', 'http://example.org/UNKNOWN/GO/') -HGNC = CurieNamespace('HGNC', 'http://example.org/UNKNOWN/HGNC/') -RO = CurieNamespace('RO', 'http://purl.obolibrary.org/obo/RO_') -BIOLINK = CurieNamespace('biolink', 'http://example.org/UNKNOWN/biolink/') -BP = CurieNamespace('bp', 'http://w3id.org/ontogpt/biological-process-template') -CORE = CurieNamespace('core', 'http://w3id.org/ontogpt/core/') -LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') -RDFS = CurieNamespace('rdfs', 'http://example.org/UNKNOWN/rdfs/') -DEFAULT_ = BP - - -# Types - -# Class references -class NamedEntityId(extended_str): - pass - - -class BiologicalProcessId(NamedEntityId): - pass - - -class GeneId(NamedEntityId): - pass - - -class MolecularActivityId(NamedEntityId): - pass - - -class ChemicalEntityId(NamedEntityId): - pass - - -class RelationshipTypeId(NamedEntityId): - pass - - -@dataclass -class GeneMolecularActivityRelationship(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = BP.GeneMolecularActivityRelationship - class_class_curie: ClassVar[str] = "bp:GeneMolecularActivityRelationship" - class_name: ClassVar[str] = "GeneMolecularActivityRelationship" - class_model_uri: ClassVar[URIRef] = BP.GeneMolecularActivityRelationship - - gene: Optional[Union[str, GeneId]] = None - molecular_activity: Optional[Union[str, MolecularActivityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.gene is not None and not isinstance(self.gene, GeneId): - self.gene = GeneId(self.gene) - - if self.molecular_activity is not None and not isinstance(self.molecular_activity, MolecularActivityId): - self.molecular_activity = MolecularActivityId(self.molecular_activity) - - super().__post_init__(**kwargs) - - -Any = Any - -@dataclass -class ExtractionResult(YAMLRoot): - """ - A result of extracting knowledge on text - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.ExtractionResult - class_class_curie: ClassVar[str] = "core:ExtractionResult" - class_name: ClassVar[str] = "ExtractionResult" - class_model_uri: ClassVar[URIRef] = BP.ExtractionResult - - input_id: Optional[str] = None - input_title: Optional[str] = None - input_text: Optional[str] = None - raw_completion_output: Optional[str] = None - prompt: Optional[str] = None - extracted_object: Optional[Union[dict, Any]] = None - named_entities: Optional[Union[Union[dict, Any], List[Union[dict, Any]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.input_id is not None and not isinstance(self.input_id, str): - self.input_id = str(self.input_id) - - if self.input_title is not None and not isinstance(self.input_title, str): - self.input_title = str(self.input_title) - - if self.input_text is not None and not isinstance(self.input_text, str): - self.input_text = str(self.input_text) - - if self.raw_completion_output is not None and not isinstance(self.raw_completion_output, str): - self.raw_completion_output = str(self.raw_completion_output) - - if self.prompt is not None and not isinstance(self.prompt, str): - self.prompt = str(self.prompt) - - super().__post_init__(**kwargs) - - -@dataclass -class NamedEntity(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.NamedEntity - class_class_curie: ClassVar[str] = "core:NamedEntity" - class_name: ClassVar[str] = "NamedEntity" - class_model_uri: ClassVar[URIRef] = BP.NamedEntity - - id: Union[str, NamedEntityId] = None - label: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, NamedEntityId): - self.id = NamedEntityId(self.id) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - super().__post_init__(**kwargs) - - -@dataclass -class BiologicalProcess(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = BP.BiologicalProcess - class_class_curie: ClassVar[str] = "bp:BiologicalProcess" - class_name: ClassVar[str] = "BiologicalProcess" - class_model_uri: ClassVar[URIRef] = BP.BiologicalProcess - - id: Union[str, BiologicalProcessId] = None - label: Optional[str] = None - description: Optional[str] = None - synonyms: Optional[Union[str, List[str]]] = empty_list() - subclass_of: Optional[Union[str, BiologicalProcessId]] = None - inputs: Optional[Union[Union[str, ChemicalEntityId], List[Union[str, ChemicalEntityId]]]] = empty_list() - outputs: Optional[Union[Union[str, ChemicalEntityId], List[Union[str, ChemicalEntityId]]]] = empty_list() - steps: Optional[Union[Union[str, MolecularActivityId], List[Union[str, MolecularActivityId]]]] = empty_list() - genes: Optional[Union[Union[str, GeneId], List[Union[str, GeneId]]]] = empty_list() - gene_activities: Optional[Union[Union[dict, "GeneMolecularActivityRelationship"], List[Union[dict, "GeneMolecularActivityRelationship"]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, BiologicalProcessId): - self.id = BiologicalProcessId(self.id) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - if self.description is not None and not isinstance(self.description, str): - self.description = str(self.description) - - if not isinstance(self.synonyms, list): - self.synonyms = [self.synonyms] if self.synonyms is not None else [] - self.synonyms = [v if isinstance(v, str) else str(v) for v in self.synonyms] - - if self.subclass_of is not None and not isinstance(self.subclass_of, BiologicalProcessId): - self.subclass_of = BiologicalProcessId(self.subclass_of) - - if not isinstance(self.inputs, list): - self.inputs = [self.inputs] if self.inputs is not None else [] - self.inputs = [v if isinstance(v, ChemicalEntityId) else ChemicalEntityId(v) for v in self.inputs] - - if not isinstance(self.outputs, list): - self.outputs = [self.outputs] if self.outputs is not None else [] - self.outputs = [v if isinstance(v, ChemicalEntityId) else ChemicalEntityId(v) for v in self.outputs] - - if not isinstance(self.steps, list): - self.steps = [self.steps] if self.steps is not None else [] - self.steps = [v if isinstance(v, MolecularActivityId) else MolecularActivityId(v) for v in self.steps] - - if not isinstance(self.genes, list): - self.genes = [self.genes] if self.genes is not None else [] - self.genes = [v if isinstance(v, GeneId) else GeneId(v) for v in self.genes] - - if not isinstance(self.gene_activities, list): - self.gene_activities = [self.gene_activities] if self.gene_activities is not None else [] - self.gene_activities = [v if isinstance(v, GeneMolecularActivityRelationship) else GeneMolecularActivityRelationship(**as_dict(v)) for v in self.gene_activities] - - super().__post_init__(**kwargs) - - -@dataclass -class Gene(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = BP.Gene - class_class_curie: ClassVar[str] = "bp:Gene" - class_name: ClassVar[str] = "Gene" - class_model_uri: ClassVar[URIRef] = BP.Gene - - id: Union[str, GeneId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, GeneId): - self.id = GeneId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class MolecularActivity(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = BP.MolecularActivity - class_class_curie: ClassVar[str] = "bp:MolecularActivity" - class_name: ClassVar[str] = "MolecularActivity" - class_model_uri: ClassVar[URIRef] = BP.MolecularActivity - - id: Union[str, MolecularActivityId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, MolecularActivityId): - self.id = MolecularActivityId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class ChemicalEntity(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = BP.ChemicalEntity - class_class_curie: ClassVar[str] = "bp:ChemicalEntity" - class_name: ClassVar[str] = "ChemicalEntity" - class_model_uri: ClassVar[URIRef] = BP.ChemicalEntity - - id: Union[str, ChemicalEntityId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, ChemicalEntityId): - self.id = ChemicalEntityId(self.id) - - super().__post_init__(**kwargs) - - -class CompoundExpression(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.CompoundExpression - class_class_curie: ClassVar[str] = "core:CompoundExpression" - class_name: ClassVar[str] = "CompoundExpression" - class_model_uri: ClassVar[URIRef] = BP.CompoundExpression - - -@dataclass -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Triple - class_class_curie: ClassVar[str] = "core:Triple" - class_name: ClassVar[str] = "Triple" - class_model_uri: ClassVar[URIRef] = BP.Triple - - subject: Optional[Union[str, NamedEntityId]] = None - predicate: Optional[Union[str, RelationshipTypeId]] = None - object: Optional[Union[str, NamedEntityId]] = None - qualifier: Optional[str] = None - subject_qualifier: Optional[Union[str, NamedEntityId]] = None - object_qualifier: Optional[Union[str, NamedEntityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, NamedEntityId): - self.subject = NamedEntityId(self.subject) - - if self.predicate is not None and not isinstance(self.predicate, RelationshipTypeId): - self.predicate = RelationshipTypeId(self.predicate) - - if self.object is not None and not isinstance(self.object, NamedEntityId): - self.object = NamedEntityId(self.object) - - if self.qualifier is not None and not isinstance(self.qualifier, str): - self.qualifier = str(self.qualifier) - - if self.subject_qualifier is not None and not isinstance(self.subject_qualifier, NamedEntityId): - self.subject_qualifier = NamedEntityId(self.subject_qualifier) - - if self.object_qualifier is not None and not isinstance(self.object_qualifier, NamedEntityId): - self.object_qualifier = NamedEntityId(self.object_qualifier) - - super().__post_init__(**kwargs) - - -@dataclass -class TextWithTriples(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.TextWithTriples - class_class_curie: ClassVar[str] = "core:TextWithTriples" - class_name: ClassVar[str] = "TextWithTriples" - class_model_uri: ClassVar[URIRef] = BP.TextWithTriples - - publication: Optional[Union[dict, "Publication"]] = None - triples: Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.publication is not None and not isinstance(self.publication, Publication): - self.publication = Publication(**as_dict(self.publication)) - - if not isinstance(self.triples, list): - self.triples = [self.triples] if self.triples is not None else [] - self.triples = [v if isinstance(v, Triple) else Triple(**as_dict(v)) for v in self.triples] - - super().__post_init__(**kwargs) - - -@dataclass -class RelationshipType(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.RelationshipType - class_class_curie: ClassVar[str] = "core:RelationshipType" - class_name: ClassVar[str] = "RelationshipType" - class_model_uri: ClassVar[URIRef] = BP.RelationshipType - - id: Union[str, RelationshipTypeId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, RelationshipTypeId): - self.id = RelationshipTypeId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Publication(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Publication - class_class_curie: ClassVar[str] = "core:Publication" - class_name: ClassVar[str] = "Publication" - class_model_uri: ClassVar[URIRef] = BP.Publication - - id: Optional[str] = None - title: Optional[str] = None - abstract: Optional[str] = None - combined_text: Optional[str] = None - full_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.id is not None and not isinstance(self.id, str): - self.id = str(self.id) - - if self.title is not None and not isinstance(self.title, str): - self.title = str(self.title) - - if self.abstract is not None and not isinstance(self.abstract, str): - self.abstract = str(self.abstract) - - if self.combined_text is not None and not isinstance(self.combined_text, str): - self.combined_text = str(self.combined_text) - - if self.full_text is not None and not isinstance(self.full_text, str): - self.full_text = str(self.full_text) - - super().__post_init__(**kwargs) - - -@dataclass -class AnnotatorResult(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.AnnotatorResult - class_class_curie: ClassVar[str] = "core:AnnotatorResult" - class_name: ClassVar[str] = "AnnotatorResult" - class_model_uri: ClassVar[URIRef] = BP.AnnotatorResult - - subject_text: Optional[str] = None - object_id: Optional[str] = None - object_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject_text is not None and not isinstance(self.subject_text, str): - self.subject_text = str(self.subject_text) - - if self.object_id is not None and not isinstance(self.object_id, str): - self.object_id = str(self.object_id) - - if self.object_text is not None and not isinstance(self.object_text, str): - self.object_text = str(self.object_text) - - super().__post_init__(**kwargs) - - -# Enumerations -class NullDataOptions(EnumDefinitionImpl): - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = PermissibleValue(text="UNSPECIFIED_METHOD_OF_ADMINISTRATION", - meaning=NCIT.C149701) - NOT_APPLICABLE = PermissibleValue(text="NOT_APPLICABLE", - meaning=NCIT.C18902) - NOT_MENTIONED = PermissibleValue(text="NOT_MENTIONED") - - _defn = EnumDefinition( - name="NullDataOptions", - ) - -# Slots -class slots: - pass - -slots.biologicalProcess__label = Slot(uri=BP.label, name="biologicalProcess__label", curie=BP.curie('label'), - model_uri=BP.biologicalProcess__label, domain=None, range=Optional[str]) - -slots.biologicalProcess__description = Slot(uri=BP.description, name="biologicalProcess__description", curie=BP.curie('description'), - model_uri=BP.biologicalProcess__description, domain=None, range=Optional[str]) - -slots.biologicalProcess__synonyms = Slot(uri=BP.synonyms, name="biologicalProcess__synonyms", curie=BP.curie('synonyms'), - model_uri=BP.biologicalProcess__synonyms, domain=None, range=Optional[Union[str, List[str]]]) - -slots.biologicalProcess__subclass_of = Slot(uri=BP.subclass_of, name="biologicalProcess__subclass_of", curie=BP.curie('subclass_of'), - model_uri=BP.biologicalProcess__subclass_of, domain=None, range=Optional[Union[str, BiologicalProcessId]]) - -slots.biologicalProcess__inputs = Slot(uri=BP.inputs, name="biologicalProcess__inputs", curie=BP.curie('inputs'), - model_uri=BP.biologicalProcess__inputs, domain=None, range=Optional[Union[Union[str, ChemicalEntityId], List[Union[str, ChemicalEntityId]]]]) - -slots.biologicalProcess__outputs = Slot(uri=BP.outputs, name="biologicalProcess__outputs", curie=BP.curie('outputs'), - model_uri=BP.biologicalProcess__outputs, domain=None, range=Optional[Union[Union[str, ChemicalEntityId], List[Union[str, ChemicalEntityId]]]]) - -slots.biologicalProcess__steps = Slot(uri=BP.steps, name="biologicalProcess__steps", curie=BP.curie('steps'), - model_uri=BP.biologicalProcess__steps, domain=None, range=Optional[Union[Union[str, MolecularActivityId], List[Union[str, MolecularActivityId]]]]) - -slots.biologicalProcess__genes = Slot(uri=BP.genes, name="biologicalProcess__genes", curie=BP.curie('genes'), - model_uri=BP.biologicalProcess__genes, domain=None, range=Optional[Union[Union[str, GeneId], List[Union[str, GeneId]]]]) - -slots.biologicalProcess__gene_activities = Slot(uri=BP.gene_activities, name="biologicalProcess__gene_activities", curie=BP.curie('gene_activities'), - model_uri=BP.biologicalProcess__gene_activities, domain=None, range=Optional[Union[Union[dict, GeneMolecularActivityRelationship], List[Union[dict, GeneMolecularActivityRelationship]]]]) - -slots.geneMolecularActivityRelationship__gene = Slot(uri=BP.gene, name="geneMolecularActivityRelationship__gene", curie=BP.curie('gene'), - model_uri=BP.geneMolecularActivityRelationship__gene, domain=None, range=Optional[Union[str, GeneId]]) - -slots.geneMolecularActivityRelationship__molecular_activity = Slot(uri=BP.molecular_activity, name="geneMolecularActivityRelationship__molecular_activity", curie=BP.curie('molecular_activity'), - model_uri=BP.geneMolecularActivityRelationship__molecular_activity, domain=None, range=Optional[Union[str, MolecularActivityId]]) - -slots.extractionResult__input_id = Slot(uri=CORE.input_id, name="extractionResult__input_id", curie=CORE.curie('input_id'), - model_uri=BP.extractionResult__input_id, domain=None, range=Optional[str]) - -slots.extractionResult__input_title = Slot(uri=CORE.input_title, name="extractionResult__input_title", curie=CORE.curie('input_title'), - model_uri=BP.extractionResult__input_title, domain=None, range=Optional[str]) - -slots.extractionResult__input_text = Slot(uri=CORE.input_text, name="extractionResult__input_text", curie=CORE.curie('input_text'), - model_uri=BP.extractionResult__input_text, domain=None, range=Optional[str]) - -slots.extractionResult__raw_completion_output = Slot(uri=CORE.raw_completion_output, name="extractionResult__raw_completion_output", curie=CORE.curie('raw_completion_output'), - model_uri=BP.extractionResult__raw_completion_output, domain=None, range=Optional[str]) - -slots.extractionResult__prompt = Slot(uri=CORE.prompt, name="extractionResult__prompt", curie=CORE.curie('prompt'), - model_uri=BP.extractionResult__prompt, domain=None, range=Optional[str]) - -slots.extractionResult__extracted_object = Slot(uri=CORE.extracted_object, name="extractionResult__extracted_object", curie=CORE.curie('extracted_object'), - model_uri=BP.extractionResult__extracted_object, domain=None, range=Optional[Union[dict, Any]]) - -slots.extractionResult__named_entities = Slot(uri=CORE.named_entities, name="extractionResult__named_entities", curie=CORE.curie('named_entities'), - model_uri=BP.extractionResult__named_entities, domain=None, range=Optional[Union[Union[dict, Any], List[Union[dict, Any]]]]) - -slots.namedEntity__id = Slot(uri=CORE.id, name="namedEntity__id", curie=CORE.curie('id'), - model_uri=BP.namedEntity__id, domain=None, range=URIRef) - -slots.namedEntity__label = Slot(uri=RDFS.label, name="namedEntity__label", curie=RDFS.curie('label'), - model_uri=BP.namedEntity__label, domain=None, range=Optional[str]) - -slots.triple__subject = Slot(uri=CORE.subject, name="triple__subject", curie=CORE.curie('subject'), - model_uri=BP.triple__subject, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__predicate = Slot(uri=CORE.predicate, name="triple__predicate", curie=CORE.curie('predicate'), - model_uri=BP.triple__predicate, domain=None, range=Optional[Union[str, RelationshipTypeId]]) - -slots.triple__object = Slot(uri=CORE.object, name="triple__object", curie=CORE.curie('object'), - model_uri=BP.triple__object, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__qualifier = Slot(uri=CORE.qualifier, name="triple__qualifier", curie=CORE.curie('qualifier'), - model_uri=BP.triple__qualifier, domain=None, range=Optional[str]) - -slots.triple__subject_qualifier = Slot(uri=CORE.subject_qualifier, name="triple__subject_qualifier", curie=CORE.curie('subject_qualifier'), - model_uri=BP.triple__subject_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__object_qualifier = Slot(uri=CORE.object_qualifier, name="triple__object_qualifier", curie=CORE.curie('object_qualifier'), - model_uri=BP.triple__object_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.textWithTriples__publication = Slot(uri=CORE.publication, name="textWithTriples__publication", curie=CORE.curie('publication'), - model_uri=BP.textWithTriples__publication, domain=None, range=Optional[Union[dict, Publication]]) - -slots.textWithTriples__triples = Slot(uri=CORE.triples, name="textWithTriples__triples", curie=CORE.curie('triples'), - model_uri=BP.textWithTriples__triples, domain=None, range=Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]]) - -slots.publication__id = Slot(uri=CORE.id, name="publication__id", curie=CORE.curie('id'), - model_uri=BP.publication__id, domain=None, range=Optional[str]) - -slots.publication__title = Slot(uri=CORE.title, name="publication__title", curie=CORE.curie('title'), - model_uri=BP.publication__title, domain=None, range=Optional[str]) - -slots.publication__abstract = Slot(uri=CORE.abstract, name="publication__abstract", curie=CORE.curie('abstract'), - model_uri=BP.publication__abstract, domain=None, range=Optional[str]) - -slots.publication__combined_text = Slot(uri=CORE.combined_text, name="publication__combined_text", curie=CORE.curie('combined_text'), - model_uri=BP.publication__combined_text, domain=None, range=Optional[str]) - -slots.publication__full_text = Slot(uri=CORE.full_text, name="publication__full_text", curie=CORE.curie('full_text'), - model_uri=BP.publication__full_text, domain=None, range=Optional[str]) - -slots.annotatorResult__subject_text = Slot(uri=CORE.subject_text, name="annotatorResult__subject_text", curie=CORE.curie('subject_text'), - model_uri=BP.annotatorResult__subject_text, domain=None, range=Optional[str]) - -slots.annotatorResult__object_id = Slot(uri=CORE.object_id, name="annotatorResult__object_id", curie=CORE.curie('object_id'), - model_uri=BP.annotatorResult__object_id, domain=None, range=Optional[str]) - -slots.annotatorResult__object_text = Slot(uri=CORE.object_text, name="annotatorResult__object_text", curie=CORE.curie('object_text'), - model_uri=BP.annotatorResult__object_text, domain=None, range=Optional[str]) \ No newline at end of file diff --git a/projects/biological_process/docs/AnnotatorResult.md b/projects/biological_process/docs/AnnotatorResult.md deleted file mode 100644 index b25d0a529..000000000 --- a/projects/biological_process/docs/AnnotatorResult.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Class: AnnotatorResult - - - - -URI: [bp:AnnotatorResult](http://w3id.org/ontogpt/biological-process-templateAnnotatorResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F])](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F]) - -## Attributes - - -### Own - - * [➞subject_text](annotatorResult__subject_text.md) 0..1 - * Range: [String](types/String.md) - * [➞object_id](annotatorResult__object_id.md) 0..1 - * Range: [String](types/String.md) - * [➞object_text](annotatorResult__object_text.md) 0..1 - * Range: [String](types/String.md) diff --git a/projects/biological_process/docs/Any.md b/projects/biological_process/docs/Any.md deleted file mode 100644 index cb46c4be4..000000000 --- a/projects/biological_process/docs/Any.md +++ /dev/null @@ -1,25 +0,0 @@ - -# Class: Any - - - - -URI: [bp:Any](http://w3id.org/ontogpt/biological-process-templateAny) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult])](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult]) - -## Referenced by Class - - * **None** *[➞extracted_object](extractionResult__extracted_object.md)* 0..1 **[Any](Any.md)** - * **None** *[➞named_entities](extractionResult__named_entities.md)* 0..\* **[Any](Any.md)** - -## Attributes - - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | linkml:Any | - diff --git a/projects/biological_process/docs/BiologicalProcess.md b/projects/biological_process/docs/BiologicalProcess.md deleted file mode 100644 index 777220560..000000000 --- a/projects/biological_process/docs/BiologicalProcess.md +++ /dev/null @@ -1,56 +0,0 @@ - -# Class: BiologicalProcess - - - - -URI: [bp:BiologicalProcess](http://w3id.org/ontogpt/biological-process-templateBiologicalProcess) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[MolecularActivity],[GeneMolecularActivityRelationship],[Gene],[ChemicalEntity],[GeneMolecularActivityRelationship]0..1 **[BiologicalProcess](BiologicalProcess.md)** - -## Attributes - - -### Own - - * [➞label](biologicalProcess__label.md) 0..1 - * Description: the name of the biological process - * Range: [String](types/String.md) - * [➞description](biologicalProcess__description.md) 0..1 - * Description: a textual description of the biological process - * Range: [String](types/String.md) - * [➞synonyms](biologicalProcess__synonyms.md) 0..\* - * Description: alternative names of the biological process - * Range: [String](types/String.md) - * [➞subclass_of](biologicalProcess__subclass_of.md) 0..1 - * Description: the category to which this biological process belongs - * Range: [BiologicalProcess](BiologicalProcess.md) - * [➞inputs](biologicalProcess__inputs.md) 0..\* - * Description: the inputs of the biological process - * Range: [ChemicalEntity](ChemicalEntity.md) - * [➞outputs](biologicalProcess__outputs.md) 0..\* - * Description: the outputs of the biological process - * Range: [ChemicalEntity](ChemicalEntity.md) - * [➞steps](biologicalProcess__steps.md) 0..\* - * Description: the steps involved in this biological process - * Range: [MolecularActivity](MolecularActivity.md) - * [➞genes](biologicalProcess__genes.md) 0..\* - * Range: [Gene](Gene.md) - * [➞gene_activities](biologicalProcess__gene_activities.md) 0..\* - * Description: semicolon-separated list of gene to molecular activity relationships - * Range: [GeneMolecularActivityRelationship](GeneMolecularActivityRelationship.md) - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) 1..1 - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) diff --git a/projects/biological_process/docs/ChemicalEntity.md b/projects/biological_process/docs/ChemicalEntity.md deleted file mode 100644 index 8d1b59df9..000000000 --- a/projects/biological_process/docs/ChemicalEntity.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: ChemicalEntity - - - - -URI: [bp:ChemicalEntity](http://w3id.org/ontogpt/biological-process-templateChemicalEntity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[BiologicalProcess]-%20inputs%200..*>[ChemicalEntity|id(i):string;label(i):string%20%3F],[BiologicalProcess]-%20outputs%200..*>[ChemicalEntity],[NamedEntity]^-[ChemicalEntity],[BiologicalProcess])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[BiologicalProcess]-%20inputs%200..*>[ChemicalEntity|id(i):string;label(i):string%20%3F],[BiologicalProcess]-%20outputs%200..*>[ChemicalEntity],[NamedEntity]^-[ChemicalEntity],[BiologicalProcess]) - -## Identifier prefixes - - * CHEBI - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞inputs](biologicalProcess__inputs.md)* 0..\* **[ChemicalEntity](ChemicalEntity.md)** - * **None** *[➞outputs](biologicalProcess__outputs.md)* 0..\* **[ChemicalEntity](ChemicalEntity.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) 1..1 - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) 0..1 - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/biological_process/docs/CompoundExpression.md b/projects/biological_process/docs/CompoundExpression.md deleted file mode 100644 index 6c1bba32f..000000000 --- a/projects/biological_process/docs/CompoundExpression.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: CompoundExpression - - - - -URI: [bp:CompoundExpression](http://w3id.org/ontogpt/biological-process-templateCompoundExpression) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[CompoundExpression]^-[Triple])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[CompoundExpression]^-[Triple]) - -## Children - - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - -## Referenced by Class - - -## Attributes - diff --git a/projects/biological_process/docs/ExtractionResult.md b/projects/biological_process/docs/ExtractionResult.md deleted file mode 100644 index 4d0ab7ab9..000000000 --- a/projects/biological_process/docs/ExtractionResult.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Class: ExtractionResult - - -A result of extracting knowledge on text - -URI: [bp:ExtractionResult](http://w3id.org/ontogpt/biological-process-templateExtractionResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]0..1 - * Range: [String](types/String.md) - * [➞input_title](extractionResult__input_title.md) 0..1 - * Range: [String](types/String.md) - * [➞input_text](extractionResult__input_text.md) 0..1 - * Range: [String](types/String.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) 0..1 - * Range: [String](types/String.md) - * [➞prompt](extractionResult__prompt.md) 0..1 - * Range: [String](types/String.md) - * [➞extracted_object](extractionResult__extracted_object.md) 0..1 - * Description: The complex objects extracted from the text - * Range: [Any](Any.md) - * [➞named_entities](extractionResult__named_entities.md) 0..\* - * Description: Named entities extracted from the text - * Range: [Any](Any.md) diff --git a/projects/biological_process/docs/Gene.md b/projects/biological_process/docs/Gene.md deleted file mode 100644 index ec2822f49..000000000 --- a/projects/biological_process/docs/Gene.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: Gene - - - - -URI: [bp:Gene](http://w3id.org/ontogpt/biological-process-templateGene) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[BiologicalProcess]-%20genes%200..*>[Gene|id(i):string;label(i):string%20%3F],[GeneMolecularActivityRelationship]-%20gene%200..1>[Gene],[NamedEntity]^-[Gene],[GeneMolecularActivityRelationship],[BiologicalProcess])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[BiologicalProcess]-%20genes%200..*>[Gene|id(i):string;label(i):string%20%3F],[GeneMolecularActivityRelationship]-%20gene%200..1>[Gene],[NamedEntity]^-[Gene],[GeneMolecularActivityRelationship],[BiologicalProcess]) - -## Identifier prefixes - - * HGNC - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞genes](biologicalProcess__genes.md)* 0..\* **[Gene](Gene.md)** - * **None** *[➞gene](geneMolecularActivityRelationship__gene.md)* 0..1 **[Gene](Gene.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) 1..1 - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) 0..1 - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/biological_process/docs/GeneMolecularActivityRelationship.md b/projects/biological_process/docs/GeneMolecularActivityRelationship.md deleted file mode 100644 index d85f3d3cf..000000000 --- a/projects/biological_process/docs/GeneMolecularActivityRelationship.md +++ /dev/null @@ -1,24 +0,0 @@ - -# Class: GeneMolecularActivityRelationship - - - - -URI: [bp:GeneMolecularActivityRelationship](http://w3id.org/ontogpt/biological-process-templateGeneMolecularActivityRelationship) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[MolecularActivity],[MolecularActivity][GeneMolecularActivityRelationship],[Gene],[BiologicalProcess])](https://yuml.me/diagram/nofunky;dir:TB/class/[MolecularActivity],[MolecularActivity][GeneMolecularActivityRelationship],[Gene],[BiologicalProcess]) - -## Referenced by Class - - * **None** *[➞gene_activities](biologicalProcess__gene_activities.md)* 0..\* **[GeneMolecularActivityRelationship](GeneMolecularActivityRelationship.md)** - -## Attributes - - -### Own - - * [➞gene](geneMolecularActivityRelationship__gene.md) 0..1 - * Range: [Gene](Gene.md) - * [➞molecular_activity](geneMolecularActivityRelationship__molecular_activity.md) 0..1 - * Range: [MolecularActivity](MolecularActivity.md) diff --git a/projects/biological_process/docs/MolecularActivity.md b/projects/biological_process/docs/MolecularActivity.md deleted file mode 100644 index d3f34ec4f..000000000 --- a/projects/biological_process/docs/MolecularActivity.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: MolecularActivity - - - - -URI: [bp:MolecularActivity](http://w3id.org/ontogpt/biological-process-templateMolecularActivity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[BiologicalProcess]-%20steps%200..*>[MolecularActivity|id(i):string;label(i):string%20%3F],[GeneMolecularActivityRelationship]-%20molecular_activity%200..1>[MolecularActivity],[NamedEntity]^-[MolecularActivity],[GeneMolecularActivityRelationship],[BiologicalProcess])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[BiologicalProcess]-%20steps%200..*>[MolecularActivity|id(i):string;label(i):string%20%3F],[GeneMolecularActivityRelationship]-%20molecular_activity%200..1>[MolecularActivity],[NamedEntity]^-[MolecularActivity],[GeneMolecularActivityRelationship],[BiologicalProcess]) - -## Identifier prefixes - - * GO - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞steps](biologicalProcess__steps.md)* 0..\* **[MolecularActivity](MolecularActivity.md)** - * **None** *[➞molecular_activity](geneMolecularActivityRelationship__molecular_activity.md)* 0..1 **[MolecularActivity](MolecularActivity.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) 1..1 - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) 0..1 - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/biological_process/docs/NamedEntity.md b/projects/biological_process/docs/NamedEntity.md deleted file mode 100644 index db2c7c939..000000000 --- a/projects/biological_process/docs/NamedEntity.md +++ /dev/null @@ -1,37 +0,0 @@ - -# Class: NamedEntity - - - - -URI: [bp:NamedEntity](http://w3id.org/ontogpt/biological-process-templateNamedEntity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[MolecularActivity],[NamedEntity]^-[Gene],[NamedEntity]^-[ChemicalEntity],[NamedEntity]^-[BiologicalProcess],[Triple],[MolecularActivity],[Gene],[ChemicalEntity],[BiologicalProcess])](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[MolecularActivity],[NamedEntity]^-[Gene],[NamedEntity]^-[ChemicalEntity],[NamedEntity]^-[BiologicalProcess],[Triple],[MolecularActivity],[Gene],[ChemicalEntity],[BiologicalProcess]) - -## Children - - * [BiologicalProcess](BiologicalProcess.md) - * [ChemicalEntity](ChemicalEntity.md) - * [Gene](Gene.md) - * [MolecularActivity](MolecularActivity.md) - * [RelationshipType](RelationshipType.md) - -## Referenced by Class - - * **None** *[➞object](triple__object.md)* 0..1 **[NamedEntity](NamedEntity.md)** - * **None** *[➞object_qualifier](triple__object_qualifier.md)* 0..1 **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject](triple__subject.md)* 0..1 **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject_qualifier](triple__subject_qualifier.md)* 0..1 **[NamedEntity](NamedEntity.md)** - -## Attributes - - -### Own - - * [➞id](namedEntity__id.md) 1..1 - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) 0..1 - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/biological_process/docs/NullDataOptions.md b/projects/biological_process/docs/NullDataOptions.md deleted file mode 100644 index 716244681..000000000 --- a/projects/biological_process/docs/NullDataOptions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Enum: NullDataOptions - - - - -URI: [bp:NullDataOptions](http://w3id.org/ontogpt/biological-process-templateNullDataOptions) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | -| UNSPECIFIED_METHOD_OF_ADMINISTRATION | | NCIT:C149701 | | -| NOT_APPLICABLE | | NCIT:C18902 | {'aliases': ['not applicable', 'N/A']} | -| NOT_MENTIONED | | | | - diff --git a/projects/biological_process/docs/Publication.md b/projects/biological_process/docs/Publication.md deleted file mode 100644 index d54b928f4..000000000 --- a/projects/biological_process/docs/Publication.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Publication - - - - -URI: [bp:Publication](http://w3id.org/ontogpt/biological-process-templatePublication) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples])](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples]) - -## Referenced by Class - - * **None** *[➞publication](textWithTriples__publication.md)* 0..1 **[Publication](Publication.md)** - -## Attributes - - -### Own - - * [➞id](publication__id.md) 0..1 - * Description: The publication identifier - * Range: [String](types/String.md) - * [➞title](publication__title.md) 0..1 - * Description: The title of the publication - * Range: [String](types/String.md) - * [➞abstract](publication__abstract.md) 0..1 - * Description: The abstract of the publication - * Range: [String](types/String.md) - * [➞combined_text](publication__combined_text.md) 0..1 - * Range: [String](types/String.md) - * [➞full_text](publication__full_text.md) 0..1 - * Description: The full text of the publication - * Range: [String](types/String.md) diff --git a/projects/biological_process/docs/RelationshipType.md b/projects/biological_process/docs/RelationshipType.md deleted file mode 100644 index 918e3647c..000000000 --- a/projects/biological_process/docs/RelationshipType.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: RelationshipType - - - - -URI: [bp:RelationshipType](http://w3id.org/ontogpt/biological-process-templateRelationshipType) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity]) - -## Identifier prefixes - - * RO - * biolink - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞predicate](triple__predicate.md)* 0..1 **[RelationshipType](RelationshipType.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) 1..1 - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) 0..1 - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/biological_process/docs/TextWithTriples.md b/projects/biological_process/docs/TextWithTriples.md deleted file mode 100644 index 4237a7785..000000000 --- a/projects/biological_process/docs/TextWithTriples.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: TextWithTriples - - - - -URI: [bp:TextWithTriples](http://w3id.org/ontogpt/biological-process-templateTextWithTriples) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]0..1 - * Range: [Publication](Publication.md) - * [➞triples](textWithTriples__triples.md) 0..\* - * Range: [Triple](Triple.md) diff --git a/projects/biological_process/docs/Triple.md b/projects/biological_process/docs/Triple.md deleted file mode 100644 index b9e6bb42d..000000000 --- a/projects/biological_process/docs/Triple.md +++ /dev/null @@ -1,39 +0,0 @@ - -# Class: Triple - - -Abstract parent for Relation Extraction tasks - -URI: [bp:Triple](http://w3id.org/ontogpt/biological-process-templateTriple) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity][Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity][Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞triples](textWithTriples__triples.md)* 0..\* **[Triple](Triple.md)** - -## Attributes - - -### Own - - * [➞subject](triple__subject.md) 0..1 - * Range: [NamedEntity](NamedEntity.md) - * [➞predicate](triple__predicate.md) 0..1 - * Range: [RelationshipType](RelationshipType.md) - * [➞object](triple__object.md) 0..1 - * Range: [NamedEntity](NamedEntity.md) - * [➞qualifier](triple__qualifier.md) 0..1 - * Description: A qualifier for the statements, e.g. "NOT" for negation - * Range: [String](types/String.md) - * [➞subject_qualifier](triple__subject_qualifier.md) 0..1 - * Description: An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - * Range: [NamedEntity](NamedEntity.md) - * [➞object_qualifier](triple__object_qualifier.md) 0..1 - * Description: An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * Range: [NamedEntity](NamedEntity.md) diff --git a/projects/biological_process/docs/annotatorResult__object_id.md b/projects/biological_process/docs/annotatorResult__object_id.md deleted file mode 100644 index ffc6bbeca..000000000 --- a/projects/biological_process/docs/annotatorResult__object_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_id - - - - -URI: [bp:annotatorResult__object_id](http://w3id.org/ontogpt/biological-process-templateannotatorResult__object_id) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/biological_process/docs/annotatorResult__object_text.md b/projects/biological_process/docs/annotatorResult__object_text.md deleted file mode 100644 index b127369af..000000000 --- a/projects/biological_process/docs/annotatorResult__object_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_text - - - - -URI: [bp:annotatorResult__object_text](http://w3id.org/ontogpt/biological-process-templateannotatorResult__object_text) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/biological_process/docs/annotatorResult__subject_text.md b/projects/biological_process/docs/annotatorResult__subject_text.md deleted file mode 100644 index 79e732b09..000000000 --- a/projects/biological_process/docs/annotatorResult__subject_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_text - - - - -URI: [bp:annotatorResult__subject_text](http://w3id.org/ontogpt/biological-process-templateannotatorResult__subject_text) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/biological_process/docs/biologicalProcess__description.md b/projects/biological_process/docs/biologicalProcess__description.md deleted file mode 100644 index dfe2423fe..000000000 --- a/projects/biological_process/docs/biologicalProcess__description.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: description - - -a textual description of the biological process - -URI: [bp:biologicalProcess__description](http://w3id.org/ontogpt/biological-process-templatebiologicalProcess__description) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [BiologicalProcess](BiologicalProcess.md) diff --git a/projects/biological_process/docs/biologicalProcess__gene_activities.md b/projects/biological_process/docs/biologicalProcess__gene_activities.md deleted file mode 100644 index 19ca2e4a1..000000000 --- a/projects/biological_process/docs/biologicalProcess__gene_activities.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: gene_activities - - -semicolon-separated list of gene to molecular activity relationships - -URI: [bp:biologicalProcess__gene_activities](http://w3id.org/ontogpt/biological-process-templatebiologicalProcess__gene_activities) - - -## Domain and Range - -None → 0..\* [GeneMolecularActivityRelationship](GeneMolecularActivityRelationship.md) - -## Parents - - -## Children - - -## Used by - - * [BiologicalProcess](BiologicalProcess.md) diff --git a/projects/biological_process/docs/biologicalProcess__genes.md b/projects/biological_process/docs/biologicalProcess__genes.md deleted file mode 100644 index f4db39472..000000000 --- a/projects/biological_process/docs/biologicalProcess__genes.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: genes - - - - -URI: [bp:biologicalProcess__genes](http://w3id.org/ontogpt/biological-process-templatebiologicalProcess__genes) - - -## Domain and Range - -None → 0..\* [Gene](Gene.md) - -## Parents - - -## Children - - -## Used by - - * [BiologicalProcess](BiologicalProcess.md) diff --git a/projects/biological_process/docs/biologicalProcess__inputs.md b/projects/biological_process/docs/biologicalProcess__inputs.md deleted file mode 100644 index b847140f1..000000000 --- a/projects/biological_process/docs/biologicalProcess__inputs.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: inputs - - -the inputs of the biological process - -URI: [bp:biologicalProcess__inputs](http://w3id.org/ontogpt/biological-process-templatebiologicalProcess__inputs) - - -## Domain and Range - -None → 0..\* [ChemicalEntity](ChemicalEntity.md) - -## Parents - - -## Children - - -## Used by - - * [BiologicalProcess](BiologicalProcess.md) diff --git a/projects/biological_process/docs/biologicalProcess__label.md b/projects/biological_process/docs/biologicalProcess__label.md deleted file mode 100644 index dbfb32e50..000000000 --- a/projects/biological_process/docs/biologicalProcess__label.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: label - - -the name of the biological process - -URI: [bp:biologicalProcess__label](http://w3id.org/ontogpt/biological-process-templatebiologicalProcess__label) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [BiologicalProcess](BiologicalProcess.md) diff --git a/projects/biological_process/docs/biologicalProcess__outputs.md b/projects/biological_process/docs/biologicalProcess__outputs.md deleted file mode 100644 index 06b35c922..000000000 --- a/projects/biological_process/docs/biologicalProcess__outputs.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: outputs - - -the outputs of the biological process - -URI: [bp:biologicalProcess__outputs](http://w3id.org/ontogpt/biological-process-templatebiologicalProcess__outputs) - - -## Domain and Range - -None → 0..\* [ChemicalEntity](ChemicalEntity.md) - -## Parents - - -## Children - - -## Used by - - * [BiologicalProcess](BiologicalProcess.md) diff --git a/projects/biological_process/docs/biologicalProcess__steps.md b/projects/biological_process/docs/biologicalProcess__steps.md deleted file mode 100644 index d7a2bf166..000000000 --- a/projects/biological_process/docs/biologicalProcess__steps.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: steps - - -the steps involved in this biological process - -URI: [bp:biologicalProcess__steps](http://w3id.org/ontogpt/biological-process-templatebiologicalProcess__steps) - - -## Domain and Range - -None → 0..\* [MolecularActivity](MolecularActivity.md) - -## Parents - - -## Children - - -## Used by - - * [BiologicalProcess](BiologicalProcess.md) diff --git a/projects/biological_process/docs/biologicalProcess__subclass_of.md b/projects/biological_process/docs/biologicalProcess__subclass_of.md deleted file mode 100644 index 1356361a6..000000000 --- a/projects/biological_process/docs/biologicalProcess__subclass_of.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subclass_of - - -the category to which this biological process belongs - -URI: [bp:biologicalProcess__subclass_of](http://w3id.org/ontogpt/biological-process-templatebiologicalProcess__subclass_of) - - -## Domain and Range - -None → 0..1 [BiologicalProcess](BiologicalProcess.md) - -## Parents - - -## Children - - -## Used by - - * [BiologicalProcess](BiologicalProcess.md) diff --git a/projects/biological_process/docs/biologicalProcess__synonyms.md b/projects/biological_process/docs/biologicalProcess__synonyms.md deleted file mode 100644 index 5a7ea0d18..000000000 --- a/projects/biological_process/docs/biologicalProcess__synonyms.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: synonyms - - -alternative names of the biological process - -URI: [bp:biologicalProcess__synonyms](http://w3id.org/ontogpt/biological-process-templatebiologicalProcess__synonyms) - - -## Domain and Range - -None → 0..\* [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [BiologicalProcess](BiologicalProcess.md) diff --git a/projects/biological_process/docs/biological_process.md b/projects/biological_process/docs/biological_process.md deleted file mode 100644 index effdf9cb9..000000000 --- a/projects/biological_process/docs/biological_process.md +++ /dev/null @@ -1,119 +0,0 @@ - -# biological-process-template - - -**metamodel version:** 1.7.0 - -**version:** None - - -A template for GO-CAMs - - -### Classes - - * [AnnotatorResult](AnnotatorResult.md) - * [Any](Any.md) - * [CompoundExpression](CompoundExpression.md) - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - * [ExtractionResult](ExtractionResult.md) - A result of extracting knowledge on text - * [GeneMolecularActivityRelationship](GeneMolecularActivityRelationship.md) - * [NamedEntity](NamedEntity.md) - * [BiologicalProcess](BiologicalProcess.md) - * [ChemicalEntity](ChemicalEntity.md) - * [Gene](Gene.md) - * [MolecularActivity](MolecularActivity.md) - * [RelationshipType](RelationshipType.md) - * [Publication](Publication.md) - * [TextWithTriples](TextWithTriples.md) - -### Mixins - - -### Slots - - * [➞object_id](annotatorResult__object_id.md) - * [➞object_text](annotatorResult__object_text.md) - * [➞subject_text](annotatorResult__subject_text.md) - * [➞description](biologicalProcess__description.md) - a textual description of the biological process - * [➞gene_activities](biologicalProcess__gene_activities.md) - semicolon-separated list of gene to molecular activity relationships - * [➞genes](biologicalProcess__genes.md) - * [➞inputs](biologicalProcess__inputs.md) - the inputs of the biological process - * [➞label](biologicalProcess__label.md) - the name of the biological process - * [➞outputs](biologicalProcess__outputs.md) - the outputs of the biological process - * [➞steps](biologicalProcess__steps.md) - the steps involved in this biological process - * [➞subclass_of](biologicalProcess__subclass_of.md) - the category to which this biological process belongs - * [➞synonyms](biologicalProcess__synonyms.md) - alternative names of the biological process - * [➞extracted_object](extractionResult__extracted_object.md) - The complex objects extracted from the text - * [➞input_id](extractionResult__input_id.md) - * [➞input_text](extractionResult__input_text.md) - * [➞input_title](extractionResult__input_title.md) - * [➞named_entities](extractionResult__named_entities.md) - Named entities extracted from the text - * [➞prompt](extractionResult__prompt.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) - * [➞gene](geneMolecularActivityRelationship__gene.md) - * [➞molecular_activity](geneMolecularActivityRelationship__molecular_activity.md) - * [➞id](namedEntity__id.md) - A unique identifier for the named entity - * [➞label](namedEntity__label.md) - The label (name) of the named thing - * [➞abstract](publication__abstract.md) - The abstract of the publication - * [➞combined_text](publication__combined_text.md) - * [➞full_text](publication__full_text.md) - The full text of the publication - * [➞id](publication__id.md) - The publication identifier - * [➞title](publication__title.md) - The title of the publication - * [➞publication](textWithTriples__publication.md) - * [➞triples](textWithTriples__triples.md) - * [➞object](triple__object.md) - * [➞object_qualifier](triple__object_qualifier.md) - An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * [➞predicate](triple__predicate.md) - * [➞qualifier](triple__qualifier.md) - A qualifier for the statements, e.g. "NOT" for negation - * [➞subject](triple__subject.md) - * [➞subject_qualifier](triple__subject_qualifier.md) - An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -### Enums - - * [NullDataOptions](NullDataOptions.md) - -### Subsets - - -### Types - - -#### Built in - - * **Bool** - * **Curie** - * **Decimal** - * **ElementIdentifier** - * **NCName** - * **NodeIdentifier** - * **URI** - * **URIorCURIE** - * **XSDDate** - * **XSDDateTime** - * **XSDTime** - * **float** - * **int** - * **str** - -#### Defined - - * [Boolean](types/Boolean.md) (**Bool**) - A binary (true or false) value - * [Curie](types/Curie.md) (**Curie**) - a compact URI - * [Date](types/Date.md) (**XSDDate**) - a date (year, month and day) in an idealized calendar - * [DateOrDatetime](types/DateOrDatetime.md) (**str**) - Either a date or a datetime - * [Datetime](types/Datetime.md) (**XSDDateTime**) - The combination of a date and time - * [Decimal](types/Decimal.md) (**Decimal**) - A real number with arbitrary precision that conforms to the xsd:decimal specification - * [Double](types/Double.md) (**float**) - A real number that conforms to the xsd:double specification - * [Float](types/Float.md) (**float**) - A real number that conforms to the xsd:float specification - * [Integer](types/Integer.md) (**int**) - An integer - * [Jsonpath](types/Jsonpath.md) (**str**) - A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - * [Jsonpointer](types/Jsonpointer.md) (**str**) - A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - * [Ncname](types/Ncname.md) (**NCName**) - Prefix part of CURIE - * [Nodeidentifier](types/Nodeidentifier.md) (**NodeIdentifier**) - A URI, CURIE or BNODE that represents a node in a model. - * [Objectidentifier](types/Objectidentifier.md) (**ElementIdentifier**) - A URI or CURIE that represents an object in the model. - * [Sparqlpath](types/Sparqlpath.md) (**str**) - A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - * [String](types/String.md) (**str**) - A character string - * [Time](types/Time.md) (**XSDTime**) - A time object represents a (local) time of day, independent of any particular day - * [Uri](types/Uri.md) (**URI**) - a complete URI - * [Uriorcurie](types/Uriorcurie.md) (**URIorCURIE**) - a URI or a CURIE diff --git a/projects/biological_process/docs/extractionResult__extracted_object.md b/projects/biological_process/docs/extractionResult__extracted_object.md deleted file mode 100644 index 9cb7fab08..000000000 --- a/projects/biological_process/docs/extractionResult__extracted_object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: extracted_object - - -The complex objects extracted from the text - -URI: [bp:extractionResult__extracted_object](http://w3id.org/ontogpt/biological-process-templateextractionResult__extracted_object) - - -## Domain and Range - -None → 0..1 [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/biological_process/docs/extractionResult__input_id.md b/projects/biological_process/docs/extractionResult__input_id.md deleted file mode 100644 index 77a58c462..000000000 --- a/projects/biological_process/docs/extractionResult__input_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_id - - - - -URI: [bp:extractionResult__input_id](http://w3id.org/ontogpt/biological-process-templateextractionResult__input_id) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/biological_process/docs/extractionResult__input_text.md b/projects/biological_process/docs/extractionResult__input_text.md deleted file mode 100644 index 0d447a742..000000000 --- a/projects/biological_process/docs/extractionResult__input_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_text - - - - -URI: [bp:extractionResult__input_text](http://w3id.org/ontogpt/biological-process-templateextractionResult__input_text) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/biological_process/docs/extractionResult__input_title.md b/projects/biological_process/docs/extractionResult__input_title.md deleted file mode 100644 index 87d22e4d5..000000000 --- a/projects/biological_process/docs/extractionResult__input_title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_title - - - - -URI: [bp:extractionResult__input_title](http://w3id.org/ontogpt/biological-process-templateextractionResult__input_title) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/biological_process/docs/extractionResult__named_entities.md b/projects/biological_process/docs/extractionResult__named_entities.md deleted file mode 100644 index 4274e9c2a..000000000 --- a/projects/biological_process/docs/extractionResult__named_entities.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: named_entities - - -Named entities extracted from the text - -URI: [bp:extractionResult__named_entities](http://w3id.org/ontogpt/biological-process-templateextractionResult__named_entities) - - -## Domain and Range - -None → 0..\* [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/biological_process/docs/extractionResult__prompt.md b/projects/biological_process/docs/extractionResult__prompt.md deleted file mode 100644 index 2d9f03d71..000000000 --- a/projects/biological_process/docs/extractionResult__prompt.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: prompt - - - - -URI: [bp:extractionResult__prompt](http://w3id.org/ontogpt/biological-process-templateextractionResult__prompt) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/biological_process/docs/extractionResult__raw_completion_output.md b/projects/biological_process/docs/extractionResult__raw_completion_output.md deleted file mode 100644 index 0e689fc73..000000000 --- a/projects/biological_process/docs/extractionResult__raw_completion_output.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: raw_completion_output - - - - -URI: [bp:extractionResult__raw_completion_output](http://w3id.org/ontogpt/biological-process-templateextractionResult__raw_completion_output) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/biological_process/docs/geneMolecularActivityRelationship__gene.md b/projects/biological_process/docs/geneMolecularActivityRelationship__gene.md deleted file mode 100644 index 3f0e4bbab..000000000 --- a/projects/biological_process/docs/geneMolecularActivityRelationship__gene.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: gene - - - - -URI: [bp:geneMolecularActivityRelationship__gene](http://w3id.org/ontogpt/biological-process-templategeneMolecularActivityRelationship__gene) - - -## Domain and Range - -None → 0..1 [Gene](Gene.md) - -## Parents - - -## Children - - -## Used by - - * [GeneMolecularActivityRelationship](GeneMolecularActivityRelationship.md) diff --git a/projects/biological_process/docs/geneMolecularActivityRelationship__molecular_activity.md b/projects/biological_process/docs/geneMolecularActivityRelationship__molecular_activity.md deleted file mode 100644 index 6fe3e9323..000000000 --- a/projects/biological_process/docs/geneMolecularActivityRelationship__molecular_activity.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: molecular_activity - - - - -URI: [bp:geneMolecularActivityRelationship__molecular_activity](http://w3id.org/ontogpt/biological-process-templategeneMolecularActivityRelationship__molecular_activity) - - -## Domain and Range - -None → 0..1 [MolecularActivity](MolecularActivity.md) - -## Parents - - -## Children - - -## Used by - - * [GeneMolecularActivityRelationship](GeneMolecularActivityRelationship.md) diff --git a/projects/biological_process/docs/namedEntity__id.md b/projects/biological_process/docs/namedEntity__id.md deleted file mode 100644 index df74e8512..000000000 --- a/projects/biological_process/docs/namedEntity__id.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Slot: id - - -A unique identifier for the named entity - -URI: [bp:namedEntity__id](http://w3id.org/ontogpt/biological-process-templatenamedEntity__id) - - -## Domain and Range - -None → 1..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [BiologicalProcess](BiologicalProcess.md) - * [ChemicalEntity](ChemicalEntity.md) - * [Gene](Gene.md) - * [MolecularActivity](MolecularActivity.md) - * [NamedEntity](NamedEntity.md) - * [RelationshipType](RelationshipType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | this is populated during the grounding and normalization step | - diff --git a/projects/biological_process/docs/namedEntity__label.md b/projects/biological_process/docs/namedEntity__label.md deleted file mode 100644 index 5db5381b4..000000000 --- a/projects/biological_process/docs/namedEntity__label.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Slot: label - - -The label (name) of the named thing - -URI: [bp:namedEntity__label](http://w3id.org/ontogpt/biological-process-templatenamedEntity__label) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ChemicalEntity](ChemicalEntity.md) - * [Gene](Gene.md) - * [MolecularActivity](MolecularActivity.md) - * [NamedEntity](NamedEntity.md) - * [RelationshipType](RelationshipType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Aliases:** | | name | -| **Mappings:** | | rdfs:label | - diff --git a/projects/biological_process/docs/publication__abstract.md b/projects/biological_process/docs/publication__abstract.md deleted file mode 100644 index 96be47057..000000000 --- a/projects/biological_process/docs/publication__abstract.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: abstract - - -The abstract of the publication - -URI: [bp:publication__abstract](http://w3id.org/ontogpt/biological-process-templatepublication__abstract) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/biological_process/docs/publication__combined_text.md b/projects/biological_process/docs/publication__combined_text.md deleted file mode 100644 index 613506acc..000000000 --- a/projects/biological_process/docs/publication__combined_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: combined_text - - - - -URI: [bp:publication__combined_text](http://w3id.org/ontogpt/biological-process-templatepublication__combined_text) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/biological_process/docs/publication__full_text.md b/projects/biological_process/docs/publication__full_text.md deleted file mode 100644 index 978e83538..000000000 --- a/projects/biological_process/docs/publication__full_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: full_text - - -The full text of the publication - -URI: [bp:publication__full_text](http://w3id.org/ontogpt/biological-process-templatepublication__full_text) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/biological_process/docs/publication__id.md b/projects/biological_process/docs/publication__id.md deleted file mode 100644 index 9c03571b0..000000000 --- a/projects/biological_process/docs/publication__id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: id - - -The publication identifier - -URI: [bp:publication__id](http://w3id.org/ontogpt/biological-process-templatepublication__id) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/biological_process/docs/publication__title.md b/projects/biological_process/docs/publication__title.md deleted file mode 100644 index 93aa90543..000000000 --- a/projects/biological_process/docs/publication__title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: title - - -The title of the publication - -URI: [bp:publication__title](http://w3id.org/ontogpt/biological-process-templatepublication__title) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/biological_process/docs/textWithTriples__publication.md b/projects/biological_process/docs/textWithTriples__publication.md deleted file mode 100644 index d5eb7b7f9..000000000 --- a/projects/biological_process/docs/textWithTriples__publication.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: publication - - - - -URI: [bp:textWithTriples__publication](http://w3id.org/ontogpt/biological-process-templatetextWithTriples__publication) - - -## Domain and Range - -None → 0..1 [Publication](Publication.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/biological_process/docs/textWithTriples__triples.md b/projects/biological_process/docs/textWithTriples__triples.md deleted file mode 100644 index 4865a084d..000000000 --- a/projects/biological_process/docs/textWithTriples__triples.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: triples - - - - -URI: [bp:textWithTriples__triples](http://w3id.org/ontogpt/biological-process-templatetextWithTriples__triples) - - -## Domain and Range - -None → 0..\* [Triple](Triple.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/biological_process/docs/triple__object.md b/projects/biological_process/docs/triple__object.md deleted file mode 100644 index bc102f3c8..000000000 --- a/projects/biological_process/docs/triple__object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object - - - - -URI: [bp:triple__object](http://w3id.org/ontogpt/biological-process-templatetriple__object) - - -## Domain and Range - -None → 0..1 [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/biological_process/docs/triple__object_qualifier.md b/projects/biological_process/docs/triple__object_qualifier.md deleted file mode 100644 index f06d74b8d..000000000 --- a/projects/biological_process/docs/triple__object_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_qualifier - - -An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - -URI: [bp:triple__object_qualifier](http://w3id.org/ontogpt/biological-process-templatetriple__object_qualifier) - - -## Domain and Range - -None → 0..1 [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/biological_process/docs/triple__predicate.md b/projects/biological_process/docs/triple__predicate.md deleted file mode 100644 index 92c257664..000000000 --- a/projects/biological_process/docs/triple__predicate.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: predicate - - - - -URI: [bp:triple__predicate](http://w3id.org/ontogpt/biological-process-templatetriple__predicate) - - -## Domain and Range - -None → 0..1 [RelationshipType](RelationshipType.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/biological_process/docs/triple__qualifier.md b/projects/biological_process/docs/triple__qualifier.md deleted file mode 100644 index 1ea0152f1..000000000 --- a/projects/biological_process/docs/triple__qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: qualifier - - -A qualifier for the statements, e.g. "NOT" for negation - -URI: [bp:triple__qualifier](http://w3id.org/ontogpt/biological-process-templatetriple__qualifier) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/biological_process/docs/triple__subject.md b/projects/biological_process/docs/triple__subject.md deleted file mode 100644 index cc0377542..000000000 --- a/projects/biological_process/docs/triple__subject.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject - - - - -URI: [bp:triple__subject](http://w3id.org/ontogpt/biological-process-templatetriple__subject) - - -## Domain and Range - -None → 0..1 [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/biological_process/docs/triple__subject_qualifier.md b/projects/biological_process/docs/triple__subject_qualifier.md deleted file mode 100644 index 998e0615e..000000000 --- a/projects/biological_process/docs/triple__subject_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_qualifier - - -An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -URI: [bp:triple__subject_qualifier](http://w3id.org/ontogpt/biological-process-templatetriple__subject_qualifier) - - -## Domain and Range - -None → 0..1 [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/biological_process/docs/types/Boolean.md b/projects/biological_process/docs/types/Boolean.md deleted file mode 100644 index dc83a9c6e..000000000 --- a/projects/biological_process/docs/types/Boolean.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: boolean - - -A binary (true or false) value - -URI: [linkml:Boolean](https://w3id.org/linkml/Boolean) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Bool** | -| Representation | | bool | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Boolean | - diff --git a/projects/biological_process/docs/types/Curie.md b/projects/biological_process/docs/types/Curie.md deleted file mode 100644 index c1803f93f..000000000 --- a/projects/biological_process/docs/types/Curie.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: curie - - -a compact URI - -URI: [linkml:Curie](https://w3id.org/linkml/Curie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Curie** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations this MUST be expanded to a URI | -| | | in non-RDF serializations MAY be serialized as the compact representation | - diff --git a/projects/biological_process/docs/types/Date.md b/projects/biological_process/docs/types/Date.md deleted file mode 100644 index 06948af97..000000000 --- a/projects/biological_process/docs/types/Date.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: date - - -a date (year, month and day) in an idealized calendar - -URI: [linkml:Date](https://w3id.org/linkml/Date) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDate** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Date | - diff --git a/projects/biological_process/docs/types/DateOrDatetime.md b/projects/biological_process/docs/types/DateOrDatetime.md deleted file mode 100644 index ef983898d..000000000 --- a/projects/biological_process/docs/types/DateOrDatetime.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: date_or_datetime - - -Either a date or a datetime - -URI: [linkml:DateOrDatetime](https://w3id.org/linkml/DateOrDatetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/biological_process/docs/types/Datetime.md b/projects/biological_process/docs/types/Datetime.md deleted file mode 100644 index 9510454a8..000000000 --- a/projects/biological_process/docs/types/Datetime.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: datetime - - -The combination of a date and time - -URI: [linkml:Datetime](https://w3id.org/linkml/Datetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDateTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:DateTime | - diff --git a/projects/biological_process/docs/types/Decimal.md b/projects/biological_process/docs/types/Decimal.md deleted file mode 100644 index a7ba14a5d..000000000 --- a/projects/biological_process/docs/types/Decimal.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: decimal - - -A real number with arbitrary precision that conforms to the xsd:decimal specification - -URI: [linkml:Decimal](https://w3id.org/linkml/Decimal) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Decimal** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Broad Mappings:** | | schema:Number | - diff --git a/projects/biological_process/docs/types/Double.md b/projects/biological_process/docs/types/Double.md deleted file mode 100644 index cfe6d71e2..000000000 --- a/projects/biological_process/docs/types/Double.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: double - - -A real number that conforms to the xsd:double specification - -URI: [linkml:Double](https://w3id.org/linkml/Double) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Close Mappings:** | | schema:Float | - diff --git a/projects/biological_process/docs/types/Float.md b/projects/biological_process/docs/types/Float.md deleted file mode 100644 index 7b303f96f..000000000 --- a/projects/biological_process/docs/types/Float.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: float - - -A real number that conforms to the xsd:float specification - -URI: [linkml:Float](https://w3id.org/linkml/Float) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Float | - diff --git a/projects/biological_process/docs/types/Integer.md b/projects/biological_process/docs/types/Integer.md deleted file mode 100644 index 3cfcc66d9..000000000 --- a/projects/biological_process/docs/types/Integer.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: integer - - -An integer - -URI: [linkml:Integer](https://w3id.org/linkml/Integer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **int** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Integer | - diff --git a/projects/biological_process/docs/types/Jsonpath.md b/projects/biological_process/docs/types/Jsonpath.md deleted file mode 100644 index a03a58e67..000000000 --- a/projects/biological_process/docs/types/Jsonpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpath - - -A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpath](https://w3id.org/linkml/Jsonpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/biological_process/docs/types/Jsonpointer.md b/projects/biological_process/docs/types/Jsonpointer.md deleted file mode 100644 index a0e1ac492..000000000 --- a/projects/biological_process/docs/types/Jsonpointer.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpointer - - -A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpointer](https://w3id.org/linkml/Jsonpointer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/biological_process/docs/types/Ncname.md b/projects/biological_process/docs/types/Ncname.md deleted file mode 100644 index 710b0b04a..000000000 --- a/projects/biological_process/docs/types/Ncname.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: ncname - - -Prefix part of CURIE - -URI: [linkml:Ncname](https://w3id.org/linkml/Ncname) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NCName** | -| Representation | | str | diff --git a/projects/biological_process/docs/types/Nodeidentifier.md b/projects/biological_process/docs/types/Nodeidentifier.md deleted file mode 100644 index f0097cdf4..000000000 --- a/projects/biological_process/docs/types/Nodeidentifier.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: nodeidentifier - - -A URI, CURIE or BNODE that represents a node in a model. - -URI: [linkml:Nodeidentifier](https://w3id.org/linkml/Nodeidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NodeIdentifier** | -| Representation | | str | diff --git a/projects/biological_process/docs/types/Objectidentifier.md b/projects/biological_process/docs/types/Objectidentifier.md deleted file mode 100644 index 454ba6be6..000000000 --- a/projects/biological_process/docs/types/Objectidentifier.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: objectidentifier - - -A URI or CURIE that represents an object in the model. - -URI: [linkml:Objectidentifier](https://w3id.org/linkml/Objectidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **ElementIdentifier** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | Used for inheritance and type checking | - diff --git a/projects/biological_process/docs/types/Sparqlpath.md b/projects/biological_process/docs/types/Sparqlpath.md deleted file mode 100644 index fd99a927e..000000000 --- a/projects/biological_process/docs/types/Sparqlpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: sparqlpath - - -A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - -URI: [linkml:Sparqlpath](https://w3id.org/linkml/Sparqlpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/biological_process/docs/types/String.md b/projects/biological_process/docs/types/String.md deleted file mode 100644 index 6e61d7081..000000000 --- a/projects/biological_process/docs/types/String.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: string - - -A character string - -URI: [linkml:String](https://w3id.org/linkml/String) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Text | - diff --git a/projects/biological_process/docs/types/Time.md b/projects/biological_process/docs/types/Time.md deleted file mode 100644 index 2b8652bcd..000000000 --- a/projects/biological_process/docs/types/Time.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: time - - -A time object represents a (local) time of day, independent of any particular day - -URI: [linkml:Time](https://w3id.org/linkml/Time) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Time | - diff --git a/projects/biological_process/docs/types/Uri.md b/projects/biological_process/docs/types/Uri.md deleted file mode 100644 index 343807a5e..000000000 --- a/projects/biological_process/docs/types/Uri.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: uri - - -a complete URI - -URI: [linkml:Uri](https://w3id.org/linkml/Uri) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URI** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node | -| **Close Mappings:** | | schema:URL | - diff --git a/projects/biological_process/docs/types/Uriorcurie.md b/projects/biological_process/docs/types/Uriorcurie.md deleted file mode 100644 index 2f7b65087..000000000 --- a/projects/biological_process/docs/types/Uriorcurie.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: uriorcurie - - -a URI or a CURIE - -URI: [linkml:Uriorcurie](https://w3id.org/linkml/Uriorcurie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URIorCURIE** | -| Representation | | str | diff --git a/projects/biological_process/excel/biological_process.xlsx b/projects/biological_process/excel/biological_process.xlsx deleted file mode 100644 index ef483dbda..000000000 Binary files a/projects/biological_process/excel/biological_process.xlsx and /dev/null differ diff --git a/projects/biological_process/graphql/biological_process.graphql b/projects/biological_process/graphql/biological_process.graphql deleted file mode 100644 index bdd010c3e..000000000 --- a/projects/biological_process/graphql/biological_process.graphql +++ /dev/null @@ -1,101 +0,0 @@ -type AnnotatorResult - { - subjectText: String - objectId: String - objectText: String - } - -type Any - { - } - -type BiologicalProcess - { - id: String! - label: String - description: String - synonyms: [String] - subclassOf: BiologicalProcess - inputs: [ChemicalEntity] - outputs: [ChemicalEntity] - steps: [MolecularActivity] - genes: [Gene] - geneActivities: [GeneMolecularActivityRelationship] - } - -type ChemicalEntity - { - id: String! - label: String - } - -interface CompoundExpression - { - } - -type ExtractionResult - { - inputId: String - inputTitle: String - inputText: String - rawCompletionOutput: String - prompt: String - extractedObject: Any - namedEntities: [Any] - } - -type Gene - { - id: String! - label: String - } - -type GeneMolecularActivityRelationship - { - gene: Gene - molecularActivity: MolecularActivity - } - -type MolecularActivity - { - id: String! - label: String - } - -interface NamedEntity - { - id: String! - label: String - } - -type Publication - { - id: String - title: String - abstract: String - combinedText: String - fullText: String - } - -type RelationshipType - { - id: String! - label: String - } - -type TextWithTriples - { - publication: Publication - triples: [Triple] - } - -interface Triple - { - subject: NamedEntity - predicate: RelationshipType - object: NamedEntity - qualifier: String - subjectQualifier: NamedEntity - objectQualifier: NamedEntity - } - diff --git a/projects/biological_process/jsonld/biological_process.context.jsonld b/projects/biological_process/jsonld/biological_process.context.jsonld deleted file mode 100644 index c38d464cb..000000000 --- a/projects/biological_process/jsonld/biological_process.context.jsonld +++ /dev/null @@ -1,157 +0,0 @@ -{ - "comments": { - "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2023-08-07T10:51:12", - "source": "biological_process.yaml" - }, - "@context": { - "CHEBI": "http://example.org/UNKNOWN/CHEBI/", - "GO": "http://example.org/UNKNOWN/GO/", - "HGNC": "http://example.org/UNKNOWN/HGNC/", - "RO": { - "@id": "http://purl.obolibrary.org/obo/RO_", - "@prefix": true - }, - "biolink": "http://example.org/UNKNOWN/biolink/", - "bp": { - "@id": "http://w3id.org/ontogpt/biological-process-template", - "@prefix": true - }, - "core": "http://w3id.org/ontogpt/core/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "@vocab": "http://w3id.org/ontogpt/biological-process-template", - "object_id": { - "@id": "core:object_id" - }, - "object_text": { - "@id": "core:object_text" - }, - "subject_text": { - "@id": "core:subject_text" - }, - "gene_activities": { - "@type": "@id" - }, - "genes": { - "@type": "@id" - }, - "inputs": { - "@type": "@id" - }, - "outputs": { - "@type": "@id" - }, - "steps": { - "@type": "@id" - }, - "subclass_of": { - "@type": "@id" - }, - "extracted_object": { - "@type": "@id", - "@id": "core:extracted_object" - }, - "input_id": { - "@id": "core:input_id" - }, - "input_text": { - "@id": "core:input_text" - }, - "input_title": { - "@id": "core:input_title" - }, - "named_entities": { - "@type": "@id", - "@id": "core:named_entities" - }, - "prompt": { - "@id": "core:prompt" - }, - "raw_completion_output": { - "@id": "core:raw_completion_output" - }, - "gene": { - "@type": "@id" - }, - "molecular_activity": { - "@type": "@id" - }, - "id": { - "@id": "core:id" - }, - "label": { - "@id": "rdfs:label" - }, - "abstract": { - "@id": "core:abstract" - }, - "combined_text": { - "@id": "core:combined_text" - }, - "full_text": { - "@id": "core:full_text" - }, - "title": { - "@id": "core:title" - }, - "publication": { - "@type": "@id", - "@id": "core:publication" - }, - "triples": { - "@type": "@id", - "@id": "core:triples" - }, - "object": { - "@type": "@id", - "@id": "core:object" - }, - "object_qualifier": { - "@type": "@id", - "@id": "core:object_qualifier" - }, - "predicate": { - "@type": "@id", - "@id": "core:predicate" - }, - "qualifier": { - "@id": "core:qualifier" - }, - "subject": { - "@type": "@id", - "@id": "core:subject" - }, - "subject_qualifier": { - "@type": "@id", - "@id": "core:subject_qualifier" - }, - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } - } -} diff --git a/projects/biological_process/jsonld/biological_process.jsonld b/projects/biological_process/jsonld/biological_process.jsonld deleted file mode 100644 index 08f54e592..000000000 --- a/projects/biological_process/jsonld/biological_process.jsonld +++ /dev/null @@ -1,1291 +0,0 @@ -{ - "name": "biological-process-template", - "description": "A template for GO-CAMs", - "title": "Biological Process Template", - "id": "https://w3id.org/ontogpt/biological_process", - "imports": [ - "linkml:types", - "core" - ], - "license": "https://creativecommons.org/publicdomain/zero/1.0/", - "prefixes": [ - { - "prefix_prefix": "linkml", - "prefix_reference": "https://w3id.org/linkml/" - }, - { - "prefix_prefix": "bp", - "prefix_reference": "http://w3id.org/ontogpt/biological-process-template" - } - ], - "default_prefix": "bp", - "default_range": "string", - "types": [ - { - "name": "string", - "definition_uri": "https://w3id.org/linkml/String", - "description": "A character string", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Text" - ], - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "@type": "TypeDefinition" - }, - { - "name": "integer", - "definition_uri": "https://w3id.org/linkml/Integer", - "description": "An integer", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Integer" - ], - "base": "int", - "uri": "http://www.w3.org/2001/XMLSchema#integer", - "@type": "TypeDefinition" - }, - { - "name": "boolean", - "definition_uri": "https://w3id.org/linkml/Boolean", - "description": "A binary (true or false) value", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Boolean" - ], - "base": "Bool", - "uri": "http://www.w3.org/2001/XMLSchema#boolean", - "repr": "bool", - "@type": "TypeDefinition" - }, - { - "name": "float", - "definition_uri": "https://w3id.org/linkml/Float", - "description": "A real number that conforms to the xsd:float specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#float", - "@type": "TypeDefinition" - }, - { - "name": "double", - "definition_uri": "https://w3id.org/linkml/Double", - "description": "A real number that conforms to the xsd:double specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#double", - "@type": "TypeDefinition" - }, - { - "name": "decimal", - "definition_uri": "https://w3id.org/linkml/Decimal", - "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "broad_mappings": [ - "schema:Number" - ], - "base": "Decimal", - "uri": "http://www.w3.org/2001/XMLSchema#decimal", - "@type": "TypeDefinition" - }, - { - "name": "time", - "definition_uri": "https://w3id.org/linkml/Time", - "description": "A time object represents a (local) time of day, independent of any particular day", - "notes": [ - "URI is dateTime because OWL reasoners do not work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Time" - ], - "base": "XSDTime", - "uri": "http://www.w3.org/2001/XMLSchema#time", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date", - "definition_uri": "https://w3id.org/linkml/Date", - "description": "a date (year, month and day) in an idealized calendar", - "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Date" - ], - "base": "XSDDate", - "uri": "http://www.w3.org/2001/XMLSchema#date", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "datetime", - "definition_uri": "https://w3id.org/linkml/Datetime", - "description": "The combination of a date and time", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:DateTime" - ], - "base": "XSDDateTime", - "uri": "http://www.w3.org/2001/XMLSchema#dateTime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date_or_datetime", - "definition_uri": "https://w3id.org/linkml/DateOrDatetime", - "description": "Either a date or a datetime", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "https://w3id.org/linkml/DateOrDatetime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uriorcurie", - "definition_uri": "https://w3id.org/linkml/Uriorcurie", - "description": "a URI or a CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "URIorCURIE", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "curie", - "definition_uri": "https://w3id.org/linkml/Curie", - "conforms_to": "https://www.w3.org/TR/curie/", - "description": "a compact URI", - "comments": [ - "in RDF serializations this MUST be expanded to a URI", - "in non-RDF serializations MAY be serialized as the compact representation" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "Curie", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uri", - "definition_uri": "https://w3id.org/linkml/Uri", - "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", - "description": "a complete URI", - "comments": [ - "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:URL" - ], - "base": "URI", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "ncname", - "definition_uri": "https://w3id.org/linkml/Ncname", - "description": "Prefix part of CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NCName", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "objectidentifier", - "definition_uri": "https://w3id.org/linkml/Objectidentifier", - "description": "A URI or CURIE that represents an object in the model.", - "comments": [ - "Used for inheritance and type checking" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "ElementIdentifier", - "uri": "http://www.w3.org/ns/shex#iri", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "nodeidentifier", - "definition_uri": "https://w3id.org/linkml/Nodeidentifier", - "description": "A URI, CURIE or BNODE that represents a node in a model.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NodeIdentifier", - "uri": "http://www.w3.org/ns/shex#nonLiteral", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpointer", - "definition_uri": "https://w3id.org/linkml/Jsonpointer", - "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901", - "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpath", - "definition_uri": "https://w3id.org/linkml/Jsonpath", - "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html", - "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "sparqlpath", - "definition_uri": "https://w3id.org/linkml/Sparqlpath", - "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths", - "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - } - ], - "enums": [ - { - "name": "NullDataOptions", - "definition_uri": "http://w3id.org/ontogpt/core/NullDataOptions", - "from_schema": "http://w3id.org/ontogpt/core", - "permissible_values": [ - { - "text": "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "meaning": "NCIT:C149701" - }, - { - "text": "NOT_APPLICABLE", - "meaning": "NCIT:C18902", - "aliases": [ - "not applicable", - "N/A" - ] - }, - { - "text": "NOT_MENTIONED" - } - ] - } - ], - "slots": [ - { - "name": "biologicalProcess__label", - "description": "the name of the biological process", - "from_schema": "https://w3id.org/ontogpt/biological_process", - "slot_uri": "http://w3id.org/ontogpt/biological-process-templatelabel", - "alias": "label", - "owner": "BiologicalProcess", - "domain_of": [ - "BiologicalProcess" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "biologicalProcess__description", - "description": "a textual description of the biological process", - "from_schema": "https://w3id.org/ontogpt/biological_process", - "slot_uri": "http://w3id.org/ontogpt/biological-process-templatedescription", - "alias": "description", - "owner": "BiologicalProcess", - "domain_of": [ - "BiologicalProcess" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "biologicalProcess__synonyms", - "description": "alternative names of the biological process", - "from_schema": "https://w3id.org/ontogpt/biological_process", - "slot_uri": "http://w3id.org/ontogpt/biological-process-templatesynonyms", - "multivalued": true, - "alias": "synonyms", - "owner": "BiologicalProcess", - "domain_of": [ - "BiologicalProcess" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "biologicalProcess__subclass_of", - "description": "the category to which this biological process belongs", - "from_schema": "https://w3id.org/ontogpt/biological_process", - "slot_uri": "http://w3id.org/ontogpt/biological-process-templatesubclass_of", - "alias": "subclass_of", - "owner": "BiologicalProcess", - "domain_of": [ - "BiologicalProcess" - ], - "range": "BiologicalProcess", - "@type": "SlotDefinition" - }, - { - "name": "biologicalProcess__inputs", - "description": "the inputs of the biological process", - "from_schema": "https://w3id.org/ontogpt/biological_process", - "slot_uri": "http://w3id.org/ontogpt/biological-process-templateinputs", - "multivalued": true, - "alias": "inputs", - "owner": "BiologicalProcess", - "domain_of": [ - "BiologicalProcess" - ], - "range": "ChemicalEntity", - "@type": "SlotDefinition" - }, - { - "name": "biologicalProcess__outputs", - "description": "the outputs of the biological process", - "from_schema": "https://w3id.org/ontogpt/biological_process", - "slot_uri": "http://w3id.org/ontogpt/biological-process-templateoutputs", - "multivalued": true, - "alias": "outputs", - "owner": "BiologicalProcess", - "domain_of": [ - "BiologicalProcess" - ], - "range": "ChemicalEntity", - "@type": "SlotDefinition" - }, - { - "name": "biologicalProcess__steps", - "description": "the steps involved in this biological process", - "from_schema": "https://w3id.org/ontogpt/biological_process", - "slot_uri": "http://w3id.org/ontogpt/biological-process-templatesteps", - "multivalued": true, - "alias": "steps", - "owner": "BiologicalProcess", - "domain_of": [ - "BiologicalProcess" - ], - "range": "MolecularActivity", - "@type": "SlotDefinition" - }, - { - "name": "biologicalProcess__genes", - "from_schema": "https://w3id.org/ontogpt/biological_process", - "slot_uri": "http://w3id.org/ontogpt/biological-process-templategenes", - "multivalued": true, - "alias": "genes", - "owner": "BiologicalProcess", - "domain_of": [ - "BiologicalProcess" - ], - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "biologicalProcess__gene_activities", - "description": "semicolon-separated list of gene to molecular activity relationships", - "from_schema": "https://w3id.org/ontogpt/biological_process", - "slot_uri": "http://w3id.org/ontogpt/biological-process-templategene_activities", - "multivalued": true, - "alias": "gene_activities", - "owner": "BiologicalProcess", - "domain_of": [ - "BiologicalProcess" - ], - "range": "GeneMolecularActivityRelationship", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "geneMolecularActivityRelationship__gene", - "from_schema": "https://w3id.org/ontogpt/biological_process", - "slot_uri": "http://w3id.org/ontogpt/biological-process-templategene", - "alias": "gene", - "owner": "GeneMolecularActivityRelationship", - "domain_of": [ - "GeneMolecularActivityRelationship" - ], - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "geneMolecularActivityRelationship__molecular_activity", - "from_schema": "https://w3id.org/ontogpt/biological_process", - "slot_uri": "http://w3id.org/ontogpt/biological-process-templatemolecular_activity", - "alias": "molecular_activity", - "owner": "GeneMolecularActivityRelationship", - "domain_of": [ - "GeneMolecularActivityRelationship" - ], - "range": "MolecularActivity", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_id", - "alias": "input_id", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_title", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_title", - "alias": "input_title", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_text", - "alias": "input_text", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__raw_completion_output", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/raw_completion_output", - "alias": "raw_completion_output", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__prompt", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/prompt", - "alias": "prompt", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__extracted_object", - "description": "The complex objects extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/extracted_object", - "alias": "extracted_object", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__named_entities", - "description": "Named entities extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/named_entities", - "multivalued": true, - "alias": "named_entities", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique 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"http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject", - "alias": "subject", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__predicate", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/predicate", - "alias": "predicate", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "triple__object", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object", - "alias": "object", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/qualifier", - "alias": "qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_qualifier", - "alias": "subject_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_qualifier", - "alias": "object_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/publication", - "alias": "publication", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__triples", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/triples", - "multivalued": true, - "alias": "triples", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "publication__id", - "description": "The publication identifier", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "alias": "id", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__title", - "description": "The title of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/title", - "alias": "title", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__abstract", - "description": "The abstract of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/abstract", - "alias": "abstract", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__combined_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/combined_text", - "alias": "combined_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__full_text", - "description": "The full text of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/full_text", - "alias": "full_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__subject_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_text", - "alias": "subject_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_id", - "alias": "object_id", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_text", - "alias": "object_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - } - ], - "classes": [ - { - "name": "BiologicalProcess", - "definition_uri": "http://w3id.org/ontogpt/biological-process-templateBiologicalProcess", - "from_schema": "https://w3id.org/ontogpt/biological_process", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "biologicalProcess__label", - "biologicalProcess__description", - "biologicalProcess__synonyms", - "biologicalProcess__subclass_of", - "biologicalProcess__inputs", - "biologicalProcess__outputs", - "biologicalProcess__steps", - "biologicalProcess__genes", - "biologicalProcess__gene_activities" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "label", - "description": "the name of the biological process", - "@type": "SlotDefinition" - }, - { - "name": "description", - "description": "a textual description of the biological process", - "@type": "SlotDefinition" - }, - { - "name": "synonyms", - "description": "alternative names of the biological process", - "multivalued": true, - "@type": "SlotDefinition" - }, - { - "name": "subclass_of", - "description": "the category to which this biological process belongs", - "range": "BiologicalProcess", - "@type": "SlotDefinition" - }, - { - "name": "inputs", - "description": "the inputs of the biological process", - "multivalued": true, - "range": "ChemicalEntity", - "@type": "SlotDefinition" - }, - { - "name": "outputs", - "description": "the outputs of the biological process", - "multivalued": true, - "range": "ChemicalEntity", - "@type": "SlotDefinition" - }, - { - "name": "steps", - "description": "the steps involved in this biological process", - "multivalued": true, - "range": "MolecularActivity", - "@type": "SlotDefinition" - }, - { - "name": "genes", - "multivalued": true, - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "gene_activities", - "description": "semicolon-separated list of gene to molecular activity relationships", - "multivalued": true, - "range": "GeneMolecularActivityRelationship", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/biological-process-templateBiologicalProcess", - "tree_root": true, - "@type": "ClassDefinition" - }, - { - "name": "Gene", - "id_prefixes": [ - "HGNC" - ], - "definition_uri": "http://w3id.org/ontogpt/biological-process-templateGene", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:hgnc", - "@type": "Annotation" - } - ], - "from_schema": "https://w3id.org/ontogpt/biological_process", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/biological-process-templateGene", - "@type": "ClassDefinition" - }, - { - "name": "MolecularActivity", - "id_prefixes": [ - "GO" - ], - "definition_uri": "http://w3id.org/ontogpt/biological-process-templateMolecularActivity", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:go", - "@type": "Annotation" - } - ], - "from_schema": "https://w3id.org/ontogpt/biological_process", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/biological-process-templateMolecularActivity", - "@type": "ClassDefinition" - }, - { - "name": "ChemicalEntity", - "id_prefixes": [ - "CHEBI" - ], - "definition_uri": "http://w3id.org/ontogpt/biological-process-templateChemicalEntity", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:chebi", - "@type": "Annotation" - } - ], - "from_schema": "https://w3id.org/ontogpt/biological_process", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/biological-process-templateChemicalEntity", - "@type": "ClassDefinition" - }, - { - "name": "GeneMolecularActivityRelationship", - "definition_uri": "http://w3id.org/ontogpt/biological-process-templateGeneMolecularActivityRelationship", - "from_schema": "https://w3id.org/ontogpt/biological_process", - "slots": [ - "geneMolecularActivityRelationship__gene", - "geneMolecularActivityRelationship__molecular_activity" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "gene", - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "molecular_activity", - "range": "MolecularActivity", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/biological-process-templateGeneMolecularActivityRelationship", - "@type": "ClassDefinition" - }, - { - "name": "Any", - "definition_uri": "http://w3id.org/ontogpt/core/Any", - "from_schema": "http://w3id.org/ontogpt/core", - "mappings": [ - "linkml:Any" - ], - "slot_usage": {}, - "class_uri": "https://w3id.org/linkml/Any", - "@type": "ClassDefinition" - }, - { - "name": "ExtractionResult", - "definition_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "description": "A result of extracting knowledge on text", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "extractionResult__input_id", - "extractionResult__input_title", - "extractionResult__input_text", - "extractionResult__raw_completion_output", - "extractionResult__prompt", - "extractionResult__extracted_object", - "extractionResult__named_entities" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "input_id", - "@type": "SlotDefinition" - }, - { - "name": "input_title", - "@type": "SlotDefinition" - }, - { - "name": "input_text", - "@type": "SlotDefinition" - }, - { - "name": "raw_completion_output", - "@type": "SlotDefinition" - }, - { - "name": "prompt", - "@type": "SlotDefinition" - }, - { - "name": "extracted_object", - "description": "The complex objects extracted from the text", - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "named_entities", - "description": "Named entities extracted from the text", - "multivalued": true, - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "@type": "ClassDefinition" - }, - { - "name": "NamedEntity", - "definition_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "identifier": true, - "@type": "SlotDefinition" - }, - { - "name": "label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "aliases": [ - "name" - ], - "slot_uri": "rdfs:label", - "range": "string", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "@type": "ClassDefinition" - }, - { - "name": "CompoundExpression", - "definition_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "@type": "ClassDefinition" - }, - { - "name": "Triple", - "definition_uri": "http://w3id.org/ontogpt/core/Triple", - "description": "Abstract parent for Relation Extraction tasks", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "CompoundExpression", - "abstract": true, - "slots": [ - "triple__subject", - "triple__predicate", - "triple__object", - "triple__qualifier", - "triple__subject_qualifier", - "triple__object_qualifier" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "predicate", - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "object", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Triple", - "@type": "ClassDefinition" - }, - { - "name": "TextWithTriples", - "definition_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "textWithTriples__publication", - "textWithTriples__triples" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "triples", - "multivalued": true, - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "@type": "ClassDefinition" - }, - { - "name": "RelationshipType", - "id_prefixes": [ - "RO", - "biolink" - ], - "definition_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "@type": "ClassDefinition" - }, - { - "name": "Publication", - "definition_uri": "http://w3id.org/ontogpt/core/Publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "publication__id", - "publication__title", - "publication__abstract", - "publication__combined_text", - "publication__full_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "description": "The publication identifier", - "@type": "SlotDefinition" - }, - { - "name": "title", - "description": "The title of the publication", - "@type": "SlotDefinition" - }, - { - "name": "abstract", - "description": "The abstract of the publication", - "@type": "SlotDefinition" - }, - { - "name": "combined_text", - "@type": "SlotDefinition" - }, - { - "name": "full_text", - "description": "The full text of the publication", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Publication", - "@type": "ClassDefinition" - }, - { - "name": "AnnotatorResult", - "definition_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "annotatorResult__subject_text", - "annotatorResult__object_id", - "annotatorResult__object_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject_text", - "@type": "SlotDefinition" - }, - { - "name": "object_id", - "@type": "SlotDefinition" - }, - { - "name": "object_text", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "@type": "ClassDefinition" - } - ], - "metamodel_version": "1.7.0", - "source_file": "biological_process.yaml", - "source_file_date": "2023-06-17T15:11:19", - "source_file_size": 2027, - "generation_date": "2023-08-07T10:51:13", - "@type": "SchemaDefinition", - "@context": [ - "projects/biological_process/jsonld/biological_process.context.jsonld", - "https://w3id.org/linkml/types.context.jsonld", - "core.context.jsonld", - { - "@base": "http://w3id.org/ontogpt/biological-process-template" - } - ] -} diff --git a/projects/biological_process/jsonschema/biological_process.schema.json b/projects/biological_process/jsonschema/biological_process.schema.json deleted file mode 100644 index fbfc40441..000000000 --- a/projects/biological_process/jsonschema/biological_process.schema.json +++ /dev/null @@ -1,342 +0,0 @@ -{ - "$defs": { - "AnnotatorResult": { - "additionalProperties": false, - "description": "", - "properties": { - "object_id": { - "type": "string" - }, - "object_text": { - "type": "string" - }, - "subject_text": { - "type": "string" - } - }, - "title": "AnnotatorResult", - "type": "object" - }, - "Any": { - "additionalProperties": true, - "description": "", - "title": "Any", - "type": "object" - }, - "BiologicalProcess": { - "additionalProperties": false, - "description": "", - "properties": { - "description": { - "description": "a textual description of the biological process", - "type": "string" - }, - "gene_activities": { - "description": "semicolon-separated list of gene to molecular activity relationships", - "items": { - "$ref": "#/$defs/GeneMolecularActivityRelationship" - }, - "type": "array" - }, - "genes": { - "items": { - "type": "string" - }, - "type": "array" - }, - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "inputs": { - "description": "the inputs of the biological process", - "items": { - "type": "string" - }, - "type": "array" - }, - "label": { - "description": "the name of the biological process", - "type": "string" - }, - "outputs": { - "description": "the outputs of the biological process", - "items": { - "type": "string" - }, - "type": "array" - }, - "steps": { - "description": "the steps involved in this biological process", - "items": { - "type": "string" - }, - "type": "array" - }, - "subclass_of": { - "description": "the category to which this biological process belongs", - "type": "string" - }, - "synonyms": { - "description": "alternative names of the biological process", - "items": { - "type": "string" - }, - "type": "array" - } - }, - "required": [ - "id" - ], - "title": "BiologicalProcess", - "type": "object" - }, - "ChemicalEntity": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "ChemicalEntity", - "type": "object" - }, - "ExtractionResult": { - "additionalProperties": false, - "description": "A result of extracting knowledge on text", - "properties": { - "extracted_object": { - "$ref": "#/$defs/Any", - "description": "The complex objects extracted from the text" - }, - "input_id": { - "type": "string" - }, - "input_text": { - "type": "string" - }, - "input_title": { - "type": "string" - }, - "named_entities": { - "description": "Named entities extracted from the text", - "items": { - "$ref": "#/$defs/Any" - }, - "type": "array" - }, - "prompt": { - "type": "string" - }, - "raw_completion_output": { - "type": "string" - } - }, - "title": "ExtractionResult", - "type": "object" - }, - "Gene": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Gene", - "type": "object" - }, - "GeneMolecularActivityRelationship": { - "additionalProperties": false, - "description": "", - "properties": { - "gene": { - "type": "string" - }, - "molecular_activity": { - "type": "string" - } - }, - "title": "GeneMolecularActivityRelationship", - "type": "object" - }, - "MolecularActivity": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "MolecularActivity", - "type": "object" - }, - "NullDataOptions": { - "description": "", - "enum": [ - "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "NOT_APPLICABLE", - "NOT_MENTIONED" - ], - "title": "NullDataOptions", - "type": "string" - }, - "Publication": { - "additionalProperties": false, - "description": "", - "properties": { - "abstract": { - "description": "The abstract of the publication", - "type": "string" - }, - "combined_text": { - "type": "string" - }, - "full_text": { - "description": "The full text of the publication", - "type": "string" - }, - "id": { - "description": "The publication identifier", - "type": "string" - }, - "title": { - "description": "The title of the publication", - "type": "string" - } - }, - "title": "Publication", - "type": "object" - }, - "RelationshipType": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "RelationshipType", - "type": "object" - }, - "TextWithTriples": { - "additionalProperties": false, - "description": "", - "properties": { - "publication": { - "$ref": "#/$defs/Publication" - }, - "triples": { - "items": { - "$ref": "#/$defs/Triple" - }, - "type": "array" - } - }, - "title": "TextWithTriples", - "type": "object" - } - }, - "$id": "https://w3id.org/ontogpt/biological_process", - "$schema": "http://json-schema.org/draft-07/schema#", - "additionalProperties": true, - "metamodel_version": "1.7.0", - "properties": { - "description": { - "description": "a textual description of the biological process", - "type": "string" - }, - "gene_activities": { - "description": "semicolon-separated list of gene to molecular activity relationships", - "items": { - "$ref": "#/$defs/GeneMolecularActivityRelationship" - }, - "type": "array" - }, - "genes": { - "items": { - "type": "string" - }, - "type": "array" - }, - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "inputs": { - "description": "the inputs of the biological process", - "items": { - "type": "string" - }, - "type": "array" - }, - "label": { - "description": "the name of the biological process", - "type": "string" - }, - "outputs": { - "description": "the outputs of the biological process", - "items": { - "type": "string" - }, - "type": "array" - }, - "steps": { - "description": "the steps involved in this biological process", - "items": { - "type": "string" - }, - "type": "array" - }, - "subclass_of": { - "description": "the category to which this biological process belongs", - "type": "string" - }, - "synonyms": { - "description": "alternative names of the biological process", - "items": { - "type": "string" - }, - "type": "array" - } - }, - "required": [ - "id" - ], - "title": "biological-process-template", - "type": "object", - "version": null -} \ No newline at end of file diff --git a/projects/biological_process/owl/biological_process.owl.ttl b/projects/biological_process/owl/biological_process.owl.ttl deleted file mode 100644 index 3649b4522..000000000 --- a/projects/biological_process/owl/biological_process.owl.ttl +++ /dev/null @@ -1,491 +0,0 @@ -@prefix IAO: . -@prefix bp: . -@prefix linkml: . -@prefix owl: . -@prefix rdf: . -@prefix rdfs: . -@prefix skos: . -@prefix xsd: . - -linkml:SubsetDefinition a owl:Class ; - rdfs:label "subset_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" . - -linkml:TypeDefinition a owl:Class ; - rdfs:label "type_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" ; - linkml:mixins "type_expression" . - -linkml:topValue a owl:DatatypeProperty ; - rdfs:label "value" . - - a owl:Ontology ; - rdfs:label "biological-process-template" ; - IAO:0000700 bp:GeneMolecularActivityRelationship, - , - , - , - , - , - , - ; - linkml:classes "{'BiologicalProcess': ClassDefinition(name='BiologicalProcess', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/biological-process-templateBiologicalProcess', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/biological_process', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'biologicalProcess__label', 'biologicalProcess__description', 'biologicalProcess__synonyms', 'biologicalProcess__subclass_of', 'biologicalProcess__inputs', 'biologicalProcess__outputs', 'biologicalProcess__steps', 'biologicalProcess__genes', 'biologicalProcess__gene_activities'], slot_usage={}, attributes={'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the name of the biological process', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'description': SlotDefinition(name='description', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a textual description of the biological process', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'synonyms': SlotDefinition(name='synonyms', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='alternative names of the biological process', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subclass_of': SlotDefinition(name='subclass_of', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the category to which this biological process belongs', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='BiologicalProcess', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'inputs': SlotDefinition(name='inputs', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the inputs of the biological process', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ChemicalEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'outputs': SlotDefinition(name='outputs', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the outputs of the biological process', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ChemicalEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'steps': SlotDefinition(name='steps', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the steps involved in this biological process', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='MolecularActivity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'genes': SlotDefinition(name='genes', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'gene_activities': SlotDefinition(name='gene_activities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of gene to molecular activity relationships', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneMolecularActivityRelationship', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='bp:BiologicalProcess', subclass_of=None, union_of=[], defining_slots=[], tree_root=True, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Gene': ClassDefinition(name='Gene', id_prefixes=['HGNC'], definition_uri='http://w3id.org/ontogpt/biological-process-templateGene', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:hgnc', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/biological_process', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='bp:Gene', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'MolecularActivity': ClassDefinition(name='MolecularActivity', id_prefixes=['GO'], definition_uri='http://w3id.org/ontogpt/biological-process-templateMolecularActivity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:go', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/biological_process', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='bp:MolecularActivity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ChemicalEntity': ClassDefinition(name='ChemicalEntity', id_prefixes=['CHEBI'], definition_uri='http://w3id.org/ontogpt/biological-process-templateChemicalEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:chebi', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/biological_process', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='bp:ChemicalEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'GeneMolecularActivityRelationship': ClassDefinition(name='GeneMolecularActivityRelationship', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/biological-process-templateGeneMolecularActivityRelationship', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/biological_process', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['geneMolecularActivityRelationship__gene', 'geneMolecularActivityRelationship__molecular_activity'], slot_usage={}, attributes={'gene': SlotDefinition(name='gene', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'molecular_activity': SlotDefinition(name='molecular_activity', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='MolecularActivity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='bp:GeneMolecularActivityRelationship', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Any': ClassDefinition(name='Any', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Any', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=['linkml:Any'], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='linkml:Any', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ExtractionResult': ClassDefinition(name='ExtractionResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/ExtractionResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A result of extracting knowledge on text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['extractionResult__input_id', 'extractionResult__input_title', 'extractionResult__input_text', 'extractionResult__raw_completion_output', 'extractionResult__prompt', 'extractionResult__extracted_object', 'extractionResult__named_entities'], slot_usage={}, attributes={'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:ExtractionResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'NamedEntity': ClassDefinition(name='NamedEntity', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NamedEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:NamedEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'CompoundExpression': ClassDefinition(name='CompoundExpression', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/CompoundExpression', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='core:CompoundExpression', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Triple': ClassDefinition(name='Triple', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Triple', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Abstract parent for Relation Extraction tasks', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['triple__subject', 'triple__predicate', 'triple__object', 'triple__qualifier', 'triple__subject_qualifier', 'triple__object_qualifier'], slot_usage={}, attributes={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Triple', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'TextWithTriples': ClassDefinition(name='TextWithTriples', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/TextWithTriples', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['textWithTriples__publication', 'textWithTriples__triples'], slot_usage={}, attributes={'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:TextWithTriples', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'RelationshipType': ClassDefinition(name='RelationshipType', id_prefixes=['RO', 'biolink'], definition_uri='http://w3id.org/ontogpt/core/RelationshipType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='core:RelationshipType', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Publication': ClassDefinition(name='Publication', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Publication', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['publication__id', 'publication__title', 'publication__abstract', 'publication__combined_text', 'publication__full_text'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Publication', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'AnnotatorResult': ClassDefinition(name='AnnotatorResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/AnnotatorResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['annotatorResult__subject_text', 'annotatorResult__object_id', 'annotatorResult__object_text'], slot_usage={}, attributes={'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:AnnotatorResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={})}" ; - linkml:enums "{'NullDataOptions': EnumDefinition(name='NullDataOptions', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NullDataOptions', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'UNSPECIFIED_METHOD_OF_ADMINISTRATION': PermissibleValue(text='UNSPECIFIED_METHOD_OF_ADMINISTRATION', description=None, meaning='NCIT:C149701', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_APPLICABLE': PermissibleValue(text='NOT_APPLICABLE', description=None, meaning='NCIT:C18902', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['not applicable', 'N/A'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_MENTIONED': PermissibleValue(text='NOT_MENTIONED', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[])}" ; - linkml:id "https://w3id.org/ontogpt/biological_process" ; - linkml:imports "core", - "linkml:types" ; - linkml:types "{'string': TypeDefinition(name='string', id_prefixes=[], definition_uri='https://w3id.org/linkml/String', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A character string', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Text'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'integer': TypeDefinition(name='integer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Integer', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An integer', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Integer'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='int', uri='xsd:integer', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'boolean': TypeDefinition(name='boolean', id_prefixes=[], definition_uri='https://w3id.org/linkml/Boolean', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A binary (true or false) value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Boolean'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Bool', uri='xsd:boolean', repr='bool', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'float': TypeDefinition(name='float', id_prefixes=[], definition_uri='https://w3id.org/linkml/Float', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:float specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Float'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:float', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'double': TypeDefinition(name='double', id_prefixes=[], definition_uri='https://w3id.org/linkml/Double', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:double specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:Float'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:double', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'decimal': TypeDefinition(name='decimal', id_prefixes=[], definition_uri='https://w3id.org/linkml/Decimal', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number with arbitrary precision that conforms to the xsd:decimal specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=['schema:Number'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Decimal', uri='xsd:decimal', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'time': TypeDefinition(name='time', id_prefixes=[], definition_uri='https://w3id.org/linkml/Time', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A time object represents a (local) time of day, independent of any particular day', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=['URI is dateTime because OWL reasoners do not work with straight date or time'], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Time'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDTime', uri='xsd:time', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date': TypeDefinition(name='date', id_prefixes=[], definition_uri='https://w3id.org/linkml/Date', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a date (year, month and day) in an idealized calendar', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[\"URI is dateTime because OWL reasoners don't work with straight date or time\"], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Date'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDate', uri='xsd:date', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'datetime': TypeDefinition(name='datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/Datetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The combination of a date and time', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:DateTime'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDateTime', uri='xsd:dateTime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date_or_datetime': TypeDefinition(name='date_or_datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/DateOrDatetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Either a date or a datetime', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='linkml:DateOrDatetime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uriorcurie': TypeDefinition(name='uriorcurie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uriorcurie', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a URI or a CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URIorCURIE', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'curie': TypeDefinition(name='curie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Curie', local_names={}, conforms_to='https://www.w3.org/TR/curie/', implements=[], extensions={}, annotations={}, description='a compact URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations this MUST be expanded to a URI', 'in non-RDF serializations MAY be serialized as the compact representation'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Curie', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uri': TypeDefinition(name='uri', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uri', local_names={}, conforms_to='https://www.ietf.org/rfc/rfc3987.txt', implements=[], extensions={}, annotations={}, description='a complete URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:URL'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URI', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ncname': TypeDefinition(name='ncname', id_prefixes=[], definition_uri='https://w3id.org/linkml/Ncname', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Prefix part of CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NCName', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'objectidentifier': TypeDefinition(name='objectidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Objectidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI or CURIE that represents an object in the model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['Used for inheritance and type checking'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='ElementIdentifier', uri='shex:iri', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'nodeidentifier': TypeDefinition(name='nodeidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Nodeidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI, CURIE or BNODE that represents a node in a model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NodeIdentifier', uri='shex:nonLiteral', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpointer': TypeDefinition(name='jsonpointer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpointer', local_names={}, conforms_to='https://datatracker.ietf.org/doc/html/rfc6901', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpath': TypeDefinition(name='jsonpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpath', local_names={}, conforms_to='https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sparqlpath': TypeDefinition(name='sparqlpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Sparqlpath', local_names={}, conforms_to='https://www.w3.org/TR/sparql11-query/#propertypaths', implements=[], extensions={}, annotations={}, description='A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -bp:description a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "description" ; - rdfs:range linkml:String ; - skos:definition "a textual description of the biological process" . - -bp:gene a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "gene" ; - rdfs:range bp:Gene . - -bp:gene_activities a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "gene_activities" ; - rdfs:range bp:GeneMolecularActivityRelationship ; - skos:definition "semicolon-separated list of gene to molecular activity relationships" . - -bp:genes a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "genes" ; - rdfs:range bp:Gene . - -bp:inputs a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "inputs" ; - rdfs:range bp:ChemicalEntity ; - skos:definition "the inputs of the biological process" . - -bp:label a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "label" ; - rdfs:range linkml:String ; - skos:definition "the name of the biological process" . - -bp:molecular_activity a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "molecular_activity" ; - rdfs:range bp:MolecularActivity . - -bp:outputs a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "outputs" ; - rdfs:range bp:ChemicalEntity ; - skos:definition "the outputs of the biological process" . - -bp:steps a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "steps" ; - rdfs:range bp:MolecularActivity ; - skos:definition "the steps involved in this biological process" . - -bp:subclass_of a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subclass_of" ; - rdfs:range bp:BiologicalProcess ; - skos:definition "the category to which this biological process belongs" . - -bp:synonyms a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "synonyms" ; - rdfs:range linkml:String ; - skos:definition "alternative names of the biological process" . - - a owl:Class, - linkml:ClassDefinition ; - rdfs:label "AnnotatorResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ] ; - linkml:attributes "{'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - - a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ExtractionResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ] ; - skos:definition "A result of extracting knowledge on text" ; - linkml:attributes "{'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - - a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TextWithTriples" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ] ; - linkml:attributes "{'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "abstract" ; - rdfs:range linkml:String ; - skos:definition "The abstract of the publication" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "combined_text" ; - rdfs:range linkml:String . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "extracted_object" ; - rdfs:range ; - skos:definition "The complex objects extracted from the text" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "full_text" ; - rdfs:range linkml:String ; - skos:definition "The full text of the publication" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_id" ; - rdfs:range linkml:String . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_text" ; - rdfs:range linkml:String . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_title" ; - rdfs:range linkml:String . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "named_entities" ; - rdfs:range ; - skos:definition "Named entities extracted from the text" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object" ; - rdfs:range . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_id" ; - rdfs:range linkml:String . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_qualifier" ; - rdfs:range ; - skos:definition "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_text" ; - rdfs:range linkml:String . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "predicate" ; - rdfs:range . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "prompt" ; - rdfs:range linkml:String . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "publication" ; - bp:prompt.skip "true" ; - rdfs:range . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "qualifier" ; - rdfs:range linkml:String ; - skos:definition "A qualifier for the statements, e.g. \"NOT\" for negation" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "raw_completion_output" ; - rdfs:range linkml:String . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject" ; - rdfs:range . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_qualifier" ; - rdfs:range ; - skos:definition "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_text" ; - rdfs:range linkml:String . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "title" ; - rdfs:range linkml:String ; - skos:definition "The title of the publication" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "triples" ; - rdfs:range . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "label" ; - bp:owl "AnnotationProperty, AnnotationAssertion" ; - rdfs:range linkml:String ; - skos:altLabel "name" ; - skos:definition "The label (name) of the named thing" ; - skos:exactMatch . - - a , - owl:Class ; - rdfs:label "UNSPECIFIED_METHOD_OF_ADMINISTRATION" . - - a , - owl:Class ; - rdfs:label "NOT_APPLICABLE" . - -bp:BiologicalProcess a owl:Class, - linkml:ClassDefinition ; - rdfs:label "BiologicalProcess" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty bp:label ], - [ a owl:Restriction ; - owl:allValuesFrom bp:ChemicalEntity ; - owl:onProperty bp:outputs ], - [ a owl:Restriction ; - owl:allValuesFrom bp:GeneMolecularActivityRelationship ; - owl:onProperty bp:gene_activities ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty bp:synonyms ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty bp:description ], - [ a owl:Restriction ; - owl:allValuesFrom bp:ChemicalEntity ; - owl:onProperty bp:inputs ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass bp:BiologicalProcess ; - owl:onProperty bp:subclass_of ], - [ a owl:Restriction ; - owl:allValuesFrom bp:MolecularActivity ; - owl:onProperty bp:steps ], - [ a owl:Restriction ; - owl:allValuesFrom bp:Gene ; - owl:onProperty bp:genes ], - ; - linkml:attributes "{'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the name of the biological process', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'description': SlotDefinition(name='description', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a textual description of the biological process', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'synonyms': SlotDefinition(name='synonyms', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='alternative names of the biological process', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subclass_of': SlotDefinition(name='subclass_of', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the category to which this biological process belongs', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='BiologicalProcess', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'inputs': SlotDefinition(name='inputs', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the inputs of the biological process', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ChemicalEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'outputs': SlotDefinition(name='outputs', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the outputs of the biological process', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ChemicalEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'steps': SlotDefinition(name='steps', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the steps involved in this biological process', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='MolecularActivity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'genes': SlotDefinition(name='genes', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'gene_activities': SlotDefinition(name='gene_activities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of gene to molecular activity relationships', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneMolecularActivityRelationship', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "NamedEntity" . - - a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CompoundExpression" ; - linkml:attributes "{}" . - - a , - owl:Class ; - rdfs:label "NOT_MENTIONED" . - - a owl:Class, - linkml:ClassDefinition ; - rdfs:label "RelationshipType" ; - rdfs:subClassOf ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - - a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Triple" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - ; - skos:definition "Abstract parent for Relation Extraction tasks" ; - linkml:attributes "{'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - - a owl:ObjectProperty, - linkml:SlotDefinition . - -bp:GeneMolecularActivityRelationship a owl:Class, - linkml:ClassDefinition ; - rdfs:label "GeneMolecularActivityRelationship" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass bp:MolecularActivity ; - owl:onProperty bp:molecular_activity ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass bp:Gene ; - owl:onProperty bp:gene ] ; - linkml:attributes "{'gene': SlotDefinition(name='gene', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'molecular_activity': SlotDefinition(name='molecular_activity', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='MolecularActivity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - - a owl:Class, - linkml:EnumDefinition ; - rdfs:label "NullDataOptions" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - . - - a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Publication" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -bp:ChemicalEntity a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ChemicalEntity" ; - bp:annotators "sqlite:obo:chebi" ; - rdfs:subClassOf ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -bp:Gene a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Gene" ; - bp:annotators "sqlite:obo:hgnc" ; - rdfs:subClassOf ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -bp:MolecularActivity a owl:Class, - linkml:ClassDefinition ; - rdfs:label "MolecularActivity" ; - bp:annotators "sqlite:obo:go" ; - rdfs:subClassOf ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - - a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Any" ; - skos:exactMatch linkml:Any ; - linkml:attributes "{}" . - - a owl:Class, - linkml:ClassDefinition ; - rdfs:label "NamedEntity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:ClassDefinition a owl:Class ; - rdfs:label "class_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "class_expression" . - -linkml:SlotDefinition a owl:Class ; - rdfs:label "slot_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "slot_expression" . - - diff --git a/projects/biological_process/prefixmap/biological_process.yaml b/projects/biological_process/prefixmap/biological_process.yaml deleted file mode 100644 index f6195251e..000000000 --- a/projects/biological_process/prefixmap/biological_process.yaml +++ /dev/null @@ -1,38 +0,0 @@ -{ - "CHEBI": "http://example.org/UNKNOWN/CHEBI/", - "GO": "http://example.org/UNKNOWN/GO/", - "HGNC": "http://example.org/UNKNOWN/HGNC/", - "RO": "http://purl.obolibrary.org/obo/RO_", - "biolink": "http://example.org/UNKNOWN/biolink/", - "bp": "http://w3id.org/ontogpt/biological-process-template", - "core": "http://w3id.org/ontogpt/core/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } -} diff --git a/projects/biological_process/protobuf/biological_process.proto b/projects/biological_process/protobuf/biological_process.proto deleted file mode 100644 index ae47a2046..000000000 --- a/projects/biological_process/protobuf/biological_process.proto +++ /dev/null @@ -1,68 +0,0 @@ -message AnnotatorResult - { - string subjectText = 0 - string objectId = 0 - string objectText = 0 - } -message BiologicalProcess - { - string id = 0 - string label = 0 - string description = 0 - repeated string synonyms = 0 - biologicalProcess subclassOf = 0 - repeated chemicalEntity inputs = 0 - repeated chemicalEntity outputs = 0 - repeated molecularActivity steps = 0 - repeated gene genes = 0 - repeated geneMolecularActivityRelationship geneActivities = 0 - } -message ChemicalEntity - { - string id = 0 - string label = 0 - } -// A result of extracting knowledge on text -message ExtractionResult - { - string inputId = 0 - string inputTitle = 0 - string inputText = 0 - string rawCompletionOutput = 0 - string prompt = 0 - any extractedObject = 0 - repeated any namedEntities = 0 - } -message Gene - { - string id = 0 - string label = 0 - } -message GeneMolecularActivityRelationship - { - gene gene = 0 - molecularActivity molecularActivity = 0 - } -message MolecularActivity - { - string id = 0 - string label = 0 - } -message Publication - { - string id = 0 - string title = 0 - string abstract = 0 - string combinedText = 0 - string fullText = 0 - } -message RelationshipType - { - string id = 0 - string label = 0 - } -message TextWithTriples - { - publication publication = 0 - repeated triple triples = 0 - } diff --git a/projects/biological_process/shacl/biological_process.shacl.ttl b/projects/biological_process/shacl/biological_process.shacl.ttl deleted file mode 100644 index 67469826f..000000000 --- a/projects/biological_process/shacl/biological_process.shacl.ttl +++ /dev/null @@ -1,272 +0,0 @@ -@prefix bp: . -@prefix linkml: . -@prefix rdf: . -@prefix sh: . -@prefix xsd: . - - a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 1 ; - sh:path ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path ] ; - sh:targetClass . - - a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass . - - a sh:NodeShape ; - sh:closed true ; - sh:description "A result of extracting knowledge on text" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 2 ; - sh:path ], - [ sh:class linkml:Any ; - sh:description "The complex objects extracted from the text" ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path ], - [ sh:maxCount 1 ; - sh:order 4 ; - sh:path ], - [ sh:class linkml:Any ; - sh:description "Named entities extracted from the text" ; - sh:nodeKind sh:BlankNode ; - sh:order 6 ; - sh:path ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path ] ; - sh:targetClass . - - a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path ], - [ sh:class ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path ] ; - sh:targetClass . - -bp:BiologicalProcess a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "alternative names of the biological process" ; - sh:order 2 ; - sh:path bp:synonyms ], - [ sh:class bp:Gene ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path bp:genes ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path ], - [ sh:class bp:ChemicalEntity ; - sh:description "the inputs of the biological process" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path bp:inputs ], - [ sh:class bp:MolecularActivity ; - sh:description "the steps involved in this biological process" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path bp:steps ], - [ sh:description "the name of the biological process" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path bp:label ], - [ sh:class bp:BiologicalProcess ; - sh:description "the category to which this biological process belongs" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path bp:subclass_of ], - [ sh:class bp:GeneMolecularActivityRelationship ; - sh:description "semicolon-separated list of gene to molecular activity relationships" ; - sh:nodeKind sh:BlankNode ; - sh:order 8 ; - sh:path bp:gene_activities ], - [ sh:class bp:ChemicalEntity ; - sh:description "the outputs of the biological process" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path bp:outputs ], - [ sh:description "a textual description of the biological process" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path bp:description ] ; - sh:targetClass bp:BiologicalProcess . - -bp:GeneMolecularActivityRelationship a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class bp:MolecularActivity ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path bp:molecular_activity ], - [ sh:class bp:Gene ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path bp:gene ] ; - sh:targetClass bp:GeneMolecularActivityRelationship . - - a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The publication identifier" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path ], - [ sh:description "The title of the publication" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path ], - [ sh:description "The abstract of the publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path ], - [ sh:description "The full text of the publication" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path ] ; - sh:targetClass . - - a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path ] ; - sh:targetClass . - - a sh:NodeShape ; - sh:closed false ; - sh:description "Abstract parent for Relation Extraction tasks" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path ], - [ sh:class ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path ], - [ sh:class ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path ], - [ sh:class ; - sh:description "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path ], - [ sh:class ; - sh:description "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path ], - [ sh:description "A qualifier for the statements, e.g. \"NOT\" for negation" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path ] ; - sh:targetClass . - -bp:ChemicalEntity a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path ] ; - sh:targetClass bp:ChemicalEntity . - -bp:Gene a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path ] ; - sh:targetClass bp:Gene . - -bp:MolecularActivity a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path ] ; - sh:targetClass bp:MolecularActivity . - -linkml:Any a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass linkml:Any . - - a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path ] ; - sh:targetClass . - diff --git a/projects/biological_process/shex/biological_process.shex b/projects/biological_process/shex/biological_process.shex deleted file mode 100644 index 2b633d066..000000000 --- a/projects/biological_process/shex/biological_process.shex +++ /dev/null @@ -1,193 +0,0 @@ -BASE -PREFIX rdf: -PREFIX xsd: -PREFIX linkml: -PREFIX core: -PREFIX rdfs1: - - -linkml:String xsd:string - -linkml:Integer xsd:integer - -linkml:Boolean xsd:boolean - -linkml:Float xsd:float - -linkml:Double xsd:double - -linkml:Decimal xsd:decimal - -linkml:Time xsd:time - -linkml:Date xsd:date - -linkml:Datetime xsd:dateTime - -linkml:DateOrDatetime linkml:DateOrDatetime - -linkml:Uriorcurie IRI - -linkml:Curie xsd:string - -linkml:Uri IRI - -linkml:Ncname xsd:string - -linkml:Objectidentifier IRI - -linkml:Nodeidentifier NONLITERAL - -linkml:Jsonpointer xsd:string - -linkml:Jsonpath xsd:string - -linkml:Sparqlpath xsd:string - -core:AnnotatorResult CLOSED { - ( $core:AnnotatorResult_tes ( core:subject_text @linkml:String ? ; - core:object_id @linkml:String ? ; - core:object_text @linkml:String ? - ) ; - rdf:type [ core:AnnotatorResult ] ? - ) -} - -core:Any CLOSED { - ( $core:Any_tes rdf:type . * ; - rdf:type [ linkml:Any ] ? - ) -} - - CLOSED { - ( $ ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? ; - @linkml:String ? ; - @linkml:String ? ; - @linkml:String * ; - - @ ? ; - - @ * ; - - @ * ; - - @ * ; - @ * ; - - @ * - ) ; - rdf:type [ ] - ) -} - - CLOSED { - ( $ ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ ] - ) -} - -core:CompoundExpression ( - { - ( $core:CompoundExpression_tes rdf:type . * ; - rdf:type [ core:CompoundExpression ] ? - ) - } OR @core:Triple -) - -core:ExtractionResult CLOSED { - ( $core:ExtractionResult_tes ( core:input_id @linkml:String ? ; - core:input_title @linkml:String ? ; - core:input_text @linkml:String ? ; - core:raw_completion_output @linkml:String ? ; - core:prompt @linkml:String ? ; - core:extracted_object @core:Any ? ; - core:named_entities @core:Any * - ) ; - rdf:type [ core:ExtractionResult ] ? - ) -} - - CLOSED { - ( $ ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ ] - ) -} - - CLOSED { - ( $ ( - @ ? ; - - @ ? - ) ; - rdf:type [ ] ? - ) -} - - CLOSED { - ( $ ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ ] - ) -} - -core:NamedEntity ( - @ OR - @ OR - @ OR - @ OR @core:RelationshipType -) - -core:NamedEntity_struct { - ( $core:NamedEntity_tes rdfs1:label @linkml:String ? ; - rdf:type [ core:NamedEntity ] - ) -} - -core:Publication CLOSED { - ( $core:Publication_tes ( core:id @linkml:String ? ; - core:title @linkml:String ? ; - core:abstract @linkml:String ? ; - core:combined_text @linkml:String ? ; - core:full_text @linkml:String ? - ) ; - rdf:type [ core:Publication ] ? - ) -} - -core:RelationshipType CLOSED { - ( $core:RelationshipType_tes ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ core:RelationshipType ] - ) -} - -core:TextWithTriples CLOSED { - ( $core:TextWithTriples_tes ( core:publication @core:Publication ? ; - core:triples @core:Triple * - ) ; - rdf:type [ core:TextWithTriples ] ? - ) -} - -core:Triple { - ( $core:Triple_tes ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - core:subject @core:NamedEntity ? ; - core:predicate @core:RelationshipType ? ; - core:object @core:NamedEntity ? ; - core:qualifier @linkml:String ? ; - core:subject_qualifier @core:NamedEntity ? ; - core:object_qualifier @core:NamedEntity ? - ) ; - rdf:type [ core:Triple ] ? - ) -} - - diff --git a/projects/biological_process/sqlschema/biological_process.sql b/projects/biological_process/sqlschema/biological_process.sql deleted file mode 100644 index 8db0a7bd9..000000000 --- a/projects/biological_process/sqlschema/biological_process.sql +++ /dev/null @@ -1,88 +0,0 @@ - - -CREATE TABLE "AnnotatorResult" ( - subject_text TEXT, - object_id TEXT, - object_text TEXT, - PRIMARY KEY (subject_text, object_id, object_text) -); - -CREATE TABLE "BiologicalProcess" ( - id TEXT NOT NULL, - label TEXT, - description TEXT, - subclass_of TEXT, - inputs TEXT, - outputs TEXT, - steps TEXT, - genes TEXT, - PRIMARY KEY (id), - FOREIGN KEY(subclass_of) REFERENCES "BiologicalProcess" (id) -); - -CREATE TABLE "ChemicalEntity" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "ExtractionResult" ( - input_id TEXT, - input_title TEXT, - input_text TEXT, - raw_completion_output TEXT, - prompt TEXT, - extracted_object TEXT, - named_entities TEXT, - PRIMARY KEY (input_id, input_title, input_text, raw_completion_output, prompt, extracted_object, named_entities) -); - -CREATE TABLE "Gene" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "MolecularActivity" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Publication" ( - id TEXT, - title TEXT, - abstract TEXT, - combined_text TEXT, - full_text TEXT, - PRIMARY KEY (id, title, abstract, combined_text, full_text) -); - -CREATE TABLE "RelationshipType" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "TextWithTriples" ( - publication TEXT, - triples TEXT, - PRIMARY KEY (publication, triples) -); - -CREATE TABLE "GeneMolecularActivityRelationship" ( - gene TEXT, - molecular_activity TEXT, - "BiologicalProcess_id" TEXT, - PRIMARY KEY (gene, molecular_activity, "BiologicalProcess_id"), - FOREIGN KEY(gene) REFERENCES "Gene" (id), - FOREIGN KEY(molecular_activity) REFERENCES "MolecularActivity" (id), - FOREIGN KEY("BiologicalProcess_id") REFERENCES "BiologicalProcess" (id) -); - -CREATE TABLE "BiologicalProcess_synonyms" ( - backref_id TEXT, - synonyms TEXT, - PRIMARY KEY (backref_id, synonyms), - FOREIGN KEY(backref_id) REFERENCES "BiologicalProcess" (id) -); diff --git a/projects/biotic_interaction/biotic_interaction.py b/projects/biotic_interaction/biotic_interaction.py deleted file mode 100644 index c44a7c2a5..000000000 --- a/projects/biotic_interaction/biotic_interaction.py +++ /dev/null @@ -1,475 +0,0 @@ -# Auto generated from biotic_interaction.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-08-07T10:51:35 -# Schema: biotic-interaction-template -# -# id: https://w3id.org/ontogpt/biotic_interaction -# description: A template for biotic interactions -# license: https://creativecommons.org/publicdomain/zero/1.0/ - -import dataclasses -import sys -import re -from jsonasobj2 import JsonObj, as_dict -from typing import Optional, List, Union, Dict, ClassVar, Any -from dataclasses import dataclass -from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions - -from linkml_runtime.utils.slot import Slot -from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode -from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int -from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs -from linkml_runtime.utils.formatutils import camelcase, underscore, sfx -from linkml_runtime.utils.enumerations import EnumDefinitionImpl -from rdflib import Namespace, URIRef -from linkml_runtime.utils.curienamespace import CurieNamespace -from linkml_runtime.linkml_model.types import String - -metamodel_version = "1.7.0" -version = None - -# Overwrite dataclasses _init_fn to add **kwargs in __init__ -dataclasses._init_fn = dataclasses_init_fn_with_kwargs - -# Namespaces -COL = CurieNamespace('COL', 'https://www.catalogueoflife.org/data/taxon/') -GBIF = CurieNamespace('GBIF', 'https://www.gbif.org/species/') -ITIS = CurieNamespace('ITIS', 'https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=') -MESH = CurieNamespace('MESH', 'http://example.org/UNKNOWN/MESH/') -NCBITAXON = CurieNamespace('NCBITaxon', 'http://purl.obolibrary.org/obo/NCBITAXON_') -RO = CurieNamespace('RO', 'http://purl.obolibrary.org/obo/RO_') -BIOLINK = CurieNamespace('biolink', 'http://example.org/UNKNOWN/biolink/') -BP = CurieNamespace('bp', 'http://w3id.org/ontogpt/biotic-interaction-template') -COL = CurieNamespace('col', 'https://www.catalogueoflife.org/data/taxon/') -CORE = CurieNamespace('core', 'http://w3id.org/ontogpt/core/') -GBIF = CurieNamespace('gbif', 'https://www.gbif.org/species/') -ITIS = CurieNamespace('itis', 'https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=') -LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') -RDFS = CurieNamespace('rdfs', 'http://example.org/UNKNOWN/rdfs/') -DEFAULT_ = BP - - -# Types - -# Class references -class NamedEntityId(extended_str): - pass - - -class TaxonId(NamedEntityId): - pass - - -class InteractionTypeId(NamedEntityId): - pass - - -class RelationshipTypeId(NamedEntityId): - pass - - -@dataclass -class Container(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = BP.Container - class_class_curie: ClassVar[str] = "bp:Container" - class_name: ClassVar[str] = "Container" - class_model_uri: ClassVar[URIRef] = BP.Container - - interactions: Optional[Union[Union[dict, "BioticInteraction"], List[Union[dict, "BioticInteraction"]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if not isinstance(self.interactions, list): - self.interactions = [self.interactions] if self.interactions is not None else [] - self.interactions = [v if isinstance(v, BioticInteraction) else BioticInteraction(**as_dict(v)) for v in self.interactions] - - super().__post_init__(**kwargs) - - -@dataclass -class BioticInteraction(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = BP.BioticInteraction - class_class_curie: ClassVar[str] = "bp:BioticInteraction" - class_name: ClassVar[str] = "BioticInteraction" - class_model_uri: ClassVar[URIRef] = BP.BioticInteraction - - source_taxon: Optional[Union[str, TaxonId]] = None - target_taxon: Optional[Union[str, TaxonId]] = None - interaction_type: Optional[Union[str, InteractionTypeId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.source_taxon is not None and not isinstance(self.source_taxon, TaxonId): - self.source_taxon = TaxonId(self.source_taxon) - - if self.target_taxon is not None and not isinstance(self.target_taxon, TaxonId): - self.target_taxon = TaxonId(self.target_taxon) - - if self.interaction_type is not None and not isinstance(self.interaction_type, InteractionTypeId): - self.interaction_type = InteractionTypeId(self.interaction_type) - - super().__post_init__(**kwargs) - - -Any = Any - -@dataclass -class ExtractionResult(YAMLRoot): - """ - A result of extracting knowledge on text - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.ExtractionResult - class_class_curie: ClassVar[str] = "core:ExtractionResult" - class_name: ClassVar[str] = "ExtractionResult" - class_model_uri: ClassVar[URIRef] = BP.ExtractionResult - - input_id: Optional[str] = None - input_title: Optional[str] = None - input_text: Optional[str] = None - raw_completion_output: Optional[str] = None - prompt: Optional[str] = None - extracted_object: Optional[Union[dict, Any]] = None - named_entities: Optional[Union[Union[dict, Any], List[Union[dict, Any]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.input_id is not None and not isinstance(self.input_id, str): - self.input_id = str(self.input_id) - - if self.input_title is not None and not isinstance(self.input_title, str): - self.input_title = str(self.input_title) - - if self.input_text is not None and not isinstance(self.input_text, str): - self.input_text = str(self.input_text) - - if self.raw_completion_output is not None and not isinstance(self.raw_completion_output, str): - self.raw_completion_output = str(self.raw_completion_output) - - if self.prompt is not None and not isinstance(self.prompt, str): - self.prompt = str(self.prompt) - - super().__post_init__(**kwargs) - - -@dataclass -class NamedEntity(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.NamedEntity - class_class_curie: ClassVar[str] = "core:NamedEntity" - class_name: ClassVar[str] = "NamedEntity" - class_model_uri: ClassVar[URIRef] = BP.NamedEntity - - id: Union[str, NamedEntityId] = None - label: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, NamedEntityId): - self.id = NamedEntityId(self.id) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - super().__post_init__(**kwargs) - - -@dataclass -class Taxon(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = BP.Taxon - class_class_curie: ClassVar[str] = "bp:Taxon" - class_name: ClassVar[str] = "Taxon" - class_model_uri: ClassVar[URIRef] = BP.Taxon - - id: Union[str, TaxonId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, TaxonId): - self.id = TaxonId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class InteractionType(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = BP.InteractionType - class_class_curie: ClassVar[str] = "bp:InteractionType" - class_name: ClassVar[str] = "InteractionType" - class_model_uri: ClassVar[URIRef] = BP.InteractionType - - id: Union[str, InteractionTypeId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, InteractionTypeId): - self.id = InteractionTypeId(self.id) - - super().__post_init__(**kwargs) - - -class CompoundExpression(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.CompoundExpression - class_class_curie: ClassVar[str] = "core:CompoundExpression" - class_name: ClassVar[str] = "CompoundExpression" - class_model_uri: ClassVar[URIRef] = BP.CompoundExpression - - -@dataclass -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Triple - class_class_curie: ClassVar[str] = "core:Triple" - class_name: ClassVar[str] = "Triple" - class_model_uri: ClassVar[URIRef] = BP.Triple - - subject: Optional[Union[str, NamedEntityId]] = None - predicate: Optional[Union[str, RelationshipTypeId]] = None - object: Optional[Union[str, NamedEntityId]] = None - qualifier: Optional[str] = None - subject_qualifier: Optional[Union[str, NamedEntityId]] = None - object_qualifier: Optional[Union[str, NamedEntityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, NamedEntityId): - self.subject = NamedEntityId(self.subject) - - if self.predicate is not None and not isinstance(self.predicate, RelationshipTypeId): - self.predicate = RelationshipTypeId(self.predicate) - - if self.object is not None and not isinstance(self.object, NamedEntityId): - self.object = NamedEntityId(self.object) - - if self.qualifier is not None and not isinstance(self.qualifier, str): - self.qualifier = str(self.qualifier) - - if self.subject_qualifier is not None and not isinstance(self.subject_qualifier, NamedEntityId): - self.subject_qualifier = NamedEntityId(self.subject_qualifier) - - if self.object_qualifier is not None and not isinstance(self.object_qualifier, NamedEntityId): - self.object_qualifier = NamedEntityId(self.object_qualifier) - - super().__post_init__(**kwargs) - - -@dataclass -class TextWithTriples(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.TextWithTriples - class_class_curie: ClassVar[str] = "core:TextWithTriples" - class_name: ClassVar[str] = "TextWithTriples" - class_model_uri: ClassVar[URIRef] = BP.TextWithTriples - - publication: Optional[Union[dict, "Publication"]] = None - triples: Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.publication is not None and not isinstance(self.publication, Publication): - self.publication = Publication(**as_dict(self.publication)) - - if not isinstance(self.triples, list): - self.triples = [self.triples] if self.triples is not None else [] - self.triples = [v if isinstance(v, Triple) else Triple(**as_dict(v)) for v in self.triples] - - super().__post_init__(**kwargs) - - -@dataclass -class RelationshipType(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.RelationshipType - class_class_curie: ClassVar[str] = "core:RelationshipType" - class_name: ClassVar[str] = "RelationshipType" - class_model_uri: ClassVar[URIRef] = BP.RelationshipType - - id: Union[str, RelationshipTypeId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, RelationshipTypeId): - self.id = RelationshipTypeId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Publication(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Publication - class_class_curie: ClassVar[str] = "core:Publication" - class_name: ClassVar[str] = "Publication" - class_model_uri: ClassVar[URIRef] = BP.Publication - - id: Optional[str] = None - title: Optional[str] = None - abstract: Optional[str] = None - combined_text: Optional[str] = None - full_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.id is not None and not isinstance(self.id, str): - self.id = str(self.id) - - if self.title is not None and not isinstance(self.title, str): - self.title = str(self.title) - - if self.abstract is not None and not isinstance(self.abstract, str): - self.abstract = str(self.abstract) - - if self.combined_text is not None and not isinstance(self.combined_text, str): - self.combined_text = str(self.combined_text) - - if self.full_text is not None and not isinstance(self.full_text, str): - self.full_text = str(self.full_text) - - super().__post_init__(**kwargs) - - -@dataclass -class AnnotatorResult(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.AnnotatorResult - class_class_curie: ClassVar[str] = "core:AnnotatorResult" - class_name: ClassVar[str] = "AnnotatorResult" - class_model_uri: ClassVar[URIRef] = BP.AnnotatorResult - - subject_text: Optional[str] = None - object_id: Optional[str] = None - object_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject_text is not None and not isinstance(self.subject_text, str): - self.subject_text = str(self.subject_text) - - if self.object_id is not None and not isinstance(self.object_id, str): - self.object_id = str(self.object_id) - - if self.object_text is not None and not isinstance(self.object_text, str): - self.object_text = str(self.object_text) - - super().__post_init__(**kwargs) - - -# Enumerations -class NullDataOptions(EnumDefinitionImpl): - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = PermissibleValue(text="UNSPECIFIED_METHOD_OF_ADMINISTRATION", - meaning=NCIT.C149701) - NOT_APPLICABLE = PermissibleValue(text="NOT_APPLICABLE", - meaning=NCIT.C18902) - NOT_MENTIONED = PermissibleValue(text="NOT_MENTIONED") - - _defn = EnumDefinition( - name="NullDataOptions", - ) - -# Slots -class slots: - pass - -slots.container__interactions = Slot(uri=BP.interactions, name="container__interactions", curie=BP.curie('interactions'), - model_uri=BP.container__interactions, domain=None, range=Optional[Union[Union[dict, BioticInteraction], List[Union[dict, BioticInteraction]]]]) - -slots.bioticInteraction__source_taxon = Slot(uri=BP.source_taxon, name="bioticInteraction__source_taxon", curie=BP.curie('source_taxon'), - model_uri=BP.bioticInteraction__source_taxon, domain=None, range=Optional[Union[str, TaxonId]]) - -slots.bioticInteraction__target_taxon = Slot(uri=BP.target_taxon, name="bioticInteraction__target_taxon", curie=BP.curie('target_taxon'), - model_uri=BP.bioticInteraction__target_taxon, domain=None, range=Optional[Union[str, TaxonId]]) - -slots.bioticInteraction__interaction_type = Slot(uri=BP.interaction_type, name="bioticInteraction__interaction_type", curie=BP.curie('interaction_type'), - model_uri=BP.bioticInteraction__interaction_type, domain=None, range=Optional[Union[str, InteractionTypeId]]) - -slots.extractionResult__input_id = Slot(uri=CORE.input_id, name="extractionResult__input_id", curie=CORE.curie('input_id'), - model_uri=BP.extractionResult__input_id, domain=None, range=Optional[str]) - -slots.extractionResult__input_title = Slot(uri=CORE.input_title, name="extractionResult__input_title", curie=CORE.curie('input_title'), - model_uri=BP.extractionResult__input_title, domain=None, range=Optional[str]) - -slots.extractionResult__input_text = Slot(uri=CORE.input_text, name="extractionResult__input_text", curie=CORE.curie('input_text'), - model_uri=BP.extractionResult__input_text, domain=None, range=Optional[str]) - -slots.extractionResult__raw_completion_output = Slot(uri=CORE.raw_completion_output, name="extractionResult__raw_completion_output", curie=CORE.curie('raw_completion_output'), - model_uri=BP.extractionResult__raw_completion_output, domain=None, range=Optional[str]) - -slots.extractionResult__prompt = Slot(uri=CORE.prompt, name="extractionResult__prompt", curie=CORE.curie('prompt'), - model_uri=BP.extractionResult__prompt, domain=None, range=Optional[str]) - -slots.extractionResult__extracted_object = Slot(uri=CORE.extracted_object, name="extractionResult__extracted_object", curie=CORE.curie('extracted_object'), - model_uri=BP.extractionResult__extracted_object, domain=None, range=Optional[Union[dict, Any]]) - -slots.extractionResult__named_entities = Slot(uri=CORE.named_entities, name="extractionResult__named_entities", curie=CORE.curie('named_entities'), - model_uri=BP.extractionResult__named_entities, domain=None, range=Optional[Union[Union[dict, Any], List[Union[dict, Any]]]]) - -slots.namedEntity__id = Slot(uri=CORE.id, name="namedEntity__id", curie=CORE.curie('id'), - model_uri=BP.namedEntity__id, domain=None, range=URIRef) - -slots.namedEntity__label = Slot(uri=RDFS.label, name="namedEntity__label", curie=RDFS.curie('label'), - model_uri=BP.namedEntity__label, domain=None, range=Optional[str]) - -slots.triple__subject = Slot(uri=CORE.subject, name="triple__subject", curie=CORE.curie('subject'), - model_uri=BP.triple__subject, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__predicate = Slot(uri=CORE.predicate, name="triple__predicate", curie=CORE.curie('predicate'), - model_uri=BP.triple__predicate, domain=None, range=Optional[Union[str, RelationshipTypeId]]) - -slots.triple__object = Slot(uri=CORE.object, name="triple__object", curie=CORE.curie('object'), - model_uri=BP.triple__object, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__qualifier = Slot(uri=CORE.qualifier, name="triple__qualifier", curie=CORE.curie('qualifier'), - model_uri=BP.triple__qualifier, domain=None, range=Optional[str]) - -slots.triple__subject_qualifier = Slot(uri=CORE.subject_qualifier, name="triple__subject_qualifier", curie=CORE.curie('subject_qualifier'), - model_uri=BP.triple__subject_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__object_qualifier = Slot(uri=CORE.object_qualifier, name="triple__object_qualifier", curie=CORE.curie('object_qualifier'), - model_uri=BP.triple__object_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.textWithTriples__publication = Slot(uri=CORE.publication, name="textWithTriples__publication", curie=CORE.curie('publication'), - model_uri=BP.textWithTriples__publication, domain=None, range=Optional[Union[dict, Publication]]) - -slots.textWithTriples__triples = Slot(uri=CORE.triples, name="textWithTriples__triples", curie=CORE.curie('triples'), - model_uri=BP.textWithTriples__triples, domain=None, range=Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]]) - -slots.publication__id = Slot(uri=CORE.id, name="publication__id", curie=CORE.curie('id'), - model_uri=BP.publication__id, domain=None, range=Optional[str]) - -slots.publication__title = Slot(uri=CORE.title, name="publication__title", curie=CORE.curie('title'), - model_uri=BP.publication__title, domain=None, range=Optional[str]) - -slots.publication__abstract = Slot(uri=CORE.abstract, name="publication__abstract", curie=CORE.curie('abstract'), - model_uri=BP.publication__abstract, domain=None, range=Optional[str]) - -slots.publication__combined_text = Slot(uri=CORE.combined_text, name="publication__combined_text", curie=CORE.curie('combined_text'), - model_uri=BP.publication__combined_text, domain=None, range=Optional[str]) - -slots.publication__full_text = Slot(uri=CORE.full_text, name="publication__full_text", curie=CORE.curie('full_text'), - model_uri=BP.publication__full_text, domain=None, range=Optional[str]) - -slots.annotatorResult__subject_text = Slot(uri=CORE.subject_text, name="annotatorResult__subject_text", curie=CORE.curie('subject_text'), - model_uri=BP.annotatorResult__subject_text, domain=None, range=Optional[str]) - -slots.annotatorResult__object_id = Slot(uri=CORE.object_id, name="annotatorResult__object_id", curie=CORE.curie('object_id'), - model_uri=BP.annotatorResult__object_id, domain=None, range=Optional[str]) - -slots.annotatorResult__object_text = Slot(uri=CORE.object_text, name="annotatorResult__object_text", curie=CORE.curie('object_text'), - model_uri=BP.annotatorResult__object_text, domain=None, range=Optional[str]) \ No newline at end of file diff --git a/projects/biotic_interaction/docs/AnnotatorResult.md b/projects/biotic_interaction/docs/AnnotatorResult.md deleted file mode 100644 index db84c2ba4..000000000 --- a/projects/biotic_interaction/docs/AnnotatorResult.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Class: AnnotatorResult - - - - -URI: [bp:AnnotatorResult](http://w3id.org/ontogpt/biotic-interaction-templateAnnotatorResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F])](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F]) - -## Attributes - - -### Own - - * [➞subject_text](annotatorResult__subject_text.md) 0..1 - * Range: [String](types/String.md) - * [➞object_id](annotatorResult__object_id.md) 0..1 - * Range: [String](types/String.md) - * [➞object_text](annotatorResult__object_text.md) 0..1 - * Range: [String](types/String.md) diff --git a/projects/biotic_interaction/docs/Any.md b/projects/biotic_interaction/docs/Any.md deleted file mode 100644 index e75fec3d0..000000000 --- a/projects/biotic_interaction/docs/Any.md +++ /dev/null @@ -1,25 +0,0 @@ - -# Class: Any - - - - -URI: [bp:Any](http://w3id.org/ontogpt/biotic-interaction-templateAny) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult])](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult]) - -## Referenced by Class - - * **None** *[➞extracted_object](extractionResult__extracted_object.md)* 0..1 **[Any](Any.md)** - * **None** *[➞named_entities](extractionResult__named_entities.md)* 0..\* **[Any](Any.md)** - -## Attributes - - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | linkml:Any | - diff --git a/projects/biotic_interaction/docs/BioticInteraction.md b/projects/biotic_interaction/docs/BioticInteraction.md deleted file mode 100644 index d7643307b..000000000 --- a/projects/biotic_interaction/docs/BioticInteraction.md +++ /dev/null @@ -1,29 +0,0 @@ - -# Class: BioticInteraction - - - - -URI: [bp:BioticInteraction](http://w3id.org/ontogpt/biotic-interaction-templateBioticInteraction) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Taxon],[InteractionType],[InteractionType][BioticInteraction],[Container])](https://yuml.me/diagram/nofunky;dir:TB/class/[Taxon],[InteractionType],[InteractionType][BioticInteraction],[Container]) - -## Referenced by Class - - * **None** *[➞interactions](container__interactions.md)* 0..\* **[BioticInteraction](BioticInteraction.md)** - -## Attributes - - -### Own - - * [➞source_taxon](bioticInteraction__source_taxon.md) 0..1 - * Description: the taxon that is the subject of the interaction - * Range: [Taxon](Taxon.md) - * [➞target_taxon](bioticInteraction__target_taxon.md) 0..1 - * Description: the taxon that is the object of the ineteraction - * Range: [Taxon](Taxon.md) - * [➞interaction_type](bioticInteraction__interaction_type.md) 0..1 - * Description: the type of interaction - * Range: [InteractionType](InteractionType.md) diff --git a/projects/biotic_interaction/docs/CompoundExpression.md b/projects/biotic_interaction/docs/CompoundExpression.md deleted file mode 100644 index 9731c53d6..000000000 --- a/projects/biotic_interaction/docs/CompoundExpression.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: CompoundExpression - - - - -URI: [bp:CompoundExpression](http://w3id.org/ontogpt/biotic-interaction-templateCompoundExpression) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[CompoundExpression]^-[Triple])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[CompoundExpression]^-[Triple]) - -## Children - - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - -## Referenced by Class - - -## Attributes - diff --git a/projects/biotic_interaction/docs/Container.md b/projects/biotic_interaction/docs/Container.md deleted file mode 100644 index ff46a8278..000000000 --- a/projects/biotic_interaction/docs/Container.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Class: Container - - - - -URI: [bp:Container](http://w3id.org/ontogpt/biotic-interaction-templateContainer) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[BioticInteraction]0..\* - * Range: [BioticInteraction](BioticInteraction.md) diff --git a/projects/biotic_interaction/docs/ExtractionResult.md b/projects/biotic_interaction/docs/ExtractionResult.md deleted file mode 100644 index 3777dbc52..000000000 --- a/projects/biotic_interaction/docs/ExtractionResult.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Class: ExtractionResult - - -A result of extracting knowledge on text - -URI: [bp:ExtractionResult](http://w3id.org/ontogpt/biotic-interaction-templateExtractionResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]0..1 - * Range: [String](types/String.md) - * [➞input_title](extractionResult__input_title.md) 0..1 - * Range: [String](types/String.md) - * [➞input_text](extractionResult__input_text.md) 0..1 - * Range: [String](types/String.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) 0..1 - * Range: [String](types/String.md) - * [➞prompt](extractionResult__prompt.md) 0..1 - * Range: [String](types/String.md) - * [➞extracted_object](extractionResult__extracted_object.md) 0..1 - * Description: The complex objects extracted from the text - * Range: [Any](Any.md) - * [➞named_entities](extractionResult__named_entities.md) 0..\* - * Description: Named entities extracted from the text - * Range: [Any](Any.md) diff --git a/projects/biotic_interaction/docs/InteractionType.md b/projects/biotic_interaction/docs/InteractionType.md deleted file mode 100644 index a7095cdb4..000000000 --- a/projects/biotic_interaction/docs/InteractionType.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: InteractionType - - - - -URI: [bp:InteractionType](http://w3id.org/ontogpt/biotic-interaction-templateInteractionType) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[BioticInteraction]-%20interaction_type%200..1>[InteractionType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[InteractionType],[BioticInteraction])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[BioticInteraction]-%20interaction_type%200..1>[InteractionType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[InteractionType],[BioticInteraction]) - -## Identifier prefixes - - * RO - * MESH - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞interaction_type](bioticInteraction__interaction_type.md)* 0..1 **[InteractionType](InteractionType.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) 1..1 - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) 0..1 - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/biotic_interaction/docs/NamedEntity.md b/projects/biotic_interaction/docs/NamedEntity.md deleted file mode 100644 index 67f9ded39..000000000 --- a/projects/biotic_interaction/docs/NamedEntity.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: NamedEntity - - - - -URI: [bp:NamedEntity](http://w3id.org/ontogpt/biotic-interaction-templateNamedEntity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Taxon],[RelationshipType],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[Taxon],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[InteractionType],[Triple],[InteractionType])](https://yuml.me/diagram/nofunky;dir:TB/class/[Taxon],[RelationshipType],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[Taxon],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[InteractionType],[Triple],[InteractionType]) - -## Children - - * [InteractionType](InteractionType.md) - * [RelationshipType](RelationshipType.md) - * [Taxon](Taxon.md) - -## Referenced by Class - - * **None** *[➞object](triple__object.md)* 0..1 **[NamedEntity](NamedEntity.md)** - * **None** *[➞object_qualifier](triple__object_qualifier.md)* 0..1 **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject](triple__subject.md)* 0..1 **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject_qualifier](triple__subject_qualifier.md)* 0..1 **[NamedEntity](NamedEntity.md)** - -## Attributes - - -### Own - - * [➞id](namedEntity__id.md) 1..1 - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) 0..1 - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/biotic_interaction/docs/NullDataOptions.md b/projects/biotic_interaction/docs/NullDataOptions.md deleted file mode 100644 index dedb0768c..000000000 --- a/projects/biotic_interaction/docs/NullDataOptions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Enum: NullDataOptions - - - - -URI: [bp:NullDataOptions](http://w3id.org/ontogpt/biotic-interaction-templateNullDataOptions) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | -| UNSPECIFIED_METHOD_OF_ADMINISTRATION | | NCIT:C149701 | | -| NOT_APPLICABLE | | NCIT:C18902 | {'aliases': ['not applicable', 'N/A']} | -| NOT_MENTIONED | | | | - diff --git a/projects/biotic_interaction/docs/Publication.md b/projects/biotic_interaction/docs/Publication.md deleted file mode 100644 index af9abc833..000000000 --- a/projects/biotic_interaction/docs/Publication.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Publication - - - - -URI: [bp:Publication](http://w3id.org/ontogpt/biotic-interaction-templatePublication) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples])](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples]) - -## Referenced by Class - - * **None** *[➞publication](textWithTriples__publication.md)* 0..1 **[Publication](Publication.md)** - -## Attributes - - -### Own - - * [➞id](publication__id.md) 0..1 - * Description: The publication identifier - * Range: [String](types/String.md) - * [➞title](publication__title.md) 0..1 - * Description: The title of the publication - * Range: [String](types/String.md) - * [➞abstract](publication__abstract.md) 0..1 - * Description: The abstract of the publication - * Range: [String](types/String.md) - * [➞combined_text](publication__combined_text.md) 0..1 - * Range: [String](types/String.md) - * [➞full_text](publication__full_text.md) 0..1 - * Description: The full text of the publication - * Range: [String](types/String.md) diff --git a/projects/biotic_interaction/docs/RelationshipType.md b/projects/biotic_interaction/docs/RelationshipType.md deleted file mode 100644 index 378def0cb..000000000 --- a/projects/biotic_interaction/docs/RelationshipType.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: RelationshipType - - - - -URI: [bp:RelationshipType](http://w3id.org/ontogpt/biotic-interaction-templateRelationshipType) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity]) - -## Identifier prefixes - - * RO - * biolink - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞predicate](triple__predicate.md)* 0..1 **[RelationshipType](RelationshipType.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) 1..1 - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) 0..1 - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/biotic_interaction/docs/Taxon.md b/projects/biotic_interaction/docs/Taxon.md deleted file mode 100644 index d53213fb9..000000000 --- a/projects/biotic_interaction/docs/Taxon.md +++ /dev/null @@ -1,38 +0,0 @@ - -# Class: Taxon - - - - -URI: [bp:Taxon](http://w3id.org/ontogpt/biotic-interaction-templateTaxon) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[BioticInteraction]-%20source_taxon%200..1>[Taxon|id(i):string;label(i):string%20%3F],[BioticInteraction]-%20target_taxon%200..1>[Taxon],[NamedEntity]^-[Taxon],[NamedEntity],[BioticInteraction])](https://yuml.me/diagram/nofunky;dir:TB/class/[BioticInteraction]-%20source_taxon%200..1>[Taxon|id(i):string;label(i):string%20%3F],[BioticInteraction]-%20target_taxon%200..1>[Taxon],[NamedEntity]^-[Taxon],[NamedEntity],[BioticInteraction]) - -## Identifier prefixes - - * NCBITaxon - * COL - * ITIS - * GBIF - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞source_taxon](bioticInteraction__source_taxon.md)* 0..1 **[Taxon](Taxon.md)** - * **None** *[➞target_taxon](bioticInteraction__target_taxon.md)* 0..1 **[Taxon](Taxon.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) 1..1 - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) 0..1 - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/biotic_interaction/docs/TextWithTriples.md b/projects/biotic_interaction/docs/TextWithTriples.md deleted file mode 100644 index f7e378a44..000000000 --- a/projects/biotic_interaction/docs/TextWithTriples.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: TextWithTriples - - - - -URI: [bp:TextWithTriples](http://w3id.org/ontogpt/biotic-interaction-templateTextWithTriples) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]0..1 - * Range: [Publication](Publication.md) - * [➞triples](textWithTriples__triples.md) 0..\* - * Range: [Triple](Triple.md) diff --git a/projects/biotic_interaction/docs/Triple.md b/projects/biotic_interaction/docs/Triple.md deleted file mode 100644 index 3024d96ee..000000000 --- a/projects/biotic_interaction/docs/Triple.md +++ /dev/null @@ -1,39 +0,0 @@ - -# Class: Triple - - -Abstract parent for Relation Extraction tasks - -URI: [bp:Triple](http://w3id.org/ontogpt/biotic-interaction-templateTriple) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity][Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity][Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞triples](textWithTriples__triples.md)* 0..\* **[Triple](Triple.md)** - -## Attributes - - -### Own - - * [➞subject](triple__subject.md) 0..1 - * Range: [NamedEntity](NamedEntity.md) - * [➞predicate](triple__predicate.md) 0..1 - * Range: [RelationshipType](RelationshipType.md) - * [➞object](triple__object.md) 0..1 - * Range: [NamedEntity](NamedEntity.md) - * [➞qualifier](triple__qualifier.md) 0..1 - * Description: A qualifier for the statements, e.g. "NOT" for negation - * Range: [String](types/String.md) - * [➞subject_qualifier](triple__subject_qualifier.md) 0..1 - * Description: An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - * Range: [NamedEntity](NamedEntity.md) - * [➞object_qualifier](triple__object_qualifier.md) 0..1 - * Description: An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * Range: [NamedEntity](NamedEntity.md) diff --git a/projects/biotic_interaction/docs/annotatorResult__object_id.md b/projects/biotic_interaction/docs/annotatorResult__object_id.md deleted file mode 100644 index 18710c6b5..000000000 --- a/projects/biotic_interaction/docs/annotatorResult__object_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_id - - - - -URI: [bp:annotatorResult__object_id](http://w3id.org/ontogpt/biotic-interaction-templateannotatorResult__object_id) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/biotic_interaction/docs/annotatorResult__object_text.md b/projects/biotic_interaction/docs/annotatorResult__object_text.md deleted file mode 100644 index d35c5967d..000000000 --- a/projects/biotic_interaction/docs/annotatorResult__object_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_text - - - - -URI: [bp:annotatorResult__object_text](http://w3id.org/ontogpt/biotic-interaction-templateannotatorResult__object_text) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/biotic_interaction/docs/annotatorResult__subject_text.md b/projects/biotic_interaction/docs/annotatorResult__subject_text.md deleted file mode 100644 index 48d7020c1..000000000 --- a/projects/biotic_interaction/docs/annotatorResult__subject_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_text - - - - -URI: [bp:annotatorResult__subject_text](http://w3id.org/ontogpt/biotic-interaction-templateannotatorResult__subject_text) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/biotic_interaction/docs/bioticInteraction__interaction_type.md b/projects/biotic_interaction/docs/bioticInteraction__interaction_type.md deleted file mode 100644 index d506fc797..000000000 --- a/projects/biotic_interaction/docs/bioticInteraction__interaction_type.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: interaction_type - - -the type of interaction - -URI: [bp:bioticInteraction__interaction_type](http://w3id.org/ontogpt/biotic-interaction-templatebioticInteraction__interaction_type) - - -## Domain and Range - -None → 0..1 [InteractionType](InteractionType.md) - -## Parents - - -## Children - - -## Used by - - * [BioticInteraction](BioticInteraction.md) diff --git a/projects/biotic_interaction/docs/bioticInteraction__source_taxon.md b/projects/biotic_interaction/docs/bioticInteraction__source_taxon.md deleted file mode 100644 index 0bb5a6319..000000000 --- a/projects/biotic_interaction/docs/bioticInteraction__source_taxon.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: source_taxon - - -the taxon that is the subject of the interaction - -URI: [bp:bioticInteraction__source_taxon](http://w3id.org/ontogpt/biotic-interaction-templatebioticInteraction__source_taxon) - - -## Domain and Range - -None → 0..1 [Taxon](Taxon.md) - -## Parents - - -## Children - - -## Used by - - * [BioticInteraction](BioticInteraction.md) diff --git a/projects/biotic_interaction/docs/bioticInteraction__target_taxon.md b/projects/biotic_interaction/docs/bioticInteraction__target_taxon.md deleted file mode 100644 index f257c11c8..000000000 --- a/projects/biotic_interaction/docs/bioticInteraction__target_taxon.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: target_taxon - - -the taxon that is the object of the ineteraction - -URI: [bp:bioticInteraction__target_taxon](http://w3id.org/ontogpt/biotic-interaction-templatebioticInteraction__target_taxon) - - -## Domain and Range - -None → 0..1 [Taxon](Taxon.md) - -## Parents - - -## Children - - -## Used by - - * [BioticInteraction](BioticInteraction.md) diff --git a/projects/biotic_interaction/docs/biotic_interaction.md b/projects/biotic_interaction/docs/biotic_interaction.md deleted file mode 100644 index 30ad25250..000000000 --- a/projects/biotic_interaction/docs/biotic_interaction.md +++ /dev/null @@ -1,111 +0,0 @@ - -# biotic-interaction-template - - -**metamodel version:** 1.7.0 - -**version:** None - - -A template for biotic interactions - - -### Classes - - * [AnnotatorResult](AnnotatorResult.md) - * [Any](Any.md) - * [BioticInteraction](BioticInteraction.md) - * [CompoundExpression](CompoundExpression.md) - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - * [Container](Container.md) - * [ExtractionResult](ExtractionResult.md) - A result of extracting knowledge on text - * [NamedEntity](NamedEntity.md) - * [InteractionType](InteractionType.md) - * [RelationshipType](RelationshipType.md) - * [Taxon](Taxon.md) - * [Publication](Publication.md) - * [TextWithTriples](TextWithTriples.md) - -### Mixins - - -### Slots - - * [➞object_id](annotatorResult__object_id.md) - * [➞object_text](annotatorResult__object_text.md) - * [➞subject_text](annotatorResult__subject_text.md) - * [➞interaction_type](bioticInteraction__interaction_type.md) - the type of interaction - * [➞source_taxon](bioticInteraction__source_taxon.md) - the taxon that is the subject of the interaction - * [➞target_taxon](bioticInteraction__target_taxon.md) - the taxon that is the object of the ineteraction - * [➞interactions](container__interactions.md) - * [➞extracted_object](extractionResult__extracted_object.md) - The complex objects extracted from the text - * [➞input_id](extractionResult__input_id.md) - * [➞input_text](extractionResult__input_text.md) - * [➞input_title](extractionResult__input_title.md) - * [➞named_entities](extractionResult__named_entities.md) - Named entities extracted from the text - * [➞prompt](extractionResult__prompt.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) - * [➞id](namedEntity__id.md) - A unique identifier for the named entity - * [➞label](namedEntity__label.md) - The label (name) of the named thing - * [➞abstract](publication__abstract.md) - The abstract of the publication - * [➞combined_text](publication__combined_text.md) - * [➞full_text](publication__full_text.md) - The full text of the publication - * [➞id](publication__id.md) - The publication identifier - * [➞title](publication__title.md) - The title of the publication - * [➞publication](textWithTriples__publication.md) - * [➞triples](textWithTriples__triples.md) - * [➞object](triple__object.md) - * [➞object_qualifier](triple__object_qualifier.md) - An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * [➞predicate](triple__predicate.md) - * [➞qualifier](triple__qualifier.md) - A qualifier for the statements, e.g. "NOT" for negation - * [➞subject](triple__subject.md) - * [➞subject_qualifier](triple__subject_qualifier.md) - An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -### Enums - - * [NullDataOptions](NullDataOptions.md) - -### Subsets - - -### Types - - -#### Built in - - * **Bool** - * **Curie** - * **Decimal** - * **ElementIdentifier** - * **NCName** - * **NodeIdentifier** - * **URI** - * **URIorCURIE** - * **XSDDate** - * **XSDDateTime** - * **XSDTime** - * **float** - * **int** - * **str** - -#### Defined - - * [Boolean](types/Boolean.md) (**Bool**) - A binary (true or false) value - * [Curie](types/Curie.md) (**Curie**) - a compact URI - * [Date](types/Date.md) (**XSDDate**) - a date (year, month and day) in an idealized calendar - * [DateOrDatetime](types/DateOrDatetime.md) (**str**) - Either a date or a datetime - * [Datetime](types/Datetime.md) (**XSDDateTime**) - The combination of a date and time - * [Decimal](types/Decimal.md) (**Decimal**) - A real number with arbitrary precision that conforms to the xsd:decimal specification - * [Double](types/Double.md) (**float**) - A real number that conforms to the xsd:double specification - * [Float](types/Float.md) (**float**) - A real number that conforms to the xsd:float specification - * [Integer](types/Integer.md) (**int**) - An integer - * [Jsonpath](types/Jsonpath.md) (**str**) - A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - * [Jsonpointer](types/Jsonpointer.md) (**str**) - A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - * [Ncname](types/Ncname.md) (**NCName**) - Prefix part of CURIE - * [Nodeidentifier](types/Nodeidentifier.md) (**NodeIdentifier**) - A URI, CURIE or BNODE that represents a node in a model. - * [Objectidentifier](types/Objectidentifier.md) (**ElementIdentifier**) - A URI or CURIE that represents an object in the model. - * [Sparqlpath](types/Sparqlpath.md) (**str**) - A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - * [String](types/String.md) (**str**) - A character string - * [Time](types/Time.md) (**XSDTime**) - A time object represents a (local) time of day, independent of any particular day - * [Uri](types/Uri.md) (**URI**) - a complete URI - * [Uriorcurie](types/Uriorcurie.md) (**URIorCURIE**) - a URI or a CURIE diff --git a/projects/biotic_interaction/docs/container__interactions.md b/projects/biotic_interaction/docs/container__interactions.md deleted file mode 100644 index 414cadbcf..000000000 --- a/projects/biotic_interaction/docs/container__interactions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: interactions - - - - -URI: [bp:container__interactions](http://w3id.org/ontogpt/biotic-interaction-templatecontainer__interactions) - - -## Domain and Range - -None → 0..\* [BioticInteraction](BioticInteraction.md) - -## Parents - - -## Children - - -## Used by - - * [Container](Container.md) diff --git a/projects/biotic_interaction/docs/extractionResult__extracted_object.md b/projects/biotic_interaction/docs/extractionResult__extracted_object.md deleted file mode 100644 index efd3d1c4c..000000000 --- a/projects/biotic_interaction/docs/extractionResult__extracted_object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: extracted_object - - -The complex objects extracted from the text - -URI: [bp:extractionResult__extracted_object](http://w3id.org/ontogpt/biotic-interaction-templateextractionResult__extracted_object) - - -## Domain and Range - -None → 0..1 [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/biotic_interaction/docs/extractionResult__input_id.md b/projects/biotic_interaction/docs/extractionResult__input_id.md deleted file mode 100644 index 87ef8b964..000000000 --- a/projects/biotic_interaction/docs/extractionResult__input_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_id - - - - -URI: [bp:extractionResult__input_id](http://w3id.org/ontogpt/biotic-interaction-templateextractionResult__input_id) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/biotic_interaction/docs/extractionResult__input_text.md b/projects/biotic_interaction/docs/extractionResult__input_text.md deleted file mode 100644 index f193ada62..000000000 --- a/projects/biotic_interaction/docs/extractionResult__input_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_text - - - - -URI: [bp:extractionResult__input_text](http://w3id.org/ontogpt/biotic-interaction-templateextractionResult__input_text) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/biotic_interaction/docs/extractionResult__input_title.md b/projects/biotic_interaction/docs/extractionResult__input_title.md deleted file mode 100644 index c663e1e7e..000000000 --- a/projects/biotic_interaction/docs/extractionResult__input_title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_title - - - - -URI: [bp:extractionResult__input_title](http://w3id.org/ontogpt/biotic-interaction-templateextractionResult__input_title) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/biotic_interaction/docs/extractionResult__named_entities.md b/projects/biotic_interaction/docs/extractionResult__named_entities.md deleted file mode 100644 index 68c893212..000000000 --- a/projects/biotic_interaction/docs/extractionResult__named_entities.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: named_entities - - -Named entities extracted from the text - -URI: [bp:extractionResult__named_entities](http://w3id.org/ontogpt/biotic-interaction-templateextractionResult__named_entities) - - -## Domain and Range - -None → 0..\* [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/biotic_interaction/docs/extractionResult__prompt.md b/projects/biotic_interaction/docs/extractionResult__prompt.md deleted file mode 100644 index 78879550a..000000000 --- a/projects/biotic_interaction/docs/extractionResult__prompt.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: prompt - - - - -URI: [bp:extractionResult__prompt](http://w3id.org/ontogpt/biotic-interaction-templateextractionResult__prompt) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/biotic_interaction/docs/extractionResult__raw_completion_output.md b/projects/biotic_interaction/docs/extractionResult__raw_completion_output.md deleted file mode 100644 index 9b6e6e45e..000000000 --- a/projects/biotic_interaction/docs/extractionResult__raw_completion_output.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: raw_completion_output - - - - -URI: [bp:extractionResult__raw_completion_output](http://w3id.org/ontogpt/biotic-interaction-templateextractionResult__raw_completion_output) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/biotic_interaction/docs/namedEntity__id.md b/projects/biotic_interaction/docs/namedEntity__id.md deleted file mode 100644 index 14356b649..000000000 --- a/projects/biotic_interaction/docs/namedEntity__id.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Slot: id - - -A unique identifier for the named entity - -URI: [bp:namedEntity__id](http://w3id.org/ontogpt/biotic-interaction-templatenamedEntity__id) - - -## Domain and Range - -None → 1..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [InteractionType](InteractionType.md) - * [NamedEntity](NamedEntity.md) - * [RelationshipType](RelationshipType.md) - * [Taxon](Taxon.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | this is populated during the grounding and normalization step | - diff --git a/projects/biotic_interaction/docs/namedEntity__label.md b/projects/biotic_interaction/docs/namedEntity__label.md deleted file mode 100644 index cde2f631a..000000000 --- a/projects/biotic_interaction/docs/namedEntity__label.md +++ /dev/null @@ -1,33 +0,0 @@ - -# Slot: label - - -The label (name) of the named thing - -URI: [bp:namedEntity__label](http://w3id.org/ontogpt/biotic-interaction-templatenamedEntity__label) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [InteractionType](InteractionType.md) - * [NamedEntity](NamedEntity.md) - * [RelationshipType](RelationshipType.md) - * [Taxon](Taxon.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Aliases:** | | name | -| **Mappings:** | | rdfs:label | - diff --git a/projects/biotic_interaction/docs/publication__abstract.md b/projects/biotic_interaction/docs/publication__abstract.md deleted file mode 100644 index af0167b2a..000000000 --- a/projects/biotic_interaction/docs/publication__abstract.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: abstract - - -The abstract of the publication - -URI: [bp:publication__abstract](http://w3id.org/ontogpt/biotic-interaction-templatepublication__abstract) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/biotic_interaction/docs/publication__combined_text.md b/projects/biotic_interaction/docs/publication__combined_text.md deleted file mode 100644 index b72ba43fd..000000000 --- a/projects/biotic_interaction/docs/publication__combined_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: combined_text - - - - -URI: [bp:publication__combined_text](http://w3id.org/ontogpt/biotic-interaction-templatepublication__combined_text) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/biotic_interaction/docs/publication__full_text.md b/projects/biotic_interaction/docs/publication__full_text.md deleted file mode 100644 index 88567808f..000000000 --- a/projects/biotic_interaction/docs/publication__full_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: full_text - - -The full text of the publication - -URI: [bp:publication__full_text](http://w3id.org/ontogpt/biotic-interaction-templatepublication__full_text) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/biotic_interaction/docs/publication__id.md b/projects/biotic_interaction/docs/publication__id.md deleted file mode 100644 index 3e49e00d9..000000000 --- a/projects/biotic_interaction/docs/publication__id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: id - - -The publication identifier - -URI: [bp:publication__id](http://w3id.org/ontogpt/biotic-interaction-templatepublication__id) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/biotic_interaction/docs/publication__title.md b/projects/biotic_interaction/docs/publication__title.md deleted file mode 100644 index 2c6e2030a..000000000 --- a/projects/biotic_interaction/docs/publication__title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: title - - -The title of the publication - -URI: [bp:publication__title](http://w3id.org/ontogpt/biotic-interaction-templatepublication__title) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/biotic_interaction/docs/textWithTriples__publication.md b/projects/biotic_interaction/docs/textWithTriples__publication.md deleted file mode 100644 index 704695d79..000000000 --- a/projects/biotic_interaction/docs/textWithTriples__publication.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: publication - - - - -URI: [bp:textWithTriples__publication](http://w3id.org/ontogpt/biotic-interaction-templatetextWithTriples__publication) - - -## Domain and Range - -None → 0..1 [Publication](Publication.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/biotic_interaction/docs/textWithTriples__triples.md b/projects/biotic_interaction/docs/textWithTriples__triples.md deleted file mode 100644 index fd4d50e1d..000000000 --- a/projects/biotic_interaction/docs/textWithTriples__triples.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: triples - - - - -URI: [bp:textWithTriples__triples](http://w3id.org/ontogpt/biotic-interaction-templatetextWithTriples__triples) - - -## Domain and Range - -None → 0..\* [Triple](Triple.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/biotic_interaction/docs/triple__object.md b/projects/biotic_interaction/docs/triple__object.md deleted file mode 100644 index 30f531cf8..000000000 --- a/projects/biotic_interaction/docs/triple__object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object - - - - -URI: [bp:triple__object](http://w3id.org/ontogpt/biotic-interaction-templatetriple__object) - - -## Domain and Range - -None → 0..1 [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/biotic_interaction/docs/triple__object_qualifier.md b/projects/biotic_interaction/docs/triple__object_qualifier.md deleted file mode 100644 index 12af0c071..000000000 --- a/projects/biotic_interaction/docs/triple__object_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_qualifier - - -An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - -URI: [bp:triple__object_qualifier](http://w3id.org/ontogpt/biotic-interaction-templatetriple__object_qualifier) - - -## Domain and Range - -None → 0..1 [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/biotic_interaction/docs/triple__predicate.md b/projects/biotic_interaction/docs/triple__predicate.md deleted file mode 100644 index 4ef988d55..000000000 --- a/projects/biotic_interaction/docs/triple__predicate.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: predicate - - - - -URI: [bp:triple__predicate](http://w3id.org/ontogpt/biotic-interaction-templatetriple__predicate) - - -## Domain and Range - -None → 0..1 [RelationshipType](RelationshipType.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/biotic_interaction/docs/triple__qualifier.md b/projects/biotic_interaction/docs/triple__qualifier.md deleted file mode 100644 index 7794cfcdf..000000000 --- a/projects/biotic_interaction/docs/triple__qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: qualifier - - -A qualifier for the statements, e.g. "NOT" for negation - -URI: [bp:triple__qualifier](http://w3id.org/ontogpt/biotic-interaction-templatetriple__qualifier) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/biotic_interaction/docs/triple__subject.md b/projects/biotic_interaction/docs/triple__subject.md deleted file mode 100644 index 9571ca4d5..000000000 --- a/projects/biotic_interaction/docs/triple__subject.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject - - - - -URI: [bp:triple__subject](http://w3id.org/ontogpt/biotic-interaction-templatetriple__subject) - - -## Domain and Range - -None → 0..1 [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/biotic_interaction/docs/triple__subject_qualifier.md b/projects/biotic_interaction/docs/triple__subject_qualifier.md deleted file mode 100644 index ed6d2dbff..000000000 --- a/projects/biotic_interaction/docs/triple__subject_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_qualifier - - -An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -URI: [bp:triple__subject_qualifier](http://w3id.org/ontogpt/biotic-interaction-templatetriple__subject_qualifier) - - -## Domain and Range - -None → 0..1 [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/biotic_interaction/docs/types/Boolean.md b/projects/biotic_interaction/docs/types/Boolean.md deleted file mode 100644 index dc83a9c6e..000000000 --- a/projects/biotic_interaction/docs/types/Boolean.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: boolean - - -A binary (true or false) value - -URI: [linkml:Boolean](https://w3id.org/linkml/Boolean) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Bool** | -| Representation | | bool | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Boolean | - diff --git a/projects/biotic_interaction/docs/types/Curie.md b/projects/biotic_interaction/docs/types/Curie.md deleted file mode 100644 index c1803f93f..000000000 --- a/projects/biotic_interaction/docs/types/Curie.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: curie - - -a compact URI - -URI: [linkml:Curie](https://w3id.org/linkml/Curie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Curie** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations this MUST be expanded to a URI | -| | | in non-RDF serializations MAY be serialized as the compact representation | - diff --git a/projects/biotic_interaction/docs/types/Date.md b/projects/biotic_interaction/docs/types/Date.md deleted file mode 100644 index 06948af97..000000000 --- a/projects/biotic_interaction/docs/types/Date.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: date - - -a date (year, month and day) in an idealized calendar - -URI: [linkml:Date](https://w3id.org/linkml/Date) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDate** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Date | - diff --git a/projects/biotic_interaction/docs/types/DateOrDatetime.md b/projects/biotic_interaction/docs/types/DateOrDatetime.md deleted file mode 100644 index ef983898d..000000000 --- a/projects/biotic_interaction/docs/types/DateOrDatetime.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: date_or_datetime - - -Either a date or a datetime - -URI: [linkml:DateOrDatetime](https://w3id.org/linkml/DateOrDatetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/biotic_interaction/docs/types/Datetime.md b/projects/biotic_interaction/docs/types/Datetime.md deleted file mode 100644 index 9510454a8..000000000 --- a/projects/biotic_interaction/docs/types/Datetime.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: datetime - - -The combination of a date and time - -URI: [linkml:Datetime](https://w3id.org/linkml/Datetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDateTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:DateTime | - diff --git a/projects/biotic_interaction/docs/types/Decimal.md b/projects/biotic_interaction/docs/types/Decimal.md deleted file mode 100644 index a7ba14a5d..000000000 --- a/projects/biotic_interaction/docs/types/Decimal.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: decimal - - -A real number with arbitrary precision that conforms to the xsd:decimal specification - -URI: [linkml:Decimal](https://w3id.org/linkml/Decimal) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Decimal** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Broad Mappings:** | | schema:Number | - diff --git a/projects/biotic_interaction/docs/types/Double.md b/projects/biotic_interaction/docs/types/Double.md deleted file mode 100644 index cfe6d71e2..000000000 --- a/projects/biotic_interaction/docs/types/Double.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: double - - -A real number that conforms to the xsd:double specification - -URI: [linkml:Double](https://w3id.org/linkml/Double) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Close Mappings:** | | schema:Float | - diff --git a/projects/biotic_interaction/docs/types/Float.md b/projects/biotic_interaction/docs/types/Float.md deleted file mode 100644 index 7b303f96f..000000000 --- a/projects/biotic_interaction/docs/types/Float.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: float - - -A real number that conforms to the xsd:float specification - -URI: [linkml:Float](https://w3id.org/linkml/Float) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Float | - diff --git a/projects/biotic_interaction/docs/types/Integer.md b/projects/biotic_interaction/docs/types/Integer.md deleted file mode 100644 index 3cfcc66d9..000000000 --- a/projects/biotic_interaction/docs/types/Integer.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: integer - - -An integer - -URI: [linkml:Integer](https://w3id.org/linkml/Integer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **int** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Integer | - diff --git a/projects/biotic_interaction/docs/types/Jsonpath.md b/projects/biotic_interaction/docs/types/Jsonpath.md deleted file mode 100644 index a03a58e67..000000000 --- a/projects/biotic_interaction/docs/types/Jsonpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpath - - -A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpath](https://w3id.org/linkml/Jsonpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/biotic_interaction/docs/types/Jsonpointer.md b/projects/biotic_interaction/docs/types/Jsonpointer.md deleted file mode 100644 index a0e1ac492..000000000 --- a/projects/biotic_interaction/docs/types/Jsonpointer.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpointer - - -A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpointer](https://w3id.org/linkml/Jsonpointer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/biotic_interaction/docs/types/Ncname.md b/projects/biotic_interaction/docs/types/Ncname.md deleted file mode 100644 index 710b0b04a..000000000 --- a/projects/biotic_interaction/docs/types/Ncname.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: ncname - - -Prefix part of CURIE - -URI: [linkml:Ncname](https://w3id.org/linkml/Ncname) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NCName** | -| Representation | | str | diff --git a/projects/biotic_interaction/docs/types/Nodeidentifier.md b/projects/biotic_interaction/docs/types/Nodeidentifier.md deleted file mode 100644 index f0097cdf4..000000000 --- a/projects/biotic_interaction/docs/types/Nodeidentifier.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: nodeidentifier - - -A URI, CURIE or BNODE that represents a node in a model. - -URI: [linkml:Nodeidentifier](https://w3id.org/linkml/Nodeidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NodeIdentifier** | -| Representation | | str | diff --git a/projects/biotic_interaction/docs/types/Objectidentifier.md b/projects/biotic_interaction/docs/types/Objectidentifier.md deleted file mode 100644 index 454ba6be6..000000000 --- a/projects/biotic_interaction/docs/types/Objectidentifier.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: objectidentifier - - -A URI or CURIE that represents an object in the model. - -URI: [linkml:Objectidentifier](https://w3id.org/linkml/Objectidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **ElementIdentifier** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | Used for inheritance and type checking | - diff --git a/projects/biotic_interaction/docs/types/Sparqlpath.md b/projects/biotic_interaction/docs/types/Sparqlpath.md deleted file mode 100644 index fd99a927e..000000000 --- a/projects/biotic_interaction/docs/types/Sparqlpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: sparqlpath - - -A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - -URI: [linkml:Sparqlpath](https://w3id.org/linkml/Sparqlpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/biotic_interaction/docs/types/String.md b/projects/biotic_interaction/docs/types/String.md deleted file mode 100644 index 6e61d7081..000000000 --- a/projects/biotic_interaction/docs/types/String.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: string - - -A character string - -URI: [linkml:String](https://w3id.org/linkml/String) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Text | - diff --git a/projects/biotic_interaction/docs/types/Time.md b/projects/biotic_interaction/docs/types/Time.md deleted file mode 100644 index 2b8652bcd..000000000 --- a/projects/biotic_interaction/docs/types/Time.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: time - - -A time object represents a (local) time of day, independent of any particular day - -URI: [linkml:Time](https://w3id.org/linkml/Time) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Time | - diff --git a/projects/biotic_interaction/docs/types/Uri.md b/projects/biotic_interaction/docs/types/Uri.md deleted file mode 100644 index 343807a5e..000000000 --- a/projects/biotic_interaction/docs/types/Uri.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: uri - - -a complete URI - -URI: [linkml:Uri](https://w3id.org/linkml/Uri) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URI** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node | -| **Close Mappings:** | | schema:URL | - diff --git a/projects/biotic_interaction/docs/types/Uriorcurie.md b/projects/biotic_interaction/docs/types/Uriorcurie.md deleted file mode 100644 index 2f7b65087..000000000 --- a/projects/biotic_interaction/docs/types/Uriorcurie.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: uriorcurie - - -a URI or a CURIE - -URI: [linkml:Uriorcurie](https://w3id.org/linkml/Uriorcurie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URIorCURIE** | -| Representation | | str | diff --git a/projects/biotic_interaction/excel/biotic_interaction.xlsx b/projects/biotic_interaction/excel/biotic_interaction.xlsx deleted file mode 100644 index 24422f1cb..000000000 Binary files a/projects/biotic_interaction/excel/biotic_interaction.xlsx and /dev/null differ diff --git a/projects/biotic_interaction/graphql/biotic_interaction.graphql b/projects/biotic_interaction/graphql/biotic_interaction.graphql deleted file mode 100644 index 021fc511c..000000000 --- a/projects/biotic_interaction/graphql/biotic_interaction.graphql +++ /dev/null @@ -1,87 +0,0 @@ -type AnnotatorResult - { - subjectText: String - objectId: String - objectText: String - } - -type Any - { - } - -type BioticInteraction - { - sourceTaxon: Taxon - targetTaxon: Taxon - interactionType: InteractionType - } - -interface CompoundExpression - { - } - -type Container - { - interactions: [BioticInteraction] - } - -type ExtractionResult - { - inputId: String - inputTitle: String - inputText: String - rawCompletionOutput: String - prompt: String - extractedObject: Any - namedEntities: [Any] - } - -type InteractionType - { - id: String! - label: String - } - -interface NamedEntity - { - id: String! - label: String - } - -type Publication - { - id: String - title: String - abstract: String - combinedText: String - fullText: String - } - -type RelationshipType - { - id: String! - label: String - } - -type Taxon - { - id: String! - label: String - } - -type TextWithTriples - { - publication: Publication - triples: [Triple] - } - -interface Triple - { - subject: NamedEntity - predicate: RelationshipType - object: NamedEntity - qualifier: String - subjectQualifier: NamedEntity - objectQualifier: NamedEntity - } - diff --git a/projects/biotic_interaction/jsonld/biotic_interaction.context.jsonld b/projects/biotic_interaction/jsonld/biotic_interaction.context.jsonld deleted file mode 100644 index 47ac9c530..000000000 --- a/projects/biotic_interaction/jsonld/biotic_interaction.context.jsonld +++ /dev/null @@ -1,159 +0,0 @@ -{ - "comments": { - "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2023-08-07T10:51:26", - "source": "biotic_interaction.yaml" - }, - "@context": { - "COL": "https://www.catalogueoflife.org/data/taxon/", - "GBIF": "https://www.gbif.org/species/", - "ITIS": { - "@id": "https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=", - "@prefix": true - }, - "MESH": "http://example.org/UNKNOWN/MESH/", - "NCBITaxon": { - "@id": "http://purl.obolibrary.org/obo/NCBITAXON_", - "@prefix": true - }, - "RO": { - "@id": "http://purl.obolibrary.org/obo/RO_", - "@prefix": true - }, - "biolink": "http://example.org/UNKNOWN/biolink/", - "bp": { - "@id": "http://w3id.org/ontogpt/biotic-interaction-template", - "@prefix": true - }, - "col": "https://www.catalogueoflife.org/data/taxon/", - "core": "http://w3id.org/ontogpt/core/", - "gbif": "https://www.gbif.org/species/", - "itis": { - "@id": "https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=", - "@prefix": true - }, - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "@vocab": "http://w3id.org/ontogpt/biotic-interaction-template", - "object_id": { - "@id": "core:object_id" - }, - "object_text": { - "@id": "core:object_text" - }, - "subject_text": { - "@id": "core:subject_text" - }, - "interaction_type": { - "@type": "@id" - }, - "source_taxon": { - "@type": "@id" - }, - "target_taxon": { - "@type": "@id" - }, - "interactions": { - "@type": "@id" - }, - "extracted_object": { - "@type": "@id", - "@id": "core:extracted_object" - }, - "input_id": { - "@id": "core:input_id" - }, - "input_text": { - "@id": "core:input_text" - }, - "input_title": { - "@id": "core:input_title" - }, - "named_entities": { - "@type": "@id", - "@id": "core:named_entities" - }, - "prompt": { - "@id": "core:prompt" - }, - "raw_completion_output": { - "@id": "core:raw_completion_output" - }, - "id": { - "@id": "core:id" - }, - "label": { - "@id": "rdfs:label" - }, - "abstract": { - "@id": "core:abstract" - }, - "combined_text": { - "@id": "core:combined_text" - }, - "full_text": { - "@id": "core:full_text" - }, - "title": { - "@id": "core:title" - }, - "publication": { - "@type": "@id", - "@id": "core:publication" - }, - "triples": { - "@type": "@id", - "@id": "core:triples" - }, - "object": { - "@type": "@id", - "@id": "core:object" - }, - "object_qualifier": { - "@type": "@id", - "@id": "core:object_qualifier" - }, - "predicate": { - "@type": "@id", - "@id": "core:predicate" - }, - "qualifier": { - "@id": "core:qualifier" - }, - "subject": { - "@type": "@id", - "@id": "core:subject" - }, - "subject_qualifier": { - "@type": "@id", - "@id": "core:subject_qualifier" - }, - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } - } -} diff --git a/projects/biotic_interaction/jsonld/biotic_interaction.jsonld b/projects/biotic_interaction/jsonld/biotic_interaction.jsonld deleted file mode 100644 index be0d0109b..000000000 --- a/projects/biotic_interaction/jsonld/biotic_interaction.jsonld +++ /dev/null @@ -1,1167 +0,0 @@ -{ - "name": "biotic-interaction-template", - "description": "A template for biotic interactions", - "title": "Biotic Interaction Template", - "id": "https://w3id.org/ontogpt/biotic_interaction", - "imports": [ - "linkml:types", - "core" - ], - "license": "https://creativecommons.org/publicdomain/zero/1.0/", - "prefixes": [ - { - "prefix_prefix": "linkml", - "prefix_reference": "https://w3id.org/linkml/" - }, - { - "prefix_prefix": "bp", - "prefix_reference": "http://w3id.org/ontogpt/biotic-interaction-template" - }, - { - "prefix_prefix": "NCBITaxon", - "prefix_reference": "http://purl.obolibrary.org/obo/NCBITAXON_" - }, - { - "prefix_prefix": "col", - "prefix_reference": "https://www.catalogueoflife.org/data/taxon/" - }, - { - "prefix_prefix": "itis", - "prefix_reference": "https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=" - }, - { - "prefix_prefix": "gbif", - "prefix_reference": "https://www.gbif.org/species/" - } - ], - "default_prefix": "bp", - "default_range": "string", - "types": [ - { - "name": "string", - "definition_uri": "https://w3id.org/linkml/String", - "description": "A character string", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Text" - ], - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "@type": "TypeDefinition" - }, - { - "name": "integer", - "definition_uri": "https://w3id.org/linkml/Integer", - "description": "An integer", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Integer" - ], - "base": "int", - "uri": "http://www.w3.org/2001/XMLSchema#integer", - "@type": "TypeDefinition" - }, - { - "name": "boolean", - "definition_uri": "https://w3id.org/linkml/Boolean", - "description": "A binary (true or false) value", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Boolean" - ], - "base": "Bool", - "uri": "http://www.w3.org/2001/XMLSchema#boolean", - "repr": "bool", - "@type": "TypeDefinition" - }, - { - "name": "float", - "definition_uri": "https://w3id.org/linkml/Float", - "description": "A real number that conforms to the xsd:float specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#float", - "@type": "TypeDefinition" - }, - { - "name": "double", - "definition_uri": "https://w3id.org/linkml/Double", - "description": "A real number that conforms to the xsd:double specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#double", - "@type": "TypeDefinition" - }, - { - "name": "decimal", - "definition_uri": "https://w3id.org/linkml/Decimal", - "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "broad_mappings": [ - "schema:Number" - ], - "base": "Decimal", - "uri": "http://www.w3.org/2001/XMLSchema#decimal", - "@type": "TypeDefinition" - }, - { - "name": "time", - "definition_uri": "https://w3id.org/linkml/Time", - "description": "A time object represents a (local) time of day, independent of any particular day", - "notes": [ - "URI is dateTime because OWL reasoners do not work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Time" - ], - "base": "XSDTime", - "uri": "http://www.w3.org/2001/XMLSchema#time", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date", - "definition_uri": "https://w3id.org/linkml/Date", - "description": "a date (year, month and day) in an idealized calendar", - "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Date" - ], - "base": "XSDDate", - "uri": "http://www.w3.org/2001/XMLSchema#date", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "datetime", - "definition_uri": "https://w3id.org/linkml/Datetime", - "description": "The combination of a date and time", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:DateTime" - ], - "base": "XSDDateTime", - "uri": "http://www.w3.org/2001/XMLSchema#dateTime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date_or_datetime", - "definition_uri": "https://w3id.org/linkml/DateOrDatetime", - "description": "Either a date or a datetime", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "https://w3id.org/linkml/DateOrDatetime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uriorcurie", - "definition_uri": "https://w3id.org/linkml/Uriorcurie", - "description": "a URI or a CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "URIorCURIE", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "curie", - "definition_uri": "https://w3id.org/linkml/Curie", - "conforms_to": "https://www.w3.org/TR/curie/", - "description": "a compact URI", - "comments": [ - "in RDF serializations this MUST be expanded to a URI", - "in non-RDF serializations MAY be serialized as the compact representation" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "Curie", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uri", - "definition_uri": "https://w3id.org/linkml/Uri", - "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", - "description": "a complete URI", - "comments": [ - "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:URL" - ], - "base": "URI", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "ncname", - "definition_uri": "https://w3id.org/linkml/Ncname", - "description": "Prefix part of CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NCName", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "objectidentifier", - "definition_uri": "https://w3id.org/linkml/Objectidentifier", - "description": "A URI or CURIE that represents an object in the model.", - "comments": [ - "Used for inheritance and type checking" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "ElementIdentifier", - "uri": "http://www.w3.org/ns/shex#iri", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "nodeidentifier", - "definition_uri": "https://w3id.org/linkml/Nodeidentifier", - "description": "A URI, CURIE or BNODE that represents a node in a model.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NodeIdentifier", - "uri": "http://www.w3.org/ns/shex#nonLiteral", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpointer", - "definition_uri": "https://w3id.org/linkml/Jsonpointer", - "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901", - "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpath", - "definition_uri": "https://w3id.org/linkml/Jsonpath", - "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html", - "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "sparqlpath", - "definition_uri": "https://w3id.org/linkml/Sparqlpath", - "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths", - "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - } - ], - "enums": [ - { - "name": "NullDataOptions", - "definition_uri": "http://w3id.org/ontogpt/core/NullDataOptions", - "from_schema": "http://w3id.org/ontogpt/core", - "permissible_values": [ - { - "text": "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "meaning": "NCIT:C149701" - }, - { - "text": "NOT_APPLICABLE", - "meaning": "NCIT:C18902", - "aliases": [ - "not applicable", - "N/A" - ] - }, - { - "text": "NOT_MENTIONED" - } - ] - } - ], - "slots": [ - { - "name": "container__interactions", - "from_schema": "https://w3id.org/ontogpt/biotic_interaction", - "slot_uri": "http://w3id.org/ontogpt/biotic-interaction-templateinteractions", - "multivalued": true, - "alias": "interactions", - "owner": "Container", - "domain_of": [ - "Container" - ], - "range": "BioticInteraction", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "bioticInteraction__source_taxon", - "description": "the taxon that is the subject of the interaction", - "from_schema": "https://w3id.org/ontogpt/biotic_interaction", - "slot_uri": "http://w3id.org/ontogpt/biotic-interaction-templatesource_taxon", - "alias": "source_taxon", - "owner": "BioticInteraction", - "domain_of": [ - "BioticInteraction" - ], - "range": "Taxon", - "@type": "SlotDefinition" - }, - { - "name": "bioticInteraction__target_taxon", - "description": "the taxon that is the object of the ineteraction", - "from_schema": "https://w3id.org/ontogpt/biotic_interaction", - "slot_uri": "http://w3id.org/ontogpt/biotic-interaction-templatetarget_taxon", - "alias": "target_taxon", - "owner": "BioticInteraction", - "domain_of": [ - "BioticInteraction" - ], - "range": "Taxon", - "@type": "SlotDefinition" - }, - { - "name": "bioticInteraction__interaction_type", - "description": "the type of interaction", - "from_schema": "https://w3id.org/ontogpt/biotic_interaction", - "slot_uri": "http://w3id.org/ontogpt/biotic-interaction-templateinteraction_type", - "alias": "interaction_type", - "owner": "BioticInteraction", - "domain_of": [ - "BioticInteraction" - ], - "range": "InteractionType", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_id", - "alias": "input_id", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_title", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_title", - "alias": "input_title", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_text", - "alias": "input_text", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__raw_completion_output", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/raw_completion_output", - "alias": "raw_completion_output", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__prompt", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/prompt", - "alias": "prompt", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__extracted_object", - "description": "The complex objects extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/extracted_object", - "alias": "extracted_object", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__named_entities", - "description": "Named entities extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/named_entities", - "multivalued": true, - "alias": "named_entities", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "identifier": true, - "alias": "id", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "required": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "from_schema": "http://w3id.org/ontogpt/core", - "aliases": [ - "name" - ], - "mappings": [ - "http://example.org/UNKNOWN/rdfs/label" - ], - "slot_uri": "http://example.org/UNKNOWN/rdfs/label", - "alias": "label", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject", - "alias": "subject", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__predicate", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/predicate", - "alias": "predicate", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "triple__object", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object", - "alias": "object", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/qualifier", - "alias": "qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_qualifier", - "alias": "subject_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_qualifier", - "alias": "object_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/publication", - "alias": "publication", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__triples", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/triples", - "multivalued": true, - "alias": "triples", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "publication__id", - "description": "The publication identifier", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "alias": "id", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__title", - "description": "The title of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/title", - "alias": "title", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__abstract", - "description": "The abstract of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/abstract", - "alias": "abstract", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__combined_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/combined_text", - "alias": "combined_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__full_text", - "description": "The full text of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/full_text", - "alias": "full_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__subject_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_text", - "alias": "subject_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_id", - "alias": "object_id", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_text", - "alias": "object_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - } - ], - "classes": [ - { - "name": "Container", - "definition_uri": "http://w3id.org/ontogpt/biotic-interaction-templateContainer", - "from_schema": "https://w3id.org/ontogpt/biotic_interaction", - "slots": [ - "container__interactions" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "interactions", - "multivalued": true, - "range": "BioticInteraction", - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/biotic-interaction-templateContainer", - "tree_root": true, - "@type": "ClassDefinition" - }, - { - "name": "BioticInteraction", - "definition_uri": "http://w3id.org/ontogpt/biotic-interaction-templateBioticInteraction", - "annotations": [ - { - "tag": "prompt", - "value": "A semi-colon separated list of taxon to taxon relationships", - "@type": "Annotation" - }, - { - "tag": "prompt.example", - "value": "Carcharodon carcharias eats elephant seal; Pandarus sinuatus parasitizes Carcharodon carcharias; orca eats Carcharodon carcharias", - "@type": "Annotation" - } - ], - "from_schema": "https://w3id.org/ontogpt/biotic_interaction", - "slots": [ - "bioticInteraction__source_taxon", - "bioticInteraction__target_taxon", - "bioticInteraction__interaction_type" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "source_taxon", - "description": "the taxon that is the subject of the interaction", - "range": "Taxon", - "@type": "SlotDefinition" - }, - { - "name": "target_taxon", - "description": "the taxon that is the object of the ineteraction", - "range": "Taxon", - "@type": "SlotDefinition" - }, - { - "name": "interaction_type", - "description": "the type of interaction", - "range": "InteractionType", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/biotic-interaction-templateBioticInteraction", - "@type": "ClassDefinition" - }, - { - "name": "Taxon", - "id_prefixes": [ - "NCBITaxon", - "COL", - "ITIS", - "GBIF" - ], - "definition_uri": "http://w3id.org/ontogpt/biotic-interaction-templateTaxon", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:ncbitaxon", - "@type": "Annotation" - }, - { - "tag": "prompt.example", - "value": "shark, Carcharodon carcharias, elephant seal, Pandarus sinuatus, orca", - "@type": "Annotation" - } - ], - "from_schema": "https://w3id.org/ontogpt/biotic_interaction", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/biotic-interaction-templateTaxon", - "@type": "ClassDefinition" - }, - { - "name": "InteractionType", - "id_prefixes": [ - "RO", - "MESH" - ], - "definition_uri": "http://w3id.org/ontogpt/biotic-interaction-templateInteractionType", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:go, sqlite:obo:ro, sqlite:obo:bero", - "@type": "Annotation" - }, - { - "tag": "prompt.example", - "value": "eats, competes with, parasitizes", - "@type": "Annotation" - } - ], - "from_schema": "https://w3id.org/ontogpt/biotic_interaction", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/biotic-interaction-templateInteractionType", - "@type": "ClassDefinition" - }, - { - "name": "Any", - "definition_uri": "http://w3id.org/ontogpt/core/Any", - "from_schema": "http://w3id.org/ontogpt/core", - "mappings": [ - "linkml:Any" - ], - "slot_usage": {}, - "class_uri": "https://w3id.org/linkml/Any", - "@type": "ClassDefinition" - }, - { - "name": "ExtractionResult", - "definition_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "description": "A result of extracting knowledge on text", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "extractionResult__input_id", - "extractionResult__input_title", - "extractionResult__input_text", - "extractionResult__raw_completion_output", - "extractionResult__prompt", - "extractionResult__extracted_object", - "extractionResult__named_entities" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "input_id", - "@type": "SlotDefinition" - }, - { - "name": "input_title", - "@type": "SlotDefinition" - }, - { - "name": "input_text", - "@type": "SlotDefinition" - }, - { - "name": "raw_completion_output", - "@type": "SlotDefinition" - }, - { - "name": "prompt", - "@type": "SlotDefinition" - }, - { - "name": "extracted_object", - "description": "The complex objects extracted from the text", - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "named_entities", - "description": "Named entities extracted from the text", - "multivalued": true, - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "@type": "ClassDefinition" - }, - { - "name": "NamedEntity", - "definition_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "identifier": true, - "@type": "SlotDefinition" - }, - { - "name": "label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "aliases": [ - "name" - ], - "slot_uri": "rdfs:label", - "range": "string", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "@type": "ClassDefinition" - }, - { - "name": "CompoundExpression", - "definition_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "@type": "ClassDefinition" - }, - { - "name": "Triple", - "definition_uri": "http://w3id.org/ontogpt/core/Triple", - "description": "Abstract parent for Relation Extraction tasks", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "CompoundExpression", - "abstract": true, - "slots": [ - "triple__subject", - "triple__predicate", - "triple__object", - "triple__qualifier", - "triple__subject_qualifier", - "triple__object_qualifier" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "predicate", - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "object", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Triple", - "@type": "ClassDefinition" - }, - { - "name": "TextWithTriples", - "definition_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "textWithTriples__publication", - "textWithTriples__triples" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "triples", - "multivalued": true, - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "@type": "ClassDefinition" - }, - { - "name": "RelationshipType", - "id_prefixes": [ - "RO", - "biolink" - ], - "definition_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "@type": "ClassDefinition" - }, - { - "name": "Publication", - "definition_uri": "http://w3id.org/ontogpt/core/Publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "publication__id", - "publication__title", - "publication__abstract", - "publication__combined_text", - "publication__full_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "description": "The publication identifier", - "@type": "SlotDefinition" - }, - { - "name": "title", - "description": "The title of the publication", - "@type": "SlotDefinition" - }, - { - "name": "abstract", - "description": "The abstract of the publication", - "@type": "SlotDefinition" - }, - { - "name": "combined_text", - "@type": "SlotDefinition" - }, - { - "name": "full_text", - "description": "The full text of the publication", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Publication", - "@type": "ClassDefinition" - }, - { - "name": "AnnotatorResult", - "definition_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "annotatorResult__subject_text", - "annotatorResult__object_id", - "annotatorResult__object_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject_text", - "@type": "SlotDefinition" - }, - { - "name": "object_id", - "@type": "SlotDefinition" - }, - { - "name": "object_text", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "@type": "ClassDefinition" - } - ], - "metamodel_version": "1.7.0", - "source_file": "biotic_interaction.yaml", - "source_file_date": "2023-06-17T15:11:19", - "source_file_size": 1886, - "generation_date": "2023-08-07T10:51:27", - "@type": "SchemaDefinition", - "@context": [ - "projects/biotic_interaction/jsonld/biotic_interaction.context.jsonld", - "https://w3id.org/linkml/types.context.jsonld", - "core.context.jsonld", - { - "@base": "http://w3id.org/ontogpt/biotic-interaction-template" - } - ] -} diff --git a/projects/biotic_interaction/jsonschema/biotic_interaction.schema.json b/projects/biotic_interaction/jsonschema/biotic_interaction.schema.json deleted file mode 100644 index 4be280452..000000000 --- a/projects/biotic_interaction/jsonschema/biotic_interaction.schema.json +++ /dev/null @@ -1,221 +0,0 @@ -{ - "$defs": { - "AnnotatorResult": { - "additionalProperties": false, - "description": "", - "properties": { - "object_id": { - "type": "string" - }, - "object_text": { - "type": "string" - }, - "subject_text": { - "type": "string" - } - }, - "title": "AnnotatorResult", - "type": "object" - }, - "Any": { - "additionalProperties": true, - "description": "", - "title": "Any", - "type": "object" - }, - "BioticInteraction": { - "additionalProperties": false, - "description": "", - "properties": { - "interaction_type": { - "description": "the type of interaction", - "type": "string" - }, - "source_taxon": { - "description": "the taxon that is the subject of the interaction", - "type": "string" - }, - "target_taxon": { - "description": "the taxon that is the object of the ineteraction", - "type": "string" - } - }, - "title": "BioticInteraction", - "type": "object" - }, - "Container": { - "additionalProperties": false, - "description": "", - "properties": { - "interactions": { - "items": { - "$ref": "#/$defs/BioticInteraction" - }, - "type": "array" - } - }, - "title": "Container", - "type": "object" - }, - "ExtractionResult": { - "additionalProperties": false, - "description": "A result of extracting knowledge on text", - "properties": { - "extracted_object": { - "$ref": "#/$defs/Any", - "description": "The complex objects extracted from the text" - }, - "input_id": { - "type": "string" - }, - "input_text": { - "type": "string" - }, - "input_title": { - "type": "string" - }, - "named_entities": { - "description": "Named entities extracted from the text", - "items": { - "$ref": "#/$defs/Any" - }, - "type": "array" - }, - "prompt": { - "type": "string" - }, - "raw_completion_output": { - "type": "string" - } - }, - "title": "ExtractionResult", - "type": "object" - }, - "InteractionType": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "InteractionType", - "type": "object" - }, - "NullDataOptions": { - "description": "", - "enum": [ - "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "NOT_APPLICABLE", - "NOT_MENTIONED" - ], - "title": "NullDataOptions", - "type": "string" - }, - "Publication": { - "additionalProperties": false, - "description": "", - "properties": { - "abstract": { - "description": "The abstract of the publication", - "type": "string" - }, - "combined_text": { - "type": "string" - }, - "full_text": { - "description": "The full text of the publication", - "type": "string" - }, - "id": { - "description": "The publication identifier", - "type": "string" - }, - "title": { - "description": "The title of the publication", - "type": "string" - } - }, - "title": "Publication", - "type": "object" - }, - "RelationshipType": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "RelationshipType", - "type": "object" - }, - "Taxon": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Taxon", - "type": "object" - }, - "TextWithTriples": { - "additionalProperties": false, - "description": "", - "properties": { - "publication": { - "$ref": "#/$defs/Publication" - }, - "triples": { - "items": { - "$ref": "#/$defs/Triple" - }, - "type": "array" - } - }, - "title": "TextWithTriples", - "type": "object" - } - }, - "$id": "https://w3id.org/ontogpt/biotic_interaction", - "$schema": "http://json-schema.org/draft-07/schema#", - "additionalProperties": true, - "metamodel_version": "1.7.0", - "properties": { - "interactions": { - "items": { - "$ref": "#/$defs/BioticInteraction" - }, - "type": "array" - } - }, - "title": "biotic-interaction-template", - "type": "object", - "version": null -} \ No newline at end of file diff --git a/projects/biotic_interaction/owl/biotic_interaction.owl.ttl b/projects/biotic_interaction/owl/biotic_interaction.owl.ttl deleted file mode 100644 index 223f3cef3..000000000 --- a/projects/biotic_interaction/owl/biotic_interaction.owl.ttl +++ /dev/null @@ -1,423 +0,0 @@ -@prefix IAO: . -@prefix bp: . -@prefix linkml: . -@prefix owl: . -@prefix rdf: . -@prefix rdfs: . -@prefix skos: . -@prefix xsd: . - -linkml:SubsetDefinition a owl:Class ; - rdfs:label "subset_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" . - -linkml:TypeDefinition a owl:Class ; - rdfs:label "type_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" ; - linkml:mixins "type_expression" . - -linkml:topValue a owl:DatatypeProperty ; - rdfs:label "value" . - - a owl:Ontology ; - rdfs:label "biotic-interaction-template" ; - IAO:0000700 bp:BioticInteraction, - bp:Container, - , - , - , - , - , - , - ; - linkml:classes "{'Container': ClassDefinition(name='Container', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/biotic-interaction-templateContainer', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/biotic_interaction', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['container__interactions'], slot_usage={}, attributes={'interactions': SlotDefinition(name='interactions', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='BioticInteraction', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='bp:Container', subclass_of=None, union_of=[], defining_slots=[], tree_root=True, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'BioticInteraction': ClassDefinition(name='BioticInteraction', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/biotic-interaction-templateBioticInteraction', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='A semi-colon separated list of taxon to taxon relationships', extensions={}, annotations={}), 'prompt.example': Annotation(tag='prompt.example', value='Carcharodon carcharias eats elephant seal; Pandarus sinuatus parasitizes Carcharodon carcharias; orca eats Carcharodon carcharias', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/biotic_interaction', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['bioticInteraction__source_taxon', 'bioticInteraction__target_taxon', 'bioticInteraction__interaction_type'], slot_usage={}, attributes={'source_taxon': SlotDefinition(name='source_taxon', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the taxon that is the subject of the interaction', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Taxon', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'target_taxon': SlotDefinition(name='target_taxon', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the taxon that is the object of the ineteraction', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Taxon', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'interaction_type': SlotDefinition(name='interaction_type', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the type of interaction', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='InteractionType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='bp:BioticInteraction', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Taxon': ClassDefinition(name='Taxon', id_prefixes=['NCBITaxon', 'COL', 'ITIS', 'GBIF'], definition_uri='http://w3id.org/ontogpt/biotic-interaction-templateTaxon', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:ncbitaxon', extensions={}, annotations={}), 'prompt.example': Annotation(tag='prompt.example', value='shark, Carcharodon carcharias, elephant seal, Pandarus sinuatus, orca', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/biotic_interaction', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='bp:Taxon', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'InteractionType': ClassDefinition(name='InteractionType', id_prefixes=['RO', 'MESH'], definition_uri='http://w3id.org/ontogpt/biotic-interaction-templateInteractionType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:go, sqlite:obo:ro, sqlite:obo:bero', extensions={}, annotations={}), 'prompt.example': Annotation(tag='prompt.example', value='eats, competes with, parasitizes', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/biotic_interaction', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='bp:InteractionType', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Any': ClassDefinition(name='Any', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Any', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=['linkml:Any'], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='linkml:Any', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ExtractionResult': ClassDefinition(name='ExtractionResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/ExtractionResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A result of extracting knowledge on text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['extractionResult__input_id', 'extractionResult__input_title', 'extractionResult__input_text', 'extractionResult__raw_completion_output', 'extractionResult__prompt', 'extractionResult__extracted_object', 'extractionResult__named_entities'], slot_usage={}, attributes={'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:ExtractionResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'NamedEntity': ClassDefinition(name='NamedEntity', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NamedEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:NamedEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'CompoundExpression': ClassDefinition(name='CompoundExpression', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/CompoundExpression', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='core:CompoundExpression', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Triple': ClassDefinition(name='Triple', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Triple', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Abstract parent for Relation Extraction tasks', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['triple__subject', 'triple__predicate', 'triple__object', 'triple__qualifier', 'triple__subject_qualifier', 'triple__object_qualifier'], slot_usage={}, attributes={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Triple', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'TextWithTriples': ClassDefinition(name='TextWithTriples', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/TextWithTriples', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['textWithTriples__publication', 'textWithTriples__triples'], slot_usage={}, attributes={'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:TextWithTriples', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'RelationshipType': ClassDefinition(name='RelationshipType', id_prefixes=['RO', 'biolink'], definition_uri='http://w3id.org/ontogpt/core/RelationshipType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='core:RelationshipType', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Publication': ClassDefinition(name='Publication', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Publication', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['publication__id', 'publication__title', 'publication__abstract', 'publication__combined_text', 'publication__full_text'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Publication', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'AnnotatorResult': ClassDefinition(name='AnnotatorResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/AnnotatorResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['annotatorResult__subject_text', 'annotatorResult__object_id', 'annotatorResult__object_text'], slot_usage={}, attributes={'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:AnnotatorResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={})}" ; - linkml:enums "{'NullDataOptions': EnumDefinition(name='NullDataOptions', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NullDataOptions', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'UNSPECIFIED_METHOD_OF_ADMINISTRATION': PermissibleValue(text='UNSPECIFIED_METHOD_OF_ADMINISTRATION', description=None, meaning='NCIT:C149701', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_APPLICABLE': PermissibleValue(text='NOT_APPLICABLE', description=None, meaning='NCIT:C18902', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['not applicable', 'N/A'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_MENTIONED': PermissibleValue(text='NOT_MENTIONED', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[])}" ; - linkml:id "https://w3id.org/ontogpt/biotic_interaction" ; - linkml:imports "core", - "linkml:types" ; - linkml:types "{'string': TypeDefinition(name='string', id_prefixes=[], definition_uri='https://w3id.org/linkml/String', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A character string', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Text'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'integer': TypeDefinition(name='integer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Integer', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An integer', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Integer'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='int', uri='xsd:integer', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'boolean': TypeDefinition(name='boolean', id_prefixes=[], definition_uri='https://w3id.org/linkml/Boolean', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A binary (true or false) value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Boolean'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Bool', uri='xsd:boolean', repr='bool', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'float': TypeDefinition(name='float', id_prefixes=[], definition_uri='https://w3id.org/linkml/Float', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:float specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Float'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:float', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'double': TypeDefinition(name='double', id_prefixes=[], definition_uri='https://w3id.org/linkml/Double', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:double specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:Float'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:double', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'decimal': TypeDefinition(name='decimal', id_prefixes=[], definition_uri='https://w3id.org/linkml/Decimal', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number with arbitrary precision that conforms to the xsd:decimal specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=['schema:Number'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Decimal', uri='xsd:decimal', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'time': TypeDefinition(name='time', id_prefixes=[], definition_uri='https://w3id.org/linkml/Time', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A time object represents a (local) time of day, independent of any particular day', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=['URI is dateTime because OWL reasoners do not work with straight date or time'], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Time'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDTime', uri='xsd:time', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date': TypeDefinition(name='date', id_prefixes=[], definition_uri='https://w3id.org/linkml/Date', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a date (year, month and day) in an idealized calendar', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[\"URI is dateTime because OWL reasoners don't work with straight date or time\"], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Date'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDate', uri='xsd:date', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'datetime': TypeDefinition(name='datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/Datetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The combination of a date and time', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:DateTime'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDateTime', uri='xsd:dateTime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date_or_datetime': TypeDefinition(name='date_or_datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/DateOrDatetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Either a date or a datetime', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='linkml:DateOrDatetime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uriorcurie': TypeDefinition(name='uriorcurie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uriorcurie', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a URI or a CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URIorCURIE', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'curie': TypeDefinition(name='curie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Curie', local_names={}, conforms_to='https://www.w3.org/TR/curie/', implements=[], extensions={}, annotations={}, description='a compact URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations this MUST be expanded to a URI', 'in non-RDF serializations MAY be serialized as the compact representation'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Curie', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uri': TypeDefinition(name='uri', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uri', local_names={}, conforms_to='https://www.ietf.org/rfc/rfc3987.txt', implements=[], extensions={}, annotations={}, description='a complete URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:URL'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URI', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ncname': TypeDefinition(name='ncname', id_prefixes=[], definition_uri='https://w3id.org/linkml/Ncname', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Prefix part of CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NCName', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'objectidentifier': TypeDefinition(name='objectidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Objectidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI or CURIE that represents an object in the model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['Used for inheritance and type checking'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='ElementIdentifier', uri='shex:iri', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'nodeidentifier': TypeDefinition(name='nodeidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Nodeidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI, CURIE or BNODE that represents a node in a model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NodeIdentifier', uri='shex:nonLiteral', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpointer': TypeDefinition(name='jsonpointer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpointer', local_names={}, conforms_to='https://datatracker.ietf.org/doc/html/rfc6901', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpath': TypeDefinition(name='jsonpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpath', local_names={}, conforms_to='https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sparqlpath': TypeDefinition(name='sparqlpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Sparqlpath', local_names={}, conforms_to='https://www.w3.org/TR/sparql11-query/#propertypaths', implements=[], extensions={}, annotations={}, description='A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -bp:Container a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Container" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom bp:BioticInteraction ; - owl:onProperty bp:interactions ] ; - linkml:attributes "{'interactions': SlotDefinition(name='interactions', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='BioticInteraction', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -bp:interaction_type a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "interaction_type" ; - rdfs:range bp:InteractionType ; - skos:definition "the type of interaction" . - -bp:interactions a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "interactions" ; - rdfs:range bp:BioticInteraction . - -bp:source_taxon a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "source_taxon" ; - rdfs:range bp:Taxon ; - skos:definition "the taxon that is the subject of the interaction" . - -bp:target_taxon a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "target_taxon" ; - rdfs:range bp:Taxon ; - skos:definition "the taxon that is the object of the ineteraction" . - - a owl:Class, - linkml:ClassDefinition ; - rdfs:label "AnnotatorResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ] ; - linkml:attributes "{'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - - a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ExtractionResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ] ; - skos:definition "A result of extracting knowledge on text" ; - linkml:attributes "{'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - - a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TextWithTriples" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty ] ; - linkml:attributes "{'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "abstract" ; - rdfs:range linkml:String ; - skos:definition "The abstract of the publication" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "combined_text" ; - rdfs:range linkml:String . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "extracted_object" ; - rdfs:range ; - skos:definition "The complex objects extracted from the text" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "full_text" ; - rdfs:range linkml:String ; - skos:definition "The full text of the publication" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_id" ; - rdfs:range linkml:String . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_text" ; - rdfs:range linkml:String . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_title" ; - rdfs:range linkml:String . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "named_entities" ; - rdfs:range ; - skos:definition "Named entities extracted from the text" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object" ; - rdfs:range . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_id" ; - rdfs:range linkml:String . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_qualifier" ; - rdfs:range ; - skos:definition "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_text" ; - rdfs:range linkml:String . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "predicate" ; - rdfs:range . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "prompt" ; - rdfs:range linkml:String . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "publication" ; - bp:prompt.skip "true" ; - rdfs:range . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "qualifier" ; - rdfs:range linkml:String ; - skos:definition "A qualifier for the statements, e.g. \"NOT\" for negation" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "raw_completion_output" ; - rdfs:range linkml:String . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject" ; - rdfs:range . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_qualifier" ; - rdfs:range ; - skos:definition "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_text" ; - rdfs:range linkml:String . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "title" ; - rdfs:range linkml:String ; - skos:definition "The title of the publication" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "triples" ; - rdfs:range . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "label" ; - bp:owl "AnnotationProperty, AnnotationAssertion" ; - rdfs:range linkml:String ; - skos:altLabel "name" ; - skos:definition "The label (name) of the named thing" ; - skos:exactMatch . - - a , - owl:Class ; - rdfs:label "UNSPECIFIED_METHOD_OF_ADMINISTRATION" . - - a , - owl:Class ; - rdfs:label "NOT_APPLICABLE" . - -bp:InteractionType a owl:Class, - linkml:ClassDefinition ; - rdfs:label "InteractionType" ; - bp:annotators "sqlite:obo:go, sqlite:obo:ro, sqlite:obo:bero" ; - bp:prompt.example "eats, competes with, parasitizes" ; - rdfs:subClassOf ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - - a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CompoundExpression" ; - linkml:attributes "{}" . - - a , - owl:Class ; - rdfs:label "NOT_MENTIONED" . - - a owl:Class, - linkml:ClassDefinition ; - rdfs:label "RelationshipType" ; - rdfs:subClassOf ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - - a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Triple" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - ; - skos:definition "Abstract parent for Relation Extraction tasks" ; - linkml:attributes "{'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - - a owl:ObjectProperty, - linkml:SlotDefinition . - -bp:BioticInteraction a owl:Class, - linkml:ClassDefinition ; - rdfs:label "BioticInteraction" ; - bp:prompt "A semi-colon separated list of taxon to taxon relationships" ; - bp:prompt.example "Carcharodon carcharias eats elephant seal; Pandarus sinuatus parasitizes Carcharodon carcharias; orca eats Carcharodon carcharias" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass bp:Taxon ; - owl:onProperty bp:source_taxon ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass bp:InteractionType ; - owl:onProperty bp:interaction_type ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass bp:Taxon ; - owl:onProperty bp:target_taxon ] ; - linkml:attributes "{'source_taxon': SlotDefinition(name='source_taxon', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the taxon that is the subject of the interaction', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Taxon', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'target_taxon': SlotDefinition(name='target_taxon', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the taxon that is the object of the ineteraction', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Taxon', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'interaction_type': SlotDefinition(name='interaction_type', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the type of interaction', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='InteractionType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - - a owl:Class, - linkml:EnumDefinition ; - rdfs:label "NullDataOptions" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - . - - a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Publication" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -bp:Taxon a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Taxon" ; - bp:annotators "sqlite:obo:ncbitaxon" ; - bp:prompt.example "shark, Carcharodon carcharias, elephant seal, Pandarus sinuatus, orca" ; - rdfs:subClassOf ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - - a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Any" ; - skos:exactMatch linkml:Any ; - linkml:attributes "{}" . - - a owl:Class, - linkml:ClassDefinition ; - rdfs:label "NamedEntity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty ; - owl:qualifiedCardinality 1 ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:ClassDefinition a owl:Class ; - rdfs:label "class_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "class_expression" . - -linkml:SlotDefinition a owl:Class ; - rdfs:label "slot_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "slot_expression" . - - diff --git a/projects/biotic_interaction/prefixmap/biotic_interaction.yaml b/projects/biotic_interaction/prefixmap/biotic_interaction.yaml deleted file mode 100644 index 1c2b0a907..000000000 --- a/projects/biotic_interaction/prefixmap/biotic_interaction.yaml +++ /dev/null @@ -1,43 +0,0 @@ -{ - "COL": "https://www.catalogueoflife.org/data/taxon/", - "GBIF": "https://www.gbif.org/species/", - "ITIS": "https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=", - "MESH": "http://example.org/UNKNOWN/MESH/", - "NCBITaxon": "http://purl.obolibrary.org/obo/NCBITAXON_", - "RO": "http://purl.obolibrary.org/obo/RO_", - "biolink": "http://example.org/UNKNOWN/biolink/", - "bp": "http://w3id.org/ontogpt/biotic-interaction-template", - "col": "https://www.catalogueoflife.org/data/taxon/", - "core": "http://w3id.org/ontogpt/core/", - "gbif": "https://www.gbif.org/species/", - "itis": "https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } -} diff --git a/projects/biotic_interaction/protobuf/biotic_interaction.proto b/projects/biotic_interaction/protobuf/biotic_interaction.proto deleted file mode 100644 index 942fa12b1..000000000 --- a/projects/biotic_interaction/protobuf/biotic_interaction.proto +++ /dev/null @@ -1,55 +0,0 @@ -message AnnotatorResult - { - string subjectText = 0 - string objectId = 0 - string objectText = 0 - } -message BioticInteraction - { - taxon sourceTaxon = 0 - taxon targetTaxon = 0 - interactionType interactionType = 0 - } -message Container - { - repeated bioticInteraction interactions = 0 - } -// A result of extracting knowledge on text -message ExtractionResult - { - string inputId = 0 - string inputTitle = 0 - string inputText = 0 - string rawCompletionOutput = 0 - string prompt = 0 - any extractedObject = 0 - repeated any namedEntities = 0 - } -message InteractionType - { - string id = 0 - string label = 0 - } -message Publication - { - string id = 0 - string title = 0 - string abstract = 0 - string combinedText = 0 - string fullText = 0 - } -message RelationshipType - { - string id = 0 - string label = 0 - } -message Taxon - { - string id = 0 - string label = 0 - } -message TextWithTriples - { - publication publication = 0 - repeated triple triples = 0 - } diff --git a/projects/biotic_interaction/shacl/biotic_interaction.shacl.ttl b/projects/biotic_interaction/shacl/biotic_interaction.shacl.ttl deleted file mode 100644 index 9f58c3138..000000000 --- a/projects/biotic_interaction/shacl/biotic_interaction.shacl.ttl +++ /dev/null @@ -1,224 +0,0 @@ -@prefix bp: . -@prefix linkml: . -@prefix rdf: . -@prefix sh: . -@prefix xsd: . - -bp:Container a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class bp:BioticInteraction ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path bp:interactions ] ; - sh:targetClass bp:Container . - - a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 0 ; - sh:path ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path ] ; - sh:targetClass . - - a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass . - - a sh:NodeShape ; - sh:closed true ; - sh:description "A result of extracting knowledge on text" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 0 ; - sh:path ], - [ sh:maxCount 1 ; - sh:order 4 ; - sh:path ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path ], - [ sh:class linkml:Any ; - sh:description "Named entities extracted from the text" ; - sh:nodeKind sh:BlankNode ; - sh:order 6 ; - sh:path ], - [ sh:class linkml:Any ; - sh:description "The complex objects extracted from the text" ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path ] ; - sh:targetClass . - - a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path ], - [ sh:class ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path ] ; - sh:targetClass . - -bp:BioticInteraction a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class bp:InteractionType ; - sh:description "the type of interaction" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path bp:interaction_type ], - [ sh:class bp:Taxon ; - sh:description "the taxon that is the subject of the interaction" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path bp:source_taxon ], - [ sh:class bp:Taxon ; - sh:description "the taxon that is the object of the ineteraction" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path bp:target_taxon ] ; - sh:targetClass bp:BioticInteraction . - -bp:InteractionType a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path ] ; - sh:targetClass bp:InteractionType . - - a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The title of the publication" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path ], - [ sh:description "The full text of the publication" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path ], - [ sh:description "The abstract of the publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path ], - [ sh:description "The publication identifier" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path ] ; - sh:targetClass . - - a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path ] ; - sh:targetClass . - - a sh:NodeShape ; - sh:closed false ; - sh:description "Abstract parent for Relation Extraction tasks" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class ; - sh:description "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path ], - [ sh:class ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path ], - [ sh:class ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path ], - [ sh:class ; - sh:description "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path ], - [ sh:class ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path ], - [ sh:description "A qualifier for the statements, e.g. \"NOT\" for negation" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path ] ; - sh:targetClass . - -bp:Taxon a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path ] ; - sh:targetClass bp:Taxon . - -linkml:Any a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass linkml:Any . - - a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path ] ; - sh:targetClass . - diff --git a/projects/biotic_interaction/shex/biotic_interaction.shex b/projects/biotic_interaction/shex/biotic_interaction.shex deleted file mode 100644 index e48f21968..000000000 --- a/projects/biotic_interaction/shex/biotic_interaction.shex +++ /dev/null @@ -1,172 +0,0 @@ -BASE -PREFIX rdf: -PREFIX xsd: -PREFIX linkml: -PREFIX core: -PREFIX rdfs1: - - -linkml:String xsd:string - -linkml:Integer xsd:integer - -linkml:Boolean xsd:boolean - -linkml:Float xsd:float - -linkml:Double xsd:double - -linkml:Decimal xsd:decimal - -linkml:Time xsd:time - -linkml:Date xsd:date - -linkml:Datetime xsd:dateTime - -linkml:DateOrDatetime linkml:DateOrDatetime - -linkml:Uriorcurie IRI - -linkml:Curie xsd:string - -linkml:Uri IRI - -linkml:Ncname xsd:string - -linkml:Objectidentifier IRI - -linkml:Nodeidentifier NONLITERAL - -linkml:Jsonpointer xsd:string - -linkml:Jsonpath xsd:string - -linkml:Sparqlpath xsd:string - -core:AnnotatorResult CLOSED { - ( $core:AnnotatorResult_tes ( core:subject_text @linkml:String ? ; - core:object_id @linkml:String ? ; - core:object_text @linkml:String ? - ) ; - rdf:type [ core:AnnotatorResult ] ? - ) -} - -core:Any CLOSED { - ( $core:Any_tes rdf:type . * ; - rdf:type [ linkml:Any ] ? - ) -} - - CLOSED { - ( $ ( - - @ ? ; - - @ ? ; - - @ ? - ) ; - rdf:type [ ] ? - ) -} - -core:CompoundExpression ( - { - ( $core:CompoundExpression_tes rdf:type . * ; - rdf:type [ core:CompoundExpression ] ? - ) - } OR @core:Triple -) - - CLOSED { - ( $ - - @ * ; - rdf:type [ ] ? - ) -} - -core:ExtractionResult CLOSED { - ( $core:ExtractionResult_tes ( core:input_id @linkml:String ? ; - core:input_title @linkml:String ? ; - core:input_text @linkml:String ? ; - core:raw_completion_output @linkml:String ? ; - core:prompt @linkml:String ? ; - core:extracted_object @core:Any ? ; - core:named_entities @core:Any * - ) ; - rdf:type [ core:ExtractionResult ] ? - ) -} - - CLOSED { - ( $ ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ ] - ) -} - -core:NamedEntity ( - @ OR @core:RelationshipType OR - @ -) - -core:NamedEntity_struct { - ( $core:NamedEntity_tes rdfs1:label @linkml:String ? ; - rdf:type [ core:NamedEntity ] - ) -} - -core:Publication CLOSED { - ( $core:Publication_tes ( core:id @linkml:String ? ; - core:title @linkml:String ? ; - core:abstract @linkml:String ? ; - core:combined_text @linkml:String ? ; - core:full_text @linkml:String ? - ) ; - rdf:type [ core:Publication ] ? - ) -} - -core:RelationshipType CLOSED { - ( $core:RelationshipType_tes ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ core:RelationshipType ] - ) -} - - CLOSED { - ( $ ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ ] - ) -} - -core:TextWithTriples CLOSED { - ( $core:TextWithTriples_tes ( core:publication @core:Publication ? ; - core:triples @core:Triple * - ) ; - rdf:type [ core:TextWithTriples ] ? - ) -} - -core:Triple { - ( $core:Triple_tes ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - core:subject @core:NamedEntity ? ; - core:predicate @core:RelationshipType ? ; - core:object @core:NamedEntity ? ; - core:qualifier @linkml:String ? ; - core:subject_qualifier @core:NamedEntity ? ; - core:object_qualifier @core:NamedEntity ? - ) ; - rdf:type [ core:Triple ] ? - ) -} - - diff --git a/projects/biotic_interaction/sqlschema/biotic_interaction.sql b/projects/biotic_interaction/sqlschema/biotic_interaction.sql deleted file mode 100644 index 28357915d..000000000 --- a/projects/biotic_interaction/sqlschema/biotic_interaction.sql +++ /dev/null @@ -1,67 +0,0 @@ - - -CREATE TABLE "AnnotatorResult" ( - subject_text TEXT, - object_id TEXT, - object_text TEXT, - PRIMARY KEY (subject_text, object_id, object_text) -); - -CREATE TABLE "Container" ( - interactions TEXT, - PRIMARY KEY (interactions) -); - -CREATE TABLE "ExtractionResult" ( - input_id TEXT, - input_title TEXT, - input_text TEXT, - raw_completion_output TEXT, - prompt TEXT, - extracted_object TEXT, - named_entities TEXT, - PRIMARY KEY (input_id, input_title, input_text, raw_completion_output, prompt, extracted_object, named_entities) -); - -CREATE TABLE "InteractionType" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Publication" ( - id TEXT, - title TEXT, - abstract TEXT, - combined_text TEXT, - full_text TEXT, - PRIMARY KEY (id, title, abstract, combined_text, full_text) -); - -CREATE TABLE "RelationshipType" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Taxon" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "TextWithTriples" ( - publication TEXT, - triples TEXT, - PRIMARY KEY (publication, triples) -); - -CREATE TABLE "BioticInteraction" ( - source_taxon TEXT, - target_taxon TEXT, - interaction_type TEXT, - PRIMARY KEY (source_taxon, target_taxon, interaction_type), - FOREIGN KEY(source_taxon) REFERENCES "Taxon" (id), - FOREIGN KEY(target_taxon) REFERENCES "Taxon" (id), - FOREIGN KEY(interaction_type) REFERENCES "InteractionType" (id) -); diff --git a/projects/class_enrichment/class_enrichment.py b/projects/class_enrichment/class_enrichment.py deleted file mode 100644 index 74d0538c3..000000000 --- a/projects/class_enrichment/class_enrichment.py +++ /dev/null @@ -1,249 +0,0 @@ -# Auto generated from class_enrichment.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-08-07T10:51:45 -# Schema: class-enrichment -# -# id: https://w3id.org/oak/class-enrichment -# description: A datamodel for representing the results of class enrichment on gene sets -# license: https://creativecommons.org/publicdomain/zero/1.0/ - -import dataclasses -import sys -import re -from jsonasobj2 import JsonObj, as_dict -from typing import Optional, List, Union, Dict, ClassVar, Any -from dataclasses import dataclass -from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions - -from linkml_runtime.utils.slot import Slot -from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode -from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int -from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs -from linkml_runtime.utils.formatutils import camelcase, underscore, sfx -from linkml_runtime.utils.enumerations import EnumDefinitionImpl -from rdflib import Namespace, URIRef -from linkml_runtime.utils.curienamespace import CurieNamespace -from linkml_runtime.linkml_model.types import Boolean, Float, Integer, String, Uriorcurie -from linkml_runtime.utils.metamodelcore import Bool, URIorCURIE - -metamodel_version = "1.7.0" -version = None - -# Overwrite dataclasses _init_fn to add **kwargs in __init__ -dataclasses._init_fn = dataclasses_init_fn_with_kwargs - -# Namespaces -OBI = CurieNamespace('OBI', 'http://purl.obolibrary.org/obo/OBI_') -STATO = CurieNamespace('STATO', 'http://purl.obolibrary.org/obo/STATO_') -BPA = CurieNamespace('bpa', 'https://bioportal.bioontology.org/annotator/') -LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') -OA = CurieNamespace('oa', 'http://www.w3.org/ns/oa#') -ONTOENRICH = CurieNamespace('ontoenrich', 'https://w3id.org/oak/class-enrichment/') -OWL = CurieNamespace('owl', 'http://www.w3.org/2002/07/owl#') -PAV = CurieNamespace('pav', 'http://purl.org/pav/') -PROV = CurieNamespace('prov', 'http://www.w3.org/ns/prov#') -RDF = CurieNamespace('rdf', 'http://www.w3.org/1999/02/22-rdf-syntax-ns#') -RDFS = CurieNamespace('rdfs', 'http://www.w3.org/2000/01/rdf-schema#') -SCHEMA = CurieNamespace('schema', 'http://schema.org/') -SH = CurieNamespace('sh', 'https://w3id.org/shacl/') -SKOS = CurieNamespace('skos', 'http://www.w3.org/2004/02/skos/core#') -SSSOM = CurieNamespace('sssom', 'http://w3id.org/sssom/') -XSD = CurieNamespace('xsd', 'http://www.w3.org/2001/XMLSchema#') -DEFAULT_ = ONTOENRICH - - -# Types -class Position(Integer): - type_class_uri = XSD.integer - type_class_curie = "xsd:integer" - type_name = "Position" - type_model_uri = ONTOENRICH.Position - - -# Class references - - - -@dataclass -class ClassEnrichmentConfiguration(YAMLRoot): - """ - configuration for search - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = ONTOENRICH.ClassEnrichmentConfiguration - class_class_curie: ClassVar[str] = "ontoenrich:ClassEnrichmentConfiguration" - class_name: ClassVar[str] = "ClassEnrichmentConfiguration" - class_model_uri: ClassVar[URIRef] = ONTOENRICH.ClassEnrichmentConfiguration - - p_value_cutoff: float = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.p_value_cutoff): - self.MissingRequiredField("p_value_cutoff") - if not isinstance(self.p_value_cutoff, float): - self.p_value_cutoff = float(self.p_value_cutoff) - - super().__post_init__(**kwargs) - - -@dataclass -class ClassEnrichmentResultSet(YAMLRoot): - """ - A collection of enrichemt results - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = ONTOENRICH.ClassEnrichmentResultSet - class_class_curie: ClassVar[str] = "ontoenrich:ClassEnrichmentResultSet" - class_name: ClassVar[str] = "ClassEnrichmentResultSet" - class_model_uri: ClassVar[URIRef] = ONTOENRICH.ClassEnrichmentResultSet - - results: Optional[Union[Union[dict, "ClassEnrichmentResult"], List[Union[dict, "ClassEnrichmentResult"]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - self._normalize_inlined_as_dict(slot_name="results", slot_type=ClassEnrichmentResult, key_name="class_id", keyed=False) - - super().__post_init__(**kwargs) - - -@dataclass -class ClassEnrichmentResult(YAMLRoot): - """ - A single enrichment result - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = ONTOENRICH.ClassEnrichmentResult - class_class_curie: ClassVar[str] = "ontoenrich:ClassEnrichmentResult" - class_name: ClassVar[str] = "ClassEnrichmentResult" - class_model_uri: ClassVar[URIRef] = ONTOENRICH.ClassEnrichmentResult - - class_id: Union[str, URIorCURIE] = None - p_value: float = None - class_label: Optional[str] = None - rank: Optional[int] = None - p_value_adjusted: Optional[float] = None - false_discovery_rate: Optional[float] = None - fold_enrichment: Optional[float] = None - probability: Optional[float] = None - sample_count: Optional[int] = None - sample_total: Optional[int] = None - background_count: Optional[int] = None - background_total: Optional[int] = None - ancestor_of_more_informative_result: Optional[Union[bool, Bool]] = None - descendant_of_more_informative_result: Optional[Union[bool, Bool]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.class_id): - self.MissingRequiredField("class_id") - if not isinstance(self.class_id, URIorCURIE): - self.class_id = URIorCURIE(self.class_id) - - if self._is_empty(self.p_value): - self.MissingRequiredField("p_value") - if not isinstance(self.p_value, float): - self.p_value = float(self.p_value) - - if self.class_label is not None and not isinstance(self.class_label, str): - self.class_label = str(self.class_label) - - if self.rank is not None and not isinstance(self.rank, int): - self.rank = int(self.rank) - - if self.p_value_adjusted is not None and not isinstance(self.p_value_adjusted, float): - self.p_value_adjusted = float(self.p_value_adjusted) - - if self.false_discovery_rate is not None and not isinstance(self.false_discovery_rate, float): - self.false_discovery_rate = float(self.false_discovery_rate) - - if self.fold_enrichment is not None and not isinstance(self.fold_enrichment, float): - self.fold_enrichment = float(self.fold_enrichment) - - if self.probability is not None and not isinstance(self.probability, float): - self.probability = float(self.probability) - - if self.sample_count is not None and not isinstance(self.sample_count, int): - self.sample_count = int(self.sample_count) - - if self.sample_total is not None and not isinstance(self.sample_total, int): - self.sample_total = int(self.sample_total) - - if self.background_count is not None and not isinstance(self.background_count, int): - self.background_count = int(self.background_count) - - if self.background_total is not None and not isinstance(self.background_total, int): - self.background_total = int(self.background_total) - - if self.ancestor_of_more_informative_result is not None and not isinstance(self.ancestor_of_more_informative_result, Bool): - self.ancestor_of_more_informative_result = Bool(self.ancestor_of_more_informative_result) - - if self.descendant_of_more_informative_result is not None and not isinstance(self.descendant_of_more_informative_result, Bool): - self.descendant_of_more_informative_result = Bool(self.descendant_of_more_informative_result) - - super().__post_init__(**kwargs) - - -# Enumerations -class SortFieldEnum(EnumDefinitionImpl): - """ - The field to sort by - """ - ANY = PermissibleValue(text="ANY") - P_VALUE = PermissibleValue(text="P_VALUE") - - _defn = EnumDefinition( - name="SortFieldEnum", - description="The field to sort by", - ) - -# Slots -class slots: - pass - -slots.classEnrichmentConfiguration__p_value_cutoff = Slot(uri=ONTOENRICH.p_value_cutoff, name="classEnrichmentConfiguration__p_value_cutoff", curie=ONTOENRICH.curie('p_value_cutoff'), - model_uri=ONTOENRICH.classEnrichmentConfiguration__p_value_cutoff, domain=None, range=float) - -slots.classEnrichmentResultSet__results = Slot(uri=ONTOENRICH.results, name="classEnrichmentResultSet__results", curie=ONTOENRICH.curie('results'), - model_uri=ONTOENRICH.classEnrichmentResultSet__results, domain=None, range=Optional[Union[Union[dict, ClassEnrichmentResult], List[Union[dict, ClassEnrichmentResult]]]]) - -slots.classEnrichmentResult__class_id = Slot(uri=ONTOENRICH.class_id, name="classEnrichmentResult__class_id", curie=ONTOENRICH.curie('class_id'), - model_uri=ONTOENRICH.classEnrichmentResult__class_id, domain=None, range=Union[str, URIorCURIE]) - -slots.classEnrichmentResult__class_label = Slot(uri=ONTOENRICH.class_label, name="classEnrichmentResult__class_label", curie=ONTOENRICH.curie('class_label'), - model_uri=ONTOENRICH.classEnrichmentResult__class_label, domain=None, range=Optional[str]) - -slots.classEnrichmentResult__rank = Slot(uri=ONTOENRICH.rank, name="classEnrichmentResult__rank", curie=ONTOENRICH.curie('rank'), - model_uri=ONTOENRICH.classEnrichmentResult__rank, domain=None, range=Optional[int]) - -slots.classEnrichmentResult__p_value = Slot(uri=OBI['0000175'], name="classEnrichmentResult__p_value", curie=OBI.curie('0000175'), - model_uri=ONTOENRICH.classEnrichmentResult__p_value, domain=None, range=float) - -slots.classEnrichmentResult__p_value_adjusted = Slot(uri=ONTOENRICH.p_value_adjusted, name="classEnrichmentResult__p_value_adjusted", curie=ONTOENRICH.curie('p_value_adjusted'), - model_uri=ONTOENRICH.classEnrichmentResult__p_value_adjusted, domain=None, range=Optional[float]) - -slots.classEnrichmentResult__false_discovery_rate = Slot(uri=ONTOENRICH.false_discovery_rate, name="classEnrichmentResult__false_discovery_rate", curie=ONTOENRICH.curie('false_discovery_rate'), - model_uri=ONTOENRICH.classEnrichmentResult__false_discovery_rate, domain=None, range=Optional[float]) - -slots.classEnrichmentResult__fold_enrichment = Slot(uri=ONTOENRICH.fold_enrichment, name="classEnrichmentResult__fold_enrichment", curie=ONTOENRICH.curie('fold_enrichment'), - model_uri=ONTOENRICH.classEnrichmentResult__fold_enrichment, domain=None, range=Optional[float]) - -slots.classEnrichmentResult__probability = Slot(uri=ONTOENRICH.probability, name="classEnrichmentResult__probability", curie=ONTOENRICH.curie('probability'), - model_uri=ONTOENRICH.classEnrichmentResult__probability, domain=None, range=Optional[float]) - -slots.classEnrichmentResult__sample_count = Slot(uri=ONTOENRICH.sample_count, name="classEnrichmentResult__sample_count", curie=ONTOENRICH.curie('sample_count'), - model_uri=ONTOENRICH.classEnrichmentResult__sample_count, domain=None, range=Optional[int]) - -slots.classEnrichmentResult__sample_total = Slot(uri=ONTOENRICH.sample_total, name="classEnrichmentResult__sample_total", curie=ONTOENRICH.curie('sample_total'), - model_uri=ONTOENRICH.classEnrichmentResult__sample_total, domain=None, range=Optional[int]) - -slots.classEnrichmentResult__background_count = Slot(uri=ONTOENRICH.background_count, name="classEnrichmentResult__background_count", curie=ONTOENRICH.curie('background_count'), - model_uri=ONTOENRICH.classEnrichmentResult__background_count, domain=None, range=Optional[int]) - -slots.classEnrichmentResult__background_total = Slot(uri=ONTOENRICH.background_total, name="classEnrichmentResult__background_total", curie=ONTOENRICH.curie('background_total'), - model_uri=ONTOENRICH.classEnrichmentResult__background_total, domain=None, range=Optional[int]) - -slots.classEnrichmentResult__ancestor_of_more_informative_result = Slot(uri=ONTOENRICH.ancestor_of_more_informative_result, name="classEnrichmentResult__ancestor_of_more_informative_result", curie=ONTOENRICH.curie('ancestor_of_more_informative_result'), - model_uri=ONTOENRICH.classEnrichmentResult__ancestor_of_more_informative_result, domain=None, range=Optional[Union[bool, Bool]]) - -slots.classEnrichmentResult__descendant_of_more_informative_result = Slot(uri=ONTOENRICH.descendant_of_more_informative_result, name="classEnrichmentResult__descendant_of_more_informative_result", curie=ONTOENRICH.curie('descendant_of_more_informative_result'), - model_uri=ONTOENRICH.classEnrichmentResult__descendant_of_more_informative_result, domain=None, range=Optional[Union[bool, Bool]]) \ No newline at end of file diff --git a/projects/class_enrichment/docs/ClassEnrichmentConfiguration.md b/projects/class_enrichment/docs/ClassEnrichmentConfiguration.md deleted file mode 100644 index bc480f79b..000000000 --- a/projects/class_enrichment/docs/ClassEnrichmentConfiguration.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Class: ClassEnrichmentConfiguration - - -configuration for search - -URI: [ontoenrich:ClassEnrichmentConfiguration](https://w3id.org/oak/class-enrichment/ClassEnrichmentConfiguration) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ClassEnrichmentConfiguration|p_value_cutoff:float])](https://yuml.me/diagram/nofunky;dir:TB/class/[ClassEnrichmentConfiguration|p_value_cutoff:float]) - -## Attributes - - -### Own - - * [➞p_value_cutoff](classEnrichmentConfiguration__p_value_cutoff.md) 1..1 - * Description: p-value cutoff for enrichment - * Range: [Float](types/Float.md) diff --git a/projects/class_enrichment/docs/ClassEnrichmentResult.md b/projects/class_enrichment/docs/ClassEnrichmentResult.md deleted file mode 100644 index b39918d32..000000000 --- a/projects/class_enrichment/docs/ClassEnrichmentResult.md +++ /dev/null @@ -1,62 +0,0 @@ - -# Class: ClassEnrichmentResult - - -A single enrichment result - -URI: [ontoenrich:ClassEnrichmentResult](https://w3id.org/oak/class-enrichment/ClassEnrichmentResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ClassEnrichmentResultSet]++-%20results%200..*>[ClassEnrichmentResult|class_id:uriorcurie;class_label:string%20%3F;rank:integer%20%3F;p_value:float;p_value_adjusted:float%20%3F;false_discovery_rate:float%20%3F;fold_enrichment:float%20%3F;probability:float%20%3F;sample_count:integer%20%3F;sample_total:integer%20%3F;background_count:integer%20%3F;background_total:integer%20%3F;ancestor_of_more_informative_result:boolean%20%3F;descendant_of_more_informative_result:boolean%20%3F],[ClassEnrichmentResultSet])](https://yuml.me/diagram/nofunky;dir:TB/class/[ClassEnrichmentResultSet]++-%20results%200..*>[ClassEnrichmentResult|class_id:uriorcurie;class_label:string%20%3F;rank:integer%20%3F;p_value:float;p_value_adjusted:float%20%3F;false_discovery_rate:float%20%3F;fold_enrichment:float%20%3F;probability:float%20%3F;sample_count:integer%20%3F;sample_total:integer%20%3F;background_count:integer%20%3F;background_total:integer%20%3F;ancestor_of_more_informative_result:boolean%20%3F;descendant_of_more_informative_result:boolean%20%3F],[ClassEnrichmentResultSet]) - -## Referenced by Class - - * **None** *[➞results](classEnrichmentResultSet__results.md)* 0..\* **[ClassEnrichmentResult](ClassEnrichmentResult.md)** - -## Attributes - - -### Own - - * [➞class_id](classEnrichmentResult__class_id.md) 1..1 - * Description: The class id - * Range: [Uriorcurie](types/Uriorcurie.md) - * [➞class_label](classEnrichmentResult__class_label.md) 0..1 - * Description: The class label - * Range: [String](types/String.md) - * [➞rank](classEnrichmentResult__rank.md) 0..1 - * Description: The rank of this result - * Range: [Integer](types/Integer.md) - * [➞p_value](classEnrichmentResult__p_value.md) 1..1 - * Description: The p-value - * Range: [Float](types/Float.md) - * [➞p_value_adjusted](classEnrichmentResult__p_value_adjusted.md) 0..1 - * Description: The adjusted p-value - * Range: [Float](types/Float.md) - * [➞false_discovery_rate](classEnrichmentResult__false_discovery_rate.md) 0..1 - * Description: The false discovery rate - * Range: [Float](types/Float.md) - * [➞fold_enrichment](classEnrichmentResult__fold_enrichment.md) 0..1 - * Description: The fold enrichment - * Range: [Float](types/Float.md) - * [➞probability](classEnrichmentResult__probability.md) 0..1 - * Description: The probability, as estimated by model-based approaches - * Range: [Float](types/Float.md) - * [➞sample_count](classEnrichmentResult__sample_count.md) 0..1 - * Description: The number of entities in the sample with this class - * Range: [Integer](types/Integer.md) - * [➞sample_total](classEnrichmentResult__sample_total.md) 0..1 - * Description: The total number of entities in the sample - * Range: [Integer](types/Integer.md) - * [➞background_count](classEnrichmentResult__background_count.md) 0..1 - * Description: The background count - * Range: [Integer](types/Integer.md) - * [➞background_total](classEnrichmentResult__background_total.md) 0..1 - * Description: The background total - * Range: [Integer](types/Integer.md) - * [➞ancestor_of_more_informative_result](classEnrichmentResult__ancestor_of_more_informative_result.md) 0..1 - * Description: This term is more general than a previously reported result - * Range: [Boolean](types/Boolean.md) - * [➞descendant_of_more_informative_result](classEnrichmentResult__descendant_of_more_informative_result.md) 0..1 - * Description: This term is more specific than a previously reported result - * Range: [Boolean](types/Boolean.md) diff --git a/projects/class_enrichment/docs/ClassEnrichmentResultSet.md b/projects/class_enrichment/docs/ClassEnrichmentResultSet.md deleted file mode 100644 index 984538cf5..000000000 --- a/projects/class_enrichment/docs/ClassEnrichmentResultSet.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Class: ClassEnrichmentResultSet - - -A collection of enrichemt results - -URI: [ontoenrich:ClassEnrichmentResultSet](https://w3id.org/oak/class-enrichment/ClassEnrichmentResultSet) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ClassEnrichmentResult]0..\* - * Description: The enrichment results - * Range: [ClassEnrichmentResult](ClassEnrichmentResult.md) diff --git a/projects/class_enrichment/docs/SortFieldEnum.md b/projects/class_enrichment/docs/SortFieldEnum.md deleted file mode 100644 index 227c37e4e..000000000 --- a/projects/class_enrichment/docs/SortFieldEnum.md +++ /dev/null @@ -1,21 +0,0 @@ - -# Enum: SortFieldEnum - - -The field to sort by - -URI: [ontoenrich:SortFieldEnum](https://w3id.org/oak/class-enrichment/SortFieldEnum) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | -| ANY | | | | -| P_VALUE | | | | - diff --git a/projects/class_enrichment/docs/classEnrichmentConfiguration__p_value_cutoff.md b/projects/class_enrichment/docs/classEnrichmentConfiguration__p_value_cutoff.md deleted file mode 100644 index a822f3cc1..000000000 --- a/projects/class_enrichment/docs/classEnrichmentConfiguration__p_value_cutoff.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: p_value_cutoff - - -p-value cutoff for enrichment - -URI: [ontoenrich:classEnrichmentConfiguration__p_value_cutoff](https://w3id.org/oak/class-enrichment/classEnrichmentConfiguration__p_value_cutoff) - - -## Domain and Range - -None → 1..1 [Float](types/Float.md) - -## Parents - - -## Children - - -## Used by - - * [ClassEnrichmentConfiguration](ClassEnrichmentConfiguration.md) diff --git a/projects/class_enrichment/docs/classEnrichmentResultSet__results.md b/projects/class_enrichment/docs/classEnrichmentResultSet__results.md deleted file mode 100644 index 2425ab9dd..000000000 --- a/projects/class_enrichment/docs/classEnrichmentResultSet__results.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: results - - -The enrichment results - -URI: [ontoenrich:classEnrichmentResultSet__results](https://w3id.org/oak/class-enrichment/classEnrichmentResultSet__results) - - -## Domain and Range - -None → 0..\* [ClassEnrichmentResult](ClassEnrichmentResult.md) - -## Parents - - -## Children - - -## Used by - - * [ClassEnrichmentResultSet](ClassEnrichmentResultSet.md) diff --git a/projects/class_enrichment/docs/classEnrichmentResult__ancestor_of_more_informative_result.md b/projects/class_enrichment/docs/classEnrichmentResult__ancestor_of_more_informative_result.md deleted file mode 100644 index 661700dbd..000000000 --- a/projects/class_enrichment/docs/classEnrichmentResult__ancestor_of_more_informative_result.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: ancestor_of_more_informative_result - - -This term is more general than a previously reported result - -URI: [ontoenrich:classEnrichmentResult__ancestor_of_more_informative_result](https://w3id.org/oak/class-enrichment/classEnrichmentResult__ancestor_of_more_informative_result) - - -## Domain and Range - -None → 0..1 [Boolean](types/Boolean.md) - -## Parents - - -## Children - - -## Used by - - * [ClassEnrichmentResult](ClassEnrichmentResult.md) diff --git a/projects/class_enrichment/docs/classEnrichmentResult__background_count.md b/projects/class_enrichment/docs/classEnrichmentResult__background_count.md deleted file mode 100644 index 032ea8941..000000000 --- a/projects/class_enrichment/docs/classEnrichmentResult__background_count.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: background_count - - -The background count - -URI: [ontoenrich:classEnrichmentResult__background_count](https://w3id.org/oak/class-enrichment/classEnrichmentResult__background_count) - - -## Domain and Range - -None → 0..1 [Integer](types/Integer.md) - -## Parents - - -## Children - - -## Used by - - * [ClassEnrichmentResult](ClassEnrichmentResult.md) diff --git a/projects/class_enrichment/docs/classEnrichmentResult__background_total.md b/projects/class_enrichment/docs/classEnrichmentResult__background_total.md deleted file mode 100644 index 3661ec524..000000000 --- a/projects/class_enrichment/docs/classEnrichmentResult__background_total.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: background_total - - -The background total - -URI: [ontoenrich:classEnrichmentResult__background_total](https://w3id.org/oak/class-enrichment/classEnrichmentResult__background_total) - - -## Domain and Range - -None → 0..1 [Integer](types/Integer.md) - -## Parents - - -## Children - - -## Used by - - * [ClassEnrichmentResult](ClassEnrichmentResult.md) diff --git a/projects/class_enrichment/docs/classEnrichmentResult__class_id.md b/projects/class_enrichment/docs/classEnrichmentResult__class_id.md deleted file mode 100644 index 6c531b5a4..000000000 --- a/projects/class_enrichment/docs/classEnrichmentResult__class_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: class_id - - -The class id - -URI: [ontoenrich:classEnrichmentResult__class_id](https://w3id.org/oak/class-enrichment/classEnrichmentResult__class_id) - - -## Domain and Range - -None → 1..1 [Uriorcurie](types/Uriorcurie.md) - -## Parents - - -## Children - - -## Used by - - * [ClassEnrichmentResult](ClassEnrichmentResult.md) diff --git a/projects/class_enrichment/docs/classEnrichmentResult__class_label.md b/projects/class_enrichment/docs/classEnrichmentResult__class_label.md deleted file mode 100644 index ae110d671..000000000 --- a/projects/class_enrichment/docs/classEnrichmentResult__class_label.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: class_label - - -The class label - -URI: [ontoenrich:classEnrichmentResult__class_label](https://w3id.org/oak/class-enrichment/classEnrichmentResult__class_label) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ClassEnrichmentResult](ClassEnrichmentResult.md) diff --git a/projects/class_enrichment/docs/classEnrichmentResult__descendant_of_more_informative_result.md b/projects/class_enrichment/docs/classEnrichmentResult__descendant_of_more_informative_result.md deleted file mode 100644 index de7b17c3f..000000000 --- a/projects/class_enrichment/docs/classEnrichmentResult__descendant_of_more_informative_result.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: descendant_of_more_informative_result - - -This term is more specific than a previously reported result - -URI: [ontoenrich:classEnrichmentResult__descendant_of_more_informative_result](https://w3id.org/oak/class-enrichment/classEnrichmentResult__descendant_of_more_informative_result) - - -## Domain and Range - -None → 0..1 [Boolean](types/Boolean.md) - -## Parents - - -## Children - - -## Used by - - * [ClassEnrichmentResult](ClassEnrichmentResult.md) diff --git a/projects/class_enrichment/docs/classEnrichmentResult__false_discovery_rate.md b/projects/class_enrichment/docs/classEnrichmentResult__false_discovery_rate.md deleted file mode 100644 index cee89a949..000000000 --- a/projects/class_enrichment/docs/classEnrichmentResult__false_discovery_rate.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: false_discovery_rate - - -The false discovery rate - -URI: [ontoenrich:classEnrichmentResult__false_discovery_rate](https://w3id.org/oak/class-enrichment/classEnrichmentResult__false_discovery_rate) - - -## Domain and Range - -None → 0..1 [Float](types/Float.md) - -## Parents - - -## Children - - -## Used by - - * [ClassEnrichmentResult](ClassEnrichmentResult.md) diff --git a/projects/class_enrichment/docs/classEnrichmentResult__fold_enrichment.md b/projects/class_enrichment/docs/classEnrichmentResult__fold_enrichment.md deleted file mode 100644 index 5f5042fa1..000000000 --- a/projects/class_enrichment/docs/classEnrichmentResult__fold_enrichment.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: fold_enrichment - - -The fold enrichment - -URI: [ontoenrich:classEnrichmentResult__fold_enrichment](https://w3id.org/oak/class-enrichment/classEnrichmentResult__fold_enrichment) - - -## Domain and Range - -None → 0..1 [Float](types/Float.md) - -## Parents - - -## Children - - -## Used by - - * [ClassEnrichmentResult](ClassEnrichmentResult.md) diff --git a/projects/class_enrichment/docs/classEnrichmentResult__p_value.md b/projects/class_enrichment/docs/classEnrichmentResult__p_value.md deleted file mode 100644 index d96b4d544..000000000 --- a/projects/class_enrichment/docs/classEnrichmentResult__p_value.md +++ /dev/null @@ -1,29 +0,0 @@ - -# Slot: p_value - - -The p-value - -URI: [ontoenrich:classEnrichmentResult__p_value](https://w3id.org/oak/class-enrichment/classEnrichmentResult__p_value) - - -## Domain and Range - -None → 1..1 [Float](types/Float.md) - -## Parents - - -## Children - - -## Used by - - * [ClassEnrichmentResult](ClassEnrichmentResult.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | OBI:0000175 | - diff --git a/projects/class_enrichment/docs/classEnrichmentResult__p_value_adjusted.md b/projects/class_enrichment/docs/classEnrichmentResult__p_value_adjusted.md deleted file mode 100644 index 26e3efb03..000000000 --- a/projects/class_enrichment/docs/classEnrichmentResult__p_value_adjusted.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: p_value_adjusted - - -The adjusted p-value - -URI: [ontoenrich:classEnrichmentResult__p_value_adjusted](https://w3id.org/oak/class-enrichment/classEnrichmentResult__p_value_adjusted) - - -## Domain and Range - -None → 0..1 [Float](types/Float.md) - -## Parents - - -## Children - - -## Used by - - * [ClassEnrichmentResult](ClassEnrichmentResult.md) diff --git a/projects/class_enrichment/docs/classEnrichmentResult__probability.md b/projects/class_enrichment/docs/classEnrichmentResult__probability.md deleted file mode 100644 index 51e5d9f30..000000000 --- a/projects/class_enrichment/docs/classEnrichmentResult__probability.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: probability - - -The probability, as estimated by model-based approaches - -URI: [ontoenrich:classEnrichmentResult__probability](https://w3id.org/oak/class-enrichment/classEnrichmentResult__probability) - - -## Domain and Range - -None → 0..1 [Float](types/Float.md) - -## Parents - - -## Children - - -## Used by - - * [ClassEnrichmentResult](ClassEnrichmentResult.md) diff --git a/projects/class_enrichment/docs/classEnrichmentResult__rank.md b/projects/class_enrichment/docs/classEnrichmentResult__rank.md deleted file mode 100644 index c129300ea..000000000 --- a/projects/class_enrichment/docs/classEnrichmentResult__rank.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: rank - - -The rank of this result - -URI: [ontoenrich:classEnrichmentResult__rank](https://w3id.org/oak/class-enrichment/classEnrichmentResult__rank) - - -## Domain and Range - -None → 0..1 [Integer](types/Integer.md) - -## Parents - - -## Children - - -## Used by - - * [ClassEnrichmentResult](ClassEnrichmentResult.md) diff --git a/projects/class_enrichment/docs/classEnrichmentResult__sample_count.md b/projects/class_enrichment/docs/classEnrichmentResult__sample_count.md deleted file mode 100644 index 0ff4e269f..000000000 --- a/projects/class_enrichment/docs/classEnrichmentResult__sample_count.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: sample_count - - -The number of entities in the sample with this class - -URI: [ontoenrich:classEnrichmentResult__sample_count](https://w3id.org/oak/class-enrichment/classEnrichmentResult__sample_count) - - -## Domain and Range - -None → 0..1 [Integer](types/Integer.md) - -## Parents - - -## Children - - -## Used by - - * [ClassEnrichmentResult](ClassEnrichmentResult.md) diff --git a/projects/class_enrichment/docs/classEnrichmentResult__sample_total.md b/projects/class_enrichment/docs/classEnrichmentResult__sample_total.md deleted file mode 100644 index 51f263d7b..000000000 --- a/projects/class_enrichment/docs/classEnrichmentResult__sample_total.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: sample_total - - -The total number of entities in the sample - -URI: [ontoenrich:classEnrichmentResult__sample_total](https://w3id.org/oak/class-enrichment/classEnrichmentResult__sample_total) - - -## Domain and Range - -None → 0..1 [Integer](types/Integer.md) - -## Parents - - -## Children - - -## Used by - - * [ClassEnrichmentResult](ClassEnrichmentResult.md) diff --git a/projects/class_enrichment/docs/class_enrichment.md b/projects/class_enrichment/docs/class_enrichment.md deleted file mode 100644 index e2cc53aa3..000000000 --- a/projects/class_enrichment/docs/class_enrichment.md +++ /dev/null @@ -1,89 +0,0 @@ - -# class-enrichment - - -**metamodel version:** 1.7.0 - -**version:** None - - -A datamodel for representing the results of class enrichment on gene sets - - -### Classes - - * [ClassEnrichmentConfiguration](ClassEnrichmentConfiguration.md) - configuration for search - * [ClassEnrichmentResult](ClassEnrichmentResult.md) - A single enrichment result - * [ClassEnrichmentResultSet](ClassEnrichmentResultSet.md) - A collection of enrichemt results - -### Mixins - - -### Slots - - * [➞p_value_cutoff](classEnrichmentConfiguration__p_value_cutoff.md) - p-value cutoff for enrichment - * [➞results](classEnrichmentResultSet__results.md) - The enrichment results - * [➞ancestor_of_more_informative_result](classEnrichmentResult__ancestor_of_more_informative_result.md) - This term is more general than a previously reported result - * [➞background_count](classEnrichmentResult__background_count.md) - The background count - * [➞background_total](classEnrichmentResult__background_total.md) - The background total - * [➞class_id](classEnrichmentResult__class_id.md) - The class id - * [➞class_label](classEnrichmentResult__class_label.md) - The class label - * [➞descendant_of_more_informative_result](classEnrichmentResult__descendant_of_more_informative_result.md) - This term is more specific than a previously reported result - * [➞false_discovery_rate](classEnrichmentResult__false_discovery_rate.md) - The false discovery rate - * [➞fold_enrichment](classEnrichmentResult__fold_enrichment.md) - The fold enrichment - * [➞p_value](classEnrichmentResult__p_value.md) - The p-value - * [➞p_value_adjusted](classEnrichmentResult__p_value_adjusted.md) - The adjusted p-value - * [➞probability](classEnrichmentResult__probability.md) - The probability, as estimated by model-based approaches - * [➞rank](classEnrichmentResult__rank.md) - The rank of this result - * [➞sample_count](classEnrichmentResult__sample_count.md) - The number of entities in the sample with this class - * [➞sample_total](classEnrichmentResult__sample_total.md) - The total number of entities in the sample - -### Enums - - * [SortFieldEnum](SortFieldEnum.md) - The field to sort by - -### Subsets - - -### Types - - -#### Built in - - * **Bool** - * **Curie** - * **Decimal** - * **ElementIdentifier** - * **NCName** - * **NodeIdentifier** - * **URI** - * **URIorCURIE** - * **XSDDate** - * **XSDDateTime** - * **XSDTime** - * **float** - * **int** - * **str** - -#### Defined - - * [Position](types/Position.md) ([Integer](types/Integer.md)) - * [Boolean](types/Boolean.md) (**Bool**) - A binary (true or false) value - * [Curie](types/Curie.md) (**Curie**) - a compact URI - * [Date](types/Date.md) (**XSDDate**) - a date (year, month and day) in an idealized calendar - * [DateOrDatetime](types/DateOrDatetime.md) (**str**) - Either a date or a datetime - * [Datetime](types/Datetime.md) (**XSDDateTime**) - The combination of a date and time - * [Decimal](types/Decimal.md) (**Decimal**) - A real number with arbitrary precision that conforms to the xsd:decimal specification - * [Double](types/Double.md) (**float**) - A real number that conforms to the xsd:double specification - * [Float](types/Float.md) (**float**) - A real number that conforms to the xsd:float specification - * [Integer](types/Integer.md) (**int**) - An integer - * [Jsonpath](types/Jsonpath.md) (**str**) - A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - * [Jsonpointer](types/Jsonpointer.md) (**str**) - A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - * [Ncname](types/Ncname.md) (**NCName**) - Prefix part of CURIE - * [Nodeidentifier](types/Nodeidentifier.md) (**NodeIdentifier**) - A URI, CURIE or BNODE that represents a node in a model. - * [Objectidentifier](types/Objectidentifier.md) (**ElementIdentifier**) - A URI or CURIE that represents an object in the model. - * [Sparqlpath](types/Sparqlpath.md) (**str**) - A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - * [String](types/String.md) (**str**) - A character string - * [Time](types/Time.md) (**XSDTime**) - A time object represents a (local) time of day, independent of any particular day - * [Uri](types/Uri.md) (**URI**) - a complete URI - * [Uriorcurie](types/Uriorcurie.md) (**URIorCURIE**) - a URI or a CURIE diff --git a/projects/class_enrichment/docs/types/Boolean.md b/projects/class_enrichment/docs/types/Boolean.md deleted file mode 100644 index dc83a9c6e..000000000 --- a/projects/class_enrichment/docs/types/Boolean.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: boolean - - -A binary (true or false) value - -URI: [linkml:Boolean](https://w3id.org/linkml/Boolean) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Bool** | -| Representation | | bool | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Boolean | - diff --git a/projects/class_enrichment/docs/types/Curie.md b/projects/class_enrichment/docs/types/Curie.md deleted file mode 100644 index c1803f93f..000000000 --- a/projects/class_enrichment/docs/types/Curie.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: curie - - -a compact URI - -URI: [linkml:Curie](https://w3id.org/linkml/Curie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Curie** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations this MUST be expanded to a URI | -| | | in non-RDF serializations MAY be serialized as the compact representation | - diff --git a/projects/class_enrichment/docs/types/Date.md b/projects/class_enrichment/docs/types/Date.md deleted file mode 100644 index 06948af97..000000000 --- a/projects/class_enrichment/docs/types/Date.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: date - - -a date (year, month and day) in an idealized calendar - -URI: [linkml:Date](https://w3id.org/linkml/Date) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDate** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Date | - diff --git a/projects/class_enrichment/docs/types/DateOrDatetime.md b/projects/class_enrichment/docs/types/DateOrDatetime.md deleted file mode 100644 index ef983898d..000000000 --- a/projects/class_enrichment/docs/types/DateOrDatetime.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: date_or_datetime - - -Either a date or a datetime - -URI: [linkml:DateOrDatetime](https://w3id.org/linkml/DateOrDatetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/class_enrichment/docs/types/Datetime.md b/projects/class_enrichment/docs/types/Datetime.md deleted file mode 100644 index 9510454a8..000000000 --- a/projects/class_enrichment/docs/types/Datetime.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: datetime - - -The combination of a date and time - -URI: [linkml:Datetime](https://w3id.org/linkml/Datetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDateTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:DateTime | - diff --git a/projects/class_enrichment/docs/types/Decimal.md b/projects/class_enrichment/docs/types/Decimal.md deleted file mode 100644 index a7ba14a5d..000000000 --- a/projects/class_enrichment/docs/types/Decimal.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: decimal - - -A real number with arbitrary precision that conforms to the xsd:decimal specification - -URI: [linkml:Decimal](https://w3id.org/linkml/Decimal) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Decimal** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Broad Mappings:** | | schema:Number | - diff --git a/projects/class_enrichment/docs/types/Double.md b/projects/class_enrichment/docs/types/Double.md deleted file mode 100644 index cfe6d71e2..000000000 --- a/projects/class_enrichment/docs/types/Double.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: double - - -A real number that conforms to the xsd:double specification - -URI: [linkml:Double](https://w3id.org/linkml/Double) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Close Mappings:** | | schema:Float | - diff --git a/projects/class_enrichment/docs/types/Float.md b/projects/class_enrichment/docs/types/Float.md deleted file mode 100644 index 7b303f96f..000000000 --- a/projects/class_enrichment/docs/types/Float.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: float - - -A real number that conforms to the xsd:float specification - -URI: [linkml:Float](https://w3id.org/linkml/Float) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Float | - diff --git a/projects/class_enrichment/docs/types/Integer.md b/projects/class_enrichment/docs/types/Integer.md deleted file mode 100644 index 3cfcc66d9..000000000 --- a/projects/class_enrichment/docs/types/Integer.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: integer - - -An integer - -URI: [linkml:Integer](https://w3id.org/linkml/Integer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **int** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Integer | - diff --git a/projects/class_enrichment/docs/types/Jsonpath.md b/projects/class_enrichment/docs/types/Jsonpath.md deleted file mode 100644 index a03a58e67..000000000 --- a/projects/class_enrichment/docs/types/Jsonpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpath - - -A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpath](https://w3id.org/linkml/Jsonpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/class_enrichment/docs/types/Jsonpointer.md b/projects/class_enrichment/docs/types/Jsonpointer.md deleted file mode 100644 index a0e1ac492..000000000 --- a/projects/class_enrichment/docs/types/Jsonpointer.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpointer - - -A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpointer](https://w3id.org/linkml/Jsonpointer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/class_enrichment/docs/types/Ncname.md b/projects/class_enrichment/docs/types/Ncname.md deleted file mode 100644 index 710b0b04a..000000000 --- a/projects/class_enrichment/docs/types/Ncname.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: ncname - - -Prefix part of CURIE - -URI: [linkml:Ncname](https://w3id.org/linkml/Ncname) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NCName** | -| Representation | | str | diff --git a/projects/class_enrichment/docs/types/Nodeidentifier.md b/projects/class_enrichment/docs/types/Nodeidentifier.md deleted file mode 100644 index f0097cdf4..000000000 --- a/projects/class_enrichment/docs/types/Nodeidentifier.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: nodeidentifier - - -A URI, CURIE or BNODE that represents a node in a model. - -URI: [linkml:Nodeidentifier](https://w3id.org/linkml/Nodeidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NodeIdentifier** | -| Representation | | str | diff --git a/projects/class_enrichment/docs/types/Objectidentifier.md b/projects/class_enrichment/docs/types/Objectidentifier.md deleted file mode 100644 index 454ba6be6..000000000 --- a/projects/class_enrichment/docs/types/Objectidentifier.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: objectidentifier - - -A URI or CURIE that represents an object in the model. - -URI: [linkml:Objectidentifier](https://w3id.org/linkml/Objectidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **ElementIdentifier** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | Used for inheritance and type checking | - diff --git a/projects/class_enrichment/docs/types/Position.md b/projects/class_enrichment/docs/types/Position.md deleted file mode 100644 index ad3e7e98d..000000000 --- a/projects/class_enrichment/docs/types/Position.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: Position - - - - -URI: [ontoenrich:Position](https://w3id.org/oak/class-enrichment/Position) - -| | | | -| --- | --- | --- | -| Parent type | | [Integer](types/Integer.md) | -| Root (builtin) type | | **int** | diff --git a/projects/class_enrichment/docs/types/Sparqlpath.md b/projects/class_enrichment/docs/types/Sparqlpath.md deleted file mode 100644 index fd99a927e..000000000 --- a/projects/class_enrichment/docs/types/Sparqlpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: sparqlpath - - -A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - -URI: [linkml:Sparqlpath](https://w3id.org/linkml/Sparqlpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/class_enrichment/docs/types/String.md b/projects/class_enrichment/docs/types/String.md deleted file mode 100644 index 6e61d7081..000000000 --- a/projects/class_enrichment/docs/types/String.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: string - - -A character string - -URI: [linkml:String](https://w3id.org/linkml/String) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Text | - diff --git a/projects/class_enrichment/docs/types/Time.md b/projects/class_enrichment/docs/types/Time.md deleted file mode 100644 index 2b8652bcd..000000000 --- a/projects/class_enrichment/docs/types/Time.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: time - - -A time object represents a (local) time of day, independent of any particular day - -URI: [linkml:Time](https://w3id.org/linkml/Time) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Time | - diff --git a/projects/class_enrichment/docs/types/Uri.md b/projects/class_enrichment/docs/types/Uri.md deleted file mode 100644 index 343807a5e..000000000 --- a/projects/class_enrichment/docs/types/Uri.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: uri - - -a complete URI - -URI: [linkml:Uri](https://w3id.org/linkml/Uri) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URI** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node | -| **Close Mappings:** | | schema:URL | - diff --git a/projects/class_enrichment/docs/types/Uriorcurie.md b/projects/class_enrichment/docs/types/Uriorcurie.md deleted file mode 100644 index 2f7b65087..000000000 --- a/projects/class_enrichment/docs/types/Uriorcurie.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: uriorcurie - - -a URI or a CURIE - -URI: [linkml:Uriorcurie](https://w3id.org/linkml/Uriorcurie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URIorCURIE** | -| Representation | | str | diff --git a/projects/class_enrichment/excel/class_enrichment.xlsx b/projects/class_enrichment/excel/class_enrichment.xlsx deleted file mode 100644 index e8edbe391..000000000 Binary files a/projects/class_enrichment/excel/class_enrichment.xlsx and /dev/null differ diff --git a/projects/class_enrichment/graphql/class_enrichment.graphql b/projects/class_enrichment/graphql/class_enrichment.graphql deleted file mode 100644 index d554fb474..000000000 --- a/projects/class_enrichment/graphql/class_enrichment.graphql +++ /dev/null @@ -1,28 +0,0 @@ -type ClassEnrichmentConfiguration - { - pValueCutoff: Float! - } - -type ClassEnrichmentResult - { - classId: Uriorcurie! - classLabel: String - rank: Integer - pValue: Float! - pValueAdjusted: Float - falseDiscoveryRate: Float - foldEnrichment: Float - probability: Float - sampleCount: Integer - sampleTotal: Integer - backgroundCount: Integer - backgroundTotal: Integer - ancestorOfMoreInformativeResult: Boolean - descendantOfMoreInformativeResult: Boolean - } - -type ClassEnrichmentResultSet - { - results: [ClassEnrichmentResult] - } - diff --git a/projects/class_enrichment/jsonld/class_enrichment.context.jsonld b/projects/class_enrichment/jsonld/class_enrichment.context.jsonld deleted file mode 100644 index 4ebfa58fc..000000000 --- a/projects/class_enrichment/jsonld/class_enrichment.context.jsonld +++ /dev/null @@ -1,78 +0,0 @@ -{ - "comments": { - "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2023-08-07T10:51:40", - "source": "class_enrichment.yaml" - }, - "@context": { - "OBI": { - "@id": "http://purl.obolibrary.org/obo/OBI_", - "@prefix": true - }, - "STATO": { - "@id": "http://purl.obolibrary.org/obo/STATO_", - "@prefix": true - }, - "bpa": "https://bioportal.bioontology.org/annotator/", - "linkml": "https://w3id.org/linkml/", - "oa": "http://www.w3.org/ns/oa#", - "ontoenrich": "https://w3id.org/oak/class-enrichment/", - "owl": "http://www.w3.org/2002/07/owl#", - "pav": "http://purl.org/pav/", - "prov": "http://www.w3.org/ns/prov#", - "rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#", - "rdfs": "http://www.w3.org/2000/01/rdf-schema#", - "schema": "http://schema.org/", - "sh": "https://w3id.org/shacl/", - "skos": "http://www.w3.org/2004/02/skos/core#", - "sssom": "http://w3id.org/sssom/", - "xsd": "http://www.w3.org/2001/XMLSchema#", - "@vocab": "https://w3id.org/oak/class-enrichment/", - "p_value_cutoff": { - "@type": "xsd:float" - }, - "ancestor_of_more_informative_result": { - "@type": "xsd:boolean" - }, - "background_count": { - "@type": "xsd:integer" - }, - "background_total": { - "@type": "xsd:integer" - }, - "class_id": { - "@type": "@id" - }, - "descendant_of_more_informative_result": { - "@type": "xsd:boolean" - }, - "false_discovery_rate": { - "@type": "xsd:float" - }, - "fold_enrichment": { - "@type": "xsd:float" - }, - "p_value": { - "@type": "xsd:float", - "@id": "OBI:0000175" - }, - "p_value_adjusted": { - "@type": "xsd:float" - }, - "probability": { - "@type": "xsd:float" - }, - "rank": { - "@type": "xsd:integer" - }, - "sample_count": { - "@type": "xsd:integer" - }, - "sample_total": { - "@type": "xsd:integer" - }, - "results": { - "@type": "@id" - } - } -} diff --git a/projects/class_enrichment/jsonld/class_enrichment.jsonld b/projects/class_enrichment/jsonld/class_enrichment.jsonld deleted file mode 100644 index 763a76a58..000000000 --- a/projects/class_enrichment/jsonld/class_enrichment.jsonld +++ /dev/null @@ -1,747 +0,0 @@ -{ - "name": "class-enrichment", - "description": "A datamodel for representing the results of class enrichment on gene sets", - "title": "Class Enrichment Datamodel", - "id": "https://w3id.org/oak/class-enrichment", - "imports": [ - "linkml:types" - ], - "license": "https://creativecommons.org/publicdomain/zero/1.0/", - "prefixes": [ - { - "prefix_prefix": "linkml", - "prefix_reference": "https://w3id.org/linkml/" - }, - { - "prefix_prefix": "ontoenrich", - "prefix_reference": "https://w3id.org/oak/class-enrichment/" - }, - { - "prefix_prefix": "skos", - "prefix_reference": "http://www.w3.org/2004/02/skos/core#" - }, - { - "prefix_prefix": "pav", - "prefix_reference": "http://purl.org/pav/" - }, - { - "prefix_prefix": "schema", - "prefix_reference": "http://schema.org/" - }, - { - "prefix_prefix": "sh", - "prefix_reference": "https://w3id.org/shacl/" - }, - { - "prefix_prefix": "prov", - "prefix_reference": "http://www.w3.org/ns/prov#" - }, - { - "prefix_prefix": "sssom", - "prefix_reference": "http://w3id.org/sssom/" - }, - { - "prefix_prefix": "bpa", - "prefix_reference": "https://bioportal.bioontology.org/annotator/" - }, - { - "prefix_prefix": "oa", - "prefix_reference": "http://www.w3.org/ns/oa#" - }, - { - "prefix_prefix": "STATO", - "prefix_reference": "http://purl.obolibrary.org/obo/STATO_" - }, - { - "prefix_prefix": "OBI", - "prefix_reference": "http://purl.obolibrary.org/obo/OBI_" - } - ], - "emit_prefixes": [ - "linkml", - "rdf", - "rdfs", - "xsd", - "owl" - ], - "default_curi_maps": [ - "semweb_context" - ], - "default_prefix": "ontoenrich", - "default_range": "string", - "types": [ - { - "name": "Position", - "definition_uri": "https://w3id.org/oak/class-enrichment/Position", - "from_schema": "https://w3id.org/oak/class-enrichment", - "typeof": "integer", - "base": "int", - "uri": "http://www.w3.org/2001/XMLSchema#integer", - "@type": "TypeDefinition" - }, - { - "name": "string", - "definition_uri": "https://w3id.org/linkml/String", - "description": "A character string", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Text" - ], - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "@type": "TypeDefinition" - }, - { - "name": "integer", - "definition_uri": "https://w3id.org/linkml/Integer", - "description": "An integer", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Integer" - ], - "base": "int", - "uri": "http://www.w3.org/2001/XMLSchema#integer", - "@type": "TypeDefinition" - }, - { - "name": "boolean", - "definition_uri": "https://w3id.org/linkml/Boolean", - "description": "A binary (true or false) value", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Boolean" - ], - "base": "Bool", - "uri": "http://www.w3.org/2001/XMLSchema#boolean", - "repr": "bool", - "@type": "TypeDefinition" - }, - { - "name": "float", - "definition_uri": "https://w3id.org/linkml/Float", - "description": "A real number that conforms to the xsd:float specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#float", - "@type": "TypeDefinition" - }, - { - "name": "double", - "definition_uri": "https://w3id.org/linkml/Double", - "description": "A real number that conforms to the xsd:double specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#double", - "@type": "TypeDefinition" - }, - { - "name": "decimal", - "definition_uri": "https://w3id.org/linkml/Decimal", - "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "broad_mappings": [ - "schema:Number" - ], - "base": "Decimal", - "uri": "http://www.w3.org/2001/XMLSchema#decimal", - "@type": "TypeDefinition" - }, - { - "name": "time", - "definition_uri": "https://w3id.org/linkml/Time", - "description": "A time object represents a (local) time of day, independent of any particular day", - "notes": [ - "URI is dateTime because OWL reasoners do not work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Time" - ], - "base": "XSDTime", - "uri": "http://www.w3.org/2001/XMLSchema#time", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date", - "definition_uri": "https://w3id.org/linkml/Date", - "description": "a date (year, month and day) in an idealized calendar", - "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Date" - ], - "base": "XSDDate", - "uri": "http://www.w3.org/2001/XMLSchema#date", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "datetime", - "definition_uri": "https://w3id.org/linkml/Datetime", - "description": "The combination of a date and time", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:DateTime" - ], - "base": "XSDDateTime", - "uri": "http://www.w3.org/2001/XMLSchema#dateTime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date_or_datetime", - "definition_uri": "https://w3id.org/linkml/DateOrDatetime", - "description": "Either a date or a datetime", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "https://w3id.org/linkml/DateOrDatetime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uriorcurie", - "definition_uri": "https://w3id.org/linkml/Uriorcurie", - "description": "a URI or a CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "URIorCURIE", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "curie", - "definition_uri": "https://w3id.org/linkml/Curie", - "conforms_to": "https://www.w3.org/TR/curie/", - "description": "a compact URI", - "comments": [ - "in RDF serializations this MUST be expanded to a URI", - "in non-RDF serializations MAY be serialized as the compact representation" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "Curie", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uri", - "definition_uri": "https://w3id.org/linkml/Uri", - "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", - "description": "a complete URI", - "comments": [ - "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:URL" - ], - "base": "URI", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "ncname", - "definition_uri": "https://w3id.org/linkml/Ncname", - "description": "Prefix part of CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NCName", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "objectidentifier", - "definition_uri": "https://w3id.org/linkml/Objectidentifier", - "description": "A URI or CURIE that represents an object in the model.", - "comments": [ - "Used for inheritance and type checking" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "ElementIdentifier", - "uri": "http://www.w3.org/ns/shex#iri", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "nodeidentifier", - "definition_uri": "https://w3id.org/linkml/Nodeidentifier", - "description": "A URI, CURIE or BNODE that represents a node in a model.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NodeIdentifier", - "uri": "http://www.w3.org/ns/shex#nonLiteral", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpointer", - "definition_uri": "https://w3id.org/linkml/Jsonpointer", - "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901", - "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpath", - "definition_uri": "https://w3id.org/linkml/Jsonpath", - "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html", - "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "sparqlpath", - "definition_uri": "https://w3id.org/linkml/Sparqlpath", - "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths", - "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - } - ], - "enums": [ - { - "name": "SortFieldEnum", - "definition_uri": "https://w3id.org/oak/class-enrichment/SortFieldEnum", - "description": "The field to sort by", - "from_schema": "https://w3id.org/oak/class-enrichment", - "permissible_values": [ - { - "text": "ANY" - }, - { - "text": "P_VALUE" - } - ] - } - ], - "slots": [ - { - "name": "classEnrichmentConfiguration__p_value_cutoff", - "description": "p-value cutoff for enrichment", - "from_schema": "https://w3id.org/oak/class-enrichment", - "slot_uri": "https://w3id.org/oak/class-enrichment/p_value_cutoff", - "alias": "p_value_cutoff", - "owner": "ClassEnrichmentConfiguration", - "domain_of": [ - "ClassEnrichmentConfiguration" - ], - "range": "float", - "required": true, - "@type": "SlotDefinition" - }, - { - "name": "classEnrichmentResultSet__results", - "description": "The enrichment results", - "from_schema": "https://w3id.org/oak/class-enrichment", - "slot_uri": "https://w3id.org/oak/class-enrichment/results", - "multivalued": true, - "alias": "results", - "owner": "ClassEnrichmentResultSet", - "domain_of": [ - "ClassEnrichmentResultSet" - ], - "range": "ClassEnrichmentResult", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "classEnrichmentResult__class_id", - "description": "The class id", - "from_schema": "https://w3id.org/oak/class-enrichment", - "slot_uri": "https://w3id.org/oak/class-enrichment/class_id", - "alias": "class_id", - "owner": "ClassEnrichmentResult", - "domain_of": [ - "ClassEnrichmentResult" - ], - "range": "uriorcurie", - "required": true, - "@type": "SlotDefinition" - }, - { - "name": "classEnrichmentResult__class_label", - "description": "The class label", - "from_schema": "https://w3id.org/oak/class-enrichment", - "slot_uri": "https://w3id.org/oak/class-enrichment/class_label", - "alias": "class_label", - "owner": "ClassEnrichmentResult", - "domain_of": [ - "ClassEnrichmentResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "classEnrichmentResult__rank", - "description": "The rank of this result", - "from_schema": "https://w3id.org/oak/class-enrichment", - "slot_uri": "https://w3id.org/oak/class-enrichment/rank", - "alias": "rank", - "owner": "ClassEnrichmentResult", - "domain_of": [ - "ClassEnrichmentResult" - ], - "range": "integer", - "@type": "SlotDefinition" - }, - { - "name": "classEnrichmentResult__p_value", - "description": "The p-value", - "from_schema": "https://w3id.org/oak/class-enrichment", - "mappings": [ - "http://purl.obolibrary.org/obo/OBI_0000175" - ], - "slot_uri": "http://purl.obolibrary.org/obo/OBI_0000175", - "alias": "p_value", - "owner": "ClassEnrichmentResult", - "domain_of": [ - "ClassEnrichmentResult" - ], - "range": "float", - "required": true, - "@type": "SlotDefinition" - }, - { - "name": "classEnrichmentResult__p_value_adjusted", - "description": "The adjusted p-value", - "from_schema": "https://w3id.org/oak/class-enrichment", - "slot_uri": "https://w3id.org/oak/class-enrichment/p_value_adjusted", - "alias": "p_value_adjusted", - "owner": "ClassEnrichmentResult", - "domain_of": [ - "ClassEnrichmentResult" - ], - "range": "float", - "@type": "SlotDefinition" - }, - { - "name": "classEnrichmentResult__false_discovery_rate", - "description": "The false discovery rate", - "from_schema": "https://w3id.org/oak/class-enrichment", - "slot_uri": "https://w3id.org/oak/class-enrichment/false_discovery_rate", - "alias": "false_discovery_rate", - "owner": "ClassEnrichmentResult", - "domain_of": [ - "ClassEnrichmentResult" - ], - "range": "float", - "@type": "SlotDefinition" - }, - { - "name": "classEnrichmentResult__fold_enrichment", - "description": "The fold enrichment", - "from_schema": "https://w3id.org/oak/class-enrichment", - "slot_uri": "https://w3id.org/oak/class-enrichment/fold_enrichment", - "alias": "fold_enrichment", - "owner": "ClassEnrichmentResult", - "domain_of": [ - "ClassEnrichmentResult" - ], - "range": "float", - "@type": "SlotDefinition" - }, - { - "name": "classEnrichmentResult__probability", - "description": "The probability, as estimated by model-based approaches", - "from_schema": "https://w3id.org/oak/class-enrichment", - "slot_uri": "https://w3id.org/oak/class-enrichment/probability", - "alias": "probability", - "owner": "ClassEnrichmentResult", - "domain_of": [ - "ClassEnrichmentResult" - ], - "range": "float", - "minimum_value": 0, - "maximum_value": 1, - "@type": "SlotDefinition" - }, - { - "name": "classEnrichmentResult__sample_count", - "description": "The number of entities in the sample with this class", - "from_schema": "https://w3id.org/oak/class-enrichment", - "slot_uri": "https://w3id.org/oak/class-enrichment/sample_count", - "alias": "sample_count", - "owner": "ClassEnrichmentResult", - "domain_of": [ - "ClassEnrichmentResult" - ], - "range": "integer", - "@type": "SlotDefinition" - }, - { - "name": "classEnrichmentResult__sample_total", - "description": "The total number of entities in the sample", - "from_schema": "https://w3id.org/oak/class-enrichment", - "slot_uri": "https://w3id.org/oak/class-enrichment/sample_total", - "alias": "sample_total", - "owner": "ClassEnrichmentResult", - "domain_of": [ - "ClassEnrichmentResult" - ], - "range": "integer", - "@type": "SlotDefinition" - }, - { - "name": "classEnrichmentResult__background_count", - "description": "The background count", - "from_schema": "https://w3id.org/oak/class-enrichment", - "slot_uri": "https://w3id.org/oak/class-enrichment/background_count", - "alias": "background_count", - "owner": "ClassEnrichmentResult", - "domain_of": [ - "ClassEnrichmentResult" - ], - "range": "integer", - "@type": "SlotDefinition" - }, - { - "name": "classEnrichmentResult__background_total", - "description": "The background total", - "from_schema": "https://w3id.org/oak/class-enrichment", - "slot_uri": "https://w3id.org/oak/class-enrichment/background_total", - "alias": "background_total", - "owner": "ClassEnrichmentResult", - "domain_of": [ - "ClassEnrichmentResult" - ], - "range": "integer", - "@type": "SlotDefinition" - }, - { - "name": "classEnrichmentResult__ancestor_of_more_informative_result", - "description": "This term is more general than a previously reported result", - "from_schema": "https://w3id.org/oak/class-enrichment", - "slot_uri": "https://w3id.org/oak/class-enrichment/ancestor_of_more_informative_result", - "alias": "ancestor_of_more_informative_result", - "owner": "ClassEnrichmentResult", - "domain_of": [ - "ClassEnrichmentResult" - ], - "range": "boolean", - "@type": "SlotDefinition" - }, - { - "name": "classEnrichmentResult__descendant_of_more_informative_result", - "description": "This term is more specific than a previously reported result", - "from_schema": "https://w3id.org/oak/class-enrichment", - "slot_uri": "https://w3id.org/oak/class-enrichment/descendant_of_more_informative_result", - "alias": "descendant_of_more_informative_result", - "owner": "ClassEnrichmentResult", - "domain_of": [ - "ClassEnrichmentResult" - ], - "range": "boolean", - "@type": "SlotDefinition" - } - ], - "classes": [ - { - "name": "ClassEnrichmentConfiguration", - "definition_uri": "https://w3id.org/oak/class-enrichment/ClassEnrichmentConfiguration", - "description": "configuration for search", - "from_schema": "https://w3id.org/oak/class-enrichment", - "slots": [ - "classEnrichmentConfiguration__p_value_cutoff" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "p_value_cutoff", - "description": "p-value cutoff for enrichment", - "range": "float", - "required": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "https://w3id.org/oak/class-enrichment/ClassEnrichmentConfiguration", - "@type": "ClassDefinition" - }, - { - "name": "ClassEnrichmentResultSet", - "definition_uri": "https://w3id.org/oak/class-enrichment/ClassEnrichmentResultSet", - "description": "A collection of enrichemt results", - "from_schema": "https://w3id.org/oak/class-enrichment", - "slots": [ - "classEnrichmentResultSet__results" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "results", - "description": "The enrichment results", - "multivalued": true, - "range": "ClassEnrichmentResult", - "@type": "SlotDefinition" - } - ], - "class_uri": "https://w3id.org/oak/class-enrichment/ClassEnrichmentResultSet", - "@type": "ClassDefinition" - }, - { - "name": "ClassEnrichmentResult", - "definition_uri": "https://w3id.org/oak/class-enrichment/ClassEnrichmentResult", - "description": "A single enrichment result", - "from_schema": "https://w3id.org/oak/class-enrichment", - "slots": [ - "classEnrichmentResult__class_id", - "classEnrichmentResult__class_label", - "classEnrichmentResult__rank", - "classEnrichmentResult__p_value", - "classEnrichmentResult__p_value_adjusted", - "classEnrichmentResult__false_discovery_rate", - "classEnrichmentResult__fold_enrichment", - "classEnrichmentResult__probability", - "classEnrichmentResult__sample_count", - "classEnrichmentResult__sample_total", - "classEnrichmentResult__background_count", - "classEnrichmentResult__background_total", - "classEnrichmentResult__ancestor_of_more_informative_result", - "classEnrichmentResult__descendant_of_more_informative_result" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "class_id", - "description": "The class id", - "range": "uriorcurie", - "required": true, - "@type": "SlotDefinition" - }, - { - "name": "class_label", - "description": "The class label", - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "rank", - "description": "The rank of this result", - "range": "integer", - "@type": "SlotDefinition" - }, - { - "name": "p_value", - "description": "The p-value", - "slot_uri": "OBI:0000175", - "range": "float", - "required": true, - "@type": "SlotDefinition" - }, - { - "name": "p_value_adjusted", - "description": "The adjusted p-value", - "range": "float", - "@type": "SlotDefinition" - }, - { - "name": "false_discovery_rate", - "description": "The false discovery rate", - "range": "float", - "@type": "SlotDefinition" - }, - { - "name": "fold_enrichment", - "description": "The fold enrichment", - "range": "float", - "@type": "SlotDefinition" - }, - { - "name": "probability", - "description": "The probability, as estimated by model-based approaches", - "range": "float", - "minimum_value": 0, - "maximum_value": 1, - "@type": "SlotDefinition" - }, - { - "name": "sample_count", - "description": "The number of entities in the sample with this class", - "range": "integer", - "@type": "SlotDefinition" - }, - { - "name": "sample_total", - "description": "The total number of entities in the sample", - "range": "integer", - "@type": "SlotDefinition" - }, - { - "name": "background_count", - "description": "The background count", - "range": "integer", - "@type": "SlotDefinition" - }, - { - "name": "background_total", - "description": "The background total", - "range": "integer", - "@type": "SlotDefinition" - }, - { - "name": "ancestor_of_more_informative_result", - "description": "This term is more general than a previously reported result", - "range": "boolean", - "@type": "SlotDefinition" - }, - { - "name": "descendant_of_more_informative_result", - "description": "This term is more specific than a previously reported result", - "range": "boolean", - "@type": "SlotDefinition" - } - ], - "class_uri": "https://w3id.org/oak/class-enrichment/ClassEnrichmentResult", - "@type": "ClassDefinition" - } - ], - "metamodel_version": "1.7.0", - "source_file": "class_enrichment.yaml", - "source_file_date": "2023-06-17T15:11:19", - "source_file_size": 3192, - "generation_date": "2023-08-07T10:51:41", - "@type": "SchemaDefinition", - "@context": [ - "projects/class_enrichment/jsonld/class_enrichment.context.jsonld", - "https://w3id.org/linkml/types.context.jsonld", - { - "@base": "https://w3id.org/oak/class-enrichment/" - } - ] -} diff --git a/projects/class_enrichment/jsonschema/class_enrichment.schema.json b/projects/class_enrichment/jsonschema/class_enrichment.schema.json deleted file mode 100644 index 4a0c9036d..000000000 --- a/projects/class_enrichment/jsonschema/class_enrichment.schema.json +++ /dev/null @@ -1,120 +0,0 @@ -{ - "$defs": { - "ClassEnrichmentConfiguration": { - "additionalProperties": false, - "description": "configuration for search", - "properties": { - "p_value_cutoff": { - "description": "p-value cutoff for enrichment", - "type": "number" - } - }, - "required": [ - "p_value_cutoff" - ], - "title": "ClassEnrichmentConfiguration", - "type": "object" - }, - "ClassEnrichmentResult": { - "additionalProperties": false, - "description": "A single enrichment result", - "properties": { - "ancestor_of_more_informative_result": { - "description": "This term is more general than a previously reported result", - "type": "boolean" - }, - "background_count": { - "description": "The background count", - "type": "integer" - }, - "background_total": { - "description": "The background total", - "type": "integer" - }, - "class_id": { - "description": "The class id", - "type": "string" - }, - "class_label": { - "description": "The class label", - "type": "string" - }, - "descendant_of_more_informative_result": { - "description": "This term is more specific than a previously reported result", - "type": "boolean" - }, - "false_discovery_rate": { - "description": "The false discovery rate", - "type": "number" - }, - "fold_enrichment": { - "description": "The fold enrichment", - "type": "number" - }, - "p_value": { - "description": "The p-value", - "type": "number" - }, - "p_value_adjusted": { - "description": "The adjusted p-value", - "type": "number" - }, - "probability": { - "description": "The probability, as estimated by model-based approaches", - "maximum": 1, - "minimum": 0, - "type": "number" - }, - "rank": { - "description": "The rank of this result", - "type": "integer" - }, - "sample_count": { - "description": "The number of entities in the sample with this class", - "type": "integer" - }, - "sample_total": { - "description": "The total number of entities in the sample", - "type": "integer" - } - }, - "required": [ - "class_id", - "p_value" - ], - "title": "ClassEnrichmentResult", - "type": "object" - }, - "ClassEnrichmentResultSet": { - "additionalProperties": false, - "description": "A collection of enrichemt results", - "properties": { - "results": { - "description": "The enrichment results", - "items": { - "$ref": "#/$defs/ClassEnrichmentResult" - }, - "type": "array" - } - }, - "title": "ClassEnrichmentResultSet", - "type": "object" - }, - "SortFieldEnum": { - "description": "The field to sort by", - "enum": [ - "ANY", - "P_VALUE" - ], - "title": "SortFieldEnum", - "type": "string" - } - }, - "$id": "https://w3id.org/oak/class-enrichment", - "$schema": "http://json-schema.org/draft-07/schema#", - "additionalProperties": true, - "metamodel_version": "1.7.0", - "title": "class-enrichment", - "type": "object", - "version": null -} \ No newline at end of file diff --git a/projects/class_enrichment/owl/class_enrichment.owl.ttl b/projects/class_enrichment/owl/class_enrichment.owl.ttl deleted file mode 100644 index 0575e121d..000000000 --- a/projects/class_enrichment/owl/class_enrichment.owl.ttl +++ /dev/null @@ -1,246 +0,0 @@ -@prefix IAO: . -@prefix OBI: . -@prefix linkml: . -@prefix ontoenrich: . -@prefix owl: . -@prefix rdf: . -@prefix rdfs: . -@prefix skos: . -@prefix xsd: . - -linkml:SubsetDefinition a owl:Class ; - rdfs:label "subset_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" . - -linkml:topValue a owl:DatatypeProperty ; - rdfs:label "value" . - - a owl:Ontology ; - rdfs:label "class-enrichment" ; - IAO:0000700 ontoenrich:ClassEnrichmentConfiguration, - ontoenrich:ClassEnrichmentResult, - ontoenrich:ClassEnrichmentResultSet ; - linkml:classes "{'ClassEnrichmentConfiguration': ClassDefinition(name='ClassEnrichmentConfiguration', id_prefixes=[], definition_uri='https://w3id.org/oak/class-enrichment/ClassEnrichmentConfiguration', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='configuration for search', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/oak/class-enrichment', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['classEnrichmentConfiguration__p_value_cutoff'], slot_usage={}, attributes={'p_value_cutoff': SlotDefinition(name='p_value_cutoff', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='p-value cutoff for enrichment', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='float', range_expression=None, enum_range=None, required=True, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='ontoenrich:ClassEnrichmentConfiguration', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ClassEnrichmentResultSet': ClassDefinition(name='ClassEnrichmentResultSet', id_prefixes=[], definition_uri='https://w3id.org/oak/class-enrichment/ClassEnrichmentResultSet', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A collection of enrichemt results', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/oak/class-enrichment', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['classEnrichmentResultSet__results'], slot_usage={}, attributes={'results': SlotDefinition(name='results', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The enrichment results', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ClassEnrichmentResult', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='ontoenrich:ClassEnrichmentResultSet', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ClassEnrichmentResult': ClassDefinition(name='ClassEnrichmentResult', id_prefixes=[], definition_uri='https://w3id.org/oak/class-enrichment/ClassEnrichmentResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A single enrichment result', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/oak/class-enrichment', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['classEnrichmentResult__class_id', 'classEnrichmentResult__class_label', 'classEnrichmentResult__rank', 'classEnrichmentResult__p_value', 'classEnrichmentResult__p_value_adjusted', 'classEnrichmentResult__false_discovery_rate', 'classEnrichmentResult__fold_enrichment', 'classEnrichmentResult__probability', 'classEnrichmentResult__sample_count', 'classEnrichmentResult__sample_total', 'classEnrichmentResult__background_count', 'classEnrichmentResult__background_total', 'classEnrichmentResult__ancestor_of_more_informative_result', 'classEnrichmentResult__descendant_of_more_informative_result'], slot_usage={}, attributes={'class_id': SlotDefinition(name='class_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The class id', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='uriorcurie', range_expression=None, enum_range=None, required=True, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'class_label': SlotDefinition(name='class_label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The class label', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'rank': SlotDefinition(name='rank', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The rank of this result', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='integer', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'p_value': SlotDefinition(name='p_value', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The p-value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='OBI:0000175', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='float', range_expression=None, enum_range=None, required=True, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'p_value_adjusted': SlotDefinition(name='p_value_adjusted', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The adjusted p-value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='float', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'false_discovery_rate': SlotDefinition(name='false_discovery_rate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The false discovery rate', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='float', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'fold_enrichment': SlotDefinition(name='fold_enrichment', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The fold enrichment', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='float', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'probability': SlotDefinition(name='probability', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The probability, as estimated by model-based approaches', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='float', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=0, maximum_value=1, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sample_count': SlotDefinition(name='sample_count', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The number of entities in the sample with this class', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='integer', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sample_total': SlotDefinition(name='sample_total', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The total number of entities in the sample', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='integer', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'background_count': SlotDefinition(name='background_count', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The background count', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='integer', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'background_total': SlotDefinition(name='background_total', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The background total', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='integer', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ancestor_of_more_informative_result': SlotDefinition(name='ancestor_of_more_informative_result', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='This term is more general than a previously reported result', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='boolean', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'descendant_of_more_informative_result': SlotDefinition(name='descendant_of_more_informative_result', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='This term is more specific than a previously reported result', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='boolean', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='ontoenrich:ClassEnrichmentResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={})}" ; - linkml:enums "{'SortFieldEnum': EnumDefinition(name='SortFieldEnum', id_prefixes=[], definition_uri='https://w3id.org/oak/class-enrichment/SortFieldEnum', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The field to sort by', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/oak/class-enrichment', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'ANY': PermissibleValue(text='ANY', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'P_VALUE': PermissibleValue(text='P_VALUE', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[])}" ; - linkml:id "https://w3id.org/oak/class-enrichment" ; - linkml:imports "linkml:types" ; - linkml:types "{'Position': TypeDefinition(name='Position', id_prefixes=[], definition_uri='https://w3id.org/oak/class-enrichment/Position', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/oak/class-enrichment', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof='integer', base='int', uri='xsd:integer', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'string': TypeDefinition(name='string', id_prefixes=[], definition_uri='https://w3id.org/linkml/String', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A character string', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Text'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'integer': TypeDefinition(name='integer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Integer', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An integer', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Integer'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='int', uri='xsd:integer', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'boolean': TypeDefinition(name='boolean', id_prefixes=[], definition_uri='https://w3id.org/linkml/Boolean', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A binary (true or false) value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Boolean'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Bool', uri='xsd:boolean', repr='bool', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'float': TypeDefinition(name='float', id_prefixes=[], definition_uri='https://w3id.org/linkml/Float', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:float specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Float'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:float', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'double': TypeDefinition(name='double', id_prefixes=[], definition_uri='https://w3id.org/linkml/Double', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:double specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:Float'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:double', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'decimal': TypeDefinition(name='decimal', id_prefixes=[], definition_uri='https://w3id.org/linkml/Decimal', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number with arbitrary precision that conforms to the xsd:decimal specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=['schema:Number'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Decimal', uri='xsd:decimal', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'time': TypeDefinition(name='time', id_prefixes=[], definition_uri='https://w3id.org/linkml/Time', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A time object represents a (local) time of day, independent of any particular day', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=['URI is dateTime because OWL reasoners do not work with straight date or time'], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Time'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDTime', uri='xsd:time', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date': TypeDefinition(name='date', id_prefixes=[], definition_uri='https://w3id.org/linkml/Date', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a date (year, month and day) in an idealized calendar', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[\"URI is dateTime because OWL reasoners don't work with straight date or time\"], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Date'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDate', uri='xsd:date', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'datetime': TypeDefinition(name='datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/Datetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The combination of a date and time', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:DateTime'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDateTime', uri='xsd:dateTime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date_or_datetime': TypeDefinition(name='date_or_datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/DateOrDatetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Either a date or a datetime', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='linkml:DateOrDatetime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uriorcurie': TypeDefinition(name='uriorcurie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uriorcurie', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a URI or a CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URIorCURIE', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'curie': TypeDefinition(name='curie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Curie', local_names={}, conforms_to='https://www.w3.org/TR/curie/', implements=[], extensions={}, annotations={}, description='a compact URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations this MUST be expanded to a URI', 'in non-RDF serializations MAY be serialized as the compact representation'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Curie', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uri': TypeDefinition(name='uri', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uri', local_names={}, conforms_to='https://www.ietf.org/rfc/rfc3987.txt', implements=[], extensions={}, annotations={}, description='a complete URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:URL'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URI', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ncname': TypeDefinition(name='ncname', id_prefixes=[], definition_uri='https://w3id.org/linkml/Ncname', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Prefix part of CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NCName', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'objectidentifier': TypeDefinition(name='objectidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Objectidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI or CURIE that represents an object in the model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['Used for inheritance and type checking'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='ElementIdentifier', uri='shex:iri', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'nodeidentifier': TypeDefinition(name='nodeidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Nodeidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI, CURIE or BNODE that represents a node in a model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NodeIdentifier', uri='shex:nonLiteral', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpointer': TypeDefinition(name='jsonpointer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpointer', local_names={}, conforms_to='https://datatracker.ietf.org/doc/html/rfc6901', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpath': TypeDefinition(name='jsonpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpath', local_names={}, conforms_to='https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sparqlpath': TypeDefinition(name='sparqlpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Sparqlpath', local_names={}, conforms_to='https://www.w3.org/TR/sparql11-query/#propertypaths', implements=[], extensions={}, annotations={}, description='A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -ontoenrich:Position a owl:Class, - linkml:TypeDefinition ; - rdfs:label "Position" ; - rdfs:subClassOf linkml:Integer . - -linkml:TypeDefinition a owl:Class ; - rdfs:label "type_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" ; - linkml:mixins "type_expression" . - -ontoenrich:ClassEnrichmentConfiguration a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ClassEnrichmentConfiguration" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:Float ; - owl:onProperty ontoenrich:p_value_cutoff ; - owl:qualifiedCardinality 1 ] ; - skos:definition "configuration for search" ; - linkml:attributes "{'p_value_cutoff': SlotDefinition(name='p_value_cutoff', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='p-value cutoff for enrichment', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='float', range_expression=None, enum_range=None, required=True, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -ontoenrich:ClassEnrichmentResultSet a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ClassEnrichmentResultSet" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom ontoenrich:ClassEnrichmentResult ; - owl:onProperty ontoenrich:results ] ; - skos:definition "A collection of enrichemt results" ; - linkml:attributes "{'results': SlotDefinition(name='results', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The enrichment results', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ClassEnrichmentResult', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -ontoenrich:ancestor_of_more_informative_result a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "ancestor_of_more_informative_result" ; - rdfs:range linkml:Boolean ; - skos:definition "This term is more general than a previously reported result" . - -ontoenrich:background_count a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "background_count" ; - rdfs:range linkml:Integer ; - skos:definition "The background count" . - -ontoenrich:background_total a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "background_total" ; - rdfs:range linkml:Integer ; - skos:definition "The background total" . - -ontoenrich:class_id a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "class_id" ; - rdfs:range linkml:Uriorcurie ; - skos:definition "The class id" . - -ontoenrich:class_label a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "class_label" ; - rdfs:range linkml:String ; - skos:definition "The class label" . - -ontoenrich:descendant_of_more_informative_result a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "descendant_of_more_informative_result" ; - rdfs:range linkml:Boolean ; - skos:definition "This term is more specific than a previously reported result" . - -ontoenrich:false_discovery_rate a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "false_discovery_rate" ; - rdfs:range linkml:Float ; - skos:definition "The false discovery rate" . - -ontoenrich:fold_enrichment a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "fold_enrichment" ; - rdfs:range linkml:Float ; - skos:definition "The fold enrichment" . - -ontoenrich:p_value_adjusted a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "p_value_adjusted" ; - rdfs:range linkml:Float ; - skos:definition "The adjusted p-value" . - -ontoenrich:p_value_cutoff a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "p_value_cutoff" ; - rdfs:range linkml:Float ; - skos:definition "p-value cutoff for enrichment" . - -ontoenrich:probability a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "probability" ; - rdfs:range linkml:Float ; - skos:definition "The probability, as estimated by model-based approaches" . - -ontoenrich:rank a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "rank" ; - rdfs:range linkml:Integer ; - skos:definition "The rank of this result" . - -ontoenrich:results a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "results" ; - rdfs:range ontoenrich:ClassEnrichmentResult ; - skos:definition "The enrichment results" . - -ontoenrich:sample_count a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "sample_count" ; - rdfs:range linkml:Integer ; - skos:definition "The number of entities in the sample with this class" . - -ontoenrich:sample_total a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "sample_total" ; - rdfs:range linkml:Integer ; - skos:definition "The total number of entities in the sample" . - -OBI:0000175 a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "p_value" ; - rdfs:range linkml:Float ; - skos:definition "The p-value" ; - skos:exactMatch OBI:0000175 . - -ontoenrich:SortFieldEnum a owl:Class, - linkml:EnumDefinition ; - rdfs:label "SortFieldEnum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - . - - a owl:Class, - ontoenrich:SortFieldEnum ; - rdfs:label "ANY" . - - a owl:Class, - ontoenrich:SortFieldEnum ; - rdfs:label "P_VALUE" . - -linkml:ClassDefinition a owl:Class ; - rdfs:label "class_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "class_expression" . - -ontoenrich:ClassEnrichmentResult a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ClassEnrichmentResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty ontoenrich:background_count ], - [ a owl:Restriction ; - owl:onClass linkml:Float ; - owl:onProperty OBI:0000175 ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty ontoenrich:p_value_adjusted ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Boolean ; - owl:onProperty ontoenrich:ancestor_of_more_informative_result ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty ontoenrich:false_discovery_rate ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ontoenrich:class_label ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty ontoenrich:sample_total ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty ontoenrich:rank ], - [ a owl:Restriction ; - owl:onClass linkml:Uriorcurie ; - owl:onProperty ontoenrich:class_id ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty ontoenrich:probability ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty ontoenrich:sample_count ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty ontoenrich:fold_enrichment ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty ontoenrich:background_total ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Boolean ; - owl:onProperty ontoenrich:descendant_of_more_informative_result ] ; - skos:definition "A single enrichment result" ; - linkml:attributes "{'class_id': SlotDefinition(name='class_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The class id', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='uriorcurie', range_expression=None, enum_range=None, required=True, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'class_label': SlotDefinition(name='class_label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The class label', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'rank': SlotDefinition(name='rank', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The rank of this result', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='integer', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'p_value': SlotDefinition(name='p_value', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The p-value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='OBI:0000175', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='float', range_expression=None, enum_range=None, required=True, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'p_value_adjusted': SlotDefinition(name='p_value_adjusted', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The adjusted p-value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='float', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'false_discovery_rate': SlotDefinition(name='false_discovery_rate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The false discovery rate', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='float', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'fold_enrichment': SlotDefinition(name='fold_enrichment', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The fold enrichment', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='float', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'probability': SlotDefinition(name='probability', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The probability, as estimated by model-based approaches', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='float', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=0, maximum_value=1, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sample_count': SlotDefinition(name='sample_count', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The number of entities in the sample with this class', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='integer', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sample_total': SlotDefinition(name='sample_total', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The total number of entities in the sample', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='integer', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'background_count': SlotDefinition(name='background_count', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The background count', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='integer', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'background_total': SlotDefinition(name='background_total', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The background total', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='integer', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ancestor_of_more_informative_result': SlotDefinition(name='ancestor_of_more_informative_result', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='This term is more general than a previously reported result', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='boolean', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'descendant_of_more_informative_result': SlotDefinition(name='descendant_of_more_informative_result', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='This term is more specific than a previously reported result', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='boolean', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:SlotDefinition a owl:Class ; - rdfs:label "slot_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "slot_expression" . - - diff --git a/projects/class_enrichment/prefixmap/class_enrichment.yaml b/projects/class_enrichment/prefixmap/class_enrichment.yaml deleted file mode 100644 index a598bd14d..000000000 --- a/projects/class_enrichment/prefixmap/class_enrichment.yaml +++ /dev/null @@ -1,18 +0,0 @@ -{ - "OBI": "http://purl.obolibrary.org/obo/OBI_", - "STATO": "http://purl.obolibrary.org/obo/STATO_", - "bpa": "https://bioportal.bioontology.org/annotator/", - "linkml": "https://w3id.org/linkml/", - "oa": "http://www.w3.org/ns/oa#", - "ontoenrich": "https://w3id.org/oak/class-enrichment/", - "owl": "http://www.w3.org/2002/07/owl#", - "pav": "http://purl.org/pav/", - "prov": "http://www.w3.org/ns/prov#", - "rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#", - "rdfs": "http://www.w3.org/2000/01/rdf-schema#", - "schema": "http://schema.org/", - "sh": "https://w3id.org/shacl/", - "skos": "http://www.w3.org/2004/02/skos/core#", - "sssom": "http://w3id.org/sssom/", - "xsd": "http://www.w3.org/2001/XMLSchema#" -} diff --git a/projects/class_enrichment/protobuf/class_enrichment.proto b/projects/class_enrichment/protobuf/class_enrichment.proto deleted file mode 100644 index 8079fd0cf..000000000 --- a/projects/class_enrichment/protobuf/class_enrichment.proto +++ /dev/null @@ -1,28 +0,0 @@ -// configuration for search -message ClassEnrichmentConfiguration - { - float pValueCutoff = 0 - } -// A single enrichment result -message ClassEnrichmentResult - { - uriorcurie classId = 0 - string classLabel = 0 - integer rank = 0 - float pValue = 0 - float pValueAdjusted = 0 - float falseDiscoveryRate = 0 - float foldEnrichment = 0 - float probability = 0 - integer sampleCount = 0 - integer sampleTotal = 0 - integer backgroundCount = 0 - integer backgroundTotal = 0 - boolean ancestorOfMoreInformativeResult = 0 - boolean descendantOfMoreInformativeResult = 0 - } -// A collection of enrichemt results -message ClassEnrichmentResultSet - { - repeated classEnrichmentResult results = 0 - } diff --git a/projects/class_enrichment/shacl/class_enrichment.shacl.ttl b/projects/class_enrichment/shacl/class_enrichment.shacl.ttl deleted file mode 100644 index 73c339319..000000000 --- a/projects/class_enrichment/shacl/class_enrichment.shacl.ttl +++ /dev/null @@ -1,94 +0,0 @@ -@prefix OBI: . -@prefix ontoenrich: . -@prefix rdf: . -@prefix sh: . -@prefix xsd: . - -ontoenrich:ClassEnrichmentConfiguration a sh:NodeShape ; - sh:closed true ; - sh:description "configuration for search" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "p-value cutoff for enrichment" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path ontoenrich:p_value_cutoff ] ; - sh:targetClass ontoenrich:ClassEnrichmentConfiguration . - -ontoenrich:ClassEnrichmentResultSet a sh:NodeShape ; - sh:closed true ; - sh:description "A collection of enrichemt results" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class ontoenrich:ClassEnrichmentResult ; - sh:description "The enrichment results" ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path ontoenrich:results ] ; - sh:targetClass ontoenrich:ClassEnrichmentResultSet . - -ontoenrich:ClassEnrichmentResult a sh:NodeShape ; - sh:closed true ; - sh:description "A single enrichment result" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The rank of this result" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path ontoenrich:rank ], - [ sh:description "The probability, as estimated by model-based approaches" ; - sh:maxCount 1 ; - sh:maxInclusive 1 ; - sh:minInclusive 0 ; - sh:order 7 ; - sh:path ontoenrich:probability ], - [ sh:description "The class label" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path ontoenrich:class_label ], - [ sh:description "The adjusted p-value" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path ontoenrich:p_value_adjusted ], - [ sh:description "The background total" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path ontoenrich:background_total ], - [ sh:description "The number of entities in the sample with this class" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path ontoenrich:sample_count ], - [ sh:description "This term is more specific than a previously reported result" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path ontoenrich:descendant_of_more_informative_result ], - [ sh:description "The class id" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path ontoenrich:class_id ], - [ sh:description "This term is more general than a previously reported result" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path ontoenrich:ancestor_of_more_informative_result ], - [ sh:description "The fold enrichment" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path ontoenrich:fold_enrichment ], - [ sh:description "The total number of entities in the sample" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path ontoenrich:sample_total ], - [ sh:description "The background count" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path ontoenrich:background_count ], - [ sh:description "The false discovery rate" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path ontoenrich:false_discovery_rate ], - [ sh:description "The p-value" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path OBI:0000175 ] ; - sh:targetClass ontoenrich:ClassEnrichmentResult . - diff --git a/projects/class_enrichment/shex/class_enrichment.shex b/projects/class_enrichment/shex/class_enrichment.shex deleted file mode 100644 index b18547db1..000000000 --- a/projects/class_enrichment/shex/class_enrichment.shex +++ /dev/null @@ -1,79 +0,0 @@ -BASE -PREFIX rdf: -PREFIX xsd: -PREFIX linkml: - - - xsd:integer - -linkml:String xsd:string - -linkml:Integer xsd:integer - -linkml:Boolean xsd:boolean - -linkml:Float xsd:float - -linkml:Double xsd:double - -linkml:Decimal xsd:decimal - -linkml:Time xsd:time - -linkml:Date xsd:date - -linkml:Datetime xsd:dateTime - -linkml:DateOrDatetime linkml:DateOrDatetime - -linkml:Uriorcurie IRI - -linkml:Curie xsd:string - -linkml:Uri IRI - -linkml:Ncname xsd:string - -linkml:Objectidentifier IRI - -linkml:Nodeidentifier NONLITERAL - -linkml:Jsonpointer xsd:string - -linkml:Jsonpath xsd:string - -linkml:Sparqlpath xsd:string - - CLOSED { - ( $ @linkml:Float ; - rdf:type [ ] ? - ) -} - - CLOSED { - ( $ ( @linkml:Uriorcurie ; - @linkml:String ? ; - @linkml:Integer ? ; - @linkml:Float ; - @linkml:Float ? ; - @linkml:Float ? ; - @linkml:Float ? ; - @linkml:Float ? ; - @linkml:Integer ? ; - @linkml:Integer ? ; - @linkml:Integer ? ; - @linkml:Integer ? ; - @linkml:Boolean ? ; - @linkml:Boolean ? - ) ; - rdf:type [ ] ? - ) -} - - CLOSED { - ( $ @ * ; - rdf:type [ ] ? - ) -} - - diff --git a/projects/class_enrichment/sqlschema/class_enrichment.sql b/projects/class_enrichment/sqlschema/class_enrichment.sql deleted file mode 100644 index dfc0b38dc..000000000 --- a/projects/class_enrichment/sqlschema/class_enrichment.sql +++ /dev/null @@ -1,29 +0,0 @@ - - -CREATE TABLE "ClassEnrichmentConfiguration" ( - p_value_cutoff FLOAT NOT NULL, - PRIMARY KEY (p_value_cutoff) -); - -CREATE TABLE "ClassEnrichmentResult" ( - class_id TEXT NOT NULL, - class_label TEXT, - rank INTEGER, - p_value FLOAT NOT NULL, - p_value_adjusted FLOAT, - false_discovery_rate FLOAT, - fold_enrichment FLOAT, - probability FLOAT, - sample_count INTEGER, - sample_total INTEGER, - background_count INTEGER, - background_total INTEGER, - ancestor_of_more_informative_result BOOLEAN, - descendant_of_more_informative_result BOOLEAN, - PRIMARY KEY (class_id, class_label, rank, p_value, p_value_adjusted, false_discovery_rate, fold_enrichment, probability, sample_count, sample_total, background_count, background_total, ancestor_of_more_informative_result, descendant_of_more_informative_result) -); - -CREATE TABLE "ClassEnrichmentResultSet" ( - results TEXT, - PRIMARY KEY (results) -); diff --git a/projects/composite_disease/composite_disease.py b/projects/composite_disease/composite_disease.py deleted file mode 100644 index 1b8a4a5c2..000000000 --- a/projects/composite_disease/composite_disease.py +++ /dev/null @@ -1,722 +0,0 @@ -# Auto generated from composite_disease.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-08-07T10:51:59 -# Schema: composite_disease -# -# id: http://w3id.org/ontogpt/composite_disease -# description: A template for representing composite disease concepts -# license: https://creativecommons.org/publicdomain/zero/1.0/ - -import dataclasses -import sys -import re -from jsonasobj2 import JsonObj, as_dict -from typing import Optional, List, Union, Dict, ClassVar, Any -from dataclasses import dataclass -from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions - -from linkml_runtime.utils.slot import Slot -from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode -from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int -from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs -from linkml_runtime.utils.formatutils import camelcase, underscore, sfx -from linkml_runtime.utils.enumerations import EnumDefinitionImpl -from rdflib import Namespace, URIRef -from linkml_runtime.utils.curienamespace import CurieNamespace -from linkml_runtime.linkml_model.types import String - -metamodel_version = "1.7.0" -version = None - -# Overwrite dataclasses _init_fn to add **kwargs in __init__ -dataclasses._init_fn = dataclasses_init_fn_with_kwargs - -# Namespaces -HGNC = CurieNamespace('HGNC', 'http://example.org/UNKNOWN/HGNC/') -HP = CurieNamespace('HP', 'http://example.org/UNKNOWN/HP/') -RO = CurieNamespace('RO', 'http://purl.obolibrary.org/obo/RO_') -BIOLINK = CurieNamespace('biolink', 'http://example.org/UNKNOWN/biolink/') -COMPOSITE_DISEASE = CurieNamespace('composite_disease', 'http://w3id.org/ontogpt/composite_disease/') -CORE = CurieNamespace('core', 'http://w3id.org/ontogpt/core/') -LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') -RDFS = CurieNamespace('rdfs', 'http://example.org/UNKNOWN/rdfs/') -DEFAULT_ = COMPOSITE_DISEASE - - -# Types - -# Class references -class NamedEntityId(extended_str): - pass - - -class GeneId(NamedEntityId): - pass - - -class SymptomId(NamedEntityId): - pass - - -class DiseaseId(NamedEntityId): - pass - - -class AdverseEffectId(NamedEntityId): - pass - - -class TreatmentId(NamedEntityId): - pass - - -class MechanismId(NamedEntityId): - pass - - -class DrugId(NamedEntityId): - pass - - -class RelationshipTypeId(NamedEntityId): - pass - - -@dataclass -class CompositeDisease(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = COMPOSITE_DISEASE.CompositeDisease - class_class_curie: ClassVar[str] = "composite_disease:CompositeDisease" - class_name: ClassVar[str] = "CompositeDisease" - class_model_uri: ClassVar[URIRef] = COMPOSITE_DISEASE.CompositeDisease - - main_disease: Optional[Union[str, DiseaseId]] = None - drugs: Optional[Union[Union[str, DrugId], List[Union[str, DrugId]]]] = empty_list() - treatments: Optional[Union[Union[str, TreatmentId], List[Union[str, TreatmentId]]]] = empty_list() - contraindications: Optional[Union[Union[str, TreatmentId], List[Union[str, TreatmentId]]]] = empty_list() - treatment_mechanisms: Optional[Union[Union[dict, "TreatmentMechanism"], List[Union[dict, "TreatmentMechanism"]]]] = empty_list() - treatment_efficacies: Optional[Union[Union[dict, "TreatmentEfficacy"], List[Union[dict, "TreatmentEfficacy"]]]] = empty_list() - treatment_adverse_effects: Optional[Union[Union[dict, "TreatmentAdverseEffect"], List[Union[dict, "TreatmentAdverseEffect"]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.main_disease is not None and not isinstance(self.main_disease, DiseaseId): - self.main_disease = DiseaseId(self.main_disease) - - if not isinstance(self.drugs, list): - self.drugs = [self.drugs] if self.drugs is not None else [] - self.drugs = [v if isinstance(v, DrugId) else DrugId(v) for v in self.drugs] - - if not isinstance(self.treatments, list): - self.treatments = [self.treatments] if self.treatments is not None else [] - self.treatments = [v if isinstance(v, TreatmentId) else TreatmentId(v) for v in self.treatments] - - if not isinstance(self.contraindications, list): - self.contraindications = [self.contraindications] if self.contraindications is not None else [] - self.contraindications = [v if isinstance(v, TreatmentId) else TreatmentId(v) for v in self.contraindications] - - if not isinstance(self.treatment_mechanisms, list): - self.treatment_mechanisms = [self.treatment_mechanisms] if self.treatment_mechanisms is not None else [] - self.treatment_mechanisms = [v if isinstance(v, TreatmentMechanism) else TreatmentMechanism(**as_dict(v)) for v in self.treatment_mechanisms] - - if not isinstance(self.treatment_efficacies, list): - self.treatment_efficacies = [self.treatment_efficacies] if self.treatment_efficacies is not None else [] - self.treatment_efficacies = [v if isinstance(v, TreatmentEfficacy) else TreatmentEfficacy(**as_dict(v)) for v in self.treatment_efficacies] - - if not isinstance(self.treatment_adverse_effects, list): - self.treatment_adverse_effects = [self.treatment_adverse_effects] if self.treatment_adverse_effects is not None else [] - self.treatment_adverse_effects = [v if isinstance(v, TreatmentAdverseEffect) else TreatmentAdverseEffect(**as_dict(v)) for v in self.treatment_adverse_effects] - - super().__post_init__(**kwargs) - - -Any = Any - -@dataclass -class ExtractionResult(YAMLRoot): - """ - A result of extracting knowledge on text - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.ExtractionResult - class_class_curie: ClassVar[str] = "core:ExtractionResult" - class_name: ClassVar[str] = "ExtractionResult" - class_model_uri: ClassVar[URIRef] = COMPOSITE_DISEASE.ExtractionResult - - input_id: Optional[str] = None - input_title: Optional[str] = None - input_text: Optional[str] = None - raw_completion_output: Optional[str] = None - prompt: Optional[str] = None - extracted_object: Optional[Union[dict, Any]] = None - named_entities: Optional[Union[Union[dict, Any], List[Union[dict, Any]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.input_id is not None and not isinstance(self.input_id, str): - self.input_id = str(self.input_id) - - if self.input_title is not None and not isinstance(self.input_title, str): - self.input_title = str(self.input_title) - - if self.input_text is not None and not isinstance(self.input_text, str): - self.input_text = str(self.input_text) - - if self.raw_completion_output is not None and not isinstance(self.raw_completion_output, str): - self.raw_completion_output = str(self.raw_completion_output) - - if self.prompt is not None and not isinstance(self.prompt, str): - self.prompt = str(self.prompt) - - super().__post_init__(**kwargs) - - -@dataclass -class NamedEntity(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.NamedEntity - class_class_curie: ClassVar[str] = "core:NamedEntity" - class_name: ClassVar[str] = "NamedEntity" - class_model_uri: ClassVar[URIRef] = COMPOSITE_DISEASE.NamedEntity - - id: Union[str, NamedEntityId] = None - label: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, NamedEntityId): - self.id = NamedEntityId(self.id) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - super().__post_init__(**kwargs) - - -@dataclass -class Gene(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = COMPOSITE_DISEASE.Gene - class_class_curie: ClassVar[str] = "composite_disease:Gene" - class_name: ClassVar[str] = "Gene" - class_model_uri: ClassVar[URIRef] = COMPOSITE_DISEASE.Gene - - id: Union[str, GeneId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, GeneId): - self.id = GeneId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Symptom(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = COMPOSITE_DISEASE.Symptom - class_class_curie: ClassVar[str] = "composite_disease:Symptom" - class_name: ClassVar[str] = "Symptom" - class_model_uri: ClassVar[URIRef] = COMPOSITE_DISEASE.Symptom - - id: Union[str, SymptomId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, SymptomId): - self.id = SymptomId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Disease(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = COMPOSITE_DISEASE.Disease - class_class_curie: ClassVar[str] = "composite_disease:Disease" - class_name: ClassVar[str] = "Disease" - class_model_uri: ClassVar[URIRef] = COMPOSITE_DISEASE.Disease - - id: Union[str, DiseaseId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, DiseaseId): - self.id = DiseaseId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class AdverseEffect(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = COMPOSITE_DISEASE.AdverseEffect - class_class_curie: ClassVar[str] = "composite_disease:AdverseEffect" - class_name: ClassVar[str] = "AdverseEffect" - class_model_uri: ClassVar[URIRef] = COMPOSITE_DISEASE.AdverseEffect - - id: Union[str, AdverseEffectId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, AdverseEffectId): - self.id = AdverseEffectId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Treatment(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = COMPOSITE_DISEASE.Treatment - class_class_curie: ClassVar[str] = "composite_disease:Treatment" - class_name: ClassVar[str] = "Treatment" - class_model_uri: ClassVar[URIRef] = COMPOSITE_DISEASE.Treatment - - id: Union[str, TreatmentId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, TreatmentId): - self.id = TreatmentId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Mechanism(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = COMPOSITE_DISEASE.Mechanism - class_class_curie: ClassVar[str] = "composite_disease:Mechanism" - class_name: ClassVar[str] = "Mechanism" - class_model_uri: ClassVar[URIRef] = COMPOSITE_DISEASE.Mechanism - - id: Union[str, MechanismId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, MechanismId): - self.id = MechanismId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Drug(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = COMPOSITE_DISEASE.Drug - class_class_curie: ClassVar[str] = "composite_disease:Drug" - class_name: ClassVar[str] = "Drug" - class_model_uri: ClassVar[URIRef] = COMPOSITE_DISEASE.Drug - - id: Union[str, DrugId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, DrugId): - self.id = DrugId(self.id) - - super().__post_init__(**kwargs) - - -class CompoundExpression(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.CompoundExpression - class_class_curie: ClassVar[str] = "core:CompoundExpression" - class_name: ClassVar[str] = "CompoundExpression" - class_model_uri: ClassVar[URIRef] = COMPOSITE_DISEASE.CompoundExpression - - -@dataclass -class TreatmentMechanism(CompoundExpression): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = COMPOSITE_DISEASE.TreatmentMechanism - class_class_curie: ClassVar[str] = "composite_disease:TreatmentMechanism" - class_name: ClassVar[str] = "TreatmentMechanism" - class_model_uri: ClassVar[URIRef] = COMPOSITE_DISEASE.TreatmentMechanism - - treatment: Optional[Union[str, TreatmentId]] = None - mechanism: Optional[Union[str, MechanismId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.treatment is not None and not isinstance(self.treatment, TreatmentId): - self.treatment = TreatmentId(self.treatment) - - if self.mechanism is not None and not isinstance(self.mechanism, MechanismId): - self.mechanism = MechanismId(self.mechanism) - - super().__post_init__(**kwargs) - - -@dataclass -class TreatmentAdverseEffect(CompoundExpression): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = COMPOSITE_DISEASE.TreatmentAdverseEffect - class_class_curie: ClassVar[str] = "composite_disease:TreatmentAdverseEffect" - class_name: ClassVar[str] = "TreatmentAdverseEffect" - class_model_uri: ClassVar[URIRef] = COMPOSITE_DISEASE.TreatmentAdverseEffect - - treatment: Optional[Union[str, TreatmentId]] = None - adverse_effects: Optional[Union[Union[str, AdverseEffectId], List[Union[str, AdverseEffectId]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.treatment is not None and not isinstance(self.treatment, TreatmentId): - self.treatment = TreatmentId(self.treatment) - - if not isinstance(self.adverse_effects, list): - self.adverse_effects = [self.adverse_effects] if self.adverse_effects is not None else [] - self.adverse_effects = [v if isinstance(v, AdverseEffectId) else AdverseEffectId(v) for v in self.adverse_effects] - - super().__post_init__(**kwargs) - - -@dataclass -class TreatmentEfficacy(CompoundExpression): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = COMPOSITE_DISEASE.TreatmentEfficacy - class_class_curie: ClassVar[str] = "composite_disease:TreatmentEfficacy" - class_name: ClassVar[str] = "TreatmentEfficacy" - class_model_uri: ClassVar[URIRef] = COMPOSITE_DISEASE.TreatmentEfficacy - - treatment: Optional[Union[str, TreatmentId]] = None - efficacy: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.treatment is not None and not isinstance(self.treatment, TreatmentId): - self.treatment = TreatmentId(self.treatment) - - if self.efficacy is not None and not isinstance(self.efficacy, str): - self.efficacy = str(self.efficacy) - - super().__post_init__(**kwargs) - - -@dataclass -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Triple - class_class_curie: ClassVar[str] = "core:Triple" - class_name: ClassVar[str] = "Triple" - class_model_uri: ClassVar[URIRef] = COMPOSITE_DISEASE.Triple - - subject: Optional[Union[str, NamedEntityId]] = None - predicate: Optional[Union[str, RelationshipTypeId]] = None - object: Optional[Union[str, NamedEntityId]] = None - qualifier: Optional[str] = None - subject_qualifier: Optional[Union[str, NamedEntityId]] = None - object_qualifier: Optional[Union[str, NamedEntityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, NamedEntityId): - self.subject = NamedEntityId(self.subject) - - if self.predicate is not None and not isinstance(self.predicate, RelationshipTypeId): - self.predicate = RelationshipTypeId(self.predicate) - - if self.object is not None and not isinstance(self.object, NamedEntityId): - self.object = NamedEntityId(self.object) - - if self.qualifier is not None and not isinstance(self.qualifier, str): - self.qualifier = str(self.qualifier) - - if self.subject_qualifier is not None and not isinstance(self.subject_qualifier, NamedEntityId): - self.subject_qualifier = NamedEntityId(self.subject_qualifier) - - if self.object_qualifier is not None and not isinstance(self.object_qualifier, NamedEntityId): - self.object_qualifier = NamedEntityId(self.object_qualifier) - - super().__post_init__(**kwargs) - - -@dataclass -class TextWithTriples(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.TextWithTriples - class_class_curie: ClassVar[str] = "core:TextWithTriples" - class_name: ClassVar[str] = "TextWithTriples" - class_model_uri: ClassVar[URIRef] = COMPOSITE_DISEASE.TextWithTriples - - publication: Optional[Union[dict, "Publication"]] = None - triples: Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.publication is not None and not isinstance(self.publication, Publication): - self.publication = Publication(**as_dict(self.publication)) - - if not isinstance(self.triples, list): - self.triples = [self.triples] if self.triples is not None else [] - self.triples = [v if isinstance(v, Triple) else Triple(**as_dict(v)) for v in self.triples] - - super().__post_init__(**kwargs) - - -@dataclass -class RelationshipType(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.RelationshipType - class_class_curie: ClassVar[str] = "core:RelationshipType" - class_name: ClassVar[str] = "RelationshipType" - class_model_uri: ClassVar[URIRef] = COMPOSITE_DISEASE.RelationshipType - - id: Union[str, RelationshipTypeId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, RelationshipTypeId): - self.id = RelationshipTypeId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Publication(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Publication - class_class_curie: ClassVar[str] = "core:Publication" - class_name: ClassVar[str] = "Publication" - class_model_uri: ClassVar[URIRef] = COMPOSITE_DISEASE.Publication - - id: Optional[str] = None - title: Optional[str] = None - abstract: Optional[str] = None - combined_text: Optional[str] = None - full_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.id is not None and not isinstance(self.id, str): - self.id = str(self.id) - - if self.title is not None and not isinstance(self.title, str): - self.title = str(self.title) - - if self.abstract is not None and not isinstance(self.abstract, str): - self.abstract = str(self.abstract) - - if self.combined_text is not None and not isinstance(self.combined_text, str): - self.combined_text = str(self.combined_text) - - if self.full_text is not None and not isinstance(self.full_text, str): - self.full_text = str(self.full_text) - - super().__post_init__(**kwargs) - - -@dataclass -class AnnotatorResult(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.AnnotatorResult - class_class_curie: ClassVar[str] = "core:AnnotatorResult" - class_name: ClassVar[str] = "AnnotatorResult" - class_model_uri: ClassVar[URIRef] = COMPOSITE_DISEASE.AnnotatorResult - - subject_text: Optional[str] = None - object_id: Optional[str] = None - object_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject_text is not None and not isinstance(self.subject_text, str): - self.subject_text = str(self.subject_text) - - if self.object_id is not None and not isinstance(self.object_id, str): - self.object_id = str(self.object_id) - - if self.object_text is not None and not isinstance(self.object_text, str): - self.object_text = str(self.object_text) - - super().__post_init__(**kwargs) - - -# Enumerations -class NCITDrugType(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="NCITDrugType", - ) - -class NCITTreatmentType(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="NCITTreatmentType", - ) - -class NCITTActivityType(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="NCITTActivityType", - ) - -class MAXOActionType(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="MAXOActionType", - ) - -class MESHTherapeuticType(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="MESHTherapeuticType", - ) - -class CHEBIDrugType(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="CHEBIDrugType", - ) - -class NullDataOptions(EnumDefinitionImpl): - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = PermissibleValue(text="UNSPECIFIED_METHOD_OF_ADMINISTRATION", - meaning=NCIT.C149701) - NOT_APPLICABLE = PermissibleValue(text="NOT_APPLICABLE", - meaning=NCIT.C18902) - NOT_MENTIONED = PermissibleValue(text="NOT_MENTIONED") - - _defn = EnumDefinition( - name="NullDataOptions", - ) - -# Slots -class slots: - pass - -slots.compositeDisease__main_disease = Slot(uri=COMPOSITE_DISEASE.main_disease, name="compositeDisease__main_disease", curie=COMPOSITE_DISEASE.curie('main_disease'), - model_uri=COMPOSITE_DISEASE.compositeDisease__main_disease, domain=None, range=Optional[Union[str, DiseaseId]]) - -slots.compositeDisease__drugs = Slot(uri=COMPOSITE_DISEASE.drugs, name="compositeDisease__drugs", curie=COMPOSITE_DISEASE.curie('drugs'), - model_uri=COMPOSITE_DISEASE.compositeDisease__drugs, domain=None, range=Optional[Union[Union[str, DrugId], List[Union[str, DrugId]]]]) - -slots.compositeDisease__treatments = Slot(uri=COMPOSITE_DISEASE.treatments, name="compositeDisease__treatments", curie=COMPOSITE_DISEASE.curie('treatments'), - model_uri=COMPOSITE_DISEASE.compositeDisease__treatments, domain=None, range=Optional[Union[Union[str, TreatmentId], List[Union[str, TreatmentId]]]]) - -slots.compositeDisease__contraindications = Slot(uri=COMPOSITE_DISEASE.contraindications, name="compositeDisease__contraindications", curie=COMPOSITE_DISEASE.curie('contraindications'), - model_uri=COMPOSITE_DISEASE.compositeDisease__contraindications, domain=None, range=Optional[Union[Union[str, TreatmentId], List[Union[str, TreatmentId]]]]) - -slots.compositeDisease__treatment_mechanisms = Slot(uri=COMPOSITE_DISEASE.treatment_mechanisms, name="compositeDisease__treatment_mechanisms", curie=COMPOSITE_DISEASE.curie('treatment_mechanisms'), - model_uri=COMPOSITE_DISEASE.compositeDisease__treatment_mechanisms, domain=None, range=Optional[Union[Union[dict, TreatmentMechanism], List[Union[dict, TreatmentMechanism]]]]) - -slots.compositeDisease__treatment_efficacies = Slot(uri=COMPOSITE_DISEASE.treatment_efficacies, name="compositeDisease__treatment_efficacies", curie=COMPOSITE_DISEASE.curie('treatment_efficacies'), - model_uri=COMPOSITE_DISEASE.compositeDisease__treatment_efficacies, domain=None, range=Optional[Union[Union[dict, TreatmentEfficacy], List[Union[dict, TreatmentEfficacy]]]]) - -slots.compositeDisease__treatment_adverse_effects = Slot(uri=COMPOSITE_DISEASE.treatment_adverse_effects, name="compositeDisease__treatment_adverse_effects", curie=COMPOSITE_DISEASE.curie('treatment_adverse_effects'), - model_uri=COMPOSITE_DISEASE.compositeDisease__treatment_adverse_effects, domain=None, range=Optional[Union[Union[dict, TreatmentAdverseEffect], List[Union[dict, TreatmentAdverseEffect]]]]) - -slots.treatmentMechanism__treatment = Slot(uri=COMPOSITE_DISEASE.treatment, name="treatmentMechanism__treatment", curie=COMPOSITE_DISEASE.curie('treatment'), - model_uri=COMPOSITE_DISEASE.treatmentMechanism__treatment, domain=None, range=Optional[Union[str, TreatmentId]]) - -slots.treatmentMechanism__mechanism = Slot(uri=COMPOSITE_DISEASE.mechanism, name="treatmentMechanism__mechanism", curie=COMPOSITE_DISEASE.curie('mechanism'), - model_uri=COMPOSITE_DISEASE.treatmentMechanism__mechanism, domain=None, range=Optional[Union[str, MechanismId]]) - -slots.treatmentAdverseEffect__treatment = Slot(uri=COMPOSITE_DISEASE.treatment, name="treatmentAdverseEffect__treatment", curie=COMPOSITE_DISEASE.curie('treatment'), - model_uri=COMPOSITE_DISEASE.treatmentAdverseEffect__treatment, domain=None, range=Optional[Union[str, TreatmentId]]) - -slots.treatmentAdverseEffect__adverse_effects = Slot(uri=COMPOSITE_DISEASE.adverse_effects, name="treatmentAdverseEffect__adverse_effects", curie=COMPOSITE_DISEASE.curie('adverse_effects'), - model_uri=COMPOSITE_DISEASE.treatmentAdverseEffect__adverse_effects, domain=None, range=Optional[Union[Union[str, AdverseEffectId], List[Union[str, AdverseEffectId]]]]) - -slots.treatmentEfficacy__treatment = Slot(uri=COMPOSITE_DISEASE.treatment, name="treatmentEfficacy__treatment", curie=COMPOSITE_DISEASE.curie('treatment'), - model_uri=COMPOSITE_DISEASE.treatmentEfficacy__treatment, domain=None, range=Optional[Union[str, TreatmentId]]) - -slots.treatmentEfficacy__efficacy = Slot(uri=COMPOSITE_DISEASE.efficacy, name="treatmentEfficacy__efficacy", curie=COMPOSITE_DISEASE.curie('efficacy'), - model_uri=COMPOSITE_DISEASE.treatmentEfficacy__efficacy, domain=None, range=Optional[str]) - -slots.extractionResult__input_id = Slot(uri=CORE.input_id, name="extractionResult__input_id", curie=CORE.curie('input_id'), - model_uri=COMPOSITE_DISEASE.extractionResult__input_id, domain=None, range=Optional[str]) - -slots.extractionResult__input_title = Slot(uri=CORE.input_title, name="extractionResult__input_title", curie=CORE.curie('input_title'), - model_uri=COMPOSITE_DISEASE.extractionResult__input_title, domain=None, range=Optional[str]) - -slots.extractionResult__input_text = Slot(uri=CORE.input_text, name="extractionResult__input_text", curie=CORE.curie('input_text'), - model_uri=COMPOSITE_DISEASE.extractionResult__input_text, domain=None, range=Optional[str]) - -slots.extractionResult__raw_completion_output = Slot(uri=CORE.raw_completion_output, name="extractionResult__raw_completion_output", curie=CORE.curie('raw_completion_output'), - model_uri=COMPOSITE_DISEASE.extractionResult__raw_completion_output, domain=None, range=Optional[str]) - -slots.extractionResult__prompt = Slot(uri=CORE.prompt, name="extractionResult__prompt", curie=CORE.curie('prompt'), - model_uri=COMPOSITE_DISEASE.extractionResult__prompt, domain=None, range=Optional[str]) - -slots.extractionResult__extracted_object = Slot(uri=CORE.extracted_object, name="extractionResult__extracted_object", curie=CORE.curie('extracted_object'), - model_uri=COMPOSITE_DISEASE.extractionResult__extracted_object, domain=None, range=Optional[Union[dict, Any]]) - -slots.extractionResult__named_entities = Slot(uri=CORE.named_entities, name="extractionResult__named_entities", curie=CORE.curie('named_entities'), - model_uri=COMPOSITE_DISEASE.extractionResult__named_entities, domain=None, range=Optional[Union[Union[dict, Any], List[Union[dict, Any]]]]) - -slots.namedEntity__id = Slot(uri=CORE.id, name="namedEntity__id", curie=CORE.curie('id'), - model_uri=COMPOSITE_DISEASE.namedEntity__id, domain=None, range=URIRef) - -slots.namedEntity__label = Slot(uri=RDFS.label, name="namedEntity__label", curie=RDFS.curie('label'), - model_uri=COMPOSITE_DISEASE.namedEntity__label, domain=None, range=Optional[str]) - -slots.triple__subject = Slot(uri=CORE.subject, name="triple__subject", curie=CORE.curie('subject'), - model_uri=COMPOSITE_DISEASE.triple__subject, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__predicate = Slot(uri=CORE.predicate, name="triple__predicate", curie=CORE.curie('predicate'), - model_uri=COMPOSITE_DISEASE.triple__predicate, domain=None, range=Optional[Union[str, RelationshipTypeId]]) - -slots.triple__object = Slot(uri=CORE.object, name="triple__object", curie=CORE.curie('object'), - model_uri=COMPOSITE_DISEASE.triple__object, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__qualifier = Slot(uri=CORE.qualifier, name="triple__qualifier", curie=CORE.curie('qualifier'), - model_uri=COMPOSITE_DISEASE.triple__qualifier, domain=None, range=Optional[str]) - -slots.triple__subject_qualifier = Slot(uri=CORE.subject_qualifier, name="triple__subject_qualifier", curie=CORE.curie('subject_qualifier'), - model_uri=COMPOSITE_DISEASE.triple__subject_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__object_qualifier = Slot(uri=CORE.object_qualifier, name="triple__object_qualifier", curie=CORE.curie('object_qualifier'), - model_uri=COMPOSITE_DISEASE.triple__object_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.textWithTriples__publication = Slot(uri=CORE.publication, name="textWithTriples__publication", curie=CORE.curie('publication'), - model_uri=COMPOSITE_DISEASE.textWithTriples__publication, domain=None, range=Optional[Union[dict, Publication]]) - -slots.textWithTriples__triples = Slot(uri=CORE.triples, name="textWithTriples__triples", curie=CORE.curie('triples'), - model_uri=COMPOSITE_DISEASE.textWithTriples__triples, domain=None, range=Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]]) - -slots.publication__id = Slot(uri=CORE.id, name="publication__id", curie=CORE.curie('id'), - model_uri=COMPOSITE_DISEASE.publication__id, domain=None, range=Optional[str]) - -slots.publication__title = Slot(uri=CORE.title, name="publication__title", curie=CORE.curie('title'), - model_uri=COMPOSITE_DISEASE.publication__title, domain=None, range=Optional[str]) - -slots.publication__abstract = Slot(uri=CORE.abstract, name="publication__abstract", curie=CORE.curie('abstract'), - model_uri=COMPOSITE_DISEASE.publication__abstract, domain=None, range=Optional[str]) - -slots.publication__combined_text = Slot(uri=CORE.combined_text, name="publication__combined_text", curie=CORE.curie('combined_text'), - model_uri=COMPOSITE_DISEASE.publication__combined_text, domain=None, range=Optional[str]) - -slots.publication__full_text = Slot(uri=CORE.full_text, name="publication__full_text", curie=CORE.curie('full_text'), - model_uri=COMPOSITE_DISEASE.publication__full_text, domain=None, range=Optional[str]) - -slots.annotatorResult__subject_text = Slot(uri=CORE.subject_text, name="annotatorResult__subject_text", curie=CORE.curie('subject_text'), - model_uri=COMPOSITE_DISEASE.annotatorResult__subject_text, domain=None, range=Optional[str]) - -slots.annotatorResult__object_id = Slot(uri=CORE.object_id, name="annotatorResult__object_id", curie=CORE.curie('object_id'), - model_uri=COMPOSITE_DISEASE.annotatorResult__object_id, domain=None, range=Optional[str]) - -slots.annotatorResult__object_text = Slot(uri=CORE.object_text, name="annotatorResult__object_text", curie=CORE.curie('object_text'), - model_uri=COMPOSITE_DISEASE.annotatorResult__object_text, domain=None, range=Optional[str]) \ No newline at end of file diff --git a/projects/composite_disease/docs/AdverseEffect.md b/projects/composite_disease/docs/AdverseEffect.md deleted file mode 100644 index d439f5a44..000000000 --- a/projects/composite_disease/docs/AdverseEffect.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Class: AdverseEffect - - - - -URI: [composite_disease:AdverseEffect](http://w3id.org/ontogpt/composite_disease/AdverseEffect) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[TreatmentAdverseEffect]-%20adverse_effects%200..*>[AdverseEffect|id(i):string;label(i):string%20%3F],[NamedEntity]^-[AdverseEffect],[TreatmentAdverseEffect])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[TreatmentAdverseEffect]-%20adverse_effects%200..*>[AdverseEffect|id(i):string;label(i):string%20%3F],[NamedEntity]^-[AdverseEffect],[TreatmentAdverseEffect]) - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞adverse_effects](treatmentAdverseEffect__adverse_effects.md)* 0..\* **[AdverseEffect](AdverseEffect.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) 1..1 - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) 0..1 - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/composite_disease/docs/AnnotatorResult.md b/projects/composite_disease/docs/AnnotatorResult.md deleted file mode 100644 index b89c1a94d..000000000 --- a/projects/composite_disease/docs/AnnotatorResult.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Class: AnnotatorResult - - - - -URI: [composite_disease:AnnotatorResult](http://w3id.org/ontogpt/composite_disease/AnnotatorResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F])](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F]) - -## Attributes - - -### Own - - * [➞subject_text](annotatorResult__subject_text.md) 0..1 - * Range: [String](types/String.md) - * [➞object_id](annotatorResult__object_id.md) 0..1 - * Range: [String](types/String.md) - * [➞object_text](annotatorResult__object_text.md) 0..1 - * Range: [String](types/String.md) diff --git a/projects/composite_disease/docs/Any.md b/projects/composite_disease/docs/Any.md deleted file mode 100644 index f5b564def..000000000 --- a/projects/composite_disease/docs/Any.md +++ /dev/null @@ -1,25 +0,0 @@ - -# Class: Any - - - - -URI: [composite_disease:Any](http://w3id.org/ontogpt/composite_disease/Any) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult])](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult]) - -## Referenced by Class - - * **None** *[➞extracted_object](extractionResult__extracted_object.md)* 0..1 **[Any](Any.md)** - * **None** *[➞named_entities](extractionResult__named_entities.md)* 0..\* **[Any](Any.md)** - -## Attributes - - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | linkml:Any | - diff --git a/projects/composite_disease/docs/CHEBIDrugType.md b/projects/composite_disease/docs/CHEBIDrugType.md deleted file mode 100644 index 4da395edc..000000000 --- a/projects/composite_disease/docs/CHEBIDrugType.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Enum: CHEBIDrugType - - - - -URI: [composite_disease:CHEBIDrugType](http://w3id.org/ontogpt/composite_disease/CHEBIDrugType) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | - diff --git a/projects/composite_disease/docs/CompositeDisease.md b/projects/composite_disease/docs/CompositeDisease.md deleted file mode 100644 index edcff906b..000000000 --- a/projects/composite_disease/docs/CompositeDisease.md +++ /dev/null @@ -1,37 +0,0 @@ - -# Class: CompositeDisease - - - - -URI: [composite_disease:CompositeDisease](http://w3id.org/ontogpt/composite_disease/CompositeDisease) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[TreatmentMechanism],[TreatmentEfficacy],[TreatmentAdverseEffect],[Treatment],[Drug],[Disease],[TreatmentAdverseEffect]0..1 - * Description: the name of the disease that is treated. - * Range: [Disease](Disease.md) - * [➞drugs](compositeDisease__drugs.md) 0..\* - * Description: semicolon-separated list of named small molecule drugs - * Range: [Drug](Drug.md) - * [➞treatments](compositeDisease__treatments.md) 0..\* - * Description: semicolon-separated list of therapies and treatments are indicated for treating the disease. - * Range: [Treatment](Treatment.md) - * [➞contraindications](compositeDisease__contraindications.md) 0..\* - * Description: semicolon-separated list of therapies and treatments that are contra-indicated for the disease, and should not be used, due to risk of adverse effects. - * Range: [Treatment](Treatment.md) - * [➞treatment_mechanisms](compositeDisease__treatment_mechanisms.md) 0..\* - * Description: semicolon-separated list of treatment to asterisk-separated mechanism associations - * Range: [TreatmentMechanism](TreatmentMechanism.md) - * [➞treatment_efficacies](compositeDisease__treatment_efficacies.md) 0..\* - * Description: semicolon-separated list of treatment to efficacy associations, e.g. Imatinib*effective - * Range: [TreatmentEfficacy](TreatmentEfficacy.md) - * [➞treatment_adverse_effects](compositeDisease__treatment_adverse_effects.md) 0..\* - * Description: semicolon-separated list of treatment to adverse effect associations, e.g. Imatinib*nausea - * Range: [TreatmentAdverseEffect](TreatmentAdverseEffect.md) diff --git a/projects/composite_disease/docs/CompoundExpression.md b/projects/composite_disease/docs/CompoundExpression.md deleted file mode 100644 index d1831129e..000000000 --- a/projects/composite_disease/docs/CompoundExpression.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Class: CompoundExpression - - - - -URI: [composite_disease:CompoundExpression](http://w3id.org/ontogpt/composite_disease/CompoundExpression) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[TreatmentMechanism],[TreatmentEfficacy],[TreatmentAdverseEffect],[CompoundExpression]^-[Triple],[CompoundExpression]^-[TreatmentMechanism],[CompoundExpression]^-[TreatmentEfficacy],[CompoundExpression]^-[TreatmentAdverseEffect])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[TreatmentMechanism],[TreatmentEfficacy],[TreatmentAdverseEffect],[CompoundExpression]^-[Triple],[CompoundExpression]^-[TreatmentMechanism],[CompoundExpression]^-[TreatmentEfficacy],[CompoundExpression]^-[TreatmentAdverseEffect]) - -## Children - - * [TreatmentAdverseEffect](TreatmentAdverseEffect.md) - * [TreatmentEfficacy](TreatmentEfficacy.md) - * [TreatmentMechanism](TreatmentMechanism.md) - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - -## Referenced by Class - - -## Attributes - diff --git a/projects/composite_disease/docs/Disease.md b/projects/composite_disease/docs/Disease.md deleted file mode 100644 index 43817a43c..000000000 --- a/projects/composite_disease/docs/Disease.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Class: Disease - - - - -URI: [composite_disease:Disease](http://w3id.org/ontogpt/composite_disease/Disease) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[CompositeDisease]-%20main_disease%200..1>[Disease|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Disease],[CompositeDisease])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[CompositeDisease]-%20main_disease%200..1>[Disease|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Disease],[CompositeDisease]) - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞main_disease](compositeDisease__main_disease.md)* 0..1 **[Disease](Disease.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) 1..1 - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) 0..1 - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/composite_disease/docs/Drug.md b/projects/composite_disease/docs/Drug.md deleted file mode 100644 index ff08bec35..000000000 --- a/projects/composite_disease/docs/Drug.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Class: Drug - - - - -URI: [composite_disease:Drug](http://w3id.org/ontogpt/composite_disease/Drug) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[CompositeDisease]-%20drugs%200..*>[Drug|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Drug],[CompositeDisease])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[CompositeDisease]-%20drugs%200..*>[Drug|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Drug],[CompositeDisease]) - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞drugs](compositeDisease__drugs.md)* 0..\* **[Drug](Drug.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) 1..1 - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) 0..1 - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/composite_disease/docs/ExtractionResult.md b/projects/composite_disease/docs/ExtractionResult.md deleted file mode 100644 index e138c25b7..000000000 --- a/projects/composite_disease/docs/ExtractionResult.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Class: ExtractionResult - - -A result of extracting knowledge on text - -URI: [composite_disease:ExtractionResult](http://w3id.org/ontogpt/composite_disease/ExtractionResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]0..1 - * Range: [String](types/String.md) - * [➞input_title](extractionResult__input_title.md) 0..1 - * Range: [String](types/String.md) - * [➞input_text](extractionResult__input_text.md) 0..1 - * Range: [String](types/String.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) 0..1 - * Range: [String](types/String.md) - * [➞prompt](extractionResult__prompt.md) 0..1 - * Range: [String](types/String.md) - * [➞extracted_object](extractionResult__extracted_object.md) 0..1 - * Description: The complex objects extracted from the text - * Range: [Any](Any.md) - * [➞named_entities](extractionResult__named_entities.md) 0..\* - * Description: Named entities extracted from the text - * Range: [Any](Any.md) diff --git a/projects/composite_disease/docs/Gene.md b/projects/composite_disease/docs/Gene.md deleted file mode 100644 index abeb93212..000000000 --- a/projects/composite_disease/docs/Gene.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Class: Gene - - - - -URI: [composite_disease:Gene](http://w3id.org/ontogpt/composite_disease/Gene) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[NamedEntity]^-[Gene|id(i):string;label(i):string%20%3F])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[NamedEntity]^-[Gene|id(i):string;label(i):string%20%3F]) - -## Identifier prefixes - - * HGNC - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) 1..1 - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) 0..1 - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/composite_disease/docs/MAXOActionType.md b/projects/composite_disease/docs/MAXOActionType.md deleted file mode 100644 index cf61778da..000000000 --- a/projects/composite_disease/docs/MAXOActionType.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Enum: MAXOActionType - - - - -URI: [composite_disease:MAXOActionType](http://w3id.org/ontogpt/composite_disease/MAXOActionType) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | - diff --git a/projects/composite_disease/docs/MESHTherapeuticType.md b/projects/composite_disease/docs/MESHTherapeuticType.md deleted file mode 100644 index d3e9d3dff..000000000 --- a/projects/composite_disease/docs/MESHTherapeuticType.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Enum: MESHTherapeuticType - - - - -URI: [composite_disease:MESHTherapeuticType](http://w3id.org/ontogpt/composite_disease/MESHTherapeuticType) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | - diff --git a/projects/composite_disease/docs/Mechanism.md b/projects/composite_disease/docs/Mechanism.md deleted file mode 100644 index f19f1dbcb..000000000 --- a/projects/composite_disease/docs/Mechanism.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Class: Mechanism - - - - -URI: [composite_disease:Mechanism](http://w3id.org/ontogpt/composite_disease/Mechanism) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[TreatmentMechanism]-%20mechanism%200..1>[Mechanism|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Mechanism],[TreatmentMechanism])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[TreatmentMechanism]-%20mechanism%200..1>[Mechanism|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Mechanism],[TreatmentMechanism]) - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞mechanism](treatmentMechanism__mechanism.md)* 0..1 **[Mechanism](Mechanism.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) 1..1 - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) 0..1 - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/composite_disease/docs/NCITDrugType.md b/projects/composite_disease/docs/NCITDrugType.md deleted file mode 100644 index 4a0d81963..000000000 --- a/projects/composite_disease/docs/NCITDrugType.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Enum: NCITDrugType - - - - -URI: [composite_disease:NCITDrugType](http://w3id.org/ontogpt/composite_disease/NCITDrugType) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | - diff --git a/projects/composite_disease/docs/NCITTActivityType.md b/projects/composite_disease/docs/NCITTActivityType.md deleted file mode 100644 index da33466d9..000000000 --- a/projects/composite_disease/docs/NCITTActivityType.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Enum: NCITTActivityType - - - - -URI: [composite_disease:NCITTActivityType](http://w3id.org/ontogpt/composite_disease/NCITTActivityType) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | - diff --git a/projects/composite_disease/docs/NCITTreatmentType.md b/projects/composite_disease/docs/NCITTreatmentType.md deleted file mode 100644 index 309c96759..000000000 --- a/projects/composite_disease/docs/NCITTreatmentType.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Enum: NCITTreatmentType - - - - -URI: [composite_disease:NCITTreatmentType](http://w3id.org/ontogpt/composite_disease/NCITTreatmentType) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | - diff --git a/projects/composite_disease/docs/NamedEntity.md b/projects/composite_disease/docs/NamedEntity.md deleted file mode 100644 index 2ca5facd0..000000000 --- a/projects/composite_disease/docs/NamedEntity.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Class: NamedEntity - - - - -URI: [composite_disease:NamedEntity](http://w3id.org/ontogpt/composite_disease/NamedEntity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Treatment],[Symptom],[RelationshipType],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[Treatment],[NamedEntity]^-[Symptom],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[Mechanism],[NamedEntity]^-[Gene],[NamedEntity]^-[Drug],[NamedEntity]^-[Disease],[NamedEntity]^-[AdverseEffect],[Triple],[Mechanism],[Gene],[Drug],[Disease],[AdverseEffect])](https://yuml.me/diagram/nofunky;dir:TB/class/[Treatment],[Symptom],[RelationshipType],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[Treatment],[NamedEntity]^-[Symptom],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[Mechanism],[NamedEntity]^-[Gene],[NamedEntity]^-[Drug],[NamedEntity]^-[Disease],[NamedEntity]^-[AdverseEffect],[Triple],[Mechanism],[Gene],[Drug],[Disease],[AdverseEffect]) - -## Children - - * [AdverseEffect](AdverseEffect.md) - * [Disease](Disease.md) - * [Drug](Drug.md) - * [Gene](Gene.md) - * [Mechanism](Mechanism.md) - * [RelationshipType](RelationshipType.md) - * [Symptom](Symptom.md) - * [Treatment](Treatment.md) - -## Referenced by Class - - * **None** *[➞object](triple__object.md)* 0..1 **[NamedEntity](NamedEntity.md)** - * **None** *[➞object_qualifier](triple__object_qualifier.md)* 0..1 **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject](triple__subject.md)* 0..1 **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject_qualifier](triple__subject_qualifier.md)* 0..1 **[NamedEntity](NamedEntity.md)** - -## Attributes - - -### Own - - * [➞id](namedEntity__id.md) 1..1 - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) 0..1 - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/composite_disease/docs/NullDataOptions.md b/projects/composite_disease/docs/NullDataOptions.md deleted file mode 100644 index e5a12b342..000000000 --- a/projects/composite_disease/docs/NullDataOptions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Enum: NullDataOptions - - - - -URI: [composite_disease:NullDataOptions](http://w3id.org/ontogpt/composite_disease/NullDataOptions) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | -| UNSPECIFIED_METHOD_OF_ADMINISTRATION | | NCIT:C149701 | | -| NOT_APPLICABLE | | NCIT:C18902 | {'aliases': ['not applicable', 'N/A']} | -| NOT_MENTIONED | | | | - diff --git a/projects/composite_disease/docs/Publication.md b/projects/composite_disease/docs/Publication.md deleted file mode 100644 index 661829a48..000000000 --- a/projects/composite_disease/docs/Publication.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Publication - - - - -URI: [composite_disease:Publication](http://w3id.org/ontogpt/composite_disease/Publication) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples])](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples]) - -## Referenced by Class - - * **None** *[➞publication](textWithTriples__publication.md)* 0..1 **[Publication](Publication.md)** - -## Attributes - - -### Own - - * [➞id](publication__id.md) 0..1 - * Description: The publication identifier - * Range: [String](types/String.md) - * [➞title](publication__title.md) 0..1 - * Description: The title of the publication - * Range: [String](types/String.md) - * [➞abstract](publication__abstract.md) 0..1 - * Description: The abstract of the publication - * Range: [String](types/String.md) - * [➞combined_text](publication__combined_text.md) 0..1 - * Range: [String](types/String.md) - * [➞full_text](publication__full_text.md) 0..1 - * Description: The full text of the publication - * Range: [String](types/String.md) diff --git a/projects/composite_disease/docs/RelationshipType.md b/projects/composite_disease/docs/RelationshipType.md deleted file mode 100644 index 6b4c516bc..000000000 --- a/projects/composite_disease/docs/RelationshipType.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: RelationshipType - - - - -URI: [composite_disease:RelationshipType](http://w3id.org/ontogpt/composite_disease/RelationshipType) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity]) - -## Identifier prefixes - - * RO - * biolink - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞predicate](triple__predicate.md)* 0..1 **[RelationshipType](RelationshipType.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) 1..1 - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) 0..1 - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/composite_disease/docs/Symptom.md b/projects/composite_disease/docs/Symptom.md deleted file mode 100644 index 06440e5f1..000000000 --- a/projects/composite_disease/docs/Symptom.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Class: Symptom - - - - -URI: [composite_disease:Symptom](http://w3id.org/ontogpt/composite_disease/Symptom) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]^-[Symptom|id(i):string;label(i):string%20%3F],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]^-[Symptom|id(i):string;label(i):string%20%3F],[NamedEntity]) - -## Identifier prefixes - - * HP - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) 1..1 - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) 0..1 - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/composite_disease/docs/TextWithTriples.md b/projects/composite_disease/docs/TextWithTriples.md deleted file mode 100644 index 132154937..000000000 --- a/projects/composite_disease/docs/TextWithTriples.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: TextWithTriples - - - - -URI: [composite_disease:TextWithTriples](http://w3id.org/ontogpt/composite_disease/TextWithTriples) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]0..1 - * Range: [Publication](Publication.md) - * [➞triples](textWithTriples__triples.md) 0..\* - * Range: [Triple](Triple.md) diff --git a/projects/composite_disease/docs/Treatment.md b/projects/composite_disease/docs/Treatment.md deleted file mode 100644 index 74b7739fd..000000000 --- a/projects/composite_disease/docs/Treatment.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Treatment - - - - -URI: [composite_disease:Treatment](http://w3id.org/ontogpt/composite_disease/Treatment) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[CompositeDisease]-%20contraindications%200..*>[Treatment|id(i):string;label(i):string%20%3F],[CompositeDisease]-%20treatments%200..*>[Treatment],[TreatmentAdverseEffect]-%20treatment%200..1>[Treatment],[TreatmentEfficacy]-%20treatment%200..1>[Treatment],[TreatmentMechanism]-%20treatment%200..1>[Treatment],[NamedEntity]^-[Treatment],[TreatmentMechanism],[TreatmentEfficacy],[TreatmentAdverseEffect],[NamedEntity],[CompositeDisease])](https://yuml.me/diagram/nofunky;dir:TB/class/[CompositeDisease]-%20contraindications%200..*>[Treatment|id(i):string;label(i):string%20%3F],[CompositeDisease]-%20treatments%200..*>[Treatment],[TreatmentAdverseEffect]-%20treatment%200..1>[Treatment],[TreatmentEfficacy]-%20treatment%200..1>[Treatment],[TreatmentMechanism]-%20treatment%200..1>[Treatment],[NamedEntity]^-[Treatment],[TreatmentMechanism],[TreatmentEfficacy],[TreatmentAdverseEffect],[NamedEntity],[CompositeDisease]) - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞contraindications](compositeDisease__contraindications.md)* 0..\* **[Treatment](Treatment.md)** - * **None** *[➞treatments](compositeDisease__treatments.md)* 0..\* **[Treatment](Treatment.md)** - * **None** *[➞treatment](treatmentAdverseEffect__treatment.md)* 0..1 **[Treatment](Treatment.md)** - * **None** *[➞treatment](treatmentEfficacy__treatment.md)* 0..1 **[Treatment](Treatment.md)** - * **None** *[➞treatment](treatmentMechanism__treatment.md)* 0..1 **[Treatment](Treatment.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) 1..1 - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) 0..1 - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/composite_disease/docs/TreatmentAdverseEffect.md b/projects/composite_disease/docs/TreatmentAdverseEffect.md deleted file mode 100644 index 5b6b0cdae..000000000 --- a/projects/composite_disease/docs/TreatmentAdverseEffect.md +++ /dev/null @@ -1,28 +0,0 @@ - -# Class: TreatmentAdverseEffect - - - - -URI: [composite_disease:TreatmentAdverseEffect](http://w3id.org/ontogpt/composite_disease/TreatmentAdverseEffect) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[AdverseEffect][TreatmentAdverseEffect],[CompoundExpression]^-[TreatmentAdverseEffect],[Treatment],[CompoundExpression],[CompositeDisease],[AdverseEffect])](https://yuml.me/diagram/nofunky;dir:TB/class/[AdverseEffect][TreatmentAdverseEffect],[CompoundExpression]^-[TreatmentAdverseEffect],[Treatment],[CompoundExpression],[CompositeDisease],[AdverseEffect]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞treatment_adverse_effects](compositeDisease__treatment_adverse_effects.md)* 0..\* **[TreatmentAdverseEffect](TreatmentAdverseEffect.md)** - -## Attributes - - -### Own - - * [➞treatment](treatmentAdverseEffect__treatment.md) 0..1 - * Range: [Treatment](Treatment.md) - * [➞adverse_effects](treatmentAdverseEffect__adverse_effects.md) 0..\* - * Range: [AdverseEffect](AdverseEffect.md) diff --git a/projects/composite_disease/docs/TreatmentEfficacy.md b/projects/composite_disease/docs/TreatmentEfficacy.md deleted file mode 100644 index b7bc0bf5a..000000000 --- a/projects/composite_disease/docs/TreatmentEfficacy.md +++ /dev/null @@ -1,28 +0,0 @@ - -# Class: TreatmentEfficacy - - - - -URI: [composite_disease:TreatmentEfficacy](http://w3id.org/ontogpt/composite_disease/TreatmentEfficacy) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Treatment][TreatmentEfficacy],[CompoundExpression]^-[TreatmentEfficacy],[Treatment],[CompoundExpression],[CompositeDisease])](https://yuml.me/diagram/nofunky;dir:TB/class/[Treatment][TreatmentEfficacy],[CompoundExpression]^-[TreatmentEfficacy],[Treatment],[CompoundExpression],[CompositeDisease]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞treatment_efficacies](compositeDisease__treatment_efficacies.md)* 0..\* **[TreatmentEfficacy](TreatmentEfficacy.md)** - -## Attributes - - -### Own - - * [➞treatment](treatmentEfficacy__treatment.md) 0..1 - * Range: [Treatment](Treatment.md) - * [➞efficacy](treatmentEfficacy__efficacy.md) 0..1 - * Range: [String](types/String.md) diff --git a/projects/composite_disease/docs/TreatmentMechanism.md b/projects/composite_disease/docs/TreatmentMechanism.md deleted file mode 100644 index b8d82b890..000000000 --- a/projects/composite_disease/docs/TreatmentMechanism.md +++ /dev/null @@ -1,28 +0,0 @@ - -# Class: TreatmentMechanism - - - - -URI: [composite_disease:TreatmentMechanism](http://w3id.org/ontogpt/composite_disease/TreatmentMechanism) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Mechanism][TreatmentMechanism],[CompoundExpression]^-[TreatmentMechanism],[Treatment],[Mechanism],[CompoundExpression],[CompositeDisease])](https://yuml.me/diagram/nofunky;dir:TB/class/[Mechanism][TreatmentMechanism],[CompoundExpression]^-[TreatmentMechanism],[Treatment],[Mechanism],[CompoundExpression],[CompositeDisease]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞treatment_mechanisms](compositeDisease__treatment_mechanisms.md)* 0..\* **[TreatmentMechanism](TreatmentMechanism.md)** - -## Attributes - - -### Own - - * [➞treatment](treatmentMechanism__treatment.md) 0..1 - * Range: [Treatment](Treatment.md) - * [➞mechanism](treatmentMechanism__mechanism.md) 0..1 - * Range: [Mechanism](Mechanism.md) diff --git a/projects/composite_disease/docs/Triple.md b/projects/composite_disease/docs/Triple.md deleted file mode 100644 index e8018eeff..000000000 --- a/projects/composite_disease/docs/Triple.md +++ /dev/null @@ -1,39 +0,0 @@ - -# Class: Triple - - -Abstract parent for Relation Extraction tasks - -URI: [composite_disease:Triple](http://w3id.org/ontogpt/composite_disease/Triple) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity][Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity][Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞triples](textWithTriples__triples.md)* 0..\* **[Triple](Triple.md)** - -## Attributes - - -### Own - - * [➞subject](triple__subject.md) 0..1 - * Range: [NamedEntity](NamedEntity.md) - * [➞predicate](triple__predicate.md) 0..1 - * Range: [RelationshipType](RelationshipType.md) - * [➞object](triple__object.md) 0..1 - * Range: [NamedEntity](NamedEntity.md) - * [➞qualifier](triple__qualifier.md) 0..1 - * Description: A qualifier for the statements, e.g. "NOT" for negation - * Range: [String](types/String.md) - * [➞subject_qualifier](triple__subject_qualifier.md) 0..1 - * Description: An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - * Range: [NamedEntity](NamedEntity.md) - * [➞object_qualifier](triple__object_qualifier.md) 0..1 - * Description: An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * Range: [NamedEntity](NamedEntity.md) diff --git a/projects/composite_disease/docs/annotatorResult__object_id.md b/projects/composite_disease/docs/annotatorResult__object_id.md deleted file mode 100644 index 21c84bac5..000000000 --- a/projects/composite_disease/docs/annotatorResult__object_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_id - - - - -URI: [composite_disease:annotatorResult__object_id](http://w3id.org/ontogpt/composite_disease/annotatorResult__object_id) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/composite_disease/docs/annotatorResult__object_text.md b/projects/composite_disease/docs/annotatorResult__object_text.md deleted file mode 100644 index 04eacc6a1..000000000 --- a/projects/composite_disease/docs/annotatorResult__object_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_text - - - - -URI: [composite_disease:annotatorResult__object_text](http://w3id.org/ontogpt/composite_disease/annotatorResult__object_text) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/composite_disease/docs/annotatorResult__subject_text.md b/projects/composite_disease/docs/annotatorResult__subject_text.md deleted file mode 100644 index 813a613dc..000000000 --- a/projects/composite_disease/docs/annotatorResult__subject_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_text - - - - -URI: [composite_disease:annotatorResult__subject_text](http://w3id.org/ontogpt/composite_disease/annotatorResult__subject_text) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/composite_disease/docs/compositeDisease__contraindications.md b/projects/composite_disease/docs/compositeDisease__contraindications.md deleted file mode 100644 index b649b37bc..000000000 --- a/projects/composite_disease/docs/compositeDisease__contraindications.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: contraindications - - -semicolon-separated list of therapies and treatments that are contra-indicated for the disease, and should not be used, due to risk of adverse effects. - -URI: [composite_disease:compositeDisease__contraindications](http://w3id.org/ontogpt/composite_disease/compositeDisease__contraindications) - - -## Domain and Range - -None → 0..\* [Treatment](Treatment.md) - -## Parents - - -## Children - - -## Used by - - * [CompositeDisease](CompositeDisease.md) diff --git a/projects/composite_disease/docs/compositeDisease__drugs.md b/projects/composite_disease/docs/compositeDisease__drugs.md deleted file mode 100644 index 0e62f267d..000000000 --- a/projects/composite_disease/docs/compositeDisease__drugs.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: drugs - - -semicolon-separated list of named small molecule drugs - -URI: [composite_disease:compositeDisease__drugs](http://w3id.org/ontogpt/composite_disease/compositeDisease__drugs) - - -## Domain and Range - -None → 0..\* [Drug](Drug.md) - -## Parents - - -## Children - - -## Used by - - * [CompositeDisease](CompositeDisease.md) diff --git a/projects/composite_disease/docs/compositeDisease__main_disease.md b/projects/composite_disease/docs/compositeDisease__main_disease.md deleted file mode 100644 index 46fb5d7f6..000000000 --- a/projects/composite_disease/docs/compositeDisease__main_disease.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: main_disease - - -the name of the disease that is treated. - -URI: [composite_disease:compositeDisease__main_disease](http://w3id.org/ontogpt/composite_disease/compositeDisease__main_disease) - - -## Domain and Range - -None → 0..1 [Disease](Disease.md) - -## Parents - - -## Children - - -## Used by - - * [CompositeDisease](CompositeDisease.md) diff --git a/projects/composite_disease/docs/compositeDisease__treatment_adverse_effects.md b/projects/composite_disease/docs/compositeDisease__treatment_adverse_effects.md deleted file mode 100644 index 59cc61e70..000000000 --- a/projects/composite_disease/docs/compositeDisease__treatment_adverse_effects.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: treatment_adverse_effects - - -semicolon-separated list of treatment to adverse effect associations, e.g. Imatinib*nausea - -URI: [composite_disease:compositeDisease__treatment_adverse_effects](http://w3id.org/ontogpt/composite_disease/compositeDisease__treatment_adverse_effects) - - -## Domain and Range - -None → 0..\* [TreatmentAdverseEffect](TreatmentAdverseEffect.md) - -## Parents - - -## Children - - -## Used by - - * [CompositeDisease](CompositeDisease.md) diff --git a/projects/composite_disease/docs/compositeDisease__treatment_efficacies.md b/projects/composite_disease/docs/compositeDisease__treatment_efficacies.md deleted file mode 100644 index 198fd7165..000000000 --- a/projects/composite_disease/docs/compositeDisease__treatment_efficacies.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: treatment_efficacies - - -semicolon-separated list of treatment to efficacy associations, e.g. Imatinib*effective - -URI: [composite_disease:compositeDisease__treatment_efficacies](http://w3id.org/ontogpt/composite_disease/compositeDisease__treatment_efficacies) - - -## Domain and Range - -None → 0..\* [TreatmentEfficacy](TreatmentEfficacy.md) - -## Parents - - -## Children - - -## Used by - - * [CompositeDisease](CompositeDisease.md) diff --git a/projects/composite_disease/docs/compositeDisease__treatment_mechanisms.md b/projects/composite_disease/docs/compositeDisease__treatment_mechanisms.md deleted file mode 100644 index 6634185bf..000000000 --- a/projects/composite_disease/docs/compositeDisease__treatment_mechanisms.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: treatment_mechanisms - - -semicolon-separated list of treatment to asterisk-separated mechanism associations - -URI: [composite_disease:compositeDisease__treatment_mechanisms](http://w3id.org/ontogpt/composite_disease/compositeDisease__treatment_mechanisms) - - -## Domain and Range - -None → 0..\* [TreatmentMechanism](TreatmentMechanism.md) - -## Parents - - -## Children - - -## Used by - - * [CompositeDisease](CompositeDisease.md) diff --git a/projects/composite_disease/docs/compositeDisease__treatments.md b/projects/composite_disease/docs/compositeDisease__treatments.md deleted file mode 100644 index 3b120d777..000000000 --- a/projects/composite_disease/docs/compositeDisease__treatments.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: treatments - - -semicolon-separated list of therapies and treatments are indicated for treating the disease. - -URI: [composite_disease:compositeDisease__treatments](http://w3id.org/ontogpt/composite_disease/compositeDisease__treatments) - - -## Domain and Range - -None → 0..\* [Treatment](Treatment.md) - -## Parents - - -## Children - - -## Used by - - * [CompositeDisease](CompositeDisease.md) diff --git a/projects/composite_disease/docs/composite_disease.md b/projects/composite_disease/docs/composite_disease.md deleted file mode 100644 index a9c889f9f..000000000 --- a/projects/composite_disease/docs/composite_disease.md +++ /dev/null @@ -1,133 +0,0 @@ - -# composite_disease - - -**metamodel version:** 1.7.0 - -**version:** None - - -A template for representing composite disease concepts - - -### Classes - - * [AnnotatorResult](AnnotatorResult.md) - * [Any](Any.md) - * [CompositeDisease](CompositeDisease.md) - * [CompoundExpression](CompoundExpression.md) - * [TreatmentAdverseEffect](TreatmentAdverseEffect.md) - * [TreatmentEfficacy](TreatmentEfficacy.md) - * [TreatmentMechanism](TreatmentMechanism.md) - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - * [ExtractionResult](ExtractionResult.md) - A result of extracting knowledge on text - * [NamedEntity](NamedEntity.md) - * [AdverseEffect](AdverseEffect.md) - * [Disease](Disease.md) - * [Drug](Drug.md) - * [Gene](Gene.md) - * [Mechanism](Mechanism.md) - * [RelationshipType](RelationshipType.md) - * [Symptom](Symptom.md) - * [Treatment](Treatment.md) - * [Publication](Publication.md) - * [TextWithTriples](TextWithTriples.md) - -### Mixins - - -### Slots - - * [➞object_id](annotatorResult__object_id.md) - * [➞object_text](annotatorResult__object_text.md) - * [➞subject_text](annotatorResult__subject_text.md) - * [➞contraindications](compositeDisease__contraindications.md) - semicolon-separated list of therapies and treatments that are contra-indicated for the disease, and should not be used, due to risk of adverse effects. - * [➞drugs](compositeDisease__drugs.md) - semicolon-separated list of named small molecule drugs - * [➞main_disease](compositeDisease__main_disease.md) - the name of the disease that is treated. - * [➞treatment_adverse_effects](compositeDisease__treatment_adverse_effects.md) - semicolon-separated list of treatment to adverse effect associations, e.g. Imatinib*nausea - * [➞treatment_efficacies](compositeDisease__treatment_efficacies.md) - semicolon-separated list of treatment to efficacy associations, e.g. Imatinib*effective - * [➞treatment_mechanisms](compositeDisease__treatment_mechanisms.md) - semicolon-separated list of treatment to asterisk-separated mechanism associations - * [➞treatments](compositeDisease__treatments.md) - semicolon-separated list of therapies and treatments are indicated for treating the disease. - * [➞extracted_object](extractionResult__extracted_object.md) - The complex objects extracted from the text - * [➞input_id](extractionResult__input_id.md) - * [➞input_text](extractionResult__input_text.md) - * [➞input_title](extractionResult__input_title.md) - * [➞named_entities](extractionResult__named_entities.md) - Named entities extracted from the text - * [➞prompt](extractionResult__prompt.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) - * [➞id](namedEntity__id.md) - A unique identifier for the named entity - * [➞label](namedEntity__label.md) - The label (name) of the named thing - * [➞abstract](publication__abstract.md) - The abstract of the publication - * [➞combined_text](publication__combined_text.md) - * [➞full_text](publication__full_text.md) - The full text of the publication - * [➞id](publication__id.md) - The publication identifier - * [➞title](publication__title.md) - The title of the publication - * [➞publication](textWithTriples__publication.md) - * [➞triples](textWithTriples__triples.md) - * [➞adverse_effects](treatmentAdverseEffect__adverse_effects.md) - * [➞treatment](treatmentAdverseEffect__treatment.md) - * [➞efficacy](treatmentEfficacy__efficacy.md) - * [➞treatment](treatmentEfficacy__treatment.md) - * [➞mechanism](treatmentMechanism__mechanism.md) - * [➞treatment](treatmentMechanism__treatment.md) - * [➞object](triple__object.md) - * [➞object_qualifier](triple__object_qualifier.md) - An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * [➞predicate](triple__predicate.md) - * [➞qualifier](triple__qualifier.md) - A qualifier for the statements, e.g. "NOT" for negation - * [➞subject](triple__subject.md) - * [➞subject_qualifier](triple__subject_qualifier.md) - An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -### Enums - - * [CHEBIDrugType](CHEBIDrugType.md) - * [MAXOActionType](MAXOActionType.md) - * [MESHTherapeuticType](MESHTherapeuticType.md) - * [NCITDrugType](NCITDrugType.md) - * [NCITTActivityType](NCITTActivityType.md) - * [NCITTreatmentType](NCITTreatmentType.md) - * [NullDataOptions](NullDataOptions.md) - -### Subsets - - -### Types - - -#### Built in - - * **Bool** - * **Curie** - * **Decimal** - * **ElementIdentifier** - * **NCName** - * **NodeIdentifier** - * **URI** - * **URIorCURIE** - * **XSDDate** - * **XSDDateTime** - * **XSDTime** - * **float** - * **int** - * **str** - -#### Defined - - * [Boolean](types/Boolean.md) (**Bool**) - A binary (true or false) value - * [Curie](types/Curie.md) (**Curie**) - a compact URI - * [Date](types/Date.md) (**XSDDate**) - a date (year, month and day) in an idealized calendar - * [DateOrDatetime](types/DateOrDatetime.md) (**str**) - Either a date or a datetime - * [Datetime](types/Datetime.md) (**XSDDateTime**) - The combination of a date and time - * [Decimal](types/Decimal.md) (**Decimal**) - A real number with arbitrary precision that conforms to the xsd:decimal specification - * [Double](types/Double.md) (**float**) - A real number that conforms to the xsd:double specification - * [Float](types/Float.md) (**float**) - A real number that conforms to the xsd:float specification - * [Integer](types/Integer.md) (**int**) - An integer - * [Jsonpath](types/Jsonpath.md) (**str**) - A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - * [Jsonpointer](types/Jsonpointer.md) (**str**) - A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - * [Ncname](types/Ncname.md) (**NCName**) - Prefix part of CURIE - * [Nodeidentifier](types/Nodeidentifier.md) (**NodeIdentifier**) - A URI, CURIE or BNODE that represents a node in a model. - * [Objectidentifier](types/Objectidentifier.md) (**ElementIdentifier**) - A URI or CURIE that represents an object in the model. - * [Sparqlpath](types/Sparqlpath.md) (**str**) - A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - * [String](types/String.md) (**str**) - A character string - * [Time](types/Time.md) (**XSDTime**) - A time object represents a (local) time of day, independent of any particular day - * [Uri](types/Uri.md) (**URI**) - a complete URI - * [Uriorcurie](types/Uriorcurie.md) (**URIorCURIE**) - a URI or a CURIE diff --git a/projects/composite_disease/docs/extractionResult__extracted_object.md b/projects/composite_disease/docs/extractionResult__extracted_object.md deleted file mode 100644 index a085be898..000000000 --- a/projects/composite_disease/docs/extractionResult__extracted_object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: extracted_object - - -The complex objects extracted from the text - -URI: [composite_disease:extractionResult__extracted_object](http://w3id.org/ontogpt/composite_disease/extractionResult__extracted_object) - - -## Domain and Range - -None → 0..1 [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/composite_disease/docs/extractionResult__input_id.md b/projects/composite_disease/docs/extractionResult__input_id.md deleted file mode 100644 index 236703e9a..000000000 --- a/projects/composite_disease/docs/extractionResult__input_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_id - - - - -URI: [composite_disease:extractionResult__input_id](http://w3id.org/ontogpt/composite_disease/extractionResult__input_id) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/composite_disease/docs/extractionResult__input_text.md b/projects/composite_disease/docs/extractionResult__input_text.md deleted file mode 100644 index e6400df0f..000000000 --- a/projects/composite_disease/docs/extractionResult__input_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_text - - - - -URI: [composite_disease:extractionResult__input_text](http://w3id.org/ontogpt/composite_disease/extractionResult__input_text) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/composite_disease/docs/extractionResult__input_title.md b/projects/composite_disease/docs/extractionResult__input_title.md deleted file mode 100644 index 52f346e83..000000000 --- a/projects/composite_disease/docs/extractionResult__input_title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_title - - - - -URI: [composite_disease:extractionResult__input_title](http://w3id.org/ontogpt/composite_disease/extractionResult__input_title) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/composite_disease/docs/extractionResult__named_entities.md b/projects/composite_disease/docs/extractionResult__named_entities.md deleted file mode 100644 index e5a31210b..000000000 --- a/projects/composite_disease/docs/extractionResult__named_entities.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: named_entities - - -Named entities extracted from the text - -URI: [composite_disease:extractionResult__named_entities](http://w3id.org/ontogpt/composite_disease/extractionResult__named_entities) - - -## Domain and Range - -None → 0..\* [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/composite_disease/docs/extractionResult__prompt.md b/projects/composite_disease/docs/extractionResult__prompt.md deleted file mode 100644 index 8b6ea40a1..000000000 --- a/projects/composite_disease/docs/extractionResult__prompt.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: prompt - - - - -URI: [composite_disease:extractionResult__prompt](http://w3id.org/ontogpt/composite_disease/extractionResult__prompt) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/composite_disease/docs/extractionResult__raw_completion_output.md b/projects/composite_disease/docs/extractionResult__raw_completion_output.md deleted file mode 100644 index c67f7ef5c..000000000 --- a/projects/composite_disease/docs/extractionResult__raw_completion_output.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: raw_completion_output - - - - -URI: [composite_disease:extractionResult__raw_completion_output](http://w3id.org/ontogpt/composite_disease/extractionResult__raw_completion_output) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/composite_disease/docs/namedEntity__id.md b/projects/composite_disease/docs/namedEntity__id.md deleted file mode 100644 index 588564cf2..000000000 --- a/projects/composite_disease/docs/namedEntity__id.md +++ /dev/null @@ -1,37 +0,0 @@ - -# Slot: id - - -A unique identifier for the named entity - -URI: [composite_disease:namedEntity__id](http://w3id.org/ontogpt/composite_disease/namedEntity__id) - - -## Domain and Range - -None → 1..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AdverseEffect](AdverseEffect.md) - * [Disease](Disease.md) - * [Drug](Drug.md) - * [Gene](Gene.md) - * [Mechanism](Mechanism.md) - * [NamedEntity](NamedEntity.md) - * [RelationshipType](RelationshipType.md) - * [Symptom](Symptom.md) - * [Treatment](Treatment.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | this is populated during the grounding and normalization step | - diff --git a/projects/composite_disease/docs/namedEntity__label.md b/projects/composite_disease/docs/namedEntity__label.md deleted file mode 100644 index 9cfef98e0..000000000 --- a/projects/composite_disease/docs/namedEntity__label.md +++ /dev/null @@ -1,38 +0,0 @@ - -# Slot: label - - -The label (name) of the named thing - -URI: [composite_disease:namedEntity__label](http://w3id.org/ontogpt/composite_disease/namedEntity__label) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AdverseEffect](AdverseEffect.md) - * [Disease](Disease.md) - * [Drug](Drug.md) - * [Gene](Gene.md) - * [Mechanism](Mechanism.md) - * [NamedEntity](NamedEntity.md) - * [RelationshipType](RelationshipType.md) - * [Symptom](Symptom.md) - * [Treatment](Treatment.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Aliases:** | | name | -| **Mappings:** | | rdfs:label | - diff --git a/projects/composite_disease/docs/publication__abstract.md b/projects/composite_disease/docs/publication__abstract.md deleted file mode 100644 index 74bb27221..000000000 --- a/projects/composite_disease/docs/publication__abstract.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: abstract - - -The abstract of the publication - -URI: [composite_disease:publication__abstract](http://w3id.org/ontogpt/composite_disease/publication__abstract) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/composite_disease/docs/publication__combined_text.md b/projects/composite_disease/docs/publication__combined_text.md deleted file mode 100644 index 7ba220d45..000000000 --- a/projects/composite_disease/docs/publication__combined_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: combined_text - - - - -URI: [composite_disease:publication__combined_text](http://w3id.org/ontogpt/composite_disease/publication__combined_text) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/composite_disease/docs/publication__full_text.md b/projects/composite_disease/docs/publication__full_text.md deleted file mode 100644 index 1053a20bb..000000000 --- a/projects/composite_disease/docs/publication__full_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: full_text - - -The full text of the publication - -URI: [composite_disease:publication__full_text](http://w3id.org/ontogpt/composite_disease/publication__full_text) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/composite_disease/docs/publication__id.md b/projects/composite_disease/docs/publication__id.md deleted file mode 100644 index 06213aeab..000000000 --- a/projects/composite_disease/docs/publication__id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: id - - -The publication identifier - -URI: [composite_disease:publication__id](http://w3id.org/ontogpt/composite_disease/publication__id) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/composite_disease/docs/publication__title.md b/projects/composite_disease/docs/publication__title.md deleted file mode 100644 index a04d513a6..000000000 --- a/projects/composite_disease/docs/publication__title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: title - - -The title of the publication - -URI: [composite_disease:publication__title](http://w3id.org/ontogpt/composite_disease/publication__title) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/composite_disease/docs/textWithTriples__publication.md b/projects/composite_disease/docs/textWithTriples__publication.md deleted file mode 100644 index 60bd567fb..000000000 --- a/projects/composite_disease/docs/textWithTriples__publication.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: publication - - - - -URI: [composite_disease:textWithTriples__publication](http://w3id.org/ontogpt/composite_disease/textWithTriples__publication) - - -## Domain and Range - -None → 0..1 [Publication](Publication.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/composite_disease/docs/textWithTriples__triples.md b/projects/composite_disease/docs/textWithTriples__triples.md deleted file mode 100644 index a05e900ee..000000000 --- a/projects/composite_disease/docs/textWithTriples__triples.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: triples - - - - -URI: [composite_disease:textWithTriples__triples](http://w3id.org/ontogpt/composite_disease/textWithTriples__triples) - - -## Domain and Range - -None → 0..\* [Triple](Triple.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/composite_disease/docs/treatmentAdverseEffect__adverse_effects.md b/projects/composite_disease/docs/treatmentAdverseEffect__adverse_effects.md deleted file mode 100644 index bca39a2dd..000000000 --- a/projects/composite_disease/docs/treatmentAdverseEffect__adverse_effects.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: adverse_effects - - - - -URI: [composite_disease:treatmentAdverseEffect__adverse_effects](http://w3id.org/ontogpt/composite_disease/treatmentAdverseEffect__adverse_effects) - - -## Domain and Range - -None → 0..\* [AdverseEffect](AdverseEffect.md) - -## Parents - - -## Children - - -## Used by - - * [TreatmentAdverseEffect](TreatmentAdverseEffect.md) diff --git a/projects/composite_disease/docs/treatmentAdverseEffect__treatment.md b/projects/composite_disease/docs/treatmentAdverseEffect__treatment.md deleted file mode 100644 index 8fa143a94..000000000 --- a/projects/composite_disease/docs/treatmentAdverseEffect__treatment.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: treatment - - - - -URI: [composite_disease:treatmentAdverseEffect__treatment](http://w3id.org/ontogpt/composite_disease/treatmentAdverseEffect__treatment) - - -## Domain and Range - -None → 0..1 [Treatment](Treatment.md) - -## Parents - - -## Children - - -## Used by - - * [TreatmentAdverseEffect](TreatmentAdverseEffect.md) diff --git a/projects/composite_disease/docs/treatmentEfficacy__efficacy.md b/projects/composite_disease/docs/treatmentEfficacy__efficacy.md deleted file mode 100644 index 7d393ac11..000000000 --- a/projects/composite_disease/docs/treatmentEfficacy__efficacy.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: efficacy - - - - -URI: [composite_disease:treatmentEfficacy__efficacy](http://w3id.org/ontogpt/composite_disease/treatmentEfficacy__efficacy) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [TreatmentEfficacy](TreatmentEfficacy.md) diff --git a/projects/composite_disease/docs/treatmentEfficacy__treatment.md b/projects/composite_disease/docs/treatmentEfficacy__treatment.md deleted file mode 100644 index 7abd2a6b6..000000000 --- a/projects/composite_disease/docs/treatmentEfficacy__treatment.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: treatment - - - - -URI: [composite_disease:treatmentEfficacy__treatment](http://w3id.org/ontogpt/composite_disease/treatmentEfficacy__treatment) - - -## Domain and Range - -None → 0..1 [Treatment](Treatment.md) - -## Parents - - -## Children - - -## Used by - - * [TreatmentEfficacy](TreatmentEfficacy.md) diff --git a/projects/composite_disease/docs/treatmentMechanism__mechanism.md b/projects/composite_disease/docs/treatmentMechanism__mechanism.md deleted file mode 100644 index 39837c489..000000000 --- a/projects/composite_disease/docs/treatmentMechanism__mechanism.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: mechanism - - - - -URI: [composite_disease:treatmentMechanism__mechanism](http://w3id.org/ontogpt/composite_disease/treatmentMechanism__mechanism) - - -## Domain and Range - -None → 0..1 [Mechanism](Mechanism.md) - -## Parents - - -## Children - - -## Used by - - * [TreatmentMechanism](TreatmentMechanism.md) diff --git a/projects/composite_disease/docs/treatmentMechanism__treatment.md b/projects/composite_disease/docs/treatmentMechanism__treatment.md deleted file mode 100644 index eb85895d5..000000000 --- a/projects/composite_disease/docs/treatmentMechanism__treatment.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: treatment - - - - -URI: [composite_disease:treatmentMechanism__treatment](http://w3id.org/ontogpt/composite_disease/treatmentMechanism__treatment) - - -## Domain and Range - -None → 0..1 [Treatment](Treatment.md) - -## Parents - - -## Children - - -## Used by - - * [TreatmentMechanism](TreatmentMechanism.md) diff --git a/projects/composite_disease/docs/triple__object.md b/projects/composite_disease/docs/triple__object.md deleted file mode 100644 index 3345909a5..000000000 --- a/projects/composite_disease/docs/triple__object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object - - - - -URI: [composite_disease:triple__object](http://w3id.org/ontogpt/composite_disease/triple__object) - - -## Domain and Range - -None → 0..1 [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/composite_disease/docs/triple__object_qualifier.md b/projects/composite_disease/docs/triple__object_qualifier.md deleted file mode 100644 index ff66108e0..000000000 --- a/projects/composite_disease/docs/triple__object_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_qualifier - - -An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - -URI: [composite_disease:triple__object_qualifier](http://w3id.org/ontogpt/composite_disease/triple__object_qualifier) - - -## Domain and Range - -None → 0..1 [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/composite_disease/docs/triple__predicate.md b/projects/composite_disease/docs/triple__predicate.md deleted file mode 100644 index 427e1e3a2..000000000 --- a/projects/composite_disease/docs/triple__predicate.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: predicate - - - - -URI: [composite_disease:triple__predicate](http://w3id.org/ontogpt/composite_disease/triple__predicate) - - -## Domain and Range - -None → 0..1 [RelationshipType](RelationshipType.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/composite_disease/docs/triple__qualifier.md b/projects/composite_disease/docs/triple__qualifier.md deleted file mode 100644 index 9cc2b96e6..000000000 --- a/projects/composite_disease/docs/triple__qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: qualifier - - -A qualifier for the statements, e.g. "NOT" for negation - -URI: [composite_disease:triple__qualifier](http://w3id.org/ontogpt/composite_disease/triple__qualifier) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/composite_disease/docs/triple__subject.md b/projects/composite_disease/docs/triple__subject.md deleted file mode 100644 index ae60b051d..000000000 --- a/projects/composite_disease/docs/triple__subject.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject - - - - -URI: [composite_disease:triple__subject](http://w3id.org/ontogpt/composite_disease/triple__subject) - - -## Domain and Range - -None → 0..1 [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/composite_disease/docs/triple__subject_qualifier.md b/projects/composite_disease/docs/triple__subject_qualifier.md deleted file mode 100644 index 5051e8af0..000000000 --- a/projects/composite_disease/docs/triple__subject_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_qualifier - - -An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -URI: [composite_disease:triple__subject_qualifier](http://w3id.org/ontogpt/composite_disease/triple__subject_qualifier) - - -## Domain and Range - -None → 0..1 [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/composite_disease/docs/types/Boolean.md b/projects/composite_disease/docs/types/Boolean.md deleted file mode 100644 index dc83a9c6e..000000000 --- a/projects/composite_disease/docs/types/Boolean.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: boolean - - -A binary (true or false) value - -URI: [linkml:Boolean](https://w3id.org/linkml/Boolean) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Bool** | -| Representation | | bool | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Boolean | - diff --git a/projects/composite_disease/docs/types/Curie.md b/projects/composite_disease/docs/types/Curie.md deleted file mode 100644 index c1803f93f..000000000 --- a/projects/composite_disease/docs/types/Curie.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: curie - - -a compact URI - -URI: [linkml:Curie](https://w3id.org/linkml/Curie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Curie** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations this MUST be expanded to a URI | -| | | in non-RDF serializations MAY be serialized as the compact representation | - diff --git a/projects/composite_disease/docs/types/Date.md b/projects/composite_disease/docs/types/Date.md deleted file mode 100644 index 06948af97..000000000 --- a/projects/composite_disease/docs/types/Date.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: date - - -a date (year, month and day) in an idealized calendar - -URI: [linkml:Date](https://w3id.org/linkml/Date) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDate** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Date | - diff --git a/projects/composite_disease/docs/types/DateOrDatetime.md b/projects/composite_disease/docs/types/DateOrDatetime.md deleted file mode 100644 index ef983898d..000000000 --- a/projects/composite_disease/docs/types/DateOrDatetime.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: date_or_datetime - - -Either a date or a datetime - -URI: [linkml:DateOrDatetime](https://w3id.org/linkml/DateOrDatetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/composite_disease/docs/types/Datetime.md b/projects/composite_disease/docs/types/Datetime.md deleted file mode 100644 index 9510454a8..000000000 --- a/projects/composite_disease/docs/types/Datetime.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: datetime - - -The combination of a date and time - -URI: [linkml:Datetime](https://w3id.org/linkml/Datetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDateTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:DateTime | - diff --git a/projects/composite_disease/docs/types/Decimal.md b/projects/composite_disease/docs/types/Decimal.md deleted file mode 100644 index a7ba14a5d..000000000 --- a/projects/composite_disease/docs/types/Decimal.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: decimal - - -A real number with arbitrary precision that conforms to the xsd:decimal specification - -URI: [linkml:Decimal](https://w3id.org/linkml/Decimal) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Decimal** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Broad Mappings:** | | schema:Number | - diff --git a/projects/composite_disease/docs/types/Double.md b/projects/composite_disease/docs/types/Double.md deleted file mode 100644 index cfe6d71e2..000000000 --- a/projects/composite_disease/docs/types/Double.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: double - - -A real number that conforms to the xsd:double specification - -URI: [linkml:Double](https://w3id.org/linkml/Double) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Close Mappings:** | | schema:Float | - diff --git a/projects/composite_disease/docs/types/Float.md b/projects/composite_disease/docs/types/Float.md deleted file mode 100644 index 7b303f96f..000000000 --- a/projects/composite_disease/docs/types/Float.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: float - - -A real number that conforms to the xsd:float specification - -URI: [linkml:Float](https://w3id.org/linkml/Float) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Float | - diff --git a/projects/composite_disease/docs/types/Integer.md b/projects/composite_disease/docs/types/Integer.md deleted file mode 100644 index 3cfcc66d9..000000000 --- a/projects/composite_disease/docs/types/Integer.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: integer - - -An integer - -URI: [linkml:Integer](https://w3id.org/linkml/Integer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **int** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Integer | - diff --git a/projects/composite_disease/docs/types/Jsonpath.md b/projects/composite_disease/docs/types/Jsonpath.md deleted file mode 100644 index a03a58e67..000000000 --- a/projects/composite_disease/docs/types/Jsonpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpath - - -A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpath](https://w3id.org/linkml/Jsonpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/composite_disease/docs/types/Jsonpointer.md b/projects/composite_disease/docs/types/Jsonpointer.md deleted file mode 100644 index a0e1ac492..000000000 --- a/projects/composite_disease/docs/types/Jsonpointer.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpointer - - -A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpointer](https://w3id.org/linkml/Jsonpointer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/composite_disease/docs/types/Ncname.md b/projects/composite_disease/docs/types/Ncname.md deleted file mode 100644 index 710b0b04a..000000000 --- a/projects/composite_disease/docs/types/Ncname.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: ncname - - -Prefix part of CURIE - -URI: [linkml:Ncname](https://w3id.org/linkml/Ncname) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NCName** | -| Representation | | str | diff --git a/projects/composite_disease/docs/types/Nodeidentifier.md b/projects/composite_disease/docs/types/Nodeidentifier.md deleted file mode 100644 index f0097cdf4..000000000 --- a/projects/composite_disease/docs/types/Nodeidentifier.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: nodeidentifier - - -A URI, CURIE or BNODE that represents a node in a model. - -URI: [linkml:Nodeidentifier](https://w3id.org/linkml/Nodeidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NodeIdentifier** | -| Representation | | str | diff --git a/projects/composite_disease/docs/types/Objectidentifier.md b/projects/composite_disease/docs/types/Objectidentifier.md deleted file mode 100644 index 454ba6be6..000000000 --- a/projects/composite_disease/docs/types/Objectidentifier.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: objectidentifier - - -A URI or CURIE that represents an object in the model. - -URI: [linkml:Objectidentifier](https://w3id.org/linkml/Objectidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **ElementIdentifier** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | Used for inheritance and type checking | - diff --git a/projects/composite_disease/docs/types/Sparqlpath.md b/projects/composite_disease/docs/types/Sparqlpath.md deleted file mode 100644 index fd99a927e..000000000 --- a/projects/composite_disease/docs/types/Sparqlpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: sparqlpath - - -A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - -URI: [linkml:Sparqlpath](https://w3id.org/linkml/Sparqlpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/composite_disease/docs/types/String.md b/projects/composite_disease/docs/types/String.md deleted file mode 100644 index 6e61d7081..000000000 --- a/projects/composite_disease/docs/types/String.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: string - - -A character string - -URI: [linkml:String](https://w3id.org/linkml/String) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Text | - diff --git a/projects/composite_disease/docs/types/Time.md b/projects/composite_disease/docs/types/Time.md deleted file mode 100644 index 2b8652bcd..000000000 --- a/projects/composite_disease/docs/types/Time.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: time - - -A time object represents a (local) time of day, independent of any particular day - -URI: [linkml:Time](https://w3id.org/linkml/Time) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Time | - diff --git a/projects/composite_disease/docs/types/Uri.md b/projects/composite_disease/docs/types/Uri.md deleted file mode 100644 index 343807a5e..000000000 --- a/projects/composite_disease/docs/types/Uri.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: uri - - -a complete URI - -URI: [linkml:Uri](https://w3id.org/linkml/Uri) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URI** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node | -| **Close Mappings:** | | schema:URL | - diff --git a/projects/composite_disease/docs/types/Uriorcurie.md b/projects/composite_disease/docs/types/Uriorcurie.md deleted file mode 100644 index 2f7b65087..000000000 --- a/projects/composite_disease/docs/types/Uriorcurie.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: uriorcurie - - -a URI or a CURIE - -URI: [linkml:Uriorcurie](https://w3id.org/linkml/Uriorcurie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URIorCURIE** | -| Representation | | str | diff --git a/projects/composite_disease/excel/composite_disease.xlsx b/projects/composite_disease/excel/composite_disease.xlsx deleted file mode 100644 index a1a5e49e8..000000000 Binary files a/projects/composite_disease/excel/composite_disease.xlsx and /dev/null differ diff --git a/projects/composite_disease/graphql/composite_disease.graphql b/projects/composite_disease/graphql/composite_disease.graphql deleted file mode 100644 index 7361ada27..000000000 --- a/projects/composite_disease/graphql/composite_disease.graphql +++ /dev/null @@ -1,134 +0,0 @@ -type AdverseEffect - { - id: String! - label: String - } - -type AnnotatorResult - { - subjectText: String - objectId: String - objectText: String - } - -type Any - { - } - -type CompositeDisease - { - mainDisease: Disease - drugs: [Drug] - treatments: [Treatment] - contraindications: [Treatment] - treatmentMechanisms: [TreatmentMechanism] - treatmentEfficacies: [TreatmentEfficacy] - treatmentAdverseEffects: [TreatmentAdverseEffect] - } - -interface CompoundExpression - { - } - -type Disease - { - id: String! - label: String - } - -type Drug - { - id: String! - label: String - } - -type ExtractionResult - { - inputId: String - inputTitle: String - inputText: String - rawCompletionOutput: String - prompt: String - extractedObject: Any - namedEntities: [Any] - } - -type Gene - { - id: String! - label: String - } - -type Mechanism - { - id: String! - label: String - } - -interface NamedEntity - { - id: String! - label: String - } - -type Publication - { - id: String - title: String - abstract: String - combinedText: String - fullText: String - } - -type RelationshipType - { - id: String! - label: String - } - -type Symptom - { - id: String! - label: String - } - -type TextWithTriples - { - publication: Publication - triples: [Triple] - } - -type Treatment - { - id: String! - label: String - } - -type TreatmentAdverseEffect - { - treatment: Treatment - adverseEffects: [AdverseEffect] - } - -type TreatmentEfficacy - { - treatment: Treatment - efficacy: String - } - -type TreatmentMechanism - { - treatment: Treatment - mechanism: Mechanism - } - -interface Triple - { - subject: NamedEntity - predicate: RelationshipType - object: NamedEntity - qualifier: String - subjectQualifier: NamedEntity - objectQualifier: NamedEntity - } - diff --git a/projects/composite_disease/jsonld/composite_disease.context.jsonld b/projects/composite_disease/jsonld/composite_disease.context.jsonld deleted file mode 100644 index b1b6f5456..000000000 --- a/projects/composite_disease/jsonld/composite_disease.context.jsonld +++ /dev/null @@ -1,159 +0,0 @@ -{ - "comments": { - "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2023-08-07T10:51:49", - "source": "composite_disease.yaml" - }, - "@context": { - "HGNC": "http://example.org/UNKNOWN/HGNC/", - "HP": "http://example.org/UNKNOWN/HP/", - "RO": { - "@id": "http://purl.obolibrary.org/obo/RO_", - "@prefix": true - }, - "biolink": "http://example.org/UNKNOWN/biolink/", - "composite_disease": "http://w3id.org/ontogpt/composite_disease/", - "core": "http://w3id.org/ontogpt/core/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "@vocab": "http://w3id.org/ontogpt/composite_disease/", - "object_id": { - "@id": "core:object_id" - }, - "object_text": { - "@id": "core:object_text" - }, - "subject_text": { - "@id": "core:subject_text" - }, - "contraindications": { - "@type": "@id" - }, - "drugs": { - "@type": "@id" - }, - "main_disease": { - "@type": "@id" - }, - "treatment_adverse_effects": { - "@type": "@id" - }, - "treatment_efficacies": { - "@type": "@id" - }, - "treatment_mechanisms": { - "@type": "@id" - }, - "treatments": { - "@type": "@id" - }, - "extracted_object": { - "@type": "@id", - "@id": "core:extracted_object" - }, - "input_id": { - "@id": "core:input_id" - }, - "input_text": { - "@id": "core:input_text" - }, - "input_title": { - "@id": "core:input_title" - }, - "named_entities": { - "@type": "@id", - "@id": "core:named_entities" - }, - "prompt": { - "@id": "core:prompt" - }, - "raw_completion_output": { - "@id": "core:raw_completion_output" - }, - "id": { - "@id": "core:id" - }, - "label": { - "@id": "rdfs:label" - }, - "abstract": { - "@id": "core:abstract" - }, - "combined_text": { - "@id": "core:combined_text" - }, - "full_text": { - "@id": "core:full_text" - }, - "title": { - "@id": "core:title" - }, - "publication": { - "@type": "@id", - "@id": "core:publication" - }, - "triples": { - "@type": "@id", - "@id": "core:triples" - }, - "adverse_effects": { - "@type": "@id" - }, - "treatment": { - "@type": "@id" - }, - "mechanism": { - "@type": "@id" - }, - "object": { - "@type": "@id", - "@id": "core:object" - }, - "object_qualifier": { - "@type": "@id", - "@id": "core:object_qualifier" - }, - "predicate": { - "@type": "@id", - "@id": "core:predicate" - }, - "qualifier": { - "@id": "core:qualifier" - }, - "subject": { - "@type": "@id", - "@id": "core:subject" - }, - "subject_qualifier": { - "@type": "@id", - "@id": "core:subject_qualifier" - }, - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } - } -} diff --git a/projects/composite_disease/jsonld/composite_disease.jsonld b/projects/composite_disease/jsonld/composite_disease.jsonld deleted file mode 100644 index 05fbc5bff..000000000 --- a/projects/composite_disease/jsonld/composite_disease.jsonld +++ /dev/null @@ -1,1586 +0,0 @@ -{ - "name": "composite_disease", - "description": "A template for representing composite disease concepts", - "title": "Composite Disease", - "id": "http://w3id.org/ontogpt/composite_disease", - "imports": [ - "linkml:types", - "core" - ], - "license": "https://creativecommons.org/publicdomain/zero/1.0/", - "prefixes": [ - { - "prefix_prefix": "linkml", - "prefix_reference": "https://w3id.org/linkml/" - }, - { - "prefix_prefix": "composite_disease", - "prefix_reference": "http://w3id.org/ontogpt/composite_disease/" - } - ], - "default_prefix": "composite_disease", - "default_range": "string", - "types": [ - { - "name": "string", - "definition_uri": "https://w3id.org/linkml/String", - "description": "A character string", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Text" - ], - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "@type": "TypeDefinition" - }, - { - "name": "integer", - "definition_uri": "https://w3id.org/linkml/Integer", - "description": "An integer", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Integer" - ], - "base": "int", - "uri": "http://www.w3.org/2001/XMLSchema#integer", - "@type": "TypeDefinition" - }, - { - "name": "boolean", - "definition_uri": "https://w3id.org/linkml/Boolean", - "description": "A binary (true or false) value", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Boolean" - ], - "base": "Bool", - "uri": "http://www.w3.org/2001/XMLSchema#boolean", - "repr": "bool", - "@type": "TypeDefinition" - }, - { - "name": "float", - "definition_uri": "https://w3id.org/linkml/Float", - "description": "A real number that conforms to the xsd:float specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#float", - "@type": "TypeDefinition" - }, - { - "name": "double", - "definition_uri": "https://w3id.org/linkml/Double", - "description": "A real number that conforms to the xsd:double specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#double", - "@type": "TypeDefinition" - }, - { - "name": "decimal", - "definition_uri": "https://w3id.org/linkml/Decimal", - "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "broad_mappings": [ - "schema:Number" - ], - "base": "Decimal", - "uri": "http://www.w3.org/2001/XMLSchema#decimal", - "@type": "TypeDefinition" - }, - { - "name": "time", - "definition_uri": "https://w3id.org/linkml/Time", - "description": "A time object represents a (local) time of day, independent of any particular day", - "notes": [ - "URI is dateTime because OWL reasoners do not work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Time" - ], - "base": "XSDTime", - "uri": "http://www.w3.org/2001/XMLSchema#time", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date", - "definition_uri": "https://w3id.org/linkml/Date", - "description": "a date (year, month and day) in an idealized calendar", - "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Date" - ], - "base": "XSDDate", - "uri": "http://www.w3.org/2001/XMLSchema#date", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "datetime", - "definition_uri": "https://w3id.org/linkml/Datetime", - "description": "The combination of a date and time", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:DateTime" - ], - "base": "XSDDateTime", - "uri": "http://www.w3.org/2001/XMLSchema#dateTime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date_or_datetime", - "definition_uri": "https://w3id.org/linkml/DateOrDatetime", - "description": "Either a date or a datetime", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "https://w3id.org/linkml/DateOrDatetime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uriorcurie", - "definition_uri": "https://w3id.org/linkml/Uriorcurie", - "description": "a URI or a CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "URIorCURIE", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "curie", - "definition_uri": "https://w3id.org/linkml/Curie", - "conforms_to": "https://www.w3.org/TR/curie/", - "description": "a compact URI", - "comments": [ - "in RDF serializations this MUST be expanded to a URI", - "in non-RDF serializations MAY be serialized as the compact representation" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "Curie", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uri", - "definition_uri": "https://w3id.org/linkml/Uri", - "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", - "description": "a complete URI", - "comments": [ - "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:URL" - ], - "base": "URI", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "ncname", - "definition_uri": "https://w3id.org/linkml/Ncname", - "description": "Prefix part of CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NCName", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "objectidentifier", - "definition_uri": "https://w3id.org/linkml/Objectidentifier", - "description": "A URI or CURIE that represents an object in the model.", - "comments": [ - "Used for inheritance and type checking" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "ElementIdentifier", - "uri": "http://www.w3.org/ns/shex#iri", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "nodeidentifier", - "definition_uri": "https://w3id.org/linkml/Nodeidentifier", - "description": "A URI, CURIE or BNODE that represents a node in a model.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NodeIdentifier", - "uri": "http://www.w3.org/ns/shex#nonLiteral", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpointer", - "definition_uri": "https://w3id.org/linkml/Jsonpointer", - "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901", - "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpath", - "definition_uri": "https://w3id.org/linkml/Jsonpath", - "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html", - "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "sparqlpath", - "definition_uri": "https://w3id.org/linkml/Sparqlpath", - "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths", - "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - } - ], - "enums": [ - { - "name": "NCITDrugType", - "definition_uri": "http://w3id.org/ontogpt/composite_disease/NCITDrugType", - "from_schema": "http://w3id.org/ontogpt/composite_disease", - "reachable_from": { - "source_ontology": "obo:ncit", - "source_nodes": [ - "NCIT:C1908" - ] - } - }, - { - "name": "NCITTreatmentType", - "definition_uri": "http://w3id.org/ontogpt/composite_disease/NCITTreatmentType", - "from_schema": "http://w3id.org/ontogpt/composite_disease", - "reachable_from": { - "source_ontology": "obo:ncit", - "source_nodes": [ - "NCIT:C25218" - ] - } - }, - { - "name": "NCITTActivityType", - "definition_uri": "http://w3id.org/ontogpt/composite_disease/NCITTActivityType", - "from_schema": "http://w3id.org/ontogpt/composite_disease", - "reachable_from": { - "source_ontology": "obo:ncit", - "source_nodes": [ - "NCIT:C43431" - ] - } - }, - { - "name": "MAXOActionType", - "definition_uri": "http://w3id.org/ontogpt/composite_disease/MAXOActionType", - "from_schema": "http://w3id.org/ontogpt/composite_disease", - "reachable_from": { - "source_ontology": "obo:maxo", - "source_nodes": [ - "MAXO:0000001" - ] - } - }, - { - "name": "MESHTherapeuticType", - "definition_uri": "http://w3id.org/ontogpt/composite_disease/MESHTherapeuticType", - "from_schema": "http://w3id.org/ontogpt/composite_disease", - "reachable_from": { - "source_ontology": "obo:mesh", - "source_nodes": [ - "MESH:D013812" - ] - } - }, - { - "name": "CHEBIDrugType", - "definition_uri": "http://w3id.org/ontogpt/composite_disease/CHEBIDrugType", - "from_schema": "http://w3id.org/ontogpt/composite_disease", - "reachable_from": { - "source_ontology": "obo:chebi", - "source_nodes": [ - "CHEBI:23888" - ], - "relationship_types": [ - "rdfs:subClassOf", - "RO:0000087" - ] - } - }, - { - "name": "NullDataOptions", - "definition_uri": "http://w3id.org/ontogpt/core/NullDataOptions", - "from_schema": "http://w3id.org/ontogpt/core", - "permissible_values": [ - { - "text": "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "meaning": "NCIT:C149701" - }, - { - "text": "NOT_APPLICABLE", - "meaning": "NCIT:C18902", - "aliases": [ - "not applicable", - "N/A" - ] - }, - { - "text": "NOT_MENTIONED" - } - ] - } - ], - "slots": [ - { - "name": "compositeDisease__main_disease", - "description": "the name of the disease that is treated.", - "from_schema": "http://w3id.org/ontogpt/composite_disease", - "slot_uri": "http://w3id.org/ontogpt/composite_disease/main_disease", - "alias": "main_disease", - "owner": "CompositeDisease", - "domain_of": [ - "CompositeDisease" - ], - "range": "Disease", - "@type": "SlotDefinition" - }, - { - "name": "compositeDisease__drugs", - "description": "semicolon-separated list of named small molecule drugs", - "from_schema": "http://w3id.org/ontogpt/composite_disease", - "slot_uri": "http://w3id.org/ontogpt/composite_disease/drugs", - "multivalued": true, - "alias": "drugs", - "owner": "CompositeDisease", - "domain_of": [ - "CompositeDisease" - ], - "range": "Drug", - "@type": "SlotDefinition" - }, - { - "name": "compositeDisease__treatments", - "annotations": [ - { - "tag": "prompt.examples", - "value": "Imatinib, exercise, surgery", - "@type": "Annotation" - } - ], - "description": "semicolon-separated list of therapies and treatments are indicated for treating the disease.", - "from_schema": "http://w3id.org/ontogpt/composite_disease", - "slot_uri": "http://w3id.org/ontogpt/composite_disease/treatments", - "multivalued": true, - "alias": "treatments", - "owner": "CompositeDisease", - "domain_of": [ - "CompositeDisease" - ], - "range": "Treatment", - "@type": "SlotDefinition" - }, - { - "name": "compositeDisease__contraindications", - "annotations": [ - { - "tag": "prompt.examples", - "value": "Beta-blockers, exercise, surgery", - "@type": "Annotation" - } - ], - "description": "semicolon-separated list of therapies and treatments that are contra-indicated for the disease, and should not be used, due to risk of adverse effects.", - "from_schema": "http://w3id.org/ontogpt/composite_disease", - "slot_uri": "http://w3id.org/ontogpt/composite_disease/contraindications", - "multivalued": true, - "alias": "contraindications", - "owner": "CompositeDisease", - "domain_of": [ - "CompositeDisease" - ], - "range": "Treatment", - "@type": "SlotDefinition" - }, - { - "name": "compositeDisease__treatment_mechanisms", - "annotations": [ - { - "tag": "prompt.separator", - "value": "*", - "@type": "Annotation" - } - ], - "description": "semicolon-separated list of treatment to asterisk-separated mechanism associations", - "from_schema": "http://w3id.org/ontogpt/composite_disease", - "slot_uri": "http://w3id.org/ontogpt/composite_disease/treatment_mechanisms", - "multivalued": true, - "alias": "treatment_mechanisms", - "owner": "CompositeDisease", - "domain_of": [ - "CompositeDisease" - ], - "range": "TreatmentMechanism", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "compositeDisease__treatment_efficacies", - "annotations": [ - { - "tag": "prompt.separator", - "value": "*", - "@type": "Annotation" - } - ], - "description": "semicolon-separated list of treatment to efficacy associations, e.g. Imatinib*effective", - "from_schema": "http://w3id.org/ontogpt/composite_disease", - "slot_uri": "http://w3id.org/ontogpt/composite_disease/treatment_efficacies", - "multivalued": true, - "alias": "treatment_efficacies", - "owner": "CompositeDisease", - "domain_of": [ - "CompositeDisease" - ], - "range": "TreatmentEfficacy", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "compositeDisease__treatment_adverse_effects", - "annotations": [ - { - "tag": "prompt.separator", - "value": "*", - "@type": "Annotation" - } - ], - "description": "semicolon-separated list of treatment to adverse effect associations, e.g. Imatinib*nausea", - "from_schema": "http://w3id.org/ontogpt/composite_disease", - "slot_uri": "http://w3id.org/ontogpt/composite_disease/treatment_adverse_effects", - "multivalued": true, - "alias": "treatment_adverse_effects", - "owner": "CompositeDisease", - "domain_of": [ - "CompositeDisease" - ], - "range": "TreatmentAdverseEffect", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "treatmentMechanism__treatment", - "from_schema": "http://w3id.org/ontogpt/composite_disease", - "slot_uri": "http://w3id.org/ontogpt/composite_disease/treatment", - "alias": "treatment", - "owner": "TreatmentMechanism", - "domain_of": [ - "TreatmentMechanism" - ], - "range": "Treatment", - "@type": "SlotDefinition" - }, - { - "name": "treatmentMechanism__mechanism", - "from_schema": "http://w3id.org/ontogpt/composite_disease", - "slot_uri": "http://w3id.org/ontogpt/composite_disease/mechanism", - "alias": "mechanism", - "owner": "TreatmentMechanism", - "domain_of": [ - "TreatmentMechanism" - ], - "range": "Mechanism", - "@type": "SlotDefinition" - }, - { - "name": "treatmentAdverseEffect__treatment", - "from_schema": "http://w3id.org/ontogpt/composite_disease", - "slot_uri": "http://w3id.org/ontogpt/composite_disease/treatment", - "alias": "treatment", - "owner": "TreatmentAdverseEffect", - "domain_of": [ - "TreatmentAdverseEffect" - ], - "range": "Treatment", - "@type": "SlotDefinition" - }, - { - "name": "treatmentAdverseEffect__adverse_effects", - "from_schema": "http://w3id.org/ontogpt/composite_disease", - "slot_uri": "http://w3id.org/ontogpt/composite_disease/adverse_effects", - "multivalued": true, - "alias": "adverse_effects", - "owner": "TreatmentAdverseEffect", - "domain_of": [ - "TreatmentAdverseEffect" - ], - "range": "AdverseEffect", - "@type": "SlotDefinition" - }, - { - "name": "treatmentEfficacy__treatment", - "from_schema": "http://w3id.org/ontogpt/composite_disease", - "slot_uri": "http://w3id.org/ontogpt/composite_disease/treatment", - "alias": "treatment", - "owner": "TreatmentEfficacy", - "domain_of": [ - "TreatmentEfficacy" - ], - "range": "Treatment", - "@type": "SlotDefinition" - }, - { - "name": "treatmentEfficacy__efficacy", - "from_schema": "http://w3id.org/ontogpt/composite_disease", - "slot_uri": "http://w3id.org/ontogpt/composite_disease/efficacy", - "alias": "efficacy", - "owner": "TreatmentEfficacy", - "domain_of": [ - "TreatmentEfficacy" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_id", - "alias": "input_id", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_title", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_title", - "alias": "input_title", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_text", - "alias": "input_text", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__raw_completion_output", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/raw_completion_output", - "alias": "raw_completion_output", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__prompt", - "from_schema": 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"annotatorResult__object_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_id", - "alias": "object_id", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_text", - "alias": "object_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - } - ], - "classes": [ - { - "name": "CompositeDisease", - "definition_uri": "http://w3id.org/ontogpt/composite_disease/CompositeDisease", - "from_schema": "http://w3id.org/ontogpt/composite_disease", - "slots": [ - "compositeDisease__main_disease", - "compositeDisease__drugs", - "compositeDisease__treatments", - "compositeDisease__contraindications", - "compositeDisease__treatment_mechanisms", - 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"http://w3id.org/ontogpt/composite_disease/Symptom", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:hp", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/composite_disease", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/composite_disease/Symptom", - "@type": "ClassDefinition" - }, - { - "name": "Disease", - "definition_uri": "http://w3id.org/ontogpt/composite_disease/Disease", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:mondo", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/composite_disease", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/composite_disease/Disease", - "@type": "ClassDefinition" - }, - { - "name": "AdverseEffect", - "definition_uri": "http://w3id.org/ontogpt/composite_disease/AdverseEffect", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:hp, sqlite:obo:ncit", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/composite_disease", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/composite_disease/AdverseEffect", - "@type": "ClassDefinition" - }, - { - "name": "Treatment", - "definition_uri": "http://w3id.org/ontogpt/composite_disease/Treatment", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:maxo, sqlite:obo:ncit, sqlite:obo:mesh, sqlite:obo:chebi", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/composite_disease", - "is_a": "NamedEntity", - "values_from": [ - "NCITDrugType", - "NCITTreatmentType", - "NCITActivityType", - "MAXOTreatmentType", - "MESHTherapeuticType", - "CHEBIDrugType" - ], - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/composite_disease/Treatment", - "@type": "ClassDefinition" - }, - { - "name": "Mechanism", - "definition_uri": "http://w3id.org/ontogpt/composite_disease/Mechanism", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:go, sqlite:obo:ncit, sqlite:obo:mesh", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/composite_disease", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/composite_disease/Mechanism", - "@type": "ClassDefinition" - }, - { - "name": "Drug", - "definition_uri": "http://w3id.org/ontogpt/composite_disease/Drug", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:chebi, sqlite:obo:drugbank", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/composite_disease", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/composite_disease/Drug", - "@type": "ClassDefinition" - }, - { - "name": "TreatmentMechanism", - "definition_uri": "http://w3id.org/ontogpt/composite_disease/TreatmentMechanism", - "from_schema": "http://w3id.org/ontogpt/composite_disease", - "is_a": "CompoundExpression", - "slots": [ - "treatmentMechanism__treatment", - "treatmentMechanism__mechanism" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "treatment", - "range": "Treatment", - "@type": "SlotDefinition" - }, - { - "name": "mechanism", - "range": "Mechanism", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/composite_disease/TreatmentMechanism", - "@type": "ClassDefinition" - }, - { - "name": "TreatmentAdverseEffect", - "definition_uri": "http://w3id.org/ontogpt/composite_disease/TreatmentAdverseEffect", - "from_schema": "http://w3id.org/ontogpt/composite_disease", - "is_a": "CompoundExpression", - "slots": [ - "treatmentAdverseEffect__treatment", - "treatmentAdverseEffect__adverse_effects" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "treatment", - "range": "Treatment", - "@type": "SlotDefinition" - }, - { - "name": "adverse_effects", - "multivalued": true, - "range": "AdverseEffect", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/composite_disease/TreatmentAdverseEffect", - "@type": "ClassDefinition" - }, - { - "name": "TreatmentEfficacy", - "definition_uri": "http://w3id.org/ontogpt/composite_disease/TreatmentEfficacy", - "from_schema": "http://w3id.org/ontogpt/composite_disease", - "is_a": "CompoundExpression", - "slots": [ - "treatmentEfficacy__treatment", - "treatmentEfficacy__efficacy" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "treatment", - "range": "Treatment", - "@type": "SlotDefinition" - }, - { - "name": "efficacy", - "range": "string", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/composite_disease/TreatmentEfficacy", - "@type": "ClassDefinition" - }, - { - "name": "Any", - "definition_uri": "http://w3id.org/ontogpt/core/Any", - "from_schema": "http://w3id.org/ontogpt/core", - "mappings": [ - "linkml:Any" - ], - "slot_usage": {}, - "class_uri": "https://w3id.org/linkml/Any", - "@type": "ClassDefinition" - }, - { - "name": "ExtractionResult", - "definition_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "description": "A result of extracting knowledge on text", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "extractionResult__input_id", - "extractionResult__input_title", - "extractionResult__input_text", - "extractionResult__raw_completion_output", - "extractionResult__prompt", - "extractionResult__extracted_object", - "extractionResult__named_entities" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "input_id", - "@type": "SlotDefinition" - }, - { - "name": "input_title", - "@type": "SlotDefinition" - 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"Triple", - "definition_uri": "http://w3id.org/ontogpt/core/Triple", - "description": "Abstract parent for Relation Extraction tasks", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "CompoundExpression", - "abstract": true, - "slots": [ - "triple__subject", - "triple__predicate", - "triple__object", - "triple__qualifier", - "triple__subject_qualifier", - "triple__object_qualifier" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "predicate", - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "object", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Triple", - "@type": "ClassDefinition" - }, - { - "name": "TextWithTriples", - "definition_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "textWithTriples__publication", - "textWithTriples__triples" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "triples", - "multivalued": true, - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "@type": "ClassDefinition" - }, - { - "name": "RelationshipType", - "id_prefixes": [ - "RO", - "biolink" - ], - "definition_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "@type": "ClassDefinition" - }, - { - "name": "Publication", - "definition_uri": "http://w3id.org/ontogpt/core/Publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "publication__id", - "publication__title", - "publication__abstract", - "publication__combined_text", - "publication__full_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "description": "The publication identifier", - "@type": "SlotDefinition" - }, - { - "name": "title", - "description": "The title of the publication", - "@type": "SlotDefinition" - }, - { - "name": "abstract", - "description": "The abstract of the publication", - "@type": "SlotDefinition" - }, - { - "name": "combined_text", - "@type": "SlotDefinition" - }, - { - "name": "full_text", - "description": "The full text of the publication", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Publication", - "@type": "ClassDefinition" - }, - { - "name": "AnnotatorResult", - "definition_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "annotatorResult__subject_text", - "annotatorResult__object_id", - "annotatorResult__object_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject_text", - "@type": "SlotDefinition" - }, - { - "name": "object_id", - "@type": "SlotDefinition" - }, - { - "name": "object_text", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "@type": "ClassDefinition" - } - ], - "metamodel_version": "1.7.0", - "source_file": "composite_disease.yaml", - "source_file_date": "2023-06-17T15:11:19", - "source_file_size": 4519, - "generation_date": "2023-08-07T10:51:50", - "keywords": [ - "disease", - "indication" - ], - "@type": "SchemaDefinition", - "@context": [ - "projects/composite_disease/jsonld/composite_disease.context.jsonld", - "https://w3id.org/linkml/types.context.jsonld", - "core.context.jsonld", - { - "@base": "http://w3id.org/ontogpt/composite_disease/" - } - ] -} diff --git a/projects/composite_disease/jsonschema/composite_disease.schema.json b/projects/composite_disease/jsonschema/composite_disease.schema.json deleted file mode 100644 index 10c5cd549..000000000 --- a/projects/composite_disease/jsonschema/composite_disease.schema.json +++ /dev/null @@ -1,457 +0,0 @@ -{ - "$defs": { - "AdverseEffect": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "AdverseEffect", - "type": "object" - }, - "AnnotatorResult": { - "additionalProperties": false, - "description": "", - "properties": { - "object_id": { - "type": "string" - }, - "object_text": { - "type": "string" - }, - "subject_text": { - "type": "string" - } - }, - "title": "AnnotatorResult", - "type": "object" - }, - "Any": { - "additionalProperties": true, - "description": "", - "title": "Any", - "type": "object" - }, - "CHEBIDrugType": { - "description": "", - "enum": [], - "title": "CHEBIDrugType", - "type": "string" - }, - "CompositeDisease": { - "additionalProperties": false, - "description": "", - "properties": { - "contraindications": { - "description": "semicolon-separated list of therapies and treatments that are contra-indicated for the disease, and should not be used, due to risk of adverse effects.", - "items": { - "type": "string" - }, - "type": "array" - }, - "drugs": { - "description": "semicolon-separated list of named small molecule drugs", - "items": { - "type": "string" - }, - "type": "array" - }, - "main_disease": { - "description": "the name of the disease that is treated.", - "type": "string" - }, - "treatment_adverse_effects": { - "description": "semicolon-separated list of treatment to adverse effect associations, e.g. Imatinib*nausea", - "items": { - "$ref": "#/$defs/TreatmentAdverseEffect" - }, - "type": "array" - }, - "treatment_efficacies": { - "description": "semicolon-separated list of treatment to efficacy associations, e.g. Imatinib*effective", - "items": { - "$ref": "#/$defs/TreatmentEfficacy" - }, - "type": "array" - }, - "treatment_mechanisms": { - "description": "semicolon-separated list of treatment to asterisk-separated mechanism associations", - "items": { - "$ref": "#/$defs/TreatmentMechanism" - }, - "type": "array" - }, - "treatments": { - "description": "semicolon-separated list of therapies and treatments are indicated for treating the disease.", - "items": { - "type": "string" - }, - "type": "array" - } - }, - "title": "CompositeDisease", - "type": "object" - }, - "Disease": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Disease", - "type": "object" - }, - "Drug": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Drug", - "type": "object" - }, - "ExtractionResult": { - "additionalProperties": false, - "description": "A result of extracting knowledge on text", - "properties": { - "extracted_object": { - "$ref": "#/$defs/Any", - "description": "The complex objects extracted from the text" - }, - "input_id": { - "type": "string" - }, - "input_text": { - "type": "string" - }, - "input_title": { - "type": "string" - }, - "named_entities": { - "description": "Named entities extracted from the text", - "items": { - "$ref": "#/$defs/Any" - }, - "type": "array" - }, - "prompt": { - "type": "string" - }, - "raw_completion_output": { - "type": "string" - } - }, - "title": "ExtractionResult", - "type": "object" - }, - "Gene": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Gene", - "type": "object" - }, - "MAXOActionType": { - "description": "", - "enum": [], - "title": "MAXOActionType", - "type": "string" - }, - "MESHTherapeuticType": { - "description": "", - "enum": [], - "title": "MESHTherapeuticType", - "type": "string" - }, - "Mechanism": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Mechanism", - "type": "object" - }, - "NCITDrugType": { - "description": "", - "enum": [], - "title": "NCITDrugType", - "type": "string" - }, - "NCITTActivityType": { - "description": "", - "enum": [], - "title": "NCITTActivityType", - "type": "string" - }, - "NCITTreatmentType": { - "description": "", - "enum": [], - "title": "NCITTreatmentType", - "type": "string" - }, - "NullDataOptions": { - "description": "", - "enum": [ - "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "NOT_APPLICABLE", - "NOT_MENTIONED" - ], - "title": "NullDataOptions", - "type": "string" - }, - "Publication": { - "additionalProperties": false, - "description": "", - "properties": { - "abstract": { - "description": "The abstract of the publication", - "type": "string" - }, - "combined_text": { - "type": "string" - }, - "full_text": { - "description": "The full text of the publication", - "type": "string" - }, - "id": { - "description": "The publication identifier", - "type": "string" - }, - "title": { - "description": "The title of the publication", - "type": "string" - } - }, - "title": "Publication", - "type": "object" - }, - "RelationshipType": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "RelationshipType", - "type": "object" - }, - "Symptom": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Symptom", - "type": "object" - }, - "TextWithTriples": { - "additionalProperties": false, - "description": "", - "properties": { - "publication": { - "$ref": "#/$defs/Publication" - }, - "triples": { - "items": { - "$ref": "#/$defs/Triple" - }, - "type": "array" - } - }, - "title": "TextWithTriples", - "type": "object" - }, - "Treatment": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Treatment", - "type": "object" - }, - "TreatmentAdverseEffect": { - "additionalProperties": false, - "description": "", - "properties": { - "adverse_effects": { - "items": { - "type": "string" - }, - "type": "array" - }, - "treatment": { - "type": "string" - } - }, - "title": "TreatmentAdverseEffect", - "type": "object" - }, - "TreatmentEfficacy": { - "additionalProperties": false, - "description": "", - "properties": { - "efficacy": { - "type": "string" - }, - "treatment": { - "type": "string" - } - }, - "title": "TreatmentEfficacy", - "type": "object" - }, - "TreatmentMechanism": { - "additionalProperties": false, - "description": "", - "properties": { - "mechanism": { - "type": "string" - }, - "treatment": { - "type": "string" - } - }, - "title": "TreatmentMechanism", - "type": "object" - } - }, - "$id": "http://w3id.org/ontogpt/composite_disease", - "$schema": "http://json-schema.org/draft-07/schema#", - "additionalProperties": true, - "metamodel_version": "1.7.0", - "properties": { - "contraindications": { - "description": "semicolon-separated list of therapies and treatments that are contra-indicated for the disease, and should not be used, due to risk of adverse effects.", - "items": { - "type": "string" - }, - "type": "array" - }, - "drugs": { - "description": "semicolon-separated list of named small molecule drugs", - "items": { - "type": "string" - }, - "type": "array" - }, - "main_disease": { - "description": "the name of the disease that is treated.", - "type": "string" - }, - "treatment_adverse_effects": { - "description": "semicolon-separated list of treatment to adverse effect associations, e.g. Imatinib*nausea", - "items": { - "$ref": "#/$defs/TreatmentAdverseEffect" - }, - "type": "array" - }, - "treatment_efficacies": { - "description": "semicolon-separated list of treatment to efficacy associations, e.g. Imatinib*effective", - "items": { - "$ref": "#/$defs/TreatmentEfficacy" - }, - "type": "array" - }, - "treatment_mechanisms": { - "description": "semicolon-separated list of treatment to asterisk-separated mechanism associations", - "items": { - "$ref": "#/$defs/TreatmentMechanism" - }, - "type": "array" - }, - "treatments": { - "description": "semicolon-separated list of therapies and treatments are indicated for treating the disease.", - "items": { - "type": "string" - }, - "type": "array" - } - }, - "title": "composite_disease", - "type": "object", - "version": null -} \ No newline at end of file diff --git a/projects/composite_disease/owl/composite_disease.owl.ttl b/projects/composite_disease/owl/composite_disease.owl.ttl deleted file mode 100644 index b9e698233..000000000 --- a/projects/composite_disease/owl/composite_disease.owl.ttl +++ /dev/null @@ -1,576 +0,0 @@ -@prefix IAO: . -@prefix composite_disease: . -@prefix linkml: . -@prefix owl: . -@prefix rdf: . -@prefix rdfs: . -@prefix skos: . -@prefix xsd: . - - a owl:Ontology ; - rdfs:label "composite_disease" ; - IAO:0000700 composite_disease:CompositeDisease, - , - , - , - , - , - , - ; - linkml:classes "{'CompositeDisease': ClassDefinition(name='CompositeDisease', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/composite_disease/CompositeDisease', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/composite_disease', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['compositeDisease__main_disease', 'compositeDisease__drugs', 'compositeDisease__treatments', 'compositeDisease__contraindications', 'compositeDisease__treatment_mechanisms', 'compositeDisease__treatment_efficacies', 'compositeDisease__treatment_adverse_effects'], slot_usage={}, attributes={'main_disease': SlotDefinition(name='main_disease', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the name of the disease that is treated.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Disease', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'drugs': SlotDefinition(name='drugs', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of named small molecule drugs', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Drug', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'treatments': SlotDefinition(name='treatments', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.examples': Annotation(tag='prompt.examples', value='Imatinib, exercise, surgery', extensions={}, annotations={})}, description='semicolon-separated list of therapies and treatments are indicated for treating the disease.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Treatment', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'contraindications': SlotDefinition(name='contraindications', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.examples': Annotation(tag='prompt.examples', value='Beta-blockers, exercise, surgery', extensions={}, annotations={})}, description='semicolon-separated list of therapies and treatments that are contra-indicated for the disease, and should not be used, due to risk of adverse effects.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Treatment', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'treatment_mechanisms': SlotDefinition(name='treatment_mechanisms', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.separator': Annotation(tag='prompt.separator', value='*', extensions={}, annotations={})}, description='semicolon-separated list of treatment to asterisk-separated mechanism associations', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='TreatmentMechanism', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'treatment_efficacies': SlotDefinition(name='treatment_efficacies', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.separator': Annotation(tag='prompt.separator', value='*', extensions={}, annotations={})}, description='semicolon-separated list of treatment to efficacy associations, e.g. Imatinib*effective', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='TreatmentEfficacy', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'treatment_adverse_effects': SlotDefinition(name='treatment_adverse_effects', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.separator': Annotation(tag='prompt.separator', value='*', extensions={}, annotations={})}, description='semicolon-separated list of treatment to adverse effect associations, e.g. Imatinib*nausea', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='TreatmentAdverseEffect', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='composite_disease:CompositeDisease', subclass_of=None, union_of=[], defining_slots=[], tree_root=True, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Gene': ClassDefinition(name='Gene', id_prefixes=['HGNC'], definition_uri='http://w3id.org/ontogpt/composite_disease/Gene', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='gilda:, obo:sql:hgnc, bioportal:hgnc-nr', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/composite_disease', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='composite_disease:Gene', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Symptom': ClassDefinition(name='Symptom', id_prefixes=['HP'], definition_uri='http://w3id.org/ontogpt/composite_disease/Symptom', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:hp', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/composite_disease', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='composite_disease:Symptom', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Disease': ClassDefinition(name='Disease', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/composite_disease/Disease', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:mondo', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/composite_disease', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='composite_disease:Disease', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'AdverseEffect': ClassDefinition(name='AdverseEffect', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/composite_disease/AdverseEffect', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:hp, sqlite:obo:ncit', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/composite_disease', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='composite_disease:AdverseEffect', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Treatment': ClassDefinition(name='Treatment', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/composite_disease/Treatment', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:maxo, sqlite:obo:ncit, sqlite:obo:mesh, sqlite:obo:chebi', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/composite_disease', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=['NCITDrugType', 'NCITTreatmentType', 'NCITActivityType', 'MAXOTreatmentType', 'MESHTherapeuticType', 'CHEBIDrugType'], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='composite_disease:Treatment', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Mechanism': ClassDefinition(name='Mechanism', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/composite_disease/Mechanism', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:go, sqlite:obo:ncit, sqlite:obo:mesh', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/composite_disease', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='composite_disease:Mechanism', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Drug': ClassDefinition(name='Drug', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/composite_disease/Drug', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:chebi, sqlite:obo:drugbank', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/composite_disease', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='composite_disease:Drug', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'TreatmentMechanism': ClassDefinition(name='TreatmentMechanism', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/composite_disease/TreatmentMechanism', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/composite_disease', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['treatmentMechanism__treatment', 'treatmentMechanism__mechanism'], slot_usage={}, attributes={'treatment': SlotDefinition(name='treatment', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Treatment', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'mechanism': SlotDefinition(name='mechanism', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Mechanism', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='composite_disease:TreatmentMechanism', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'TreatmentAdverseEffect': ClassDefinition(name='TreatmentAdverseEffect', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/composite_disease/TreatmentAdverseEffect', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/composite_disease', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['treatmentAdverseEffect__treatment', 'treatmentAdverseEffect__adverse_effects'], slot_usage={}, attributes={'treatment': SlotDefinition(name='treatment', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Treatment', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'adverse_effects': SlotDefinition(name='adverse_effects', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='AdverseEffect', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='composite_disease:TreatmentAdverseEffect', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'TreatmentEfficacy': ClassDefinition(name='TreatmentEfficacy', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/composite_disease/TreatmentEfficacy', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/composite_disease', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['treatmentEfficacy__treatment', 'treatmentEfficacy__efficacy'], slot_usage={}, attributes={'treatment': SlotDefinition(name='treatment', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Treatment', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'efficacy': SlotDefinition(name='efficacy', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='composite_disease:TreatmentEfficacy', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Any': ClassDefinition(name='Any', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Any', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=['linkml:Any'], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='linkml:Any', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ExtractionResult': ClassDefinition(name='ExtractionResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/ExtractionResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A result of extracting knowledge on text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['extractionResult__input_id', 'extractionResult__input_title', 'extractionResult__input_text', 'extractionResult__raw_completion_output', 'extractionResult__prompt', 'extractionResult__extracted_object', 'extractionResult__named_entities'], slot_usage={}, attributes={'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:ExtractionResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'NamedEntity': ClassDefinition(name='NamedEntity', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NamedEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:NamedEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'CompoundExpression': ClassDefinition(name='CompoundExpression', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/CompoundExpression', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='core:CompoundExpression', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Triple': ClassDefinition(name='Triple', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Triple', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Abstract parent for Relation Extraction tasks', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['triple__subject', 'triple__predicate', 'triple__object', 'triple__qualifier', 'triple__subject_qualifier', 'triple__object_qualifier'], slot_usage={}, attributes={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Triple', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'TextWithTriples': ClassDefinition(name='TextWithTriples', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/TextWithTriples', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['textWithTriples__publication', 'textWithTriples__triples'], slot_usage={}, attributes={'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:TextWithTriples', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'RelationshipType': ClassDefinition(name='RelationshipType', id_prefixes=['RO', 'biolink'], definition_uri='http://w3id.org/ontogpt/core/RelationshipType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='core:RelationshipType', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Publication': ClassDefinition(name='Publication', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Publication', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['publication__id', 'publication__title', 'publication__abstract', 'publication__combined_text', 'publication__full_text'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Publication', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'AnnotatorResult': ClassDefinition(name='AnnotatorResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/AnnotatorResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['annotatorResult__subject_text', 'annotatorResult__object_id', 'annotatorResult__object_text'], slot_usage={}, attributes={'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:AnnotatorResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={})}" ; - linkml:enums "{'NCITDrugType': EnumDefinition(name='NCITDrugType', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/composite_disease/NCITDrugType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/composite_disease', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={}, include=[], minus=[], inherits=[], reachable_from=ReachabilityQuery(source_ontology='obo:ncit', source_nodes=['NCIT:C1908'], relationship_types=[], is_direct=None, include_self=None, traverse_up=None), matches=None, concepts=[]), 'NCITTreatmentType': EnumDefinition(name='NCITTreatmentType', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/composite_disease/NCITTreatmentType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/composite_disease', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={}, include=[], minus=[], inherits=[], reachable_from=ReachabilityQuery(source_ontology='obo:ncit', source_nodes=['NCIT:C25218'], relationship_types=[], is_direct=None, include_self=None, traverse_up=None), matches=None, concepts=[]), 'NCITTActivityType': EnumDefinition(name='NCITTActivityType', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/composite_disease/NCITTActivityType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/composite_disease', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={}, include=[], minus=[], inherits=[], reachable_from=ReachabilityQuery(source_ontology='obo:ncit', source_nodes=['NCIT:C43431'], relationship_types=[], is_direct=None, include_self=None, traverse_up=None), matches=None, concepts=[]), 'MAXOActionType': EnumDefinition(name='MAXOActionType', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/composite_disease/MAXOActionType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/composite_disease', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={}, include=[], minus=[], inherits=[], reachable_from=ReachabilityQuery(source_ontology='obo:maxo', source_nodes=['MAXO:0000001'], relationship_types=[], is_direct=None, include_self=None, traverse_up=None), matches=None, concepts=[]), 'MESHTherapeuticType': EnumDefinition(name='MESHTherapeuticType', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/composite_disease/MESHTherapeuticType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/composite_disease', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={}, include=[], minus=[], inherits=[], reachable_from=ReachabilityQuery(source_ontology='obo:mesh', source_nodes=['MESH:D013812'], relationship_types=[], is_direct=None, include_self=None, traverse_up=None), matches=None, concepts=[]), 'CHEBIDrugType': EnumDefinition(name='CHEBIDrugType', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/composite_disease/CHEBIDrugType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/composite_disease', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={}, include=[], minus=[], inherits=[], reachable_from=ReachabilityQuery(source_ontology='obo:chebi', source_nodes=['CHEBI:23888'], relationship_types=['rdfs:subClassOf', 'RO:0000087'], is_direct=None, include_self=None, traverse_up=None), matches=None, concepts=[]), 'NullDataOptions': EnumDefinition(name='NullDataOptions', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NullDataOptions', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'UNSPECIFIED_METHOD_OF_ADMINISTRATION': PermissibleValue(text='UNSPECIFIED_METHOD_OF_ADMINISTRATION', description=None, meaning='NCIT:C149701', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_APPLICABLE': PermissibleValue(text='NOT_APPLICABLE', description=None, meaning='NCIT:C18902', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['not applicable', 'N/A'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_MENTIONED': PermissibleValue(text='NOT_MENTIONED', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[])}" ; - linkml:id "http://w3id.org/ontogpt/composite_disease" ; - linkml:imports "core", - "linkml:types" ; - linkml:types "{'string': TypeDefinition(name='string', id_prefixes=[], definition_uri='https://w3id.org/linkml/String', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A character string', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Text'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'integer': TypeDefinition(name='integer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Integer', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An integer', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Integer'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='int', uri='xsd:integer', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'boolean': TypeDefinition(name='boolean', id_prefixes=[], definition_uri='https://w3id.org/linkml/Boolean', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A binary (true or false) value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Boolean'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Bool', uri='xsd:boolean', repr='bool', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'float': TypeDefinition(name='float', id_prefixes=[], definition_uri='https://w3id.org/linkml/Float', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:float specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Float'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:float', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'double': TypeDefinition(name='double', id_prefixes=[], definition_uri='https://w3id.org/linkml/Double', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:double specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:Float'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:double', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'decimal': TypeDefinition(name='decimal', id_prefixes=[], definition_uri='https://w3id.org/linkml/Decimal', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number with arbitrary precision that conforms to the xsd:decimal specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=['schema:Number'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Decimal', uri='xsd:decimal', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'time': TypeDefinition(name='time', id_prefixes=[], definition_uri='https://w3id.org/linkml/Time', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A time object represents a (local) time of day, independent of any particular day', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=['URI is dateTime because OWL reasoners do not work with straight date or time'], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Time'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDTime', uri='xsd:time', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date': TypeDefinition(name='date', id_prefixes=[], definition_uri='https://w3id.org/linkml/Date', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a date (year, month and day) in an idealized calendar', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[\"URI is dateTime because OWL reasoners don't work with straight date or time\"], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Date'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDate', uri='xsd:date', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'datetime': TypeDefinition(name='datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/Datetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The combination of a date and time', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:DateTime'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDateTime', uri='xsd:dateTime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date_or_datetime': TypeDefinition(name='date_or_datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/DateOrDatetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Either a date or a datetime', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='linkml:DateOrDatetime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uriorcurie': TypeDefinition(name='uriorcurie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uriorcurie', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a URI or a CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URIorCURIE', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'curie': TypeDefinition(name='curie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Curie', local_names={}, conforms_to='https://www.w3.org/TR/curie/', implements=[], extensions={}, annotations={}, description='a compact URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations this MUST be expanded to a URI', 'in non-RDF serializations MAY be serialized as the compact representation'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Curie', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uri': TypeDefinition(name='uri', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uri', local_names={}, conforms_to='https://www.ietf.org/rfc/rfc3987.txt', implements=[], extensions={}, annotations={}, description='a complete URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:URL'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URI', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ncname': TypeDefinition(name='ncname', id_prefixes=[], definition_uri='https://w3id.org/linkml/Ncname', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Prefix part of CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NCName', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'objectidentifier': TypeDefinition(name='objectidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Objectidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI or CURIE that represents an object in the model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['Used for inheritance and type checking'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='ElementIdentifier', uri='shex:iri', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'nodeidentifier': TypeDefinition(name='nodeidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Nodeidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI, CURIE or BNODE that represents a node in a model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NodeIdentifier', uri='shex:nonLiteral', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpointer': TypeDefinition(name='jsonpointer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpointer', local_names={}, conforms_to='https://datatracker.ietf.org/doc/html/rfc6901', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpath': TypeDefinition(name='jsonpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpath', local_names={}, conforms_to='https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sparqlpath': TypeDefinition(name='sparqlpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Sparqlpath', local_names={}, conforms_to='https://www.w3.org/TR/sparql11-query/#propertypaths', implements=[], extensions={}, annotations={}, description='A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -composite_disease:CHEBIDrugType a owl:Class, - linkml:EnumDefinition ; - rdfs:label "CHEBIDrugType" ; - owl:unionOf [ rdf:rest () ] . - -composite_disease:Gene a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Gene" ; - composite_disease:annotators "gilda:, obo:sql:hgnc, bioportal:hgnc-nr" ; - rdfs:subClassOf ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -composite_disease:MAXOActionType a owl:Class, - linkml:EnumDefinition ; - rdfs:label "MAXOActionType" ; - owl:unionOf [ rdf:rest () ] . - -composite_disease:MESHTherapeuticType a owl:Class, - linkml:EnumDefinition ; - rdfs:label "MESHTherapeuticType" ; - owl:unionOf [ rdf:rest () ] . - -composite_disease:NCITDrugType a owl:Class, - linkml:EnumDefinition ; - rdfs:label "NCITDrugType" ; - owl:unionOf [ rdf:rest () ] . - -composite_disease:NCITTActivityType a owl:Class, - linkml:EnumDefinition ; - rdfs:label "NCITTActivityType" ; - owl:unionOf [ rdf:rest () ] . - -composite_disease:NCITTreatmentType a owl:Class, - linkml:EnumDefinition ; - rdfs:label "NCITTreatmentType" ; - owl:unionOf [ rdf:rest () ] . - -composite_disease:Symptom a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Symptom" ; - composite_disease:annotators "sqlite:obo:hp" ; - rdfs:subClassOf ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -linkml:SubsetDefinition a owl:Class ; - rdfs:label "subset_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" . - -linkml:TypeDefinition a owl:Class ; - rdfs:label "type_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" ; - linkml:mixins "type_expression" . - -linkml:topValue a owl:DatatypeProperty ; - rdfs:label "value" . - -composite_disease:CompositeDisease a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CompositeDisease" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass composite_disease:Disease ; - owl:onProperty composite_disease:main_disease ], - [ a owl:Restriction ; - owl:allValuesFrom composite_disease:TreatmentMechanism ; - owl:onProperty composite_disease:treatment_mechanisms ], - [ a owl:Restriction ; - owl:allValuesFrom composite_disease:TreatmentAdverseEffect ; - owl:onProperty composite_disease:treatment_adverse_effects ], - [ a owl:Restriction ; - owl:allValuesFrom composite_disease:Treatment ; - owl:onProperty composite_disease:contraindications ], - [ a owl:Restriction ; - owl:allValuesFrom composite_disease:TreatmentEfficacy ; - owl:onProperty composite_disease:treatment_efficacies ], - [ a owl:Restriction ; - owl:allValuesFrom composite_disease:Treatment ; - owl:onProperty composite_disease:treatments ], - [ a owl:Restriction ; - owl:allValuesFrom composite_disease:Drug ; - owl:onProperty composite_disease:drugs ] ; - linkml:attributes "{'main_disease': SlotDefinition(name='main_disease', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the name of the disease that is treated.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Disease', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'drugs': SlotDefinition(name='drugs', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of named small molecule drugs', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Drug', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'treatments': SlotDefinition(name='treatments', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.examples': Annotation(tag='prompt.examples', value='Imatinib, exercise, surgery', extensions={}, annotations={})}, description='semicolon-separated list of therapies and treatments are indicated for treating the disease.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Treatment', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'contraindications': SlotDefinition(name='contraindications', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.examples': Annotation(tag='prompt.examples', value='Beta-blockers, exercise, surgery', extensions={}, annotations={})}, description='semicolon-separated list of therapies and treatments that are contra-indicated for the disease, and should not be used, due to risk of adverse effects.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Treatment', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'treatment_mechanisms': SlotDefinition(name='treatment_mechanisms', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.separator': Annotation(tag='prompt.separator', value='*', extensions={}, annotations={})}, description='semicolon-separated list of treatment to asterisk-separated mechanism associations', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='TreatmentMechanism', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'treatment_efficacies': SlotDefinition(name='treatment_efficacies', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.separator': Annotation(tag='prompt.separator', value='*', extensions={}, annotations={})}, description='semicolon-separated list of treatment to efficacy associations, e.g. Imatinib*effective', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='TreatmentEfficacy', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'treatment_adverse_effects': SlotDefinition(name='treatment_adverse_effects', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.separator': Annotation(tag='prompt.separator', value='*', extensions={}, annotations={})}, description='semicolon-separated list of treatment to adverse effect associations, e.g. Imatinib*nausea', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='TreatmentAdverseEffect', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -composite_disease:adverse_effects a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "adverse_effects" ; - rdfs:range composite_disease:AdverseEffect . - -composite_disease:contraindications a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "contraindications" ; - composite_disease:prompt.examples "Beta-blockers, exercise, surgery" ; - rdfs:range composite_disease:Treatment ; - skos:definition "semicolon-separated list of therapies and treatments that are contra-indicated for the disease, and should not be used, due to risk of adverse effects." . - -composite_disease:drugs a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "drugs" ; - rdfs:range composite_disease:Drug ; - skos:definition "semicolon-separated list of named small molecule drugs" . - -composite_disease:efficacy a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "efficacy" ; - rdfs:range linkml:String . - -composite_disease:main_disease a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "main_disease" ; - rdfs:range composite_disease:Disease ; - skos:definition "the name of the disease that is treated." . - -composite_disease:mechanism a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "mechanism" ; - rdfs:range composite_disease:Mechanism . - -composite_disease:treatment_adverse_effects a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "treatment_adverse_effects" ; - composite_disease:prompt.separator "*" ; - rdfs:range composite_disease:TreatmentAdverseEffect ; - skos:definition "semicolon-separated list of treatment to adverse effect associations, e.g. Imatinib*nausea" . - -composite_disease:treatment_efficacies a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "treatment_efficacies" ; - composite_disease:prompt.separator "*" ; - rdfs:range composite_disease:TreatmentEfficacy ; - skos:definition "semicolon-separated list of treatment to efficacy associations, e.g. Imatinib*effective" . - -composite_disease:treatment_mechanisms a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "treatment_mechanisms" ; - composite_disease:prompt.separator "*" ; - rdfs:range composite_disease:TreatmentMechanism ; - skos:definition "semicolon-separated list of treatment to asterisk-separated mechanism associations" . - -composite_disease:treatments a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "treatments" ; - composite_disease:prompt.examples "Imatinib, exercise, surgery" ; - rdfs:range composite_disease:Treatment ; - skos:definition "semicolon-separated list of therapies and treatments are indicated for treating the disease." . - - a owl:Class, - linkml:ClassDefinition ; - rdfs:label "AnnotatorResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ] ; - linkml:attributes "{'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - - a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ExtractionResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ] ; - skos:definition "A result of extracting knowledge on text" ; - linkml:attributes "{'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - - a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TextWithTriples" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty ] ; - linkml:attributes "{'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "abstract" ; - rdfs:range linkml:String ; - skos:definition "The abstract of the publication" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "combined_text" ; - rdfs:range linkml:String . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "extracted_object" ; - rdfs:range ; - skos:definition "The complex objects extracted from the text" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "full_text" ; - rdfs:range linkml:String ; - skos:definition "The full text of the publication" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_id" ; - rdfs:range linkml:String . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_text" ; - rdfs:range linkml:String . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_title" ; - rdfs:range linkml:String . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "named_entities" ; - rdfs:range ; - skos:definition "Named entities extracted from the text" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object" ; - rdfs:range . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_id" ; - rdfs:range linkml:String . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_qualifier" ; - rdfs:range ; - skos:definition "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_text" ; - rdfs:range linkml:String . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "predicate" ; - rdfs:range . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "prompt" ; - rdfs:range linkml:String . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "publication" ; - composite_disease:prompt.skip "true" ; - rdfs:range . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "qualifier" ; - rdfs:range linkml:String ; - skos:definition "A qualifier for the statements, e.g. \"NOT\" for negation" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "raw_completion_output" ; - rdfs:range linkml:String . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject" ; - rdfs:range . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_qualifier" ; - rdfs:range ; - skos:definition "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_text" ; - rdfs:range linkml:String . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "title" ; - rdfs:range linkml:String ; - skos:definition "The title of the publication" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "triples" ; - rdfs:range . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "label" ; - composite_disease:owl "AnnotationProperty, AnnotationAssertion" ; - rdfs:range linkml:String ; - skos:altLabel "name" ; - skos:definition "The label (name) of the named thing" ; - skos:exactMatch . - - a , - owl:Class ; - rdfs:label "UNSPECIFIED_METHOD_OF_ADMINISTRATION" . - - a , - owl:Class ; - rdfs:label "NOT_APPLICABLE" . - -composite_disease:AdverseEffect a owl:Class, - linkml:ClassDefinition ; - rdfs:label "AdverseEffect" ; - composite_disease:annotators "sqlite:obo:hp, sqlite:obo:ncit" ; - rdfs:subClassOf ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -composite_disease:Disease a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Disease" ; - composite_disease:annotators "sqlite:obo:mondo" ; - rdfs:subClassOf ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -composite_disease:Drug a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Drug" ; - composite_disease:annotators "sqlite:obo:chebi, sqlite:obo:drugbank" ; - rdfs:subClassOf ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -composite_disease:Mechanism a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Mechanism" ; - composite_disease:annotators "sqlite:obo:go, sqlite:obo:ncit, sqlite:obo:mesh" ; - rdfs:subClassOf ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -composite_disease:TreatmentAdverseEffect a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TreatmentAdverseEffect" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass composite_disease:Treatment ; - owl:onProperty composite_disease:treatment ], - [ a owl:Restriction ; - owl:allValuesFrom composite_disease:AdverseEffect ; - owl:onProperty composite_disease:adverse_effects ], - ; - linkml:attributes "{'treatment': SlotDefinition(name='treatment', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Treatment', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'adverse_effects': SlotDefinition(name='adverse_effects', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='AdverseEffect', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -composite_disease:TreatmentEfficacy a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TreatmentEfficacy" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass composite_disease:Treatment ; - owl:onProperty composite_disease:treatment ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty composite_disease:efficacy ], - ; - linkml:attributes "{'treatment': SlotDefinition(name='treatment', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Treatment', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'efficacy': SlotDefinition(name='efficacy', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -composite_disease:TreatmentMechanism a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TreatmentMechanism" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass composite_disease:Treatment ; - owl:onProperty composite_disease:treatment ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass composite_disease:Mechanism ; - owl:onProperty composite_disease:mechanism ], - ; - linkml:attributes "{'treatment': SlotDefinition(name='treatment', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Treatment', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'mechanism': SlotDefinition(name='mechanism', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Mechanism', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - - a , - owl:Class ; - rdfs:label "NOT_MENTIONED" . - - a owl:Class, - linkml:ClassDefinition ; - rdfs:label "RelationshipType" ; - rdfs:subClassOf ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - - a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Triple" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - ; - skos:definition "Abstract parent for Relation Extraction tasks" ; - linkml:attributes "{'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - - a owl:ObjectProperty, - linkml:SlotDefinition . - -composite_disease:treatment a owl:ObjectProperty, - linkml:SlotDefinition . - - a owl:Class, - linkml:EnumDefinition ; - rdfs:label "NullDataOptions" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - . - - a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Publication" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - - a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Any" ; - skos:exactMatch linkml:Any ; - linkml:attributes "{}" . - - a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CompoundExpression" ; - linkml:attributes "{}" . - -composite_disease:Treatment a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Treatment" ; - composite_disease:annotators "sqlite:obo:maxo, sqlite:obo:ncit, sqlite:obo:mesh, sqlite:obo:chebi" ; - rdfs:subClassOf ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - - a owl:Class, - linkml:ClassDefinition ; - rdfs:label "NamedEntity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:ClassDefinition a owl:Class ; - rdfs:label "class_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "class_expression" . - -linkml:SlotDefinition a owl:Class ; - rdfs:label "slot_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "slot_expression" . - - diff --git a/projects/composite_disease/prefixmap/composite_disease.yaml b/projects/composite_disease/prefixmap/composite_disease.yaml deleted file mode 100644 index 2a737b3b7..000000000 --- a/projects/composite_disease/prefixmap/composite_disease.yaml +++ /dev/null @@ -1,37 +0,0 @@ -{ - "HGNC": "http://example.org/UNKNOWN/HGNC/", - "HP": "http://example.org/UNKNOWN/HP/", - "RO": "http://purl.obolibrary.org/obo/RO_", - "biolink": "http://example.org/UNKNOWN/biolink/", - "composite_disease": "http://w3id.org/ontogpt/composite_disease/", - "core": "http://w3id.org/ontogpt/core/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } -} diff --git a/projects/composite_disease/protobuf/composite_disease.proto b/projects/composite_disease/protobuf/composite_disease.proto deleted file mode 100644 index 0a2324473..000000000 --- a/projects/composite_disease/protobuf/composite_disease.proto +++ /dev/null @@ -1,95 +0,0 @@ -message AdverseEffect - { - string id = 0 - string label = 0 - } -message AnnotatorResult - { - string subjectText = 0 - string objectId = 0 - string objectText = 0 - } -message CompositeDisease - { - disease mainDisease = 0 - repeated drug drugs = 0 - repeated treatment treatments = 0 - repeated treatment contraindications = 0 - repeated treatmentMechanism treatmentMechanisms = 0 - repeated treatmentEfficacy treatmentEfficacies = 0 - repeated treatmentAdverseEffect treatmentAdverseEffects = 0 - } -message Disease - { - string id = 0 - string label = 0 - } -message Drug - { - string id = 0 - string label = 0 - } -// A result of extracting knowledge on text -message ExtractionResult - { - string inputId = 0 - string inputTitle = 0 - string inputText = 0 - string rawCompletionOutput = 0 - string prompt = 0 - any extractedObject = 0 - repeated any namedEntities = 0 - } -message Gene - { - string id = 0 - string label = 0 - } -message Mechanism - { - string id = 0 - string label = 0 - } -message Publication - { - string id = 0 - string title = 0 - string abstract = 0 - string combinedText = 0 - string fullText = 0 - } -message RelationshipType - { - string id = 0 - string label = 0 - } -message Symptom - { - string id = 0 - string label = 0 - } -message TextWithTriples - { - publication publication = 0 - repeated triple triples = 0 - } -message Treatment - { - string id = 0 - string label = 0 - } -message TreatmentAdverseEffect - { - treatment treatment = 0 - repeated adverseEffect adverseEffects = 0 - } -message TreatmentEfficacy - { - treatment treatment = 0 - string efficacy = 0 - } -message TreatmentMechanism - { - treatment treatment = 0 - mechanism mechanism = 0 - } diff --git a/projects/composite_disease/shacl/composite_disease.shacl.ttl b/projects/composite_disease/shacl/composite_disease.shacl.ttl deleted file mode 100644 index 8053d0fd7..000000000 --- a/projects/composite_disease/shacl/composite_disease.shacl.ttl +++ /dev/null @@ -1,345 +0,0 @@ -@prefix composite_disease: . -@prefix linkml: . -@prefix rdf: . -@prefix sh: . -@prefix xsd: . - -composite_disease:CompositeDisease a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class composite_disease:TreatmentMechanism ; - sh:description "semicolon-separated list of treatment to asterisk-separated mechanism associations" ; - sh:nodeKind sh:BlankNode ; - sh:order 4 ; - sh:path composite_disease:treatment_mechanisms ], - [ sh:class composite_disease:Treatment ; - sh:description "semicolon-separated list of therapies and treatments that are contra-indicated for the disease, and should not be used, due to risk of adverse effects." ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path composite_disease:contraindications ], - [ sh:class composite_disease:Disease ; - sh:description "the name of the disease that is treated." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path composite_disease:main_disease ], - [ sh:class composite_disease:TreatmentEfficacy ; - sh:description "semicolon-separated list of treatment to efficacy associations, e.g. Imatinib*effective" ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path composite_disease:treatment_efficacies ], - [ sh:class composite_disease:Drug ; - sh:description "semicolon-separated list of named small molecule drugs" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path composite_disease:drugs ], - [ sh:class composite_disease:TreatmentAdverseEffect ; - sh:description "semicolon-separated list of treatment to adverse effect associations, e.g. Imatinib*nausea" ; - sh:nodeKind sh:BlankNode ; - sh:order 6 ; - sh:path composite_disease:treatment_adverse_effects ], - [ sh:class composite_disease:Treatment ; - sh:description "semicolon-separated list of therapies and treatments are indicated for treating the disease." ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path composite_disease:treatments ] ; - sh:targetClass composite_disease:CompositeDisease . - -composite_disease:Gene a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path ] ; - sh:targetClass composite_disease:Gene . - -composite_disease:Symptom a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path ] ; - sh:targetClass composite_disease:Symptom . - - a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 1 ; - sh:path ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path ] ; - sh:targetClass . - - a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass . - - a sh:NodeShape ; - sh:closed true ; - sh:description "A result of extracting knowledge on text" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 2 ; - sh:path ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path ], - [ sh:maxCount 1 ; - sh:order 4 ; - sh:path ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path ], - [ sh:class linkml:Any ; - sh:description "The complex objects extracted from the text" ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path ], - [ sh:class linkml:Any ; - sh:description "Named entities extracted from the text" ; - sh:nodeKind sh:BlankNode ; - sh:order 6 ; - sh:path ] ; - sh:targetClass . - - a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path ], - [ sh:class ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path ] ; - sh:targetClass . - -composite_disease:AdverseEffect a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path ] ; - sh:targetClass composite_disease:AdverseEffect . - -composite_disease:Disease a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path ] ; - sh:targetClass composite_disease:Disease . - -composite_disease:Drug a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path ] ; - sh:targetClass composite_disease:Drug . - -composite_disease:Mechanism a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path ] ; - sh:targetClass composite_disease:Mechanism . - -composite_disease:TreatmentAdverseEffect a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class composite_disease:AdverseEffect ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path composite_disease:adverse_effects ], - [ sh:class composite_disease:Treatment ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path composite_disease:treatment ] ; - sh:targetClass composite_disease:TreatmentAdverseEffect . - -composite_disease:TreatmentEfficacy a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class composite_disease:Treatment ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path composite_disease:treatment ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path composite_disease:efficacy ] ; - sh:targetClass composite_disease:TreatmentEfficacy . - -composite_disease:TreatmentMechanism a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class composite_disease:Treatment ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path composite_disease:treatment ], - [ sh:class composite_disease:Mechanism ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path composite_disease:mechanism ] ; - sh:targetClass composite_disease:TreatmentMechanism . - - a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The abstract of the publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path ], - [ sh:description "The full text of the publication" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path ], - [ sh:description "The publication identifier" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path ], - [ sh:description "The title of the publication" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path ] ; - sh:targetClass . - - a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path ] ; - sh:targetClass . - - a sh:NodeShape ; - sh:closed false ; - sh:description "Abstract parent for Relation Extraction tasks" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path ], - [ sh:class ; - sh:description "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path ], - [ sh:class ; - sh:description "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path ], - [ sh:class ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path ], - [ sh:description "A qualifier for the statements, e.g. \"NOT\" for negation" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path ], - [ sh:class ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path ] ; - sh:targetClass . - -linkml:Any a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass linkml:Any . - - a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path ] ; - sh:targetClass . - -composite_disease:Treatment a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path ] ; - sh:targetClass composite_disease:Treatment . - diff --git a/projects/composite_disease/shex/composite_disease.shex b/projects/composite_disease/shex/composite_disease.shex deleted file mode 100644 index f59e6d75b..000000000 --- a/projects/composite_disease/shex/composite_disease.shex +++ /dev/null @@ -1,235 +0,0 @@ -BASE -PREFIX rdf: -PREFIX xsd: -PREFIX linkml: -PREFIX core: -PREFIX rdfs1: - - -linkml:String xsd:string - -linkml:Integer xsd:integer - -linkml:Boolean xsd:boolean - -linkml:Float xsd:float - -linkml:Double xsd:double - -linkml:Decimal xsd:decimal - -linkml:Time xsd:time - -linkml:Date xsd:date - -linkml:Datetime xsd:dateTime - -linkml:DateOrDatetime linkml:DateOrDatetime - -linkml:Uriorcurie IRI - -linkml:Curie xsd:string - -linkml:Uri IRI - -linkml:Ncname xsd:string - -linkml:Objectidentifier IRI - -linkml:Nodeidentifier NONLITERAL - -linkml:Jsonpointer xsd:string - -linkml:Jsonpath xsd:string - -linkml:Sparqlpath xsd:string - - CLOSED { - ( $ ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ ] - ) -} - -core:AnnotatorResult CLOSED { - ( $core:AnnotatorResult_tes ( core:subject_text @linkml:String ? ; - core:object_id @linkml:String ? ; - core:object_text @linkml:String ? - ) ; - rdf:type [ core:AnnotatorResult ] ? - ) -} - -core:Any CLOSED { - ( $core:Any_tes rdf:type . * ; - rdf:type [ linkml:Any ] ? - ) -} - - CLOSED { - ( $ ( @ ? ; - @ * ; - @ * ; - @ * ; - @ * ; - @ * ; - @ * - ) ; - rdf:type [ ] ? - ) -} - -core:CompoundExpression ( - @ OR @ OR @ OR @core:Triple -) - -core:CompoundExpression_struct { - ( $core:CompoundExpression_tes rdf:type . * ; - rdf:type [ core:CompoundExpression ] ? - ) -} - - CLOSED { - ( $ ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ ] - ) -} - - CLOSED { - ( $ ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ ] - ) -} - -core:ExtractionResult CLOSED { - ( $core:ExtractionResult_tes ( core:input_id @linkml:String ? ; - core:input_title @linkml:String ? ; - core:input_text @linkml:String ? ; - core:raw_completion_output @linkml:String ? ; - core:prompt @linkml:String ? ; - core:extracted_object @core:Any ? ; - core:named_entities @core:Any * - ) ; - rdf:type [ core:ExtractionResult ] ? - ) -} - - CLOSED { - ( $ ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ ] - ) -} - - CLOSED { - ( $ ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ ] - ) -} - -core:NamedEntity ( - @ OR @ OR @ OR @ OR @ OR @core:RelationshipType OR @ OR @ -) - -core:NamedEntity_struct { - ( $core:NamedEntity_tes rdfs1:label @linkml:String ? ; - rdf:type [ core:NamedEntity ] - ) -} - -core:Publication CLOSED { - ( $core:Publication_tes ( core:id @linkml:String ? ; - core:title @linkml:String ? ; - core:abstract @linkml:String ? ; - core:combined_text @linkml:String ? ; - core:full_text @linkml:String ? - ) ; - rdf:type [ core:Publication ] ? - ) -} - -core:RelationshipType CLOSED { - ( $core:RelationshipType_tes ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ core:RelationshipType ] - ) -} - - CLOSED { - ( $ ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ ] - ) -} - -core:TextWithTriples CLOSED { - ( $core:TextWithTriples_tes ( core:publication @core:Publication ? ; - core:triples @core:Triple * - ) ; - rdf:type [ core:TextWithTriples ] ? - ) -} - - CLOSED { - ( $ ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ ] - ) -} - - CLOSED { - ( $ ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - @ ? ; - @ * - ) ; - rdf:type [ ] ? - ) -} - - CLOSED { - ( $ ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - @ ? ; - @linkml:String ? - ) ; - rdf:type [ ] ? - ) -} - - CLOSED { - ( $ ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - @ ? ; - @ ? - ) ; - rdf:type [ ] ? - ) -} - -core:Triple { - ( $core:Triple_tes ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - core:subject @core:NamedEntity ? ; - core:predicate @core:RelationshipType ? ; - core:object @core:NamedEntity ? ; - core:qualifier @linkml:String ? ; - core:subject_qualifier @core:NamedEntity ? ; - core:object_qualifier @core:NamedEntity ? - ) ; - rdf:type [ core:Triple ] ? - ) -} - - diff --git a/projects/composite_disease/sqlschema/composite_disease.sql b/projects/composite_disease/sqlschema/composite_disease.sql deleted file mode 100644 index 845d50f11..000000000 --- a/projects/composite_disease/sqlschema/composite_disease.sql +++ /dev/null @@ -1,116 +0,0 @@ - - -CREATE TABLE "AdverseEffect" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "AnnotatorResult" ( - subject_text TEXT, - object_id TEXT, - object_text TEXT, - PRIMARY KEY (subject_text, object_id, object_text) -); - -CREATE TABLE "Disease" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Drug" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "ExtractionResult" ( - input_id TEXT, - input_title TEXT, - input_text TEXT, - raw_completion_output TEXT, - prompt TEXT, - extracted_object TEXT, - named_entities TEXT, - PRIMARY KEY (input_id, input_title, input_text, raw_completion_output, prompt, extracted_object, named_entities) -); - -CREATE TABLE "Gene" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Mechanism" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Publication" ( - id TEXT, - title TEXT, - abstract TEXT, - combined_text TEXT, - full_text TEXT, - PRIMARY KEY (id, title, abstract, combined_text, full_text) -); - -CREATE TABLE "RelationshipType" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Symptom" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "TextWithTriples" ( - publication TEXT, - triples TEXT, - PRIMARY KEY (publication, triples) -); - -CREATE TABLE "Treatment" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "CompositeDisease" ( - main_disease TEXT, - drugs TEXT, - treatments TEXT, - contraindications TEXT, - treatment_mechanisms TEXT, - treatment_efficacies TEXT, - treatment_adverse_effects TEXT, - PRIMARY KEY (main_disease, drugs, treatments, contraindications, treatment_mechanisms, treatment_efficacies, treatment_adverse_effects), - FOREIGN KEY(main_disease) REFERENCES "Disease" (id) -); - -CREATE TABLE "TreatmentAdverseEffect" ( - treatment TEXT, - adverse_effects TEXT, - PRIMARY KEY (treatment, adverse_effects), - FOREIGN KEY(treatment) REFERENCES "Treatment" (id) -); - -CREATE TABLE "TreatmentEfficacy" ( - treatment TEXT, - efficacy TEXT, - PRIMARY KEY (treatment, efficacy), - FOREIGN KEY(treatment) REFERENCES "Treatment" (id) -); - -CREATE TABLE "TreatmentMechanism" ( - treatment TEXT, - mechanism TEXT, - PRIMARY KEY (treatment, mechanism), - FOREIGN KEY(treatment) REFERENCES "Treatment" (id), - FOREIGN KEY(mechanism) REFERENCES "Mechanism" (id) -); diff --git a/projects/core/core.py b/projects/core/core.py deleted file mode 100644 index 42c1e37f7..000000000 --- a/projects/core/core.py +++ /dev/null @@ -1,362 +0,0 @@ -# Auto generated from core.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-08-07T10:52:11 -# Schema: core -# -# id: http://w3id.org/ontogpt/core -# description: Core upper level -# license: https://creativecommons.org/publicdomain/zero/1.0/ - -import dataclasses -import sys -import re -from jsonasobj2 import JsonObj, as_dict -from typing import Optional, List, Union, Dict, ClassVar, Any -from dataclasses import dataclass -from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions - -from linkml_runtime.utils.slot import Slot -from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode -from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int -from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs -from linkml_runtime.utils.formatutils import camelcase, underscore, sfx -from linkml_runtime.utils.enumerations import EnumDefinitionImpl -from rdflib import Namespace, URIRef -from linkml_runtime.utils.curienamespace import CurieNamespace -from linkml_runtime.linkml_model.types import String - -metamodel_version = "1.7.0" -version = None - -# Overwrite dataclasses _init_fn to add **kwargs in __init__ -dataclasses._init_fn = dataclasses_init_fn_with_kwargs - -# Namespaces -NCIT = CurieNamespace('NCIT', 'http://purl.obolibrary.org/obo/NCIT_') -RO = CurieNamespace('RO', 'http://purl.obolibrary.org/obo/RO_') -BIOLINK = CurieNamespace('biolink', 'http://example.org/UNKNOWN/biolink/') -CORE = CurieNamespace('core', 'http://w3id.org/ontogpt/core/') -LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') -RDFS = CurieNamespace('rdfs', 'http://example.org/UNKNOWN/rdfs/') -DEFAULT_ = CORE - - -# Types - -# Class references -class NamedEntityId(extended_str): - pass - - -class RelationshipTypeId(NamedEntityId): - pass - - -Any = Any - -@dataclass -class ExtractionResult(YAMLRoot): - """ - A result of extracting knowledge on text - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.ExtractionResult - class_class_curie: ClassVar[str] = "core:ExtractionResult" - class_name: ClassVar[str] = "ExtractionResult" - class_model_uri: ClassVar[URIRef] = CORE.ExtractionResult - - input_id: Optional[str] = None - input_title: Optional[str] = None - input_text: Optional[str] = None - raw_completion_output: Optional[str] = None - prompt: Optional[str] = None - extracted_object: Optional[Union[dict, Any]] = None - named_entities: Optional[Union[Union[dict, Any], List[Union[dict, Any]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.input_id is not None and not isinstance(self.input_id, str): - self.input_id = str(self.input_id) - - if self.input_title is not None and not isinstance(self.input_title, str): - self.input_title = str(self.input_title) - - if self.input_text is not None and not isinstance(self.input_text, str): - self.input_text = str(self.input_text) - - if self.raw_completion_output is not None and not isinstance(self.raw_completion_output, str): - self.raw_completion_output = str(self.raw_completion_output) - - if self.prompt is not None and not isinstance(self.prompt, str): - self.prompt = str(self.prompt) - - super().__post_init__(**kwargs) - - -@dataclass -class NamedEntity(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.NamedEntity - class_class_curie: ClassVar[str] = "core:NamedEntity" - class_name: ClassVar[str] = "NamedEntity" - class_model_uri: ClassVar[URIRef] = CORE.NamedEntity - - id: Union[str, NamedEntityId] = None - label: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, NamedEntityId): - self.id = NamedEntityId(self.id) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - super().__post_init__(**kwargs) - - -class CompoundExpression(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.CompoundExpression - class_class_curie: ClassVar[str] = "core:CompoundExpression" - class_name: ClassVar[str] = "CompoundExpression" - class_model_uri: ClassVar[URIRef] = CORE.CompoundExpression - - -@dataclass -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Triple - class_class_curie: ClassVar[str] = "core:Triple" - class_name: ClassVar[str] = "Triple" - class_model_uri: ClassVar[URIRef] = CORE.Triple - - subject: Optional[Union[str, NamedEntityId]] = None - predicate: Optional[Union[str, RelationshipTypeId]] = None - object: Optional[Union[str, NamedEntityId]] = None - qualifier: Optional[str] = None - subject_qualifier: Optional[Union[str, NamedEntityId]] = None - object_qualifier: Optional[Union[str, NamedEntityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, NamedEntityId): - self.subject = NamedEntityId(self.subject) - - if self.predicate is not None and not isinstance(self.predicate, RelationshipTypeId): - self.predicate = RelationshipTypeId(self.predicate) - - if self.object is not None and not isinstance(self.object, NamedEntityId): - self.object = NamedEntityId(self.object) - - if self.qualifier is not None and not isinstance(self.qualifier, str): - self.qualifier = str(self.qualifier) - - if self.subject_qualifier is not None and not isinstance(self.subject_qualifier, NamedEntityId): - self.subject_qualifier = NamedEntityId(self.subject_qualifier) - - if self.object_qualifier is not None and not isinstance(self.object_qualifier, NamedEntityId): - self.object_qualifier = NamedEntityId(self.object_qualifier) - - super().__post_init__(**kwargs) - - -@dataclass -class TextWithTriples(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.TextWithTriples - class_class_curie: ClassVar[str] = "core:TextWithTriples" - class_name: ClassVar[str] = "TextWithTriples" - class_model_uri: ClassVar[URIRef] = CORE.TextWithTriples - - publication: Optional[Union[dict, "Publication"]] = None - triples: Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.publication is not None and not isinstance(self.publication, Publication): - self.publication = Publication(**as_dict(self.publication)) - - if not isinstance(self.triples, list): - self.triples = [self.triples] if self.triples is not None else [] - self.triples = [v if isinstance(v, Triple) else Triple(**as_dict(v)) for v in self.triples] - - super().__post_init__(**kwargs) - - -@dataclass -class RelationshipType(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.RelationshipType - class_class_curie: ClassVar[str] = "core:RelationshipType" - class_name: ClassVar[str] = "RelationshipType" - class_model_uri: ClassVar[URIRef] = CORE.RelationshipType - - id: Union[str, RelationshipTypeId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, RelationshipTypeId): - self.id = RelationshipTypeId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Publication(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Publication - class_class_curie: ClassVar[str] = "core:Publication" - class_name: ClassVar[str] = "Publication" - class_model_uri: ClassVar[URIRef] = CORE.Publication - - id: Optional[str] = None - title: Optional[str] = None - abstract: Optional[str] = None - combined_text: Optional[str] = None - full_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.id is not None and not isinstance(self.id, str): - self.id = str(self.id) - - if self.title is not None and not isinstance(self.title, str): - self.title = str(self.title) - - if self.abstract is not None and not isinstance(self.abstract, str): - self.abstract = str(self.abstract) - - if self.combined_text is not None and not isinstance(self.combined_text, str): - self.combined_text = str(self.combined_text) - - if self.full_text is not None and not isinstance(self.full_text, str): - self.full_text = str(self.full_text) - - super().__post_init__(**kwargs) - - -@dataclass -class AnnotatorResult(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.AnnotatorResult - class_class_curie: ClassVar[str] = "core:AnnotatorResult" - class_name: ClassVar[str] = "AnnotatorResult" - class_model_uri: ClassVar[URIRef] = CORE.AnnotatorResult - - subject_text: Optional[str] = None - object_id: Optional[str] = None - object_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject_text is not None and not isinstance(self.subject_text, str): - self.subject_text = str(self.subject_text) - - if self.object_id is not None and not isinstance(self.object_id, str): - self.object_id = str(self.object_id) - - if self.object_text is not None and not isinstance(self.object_text, str): - self.object_text = str(self.object_text) - - super().__post_init__(**kwargs) - - -# Enumerations -class NullDataOptions(EnumDefinitionImpl): - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = PermissibleValue(text="UNSPECIFIED_METHOD_OF_ADMINISTRATION", - meaning=NCIT.C149701) - NOT_APPLICABLE = PermissibleValue(text="NOT_APPLICABLE", - meaning=NCIT.C18902) - NOT_MENTIONED = PermissibleValue(text="NOT_MENTIONED") - - _defn = EnumDefinition( - name="NullDataOptions", - ) - -# Slots -class slots: - pass - -slots.extractionResult__input_id = Slot(uri=CORE.input_id, name="extractionResult__input_id", curie=CORE.curie('input_id'), - model_uri=CORE.extractionResult__input_id, domain=None, range=Optional[str]) - -slots.extractionResult__input_title = Slot(uri=CORE.input_title, name="extractionResult__input_title", curie=CORE.curie('input_title'), - model_uri=CORE.extractionResult__input_title, domain=None, range=Optional[str]) - -slots.extractionResult__input_text = Slot(uri=CORE.input_text, name="extractionResult__input_text", curie=CORE.curie('input_text'), - model_uri=CORE.extractionResult__input_text, domain=None, range=Optional[str]) - -slots.extractionResult__raw_completion_output = Slot(uri=CORE.raw_completion_output, name="extractionResult__raw_completion_output", curie=CORE.curie('raw_completion_output'), - model_uri=CORE.extractionResult__raw_completion_output, domain=None, range=Optional[str]) - -slots.extractionResult__prompt = Slot(uri=CORE.prompt, name="extractionResult__prompt", curie=CORE.curie('prompt'), - model_uri=CORE.extractionResult__prompt, domain=None, range=Optional[str]) - -slots.extractionResult__extracted_object = Slot(uri=CORE.extracted_object, name="extractionResult__extracted_object", curie=CORE.curie('extracted_object'), - model_uri=CORE.extractionResult__extracted_object, domain=None, range=Optional[Union[dict, Any]]) - -slots.extractionResult__named_entities = Slot(uri=CORE.named_entities, name="extractionResult__named_entities", curie=CORE.curie('named_entities'), - model_uri=CORE.extractionResult__named_entities, domain=None, range=Optional[Union[Union[dict, Any], List[Union[dict, Any]]]]) - -slots.namedEntity__id = Slot(uri=CORE.id, name="namedEntity__id", curie=CORE.curie('id'), - model_uri=CORE.namedEntity__id, domain=None, range=URIRef) - -slots.namedEntity__label = Slot(uri=RDFS.label, name="namedEntity__label", curie=RDFS.curie('label'), - model_uri=CORE.namedEntity__label, domain=None, range=Optional[str]) - -slots.triple__subject = Slot(uri=CORE.subject, name="triple__subject", curie=CORE.curie('subject'), - model_uri=CORE.triple__subject, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__predicate = Slot(uri=CORE.predicate, name="triple__predicate", curie=CORE.curie('predicate'), - model_uri=CORE.triple__predicate, domain=None, range=Optional[Union[str, RelationshipTypeId]]) - -slots.triple__object = Slot(uri=CORE.object, name="triple__object", curie=CORE.curie('object'), - model_uri=CORE.triple__object, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__qualifier = Slot(uri=CORE.qualifier, name="triple__qualifier", curie=CORE.curie('qualifier'), - model_uri=CORE.triple__qualifier, domain=None, range=Optional[str]) - -slots.triple__subject_qualifier = Slot(uri=CORE.subject_qualifier, name="triple__subject_qualifier", curie=CORE.curie('subject_qualifier'), - model_uri=CORE.triple__subject_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__object_qualifier = Slot(uri=CORE.object_qualifier, name="triple__object_qualifier", curie=CORE.curie('object_qualifier'), - model_uri=CORE.triple__object_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.textWithTriples__publication = Slot(uri=CORE.publication, name="textWithTriples__publication", curie=CORE.curie('publication'), - model_uri=CORE.textWithTriples__publication, domain=None, range=Optional[Union[dict, Publication]]) - -slots.textWithTriples__triples = Slot(uri=CORE.triples, name="textWithTriples__triples", curie=CORE.curie('triples'), - model_uri=CORE.textWithTriples__triples, domain=None, range=Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]]) - -slots.publication__id = Slot(uri=CORE.id, name="publication__id", curie=CORE.curie('id'), - model_uri=CORE.publication__id, domain=None, range=Optional[str]) - -slots.publication__title = Slot(uri=CORE.title, name="publication__title", curie=CORE.curie('title'), - model_uri=CORE.publication__title, domain=None, range=Optional[str]) - -slots.publication__abstract = Slot(uri=CORE.abstract, name="publication__abstract", curie=CORE.curie('abstract'), - model_uri=CORE.publication__abstract, domain=None, range=Optional[str]) - -slots.publication__combined_text = Slot(uri=CORE.combined_text, name="publication__combined_text", curie=CORE.curie('combined_text'), - model_uri=CORE.publication__combined_text, domain=None, range=Optional[str]) - -slots.publication__full_text = Slot(uri=CORE.full_text, name="publication__full_text", curie=CORE.curie('full_text'), - model_uri=CORE.publication__full_text, domain=None, range=Optional[str]) - -slots.annotatorResult__subject_text = Slot(uri=CORE.subject_text, name="annotatorResult__subject_text", curie=CORE.curie('subject_text'), - model_uri=CORE.annotatorResult__subject_text, domain=None, range=Optional[str]) - -slots.annotatorResult__object_id = Slot(uri=CORE.object_id, name="annotatorResult__object_id", curie=CORE.curie('object_id'), - model_uri=CORE.annotatorResult__object_id, domain=None, range=Optional[str]) - -slots.annotatorResult__object_text = Slot(uri=CORE.object_text, name="annotatorResult__object_text", curie=CORE.curie('object_text'), - model_uri=CORE.annotatorResult__object_text, domain=None, range=Optional[str]) \ No newline at end of file diff --git a/projects/core/docs/AnnotatorResult.md b/projects/core/docs/AnnotatorResult.md deleted file mode 100644 index 64a2e261b..000000000 --- a/projects/core/docs/AnnotatorResult.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Class: AnnotatorResult - - - - -URI: [core:AnnotatorResult](http://w3id.org/ontogpt/core/AnnotatorResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F])](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F]) - -## Attributes - - -### Own - - * [➞subject_text](annotatorResult__subject_text.md) 0..1 - * Range: [String](types/String.md) - * [➞object_id](annotatorResult__object_id.md) 0..1 - * Range: [String](types/String.md) - * [➞object_text](annotatorResult__object_text.md) 0..1 - * Range: [String](types/String.md) diff --git a/projects/core/docs/Any.md b/projects/core/docs/Any.md deleted file mode 100644 index 109c12ca2..000000000 --- a/projects/core/docs/Any.md +++ /dev/null @@ -1,25 +0,0 @@ - -# Class: Any - - - - -URI: [core:Any](http://w3id.org/ontogpt/core/Any) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult])](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult]) - -## Referenced by Class - - * **None** *[➞extracted_object](extractionResult__extracted_object.md)* 0..1 **[Any](Any.md)** - * **None** *[➞named_entities](extractionResult__named_entities.md)* 0..\* **[Any](Any.md)** - -## Attributes - - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | linkml:Any | - diff --git a/projects/core/docs/CompoundExpression.md b/projects/core/docs/CompoundExpression.md deleted file mode 100644 index 2f73ec8dd..000000000 --- a/projects/core/docs/CompoundExpression.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: CompoundExpression - - - - -URI: [core:CompoundExpression](http://w3id.org/ontogpt/core/CompoundExpression) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[CompoundExpression]^-[Triple])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[CompoundExpression]^-[Triple]) - -## Children - - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - -## Referenced by Class - - -## Attributes - diff --git a/projects/core/docs/ExtractionResult.md b/projects/core/docs/ExtractionResult.md deleted file mode 100644 index dcb9d4665..000000000 --- a/projects/core/docs/ExtractionResult.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Class: ExtractionResult - - -A result of extracting knowledge on text - -URI: [core:ExtractionResult](http://w3id.org/ontogpt/core/ExtractionResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]0..1 - * Range: [String](types/String.md) - * [➞input_title](extractionResult__input_title.md) 0..1 - * Range: [String](types/String.md) - * [➞input_text](extractionResult__input_text.md) 0..1 - * Range: [String](types/String.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) 0..1 - * Range: [String](types/String.md) - * [➞prompt](extractionResult__prompt.md) 0..1 - * Range: [String](types/String.md) - * [➞extracted_object](extractionResult__extracted_object.md) 0..1 - * Description: The complex objects extracted from the text - * Range: [Any](Any.md) - * [➞named_entities](extractionResult__named_entities.md) 0..\* - * Description: Named entities extracted from the text - * Range: [Any](Any.md) diff --git a/projects/core/docs/NamedEntity.md b/projects/core/docs/NamedEntity.md deleted file mode 100644 index 356e8abf6..000000000 --- a/projects/core/docs/NamedEntity.md +++ /dev/null @@ -1,33 +0,0 @@ - -# Class: NamedEntity - - - - -URI: [core:NamedEntity](http://w3id.org/ontogpt/core/NamedEntity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[RelationshipType],[Triple])](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[RelationshipType],[Triple]) - -## Children - - * [RelationshipType](RelationshipType.md) - -## Referenced by Class - - * **None** *[➞object](triple__object.md)* 0..1 **[NamedEntity](NamedEntity.md)** - * **None** *[➞object_qualifier](triple__object_qualifier.md)* 0..1 **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject](triple__subject.md)* 0..1 **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject_qualifier](triple__subject_qualifier.md)* 0..1 **[NamedEntity](NamedEntity.md)** - -## Attributes - - -### Own - - * [➞id](namedEntity__id.md) 1..1 - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) 0..1 - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/core/docs/NullDataOptions.md b/projects/core/docs/NullDataOptions.md deleted file mode 100644 index fae7f8f08..000000000 --- a/projects/core/docs/NullDataOptions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Enum: NullDataOptions - - - - -URI: [core:NullDataOptions](http://w3id.org/ontogpt/core/NullDataOptions) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | -| UNSPECIFIED_METHOD_OF_ADMINISTRATION | | NCIT:C149701 | | -| NOT_APPLICABLE | | NCIT:C18902 | {'aliases': ['not applicable', 'N/A']} | -| NOT_MENTIONED | | | | - diff --git a/projects/core/docs/Publication.md b/projects/core/docs/Publication.md deleted file mode 100644 index 0a70ed378..000000000 --- a/projects/core/docs/Publication.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Publication - - - - -URI: [core:Publication](http://w3id.org/ontogpt/core/Publication) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples])](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples]) - -## Referenced by Class - - * **None** *[➞publication](textWithTriples__publication.md)* 0..1 **[Publication](Publication.md)** - -## Attributes - - -### Own - - * [➞id](publication__id.md) 0..1 - * Description: The publication identifier - * Range: [String](types/String.md) - * [➞title](publication__title.md) 0..1 - * Description: The title of the publication - * Range: [String](types/String.md) - * [➞abstract](publication__abstract.md) 0..1 - * Description: The abstract of the publication - * Range: [String](types/String.md) - * [➞combined_text](publication__combined_text.md) 0..1 - * Range: [String](types/String.md) - * [➞full_text](publication__full_text.md) 0..1 - * Description: The full text of the publication - * Range: [String](types/String.md) diff --git a/projects/core/docs/RelationshipType.md b/projects/core/docs/RelationshipType.md deleted file mode 100644 index 83361ef96..000000000 --- a/projects/core/docs/RelationshipType.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: RelationshipType - - - - -URI: [core:RelationshipType](http://w3id.org/ontogpt/core/RelationshipType) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity]) - -## Identifier prefixes - - * RO - * biolink - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞predicate](triple__predicate.md)* 0..1 **[RelationshipType](RelationshipType.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) 1..1 - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) 0..1 - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/core/docs/TextWithTriples.md b/projects/core/docs/TextWithTriples.md deleted file mode 100644 index 4b9147f9d..000000000 --- a/projects/core/docs/TextWithTriples.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: TextWithTriples - - - - -URI: [core:TextWithTriples](http://w3id.org/ontogpt/core/TextWithTriples) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]0..1 - * Range: [Publication](Publication.md) - * [➞triples](textWithTriples__triples.md) 0..\* - * Range: [Triple](Triple.md) diff --git a/projects/core/docs/Triple.md b/projects/core/docs/Triple.md deleted file mode 100644 index 70645a204..000000000 --- a/projects/core/docs/Triple.md +++ /dev/null @@ -1,39 +0,0 @@ - -# Class: Triple - - -Abstract parent for Relation Extraction tasks - -URI: [core:Triple](http://w3id.org/ontogpt/core/Triple) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity][Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity][Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞triples](textWithTriples__triples.md)* 0..\* **[Triple](Triple.md)** - -## Attributes - - -### Own - - * [➞subject](triple__subject.md) 0..1 - * Range: [NamedEntity](NamedEntity.md) - * [➞predicate](triple__predicate.md) 0..1 - * Range: [RelationshipType](RelationshipType.md) - * [➞object](triple__object.md) 0..1 - * Range: [NamedEntity](NamedEntity.md) - * [➞qualifier](triple__qualifier.md) 0..1 - * Description: A qualifier for the statements, e.g. "NOT" for negation - * Range: [String](types/String.md) - * [➞subject_qualifier](triple__subject_qualifier.md) 0..1 - * Description: An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - * Range: [NamedEntity](NamedEntity.md) - * [➞object_qualifier](triple__object_qualifier.md) 0..1 - * Description: An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * Range: [NamedEntity](NamedEntity.md) diff --git a/projects/core/docs/annotatorResult__object_id.md b/projects/core/docs/annotatorResult__object_id.md deleted file mode 100644 index 43da8c67b..000000000 --- a/projects/core/docs/annotatorResult__object_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_id - - - - -URI: [core:annotatorResult__object_id](http://w3id.org/ontogpt/core/annotatorResult__object_id) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/core/docs/annotatorResult__object_text.md b/projects/core/docs/annotatorResult__object_text.md deleted file mode 100644 index fd16826f3..000000000 --- a/projects/core/docs/annotatorResult__object_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_text - - - - -URI: [core:annotatorResult__object_text](http://w3id.org/ontogpt/core/annotatorResult__object_text) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/core/docs/annotatorResult__subject_text.md b/projects/core/docs/annotatorResult__subject_text.md deleted file mode 100644 index 6f954fd44..000000000 --- a/projects/core/docs/annotatorResult__subject_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_text - - - - -URI: [core:annotatorResult__subject_text](http://w3id.org/ontogpt/core/annotatorResult__subject_text) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/core/docs/core.md b/projects/core/docs/core.md deleted file mode 100644 index 325d6b2ff..000000000 --- a/projects/core/docs/core.md +++ /dev/null @@ -1,103 +0,0 @@ - -# core - - -**metamodel version:** 1.7.0 - -**version:** None - - -Core upper level - - -### Classes - - * [AnnotatorResult](AnnotatorResult.md) - * [Any](Any.md) - * [CompoundExpression](CompoundExpression.md) - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - * [ExtractionResult](ExtractionResult.md) - A result of extracting knowledge on text - * [NamedEntity](NamedEntity.md) - * [RelationshipType](RelationshipType.md) - * [Publication](Publication.md) - * [TextWithTriples](TextWithTriples.md) - -### Mixins - - -### Slots - - * [➞object_id](annotatorResult__object_id.md) - * [➞object_text](annotatorResult__object_text.md) - * [➞subject_text](annotatorResult__subject_text.md) - * [➞extracted_object](extractionResult__extracted_object.md) - The complex objects extracted from the text - * [➞input_id](extractionResult__input_id.md) - * [➞input_text](extractionResult__input_text.md) - * [➞input_title](extractionResult__input_title.md) - * [➞named_entities](extractionResult__named_entities.md) - Named entities extracted from the text - * [➞prompt](extractionResult__prompt.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) - * [➞id](namedEntity__id.md) - A unique identifier for the named entity - * [➞label](namedEntity__label.md) - The label (name) of the named thing - * [➞abstract](publication__abstract.md) - The abstract of the publication - * [➞combined_text](publication__combined_text.md) - * [➞full_text](publication__full_text.md) - The full text of the publication - * [➞id](publication__id.md) - The publication identifier - * [➞title](publication__title.md) - The title of the publication - * [➞publication](textWithTriples__publication.md) - * [➞triples](textWithTriples__triples.md) - * [➞object](triple__object.md) - * [➞object_qualifier](triple__object_qualifier.md) - An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * [➞predicate](triple__predicate.md) - * [➞qualifier](triple__qualifier.md) - A qualifier for the statements, e.g. "NOT" for negation - * [➞subject](triple__subject.md) - * [➞subject_qualifier](triple__subject_qualifier.md) - An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -### Enums - - * [NullDataOptions](NullDataOptions.md) - -### Subsets - - -### Types - - -#### Built in - - * **Bool** - * **Curie** - * **Decimal** - * **ElementIdentifier** - * **NCName** - * **NodeIdentifier** - * **URI** - * **URIorCURIE** - * **XSDDate** - * **XSDDateTime** - * **XSDTime** - * **float** - * **int** - * **str** - -#### Defined - - * [Boolean](types/Boolean.md) (**Bool**) - A binary (true or false) value - * [Curie](types/Curie.md) (**Curie**) - a compact URI - * [Date](types/Date.md) (**XSDDate**) - a date (year, month and day) in an idealized calendar - * [DateOrDatetime](types/DateOrDatetime.md) (**str**) - Either a date or a datetime - * [Datetime](types/Datetime.md) (**XSDDateTime**) - The combination of a date and time - * [Decimal](types/Decimal.md) (**Decimal**) - A real number with arbitrary precision that conforms to the xsd:decimal specification - * [Double](types/Double.md) (**float**) - A real number that conforms to the xsd:double specification - * [Float](types/Float.md) (**float**) - A real number that conforms to the xsd:float specification - * [Integer](types/Integer.md) (**int**) - An integer - * [Jsonpath](types/Jsonpath.md) (**str**) - A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - * [Jsonpointer](types/Jsonpointer.md) (**str**) - A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - * [Ncname](types/Ncname.md) (**NCName**) - Prefix part of CURIE - * [Nodeidentifier](types/Nodeidentifier.md) (**NodeIdentifier**) - A URI, CURIE or BNODE that represents a node in a model. - * [Objectidentifier](types/Objectidentifier.md) (**ElementIdentifier**) - A URI or CURIE that represents an object in the model. - * [Sparqlpath](types/Sparqlpath.md) (**str**) - A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - * [String](types/String.md) (**str**) - A character string - * [Time](types/Time.md) (**XSDTime**) - A time object represents a (local) time of day, independent of any particular day - * [Uri](types/Uri.md) (**URI**) - a complete URI - * [Uriorcurie](types/Uriorcurie.md) (**URIorCURIE**) - a URI or a CURIE diff --git a/projects/core/docs/extractionResult__extracted_object.md b/projects/core/docs/extractionResult__extracted_object.md deleted file mode 100644 index 4df7da90c..000000000 --- a/projects/core/docs/extractionResult__extracted_object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: extracted_object - - -The complex objects extracted from the text - -URI: [core:extractionResult__extracted_object](http://w3id.org/ontogpt/core/extractionResult__extracted_object) - - -## Domain and Range - -None → 0..1 [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/core/docs/extractionResult__input_id.md b/projects/core/docs/extractionResult__input_id.md deleted file mode 100644 index 06b56bf83..000000000 --- a/projects/core/docs/extractionResult__input_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_id - - - - -URI: [core:extractionResult__input_id](http://w3id.org/ontogpt/core/extractionResult__input_id) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/core/docs/extractionResult__input_text.md b/projects/core/docs/extractionResult__input_text.md deleted file mode 100644 index 12569eae8..000000000 --- a/projects/core/docs/extractionResult__input_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_text - - - - -URI: [core:extractionResult__input_text](http://w3id.org/ontogpt/core/extractionResult__input_text) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/core/docs/extractionResult__input_title.md b/projects/core/docs/extractionResult__input_title.md deleted file mode 100644 index 07700cc95..000000000 --- a/projects/core/docs/extractionResult__input_title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_title - - - - -URI: [core:extractionResult__input_title](http://w3id.org/ontogpt/core/extractionResult__input_title) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/core/docs/extractionResult__named_entities.md b/projects/core/docs/extractionResult__named_entities.md deleted file mode 100644 index 830aeca3f..000000000 --- a/projects/core/docs/extractionResult__named_entities.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: named_entities - - -Named entities extracted from the text - -URI: [core:extractionResult__named_entities](http://w3id.org/ontogpt/core/extractionResult__named_entities) - - -## Domain and Range - -None → 0..\* [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/core/docs/extractionResult__prompt.md b/projects/core/docs/extractionResult__prompt.md deleted file mode 100644 index 04bf5d29b..000000000 --- a/projects/core/docs/extractionResult__prompt.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: prompt - - - - -URI: [core:extractionResult__prompt](http://w3id.org/ontogpt/core/extractionResult__prompt) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/core/docs/extractionResult__raw_completion_output.md b/projects/core/docs/extractionResult__raw_completion_output.md deleted file mode 100644 index 6f86f7266..000000000 --- a/projects/core/docs/extractionResult__raw_completion_output.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: raw_completion_output - - - - -URI: [core:extractionResult__raw_completion_output](http://w3id.org/ontogpt/core/extractionResult__raw_completion_output) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/core/docs/namedEntity__id.md b/projects/core/docs/namedEntity__id.md deleted file mode 100644 index c4285c132..000000000 --- a/projects/core/docs/namedEntity__id.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Slot: id - - -A unique identifier for the named entity - -URI: [core:namedEntity__id](http://w3id.org/ontogpt/core/namedEntity__id) - - -## Domain and Range - -None → 1..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [NamedEntity](NamedEntity.md) - * [RelationshipType](RelationshipType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | this is populated during the grounding and normalization step | - diff --git a/projects/core/docs/namedEntity__label.md b/projects/core/docs/namedEntity__label.md deleted file mode 100644 index 8310a070f..000000000 --- a/projects/core/docs/namedEntity__label.md +++ /dev/null @@ -1,31 +0,0 @@ - -# Slot: label - - -The label (name) of the named thing - -URI: [core:namedEntity__label](http://w3id.org/ontogpt/core/namedEntity__label) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [NamedEntity](NamedEntity.md) - * [RelationshipType](RelationshipType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Aliases:** | | name | -| **Mappings:** | | rdfs:label | - diff --git a/projects/core/docs/publication__abstract.md b/projects/core/docs/publication__abstract.md deleted file mode 100644 index 6345cf85f..000000000 --- a/projects/core/docs/publication__abstract.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: abstract - - -The abstract of the publication - -URI: [core:publication__abstract](http://w3id.org/ontogpt/core/publication__abstract) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/core/docs/publication__combined_text.md b/projects/core/docs/publication__combined_text.md deleted file mode 100644 index fc0082cbe..000000000 --- a/projects/core/docs/publication__combined_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: combined_text - - - - -URI: [core:publication__combined_text](http://w3id.org/ontogpt/core/publication__combined_text) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/core/docs/publication__full_text.md b/projects/core/docs/publication__full_text.md deleted file mode 100644 index 60df5cc89..000000000 --- a/projects/core/docs/publication__full_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: full_text - - -The full text of the publication - -URI: [core:publication__full_text](http://w3id.org/ontogpt/core/publication__full_text) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/core/docs/publication__id.md b/projects/core/docs/publication__id.md deleted file mode 100644 index 9cc7a1bec..000000000 --- a/projects/core/docs/publication__id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: id - - -The publication identifier - -URI: [core:publication__id](http://w3id.org/ontogpt/core/publication__id) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/core/docs/publication__title.md b/projects/core/docs/publication__title.md deleted file mode 100644 index 01cf66963..000000000 --- a/projects/core/docs/publication__title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: title - - -The title of the publication - -URI: [core:publication__title](http://w3id.org/ontogpt/core/publication__title) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/core/docs/textWithTriples__publication.md b/projects/core/docs/textWithTriples__publication.md deleted file mode 100644 index 3d3b57bd1..000000000 --- a/projects/core/docs/textWithTriples__publication.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: publication - - - - -URI: [core:textWithTriples__publication](http://w3id.org/ontogpt/core/textWithTriples__publication) - - -## Domain and Range - -None → 0..1 [Publication](Publication.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/core/docs/textWithTriples__triples.md b/projects/core/docs/textWithTriples__triples.md deleted file mode 100644 index bf9ab7a93..000000000 --- a/projects/core/docs/textWithTriples__triples.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: triples - - - - -URI: [core:textWithTriples__triples](http://w3id.org/ontogpt/core/textWithTriples__triples) - - -## Domain and Range - -None → 0..\* [Triple](Triple.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/core/docs/triple__object.md b/projects/core/docs/triple__object.md deleted file mode 100644 index 906a3f8c9..000000000 --- a/projects/core/docs/triple__object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object - - - - -URI: [core:triple__object](http://w3id.org/ontogpt/core/triple__object) - - -## Domain and Range - -None → 0..1 [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/core/docs/triple__object_qualifier.md b/projects/core/docs/triple__object_qualifier.md deleted file mode 100644 index e599434ac..000000000 --- a/projects/core/docs/triple__object_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_qualifier - - -An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - -URI: [core:triple__object_qualifier](http://w3id.org/ontogpt/core/triple__object_qualifier) - - -## Domain and Range - -None → 0..1 [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/core/docs/triple__predicate.md b/projects/core/docs/triple__predicate.md deleted file mode 100644 index 2a475a200..000000000 --- a/projects/core/docs/triple__predicate.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: predicate - - - - -URI: [core:triple__predicate](http://w3id.org/ontogpt/core/triple__predicate) - - -## Domain and Range - -None → 0..1 [RelationshipType](RelationshipType.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/core/docs/triple__qualifier.md b/projects/core/docs/triple__qualifier.md deleted file mode 100644 index 5488b6a06..000000000 --- a/projects/core/docs/triple__qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: qualifier - - -A qualifier for the statements, e.g. "NOT" for negation - -URI: [core:triple__qualifier](http://w3id.org/ontogpt/core/triple__qualifier) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/core/docs/triple__subject.md b/projects/core/docs/triple__subject.md deleted file mode 100644 index d054483fb..000000000 --- a/projects/core/docs/triple__subject.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject - - - - -URI: [core:triple__subject](http://w3id.org/ontogpt/core/triple__subject) - - -## Domain and Range - -None → 0..1 [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/core/docs/triple__subject_qualifier.md b/projects/core/docs/triple__subject_qualifier.md deleted file mode 100644 index 628145a99..000000000 --- a/projects/core/docs/triple__subject_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_qualifier - - -An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -URI: [core:triple__subject_qualifier](http://w3id.org/ontogpt/core/triple__subject_qualifier) - - -## Domain and Range - -None → 0..1 [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/core/docs/types/Boolean.md b/projects/core/docs/types/Boolean.md deleted file mode 100644 index dc83a9c6e..000000000 --- a/projects/core/docs/types/Boolean.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: boolean - - -A binary (true or false) value - -URI: [linkml:Boolean](https://w3id.org/linkml/Boolean) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Bool** | -| Representation | | bool | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Boolean | - diff --git a/projects/core/docs/types/Curie.md b/projects/core/docs/types/Curie.md deleted file mode 100644 index c1803f93f..000000000 --- a/projects/core/docs/types/Curie.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: curie - - -a compact URI - -URI: [linkml:Curie](https://w3id.org/linkml/Curie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Curie** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations this MUST be expanded to a URI | -| | | in non-RDF serializations MAY be serialized as the compact representation | - diff --git a/projects/core/docs/types/Date.md b/projects/core/docs/types/Date.md deleted file mode 100644 index 06948af97..000000000 --- a/projects/core/docs/types/Date.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: date - - -a date (year, month and day) in an idealized calendar - -URI: [linkml:Date](https://w3id.org/linkml/Date) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDate** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Date | - diff --git a/projects/core/docs/types/DateOrDatetime.md b/projects/core/docs/types/DateOrDatetime.md deleted file mode 100644 index ef983898d..000000000 --- a/projects/core/docs/types/DateOrDatetime.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: date_or_datetime - - -Either a date or a datetime - -URI: [linkml:DateOrDatetime](https://w3id.org/linkml/DateOrDatetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/core/docs/types/Datetime.md b/projects/core/docs/types/Datetime.md deleted file mode 100644 index 9510454a8..000000000 --- a/projects/core/docs/types/Datetime.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: datetime - - -The combination of a date and time - -URI: [linkml:Datetime](https://w3id.org/linkml/Datetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDateTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:DateTime | - diff --git a/projects/core/docs/types/Decimal.md b/projects/core/docs/types/Decimal.md deleted file mode 100644 index a7ba14a5d..000000000 --- a/projects/core/docs/types/Decimal.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: decimal - - -A real number with arbitrary precision that conforms to the xsd:decimal specification - -URI: [linkml:Decimal](https://w3id.org/linkml/Decimal) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Decimal** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Broad Mappings:** | | schema:Number | - diff --git a/projects/core/docs/types/Double.md b/projects/core/docs/types/Double.md deleted file mode 100644 index cfe6d71e2..000000000 --- a/projects/core/docs/types/Double.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: double - - -A real number that conforms to the xsd:double specification - -URI: [linkml:Double](https://w3id.org/linkml/Double) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Close Mappings:** | | schema:Float | - diff --git a/projects/core/docs/types/Float.md b/projects/core/docs/types/Float.md deleted file mode 100644 index 7b303f96f..000000000 --- a/projects/core/docs/types/Float.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: float - - -A real number that conforms to the xsd:float specification - -URI: [linkml:Float](https://w3id.org/linkml/Float) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Float | - diff --git a/projects/core/docs/types/Integer.md b/projects/core/docs/types/Integer.md deleted file mode 100644 index 3cfcc66d9..000000000 --- a/projects/core/docs/types/Integer.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: integer - - -An integer - -URI: [linkml:Integer](https://w3id.org/linkml/Integer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **int** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Integer | - diff --git a/projects/core/docs/types/Jsonpath.md b/projects/core/docs/types/Jsonpath.md deleted file mode 100644 index a03a58e67..000000000 --- a/projects/core/docs/types/Jsonpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpath - - -A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpath](https://w3id.org/linkml/Jsonpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/core/docs/types/Jsonpointer.md b/projects/core/docs/types/Jsonpointer.md deleted file mode 100644 index a0e1ac492..000000000 --- a/projects/core/docs/types/Jsonpointer.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpointer - - -A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpointer](https://w3id.org/linkml/Jsonpointer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/core/docs/types/Ncname.md b/projects/core/docs/types/Ncname.md deleted file mode 100644 index 710b0b04a..000000000 --- a/projects/core/docs/types/Ncname.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: ncname - - -Prefix part of CURIE - -URI: [linkml:Ncname](https://w3id.org/linkml/Ncname) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NCName** | -| Representation | | str | diff --git a/projects/core/docs/types/Nodeidentifier.md b/projects/core/docs/types/Nodeidentifier.md deleted file mode 100644 index f0097cdf4..000000000 --- a/projects/core/docs/types/Nodeidentifier.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: nodeidentifier - - -A URI, CURIE or BNODE that represents a node in a model. - -URI: [linkml:Nodeidentifier](https://w3id.org/linkml/Nodeidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NodeIdentifier** | -| Representation | | str | diff --git a/projects/core/docs/types/Objectidentifier.md b/projects/core/docs/types/Objectidentifier.md deleted file mode 100644 index 454ba6be6..000000000 --- a/projects/core/docs/types/Objectidentifier.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: objectidentifier - - -A URI or CURIE that represents an object in the model. - -URI: [linkml:Objectidentifier](https://w3id.org/linkml/Objectidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **ElementIdentifier** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | Used for inheritance and type checking | - diff --git a/projects/core/docs/types/Sparqlpath.md b/projects/core/docs/types/Sparqlpath.md deleted file mode 100644 index fd99a927e..000000000 --- a/projects/core/docs/types/Sparqlpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: sparqlpath - - -A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - -URI: [linkml:Sparqlpath](https://w3id.org/linkml/Sparqlpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/core/docs/types/String.md b/projects/core/docs/types/String.md deleted file mode 100644 index 6e61d7081..000000000 --- a/projects/core/docs/types/String.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: string - - -A character string - -URI: [linkml:String](https://w3id.org/linkml/String) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Text | - diff --git a/projects/core/docs/types/Time.md b/projects/core/docs/types/Time.md deleted file mode 100644 index 2b8652bcd..000000000 --- a/projects/core/docs/types/Time.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: time - - -A time object represents a (local) time of day, independent of any particular day - -URI: [linkml:Time](https://w3id.org/linkml/Time) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Time | - diff --git a/projects/core/docs/types/Uri.md b/projects/core/docs/types/Uri.md deleted file mode 100644 index 343807a5e..000000000 --- a/projects/core/docs/types/Uri.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: uri - - -a complete URI - -URI: [linkml:Uri](https://w3id.org/linkml/Uri) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URI** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node | -| **Close Mappings:** | | schema:URL | - diff --git a/projects/core/docs/types/Uriorcurie.md b/projects/core/docs/types/Uriorcurie.md deleted file mode 100644 index 2f7b65087..000000000 --- a/projects/core/docs/types/Uriorcurie.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: uriorcurie - - -a URI or a CURIE - -URI: [linkml:Uriorcurie](https://w3id.org/linkml/Uriorcurie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URIorCURIE** | -| Representation | | str | diff --git a/projects/core/excel/core.xlsx b/projects/core/excel/core.xlsx deleted file mode 100644 index 29894fd7a..000000000 Binary files a/projects/core/excel/core.xlsx and /dev/null differ diff --git a/projects/core/graphql/core.graphql b/projects/core/graphql/core.graphql deleted file mode 100644 index 62c0b9d87..000000000 --- a/projects/core/graphql/core.graphql +++ /dev/null @@ -1,63 +0,0 @@ -type AnnotatorResult - { - subjectText: String - objectId: String - objectText: String - } - -type Any - { - } - -interface CompoundExpression - { - } - -type ExtractionResult - { - inputId: String - inputTitle: String - inputText: String - rawCompletionOutput: String - prompt: String - extractedObject: Any - namedEntities: [Any] - } - -interface NamedEntity - { - id: String! - label: String - } - -type Publication - { - id: String - title: String - abstract: String - combinedText: String - fullText: String - } - -type RelationshipType - { - id: String! - label: String - } - -type TextWithTriples - { - publication: Publication - triples: [Triple] - } - -interface Triple - { - subject: NamedEntity - predicate: RelationshipType - object: NamedEntity - qualifier: String - subjectQualifier: NamedEntity - objectQualifier: NamedEntity - } - diff --git a/projects/core/jsonld/core.context.jsonld b/projects/core/jsonld/core.context.jsonld deleted file mode 100644 index 051442c6c..000000000 --- a/projects/core/jsonld/core.context.jsonld +++ /dev/null @@ -1,56 +0,0 @@ -{ - "comments": { - "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2023-08-07T10:52:04", - "source": "core.yaml" - }, - "@context": { - "NCIT": { - "@id": "http://purl.obolibrary.org/obo/NCIT_", - "@prefix": true - }, - "RO": { - "@id": "http://purl.obolibrary.org/obo/RO_", - "@prefix": true - }, - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "@vocab": "http://w3id.org/ontogpt/core/", - "extracted_object": { - "@type": "@id" - }, - "named_entities": { - "@type": "@id" - }, - "id": "@id", - "label": { - "@id": "rdfs:label" - }, - "publication": { - "@type": "@id" - }, - "triples": { - "@type": "@id" - }, - "object": { - "@type": "@id" - }, - "object_qualifier": { - "@type": "@id" - }, - "predicate": { - "@type": "@id" - }, - "subject": { - "@type": "@id" - }, - "subject_qualifier": { - "@type": "@id" - }, - "Any": { - "@id": "linkml:Any" - } - } -} diff --git a/projects/core/jsonld/core.jsonld b/projects/core/jsonld/core.jsonld deleted file mode 100644 index d0afe9a72..000000000 --- a/projects/core/jsonld/core.jsonld +++ /dev/null @@ -1,977 +0,0 @@ -{ - "name": "core", - "description": "Core upper level", - "title": "AI core Template", - "id": "http://w3id.org/ontogpt/core", - "imports": [ - "linkml:types" - ], - "license": "https://creativecommons.org/publicdomain/zero/1.0/", - "prefixes": [ - { - "prefix_prefix": "linkml", - "prefix_reference": "https://w3id.org/linkml/" - }, - { - "prefix_prefix": "core", - "prefix_reference": "http://w3id.org/ontogpt/core/" - }, - { - "prefix_prefix": "NCIT", - "prefix_reference": "http://purl.obolibrary.org/obo/NCIT_" - }, - { - "prefix_prefix": "RO", - "prefix_reference": "http://purl.obolibrary.org/obo/RO_" - } - ], - "default_prefix": "core", - "default_range": "string", - "types": [ - { - "name": "string", - "definition_uri": "https://w3id.org/linkml/String", - "description": "A character string", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Text" - ], - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "@type": "TypeDefinition" - }, - { - "name": "integer", - "definition_uri": "https://w3id.org/linkml/Integer", - "description": "An integer", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Integer" - ], - "base": "int", - "uri": "http://www.w3.org/2001/XMLSchema#integer", - "@type": "TypeDefinition" - }, - { - "name": "boolean", - "definition_uri": "https://w3id.org/linkml/Boolean", - "description": "A binary (true or false) value", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Boolean" - ], - "base": "Bool", - "uri": "http://www.w3.org/2001/XMLSchema#boolean", - "repr": "bool", - "@type": "TypeDefinition" - }, - { - "name": "float", - "definition_uri": "https://w3id.org/linkml/Float", - "description": "A real number that conforms to the xsd:float specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#float", - "@type": "TypeDefinition" - }, - { - "name": "double", - "definition_uri": "https://w3id.org/linkml/Double", - "description": "A real number that conforms to the xsd:double specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#double", - "@type": "TypeDefinition" - }, - { - "name": "decimal", - "definition_uri": "https://w3id.org/linkml/Decimal", - "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "broad_mappings": [ - "schema:Number" - ], - "base": "Decimal", - "uri": "http://www.w3.org/2001/XMLSchema#decimal", - "@type": "TypeDefinition" - }, - { - "name": "time", - "definition_uri": "https://w3id.org/linkml/Time", - "description": "A time object represents a (local) time of day, independent of any particular day", - "notes": [ - "URI is dateTime because OWL reasoners do not work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Time" - ], - "base": "XSDTime", - "uri": "http://www.w3.org/2001/XMLSchema#time", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date", - "definition_uri": "https://w3id.org/linkml/Date", - "description": "a date (year, month and day) in an idealized calendar", - "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Date" - ], - "base": "XSDDate", - "uri": "http://www.w3.org/2001/XMLSchema#date", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "datetime", - "definition_uri": "https://w3id.org/linkml/Datetime", - "description": "The combination of a date and time", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:DateTime" - ], - "base": "XSDDateTime", - "uri": "http://www.w3.org/2001/XMLSchema#dateTime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date_or_datetime", - "definition_uri": "https://w3id.org/linkml/DateOrDatetime", - "description": "Either a date or a datetime", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "https://w3id.org/linkml/DateOrDatetime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uriorcurie", - "definition_uri": "https://w3id.org/linkml/Uriorcurie", - "description": "a URI or a CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "URIorCURIE", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "curie", - "definition_uri": "https://w3id.org/linkml/Curie", - "conforms_to": "https://www.w3.org/TR/curie/", - "description": "a compact URI", - "comments": [ - "in RDF serializations this MUST be expanded to a URI", - "in non-RDF serializations MAY be serialized as the compact representation" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "Curie", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uri", - "definition_uri": "https://w3id.org/linkml/Uri", - "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", - "description": "a complete URI", - "comments": [ - "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:URL" - ], - "base": "URI", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "ncname", - "definition_uri": "https://w3id.org/linkml/Ncname", - "description": "Prefix part of CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NCName", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "objectidentifier", - "definition_uri": "https://w3id.org/linkml/Objectidentifier", - "description": "A URI or CURIE that represents an object in the model.", - "comments": [ - "Used for inheritance and type checking" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "ElementIdentifier", - "uri": "http://www.w3.org/ns/shex#iri", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "nodeidentifier", - "definition_uri": "https://w3id.org/linkml/Nodeidentifier", - "description": "A URI, CURIE or BNODE that represents a node in a model.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NodeIdentifier", - "uri": "http://www.w3.org/ns/shex#nonLiteral", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpointer", - "definition_uri": "https://w3id.org/linkml/Jsonpointer", - "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901", - "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpath", - "definition_uri": "https://w3id.org/linkml/Jsonpath", - "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html", - "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "sparqlpath", - "definition_uri": "https://w3id.org/linkml/Sparqlpath", - "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths", - "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - } - ], - "enums": [ - { - "name": "NullDataOptions", - "definition_uri": "http://w3id.org/ontogpt/core/NullDataOptions", - "from_schema": "http://w3id.org/ontogpt/core", - "permissible_values": [ - { - "text": "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "meaning": "NCIT:C149701" - }, - { - "text": "NOT_APPLICABLE", - "meaning": "NCIT:C18902", - "aliases": [ - "not applicable", - "N/A" - ] - }, - { - "text": "NOT_MENTIONED" - } - ] - } - ], - "slots": [ - { - "name": "extractionResult__input_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_id", - "alias": "input_id", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_title", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_title", - "alias": "input_title", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_text", - "alias": "input_text", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__raw_completion_output", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/raw_completion_output", - "alias": "raw_completion_output", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__prompt", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/prompt", - "alias": "prompt", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__extracted_object", - "description": "The complex objects extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/extracted_object", - "alias": "extracted_object", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__named_entities", - "description": "Named entities extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/named_entities", - "multivalued": true, - "alias": "named_entities", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "identifier": true, - "alias": "id", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "required": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "from_schema": "http://w3id.org/ontogpt/core", - "aliases": [ - "name" - ], - "mappings": [ - "http://example.org/UNKNOWN/rdfs/label" - ], - "slot_uri": "http://example.org/UNKNOWN/rdfs/label", - "alias": "label", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject", - "alias": "subject", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__predicate", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/predicate", - "alias": "predicate", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "triple__object", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object", - "alias": "object", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/qualifier", - "alias": "qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_qualifier", - "alias": "subject_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_qualifier", - "alias": "object_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/publication", - "alias": "publication", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__triples", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/triples", - "multivalued": true, - "alias": "triples", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "publication__id", - "description": "The publication identifier", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "alias": "id", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__title", - "description": "The title of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/title", - "alias": "title", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__abstract", - "description": "The abstract of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/abstract", - "alias": "abstract", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__combined_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/combined_text", - "alias": "combined_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__full_text", - "description": "The full text of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/full_text", - "alias": "full_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__subject_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_text", - "alias": "subject_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_id", - "alias": "object_id", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_text", - "alias": "object_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - } - ], - "classes": [ - { - "name": "Any", - "definition_uri": "http://w3id.org/ontogpt/core/Any", - "from_schema": "http://w3id.org/ontogpt/core", - "mappings": [ - "linkml:Any" - ], - "slot_usage": {}, - "class_uri": "https://w3id.org/linkml/Any", - "@type": "ClassDefinition" - }, - { - "name": "ExtractionResult", - "definition_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "description": "A result of extracting knowledge on text", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "extractionResult__input_id", - "extractionResult__input_title", - "extractionResult__input_text", - "extractionResult__raw_completion_output", - "extractionResult__prompt", - "extractionResult__extracted_object", - "extractionResult__named_entities" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "input_id", - "@type": "SlotDefinition" - }, - { - "name": "input_title", - "@type": "SlotDefinition" - }, - { - "name": "input_text", - "@type": "SlotDefinition" - }, - { - "name": "raw_completion_output", - "@type": "SlotDefinition" - }, - { - "name": "prompt", - "@type": "SlotDefinition" - }, - { - "name": "extracted_object", - "description": "The complex objects extracted from the text", - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "named_entities", - "description": "Named entities extracted from the text", - "multivalued": true, - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "@type": "ClassDefinition" - }, - { - "name": "NamedEntity", - "definition_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "identifier": true, - "@type": "SlotDefinition" - }, - { - "name": "label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "aliases": [ - "name" - ], - "slot_uri": "rdfs:label", - "range": "string", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "@type": "ClassDefinition" - }, - { - "name": "CompoundExpression", - "definition_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "@type": "ClassDefinition" - }, - { - "name": "Triple", - "definition_uri": "http://w3id.org/ontogpt/core/Triple", - "description": "Abstract parent for Relation Extraction tasks", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "CompoundExpression", - "abstract": true, - "slots": [ - "triple__subject", - "triple__predicate", - "triple__object", - "triple__qualifier", - "triple__subject_qualifier", - "triple__object_qualifier" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "predicate", - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "object", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Triple", - "@type": "ClassDefinition" - }, - { - "name": "TextWithTriples", - "definition_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "textWithTriples__publication", - "textWithTriples__triples" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "triples", - "multivalued": true, - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "@type": "ClassDefinition" - }, - { - "name": "RelationshipType", - "id_prefixes": [ - "RO", - "biolink" - ], - "definition_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "@type": "ClassDefinition" - }, - { - "name": "Publication", - "definition_uri": "http://w3id.org/ontogpt/core/Publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "publication__id", - "publication__title", - "publication__abstract", - "publication__combined_text", - "publication__full_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "description": "The publication identifier", - "@type": "SlotDefinition" - }, - { - "name": "title", - "description": "The title of the publication", - "@type": "SlotDefinition" - }, - { - "name": "abstract", - "description": "The abstract of the publication", - "@type": "SlotDefinition" - }, - { - "name": "combined_text", - "@type": "SlotDefinition" - }, - { - "name": "full_text", - "description": "The full text of the publication", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Publication", - "@type": "ClassDefinition" - }, - { - "name": "AnnotatorResult", - "definition_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "annotatorResult__subject_text", - "annotatorResult__object_id", - "annotatorResult__object_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject_text", - "@type": "SlotDefinition" - }, - { - "name": "object_id", - "@type": "SlotDefinition" - }, - { - "name": "object_text", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "@type": "ClassDefinition" - } - ], - "metamodel_version": "1.7.0", - "source_file": "core.yaml", - "source_file_date": "2023-06-17T15:11:19", - "source_file_size": 3446, - "generation_date": "2023-08-07T10:52:05", - "@type": "SchemaDefinition", - "@context": [ - "projects/core/jsonld/core.context.jsonld", - "https://w3id.org/linkml/types.context.jsonld", - { - "@base": "http://w3id.org/ontogpt/core/" - } - ] -} diff --git a/projects/core/jsonschema/core.schema.json b/projects/core/jsonschema/core.schema.json deleted file mode 100644 index a51b370dd..000000000 --- a/projects/core/jsonschema/core.schema.json +++ /dev/null @@ -1,141 +0,0 @@ -{ - "$defs": { - "AnnotatorResult": { - "additionalProperties": false, - "description": "", - "properties": { - "object_id": { - "type": "string" - }, - "object_text": { - "type": "string" - }, - "subject_text": { - "type": "string" - } - }, - "title": "AnnotatorResult", - "type": "object" - }, - "Any": { - "additionalProperties": true, - "description": "", - "title": "Any", - "type": "object" - }, - "ExtractionResult": { - "additionalProperties": false, - "description": "A result of extracting knowledge on text", - "properties": { - "extracted_object": { - "$ref": "#/$defs/Any", - "description": "The complex objects extracted from the text" - }, - "input_id": { - "type": "string" - }, - "input_text": { - "type": "string" - }, - "input_title": { - "type": "string" - }, - "named_entities": { - "description": "Named entities extracted from the text", - "items": { - "$ref": "#/$defs/Any" - }, - "type": "array" - }, - "prompt": { - "type": "string" - }, - "raw_completion_output": { - "type": "string" - } - }, - "title": "ExtractionResult", - "type": "object" - }, - "NullDataOptions": { - "description": "", - "enum": [ - "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "NOT_APPLICABLE", - "NOT_MENTIONED" - ], - "title": "NullDataOptions", - "type": "string" - }, - "Publication": { - "additionalProperties": false, - "description": "", - "properties": { - "abstract": { - "description": "The abstract of the publication", - "type": "string" - }, - "combined_text": { - "type": "string" - }, - "full_text": { - "description": "The full text of the publication", - "type": "string" - }, - "id": { - "description": "The publication identifier", - "type": "string" - }, - "title": { - "description": "The title of the publication", - "type": "string" - } - }, - "title": "Publication", - "type": "object" - }, - "RelationshipType": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "RelationshipType", - "type": "object" - }, - "TextWithTriples": { - "additionalProperties": false, - "description": "", - "properties": { - "publication": { - "$ref": "#/$defs/Publication" - }, - "triples": { - "items": { - "$ref": "#/$defs/Triple" - }, - "type": "array" - } - }, - "title": "TextWithTriples", - "type": "object" - } - }, - "$id": "http://w3id.org/ontogpt/core", - "$schema": "http://json-schema.org/draft-07/schema#", - "additionalProperties": true, - "metamodel_version": "1.7.0", - "title": "core", - "type": "object", - "version": null -} \ No newline at end of file diff --git a/projects/core/owl/core.owl.ttl b/projects/core/owl/core.owl.ttl deleted file mode 100644 index e9faa8a12..000000000 --- a/projects/core/owl/core.owl.ttl +++ /dev/null @@ -1,353 +0,0 @@ -@prefix IAO: . -@prefix NCIT: . -@prefix core: . -@prefix linkml: . -@prefix owl: . -@prefix rdf: . -@prefix rdfs: . -@prefix skos: . -@prefix xsd: . - - a owl:Ontology ; - rdfs:label "core" ; - IAO:0000700 core:AnnotatorResult, - core:Any, - core:CompoundExpression, - core:ExtractionResult, - core:NamedEntity, - core:Publication, - core:TextWithTriples ; - linkml:classes "{'Any': ClassDefinition(name='Any', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Any', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=['linkml:Any'], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='linkml:Any', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ExtractionResult': ClassDefinition(name='ExtractionResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/ExtractionResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A result of extracting knowledge on text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['extractionResult__input_id', 'extractionResult__input_title', 'extractionResult__input_text', 'extractionResult__raw_completion_output', 'extractionResult__prompt', 'extractionResult__extracted_object', 'extractionResult__named_entities'], slot_usage={}, attributes={'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:ExtractionResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'NamedEntity': ClassDefinition(name='NamedEntity', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NamedEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:NamedEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'CompoundExpression': ClassDefinition(name='CompoundExpression', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/CompoundExpression', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='core:CompoundExpression', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Triple': ClassDefinition(name='Triple', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Triple', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Abstract parent for Relation Extraction tasks', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['triple__subject', 'triple__predicate', 'triple__object', 'triple__qualifier', 'triple__subject_qualifier', 'triple__object_qualifier'], slot_usage={}, attributes={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Triple', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'TextWithTriples': ClassDefinition(name='TextWithTriples', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/TextWithTriples', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['textWithTriples__publication', 'textWithTriples__triples'], slot_usage={}, attributes={'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:TextWithTriples', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'RelationshipType': ClassDefinition(name='RelationshipType', id_prefixes=['RO', 'biolink'], definition_uri='http://w3id.org/ontogpt/core/RelationshipType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='core:RelationshipType', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Publication': ClassDefinition(name='Publication', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Publication', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['publication__id', 'publication__title', 'publication__abstract', 'publication__combined_text', 'publication__full_text'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Publication', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'AnnotatorResult': ClassDefinition(name='AnnotatorResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/AnnotatorResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['annotatorResult__subject_text', 'annotatorResult__object_id', 'annotatorResult__object_text'], slot_usage={}, attributes={'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:AnnotatorResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={})}" ; - linkml:enums "{'NullDataOptions': EnumDefinition(name='NullDataOptions', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NullDataOptions', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'UNSPECIFIED_METHOD_OF_ADMINISTRATION': PermissibleValue(text='UNSPECIFIED_METHOD_OF_ADMINISTRATION', description=None, meaning='NCIT:C149701', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_APPLICABLE': PermissibleValue(text='NOT_APPLICABLE', description=None, meaning='NCIT:C18902', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['not applicable', 'N/A'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_MENTIONED': PermissibleValue(text='NOT_MENTIONED', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[])}" ; - linkml:id "http://w3id.org/ontogpt/core" ; - linkml:imports "linkml:types" ; - linkml:types "{'string': TypeDefinition(name='string', id_prefixes=[], definition_uri='https://w3id.org/linkml/String', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A character string', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Text'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'integer': TypeDefinition(name='integer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Integer', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An integer', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Integer'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='int', uri='xsd:integer', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'boolean': TypeDefinition(name='boolean', id_prefixes=[], definition_uri='https://w3id.org/linkml/Boolean', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A binary (true or false) value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Boolean'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Bool', uri='xsd:boolean', repr='bool', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'float': TypeDefinition(name='float', id_prefixes=[], definition_uri='https://w3id.org/linkml/Float', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:float specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Float'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:float', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'double': TypeDefinition(name='double', id_prefixes=[], definition_uri='https://w3id.org/linkml/Double', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:double specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:Float'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:double', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'decimal': TypeDefinition(name='decimal', id_prefixes=[], definition_uri='https://w3id.org/linkml/Decimal', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number with arbitrary precision that conforms to the xsd:decimal specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=['schema:Number'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Decimal', uri='xsd:decimal', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'time': TypeDefinition(name='time', id_prefixes=[], definition_uri='https://w3id.org/linkml/Time', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A time object represents a (local) time of day, independent of any particular day', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=['URI is dateTime because OWL reasoners do not work with straight date or time'], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Time'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDTime', uri='xsd:time', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date': TypeDefinition(name='date', id_prefixes=[], definition_uri='https://w3id.org/linkml/Date', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a date (year, month and day) in an idealized calendar', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[\"URI is dateTime because OWL reasoners don't work with straight date or time\"], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Date'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDate', uri='xsd:date', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'datetime': TypeDefinition(name='datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/Datetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The combination of a date and time', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:DateTime'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDateTime', uri='xsd:dateTime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date_or_datetime': TypeDefinition(name='date_or_datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/DateOrDatetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Either a date or a datetime', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='linkml:DateOrDatetime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uriorcurie': TypeDefinition(name='uriorcurie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uriorcurie', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a URI or a CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URIorCURIE', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'curie': TypeDefinition(name='curie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Curie', local_names={}, conforms_to='https://www.w3.org/TR/curie/', implements=[], extensions={}, annotations={}, description='a compact URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations this MUST be expanded to a URI', 'in non-RDF serializations MAY be serialized as the compact representation'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Curie', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uri': TypeDefinition(name='uri', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uri', local_names={}, conforms_to='https://www.ietf.org/rfc/rfc3987.txt', implements=[], extensions={}, annotations={}, description='a complete URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:URL'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URI', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ncname': TypeDefinition(name='ncname', id_prefixes=[], definition_uri='https://w3id.org/linkml/Ncname', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Prefix part of CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NCName', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'objectidentifier': TypeDefinition(name='objectidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Objectidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI or CURIE that represents an object in the model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['Used for inheritance and type checking'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='ElementIdentifier', uri='shex:iri', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'nodeidentifier': TypeDefinition(name='nodeidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Nodeidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI, CURIE or BNODE that represents a node in a model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NodeIdentifier', uri='shex:nonLiteral', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpointer': TypeDefinition(name='jsonpointer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpointer', local_names={}, conforms_to='https://datatracker.ietf.org/doc/html/rfc6901', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpath': TypeDefinition(name='jsonpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpath', local_names={}, conforms_to='https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sparqlpath': TypeDefinition(name='sparqlpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Sparqlpath', local_names={}, conforms_to='https://www.w3.org/TR/sparql11-query/#propertypaths', implements=[], extensions={}, annotations={}, description='A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:SubsetDefinition a owl:Class ; - rdfs:label "subset_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" . - -linkml:TypeDefinition a owl:Class ; - rdfs:label "type_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" ; - linkml:mixins "type_expression" . - -linkml:topValue a owl:DatatypeProperty ; - rdfs:label "value" . - -core:AnnotatorResult a owl:Class, - linkml:ClassDefinition ; - rdfs:label "AnnotatorResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty core:object_text ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty core:subject_text ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty core:object_id ] ; - linkml:attributes "{'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -core:ExtractionResult a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ExtractionResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty core:prompt ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty core:input_title ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty core:input_text ], - [ a owl:Restriction ; - owl:allValuesFrom core:Any ; - owl:onProperty core:named_entities ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty core:input_id ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty core:raw_completion_output ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass core:Any ; - owl:onProperty core:extracted_object ] ; - skos:definition "A result of extracting knowledge on text" ; - linkml:attributes "{'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -core:TextWithTriples a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TextWithTriples" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom core:Triple ; - owl:onProperty core:triples ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass core:Publication ; - owl:onProperty core:publication ] ; - linkml:attributes "{'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -core:abstract a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "abstract" ; - rdfs:range linkml:String ; - skos:definition "The abstract of the publication" . - -core:combined_text a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "combined_text" ; - rdfs:range linkml:String . - -core:extracted_object a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "extracted_object" ; - rdfs:range core:Any ; - skos:definition "The complex objects extracted from the text" . - -core:full_text a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "full_text" ; - rdfs:range linkml:String ; - skos:definition "The full text of the publication" . - -core:input_id a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_id" ; - rdfs:range linkml:String . - -core:input_text a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_text" ; - rdfs:range linkml:String . - -core:input_title a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_title" ; - rdfs:range linkml:String . - -core:named_entities a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "named_entities" ; - rdfs:range core:Any ; - skos:definition "Named entities extracted from the text" . - -core:object a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object" ; - rdfs:range core:NamedEntity . - -core:object_id a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_id" ; - rdfs:range linkml:String . - -core:object_qualifier a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_qualifier" ; - rdfs:range core:NamedEntity ; - skos:definition "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" . - -core:object_text a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_text" ; - rdfs:range linkml:String . - -core:predicate a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "predicate" ; - rdfs:range core:RelationshipType . - -core:prompt a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "prompt" ; - rdfs:range linkml:String . - -core:publication a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "publication" ; - core:prompt.skip "true" ; - rdfs:range core:Publication . - -core:qualifier a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "qualifier" ; - rdfs:range linkml:String ; - skos:definition "A qualifier for the statements, e.g. \"NOT\" for negation" . - -core:raw_completion_output a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "raw_completion_output" ; - rdfs:range linkml:String . - -core:subject a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject" ; - rdfs:range core:NamedEntity . - -core:subject_qualifier a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_qualifier" ; - rdfs:range core:NamedEntity ; - skos:definition "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" . - -core:subject_text a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_text" ; - rdfs:range linkml:String . - -core:title a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "title" ; - rdfs:range linkml:String ; - skos:definition "The title of the publication" . - -core:triples a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "triples" ; - rdfs:range core:Triple . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "label" ; - core:owl "AnnotationProperty, AnnotationAssertion" ; - rdfs:range linkml:String ; - skos:altLabel "name" ; - skos:definition "The label (name) of the named thing" ; - skos:exactMatch . - -NCIT:C149701 a core:NullDataOptions, - owl:Class ; - rdfs:label "UNSPECIFIED_METHOD_OF_ADMINISTRATION" . - -NCIT:C18902 a core:NullDataOptions, - owl:Class ; - rdfs:label "NOT_APPLICABLE" . - -core:CompoundExpression a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CompoundExpression" ; - linkml:attributes "{}" . - - a core:NullDataOptions, - owl:Class ; - rdfs:label "NOT_MENTIONED" . - -core:RelationshipType a owl:Class, - linkml:ClassDefinition ; - rdfs:label "RelationshipType" ; - rdfs:subClassOf core:NamedEntity ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -core:Triple a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Triple" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass core:NamedEntity ; - owl:onProperty core:subject_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass core:NamedEntity ; - owl:onProperty core:object_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass core:NamedEntity ; - owl:onProperty core:object ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass core:RelationshipType ; - owl:onProperty core:predicate ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass core:NamedEntity ; - owl:onProperty core:subject ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty core:qualifier ], - core:CompoundExpression ; - skos:definition "Abstract parent for Relation Extraction tasks" ; - linkml:attributes "{'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -core:id a owl:ObjectProperty, - linkml:SlotDefinition . - -core:NullDataOptions a owl:Class, - linkml:EnumDefinition ; - rdfs:label "NullDataOptions" ; - owl:unionOf ( NCIT:C149701 NCIT:C18902 ) ; - linkml:permissible_values NCIT:C149701, - NCIT:C18902, - . - -core:Publication a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Publication" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty core:abstract ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty core:id ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty core:title ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty core:combined_text ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty core:full_text ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -core:Any a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Any" ; - skos:exactMatch linkml:Any ; - linkml:attributes "{}" . - -linkml:ClassDefinition a owl:Class ; - rdfs:label "class_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "class_expression" . - -core:NamedEntity a owl:Class, - linkml:ClassDefinition ; - rdfs:label "NamedEntity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty core:id ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:SlotDefinition a owl:Class ; - rdfs:label "slot_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "slot_expression" . - - diff --git a/projects/core/prefixmap/core.yaml b/projects/core/prefixmap/core.yaml deleted file mode 100644 index 5bb6968d5..000000000 --- a/projects/core/prefixmap/core.yaml +++ /dev/null @@ -1,11 +0,0 @@ -{ - "NCIT": "http://purl.obolibrary.org/obo/NCIT_", - "RO": "http://purl.obolibrary.org/obo/RO_", - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "Any": { - "@id": "linkml:Any" - } -} diff --git a/projects/core/protobuf/core.proto b/projects/core/protobuf/core.proto deleted file mode 100644 index c3cc6b1ba..000000000 --- a/projects/core/protobuf/core.proto +++ /dev/null @@ -1,35 +0,0 @@ -message AnnotatorResult - { - string subjectText = 0 - string objectId = 0 - string objectText = 0 - } -// A result of extracting knowledge on text -message ExtractionResult - { - string inputId = 0 - string inputTitle = 0 - string inputText = 0 - string rawCompletionOutput = 0 - string prompt = 0 - any extractedObject = 0 - repeated any namedEntities = 0 - } -message Publication - { - string id = 0 - string title = 0 - string abstract = 0 - string combinedText = 0 - string fullText = 0 - } -message RelationshipType - { - string id = 0 - string label = 0 - } -message TextWithTriples - { - publication publication = 0 - repeated triple triples = 0 - } diff --git a/projects/core/shacl/core.shacl.ttl b/projects/core/shacl/core.shacl.ttl deleted file mode 100644 index 9ee4c542b..000000000 --- a/projects/core/shacl/core.shacl.ttl +++ /dev/null @@ -1,164 +0,0 @@ -@prefix core: . -@prefix linkml: . -@prefix rdf: . -@prefix sh: . -@prefix xsd: . - -core:AnnotatorResult a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 1 ; - sh:path core:object_id ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path core:object_text ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path core:subject_text ] ; - sh:targetClass core:AnnotatorResult . - -core:CompoundExpression a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass core:CompoundExpression . - -core:ExtractionResult a sh:NodeShape ; - sh:closed true ; - sh:description "A result of extracting knowledge on text" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 1 ; - sh:path core:input_title ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path core:input_id ], - [ sh:class linkml:Any ; - sh:description "Named entities extracted from the text" ; - sh:nodeKind sh:BlankNode ; - sh:order 6 ; - sh:path core:named_entities ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path core:input_text ], - [ sh:class linkml:Any ; - sh:description "The complex objects extracted from the text" ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path core:extracted_object ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path core:raw_completion_output ], - [ sh:maxCount 1 ; - sh:order 4 ; - sh:path core:prompt ] ; - sh:targetClass core:ExtractionResult . - -core:TextWithTriples a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class core:Triple ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path core:triples ], - [ sh:class core:Publication ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path core:publication ] ; - sh:targetClass core:TextWithTriples . - -core:Publication a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The title of the publication" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path core:title ], - [ sh:description "The abstract of the publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path core:abstract ], - [ sh:description "The full text of the publication" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path core:full_text ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path core:combined_text ], - [ sh:description "The publication identifier" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path core:id ] ; - sh:targetClass core:Publication . - -core:RelationshipType a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path core:id ] ; - sh:targetClass core:RelationshipType . - -core:Triple a sh:NodeShape ; - sh:closed false ; - sh:description "Abstract parent for Relation Extraction tasks" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class core:NamedEntity ; - sh:description "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path core:subject_qualifier ], - [ sh:class core:RelationshipType ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path core:predicate ], - [ sh:description "A qualifier for the statements, e.g. \"NOT\" for negation" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path core:qualifier ], - [ sh:class core:NamedEntity ; - sh:description "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path core:object_qualifier ], - [ sh:class core:NamedEntity ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path core:subject ], - [ sh:class core:NamedEntity ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path core:object ] ; - sh:targetClass core:Triple . - -linkml:Any a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass linkml:Any . - -core:NamedEntity a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path core:id ] ; - sh:targetClass core:NamedEntity . - diff --git a/projects/core/shex/core.shex b/projects/core/shex/core.shex deleted file mode 100644 index 35be31fb3..000000000 --- a/projects/core/shex/core.shex +++ /dev/null @@ -1,131 +0,0 @@ -BASE -PREFIX rdf: -PREFIX xsd: -PREFIX linkml: -PREFIX rdfs1: - - -linkml:String xsd:string - -linkml:Integer xsd:integer - -linkml:Boolean xsd:boolean - -linkml:Float xsd:float - -linkml:Double xsd:double - -linkml:Decimal xsd:decimal - -linkml:Time xsd:time - -linkml:Date xsd:date - -linkml:Datetime xsd:dateTime - -linkml:DateOrDatetime linkml:DateOrDatetime - -linkml:Uriorcurie IRI - -linkml:Curie xsd:string - -linkml:Uri IRI - -linkml:Ncname xsd:string - -linkml:Objectidentifier IRI - -linkml:Nodeidentifier NONLITERAL - -linkml:Jsonpointer xsd:string - -linkml:Jsonpath xsd:string - -linkml:Sparqlpath xsd:string - - CLOSED { - ( $ ( @linkml:String ? ; - @linkml:String ? ; - @linkml:String ? - ) ; - rdf:type [ ] ? - ) -} - - CLOSED { - ( $ rdf:type . * ; - rdf:type [ linkml:Any ] ? - ) -} - - ( - { - ( $ rdf:type . * ; - rdf:type [ ] ? - ) - } OR @ -) - - CLOSED { - ( $ ( @linkml:String ? ; - @linkml:String ? ; - @linkml:String ? ; - @linkml:String ? ; - @linkml:String ? ; - @ ? ; - @ * - ) ; - rdf:type [ ] ? - ) -} - - ( - { - ( $ rdfs1:label @linkml:String ? ; - rdf:type [ ] - ) - } OR @ -) - - CLOSED { - ( $ ( @linkml:String ? ; - @linkml:String ? ; - <abstract> @linkml:String ? ; - <combined_text> @linkml:String ? ; - <full_text> @linkml:String ? - ) ; - rdf:type [ <Publication> ] ? - ) -} - -<RelationshipType> CLOSED { - ( $<RelationshipType_tes> ( &<NamedEntity_tes> ; - rdf:type [ <NamedEntity> ] ? - ) ; - rdf:type [ <RelationshipType> ] - ) -} - -<TextWithTriples> CLOSED { - ( $<TextWithTriples_tes> ( <publication> @<Publication> ? ; - <triples> @<Triple> * - ) ; - rdf:type [ <TextWithTriples> ] ? - ) -} - -<Triple> { - ( $<Triple_tes> ( &<CompoundExpression_tes> ; - rdf:type [ <CompoundExpression> ] ? ; - <subject> @<NamedEntity> ? ; - <predicate> @<RelationshipType> ? ; - <object> @<NamedEntity> ? ; - <qualifier> @linkml:String ? ; - <subject_qualifier> @<NamedEntity> ? ; - <object_qualifier> @<NamedEntity> ? - ) ; - rdf:type [ <Triple> ] ? - ) -} - - diff --git a/projects/core/sqlschema/core.sql b/projects/core/sqlschema/core.sql deleted file mode 100644 index 0d5e7d23b..000000000 --- a/projects/core/sqlschema/core.sql +++ /dev/null @@ -1,40 +0,0 @@ - - -CREATE TABLE "AnnotatorResult" ( - subject_text TEXT, - object_id TEXT, - object_text TEXT, - PRIMARY KEY (subject_text, object_id, object_text) -); - -CREATE TABLE "ExtractionResult" ( - input_id TEXT, - input_title TEXT, - input_text TEXT, - raw_completion_output TEXT, - prompt TEXT, - extracted_object TEXT, - named_entities TEXT, - PRIMARY KEY (input_id, input_title, input_text, raw_completion_output, prompt, extracted_object, named_entities) -); - -CREATE TABLE "Publication" ( - id TEXT, - title TEXT, - abstract TEXT, - combined_text TEXT, - full_text TEXT, - PRIMARY KEY (id, title, abstract, combined_text, full_text) -); - -CREATE TABLE "RelationshipType" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "TextWithTriples" ( - publication TEXT, - triples TEXT, - PRIMARY KEY (publication, triples) -); diff --git a/projects/ctd/ctd.py b/projects/ctd/ctd.py deleted file mode 100644 index 9fa39d8ce..000000000 --- a/projects/ctd/ctd.py +++ /dev/null @@ -1,537 +0,0 @@ -# Auto generated from ctd.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-08-07T10:52:24 -# Schema: ctd -# -# id: http://w3id.org/ontogpt/ctd -# description: A template for Chemical to Disease associations. This template is intended to represent -# associations between chemicals and diseases, and for evaluating Semantic Llama against BioCreative -# V Chemical Disease Relation (CDR) Task (BC5CDR). -# license: https://creativecommons.org/publicdomain/zero/1.0/ - -import dataclasses -import sys -import re -from jsonasobj2 import JsonObj, as_dict -from typing import Optional, List, Union, Dict, ClassVar, Any -from dataclasses import dataclass -from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions - -from linkml_runtime.utils.slot import Slot -from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode -from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int -from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs -from linkml_runtime.utils.formatutils import camelcase, underscore, sfx -from linkml_runtime.utils.enumerations import EnumDefinitionImpl -from rdflib import Namespace, URIRef -from linkml_runtime.utils.curienamespace import CurieNamespace -from linkml_runtime.linkml_model.types import String - -metamodel_version = "1.7.0" -version = None - -# Overwrite dataclasses _init_fn to add **kwargs in __init__ -dataclasses._init_fn = dataclasses_init_fn_with_kwargs - -# Namespaces -MESH = CurieNamespace('MESH', 'http://example.org/UNKNOWN/MESH/') -RO = CurieNamespace('RO', 'http://purl.obolibrary.org/obo/RO_') -BIOLINK = CurieNamespace('biolink', 'http://example.org/UNKNOWN/biolink/') -CORE = CurieNamespace('core', 'http://w3id.org/ontogpt/core/') -DRUG = CurieNamespace('drug', 'http://w3id.org/ontogpt/drug/') -LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') -RDFS = CurieNamespace('rdfs', 'http://example.org/UNKNOWN/rdfs/') -DEFAULT_ = DRUG - - -# Types - -# Class references -class NamedEntityId(extended_str): - pass - - -class DiseaseId(NamedEntityId): - pass - - -class ChemicalId(NamedEntityId): - pass - - -class RelationshipTypeId(NamedEntityId): - pass - - -class ChemicalToDiseasePredicateId(RelationshipTypeId): - pass - - -Any = Any - -@dataclass -class ExtractionResult(YAMLRoot): - """ - A result of extracting knowledge on text - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.ExtractionResult - class_class_curie: ClassVar[str] = "core:ExtractionResult" - class_name: ClassVar[str] = "ExtractionResult" - class_model_uri: ClassVar[URIRef] = DRUG.ExtractionResult - - input_id: Optional[str] = None - input_title: Optional[str] = None - input_text: Optional[str] = None - raw_completion_output: Optional[str] = None - prompt: Optional[str] = None - extracted_object: Optional[Union[dict, Any]] = None - named_entities: Optional[Union[Union[dict, Any], List[Union[dict, Any]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.input_id is not None and not isinstance(self.input_id, str): - self.input_id = str(self.input_id) - - if self.input_title is not None and not isinstance(self.input_title, str): - self.input_title = str(self.input_title) - - if self.input_text is not None and not isinstance(self.input_text, str): - self.input_text = str(self.input_text) - - if self.raw_completion_output is not None and not isinstance(self.raw_completion_output, str): - self.raw_completion_output = str(self.raw_completion_output) - - if self.prompt is not None and not isinstance(self.prompt, str): - self.prompt = str(self.prompt) - - super().__post_init__(**kwargs) - - -@dataclass -class NamedEntity(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.NamedEntity - class_class_curie: ClassVar[str] = "core:NamedEntity" - class_name: ClassVar[str] = "NamedEntity" - class_model_uri: ClassVar[URIRef] = DRUG.NamedEntity - - id: Union[str, NamedEntityId] = None - label: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, NamedEntityId): - self.id = NamedEntityId(self.id) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - super().__post_init__(**kwargs) - - -@dataclass -class Disease(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = DRUG.Disease - class_class_curie: ClassVar[str] = "drug:Disease" - class_name: ClassVar[str] = "Disease" - class_model_uri: ClassVar[URIRef] = DRUG.Disease - - id: Union[str, DiseaseId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, DiseaseId): - self.id = DiseaseId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Chemical(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = DRUG.Chemical - class_class_curie: ClassVar[str] = "drug:Chemical" - class_name: ClassVar[str] = "Chemical" - class_model_uri: ClassVar[URIRef] = DRUG.Chemical - - id: Union[str, ChemicalId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, ChemicalId): - self.id = ChemicalId(self.id) - - super().__post_init__(**kwargs) - - -class CompoundExpression(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.CompoundExpression - class_class_curie: ClassVar[str] = "core:CompoundExpression" - class_name: ClassVar[str] = "CompoundExpression" - class_model_uri: ClassVar[URIRef] = DRUG.CompoundExpression - - -@dataclass -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Triple - class_class_curie: ClassVar[str] = "core:Triple" - class_name: ClassVar[str] = "Triple" - class_model_uri: ClassVar[URIRef] = DRUG.Triple - - subject: Optional[Union[str, NamedEntityId]] = None - predicate: Optional[Union[str, RelationshipTypeId]] = None - object: Optional[Union[str, NamedEntityId]] = None - qualifier: Optional[str] = None - subject_qualifier: Optional[Union[str, NamedEntityId]] = None - object_qualifier: Optional[Union[str, NamedEntityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, NamedEntityId): - self.subject = NamedEntityId(self.subject) - - if self.predicate is not None and not isinstance(self.predicate, RelationshipTypeId): - self.predicate = RelationshipTypeId(self.predicate) - - if self.object is not None and not isinstance(self.object, NamedEntityId): - self.object = NamedEntityId(self.object) - - if self.qualifier is not None and not isinstance(self.qualifier, str): - self.qualifier = str(self.qualifier) - - if self.subject_qualifier is not None and not isinstance(self.subject_qualifier, NamedEntityId): - self.subject_qualifier = NamedEntityId(self.subject_qualifier) - - if self.object_qualifier is not None and not isinstance(self.object_qualifier, NamedEntityId): - self.object_qualifier = NamedEntityId(self.object_qualifier) - - super().__post_init__(**kwargs) - - -@dataclass -class ChemicalToDiseaseRelationship(Triple): - """ - A triple where the subject is a chemical and the object is a disease. - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = DRUG.ChemicalToDiseaseRelationship - class_class_curie: ClassVar[str] = "drug:ChemicalToDiseaseRelationship" - class_name: ClassVar[str] = "ChemicalToDiseaseRelationship" - class_model_uri: ClassVar[URIRef] = DRUG.ChemicalToDiseaseRelationship - - subject: Optional[Union[str, ChemicalId]] = None - object: Optional[Union[str, DiseaseId]] = None - predicate: Optional[Union[str, ChemicalToDiseasePredicateId]] = None - subject_qualifier: Optional[Union[str, NamedEntityId]] = None - object_qualifier: Optional[Union[str, NamedEntityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, ChemicalId): - self.subject = ChemicalId(self.subject) - - if self.object is not None and not isinstance(self.object, DiseaseId): - self.object = DiseaseId(self.object) - - if self.predicate is not None and not isinstance(self.predicate, ChemicalToDiseasePredicateId): - self.predicate = ChemicalToDiseasePredicateId(self.predicate) - - if self.subject_qualifier is not None and not isinstance(self.subject_qualifier, NamedEntityId): - self.subject_qualifier = NamedEntityId(self.subject_qualifier) - - if self.object_qualifier is not None and not isinstance(self.object_qualifier, NamedEntityId): - self.object_qualifier = NamedEntityId(self.object_qualifier) - - super().__post_init__(**kwargs) - - -@dataclass -class TextWithTriples(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.TextWithTriples - class_class_curie: ClassVar[str] = "core:TextWithTriples" - class_name: ClassVar[str] = "TextWithTriples" - class_model_uri: ClassVar[URIRef] = DRUG.TextWithTriples - - publication: Optional[Union[dict, "Publication"]] = None - triples: Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.publication is not None and not isinstance(self.publication, Publication): - self.publication = Publication(**as_dict(self.publication)) - - if not isinstance(self.triples, list): - self.triples = [self.triples] if self.triples is not None else [] - self.triples = [v if isinstance(v, Triple) else Triple(**as_dict(v)) for v in self.triples] - - super().__post_init__(**kwargs) - - -@dataclass -class ChemicalToDiseaseDocument(TextWithTriples): - """ - A document that contains chemical to disease relations. - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = DRUG.ChemicalToDiseaseDocument - class_class_curie: ClassVar[str] = "drug:ChemicalToDiseaseDocument" - class_name: ClassVar[str] = "ChemicalToDiseaseDocument" - class_model_uri: ClassVar[URIRef] = DRUG.ChemicalToDiseaseDocument - - triples: Optional[Union[Union[dict, "ChemicalToDiseaseRelationship"], List[Union[dict, "ChemicalToDiseaseRelationship"]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if not isinstance(self.triples, list): - self.triples = [self.triples] if self.triples is not None else [] - self.triples = [v if isinstance(v, ChemicalToDiseaseRelationship) else ChemicalToDiseaseRelationship(**as_dict(v)) for v in self.triples] - - super().__post_init__(**kwargs) - - -@dataclass -class RelationshipType(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.RelationshipType - class_class_curie: ClassVar[str] = "core:RelationshipType" - class_name: ClassVar[str] = "RelationshipType" - class_model_uri: ClassVar[URIRef] = DRUG.RelationshipType - - id: Union[str, RelationshipTypeId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, RelationshipTypeId): - self.id = RelationshipTypeId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class ChemicalToDiseasePredicate(RelationshipType): - """ - A predicate for chemical to disease relationships - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = DRUG.ChemicalToDiseasePredicate - class_class_curie: ClassVar[str] = "drug:ChemicalToDiseasePredicate" - class_name: ClassVar[str] = "ChemicalToDiseasePredicate" - class_model_uri: ClassVar[URIRef] = DRUG.ChemicalToDiseasePredicate - - id: Union[str, ChemicalToDiseasePredicateId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, ChemicalToDiseasePredicateId): - self.id = ChemicalToDiseasePredicateId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Publication(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Publication - class_class_curie: ClassVar[str] = "core:Publication" - class_name: ClassVar[str] = "Publication" - class_model_uri: ClassVar[URIRef] = DRUG.Publication - - id: Optional[str] = None - title: Optional[str] = None - abstract: Optional[str] = None - combined_text: Optional[str] = None - full_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.id is not None and not isinstance(self.id, str): - self.id = str(self.id) - - if self.title is not None and not isinstance(self.title, str): - self.title = str(self.title) - - if self.abstract is not None and not isinstance(self.abstract, str): - self.abstract = str(self.abstract) - - if self.combined_text is not None and not isinstance(self.combined_text, str): - self.combined_text = str(self.combined_text) - - if self.full_text is not None and not isinstance(self.full_text, str): - self.full_text = str(self.full_text) - - super().__post_init__(**kwargs) - - -@dataclass -class AnnotatorResult(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.AnnotatorResult - class_class_curie: ClassVar[str] = "core:AnnotatorResult" - class_name: ClassVar[str] = "AnnotatorResult" - class_model_uri: ClassVar[URIRef] = DRUG.AnnotatorResult - - subject_text: Optional[str] = None - object_id: Optional[str] = None - object_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject_text is not None and not isinstance(self.subject_text, str): - self.subject_text = str(self.subject_text) - - if self.object_id is not None and not isinstance(self.object_id, str): - self.object_id = str(self.object_id) - - if self.object_text is not None and not isinstance(self.object_text, str): - self.object_text = str(self.object_text) - - super().__post_init__(**kwargs) - - -# Enumerations -class MeshChemicalIdentifier(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="MeshChemicalIdentifier", - ) - -class MeshDiseaseIdentifier(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="MeshDiseaseIdentifier", - ) - -class NullDataOptions(EnumDefinitionImpl): - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = PermissibleValue(text="UNSPECIFIED_METHOD_OF_ADMINISTRATION", - meaning=NCIT.C149701) - NOT_APPLICABLE = PermissibleValue(text="NOT_APPLICABLE", - meaning=NCIT.C18902) - NOT_MENTIONED = PermissibleValue(text="NOT_MENTIONED") - - _defn = EnumDefinition( - name="NullDataOptions", - ) - -# Slots -class slots: - pass - -slots.extractionResult__input_id = Slot(uri=CORE.input_id, name="extractionResult__input_id", curie=CORE.curie('input_id'), - model_uri=DRUG.extractionResult__input_id, domain=None, range=Optional[str]) - -slots.extractionResult__input_title = Slot(uri=CORE.input_title, name="extractionResult__input_title", curie=CORE.curie('input_title'), - model_uri=DRUG.extractionResult__input_title, domain=None, range=Optional[str]) - -slots.extractionResult__input_text = Slot(uri=CORE.input_text, name="extractionResult__input_text", curie=CORE.curie('input_text'), - model_uri=DRUG.extractionResult__input_text, domain=None, range=Optional[str]) - -slots.extractionResult__raw_completion_output = Slot(uri=CORE.raw_completion_output, name="extractionResult__raw_completion_output", curie=CORE.curie('raw_completion_output'), - model_uri=DRUG.extractionResult__raw_completion_output, domain=None, range=Optional[str]) - -slots.extractionResult__prompt = Slot(uri=CORE.prompt, name="extractionResult__prompt", curie=CORE.curie('prompt'), - model_uri=DRUG.extractionResult__prompt, domain=None, range=Optional[str]) - -slots.extractionResult__extracted_object = Slot(uri=CORE.extracted_object, name="extractionResult__extracted_object", curie=CORE.curie('extracted_object'), - model_uri=DRUG.extractionResult__extracted_object, domain=None, range=Optional[Union[dict, Any]]) - -slots.extractionResult__named_entities = Slot(uri=CORE.named_entities, name="extractionResult__named_entities", curie=CORE.curie('named_entities'), - model_uri=DRUG.extractionResult__named_entities, domain=None, range=Optional[Union[Union[dict, Any], List[Union[dict, Any]]]]) - -slots.namedEntity__id = Slot(uri=CORE.id, name="namedEntity__id", curie=CORE.curie('id'), - model_uri=DRUG.namedEntity__id, domain=None, range=URIRef) - -slots.namedEntity__label = Slot(uri=RDFS.label, name="namedEntity__label", curie=RDFS.curie('label'), - model_uri=DRUG.namedEntity__label, domain=None, range=Optional[str]) - -slots.triple__subject = Slot(uri=CORE.subject, name="triple__subject", curie=CORE.curie('subject'), - model_uri=DRUG.triple__subject, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__predicate = Slot(uri=CORE.predicate, name="triple__predicate", curie=CORE.curie('predicate'), - model_uri=DRUG.triple__predicate, domain=None, range=Optional[Union[str, RelationshipTypeId]]) - -slots.triple__object = Slot(uri=CORE.object, name="triple__object", curie=CORE.curie('object'), - model_uri=DRUG.triple__object, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__qualifier = Slot(uri=CORE.qualifier, name="triple__qualifier", curie=CORE.curie('qualifier'), - model_uri=DRUG.triple__qualifier, domain=None, range=Optional[str]) - -slots.triple__subject_qualifier = Slot(uri=CORE.subject_qualifier, name="triple__subject_qualifier", curie=CORE.curie('subject_qualifier'), - model_uri=DRUG.triple__subject_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__object_qualifier = Slot(uri=CORE.object_qualifier, name="triple__object_qualifier", curie=CORE.curie('object_qualifier'), - model_uri=DRUG.triple__object_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.textWithTriples__publication = Slot(uri=CORE.publication, name="textWithTriples__publication", curie=CORE.curie('publication'), - model_uri=DRUG.textWithTriples__publication, domain=None, range=Optional[Union[dict, Publication]]) - -slots.textWithTriples__triples = Slot(uri=CORE.triples, name="textWithTriples__triples", curie=CORE.curie('triples'), - model_uri=DRUG.textWithTriples__triples, domain=None, range=Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]]) - -slots.publication__id = Slot(uri=CORE.id, name="publication__id", curie=CORE.curie('id'), - model_uri=DRUG.publication__id, domain=None, range=Optional[str]) - -slots.publication__title = Slot(uri=CORE.title, name="publication__title", curie=CORE.curie('title'), - model_uri=DRUG.publication__title, domain=None, range=Optional[str]) - -slots.publication__abstract = Slot(uri=CORE.abstract, name="publication__abstract", curie=CORE.curie('abstract'), - model_uri=DRUG.publication__abstract, domain=None, range=Optional[str]) - -slots.publication__combined_text = Slot(uri=CORE.combined_text, name="publication__combined_text", curie=CORE.curie('combined_text'), - model_uri=DRUG.publication__combined_text, domain=None, range=Optional[str]) - -slots.publication__full_text = Slot(uri=CORE.full_text, name="publication__full_text", curie=CORE.curie('full_text'), - model_uri=DRUG.publication__full_text, domain=None, range=Optional[str]) - -slots.annotatorResult__subject_text = Slot(uri=CORE.subject_text, name="annotatorResult__subject_text", curie=CORE.curie('subject_text'), - model_uri=DRUG.annotatorResult__subject_text, domain=None, range=Optional[str]) - -slots.annotatorResult__object_id = Slot(uri=CORE.object_id, name="annotatorResult__object_id", curie=CORE.curie('object_id'), - model_uri=DRUG.annotatorResult__object_id, domain=None, range=Optional[str]) - -slots.annotatorResult__object_text = Slot(uri=CORE.object_text, name="annotatorResult__object_text", curie=CORE.curie('object_text'), - model_uri=DRUG.annotatorResult__object_text, domain=None, range=Optional[str]) - -slots.ChemicalToDiseaseDocument_triples = Slot(uri=DRUG.triples, name="ChemicalToDiseaseDocument_triples", curie=DRUG.curie('triples'), - model_uri=DRUG.ChemicalToDiseaseDocument_triples, domain=ChemicalToDiseaseDocument, range=Optional[Union[Union[dict, "ChemicalToDiseaseRelationship"], List[Union[dict, "ChemicalToDiseaseRelationship"]]]]) - -slots.ChemicalToDiseaseRelationship_subject = Slot(uri=DRUG.subject, name="ChemicalToDiseaseRelationship_subject", curie=DRUG.curie('subject'), - model_uri=DRUG.ChemicalToDiseaseRelationship_subject, domain=ChemicalToDiseaseRelationship, range=Optional[Union[str, ChemicalId]]) - -slots.ChemicalToDiseaseRelationship_object = Slot(uri=DRUG.object, name="ChemicalToDiseaseRelationship_object", curie=DRUG.curie('object'), - model_uri=DRUG.ChemicalToDiseaseRelationship_object, domain=ChemicalToDiseaseRelationship, range=Optional[Union[str, DiseaseId]]) - -slots.ChemicalToDiseaseRelationship_predicate = Slot(uri=DRUG.predicate, name="ChemicalToDiseaseRelationship_predicate", curie=DRUG.curie('predicate'), - model_uri=DRUG.ChemicalToDiseaseRelationship_predicate, domain=ChemicalToDiseaseRelationship, range=Optional[Union[str, ChemicalToDiseasePredicateId]]) - -slots.ChemicalToDiseaseRelationship_subject_qualifier = Slot(uri=DRUG.subject_qualifier, name="ChemicalToDiseaseRelationship_subject_qualifier", curie=DRUG.curie('subject_qualifier'), - model_uri=DRUG.ChemicalToDiseaseRelationship_subject_qualifier, domain=ChemicalToDiseaseRelationship, range=Optional[Union[str, NamedEntityId]]) - -slots.ChemicalToDiseaseRelationship_object_qualifier = Slot(uri=DRUG.object_qualifier, name="ChemicalToDiseaseRelationship_object_qualifier", curie=DRUG.curie('object_qualifier'), - model_uri=DRUG.ChemicalToDiseaseRelationship_object_qualifier, domain=ChemicalToDiseaseRelationship, range=Optional[Union[str, NamedEntityId]]) - -slots.Disease_id = Slot(uri=DRUG.id, name="Disease_id", curie=DRUG.curie('id'), - model_uri=DRUG.Disease_id, domain=Disease, range=Union[str, DiseaseId], - pattern=re.compile(r'^MESH:[CD][0-9]{6}$')) - -slots.Chemical_id = Slot(uri=DRUG.id, name="Chemical_id", curie=DRUG.curie('id'), - model_uri=DRUG.Chemical_id, domain=Chemical, range=Union[str, ChemicalId], - pattern=re.compile(r'^MESH:[CD][0-9]{6}$')) \ No newline at end of file diff --git a/projects/ctd/docs/AnnotatorResult.md b/projects/ctd/docs/AnnotatorResult.md deleted file mode 100644 index 1ea640ba8..000000000 --- a/projects/ctd/docs/AnnotatorResult.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Class: AnnotatorResult - - - - -URI: [drug:AnnotatorResult](http://w3id.org/ontogpt/drug/AnnotatorResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F])](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F]) - -## Attributes - - -### Own - - * [➞subject_text](annotatorResult__subject_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_id](annotatorResult__object_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_text](annotatorResult__object_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) diff --git a/projects/ctd/docs/Any.md b/projects/ctd/docs/Any.md deleted file mode 100644 index 4da2d3785..000000000 --- a/projects/ctd/docs/Any.md +++ /dev/null @@ -1,25 +0,0 @@ - -# Class: Any - - - - -URI: [drug:Any](http://w3id.org/ontogpt/drug/Any) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult])](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult]) - -## Referenced by Class - - * **None** *[➞extracted_object](extractionResult__extracted_object.md)* <sub>0..1</sub> **[Any](Any.md)** - * **None** *[➞named_entities](extractionResult__named_entities.md)* <sub>0..\*</sub> **[Any](Any.md)** - -## Attributes - - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | linkml:Any | - diff --git a/projects/ctd/docs/Chemical.md b/projects/ctd/docs/Chemical.md deleted file mode 100644 index 583be8e98..000000000 --- a/projects/ctd/docs/Chemical.md +++ /dev/null @@ -1,36 +0,0 @@ - -# Class: Chemical - - - - -URI: [drug:Chemical](http://w3id.org/ontogpt/drug/Chemical) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[ChemicalToDiseaseRelationship],[ChemicalToDiseaseRelationship]-%20subject%200..1>[Chemical|id:string;label(i):string%20%3F],[NamedEntity]^-[Chemical])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[ChemicalToDiseaseRelationship],[ChemicalToDiseaseRelationship]-%20subject%200..1>[Chemical|id:string;label(i):string%20%3F],[NamedEntity]^-[Chemical]) - -## Identifier prefixes - - * MESH - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **[ChemicalToDiseaseRelationship](ChemicalToDiseaseRelationship.md)** *[ChemicalToDiseaseRelationship➞subject](ChemicalToDiseaseRelationship_subject.md)* <sub>0..1</sub> **[Chemical](Chemical.md)** - -## Attributes - - -### Own - - * [Chemical➞id](Chemical_id.md) <sub>1..1</sub> - * Range: [String](types/String.md) - -### Inherited from NamedEntity: - - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/ctd/docs/ChemicalToDiseaseDocument.md b/projects/ctd/docs/ChemicalToDiseaseDocument.md deleted file mode 100644 index cfb2836e8..000000000 --- a/projects/ctd/docs/ChemicalToDiseaseDocument.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Class: ChemicalToDiseaseDocument - - -A document that contains chemical to disease relations. - -URI: [drug:ChemicalToDiseaseDocument](http://w3id.org/ontogpt/drug/ChemicalToDiseaseDocument) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples],[Publication],[ChemicalToDiseaseRelationship],[ChemicalToDiseaseRelationship]<triples%200..*-++[ChemicalToDiseaseDocument],[TextWithTriples]^-[ChemicalToDiseaseDocument])](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples],[Publication],[ChemicalToDiseaseRelationship],[ChemicalToDiseaseRelationship]<triples%200..*-++[ChemicalToDiseaseDocument],[TextWithTriples]^-[ChemicalToDiseaseDocument]) - -## Parents - - * is_a: [TextWithTriples](TextWithTriples.md) - -## Referenced by Class - - -## Attributes - - -### Own - - * [ChemicalToDiseaseDocument➞triples](ChemicalToDiseaseDocument_triples.md) <sub>0..\*</sub> - * Range: [ChemicalToDiseaseRelationship](ChemicalToDiseaseRelationship.md) - -### Inherited from TextWithTriples: - - * [➞publication](textWithTriples__publication.md) <sub>0..1</sub> - * Range: [Publication](Publication.md) diff --git a/projects/ctd/docs/ChemicalToDiseaseDocument_triples.md b/projects/ctd/docs/ChemicalToDiseaseDocument_triples.md deleted file mode 100644 index 3c08f751c..000000000 --- a/projects/ctd/docs/ChemicalToDiseaseDocument_triples.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: triples - - - - -URI: [drug:ChemicalToDiseaseDocument_triples](http://w3id.org/ontogpt/drug/ChemicalToDiseaseDocument_triples) - - -## Domain and Range - -[ChemicalToDiseaseDocument](ChemicalToDiseaseDocument.md) → <sub>0..\*</sub> [ChemicalToDiseaseRelationship](ChemicalToDiseaseRelationship.md) - -## Parents - - * is_a: [➞triples](textWithTriples__triples.md) - -## Children - - -## Used by - - * [ChemicalToDiseaseDocument](ChemicalToDiseaseDocument.md) diff --git a/projects/ctd/docs/ChemicalToDiseasePredicate.md b/projects/ctd/docs/ChemicalToDiseasePredicate.md deleted file mode 100644 index d41c9ffb4..000000000 --- a/projects/ctd/docs/ChemicalToDiseasePredicate.md +++ /dev/null @@ -1,37 +0,0 @@ - -# Class: ChemicalToDiseasePredicate - - -A predicate for chemical to disease relationships - -URI: [drug:ChemicalToDiseasePredicate](http://w3id.org/ontogpt/drug/ChemicalToDiseasePredicate) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[ChemicalToDiseaseRelationship],[ChemicalToDiseaseRelationship]-%20predicate%200..1>[ChemicalToDiseasePredicate|id(i):string;label(i):string%20%3F],[RelationshipType]^-[ChemicalToDiseasePredicate])](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[ChemicalToDiseaseRelationship],[ChemicalToDiseaseRelationship]-%20predicate%200..1>[ChemicalToDiseasePredicate|id(i):string;label(i):string%20%3F],[RelationshipType]^-[ChemicalToDiseasePredicate]) - -## Parents - - * is_a: [RelationshipType](RelationshipType.md) - -## Referenced by Class - - * **[ChemicalToDiseaseRelationship](ChemicalToDiseaseRelationship.md)** *[ChemicalToDiseaseRelationship➞predicate](ChemicalToDiseaseRelationship_predicate.md)* <sub>0..1</sub> **[ChemicalToDiseasePredicate](ChemicalToDiseasePredicate.md)** - -## Attributes - - -### Inherited from RelationshipType: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | for the purposes of evaluation against BC5CDR, any predicate other than INDUCES is ignored. | - diff --git a/projects/ctd/docs/ChemicalToDiseaseRelationship.md b/projects/ctd/docs/ChemicalToDiseaseRelationship.md deleted file mode 100644 index 5fa4aa7b2..000000000 --- a/projects/ctd/docs/ChemicalToDiseaseRelationship.md +++ /dev/null @@ -1,45 +0,0 @@ - -# Class: ChemicalToDiseaseRelationship - - -A triple where the subject is a chemical and the object is a disease. - -URI: [drug:ChemicalToDiseaseRelationship](http://w3id.org/ontogpt/drug/ChemicalToDiseaseRelationship) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[NamedEntity],[Disease],[NamedEntity]<object_qualifier%200..1-%20[ChemicalToDiseaseRelationship|qualifier(i):string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[ChemicalToDiseaseRelationship],[ChemicalToDiseasePredicate]<predicate%200..1-%20[ChemicalToDiseaseRelationship],[Disease]<object%200..1-%20[ChemicalToDiseaseRelationship],[Chemical]<subject%200..1-%20[ChemicalToDiseaseRelationship],[ChemicalToDiseaseDocument]++-%20triples%200..*>[ChemicalToDiseaseRelationship],[Triple]^-[ChemicalToDiseaseRelationship],[ChemicalToDiseasePredicate],[ChemicalToDiseaseDocument],[Chemical])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[NamedEntity],[Disease],[NamedEntity]<object_qualifier%200..1-%20[ChemicalToDiseaseRelationship|qualifier(i):string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[ChemicalToDiseaseRelationship],[ChemicalToDiseasePredicate]<predicate%200..1-%20[ChemicalToDiseaseRelationship],[Disease]<object%200..1-%20[ChemicalToDiseaseRelationship],[Chemical]<subject%200..1-%20[ChemicalToDiseaseRelationship],[ChemicalToDiseaseDocument]++-%20triples%200..*>[ChemicalToDiseaseRelationship],[Triple]^-[ChemicalToDiseaseRelationship],[ChemicalToDiseasePredicate],[ChemicalToDiseaseDocument],[Chemical]) - -## Parents - - * is_a: [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - -## Referenced by Class - - * **[ChemicalToDiseaseDocument](ChemicalToDiseaseDocument.md)** *[ChemicalToDiseaseDocument➞triples](ChemicalToDiseaseDocument_triples.md)* <sub>0..\*</sub> **[ChemicalToDiseaseRelationship](ChemicalToDiseaseRelationship.md)** - -## Attributes - - -### Own - - * [ChemicalToDiseaseRelationship➞subject](ChemicalToDiseaseRelationship_subject.md) <sub>0..1</sub> - * Description: The chemical substance, drug, or small molecule. For example: Lidocaine, Monosodium Glutamate, Imatinib. - * Range: [Chemical](Chemical.md) - * [ChemicalToDiseaseRelationship➞object](ChemicalToDiseaseRelationship_object.md) <sub>0..1</sub> - * Description: The disease or condition that is being treated or induced by the chemical. For example, asthma, cancer, covid-19, cardiac asystole, Hypotension, Headache. - * Range: [Disease](Disease.md) - * [ChemicalToDiseaseRelationship➞predicate](ChemicalToDiseaseRelationship_predicate.md) <sub>0..1</sub> - * Description: The relationship type, e.g. INDUCES, TREATS. - * Range: [ChemicalToDiseasePredicate](ChemicalToDiseasePredicate.md) - * [ChemicalToDiseaseRelationship➞subject_qualifier](ChemicalToDiseaseRelationship_subject_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the chemical, e.g. "high dose" or "intravenously administered" - * Range: [NamedEntity](NamedEntity.md) - * [ChemicalToDiseaseRelationship➞object_qualifier](ChemicalToDiseaseRelationship_object_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the disease, e.g. "severe" or "with additional complications" - * Range: [NamedEntity](NamedEntity.md) - -### Inherited from Triple: - - * [➞qualifier](triple__qualifier.md) <sub>0..1</sub> - * Description: A qualifier for the statements, e.g. "NOT" for negation - * Range: [String](types/String.md) diff --git a/projects/ctd/docs/ChemicalToDiseaseRelationship_object.md b/projects/ctd/docs/ChemicalToDiseaseRelationship_object.md deleted file mode 100644 index 60be4e509..000000000 --- a/projects/ctd/docs/ChemicalToDiseaseRelationship_object.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: object - - -The disease or condition that is being treated or induced by the chemical. For example, asthma, cancer, covid-19, cardiac asystole, Hypotension, Headache. - -URI: [drug:ChemicalToDiseaseRelationship_object](http://w3id.org/ontogpt/drug/ChemicalToDiseaseRelationship_object) - - -## Domain and Range - -[ChemicalToDiseaseRelationship](ChemicalToDiseaseRelationship.md) → <sub>0..1</sub> [Disease](Disease.md) - -## Parents - - * is_a: [➞object](triple__object.md) - -## Children - - -## Used by - - * [ChemicalToDiseaseRelationship](ChemicalToDiseaseRelationship.md) diff --git a/projects/ctd/docs/ChemicalToDiseaseRelationship_object_qualifier.md b/projects/ctd/docs/ChemicalToDiseaseRelationship_object_qualifier.md deleted file mode 100644 index 41cbc9363..000000000 --- a/projects/ctd/docs/ChemicalToDiseaseRelationship_object_qualifier.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: object_qualifier - - -An optional qualifier or modifier for the disease, e.g. "severe" or "with additional complications" - -URI: [drug:ChemicalToDiseaseRelationship_object_qualifier](http://w3id.org/ontogpt/drug/ChemicalToDiseaseRelationship_object_qualifier) - - -## Domain and Range - -[ChemicalToDiseaseRelationship](ChemicalToDiseaseRelationship.md) → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - * is_a: [➞object_qualifier](triple__object_qualifier.md) - -## Children - - -## Used by - - * [ChemicalToDiseaseRelationship](ChemicalToDiseaseRelationship.md) diff --git a/projects/ctd/docs/ChemicalToDiseaseRelationship_predicate.md b/projects/ctd/docs/ChemicalToDiseaseRelationship_predicate.md deleted file mode 100644 index 1bc5f372a..000000000 --- a/projects/ctd/docs/ChemicalToDiseaseRelationship_predicate.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: predicate - - -The relationship type, e.g. INDUCES, TREATS. - -URI: [drug:ChemicalToDiseaseRelationship_predicate](http://w3id.org/ontogpt/drug/ChemicalToDiseaseRelationship_predicate) - - -## Domain and Range - -[ChemicalToDiseaseRelationship](ChemicalToDiseaseRelationship.md) → <sub>0..1</sub> [ChemicalToDiseasePredicate](ChemicalToDiseasePredicate.md) - -## Parents - - * is_a: [➞predicate](triple__predicate.md) - -## Children - - -## Used by - - * [ChemicalToDiseaseRelationship](ChemicalToDiseaseRelationship.md) diff --git a/projects/ctd/docs/ChemicalToDiseaseRelationship_subject.md b/projects/ctd/docs/ChemicalToDiseaseRelationship_subject.md deleted file mode 100644 index e4bee707d..000000000 --- a/projects/ctd/docs/ChemicalToDiseaseRelationship_subject.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: subject - - -The chemical substance, drug, or small molecule. For example: Lidocaine, Monosodium Glutamate, Imatinib. - -URI: [drug:ChemicalToDiseaseRelationship_subject](http://w3id.org/ontogpt/drug/ChemicalToDiseaseRelationship_subject) - - -## Domain and Range - -[ChemicalToDiseaseRelationship](ChemicalToDiseaseRelationship.md) → <sub>0..1</sub> [Chemical](Chemical.md) - -## Parents - - * is_a: [➞subject](triple__subject.md) - -## Children - - -## Used by - - * [ChemicalToDiseaseRelationship](ChemicalToDiseaseRelationship.md) diff --git a/projects/ctd/docs/ChemicalToDiseaseRelationship_subject_qualifier.md b/projects/ctd/docs/ChemicalToDiseaseRelationship_subject_qualifier.md deleted file mode 100644 index 8a2ecee11..000000000 --- a/projects/ctd/docs/ChemicalToDiseaseRelationship_subject_qualifier.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: subject_qualifier - - -An optional qualifier or modifier for the chemical, e.g. "high dose" or "intravenously administered" - -URI: [drug:ChemicalToDiseaseRelationship_subject_qualifier](http://w3id.org/ontogpt/drug/ChemicalToDiseaseRelationship_subject_qualifier) - - -## Domain and Range - -[ChemicalToDiseaseRelationship](ChemicalToDiseaseRelationship.md) → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - * is_a: [➞subject_qualifier](triple__subject_qualifier.md) - -## Children - - -## Used by - - * [ChemicalToDiseaseRelationship](ChemicalToDiseaseRelationship.md) diff --git a/projects/ctd/docs/Chemical_id.md b/projects/ctd/docs/Chemical_id.md deleted file mode 100644 index 115bd91d8..000000000 --- a/projects/ctd/docs/Chemical_id.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: id - - - - -URI: [drug:Chemical_id](http://w3id.org/ontogpt/drug/Chemical_id) - - -## Domain and Range - -[Chemical](Chemical.md) → <sub>1..1</sub> [String](types/String.md) - -## Parents - - * is_a: [➞id](namedEntity__id.md) - -## Children - - -## Used by - - * [Chemical](Chemical.md) diff --git a/projects/ctd/docs/CompoundExpression.md b/projects/ctd/docs/CompoundExpression.md deleted file mode 100644 index 6c3865064..000000000 --- a/projects/ctd/docs/CompoundExpression.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: CompoundExpression - - - - -URI: [drug:CompoundExpression](http://w3id.org/ontogpt/drug/CompoundExpression) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[CompoundExpression]^-[Triple])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[CompoundExpression]^-[Triple]) - -## Children - - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - -## Referenced by Class - - -## Attributes - diff --git a/projects/ctd/docs/Disease.md b/projects/ctd/docs/Disease.md deleted file mode 100644 index f8468fbe8..000000000 --- a/projects/ctd/docs/Disease.md +++ /dev/null @@ -1,36 +0,0 @@ - -# Class: Disease - - - - -URI: [drug:Disease](http://w3id.org/ontogpt/drug/Disease) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[ChemicalToDiseaseRelationship]-%20object%200..1>[Disease|id:string;label(i):string%20%3F],[NamedEntity]^-[Disease],[ChemicalToDiseaseRelationship])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[ChemicalToDiseaseRelationship]-%20object%200..1>[Disease|id:string;label(i):string%20%3F],[NamedEntity]^-[Disease],[ChemicalToDiseaseRelationship]) - -## Identifier prefixes - - * MESH - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **[ChemicalToDiseaseRelationship](ChemicalToDiseaseRelationship.md)** *[ChemicalToDiseaseRelationship➞object](ChemicalToDiseaseRelationship_object.md)* <sub>0..1</sub> **[Disease](Disease.md)** - -## Attributes - - -### Own - - * [Disease➞id](Disease_id.md) <sub>1..1</sub> - * Range: [String](types/String.md) - -### Inherited from NamedEntity: - - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/ctd/docs/Disease_id.md b/projects/ctd/docs/Disease_id.md deleted file mode 100644 index 27b010dc2..000000000 --- a/projects/ctd/docs/Disease_id.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: id - - - - -URI: [drug:Disease_id](http://w3id.org/ontogpt/drug/Disease_id) - - -## Domain and Range - -[Disease](Disease.md) → <sub>1..1</sub> [String](types/String.md) - -## Parents - - * is_a: [➞id](namedEntity__id.md) - -## Children - - -## Used by - - * [Disease](Disease.md) diff --git a/projects/ctd/docs/ExtractionResult.md b/projects/ctd/docs/ExtractionResult.md deleted file mode 100644 index 7d07c8ae7..000000000 --- a/projects/ctd/docs/ExtractionResult.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Class: ExtractionResult - - -A result of extracting knowledge on text - -URI: [drug:ExtractionResult](http://w3id.org/ontogpt/drug/ExtractionResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any])](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any]) - -## Attributes - - -### Own - - * [➞input_id](extractionResult__input_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_title](extractionResult__input_title.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_text](extractionResult__input_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞prompt](extractionResult__prompt.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞extracted_object](extractionResult__extracted_object.md) <sub>0..1</sub> - * Description: The complex objects extracted from the text - * Range: [Any](Any.md) - * [➞named_entities](extractionResult__named_entities.md) <sub>0..\*</sub> - * Description: Named entities extracted from the text - * Range: [Any](Any.md) diff --git a/projects/ctd/docs/MeshChemicalIdentifier.md b/projects/ctd/docs/MeshChemicalIdentifier.md deleted file mode 100644 index 689558de6..000000000 --- a/projects/ctd/docs/MeshChemicalIdentifier.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Enum: MeshChemicalIdentifier - - - - -URI: [drug:MeshChemicalIdentifier](http://w3id.org/ontogpt/drug/MeshChemicalIdentifier) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | - diff --git a/projects/ctd/docs/MeshDiseaseIdentifier.md b/projects/ctd/docs/MeshDiseaseIdentifier.md deleted file mode 100644 index 7ae12796d..000000000 --- a/projects/ctd/docs/MeshDiseaseIdentifier.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Enum: MeshDiseaseIdentifier - - - - -URI: [drug:MeshDiseaseIdentifier](http://w3id.org/ontogpt/drug/MeshDiseaseIdentifier) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | - diff --git a/projects/ctd/docs/NamedEntity.md b/projects/ctd/docs/NamedEntity.md deleted file mode 100644 index b06a1df18..000000000 --- a/projects/ctd/docs/NamedEntity.md +++ /dev/null @@ -1,37 +0,0 @@ - -# Class: NamedEntity - - - - -URI: [drug:NamedEntity](http://w3id.org/ontogpt/drug/NamedEntity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[ChemicalToDiseaseRelationship]-%20object_qualifier%200..1>[NamedEntity|id:string;label:string%20%3F],[ChemicalToDiseaseRelationship]-%20subject_qualifier%200..1>[NamedEntity],[Triple]-%20object%200..1>[NamedEntity],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[Disease],[NamedEntity]^-[Chemical],[Triple],[Disease],[ChemicalToDiseaseRelationship],[Chemical])](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[ChemicalToDiseaseRelationship]-%20object_qualifier%200..1>[NamedEntity|id:string;label:string%20%3F],[ChemicalToDiseaseRelationship]-%20subject_qualifier%200..1>[NamedEntity],[Triple]-%20object%200..1>[NamedEntity],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[Disease],[NamedEntity]^-[Chemical],[Triple],[Disease],[ChemicalToDiseaseRelationship],[Chemical]) - -## Children - - * [Chemical](Chemical.md) - * [Disease](Disease.md) - * [RelationshipType](RelationshipType.md) - -## Referenced by Class - - * **[ChemicalToDiseaseRelationship](ChemicalToDiseaseRelationship.md)** *[ChemicalToDiseaseRelationship➞object_qualifier](ChemicalToDiseaseRelationship_object_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **[ChemicalToDiseaseRelationship](ChemicalToDiseaseRelationship.md)** *[ChemicalToDiseaseRelationship➞subject_qualifier](ChemicalToDiseaseRelationship_subject_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞object](triple__object.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞object_qualifier](triple__object_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject](triple__subject.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject_qualifier](triple__subject_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - -## Attributes - - -### Own - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/ctd/docs/NullDataOptions.md b/projects/ctd/docs/NullDataOptions.md deleted file mode 100644 index 25c94dc0c..000000000 --- a/projects/ctd/docs/NullDataOptions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Enum: NullDataOptions - - - - -URI: [drug:NullDataOptions](http://w3id.org/ontogpt/drug/NullDataOptions) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | -| UNSPECIFIED_METHOD_OF_ADMINISTRATION | | NCIT:C149701 | | -| NOT_APPLICABLE | | NCIT:C18902 | {'aliases': ['not applicable', 'N/A']} | -| NOT_MENTIONED | | | | - diff --git a/projects/ctd/docs/Publication.md b/projects/ctd/docs/Publication.md deleted file mode 100644 index 838ef88ac..000000000 --- a/projects/ctd/docs/Publication.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Publication - - - - -URI: [drug:Publication](http://w3id.org/ontogpt/drug/Publication) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples])](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples]) - -## Referenced by Class - - * **None** *[➞publication](textWithTriples__publication.md)* <sub>0..1</sub> **[Publication](Publication.md)** - -## Attributes - - -### Own - - * [➞id](publication__id.md) <sub>0..1</sub> - * Description: The publication identifier - * Range: [String](types/String.md) - * [➞title](publication__title.md) <sub>0..1</sub> - * Description: The title of the publication - * Range: [String](types/String.md) - * [➞abstract](publication__abstract.md) <sub>0..1</sub> - * Description: The abstract of the publication - * Range: [String](types/String.md) - * [➞combined_text](publication__combined_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞full_text](publication__full_text.md) <sub>0..1</sub> - * Description: The full text of the publication - * Range: [String](types/String.md) diff --git a/projects/ctd/docs/RelationshipType.md b/projects/ctd/docs/RelationshipType.md deleted file mode 100644 index 937f4ba51..000000000 --- a/projects/ctd/docs/RelationshipType.md +++ /dev/null @@ -1,39 +0,0 @@ - -# Class: RelationshipType - - - - -URI: [drug:RelationshipType](http://w3id.org/ontogpt/drug/RelationshipType) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[RelationshipType]^-[ChemicalToDiseasePredicate],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity],[ChemicalToDiseasePredicate])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[RelationshipType]^-[ChemicalToDiseasePredicate],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity],[ChemicalToDiseasePredicate]) - -## Identifier prefixes - - * RO - * biolink - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Children - - * [ChemicalToDiseasePredicate](ChemicalToDiseasePredicate.md) - A predicate for chemical to disease relationships - -## Referenced by Class - - * **None** *[➞predicate](triple__predicate.md)* <sub>0..1</sub> **[RelationshipType](RelationshipType.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/ctd/docs/TextWithTriples.md b/projects/ctd/docs/TextWithTriples.md deleted file mode 100644 index 3e244027c..000000000 --- a/projects/ctd/docs/TextWithTriples.md +++ /dev/null @@ -1,27 +0,0 @@ - -# Class: TextWithTriples - - - - -URI: [drug:TextWithTriples](http://w3id.org/ontogpt/drug/TextWithTriples) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[TextWithTriples]^-[ChemicalToDiseaseDocument],[Publication],[ChemicalToDiseaseDocument])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[TextWithTriples]^-[ChemicalToDiseaseDocument],[Publication],[ChemicalToDiseaseDocument]) - -## Children - - * [ChemicalToDiseaseDocument](ChemicalToDiseaseDocument.md) - A document that contains chemical to disease relations. - -## Referenced by Class - - -## Attributes - - -### Own - - * [➞publication](textWithTriples__publication.md) <sub>0..1</sub> - * Range: [Publication](Publication.md) - * [➞triples](textWithTriples__triples.md) <sub>0..\*</sub> - * Range: [Triple](Triple.md) diff --git a/projects/ctd/docs/Triple.md b/projects/ctd/docs/Triple.md deleted file mode 100644 index 6768bc705..000000000 --- a/projects/ctd/docs/Triple.md +++ /dev/null @@ -1,43 +0,0 @@ - -# Class: Triple - - -Abstract parent for Relation Extraction tasks - -URI: [drug:Triple](http://w3id.org/ontogpt/drug/Triple) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[Triple]^-[ChemicalToDiseaseRelationship],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression],[ChemicalToDiseaseRelationship])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[Triple]^-[ChemicalToDiseaseRelationship],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression],[ChemicalToDiseaseRelationship]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Children - - * [ChemicalToDiseaseRelationship](ChemicalToDiseaseRelationship.md) - A triple where the subject is a chemical and the object is a disease. - -## Referenced by Class - - * **None** *[➞triples](textWithTriples__triples.md)* <sub>0..\*</sub> **[Triple](Triple.md)** - -## Attributes - - -### Own - - * [➞subject](triple__subject.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞predicate](triple__predicate.md) <sub>0..1</sub> - * Range: [RelationshipType](RelationshipType.md) - * [➞object](triple__object.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞qualifier](triple__qualifier.md) <sub>0..1</sub> - * Description: A qualifier for the statements, e.g. "NOT" for negation - * Range: [String](types/String.md) - * [➞subject_qualifier](triple__subject_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - * Range: [NamedEntity](NamedEntity.md) - * [➞object_qualifier](triple__object_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * Range: [NamedEntity](NamedEntity.md) diff --git a/projects/ctd/docs/annotatorResult__object_id.md b/projects/ctd/docs/annotatorResult__object_id.md deleted file mode 100644 index 3be702157..000000000 --- a/projects/ctd/docs/annotatorResult__object_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_id - - - - -URI: [drug:annotatorResult__object_id](http://w3id.org/ontogpt/drug/annotatorResult__object_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/ctd/docs/annotatorResult__object_text.md b/projects/ctd/docs/annotatorResult__object_text.md deleted file mode 100644 index 69b131f6a..000000000 --- a/projects/ctd/docs/annotatorResult__object_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_text - - - - -URI: [drug:annotatorResult__object_text](http://w3id.org/ontogpt/drug/annotatorResult__object_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/ctd/docs/annotatorResult__subject_text.md b/projects/ctd/docs/annotatorResult__subject_text.md deleted file mode 100644 index c72ea9131..000000000 --- a/projects/ctd/docs/annotatorResult__subject_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_text - - - - -URI: [drug:annotatorResult__subject_text](http://w3id.org/ontogpt/drug/annotatorResult__subject_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/ctd/docs/ctd.md b/projects/ctd/docs/ctd.md deleted file mode 100644 index 3388ac776..000000000 --- a/projects/ctd/docs/ctd.md +++ /dev/null @@ -1,119 +0,0 @@ - -# ctd - - -**metamodel version:** 1.7.0 - -**version:** None - - -A template for Chemical to Disease associations. -This template is intended to represent associations between chemicals and diseases, and for evaluating Semantic Llama against BioCreative V Chemical Disease Relation (CDR) Task (BC5CDR). - - -### Classes - - * [AnnotatorResult](AnnotatorResult.md) - * [Any](Any.md) - * [CompoundExpression](CompoundExpression.md) - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - * [ChemicalToDiseaseRelationship](ChemicalToDiseaseRelationship.md) - A triple where the subject is a chemical and the object is a disease. - * [ExtractionResult](ExtractionResult.md) - A result of extracting knowledge on text - * [NamedEntity](NamedEntity.md) - * [Chemical](Chemical.md) - * [Disease](Disease.md) - * [RelationshipType](RelationshipType.md) - * [ChemicalToDiseasePredicate](ChemicalToDiseasePredicate.md) - A predicate for chemical to disease relationships - * [Publication](Publication.md) - * [TextWithTriples](TextWithTriples.md) - * [ChemicalToDiseaseDocument](ChemicalToDiseaseDocument.md) - A document that contains chemical to disease relations. - -### Mixins - - -### Slots - - * [➞object_id](annotatorResult__object_id.md) - * [➞object_text](annotatorResult__object_text.md) - * [➞subject_text](annotatorResult__subject_text.md) - * [➞extracted_object](extractionResult__extracted_object.md) - The complex objects extracted from the text - * [➞input_id](extractionResult__input_id.md) - * [➞input_text](extractionResult__input_text.md) - * [➞input_title](extractionResult__input_title.md) - * [➞named_entities](extractionResult__named_entities.md) - Named entities extracted from the text - * [➞prompt](extractionResult__prompt.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) - * [➞id](namedEntity__id.md) - A unique identifier for the named entity - * [Chemical➞id](Chemical_id.md) - * [Disease➞id](Disease_id.md) - * [➞label](namedEntity__label.md) - The label (name) of the named thing - * [➞abstract](publication__abstract.md) - The abstract of the publication - * [➞combined_text](publication__combined_text.md) - * [➞full_text](publication__full_text.md) - The full text of the publication - * [➞id](publication__id.md) - The publication identifier - * [➞title](publication__title.md) - The title of the publication - * [➞publication](textWithTriples__publication.md) - * [➞triples](textWithTriples__triples.md) - * [ChemicalToDiseaseDocument➞triples](ChemicalToDiseaseDocument_triples.md) - * [➞object](triple__object.md) - * [ChemicalToDiseaseRelationship➞object](ChemicalToDiseaseRelationship_object.md) - The disease or condition that is being treated or induced by the chemical. For example, asthma, cancer, covid-19, cardiac asystole, Hypotension, Headache. - * [➞object_qualifier](triple__object_qualifier.md) - An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * [ChemicalToDiseaseRelationship➞object_qualifier](ChemicalToDiseaseRelationship_object_qualifier.md) - An optional qualifier or modifier for the disease, e.g. "severe" or "with additional complications" - * [➞predicate](triple__predicate.md) - * [ChemicalToDiseaseRelationship➞predicate](ChemicalToDiseaseRelationship_predicate.md) - The relationship type, e.g. INDUCES, TREATS. - * [➞qualifier](triple__qualifier.md) - A qualifier for the statements, e.g. "NOT" for negation - * [➞subject](triple__subject.md) - * [ChemicalToDiseaseRelationship➞subject](ChemicalToDiseaseRelationship_subject.md) - The chemical substance, drug, or small molecule. For example: Lidocaine, Monosodium Glutamate, Imatinib. - * [➞subject_qualifier](triple__subject_qualifier.md) - An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - * [ChemicalToDiseaseRelationship➞subject_qualifier](ChemicalToDiseaseRelationship_subject_qualifier.md) - An optional qualifier or modifier for the chemical, e.g. "high dose" or "intravenously administered" - -### Enums - - * [MeshChemicalIdentifier](MeshChemicalIdentifier.md) - * [MeshDiseaseIdentifier](MeshDiseaseIdentifier.md) - * [NullDataOptions](NullDataOptions.md) - -### Subsets - - -### Types - - -#### Built in - - * **Bool** - * **Curie** - * **Decimal** - * **ElementIdentifier** - * **NCName** - * **NodeIdentifier** - * **URI** - * **URIorCURIE** - * **XSDDate** - * **XSDDateTime** - * **XSDTime** - * **float** - * **int** - * **str** - -#### Defined - - * [Boolean](types/Boolean.md) (**Bool**) - A binary (true or false) value - * [Curie](types/Curie.md) (**Curie**) - a compact URI - * [Date](types/Date.md) (**XSDDate**) - a date (year, month and day) in an idealized calendar - * [DateOrDatetime](types/DateOrDatetime.md) (**str**) - Either a date or a datetime - * [Datetime](types/Datetime.md) (**XSDDateTime**) - The combination of a date and time - * [Decimal](types/Decimal.md) (**Decimal**) - A real number with arbitrary precision that conforms to the xsd:decimal specification - * [Double](types/Double.md) (**float**) - A real number that conforms to the xsd:double specification - * [Float](types/Float.md) (**float**) - A real number that conforms to the xsd:float specification - * [Integer](types/Integer.md) (**int**) - An integer - * [Jsonpath](types/Jsonpath.md) (**str**) - A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - * [Jsonpointer](types/Jsonpointer.md) (**str**) - A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - * [Ncname](types/Ncname.md) (**NCName**) - Prefix part of CURIE - * [Nodeidentifier](types/Nodeidentifier.md) (**NodeIdentifier**) - A URI, CURIE or BNODE that represents a node in a model. - * [Objectidentifier](types/Objectidentifier.md) (**ElementIdentifier**) - A URI or CURIE that represents an object in the model. - * [Sparqlpath](types/Sparqlpath.md) (**str**) - A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - * [String](types/String.md) (**str**) - A character string - * [Time](types/Time.md) (**XSDTime**) - A time object represents a (local) time of day, independent of any particular day - * [Uri](types/Uri.md) (**URI**) - a complete URI - * [Uriorcurie](types/Uriorcurie.md) (**URIorCURIE**) - a URI or a CURIE diff --git a/projects/ctd/docs/extractionResult__extracted_object.md b/projects/ctd/docs/extractionResult__extracted_object.md deleted file mode 100644 index 9e1ffec86..000000000 --- a/projects/ctd/docs/extractionResult__extracted_object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: extracted_object - - -The complex objects extracted from the text - -URI: [drug:extractionResult__extracted_object](http://w3id.org/ontogpt/drug/extractionResult__extracted_object) - - -## Domain and Range - -None → <sub>0..1</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ctd/docs/extractionResult__input_id.md b/projects/ctd/docs/extractionResult__input_id.md deleted file mode 100644 index 3091924ef..000000000 --- a/projects/ctd/docs/extractionResult__input_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_id - - - - -URI: [drug:extractionResult__input_id](http://w3id.org/ontogpt/drug/extractionResult__input_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ctd/docs/extractionResult__input_text.md b/projects/ctd/docs/extractionResult__input_text.md deleted file mode 100644 index e52590f86..000000000 --- a/projects/ctd/docs/extractionResult__input_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_text - - - - -URI: [drug:extractionResult__input_text](http://w3id.org/ontogpt/drug/extractionResult__input_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ctd/docs/extractionResult__input_title.md b/projects/ctd/docs/extractionResult__input_title.md deleted file mode 100644 index db5911166..000000000 --- a/projects/ctd/docs/extractionResult__input_title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_title - - - - -URI: [drug:extractionResult__input_title](http://w3id.org/ontogpt/drug/extractionResult__input_title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ctd/docs/extractionResult__named_entities.md b/projects/ctd/docs/extractionResult__named_entities.md deleted file mode 100644 index 5d7701c98..000000000 --- a/projects/ctd/docs/extractionResult__named_entities.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: named_entities - - -Named entities extracted from the text - -URI: [drug:extractionResult__named_entities](http://w3id.org/ontogpt/drug/extractionResult__named_entities) - - -## Domain and Range - -None → <sub>0..\*</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ctd/docs/extractionResult__prompt.md b/projects/ctd/docs/extractionResult__prompt.md deleted file mode 100644 index dc94587a9..000000000 --- a/projects/ctd/docs/extractionResult__prompt.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: prompt - - - - -URI: [drug:extractionResult__prompt](http://w3id.org/ontogpt/drug/extractionResult__prompt) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ctd/docs/extractionResult__raw_completion_output.md b/projects/ctd/docs/extractionResult__raw_completion_output.md deleted file mode 100644 index 1e77ca0a5..000000000 --- a/projects/ctd/docs/extractionResult__raw_completion_output.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: raw_completion_output - - - - -URI: [drug:extractionResult__raw_completion_output](http://w3id.org/ontogpt/drug/extractionResult__raw_completion_output) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ctd/docs/namedEntity__id.md b/projects/ctd/docs/namedEntity__id.md deleted file mode 100644 index d5667e862..000000000 --- a/projects/ctd/docs/namedEntity__id.md +++ /dev/null @@ -1,33 +0,0 @@ - -# Slot: id - - -A unique identifier for the named entity - -URI: [drug:namedEntity__id](http://w3id.org/ontogpt/drug/namedEntity__id) - - -## Domain and Range - -None → <sub>1..1</sub> [String](types/String.md) - -## Parents - - -## Children - - * [Chemical➞id](Chemical_id.md) - * [Disease➞id](Disease_id.md) - -## Used by - - * [ChemicalToDiseasePredicate](ChemicalToDiseasePredicate.md) - * [NamedEntity](NamedEntity.md) - * [RelationshipType](RelationshipType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | this is populated during the grounding and normalization step | - diff --git a/projects/ctd/docs/namedEntity__label.md b/projects/ctd/docs/namedEntity__label.md deleted file mode 100644 index 23898591a..000000000 --- a/projects/ctd/docs/namedEntity__label.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Slot: label - - -The label (name) of the named thing - -URI: [drug:namedEntity__label](http://w3id.org/ontogpt/drug/namedEntity__label) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Chemical](Chemical.md) - * [ChemicalToDiseasePredicate](ChemicalToDiseasePredicate.md) - * [Disease](Disease.md) - * [NamedEntity](NamedEntity.md) - * [RelationshipType](RelationshipType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Aliases:** | | name | -| **Mappings:** | | rdfs:label | - diff --git a/projects/ctd/docs/publication__abstract.md b/projects/ctd/docs/publication__abstract.md deleted file mode 100644 index f72aeea74..000000000 --- a/projects/ctd/docs/publication__abstract.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: abstract - - -The abstract of the publication - -URI: [drug:publication__abstract](http://w3id.org/ontogpt/drug/publication__abstract) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/ctd/docs/publication__combined_text.md b/projects/ctd/docs/publication__combined_text.md deleted file mode 100644 index 5e743fb57..000000000 --- a/projects/ctd/docs/publication__combined_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: combined_text - - - - -URI: [drug:publication__combined_text](http://w3id.org/ontogpt/drug/publication__combined_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/ctd/docs/publication__full_text.md b/projects/ctd/docs/publication__full_text.md deleted file mode 100644 index 7612a1e21..000000000 --- a/projects/ctd/docs/publication__full_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: full_text - - -The full text of the publication - -URI: [drug:publication__full_text](http://w3id.org/ontogpt/drug/publication__full_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/ctd/docs/publication__id.md b/projects/ctd/docs/publication__id.md deleted file mode 100644 index 6559e9615..000000000 --- a/projects/ctd/docs/publication__id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: id - - -The publication identifier - -URI: [drug:publication__id](http://w3id.org/ontogpt/drug/publication__id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/ctd/docs/publication__title.md b/projects/ctd/docs/publication__title.md deleted file mode 100644 index 5f67aee85..000000000 --- a/projects/ctd/docs/publication__title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: title - - -The title of the publication - -URI: [drug:publication__title](http://w3id.org/ontogpt/drug/publication__title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/ctd/docs/textWithTriples__publication.md b/projects/ctd/docs/textWithTriples__publication.md deleted file mode 100644 index d6b4fa34d..000000000 --- a/projects/ctd/docs/textWithTriples__publication.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: publication - - - - -URI: [drug:textWithTriples__publication](http://w3id.org/ontogpt/drug/textWithTriples__publication) - - -## Domain and Range - -None → <sub>0..1</sub> [Publication](Publication.md) - -## Parents - - -## Children - - -## Used by - - * [ChemicalToDiseaseDocument](ChemicalToDiseaseDocument.md) - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/ctd/docs/textWithTriples__triples.md b/projects/ctd/docs/textWithTriples__triples.md deleted file mode 100644 index c7cf5bb44..000000000 --- a/projects/ctd/docs/textWithTriples__triples.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: triples - - - - -URI: [drug:textWithTriples__triples](http://w3id.org/ontogpt/drug/textWithTriples__triples) - - -## Domain and Range - -None → <sub>0..\*</sub> [Triple](Triple.md) - -## Parents - - -## Children - - * [ChemicalToDiseaseDocument➞triples](ChemicalToDiseaseDocument_triples.md) - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/ctd/docs/triple__object.md b/projects/ctd/docs/triple__object.md deleted file mode 100644 index a2b3698de..000000000 --- a/projects/ctd/docs/triple__object.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: object - - - - -URI: [drug:triple__object](http://w3id.org/ontogpt/drug/triple__object) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - * [ChemicalToDiseaseRelationship➞object](ChemicalToDiseaseRelationship_object.md) - -## Used by - - * [Triple](Triple.md) diff --git a/projects/ctd/docs/triple__object_qualifier.md b/projects/ctd/docs/triple__object_qualifier.md deleted file mode 100644 index dc1efb4ab..000000000 --- a/projects/ctd/docs/triple__object_qualifier.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: object_qualifier - - -An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - -URI: [drug:triple__object_qualifier](http://w3id.org/ontogpt/drug/triple__object_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - * [ChemicalToDiseaseRelationship➞object_qualifier](ChemicalToDiseaseRelationship_object_qualifier.md) - -## Used by - - * [Triple](Triple.md) diff --git a/projects/ctd/docs/triple__predicate.md b/projects/ctd/docs/triple__predicate.md deleted file mode 100644 index a9b9ac83a..000000000 --- a/projects/ctd/docs/triple__predicate.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: predicate - - - - -URI: [drug:triple__predicate](http://w3id.org/ontogpt/drug/triple__predicate) - - -## Domain and Range - -None → <sub>0..1</sub> [RelationshipType](RelationshipType.md) - -## Parents - - -## Children - - * [ChemicalToDiseaseRelationship➞predicate](ChemicalToDiseaseRelationship_predicate.md) - -## Used by - - * [Triple](Triple.md) diff --git a/projects/ctd/docs/triple__qualifier.md b/projects/ctd/docs/triple__qualifier.md deleted file mode 100644 index 9ecf6f540..000000000 --- a/projects/ctd/docs/triple__qualifier.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: qualifier - - -A qualifier for the statements, e.g. "NOT" for negation - -URI: [drug:triple__qualifier](http://w3id.org/ontogpt/drug/triple__qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ChemicalToDiseaseRelationship](ChemicalToDiseaseRelationship.md) - * [Triple](Triple.md) diff --git a/projects/ctd/docs/triple__subject.md b/projects/ctd/docs/triple__subject.md deleted file mode 100644 index 9378144c0..000000000 --- a/projects/ctd/docs/triple__subject.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: subject - - - - -URI: [drug:triple__subject](http://w3id.org/ontogpt/drug/triple__subject) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - * [ChemicalToDiseaseRelationship➞subject](ChemicalToDiseaseRelationship_subject.md) - -## Used by - - * [Triple](Triple.md) diff --git a/projects/ctd/docs/triple__subject_qualifier.md b/projects/ctd/docs/triple__subject_qualifier.md deleted file mode 100644 index 05061102a..000000000 --- a/projects/ctd/docs/triple__subject_qualifier.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: subject_qualifier - - -An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -URI: [drug:triple__subject_qualifier](http://w3id.org/ontogpt/drug/triple__subject_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - * [ChemicalToDiseaseRelationship➞subject_qualifier](ChemicalToDiseaseRelationship_subject_qualifier.md) - -## Used by - - * [Triple](Triple.md) diff --git a/projects/ctd/docs/types/Boolean.md b/projects/ctd/docs/types/Boolean.md deleted file mode 100644 index dc83a9c6e..000000000 --- a/projects/ctd/docs/types/Boolean.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: boolean - - -A binary (true or false) value - -URI: [linkml:Boolean](https://w3id.org/linkml/Boolean) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Bool** | -| Representation | | bool | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Boolean | - diff --git a/projects/ctd/docs/types/Curie.md b/projects/ctd/docs/types/Curie.md deleted file mode 100644 index c1803f93f..000000000 --- a/projects/ctd/docs/types/Curie.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: curie - - -a compact URI - -URI: [linkml:Curie](https://w3id.org/linkml/Curie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Curie** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations this MUST be expanded to a URI | -| | | in non-RDF serializations MAY be serialized as the compact representation | - diff --git a/projects/ctd/docs/types/Date.md b/projects/ctd/docs/types/Date.md deleted file mode 100644 index 06948af97..000000000 --- a/projects/ctd/docs/types/Date.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: date - - -a date (year, month and day) in an idealized calendar - -URI: [linkml:Date](https://w3id.org/linkml/Date) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDate** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Date | - diff --git a/projects/ctd/docs/types/DateOrDatetime.md b/projects/ctd/docs/types/DateOrDatetime.md deleted file mode 100644 index ef983898d..000000000 --- a/projects/ctd/docs/types/DateOrDatetime.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: date_or_datetime - - -Either a date or a datetime - -URI: [linkml:DateOrDatetime](https://w3id.org/linkml/DateOrDatetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/ctd/docs/types/Datetime.md b/projects/ctd/docs/types/Datetime.md deleted file mode 100644 index 9510454a8..000000000 --- a/projects/ctd/docs/types/Datetime.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: datetime - - -The combination of a date and time - -URI: [linkml:Datetime](https://w3id.org/linkml/Datetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDateTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:DateTime | - diff --git a/projects/ctd/docs/types/Decimal.md b/projects/ctd/docs/types/Decimal.md deleted file mode 100644 index a7ba14a5d..000000000 --- a/projects/ctd/docs/types/Decimal.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: decimal - - -A real number with arbitrary precision that conforms to the xsd:decimal specification - -URI: [linkml:Decimal](https://w3id.org/linkml/Decimal) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Decimal** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Broad Mappings:** | | schema:Number | - diff --git a/projects/ctd/docs/types/Double.md b/projects/ctd/docs/types/Double.md deleted file mode 100644 index cfe6d71e2..000000000 --- a/projects/ctd/docs/types/Double.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: double - - -A real number that conforms to the xsd:double specification - -URI: [linkml:Double](https://w3id.org/linkml/Double) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Close Mappings:** | | schema:Float | - diff --git a/projects/ctd/docs/types/Float.md b/projects/ctd/docs/types/Float.md deleted file mode 100644 index 7b303f96f..000000000 --- a/projects/ctd/docs/types/Float.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: float - - -A real number that conforms to the xsd:float specification - -URI: [linkml:Float](https://w3id.org/linkml/Float) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Float | - diff --git a/projects/ctd/docs/types/Integer.md b/projects/ctd/docs/types/Integer.md deleted file mode 100644 index 3cfcc66d9..000000000 --- a/projects/ctd/docs/types/Integer.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: integer - - -An integer - -URI: [linkml:Integer](https://w3id.org/linkml/Integer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **int** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Integer | - diff --git a/projects/ctd/docs/types/Jsonpath.md b/projects/ctd/docs/types/Jsonpath.md deleted file mode 100644 index a03a58e67..000000000 --- a/projects/ctd/docs/types/Jsonpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpath - - -A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpath](https://w3id.org/linkml/Jsonpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/ctd/docs/types/Jsonpointer.md b/projects/ctd/docs/types/Jsonpointer.md deleted file mode 100644 index a0e1ac492..000000000 --- a/projects/ctd/docs/types/Jsonpointer.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpointer - - -A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpointer](https://w3id.org/linkml/Jsonpointer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/ctd/docs/types/Ncname.md b/projects/ctd/docs/types/Ncname.md deleted file mode 100644 index 710b0b04a..000000000 --- a/projects/ctd/docs/types/Ncname.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: ncname - - -Prefix part of CURIE - -URI: [linkml:Ncname](https://w3id.org/linkml/Ncname) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NCName** | -| Representation | | str | diff --git a/projects/ctd/docs/types/Nodeidentifier.md b/projects/ctd/docs/types/Nodeidentifier.md deleted file mode 100644 index f0097cdf4..000000000 --- a/projects/ctd/docs/types/Nodeidentifier.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: nodeidentifier - - -A URI, CURIE or BNODE that represents a node in a model. - -URI: [linkml:Nodeidentifier](https://w3id.org/linkml/Nodeidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NodeIdentifier** | -| Representation | | str | diff --git a/projects/ctd/docs/types/Objectidentifier.md b/projects/ctd/docs/types/Objectidentifier.md deleted file mode 100644 index 454ba6be6..000000000 --- a/projects/ctd/docs/types/Objectidentifier.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: objectidentifier - - -A URI or CURIE that represents an object in the model. - -URI: [linkml:Objectidentifier](https://w3id.org/linkml/Objectidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **ElementIdentifier** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | Used for inheritance and type checking | - diff --git a/projects/ctd/docs/types/Sparqlpath.md b/projects/ctd/docs/types/Sparqlpath.md deleted file mode 100644 index fd99a927e..000000000 --- a/projects/ctd/docs/types/Sparqlpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: sparqlpath - - -A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - -URI: [linkml:Sparqlpath](https://w3id.org/linkml/Sparqlpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/ctd/docs/types/String.md b/projects/ctd/docs/types/String.md deleted file mode 100644 index 6e61d7081..000000000 --- a/projects/ctd/docs/types/String.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: string - - -A character string - -URI: [linkml:String](https://w3id.org/linkml/String) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Text | - diff --git a/projects/ctd/docs/types/Time.md b/projects/ctd/docs/types/Time.md deleted file mode 100644 index 2b8652bcd..000000000 --- a/projects/ctd/docs/types/Time.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: time - - -A time object represents a (local) time of day, independent of any particular day - -URI: [linkml:Time](https://w3id.org/linkml/Time) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Time | - diff --git a/projects/ctd/docs/types/Uri.md b/projects/ctd/docs/types/Uri.md deleted file mode 100644 index 343807a5e..000000000 --- a/projects/ctd/docs/types/Uri.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: uri - - -a complete URI - -URI: [linkml:Uri](https://w3id.org/linkml/Uri) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URI** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node | -| **Close Mappings:** | | schema:URL | - diff --git a/projects/ctd/docs/types/Uriorcurie.md b/projects/ctd/docs/types/Uriorcurie.md deleted file mode 100644 index 2f7b65087..000000000 --- a/projects/ctd/docs/types/Uriorcurie.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: uriorcurie - - -a URI or a CURIE - -URI: [linkml:Uriorcurie](https://w3id.org/linkml/Uriorcurie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URIorCURIE** | -| Representation | | str | diff --git a/projects/ctd/excel/ctd.xlsx b/projects/ctd/excel/ctd.xlsx deleted file mode 100644 index 68d93db87..000000000 Binary files a/projects/ctd/excel/ctd.xlsx and /dev/null differ diff --git a/projects/ctd/graphql/ctd.graphql b/projects/ctd/graphql/ctd.graphql deleted file mode 100644 index 0c020b012..000000000 --- a/projects/ctd/graphql/ctd.graphql +++ /dev/null @@ -1,97 +0,0 @@ -type AnnotatorResult - { - subjectText: String - objectId: String - objectText: String - } - -type Any - { - } - -type Chemical - { - label: String - id: String! - } - -type ChemicalToDiseaseDocument - { - publication: Publication - triples: [ChemicalToDiseaseRelationship] - } - -type ChemicalToDiseasePredicate - { - id: String! - label: String - } - -type ChemicalToDiseaseRelationship - { - qualifier: String - subject: Chemical - object: Disease - predicate: ChemicalToDiseasePredicate - subjectQualifier: NamedEntity - objectQualifier: NamedEntity - } - -interface CompoundExpression - { - } - -type Disease - { - label: String - id: String! - } - -type ExtractionResult - { - inputId: String - inputTitle: String - inputText: String - rawCompletionOutput: String - prompt: String - extractedObject: Any - namedEntities: [Any] - } - -interface NamedEntity - { - id: String! - label: String - } - -type Publication - { - id: String - title: String - abstract: String - combinedText: String - fullText: String - } - -type RelationshipType - { - id: String! - label: String - } - -type TextWithTriples - { - publication: Publication - triples: [Triple] - } - -interface Triple - { - subject: NamedEntity - predicate: RelationshipType - object: NamedEntity - qualifier: String - subjectQualifier: NamedEntity - objectQualifier: NamedEntity - } - diff --git a/projects/ctd/jsonld/ctd.context.jsonld b/projects/ctd/jsonld/ctd.context.jsonld deleted file mode 100644 index b400329ed..000000000 --- a/projects/ctd/jsonld/ctd.context.jsonld +++ /dev/null @@ -1,128 +0,0 @@ -{ - "comments": { - "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2023-08-07T10:52:15", - "source": "ctd.yaml" - }, - "@context": { - "MESH": "http://example.org/UNKNOWN/MESH/", - "RO": { - "@id": "http://purl.obolibrary.org/obo/RO_", - "@prefix": true - }, - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "drug": "http://w3id.org/ontogpt/drug/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "@vocab": "http://w3id.org/ontogpt/drug/", - "object_id": { - "@id": "core:object_id" - }, - "object_text": { - "@id": "core:object_text" - }, - "subject_text": { - "@id": "core:subject_text" - }, - "id": { - "@id": "core:id" - }, - "extracted_object": { - "@type": "@id", - "@id": "core:extracted_object" - }, - "input_id": { - "@id": "core:input_id" - }, - "input_text": { - "@id": "core:input_text" - }, - "input_title": { - "@id": "core:input_title" - }, - "named_entities": { - "@type": "@id", - "@id": "core:named_entities" - }, - "prompt": { - "@id": "core:prompt" - }, - "raw_completion_output": { - "@id": "core:raw_completion_output" - }, - "label": { - "@id": "rdfs:label" - }, - "abstract": { - "@id": "core:abstract" - }, - "combined_text": { - "@id": "core:combined_text" - }, - "full_text": { - "@id": "core:full_text" - }, - "title": { - "@id": "core:title" - }, - "publication": { - "@type": "@id", - "@id": "core:publication" - }, - "triples": { - "@type": "@id", - "@id": "core:triples" - }, - "object": { - "@type": "@id", - "@id": "core:object" - }, - "object_qualifier": { - "@type": "@id", - "@id": "core:object_qualifier" - }, - "predicate": { - "@type": "@id", - "@id": "core:predicate" - }, - "qualifier": { - "@id": "core:qualifier" - }, - "subject": { - "@type": "@id", - "@id": "core:subject" - }, - "subject_qualifier": { - "@type": "@id", - "@id": "core:subject_qualifier" - }, - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } - } -} diff --git a/projects/ctd/jsonld/ctd.jsonld b/projects/ctd/jsonld/ctd.jsonld deleted file mode 100644 index e92a5d975..000000000 --- a/projects/ctd/jsonld/ctd.jsonld +++ /dev/null @@ -1,1303 +0,0 @@ -{ - "name": "ctd", - "description": "A template for Chemical to Disease associations.\nThis template is intended to represent associations between chemicals and diseases, and for evaluating Semantic Llama against BioCreative V Chemical Disease Relation (CDR) Task (BC5CDR).", - "title": "Chemical to Disease Template", - "source": "https://biocreative.bioinformatics.udel.edu/tasks/biocreative-v/track-3-cdr/", - "see_also": [ - "https://biocreative.bioinformatics.udel.edu/media/store/files/2015/BC5CDR_overview.final.pdf", - "https://academic.oup.com/database/article/doi/10.1093/database/baw068/2630414" - ], - "id": "http://w3id.org/ontogpt/ctd", - "imports": [ - "linkml:types", - "core" - ], - "license": "https://creativecommons.org/publicdomain/zero/1.0/", - "prefixes": [ - { - "prefix_prefix": "linkml", - "prefix_reference": "https://w3id.org/linkml/" - }, - { - "prefix_prefix": "drug", - "prefix_reference": "http://w3id.org/ontogpt/drug/" - } - ], - "default_prefix": "drug", - "default_range": "string", - "types": [ - { - "name": "string", - "definition_uri": "https://w3id.org/linkml/String", - "description": "A character string", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Text" - ], - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "@type": "TypeDefinition" - }, - { - "name": "integer", - "definition_uri": "https://w3id.org/linkml/Integer", - "description": "An integer", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Integer" - ], - "base": "int", - "uri": "http://www.w3.org/2001/XMLSchema#integer", - "@type": "TypeDefinition" - }, - { - "name": "boolean", - "definition_uri": "https://w3id.org/linkml/Boolean", - "description": "A binary (true or false) value", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Boolean" - ], - "base": "Bool", - "uri": "http://www.w3.org/2001/XMLSchema#boolean", - "repr": "bool", - "@type": "TypeDefinition" - }, - { - "name": "float", - "definition_uri": "https://w3id.org/linkml/Float", - "description": "A real number that conforms to the xsd:float specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#float", - "@type": "TypeDefinition" - }, - { - "name": "double", - "definition_uri": "https://w3id.org/linkml/Double", - "description": "A real number that conforms to the xsd:double specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#double", - "@type": "TypeDefinition" - }, - { - "name": "decimal", - "definition_uri": "https://w3id.org/linkml/Decimal", - "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "broad_mappings": [ - "schema:Number" - ], - "base": "Decimal", - "uri": "http://www.w3.org/2001/XMLSchema#decimal", - "@type": "TypeDefinition" - }, - { - "name": "time", - "definition_uri": "https://w3id.org/linkml/Time", - "description": "A time object represents a (local) time of day, independent of any particular day", - "notes": [ - "URI is dateTime because OWL reasoners do not work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Time" - ], - "base": "XSDTime", - "uri": "http://www.w3.org/2001/XMLSchema#time", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date", - "definition_uri": "https://w3id.org/linkml/Date", - "description": "a date (year, month and day) in an idealized calendar", - "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Date" - ], - "base": "XSDDate", - "uri": "http://www.w3.org/2001/XMLSchema#date", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "datetime", - "definition_uri": "https://w3id.org/linkml/Datetime", - "description": "The combination of a date and time", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:DateTime" - ], - "base": "XSDDateTime", - "uri": "http://www.w3.org/2001/XMLSchema#dateTime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date_or_datetime", - "definition_uri": "https://w3id.org/linkml/DateOrDatetime", - "description": "Either a date or a datetime", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "https://w3id.org/linkml/DateOrDatetime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uriorcurie", - "definition_uri": "https://w3id.org/linkml/Uriorcurie", - "description": "a URI or a CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "URIorCURIE", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "curie", - "definition_uri": "https://w3id.org/linkml/Curie", - "conforms_to": "https://www.w3.org/TR/curie/", - "description": "a compact URI", - "comments": [ - "in RDF serializations this MUST be expanded to a URI", - "in non-RDF serializations MAY be serialized as the compact representation" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "Curie", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uri", - "definition_uri": "https://w3id.org/linkml/Uri", - "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", - "description": "a complete URI", - "comments": [ - "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:URL" - ], - "base": "URI", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "ncname", - "definition_uri": "https://w3id.org/linkml/Ncname", - "description": "Prefix part of CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NCName", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "objectidentifier", - "definition_uri": "https://w3id.org/linkml/Objectidentifier", - "description": "A URI or CURIE that represents an object in the model.", - "comments": [ - "Used for inheritance and type checking" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "ElementIdentifier", - "uri": "http://www.w3.org/ns/shex#iri", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "nodeidentifier", - "definition_uri": "https://w3id.org/linkml/Nodeidentifier", - "description": "A URI, CURIE or BNODE that represents a node in a model.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NodeIdentifier", - "uri": "http://www.w3.org/ns/shex#nonLiteral", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpointer", - "definition_uri": "https://w3id.org/linkml/Jsonpointer", - "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901", - "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpath", - "definition_uri": "https://w3id.org/linkml/Jsonpath", - "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html", - "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "sparqlpath", - "definition_uri": "https://w3id.org/linkml/Sparqlpath", - "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths", - "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - } - ], - "enums": [ - { - "name": "MeshChemicalIdentifier", - "definition_uri": "http://w3id.org/ontogpt/drug/MeshChemicalIdentifier", - "from_schema": "http://w3id.org/ontogpt/ctd", - "reachable_from": { - "source_ontology": "obo:mesh", - "source_nodes": [ - "MESH:D000602", - "MESH:D001685", - "MESH:D002241", - "MESH:D004364", - "MESH:D006571", - "MESH:D007287", - "MESH:D008055", - "MESH:D009706", - "MESH:D009930", - "MESH:D011083", - "MESH:D013812", - "MESH:D019602", - "MESH:D045424", - "MESH:D045762", - "MESH:D046911" - ] - } - }, - { - "name": "MeshDiseaseIdentifier", - "definition_uri": "http://w3id.org/ontogpt/drug/MeshDiseaseIdentifier", - "from_schema": "http://w3id.org/ontogpt/ctd", - "reachable_from": { - "source_ontology": "obo:mesh", - "source_nodes": [ - "MESH:D001423", - "MESH:D001523", - "MESH:D002318", - "MESH:D002943", - "MESH:D004066", - "MESH:D004700", - "MESH:D005128", - "MESH:D005261", - "MESH:D006425", - "MESH:D007154", - "MESH:D007280", - "MESH:D009057", - "MESH:D009140", - "MESH:D009358", - "MESH:D009369", - "MESH:D009422", - "MESH:D009750", - "MESH:D009784", - "MESH:D010038", - "MESH:D010272", - "MESH:D012140", - "MESH:D013568", - "MESH:D014777", - "MESH:D014947", - "MESH:D017437", - "MESH:D052801", - "MESH:D064419" - ] - } - }, - { - "name": "NullDataOptions", - "definition_uri": "http://w3id.org/ontogpt/core/NullDataOptions", - "from_schema": "http://w3id.org/ontogpt/core", - "permissible_values": [ - { - "text": "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "meaning": "NCIT:C149701" - }, - { - "text": "NOT_APPLICABLE", - "meaning": "NCIT:C18902", - "aliases": [ - "not applicable", - "N/A" - ] - }, - { - "text": "NOT_MENTIONED" - } - ] - } - ], - "slots": [ - { - "name": "extractionResult__input_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_id", - "alias": "input_id", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_title", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_title", - "alias": "input_title", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_text", - "alias": "input_text", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__raw_completion_output", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/raw_completion_output", - "alias": "raw_completion_output", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__prompt", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/prompt", - "alias": "prompt", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__extracted_object", - "description": "The complex objects extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/extracted_object", - "alias": "extracted_object", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__named_entities", - "description": "Named entities extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/named_entities", - "multivalued": true, - "alias": "named_entities", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "identifier": true, - "alias": "id", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "required": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "from_schema": "http://w3id.org/ontogpt/core", - "aliases": [ - "name" - ], - "mappings": [ - "http://example.org/UNKNOWN/rdfs/label" - ], - "slot_uri": "http://example.org/UNKNOWN/rdfs/label", - "alias": "label", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject", - "alias": "subject", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__predicate", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/predicate", - "alias": "predicate", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "triple__object", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object", - "alias": "object", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/qualifier", - "alias": "qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_qualifier", - "alias": "subject_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_qualifier", - "alias": "object_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/publication", - "alias": "publication", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__triples", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/triples", - "multivalued": true, - "alias": "triples", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "publication__id", - "description": "The publication identifier", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "alias": "id", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__title", - "description": "The title of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/title", - "alias": "title", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__abstract", - "description": "The abstract of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/abstract", - "alias": "abstract", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__combined_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/combined_text", - "alias": "combined_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__full_text", - "description": "The full text of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/full_text", - "alias": "full_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__subject_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_text", - "alias": "subject_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_id", - "alias": "object_id", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_text", - "alias": "object_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "ChemicalToDiseaseDocument_triples", - "annotations": [ - { - "tag": "prompt", - "value": "A semi-colon separated list of chemical to disease relationships, where the relationship is either INDUCES or TREATS. for example: Lidocaine INDUCES cardiac asystole; Hydroxychloroquine NOT TREATS COVID-19; Methyldopa INDUCES Hypotension; Monosodium Glutamate NOT INDUCES Headache; Imatinib TREATS cancer", - "@type": "Annotation" - }, - { - "tag": "exclude", - "value": "Lidocaine, cardiac asystole, Hydroxychloroquine, COVID-19, Methyldopa, Headache, Imatinib, cancer", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/ctd", - "is_a": "textWithTriples__triples", - "domain": "ChemicalToDiseaseDocument", - "slot_uri": "http://w3id.org/ontogpt/drug/triples", - "multivalued": true, - "alias": "triples", - "owner": "ChemicalToDiseaseDocument", - "domain_of": [ - "ChemicalToDiseaseDocument" - ], - "is_usage_slot": true, - "usage_slot_name": "triples", - "range": "ChemicalToDiseaseRelationship", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "ChemicalToDiseaseRelationship_subject", - "description": "The chemical substance, drug, or small molecule. For example: Lidocaine, Monosodium Glutamate, Imatinib.", - "from_schema": "http://w3id.org/ontogpt/ctd", - "is_a": "triple__subject", - "domain": "ChemicalToDiseaseRelationship", - "slot_uri": "http://w3id.org/ontogpt/drug/subject", - "alias": "subject", - "owner": "ChemicalToDiseaseRelationship", - "domain_of": [ - "ChemicalToDiseaseRelationship" - ], - "is_usage_slot": true, - "usage_slot_name": "subject", - "range": "Chemical", - "@type": "SlotDefinition" - }, - { - "name": "ChemicalToDiseaseRelationship_object", - "description": "The disease or condition that is being treated or induced by the chemical. For example, asthma, cancer, covid-19, cardiac asystole, Hypotension, Headache.", - "from_schema": "http://w3id.org/ontogpt/ctd", - "is_a": "triple__object", - "domain": "ChemicalToDiseaseRelationship", - "slot_uri": "http://w3id.org/ontogpt/drug/object", - "alias": "object", - "owner": "ChemicalToDiseaseRelationship", - "domain_of": [ - "ChemicalToDiseaseRelationship" - ], - "is_usage_slot": true, - "usage_slot_name": "object", - "range": "Disease", - "@type": "SlotDefinition" - }, - { - "name": "ChemicalToDiseaseRelationship_predicate", - "description": "The relationship type, e.g. INDUCES, TREATS.", - "from_schema": "http://w3id.org/ontogpt/ctd", - "is_a": "triple__predicate", - "domain": "ChemicalToDiseaseRelationship", - "slot_uri": "http://w3id.org/ontogpt/drug/predicate", - "alias": "predicate", - "owner": "ChemicalToDiseaseRelationship", - "domain_of": [ - "ChemicalToDiseaseRelationship" - ], - "is_usage_slot": true, - "usage_slot_name": "predicate", - "range": "ChemicalToDiseasePredicate", - "@type": "SlotDefinition" - }, - { - "name": "ChemicalToDiseaseRelationship_subject_qualifier", - "description": "An optional qualifier or modifier for the chemical, e.g. \"high dose\" or \"intravenously administered\"", - "from_schema": "http://w3id.org/ontogpt/ctd", - "is_a": "triple__subject_qualifier", - "domain": "ChemicalToDiseaseRelationship", - "slot_uri": "http://w3id.org/ontogpt/drug/subject_qualifier", - "alias": "subject_qualifier", - "owner": "ChemicalToDiseaseRelationship", - "domain_of": [ - "ChemicalToDiseaseRelationship" - ], - "is_usage_slot": true, - "usage_slot_name": "subject_qualifier", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "ChemicalToDiseaseRelationship_object_qualifier", - "description": "An optional qualifier or modifier for the disease, e.g. \"severe\" or \"with additional complications\"", - "from_schema": "http://w3id.org/ontogpt/ctd", - "is_a": "triple__object_qualifier", - "domain": "ChemicalToDiseaseRelationship", - "slot_uri": "http://w3id.org/ontogpt/drug/object_qualifier", - "alias": "object_qualifier", - "owner": "ChemicalToDiseaseRelationship", - "domain_of": [ - "ChemicalToDiseaseRelationship" - ], - "is_usage_slot": true, - "usage_slot_name": "object_qualifier", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "Disease_id", - "from_schema": "http://w3id.org/ontogpt/ctd", - "is_a": "namedEntity__id", - "values_from": [ - "MeshDiseaseIdentifier" - ], - "domain": "Disease", - "slot_uri": "http://w3id.org/ontogpt/drug/id", - "identifier": true, - "alias": "id", - "owner": "Disease", - "domain_of": [ - "Disease" - ], - "is_usage_slot": true, - "usage_slot_name": "id", - "range": "string", - "required": true, - "pattern": "^MESH:[CD][0-9]{6}$", - "@type": "SlotDefinition" - }, - { - "name": "Chemical_id", - "from_schema": "http://w3id.org/ontogpt/ctd", - "is_a": "namedEntity__id", - "values_from": [ - "MeshChemicalIdentifier" - ], - "domain": "Chemical", - "slot_uri": "http://w3id.org/ontogpt/drug/id", - "identifier": true, - "alias": "id", - "owner": "Chemical", - "domain_of": [ - "Chemical" - ], - "is_usage_slot": true, - "usage_slot_name": "id", - "range": "string", - "required": true, - "pattern": "^MESH:[CD][0-9]{6}$", - "@type": "SlotDefinition" - } - ], - "classes": [ - { - "name": "ChemicalToDiseaseDocument", - "definition_uri": "http://w3id.org/ontogpt/drug/ChemicalToDiseaseDocument", - "description": "A document that contains chemical to disease relations.", - "from_schema": "http://w3id.org/ontogpt/ctd", - "is_a": "TextWithTriples", - "slots": [ - "textWithTriples__publication", - "ChemicalToDiseaseDocument_triples" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/drug/ChemicalToDiseaseDocument", - "@type": "ClassDefinition" - }, - { - "name": "ChemicalToDiseaseRelationship", - "definition_uri": "http://w3id.org/ontogpt/drug/ChemicalToDiseaseRelationship", - "description": "A triple where the subject is a chemical and the object is a disease.", - "from_schema": "http://w3id.org/ontogpt/ctd", - "is_a": "Triple", - "slots": [ - "triple__qualifier", - "ChemicalToDiseaseRelationship_subject", - "ChemicalToDiseaseRelationship_object", - "ChemicalToDiseaseRelationship_predicate", - "ChemicalToDiseaseRelationship_subject_qualifier", - "ChemicalToDiseaseRelationship_object_qualifier" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/drug/ChemicalToDiseaseRelationship", - "@type": "ClassDefinition" - }, - { - "name": "Disease", - "id_prefixes": [ - "MESH" - ], - "definition_uri": "http://w3id.org/ontogpt/drug/Disease", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:mesh, sqlite:obo:mondo, sqlite:obo:hp, sqlite:obo:ncit, sqlite:obo:doid, bioportal:meddra", - "@type": "Annotation" - }, - { - "tag": "prompt.examples", - "value": "cardiac asystole, COVID-19, Headache, cancer", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/ctd", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__label", - "Disease_id" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/drug/Disease", - "@type": "ClassDefinition" - }, - { - "name": "Chemical", - "id_prefixes": [ - "MESH" - ], - "definition_uri": "http://w3id.org/ontogpt/drug/Chemical", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:mesh, sqlite:obo:chebi, sqlite:obo:ncit, bioportal:mdm, sqlite:obo:drugbank, gilda:", - "@type": "Annotation" - }, - { - "tag": "prompt.examples", - "value": "Lidocaine, Hydroxychloroquine, Methyldopa, Imatinib", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/ctd", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__label", - "Chemical_id" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/drug/Chemical", - "@type": "ClassDefinition" - }, - { - "name": "ChemicalToDiseasePredicate", - "definition_uri": "http://w3id.org/ontogpt/drug/ChemicalToDiseasePredicate", - "description": "A predicate for chemical to disease relationships", - "comments": [ - "for the purposes of evaluation against BC5CDR, any predicate other than INDUCES is ignored." - ], - "from_schema": "http://w3id.org/ontogpt/ctd", - "is_a": "RelationshipType", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/drug/ChemicalToDiseasePredicate", - "@type": "ClassDefinition" - }, - { - "name": "Any", - "definition_uri": "http://w3id.org/ontogpt/core/Any", - "from_schema": "http://w3id.org/ontogpt/core", - "mappings": [ - "linkml:Any" - ], - "slot_usage": {}, - "class_uri": "https://w3id.org/linkml/Any", - "@type": "ClassDefinition" - }, - { - "name": "ExtractionResult", - "definition_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "description": "A result of extracting knowledge on text", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "extractionResult__input_id", - "extractionResult__input_title", - "extractionResult__input_text", - "extractionResult__raw_completion_output", - "extractionResult__prompt", - "extractionResult__extracted_object", - "extractionResult__named_entities" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "input_id", - "@type": "SlotDefinition" - }, - { - "name": "input_title", - "@type": "SlotDefinition" - }, - { - "name": "input_text", - "@type": "SlotDefinition" - }, - { - "name": "raw_completion_output", - "@type": "SlotDefinition" - }, - { - "name": "prompt", - "@type": "SlotDefinition" - }, - { - "name": "extracted_object", - "description": "The complex objects extracted from the text", - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "named_entities", - "description": "Named entities extracted from the text", - "multivalued": true, - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "@type": "ClassDefinition" - }, - { - "name": "NamedEntity", - "definition_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "identifier": true, - "@type": "SlotDefinition" - }, - { - "name": "label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "aliases": [ - "name" - ], - "slot_uri": "rdfs:label", - "range": "string", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "@type": "ClassDefinition" - }, - { - "name": "CompoundExpression", - "definition_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "@type": "ClassDefinition" - }, - { - "name": "Triple", - "definition_uri": "http://w3id.org/ontogpt/core/Triple", - "description": "Abstract parent for Relation Extraction tasks", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "CompoundExpression", - "abstract": true, - "slots": [ - "triple__subject", - "triple__predicate", - "triple__object", - "triple__qualifier", - "triple__subject_qualifier", - "triple__object_qualifier" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "predicate", - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "object", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Triple", - "@type": "ClassDefinition" - }, - { - "name": "TextWithTriples", - "definition_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "textWithTriples__publication", - "textWithTriples__triples" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "triples", - "multivalued": true, - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "@type": "ClassDefinition" - }, - { - "name": "RelationshipType", - "id_prefixes": [ - "RO", - "biolink" - ], - "definition_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "@type": "ClassDefinition" - }, - { - "name": "Publication", - "definition_uri": "http://w3id.org/ontogpt/core/Publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "publication__id", - "publication__title", - "publication__abstract", - "publication__combined_text", - "publication__full_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "description": "The publication identifier", - "@type": "SlotDefinition" - }, - { - "name": "title", - "description": "The title of the publication", - "@type": "SlotDefinition" - }, - { - "name": "abstract", - "description": "The abstract of the publication", - "@type": "SlotDefinition" - }, - { - "name": "combined_text", - "@type": "SlotDefinition" - }, - { - "name": "full_text", - "description": "The full text of the publication", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Publication", - "@type": "ClassDefinition" - }, - { - "name": "AnnotatorResult", - "definition_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "annotatorResult__subject_text", - "annotatorResult__object_id", - "annotatorResult__object_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject_text", - "@type": "SlotDefinition" - }, - { - "name": "object_id", - "@type": "SlotDefinition" - }, - { - "name": "object_text", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "@type": "ClassDefinition" - } - ], - "metamodel_version": "1.7.0", - "source_file": "ctd.yaml", - "source_file_date": "2023-06-17T15:11:19", - "source_file_size": 6683, - "generation_date": "2023-08-07T10:52:16", - "@type": "SchemaDefinition", - "@context": [ - "projects/ctd/jsonld/ctd.context.jsonld", - "https://w3id.org/linkml/types.context.jsonld", - "core.context.jsonld", - { - "@base": "http://w3id.org/ontogpt/drug/" - } - ] -} diff --git a/projects/ctd/jsonschema/ctd.schema.json b/projects/ctd/jsonschema/ctd.schema.json deleted file mode 100644 index 81c32600a..000000000 --- a/projects/ctd/jsonschema/ctd.schema.json +++ /dev/null @@ -1,261 +0,0 @@ -{ - "$defs": { - "AnnotatorResult": { - "additionalProperties": false, - "description": "", - "properties": { - "object_id": { - "type": "string" - }, - "object_text": { - "type": "string" - }, - "subject_text": { - "type": "string" - } - }, - "title": "AnnotatorResult", - "type": "object" - }, - "Any": { - "additionalProperties": true, - "description": "", - "title": "Any", - "type": "object" - }, - "Chemical": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "pattern": "^MESH:[CD][0-9]{6}$", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Chemical", - "type": "object" - }, - "ChemicalToDiseaseDocument": { - "additionalProperties": false, - "description": "A document that contains chemical to disease relations.", - "properties": { - "publication": { - "$ref": "#/$defs/Publication" - }, - "triples": { - "items": { - "$ref": "#/$defs/ChemicalToDiseaseRelationship" - }, - "type": "array" - } - }, - "title": "ChemicalToDiseaseDocument", - "type": "object" - }, - "ChemicalToDiseasePredicate": { - "additionalProperties": false, - "description": "A predicate for chemical to disease relationships", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "ChemicalToDiseasePredicate", - "type": "object" - }, - "ChemicalToDiseaseRelationship": { - "additionalProperties": false, - "description": "A triple where the subject is a chemical and the object is a disease.", - "properties": { - "object": { - "description": "The disease or condition that is being treated or induced by the chemical. For example, asthma, cancer, covid-19, cardiac asystole, Hypotension, Headache.", - "type": "string" - }, - "object_qualifier": { - "description": "An optional qualifier or modifier for the disease, e.g. \"severe\" or \"with additional complications\"", - "type": "string" - }, - "predicate": { - "description": "The relationship type, e.g. INDUCES, TREATS.", - "type": "string" - }, - "qualifier": { - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "type": "string" - }, - "subject": { - "description": "The chemical substance, drug, or small molecule. For example: Lidocaine, Monosodium Glutamate, Imatinib.", - "type": "string" - }, - "subject_qualifier": { - "description": "An optional qualifier or modifier for the chemical, e.g. \"high dose\" or \"intravenously administered\"", - "type": "string" - } - }, - "title": "ChemicalToDiseaseRelationship", - "type": "object" - }, - "Disease": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "pattern": "^MESH:[CD][0-9]{6}$", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Disease", - "type": "object" - }, - "ExtractionResult": { - "additionalProperties": false, - "description": "A result of extracting knowledge on text", - "properties": { - "extracted_object": { - "$ref": "#/$defs/Any", - "description": "The complex objects extracted from the text" - }, - "input_id": { - "type": "string" - }, - "input_text": { - "type": "string" - }, - "input_title": { - "type": "string" - }, - "named_entities": { - "description": "Named entities extracted from the text", - "items": { - "$ref": "#/$defs/Any" - }, - "type": "array" - }, - "prompt": { - "type": "string" - }, - "raw_completion_output": { - "type": "string" - } - }, - "title": "ExtractionResult", - "type": "object" - }, - "MeshChemicalIdentifier": { - "description": "", - "enum": [], - "title": "MeshChemicalIdentifier", - "type": "string" - }, - "MeshDiseaseIdentifier": { - "description": "", - "enum": [], - "title": "MeshDiseaseIdentifier", - "type": "string" - }, - "NullDataOptions": { - "description": "", - "enum": [ - "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "NOT_APPLICABLE", - "NOT_MENTIONED" - ], - "title": "NullDataOptions", - "type": "string" - }, - "Publication": { - "additionalProperties": false, - "description": "", - "properties": { - "abstract": { - "description": "The abstract of the publication", - "type": "string" - }, - "combined_text": { - "type": "string" - }, - "full_text": { - "description": "The full text of the publication", - "type": "string" - }, - "id": { - "description": "The publication identifier", - "type": "string" - }, - "title": { - "description": "The title of the publication", - "type": "string" - } - }, - "title": "Publication", - "type": "object" - }, - "RelationshipType": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "RelationshipType", - "type": "object" - }, - "TextWithTriples": { - "additionalProperties": false, - "description": "", - "properties": { - "publication": { - "$ref": "#/$defs/Publication" - }, - "triples": { - "items": { - "$ref": "#/$defs/Triple" - }, - "type": "array" - } - }, - "title": "TextWithTriples", - "type": "object" - } - }, - "$id": "http://w3id.org/ontogpt/ctd", - "$schema": "http://json-schema.org/draft-07/schema#", - "additionalProperties": true, - "metamodel_version": "1.7.0", - "title": "ctd", - "type": "object", - "version": null -} \ No newline at end of file diff --git a/projects/ctd/owl/ctd.owl.ttl b/projects/ctd/owl/ctd.owl.ttl deleted file mode 100644 index 699f47674..000000000 --- a/projects/ctd/owl/ctd.owl.ttl +++ /dev/null @@ -1,500 +0,0 @@ -@prefix IAO: <http://purl.obolibrary.org/obo/IAO_> . -@prefix drug: <http://w3id.org/ontogpt/drug/> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix owl: <http://www.w3.org/2002/07/owl#> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . -@prefix skos: <http://www.w3.org/2004/02/skos/core#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -<http://w3id.org/ontogpt/ctd> a owl:Ontology ; - rdfs:label "ctd" ; - IAO:0000700 <http://w3id.org/ontogpt/core/AnnotatorResult>, - <http://w3id.org/ontogpt/core/Any>, - <http://w3id.org/ontogpt/core/CompoundExpression>, - <http://w3id.org/ontogpt/core/ExtractionResult>, - <http://w3id.org/ontogpt/core/NamedEntity>, - <http://w3id.org/ontogpt/core/Publication>, - <http://w3id.org/ontogpt/core/TextWithTriples> ; - linkml:classes "{'ChemicalToDiseaseDocument': ClassDefinition(name='ChemicalToDiseaseDocument', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/drug/ChemicalToDiseaseDocument', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A document that contains chemical to disease relations.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/ctd', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='TextWithTriples', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['textWithTriples__publication', 'ChemicalToDiseaseDocument_triples'], slot_usage={'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='A semi-colon separated list of chemical to disease relationships, where the relationship is either INDUCES or TREATS. for example: Lidocaine INDUCES cardiac asystole; Hydroxychloroquine NOT TREATS COVID-19; Methyldopa INDUCES Hypotension; Monosodium Glutamate NOT INDUCES Headache; Imatinib TREATS cancer', extensions={}, annotations={}), 'exclude': Annotation(tag='exclude', value='Lidocaine, cardiac asystole, Hydroxychloroquine, COVID-19, Methyldopa, Headache, Imatinib, cancer', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='textWithTriples__triples', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ChemicalToDiseaseRelationship', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='drug:ChemicalToDiseaseDocument', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ChemicalToDiseaseRelationship': ClassDefinition(name='ChemicalToDiseaseRelationship', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/drug/ChemicalToDiseaseRelationship', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A triple where the subject is a chemical and the object is a disease.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/ctd', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='Triple', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['triple__qualifier', 'ChemicalToDiseaseRelationship_subject', 'ChemicalToDiseaseRelationship_object', 'ChemicalToDiseaseRelationship_predicate', 'ChemicalToDiseaseRelationship_subject_qualifier', 'ChemicalToDiseaseRelationship_object_qualifier'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The chemical substance, drug, or small molecule. For example: Lidocaine, Monosodium Glutamate, Imatinib.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='triple__subject', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Chemical', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The disease or condition that is being treated or induced by the chemical. For example, asthma, cancer, covid-19, cardiac asystole, Hypotension, Headache.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='triple__object', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Disease', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The relationship type, e.g. INDUCES, TREATS.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='triple__predicate', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ChemicalToDiseasePredicate', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the chemical, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='triple__subject_qualifier', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the disease, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='triple__object_qualifier', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='drug:ChemicalToDiseaseRelationship', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Disease': ClassDefinition(name='Disease', id_prefixes=['MESH'], definition_uri='http://w3id.org/ontogpt/drug/Disease', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:mesh, sqlite:obo:mondo, sqlite:obo:hp, sqlite:obo:ncit, sqlite:obo:doid, bioportal:meddra', extensions={}, annotations={}), 'prompt.examples': Annotation(tag='prompt.examples', value='cardiac asystole, COVID-19, Headache, cancer', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/ctd', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__label', 'Disease_id'], slot_usage={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='namedEntity__id', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=['MeshDiseaseIdentifier'], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern='^MESH:[CD][0-9]{6}$', structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='drug:Disease', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Chemical': ClassDefinition(name='Chemical', id_prefixes=['MESH'], definition_uri='http://w3id.org/ontogpt/drug/Chemical', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:mesh, sqlite:obo:chebi, sqlite:obo:ncit, bioportal:mdm, sqlite:obo:drugbank, gilda:', extensions={}, annotations={}), 'prompt.examples': Annotation(tag='prompt.examples', value='Lidocaine, Hydroxychloroquine, Methyldopa, Imatinib', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/ctd', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__label', 'Chemical_id'], slot_usage={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='namedEntity__id', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=['MeshChemicalIdentifier'], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern='^MESH:[CD][0-9]{6}$', structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='drug:Chemical', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ChemicalToDiseasePredicate': ClassDefinition(name='ChemicalToDiseasePredicate', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/drug/ChemicalToDiseasePredicate', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A predicate for chemical to disease relationships', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['for the purposes of evaluation against BC5CDR, any predicate other than INDUCES is ignored.'], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/ctd', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='RelationshipType', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='drug:ChemicalToDiseasePredicate', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Any': ClassDefinition(name='Any', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Any', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=['linkml:Any'], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='linkml:Any', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ExtractionResult': ClassDefinition(name='ExtractionResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/ExtractionResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A result of extracting knowledge on text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['extractionResult__input_id', 'extractionResult__input_title', 'extractionResult__input_text', 'extractionResult__raw_completion_output', 'extractionResult__prompt', 'extractionResult__extracted_object', 'extractionResult__named_entities'], slot_usage={}, attributes={'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:ExtractionResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'NamedEntity': ClassDefinition(name='NamedEntity', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NamedEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:NamedEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'CompoundExpression': ClassDefinition(name='CompoundExpression', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/CompoundExpression', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='core:CompoundExpression', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Triple': ClassDefinition(name='Triple', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Triple', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Abstract parent for Relation Extraction tasks', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['triple__subject', 'triple__predicate', 'triple__object', 'triple__qualifier', 'triple__subject_qualifier', 'triple__object_qualifier'], slot_usage={}, attributes={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Triple', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'TextWithTriples': ClassDefinition(name='TextWithTriples', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/TextWithTriples', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['textWithTriples__publication', 'textWithTriples__triples'], slot_usage={}, attributes={'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:TextWithTriples', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'RelationshipType': ClassDefinition(name='RelationshipType', id_prefixes=['RO', 'biolink'], definition_uri='http://w3id.org/ontogpt/core/RelationshipType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='core:RelationshipType', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Publication': ClassDefinition(name='Publication', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Publication', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['publication__id', 'publication__title', 'publication__abstract', 'publication__combined_text', 'publication__full_text'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Publication', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'AnnotatorResult': ClassDefinition(name='AnnotatorResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/AnnotatorResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['annotatorResult__subject_text', 'annotatorResult__object_id', 'annotatorResult__object_text'], slot_usage={}, attributes={'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:AnnotatorResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={})}" ; - linkml:enums "{'MeshChemicalIdentifier': EnumDefinition(name='MeshChemicalIdentifier', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/drug/MeshChemicalIdentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/ctd', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={}, include=[], minus=[], inherits=[], reachable_from=ReachabilityQuery(source_ontology='obo:mesh', source_nodes=['MESH:D000602', 'MESH:D001685', 'MESH:D002241', 'MESH:D004364', 'MESH:D006571', 'MESH:D007287', 'MESH:D008055', 'MESH:D009706', 'MESH:D009930', 'MESH:D011083', 'MESH:D013812', 'MESH:D019602', 'MESH:D045424', 'MESH:D045762', 'MESH:D046911'], relationship_types=[], is_direct=None, include_self=None, traverse_up=None), matches=None, concepts=[]), 'MeshDiseaseIdentifier': EnumDefinition(name='MeshDiseaseIdentifier', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/drug/MeshDiseaseIdentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/ctd', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={}, include=[], minus=[], inherits=[], reachable_from=ReachabilityQuery(source_ontology='obo:mesh', source_nodes=['MESH:D001423', 'MESH:D001523', 'MESH:D002318', 'MESH:D002943', 'MESH:D004066', 'MESH:D004700', 'MESH:D005128', 'MESH:D005261', 'MESH:D006425', 'MESH:D007154', 'MESH:D007280', 'MESH:D009057', 'MESH:D009140', 'MESH:D009358', 'MESH:D009369', 'MESH:D009422', 'MESH:D009750', 'MESH:D009784', 'MESH:D010038', 'MESH:D010272', 'MESH:D012140', 'MESH:D013568', 'MESH:D014777', 'MESH:D014947', 'MESH:D017437', 'MESH:D052801', 'MESH:D064419'], relationship_types=[], is_direct=None, include_self=None, traverse_up=None), matches=None, concepts=[]), 'NullDataOptions': EnumDefinition(name='NullDataOptions', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NullDataOptions', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'UNSPECIFIED_METHOD_OF_ADMINISTRATION': PermissibleValue(text='UNSPECIFIED_METHOD_OF_ADMINISTRATION', description=None, meaning='NCIT:C149701', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_APPLICABLE': PermissibleValue(text='NOT_APPLICABLE', description=None, meaning='NCIT:C18902', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['not applicable', 'N/A'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_MENTIONED': PermissibleValue(text='NOT_MENTIONED', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[])}" ; - linkml:id "http://w3id.org/ontogpt/ctd" ; - linkml:imports "core", - "linkml:types" ; - linkml:types "{'string': TypeDefinition(name='string', id_prefixes=[], definition_uri='https://w3id.org/linkml/String', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A character string', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Text'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'integer': TypeDefinition(name='integer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Integer', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An integer', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Integer'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='int', uri='xsd:integer', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'boolean': TypeDefinition(name='boolean', id_prefixes=[], definition_uri='https://w3id.org/linkml/Boolean', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A binary (true or false) value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Boolean'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Bool', uri='xsd:boolean', repr='bool', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'float': TypeDefinition(name='float', id_prefixes=[], definition_uri='https://w3id.org/linkml/Float', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:float specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Float'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:float', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'double': TypeDefinition(name='double', id_prefixes=[], definition_uri='https://w3id.org/linkml/Double', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:double specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:Float'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:double', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'decimal': TypeDefinition(name='decimal', id_prefixes=[], definition_uri='https://w3id.org/linkml/Decimal', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number with arbitrary precision that conforms to the xsd:decimal specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=['schema:Number'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Decimal', uri='xsd:decimal', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'time': TypeDefinition(name='time', id_prefixes=[], definition_uri='https://w3id.org/linkml/Time', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A time object represents a (local) time of day, independent of any particular day', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=['URI is dateTime because OWL reasoners do not work with straight date or time'], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Time'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDTime', uri='xsd:time', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date': TypeDefinition(name='date', id_prefixes=[], definition_uri='https://w3id.org/linkml/Date', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a date (year, month and day) in an idealized calendar', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[\"URI is dateTime because OWL reasoners don't work with straight date or time\"], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Date'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDate', uri='xsd:date', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'datetime': TypeDefinition(name='datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/Datetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The combination of a date and time', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:DateTime'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDateTime', uri='xsd:dateTime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date_or_datetime': TypeDefinition(name='date_or_datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/DateOrDatetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Either a date or a datetime', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='linkml:DateOrDatetime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uriorcurie': TypeDefinition(name='uriorcurie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uriorcurie', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a URI or a CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URIorCURIE', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'curie': TypeDefinition(name='curie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Curie', local_names={}, conforms_to='https://www.w3.org/TR/curie/', implements=[], extensions={}, annotations={}, description='a compact URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations this MUST be expanded to a URI', 'in non-RDF serializations MAY be serialized as the compact representation'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Curie', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uri': TypeDefinition(name='uri', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uri', local_names={}, conforms_to='https://www.ietf.org/rfc/rfc3987.txt', implements=[], extensions={}, annotations={}, description='a complete URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:URL'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URI', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ncname': TypeDefinition(name='ncname', id_prefixes=[], definition_uri='https://w3id.org/linkml/Ncname', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Prefix part of CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NCName', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'objectidentifier': TypeDefinition(name='objectidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Objectidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI or CURIE that represents an object in the model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['Used for inheritance and type checking'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='ElementIdentifier', uri='shex:iri', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'nodeidentifier': TypeDefinition(name='nodeidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Nodeidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI, CURIE or BNODE that represents a node in a model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NodeIdentifier', uri='shex:nonLiteral', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpointer': TypeDefinition(name='jsonpointer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpointer', local_names={}, conforms_to='https://datatracker.ietf.org/doc/html/rfc6901', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpath': TypeDefinition(name='jsonpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpath', local_names={}, conforms_to='https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sparqlpath': TypeDefinition(name='sparqlpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Sparqlpath', local_names={}, conforms_to='https://www.w3.org/TR/sparql11-query/#propertypaths', implements=[], extensions={}, annotations={}, description='A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -drug:MeshChemicalIdentifier a owl:Class, - linkml:EnumDefinition ; - rdfs:label "MeshChemicalIdentifier" ; - owl:unionOf [ rdf:rest () ] . - -drug:MeshDiseaseIdentifier a owl:Class, - linkml:EnumDefinition ; - rdfs:label "MeshDiseaseIdentifier" ; - owl:unionOf [ rdf:rest () ] . - -linkml:SubsetDefinition a owl:Class ; - rdfs:label "subset_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" . - -linkml:TypeDefinition a owl:Class ; - rdfs:label "type_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" ; - linkml:mixins "type_expression" . - -linkml:topValue a owl:DatatypeProperty ; - rdfs:label "value" . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "AnnotatorResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_text> ] ; - linkml:attributes "{'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/ExtractionResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ExtractionResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/prompt> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_title> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/extracted_object> ], - [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/named_entities> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_text> ] ; - skos:definition "A result of extracting knowledge on text" ; - linkml:attributes "{'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/abstract> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "abstract" ; - rdfs:range linkml:String ; - skos:definition "The abstract of the publication" . - -<http://w3id.org/ontogpt/core/combined_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "combined_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/extracted_object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "extracted_object" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "The complex objects extracted from the text" . - -<http://w3id.org/ontogpt/core/full_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "full_text" ; - rdfs:range linkml:String ; - skos:definition "The full text of the publication" . - -<http://w3id.org/ontogpt/core/input_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_title" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/named_entities> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "named_entities" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "Named entities extracted from the text" . - -<http://w3id.org/ontogpt/core/object_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/object_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/prompt> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "prompt" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/publication> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "publication" ; - drug:prompt.skip "true" ; - rdfs:range <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "qualifier" ; - rdfs:range linkml:String ; - skos:definition "A qualifier for the statements, e.g. \"NOT\" for negation" . - -<http://w3id.org/ontogpt/core/raw_completion_output> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "raw_completion_output" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/subject_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "title" ; - rdfs:range linkml:String ; - skos:definition "The title of the publication" . - -drug:ChemicalToDiseaseDocument a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ChemicalToDiseaseDocument" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom drug:ChemicalToDiseaseRelationship ; - owl:onProperty drug:triples ], - <http://w3id.org/ontogpt/core/TextWithTriples> ; - skos:definition "A document that contains chemical to disease relations." ; - linkml:attributes "{}" ; - linkml:is_a "TextWithTriples" . - -drug:object a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object" ; - rdfs:domain drug:ChemicalToDiseaseRelationship ; - rdfs:range drug:Disease ; - rdfs:subPropertyOf <http://w3id.org/ontogpt/core/object> ; - skos:definition "The disease or condition that is being treated or induced by the chemical. For example, asthma, cancer, covid-19, cardiac asystole, Hypotension, Headache." ; - linkml:is_a "triple__object" . - -drug:object_qualifier a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_qualifier" ; - rdfs:domain drug:ChemicalToDiseaseRelationship ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - rdfs:subPropertyOf <http://w3id.org/ontogpt/core/object_qualifier> ; - skos:definition "An optional qualifier or modifier for the disease, e.g. \"severe\" or \"with additional complications\"" ; - linkml:is_a "triple__object_qualifier" . - -drug:predicate a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "predicate" ; - rdfs:domain drug:ChemicalToDiseaseRelationship ; - rdfs:range drug:ChemicalToDiseasePredicate ; - rdfs:subPropertyOf <http://w3id.org/ontogpt/core/predicate> ; - skos:definition "The relationship type, e.g. INDUCES, TREATS." ; - linkml:is_a "triple__predicate" . - -drug:subject a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject" ; - rdfs:domain drug:ChemicalToDiseaseRelationship ; - rdfs:range drug:Chemical ; - rdfs:subPropertyOf <http://w3id.org/ontogpt/core/subject> ; - skos:definition "The chemical substance, drug, or small molecule. For example: Lidocaine, Monosodium Glutamate, Imatinib." ; - linkml:is_a "triple__subject" . - -drug:subject_qualifier a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_qualifier" ; - rdfs:domain drug:ChemicalToDiseaseRelationship ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - rdfs:subPropertyOf <http://w3id.org/ontogpt/core/subject_qualifier> ; - skos:definition "An optional qualifier or modifier for the chemical, e.g. \"high dose\" or \"intravenously administered\"" ; - linkml:is_a "triple__subject_qualifier" . - -drug:triples a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "triples" ; - drug:exclude "Lidocaine, cardiac asystole, Hydroxychloroquine, COVID-19, Methyldopa, Headache, Imatinib, cancer" ; - drug:prompt "A semi-colon separated list of chemical to disease relationships, where the relationship is either INDUCES or TREATS. for example: Lidocaine INDUCES cardiac asystole; Hydroxychloroquine NOT TREATS COVID-19; Methyldopa INDUCES Hypotension; Monosodium Glutamate NOT INDUCES Headache; Imatinib TREATS cancer" ; - rdfs:domain drug:ChemicalToDiseaseDocument ; - rdfs:range drug:ChemicalToDiseaseRelationship ; - rdfs:subPropertyOf <http://w3id.org/ontogpt/core/triples> ; - linkml:is_a "textWithTriples__triples" . - -<http://example.org/UNKNOWN/rdfs/label> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "label" ; - drug:owl "AnnotationProperty, AnnotationAssertion" ; - rdfs:range linkml:String ; - skos:altLabel "name" ; - skos:definition "The label (name) of the named thing" ; - skos:exactMatch <http://example.org/UNKNOWN/rdfs/label> . - -<http://purl.obolibrary.org/obo/NCIT_C149701> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "UNSPECIFIED_METHOD_OF_ADMINISTRATION" . - -<http://purl.obolibrary.org/obo/NCIT_C18902> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_APPLICABLE" . - -<http://w3id.org/ontogpt/core/CompoundExpression> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CompoundExpression" ; - linkml:attributes "{}" . - -<http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_MENTIONED" . - -<http://w3id.org/ontogpt/core/TextWithTriples> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TextWithTriples" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Publication> ; - owl:onProperty <http://w3id.org/ontogpt/core/publication> ], - [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Triple> ; - owl:onProperty <http://w3id.org/ontogpt/core/triples> ] ; - linkml:attributes "{'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/object_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" . - -<http://w3id.org/ontogpt/core/predicate> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "predicate" ; - rdfs:range <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/subject> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/subject_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" . - -<http://w3id.org/ontogpt/core/triples> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "triples" ; - rdfs:range <http://w3id.org/ontogpt/core/Triple> . - -drug:ChemicalToDiseasePredicate a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ChemicalToDiseasePredicate" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/RelationshipType> ; - skos:definition "A predicate for chemical to disease relationships" ; - linkml:attributes "{}" ; - linkml:is_a "RelationshipType" . - -drug:id a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "id" ; - rdfs:domain drug:Chemical, - drug:Disease ; - rdfs:range linkml:String ; - rdfs:subPropertyOf <http://w3id.org/ontogpt/core/id> ; - linkml:is_a "namedEntity__id" . - -<http://w3id.org/ontogpt/core/NullDataOptions> a owl:Class, - linkml:EnumDefinition ; - rdfs:label "NullDataOptions" ; - owl:unionOf ( <http://purl.obolibrary.org/obo/NCIT_C149701> <http://purl.obolibrary.org/obo/NCIT_C18902> <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> ) ; - linkml:permissible_values <http://purl.obolibrary.org/obo/NCIT_C149701>, - <http://purl.obolibrary.org/obo/NCIT_C18902>, - <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> . - -<http://w3id.org/ontogpt/core/Publication> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Publication" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/full_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/combined_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/abstract> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/title> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/RelationshipType> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "RelationshipType" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/Triple> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Triple" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/RelationshipType> ; - owl:onProperty <http://w3id.org/ontogpt/core/predicate> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object_qualifier> ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - skos:definition "Abstract parent for Relation Extraction tasks" ; - linkml:attributes "{'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -<http://w3id.org/ontogpt/core/id> a owl:ObjectProperty, - linkml:SlotDefinition . - -drug:Chemical a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Chemical" ; - drug:annotators "sqlite:obo:mesh, sqlite:obo:chebi, sqlite:obo:ncit, bioportal:mdm, sqlite:obo:drugbank, gilda:" ; - drug:prompt.examples "Lidocaine, Hydroxychloroquine, Methyldopa, Imatinib" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty drug:id ; - owl:qualifiedCardinality 1 ], - <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -drug:Disease a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Disease" ; - drug:annotators "sqlite:obo:mesh, sqlite:obo:mondo, sqlite:obo:hp, sqlite:obo:ncit, sqlite:obo:doid, bioportal:meddra" ; - drug:prompt.examples "cardiac asystole, COVID-19, Headache, cancer" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty drug:id ; - owl:qualifiedCardinality 1 ], - <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/Any> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Any" ; - skos:exactMatch linkml:Any ; - linkml:attributes "{}" . - -drug:ChemicalToDiseaseRelationship a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ChemicalToDiseaseRelationship" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass drug:Chemical ; - owl:onProperty drug:subject ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass drug:ChemicalToDiseasePredicate ; - owl:onProperty drug:predicate ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty drug:subject_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty drug:object_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass drug:Disease ; - owl:onProperty drug:object ], - <http://w3id.org/ontogpt/core/Triple> ; - skos:definition "A triple where the subject is a chemical and the object is a disease." ; - linkml:attributes "{}" ; - linkml:is_a "Triple" . - -linkml:ClassDefinition a owl:Class ; - rdfs:label "class_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "class_expression" . - -<http://w3id.org/ontogpt/core/NamedEntity> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "NamedEntity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://example.org/UNKNOWN/rdfs/label> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:SlotDefinition a owl:Class ; - rdfs:label "slot_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "slot_expression" . - - diff --git a/projects/ctd/prefixmap/ctd.yaml b/projects/ctd/prefixmap/ctd.yaml deleted file mode 100644 index 4100280b3..000000000 --- a/projects/ctd/prefixmap/ctd.yaml +++ /dev/null @@ -1,36 +0,0 @@ -{ - "MESH": "http://example.org/UNKNOWN/MESH/", - "RO": "http://purl.obolibrary.org/obo/RO_", - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "drug": "http://w3id.org/ontogpt/drug/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } -} diff --git a/projects/ctd/protobuf/ctd.proto b/projects/ctd/protobuf/ctd.proto deleted file mode 100644 index 5fd0e70fe..000000000 --- a/projects/ctd/protobuf/ctd.proto +++ /dev/null @@ -1,67 +0,0 @@ -message AnnotatorResult - { - string subjectText = 0 - string objectId = 0 - string objectText = 0 - } -message Chemical - { - string label = 0 - string id = 0 - } -// A document that contains chemical to disease relations. -message ChemicalToDiseaseDocument - { - publication publication = 0 - repeated chemicalToDiseaseRelationship triples = 0 - } -// A predicate for chemical to disease relationships -message ChemicalToDiseasePredicate - { - string id = 0 - string label = 0 - } -// A triple where the subject is a chemical and the object is a disease. -message ChemicalToDiseaseRelationship - { - string qualifier = 0 - chemical subject = 0 - disease object = 0 - chemicalToDiseasePredicate predicate = 0 - namedEntity subjectQualifier = 0 - namedEntity objectQualifier = 0 - } -message Disease - { - string label = 0 - string id = 0 - } -// A result of extracting knowledge on text -message ExtractionResult - { - string inputId = 0 - string inputTitle = 0 - string inputText = 0 - string rawCompletionOutput = 0 - string prompt = 0 - any extractedObject = 0 - repeated any namedEntities = 0 - } -message Publication - { - string id = 0 - string title = 0 - string abstract = 0 - string combinedText = 0 - string fullText = 0 - } -message RelationshipType - { - string id = 0 - string label = 0 - } -message TextWithTriples - { - publication publication = 0 - repeated triple triples = 0 - } diff --git a/projects/ctd/shacl/ctd.shacl.ttl b/projects/ctd/shacl/ctd.shacl.ttl deleted file mode 100644 index 9dd8fa86c..000000000 --- a/projects/ctd/shacl/ctd.shacl.ttl +++ /dev/null @@ -1,264 +0,0 @@ -@prefix drug: <http://w3id.org/ontogpt/drug/> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix sh: <http://www.w3.org/ns/shacl#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/object_id> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object_text> ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject_text> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/AnnotatorResult> . - -<http://w3id.org/ontogpt/core/CompoundExpression> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass <http://w3id.org/ontogpt/core/CompoundExpression> . - -<http://w3id.org/ontogpt/core/ExtractionResult> a sh:NodeShape ; - sh:closed true ; - sh:description "A result of extracting knowledge on text" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/input_id> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ sh:class linkml:Any ; - sh:description "The complex objects extracted from the text" ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/extracted_object> ], - [ sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/prompt> ], - [ sh:class linkml:Any ; - sh:description "Named entities extracted from the text" ; - sh:nodeKind sh:BlankNode ; - sh:order 6 ; - sh:path <http://w3id.org/ontogpt/core/named_entities> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/input_text> ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/input_title> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/ExtractionResult> . - -<http://w3id.org/ontogpt/core/TextWithTriples> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/Triple> ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/triples> ], - [ sh:class <http://w3id.org/ontogpt/core/Publication> ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/publication> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/TextWithTriples> . - -drug:ChemicalToDiseaseDocument a sh:NodeShape ; - sh:closed true ; - sh:description "A document that contains chemical to disease relations." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class drug:ChemicalToDiseaseRelationship ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/triples> ], - [ sh:class <http://w3id.org/ontogpt/core/Publication> ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/publication> ] ; - sh:targetClass drug:ChemicalToDiseaseDocument . - -<http://w3id.org/ontogpt/core/RelationshipType> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/Triple> a sh:NodeShape ; - sh:closed false ; - sh:description "Abstract parent for Relation Extraction tasks" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/object_qualifier> ], - [ sh:description "A qualifier for the statements, e.g. \"NOT\" for negation" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject> ], - [ sh:class <http://w3id.org/ontogpt/core/RelationshipType> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/predicate> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Triple> . - -drug:Chemical a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ; - sh:pattern "^MESH:[CD][0-9]{6}$" ] ; - sh:targetClass drug:Chemical . - -drug:ChemicalToDiseasePredicate a sh:NodeShape ; - sh:closed true ; - sh:description "A predicate for chemical to disease relationships" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass drug:ChemicalToDiseasePredicate . - -drug:ChemicalToDiseaseRelationship a sh:NodeShape ; - sh:closed true ; - sh:description "A triple where the subject is a chemical and the object is a disease." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the chemical, e.g. \"high dose\" or \"intravenously administered\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ sh:class drug:Disease ; - sh:description "The disease or condition that is being treated or induced by the chemical. For example, asthma, cancer, covid-19, cardiac asystole, Hypotension, Headache." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object> ], - [ sh:class drug:ChemicalToDiseasePredicate ; - sh:description "The relationship type, e.g. INDUCES, TREATS." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/predicate> ], - [ sh:class drug:Chemical ; - sh:description "The chemical substance, drug, or small molecule. For example: Lidocaine, Monosodium Glutamate, Imatinib." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject> ], - [ sh:description "A qualifier for the statements, e.g. \"NOT\" for negation" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the disease, e.g. \"severe\" or \"with additional complications\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/object_qualifier> ] ; - sh:targetClass drug:ChemicalToDiseaseRelationship . - -drug:Disease a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ; - sh:pattern "^MESH:[CD][0-9]{6}$" ] ; - sh:targetClass drug:Disease . - -<http://w3id.org/ontogpt/core/Publication> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The abstract of the publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/abstract> ], - [ sh:description "The publication identifier" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The title of the publication" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/title> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/combined_text> ], - [ sh:description "The full text of the publication" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/full_text> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Publication> . - -linkml:Any a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass linkml:Any . - -<http://w3id.org/ontogpt/core/NamedEntity> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/NamedEntity> . - diff --git a/projects/ctd/shex/ctd.shex b/projects/ctd/shex/ctd.shex deleted file mode 100644 index 89f380355..000000000 --- a/projects/ctd/shex/ctd.shex +++ /dev/null @@ -1,186 +0,0 @@ -BASE <http://w3id.org/ontogpt/drug/> -PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> -PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> -PREFIX linkml: <https://w3id.org/linkml/> -PREFIX core: <http://w3id.org/ontogpt/core/> -PREFIX rdfs1: <http://example.org/UNKNOWN/rdfs/> - - -linkml:String xsd:string - -linkml:Integer xsd:integer - -linkml:Boolean xsd:boolean - -linkml:Float xsd:float - -linkml:Double xsd:double - -linkml:Decimal xsd:decimal - -linkml:Time xsd:time - -linkml:Date xsd:date - -linkml:Datetime xsd:dateTime - -linkml:DateOrDatetime linkml:DateOrDatetime - -linkml:Uriorcurie IRI - -linkml:Curie xsd:string - -linkml:Uri IRI - -linkml:Ncname xsd:string - -linkml:Objectidentifier IRI - -linkml:Nodeidentifier NONLITERAL - -linkml:Jsonpointer xsd:string - -linkml:Jsonpath xsd:string - -linkml:Sparqlpath xsd:string - -core:AnnotatorResult CLOSED { - ( $core:AnnotatorResult_tes ( core:subject_text @linkml:String ? ; - core:object_id @linkml:String ? ; - core:object_text @linkml:String ? - ) ; - rdf:type [ core:AnnotatorResult ] ? - ) -} - -core:Any CLOSED { - ( $core:Any_tes rdf:type . * ; - rdf:type [ linkml:Any ] ? - ) -} - -<Chemical> CLOSED { - ( $<Chemical_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Chemical> ] - ) -} - -<ChemicalToDiseaseDocument> CLOSED { - ( $<ChemicalToDiseaseDocument_tes> ( &core:TextWithTriples_tes ; - rdf:type [ core:TextWithTriples ] ? ; - <triples> @<ChemicalToDiseaseRelationship> * - ) ; - rdf:type [ <ChemicalToDiseaseDocument> ] ? - ) -} - -<ChemicalToDiseasePredicate> CLOSED { - ( $<ChemicalToDiseasePredicate_tes> ( &core:RelationshipType_tes ; - rdf:type [ core:RelationshipType ] ? - ) ; - rdf:type [ <ChemicalToDiseasePredicate> ] - ) -} - -<ChemicalToDiseaseRelationship> CLOSED { - ( $<ChemicalToDiseaseRelationship_tes> ( &core:Triple_tes ; - rdf:type [ core:Triple ] ? ; - <subject> @<Chemical> ? ; - <object> @<Disease> ? ; - <predicate> @<ChemicalToDiseasePredicate> ? ; - <subject_qualifier> @core:NamedEntity ? ; - <object_qualifier> @core:NamedEntity ? - ) ; - rdf:type [ <ChemicalToDiseaseRelationship> ] ? - ) -} - -core:CompoundExpression ( - { - ( $core:CompoundExpression_tes rdf:type . * ; - rdf:type [ core:CompoundExpression ] ? - ) - } OR @core:Triple -) - -<Disease> CLOSED { - ( $<Disease_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Disease> ] - ) -} - -core:ExtractionResult CLOSED { - ( $core:ExtractionResult_tes ( core:input_id @linkml:String ? ; - core:input_title @linkml:String ? ; - core:input_text @linkml:String ? ; - core:raw_completion_output @linkml:String ? ; - core:prompt @linkml:String ? ; - core:extracted_object @core:Any ? ; - core:named_entities @core:Any * - ) ; - rdf:type [ core:ExtractionResult ] ? - ) -} - -core:NamedEntity ( - @<Chemical> OR @<Disease> OR @core:RelationshipType -) - -core:NamedEntity_struct { - ( $core:NamedEntity_tes rdfs1:label @linkml:String ? ; - rdf:type [ core:NamedEntity ] - ) -} - -core:Publication CLOSED { - ( $core:Publication_tes ( core:id @linkml:String ? ; - core:title @linkml:String ? ; - core:abstract @linkml:String ? ; - core:combined_text @linkml:String ? ; - core:full_text @linkml:String ? - ) ; - rdf:type [ core:Publication ] ? - ) -} - -core:RelationshipType ( - CLOSED { - ( $core:RelationshipType_tes ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ core:RelationshipType ] - ) - } OR @<ChemicalToDiseasePredicate> -) - -core:TextWithTriples ( - CLOSED { - ( $core:TextWithTriples_tes ( core:publication @core:Publication ? ; - core:triples @core:Triple * - ) ; - rdf:type [ core:TextWithTriples ] ? - ) - } OR @<ChemicalToDiseaseDocument> -) - -core:Triple ( - { - ( $core:Triple_tes ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - core:subject @core:NamedEntity ? ; - core:predicate @core:RelationshipType ? ; - core:object @core:NamedEntity ? ; - core:qualifier @linkml:String ? ; - core:subject_qualifier @core:NamedEntity ? ; - core:object_qualifier @core:NamedEntity ? - ) ; - rdf:type [ core:Triple ] ? - ) - } OR @<ChemicalToDiseaseRelationship> -) - - diff --git a/projects/ctd/sqlschema/ctd.sql b/projects/ctd/sqlschema/ctd.sql deleted file mode 100644 index c460b2ab7..000000000 --- a/projects/ctd/sqlschema/ctd.sql +++ /dev/null @@ -1,77 +0,0 @@ - - -CREATE TABLE "AnnotatorResult" ( - subject_text TEXT, - object_id TEXT, - object_text TEXT, - PRIMARY KEY (subject_text, object_id, object_text) -); - -CREATE TABLE "Chemical" ( - label TEXT, - id TEXT NOT NULL, - PRIMARY KEY (id) -); - -CREATE TABLE "ChemicalToDiseaseDocument" ( - publication TEXT, - triples TEXT, - PRIMARY KEY (publication, triples) -); - -CREATE TABLE "ChemicalToDiseasePredicate" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Disease" ( - label TEXT, - id TEXT NOT NULL, - PRIMARY KEY (id) -); - -CREATE TABLE "ExtractionResult" ( - input_id TEXT, - input_title TEXT, - input_text TEXT, - raw_completion_output TEXT, - prompt TEXT, - extracted_object TEXT, - named_entities TEXT, - PRIMARY KEY (input_id, input_title, input_text, raw_completion_output, prompt, extracted_object, named_entities) -); - -CREATE TABLE "Publication" ( - id TEXT, - title TEXT, - abstract TEXT, - combined_text TEXT, - full_text TEXT, - PRIMARY KEY (id, title, abstract, combined_text, full_text) -); - -CREATE TABLE "RelationshipType" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "TextWithTriples" ( - publication TEXT, - triples TEXT, - PRIMARY KEY (publication, triples) -); - -CREATE TABLE "ChemicalToDiseaseRelationship" ( - qualifier TEXT, - subject TEXT, - object TEXT, - predicate TEXT, - subject_qualifier TEXT, - object_qualifier TEXT, - PRIMARY KEY (qualifier, subject, object, predicate, subject_qualifier, object_qualifier), - FOREIGN KEY(subject) REFERENCES "Chemical" (id), - FOREIGN KEY(object) REFERENCES "Disease" (id), - FOREIGN KEY(predicate) REFERENCES "ChemicalToDiseasePredicate" (id) -); diff --git a/projects/diagnostic_procedure/diagnostic_procedure.py b/projects/diagnostic_procedure/diagnostic_procedure.py deleted file mode 100644 index fc07e9b51..000000000 --- a/projects/diagnostic_procedure/diagnostic_procedure.py +++ /dev/null @@ -1,658 +0,0 @@ -# Auto generated from diagnostic_procedure.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-08-07T10:52:38 -# Schema: diagnostic_procedure -# -# id: http://w3id.org/ontogpt/diagnostic_procedure -# description: A template for clinical diagnostic procedures and the phenotypes they may contribute to. -# license: https://creativecommons.org/publicdomain/zero/1.0/ - -import dataclasses -import sys -import re -from jsonasobj2 import JsonObj, as_dict -from typing import Optional, List, Union, Dict, ClassVar, Any -from dataclasses import dataclass -from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions - -from linkml_runtime.utils.slot import Slot -from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode -from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int -from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs -from linkml_runtime.utils.formatutils import camelcase, underscore, sfx -from linkml_runtime.utils.enumerations import EnumDefinitionImpl -from rdflib import Namespace, URIRef -from linkml_runtime.utils.curienamespace import CurieNamespace -from linkml_runtime.linkml_model.types import String - -metamodel_version = "1.7.0" -version = None - -# Overwrite dataclasses _init_fn to add **kwargs in __init__ -dataclasses._init_fn = dataclasses_init_fn_with_kwargs - -# Namespaces -HP = CurieNamespace('HP', 'http://purl.obolibrary.org/obo/HP_') -LOINC = CurieNamespace('LOINC', 'http://loinc.org/rdf/') -OBA = CurieNamespace('OBA', 'http://purl.obolibrary.org/obo/OBA_') -PATO = CurieNamespace('PATO', 'http://purl.obolibrary.org/obo/PATO_') -RO = CurieNamespace('RO', 'http://purl.obolibrary.org/obo/RO_') -UO = CurieNamespace('UO', 'http://example.org/UNKNOWN/UO/') -BIOLINK = CurieNamespace('biolink', 'https://w3id.org/biolink/vocab/') -CORE = CurieNamespace('core', 'http://w3id.org/ontogpt/core/') -DIAG = CurieNamespace('diag', 'http://w3id.org/ontogpt/diagnostic_procedure/') -LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') -RDFS = CurieNamespace('rdfs', 'http://example.org/UNKNOWN/rdfs/') -DEFAULT_ = DIAG - - -# Types - -# Class references -class NamedEntityId(extended_str): - pass - - -class DiagnosticProcedureId(NamedEntityId): - pass - - -class PhenotypeId(NamedEntityId): - pass - - -class ClinicalAttributeId(NamedEntityId): - pass - - -class QualityId(NamedEntityId): - pass - - -class UnitId(NamedEntityId): - pass - - -class RelationshipTypeId(NamedEntityId): - pass - - -class ProcedureToPhenotypePredicateId(RelationshipTypeId): - pass - - -class ProcedureToAttributePredicateId(RelationshipTypeId): - pass - - -Any = Any - -@dataclass -class ExtractionResult(YAMLRoot): - """ - A result of extracting knowledge on text - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.ExtractionResult - class_class_curie: ClassVar[str] = "core:ExtractionResult" - class_name: ClassVar[str] = "ExtractionResult" - class_model_uri: ClassVar[URIRef] = DIAG.ExtractionResult - - input_id: Optional[str] = None - input_title: Optional[str] = None - input_text: Optional[str] = None - raw_completion_output: Optional[str] = None - prompt: Optional[str] = None - extracted_object: Optional[Union[dict, Any]] = None - named_entities: Optional[Union[Union[dict, Any], List[Union[dict, Any]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.input_id is not None and not isinstance(self.input_id, str): - self.input_id = str(self.input_id) - - if self.input_title is not None and not isinstance(self.input_title, str): - self.input_title = str(self.input_title) - - if self.input_text is not None and not isinstance(self.input_text, str): - self.input_text = str(self.input_text) - - if self.raw_completion_output is not None and not isinstance(self.raw_completion_output, str): - self.raw_completion_output = str(self.raw_completion_output) - - if self.prompt is not None and not isinstance(self.prompt, str): - self.prompt = str(self.prompt) - - super().__post_init__(**kwargs) - - -@dataclass -class NamedEntity(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.NamedEntity - class_class_curie: ClassVar[str] = "core:NamedEntity" - class_name: ClassVar[str] = "NamedEntity" - class_model_uri: ClassVar[URIRef] = DIAG.NamedEntity - - id: Union[str, NamedEntityId] = None - label: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, NamedEntityId): - self.id = NamedEntityId(self.id) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - super().__post_init__(**kwargs) - - -@dataclass -class DiagnosticProcedure(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = DIAG.DiagnosticProcedure - class_class_curie: ClassVar[str] = "diag:DiagnosticProcedure" - class_name: ClassVar[str] = "DiagnosticProcedure" - class_model_uri: ClassVar[URIRef] = DIAG.DiagnosticProcedure - - id: Union[str, DiagnosticProcedureId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, DiagnosticProcedureId): - self.id = DiagnosticProcedureId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Phenotype(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = DIAG.Phenotype - class_class_curie: ClassVar[str] = "diag:Phenotype" - class_name: ClassVar[str] = "Phenotype" - class_model_uri: ClassVar[URIRef] = DIAG.Phenotype - - id: Union[str, PhenotypeId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, PhenotypeId): - self.id = PhenotypeId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class ClinicalAttribute(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = DIAG.ClinicalAttribute - class_class_curie: ClassVar[str] = "diag:ClinicalAttribute" - class_name: ClassVar[str] = "ClinicalAttribute" - class_model_uri: ClassVar[URIRef] = DIAG.ClinicalAttribute - - id: Union[str, ClinicalAttributeId] = None - unit: Optional[Union[str, UnitId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, ClinicalAttributeId): - self.id = ClinicalAttributeId(self.id) - - if self.unit is not None and not isinstance(self.unit, UnitId): - self.unit = UnitId(self.unit) - - super().__post_init__(**kwargs) - - -@dataclass -class Quality(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = DIAG.Quality - class_class_curie: ClassVar[str] = "diag:Quality" - class_name: ClassVar[str] = "Quality" - class_model_uri: ClassVar[URIRef] = DIAG.Quality - - id: Union[str, QualityId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, QualityId): - self.id = QualityId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Unit(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = DIAG.Unit - class_class_curie: ClassVar[str] = "diag:Unit" - class_name: ClassVar[str] = "Unit" - class_model_uri: ClassVar[URIRef] = DIAG.Unit - - id: Union[str, UnitId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, UnitId): - self.id = UnitId(self.id) - - super().__post_init__(**kwargs) - - -class CompoundExpression(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.CompoundExpression - class_class_curie: ClassVar[str] = "core:CompoundExpression" - class_name: ClassVar[str] = "CompoundExpression" - class_model_uri: ClassVar[URIRef] = DIAG.CompoundExpression - - -@dataclass -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Triple - class_class_curie: ClassVar[str] = "core:Triple" - class_name: ClassVar[str] = "Triple" - class_model_uri: ClassVar[URIRef] = DIAG.Triple - - subject: Optional[Union[str, NamedEntityId]] = None - predicate: Optional[Union[str, RelationshipTypeId]] = None - object: Optional[Union[str, NamedEntityId]] = None - qualifier: Optional[str] = None - subject_qualifier: Optional[Union[str, NamedEntityId]] = None - object_qualifier: Optional[Union[str, NamedEntityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, NamedEntityId): - self.subject = NamedEntityId(self.subject) - - if self.predicate is not None and not isinstance(self.predicate, RelationshipTypeId): - self.predicate = RelationshipTypeId(self.predicate) - - if self.object is not None and not isinstance(self.object, NamedEntityId): - self.object = NamedEntityId(self.object) - - if self.qualifier is not None and not isinstance(self.qualifier, str): - self.qualifier = str(self.qualifier) - - if self.subject_qualifier is not None and not isinstance(self.subject_qualifier, NamedEntityId): - self.subject_qualifier = NamedEntityId(self.subject_qualifier) - - if self.object_qualifier is not None and not isinstance(self.object_qualifier, NamedEntityId): - self.object_qualifier = NamedEntityId(self.object_qualifier) - - super().__post_init__(**kwargs) - - -@dataclass -class DiagnosticProceduretoPhenotypeAssociation(Triple): - """ - A triple representing a relationship between a diagnostic procedure and an associated phenotype, e.g., "blood - pressure measurement" is associated with "high blood pressure". - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = DIAG.DiagnosticProceduretoPhenotypeAssociation - class_class_curie: ClassVar[str] = "diag:DiagnosticProceduretoPhenotypeAssociation" - class_name: ClassVar[str] = "DiagnosticProceduretoPhenotypeAssociation" - class_model_uri: ClassVar[URIRef] = DIAG.DiagnosticProceduretoPhenotypeAssociation - - subject: Optional[Union[str, DiagnosticProcedureId]] = None - object: Optional[Union[Union[str, PhenotypeId], List[Union[str, PhenotypeId]]]] = empty_list() - predicate: Optional[Union[str, ProcedureToPhenotypePredicateId]] = None - subject_qualifier: Optional[Union[str, NamedEntityId]] = None - object_qualifier: Optional[Union[str, NamedEntityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, DiagnosticProcedureId): - self.subject = DiagnosticProcedureId(self.subject) - - if not isinstance(self.object, list): - self.object = [self.object] if self.object is not None else [] - self.object = [v if isinstance(v, PhenotypeId) else PhenotypeId(v) for v in self.object] - - if self.predicate is not None and not isinstance(self.predicate, ProcedureToPhenotypePredicateId): - self.predicate = ProcedureToPhenotypePredicateId(self.predicate) - - if self.subject_qualifier is not None and not isinstance(self.subject_qualifier, NamedEntityId): - self.subject_qualifier = NamedEntityId(self.subject_qualifier) - - if self.object_qualifier is not None and not isinstance(self.object_qualifier, NamedEntityId): - self.object_qualifier = NamedEntityId(self.object_qualifier) - - super().__post_init__(**kwargs) - - -@dataclass -class DiagnosticProceduretoAttributeAssociation(Triple): - """ - A triple representing a relationship between a diagnostic procedure and a measured attribute, e.g., "blood - pressure measurement" is associated with "blood pressure" (or in OBA, something like OBA:VT0000183, "blood - pressure trait"). - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = DIAG.DiagnosticProceduretoAttributeAssociation - class_class_curie: ClassVar[str] = "diag:DiagnosticProceduretoAttributeAssociation" - class_name: ClassVar[str] = "DiagnosticProceduretoAttributeAssociation" - class_model_uri: ClassVar[URIRef] = DIAG.DiagnosticProceduretoAttributeAssociation - - subject: Optional[Union[str, DiagnosticProcedureId]] = None - object: Optional[Union[Union[str, ClinicalAttributeId], List[Union[str, ClinicalAttributeId]]]] = empty_list() - predicate: Optional[Union[str, ProcedureToAttributePredicateId]] = None - subject_qualifier: Optional[Union[str, NamedEntityId]] = None - object_qualifier: Optional[Union[str, QualityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, DiagnosticProcedureId): - self.subject = DiagnosticProcedureId(self.subject) - - if not isinstance(self.object, list): - self.object = [self.object] if self.object is not None else [] - self.object = [v if isinstance(v, ClinicalAttributeId) else ClinicalAttributeId(v) for v in self.object] - - if self.predicate is not None and not isinstance(self.predicate, ProcedureToAttributePredicateId): - self.predicate = ProcedureToAttributePredicateId(self.predicate) - - if self.subject_qualifier is not None and not isinstance(self.subject_qualifier, NamedEntityId): - self.subject_qualifier = NamedEntityId(self.subject_qualifier) - - if self.object_qualifier is not None and not isinstance(self.object_qualifier, QualityId): - self.object_qualifier = QualityId(self.object_qualifier) - - super().__post_init__(**kwargs) - - -@dataclass -class TextWithTriples(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.TextWithTriples - class_class_curie: ClassVar[str] = "core:TextWithTriples" - class_name: ClassVar[str] = "TextWithTriples" - class_model_uri: ClassVar[URIRef] = DIAG.TextWithTriples - - publication: Optional[Union[dict, "Publication"]] = None - triples: Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.publication is not None and not isinstance(self.publication, Publication): - self.publication = Publication(**as_dict(self.publication)) - - if not isinstance(self.triples, list): - self.triples = [self.triples] if self.triples is not None else [] - self.triples = [v if isinstance(v, Triple) else Triple(**as_dict(v)) for v in self.triples] - - super().__post_init__(**kwargs) - - -@dataclass -class RelationshipType(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.RelationshipType - class_class_curie: ClassVar[str] = "core:RelationshipType" - class_name: ClassVar[str] = "RelationshipType" - class_model_uri: ClassVar[URIRef] = DIAG.RelationshipType - - id: Union[str, RelationshipTypeId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, RelationshipTypeId): - self.id = RelationshipTypeId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class ProcedureToPhenotypePredicate(RelationshipType): - """ - A predicate for procedure to phenotype relationships, defining "this procedure is intended to provide support - for/against this phenotype". - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = DIAG.ProcedureToPhenotypePredicate - class_class_curie: ClassVar[str] = "diag:ProcedureToPhenotypePredicate" - class_name: ClassVar[str] = "ProcedureToPhenotypePredicate" - class_model_uri: ClassVar[URIRef] = DIAG.ProcedureToPhenotypePredicate - - id: Union[str, ProcedureToPhenotypePredicateId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, ProcedureToPhenotypePredicateId): - self.id = ProcedureToPhenotypePredicateId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class ProcedureToAttributePredicate(RelationshipType): - """ - A predicate for procedure to attribute relationships, defining "this procedure is a measurement of this attribute". - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = DIAG.ProcedureToAttributePredicate - class_class_curie: ClassVar[str] = "diag:ProcedureToAttributePredicate" - class_name: ClassVar[str] = "ProcedureToAttributePredicate" - class_model_uri: ClassVar[URIRef] = DIAG.ProcedureToAttributePredicate - - id: Union[str, ProcedureToAttributePredicateId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, ProcedureToAttributePredicateId): - self.id = ProcedureToAttributePredicateId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Publication(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Publication - class_class_curie: ClassVar[str] = "core:Publication" - class_name: ClassVar[str] = "Publication" - class_model_uri: ClassVar[URIRef] = DIAG.Publication - - id: Optional[str] = None - title: Optional[str] = None - abstract: Optional[str] = None - combined_text: Optional[str] = None - full_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.id is not None and not isinstance(self.id, str): - self.id = str(self.id) - - if self.title is not None and not isinstance(self.title, str): - self.title = str(self.title) - - if self.abstract is not None and not isinstance(self.abstract, str): - self.abstract = str(self.abstract) - - if self.combined_text is not None and not isinstance(self.combined_text, str): - self.combined_text = str(self.combined_text) - - if self.full_text is not None and not isinstance(self.full_text, str): - self.full_text = str(self.full_text) - - super().__post_init__(**kwargs) - - -@dataclass -class AnnotatorResult(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.AnnotatorResult - class_class_curie: ClassVar[str] = "core:AnnotatorResult" - class_name: ClassVar[str] = "AnnotatorResult" - class_model_uri: ClassVar[URIRef] = DIAG.AnnotatorResult - - subject_text: Optional[str] = None - object_id: Optional[str] = None - object_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject_text is not None and not isinstance(self.subject_text, str): - self.subject_text = str(self.subject_text) - - if self.object_id is not None and not isinstance(self.object_id, str): - self.object_id = str(self.object_id) - - if self.object_text is not None and not isinstance(self.object_text, str): - self.object_text = str(self.object_text) - - super().__post_init__(**kwargs) - - -# Enumerations -class NullDataOptions(EnumDefinitionImpl): - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = PermissibleValue(text="UNSPECIFIED_METHOD_OF_ADMINISTRATION", - meaning=NCIT.C149701) - NOT_APPLICABLE = PermissibleValue(text="NOT_APPLICABLE", - meaning=NCIT.C18902) - NOT_MENTIONED = PermissibleValue(text="NOT_MENTIONED") - - _defn = EnumDefinition( - name="NullDataOptions", - ) - -# Slots -class slots: - pass - -slots.clinicalAttribute__unit = Slot(uri=DIAG.unit, name="clinicalAttribute__unit", curie=DIAG.curie('unit'), - model_uri=DIAG.clinicalAttribute__unit, domain=None, range=Optional[Union[str, UnitId]]) - -slots.extractionResult__input_id = Slot(uri=CORE.input_id, name="extractionResult__input_id", curie=CORE.curie('input_id'), - model_uri=DIAG.extractionResult__input_id, domain=None, range=Optional[str]) - -slots.extractionResult__input_title = Slot(uri=CORE.input_title, name="extractionResult__input_title", curie=CORE.curie('input_title'), - model_uri=DIAG.extractionResult__input_title, domain=None, range=Optional[str]) - -slots.extractionResult__input_text = Slot(uri=CORE.input_text, name="extractionResult__input_text", curie=CORE.curie('input_text'), - model_uri=DIAG.extractionResult__input_text, domain=None, range=Optional[str]) - -slots.extractionResult__raw_completion_output = Slot(uri=CORE.raw_completion_output, name="extractionResult__raw_completion_output", curie=CORE.curie('raw_completion_output'), - model_uri=DIAG.extractionResult__raw_completion_output, domain=None, range=Optional[str]) - -slots.extractionResult__prompt = Slot(uri=CORE.prompt, name="extractionResult__prompt", curie=CORE.curie('prompt'), - model_uri=DIAG.extractionResult__prompt, domain=None, range=Optional[str]) - -slots.extractionResult__extracted_object = Slot(uri=CORE.extracted_object, name="extractionResult__extracted_object", curie=CORE.curie('extracted_object'), - model_uri=DIAG.extractionResult__extracted_object, domain=None, range=Optional[Union[dict, Any]]) - -slots.extractionResult__named_entities = Slot(uri=CORE.named_entities, name="extractionResult__named_entities", curie=CORE.curie('named_entities'), - model_uri=DIAG.extractionResult__named_entities, domain=None, range=Optional[Union[Union[dict, Any], List[Union[dict, Any]]]]) - -slots.namedEntity__id = Slot(uri=CORE.id, name="namedEntity__id", curie=CORE.curie('id'), - model_uri=DIAG.namedEntity__id, domain=None, range=URIRef) - -slots.namedEntity__label = Slot(uri=RDFS.label, name="namedEntity__label", curie=RDFS.curie('label'), - model_uri=DIAG.namedEntity__label, domain=None, range=Optional[str]) - -slots.triple__subject = Slot(uri=CORE.subject, name="triple__subject", curie=CORE.curie('subject'), - model_uri=DIAG.triple__subject, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__predicate = Slot(uri=CORE.predicate, name="triple__predicate", curie=CORE.curie('predicate'), - model_uri=DIAG.triple__predicate, domain=None, range=Optional[Union[str, RelationshipTypeId]]) - -slots.triple__object = Slot(uri=CORE.object, name="triple__object", curie=CORE.curie('object'), - model_uri=DIAG.triple__object, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__qualifier = Slot(uri=CORE.qualifier, name="triple__qualifier", curie=CORE.curie('qualifier'), - model_uri=DIAG.triple__qualifier, domain=None, range=Optional[str]) - -slots.triple__subject_qualifier = Slot(uri=CORE.subject_qualifier, name="triple__subject_qualifier", curie=CORE.curie('subject_qualifier'), - model_uri=DIAG.triple__subject_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__object_qualifier = Slot(uri=CORE.object_qualifier, name="triple__object_qualifier", curie=CORE.curie('object_qualifier'), - model_uri=DIAG.triple__object_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.textWithTriples__publication = Slot(uri=CORE.publication, name="textWithTriples__publication", curie=CORE.curie('publication'), - model_uri=DIAG.textWithTriples__publication, domain=None, range=Optional[Union[dict, Publication]]) - -slots.textWithTriples__triples = Slot(uri=CORE.triples, name="textWithTriples__triples", curie=CORE.curie('triples'), - model_uri=DIAG.textWithTriples__triples, domain=None, range=Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]]) - -slots.publication__id = Slot(uri=CORE.id, name="publication__id", curie=CORE.curie('id'), - model_uri=DIAG.publication__id, domain=None, range=Optional[str]) - -slots.publication__title = Slot(uri=CORE.title, name="publication__title", curie=CORE.curie('title'), - model_uri=DIAG.publication__title, domain=None, range=Optional[str]) - -slots.publication__abstract = Slot(uri=CORE.abstract, name="publication__abstract", curie=CORE.curie('abstract'), - model_uri=DIAG.publication__abstract, domain=None, range=Optional[str]) - -slots.publication__combined_text = Slot(uri=CORE.combined_text, name="publication__combined_text", curie=CORE.curie('combined_text'), - model_uri=DIAG.publication__combined_text, domain=None, range=Optional[str]) - -slots.publication__full_text = Slot(uri=CORE.full_text, name="publication__full_text", curie=CORE.curie('full_text'), - model_uri=DIAG.publication__full_text, domain=None, range=Optional[str]) - -slots.annotatorResult__subject_text = Slot(uri=CORE.subject_text, name="annotatorResult__subject_text", curie=CORE.curie('subject_text'), - model_uri=DIAG.annotatorResult__subject_text, domain=None, range=Optional[str]) - -slots.annotatorResult__object_id = Slot(uri=CORE.object_id, name="annotatorResult__object_id", curie=CORE.curie('object_id'), - model_uri=DIAG.annotatorResult__object_id, domain=None, range=Optional[str]) - -slots.annotatorResult__object_text = Slot(uri=CORE.object_text, name="annotatorResult__object_text", curie=CORE.curie('object_text'), - model_uri=DIAG.annotatorResult__object_text, domain=None, range=Optional[str]) - -slots.DiagnosticProceduretoPhenotypeAssociation_subject = Slot(uri=DIAG.subject, name="DiagnosticProceduretoPhenotypeAssociation_subject", curie=DIAG.curie('subject'), - model_uri=DIAG.DiagnosticProceduretoPhenotypeAssociation_subject, domain=DiagnosticProceduretoPhenotypeAssociation, range=Optional[Union[str, DiagnosticProcedureId]]) - -slots.DiagnosticProceduretoPhenotypeAssociation_object = Slot(uri=DIAG.object, name="DiagnosticProceduretoPhenotypeAssociation_object", curie=DIAG.curie('object'), - model_uri=DIAG.DiagnosticProceduretoPhenotypeAssociation_object, domain=DiagnosticProceduretoPhenotypeAssociation, range=Optional[Union[Union[str, PhenotypeId], List[Union[str, PhenotypeId]]]]) - -slots.DiagnosticProceduretoPhenotypeAssociation_predicate = Slot(uri=DIAG.predicate, name="DiagnosticProceduretoPhenotypeAssociation_predicate", curie=DIAG.curie('predicate'), - model_uri=DIAG.DiagnosticProceduretoPhenotypeAssociation_predicate, domain=DiagnosticProceduretoPhenotypeAssociation, range=Optional[Union[str, ProcedureToPhenotypePredicateId]]) - -slots.DiagnosticProceduretoPhenotypeAssociation_subject_qualifier = Slot(uri=DIAG.subject_qualifier, name="DiagnosticProceduretoPhenotypeAssociation_subject_qualifier", curie=DIAG.curie('subject_qualifier'), - model_uri=DIAG.DiagnosticProceduretoPhenotypeAssociation_subject_qualifier, domain=DiagnosticProceduretoPhenotypeAssociation, range=Optional[Union[str, NamedEntityId]]) - -slots.DiagnosticProceduretoPhenotypeAssociation_object_qualifier = Slot(uri=DIAG.object_qualifier, name="DiagnosticProceduretoPhenotypeAssociation_object_qualifier", curie=DIAG.curie('object_qualifier'), - model_uri=DIAG.DiagnosticProceduretoPhenotypeAssociation_object_qualifier, domain=DiagnosticProceduretoPhenotypeAssociation, range=Optional[Union[str, NamedEntityId]]) - -slots.DiagnosticProceduretoAttributeAssociation_subject = Slot(uri=DIAG.subject, name="DiagnosticProceduretoAttributeAssociation_subject", curie=DIAG.curie('subject'), - model_uri=DIAG.DiagnosticProceduretoAttributeAssociation_subject, domain=DiagnosticProceduretoAttributeAssociation, range=Optional[Union[str, DiagnosticProcedureId]]) - -slots.DiagnosticProceduretoAttributeAssociation_object = Slot(uri=DIAG.object, name="DiagnosticProceduretoAttributeAssociation_object", curie=DIAG.curie('object'), - model_uri=DIAG.DiagnosticProceduretoAttributeAssociation_object, domain=DiagnosticProceduretoAttributeAssociation, range=Optional[Union[Union[str, ClinicalAttributeId], List[Union[str, ClinicalAttributeId]]]]) - -slots.DiagnosticProceduretoAttributeAssociation_predicate = Slot(uri=DIAG.predicate, name="DiagnosticProceduretoAttributeAssociation_predicate", curie=DIAG.curie('predicate'), - model_uri=DIAG.DiagnosticProceduretoAttributeAssociation_predicate, domain=DiagnosticProceduretoAttributeAssociation, range=Optional[Union[str, ProcedureToAttributePredicateId]]) - -slots.DiagnosticProceduretoAttributeAssociation_subject_qualifier = Slot(uri=DIAG.subject_qualifier, name="DiagnosticProceduretoAttributeAssociation_subject_qualifier", curie=DIAG.curie('subject_qualifier'), - model_uri=DIAG.DiagnosticProceduretoAttributeAssociation_subject_qualifier, domain=DiagnosticProceduretoAttributeAssociation, range=Optional[Union[str, NamedEntityId]]) - -slots.DiagnosticProceduretoAttributeAssociation_object_qualifier = Slot(uri=DIAG.object_qualifier, name="DiagnosticProceduretoAttributeAssociation_object_qualifier", curie=DIAG.curie('object_qualifier'), - model_uri=DIAG.DiagnosticProceduretoAttributeAssociation_object_qualifier, domain=DiagnosticProceduretoAttributeAssociation, range=Optional[Union[str, QualityId]]) \ No newline at end of file diff --git a/projects/diagnostic_procedure/docs/AnnotatorResult.md b/projects/diagnostic_procedure/docs/AnnotatorResult.md deleted file mode 100644 index 9123f01ac..000000000 --- a/projects/diagnostic_procedure/docs/AnnotatorResult.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Class: AnnotatorResult - - - - -URI: [diag:AnnotatorResult](http://w3id.org/ontogpt/diagnostic_procedure/AnnotatorResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F])](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F]) - -## Attributes - - -### Own - - * [➞subject_text](annotatorResult__subject_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_id](annotatorResult__object_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_text](annotatorResult__object_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) diff --git a/projects/diagnostic_procedure/docs/Any.md b/projects/diagnostic_procedure/docs/Any.md deleted file mode 100644 index 198c529ab..000000000 --- a/projects/diagnostic_procedure/docs/Any.md +++ /dev/null @@ -1,25 +0,0 @@ - -# Class: Any - - - - -URI: [diag:Any](http://w3id.org/ontogpt/diagnostic_procedure/Any) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult])](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult]) - -## Referenced by Class - - * **None** *[➞extracted_object](extractionResult__extracted_object.md)* <sub>0..1</sub> **[Any](Any.md)** - * **None** *[➞named_entities](extractionResult__named_entities.md)* <sub>0..\*</sub> **[Any](Any.md)** - -## Attributes - - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | linkml:Any | - diff --git a/projects/diagnostic_procedure/docs/ClinicalAttribute.md b/projects/diagnostic_procedure/docs/ClinicalAttribute.md deleted file mode 100644 index a1ebe4855..000000000 --- a/projects/diagnostic_procedure/docs/ClinicalAttribute.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Class: ClinicalAttribute - - - - -URI: [diag:ClinicalAttribute](http://w3id.org/ontogpt/diagnostic_procedure/ClinicalAttribute) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Unit],[NamedEntity],[DiagnosticProceduretoAttributeAssociation],[Unit]<unit%200..1-%20[ClinicalAttribute|id(i):string;label(i):string%20%3F],[DiagnosticProceduretoAttributeAssociation]-%20object%200..*>[ClinicalAttribute],[NamedEntity]^-[ClinicalAttribute])](https://yuml.me/diagram/nofunky;dir:TB/class/[Unit],[NamedEntity],[DiagnosticProceduretoAttributeAssociation],[Unit]<unit%200..1-%20[ClinicalAttribute|id(i):string;label(i):string%20%3F],[DiagnosticProceduretoAttributeAssociation]-%20object%200..*>[ClinicalAttribute],[NamedEntity]^-[ClinicalAttribute]) - -## Identifier prefixes - - * OBA - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **[DiagnosticProceduretoAttributeAssociation](DiagnosticProceduretoAttributeAssociation.md)** *[DiagnosticProceduretoAttributeAssociation➞object](DiagnosticProceduretoAttributeAssociation_object.md)* <sub>0..\*</sub> **[ClinicalAttribute](ClinicalAttribute.md)** - -## Attributes - - -### Own - - * [➞unit](clinicalAttribute__unit.md) <sub>0..1</sub> - * Description: the unit used to measure the attribute - * Range: [Unit](Unit.md) - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/diagnostic_procedure/docs/CompoundExpression.md b/projects/diagnostic_procedure/docs/CompoundExpression.md deleted file mode 100644 index ceff89418..000000000 --- a/projects/diagnostic_procedure/docs/CompoundExpression.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: CompoundExpression - - - - -URI: [diag:CompoundExpression](http://w3id.org/ontogpt/diagnostic_procedure/CompoundExpression) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[CompoundExpression]^-[Triple])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[CompoundExpression]^-[Triple]) - -## Children - - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - -## Referenced by Class - - -## Attributes - diff --git a/projects/diagnostic_procedure/docs/DiagnosticProcedure.md b/projects/diagnostic_procedure/docs/DiagnosticProcedure.md deleted file mode 100644 index 117f9269d..000000000 --- a/projects/diagnostic_procedure/docs/DiagnosticProcedure.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: DiagnosticProcedure - - - - -URI: [diag:DiagnosticProcedure](http://w3id.org/ontogpt/diagnostic_procedure/DiagnosticProcedure) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[DiagnosticProceduretoPhenotypeAssociation],[DiagnosticProceduretoAttributeAssociation],[DiagnosticProceduretoAttributeAssociation]-%20subject%200..1>[DiagnosticProcedure|id(i):string;label(i):string%20%3F],[DiagnosticProceduretoPhenotypeAssociation]-%20subject%200..1>[DiagnosticProcedure],[NamedEntity]^-[DiagnosticProcedure])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[DiagnosticProceduretoPhenotypeAssociation],[DiagnosticProceduretoAttributeAssociation],[DiagnosticProceduretoAttributeAssociation]-%20subject%200..1>[DiagnosticProcedure|id(i):string;label(i):string%20%3F],[DiagnosticProceduretoPhenotypeAssociation]-%20subject%200..1>[DiagnosticProcedure],[NamedEntity]^-[DiagnosticProcedure]) - -## Identifier prefixes - - * LOINC - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **[DiagnosticProceduretoAttributeAssociation](DiagnosticProceduretoAttributeAssociation.md)** *[DiagnosticProceduretoAttributeAssociation➞subject](DiagnosticProceduretoAttributeAssociation_subject.md)* <sub>0..1</sub> **[DiagnosticProcedure](DiagnosticProcedure.md)** - * **[DiagnosticProceduretoPhenotypeAssociation](DiagnosticProceduretoPhenotypeAssociation.md)** *[DiagnosticProceduretoPhenotypeAssociation➞subject](DiagnosticProceduretoPhenotypeAssociation_subject.md)* <sub>0..1</sub> **[DiagnosticProcedure](DiagnosticProcedure.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/diagnostic_procedure/docs/DiagnosticProceduretoAttributeAssociation.md b/projects/diagnostic_procedure/docs/DiagnosticProceduretoAttributeAssociation.md deleted file mode 100644 index 73abb979d..000000000 --- a/projects/diagnostic_procedure/docs/DiagnosticProceduretoAttributeAssociation.md +++ /dev/null @@ -1,44 +0,0 @@ - -# Class: DiagnosticProceduretoAttributeAssociation - - -A triple representing a relationship between a diagnostic procedure and a measured attribute, e.g., "blood pressure measurement" is associated with "blood pressure" (or in OBA, something like OBA:VT0000183, "blood pressure trait"). - -URI: [diag:DiagnosticProceduretoAttributeAssociation](http://w3id.org/ontogpt/diagnostic_procedure/DiagnosticProceduretoAttributeAssociation) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Quality],[ProcedureToAttributePredicate],[NamedEntity],[Quality]<object_qualifier%200..1-%20[DiagnosticProceduretoAttributeAssociation|qualifier(i):string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[DiagnosticProceduretoAttributeAssociation],[ProcedureToAttributePredicate]<predicate%200..1-%20[DiagnosticProceduretoAttributeAssociation],[ClinicalAttribute]<object%200..*-%20[DiagnosticProceduretoAttributeAssociation],[DiagnosticProcedure]<subject%200..1-%20[DiagnosticProceduretoAttributeAssociation],[Triple]^-[DiagnosticProceduretoAttributeAssociation],[DiagnosticProcedure],[ClinicalAttribute])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Quality],[ProcedureToAttributePredicate],[NamedEntity],[Quality]<object_qualifier%200..1-%20[DiagnosticProceduretoAttributeAssociation|qualifier(i):string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[DiagnosticProceduretoAttributeAssociation],[ProcedureToAttributePredicate]<predicate%200..1-%20[DiagnosticProceduretoAttributeAssociation],[ClinicalAttribute]<object%200..*-%20[DiagnosticProceduretoAttributeAssociation],[DiagnosticProcedure]<subject%200..1-%20[DiagnosticProceduretoAttributeAssociation],[Triple]^-[DiagnosticProceduretoAttributeAssociation],[DiagnosticProcedure],[ClinicalAttribute]) - -## Parents - - * is_a: [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - -## Referenced by Class - - -## Attributes - - -### Own - - * [DiagnosticProceduretoAttributeAssociation➞subject](DiagnosticProceduretoAttributeAssociation_subject.md) <sub>0..1</sub> - * Description: A diagnostic procedure yielding a result, which in turn may be interpreted as a phenotype. Procedures include "heart rate measurement", "blood pressure measurement", "oxygen saturation measurement", etc. In practice, procedures may be named based on what they measure, with the "measurement" part left implicit. - * Range: [DiagnosticProcedure](DiagnosticProcedure.md) - * [DiagnosticProceduretoAttributeAssociation➞object](DiagnosticProceduretoAttributeAssociation_object.md) <sub>0..\*</sub> - * Description: Any measurable clinical attribute. - * Range: [ClinicalAttribute](ClinicalAttribute.md) - * [DiagnosticProceduretoAttributeAssociation➞predicate](DiagnosticProceduretoAttributeAssociation_predicate.md) <sub>0..1</sub> - * Description: The relationship type, e.g. RELATED_TO - * Range: [ProcedureToAttributePredicate](ProcedureToAttributePredicate.md) - * [DiagnosticProceduretoAttributeAssociation➞subject_qualifier](DiagnosticProceduretoAttributeAssociation_subject_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the procedure. - * Range: [NamedEntity](NamedEntity.md) - * [DiagnosticProceduretoAttributeAssociation➞object_qualifier](DiagnosticProceduretoAttributeAssociation_object_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the phenotype. - * Range: [Quality](Quality.md) - -### Inherited from Triple: - - * [➞qualifier](triple__qualifier.md) <sub>0..1</sub> - * Description: A qualifier for the statements, e.g. "NOT" for negation - * Range: [String](types/String.md) diff --git a/projects/diagnostic_procedure/docs/DiagnosticProceduretoAttributeAssociation_object.md b/projects/diagnostic_procedure/docs/DiagnosticProceduretoAttributeAssociation_object.md deleted file mode 100644 index 03a929c8a..000000000 --- a/projects/diagnostic_procedure/docs/DiagnosticProceduretoAttributeAssociation_object.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: object - - -Any measurable clinical attribute. - -URI: [diag:DiagnosticProceduretoAttributeAssociation_object](http://w3id.org/ontogpt/diagnostic_procedure/DiagnosticProceduretoAttributeAssociation_object) - - -## Domain and Range - -[DiagnosticProceduretoAttributeAssociation](DiagnosticProceduretoAttributeAssociation.md) → <sub>0..\*</sub> [ClinicalAttribute](ClinicalAttribute.md) - -## Parents - - * is_a: [➞object](triple__object.md) - -## Children - - -## Used by - - * [DiagnosticProceduretoAttributeAssociation](DiagnosticProceduretoAttributeAssociation.md) diff --git a/projects/diagnostic_procedure/docs/DiagnosticProceduretoAttributeAssociation_object_qualifier.md b/projects/diagnostic_procedure/docs/DiagnosticProceduretoAttributeAssociation_object_qualifier.md deleted file mode 100644 index 811c766fa..000000000 --- a/projects/diagnostic_procedure/docs/DiagnosticProceduretoAttributeAssociation_object_qualifier.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: object_qualifier - - -An optional qualifier or modifier for the phenotype. - -URI: [diag:DiagnosticProceduretoAttributeAssociation_object_qualifier](http://w3id.org/ontogpt/diagnostic_procedure/DiagnosticProceduretoAttributeAssociation_object_qualifier) - - -## Domain and Range - -[DiagnosticProceduretoAttributeAssociation](DiagnosticProceduretoAttributeAssociation.md) → <sub>0..1</sub> [Quality](Quality.md) - -## Parents - - * is_a: [➞object_qualifier](triple__object_qualifier.md) - -## Children - - -## Used by - - * [DiagnosticProceduretoAttributeAssociation](DiagnosticProceduretoAttributeAssociation.md) diff --git a/projects/diagnostic_procedure/docs/DiagnosticProceduretoAttributeAssociation_predicate.md b/projects/diagnostic_procedure/docs/DiagnosticProceduretoAttributeAssociation_predicate.md deleted file mode 100644 index 3ddf05152..000000000 --- a/projects/diagnostic_procedure/docs/DiagnosticProceduretoAttributeAssociation_predicate.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: predicate - - -The relationship type, e.g. RELATED_TO - -URI: [diag:DiagnosticProceduretoAttributeAssociation_predicate](http://w3id.org/ontogpt/diagnostic_procedure/DiagnosticProceduretoAttributeAssociation_predicate) - - -## Domain and Range - -[DiagnosticProceduretoAttributeAssociation](DiagnosticProceduretoAttributeAssociation.md) → <sub>0..1</sub> [ProcedureToAttributePredicate](ProcedureToAttributePredicate.md) - -## Parents - - * is_a: [➞predicate](triple__predicate.md) - -## Children - - -## Used by - - * [DiagnosticProceduretoAttributeAssociation](DiagnosticProceduretoAttributeAssociation.md) diff --git a/projects/diagnostic_procedure/docs/DiagnosticProceduretoAttributeAssociation_subject.md b/projects/diagnostic_procedure/docs/DiagnosticProceduretoAttributeAssociation_subject.md deleted file mode 100644 index fcb44273f..000000000 --- a/projects/diagnostic_procedure/docs/DiagnosticProceduretoAttributeAssociation_subject.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: subject - - -A diagnostic procedure yielding a result, which in turn may be interpreted as a phenotype. Procedures include "heart rate measurement", "blood pressure measurement", "oxygen saturation measurement", etc. In practice, procedures may be named based on what they measure, with the "measurement" part left implicit. - -URI: [diag:DiagnosticProceduretoAttributeAssociation_subject](http://w3id.org/ontogpt/diagnostic_procedure/DiagnosticProceduretoAttributeAssociation_subject) - - -## Domain and Range - -[DiagnosticProceduretoAttributeAssociation](DiagnosticProceduretoAttributeAssociation.md) → <sub>0..1</sub> [DiagnosticProcedure](DiagnosticProcedure.md) - -## Parents - - * is_a: [➞subject](triple__subject.md) - -## Children - - -## Used by - - * [DiagnosticProceduretoAttributeAssociation](DiagnosticProceduretoAttributeAssociation.md) diff --git a/projects/diagnostic_procedure/docs/DiagnosticProceduretoAttributeAssociation_subject_qualifier.md b/projects/diagnostic_procedure/docs/DiagnosticProceduretoAttributeAssociation_subject_qualifier.md deleted file mode 100644 index 8554c92e1..000000000 --- a/projects/diagnostic_procedure/docs/DiagnosticProceduretoAttributeAssociation_subject_qualifier.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: subject_qualifier - - -An optional qualifier or modifier for the procedure. - -URI: [diag:DiagnosticProceduretoAttributeAssociation_subject_qualifier](http://w3id.org/ontogpt/diagnostic_procedure/DiagnosticProceduretoAttributeAssociation_subject_qualifier) - - -## Domain and Range - -[DiagnosticProceduretoAttributeAssociation](DiagnosticProceduretoAttributeAssociation.md) → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - * is_a: [➞subject_qualifier](triple__subject_qualifier.md) - -## Children - - -## Used by - - * [DiagnosticProceduretoAttributeAssociation](DiagnosticProceduretoAttributeAssociation.md) diff --git a/projects/diagnostic_procedure/docs/DiagnosticProceduretoPhenotypeAssociation.md b/projects/diagnostic_procedure/docs/DiagnosticProceduretoPhenotypeAssociation.md deleted file mode 100644 index 13a206e17..000000000 --- a/projects/diagnostic_procedure/docs/DiagnosticProceduretoPhenotypeAssociation.md +++ /dev/null @@ -1,44 +0,0 @@ - -# Class: DiagnosticProceduretoPhenotypeAssociation - - -A triple representing a relationship between a diagnostic procedure and an associated phenotype, e.g., "blood pressure measurement" is associated with "high blood pressure". - -URI: [diag:DiagnosticProceduretoPhenotypeAssociation](http://w3id.org/ontogpt/diagnostic_procedure/DiagnosticProceduretoPhenotypeAssociation) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[ProcedureToPhenotypePredicate],[Phenotype],[NamedEntity],[NamedEntity]<object_qualifier%200..1-%20[DiagnosticProceduretoPhenotypeAssociation|qualifier(i):string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[DiagnosticProceduretoPhenotypeAssociation],[ProcedureToPhenotypePredicate]<predicate%200..1-%20[DiagnosticProceduretoPhenotypeAssociation],[Phenotype]<object%200..*-%20[DiagnosticProceduretoPhenotypeAssociation],[DiagnosticProcedure]<subject%200..1-%20[DiagnosticProceduretoPhenotypeAssociation],[Triple]^-[DiagnosticProceduretoPhenotypeAssociation],[DiagnosticProcedure])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[ProcedureToPhenotypePredicate],[Phenotype],[NamedEntity],[NamedEntity]<object_qualifier%200..1-%20[DiagnosticProceduretoPhenotypeAssociation|qualifier(i):string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[DiagnosticProceduretoPhenotypeAssociation],[ProcedureToPhenotypePredicate]<predicate%200..1-%20[DiagnosticProceduretoPhenotypeAssociation],[Phenotype]<object%200..*-%20[DiagnosticProceduretoPhenotypeAssociation],[DiagnosticProcedure]<subject%200..1-%20[DiagnosticProceduretoPhenotypeAssociation],[Triple]^-[DiagnosticProceduretoPhenotypeAssociation],[DiagnosticProcedure]) - -## Parents - - * is_a: [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - -## Referenced by Class - - -## Attributes - - -### Own - - * [DiagnosticProceduretoPhenotypeAssociation➞subject](DiagnosticProceduretoPhenotypeAssociation_subject.md) <sub>0..1</sub> - * Description: A diagnostic procedure yielding a result, which in turn may be interpreted as a phenotype. Procedures include "heart rate measurement", "blood pressure measurement", "oxygen saturation measurement", etc. In practice, procedures may be named based on what they measure, with the "measurement" part left implicit. - * Range: [DiagnosticProcedure](DiagnosticProcedure.md) - * [DiagnosticProceduretoPhenotypeAssociation➞object](DiagnosticProceduretoPhenotypeAssociation_object.md) <sub>0..\*</sub> - * Description: The observable physical or biochemical characteristics of a patient. Not equivalent to a disease state, but may contribute to a diagnosis. - * Range: [Phenotype](Phenotype.md) - * [DiagnosticProceduretoPhenotypeAssociation➞predicate](DiagnosticProceduretoPhenotypeAssociation_predicate.md) <sub>0..1</sub> - * Description: The relationship type, e.g. RELATED_TO - * Range: [ProcedureToPhenotypePredicate](ProcedureToPhenotypePredicate.md) - * [DiagnosticProceduretoPhenotypeAssociation➞subject_qualifier](DiagnosticProceduretoPhenotypeAssociation_subject_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the procedure. - * Range: [NamedEntity](NamedEntity.md) - * [DiagnosticProceduretoPhenotypeAssociation➞object_qualifier](DiagnosticProceduretoPhenotypeAssociation_object_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the phenotype. - * Range: [NamedEntity](NamedEntity.md) - -### Inherited from Triple: - - * [➞qualifier](triple__qualifier.md) <sub>0..1</sub> - * Description: A qualifier for the statements, e.g. "NOT" for negation - * Range: [String](types/String.md) diff --git a/projects/diagnostic_procedure/docs/DiagnosticProceduretoPhenotypeAssociation_object.md b/projects/diagnostic_procedure/docs/DiagnosticProceduretoPhenotypeAssociation_object.md deleted file mode 100644 index 3aa84aeef..000000000 --- a/projects/diagnostic_procedure/docs/DiagnosticProceduretoPhenotypeAssociation_object.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: object - - -The observable physical or biochemical characteristics of a patient. Not equivalent to a disease state, but may contribute to a diagnosis. - -URI: [diag:DiagnosticProceduretoPhenotypeAssociation_object](http://w3id.org/ontogpt/diagnostic_procedure/DiagnosticProceduretoPhenotypeAssociation_object) - - -## Domain and Range - -[DiagnosticProceduretoPhenotypeAssociation](DiagnosticProceduretoPhenotypeAssociation.md) → <sub>0..\*</sub> [Phenotype](Phenotype.md) - -## Parents - - * is_a: [➞object](triple__object.md) - -## Children - - -## Used by - - * [DiagnosticProceduretoPhenotypeAssociation](DiagnosticProceduretoPhenotypeAssociation.md) diff --git a/projects/diagnostic_procedure/docs/DiagnosticProceduretoPhenotypeAssociation_object_qualifier.md b/projects/diagnostic_procedure/docs/DiagnosticProceduretoPhenotypeAssociation_object_qualifier.md deleted file mode 100644 index cc6d50b0a..000000000 --- a/projects/diagnostic_procedure/docs/DiagnosticProceduretoPhenotypeAssociation_object_qualifier.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: object_qualifier - - -An optional qualifier or modifier for the phenotype. - -URI: [diag:DiagnosticProceduretoPhenotypeAssociation_object_qualifier](http://w3id.org/ontogpt/diagnostic_procedure/DiagnosticProceduretoPhenotypeAssociation_object_qualifier) - - -## Domain and Range - -[DiagnosticProceduretoPhenotypeAssociation](DiagnosticProceduretoPhenotypeAssociation.md) → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - * is_a: [➞object_qualifier](triple__object_qualifier.md) - -## Children - - -## Used by - - * [DiagnosticProceduretoPhenotypeAssociation](DiagnosticProceduretoPhenotypeAssociation.md) diff --git a/projects/diagnostic_procedure/docs/DiagnosticProceduretoPhenotypeAssociation_predicate.md b/projects/diagnostic_procedure/docs/DiagnosticProceduretoPhenotypeAssociation_predicate.md deleted file mode 100644 index aa7230fd3..000000000 --- a/projects/diagnostic_procedure/docs/DiagnosticProceduretoPhenotypeAssociation_predicate.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: predicate - - -The relationship type, e.g. RELATED_TO - -URI: [diag:DiagnosticProceduretoPhenotypeAssociation_predicate](http://w3id.org/ontogpt/diagnostic_procedure/DiagnosticProceduretoPhenotypeAssociation_predicate) - - -## Domain and Range - -[DiagnosticProceduretoPhenotypeAssociation](DiagnosticProceduretoPhenotypeAssociation.md) → <sub>0..1</sub> [ProcedureToPhenotypePredicate](ProcedureToPhenotypePredicate.md) - -## Parents - - * is_a: [➞predicate](triple__predicate.md) - -## Children - - -## Used by - - * [DiagnosticProceduretoPhenotypeAssociation](DiagnosticProceduretoPhenotypeAssociation.md) diff --git a/projects/diagnostic_procedure/docs/DiagnosticProceduretoPhenotypeAssociation_subject.md b/projects/diagnostic_procedure/docs/DiagnosticProceduretoPhenotypeAssociation_subject.md deleted file mode 100644 index 5fc29c421..000000000 --- a/projects/diagnostic_procedure/docs/DiagnosticProceduretoPhenotypeAssociation_subject.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: subject - - -A diagnostic procedure yielding a result, which in turn may be interpreted as a phenotype. Procedures include "heart rate measurement", "blood pressure measurement", "oxygen saturation measurement", etc. In practice, procedures may be named based on what they measure, with the "measurement" part left implicit. - -URI: [diag:DiagnosticProceduretoPhenotypeAssociation_subject](http://w3id.org/ontogpt/diagnostic_procedure/DiagnosticProceduretoPhenotypeAssociation_subject) - - -## Domain and Range - -[DiagnosticProceduretoPhenotypeAssociation](DiagnosticProceduretoPhenotypeAssociation.md) → <sub>0..1</sub> [DiagnosticProcedure](DiagnosticProcedure.md) - -## Parents - - * is_a: [➞subject](triple__subject.md) - -## Children - - -## Used by - - * [DiagnosticProceduretoPhenotypeAssociation](DiagnosticProceduretoPhenotypeAssociation.md) diff --git a/projects/diagnostic_procedure/docs/DiagnosticProceduretoPhenotypeAssociation_subject_qualifier.md b/projects/diagnostic_procedure/docs/DiagnosticProceduretoPhenotypeAssociation_subject_qualifier.md deleted file mode 100644 index 705e762d7..000000000 --- a/projects/diagnostic_procedure/docs/DiagnosticProceduretoPhenotypeAssociation_subject_qualifier.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: subject_qualifier - - -An optional qualifier or modifier for the procedure. - -URI: [diag:DiagnosticProceduretoPhenotypeAssociation_subject_qualifier](http://w3id.org/ontogpt/diagnostic_procedure/DiagnosticProceduretoPhenotypeAssociation_subject_qualifier) - - -## Domain and Range - -[DiagnosticProceduretoPhenotypeAssociation](DiagnosticProceduretoPhenotypeAssociation.md) → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - * is_a: [➞subject_qualifier](triple__subject_qualifier.md) - -## Children - - -## Used by - - * [DiagnosticProceduretoPhenotypeAssociation](DiagnosticProceduretoPhenotypeAssociation.md) diff --git a/projects/diagnostic_procedure/docs/ExtractionResult.md b/projects/diagnostic_procedure/docs/ExtractionResult.md deleted file mode 100644 index d0c5a25fc..000000000 --- a/projects/diagnostic_procedure/docs/ExtractionResult.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Class: ExtractionResult - - -A result of extracting knowledge on text - -URI: [diag:ExtractionResult](http://w3id.org/ontogpt/diagnostic_procedure/ExtractionResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any])](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any]) - -## Attributes - - -### Own - - * [➞input_id](extractionResult__input_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_title](extractionResult__input_title.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_text](extractionResult__input_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞prompt](extractionResult__prompt.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞extracted_object](extractionResult__extracted_object.md) <sub>0..1</sub> - * Description: The complex objects extracted from the text - * Range: [Any](Any.md) - * [➞named_entities](extractionResult__named_entities.md) <sub>0..\*</sub> - * Description: Named entities extracted from the text - * Range: [Any](Any.md) diff --git a/projects/diagnostic_procedure/docs/NamedEntity.md b/projects/diagnostic_procedure/docs/NamedEntity.md deleted file mode 100644 index 62b033567..000000000 --- a/projects/diagnostic_procedure/docs/NamedEntity.md +++ /dev/null @@ -1,41 +0,0 @@ - -# Class: NamedEntity - - - - -URI: [diag:NamedEntity](http://w3id.org/ontogpt/diagnostic_procedure/NamedEntity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Unit],[RelationshipType],[Quality],[Phenotype],[DiagnosticProceduretoAttributeAssociation]-%20subject_qualifier%200..1>[NamedEntity|id:string;label:string%20%3F],[DiagnosticProceduretoPhenotypeAssociation]-%20object_qualifier%200..1>[NamedEntity],[DiagnosticProceduretoPhenotypeAssociation]-%20subject_qualifier%200..1>[NamedEntity],[Triple]-%20object%200..1>[NamedEntity],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[Unit],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[Quality],[NamedEntity]^-[Phenotype],[NamedEntity]^-[DiagnosticProcedure],[NamedEntity]^-[ClinicalAttribute],[Triple],[DiagnosticProceduretoPhenotypeAssociation],[DiagnosticProceduretoAttributeAssociation],[DiagnosticProcedure],[ClinicalAttribute])](https://yuml.me/diagram/nofunky;dir:TB/class/[Unit],[RelationshipType],[Quality],[Phenotype],[DiagnosticProceduretoAttributeAssociation]-%20subject_qualifier%200..1>[NamedEntity|id:string;label:string%20%3F],[DiagnosticProceduretoPhenotypeAssociation]-%20object_qualifier%200..1>[NamedEntity],[DiagnosticProceduretoPhenotypeAssociation]-%20subject_qualifier%200..1>[NamedEntity],[Triple]-%20object%200..1>[NamedEntity],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[Unit],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[Quality],[NamedEntity]^-[Phenotype],[NamedEntity]^-[DiagnosticProcedure],[NamedEntity]^-[ClinicalAttribute],[Triple],[DiagnosticProceduretoPhenotypeAssociation],[DiagnosticProceduretoAttributeAssociation],[DiagnosticProcedure],[ClinicalAttribute]) - -## Children - - * [ClinicalAttribute](ClinicalAttribute.md) - * [DiagnosticProcedure](DiagnosticProcedure.md) - * [Phenotype](Phenotype.md) - * [Quality](Quality.md) - * [RelationshipType](RelationshipType.md) - * [Unit](Unit.md) - -## Referenced by Class - - * **[DiagnosticProceduretoAttributeAssociation](DiagnosticProceduretoAttributeAssociation.md)** *[DiagnosticProceduretoAttributeAssociation➞subject_qualifier](DiagnosticProceduretoAttributeAssociation_subject_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **[DiagnosticProceduretoPhenotypeAssociation](DiagnosticProceduretoPhenotypeAssociation.md)** *[DiagnosticProceduretoPhenotypeAssociation➞object_qualifier](DiagnosticProceduretoPhenotypeAssociation_object_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **[DiagnosticProceduretoPhenotypeAssociation](DiagnosticProceduretoPhenotypeAssociation.md)** *[DiagnosticProceduretoPhenotypeAssociation➞subject_qualifier](DiagnosticProceduretoPhenotypeAssociation_subject_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞object](triple__object.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞object_qualifier](triple__object_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject](triple__subject.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject_qualifier](triple__subject_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - -## Attributes - - -### Own - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/diagnostic_procedure/docs/NullDataOptions.md b/projects/diagnostic_procedure/docs/NullDataOptions.md deleted file mode 100644 index d738f531e..000000000 --- a/projects/diagnostic_procedure/docs/NullDataOptions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Enum: NullDataOptions - - - - -URI: [diag:NullDataOptions](http://w3id.org/ontogpt/diagnostic_procedure/NullDataOptions) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | -| UNSPECIFIED_METHOD_OF_ADMINISTRATION | | NCIT:C149701 | | -| NOT_APPLICABLE | | NCIT:C18902 | {'aliases': ['not applicable', 'N/A']} | -| NOT_MENTIONED | | | | - diff --git a/projects/diagnostic_procedure/docs/Phenotype.md b/projects/diagnostic_procedure/docs/Phenotype.md deleted file mode 100644 index cf80c0771..000000000 --- a/projects/diagnostic_procedure/docs/Phenotype.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Phenotype - - - - -URI: [diag:Phenotype](http://w3id.org/ontogpt/diagnostic_procedure/Phenotype) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[DiagnosticProceduretoPhenotypeAssociation]-%20object%200..*>[Phenotype|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Phenotype],[NamedEntity],[DiagnosticProceduretoPhenotypeAssociation])](https://yuml.me/diagram/nofunky;dir:TB/class/[DiagnosticProceduretoPhenotypeAssociation]-%20object%200..*>[Phenotype|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Phenotype],[NamedEntity],[DiagnosticProceduretoPhenotypeAssociation]) - -## Identifier prefixes - - * HP - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **[DiagnosticProceduretoPhenotypeAssociation](DiagnosticProceduretoPhenotypeAssociation.md)** *[DiagnosticProceduretoPhenotypeAssociation➞object](DiagnosticProceduretoPhenotypeAssociation_object.md)* <sub>0..\*</sub> **[Phenotype](Phenotype.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/diagnostic_procedure/docs/ProcedureToAttributePredicate.md b/projects/diagnostic_procedure/docs/ProcedureToAttributePredicate.md deleted file mode 100644 index a7476bca7..000000000 --- a/projects/diagnostic_procedure/docs/ProcedureToAttributePredicate.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Class: ProcedureToAttributePredicate - - -A predicate for procedure to attribute relationships, defining "this procedure is a measurement of this attribute". - -URI: [diag:ProcedureToAttributePredicate](http://w3id.org/ontogpt/diagnostic_procedure/ProcedureToAttributePredicate) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[DiagnosticProceduretoAttributeAssociation]-%20predicate%200..1>[ProcedureToAttributePredicate|id(i):string;label(i):string%20%3F],[RelationshipType]^-[ProcedureToAttributePredicate],[DiagnosticProceduretoAttributeAssociation])](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[DiagnosticProceduretoAttributeAssociation]-%20predicate%200..1>[ProcedureToAttributePredicate|id(i):string;label(i):string%20%3F],[RelationshipType]^-[ProcedureToAttributePredicate],[DiagnosticProceduretoAttributeAssociation]) - -## Parents - - * is_a: [RelationshipType](RelationshipType.md) - -## Referenced by Class - - * **[DiagnosticProceduretoAttributeAssociation](DiagnosticProceduretoAttributeAssociation.md)** *[DiagnosticProceduretoAttributeAssociation➞predicate](DiagnosticProceduretoAttributeAssociation_predicate.md)* <sub>0..1</sub> **[ProcedureToAttributePredicate](ProcedureToAttributePredicate.md)** - -## Attributes - - -### Inherited from RelationshipType: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/diagnostic_procedure/docs/ProcedureToPhenotypePredicate.md b/projects/diagnostic_procedure/docs/ProcedureToPhenotypePredicate.md deleted file mode 100644 index 98caa15f3..000000000 --- a/projects/diagnostic_procedure/docs/ProcedureToPhenotypePredicate.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Class: ProcedureToPhenotypePredicate - - -A predicate for procedure to phenotype relationships, defining "this procedure is intended to provide support for/against this phenotype". - -URI: [diag:ProcedureToPhenotypePredicate](http://w3id.org/ontogpt/diagnostic_procedure/ProcedureToPhenotypePredicate) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[DiagnosticProceduretoPhenotypeAssociation]-%20predicate%200..1>[ProcedureToPhenotypePredicate|id(i):string;label(i):string%20%3F],[RelationshipType]^-[ProcedureToPhenotypePredicate],[DiagnosticProceduretoPhenotypeAssociation])](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[DiagnosticProceduretoPhenotypeAssociation]-%20predicate%200..1>[ProcedureToPhenotypePredicate|id(i):string;label(i):string%20%3F],[RelationshipType]^-[ProcedureToPhenotypePredicate],[DiagnosticProceduretoPhenotypeAssociation]) - -## Parents - - * is_a: [RelationshipType](RelationshipType.md) - -## Referenced by Class - - * **[DiagnosticProceduretoPhenotypeAssociation](DiagnosticProceduretoPhenotypeAssociation.md)** *[DiagnosticProceduretoPhenotypeAssociation➞predicate](DiagnosticProceduretoPhenotypeAssociation_predicate.md)* <sub>0..1</sub> **[ProcedureToPhenotypePredicate](ProcedureToPhenotypePredicate.md)** - -## Attributes - - -### Inherited from RelationshipType: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/diagnostic_procedure/docs/Publication.md b/projects/diagnostic_procedure/docs/Publication.md deleted file mode 100644 index e43e6814e..000000000 --- a/projects/diagnostic_procedure/docs/Publication.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Publication - - - - -URI: [diag:Publication](http://w3id.org/ontogpt/diagnostic_procedure/Publication) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples])](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples]) - -## Referenced by Class - - * **None** *[➞publication](textWithTriples__publication.md)* <sub>0..1</sub> **[Publication](Publication.md)** - -## Attributes - - -### Own - - * [➞id](publication__id.md) <sub>0..1</sub> - * Description: The publication identifier - * Range: [String](types/String.md) - * [➞title](publication__title.md) <sub>0..1</sub> - * Description: The title of the publication - * Range: [String](types/String.md) - * [➞abstract](publication__abstract.md) <sub>0..1</sub> - * Description: The abstract of the publication - * Range: [String](types/String.md) - * [➞combined_text](publication__combined_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞full_text](publication__full_text.md) <sub>0..1</sub> - * Description: The full text of the publication - * Range: [String](types/String.md) diff --git a/projects/diagnostic_procedure/docs/Quality.md b/projects/diagnostic_procedure/docs/Quality.md deleted file mode 100644 index f8f84ec4b..000000000 --- a/projects/diagnostic_procedure/docs/Quality.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Quality - - - - -URI: [diag:Quality](http://w3id.org/ontogpt/diagnostic_procedure/Quality) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[DiagnosticProceduretoAttributeAssociation]-%20object_qualifier%200..1>[Quality|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Quality],[NamedEntity],[DiagnosticProceduretoAttributeAssociation])](https://yuml.me/diagram/nofunky;dir:TB/class/[DiagnosticProceduretoAttributeAssociation]-%20object_qualifier%200..1>[Quality|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Quality],[NamedEntity],[DiagnosticProceduretoAttributeAssociation]) - -## Identifier prefixes - - * PATO - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **[DiagnosticProceduretoAttributeAssociation](DiagnosticProceduretoAttributeAssociation.md)** *[DiagnosticProceduretoAttributeAssociation➞object_qualifier](DiagnosticProceduretoAttributeAssociation_object_qualifier.md)* <sub>0..1</sub> **[Quality](Quality.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/diagnostic_procedure/docs/RelationshipType.md b/projects/diagnostic_procedure/docs/RelationshipType.md deleted file mode 100644 index e5f7930cc..000000000 --- a/projects/diagnostic_procedure/docs/RelationshipType.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Class: RelationshipType - - - - -URI: [diag:RelationshipType](http://w3id.org/ontogpt/diagnostic_procedure/RelationshipType) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[RelationshipType]^-[ProcedureToPhenotypePredicate],[RelationshipType]^-[ProcedureToAttributePredicate],[NamedEntity]^-[RelationshipType],[Triple],[ProcedureToPhenotypePredicate],[ProcedureToAttributePredicate],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[RelationshipType]^-[ProcedureToPhenotypePredicate],[RelationshipType]^-[ProcedureToAttributePredicate],[NamedEntity]^-[RelationshipType],[Triple],[ProcedureToPhenotypePredicate],[ProcedureToAttributePredicate],[NamedEntity]) - -## Identifier prefixes - - * RO - * biolink - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Children - - * [ProcedureToAttributePredicate](ProcedureToAttributePredicate.md) - A predicate for procedure to attribute relationships, defining "this procedure is a measurement of this attribute". - * [ProcedureToPhenotypePredicate](ProcedureToPhenotypePredicate.md) - A predicate for procedure to phenotype relationships, defining "this procedure is intended to provide support for/against this phenotype". - -## Referenced by Class - - * **None** *[➞predicate](triple__predicate.md)* <sub>0..1</sub> **[RelationshipType](RelationshipType.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/diagnostic_procedure/docs/TextWithTriples.md b/projects/diagnostic_procedure/docs/TextWithTriples.md deleted file mode 100644 index 509967bdd..000000000 --- a/projects/diagnostic_procedure/docs/TextWithTriples.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: TextWithTriples - - - - -URI: [diag:TextWithTriples](http://w3id.org/ontogpt/diagnostic_procedure/TextWithTriples) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication]) - -## Attributes - - -### Own - - * [➞publication](textWithTriples__publication.md) <sub>0..1</sub> - * Range: [Publication](Publication.md) - * [➞triples](textWithTriples__triples.md) <sub>0..\*</sub> - * Range: [Triple](Triple.md) diff --git a/projects/diagnostic_procedure/docs/Triple.md b/projects/diagnostic_procedure/docs/Triple.md deleted file mode 100644 index 999cbff06..000000000 --- a/projects/diagnostic_procedure/docs/Triple.md +++ /dev/null @@ -1,44 +0,0 @@ - -# Class: Triple - - -Abstract parent for Relation Extraction tasks - -URI: [diag:Triple](http://w3id.org/ontogpt/diagnostic_procedure/Triple) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[Triple]^-[DiagnosticProceduretoPhenotypeAssociation],[Triple]^-[DiagnosticProceduretoAttributeAssociation],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[DiagnosticProceduretoPhenotypeAssociation],[DiagnosticProceduretoAttributeAssociation],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[Triple]^-[DiagnosticProceduretoPhenotypeAssociation],[Triple]^-[DiagnosticProceduretoAttributeAssociation],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[DiagnosticProceduretoPhenotypeAssociation],[DiagnosticProceduretoAttributeAssociation],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Children - - * [DiagnosticProceduretoAttributeAssociation](DiagnosticProceduretoAttributeAssociation.md) - A triple representing a relationship between a diagnostic procedure and a measured attribute, e.g., "blood pressure measurement" is associated with "blood pressure" (or in OBA, something like OBA:VT0000183, "blood pressure trait"). - * [DiagnosticProceduretoPhenotypeAssociation](DiagnosticProceduretoPhenotypeAssociation.md) - A triple representing a relationship between a diagnostic procedure and an associated phenotype, e.g., "blood pressure measurement" is associated with "high blood pressure". - -## Referenced by Class - - * **None** *[➞triples](textWithTriples__triples.md)* <sub>0..\*</sub> **[Triple](Triple.md)** - -## Attributes - - -### Own - - * [➞subject](triple__subject.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞predicate](triple__predicate.md) <sub>0..1</sub> - * Range: [RelationshipType](RelationshipType.md) - * [➞object](triple__object.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞qualifier](triple__qualifier.md) <sub>0..1</sub> - * Description: A qualifier for the statements, e.g. "NOT" for negation - * Range: [String](types/String.md) - * [➞subject_qualifier](triple__subject_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - * Range: [NamedEntity](NamedEntity.md) - * [➞object_qualifier](triple__object_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * Range: [NamedEntity](NamedEntity.md) diff --git a/projects/diagnostic_procedure/docs/Unit.md b/projects/diagnostic_procedure/docs/Unit.md deleted file mode 100644 index 9071553fc..000000000 --- a/projects/diagnostic_procedure/docs/Unit.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Unit - - - - -URI: [diag:Unit](http://w3id.org/ontogpt/diagnostic_procedure/Unit) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ClinicalAttribute]-%20unit%200..1>[Unit|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Unit],[NamedEntity],[ClinicalAttribute])](https://yuml.me/diagram/nofunky;dir:TB/class/[ClinicalAttribute]-%20unit%200..1>[Unit|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Unit],[NamedEntity],[ClinicalAttribute]) - -## Identifier prefixes - - * UO - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞unit](clinicalAttribute__unit.md)* <sub>0..1</sub> **[Unit](Unit.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/diagnostic_procedure/docs/annotatorResult__object_id.md b/projects/diagnostic_procedure/docs/annotatorResult__object_id.md deleted file mode 100644 index e111af098..000000000 --- a/projects/diagnostic_procedure/docs/annotatorResult__object_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_id - - - - -URI: [diag:annotatorResult__object_id](http://w3id.org/ontogpt/diagnostic_procedure/annotatorResult__object_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/diagnostic_procedure/docs/annotatorResult__object_text.md b/projects/diagnostic_procedure/docs/annotatorResult__object_text.md deleted file mode 100644 index 281f17ec2..000000000 --- a/projects/diagnostic_procedure/docs/annotatorResult__object_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_text - - - - -URI: [diag:annotatorResult__object_text](http://w3id.org/ontogpt/diagnostic_procedure/annotatorResult__object_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/diagnostic_procedure/docs/annotatorResult__subject_text.md b/projects/diagnostic_procedure/docs/annotatorResult__subject_text.md deleted file mode 100644 index 715163dfa..000000000 --- a/projects/diagnostic_procedure/docs/annotatorResult__subject_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_text - - - - -URI: [diag:annotatorResult__subject_text](http://w3id.org/ontogpt/diagnostic_procedure/annotatorResult__subject_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/diagnostic_procedure/docs/clinicalAttribute__unit.md b/projects/diagnostic_procedure/docs/clinicalAttribute__unit.md deleted file mode 100644 index 1963ae530..000000000 --- a/projects/diagnostic_procedure/docs/clinicalAttribute__unit.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: unit - - -the unit used to measure the attribute - -URI: [diag:clinicalAttribute__unit](http://w3id.org/ontogpt/diagnostic_procedure/clinicalAttribute__unit) - - -## Domain and Range - -None → <sub>0..1</sub> [Unit](Unit.md) - -## Parents - - -## Children - - -## Used by - - * [ClinicalAttribute](ClinicalAttribute.md) diff --git a/projects/diagnostic_procedure/docs/diagnostic_procedure.md b/projects/diagnostic_procedure/docs/diagnostic_procedure.md deleted file mode 100644 index 53ad1538d..000000000 --- a/projects/diagnostic_procedure/docs/diagnostic_procedure.md +++ /dev/null @@ -1,123 +0,0 @@ - -# diagnostic_procedure - - -**metamodel version:** 1.7.0 - -**version:** None - - -A template for clinical diagnostic procedures and the phenotypes they may contribute to. - - -### Classes - - * [AnnotatorResult](AnnotatorResult.md) - * [Any](Any.md) - * [CompoundExpression](CompoundExpression.md) - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - * [DiagnosticProceduretoAttributeAssociation](DiagnosticProceduretoAttributeAssociation.md) - A triple representing a relationship between a diagnostic procedure and a measured attribute, e.g., "blood pressure measurement" is associated with "blood pressure" (or in OBA, something like OBA:VT0000183, "blood pressure trait"). - * [DiagnosticProceduretoPhenotypeAssociation](DiagnosticProceduretoPhenotypeAssociation.md) - A triple representing a relationship between a diagnostic procedure and an associated phenotype, e.g., "blood pressure measurement" is associated with "high blood pressure". - * [ExtractionResult](ExtractionResult.md) - A result of extracting knowledge on text - * [NamedEntity](NamedEntity.md) - * [ClinicalAttribute](ClinicalAttribute.md) - * [DiagnosticProcedure](DiagnosticProcedure.md) - * [Phenotype](Phenotype.md) - * [Quality](Quality.md) - * [RelationshipType](RelationshipType.md) - * [ProcedureToAttributePredicate](ProcedureToAttributePredicate.md) - A predicate for procedure to attribute relationships, defining "this procedure is a measurement of this attribute". - * [ProcedureToPhenotypePredicate](ProcedureToPhenotypePredicate.md) - A predicate for procedure to phenotype relationships, defining "this procedure is intended to provide support for/against this phenotype". - * [Unit](Unit.md) - * [Publication](Publication.md) - * [TextWithTriples](TextWithTriples.md) - -### Mixins - - -### Slots - - * [➞object_id](annotatorResult__object_id.md) - * [➞object_text](annotatorResult__object_text.md) - * [➞subject_text](annotatorResult__subject_text.md) - * [➞unit](clinicalAttribute__unit.md) - the unit used to measure the attribute - * [➞extracted_object](extractionResult__extracted_object.md) - The complex objects extracted from the text - * [➞input_id](extractionResult__input_id.md) - * [➞input_text](extractionResult__input_text.md) - * [➞input_title](extractionResult__input_title.md) - * [➞named_entities](extractionResult__named_entities.md) - Named entities extracted from the text - * [➞prompt](extractionResult__prompt.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) - * [➞id](namedEntity__id.md) - A unique identifier for the named entity - * [➞label](namedEntity__label.md) - The label (name) of the named thing - * [➞abstract](publication__abstract.md) - The abstract of the publication - * [➞combined_text](publication__combined_text.md) - * [➞full_text](publication__full_text.md) - The full text of the publication - * [➞id](publication__id.md) - The publication identifier - * [➞title](publication__title.md) - The title of the publication - * [➞publication](textWithTriples__publication.md) - * [➞triples](textWithTriples__triples.md) - * [➞object](triple__object.md) - * [DiagnosticProceduretoAttributeAssociation➞object](DiagnosticProceduretoAttributeAssociation_object.md) - Any measurable clinical attribute. - * [DiagnosticProceduretoPhenotypeAssociation➞object](DiagnosticProceduretoPhenotypeAssociation_object.md) - The observable physical or biochemical characteristics of a patient. Not equivalent to a disease state, but may contribute to a diagnosis. - * [➞object_qualifier](triple__object_qualifier.md) - An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * [DiagnosticProceduretoAttributeAssociation➞object_qualifier](DiagnosticProceduretoAttributeAssociation_object_qualifier.md) - An optional qualifier or modifier for the phenotype. - * [DiagnosticProceduretoPhenotypeAssociation➞object_qualifier](DiagnosticProceduretoPhenotypeAssociation_object_qualifier.md) - An optional qualifier or modifier for the phenotype. - * [➞predicate](triple__predicate.md) - * [DiagnosticProceduretoAttributeAssociation➞predicate](DiagnosticProceduretoAttributeAssociation_predicate.md) - The relationship type, e.g. RELATED_TO - * [DiagnosticProceduretoPhenotypeAssociation➞predicate](DiagnosticProceduretoPhenotypeAssociation_predicate.md) - The relationship type, e.g. RELATED_TO - * [➞qualifier](triple__qualifier.md) - A qualifier for the statements, e.g. "NOT" for negation - * [➞subject](triple__subject.md) - * [DiagnosticProceduretoAttributeAssociation➞subject](DiagnosticProceduretoAttributeAssociation_subject.md) - A diagnostic procedure yielding a result, which in turn may be interpreted as a phenotype. Procedures include "heart rate measurement", "blood pressure measurement", "oxygen saturation measurement", etc. In practice, procedures may be named based on what they measure, with the "measurement" part left implicit. - * [DiagnosticProceduretoPhenotypeAssociation➞subject](DiagnosticProceduretoPhenotypeAssociation_subject.md) - A diagnostic procedure yielding a result, which in turn may be interpreted as a phenotype. Procedures include "heart rate measurement", "blood pressure measurement", "oxygen saturation measurement", etc. In practice, procedures may be named based on what they measure, with the "measurement" part left implicit. - * [➞subject_qualifier](triple__subject_qualifier.md) - An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - * [DiagnosticProceduretoAttributeAssociation➞subject_qualifier](DiagnosticProceduretoAttributeAssociation_subject_qualifier.md) - An optional qualifier or modifier for the procedure. - * [DiagnosticProceduretoPhenotypeAssociation➞subject_qualifier](DiagnosticProceduretoPhenotypeAssociation_subject_qualifier.md) - An optional qualifier or modifier for the procedure. - -### Enums - - * [NullDataOptions](NullDataOptions.md) - -### Subsets - - -### Types - - -#### Built in - - * **Bool** - * **Curie** - * **Decimal** - * **ElementIdentifier** - * **NCName** - * **NodeIdentifier** - * **URI** - * **URIorCURIE** - * **XSDDate** - * **XSDDateTime** - * **XSDTime** - * **float** - * **int** - * **str** - -#### Defined - - * [Boolean](types/Boolean.md) (**Bool**) - A binary (true or false) value - * [Curie](types/Curie.md) (**Curie**) - a compact URI - * [Date](types/Date.md) (**XSDDate**) - a date (year, month and day) in an idealized calendar - * [DateOrDatetime](types/DateOrDatetime.md) (**str**) - Either a date or a datetime - * [Datetime](types/Datetime.md) (**XSDDateTime**) - The combination of a date and time - * [Decimal](types/Decimal.md) (**Decimal**) - A real number with arbitrary precision that conforms to the xsd:decimal specification - * [Double](types/Double.md) (**float**) - A real number that conforms to the xsd:double specification - * [Float](types/Float.md) (**float**) - A real number that conforms to the xsd:float specification - * [Integer](types/Integer.md) (**int**) - An integer - * [Jsonpath](types/Jsonpath.md) (**str**) - A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - * [Jsonpointer](types/Jsonpointer.md) (**str**) - A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - * [Ncname](types/Ncname.md) (**NCName**) - Prefix part of CURIE - * [Nodeidentifier](types/Nodeidentifier.md) (**NodeIdentifier**) - A URI, CURIE or BNODE that represents a node in a model. - * [Objectidentifier](types/Objectidentifier.md) (**ElementIdentifier**) - A URI or CURIE that represents an object in the model. - * [Sparqlpath](types/Sparqlpath.md) (**str**) - A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - * [String](types/String.md) (**str**) - A character string - * [Time](types/Time.md) (**XSDTime**) - A time object represents a (local) time of day, independent of any particular day - * [Uri](types/Uri.md) (**URI**) - a complete URI - * [Uriorcurie](types/Uriorcurie.md) (**URIorCURIE**) - a URI or a CURIE diff --git a/projects/diagnostic_procedure/docs/extractionResult__extracted_object.md b/projects/diagnostic_procedure/docs/extractionResult__extracted_object.md deleted file mode 100644 index 030afba49..000000000 --- a/projects/diagnostic_procedure/docs/extractionResult__extracted_object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: extracted_object - - -The complex objects extracted from the text - -URI: [diag:extractionResult__extracted_object](http://w3id.org/ontogpt/diagnostic_procedure/extractionResult__extracted_object) - - -## Domain and Range - -None → <sub>0..1</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/diagnostic_procedure/docs/extractionResult__input_id.md b/projects/diagnostic_procedure/docs/extractionResult__input_id.md deleted file mode 100644 index 4e5ce054c..000000000 --- a/projects/diagnostic_procedure/docs/extractionResult__input_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_id - - - - -URI: [diag:extractionResult__input_id](http://w3id.org/ontogpt/diagnostic_procedure/extractionResult__input_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/diagnostic_procedure/docs/extractionResult__input_text.md b/projects/diagnostic_procedure/docs/extractionResult__input_text.md deleted file mode 100644 index 3b6dcc5cb..000000000 --- a/projects/diagnostic_procedure/docs/extractionResult__input_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_text - - - - -URI: [diag:extractionResult__input_text](http://w3id.org/ontogpt/diagnostic_procedure/extractionResult__input_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/diagnostic_procedure/docs/extractionResult__input_title.md b/projects/diagnostic_procedure/docs/extractionResult__input_title.md deleted file mode 100644 index e37e7429b..000000000 --- a/projects/diagnostic_procedure/docs/extractionResult__input_title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_title - - - - -URI: [diag:extractionResult__input_title](http://w3id.org/ontogpt/diagnostic_procedure/extractionResult__input_title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/diagnostic_procedure/docs/extractionResult__named_entities.md b/projects/diagnostic_procedure/docs/extractionResult__named_entities.md deleted file mode 100644 index 2246afb9c..000000000 --- a/projects/diagnostic_procedure/docs/extractionResult__named_entities.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: named_entities - - -Named entities extracted from the text - -URI: [diag:extractionResult__named_entities](http://w3id.org/ontogpt/diagnostic_procedure/extractionResult__named_entities) - - -## Domain and Range - -None → <sub>0..\*</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/diagnostic_procedure/docs/extractionResult__prompt.md b/projects/diagnostic_procedure/docs/extractionResult__prompt.md deleted file mode 100644 index 20fdaaccf..000000000 --- a/projects/diagnostic_procedure/docs/extractionResult__prompt.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: prompt - - - - -URI: [diag:extractionResult__prompt](http://w3id.org/ontogpt/diagnostic_procedure/extractionResult__prompt) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/diagnostic_procedure/docs/extractionResult__raw_completion_output.md b/projects/diagnostic_procedure/docs/extractionResult__raw_completion_output.md deleted file mode 100644 index 554805c0f..000000000 --- a/projects/diagnostic_procedure/docs/extractionResult__raw_completion_output.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: raw_completion_output - - - - -URI: [diag:extractionResult__raw_completion_output](http://w3id.org/ontogpt/diagnostic_procedure/extractionResult__raw_completion_output) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/diagnostic_procedure/docs/namedEntity__id.md b/projects/diagnostic_procedure/docs/namedEntity__id.md deleted file mode 100644 index 7413eb383..000000000 --- a/projects/diagnostic_procedure/docs/namedEntity__id.md +++ /dev/null @@ -1,37 +0,0 @@ - -# Slot: id - - -A unique identifier for the named entity - -URI: [diag:namedEntity__id](http://w3id.org/ontogpt/diagnostic_procedure/namedEntity__id) - - -## Domain and Range - -None → <sub>1..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ClinicalAttribute](ClinicalAttribute.md) - * [DiagnosticProcedure](DiagnosticProcedure.md) - * [NamedEntity](NamedEntity.md) - * [Phenotype](Phenotype.md) - * [ProcedureToAttributePredicate](ProcedureToAttributePredicate.md) - * [ProcedureToPhenotypePredicate](ProcedureToPhenotypePredicate.md) - * [Quality](Quality.md) - * [RelationshipType](RelationshipType.md) - * [Unit](Unit.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | this is populated during the grounding and normalization step | - diff --git a/projects/diagnostic_procedure/docs/namedEntity__label.md b/projects/diagnostic_procedure/docs/namedEntity__label.md deleted file mode 100644 index 2c32cb0e8..000000000 --- a/projects/diagnostic_procedure/docs/namedEntity__label.md +++ /dev/null @@ -1,38 +0,0 @@ - -# Slot: label - - -The label (name) of the named thing - -URI: [diag:namedEntity__label](http://w3id.org/ontogpt/diagnostic_procedure/namedEntity__label) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ClinicalAttribute](ClinicalAttribute.md) - * [DiagnosticProcedure](DiagnosticProcedure.md) - * [NamedEntity](NamedEntity.md) - * [Phenotype](Phenotype.md) - * [ProcedureToAttributePredicate](ProcedureToAttributePredicate.md) - * [ProcedureToPhenotypePredicate](ProcedureToPhenotypePredicate.md) - * [Quality](Quality.md) - * [RelationshipType](RelationshipType.md) - * [Unit](Unit.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Aliases:** | | name | -| **Mappings:** | | rdfs:label | - diff --git a/projects/diagnostic_procedure/docs/publication__abstract.md b/projects/diagnostic_procedure/docs/publication__abstract.md deleted file mode 100644 index a23d8005d..000000000 --- a/projects/diagnostic_procedure/docs/publication__abstract.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: abstract - - -The abstract of the publication - -URI: [diag:publication__abstract](http://w3id.org/ontogpt/diagnostic_procedure/publication__abstract) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/diagnostic_procedure/docs/publication__combined_text.md b/projects/diagnostic_procedure/docs/publication__combined_text.md deleted file mode 100644 index 8d5296d47..000000000 --- a/projects/diagnostic_procedure/docs/publication__combined_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: combined_text - - - - -URI: [diag:publication__combined_text](http://w3id.org/ontogpt/diagnostic_procedure/publication__combined_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/diagnostic_procedure/docs/publication__full_text.md b/projects/diagnostic_procedure/docs/publication__full_text.md deleted file mode 100644 index 770358251..000000000 --- a/projects/diagnostic_procedure/docs/publication__full_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: full_text - - -The full text of the publication - -URI: [diag:publication__full_text](http://w3id.org/ontogpt/diagnostic_procedure/publication__full_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/diagnostic_procedure/docs/publication__id.md b/projects/diagnostic_procedure/docs/publication__id.md deleted file mode 100644 index b301de365..000000000 --- a/projects/diagnostic_procedure/docs/publication__id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: id - - -The publication identifier - -URI: [diag:publication__id](http://w3id.org/ontogpt/diagnostic_procedure/publication__id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/diagnostic_procedure/docs/publication__title.md b/projects/diagnostic_procedure/docs/publication__title.md deleted file mode 100644 index a29167a8e..000000000 --- a/projects/diagnostic_procedure/docs/publication__title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: title - - -The title of the publication - -URI: [diag:publication__title](http://w3id.org/ontogpt/diagnostic_procedure/publication__title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/diagnostic_procedure/docs/textWithTriples__publication.md b/projects/diagnostic_procedure/docs/textWithTriples__publication.md deleted file mode 100644 index 69860f0a5..000000000 --- a/projects/diagnostic_procedure/docs/textWithTriples__publication.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: publication - - - - -URI: [diag:textWithTriples__publication](http://w3id.org/ontogpt/diagnostic_procedure/textWithTriples__publication) - - -## Domain and Range - -None → <sub>0..1</sub> [Publication](Publication.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/diagnostic_procedure/docs/textWithTriples__triples.md b/projects/diagnostic_procedure/docs/textWithTriples__triples.md deleted file mode 100644 index 7da8f2bbc..000000000 --- a/projects/diagnostic_procedure/docs/textWithTriples__triples.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: triples - - - - -URI: [diag:textWithTriples__triples](http://w3id.org/ontogpt/diagnostic_procedure/textWithTriples__triples) - - -## Domain and Range - -None → <sub>0..\*</sub> [Triple](Triple.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/diagnostic_procedure/docs/triple__object.md b/projects/diagnostic_procedure/docs/triple__object.md deleted file mode 100644 index 9867ef445..000000000 --- a/projects/diagnostic_procedure/docs/triple__object.md +++ /dev/null @@ -1,24 +0,0 @@ - -# Slot: object - - - - -URI: [diag:triple__object](http://w3id.org/ontogpt/diagnostic_procedure/triple__object) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - * [DiagnosticProceduretoAttributeAssociation➞object](DiagnosticProceduretoAttributeAssociation_object.md) - * [DiagnosticProceduretoPhenotypeAssociation➞object](DiagnosticProceduretoPhenotypeAssociation_object.md) - -## Used by - - * [Triple](Triple.md) diff --git a/projects/diagnostic_procedure/docs/triple__object_qualifier.md b/projects/diagnostic_procedure/docs/triple__object_qualifier.md deleted file mode 100644 index 4bd449f17..000000000 --- a/projects/diagnostic_procedure/docs/triple__object_qualifier.md +++ /dev/null @@ -1,24 +0,0 @@ - -# Slot: object_qualifier - - -An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - -URI: [diag:triple__object_qualifier](http://w3id.org/ontogpt/diagnostic_procedure/triple__object_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - * [DiagnosticProceduretoAttributeAssociation➞object_qualifier](DiagnosticProceduretoAttributeAssociation_object_qualifier.md) - * [DiagnosticProceduretoPhenotypeAssociation➞object_qualifier](DiagnosticProceduretoPhenotypeAssociation_object_qualifier.md) - -## Used by - - * [Triple](Triple.md) diff --git a/projects/diagnostic_procedure/docs/triple__predicate.md b/projects/diagnostic_procedure/docs/triple__predicate.md deleted file mode 100644 index 79146dc19..000000000 --- a/projects/diagnostic_procedure/docs/triple__predicate.md +++ /dev/null @@ -1,24 +0,0 @@ - -# Slot: predicate - - - - -URI: [diag:triple__predicate](http://w3id.org/ontogpt/diagnostic_procedure/triple__predicate) - - -## Domain and Range - -None → <sub>0..1</sub> [RelationshipType](RelationshipType.md) - -## Parents - - -## Children - - * [DiagnosticProceduretoAttributeAssociation➞predicate](DiagnosticProceduretoAttributeAssociation_predicate.md) - * [DiagnosticProceduretoPhenotypeAssociation➞predicate](DiagnosticProceduretoPhenotypeAssociation_predicate.md) - -## Used by - - * [Triple](Triple.md) diff --git a/projects/diagnostic_procedure/docs/triple__qualifier.md b/projects/diagnostic_procedure/docs/triple__qualifier.md deleted file mode 100644 index baeed3656..000000000 --- a/projects/diagnostic_procedure/docs/triple__qualifier.md +++ /dev/null @@ -1,24 +0,0 @@ - -# Slot: qualifier - - -A qualifier for the statements, e.g. "NOT" for negation - -URI: [diag:triple__qualifier](http://w3id.org/ontogpt/diagnostic_procedure/triple__qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [DiagnosticProceduretoAttributeAssociation](DiagnosticProceduretoAttributeAssociation.md) - * [DiagnosticProceduretoPhenotypeAssociation](DiagnosticProceduretoPhenotypeAssociation.md) - * [Triple](Triple.md) diff --git a/projects/diagnostic_procedure/docs/triple__subject.md b/projects/diagnostic_procedure/docs/triple__subject.md deleted file mode 100644 index ef43fd56e..000000000 --- a/projects/diagnostic_procedure/docs/triple__subject.md +++ /dev/null @@ -1,24 +0,0 @@ - -# Slot: subject - - - - -URI: [diag:triple__subject](http://w3id.org/ontogpt/diagnostic_procedure/triple__subject) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - * [DiagnosticProceduretoAttributeAssociation➞subject](DiagnosticProceduretoAttributeAssociation_subject.md) - * [DiagnosticProceduretoPhenotypeAssociation➞subject](DiagnosticProceduretoPhenotypeAssociation_subject.md) - -## Used by - - * [Triple](Triple.md) diff --git a/projects/diagnostic_procedure/docs/triple__subject_qualifier.md b/projects/diagnostic_procedure/docs/triple__subject_qualifier.md deleted file mode 100644 index c0f1c2604..000000000 --- a/projects/diagnostic_procedure/docs/triple__subject_qualifier.md +++ /dev/null @@ -1,24 +0,0 @@ - -# Slot: subject_qualifier - - -An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -URI: [diag:triple__subject_qualifier](http://w3id.org/ontogpt/diagnostic_procedure/triple__subject_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - * [DiagnosticProceduretoAttributeAssociation➞subject_qualifier](DiagnosticProceduretoAttributeAssociation_subject_qualifier.md) - * [DiagnosticProceduretoPhenotypeAssociation➞subject_qualifier](DiagnosticProceduretoPhenotypeAssociation_subject_qualifier.md) - -## Used by - - * [Triple](Triple.md) diff --git a/projects/diagnostic_procedure/docs/types/Boolean.md b/projects/diagnostic_procedure/docs/types/Boolean.md deleted file mode 100644 index dc83a9c6e..000000000 --- a/projects/diagnostic_procedure/docs/types/Boolean.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: boolean - - -A binary (true or false) value - -URI: [linkml:Boolean](https://w3id.org/linkml/Boolean) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Bool** | -| Representation | | bool | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Boolean | - diff --git a/projects/diagnostic_procedure/docs/types/Curie.md b/projects/diagnostic_procedure/docs/types/Curie.md deleted file mode 100644 index c1803f93f..000000000 --- a/projects/diagnostic_procedure/docs/types/Curie.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: curie - - -a compact URI - -URI: [linkml:Curie](https://w3id.org/linkml/Curie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Curie** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations this MUST be expanded to a URI | -| | | in non-RDF serializations MAY be serialized as the compact representation | - diff --git a/projects/diagnostic_procedure/docs/types/Date.md b/projects/diagnostic_procedure/docs/types/Date.md deleted file mode 100644 index 06948af97..000000000 --- a/projects/diagnostic_procedure/docs/types/Date.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: date - - -a date (year, month and day) in an idealized calendar - -URI: [linkml:Date](https://w3id.org/linkml/Date) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDate** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Date | - diff --git a/projects/diagnostic_procedure/docs/types/DateOrDatetime.md b/projects/diagnostic_procedure/docs/types/DateOrDatetime.md deleted file mode 100644 index ef983898d..000000000 --- a/projects/diagnostic_procedure/docs/types/DateOrDatetime.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: date_or_datetime - - -Either a date or a datetime - -URI: [linkml:DateOrDatetime](https://w3id.org/linkml/DateOrDatetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/diagnostic_procedure/docs/types/Datetime.md b/projects/diagnostic_procedure/docs/types/Datetime.md deleted file mode 100644 index 9510454a8..000000000 --- a/projects/diagnostic_procedure/docs/types/Datetime.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: datetime - - -The combination of a date and time - -URI: [linkml:Datetime](https://w3id.org/linkml/Datetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDateTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:DateTime | - diff --git a/projects/diagnostic_procedure/docs/types/Decimal.md b/projects/diagnostic_procedure/docs/types/Decimal.md deleted file mode 100644 index a7ba14a5d..000000000 --- a/projects/diagnostic_procedure/docs/types/Decimal.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: decimal - - -A real number with arbitrary precision that conforms to the xsd:decimal specification - -URI: [linkml:Decimal](https://w3id.org/linkml/Decimal) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Decimal** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Broad Mappings:** | | schema:Number | - diff --git a/projects/diagnostic_procedure/docs/types/Double.md b/projects/diagnostic_procedure/docs/types/Double.md deleted file mode 100644 index cfe6d71e2..000000000 --- a/projects/diagnostic_procedure/docs/types/Double.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: double - - -A real number that conforms to the xsd:double specification - -URI: [linkml:Double](https://w3id.org/linkml/Double) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Close Mappings:** | | schema:Float | - diff --git a/projects/diagnostic_procedure/docs/types/Float.md b/projects/diagnostic_procedure/docs/types/Float.md deleted file mode 100644 index 7b303f96f..000000000 --- a/projects/diagnostic_procedure/docs/types/Float.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: float - - -A real number that conforms to the xsd:float specification - -URI: [linkml:Float](https://w3id.org/linkml/Float) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Float | - diff --git a/projects/diagnostic_procedure/docs/types/Integer.md b/projects/diagnostic_procedure/docs/types/Integer.md deleted file mode 100644 index 3cfcc66d9..000000000 --- a/projects/diagnostic_procedure/docs/types/Integer.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: integer - - -An integer - -URI: [linkml:Integer](https://w3id.org/linkml/Integer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **int** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Integer | - diff --git a/projects/diagnostic_procedure/docs/types/Jsonpath.md b/projects/diagnostic_procedure/docs/types/Jsonpath.md deleted file mode 100644 index a03a58e67..000000000 --- a/projects/diagnostic_procedure/docs/types/Jsonpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpath - - -A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpath](https://w3id.org/linkml/Jsonpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/diagnostic_procedure/docs/types/Jsonpointer.md b/projects/diagnostic_procedure/docs/types/Jsonpointer.md deleted file mode 100644 index a0e1ac492..000000000 --- a/projects/diagnostic_procedure/docs/types/Jsonpointer.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpointer - - -A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpointer](https://w3id.org/linkml/Jsonpointer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/diagnostic_procedure/docs/types/Ncname.md b/projects/diagnostic_procedure/docs/types/Ncname.md deleted file mode 100644 index 710b0b04a..000000000 --- a/projects/diagnostic_procedure/docs/types/Ncname.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: ncname - - -Prefix part of CURIE - -URI: [linkml:Ncname](https://w3id.org/linkml/Ncname) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NCName** | -| Representation | | str | diff --git a/projects/diagnostic_procedure/docs/types/Nodeidentifier.md b/projects/diagnostic_procedure/docs/types/Nodeidentifier.md deleted file mode 100644 index f0097cdf4..000000000 --- a/projects/diagnostic_procedure/docs/types/Nodeidentifier.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: nodeidentifier - - -A URI, CURIE or BNODE that represents a node in a model. - -URI: [linkml:Nodeidentifier](https://w3id.org/linkml/Nodeidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NodeIdentifier** | -| Representation | | str | diff --git a/projects/diagnostic_procedure/docs/types/Objectidentifier.md b/projects/diagnostic_procedure/docs/types/Objectidentifier.md deleted file mode 100644 index 454ba6be6..000000000 --- a/projects/diagnostic_procedure/docs/types/Objectidentifier.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: objectidentifier - - -A URI or CURIE that represents an object in the model. - -URI: [linkml:Objectidentifier](https://w3id.org/linkml/Objectidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **ElementIdentifier** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | Used for inheritance and type checking | - diff --git a/projects/diagnostic_procedure/docs/types/Sparqlpath.md b/projects/diagnostic_procedure/docs/types/Sparqlpath.md deleted file mode 100644 index fd99a927e..000000000 --- a/projects/diagnostic_procedure/docs/types/Sparqlpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: sparqlpath - - -A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - -URI: [linkml:Sparqlpath](https://w3id.org/linkml/Sparqlpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/diagnostic_procedure/docs/types/String.md b/projects/diagnostic_procedure/docs/types/String.md deleted file mode 100644 index 6e61d7081..000000000 --- a/projects/diagnostic_procedure/docs/types/String.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: string - - -A character string - -URI: [linkml:String](https://w3id.org/linkml/String) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Text | - diff --git a/projects/diagnostic_procedure/docs/types/Time.md b/projects/diagnostic_procedure/docs/types/Time.md deleted file mode 100644 index 2b8652bcd..000000000 --- a/projects/diagnostic_procedure/docs/types/Time.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: time - - -A time object represents a (local) time of day, independent of any particular day - -URI: [linkml:Time](https://w3id.org/linkml/Time) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Time | - diff --git a/projects/diagnostic_procedure/docs/types/Uri.md b/projects/diagnostic_procedure/docs/types/Uri.md deleted file mode 100644 index 343807a5e..000000000 --- a/projects/diagnostic_procedure/docs/types/Uri.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: uri - - -a complete URI - -URI: [linkml:Uri](https://w3id.org/linkml/Uri) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URI** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node | -| **Close Mappings:** | | schema:URL | - diff --git a/projects/diagnostic_procedure/docs/types/Uriorcurie.md b/projects/diagnostic_procedure/docs/types/Uriorcurie.md deleted file mode 100644 index 2f7b65087..000000000 --- a/projects/diagnostic_procedure/docs/types/Uriorcurie.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: uriorcurie - - -a URI or a CURIE - -URI: [linkml:Uriorcurie](https://w3id.org/linkml/Uriorcurie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URIorCURIE** | -| Representation | | str | diff --git a/projects/diagnostic_procedure/excel/diagnostic_procedure.xlsx b/projects/diagnostic_procedure/excel/diagnostic_procedure.xlsx deleted file mode 100644 index 03e0b49f0..000000000 Binary files a/projects/diagnostic_procedure/excel/diagnostic_procedure.xlsx and /dev/null differ diff --git a/projects/diagnostic_procedure/graphql/diagnostic_procedure.graphql b/projects/diagnostic_procedure/graphql/diagnostic_procedure.graphql deleted file mode 100644 index 152e88aac..000000000 --- a/projects/diagnostic_procedure/graphql/diagnostic_procedure.graphql +++ /dev/null @@ -1,126 +0,0 @@ -type AnnotatorResult - { - subjectText: String - objectId: String - objectText: String - } - -type Any - { - } - -type ClinicalAttribute - { - id: String! - label: String - unit: Unit - } - -interface CompoundExpression - { - } - -type DiagnosticProcedure - { - id: String! - label: String - } - -type DiagnosticProceduretoAttributeAssociation - { - qualifier: String - subject: DiagnosticProcedure - object: [ClinicalAttribute] - predicate: ProcedureToAttributePredicate - subjectQualifier: NamedEntity - objectQualifier: Quality - } - -type DiagnosticProceduretoPhenotypeAssociation - { - qualifier: String - subject: DiagnosticProcedure - object: [Phenotype] - predicate: ProcedureToPhenotypePredicate - subjectQualifier: NamedEntity - objectQualifier: NamedEntity - } - -type ExtractionResult - { - inputId: String - inputTitle: String - inputText: String - rawCompletionOutput: String - prompt: String - extractedObject: Any - namedEntities: [Any] - } - -interface NamedEntity - { - id: String! - label: String - } - -type Phenotype - { - id: String! - label: String - } - -type ProcedureToAttributePredicate - { - id: String! - label: String - } - -type ProcedureToPhenotypePredicate - { - id: String! - label: String - } - -type Publication - { - id: String - title: String - abstract: String - combinedText: String - fullText: String - } - -type Quality - { - id: String! - label: String - } - -type RelationshipType - { - id: String! - label: String - } - -type TextWithTriples - { - publication: Publication - triples: [Triple] - } - -interface Triple - { - subject: NamedEntity - predicate: RelationshipType - object: NamedEntity - qualifier: String - subjectQualifier: NamedEntity - objectQualifier: NamedEntity - } - -type Unit - { - id: String! - label: String - } - diff --git a/projects/diagnostic_procedure/jsonld/diagnostic_procedure.context.jsonld b/projects/diagnostic_procedure/jsonld/diagnostic_procedure.context.jsonld deleted file mode 100644 index d5d39d283..000000000 --- a/projects/diagnostic_procedure/jsonld/diagnostic_procedure.context.jsonld +++ /dev/null @@ -1,144 +0,0 @@ -{ - "comments": { - "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2023-08-07T10:52:28", - "source": "diagnostic_procedure.yaml" - }, - "@context": { - "HP": { - "@id": "http://purl.obolibrary.org/obo/HP_", - "@prefix": true - }, - "LOINC": "http://loinc.org/rdf/", - "OBA": { - "@id": "http://purl.obolibrary.org/obo/OBA_", - "@prefix": true - }, - "PATO": { - "@id": "http://purl.obolibrary.org/obo/PATO_", - "@prefix": true - }, - "RO": { - "@id": "http://purl.obolibrary.org/obo/RO_", - "@prefix": true - }, - "UO": "http://example.org/UNKNOWN/UO/", - "biolink": "https://w3id.org/biolink/vocab/", - "core": "http://w3id.org/ontogpt/core/", - "diag": "http://w3id.org/ontogpt/diagnostic_procedure/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "@vocab": "http://w3id.org/ontogpt/diagnostic_procedure/", - "object_id": { - "@id": "core:object_id" - }, - "object_text": { - "@id": "core:object_text" - }, - "subject_text": { - "@id": "core:subject_text" - }, - "unit": { - "@type": "@id" - }, - "extracted_object": { - "@type": "@id", - "@id": "core:extracted_object" - }, - "input_id": { - "@id": "core:input_id" - }, - "input_text": { - "@id": "core:input_text" - }, - "input_title": { - "@id": "core:input_title" - }, - "named_entities": { - "@type": "@id", - "@id": "core:named_entities" - }, - "prompt": { - "@id": "core:prompt" - }, - "raw_completion_output": { - "@id": "core:raw_completion_output" - }, - "id": { - "@id": "core:id" - }, - "label": { - "@id": "rdfs:label" - }, - "abstract": { - "@id": "core:abstract" - }, - "combined_text": { - "@id": "core:combined_text" - }, - "full_text": { - "@id": "core:full_text" - }, - "title": { - "@id": "core:title" - }, - "publication": { - "@type": "@id", - "@id": "core:publication" - }, - "triples": { - "@type": "@id", - "@id": "core:triples" - }, - "object": { - "@type": "@id", - "@id": "core:object" - }, - "object_qualifier": { - "@type": "@id", - "@id": "core:object_qualifier" - }, - "predicate": { - "@type": "@id", - "@id": "core:predicate" - }, - "qualifier": { - "@id": "core:qualifier" - }, - "subject": { - "@type": "@id", - "@id": "core:subject" - }, - "subject_qualifier": { - "@type": "@id", - "@id": "core:subject_qualifier" - }, - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } - } -} diff --git a/projects/diagnostic_procedure/jsonld/diagnostic_procedure.jsonld b/projects/diagnostic_procedure/jsonld/diagnostic_procedure.jsonld deleted file mode 100644 index 93b7cfd9e..000000000 --- a/projects/diagnostic_procedure/jsonld/diagnostic_procedure.jsonld +++ /dev/null @@ -1,1368 +0,0 @@ -{ - "name": "diagnostic_procedure", - "description": "A template for clinical diagnostic procedures and the phenotypes they may contribute to.", - "title": "Diagnostic Procedure Template", - "id": "http://w3id.org/ontogpt/diagnostic_procedure", - "imports": [ - "linkml:types", - "core" - ], - "license": "https://creativecommons.org/publicdomain/zero/1.0/", - "prefixes": [ - { - "prefix_prefix": "linkml", - "prefix_reference": "https://w3id.org/linkml/" - }, - { - "prefix_prefix": "diag", - "prefix_reference": "http://w3id.org/ontogpt/diagnostic_procedure/" - }, - { - "prefix_prefix": "LOINC", - "prefix_reference": "http://loinc.org/rdf/" - }, - { - "prefix_prefix": "HP", - "prefix_reference": "http://purl.obolibrary.org/obo/HP_" - }, - { - "prefix_prefix": "RO", - "prefix_reference": "http://purl.obolibrary.org/obo/RO_" - }, - { - "prefix_prefix": "OBA", - "prefix_reference": "http://purl.obolibrary.org/obo/OBA_" - }, - { - "prefix_prefix": "PATO", - "prefix_reference": "http://purl.obolibrary.org/obo/PATO_" - }, - { - "prefix_prefix": "biolink", - "prefix_reference": "https://w3id.org/biolink/vocab/" - } - ], - "default_prefix": "diag", - "default_range": "string", - "types": [ - { - "name": "string", - "definition_uri": "https://w3id.org/linkml/String", - "description": "A character string", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Text" - ], - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "@type": "TypeDefinition" - }, - { - "name": "integer", - "definition_uri": "https://w3id.org/linkml/Integer", - "description": "An integer", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Integer" - ], - "base": "int", - "uri": "http://www.w3.org/2001/XMLSchema#integer", - "@type": "TypeDefinition" - }, - { - "name": "boolean", - "definition_uri": "https://w3id.org/linkml/Boolean", - "description": "A binary (true or false) value", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Boolean" - ], - "base": "Bool", - "uri": "http://www.w3.org/2001/XMLSchema#boolean", - "repr": "bool", - "@type": "TypeDefinition" - }, - { - "name": "float", - "definition_uri": "https://w3id.org/linkml/Float", - "description": "A real number that conforms to the xsd:float specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#float", - "@type": "TypeDefinition" - }, - { - "name": "double", - "definition_uri": "https://w3id.org/linkml/Double", - "description": "A real number that conforms to the xsd:double specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#double", - "@type": "TypeDefinition" - }, - { - "name": "decimal", - "definition_uri": "https://w3id.org/linkml/Decimal", - "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "broad_mappings": [ - "schema:Number" - ], - "base": "Decimal", - "uri": "http://www.w3.org/2001/XMLSchema#decimal", - "@type": "TypeDefinition" - }, - { - "name": "time", - "definition_uri": "https://w3id.org/linkml/Time", - "description": "A time object represents a (local) time of day, independent of any particular day", - "notes": [ - "URI is dateTime because OWL reasoners do not work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Time" - ], - "base": "XSDTime", - "uri": "http://www.w3.org/2001/XMLSchema#time", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date", - "definition_uri": "https://w3id.org/linkml/Date", - "description": "a date (year, month and day) in an idealized calendar", - "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Date" - ], - "base": "XSDDate", - "uri": "http://www.w3.org/2001/XMLSchema#date", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "datetime", - "definition_uri": "https://w3id.org/linkml/Datetime", - "description": "The combination of a date and time", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:DateTime" - ], - "base": "XSDDateTime", - "uri": "http://www.w3.org/2001/XMLSchema#dateTime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date_or_datetime", - "definition_uri": "https://w3id.org/linkml/DateOrDatetime", - "description": "Either a date or a datetime", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "https://w3id.org/linkml/DateOrDatetime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uriorcurie", - "definition_uri": "https://w3id.org/linkml/Uriorcurie", - "description": "a URI or a CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "URIorCURIE", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "curie", - "definition_uri": "https://w3id.org/linkml/Curie", - "conforms_to": "https://www.w3.org/TR/curie/", - "description": "a compact URI", - "comments": [ - "in RDF serializations this MUST be expanded to a URI", - "in non-RDF serializations MAY be serialized as the compact representation" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "Curie", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uri", - "definition_uri": "https://w3id.org/linkml/Uri", - "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", - "description": "a complete URI", - "comments": [ - "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:URL" - ], - "base": "URI", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "ncname", - "definition_uri": "https://w3id.org/linkml/Ncname", - "description": "Prefix part of CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NCName", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "objectidentifier", - "definition_uri": "https://w3id.org/linkml/Objectidentifier", - "description": "A URI or CURIE that represents an object in the model.", - "comments": [ - "Used for inheritance and type checking" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "ElementIdentifier", - "uri": "http://www.w3.org/ns/shex#iri", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "nodeidentifier", - "definition_uri": "https://w3id.org/linkml/Nodeidentifier", - "description": "A URI, CURIE or BNODE that represents a node in a model.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NodeIdentifier", - "uri": "http://www.w3.org/ns/shex#nonLiteral", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpointer", - "definition_uri": "https://w3id.org/linkml/Jsonpointer", - "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901", - "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpath", - "definition_uri": "https://w3id.org/linkml/Jsonpath", - "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html", - "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "sparqlpath", - "definition_uri": "https://w3id.org/linkml/Sparqlpath", - "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths", - "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - } - ], - "enums": [ - { - "name": "NullDataOptions", - "definition_uri": "http://w3id.org/ontogpt/core/NullDataOptions", - "from_schema": "http://w3id.org/ontogpt/core", - "permissible_values": [ - { - "text": "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "meaning": "NCIT:C149701" - }, - { - "text": "NOT_APPLICABLE", - "meaning": "NCIT:C18902", - "aliases": [ - "not applicable", - "N/A" - ] - }, - { - "text": "NOT_MENTIONED" - } - ] - } - ], - "slots": [ - { - "name": "clinicalAttribute__unit", - "description": "the unit used to measure the attribute", - "from_schema": "http://w3id.org/ontogpt/diagnostic_procedure", - "slot_uri": "http://w3id.org/ontogpt/diagnostic_procedure/unit", - "alias": "unit", - "owner": "ClinicalAttribute", - "domain_of": [ - "ClinicalAttribute" - ], - "range": "Unit", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_id", - "alias": "input_id", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_title", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_title", - "alias": "input_title", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_text", - "alias": "input_text", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__raw_completion_output", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/raw_completion_output", - "alias": "raw_completion_output", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__prompt", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/prompt", - "alias": "prompt", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__extracted_object", - "description": "The complex objects extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/extracted_object", - "alias": "extracted_object", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__named_entities", - "description": "Named entities extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/named_entities", - "multivalued": true, - "alias": "named_entities", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "identifier": true, - "alias": "id", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "required": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "from_schema": "http://w3id.org/ontogpt/core", - "aliases": [ - "name" - ], - "mappings": [ - "http://example.org/UNKNOWN/rdfs/label" - ], - "slot_uri": "http://example.org/UNKNOWN/rdfs/label", - "alias": "label", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject", - "alias": "subject", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__predicate", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/predicate", - "alias": "predicate", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "triple__object", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object", - "alias": "object", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/qualifier", - "alias": "qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_qualifier", - "alias": "subject_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_qualifier", - "alias": "object_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/publication", - "alias": "publication", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__triples", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/triples", - "multivalued": true, - "alias": "triples", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "publication__id", - "description": "The publication identifier", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "alias": "id", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__title", - "description": "The title of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/title", - "alias": "title", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__abstract", - "description": "The abstract of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/abstract", - "alias": "abstract", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__combined_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/combined_text", - "alias": "combined_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__full_text", - "description": "The full text of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/full_text", - "alias": "full_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__subject_text", - 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"source_file_size": 4774, - "generation_date": "2023-08-07T10:52:29", - "@type": "SchemaDefinition", - "@context": [ - "projects/diagnostic_procedure/jsonld/diagnostic_procedure.context.jsonld", - "https://w3id.org/linkml/types.context.jsonld", - "core.context.jsonld", - { - "@base": "http://w3id.org/ontogpt/diagnostic_procedure/" - } - ] -} diff --git a/projects/diagnostic_procedure/jsonschema/diagnostic_procedure.schema.json b/projects/diagnostic_procedure/jsonschema/diagnostic_procedure.schema.json deleted file mode 100644 index d573d848c..000000000 --- a/projects/diagnostic_procedure/jsonschema/diagnostic_procedure.schema.json +++ /dev/null @@ -1,348 +0,0 @@ -{ - "$defs": { - "AnnotatorResult": { - "additionalProperties": false, - "description": "", - "properties": { - "object_id": { - "type": "string" - }, - "object_text": { - "type": "string" - }, - "subject_text": { - "type": "string" - } - }, - "title": "AnnotatorResult", - "type": "object" - }, - "Any": { - "additionalProperties": true, - "description": "", - "title": "Any", - "type": "object" - }, - "ClinicalAttribute": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - }, - "unit": { - "description": "the unit used to measure the attribute", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "ClinicalAttribute", - "type": "object" - }, - "DiagnosticProcedure": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "DiagnosticProcedure", - "type": "object" - }, - "DiagnosticProceduretoAttributeAssociation": { - "additionalProperties": false, - "description": "A triple representing a relationship between a diagnostic procedure and a measured attribute, e.g., \"blood pressure measurement\" is associated with \"blood pressure\" (or in OBA, something like OBA:VT0000183, \"blood pressure trait\").", - "properties": { - "object": { - "description": "Any measurable clinical attribute.", - "items": { - "type": "string" - }, - "type": "array" - }, - "object_qualifier": { - "description": "An optional qualifier or modifier for the phenotype.", - "type": "string" - }, - "predicate": { - "description": "The relationship type, e.g. RELATED_TO", - "type": "string" - }, - "qualifier": { - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "type": "string" - }, - "subject": { - "description": "A diagnostic procedure yielding a result, which in turn may be interpreted as a phenotype. Procedures include \"heart rate measurement\", \"blood pressure measurement\", \"oxygen saturation measurement\", etc. In practice, procedures may be named based on what they measure, with the \"measurement\" part left implicit.", - "type": "string" - }, - "subject_qualifier": { - "description": "An optional qualifier or modifier for the procedure.", - "type": "string" - } - }, - "title": "DiagnosticProceduretoAttributeAssociation", - "type": "object" - }, - "DiagnosticProceduretoPhenotypeAssociation": { - "additionalProperties": false, - "description": "A triple representing a relationship between a diagnostic procedure and an associated phenotype, e.g., \"blood pressure measurement\" is associated with \"high blood pressure\".", - "properties": { - "object": { - "description": "The observable physical or biochemical characteristics of a patient. Not equivalent to a disease state, but may contribute to a diagnosis.", - "items": { - "type": "string" - }, - "type": "array" - }, - "object_qualifier": { - "description": "An optional qualifier or modifier for the phenotype.", - "type": "string" - }, - "predicate": { - "description": "The relationship type, e.g. RELATED_TO", - "type": "string" - }, - "qualifier": { - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "type": "string" - }, - "subject": { - "description": "A diagnostic procedure yielding a result, which in turn may be interpreted as a phenotype. Procedures include \"heart rate measurement\", \"blood pressure measurement\", \"oxygen saturation measurement\", etc. In practice, procedures may be named based on what they measure, with the \"measurement\" part left implicit.", - "type": "string" - }, - "subject_qualifier": { - "description": "An optional qualifier or modifier for the procedure.", - "type": "string" - } - }, - "title": "DiagnosticProceduretoPhenotypeAssociation", - "type": "object" - }, - "ExtractionResult": { - "additionalProperties": false, - "description": "A result of extracting knowledge on text", - "properties": { - "extracted_object": { - "$ref": "#/$defs/Any", - "description": "The complex objects extracted from the text" - }, - "input_id": { - "type": "string" - }, - "input_text": { - "type": "string" - }, - "input_title": { - "type": "string" - }, - "named_entities": { - "description": "Named entities extracted from the text", - "items": { - "$ref": "#/$defs/Any" - }, - "type": "array" - }, - "prompt": { - "type": "string" - }, - "raw_completion_output": { - "type": "string" - } - }, - "title": "ExtractionResult", - "type": "object" - }, - "NullDataOptions": { - "description": "", - "enum": [ - "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "NOT_APPLICABLE", - "NOT_MENTIONED" - ], - "title": "NullDataOptions", - "type": "string" - }, - "Phenotype": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Phenotype", - "type": "object" - }, - "ProcedureToAttributePredicate": { - "additionalProperties": false, - "description": "A predicate for procedure to attribute relationships, defining \"this procedure is a measurement of this attribute\".", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "ProcedureToAttributePredicate", - "type": "object" - }, - "ProcedureToPhenotypePredicate": { - "additionalProperties": false, - "description": "A predicate for procedure to phenotype relationships, defining \"this procedure is intended to provide support for/against this phenotype\".", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "ProcedureToPhenotypePredicate", - "type": "object" - }, - "Publication": { - "additionalProperties": false, - "description": "", - "properties": { - "abstract": { - "description": "The abstract of the publication", - "type": "string" - }, - "combined_text": { - "type": "string" - }, - "full_text": { - "description": "The full text of the publication", - "type": "string" - }, - "id": { - "description": "The publication identifier", - "type": "string" - }, - "title": { - "description": "The title of the publication", - "type": "string" - } - }, - "title": "Publication", - "type": "object" - }, - "Quality": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Quality", - "type": "object" - }, - "RelationshipType": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "RelationshipType", - "type": "object" - }, - "TextWithTriples": { - "additionalProperties": false, - "description": "", - "properties": { - "publication": { - "$ref": "#/$defs/Publication" - }, - "triples": { - "items": { - "$ref": "#/$defs/Triple" - }, - "type": "array" - } - }, - "title": "TextWithTriples", - "type": "object" - }, - "Unit": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Unit", - "type": "object" - } - }, - "$id": "http://w3id.org/ontogpt/diagnostic_procedure", - "$schema": "http://json-schema.org/draft-07/schema#", - "additionalProperties": true, - "metamodel_version": "1.7.0", - "title": "diagnostic_procedure", - "type": "object", - "version": null -} \ No newline at end of file diff --git a/projects/diagnostic_procedure/owl/diagnostic_procedure.owl.ttl b/projects/diagnostic_procedure/owl/diagnostic_procedure.owl.ttl deleted file mode 100644 index 9b827e802..000000000 --- a/projects/diagnostic_procedure/owl/diagnostic_procedure.owl.ttl +++ /dev/null @@ -1,527 +0,0 @@ -@prefix IAO: <http://purl.obolibrary.org/obo/IAO_> . -@prefix diag: <http://w3id.org/ontogpt/diagnostic_procedure/> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix owl: <http://www.w3.org/2002/07/owl#> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . -@prefix skos: <http://www.w3.org/2004/02/skos/core#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -<http://w3id.org/ontogpt/diagnostic_procedure> a owl:Ontology ; - rdfs:label "diagnostic_procedure" ; - IAO:0000700 <http://w3id.org/ontogpt/core/AnnotatorResult>, - <http://w3id.org/ontogpt/core/Any>, - <http://w3id.org/ontogpt/core/CompoundExpression>, - <http://w3id.org/ontogpt/core/ExtractionResult>, - <http://w3id.org/ontogpt/core/NamedEntity>, - <http://w3id.org/ontogpt/core/Publication>, - <http://w3id.org/ontogpt/core/TextWithTriples> ; - linkml:classes "{'DiagnosticProceduretoPhenotypeAssociation': ClassDefinition(name='DiagnosticProceduretoPhenotypeAssociation', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/diagnostic_procedure/DiagnosticProceduretoPhenotypeAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A triple representing a relationship between a diagnostic procedure and an associated phenotype, e.g., \"blood pressure measurement\" is associated with \"high blood pressure\".', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/diagnostic_procedure', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='Triple', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['triple__qualifier', 'DiagnosticProceduretoPhenotypeAssociation_subject', 'DiagnosticProceduretoPhenotypeAssociation_object', 'DiagnosticProceduretoPhenotypeAssociation_predicate', 'DiagnosticProceduretoPhenotypeAssociation_subject_qualifier', 'DiagnosticProceduretoPhenotypeAssociation_object_qualifier'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A diagnostic procedure yielding a result, which in turn may be interpreted as a phenotype. Procedures include \"heart rate measurement\", \"blood pressure measurement\", \"oxygen saturation measurement\", etc. In practice, procedures may be named based on what they measure, with the \"measurement\" part left implicit.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='triple__subject', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='DiagnosticProcedure', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The observable physical or biochemical characteristics of a patient. Not equivalent to a disease state, but may contribute to a diagnosis.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='triple__object', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Phenotype', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The relationship type, e.g. RELATED_TO', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='triple__predicate', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ProcedureToPhenotypePredicate', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the procedure.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='triple__subject_qualifier', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the phenotype.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='triple__object_qualifier', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='diag:DiagnosticProceduretoPhenotypeAssociation', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'DiagnosticProceduretoAttributeAssociation': ClassDefinition(name='DiagnosticProceduretoAttributeAssociation', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/diagnostic_procedure/DiagnosticProceduretoAttributeAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A triple representing a relationship between a diagnostic procedure and a measured attribute, e.g., \"blood pressure measurement\" is associated with \"blood pressure\" (or in OBA, something like OBA:VT0000183, \"blood pressure trait\").', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/diagnostic_procedure', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='Triple', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['triple__qualifier', 'DiagnosticProceduretoAttributeAssociation_subject', 'DiagnosticProceduretoAttributeAssociation_object', 'DiagnosticProceduretoAttributeAssociation_predicate', 'DiagnosticProceduretoAttributeAssociation_subject_qualifier', 'DiagnosticProceduretoAttributeAssociation_object_qualifier'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A diagnostic procedure yielding a result, which in turn may be interpreted as a phenotype. Procedures include \"heart rate measurement\", \"blood pressure measurement\", \"oxygen saturation measurement\", etc. In practice, procedures may be named based on what they measure, with the \"measurement\" part left implicit.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='triple__subject', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='DiagnosticProcedure', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Any measurable clinical attribute.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='triple__object', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ClinicalAttribute', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The relationship type, e.g. RELATED_TO', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='triple__predicate', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ProcedureToAttributePredicate', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the procedure.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='triple__subject_qualifier', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the phenotype.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='triple__object_qualifier', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Quality', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='diag:DiagnosticProceduretoAttributeAssociation', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'DiagnosticProcedure': ClassDefinition(name='DiagnosticProcedure', id_prefixes=['LOINC'], definition_uri='http://w3id.org/ontogpt/diagnostic_procedure/DiagnosticProcedure', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='bioportal:loinc, sqlite:obo:ncit', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/diagnostic_procedure', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='diag:DiagnosticProcedure', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Phenotype': ClassDefinition(name='Phenotype', id_prefixes=['HP'], definition_uri='http://w3id.org/ontogpt/diagnostic_procedure/Phenotype', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:hp', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/diagnostic_procedure', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='diag:Phenotype', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ClinicalAttribute': ClassDefinition(name='ClinicalAttribute', id_prefixes=['OBA'], definition_uri='http://w3id.org/ontogpt/diagnostic_procedure/ClinicalAttribute', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:oba, sqlite:obo:ncit', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/diagnostic_procedure', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label', 'clinicalAttribute__unit'], slot_usage={}, attributes={'unit': SlotDefinition(name='unit', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the unit used to measure the attribute', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Unit', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='diag:ClinicalAttribute', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Quality': ClassDefinition(name='Quality', id_prefixes=['PATO'], definition_uri='http://w3id.org/ontogpt/diagnostic_procedure/Quality', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:pato', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/diagnostic_procedure', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='diag:Quality', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ProcedureToPhenotypePredicate': ClassDefinition(name='ProcedureToPhenotypePredicate', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/diagnostic_procedure/ProcedureToPhenotypePredicate', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A predicate for procedure to phenotype relationships, defining \"this procedure is intended to provide support for/against this phenotype\".', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/diagnostic_procedure', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='RelationshipType', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='diag:ProcedureToPhenotypePredicate', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ProcedureToAttributePredicate': ClassDefinition(name='ProcedureToAttributePredicate', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/diagnostic_procedure/ProcedureToAttributePredicate', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A predicate for procedure to attribute relationships, defining \"this procedure is a measurement of this attribute\".', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/diagnostic_procedure', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='RelationshipType', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='diag:ProcedureToAttributePredicate', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Unit': ClassDefinition(name='Unit', id_prefixes=['UO'], definition_uri='http://w3id.org/ontogpt/diagnostic_procedure/Unit', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:uo', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/diagnostic_procedure', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='diag:Unit', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Any': ClassDefinition(name='Any', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Any', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=['linkml:Any'], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='linkml:Any', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ExtractionResult': ClassDefinition(name='ExtractionResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/ExtractionResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A result of extracting knowledge on text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['extractionResult__input_id', 'extractionResult__input_title', 'extractionResult__input_text', 'extractionResult__raw_completion_output', 'extractionResult__prompt', 'extractionResult__extracted_object', 'extractionResult__named_entities'], slot_usage={}, attributes={'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:ExtractionResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'NamedEntity': ClassDefinition(name='NamedEntity', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NamedEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:NamedEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'CompoundExpression': ClassDefinition(name='CompoundExpression', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/CompoundExpression', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='core:CompoundExpression', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Triple': ClassDefinition(name='Triple', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Triple', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Abstract parent for Relation Extraction tasks', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['triple__subject', 'triple__predicate', 'triple__object', 'triple__qualifier', 'triple__subject_qualifier', 'triple__object_qualifier'], slot_usage={}, attributes={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Triple', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'TextWithTriples': ClassDefinition(name='TextWithTriples', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/TextWithTriples', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['textWithTriples__publication', 'textWithTriples__triples'], slot_usage={}, attributes={'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:TextWithTriples', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'RelationshipType': ClassDefinition(name='RelationshipType', id_prefixes=['RO', 'biolink'], definition_uri='http://w3id.org/ontogpt/core/RelationshipType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='core:RelationshipType', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Publication': ClassDefinition(name='Publication', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Publication', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['publication__id', 'publication__title', 'publication__abstract', 'publication__combined_text', 'publication__full_text'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Publication', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'AnnotatorResult': ClassDefinition(name='AnnotatorResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/AnnotatorResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['annotatorResult__subject_text', 'annotatorResult__object_id', 'annotatorResult__object_text'], slot_usage={}, attributes={'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:AnnotatorResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={})}" ; - linkml:enums "{'NullDataOptions': EnumDefinition(name='NullDataOptions', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NullDataOptions', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'UNSPECIFIED_METHOD_OF_ADMINISTRATION': PermissibleValue(text='UNSPECIFIED_METHOD_OF_ADMINISTRATION', description=None, meaning='NCIT:C149701', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_APPLICABLE': PermissibleValue(text='NOT_APPLICABLE', description=None, meaning='NCIT:C18902', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['not applicable', 'N/A'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_MENTIONED': PermissibleValue(text='NOT_MENTIONED', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[])}" ; - linkml:id "http://w3id.org/ontogpt/diagnostic_procedure" ; - linkml:imports "core", - "linkml:types" ; - linkml:types "{'string': TypeDefinition(name='string', id_prefixes=[], definition_uri='https://w3id.org/linkml/String', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A character string', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Text'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'integer': TypeDefinition(name='integer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Integer', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An integer', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Integer'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='int', uri='xsd:integer', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'boolean': TypeDefinition(name='boolean', id_prefixes=[], definition_uri='https://w3id.org/linkml/Boolean', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A binary (true or false) value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Boolean'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Bool', uri='xsd:boolean', repr='bool', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'float': TypeDefinition(name='float', id_prefixes=[], definition_uri='https://w3id.org/linkml/Float', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:float specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Float'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:float', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'double': TypeDefinition(name='double', id_prefixes=[], definition_uri='https://w3id.org/linkml/Double', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:double specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:Float'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:double', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'decimal': TypeDefinition(name='decimal', id_prefixes=[], definition_uri='https://w3id.org/linkml/Decimal', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number with arbitrary precision that conforms to the xsd:decimal specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=['schema:Number'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Decimal', uri='xsd:decimal', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'time': TypeDefinition(name='time', id_prefixes=[], definition_uri='https://w3id.org/linkml/Time', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A time object represents a (local) time of day, independent of any particular day', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=['URI is dateTime because OWL reasoners do not work with straight date or time'], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Time'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDTime', uri='xsd:time', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date': TypeDefinition(name='date', id_prefixes=[], definition_uri='https://w3id.org/linkml/Date', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a date (year, month and day) in an idealized calendar', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[\"URI is dateTime because OWL reasoners don't work with straight date or time\"], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Date'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDate', uri='xsd:date', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'datetime': TypeDefinition(name='datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/Datetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The combination of a date and time', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:DateTime'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDateTime', uri='xsd:dateTime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date_or_datetime': TypeDefinition(name='date_or_datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/DateOrDatetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Either a date or a datetime', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='linkml:DateOrDatetime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uriorcurie': TypeDefinition(name='uriorcurie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uriorcurie', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a URI or a CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URIorCURIE', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'curie': TypeDefinition(name='curie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Curie', local_names={}, conforms_to='https://www.w3.org/TR/curie/', implements=[], extensions={}, annotations={}, description='a compact URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations this MUST be expanded to a URI', 'in non-RDF serializations MAY be serialized as the compact representation'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Curie', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uri': TypeDefinition(name='uri', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uri', local_names={}, conforms_to='https://www.ietf.org/rfc/rfc3987.txt', implements=[], extensions={}, annotations={}, description='a complete URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:URL'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URI', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ncname': TypeDefinition(name='ncname', id_prefixes=[], definition_uri='https://w3id.org/linkml/Ncname', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Prefix part of CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NCName', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'objectidentifier': TypeDefinition(name='objectidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Objectidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI or CURIE that represents an object in the model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['Used for inheritance and type checking'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='ElementIdentifier', uri='shex:iri', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'nodeidentifier': TypeDefinition(name='nodeidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Nodeidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI, CURIE or BNODE that represents a node in a model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NodeIdentifier', uri='shex:nonLiteral', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpointer': TypeDefinition(name='jsonpointer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpointer', local_names={}, conforms_to='https://datatracker.ietf.org/doc/html/rfc6901', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpath': TypeDefinition(name='jsonpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpath', local_names={}, conforms_to='https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sparqlpath': TypeDefinition(name='sparqlpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Sparqlpath', local_names={}, conforms_to='https://www.w3.org/TR/sparql11-query/#propertypaths', implements=[], extensions={}, annotations={}, description='A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:SubsetDefinition a owl:Class ; - rdfs:label "subset_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" . - -linkml:TypeDefinition a owl:Class ; - rdfs:label "type_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" ; - linkml:mixins "type_expression" . - -linkml:topValue a owl:DatatypeProperty ; - rdfs:label "value" . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "AnnotatorResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_id> ] ; - linkml:attributes "{'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/ExtractionResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ExtractionResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/prompt> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_title> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/extracted_object> ], - [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/named_entities> ] ; - skos:definition "A result of extracting knowledge on text" ; - linkml:attributes "{'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/TextWithTriples> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TextWithTriples" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Publication> ; - owl:onProperty <http://w3id.org/ontogpt/core/publication> ], - [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Triple> ; - owl:onProperty <http://w3id.org/ontogpt/core/triples> ] ; - linkml:attributes "{'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/abstract> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "abstract" ; - rdfs:range linkml:String ; - skos:definition "The abstract of the publication" . - -<http://w3id.org/ontogpt/core/combined_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "combined_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/extracted_object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "extracted_object" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "The complex objects extracted from the text" . - -<http://w3id.org/ontogpt/core/full_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "full_text" ; - rdfs:range linkml:String ; - skos:definition "The full text of the publication" . - -<http://w3id.org/ontogpt/core/input_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_title" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/named_entities> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "named_entities" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "Named entities extracted from the text" . - -<http://w3id.org/ontogpt/core/object_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/object_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/prompt> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "prompt" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/publication> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "publication" ; - diag:prompt.skip "true" ; - rdfs:range <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "qualifier" ; - rdfs:range linkml:String ; - skos:definition "A qualifier for the statements, e.g. \"NOT\" for negation" . - -<http://w3id.org/ontogpt/core/raw_completion_output> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "raw_completion_output" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/subject_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "title" ; - rdfs:range linkml:String ; - skos:definition "The title of the publication" . - -<http://w3id.org/ontogpt/core/triples> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "triples" ; - rdfs:range <http://w3id.org/ontogpt/core/Triple> . - -diag:unit a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "unit" ; - rdfs:range diag:Unit ; - skos:definition "the unit used to measure the attribute" . - -<http://example.org/UNKNOWN/rdfs/label> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "label" ; - diag:owl "AnnotationProperty, AnnotationAssertion" ; - rdfs:range linkml:String ; - skos:altLabel "name" ; - skos:definition "The label (name) of the named thing" ; - skos:exactMatch <http://example.org/UNKNOWN/rdfs/label> . - -<http://purl.obolibrary.org/obo/NCIT_C149701> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "UNSPECIFIED_METHOD_OF_ADMINISTRATION" . - -<http://purl.obolibrary.org/obo/NCIT_C18902> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_APPLICABLE" . - -<http://w3id.org/ontogpt/core/CompoundExpression> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CompoundExpression" ; - linkml:attributes "{}" . - -<http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_MENTIONED" . - -<http://w3id.org/ontogpt/core/id> a owl:ObjectProperty, - linkml:SlotDefinition . - -<http://w3id.org/ontogpt/core/object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/object_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" . - -<http://w3id.org/ontogpt/core/predicate> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "predicate" ; - rdfs:range <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/subject> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/subject_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" . - -diag:ClinicalAttribute a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ClinicalAttribute" ; - diag:annotators "sqlite:obo:oba, sqlite:obo:ncit" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass diag:Unit ; - owl:onProperty diag:unit ], - <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{'unit': SlotDefinition(name='unit', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the unit used to measure the attribute', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Unit', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "NamedEntity" . - -diag:Phenotype a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Phenotype" ; - diag:annotators "sqlite:obo:hp" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -diag:ProcedureToAttributePredicate a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ProcedureToAttributePredicate" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/RelationshipType> ; - skos:definition "A predicate for procedure to attribute relationships, defining \"this procedure is a measurement of this attribute\"." ; - linkml:attributes "{}" ; - linkml:is_a "RelationshipType" . - -diag:ProcedureToPhenotypePredicate a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ProcedureToPhenotypePredicate" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/RelationshipType> ; - skos:definition "A predicate for procedure to phenotype relationships, defining \"this procedure is intended to provide support for/against this phenotype\"." ; - linkml:attributes "{}" ; - linkml:is_a "RelationshipType" . - -diag:Quality a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Quality" ; - diag:annotators "sqlite:obo:pato" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -diag:Unit a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Unit" ; - diag:annotators "sqlite:obo:uo" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -diag:object a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object" ; - rdfs:domain diag:DiagnosticProceduretoAttributeAssociation, - diag:DiagnosticProceduretoPhenotypeAssociation ; - rdfs:range diag:ClinicalAttribute, - diag:Phenotype ; - rdfs:subPropertyOf <http://w3id.org/ontogpt/core/object> ; - skos:definition "Any measurable clinical attribute.", - "The observable physical or biochemical characteristics of a patient. Not equivalent to a disease state, but may contribute to a diagnosis." ; - linkml:is_a "triple__object" . - -diag:object_qualifier a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_qualifier" ; - rdfs:domain diag:DiagnosticProceduretoAttributeAssociation, - diag:DiagnosticProceduretoPhenotypeAssociation ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity>, - diag:Quality ; - rdfs:subPropertyOf <http://w3id.org/ontogpt/core/object_qualifier> ; - skos:definition "An optional qualifier or modifier for the phenotype." ; - linkml:is_a "triple__object_qualifier" . - -diag:predicate a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "predicate" ; - rdfs:domain diag:DiagnosticProceduretoAttributeAssociation, - diag:DiagnosticProceduretoPhenotypeAssociation ; - rdfs:range diag:ProcedureToAttributePredicate, - diag:ProcedureToPhenotypePredicate ; - rdfs:subPropertyOf <http://w3id.org/ontogpt/core/predicate> ; - skos:definition "The relationship type, e.g. RELATED_TO" ; - linkml:is_a "triple__predicate" . - -diag:subject a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject" ; - rdfs:domain diag:DiagnosticProceduretoAttributeAssociation, - diag:DiagnosticProceduretoPhenotypeAssociation ; - rdfs:range diag:DiagnosticProcedure ; - rdfs:subPropertyOf <http://w3id.org/ontogpt/core/subject> ; - skos:definition "A diagnostic procedure yielding a result, which in turn may be interpreted as a phenotype. Procedures include \"heart rate measurement\", \"blood pressure measurement\", \"oxygen saturation measurement\", etc. In practice, procedures may be named based on what they measure, with the \"measurement\" part left implicit." ; - linkml:is_a "triple__subject" . - -diag:subject_qualifier a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_qualifier" ; - rdfs:domain diag:DiagnosticProceduretoAttributeAssociation, - diag:DiagnosticProceduretoPhenotypeAssociation ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - rdfs:subPropertyOf <http://w3id.org/ontogpt/core/subject_qualifier> ; - skos:definition "An optional qualifier or modifier for the procedure." ; - linkml:is_a "triple__subject_qualifier" . - -<http://w3id.org/ontogpt/core/NullDataOptions> a owl:Class, - linkml:EnumDefinition ; - rdfs:label "NullDataOptions" ; - owl:unionOf ( <http://purl.obolibrary.org/obo/NCIT_C149701> <http://purl.obolibrary.org/obo/NCIT_C18902> <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> ) ; - linkml:permissible_values <http://purl.obolibrary.org/obo/NCIT_C149701>, - <http://purl.obolibrary.org/obo/NCIT_C18902>, - <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> . - -<http://w3id.org/ontogpt/core/Publication> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Publication" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/title> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/abstract> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/full_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/combined_text> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -diag:DiagnosticProcedure a owl:Class, - linkml:ClassDefinition ; - rdfs:label "DiagnosticProcedure" ; - diag:annotators "bioportal:loinc, sqlite:obo:ncit" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/RelationshipType> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "RelationshipType" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/Triple> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Triple" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/RelationshipType> ; - owl:onProperty <http://w3id.org/ontogpt/core/predicate> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object_qualifier> ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - skos:definition "Abstract parent for Relation Extraction tasks" ; - linkml:attributes "{'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -<http://w3id.org/ontogpt/core/Any> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Any" ; - skos:exactMatch linkml:Any ; - linkml:attributes "{}" . - -diag:DiagnosticProceduretoAttributeAssociation a owl:Class, - linkml:ClassDefinition ; - rdfs:label "DiagnosticProceduretoAttributeAssociation" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass diag:Quality ; - owl:onProperty diag:object_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass diag:ProcedureToAttributePredicate ; - owl:onProperty diag:predicate ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass diag:DiagnosticProcedure ; - owl:onProperty diag:subject ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty diag:subject_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom diag:ClinicalAttribute ; - owl:onProperty diag:object ], - <http://w3id.org/ontogpt/core/Triple> ; - skos:definition "A triple representing a relationship between a diagnostic procedure and a measured attribute, e.g., \"blood pressure measurement\" is associated with \"blood pressure\" (or in OBA, something like OBA:VT0000183, \"blood pressure trait\")." ; - linkml:attributes "{}" ; - linkml:is_a "Triple" . - -diag:DiagnosticProceduretoPhenotypeAssociation a owl:Class, - linkml:ClassDefinition ; - rdfs:label "DiagnosticProceduretoPhenotypeAssociation" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass diag:ProcedureToPhenotypePredicate ; - owl:onProperty diag:predicate ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty diag:subject_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty diag:object_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom diag:Phenotype ; - owl:onProperty diag:object ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass diag:DiagnosticProcedure ; - owl:onProperty diag:subject ], - <http://w3id.org/ontogpt/core/Triple> ; - skos:definition "A triple representing a relationship between a diagnostic procedure and an associated phenotype, e.g., \"blood pressure measurement\" is associated with \"high blood pressure\"." ; - linkml:attributes "{}" ; - linkml:is_a "Triple" . - -linkml:ClassDefinition a owl:Class ; - rdfs:label "class_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "class_expression" . - -<http://w3id.org/ontogpt/core/NamedEntity> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "NamedEntity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://example.org/UNKNOWN/rdfs/label> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:SlotDefinition a owl:Class ; - rdfs:label "slot_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "slot_expression" . - - diff --git a/projects/diagnostic_procedure/prefixmap/diagnostic_procedure.yaml b/projects/diagnostic_procedure/prefixmap/diagnostic_procedure.yaml deleted file mode 100644 index 5f652360b..000000000 --- a/projects/diagnostic_procedure/prefixmap/diagnostic_procedure.yaml +++ /dev/null @@ -1,40 +0,0 @@ -{ - "HP": "http://purl.obolibrary.org/obo/HP_", - "LOINC": "http://loinc.org/rdf/", - "OBA": "http://purl.obolibrary.org/obo/OBA_", - "PATO": "http://purl.obolibrary.org/obo/PATO_", - "RO": "http://purl.obolibrary.org/obo/RO_", - "UO": "http://example.org/UNKNOWN/UO/", - "biolink": "https://w3id.org/biolink/vocab/", - "core": "http://w3id.org/ontogpt/core/", - "diag": "http://w3id.org/ontogpt/diagnostic_procedure/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } -} diff --git a/projects/diagnostic_procedure/protobuf/diagnostic_procedure.proto b/projects/diagnostic_procedure/protobuf/diagnostic_procedure.proto deleted file mode 100644 index d888ad452..000000000 --- a/projects/diagnostic_procedure/protobuf/diagnostic_procedure.proto +++ /dev/null @@ -1,93 +0,0 @@ -message AnnotatorResult - { - string subjectText = 0 - string objectId = 0 - string objectText = 0 - } -message ClinicalAttribute - { - string id = 0 - string label = 0 - unit unit = 0 - } -message DiagnosticProcedure - { - string id = 0 - string label = 0 - } -// A triple representing a relationship between a diagnostic procedure and a measured attribute, e.g., "blood pressure measurement" is associated with "blood pressure" (or in OBA, something like OBA:VT0000183, "blood pressure trait"). -message DiagnosticProceduretoAttributeAssociation - { - string qualifier = 0 - diagnosticProcedure subject = 0 - repeated clinicalAttribute object = 0 - procedureToAttributePredicate predicate = 0 - namedEntity subjectQualifier = 0 - quality objectQualifier = 0 - } -// A triple representing a relationship between a diagnostic procedure and an associated phenotype, e.g., "blood pressure measurement" is associated with "high blood pressure". -message DiagnosticProceduretoPhenotypeAssociation - { - string qualifier = 0 - diagnosticProcedure subject = 0 - repeated phenotype object = 0 - procedureToPhenotypePredicate predicate = 0 - namedEntity subjectQualifier = 0 - namedEntity objectQualifier = 0 - } -// A result of extracting knowledge on text -message ExtractionResult - { - string inputId = 0 - string inputTitle = 0 - string inputText = 0 - string rawCompletionOutput = 0 - string prompt = 0 - any extractedObject = 0 - repeated any namedEntities = 0 - } -message Phenotype - { - string id = 0 - string label = 0 - } -// A predicate for procedure to attribute relationships, defining "this procedure is a measurement of this attribute". -message ProcedureToAttributePredicate - { - string id = 0 - string label = 0 - } -// A predicate for procedure to phenotype relationships, defining "this procedure is intended to provide support for/against this phenotype". -message ProcedureToPhenotypePredicate - { - string id = 0 - string label = 0 - } -message Publication - { - string id = 0 - string title = 0 - string abstract = 0 - string combinedText = 0 - string fullText = 0 - } -message Quality - { - string id = 0 - string label = 0 - } -message RelationshipType - { - string id = 0 - string label = 0 - } -message TextWithTriples - { - publication publication = 0 - repeated triple triples = 0 - } -message Unit - { - string id = 0 - string label = 0 - } diff --git a/projects/diagnostic_procedure/shacl/diagnostic_procedure.shacl.ttl b/projects/diagnostic_procedure/shacl/diagnostic_procedure.shacl.ttl deleted file mode 100644 index 811707381..000000000 --- a/projects/diagnostic_procedure/shacl/diagnostic_procedure.shacl.ttl +++ /dev/null @@ -1,348 +0,0 @@ -@prefix diag: <http://w3id.org/ontogpt/diagnostic_procedure/> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix sh: <http://www.w3.org/ns/shacl#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject_text> ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/object_id> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object_text> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/AnnotatorResult> . - -<http://w3id.org/ontogpt/core/CompoundExpression> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass <http://w3id.org/ontogpt/core/CompoundExpression> . - -<http://w3id.org/ontogpt/core/ExtractionResult> a sh:NodeShape ; - sh:closed true ; - sh:description "A result of extracting knowledge on text" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class linkml:Any ; - sh:description "Named entities extracted from the text" ; - sh:nodeKind sh:BlankNode ; - sh:order 6 ; - sh:path <http://w3id.org/ontogpt/core/named_entities> ], - [ sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/prompt> ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/input_title> ], - [ sh:class linkml:Any ; - sh:description "The complex objects extracted from the text" ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/extracted_object> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/input_text> ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/input_id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/ExtractionResult> . - -<http://w3id.org/ontogpt/core/TextWithTriples> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/Triple> ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/triples> ], - [ sh:class <http://w3id.org/ontogpt/core/Publication> ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/publication> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/TextWithTriples> . - -diag:DiagnosticProceduretoAttributeAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "A triple representing a relationship between a diagnostic procedure and a measured attribute, e.g., \"blood pressure measurement\" is associated with \"blood pressure\" (or in OBA, something like OBA:VT0000183, \"blood pressure trait\")." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A qualifier for the statements, e.g. \"NOT\" for negation" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/qualifier> ], - [ sh:class diag:ProcedureToAttributePredicate ; - sh:description "The relationship type, e.g. RELATED_TO" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/predicate> ], - [ sh:class diag:DiagnosticProcedure ; - sh:description "A diagnostic procedure yielding a result, which in turn may be interpreted as a phenotype. Procedures include \"heart rate measurement\", \"blood pressure measurement\", \"oxygen saturation measurement\", etc. In practice, procedures may be named based on what they measure, with the \"measurement\" part left implicit." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject> ], - [ sh:class diag:ClinicalAttribute ; - sh:description "Any measurable clinical attribute." ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object> ], - [ sh:class diag:Quality ; - sh:description "An optional qualifier or modifier for the phenotype." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/object_qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the procedure." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/subject_qualifier> ] ; - sh:targetClass diag:DiagnosticProceduretoAttributeAssociation . - -diag:DiagnosticProceduretoPhenotypeAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "A triple representing a relationship between a diagnostic procedure and an associated phenotype, e.g., \"blood pressure measurement\" is associated with \"high blood pressure\"." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class diag:DiagnosticProcedure ; - sh:description "A diagnostic procedure yielding a result, which in turn may be interpreted as a phenotype. Procedures include \"heart rate measurement\", \"blood pressure measurement\", \"oxygen saturation measurement\", etc. In practice, procedures may be named based on what they measure, with the \"measurement\" part left implicit." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject> ], - [ sh:class diag:ProcedureToPhenotypePredicate ; - sh:description "The relationship type, e.g. RELATED_TO" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/predicate> ], - [ sh:class diag:Phenotype ; - sh:description "The observable physical or biochemical characteristics of a patient. Not equivalent to a disease state, but may contribute to a diagnosis." ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the procedure." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the phenotype." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/object_qualifier> ], - [ sh:description "A qualifier for the statements, e.g. \"NOT\" for negation" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/qualifier> ] ; - sh:targetClass diag:DiagnosticProceduretoPhenotypeAssociation . - -<http://w3id.org/ontogpt/core/Publication> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The full text of the publication" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/full_text> ], - [ sh:description "The publication identifier" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/combined_text> ], - [ sh:description "The title of the publication" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/title> ], - [ sh:description "The abstract of the publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/abstract> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/RelationshipType> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/Triple> a sh:NodeShape ; - sh:closed false ; - sh:description "Abstract parent for Relation Extraction tasks" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object> ], - [ sh:class <http://w3id.org/ontogpt/core/RelationshipType> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/predicate> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/object_qualifier> ], - [ sh:description "A qualifier for the statements, e.g. \"NOT\" for negation" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/qualifier> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Triple> . - -diag:ClinicalAttribute a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:class diag:Unit ; - sh:description "the unit used to measure the attribute" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path diag:unit ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path <rdfs:label> ] ; - sh:targetClass diag:ClinicalAttribute . - -diag:Phenotype a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass diag:Phenotype . - -diag:ProcedureToAttributePredicate a sh:NodeShape ; - sh:closed true ; - sh:description "A predicate for procedure to attribute relationships, defining \"this procedure is a measurement of this attribute\"." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass diag:ProcedureToAttributePredicate . - -diag:ProcedureToPhenotypePredicate a sh:NodeShape ; - sh:closed true ; - sh:description "A predicate for procedure to phenotype relationships, defining \"this procedure is intended to provide support for/against this phenotype\"." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass diag:ProcedureToPhenotypePredicate . - -diag:Quality a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass diag:Quality . - -diag:Unit a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass diag:Unit . - -diag:DiagnosticProcedure a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass diag:DiagnosticProcedure . - -linkml:Any a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass linkml:Any . - -<http://w3id.org/ontogpt/core/NamedEntity> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/NamedEntity> . - diff --git a/projects/diagnostic_procedure/shex/diagnostic_procedure.shex b/projects/diagnostic_procedure/shex/diagnostic_procedure.shex deleted file mode 100644 index 13472bbc3..000000000 --- a/projects/diagnostic_procedure/shex/diagnostic_procedure.shex +++ /dev/null @@ -1,223 +0,0 @@ -BASE <http://w3id.org/ontogpt/diagnostic_procedure/> -PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> -PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> -PREFIX linkml: <https://w3id.org/linkml/> -PREFIX core: <http://w3id.org/ontogpt/core/> -PREFIX rdfs1: <http://example.org/UNKNOWN/rdfs/> - - -linkml:String xsd:string - -linkml:Integer xsd:integer - -linkml:Boolean xsd:boolean - -linkml:Float xsd:float - -linkml:Double xsd:double - -linkml:Decimal xsd:decimal - -linkml:Time xsd:time - -linkml:Date xsd:date - -linkml:Datetime xsd:dateTime - -linkml:DateOrDatetime linkml:DateOrDatetime - -linkml:Uriorcurie IRI - -linkml:Curie xsd:string - -linkml:Uri IRI - -linkml:Ncname xsd:string - -linkml:Objectidentifier IRI - -linkml:Nodeidentifier NONLITERAL - -linkml:Jsonpointer xsd:string - -linkml:Jsonpath xsd:string - -linkml:Sparqlpath xsd:string - -core:AnnotatorResult CLOSED { - ( $core:AnnotatorResult_tes ( core:subject_text @linkml:String ? ; - core:object_id @linkml:String ? ; - core:object_text @linkml:String ? - ) ; - rdf:type [ core:AnnotatorResult ] ? - ) -} - -core:Any CLOSED { - ( $core:Any_tes rdf:type . * ; - rdf:type [ linkml:Any ] ? - ) -} - -<ClinicalAttribute> CLOSED { - ( $<ClinicalAttribute_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? ; - <unit> @<Unit> ? - ) ; - rdf:type [ <ClinicalAttribute> ] - ) -} - -core:CompoundExpression ( - { - ( $core:CompoundExpression_tes rdf:type . * ; - rdf:type [ core:CompoundExpression ] ? - ) - } OR @core:Triple -) - -<DiagnosticProcedure> CLOSED { - ( $<DiagnosticProcedure_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <DiagnosticProcedure> ] - ) -} - -<DiagnosticProceduretoAttributeAssociation> CLOSED { - ( $<DiagnosticProceduretoAttributeAssociation_tes> ( &core:Triple_tes ; - rdf:type [ core:Triple ] ? ; - <subject> @<DiagnosticProcedure> ? ; - <object> @<ClinicalAttribute> * ; - <predicate> @<ProcedureToAttributePredicate> ? ; - <subject_qualifier> @core:NamedEntity ? ; - <object_qualifier> @<Quality> ? - ) ; - rdf:type [ <DiagnosticProceduretoAttributeAssociation> ] ? - ) -} - -<DiagnosticProceduretoPhenotypeAssociation> CLOSED { - ( $<DiagnosticProceduretoPhenotypeAssociation_tes> ( &core:Triple_tes ; - rdf:type [ core:Triple ] ? ; - <subject> @<DiagnosticProcedure> ? ; - <object> @<Phenotype> * ; - <predicate> @<ProcedureToPhenotypePredicate> ? ; - <subject_qualifier> @core:NamedEntity ? ; - <object_qualifier> @core:NamedEntity ? - ) ; - rdf:type [ <DiagnosticProceduretoPhenotypeAssociation> ] ? - ) -} - -core:ExtractionResult CLOSED { - ( $core:ExtractionResult_tes ( core:input_id @linkml:String ? ; - core:input_title @linkml:String ? ; - core:input_text @linkml:String ? ; - core:raw_completion_output @linkml:String ? ; - core:prompt @linkml:String ? ; - core:extracted_object @core:Any ? ; - core:named_entities @core:Any * - ) ; - rdf:type [ core:ExtractionResult ] ? - ) -} - -core:NamedEntity ( - @<ClinicalAttribute> OR @<DiagnosticProcedure> OR @<Phenotype> OR @<Quality> OR @core:RelationshipType OR @<Unit> -) - -core:NamedEntity_struct { - ( $core:NamedEntity_tes rdfs1:label @linkml:String ? ; - rdf:type [ core:NamedEntity ] - ) -} - -<Phenotype> CLOSED { - ( $<Phenotype_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Phenotype> ] - ) -} - -<ProcedureToAttributePredicate> CLOSED { - ( $<ProcedureToAttributePredicate_tes> ( &core:RelationshipType_tes ; - rdf:type [ core:RelationshipType ] ? - ) ; - rdf:type [ <ProcedureToAttributePredicate> ] - ) -} - -<ProcedureToPhenotypePredicate> CLOSED { - ( $<ProcedureToPhenotypePredicate_tes> ( &core:RelationshipType_tes ; - rdf:type [ core:RelationshipType ] ? - ) ; - rdf:type [ <ProcedureToPhenotypePredicate> ] - ) -} - -core:Publication CLOSED { - ( $core:Publication_tes ( core:id @linkml:String ? ; - core:title @linkml:String ? ; - core:abstract @linkml:String ? ; - core:combined_text @linkml:String ? ; - core:full_text @linkml:String ? - ) ; - rdf:type [ core:Publication ] ? - ) -} - -<Quality> CLOSED { - ( $<Quality_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Quality> ] - ) -} - -core:RelationshipType ( - CLOSED { - ( $core:RelationshipType_tes ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ core:RelationshipType ] - ) - } OR @<ProcedureToAttributePredicate> OR @<ProcedureToPhenotypePredicate> -) - -core:TextWithTriples CLOSED { - ( $core:TextWithTriples_tes ( core:publication @core:Publication ? ; - core:triples @core:Triple * - ) ; - rdf:type [ core:TextWithTriples ] ? - ) -} - -core:Triple ( - @<DiagnosticProceduretoAttributeAssociation> OR @<DiagnosticProceduretoPhenotypeAssociation> -) - -core:Triple_struct { - ( $core:Triple_tes ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - core:subject @core:NamedEntity ? ; - core:predicate @core:RelationshipType ? ; - core:object @core:NamedEntity ? ; - core:qualifier @linkml:String ? ; - core:subject_qualifier @core:NamedEntity ? ; - core:object_qualifier @core:NamedEntity ? - ) ; - rdf:type [ core:Triple ] ? - ) -} - -<Unit> CLOSED { - ( $<Unit_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Unit> ] - ) -} - - diff --git a/projects/diagnostic_procedure/sqlschema/diagnostic_procedure.sql b/projects/diagnostic_procedure/sqlschema/diagnostic_procedure.sql deleted file mode 100644 index e36f64286..000000000 --- a/projects/diagnostic_procedure/sqlschema/diagnostic_procedure.sql +++ /dev/null @@ -1,109 +0,0 @@ - - -CREATE TABLE "AnnotatorResult" ( - subject_text TEXT, - object_id TEXT, - object_text TEXT, - PRIMARY KEY (subject_text, object_id, object_text) -); - -CREATE TABLE "DiagnosticProcedure" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "ExtractionResult" ( - input_id TEXT, - input_title TEXT, - input_text TEXT, - raw_completion_output TEXT, - prompt TEXT, - extracted_object TEXT, - named_entities TEXT, - PRIMARY KEY (input_id, input_title, input_text, raw_completion_output, prompt, extracted_object, named_entities) -); - -CREATE TABLE "Phenotype" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "ProcedureToAttributePredicate" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "ProcedureToPhenotypePredicate" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Publication" ( - id TEXT, - title TEXT, - abstract TEXT, - combined_text TEXT, - full_text TEXT, - PRIMARY KEY (id, title, abstract, combined_text, full_text) -); - -CREATE TABLE "Quality" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "RelationshipType" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "TextWithTriples" ( - publication TEXT, - triples TEXT, - PRIMARY KEY (publication, triples) -); - -CREATE TABLE "Unit" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "ClinicalAttribute" ( - id TEXT NOT NULL, - label TEXT, - unit TEXT, - PRIMARY KEY (id), - FOREIGN KEY(unit) REFERENCES "Unit" (id) -); - -CREATE TABLE "DiagnosticProceduretoAttributeAssociation" ( - qualifier TEXT, - subject TEXT, - object TEXT, - predicate TEXT, - subject_qualifier TEXT, - object_qualifier TEXT, - PRIMARY KEY (qualifier, subject, object, predicate, subject_qualifier, object_qualifier), - FOREIGN KEY(subject) REFERENCES "DiagnosticProcedure" (id), - FOREIGN KEY(predicate) REFERENCES "ProcedureToAttributePredicate" (id), - FOREIGN KEY(object_qualifier) REFERENCES "Quality" (id) -); - -CREATE TABLE "DiagnosticProceduretoPhenotypeAssociation" ( - qualifier TEXT, - subject TEXT, - object TEXT, - predicate TEXT, - subject_qualifier TEXT, - object_qualifier TEXT, - PRIMARY KEY (qualifier, subject, object, predicate, subject_qualifier, object_qualifier), - FOREIGN KEY(subject) REFERENCES "DiagnosticProcedure" (id), - FOREIGN KEY(predicate) REFERENCES "ProcedureToPhenotypePredicate" (id) -); diff --git a/projects/drug/docs/AnnotatorResult.md b/projects/drug/docs/AnnotatorResult.md deleted file mode 100644 index 1ea640ba8..000000000 --- a/projects/drug/docs/AnnotatorResult.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Class: AnnotatorResult - - - - -URI: [drug:AnnotatorResult](http://w3id.org/ontogpt/drug/AnnotatorResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F])](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F]) - -## Attributes - - -### Own - - * [➞subject_text](annotatorResult__subject_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_id](annotatorResult__object_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_text](annotatorResult__object_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) diff --git a/projects/drug/docs/Any.md b/projects/drug/docs/Any.md deleted file mode 100644 index 4da2d3785..000000000 --- a/projects/drug/docs/Any.md +++ /dev/null @@ -1,25 +0,0 @@ - -# Class: Any - - - - -URI: [drug:Any](http://w3id.org/ontogpt/drug/Any) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult])](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult]) - -## Referenced by Class - - * **None** *[➞extracted_object](extractionResult__extracted_object.md)* <sub>0..1</sub> **[Any](Any.md)** - * **None** *[➞named_entities](extractionResult__named_entities.md)* <sub>0..\*</sub> **[Any](Any.md)** - -## Attributes - - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | linkml:Any | - diff --git a/projects/drug/docs/CompoundExpression.md b/projects/drug/docs/CompoundExpression.md deleted file mode 100644 index 6478dc584..000000000 --- a/projects/drug/docs/CompoundExpression.md +++ /dev/null @@ -1,21 +0,0 @@ - -# Class: CompoundExpression - - - - -URI: [drug:CompoundExpression](http://w3id.org/ontogpt/drug/CompoundExpression) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[MechanismLink],[CompoundExpression]^-[Triple],[CompoundExpression]^-[MechanismLink])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[MechanismLink],[CompoundExpression]^-[Triple],[CompoundExpression]^-[MechanismLink]) - -## Children - - * [MechanismLink](MechanismLink.md) - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - -## Referenced by Class - - -## Attributes - diff --git a/projects/drug/docs/Disease.md b/projects/drug/docs/Disease.md deleted file mode 100644 index 3d32596fc..000000000 --- a/projects/drug/docs/Disease.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Class: Disease - - - - -URI: [drug:Disease](http://w3id.org/ontogpt/drug/Disease) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[DrugMechanism]-%20disease%200..1>[Disease|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Disease],[DrugMechanism])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[DrugMechanism]-%20disease%200..1>[Disease|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Disease],[DrugMechanism]) - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞disease](drugMechanism__disease.md)* <sub>0..1</sub> **[Disease](Disease.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/drug/docs/DrugMechanism.md b/projects/drug/docs/DrugMechanism.md deleted file mode 100644 index 4e2e63001..000000000 --- a/projects/drug/docs/DrugMechanism.md +++ /dev/null @@ -1,29 +0,0 @@ - -# Class: DrugMechanism - - - - -URI: [drug:DrugMechanism](http://w3id.org/ontogpt/drug/DrugMechanism) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[MechanismLink],[MechanismLink]<mechanism_links%200..*-++[DrugMechanism|references:string%20*;source_text:string%20%3F],[Drug]<drug%200..1-%20[DrugMechanism],[Disease]<disease%200..1-%20[DrugMechanism],[Drug],[Disease])](https://yuml.me/diagram/nofunky;dir:TB/class/[MechanismLink],[MechanismLink]<mechanism_links%200..*-++[DrugMechanism|references:string%20*;source_text:string%20%3F],[Drug]<drug%200..1-%20[DrugMechanism],[Disease]<disease%200..1-%20[DrugMechanism],[Drug],[Disease]) - -## Attributes - - -### Own - - * [➞disease](drugMechanism__disease.md) <sub>0..1</sub> - * Description: the name of the disease that is treated - * Range: [Disease](Disease.md) - * [➞drug](drugMechanism__drug.md) <sub>0..1</sub> - * Description: the name of the drug that treats the disease - * Range: [Drug](Drug.md) - * [➞mechanism_links](drugMechanism__mechanism_links.md) <sub>0..\*</sub> - * Description: semicolon-separated list of links, where each link is a triple connecting two entities via a relationship type - * Range: [MechanismLink](MechanismLink.md) - * [➞references](drugMechanism__references.md) <sub>0..\*</sub> - * Range: [String](types/String.md) - * [➞source_text](drugMechanism__source_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) diff --git a/projects/drug/docs/ExtractionResult.md b/projects/drug/docs/ExtractionResult.md deleted file mode 100644 index 7d07c8ae7..000000000 --- a/projects/drug/docs/ExtractionResult.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Class: ExtractionResult - - -A result of extracting knowledge on text - -URI: [drug:ExtractionResult](http://w3id.org/ontogpt/drug/ExtractionResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any])](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any]) - -## Attributes - - -### Own - - * [➞input_id](extractionResult__input_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_title](extractionResult__input_title.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_text](extractionResult__input_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞prompt](extractionResult__prompt.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞extracted_object](extractionResult__extracted_object.md) <sub>0..1</sub> - * Description: The complex objects extracted from the text - * Range: [Any](Any.md) - * [➞named_entities](extractionResult__named_entities.md) <sub>0..\*</sub> - * Description: Named entities extracted from the text - * Range: [Any](Any.md) diff --git a/projects/drug/docs/MechanismElement.md b/projects/drug/docs/MechanismElement.md deleted file mode 100644 index a7c61c9bd..000000000 --- a/projects/drug/docs/MechanismElement.md +++ /dev/null @@ -1,36 +0,0 @@ - -# Class: MechanismElement - - - - -URI: [drug:MechanismElement](http://w3id.org/ontogpt/drug/MechanismElement) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[MechanismLink]-%20object%200..1>[MechanismElement|id(i):string;label(i):string%20%3F],[MechanismLink]-%20subject%200..1>[MechanismElement],[NamedEntity]^-[MechanismElement],[MechanismLink])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[MechanismLink]-%20object%200..1>[MechanismElement|id(i):string;label(i):string%20%3F],[MechanismLink]-%20subject%200..1>[MechanismElement],[NamedEntity]^-[MechanismElement],[MechanismLink]) - -## Identifier prefixes - - * HGNC - * MESH - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞object](mechanismLink__object.md)* <sub>0..1</sub> **[MechanismElement](MechanismElement.md)** - * **None** *[➞subject](mechanismLink__subject.md)* <sub>0..1</sub> **[MechanismElement](MechanismElement.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/drug/docs/MechanismLink.md b/projects/drug/docs/MechanismLink.md deleted file mode 100644 index 7f5733162..000000000 --- a/projects/drug/docs/MechanismLink.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Class: MechanismLink - - - - -URI: [drug:MechanismLink](http://w3id.org/ontogpt/drug/MechanismLink) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Predicate],[MechanismElement]<object%200..1-%20[MechanismLink],[Predicate]<predicate%200..1-%20[MechanismLink],[MechanismElement]<subject%200..1-%20[MechanismLink],[DrugMechanism]++-%20mechanism_links%200..*>[MechanismLink],[CompoundExpression]^-[MechanismLink],[MechanismElement],[DrugMechanism],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[Predicate],[MechanismElement]<object%200..1-%20[MechanismLink],[Predicate]<predicate%200..1-%20[MechanismLink],[MechanismElement]<subject%200..1-%20[MechanismLink],[DrugMechanism]++-%20mechanism_links%200..*>[MechanismLink],[CompoundExpression]^-[MechanismLink],[MechanismElement],[DrugMechanism],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞mechanism_links](drugMechanism__mechanism_links.md)* <sub>0..\*</sub> **[MechanismLink](MechanismLink.md)** - -## Attributes - - -### Own - - * [➞subject](mechanismLink__subject.md) <sub>0..1</sub> - * Range: [MechanismElement](MechanismElement.md) - * [➞predicate](mechanismLink__predicate.md) <sub>0..1</sub> - * Range: [Predicate](Predicate.md) - * [➞object](mechanismLink__object.md) <sub>0..1</sub> - * Range: [MechanismElement](MechanismElement.md) diff --git a/projects/drug/docs/NamedEntity.md b/projects/drug/docs/NamedEntity.md deleted file mode 100644 index 4b94cf76b..000000000 --- a/projects/drug/docs/NamedEntity.md +++ /dev/null @@ -1,37 +0,0 @@ - -# Class: NamedEntity - - - - -URI: [drug:NamedEntity](http://w3id.org/ontogpt/drug/NamedEntity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[Predicate],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[Predicate],[NamedEntity]^-[MechanismElement],[NamedEntity]^-[Drug],[NamedEntity]^-[Disease],[Triple],[MechanismElement],[Drug],[Disease])](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[Predicate],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[Predicate],[NamedEntity]^-[MechanismElement],[NamedEntity]^-[Drug],[NamedEntity]^-[Disease],[Triple],[MechanismElement],[Drug],[Disease]) - -## Children - - * [Disease](Disease.md) - * [Drug](Drug.md) - * [MechanismElement](MechanismElement.md) - * [Predicate](Predicate.md) - * [RelationshipType](RelationshipType.md) - -## Referenced by Class - - * **None** *[➞object](triple__object.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞object_qualifier](triple__object_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject](triple__subject.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject_qualifier](triple__subject_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - -## Attributes - - -### Own - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/drug/docs/NullDataOptions.md b/projects/drug/docs/NullDataOptions.md deleted file mode 100644 index 25c94dc0c..000000000 --- a/projects/drug/docs/NullDataOptions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Enum: NullDataOptions - - - - -URI: [drug:NullDataOptions](http://w3id.org/ontogpt/drug/NullDataOptions) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | -| UNSPECIFIED_METHOD_OF_ADMINISTRATION | | NCIT:C149701 | | -| NOT_APPLICABLE | | NCIT:C18902 | {'aliases': ['not applicable', 'N/A']} | -| NOT_MENTIONED | | | | - diff --git a/projects/drug/docs/Predicate.md b/projects/drug/docs/Predicate.md deleted file mode 100644 index 6d81fd633..000000000 --- a/projects/drug/docs/Predicate.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Class: Predicate - - - - -URI: [drug:Predicate](http://w3id.org/ontogpt/drug/Predicate) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[MechanismLink]-%20predicate%200..1>[Predicate|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Predicate],[NamedEntity],[MechanismLink])](https://yuml.me/diagram/nofunky;dir:TB/class/[MechanismLink]-%20predicate%200..1>[Predicate|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Predicate],[NamedEntity],[MechanismLink]) - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞predicate](mechanismLink__predicate.md)* <sub>0..1</sub> **[Predicate](Predicate.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/drug/docs/Publication.md b/projects/drug/docs/Publication.md deleted file mode 100644 index 838ef88ac..000000000 --- a/projects/drug/docs/Publication.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Publication - - - - -URI: [drug:Publication](http://w3id.org/ontogpt/drug/Publication) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples])](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples]) - -## Referenced by Class - - * **None** *[➞publication](textWithTriples__publication.md)* <sub>0..1</sub> **[Publication](Publication.md)** - -## Attributes - - -### Own - - * [➞id](publication__id.md) <sub>0..1</sub> - * Description: The publication identifier - * Range: [String](types/String.md) - * [➞title](publication__title.md) <sub>0..1</sub> - * Description: The title of the publication - * Range: [String](types/String.md) - * [➞abstract](publication__abstract.md) <sub>0..1</sub> - * Description: The abstract of the publication - * Range: [String](types/String.md) - * [➞combined_text](publication__combined_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞full_text](publication__full_text.md) <sub>0..1</sub> - * Description: The full text of the publication - * Range: [String](types/String.md) diff --git a/projects/drug/docs/RelationshipType.md b/projects/drug/docs/RelationshipType.md deleted file mode 100644 index f59ebdaed..000000000 --- a/projects/drug/docs/RelationshipType.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: RelationshipType - - - - -URI: [drug:RelationshipType](http://w3id.org/ontogpt/drug/RelationshipType) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity]) - -## Identifier prefixes - - * RO - * biolink - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞predicate](triple__predicate.md)* <sub>0..1</sub> **[RelationshipType](RelationshipType.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/drug/docs/TextWithTriples.md b/projects/drug/docs/TextWithTriples.md deleted file mode 100644 index 21688ca7d..000000000 --- a/projects/drug/docs/TextWithTriples.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: TextWithTriples - - - - -URI: [drug:TextWithTriples](http://w3id.org/ontogpt/drug/TextWithTriples) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication]) - -## Attributes - - -### Own - - * [➞publication](textWithTriples__publication.md) <sub>0..1</sub> - * Range: [Publication](Publication.md) - * [➞triples](textWithTriples__triples.md) <sub>0..\*</sub> - * Range: [Triple](Triple.md) diff --git a/projects/drug/docs/Triple.md b/projects/drug/docs/Triple.md deleted file mode 100644 index d56fd4260..000000000 --- a/projects/drug/docs/Triple.md +++ /dev/null @@ -1,39 +0,0 @@ - -# Class: Triple - - -Abstract parent for Relation Extraction tasks - -URI: [drug:Triple](http://w3id.org/ontogpt/drug/Triple) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞triples](textWithTriples__triples.md)* <sub>0..\*</sub> **[Triple](Triple.md)** - -## Attributes - - -### Own - - * [➞subject](triple__subject.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞predicate](triple__predicate.md) <sub>0..1</sub> - * Range: [RelationshipType](RelationshipType.md) - * [➞object](triple__object.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞qualifier](triple__qualifier.md) <sub>0..1</sub> - * Description: A qualifier for the statements, e.g. "NOT" for negation - * Range: [String](types/String.md) - * [➞subject_qualifier](triple__subject_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - * Range: [NamedEntity](NamedEntity.md) - * [➞object_qualifier](triple__object_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * Range: [NamedEntity](NamedEntity.md) diff --git a/projects/drug/docs/annotatorResult__object_id.md b/projects/drug/docs/annotatorResult__object_id.md deleted file mode 100644 index 3be702157..000000000 --- a/projects/drug/docs/annotatorResult__object_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_id - - - - -URI: [drug:annotatorResult__object_id](http://w3id.org/ontogpt/drug/annotatorResult__object_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/drug/docs/annotatorResult__object_text.md b/projects/drug/docs/annotatorResult__object_text.md deleted file mode 100644 index 69b131f6a..000000000 --- a/projects/drug/docs/annotatorResult__object_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_text - - - - -URI: [drug:annotatorResult__object_text](http://w3id.org/ontogpt/drug/annotatorResult__object_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/drug/docs/annotatorResult__subject_text.md b/projects/drug/docs/annotatorResult__subject_text.md deleted file mode 100644 index c72ea9131..000000000 --- a/projects/drug/docs/annotatorResult__subject_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_text - - - - -URI: [drug:annotatorResult__subject_text](http://w3id.org/ontogpt/drug/annotatorResult__subject_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/drug/docs/drug.md b/projects/drug/docs/drug.md deleted file mode 100644 index 839797c32..000000000 --- a/projects/drug/docs/drug.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Class: Drug - - - - -URI: [drug:Drug](http://w3id.org/ontogpt/drug/Drug) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[DrugMechanism]-%20drug%200..1>[Drug|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Drug],[DrugMechanism])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[DrugMechanism]-%20drug%200..1>[Drug|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Drug],[DrugMechanism]) - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞drug](drugMechanism__drug.md)* <sub>0..1</sub> **[Drug](Drug.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/drug/docs/drugMechanism__disease.md b/projects/drug/docs/drugMechanism__disease.md deleted file mode 100644 index aafd767bb..000000000 --- a/projects/drug/docs/drugMechanism__disease.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: disease - - -the name of the disease that is treated - -URI: [drug:drugMechanism__disease](http://w3id.org/ontogpt/drug/drugMechanism__disease) - - -## Domain and Range - -None → <sub>0..1</sub> [Disease](Disease.md) - -## Parents - - -## Children - - -## Used by - - * [DrugMechanism](DrugMechanism.md) diff --git a/projects/drug/docs/drugMechanism__drug.md b/projects/drug/docs/drugMechanism__drug.md deleted file mode 100644 index a17312acb..000000000 --- a/projects/drug/docs/drugMechanism__drug.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: drug - - -the name of the drug that treats the disease - -URI: [drug:drugMechanism__drug](http://w3id.org/ontogpt/drug/drugMechanism__drug) - - -## Domain and Range - -None → <sub>0..1</sub> [Drug](Drug.md) - -## Parents - - -## Children - - -## Used by - - * [DrugMechanism](DrugMechanism.md) diff --git a/projects/drug/docs/drugMechanism__mechanism_links.md b/projects/drug/docs/drugMechanism__mechanism_links.md deleted file mode 100644 index 9121fd44c..000000000 --- a/projects/drug/docs/drugMechanism__mechanism_links.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: mechanism_links - - -semicolon-separated list of links, where each link is a triple connecting two entities via a relationship type - -URI: [drug:drugMechanism__mechanism_links](http://w3id.org/ontogpt/drug/drugMechanism__mechanism_links) - - -## Domain and Range - -None → <sub>0..\*</sub> [MechanismLink](MechanismLink.md) - -## Parents - - -## Children - - -## Used by - - * [DrugMechanism](DrugMechanism.md) diff --git a/projects/drug/docs/drugMechanism__references.md b/projects/drug/docs/drugMechanism__references.md deleted file mode 100644 index be2074040..000000000 --- a/projects/drug/docs/drugMechanism__references.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: references - - - - -URI: [drug:drugMechanism__references](http://w3id.org/ontogpt/drug/drugMechanism__references) - - -## Domain and Range - -None → <sub>0..\*</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [DrugMechanism](DrugMechanism.md) diff --git a/projects/drug/docs/drugMechanism__source_text.md b/projects/drug/docs/drugMechanism__source_text.md deleted file mode 100644 index 5ddd93aad..000000000 --- a/projects/drug/docs/drugMechanism__source_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: source_text - - - - -URI: [drug:drugMechanism__source_text](http://w3id.org/ontogpt/drug/drugMechanism__source_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [DrugMechanism](DrugMechanism.md) diff --git a/projects/drug/docs/extractionResult__extracted_object.md b/projects/drug/docs/extractionResult__extracted_object.md deleted file mode 100644 index 9e1ffec86..000000000 --- a/projects/drug/docs/extractionResult__extracted_object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: extracted_object - - -The complex objects extracted from the text - -URI: [drug:extractionResult__extracted_object](http://w3id.org/ontogpt/drug/extractionResult__extracted_object) - - -## Domain and Range - -None → <sub>0..1</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/drug/docs/extractionResult__input_id.md b/projects/drug/docs/extractionResult__input_id.md deleted file mode 100644 index 3091924ef..000000000 --- a/projects/drug/docs/extractionResult__input_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_id - - - - -URI: [drug:extractionResult__input_id](http://w3id.org/ontogpt/drug/extractionResult__input_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/drug/docs/extractionResult__input_text.md b/projects/drug/docs/extractionResult__input_text.md deleted file mode 100644 index e52590f86..000000000 --- a/projects/drug/docs/extractionResult__input_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_text - - - - -URI: [drug:extractionResult__input_text](http://w3id.org/ontogpt/drug/extractionResult__input_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/drug/docs/extractionResult__input_title.md b/projects/drug/docs/extractionResult__input_title.md deleted file mode 100644 index db5911166..000000000 --- a/projects/drug/docs/extractionResult__input_title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_title - - - - -URI: [drug:extractionResult__input_title](http://w3id.org/ontogpt/drug/extractionResult__input_title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/drug/docs/extractionResult__named_entities.md b/projects/drug/docs/extractionResult__named_entities.md deleted file mode 100644 index 5d7701c98..000000000 --- a/projects/drug/docs/extractionResult__named_entities.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: named_entities - - -Named entities extracted from the text - -URI: [drug:extractionResult__named_entities](http://w3id.org/ontogpt/drug/extractionResult__named_entities) - - -## Domain and Range - -None → <sub>0..\*</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/drug/docs/extractionResult__prompt.md b/projects/drug/docs/extractionResult__prompt.md deleted file mode 100644 index dc94587a9..000000000 --- a/projects/drug/docs/extractionResult__prompt.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: prompt - - - - -URI: [drug:extractionResult__prompt](http://w3id.org/ontogpt/drug/extractionResult__prompt) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/drug/docs/extractionResult__raw_completion_output.md b/projects/drug/docs/extractionResult__raw_completion_output.md deleted file mode 100644 index 1e77ca0a5..000000000 --- a/projects/drug/docs/extractionResult__raw_completion_output.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: raw_completion_output - - - - -URI: [drug:extractionResult__raw_completion_output](http://w3id.org/ontogpt/drug/extractionResult__raw_completion_output) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/drug/docs/mechanismLink__object.md b/projects/drug/docs/mechanismLink__object.md deleted file mode 100644 index 01aff3202..000000000 --- a/projects/drug/docs/mechanismLink__object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object - - - - -URI: [drug:mechanismLink__object](http://w3id.org/ontogpt/drug/mechanismLink__object) - - -## Domain and Range - -None → <sub>0..1</sub> [MechanismElement](MechanismElement.md) - -## Parents - - -## Children - - -## Used by - - * [MechanismLink](MechanismLink.md) diff --git a/projects/drug/docs/mechanismLink__predicate.md b/projects/drug/docs/mechanismLink__predicate.md deleted file mode 100644 index 83bf0fd17..000000000 --- a/projects/drug/docs/mechanismLink__predicate.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: predicate - - - - -URI: [drug:mechanismLink__predicate](http://w3id.org/ontogpt/drug/mechanismLink__predicate) - - -## Domain and Range - -None → <sub>0..1</sub> [Predicate](Predicate.md) - -## Parents - - -## Children - - -## Used by - - * [MechanismLink](MechanismLink.md) diff --git a/projects/drug/docs/mechanismLink__subject.md b/projects/drug/docs/mechanismLink__subject.md deleted file mode 100644 index c1f1270ae..000000000 --- a/projects/drug/docs/mechanismLink__subject.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject - - - - -URI: [drug:mechanismLink__subject](http://w3id.org/ontogpt/drug/mechanismLink__subject) - - -## Domain and Range - -None → <sub>0..1</sub> [MechanismElement](MechanismElement.md) - -## Parents - - -## Children - - -## Used by - - * [MechanismLink](MechanismLink.md) diff --git a/projects/drug/docs/namedEntity__id.md b/projects/drug/docs/namedEntity__id.md deleted file mode 100644 index 4cde4a702..000000000 --- a/projects/drug/docs/namedEntity__id.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Slot: id - - -A unique identifier for the named entity - -URI: [drug:namedEntity__id](http://w3id.org/ontogpt/drug/namedEntity__id) - - -## Domain and Range - -None → <sub>1..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Disease](Disease.md) - * [Drug](Drug.md) - * [MechanismElement](MechanismElement.md) - * [NamedEntity](NamedEntity.md) - * [Predicate](Predicate.md) - * [RelationshipType](RelationshipType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | this is populated during the grounding and normalization step | - diff --git a/projects/drug/docs/namedEntity__label.md b/projects/drug/docs/namedEntity__label.md deleted file mode 100644 index ce578146f..000000000 --- a/projects/drug/docs/namedEntity__label.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Slot: label - - -The label (name) of the named thing - -URI: [drug:namedEntity__label](http://w3id.org/ontogpt/drug/namedEntity__label) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Disease](Disease.md) - * [Drug](Drug.md) - * [MechanismElement](MechanismElement.md) - * [NamedEntity](NamedEntity.md) - * [Predicate](Predicate.md) - * [RelationshipType](RelationshipType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Aliases:** | | name | -| **Mappings:** | | rdfs:label | - diff --git a/projects/drug/docs/publication__abstract.md b/projects/drug/docs/publication__abstract.md deleted file mode 100644 index f72aeea74..000000000 --- a/projects/drug/docs/publication__abstract.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: abstract - - -The abstract of the publication - -URI: [drug:publication__abstract](http://w3id.org/ontogpt/drug/publication__abstract) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/drug/docs/publication__combined_text.md b/projects/drug/docs/publication__combined_text.md deleted file mode 100644 index 5e743fb57..000000000 --- a/projects/drug/docs/publication__combined_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: combined_text - - - - -URI: [drug:publication__combined_text](http://w3id.org/ontogpt/drug/publication__combined_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/drug/docs/publication__full_text.md b/projects/drug/docs/publication__full_text.md deleted file mode 100644 index 7612a1e21..000000000 --- a/projects/drug/docs/publication__full_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: full_text - - -The full text of the publication - -URI: [drug:publication__full_text](http://w3id.org/ontogpt/drug/publication__full_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/drug/docs/publication__id.md b/projects/drug/docs/publication__id.md deleted file mode 100644 index 6559e9615..000000000 --- a/projects/drug/docs/publication__id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: id - - -The publication identifier - -URI: [drug:publication__id](http://w3id.org/ontogpt/drug/publication__id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/drug/docs/publication__title.md b/projects/drug/docs/publication__title.md deleted file mode 100644 index 5f67aee85..000000000 --- a/projects/drug/docs/publication__title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: title - - -The title of the publication - -URI: [drug:publication__title](http://w3id.org/ontogpt/drug/publication__title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/drug/docs/textWithTriples__publication.md b/projects/drug/docs/textWithTriples__publication.md deleted file mode 100644 index d4cad2729..000000000 --- a/projects/drug/docs/textWithTriples__publication.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: publication - - - - -URI: [drug:textWithTriples__publication](http://w3id.org/ontogpt/drug/textWithTriples__publication) - - -## Domain and Range - -None → <sub>0..1</sub> [Publication](Publication.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/drug/docs/textWithTriples__triples.md b/projects/drug/docs/textWithTriples__triples.md deleted file mode 100644 index a8f3c7d31..000000000 --- a/projects/drug/docs/textWithTriples__triples.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: triples - - - - -URI: [drug:textWithTriples__triples](http://w3id.org/ontogpt/drug/textWithTriples__triples) - - -## Domain and Range - -None → <sub>0..\*</sub> [Triple](Triple.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/drug/docs/triple__object.md b/projects/drug/docs/triple__object.md deleted file mode 100644 index a2e0c615d..000000000 --- a/projects/drug/docs/triple__object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object - - - - -URI: [drug:triple__object](http://w3id.org/ontogpt/drug/triple__object) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/drug/docs/triple__object_qualifier.md b/projects/drug/docs/triple__object_qualifier.md deleted file mode 100644 index c34b7cd0b..000000000 --- a/projects/drug/docs/triple__object_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_qualifier - - -An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - -URI: [drug:triple__object_qualifier](http://w3id.org/ontogpt/drug/triple__object_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/drug/docs/triple__predicate.md b/projects/drug/docs/triple__predicate.md deleted file mode 100644 index b8c744fdf..000000000 --- a/projects/drug/docs/triple__predicate.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: predicate - - - - -URI: [drug:triple__predicate](http://w3id.org/ontogpt/drug/triple__predicate) - - -## Domain and Range - -None → <sub>0..1</sub> [RelationshipType](RelationshipType.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/drug/docs/triple__qualifier.md b/projects/drug/docs/triple__qualifier.md deleted file mode 100644 index 5e6c0ade3..000000000 --- a/projects/drug/docs/triple__qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: qualifier - - -A qualifier for the statements, e.g. "NOT" for negation - -URI: [drug:triple__qualifier](http://w3id.org/ontogpt/drug/triple__qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/drug/docs/triple__subject.md b/projects/drug/docs/triple__subject.md deleted file mode 100644 index 13d718c66..000000000 --- a/projects/drug/docs/triple__subject.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject - - - - -URI: [drug:triple__subject](http://w3id.org/ontogpt/drug/triple__subject) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/drug/docs/triple__subject_qualifier.md b/projects/drug/docs/triple__subject_qualifier.md deleted file mode 100644 index 50842f269..000000000 --- a/projects/drug/docs/triple__subject_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_qualifier - - -An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -URI: [drug:triple__subject_qualifier](http://w3id.org/ontogpt/drug/triple__subject_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/drug/docs/types/Boolean.md b/projects/drug/docs/types/Boolean.md deleted file mode 100644 index dc83a9c6e..000000000 --- a/projects/drug/docs/types/Boolean.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: boolean - - -A binary (true or false) value - -URI: [linkml:Boolean](https://w3id.org/linkml/Boolean) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Bool** | -| Representation | | bool | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Boolean | - diff --git a/projects/drug/docs/types/Curie.md b/projects/drug/docs/types/Curie.md deleted file mode 100644 index c1803f93f..000000000 --- a/projects/drug/docs/types/Curie.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: curie - - -a compact URI - -URI: [linkml:Curie](https://w3id.org/linkml/Curie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Curie** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations this MUST be expanded to a URI | -| | | in non-RDF serializations MAY be serialized as the compact representation | - diff --git a/projects/drug/docs/types/Date.md b/projects/drug/docs/types/Date.md deleted file mode 100644 index 06948af97..000000000 --- a/projects/drug/docs/types/Date.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: date - - -a date (year, month and day) in an idealized calendar - -URI: [linkml:Date](https://w3id.org/linkml/Date) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDate** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Date | - diff --git a/projects/drug/docs/types/DateOrDatetime.md b/projects/drug/docs/types/DateOrDatetime.md deleted file mode 100644 index ef983898d..000000000 --- a/projects/drug/docs/types/DateOrDatetime.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: date_or_datetime - - -Either a date or a datetime - -URI: [linkml:DateOrDatetime](https://w3id.org/linkml/DateOrDatetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/drug/docs/types/Datetime.md b/projects/drug/docs/types/Datetime.md deleted file mode 100644 index 9510454a8..000000000 --- a/projects/drug/docs/types/Datetime.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: datetime - - -The combination of a date and time - -URI: [linkml:Datetime](https://w3id.org/linkml/Datetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDateTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:DateTime | - diff --git a/projects/drug/docs/types/Decimal.md b/projects/drug/docs/types/Decimal.md deleted file mode 100644 index a7ba14a5d..000000000 --- a/projects/drug/docs/types/Decimal.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: decimal - - -A real number with arbitrary precision that conforms to the xsd:decimal specification - -URI: [linkml:Decimal](https://w3id.org/linkml/Decimal) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Decimal** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Broad Mappings:** | | schema:Number | - diff --git a/projects/drug/docs/types/Double.md b/projects/drug/docs/types/Double.md deleted file mode 100644 index cfe6d71e2..000000000 --- a/projects/drug/docs/types/Double.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: double - - -A real number that conforms to the xsd:double specification - -URI: [linkml:Double](https://w3id.org/linkml/Double) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Close Mappings:** | | schema:Float | - diff --git a/projects/drug/docs/types/Float.md b/projects/drug/docs/types/Float.md deleted file mode 100644 index 7b303f96f..000000000 --- a/projects/drug/docs/types/Float.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: float - - -A real number that conforms to the xsd:float specification - -URI: [linkml:Float](https://w3id.org/linkml/Float) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Float | - diff --git a/projects/drug/docs/types/Integer.md b/projects/drug/docs/types/Integer.md deleted file mode 100644 index 3cfcc66d9..000000000 --- a/projects/drug/docs/types/Integer.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: integer - - -An integer - -URI: [linkml:Integer](https://w3id.org/linkml/Integer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **int** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Integer | - diff --git a/projects/drug/docs/types/Jsonpath.md b/projects/drug/docs/types/Jsonpath.md deleted file mode 100644 index a03a58e67..000000000 --- a/projects/drug/docs/types/Jsonpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpath - - -A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpath](https://w3id.org/linkml/Jsonpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/drug/docs/types/Jsonpointer.md b/projects/drug/docs/types/Jsonpointer.md deleted file mode 100644 index a0e1ac492..000000000 --- a/projects/drug/docs/types/Jsonpointer.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpointer - - -A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpointer](https://w3id.org/linkml/Jsonpointer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/drug/docs/types/Ncname.md b/projects/drug/docs/types/Ncname.md deleted file mode 100644 index 710b0b04a..000000000 --- a/projects/drug/docs/types/Ncname.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: ncname - - -Prefix part of CURIE - -URI: [linkml:Ncname](https://w3id.org/linkml/Ncname) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NCName** | -| Representation | | str | diff --git a/projects/drug/docs/types/Nodeidentifier.md b/projects/drug/docs/types/Nodeidentifier.md deleted file mode 100644 index f0097cdf4..000000000 --- a/projects/drug/docs/types/Nodeidentifier.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: nodeidentifier - - -A URI, CURIE or BNODE that represents a node in a model. - -URI: [linkml:Nodeidentifier](https://w3id.org/linkml/Nodeidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NodeIdentifier** | -| Representation | | str | diff --git a/projects/drug/docs/types/Objectidentifier.md b/projects/drug/docs/types/Objectidentifier.md deleted file mode 100644 index 454ba6be6..000000000 --- a/projects/drug/docs/types/Objectidentifier.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: objectidentifier - - -A URI or CURIE that represents an object in the model. - -URI: [linkml:Objectidentifier](https://w3id.org/linkml/Objectidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **ElementIdentifier** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | Used for inheritance and type checking | - diff --git a/projects/drug/docs/types/Sparqlpath.md b/projects/drug/docs/types/Sparqlpath.md deleted file mode 100644 index fd99a927e..000000000 --- a/projects/drug/docs/types/Sparqlpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: sparqlpath - - -A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - -URI: [linkml:Sparqlpath](https://w3id.org/linkml/Sparqlpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/drug/docs/types/String.md b/projects/drug/docs/types/String.md deleted file mode 100644 index 6e61d7081..000000000 --- a/projects/drug/docs/types/String.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: string - - -A character string - -URI: [linkml:String](https://w3id.org/linkml/String) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Text | - diff --git a/projects/drug/docs/types/Time.md b/projects/drug/docs/types/Time.md deleted file mode 100644 index 2b8652bcd..000000000 --- a/projects/drug/docs/types/Time.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: time - - -A time object represents a (local) time of day, independent of any particular day - -URI: [linkml:Time](https://w3id.org/linkml/Time) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Time | - diff --git a/projects/drug/docs/types/Uri.md b/projects/drug/docs/types/Uri.md deleted file mode 100644 index 343807a5e..000000000 --- a/projects/drug/docs/types/Uri.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: uri - - -a complete URI - -URI: [linkml:Uri](https://w3id.org/linkml/Uri) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URI** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node | -| **Close Mappings:** | | schema:URL | - diff --git a/projects/drug/docs/types/Uriorcurie.md b/projects/drug/docs/types/Uriorcurie.md deleted file mode 100644 index 2f7b65087..000000000 --- a/projects/drug/docs/types/Uriorcurie.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: uriorcurie - - -a URI or a CURIE - -URI: [linkml:Uriorcurie](https://w3id.org/linkml/Uriorcurie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URIorCURIE** | -| Representation | | str | diff --git a/projects/drug/drug.py b/projects/drug/drug.py deleted file mode 100644 index 306776729..000000000 --- a/projects/drug/drug.py +++ /dev/null @@ -1,546 +0,0 @@ -# Auto generated from drug.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-08-07T10:52:51 -# Schema: drug -# -# id: http://w3id.org/ontogpt/drug -# description: A template for Drugs and drug mechanism -# license: https://creativecommons.org/publicdomain/zero/1.0/ - -import dataclasses -import sys -import re -from jsonasobj2 import JsonObj, as_dict -from typing import Optional, List, Union, Dict, ClassVar, Any -from dataclasses import dataclass -from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions - -from linkml_runtime.utils.slot import Slot -from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode -from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int -from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs -from linkml_runtime.utils.formatutils import camelcase, underscore, sfx -from linkml_runtime.utils.enumerations import EnumDefinitionImpl -from rdflib import Namespace, URIRef -from linkml_runtime.utils.curienamespace import CurieNamespace -from linkml_runtime.linkml_model.types import String - -metamodel_version = "1.7.0" -version = None - -# Overwrite dataclasses _init_fn to add **kwargs in __init__ -dataclasses._init_fn = dataclasses_init_fn_with_kwargs - -# Namespaces -HGNC = CurieNamespace('HGNC', 'http://example.org/UNKNOWN/HGNC/') -MESH = CurieNamespace('MESH', 'http://example.org/UNKNOWN/MESH/') -RO = CurieNamespace('RO', 'http://purl.obolibrary.org/obo/RO_') -BIOLINK = CurieNamespace('biolink', 'http://example.org/UNKNOWN/biolink/') -CORE = CurieNamespace('core', 'http://w3id.org/ontogpt/core/') -DRUG = CurieNamespace('drug', 'http://w3id.org/ontogpt/drug/') -LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') -RDFS = CurieNamespace('rdfs', 'http://example.org/UNKNOWN/rdfs/') -DEFAULT_ = DRUG - - -# Types - -# Class references -class NamedEntityId(extended_str): - pass - - -class MechanismElementId(NamedEntityId): - pass - - -class DiseaseId(NamedEntityId): - pass - - -class DrugId(NamedEntityId): - pass - - -class PredicateId(NamedEntityId): - pass - - -class RelationshipTypeId(NamedEntityId): - pass - - -@dataclass -class DrugMechanism(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = DRUG.DrugMechanism - class_class_curie: ClassVar[str] = "drug:DrugMechanism" - class_name: ClassVar[str] = "DrugMechanism" - class_model_uri: ClassVar[URIRef] = DRUG.DrugMechanism - - disease: Optional[Union[str, DiseaseId]] = None - drug: Optional[Union[str, DrugId]] = None - mechanism_links: Optional[Union[Union[dict, "MechanismLink"], List[Union[dict, "MechanismLink"]]]] = empty_list() - references: Optional[Union[str, List[str]]] = empty_list() - source_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.disease is not None and not isinstance(self.disease, DiseaseId): - self.disease = DiseaseId(self.disease) - - if self.drug is not None and not isinstance(self.drug, DrugId): - self.drug = DrugId(self.drug) - - if not isinstance(self.mechanism_links, list): - self.mechanism_links = [self.mechanism_links] if self.mechanism_links is not None else [] - self.mechanism_links = [v if isinstance(v, MechanismLink) else MechanismLink(**as_dict(v)) for v in self.mechanism_links] - - if not isinstance(self.references, list): - self.references = [self.references] if self.references is not None else [] - self.references = [v if isinstance(v, str) else str(v) for v in self.references] - - if self.source_text is not None and not isinstance(self.source_text, str): - self.source_text = str(self.source_text) - - super().__post_init__(**kwargs) - - -Any = Any - -@dataclass -class ExtractionResult(YAMLRoot): - """ - A result of extracting knowledge on text - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.ExtractionResult - class_class_curie: ClassVar[str] = "core:ExtractionResult" - class_name: ClassVar[str] = "ExtractionResult" - class_model_uri: ClassVar[URIRef] = DRUG.ExtractionResult - - input_id: Optional[str] = None - input_title: Optional[str] = None - input_text: Optional[str] = None - raw_completion_output: Optional[str] = None - prompt: Optional[str] = None - extracted_object: Optional[Union[dict, Any]] = None - named_entities: Optional[Union[Union[dict, Any], List[Union[dict, Any]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.input_id is not None and not isinstance(self.input_id, str): - self.input_id = str(self.input_id) - - if self.input_title is not None and not isinstance(self.input_title, str): - self.input_title = str(self.input_title) - - if self.input_text is not None and not isinstance(self.input_text, str): - self.input_text = str(self.input_text) - - if self.raw_completion_output is not None and not isinstance(self.raw_completion_output, str): - self.raw_completion_output = str(self.raw_completion_output) - - if self.prompt is not None and not isinstance(self.prompt, str): - self.prompt = str(self.prompt) - - super().__post_init__(**kwargs) - - -@dataclass -class NamedEntity(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.NamedEntity - class_class_curie: ClassVar[str] = "core:NamedEntity" - class_name: ClassVar[str] = "NamedEntity" - class_model_uri: ClassVar[URIRef] = DRUG.NamedEntity - - id: Union[str, NamedEntityId] = None - label: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, NamedEntityId): - self.id = NamedEntityId(self.id) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - super().__post_init__(**kwargs) - - -@dataclass -class MechanismElement(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = DRUG.MechanismElement - class_class_curie: ClassVar[str] = "drug:MechanismElement" - class_name: ClassVar[str] = "MechanismElement" - class_model_uri: ClassVar[URIRef] = DRUG.MechanismElement - - id: Union[str, MechanismElementId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, MechanismElementId): - self.id = MechanismElementId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Disease(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = DRUG.Disease - class_class_curie: ClassVar[str] = "drug:Disease" - class_name: ClassVar[str] = "Disease" - class_model_uri: ClassVar[URIRef] = DRUG.Disease - - id: Union[str, DiseaseId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, DiseaseId): - self.id = DiseaseId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Drug(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = DRUG.Drug - class_class_curie: ClassVar[str] = "drug:Drug" - class_name: ClassVar[str] = "Drug" - class_model_uri: ClassVar[URIRef] = DRUG.Drug - - id: Union[str, DrugId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, DrugId): - self.id = DrugId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Predicate(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = DRUG.Predicate - class_class_curie: ClassVar[str] = "drug:Predicate" - class_name: ClassVar[str] = "Predicate" - class_model_uri: ClassVar[URIRef] = DRUG.Predicate - - id: Union[str, PredicateId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, PredicateId): - self.id = PredicateId(self.id) - - super().__post_init__(**kwargs) - - -class CompoundExpression(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.CompoundExpression - class_class_curie: ClassVar[str] = "core:CompoundExpression" - class_name: ClassVar[str] = "CompoundExpression" - class_model_uri: ClassVar[URIRef] = DRUG.CompoundExpression - - -@dataclass -class MechanismLink(CompoundExpression): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = DRUG.MechanismLink - class_class_curie: ClassVar[str] = "drug:MechanismLink" - class_name: ClassVar[str] = "MechanismLink" - class_model_uri: ClassVar[URIRef] = DRUG.MechanismLink - - subject: Optional[Union[str, MechanismElementId]] = None - predicate: Optional[Union[str, PredicateId]] = None - object: Optional[Union[str, MechanismElementId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, MechanismElementId): - self.subject = MechanismElementId(self.subject) - - if self.predicate is not None and not isinstance(self.predicate, PredicateId): - self.predicate = PredicateId(self.predicate) - - if self.object is not None and not isinstance(self.object, MechanismElementId): - self.object = MechanismElementId(self.object) - - super().__post_init__(**kwargs) - - -@dataclass -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Triple - class_class_curie: ClassVar[str] = "core:Triple" - class_name: ClassVar[str] = "Triple" - class_model_uri: ClassVar[URIRef] = DRUG.Triple - - subject: Optional[Union[str, NamedEntityId]] = None - predicate: Optional[Union[str, RelationshipTypeId]] = None - object: Optional[Union[str, NamedEntityId]] = None - qualifier: Optional[str] = None - subject_qualifier: Optional[Union[str, NamedEntityId]] = None - object_qualifier: Optional[Union[str, NamedEntityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, NamedEntityId): - self.subject = NamedEntityId(self.subject) - - if self.predicate is not None and not isinstance(self.predicate, RelationshipTypeId): - self.predicate = RelationshipTypeId(self.predicate) - - if self.object is not None and not isinstance(self.object, NamedEntityId): - self.object = NamedEntityId(self.object) - - if self.qualifier is not None and not isinstance(self.qualifier, str): - self.qualifier = str(self.qualifier) - - if self.subject_qualifier is not None and not isinstance(self.subject_qualifier, NamedEntityId): - self.subject_qualifier = NamedEntityId(self.subject_qualifier) - - if self.object_qualifier is not None and not isinstance(self.object_qualifier, NamedEntityId): - self.object_qualifier = NamedEntityId(self.object_qualifier) - - super().__post_init__(**kwargs) - - -@dataclass -class TextWithTriples(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.TextWithTriples - class_class_curie: ClassVar[str] = "core:TextWithTriples" - class_name: ClassVar[str] = "TextWithTriples" - class_model_uri: ClassVar[URIRef] = DRUG.TextWithTriples - - publication: Optional[Union[dict, "Publication"]] = None - triples: Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.publication is not None and not isinstance(self.publication, Publication): - self.publication = Publication(**as_dict(self.publication)) - - if not isinstance(self.triples, list): - self.triples = [self.triples] if self.triples is not None else [] - self.triples = [v if isinstance(v, Triple) else Triple(**as_dict(v)) for v in self.triples] - - super().__post_init__(**kwargs) - - -@dataclass -class RelationshipType(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.RelationshipType - class_class_curie: ClassVar[str] = "core:RelationshipType" - class_name: ClassVar[str] = "RelationshipType" - class_model_uri: ClassVar[URIRef] = DRUG.RelationshipType - - id: Union[str, RelationshipTypeId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, RelationshipTypeId): - self.id = RelationshipTypeId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Publication(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Publication - class_class_curie: ClassVar[str] = "core:Publication" - class_name: ClassVar[str] = "Publication" - class_model_uri: ClassVar[URIRef] = DRUG.Publication - - id: Optional[str] = None - title: Optional[str] = None - abstract: Optional[str] = None - combined_text: Optional[str] = None - full_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.id is not None and not isinstance(self.id, str): - self.id = str(self.id) - - if self.title is not None and not isinstance(self.title, str): - self.title = str(self.title) - - if self.abstract is not None and not isinstance(self.abstract, str): - self.abstract = str(self.abstract) - - if self.combined_text is not None and not isinstance(self.combined_text, str): - self.combined_text = str(self.combined_text) - - if self.full_text is not None and not isinstance(self.full_text, str): - self.full_text = str(self.full_text) - - super().__post_init__(**kwargs) - - -@dataclass -class AnnotatorResult(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.AnnotatorResult - class_class_curie: ClassVar[str] = "core:AnnotatorResult" - class_name: ClassVar[str] = "AnnotatorResult" - class_model_uri: ClassVar[URIRef] = DRUG.AnnotatorResult - - subject_text: Optional[str] = None - object_id: Optional[str] = None - object_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject_text is not None and not isinstance(self.subject_text, str): - self.subject_text = str(self.subject_text) - - if self.object_id is not None and not isinstance(self.object_id, str): - self.object_id = str(self.object_id) - - if self.object_text is not None and not isinstance(self.object_text, str): - self.object_text = str(self.object_text) - - super().__post_init__(**kwargs) - - -# Enumerations -class NullDataOptions(EnumDefinitionImpl): - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = PermissibleValue(text="UNSPECIFIED_METHOD_OF_ADMINISTRATION", - meaning=NCIT.C149701) - NOT_APPLICABLE = PermissibleValue(text="NOT_APPLICABLE", - meaning=NCIT.C18902) - NOT_MENTIONED = PermissibleValue(text="NOT_MENTIONED") - - _defn = EnumDefinition( - name="NullDataOptions", - ) - -# Slots -class slots: - pass - -slots.drugMechanism__disease = Slot(uri=DRUG.disease, name="drugMechanism__disease", curie=DRUG.curie('disease'), - model_uri=DRUG.drugMechanism__disease, domain=None, range=Optional[Union[str, DiseaseId]]) - -slots.drugMechanism__drug = Slot(uri=DRUG.drug, name="drugMechanism__drug", curie=DRUG.curie('drug'), - model_uri=DRUG.drugMechanism__drug, domain=None, range=Optional[Union[str, DrugId]]) - -slots.drugMechanism__mechanism_links = Slot(uri=DRUG.mechanism_links, name="drugMechanism__mechanism_links", curie=DRUG.curie('mechanism_links'), - model_uri=DRUG.drugMechanism__mechanism_links, domain=None, range=Optional[Union[Union[dict, MechanismLink], List[Union[dict, MechanismLink]]]]) - -slots.drugMechanism__references = Slot(uri=DRUG.references, name="drugMechanism__references", curie=DRUG.curie('references'), - model_uri=DRUG.drugMechanism__references, domain=None, range=Optional[Union[str, List[str]]]) - -slots.drugMechanism__source_text = Slot(uri=DRUG.source_text, name="drugMechanism__source_text", curie=DRUG.curie('source_text'), - model_uri=DRUG.drugMechanism__source_text, domain=None, range=Optional[str]) - -slots.mechanismLink__subject = Slot(uri=DRUG.subject, name="mechanismLink__subject", curie=DRUG.curie('subject'), - model_uri=DRUG.mechanismLink__subject, domain=None, range=Optional[Union[str, MechanismElementId]]) - -slots.mechanismLink__predicate = Slot(uri=DRUG.predicate, name="mechanismLink__predicate", curie=DRUG.curie('predicate'), - model_uri=DRUG.mechanismLink__predicate, domain=None, range=Optional[Union[str, PredicateId]]) - -slots.mechanismLink__object = Slot(uri=DRUG.object, name="mechanismLink__object", curie=DRUG.curie('object'), - model_uri=DRUG.mechanismLink__object, domain=None, range=Optional[Union[str, MechanismElementId]]) - -slots.extractionResult__input_id = Slot(uri=CORE.input_id, name="extractionResult__input_id", curie=CORE.curie('input_id'), - model_uri=DRUG.extractionResult__input_id, domain=None, range=Optional[str]) - -slots.extractionResult__input_title = Slot(uri=CORE.input_title, name="extractionResult__input_title", curie=CORE.curie('input_title'), - model_uri=DRUG.extractionResult__input_title, domain=None, range=Optional[str]) - -slots.extractionResult__input_text = Slot(uri=CORE.input_text, name="extractionResult__input_text", curie=CORE.curie('input_text'), - model_uri=DRUG.extractionResult__input_text, domain=None, range=Optional[str]) - -slots.extractionResult__raw_completion_output = Slot(uri=CORE.raw_completion_output, name="extractionResult__raw_completion_output", curie=CORE.curie('raw_completion_output'), - model_uri=DRUG.extractionResult__raw_completion_output, domain=None, range=Optional[str]) - -slots.extractionResult__prompt = Slot(uri=CORE.prompt, name="extractionResult__prompt", curie=CORE.curie('prompt'), - model_uri=DRUG.extractionResult__prompt, domain=None, range=Optional[str]) - -slots.extractionResult__extracted_object = Slot(uri=CORE.extracted_object, name="extractionResult__extracted_object", curie=CORE.curie('extracted_object'), - model_uri=DRUG.extractionResult__extracted_object, domain=None, range=Optional[Union[dict, Any]]) - -slots.extractionResult__named_entities = Slot(uri=CORE.named_entities, name="extractionResult__named_entities", curie=CORE.curie('named_entities'), - model_uri=DRUG.extractionResult__named_entities, domain=None, range=Optional[Union[Union[dict, Any], List[Union[dict, Any]]]]) - -slots.namedEntity__id = Slot(uri=CORE.id, name="namedEntity__id", curie=CORE.curie('id'), - model_uri=DRUG.namedEntity__id, domain=None, range=URIRef) - -slots.namedEntity__label = Slot(uri=RDFS.label, name="namedEntity__label", curie=RDFS.curie('label'), - model_uri=DRUG.namedEntity__label, domain=None, range=Optional[str]) - -slots.triple__subject = Slot(uri=CORE.subject, name="triple__subject", curie=CORE.curie('subject'), - model_uri=DRUG.triple__subject, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__predicate = Slot(uri=CORE.predicate, name="triple__predicate", curie=CORE.curie('predicate'), - model_uri=DRUG.triple__predicate, domain=None, range=Optional[Union[str, RelationshipTypeId]]) - -slots.triple__object = Slot(uri=CORE.object, name="triple__object", curie=CORE.curie('object'), - model_uri=DRUG.triple__object, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__qualifier = Slot(uri=CORE.qualifier, name="triple__qualifier", curie=CORE.curie('qualifier'), - model_uri=DRUG.triple__qualifier, domain=None, range=Optional[str]) - -slots.triple__subject_qualifier = Slot(uri=CORE.subject_qualifier, name="triple__subject_qualifier", curie=CORE.curie('subject_qualifier'), - model_uri=DRUG.triple__subject_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__object_qualifier = Slot(uri=CORE.object_qualifier, name="triple__object_qualifier", curie=CORE.curie('object_qualifier'), - model_uri=DRUG.triple__object_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.textWithTriples__publication = Slot(uri=CORE.publication, name="textWithTriples__publication", curie=CORE.curie('publication'), - model_uri=DRUG.textWithTriples__publication, domain=None, range=Optional[Union[dict, Publication]]) - -slots.textWithTriples__triples = Slot(uri=CORE.triples, name="textWithTriples__triples", curie=CORE.curie('triples'), - model_uri=DRUG.textWithTriples__triples, domain=None, range=Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]]) - -slots.publication__id = Slot(uri=CORE.id, name="publication__id", curie=CORE.curie('id'), - model_uri=DRUG.publication__id, domain=None, range=Optional[str]) - -slots.publication__title = Slot(uri=CORE.title, name="publication__title", curie=CORE.curie('title'), - model_uri=DRUG.publication__title, domain=None, range=Optional[str]) - -slots.publication__abstract = Slot(uri=CORE.abstract, name="publication__abstract", curie=CORE.curie('abstract'), - model_uri=DRUG.publication__abstract, domain=None, range=Optional[str]) - -slots.publication__combined_text = Slot(uri=CORE.combined_text, name="publication__combined_text", curie=CORE.curie('combined_text'), - model_uri=DRUG.publication__combined_text, domain=None, range=Optional[str]) - -slots.publication__full_text = Slot(uri=CORE.full_text, name="publication__full_text", curie=CORE.curie('full_text'), - model_uri=DRUG.publication__full_text, domain=None, range=Optional[str]) - -slots.annotatorResult__subject_text = Slot(uri=CORE.subject_text, name="annotatorResult__subject_text", curie=CORE.curie('subject_text'), - model_uri=DRUG.annotatorResult__subject_text, domain=None, range=Optional[str]) - -slots.annotatorResult__object_id = Slot(uri=CORE.object_id, name="annotatorResult__object_id", curie=CORE.curie('object_id'), - model_uri=DRUG.annotatorResult__object_id, domain=None, range=Optional[str]) - -slots.annotatorResult__object_text = Slot(uri=CORE.object_text, name="annotatorResult__object_text", curie=CORE.curie('object_text'), - model_uri=DRUG.annotatorResult__object_text, domain=None, range=Optional[str]) \ No newline at end of file diff --git a/projects/drug/excel/drug.xlsx b/projects/drug/excel/drug.xlsx deleted file mode 100644 index c439fd633..000000000 Binary files a/projects/drug/excel/drug.xlsx and /dev/null differ diff --git a/projects/drug/graphql/drug.graphql b/projects/drug/graphql/drug.graphql deleted file mode 100644 index e0915eee8..000000000 --- a/projects/drug/graphql/drug.graphql +++ /dev/null @@ -1,103 +0,0 @@ -type AnnotatorResult - { - subjectText: String - objectId: String - objectText: String - } - -type Any - { - } - -interface CompoundExpression - { - } - -type Disease - { - id: String! - label: String - } - -type Drug - { - id: String! - label: String - } - -type DrugMechanism - { - disease: Disease - drug: Drug - mechanismLinks: [MechanismLink] - references: [String] - sourceText: String - } - -type ExtractionResult - { - inputId: String - inputTitle: String - inputText: String - rawCompletionOutput: String - prompt: String - extractedObject: Any - namedEntities: [Any] - } - -type MechanismElement - { - id: String! - label: String - } - -type MechanismLink - { - subject: MechanismElement - predicate: Predicate - object: MechanismElement - } - -interface NamedEntity - { - id: String! - label: String - } - -type Predicate - { - id: String! - label: String - } - -type Publication - { - id: String - title: String - abstract: String - combinedText: String - fullText: String - } - -type RelationshipType - { - id: String! - label: String - } - -type TextWithTriples - { - publication: Publication - triples: [Triple] - } - -interface Triple - { - subject: NamedEntity - predicate: RelationshipType - object: NamedEntity - qualifier: String - subjectQualifier: NamedEntity - objectQualifier: NamedEntity - } - diff --git a/projects/drug/jsonld/drug.context.jsonld b/projects/drug/jsonld/drug.context.jsonld deleted file mode 100644 index 55aab6d3c..000000000 --- a/projects/drug/jsonld/drug.context.jsonld +++ /dev/null @@ -1,137 +0,0 @@ -{ - "comments": { - "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2023-08-07T10:52:43", - "source": "drug.yaml" - }, - "@context": { - "HGNC": "http://example.org/UNKNOWN/HGNC/", - "MESH": "http://example.org/UNKNOWN/MESH/", - "RO": { - "@id": "http://purl.obolibrary.org/obo/RO_", - "@prefix": true - }, - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "drug": { - "@type": "@id" - }, - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "@vocab": "http://w3id.org/ontogpt/drug/", - "object_id": { - "@id": "core:object_id" - }, - "object_text": { - "@id": "core:object_text" - }, - "subject_text": { - "@id": "core:subject_text" - }, - "disease": { - "@type": "@id" - }, - "mechanism_links": { - "@type": "@id" - }, - "extracted_object": { - "@type": "@id", - "@id": "core:extracted_object" - }, - "input_id": { - "@id": "core:input_id" - }, - "input_text": { - "@id": "core:input_text" - }, - "input_title": { - "@id": "core:input_title" - }, - "named_entities": { - "@type": "@id", - "@id": "core:named_entities" - }, - "prompt": { - "@id": "core:prompt" - }, - "raw_completion_output": { - "@id": "core:raw_completion_output" - }, - "object": { - "@type": "@id", - "@id": "core:object" - }, - "predicate": { - "@type": "@id", - "@id": "core:predicate" - }, - "subject": { - "@type": "@id", - "@id": "core:subject" - }, - "id": { - "@id": "core:id" - }, - "label": { - "@id": "rdfs:label" - }, - "abstract": { - "@id": "core:abstract" - }, - "combined_text": { - "@id": "core:combined_text" - }, - "full_text": { - "@id": "core:full_text" - }, - "title": { - "@id": "core:title" - }, - "publication": { - "@type": "@id", - "@id": "core:publication" - }, - "triples": { - "@type": "@id", - "@id": "core:triples" - }, - "object_qualifier": { - "@type": "@id", - "@id": "core:object_qualifier" - }, - "qualifier": { - "@id": "core:qualifier" - }, - "subject_qualifier": { - "@type": "@id", - "@id": "core:subject_qualifier" - }, - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } - } -} diff --git a/projects/drug/jsonld/drug.jsonld b/projects/drug/jsonld/drug.jsonld deleted file mode 100644 index bacf82f23..000000000 --- a/projects/drug/jsonld/drug.jsonld +++ /dev/null @@ -1,1264 +0,0 @@ -{ - "name": "drug", - "description": "A template for Drugs and drug mechanism", - "title": "Drug Template", - "id": "http://w3id.org/ontogpt/drug", - "imports": [ - "linkml:types", - "core" - ], - "license": "https://creativecommons.org/publicdomain/zero/1.0/", - "prefixes": [ - { - "prefix_prefix": "linkml", - "prefix_reference": "https://w3id.org/linkml/" - }, - { - "prefix_prefix": "drug", - "prefix_reference": "http://w3id.org/ontogpt/drug/" - } - ], - "default_prefix": "drug", - "default_range": "string", - "types": [ - { - "name": "string", - "definition_uri": "https://w3id.org/linkml/String", - "description": "A character string", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Text" - ], - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "@type": "TypeDefinition" - }, - { - "name": "integer", - "definition_uri": "https://w3id.org/linkml/Integer", - "description": "An integer", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Integer" - ], - "base": "int", - "uri": "http://www.w3.org/2001/XMLSchema#integer", - "@type": "TypeDefinition" - }, - { - "name": "boolean", - "definition_uri": "https://w3id.org/linkml/Boolean", - "description": "A binary (true or false) value", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Boolean" - ], - "base": "Bool", - "uri": "http://www.w3.org/2001/XMLSchema#boolean", - "repr": "bool", - "@type": "TypeDefinition" - }, - { - "name": "float", - "definition_uri": "https://w3id.org/linkml/Float", - "description": "A real number that conforms to the xsd:float specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#float", - "@type": "TypeDefinition" - }, - { - "name": "double", - "definition_uri": "https://w3id.org/linkml/Double", - "description": "A real number that conforms to the xsd:double specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#double", - "@type": "TypeDefinition" - }, - { - "name": "decimal", - "definition_uri": "https://w3id.org/linkml/Decimal", - "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "broad_mappings": [ - "schema:Number" - ], - "base": "Decimal", - "uri": "http://www.w3.org/2001/XMLSchema#decimal", - "@type": "TypeDefinition" - }, - { - "name": "time", - "definition_uri": "https://w3id.org/linkml/Time", - "description": "A time object represents a (local) time of day, independent of any particular day", - "notes": [ - "URI is dateTime because OWL reasoners do not work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Time" - ], - "base": "XSDTime", - "uri": "http://www.w3.org/2001/XMLSchema#time", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date", - "definition_uri": "https://w3id.org/linkml/Date", - "description": "a date (year, month and day) in an idealized calendar", - "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Date" - ], - "base": "XSDDate", - "uri": "http://www.w3.org/2001/XMLSchema#date", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "datetime", - "definition_uri": "https://w3id.org/linkml/Datetime", - "description": "The combination of a date and time", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:DateTime" - ], - "base": "XSDDateTime", - "uri": "http://www.w3.org/2001/XMLSchema#dateTime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date_or_datetime", - "definition_uri": "https://w3id.org/linkml/DateOrDatetime", - "description": "Either a date or a datetime", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "https://w3id.org/linkml/DateOrDatetime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uriorcurie", - "definition_uri": "https://w3id.org/linkml/Uriorcurie", - "description": "a URI or a CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "URIorCURIE", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "curie", - "definition_uri": "https://w3id.org/linkml/Curie", - "conforms_to": "https://www.w3.org/TR/curie/", - "description": "a compact URI", - "comments": [ - "in RDF serializations this MUST be expanded to a URI", - "in non-RDF serializations MAY be serialized as the compact representation" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "Curie", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uri", - "definition_uri": "https://w3id.org/linkml/Uri", - "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", - "description": "a complete URI", - "comments": [ - "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:URL" - ], - "base": "URI", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "ncname", - "definition_uri": "https://w3id.org/linkml/Ncname", - "description": "Prefix part of CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NCName", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "objectidentifier", - "definition_uri": "https://w3id.org/linkml/Objectidentifier", - "description": "A URI or CURIE that represents an object in the model.", - "comments": [ - "Used for inheritance and type checking" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "ElementIdentifier", - "uri": "http://www.w3.org/ns/shex#iri", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "nodeidentifier", - "definition_uri": "https://w3id.org/linkml/Nodeidentifier", - "description": "A URI, CURIE or BNODE that represents a node in a model.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NodeIdentifier", - "uri": "http://www.w3.org/ns/shex#nonLiteral", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpointer", - "definition_uri": "https://w3id.org/linkml/Jsonpointer", - "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901", - "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpath", - "definition_uri": "https://w3id.org/linkml/Jsonpath", - "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html", - "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "sparqlpath", - "definition_uri": "https://w3id.org/linkml/Sparqlpath", - "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths", - "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - } - ], - "enums": [ - { - "name": "NullDataOptions", - "definition_uri": "http://w3id.org/ontogpt/core/NullDataOptions", - "from_schema": "http://w3id.org/ontogpt/core", - "permissible_values": [ - { - "text": "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "meaning": "NCIT:C149701" - }, - { - "text": "NOT_APPLICABLE", - "meaning": "NCIT:C18902", - "aliases": [ - "not applicable", - "N/A" - ] - }, - { - "text": "NOT_MENTIONED" - } - ] - } - ], - "slots": [ - { - "name": "drugMechanism__disease", - "description": "the name of the disease that is treated", - "from_schema": "http://w3id.org/ontogpt/drug", - "slot_uri": "http://w3id.org/ontogpt/drug/disease", - "alias": "disease", - "owner": "DrugMechanism", - "domain_of": [ - "DrugMechanism" - ], - "range": "Disease", - "@type": "SlotDefinition" - }, - { - "name": "drugMechanism__drug", - "description": "the name of the drug that treats the disease", - "from_schema": "http://w3id.org/ontogpt/drug", - "slot_uri": "http://w3id.org/ontogpt/drug/drug", - "alias": "drug", - "owner": "DrugMechanism", - "domain_of": [ - "DrugMechanism" - ], - "range": "Drug", - "@type": "SlotDefinition" - }, - { - "name": "drugMechanism__mechanism_links", - "description": "semicolon-separated list of links, where each link is a triple connecting two entities via a relationship type", - "from_schema": "http://w3id.org/ontogpt/drug", - "slot_uri": "http://w3id.org/ontogpt/drug/mechanism_links", - "multivalued": true, - "alias": "mechanism_links", - "owner": "DrugMechanism", - "domain_of": [ - "DrugMechanism" - ], - "range": "MechanismLink", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "drugMechanism__references", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/drug", - "slot_uri": "http://w3id.org/ontogpt/drug/references", - "multivalued": true, - "alias": "references", - "owner": "DrugMechanism", - "domain_of": [ - "DrugMechanism" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "drugMechanism__source_text", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/drug", - "slot_uri": "http://w3id.org/ontogpt/drug/source_text", - "alias": "source_text", - "owner": "DrugMechanism", - "domain_of": [ - "DrugMechanism" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "mechanismLink__subject", - "from_schema": "http://w3id.org/ontogpt/drug", - "slot_uri": "http://w3id.org/ontogpt/drug/subject", - "alias": "subject", - "owner": "MechanismLink", - "domain_of": [ - "MechanismLink" - ], - "range": "MechanismElement", - "@type": "SlotDefinition" - }, - { - "name": "mechanismLink__predicate", - "from_schema": "http://w3id.org/ontogpt/drug", - "slot_uri": "http://w3id.org/ontogpt/drug/predicate", - "alias": "predicate", - "owner": "MechanismLink", - "domain_of": [ - "MechanismLink" - ], - "range": "Predicate", - "@type": "SlotDefinition" - }, - { - "name": "mechanismLink__object", - "from_schema": "http://w3id.org/ontogpt/drug", - "slot_uri": "http://w3id.org/ontogpt/drug/object", - "alias": "object", - "owner": "MechanismLink", - "domain_of": [ - "MechanismLink" - ], - "range": "MechanismElement", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_id", - "alias": "input_id", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_title", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_title", - "alias": "input_title", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_text", - "alias": "input_text", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__raw_completion_output", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/raw_completion_output", - "alias": "raw_completion_output", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__prompt", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/prompt", - "alias": "prompt", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__extracted_object", - "description": "The complex objects extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/extracted_object", - "alias": "extracted_object", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__named_entities", - "description": "Named entities extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/named_entities", - "multivalued": true, - "alias": "named_entities", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "identifier": true, - "alias": "id", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "required": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "from_schema": "http://w3id.org/ontogpt/core", - "aliases": [ - "name" - ], - "mappings": [ - "http://example.org/UNKNOWN/rdfs/label" - ], - "slot_uri": "http://example.org/UNKNOWN/rdfs/label", - "alias": "label", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject", - "alias": "subject", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__predicate", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/predicate", - "alias": "predicate", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "triple__object", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object", - "alias": "object", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/qualifier", - "alias": "qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_qualifier", - "alias": "subject_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_qualifier", - "alias": "object_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/publication", - "alias": "publication", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__triples", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/triples", - "multivalued": true, - "alias": "triples", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "publication__id", - "description": "The publication identifier", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "alias": "id", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__title", - "description": "The title of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/title", - "alias": "title", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__abstract", - "description": "The abstract of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/abstract", - "alias": "abstract", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__combined_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/combined_text", - "alias": "combined_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__full_text", - "description": "The full text of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/full_text", - "alias": "full_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__subject_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_text", - "alias": "subject_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_id", - "alias": "object_id", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_text", - "alias": "object_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - } - ], - "classes": [ - { - "name": "DrugMechanism", - "definition_uri": "http://w3id.org/ontogpt/drug/DrugMechanism", - "from_schema": "http://w3id.org/ontogpt/drug", - "slots": [ - "drugMechanism__disease", - "drugMechanism__drug", - "drugMechanism__mechanism_links", - "drugMechanism__references", - "drugMechanism__source_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "disease", - "description": "the name of the disease that is treated", - "range": "Disease", - "@type": "SlotDefinition" - }, - { - "name": "drug", - "description": "the name of the drug that treats the disease", - "range": "Drug", - "@type": "SlotDefinition" - }, - { - "name": "mechanism_links", - "description": "semicolon-separated list of links, where each link is a triple connecting two entities via a relationship type", - "multivalued": true, - "range": "MechanismLink", - "@type": "SlotDefinition" - }, - { - "name": "references", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "multivalued": true, - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "source_text", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "range": "string", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/drug/DrugMechanism", - "tree_root": true, - "@type": "ClassDefinition" - }, - { - "name": "MechanismElement", - "id_prefixes": [ - "HGNC", - "MESH" - ], - "definition_uri": "http://w3id.org/ontogpt/drug/MechanismElement", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:go, sqlite:obo:mesh, sqlite:obo:uberon, sqlite:obo:pr, sqlite:obo:ncbitaxon, sqlite:obo:cl", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/drug", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/drug/MechanismElement", - "@type": "ClassDefinition" - }, - { - "name": "Disease", - "definition_uri": "http://w3id.org/ontogpt/drug/Disease", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:mesh, sqlite:obo:mondo", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/drug", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/drug/Disease", - "@type": "ClassDefinition" - }, - { - "name": "Drug", - "definition_uri": "http://w3id.org/ontogpt/drug/Drug", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:drugbank, sqlite:obo:chebi, sqlite:obo:mesh", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/drug", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/drug/Drug", - "@type": "ClassDefinition" - }, - { - "name": "Predicate", - "definition_uri": "http://w3id.org/ontogpt/drug/Predicate", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:biolink, sqlite:obo:ro", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/drug", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/drug/Predicate", - "@type": "ClassDefinition" - }, - { - "name": "MechanismLink", - "definition_uri": "http://w3id.org/ontogpt/drug/MechanismLink", - "from_schema": "http://w3id.org/ontogpt/drug", - "is_a": "CompoundExpression", - "slots": [ - "mechanismLink__subject", - "mechanismLink__predicate", - "mechanismLink__object" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject", - "range": "MechanismElement", - "@type": "SlotDefinition" - }, - { - "name": "predicate", - "range": "Predicate", - "@type": "SlotDefinition" - }, - { - "name": "object", - "range": "MechanismElement", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/drug/MechanismLink", - "@type": "ClassDefinition" - }, - { - "name": "Any", - "definition_uri": "http://w3id.org/ontogpt/core/Any", - "from_schema": "http://w3id.org/ontogpt/core", - "mappings": [ - "linkml:Any" - ], - "slot_usage": {}, - "class_uri": "https://w3id.org/linkml/Any", - "@type": "ClassDefinition" - }, - { - "name": "ExtractionResult", - "definition_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "description": "A result of extracting knowledge on text", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "extractionResult__input_id", - "extractionResult__input_title", - "extractionResult__input_text", - "extractionResult__raw_completion_output", - "extractionResult__prompt", - "extractionResult__extracted_object", - "extractionResult__named_entities" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "input_id", - "@type": "SlotDefinition" - }, - { - "name": "input_title", - "@type": "SlotDefinition" - }, - { - "name": "input_text", - "@type": "SlotDefinition" - }, - { - "name": "raw_completion_output", - "@type": "SlotDefinition" - }, - { - "name": "prompt", - "@type": "SlotDefinition" - }, - { - "name": "extracted_object", - "description": "The complex objects extracted from the text", - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "named_entities", - "description": "Named entities extracted from the text", - "multivalued": true, - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "@type": "ClassDefinition" - }, - { - "name": "NamedEntity", - "definition_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "identifier": true, - "@type": "SlotDefinition" - }, - { - "name": "label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "aliases": [ - "name" - ], - "slot_uri": "rdfs:label", - "range": "string", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "@type": "ClassDefinition" - }, - { - "name": "CompoundExpression", - "definition_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "@type": "ClassDefinition" - }, - { - "name": "Triple", - "definition_uri": "http://w3id.org/ontogpt/core/Triple", - "description": "Abstract parent for Relation Extraction tasks", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "CompoundExpression", - "abstract": true, - "slots": [ - "triple__subject", - "triple__predicate", - "triple__object", - "triple__qualifier", - "triple__subject_qualifier", - "triple__object_qualifier" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "predicate", - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "object", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Triple", - "@type": "ClassDefinition" - }, - { - "name": "TextWithTriples", - "definition_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "textWithTriples__publication", - "textWithTriples__triples" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "triples", - "multivalued": true, - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "@type": "ClassDefinition" - }, - { - "name": "RelationshipType", - "id_prefixes": [ - "RO", - "biolink" - ], - "definition_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "@type": "ClassDefinition" - }, - { - "name": "Publication", - "definition_uri": "http://w3id.org/ontogpt/core/Publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "publication__id", - "publication__title", - "publication__abstract", - "publication__combined_text", - "publication__full_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "description": "The publication identifier", - "@type": "SlotDefinition" - }, - { - "name": "title", - "description": "The title of the publication", - "@type": "SlotDefinition" - }, - { - "name": "abstract", - "description": "The abstract of the publication", - "@type": "SlotDefinition" - }, - { - "name": "combined_text", - "@type": "SlotDefinition" - }, - { - "name": "full_text", - "description": "The full text of the publication", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Publication", - "@type": "ClassDefinition" - }, - { - "name": "AnnotatorResult", - "definition_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "annotatorResult__subject_text", - "annotatorResult__object_id", - "annotatorResult__object_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject_text", - "@type": "SlotDefinition" - }, - { - "name": "object_id", - "@type": "SlotDefinition" - }, - { - "name": "object_text", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "@type": "ClassDefinition" - } - ], - "metamodel_version": "1.7.0", - "source_file": "drug.yaml", - "source_file_date": "2023-06-17T15:11:19", - "source_file_size": 1856, - "generation_date": "2023-08-07T10:52:43", - "@type": "SchemaDefinition", - "@context": [ - "projects/drug/jsonld/drug.context.jsonld", - "https://w3id.org/linkml/types.context.jsonld", - "core.context.jsonld", - { - "@base": "http://w3id.org/ontogpt/drug/" - } - ] -} diff --git a/projects/drug/jsonschema/drug.schema.json b/projects/drug/jsonschema/drug.schema.json deleted file mode 100644 index 46c9c9bf6..000000000 --- a/projects/drug/jsonschema/drug.schema.json +++ /dev/null @@ -1,292 +0,0 @@ -{ - "$defs": { - "AnnotatorResult": { - "additionalProperties": false, - "description": "", - "properties": { - "object_id": { - "type": "string" - }, - "object_text": { - "type": "string" - }, - "subject_text": { - "type": "string" - } - }, - "title": "AnnotatorResult", - "type": "object" - }, - "Any": { - "additionalProperties": true, - "description": "", - "title": "Any", - "type": "object" - }, - "Disease": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Disease", - "type": "object" - }, - "Drug": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Drug", - "type": "object" - }, - "DrugMechanism": { - "additionalProperties": false, - "description": "", - "properties": { - "disease": { - "description": "the name of the disease that is treated", - "type": "string" - }, - "drug": { - "description": "the name of the drug that treats the disease", - "type": "string" - }, - "mechanism_links": { - "description": "semicolon-separated list of links, where each link is a triple connecting two entities via a relationship type", - "items": { - "$ref": "#/$defs/MechanismLink" - }, - "type": "array" - }, - "references": { - "items": { - "type": "string" - }, - "type": "array" - }, - "source_text": { - "type": "string" - } - }, - "title": "DrugMechanism", - "type": "object" - }, - "ExtractionResult": { - "additionalProperties": false, - "description": "A result of extracting knowledge on text", - "properties": { - "extracted_object": { - "$ref": "#/$defs/Any", - "description": "The complex objects extracted from the text" - }, - "input_id": { - "type": "string" - }, - "input_text": { - "type": "string" - }, - "input_title": { - "type": "string" - }, - "named_entities": { - "description": "Named entities extracted from the text", - "items": { - "$ref": "#/$defs/Any" - }, - "type": "array" - }, - "prompt": { - "type": "string" - }, - "raw_completion_output": { - "type": "string" - } - }, - "title": "ExtractionResult", - "type": "object" - }, - "MechanismElement": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "MechanismElement", - "type": "object" - }, - "MechanismLink": { - "additionalProperties": false, - "description": "", - "properties": { - "object": { - "type": "string" - }, - "predicate": { - "type": "string" - }, - "subject": { - "type": "string" - } - }, - "title": "MechanismLink", - "type": "object" - }, - "NullDataOptions": { - "description": "", - "enum": [ - "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "NOT_APPLICABLE", - "NOT_MENTIONED" - ], - "title": "NullDataOptions", - "type": "string" - }, - "Predicate": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Predicate", - "type": "object" - }, - "Publication": { - "additionalProperties": false, - "description": "", - "properties": { - "abstract": { - "description": "The abstract of the publication", - "type": "string" - }, - "combined_text": { - "type": "string" - }, - "full_text": { - "description": "The full text of the publication", - "type": "string" - }, - "id": { - "description": "The publication identifier", - "type": "string" - }, - "title": { - "description": "The title of the publication", - "type": "string" - } - }, - "title": "Publication", - "type": "object" - }, - "RelationshipType": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "RelationshipType", - "type": "object" - }, - "TextWithTriples": { - "additionalProperties": false, - "description": "", - "properties": { - "publication": { - "$ref": "#/$defs/Publication" - }, - "triples": { - "items": { - "$ref": "#/$defs/Triple" - }, - "type": "array" - } - }, - "title": "TextWithTriples", - "type": "object" - } - }, - "$id": "http://w3id.org/ontogpt/drug", - "$schema": "http://json-schema.org/draft-07/schema#", - "additionalProperties": true, - "metamodel_version": "1.7.0", - "properties": { - "disease": { - "description": "the name of the disease that is treated", - "type": "string" - }, - "drug": { - "description": "the name of the drug that treats the disease", - "type": "string" - }, - "mechanism_links": { - "description": "semicolon-separated list of links, where each link is a triple connecting two entities via a relationship type", - "items": { - "$ref": "#/$defs/MechanismLink" - }, - "type": "array" - }, - "references": { - "items": { - "type": "string" - }, - "type": "array" - }, - "source_text": { - "type": "string" - } - }, - "title": "drug", - "type": "object", - "version": null -} \ No newline at end of file diff --git a/projects/drug/owl/drug.owl.ttl b/projects/drug/owl/drug.owl.ttl deleted file mode 100644 index 6fce7c4b0..000000000 --- a/projects/drug/owl/drug.owl.ttl +++ /dev/null @@ -1,473 +0,0 @@ -@prefix IAO: <http://purl.obolibrary.org/obo/IAO_> . -@prefix drug: <http://w3id.org/ontogpt/drug/> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix owl: <http://www.w3.org/2002/07/owl#> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . -@prefix skos: <http://www.w3.org/2004/02/skos/core#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -<http://w3id.org/ontogpt/drug> a owl:Ontology ; - rdfs:label "drug" ; - IAO:0000700 <http://w3id.org/ontogpt/core/AnnotatorResult>, - <http://w3id.org/ontogpt/core/Any>, - <http://w3id.org/ontogpt/core/CompoundExpression>, - <http://w3id.org/ontogpt/core/ExtractionResult>, - <http://w3id.org/ontogpt/core/NamedEntity>, - <http://w3id.org/ontogpt/core/Publication>, - <http://w3id.org/ontogpt/core/TextWithTriples>, - drug:DrugMechanism ; - linkml:classes "{'DrugMechanism': ClassDefinition(name='DrugMechanism', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/drug/DrugMechanism', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/drug', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['drugMechanism__disease', 'drugMechanism__drug', 'drugMechanism__mechanism_links', 'drugMechanism__references', 'drugMechanism__source_text'], slot_usage={}, attributes={'disease': SlotDefinition(name='disease', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the name of the disease that is treated', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Disease', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'drug': SlotDefinition(name='drug', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the name of the drug that treats the disease', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Drug', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'mechanism_links': SlotDefinition(name='mechanism_links', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of links, where each link is a triple connecting two entities via a relationship type', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='MechanismLink', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'references': SlotDefinition(name='references', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'source_text': SlotDefinition(name='source_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='drug:DrugMechanism', subclass_of=None, union_of=[], defining_slots=[], tree_root=True, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'MechanismElement': ClassDefinition(name='MechanismElement', id_prefixes=['HGNC', 'MESH'], definition_uri='http://w3id.org/ontogpt/drug/MechanismElement', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:go, sqlite:obo:mesh, sqlite:obo:uberon, sqlite:obo:pr, sqlite:obo:ncbitaxon, sqlite:obo:cl', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/drug', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='drug:MechanismElement', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Disease': ClassDefinition(name='Disease', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/drug/Disease', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:mesh, sqlite:obo:mondo', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/drug', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='drug:Disease', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Drug': ClassDefinition(name='Drug', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/drug/Drug', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:drugbank, sqlite:obo:chebi, sqlite:obo:mesh', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/drug', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='drug:Drug', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Predicate': ClassDefinition(name='Predicate', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/drug/Predicate', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:biolink, sqlite:obo:ro', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/drug', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='drug:Predicate', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'MechanismLink': ClassDefinition(name='MechanismLink', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/drug/MechanismLink', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/drug', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['mechanismLink__subject', 'mechanismLink__predicate', 'mechanismLink__object'], slot_usage={}, attributes={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='MechanismElement', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Predicate', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='MechanismElement', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='drug:MechanismLink', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Any': ClassDefinition(name='Any', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Any', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=['linkml:Any'], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='linkml:Any', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ExtractionResult': ClassDefinition(name='ExtractionResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/ExtractionResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A result of extracting knowledge on text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['extractionResult__input_id', 'extractionResult__input_title', 'extractionResult__input_text', 'extractionResult__raw_completion_output', 'extractionResult__prompt', 'extractionResult__extracted_object', 'extractionResult__named_entities'], slot_usage={}, attributes={'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:ExtractionResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'NamedEntity': ClassDefinition(name='NamedEntity', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NamedEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:NamedEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'CompoundExpression': ClassDefinition(name='CompoundExpression', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/CompoundExpression', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='core:CompoundExpression', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Triple': ClassDefinition(name='Triple', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Triple', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Abstract parent for Relation Extraction tasks', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['triple__subject', 'triple__predicate', 'triple__object', 'triple__qualifier', 'triple__subject_qualifier', 'triple__object_qualifier'], slot_usage={}, attributes={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Triple', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'TextWithTriples': ClassDefinition(name='TextWithTriples', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/TextWithTriples', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['textWithTriples__publication', 'textWithTriples__triples'], slot_usage={}, attributes={'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:TextWithTriples', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'RelationshipType': ClassDefinition(name='RelationshipType', id_prefixes=['RO', 'biolink'], definition_uri='http://w3id.org/ontogpt/core/RelationshipType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='core:RelationshipType', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Publication': ClassDefinition(name='Publication', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Publication', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['publication__id', 'publication__title', 'publication__abstract', 'publication__combined_text', 'publication__full_text'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Publication', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'AnnotatorResult': ClassDefinition(name='AnnotatorResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/AnnotatorResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['annotatorResult__subject_text', 'annotatorResult__object_id', 'annotatorResult__object_text'], slot_usage={}, attributes={'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:AnnotatorResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={})}" ; - linkml:enums "{'NullDataOptions': EnumDefinition(name='NullDataOptions', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NullDataOptions', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'UNSPECIFIED_METHOD_OF_ADMINISTRATION': PermissibleValue(text='UNSPECIFIED_METHOD_OF_ADMINISTRATION', description=None, meaning='NCIT:C149701', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_APPLICABLE': PermissibleValue(text='NOT_APPLICABLE', description=None, meaning='NCIT:C18902', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['not applicable', 'N/A'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_MENTIONED': PermissibleValue(text='NOT_MENTIONED', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[])}" ; - linkml:id "http://w3id.org/ontogpt/drug" ; - linkml:imports "core", - "linkml:types" ; - linkml:types "{'string': TypeDefinition(name='string', id_prefixes=[], definition_uri='https://w3id.org/linkml/String', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A character string', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Text'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'integer': TypeDefinition(name='integer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Integer', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An integer', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Integer'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='int', uri='xsd:integer', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'boolean': TypeDefinition(name='boolean', id_prefixes=[], definition_uri='https://w3id.org/linkml/Boolean', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A binary (true or false) value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Boolean'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Bool', uri='xsd:boolean', repr='bool', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'float': TypeDefinition(name='float', id_prefixes=[], definition_uri='https://w3id.org/linkml/Float', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:float specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Float'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:float', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'double': TypeDefinition(name='double', id_prefixes=[], definition_uri='https://w3id.org/linkml/Double', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:double specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:Float'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:double', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'decimal': TypeDefinition(name='decimal', id_prefixes=[], definition_uri='https://w3id.org/linkml/Decimal', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number with arbitrary precision that conforms to the xsd:decimal specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=['schema:Number'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Decimal', uri='xsd:decimal', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'time': TypeDefinition(name='time', id_prefixes=[], definition_uri='https://w3id.org/linkml/Time', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A time object represents a (local) time of day, independent of any particular day', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=['URI is dateTime because OWL reasoners do not work with straight date or time'], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Time'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDTime', uri='xsd:time', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date': TypeDefinition(name='date', id_prefixes=[], definition_uri='https://w3id.org/linkml/Date', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a date (year, month and day) in an idealized calendar', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[\"URI is dateTime because OWL reasoners don't work with straight date or time\"], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Date'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDate', uri='xsd:date', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'datetime': TypeDefinition(name='datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/Datetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The combination of a date and time', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:DateTime'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDateTime', uri='xsd:dateTime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date_or_datetime': TypeDefinition(name='date_or_datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/DateOrDatetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Either a date or a datetime', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='linkml:DateOrDatetime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uriorcurie': TypeDefinition(name='uriorcurie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uriorcurie', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a URI or a CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URIorCURIE', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'curie': TypeDefinition(name='curie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Curie', local_names={}, conforms_to='https://www.w3.org/TR/curie/', implements=[], extensions={}, annotations={}, description='a compact URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations this MUST be expanded to a URI', 'in non-RDF serializations MAY be serialized as the compact representation'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Curie', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uri': TypeDefinition(name='uri', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uri', local_names={}, conforms_to='https://www.ietf.org/rfc/rfc3987.txt', implements=[], extensions={}, annotations={}, description='a complete URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:URL'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URI', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ncname': TypeDefinition(name='ncname', id_prefixes=[], definition_uri='https://w3id.org/linkml/Ncname', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Prefix part of CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NCName', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'objectidentifier': TypeDefinition(name='objectidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Objectidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI or CURIE that represents an object in the model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['Used for inheritance and type checking'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='ElementIdentifier', uri='shex:iri', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'nodeidentifier': TypeDefinition(name='nodeidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Nodeidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI, CURIE or BNODE that represents a node in a model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NodeIdentifier', uri='shex:nonLiteral', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpointer': TypeDefinition(name='jsonpointer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpointer', local_names={}, conforms_to='https://datatracker.ietf.org/doc/html/rfc6901', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpath': TypeDefinition(name='jsonpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpath', local_names={}, conforms_to='https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sparqlpath': TypeDefinition(name='sparqlpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Sparqlpath', local_names={}, conforms_to='https://www.w3.org/TR/sparql11-query/#propertypaths', implements=[], extensions={}, annotations={}, description='A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:SubsetDefinition a owl:Class ; - rdfs:label "subset_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" . - -linkml:TypeDefinition a owl:Class ; - rdfs:label "type_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" ; - linkml:mixins "type_expression" . - -linkml:topValue a owl:DatatypeProperty ; - rdfs:label "value" . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "AnnotatorResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_text> ] ; - linkml:attributes "{'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/ExtractionResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ExtractionResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_title> ], - [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/named_entities> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/extracted_object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/prompt> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_id> ] ; - skos:definition "A result of extracting knowledge on text" ; - linkml:attributes "{'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/TextWithTriples> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TextWithTriples" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Triple> ; - owl:onProperty <http://w3id.org/ontogpt/core/triples> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Publication> ; - owl:onProperty <http://w3id.org/ontogpt/core/publication> ] ; - linkml:attributes "{'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/abstract> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "abstract" ; - rdfs:range linkml:String ; - skos:definition "The abstract of the publication" . - -<http://w3id.org/ontogpt/core/combined_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "combined_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/extracted_object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "extracted_object" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "The complex objects extracted from the text" . - -<http://w3id.org/ontogpt/core/full_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "full_text" ; - rdfs:range linkml:String ; - skos:definition "The full text of the publication" . - -<http://w3id.org/ontogpt/core/input_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_title" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/named_entities> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "named_entities" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "Named entities extracted from the text" . - -<http://w3id.org/ontogpt/core/object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/object_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/object_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" . - -<http://w3id.org/ontogpt/core/object_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/predicate> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "predicate" ; - rdfs:range <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/prompt> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "prompt" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/publication> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "publication" ; - drug:prompt.skip "true" ; - rdfs:range <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "qualifier" ; - rdfs:range linkml:String ; - skos:definition "A qualifier for the statements, e.g. \"NOT\" for negation" . - -<http://w3id.org/ontogpt/core/raw_completion_output> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "raw_completion_output" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/subject> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/subject_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" . - -<http://w3id.org/ontogpt/core/subject_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "title" ; - rdfs:range linkml:String ; - skos:definition "The title of the publication" . - -<http://w3id.org/ontogpt/core/triples> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "triples" ; - rdfs:range <http://w3id.org/ontogpt/core/Triple> . - -drug:DrugMechanism a owl:Class, - linkml:ClassDefinition ; - rdfs:label "DrugMechanism" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom drug:MechanismLink ; - owl:onProperty drug:mechanism_links ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass drug:Disease ; - owl:onProperty drug:disease ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass drug:Drug ; - owl:onProperty drug:drug ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty drug:source_text ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty drug:references ] ; - linkml:attributes "{'disease': SlotDefinition(name='disease', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the name of the disease that is treated', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Disease', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'drug': SlotDefinition(name='drug', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the name of the drug that treats the disease', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Drug', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'mechanism_links': SlotDefinition(name='mechanism_links', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of links, where each link is a triple connecting two entities via a relationship type', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='MechanismLink', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'references': SlotDefinition(name='references', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'source_text': SlotDefinition(name='source_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -drug:disease a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "disease" ; - rdfs:range drug:Disease ; - skos:definition "the name of the disease that is treated" . - -drug:drug a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "drug" ; - rdfs:range drug:Drug ; - skos:definition "the name of the drug that treats the disease" . - -drug:mechanism_links a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "mechanism_links" ; - rdfs:range drug:MechanismLink ; - skos:definition "semicolon-separated list of links, where each link is a triple connecting two entities via a relationship type" . - -drug:object a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object" ; - rdfs:range drug:MechanismElement . - -drug:predicate a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "predicate" ; - rdfs:range drug:Predicate . - -drug:references a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "references" ; - drug:prompt.skip "true" ; - rdfs:range linkml:String . - -drug:source_text a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "source_text" ; - drug:prompt.skip "true" ; - rdfs:range linkml:String . - -drug:subject a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject" ; - rdfs:range drug:MechanismElement . - -<http://example.org/UNKNOWN/rdfs/label> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "label" ; - drug:owl "AnnotationProperty, AnnotationAssertion" ; - rdfs:range linkml:String ; - skos:altLabel "name" ; - skos:definition "The label (name) of the named thing" ; - skos:exactMatch <http://example.org/UNKNOWN/rdfs/label> . - -<http://purl.obolibrary.org/obo/NCIT_C149701> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "UNSPECIFIED_METHOD_OF_ADMINISTRATION" . - -<http://purl.obolibrary.org/obo/NCIT_C18902> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_APPLICABLE" . - -<http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_MENTIONED" . - -<http://w3id.org/ontogpt/core/RelationshipType> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "RelationshipType" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/Triple> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Triple" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/RelationshipType> ; - owl:onProperty <http://w3id.org/ontogpt/core/predicate> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject> ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - skos:definition "Abstract parent for Relation Extraction tasks" ; - linkml:attributes "{'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -<http://w3id.org/ontogpt/core/id> a owl:ObjectProperty, - linkml:SlotDefinition . - -drug:Disease a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Disease" ; - drug:annotators "sqlite:obo:mesh, sqlite:obo:mondo" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -drug:Drug a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Drug" ; - drug:annotators "sqlite:obo:drugbank, sqlite:obo:chebi, sqlite:obo:mesh" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -drug:MechanismLink a owl:Class, - linkml:ClassDefinition ; - rdfs:label "MechanismLink" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass drug:MechanismElement ; - owl:onProperty drug:object ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass drug:Predicate ; - owl:onProperty drug:predicate ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass drug:MechanismElement ; - owl:onProperty drug:subject ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - linkml:attributes "{'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='MechanismElement', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Predicate', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='MechanismElement', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -drug:Predicate a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Predicate" ; - drug:annotators "sqlite:obo:biolink, sqlite:obo:ro" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/CompoundExpression> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CompoundExpression" ; - linkml:attributes "{}" . - -<http://w3id.org/ontogpt/core/NullDataOptions> a owl:Class, - linkml:EnumDefinition ; - rdfs:label "NullDataOptions" ; - owl:unionOf ( <http://purl.obolibrary.org/obo/NCIT_C149701> <http://purl.obolibrary.org/obo/NCIT_C18902> <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> ) ; - linkml:permissible_values <http://purl.obolibrary.org/obo/NCIT_C149701>, - <http://purl.obolibrary.org/obo/NCIT_C18902>, - <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> . - -<http://w3id.org/ontogpt/core/Publication> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Publication" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/abstract> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/title> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/combined_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/full_text> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -drug:MechanismElement a owl:Class, - linkml:ClassDefinition ; - rdfs:label "MechanismElement" ; - drug:annotators "sqlite:obo:go, sqlite:obo:mesh, sqlite:obo:uberon, sqlite:obo:pr, sqlite:obo:ncbitaxon, sqlite:obo:cl" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/Any> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Any" ; - skos:exactMatch linkml:Any ; - linkml:attributes "{}" . - -<http://w3id.org/ontogpt/core/NamedEntity> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "NamedEntity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://example.org/UNKNOWN/rdfs/label> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:ClassDefinition a owl:Class ; - rdfs:label "class_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "class_expression" . - -linkml:SlotDefinition a owl:Class ; - rdfs:label "slot_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "slot_expression" . - - diff --git a/projects/drug/prefixmap/drug.yaml b/projects/drug/prefixmap/drug.yaml deleted file mode 100644 index bda25fa94..000000000 --- a/projects/drug/prefixmap/drug.yaml +++ /dev/null @@ -1,37 +0,0 @@ -{ - "HGNC": "http://example.org/UNKNOWN/HGNC/", - "MESH": "http://example.org/UNKNOWN/MESH/", - "RO": "http://purl.obolibrary.org/obo/RO_", - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "drug": "http://w3id.org/ontogpt/drug/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } -} diff --git a/projects/drug/protobuf/drug.proto b/projects/drug/protobuf/drug.proto deleted file mode 100644 index fa063bf0e..000000000 --- a/projects/drug/protobuf/drug.proto +++ /dev/null @@ -1,69 +0,0 @@ -message AnnotatorResult - { - string subjectText = 0 - string objectId = 0 - string objectText = 0 - } -message Disease - { - string id = 0 - string label = 0 - } -message Drug - { - string id = 0 - string label = 0 - } -message DrugMechanism - { - disease disease = 0 - drug drug = 0 - repeated mechanismLink mechanismLinks = 0 - repeated string references = 0 - string sourceText = 0 - } -// A result of extracting knowledge on text -message ExtractionResult - { - string inputId = 0 - string inputTitle = 0 - string inputText = 0 - string rawCompletionOutput = 0 - string prompt = 0 - any extractedObject = 0 - repeated any namedEntities = 0 - } -message MechanismElement - { - string id = 0 - string label = 0 - } -message MechanismLink - { - mechanismElement subject = 0 - predicate predicate = 0 - mechanismElement object = 0 - } -message Predicate - { - string id = 0 - string label = 0 - } -message Publication - { - string id = 0 - string title = 0 - string abstract = 0 - string combinedText = 0 - string fullText = 0 - } -message RelationshipType - { - string id = 0 - string label = 0 - } -message TextWithTriples - { - publication publication = 0 - repeated triple triples = 0 - } diff --git a/projects/drug/shacl/drug.shacl.ttl b/projects/drug/shacl/drug.shacl.ttl deleted file mode 100644 index fd3029861..000000000 --- a/projects/drug/shacl/drug.shacl.ttl +++ /dev/null @@ -1,267 +0,0 @@ -@prefix drug: <http://w3id.org/ontogpt/drug/> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix sh: <http://www.w3.org/ns/shacl#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/object_id> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object_text> ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject_text> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/AnnotatorResult> . - -<http://w3id.org/ontogpt/core/CompoundExpression> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass <http://w3id.org/ontogpt/core/CompoundExpression> . - -<http://w3id.org/ontogpt/core/ExtractionResult> a sh:NodeShape ; - sh:closed true ; - sh:description "A result of extracting knowledge on text" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/prompt> ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/input_title> ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/input_id> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/input_text> ], - [ sh:class linkml:Any ; - sh:description "Named entities extracted from the text" ; - sh:nodeKind sh:BlankNode ; - sh:order 6 ; - sh:path <http://w3id.org/ontogpt/core/named_entities> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ sh:class linkml:Any ; - sh:description "The complex objects extracted from the text" ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/extracted_object> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/ExtractionResult> . - -<http://w3id.org/ontogpt/core/TextWithTriples> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/Publication> ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/publication> ], - [ sh:class <http://w3id.org/ontogpt/core/Triple> ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/triples> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/TextWithTriples> . - -drug:DrugMechanism a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class drug:Drug ; - sh:description "the name of the drug that treats the disease" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path drug:drug ], - [ sh:class drug:Disease ; - sh:description "the name of the disease that is treated" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path drug:disease ], - [ sh:maxCount 1 ; - sh:order 4 ; - sh:path drug:source_text ], - [ sh:order 3 ; - sh:path drug:references ], - [ sh:class drug:MechanismLink ; - sh:description "semicolon-separated list of links, where each link is a triple connecting two entities via a relationship type" ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path drug:mechanism_links ] ; - sh:targetClass drug:DrugMechanism . - -<http://w3id.org/ontogpt/core/Publication> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The abstract of the publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/abstract> ], - [ sh:description "The full text of the publication" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/full_text> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/combined_text> ], - [ sh:description "The title of the publication" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/title> ], - [ sh:description "The publication identifier" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/RelationshipType> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/Triple> a sh:NodeShape ; - sh:closed false ; - sh:description "Abstract parent for Relation Extraction tasks" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/object_qualifier> ], - [ sh:description "A qualifier for the statements, e.g. \"NOT\" for negation" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/RelationshipType> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/predicate> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Triple> . - -drug:Disease a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass drug:Disease . - -drug:Drug a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass drug:Drug . - -drug:MechanismLink a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class drug:MechanismElement ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path drug:object ], - [ sh:class drug:Predicate ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path drug:predicate ], - [ sh:class drug:MechanismElement ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path drug:subject ] ; - sh:targetClass drug:MechanismLink . - -drug:Predicate a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass drug:Predicate . - -drug:MechanismElement a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass drug:MechanismElement . - -linkml:Any a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass linkml:Any . - -<http://w3id.org/ontogpt/core/NamedEntity> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/NamedEntity> . - diff --git a/projects/drug/shex/drug.shex b/projects/drug/shex/drug.shex deleted file mode 100644 index 00f492f4d..000000000 --- a/projects/drug/shex/drug.shex +++ /dev/null @@ -1,190 +0,0 @@ -BASE <http://w3id.org/ontogpt/drug/> -PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> -PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> -PREFIX linkml: <https://w3id.org/linkml/> -PREFIX core: <http://w3id.org/ontogpt/core/> -PREFIX rdfs1: <http://example.org/UNKNOWN/rdfs/> - - -linkml:String xsd:string - -linkml:Integer xsd:integer - -linkml:Boolean xsd:boolean - -linkml:Float xsd:float - -linkml:Double xsd:double - -linkml:Decimal xsd:decimal - -linkml:Time xsd:time - -linkml:Date xsd:date - -linkml:Datetime xsd:dateTime - -linkml:DateOrDatetime linkml:DateOrDatetime - -linkml:Uriorcurie IRI - -linkml:Curie xsd:string - -linkml:Uri IRI - -linkml:Ncname xsd:string - -linkml:Objectidentifier IRI - -linkml:Nodeidentifier NONLITERAL - -linkml:Jsonpointer xsd:string - -linkml:Jsonpath xsd:string - -linkml:Sparqlpath xsd:string - -core:AnnotatorResult CLOSED { - ( $core:AnnotatorResult_tes ( core:subject_text @linkml:String ? ; - core:object_id @linkml:String ? ; - core:object_text @linkml:String ? - ) ; - rdf:type [ core:AnnotatorResult ] ? - ) -} - -core:Any CLOSED { - ( $core:Any_tes rdf:type . * ; - rdf:type [ linkml:Any ] ? - ) -} - -core:CompoundExpression ( - @<MechanismLink> OR @core:Triple -) - -core:CompoundExpression_struct { - ( $core:CompoundExpression_tes rdf:type . * ; - rdf:type [ core:CompoundExpression ] ? - ) -} - -<Disease> CLOSED { - ( $<Disease_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Disease> ] - ) -} - -<Drug> CLOSED { - ( $<Drug_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Drug> ] - ) -} - -<DrugMechanism> CLOSED { - ( $<DrugMechanism_tes> ( <disease> @<Disease> ? ; - <drug> @<Drug> ? ; - <mechanism_links> @<MechanismLink> * ; - <references> @linkml:String * ; - <source_text> @linkml:String ? - ) ; - rdf:type [ <DrugMechanism> ] ? - ) -} - -core:ExtractionResult CLOSED { - ( $core:ExtractionResult_tes ( core:input_id @linkml:String ? ; - core:input_title @linkml:String ? ; - core:input_text @linkml:String ? ; - core:raw_completion_output @linkml:String ? ; - core:prompt @linkml:String ? ; - core:extracted_object @core:Any ? ; - core:named_entities @core:Any * - ) ; - rdf:type [ core:ExtractionResult ] ? - ) -} - -<MechanismElement> CLOSED { - ( $<MechanismElement_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <MechanismElement> ] - ) -} - -<MechanismLink> CLOSED { - ( $<MechanismLink_tes> ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - <subject> @<MechanismElement> ? ; - <predicate> @<Predicate> ? ; - <object> @<MechanismElement> ? - ) ; - rdf:type [ <MechanismLink> ] ? - ) -} - -core:NamedEntity ( - @<Disease> OR @<Drug> OR @<MechanismElement> OR @<Predicate> OR @core:RelationshipType -) - -core:NamedEntity_struct { - ( $core:NamedEntity_tes rdfs1:label @linkml:String ? ; - rdf:type [ core:NamedEntity ] - ) -} - -<Predicate> CLOSED { - ( $<Predicate_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Predicate> ] - ) -} - -core:Publication CLOSED { - ( $core:Publication_tes ( core:id @linkml:String ? ; - core:title @linkml:String ? ; - core:abstract @linkml:String ? ; - core:combined_text @linkml:String ? ; - core:full_text @linkml:String ? - ) ; - rdf:type [ core:Publication ] ? - ) -} - -core:RelationshipType CLOSED { - ( $core:RelationshipType_tes ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ core:RelationshipType ] - ) -} - -core:TextWithTriples CLOSED { - ( $core:TextWithTriples_tes ( core:publication @core:Publication ? ; - core:triples @core:Triple * - ) ; - rdf:type [ core:TextWithTriples ] ? - ) -} - -core:Triple { - ( $core:Triple_tes ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - core:subject @core:NamedEntity ? ; - core:predicate @core:RelationshipType ? ; - core:object @core:NamedEntity ? ; - core:qualifier @linkml:String ? ; - core:subject_qualifier @core:NamedEntity ? ; - core:object_qualifier @core:NamedEntity ? - ) ; - rdf:type [ core:Triple ] ? - ) -} - - diff --git a/projects/drug/sqlschema/drug.sql b/projects/drug/sqlschema/drug.sql deleted file mode 100644 index ab9ffe6b0..000000000 --- a/projects/drug/sqlschema/drug.sql +++ /dev/null @@ -1,85 +0,0 @@ - - -CREATE TABLE "AnnotatorResult" ( - subject_text TEXT, - object_id TEXT, - object_text TEXT, - PRIMARY KEY (subject_text, object_id, object_text) -); - -CREATE TABLE "Disease" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Drug" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "ExtractionResult" ( - input_id TEXT, - input_title TEXT, - input_text TEXT, - raw_completion_output TEXT, - prompt TEXT, - extracted_object TEXT, - named_entities TEXT, - PRIMARY KEY (input_id, input_title, input_text, raw_completion_output, prompt, extracted_object, named_entities) -); - -CREATE TABLE "MechanismElement" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Predicate" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Publication" ( - id TEXT, - title TEXT, - abstract TEXT, - combined_text TEXT, - full_text TEXT, - PRIMARY KEY (id, title, abstract, combined_text, full_text) -); - -CREATE TABLE "RelationshipType" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "TextWithTriples" ( - publication TEXT, - triples TEXT, - PRIMARY KEY (publication, triples) -); - -CREATE TABLE "DrugMechanism" ( - disease TEXT, - drug TEXT, - mechanism_links TEXT, - "references" TEXT, - source_text TEXT, - PRIMARY KEY (disease, drug, mechanism_links, "references", source_text), - FOREIGN KEY(disease) REFERENCES "Disease" (id), - FOREIGN KEY(drug) REFERENCES "Drug" (id) -); - -CREATE TABLE "MechanismLink" ( - subject TEXT, - predicate TEXT, - object TEXT, - PRIMARY KEY (subject, predicate, object), - FOREIGN KEY(subject) REFERENCES "MechanismElement" (id), - FOREIGN KEY(predicate) REFERENCES "Predicate" (id), - FOREIGN KEY(object) REFERENCES "MechanismElement" (id) -); diff --git a/projects/environmental_metadata/docs/AnnotatorResult.md b/projects/environmental_metadata/docs/AnnotatorResult.md deleted file mode 100644 index 6060db730..000000000 --- a/projects/environmental_metadata/docs/AnnotatorResult.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Class: AnnotatorResult - - - - -URI: [envmd:AnnotatorResult](http://w3id.org/ontogpt/environmental-metadataAnnotatorResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F])](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F]) - -## Attributes - - -### Own - - * [➞subject_text](annotatorResult__subject_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_id](annotatorResult__object_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_text](annotatorResult__object_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) diff --git a/projects/environmental_metadata/docs/Any.md b/projects/environmental_metadata/docs/Any.md deleted file mode 100644 index e42f52283..000000000 --- a/projects/environmental_metadata/docs/Any.md +++ /dev/null @@ -1,25 +0,0 @@ - -# Class: Any - - - - -URI: [envmd:Any](http://w3id.org/ontogpt/environmental-metadataAny) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult])](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult]) - -## Referenced by Class - - * **None** *[➞extracted_object](extractionResult__extracted_object.md)* <sub>0..1</sub> **[Any](Any.md)** - * **None** *[➞named_entities](extractionResult__named_entities.md)* <sub>0..\*</sub> **[Any](Any.md)** - -## Attributes - - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | linkml:Any | - diff --git a/projects/environmental_metadata/docs/CompoundExpression.md b/projects/environmental_metadata/docs/CompoundExpression.md deleted file mode 100644 index eff1887aa..000000000 --- a/projects/environmental_metadata/docs/CompoundExpression.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: CompoundExpression - - - - -URI: [envmd:CompoundExpression](http://w3id.org/ontogpt/environmental-metadataCompoundExpression) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[CompoundExpression]^-[Triple])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[CompoundExpression]^-[Triple]) - -## Children - - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - -## Referenced by Class - - -## Attributes - diff --git a/projects/environmental_metadata/docs/Dataset.md b/projects/environmental_metadata/docs/Dataset.md deleted file mode 100644 index d54b0e9e2..000000000 --- a/projects/environmental_metadata/docs/Dataset.md +++ /dev/null @@ -1,33 +0,0 @@ - -# Class: Dataset - - - - -URI: [envmd:Dataset](http://w3id.org/ontogpt/environmental-metadataDataset) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Topic],[Method],[Location],[EnvironmentalMaterial],[Environment],[Method]<methods%200..*-%20[Dataset|packageid:string%20%3F],[Environment]<environments%200..*-%20[Dataset],[EnvironmentalMaterial]<environmental_material%200..*-%20[Dataset],[Location]<location%200..*-%20[Dataset],[Topic]<topic%200..*-%20[Dataset])](https://yuml.me/diagram/nofunky;dir:TB/class/[Topic],[Method],[Location],[EnvironmentalMaterial],[Environment],[Method]<methods%200..*-%20[Dataset|packageid:string%20%3F],[Environment]<environments%200..*-%20[Dataset],[EnvironmentalMaterial]<environmental_material%200..*-%20[Dataset],[Location]<location%200..*-%20[Dataset],[Topic]<topic%200..*-%20[Dataset]) - -## Attributes - - -### Own - - * [➞packageid](dataset__packageid.md) <sub>0..1</sub> - * Description: The internal identifier for the dataset - * Range: [String](types/String.md) - * [➞topic](dataset__topic.md) <sub>0..\*</sub> - * Description: the general scientific area of study concerning the sample(s) - * Range: [Topic](Topic.md) - * [➞location](dataset__location.md) <sub>0..\*</sub> - * Description: the geographic location where the sample was isolated - * Range: [Location](Location.md) - * [➞environmental_material](dataset__environmental_material.md) <sub>0..\*</sub> - * Description: the environmental material that was sampled - * Range: [EnvironmentalMaterial](EnvironmentalMaterial.md) - * [➞environments](dataset__environments.md) <sub>0..\*</sub> - * Description: the environmental context in which the study was conducted - * Range: [Environment](Environment.md) - * [➞methods](dataset__methods.md) <sub>0..\*</sub> - * Range: [Method](Method.md) diff --git a/projects/environmental_metadata/docs/Environment.md b/projects/environmental_metadata/docs/Environment.md deleted file mode 100644 index 851d23f7a..000000000 --- a/projects/environmental_metadata/docs/Environment.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: Environment - - - - -URI: [envmd:Environment](http://w3id.org/ontogpt/environmental-metadataEnvironment) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[Dataset]-%20environments%200..*>[Environment|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Environment],[Dataset])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[Dataset]-%20environments%200..*>[Environment|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Environment],[Dataset]) - -## Identifier prefixes - - * ENVO - * ENVTHES - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞environments](dataset__environments.md)* <sub>0..\*</sub> **[Environment](Environment.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/environmental_metadata/docs/EnvironmentalMaterial.md b/projects/environmental_metadata/docs/EnvironmentalMaterial.md deleted file mode 100644 index 79a2834c0..000000000 --- a/projects/environmental_metadata/docs/EnvironmentalMaterial.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: EnvironmentalMaterial - - - - -URI: [envmd:EnvironmentalMaterial](http://w3id.org/ontogpt/environmental-metadataEnvironmentalMaterial) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[Dataset]-%20environmental_material%200..*>[EnvironmentalMaterial|id(i):string;label(i):string%20%3F],[NamedEntity]^-[EnvironmentalMaterial],[Dataset])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[Dataset]-%20environmental_material%200..*>[EnvironmentalMaterial|id(i):string;label(i):string%20%3F],[NamedEntity]^-[EnvironmentalMaterial],[Dataset]) - -## Identifier prefixes - - * ENVO - * ENVTHES - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞environmental_material](dataset__environmental_material.md)* <sub>0..\*</sub> **[EnvironmentalMaterial](EnvironmentalMaterial.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/environmental_metadata/docs/ExtractionResult.md b/projects/environmental_metadata/docs/ExtractionResult.md deleted file mode 100644 index e390e42ee..000000000 --- a/projects/environmental_metadata/docs/ExtractionResult.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Class: ExtractionResult - - -A result of extracting knowledge on text - -URI: [envmd:ExtractionResult](http://w3id.org/ontogpt/environmental-metadataExtractionResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any])](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any]) - -## Attributes - - -### Own - - * [➞input_id](extractionResult__input_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_title](extractionResult__input_title.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_text](extractionResult__input_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞prompt](extractionResult__prompt.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞extracted_object](extractionResult__extracted_object.md) <sub>0..1</sub> - * Description: The complex objects extracted from the text - * Range: [Any](Any.md) - * [➞named_entities](extractionResult__named_entities.md) <sub>0..\*</sub> - * Description: Named entities extracted from the text - * Range: [Any](Any.md) diff --git a/projects/environmental_metadata/docs/Location.md b/projects/environmental_metadata/docs/Location.md deleted file mode 100644 index 10fcdee28..000000000 --- a/projects/environmental_metadata/docs/Location.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: Location - - - - -URI: [envmd:Location](http://w3id.org/ontogpt/environmental-metadataLocation) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[Dataset]-%20location%200..*>[Location|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Location],[Dataset])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[Dataset]-%20location%200..*>[Location|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Location],[Dataset]) - -## Identifier prefixes - - * ENVO - * GAZ - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞location](dataset__location.md)* <sub>0..\*</sub> **[Location](Location.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/environmental_metadata/docs/Method.md b/projects/environmental_metadata/docs/Method.md deleted file mode 100644 index dec9980fb..000000000 --- a/projects/environmental_metadata/docs/Method.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Method - - - - -URI: [envmd:Method](http://w3id.org/ontogpt/environmental-metadataMethod) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[Dataset]-%20methods%200..*>[Method|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Method],[Dataset])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[Dataset]-%20methods%200..*>[Method|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Method],[Dataset]) - -## Identifier prefixes - - * ENVTHES - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞methods](dataset__methods.md)* <sub>0..\*</sub> **[Method](Method.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/environmental_metadata/docs/NamedEntity.md b/projects/environmental_metadata/docs/NamedEntity.md deleted file mode 100644 index 1c075c09f..000000000 --- a/projects/environmental_metadata/docs/NamedEntity.md +++ /dev/null @@ -1,38 +0,0 @@ - -# Class: NamedEntity - - - - -URI: [envmd:NamedEntity](http://w3id.org/ontogpt/environmental-metadataNamedEntity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Topic],[RelationshipType],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[Topic],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[Method],[NamedEntity]^-[Location],[NamedEntity]^-[EnvironmentalMaterial],[NamedEntity]^-[Environment],[Triple],[Method],[Location],[EnvironmentalMaterial],[Environment])](https://yuml.me/diagram/nofunky;dir:TB/class/[Topic],[RelationshipType],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[Topic],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[Method],[NamedEntity]^-[Location],[NamedEntity]^-[EnvironmentalMaterial],[NamedEntity]^-[Environment],[Triple],[Method],[Location],[EnvironmentalMaterial],[Environment]) - -## Children - - * [Environment](Environment.md) - * [EnvironmentalMaterial](EnvironmentalMaterial.md) - * [Location](Location.md) - * [Method](Method.md) - * [RelationshipType](RelationshipType.md) - * [Topic](Topic.md) - -## Referenced by Class - - * **None** *[➞object](triple__object.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞object_qualifier](triple__object_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject](triple__subject.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject_qualifier](triple__subject_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - -## Attributes - - -### Own - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/environmental_metadata/docs/NullDataOptions.md b/projects/environmental_metadata/docs/NullDataOptions.md deleted file mode 100644 index 25a33076d..000000000 --- a/projects/environmental_metadata/docs/NullDataOptions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Enum: NullDataOptions - - - - -URI: [envmd:NullDataOptions](http://w3id.org/ontogpt/environmental-metadataNullDataOptions) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | -| UNSPECIFIED_METHOD_OF_ADMINISTRATION | | NCIT:C149701 | | -| NOT_APPLICABLE | | NCIT:C18902 | {'aliases': ['not applicable', 'N/A']} | -| NOT_MENTIONED | | | | - diff --git a/projects/environmental_metadata/docs/Publication.md b/projects/environmental_metadata/docs/Publication.md deleted file mode 100644 index 46dd3ee50..000000000 --- a/projects/environmental_metadata/docs/Publication.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Publication - - - - -URI: [envmd:Publication](http://w3id.org/ontogpt/environmental-metadataPublication) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples])](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples]) - -## Referenced by Class - - * **None** *[➞publication](textWithTriples__publication.md)* <sub>0..1</sub> **[Publication](Publication.md)** - -## Attributes - - -### Own - - * [➞id](publication__id.md) <sub>0..1</sub> - * Description: The publication identifier - * Range: [String](types/String.md) - * [➞title](publication__title.md) <sub>0..1</sub> - * Description: The title of the publication - * Range: [String](types/String.md) - * [➞abstract](publication__abstract.md) <sub>0..1</sub> - * Description: The abstract of the publication - * Range: [String](types/String.md) - * [➞combined_text](publication__combined_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞full_text](publication__full_text.md) <sub>0..1</sub> - * Description: The full text of the publication - * Range: [String](types/String.md) diff --git a/projects/environmental_metadata/docs/RelationshipType.md b/projects/environmental_metadata/docs/RelationshipType.md deleted file mode 100644 index 3145f0773..000000000 --- a/projects/environmental_metadata/docs/RelationshipType.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: RelationshipType - - - - -URI: [envmd:RelationshipType](http://w3id.org/ontogpt/environmental-metadataRelationshipType) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity]) - -## Identifier prefixes - - * RO - * biolink - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞predicate](triple__predicate.md)* <sub>0..1</sub> **[RelationshipType](RelationshipType.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/environmental_metadata/docs/TextWithTriples.md b/projects/environmental_metadata/docs/TextWithTriples.md deleted file mode 100644 index e67af9874..000000000 --- a/projects/environmental_metadata/docs/TextWithTriples.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: TextWithTriples - - - - -URI: [envmd:TextWithTriples](http://w3id.org/ontogpt/environmental-metadataTextWithTriples) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication]) - -## Attributes - - -### Own - - * [➞publication](textWithTriples__publication.md) <sub>0..1</sub> - * Range: [Publication](Publication.md) - * [➞triples](textWithTriples__triples.md) <sub>0..\*</sub> - * Range: [Triple](Triple.md) diff --git a/projects/environmental_metadata/docs/Topic.md b/projects/environmental_metadata/docs/Topic.md deleted file mode 100644 index 01162867d..000000000 --- a/projects/environmental_metadata/docs/Topic.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Topic - - - - -URI: [envmd:Topic](http://w3id.org/ontogpt/environmental-metadataTopic) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Dataset]-%20topic%200..*>[Topic|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Topic],[NamedEntity],[Dataset])](https://yuml.me/diagram/nofunky;dir:TB/class/[Dataset]-%20topic%200..*>[Topic|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Topic],[NamedEntity],[Dataset]) - -## Identifier prefixes - - * ENVTHES - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞topic](dataset__topic.md)* <sub>0..\*</sub> **[Topic](Topic.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/environmental_metadata/docs/Triple.md b/projects/environmental_metadata/docs/Triple.md deleted file mode 100644 index afeb4ff25..000000000 --- a/projects/environmental_metadata/docs/Triple.md +++ /dev/null @@ -1,39 +0,0 @@ - -# Class: Triple - - -Abstract parent for Relation Extraction tasks - -URI: [envmd:Triple](http://w3id.org/ontogpt/environmental-metadataTriple) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞triples](textWithTriples__triples.md)* <sub>0..\*</sub> **[Triple](Triple.md)** - -## Attributes - - -### Own - - * [➞subject](triple__subject.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞predicate](triple__predicate.md) <sub>0..1</sub> - * Range: [RelationshipType](RelationshipType.md) - * [➞object](triple__object.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞qualifier](triple__qualifier.md) <sub>0..1</sub> - * Description: A qualifier for the statements, e.g. "NOT" for negation - * Range: [String](types/String.md) - * [➞subject_qualifier](triple__subject_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - * Range: [NamedEntity](NamedEntity.md) - * [➞object_qualifier](triple__object_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * Range: [NamedEntity](NamedEntity.md) diff --git a/projects/environmental_metadata/docs/annotatorResult__object_id.md b/projects/environmental_metadata/docs/annotatorResult__object_id.md deleted file mode 100644 index 918a3ec02..000000000 --- a/projects/environmental_metadata/docs/annotatorResult__object_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_id - - - - -URI: [envmd:annotatorResult__object_id](http://w3id.org/ontogpt/environmental-metadataannotatorResult__object_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/environmental_metadata/docs/annotatorResult__object_text.md b/projects/environmental_metadata/docs/annotatorResult__object_text.md deleted file mode 100644 index 7c75cb72f..000000000 --- a/projects/environmental_metadata/docs/annotatorResult__object_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_text - - - - -URI: [envmd:annotatorResult__object_text](http://w3id.org/ontogpt/environmental-metadataannotatorResult__object_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/environmental_metadata/docs/annotatorResult__subject_text.md b/projects/environmental_metadata/docs/annotatorResult__subject_text.md deleted file mode 100644 index 4fadfa223..000000000 --- a/projects/environmental_metadata/docs/annotatorResult__subject_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_text - - - - -URI: [envmd:annotatorResult__subject_text](http://w3id.org/ontogpt/environmental-metadataannotatorResult__subject_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/environmental_metadata/docs/dataset__environmental_material.md b/projects/environmental_metadata/docs/dataset__environmental_material.md deleted file mode 100644 index c3140a16b..000000000 --- a/projects/environmental_metadata/docs/dataset__environmental_material.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: environmental_material - - -the environmental material that was sampled - -URI: [envmd:dataset__environmental_material](http://w3id.org/ontogpt/environmental-metadatadataset__environmental_material) - - -## Domain and Range - -None → <sub>0..\*</sub> [EnvironmentalMaterial](EnvironmentalMaterial.md) - -## Parents - - -## Children - - -## Used by - - * [Dataset](Dataset.md) diff --git a/projects/environmental_metadata/docs/dataset__environments.md b/projects/environmental_metadata/docs/dataset__environments.md deleted file mode 100644 index b721c3c1c..000000000 --- a/projects/environmental_metadata/docs/dataset__environments.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: environments - - -the environmental context in which the study was conducted - -URI: [envmd:dataset__environments](http://w3id.org/ontogpt/environmental-metadatadataset__environments) - - -## Domain and Range - -None → <sub>0..\*</sub> [Environment](Environment.md) - -## Parents - - -## Children - - -## Used by - - * [Dataset](Dataset.md) diff --git a/projects/environmental_metadata/docs/dataset__location.md b/projects/environmental_metadata/docs/dataset__location.md deleted file mode 100644 index 25e4348c9..000000000 --- a/projects/environmental_metadata/docs/dataset__location.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: location - - -the geographic location where the sample was isolated - -URI: [envmd:dataset__location](http://w3id.org/ontogpt/environmental-metadatadataset__location) - - -## Domain and Range - -None → <sub>0..\*</sub> [Location](Location.md) - -## Parents - - -## Children - - -## Used by - - * [Dataset](Dataset.md) diff --git a/projects/environmental_metadata/docs/dataset__methods.md b/projects/environmental_metadata/docs/dataset__methods.md deleted file mode 100644 index 6917e6adb..000000000 --- a/projects/environmental_metadata/docs/dataset__methods.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: methods - - - - -URI: [envmd:dataset__methods](http://w3id.org/ontogpt/environmental-metadatadataset__methods) - - -## Domain and Range - -None → <sub>0..\*</sub> [Method](Method.md) - -## Parents - - -## Children - - -## Used by - - * [Dataset](Dataset.md) diff --git a/projects/environmental_metadata/docs/dataset__packageid.md b/projects/environmental_metadata/docs/dataset__packageid.md deleted file mode 100644 index 892be96ae..000000000 --- a/projects/environmental_metadata/docs/dataset__packageid.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: packageid - - -The internal identifier for the dataset - -URI: [envmd:dataset__packageid](http://w3id.org/ontogpt/environmental-metadatadataset__packageid) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Dataset](Dataset.md) diff --git a/projects/environmental_metadata/docs/dataset__topic.md b/projects/environmental_metadata/docs/dataset__topic.md deleted file mode 100644 index c14c6d825..000000000 --- a/projects/environmental_metadata/docs/dataset__topic.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: topic - - -the general scientific area of study concerning the sample(s) - -URI: [envmd:dataset__topic](http://w3id.org/ontogpt/environmental-metadatadataset__topic) - - -## Domain and Range - -None → <sub>0..\*</sub> [Topic](Topic.md) - -## Parents - - -## Children - - -## Used by - - * [Dataset](Dataset.md) diff --git a/projects/environmental_metadata/docs/environmental_metadata.md b/projects/environmental_metadata/docs/environmental_metadata.md deleted file mode 100644 index ece03a5d6..000000000 --- a/projects/environmental_metadata/docs/environmental_metadata.md +++ /dev/null @@ -1,115 +0,0 @@ - -# environmental-metadata - - -**metamodel version:** 1.7.0 - -**version:** None - - -A template for categorizing Environmental Data Initiative data entries. See https://github.com/EDIorg/EDIorg-repository-index - - -### Classes - - * [AnnotatorResult](AnnotatorResult.md) - * [Any](Any.md) - * [CompoundExpression](CompoundExpression.md) - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - * [Dataset](Dataset.md) - * [ExtractionResult](ExtractionResult.md) - A result of extracting knowledge on text - * [NamedEntity](NamedEntity.md) - * [Environment](Environment.md) - * [EnvironmentalMaterial](EnvironmentalMaterial.md) - * [Location](Location.md) - * [Method](Method.md) - * [RelationshipType](RelationshipType.md) - * [Topic](Topic.md) - * [Publication](Publication.md) - * [TextWithTriples](TextWithTriples.md) - -### Mixins - - -### Slots - - * [➞object_id](annotatorResult__object_id.md) - * [➞object_text](annotatorResult__object_text.md) - * [➞subject_text](annotatorResult__subject_text.md) - * [➞environmental_material](dataset__environmental_material.md) - the environmental material that was sampled - * [➞environments](dataset__environments.md) - the environmental context in which the study was conducted - * [➞location](dataset__location.md) - the geographic location where the sample was isolated - * [➞methods](dataset__methods.md) - * [➞packageid](dataset__packageid.md) - The internal identifier for the dataset - * [➞topic](dataset__topic.md) - the general scientific area of study concerning the sample(s) - * [➞extracted_object](extractionResult__extracted_object.md) - The complex objects extracted from the text - * [➞input_id](extractionResult__input_id.md) - * [➞input_text](extractionResult__input_text.md) - * [➞input_title](extractionResult__input_title.md) - * [➞named_entities](extractionResult__named_entities.md) - Named entities extracted from the text - * [➞prompt](extractionResult__prompt.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) - * [➞id](namedEntity__id.md) - A unique identifier for the named entity - * [➞label](namedEntity__label.md) - The label (name) of the named thing - * [➞abstract](publication__abstract.md) - The abstract of the publication - * [➞combined_text](publication__combined_text.md) - * [➞full_text](publication__full_text.md) - The full text of the publication - * [➞id](publication__id.md) - The publication identifier - * [➞title](publication__title.md) - The title of the publication - * [➞publication](textWithTriples__publication.md) - * [➞triples](textWithTriples__triples.md) - * [➞object](triple__object.md) - * [➞object_qualifier](triple__object_qualifier.md) - An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * [➞predicate](triple__predicate.md) - * [➞qualifier](triple__qualifier.md) - A qualifier for the statements, e.g. "NOT" for negation - * [➞subject](triple__subject.md) - * [➞subject_qualifier](triple__subject_qualifier.md) - An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -### Enums - - * [NullDataOptions](NullDataOptions.md) - -### Subsets - - -### Types - - -#### Built in - - * **Bool** - * **Curie** - * **Decimal** - * **ElementIdentifier** - * **NCName** - * **NodeIdentifier** - * **URI** - * **URIorCURIE** - * **XSDDate** - * **XSDDateTime** - * **XSDTime** - * **float** - * **int** - * **str** - -#### Defined - - * [Boolean](types/Boolean.md) (**Bool**) - A binary (true or false) value - * [Curie](types/Curie.md) (**Curie**) - a compact URI - * [Date](types/Date.md) (**XSDDate**) - a date (year, month and day) in an idealized calendar - * [DateOrDatetime](types/DateOrDatetime.md) (**str**) - Either a date or a datetime - * [Datetime](types/Datetime.md) (**XSDDateTime**) - The combination of a date and time - * [Decimal](types/Decimal.md) (**Decimal**) - A real number with arbitrary precision that conforms to the xsd:decimal specification - * [Double](types/Double.md) (**float**) - A real number that conforms to the xsd:double specification - * [Float](types/Float.md) (**float**) - A real number that conforms to the xsd:float specification - * [Integer](types/Integer.md) (**int**) - An integer - * [Jsonpath](types/Jsonpath.md) (**str**) - A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - * [Jsonpointer](types/Jsonpointer.md) (**str**) - A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - * [Ncname](types/Ncname.md) (**NCName**) - Prefix part of CURIE - * [Nodeidentifier](types/Nodeidentifier.md) (**NodeIdentifier**) - A URI, CURIE or BNODE that represents a node in a model. - * [Objectidentifier](types/Objectidentifier.md) (**ElementIdentifier**) - A URI or CURIE that represents an object in the model. - * [Sparqlpath](types/Sparqlpath.md) (**str**) - A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - * [String](types/String.md) (**str**) - A character string - * [Time](types/Time.md) (**XSDTime**) - A time object represents a (local) time of day, independent of any particular day - * [Uri](types/Uri.md) (**URI**) - a complete URI - * [Uriorcurie](types/Uriorcurie.md) (**URIorCURIE**) - a URI or a CURIE diff --git a/projects/environmental_metadata/docs/extractionResult__extracted_object.md b/projects/environmental_metadata/docs/extractionResult__extracted_object.md deleted file mode 100644 index c6f5f2ff0..000000000 --- a/projects/environmental_metadata/docs/extractionResult__extracted_object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: extracted_object - - -The complex objects extracted from the text - -URI: [envmd:extractionResult__extracted_object](http://w3id.org/ontogpt/environmental-metadataextractionResult__extracted_object) - - -## Domain and Range - -None → <sub>0..1</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/environmental_metadata/docs/extractionResult__input_id.md b/projects/environmental_metadata/docs/extractionResult__input_id.md deleted file mode 100644 index 4d84e2add..000000000 --- a/projects/environmental_metadata/docs/extractionResult__input_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_id - - - - -URI: [envmd:extractionResult__input_id](http://w3id.org/ontogpt/environmental-metadataextractionResult__input_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/environmental_metadata/docs/extractionResult__input_text.md b/projects/environmental_metadata/docs/extractionResult__input_text.md deleted file mode 100644 index 542145654..000000000 --- a/projects/environmental_metadata/docs/extractionResult__input_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_text - - - - -URI: [envmd:extractionResult__input_text](http://w3id.org/ontogpt/environmental-metadataextractionResult__input_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/environmental_metadata/docs/extractionResult__input_title.md b/projects/environmental_metadata/docs/extractionResult__input_title.md deleted file mode 100644 index b3df32354..000000000 --- a/projects/environmental_metadata/docs/extractionResult__input_title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_title - - - - -URI: [envmd:extractionResult__input_title](http://w3id.org/ontogpt/environmental-metadataextractionResult__input_title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/environmental_metadata/docs/extractionResult__named_entities.md b/projects/environmental_metadata/docs/extractionResult__named_entities.md deleted file mode 100644 index f24f0474b..000000000 --- a/projects/environmental_metadata/docs/extractionResult__named_entities.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: named_entities - - -Named entities extracted from the text - -URI: [envmd:extractionResult__named_entities](http://w3id.org/ontogpt/environmental-metadataextractionResult__named_entities) - - -## Domain and Range - -None → <sub>0..\*</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/environmental_metadata/docs/extractionResult__prompt.md b/projects/environmental_metadata/docs/extractionResult__prompt.md deleted file mode 100644 index e1ee7b2f6..000000000 --- a/projects/environmental_metadata/docs/extractionResult__prompt.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: prompt - - - - -URI: [envmd:extractionResult__prompt](http://w3id.org/ontogpt/environmental-metadataextractionResult__prompt) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/environmental_metadata/docs/extractionResult__raw_completion_output.md b/projects/environmental_metadata/docs/extractionResult__raw_completion_output.md deleted file mode 100644 index f586d0a1a..000000000 --- a/projects/environmental_metadata/docs/extractionResult__raw_completion_output.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: raw_completion_output - - - - -URI: [envmd:extractionResult__raw_completion_output](http://w3id.org/ontogpt/environmental-metadataextractionResult__raw_completion_output) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/environmental_metadata/docs/namedEntity__id.md b/projects/environmental_metadata/docs/namedEntity__id.md deleted file mode 100644 index 6f78c52a8..000000000 --- a/projects/environmental_metadata/docs/namedEntity__id.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Slot: id - - -A unique identifier for the named entity - -URI: [envmd:namedEntity__id](http://w3id.org/ontogpt/environmental-metadatanamedEntity__id) - - -## Domain and Range - -None → <sub>1..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Environment](Environment.md) - * [EnvironmentalMaterial](EnvironmentalMaterial.md) - * [Location](Location.md) - * [Method](Method.md) - * [NamedEntity](NamedEntity.md) - * [RelationshipType](RelationshipType.md) - * [Topic](Topic.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | this is populated during the grounding and normalization step | - diff --git a/projects/environmental_metadata/docs/namedEntity__label.md b/projects/environmental_metadata/docs/namedEntity__label.md deleted file mode 100644 index 49ba1372c..000000000 --- a/projects/environmental_metadata/docs/namedEntity__label.md +++ /dev/null @@ -1,36 +0,0 @@ - -# Slot: label - - -The label (name) of the named thing - -URI: [envmd:namedEntity__label](http://w3id.org/ontogpt/environmental-metadatanamedEntity__label) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Environment](Environment.md) - * [EnvironmentalMaterial](EnvironmentalMaterial.md) - * [Location](Location.md) - * [Method](Method.md) - * [NamedEntity](NamedEntity.md) - * [RelationshipType](RelationshipType.md) - * [Topic](Topic.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Aliases:** | | name | -| **Mappings:** | | rdfs:label | - diff --git a/projects/environmental_metadata/docs/publication__abstract.md b/projects/environmental_metadata/docs/publication__abstract.md deleted file mode 100644 index 42f059d76..000000000 --- a/projects/environmental_metadata/docs/publication__abstract.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: abstract - - -The abstract of the publication - -URI: [envmd:publication__abstract](http://w3id.org/ontogpt/environmental-metadatapublication__abstract) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/environmental_metadata/docs/publication__combined_text.md b/projects/environmental_metadata/docs/publication__combined_text.md deleted file mode 100644 index c0c440dda..000000000 --- a/projects/environmental_metadata/docs/publication__combined_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: combined_text - - - - -URI: [envmd:publication__combined_text](http://w3id.org/ontogpt/environmental-metadatapublication__combined_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/environmental_metadata/docs/publication__full_text.md b/projects/environmental_metadata/docs/publication__full_text.md deleted file mode 100644 index 765dac52b..000000000 --- a/projects/environmental_metadata/docs/publication__full_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: full_text - - -The full text of the publication - -URI: [envmd:publication__full_text](http://w3id.org/ontogpt/environmental-metadatapublication__full_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/environmental_metadata/docs/publication__id.md b/projects/environmental_metadata/docs/publication__id.md deleted file mode 100644 index 14fcd1d7e..000000000 --- a/projects/environmental_metadata/docs/publication__id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: id - - -The publication identifier - -URI: [envmd:publication__id](http://w3id.org/ontogpt/environmental-metadatapublication__id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/environmental_metadata/docs/publication__title.md b/projects/environmental_metadata/docs/publication__title.md deleted file mode 100644 index d821363aa..000000000 --- a/projects/environmental_metadata/docs/publication__title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: title - - -The title of the publication - -URI: [envmd:publication__title](http://w3id.org/ontogpt/environmental-metadatapublication__title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/environmental_metadata/docs/textWithTriples__publication.md b/projects/environmental_metadata/docs/textWithTriples__publication.md deleted file mode 100644 index d10a4d087..000000000 --- a/projects/environmental_metadata/docs/textWithTriples__publication.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: publication - - - - -URI: [envmd:textWithTriples__publication](http://w3id.org/ontogpt/environmental-metadatatextWithTriples__publication) - - -## Domain and Range - -None → <sub>0..1</sub> [Publication](Publication.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/environmental_metadata/docs/textWithTriples__triples.md b/projects/environmental_metadata/docs/textWithTriples__triples.md deleted file mode 100644 index 9a47988e7..000000000 --- a/projects/environmental_metadata/docs/textWithTriples__triples.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: triples - - - - -URI: [envmd:textWithTriples__triples](http://w3id.org/ontogpt/environmental-metadatatextWithTriples__triples) - - -## Domain and Range - -None → <sub>0..\*</sub> [Triple](Triple.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/environmental_metadata/docs/triple__object.md b/projects/environmental_metadata/docs/triple__object.md deleted file mode 100644 index 8034d4a8f..000000000 --- a/projects/environmental_metadata/docs/triple__object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object - - - - -URI: [envmd:triple__object](http://w3id.org/ontogpt/environmental-metadatatriple__object) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/environmental_metadata/docs/triple__object_qualifier.md b/projects/environmental_metadata/docs/triple__object_qualifier.md deleted file mode 100644 index d89d30add..000000000 --- a/projects/environmental_metadata/docs/triple__object_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_qualifier - - -An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - -URI: [envmd:triple__object_qualifier](http://w3id.org/ontogpt/environmental-metadatatriple__object_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/environmental_metadata/docs/triple__predicate.md b/projects/environmental_metadata/docs/triple__predicate.md deleted file mode 100644 index 465230d47..000000000 --- a/projects/environmental_metadata/docs/triple__predicate.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: predicate - - - - -URI: [envmd:triple__predicate](http://w3id.org/ontogpt/environmental-metadatatriple__predicate) - - -## Domain and Range - -None → <sub>0..1</sub> [RelationshipType](RelationshipType.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/environmental_metadata/docs/triple__qualifier.md b/projects/environmental_metadata/docs/triple__qualifier.md deleted file mode 100644 index 0f0a895af..000000000 --- a/projects/environmental_metadata/docs/triple__qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: qualifier - - -A qualifier for the statements, e.g. "NOT" for negation - -URI: [envmd:triple__qualifier](http://w3id.org/ontogpt/environmental-metadatatriple__qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/environmental_metadata/docs/triple__subject.md b/projects/environmental_metadata/docs/triple__subject.md deleted file mode 100644 index 496fbcfc0..000000000 --- a/projects/environmental_metadata/docs/triple__subject.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject - - - - -URI: [envmd:triple__subject](http://w3id.org/ontogpt/environmental-metadatatriple__subject) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/environmental_metadata/docs/triple__subject_qualifier.md b/projects/environmental_metadata/docs/triple__subject_qualifier.md deleted file mode 100644 index 57598e405..000000000 --- a/projects/environmental_metadata/docs/triple__subject_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_qualifier - - -An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -URI: [envmd:triple__subject_qualifier](http://w3id.org/ontogpt/environmental-metadatatriple__subject_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/environmental_metadata/docs/types/Boolean.md b/projects/environmental_metadata/docs/types/Boolean.md deleted file mode 100644 index dc83a9c6e..000000000 --- a/projects/environmental_metadata/docs/types/Boolean.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: boolean - - -A binary (true or false) value - -URI: [linkml:Boolean](https://w3id.org/linkml/Boolean) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Bool** | -| Representation | | bool | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Boolean | - diff --git a/projects/environmental_metadata/docs/types/Curie.md b/projects/environmental_metadata/docs/types/Curie.md deleted file mode 100644 index c1803f93f..000000000 --- a/projects/environmental_metadata/docs/types/Curie.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: curie - - -a compact URI - -URI: [linkml:Curie](https://w3id.org/linkml/Curie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Curie** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations this MUST be expanded to a URI | -| | | in non-RDF serializations MAY be serialized as the compact representation | - diff --git a/projects/environmental_metadata/docs/types/Date.md b/projects/environmental_metadata/docs/types/Date.md deleted file mode 100644 index 06948af97..000000000 --- a/projects/environmental_metadata/docs/types/Date.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: date - - -a date (year, month and day) in an idealized calendar - -URI: [linkml:Date](https://w3id.org/linkml/Date) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDate** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Date | - diff --git a/projects/environmental_metadata/docs/types/DateOrDatetime.md b/projects/environmental_metadata/docs/types/DateOrDatetime.md deleted file mode 100644 index ef983898d..000000000 --- a/projects/environmental_metadata/docs/types/DateOrDatetime.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: date_or_datetime - - -Either a date or a datetime - -URI: [linkml:DateOrDatetime](https://w3id.org/linkml/DateOrDatetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/environmental_metadata/docs/types/Datetime.md b/projects/environmental_metadata/docs/types/Datetime.md deleted file mode 100644 index 9510454a8..000000000 --- a/projects/environmental_metadata/docs/types/Datetime.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: datetime - - -The combination of a date and time - -URI: [linkml:Datetime](https://w3id.org/linkml/Datetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDateTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:DateTime | - diff --git a/projects/environmental_metadata/docs/types/Decimal.md b/projects/environmental_metadata/docs/types/Decimal.md deleted file mode 100644 index a7ba14a5d..000000000 --- a/projects/environmental_metadata/docs/types/Decimal.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: decimal - - -A real number with arbitrary precision that conforms to the xsd:decimal specification - -URI: [linkml:Decimal](https://w3id.org/linkml/Decimal) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Decimal** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Broad Mappings:** | | schema:Number | - diff --git a/projects/environmental_metadata/docs/types/Double.md b/projects/environmental_metadata/docs/types/Double.md deleted file mode 100644 index cfe6d71e2..000000000 --- a/projects/environmental_metadata/docs/types/Double.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: double - - -A real number that conforms to the xsd:double specification - -URI: [linkml:Double](https://w3id.org/linkml/Double) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Close Mappings:** | | schema:Float | - diff --git a/projects/environmental_metadata/docs/types/Float.md b/projects/environmental_metadata/docs/types/Float.md deleted file mode 100644 index 7b303f96f..000000000 --- a/projects/environmental_metadata/docs/types/Float.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: float - - -A real number that conforms to the xsd:float specification - -URI: [linkml:Float](https://w3id.org/linkml/Float) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Float | - diff --git a/projects/environmental_metadata/docs/types/Integer.md b/projects/environmental_metadata/docs/types/Integer.md deleted file mode 100644 index 3cfcc66d9..000000000 --- a/projects/environmental_metadata/docs/types/Integer.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: integer - - -An integer - -URI: [linkml:Integer](https://w3id.org/linkml/Integer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **int** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Integer | - diff --git a/projects/environmental_metadata/docs/types/Jsonpath.md b/projects/environmental_metadata/docs/types/Jsonpath.md deleted file mode 100644 index a03a58e67..000000000 --- a/projects/environmental_metadata/docs/types/Jsonpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpath - - -A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpath](https://w3id.org/linkml/Jsonpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/environmental_metadata/docs/types/Jsonpointer.md b/projects/environmental_metadata/docs/types/Jsonpointer.md deleted file mode 100644 index a0e1ac492..000000000 --- a/projects/environmental_metadata/docs/types/Jsonpointer.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpointer - - -A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpointer](https://w3id.org/linkml/Jsonpointer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/environmental_metadata/docs/types/Ncname.md b/projects/environmental_metadata/docs/types/Ncname.md deleted file mode 100644 index 710b0b04a..000000000 --- a/projects/environmental_metadata/docs/types/Ncname.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: ncname - - -Prefix part of CURIE - -URI: [linkml:Ncname](https://w3id.org/linkml/Ncname) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NCName** | -| Representation | | str | diff --git a/projects/environmental_metadata/docs/types/Nodeidentifier.md b/projects/environmental_metadata/docs/types/Nodeidentifier.md deleted file mode 100644 index f0097cdf4..000000000 --- a/projects/environmental_metadata/docs/types/Nodeidentifier.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: nodeidentifier - - -A URI, CURIE or BNODE that represents a node in a model. - -URI: [linkml:Nodeidentifier](https://w3id.org/linkml/Nodeidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NodeIdentifier** | -| Representation | | str | diff --git a/projects/environmental_metadata/docs/types/Objectidentifier.md b/projects/environmental_metadata/docs/types/Objectidentifier.md deleted file mode 100644 index 454ba6be6..000000000 --- a/projects/environmental_metadata/docs/types/Objectidentifier.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: objectidentifier - - -A URI or CURIE that represents an object in the model. - -URI: [linkml:Objectidentifier](https://w3id.org/linkml/Objectidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **ElementIdentifier** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | Used for inheritance and type checking | - diff --git a/projects/environmental_metadata/docs/types/Sparqlpath.md b/projects/environmental_metadata/docs/types/Sparqlpath.md deleted file mode 100644 index fd99a927e..000000000 --- a/projects/environmental_metadata/docs/types/Sparqlpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: sparqlpath - - -A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - -URI: [linkml:Sparqlpath](https://w3id.org/linkml/Sparqlpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/environmental_metadata/docs/types/String.md b/projects/environmental_metadata/docs/types/String.md deleted file mode 100644 index 6e61d7081..000000000 --- a/projects/environmental_metadata/docs/types/String.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: string - - -A character string - -URI: [linkml:String](https://w3id.org/linkml/String) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Text | - diff --git a/projects/environmental_metadata/docs/types/Time.md b/projects/environmental_metadata/docs/types/Time.md deleted file mode 100644 index 2b8652bcd..000000000 --- a/projects/environmental_metadata/docs/types/Time.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: time - - -A time object represents a (local) time of day, independent of any particular day - -URI: [linkml:Time](https://w3id.org/linkml/Time) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Time | - diff --git a/projects/environmental_metadata/docs/types/Uri.md b/projects/environmental_metadata/docs/types/Uri.md deleted file mode 100644 index 343807a5e..000000000 --- a/projects/environmental_metadata/docs/types/Uri.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: uri - - -a complete URI - -URI: [linkml:Uri](https://w3id.org/linkml/Uri) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URI** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node | -| **Close Mappings:** | | schema:URL | - diff --git a/projects/environmental_metadata/docs/types/Uriorcurie.md b/projects/environmental_metadata/docs/types/Uriorcurie.md deleted file mode 100644 index 2f7b65087..000000000 --- a/projects/environmental_metadata/docs/types/Uriorcurie.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: uriorcurie - - -a URI or a CURIE - -URI: [linkml:Uriorcurie](https://w3id.org/linkml/Uriorcurie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URIorCURIE** | -| Representation | | str | diff --git a/projects/environmental_metadata/environmental_metadata.py b/projects/environmental_metadata/environmental_metadata.py deleted file mode 100644 index c1dbceb02..000000000 --- a/projects/environmental_metadata/environmental_metadata.py +++ /dev/null @@ -1,547 +0,0 @@ -# Auto generated from environmental_metadata.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-08-07T10:53:05 -# Schema: environmental-metadata -# -# id: http://w3id.org/ontogpt/environmental-metadata -# description: A template for categorizing Environmental Data Initiative data entries. See -# https://github.com/EDIorg/EDIorg-repository-index -# license: https://creativecommons.org/publicdomain/zero/1.0/ - -import dataclasses -import sys -import re -from jsonasobj2 import JsonObj, as_dict -from typing import Optional, List, Union, Dict, ClassVar, Any -from dataclasses import dataclass -from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions - -from linkml_runtime.utils.slot import Slot -from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode -from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int -from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs -from linkml_runtime.utils.formatutils import camelcase, underscore, sfx -from linkml_runtime.utils.enumerations import EnumDefinitionImpl -from rdflib import Namespace, URIRef -from linkml_runtime.utils.curienamespace import CurieNamespace -from linkml_runtime.linkml_model.types import String - -metamodel_version = "1.7.0" -version = None - -# Overwrite dataclasses _init_fn to add **kwargs in __init__ -dataclasses._init_fn = dataclasses_init_fn_with_kwargs - -# Namespaces -ENVO = CurieNamespace('ENVO', 'http://example.org/UNKNOWN/ENVO/') -ENVTHES = CurieNamespace('ENVTHES', 'http://example.org/UNKNOWN/ENVTHES/') -GAZ = CurieNamespace('GAZ', 'http://example.org/UNKNOWN/GAZ/') -RO = CurieNamespace('RO', 'http://purl.obolibrary.org/obo/RO_') -BIOLINK = CurieNamespace('biolink', 'http://example.org/UNKNOWN/biolink/') -CORE = CurieNamespace('core', 'http://w3id.org/ontogpt/core/') -ENVMD = CurieNamespace('envmd', 'http://w3id.org/ontogpt/environmental-metadata') -LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') -RDFS = CurieNamespace('rdfs', 'http://example.org/UNKNOWN/rdfs/') -DEFAULT_ = ENVMD - - -# Types - -# Class references -class NamedEntityId(extended_str): - pass - - -class TopicId(NamedEntityId): - pass - - -class LocationId(NamedEntityId): - pass - - -class EnvironmentalMaterialId(NamedEntityId): - pass - - -class EnvironmentId(NamedEntityId): - pass - - -class MethodId(NamedEntityId): - pass - - -class RelationshipTypeId(NamedEntityId): - pass - - -@dataclass -class Dataset(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = ENVMD.Dataset - class_class_curie: ClassVar[str] = "envmd:Dataset" - class_name: ClassVar[str] = "Dataset" - class_model_uri: ClassVar[URIRef] = ENVMD.Dataset - - packageid: Optional[str] = None - topic: Optional[Union[Union[str, TopicId], List[Union[str, TopicId]]]] = empty_list() - location: Optional[Union[Union[str, LocationId], List[Union[str, LocationId]]]] = empty_list() - environmental_material: Optional[Union[Union[str, EnvironmentalMaterialId], List[Union[str, EnvironmentalMaterialId]]]] = empty_list() - environments: Optional[Union[Union[str, EnvironmentId], List[Union[str, EnvironmentId]]]] = empty_list() - methods: Optional[Union[Union[str, MethodId], List[Union[str, MethodId]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.packageid is not None and not isinstance(self.packageid, str): - self.packageid = str(self.packageid) - - if not isinstance(self.topic, list): - self.topic = [self.topic] if self.topic is not None else [] - self.topic = [v if isinstance(v, TopicId) else TopicId(v) for v in self.topic] - - if not isinstance(self.location, list): - self.location = [self.location] if self.location is not None else [] - self.location = [v if isinstance(v, LocationId) else LocationId(v) for v in self.location] - - if not isinstance(self.environmental_material, list): - self.environmental_material = [self.environmental_material] if self.environmental_material is not None else [] - self.environmental_material = [v if isinstance(v, EnvironmentalMaterialId) else EnvironmentalMaterialId(v) for v in self.environmental_material] - - if not isinstance(self.environments, list): - self.environments = [self.environments] if self.environments is not None else [] - self.environments = [v if isinstance(v, EnvironmentId) else EnvironmentId(v) for v in self.environments] - - if not isinstance(self.methods, list): - self.methods = [self.methods] if self.methods is not None else [] - self.methods = [v if isinstance(v, MethodId) else MethodId(v) for v in self.methods] - - super().__post_init__(**kwargs) - - -Any = Any - -@dataclass -class ExtractionResult(YAMLRoot): - """ - A result of extracting knowledge on text - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.ExtractionResult - class_class_curie: ClassVar[str] = "core:ExtractionResult" - class_name: ClassVar[str] = "ExtractionResult" - class_model_uri: ClassVar[URIRef] = ENVMD.ExtractionResult - - input_id: Optional[str] = None - input_title: Optional[str] = None - input_text: Optional[str] = None - raw_completion_output: Optional[str] = None - prompt: Optional[str] = None - extracted_object: Optional[Union[dict, Any]] = None - named_entities: Optional[Union[Union[dict, Any], List[Union[dict, Any]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.input_id is not None and not isinstance(self.input_id, str): - self.input_id = str(self.input_id) - - if self.input_title is not None and not isinstance(self.input_title, str): - self.input_title = str(self.input_title) - - if self.input_text is not None and not isinstance(self.input_text, str): - self.input_text = str(self.input_text) - - if self.raw_completion_output is not None and not isinstance(self.raw_completion_output, str): - self.raw_completion_output = str(self.raw_completion_output) - - if self.prompt is not None and not isinstance(self.prompt, str): - self.prompt = str(self.prompt) - - super().__post_init__(**kwargs) - - -@dataclass -class NamedEntity(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.NamedEntity - class_class_curie: ClassVar[str] = "core:NamedEntity" - class_name: ClassVar[str] = "NamedEntity" - class_model_uri: ClassVar[URIRef] = ENVMD.NamedEntity - - id: Union[str, NamedEntityId] = None - label: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, NamedEntityId): - self.id = NamedEntityId(self.id) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - super().__post_init__(**kwargs) - - -@dataclass -class Topic(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = ENVMD.Topic - class_class_curie: ClassVar[str] = "envmd:Topic" - class_name: ClassVar[str] = "Topic" - class_model_uri: ClassVar[URIRef] = ENVMD.Topic - - id: Union[str, TopicId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, TopicId): - self.id = TopicId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Location(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = ENVMD.Location - class_class_curie: ClassVar[str] = "envmd:Location" - class_name: ClassVar[str] = "Location" - class_model_uri: ClassVar[URIRef] = ENVMD.Location - - id: Union[str, LocationId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, LocationId): - self.id = LocationId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class EnvironmentalMaterial(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = ENVMD.EnvironmentalMaterial - class_class_curie: ClassVar[str] = "envmd:EnvironmentalMaterial" - class_name: ClassVar[str] = "EnvironmentalMaterial" - class_model_uri: ClassVar[URIRef] = ENVMD.EnvironmentalMaterial - - id: Union[str, EnvironmentalMaterialId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, EnvironmentalMaterialId): - self.id = EnvironmentalMaterialId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Environment(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = ENVMD.Environment - class_class_curie: ClassVar[str] = "envmd:Environment" - class_name: ClassVar[str] = "Environment" - class_model_uri: ClassVar[URIRef] = ENVMD.Environment - - id: Union[str, EnvironmentId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, EnvironmentId): - self.id = EnvironmentId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Method(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = ENVMD.Method - class_class_curie: ClassVar[str] = "envmd:Method" - class_name: ClassVar[str] = "Method" - class_model_uri: ClassVar[URIRef] = ENVMD.Method - - id: Union[str, MethodId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, MethodId): - self.id = MethodId(self.id) - - super().__post_init__(**kwargs) - - -class CompoundExpression(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.CompoundExpression - class_class_curie: ClassVar[str] = "core:CompoundExpression" - class_name: ClassVar[str] = "CompoundExpression" - class_model_uri: ClassVar[URIRef] = ENVMD.CompoundExpression - - -@dataclass -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Triple - class_class_curie: ClassVar[str] = "core:Triple" - class_name: ClassVar[str] = "Triple" - class_model_uri: ClassVar[URIRef] = ENVMD.Triple - - subject: Optional[Union[str, NamedEntityId]] = None - predicate: Optional[Union[str, RelationshipTypeId]] = None - object: Optional[Union[str, NamedEntityId]] = None - qualifier: Optional[str] = None - subject_qualifier: Optional[Union[str, NamedEntityId]] = None - object_qualifier: Optional[Union[str, NamedEntityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, NamedEntityId): - self.subject = NamedEntityId(self.subject) - - if self.predicate is not None and not isinstance(self.predicate, RelationshipTypeId): - self.predicate = RelationshipTypeId(self.predicate) - - if self.object is not None and not isinstance(self.object, NamedEntityId): - self.object = NamedEntityId(self.object) - - if self.qualifier is not None and not isinstance(self.qualifier, str): - self.qualifier = str(self.qualifier) - - if self.subject_qualifier is not None and not isinstance(self.subject_qualifier, NamedEntityId): - self.subject_qualifier = NamedEntityId(self.subject_qualifier) - - if self.object_qualifier is not None and not isinstance(self.object_qualifier, NamedEntityId): - self.object_qualifier = NamedEntityId(self.object_qualifier) - - super().__post_init__(**kwargs) - - -@dataclass -class TextWithTriples(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.TextWithTriples - class_class_curie: ClassVar[str] = "core:TextWithTriples" - class_name: ClassVar[str] = "TextWithTriples" - class_model_uri: ClassVar[URIRef] = ENVMD.TextWithTriples - - publication: Optional[Union[dict, "Publication"]] = None - triples: Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.publication is not None and not isinstance(self.publication, Publication): - self.publication = Publication(**as_dict(self.publication)) - - if not isinstance(self.triples, list): - self.triples = [self.triples] if self.triples is not None else [] - self.triples = [v if isinstance(v, Triple) else Triple(**as_dict(v)) for v in self.triples] - - super().__post_init__(**kwargs) - - -@dataclass -class RelationshipType(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.RelationshipType - class_class_curie: ClassVar[str] = "core:RelationshipType" - class_name: ClassVar[str] = "RelationshipType" - class_model_uri: ClassVar[URIRef] = ENVMD.RelationshipType - - id: Union[str, RelationshipTypeId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, RelationshipTypeId): - self.id = RelationshipTypeId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Publication(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Publication - class_class_curie: ClassVar[str] = "core:Publication" - class_name: ClassVar[str] = "Publication" - class_model_uri: ClassVar[URIRef] = ENVMD.Publication - - id: Optional[str] = None - title: Optional[str] = None - abstract: Optional[str] = None - combined_text: Optional[str] = None - full_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.id is not None and not isinstance(self.id, str): - self.id = str(self.id) - - if self.title is not None and not isinstance(self.title, str): - self.title = str(self.title) - - if self.abstract is not None and not isinstance(self.abstract, str): - self.abstract = str(self.abstract) - - if self.combined_text is not None and not isinstance(self.combined_text, str): - self.combined_text = str(self.combined_text) - - if self.full_text is not None and not isinstance(self.full_text, str): - self.full_text = str(self.full_text) - - super().__post_init__(**kwargs) - - -@dataclass -class AnnotatorResult(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.AnnotatorResult - class_class_curie: ClassVar[str] = "core:AnnotatorResult" - class_name: ClassVar[str] = "AnnotatorResult" - class_model_uri: ClassVar[URIRef] = ENVMD.AnnotatorResult - - subject_text: Optional[str] = None - object_id: Optional[str] = None - object_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject_text is not None and not isinstance(self.subject_text, str): - self.subject_text = str(self.subject_text) - - if self.object_id is not None and not isinstance(self.object_id, str): - self.object_id = str(self.object_id) - - if self.object_text is not None and not isinstance(self.object_text, str): - self.object_text = str(self.object_text) - - super().__post_init__(**kwargs) - - -# Enumerations -class NullDataOptions(EnumDefinitionImpl): - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = PermissibleValue(text="UNSPECIFIED_METHOD_OF_ADMINISTRATION", - meaning=NCIT.C149701) - NOT_APPLICABLE = PermissibleValue(text="NOT_APPLICABLE", - meaning=NCIT.C18902) - NOT_MENTIONED = PermissibleValue(text="NOT_MENTIONED") - - _defn = EnumDefinition( - name="NullDataOptions", - ) - -# Slots -class slots: - pass - -slots.dataset__packageid = Slot(uri=ENVMD.packageid, name="dataset__packageid", curie=ENVMD.curie('packageid'), - model_uri=ENVMD.dataset__packageid, domain=None, range=Optional[str]) - -slots.dataset__topic = Slot(uri=ENVMD.topic, name="dataset__topic", curie=ENVMD.curie('topic'), - model_uri=ENVMD.dataset__topic, domain=None, range=Optional[Union[Union[str, TopicId], List[Union[str, TopicId]]]]) - -slots.dataset__location = Slot(uri=ENVMD.location, name="dataset__location", curie=ENVMD.curie('location'), - model_uri=ENVMD.dataset__location, domain=None, range=Optional[Union[Union[str, LocationId], List[Union[str, LocationId]]]]) - -slots.dataset__environmental_material = Slot(uri=ENVMD.environmental_material, name="dataset__environmental_material", curie=ENVMD.curie('environmental_material'), - model_uri=ENVMD.dataset__environmental_material, domain=None, range=Optional[Union[Union[str, EnvironmentalMaterialId], List[Union[str, EnvironmentalMaterialId]]]]) - -slots.dataset__environments = Slot(uri=ENVMD.environments, name="dataset__environments", curie=ENVMD.curie('environments'), - model_uri=ENVMD.dataset__environments, domain=None, range=Optional[Union[Union[str, EnvironmentId], List[Union[str, EnvironmentId]]]]) - -slots.dataset__methods = Slot(uri=ENVMD.methods, name="dataset__methods", curie=ENVMD.curie('methods'), - model_uri=ENVMD.dataset__methods, domain=None, range=Optional[Union[Union[str, MethodId], List[Union[str, MethodId]]]]) - -slots.extractionResult__input_id = Slot(uri=CORE.input_id, name="extractionResult__input_id", curie=CORE.curie('input_id'), - model_uri=ENVMD.extractionResult__input_id, domain=None, range=Optional[str]) - -slots.extractionResult__input_title = Slot(uri=CORE.input_title, name="extractionResult__input_title", curie=CORE.curie('input_title'), - model_uri=ENVMD.extractionResult__input_title, domain=None, range=Optional[str]) - -slots.extractionResult__input_text = Slot(uri=CORE.input_text, name="extractionResult__input_text", curie=CORE.curie('input_text'), - model_uri=ENVMD.extractionResult__input_text, domain=None, range=Optional[str]) - -slots.extractionResult__raw_completion_output = Slot(uri=CORE.raw_completion_output, name="extractionResult__raw_completion_output", curie=CORE.curie('raw_completion_output'), - model_uri=ENVMD.extractionResult__raw_completion_output, domain=None, range=Optional[str]) - -slots.extractionResult__prompt = Slot(uri=CORE.prompt, name="extractionResult__prompt", curie=CORE.curie('prompt'), - model_uri=ENVMD.extractionResult__prompt, domain=None, range=Optional[str]) - -slots.extractionResult__extracted_object = Slot(uri=CORE.extracted_object, name="extractionResult__extracted_object", curie=CORE.curie('extracted_object'), - model_uri=ENVMD.extractionResult__extracted_object, domain=None, range=Optional[Union[dict, Any]]) - -slots.extractionResult__named_entities = Slot(uri=CORE.named_entities, name="extractionResult__named_entities", curie=CORE.curie('named_entities'), - model_uri=ENVMD.extractionResult__named_entities, domain=None, range=Optional[Union[Union[dict, Any], List[Union[dict, Any]]]]) - -slots.namedEntity__id = Slot(uri=CORE.id, name="namedEntity__id", curie=CORE.curie('id'), - model_uri=ENVMD.namedEntity__id, domain=None, range=URIRef) - -slots.namedEntity__label = Slot(uri=RDFS.label, name="namedEntity__label", curie=RDFS.curie('label'), - model_uri=ENVMD.namedEntity__label, domain=None, range=Optional[str]) - -slots.triple__subject = Slot(uri=CORE.subject, name="triple__subject", curie=CORE.curie('subject'), - model_uri=ENVMD.triple__subject, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__predicate = Slot(uri=CORE.predicate, name="triple__predicate", curie=CORE.curie('predicate'), - model_uri=ENVMD.triple__predicate, domain=None, range=Optional[Union[str, RelationshipTypeId]]) - -slots.triple__object = Slot(uri=CORE.object, name="triple__object", curie=CORE.curie('object'), - model_uri=ENVMD.triple__object, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__qualifier = Slot(uri=CORE.qualifier, name="triple__qualifier", curie=CORE.curie('qualifier'), - model_uri=ENVMD.triple__qualifier, domain=None, range=Optional[str]) - -slots.triple__subject_qualifier = Slot(uri=CORE.subject_qualifier, name="triple__subject_qualifier", curie=CORE.curie('subject_qualifier'), - model_uri=ENVMD.triple__subject_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__object_qualifier = Slot(uri=CORE.object_qualifier, name="triple__object_qualifier", curie=CORE.curie('object_qualifier'), - model_uri=ENVMD.triple__object_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.textWithTriples__publication = Slot(uri=CORE.publication, name="textWithTriples__publication", curie=CORE.curie('publication'), - model_uri=ENVMD.textWithTriples__publication, domain=None, range=Optional[Union[dict, Publication]]) - -slots.textWithTriples__triples = Slot(uri=CORE.triples, name="textWithTriples__triples", curie=CORE.curie('triples'), - model_uri=ENVMD.textWithTriples__triples, domain=None, range=Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]]) - -slots.publication__id = Slot(uri=CORE.id, name="publication__id", curie=CORE.curie('id'), - model_uri=ENVMD.publication__id, domain=None, range=Optional[str]) - -slots.publication__title = Slot(uri=CORE.title, name="publication__title", curie=CORE.curie('title'), - model_uri=ENVMD.publication__title, domain=None, range=Optional[str]) - -slots.publication__abstract = Slot(uri=CORE.abstract, name="publication__abstract", curie=CORE.curie('abstract'), - model_uri=ENVMD.publication__abstract, domain=None, range=Optional[str]) - -slots.publication__combined_text = Slot(uri=CORE.combined_text, name="publication__combined_text", curie=CORE.curie('combined_text'), - model_uri=ENVMD.publication__combined_text, domain=None, range=Optional[str]) - -slots.publication__full_text = Slot(uri=CORE.full_text, name="publication__full_text", curie=CORE.curie('full_text'), - model_uri=ENVMD.publication__full_text, domain=None, range=Optional[str]) - -slots.annotatorResult__subject_text = Slot(uri=CORE.subject_text, name="annotatorResult__subject_text", curie=CORE.curie('subject_text'), - model_uri=ENVMD.annotatorResult__subject_text, domain=None, range=Optional[str]) - -slots.annotatorResult__object_id = Slot(uri=CORE.object_id, name="annotatorResult__object_id", curie=CORE.curie('object_id'), - model_uri=ENVMD.annotatorResult__object_id, domain=None, range=Optional[str]) - -slots.annotatorResult__object_text = Slot(uri=CORE.object_text, name="annotatorResult__object_text", curie=CORE.curie('object_text'), - model_uri=ENVMD.annotatorResult__object_text, domain=None, range=Optional[str]) \ No newline at end of file diff --git a/projects/environmental_metadata/excel/environmental_metadata.xlsx b/projects/environmental_metadata/excel/environmental_metadata.xlsx deleted file mode 100644 index dabb22828..000000000 Binary files a/projects/environmental_metadata/excel/environmental_metadata.xlsx and /dev/null differ diff --git a/projects/environmental_metadata/graphql/environmental_metadata.graphql b/projects/environmental_metadata/graphql/environmental_metadata.graphql deleted file mode 100644 index 40a51ae25..000000000 --- a/projects/environmental_metadata/graphql/environmental_metadata.graphql +++ /dev/null @@ -1,103 +0,0 @@ -type AnnotatorResult - { - subjectText: String - objectId: String - objectText: String - } - -type Any - { - } - -interface CompoundExpression - { - } - -type Dataset - { - packageid: String - topic: [Topic] - location: [Location] - environmentalMaterial: [EnvironmentalMaterial] - environments: [Environment] - methods: [Method] - } - -type Environment - { - id: String! - label: String - } - -type EnvironmentalMaterial - { - id: String! - label: String - } - -type ExtractionResult - { - inputId: String - inputTitle: String - inputText: String - rawCompletionOutput: String - prompt: String - extractedObject: Any - namedEntities: [Any] - } - -type Location - { - id: String! - label: String - } - -type Method - { - id: String! - label: String - } - -interface NamedEntity - { - id: String! - label: String - } - -type Publication - { - id: String - title: String - abstract: String - combinedText: String - fullText: String - } - -type RelationshipType - { - id: String! - label: String - } - -type TextWithTriples - { - publication: Publication - triples: [Triple] - } - -type Topic - { - id: String! - label: String - } - -interface Triple - { - subject: NamedEntity - predicate: RelationshipType - object: NamedEntity - qualifier: String - subjectQualifier: NamedEntity - objectQualifier: NamedEntity - } - diff --git a/projects/environmental_metadata/jsonld/environmental_metadata.context.jsonld b/projects/environmental_metadata/jsonld/environmental_metadata.context.jsonld deleted file mode 100644 index 68eaa9ed2..000000000 --- a/projects/environmental_metadata/jsonld/environmental_metadata.context.jsonld +++ /dev/null @@ -1,148 +0,0 @@ -{ - "comments": { - "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2023-08-07T10:52:56", - "source": "environmental_metadata.yaml" - }, - "@context": { - "ENVO": "http://example.org/UNKNOWN/ENVO/", - "ENVTHES": "http://example.org/UNKNOWN/ENVTHES/", - "GAZ": "http://example.org/UNKNOWN/GAZ/", - "RO": { - "@id": "http://purl.obolibrary.org/obo/RO_", - "@prefix": true - }, - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "envmd": { - "@id": "http://w3id.org/ontogpt/environmental-metadata", - "@prefix": true - }, - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "@vocab": "http://w3id.org/ontogpt/environmental-metadata", - "object_id": { - "@id": "core:object_id" - }, - "object_text": { - "@id": "core:object_text" - }, - "subject_text": { - "@id": "core:subject_text" - }, - "environmental_material": { - "@type": "@id" - }, - "environments": { - "@type": "@id" - }, - "location": { - "@type": "@id" - }, - "methods": { - "@type": "@id" - }, - "topic": { - "@type": "@id" - }, - "extracted_object": { - "@type": "@id", - "@id": "core:extracted_object" - }, - "input_id": { - "@id": "core:input_id" - }, - "input_text": { - "@id": "core:input_text" - }, - "input_title": { - "@id": "core:input_title" - }, - "named_entities": { - "@type": "@id", - "@id": "core:named_entities" - }, - "prompt": { - "@id": "core:prompt" - }, - "raw_completion_output": { - "@id": "core:raw_completion_output" - }, - "id": { - "@id": "core:id" - }, - "label": { - "@id": "rdfs:label" - }, - "abstract": { - "@id": "core:abstract" - }, - "combined_text": { - "@id": "core:combined_text" - }, - "full_text": { - "@id": "core:full_text" - }, - "title": { - "@id": "core:title" - }, - "publication": { - "@type": "@id", - "@id": "core:publication" - }, - "triples": { - "@type": "@id", - "@id": "core:triples" - }, - "object": { - "@type": "@id", - "@id": "core:object" - }, - "object_qualifier": { - "@type": "@id", - "@id": "core:object_qualifier" - }, - "predicate": { - "@type": "@id", - "@id": "core:predicate" - }, - "qualifier": { - "@id": "core:qualifier" - }, - "subject": { - "@type": "@id", - "@id": "core:subject" - }, - "subject_qualifier": { - "@type": "@id", - "@id": "core:subject_qualifier" - }, - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } - } -} diff --git a/projects/environmental_metadata/jsonld/environmental_metadata.jsonld b/projects/environmental_metadata/jsonld/environmental_metadata.jsonld deleted file mode 100644 index 7a10880a5..000000000 --- a/projects/environmental_metadata/jsonld/environmental_metadata.jsonld +++ /dev/null @@ -1,1314 +0,0 @@ -{ - "name": "environmental-metadata", - "description": "A template for categorizing Environmental Data Initiative data entries. See https://github.com/EDIorg/EDIorg-repository-index", - "title": "Environmental sample metadata", - "id": "http://w3id.org/ontogpt/environmental-metadata", - "imports": [ - "linkml:types", - "core" - ], - "license": "https://creativecommons.org/publicdomain/zero/1.0/", - "prefixes": [ - { - "prefix_prefix": "linkml", - "prefix_reference": "https://w3id.org/linkml/" - }, - { - "prefix_prefix": "envmd", - "prefix_reference": "http://w3id.org/ontogpt/environmental-metadata" - } - ], - "default_prefix": "envmd", - "default_range": "string", - "types": [ - { - "name": "string", - "definition_uri": "https://w3id.org/linkml/String", - "description": "A character string", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Text" - ], - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "@type": "TypeDefinition" - }, - { - "name": "integer", - "definition_uri": "https://w3id.org/linkml/Integer", - "description": "An integer", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Integer" - ], - "base": "int", - "uri": "http://www.w3.org/2001/XMLSchema#integer", - "@type": "TypeDefinition" - }, - { - "name": "boolean", - "definition_uri": "https://w3id.org/linkml/Boolean", - "description": "A binary (true or false) value", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Boolean" - ], - "base": "Bool", - "uri": "http://www.w3.org/2001/XMLSchema#boolean", - "repr": "bool", - "@type": "TypeDefinition" - }, - { - "name": "float", - "definition_uri": "https://w3id.org/linkml/Float", - "description": "A real number that conforms to the xsd:float specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#float", - "@type": "TypeDefinition" - }, - { - "name": "double", - "definition_uri": "https://w3id.org/linkml/Double", - "description": "A real number that conforms to the xsd:double specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#double", - "@type": "TypeDefinition" - }, - { - "name": "decimal", - "definition_uri": "https://w3id.org/linkml/Decimal", - "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "broad_mappings": [ - "schema:Number" - ], - "base": "Decimal", - "uri": "http://www.w3.org/2001/XMLSchema#decimal", - "@type": "TypeDefinition" - }, - { - "name": "time", - "definition_uri": "https://w3id.org/linkml/Time", - "description": "A time object represents a (local) time of day, independent of any particular day", - "notes": [ - "URI is dateTime because OWL reasoners do not work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Time" - ], - "base": "XSDTime", - "uri": "http://www.w3.org/2001/XMLSchema#time", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date", - "definition_uri": "https://w3id.org/linkml/Date", - "description": "a date (year, month and day) in an idealized calendar", - "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Date" - ], - "base": "XSDDate", - "uri": "http://www.w3.org/2001/XMLSchema#date", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "datetime", - "definition_uri": "https://w3id.org/linkml/Datetime", - "description": "The combination of a date and time", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:DateTime" - ], - "base": "XSDDateTime", - "uri": "http://www.w3.org/2001/XMLSchema#dateTime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date_or_datetime", - "definition_uri": "https://w3id.org/linkml/DateOrDatetime", - "description": "Either a date or a datetime", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "https://w3id.org/linkml/DateOrDatetime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uriorcurie", - "definition_uri": "https://w3id.org/linkml/Uriorcurie", - "description": "a URI or a CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "URIorCURIE", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "curie", - "definition_uri": "https://w3id.org/linkml/Curie", - "conforms_to": "https://www.w3.org/TR/curie/", - "description": "a compact URI", - "comments": [ - "in RDF serializations this MUST be expanded to a URI", - "in non-RDF serializations MAY be serialized as the compact representation" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "Curie", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uri", - "definition_uri": "https://w3id.org/linkml/Uri", - "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", - "description": "a complete URI", - "comments": [ - "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:URL" - ], - "base": "URI", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "ncname", - "definition_uri": "https://w3id.org/linkml/Ncname", - "description": "Prefix part of CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NCName", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "objectidentifier", - "definition_uri": "https://w3id.org/linkml/Objectidentifier", - "description": "A URI or CURIE that represents an object in the model.", - "comments": [ - "Used for inheritance and type checking" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "ElementIdentifier", - "uri": "http://www.w3.org/ns/shex#iri", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "nodeidentifier", - "definition_uri": "https://w3id.org/linkml/Nodeidentifier", - "description": "A URI, CURIE or BNODE that represents a node in a model.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NodeIdentifier", - "uri": "http://www.w3.org/ns/shex#nonLiteral", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpointer", - "definition_uri": "https://w3id.org/linkml/Jsonpointer", - "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901", - "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpath", - "definition_uri": "https://w3id.org/linkml/Jsonpath", - "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html", - "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "sparqlpath", - "definition_uri": "https://w3id.org/linkml/Sparqlpath", - "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths", - "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - } - ], - "enums": [ - { - "name": "NullDataOptions", - "definition_uri": "http://w3id.org/ontogpt/core/NullDataOptions", - "from_schema": "http://w3id.org/ontogpt/core", - "permissible_values": [ - { - "text": "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "meaning": "NCIT:C149701" - }, - { - "text": "NOT_APPLICABLE", - "meaning": "NCIT:C18902", - "aliases": [ - "not applicable", - "N/A" - ] - }, - { - "text": "NOT_MENTIONED" - } - ] - } - ], - "slots": [ - { - "name": "dataset__packageid", - "annotations": [ - { - "tag": "prompt", - "value": "single unique identifier for the dataset", - "@type": "Annotation" - } - ], - "description": "The internal identifier for the dataset", - "from_schema": "http://w3id.org/ontogpt/environmental-metadata", - "slot_uri": "http://w3id.org/ontogpt/environmental-metadatapackageid", - "alias": "packageid", - "owner": "Dataset", - "domain_of": [ - "Dataset" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "dataset__topic", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of scientific areas of study concerning the sample(s)", - "@type": "Annotation" - } - ], - "description": "the general scientific area of study concerning the sample(s)", - "from_schema": "http://w3id.org/ontogpt/environmental-metadata", - "slot_uri": "http://w3id.org/ontogpt/environmental-metadatatopic", - "multivalued": true, - "alias": "topic", - "owner": "Dataset", - "domain_of": [ - "Dataset" - ], - "range": "Topic", - "@type": "SlotDefinition" - }, - { - "name": "dataset__location", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of geographic locations of sample isolations", - "@type": "Annotation" - } - ], - "description": "the geographic location where the sample was isolated", - "from_schema": "http://w3id.org/ontogpt/environmental-metadata", - "slot_uri": "http://w3id.org/ontogpt/environmental-metadatalocation", - "multivalued": true, - "alias": "location", - "owner": "Dataset", - "domain_of": [ - "Dataset" - ], - "range": "Location", - "@type": "SlotDefinition" - }, - { - "name": "dataset__environmental_material", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of environmental materials", - "@type": "Annotation" - } - ], - "description": "the environmental material that was sampled", - "from_schema": "http://w3id.org/ontogpt/environmental-metadata", - "slot_uri": "http://w3id.org/ontogpt/environmental-metadataenvironmental_material", - "multivalued": true, - "alias": "environmental_material", - "owner": "Dataset", - "domain_of": [ - "Dataset" - ], - "range": "EnvironmentalMaterial", - "@type": "SlotDefinition" - }, - { - "name": "dataset__environments", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of environmental contexts in which the study was conducted", - "@type": "Annotation" - } - ], - "description": "the environmental context in which the study was conducted", - "from_schema": "http://w3id.org/ontogpt/environmental-metadata", - "slot_uri": "http://w3id.org/ontogpt/environmental-metadataenvironments", - "multivalued": true, - "alias": "environments", - "owner": "Dataset", - "domain_of": [ - "Dataset" - ], - "range": "Environment", - "@type": "SlotDefinition" - }, - { - "name": "dataset__methods", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of methods used in measuring sample variables", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/environmental-metadata", - "slot_uri": "http://w3id.org/ontogpt/environmental-metadatamethods", - "multivalued": true, - "alias": "methods", - "owner": "Dataset", - "domain_of": [ - "Dataset" - ], - "range": "Method", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_id", - "alias": "input_id", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_title", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_title", - "alias": "input_title", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_text", - "alias": "input_text", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__raw_completion_output", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/raw_completion_output", - "alias": "raw_completion_output", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__prompt", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/prompt", - "alias": "prompt", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__extracted_object", - "description": "The complex objects extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/extracted_object", - "alias": "extracted_object", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__named_entities", - "description": "Named entities extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/named_entities", - "multivalued": true, - "alias": "named_entities", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "identifier": true, - "alias": "id", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "required": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "from_schema": "http://w3id.org/ontogpt/core", - "aliases": [ - "name" - ], - "mappings": [ - "http://example.org/UNKNOWN/rdfs/label" - ], - "slot_uri": "http://example.org/UNKNOWN/rdfs/label", - "alias": "label", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject", - "alias": "subject", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__predicate", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/predicate", - "alias": "predicate", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "triple__object", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object", - "alias": "object", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/qualifier", - "alias": "qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_qualifier", - "alias": "subject_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_qualifier", - "alias": "object_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/publication", - "alias": "publication", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__triples", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/triples", - "multivalued": true, - "alias": "triples", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "publication__id", - "description": "The publication identifier", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "alias": "id", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__title", - "description": "The title of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/title", - "alias": "title", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__abstract", - "description": "The abstract of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/abstract", - "alias": "abstract", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__combined_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/combined_text", - "alias": "combined_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__full_text", - "description": "The full text of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/full_text", - "alias": "full_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__subject_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_text", - "alias": "subject_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_id", - "alias": "object_id", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_text", - "alias": "object_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - } - ], - "classes": [ - { - "name": "Dataset", - "definition_uri": "http://w3id.org/ontogpt/environmental-metadataDataset", - "from_schema": "http://w3id.org/ontogpt/environmental-metadata", - "slots": [ - "dataset__packageid", - "dataset__topic", - "dataset__location", - "dataset__environmental_material", - "dataset__environments", - "dataset__methods" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "packageid", - "annotations": [ - { - "tag": "prompt", - "value": "single unique identifier for the dataset", - "@type": "Annotation" - } - ], - "description": "The internal identifier for the dataset", - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "topic", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of scientific areas of study concerning the sample(s)", - "@type": "Annotation" - } - ], - "description": "the general scientific area of study concerning the sample(s)", - "multivalued": true, - "range": "Topic", - "@type": "SlotDefinition" - }, - { - "name": "location", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of geographic locations of sample isolations", - "@type": "Annotation" - } - ], - "description": "the geographic location where the sample was isolated", - "multivalued": true, - "range": "Location", - "@type": "SlotDefinition" - }, - { - "name": "environmental_material", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of environmental materials", - "@type": "Annotation" - } - ], - "description": "the environmental material that was sampled", - "multivalued": true, - "range": "EnvironmentalMaterial", - "@type": "SlotDefinition" - }, - { - "name": "environments", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of environmental contexts in which the study was conducted", - "@type": "Annotation" - } - ], - "description": "the environmental context in which the study was conducted", - "multivalued": true, - "range": "Environment", - "@type": "SlotDefinition" - }, - { - "name": "methods", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of methods used in measuring sample variables", - "@type": "Annotation" - } - ], - "multivalued": true, - "range": "Method", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/environmental-metadataDataset", - "tree_root": true, - "@type": "ClassDefinition" - }, - { - "name": "Topic", - "id_prefixes": [ - "ENVTHES" - ], - "definition_uri": "http://w3id.org/ontogpt/environmental-metadataTopic", - "annotations": [ - { - "tag": "annotators", - "value": "bioportal:ENVTHES", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/environmental-metadata", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/environmental-metadataTopic", - "@type": "ClassDefinition" - }, - { - "name": "Location", - "id_prefixes": [ - "ENVO", - "GAZ" - ], - "definition_uri": "http://w3id.org/ontogpt/environmental-metadataLocation", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:envo, bioportal:GAZ", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/environmental-metadata", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/environmental-metadataLocation", - "@type": "ClassDefinition" - }, - { - "name": "EnvironmentalMaterial", - "id_prefixes": [ - "ENVO", - "ENVTHES" - ], - "definition_uri": "http://w3id.org/ontogpt/environmental-metadataEnvironmentalMaterial", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:envo, bioportal:ENVTHES", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/environmental-metadata", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/environmental-metadataEnvironmentalMaterial", - "@type": "ClassDefinition" - }, - { - "name": "Environment", - "id_prefixes": [ - "ENVO", - "ENVTHES" - ], - "definition_uri": "http://w3id.org/ontogpt/environmental-metadataEnvironment", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:envo, bioportal:ENVTHES", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/environmental-metadata", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/environmental-metadataEnvironment", - "@type": "ClassDefinition" - }, - { - "name": "Method", - "id_prefixes": [ - "ENVTHES" - ], - "definition_uri": "http://w3id.org/ontogpt/environmental-metadataMethod", - "annotations": [ - { - "tag": "annotators", - "value": "bioportal:ENVTHES", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/environmental-metadata", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/environmental-metadataMethod", - "@type": "ClassDefinition" - }, - { - "name": "Any", - "definition_uri": "http://w3id.org/ontogpt/core/Any", - "from_schema": "http://w3id.org/ontogpt/core", - "mappings": [ - "linkml:Any" - ], - "slot_usage": {}, - "class_uri": "https://w3id.org/linkml/Any", - "@type": "ClassDefinition" - }, - { - "name": "ExtractionResult", - "definition_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "description": "A result of extracting knowledge on text", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "extractionResult__input_id", - "extractionResult__input_title", - "extractionResult__input_text", - "extractionResult__raw_completion_output", - "extractionResult__prompt", - "extractionResult__extracted_object", - "extractionResult__named_entities" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "input_id", - "@type": "SlotDefinition" - }, - { - "name": "input_title", - "@type": "SlotDefinition" - }, - { - "name": "input_text", - "@type": "SlotDefinition" - }, - { - "name": "raw_completion_output", - "@type": "SlotDefinition" - }, - { - "name": "prompt", - "@type": "SlotDefinition" - }, - { - "name": "extracted_object", - "description": "The complex objects extracted from the text", - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "named_entities", - "description": "Named entities extracted from the text", - "multivalued": true, - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "@type": "ClassDefinition" - }, - { - "name": "NamedEntity", - "definition_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "identifier": true, - "@type": "SlotDefinition" - }, - { - "name": "label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "aliases": [ - "name" - ], - "slot_uri": "rdfs:label", - "range": "string", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "@type": "ClassDefinition" - }, - { - "name": "CompoundExpression", - "definition_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "@type": "ClassDefinition" - }, - { - "name": "Triple", - "definition_uri": "http://w3id.org/ontogpt/core/Triple", - "description": "Abstract parent for Relation Extraction tasks", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "CompoundExpression", - "abstract": true, - "slots": [ - "triple__subject", - "triple__predicate", - "triple__object", - "triple__qualifier", - "triple__subject_qualifier", - "triple__object_qualifier" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "predicate", - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "object", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Triple", - "@type": "ClassDefinition" - }, - { - "name": "TextWithTriples", - "definition_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "textWithTriples__publication", - "textWithTriples__triples" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "triples", - "multivalued": true, - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "@type": "ClassDefinition" - }, - { - "name": "RelationshipType", - "id_prefixes": [ - "RO", - "biolink" - ], - "definition_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "@type": "ClassDefinition" - }, - { - "name": "Publication", - "definition_uri": "http://w3id.org/ontogpt/core/Publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "publication__id", - "publication__title", - "publication__abstract", - "publication__combined_text", - "publication__full_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "description": "The publication identifier", - "@type": "SlotDefinition" - }, - { - "name": "title", - "description": "The title of the publication", - "@type": "SlotDefinition" - }, - { - "name": "abstract", - "description": "The abstract of the publication", - "@type": "SlotDefinition" - }, - { - "name": "combined_text", - "@type": "SlotDefinition" - }, - { - "name": "full_text", - "description": "The full text of the publication", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Publication", - "@type": "ClassDefinition" - }, - { - "name": "AnnotatorResult", - "definition_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "annotatorResult__subject_text", - "annotatorResult__object_id", - "annotatorResult__object_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject_text", - "@type": "SlotDefinition" - }, - { - "name": "object_id", - "@type": "SlotDefinition" - }, - { - "name": "object_text", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "@type": "ClassDefinition" - } - ], - "metamodel_version": "1.7.0", - "source_file": "environmental_metadata.yaml", - "source_file_date": "2023-06-24T17:09:53", - "source_file_size": 2681, - "generation_date": "2023-08-07T10:52:57", - "@type": "SchemaDefinition", - "@context": [ - "projects/environmental_metadata/jsonld/environmental_metadata.context.jsonld", - "https://w3id.org/linkml/types.context.jsonld", - "core.context.jsonld", - { - "@base": "http://w3id.org/ontogpt/environmental-metadata" - } - ] -} diff --git a/projects/environmental_metadata/jsonschema/environmental_metadata.schema.json b/projects/environmental_metadata/jsonschema/environmental_metadata.schema.json deleted file mode 100644 index ab7b0059c..000000000 --- a/projects/environmental_metadata/jsonschema/environmental_metadata.schema.json +++ /dev/null @@ -1,322 +0,0 @@ -{ - "$defs": { - "AnnotatorResult": { - "additionalProperties": false, - "description": "", - "properties": { - "object_id": { - "type": "string" - }, - "object_text": { - "type": "string" - }, - "subject_text": { - "type": "string" - } - }, - "title": "AnnotatorResult", - "type": "object" - }, - "Any": { - "additionalProperties": true, - "description": "", - "title": "Any", - "type": "object" - }, - "Dataset": { - "additionalProperties": false, - "description": "", - "properties": { - "environmental_material": { - "description": "the environmental material that was sampled", - "items": { - "type": "string" - }, - "type": "array" - }, - "environments": { - "description": "the environmental context in which the study was conducted", - "items": { - "type": "string" - }, - "type": "array" - }, - "location": { - "description": "the geographic location where the sample was isolated", - "items": { - "type": "string" - }, - "type": "array" - }, - "methods": { - "items": { - "type": "string" - }, - "type": "array" - }, - "packageid": { - "description": "The internal identifier for the dataset", - "type": "string" - }, - "topic": { - "description": "the general scientific area of study concerning the sample(s)", - "items": { - "type": "string" - }, - "type": "array" - } - }, - "title": "Dataset", - "type": "object" - }, - "Environment": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Environment", - "type": "object" - }, - "EnvironmentalMaterial": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "EnvironmentalMaterial", - "type": "object" - }, - "ExtractionResult": { - "additionalProperties": false, - "description": "A result of extracting knowledge on text", - "properties": { - "extracted_object": { - "$ref": "#/$defs/Any", - "description": "The complex objects extracted from the text" - }, - "input_id": { - "type": "string" - }, - "input_text": { - "type": "string" - }, - "input_title": { - "type": "string" - }, - "named_entities": { - "description": "Named entities extracted from the text", - "items": { - "$ref": "#/$defs/Any" - }, - "type": "array" - }, - "prompt": { - "type": "string" - }, - "raw_completion_output": { - "type": "string" - } - }, - "title": "ExtractionResult", - "type": "object" - }, - "Location": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Location", - "type": "object" - }, - "Method": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Method", - "type": "object" - }, - "NullDataOptions": { - "description": "", - "enum": [ - "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "NOT_APPLICABLE", - "NOT_MENTIONED" - ], - "title": "NullDataOptions", - "type": "string" - }, - "Publication": { - "additionalProperties": false, - "description": "", - "properties": { - "abstract": { - "description": "The abstract of the publication", - "type": "string" - }, - "combined_text": { - "type": "string" - }, - "full_text": { - "description": "The full text of the publication", - "type": "string" - }, - "id": { - "description": "The publication identifier", - "type": "string" - }, - "title": { - "description": "The title of the publication", - "type": "string" - } - }, - "title": "Publication", - "type": "object" - }, - "RelationshipType": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "RelationshipType", - "type": "object" - }, - "TextWithTriples": { - "additionalProperties": false, - "description": "", - "properties": { - "publication": { - "$ref": "#/$defs/Publication" - }, - "triples": { - "items": { - "$ref": "#/$defs/Triple" - }, - "type": "array" - } - }, - "title": "TextWithTriples", - "type": "object" - }, - "Topic": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Topic", - "type": "object" - } - }, - "$id": "http://w3id.org/ontogpt/environmental-metadata", - "$schema": "http://json-schema.org/draft-07/schema#", - "additionalProperties": true, - "metamodel_version": "1.7.0", - "properties": { - "environmental_material": { - "description": "the environmental material that was sampled", - "items": { - "type": "string" - }, - "type": "array" - }, - "environments": { - "description": "the environmental context in which the study was conducted", - "items": { - "type": "string" - }, - "type": "array" - }, - "location": { - "description": "the geographic location where the sample was isolated", - "items": { - "type": "string" - }, - "type": "array" - }, - "methods": { - "items": { - "type": "string" - }, - "type": "array" - }, - "packageid": { - "description": "The internal identifier for the dataset", - "type": "string" - }, - "topic": { - "description": "the general scientific area of study concerning the sample(s)", - "items": { - "type": "string" - }, - "type": "array" - } - }, - "title": "environmental-metadata", - "type": "object", - "version": null -} \ No newline at end of file diff --git a/projects/environmental_metadata/owl/environmental_metadata.owl.ttl b/projects/environmental_metadata/owl/environmental_metadata.owl.ttl deleted file mode 100644 index 9da750475..000000000 --- a/projects/environmental_metadata/owl/environmental_metadata.owl.ttl +++ /dev/null @@ -1,459 +0,0 @@ -@prefix IAO: <http://purl.obolibrary.org/obo/IAO_> . -@prefix envmd: <http://w3id.org/ontogpt/environmental-metadata> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix owl: <http://www.w3.org/2002/07/owl#> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . -@prefix skos: <http://www.w3.org/2004/02/skos/core#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -envmd: a owl:Ontology ; - rdfs:label "environmental-metadata" ; - IAO:0000700 <http://w3id.org/ontogpt/core/AnnotatorResult>, - <http://w3id.org/ontogpt/core/Any>, - <http://w3id.org/ontogpt/core/CompoundExpression>, - <http://w3id.org/ontogpt/core/ExtractionResult>, - <http://w3id.org/ontogpt/core/NamedEntity>, - <http://w3id.org/ontogpt/core/Publication>, - <http://w3id.org/ontogpt/core/TextWithTriples>, - envmd:Dataset ; - linkml:classes "{'Dataset': ClassDefinition(name='Dataset', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/environmental-metadataDataset', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/environmental-metadata', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['dataset__packageid', 'dataset__topic', 'dataset__location', 'dataset__environmental_material', 'dataset__environments', 'dataset__methods'], slot_usage={}, attributes={'packageid': SlotDefinition(name='packageid', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='single unique identifier for the dataset', extensions={}, annotations={})}, description='The internal identifier for the dataset', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=False, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'topic': SlotDefinition(name='topic', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of scientific areas of study concerning the sample(s)', extensions={}, annotations={})}, description='the general scientific area of study concerning the sample(s)', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Topic', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'location': SlotDefinition(name='location', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of geographic locations of sample isolations', extensions={}, annotations={})}, description='the geographic location where the sample was isolated', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Location', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'environmental_material': SlotDefinition(name='environmental_material', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of environmental materials', extensions={}, annotations={})}, description='the environmental material that was sampled', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='EnvironmentalMaterial', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'environments': SlotDefinition(name='environments', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of environmental contexts in which the study was conducted', extensions={}, annotations={})}, description='the environmental context in which the study was conducted', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Environment', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'methods': SlotDefinition(name='methods', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of methods used in measuring sample variables', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Method', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='envmd:Dataset', subclass_of=None, union_of=[], defining_slots=[], tree_root=True, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Topic': ClassDefinition(name='Topic', id_prefixes=['ENVTHES'], definition_uri='http://w3id.org/ontogpt/environmental-metadataTopic', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='bioportal:ENVTHES', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/environmental-metadata', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='envmd:Topic', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Location': ClassDefinition(name='Location', id_prefixes=['ENVO', 'GAZ'], definition_uri='http://w3id.org/ontogpt/environmental-metadataLocation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:envo, bioportal:GAZ', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/environmental-metadata', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='envmd:Location', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'EnvironmentalMaterial': ClassDefinition(name='EnvironmentalMaterial', id_prefixes=['ENVO', 'ENVTHES'], definition_uri='http://w3id.org/ontogpt/environmental-metadataEnvironmentalMaterial', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:envo, bioportal:ENVTHES', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/environmental-metadata', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='envmd:EnvironmentalMaterial', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Environment': ClassDefinition(name='Environment', id_prefixes=['ENVO', 'ENVTHES'], definition_uri='http://w3id.org/ontogpt/environmental-metadataEnvironment', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:envo, bioportal:ENVTHES', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/environmental-metadata', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='envmd:Environment', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Method': ClassDefinition(name='Method', id_prefixes=['ENVTHES'], definition_uri='http://w3id.org/ontogpt/environmental-metadataMethod', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='bioportal:ENVTHES', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/environmental-metadata', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='envmd:Method', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Any': ClassDefinition(name='Any', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Any', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=['linkml:Any'], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='linkml:Any', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ExtractionResult': ClassDefinition(name='ExtractionResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/ExtractionResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A result of extracting knowledge on text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['extractionResult__input_id', 'extractionResult__input_title', 'extractionResult__input_text', 'extractionResult__raw_completion_output', 'extractionResult__prompt', 'extractionResult__extracted_object', 'extractionResult__named_entities'], slot_usage={}, attributes={'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:ExtractionResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'NamedEntity': ClassDefinition(name='NamedEntity', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NamedEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:NamedEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'CompoundExpression': ClassDefinition(name='CompoundExpression', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/CompoundExpression', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='core:CompoundExpression', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Triple': ClassDefinition(name='Triple', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Triple', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Abstract parent for Relation Extraction tasks', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['triple__subject', 'triple__predicate', 'triple__object', 'triple__qualifier', 'triple__subject_qualifier', 'triple__object_qualifier'], slot_usage={}, attributes={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Triple', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'TextWithTriples': ClassDefinition(name='TextWithTriples', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/TextWithTriples', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['textWithTriples__publication', 'textWithTriples__triples'], slot_usage={}, attributes={'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:TextWithTriples', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'RelationshipType': ClassDefinition(name='RelationshipType', id_prefixes=['RO', 'biolink'], definition_uri='http://w3id.org/ontogpt/core/RelationshipType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='core:RelationshipType', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Publication': ClassDefinition(name='Publication', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Publication', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['publication__id', 'publication__title', 'publication__abstract', 'publication__combined_text', 'publication__full_text'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Publication', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'AnnotatorResult': ClassDefinition(name='AnnotatorResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/AnnotatorResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['annotatorResult__subject_text', 'annotatorResult__object_id', 'annotatorResult__object_text'], slot_usage={}, attributes={'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:AnnotatorResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={})}" ; - linkml:enums "{'NullDataOptions': EnumDefinition(name='NullDataOptions', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NullDataOptions', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'UNSPECIFIED_METHOD_OF_ADMINISTRATION': PermissibleValue(text='UNSPECIFIED_METHOD_OF_ADMINISTRATION', description=None, meaning='NCIT:C149701', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_APPLICABLE': PermissibleValue(text='NOT_APPLICABLE', description=None, meaning='NCIT:C18902', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['not applicable', 'N/A'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_MENTIONED': PermissibleValue(text='NOT_MENTIONED', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[])}" ; - linkml:id "http://w3id.org/ontogpt/environmental-metadata" ; - linkml:imports "core", - "linkml:types" ; - linkml:types "{'string': TypeDefinition(name='string', id_prefixes=[], definition_uri='https://w3id.org/linkml/String', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A character string', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Text'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'integer': TypeDefinition(name='integer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Integer', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An integer', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Integer'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='int', uri='xsd:integer', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'boolean': TypeDefinition(name='boolean', id_prefixes=[], definition_uri='https://w3id.org/linkml/Boolean', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A binary (true or false) value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Boolean'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Bool', uri='xsd:boolean', repr='bool', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'float': TypeDefinition(name='float', id_prefixes=[], definition_uri='https://w3id.org/linkml/Float', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:float specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Float'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:float', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'double': TypeDefinition(name='double', id_prefixes=[], definition_uri='https://w3id.org/linkml/Double', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:double specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:Float'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:double', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'decimal': TypeDefinition(name='decimal', id_prefixes=[], definition_uri='https://w3id.org/linkml/Decimal', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number with arbitrary precision that conforms to the xsd:decimal specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=['schema:Number'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Decimal', uri='xsd:decimal', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'time': TypeDefinition(name='time', id_prefixes=[], definition_uri='https://w3id.org/linkml/Time', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A time object represents a (local) time of day, independent of any particular day', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=['URI is dateTime because OWL reasoners do not work with straight date or time'], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Time'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDTime', uri='xsd:time', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date': TypeDefinition(name='date', id_prefixes=[], definition_uri='https://w3id.org/linkml/Date', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a date (year, month and day) in an idealized calendar', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[\"URI is dateTime because OWL reasoners don't work with straight date or time\"], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Date'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDate', uri='xsd:date', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'datetime': TypeDefinition(name='datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/Datetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The combination of a date and time', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:DateTime'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDateTime', uri='xsd:dateTime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date_or_datetime': TypeDefinition(name='date_or_datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/DateOrDatetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Either a date or a datetime', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='linkml:DateOrDatetime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uriorcurie': TypeDefinition(name='uriorcurie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uriorcurie', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a URI or a CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URIorCURIE', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'curie': TypeDefinition(name='curie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Curie', local_names={}, conforms_to='https://www.w3.org/TR/curie/', implements=[], extensions={}, annotations={}, description='a compact URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations this MUST be expanded to a URI', 'in non-RDF serializations MAY be serialized as the compact representation'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Curie', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uri': TypeDefinition(name='uri', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uri', local_names={}, conforms_to='https://www.ietf.org/rfc/rfc3987.txt', implements=[], extensions={}, annotations={}, description='a complete URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:URL'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URI', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ncname': TypeDefinition(name='ncname', id_prefixes=[], definition_uri='https://w3id.org/linkml/Ncname', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Prefix part of CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NCName', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'objectidentifier': TypeDefinition(name='objectidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Objectidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI or CURIE that represents an object in the model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['Used for inheritance and type checking'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='ElementIdentifier', uri='shex:iri', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'nodeidentifier': TypeDefinition(name='nodeidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Nodeidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI, CURIE or BNODE that represents a node in a model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NodeIdentifier', uri='shex:nonLiteral', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpointer': TypeDefinition(name='jsonpointer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpointer', local_names={}, conforms_to='https://datatracker.ietf.org/doc/html/rfc6901', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpath': TypeDefinition(name='jsonpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpath', local_names={}, conforms_to='https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sparqlpath': TypeDefinition(name='sparqlpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Sparqlpath', local_names={}, conforms_to='https://www.w3.org/TR/sparql11-query/#propertypaths', implements=[], extensions={}, annotations={}, description='A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:SubsetDefinition a owl:Class ; - rdfs:label "subset_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" . - -linkml:TypeDefinition a owl:Class ; - rdfs:label "type_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" ; - linkml:mixins "type_expression" . - -linkml:topValue a owl:DatatypeProperty ; - rdfs:label "value" . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "AnnotatorResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_text> ] ; - linkml:attributes "{'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/ExtractionResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ExtractionResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_text> ], - [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/named_entities> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/prompt> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_title> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/extracted_object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_id> ] ; - skos:definition "A result of extracting knowledge on text" ; - linkml:attributes "{'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/TextWithTriples> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TextWithTriples" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Publication> ; - owl:onProperty <http://w3id.org/ontogpt/core/publication> ], - [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Triple> ; - owl:onProperty <http://w3id.org/ontogpt/core/triples> ] ; - linkml:attributes "{'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/abstract> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "abstract" ; - rdfs:range linkml:String ; - skos:definition "The abstract of the publication" . - -<http://w3id.org/ontogpt/core/combined_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "combined_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/extracted_object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "extracted_object" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "The complex objects extracted from the text" . - -<http://w3id.org/ontogpt/core/full_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "full_text" ; - rdfs:range linkml:String ; - skos:definition "The full text of the publication" . - -<http://w3id.org/ontogpt/core/input_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_title" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/named_entities> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "named_entities" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "Named entities extracted from the text" . - -<http://w3id.org/ontogpt/core/object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/object_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/object_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" . - -<http://w3id.org/ontogpt/core/object_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/predicate> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "predicate" ; - rdfs:range <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/prompt> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "prompt" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/publication> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "publication" ; - envmd:prompt.skip "true" ; - rdfs:range <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "qualifier" ; - rdfs:range linkml:String ; - skos:definition "A qualifier for the statements, e.g. \"NOT\" for negation" . - -<http://w3id.org/ontogpt/core/raw_completion_output> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "raw_completion_output" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/subject> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/subject_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" . - -<http://w3id.org/ontogpt/core/subject_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "title" ; - rdfs:range linkml:String ; - skos:definition "The title of the publication" . - -<http://w3id.org/ontogpt/core/triples> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "triples" ; - rdfs:range <http://w3id.org/ontogpt/core/Triple> . - -envmd:Dataset a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Dataset" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom envmd:Location ; - owl:onProperty envmd:location ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty envmd:packageid ], - [ a owl:Restriction ; - owl:allValuesFrom envmd:Environment ; - owl:onProperty envmd:environments ], - [ a owl:Restriction ; - owl:allValuesFrom envmd:Method ; - owl:onProperty envmd:methods ], - [ a owl:Restriction ; - owl:allValuesFrom envmd:Topic ; - owl:onProperty envmd:topic ], - [ a owl:Restriction ; - owl:allValuesFrom envmd:EnvironmentalMaterial ; - owl:onProperty envmd:environmental_material ] ; - linkml:attributes "{'packageid': SlotDefinition(name='packageid', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='single unique identifier for the dataset', extensions={}, annotations={})}, description='The internal identifier for the dataset', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=False, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'topic': SlotDefinition(name='topic', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of scientific areas of study concerning the sample(s)', extensions={}, annotations={})}, description='the general scientific area of study concerning the sample(s)', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Topic', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'location': SlotDefinition(name='location', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of geographic locations of sample isolations', extensions={}, annotations={})}, description='the geographic location where the sample was isolated', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Location', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'environmental_material': SlotDefinition(name='environmental_material', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of environmental materials', extensions={}, annotations={})}, description='the environmental material that was sampled', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='EnvironmentalMaterial', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'environments': SlotDefinition(name='environments', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of environmental contexts in which the study was conducted', extensions={}, annotations={})}, description='the environmental context in which the study was conducted', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Environment', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'methods': SlotDefinition(name='methods', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of methods used in measuring sample variables', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Method', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -envmd:environmental_material a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "environmental_material" ; - envmd:prompt "semicolon-separated list of environmental materials" ; - rdfs:range envmd:EnvironmentalMaterial ; - skos:definition "the environmental material that was sampled" . - -envmd:environments a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "environments" ; - envmd:prompt "semicolon-separated list of environmental contexts in which the study was conducted" ; - rdfs:range envmd:Environment ; - skos:definition "the environmental context in which the study was conducted" . - -envmd:location a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "location" ; - envmd:prompt "semicolon-separated list of geographic locations of sample isolations" ; - rdfs:range envmd:Location ; - skos:definition "the geographic location where the sample was isolated" . - -envmd:methods a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "methods" ; - envmd:prompt "semicolon-separated list of methods used in measuring sample variables" ; - rdfs:range envmd:Method . - -envmd:packageid a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "packageid" ; - envmd:prompt "single unique identifier for the dataset" ; - rdfs:range linkml:String ; - skos:definition "The internal identifier for the dataset" . - -envmd:topic a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "topic" ; - envmd:prompt "semicolon-separated list of scientific areas of study concerning the sample(s)" ; - rdfs:range envmd:Topic ; - skos:definition "the general scientific area of study concerning the sample(s)" . - -<http://example.org/UNKNOWN/rdfs/label> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "label" ; - envmd:owl "AnnotationProperty, AnnotationAssertion" ; - rdfs:range linkml:String ; - skos:altLabel "name" ; - skos:definition "The label (name) of the named thing" ; - skos:exactMatch <http://example.org/UNKNOWN/rdfs/label> . - -<http://purl.obolibrary.org/obo/NCIT_C149701> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "UNSPECIFIED_METHOD_OF_ADMINISTRATION" . - -<http://purl.obolibrary.org/obo/NCIT_C18902> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_APPLICABLE" . - -<http://w3id.org/ontogpt/core/CompoundExpression> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CompoundExpression" ; - linkml:attributes "{}" . - -<http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_MENTIONED" . - -<http://w3id.org/ontogpt/core/RelationshipType> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "RelationshipType" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/Triple> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Triple" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/RelationshipType> ; - owl:onProperty <http://w3id.org/ontogpt/core/predicate> ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - skos:definition "Abstract parent for Relation Extraction tasks" ; - linkml:attributes "{'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -<http://w3id.org/ontogpt/core/id> a owl:ObjectProperty, - linkml:SlotDefinition . - -envmd:Environment a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Environment" ; - envmd:annotators "sqlite:obo:envo, bioportal:ENVTHES" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -envmd:EnvironmentalMaterial a owl:Class, - linkml:ClassDefinition ; - rdfs:label "EnvironmentalMaterial" ; - envmd:annotators "sqlite:obo:envo, bioportal:ENVTHES" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -envmd:Location a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Location" ; - envmd:annotators "sqlite:obo:envo, bioportal:GAZ" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -envmd:Method a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Method" ; - envmd:annotators "bioportal:ENVTHES" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -envmd:Topic a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Topic" ; - envmd:annotators "bioportal:ENVTHES" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/NullDataOptions> a owl:Class, - linkml:EnumDefinition ; - rdfs:label "NullDataOptions" ; - owl:unionOf ( <http://purl.obolibrary.org/obo/NCIT_C149701> <http://purl.obolibrary.org/obo/NCIT_C18902> <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> ) ; - linkml:permissible_values <http://purl.obolibrary.org/obo/NCIT_C149701>, - <http://purl.obolibrary.org/obo/NCIT_C18902>, - <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> . - -<http://w3id.org/ontogpt/core/Publication> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Publication" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/full_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/title> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/combined_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/abstract> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/Any> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Any" ; - skos:exactMatch linkml:Any ; - linkml:attributes "{}" . - -<http://w3id.org/ontogpt/core/NamedEntity> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "NamedEntity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://example.org/UNKNOWN/rdfs/label> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:ClassDefinition a owl:Class ; - rdfs:label "class_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "class_expression" . - -linkml:SlotDefinition a owl:Class ; - rdfs:label "slot_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "slot_expression" . - - diff --git a/projects/environmental_metadata/prefixmap/environmental_metadata.yaml b/projects/environmental_metadata/prefixmap/environmental_metadata.yaml deleted file mode 100644 index 43f93149a..000000000 --- a/projects/environmental_metadata/prefixmap/environmental_metadata.yaml +++ /dev/null @@ -1,38 +0,0 @@ -{ - "ENVO": "http://example.org/UNKNOWN/ENVO/", - "ENVTHES": "http://example.org/UNKNOWN/ENVTHES/", - "GAZ": "http://example.org/UNKNOWN/GAZ/", - "RO": "http://purl.obolibrary.org/obo/RO_", - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "envmd": "http://w3id.org/ontogpt/environmental-metadata", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } -} diff --git a/projects/environmental_metadata/protobuf/environmental_metadata.proto b/projects/environmental_metadata/protobuf/environmental_metadata.proto deleted file mode 100644 index 5ce9c7df5..000000000 --- a/projects/environmental_metadata/protobuf/environmental_metadata.proto +++ /dev/null @@ -1,69 +0,0 @@ -message AnnotatorResult - { - string subjectText = 0 - string objectId = 0 - string objectText = 0 - } -message Dataset - { - string packageid = 0 - repeated topic topic = 0 - repeated location location = 0 - repeated environmentalMaterial environmentalMaterial = 0 - repeated environment environments = 0 - repeated method methods = 0 - } -message Environment - { - string id = 0 - string label = 0 - } -message EnvironmentalMaterial - { - string id = 0 - string label = 0 - } -// A result of extracting knowledge on text -message ExtractionResult - { - string inputId = 0 - string inputTitle = 0 - string inputText = 0 - string rawCompletionOutput = 0 - string prompt = 0 - any extractedObject = 0 - repeated any namedEntities = 0 - } -message Location - { - string id = 0 - string label = 0 - } -message Method - { - string id = 0 - string label = 0 - } -message Publication - { - string id = 0 - string title = 0 - string abstract = 0 - string combinedText = 0 - string fullText = 0 - } -message RelationshipType - { - string id = 0 - string label = 0 - } -message TextWithTriples - { - publication publication = 0 - repeated triple triples = 0 - } -message Topic - { - string id = 0 - string label = 0 - } diff --git a/projects/environmental_metadata/shacl/environmental_metadata.shacl.ttl b/projects/environmental_metadata/shacl/environmental_metadata.shacl.ttl deleted file mode 100644 index b45ae3a9b..000000000 --- a/projects/environmental_metadata/shacl/environmental_metadata.shacl.ttl +++ /dev/null @@ -1,267 +0,0 @@ -@prefix envmd: <http://w3id.org/ontogpt/environmental-metadata> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix sh: <http://www.w3.org/ns/shacl#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject_text> ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/object_id> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object_text> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/AnnotatorResult> . - -<http://w3id.org/ontogpt/core/CompoundExpression> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass <http://w3id.org/ontogpt/core/CompoundExpression> . - -<http://w3id.org/ontogpt/core/ExtractionResult> a sh:NodeShape ; - sh:closed true ; - sh:description "A result of extracting knowledge on text" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/input_text> ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/input_id> ], - [ sh:class linkml:Any ; - sh:description "The complex objects extracted from the text" ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/extracted_object> ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/input_title> ], - [ sh:class linkml:Any ; - sh:description "Named entities extracted from the text" ; - sh:nodeKind sh:BlankNode ; - sh:order 6 ; - sh:path <http://w3id.org/ontogpt/core/named_entities> ], - [ sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/prompt> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/raw_completion_output> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/ExtractionResult> . - -<http://w3id.org/ontogpt/core/TextWithTriples> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/Publication> ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/publication> ], - [ sh:class <http://w3id.org/ontogpt/core/Triple> ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/triples> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/TextWithTriples> . - -envmd:Dataset a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class envmd:EnvironmentalMaterial ; - sh:description "the environmental material that was sampled" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path envmd:environmental_material ], - [ sh:class envmd:Method ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path envmd:methods ], - [ sh:class envmd:Topic ; - sh:description "the general scientific area of study concerning the sample(s)" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path envmd:topic ], - [ sh:class envmd:Location ; - sh:description "the geographic location where the sample was isolated" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path envmd:location ], - [ sh:description "The internal identifier for the dataset" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path envmd:packageid ], - [ sh:class envmd:Environment ; - sh:description "the environmental context in which the study was conducted" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path envmd:environments ] ; - sh:targetClass envmd:Dataset . - -<http://w3id.org/ontogpt/core/Publication> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The title of the publication" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/title> ], - [ sh:description "The publication identifier" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/combined_text> ], - [ sh:description "The full text of the publication" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/full_text> ], - [ sh:description "The abstract of the publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/abstract> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/RelationshipType> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/Triple> a sh:NodeShape ; - sh:closed false ; - sh:description "Abstract parent for Relation Extraction tasks" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/object_qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/RelationshipType> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/predicate> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object> ], - [ sh:description "A qualifier for the statements, e.g. \"NOT\" for negation" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/subject_qualifier> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Triple> . - -envmd:Environment a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass envmd:Environment . - -envmd:EnvironmentalMaterial a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass envmd:EnvironmentalMaterial . - -envmd:Location a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass envmd:Location . - -envmd:Method a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass envmd:Method . - -envmd:Topic a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass envmd:Topic . - -linkml:Any a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass linkml:Any . - -<http://w3id.org/ontogpt/core/NamedEntity> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/NamedEntity> . - diff --git a/projects/environmental_metadata/shex/environmental_metadata.shex b/projects/environmental_metadata/shex/environmental_metadata.shex deleted file mode 100644 index cd72663c0..000000000 --- a/projects/environmental_metadata/shex/environmental_metadata.shex +++ /dev/null @@ -1,192 +0,0 @@ -BASE <http://w3id.org/ontogpt/environmental-metadata/> -PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> -PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> -PREFIX linkml: <https://w3id.org/linkml/> -PREFIX core: <http://w3id.org/ontogpt/core/> -PREFIX rdfs1: <http://example.org/UNKNOWN/rdfs/> - - -linkml:String xsd:string - -linkml:Integer xsd:integer - -linkml:Boolean xsd:boolean - -linkml:Float xsd:float - -linkml:Double xsd:double - -linkml:Decimal xsd:decimal - -linkml:Time xsd:time - -linkml:Date xsd:date - -linkml:Datetime xsd:dateTime - -linkml:DateOrDatetime linkml:DateOrDatetime - -linkml:Uriorcurie IRI - -linkml:Curie xsd:string - -linkml:Uri IRI - -linkml:Ncname xsd:string - -linkml:Objectidentifier IRI - -linkml:Nodeidentifier NONLITERAL - -linkml:Jsonpointer xsd:string - -linkml:Jsonpath xsd:string - -linkml:Sparqlpath xsd:string - -core:AnnotatorResult CLOSED { - ( $core:AnnotatorResult_tes ( core:subject_text @linkml:String ? ; - core:object_id @linkml:String ? ; - core:object_text @linkml:String ? - ) ; - rdf:type [ core:AnnotatorResult ] ? - ) -} - -core:Any CLOSED { - ( $core:Any_tes rdf:type . * ; - rdf:type [ linkml:Any ] ? - ) -} - -core:CompoundExpression ( - { - ( $core:CompoundExpression_tes rdf:type . * ; - rdf:type [ core:CompoundExpression ] ? - ) - } OR @core:Triple -) - -<http://w3id.org/ontogpt/environmental-metadataDataset> CLOSED { - ( $<http://w3id.org/ontogpt/environmental-metadataDataset_tes> ( <http://w3id.org/ontogpt/environmental-metadatapackageid> - @linkml:String ? ; - <http://w3id.org/ontogpt/environmental-metadatatopic> @<http://w3id.org/ontogpt/environmental-metadataTopic> * ; - <http://w3id.org/ontogpt/environmental-metadatalocation> @<http://w3id.org/ontogpt/environmental-metadataLocation> * ; - <http://w3id.org/ontogpt/environmental-metadataenvironmental_material> - @<http://w3id.org/ontogpt/environmental-metadataEnvironmentalMaterial> * ; - <http://w3id.org/ontogpt/environmental-metadataenvironments> @<http://w3id.org/ontogpt/environmental-metadataEnvironment> - * ; - <http://w3id.org/ontogpt/environmental-metadatamethods> @<http://w3id.org/ontogpt/environmental-metadataMethod> * - ) ; - rdf:type [ <http://w3id.org/ontogpt/environmental-metadataDataset> ] ? - ) -} - -<http://w3id.org/ontogpt/environmental-metadataEnvironment> CLOSED { - ( $<http://w3id.org/ontogpt/environmental-metadataEnvironment_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <http://w3id.org/ontogpt/environmental-metadataEnvironment> ] - ) -} - -<http://w3id.org/ontogpt/environmental-metadataEnvironmentalMaterial> CLOSED { - ( $<http://w3id.org/ontogpt/environmental-metadataEnvironmentalMaterial_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <http://w3id.org/ontogpt/environmental-metadataEnvironmentalMaterial> ] - ) -} - -core:ExtractionResult CLOSED { - ( $core:ExtractionResult_tes ( core:input_id @linkml:String ? ; - core:input_title @linkml:String ? ; - core:input_text @linkml:String ? ; - core:raw_completion_output @linkml:String ? ; - core:prompt @linkml:String ? ; - core:extracted_object @core:Any ? ; - core:named_entities @core:Any * - ) ; - rdf:type [ core:ExtractionResult ] ? - ) -} - -<http://w3id.org/ontogpt/environmental-metadataLocation> CLOSED { - ( $<http://w3id.org/ontogpt/environmental-metadataLocation_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <http://w3id.org/ontogpt/environmental-metadataLocation> ] - ) -} - -<http://w3id.org/ontogpt/environmental-metadataMethod> CLOSED { - ( $<http://w3id.org/ontogpt/environmental-metadataMethod_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <http://w3id.org/ontogpt/environmental-metadataMethod> ] - ) -} - -core:NamedEntity ( - @<http://w3id.org/ontogpt/environmental-metadataEnvironment> OR - @<http://w3id.org/ontogpt/environmental-metadataEnvironmentalMaterial> OR - @<http://w3id.org/ontogpt/environmental-metadataLocation> OR @<http://w3id.org/ontogpt/environmental-metadataMethod> OR - @core:RelationshipType OR @<http://w3id.org/ontogpt/environmental-metadataTopic> -) - -core:NamedEntity_struct { - ( $core:NamedEntity_tes rdfs1:label @linkml:String ? ; - rdf:type [ core:NamedEntity ] - ) -} - -core:Publication CLOSED { - ( $core:Publication_tes ( core:id @linkml:String ? ; - core:title @linkml:String ? ; - core:abstract @linkml:String ? ; - core:combined_text @linkml:String ? ; - core:full_text @linkml:String ? - ) ; - rdf:type [ core:Publication ] ? - ) -} - -core:RelationshipType CLOSED { - ( $core:RelationshipType_tes ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ core:RelationshipType ] - ) -} - -core:TextWithTriples CLOSED { - ( $core:TextWithTriples_tes ( core:publication @core:Publication ? ; - core:triples @core:Triple * - ) ; - rdf:type [ core:TextWithTriples ] ? - ) -} - -<http://w3id.org/ontogpt/environmental-metadataTopic> CLOSED { - ( $<http://w3id.org/ontogpt/environmental-metadataTopic_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <http://w3id.org/ontogpt/environmental-metadataTopic> ] - ) -} - -core:Triple { - ( $core:Triple_tes ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - core:subject @core:NamedEntity ? ; - core:predicate @core:RelationshipType ? ; - core:object @core:NamedEntity ? ; - core:qualifier @linkml:String ? ; - core:subject_qualifier @core:NamedEntity ? ; - core:object_qualifier @core:NamedEntity ? - ) ; - rdf:type [ core:Triple ] ? - ) -} - - diff --git a/projects/environmental_metadata/sqlschema/environmental_metadata.sql b/projects/environmental_metadata/sqlschema/environmental_metadata.sql deleted file mode 100644 index db165bba3..000000000 --- a/projects/environmental_metadata/sqlschema/environmental_metadata.sql +++ /dev/null @@ -1,80 +0,0 @@ - - -CREATE TABLE "AnnotatorResult" ( - subject_text TEXT, - object_id TEXT, - object_text TEXT, - PRIMARY KEY (subject_text, object_id, object_text) -); - -CREATE TABLE "Dataset" ( - packageid TEXT, - topic TEXT, - location TEXT, - environmental_material TEXT, - environments TEXT, - methods TEXT, - PRIMARY KEY (packageid, topic, location, environmental_material, environments, methods) -); - -CREATE TABLE "Environment" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "EnvironmentalMaterial" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "ExtractionResult" ( - input_id TEXT, - input_title TEXT, - input_text TEXT, - raw_completion_output TEXT, - prompt TEXT, - extracted_object TEXT, - named_entities TEXT, - PRIMARY KEY (input_id, input_title, input_text, raw_completion_output, prompt, extracted_object, named_entities) -); - -CREATE TABLE "Location" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Method" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Publication" ( - id TEXT, - title TEXT, - abstract TEXT, - combined_text TEXT, - full_text TEXT, - PRIMARY KEY (id, title, abstract, combined_text, full_text) -); - -CREATE TABLE "RelationshipType" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "TextWithTriples" ( - publication TEXT, - triples TEXT, - PRIMARY KEY (publication, triples) -); - -CREATE TABLE "Topic" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); diff --git a/projects/environmental_sample/docs/AnnotatorResult.md b/projects/environmental_sample/docs/AnnotatorResult.md deleted file mode 100644 index 47c39c704..000000000 --- a/projects/environmental_sample/docs/AnnotatorResult.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Class: AnnotatorResult - - - - -URI: [sample:AnnotatorResult](http://w3id.org/ontogpt/environmental-sample/AnnotatorResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F])](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F]) - -## Attributes - - -### Own - - * [➞subject_text](annotatorResult__subject_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_id](annotatorResult__object_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_text](annotatorResult__object_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) diff --git a/projects/environmental_sample/docs/Any.md b/projects/environmental_sample/docs/Any.md deleted file mode 100644 index fa11e8c74..000000000 --- a/projects/environmental_sample/docs/Any.md +++ /dev/null @@ -1,25 +0,0 @@ - -# Class: Any - - - - -URI: [sample:Any](http://w3id.org/ontogpt/environmental-sample/Any) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult])](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult]) - -## Referenced by Class - - * **None** *[➞extracted_object](extractionResult__extracted_object.md)* <sub>0..1</sub> **[Any](Any.md)** - * **None** *[➞named_entities](extractionResult__named_entities.md)* <sub>0..\*</sub> **[Any](Any.md)** - -## Attributes - - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | linkml:Any | - diff --git a/projects/environmental_sample/docs/CausalRelationship.md b/projects/environmental_sample/docs/CausalRelationship.md deleted file mode 100644 index 983312157..000000000 --- a/projects/environmental_sample/docs/CausalRelationship.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Class: CausalRelationship - - - - -URI: [sample:CausalRelationship](http://w3id.org/ontogpt/environmental-sample/CausalRelationship) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Variable],[CompoundExpression],[Variable]<effect%200..1-%20[CausalRelationship],[Variable]<cause%200..1-%20[CausalRelationship],[Study]++-%20causal_relationships%200..*>[CausalRelationship],[CompoundExpression]^-[CausalRelationship],[Study])](https://yuml.me/diagram/nofunky;dir:TB/class/[Variable],[CompoundExpression],[Variable]<effect%200..1-%20[CausalRelationship],[Variable]<cause%200..1-%20[CausalRelationship],[Study]++-%20causal_relationships%200..*>[CausalRelationship],[CompoundExpression]^-[CausalRelationship],[Study]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞causal_relationships](study__causal_relationships.md)* <sub>0..\*</sub> **[CausalRelationship](CausalRelationship.md)** - -## Attributes - - -### Own - - * [➞cause](causalRelationship__cause.md) <sub>0..1</sub> - * Description: the variable that is the cause of the effect - * Range: [Variable](Variable.md) - * [➞effect](causalRelationship__effect.md) <sub>0..1</sub> - * Description: the things that is affected - * Range: [Variable](Variable.md) diff --git a/projects/environmental_sample/docs/CompoundExpression.md b/projects/environmental_sample/docs/CompoundExpression.md deleted file mode 100644 index 26b43451d..000000000 --- a/projects/environmental_sample/docs/CompoundExpression.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Class: CompoundExpression - - - - -URI: [sample:CompoundExpression](http://w3id.org/ontogpt/environmental-sample/CompoundExpression) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Measurement],[CompoundExpression]^-[Triple],[CompoundExpression]^-[Measurement],[CompoundExpression]^-[CausalRelationship],[CausalRelationship])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Measurement],[CompoundExpression]^-[Triple],[CompoundExpression]^-[Measurement],[CompoundExpression]^-[CausalRelationship],[CausalRelationship]) - -## Children - - * [CausalRelationship](CausalRelationship.md) - * [Measurement](Measurement.md) - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - -## Referenced by Class - - -## Attributes - diff --git a/projects/environmental_sample/docs/Environment.md b/projects/environmental_sample/docs/Environment.md deleted file mode 100644 index 424cc54eb..000000000 --- a/projects/environmental_sample/docs/Environment.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: Environment - - - - -URI: [sample:Environment](http://w3id.org/ontogpt/environmental-sample/Environment) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[Study]-%20environments%200..*>[Environment|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Environment],[Study])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[Study]-%20environments%200..*>[Environment|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Environment],[Study]) - -## Identifier prefixes - - * ENVO - * ENVTHES - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞environments](study__environments.md)* <sub>0..\*</sub> **[Environment](Environment.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/environmental_sample/docs/EnvironmentalMaterial.md b/projects/environmental_sample/docs/EnvironmentalMaterial.md deleted file mode 100644 index 79a700713..000000000 --- a/projects/environmental_sample/docs/EnvironmentalMaterial.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: EnvironmentalMaterial - - - - -URI: [sample:EnvironmentalMaterial](http://w3id.org/ontogpt/environmental-sample/EnvironmentalMaterial) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[Study]-%20environmental_material%200..*>[EnvironmentalMaterial|id(i):string;label(i):string%20%3F],[NamedEntity]^-[EnvironmentalMaterial],[Study])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[Study]-%20environmental_material%200..*>[EnvironmentalMaterial|id(i):string;label(i):string%20%3F],[NamedEntity]^-[EnvironmentalMaterial],[Study]) - -## Identifier prefixes - - * ENVO - * ENVTHES - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞environmental_material](study__environmental_material.md)* <sub>0..\*</sub> **[EnvironmentalMaterial](EnvironmentalMaterial.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/environmental_sample/docs/ExtractionResult.md b/projects/environmental_sample/docs/ExtractionResult.md deleted file mode 100644 index 4fbd920ef..000000000 --- a/projects/environmental_sample/docs/ExtractionResult.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Class: ExtractionResult - - -A result of extracting knowledge on text - -URI: [sample:ExtractionResult](http://w3id.org/ontogpt/environmental-sample/ExtractionResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any])](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any]) - -## Attributes - - -### Own - - * [➞input_id](extractionResult__input_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_title](extractionResult__input_title.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_text](extractionResult__input_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞prompt](extractionResult__prompt.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞extracted_object](extractionResult__extracted_object.md) <sub>0..1</sub> - * Description: The complex objects extracted from the text - * Range: [Any](Any.md) - * [➞named_entities](extractionResult__named_entities.md) <sub>0..\*</sub> - * Description: Named entities extracted from the text - * Range: [Any](Any.md) diff --git a/projects/environmental_sample/docs/Location.md b/projects/environmental_sample/docs/Location.md deleted file mode 100644 index ee259f0c9..000000000 --- a/projects/environmental_sample/docs/Location.md +++ /dev/null @@ -1,36 +0,0 @@ - -# Class: Location - - - - -URI: [sample:Location](http://w3id.org/ontogpt/environmental-sample/Location) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[Study]-%20location%200..*>[Location|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Location],[Study])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[Study]-%20location%200..*>[Location|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Location],[Study]) - -## Identifier prefixes - - * ENVO - * GAZ - * ENVTHES - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞location](study__location.md)* <sub>0..\*</sub> **[Location](Location.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/environmental_sample/docs/Measurement.md b/projects/environmental_sample/docs/Measurement.md deleted file mode 100644 index 47e7284cc..000000000 --- a/projects/environmental_sample/docs/Measurement.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Class: Measurement - - - - -URI: [sample:Measurement](http://w3id.org/ontogpt/environmental-sample/Measurement) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Unit],[Unit]<unit%200..1-%20[Measurement|value:string%20%3F],[Study]++-%20measurements%200..*>[Measurement],[CompoundExpression]^-[Measurement],[Study],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[Unit],[Unit]<unit%200..1-%20[Measurement|value:string%20%3F],[Study]++-%20measurements%200..*>[Measurement],[CompoundExpression]^-[Measurement],[Study],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞measurements](study__measurements.md)* <sub>0..\*</sub> **[Measurement](Measurement.md)** - -## Attributes - - -### Own - - * [➞value](measurement__value.md) <sub>0..1</sub> - * Description: the value of the measurement - * Range: [String](types/String.md) - * [➞unit](measurement__unit.md) <sub>0..1</sub> - * Description: the unit of the measurement - * Range: [Unit](Unit.md) diff --git a/projects/environmental_sample/docs/NamedEntity.md b/projects/environmental_sample/docs/NamedEntity.md deleted file mode 100644 index ac02541b8..000000000 --- a/projects/environmental_sample/docs/NamedEntity.md +++ /dev/null @@ -1,38 +0,0 @@ - -# Class: NamedEntity - - - - -URI: [sample:NamedEntity](http://w3id.org/ontogpt/environmental-sample/NamedEntity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Variable],[Unit],[RelationshipType],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[Variable],[NamedEntity]^-[Unit],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[Location],[NamedEntity]^-[EnvironmentalMaterial],[NamedEntity]^-[Environment],[Triple],[Location],[EnvironmentalMaterial],[Environment])](https://yuml.me/diagram/nofunky;dir:TB/class/[Variable],[Unit],[RelationshipType],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[Variable],[NamedEntity]^-[Unit],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[Location],[NamedEntity]^-[EnvironmentalMaterial],[NamedEntity]^-[Environment],[Triple],[Location],[EnvironmentalMaterial],[Environment]) - -## Children - - * [Environment](Environment.md) - * [EnvironmentalMaterial](EnvironmentalMaterial.md) - * [Location](Location.md) - * [RelationshipType](RelationshipType.md) - * [Unit](Unit.md) - * [Variable](Variable.md) - -## Referenced by Class - - * **None** *[➞object](triple__object.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞object_qualifier](triple__object_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject](triple__subject.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject_qualifier](triple__subject_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - -## Attributes - - -### Own - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/environmental_sample/docs/NullDataOptions.md b/projects/environmental_sample/docs/NullDataOptions.md deleted file mode 100644 index d8cfd2ea1..000000000 --- a/projects/environmental_sample/docs/NullDataOptions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Enum: NullDataOptions - - - - -URI: [sample:NullDataOptions](http://w3id.org/ontogpt/environmental-sample/NullDataOptions) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | -| UNSPECIFIED_METHOD_OF_ADMINISTRATION | | NCIT:C149701 | | -| NOT_APPLICABLE | | NCIT:C18902 | {'aliases': ['not applicable', 'N/A']} | -| NOT_MENTIONED | | | | - diff --git a/projects/environmental_sample/docs/Publication.md b/projects/environmental_sample/docs/Publication.md deleted file mode 100644 index 03a8cab13..000000000 --- a/projects/environmental_sample/docs/Publication.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Publication - - - - -URI: [sample:Publication](http://w3id.org/ontogpt/environmental-sample/Publication) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples])](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples]) - -## Referenced by Class - - * **None** *[➞publication](textWithTriples__publication.md)* <sub>0..1</sub> **[Publication](Publication.md)** - -## Attributes - - -### Own - - * [➞id](publication__id.md) <sub>0..1</sub> - * Description: The publication identifier - * Range: [String](types/String.md) - * [➞title](publication__title.md) <sub>0..1</sub> - * Description: The title of the publication - * Range: [String](types/String.md) - * [➞abstract](publication__abstract.md) <sub>0..1</sub> - * Description: The abstract of the publication - * Range: [String](types/String.md) - * [➞combined_text](publication__combined_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞full_text](publication__full_text.md) <sub>0..1</sub> - * Description: The full text of the publication - * Range: [String](types/String.md) diff --git a/projects/environmental_sample/docs/RelationshipType.md b/projects/environmental_sample/docs/RelationshipType.md deleted file mode 100644 index 833b5a697..000000000 --- a/projects/environmental_sample/docs/RelationshipType.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: RelationshipType - - - - -URI: [sample:RelationshipType](http://w3id.org/ontogpt/environmental-sample/RelationshipType) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity]) - -## Identifier prefixes - - * RO - * biolink - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞predicate](triple__predicate.md)* <sub>0..1</sub> **[RelationshipType](RelationshipType.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/environmental_sample/docs/Study.md b/projects/environmental_sample/docs/Study.md deleted file mode 100644 index cdffa2f40..000000000 --- a/projects/environmental_sample/docs/Study.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Class: Study - - - - -URI: [sample:Study](http://w3id.org/ontogpt/environmental-sample/Study) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Variable],[Measurement]<measurements%200..*-++[Study],[Variable]<variables%200..*-%20[Study],[CausalRelationship]<causal_relationships%200..*-++[Study],[Environment]<environments%200..*-%20[Study],[EnvironmentalMaterial]<environmental_material%200..*-%20[Study],[Location]<location%200..*-%20[Study],[Measurement],[Location],[EnvironmentalMaterial],[Environment],[CausalRelationship])](https://yuml.me/diagram/nofunky;dir:TB/class/[Variable],[Measurement]<measurements%200..*-++[Study],[Variable]<variables%200..*-%20[Study],[CausalRelationship]<causal_relationships%200..*-++[Study],[Environment]<environments%200..*-%20[Study],[EnvironmentalMaterial]<environmental_material%200..*-%20[Study],[Location]<location%200..*-%20[Study],[Measurement],[Location],[EnvironmentalMaterial],[Environment],[CausalRelationship]) - -## Attributes - - -### Own - - * [➞location](study__location.md) <sub>0..\*</sub> - * Description: the sites at which the study was conducted - * Range: [Location](Location.md) - * [➞environmental_material](study__environmental_material.md) <sub>0..\*</sub> - * Description: the environmental material that was sampled - * Range: [EnvironmentalMaterial](EnvironmentalMaterial.md) - * [➞environments](study__environments.md) <sub>0..\*</sub> - * Range: [Environment](Environment.md) - * [➞causal_relationships](study__causal_relationships.md) <sub>0..\*</sub> - * Range: [CausalRelationship](CausalRelationship.md) - * [➞variables](study__variables.md) <sub>0..\*</sub> - * Range: [Variable](Variable.md) - * [➞measurements](study__measurements.md) <sub>0..\*</sub> - * Range: [Measurement](Measurement.md) diff --git a/projects/environmental_sample/docs/TextWithTriples.md b/projects/environmental_sample/docs/TextWithTriples.md deleted file mode 100644 index 966723bb6..000000000 --- a/projects/environmental_sample/docs/TextWithTriples.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: TextWithTriples - - - - -URI: [sample:TextWithTriples](http://w3id.org/ontogpt/environmental-sample/TextWithTriples) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication]) - -## Attributes - - -### Own - - * [➞publication](textWithTriples__publication.md) <sub>0..1</sub> - * Range: [Publication](Publication.md) - * [➞triples](textWithTriples__triples.md) <sub>0..\*</sub> - * Range: [Triple](Triple.md) diff --git a/projects/environmental_sample/docs/Triple.md b/projects/environmental_sample/docs/Triple.md deleted file mode 100644 index 4d4252eaf..000000000 --- a/projects/environmental_sample/docs/Triple.md +++ /dev/null @@ -1,39 +0,0 @@ - -# Class: Triple - - -Abstract parent for Relation Extraction tasks - -URI: [sample:Triple](http://w3id.org/ontogpt/environmental-sample/Triple) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞triples](textWithTriples__triples.md)* <sub>0..\*</sub> **[Triple](Triple.md)** - -## Attributes - - -### Own - - * [➞subject](triple__subject.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞predicate](triple__predicate.md) <sub>0..1</sub> - * Range: [RelationshipType](RelationshipType.md) - * [➞object](triple__object.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞qualifier](triple__qualifier.md) <sub>0..1</sub> - * Description: A qualifier for the statements, e.g. "NOT" for negation - * Range: [String](types/String.md) - * [➞subject_qualifier](triple__subject_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - * Range: [NamedEntity](NamedEntity.md) - * [➞object_qualifier](triple__object_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * Range: [NamedEntity](NamedEntity.md) diff --git a/projects/environmental_sample/docs/Unit.md b/projects/environmental_sample/docs/Unit.md deleted file mode 100644 index e52b832f4..000000000 --- a/projects/environmental_sample/docs/Unit.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: Unit - - - - -URI: [sample:Unit](http://w3id.org/ontogpt/environmental-sample/Unit) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Measurement]-%20unit%200..1>[Unit|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Unit],[NamedEntity],[Measurement])](https://yuml.me/diagram/nofunky;dir:TB/class/[Measurement]-%20unit%200..1>[Unit|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Unit],[NamedEntity],[Measurement]) - -## Identifier prefixes - - * UO - * NCIT - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞unit](measurement__unit.md)* <sub>0..1</sub> **[Unit](Unit.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/environmental_sample/docs/Variable.md b/projects/environmental_sample/docs/Variable.md deleted file mode 100644 index 90bfc2919..000000000 --- a/projects/environmental_sample/docs/Variable.md +++ /dev/null @@ -1,39 +0,0 @@ - -# Class: Variable - - - - -URI: [sample:Variable](http://w3id.org/ontogpt/environmental-sample/Variable) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[CausalRelationship]-%20cause%200..1>[Variable|id(i):string;label(i):string%20%3F],[CausalRelationship]-%20effect%200..1>[Variable],[Study]-%20variables%200..*>[Variable],[NamedEntity]^-[Variable],[Study],[NamedEntity],[CausalRelationship])](https://yuml.me/diagram/nofunky;dir:TB/class/[CausalRelationship]-%20cause%200..1>[Variable|id(i):string;label(i):string%20%3F],[CausalRelationship]-%20effect%200..1>[Variable],[Study]-%20variables%200..*>[Variable],[NamedEntity]^-[Variable],[Study],[NamedEntity],[CausalRelationship]) - -## Identifier prefixes - - * ENVO - * MIXS - * PATO - * ENVTHES - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞cause](causalRelationship__cause.md)* <sub>0..1</sub> **[Variable](Variable.md)** - * **None** *[➞effect](causalRelationship__effect.md)* <sub>0..1</sub> **[Variable](Variable.md)** - * **None** *[➞variables](study__variables.md)* <sub>0..\*</sub> **[Variable](Variable.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/environmental_sample/docs/annotatorResult__object_id.md b/projects/environmental_sample/docs/annotatorResult__object_id.md deleted file mode 100644 index 0c6c250bc..000000000 --- a/projects/environmental_sample/docs/annotatorResult__object_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_id - - - - -URI: [sample:annotatorResult__object_id](http://w3id.org/ontogpt/environmental-sample/annotatorResult__object_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/environmental_sample/docs/annotatorResult__object_text.md b/projects/environmental_sample/docs/annotatorResult__object_text.md deleted file mode 100644 index 82aa42a0f..000000000 --- a/projects/environmental_sample/docs/annotatorResult__object_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_text - - - - -URI: [sample:annotatorResult__object_text](http://w3id.org/ontogpt/environmental-sample/annotatorResult__object_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/environmental_sample/docs/annotatorResult__subject_text.md b/projects/environmental_sample/docs/annotatorResult__subject_text.md deleted file mode 100644 index caf48ada0..000000000 --- a/projects/environmental_sample/docs/annotatorResult__subject_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_text - - - - -URI: [sample:annotatorResult__subject_text](http://w3id.org/ontogpt/environmental-sample/annotatorResult__subject_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/environmental_sample/docs/causalRelationship__cause.md b/projects/environmental_sample/docs/causalRelationship__cause.md deleted file mode 100644 index dd0594271..000000000 --- a/projects/environmental_sample/docs/causalRelationship__cause.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: cause - - -the variable that is the cause of the effect - -URI: [sample:causalRelationship__cause](http://w3id.org/ontogpt/environmental-sample/causalRelationship__cause) - - -## Domain and Range - -None → <sub>0..1</sub> [Variable](Variable.md) - -## Parents - - -## Children - - -## Used by - - * [CausalRelationship](CausalRelationship.md) diff --git a/projects/environmental_sample/docs/causalRelationship__effect.md b/projects/environmental_sample/docs/causalRelationship__effect.md deleted file mode 100644 index bfa059238..000000000 --- a/projects/environmental_sample/docs/causalRelationship__effect.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: effect - - -the things that is affected - -URI: [sample:causalRelationship__effect](http://w3id.org/ontogpt/environmental-sample/causalRelationship__effect) - - -## Domain and Range - -None → <sub>0..1</sub> [Variable](Variable.md) - -## Parents - - -## Children - - -## Used by - - * [CausalRelationship](CausalRelationship.md) diff --git a/projects/environmental_sample/docs/environmental_sample.md b/projects/environmental_sample/docs/environmental_sample.md deleted file mode 100644 index f40df4349..000000000 --- a/projects/environmental_sample/docs/environmental_sample.md +++ /dev/null @@ -1,121 +0,0 @@ - -# environmental-sample - - -**metamodel version:** 1.7.0 - -**version:** None - - -A template for Environmental Samples - - -### Classes - - * [AnnotatorResult](AnnotatorResult.md) - * [Any](Any.md) - * [CompoundExpression](CompoundExpression.md) - * [CausalRelationship](CausalRelationship.md) - * [Measurement](Measurement.md) - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - * [ExtractionResult](ExtractionResult.md) - A result of extracting knowledge on text - * [NamedEntity](NamedEntity.md) - * [Environment](Environment.md) - * [EnvironmentalMaterial](EnvironmentalMaterial.md) - * [Location](Location.md) - * [RelationshipType](RelationshipType.md) - * [Unit](Unit.md) - * [Variable](Variable.md) - * [Publication](Publication.md) - * [Study](Study.md) - * [TextWithTriples](TextWithTriples.md) - -### Mixins - - -### Slots - - * [➞object_id](annotatorResult__object_id.md) - * [➞object_text](annotatorResult__object_text.md) - * [➞subject_text](annotatorResult__subject_text.md) - * [➞cause](causalRelationship__cause.md) - the variable that is the cause of the effect - * [➞effect](causalRelationship__effect.md) - the things that is affected - * [➞extracted_object](extractionResult__extracted_object.md) - The complex objects extracted from the text - * [➞input_id](extractionResult__input_id.md) - * [➞input_text](extractionResult__input_text.md) - * [➞input_title](extractionResult__input_title.md) - * [➞named_entities](extractionResult__named_entities.md) - Named entities extracted from the text - * [➞prompt](extractionResult__prompt.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) - * [➞unit](measurement__unit.md) - the unit of the measurement - * [➞value](measurement__value.md) - the value of the measurement - * [➞id](namedEntity__id.md) - A unique identifier for the named entity - * [➞label](namedEntity__label.md) - The label (name) of the named thing - * [➞abstract](publication__abstract.md) - The abstract of the publication - * [➞combined_text](publication__combined_text.md) - * [➞full_text](publication__full_text.md) - The full text of the publication - * [➞id](publication__id.md) - The publication identifier - * [➞title](publication__title.md) - The title of the publication - * [➞causal_relationships](study__causal_relationships.md) - * [➞environmental_material](study__environmental_material.md) - the environmental material that was sampled - * [➞environments](study__environments.md) - * [➞location](study__location.md) - the sites at which the study was conducted - * [➞measurements](study__measurements.md) - * [➞variables](study__variables.md) - * [➞publication](textWithTriples__publication.md) - * [➞triples](textWithTriples__triples.md) - * [➞object](triple__object.md) - * [➞object_qualifier](triple__object_qualifier.md) - An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * [➞predicate](triple__predicate.md) - * [➞qualifier](triple__qualifier.md) - A qualifier for the statements, e.g. "NOT" for negation - * [➞subject](triple__subject.md) - * [➞subject_qualifier](triple__subject_qualifier.md) - An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -### Enums - - * [NullDataOptions](NullDataOptions.md) - -### Subsets - - -### Types - - -#### Built in - - * **Bool** - * **Curie** - * **Decimal** - * **ElementIdentifier** - * **NCName** - * **NodeIdentifier** - * **URI** - * **URIorCURIE** - * **XSDDate** - * **XSDDateTime** - * **XSDTime** - * **float** - * **int** - * **str** - -#### Defined - - * [Boolean](types/Boolean.md) (**Bool**) - A binary (true or false) value - * [Curie](types/Curie.md) (**Curie**) - a compact URI - * [Date](types/Date.md) (**XSDDate**) - a date (year, month and day) in an idealized calendar - * [DateOrDatetime](types/DateOrDatetime.md) (**str**) - Either a date or a datetime - * [Datetime](types/Datetime.md) (**XSDDateTime**) - The combination of a date and time - * [Decimal](types/Decimal.md) (**Decimal**) - A real number with arbitrary precision that conforms to the xsd:decimal specification - * [Double](types/Double.md) (**float**) - A real number that conforms to the xsd:double specification - * [Float](types/Float.md) (**float**) - A real number that conforms to the xsd:float specification - * [Integer](types/Integer.md) (**int**) - An integer - * [Jsonpath](types/Jsonpath.md) (**str**) - A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - * [Jsonpointer](types/Jsonpointer.md) (**str**) - A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - * [Ncname](types/Ncname.md) (**NCName**) - Prefix part of CURIE - * [Nodeidentifier](types/Nodeidentifier.md) (**NodeIdentifier**) - A URI, CURIE or BNODE that represents a node in a model. - * [Objectidentifier](types/Objectidentifier.md) (**ElementIdentifier**) - A URI or CURIE that represents an object in the model. - * [Sparqlpath](types/Sparqlpath.md) (**str**) - A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - * [String](types/String.md) (**str**) - A character string - * [Time](types/Time.md) (**XSDTime**) - A time object represents a (local) time of day, independent of any particular day - * [Uri](types/Uri.md) (**URI**) - a complete URI - * [Uriorcurie](types/Uriorcurie.md) (**URIorCURIE**) - a URI or a CURIE diff --git a/projects/environmental_sample/docs/extractionResult__extracted_object.md b/projects/environmental_sample/docs/extractionResult__extracted_object.md deleted file mode 100644 index 19207749e..000000000 --- a/projects/environmental_sample/docs/extractionResult__extracted_object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: extracted_object - - -The complex objects extracted from the text - -URI: [sample:extractionResult__extracted_object](http://w3id.org/ontogpt/environmental-sample/extractionResult__extracted_object) - - -## Domain and Range - -None → <sub>0..1</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/environmental_sample/docs/extractionResult__input_id.md b/projects/environmental_sample/docs/extractionResult__input_id.md deleted file mode 100644 index dd7b61fc6..000000000 --- a/projects/environmental_sample/docs/extractionResult__input_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_id - - - - -URI: [sample:extractionResult__input_id](http://w3id.org/ontogpt/environmental-sample/extractionResult__input_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/environmental_sample/docs/extractionResult__input_text.md b/projects/environmental_sample/docs/extractionResult__input_text.md deleted file mode 100644 index 247ac72cd..000000000 --- a/projects/environmental_sample/docs/extractionResult__input_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_text - - - - -URI: [sample:extractionResult__input_text](http://w3id.org/ontogpt/environmental-sample/extractionResult__input_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/environmental_sample/docs/extractionResult__input_title.md b/projects/environmental_sample/docs/extractionResult__input_title.md deleted file mode 100644 index 9fa9579bd..000000000 --- a/projects/environmental_sample/docs/extractionResult__input_title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_title - - - - -URI: [sample:extractionResult__input_title](http://w3id.org/ontogpt/environmental-sample/extractionResult__input_title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/environmental_sample/docs/extractionResult__named_entities.md b/projects/environmental_sample/docs/extractionResult__named_entities.md deleted file mode 100644 index 727eae8e0..000000000 --- a/projects/environmental_sample/docs/extractionResult__named_entities.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: named_entities - - -Named entities extracted from the text - -URI: [sample:extractionResult__named_entities](http://w3id.org/ontogpt/environmental-sample/extractionResult__named_entities) - - -## Domain and Range - -None → <sub>0..\*</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/environmental_sample/docs/extractionResult__prompt.md b/projects/environmental_sample/docs/extractionResult__prompt.md deleted file mode 100644 index 6b58c69e9..000000000 --- a/projects/environmental_sample/docs/extractionResult__prompt.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: prompt - - - - -URI: [sample:extractionResult__prompt](http://w3id.org/ontogpt/environmental-sample/extractionResult__prompt) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/environmental_sample/docs/extractionResult__raw_completion_output.md b/projects/environmental_sample/docs/extractionResult__raw_completion_output.md deleted file mode 100644 index d2ebc054e..000000000 --- a/projects/environmental_sample/docs/extractionResult__raw_completion_output.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: raw_completion_output - - - - -URI: [sample:extractionResult__raw_completion_output](http://w3id.org/ontogpt/environmental-sample/extractionResult__raw_completion_output) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/environmental_sample/docs/measurement__unit.md b/projects/environmental_sample/docs/measurement__unit.md deleted file mode 100644 index 5b8c73c70..000000000 --- a/projects/environmental_sample/docs/measurement__unit.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: unit - - -the unit of the measurement - -URI: [sample:measurement__unit](http://w3id.org/ontogpt/environmental-sample/measurement__unit) - - -## Domain and Range - -None → <sub>0..1</sub> [Unit](Unit.md) - -## Parents - - -## Children - - -## Used by - - * [Measurement](Measurement.md) diff --git a/projects/environmental_sample/docs/measurement__value.md b/projects/environmental_sample/docs/measurement__value.md deleted file mode 100644 index 7409934f3..000000000 --- a/projects/environmental_sample/docs/measurement__value.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: value - - -the value of the measurement - -URI: [sample:measurement__value](http://w3id.org/ontogpt/environmental-sample/measurement__value) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Measurement](Measurement.md) diff --git a/projects/environmental_sample/docs/namedEntity__id.md b/projects/environmental_sample/docs/namedEntity__id.md deleted file mode 100644 index 8b066b213..000000000 --- a/projects/environmental_sample/docs/namedEntity__id.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Slot: id - - -A unique identifier for the named entity - -URI: [sample:namedEntity__id](http://w3id.org/ontogpt/environmental-sample/namedEntity__id) - - -## Domain and Range - -None → <sub>1..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Environment](Environment.md) - * [EnvironmentalMaterial](EnvironmentalMaterial.md) - * [Location](Location.md) - * [NamedEntity](NamedEntity.md) - * [RelationshipType](RelationshipType.md) - * [Unit](Unit.md) - * [Variable](Variable.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | this is populated during the grounding and normalization step | - diff --git a/projects/environmental_sample/docs/namedEntity__label.md b/projects/environmental_sample/docs/namedEntity__label.md deleted file mode 100644 index 746d61cb4..000000000 --- a/projects/environmental_sample/docs/namedEntity__label.md +++ /dev/null @@ -1,36 +0,0 @@ - -# Slot: label - - -The label (name) of the named thing - -URI: [sample:namedEntity__label](http://w3id.org/ontogpt/environmental-sample/namedEntity__label) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Environment](Environment.md) - * [EnvironmentalMaterial](EnvironmentalMaterial.md) - * [Location](Location.md) - * [NamedEntity](NamedEntity.md) - * [RelationshipType](RelationshipType.md) - * [Unit](Unit.md) - * [Variable](Variable.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Aliases:** | | name | -| **Mappings:** | | rdfs:label | - diff --git a/projects/environmental_sample/docs/publication__abstract.md b/projects/environmental_sample/docs/publication__abstract.md deleted file mode 100644 index b02cadb58..000000000 --- a/projects/environmental_sample/docs/publication__abstract.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: abstract - - -The abstract of the publication - -URI: [sample:publication__abstract](http://w3id.org/ontogpt/environmental-sample/publication__abstract) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/environmental_sample/docs/publication__combined_text.md b/projects/environmental_sample/docs/publication__combined_text.md deleted file mode 100644 index 6c8e47f42..000000000 --- a/projects/environmental_sample/docs/publication__combined_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: combined_text - - - - -URI: [sample:publication__combined_text](http://w3id.org/ontogpt/environmental-sample/publication__combined_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/environmental_sample/docs/publication__full_text.md b/projects/environmental_sample/docs/publication__full_text.md deleted file mode 100644 index d844ec02c..000000000 --- a/projects/environmental_sample/docs/publication__full_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: full_text - - -The full text of the publication - -URI: [sample:publication__full_text](http://w3id.org/ontogpt/environmental-sample/publication__full_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/environmental_sample/docs/publication__id.md b/projects/environmental_sample/docs/publication__id.md deleted file mode 100644 index 5b8e23e69..000000000 --- a/projects/environmental_sample/docs/publication__id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: id - - -The publication identifier - -URI: [sample:publication__id](http://w3id.org/ontogpt/environmental-sample/publication__id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/environmental_sample/docs/publication__title.md b/projects/environmental_sample/docs/publication__title.md deleted file mode 100644 index c031cc577..000000000 --- a/projects/environmental_sample/docs/publication__title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: title - - -The title of the publication - -URI: [sample:publication__title](http://w3id.org/ontogpt/environmental-sample/publication__title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/environmental_sample/docs/study__causal_relationships.md b/projects/environmental_sample/docs/study__causal_relationships.md deleted file mode 100644 index 755de60e3..000000000 --- a/projects/environmental_sample/docs/study__causal_relationships.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: causal_relationships - - - - -URI: [sample:study__causal_relationships](http://w3id.org/ontogpt/environmental-sample/study__causal_relationships) - - -## Domain and Range - -None → <sub>0..\*</sub> [CausalRelationship](CausalRelationship.md) - -## Parents - - -## Children - - -## Used by - - * [Study](Study.md) diff --git a/projects/environmental_sample/docs/study__environmental_material.md b/projects/environmental_sample/docs/study__environmental_material.md deleted file mode 100644 index f654199dd..000000000 --- a/projects/environmental_sample/docs/study__environmental_material.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: environmental_material - - -the environmental material that was sampled - -URI: [sample:study__environmental_material](http://w3id.org/ontogpt/environmental-sample/study__environmental_material) - - -## Domain and Range - -None → <sub>0..\*</sub> [EnvironmentalMaterial](EnvironmentalMaterial.md) - -## Parents - - -## Children - - -## Used by - - * [Study](Study.md) diff --git a/projects/environmental_sample/docs/study__environments.md b/projects/environmental_sample/docs/study__environments.md deleted file mode 100644 index 3b10f1357..000000000 --- a/projects/environmental_sample/docs/study__environments.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: environments - - - - -URI: [sample:study__environments](http://w3id.org/ontogpt/environmental-sample/study__environments) - - -## Domain and Range - -None → <sub>0..\*</sub> [Environment](Environment.md) - -## Parents - - -## Children - - -## Used by - - * [Study](Study.md) diff --git a/projects/environmental_sample/docs/study__location.md b/projects/environmental_sample/docs/study__location.md deleted file mode 100644 index 90d1118fc..000000000 --- a/projects/environmental_sample/docs/study__location.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: location - - -the sites at which the study was conducted - -URI: [sample:study__location](http://w3id.org/ontogpt/environmental-sample/study__location) - - -## Domain and Range - -None → <sub>0..\*</sub> [Location](Location.md) - -## Parents - - -## Children - - -## Used by - - * [Study](Study.md) diff --git a/projects/environmental_sample/docs/study__measurements.md b/projects/environmental_sample/docs/study__measurements.md deleted file mode 100644 index 1905c2405..000000000 --- a/projects/environmental_sample/docs/study__measurements.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: measurements - - - - -URI: [sample:study__measurements](http://w3id.org/ontogpt/environmental-sample/study__measurements) - - -## Domain and Range - -None → <sub>0..\*</sub> [Measurement](Measurement.md) - -## Parents - - -## Children - - -## Used by - - * [Study](Study.md) diff --git a/projects/environmental_sample/docs/study__variables.md b/projects/environmental_sample/docs/study__variables.md deleted file mode 100644 index d0e9b4246..000000000 --- a/projects/environmental_sample/docs/study__variables.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: variables - - - - -URI: [sample:study__variables](http://w3id.org/ontogpt/environmental-sample/study__variables) - - -## Domain and Range - -None → <sub>0..\*</sub> [Variable](Variable.md) - -## Parents - - -## Children - - -## Used by - - * [Study](Study.md) diff --git a/projects/environmental_sample/docs/textWithTriples__publication.md b/projects/environmental_sample/docs/textWithTriples__publication.md deleted file mode 100644 index 5dc028075..000000000 --- a/projects/environmental_sample/docs/textWithTriples__publication.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: publication - - - - -URI: [sample:textWithTriples__publication](http://w3id.org/ontogpt/environmental-sample/textWithTriples__publication) - - -## Domain and Range - -None → <sub>0..1</sub> [Publication](Publication.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/environmental_sample/docs/textWithTriples__triples.md b/projects/environmental_sample/docs/textWithTriples__triples.md deleted file mode 100644 index ba158bb7e..000000000 --- a/projects/environmental_sample/docs/textWithTriples__triples.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: triples - - - - -URI: [sample:textWithTriples__triples](http://w3id.org/ontogpt/environmental-sample/textWithTriples__triples) - - -## Domain and Range - -None → <sub>0..\*</sub> [Triple](Triple.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/environmental_sample/docs/triple__object.md b/projects/environmental_sample/docs/triple__object.md deleted file mode 100644 index 1b6e085ae..000000000 --- a/projects/environmental_sample/docs/triple__object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object - - - - -URI: [sample:triple__object](http://w3id.org/ontogpt/environmental-sample/triple__object) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/environmental_sample/docs/triple__object_qualifier.md b/projects/environmental_sample/docs/triple__object_qualifier.md deleted file mode 100644 index 861af5475..000000000 --- a/projects/environmental_sample/docs/triple__object_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_qualifier - - -An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - -URI: [sample:triple__object_qualifier](http://w3id.org/ontogpt/environmental-sample/triple__object_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/environmental_sample/docs/triple__predicate.md b/projects/environmental_sample/docs/triple__predicate.md deleted file mode 100644 index 1c9dbb4f8..000000000 --- a/projects/environmental_sample/docs/triple__predicate.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: predicate - - - - -URI: [sample:triple__predicate](http://w3id.org/ontogpt/environmental-sample/triple__predicate) - - -## Domain and Range - -None → <sub>0..1</sub> [RelationshipType](RelationshipType.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/environmental_sample/docs/triple__qualifier.md b/projects/environmental_sample/docs/triple__qualifier.md deleted file mode 100644 index 822e39281..000000000 --- a/projects/environmental_sample/docs/triple__qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: qualifier - - -A qualifier for the statements, e.g. "NOT" for negation - -URI: [sample:triple__qualifier](http://w3id.org/ontogpt/environmental-sample/triple__qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/environmental_sample/docs/triple__subject.md b/projects/environmental_sample/docs/triple__subject.md deleted file mode 100644 index f0761f24f..000000000 --- a/projects/environmental_sample/docs/triple__subject.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject - - - - -URI: [sample:triple__subject](http://w3id.org/ontogpt/environmental-sample/triple__subject) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/environmental_sample/docs/triple__subject_qualifier.md b/projects/environmental_sample/docs/triple__subject_qualifier.md deleted file mode 100644 index b8dcab9fe..000000000 --- a/projects/environmental_sample/docs/triple__subject_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_qualifier - - -An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -URI: [sample:triple__subject_qualifier](http://w3id.org/ontogpt/environmental-sample/triple__subject_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/environmental_sample/docs/types/Boolean.md b/projects/environmental_sample/docs/types/Boolean.md deleted file mode 100644 index dc83a9c6e..000000000 --- a/projects/environmental_sample/docs/types/Boolean.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: boolean - - -A binary (true or false) value - -URI: [linkml:Boolean](https://w3id.org/linkml/Boolean) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Bool** | -| Representation | | bool | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Boolean | - diff --git a/projects/environmental_sample/docs/types/Curie.md b/projects/environmental_sample/docs/types/Curie.md deleted file mode 100644 index c1803f93f..000000000 --- a/projects/environmental_sample/docs/types/Curie.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: curie - - -a compact URI - -URI: [linkml:Curie](https://w3id.org/linkml/Curie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Curie** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations this MUST be expanded to a URI | -| | | in non-RDF serializations MAY be serialized as the compact representation | - diff --git a/projects/environmental_sample/docs/types/Date.md b/projects/environmental_sample/docs/types/Date.md deleted file mode 100644 index 06948af97..000000000 --- a/projects/environmental_sample/docs/types/Date.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: date - - -a date (year, month and day) in an idealized calendar - -URI: [linkml:Date](https://w3id.org/linkml/Date) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDate** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Date | - diff --git a/projects/environmental_sample/docs/types/DateOrDatetime.md b/projects/environmental_sample/docs/types/DateOrDatetime.md deleted file mode 100644 index ef983898d..000000000 --- a/projects/environmental_sample/docs/types/DateOrDatetime.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: date_or_datetime - - -Either a date or a datetime - -URI: [linkml:DateOrDatetime](https://w3id.org/linkml/DateOrDatetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/environmental_sample/docs/types/Datetime.md b/projects/environmental_sample/docs/types/Datetime.md deleted file mode 100644 index 9510454a8..000000000 --- a/projects/environmental_sample/docs/types/Datetime.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: datetime - - -The combination of a date and time - -URI: [linkml:Datetime](https://w3id.org/linkml/Datetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDateTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:DateTime | - diff --git a/projects/environmental_sample/docs/types/Decimal.md b/projects/environmental_sample/docs/types/Decimal.md deleted file mode 100644 index a7ba14a5d..000000000 --- a/projects/environmental_sample/docs/types/Decimal.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: decimal - - -A real number with arbitrary precision that conforms to the xsd:decimal specification - -URI: [linkml:Decimal](https://w3id.org/linkml/Decimal) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Decimal** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Broad Mappings:** | | schema:Number | - diff --git a/projects/environmental_sample/docs/types/Double.md b/projects/environmental_sample/docs/types/Double.md deleted file mode 100644 index cfe6d71e2..000000000 --- a/projects/environmental_sample/docs/types/Double.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: double - - -A real number that conforms to the xsd:double specification - -URI: [linkml:Double](https://w3id.org/linkml/Double) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Close Mappings:** | | schema:Float | - diff --git a/projects/environmental_sample/docs/types/Float.md b/projects/environmental_sample/docs/types/Float.md deleted file mode 100644 index 7b303f96f..000000000 --- a/projects/environmental_sample/docs/types/Float.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: float - - -A real number that conforms to the xsd:float specification - -URI: [linkml:Float](https://w3id.org/linkml/Float) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Float | - diff --git a/projects/environmental_sample/docs/types/Integer.md b/projects/environmental_sample/docs/types/Integer.md deleted file mode 100644 index 3cfcc66d9..000000000 --- a/projects/environmental_sample/docs/types/Integer.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: integer - - -An integer - -URI: [linkml:Integer](https://w3id.org/linkml/Integer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **int** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Integer | - diff --git a/projects/environmental_sample/docs/types/Jsonpath.md b/projects/environmental_sample/docs/types/Jsonpath.md deleted file mode 100644 index a03a58e67..000000000 --- a/projects/environmental_sample/docs/types/Jsonpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpath - - -A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpath](https://w3id.org/linkml/Jsonpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/environmental_sample/docs/types/Jsonpointer.md b/projects/environmental_sample/docs/types/Jsonpointer.md deleted file mode 100644 index a0e1ac492..000000000 --- a/projects/environmental_sample/docs/types/Jsonpointer.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpointer - - -A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpointer](https://w3id.org/linkml/Jsonpointer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/environmental_sample/docs/types/Ncname.md b/projects/environmental_sample/docs/types/Ncname.md deleted file mode 100644 index 710b0b04a..000000000 --- a/projects/environmental_sample/docs/types/Ncname.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: ncname - - -Prefix part of CURIE - -URI: [linkml:Ncname](https://w3id.org/linkml/Ncname) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NCName** | -| Representation | | str | diff --git a/projects/environmental_sample/docs/types/Nodeidentifier.md b/projects/environmental_sample/docs/types/Nodeidentifier.md deleted file mode 100644 index f0097cdf4..000000000 --- a/projects/environmental_sample/docs/types/Nodeidentifier.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: nodeidentifier - - -A URI, CURIE or BNODE that represents a node in a model. - -URI: [linkml:Nodeidentifier](https://w3id.org/linkml/Nodeidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NodeIdentifier** | -| Representation | | str | diff --git a/projects/environmental_sample/docs/types/Objectidentifier.md b/projects/environmental_sample/docs/types/Objectidentifier.md deleted file mode 100644 index 454ba6be6..000000000 --- a/projects/environmental_sample/docs/types/Objectidentifier.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: objectidentifier - - -A URI or CURIE that represents an object in the model. - -URI: [linkml:Objectidentifier](https://w3id.org/linkml/Objectidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **ElementIdentifier** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | Used for inheritance and type checking | - diff --git a/projects/environmental_sample/docs/types/Sparqlpath.md b/projects/environmental_sample/docs/types/Sparqlpath.md deleted file mode 100644 index fd99a927e..000000000 --- a/projects/environmental_sample/docs/types/Sparqlpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: sparqlpath - - -A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - -URI: [linkml:Sparqlpath](https://w3id.org/linkml/Sparqlpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/environmental_sample/docs/types/String.md b/projects/environmental_sample/docs/types/String.md deleted file mode 100644 index 6e61d7081..000000000 --- a/projects/environmental_sample/docs/types/String.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: string - - -A character string - -URI: [linkml:String](https://w3id.org/linkml/String) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Text | - diff --git a/projects/environmental_sample/docs/types/Time.md b/projects/environmental_sample/docs/types/Time.md deleted file mode 100644 index 2b8652bcd..000000000 --- a/projects/environmental_sample/docs/types/Time.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: time - - -A time object represents a (local) time of day, independent of any particular day - -URI: [linkml:Time](https://w3id.org/linkml/Time) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Time | - diff --git a/projects/environmental_sample/docs/types/Uri.md b/projects/environmental_sample/docs/types/Uri.md deleted file mode 100644 index 343807a5e..000000000 --- a/projects/environmental_sample/docs/types/Uri.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: uri - - -a complete URI - -URI: [linkml:Uri](https://w3id.org/linkml/Uri) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URI** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node | -| **Close Mappings:** | | schema:URL | - diff --git a/projects/environmental_sample/docs/types/Uriorcurie.md b/projects/environmental_sample/docs/types/Uriorcurie.md deleted file mode 100644 index 2f7b65087..000000000 --- a/projects/environmental_sample/docs/types/Uriorcurie.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: uriorcurie - - -a URI or a CURIE - -URI: [linkml:Uriorcurie](https://w3id.org/linkml/Uriorcurie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URIorCURIE** | -| Representation | | str | diff --git a/projects/environmental_sample/environmental_sample.py b/projects/environmental_sample/environmental_sample.py deleted file mode 100644 index 9fad60554..000000000 --- a/projects/environmental_sample/environmental_sample.py +++ /dev/null @@ -1,607 +0,0 @@ -# Auto generated from environmental_sample.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-08-07T10:53:18 -# Schema: environmental-sample -# -# id: http://w3id.org/ontogpt/environmental-sample -# description: A template for Environmental Samples -# license: https://creativecommons.org/publicdomain/zero/1.0/ - -import dataclasses -import sys -import re -from jsonasobj2 import JsonObj, as_dict -from typing import Optional, List, Union, Dict, ClassVar, Any -from dataclasses import dataclass -from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions - -from linkml_runtime.utils.slot import Slot -from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode -from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int -from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs -from linkml_runtime.utils.formatutils import camelcase, underscore, sfx -from linkml_runtime.utils.enumerations import EnumDefinitionImpl -from rdflib import Namespace, URIRef -from linkml_runtime.utils.curienamespace import CurieNamespace -from linkml_runtime.linkml_model.types import String - -metamodel_version = "1.7.0" -version = None - -# Overwrite dataclasses _init_fn to add **kwargs in __init__ -dataclasses._init_fn = dataclasses_init_fn_with_kwargs - -# Namespaces -ENVO = CurieNamespace('ENVO', 'http://example.org/UNKNOWN/ENVO/') -ENVTHES = CurieNamespace('ENVTHES', 'http://example.org/UNKNOWN/ENVTHES/') -GAZ = CurieNamespace('GAZ', 'http://example.org/UNKNOWN/GAZ/') -MIXS = CurieNamespace('MIXS', 'http://example.org/UNKNOWN/MIXS/') -NCIT = CurieNamespace('NCIT', 'http://purl.obolibrary.org/obo/NCIT_') -PATO = CurieNamespace('PATO', 'http://example.org/UNKNOWN/PATO/') -RO = CurieNamespace('RO', 'http://purl.obolibrary.org/obo/RO_') -UO = CurieNamespace('UO', 'http://example.org/UNKNOWN/UO/') -BIOLINK = CurieNamespace('biolink', 'http://example.org/UNKNOWN/biolink/') -CORE = CurieNamespace('core', 'http://w3id.org/ontogpt/core/') -LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') -RDFS = CurieNamespace('rdfs', 'http://example.org/UNKNOWN/rdfs/') -SAMPLE = CurieNamespace('sample', 'http://w3id.org/ontogpt/environmental-sample/') -DEFAULT_ = SAMPLE - - -# Types - -# Class references -class NamedEntityId(extended_str): - pass - - -class LocationId(NamedEntityId): - pass - - -class EnvironmentalMaterialId(NamedEntityId): - pass - - -class EnvironmentId(NamedEntityId): - pass - - -class VariableId(NamedEntityId): - pass - - -class UnitId(NamedEntityId): - pass - - -class RelationshipTypeId(NamedEntityId): - pass - - -@dataclass -class Study(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = SAMPLE.Study - class_class_curie: ClassVar[str] = "sample:Study" - class_name: ClassVar[str] = "Study" - class_model_uri: ClassVar[URIRef] = SAMPLE.Study - - location: Optional[Union[Union[str, LocationId], List[Union[str, LocationId]]]] = empty_list() - environmental_material: Optional[Union[Union[str, EnvironmentalMaterialId], List[Union[str, EnvironmentalMaterialId]]]] = empty_list() - environments: Optional[Union[Union[str, EnvironmentId], List[Union[str, EnvironmentId]]]] = empty_list() - causal_relationships: Optional[Union[Union[dict, "CausalRelationship"], List[Union[dict, "CausalRelationship"]]]] = empty_list() - variables: Optional[Union[Union[str, VariableId], List[Union[str, VariableId]]]] = empty_list() - measurements: Optional[Union[Union[dict, "Measurement"], List[Union[dict, "Measurement"]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if not isinstance(self.location, list): - self.location = [self.location] if self.location is not None else [] - self.location = [v if isinstance(v, LocationId) else LocationId(v) for v in self.location] - - if not isinstance(self.environmental_material, list): - self.environmental_material = [self.environmental_material] if self.environmental_material is not None else [] - self.environmental_material = [v if isinstance(v, EnvironmentalMaterialId) else EnvironmentalMaterialId(v) for v in self.environmental_material] - - if not isinstance(self.environments, list): - self.environments = [self.environments] if self.environments is not None else [] - self.environments = [v if isinstance(v, EnvironmentId) else EnvironmentId(v) for v in self.environments] - - if not isinstance(self.causal_relationships, list): - self.causal_relationships = [self.causal_relationships] if self.causal_relationships is not None else [] - self.causal_relationships = [v if isinstance(v, CausalRelationship) else CausalRelationship(**as_dict(v)) for v in self.causal_relationships] - - if not isinstance(self.variables, list): - self.variables = [self.variables] if self.variables is not None else [] - self.variables = [v if isinstance(v, VariableId) else VariableId(v) for v in self.variables] - - if not isinstance(self.measurements, list): - self.measurements = [self.measurements] if self.measurements is not None else [] - self.measurements = [v if isinstance(v, Measurement) else Measurement(**as_dict(v)) for v in self.measurements] - - super().__post_init__(**kwargs) - - -Any = Any - -@dataclass -class ExtractionResult(YAMLRoot): - """ - A result of extracting knowledge on text - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.ExtractionResult - class_class_curie: ClassVar[str] = "core:ExtractionResult" - class_name: ClassVar[str] = "ExtractionResult" - class_model_uri: ClassVar[URIRef] = SAMPLE.ExtractionResult - - input_id: Optional[str] = None - input_title: Optional[str] = None - input_text: Optional[str] = None - raw_completion_output: Optional[str] = None - prompt: Optional[str] = None - extracted_object: Optional[Union[dict, Any]] = None - named_entities: Optional[Union[Union[dict, Any], List[Union[dict, Any]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.input_id is not None and not isinstance(self.input_id, str): - self.input_id = str(self.input_id) - - if self.input_title is not None and not isinstance(self.input_title, str): - self.input_title = str(self.input_title) - - if self.input_text is not None and not isinstance(self.input_text, str): - self.input_text = str(self.input_text) - - if self.raw_completion_output is not None and not isinstance(self.raw_completion_output, str): - self.raw_completion_output = str(self.raw_completion_output) - - if self.prompt is not None and not isinstance(self.prompt, str): - self.prompt = str(self.prompt) - - super().__post_init__(**kwargs) - - -@dataclass -class NamedEntity(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.NamedEntity - class_class_curie: ClassVar[str] = "core:NamedEntity" - class_name: ClassVar[str] = "NamedEntity" - class_model_uri: ClassVar[URIRef] = SAMPLE.NamedEntity - - id: Union[str, NamedEntityId] = None - label: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, NamedEntityId): - self.id = NamedEntityId(self.id) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - super().__post_init__(**kwargs) - - -@dataclass -class Location(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = SAMPLE.Location - class_class_curie: ClassVar[str] = "sample:Location" - class_name: ClassVar[str] = "Location" - class_model_uri: ClassVar[URIRef] = SAMPLE.Location - - id: Union[str, LocationId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, LocationId): - self.id = LocationId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class EnvironmentalMaterial(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = SAMPLE.EnvironmentalMaterial - class_class_curie: ClassVar[str] = "sample:EnvironmentalMaterial" - class_name: ClassVar[str] = "EnvironmentalMaterial" - class_model_uri: ClassVar[URIRef] = SAMPLE.EnvironmentalMaterial - - id: Union[str, EnvironmentalMaterialId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, EnvironmentalMaterialId): - self.id = EnvironmentalMaterialId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Environment(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = SAMPLE.Environment - class_class_curie: ClassVar[str] = "sample:Environment" - class_name: ClassVar[str] = "Environment" - class_model_uri: ClassVar[URIRef] = SAMPLE.Environment - - id: Union[str, EnvironmentId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, EnvironmentId): - self.id = EnvironmentId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Variable(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = SAMPLE.Variable - class_class_curie: ClassVar[str] = "sample:Variable" - class_name: ClassVar[str] = "Variable" - class_model_uri: ClassVar[URIRef] = SAMPLE.Variable - - id: Union[str, VariableId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, VariableId): - self.id = VariableId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Unit(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = SAMPLE.Unit - class_class_curie: ClassVar[str] = "sample:Unit" - class_name: ClassVar[str] = "Unit" - class_model_uri: ClassVar[URIRef] = SAMPLE.Unit - - id: Union[str, UnitId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, UnitId): - self.id = UnitId(self.id) - - super().__post_init__(**kwargs) - - -class CompoundExpression(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.CompoundExpression - class_class_curie: ClassVar[str] = "core:CompoundExpression" - class_name: ClassVar[str] = "CompoundExpression" - class_model_uri: ClassVar[URIRef] = SAMPLE.CompoundExpression - - -@dataclass -class Measurement(CompoundExpression): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = SAMPLE.Measurement - class_class_curie: ClassVar[str] = "sample:Measurement" - class_name: ClassVar[str] = "Measurement" - class_model_uri: ClassVar[URIRef] = SAMPLE.Measurement - - value: Optional[str] = None - unit: Optional[Union[str, UnitId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.value is not None and not isinstance(self.value, str): - self.value = str(self.value) - - if self.unit is not None and not isinstance(self.unit, UnitId): - self.unit = UnitId(self.unit) - - super().__post_init__(**kwargs) - - -@dataclass -class CausalRelationship(CompoundExpression): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = SAMPLE.CausalRelationship - class_class_curie: ClassVar[str] = "sample:CausalRelationship" - class_name: ClassVar[str] = "CausalRelationship" - class_model_uri: ClassVar[URIRef] = SAMPLE.CausalRelationship - - cause: Optional[Union[str, VariableId]] = None - effect: Optional[Union[str, VariableId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.cause is not None and not isinstance(self.cause, VariableId): - self.cause = VariableId(self.cause) - - if self.effect is not None and not isinstance(self.effect, VariableId): - self.effect = VariableId(self.effect) - - super().__post_init__(**kwargs) - - -@dataclass -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Triple - class_class_curie: ClassVar[str] = "core:Triple" - class_name: ClassVar[str] = "Triple" - class_model_uri: ClassVar[URIRef] = SAMPLE.Triple - - subject: Optional[Union[str, NamedEntityId]] = None - predicate: Optional[Union[str, RelationshipTypeId]] = None - object: Optional[Union[str, NamedEntityId]] = None - qualifier: Optional[str] = None - subject_qualifier: Optional[Union[str, NamedEntityId]] = None - object_qualifier: Optional[Union[str, NamedEntityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, NamedEntityId): - self.subject = NamedEntityId(self.subject) - - if self.predicate is not None and not isinstance(self.predicate, RelationshipTypeId): - self.predicate = RelationshipTypeId(self.predicate) - - if self.object is not None and not isinstance(self.object, NamedEntityId): - self.object = NamedEntityId(self.object) - - if self.qualifier is not None and not isinstance(self.qualifier, str): - self.qualifier = str(self.qualifier) - - if self.subject_qualifier is not None and not isinstance(self.subject_qualifier, NamedEntityId): - self.subject_qualifier = NamedEntityId(self.subject_qualifier) - - if self.object_qualifier is not None and not isinstance(self.object_qualifier, NamedEntityId): - self.object_qualifier = NamedEntityId(self.object_qualifier) - - super().__post_init__(**kwargs) - - -@dataclass -class TextWithTriples(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.TextWithTriples - class_class_curie: ClassVar[str] = "core:TextWithTriples" - class_name: ClassVar[str] = "TextWithTriples" - class_model_uri: ClassVar[URIRef] = SAMPLE.TextWithTriples - - publication: Optional[Union[dict, "Publication"]] = None - triples: Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.publication is not None and not isinstance(self.publication, Publication): - self.publication = Publication(**as_dict(self.publication)) - - if not isinstance(self.triples, list): - self.triples = [self.triples] if self.triples is not None else [] - self.triples = [v if isinstance(v, Triple) else Triple(**as_dict(v)) for v in self.triples] - - super().__post_init__(**kwargs) - - -@dataclass -class RelationshipType(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.RelationshipType - class_class_curie: ClassVar[str] = "core:RelationshipType" - class_name: ClassVar[str] = "RelationshipType" - class_model_uri: ClassVar[URIRef] = SAMPLE.RelationshipType - - id: Union[str, RelationshipTypeId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, RelationshipTypeId): - self.id = RelationshipTypeId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Publication(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Publication - class_class_curie: ClassVar[str] = "core:Publication" - class_name: ClassVar[str] = "Publication" - class_model_uri: ClassVar[URIRef] = SAMPLE.Publication - - id: Optional[str] = None - title: Optional[str] = None - abstract: Optional[str] = None - combined_text: Optional[str] = None - full_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.id is not None and not isinstance(self.id, str): - self.id = str(self.id) - - if self.title is not None and not isinstance(self.title, str): - self.title = str(self.title) - - if self.abstract is not None and not isinstance(self.abstract, str): - self.abstract = str(self.abstract) - - if self.combined_text is not None and not isinstance(self.combined_text, str): - self.combined_text = str(self.combined_text) - - if self.full_text is not None and not isinstance(self.full_text, str): - self.full_text = str(self.full_text) - - super().__post_init__(**kwargs) - - -@dataclass -class AnnotatorResult(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.AnnotatorResult - class_class_curie: ClassVar[str] = "core:AnnotatorResult" - class_name: ClassVar[str] = "AnnotatorResult" - class_model_uri: ClassVar[URIRef] = SAMPLE.AnnotatorResult - - subject_text: Optional[str] = None - object_id: Optional[str] = None - object_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject_text is not None and not isinstance(self.subject_text, str): - self.subject_text = str(self.subject_text) - - if self.object_id is not None and not isinstance(self.object_id, str): - self.object_id = str(self.object_id) - - if self.object_text is not None and not isinstance(self.object_text, str): - self.object_text = str(self.object_text) - - super().__post_init__(**kwargs) - - -# Enumerations -class NullDataOptions(EnumDefinitionImpl): - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = PermissibleValue(text="UNSPECIFIED_METHOD_OF_ADMINISTRATION", - meaning=NCIT.C149701) - NOT_APPLICABLE = PermissibleValue(text="NOT_APPLICABLE", - meaning=NCIT.C18902) - NOT_MENTIONED = PermissibleValue(text="NOT_MENTIONED") - - _defn = EnumDefinition( - name="NullDataOptions", - ) - -# Slots -class slots: - pass - -slots.study__location = Slot(uri=SAMPLE.location, name="study__location", curie=SAMPLE.curie('location'), - model_uri=SAMPLE.study__location, domain=None, range=Optional[Union[Union[str, LocationId], List[Union[str, LocationId]]]]) - -slots.study__environmental_material = Slot(uri=SAMPLE.environmental_material, name="study__environmental_material", curie=SAMPLE.curie('environmental_material'), - model_uri=SAMPLE.study__environmental_material, domain=None, range=Optional[Union[Union[str, EnvironmentalMaterialId], List[Union[str, EnvironmentalMaterialId]]]]) - -slots.study__environments = Slot(uri=SAMPLE.environments, name="study__environments", curie=SAMPLE.curie('environments'), - model_uri=SAMPLE.study__environments, domain=None, range=Optional[Union[Union[str, EnvironmentId], List[Union[str, EnvironmentId]]]]) - -slots.study__causal_relationships = Slot(uri=SAMPLE.causal_relationships, name="study__causal_relationships", curie=SAMPLE.curie('causal_relationships'), - model_uri=SAMPLE.study__causal_relationships, domain=None, range=Optional[Union[Union[dict, CausalRelationship], List[Union[dict, CausalRelationship]]]]) - -slots.study__variables = Slot(uri=SAMPLE.variables, name="study__variables", curie=SAMPLE.curie('variables'), - model_uri=SAMPLE.study__variables, domain=None, range=Optional[Union[Union[str, VariableId], List[Union[str, VariableId]]]]) - -slots.study__measurements = Slot(uri=SAMPLE.measurements, name="study__measurements", curie=SAMPLE.curie('measurements'), - model_uri=SAMPLE.study__measurements, domain=None, range=Optional[Union[Union[dict, Measurement], List[Union[dict, Measurement]]]]) - -slots.measurement__value = Slot(uri=SAMPLE.value, name="measurement__value", curie=SAMPLE.curie('value'), - model_uri=SAMPLE.measurement__value, domain=None, range=Optional[str]) - -slots.measurement__unit = Slot(uri=SAMPLE.unit, name="measurement__unit", curie=SAMPLE.curie('unit'), - model_uri=SAMPLE.measurement__unit, domain=None, range=Optional[Union[str, UnitId]]) - -slots.causalRelationship__cause = Slot(uri=SAMPLE.cause, name="causalRelationship__cause", curie=SAMPLE.curie('cause'), - model_uri=SAMPLE.causalRelationship__cause, domain=None, range=Optional[Union[str, VariableId]]) - -slots.causalRelationship__effect = Slot(uri=SAMPLE.effect, name="causalRelationship__effect", curie=SAMPLE.curie('effect'), - model_uri=SAMPLE.causalRelationship__effect, domain=None, range=Optional[Union[str, VariableId]]) - -slots.extractionResult__input_id = Slot(uri=CORE.input_id, name="extractionResult__input_id", curie=CORE.curie('input_id'), - model_uri=SAMPLE.extractionResult__input_id, domain=None, range=Optional[str]) - -slots.extractionResult__input_title = Slot(uri=CORE.input_title, name="extractionResult__input_title", curie=CORE.curie('input_title'), - model_uri=SAMPLE.extractionResult__input_title, domain=None, range=Optional[str]) - -slots.extractionResult__input_text = Slot(uri=CORE.input_text, name="extractionResult__input_text", curie=CORE.curie('input_text'), - model_uri=SAMPLE.extractionResult__input_text, domain=None, range=Optional[str]) - -slots.extractionResult__raw_completion_output = Slot(uri=CORE.raw_completion_output, name="extractionResult__raw_completion_output", curie=CORE.curie('raw_completion_output'), - model_uri=SAMPLE.extractionResult__raw_completion_output, domain=None, range=Optional[str]) - -slots.extractionResult__prompt = Slot(uri=CORE.prompt, name="extractionResult__prompt", curie=CORE.curie('prompt'), - model_uri=SAMPLE.extractionResult__prompt, domain=None, range=Optional[str]) - -slots.extractionResult__extracted_object = Slot(uri=CORE.extracted_object, name="extractionResult__extracted_object", curie=CORE.curie('extracted_object'), - model_uri=SAMPLE.extractionResult__extracted_object, domain=None, range=Optional[Union[dict, Any]]) - -slots.extractionResult__named_entities = Slot(uri=CORE.named_entities, name="extractionResult__named_entities", curie=CORE.curie('named_entities'), - model_uri=SAMPLE.extractionResult__named_entities, domain=None, range=Optional[Union[Union[dict, Any], List[Union[dict, Any]]]]) - -slots.namedEntity__id = Slot(uri=CORE.id, name="namedEntity__id", curie=CORE.curie('id'), - model_uri=SAMPLE.namedEntity__id, domain=None, range=URIRef) - -slots.namedEntity__label = Slot(uri=RDFS.label, name="namedEntity__label", curie=RDFS.curie('label'), - model_uri=SAMPLE.namedEntity__label, domain=None, range=Optional[str]) - -slots.triple__subject = Slot(uri=CORE.subject, name="triple__subject", curie=CORE.curie('subject'), - model_uri=SAMPLE.triple__subject, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__predicate = Slot(uri=CORE.predicate, name="triple__predicate", curie=CORE.curie('predicate'), - model_uri=SAMPLE.triple__predicate, domain=None, range=Optional[Union[str, RelationshipTypeId]]) - -slots.triple__object = Slot(uri=CORE.object, name="triple__object", curie=CORE.curie('object'), - model_uri=SAMPLE.triple__object, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__qualifier = Slot(uri=CORE.qualifier, name="triple__qualifier", curie=CORE.curie('qualifier'), - model_uri=SAMPLE.triple__qualifier, domain=None, range=Optional[str]) - -slots.triple__subject_qualifier = Slot(uri=CORE.subject_qualifier, name="triple__subject_qualifier", curie=CORE.curie('subject_qualifier'), - model_uri=SAMPLE.triple__subject_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__object_qualifier = Slot(uri=CORE.object_qualifier, name="triple__object_qualifier", curie=CORE.curie('object_qualifier'), - model_uri=SAMPLE.triple__object_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.textWithTriples__publication = Slot(uri=CORE.publication, name="textWithTriples__publication", curie=CORE.curie('publication'), - model_uri=SAMPLE.textWithTriples__publication, domain=None, range=Optional[Union[dict, Publication]]) - -slots.textWithTriples__triples = Slot(uri=CORE.triples, name="textWithTriples__triples", curie=CORE.curie('triples'), - model_uri=SAMPLE.textWithTriples__triples, domain=None, range=Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]]) - -slots.publication__id = Slot(uri=CORE.id, name="publication__id", curie=CORE.curie('id'), - model_uri=SAMPLE.publication__id, domain=None, range=Optional[str]) - -slots.publication__title = Slot(uri=CORE.title, name="publication__title", curie=CORE.curie('title'), - model_uri=SAMPLE.publication__title, domain=None, range=Optional[str]) - -slots.publication__abstract = Slot(uri=CORE.abstract, name="publication__abstract", curie=CORE.curie('abstract'), - model_uri=SAMPLE.publication__abstract, domain=None, range=Optional[str]) - -slots.publication__combined_text = Slot(uri=CORE.combined_text, name="publication__combined_text", curie=CORE.curie('combined_text'), - model_uri=SAMPLE.publication__combined_text, domain=None, range=Optional[str]) - -slots.publication__full_text = Slot(uri=CORE.full_text, name="publication__full_text", curie=CORE.curie('full_text'), - model_uri=SAMPLE.publication__full_text, domain=None, range=Optional[str]) - -slots.annotatorResult__subject_text = Slot(uri=CORE.subject_text, name="annotatorResult__subject_text", curie=CORE.curie('subject_text'), - model_uri=SAMPLE.annotatorResult__subject_text, domain=None, range=Optional[str]) - -slots.annotatorResult__object_id = Slot(uri=CORE.object_id, name="annotatorResult__object_id", curie=CORE.curie('object_id'), - model_uri=SAMPLE.annotatorResult__object_id, domain=None, range=Optional[str]) - -slots.annotatorResult__object_text = Slot(uri=CORE.object_text, name="annotatorResult__object_text", curie=CORE.curie('object_text'), - model_uri=SAMPLE.annotatorResult__object_text, domain=None, range=Optional[str]) \ No newline at end of file diff --git a/projects/environmental_sample/excel/environmental_sample.xlsx b/projects/environmental_sample/excel/environmental_sample.xlsx deleted file mode 100644 index 98f7f4c97..000000000 Binary files a/projects/environmental_sample/excel/environmental_sample.xlsx and /dev/null differ diff --git a/projects/environmental_sample/graphql/environmental_sample.graphql b/projects/environmental_sample/graphql/environmental_sample.graphql deleted file mode 100644 index 9b059b204..000000000 --- a/projects/environmental_sample/graphql/environmental_sample.graphql +++ /dev/null @@ -1,115 +0,0 @@ -type AnnotatorResult - { - subjectText: String - objectId: String - objectText: String - } - -type Any - { - } - -type CausalRelationship - { - cause: Variable - effect: Variable - } - -interface CompoundExpression - { - } - -type Environment - { - id: String! - label: String - } - -type EnvironmentalMaterial - { - id: String! - label: String - } - -type ExtractionResult - { - inputId: String - inputTitle: String - inputText: String - rawCompletionOutput: String - prompt: String - extractedObject: Any - namedEntities: [Any] - } - -type Location - { - id: String! - label: String - } - -type Measurement - { - value: String - unit: Unit - } - -interface NamedEntity - { - id: String! - label: String - } - -type Publication - { - id: String - title: String - abstract: String - combinedText: String - fullText: String - } - -type RelationshipType - { - id: String! - label: String - } - -type Study - { - location: [Location] - environmentalMaterial: [EnvironmentalMaterial] - environments: [Environment] - causalRelationships: [CausalRelationship] - variables: [Variable] - measurements: [Measurement] - } - -type TextWithTriples - { - publication: Publication - triples: [Triple] - } - -interface Triple - { - subject: NamedEntity - predicate: RelationshipType - object: NamedEntity - qualifier: String - subjectQualifier: NamedEntity - objectQualifier: NamedEntity - } - -type Unit - { - id: String! - label: String - } - -type Variable - { - id: String! - label: String - } - diff --git a/projects/environmental_sample/jsonld/environmental_sample.context.jsonld b/projects/environmental_sample/jsonld/environmental_sample.context.jsonld deleted file mode 100644 index e8fea7e3d..000000000 --- a/projects/environmental_sample/jsonld/environmental_sample.context.jsonld +++ /dev/null @@ -1,164 +0,0 @@ -{ - "comments": { - "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2023-08-07T10:53:09", - "source": "environmental_sample.yaml" - }, - "@context": { - "ENVO": "http://example.org/UNKNOWN/ENVO/", - "ENVTHES": "http://example.org/UNKNOWN/ENVTHES/", - "GAZ": "http://example.org/UNKNOWN/GAZ/", - "MIXS": "http://example.org/UNKNOWN/MIXS/", - "NCIT": { - "@id": "http://purl.obolibrary.org/obo/NCIT_", - "@prefix": true - }, - "PATO": "http://example.org/UNKNOWN/PATO/", - "RO": { - "@id": "http://purl.obolibrary.org/obo/RO_", - "@prefix": true - }, - "UO": "http://example.org/UNKNOWN/UO/", - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "sample": "http://w3id.org/ontogpt/environmental-sample/", - "@vocab": "http://w3id.org/ontogpt/environmental-sample/", - "object_id": { - "@id": "core:object_id" - }, - "object_text": { - "@id": "core:object_text" - }, - "subject_text": { - "@id": "core:subject_text" - }, - "cause": { - "@type": "@id" - }, - "effect": { - "@type": "@id" - }, - "extracted_object": { - "@type": "@id", - "@id": "core:extracted_object" - }, - "input_id": { - "@id": "core:input_id" - }, - "input_text": { - "@id": "core:input_text" - }, - "input_title": { - "@id": "core:input_title" - }, - "named_entities": { - "@type": "@id", - "@id": "core:named_entities" - }, - "prompt": { - "@id": "core:prompt" - }, - "raw_completion_output": { - "@id": "core:raw_completion_output" - }, - "unit": { - "@type": "@id" - }, - "id": { - "@id": "core:id" - }, - "label": { - "@id": "rdfs:label" - }, - "abstract": { - "@id": "core:abstract" - }, - "combined_text": { - "@id": "core:combined_text" - }, - "full_text": { - "@id": "core:full_text" - }, - "title": { - "@id": "core:title" - }, - "causal_relationships": { - "@type": "@id" - }, - "environmental_material": { - "@type": "@id" - }, - "environments": { - "@type": "@id" - }, - "location": { - "@type": "@id" - }, - "measurements": { - "@type": "@id" - }, - "variables": { - "@type": "@id" - }, - "publication": { - "@type": "@id", - "@id": "core:publication" - }, - "triples": { - "@type": "@id", - "@id": "core:triples" - }, - "object": { - "@type": "@id", - "@id": "core:object" - }, - "object_qualifier": { - "@type": "@id", - "@id": "core:object_qualifier" - }, - "predicate": { - "@type": "@id", - "@id": "core:predicate" - }, - "qualifier": { - "@id": "core:qualifier" - }, - "subject": { - "@type": "@id", - "@id": "core:subject" - }, - "subject_qualifier": { - "@type": "@id", - "@id": "core:subject_qualifier" - }, - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } - } -} diff --git a/projects/environmental_sample/jsonld/environmental_sample.jsonld b/projects/environmental_sample/jsonld/environmental_sample.jsonld deleted file mode 100644 index a1c9df94a..000000000 --- a/projects/environmental_sample/jsonld/environmental_sample.jsonld +++ /dev/null @@ -1,1422 +0,0 @@ -{ - "name": "environmental-sample", - "description": "A template for Environmental Samples", - "title": "Environmental Sample Template", - "id": "http://w3id.org/ontogpt/environmental-sample", - "imports": [ - "linkml:types", - "core" - ], - "license": "https://creativecommons.org/publicdomain/zero/1.0/", - "prefixes": [ - { - "prefix_prefix": "linkml", - "prefix_reference": "https://w3id.org/linkml/" - }, - { - "prefix_prefix": "sample", - "prefix_reference": "http://w3id.org/ontogpt/environmental-sample/" - } - ], - "default_prefix": "sample", - "default_range": "string", - "types": [ - { - "name": "string", - "definition_uri": "https://w3id.org/linkml/String", - "description": "A character string", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Text" - ], - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "@type": "TypeDefinition" - }, - { - "name": "integer", - "definition_uri": "https://w3id.org/linkml/Integer", - "description": "An integer", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Integer" - ], - "base": "int", - "uri": "http://www.w3.org/2001/XMLSchema#integer", - "@type": "TypeDefinition" - }, - { - "name": "boolean", - "definition_uri": "https://w3id.org/linkml/Boolean", - "description": "A binary (true or false) value", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Boolean" - ], - "base": "Bool", - "uri": "http://www.w3.org/2001/XMLSchema#boolean", - "repr": "bool", - "@type": "TypeDefinition" - }, - { - "name": "float", - "definition_uri": "https://w3id.org/linkml/Float", - "description": "A real number that conforms to the xsd:float specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#float", - "@type": "TypeDefinition" - }, - { - "name": "double", - "definition_uri": "https://w3id.org/linkml/Double", - "description": "A real number that conforms to the xsd:double specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#double", - "@type": "TypeDefinition" - }, - { - "name": "decimal", - "definition_uri": "https://w3id.org/linkml/Decimal", - "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "broad_mappings": [ - "schema:Number" - ], - "base": "Decimal", - "uri": "http://www.w3.org/2001/XMLSchema#decimal", - "@type": "TypeDefinition" - }, - { - "name": "time", - "definition_uri": "https://w3id.org/linkml/Time", - "description": "A time object represents a (local) time of day, independent of any particular day", - "notes": [ - "URI is dateTime because OWL reasoners do not work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Time" - ], - "base": "XSDTime", - "uri": "http://www.w3.org/2001/XMLSchema#time", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date", - "definition_uri": "https://w3id.org/linkml/Date", - "description": "a date (year, month and day) in an idealized calendar", - "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Date" - ], - "base": "XSDDate", - "uri": "http://www.w3.org/2001/XMLSchema#date", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "datetime", - "definition_uri": "https://w3id.org/linkml/Datetime", - "description": "The combination of a date and time", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:DateTime" - ], - "base": "XSDDateTime", - "uri": "http://www.w3.org/2001/XMLSchema#dateTime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date_or_datetime", - "definition_uri": "https://w3id.org/linkml/DateOrDatetime", - "description": "Either a date or a datetime", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "https://w3id.org/linkml/DateOrDatetime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uriorcurie", - "definition_uri": "https://w3id.org/linkml/Uriorcurie", - "description": "a URI or a CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "URIorCURIE", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "curie", - "definition_uri": "https://w3id.org/linkml/Curie", - "conforms_to": "https://www.w3.org/TR/curie/", - "description": "a compact URI", - "comments": [ - "in RDF serializations this MUST be expanded to a URI", - "in non-RDF serializations MAY be serialized as the compact representation" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "Curie", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uri", - "definition_uri": "https://w3id.org/linkml/Uri", - "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", - "description": "a complete URI", - "comments": [ - "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:URL" - ], - "base": "URI", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "ncname", - "definition_uri": "https://w3id.org/linkml/Ncname", - "description": "Prefix part of CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NCName", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "objectidentifier", - "definition_uri": "https://w3id.org/linkml/Objectidentifier", - "description": "A URI or CURIE that represents an object in the model.", - "comments": [ - "Used for inheritance and type checking" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "ElementIdentifier", - "uri": "http://www.w3.org/ns/shex#iri", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "nodeidentifier", - "definition_uri": "https://w3id.org/linkml/Nodeidentifier", - "description": "A URI, CURIE or BNODE that represents a node in a model.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NodeIdentifier", - "uri": "http://www.w3.org/ns/shex#nonLiteral", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpointer", - "definition_uri": "https://w3id.org/linkml/Jsonpointer", - "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901", - "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpath", - "definition_uri": "https://w3id.org/linkml/Jsonpath", - "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html", - "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "sparqlpath", - "definition_uri": "https://w3id.org/linkml/Sparqlpath", - "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths", - "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - } - ], - "enums": [ - { - "name": "NullDataOptions", - "definition_uri": "http://w3id.org/ontogpt/core/NullDataOptions", - "from_schema": "http://w3id.org/ontogpt/core", - "permissible_values": [ - { - "text": "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "meaning": "NCIT:C149701" - }, - { - "text": "NOT_APPLICABLE", - "meaning": "NCIT:C18902", - "aliases": [ - "not applicable", - "N/A" - ] - }, - { - "text": "NOT_MENTIONED" - } - ] - } - ], - "slots": [ - { - "name": "study__location", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of sites at which the study was conducted. give specific place names. if you cannot find a specific place name leave the field as empty.", - "@type": "Annotation" - } - ], - "description": "the sites at which the study was conducted", - "from_schema": "http://w3id.org/ontogpt/environmental-sample", - "slot_uri": "http://w3id.org/ontogpt/environmental-sample/location", - "multivalued": true, - "alias": "location", - "owner": "Study", - "domain_of": [ - "Study" - ], - "range": "Location", - "@type": "SlotDefinition" - }, - { - "name": "study__environmental_material", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of environmental materials", - "@type": "Annotation" - } - ], - "description": "the environmental material that was sampled", - "from_schema": "http://w3id.org/ontogpt/environmental-sample", - "slot_uri": "http://w3id.org/ontogpt/environmental-sample/environmental_material", - "multivalued": true, - "alias": "environmental_material", - "owner": "Study", - "domain_of": [ - "Study" - ], - "range": "EnvironmentalMaterial", - "@type": "SlotDefinition" - }, - { - "name": "study__environments", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of environment terms for the location in which the study was conducted", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/environmental-sample", - "slot_uri": "http://w3id.org/ontogpt/environmental-sample/environments", - "multivalued": true, - "alias": "environments", - "owner": "Study", - "domain_of": [ - "Study" - ], - "range": "Environment", - "@type": "SlotDefinition" - }, - { - "name": "study__causal_relationships", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of cause-effect pairs, for example, effect of temperature on growth", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/environmental-sample", - "slot_uri": "http://w3id.org/ontogpt/environmental-sample/causal_relationships", - "multivalued": true, - "alias": "causal_relationships", - "owner": "Study", - "domain_of": [ - "Study" - ], - "range": "CausalRelationship", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "study__variables", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of study variables", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/environmental-sample", - "slot_uri": "http://w3id.org/ontogpt/environmental-sample/variables", - "multivalued": true, - "alias": "variables", - "owner": "Study", - "domain_of": [ - "Study" - ], - "range": "Variable", - "@type": "SlotDefinition" - }, - { - "name": "study__measurements", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of value-measurement pairs", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/environmental-sample", - "slot_uri": "http://w3id.org/ontogpt/environmental-sample/measurements", - "multivalued": true, - "alias": "measurements", - "owner": "Study", - "domain_of": [ - "Study" - ], - "range": "Measurement", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "measurement__value", - "description": "the value of the measurement", - "from_schema": "http://w3id.org/ontogpt/environmental-sample", - "slot_uri": "http://w3id.org/ontogpt/environmental-sample/value", - "alias": "value", - "owner": "Measurement", - "domain_of": [ - "Measurement" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "measurement__unit", - "description": "the unit of the measurement", - "from_schema": "http://w3id.org/ontogpt/environmental-sample", - "slot_uri": "http://w3id.org/ontogpt/environmental-sample/unit", - "alias": "unit", - "owner": "Measurement", - "domain_of": [ - "Measurement" - ], - "range": "Unit", - "@type": "SlotDefinition" - }, - { - "name": "causalRelationship__cause", - "description": "the variable that is the cause of the effect", - "from_schema": "http://w3id.org/ontogpt/environmental-sample", - "slot_uri": "http://w3id.org/ontogpt/environmental-sample/cause", - "alias": "cause", - "owner": "CausalRelationship", - "domain_of": [ - "CausalRelationship" - ], - "range": "Variable", - "@type": "SlotDefinition" - }, - { - "name": "causalRelationship__effect", - "description": "the things that is affected", - "from_schema": "http://w3id.org/ontogpt/environmental-sample", - "slot_uri": "http://w3id.org/ontogpt/environmental-sample/effect", - "alias": "effect", - "owner": "CausalRelationship", - "domain_of": [ - "CausalRelationship" - ], - "range": "Variable", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_id", - "alias": "input_id", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_title", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_title", - "alias": "input_title", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_text", - "alias": "input_text", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__raw_completion_output", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/raw_completion_output", - "alias": "raw_completion_output", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__prompt", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/prompt", - "alias": "prompt", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__extracted_object", - "description": "The complex objects extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/extracted_object", - "alias": "extracted_object", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__named_entities", - "description": "Named entities extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/named_entities", - "multivalued": true, - "alias": "named_entities", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "identifier": true, - "alias": "id", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "required": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "from_schema": "http://w3id.org/ontogpt/core", - "aliases": [ - "name" - ], - "mappings": [ - "http://example.org/UNKNOWN/rdfs/label" - ], - "slot_uri": "http://example.org/UNKNOWN/rdfs/label", - "alias": "label", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject", - "alias": "subject", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__predicate", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/predicate", - "alias": "predicate", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "triple__object", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object", - "alias": "object", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/qualifier", - "alias": "qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_qualifier", - "alias": "subject_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_qualifier", - "alias": "object_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/publication", - "alias": "publication", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__triples", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/triples", - "multivalued": true, - "alias": "triples", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "publication__id", - "description": "The publication identifier", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "alias": "id", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__title", - "description": "The title of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/title", - "alias": "title", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__abstract", - "description": "The abstract of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/abstract", - "alias": "abstract", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__combined_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/combined_text", - "alias": "combined_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__full_text", - "description": "The full text of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/full_text", - "alias": "full_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__subject_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_text", - "alias": "subject_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_id", - "alias": "object_id", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_text", - "alias": "object_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - } - ], - "classes": [ - { - "name": "Study", - "definition_uri": "http://w3id.org/ontogpt/environmental-sample/Study", - "from_schema": "http://w3id.org/ontogpt/environmental-sample", - "slots": [ - "study__location", - "study__environmental_material", - "study__environments", - "study__causal_relationships", - "study__variables", - "study__measurements" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "location", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of sites at which the study was conducted. give specific place names. if you cannot find a specific place name leave the field as empty.", - "@type": "Annotation" - } - ], - "description": "the sites at which the study was conducted", - "multivalued": true, - "range": "Location", - "@type": "SlotDefinition" - }, - { - "name": "environmental_material", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of environmental materials", - "@type": "Annotation" - } - ], - "description": "the environmental material that was sampled", - "multivalued": true, - "range": "EnvironmentalMaterial", - "@type": "SlotDefinition" - }, - { - "name": "environments", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of environment terms for the location in which the study was conducted", - "@type": "Annotation" - } - ], - "multivalued": true, - "range": "Environment", - "@type": "SlotDefinition" - }, - { - "name": "causal_relationships", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of cause-effect pairs, for example, effect of temperature on growth", - "@type": "Annotation" - } - ], - "multivalued": true, - "range": "CausalRelationship", - "@type": "SlotDefinition" - }, - { - "name": "variables", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of study variables", - "@type": "Annotation" - } - ], - "multivalued": true, - "range": "Variable", - "@type": "SlotDefinition" - }, - { - "name": "measurements", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of value-measurement pairs", - "@type": "Annotation" - } - ], - "multivalued": true, - "range": "Measurement", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/environmental-sample/Study", - "tree_root": true, - "@type": "ClassDefinition" - }, - { - "name": "Location", - "id_prefixes": [ - "ENVO", - "GAZ", - "ENVTHES" - ], - "definition_uri": "http://w3id.org/ontogpt/environmental-sample/Location", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:envo, bioportal:gaz, bioportal:envthes", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/environmental-sample", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/environmental-sample/Location", - "@type": "ClassDefinition" - }, - { - "name": "EnvironmentalMaterial", - "id_prefixes": [ - "ENVO", - "ENVTHES" - ], - "definition_uri": "http://w3id.org/ontogpt/environmental-sample/EnvironmentalMaterial", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:envo, bioportal:envthes", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/environmental-sample", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/environmental-sample/EnvironmentalMaterial", - "@type": "ClassDefinition" - }, - { - "name": "Environment", - "id_prefixes": [ - "ENVO", - "ENVTHES" - ], - "definition_uri": "http://w3id.org/ontogpt/environmental-sample/Environment", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:envo, bioportal:envthes", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/environmental-sample", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/environmental-sample/Environment", - "@type": "ClassDefinition" - }, - { - "name": "Variable", - "id_prefixes": [ - "ENVO", - "MIXS", - "PATO", - "ENVTHES" - ], - "definition_uri": "http://w3id.org/ontogpt/environmental-sample/Variable", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:envo, bioportal:bero, bioportal:envthes", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/environmental-sample", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/environmental-sample/Variable", - "@type": "ClassDefinition" - }, - { - "name": "Unit", - "id_prefixes": [ - "UO", - "NCIT" - ], - "definition_uri": "http://w3id.org/ontogpt/environmental-sample/Unit", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:uo, bioportal:ncit", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/environmental-sample", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/environmental-sample/Unit", - "@type": "ClassDefinition" - }, - { - "name": "Measurement", - "definition_uri": "http://w3id.org/ontogpt/environmental-sample/Measurement", - "from_schema": "http://w3id.org/ontogpt/environmental-sample", - "is_a": "CompoundExpression", - "slots": [ - "measurement__value", - "measurement__unit" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "value", - "description": "the value of the measurement", - "@type": "SlotDefinition" - }, - { - "name": "unit", - "description": "the unit of the measurement", - "range": "Unit", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/environmental-sample/Measurement", - "@type": "ClassDefinition" - }, - { - "name": "CausalRelationship", - "definition_uri": "http://w3id.org/ontogpt/environmental-sample/CausalRelationship", - "from_schema": "http://w3id.org/ontogpt/environmental-sample", - "is_a": "CompoundExpression", - "slots": [ - "causalRelationship__cause", - "causalRelationship__effect" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "cause", - "description": "the variable that is the cause of the effect", - "range": "Variable", - "@type": "SlotDefinition" - }, - { - "name": "effect", - "description": "the things that is affected", - "range": "Variable", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/environmental-sample/CausalRelationship", - "@type": "ClassDefinition" - }, - { - "name": "Any", - "definition_uri": "http://w3id.org/ontogpt/core/Any", - "from_schema": "http://w3id.org/ontogpt/core", - "mappings": [ - "linkml:Any" - ], - "slot_usage": {}, - "class_uri": "https://w3id.org/linkml/Any", - "@type": "ClassDefinition" - }, - { - "name": "ExtractionResult", - "definition_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "description": "A result of extracting knowledge on text", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "extractionResult__input_id", - "extractionResult__input_title", - "extractionResult__input_text", - "extractionResult__raw_completion_output", - "extractionResult__prompt", - "extractionResult__extracted_object", - "extractionResult__named_entities" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "input_id", - "@type": "SlotDefinition" - }, - { - "name": "input_title", - "@type": "SlotDefinition" - }, - { - "name": "input_text", - "@type": "SlotDefinition" - }, - { - "name": "raw_completion_output", - "@type": "SlotDefinition" - }, - { - "name": "prompt", - "@type": "SlotDefinition" - }, - { - "name": "extracted_object", - "description": "The complex objects extracted from the text", - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "named_entities", - "description": "Named entities extracted from the text", - "multivalued": true, - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "@type": "ClassDefinition" - }, - { - "name": "NamedEntity", - "definition_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "identifier": true, - "@type": "SlotDefinition" - }, - { - "name": "label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "aliases": [ - "name" - ], - "slot_uri": "rdfs:label", - "range": "string", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "@type": "ClassDefinition" - }, - { - "name": "CompoundExpression", - "definition_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "@type": "ClassDefinition" - }, - { - "name": "Triple", - "definition_uri": "http://w3id.org/ontogpt/core/Triple", - "description": "Abstract parent for Relation Extraction tasks", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "CompoundExpression", - "abstract": true, - "slots": [ - "triple__subject", - "triple__predicate", - "triple__object", - "triple__qualifier", - "triple__subject_qualifier", - "triple__object_qualifier" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "predicate", - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "object", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Triple", - "@type": "ClassDefinition" - }, - { - "name": "TextWithTriples", - "definition_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "textWithTriples__publication", - "textWithTriples__triples" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "triples", - "multivalued": true, - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "@type": "ClassDefinition" - }, - { - "name": "RelationshipType", - "id_prefixes": [ - "RO", - "biolink" - ], - "definition_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "@type": "ClassDefinition" - }, - { - "name": "Publication", - "definition_uri": "http://w3id.org/ontogpt/core/Publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "publication__id", - "publication__title", - "publication__abstract", - "publication__combined_text", - "publication__full_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "description": "The publication identifier", - "@type": "SlotDefinition" - }, - { - "name": "title", - "description": "The title of the publication", - "@type": "SlotDefinition" - }, - { - "name": "abstract", - "description": "The abstract of the publication", - "@type": "SlotDefinition" - }, - { - "name": "combined_text", - "@type": "SlotDefinition" - }, - { - "name": "full_text", - "description": "The full text of the publication", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Publication", - "@type": "ClassDefinition" - }, - { - "name": "AnnotatorResult", - "definition_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "annotatorResult__subject_text", - "annotatorResult__object_id", - "annotatorResult__object_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject_text", - "@type": "SlotDefinition" - }, - { - "name": "object_id", - "@type": "SlotDefinition" - }, - { - "name": "object_text", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "@type": "ClassDefinition" - } - ], - "metamodel_version": "1.7.0", - "source_file": "environmental_sample.yaml", - "source_file_date": "2023-06-17T15:11:19", - "source_file_size": 3147, - "generation_date": "2023-08-07T10:53:10", - "@type": "SchemaDefinition", - "@context": [ - "projects/environmental_sample/jsonld/environmental_sample.context.jsonld", - "https://w3id.org/linkml/types.context.jsonld", - "core.context.jsonld", - { - "@base": "http://w3id.org/ontogpt/environmental-sample/" - } - ] -} diff --git a/projects/environmental_sample/jsonschema/environmental_sample.schema.json b/projects/environmental_sample/jsonschema/environmental_sample.schema.json deleted file mode 100644 index 551239e45..000000000 --- a/projects/environmental_sample/jsonschema/environmental_sample.schema.json +++ /dev/null @@ -1,354 +0,0 @@ -{ - "$defs": { - "AnnotatorResult": { - "additionalProperties": false, - "description": "", - "properties": { - "object_id": { - "type": "string" - }, - "object_text": { - "type": "string" - }, - "subject_text": { - "type": "string" - } - }, - "title": "AnnotatorResult", - "type": "object" - }, - "Any": { - "additionalProperties": true, - "description": "", - "title": "Any", - "type": "object" - }, - "CausalRelationship": { - "additionalProperties": false, - "description": "", - "properties": { - "cause": { - "description": "the variable that is the cause of the effect", - "type": "string" - }, - "effect": { - "description": "the things that is affected", - "type": "string" - } - }, - "title": "CausalRelationship", - "type": "object" - }, - "Environment": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Environment", - "type": "object" - }, - "EnvironmentalMaterial": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "EnvironmentalMaterial", - "type": "object" - }, - "ExtractionResult": { - "additionalProperties": false, - "description": "A result of extracting knowledge on text", - "properties": { - "extracted_object": { - "$ref": "#/$defs/Any", - "description": "The complex objects extracted from the text" - }, - "input_id": { - "type": "string" - }, - "input_text": { - "type": "string" - }, - "input_title": { - "type": "string" - }, - "named_entities": { - "description": "Named entities extracted from the text", - "items": { - "$ref": "#/$defs/Any" - }, - "type": "array" - }, - "prompt": { - "type": "string" - }, - "raw_completion_output": { - "type": "string" - } - }, - "title": "ExtractionResult", - "type": "object" - }, - "Location": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Location", - "type": "object" - }, - "Measurement": { - "additionalProperties": false, - "description": "", - "properties": { - "unit": { - "description": "the unit of the measurement", - "type": "string" - }, - "value": { - "description": "the value of the measurement", - "type": "string" - } - }, - "title": "Measurement", - "type": "object" - }, - "NullDataOptions": { - "description": "", - "enum": [ - "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "NOT_APPLICABLE", - "NOT_MENTIONED" - ], - "title": "NullDataOptions", - "type": "string" - }, - "Publication": { - "additionalProperties": false, - "description": "", - "properties": { - "abstract": { - "description": "The abstract of the publication", - "type": "string" - }, - "combined_text": { - "type": "string" - }, - "full_text": { - "description": "The full text of the publication", - "type": "string" - }, - "id": { - "description": "The publication identifier", - "type": "string" - }, - "title": { - "description": "The title of the publication", - "type": "string" - } - }, - "title": "Publication", - "type": "object" - }, - "RelationshipType": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "RelationshipType", - "type": "object" - }, - "Study": { - "additionalProperties": false, - "description": "", - "properties": { - "causal_relationships": { - "items": { - "$ref": "#/$defs/CausalRelationship" - }, - "type": "array" - }, - "environmental_material": { - "description": "the environmental material that was sampled", - "items": { - "type": "string" - }, - "type": "array" - }, - "environments": { - "items": { - "type": "string" - }, - "type": "array" - }, - "location": { - "description": "the sites at which the study was conducted", - "items": { - "type": "string" - }, - "type": "array" - }, - "measurements": { - "items": { - "$ref": "#/$defs/Measurement" - }, - "type": "array" - }, - "variables": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "title": "Study", - "type": "object" - }, - "TextWithTriples": { - "additionalProperties": false, - "description": "", - "properties": { - "publication": { - "$ref": "#/$defs/Publication" - }, - "triples": { - "items": { - "$ref": "#/$defs/Triple" - }, - "type": "array" - } - }, - "title": "TextWithTriples", - "type": "object" - }, - "Unit": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Unit", - "type": "object" - }, - "Variable": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Variable", - "type": "object" - } - }, - "$id": "http://w3id.org/ontogpt/environmental-sample", - "$schema": "http://json-schema.org/draft-07/schema#", - "additionalProperties": true, - "metamodel_version": "1.7.0", - "properties": { - "causal_relationships": { - "items": { - "$ref": "#/$defs/CausalRelationship" - }, - "type": "array" - }, - "environmental_material": { - "description": "the environmental material that was sampled", - "items": { - "type": "string" - }, - "type": "array" - }, - "environments": { - "items": { - "type": "string" - }, - "type": "array" - }, - "location": { - "description": "the sites at which the study was conducted", - "items": { - "type": "string" - }, - "type": "array" - }, - "measurements": { - "items": { - "$ref": "#/$defs/Measurement" - }, - "type": "array" - }, - "variables": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "title": "environmental-sample", - "type": "object", - "version": null -} \ No newline at end of file diff --git a/projects/environmental_sample/owl/environmental_sample.owl.ttl b/projects/environmental_sample/owl/environmental_sample.owl.ttl deleted file mode 100644 index 11e703611..000000000 --- a/projects/environmental_sample/owl/environmental_sample.owl.ttl +++ /dev/null @@ -1,509 +0,0 @@ -@prefix IAO: <http://purl.obolibrary.org/obo/IAO_> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix owl: <http://www.w3.org/2002/07/owl#> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . -@prefix sample: <http://w3id.org/ontogpt/environmental-sample/> . -@prefix skos: <http://www.w3.org/2004/02/skos/core#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -<http://w3id.org/ontogpt/environmental-sample> a owl:Ontology ; - rdfs:label "environmental-sample" ; - IAO:0000700 <http://w3id.org/ontogpt/core/AnnotatorResult>, - <http://w3id.org/ontogpt/core/Any>, - <http://w3id.org/ontogpt/core/CompoundExpression>, - <http://w3id.org/ontogpt/core/ExtractionResult>, - <http://w3id.org/ontogpt/core/NamedEntity>, - <http://w3id.org/ontogpt/core/Publication>, - <http://w3id.org/ontogpt/core/TextWithTriples>, - sample:Study ; - linkml:classes "{'Study': ClassDefinition(name='Study', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/environmental-sample/Study', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/environmental-sample', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['study__location', 'study__environmental_material', 'study__environments', 'study__causal_relationships', 'study__variables', 'study__measurements'], slot_usage={}, attributes={'location': SlotDefinition(name='location', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of sites at which the study was conducted. give specific place names. if you cannot find a specific place name leave the field as empty.', extensions={}, annotations={})}, description='the sites at which the study was conducted', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Location', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'environmental_material': SlotDefinition(name='environmental_material', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of environmental materials', extensions={}, annotations={})}, description='the environmental material that was sampled', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='EnvironmentalMaterial', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'environments': SlotDefinition(name='environments', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of environment terms for the location in which the study was conducted', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Environment', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'causal_relationships': SlotDefinition(name='causal_relationships', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of cause-effect pairs, for example, effect of temperature on growth', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='CausalRelationship', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'variables': SlotDefinition(name='variables', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of study variables', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Variable', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'measurements': SlotDefinition(name='measurements', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of value-measurement pairs', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Measurement', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='sample:Study', subclass_of=None, union_of=[], defining_slots=[], tree_root=True, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Location': ClassDefinition(name='Location', id_prefixes=['ENVO', 'GAZ', 'ENVTHES'], definition_uri='http://w3id.org/ontogpt/environmental-sample/Location', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:envo, bioportal:gaz, bioportal:envthes', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/environmental-sample', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='sample:Location', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'EnvironmentalMaterial': ClassDefinition(name='EnvironmentalMaterial', id_prefixes=['ENVO', 'ENVTHES'], definition_uri='http://w3id.org/ontogpt/environmental-sample/EnvironmentalMaterial', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:envo, bioportal:envthes', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/environmental-sample', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='sample:EnvironmentalMaterial', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Environment': ClassDefinition(name='Environment', id_prefixes=['ENVO', 'ENVTHES'], definition_uri='http://w3id.org/ontogpt/environmental-sample/Environment', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:envo, bioportal:envthes', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/environmental-sample', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='sample:Environment', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Variable': ClassDefinition(name='Variable', id_prefixes=['ENVO', 'MIXS', 'PATO', 'ENVTHES'], definition_uri='http://w3id.org/ontogpt/environmental-sample/Variable', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:envo, bioportal:bero, bioportal:envthes', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/environmental-sample', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='sample:Variable', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Unit': ClassDefinition(name='Unit', id_prefixes=['UO', 'NCIT'], definition_uri='http://w3id.org/ontogpt/environmental-sample/Unit', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:uo, bioportal:ncit', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/environmental-sample', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='sample:Unit', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Measurement': ClassDefinition(name='Measurement', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/environmental-sample/Measurement', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/environmental-sample', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['measurement__value', 'measurement__unit'], slot_usage={}, attributes={'value': SlotDefinition(name='value', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the value of the measurement', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'unit': SlotDefinition(name='unit', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the unit of the measurement', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Unit', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='sample:Measurement', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'CausalRelationship': ClassDefinition(name='CausalRelationship', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/environmental-sample/CausalRelationship', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/environmental-sample', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['causalRelationship__cause', 'causalRelationship__effect'], slot_usage={}, attributes={'cause': SlotDefinition(name='cause', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the variable that is the cause of the effect', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Variable', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'effect': SlotDefinition(name='effect', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the things that is affected', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Variable', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='sample:CausalRelationship', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Any': ClassDefinition(name='Any', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Any', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=['linkml:Any'], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='linkml:Any', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ExtractionResult': ClassDefinition(name='ExtractionResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/ExtractionResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A result of extracting knowledge on text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['extractionResult__input_id', 'extractionResult__input_title', 'extractionResult__input_text', 'extractionResult__raw_completion_output', 'extractionResult__prompt', 'extractionResult__extracted_object', 'extractionResult__named_entities'], slot_usage={}, attributes={'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:ExtractionResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'NamedEntity': ClassDefinition(name='NamedEntity', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NamedEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:NamedEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'CompoundExpression': ClassDefinition(name='CompoundExpression', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/CompoundExpression', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='core:CompoundExpression', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Triple': ClassDefinition(name='Triple', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Triple', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Abstract parent for Relation Extraction tasks', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['triple__subject', 'triple__predicate', 'triple__object', 'triple__qualifier', 'triple__subject_qualifier', 'triple__object_qualifier'], slot_usage={}, attributes={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Triple', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'TextWithTriples': ClassDefinition(name='TextWithTriples', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/TextWithTriples', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['textWithTriples__publication', 'textWithTriples__triples'], slot_usage={}, attributes={'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:TextWithTriples', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'RelationshipType': ClassDefinition(name='RelationshipType', id_prefixes=['RO', 'biolink'], definition_uri='http://w3id.org/ontogpt/core/RelationshipType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='core:RelationshipType', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Publication': ClassDefinition(name='Publication', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Publication', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['publication__id', 'publication__title', 'publication__abstract', 'publication__combined_text', 'publication__full_text'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Publication', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'AnnotatorResult': ClassDefinition(name='AnnotatorResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/AnnotatorResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['annotatorResult__subject_text', 'annotatorResult__object_id', 'annotatorResult__object_text'], slot_usage={}, attributes={'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:AnnotatorResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={})}" ; - linkml:enums "{'NullDataOptions': EnumDefinition(name='NullDataOptions', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NullDataOptions', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'UNSPECIFIED_METHOD_OF_ADMINISTRATION': PermissibleValue(text='UNSPECIFIED_METHOD_OF_ADMINISTRATION', description=None, meaning='NCIT:C149701', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_APPLICABLE': PermissibleValue(text='NOT_APPLICABLE', description=None, meaning='NCIT:C18902', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['not applicable', 'N/A'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_MENTIONED': PermissibleValue(text='NOT_MENTIONED', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[])}" ; - linkml:id "http://w3id.org/ontogpt/environmental-sample" ; - linkml:imports "core", - "linkml:types" ; - linkml:types "{'string': TypeDefinition(name='string', id_prefixes=[], definition_uri='https://w3id.org/linkml/String', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A character string', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Text'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'integer': TypeDefinition(name='integer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Integer', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An integer', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Integer'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='int', uri='xsd:integer', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'boolean': TypeDefinition(name='boolean', id_prefixes=[], definition_uri='https://w3id.org/linkml/Boolean', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A binary (true or false) value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Boolean'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Bool', uri='xsd:boolean', repr='bool', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'float': TypeDefinition(name='float', id_prefixes=[], definition_uri='https://w3id.org/linkml/Float', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:float specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Float'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:float', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'double': TypeDefinition(name='double', id_prefixes=[], definition_uri='https://w3id.org/linkml/Double', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:double specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:Float'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:double', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'decimal': TypeDefinition(name='decimal', id_prefixes=[], definition_uri='https://w3id.org/linkml/Decimal', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number with arbitrary precision that conforms to the xsd:decimal specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=['schema:Number'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Decimal', uri='xsd:decimal', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'time': TypeDefinition(name='time', id_prefixes=[], definition_uri='https://w3id.org/linkml/Time', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A time object represents a (local) time of day, independent of any particular day', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=['URI is dateTime because OWL reasoners do not work with straight date or time'], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Time'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDTime', uri='xsd:time', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date': TypeDefinition(name='date', id_prefixes=[], definition_uri='https://w3id.org/linkml/Date', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a date (year, month and day) in an idealized calendar', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[\"URI is dateTime because OWL reasoners don't work with straight date or time\"], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Date'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDate', uri='xsd:date', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'datetime': TypeDefinition(name='datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/Datetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The combination of a date and time', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:DateTime'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDateTime', uri='xsd:dateTime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date_or_datetime': TypeDefinition(name='date_or_datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/DateOrDatetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Either a date or a datetime', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='linkml:DateOrDatetime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uriorcurie': TypeDefinition(name='uriorcurie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uriorcurie', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a URI or a CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URIorCURIE', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'curie': TypeDefinition(name='curie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Curie', local_names={}, conforms_to='https://www.w3.org/TR/curie/', implements=[], extensions={}, annotations={}, description='a compact URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations this MUST be expanded to a URI', 'in non-RDF serializations MAY be serialized as the compact representation'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Curie', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uri': TypeDefinition(name='uri', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uri', local_names={}, conforms_to='https://www.ietf.org/rfc/rfc3987.txt', implements=[], extensions={}, annotations={}, description='a complete URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:URL'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URI', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ncname': TypeDefinition(name='ncname', id_prefixes=[], definition_uri='https://w3id.org/linkml/Ncname', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Prefix part of CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NCName', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'objectidentifier': TypeDefinition(name='objectidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Objectidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI or CURIE that represents an object in the model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['Used for inheritance and type checking'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='ElementIdentifier', uri='shex:iri', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'nodeidentifier': TypeDefinition(name='nodeidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Nodeidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI, CURIE or BNODE that represents a node in a model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NodeIdentifier', uri='shex:nonLiteral', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpointer': TypeDefinition(name='jsonpointer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpointer', local_names={}, conforms_to='https://datatracker.ietf.org/doc/html/rfc6901', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpath': TypeDefinition(name='jsonpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpath', local_names={}, conforms_to='https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sparqlpath': TypeDefinition(name='sparqlpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Sparqlpath', local_names={}, conforms_to='https://www.w3.org/TR/sparql11-query/#propertypaths', implements=[], extensions={}, annotations={}, description='A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:SubsetDefinition a owl:Class ; - rdfs:label "subset_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" . - -linkml:TypeDefinition a owl:Class ; - rdfs:label "type_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" ; - linkml:mixins "type_expression" . - -linkml:topValue a owl:DatatypeProperty ; - rdfs:label "value" . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "AnnotatorResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_text> ] ; - linkml:attributes "{'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/ExtractionResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ExtractionResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_title> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/prompt> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/extracted_object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_text> ], - [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/named_entities> ] ; - skos:definition "A result of extracting knowledge on text" ; - linkml:attributes "{'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/TextWithTriples> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TextWithTriples" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Triple> ; - owl:onProperty <http://w3id.org/ontogpt/core/triples> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Publication> ; - owl:onProperty <http://w3id.org/ontogpt/core/publication> ] ; - linkml:attributes "{'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/abstract> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "abstract" ; - rdfs:range linkml:String ; - skos:definition "The abstract of the publication" . - -<http://w3id.org/ontogpt/core/combined_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "combined_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/extracted_object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "extracted_object" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "The complex objects extracted from the text" . - -<http://w3id.org/ontogpt/core/full_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "full_text" ; - rdfs:range linkml:String ; - skos:definition "The full text of the publication" . - -<http://w3id.org/ontogpt/core/input_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_title" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/named_entities> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "named_entities" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "Named entities extracted from the text" . - -<http://w3id.org/ontogpt/core/object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/object_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/object_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" . - -<http://w3id.org/ontogpt/core/object_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/predicate> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "predicate" ; - rdfs:range <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/prompt> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "prompt" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/publication> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "publication" ; - sample:prompt.skip "true" ; - rdfs:range <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "qualifier" ; - rdfs:range linkml:String ; - skos:definition "A qualifier for the statements, e.g. \"NOT\" for negation" . - -<http://w3id.org/ontogpt/core/raw_completion_output> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "raw_completion_output" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/subject> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/subject_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" . - -<http://w3id.org/ontogpt/core/subject_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "title" ; - rdfs:range linkml:String ; - skos:definition "The title of the publication" . - -<http://w3id.org/ontogpt/core/triples> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "triples" ; - rdfs:range <http://w3id.org/ontogpt/core/Triple> . - -sample:Study a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Study" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom sample:Variable ; - owl:onProperty sample:variables ], - [ a owl:Restriction ; - owl:allValuesFrom sample:Measurement ; - owl:onProperty sample:measurements ], - [ a owl:Restriction ; - owl:allValuesFrom sample:Environment ; - owl:onProperty sample:environments ], - [ a owl:Restriction ; - owl:allValuesFrom sample:CausalRelationship ; - owl:onProperty sample:causal_relationships ], - [ a owl:Restriction ; - owl:allValuesFrom sample:Location ; - owl:onProperty sample:location ], - [ a owl:Restriction ; - owl:allValuesFrom sample:EnvironmentalMaterial ; - owl:onProperty sample:environmental_material ] ; - linkml:attributes "{'location': SlotDefinition(name='location', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of sites at which the study was conducted. give specific place names. if you cannot find a specific place name leave the field as empty.', extensions={}, annotations={})}, description='the sites at which the study was conducted', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Location', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'environmental_material': SlotDefinition(name='environmental_material', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of environmental materials', extensions={}, annotations={})}, description='the environmental material that was sampled', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='EnvironmentalMaterial', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'environments': SlotDefinition(name='environments', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of environment terms for the location in which the study was conducted', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Environment', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'causal_relationships': SlotDefinition(name='causal_relationships', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of cause-effect pairs, for example, effect of temperature on growth', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='CausalRelationship', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'variables': SlotDefinition(name='variables', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of study variables', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Variable', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'measurements': SlotDefinition(name='measurements', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of value-measurement pairs', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Measurement', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -sample:causal_relationships a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "causal_relationships" ; - sample:prompt "semicolon-separated list of cause-effect pairs, for example, effect of temperature on growth" ; - rdfs:range sample:CausalRelationship . - -sample:cause a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "cause" ; - rdfs:range sample:Variable ; - skos:definition "the variable that is the cause of the effect" . - -sample:effect a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "effect" ; - rdfs:range sample:Variable ; - skos:definition "the things that is affected" . - -sample:environmental_material a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "environmental_material" ; - sample:prompt "semicolon-separated list of environmental materials" ; - rdfs:range sample:EnvironmentalMaterial ; - skos:definition "the environmental material that was sampled" . - -sample:environments a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "environments" ; - sample:prompt "semicolon-separated list of environment terms for the location in which the study was conducted" ; - rdfs:range sample:Environment . - -sample:location a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "location" ; - sample:prompt "semicolon-separated list of sites at which the study was conducted. give specific place names. if you cannot find a specific place name leave the field as empty." ; - rdfs:range sample:Location ; - skos:definition "the sites at which the study was conducted" . - -sample:measurements a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "measurements" ; - sample:prompt "semicolon-separated list of value-measurement pairs" ; - rdfs:range sample:Measurement . - -sample:unit a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "unit" ; - rdfs:range sample:Unit ; - skos:definition "the unit of the measurement" . - -sample:value a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "value" ; - rdfs:range linkml:String ; - skos:definition "the value of the measurement" . - -sample:variables a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "variables" ; - sample:prompt "semicolon-separated list of study variables" ; - rdfs:range sample:Variable . - -<http://example.org/UNKNOWN/rdfs/label> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "label" ; - sample:owl "AnnotationProperty, AnnotationAssertion" ; - rdfs:range linkml:String ; - skos:altLabel "name" ; - skos:definition "The label (name) of the named thing" ; - skos:exactMatch <http://example.org/UNKNOWN/rdfs/label> . - -<http://purl.obolibrary.org/obo/NCIT_C149701> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "UNSPECIFIED_METHOD_OF_ADMINISTRATION" . - -<http://purl.obolibrary.org/obo/NCIT_C18902> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_APPLICABLE" . - -<http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_MENTIONED" . - -<http://w3id.org/ontogpt/core/RelationshipType> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "RelationshipType" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/Triple> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Triple" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/RelationshipType> ; - owl:onProperty <http://w3id.org/ontogpt/core/predicate> ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - skos:definition "Abstract parent for Relation Extraction tasks" ; - linkml:attributes "{'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -<http://w3id.org/ontogpt/core/id> a owl:ObjectProperty, - linkml:SlotDefinition . - -sample:CausalRelationship a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CausalRelationship" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass sample:Variable ; - owl:onProperty sample:effect ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass sample:Variable ; - owl:onProperty sample:cause ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - linkml:attributes "{'cause': SlotDefinition(name='cause', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the variable that is the cause of the effect', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Variable', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'effect': SlotDefinition(name='effect', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the things that is affected', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Variable', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -sample:Environment a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Environment" ; - sample:annotators "sqlite:obo:envo, bioportal:envthes" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -sample:EnvironmentalMaterial a owl:Class, - linkml:ClassDefinition ; - rdfs:label "EnvironmentalMaterial" ; - sample:annotators "sqlite:obo:envo, bioportal:envthes" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -sample:Location a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Location" ; - sample:annotators "sqlite:obo:envo, bioportal:gaz, bioportal:envthes" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -sample:Measurement a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Measurement" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty sample:value ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass sample:Unit ; - owl:onProperty sample:unit ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - linkml:attributes "{'value': SlotDefinition(name='value', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the value of the measurement', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'unit': SlotDefinition(name='unit', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the unit of the measurement', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Unit', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -sample:Unit a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Unit" ; - sample:annotators "sqlite:obo:uo, bioportal:ncit" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/NullDataOptions> a owl:Class, - linkml:EnumDefinition ; - rdfs:label "NullDataOptions" ; - owl:unionOf ( <http://purl.obolibrary.org/obo/NCIT_C149701> <http://purl.obolibrary.org/obo/NCIT_C18902> <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> ) ; - linkml:permissible_values <http://purl.obolibrary.org/obo/NCIT_C149701>, - <http://purl.obolibrary.org/obo/NCIT_C18902>, - <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> . - -<http://w3id.org/ontogpt/core/Publication> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Publication" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/combined_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/title> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/full_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/abstract> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/CompoundExpression> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CompoundExpression" ; - linkml:attributes "{}" . - -<http://w3id.org/ontogpt/core/Any> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Any" ; - skos:exactMatch linkml:Any ; - linkml:attributes "{}" . - -sample:Variable a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Variable" ; - sample:annotators "sqlite:obo:envo, bioportal:bero, bioportal:envthes" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/NamedEntity> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "NamedEntity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://example.org/UNKNOWN/rdfs/label> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:ClassDefinition a owl:Class ; - rdfs:label "class_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "class_expression" . - -linkml:SlotDefinition a owl:Class ; - rdfs:label "slot_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "slot_expression" . - - diff --git a/projects/environmental_sample/prefixmap/environmental_sample.yaml b/projects/environmental_sample/prefixmap/environmental_sample.yaml deleted file mode 100644 index c6e700268..000000000 --- a/projects/environmental_sample/prefixmap/environmental_sample.yaml +++ /dev/null @@ -1,42 +0,0 @@ -{ - "ENVO": "http://example.org/UNKNOWN/ENVO/", - "ENVTHES": "http://example.org/UNKNOWN/ENVTHES/", - "GAZ": "http://example.org/UNKNOWN/GAZ/", - "MIXS": "http://example.org/UNKNOWN/MIXS/", - "NCIT": "http://purl.obolibrary.org/obo/NCIT_", - "PATO": "http://example.org/UNKNOWN/PATO/", - "RO": "http://purl.obolibrary.org/obo/RO_", - "UO": "http://example.org/UNKNOWN/UO/", - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "sample": "http://w3id.org/ontogpt/environmental-sample/", - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } -} diff --git a/projects/environmental_sample/protobuf/environmental_sample.proto b/projects/environmental_sample/protobuf/environmental_sample.proto deleted file mode 100644 index 195a6f5e5..000000000 --- a/projects/environmental_sample/protobuf/environmental_sample.proto +++ /dev/null @@ -1,79 +0,0 @@ -message AnnotatorResult - { - string subjectText = 0 - string objectId = 0 - string objectText = 0 - } -message CausalRelationship - { - variable cause = 0 - variable effect = 0 - } -message Environment - { - string id = 0 - string label = 0 - } -message EnvironmentalMaterial - { - string id = 0 - string label = 0 - } -// A result of extracting knowledge on text -message ExtractionResult - { - string inputId = 0 - string inputTitle = 0 - string inputText = 0 - string rawCompletionOutput = 0 - string prompt = 0 - any extractedObject = 0 - repeated any namedEntities = 0 - } -message Location - { - string id = 0 - string label = 0 - } -message Measurement - { - string value = 0 - unit unit = 0 - } -message Publication - { - string id = 0 - string title = 0 - string abstract = 0 - string combinedText = 0 - string fullText = 0 - } -message RelationshipType - { - string id = 0 - string label = 0 - } -message Study - { - repeated location location = 0 - repeated environmentalMaterial environmentalMaterial = 0 - repeated environment environments = 0 - repeated causalRelationship causalRelationships = 0 - repeated variable variables = 0 - repeated measurement measurements = 0 - } -message TextWithTriples - { - publication publication = 0 - repeated triple triples = 0 - } -message Unit - { - string id = 0 - string label = 0 - } -message Variable - { - string id = 0 - string label = 0 - } diff --git a/projects/environmental_sample/shacl/environmental_sample.shacl.ttl b/projects/environmental_sample/shacl/environmental_sample.shacl.ttl deleted file mode 100644 index f0d0f8b35..000000000 --- a/projects/environmental_sample/shacl/environmental_sample.shacl.ttl +++ /dev/null @@ -1,297 +0,0 @@ -@prefix linkml: <https://w3id.org/linkml/> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix sample: <http://w3id.org/ontogpt/environmental-sample/> . -@prefix sh: <http://www.w3.org/ns/shacl#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/object_id> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object_text> ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject_text> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/AnnotatorResult> . - -<http://w3id.org/ontogpt/core/CompoundExpression> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass <http://w3id.org/ontogpt/core/CompoundExpression> . - -<http://w3id.org/ontogpt/core/ExtractionResult> a sh:NodeShape ; - sh:closed true ; - sh:description "A result of extracting knowledge on text" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class linkml:Any ; - sh:description "The complex objects extracted from the text" ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/extracted_object> ], - [ sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/prompt> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/input_text> ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/input_title> ], - [ sh:class linkml:Any ; - sh:description "Named entities extracted from the text" ; - sh:nodeKind sh:BlankNode ; - sh:order 6 ; - sh:path <http://w3id.org/ontogpt/core/named_entities> ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/input_id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/ExtractionResult> . - -<http://w3id.org/ontogpt/core/TextWithTriples> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/Publication> ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/publication> ], - [ sh:class <http://w3id.org/ontogpt/core/Triple> ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/triples> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/TextWithTriples> . - -sample:Study a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class sample:Measurement ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path sample:measurements ], - [ sh:class sample:CausalRelationship ; - sh:nodeKind sh:BlankNode ; - sh:order 3 ; - sh:path sample:causal_relationships ], - [ sh:class sample:Location ; - sh:description "the sites at which the study was conducted" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path sample:location ], - [ sh:class sample:Environment ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path sample:environments ], - [ sh:class sample:Variable ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path sample:variables ], - [ sh:class sample:EnvironmentalMaterial ; - sh:description "the environmental material that was sampled" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path sample:environmental_material ] ; - sh:targetClass sample:Study . - -<http://w3id.org/ontogpt/core/Publication> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The title of the publication" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/title> ], - [ sh:description "The abstract of the publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/abstract> ], - [ sh:description "The full text of the publication" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/full_text> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/combined_text> ], - [ sh:description "The publication identifier" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/RelationshipType> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/Triple> a sh:NodeShape ; - sh:closed false ; - sh:description "Abstract parent for Relation Extraction tasks" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A qualifier for the statements, e.g. \"NOT\" for negation" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/object_qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object> ], - [ sh:class <http://w3id.org/ontogpt/core/RelationshipType> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/predicate> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Triple> . - -sample:CausalRelationship a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class sample:Variable ; - sh:description "the variable that is the cause of the effect" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path sample:cause ], - [ sh:class sample:Variable ; - sh:description "the things that is affected" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path sample:effect ] ; - sh:targetClass sample:CausalRelationship . - -sample:Environment a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass sample:Environment . - -sample:EnvironmentalMaterial a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass sample:EnvironmentalMaterial . - -sample:Location a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass sample:Location . - -sample:Measurement a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "the value of the measurement" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path sample:value ], - [ sh:class sample:Unit ; - sh:description "the unit of the measurement" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path sample:unit ] ; - sh:targetClass sample:Measurement . - -sample:Unit a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass sample:Unit . - -linkml:Any a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass linkml:Any . - -sample:Variable a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass sample:Variable . - -<http://w3id.org/ontogpt/core/NamedEntity> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/NamedEntity> . - diff --git a/projects/environmental_sample/shex/environmental_sample.shex b/projects/environmental_sample/shex/environmental_sample.shex deleted file mode 100644 index 49dafa259..000000000 --- a/projects/environmental_sample/shex/environmental_sample.shex +++ /dev/null @@ -1,208 +0,0 @@ -BASE <http://w3id.org/ontogpt/environmental-sample/> -PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> -PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> -PREFIX linkml: <https://w3id.org/linkml/> -PREFIX core: <http://w3id.org/ontogpt/core/> -PREFIX rdfs1: <http://example.org/UNKNOWN/rdfs/> - - -linkml:String xsd:string - -linkml:Integer xsd:integer - -linkml:Boolean xsd:boolean - -linkml:Float xsd:float - -linkml:Double xsd:double - -linkml:Decimal xsd:decimal - -linkml:Time xsd:time - -linkml:Date xsd:date - -linkml:Datetime xsd:dateTime - -linkml:DateOrDatetime linkml:DateOrDatetime - -linkml:Uriorcurie IRI - -linkml:Curie xsd:string - -linkml:Uri IRI - -linkml:Ncname xsd:string - -linkml:Objectidentifier IRI - -linkml:Nodeidentifier NONLITERAL - -linkml:Jsonpointer xsd:string - -linkml:Jsonpath xsd:string - -linkml:Sparqlpath xsd:string - -core:AnnotatorResult CLOSED { - ( $core:AnnotatorResult_tes ( core:subject_text @linkml:String ? ; - core:object_id @linkml:String ? ; - core:object_text @linkml:String ? - ) ; - rdf:type [ core:AnnotatorResult ] ? - ) -} - -core:Any CLOSED { - ( $core:Any_tes rdf:type . * ; - rdf:type [ linkml:Any ] ? - ) -} - -<CausalRelationship> CLOSED { - ( $<CausalRelationship_tes> ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - <cause> @<Variable> ? ; - <effect> @<Variable> ? - ) ; - rdf:type [ <CausalRelationship> ] ? - ) -} - -core:CompoundExpression ( - @<CausalRelationship> OR @<Measurement> OR @core:Triple -) - -core:CompoundExpression_struct { - ( $core:CompoundExpression_tes rdf:type . * ; - rdf:type [ core:CompoundExpression ] ? - ) -} - -<Environment> CLOSED { - ( $<Environment_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Environment> ] - ) -} - -<EnvironmentalMaterial> CLOSED { - ( $<EnvironmentalMaterial_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <EnvironmentalMaterial> ] - ) -} - -core:ExtractionResult CLOSED { - ( $core:ExtractionResult_tes ( core:input_id @linkml:String ? ; - core:input_title @linkml:String ? ; - core:input_text @linkml:String ? ; - core:raw_completion_output @linkml:String ? ; - core:prompt @linkml:String ? ; - core:extracted_object @core:Any ? ; - core:named_entities @core:Any * - ) ; - rdf:type [ core:ExtractionResult ] ? - ) -} - -<Location> CLOSED { - ( $<Location_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Location> ] - ) -} - -<Measurement> CLOSED { - ( $<Measurement_tes> ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - <value> @linkml:String ? ; - <unit> @<Unit> ? - ) ; - rdf:type [ <Measurement> ] ? - ) -} - -core:NamedEntity ( - @<Environment> OR @<EnvironmentalMaterial> OR @<Location> OR @core:RelationshipType OR @<Unit> OR @<Variable> -) - -core:NamedEntity_struct { - ( $core:NamedEntity_tes rdfs1:label @linkml:String ? ; - rdf:type [ core:NamedEntity ] - ) -} - -core:Publication CLOSED { - ( $core:Publication_tes ( core:id @linkml:String ? ; - core:title @linkml:String ? ; - core:abstract @linkml:String ? ; - core:combined_text @linkml:String ? ; - core:full_text @linkml:String ? - ) ; - rdf:type [ core:Publication ] ? - ) -} - -core:RelationshipType CLOSED { - ( $core:RelationshipType_tes ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ core:RelationshipType ] - ) -} - -<Study> CLOSED { - ( $<Study_tes> ( <location> @<Location> * ; - <environmental_material> @<EnvironmentalMaterial> * ; - <environments> @<Environment> * ; - <causal_relationships> @<CausalRelationship> * ; - <variables> @<Variable> * ; - <measurements> @<Measurement> * - ) ; - rdf:type [ <Study> ] ? - ) -} - -core:TextWithTriples CLOSED { - ( $core:TextWithTriples_tes ( core:publication @core:Publication ? ; - core:triples @core:Triple * - ) ; - rdf:type [ core:TextWithTriples ] ? - ) -} - -core:Triple { - ( $core:Triple_tes ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - core:subject @core:NamedEntity ? ; - core:predicate @core:RelationshipType ? ; - core:object @core:NamedEntity ? ; - core:qualifier @linkml:String ? ; - core:subject_qualifier @core:NamedEntity ? ; - core:object_qualifier @core:NamedEntity ? - ) ; - rdf:type [ core:Triple ] ? - ) -} - -<Unit> CLOSED { - ( $<Unit_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Unit> ] - ) -} - -<Variable> CLOSED { - ( $<Variable_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Variable> ] - ) -} - - diff --git a/projects/environmental_sample/sqlschema/environmental_sample.sql b/projects/environmental_sample/sqlschema/environmental_sample.sql deleted file mode 100644 index b76f935e7..000000000 --- a/projects/environmental_sample/sqlschema/environmental_sample.sql +++ /dev/null @@ -1,95 +0,0 @@ - - -CREATE TABLE "AnnotatorResult" ( - subject_text TEXT, - object_id TEXT, - object_text TEXT, - PRIMARY KEY (subject_text, object_id, object_text) -); - -CREATE TABLE "Environment" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "EnvironmentalMaterial" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "ExtractionResult" ( - input_id TEXT, - input_title TEXT, - input_text TEXT, - raw_completion_output TEXT, - prompt TEXT, - extracted_object TEXT, - named_entities TEXT, - PRIMARY KEY (input_id, input_title, input_text, raw_completion_output, prompt, extracted_object, named_entities) -); - -CREATE TABLE "Location" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Publication" ( - id TEXT, - title TEXT, - abstract TEXT, - combined_text TEXT, - full_text TEXT, - PRIMARY KEY (id, title, abstract, combined_text, full_text) -); - -CREATE TABLE "RelationshipType" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Study" ( - location TEXT, - environmental_material TEXT, - environments TEXT, - causal_relationships TEXT, - variables TEXT, - measurements TEXT, - PRIMARY KEY (location, environmental_material, environments, causal_relationships, variables, measurements) -); - -CREATE TABLE "TextWithTriples" ( - publication TEXT, - triples TEXT, - PRIMARY KEY (publication, triples) -); - -CREATE TABLE "Unit" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Variable" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "CausalRelationship" ( - cause TEXT, - effect TEXT, - PRIMARY KEY (cause, effect), - FOREIGN KEY(cause) REFERENCES "Variable" (id), - FOREIGN KEY(effect) REFERENCES "Variable" (id) -); - -CREATE TABLE "Measurement" ( - value TEXT, - unit TEXT, - PRIMARY KEY (value, unit), - FOREIGN KEY(unit) REFERENCES "Unit" (id) -); diff --git a/projects/gene_description_term/docs/AnnotatorResult.md b/projects/gene_description_term/docs/AnnotatorResult.md deleted file mode 100644 index b25d0a529..000000000 --- a/projects/gene_description_term/docs/AnnotatorResult.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Class: AnnotatorResult - - - - -URI: [bp:AnnotatorResult](http://w3id.org/ontogpt/biological-process-templateAnnotatorResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F])](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F]) - -## Attributes - - -### Own - - * [➞subject_text](annotatorResult__subject_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_id](annotatorResult__object_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_text](annotatorResult__object_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) diff --git a/projects/gene_description_term/docs/Any.md b/projects/gene_description_term/docs/Any.md deleted file mode 100644 index cb46c4be4..000000000 --- a/projects/gene_description_term/docs/Any.md +++ /dev/null @@ -1,25 +0,0 @@ - -# Class: Any - - - - -URI: [bp:Any](http://w3id.org/ontogpt/biological-process-templateAny) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult])](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult]) - -## Referenced by Class - - * **None** *[➞extracted_object](extractionResult__extracted_object.md)* <sub>0..1</sub> **[Any](Any.md)** - * **None** *[➞named_entities](extractionResult__named_entities.md)* <sub>0..\*</sub> **[Any](Any.md)** - -## Attributes - - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | linkml:Any | - diff --git a/projects/gene_description_term/docs/CompoundExpression.md b/projects/gene_description_term/docs/CompoundExpression.md deleted file mode 100644 index 6c1bba32f..000000000 --- a/projects/gene_description_term/docs/CompoundExpression.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: CompoundExpression - - - - -URI: [bp:CompoundExpression](http://w3id.org/ontogpt/biological-process-templateCompoundExpression) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[CompoundExpression]^-[Triple])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[CompoundExpression]^-[Triple]) - -## Children - - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - -## Referenced by Class - - -## Attributes - diff --git a/projects/gene_description_term/docs/ExtractionResult.md b/projects/gene_description_term/docs/ExtractionResult.md deleted file mode 100644 index 4d0ab7ab9..000000000 --- a/projects/gene_description_term/docs/ExtractionResult.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Class: ExtractionResult - - -A result of extracting knowledge on text - -URI: [bp:ExtractionResult](http://w3id.org/ontogpt/biological-process-templateExtractionResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any])](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any]) - -## Attributes - - -### Own - - * [➞input_id](extractionResult__input_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_title](extractionResult__input_title.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_text](extractionResult__input_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞prompt](extractionResult__prompt.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞extracted_object](extractionResult__extracted_object.md) <sub>0..1</sub> - * Description: The complex objects extracted from the text - * Range: [Any](Any.md) - * [➞named_entities](extractionResult__named_entities.md) <sub>0..\*</sub> - * Description: Named entities extracted from the text - * Range: [Any](Any.md) diff --git a/projects/gene_description_term/docs/Gene.md b/projects/gene_description_term/docs/Gene.md deleted file mode 100644 index cd7be180a..000000000 --- a/projects/gene_description_term/docs/Gene.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Gene - - - - -URI: [bp:Gene](http://w3id.org/ontogpt/biological-process-templateGene) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[GeneDescription]-%20about%200..1>[Gene|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Gene],[GeneDescription])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[GeneDescription]-%20about%200..1>[Gene|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Gene],[GeneDescription]) - -## Identifier prefixes - - * HGNC - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞about](geneDescription__about.md)* <sub>0..1</sub> **[Gene](Gene.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/gene_description_term/docs/GeneDescription.md b/projects/gene_description_term/docs/GeneDescription.md deleted file mode 100644 index 2744f59a5..000000000 --- a/projects/gene_description_term/docs/GeneDescription.md +++ /dev/null @@ -1,25 +0,0 @@ - -# Class: GeneDescription - - -A summarization of an individual gene - -URI: [bp:GeneDescription](http://w3id.org/ontogpt/biological-process-templateGeneDescription) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[GeneDescriptionTerm],[GeneDescriptionTerm]<terms%200..*-%20[GeneDescription|narrative_summary:string%20%3F],[Gene]<about%200..1-%20[GeneDescription],[Gene])](https://yuml.me/diagram/nofunky;dir:TB/class/[GeneDescriptionTerm],[GeneDescriptionTerm]<terms%200..*-%20[GeneDescription|narrative_summary:string%20%3F],[Gene]<about%200..1-%20[GeneDescription],[Gene]) - -## Attributes - - -### Own - - * [➞about](geneDescription__about.md) <sub>0..1</sub> - * Description: The official symbol of the gene that is described. For example "TP53". Do not include the word "gene" in the answer. - * Range: [Gene](Gene.md) - * [➞narrative_summary](geneDescription__narrative_summary.md) <sub>0..1</sub> - * Description: A free text summary describing the function of the gene - * Range: [String](types/String.md) - * [➞terms](geneDescription__terms.md) <sub>0..\*</sub> - * Description: A semicolon separated list of controlled terms drawn from the Gene Ontology that describe the function of the gene - * Range: [GeneDescriptionTerm](GeneDescriptionTerm.md) diff --git a/projects/gene_description_term/docs/GeneDescriptionTerm.md b/projects/gene_description_term/docs/GeneDescriptionTerm.md deleted file mode 100644 index 028c649b7..000000000 --- a/projects/gene_description_term/docs/GeneDescriptionTerm.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Class: GeneDescriptionTerm - - - - -URI: [bp:GeneDescriptionTerm](http://w3id.org/ontogpt/biological-process-templateGeneDescriptionTerm) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[GeneDescription]-%20terms%200..*>[GeneDescriptionTerm|label:string%20%3F;id(i):string],[NamedEntity]^-[GeneDescriptionTerm],[GeneDescription])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[GeneDescription]-%20terms%200..*>[GeneDescriptionTerm|label:string%20%3F;id(i):string],[NamedEntity]^-[GeneDescriptionTerm],[GeneDescription]) - -## Identifier prefixes - - * GO - * MONDO - * UBERON - * MESH - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞terms](geneDescription__terms.md)* <sub>0..\*</sub> **[GeneDescriptionTerm](GeneDescriptionTerm.md)** - -## Attributes - - -### Own - - * [➞label](geneDescriptionTerm__label.md) <sub>0..1</sub> - * Description: the name of the GO term - * Range: [String](types/String.md) - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) diff --git a/projects/gene_description_term/docs/NamedEntity.md b/projects/gene_description_term/docs/NamedEntity.md deleted file mode 100644 index f65bbcc78..000000000 --- a/projects/gene_description_term/docs/NamedEntity.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: NamedEntity - - - - -URI: [bp:NamedEntity](http://w3id.org/ontogpt/biological-process-templateNamedEntity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[GeneDescriptionTerm],[NamedEntity]^-[Gene],[Triple],[GeneDescriptionTerm],[Gene])](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[GeneDescriptionTerm],[NamedEntity]^-[Gene],[Triple],[GeneDescriptionTerm],[Gene]) - -## Children - - * [Gene](Gene.md) - * [GeneDescriptionTerm](GeneDescriptionTerm.md) - * [RelationshipType](RelationshipType.md) - -## Referenced by Class - - * **None** *[➞object](triple__object.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞object_qualifier](triple__object_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject](triple__subject.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject_qualifier](triple__subject_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - -## Attributes - - -### Own - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/gene_description_term/docs/NullDataOptions.md b/projects/gene_description_term/docs/NullDataOptions.md deleted file mode 100644 index 716244681..000000000 --- a/projects/gene_description_term/docs/NullDataOptions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Enum: NullDataOptions - - - - -URI: [bp:NullDataOptions](http://w3id.org/ontogpt/biological-process-templateNullDataOptions) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | -| UNSPECIFIED_METHOD_OF_ADMINISTRATION | | NCIT:C149701 | | -| NOT_APPLICABLE | | NCIT:C18902 | {'aliases': ['not applicable', 'N/A']} | -| NOT_MENTIONED | | | | - diff --git a/projects/gene_description_term/docs/Publication.md b/projects/gene_description_term/docs/Publication.md deleted file mode 100644 index d54b928f4..000000000 --- a/projects/gene_description_term/docs/Publication.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Publication - - - - -URI: [bp:Publication](http://w3id.org/ontogpt/biological-process-templatePublication) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples])](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples]) - -## Referenced by Class - - * **None** *[➞publication](textWithTriples__publication.md)* <sub>0..1</sub> **[Publication](Publication.md)** - -## Attributes - - -### Own - - * [➞id](publication__id.md) <sub>0..1</sub> - * Description: The publication identifier - * Range: [String](types/String.md) - * [➞title](publication__title.md) <sub>0..1</sub> - * Description: The title of the publication - * Range: [String](types/String.md) - * [➞abstract](publication__abstract.md) <sub>0..1</sub> - * Description: The abstract of the publication - * Range: [String](types/String.md) - * [➞combined_text](publication__combined_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞full_text](publication__full_text.md) <sub>0..1</sub> - * Description: The full text of the publication - * Range: [String](types/String.md) diff --git a/projects/gene_description_term/docs/RelationshipType.md b/projects/gene_description_term/docs/RelationshipType.md deleted file mode 100644 index 918e3647c..000000000 --- a/projects/gene_description_term/docs/RelationshipType.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: RelationshipType - - - - -URI: [bp:RelationshipType](http://w3id.org/ontogpt/biological-process-templateRelationshipType) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity]) - -## Identifier prefixes - - * RO - * biolink - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞predicate](triple__predicate.md)* <sub>0..1</sub> **[RelationshipType](RelationshipType.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/gene_description_term/docs/TextWithTriples.md b/projects/gene_description_term/docs/TextWithTriples.md deleted file mode 100644 index 4237a7785..000000000 --- a/projects/gene_description_term/docs/TextWithTriples.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: TextWithTriples - - - - -URI: [bp:TextWithTriples](http://w3id.org/ontogpt/biological-process-templateTextWithTriples) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication]) - -## Attributes - - -### Own - - * [➞publication](textWithTriples__publication.md) <sub>0..1</sub> - * Range: [Publication](Publication.md) - * [➞triples](textWithTriples__triples.md) <sub>0..\*</sub> - * Range: [Triple](Triple.md) diff --git a/projects/gene_description_term/docs/Triple.md b/projects/gene_description_term/docs/Triple.md deleted file mode 100644 index b9e6bb42d..000000000 --- a/projects/gene_description_term/docs/Triple.md +++ /dev/null @@ -1,39 +0,0 @@ - -# Class: Triple - - -Abstract parent for Relation Extraction tasks - -URI: [bp:Triple](http://w3id.org/ontogpt/biological-process-templateTriple) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞triples](textWithTriples__triples.md)* <sub>0..\*</sub> **[Triple](Triple.md)** - -## Attributes - - -### Own - - * [➞subject](triple__subject.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞predicate](triple__predicate.md) <sub>0..1</sub> - * Range: [RelationshipType](RelationshipType.md) - * [➞object](triple__object.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞qualifier](triple__qualifier.md) <sub>0..1</sub> - * Description: A qualifier for the statements, e.g. "NOT" for negation - * Range: [String](types/String.md) - * [➞subject_qualifier](triple__subject_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - * Range: [NamedEntity](NamedEntity.md) - * [➞object_qualifier](triple__object_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * Range: [NamedEntity](NamedEntity.md) diff --git a/projects/gene_description_term/docs/annotatorResult__object_id.md b/projects/gene_description_term/docs/annotatorResult__object_id.md deleted file mode 100644 index ffc6bbeca..000000000 --- a/projects/gene_description_term/docs/annotatorResult__object_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_id - - - - -URI: [bp:annotatorResult__object_id](http://w3id.org/ontogpt/biological-process-templateannotatorResult__object_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/gene_description_term/docs/annotatorResult__object_text.md b/projects/gene_description_term/docs/annotatorResult__object_text.md deleted file mode 100644 index b127369af..000000000 --- a/projects/gene_description_term/docs/annotatorResult__object_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_text - - - - -URI: [bp:annotatorResult__object_text](http://w3id.org/ontogpt/biological-process-templateannotatorResult__object_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/gene_description_term/docs/annotatorResult__subject_text.md b/projects/gene_description_term/docs/annotatorResult__subject_text.md deleted file mode 100644 index 79e732b09..000000000 --- a/projects/gene_description_term/docs/annotatorResult__subject_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_text - - - - -URI: [bp:annotatorResult__subject_text](http://w3id.org/ontogpt/biological-process-templateannotatorResult__subject_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/gene_description_term/docs/extractionResult__extracted_object.md b/projects/gene_description_term/docs/extractionResult__extracted_object.md deleted file mode 100644 index 9cb7fab08..000000000 --- a/projects/gene_description_term/docs/extractionResult__extracted_object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: extracted_object - - -The complex objects extracted from the text - -URI: [bp:extractionResult__extracted_object](http://w3id.org/ontogpt/biological-process-templateextractionResult__extracted_object) - - -## Domain and Range - -None → <sub>0..1</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/gene_description_term/docs/extractionResult__input_id.md b/projects/gene_description_term/docs/extractionResult__input_id.md deleted file mode 100644 index 77a58c462..000000000 --- a/projects/gene_description_term/docs/extractionResult__input_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_id - - - - -URI: [bp:extractionResult__input_id](http://w3id.org/ontogpt/biological-process-templateextractionResult__input_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/gene_description_term/docs/extractionResult__input_text.md b/projects/gene_description_term/docs/extractionResult__input_text.md deleted file mode 100644 index 0d447a742..000000000 --- a/projects/gene_description_term/docs/extractionResult__input_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_text - - - - -URI: [bp:extractionResult__input_text](http://w3id.org/ontogpt/biological-process-templateextractionResult__input_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/gene_description_term/docs/extractionResult__input_title.md b/projects/gene_description_term/docs/extractionResult__input_title.md deleted file mode 100644 index 87d22e4d5..000000000 --- a/projects/gene_description_term/docs/extractionResult__input_title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_title - - - - -URI: [bp:extractionResult__input_title](http://w3id.org/ontogpt/biological-process-templateextractionResult__input_title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/gene_description_term/docs/extractionResult__named_entities.md b/projects/gene_description_term/docs/extractionResult__named_entities.md deleted file mode 100644 index 4274e9c2a..000000000 --- a/projects/gene_description_term/docs/extractionResult__named_entities.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: named_entities - - -Named entities extracted from the text - -URI: [bp:extractionResult__named_entities](http://w3id.org/ontogpt/biological-process-templateextractionResult__named_entities) - - -## Domain and Range - -None → <sub>0..\*</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/gene_description_term/docs/extractionResult__prompt.md b/projects/gene_description_term/docs/extractionResult__prompt.md deleted file mode 100644 index 2d9f03d71..000000000 --- a/projects/gene_description_term/docs/extractionResult__prompt.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: prompt - - - - -URI: [bp:extractionResult__prompt](http://w3id.org/ontogpt/biological-process-templateextractionResult__prompt) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/gene_description_term/docs/extractionResult__raw_completion_output.md b/projects/gene_description_term/docs/extractionResult__raw_completion_output.md deleted file mode 100644 index 0e689fc73..000000000 --- a/projects/gene_description_term/docs/extractionResult__raw_completion_output.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: raw_completion_output - - - - -URI: [bp:extractionResult__raw_completion_output](http://w3id.org/ontogpt/biological-process-templateextractionResult__raw_completion_output) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/gene_description_term/docs/geneDescriptionTerm__label.md b/projects/gene_description_term/docs/geneDescriptionTerm__label.md deleted file mode 100644 index 2f6e328d6..000000000 --- a/projects/gene_description_term/docs/geneDescriptionTerm__label.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: label - - -the name of the GO term - -URI: [bp:geneDescriptionTerm__label](http://w3id.org/ontogpt/biological-process-templategeneDescriptionTerm__label) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [GeneDescriptionTerm](GeneDescriptionTerm.md) diff --git a/projects/gene_description_term/docs/geneDescription__about.md b/projects/gene_description_term/docs/geneDescription__about.md deleted file mode 100644 index 5630fc47d..000000000 --- a/projects/gene_description_term/docs/geneDescription__about.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: about - - -The official symbol of the gene that is described. For example "TP53". Do not include the word "gene" in the answer. - -URI: [bp:geneDescription__about](http://w3id.org/ontogpt/biological-process-templategeneDescription__about) - - -## Domain and Range - -None → <sub>0..1</sub> [Gene](Gene.md) - -## Parents - - -## Children - - -## Used by - - * [GeneDescription](GeneDescription.md) diff --git a/projects/gene_description_term/docs/geneDescription__narrative_summary.md b/projects/gene_description_term/docs/geneDescription__narrative_summary.md deleted file mode 100644 index 7f5677e2e..000000000 --- a/projects/gene_description_term/docs/geneDescription__narrative_summary.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: narrative_summary - - -A free text summary describing the function of the gene - -URI: [bp:geneDescription__narrative_summary](http://w3id.org/ontogpt/biological-process-templategeneDescription__narrative_summary) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [GeneDescription](GeneDescription.md) diff --git a/projects/gene_description_term/docs/geneDescription__terms.md b/projects/gene_description_term/docs/geneDescription__terms.md deleted file mode 100644 index 9a45946fb..000000000 --- a/projects/gene_description_term/docs/geneDescription__terms.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: terms - - -A semicolon separated list of controlled terms drawn from the Gene Ontology that describe the function of the gene - -URI: [bp:geneDescription__terms](http://w3id.org/ontogpt/biological-process-templategeneDescription__terms) - - -## Domain and Range - -None → <sub>0..\*</sub> [GeneDescriptionTerm](GeneDescriptionTerm.md) - -## Parents - - -## Children - - -## Used by - - * [GeneDescription](GeneDescription.md) diff --git a/projects/gene_description_term/docs/gene_description_term.md b/projects/gene_description_term/docs/gene_description_term.md deleted file mode 100644 index 410c3467d..000000000 --- a/projects/gene_description_term/docs/gene_description_term.md +++ /dev/null @@ -1,110 +0,0 @@ - -# go-term-template - - -**metamodel version:** 1.7.0 - -**version:** None - - -A simple GO term template for NER - - -### Classes - - * [AnnotatorResult](AnnotatorResult.md) - * [Any](Any.md) - * [CompoundExpression](CompoundExpression.md) - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - * [ExtractionResult](ExtractionResult.md) - A result of extracting knowledge on text - * [GeneDescription](GeneDescription.md) - A summarization of an individual gene - * [NamedEntity](NamedEntity.md) - * [Gene](Gene.md) - * [GeneDescriptionTerm](GeneDescriptionTerm.md) - * [RelationshipType](RelationshipType.md) - * [Publication](Publication.md) - * [TextWithTriples](TextWithTriples.md) - -### Mixins - - -### Slots - - * [➞object_id](annotatorResult__object_id.md) - * [➞object_text](annotatorResult__object_text.md) - * [➞subject_text](annotatorResult__subject_text.md) - * [➞extracted_object](extractionResult__extracted_object.md) - The complex objects extracted from the text - * [➞input_id](extractionResult__input_id.md) - * [➞input_text](extractionResult__input_text.md) - * [➞input_title](extractionResult__input_title.md) - * [➞named_entities](extractionResult__named_entities.md) - Named entities extracted from the text - * [➞prompt](extractionResult__prompt.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) - * [➞label](geneDescriptionTerm__label.md) - the name of the GO term - * [➞about](geneDescription__about.md) - The official symbol of the gene that is described. For example "TP53". Do not include the word "gene" in the answer. - * [➞narrative_summary](geneDescription__narrative_summary.md) - A free text summary describing the function of the gene - * [➞terms](geneDescription__terms.md) - A semicolon separated list of controlled terms drawn from the Gene Ontology that describe the function of the gene - * [➞id](namedEntity__id.md) - A unique identifier for the named entity - * [➞label](namedEntity__label.md) - The label (name) of the named thing - * [➞abstract](publication__abstract.md) - The abstract of the publication - * [➞combined_text](publication__combined_text.md) - * [➞full_text](publication__full_text.md) - The full text of the publication - * [➞id](publication__id.md) - The publication identifier - * [➞title](publication__title.md) - The title of the publication - * [➞publication](textWithTriples__publication.md) - * [➞triples](textWithTriples__triples.md) - * [➞object](triple__object.md) - * [➞object_qualifier](triple__object_qualifier.md) - An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * [➞predicate](triple__predicate.md) - * [➞qualifier](triple__qualifier.md) - A qualifier for the statements, e.g. "NOT" for negation - * [➞subject](triple__subject.md) - * [➞subject_qualifier](triple__subject_qualifier.md) - An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -### Enums - - * [NullDataOptions](NullDataOptions.md) - -### Subsets - - -### Types - - -#### Built in - - * **Bool** - * **Curie** - * **Decimal** - * **ElementIdentifier** - * **NCName** - * **NodeIdentifier** - * **URI** - * **URIorCURIE** - * **XSDDate** - * **XSDDateTime** - * **XSDTime** - * **float** - * **int** - * **str** - -#### Defined - - * [Boolean](types/Boolean.md) (**Bool**) - A binary (true or false) value - * [Curie](types/Curie.md) (**Curie**) - a compact URI - * [Date](types/Date.md) (**XSDDate**) - a date (year, month and day) in an idealized calendar - * [DateOrDatetime](types/DateOrDatetime.md) (**str**) - Either a date or a datetime - * [Datetime](types/Datetime.md) (**XSDDateTime**) - The combination of a date and time - * [Decimal](types/Decimal.md) (**Decimal**) - A real number with arbitrary precision that conforms to the xsd:decimal specification - * [Double](types/Double.md) (**float**) - A real number that conforms to the xsd:double specification - * [Float](types/Float.md) (**float**) - A real number that conforms to the xsd:float specification - * [Integer](types/Integer.md) (**int**) - An integer - * [Jsonpath](types/Jsonpath.md) (**str**) - A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - * [Jsonpointer](types/Jsonpointer.md) (**str**) - A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - * [Ncname](types/Ncname.md) (**NCName**) - Prefix part of CURIE - * [Nodeidentifier](types/Nodeidentifier.md) (**NodeIdentifier**) - A URI, CURIE or BNODE that represents a node in a model. - * [Objectidentifier](types/Objectidentifier.md) (**ElementIdentifier**) - A URI or CURIE that represents an object in the model. - * [Sparqlpath](types/Sparqlpath.md) (**str**) - A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - * [String](types/String.md) (**str**) - A character string - * [Time](types/Time.md) (**XSDTime**) - A time object represents a (local) time of day, independent of any particular day - * [Uri](types/Uri.md) (**URI**) - a complete URI - * [Uriorcurie](types/Uriorcurie.md) (**URIorCURIE**) - a URI or a CURIE diff --git a/projects/gene_description_term/docs/namedEntity__id.md b/projects/gene_description_term/docs/namedEntity__id.md deleted file mode 100644 index 4cf1e966f..000000000 --- a/projects/gene_description_term/docs/namedEntity__id.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Slot: id - - -A unique identifier for the named entity - -URI: [bp:namedEntity__id](http://w3id.org/ontogpt/biological-process-templatenamedEntity__id) - - -## Domain and Range - -None → <sub>1..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Gene](Gene.md) - * [GeneDescriptionTerm](GeneDescriptionTerm.md) - * [NamedEntity](NamedEntity.md) - * [RelationshipType](RelationshipType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | this is populated during the grounding and normalization step | - diff --git a/projects/gene_description_term/docs/namedEntity__label.md b/projects/gene_description_term/docs/namedEntity__label.md deleted file mode 100644 index ace66ab52..000000000 --- a/projects/gene_description_term/docs/namedEntity__label.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Slot: label - - -The label (name) of the named thing - -URI: [bp:namedEntity__label](http://w3id.org/ontogpt/biological-process-templatenamedEntity__label) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Gene](Gene.md) - * [NamedEntity](NamedEntity.md) - * [RelationshipType](RelationshipType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Aliases:** | | name | -| **Mappings:** | | rdfs:label | - diff --git a/projects/gene_description_term/docs/publication__abstract.md b/projects/gene_description_term/docs/publication__abstract.md deleted file mode 100644 index 96be47057..000000000 --- a/projects/gene_description_term/docs/publication__abstract.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: abstract - - -The abstract of the publication - -URI: [bp:publication__abstract](http://w3id.org/ontogpt/biological-process-templatepublication__abstract) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/gene_description_term/docs/publication__combined_text.md b/projects/gene_description_term/docs/publication__combined_text.md deleted file mode 100644 index 613506acc..000000000 --- a/projects/gene_description_term/docs/publication__combined_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: combined_text - - - - -URI: [bp:publication__combined_text](http://w3id.org/ontogpt/biological-process-templatepublication__combined_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/gene_description_term/docs/publication__full_text.md b/projects/gene_description_term/docs/publication__full_text.md deleted file mode 100644 index 978e83538..000000000 --- a/projects/gene_description_term/docs/publication__full_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: full_text - - -The full text of the publication - -URI: [bp:publication__full_text](http://w3id.org/ontogpt/biological-process-templatepublication__full_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/gene_description_term/docs/publication__id.md b/projects/gene_description_term/docs/publication__id.md deleted file mode 100644 index 9c03571b0..000000000 --- a/projects/gene_description_term/docs/publication__id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: id - - -The publication identifier - -URI: [bp:publication__id](http://w3id.org/ontogpt/biological-process-templatepublication__id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/gene_description_term/docs/publication__title.md b/projects/gene_description_term/docs/publication__title.md deleted file mode 100644 index 93aa90543..000000000 --- a/projects/gene_description_term/docs/publication__title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: title - - -The title of the publication - -URI: [bp:publication__title](http://w3id.org/ontogpt/biological-process-templatepublication__title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/gene_description_term/docs/textWithTriples__publication.md b/projects/gene_description_term/docs/textWithTriples__publication.md deleted file mode 100644 index d5eb7b7f9..000000000 --- a/projects/gene_description_term/docs/textWithTriples__publication.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: publication - - - - -URI: [bp:textWithTriples__publication](http://w3id.org/ontogpt/biological-process-templatetextWithTriples__publication) - - -## Domain and Range - -None → <sub>0..1</sub> [Publication](Publication.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/gene_description_term/docs/textWithTriples__triples.md b/projects/gene_description_term/docs/textWithTriples__triples.md deleted file mode 100644 index 4865a084d..000000000 --- a/projects/gene_description_term/docs/textWithTriples__triples.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: triples - - - - -URI: [bp:textWithTriples__triples](http://w3id.org/ontogpt/biological-process-templatetextWithTriples__triples) - - -## Domain and Range - -None → <sub>0..\*</sub> [Triple](Triple.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/gene_description_term/docs/triple__object.md b/projects/gene_description_term/docs/triple__object.md deleted file mode 100644 index bc102f3c8..000000000 --- a/projects/gene_description_term/docs/triple__object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object - - - - -URI: [bp:triple__object](http://w3id.org/ontogpt/biological-process-templatetriple__object) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/gene_description_term/docs/triple__object_qualifier.md b/projects/gene_description_term/docs/triple__object_qualifier.md deleted file mode 100644 index f06d74b8d..000000000 --- a/projects/gene_description_term/docs/triple__object_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_qualifier - - -An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - -URI: [bp:triple__object_qualifier](http://w3id.org/ontogpt/biological-process-templatetriple__object_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/gene_description_term/docs/triple__predicate.md b/projects/gene_description_term/docs/triple__predicate.md deleted file mode 100644 index 92c257664..000000000 --- a/projects/gene_description_term/docs/triple__predicate.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: predicate - - - - -URI: [bp:triple__predicate](http://w3id.org/ontogpt/biological-process-templatetriple__predicate) - - -## Domain and Range - -None → <sub>0..1</sub> [RelationshipType](RelationshipType.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/gene_description_term/docs/triple__qualifier.md b/projects/gene_description_term/docs/triple__qualifier.md deleted file mode 100644 index 1ea0152f1..000000000 --- a/projects/gene_description_term/docs/triple__qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: qualifier - - -A qualifier for the statements, e.g. "NOT" for negation - -URI: [bp:triple__qualifier](http://w3id.org/ontogpt/biological-process-templatetriple__qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/gene_description_term/docs/triple__subject.md b/projects/gene_description_term/docs/triple__subject.md deleted file mode 100644 index cc0377542..000000000 --- a/projects/gene_description_term/docs/triple__subject.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject - - - - -URI: [bp:triple__subject](http://w3id.org/ontogpt/biological-process-templatetriple__subject) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/gene_description_term/docs/triple__subject_qualifier.md b/projects/gene_description_term/docs/triple__subject_qualifier.md deleted file mode 100644 index 998e0615e..000000000 --- a/projects/gene_description_term/docs/triple__subject_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_qualifier - - -An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -URI: [bp:triple__subject_qualifier](http://w3id.org/ontogpt/biological-process-templatetriple__subject_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/gene_description_term/docs/types/Boolean.md b/projects/gene_description_term/docs/types/Boolean.md deleted file mode 100644 index dc83a9c6e..000000000 --- a/projects/gene_description_term/docs/types/Boolean.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: boolean - - -A binary (true or false) value - -URI: [linkml:Boolean](https://w3id.org/linkml/Boolean) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Bool** | -| Representation | | bool | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Boolean | - diff --git a/projects/gene_description_term/docs/types/Curie.md b/projects/gene_description_term/docs/types/Curie.md deleted file mode 100644 index c1803f93f..000000000 --- a/projects/gene_description_term/docs/types/Curie.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: curie - - -a compact URI - -URI: [linkml:Curie](https://w3id.org/linkml/Curie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Curie** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations this MUST be expanded to a URI | -| | | in non-RDF serializations MAY be serialized as the compact representation | - diff --git a/projects/gene_description_term/docs/types/Date.md b/projects/gene_description_term/docs/types/Date.md deleted file mode 100644 index 06948af97..000000000 --- a/projects/gene_description_term/docs/types/Date.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: date - - -a date (year, month and day) in an idealized calendar - -URI: [linkml:Date](https://w3id.org/linkml/Date) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDate** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Date | - diff --git a/projects/gene_description_term/docs/types/DateOrDatetime.md b/projects/gene_description_term/docs/types/DateOrDatetime.md deleted file mode 100644 index ef983898d..000000000 --- a/projects/gene_description_term/docs/types/DateOrDatetime.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: date_or_datetime - - -Either a date or a datetime - -URI: [linkml:DateOrDatetime](https://w3id.org/linkml/DateOrDatetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/gene_description_term/docs/types/Datetime.md b/projects/gene_description_term/docs/types/Datetime.md deleted file mode 100644 index 9510454a8..000000000 --- a/projects/gene_description_term/docs/types/Datetime.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: datetime - - -The combination of a date and time - -URI: [linkml:Datetime](https://w3id.org/linkml/Datetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDateTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:DateTime | - diff --git a/projects/gene_description_term/docs/types/Decimal.md b/projects/gene_description_term/docs/types/Decimal.md deleted file mode 100644 index a7ba14a5d..000000000 --- a/projects/gene_description_term/docs/types/Decimal.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: decimal - - -A real number with arbitrary precision that conforms to the xsd:decimal specification - -URI: [linkml:Decimal](https://w3id.org/linkml/Decimal) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Decimal** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Broad Mappings:** | | schema:Number | - diff --git a/projects/gene_description_term/docs/types/Double.md b/projects/gene_description_term/docs/types/Double.md deleted file mode 100644 index cfe6d71e2..000000000 --- a/projects/gene_description_term/docs/types/Double.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: double - - -A real number that conforms to the xsd:double specification - -URI: [linkml:Double](https://w3id.org/linkml/Double) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Close Mappings:** | | schema:Float | - diff --git a/projects/gene_description_term/docs/types/Float.md b/projects/gene_description_term/docs/types/Float.md deleted file mode 100644 index 7b303f96f..000000000 --- a/projects/gene_description_term/docs/types/Float.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: float - - -A real number that conforms to the xsd:float specification - -URI: [linkml:Float](https://w3id.org/linkml/Float) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Float | - diff --git a/projects/gene_description_term/docs/types/Integer.md b/projects/gene_description_term/docs/types/Integer.md deleted file mode 100644 index 3cfcc66d9..000000000 --- a/projects/gene_description_term/docs/types/Integer.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: integer - - -An integer - -URI: [linkml:Integer](https://w3id.org/linkml/Integer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **int** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Integer | - diff --git a/projects/gene_description_term/docs/types/Jsonpath.md b/projects/gene_description_term/docs/types/Jsonpath.md deleted file mode 100644 index a03a58e67..000000000 --- a/projects/gene_description_term/docs/types/Jsonpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpath - - -A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpath](https://w3id.org/linkml/Jsonpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/gene_description_term/docs/types/Jsonpointer.md b/projects/gene_description_term/docs/types/Jsonpointer.md deleted file mode 100644 index a0e1ac492..000000000 --- a/projects/gene_description_term/docs/types/Jsonpointer.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpointer - - -A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpointer](https://w3id.org/linkml/Jsonpointer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/gene_description_term/docs/types/Ncname.md b/projects/gene_description_term/docs/types/Ncname.md deleted file mode 100644 index 710b0b04a..000000000 --- a/projects/gene_description_term/docs/types/Ncname.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: ncname - - -Prefix part of CURIE - -URI: [linkml:Ncname](https://w3id.org/linkml/Ncname) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NCName** | -| Representation | | str | diff --git a/projects/gene_description_term/docs/types/Nodeidentifier.md b/projects/gene_description_term/docs/types/Nodeidentifier.md deleted file mode 100644 index f0097cdf4..000000000 --- a/projects/gene_description_term/docs/types/Nodeidentifier.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: nodeidentifier - - -A URI, CURIE or BNODE that represents a node in a model. - -URI: [linkml:Nodeidentifier](https://w3id.org/linkml/Nodeidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NodeIdentifier** | -| Representation | | str | diff --git a/projects/gene_description_term/docs/types/Objectidentifier.md b/projects/gene_description_term/docs/types/Objectidentifier.md deleted file mode 100644 index 454ba6be6..000000000 --- a/projects/gene_description_term/docs/types/Objectidentifier.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: objectidentifier - - -A URI or CURIE that represents an object in the model. - -URI: [linkml:Objectidentifier](https://w3id.org/linkml/Objectidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **ElementIdentifier** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | Used for inheritance and type checking | - diff --git a/projects/gene_description_term/docs/types/Sparqlpath.md b/projects/gene_description_term/docs/types/Sparqlpath.md deleted file mode 100644 index fd99a927e..000000000 --- a/projects/gene_description_term/docs/types/Sparqlpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: sparqlpath - - -A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - -URI: [linkml:Sparqlpath](https://w3id.org/linkml/Sparqlpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/gene_description_term/docs/types/String.md b/projects/gene_description_term/docs/types/String.md deleted file mode 100644 index 6e61d7081..000000000 --- a/projects/gene_description_term/docs/types/String.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: string - - -A character string - -URI: [linkml:String](https://w3id.org/linkml/String) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Text | - diff --git a/projects/gene_description_term/docs/types/Time.md b/projects/gene_description_term/docs/types/Time.md deleted file mode 100644 index 2b8652bcd..000000000 --- a/projects/gene_description_term/docs/types/Time.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: time - - -A time object represents a (local) time of day, independent of any particular day - -URI: [linkml:Time](https://w3id.org/linkml/Time) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Time | - diff --git a/projects/gene_description_term/docs/types/Uri.md b/projects/gene_description_term/docs/types/Uri.md deleted file mode 100644 index 343807a5e..000000000 --- a/projects/gene_description_term/docs/types/Uri.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: uri - - -a complete URI - -URI: [linkml:Uri](https://w3id.org/linkml/Uri) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URI** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node | -| **Close Mappings:** | | schema:URL | - diff --git a/projects/gene_description_term/docs/types/Uriorcurie.md b/projects/gene_description_term/docs/types/Uriorcurie.md deleted file mode 100644 index 2f7b65087..000000000 --- a/projects/gene_description_term/docs/types/Uriorcurie.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: uriorcurie - - -a URI or a CURIE - -URI: [linkml:Uriorcurie](https://w3id.org/linkml/Uriorcurie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URIorCURIE** | -| Representation | | str | diff --git a/projects/gene_description_term/excel/gene_description_term.xlsx b/projects/gene_description_term/excel/gene_description_term.xlsx deleted file mode 100644 index c249ee2a2..000000000 Binary files a/projects/gene_description_term/excel/gene_description_term.xlsx and /dev/null differ diff --git a/projects/gene_description_term/gene_description_term.py b/projects/gene_description_term/gene_description_term.py deleted file mode 100644 index 481cc8f8e..000000000 --- a/projects/gene_description_term/gene_description_term.py +++ /dev/null @@ -1,461 +0,0 @@ -# Auto generated from gene_description_term.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-08-07T10:53:31 -# Schema: go-term-template -# -# id: https://w3id.org/ontogpt/go_term -# description: A simple GO term template for NER -# license: https://creativecommons.org/publicdomain/zero/1.0/ - -import dataclasses -import sys -import re -from jsonasobj2 import JsonObj, as_dict -from typing import Optional, List, Union, Dict, ClassVar, Any -from dataclasses import dataclass -from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions - -from linkml_runtime.utils.slot import Slot -from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode -from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int -from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs -from linkml_runtime.utils.formatutils import camelcase, underscore, sfx -from linkml_runtime.utils.enumerations import EnumDefinitionImpl -from rdflib import Namespace, URIRef -from linkml_runtime.utils.curienamespace import CurieNamespace -from linkml_runtime.linkml_model.types import String - -metamodel_version = "1.7.0" -version = None - -# Overwrite dataclasses _init_fn to add **kwargs in __init__ -dataclasses._init_fn = dataclasses_init_fn_with_kwargs - -# Namespaces -GO = CurieNamespace('GO', 'http://purl.obolibrary.org/obo/GO_') -HGNC = CurieNamespace('HGNC', 'http://identifiers.org/hgnc/') -MESH = CurieNamespace('MESH', 'http://identifiers.org/mesh/') -MONDO = CurieNamespace('MONDO', 'http://purl.obolibrary.org/obo/MONDO_') -RO = CurieNamespace('RO', 'http://purl.obolibrary.org/obo/RO_') -UBERON = CurieNamespace('UBERON', 'http://example.org/UNKNOWN/UBERON/') -BIOLINK = CurieNamespace('biolink', 'http://example.org/UNKNOWN/biolink/') -BP = CurieNamespace('bp', 'http://w3id.org/ontogpt/biological-process-template') -CORE = CurieNamespace('core', 'http://w3id.org/ontogpt/core/') -LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') -RDFS = CurieNamespace('rdfs', 'http://example.org/UNKNOWN/rdfs/') -DEFAULT_ = BP - - -# Types - -# Class references -class NamedEntityId(extended_str): - pass - - -class GeneId(NamedEntityId): - pass - - -class GeneDescriptionTermId(NamedEntityId): - pass - - -class RelationshipTypeId(NamedEntityId): - pass - - -@dataclass -class GeneDescription(YAMLRoot): - """ - A summarization of an individual gene - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = BP.GeneDescription - class_class_curie: ClassVar[str] = "bp:GeneDescription" - class_name: ClassVar[str] = "GeneDescription" - class_model_uri: ClassVar[URIRef] = BP.GeneDescription - - about: Optional[Union[str, GeneId]] = None - narrative_summary: Optional[str] = None - terms: Optional[Union[Union[str, GeneDescriptionTermId], List[Union[str, GeneDescriptionTermId]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.about is not None and not isinstance(self.about, GeneId): - self.about = GeneId(self.about) - - if self.narrative_summary is not None and not isinstance(self.narrative_summary, str): - self.narrative_summary = str(self.narrative_summary) - - if not isinstance(self.terms, list): - self.terms = [self.terms] if self.terms is not None else [] - self.terms = [v if isinstance(v, GeneDescriptionTermId) else GeneDescriptionTermId(v) for v in self.terms] - - super().__post_init__(**kwargs) - - -Any = Any - -@dataclass -class ExtractionResult(YAMLRoot): - """ - A result of extracting knowledge on text - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.ExtractionResult - class_class_curie: ClassVar[str] = "core:ExtractionResult" - class_name: ClassVar[str] = "ExtractionResult" - class_model_uri: ClassVar[URIRef] = BP.ExtractionResult - - input_id: Optional[str] = None - input_title: Optional[str] = None - input_text: Optional[str] = None - raw_completion_output: Optional[str] = None - prompt: Optional[str] = None - extracted_object: Optional[Union[dict, Any]] = None - named_entities: Optional[Union[Union[dict, Any], List[Union[dict, Any]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.input_id is not None and not isinstance(self.input_id, str): - self.input_id = str(self.input_id) - - if self.input_title is not None and not isinstance(self.input_title, str): - self.input_title = str(self.input_title) - - if self.input_text is not None and not isinstance(self.input_text, str): - self.input_text = str(self.input_text) - - if self.raw_completion_output is not None and not isinstance(self.raw_completion_output, str): - self.raw_completion_output = str(self.raw_completion_output) - - if self.prompt is not None and not isinstance(self.prompt, str): - self.prompt = str(self.prompt) - - super().__post_init__(**kwargs) - - -@dataclass -class NamedEntity(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.NamedEntity - class_class_curie: ClassVar[str] = "core:NamedEntity" - class_name: ClassVar[str] = "NamedEntity" - class_model_uri: ClassVar[URIRef] = BP.NamedEntity - - id: Union[str, NamedEntityId] = None - label: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, NamedEntityId): - self.id = NamedEntityId(self.id) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - super().__post_init__(**kwargs) - - -@dataclass -class Gene(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = BP.Gene - class_class_curie: ClassVar[str] = "bp:Gene" - class_name: ClassVar[str] = "Gene" - class_model_uri: ClassVar[URIRef] = BP.Gene - - id: Union[str, GeneId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, GeneId): - self.id = GeneId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class GeneDescriptionTerm(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = BP.GeneDescriptionTerm - class_class_curie: ClassVar[str] = "bp:GeneDescriptionTerm" - class_name: ClassVar[str] = "GeneDescriptionTerm" - class_model_uri: ClassVar[URIRef] = BP.GeneDescriptionTerm - - id: Union[str, GeneDescriptionTermId] = None - label: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, GeneDescriptionTermId): - self.id = GeneDescriptionTermId(self.id) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - super().__post_init__(**kwargs) - - -class CompoundExpression(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.CompoundExpression - class_class_curie: ClassVar[str] = "core:CompoundExpression" - class_name: ClassVar[str] = "CompoundExpression" - class_model_uri: ClassVar[URIRef] = BP.CompoundExpression - - -@dataclass -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Triple - class_class_curie: ClassVar[str] = "core:Triple" - class_name: ClassVar[str] = "Triple" - class_model_uri: ClassVar[URIRef] = BP.Triple - - subject: Optional[Union[str, NamedEntityId]] = None - predicate: Optional[Union[str, RelationshipTypeId]] = None - object: Optional[Union[str, NamedEntityId]] = None - qualifier: Optional[str] = None - subject_qualifier: Optional[Union[str, NamedEntityId]] = None - object_qualifier: Optional[Union[str, NamedEntityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, NamedEntityId): - self.subject = NamedEntityId(self.subject) - - if self.predicate is not None and not isinstance(self.predicate, RelationshipTypeId): - self.predicate = RelationshipTypeId(self.predicate) - - if self.object is not None and not isinstance(self.object, NamedEntityId): - self.object = NamedEntityId(self.object) - - if self.qualifier is not None and not isinstance(self.qualifier, str): - self.qualifier = str(self.qualifier) - - if self.subject_qualifier is not None and not isinstance(self.subject_qualifier, NamedEntityId): - self.subject_qualifier = NamedEntityId(self.subject_qualifier) - - if self.object_qualifier is not None and not isinstance(self.object_qualifier, NamedEntityId): - self.object_qualifier = NamedEntityId(self.object_qualifier) - - super().__post_init__(**kwargs) - - -@dataclass -class TextWithTriples(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.TextWithTriples - class_class_curie: ClassVar[str] = "core:TextWithTriples" - class_name: ClassVar[str] = "TextWithTriples" - class_model_uri: ClassVar[URIRef] = BP.TextWithTriples - - publication: Optional[Union[dict, "Publication"]] = None - triples: Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.publication is not None and not isinstance(self.publication, Publication): - self.publication = Publication(**as_dict(self.publication)) - - if not isinstance(self.triples, list): - self.triples = [self.triples] if self.triples is not None else [] - self.triples = [v if isinstance(v, Triple) else Triple(**as_dict(v)) for v in self.triples] - - super().__post_init__(**kwargs) - - -@dataclass -class RelationshipType(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.RelationshipType - class_class_curie: ClassVar[str] = "core:RelationshipType" - class_name: ClassVar[str] = "RelationshipType" - class_model_uri: ClassVar[URIRef] = BP.RelationshipType - - id: Union[str, RelationshipTypeId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, RelationshipTypeId): - self.id = RelationshipTypeId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Publication(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Publication - class_class_curie: ClassVar[str] = "core:Publication" - class_name: ClassVar[str] = "Publication" - class_model_uri: ClassVar[URIRef] = BP.Publication - - id: Optional[str] = None - title: Optional[str] = None - abstract: Optional[str] = None - combined_text: Optional[str] = None - full_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.id is not None and not isinstance(self.id, str): - self.id = str(self.id) - - if self.title is not None and not isinstance(self.title, str): - self.title = str(self.title) - - if self.abstract is not None and not isinstance(self.abstract, str): - self.abstract = str(self.abstract) - - if self.combined_text is not None and not isinstance(self.combined_text, str): - self.combined_text = str(self.combined_text) - - if self.full_text is not None and not isinstance(self.full_text, str): - self.full_text = str(self.full_text) - - super().__post_init__(**kwargs) - - -@dataclass -class AnnotatorResult(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.AnnotatorResult - class_class_curie: ClassVar[str] = "core:AnnotatorResult" - class_name: ClassVar[str] = "AnnotatorResult" - class_model_uri: ClassVar[URIRef] = BP.AnnotatorResult - - subject_text: Optional[str] = None - object_id: Optional[str] = None - object_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject_text is not None and not isinstance(self.subject_text, str): - self.subject_text = str(self.subject_text) - - if self.object_id is not None and not isinstance(self.object_id, str): - self.object_id = str(self.object_id) - - if self.object_text is not None and not isinstance(self.object_text, str): - self.object_text = str(self.object_text) - - super().__post_init__(**kwargs) - - -# Enumerations -class NullDataOptions(EnumDefinitionImpl): - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = PermissibleValue(text="UNSPECIFIED_METHOD_OF_ADMINISTRATION", - meaning=NCIT.C149701) - NOT_APPLICABLE = PermissibleValue(text="NOT_APPLICABLE", - meaning=NCIT.C18902) - NOT_MENTIONED = PermissibleValue(text="NOT_MENTIONED") - - _defn = EnumDefinition( - name="NullDataOptions", - ) - -# Slots -class slots: - pass - -slots.geneDescription__about = Slot(uri=BP.about, name="geneDescription__about", curie=BP.curie('about'), - model_uri=BP.geneDescription__about, domain=None, range=Optional[Union[str, GeneId]]) - -slots.geneDescription__narrative_summary = Slot(uri=BP.narrative_summary, name="geneDescription__narrative_summary", curie=BP.curie('narrative_summary'), - model_uri=BP.geneDescription__narrative_summary, domain=None, range=Optional[str]) - -slots.geneDescription__terms = Slot(uri=BP.terms, name="geneDescription__terms", curie=BP.curie('terms'), - model_uri=BP.geneDescription__terms, domain=None, range=Optional[Union[Union[str, GeneDescriptionTermId], List[Union[str, GeneDescriptionTermId]]]]) - -slots.geneDescriptionTerm__label = Slot(uri=BP.label, name="geneDescriptionTerm__label", curie=BP.curie('label'), - model_uri=BP.geneDescriptionTerm__label, domain=None, range=Optional[str]) - -slots.extractionResult__input_id = Slot(uri=CORE.input_id, name="extractionResult__input_id", curie=CORE.curie('input_id'), - model_uri=BP.extractionResult__input_id, domain=None, range=Optional[str]) - -slots.extractionResult__input_title = Slot(uri=CORE.input_title, name="extractionResult__input_title", curie=CORE.curie('input_title'), - model_uri=BP.extractionResult__input_title, domain=None, range=Optional[str]) - -slots.extractionResult__input_text = Slot(uri=CORE.input_text, name="extractionResult__input_text", curie=CORE.curie('input_text'), - model_uri=BP.extractionResult__input_text, domain=None, range=Optional[str]) - -slots.extractionResult__raw_completion_output = Slot(uri=CORE.raw_completion_output, name="extractionResult__raw_completion_output", curie=CORE.curie('raw_completion_output'), - model_uri=BP.extractionResult__raw_completion_output, domain=None, range=Optional[str]) - -slots.extractionResult__prompt = Slot(uri=CORE.prompt, name="extractionResult__prompt", curie=CORE.curie('prompt'), - model_uri=BP.extractionResult__prompt, domain=None, range=Optional[str]) - -slots.extractionResult__extracted_object = Slot(uri=CORE.extracted_object, name="extractionResult__extracted_object", curie=CORE.curie('extracted_object'), - model_uri=BP.extractionResult__extracted_object, domain=None, range=Optional[Union[dict, Any]]) - -slots.extractionResult__named_entities = Slot(uri=CORE.named_entities, name="extractionResult__named_entities", curie=CORE.curie('named_entities'), - model_uri=BP.extractionResult__named_entities, domain=None, range=Optional[Union[Union[dict, Any], List[Union[dict, Any]]]]) - -slots.namedEntity__id = Slot(uri=CORE.id, name="namedEntity__id", curie=CORE.curie('id'), - model_uri=BP.namedEntity__id, domain=None, range=URIRef) - -slots.namedEntity__label = Slot(uri=RDFS.label, name="namedEntity__label", curie=RDFS.curie('label'), - model_uri=BP.namedEntity__label, domain=None, range=Optional[str]) - -slots.triple__subject = Slot(uri=CORE.subject, name="triple__subject", curie=CORE.curie('subject'), - model_uri=BP.triple__subject, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__predicate = Slot(uri=CORE.predicate, name="triple__predicate", curie=CORE.curie('predicate'), - model_uri=BP.triple__predicate, domain=None, range=Optional[Union[str, RelationshipTypeId]]) - -slots.triple__object = Slot(uri=CORE.object, name="triple__object", curie=CORE.curie('object'), - model_uri=BP.triple__object, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__qualifier = Slot(uri=CORE.qualifier, name="triple__qualifier", curie=CORE.curie('qualifier'), - model_uri=BP.triple__qualifier, domain=None, range=Optional[str]) - -slots.triple__subject_qualifier = Slot(uri=CORE.subject_qualifier, name="triple__subject_qualifier", curie=CORE.curie('subject_qualifier'), - model_uri=BP.triple__subject_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__object_qualifier = Slot(uri=CORE.object_qualifier, name="triple__object_qualifier", curie=CORE.curie('object_qualifier'), - model_uri=BP.triple__object_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.textWithTriples__publication = Slot(uri=CORE.publication, name="textWithTriples__publication", curie=CORE.curie('publication'), - model_uri=BP.textWithTriples__publication, domain=None, range=Optional[Union[dict, Publication]]) - -slots.textWithTriples__triples = Slot(uri=CORE.triples, name="textWithTriples__triples", curie=CORE.curie('triples'), - model_uri=BP.textWithTriples__triples, domain=None, range=Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]]) - -slots.publication__id = Slot(uri=CORE.id, name="publication__id", curie=CORE.curie('id'), - model_uri=BP.publication__id, domain=None, range=Optional[str]) - -slots.publication__title = Slot(uri=CORE.title, name="publication__title", curie=CORE.curie('title'), - model_uri=BP.publication__title, domain=None, range=Optional[str]) - -slots.publication__abstract = Slot(uri=CORE.abstract, name="publication__abstract", curie=CORE.curie('abstract'), - model_uri=BP.publication__abstract, domain=None, range=Optional[str]) - -slots.publication__combined_text = Slot(uri=CORE.combined_text, name="publication__combined_text", curie=CORE.curie('combined_text'), - model_uri=BP.publication__combined_text, domain=None, range=Optional[str]) - -slots.publication__full_text = Slot(uri=CORE.full_text, name="publication__full_text", curie=CORE.curie('full_text'), - model_uri=BP.publication__full_text, domain=None, range=Optional[str]) - -slots.annotatorResult__subject_text = Slot(uri=CORE.subject_text, name="annotatorResult__subject_text", curie=CORE.curie('subject_text'), - model_uri=BP.annotatorResult__subject_text, domain=None, range=Optional[str]) - -slots.annotatorResult__object_id = Slot(uri=CORE.object_id, name="annotatorResult__object_id", curie=CORE.curie('object_id'), - model_uri=BP.annotatorResult__object_id, domain=None, range=Optional[str]) - -slots.annotatorResult__object_text = Slot(uri=CORE.object_text, name="annotatorResult__object_text", curie=CORE.curie('object_text'), - model_uri=BP.annotatorResult__object_text, domain=None, range=Optional[str]) \ No newline at end of file diff --git a/projects/gene_description_term/graphql/gene_description_term.graphql b/projects/gene_description_term/graphql/gene_description_term.graphql deleted file mode 100644 index 70be47e72..000000000 --- a/projects/gene_description_term/graphql/gene_description_term.graphql +++ /dev/null @@ -1,82 +0,0 @@ -type AnnotatorResult - { - subjectText: String - objectId: String - objectText: String - } - -type Any - { - } - -interface CompoundExpression - { - } - -type ExtractionResult - { - inputId: String - inputTitle: String - inputText: String - rawCompletionOutput: String - prompt: String - extractedObject: Any - namedEntities: [Any] - } - -type Gene - { - id: String! - label: String - } - -type GeneDescription - { - about: Gene - narrativeSummary: String - terms: [GeneDescriptionTerm] - } - -type GeneDescriptionTerm - { - id: String! - label: String - } - -interface NamedEntity - { - id: String! - label: String - } - -type Publication - { - id: String - title: String - abstract: String - combinedText: String - fullText: String - } - -type RelationshipType - { - id: String! - label: String - } - -type TextWithTriples - { - publication: Publication - triples: [Triple] - } - -interface Triple - { - subject: NamedEntity - predicate: RelationshipType - object: NamedEntity - qualifier: String - subjectQualifier: NamedEntity - objectQualifier: NamedEntity - } - diff --git a/projects/gene_description_term/jsonld/gene_description_term.context.jsonld b/projects/gene_description_term/jsonld/gene_description_term.context.jsonld deleted file mode 100644 index c01be5aa2..000000000 --- a/projects/gene_description_term/jsonld/gene_description_term.context.jsonld +++ /dev/null @@ -1,147 +0,0 @@ -{ - "comments": { - "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2023-08-07T10:53:23", - "source": "gene_description_term.yaml" - }, - "@context": { - "GO": { - "@id": "http://purl.obolibrary.org/obo/GO_", - "@prefix": true - }, - "HGNC": "http://identifiers.org/hgnc/", - "MESH": "http://identifiers.org/mesh/", - "MONDO": { - "@id": "http://purl.obolibrary.org/obo/MONDO_", - "@prefix": true - }, - "RO": { - "@id": "http://purl.obolibrary.org/obo/RO_", - "@prefix": true - }, - "UBERON": "http://example.org/UNKNOWN/UBERON/", - "biolink": "http://example.org/UNKNOWN/biolink/", - "bp": { - "@id": "http://w3id.org/ontogpt/biological-process-template", - "@prefix": true - }, - "core": "http://w3id.org/ontogpt/core/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "@vocab": "http://w3id.org/ontogpt/biological-process-template", - "object_id": { - "@id": "core:object_id" - }, - "object_text": { - "@id": "core:object_text" - }, - "subject_text": { - "@id": "core:subject_text" - }, - "extracted_object": { - "@type": "@id", - "@id": "core:extracted_object" - }, - "input_id": { - "@id": "core:input_id" - }, - "input_text": { - "@id": "core:input_text" - }, - "input_title": { - "@id": "core:input_title" - }, - "named_entities": { - "@type": "@id", - "@id": "core:named_entities" - }, - "prompt": { - "@id": "core:prompt" - }, - "raw_completion_output": { - "@id": "core:raw_completion_output" - }, - "about": { - "@type": "@id" - }, - "terms": { - "@type": "@id" - }, - "id": { - "@id": "core:id" - }, - "label": { - "@id": "rdfs:label" - }, - "abstract": { - "@id": "core:abstract" - }, - "combined_text": { - "@id": "core:combined_text" - }, - "full_text": { - "@id": "core:full_text" - }, - "title": { - "@id": "core:title" - }, - "publication": { - "@type": "@id", - "@id": "core:publication" - }, - "triples": { - "@type": "@id", - "@id": "core:triples" - }, - "object": { - "@type": "@id", - "@id": "core:object" - }, - "object_qualifier": { - "@type": "@id", - "@id": "core:object_qualifier" - }, - "predicate": { - "@type": "@id", - "@id": "core:predicate" - }, - "qualifier": { - "@id": "core:qualifier" - }, - "subject": { - "@type": "@id", - "@id": "core:subject" - }, - "subject_qualifier": { - "@type": "@id", - "@id": "core:subject_qualifier" - }, - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } - } -} diff --git a/projects/gene_description_term/jsonld/gene_description_term.jsonld b/projects/gene_description_term/jsonld/gene_description_term.jsonld deleted file mode 100644 index 96affc5f4..000000000 --- a/projects/gene_description_term/jsonld/gene_description_term.jsonld +++ /dev/null @@ -1,1132 +0,0 @@ -{ - "name": "go-term-template", - "description": "A simple GO term template for NER", - "title": "GO Term Template", - "id": "https://w3id.org/ontogpt/go_term", - "imports": [ - "linkml:types", - "core" - ], - "license": "https://creativecommons.org/publicdomain/zero/1.0/", - "prefixes": [ - { - "prefix_prefix": "linkml", - "prefix_reference": "https://w3id.org/linkml/" - }, - { - "prefix_prefix": "bp", - "prefix_reference": "http://w3id.org/ontogpt/biological-process-template" - }, - { - "prefix_prefix": "HGNC", - "prefix_reference": "http://identifiers.org/hgnc/" - }, - { - "prefix_prefix": "GO", - "prefix_reference": "http://purl.obolibrary.org/obo/GO_" - }, - { - "prefix_prefix": "MONDO", - "prefix_reference": "http://purl.obolibrary.org/obo/MONDO_" - }, - { - "prefix_prefix": "MESH", - "prefix_reference": "http://identifiers.org/mesh/" - } - ], - "default_prefix": "bp", - "default_range": "string", - "types": [ - { - "name": "string", - "definition_uri": "https://w3id.org/linkml/String", - "description": "A character string", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Text" - ], - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "@type": "TypeDefinition" - }, - { - "name": "integer", - "definition_uri": "https://w3id.org/linkml/Integer", - "description": "An integer", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Integer" - ], - "base": "int", - "uri": "http://www.w3.org/2001/XMLSchema#integer", - "@type": "TypeDefinition" - }, - { - "name": "boolean", - "definition_uri": "https://w3id.org/linkml/Boolean", - "description": "A binary (true or false) value", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Boolean" - ], - "base": "Bool", - "uri": "http://www.w3.org/2001/XMLSchema#boolean", - "repr": "bool", - "@type": "TypeDefinition" - }, - { - "name": "float", - "definition_uri": "https://w3id.org/linkml/Float", - "description": "A real number that conforms to the xsd:float specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#float", - "@type": "TypeDefinition" - }, - { - "name": "double", - "definition_uri": "https://w3id.org/linkml/Double", - "description": "A real number that conforms to the xsd:double specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#double", - "@type": "TypeDefinition" - }, - { - "name": "decimal", - "definition_uri": "https://w3id.org/linkml/Decimal", - "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "broad_mappings": [ - "schema:Number" - ], - "base": "Decimal", - "uri": "http://www.w3.org/2001/XMLSchema#decimal", - "@type": "TypeDefinition" - }, - { - "name": "time", - "definition_uri": "https://w3id.org/linkml/Time", - "description": "A time object represents a (local) time of day, independent of any particular day", - "notes": [ - "URI is dateTime because OWL reasoners do not work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Time" - ], - "base": "XSDTime", - "uri": "http://www.w3.org/2001/XMLSchema#time", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date", - "definition_uri": "https://w3id.org/linkml/Date", - "description": "a date (year, month and day) in an idealized calendar", - "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Date" - ], - "base": "XSDDate", - "uri": "http://www.w3.org/2001/XMLSchema#date", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "datetime", - "definition_uri": "https://w3id.org/linkml/Datetime", - "description": "The combination of a date and time", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:DateTime" - ], - "base": "XSDDateTime", - "uri": "http://www.w3.org/2001/XMLSchema#dateTime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date_or_datetime", - "definition_uri": "https://w3id.org/linkml/DateOrDatetime", - "description": "Either a date or a datetime", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "https://w3id.org/linkml/DateOrDatetime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uriorcurie", - "definition_uri": "https://w3id.org/linkml/Uriorcurie", - "description": "a URI or a CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "URIorCURIE", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "curie", - "definition_uri": "https://w3id.org/linkml/Curie", - "conforms_to": "https://www.w3.org/TR/curie/", - "description": "a compact URI", - "comments": [ - "in RDF serializations this MUST be expanded to a URI", - "in non-RDF serializations MAY be serialized as the compact representation" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "Curie", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uri", - "definition_uri": "https://w3id.org/linkml/Uri", - "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", - "description": "a complete URI", - "comments": [ - "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:URL" - ], - "base": "URI", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "ncname", - "definition_uri": "https://w3id.org/linkml/Ncname", - "description": "Prefix part of CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NCName", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "objectidentifier", - "definition_uri": "https://w3id.org/linkml/Objectidentifier", - "description": "A URI or CURIE that represents an object in the model.", - "comments": [ - "Used for inheritance and type checking" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "ElementIdentifier", - "uri": "http://www.w3.org/ns/shex#iri", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "nodeidentifier", - "definition_uri": "https://w3id.org/linkml/Nodeidentifier", - "description": "A URI, CURIE or BNODE that represents a node in a model.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NodeIdentifier", - "uri": "http://www.w3.org/ns/shex#nonLiteral", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpointer", - "definition_uri": "https://w3id.org/linkml/Jsonpointer", - "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901", - "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpath", - "definition_uri": "https://w3id.org/linkml/Jsonpath", - "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html", - "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "sparqlpath", - "definition_uri": "https://w3id.org/linkml/Sparqlpath", - "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths", - "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - } - ], - "enums": [ - { - "name": "NullDataOptions", - "definition_uri": "http://w3id.org/ontogpt/core/NullDataOptions", - "from_schema": "http://w3id.org/ontogpt/core", - "permissible_values": [ - { - "text": "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "meaning": "NCIT:C149701" - }, - { - "text": "NOT_APPLICABLE", - "meaning": "NCIT:C18902", - "aliases": [ - "not applicable", - "N/A" - ] - }, - { - "text": "NOT_MENTIONED" - } - ] - } - ], - "slots": [ - { - "name": "geneDescription__about", - "description": "The official symbol of the gene that is described. For example \"TP53\". Do not include the word \"gene\" in the answer.", - "from_schema": "https://w3id.org/ontogpt/go_term", - "slot_uri": "http://w3id.org/ontogpt/biological-process-templateabout", - "alias": "about", - "owner": "GeneDescription", - "domain_of": [ - "GeneDescription" - ], - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "geneDescription__narrative_summary", - "description": "A free text summary describing the function of the gene", - "from_schema": "https://w3id.org/ontogpt/go_term", - "slot_uri": "http://w3id.org/ontogpt/biological-process-templatenarrative_summary", - "alias": "narrative_summary", - "owner": "GeneDescription", - "domain_of": [ - "GeneDescription" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "geneDescription__terms", - "description": "A semicolon separated list of controlled terms drawn from the Gene Ontology that describe the function of the gene", - "from_schema": "https://w3id.org/ontogpt/go_term", - "slot_uri": "http://w3id.org/ontogpt/biological-process-templateterms", - "multivalued": true, - "alias": "terms", - "owner": "GeneDescription", - "domain_of": [ - "GeneDescription" - ], - "range": "GeneDescriptionTerm", - "@type": "SlotDefinition" - }, - { - "name": "geneDescriptionTerm__label", - "description": "the name of the GO term", - "from_schema": "https://w3id.org/ontogpt/go_term", - "slot_uri": "http://w3id.org/ontogpt/biological-process-templatelabel", - "alias": "label", - "owner": "GeneDescriptionTerm", - "domain_of": [ - "GeneDescriptionTerm" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_id", - "alias": "input_id", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_title", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_title", - "alias": "input_title", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_text", - "alias": "input_text", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__raw_completion_output", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/raw_completion_output", - "alias": "raw_completion_output", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__prompt", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/prompt", - "alias": "prompt", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__extracted_object", - "description": "The complex objects extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/extracted_object", - "alias": "extracted_object", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__named_entities", - "description": "Named entities extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/named_entities", - "multivalued": true, - "alias": "named_entities", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "identifier": true, - "alias": "id", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "required": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "from_schema": "http://w3id.org/ontogpt/core", - "aliases": [ - "name" - ], - "mappings": [ - "http://example.org/UNKNOWN/rdfs/label" - ], - "slot_uri": "http://example.org/UNKNOWN/rdfs/label", - "alias": "label", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject", - "alias": "subject", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__predicate", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/predicate", - "alias": "predicate", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "triple__object", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object", - "alias": "object", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/qualifier", - "alias": "qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_qualifier", - "alias": "subject_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_qualifier", - "alias": "object_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/publication", - "alias": "publication", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__triples", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/triples", - "multivalued": true, - "alias": "triples", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "publication__id", - "description": "The publication identifier", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "alias": "id", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__title", - "description": "The title of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/title", - "alias": "title", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__abstract", - "description": "The abstract of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/abstract", - "alias": "abstract", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__combined_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/combined_text", - "alias": "combined_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__full_text", - "description": "The full text of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/full_text", - "alias": "full_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__subject_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_text", - "alias": "subject_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_id", - "alias": "object_id", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_text", - "alias": "object_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - } - ], - "classes": [ - { - "name": "Gene", - "id_prefixes": [ - "HGNC" - ], - "definition_uri": "http://w3id.org/ontogpt/biological-process-templateGene", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:hgnc", - "@type": "Annotation" - } - ], - "from_schema": "https://w3id.org/ontogpt/go_term", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/biological-process-templateGene", - "@type": "ClassDefinition" - }, - { - "name": "GeneDescription", - "definition_uri": "http://w3id.org/ontogpt/biological-process-templateGeneDescription", - "description": "A summarization of an individual gene", - "from_schema": "https://w3id.org/ontogpt/go_term", - "slots": [ - "geneDescription__about", - "geneDescription__narrative_summary", - "geneDescription__terms" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "about", - "description": "The official symbol of the gene that is described. For example \"TP53\". Do not include the word \"gene\" in the answer.", - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "narrative_summary", - "description": "A free text summary describing the function of the gene", - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "terms", - "description": "A semicolon separated list of controlled terms drawn from the Gene Ontology that describe the function of the gene", - "multivalued": true, - "range": "GeneDescriptionTerm", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/biological-process-templateGeneDescription", - "@type": "ClassDefinition" - }, - { - "name": "GeneDescriptionTerm", - "id_prefixes": [ - "GO", - "MONDO", - "UBERON", - "MESH" - ], - "definition_uri": "http://w3id.org/ontogpt/biological-process-templateGeneDescriptionTerm", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:go, sqlite:obo:mondo, sqlite:obo:uberon, sqlite:obo:mesh", - "@type": "Annotation" - } - ], - "from_schema": "https://w3id.org/ontogpt/go_term", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "geneDescriptionTerm__label" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "label", - "description": "the name of the GO term", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/biological-process-templateGeneDescriptionTerm", - "tree_root": true, - "@type": "ClassDefinition" - }, - { - "name": "Any", - "definition_uri": "http://w3id.org/ontogpt/core/Any", - "from_schema": "http://w3id.org/ontogpt/core", - "mappings": [ - "linkml:Any" - ], - "slot_usage": {}, - "class_uri": "https://w3id.org/linkml/Any", - "@type": "ClassDefinition" - }, - { - "name": "ExtractionResult", - "definition_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "description": "A result of extracting knowledge on text", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "extractionResult__input_id", - "extractionResult__input_title", - "extractionResult__input_text", - "extractionResult__raw_completion_output", - "extractionResult__prompt", - "extractionResult__extracted_object", - "extractionResult__named_entities" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "input_id", - "@type": "SlotDefinition" - }, - { - "name": "input_title", - "@type": "SlotDefinition" - }, - { - "name": "input_text", - "@type": "SlotDefinition" - }, - { - "name": "raw_completion_output", - "@type": "SlotDefinition" - }, - { - "name": "prompt", - "@type": "SlotDefinition" - }, - { - "name": "extracted_object", - "description": "The complex objects extracted from the text", - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "named_entities", - "description": "Named entities extracted from the text", - "multivalued": true, - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "@type": "ClassDefinition" - }, - { - "name": "NamedEntity", - "definition_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "identifier": true, - "@type": "SlotDefinition" - }, - { - "name": "label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "aliases": [ - "name" - ], - "slot_uri": "rdfs:label", - "range": "string", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "@type": "ClassDefinition" - }, - { - "name": "CompoundExpression", - "definition_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "@type": "ClassDefinition" - }, - { - "name": "Triple", - "definition_uri": "http://w3id.org/ontogpt/core/Triple", - "description": "Abstract parent for Relation Extraction tasks", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "CompoundExpression", - "abstract": true, - "slots": [ - "triple__subject", - "triple__predicate", - "triple__object", - "triple__qualifier", - "triple__subject_qualifier", - "triple__object_qualifier" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "predicate", - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "object", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Triple", - "@type": "ClassDefinition" - }, - { - "name": "TextWithTriples", - "definition_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "textWithTriples__publication", - "textWithTriples__triples" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "triples", - "multivalued": true, - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "@type": "ClassDefinition" - }, - { - "name": "RelationshipType", - "id_prefixes": [ - "RO", - "biolink" - ], - "definition_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "@type": "ClassDefinition" - }, - { - "name": "Publication", - "definition_uri": "http://w3id.org/ontogpt/core/Publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "publication__id", - "publication__title", - "publication__abstract", - "publication__combined_text", - "publication__full_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "description": "The publication identifier", - "@type": "SlotDefinition" - }, - { - "name": "title", - "description": "The title of the publication", - "@type": "SlotDefinition" - }, - { - "name": "abstract", - "description": "The abstract of the publication", - "@type": "SlotDefinition" - }, - { - "name": "combined_text", - "@type": "SlotDefinition" - }, - { - "name": "full_text", - "description": "The full text of the publication", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Publication", - "@type": "ClassDefinition" - }, - { - "name": "AnnotatorResult", - "definition_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "annotatorResult__subject_text", - "annotatorResult__object_id", - "annotatorResult__object_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject_text", - "@type": "SlotDefinition" - }, - { - "name": "object_id", - "@type": "SlotDefinition" - }, - { - "name": "object_text", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "@type": "ClassDefinition" - } - ], - "metamodel_version": "1.7.0", - "source_file": "gene_description_term.yaml", - "source_file_date": "2023-06-17T15:11:19", - "source_file_size": 1614, - "generation_date": "2023-08-07T10:53:24", - "@type": "SchemaDefinition", - "@context": [ - "projects/gene_description_term/jsonld/gene_description_term.context.jsonld", - "https://w3id.org/linkml/types.context.jsonld", - "core.context.jsonld", - { - "@base": "http://w3id.org/ontogpt/biological-process-template" - } - ] -} diff --git a/projects/gene_description_term/jsonschema/gene_description_term.schema.json b/projects/gene_description_term/jsonschema/gene_description_term.schema.json deleted file mode 100644 index c098ee47a..000000000 --- a/projects/gene_description_term/jsonschema/gene_description_term.schema.json +++ /dev/null @@ -1,215 +0,0 @@ -{ - "$defs": { - "AnnotatorResult": { - "additionalProperties": false, - "description": "", - "properties": { - "object_id": { - "type": "string" - }, - "object_text": { - "type": "string" - }, - "subject_text": { - "type": "string" - } - }, - "title": "AnnotatorResult", - "type": "object" - }, - "Any": { - "additionalProperties": true, - "description": "", - "title": "Any", - "type": "object" - }, - "ExtractionResult": { - "additionalProperties": false, - "description": "A result of extracting knowledge on text", - "properties": { - "extracted_object": { - "$ref": "#/$defs/Any", - "description": "The complex objects extracted from the text" - }, - "input_id": { - "type": "string" - }, - "input_text": { - "type": "string" - }, - "input_title": { - "type": "string" - }, - "named_entities": { - "description": "Named entities extracted from the text", - "items": { - "$ref": "#/$defs/Any" - }, - "type": "array" - }, - "prompt": { - "type": "string" - }, - "raw_completion_output": { - "type": "string" - } - }, - "title": "ExtractionResult", - "type": "object" - }, - "Gene": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Gene", - "type": "object" - }, - "GeneDescription": { - "additionalProperties": false, - "description": "A summarization of an individual gene", - "properties": { - "about": { - "description": "The official symbol of the gene that is described. For example \"TP53\". Do not include the word \"gene\" in the answer.", - "type": "string" - }, - "narrative_summary": { - "description": "A free text summary describing the function of the gene", - "type": "string" - }, - "terms": { - "description": "A semicolon separated list of controlled terms drawn from the Gene Ontology that describe the function of the gene", - "items": { - "type": "string" - }, - "type": "array" - } - }, - "title": "GeneDescription", - "type": "object" - }, - "GeneDescriptionTerm": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "the name of the GO term", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "GeneDescriptionTerm", - "type": "object" - }, - "NullDataOptions": { - "description": "", - "enum": [ - "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "NOT_APPLICABLE", - "NOT_MENTIONED" - ], - "title": "NullDataOptions", - "type": "string" - }, - "Publication": { - "additionalProperties": false, - "description": "", - "properties": { - "abstract": { - "description": "The abstract of the publication", - "type": "string" - }, - "combined_text": { - "type": "string" - }, - "full_text": { - "description": "The full text of the publication", - "type": "string" - }, - "id": { - "description": "The publication identifier", - "type": "string" - }, - "title": { - "description": "The title of the publication", - "type": "string" - } - }, - "title": "Publication", - "type": "object" - }, - "RelationshipType": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "RelationshipType", - "type": "object" - }, - "TextWithTriples": { - "additionalProperties": false, - "description": "", - "properties": { - "publication": { - "$ref": "#/$defs/Publication" - }, - "triples": { - "items": { - "$ref": "#/$defs/Triple" - }, - "type": "array" - } - }, - "title": "TextWithTriples", - "type": "object" - } - }, - "$id": "https://w3id.org/ontogpt/go_term", - "$schema": "http://json-schema.org/draft-07/schema#", - "additionalProperties": true, - "metamodel_version": "1.7.0", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "the name of the GO term", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "go-term-template", - "type": "object", - "version": null -} \ No newline at end of file diff --git a/projects/gene_description_term/owl/gene_description_term.owl.ttl b/projects/gene_description_term/owl/gene_description_term.owl.ttl deleted file mode 100644 index fb63ae60d..000000000 --- a/projects/gene_description_term/owl/gene_description_term.owl.ttl +++ /dev/null @@ -1,415 +0,0 @@ -@prefix IAO: <http://purl.obolibrary.org/obo/IAO_> . -@prefix bp: <http://w3id.org/ontogpt/biological-process-template> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix owl: <http://www.w3.org/2002/07/owl#> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . -@prefix skos: <http://www.w3.org/2004/02/skos/core#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -linkml:SubsetDefinition a owl:Class ; - rdfs:label "subset_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" . - -linkml:TypeDefinition a owl:Class ; - rdfs:label "type_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" ; - linkml:mixins "type_expression" . - -linkml:topValue a owl:DatatypeProperty ; - rdfs:label "value" . - -<https://w3id.org/ontogpt/go_term> a owl:Ontology ; - rdfs:label "go-term-template" ; - IAO:0000700 bp:GeneDescription, - <http://w3id.org/ontogpt/core/AnnotatorResult>, - <http://w3id.org/ontogpt/core/Any>, - <http://w3id.org/ontogpt/core/CompoundExpression>, - <http://w3id.org/ontogpt/core/ExtractionResult>, - <http://w3id.org/ontogpt/core/NamedEntity>, - <http://w3id.org/ontogpt/core/Publication>, - <http://w3id.org/ontogpt/core/TextWithTriples> ; - linkml:classes "{'Gene': ClassDefinition(name='Gene', id_prefixes=['HGNC'], definition_uri='http://w3id.org/ontogpt/biological-process-templateGene', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:hgnc', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/go_term', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='bp:Gene', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'GeneDescription': ClassDefinition(name='GeneDescription', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/biological-process-templateGeneDescription', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A summarization of an individual gene', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/go_term', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['geneDescription__about', 'geneDescription__narrative_summary', 'geneDescription__terms'], slot_usage={}, attributes={'about': SlotDefinition(name='about', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The official symbol of the gene that is described. For example \"TP53\". Do not include the word \"gene\" in the answer.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'narrative_summary': SlotDefinition(name='narrative_summary', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A free text summary describing the function of the gene', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'terms': SlotDefinition(name='terms', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A semicolon separated list of controlled terms drawn from the Gene Ontology that describe the function of the gene', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneDescriptionTerm', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='bp:GeneDescription', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'GeneDescriptionTerm': ClassDefinition(name='GeneDescriptionTerm', id_prefixes=['GO', 'MONDO', 'UBERON', 'MESH'], definition_uri='http://w3id.org/ontogpt/biological-process-templateGeneDescriptionTerm', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:go, sqlite:obo:mondo, sqlite:obo:uberon, sqlite:obo:mesh', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/go_term', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'geneDescriptionTerm__label'], slot_usage={}, attributes={'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the name of the GO term', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='bp:GeneDescriptionTerm', subclass_of=None, union_of=[], defining_slots=[], tree_root=True, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Any': ClassDefinition(name='Any', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Any', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=['linkml:Any'], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='linkml:Any', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ExtractionResult': ClassDefinition(name='ExtractionResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/ExtractionResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A result of extracting knowledge on text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['extractionResult__input_id', 'extractionResult__input_title', 'extractionResult__input_text', 'extractionResult__raw_completion_output', 'extractionResult__prompt', 'extractionResult__extracted_object', 'extractionResult__named_entities'], slot_usage={}, attributes={'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:ExtractionResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'NamedEntity': ClassDefinition(name='NamedEntity', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NamedEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:NamedEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'CompoundExpression': ClassDefinition(name='CompoundExpression', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/CompoundExpression', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='core:CompoundExpression', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Triple': ClassDefinition(name='Triple', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Triple', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Abstract parent for Relation Extraction tasks', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['triple__subject', 'triple__predicate', 'triple__object', 'triple__qualifier', 'triple__subject_qualifier', 'triple__object_qualifier'], slot_usage={}, attributes={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Triple', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'TextWithTriples': ClassDefinition(name='TextWithTriples', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/TextWithTriples', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['textWithTriples__publication', 'textWithTriples__triples'], slot_usage={}, attributes={'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:TextWithTriples', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'RelationshipType': ClassDefinition(name='RelationshipType', id_prefixes=['RO', 'biolink'], definition_uri='http://w3id.org/ontogpt/core/RelationshipType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='core:RelationshipType', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Publication': ClassDefinition(name='Publication', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Publication', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['publication__id', 'publication__title', 'publication__abstract', 'publication__combined_text', 'publication__full_text'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Publication', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'AnnotatorResult': ClassDefinition(name='AnnotatorResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/AnnotatorResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['annotatorResult__subject_text', 'annotatorResult__object_id', 'annotatorResult__object_text'], slot_usage={}, attributes={'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:AnnotatorResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={})}" ; - linkml:enums "{'NullDataOptions': EnumDefinition(name='NullDataOptions', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NullDataOptions', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'UNSPECIFIED_METHOD_OF_ADMINISTRATION': PermissibleValue(text='UNSPECIFIED_METHOD_OF_ADMINISTRATION', description=None, meaning='NCIT:C149701', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_APPLICABLE': PermissibleValue(text='NOT_APPLICABLE', description=None, meaning='NCIT:C18902', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['not applicable', 'N/A'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_MENTIONED': PermissibleValue(text='NOT_MENTIONED', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[])}" ; - linkml:id "https://w3id.org/ontogpt/go_term" ; - linkml:imports "core", - "linkml:types" ; - linkml:types "{'string': TypeDefinition(name='string', id_prefixes=[], definition_uri='https://w3id.org/linkml/String', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A character string', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Text'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'integer': TypeDefinition(name='integer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Integer', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An integer', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Integer'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='int', uri='xsd:integer', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'boolean': TypeDefinition(name='boolean', id_prefixes=[], definition_uri='https://w3id.org/linkml/Boolean', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A binary (true or false) value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Boolean'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Bool', uri='xsd:boolean', repr='bool', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'float': TypeDefinition(name='float', id_prefixes=[], definition_uri='https://w3id.org/linkml/Float', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:float specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Float'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:float', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'double': TypeDefinition(name='double', id_prefixes=[], definition_uri='https://w3id.org/linkml/Double', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:double specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:Float'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:double', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'decimal': TypeDefinition(name='decimal', id_prefixes=[], definition_uri='https://w3id.org/linkml/Decimal', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number with arbitrary precision that conforms to the xsd:decimal specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=['schema:Number'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Decimal', uri='xsd:decimal', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'time': TypeDefinition(name='time', id_prefixes=[], definition_uri='https://w3id.org/linkml/Time', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A time object represents a (local) time of day, independent of any particular day', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=['URI is dateTime because OWL reasoners do not work with straight date or time'], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Time'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDTime', uri='xsd:time', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date': TypeDefinition(name='date', id_prefixes=[], definition_uri='https://w3id.org/linkml/Date', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a date (year, month and day) in an idealized calendar', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[\"URI is dateTime because OWL reasoners don't work with straight date or time\"], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Date'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDate', uri='xsd:date', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'datetime': TypeDefinition(name='datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/Datetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The combination of a date and time', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:DateTime'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDateTime', uri='xsd:dateTime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date_or_datetime': TypeDefinition(name='date_or_datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/DateOrDatetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Either a date or a datetime', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='linkml:DateOrDatetime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uriorcurie': TypeDefinition(name='uriorcurie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uriorcurie', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a URI or a CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URIorCURIE', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'curie': TypeDefinition(name='curie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Curie', local_names={}, conforms_to='https://www.w3.org/TR/curie/', implements=[], extensions={}, annotations={}, description='a compact URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations this MUST be expanded to a URI', 'in non-RDF serializations MAY be serialized as the compact representation'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Curie', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uri': TypeDefinition(name='uri', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uri', local_names={}, conforms_to='https://www.ietf.org/rfc/rfc3987.txt', implements=[], extensions={}, annotations={}, description='a complete URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:URL'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URI', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ncname': TypeDefinition(name='ncname', id_prefixes=[], definition_uri='https://w3id.org/linkml/Ncname', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Prefix part of CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NCName', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'objectidentifier': TypeDefinition(name='objectidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Objectidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI or CURIE that represents an object in the model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['Used for inheritance and type checking'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='ElementIdentifier', uri='shex:iri', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'nodeidentifier': TypeDefinition(name='nodeidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Nodeidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI, CURIE or BNODE that represents a node in a model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NodeIdentifier', uri='shex:nonLiteral', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpointer': TypeDefinition(name='jsonpointer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpointer', local_names={}, conforms_to='https://datatracker.ietf.org/doc/html/rfc6901', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpath': TypeDefinition(name='jsonpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpath', local_names={}, conforms_to='https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sparqlpath': TypeDefinition(name='sparqlpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Sparqlpath', local_names={}, conforms_to='https://www.w3.org/TR/sparql11-query/#propertypaths', implements=[], extensions={}, annotations={}, description='A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -bp:GeneDescription a owl:Class, - linkml:ClassDefinition ; - rdfs:label "GeneDescription" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty bp:narrative_summary ], - [ a owl:Restriction ; - owl:allValuesFrom bp:GeneDescriptionTerm ; - owl:onProperty bp:terms ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass bp:Gene ; - owl:onProperty bp:about ] ; - skos:definition "A summarization of an individual gene" ; - linkml:attributes "{'about': SlotDefinition(name='about', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The official symbol of the gene that is described. For example \"TP53\". Do not include the word \"gene\" in the answer.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'narrative_summary': SlotDefinition(name='narrative_summary', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A free text summary describing the function of the gene', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'terms': SlotDefinition(name='terms', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A semicolon separated list of controlled terms drawn from the Gene Ontology that describe the function of the gene', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneDescriptionTerm', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -bp:about a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "about" ; - rdfs:range bp:Gene ; - skos:definition "The official symbol of the gene that is described. For example \"TP53\". Do not include the word \"gene\" in the answer." . - -bp:label a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "label" ; - rdfs:range linkml:String ; - skos:definition "the name of the GO term" . - -bp:narrative_summary a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "narrative_summary" ; - rdfs:range linkml:String ; - skos:definition "A free text summary describing the function of the gene" . - -bp:terms a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "terms" ; - rdfs:range bp:GeneDescriptionTerm ; - skos:definition "A semicolon separated list of controlled terms drawn from the Gene Ontology that describe the function of the gene" . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "AnnotatorResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_text> ] ; - linkml:attributes "{'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/ExtractionResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ExtractionResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/extracted_object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_title> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/prompt> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_text> ], - [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/named_entities> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_id> ] ; - skos:definition "A result of extracting knowledge on text" ; - linkml:attributes "{'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/TextWithTriples> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TextWithTriples" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Triple> ; - owl:onProperty <http://w3id.org/ontogpt/core/triples> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Publication> ; - owl:onProperty <http://w3id.org/ontogpt/core/publication> ] ; - linkml:attributes "{'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/abstract> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "abstract" ; - rdfs:range linkml:String ; - skos:definition "The abstract of the publication" . - -<http://w3id.org/ontogpt/core/combined_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "combined_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/extracted_object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "extracted_object" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "The complex objects extracted from the text" . - -<http://w3id.org/ontogpt/core/full_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "full_text" ; - rdfs:range linkml:String ; - skos:definition "The full text of the publication" . - -<http://w3id.org/ontogpt/core/input_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_title" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/named_entities> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "named_entities" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "Named entities extracted from the text" . - -<http://w3id.org/ontogpt/core/object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/object_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/object_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" . - -<http://w3id.org/ontogpt/core/object_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/predicate> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "predicate" ; - rdfs:range <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/prompt> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "prompt" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/publication> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "publication" ; - bp:prompt.skip "true" ; - rdfs:range <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "qualifier" ; - rdfs:range linkml:String ; - skos:definition "A qualifier for the statements, e.g. \"NOT\" for negation" . - -<http://w3id.org/ontogpt/core/raw_completion_output> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "raw_completion_output" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/subject> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/subject_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" . - -<http://w3id.org/ontogpt/core/subject_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "title" ; - rdfs:range linkml:String ; - skos:definition "The title of the publication" . - -<http://w3id.org/ontogpt/core/triples> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "triples" ; - rdfs:range <http://w3id.org/ontogpt/core/Triple> . - -<http://example.org/UNKNOWN/rdfs/label> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "label" ; - bp:owl "AnnotationProperty, AnnotationAssertion" ; - rdfs:range linkml:String ; - skos:altLabel "name" ; - skos:definition "The label (name) of the named thing" ; - skos:exactMatch <http://example.org/UNKNOWN/rdfs/label> . - -<http://purl.obolibrary.org/obo/NCIT_C149701> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "UNSPECIFIED_METHOD_OF_ADMINISTRATION" . - -<http://purl.obolibrary.org/obo/NCIT_C18902> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_APPLICABLE" . - -bp:Gene a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Gene" ; - bp:annotators "sqlite:obo:hgnc" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -bp:GeneDescriptionTerm a owl:Class, - linkml:ClassDefinition ; - rdfs:label "GeneDescriptionTerm" ; - bp:annotators "sqlite:obo:go, sqlite:obo:mondo, sqlite:obo:uberon, sqlite:obo:mesh" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty bp:label ], - <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the name of the GO term', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/CompoundExpression> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CompoundExpression" ; - linkml:attributes "{}" . - -<http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_MENTIONED" . - -<http://w3id.org/ontogpt/core/RelationshipType> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "RelationshipType" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/Triple> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Triple" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/RelationshipType> ; - owl:onProperty <http://w3id.org/ontogpt/core/predicate> ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - skos:definition "Abstract parent for Relation Extraction tasks" ; - linkml:attributes "{'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -<http://w3id.org/ontogpt/core/id> a owl:ObjectProperty, - linkml:SlotDefinition . - -<http://w3id.org/ontogpt/core/NullDataOptions> a owl:Class, - linkml:EnumDefinition ; - rdfs:label "NullDataOptions" ; - owl:unionOf ( <http://purl.obolibrary.org/obo/NCIT_C149701> <http://purl.obolibrary.org/obo/NCIT_C18902> <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> ) ; - linkml:permissible_values <http://purl.obolibrary.org/obo/NCIT_C149701>, - <http://purl.obolibrary.org/obo/NCIT_C18902>, - <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> . - -<http://w3id.org/ontogpt/core/Publication> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Publication" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/abstract> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/combined_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/full_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/title> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/Any> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Any" ; - skos:exactMatch linkml:Any ; - linkml:attributes "{}" . - -<http://w3id.org/ontogpt/core/NamedEntity> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "NamedEntity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://example.org/UNKNOWN/rdfs/label> ], - [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ; - owl:qualifiedCardinality 1 ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:ClassDefinition a owl:Class ; - rdfs:label "class_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "class_expression" . - -linkml:SlotDefinition a owl:Class ; - rdfs:label "slot_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "slot_expression" . - - diff --git a/projects/gene_description_term/prefixmap/gene_description_term.yaml b/projects/gene_description_term/prefixmap/gene_description_term.yaml deleted file mode 100644 index 0ea758005..000000000 --- a/projects/gene_description_term/prefixmap/gene_description_term.yaml +++ /dev/null @@ -1,40 +0,0 @@ -{ - "GO": "http://purl.obolibrary.org/obo/GO_", - "HGNC": "http://identifiers.org/hgnc/", - "MESH": "http://identifiers.org/mesh/", - "MONDO": "http://purl.obolibrary.org/obo/MONDO_", - "RO": "http://purl.obolibrary.org/obo/RO_", - "UBERON": "http://example.org/UNKNOWN/UBERON/", - "biolink": "http://example.org/UNKNOWN/biolink/", - "bp": "http://w3id.org/ontogpt/biological-process-template", - "core": "http://w3id.org/ontogpt/core/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } -} diff --git a/projects/gene_description_term/protobuf/gene_description_term.proto b/projects/gene_description_term/protobuf/gene_description_term.proto deleted file mode 100644 index 7d2bd9128..000000000 --- a/projects/gene_description_term/protobuf/gene_description_term.proto +++ /dev/null @@ -1,52 +0,0 @@ -message AnnotatorResult - { - string subjectText = 0 - string objectId = 0 - string objectText = 0 - } -// A result of extracting knowledge on text -message ExtractionResult - { - string inputId = 0 - string inputTitle = 0 - string inputText = 0 - string rawCompletionOutput = 0 - string prompt = 0 - any extractedObject = 0 - repeated any namedEntities = 0 - } -message Gene - { - string id = 0 - string label = 0 - } -// A summarization of an individual gene -message GeneDescription - { - gene about = 0 - string narrativeSummary = 0 - repeated geneDescriptionTerm terms = 0 - } -message GeneDescriptionTerm - { - string id = 0 - string label = 0 - } -message Publication - { - string id = 0 - string title = 0 - string abstract = 0 - string combinedText = 0 - string fullText = 0 - } -message RelationshipType - { - string id = 0 - string label = 0 - } -message TextWithTriples - { - publication publication = 0 - repeated triple triples = 0 - } diff --git a/projects/gene_description_term/shacl/gene_description_term.shacl.ttl b/projects/gene_description_term/shacl/gene_description_term.shacl.ttl deleted file mode 100644 index e33c3129c..000000000 --- a/projects/gene_description_term/shacl/gene_description_term.shacl.ttl +++ /dev/null @@ -1,213 +0,0 @@ -@prefix bp: <http://w3id.org/ontogpt/biological-process-template> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix sh: <http://www.w3.org/ns/shacl#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -bp:GeneDescription a sh:NodeShape ; - sh:closed true ; - sh:description "A summarization of an individual gene" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class bp:Gene ; - sh:description "The official symbol of the gene that is described. For example \"TP53\". Do not include the word \"gene\" in the answer." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path bp:about ], - [ sh:class bp:GeneDescriptionTerm ; - sh:description "A semicolon separated list of controlled terms drawn from the Gene Ontology that describe the function of the gene" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path bp:terms ], - [ sh:description "A free text summary describing the function of the gene" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path bp:narrative_summary ] ; - sh:targetClass bp:GeneDescription . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/object_id> ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject_text> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object_text> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/AnnotatorResult> . - -<http://w3id.org/ontogpt/core/CompoundExpression> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass <http://w3id.org/ontogpt/core/CompoundExpression> . - -<http://w3id.org/ontogpt/core/ExtractionResult> a sh:NodeShape ; - sh:closed true ; - sh:description "A result of extracting knowledge on text" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class linkml:Any ; - sh:description "The complex objects extracted from the text" ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/extracted_object> ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/input_id> ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/input_title> ], - [ sh:class linkml:Any ; - sh:description "Named entities extracted from the text" ; - sh:nodeKind sh:BlankNode ; - sh:order 6 ; - sh:path <http://w3id.org/ontogpt/core/named_entities> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/input_text> ], - [ sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/prompt> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/ExtractionResult> . - -<http://w3id.org/ontogpt/core/TextWithTriples> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/Triple> ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/triples> ], - [ sh:class <http://w3id.org/ontogpt/core/Publication> ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/publication> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/TextWithTriples> . - -bp:Gene a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass bp:Gene . - -bp:GeneDescriptionTerm a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "the name of the GO term" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path bp:label ] ; - sh:targetClass bp:GeneDescriptionTerm . - -<http://w3id.org/ontogpt/core/Publication> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The full text of the publication" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/full_text> ], - [ sh:description "The title of the publication" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/title> ], - [ sh:description "The publication identifier" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/combined_text> ], - [ sh:description "The abstract of the publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/abstract> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/RelationshipType> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/Triple> a sh:NodeShape ; - sh:closed false ; - sh:description "Abstract parent for Relation Extraction tasks" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A qualifier for the statements, e.g. \"NOT\" for negation" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/RelationshipType> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/predicate> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/object_qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Triple> . - -linkml:Any a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass linkml:Any . - -<http://w3id.org/ontogpt/core/NamedEntity> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/NamedEntity> . - diff --git a/projects/gene_description_term/shex/gene_description_term.shex b/projects/gene_description_term/shex/gene_description_term.shex deleted file mode 100644 index 83279f026..000000000 --- a/projects/gene_description_term/shex/gene_description_term.shex +++ /dev/null @@ -1,163 +0,0 @@ -BASE <http://w3id.org/ontogpt/biological-process-template/> -PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> -PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> -PREFIX linkml: <https://w3id.org/linkml/> -PREFIX core: <http://w3id.org/ontogpt/core/> -PREFIX rdfs1: <http://example.org/UNKNOWN/rdfs/> - - -linkml:String xsd:string - -linkml:Integer xsd:integer - -linkml:Boolean xsd:boolean - -linkml:Float xsd:float - -linkml:Double xsd:double - -linkml:Decimal xsd:decimal - -linkml:Time xsd:time - -linkml:Date xsd:date - -linkml:Datetime xsd:dateTime - -linkml:DateOrDatetime linkml:DateOrDatetime - -linkml:Uriorcurie IRI - -linkml:Curie xsd:string - -linkml:Uri IRI - -linkml:Ncname xsd:string - -linkml:Objectidentifier IRI - -linkml:Nodeidentifier NONLITERAL - -linkml:Jsonpointer xsd:string - -linkml:Jsonpath xsd:string - -linkml:Sparqlpath xsd:string - -core:AnnotatorResult CLOSED { - ( $core:AnnotatorResult_tes ( core:subject_text @linkml:String ? ; - core:object_id @linkml:String ? ; - core:object_text @linkml:String ? - ) ; - rdf:type [ core:AnnotatorResult ] ? - ) -} - -core:Any CLOSED { - ( $core:Any_tes rdf:type . * ; - rdf:type [ linkml:Any ] ? - ) -} - -core:CompoundExpression ( - { - ( $core:CompoundExpression_tes rdf:type . * ; - rdf:type [ core:CompoundExpression ] ? - ) - } OR @core:Triple -) - -core:ExtractionResult CLOSED { - ( $core:ExtractionResult_tes ( core:input_id @linkml:String ? ; - core:input_title @linkml:String ? ; - core:input_text @linkml:String ? ; - core:raw_completion_output @linkml:String ? ; - core:prompt @linkml:String ? ; - core:extracted_object @core:Any ? ; - core:named_entities @core:Any * - ) ; - rdf:type [ core:ExtractionResult ] ? - ) -} - -<http://w3id.org/ontogpt/biological-process-templateGene> CLOSED { - ( $<http://w3id.org/ontogpt/biological-process-templateGene_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <http://w3id.org/ontogpt/biological-process-templateGene> ] - ) -} - -<http://w3id.org/ontogpt/biological-process-templateGeneDescription> CLOSED { - ( $<http://w3id.org/ontogpt/biological-process-templateGeneDescription_tes> ( - <http://w3id.org/ontogpt/biological-process-templateabout> @<http://w3id.org/ontogpt/biological-process-templateGene> ? ; - <http://w3id.org/ontogpt/biological-process-templatenarrative_summary> @linkml:String ? ; - <http://w3id.org/ontogpt/biological-process-templateterms> - @<http://w3id.org/ontogpt/biological-process-templateGeneDescriptionTerm> * - ) ; - rdf:type [ <http://w3id.org/ontogpt/biological-process-templateGeneDescription> ] ? - ) -} - -<http://w3id.org/ontogpt/biological-process-templateGeneDescriptionTerm> CLOSED { - ( $<http://w3id.org/ontogpt/biological-process-templateGeneDescriptionTerm_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? ; - <http://w3id.org/ontogpt/biological-process-templatelabel> @linkml:String ? - ) ; - rdf:type [ <http://w3id.org/ontogpt/biological-process-templateGeneDescriptionTerm> ] - ) -} - -core:NamedEntity ( - @<http://w3id.org/ontogpt/biological-process-templateGene> OR - @<http://w3id.org/ontogpt/biological-process-templateGeneDescriptionTerm> OR @core:RelationshipType -) - -core:NamedEntity_struct { - ( $core:NamedEntity_tes rdfs1:label @linkml:String ? ; - rdf:type [ core:NamedEntity ] - ) -} - -core:Publication CLOSED { - ( $core:Publication_tes ( core:id @linkml:String ? ; - core:title @linkml:String ? ; - core:abstract @linkml:String ? ; - core:combined_text @linkml:String ? ; - core:full_text @linkml:String ? - ) ; - rdf:type [ core:Publication ] ? - ) -} - -core:RelationshipType CLOSED { - ( $core:RelationshipType_tes ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ core:RelationshipType ] - ) -} - -core:TextWithTriples CLOSED { - ( $core:TextWithTriples_tes ( core:publication @core:Publication ? ; - core:triples @core:Triple * - ) ; - rdf:type [ core:TextWithTriples ] ? - ) -} - -core:Triple { - ( $core:Triple_tes ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - core:subject @core:NamedEntity ? ; - core:predicate @core:RelationshipType ? ; - core:object @core:NamedEntity ? ; - core:qualifier @linkml:String ? ; - core:subject_qualifier @core:NamedEntity ? ; - core:object_qualifier @core:NamedEntity ? - ) ; - rdf:type [ core:Triple ] ? - ) -} - - diff --git a/projects/gene_description_term/sqlschema/gene_description_term.sql b/projects/gene_description_term/sqlschema/gene_description_term.sql deleted file mode 100644 index 37e47244b..000000000 --- a/projects/gene_description_term/sqlschema/gene_description_term.sql +++ /dev/null @@ -1,60 +0,0 @@ - - -CREATE TABLE "AnnotatorResult" ( - subject_text TEXT, - object_id TEXT, - object_text TEXT, - PRIMARY KEY (subject_text, object_id, object_text) -); - -CREATE TABLE "ExtractionResult" ( - input_id TEXT, - input_title TEXT, - input_text TEXT, - raw_completion_output TEXT, - prompt TEXT, - extracted_object TEXT, - named_entities TEXT, - PRIMARY KEY (input_id, input_title, input_text, raw_completion_output, prompt, extracted_object, named_entities) -); - -CREATE TABLE "Gene" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "GeneDescriptionTerm" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Publication" ( - id TEXT, - title TEXT, - abstract TEXT, - combined_text TEXT, - full_text TEXT, - PRIMARY KEY (id, title, abstract, combined_text, full_text) -); - -CREATE TABLE "RelationshipType" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "TextWithTriples" ( - publication TEXT, - triples TEXT, - PRIMARY KEY (publication, triples) -); - -CREATE TABLE "GeneDescription" ( - about TEXT, - narrative_summary TEXT, - terms TEXT, - PRIMARY KEY (about, narrative_summary, terms), - FOREIGN KEY(about) REFERENCES "Gene" (id) -); diff --git a/projects/gocam/docs/AnnotatorResult.md b/projects/gocam/docs/AnnotatorResult.md deleted file mode 100644 index b21f75a37..000000000 --- a/projects/gocam/docs/AnnotatorResult.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Class: AnnotatorResult - - - - -URI: [gocam:AnnotatorResult](http://w3id.org/ontogpt/gocam/AnnotatorResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F])](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F]) - -## Attributes - - -### Own - - * [➞subject_text](annotatorResult__subject_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_id](annotatorResult__object_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_text](annotatorResult__object_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) diff --git a/projects/gocam/docs/Any.md b/projects/gocam/docs/Any.md deleted file mode 100644 index 294c64451..000000000 --- a/projects/gocam/docs/Any.md +++ /dev/null @@ -1,25 +0,0 @@ - -# Class: Any - - - - -URI: [gocam:Any](http://w3id.org/ontogpt/gocam/Any) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult])](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult]) - -## Referenced by Class - - * **None** *[➞extracted_object](extractionResult__extracted_object.md)* <sub>0..1</sub> **[Any](Any.md)** - * **None** *[➞named_entities](extractionResult__named_entities.md)* <sub>0..\*</sub> **[Any](Any.md)** - -## Attributes - - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | linkml:Any | - diff --git a/projects/gocam/docs/CellType.md b/projects/gocam/docs/CellType.md deleted file mode 100644 index cce37c2b0..000000000 --- a/projects/gocam/docs/CellType.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Enum: CellType - - - - -URI: [gocam:CellType](http://w3id.org/ontogpt/gocam/CellType) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | - diff --git a/projects/gocam/docs/CellularProcess.md b/projects/gocam/docs/CellularProcess.md deleted file mode 100644 index 6655db07f..000000000 --- a/projects/gocam/docs/CellularProcess.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: CellularProcess - - - - -URI: [gocam:CellularProcess](http://w3id.org/ontogpt/gocam/CellularProcess) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[GoCamAnnotations]-%20cellular_processes%200..*>[CellularProcess|id(i):string;label(i):string%20%3F],[NamedEntity]^-[CellularProcess],[GoCamAnnotations])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[GoCamAnnotations]-%20cellular_processes%200..*>[CellularProcess|id(i):string;label(i):string%20%3F],[NamedEntity]^-[CellularProcess],[GoCamAnnotations]) - -## Identifier prefixes - - * GO - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞cellular_processes](goCamAnnotations__cellular_processes.md)* <sub>0..\*</sub> **[CellularProcess](CellularProcess.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/gocam/docs/CompoundExpression.md b/projects/gocam/docs/CompoundExpression.md deleted file mode 100644 index 2c710a723..000000000 --- a/projects/gocam/docs/CompoundExpression.md +++ /dev/null @@ -1,25 +0,0 @@ - -# Class: CompoundExpression - - - - -URI: [gocam:CompoundExpression](http://w3id.org/ontogpt/gocam/CompoundExpression) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[GeneSubcellularLocalizationRelationship],[GeneOrganismRelationship],[GeneMolecularActivityRelationship2],[GeneMolecularActivityRelationship],[GeneGeneInteraction],[CompoundExpression]^-[Triple],[CompoundExpression]^-[GeneSubcellularLocalizationRelationship],[CompoundExpression]^-[GeneOrganismRelationship],[CompoundExpression]^-[GeneMolecularActivityRelationship2],[CompoundExpression]^-[GeneMolecularActivityRelationship],[CompoundExpression]^-[GeneGeneInteraction])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[GeneSubcellularLocalizationRelationship],[GeneOrganismRelationship],[GeneMolecularActivityRelationship2],[GeneMolecularActivityRelationship],[GeneGeneInteraction],[CompoundExpression]^-[Triple],[CompoundExpression]^-[GeneSubcellularLocalizationRelationship],[CompoundExpression]^-[GeneOrganismRelationship],[CompoundExpression]^-[GeneMolecularActivityRelationship2],[CompoundExpression]^-[GeneMolecularActivityRelationship],[CompoundExpression]^-[GeneGeneInteraction]) - -## Children - - * [GeneGeneInteraction](GeneGeneInteraction.md) - * [GeneMolecularActivityRelationship](GeneMolecularActivityRelationship.md) - * [GeneMolecularActivityRelationship2](GeneMolecularActivityRelationship2.md) - * [GeneOrganismRelationship](GeneOrganismRelationship.md) - * [GeneSubcellularLocalizationRelationship](GeneSubcellularLocalizationRelationship.md) - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - -## Referenced by Class - - -## Attributes - diff --git a/projects/gocam/docs/ExtractionResult.md b/projects/gocam/docs/ExtractionResult.md deleted file mode 100644 index 5fd1b0627..000000000 --- a/projects/gocam/docs/ExtractionResult.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Class: ExtractionResult - - -A result of extracting knowledge on text - -URI: [gocam:ExtractionResult](http://w3id.org/ontogpt/gocam/ExtractionResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any])](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any]) - -## Attributes - - -### Own - - * [➞input_id](extractionResult__input_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_title](extractionResult__input_title.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_text](extractionResult__input_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞prompt](extractionResult__prompt.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞extracted_object](extractionResult__extracted_object.md) <sub>0..1</sub> - * Description: The complex objects extracted from the text - * Range: [Any](Any.md) - * [➞named_entities](extractionResult__named_entities.md) <sub>0..\*</sub> - * Description: Named entities extracted from the text - * Range: [Any](Any.md) diff --git a/projects/gocam/docs/GOCellComponentType.md b/projects/gocam/docs/GOCellComponentType.md deleted file mode 100644 index e2e6fcda9..000000000 --- a/projects/gocam/docs/GOCellComponentType.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Enum: GOCellComponentType - - - - -URI: [gocam:GOCellComponentType](http://w3id.org/ontogpt/gocam/GOCellComponentType) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | - diff --git a/projects/gocam/docs/Gene.md b/projects/gocam/docs/Gene.md deleted file mode 100644 index 2a66c7056..000000000 --- a/projects/gocam/docs/Gene.md +++ /dev/null @@ -1,42 +0,0 @@ - -# Class: Gene - - - - -URI: [gocam:Gene](http://w3id.org/ontogpt/gocam/Gene) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[GeneGeneInteraction]-%20gene1%200..1>[Gene|id(i):string;label(i):string%20%3F],[GeneGeneInteraction]-%20gene2%200..1>[Gene],[GeneMolecularActivityRelationship2]-%20gene%200..1>[Gene],[GeneMolecularActivityRelationship]-%20gene%200..1>[Gene],[GeneOrganismRelationship]-%20gene%200..1>[Gene],[GeneSubcellularLocalizationRelationship]-%20gene%200..1>[Gene],[GoCamAnnotations]-%20genes%200..*>[Gene],[NamedEntity]^-[Gene],[GoCamAnnotations],[GeneSubcellularLocalizationRelationship],[GeneOrganismRelationship],[GeneMolecularActivityRelationship2],[GeneMolecularActivityRelationship],[GeneGeneInteraction])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[GeneGeneInteraction]-%20gene1%200..1>[Gene|id(i):string;label(i):string%20%3F],[GeneGeneInteraction]-%20gene2%200..1>[Gene],[GeneMolecularActivityRelationship2]-%20gene%200..1>[Gene],[GeneMolecularActivityRelationship]-%20gene%200..1>[Gene],[GeneOrganismRelationship]-%20gene%200..1>[Gene],[GeneSubcellularLocalizationRelationship]-%20gene%200..1>[Gene],[GoCamAnnotations]-%20genes%200..*>[Gene],[NamedEntity]^-[Gene],[GoCamAnnotations],[GeneSubcellularLocalizationRelationship],[GeneOrganismRelationship],[GeneMolecularActivityRelationship2],[GeneMolecularActivityRelationship],[GeneGeneInteraction]) - -## Identifier prefixes - - * HGNC - * PR - * UniProtKB - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞gene1](geneGeneInteraction__gene1.md)* <sub>0..1</sub> **[Gene](Gene.md)** - * **None** *[➞gene2](geneGeneInteraction__gene2.md)* <sub>0..1</sub> **[Gene](Gene.md)** - * **None** *[➞gene](geneMolecularActivityRelationship2__gene.md)* <sub>0..1</sub> **[Gene](Gene.md)** - * **None** *[➞gene](geneMolecularActivityRelationship__gene.md)* <sub>0..1</sub> **[Gene](Gene.md)** - * **None** *[➞gene](geneOrganismRelationship__gene.md)* <sub>0..1</sub> **[Gene](Gene.md)** - * **None** *[➞gene](geneSubcellularLocalizationRelationship__gene.md)* <sub>0..1</sub> **[Gene](Gene.md)** - * **None** *[➞genes](goCamAnnotations__genes.md)* <sub>0..\*</sub> **[Gene](Gene.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/gocam/docs/GeneGeneInteraction.md b/projects/gocam/docs/GeneGeneInteraction.md deleted file mode 100644 index 579fc263d..000000000 --- a/projects/gocam/docs/GeneGeneInteraction.md +++ /dev/null @@ -1,28 +0,0 @@ - -# Class: GeneGeneInteraction - - - - -URI: [gocam:GeneGeneInteraction](http://w3id.org/ontogpt/gocam/GeneGeneInteraction) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Gene]<gene2%200..1-%20[GeneGeneInteraction],[Gene]<gene1%200..1-%20[GeneGeneInteraction],[GoCamAnnotations]++-%20gene_gene_interactions%200..*>[GeneGeneInteraction],[CompoundExpression]^-[GeneGeneInteraction],[GoCamAnnotations],[Gene],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[Gene]<gene2%200..1-%20[GeneGeneInteraction],[Gene]<gene1%200..1-%20[GeneGeneInteraction],[GoCamAnnotations]++-%20gene_gene_interactions%200..*>[GeneGeneInteraction],[CompoundExpression]^-[GeneGeneInteraction],[GoCamAnnotations],[Gene],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞gene_gene_interactions](goCamAnnotations__gene_gene_interactions.md)* <sub>0..\*</sub> **[GeneGeneInteraction](GeneGeneInteraction.md)** - -## Attributes - - -### Own - - * [➞gene1](geneGeneInteraction__gene1.md) <sub>0..1</sub> - * Range: [Gene](Gene.md) - * [➞gene2](geneGeneInteraction__gene2.md) <sub>0..1</sub> - * Range: [Gene](Gene.md) diff --git a/projects/gocam/docs/GeneLocation.md b/projects/gocam/docs/GeneLocation.md deleted file mode 100644 index d54b4da61..000000000 --- a/projects/gocam/docs/GeneLocation.md +++ /dev/null @@ -1,38 +0,0 @@ - -# Class: GeneLocation - - - - -URI: [gocam:GeneLocation](http://w3id.org/ontogpt/gocam/GeneLocation) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[GeneSubcellularLocalizationRelationship]-%20location%200..1>[GeneLocation|id:string;label(i):string%20%3F],[NamedEntity]^-[GeneLocation],[GeneSubcellularLocalizationRelationship])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[GeneSubcellularLocalizationRelationship]-%20location%200..1>[GeneLocation|id:string;label(i):string%20%3F],[NamedEntity]^-[GeneLocation],[GeneSubcellularLocalizationRelationship]) - -## Identifier prefixes - - * GO - * CL - * UBERON - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞location](geneSubcellularLocalizationRelationship__location.md)* <sub>0..1</sub> **[GeneLocation](GeneLocation.md)** - -## Attributes - - -### Own - - * [GeneLocation➞id](GeneLocation_id.md) <sub>1..1</sub> - * Range: [String](types/String.md) - -### Inherited from NamedEntity: - - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/gocam/docs/GeneLocationEnum.md b/projects/gocam/docs/GeneLocationEnum.md deleted file mode 100644 index 67626c0d9..000000000 --- a/projects/gocam/docs/GeneLocationEnum.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Enum: GeneLocationEnum - - - - -URI: [gocam:GeneLocationEnum](http://w3id.org/ontogpt/gocam/GeneLocationEnum) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | - diff --git a/projects/gocam/docs/GeneLocation_id.md b/projects/gocam/docs/GeneLocation_id.md deleted file mode 100644 index 1357ee5d7..000000000 --- a/projects/gocam/docs/GeneLocation_id.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: id - - - - -URI: [gocam:GeneLocation_id](http://w3id.org/ontogpt/gocam/GeneLocation_id) - - -## Domain and Range - -[GeneLocation](GeneLocation.md) → <sub>1..1</sub> [String](types/String.md) - -## Parents - - * is_a: [➞id](namedEntity__id.md) - -## Children - - -## Used by - - * [GeneLocation](GeneLocation.md) diff --git a/projects/gocam/docs/GeneMolecularActivityRelationship.md b/projects/gocam/docs/GeneMolecularActivityRelationship.md deleted file mode 100644 index b605122de..000000000 --- a/projects/gocam/docs/GeneMolecularActivityRelationship.md +++ /dev/null @@ -1,28 +0,0 @@ - -# Class: GeneMolecularActivityRelationship - - - - -URI: [gocam:GeneMolecularActivityRelationship](http://w3id.org/ontogpt/gocam/GeneMolecularActivityRelationship) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[MolecularActivity],[MolecularActivity]<molecular_activity%200..1-%20[GeneMolecularActivityRelationship],[Gene]<gene%200..1-%20[GeneMolecularActivityRelationship],[GoCamAnnotations]++-%20gene_functions%200..*>[GeneMolecularActivityRelationship],[CompoundExpression]^-[GeneMolecularActivityRelationship],[GoCamAnnotations],[Gene],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[MolecularActivity],[MolecularActivity]<molecular_activity%200..1-%20[GeneMolecularActivityRelationship],[Gene]<gene%200..1-%20[GeneMolecularActivityRelationship],[GoCamAnnotations]++-%20gene_functions%200..*>[GeneMolecularActivityRelationship],[CompoundExpression]^-[GeneMolecularActivityRelationship],[GoCamAnnotations],[Gene],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞gene_functions](goCamAnnotations__gene_functions.md)* <sub>0..\*</sub> **[GeneMolecularActivityRelationship](GeneMolecularActivityRelationship.md)** - -## Attributes - - -### Own - - * [➞gene](geneMolecularActivityRelationship__gene.md) <sub>0..1</sub> - * Range: [Gene](Gene.md) - * [➞molecular_activity](geneMolecularActivityRelationship__molecular_activity.md) <sub>0..1</sub> - * Range: [MolecularActivity](MolecularActivity.md) diff --git a/projects/gocam/docs/GeneMolecularActivityRelationship2.md b/projects/gocam/docs/GeneMolecularActivityRelationship2.md deleted file mode 100644 index 395313a4f..000000000 --- a/projects/gocam/docs/GeneMolecularActivityRelationship2.md +++ /dev/null @@ -1,26 +0,0 @@ - -# Class: GeneMolecularActivityRelationship2 - - - - -URI: [gocam:GeneMolecularActivityRelationship2](http://w3id.org/ontogpt/gocam/GeneMolecularActivityRelationship2) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Molecule],[MolecularActivity],[Molecule]<target%200..1-%20[GeneMolecularActivityRelationship2],[MolecularActivity]<molecular_activity%200..1-%20[GeneMolecularActivityRelationship2],[Gene]<gene%200..1-%20[GeneMolecularActivityRelationship2],[CompoundExpression]^-[GeneMolecularActivityRelationship2],[Gene],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[Molecule],[MolecularActivity],[Molecule]<target%200..1-%20[GeneMolecularActivityRelationship2],[MolecularActivity]<molecular_activity%200..1-%20[GeneMolecularActivityRelationship2],[Gene]<gene%200..1-%20[GeneMolecularActivityRelationship2],[CompoundExpression]^-[GeneMolecularActivityRelationship2],[Gene],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Attributes - - -### Own - - * [➞gene](geneMolecularActivityRelationship2__gene.md) <sub>0..1</sub> - * Range: [Gene](Gene.md) - * [➞molecular_activity](geneMolecularActivityRelationship2__molecular_activity.md) <sub>0..1</sub> - * Range: [MolecularActivity](MolecularActivity.md) - * [➞target](geneMolecularActivityRelationship2__target.md) <sub>0..1</sub> - * Range: [Molecule](Molecule.md) diff --git a/projects/gocam/docs/GeneOrganismRelationship.md b/projects/gocam/docs/GeneOrganismRelationship.md deleted file mode 100644 index 652185c57..000000000 --- a/projects/gocam/docs/GeneOrganismRelationship.md +++ /dev/null @@ -1,28 +0,0 @@ - -# Class: GeneOrganismRelationship - - - - -URI: [gocam:GeneOrganismRelationship](http://w3id.org/ontogpt/gocam/GeneOrganismRelationship) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Organism],[Organism]<organism%200..1-%20[GeneOrganismRelationship],[Gene]<gene%200..1-%20[GeneOrganismRelationship],[GoCamAnnotations]++-%20gene_organisms%200..*>[GeneOrganismRelationship],[CompoundExpression]^-[GeneOrganismRelationship],[GoCamAnnotations],[Gene],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[Organism],[Organism]<organism%200..1-%20[GeneOrganismRelationship],[Gene]<gene%200..1-%20[GeneOrganismRelationship],[GoCamAnnotations]++-%20gene_organisms%200..*>[GeneOrganismRelationship],[CompoundExpression]^-[GeneOrganismRelationship],[GoCamAnnotations],[Gene],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞gene_organisms](goCamAnnotations__gene_organisms.md)* <sub>0..\*</sub> **[GeneOrganismRelationship](GeneOrganismRelationship.md)** - -## Attributes - - -### Own - - * [➞gene](geneOrganismRelationship__gene.md) <sub>0..1</sub> - * Range: [Gene](Gene.md) - * [➞organism](geneOrganismRelationship__organism.md) <sub>0..1</sub> - * Range: [Organism](Organism.md) diff --git a/projects/gocam/docs/GeneSubcellularLocalizationRelationship.md b/projects/gocam/docs/GeneSubcellularLocalizationRelationship.md deleted file mode 100644 index d9f8648b4..000000000 --- a/projects/gocam/docs/GeneSubcellularLocalizationRelationship.md +++ /dev/null @@ -1,28 +0,0 @@ - -# Class: GeneSubcellularLocalizationRelationship - - - - -URI: [gocam:GeneSubcellularLocalizationRelationship](http://w3id.org/ontogpt/gocam/GeneSubcellularLocalizationRelationship) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[GeneLocation]<location%200..1-%20[GeneSubcellularLocalizationRelationship],[Gene]<gene%200..1-%20[GeneSubcellularLocalizationRelationship],[GoCamAnnotations]++-%20gene_localizations%200..*>[GeneSubcellularLocalizationRelationship],[CompoundExpression]^-[GeneSubcellularLocalizationRelationship],[GoCamAnnotations],[GeneLocation],[Gene],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[GeneLocation]<location%200..1-%20[GeneSubcellularLocalizationRelationship],[Gene]<gene%200..1-%20[GeneSubcellularLocalizationRelationship],[GoCamAnnotations]++-%20gene_localizations%200..*>[GeneSubcellularLocalizationRelationship],[CompoundExpression]^-[GeneSubcellularLocalizationRelationship],[GoCamAnnotations],[GeneLocation],[Gene],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞gene_localizations](goCamAnnotations__gene_localizations.md)* <sub>0..\*</sub> **[GeneSubcellularLocalizationRelationship](GeneSubcellularLocalizationRelationship.md)** - -## Attributes - - -### Own - - * [➞gene](geneSubcellularLocalizationRelationship__gene.md) <sub>0..1</sub> - * Range: [Gene](Gene.md) - * [➞location](geneSubcellularLocalizationRelationship__location.md) <sub>0..1</sub> - * Range: [GeneLocation](GeneLocation.md) diff --git a/projects/gocam/docs/GoCamAnnotations.md b/projects/gocam/docs/GoCamAnnotations.md deleted file mode 100644 index e23722b20..000000000 --- a/projects/gocam/docs/GoCamAnnotations.md +++ /dev/null @@ -1,42 +0,0 @@ - -# Class: GoCamAnnotations - - - - -URI: [gocam:GoCamAnnotations](http://w3id.org/ontogpt/gocam/GoCamAnnotations) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Pathway],[Organism],[MolecularActivity],[GeneSubcellularLocalizationRelationship]<gene_localizations%200..*-++[GoCamAnnotations],[GeneGeneInteraction]<gene_gene_interactions%200..*-++[GoCamAnnotations],[Pathway]<pathways%200..*-%20[GoCamAnnotations],[CellularProcess]<cellular_processes%200..*-%20[GoCamAnnotations],[GeneMolecularActivityRelationship]<gene_functions%200..*-++[GoCamAnnotations],[MolecularActivity]<activities%200..*-%20[GoCamAnnotations],[GeneOrganismRelationship]<gene_organisms%200..*-++[GoCamAnnotations],[Organism]<organisms%200..*-%20[GoCamAnnotations],[Gene]<genes%200..*-%20[GoCamAnnotations],[GeneSubcellularLocalizationRelationship],[GeneOrganismRelationship],[GeneMolecularActivityRelationship],[GeneGeneInteraction],[Gene],[CellularProcess])](https://yuml.me/diagram/nofunky;dir:TB/class/[Pathway],[Organism],[MolecularActivity],[GeneSubcellularLocalizationRelationship]<gene_localizations%200..*-++[GoCamAnnotations],[GeneGeneInteraction]<gene_gene_interactions%200..*-++[GoCamAnnotations],[Pathway]<pathways%200..*-%20[GoCamAnnotations],[CellularProcess]<cellular_processes%200..*-%20[GoCamAnnotations],[GeneMolecularActivityRelationship]<gene_functions%200..*-++[GoCamAnnotations],[MolecularActivity]<activities%200..*-%20[GoCamAnnotations],[GeneOrganismRelationship]<gene_organisms%200..*-++[GoCamAnnotations],[Organism]<organisms%200..*-%20[GoCamAnnotations],[Gene]<genes%200..*-%20[GoCamAnnotations],[GeneSubcellularLocalizationRelationship],[GeneOrganismRelationship],[GeneMolecularActivityRelationship],[GeneGeneInteraction],[Gene],[CellularProcess]) - -## Attributes - - -### Own - - * [➞genes](goCamAnnotations__genes.md) <sub>0..\*</sub> - * Description: semicolon-separated list of genes - * Range: [Gene](Gene.md) - * [➞organisms](goCamAnnotations__organisms.md) <sub>0..\*</sub> - * Description: semicolon-separated list of organism taxons - * Range: [Organism](Organism.md) - * [➞gene_organisms](goCamAnnotations__gene_organisms.md) <sub>0..\*</sub> - * Range: [GeneOrganismRelationship](GeneOrganismRelationship.md) - * [➞activities](goCamAnnotations__activities.md) <sub>0..\*</sub> - * Description: semicolon-separated list of molecular activities - * Range: [MolecularActivity](MolecularActivity.md) - * [➞gene_functions](goCamAnnotations__gene_functions.md) <sub>0..\*</sub> - * Description: semicolon-separated list of gene to molecular activity relationships - * Range: [GeneMolecularActivityRelationship](GeneMolecularActivityRelationship.md) - * [➞cellular_processes](goCamAnnotations__cellular_processes.md) <sub>0..\*</sub> - * Description: semicolon-separated list of cellular processes - * Range: [CellularProcess](CellularProcess.md) - * [➞pathways](goCamAnnotations__pathways.md) <sub>0..\*</sub> - * Description: semicolon-separated list of pathways - * Range: [Pathway](Pathway.md) - * [➞gene_gene_interactions](goCamAnnotations__gene_gene_interactions.md) <sub>0..\*</sub> - * Description: semicolon-separated list of gene to gene interactions - * Range: [GeneGeneInteraction](GeneGeneInteraction.md) - * [➞gene_localizations](goCamAnnotations__gene_localizations.md) <sub>0..\*</sub> - * Description: semicolon-separated list of genes plus their location in the cell; for example, "gene1 / cytoplasm; gene2 / mitochondrion" - * Range: [GeneSubcellularLocalizationRelationship](GeneSubcellularLocalizationRelationship.md) diff --git a/projects/gocam/docs/MolecularActivity.md b/projects/gocam/docs/MolecularActivity.md deleted file mode 100644 index 2fa43b454..000000000 --- a/projects/gocam/docs/MolecularActivity.md +++ /dev/null @@ -1,36 +0,0 @@ - -# Class: MolecularActivity - - - - -URI: [gocam:MolecularActivity](http://w3id.org/ontogpt/gocam/MolecularActivity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[GeneMolecularActivityRelationship2]-%20molecular_activity%200..1>[MolecularActivity|id(i):string;label(i):string%20%3F],[GeneMolecularActivityRelationship]-%20molecular_activity%200..1>[MolecularActivity],[GoCamAnnotations]-%20activities%200..*>[MolecularActivity],[NamedEntity]^-[MolecularActivity],[GoCamAnnotations],[GeneMolecularActivityRelationship2],[GeneMolecularActivityRelationship])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[GeneMolecularActivityRelationship2]-%20molecular_activity%200..1>[MolecularActivity|id(i):string;label(i):string%20%3F],[GeneMolecularActivityRelationship]-%20molecular_activity%200..1>[MolecularActivity],[GoCamAnnotations]-%20activities%200..*>[MolecularActivity],[NamedEntity]^-[MolecularActivity],[GoCamAnnotations],[GeneMolecularActivityRelationship2],[GeneMolecularActivityRelationship]) - -## Identifier prefixes - - * GO - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞molecular_activity](geneMolecularActivityRelationship2__molecular_activity.md)* <sub>0..1</sub> **[MolecularActivity](MolecularActivity.md)** - * **None** *[➞molecular_activity](geneMolecularActivityRelationship__molecular_activity.md)* <sub>0..1</sub> **[MolecularActivity](MolecularActivity.md)** - * **None** *[➞activities](goCamAnnotations__activities.md)* <sub>0..\*</sub> **[MolecularActivity](MolecularActivity.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/gocam/docs/Molecule.md b/projects/gocam/docs/Molecule.md deleted file mode 100644 index 2dc4c84f4..000000000 --- a/projects/gocam/docs/Molecule.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: Molecule - - - - -URI: [gocam:Molecule](http://w3id.org/ontogpt/gocam/Molecule) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[GeneMolecularActivityRelationship2]-%20target%200..1>[Molecule|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Molecule],[GeneMolecularActivityRelationship2])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[GeneMolecularActivityRelationship2]-%20target%200..1>[Molecule|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Molecule],[GeneMolecularActivityRelationship2]) - -## Identifier prefixes - - * CHEBI - * PR - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞target](geneMolecularActivityRelationship2__target.md)* <sub>0..1</sub> **[Molecule](Molecule.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/gocam/docs/NamedEntity.md b/projects/gocam/docs/NamedEntity.md deleted file mode 100644 index 3896f74ca..000000000 --- a/projects/gocam/docs/NamedEntity.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Class: NamedEntity - - - - -URI: [gocam:NamedEntity](http://w3id.org/ontogpt/gocam/NamedEntity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[Pathway],[Organism],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[Pathway],[NamedEntity]^-[Organism],[NamedEntity]^-[Molecule],[NamedEntity]^-[MolecularActivity],[NamedEntity]^-[GeneLocation],[NamedEntity]^-[Gene],[NamedEntity]^-[CellularProcess],[Triple],[Molecule],[MolecularActivity],[GeneLocation],[Gene],[CellularProcess])](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[Pathway],[Organism],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[Pathway],[NamedEntity]^-[Organism],[NamedEntity]^-[Molecule],[NamedEntity]^-[MolecularActivity],[NamedEntity]^-[GeneLocation],[NamedEntity]^-[Gene],[NamedEntity]^-[CellularProcess],[Triple],[Molecule],[MolecularActivity],[GeneLocation],[Gene],[CellularProcess]) - -## Children - - * [CellularProcess](CellularProcess.md) - * [Gene](Gene.md) - * [GeneLocation](GeneLocation.md) - * [MolecularActivity](MolecularActivity.md) - * [Molecule](Molecule.md) - * [Organism](Organism.md) - * [Pathway](Pathway.md) - * [RelationshipType](RelationshipType.md) - -## Referenced by Class - - * **None** *[➞object](triple__object.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞object_qualifier](triple__object_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject](triple__subject.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject_qualifier](triple__subject_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - -## Attributes - - -### Own - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/gocam/docs/NullDataOptions.md b/projects/gocam/docs/NullDataOptions.md deleted file mode 100644 index abbb7e68a..000000000 --- a/projects/gocam/docs/NullDataOptions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Enum: NullDataOptions - - - - -URI: [gocam:NullDataOptions](http://w3id.org/ontogpt/gocam/NullDataOptions) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | -| UNSPECIFIED_METHOD_OF_ADMINISTRATION | | NCIT:C149701 | | -| NOT_APPLICABLE | | NCIT:C18902 | {'aliases': ['not applicable', 'N/A']} | -| NOT_MENTIONED | | | | - diff --git a/projects/gocam/docs/Organism.md b/projects/gocam/docs/Organism.md deleted file mode 100644 index 9eb2f72e8..000000000 --- a/projects/gocam/docs/Organism.md +++ /dev/null @@ -1,36 +0,0 @@ - -# Class: Organism - - - - -URI: [gocam:Organism](http://w3id.org/ontogpt/gocam/Organism) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[GeneOrganismRelationship]-%20organism%200..1>[Organism|id(i):string;label(i):string%20%3F],[GoCamAnnotations]-%20organisms%200..*>[Organism],[NamedEntity]^-[Organism],[NamedEntity],[GoCamAnnotations],[GeneOrganismRelationship])](https://yuml.me/diagram/nofunky;dir:TB/class/[GeneOrganismRelationship]-%20organism%200..1>[Organism|id(i):string;label(i):string%20%3F],[GoCamAnnotations]-%20organisms%200..*>[Organism],[NamedEntity]^-[Organism],[NamedEntity],[GoCamAnnotations],[GeneOrganismRelationship]) - -## Identifier prefixes - - * NCBITaxon - * EFO - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞organism](geneOrganismRelationship__organism.md)* <sub>0..1</sub> **[Organism](Organism.md)** - * **None** *[➞organisms](goCamAnnotations__organisms.md)* <sub>0..\*</sub> **[Organism](Organism.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/gocam/docs/Pathway.md b/projects/gocam/docs/Pathway.md deleted file mode 100644 index d64e098ef..000000000 --- a/projects/gocam/docs/Pathway.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: Pathway - - - - -URI: [gocam:Pathway](http://w3id.org/ontogpt/gocam/Pathway) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[GoCamAnnotations]-%20pathways%200..*>[Pathway|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Pathway],[NamedEntity],[GoCamAnnotations])](https://yuml.me/diagram/nofunky;dir:TB/class/[GoCamAnnotations]-%20pathways%200..*>[Pathway|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Pathway],[NamedEntity],[GoCamAnnotations]) - -## Identifier prefixes - - * GO - * PW - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞pathways](goCamAnnotations__pathways.md)* <sub>0..\*</sub> **[Pathway](Pathway.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/gocam/docs/Publication.md b/projects/gocam/docs/Publication.md deleted file mode 100644 index 64d87f10d..000000000 --- a/projects/gocam/docs/Publication.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Publication - - - - -URI: [gocam:Publication](http://w3id.org/ontogpt/gocam/Publication) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples])](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples]) - -## Referenced by Class - - * **None** *[➞publication](textWithTriples__publication.md)* <sub>0..1</sub> **[Publication](Publication.md)** - -## Attributes - - -### Own - - * [➞id](publication__id.md) <sub>0..1</sub> - * Description: The publication identifier - * Range: [String](types/String.md) - * [➞title](publication__title.md) <sub>0..1</sub> - * Description: The title of the publication - * Range: [String](types/String.md) - * [➞abstract](publication__abstract.md) <sub>0..1</sub> - * Description: The abstract of the publication - * Range: [String](types/String.md) - * [➞combined_text](publication__combined_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞full_text](publication__full_text.md) <sub>0..1</sub> - * Description: The full text of the publication - * Range: [String](types/String.md) diff --git a/projects/gocam/docs/RelationshipType.md b/projects/gocam/docs/RelationshipType.md deleted file mode 100644 index ea382170c..000000000 --- a/projects/gocam/docs/RelationshipType.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: RelationshipType - - - - -URI: [gocam:RelationshipType](http://w3id.org/ontogpt/gocam/RelationshipType) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity]) - -## Identifier prefixes - - * RO - * biolink - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞predicate](triple__predicate.md)* <sub>0..1</sub> **[RelationshipType](RelationshipType.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/gocam/docs/TextWithTriples.md b/projects/gocam/docs/TextWithTriples.md deleted file mode 100644 index 77200b9c3..000000000 --- a/projects/gocam/docs/TextWithTriples.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: TextWithTriples - - - - -URI: [gocam:TextWithTriples](http://w3id.org/ontogpt/gocam/TextWithTriples) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication]) - -## Attributes - - -### Own - - * [➞publication](textWithTriples__publication.md) <sub>0..1</sub> - * Range: [Publication](Publication.md) - * [➞triples](textWithTriples__triples.md) <sub>0..\*</sub> - * Range: [Triple](Triple.md) diff --git a/projects/gocam/docs/Triple.md b/projects/gocam/docs/Triple.md deleted file mode 100644 index 77c3e9483..000000000 --- a/projects/gocam/docs/Triple.md +++ /dev/null @@ -1,39 +0,0 @@ - -# Class: Triple - - -Abstract parent for Relation Extraction tasks - -URI: [gocam:Triple](http://w3id.org/ontogpt/gocam/Triple) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞triples](textWithTriples__triples.md)* <sub>0..\*</sub> **[Triple](Triple.md)** - -## Attributes - - -### Own - - * [➞subject](triple__subject.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞predicate](triple__predicate.md) <sub>0..1</sub> - * Range: [RelationshipType](RelationshipType.md) - * [➞object](triple__object.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞qualifier](triple__qualifier.md) <sub>0..1</sub> - * Description: A qualifier for the statements, e.g. "NOT" for negation - * Range: [String](types/String.md) - * [➞subject_qualifier](triple__subject_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - * Range: [NamedEntity](NamedEntity.md) - * [➞object_qualifier](triple__object_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * Range: [NamedEntity](NamedEntity.md) diff --git a/projects/gocam/docs/annotatorResult__object_id.md b/projects/gocam/docs/annotatorResult__object_id.md deleted file mode 100644 index 77a3040ba..000000000 --- a/projects/gocam/docs/annotatorResult__object_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_id - - - - -URI: [gocam:annotatorResult__object_id](http://w3id.org/ontogpt/gocam/annotatorResult__object_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/gocam/docs/annotatorResult__object_text.md b/projects/gocam/docs/annotatorResult__object_text.md deleted file mode 100644 index 2869435f2..000000000 --- a/projects/gocam/docs/annotatorResult__object_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_text - - - - -URI: [gocam:annotatorResult__object_text](http://w3id.org/ontogpt/gocam/annotatorResult__object_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/gocam/docs/annotatorResult__subject_text.md b/projects/gocam/docs/annotatorResult__subject_text.md deleted file mode 100644 index 6f92b2c48..000000000 --- a/projects/gocam/docs/annotatorResult__subject_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_text - - - - -URI: [gocam:annotatorResult__subject_text](http://w3id.org/ontogpt/gocam/annotatorResult__subject_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/gocam/docs/extractionResult__extracted_object.md b/projects/gocam/docs/extractionResult__extracted_object.md deleted file mode 100644 index 8e46f1540..000000000 --- a/projects/gocam/docs/extractionResult__extracted_object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: extracted_object - - -The complex objects extracted from the text - -URI: [gocam:extractionResult__extracted_object](http://w3id.org/ontogpt/gocam/extractionResult__extracted_object) - - -## Domain and Range - -None → <sub>0..1</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/gocam/docs/extractionResult__input_id.md b/projects/gocam/docs/extractionResult__input_id.md deleted file mode 100644 index d667d9cc3..000000000 --- a/projects/gocam/docs/extractionResult__input_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_id - - - - -URI: [gocam:extractionResult__input_id](http://w3id.org/ontogpt/gocam/extractionResult__input_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/gocam/docs/extractionResult__input_text.md b/projects/gocam/docs/extractionResult__input_text.md deleted file mode 100644 index 5d130aab5..000000000 --- a/projects/gocam/docs/extractionResult__input_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_text - - - - -URI: [gocam:extractionResult__input_text](http://w3id.org/ontogpt/gocam/extractionResult__input_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/gocam/docs/extractionResult__input_title.md b/projects/gocam/docs/extractionResult__input_title.md deleted file mode 100644 index 80c0a0585..000000000 --- a/projects/gocam/docs/extractionResult__input_title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_title - - - - -URI: [gocam:extractionResult__input_title](http://w3id.org/ontogpt/gocam/extractionResult__input_title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/gocam/docs/extractionResult__named_entities.md b/projects/gocam/docs/extractionResult__named_entities.md deleted file mode 100644 index 6680295e3..000000000 --- a/projects/gocam/docs/extractionResult__named_entities.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: named_entities - - -Named entities extracted from the text - -URI: [gocam:extractionResult__named_entities](http://w3id.org/ontogpt/gocam/extractionResult__named_entities) - - -## Domain and Range - -None → <sub>0..\*</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/gocam/docs/extractionResult__prompt.md b/projects/gocam/docs/extractionResult__prompt.md deleted file mode 100644 index 0bc5b4d86..000000000 --- a/projects/gocam/docs/extractionResult__prompt.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: prompt - - - - -URI: [gocam:extractionResult__prompt](http://w3id.org/ontogpt/gocam/extractionResult__prompt) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/gocam/docs/extractionResult__raw_completion_output.md b/projects/gocam/docs/extractionResult__raw_completion_output.md deleted file mode 100644 index d5b8ad15b..000000000 --- a/projects/gocam/docs/extractionResult__raw_completion_output.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: raw_completion_output - - - - -URI: [gocam:extractionResult__raw_completion_output](http://w3id.org/ontogpt/gocam/extractionResult__raw_completion_output) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/gocam/docs/geneGeneInteraction__gene1.md b/projects/gocam/docs/geneGeneInteraction__gene1.md deleted file mode 100644 index 25ff5d3e1..000000000 --- a/projects/gocam/docs/geneGeneInteraction__gene1.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: gene1 - - - - -URI: [gocam:geneGeneInteraction__gene1](http://w3id.org/ontogpt/gocam/geneGeneInteraction__gene1) - - -## Domain and Range - -None → <sub>0..1</sub> [Gene](Gene.md) - -## Parents - - -## Children - - -## Used by - - * [GeneGeneInteraction](GeneGeneInteraction.md) diff --git a/projects/gocam/docs/geneGeneInteraction__gene2.md b/projects/gocam/docs/geneGeneInteraction__gene2.md deleted file mode 100644 index 8ad830681..000000000 --- a/projects/gocam/docs/geneGeneInteraction__gene2.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: gene2 - - - - -URI: [gocam:geneGeneInteraction__gene2](http://w3id.org/ontogpt/gocam/geneGeneInteraction__gene2) - - -## Domain and Range - -None → <sub>0..1</sub> [Gene](Gene.md) - -## Parents - - -## Children - - -## Used by - - * [GeneGeneInteraction](GeneGeneInteraction.md) diff --git a/projects/gocam/docs/geneMolecularActivityRelationship2__gene.md b/projects/gocam/docs/geneMolecularActivityRelationship2__gene.md deleted file mode 100644 index 29e3876af..000000000 --- a/projects/gocam/docs/geneMolecularActivityRelationship2__gene.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: gene - - - - -URI: [gocam:geneMolecularActivityRelationship2__gene](http://w3id.org/ontogpt/gocam/geneMolecularActivityRelationship2__gene) - - -## Domain and Range - -None → <sub>0..1</sub> [Gene](Gene.md) - -## Parents - - -## Children - - -## Used by - - * [GeneMolecularActivityRelationship2](GeneMolecularActivityRelationship2.md) diff --git a/projects/gocam/docs/geneMolecularActivityRelationship2__molecular_activity.md b/projects/gocam/docs/geneMolecularActivityRelationship2__molecular_activity.md deleted file mode 100644 index db47a4345..000000000 --- a/projects/gocam/docs/geneMolecularActivityRelationship2__molecular_activity.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: molecular_activity - - - - -URI: [gocam:geneMolecularActivityRelationship2__molecular_activity](http://w3id.org/ontogpt/gocam/geneMolecularActivityRelationship2__molecular_activity) - - -## Domain and Range - -None → <sub>0..1</sub> [MolecularActivity](MolecularActivity.md) - -## Parents - - -## Children - - -## Used by - - * [GeneMolecularActivityRelationship2](GeneMolecularActivityRelationship2.md) diff --git a/projects/gocam/docs/geneMolecularActivityRelationship2__target.md b/projects/gocam/docs/geneMolecularActivityRelationship2__target.md deleted file mode 100644 index bb68d8cef..000000000 --- a/projects/gocam/docs/geneMolecularActivityRelationship2__target.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: target - - - - -URI: [gocam:geneMolecularActivityRelationship2__target](http://w3id.org/ontogpt/gocam/geneMolecularActivityRelationship2__target) - - -## Domain and Range - -None → <sub>0..1</sub> [Molecule](Molecule.md) - -## Parents - - -## Children - - -## Used by - - * [GeneMolecularActivityRelationship2](GeneMolecularActivityRelationship2.md) diff --git a/projects/gocam/docs/geneMolecularActivityRelationship__gene.md b/projects/gocam/docs/geneMolecularActivityRelationship__gene.md deleted file mode 100644 index e4df4fa20..000000000 --- a/projects/gocam/docs/geneMolecularActivityRelationship__gene.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: gene - - - - -URI: [gocam:geneMolecularActivityRelationship__gene](http://w3id.org/ontogpt/gocam/geneMolecularActivityRelationship__gene) - - -## Domain and Range - -None → <sub>0..1</sub> [Gene](Gene.md) - -## Parents - - -## Children - - -## Used by - - * [GeneMolecularActivityRelationship](GeneMolecularActivityRelationship.md) diff --git a/projects/gocam/docs/geneMolecularActivityRelationship__molecular_activity.md b/projects/gocam/docs/geneMolecularActivityRelationship__molecular_activity.md deleted file mode 100644 index 42577e0a6..000000000 --- a/projects/gocam/docs/geneMolecularActivityRelationship__molecular_activity.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: molecular_activity - - - - -URI: [gocam:geneMolecularActivityRelationship__molecular_activity](http://w3id.org/ontogpt/gocam/geneMolecularActivityRelationship__molecular_activity) - - -## Domain and Range - -None → <sub>0..1</sub> [MolecularActivity](MolecularActivity.md) - -## Parents - - -## Children - - -## Used by - - * [GeneMolecularActivityRelationship](GeneMolecularActivityRelationship.md) diff --git a/projects/gocam/docs/geneOrganismRelationship__gene.md b/projects/gocam/docs/geneOrganismRelationship__gene.md deleted file mode 100644 index 7071e06cd..000000000 --- a/projects/gocam/docs/geneOrganismRelationship__gene.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: gene - - - - -URI: [gocam:geneOrganismRelationship__gene](http://w3id.org/ontogpt/gocam/geneOrganismRelationship__gene) - - -## Domain and Range - -None → <sub>0..1</sub> [Gene](Gene.md) - -## Parents - - -## Children - - -## Used by - - * [GeneOrganismRelationship](GeneOrganismRelationship.md) diff --git a/projects/gocam/docs/geneOrganismRelationship__organism.md b/projects/gocam/docs/geneOrganismRelationship__organism.md deleted file mode 100644 index 80ad6c95a..000000000 --- a/projects/gocam/docs/geneOrganismRelationship__organism.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: organism - - - - -URI: [gocam:geneOrganismRelationship__organism](http://w3id.org/ontogpt/gocam/geneOrganismRelationship__organism) - - -## Domain and Range - -None → <sub>0..1</sub> [Organism](Organism.md) - -## Parents - - -## Children - - -## Used by - - * [GeneOrganismRelationship](GeneOrganismRelationship.md) diff --git a/projects/gocam/docs/geneSubcellularLocalizationRelationship__gene.md b/projects/gocam/docs/geneSubcellularLocalizationRelationship__gene.md deleted file mode 100644 index 719048841..000000000 --- a/projects/gocam/docs/geneSubcellularLocalizationRelationship__gene.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: gene - - - - -URI: [gocam:geneSubcellularLocalizationRelationship__gene](http://w3id.org/ontogpt/gocam/geneSubcellularLocalizationRelationship__gene) - - -## Domain and Range - -None → <sub>0..1</sub> [Gene](Gene.md) - -## Parents - - -## Children - - -## Used by - - * [GeneSubcellularLocalizationRelationship](GeneSubcellularLocalizationRelationship.md) diff --git a/projects/gocam/docs/geneSubcellularLocalizationRelationship__location.md b/projects/gocam/docs/geneSubcellularLocalizationRelationship__location.md deleted file mode 100644 index c5e53c56a..000000000 --- a/projects/gocam/docs/geneSubcellularLocalizationRelationship__location.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: location - - - - -URI: [gocam:geneSubcellularLocalizationRelationship__location](http://w3id.org/ontogpt/gocam/geneSubcellularLocalizationRelationship__location) - - -## Domain and Range - -None → <sub>0..1</sub> [GeneLocation](GeneLocation.md) - -## Parents - - -## Children - - -## Used by - - * [GeneSubcellularLocalizationRelationship](GeneSubcellularLocalizationRelationship.md) diff --git a/projects/gocam/docs/goCamAnnotations__activities.md b/projects/gocam/docs/goCamAnnotations__activities.md deleted file mode 100644 index bf256fa2a..000000000 --- a/projects/gocam/docs/goCamAnnotations__activities.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: activities - - -semicolon-separated list of molecular activities - -URI: [gocam:goCamAnnotations__activities](http://w3id.org/ontogpt/gocam/goCamAnnotations__activities) - - -## Domain and Range - -None → <sub>0..\*</sub> [MolecularActivity](MolecularActivity.md) - -## Parents - - -## Children - - -## Used by - - * [GoCamAnnotations](GoCamAnnotations.md) diff --git a/projects/gocam/docs/goCamAnnotations__cellular_processes.md b/projects/gocam/docs/goCamAnnotations__cellular_processes.md deleted file mode 100644 index bdd8d8787..000000000 --- a/projects/gocam/docs/goCamAnnotations__cellular_processes.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: cellular_processes - - -semicolon-separated list of cellular processes - -URI: [gocam:goCamAnnotations__cellular_processes](http://w3id.org/ontogpt/gocam/goCamAnnotations__cellular_processes) - - -## Domain and Range - -None → <sub>0..\*</sub> [CellularProcess](CellularProcess.md) - -## Parents - - -## Children - - -## Used by - - * [GoCamAnnotations](GoCamAnnotations.md) diff --git a/projects/gocam/docs/goCamAnnotations__gene_functions.md b/projects/gocam/docs/goCamAnnotations__gene_functions.md deleted file mode 100644 index 47da49890..000000000 --- a/projects/gocam/docs/goCamAnnotations__gene_functions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: gene_functions - - -semicolon-separated list of gene to molecular activity relationships - -URI: [gocam:goCamAnnotations__gene_functions](http://w3id.org/ontogpt/gocam/goCamAnnotations__gene_functions) - - -## Domain and Range - -None → <sub>0..\*</sub> [GeneMolecularActivityRelationship](GeneMolecularActivityRelationship.md) - -## Parents - - -## Children - - -## Used by - - * [GoCamAnnotations](GoCamAnnotations.md) diff --git a/projects/gocam/docs/goCamAnnotations__gene_gene_interactions.md b/projects/gocam/docs/goCamAnnotations__gene_gene_interactions.md deleted file mode 100644 index 5eb3bea2e..000000000 --- a/projects/gocam/docs/goCamAnnotations__gene_gene_interactions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: gene_gene_interactions - - -semicolon-separated list of gene to gene interactions - -URI: [gocam:goCamAnnotations__gene_gene_interactions](http://w3id.org/ontogpt/gocam/goCamAnnotations__gene_gene_interactions) - - -## Domain and Range - -None → <sub>0..\*</sub> [GeneGeneInteraction](GeneGeneInteraction.md) - -## Parents - - -## Children - - -## Used by - - * [GoCamAnnotations](GoCamAnnotations.md) diff --git a/projects/gocam/docs/goCamAnnotations__gene_localizations.md b/projects/gocam/docs/goCamAnnotations__gene_localizations.md deleted file mode 100644 index 6815039e0..000000000 --- a/projects/gocam/docs/goCamAnnotations__gene_localizations.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: gene_localizations - - -semicolon-separated list of genes plus their location in the cell; for example, "gene1 / cytoplasm; gene2 / mitochondrion" - -URI: [gocam:goCamAnnotations__gene_localizations](http://w3id.org/ontogpt/gocam/goCamAnnotations__gene_localizations) - - -## Domain and Range - -None → <sub>0..\*</sub> [GeneSubcellularLocalizationRelationship](GeneSubcellularLocalizationRelationship.md) - -## Parents - - -## Children - - -## Used by - - * [GoCamAnnotations](GoCamAnnotations.md) diff --git a/projects/gocam/docs/goCamAnnotations__gene_organisms.md b/projects/gocam/docs/goCamAnnotations__gene_organisms.md deleted file mode 100644 index 946e06471..000000000 --- a/projects/gocam/docs/goCamAnnotations__gene_organisms.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: gene_organisms - - - - -URI: [gocam:goCamAnnotations__gene_organisms](http://w3id.org/ontogpt/gocam/goCamAnnotations__gene_organisms) - - -## Domain and Range - -None → <sub>0..\*</sub> [GeneOrganismRelationship](GeneOrganismRelationship.md) - -## Parents - - -## Children - - -## Used by - - * [GoCamAnnotations](GoCamAnnotations.md) diff --git a/projects/gocam/docs/goCamAnnotations__genes.md b/projects/gocam/docs/goCamAnnotations__genes.md deleted file mode 100644 index c505077b7..000000000 --- a/projects/gocam/docs/goCamAnnotations__genes.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: genes - - -semicolon-separated list of genes - -URI: [gocam:goCamAnnotations__genes](http://w3id.org/ontogpt/gocam/goCamAnnotations__genes) - - -## Domain and Range - -None → <sub>0..\*</sub> [Gene](Gene.md) - -## Parents - - -## Children - - -## Used by - - * [GoCamAnnotations](GoCamAnnotations.md) diff --git a/projects/gocam/docs/goCamAnnotations__organisms.md b/projects/gocam/docs/goCamAnnotations__organisms.md deleted file mode 100644 index 9e4d3b2d5..000000000 --- a/projects/gocam/docs/goCamAnnotations__organisms.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: organisms - - -semicolon-separated list of organism taxons - -URI: [gocam:goCamAnnotations__organisms](http://w3id.org/ontogpt/gocam/goCamAnnotations__organisms) - - -## Domain and Range - -None → <sub>0..\*</sub> [Organism](Organism.md) - -## Parents - - -## Children - - -## Used by - - * [GoCamAnnotations](GoCamAnnotations.md) diff --git a/projects/gocam/docs/goCamAnnotations__pathways.md b/projects/gocam/docs/goCamAnnotations__pathways.md deleted file mode 100644 index 5c47b4bda..000000000 --- a/projects/gocam/docs/goCamAnnotations__pathways.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: pathways - - -semicolon-separated list of pathways - -URI: [gocam:goCamAnnotations__pathways](http://w3id.org/ontogpt/gocam/goCamAnnotations__pathways) - - -## Domain and Range - -None → <sub>0..\*</sub> [Pathway](Pathway.md) - -## Parents - - -## Children - - -## Used by - - * [GoCamAnnotations](GoCamAnnotations.md) diff --git a/projects/gocam/docs/gocam.md b/projects/gocam/docs/gocam.md deleted file mode 100644 index b13277173..000000000 --- a/projects/gocam/docs/gocam.md +++ /dev/null @@ -1,140 +0,0 @@ - -# gocam-template - - -**metamodel version:** 1.7.0 - -**version:** None - - -A template for GO-CAMs - - -### Classes - - * [AnnotatorResult](AnnotatorResult.md) - * [Any](Any.md) - * [CompoundExpression](CompoundExpression.md) - * [GeneGeneInteraction](GeneGeneInteraction.md) - * [GeneMolecularActivityRelationship](GeneMolecularActivityRelationship.md) - * [GeneMolecularActivityRelationship2](GeneMolecularActivityRelationship2.md) - * [GeneOrganismRelationship](GeneOrganismRelationship.md) - * [GeneSubcellularLocalizationRelationship](GeneSubcellularLocalizationRelationship.md) - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - * [ExtractionResult](ExtractionResult.md) - A result of extracting knowledge on text - * [GoCamAnnotations](GoCamAnnotations.md) - * [NamedEntity](NamedEntity.md) - * [CellularProcess](CellularProcess.md) - * [Gene](Gene.md) - * [GeneLocation](GeneLocation.md) - * [MolecularActivity](MolecularActivity.md) - * [Molecule](Molecule.md) - * [Organism](Organism.md) - * [Pathway](Pathway.md) - * [RelationshipType](RelationshipType.md) - * [Publication](Publication.md) - * [TextWithTriples](TextWithTriples.md) - -### Mixins - - -### Slots - - * [➞object_id](annotatorResult__object_id.md) - * [➞object_text](annotatorResult__object_text.md) - * [➞subject_text](annotatorResult__subject_text.md) - * [➞extracted_object](extractionResult__extracted_object.md) - The complex objects extracted from the text - * [➞input_id](extractionResult__input_id.md) - * [➞input_text](extractionResult__input_text.md) - * [➞input_title](extractionResult__input_title.md) - * [➞named_entities](extractionResult__named_entities.md) - Named entities extracted from the text - * [➞prompt](extractionResult__prompt.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) - * [➞gene1](geneGeneInteraction__gene1.md) - * [➞gene2](geneGeneInteraction__gene2.md) - * [➞gene](geneMolecularActivityRelationship2__gene.md) - * [➞molecular_activity](geneMolecularActivityRelationship2__molecular_activity.md) - * [➞target](geneMolecularActivityRelationship2__target.md) - * [➞gene](geneMolecularActivityRelationship__gene.md) - * [➞molecular_activity](geneMolecularActivityRelationship__molecular_activity.md) - * [➞gene](geneOrganismRelationship__gene.md) - * [➞organism](geneOrganismRelationship__organism.md) - * [➞gene](geneSubcellularLocalizationRelationship__gene.md) - * [➞location](geneSubcellularLocalizationRelationship__location.md) - * [➞activities](goCamAnnotations__activities.md) - semicolon-separated list of molecular activities - * [➞cellular_processes](goCamAnnotations__cellular_processes.md) - semicolon-separated list of cellular processes - * [➞gene_functions](goCamAnnotations__gene_functions.md) - semicolon-separated list of gene to molecular activity relationships - * [➞gene_gene_interactions](goCamAnnotations__gene_gene_interactions.md) - semicolon-separated list of gene to gene interactions - * [➞gene_localizations](goCamAnnotations__gene_localizations.md) - semicolon-separated list of genes plus their location in the cell; for example, "gene1 / cytoplasm; gene2 / mitochondrion" - * [➞gene_organisms](goCamAnnotations__gene_organisms.md) - * [➞genes](goCamAnnotations__genes.md) - semicolon-separated list of genes - * [➞organisms](goCamAnnotations__organisms.md) - semicolon-separated list of organism taxons - * [➞pathways](goCamAnnotations__pathways.md) - semicolon-separated list of pathways - * [➞id](namedEntity__id.md) - A unique identifier for the named entity - * [GeneLocation➞id](GeneLocation_id.md) - * [➞label](namedEntity__label.md) - The label (name) of the named thing - * [➞abstract](publication__abstract.md) - The abstract of the publication - * [➞combined_text](publication__combined_text.md) - * [➞full_text](publication__full_text.md) - The full text of the publication - * [➞id](publication__id.md) - The publication identifier - * [➞title](publication__title.md) - The title of the publication - * [➞publication](textWithTriples__publication.md) - * [➞triples](textWithTriples__triples.md) - * [➞object](triple__object.md) - * [➞object_qualifier](triple__object_qualifier.md) - An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * [➞predicate](triple__predicate.md) - * [➞qualifier](triple__qualifier.md) - A qualifier for the statements, e.g. "NOT" for negation - * [➞subject](triple__subject.md) - * [➞subject_qualifier](triple__subject_qualifier.md) - An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -### Enums - - * [CellType](CellType.md) - * [GOCellComponentType](GOCellComponentType.md) - * [GeneLocationEnum](GeneLocationEnum.md) - * [NullDataOptions](NullDataOptions.md) - -### Subsets - - -### Types - - -#### Built in - - * **Bool** - * **Curie** - * **Decimal** - * **ElementIdentifier** - * **NCName** - * **NodeIdentifier** - * **URI** - * **URIorCURIE** - * **XSDDate** - * **XSDDateTime** - * **XSDTime** - * **float** - * **int** - * **str** - -#### Defined - - * [Boolean](types/Boolean.md) (**Bool**) - A binary (true or false) value - * [Curie](types/Curie.md) (**Curie**) - a compact URI - * [Date](types/Date.md) (**XSDDate**) - a date (year, month and day) in an idealized calendar - * [DateOrDatetime](types/DateOrDatetime.md) (**str**) - Either a date or a datetime - * [Datetime](types/Datetime.md) (**XSDDateTime**) - The combination of a date and time - * [Decimal](types/Decimal.md) (**Decimal**) - A real number with arbitrary precision that conforms to the xsd:decimal specification - * [Double](types/Double.md) (**float**) - A real number that conforms to the xsd:double specification - * [Float](types/Float.md) (**float**) - A real number that conforms to the xsd:float specification - * [Integer](types/Integer.md) (**int**) - An integer - * [Jsonpath](types/Jsonpath.md) (**str**) - A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - * [Jsonpointer](types/Jsonpointer.md) (**str**) - A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - * [Ncname](types/Ncname.md) (**NCName**) - Prefix part of CURIE - * [Nodeidentifier](types/Nodeidentifier.md) (**NodeIdentifier**) - A URI, CURIE or BNODE that represents a node in a model. - * [Objectidentifier](types/Objectidentifier.md) (**ElementIdentifier**) - A URI or CURIE that represents an object in the model. - * [Sparqlpath](types/Sparqlpath.md) (**str**) - A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - * [String](types/String.md) (**str**) - A character string - * [Time](types/Time.md) (**XSDTime**) - A time object represents a (local) time of day, independent of any particular day - * [Uri](types/Uri.md) (**URI**) - a complete URI - * [Uriorcurie](types/Uriorcurie.md) (**URIorCURIE**) - a URI or a CURIE diff --git a/projects/gocam/docs/namedEntity__id.md b/projects/gocam/docs/namedEntity__id.md deleted file mode 100644 index 0555a9f73..000000000 --- a/projects/gocam/docs/namedEntity__id.md +++ /dev/null @@ -1,37 +0,0 @@ - -# Slot: id - - -A unique identifier for the named entity - -URI: [gocam:namedEntity__id](http://w3id.org/ontogpt/gocam/namedEntity__id) - - -## Domain and Range - -None → <sub>1..1</sub> [String](types/String.md) - -## Parents - - -## Children - - * [GeneLocation➞id](GeneLocation_id.md) - -## Used by - - * [CellularProcess](CellularProcess.md) - * [Gene](Gene.md) - * [MolecularActivity](MolecularActivity.md) - * [Molecule](Molecule.md) - * [NamedEntity](NamedEntity.md) - * [Organism](Organism.md) - * [Pathway](Pathway.md) - * [RelationshipType](RelationshipType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | this is populated during the grounding and normalization step | - diff --git a/projects/gocam/docs/namedEntity__label.md b/projects/gocam/docs/namedEntity__label.md deleted file mode 100644 index 2b599b1cc..000000000 --- a/projects/gocam/docs/namedEntity__label.md +++ /dev/null @@ -1,38 +0,0 @@ - -# Slot: label - - -The label (name) of the named thing - -URI: [gocam:namedEntity__label](http://w3id.org/ontogpt/gocam/namedEntity__label) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [CellularProcess](CellularProcess.md) - * [Gene](Gene.md) - * [GeneLocation](GeneLocation.md) - * [MolecularActivity](MolecularActivity.md) - * [Molecule](Molecule.md) - * [NamedEntity](NamedEntity.md) - * [Organism](Organism.md) - * [Pathway](Pathway.md) - * [RelationshipType](RelationshipType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Aliases:** | | name | -| **Mappings:** | | rdfs:label | - diff --git a/projects/gocam/docs/publication__abstract.md b/projects/gocam/docs/publication__abstract.md deleted file mode 100644 index dd434bed1..000000000 --- a/projects/gocam/docs/publication__abstract.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: abstract - - -The abstract of the publication - -URI: [gocam:publication__abstract](http://w3id.org/ontogpt/gocam/publication__abstract) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/gocam/docs/publication__combined_text.md b/projects/gocam/docs/publication__combined_text.md deleted file mode 100644 index 128ca7aed..000000000 --- a/projects/gocam/docs/publication__combined_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: combined_text - - - - -URI: [gocam:publication__combined_text](http://w3id.org/ontogpt/gocam/publication__combined_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/gocam/docs/publication__full_text.md b/projects/gocam/docs/publication__full_text.md deleted file mode 100644 index be255126c..000000000 --- a/projects/gocam/docs/publication__full_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: full_text - - -The full text of the publication - -URI: [gocam:publication__full_text](http://w3id.org/ontogpt/gocam/publication__full_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/gocam/docs/publication__id.md b/projects/gocam/docs/publication__id.md deleted file mode 100644 index 583585698..000000000 --- a/projects/gocam/docs/publication__id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: id - - -The publication identifier - -URI: [gocam:publication__id](http://w3id.org/ontogpt/gocam/publication__id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/gocam/docs/publication__title.md b/projects/gocam/docs/publication__title.md deleted file mode 100644 index af7b52d3f..000000000 --- a/projects/gocam/docs/publication__title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: title - - -The title of the publication - -URI: [gocam:publication__title](http://w3id.org/ontogpt/gocam/publication__title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/gocam/docs/textWithTriples__publication.md b/projects/gocam/docs/textWithTriples__publication.md deleted file mode 100644 index f2480d2c2..000000000 --- a/projects/gocam/docs/textWithTriples__publication.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: publication - - - - -URI: [gocam:textWithTriples__publication](http://w3id.org/ontogpt/gocam/textWithTriples__publication) - - -## Domain and Range - -None → <sub>0..1</sub> [Publication](Publication.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/gocam/docs/textWithTriples__triples.md b/projects/gocam/docs/textWithTriples__triples.md deleted file mode 100644 index 8fe102100..000000000 --- a/projects/gocam/docs/textWithTriples__triples.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: triples - - - - -URI: [gocam:textWithTriples__triples](http://w3id.org/ontogpt/gocam/textWithTriples__triples) - - -## Domain and Range - -None → <sub>0..\*</sub> [Triple](Triple.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/gocam/docs/triple__object.md b/projects/gocam/docs/triple__object.md deleted file mode 100644 index 38e4c4c25..000000000 --- a/projects/gocam/docs/triple__object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object - - - - -URI: [gocam:triple__object](http://w3id.org/ontogpt/gocam/triple__object) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/gocam/docs/triple__object_qualifier.md b/projects/gocam/docs/triple__object_qualifier.md deleted file mode 100644 index 21bae818d..000000000 --- a/projects/gocam/docs/triple__object_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_qualifier - - -An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - -URI: [gocam:triple__object_qualifier](http://w3id.org/ontogpt/gocam/triple__object_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/gocam/docs/triple__predicate.md b/projects/gocam/docs/triple__predicate.md deleted file mode 100644 index 3c7c729c3..000000000 --- a/projects/gocam/docs/triple__predicate.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: predicate - - - - -URI: [gocam:triple__predicate](http://w3id.org/ontogpt/gocam/triple__predicate) - - -## Domain and Range - -None → <sub>0..1</sub> [RelationshipType](RelationshipType.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/gocam/docs/triple__qualifier.md b/projects/gocam/docs/triple__qualifier.md deleted file mode 100644 index 7f62d89e8..000000000 --- a/projects/gocam/docs/triple__qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: qualifier - - -A qualifier for the statements, e.g. "NOT" for negation - -URI: [gocam:triple__qualifier](http://w3id.org/ontogpt/gocam/triple__qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/gocam/docs/triple__subject.md b/projects/gocam/docs/triple__subject.md deleted file mode 100644 index 9b9ece18a..000000000 --- a/projects/gocam/docs/triple__subject.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject - - - - -URI: [gocam:triple__subject](http://w3id.org/ontogpt/gocam/triple__subject) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/gocam/docs/triple__subject_qualifier.md b/projects/gocam/docs/triple__subject_qualifier.md deleted file mode 100644 index 588c54157..000000000 --- a/projects/gocam/docs/triple__subject_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_qualifier - - -An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -URI: [gocam:triple__subject_qualifier](http://w3id.org/ontogpt/gocam/triple__subject_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/gocam/docs/types/Boolean.md b/projects/gocam/docs/types/Boolean.md deleted file mode 100644 index dc83a9c6e..000000000 --- a/projects/gocam/docs/types/Boolean.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: boolean - - -A binary (true or false) value - -URI: [linkml:Boolean](https://w3id.org/linkml/Boolean) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Bool** | -| Representation | | bool | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Boolean | - diff --git a/projects/gocam/docs/types/Curie.md b/projects/gocam/docs/types/Curie.md deleted file mode 100644 index c1803f93f..000000000 --- a/projects/gocam/docs/types/Curie.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: curie - - -a compact URI - -URI: [linkml:Curie](https://w3id.org/linkml/Curie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Curie** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations this MUST be expanded to a URI | -| | | in non-RDF serializations MAY be serialized as the compact representation | - diff --git a/projects/gocam/docs/types/Date.md b/projects/gocam/docs/types/Date.md deleted file mode 100644 index 06948af97..000000000 --- a/projects/gocam/docs/types/Date.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: date - - -a date (year, month and day) in an idealized calendar - -URI: [linkml:Date](https://w3id.org/linkml/Date) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDate** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Date | - diff --git a/projects/gocam/docs/types/DateOrDatetime.md b/projects/gocam/docs/types/DateOrDatetime.md deleted file mode 100644 index ef983898d..000000000 --- a/projects/gocam/docs/types/DateOrDatetime.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: date_or_datetime - - -Either a date or a datetime - -URI: [linkml:DateOrDatetime](https://w3id.org/linkml/DateOrDatetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/gocam/docs/types/Datetime.md b/projects/gocam/docs/types/Datetime.md deleted file mode 100644 index 9510454a8..000000000 --- a/projects/gocam/docs/types/Datetime.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: datetime - - -The combination of a date and time - -URI: [linkml:Datetime](https://w3id.org/linkml/Datetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDateTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:DateTime | - diff --git a/projects/gocam/docs/types/Decimal.md b/projects/gocam/docs/types/Decimal.md deleted file mode 100644 index a7ba14a5d..000000000 --- a/projects/gocam/docs/types/Decimal.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: decimal - - -A real number with arbitrary precision that conforms to the xsd:decimal specification - -URI: [linkml:Decimal](https://w3id.org/linkml/Decimal) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Decimal** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Broad Mappings:** | | schema:Number | - diff --git a/projects/gocam/docs/types/Double.md b/projects/gocam/docs/types/Double.md deleted file mode 100644 index cfe6d71e2..000000000 --- a/projects/gocam/docs/types/Double.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: double - - -A real number that conforms to the xsd:double specification - -URI: [linkml:Double](https://w3id.org/linkml/Double) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Close Mappings:** | | schema:Float | - diff --git a/projects/gocam/docs/types/Float.md b/projects/gocam/docs/types/Float.md deleted file mode 100644 index 7b303f96f..000000000 --- a/projects/gocam/docs/types/Float.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: float - - -A real number that conforms to the xsd:float specification - -URI: [linkml:Float](https://w3id.org/linkml/Float) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Float | - diff --git a/projects/gocam/docs/types/Integer.md b/projects/gocam/docs/types/Integer.md deleted file mode 100644 index 3cfcc66d9..000000000 --- a/projects/gocam/docs/types/Integer.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: integer - - -An integer - -URI: [linkml:Integer](https://w3id.org/linkml/Integer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **int** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Integer | - diff --git a/projects/gocam/docs/types/Jsonpath.md b/projects/gocam/docs/types/Jsonpath.md deleted file mode 100644 index a03a58e67..000000000 --- a/projects/gocam/docs/types/Jsonpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpath - - -A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpath](https://w3id.org/linkml/Jsonpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/gocam/docs/types/Jsonpointer.md b/projects/gocam/docs/types/Jsonpointer.md deleted file mode 100644 index a0e1ac492..000000000 --- a/projects/gocam/docs/types/Jsonpointer.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpointer - - -A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpointer](https://w3id.org/linkml/Jsonpointer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/gocam/docs/types/Ncname.md b/projects/gocam/docs/types/Ncname.md deleted file mode 100644 index 710b0b04a..000000000 --- a/projects/gocam/docs/types/Ncname.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: ncname - - -Prefix part of CURIE - -URI: [linkml:Ncname](https://w3id.org/linkml/Ncname) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NCName** | -| Representation | | str | diff --git a/projects/gocam/docs/types/Nodeidentifier.md b/projects/gocam/docs/types/Nodeidentifier.md deleted file mode 100644 index f0097cdf4..000000000 --- a/projects/gocam/docs/types/Nodeidentifier.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: nodeidentifier - - -A URI, CURIE or BNODE that represents a node in a model. - -URI: [linkml:Nodeidentifier](https://w3id.org/linkml/Nodeidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NodeIdentifier** | -| Representation | | str | diff --git a/projects/gocam/docs/types/Objectidentifier.md b/projects/gocam/docs/types/Objectidentifier.md deleted file mode 100644 index 454ba6be6..000000000 --- a/projects/gocam/docs/types/Objectidentifier.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: objectidentifier - - -A URI or CURIE that represents an object in the model. - -URI: [linkml:Objectidentifier](https://w3id.org/linkml/Objectidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **ElementIdentifier** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | Used for inheritance and type checking | - diff --git a/projects/gocam/docs/types/Sparqlpath.md b/projects/gocam/docs/types/Sparqlpath.md deleted file mode 100644 index fd99a927e..000000000 --- a/projects/gocam/docs/types/Sparqlpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: sparqlpath - - -A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - -URI: [linkml:Sparqlpath](https://w3id.org/linkml/Sparqlpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/gocam/docs/types/String.md b/projects/gocam/docs/types/String.md deleted file mode 100644 index 6e61d7081..000000000 --- a/projects/gocam/docs/types/String.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: string - - -A character string - -URI: [linkml:String](https://w3id.org/linkml/String) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Text | - diff --git a/projects/gocam/docs/types/Time.md b/projects/gocam/docs/types/Time.md deleted file mode 100644 index 2b8652bcd..000000000 --- a/projects/gocam/docs/types/Time.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: time - - -A time object represents a (local) time of day, independent of any particular day - -URI: [linkml:Time](https://w3id.org/linkml/Time) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Time | - diff --git a/projects/gocam/docs/types/Uri.md b/projects/gocam/docs/types/Uri.md deleted file mode 100644 index 343807a5e..000000000 --- a/projects/gocam/docs/types/Uri.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: uri - - -a complete URI - -URI: [linkml:Uri](https://w3id.org/linkml/Uri) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URI** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node | -| **Close Mappings:** | | schema:URL | - diff --git a/projects/gocam/docs/types/Uriorcurie.md b/projects/gocam/docs/types/Uriorcurie.md deleted file mode 100644 index 2f7b65087..000000000 --- a/projects/gocam/docs/types/Uriorcurie.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: uriorcurie - - -a URI or a CURIE - -URI: [linkml:Uriorcurie](https://w3id.org/linkml/Uriorcurie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URIorCURIE** | -| Representation | | str | diff --git a/projects/gocam/excel/gocam.xlsx b/projects/gocam/excel/gocam.xlsx deleted file mode 100644 index c51f66c3a..000000000 Binary files a/projects/gocam/excel/gocam.xlsx and /dev/null differ diff --git a/projects/gocam/gocam.py b/projects/gocam/gocam.py deleted file mode 100644 index ee7727d40..000000000 --- a/projects/gocam/gocam.py +++ /dev/null @@ -1,794 +0,0 @@ -# Auto generated from gocam.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-08-07T10:53:47 -# Schema: gocam-template -# -# id: http://w3id.org/ontogpt/gocam -# description: A template for GO-CAMs -# license: https://creativecommons.org/publicdomain/zero/1.0/ - -import dataclasses -import sys -import re -from jsonasobj2 import JsonObj, as_dict -from typing import Optional, List, Union, Dict, ClassVar, Any -from dataclasses import dataclass -from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions - -from linkml_runtime.utils.slot import Slot -from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode -from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int -from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs -from linkml_runtime.utils.formatutils import camelcase, underscore, sfx -from linkml_runtime.utils.enumerations import EnumDefinitionImpl -from rdflib import Namespace, URIRef -from linkml_runtime.utils.curienamespace import CurieNamespace -from linkml_runtime.linkml_model.types import String - -metamodel_version = "1.7.0" -version = None - -# Overwrite dataclasses _init_fn to add **kwargs in __init__ -dataclasses._init_fn = dataclasses_init_fn_with_kwargs - -# Namespaces -CHEBI = CurieNamespace('CHEBI', 'http://example.org/UNKNOWN/CHEBI/') -CL = CurieNamespace('CL', 'http://purl.obolibrary.org/obo/CL_') -EFO = CurieNamespace('EFO', 'http://example.org/UNKNOWN/EFO/') -GO = CurieNamespace('GO', 'http://purl.obolibrary.org/obo/GO_') -HGNC = CurieNamespace('HGNC', 'http://example.org/UNKNOWN/HGNC/') -NCBITAXON = CurieNamespace('NCBITaxon', 'http://example.org/UNKNOWN/NCBITaxon/') -PR = CurieNamespace('PR', 'http://example.org/UNKNOWN/PR/') -PW = CurieNamespace('PW', 'http://example.org/UNKNOWN/PW/') -RO = CurieNamespace('RO', 'http://purl.obolibrary.org/obo/RO_') -UBERON = CurieNamespace('UBERON', 'http://example.org/UNKNOWN/UBERON/') -UNIPROTKB = CurieNamespace('UniProtKB', 'http://example.org/UNKNOWN/UniProtKB/') -BIOLINK = CurieNamespace('biolink', 'http://example.org/UNKNOWN/biolink/') -CORE = CurieNamespace('core', 'http://w3id.org/ontogpt/core/') -GOCAM = CurieNamespace('gocam', 'http://w3id.org/ontogpt/gocam/') -LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') -RDFS = CurieNamespace('rdfs', 'http://example.org/UNKNOWN/rdfs/') -DEFAULT_ = GOCAM - - -# Types - -# Class references -class NamedEntityId(extended_str): - pass - - -class GeneId(NamedEntityId): - pass - - -class PathwayId(NamedEntityId): - pass - - -class CellularProcessId(NamedEntityId): - pass - - -class MolecularActivityId(NamedEntityId): - pass - - -class GeneLocationId(NamedEntityId): - pass - - -class OrganismId(NamedEntityId): - pass - - -class MoleculeId(NamedEntityId): - pass - - -class RelationshipTypeId(NamedEntityId): - pass - - -@dataclass -class GoCamAnnotations(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = GOCAM.GoCamAnnotations - class_class_curie: ClassVar[str] = "gocam:GoCamAnnotations" - class_name: ClassVar[str] = "GoCamAnnotations" - class_model_uri: ClassVar[URIRef] = GOCAM.GoCamAnnotations - - genes: Optional[Union[Union[str, GeneId], List[Union[str, GeneId]]]] = empty_list() - organisms: Optional[Union[Union[str, OrganismId], List[Union[str, OrganismId]]]] = empty_list() - gene_organisms: Optional[Union[Union[dict, "GeneOrganismRelationship"], List[Union[dict, "GeneOrganismRelationship"]]]] = empty_list() - activities: Optional[Union[Union[str, MolecularActivityId], List[Union[str, MolecularActivityId]]]] = empty_list() - gene_functions: Optional[Union[Union[dict, "GeneMolecularActivityRelationship"], List[Union[dict, "GeneMolecularActivityRelationship"]]]] = empty_list() - cellular_processes: Optional[Union[Union[str, CellularProcessId], List[Union[str, CellularProcessId]]]] = empty_list() - pathways: Optional[Union[Union[str, PathwayId], List[Union[str, PathwayId]]]] = empty_list() - gene_gene_interactions: Optional[Union[Union[dict, "GeneGeneInteraction"], List[Union[dict, "GeneGeneInteraction"]]]] = empty_list() - gene_localizations: Optional[Union[Union[dict, "GeneSubcellularLocalizationRelationship"], List[Union[dict, "GeneSubcellularLocalizationRelationship"]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if not isinstance(self.genes, list): - self.genes = [self.genes] if self.genes is not None else [] - self.genes = [v if isinstance(v, GeneId) else GeneId(v) for v in self.genes] - - if not isinstance(self.organisms, list): - self.organisms = [self.organisms] if self.organisms is not None else [] - self.organisms = [v if isinstance(v, OrganismId) else OrganismId(v) for v in self.organisms] - - if not isinstance(self.gene_organisms, list): - self.gene_organisms = [self.gene_organisms] if self.gene_organisms is not None else [] - self.gene_organisms = [v if isinstance(v, GeneOrganismRelationship) else GeneOrganismRelationship(**as_dict(v)) for v in self.gene_organisms] - - if not isinstance(self.activities, list): - self.activities = [self.activities] if self.activities is not None else [] - self.activities = [v if isinstance(v, MolecularActivityId) else MolecularActivityId(v) for v in self.activities] - - if not isinstance(self.gene_functions, list): - self.gene_functions = [self.gene_functions] if self.gene_functions is not None else [] - self.gene_functions = [v if isinstance(v, GeneMolecularActivityRelationship) else GeneMolecularActivityRelationship(**as_dict(v)) for v in self.gene_functions] - - if not isinstance(self.cellular_processes, list): - self.cellular_processes = [self.cellular_processes] if self.cellular_processes is not None else [] - self.cellular_processes = [v if isinstance(v, CellularProcessId) else CellularProcessId(v) for v in self.cellular_processes] - - if not isinstance(self.pathways, list): - self.pathways = [self.pathways] if self.pathways is not None else [] - self.pathways = [v if isinstance(v, PathwayId) else PathwayId(v) for v in self.pathways] - - if not isinstance(self.gene_gene_interactions, list): - self.gene_gene_interactions = [self.gene_gene_interactions] if self.gene_gene_interactions is not None else [] - self.gene_gene_interactions = [v if isinstance(v, GeneGeneInteraction) else GeneGeneInteraction(**as_dict(v)) for v in self.gene_gene_interactions] - - if not isinstance(self.gene_localizations, list): - self.gene_localizations = [self.gene_localizations] if self.gene_localizations is not None else [] - self.gene_localizations = [v if isinstance(v, GeneSubcellularLocalizationRelationship) else GeneSubcellularLocalizationRelationship(**as_dict(v)) for v in self.gene_localizations] - - super().__post_init__(**kwargs) - - -Any = Any - -@dataclass -class ExtractionResult(YAMLRoot): - """ - A result of extracting knowledge on text - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.ExtractionResult - class_class_curie: ClassVar[str] = "core:ExtractionResult" - class_name: ClassVar[str] = "ExtractionResult" - class_model_uri: ClassVar[URIRef] = GOCAM.ExtractionResult - - input_id: Optional[str] = None - input_title: Optional[str] = None - input_text: Optional[str] = None - raw_completion_output: Optional[str] = None - prompt: Optional[str] = None - extracted_object: Optional[Union[dict, Any]] = None - named_entities: Optional[Union[Union[dict, Any], List[Union[dict, Any]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.input_id is not None and not isinstance(self.input_id, str): - self.input_id = str(self.input_id) - - if self.input_title is not None and not isinstance(self.input_title, str): - self.input_title = str(self.input_title) - - if self.input_text is not None and not isinstance(self.input_text, str): - self.input_text = str(self.input_text) - - if self.raw_completion_output is not None and not isinstance(self.raw_completion_output, str): - self.raw_completion_output = str(self.raw_completion_output) - - if self.prompt is not None and not isinstance(self.prompt, str): - self.prompt = str(self.prompt) - - super().__post_init__(**kwargs) - - -@dataclass -class NamedEntity(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.NamedEntity - class_class_curie: ClassVar[str] = "core:NamedEntity" - class_name: ClassVar[str] = "NamedEntity" - class_model_uri: ClassVar[URIRef] = GOCAM.NamedEntity - - id: Union[str, NamedEntityId] = None - label: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, NamedEntityId): - self.id = NamedEntityId(self.id) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - super().__post_init__(**kwargs) - - -@dataclass -class Gene(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = GOCAM.Gene - class_class_curie: ClassVar[str] = "gocam:Gene" - class_name: ClassVar[str] = "Gene" - class_model_uri: ClassVar[URIRef] = GOCAM.Gene - - id: Union[str, GeneId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, GeneId): - self.id = GeneId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Pathway(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = GOCAM.Pathway - class_class_curie: ClassVar[str] = "gocam:Pathway" - class_name: ClassVar[str] = "Pathway" - class_model_uri: ClassVar[URIRef] = GOCAM.Pathway - - id: Union[str, PathwayId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, PathwayId): - self.id = PathwayId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class CellularProcess(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = GOCAM.CellularProcess - class_class_curie: ClassVar[str] = "gocam:CellularProcess" - class_name: ClassVar[str] = "CellularProcess" - class_model_uri: ClassVar[URIRef] = GOCAM.CellularProcess - - id: Union[str, CellularProcessId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, CellularProcessId): - self.id = CellularProcessId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class MolecularActivity(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = GOCAM.MolecularActivity - class_class_curie: ClassVar[str] = "gocam:MolecularActivity" - class_name: ClassVar[str] = "MolecularActivity" - class_model_uri: ClassVar[URIRef] = GOCAM.MolecularActivity - - id: Union[str, MolecularActivityId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, MolecularActivityId): - self.id = MolecularActivityId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class GeneLocation(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = GOCAM.GeneLocation - class_class_curie: ClassVar[str] = "gocam:GeneLocation" - class_name: ClassVar[str] = "GeneLocation" - class_model_uri: ClassVar[URIRef] = GOCAM.GeneLocation - - id: Union[str, GeneLocationId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, GeneLocationId): - self.id = GeneLocationId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Organism(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = GOCAM.Organism - class_class_curie: ClassVar[str] = "gocam:Organism" - class_name: ClassVar[str] = "Organism" - class_model_uri: ClassVar[URIRef] = GOCAM.Organism - - id: Union[str, OrganismId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, OrganismId): - self.id = OrganismId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Molecule(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = GOCAM.Molecule - class_class_curie: ClassVar[str] = "gocam:Molecule" - class_name: ClassVar[str] = "Molecule" - class_model_uri: ClassVar[URIRef] = GOCAM.Molecule - - id: Union[str, MoleculeId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, MoleculeId): - self.id = MoleculeId(self.id) - - super().__post_init__(**kwargs) - - -class CompoundExpression(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.CompoundExpression - class_class_curie: ClassVar[str] = "core:CompoundExpression" - class_name: ClassVar[str] = "CompoundExpression" - class_model_uri: ClassVar[URIRef] = GOCAM.CompoundExpression - - -@dataclass -class GeneOrganismRelationship(CompoundExpression): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = GOCAM.GeneOrganismRelationship - class_class_curie: ClassVar[str] = "gocam:GeneOrganismRelationship" - class_name: ClassVar[str] = "GeneOrganismRelationship" - class_model_uri: ClassVar[URIRef] = GOCAM.GeneOrganismRelationship - - gene: Optional[Union[str, GeneId]] = None - organism: Optional[Union[str, OrganismId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.gene is not None and not isinstance(self.gene, GeneId): - self.gene = GeneId(self.gene) - - if self.organism is not None and not isinstance(self.organism, OrganismId): - self.organism = OrganismId(self.organism) - - super().__post_init__(**kwargs) - - -@dataclass -class GeneMolecularActivityRelationship(CompoundExpression): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = GOCAM.GeneMolecularActivityRelationship - class_class_curie: ClassVar[str] = "gocam:GeneMolecularActivityRelationship" - class_name: ClassVar[str] = "GeneMolecularActivityRelationship" - class_model_uri: ClassVar[URIRef] = GOCAM.GeneMolecularActivityRelationship - - gene: Optional[Union[str, GeneId]] = None - molecular_activity: Optional[Union[str, MolecularActivityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.gene is not None and not isinstance(self.gene, GeneId): - self.gene = GeneId(self.gene) - - if self.molecular_activity is not None and not isinstance(self.molecular_activity, MolecularActivityId): - self.molecular_activity = MolecularActivityId(self.molecular_activity) - - super().__post_init__(**kwargs) - - -@dataclass -class GeneMolecularActivityRelationship2(CompoundExpression): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = GOCAM.GeneMolecularActivityRelationship2 - class_class_curie: ClassVar[str] = "gocam:GeneMolecularActivityRelationship2" - class_name: ClassVar[str] = "GeneMolecularActivityRelationship2" - class_model_uri: ClassVar[URIRef] = GOCAM.GeneMolecularActivityRelationship2 - - gene: Optional[Union[str, GeneId]] = None - molecular_activity: Optional[Union[str, MolecularActivityId]] = None - target: Optional[Union[str, MoleculeId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.gene is not None and not isinstance(self.gene, GeneId): - self.gene = GeneId(self.gene) - - if self.molecular_activity is not None and not isinstance(self.molecular_activity, MolecularActivityId): - self.molecular_activity = MolecularActivityId(self.molecular_activity) - - if self.target is not None and not isinstance(self.target, MoleculeId): - self.target = MoleculeId(self.target) - - super().__post_init__(**kwargs) - - -@dataclass -class GeneSubcellularLocalizationRelationship(CompoundExpression): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = GOCAM.GeneSubcellularLocalizationRelationship - class_class_curie: ClassVar[str] = "gocam:GeneSubcellularLocalizationRelationship" - class_name: ClassVar[str] = "GeneSubcellularLocalizationRelationship" - class_model_uri: ClassVar[URIRef] = GOCAM.GeneSubcellularLocalizationRelationship - - gene: Optional[Union[str, GeneId]] = None - location: Optional[Union[str, GeneLocationId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.gene is not None and not isinstance(self.gene, GeneId): - self.gene = GeneId(self.gene) - - if self.location is not None and not isinstance(self.location, GeneLocationId): - self.location = GeneLocationId(self.location) - - super().__post_init__(**kwargs) - - -@dataclass -class GeneGeneInteraction(CompoundExpression): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = GOCAM.GeneGeneInteraction - class_class_curie: ClassVar[str] = "gocam:GeneGeneInteraction" - class_name: ClassVar[str] = "GeneGeneInteraction" - class_model_uri: ClassVar[URIRef] = GOCAM.GeneGeneInteraction - - gene1: Optional[Union[str, GeneId]] = None - gene2: Optional[Union[str, GeneId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.gene1 is not None and not isinstance(self.gene1, GeneId): - self.gene1 = GeneId(self.gene1) - - if self.gene2 is not None and not isinstance(self.gene2, GeneId): - self.gene2 = GeneId(self.gene2) - - super().__post_init__(**kwargs) - - -@dataclass -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Triple - class_class_curie: ClassVar[str] = "core:Triple" - class_name: ClassVar[str] = "Triple" - class_model_uri: ClassVar[URIRef] = GOCAM.Triple - - subject: Optional[Union[str, NamedEntityId]] = None - predicate: Optional[Union[str, RelationshipTypeId]] = None - object: Optional[Union[str, NamedEntityId]] = None - qualifier: Optional[str] = None - subject_qualifier: Optional[Union[str, NamedEntityId]] = None - object_qualifier: Optional[Union[str, NamedEntityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, NamedEntityId): - self.subject = NamedEntityId(self.subject) - - if self.predicate is not None and not isinstance(self.predicate, RelationshipTypeId): - self.predicate = RelationshipTypeId(self.predicate) - - if self.object is not None and not isinstance(self.object, NamedEntityId): - self.object = NamedEntityId(self.object) - - if self.qualifier is not None and not isinstance(self.qualifier, str): - self.qualifier = str(self.qualifier) - - if self.subject_qualifier is not None and not isinstance(self.subject_qualifier, NamedEntityId): - self.subject_qualifier = NamedEntityId(self.subject_qualifier) - - if self.object_qualifier is not None and not isinstance(self.object_qualifier, NamedEntityId): - self.object_qualifier = NamedEntityId(self.object_qualifier) - - super().__post_init__(**kwargs) - - -@dataclass -class TextWithTriples(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.TextWithTriples - class_class_curie: ClassVar[str] = "core:TextWithTriples" - class_name: ClassVar[str] = "TextWithTriples" - class_model_uri: ClassVar[URIRef] = GOCAM.TextWithTriples - - publication: Optional[Union[dict, "Publication"]] = None - triples: Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.publication is not None and not isinstance(self.publication, Publication): - self.publication = Publication(**as_dict(self.publication)) - - if not isinstance(self.triples, list): - self.triples = [self.triples] if self.triples is not None else [] - self.triples = [v if isinstance(v, Triple) else Triple(**as_dict(v)) for v in self.triples] - - super().__post_init__(**kwargs) - - -@dataclass -class RelationshipType(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.RelationshipType - class_class_curie: ClassVar[str] = "core:RelationshipType" - class_name: ClassVar[str] = "RelationshipType" - class_model_uri: ClassVar[URIRef] = GOCAM.RelationshipType - - id: Union[str, RelationshipTypeId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, RelationshipTypeId): - self.id = RelationshipTypeId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Publication(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Publication - class_class_curie: ClassVar[str] = "core:Publication" - class_name: ClassVar[str] = "Publication" - class_model_uri: ClassVar[URIRef] = GOCAM.Publication - - id: Optional[str] = None - title: Optional[str] = None - abstract: Optional[str] = None - combined_text: Optional[str] = None - full_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.id is not None and not isinstance(self.id, str): - self.id = str(self.id) - - if self.title is not None and not isinstance(self.title, str): - self.title = str(self.title) - - if self.abstract is not None and not isinstance(self.abstract, str): - self.abstract = str(self.abstract) - - if self.combined_text is not None and not isinstance(self.combined_text, str): - self.combined_text = str(self.combined_text) - - if self.full_text is not None and not isinstance(self.full_text, str): - self.full_text = str(self.full_text) - - super().__post_init__(**kwargs) - - -@dataclass -class AnnotatorResult(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.AnnotatorResult - class_class_curie: ClassVar[str] = "core:AnnotatorResult" - class_name: ClassVar[str] = "AnnotatorResult" - class_model_uri: ClassVar[URIRef] = GOCAM.AnnotatorResult - - subject_text: Optional[str] = None - object_id: Optional[str] = None - object_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject_text is not None and not isinstance(self.subject_text, str): - self.subject_text = str(self.subject_text) - - if self.object_id is not None and not isinstance(self.object_id, str): - self.object_id = str(self.object_id) - - if self.object_text is not None and not isinstance(self.object_text, str): - self.object_text = str(self.object_text) - - super().__post_init__(**kwargs) - - -# Enumerations -class GeneLocationEnum(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="GeneLocationEnum", - ) - -class GOCellComponentType(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="GOCellComponentType", - ) - -class CellType(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="CellType", - ) - -class NullDataOptions(EnumDefinitionImpl): - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = PermissibleValue(text="UNSPECIFIED_METHOD_OF_ADMINISTRATION", - meaning=NCIT.C149701) - NOT_APPLICABLE = PermissibleValue(text="NOT_APPLICABLE", - meaning=NCIT.C18902) - NOT_MENTIONED = PermissibleValue(text="NOT_MENTIONED") - - _defn = EnumDefinition( - name="NullDataOptions", - ) - -# Slots -class slots: - pass - -slots.goCamAnnotations__genes = Slot(uri=GOCAM.genes, name="goCamAnnotations__genes", curie=GOCAM.curie('genes'), - model_uri=GOCAM.goCamAnnotations__genes, domain=None, range=Optional[Union[Union[str, GeneId], List[Union[str, GeneId]]]]) - -slots.goCamAnnotations__organisms = Slot(uri=GOCAM.organisms, name="goCamAnnotations__organisms", curie=GOCAM.curie('organisms'), - model_uri=GOCAM.goCamAnnotations__organisms, domain=None, range=Optional[Union[Union[str, OrganismId], List[Union[str, OrganismId]]]]) - -slots.goCamAnnotations__gene_organisms = Slot(uri=GOCAM.gene_organisms, name="goCamAnnotations__gene_organisms", curie=GOCAM.curie('gene_organisms'), - model_uri=GOCAM.goCamAnnotations__gene_organisms, domain=None, range=Optional[Union[Union[dict, GeneOrganismRelationship], List[Union[dict, GeneOrganismRelationship]]]]) - -slots.goCamAnnotations__activities = Slot(uri=GOCAM.activities, name="goCamAnnotations__activities", curie=GOCAM.curie('activities'), - model_uri=GOCAM.goCamAnnotations__activities, domain=None, range=Optional[Union[Union[str, MolecularActivityId], List[Union[str, MolecularActivityId]]]]) - -slots.goCamAnnotations__gene_functions = Slot(uri=GOCAM.gene_functions, name="goCamAnnotations__gene_functions", curie=GOCAM.curie('gene_functions'), - model_uri=GOCAM.goCamAnnotations__gene_functions, domain=None, range=Optional[Union[Union[dict, GeneMolecularActivityRelationship], List[Union[dict, GeneMolecularActivityRelationship]]]]) - -slots.goCamAnnotations__cellular_processes = Slot(uri=GOCAM.cellular_processes, name="goCamAnnotations__cellular_processes", curie=GOCAM.curie('cellular_processes'), - model_uri=GOCAM.goCamAnnotations__cellular_processes, domain=None, range=Optional[Union[Union[str, CellularProcessId], List[Union[str, CellularProcessId]]]]) - -slots.goCamAnnotations__pathways = Slot(uri=GOCAM.pathways, name="goCamAnnotations__pathways", curie=GOCAM.curie('pathways'), - model_uri=GOCAM.goCamAnnotations__pathways, domain=None, range=Optional[Union[Union[str, PathwayId], List[Union[str, PathwayId]]]]) - -slots.goCamAnnotations__gene_gene_interactions = Slot(uri=GOCAM.gene_gene_interactions, name="goCamAnnotations__gene_gene_interactions", curie=GOCAM.curie('gene_gene_interactions'), - model_uri=GOCAM.goCamAnnotations__gene_gene_interactions, domain=None, range=Optional[Union[Union[dict, GeneGeneInteraction], List[Union[dict, GeneGeneInteraction]]]]) - -slots.goCamAnnotations__gene_localizations = Slot(uri=GOCAM.gene_localizations, name="goCamAnnotations__gene_localizations", curie=GOCAM.curie('gene_localizations'), - model_uri=GOCAM.goCamAnnotations__gene_localizations, domain=None, range=Optional[Union[Union[dict, GeneSubcellularLocalizationRelationship], List[Union[dict, GeneSubcellularLocalizationRelationship]]]]) - -slots.geneOrganismRelationship__gene = Slot(uri=GOCAM.gene, name="geneOrganismRelationship__gene", curie=GOCAM.curie('gene'), - model_uri=GOCAM.geneOrganismRelationship__gene, domain=None, range=Optional[Union[str, GeneId]]) - -slots.geneOrganismRelationship__organism = Slot(uri=GOCAM.organism, name="geneOrganismRelationship__organism", curie=GOCAM.curie('organism'), - model_uri=GOCAM.geneOrganismRelationship__organism, domain=None, range=Optional[Union[str, OrganismId]]) - -slots.geneMolecularActivityRelationship__gene = Slot(uri=GOCAM.gene, name="geneMolecularActivityRelationship__gene", curie=GOCAM.curie('gene'), - model_uri=GOCAM.geneMolecularActivityRelationship__gene, domain=None, range=Optional[Union[str, GeneId]]) - -slots.geneMolecularActivityRelationship__molecular_activity = Slot(uri=GOCAM.molecular_activity, name="geneMolecularActivityRelationship__molecular_activity", curie=GOCAM.curie('molecular_activity'), - model_uri=GOCAM.geneMolecularActivityRelationship__molecular_activity, domain=None, range=Optional[Union[str, MolecularActivityId]]) - -slots.geneMolecularActivityRelationship2__gene = Slot(uri=GOCAM.gene, name="geneMolecularActivityRelationship2__gene", curie=GOCAM.curie('gene'), - model_uri=GOCAM.geneMolecularActivityRelationship2__gene, domain=None, range=Optional[Union[str, GeneId]]) - -slots.geneMolecularActivityRelationship2__molecular_activity = Slot(uri=GOCAM.molecular_activity, name="geneMolecularActivityRelationship2__molecular_activity", curie=GOCAM.curie('molecular_activity'), - model_uri=GOCAM.geneMolecularActivityRelationship2__molecular_activity, domain=None, range=Optional[Union[str, MolecularActivityId]]) - -slots.geneMolecularActivityRelationship2__target = Slot(uri=GOCAM.target, name="geneMolecularActivityRelationship2__target", curie=GOCAM.curie('target'), - model_uri=GOCAM.geneMolecularActivityRelationship2__target, domain=None, range=Optional[Union[str, MoleculeId]]) - -slots.geneSubcellularLocalizationRelationship__gene = Slot(uri=GOCAM.gene, name="geneSubcellularLocalizationRelationship__gene", curie=GOCAM.curie('gene'), - model_uri=GOCAM.geneSubcellularLocalizationRelationship__gene, domain=None, range=Optional[Union[str, GeneId]]) - -slots.geneSubcellularLocalizationRelationship__location = Slot(uri=GOCAM.location, name="geneSubcellularLocalizationRelationship__location", curie=GOCAM.curie('location'), - model_uri=GOCAM.geneSubcellularLocalizationRelationship__location, domain=None, range=Optional[Union[str, GeneLocationId]]) - -slots.geneGeneInteraction__gene1 = Slot(uri=GOCAM.gene1, name="geneGeneInteraction__gene1", curie=GOCAM.curie('gene1'), - model_uri=GOCAM.geneGeneInteraction__gene1, domain=None, range=Optional[Union[str, GeneId]]) - -slots.geneGeneInteraction__gene2 = Slot(uri=GOCAM.gene2, name="geneGeneInteraction__gene2", curie=GOCAM.curie('gene2'), - model_uri=GOCAM.geneGeneInteraction__gene2, domain=None, range=Optional[Union[str, GeneId]]) - -slots.extractionResult__input_id = Slot(uri=CORE.input_id, name="extractionResult__input_id", curie=CORE.curie('input_id'), - model_uri=GOCAM.extractionResult__input_id, domain=None, range=Optional[str]) - -slots.extractionResult__input_title = Slot(uri=CORE.input_title, name="extractionResult__input_title", curie=CORE.curie('input_title'), - model_uri=GOCAM.extractionResult__input_title, domain=None, range=Optional[str]) - -slots.extractionResult__input_text = Slot(uri=CORE.input_text, name="extractionResult__input_text", curie=CORE.curie('input_text'), - model_uri=GOCAM.extractionResult__input_text, domain=None, range=Optional[str]) - -slots.extractionResult__raw_completion_output = Slot(uri=CORE.raw_completion_output, name="extractionResult__raw_completion_output", curie=CORE.curie('raw_completion_output'), - model_uri=GOCAM.extractionResult__raw_completion_output, domain=None, range=Optional[str]) - -slots.extractionResult__prompt = Slot(uri=CORE.prompt, name="extractionResult__prompt", curie=CORE.curie('prompt'), - model_uri=GOCAM.extractionResult__prompt, domain=None, range=Optional[str]) - -slots.extractionResult__extracted_object = Slot(uri=CORE.extracted_object, name="extractionResult__extracted_object", curie=CORE.curie('extracted_object'), - model_uri=GOCAM.extractionResult__extracted_object, domain=None, range=Optional[Union[dict, Any]]) - -slots.extractionResult__named_entities = Slot(uri=CORE.named_entities, name="extractionResult__named_entities", curie=CORE.curie('named_entities'), - model_uri=GOCAM.extractionResult__named_entities, domain=None, range=Optional[Union[Union[dict, Any], List[Union[dict, Any]]]]) - -slots.namedEntity__id = Slot(uri=CORE.id, name="namedEntity__id", curie=CORE.curie('id'), - model_uri=GOCAM.namedEntity__id, domain=None, range=URIRef) - -slots.namedEntity__label = Slot(uri=RDFS.label, name="namedEntity__label", curie=RDFS.curie('label'), - model_uri=GOCAM.namedEntity__label, domain=None, range=Optional[str]) - -slots.triple__subject = Slot(uri=CORE.subject, name="triple__subject", curie=CORE.curie('subject'), - model_uri=GOCAM.triple__subject, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__predicate = Slot(uri=CORE.predicate, name="triple__predicate", curie=CORE.curie('predicate'), - model_uri=GOCAM.triple__predicate, domain=None, range=Optional[Union[str, RelationshipTypeId]]) - -slots.triple__object = Slot(uri=CORE.object, name="triple__object", curie=CORE.curie('object'), - model_uri=GOCAM.triple__object, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__qualifier = Slot(uri=CORE.qualifier, name="triple__qualifier", curie=CORE.curie('qualifier'), - model_uri=GOCAM.triple__qualifier, domain=None, range=Optional[str]) - -slots.triple__subject_qualifier = Slot(uri=CORE.subject_qualifier, name="triple__subject_qualifier", curie=CORE.curie('subject_qualifier'), - model_uri=GOCAM.triple__subject_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__object_qualifier = Slot(uri=CORE.object_qualifier, name="triple__object_qualifier", curie=CORE.curie('object_qualifier'), - model_uri=GOCAM.triple__object_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.textWithTriples__publication = Slot(uri=CORE.publication, name="textWithTriples__publication", curie=CORE.curie('publication'), - model_uri=GOCAM.textWithTriples__publication, domain=None, range=Optional[Union[dict, Publication]]) - -slots.textWithTriples__triples = Slot(uri=CORE.triples, name="textWithTriples__triples", curie=CORE.curie('triples'), - model_uri=GOCAM.textWithTriples__triples, domain=None, range=Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]]) - -slots.publication__id = Slot(uri=CORE.id, name="publication__id", curie=CORE.curie('id'), - model_uri=GOCAM.publication__id, domain=None, range=Optional[str]) - -slots.publication__title = Slot(uri=CORE.title, name="publication__title", curie=CORE.curie('title'), - model_uri=GOCAM.publication__title, domain=None, range=Optional[str]) - -slots.publication__abstract = Slot(uri=CORE.abstract, name="publication__abstract", curie=CORE.curie('abstract'), - model_uri=GOCAM.publication__abstract, domain=None, range=Optional[str]) - -slots.publication__combined_text = Slot(uri=CORE.combined_text, name="publication__combined_text", curie=CORE.curie('combined_text'), - model_uri=GOCAM.publication__combined_text, domain=None, range=Optional[str]) - -slots.publication__full_text = Slot(uri=CORE.full_text, name="publication__full_text", curie=CORE.curie('full_text'), - model_uri=GOCAM.publication__full_text, domain=None, range=Optional[str]) - -slots.annotatorResult__subject_text = Slot(uri=CORE.subject_text, name="annotatorResult__subject_text", curie=CORE.curie('subject_text'), - model_uri=GOCAM.annotatorResult__subject_text, domain=None, range=Optional[str]) - -slots.annotatorResult__object_id = Slot(uri=CORE.object_id, name="annotatorResult__object_id", curie=CORE.curie('object_id'), - model_uri=GOCAM.annotatorResult__object_id, domain=None, range=Optional[str]) - -slots.annotatorResult__object_text = Slot(uri=CORE.object_text, name="annotatorResult__object_text", curie=CORE.curie('object_text'), - model_uri=GOCAM.annotatorResult__object_text, domain=None, range=Optional[str]) - -slots.GeneLocation_id = Slot(uri=GOCAM.id, name="GeneLocation_id", curie=GOCAM.curie('id'), - model_uri=GOCAM.GeneLocation_id, domain=GeneLocation, range=Union[str, GeneLocationId]) \ No newline at end of file diff --git a/projects/gocam/graphql/gocam.graphql b/projects/gocam/graphql/gocam.graphql deleted file mode 100644 index 56eed285d..000000000 --- a/projects/gocam/graphql/gocam.graphql +++ /dev/null @@ -1,149 +0,0 @@ -type AnnotatorResult - { - subjectText: String - objectId: String - objectText: String - } - -type Any - { - } - -type CellularProcess - { - id: String! - label: String - } - -interface CompoundExpression - { - } - -type ExtractionResult - { - inputId: String - inputTitle: String - inputText: String - rawCompletionOutput: String - prompt: String - extractedObject: Any - namedEntities: [Any] - } - -type Gene - { - id: String! - label: String - } - -type GeneGeneInteraction - { - gene1: Gene - gene2: Gene - } - -type GeneLocation - { - label: String - id: String! - } - -type GeneMolecularActivityRelationship - { - gene: Gene - molecularActivity: MolecularActivity - } - -type GeneMolecularActivityRelationship2 - { - gene: Gene - molecularActivity: MolecularActivity - target: Molecule - } - -type GeneOrganismRelationship - { - gene: Gene - organism: Organism - } - -type GeneSubcellularLocalizationRelationship - { - gene: Gene - location: GeneLocation - } - -type GoCamAnnotations - { - genes: [Gene] - organisms: [Organism] - geneOrganisms: [GeneOrganismRelationship] - activities: [MolecularActivity] - geneFunctions: [GeneMolecularActivityRelationship] - cellularProcesses: [CellularProcess] - pathways: [Pathway] - geneGeneInteractions: [GeneGeneInteraction] - geneLocalizations: [GeneSubcellularLocalizationRelationship] - } - -type MolecularActivity - { - id: String! - label: String - } - -type Molecule - { - id: String! - label: String - } - -interface NamedEntity - { - id: String! - label: String - } - -type Organism - { - id: String! - label: String - } - -type Pathway - { - id: String! - label: String - } - -type Publication - { - id: String - title: String - abstract: String - combinedText: String - fullText: String - } - -type RelationshipType - { - id: String! - label: String - } - -type TextWithTriples - { - publication: Publication - triples: [Triple] - } - -interface Triple - { - subject: NamedEntity - predicate: RelationshipType - object: NamedEntity - qualifier: String - subjectQualifier: NamedEntity - objectQualifier: NamedEntity - } - diff --git a/projects/gocam/jsonld/gocam.context.jsonld b/projects/gocam/jsonld/gocam.context.jsonld deleted file mode 100644 index 400a8db89..000000000 --- a/projects/gocam/jsonld/gocam.context.jsonld +++ /dev/null @@ -1,191 +0,0 @@ -{ - "comments": { - "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2023-08-07T10:53:36", - "source": "gocam.yaml" - }, - "@context": { - "CHEBI": "http://example.org/UNKNOWN/CHEBI/", - "CL": { - "@id": "http://purl.obolibrary.org/obo/CL_", - "@prefix": true - }, - "EFO": "http://example.org/UNKNOWN/EFO/", - "GO": { - "@id": "http://purl.obolibrary.org/obo/GO_", - "@prefix": true - }, - "HGNC": "http://example.org/UNKNOWN/HGNC/", - "NCBITaxon": "http://example.org/UNKNOWN/NCBITaxon/", - "PR": "http://example.org/UNKNOWN/PR/", - "PW": "http://example.org/UNKNOWN/PW/", - "RO": { - "@id": "http://purl.obolibrary.org/obo/RO_", - "@prefix": true - }, - "UBERON": "http://example.org/UNKNOWN/UBERON/", - "UniProtKB": "http://example.org/UNKNOWN/UniProtKB/", - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "gocam": "http://w3id.org/ontogpt/gocam/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "@vocab": "http://w3id.org/ontogpt/gocam/", - "object_id": { - "@id": "core:object_id" - }, - "object_text": { - "@id": "core:object_text" - }, - "subject_text": { - "@id": "core:subject_text" - }, - "extracted_object": { - "@type": "@id", - "@id": "core:extracted_object" - }, - "input_id": { - "@id": "core:input_id" - }, - "input_text": { - "@id": "core:input_text" - }, - "input_title": { - "@id": "core:input_title" - }, - "named_entities": { - "@type": "@id", - "@id": "core:named_entities" - }, - "prompt": { - "@id": "core:prompt" - }, - "raw_completion_output": { - "@id": "core:raw_completion_output" - }, - "gene1": { - "@type": "@id" - }, - "gene2": { - "@type": "@id" - }, - "id": { - "@id": "core:id" - }, - "gene": { - "@type": "@id" - }, - "molecular_activity": { - "@type": "@id" - }, - "target": { - "@type": "@id" - }, - "organism": { - "@type": "@id" - }, - "location": { - "@type": "@id" - }, - "activities": { - "@type": "@id" - }, - "cellular_processes": { - "@type": "@id" - }, - "gene_functions": { - "@type": "@id" - }, - "gene_gene_interactions": { - "@type": "@id" - }, - "gene_localizations": { - "@type": "@id" - }, - "gene_organisms": { - "@type": "@id" - }, - "genes": { - "@type": "@id" - }, - "organisms": { - "@type": "@id" - }, - "pathways": { - "@type": "@id" - }, - "label": { - "@id": "rdfs:label" - }, - "abstract": { - "@id": "core:abstract" - }, - "combined_text": { - "@id": "core:combined_text" - }, - "full_text": { - "@id": "core:full_text" - }, - "title": { - "@id": "core:title" - }, - "publication": { - "@type": "@id", - "@id": "core:publication" - }, - "triples": { - "@type": "@id", - "@id": "core:triples" - }, - "object": { - "@type": "@id", - "@id": "core:object" - }, - "object_qualifier": { - "@type": "@id", - "@id": "core:object_qualifier" - }, - "predicate": { - "@type": "@id", - "@id": "core:predicate" - }, - "qualifier": { - "@id": "core:qualifier" - }, - "subject": { - "@type": "@id", - "@id": "core:subject" - }, - "subject_qualifier": { - "@type": "@id", - "@id": "core:subject_qualifier" - }, - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } - } -} diff --git a/projects/gocam/jsonld/gocam.jsonld b/projects/gocam/jsonld/gocam.jsonld deleted file mode 100644 index aeb88ea1d..000000000 --- a/projects/gocam/jsonld/gocam.jsonld +++ /dev/null @@ -1,1767 +0,0 @@ -{ - "name": "gocam-template", - "description": "A template for GO-CAMs", - "title": "GO-CAM Template", - "id": "http://w3id.org/ontogpt/gocam", - "imports": [ - "linkml:types", - "core" - ], - "license": "https://creativecommons.org/publicdomain/zero/1.0/", - "prefixes": [ - { - "prefix_prefix": "linkml", - "prefix_reference": "https://w3id.org/linkml/" - }, - { - "prefix_prefix": "gocam", - "prefix_reference": "http://w3id.org/ontogpt/gocam/" - }, - { - "prefix_prefix": "GO", - "prefix_reference": "http://purl.obolibrary.org/obo/GO_" - }, - { - "prefix_prefix": "CL", - "prefix_reference": "http://purl.obolibrary.org/obo/CL_" - } - ], - "default_prefix": "gocam", - "default_range": "string", - "types": [ - { - "name": "string", - "definition_uri": "https://w3id.org/linkml/String", - "description": "A character string", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Text" - ], - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "@type": "TypeDefinition" - }, - { - "name": "integer", - "definition_uri": "https://w3id.org/linkml/Integer", - "description": "An integer", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Integer" - ], - "base": "int", - "uri": "http://www.w3.org/2001/XMLSchema#integer", - "@type": "TypeDefinition" - }, - { - "name": "boolean", - "definition_uri": "https://w3id.org/linkml/Boolean", - "description": "A binary (true or false) value", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Boolean" - ], - "base": "Bool", - "uri": "http://www.w3.org/2001/XMLSchema#boolean", - "repr": "bool", - "@type": "TypeDefinition" - }, - { - "name": "float", - "definition_uri": "https://w3id.org/linkml/Float", - "description": "A real number that conforms to the xsd:float specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#float", - "@type": "TypeDefinition" - }, - { - "name": "double", - "definition_uri": "https://w3id.org/linkml/Double", - "description": "A real number that conforms to the xsd:double specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#double", - "@type": "TypeDefinition" - }, - { - "name": "decimal", - "definition_uri": "https://w3id.org/linkml/Decimal", - "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "broad_mappings": [ - "schema:Number" - ], - "base": "Decimal", - "uri": "http://www.w3.org/2001/XMLSchema#decimal", - "@type": "TypeDefinition" - }, - { - "name": "time", - "definition_uri": "https://w3id.org/linkml/Time", - "description": "A time object represents a (local) time of day, independent of any particular day", - "notes": [ - "URI is dateTime because OWL reasoners do not work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Time" - ], - "base": "XSDTime", - "uri": "http://www.w3.org/2001/XMLSchema#time", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date", - "definition_uri": "https://w3id.org/linkml/Date", - "description": "a date (year, month and day) in an idealized calendar", - "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Date" - ], - "base": "XSDDate", - "uri": "http://www.w3.org/2001/XMLSchema#date", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "datetime", - "definition_uri": "https://w3id.org/linkml/Datetime", - "description": "The combination of a date and time", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:DateTime" - ], - "base": "XSDDateTime", - "uri": "http://www.w3.org/2001/XMLSchema#dateTime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date_or_datetime", - "definition_uri": "https://w3id.org/linkml/DateOrDatetime", - "description": "Either a date or a datetime", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "https://w3id.org/linkml/DateOrDatetime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uriorcurie", - "definition_uri": "https://w3id.org/linkml/Uriorcurie", - "description": "a URI or a CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "URIorCURIE", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "curie", - "definition_uri": "https://w3id.org/linkml/Curie", - "conforms_to": "https://www.w3.org/TR/curie/", - "description": "a compact URI", - "comments": [ - "in RDF serializations this MUST be expanded to a URI", - "in non-RDF serializations MAY be serialized as the compact representation" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "Curie", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uri", - "definition_uri": "https://w3id.org/linkml/Uri", - "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", - "description": "a complete URI", - "comments": [ - "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:URL" - ], - "base": "URI", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "ncname", - "definition_uri": "https://w3id.org/linkml/Ncname", - "description": "Prefix part of CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NCName", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "objectidentifier", - "definition_uri": "https://w3id.org/linkml/Objectidentifier", - "description": "A URI or CURIE that represents an object in the model.", - "comments": [ - "Used for inheritance and type checking" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "ElementIdentifier", - "uri": "http://www.w3.org/ns/shex#iri", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "nodeidentifier", - "definition_uri": "https://w3id.org/linkml/Nodeidentifier", - "description": "A URI, CURIE or BNODE that represents a node in a model.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NodeIdentifier", - "uri": "http://www.w3.org/ns/shex#nonLiteral", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpointer", - "definition_uri": "https://w3id.org/linkml/Jsonpointer", - "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901", - "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpath", - "definition_uri": "https://w3id.org/linkml/Jsonpath", - "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html", - "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "sparqlpath", - "definition_uri": "https://w3id.org/linkml/Sparqlpath", - "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths", - "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - } - ], - "enums": [ - { - "name": "GeneLocationEnum", - "definition_uri": "http://w3id.org/ontogpt/gocam/GeneLocationEnum", - "from_schema": "http://w3id.org/ontogpt/gocam", - "inherits": [ - "GOCellComponent", - "CellType" - ] - }, - { - "name": "GOCellComponentType", - "definition_uri": "http://w3id.org/ontogpt/gocam/GOCellComponentType", - "from_schema": "http://w3id.org/ontogpt/gocam", - "reachable_from": { - "source_ontology": "obo:go", - "source_nodes": [ - "GO:0005575" - ] - } - }, - { - "name": "CellType", - "definition_uri": "http://w3id.org/ontogpt/gocam/CellType", - "from_schema": "http://w3id.org/ontogpt/gocam", - "reachable_from": { - "source_ontology": "obo:cl", - "source_nodes": [ - "CL:0000000" - ] - } - }, - { - "name": "NullDataOptions", - "definition_uri": "http://w3id.org/ontogpt/core/NullDataOptions", - "from_schema": "http://w3id.org/ontogpt/core", - "permissible_values": [ - { - "text": "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "meaning": "NCIT:C149701" - }, - { - "text": "NOT_APPLICABLE", - "meaning": "NCIT:C18902", - "aliases": [ - "not applicable", - "N/A" - ] - }, - { - "text": "NOT_MENTIONED" - } - ] - } - ], - "slots": [ - { - "name": "goCamAnnotations__genes", - "description": "semicolon-separated list of genes", - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/genes", - "multivalued": true, - "alias": "genes", - "owner": "GoCamAnnotations", - "domain_of": [ - "GoCamAnnotations" - ], - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "goCamAnnotations__organisms", - "description": "semicolon-separated list of organism taxons", - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/organisms", - "multivalued": true, - "alias": "organisms", - "owner": "GoCamAnnotations", - "domain_of": [ - "GoCamAnnotations" - ], - "range": "Organism", - "@type": "SlotDefinition" - }, - { - "name": "goCamAnnotations__gene_organisms", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of asterisk separated gene to organism relationships", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/gene_organisms", - "multivalued": true, - "alias": "gene_organisms", - "owner": "GoCamAnnotations", - "domain_of": [ - "GoCamAnnotations" - ], - "range": "GeneOrganismRelationship", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "goCamAnnotations__activities", - "description": "semicolon-separated list of molecular activities", - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/activities", - "multivalued": true, - "alias": "activities", - "owner": "GoCamAnnotations", - "domain_of": [ - "GoCamAnnotations" - ], - "range": "MolecularActivity", - "@type": "SlotDefinition" - }, - { - "name": "goCamAnnotations__gene_functions", - "description": "semicolon-separated list of gene to molecular activity relationships", - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/gene_functions", - "multivalued": true, - "alias": "gene_functions", - "owner": "GoCamAnnotations", - "domain_of": [ - "GoCamAnnotations" - ], - "range": "GeneMolecularActivityRelationship", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "goCamAnnotations__cellular_processes", - "description": "semicolon-separated list of cellular processes", - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/cellular_processes", - "multivalued": true, - "alias": "cellular_processes", - "owner": "GoCamAnnotations", - "domain_of": [ - "GoCamAnnotations" - ], - "range": "CellularProcess", - "@type": "SlotDefinition" - }, - { - "name": "goCamAnnotations__pathways", - "description": "semicolon-separated list of pathways", - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/pathways", - "multivalued": true, - "alias": "pathways", - "owner": "GoCamAnnotations", - "domain_of": [ - "GoCamAnnotations" - ], - "range": "Pathway", - "@type": "SlotDefinition" - }, - { - "name": "goCamAnnotations__gene_gene_interactions", - "description": "semicolon-separated list of gene to gene interactions", - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/gene_gene_interactions", - "multivalued": true, - "alias": "gene_gene_interactions", - "owner": "GoCamAnnotations", - "domain_of": [ - "GoCamAnnotations" - ], - "range": "GeneGeneInteraction", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "goCamAnnotations__gene_localizations", - "description": "semicolon-separated list of genes plus their location in the cell; for example, \"gene1 / cytoplasm; gene2 / mitochondrion\"", - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/gene_localizations", - "multivalued": true, - "alias": "gene_localizations", - "owner": "GoCamAnnotations", - "domain_of": [ - "GoCamAnnotations" - ], - "range": "GeneSubcellularLocalizationRelationship", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "geneOrganismRelationship__gene", - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/gene", - "alias": "gene", - "owner": "GeneOrganismRelationship", - "domain_of": [ - "GeneOrganismRelationship" - ], - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "geneOrganismRelationship__organism", - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/organism", - "alias": "organism", - "owner": "GeneOrganismRelationship", - "domain_of": [ - "GeneOrganismRelationship" - ], - "range": "Organism", - "@type": "SlotDefinition" - }, - { - "name": "geneMolecularActivityRelationship__gene", - "annotations": [ - { - "tag": "prompt", - "value": "the name of the gene in the pair. This comes first.", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/gene", - "alias": "gene", - "owner": "GeneMolecularActivityRelationship", - "domain_of": [ - "GeneMolecularActivityRelationship" - ], - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "geneMolecularActivityRelationship__molecular_activity", - "annotations": [ - { - "tag": "prompt", - "value": "the name of the molecular function in the pair. This comes second. May be a GO term.", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/molecular_activity", - "alias": "molecular_activity", - "owner": "GeneMolecularActivityRelationship", - "domain_of": [ - "GeneMolecularActivityRelationship" - ], - "range": "MolecularActivity", - "@type": "SlotDefinition" - }, - { - "name": "geneMolecularActivityRelationship2__gene", - "annotations": [ - { - "tag": "prompt", - "value": "the name of the gene.", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/gene", - "alias": "gene", - "owner": "GeneMolecularActivityRelationship2", - "domain_of": [ - "GeneMolecularActivityRelationship2" - ], - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "geneMolecularActivityRelationship2__molecular_activity", - "annotations": [ - { - "tag": "prompt", - "value": "the name of the molecular activity, for example, ubiquitination. May be a GO term.", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/molecular_activity", - "alias": "molecular_activity", - "owner": "GeneMolecularActivityRelationship2", - "domain_of": [ - "GeneMolecularActivityRelationship2" - ], - "range": "MolecularActivity", - "@type": "SlotDefinition" - }, - { - "name": "geneMolecularActivityRelationship2__target", - "annotations": [ - { - "tag": "prompt", - "value": "the name of the molecular entity that is the target of the molecular activity.", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/target", - "alias": "target", - "owner": "GeneMolecularActivityRelationship2", - "domain_of": [ - "GeneMolecularActivityRelationship2" - ], - "range": "Molecule", - "@type": "SlotDefinition" - }, - { - "name": "geneSubcellularLocalizationRelationship__gene", - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/gene", - "alias": "gene", - "owner": "GeneSubcellularLocalizationRelationship", - "domain_of": [ - "GeneSubcellularLocalizationRelationship" - ], - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "geneSubcellularLocalizationRelationship__location", - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/location", - "alias": "location", - "owner": "GeneSubcellularLocalizationRelationship", - "domain_of": [ - "GeneSubcellularLocalizationRelationship" - ], - "range": "GeneLocation", - "@type": "SlotDefinition" - }, - { - "name": "geneGeneInteraction__gene1", - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/gene1", - "alias": "gene1", - "owner": "GeneGeneInteraction", - "domain_of": [ - "GeneGeneInteraction" - ], - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "geneGeneInteraction__gene2", - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/gene2", - "alias": "gene2", - "owner": "GeneGeneInteraction", - "domain_of": [ - "GeneGeneInteraction" - ], - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_id", - "alias": "input_id", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_title", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_title", - "alias": "input_title", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_text", - "alias": "input_text", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__raw_completion_output", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/raw_completion_output", - "alias": "raw_completion_output", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__prompt", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/prompt", - "alias": "prompt", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__extracted_object", - "description": "The complex objects extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/extracted_object", - "alias": "extracted_object", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__named_entities", - "description": "Named entities extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/named_entities", - "multivalued": true, - "alias": "named_entities", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "identifier": true, - "alias": "id", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "required": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "from_schema": "http://w3id.org/ontogpt/core", - "aliases": [ - "name" - ], - "mappings": [ - "http://example.org/UNKNOWN/rdfs/label" - ], - "slot_uri": "http://example.org/UNKNOWN/rdfs/label", - "alias": "label", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject", - "alias": "subject", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__predicate", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/predicate", - "alias": "predicate", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "triple__object", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object", - "alias": "object", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/qualifier", - "alias": "qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_qualifier", - "alias": "subject_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_qualifier", - "alias": "object_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/publication", - "alias": "publication", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__triples", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/triples", - "multivalued": true, - "alias": "triples", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "publication__id", - "description": "The publication identifier", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "alias": "id", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__title", - "description": "The title of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/title", - "alias": "title", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__abstract", - "description": "The abstract of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/abstract", - "alias": "abstract", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__combined_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/combined_text", - "alias": "combined_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__full_text", - "description": "The full text of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/full_text", - "alias": "full_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__subject_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_text", - "alias": "subject_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_id", - "alias": "object_id", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_text", - "alias": "object_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "GeneLocation_id", - "from_schema": "http://w3id.org/ontogpt/gocam", - "is_a": "namedEntity__id", - "values_from": [ - "GOCellComponentType", - "CellType" - ], - "domain": "GeneLocation", - "slot_uri": "http://w3id.org/ontogpt/gocam/id", - "identifier": true, - "alias": "id", - "owner": "GeneLocation", - "domain_of": [ - "GeneLocation" - ], - "is_usage_slot": true, - "usage_slot_name": "id", - "range": "string", - "required": true, - "@type": "SlotDefinition" - } - ], - "classes": [ - { - "name": "GoCamAnnotations", - "definition_uri": "http://w3id.org/ontogpt/gocam/GoCamAnnotations", - "from_schema": "http://w3id.org/ontogpt/gocam", - "slots": [ - "goCamAnnotations__genes", - "goCamAnnotations__organisms", - "goCamAnnotations__gene_organisms", - "goCamAnnotations__activities", - "goCamAnnotations__gene_functions", - "goCamAnnotations__cellular_processes", - "goCamAnnotations__pathways", - "goCamAnnotations__gene_gene_interactions", - "goCamAnnotations__gene_localizations" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "genes", - "description": "semicolon-separated list of genes", - "multivalued": true, - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "organisms", - "description": "semicolon-separated list of organism taxons", - "multivalued": true, - "range": "Organism", - "@type": "SlotDefinition" - }, - { - "name": "gene_organisms", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of asterisk separated gene to organism relationships", - "@type": "Annotation" - } - ], - "multivalued": true, - "range": "GeneOrganismRelationship", - "@type": "SlotDefinition" - }, - { - "name": "activities", - "description": "semicolon-separated list of molecular activities", - "multivalued": true, - "range": "MolecularActivity", - "@type": "SlotDefinition" - }, - { - "name": "gene_functions", - "description": "semicolon-separated list of gene to molecular activity relationships", - "multivalued": true, - "range": "GeneMolecularActivityRelationship", - "@type": "SlotDefinition" - }, - { - "name": "cellular_processes", - "description": "semicolon-separated list of cellular processes", - "multivalued": true, - "range": "CellularProcess", - "@type": "SlotDefinition" - }, - { - "name": "pathways", - "description": "semicolon-separated list of pathways", - "multivalued": true, - "range": "Pathway", - "@type": "SlotDefinition" - }, - { - "name": "gene_gene_interactions", - "description": "semicolon-separated list of gene to gene interactions", - "multivalued": true, - "range": "GeneGeneInteraction", - "@type": "SlotDefinition" - }, - { - "name": "gene_localizations", - "description": "semicolon-separated list of genes plus their location in the cell; for example, \"gene1 / cytoplasm; gene2 / mitochondrion\"", - "multivalued": true, - "range": "GeneSubcellularLocalizationRelationship", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/gocam/GoCamAnnotations", - "tree_root": true, - "@type": "ClassDefinition" - }, - { - "name": "Gene", - "id_prefixes": [ - "HGNC", - "PR", - "UniProtKB" - ], - "definition_uri": "http://w3id.org/ontogpt/gocam/Gene", - "annotations": [ - { - "tag": "annotators", - "value": "gilda:, bioportal:hgnc-nr", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/gocam", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/gocam/Gene", - "@type": "ClassDefinition" - }, - { - "name": "Pathway", - "id_prefixes": [ - "GO", - "PW" - ], - "definition_uri": "http://w3id.org/ontogpt/gocam/Pathway", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:go, sqlite:obo:pw", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/gocam", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/gocam/Pathway", - "@type": "ClassDefinition" - }, - { - "name": "CellularProcess", - "id_prefixes": [ - "GO" - ], - "definition_uri": "http://w3id.org/ontogpt/gocam/CellularProcess", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:go", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/gocam", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/gocam/CellularProcess", - "@type": "ClassDefinition" - }, - { - "name": "MolecularActivity", - "id_prefixes": [ - "GO" - ], - "definition_uri": "http://w3id.org/ontogpt/gocam/MolecularActivity", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:go", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/gocam", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/gocam/MolecularActivity", - "@type": "ClassDefinition" - }, - { - "name": "GeneLocation", - "id_prefixes": [ - "GO", - "CL", - "UBERON" - ], - "definition_uri": "http://w3id.org/ontogpt/gocam/GeneLocation", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:go, sqlite:obo:cl", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/gocam", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__label", - "GeneLocation_id" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/gocam/GeneLocation", - "@type": "ClassDefinition" - }, - { - "name": "Organism", - "id_prefixes": [ - "NCBITaxon", - "EFO" - ], - "definition_uri": "http://w3id.org/ontogpt/gocam/Organism", - "annotations": [ - { - "tag": "annotators", - "value": "gilda:, sqlite:obo:ncbitaxon", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/gocam", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/gocam/Organism", - "@type": "ClassDefinition" - }, - { - "name": "Molecule", - "id_prefixes": [ - "CHEBI", - "PR" - ], - "definition_uri": "http://w3id.org/ontogpt/gocam/Molecule", - "annotations": [ - { - "tag": "annotators", - "value": "gilda:, sqlite:obo:chebi", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/gocam", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/gocam/Molecule", - "@type": "ClassDefinition" - }, - { - "name": "GeneOrganismRelationship", - "definition_uri": "http://w3id.org/ontogpt/gocam/GeneOrganismRelationship", - "from_schema": "http://w3id.org/ontogpt/gocam", - "is_a": "CompoundExpression", - "slots": [ - "geneOrganismRelationship__gene", - "geneOrganismRelationship__organism" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "gene", - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "organism", - "range": "Organism", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/gocam/GeneOrganismRelationship", - "@type": "ClassDefinition" - }, - { - "name": "GeneMolecularActivityRelationship", - "definition_uri": "http://w3id.org/ontogpt/gocam/GeneMolecularActivityRelationship", - "annotations": [ - { - "tag": "prompt.example", - "value": "TODO\n\ngene: HGNC:1234\nmolecular_activity: GO:0003674", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/gocam", - "is_a": "CompoundExpression", - "slots": [ - "geneMolecularActivityRelationship__gene", - "geneMolecularActivityRelationship__molecular_activity" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "gene", - "annotations": [ - { - "tag": "prompt", - "value": "the name of the gene in the pair. This comes first.", - "@type": "Annotation" - } - ], - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "molecular_activity", - "annotations": [ - { - "tag": "prompt", - "value": "the name of the molecular function in the pair. This comes second. May be a GO term.", - "@type": "Annotation" - } - ], - "range": "MolecularActivity", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/gocam/GeneMolecularActivityRelationship", - "@type": "ClassDefinition" - }, - { - "name": "GeneMolecularActivityRelationship2", - "definition_uri": "http://w3id.org/ontogpt/gocam/GeneMolecularActivityRelationship2", - "from_schema": "http://w3id.org/ontogpt/gocam", - "is_a": "CompoundExpression", - "slots": [ - "geneMolecularActivityRelationship2__gene", - "geneMolecularActivityRelationship2__molecular_activity", - "geneMolecularActivityRelationship2__target" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "gene", - "annotations": [ - { - "tag": "prompt", - "value": "the name of the gene.", - "@type": "Annotation" - } - ], - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "molecular_activity", - "annotations": [ - { - "tag": "prompt", - "value": "the name of the molecular activity, for example, ubiquitination. May be a GO term.", - "@type": "Annotation" - } - ], - "range": "MolecularActivity", - "@type": "SlotDefinition" - }, - { - "name": "target", - "annotations": [ - { - "tag": "prompt", - "value": "the name of the molecular entity that is the target of the molecular activity.", - "@type": "Annotation" - } - ], - "range": "Molecule", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/gocam/GeneMolecularActivityRelationship2", - "@type": "ClassDefinition" - }, - { - "name": "GeneSubcellularLocalizationRelationship", - "definition_uri": "http://w3id.org/ontogpt/gocam/GeneSubcellularLocalizationRelationship", - "from_schema": "http://w3id.org/ontogpt/gocam", - "is_a": "CompoundExpression", - "slots": [ - "geneSubcellularLocalizationRelationship__gene", - "geneSubcellularLocalizationRelationship__location" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "gene", - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "location", - "range": "GeneLocation", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/gocam/GeneSubcellularLocalizationRelationship", - "@type": "ClassDefinition" - }, - { - "name": "GeneGeneInteraction", - "definition_uri": "http://w3id.org/ontogpt/gocam/GeneGeneInteraction", - "from_schema": "http://w3id.org/ontogpt/gocam", - "is_a": "CompoundExpression", - "slots": [ - "geneGeneInteraction__gene1", - "geneGeneInteraction__gene2" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "gene1", - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "gene2", - "range": "Gene", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/gocam/GeneGeneInteraction", - "@type": "ClassDefinition" - }, - { - "name": "Any", - "definition_uri": "http://w3id.org/ontogpt/core/Any", - "from_schema": "http://w3id.org/ontogpt/core", - "mappings": [ - "linkml:Any" - ], - "slot_usage": {}, - "class_uri": "https://w3id.org/linkml/Any", - "@type": "ClassDefinition" - }, - { - "name": "ExtractionResult", - "definition_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "description": "A result of extracting knowledge on text", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "extractionResult__input_id", - "extractionResult__input_title", - "extractionResult__input_text", - "extractionResult__raw_completion_output", - "extractionResult__prompt", - "extractionResult__extracted_object", - "extractionResult__named_entities" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "input_id", - "@type": "SlotDefinition" - }, - { - "name": "input_title", - "@type": "SlotDefinition" - }, - { - "name": "input_text", - "@type": "SlotDefinition" - }, - { - "name": "raw_completion_output", - "@type": "SlotDefinition" - }, - { - "name": "prompt", - "@type": "SlotDefinition" - }, - { - "name": "extracted_object", - "description": "The complex objects extracted from the text", - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "named_entities", - "description": "Named entities extracted from the text", - "multivalued": true, - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "@type": "ClassDefinition" - }, - { - "name": "NamedEntity", - "definition_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "identifier": true, - "@type": "SlotDefinition" - }, - { - "name": "label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "aliases": [ - "name" - ], - "slot_uri": "rdfs:label", - "range": "string", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "@type": "ClassDefinition" - }, - { - "name": "CompoundExpression", - "definition_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "@type": "ClassDefinition" - }, - { - "name": "Triple", - "definition_uri": "http://w3id.org/ontogpt/core/Triple", - "description": "Abstract parent for Relation Extraction tasks", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "CompoundExpression", - "abstract": true, - "slots": [ - "triple__subject", - "triple__predicate", - "triple__object", - "triple__qualifier", - "triple__subject_qualifier", - "triple__object_qualifier" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "predicate", - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "object", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Triple", - "@type": "ClassDefinition" - }, - { - "name": "TextWithTriples", - "definition_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "textWithTriples__publication", - "textWithTriples__triples" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "triples", - "multivalued": true, - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "@type": "ClassDefinition" - }, - { - "name": "RelationshipType", - "id_prefixes": [ - "RO", - "biolink" - ], - "definition_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "@type": "ClassDefinition" - }, - { - "name": "Publication", - "definition_uri": "http://w3id.org/ontogpt/core/Publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "publication__id", - "publication__title", - "publication__abstract", - "publication__combined_text", - "publication__full_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "description": "The publication identifier", - "@type": "SlotDefinition" - }, - { - "name": "title", - "description": "The title of the publication", - "@type": "SlotDefinition" - }, - { - "name": "abstract", - "description": "The abstract of the publication", - "@type": "SlotDefinition" - }, - { - "name": "combined_text", - "@type": "SlotDefinition" - }, - { - "name": "full_text", - "description": "The full text of the publication", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Publication", - "@type": "ClassDefinition" - }, - { - "name": "AnnotatorResult", - "definition_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "annotatorResult__subject_text", - "annotatorResult__object_id", - "annotatorResult__object_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject_text", - "@type": "SlotDefinition" - }, - { - "name": "object_id", - "@type": "SlotDefinition" - }, - { - "name": "object_text", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "@type": "ClassDefinition" - } - ], - "metamodel_version": "1.7.0", - "source_file": "gocam.yaml", - "source_file_date": "2023-06-17T15:11:19", - "source_file_size": 4871, - "generation_date": "2023-08-07T10:53:37", - "@type": "SchemaDefinition", - "@context": [ - "projects/gocam/jsonld/gocam.context.jsonld", - "https://w3id.org/linkml/types.context.jsonld", - "core.context.jsonld", - { - "@base": "http://w3id.org/ontogpt/gocam/" - } - ] -} diff --git a/projects/gocam/jsonschema/gocam.schema.json b/projects/gocam/jsonschema/gocam.schema.json deleted file mode 100644 index 205c90561..000000000 --- a/projects/gocam/jsonschema/gocam.schema.json +++ /dev/null @@ -1,499 +0,0 @@ -{ - "$defs": { - "AnnotatorResult": { - "additionalProperties": false, - "description": "", - "properties": { - "object_id": { - "type": "string" - }, - "object_text": { - "type": "string" - }, - "subject_text": { - "type": "string" - } - }, - "title": "AnnotatorResult", - "type": "object" - }, - "Any": { - "additionalProperties": true, - "description": "", - "title": "Any", - "type": "object" - }, - "CellType": { - "description": "", - "enum": [], - "title": "CellType", - "type": "string" - }, - "CellularProcess": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "CellularProcess", - "type": "object" - }, - "ExtractionResult": { - "additionalProperties": false, - "description": "A result of extracting knowledge on text", - "properties": { - "extracted_object": { - "$ref": "#/$defs/Any", - "description": "The complex objects extracted from the text" - }, - "input_id": { - "type": "string" - }, - "input_text": { - "type": "string" - }, - "input_title": { - "type": "string" - }, - "named_entities": { - "description": "Named entities extracted from the text", - "items": { - "$ref": "#/$defs/Any" - }, - "type": "array" - }, - "prompt": { - "type": "string" - }, - "raw_completion_output": { - "type": "string" - } - }, - "title": "ExtractionResult", - "type": "object" - }, - "GOCellComponentType": { - "description": "", - "enum": [], - "title": "GOCellComponentType", - "type": "string" - }, - "Gene": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Gene", - "type": "object" - }, - "GeneGeneInteraction": { - "additionalProperties": false, - "description": "", - "properties": { - "gene1": { - "type": "string" - }, - "gene2": { - "type": "string" - } - }, - "title": "GeneGeneInteraction", - "type": "object" - }, - "GeneLocation": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "GeneLocation", - "type": "object" - }, - "GeneLocationEnum": { - "description": "", - "enum": [], - "title": "GeneLocationEnum", - "type": "string" - }, - "GeneMolecularActivityRelationship": { - "additionalProperties": false, - "description": "", - "properties": { - "gene": { - "type": "string" - }, - "molecular_activity": { - "type": "string" - } - }, - "title": "GeneMolecularActivityRelationship", - "type": "object" - }, - "GeneMolecularActivityRelationship2": { - "additionalProperties": false, - "description": "", - "properties": { - "gene": { - "type": "string" - }, - "molecular_activity": { - "type": "string" - }, - "target": { - "type": "string" - } - }, - "title": "GeneMolecularActivityRelationship2", - "type": "object" - }, - "GeneOrganismRelationship": { - "additionalProperties": false, - "description": "", - "properties": { - "gene": { - "type": "string" - }, - "organism": { - "type": "string" - } - }, - "title": "GeneOrganismRelationship", - "type": "object" - }, - "GeneSubcellularLocalizationRelationship": { - "additionalProperties": false, - "description": "", - "properties": { - "gene": { - "type": "string" - }, - "location": { - "type": "string" - } - }, - "title": "GeneSubcellularLocalizationRelationship", - "type": "object" - }, - "GoCamAnnotations": { - "additionalProperties": false, - "description": "", - "properties": { - "activities": { - "description": "semicolon-separated list of molecular activities", - "items": { - "type": "string" - }, - "type": "array" - }, - "cellular_processes": { - "description": "semicolon-separated list of cellular processes", - "items": { - "type": "string" - }, - "type": "array" - }, - "gene_functions": { - "description": "semicolon-separated list of gene to molecular activity relationships", - "items": { - "$ref": "#/$defs/GeneMolecularActivityRelationship" - }, - "type": "array" - }, - "gene_gene_interactions": { - "description": "semicolon-separated list of gene to gene interactions", - "items": { - "$ref": "#/$defs/GeneGeneInteraction" - }, - "type": "array" - }, - "gene_localizations": { - "description": "semicolon-separated list of genes plus their location in the cell; for example, \"gene1 / cytoplasm; gene2 / mitochondrion\"", - "items": { - "$ref": "#/$defs/GeneSubcellularLocalizationRelationship" - }, - "type": "array" - }, - "gene_organisms": { - "items": { - "$ref": "#/$defs/GeneOrganismRelationship" - }, - "type": "array" - }, - "genes": { - "description": "semicolon-separated list of genes", - "items": { - "type": "string" - }, - "type": "array" - }, - "organisms": { - "description": "semicolon-separated list of organism taxons", - "items": { - "type": "string" - }, - "type": "array" - }, - "pathways": { - "description": "semicolon-separated list of pathways", - "items": { - "type": "string" - }, - "type": "array" - } - }, - "title": "GoCamAnnotations", - "type": "object" - }, - "MolecularActivity": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "MolecularActivity", - "type": "object" - }, - "Molecule": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Molecule", - "type": "object" - }, - "NullDataOptions": { - "description": "", - "enum": [ - "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "NOT_APPLICABLE", - "NOT_MENTIONED" - ], - "title": "NullDataOptions", - "type": "string" - }, - "Organism": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Organism", - "type": "object" - }, - "Pathway": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Pathway", - "type": "object" - }, - "Publication": { - "additionalProperties": false, - "description": "", - "properties": { - "abstract": { - "description": "The abstract of the publication", - "type": "string" - }, - "combined_text": { - "type": "string" - }, - "full_text": { - "description": "The full text of the publication", - "type": "string" - }, - "id": { - "description": "The publication identifier", - "type": "string" - }, - "title": { - "description": "The title of the publication", - "type": "string" - } - }, - "title": "Publication", - "type": "object" - }, - "RelationshipType": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "RelationshipType", - "type": "object" - }, - "TextWithTriples": { - "additionalProperties": false, - "description": "", - "properties": { - "publication": { - "$ref": "#/$defs/Publication" - }, - "triples": { - "items": { - "$ref": "#/$defs/Triple" - }, - "type": "array" - } - }, - "title": "TextWithTriples", - "type": "object" - } - }, - "$id": "http://w3id.org/ontogpt/gocam", - "$schema": "http://json-schema.org/draft-07/schema#", - "additionalProperties": true, - "metamodel_version": "1.7.0", - "properties": { - "activities": { - "description": "semicolon-separated list of molecular activities", - "items": { - "type": "string" - }, - "type": "array" - }, - "cellular_processes": { - "description": "semicolon-separated list of cellular processes", - "items": { - "type": "string" - }, - "type": "array" - }, - "gene_functions": { - "description": "semicolon-separated list of gene to molecular activity relationships", - "items": { - "$ref": "#/$defs/GeneMolecularActivityRelationship" - }, - "type": "array" - }, - "gene_gene_interactions": { - "description": "semicolon-separated list of gene to gene interactions", - "items": { - "$ref": "#/$defs/GeneGeneInteraction" - }, - "type": "array" - }, - "gene_localizations": { - "description": "semicolon-separated list of genes plus their location in the cell; for example, \"gene1 / cytoplasm; gene2 / mitochondrion\"", - "items": { - "$ref": "#/$defs/GeneSubcellularLocalizationRelationship" - }, - "type": "array" - }, - "gene_organisms": { - "items": { - "$ref": "#/$defs/GeneOrganismRelationship" - }, - "type": "array" - }, - "genes": { - "description": "semicolon-separated list of genes", - "items": { - "type": "string" - }, - "type": "array" - }, - "organisms": { - "description": "semicolon-separated list of organism taxons", - "items": { - "type": "string" - }, - "type": "array" - }, - "pathways": { - "description": "semicolon-separated list of pathways", - "items": { - "type": "string" - }, - "type": "array" - } - }, - "title": "gocam-template", - "type": "object", - "version": null -} \ No newline at end of file diff --git a/projects/gocam/owl/gocam.owl.ttl b/projects/gocam/owl/gocam.owl.ttl deleted file mode 100644 index 2db2938c3..000000000 --- a/projects/gocam/owl/gocam.owl.ttl +++ /dev/null @@ -1,638 +0,0 @@ -@prefix IAO: <http://purl.obolibrary.org/obo/IAO_> . -@prefix gocam: <http://w3id.org/ontogpt/gocam/> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix owl: <http://www.w3.org/2002/07/owl#> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . -@prefix skos: <http://www.w3.org/2004/02/skos/core#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -<http://w3id.org/ontogpt/gocam> a owl:Ontology ; - rdfs:label "gocam-template" ; - IAO:0000700 <http://w3id.org/ontogpt/core/AnnotatorResult>, - <http://w3id.org/ontogpt/core/Any>, - <http://w3id.org/ontogpt/core/CompoundExpression>, - <http://w3id.org/ontogpt/core/ExtractionResult>, - <http://w3id.org/ontogpt/core/NamedEntity>, - <http://w3id.org/ontogpt/core/Publication>, - <http://w3id.org/ontogpt/core/TextWithTriples>, - gocam:GoCamAnnotations ; - linkml:classes "{'GoCamAnnotations': ClassDefinition(name='GoCamAnnotations', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/gocam/GoCamAnnotations', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['goCamAnnotations__genes', 'goCamAnnotations__organisms', 'goCamAnnotations__gene_organisms', 'goCamAnnotations__activities', 'goCamAnnotations__gene_functions', 'goCamAnnotations__cellular_processes', 'goCamAnnotations__pathways', 'goCamAnnotations__gene_gene_interactions', 'goCamAnnotations__gene_localizations'], slot_usage={}, attributes={'genes': SlotDefinition(name='genes', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of genes', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'organisms': SlotDefinition(name='organisms', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of organism taxons', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Organism', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'gene_organisms': SlotDefinition(name='gene_organisms', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of asterisk separated gene to organism relationships', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneOrganismRelationship', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'activities': SlotDefinition(name='activities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of molecular activities', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='MolecularActivity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'gene_functions': SlotDefinition(name='gene_functions', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of gene to molecular activity relationships', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneMolecularActivityRelationship', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'cellular_processes': SlotDefinition(name='cellular_processes', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of cellular processes', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='CellularProcess', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'pathways': SlotDefinition(name='pathways', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of pathways', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Pathway', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'gene_gene_interactions': SlotDefinition(name='gene_gene_interactions', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of gene to gene interactions', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneGeneInteraction', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'gene_localizations': SlotDefinition(name='gene_localizations', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of genes plus their location in the cell; for example, \"gene1 / cytoplasm; gene2 / mitochondrion\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneSubcellularLocalizationRelationship', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='gocam:GoCamAnnotations', subclass_of=None, union_of=[], defining_slots=[], tree_root=True, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Gene': ClassDefinition(name='Gene', id_prefixes=['HGNC', 'PR', 'UniProtKB'], definition_uri='http://w3id.org/ontogpt/gocam/Gene', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='gilda:, bioportal:hgnc-nr', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='gocam:Gene', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Pathway': ClassDefinition(name='Pathway', id_prefixes=['GO', 'PW'], definition_uri='http://w3id.org/ontogpt/gocam/Pathway', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:go, sqlite:obo:pw', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='gocam:Pathway', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'CellularProcess': ClassDefinition(name='CellularProcess', id_prefixes=['GO'], definition_uri='http://w3id.org/ontogpt/gocam/CellularProcess', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:go', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='gocam:CellularProcess', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'MolecularActivity': ClassDefinition(name='MolecularActivity', id_prefixes=['GO'], definition_uri='http://w3id.org/ontogpt/gocam/MolecularActivity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:go', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='gocam:MolecularActivity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'GeneLocation': ClassDefinition(name='GeneLocation', id_prefixes=['GO', 'CL', 'UBERON'], definition_uri='http://w3id.org/ontogpt/gocam/GeneLocation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:go, sqlite:obo:cl', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__label', 'GeneLocation_id'], slot_usage={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='namedEntity__id', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=['GOCellComponentType', 'CellType'], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='gocam:GeneLocation', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Organism': ClassDefinition(name='Organism', id_prefixes=['NCBITaxon', 'EFO'], definition_uri='http://w3id.org/ontogpt/gocam/Organism', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='gilda:, sqlite:obo:ncbitaxon', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='gocam:Organism', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Molecule': ClassDefinition(name='Molecule', id_prefixes=['CHEBI', 'PR'], definition_uri='http://w3id.org/ontogpt/gocam/Molecule', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='gilda:, sqlite:obo:chebi', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='gocam:Molecule', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'GeneOrganismRelationship': ClassDefinition(name='GeneOrganismRelationship', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/gocam/GeneOrganismRelationship', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['geneOrganismRelationship__gene', 'geneOrganismRelationship__organism'], slot_usage={}, attributes={'gene': SlotDefinition(name='gene', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'organism': SlotDefinition(name='organism', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Organism', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='gocam:GeneOrganismRelationship', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'GeneMolecularActivityRelationship': ClassDefinition(name='GeneMolecularActivityRelationship', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/gocam/GeneMolecularActivityRelationship', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.example': Annotation(tag='prompt.example', value='TODO\\n\\ngene: HGNC:1234\\nmolecular_activity: GO:0003674', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['geneMolecularActivityRelationship__gene', 'geneMolecularActivityRelationship__molecular_activity'], slot_usage={}, attributes={'gene': SlotDefinition(name='gene', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='the name of the gene in the pair. This comes first.', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'molecular_activity': SlotDefinition(name='molecular_activity', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='the name of the molecular function in the pair. This comes second. May be a GO term.', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='MolecularActivity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='gocam:GeneMolecularActivityRelationship', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'GeneMolecularActivityRelationship2': ClassDefinition(name='GeneMolecularActivityRelationship2', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/gocam/GeneMolecularActivityRelationship2', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['geneMolecularActivityRelationship2__gene', 'geneMolecularActivityRelationship2__molecular_activity', 'geneMolecularActivityRelationship2__target'], slot_usage={}, attributes={'gene': SlotDefinition(name='gene', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='the name of the gene.', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'molecular_activity': SlotDefinition(name='molecular_activity', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='the name of the molecular activity, for example, ubiquitination. May be a GO term.', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='MolecularActivity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'target': SlotDefinition(name='target', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='the name of the molecular entity that is the target of the molecular activity.', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Molecule', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='gocam:GeneMolecularActivityRelationship2', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'GeneSubcellularLocalizationRelationship': ClassDefinition(name='GeneSubcellularLocalizationRelationship', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/gocam/GeneSubcellularLocalizationRelationship', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['geneSubcellularLocalizationRelationship__gene', 'geneSubcellularLocalizationRelationship__location'], slot_usage={}, attributes={'gene': SlotDefinition(name='gene', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'location': SlotDefinition(name='location', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneLocation', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='gocam:GeneSubcellularLocalizationRelationship', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'GeneGeneInteraction': ClassDefinition(name='GeneGeneInteraction', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/gocam/GeneGeneInteraction', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['geneGeneInteraction__gene1', 'geneGeneInteraction__gene2'], slot_usage={}, attributes={'gene1': SlotDefinition(name='gene1', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'gene2': SlotDefinition(name='gene2', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='gocam:GeneGeneInteraction', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Any': ClassDefinition(name='Any', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Any', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=['linkml:Any'], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='linkml:Any', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ExtractionResult': ClassDefinition(name='ExtractionResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/ExtractionResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A result of extracting knowledge on text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['extractionResult__input_id', 'extractionResult__input_title', 'extractionResult__input_text', 'extractionResult__raw_completion_output', 'extractionResult__prompt', 'extractionResult__extracted_object', 'extractionResult__named_entities'], slot_usage={}, attributes={'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:ExtractionResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'NamedEntity': ClassDefinition(name='NamedEntity', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NamedEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:NamedEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'CompoundExpression': ClassDefinition(name='CompoundExpression', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/CompoundExpression', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='core:CompoundExpression', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Triple': ClassDefinition(name='Triple', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Triple', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Abstract parent for Relation Extraction tasks', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['triple__subject', 'triple__predicate', 'triple__object', 'triple__qualifier', 'triple__subject_qualifier', 'triple__object_qualifier'], slot_usage={}, attributes={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Triple', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'TextWithTriples': ClassDefinition(name='TextWithTriples', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/TextWithTriples', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['textWithTriples__publication', 'textWithTriples__triples'], slot_usage={}, attributes={'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:TextWithTriples', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'RelationshipType': ClassDefinition(name='RelationshipType', id_prefixes=['RO', 'biolink'], definition_uri='http://w3id.org/ontogpt/core/RelationshipType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='core:RelationshipType', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Publication': ClassDefinition(name='Publication', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Publication', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['publication__id', 'publication__title', 'publication__abstract', 'publication__combined_text', 'publication__full_text'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Publication', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'AnnotatorResult': ClassDefinition(name='AnnotatorResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/AnnotatorResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['annotatorResult__subject_text', 'annotatorResult__object_id', 'annotatorResult__object_text'], slot_usage={}, attributes={'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:AnnotatorResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={})}" ; - linkml:enums "{'GeneLocationEnum': EnumDefinition(name='GeneLocationEnum', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/gocam/GeneLocationEnum', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={}, include=[], minus=[], inherits=['GOCellComponent', 'CellType'], reachable_from=None, matches=None, concepts=[]), 'GOCellComponentType': EnumDefinition(name='GOCellComponentType', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/gocam/GOCellComponentType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={}, include=[], minus=[], inherits=[], reachable_from=ReachabilityQuery(source_ontology='obo:go', source_nodes=['GO:0005575'], relationship_types=[], is_direct=None, include_self=None, traverse_up=None), matches=None, concepts=[]), 'CellType': EnumDefinition(name='CellType', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/gocam/CellType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={}, include=[], minus=[], inherits=[], reachable_from=ReachabilityQuery(source_ontology='obo:cl', source_nodes=['CL:0000000'], relationship_types=[], is_direct=None, include_self=None, traverse_up=None), matches=None, concepts=[]), 'NullDataOptions': EnumDefinition(name='NullDataOptions', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NullDataOptions', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'UNSPECIFIED_METHOD_OF_ADMINISTRATION': PermissibleValue(text='UNSPECIFIED_METHOD_OF_ADMINISTRATION', description=None, meaning='NCIT:C149701', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_APPLICABLE': PermissibleValue(text='NOT_APPLICABLE', description=None, meaning='NCIT:C18902', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['not applicable', 'N/A'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_MENTIONED': PermissibleValue(text='NOT_MENTIONED', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[])}" ; - linkml:id "http://w3id.org/ontogpt/gocam" ; - linkml:imports "core", - "linkml:types" ; - linkml:types "{'string': TypeDefinition(name='string', id_prefixes=[], definition_uri='https://w3id.org/linkml/String', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A character string', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Text'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'integer': TypeDefinition(name='integer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Integer', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An integer', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Integer'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='int', uri='xsd:integer', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'boolean': TypeDefinition(name='boolean', id_prefixes=[], definition_uri='https://w3id.org/linkml/Boolean', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A binary (true or false) value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Boolean'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Bool', uri='xsd:boolean', repr='bool', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'float': TypeDefinition(name='float', id_prefixes=[], definition_uri='https://w3id.org/linkml/Float', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:float specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Float'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:float', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'double': TypeDefinition(name='double', id_prefixes=[], definition_uri='https://w3id.org/linkml/Double', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:double specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:Float'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:double', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'decimal': TypeDefinition(name='decimal', id_prefixes=[], definition_uri='https://w3id.org/linkml/Decimal', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number with arbitrary precision that conforms to the xsd:decimal specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=['schema:Number'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Decimal', uri='xsd:decimal', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'time': TypeDefinition(name='time', id_prefixes=[], definition_uri='https://w3id.org/linkml/Time', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A time object represents a (local) time of day, independent of any particular day', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=['URI is dateTime because OWL reasoners do not work with straight date or time'], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Time'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDTime', uri='xsd:time', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date': TypeDefinition(name='date', id_prefixes=[], definition_uri='https://w3id.org/linkml/Date', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a date (year, month and day) in an idealized calendar', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[\"URI is dateTime because OWL reasoners don't work with straight date or time\"], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Date'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDate', uri='xsd:date', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'datetime': TypeDefinition(name='datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/Datetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The combination of a date and time', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:DateTime'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDateTime', uri='xsd:dateTime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date_or_datetime': TypeDefinition(name='date_or_datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/DateOrDatetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Either a date or a datetime', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='linkml:DateOrDatetime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uriorcurie': TypeDefinition(name='uriorcurie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uriorcurie', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a URI or a CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URIorCURIE', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'curie': TypeDefinition(name='curie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Curie', local_names={}, conforms_to='https://www.w3.org/TR/curie/', implements=[], extensions={}, annotations={}, description='a compact URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations this MUST be expanded to a URI', 'in non-RDF serializations MAY be serialized as the compact representation'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Curie', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uri': TypeDefinition(name='uri', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uri', local_names={}, conforms_to='https://www.ietf.org/rfc/rfc3987.txt', implements=[], extensions={}, annotations={}, description='a complete URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:URL'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URI', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ncname': TypeDefinition(name='ncname', id_prefixes=[], definition_uri='https://w3id.org/linkml/Ncname', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Prefix part of CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NCName', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'objectidentifier': TypeDefinition(name='objectidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Objectidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI or CURIE that represents an object in the model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['Used for inheritance and type checking'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='ElementIdentifier', uri='shex:iri', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'nodeidentifier': TypeDefinition(name='nodeidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Nodeidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI, CURIE or BNODE that represents a node in a model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NodeIdentifier', uri='shex:nonLiteral', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpointer': TypeDefinition(name='jsonpointer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpointer', local_names={}, conforms_to='https://datatracker.ietf.org/doc/html/rfc6901', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpath': TypeDefinition(name='jsonpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpath', local_names={}, conforms_to='https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sparqlpath': TypeDefinition(name='sparqlpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Sparqlpath', local_names={}, conforms_to='https://www.w3.org/TR/sparql11-query/#propertypaths', implements=[], extensions={}, annotations={}, description='A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -gocam:CellType a owl:Class, - linkml:EnumDefinition ; - rdfs:label "CellType" ; - owl:unionOf [ rdf:rest () ] . - -gocam:GOCellComponentType a owl:Class, - linkml:EnumDefinition ; - rdfs:label "GOCellComponentType" ; - owl:unionOf [ rdf:rest () ] . - -gocam:GeneLocationEnum a owl:Class, - linkml:EnumDefinition ; - rdfs:label "GeneLocationEnum" ; - owl:unionOf [ rdf:rest () ] . - -gocam:GeneMolecularActivityRelationship2 a owl:Class, - linkml:ClassDefinition ; - rdfs:label "GeneMolecularActivityRelationship2" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass gocam:MolecularActivity ; - owl:onProperty gocam:molecular_activity ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass gocam:Gene ; - owl:onProperty gocam:gene ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass gocam:Molecule ; - owl:onProperty gocam:target ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - linkml:attributes "{'gene': SlotDefinition(name='gene', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='the name of the gene.', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'molecular_activity': SlotDefinition(name='molecular_activity', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='the name of the molecular activity, for example, ubiquitination. May be a GO term.', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='MolecularActivity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'target': SlotDefinition(name='target', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='the name of the molecular entity that is the target of the molecular activity.', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Molecule', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -linkml:SubsetDefinition a owl:Class ; - rdfs:label "subset_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" . - -linkml:TypeDefinition a owl:Class ; - rdfs:label "type_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" ; - linkml:mixins "type_expression" . - -linkml:topValue a owl:DatatypeProperty ; - rdfs:label "value" . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "AnnotatorResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_text> ] ; - linkml:attributes "{'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/ExtractionResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ExtractionResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/named_entities> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/extracted_object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_title> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/prompt> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_text> ] ; - skos:definition "A result of extracting knowledge on text" ; - linkml:attributes "{'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/TextWithTriples> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TextWithTriples" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Triple> ; - owl:onProperty <http://w3id.org/ontogpt/core/triples> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Publication> ; - owl:onProperty <http://w3id.org/ontogpt/core/publication> ] ; - linkml:attributes "{'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/abstract> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "abstract" ; - rdfs:range linkml:String ; - skos:definition "The abstract of the publication" . - -<http://w3id.org/ontogpt/core/combined_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "combined_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/extracted_object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "extracted_object" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "The complex objects extracted from the text" . - -<http://w3id.org/ontogpt/core/full_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "full_text" ; - rdfs:range linkml:String ; - skos:definition "The full text of the publication" . - -<http://w3id.org/ontogpt/core/input_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_title" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/named_entities> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "named_entities" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "Named entities extracted from the text" . - -<http://w3id.org/ontogpt/core/object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/object_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/object_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" . - -<http://w3id.org/ontogpt/core/object_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/predicate> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "predicate" ; - rdfs:range <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/prompt> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "prompt" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/publication> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "publication" ; - gocam:prompt.skip "true" ; - rdfs:range <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "qualifier" ; - rdfs:range linkml:String ; - skos:definition "A qualifier for the statements, e.g. \"NOT\" for negation" . - -<http://w3id.org/ontogpt/core/raw_completion_output> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "raw_completion_output" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/subject> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/subject_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" . - -<http://w3id.org/ontogpt/core/subject_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "title" ; - rdfs:range linkml:String ; - skos:definition "The title of the publication" . - -<http://w3id.org/ontogpt/core/triples> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "triples" ; - rdfs:range <http://w3id.org/ontogpt/core/Triple> . - -gocam:GoCamAnnotations a owl:Class, - linkml:ClassDefinition ; - rdfs:label "GoCamAnnotations" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom gocam:Pathway ; - owl:onProperty gocam:pathways ], - [ a owl:Restriction ; - owl:allValuesFrom gocam:GeneSubcellularLocalizationRelationship ; - owl:onProperty gocam:gene_localizations ], - [ a owl:Restriction ; - owl:allValuesFrom gocam:GeneGeneInteraction ; - owl:onProperty gocam:gene_gene_interactions ], - [ a owl:Restriction ; - owl:allValuesFrom gocam:Organism ; - owl:onProperty gocam:organisms ], - [ a owl:Restriction ; - owl:allValuesFrom gocam:CellularProcess ; - owl:onProperty gocam:cellular_processes ], - [ a owl:Restriction ; - owl:allValuesFrom gocam:GeneMolecularActivityRelationship ; - owl:onProperty gocam:gene_functions ], - [ a owl:Restriction ; - owl:allValuesFrom gocam:Gene ; - owl:onProperty gocam:genes ], - [ a owl:Restriction ; - owl:allValuesFrom gocam:GeneOrganismRelationship ; - owl:onProperty gocam:gene_organisms ], - [ a owl:Restriction ; - owl:allValuesFrom gocam:MolecularActivity ; - owl:onProperty gocam:activities ] ; - linkml:attributes "{'genes': SlotDefinition(name='genes', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of genes', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'organisms': SlotDefinition(name='organisms', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of organism taxons', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Organism', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'gene_organisms': SlotDefinition(name='gene_organisms', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of asterisk separated gene to organism relationships', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneOrganismRelationship', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'activities': SlotDefinition(name='activities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of molecular activities', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='MolecularActivity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'gene_functions': SlotDefinition(name='gene_functions', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of gene to molecular activity relationships', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneMolecularActivityRelationship', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'cellular_processes': SlotDefinition(name='cellular_processes', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of cellular processes', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='CellularProcess', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'pathways': SlotDefinition(name='pathways', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of pathways', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Pathway', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'gene_gene_interactions': SlotDefinition(name='gene_gene_interactions', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of gene to gene interactions', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneGeneInteraction', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'gene_localizations': SlotDefinition(name='gene_localizations', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of genes plus their location in the cell; for example, \"gene1 / cytoplasm; gene2 / mitochondrion\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneSubcellularLocalizationRelationship', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -gocam:activities a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "activities" ; - rdfs:range gocam:MolecularActivity ; - skos:definition "semicolon-separated list of molecular activities" . - -gocam:cellular_processes a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "cellular_processes" ; - rdfs:range gocam:CellularProcess ; - skos:definition "semicolon-separated list of cellular processes" . - -gocam:gene1 a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "gene1" ; - rdfs:range gocam:Gene . - -gocam:gene2 a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "gene2" ; - rdfs:range gocam:Gene . - -gocam:gene_functions a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "gene_functions" ; - rdfs:range gocam:GeneMolecularActivityRelationship ; - skos:definition "semicolon-separated list of gene to molecular activity relationships" . - -gocam:gene_gene_interactions a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "gene_gene_interactions" ; - rdfs:range gocam:GeneGeneInteraction ; - skos:definition "semicolon-separated list of gene to gene interactions" . - -gocam:gene_localizations a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "gene_localizations" ; - rdfs:range gocam:GeneSubcellularLocalizationRelationship ; - skos:definition "semicolon-separated list of genes plus their location in the cell; for example, \"gene1 / cytoplasm; gene2 / mitochondrion\"" . - -gocam:gene_organisms a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "gene_organisms" ; - gocam:prompt "semicolon-separated list of asterisk separated gene to organism relationships" ; - rdfs:range gocam:GeneOrganismRelationship . - -gocam:genes a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "genes" ; - rdfs:range gocam:Gene ; - skos:definition "semicolon-separated list of genes" . - -gocam:id a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "id" ; - rdfs:domain gocam:GeneLocation ; - rdfs:range linkml:String ; - rdfs:subPropertyOf <http://w3id.org/ontogpt/core/id> ; - linkml:is_a "namedEntity__id" . - -gocam:location a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "location" ; - rdfs:range gocam:GeneLocation . - -gocam:organism a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "organism" ; - rdfs:range gocam:Organism . - -gocam:organisms a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "organisms" ; - rdfs:range gocam:Organism ; - skos:definition "semicolon-separated list of organism taxons" . - -gocam:pathways a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "pathways" ; - rdfs:range gocam:Pathway ; - skos:definition "semicolon-separated list of pathways" . - -gocam:target a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "target" ; - gocam:prompt "the name of the molecular entity that is the target of the molecular activity." ; - rdfs:range gocam:Molecule . - -<http://example.org/UNKNOWN/rdfs/label> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "label" ; - gocam:owl "AnnotationProperty, AnnotationAssertion" ; - rdfs:range linkml:String ; - skos:altLabel "name" ; - skos:definition "The label (name) of the named thing" ; - skos:exactMatch <http://example.org/UNKNOWN/rdfs/label> . - -<http://purl.obolibrary.org/obo/NCIT_C149701> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "UNSPECIFIED_METHOD_OF_ADMINISTRATION" . - -<http://purl.obolibrary.org/obo/NCIT_C18902> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_APPLICABLE" . - -<http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_MENTIONED" . - -<http://w3id.org/ontogpt/core/RelationshipType> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "RelationshipType" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/Triple> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Triple" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/RelationshipType> ; - owl:onProperty <http://w3id.org/ontogpt/core/predicate> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject> ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - skos:definition "Abstract parent for Relation Extraction tasks" ; - linkml:attributes "{'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -gocam:CellularProcess a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CellularProcess" ; - gocam:annotators "sqlite:obo:go" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -gocam:GeneGeneInteraction a owl:Class, - linkml:ClassDefinition ; - rdfs:label "GeneGeneInteraction" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass gocam:Gene ; - owl:onProperty gocam:gene1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass gocam:Gene ; - owl:onProperty gocam:gene2 ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - linkml:attributes "{'gene1': SlotDefinition(name='gene1', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'gene2': SlotDefinition(name='gene2', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -gocam:GeneMolecularActivityRelationship a owl:Class, - linkml:ClassDefinition ; - rdfs:label "GeneMolecularActivityRelationship" ; - gocam:prompt.example """TODO - -gene: HGNC:1234 -molecular_activity: GO:0003674""" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass gocam:MolecularActivity ; - owl:onProperty gocam:molecular_activity ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass gocam:Gene ; - owl:onProperty gocam:gene ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - linkml:attributes "{'gene': SlotDefinition(name='gene', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='the name of the gene in the pair. This comes first.', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'molecular_activity': SlotDefinition(name='molecular_activity', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='the name of the molecular function in the pair. This comes second. May be a GO term.', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='MolecularActivity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -gocam:GeneOrganismRelationship a owl:Class, - linkml:ClassDefinition ; - rdfs:label "GeneOrganismRelationship" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass gocam:Gene ; - owl:onProperty gocam:gene ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass gocam:Organism ; - owl:onProperty gocam:organism ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - linkml:attributes "{'gene': SlotDefinition(name='gene', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'organism': SlotDefinition(name='organism', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Organism', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -gocam:GeneSubcellularLocalizationRelationship a owl:Class, - linkml:ClassDefinition ; - rdfs:label "GeneSubcellularLocalizationRelationship" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass gocam:Gene ; - owl:onProperty gocam:gene ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass gocam:GeneLocation ; - owl:onProperty gocam:location ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - linkml:attributes "{'gene': SlotDefinition(name='gene', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'location': SlotDefinition(name='location', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneLocation', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -gocam:Molecule a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Molecule" ; - gocam:annotators "gilda:, sqlite:obo:chebi" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -gocam:Pathway a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Pathway" ; - gocam:annotators "sqlite:obo:go, sqlite:obo:pw" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -gocam:molecular_activity a owl:ObjectProperty, - linkml:SlotDefinition . - -<http://w3id.org/ontogpt/core/NullDataOptions> a owl:Class, - linkml:EnumDefinition ; - rdfs:label "NullDataOptions" ; - owl:unionOf ( <http://purl.obolibrary.org/obo/NCIT_C149701> <http://purl.obolibrary.org/obo/NCIT_C18902> <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> ) ; - linkml:permissible_values <http://purl.obolibrary.org/obo/NCIT_C149701>, - <http://purl.obolibrary.org/obo/NCIT_C18902>, - <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> . - -<http://w3id.org/ontogpt/core/Publication> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Publication" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/abstract> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/title> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/combined_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/full_text> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/id> a owl:ObjectProperty, - linkml:SlotDefinition . - -gocam:GeneLocation a owl:Class, - linkml:ClassDefinition ; - rdfs:label "GeneLocation" ; - gocam:annotators "sqlite:obo:go, sqlite:obo:cl" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty gocam:id ; - owl:qualifiedCardinality 1 ], - <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -gocam:MolecularActivity a owl:Class, - linkml:ClassDefinition ; - rdfs:label "MolecularActivity" ; - gocam:annotators "sqlite:obo:go" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -gocam:Organism a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Organism" ; - gocam:annotators "gilda:, sqlite:obo:ncbitaxon" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -gocam:gene a owl:ObjectProperty, - linkml:SlotDefinition . - -<http://w3id.org/ontogpt/core/Any> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Any" ; - skos:exactMatch linkml:Any ; - linkml:attributes "{}" . - -<http://w3id.org/ontogpt/core/CompoundExpression> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CompoundExpression" ; - linkml:attributes "{}" . - -gocam:Gene a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Gene" ; - gocam:annotators "gilda:, bioportal:hgnc-nr" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/NamedEntity> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "NamedEntity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://example.org/UNKNOWN/rdfs/label> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:ClassDefinition a owl:Class ; - rdfs:label "class_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "class_expression" . - -linkml:SlotDefinition a owl:Class ; - rdfs:label "slot_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "slot_expression" . - - diff --git a/projects/gocam/prefixmap/gocam.yaml b/projects/gocam/prefixmap/gocam.yaml deleted file mode 100644 index e38e646ee..000000000 --- a/projects/gocam/prefixmap/gocam.yaml +++ /dev/null @@ -1,45 +0,0 @@ -{ - "CHEBI": "http://example.org/UNKNOWN/CHEBI/", - "CL": "http://purl.obolibrary.org/obo/CL_", - "EFO": "http://example.org/UNKNOWN/EFO/", - "GO": "http://purl.obolibrary.org/obo/GO_", - "HGNC": "http://example.org/UNKNOWN/HGNC/", - "NCBITaxon": "http://example.org/UNKNOWN/NCBITaxon/", - "PR": "http://example.org/UNKNOWN/PR/", - "PW": "http://example.org/UNKNOWN/PW/", - "RO": "http://purl.obolibrary.org/obo/RO_", - "UBERON": "http://example.org/UNKNOWN/UBERON/", - "UniProtKB": "http://example.org/UNKNOWN/UniProtKB/", - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "gocam": "http://w3id.org/ontogpt/gocam/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } -} diff --git a/projects/gocam/protobuf/gocam.proto b/projects/gocam/protobuf/gocam.proto deleted file mode 100644 index 135e40a64..000000000 --- a/projects/gocam/protobuf/gocam.proto +++ /dev/null @@ -1,108 +0,0 @@ -message AnnotatorResult - { - string subjectText = 0 - string objectId = 0 - string objectText = 0 - } -message CellularProcess - { - string id = 0 - string label = 0 - } -// A result of extracting knowledge on text -message ExtractionResult - { - string inputId = 0 - string inputTitle = 0 - string inputText = 0 - string rawCompletionOutput = 0 - string prompt = 0 - any extractedObject = 0 - repeated any namedEntities = 0 - } -message Gene - { - string id = 0 - string label = 0 - } -message GeneGeneInteraction - { - gene gene1 = 0 - gene gene2 = 0 - } -message GeneLocation - { - string label = 0 - string id = 0 - } -message GeneMolecularActivityRelationship - { - gene gene = 0 - molecularActivity molecularActivity = 0 - } -message GeneMolecularActivityRelationship2 - { - gene gene = 0 - molecularActivity molecularActivity = 0 - molecule target = 0 - } -message GeneOrganismRelationship - { - gene gene = 0 - organism organism = 0 - } -message GeneSubcellularLocalizationRelationship - { - gene gene = 0 - geneLocation location = 0 - } -message GoCamAnnotations - { - repeated gene genes = 0 - repeated organism organisms = 0 - repeated geneOrganismRelationship geneOrganisms = 0 - repeated molecularActivity activities = 0 - repeated geneMolecularActivityRelationship geneFunctions = 0 - repeated cellularProcess cellularProcesses = 0 - repeated pathway pathways = 0 - repeated geneGeneInteraction geneGeneInteractions = 0 - repeated geneSubcellularLocalizationRelationship geneLocalizations = 0 - } -message MolecularActivity - { - string id = 0 - string label = 0 - } -message Molecule - { - string id = 0 - string label = 0 - } -message Organism - { - string id = 0 - string label = 0 - } -message Pathway - { - string id = 0 - string label = 0 - } -message Publication - { - string id = 0 - string title = 0 - string abstract = 0 - string combinedText = 0 - string fullText = 0 - } -message RelationshipType - { - string id = 0 - string label = 0 - } -message TextWithTriples - { - publication publication = 0 - repeated triple triples = 0 - } diff --git a/projects/gocam/shacl/gocam.shacl.ttl b/projects/gocam/shacl/gocam.shacl.ttl deleted file mode 100644 index ffecaeba0..000000000 --- a/projects/gocam/shacl/gocam.shacl.ttl +++ /dev/null @@ -1,391 +0,0 @@ -@prefix gocam: <http://w3id.org/ontogpt/gocam/> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix sh: <http://www.w3.org/ns/shacl#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object_text> ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/object_id> ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject_text> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/AnnotatorResult> . - -<http://w3id.org/ontogpt/core/CompoundExpression> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass <http://w3id.org/ontogpt/core/CompoundExpression> . - -<http://w3id.org/ontogpt/core/ExtractionResult> a sh:NodeShape ; - sh:closed true ; - sh:description "A result of extracting knowledge on text" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class linkml:Any ; - sh:description "Named entities extracted from the text" ; - sh:nodeKind sh:BlankNode ; - sh:order 6 ; - sh:path <http://w3id.org/ontogpt/core/named_entities> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/input_id> ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/input_title> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/input_text> ], - [ sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/prompt> ], - [ sh:class linkml:Any ; - sh:description "The complex objects extracted from the text" ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/extracted_object> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/ExtractionResult> . - -<http://w3id.org/ontogpt/core/TextWithTriples> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/Triple> ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/triples> ], - [ sh:class <http://w3id.org/ontogpt/core/Publication> ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/publication> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/TextWithTriples> . - -gocam:GeneMolecularActivityRelationship2 a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class gocam:Molecule ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path gocam:target ], - [ sh:class gocam:Gene ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path gocam:gene ], - [ sh:class gocam:MolecularActivity ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path gocam:molecular_activity ] ; - sh:targetClass gocam:GeneMolecularActivityRelationship2 . - -gocam:GoCamAnnotations a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class gocam:CellularProcess ; - sh:description "semicolon-separated list of cellular processes" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path gocam:cellular_processes ], - [ sh:class gocam:GeneSubcellularLocalizationRelationship ; - sh:description "semicolon-separated list of genes plus their location in the cell; for example, \"gene1 / cytoplasm; gene2 / mitochondrion\"" ; - sh:nodeKind sh:BlankNode ; - sh:order 8 ; - sh:path gocam:gene_localizations ], - [ sh:class gocam:MolecularActivity ; - sh:description "semicolon-separated list of molecular activities" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path gocam:activities ], - [ sh:class gocam:GeneOrganismRelationship ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path gocam:gene_organisms ], - [ sh:class gocam:GeneGeneInteraction ; - sh:description "semicolon-separated list of gene to gene interactions" ; - sh:nodeKind sh:BlankNode ; - sh:order 7 ; - sh:path gocam:gene_gene_interactions ], - [ sh:class gocam:GeneMolecularActivityRelationship ; - sh:description "semicolon-separated list of gene to molecular activity relationships" ; - sh:nodeKind sh:BlankNode ; - sh:order 4 ; - sh:path gocam:gene_functions ], - [ sh:class gocam:Gene ; - sh:description "semicolon-separated list of genes" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path gocam:genes ], - [ sh:class gocam:Organism ; - sh:description "semicolon-separated list of organism taxons" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path gocam:organisms ], - [ sh:class gocam:Pathway ; - sh:description "semicolon-separated list of pathways" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path gocam:pathways ] ; - sh:targetClass gocam:GoCamAnnotations . - -<http://w3id.org/ontogpt/core/Publication> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The publication identifier" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The full text of the publication" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/full_text> ], - [ sh:description "The title of the publication" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/title> ], - [ sh:description "The abstract of the publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/abstract> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/combined_text> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/RelationshipType> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/Triple> a sh:NodeShape ; - sh:closed false ; - sh:description "Abstract parent for Relation Extraction tasks" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/object_qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/RelationshipType> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/predicate> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ sh:description "A qualifier for the statements, e.g. \"NOT\" for negation" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/qualifier> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Triple> . - -gocam:CellularProcess a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass gocam:CellularProcess . - -gocam:GeneGeneInteraction a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class gocam:Gene ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path gocam:gene1 ], - [ sh:class gocam:Gene ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path gocam:gene2 ] ; - sh:targetClass gocam:GeneGeneInteraction . - -gocam:GeneLocation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass gocam:GeneLocation . - -gocam:GeneMolecularActivityRelationship a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class gocam:Gene ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path gocam:gene ], - [ sh:class gocam:MolecularActivity ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path gocam:molecular_activity ] ; - sh:targetClass gocam:GeneMolecularActivityRelationship . - -gocam:GeneOrganismRelationship a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class gocam:Gene ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path gocam:gene ], - [ sh:class gocam:Organism ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path gocam:organism ] ; - sh:targetClass gocam:GeneOrganismRelationship . - -gocam:GeneSubcellularLocalizationRelationship a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class gocam:GeneLocation ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path gocam:location ], - [ sh:class gocam:Gene ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path gocam:gene ] ; - sh:targetClass gocam:GeneSubcellularLocalizationRelationship . - -gocam:Molecule a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass gocam:Molecule . - -gocam:Pathway a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass gocam:Pathway . - -gocam:Organism a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass gocam:Organism . - -linkml:Any a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass linkml:Any . - -gocam:MolecularActivity a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass gocam:MolecularActivity . - -<http://w3id.org/ontogpt/core/NamedEntity> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/NamedEntity> . - -gocam:Gene a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass gocam:Gene . - diff --git a/projects/gocam/shex/gocam.shex b/projects/gocam/shex/gocam.shex deleted file mode 100644 index fb81046aa..000000000 --- a/projects/gocam/shex/gocam.shex +++ /dev/null @@ -1,260 +0,0 @@ -BASE <http://w3id.org/ontogpt/gocam/> -PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> -PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> -PREFIX linkml: <https://w3id.org/linkml/> -PREFIX core: <http://w3id.org/ontogpt/core/> -PREFIX rdfs1: <http://example.org/UNKNOWN/rdfs/> - - -linkml:String xsd:string - -linkml:Integer xsd:integer - -linkml:Boolean xsd:boolean - -linkml:Float xsd:float - -linkml:Double xsd:double - -linkml:Decimal xsd:decimal - -linkml:Time xsd:time - -linkml:Date xsd:date - -linkml:Datetime xsd:dateTime - -linkml:DateOrDatetime linkml:DateOrDatetime - -linkml:Uriorcurie IRI - -linkml:Curie xsd:string - -linkml:Uri IRI - -linkml:Ncname xsd:string - -linkml:Objectidentifier IRI - -linkml:Nodeidentifier NONLITERAL - -linkml:Jsonpointer xsd:string - -linkml:Jsonpath xsd:string - -linkml:Sparqlpath xsd:string - -core:AnnotatorResult CLOSED { - ( $core:AnnotatorResult_tes ( core:subject_text @linkml:String ? ; - core:object_id @linkml:String ? ; - core:object_text @linkml:String ? - ) ; - rdf:type [ core:AnnotatorResult ] ? - ) -} - -core:Any CLOSED { - ( $core:Any_tes rdf:type . * ; - rdf:type [ linkml:Any ] ? - ) -} - -<CellularProcess> CLOSED { - ( $<CellularProcess_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <CellularProcess> ] - ) -} - -core:CompoundExpression ( - @<GeneGeneInteraction> OR @<GeneMolecularActivityRelationship> OR @<GeneMolecularActivityRelationship2> OR - @<GeneOrganismRelationship> OR @<GeneSubcellularLocalizationRelationship> OR @core:Triple -) - -core:CompoundExpression_struct { - ( $core:CompoundExpression_tes rdf:type . * ; - rdf:type [ core:CompoundExpression ] ? - ) -} - -core:ExtractionResult CLOSED { - ( $core:ExtractionResult_tes ( core:input_id @linkml:String ? ; - core:input_title @linkml:String ? ; - core:input_text @linkml:String ? ; - core:raw_completion_output @linkml:String ? ; - core:prompt @linkml:String ? ; - core:extracted_object @core:Any ? ; - core:named_entities @core:Any * - ) ; - rdf:type [ core:ExtractionResult ] ? - ) -} - -<Gene> CLOSED { - ( $<Gene_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Gene> ] - ) -} - -<GeneGeneInteraction> CLOSED { - ( $<GeneGeneInteraction_tes> ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - <gene1> @<Gene> ? ; - <gene2> @<Gene> ? - ) ; - rdf:type [ <GeneGeneInteraction> ] ? - ) -} - -<GeneLocation> CLOSED { - ( $<GeneLocation_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <GeneLocation> ] - ) -} - -<GeneMolecularActivityRelationship> CLOSED { - ( $<GeneMolecularActivityRelationship_tes> ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - <gene> @<Gene> ? ; - <molecular_activity> @<MolecularActivity> ? - ) ; - rdf:type [ <GeneMolecularActivityRelationship> ] ? - ) -} - -<GeneMolecularActivityRelationship2> CLOSED { - ( $<GeneMolecularActivityRelationship2_tes> ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - <gene> @<Gene> ? ; - <molecular_activity> @<MolecularActivity> ? ; - <target> @<Molecule> ? - ) ; - rdf:type [ <GeneMolecularActivityRelationship2> ] ? - ) -} - -<GeneOrganismRelationship> CLOSED { - ( $<GeneOrganismRelationship_tes> ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - <gene> @<Gene> ? ; - <organism> @<Organism> ? - ) ; - rdf:type [ <GeneOrganismRelationship> ] ? - ) -} - -<GeneSubcellularLocalizationRelationship> CLOSED { - ( $<GeneSubcellularLocalizationRelationship_tes> ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - <gene> @<Gene> ? ; - <location> @<GeneLocation> ? - ) ; - rdf:type [ <GeneSubcellularLocalizationRelationship> ] ? - ) -} - -<GoCamAnnotations> CLOSED { - ( $<GoCamAnnotations_tes> ( <genes> @<Gene> * ; - <organisms> @<Organism> * ; - <gene_organisms> @<GeneOrganismRelationship> * ; - <activities> @<MolecularActivity> * ; - <gene_functions> @<GeneMolecularActivityRelationship> * ; - <cellular_processes> @<CellularProcess> * ; - <pathways> @<Pathway> * ; - <gene_gene_interactions> @<GeneGeneInteraction> * ; - <gene_localizations> @<GeneSubcellularLocalizationRelationship> * - ) ; - rdf:type [ <GoCamAnnotations> ] ? - ) -} - -<MolecularActivity> CLOSED { - ( $<MolecularActivity_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <MolecularActivity> ] - ) -} - -<Molecule> CLOSED { - ( $<Molecule_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Molecule> ] - ) -} - -core:NamedEntity ( - @<CellularProcess> OR @<Gene> OR @<GeneLocation> OR @<MolecularActivity> OR @<Molecule> OR @<Organism> OR @<Pathway> OR - @core:RelationshipType -) - -core:NamedEntity_struct { - ( $core:NamedEntity_tes rdfs1:label @linkml:String ? ; - rdf:type [ core:NamedEntity ] - ) -} - -<Organism> CLOSED { - ( $<Organism_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Organism> ] - ) -} - -<Pathway> CLOSED { - ( $<Pathway_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Pathway> ] - ) -} - -core:Publication CLOSED { - ( $core:Publication_tes ( core:id @linkml:String ? ; - core:title @linkml:String ? ; - core:abstract @linkml:String ? ; - core:combined_text @linkml:String ? ; - core:full_text @linkml:String ? - ) ; - rdf:type [ core:Publication ] ? - ) -} - -core:RelationshipType CLOSED { - ( $core:RelationshipType_tes ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ core:RelationshipType ] - ) -} - -core:TextWithTriples CLOSED { - ( $core:TextWithTriples_tes ( core:publication @core:Publication ? ; - core:triples @core:Triple * - ) ; - rdf:type [ core:TextWithTriples ] ? - ) -} - -core:Triple { - ( $core:Triple_tes ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - core:subject @core:NamedEntity ? ; - core:predicate @core:RelationshipType ? ; - core:object @core:NamedEntity ? ; - core:qualifier @linkml:String ? ; - core:subject_qualifier @core:NamedEntity ? ; - core:object_qualifier @core:NamedEntity ? - ) ; - rdf:type [ core:Triple ] ? - ) -} - - diff --git a/projects/gocam/sqlschema/gocam.sql b/projects/gocam/sqlschema/gocam.sql deleted file mode 100644 index d1a86a14d..000000000 --- a/projects/gocam/sqlschema/gocam.sql +++ /dev/null @@ -1,137 +0,0 @@ - - -CREATE TABLE "AnnotatorResult" ( - subject_text TEXT, - object_id TEXT, - object_text TEXT, - PRIMARY KEY (subject_text, object_id, object_text) -); - -CREATE TABLE "CellularProcess" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "ExtractionResult" ( - input_id TEXT, - input_title TEXT, - input_text TEXT, - raw_completion_output TEXT, - prompt TEXT, - extracted_object TEXT, - named_entities TEXT, - PRIMARY KEY (input_id, input_title, input_text, raw_completion_output, prompt, extracted_object, named_entities) -); - -CREATE TABLE "Gene" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "GeneLocation" ( - label TEXT, - id TEXT NOT NULL, - PRIMARY KEY (id) -); - -CREATE TABLE "GoCamAnnotations" ( - genes TEXT, - organisms TEXT, - gene_organisms TEXT, - activities TEXT, - gene_functions TEXT, - cellular_processes TEXT, - pathways TEXT, - gene_gene_interactions TEXT, - gene_localizations TEXT, - PRIMARY KEY (genes, organisms, gene_organisms, activities, gene_functions, cellular_processes, pathways, gene_gene_interactions, gene_localizations) -); - -CREATE TABLE "MolecularActivity" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Molecule" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Organism" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Pathway" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Publication" ( - id TEXT, - title TEXT, - abstract TEXT, - combined_text TEXT, - full_text TEXT, - PRIMARY KEY (id, title, abstract, combined_text, full_text) -); - -CREATE TABLE "RelationshipType" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "TextWithTriples" ( - publication TEXT, - triples TEXT, - PRIMARY KEY (publication, triples) -); - -CREATE TABLE "GeneGeneInteraction" ( - gene1 TEXT, - gene2 TEXT, - PRIMARY KEY (gene1, gene2), - FOREIGN KEY(gene1) REFERENCES "Gene" (id), - FOREIGN KEY(gene2) REFERENCES "Gene" (id) -); - -CREATE TABLE "GeneMolecularActivityRelationship" ( - gene TEXT, - molecular_activity TEXT, - PRIMARY KEY (gene, molecular_activity), - FOREIGN KEY(gene) REFERENCES "Gene" (id), - FOREIGN KEY(molecular_activity) REFERENCES "MolecularActivity" (id) -); - -CREATE TABLE "GeneMolecularActivityRelationship2" ( - gene TEXT, - molecular_activity TEXT, - target TEXT, - PRIMARY KEY (gene, molecular_activity, target), - FOREIGN KEY(gene) REFERENCES "Gene" (id), - FOREIGN KEY(molecular_activity) REFERENCES "MolecularActivity" (id), - FOREIGN KEY(target) REFERENCES "Molecule" (id) -); - -CREATE TABLE "GeneOrganismRelationship" ( - gene TEXT, - organism TEXT, - PRIMARY KEY (gene, organism), - FOREIGN KEY(gene) REFERENCES "Gene" (id), - FOREIGN KEY(organism) REFERENCES "Organism" (id) -); - -CREATE TABLE "GeneSubcellularLocalizationRelationship" ( - gene TEXT, - location TEXT, - PRIMARY KEY (gene, location), - FOREIGN KEY(gene) REFERENCES "Gene" (id), - FOREIGN KEY(location) REFERENCES "GeneLocation" (id) -); diff --git a/projects/halo/docs/AnnotatorResult.md b/projects/halo/docs/AnnotatorResult.md deleted file mode 100644 index 4f189092b..000000000 --- a/projects/halo/docs/AnnotatorResult.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Class: AnnotatorResult - - - - -URI: [oc:AnnotatorResult](http://w3id.org/ontogpt/ontology-class-templateAnnotatorResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F])](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F]) - -## Attributes - - -### Own - - * [➞subject_text](annotatorResult__subject_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_id](annotatorResult__object_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_text](annotatorResult__object_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) diff --git a/projects/halo/docs/Any.md b/projects/halo/docs/Any.md deleted file mode 100644 index 75c20f2f8..000000000 --- a/projects/halo/docs/Any.md +++ /dev/null @@ -1,25 +0,0 @@ - -# Class: Any - - - - -URI: [oc:Any](http://w3id.org/ontogpt/ontology-class-templateAny) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult])](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult]) - -## Referenced by Class - - * **None** *[➞extracted_object](extractionResult__extracted_object.md)* <sub>0..1</sub> **[Any](Any.md)** - * **None** *[➞named_entities](extractionResult__named_entities.md)* <sub>0..\*</sub> **[Any](Any.md)** - -## Attributes - - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | linkml:Any | - diff --git a/projects/halo/docs/Category.md b/projects/halo/docs/Category.md deleted file mode 100644 index 0b363a659..000000000 --- a/projects/halo/docs/Category.md +++ /dev/null @@ -1,54 +0,0 @@ - -# Class: Category - - - - -URI: [oc:Category](http://w3id.org/ontogpt/ontology-class-templateCategory) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[OntologyElement],[OntologyElement]-%20categories%200..*>[Category|name(i):string;context(i):string%20%3F;description(i):string%20%3F;synonyms(i):string%20*;equivalent_to(i):string%20%3F],[OntologyElement]^-[Category])](https://yuml.me/diagram/nofunky;dir:TB/class/[OntologyElement],[OntologyElement]-%20categories%200..*>[Category|name(i):string;context(i):string%20%3F;description(i):string%20%3F;synonyms(i):string%20*;equivalent_to(i):string%20%3F],[OntologyElement]^-[Category]) - -## Parents - - * is_a: [OntologyElement](OntologyElement.md) - -## Referenced by Class - - * **None** *[➞categories](ontologyElement__categories.md)* <sub>0..\*</sub> **[Category](Category.md)** - -## Attributes - - -### Inherited from OntologyElement: - - * [➞name](ontologyElement__name.md) <sub>1..1</sub> - * Description: the name of the entity - * Range: [String](types/String.md) - * [➞context](ontologyElement__context.md) <sub>0..1</sub> - * Description: the ontology to which this belongs (single-valued) - * Range: [String](types/String.md) - * [➞description](ontologyElement__description.md) <sub>0..1</sub> - * Description: a textual description of the entity (single-valued) - * Range: [String](types/String.md) - * [➞synonyms](ontologyElement__synonyms.md) <sub>0..\*</sub> - * Description: a list of alternative names of the entity - * Range: [String](types/String.md) - * [➞categories](ontologyElement__categories.md) <sub>0..\*</sub> - * Description: a list of the categories to which this entity belongs - * Range: [Category](Category.md) - * [➞subclass_of](ontologyElement__subclass_of.md) <sub>0..\*</sub> - * Description: a list of parent class (superclasses) of this entity - * Range: [OntologyElement](OntologyElement.md) - * [➞part_of](ontologyElement__part_of.md) <sub>0..\*</sub> - * Description: a list of things this element is part of - * Range: [OntologyElement](OntologyElement.md) - * [➞subtypes](ontologyElement__subtypes.md) <sub>0..\*</sub> - * Description: a list of child classes (subclasses) of this entity - * Range: [OntologyElement](OntologyElement.md) - * [➞parts](ontologyElement__parts.md) <sub>0..\*</sub> - * Description: a list of names of things this element has as parts (components) - * Range: [OntologyElement](OntologyElement.md) - * [➞equivalent_to](ontologyElement__equivalent_to.md) <sub>0..1</sub> - * Description: an OWL class expression with the necessary and sufficient conditions for this entity to be an instance of this class - * Range: [String](types/String.md) diff --git a/projects/halo/docs/CompoundExpression.md b/projects/halo/docs/CompoundExpression.md deleted file mode 100644 index 35fe2b15a..000000000 --- a/projects/halo/docs/CompoundExpression.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: CompoundExpression - - - - -URI: [oc:CompoundExpression](http://w3id.org/ontogpt/ontology-class-templateCompoundExpression) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[CompoundExpression]^-[Triple])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[CompoundExpression]^-[Triple]) - -## Children - - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - -## Referenced by Class - - -## Attributes - diff --git a/projects/halo/docs/ExtractionResult.md b/projects/halo/docs/ExtractionResult.md deleted file mode 100644 index fe7d19bb9..000000000 --- a/projects/halo/docs/ExtractionResult.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Class: ExtractionResult - - -A result of extracting knowledge on text - -URI: [oc:ExtractionResult](http://w3id.org/ontogpt/ontology-class-templateExtractionResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any])](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any]) - -## Attributes - - -### Own - - * [➞input_id](extractionResult__input_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_title](extractionResult__input_title.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_text](extractionResult__input_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞prompt](extractionResult__prompt.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞extracted_object](extractionResult__extracted_object.md) <sub>0..1</sub> - * Description: The complex objects extracted from the text - * Range: [Any](Any.md) - * [➞named_entities](extractionResult__named_entities.md) <sub>0..\*</sub> - * Description: Named entities extracted from the text - * Range: [Any](Any.md) diff --git a/projects/halo/docs/NamedEntity.md b/projects/halo/docs/NamedEntity.md deleted file mode 100644 index 12879e464..000000000 --- a/projects/halo/docs/NamedEntity.md +++ /dev/null @@ -1,33 +0,0 @@ - -# Class: NamedEntity - - - - -URI: [oc:NamedEntity](http://w3id.org/ontogpt/ontology-class-templateNamedEntity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[RelationshipType],[Triple])](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[RelationshipType],[Triple]) - -## Children - - * [RelationshipType](RelationshipType.md) - -## Referenced by Class - - * **None** *[➞object](triple__object.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞object_qualifier](triple__object_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject](triple__subject.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject_qualifier](triple__subject_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - -## Attributes - - -### Own - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/halo/docs/NullDataOptions.md b/projects/halo/docs/NullDataOptions.md deleted file mode 100644 index 4b9a6758e..000000000 --- a/projects/halo/docs/NullDataOptions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Enum: NullDataOptions - - - - -URI: [oc:NullDataOptions](http://w3id.org/ontogpt/ontology-class-templateNullDataOptions) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | -| UNSPECIFIED_METHOD_OF_ADMINISTRATION | | NCIT:C149701 | | -| NOT_APPLICABLE | | NCIT:C18902 | {'aliases': ['not applicable', 'N/A']} | -| NOT_MENTIONED | | | | - diff --git a/projects/halo/docs/Ontology.md b/projects/halo/docs/Ontology.md deleted file mode 100644 index f210fae5d..000000000 --- a/projects/halo/docs/Ontology.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Class: Ontology - - - - -URI: [oc:Ontology](http://w3id.org/ontogpt/ontology-class-templateOntology) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[OntologyElement],[OntologyElement]<elements%200..*-++[Ontology])](https://yuml.me/diagram/nofunky;dir:TB/class/[OntologyElement],[OntologyElement]<elements%200..*-++[Ontology]) - -## Attributes - - -### Own - - * [➞elements](ontology__elements.md) <sub>0..\*</sub> - * Range: [OntologyElement](OntologyElement.md) diff --git a/projects/halo/docs/OntologyElement.md b/projects/halo/docs/OntologyElement.md deleted file mode 100644 index 98acc2bf4..000000000 --- a/projects/halo/docs/OntologyElement.md +++ /dev/null @@ -1,60 +0,0 @@ - -# Class: OntologyElement - - - - -URI: [oc:OntologyElement](http://w3id.org/ontogpt/ontology-class-templateOntologyElement) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[OntologyElement]<parts%200..*-%20[OntologyElement|name:string;context:string%20%3F;description:string%20%3F;synonyms:string%20*;equivalent_to:string%20%3F],[OntologyElement]<subtypes%200..*-%20[OntologyElement],[OntologyElement]<part_of%200..*-%20[OntologyElement],[OntologyElement]<subclass_of%200..*-%20[OntologyElement],[Category]<categories%200..*-%20[OntologyElement],[Ontology]++-%20elements%200..*>[OntologyElement],[OntologyElement]^-[Category],[Ontology],[Category])](https://yuml.me/diagram/nofunky;dir:TB/class/[OntologyElement]<parts%200..*-%20[OntologyElement|name:string;context:string%20%3F;description:string%20%3F;synonyms:string%20*;equivalent_to:string%20%3F],[OntologyElement]<subtypes%200..*-%20[OntologyElement],[OntologyElement]<part_of%200..*-%20[OntologyElement],[OntologyElement]<subclass_of%200..*-%20[OntologyElement],[Category]<categories%200..*-%20[OntologyElement],[Ontology]++-%20elements%200..*>[OntologyElement],[OntologyElement]^-[Category],[Ontology],[Category]) - -## Children - - * [Category](Category.md) - -## Referenced by Class - - * **None** *[➞part_of](ontologyElement__part_of.md)* <sub>0..\*</sub> **[OntologyElement](OntologyElement.md)** - * **None** *[➞parts](ontologyElement__parts.md)* <sub>0..\*</sub> **[OntologyElement](OntologyElement.md)** - * **None** *[➞subclass_of](ontologyElement__subclass_of.md)* <sub>0..\*</sub> **[OntologyElement](OntologyElement.md)** - * **None** *[➞subtypes](ontologyElement__subtypes.md)* <sub>0..\*</sub> **[OntologyElement](OntologyElement.md)** - * **None** *[➞elements](ontology__elements.md)* <sub>0..\*</sub> **[OntologyElement](OntologyElement.md)** - * **[OntologyElement](OntologyElement.md)** *[part_of](part_of.md)* <sub>0..\*</sub> **[OntologyElement](OntologyElement.md)** - * **[OntologyElement](OntologyElement.md)** *[subclass_of](subclass_of.md)* <sub>0..\*</sub> **[OntologyElement](OntologyElement.md)** - -## Attributes - - -### Own - - * [➞name](ontologyElement__name.md) <sub>1..1</sub> - * Description: the name of the entity - * Range: [String](types/String.md) - * [➞context](ontologyElement__context.md) <sub>0..1</sub> - * Description: the ontology to which this belongs (single-valued) - * Range: [String](types/String.md) - * [➞description](ontologyElement__description.md) <sub>0..1</sub> - * Description: a textual description of the entity (single-valued) - * Range: [String](types/String.md) - * [➞synonyms](ontologyElement__synonyms.md) <sub>0..\*</sub> - * Description: a list of alternative names of the entity - * Range: [String](types/String.md) - * [➞categories](ontologyElement__categories.md) <sub>0..\*</sub> - * Description: a list of the categories to which this entity belongs - * Range: [Category](Category.md) - * [➞subclass_of](ontologyElement__subclass_of.md) <sub>0..\*</sub> - * Description: a list of parent class (superclasses) of this entity - * Range: [OntologyElement](OntologyElement.md) - * [➞part_of](ontologyElement__part_of.md) <sub>0..\*</sub> - * Description: a list of things this element is part of - * Range: [OntologyElement](OntologyElement.md) - * [➞subtypes](ontologyElement__subtypes.md) <sub>0..\*</sub> - * Description: a list of child classes (subclasses) of this entity - * Range: [OntologyElement](OntologyElement.md) - * [➞parts](ontologyElement__parts.md) <sub>0..\*</sub> - * Description: a list of names of things this element has as parts (components) - * Range: [OntologyElement](OntologyElement.md) - * [➞equivalent_to](ontologyElement__equivalent_to.md) <sub>0..1</sub> - * Description: an OWL class expression with the necessary and sufficient conditions for this entity to be an instance of this class - * Range: [String](types/String.md) diff --git a/projects/halo/docs/Publication.md b/projects/halo/docs/Publication.md deleted file mode 100644 index a55c2f8cc..000000000 --- a/projects/halo/docs/Publication.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Publication - - - - -URI: [oc:Publication](http://w3id.org/ontogpt/ontology-class-templatePublication) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples])](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples]) - -## Referenced by Class - - * **None** *[➞publication](textWithTriples__publication.md)* <sub>0..1</sub> **[Publication](Publication.md)** - -## Attributes - - -### Own - - * [➞id](publication__id.md) <sub>0..1</sub> - * Description: The publication identifier - * Range: [String](types/String.md) - * [➞title](publication__title.md) <sub>0..1</sub> - * Description: The title of the publication - * Range: [String](types/String.md) - * [➞abstract](publication__abstract.md) <sub>0..1</sub> - * Description: The abstract of the publication - * Range: [String](types/String.md) - * [➞combined_text](publication__combined_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞full_text](publication__full_text.md) <sub>0..1</sub> - * Description: The full text of the publication - * Range: [String](types/String.md) diff --git a/projects/halo/docs/RelationshipType.md b/projects/halo/docs/RelationshipType.md deleted file mode 100644 index 4adecdef0..000000000 --- a/projects/halo/docs/RelationshipType.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: RelationshipType - - - - -URI: [oc:RelationshipType](http://w3id.org/ontogpt/ontology-class-templateRelationshipType) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity]) - -## Identifier prefixes - - * RO - * biolink - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞predicate](triple__predicate.md)* <sub>0..1</sub> **[RelationshipType](RelationshipType.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/halo/docs/TextWithTriples.md b/projects/halo/docs/TextWithTriples.md deleted file mode 100644 index e94121934..000000000 --- a/projects/halo/docs/TextWithTriples.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: TextWithTriples - - - - -URI: [oc:TextWithTriples](http://w3id.org/ontogpt/ontology-class-templateTextWithTriples) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication]) - -## Attributes - - -### Own - - * [➞publication](textWithTriples__publication.md) <sub>0..1</sub> - * Range: [Publication](Publication.md) - * [➞triples](textWithTriples__triples.md) <sub>0..\*</sub> - * Range: [Triple](Triple.md) diff --git a/projects/halo/docs/Triple.md b/projects/halo/docs/Triple.md deleted file mode 100644 index 5a0ca3d43..000000000 --- a/projects/halo/docs/Triple.md +++ /dev/null @@ -1,39 +0,0 @@ - -# Class: Triple - - -Abstract parent for Relation Extraction tasks - -URI: [oc:Triple](http://w3id.org/ontogpt/ontology-class-templateTriple) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞triples](textWithTriples__triples.md)* <sub>0..\*</sub> **[Triple](Triple.md)** - -## Attributes - - -### Own - - * [➞subject](triple__subject.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞predicate](triple__predicate.md) <sub>0..1</sub> - * Range: [RelationshipType](RelationshipType.md) - * [➞object](triple__object.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞qualifier](triple__qualifier.md) <sub>0..1</sub> - * Description: A qualifier for the statements, e.g. "NOT" for negation - * Range: [String](types/String.md) - * [➞subject_qualifier](triple__subject_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - * Range: [NamedEntity](NamedEntity.md) - * [➞object_qualifier](triple__object_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * Range: [NamedEntity](NamedEntity.md) diff --git a/projects/halo/docs/annotatorResult__object_id.md b/projects/halo/docs/annotatorResult__object_id.md deleted file mode 100644 index be14e5b97..000000000 --- a/projects/halo/docs/annotatorResult__object_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_id - - - - -URI: [oc:annotatorResult__object_id](http://w3id.org/ontogpt/ontology-class-templateannotatorResult__object_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/halo/docs/annotatorResult__object_text.md b/projects/halo/docs/annotatorResult__object_text.md deleted file mode 100644 index fbf16b458..000000000 --- a/projects/halo/docs/annotatorResult__object_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_text - - - - -URI: [oc:annotatorResult__object_text](http://w3id.org/ontogpt/ontology-class-templateannotatorResult__object_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/halo/docs/annotatorResult__subject_text.md b/projects/halo/docs/annotatorResult__subject_text.md deleted file mode 100644 index 1525bf843..000000000 --- a/projects/halo/docs/annotatorResult__subject_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_text - - - - -URI: [oc:annotatorResult__subject_text](http://w3id.org/ontogpt/ontology-class-templateannotatorResult__subject_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/halo/docs/extractionResult__extracted_object.md b/projects/halo/docs/extractionResult__extracted_object.md deleted file mode 100644 index b1bc7ddff..000000000 --- a/projects/halo/docs/extractionResult__extracted_object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: extracted_object - - -The complex objects extracted from the text - -URI: [oc:extractionResult__extracted_object](http://w3id.org/ontogpt/ontology-class-templateextractionResult__extracted_object) - - -## Domain and Range - -None → <sub>0..1</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/halo/docs/extractionResult__input_id.md b/projects/halo/docs/extractionResult__input_id.md deleted file mode 100644 index 06eab71c1..000000000 --- a/projects/halo/docs/extractionResult__input_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_id - - - - -URI: [oc:extractionResult__input_id](http://w3id.org/ontogpt/ontology-class-templateextractionResult__input_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/halo/docs/extractionResult__input_text.md b/projects/halo/docs/extractionResult__input_text.md deleted file mode 100644 index 1dc6a7221..000000000 --- a/projects/halo/docs/extractionResult__input_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_text - - - - -URI: [oc:extractionResult__input_text](http://w3id.org/ontogpt/ontology-class-templateextractionResult__input_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/halo/docs/extractionResult__input_title.md b/projects/halo/docs/extractionResult__input_title.md deleted file mode 100644 index 2d7893d36..000000000 --- a/projects/halo/docs/extractionResult__input_title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_title - - - - -URI: [oc:extractionResult__input_title](http://w3id.org/ontogpt/ontology-class-templateextractionResult__input_title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/halo/docs/extractionResult__named_entities.md b/projects/halo/docs/extractionResult__named_entities.md deleted file mode 100644 index 37772a93c..000000000 --- a/projects/halo/docs/extractionResult__named_entities.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: named_entities - - -Named entities extracted from the text - -URI: [oc:extractionResult__named_entities](http://w3id.org/ontogpt/ontology-class-templateextractionResult__named_entities) - - -## Domain and Range - -None → <sub>0..\*</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/halo/docs/extractionResult__prompt.md b/projects/halo/docs/extractionResult__prompt.md deleted file mode 100644 index 8ba0ddcab..000000000 --- a/projects/halo/docs/extractionResult__prompt.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: prompt - - - - -URI: [oc:extractionResult__prompt](http://w3id.org/ontogpt/ontology-class-templateextractionResult__prompt) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/halo/docs/extractionResult__raw_completion_output.md b/projects/halo/docs/extractionResult__raw_completion_output.md deleted file mode 100644 index ec9df2512..000000000 --- a/projects/halo/docs/extractionResult__raw_completion_output.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: raw_completion_output - - - - -URI: [oc:extractionResult__raw_completion_output](http://w3id.org/ontogpt/ontology-class-templateextractionResult__raw_completion_output) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/halo/docs/halo.md b/projects/halo/docs/halo.md deleted file mode 100644 index 03a30c543..000000000 --- a/projects/halo/docs/halo.md +++ /dev/null @@ -1,119 +0,0 @@ - -# ontology-class - - -**metamodel version:** 1.7.0 - -**version:** None - - -A template for Ontology Classes - - -### Classes - - * [AnnotatorResult](AnnotatorResult.md) - * [Any](Any.md) - * [CompoundExpression](CompoundExpression.md) - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - * [ExtractionResult](ExtractionResult.md) - A result of extracting knowledge on text - * [NamedEntity](NamedEntity.md) - * [RelationshipType](RelationshipType.md) - * [Ontology](Ontology.md) - * [OntologyElement](OntologyElement.md) - * [Category](Category.md) - * [Publication](Publication.md) - * [TextWithTriples](TextWithTriples.md) - -### Mixins - - -### Slots - - * [➞object_id](annotatorResult__object_id.md) - * [➞object_text](annotatorResult__object_text.md) - * [➞subject_text](annotatorResult__subject_text.md) - * [➞extracted_object](extractionResult__extracted_object.md) - The complex objects extracted from the text - * [➞input_id](extractionResult__input_id.md) - * [➞input_text](extractionResult__input_text.md) - * [➞input_title](extractionResult__input_title.md) - * [➞named_entities](extractionResult__named_entities.md) - Named entities extracted from the text - * [➞prompt](extractionResult__prompt.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) - * [➞id](namedEntity__id.md) - A unique identifier for the named entity - * [➞label](namedEntity__label.md) - The label (name) of the named thing - * [➞categories](ontologyElement__categories.md) - a list of the categories to which this entity belongs - * [➞context](ontologyElement__context.md) - the ontology to which this belongs (single-valued) - * [➞description](ontologyElement__description.md) - a textual description of the entity (single-valued) - * [➞equivalent_to](ontologyElement__equivalent_to.md) - an OWL class expression with the necessary and sufficient conditions for this entity to be an instance of this class - * [➞name](ontologyElement__name.md) - the name of the entity - * [➞part_of](ontologyElement__part_of.md) - a list of things this element is part of - * [➞parts](ontologyElement__parts.md) - a list of names of things this element has as parts (components) - * [➞subclass_of](ontologyElement__subclass_of.md) - a list of parent class (superclasses) of this entity - * [➞subtypes](ontologyElement__subtypes.md) - a list of child classes (subclasses) of this entity - * [➞synonyms](ontologyElement__synonyms.md) - a list of alternative names of the entity - * [➞elements](ontology__elements.md) - * [part_of](part_of.md) - a list of things this element is part of - * [➞abstract](publication__abstract.md) - The abstract of the publication - * [➞combined_text](publication__combined_text.md) - * [➞full_text](publication__full_text.md) - The full text of the publication - * [➞id](publication__id.md) - The publication identifier - * [➞title](publication__title.md) - The title of the publication - * [subclass_of](subclass_of.md) - a list of parent class (superclasses) of this entity - * [➞publication](textWithTriples__publication.md) - * [➞triples](textWithTriples__triples.md) - * [➞object](triple__object.md) - * [➞object_qualifier](triple__object_qualifier.md) - An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * [➞predicate](triple__predicate.md) - * [➞qualifier](triple__qualifier.md) - A qualifier for the statements, e.g. "NOT" for negation - * [➞subject](triple__subject.md) - * [➞subject_qualifier](triple__subject_qualifier.md) - An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -### Enums - - * [NullDataOptions](NullDataOptions.md) - -### Subsets - - -### Types - - -#### Built in - - * **Bool** - * **Curie** - * **Decimal** - * **ElementIdentifier** - * **NCName** - * **NodeIdentifier** - * **URI** - * **URIorCURIE** - * **XSDDate** - * **XSDDateTime** - * **XSDTime** - * **float** - * **int** - * **str** - -#### Defined - - * [Boolean](types/Boolean.md) (**Bool**) - A binary (true or false) value - * [Curie](types/Curie.md) (**Curie**) - a compact URI - * [Date](types/Date.md) (**XSDDate**) - a date (year, month and day) in an idealized calendar - * [DateOrDatetime](types/DateOrDatetime.md) (**str**) - Either a date or a datetime - * [Datetime](types/Datetime.md) (**XSDDateTime**) - The combination of a date and time - * [Decimal](types/Decimal.md) (**Decimal**) - A real number with arbitrary precision that conforms to the xsd:decimal specification - * [Double](types/Double.md) (**float**) - A real number that conforms to the xsd:double specification - * [Float](types/Float.md) (**float**) - A real number that conforms to the xsd:float specification - * [Integer](types/Integer.md) (**int**) - An integer - * [Jsonpath](types/Jsonpath.md) (**str**) - A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - * [Jsonpointer](types/Jsonpointer.md) (**str**) - A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - * [Ncname](types/Ncname.md) (**NCName**) - Prefix part of CURIE - * [Nodeidentifier](types/Nodeidentifier.md) (**NodeIdentifier**) - A URI, CURIE or BNODE that represents a node in a model. - * [Objectidentifier](types/Objectidentifier.md) (**ElementIdentifier**) - A URI or CURIE that represents an object in the model. - * [Sparqlpath](types/Sparqlpath.md) (**str**) - A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - * [String](types/String.md) (**str**) - A character string - * [Time](types/Time.md) (**XSDTime**) - A time object represents a (local) time of day, independent of any particular day - * [Uri](types/Uri.md) (**URI**) - a complete URI - * [Uriorcurie](types/Uriorcurie.md) (**URIorCURIE**) - a URI or a CURIE diff --git a/projects/halo/docs/namedEntity__id.md b/projects/halo/docs/namedEntity__id.md deleted file mode 100644 index 0764cce7f..000000000 --- a/projects/halo/docs/namedEntity__id.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Slot: id - - -A unique identifier for the named entity - -URI: [oc:namedEntity__id](http://w3id.org/ontogpt/ontology-class-templatenamedEntity__id) - - -## Domain and Range - -None → <sub>1..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [NamedEntity](NamedEntity.md) - * [RelationshipType](RelationshipType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | this is populated during the grounding and normalization step | - diff --git a/projects/halo/docs/namedEntity__label.md b/projects/halo/docs/namedEntity__label.md deleted file mode 100644 index 0ce06a4ef..000000000 --- a/projects/halo/docs/namedEntity__label.md +++ /dev/null @@ -1,31 +0,0 @@ - -# Slot: label - - -The label (name) of the named thing - -URI: [oc:namedEntity__label](http://w3id.org/ontogpt/ontology-class-templatenamedEntity__label) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [NamedEntity](NamedEntity.md) - * [RelationshipType](RelationshipType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Aliases:** | | name | -| **Mappings:** | | rdfs:label | - diff --git a/projects/halo/docs/ontologyElement__categories.md b/projects/halo/docs/ontologyElement__categories.md deleted file mode 100644 index d5d3eef1a..000000000 --- a/projects/halo/docs/ontologyElement__categories.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: categories - - -a list of the categories to which this entity belongs - -URI: [oc:ontologyElement__categories](http://w3id.org/ontogpt/ontology-class-templateontologyElement__categories) - - -## Domain and Range - -None → <sub>0..\*</sub> [Category](Category.md) - -## Parents - - -## Children - - -## Used by - - * [Category](Category.md) - * [OntologyElement](OntologyElement.md) diff --git a/projects/halo/docs/ontologyElement__context.md b/projects/halo/docs/ontologyElement__context.md deleted file mode 100644 index 519b959dd..000000000 --- a/projects/halo/docs/ontologyElement__context.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: context - - -the ontology to which this belongs (single-valued) - -URI: [oc:ontologyElement__context](http://w3id.org/ontogpt/ontology-class-templateontologyElement__context) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Category](Category.md) - * [OntologyElement](OntologyElement.md) diff --git a/projects/halo/docs/ontologyElement__description.md b/projects/halo/docs/ontologyElement__description.md deleted file mode 100644 index 897c5f635..000000000 --- a/projects/halo/docs/ontologyElement__description.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: description - - -a textual description of the entity (single-valued) - -URI: [oc:ontologyElement__description](http://w3id.org/ontogpt/ontology-class-templateontologyElement__description) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Category](Category.md) - * [OntologyElement](OntologyElement.md) diff --git a/projects/halo/docs/ontologyElement__equivalent_to.md b/projects/halo/docs/ontologyElement__equivalent_to.md deleted file mode 100644 index 5e9443d52..000000000 --- a/projects/halo/docs/ontologyElement__equivalent_to.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: equivalent_to - - -an OWL class expression with the necessary and sufficient conditions for this entity to be an instance of this class - -URI: [oc:ontologyElement__equivalent_to](http://w3id.org/ontogpt/ontology-class-templateontologyElement__equivalent_to) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Category](Category.md) - * [OntologyElement](OntologyElement.md) diff --git a/projects/halo/docs/ontologyElement__name.md b/projects/halo/docs/ontologyElement__name.md deleted file mode 100644 index de297854e..000000000 --- a/projects/halo/docs/ontologyElement__name.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: name - - -the name of the entity - -URI: [oc:ontologyElement__name](http://w3id.org/ontogpt/ontology-class-templateontologyElement__name) - - -## Domain and Range - -None → <sub>1..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Category](Category.md) - * [OntologyElement](OntologyElement.md) diff --git a/projects/halo/docs/ontologyElement__part_of.md b/projects/halo/docs/ontologyElement__part_of.md deleted file mode 100644 index 0456bb123..000000000 --- a/projects/halo/docs/ontologyElement__part_of.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Slot: part_of - - -a list of things this element is part of - -URI: [oc:ontologyElement__part_of](http://w3id.org/ontogpt/ontology-class-templateontologyElement__part_of) - - -## Domain and Range - -None → <sub>0..\*</sub> [OntologyElement](OntologyElement.md) - -## Parents - - -## Children - - -## Used by - - * [Category](Category.md) - * [OntologyElement](OntologyElement.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | BFO:0000050 | - diff --git a/projects/halo/docs/ontologyElement__parts.md b/projects/halo/docs/ontologyElement__parts.md deleted file mode 100644 index 32c6f3f15..000000000 --- a/projects/halo/docs/ontologyElement__parts.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: parts - - -a list of names of things this element has as parts (components) - -URI: [oc:ontologyElement__parts](http://w3id.org/ontogpt/ontology-class-templateontologyElement__parts) - - -## Domain and Range - -None → <sub>0..\*</sub> [OntologyElement](OntologyElement.md) - -## Parents - - -## Children - - -## Used by - - * [Category](Category.md) - * [OntologyElement](OntologyElement.md) diff --git a/projects/halo/docs/ontologyElement__subclass_of.md b/projects/halo/docs/ontologyElement__subclass_of.md deleted file mode 100644 index 50bf9936d..000000000 --- a/projects/halo/docs/ontologyElement__subclass_of.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Slot: subclass_of - - -a list of parent class (superclasses) of this entity - -URI: [oc:ontologyElement__subclass_of](http://w3id.org/ontogpt/ontology-class-templateontologyElement__subclass_of) - - -## Domain and Range - -None → <sub>0..\*</sub> [OntologyElement](OntologyElement.md) - -## Parents - - -## Children - - -## Used by - - * [Category](Category.md) - * [OntologyElement](OntologyElement.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | rdfs:subClassOf | - diff --git a/projects/halo/docs/ontologyElement__subtypes.md b/projects/halo/docs/ontologyElement__subtypes.md deleted file mode 100644 index 71f378eb9..000000000 --- a/projects/halo/docs/ontologyElement__subtypes.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: subtypes - - -a list of child classes (subclasses) of this entity - -URI: [oc:ontologyElement__subtypes](http://w3id.org/ontogpt/ontology-class-templateontologyElement__subtypes) - - -## Domain and Range - -None → <sub>0..\*</sub> [OntologyElement](OntologyElement.md) - -## Parents - - -## Children - - -## Used by - - * [Category](Category.md) - * [OntologyElement](OntologyElement.md) diff --git a/projects/halo/docs/ontologyElement__synonyms.md b/projects/halo/docs/ontologyElement__synonyms.md deleted file mode 100644 index dae57a11b..000000000 --- a/projects/halo/docs/ontologyElement__synonyms.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: synonyms - - -a list of alternative names of the entity - -URI: [oc:ontologyElement__synonyms](http://w3id.org/ontogpt/ontology-class-templateontologyElement__synonyms) - - -## Domain and Range - -None → <sub>0..\*</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Category](Category.md) - * [OntologyElement](OntologyElement.md) diff --git a/projects/halo/docs/ontology__elements.md b/projects/halo/docs/ontology__elements.md deleted file mode 100644 index 57d0fb5da..000000000 --- a/projects/halo/docs/ontology__elements.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: elements - - - - -URI: [oc:ontology__elements](http://w3id.org/ontogpt/ontology-class-templateontology__elements) - - -## Domain and Range - -None → <sub>0..\*</sub> [OntologyElement](OntologyElement.md) - -## Parents - - -## Children - - -## Used by - - * [Ontology](Ontology.md) diff --git a/projects/halo/docs/part_of.md b/projects/halo/docs/part_of.md deleted file mode 100644 index 58621e4f3..000000000 --- a/projects/halo/docs/part_of.md +++ /dev/null @@ -1,28 +0,0 @@ - -# Slot: part_of - - -a list of things this element is part of - -URI: [oc:part_of](http://w3id.org/ontogpt/ontology-class-templatepart_of) - - -## Domain and Range - -[OntologyElement](OntologyElement.md) → <sub>0..\*</sub> [OntologyElement](OntologyElement.md) - -## Parents - - -## Children - - -## Used by - - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | BFO:0000050 | - diff --git a/projects/halo/docs/publication__abstract.md b/projects/halo/docs/publication__abstract.md deleted file mode 100644 index 7e1c7ff37..000000000 --- a/projects/halo/docs/publication__abstract.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: abstract - - -The abstract of the publication - -URI: [oc:publication__abstract](http://w3id.org/ontogpt/ontology-class-templatepublication__abstract) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/halo/docs/publication__combined_text.md b/projects/halo/docs/publication__combined_text.md deleted file mode 100644 index de03f19fd..000000000 --- a/projects/halo/docs/publication__combined_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: combined_text - - - - -URI: [oc:publication__combined_text](http://w3id.org/ontogpt/ontology-class-templatepublication__combined_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/halo/docs/publication__full_text.md b/projects/halo/docs/publication__full_text.md deleted file mode 100644 index ae02a60d4..000000000 --- a/projects/halo/docs/publication__full_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: full_text - - -The full text of the publication - -URI: [oc:publication__full_text](http://w3id.org/ontogpt/ontology-class-templatepublication__full_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/halo/docs/publication__id.md b/projects/halo/docs/publication__id.md deleted file mode 100644 index 3fbcffacd..000000000 --- a/projects/halo/docs/publication__id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: id - - -The publication identifier - -URI: [oc:publication__id](http://w3id.org/ontogpt/ontology-class-templatepublication__id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/halo/docs/publication__title.md b/projects/halo/docs/publication__title.md deleted file mode 100644 index 5f9f7ed69..000000000 --- a/projects/halo/docs/publication__title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: title - - -The title of the publication - -URI: [oc:publication__title](http://w3id.org/ontogpt/ontology-class-templatepublication__title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/halo/docs/subclass_of.md b/projects/halo/docs/subclass_of.md deleted file mode 100644 index 76fe3918b..000000000 --- a/projects/halo/docs/subclass_of.md +++ /dev/null @@ -1,28 +0,0 @@ - -# Slot: subclass_of - - -a list of parent class (superclasses) of this entity - -URI: [oc:subclass_of](http://w3id.org/ontogpt/ontology-class-templatesubclass_of) - - -## Domain and Range - -[OntologyElement](OntologyElement.md) → <sub>0..\*</sub> [OntologyElement](OntologyElement.md) - -## Parents - - -## Children - - -## Used by - - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | rdfs:subClassOf | - diff --git a/projects/halo/docs/textWithTriples__publication.md b/projects/halo/docs/textWithTriples__publication.md deleted file mode 100644 index 27b0af18d..000000000 --- a/projects/halo/docs/textWithTriples__publication.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: publication - - - - -URI: [oc:textWithTriples__publication](http://w3id.org/ontogpt/ontology-class-templatetextWithTriples__publication) - - -## Domain and Range - -None → <sub>0..1</sub> [Publication](Publication.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/halo/docs/textWithTriples__triples.md b/projects/halo/docs/textWithTriples__triples.md deleted file mode 100644 index d3a729b64..000000000 --- a/projects/halo/docs/textWithTriples__triples.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: triples - - - - -URI: [oc:textWithTriples__triples](http://w3id.org/ontogpt/ontology-class-templatetextWithTriples__triples) - - -## Domain and Range - -None → <sub>0..\*</sub> [Triple](Triple.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/halo/docs/triple__object.md b/projects/halo/docs/triple__object.md deleted file mode 100644 index 19c663552..000000000 --- a/projects/halo/docs/triple__object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object - - - - -URI: [oc:triple__object](http://w3id.org/ontogpt/ontology-class-templatetriple__object) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/halo/docs/triple__object_qualifier.md b/projects/halo/docs/triple__object_qualifier.md deleted file mode 100644 index bead5d4a5..000000000 --- a/projects/halo/docs/triple__object_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_qualifier - - -An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - -URI: [oc:triple__object_qualifier](http://w3id.org/ontogpt/ontology-class-templatetriple__object_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/halo/docs/triple__predicate.md b/projects/halo/docs/triple__predicate.md deleted file mode 100644 index 425642196..000000000 --- a/projects/halo/docs/triple__predicate.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: predicate - - - - -URI: [oc:triple__predicate](http://w3id.org/ontogpt/ontology-class-templatetriple__predicate) - - -## Domain and Range - -None → <sub>0..1</sub> [RelationshipType](RelationshipType.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/halo/docs/triple__qualifier.md b/projects/halo/docs/triple__qualifier.md deleted file mode 100644 index 9277dabfe..000000000 --- a/projects/halo/docs/triple__qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: qualifier - - -A qualifier for the statements, e.g. "NOT" for negation - -URI: [oc:triple__qualifier](http://w3id.org/ontogpt/ontology-class-templatetriple__qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/halo/docs/triple__subject.md b/projects/halo/docs/triple__subject.md deleted file mode 100644 index 89487785e..000000000 --- a/projects/halo/docs/triple__subject.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject - - - - -URI: [oc:triple__subject](http://w3id.org/ontogpt/ontology-class-templatetriple__subject) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/halo/docs/triple__subject_qualifier.md b/projects/halo/docs/triple__subject_qualifier.md deleted file mode 100644 index e63c6bbd8..000000000 --- a/projects/halo/docs/triple__subject_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_qualifier - - -An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -URI: [oc:triple__subject_qualifier](http://w3id.org/ontogpt/ontology-class-templatetriple__subject_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/halo/docs/types/Boolean.md b/projects/halo/docs/types/Boolean.md deleted file mode 100644 index dc83a9c6e..000000000 --- a/projects/halo/docs/types/Boolean.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: boolean - - -A binary (true or false) value - -URI: [linkml:Boolean](https://w3id.org/linkml/Boolean) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Bool** | -| Representation | | bool | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Boolean | - diff --git a/projects/halo/docs/types/Curie.md b/projects/halo/docs/types/Curie.md deleted file mode 100644 index c1803f93f..000000000 --- a/projects/halo/docs/types/Curie.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: curie - - -a compact URI - -URI: [linkml:Curie](https://w3id.org/linkml/Curie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Curie** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations this MUST be expanded to a URI | -| | | in non-RDF serializations MAY be serialized as the compact representation | - diff --git a/projects/halo/docs/types/Date.md b/projects/halo/docs/types/Date.md deleted file mode 100644 index 06948af97..000000000 --- a/projects/halo/docs/types/Date.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: date - - -a date (year, month and day) in an idealized calendar - -URI: [linkml:Date](https://w3id.org/linkml/Date) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDate** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Date | - diff --git a/projects/halo/docs/types/DateOrDatetime.md b/projects/halo/docs/types/DateOrDatetime.md deleted file mode 100644 index ef983898d..000000000 --- a/projects/halo/docs/types/DateOrDatetime.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: date_or_datetime - - -Either a date or a datetime - -URI: [linkml:DateOrDatetime](https://w3id.org/linkml/DateOrDatetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/halo/docs/types/Datetime.md b/projects/halo/docs/types/Datetime.md deleted file mode 100644 index 9510454a8..000000000 --- a/projects/halo/docs/types/Datetime.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: datetime - - -The combination of a date and time - -URI: [linkml:Datetime](https://w3id.org/linkml/Datetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDateTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:DateTime | - diff --git a/projects/halo/docs/types/Decimal.md b/projects/halo/docs/types/Decimal.md deleted file mode 100644 index a7ba14a5d..000000000 --- a/projects/halo/docs/types/Decimal.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: decimal - - -A real number with arbitrary precision that conforms to the xsd:decimal specification - -URI: [linkml:Decimal](https://w3id.org/linkml/Decimal) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Decimal** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Broad Mappings:** | | schema:Number | - diff --git a/projects/halo/docs/types/Double.md b/projects/halo/docs/types/Double.md deleted file mode 100644 index cfe6d71e2..000000000 --- a/projects/halo/docs/types/Double.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: double - - -A real number that conforms to the xsd:double specification - -URI: [linkml:Double](https://w3id.org/linkml/Double) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Close Mappings:** | | schema:Float | - diff --git a/projects/halo/docs/types/Float.md b/projects/halo/docs/types/Float.md deleted file mode 100644 index 7b303f96f..000000000 --- a/projects/halo/docs/types/Float.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: float - - -A real number that conforms to the xsd:float specification - -URI: [linkml:Float](https://w3id.org/linkml/Float) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Float | - diff --git a/projects/halo/docs/types/Integer.md b/projects/halo/docs/types/Integer.md deleted file mode 100644 index 3cfcc66d9..000000000 --- a/projects/halo/docs/types/Integer.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: integer - - -An integer - -URI: [linkml:Integer](https://w3id.org/linkml/Integer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **int** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Integer | - diff --git a/projects/halo/docs/types/Jsonpath.md b/projects/halo/docs/types/Jsonpath.md deleted file mode 100644 index a03a58e67..000000000 --- a/projects/halo/docs/types/Jsonpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpath - - -A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpath](https://w3id.org/linkml/Jsonpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/halo/docs/types/Jsonpointer.md b/projects/halo/docs/types/Jsonpointer.md deleted file mode 100644 index a0e1ac492..000000000 --- a/projects/halo/docs/types/Jsonpointer.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpointer - - -A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpointer](https://w3id.org/linkml/Jsonpointer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/halo/docs/types/Ncname.md b/projects/halo/docs/types/Ncname.md deleted file mode 100644 index 710b0b04a..000000000 --- a/projects/halo/docs/types/Ncname.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: ncname - - -Prefix part of CURIE - -URI: [linkml:Ncname](https://w3id.org/linkml/Ncname) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NCName** | -| Representation | | str | diff --git a/projects/halo/docs/types/Nodeidentifier.md b/projects/halo/docs/types/Nodeidentifier.md deleted file mode 100644 index f0097cdf4..000000000 --- a/projects/halo/docs/types/Nodeidentifier.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: nodeidentifier - - -A URI, CURIE or BNODE that represents a node in a model. - -URI: [linkml:Nodeidentifier](https://w3id.org/linkml/Nodeidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NodeIdentifier** | -| Representation | | str | diff --git a/projects/halo/docs/types/Objectidentifier.md b/projects/halo/docs/types/Objectidentifier.md deleted file mode 100644 index 454ba6be6..000000000 --- a/projects/halo/docs/types/Objectidentifier.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: objectidentifier - - -A URI or CURIE that represents an object in the model. - -URI: [linkml:Objectidentifier](https://w3id.org/linkml/Objectidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **ElementIdentifier** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | Used for inheritance and type checking | - diff --git a/projects/halo/docs/types/Sparqlpath.md b/projects/halo/docs/types/Sparqlpath.md deleted file mode 100644 index fd99a927e..000000000 --- a/projects/halo/docs/types/Sparqlpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: sparqlpath - - -A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - -URI: [linkml:Sparqlpath](https://w3id.org/linkml/Sparqlpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/halo/docs/types/String.md b/projects/halo/docs/types/String.md deleted file mode 100644 index 6e61d7081..000000000 --- a/projects/halo/docs/types/String.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: string - - -A character string - -URI: [linkml:String](https://w3id.org/linkml/String) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Text | - diff --git a/projects/halo/docs/types/Time.md b/projects/halo/docs/types/Time.md deleted file mode 100644 index 2b8652bcd..000000000 --- a/projects/halo/docs/types/Time.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: time - - -A time object represents a (local) time of day, independent of any particular day - -URI: [linkml:Time](https://w3id.org/linkml/Time) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Time | - diff --git a/projects/halo/docs/types/Uri.md b/projects/halo/docs/types/Uri.md deleted file mode 100644 index 343807a5e..000000000 --- a/projects/halo/docs/types/Uri.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: uri - - -a complete URI - -URI: [linkml:Uri](https://w3id.org/linkml/Uri) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URI** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node | -| **Close Mappings:** | | schema:URL | - diff --git a/projects/halo/docs/types/Uriorcurie.md b/projects/halo/docs/types/Uriorcurie.md deleted file mode 100644 index 2f7b65087..000000000 --- a/projects/halo/docs/types/Uriorcurie.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: uriorcurie - - -a URI or a CURIE - -URI: [linkml:Uriorcurie](https://w3id.org/linkml/Uriorcurie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URIorCURIE** | -| Representation | | str | diff --git a/projects/halo/excel/halo.xlsx b/projects/halo/excel/halo.xlsx deleted file mode 100644 index 8bc324a24..000000000 Binary files a/projects/halo/excel/halo.xlsx and /dev/null differ diff --git a/projects/halo/graphql/halo.graphql b/projects/halo/graphql/halo.graphql deleted file mode 100644 index 16f95365e..000000000 --- a/projects/halo/graphql/halo.graphql +++ /dev/null @@ -1,96 +0,0 @@ -type AnnotatorResult - { - subjectText: String - objectId: String - objectText: String - } - -type Any - { - } - -type Category - { - name: String! - context: String - description: String - synonyms: [String] - categories: [Category] - subclassOf: [OntologyElement] - partOf: [OntologyElement] - subtypes: [OntologyElement] - parts: [OntologyElement] - equivalentTo: String - } - -interface CompoundExpression - { - } - -type ExtractionResult - { - inputId: String - inputTitle: String - inputText: String - rawCompletionOutput: String - prompt: String - extractedObject: Any - namedEntities: [Any] - } - -interface NamedEntity - { - id: String! - label: String - } - -type Ontology - { - elements: [OntologyElement] - } - -type OntologyElement - { - name: String! - context: String - description: String - synonyms: [String] - categories: [Category] - subclassOf: [OntologyElement] - partOf: [OntologyElement] - subtypes: [OntologyElement] - parts: [OntologyElement] - equivalentTo: String - } - -type Publication - { - id: String - title: String - abstract: String - combinedText: String - fullText: String - } - -type RelationshipType - { - id: String! - label: String - } - -type TextWithTriples - { - publication: Publication - triples: [Triple] - } - -interface Triple - { - subject: NamedEntity - predicate: RelationshipType - object: NamedEntity - qualifier: String - subjectQualifier: NamedEntity - objectQualifier: NamedEntity - } - diff --git a/projects/halo/halo.py b/projects/halo/halo.py deleted file mode 100644 index 42d6d1376..000000000 --- a/projects/halo/halo.py +++ /dev/null @@ -1,509 +0,0 @@ -# Auto generated from halo.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-08-07T10:54:01 -# Schema: ontology-class -# -# id: https://w3id.org/ontogpt/halo -# description: A template for Ontology Classes -# license: https://creativecommons.org/publicdomain/zero/1.0/ - -import dataclasses -import sys -import re -from jsonasobj2 import JsonObj, as_dict -from typing import Optional, List, Union, Dict, ClassVar, Any -from dataclasses import dataclass -from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions - -from linkml_runtime.utils.slot import Slot -from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode -from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int -from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs -from linkml_runtime.utils.formatutils import camelcase, underscore, sfx -from linkml_runtime.utils.enumerations import EnumDefinitionImpl -from rdflib import Namespace, URIRef -from linkml_runtime.utils.curienamespace import CurieNamespace -from linkml_runtime.linkml_model.types import String - -metamodel_version = "1.7.0" -version = None - -# Overwrite dataclasses _init_fn to add **kwargs in __init__ -dataclasses._init_fn = dataclasses_init_fn_with_kwargs - -# Namespaces -BFO = CurieNamespace('BFO', 'http://purl.obolibrary.org/obo/BFO_') -RO = CurieNamespace('RO', 'http://purl.obolibrary.org/obo/RO_') -BIOLINK = CurieNamespace('biolink', 'http://example.org/UNKNOWN/biolink/') -CORE = CurieNamespace('core', 'http://w3id.org/ontogpt/core/') -LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') -OC = CurieNamespace('oc', 'http://w3id.org/ontogpt/ontology-class-template') -RDFS = CurieNamespace('rdfs', 'http://example.org/UNKNOWN/rdfs/') -DEFAULT_ = OC - - -# Types - -# Class references -class OntologyElementName(extended_str): - pass - - -class CategoryName(OntologyElementName): - pass - - -class NamedEntityId(extended_str): - pass - - -class RelationshipTypeId(NamedEntityId): - pass - - -@dataclass -class Ontology(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = OC.Ontology - class_class_curie: ClassVar[str] = "oc:Ontology" - class_name: ClassVar[str] = "Ontology" - class_model_uri: ClassVar[URIRef] = OC.Ontology - - elements: Optional[Union[Dict[Union[str, OntologyElementName], Union[dict, "OntologyElement"]], List[Union[dict, "OntologyElement"]]]] = empty_dict() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - self._normalize_inlined_as_list(slot_name="elements", slot_type=OntologyElement, key_name="name", keyed=True) - - super().__post_init__(**kwargs) - - -@dataclass -class OntologyElement(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = OC.OntologyElement - class_class_curie: ClassVar[str] = "oc:OntologyElement" - class_name: ClassVar[str] = "OntologyElement" - class_model_uri: ClassVar[URIRef] = OC.OntologyElement - - name: Union[str, OntologyElementName] = None - context: Optional[str] = None - description: Optional[str] = None - synonyms: Optional[Union[str, List[str]]] = empty_list() - categories: Optional[Union[Union[str, CategoryName], List[Union[str, CategoryName]]]] = empty_list() - subclass_of: Optional[Union[Union[str, OntologyElementName], List[Union[str, OntologyElementName]]]] = empty_list() - part_of: Optional[Union[Union[str, OntologyElementName], List[Union[str, OntologyElementName]]]] = empty_list() - subtypes: Optional[Union[Union[str, OntologyElementName], List[Union[str, OntologyElementName]]]] = empty_list() - parts: Optional[Union[Union[str, OntologyElementName], List[Union[str, OntologyElementName]]]] = empty_list() - equivalent_to: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.name): - self.MissingRequiredField("name") - if not isinstance(self.name, OntologyElementName): - self.name = OntologyElementName(self.name) - - if self.context is not None and not isinstance(self.context, str): - self.context = str(self.context) - - if self.description is not None and not isinstance(self.description, str): - self.description = str(self.description) - - if not isinstance(self.synonyms, list): - self.synonyms = [self.synonyms] if self.synonyms is not None else [] - self.synonyms = [v if isinstance(v, str) else str(v) for v in self.synonyms] - - if not isinstance(self.categories, list): - self.categories = [self.categories] if self.categories is not None else [] - self.categories = [v if isinstance(v, CategoryName) else CategoryName(v) for v in self.categories] - - if not isinstance(self.subclass_of, list): - self.subclass_of = [self.subclass_of] if self.subclass_of is not None else [] - self.subclass_of = [v if isinstance(v, OntologyElementName) else OntologyElementName(v) for v in self.subclass_of] - - if not isinstance(self.part_of, list): - self.part_of = [self.part_of] if self.part_of is not None else [] - self.part_of = [v if isinstance(v, OntologyElementName) else OntologyElementName(v) for v in self.part_of] - - if not isinstance(self.subtypes, list): - self.subtypes = [self.subtypes] if self.subtypes is not None else [] - self.subtypes = [v if isinstance(v, OntologyElementName) else OntologyElementName(v) for v in self.subtypes] - - if not isinstance(self.parts, list): - self.parts = [self.parts] if self.parts is not None else [] - self.parts = [v if isinstance(v, OntologyElementName) else OntologyElementName(v) for v in self.parts] - - if self.equivalent_to is not None and not isinstance(self.equivalent_to, str): - self.equivalent_to = str(self.equivalent_to) - - super().__post_init__(**kwargs) - - -@dataclass -class Category(OntologyElement): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = OC.Category - class_class_curie: ClassVar[str] = "oc:Category" - class_name: ClassVar[str] = "Category" - class_model_uri: ClassVar[URIRef] = OC.Category - - name: Union[str, CategoryName] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.name): - self.MissingRequiredField("name") - if not isinstance(self.name, CategoryName): - self.name = CategoryName(self.name) - - super().__post_init__(**kwargs) - - -Any = Any - -@dataclass -class ExtractionResult(YAMLRoot): - """ - A result of extracting knowledge on text - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.ExtractionResult - class_class_curie: ClassVar[str] = "core:ExtractionResult" - class_name: ClassVar[str] = "ExtractionResult" - class_model_uri: ClassVar[URIRef] = OC.ExtractionResult - - input_id: Optional[str] = None - input_title: Optional[str] = None - input_text: Optional[str] = None - raw_completion_output: Optional[str] = None - prompt: Optional[str] = None - extracted_object: Optional[Union[dict, Any]] = None - named_entities: Optional[Union[Union[dict, Any], List[Union[dict, Any]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.input_id is not None and not isinstance(self.input_id, str): - self.input_id = str(self.input_id) - - if self.input_title is not None and not isinstance(self.input_title, str): - self.input_title = str(self.input_title) - - if self.input_text is not None and not isinstance(self.input_text, str): - self.input_text = str(self.input_text) - - if self.raw_completion_output is not None and not isinstance(self.raw_completion_output, str): - self.raw_completion_output = str(self.raw_completion_output) - - if self.prompt is not None and not isinstance(self.prompt, str): - self.prompt = str(self.prompt) - - super().__post_init__(**kwargs) - - -@dataclass -class NamedEntity(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.NamedEntity - class_class_curie: ClassVar[str] = "core:NamedEntity" - class_name: ClassVar[str] = "NamedEntity" - class_model_uri: ClassVar[URIRef] = OC.NamedEntity - - id: Union[str, NamedEntityId] = None - label: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, NamedEntityId): - self.id = NamedEntityId(self.id) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - super().__post_init__(**kwargs) - - -class CompoundExpression(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.CompoundExpression - class_class_curie: ClassVar[str] = "core:CompoundExpression" - class_name: ClassVar[str] = "CompoundExpression" - class_model_uri: ClassVar[URIRef] = OC.CompoundExpression - - -@dataclass -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Triple - class_class_curie: ClassVar[str] = "core:Triple" - class_name: ClassVar[str] = "Triple" - class_model_uri: ClassVar[URIRef] = OC.Triple - - subject: Optional[Union[str, NamedEntityId]] = None - predicate: Optional[Union[str, RelationshipTypeId]] = None - object: Optional[Union[str, NamedEntityId]] = None - qualifier: Optional[str] = None - subject_qualifier: Optional[Union[str, NamedEntityId]] = None - object_qualifier: Optional[Union[str, NamedEntityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, NamedEntityId): - self.subject = NamedEntityId(self.subject) - - if self.predicate is not None and not isinstance(self.predicate, RelationshipTypeId): - self.predicate = RelationshipTypeId(self.predicate) - - if self.object is not None and not isinstance(self.object, NamedEntityId): - self.object = NamedEntityId(self.object) - - if self.qualifier is not None and not isinstance(self.qualifier, str): - self.qualifier = str(self.qualifier) - - if self.subject_qualifier is not None and not isinstance(self.subject_qualifier, NamedEntityId): - self.subject_qualifier = NamedEntityId(self.subject_qualifier) - - if self.object_qualifier is not None and not isinstance(self.object_qualifier, NamedEntityId): - self.object_qualifier = NamedEntityId(self.object_qualifier) - - super().__post_init__(**kwargs) - - -@dataclass -class TextWithTriples(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.TextWithTriples - class_class_curie: ClassVar[str] = "core:TextWithTriples" - class_name: ClassVar[str] = "TextWithTriples" - class_model_uri: ClassVar[URIRef] = OC.TextWithTriples - - publication: Optional[Union[dict, "Publication"]] = None - triples: Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.publication is not None and not isinstance(self.publication, Publication): - self.publication = Publication(**as_dict(self.publication)) - - if not isinstance(self.triples, list): - self.triples = [self.triples] if self.triples is not None else [] - self.triples = [v if isinstance(v, Triple) else Triple(**as_dict(v)) for v in self.triples] - - super().__post_init__(**kwargs) - - -@dataclass -class RelationshipType(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.RelationshipType - class_class_curie: ClassVar[str] = "core:RelationshipType" - class_name: ClassVar[str] = "RelationshipType" - class_model_uri: ClassVar[URIRef] = OC.RelationshipType - - id: Union[str, RelationshipTypeId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, RelationshipTypeId): - self.id = RelationshipTypeId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Publication(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Publication - class_class_curie: ClassVar[str] = "core:Publication" - class_name: ClassVar[str] = "Publication" - class_model_uri: ClassVar[URIRef] = OC.Publication - - id: Optional[str] = None - title: Optional[str] = None - abstract: Optional[str] = None - combined_text: Optional[str] = None - full_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.id is not None and not isinstance(self.id, str): - self.id = str(self.id) - - if self.title is not None and not isinstance(self.title, str): - self.title = str(self.title) - - if self.abstract is not None and not isinstance(self.abstract, str): - self.abstract = str(self.abstract) - - if self.combined_text is not None and not isinstance(self.combined_text, str): - self.combined_text = str(self.combined_text) - - if self.full_text is not None and not isinstance(self.full_text, str): - self.full_text = str(self.full_text) - - super().__post_init__(**kwargs) - - -@dataclass -class AnnotatorResult(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.AnnotatorResult - class_class_curie: ClassVar[str] = "core:AnnotatorResult" - class_name: ClassVar[str] = "AnnotatorResult" - class_model_uri: ClassVar[URIRef] = OC.AnnotatorResult - - subject_text: Optional[str] = None - object_id: Optional[str] = None - object_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject_text is not None and not isinstance(self.subject_text, str): - self.subject_text = str(self.subject_text) - - if self.object_id is not None and not isinstance(self.object_id, str): - self.object_id = str(self.object_id) - - if self.object_text is not None and not isinstance(self.object_text, str): - self.object_text = str(self.object_text) - - super().__post_init__(**kwargs) - - -# Enumerations -class NullDataOptions(EnumDefinitionImpl): - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = PermissibleValue(text="UNSPECIFIED_METHOD_OF_ADMINISTRATION", - meaning=NCIT.C149701) - NOT_APPLICABLE = PermissibleValue(text="NOT_APPLICABLE", - meaning=NCIT.C18902) - NOT_MENTIONED = PermissibleValue(text="NOT_MENTIONED") - - _defn = EnumDefinition( - name="NullDataOptions", - ) - -# Slots -class slots: - pass - -slots.subclass_of = Slot(uri=RDFS.subClassOf, name="subclass_of", curie=RDFS.curie('subClassOf'), - model_uri=OC.subclass_of, domain=OntologyElement, range=Optional[Union[Union[str, OntologyElementName], List[Union[str, OntologyElementName]]]]) - -slots.part_of = Slot(uri=BFO['0000050'], name="part_of", curie=BFO.curie('0000050'), - model_uri=OC.part_of, domain=OntologyElement, range=Optional[Union[Union[str, OntologyElementName], List[Union[str, OntologyElementName]]]]) - -slots.ontology__elements = Slot(uri=OC.elements, name="ontology__elements", curie=OC.curie('elements'), - model_uri=OC.ontology__elements, domain=None, range=Optional[Union[Dict[Union[str, OntologyElementName], Union[dict, OntologyElement]], List[Union[dict, OntologyElement]]]]) - -slots.ontologyElement__name = Slot(uri=OC.name, name="ontologyElement__name", curie=OC.curie('name'), - model_uri=OC.ontologyElement__name, domain=None, range=URIRef) - -slots.ontologyElement__context = Slot(uri=OC.context, name="ontologyElement__context", curie=OC.curie('context'), - model_uri=OC.ontologyElement__context, domain=None, range=Optional[str]) - -slots.ontologyElement__description = Slot(uri=OC.description, name="ontologyElement__description", curie=OC.curie('description'), - model_uri=OC.ontologyElement__description, domain=None, range=Optional[str]) - -slots.ontologyElement__synonyms = Slot(uri=OC.synonyms, name="ontologyElement__synonyms", curie=OC.curie('synonyms'), - model_uri=OC.ontologyElement__synonyms, domain=None, range=Optional[Union[str, List[str]]]) - -slots.ontologyElement__categories = Slot(uri=OC.categories, name="ontologyElement__categories", curie=OC.curie('categories'), - model_uri=OC.ontologyElement__categories, domain=None, range=Optional[Union[Union[str, CategoryName], List[Union[str, CategoryName]]]]) - -slots.ontologyElement__subclass_of = Slot(uri=RDFS.subClassOf, name="ontologyElement__subclass_of", curie=RDFS.curie('subClassOf'), - model_uri=OC.ontologyElement__subclass_of, domain=None, range=Optional[Union[Union[str, OntologyElementName], List[Union[str, OntologyElementName]]]]) - -slots.ontologyElement__part_of = Slot(uri=BFO['0000050'], name="ontologyElement__part_of", curie=BFO.curie('0000050'), - model_uri=OC.ontologyElement__part_of, domain=None, range=Optional[Union[Union[str, OntologyElementName], List[Union[str, OntologyElementName]]]]) - -slots.ontologyElement__subtypes = Slot(uri=OC.subtypes, name="ontologyElement__subtypes", curie=OC.curie('subtypes'), - model_uri=OC.ontologyElement__subtypes, domain=None, range=Optional[Union[Union[str, OntologyElementName], List[Union[str, OntologyElementName]]]]) - -slots.ontologyElement__parts = Slot(uri=OC.parts, name="ontologyElement__parts", curie=OC.curie('parts'), - model_uri=OC.ontologyElement__parts, domain=None, range=Optional[Union[Union[str, OntologyElementName], List[Union[str, OntologyElementName]]]]) - -slots.ontologyElement__equivalent_to = Slot(uri=OC.equivalent_to, name="ontologyElement__equivalent_to", curie=OC.curie('equivalent_to'), - model_uri=OC.ontologyElement__equivalent_to, domain=None, range=Optional[str]) - -slots.extractionResult__input_id = Slot(uri=CORE.input_id, name="extractionResult__input_id", curie=CORE.curie('input_id'), - model_uri=OC.extractionResult__input_id, domain=None, range=Optional[str]) - -slots.extractionResult__input_title = Slot(uri=CORE.input_title, name="extractionResult__input_title", curie=CORE.curie('input_title'), - model_uri=OC.extractionResult__input_title, domain=None, range=Optional[str]) - -slots.extractionResult__input_text = Slot(uri=CORE.input_text, name="extractionResult__input_text", curie=CORE.curie('input_text'), - model_uri=OC.extractionResult__input_text, domain=None, range=Optional[str]) - -slots.extractionResult__raw_completion_output = Slot(uri=CORE.raw_completion_output, name="extractionResult__raw_completion_output", curie=CORE.curie('raw_completion_output'), - model_uri=OC.extractionResult__raw_completion_output, domain=None, range=Optional[str]) - -slots.extractionResult__prompt = Slot(uri=CORE.prompt, name="extractionResult__prompt", curie=CORE.curie('prompt'), - model_uri=OC.extractionResult__prompt, domain=None, range=Optional[str]) - -slots.extractionResult__extracted_object = Slot(uri=CORE.extracted_object, name="extractionResult__extracted_object", curie=CORE.curie('extracted_object'), - model_uri=OC.extractionResult__extracted_object, domain=None, range=Optional[Union[dict, Any]]) - -slots.extractionResult__named_entities = Slot(uri=CORE.named_entities, name="extractionResult__named_entities", curie=CORE.curie('named_entities'), - model_uri=OC.extractionResult__named_entities, domain=None, range=Optional[Union[Union[dict, Any], List[Union[dict, Any]]]]) - -slots.namedEntity__id = Slot(uri=CORE.id, name="namedEntity__id", curie=CORE.curie('id'), - model_uri=OC.namedEntity__id, domain=None, range=URIRef) - -slots.namedEntity__label = Slot(uri=RDFS.label, name="namedEntity__label", curie=RDFS.curie('label'), - model_uri=OC.namedEntity__label, domain=None, range=Optional[str]) - -slots.triple__subject = Slot(uri=CORE.subject, name="triple__subject", curie=CORE.curie('subject'), - model_uri=OC.triple__subject, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__predicate = Slot(uri=CORE.predicate, name="triple__predicate", curie=CORE.curie('predicate'), - model_uri=OC.triple__predicate, domain=None, range=Optional[Union[str, RelationshipTypeId]]) - -slots.triple__object = Slot(uri=CORE.object, name="triple__object", curie=CORE.curie('object'), - model_uri=OC.triple__object, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__qualifier = Slot(uri=CORE.qualifier, name="triple__qualifier", curie=CORE.curie('qualifier'), - model_uri=OC.triple__qualifier, domain=None, range=Optional[str]) - -slots.triple__subject_qualifier = Slot(uri=CORE.subject_qualifier, name="triple__subject_qualifier", curie=CORE.curie('subject_qualifier'), - model_uri=OC.triple__subject_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__object_qualifier = Slot(uri=CORE.object_qualifier, name="triple__object_qualifier", curie=CORE.curie('object_qualifier'), - model_uri=OC.triple__object_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.textWithTriples__publication = Slot(uri=CORE.publication, name="textWithTriples__publication", curie=CORE.curie('publication'), - model_uri=OC.textWithTriples__publication, domain=None, range=Optional[Union[dict, Publication]]) - -slots.textWithTriples__triples = Slot(uri=CORE.triples, name="textWithTriples__triples", curie=CORE.curie('triples'), - model_uri=OC.textWithTriples__triples, domain=None, range=Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]]) - -slots.publication__id = Slot(uri=CORE.id, name="publication__id", curie=CORE.curie('id'), - model_uri=OC.publication__id, domain=None, range=Optional[str]) - -slots.publication__title = Slot(uri=CORE.title, name="publication__title", curie=CORE.curie('title'), - model_uri=OC.publication__title, domain=None, range=Optional[str]) - -slots.publication__abstract = Slot(uri=CORE.abstract, name="publication__abstract", curie=CORE.curie('abstract'), - model_uri=OC.publication__abstract, domain=None, range=Optional[str]) - -slots.publication__combined_text = Slot(uri=CORE.combined_text, name="publication__combined_text", curie=CORE.curie('combined_text'), - model_uri=OC.publication__combined_text, domain=None, range=Optional[str]) - -slots.publication__full_text = Slot(uri=CORE.full_text, name="publication__full_text", curie=CORE.curie('full_text'), - model_uri=OC.publication__full_text, domain=None, range=Optional[str]) - -slots.annotatorResult__subject_text = Slot(uri=CORE.subject_text, name="annotatorResult__subject_text", curie=CORE.curie('subject_text'), - model_uri=OC.annotatorResult__subject_text, domain=None, range=Optional[str]) - -slots.annotatorResult__object_id = Slot(uri=CORE.object_id, name="annotatorResult__object_id", curie=CORE.curie('object_id'), - model_uri=OC.annotatorResult__object_id, domain=None, range=Optional[str]) - -slots.annotatorResult__object_text = Slot(uri=CORE.object_text, name="annotatorResult__object_text", curie=CORE.curie('object_text'), - model_uri=OC.annotatorResult__object_text, domain=None, range=Optional[str]) \ No newline at end of file diff --git a/projects/halo/jsonld/halo.context.jsonld b/projects/halo/jsonld/halo.context.jsonld deleted file mode 100644 index a9d057eb0..000000000 --- a/projects/halo/jsonld/halo.context.jsonld +++ /dev/null @@ -1,155 +0,0 @@ -{ - "comments": { - "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2023-08-07T10:53:52", - "source": "halo.yaml" - }, - "@context": { - "BFO": { - "@id": "http://purl.obolibrary.org/obo/BFO_", - "@prefix": true - }, - "RO": { - "@id": "http://purl.obolibrary.org/obo/RO_", - "@prefix": true - }, - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "linkml": "https://w3id.org/linkml/", - "oc": { - "@id": "http://w3id.org/ontogpt/ontology-class-template", - "@prefix": true - }, - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "@vocab": "http://w3id.org/ontogpt/ontology-class-template", - "object_id": { - "@id": "core:object_id" - }, - "object_text": { - "@id": "core:object_text" - }, - "subject_text": { - "@id": "core:subject_text" - }, - "extracted_object": { - "@type": "@id", - "@id": "core:extracted_object" - }, - "input_id": { - "@id": "core:input_id" - }, - "input_text": { - "@id": "core:input_text" - }, - "input_title": { - "@id": "core:input_title" - }, - "named_entities": { - "@type": "@id", - "@id": "core:named_entities" - }, - "prompt": { - "@id": "core:prompt" - }, - "raw_completion_output": { - "@id": "core:raw_completion_output" - }, - "id": { - "@id": "core:id" - }, - "label": { - "@id": "rdfs:label" - }, - "elements": { - "@type": "@id" - }, - "categories": { - "@type": "@id" - }, - "name": "@id", - "part_of": { - "@type": "@id", - "@id": "BFO:0000050" - }, - "parts": { - "@type": "@id" - }, - "subclass_of": { - "@type": "@id", - "@id": "rdfs:subClassOf" - }, - "subtypes": { - "@type": "@id" - }, - "abstract": { - "@id": "core:abstract" - }, - "combined_text": { - "@id": "core:combined_text" - }, - "full_text": { - "@id": "core:full_text" - }, - "title": { - "@id": "core:title" - }, - "publication": { - "@type": "@id", - "@id": "core:publication" - }, - "triples": { - "@type": "@id", - "@id": "core:triples" - }, - "object": { - "@type": "@id", - "@id": "core:object" - }, - "object_qualifier": { - "@type": "@id", - "@id": "core:object_qualifier" - }, - "predicate": { - "@type": "@id", - "@id": "core:predicate" - }, - "qualifier": { - "@id": "core:qualifier" - }, - "subject": { - "@type": "@id", - "@id": "core:subject" - }, - "subject_qualifier": { - "@type": "@id", - "@id": "core:subject_qualifier" - }, - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } - } -} diff --git a/projects/halo/jsonld/halo.jsonld b/projects/halo/jsonld/halo.jsonld deleted file mode 100644 index 6409ea842..000000000 --- a/projects/halo/jsonld/halo.jsonld +++ /dev/null @@ -1,1297 +0,0 @@ -{ - "name": "ontology-class", - "description": "A template for Ontology Classes", - "title": "Ontology Class Template", - "id": "https://w3id.org/ontogpt/halo", - "imports": [ - "linkml:types", - "core" - ], - "license": "https://creativecommons.org/publicdomain/zero/1.0/", - "prefixes": [ - { - "prefix_prefix": "linkml", - "prefix_reference": "https://w3id.org/linkml/" - }, - { - "prefix_prefix": "oc", - "prefix_reference": "http://w3id.org/ontogpt/ontology-class-template" - }, - { - "prefix_prefix": "BFO", - "prefix_reference": "http://purl.obolibrary.org/obo/BFO_" - } - ], - "default_prefix": "oc", - "default_range": "string", - "types": [ - { - "name": "string", - "definition_uri": "https://w3id.org/linkml/String", - "description": "A character string", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Text" - ], - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "@type": "TypeDefinition" - }, - { - "name": "integer", - "definition_uri": "https://w3id.org/linkml/Integer", - "description": "An integer", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Integer" - ], - "base": "int", - "uri": "http://www.w3.org/2001/XMLSchema#integer", - "@type": "TypeDefinition" - }, - { - "name": "boolean", - "definition_uri": "https://w3id.org/linkml/Boolean", - "description": "A binary (true or false) value", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Boolean" - ], - "base": "Bool", - "uri": "http://www.w3.org/2001/XMLSchema#boolean", - "repr": "bool", - "@type": "TypeDefinition" - }, - { - "name": "float", - "definition_uri": "https://w3id.org/linkml/Float", - "description": "A real number that conforms to the xsd:float specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#float", - "@type": "TypeDefinition" - }, - { - "name": "double", - "definition_uri": "https://w3id.org/linkml/Double", - "description": "A real number that conforms to the xsd:double specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#double", - "@type": "TypeDefinition" - }, - { - "name": "decimal", - "definition_uri": "https://w3id.org/linkml/Decimal", - "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "broad_mappings": [ - "schema:Number" - ], - "base": "Decimal", - "uri": "http://www.w3.org/2001/XMLSchema#decimal", - "@type": "TypeDefinition" - }, - { - "name": "time", - "definition_uri": "https://w3id.org/linkml/Time", - "description": "A time object represents a (local) time of day, independent of any particular day", - "notes": [ - "URI is dateTime because OWL reasoners do not work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Time" - ], - "base": "XSDTime", - "uri": "http://www.w3.org/2001/XMLSchema#time", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date", - "definition_uri": "https://w3id.org/linkml/Date", - "description": "a date (year, month and day) in an idealized calendar", - "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Date" - ], - "base": "XSDDate", - "uri": "http://www.w3.org/2001/XMLSchema#date", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "datetime", - "definition_uri": "https://w3id.org/linkml/Datetime", - "description": "The combination of a date and time", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:DateTime" - ], - "base": "XSDDateTime", - "uri": "http://www.w3.org/2001/XMLSchema#dateTime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date_or_datetime", - "definition_uri": "https://w3id.org/linkml/DateOrDatetime", - "description": "Either a date or a datetime", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "https://w3id.org/linkml/DateOrDatetime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uriorcurie", - "definition_uri": "https://w3id.org/linkml/Uriorcurie", - "description": "a URI or a CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "URIorCURIE", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "curie", - "definition_uri": "https://w3id.org/linkml/Curie", - "conforms_to": "https://www.w3.org/TR/curie/", - "description": "a compact URI", - "comments": [ - "in RDF serializations this MUST be expanded to a URI", - "in non-RDF serializations MAY be serialized as the compact representation" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "Curie", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uri", - "definition_uri": "https://w3id.org/linkml/Uri", - "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", - "description": "a complete URI", - "comments": [ - "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:URL" - ], - "base": "URI", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "ncname", - "definition_uri": "https://w3id.org/linkml/Ncname", - "description": "Prefix part of CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NCName", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "objectidentifier", - "definition_uri": "https://w3id.org/linkml/Objectidentifier", - "description": "A URI or CURIE that represents an object in the model.", - "comments": [ - "Used for inheritance and type checking" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "ElementIdentifier", - "uri": "http://www.w3.org/ns/shex#iri", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "nodeidentifier", - "definition_uri": "https://w3id.org/linkml/Nodeidentifier", - "description": "A URI, CURIE or BNODE that represents a node in a model.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NodeIdentifier", - "uri": "http://www.w3.org/ns/shex#nonLiteral", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpointer", - "definition_uri": "https://w3id.org/linkml/Jsonpointer", - "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901", - "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpath", - "definition_uri": "https://w3id.org/linkml/Jsonpath", - "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html", - "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "sparqlpath", - "definition_uri": "https://w3id.org/linkml/Sparqlpath", - "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths", - "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - } - ], - "enums": [ - { - "name": "NullDataOptions", - "definition_uri": "http://w3id.org/ontogpt/core/NullDataOptions", - "from_schema": "http://w3id.org/ontogpt/core", - "permissible_values": [ - { - "text": "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "meaning": "NCIT:C149701" - }, - { - "text": "NOT_APPLICABLE", - "meaning": "NCIT:C18902", - "aliases": [ - "not applicable", - "N/A" - ] - }, - { - "text": "NOT_MENTIONED" - } - ] - } - ], - "slots": [ - { - "name": "subclass_of", - "definition_uri": "http://w3id.org/ontogpt/ontology-class-templatesubclass_of", - "description": "a list of parent class (superclasses) of this entity", - "from_schema": "https://w3id.org/ontogpt/halo", - "mappings": [ - "http://example.org/UNKNOWN/rdfs/subClassOf" - ], - "domain": "OntologyElement", - "slot_uri": "http://example.org/UNKNOWN/rdfs/subClassOf", - "multivalued": true, - "inverse": "ontologyElement__subtypes", - "range": "OntologyElement", - "@type": "SlotDefinition" - }, - { - "name": "part_of", - "definition_uri": "http://w3id.org/ontogpt/ontology-class-templatepart_of", - "description": "a list of things this element is part of", - "from_schema": "https://w3id.org/ontogpt/halo", - "mappings": [ - "http://purl.obolibrary.org/obo/BFO_0000050" - ], - "domain": "OntologyElement", - "slot_uri": "http://purl.obolibrary.org/obo/BFO_0000050", - "multivalued": true, - "inverse": "ontologyElement__parts", - "range": "OntologyElement", - "@type": "SlotDefinition" - }, - { - "name": "ontology__elements", - "from_schema": "https://w3id.org/ontogpt/halo", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templateelements", - "multivalued": true, - "alias": "elements", - "owner": "Ontology", - "domain_of": [ - "Ontology" - ], - "range": "OntologyElement", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "ontologyElement__name", - "description": "the name of the entity", - "from_schema": "https://w3id.org/ontogpt/halo", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templatename", - "identifier": true, - "alias": "name", - "owner": "OntologyElement", - "domain_of": [ - "OntologyElement" - ], - "range": "string", - "required": true, - "@type": "SlotDefinition" - }, - { - "name": "ontologyElement__context", - "description": "the ontology to which this belongs (single-valued)", - "from_schema": "https://w3id.org/ontogpt/halo", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templatecontext", - "alias": "context", - "owner": "OntologyElement", - "domain_of": [ - "OntologyElement" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "ontologyElement__description", - "description": "a textual description of the entity (single-valued)", - "from_schema": "https://w3id.org/ontogpt/halo", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templatedescription", - "alias": "description", - "owner": "OntologyElement", - "domain_of": [ - "OntologyElement" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "ontologyElement__synonyms", - "description": "a list of alternative names of the entity", - "from_schema": "https://w3id.org/ontogpt/halo", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templatesynonyms", - "multivalued": true, - "alias": "synonyms", - "owner": "OntologyElement", - "domain_of": [ - "OntologyElement" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "ontologyElement__categories", - "description": "a list of the categories to which this entity belongs", - "from_schema": "https://w3id.org/ontogpt/halo", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templatecategories", - "multivalued": true, - "alias": "categories", - "owner": "OntologyElement", - "domain_of": [ - "OntologyElement" - ], - "range": "Category", - "@type": "SlotDefinition" - }, - { - "name": "ontologyElement__subclass_of", - "description": "a list of parent class (superclasses) of this entity", - "from_schema": "https://w3id.org/ontogpt/halo", - "mappings": [ - "http://example.org/UNKNOWN/rdfs/subClassOf" - ], - "slot_uri": "http://example.org/UNKNOWN/rdfs/subClassOf", - "multivalued": true, - "alias": "subclass_of", - "owner": "OntologyElement", - "domain_of": [ - "OntologyElement" - ], - "range": "OntologyElement", - "@type": "SlotDefinition" - }, - { - "name": "ontologyElement__part_of", - "description": "a list of things this element is part of", - "from_schema": "https://w3id.org/ontogpt/halo", - "mappings": [ - "http://purl.obolibrary.org/obo/BFO_0000050" - ], - "slot_uri": "http://purl.obolibrary.org/obo/BFO_0000050", - "multivalued": true, - "alias": "part_of", - "owner": "OntologyElement", - "domain_of": [ - "OntologyElement" - ], - "range": "OntologyElement", - "@type": "SlotDefinition" - }, - { - "name": "ontologyElement__subtypes", - "description": "a list of child classes (subclasses) of this entity", - "from_schema": "https://w3id.org/ontogpt/halo", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templatesubtypes", - "multivalued": true, - "alias": "subtypes", - "owner": "OntologyElement", - "domain_of": [ - "OntologyElement" - ], - "inverse": "subclass_of", - "range": "OntologyElement", - "@type": "SlotDefinition" - }, - { - "name": "ontologyElement__parts", - "description": "a list of names of things this element has as parts (components)", - "from_schema": "https://w3id.org/ontogpt/halo", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templateparts", - "multivalued": true, - "alias": "parts", - "owner": "OntologyElement", - "domain_of": [ - "OntologyElement" - ], - "inverse": "part_of", - "range": "OntologyElement", - "@type": "SlotDefinition" - }, - { - "name": "ontologyElement__equivalent_to", - "description": "an OWL class expression with the necessary and sufficient conditions for this entity to be an instance of this class", - "from_schema": "https://w3id.org/ontogpt/halo", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templateequivalent_to", - "alias": "equivalent_to", - "owner": "OntologyElement", - "domain_of": [ - "OntologyElement" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_id", - "alias": "input_id", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_title", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_title", - "alias": "input_title", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_text", - "alias": "input_text", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__raw_completion_output", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/raw_completion_output", - "alias": "raw_completion_output", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__prompt", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/prompt", - "alias": "prompt", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__extracted_object", - "description": "The complex objects extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/extracted_object", - "alias": "extracted_object", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__named_entities", - "description": "Named entities extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/named_entities", - "multivalued": true, - "alias": "named_entities", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "identifier": true, - "alias": "id", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "required": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "from_schema": "http://w3id.org/ontogpt/core", - "aliases": [ - "name" - ], - "mappings": [ - "http://example.org/UNKNOWN/rdfs/label" - ], - "slot_uri": "http://example.org/UNKNOWN/rdfs/label", - "alias": "label", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject", - "alias": "subject", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__predicate", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/predicate", - "alias": "predicate", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "triple__object", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object", - "alias": "object", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/qualifier", - "alias": "qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_qualifier", - "alias": "subject_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_qualifier", - "alias": "object_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/publication", - "alias": "publication", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__triples", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/triples", - "multivalued": true, - "alias": "triples", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "publication__id", - "description": "The publication identifier", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "alias": "id", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__title", - "description": "The title of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/title", - "alias": "title", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__abstract", - "description": "The abstract of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/abstract", - "alias": "abstract", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__combined_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/combined_text", - "alias": "combined_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__full_text", - "description": "The full text of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/full_text", - "alias": "full_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__subject_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_text", - "alias": "subject_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_id", - "alias": "object_id", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_text", - "alias": "object_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - } - ], - "classes": [ - { - "name": "Ontology", - "definition_uri": "http://w3id.org/ontogpt/ontology-class-templateOntology", - "from_schema": "https://w3id.org/ontogpt/halo", - "slots": [ - "ontology__elements" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "elements", - "multivalued": true, - "range": "OntologyElement", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/ontology-class-templateOntology", - "@type": "ClassDefinition" - }, - { - "name": "OntologyElement", - "definition_uri": "http://w3id.org/ontogpt/ontology-class-templateOntologyElement", - "from_schema": "https://w3id.org/ontogpt/halo", - "slots": [ - "ontologyElement__name", - "ontologyElement__context", - "ontologyElement__description", - "ontologyElement__synonyms", - "ontologyElement__categories", - "ontologyElement__subclass_of", - "ontologyElement__part_of", - "ontologyElement__subtypes", - "ontologyElement__parts", - "ontologyElement__equivalent_to" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "name", - "description": "the name of the entity", - "identifier": true, - "@type": "SlotDefinition" - }, - { - "name": "context", - "description": "the ontology to which this belongs (single-valued)", - "@type": "SlotDefinition" - }, - { - "name": "description", - "description": "a textual description of the entity (single-valued)", - "@type": "SlotDefinition" - }, - { - "name": "synonyms", - "description": "a list of alternative names of the entity", - "multivalued": true, - "@type": "SlotDefinition" - }, - { - "name": "categories", - "description": "a list of the categories to which this entity belongs", - "multivalued": true, - "range": "Category", - "@type": "SlotDefinition" - }, - { - "name": "subclass_of", - "description": "a list of parent class (superclasses) of this entity", - "slot_uri": "rdfs:subClassOf", - "multivalued": true, - "range": "OntologyElement", - "@type": "SlotDefinition" - }, - { - "name": "part_of", - "description": "a list of things this element is part of", - "slot_uri": "BFO:0000050", - "multivalued": true, - "range": "OntologyElement", - "@type": "SlotDefinition" - }, - { - "name": "subtypes", - "description": "a list of child classes (subclasses) of this entity", - "multivalued": true, - "inverse": "subclass_of", - "range": "OntologyElement", - "@type": "SlotDefinition" - }, - { - "name": "parts", - "description": "a list of names of things this element has as parts (components)", - "multivalued": true, - "inverse": "part_of", - "range": "OntologyElement", - "@type": "SlotDefinition" - }, - { - "name": "equivalent_to", - "description": "an OWL class expression with the necessary and sufficient conditions for this entity to be an instance of this class", - "range": "string", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/ontology-class-templateOntologyElement", - "@type": "ClassDefinition" - }, - { - "name": "Category", - "definition_uri": "http://w3id.org/ontogpt/ontology-class-templateCategory", - "from_schema": "https://w3id.org/ontogpt/halo", - "is_a": "OntologyElement", - "slots": [ - "ontologyElement__name", - "ontologyElement__context", - "ontologyElement__description", - "ontologyElement__synonyms", - "ontologyElement__categories", - "ontologyElement__subclass_of", - "ontologyElement__part_of", - "ontologyElement__subtypes", - "ontologyElement__parts", - "ontologyElement__equivalent_to" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/ontology-class-templateCategory", - "@type": "ClassDefinition" - }, - { - "name": "Any", - "definition_uri": "http://w3id.org/ontogpt/core/Any", - "from_schema": "http://w3id.org/ontogpt/core", - "mappings": [ - "linkml:Any" - ], - "slot_usage": {}, - "class_uri": "https://w3id.org/linkml/Any", - "@type": "ClassDefinition" - }, - { - "name": "ExtractionResult", - "definition_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "description": "A result of extracting knowledge on text", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "extractionResult__input_id", - "extractionResult__input_title", - "extractionResult__input_text", - "extractionResult__raw_completion_output", - "extractionResult__prompt", - "extractionResult__extracted_object", - "extractionResult__named_entities" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "input_id", - "@type": "SlotDefinition" - }, - { - "name": "input_title", - "@type": "SlotDefinition" - }, - { - "name": "input_text", - "@type": "SlotDefinition" - }, - { - "name": "raw_completion_output", - "@type": "SlotDefinition" - }, - { - "name": "prompt", - "@type": "SlotDefinition" - }, - { - "name": "extracted_object", - "description": "The complex objects extracted from the text", - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "named_entities", - "description": "Named entities extracted from the text", - "multivalued": true, - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "@type": "ClassDefinition" - }, - { - "name": "NamedEntity", - "definition_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "identifier": true, - "@type": "SlotDefinition" - }, - { - "name": "label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "aliases": [ - "name" - ], - "slot_uri": "rdfs:label", - "range": "string", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "@type": "ClassDefinition" - }, - { - "name": "CompoundExpression", - "definition_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "@type": "ClassDefinition" - }, - { - "name": "Triple", - "definition_uri": "http://w3id.org/ontogpt/core/Triple", - "description": "Abstract parent for Relation Extraction tasks", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "CompoundExpression", - "abstract": true, - "slots": [ - "triple__subject", - "triple__predicate", - "triple__object", - "triple__qualifier", - "triple__subject_qualifier", - "triple__object_qualifier" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "predicate", - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "object", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Triple", - "@type": "ClassDefinition" - }, - { - "name": "TextWithTriples", - "definition_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "textWithTriples__publication", - "textWithTriples__triples" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "triples", - "multivalued": true, - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "@type": "ClassDefinition" - }, - { - "name": "RelationshipType", - "id_prefixes": [ - "RO", - "biolink" - ], - "definition_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "@type": "ClassDefinition" - }, - { - "name": "Publication", - "definition_uri": "http://w3id.org/ontogpt/core/Publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "publication__id", - "publication__title", - "publication__abstract", - "publication__combined_text", - "publication__full_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "description": "The publication identifier", - "@type": "SlotDefinition" - }, - { - "name": "title", - "description": "The title of the publication", - "@type": "SlotDefinition" - }, - { - "name": "abstract", - "description": "The abstract of the publication", - "@type": "SlotDefinition" - }, - { - "name": "combined_text", - "@type": "SlotDefinition" - }, - { - "name": "full_text", - "description": "The full text of the publication", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Publication", - "@type": "ClassDefinition" - }, - { - "name": "AnnotatorResult", - "definition_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "annotatorResult__subject_text", - "annotatorResult__object_id", - "annotatorResult__object_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject_text", - "@type": "SlotDefinition" - }, - { - "name": "object_id", - "@type": "SlotDefinition" - }, - { - "name": "object_text", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "@type": "ClassDefinition" - } - ], - "metamodel_version": "1.7.0", - "source_file": "halo.yaml", - "source_file_date": "2023-06-17T15:11:19", - "source_file_size": 2367, - "generation_date": "2023-08-07T10:53:53", - "@type": "SchemaDefinition", - "@context": [ - "projects/halo/jsonld/halo.context.jsonld", - "https://w3id.org/linkml/types.context.jsonld", - "core.context.jsonld", - { - "@base": "http://w3id.org/ontogpt/ontology-class-template" - } - ] -} diff --git a/projects/halo/jsonschema/halo.schema.json b/projects/halo/jsonschema/halo.schema.json deleted file mode 100644 index 15aa2278e..000000000 --- a/projects/halo/jsonschema/halo.schema.json +++ /dev/null @@ -1,293 +0,0 @@ -{ - "$defs": { - "AnnotatorResult": { - "additionalProperties": false, - "description": "", - "properties": { - "object_id": { - "type": "string" - }, - "object_text": { - "type": "string" - }, - "subject_text": { - "type": "string" - } - }, - "title": "AnnotatorResult", - "type": "object" - }, - "Any": { - "additionalProperties": true, - "description": "", - "title": "Any", - "type": "object" - }, - "Category": { - "additionalProperties": false, - "description": "", - "properties": { - "categories": { - "description": "a list of the categories to which this entity belongs", - "items": { - "type": "string" - }, - "type": "array" - }, - "context": { - "description": "the ontology to which this belongs (single-valued)", - "type": "string" - }, - "description": { - "description": "a textual description of the entity (single-valued)", - "type": "string" - }, - "equivalent_to": { - "description": "an OWL class expression with the necessary and sufficient conditions for this entity to be an instance of this class", - "type": "string" - }, - "name": { - "description": "the name of the entity", - "type": "string" - }, - "part_of": { - "description": "a list of things this element is part of", - "items": { - "type": "string" - }, - "type": "array" - }, - "parts": { - "description": "a list of names of things this element has as parts (components)", - "items": { - "type": "string" - }, - "type": "array" - }, - "subclass_of": { - "description": "a list of parent class (superclasses) of this entity", - "items": { - "type": "string" - }, - "type": "array" - }, - "subtypes": { - "description": "a list of child classes (subclasses) of this entity", - "items": { - "type": "string" - }, - "type": "array" - }, - "synonyms": { - "description": "a list of alternative names of the entity", - "items": { - "type": "string" - }, - "type": "array" - } - }, - "required": [ - "name" - ], - "title": "Category", - "type": "object" - }, - "ExtractionResult": { - "additionalProperties": false, - "description": "A result of extracting knowledge on text", - "properties": { - "extracted_object": { - "$ref": "#/$defs/Any", - "description": "The complex objects extracted from the text" - }, - "input_id": { - "type": "string" - }, - "input_text": { - "type": "string" - }, - "input_title": { - "type": "string" - }, - "named_entities": { - "description": "Named entities extracted from the text", - "items": { - "$ref": "#/$defs/Any" - }, - "type": "array" - }, - "prompt": { - "type": "string" - }, - "raw_completion_output": { - "type": "string" - } - }, - "title": "ExtractionResult", - "type": "object" - }, - "NullDataOptions": { - "description": "", - "enum": [ - "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "NOT_APPLICABLE", - "NOT_MENTIONED" - ], - "title": "NullDataOptions", - "type": "string" - }, - "Ontology": { - "additionalProperties": false, - "description": "", - "properties": { - "elements": { - "items": { - "$ref": "#/$defs/OntologyElement" - }, - "type": "array" - } - }, - "title": "Ontology", - "type": "object" - }, - "OntologyElement": { - "additionalProperties": false, - "description": "", - "properties": { - "categories": { - "description": "a list of the categories to which this entity belongs", - "items": { - "type": "string" - }, - "type": "array" - }, - "context": { - "description": "the ontology to which this belongs (single-valued)", - "type": "string" - }, - "description": { - "description": "a textual description of the entity (single-valued)", - "type": "string" - }, - "equivalent_to": { - "description": "an OWL class expression with the necessary and sufficient conditions for this entity to be an instance of this class", - "type": "string" - }, - "name": { - "description": "the name of the entity", - "type": "string" - }, - "part_of": { - "description": "a list of things this element is part of", - "items": { - "type": "string" - }, - "type": "array" - }, - "parts": { - "description": "a list of names of things this element has as parts (components)", - "items": { - "type": "string" - }, - "type": "array" - }, - "subclass_of": { - "description": "a list of parent class (superclasses) of this entity", - "items": { - "type": "string" - }, - "type": "array" - }, - "subtypes": { - "description": "a list of child classes (subclasses) of this entity", - "items": { - "type": "string" - }, - "type": "array" - }, - "synonyms": { - "description": "a list of alternative names of the entity", - "items": { - "type": "string" - }, - "type": "array" - } - }, - "required": [ - "name" - ], - "title": "OntologyElement", - "type": "object" - }, - "Publication": { - "additionalProperties": false, - "description": "", - "properties": { - "abstract": { - "description": "The abstract of the publication", - "type": "string" - }, - "combined_text": { - "type": "string" - }, - "full_text": { - "description": "The full text of the publication", - "type": "string" - }, - "id": { - "description": "The publication identifier", - "type": "string" - }, - "title": { - "description": "The title of the publication", - "type": "string" - } - }, - "title": "Publication", - "type": "object" - }, - "RelationshipType": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "RelationshipType", - "type": "object" - }, - "TextWithTriples": { - "additionalProperties": false, - "description": "", - "properties": { - "publication": { - "$ref": "#/$defs/Publication" - }, - "triples": { - "items": { - "$ref": "#/$defs/Triple" - }, - "type": "array" - } - }, - "title": "TextWithTriples", - "type": "object" - } - }, - "$id": "https://w3id.org/ontogpt/halo", - "$schema": "http://json-schema.org/draft-07/schema#", - "additionalProperties": true, - "metamodel_version": "1.7.0", - "title": "ontology-class", - "type": "object", - "version": null -} \ No newline at end of file diff --git a/projects/halo/owl/halo.owl.ttl b/projects/halo/owl/halo.owl.ttl deleted file mode 100644 index 1ce5232f5..000000000 --- a/projects/halo/owl/halo.owl.ttl +++ /dev/null @@ -1,471 +0,0 @@ -@prefix BFO: <http://purl.obolibrary.org/obo/BFO_> . -@prefix IAO: <http://purl.obolibrary.org/obo/IAO_> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix oc: <http://w3id.org/ontogpt/ontology-class-template> . -@prefix owl: <http://www.w3.org/2002/07/owl#> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . -@prefix skos: <http://www.w3.org/2004/02/skos/core#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -linkml:SubsetDefinition a owl:Class ; - rdfs:label "subset_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" . - -linkml:TypeDefinition a owl:Class ; - rdfs:label "type_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" ; - linkml:mixins "type_expression" . - -linkml:topValue a owl:DatatypeProperty ; - rdfs:label "value" . - -<https://w3id.org/ontogpt/halo> a owl:Ontology ; - rdfs:label "ontology-class" ; - IAO:0000700 <http://w3id.org/ontogpt/core/AnnotatorResult>, - <http://w3id.org/ontogpt/core/Any>, - <http://w3id.org/ontogpt/core/CompoundExpression>, - <http://w3id.org/ontogpt/core/ExtractionResult>, - <http://w3id.org/ontogpt/core/NamedEntity>, - <http://w3id.org/ontogpt/core/Publication>, - <http://w3id.org/ontogpt/core/TextWithTriples>, - oc:Ontology, - oc:OntologyElement ; - linkml:classes "{'Ontology': ClassDefinition(name='Ontology', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/ontology-class-templateOntology', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/halo', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['ontology__elements'], slot_usage={}, attributes={'elements': SlotDefinition(name='elements', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='OntologyElement', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='oc:Ontology', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'OntologyElement': ClassDefinition(name='OntologyElement', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/ontology-class-templateOntologyElement', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/halo', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['ontologyElement__name', 'ontologyElement__context', 'ontologyElement__description', 'ontologyElement__synonyms', 'ontologyElement__categories', 'ontologyElement__subclass_of', 'ontologyElement__part_of', 'ontologyElement__subtypes', 'ontologyElement__parts', 'ontologyElement__equivalent_to'], slot_usage={}, attributes={'name': SlotDefinition(name='name', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the name of the entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'context': SlotDefinition(name='context', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the ontology to which this belongs (single-valued)', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'description': SlotDefinition(name='description', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a textual description of the entity (single-valued)', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'synonyms': SlotDefinition(name='synonyms', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a list of alternative names of the entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'categories': SlotDefinition(name='categories', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a list of the categories to which this entity belongs', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Category', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subclass_of': SlotDefinition(name='subclass_of', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a list of parent class (superclasses) of this entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:subClassOf', multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='OntologyElement', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'part_of': SlotDefinition(name='part_of', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a list of things this element is part of', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='BFO:0000050', multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='OntologyElement', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subtypes': SlotDefinition(name='subtypes', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a list of child classes (subclasses) of this entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse='subclass_of', is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='OntologyElement', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'parts': SlotDefinition(name='parts', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a list of names of things this element has as parts (components)', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse='part_of', is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='OntologyElement', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'equivalent_to': SlotDefinition(name='equivalent_to', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='an OWL class expression with the necessary and sufficient conditions for this entity to be an instance of this class', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='oc:OntologyElement', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Category': ClassDefinition(name='Category', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/ontology-class-templateCategory', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/halo', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='OntologyElement', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['ontologyElement__name', 'ontologyElement__context', 'ontologyElement__description', 'ontologyElement__synonyms', 'ontologyElement__categories', 'ontologyElement__subclass_of', 'ontologyElement__part_of', 'ontologyElement__subtypes', 'ontologyElement__parts', 'ontologyElement__equivalent_to'], slot_usage={}, attributes={}, class_uri='oc:Category', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Any': ClassDefinition(name='Any', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Any', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=['linkml:Any'], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='linkml:Any', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ExtractionResult': ClassDefinition(name='ExtractionResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/ExtractionResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A result of extracting knowledge on text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['extractionResult__input_id', 'extractionResult__input_title', 'extractionResult__input_text', 'extractionResult__raw_completion_output', 'extractionResult__prompt', 'extractionResult__extracted_object', 'extractionResult__named_entities'], slot_usage={}, attributes={'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:ExtractionResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'NamedEntity': ClassDefinition(name='NamedEntity', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NamedEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:NamedEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'CompoundExpression': ClassDefinition(name='CompoundExpression', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/CompoundExpression', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='core:CompoundExpression', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Triple': ClassDefinition(name='Triple', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Triple', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Abstract parent for Relation Extraction tasks', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['triple__subject', 'triple__predicate', 'triple__object', 'triple__qualifier', 'triple__subject_qualifier', 'triple__object_qualifier'], slot_usage={}, attributes={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Triple', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'TextWithTriples': ClassDefinition(name='TextWithTriples', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/TextWithTriples', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['textWithTriples__publication', 'textWithTriples__triples'], slot_usage={}, attributes={'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:TextWithTriples', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'RelationshipType': ClassDefinition(name='RelationshipType', id_prefixes=['RO', 'biolink'], definition_uri='http://w3id.org/ontogpt/core/RelationshipType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='core:RelationshipType', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Publication': ClassDefinition(name='Publication', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Publication', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['publication__id', 'publication__title', 'publication__abstract', 'publication__combined_text', 'publication__full_text'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Publication', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'AnnotatorResult': ClassDefinition(name='AnnotatorResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/AnnotatorResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['annotatorResult__subject_text', 'annotatorResult__object_id', 'annotatorResult__object_text'], slot_usage={}, attributes={'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:AnnotatorResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={})}" ; - linkml:enums "{'NullDataOptions': EnumDefinition(name='NullDataOptions', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NullDataOptions', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'UNSPECIFIED_METHOD_OF_ADMINISTRATION': PermissibleValue(text='UNSPECIFIED_METHOD_OF_ADMINISTRATION', description=None, meaning='NCIT:C149701', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_APPLICABLE': PermissibleValue(text='NOT_APPLICABLE', description=None, meaning='NCIT:C18902', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['not applicable', 'N/A'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_MENTIONED': PermissibleValue(text='NOT_MENTIONED', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[])}" ; - linkml:id "https://w3id.org/ontogpt/halo" ; - linkml:imports "core", - "linkml:types" ; - linkml:types "{'string': TypeDefinition(name='string', id_prefixes=[], definition_uri='https://w3id.org/linkml/String', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A character string', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Text'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'integer': TypeDefinition(name='integer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Integer', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An integer', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Integer'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='int', uri='xsd:integer', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'boolean': TypeDefinition(name='boolean', id_prefixes=[], definition_uri='https://w3id.org/linkml/Boolean', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A binary (true or false) value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Boolean'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Bool', uri='xsd:boolean', repr='bool', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'float': TypeDefinition(name='float', id_prefixes=[], definition_uri='https://w3id.org/linkml/Float', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:float specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Float'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:float', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'double': TypeDefinition(name='double', id_prefixes=[], definition_uri='https://w3id.org/linkml/Double', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:double specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:Float'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:double', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'decimal': TypeDefinition(name='decimal', id_prefixes=[], definition_uri='https://w3id.org/linkml/Decimal', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number with arbitrary precision that conforms to the xsd:decimal specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=['schema:Number'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Decimal', uri='xsd:decimal', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'time': TypeDefinition(name='time', id_prefixes=[], definition_uri='https://w3id.org/linkml/Time', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A time object represents a (local) time of day, independent of any particular day', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=['URI is dateTime because OWL reasoners do not work with straight date or time'], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Time'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDTime', uri='xsd:time', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date': TypeDefinition(name='date', id_prefixes=[], definition_uri='https://w3id.org/linkml/Date', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a date (year, month and day) in an idealized calendar', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[\"URI is dateTime because OWL reasoners don't work with straight date or time\"], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Date'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDate', uri='xsd:date', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'datetime': TypeDefinition(name='datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/Datetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The combination of a date and time', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:DateTime'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDateTime', uri='xsd:dateTime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date_or_datetime': TypeDefinition(name='date_or_datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/DateOrDatetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Either a date or a datetime', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='linkml:DateOrDatetime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uriorcurie': TypeDefinition(name='uriorcurie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uriorcurie', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a URI or a CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URIorCURIE', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'curie': TypeDefinition(name='curie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Curie', local_names={}, conforms_to='https://www.w3.org/TR/curie/', implements=[], extensions={}, annotations={}, description='a compact URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations this MUST be expanded to a URI', 'in non-RDF serializations MAY be serialized as the compact representation'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Curie', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uri': TypeDefinition(name='uri', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uri', local_names={}, conforms_to='https://www.ietf.org/rfc/rfc3987.txt', implements=[], extensions={}, annotations={}, description='a complete URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:URL'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URI', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ncname': TypeDefinition(name='ncname', id_prefixes=[], definition_uri='https://w3id.org/linkml/Ncname', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Prefix part of CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NCName', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'objectidentifier': TypeDefinition(name='objectidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Objectidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI or CURIE that represents an object in the model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['Used for inheritance and type checking'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='ElementIdentifier', uri='shex:iri', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'nodeidentifier': TypeDefinition(name='nodeidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Nodeidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI, CURIE or BNODE that represents a node in a model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NodeIdentifier', uri='shex:nonLiteral', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpointer': TypeDefinition(name='jsonpointer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpointer', local_names={}, conforms_to='https://datatracker.ietf.org/doc/html/rfc6901', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpath': TypeDefinition(name='jsonpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpath', local_names={}, conforms_to='https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sparqlpath': TypeDefinition(name='sparqlpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Sparqlpath', local_names={}, conforms_to='https://www.w3.org/TR/sparql11-query/#propertypaths', implements=[], extensions={}, annotations={}, description='A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "AnnotatorResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_id> ] ; - linkml:attributes "{'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/ExtractionResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ExtractionResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/extracted_object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_title> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/prompt> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_text> ], - [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/named_entities> ] ; - skos:definition "A result of extracting knowledge on text" ; - linkml:attributes "{'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/TextWithTriples> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TextWithTriples" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Publication> ; - owl:onProperty <http://w3id.org/ontogpt/core/publication> ], - [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Triple> ; - owl:onProperty <http://w3id.org/ontogpt/core/triples> ] ; - linkml:attributes "{'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/abstract> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "abstract" ; - rdfs:range linkml:String ; - skos:definition "The abstract of the publication" . - -<http://w3id.org/ontogpt/core/combined_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "combined_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/extracted_object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "extracted_object" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "The complex objects extracted from the text" . - -<http://w3id.org/ontogpt/core/full_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "full_text" ; - rdfs:range linkml:String ; - skos:definition "The full text of the publication" . - -<http://w3id.org/ontogpt/core/input_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_title" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/named_entities> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "named_entities" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "Named entities extracted from the text" . - -<http://w3id.org/ontogpt/core/object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/object_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/object_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" . - -<http://w3id.org/ontogpt/core/object_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/predicate> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "predicate" ; - rdfs:range <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/prompt> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "prompt" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/publication> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "publication" ; - oc:prompt.skip "true" ; - rdfs:range <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "qualifier" ; - rdfs:range linkml:String ; - skos:definition "A qualifier for the statements, e.g. \"NOT\" for negation" . - -<http://w3id.org/ontogpt/core/raw_completion_output> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "raw_completion_output" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/subject> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/subject_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" . - -<http://w3id.org/ontogpt/core/subject_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "title" ; - rdfs:range linkml:String ; - skos:definition "The title of the publication" . - -<http://w3id.org/ontogpt/core/triples> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "triples" ; - rdfs:range <http://w3id.org/ontogpt/core/Triple> . - -oc:Ontology a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Ontology" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom oc:OntologyElement ; - owl:onProperty oc:elements ] ; - linkml:attributes "{'elements': SlotDefinition(name='elements', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='OntologyElement', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -oc:categories a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "categories" ; - rdfs:range oc:Category ; - skos:definition "a list of the categories to which this entity belongs" . - -oc:context a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "context" ; - rdfs:range linkml:String ; - skos:definition "the ontology to which this belongs (single-valued)" . - -oc:description a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "description" ; - rdfs:range linkml:String ; - skos:definition "a textual description of the entity (single-valued)" . - -oc:elements a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "elements" ; - rdfs:range oc:OntologyElement . - -oc:equivalent_to a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "equivalent_to" ; - rdfs:range linkml:String ; - skos:definition "an OWL class expression with the necessary and sufficient conditions for this entity to be an instance of this class" . - -oc:name a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "name" ; - rdfs:range linkml:String ; - skos:definition "the name of the entity" . - -oc:parts a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "parts" ; - rdfs:range oc:OntologyElement ; - owl:inverseOf BFO:0000050 ; - skos:definition "a list of names of things this element has as parts (components)" . - -oc:subtypes a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subtypes" ; - rdfs:range oc:OntologyElement ; - owl:inverseOf <http://example.org/UNKNOWN/rdfs/subClassOf> ; - skos:definition "a list of child classes (subclasses) of this entity" . - -oc:synonyms a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "synonyms" ; - rdfs:range linkml:String ; - skos:definition "a list of alternative names of the entity" . - -<http://example.org/UNKNOWN/rdfs/label> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "label" ; - oc:owl "AnnotationProperty, AnnotationAssertion" ; - rdfs:range linkml:String ; - skos:altLabel "name" ; - skos:definition "The label (name) of the named thing" ; - skos:exactMatch <http://example.org/UNKNOWN/rdfs/label> . - -<http://example.org/UNKNOWN/rdfs/subClassOf> a owl:ObjectProperty, - linkml:SlotDefinition . - -BFO:0000050 a owl:ObjectProperty, - linkml:SlotDefinition . - -<http://purl.obolibrary.org/obo/NCIT_C149701> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "UNSPECIFIED_METHOD_OF_ADMINISTRATION" . - -<http://purl.obolibrary.org/obo/NCIT_C18902> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_APPLICABLE" . - -<http://w3id.org/ontogpt/core/CompoundExpression> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CompoundExpression" ; - linkml:attributes "{}" . - -<http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_MENTIONED" . - -<http://w3id.org/ontogpt/core/RelationshipType> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "RelationshipType" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/Triple> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Triple" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/RelationshipType> ; - owl:onProperty <http://w3id.org/ontogpt/core/predicate> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject> ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - skos:definition "Abstract parent for Relation Extraction tasks" ; - linkml:attributes "{'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -<http://w3id.org/ontogpt/core/id> a owl:ObjectProperty, - linkml:SlotDefinition . - -oc:Category a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Category" ; - rdfs:subClassOf oc:OntologyElement ; - linkml:attributes "{}" ; - linkml:is_a "OntologyElement" . - -<http://w3id.org/ontogpt/core/NullDataOptions> a owl:Class, - linkml:EnumDefinition ; - rdfs:label "NullDataOptions" ; - owl:unionOf ( <http://purl.obolibrary.org/obo/NCIT_C149701> <http://purl.obolibrary.org/obo/NCIT_C18902> <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> ) ; - linkml:permissible_values <http://purl.obolibrary.org/obo/NCIT_C149701>, - <http://purl.obolibrary.org/obo/NCIT_C18902>, - <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> . - -<http://w3id.org/ontogpt/core/Publication> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Publication" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/full_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/title> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/abstract> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/combined_text> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/Any> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Any" ; - skos:exactMatch linkml:Any ; - linkml:attributes "{}" . - -<http://w3id.org/ontogpt/core/NamedEntity> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "NamedEntity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://example.org/UNKNOWN/rdfs/label> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -oc:OntologyElement a owl:Class, - linkml:ClassDefinition ; - rdfs:label "OntologyElement" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty oc:synonyms ], - [ a owl:Restriction ; - owl:allValuesFrom oc:OntologyElement ; - owl:onProperty oc:parts ], - [ a owl:Restriction ; - owl:allValuesFrom oc:OntologyElement ; - owl:onProperty oc:subtypes ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty oc:context ], - [ a owl:Restriction ; - owl:allValuesFrom oc:Category ; - owl:onProperty oc:categories ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty oc:equivalent_to ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty oc:description ], - [ a owl:Restriction ; - owl:allValuesFrom oc:OntologyElement ; - owl:onProperty BFO:0000050 ], - [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty oc:name ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:allValuesFrom oc:OntologyElement ; - owl:onProperty <http://example.org/UNKNOWN/rdfs/subClassOf> ] ; - linkml:attributes "{'name': SlotDefinition(name='name', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the name of the entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'context': SlotDefinition(name='context', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the ontology to which this belongs (single-valued)', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'description': SlotDefinition(name='description', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a textual description of the entity (single-valued)', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'synonyms': SlotDefinition(name='synonyms', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a list of alternative names of the entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'categories': SlotDefinition(name='categories', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a list of the categories to which this entity belongs', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Category', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subclass_of': SlotDefinition(name='subclass_of', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a list of parent class (superclasses) of this entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:subClassOf', multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='OntologyElement', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'part_of': SlotDefinition(name='part_of', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a list of things this element is part of', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='BFO:0000050', multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='OntologyElement', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subtypes': SlotDefinition(name='subtypes', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a list of child classes (subclasses) of this entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse='subclass_of', is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='OntologyElement', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'parts': SlotDefinition(name='parts', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a list of names of things this element has as parts (components)', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse='part_of', is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='OntologyElement', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'equivalent_to': SlotDefinition(name='equivalent_to', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='an OWL class expression with the necessary and sufficient conditions for this entity to be an instance of this class', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:ClassDefinition a owl:Class ; - rdfs:label "class_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "class_expression" . - -linkml:SlotDefinition a owl:Class ; - rdfs:label "slot_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "slot_expression" . - - diff --git a/projects/halo/prefixmap/halo.yaml b/projects/halo/prefixmap/halo.yaml deleted file mode 100644 index 9067c91e2..000000000 --- a/projects/halo/prefixmap/halo.yaml +++ /dev/null @@ -1,36 +0,0 @@ -{ - "BFO": "http://purl.obolibrary.org/obo/BFO_", - "RO": "http://purl.obolibrary.org/obo/RO_", - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "linkml": "https://w3id.org/linkml/", - "oc": "http://w3id.org/ontogpt/ontology-class-template", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } -} diff --git a/projects/halo/protobuf/halo.proto b/projects/halo/protobuf/halo.proto deleted file mode 100644 index 51c92e48c..000000000 --- a/projects/halo/protobuf/halo.proto +++ /dev/null @@ -1,65 +0,0 @@ -message AnnotatorResult - { - string subjectText = 0 - string objectId = 0 - string objectText = 0 - } -message Category - { - string name = 0 - string context = 0 - string description = 0 - repeated string synonyms = 0 - repeated category categories = 0 - repeated ontologyElement subclassOf = 0 - repeated ontologyElement partOf = 0 - repeated ontologyElement subtypes = 0 - repeated ontologyElement parts = 0 - string equivalentTo = 0 - } -// A result of extracting knowledge on text -message ExtractionResult - { - string inputId = 0 - string inputTitle = 0 - string inputText = 0 - string rawCompletionOutput = 0 - string prompt = 0 - any extractedObject = 0 - repeated any namedEntities = 0 - } -message Ontology - { - repeated ontologyElement elements = 0 - } -message OntologyElement - { - string name = 0 - string context = 0 - string description = 0 - repeated string synonyms = 0 - repeated category categories = 0 - repeated ontologyElement subclassOf = 0 - repeated ontologyElement partOf = 0 - repeated ontologyElement subtypes = 0 - repeated ontologyElement parts = 0 - string equivalentTo = 0 - } -message Publication - { - string id = 0 - string title = 0 - string abstract = 0 - string combinedText = 0 - string fullText = 0 - } -message RelationshipType - { - string id = 0 - string label = 0 - } -message TextWithTriples - { - publication publication = 0 - repeated triple triples = 0 - } diff --git a/projects/halo/shacl/halo.shacl.ttl b/projects/halo/shacl/halo.shacl.ttl deleted file mode 100644 index e72f9090d..000000000 --- a/projects/halo/shacl/halo.shacl.ttl +++ /dev/null @@ -1,273 +0,0 @@ -@prefix BFO: <http://purl.obolibrary.org/obo/BFO_> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix oc: <http://w3id.org/ontogpt/ontology-class-template> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix sh: <http://www.w3.org/ns/shacl#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject_text> ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/object_id> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object_text> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/AnnotatorResult> . - -<http://w3id.org/ontogpt/core/CompoundExpression> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass <http://w3id.org/ontogpt/core/CompoundExpression> . - -<http://w3id.org/ontogpt/core/ExtractionResult> a sh:NodeShape ; - sh:closed true ; - sh:description "A result of extracting knowledge on text" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class linkml:Any ; - sh:description "Named entities extracted from the text" ; - sh:nodeKind sh:BlankNode ; - sh:order 6 ; - sh:path <http://w3id.org/ontogpt/core/named_entities> ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/input_title> ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/input_id> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/input_text> ], - [ sh:class linkml:Any ; - sh:description "The complex objects extracted from the text" ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/extracted_object> ], - [ sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/prompt> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/raw_completion_output> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/ExtractionResult> . - -<http://w3id.org/ontogpt/core/TextWithTriples> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/Publication> ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/publication> ], - [ sh:class <http://w3id.org/ontogpt/core/Triple> ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/triples> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/TextWithTriples> . - -oc:Ontology a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class oc:OntologyElement ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path oc:elements ] ; - sh:targetClass oc:Ontology . - -<http://w3id.org/ontogpt/core/Publication> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The publication identifier" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The abstract of the publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/abstract> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/combined_text> ], - [ sh:description "The title of the publication" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/title> ], - [ sh:description "The full text of the publication" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/full_text> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/RelationshipType> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/Triple> a sh:NodeShape ; - sh:closed false ; - sh:description "Abstract parent for Relation Extraction tasks" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/RelationshipType> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/predicate> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject> ], - [ sh:description "A qualifier for the statements, e.g. \"NOT\" for negation" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/object_qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Triple> . - -oc:Category a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "an OWL class expression with the necessary and sufficient conditions for this entity to be an instance of this class" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path oc:equivalent_to ], - [ sh:description "the name of the entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path oc:name ], - [ sh:class oc:Category ; - sh:description "a list of the categories to which this entity belongs" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path oc:categories ], - [ sh:class oc:OntologyElement ; - sh:description "a list of names of things this element has as parts (components)" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path oc:parts ], - [ sh:description "a textual description of the entity (single-valued)" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path oc:description ], - [ sh:description "a list of alternative names of the entity" ; - sh:order 3 ; - sh:path oc:synonyms ], - [ sh:class oc:OntologyElement ; - sh:description "a list of child classes (subclasses) of this entity" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path oc:subtypes ], - [ sh:class oc:OntologyElement ; - sh:description "a list of things this element is part of" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path BFO:0000050 ], - [ sh:class oc:OntologyElement ; - sh:description "a list of parent class (superclasses) of this entity" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path <rdfs:subClassOf> ], - [ sh:description "the ontology to which this belongs (single-valued)" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path oc:context ] ; - sh:targetClass oc:Category . - -linkml:Any a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass linkml:Any . - -<http://w3id.org/ontogpt/core/NamedEntity> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/NamedEntity> . - -oc:OntologyElement a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class oc:OntologyElement ; - sh:description "a list of child classes (subclasses) of this entity" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path oc:subtypes ], - [ sh:class oc:OntologyElement ; - sh:description "a list of things this element is part of" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path BFO:0000050 ], - [ sh:class oc:OntologyElement ; - sh:description "a list of parent class (superclasses) of this entity" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path <rdfs:subClassOf> ], - [ sh:description "an OWL class expression with the necessary and sufficient conditions for this entity to be an instance of this class" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path oc:equivalent_to ], - [ sh:description "a textual description of the entity (single-valued)" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path oc:description ], - [ sh:description "the ontology to which this belongs (single-valued)" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path oc:context ], - [ sh:class oc:OntologyElement ; - sh:description "a list of names of things this element has as parts (components)" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path oc:parts ], - [ sh:class oc:Category ; - sh:description "a list of the categories to which this entity belongs" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path oc:categories ], - [ sh:description "a list of alternative names of the entity" ; - sh:order 3 ; - sh:path oc:synonyms ], - [ sh:description "the name of the entity" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path oc:name ] ; - sh:targetClass oc:OntologyElement . - diff --git a/projects/halo/shex/halo.shex b/projects/halo/shex/halo.shex deleted file mode 100644 index cce79a67b..000000000 --- a/projects/halo/shex/halo.shex +++ /dev/null @@ -1,169 +0,0 @@ -BASE <http://w3id.org/ontogpt/ontology-class-template/> -PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> -PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> -PREFIX linkml: <https://w3id.org/linkml/> -PREFIX core: <http://w3id.org/ontogpt/core/> -PREFIX rdfs1: <http://example.org/UNKNOWN/rdfs/> - - -linkml:String xsd:string - -linkml:Integer xsd:integer - -linkml:Boolean xsd:boolean - -linkml:Float xsd:float - -linkml:Double xsd:double - -linkml:Decimal xsd:decimal - -linkml:Time xsd:time - -linkml:Date xsd:date - -linkml:Datetime xsd:dateTime - -linkml:DateOrDatetime linkml:DateOrDatetime - -linkml:Uriorcurie IRI - -linkml:Curie xsd:string - -linkml:Uri IRI - -linkml:Ncname xsd:string - -linkml:Objectidentifier IRI - -linkml:Nodeidentifier NONLITERAL - -linkml:Jsonpointer xsd:string - -linkml:Jsonpath xsd:string - -linkml:Sparqlpath xsd:string - -core:AnnotatorResult CLOSED { - ( $core:AnnotatorResult_tes ( core:subject_text @linkml:String ? ; - core:object_id @linkml:String ? ; - core:object_text @linkml:String ? - ) ; - rdf:type [ core:AnnotatorResult ] ? - ) -} - -core:Any CLOSED { - ( $core:Any_tes rdf:type . * ; - rdf:type [ linkml:Any ] ? - ) -} - -<http://w3id.org/ontogpt/ontology-class-templateCategory> CLOSED { - ( $<http://w3id.org/ontogpt/ontology-class-templateCategory_tes> ( - &<http://w3id.org/ontogpt/ontology-class-templateOntologyElement_tes> ; - rdf:type [ <http://w3id.org/ontogpt/ontology-class-templateOntologyElement> ] ? - ) ; - rdf:type [ <http://w3id.org/ontogpt/ontology-class-templateCategory> ] - ) -} - -core:CompoundExpression ( - { - ( $core:CompoundExpression_tes rdf:type . * ; - rdf:type [ core:CompoundExpression ] ? - ) - } OR @core:Triple -) - -core:ExtractionResult CLOSED { - ( $core:ExtractionResult_tes ( core:input_id @linkml:String ? ; - core:input_title @linkml:String ? ; - core:input_text @linkml:String ? ; - core:raw_completion_output @linkml:String ? ; - core:prompt @linkml:String ? ; - core:extracted_object @core:Any ? ; - core:named_entities @core:Any * - ) ; - rdf:type [ core:ExtractionResult ] ? - ) -} - -core:NamedEntity ( - { - ( $core:NamedEntity_tes rdfs1:label @linkml:String ? ; - rdf:type [ core:NamedEntity ] - ) - } OR @core:RelationshipType -) - -<http://w3id.org/ontogpt/ontology-class-templateOntology> CLOSED { - ( $<http://w3id.org/ontogpt/ontology-class-templateOntology_tes> <http://w3id.org/ontogpt/ontology-class-templateelements> - @<http://w3id.org/ontogpt/ontology-class-templateOntologyElement> * ; - rdf:type [ <http://w3id.org/ontogpt/ontology-class-templateOntology> ] ? - ) -} - -<http://w3id.org/ontogpt/ontology-class-templateOntologyElement> ( - CLOSED { - ( $<http://w3id.org/ontogpt/ontology-class-templateOntologyElement_tes> ( - <http://w3id.org/ontogpt/ontology-class-templatecontext> @linkml:String ? ; - <http://w3id.org/ontogpt/ontology-class-templatedescription> @linkml:String ? ; - <http://w3id.org/ontogpt/ontology-class-templatesynonyms> @linkml:String * ; - <http://w3id.org/ontogpt/ontology-class-templatecategories> @<http://w3id.org/ontogpt/ontology-class-templateCategory> - * ; - rdfs1:subClassOf @<http://w3id.org/ontogpt/ontology-class-templateOntologyElement> * ; - <http://purl.obolibrary.org/obo/BFO_0000050> @<http://w3id.org/ontogpt/ontology-class-templateOntologyElement> * ; - <http://w3id.org/ontogpt/ontology-class-templatesubtypes> - @<http://w3id.org/ontogpt/ontology-class-templateOntologyElement> * ; - <http://w3id.org/ontogpt/ontology-class-templateparts> - @<http://w3id.org/ontogpt/ontology-class-templateOntologyElement> * ; - <http://w3id.org/ontogpt/ontology-class-templateequivalent_to> @linkml:String ? - ) ; - rdf:type [ <http://w3id.org/ontogpt/ontology-class-templateOntologyElement> ] - ) - } OR @<http://w3id.org/ontogpt/ontology-class-templateCategory> -) - -core:Publication CLOSED { - ( $core:Publication_tes ( core:id @linkml:String ? ; - core:title @linkml:String ? ; - core:abstract @linkml:String ? ; - core:combined_text @linkml:String ? ; - core:full_text @linkml:String ? - ) ; - rdf:type [ core:Publication ] ? - ) -} - -core:RelationshipType CLOSED { - ( $core:RelationshipType_tes ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ core:RelationshipType ] - ) -} - -core:TextWithTriples CLOSED { - ( $core:TextWithTriples_tes ( core:publication @core:Publication ? ; - core:triples @core:Triple * - ) ; - rdf:type [ core:TextWithTriples ] ? - ) -} - -core:Triple { - ( $core:Triple_tes ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - core:subject @core:NamedEntity ? ; - core:predicate @core:RelationshipType ? ; - core:object @core:NamedEntity ? ; - core:qualifier @linkml:String ? ; - core:subject_qualifier @core:NamedEntity ? ; - core:object_qualifier @core:NamedEntity ? - ) ; - rdf:type [ core:Triple ] ? - ) -} - - diff --git a/projects/halo/sqlschema/halo.sql b/projects/halo/sqlschema/halo.sql deleted file mode 100644 index 97cfaad80..000000000 --- a/projects/halo/sqlschema/halo.sql +++ /dev/null @@ -1,85 +0,0 @@ - - -CREATE TABLE "AnnotatorResult" ( - subject_text TEXT, - object_id TEXT, - object_text TEXT, - PRIMARY KEY (subject_text, object_id, object_text) -); - -CREATE TABLE "Category" ( - name TEXT NOT NULL, - context TEXT, - description TEXT, - categories TEXT, - subclass_of TEXT, - part_of TEXT, - subtypes TEXT, - parts TEXT, - equivalent_to TEXT, - PRIMARY KEY (name) -); - -CREATE TABLE "ExtractionResult" ( - input_id TEXT, - input_title TEXT, - input_text TEXT, - raw_completion_output TEXT, - prompt TEXT, - extracted_object TEXT, - named_entities TEXT, - PRIMARY KEY (input_id, input_title, input_text, raw_completion_output, prompt, extracted_object, named_entities) -); - -CREATE TABLE "Ontology" ( - elements TEXT, - PRIMARY KEY (elements) -); - -CREATE TABLE "OntologyElement" ( - name TEXT NOT NULL, - context TEXT, - description TEXT, - categories TEXT, - subclass_of TEXT, - part_of TEXT, - subtypes TEXT, - parts TEXT, - equivalent_to TEXT, - PRIMARY KEY (name) -); - -CREATE TABLE "Publication" ( - id TEXT, - title TEXT, - abstract TEXT, - combined_text TEXT, - full_text TEXT, - PRIMARY KEY (id, title, abstract, combined_text, full_text) -); - -CREATE TABLE "RelationshipType" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "TextWithTriples" ( - publication TEXT, - triples TEXT, - PRIMARY KEY (publication, triples) -); - -CREATE TABLE "Category_synonyms" ( - backref_id TEXT, - synonyms TEXT, - PRIMARY KEY (backref_id, synonyms), - FOREIGN KEY(backref_id) REFERENCES "Category" (name) -); - -CREATE TABLE "OntologyElement_synonyms" ( - backref_id TEXT, - synonyms TEXT, - PRIMARY KEY (backref_id, synonyms), - FOREIGN KEY(backref_id) REFERENCES "OntologyElement" (name) -); diff --git a/projects/ibd/docs/AnnotatorResult.md b/projects/ibd/docs/AnnotatorResult.md deleted file mode 100644 index b21f75a37..000000000 --- a/projects/ibd/docs/AnnotatorResult.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Class: AnnotatorResult - - - - -URI: [gocam:AnnotatorResult](http://w3id.org/ontogpt/gocam/AnnotatorResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F])](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F]) - -## Attributes - - -### Own - - * [➞subject_text](annotatorResult__subject_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_id](annotatorResult__object_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_text](annotatorResult__object_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) diff --git a/projects/ibd/docs/Any.md b/projects/ibd/docs/Any.md deleted file mode 100644 index 294c64451..000000000 --- a/projects/ibd/docs/Any.md +++ /dev/null @@ -1,25 +0,0 @@ - -# Class: Any - - - - -URI: [gocam:Any](http://w3id.org/ontogpt/gocam/Any) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult])](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult]) - -## Referenced by Class - - * **None** *[➞extracted_object](extractionResult__extracted_object.md)* <sub>0..1</sub> **[Any](Any.md)** - * **None** *[➞named_entities](extractionResult__named_entities.md)* <sub>0..\*</sub> **[Any](Any.md)** - -## Attributes - - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | linkml:Any | - diff --git a/projects/ibd/docs/CellType.md b/projects/ibd/docs/CellType.md deleted file mode 100644 index cce37c2b0..000000000 --- a/projects/ibd/docs/CellType.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Enum: CellType - - - - -URI: [gocam:CellType](http://w3id.org/ontogpt/gocam/CellType) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | - diff --git a/projects/ibd/docs/CellularProcess.md b/projects/ibd/docs/CellularProcess.md deleted file mode 100644 index a97d8ea79..000000000 --- a/projects/ibd/docs/CellularProcess.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: CellularProcess - - - - -URI: [gocam:CellularProcess](http://w3id.org/ontogpt/gocam/CellularProcess) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[IBDAnnotations]-%20cellular_processes%200..*>[CellularProcess|id(i):string;label(i):string%20%3F],[NamedEntity]^-[CellularProcess],[IBDAnnotations])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[IBDAnnotations]-%20cellular_processes%200..*>[CellularProcess|id(i):string;label(i):string%20%3F],[NamedEntity]^-[CellularProcess],[IBDAnnotations]) - -## Identifier prefixes - - * GO - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞cellular_processes](iBDAnnotations__cellular_processes.md)* <sub>0..\*</sub> **[CellularProcess](CellularProcess.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/ibd/docs/CompoundExpression.md b/projects/ibd/docs/CompoundExpression.md deleted file mode 100644 index 2c710a723..000000000 --- a/projects/ibd/docs/CompoundExpression.md +++ /dev/null @@ -1,25 +0,0 @@ - -# Class: CompoundExpression - - - - -URI: [gocam:CompoundExpression](http://w3id.org/ontogpt/gocam/CompoundExpression) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[GeneSubcellularLocalizationRelationship],[GeneOrganismRelationship],[GeneMolecularActivityRelationship2],[GeneMolecularActivityRelationship],[GeneGeneInteraction],[CompoundExpression]^-[Triple],[CompoundExpression]^-[GeneSubcellularLocalizationRelationship],[CompoundExpression]^-[GeneOrganismRelationship],[CompoundExpression]^-[GeneMolecularActivityRelationship2],[CompoundExpression]^-[GeneMolecularActivityRelationship],[CompoundExpression]^-[GeneGeneInteraction])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[GeneSubcellularLocalizationRelationship],[GeneOrganismRelationship],[GeneMolecularActivityRelationship2],[GeneMolecularActivityRelationship],[GeneGeneInteraction],[CompoundExpression]^-[Triple],[CompoundExpression]^-[GeneSubcellularLocalizationRelationship],[CompoundExpression]^-[GeneOrganismRelationship],[CompoundExpression]^-[GeneMolecularActivityRelationship2],[CompoundExpression]^-[GeneMolecularActivityRelationship],[CompoundExpression]^-[GeneGeneInteraction]) - -## Children - - * [GeneGeneInteraction](GeneGeneInteraction.md) - * [GeneMolecularActivityRelationship](GeneMolecularActivityRelationship.md) - * [GeneMolecularActivityRelationship2](GeneMolecularActivityRelationship2.md) - * [GeneOrganismRelationship](GeneOrganismRelationship.md) - * [GeneSubcellularLocalizationRelationship](GeneSubcellularLocalizationRelationship.md) - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - -## Referenced by Class - - -## Attributes - diff --git a/projects/ibd/docs/ExtractionResult.md b/projects/ibd/docs/ExtractionResult.md deleted file mode 100644 index 5fd1b0627..000000000 --- a/projects/ibd/docs/ExtractionResult.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Class: ExtractionResult - - -A result of extracting knowledge on text - -URI: [gocam:ExtractionResult](http://w3id.org/ontogpt/gocam/ExtractionResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any])](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any]) - -## Attributes - - -### Own - - * [➞input_id](extractionResult__input_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_title](extractionResult__input_title.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_text](extractionResult__input_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞prompt](extractionResult__prompt.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞extracted_object](extractionResult__extracted_object.md) <sub>0..1</sub> - * Description: The complex objects extracted from the text - * Range: [Any](Any.md) - * [➞named_entities](extractionResult__named_entities.md) <sub>0..\*</sub> - * Description: Named entities extracted from the text - * Range: [Any](Any.md) diff --git a/projects/ibd/docs/GOCellComponentType.md b/projects/ibd/docs/GOCellComponentType.md deleted file mode 100644 index e2e6fcda9..000000000 --- a/projects/ibd/docs/GOCellComponentType.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Enum: GOCellComponentType - - - - -URI: [gocam:GOCellComponentType](http://w3id.org/ontogpt/gocam/GOCellComponentType) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | - diff --git a/projects/ibd/docs/Gene.md b/projects/ibd/docs/Gene.md deleted file mode 100644 index 582d0b4b8..000000000 --- a/projects/ibd/docs/Gene.md +++ /dev/null @@ -1,42 +0,0 @@ - -# Class: Gene - - - - -URI: [gocam:Gene](http://w3id.org/ontogpt/gocam/Gene) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[GeneGeneInteraction]-%20gene1%200..1>[Gene|id(i):string;label(i):string%20%3F],[GeneGeneInteraction]-%20gene2%200..1>[Gene],[GeneMolecularActivityRelationship2]-%20gene%200..1>[Gene],[GeneMolecularActivityRelationship]-%20gene%200..1>[Gene],[GeneOrganismRelationship]-%20gene%200..1>[Gene],[GeneSubcellularLocalizationRelationship]-%20gene%200..1>[Gene],[IBDAnnotations]-%20genes%200..*>[Gene],[NamedEntity]^-[Gene],[IBDAnnotations],[GeneSubcellularLocalizationRelationship],[GeneOrganismRelationship],[GeneMolecularActivityRelationship2],[GeneMolecularActivityRelationship],[GeneGeneInteraction])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[GeneGeneInteraction]-%20gene1%200..1>[Gene|id(i):string;label(i):string%20%3F],[GeneGeneInteraction]-%20gene2%200..1>[Gene],[GeneMolecularActivityRelationship2]-%20gene%200..1>[Gene],[GeneMolecularActivityRelationship]-%20gene%200..1>[Gene],[GeneOrganismRelationship]-%20gene%200..1>[Gene],[GeneSubcellularLocalizationRelationship]-%20gene%200..1>[Gene],[IBDAnnotations]-%20genes%200..*>[Gene],[NamedEntity]^-[Gene],[IBDAnnotations],[GeneSubcellularLocalizationRelationship],[GeneOrganismRelationship],[GeneMolecularActivityRelationship2],[GeneMolecularActivityRelationship],[GeneGeneInteraction]) - -## Identifier prefixes - - * HGNC - * PR - * UniProtKB - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞gene1](geneGeneInteraction__gene1.md)* <sub>0..1</sub> **[Gene](Gene.md)** - * **None** *[➞gene2](geneGeneInteraction__gene2.md)* <sub>0..1</sub> **[Gene](Gene.md)** - * **None** *[➞gene](geneMolecularActivityRelationship2__gene.md)* <sub>0..1</sub> **[Gene](Gene.md)** - * **None** *[➞gene](geneMolecularActivityRelationship__gene.md)* <sub>0..1</sub> **[Gene](Gene.md)** - * **None** *[➞gene](geneOrganismRelationship__gene.md)* <sub>0..1</sub> **[Gene](Gene.md)** - * **None** *[➞gene](geneSubcellularLocalizationRelationship__gene.md)* <sub>0..1</sub> **[Gene](Gene.md)** - * **None** *[➞genes](iBDAnnotations__genes.md)* <sub>0..\*</sub> **[Gene](Gene.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/ibd/docs/GeneGeneInteraction.md b/projects/ibd/docs/GeneGeneInteraction.md deleted file mode 100644 index 805d01b25..000000000 --- a/projects/ibd/docs/GeneGeneInteraction.md +++ /dev/null @@ -1,28 +0,0 @@ - -# Class: GeneGeneInteraction - - - - -URI: [gocam:GeneGeneInteraction](http://w3id.org/ontogpt/gocam/GeneGeneInteraction) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Gene]<gene2%200..1-%20[GeneGeneInteraction],[Gene]<gene1%200..1-%20[GeneGeneInteraction],[IBDAnnotations]++-%20gene_gene_interactions%200..*>[GeneGeneInteraction],[CompoundExpression]^-[GeneGeneInteraction],[IBDAnnotations],[Gene],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[Gene]<gene2%200..1-%20[GeneGeneInteraction],[Gene]<gene1%200..1-%20[GeneGeneInteraction],[IBDAnnotations]++-%20gene_gene_interactions%200..*>[GeneGeneInteraction],[CompoundExpression]^-[GeneGeneInteraction],[IBDAnnotations],[Gene],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞gene_gene_interactions](iBDAnnotations__gene_gene_interactions.md)* <sub>0..\*</sub> **[GeneGeneInteraction](GeneGeneInteraction.md)** - -## Attributes - - -### Own - - * [➞gene1](geneGeneInteraction__gene1.md) <sub>0..1</sub> - * Range: [Gene](Gene.md) - * [➞gene2](geneGeneInteraction__gene2.md) <sub>0..1</sub> - * Range: [Gene](Gene.md) diff --git a/projects/ibd/docs/GeneLocation.md b/projects/ibd/docs/GeneLocation.md deleted file mode 100644 index d54b4da61..000000000 --- a/projects/ibd/docs/GeneLocation.md +++ /dev/null @@ -1,38 +0,0 @@ - -# Class: GeneLocation - - - - -URI: [gocam:GeneLocation](http://w3id.org/ontogpt/gocam/GeneLocation) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[GeneSubcellularLocalizationRelationship]-%20location%200..1>[GeneLocation|id:string;label(i):string%20%3F],[NamedEntity]^-[GeneLocation],[GeneSubcellularLocalizationRelationship])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[GeneSubcellularLocalizationRelationship]-%20location%200..1>[GeneLocation|id:string;label(i):string%20%3F],[NamedEntity]^-[GeneLocation],[GeneSubcellularLocalizationRelationship]) - -## Identifier prefixes - - * GO - * CL - * UBERON - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞location](geneSubcellularLocalizationRelationship__location.md)* <sub>0..1</sub> **[GeneLocation](GeneLocation.md)** - -## Attributes - - -### Own - - * [GeneLocation➞id](GeneLocation_id.md) <sub>1..1</sub> - * Range: [String](types/String.md) - -### Inherited from NamedEntity: - - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/ibd/docs/GeneLocationEnum.md b/projects/ibd/docs/GeneLocationEnum.md deleted file mode 100644 index 67626c0d9..000000000 --- a/projects/ibd/docs/GeneLocationEnum.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Enum: GeneLocationEnum - - - - -URI: [gocam:GeneLocationEnum](http://w3id.org/ontogpt/gocam/GeneLocationEnum) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | - diff --git a/projects/ibd/docs/GeneLocation_id.md b/projects/ibd/docs/GeneLocation_id.md deleted file mode 100644 index 1357ee5d7..000000000 --- a/projects/ibd/docs/GeneLocation_id.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: id - - - - -URI: [gocam:GeneLocation_id](http://w3id.org/ontogpt/gocam/GeneLocation_id) - - -## Domain and Range - -[GeneLocation](GeneLocation.md) → <sub>1..1</sub> [String](types/String.md) - -## Parents - - * is_a: [➞id](namedEntity__id.md) - -## Children - - -## Used by - - * [GeneLocation](GeneLocation.md) diff --git a/projects/ibd/docs/GeneMolecularActivityRelationship.md b/projects/ibd/docs/GeneMolecularActivityRelationship.md deleted file mode 100644 index d6e7a741d..000000000 --- a/projects/ibd/docs/GeneMolecularActivityRelationship.md +++ /dev/null @@ -1,28 +0,0 @@ - -# Class: GeneMolecularActivityRelationship - - - - -URI: [gocam:GeneMolecularActivityRelationship](http://w3id.org/ontogpt/gocam/GeneMolecularActivityRelationship) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[MolecularActivity],[MolecularActivity]<molecular_activity%200..1-%20[GeneMolecularActivityRelationship],[Gene]<gene%200..1-%20[GeneMolecularActivityRelationship],[IBDAnnotations]++-%20gene_functions%200..*>[GeneMolecularActivityRelationship],[CompoundExpression]^-[GeneMolecularActivityRelationship],[IBDAnnotations],[Gene],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[MolecularActivity],[MolecularActivity]<molecular_activity%200..1-%20[GeneMolecularActivityRelationship],[Gene]<gene%200..1-%20[GeneMolecularActivityRelationship],[IBDAnnotations]++-%20gene_functions%200..*>[GeneMolecularActivityRelationship],[CompoundExpression]^-[GeneMolecularActivityRelationship],[IBDAnnotations],[Gene],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞gene_functions](iBDAnnotations__gene_functions.md)* <sub>0..\*</sub> **[GeneMolecularActivityRelationship](GeneMolecularActivityRelationship.md)** - -## Attributes - - -### Own - - * [➞gene](geneMolecularActivityRelationship__gene.md) <sub>0..1</sub> - * Range: [Gene](Gene.md) - * [➞molecular_activity](geneMolecularActivityRelationship__molecular_activity.md) <sub>0..1</sub> - * Range: [MolecularActivity](MolecularActivity.md) diff --git a/projects/ibd/docs/GeneMolecularActivityRelationship2.md b/projects/ibd/docs/GeneMolecularActivityRelationship2.md deleted file mode 100644 index 395313a4f..000000000 --- a/projects/ibd/docs/GeneMolecularActivityRelationship2.md +++ /dev/null @@ -1,26 +0,0 @@ - -# Class: GeneMolecularActivityRelationship2 - - - - -URI: [gocam:GeneMolecularActivityRelationship2](http://w3id.org/ontogpt/gocam/GeneMolecularActivityRelationship2) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Molecule],[MolecularActivity],[Molecule]<target%200..1-%20[GeneMolecularActivityRelationship2],[MolecularActivity]<molecular_activity%200..1-%20[GeneMolecularActivityRelationship2],[Gene]<gene%200..1-%20[GeneMolecularActivityRelationship2],[CompoundExpression]^-[GeneMolecularActivityRelationship2],[Gene],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[Molecule],[MolecularActivity],[Molecule]<target%200..1-%20[GeneMolecularActivityRelationship2],[MolecularActivity]<molecular_activity%200..1-%20[GeneMolecularActivityRelationship2],[Gene]<gene%200..1-%20[GeneMolecularActivityRelationship2],[CompoundExpression]^-[GeneMolecularActivityRelationship2],[Gene],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Attributes - - -### Own - - * [➞gene](geneMolecularActivityRelationship2__gene.md) <sub>0..1</sub> - * Range: [Gene](Gene.md) - * [➞molecular_activity](geneMolecularActivityRelationship2__molecular_activity.md) <sub>0..1</sub> - * Range: [MolecularActivity](MolecularActivity.md) - * [➞target](geneMolecularActivityRelationship2__target.md) <sub>0..1</sub> - * Range: [Molecule](Molecule.md) diff --git a/projects/ibd/docs/GeneOrganismRelationship.md b/projects/ibd/docs/GeneOrganismRelationship.md deleted file mode 100644 index d5c29e09a..000000000 --- a/projects/ibd/docs/GeneOrganismRelationship.md +++ /dev/null @@ -1,28 +0,0 @@ - -# Class: GeneOrganismRelationship - - - - -URI: [gocam:GeneOrganismRelationship](http://w3id.org/ontogpt/gocam/GeneOrganismRelationship) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Organism],[Organism]<organism%200..1-%20[GeneOrganismRelationship],[Gene]<gene%200..1-%20[GeneOrganismRelationship],[IBDAnnotations]++-%20gene_organisms%200..*>[GeneOrganismRelationship],[CompoundExpression]^-[GeneOrganismRelationship],[IBDAnnotations],[Gene],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[Organism],[Organism]<organism%200..1-%20[GeneOrganismRelationship],[Gene]<gene%200..1-%20[GeneOrganismRelationship],[IBDAnnotations]++-%20gene_organisms%200..*>[GeneOrganismRelationship],[CompoundExpression]^-[GeneOrganismRelationship],[IBDAnnotations],[Gene],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞gene_organisms](iBDAnnotations__gene_organisms.md)* <sub>0..\*</sub> **[GeneOrganismRelationship](GeneOrganismRelationship.md)** - -## Attributes - - -### Own - - * [➞gene](geneOrganismRelationship__gene.md) <sub>0..1</sub> - * Range: [Gene](Gene.md) - * [➞organism](geneOrganismRelationship__organism.md) <sub>0..1</sub> - * Range: [Organism](Organism.md) diff --git a/projects/ibd/docs/GeneSubcellularLocalizationRelationship.md b/projects/ibd/docs/GeneSubcellularLocalizationRelationship.md deleted file mode 100644 index c7de454f4..000000000 --- a/projects/ibd/docs/GeneSubcellularLocalizationRelationship.md +++ /dev/null @@ -1,28 +0,0 @@ - -# Class: GeneSubcellularLocalizationRelationship - - - - -URI: [gocam:GeneSubcellularLocalizationRelationship](http://w3id.org/ontogpt/gocam/GeneSubcellularLocalizationRelationship) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[GeneLocation]<location%200..1-%20[GeneSubcellularLocalizationRelationship],[Gene]<gene%200..1-%20[GeneSubcellularLocalizationRelationship],[IBDAnnotations]++-%20gene_localizations%200..*>[GeneSubcellularLocalizationRelationship],[CompoundExpression]^-[GeneSubcellularLocalizationRelationship],[IBDAnnotations],[GeneLocation],[Gene],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[GeneLocation]<location%200..1-%20[GeneSubcellularLocalizationRelationship],[Gene]<gene%200..1-%20[GeneSubcellularLocalizationRelationship],[IBDAnnotations]++-%20gene_localizations%200..*>[GeneSubcellularLocalizationRelationship],[CompoundExpression]^-[GeneSubcellularLocalizationRelationship],[IBDAnnotations],[GeneLocation],[Gene],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞gene_localizations](iBDAnnotations__gene_localizations.md)* <sub>0..\*</sub> **[GeneSubcellularLocalizationRelationship](GeneSubcellularLocalizationRelationship.md)** - -## Attributes - - -### Own - - * [➞gene](geneSubcellularLocalizationRelationship__gene.md) <sub>0..1</sub> - * Range: [Gene](Gene.md) - * [➞location](geneSubcellularLocalizationRelationship__location.md) <sub>0..1</sub> - * Range: [GeneLocation](GeneLocation.md) diff --git a/projects/ibd/docs/IBDAnnotations.md b/projects/ibd/docs/IBDAnnotations.md deleted file mode 100644 index f37991365..000000000 --- a/projects/ibd/docs/IBDAnnotations.md +++ /dev/null @@ -1,42 +0,0 @@ - -# Class: IBDAnnotations - - - - -URI: [gocam:IBDAnnotations](http://w3id.org/ontogpt/gocam/IBDAnnotations) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Pathway],[Organism],[MolecularActivity],[GeneSubcellularLocalizationRelationship]<gene_localizations%200..*-++[IBDAnnotations],[GeneGeneInteraction]<gene_gene_interactions%200..*-++[IBDAnnotations],[Pathway]<pathways%200..*-%20[IBDAnnotations],[CellularProcess]<cellular_processes%200..*-%20[IBDAnnotations],[GeneMolecularActivityRelationship]<gene_functions%200..*-++[IBDAnnotations],[MolecularActivity]<activities%200..*-%20[IBDAnnotations],[GeneOrganismRelationship]<gene_organisms%200..*-++[IBDAnnotations],[Organism]<organisms%200..*-%20[IBDAnnotations],[Gene]<genes%200..*-%20[IBDAnnotations],[GeneSubcellularLocalizationRelationship],[GeneOrganismRelationship],[GeneMolecularActivityRelationship],[GeneGeneInteraction],[Gene],[CellularProcess])](https://yuml.me/diagram/nofunky;dir:TB/class/[Pathway],[Organism],[MolecularActivity],[GeneSubcellularLocalizationRelationship]<gene_localizations%200..*-++[IBDAnnotations],[GeneGeneInteraction]<gene_gene_interactions%200..*-++[IBDAnnotations],[Pathway]<pathways%200..*-%20[IBDAnnotations],[CellularProcess]<cellular_processes%200..*-%20[IBDAnnotations],[GeneMolecularActivityRelationship]<gene_functions%200..*-++[IBDAnnotations],[MolecularActivity]<activities%200..*-%20[IBDAnnotations],[GeneOrganismRelationship]<gene_organisms%200..*-++[IBDAnnotations],[Organism]<organisms%200..*-%20[IBDAnnotations],[Gene]<genes%200..*-%20[IBDAnnotations],[GeneSubcellularLocalizationRelationship],[GeneOrganismRelationship],[GeneMolecularActivityRelationship],[GeneGeneInteraction],[Gene],[CellularProcess]) - -## Attributes - - -### Own - - * [➞genes](iBDAnnotations__genes.md) <sub>0..\*</sub> - * Description: semicolon-separated list of genes - * Range: [Gene](Gene.md) - * [➞organisms](iBDAnnotations__organisms.md) <sub>0..\*</sub> - * Description: semicolon-separated list of organism taxons - * Range: [Organism](Organism.md) - * [➞gene_organisms](iBDAnnotations__gene_organisms.md) <sub>0..\*</sub> - * Range: [GeneOrganismRelationship](GeneOrganismRelationship.md) - * [➞activities](iBDAnnotations__activities.md) <sub>0..\*</sub> - * Description: semicolon-separated list of molecular activities - * Range: [MolecularActivity](MolecularActivity.md) - * [➞gene_functions](iBDAnnotations__gene_functions.md) <sub>0..\*</sub> - * Description: semicolon-separated list of gene to molecular activity relationships - * Range: [GeneMolecularActivityRelationship](GeneMolecularActivityRelationship.md) - * [➞cellular_processes](iBDAnnotations__cellular_processes.md) <sub>0..\*</sub> - * Description: semicolon-separated list of cellular processes - * Range: [CellularProcess](CellularProcess.md) - * [➞pathways](iBDAnnotations__pathways.md) <sub>0..\*</sub> - * Description: semicolon-separated list of pathways - * Range: [Pathway](Pathway.md) - * [➞gene_gene_interactions](iBDAnnotations__gene_gene_interactions.md) <sub>0..\*</sub> - * Description: semicolon-separated list of gene to gene interactions - * Range: [GeneGeneInteraction](GeneGeneInteraction.md) - * [➞gene_localizations](iBDAnnotations__gene_localizations.md) <sub>0..\*</sub> - * Description: semicolon-separated list of genes plus their location in the cell; for example, "gene1 / cytoplasm; gene2 / mitochondrion" - * Range: [GeneSubcellularLocalizationRelationship](GeneSubcellularLocalizationRelationship.md) diff --git a/projects/ibd/docs/MolecularActivity.md b/projects/ibd/docs/MolecularActivity.md deleted file mode 100644 index bc4583fba..000000000 --- a/projects/ibd/docs/MolecularActivity.md +++ /dev/null @@ -1,36 +0,0 @@ - -# Class: MolecularActivity - - - - -URI: [gocam:MolecularActivity](http://w3id.org/ontogpt/gocam/MolecularActivity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[GeneMolecularActivityRelationship2]-%20molecular_activity%200..1>[MolecularActivity|id(i):string;label(i):string%20%3F],[GeneMolecularActivityRelationship]-%20molecular_activity%200..1>[MolecularActivity],[IBDAnnotations]-%20activities%200..*>[MolecularActivity],[NamedEntity]^-[MolecularActivity],[IBDAnnotations],[GeneMolecularActivityRelationship2],[GeneMolecularActivityRelationship])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[GeneMolecularActivityRelationship2]-%20molecular_activity%200..1>[MolecularActivity|id(i):string;label(i):string%20%3F],[GeneMolecularActivityRelationship]-%20molecular_activity%200..1>[MolecularActivity],[IBDAnnotations]-%20activities%200..*>[MolecularActivity],[NamedEntity]^-[MolecularActivity],[IBDAnnotations],[GeneMolecularActivityRelationship2],[GeneMolecularActivityRelationship]) - -## Identifier prefixes - - * GO - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞molecular_activity](geneMolecularActivityRelationship2__molecular_activity.md)* <sub>0..1</sub> **[MolecularActivity](MolecularActivity.md)** - * **None** *[➞molecular_activity](geneMolecularActivityRelationship__molecular_activity.md)* <sub>0..1</sub> **[MolecularActivity](MolecularActivity.md)** - * **None** *[➞activities](iBDAnnotations__activities.md)* <sub>0..\*</sub> **[MolecularActivity](MolecularActivity.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/ibd/docs/Molecule.md b/projects/ibd/docs/Molecule.md deleted file mode 100644 index 2dc4c84f4..000000000 --- a/projects/ibd/docs/Molecule.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: Molecule - - - - -URI: [gocam:Molecule](http://w3id.org/ontogpt/gocam/Molecule) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[GeneMolecularActivityRelationship2]-%20target%200..1>[Molecule|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Molecule],[GeneMolecularActivityRelationship2])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[GeneMolecularActivityRelationship2]-%20target%200..1>[Molecule|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Molecule],[GeneMolecularActivityRelationship2]) - -## Identifier prefixes - - * CHEBI - * PR - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞target](geneMolecularActivityRelationship2__target.md)* <sub>0..1</sub> **[Molecule](Molecule.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/ibd/docs/NamedEntity.md b/projects/ibd/docs/NamedEntity.md deleted file mode 100644 index 3896f74ca..000000000 --- a/projects/ibd/docs/NamedEntity.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Class: NamedEntity - - - - -URI: [gocam:NamedEntity](http://w3id.org/ontogpt/gocam/NamedEntity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[Pathway],[Organism],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[Pathway],[NamedEntity]^-[Organism],[NamedEntity]^-[Molecule],[NamedEntity]^-[MolecularActivity],[NamedEntity]^-[GeneLocation],[NamedEntity]^-[Gene],[NamedEntity]^-[CellularProcess],[Triple],[Molecule],[MolecularActivity],[GeneLocation],[Gene],[CellularProcess])](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[Pathway],[Organism],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[Pathway],[NamedEntity]^-[Organism],[NamedEntity]^-[Molecule],[NamedEntity]^-[MolecularActivity],[NamedEntity]^-[GeneLocation],[NamedEntity]^-[Gene],[NamedEntity]^-[CellularProcess],[Triple],[Molecule],[MolecularActivity],[GeneLocation],[Gene],[CellularProcess]) - -## Children - - * [CellularProcess](CellularProcess.md) - * [Gene](Gene.md) - * [GeneLocation](GeneLocation.md) - * [MolecularActivity](MolecularActivity.md) - * [Molecule](Molecule.md) - * [Organism](Organism.md) - * [Pathway](Pathway.md) - * [RelationshipType](RelationshipType.md) - -## Referenced by Class - - * **None** *[➞object](triple__object.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞object_qualifier](triple__object_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject](triple__subject.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject_qualifier](triple__subject_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - -## Attributes - - -### Own - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/ibd/docs/NullDataOptions.md b/projects/ibd/docs/NullDataOptions.md deleted file mode 100644 index abbb7e68a..000000000 --- a/projects/ibd/docs/NullDataOptions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Enum: NullDataOptions - - - - -URI: [gocam:NullDataOptions](http://w3id.org/ontogpt/gocam/NullDataOptions) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | -| UNSPECIFIED_METHOD_OF_ADMINISTRATION | | NCIT:C149701 | | -| NOT_APPLICABLE | | NCIT:C18902 | {'aliases': ['not applicable', 'N/A']} | -| NOT_MENTIONED | | | | - diff --git a/projects/ibd/docs/Organism.md b/projects/ibd/docs/Organism.md deleted file mode 100644 index c9826ae6b..000000000 --- a/projects/ibd/docs/Organism.md +++ /dev/null @@ -1,36 +0,0 @@ - -# Class: Organism - - - - -URI: [gocam:Organism](http://w3id.org/ontogpt/gocam/Organism) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[GeneOrganismRelationship]-%20organism%200..1>[Organism|id(i):string;label(i):string%20%3F],[IBDAnnotations]-%20organisms%200..*>[Organism],[NamedEntity]^-[Organism],[NamedEntity],[IBDAnnotations],[GeneOrganismRelationship])](https://yuml.me/diagram/nofunky;dir:TB/class/[GeneOrganismRelationship]-%20organism%200..1>[Organism|id(i):string;label(i):string%20%3F],[IBDAnnotations]-%20organisms%200..*>[Organism],[NamedEntity]^-[Organism],[NamedEntity],[IBDAnnotations],[GeneOrganismRelationship]) - -## Identifier prefixes - - * NCBITaxon - * EFO - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞organism](geneOrganismRelationship__organism.md)* <sub>0..1</sub> **[Organism](Organism.md)** - * **None** *[➞organisms](iBDAnnotations__organisms.md)* <sub>0..\*</sub> **[Organism](Organism.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/ibd/docs/Pathway.md b/projects/ibd/docs/Pathway.md deleted file mode 100644 index 3028f7bf2..000000000 --- a/projects/ibd/docs/Pathway.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: Pathway - - - - -URI: [gocam:Pathway](http://w3id.org/ontogpt/gocam/Pathway) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[IBDAnnotations]-%20pathways%200..*>[Pathway|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Pathway],[NamedEntity],[IBDAnnotations])](https://yuml.me/diagram/nofunky;dir:TB/class/[IBDAnnotations]-%20pathways%200..*>[Pathway|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Pathway],[NamedEntity],[IBDAnnotations]) - -## Identifier prefixes - - * GO - * PW - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞pathways](iBDAnnotations__pathways.md)* <sub>0..\*</sub> **[Pathway](Pathway.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/ibd/docs/Publication.md b/projects/ibd/docs/Publication.md deleted file mode 100644 index 64d87f10d..000000000 --- a/projects/ibd/docs/Publication.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Publication - - - - -URI: [gocam:Publication](http://w3id.org/ontogpt/gocam/Publication) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples])](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples]) - -## Referenced by Class - - * **None** *[➞publication](textWithTriples__publication.md)* <sub>0..1</sub> **[Publication](Publication.md)** - -## Attributes - - -### Own - - * [➞id](publication__id.md) <sub>0..1</sub> - * Description: The publication identifier - * Range: [String](types/String.md) - * [➞title](publication__title.md) <sub>0..1</sub> - * Description: The title of the publication - * Range: [String](types/String.md) - * [➞abstract](publication__abstract.md) <sub>0..1</sub> - * Description: The abstract of the publication - * Range: [String](types/String.md) - * [➞combined_text](publication__combined_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞full_text](publication__full_text.md) <sub>0..1</sub> - * Description: The full text of the publication - * Range: [String](types/String.md) diff --git a/projects/ibd/docs/RelationshipType.md b/projects/ibd/docs/RelationshipType.md deleted file mode 100644 index ea382170c..000000000 --- a/projects/ibd/docs/RelationshipType.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: RelationshipType - - - - -URI: [gocam:RelationshipType](http://w3id.org/ontogpt/gocam/RelationshipType) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity]) - -## Identifier prefixes - - * RO - * biolink - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞predicate](triple__predicate.md)* <sub>0..1</sub> **[RelationshipType](RelationshipType.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/ibd/docs/TextWithTriples.md b/projects/ibd/docs/TextWithTriples.md deleted file mode 100644 index 77200b9c3..000000000 --- a/projects/ibd/docs/TextWithTriples.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: TextWithTriples - - - - -URI: [gocam:TextWithTriples](http://w3id.org/ontogpt/gocam/TextWithTriples) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication]) - -## Attributes - - -### Own - - * [➞publication](textWithTriples__publication.md) <sub>0..1</sub> - * Range: [Publication](Publication.md) - * [➞triples](textWithTriples__triples.md) <sub>0..\*</sub> - * Range: [Triple](Triple.md) diff --git a/projects/ibd/docs/Triple.md b/projects/ibd/docs/Triple.md deleted file mode 100644 index 77c3e9483..000000000 --- a/projects/ibd/docs/Triple.md +++ /dev/null @@ -1,39 +0,0 @@ - -# Class: Triple - - -Abstract parent for Relation Extraction tasks - -URI: [gocam:Triple](http://w3id.org/ontogpt/gocam/Triple) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞triples](textWithTriples__triples.md)* <sub>0..\*</sub> **[Triple](Triple.md)** - -## Attributes - - -### Own - - * [➞subject](triple__subject.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞predicate](triple__predicate.md) <sub>0..1</sub> - * Range: [RelationshipType](RelationshipType.md) - * [➞object](triple__object.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞qualifier](triple__qualifier.md) <sub>0..1</sub> - * Description: A qualifier for the statements, e.g. "NOT" for negation - * Range: [String](types/String.md) - * [➞subject_qualifier](triple__subject_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - * Range: [NamedEntity](NamedEntity.md) - * [➞object_qualifier](triple__object_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * Range: [NamedEntity](NamedEntity.md) diff --git a/projects/ibd/docs/annotatorResult__object_id.md b/projects/ibd/docs/annotatorResult__object_id.md deleted file mode 100644 index 77a3040ba..000000000 --- a/projects/ibd/docs/annotatorResult__object_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_id - - - - -URI: [gocam:annotatorResult__object_id](http://w3id.org/ontogpt/gocam/annotatorResult__object_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/ibd/docs/annotatorResult__object_text.md b/projects/ibd/docs/annotatorResult__object_text.md deleted file mode 100644 index 2869435f2..000000000 --- a/projects/ibd/docs/annotatorResult__object_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_text - - - - -URI: [gocam:annotatorResult__object_text](http://w3id.org/ontogpt/gocam/annotatorResult__object_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/ibd/docs/annotatorResult__subject_text.md b/projects/ibd/docs/annotatorResult__subject_text.md deleted file mode 100644 index 6f92b2c48..000000000 --- a/projects/ibd/docs/annotatorResult__subject_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_text - - - - -URI: [gocam:annotatorResult__subject_text](http://w3id.org/ontogpt/gocam/annotatorResult__subject_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/ibd/docs/extractionResult__extracted_object.md b/projects/ibd/docs/extractionResult__extracted_object.md deleted file mode 100644 index 8e46f1540..000000000 --- a/projects/ibd/docs/extractionResult__extracted_object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: extracted_object - - -The complex objects extracted from the text - -URI: [gocam:extractionResult__extracted_object](http://w3id.org/ontogpt/gocam/extractionResult__extracted_object) - - -## Domain and Range - -None → <sub>0..1</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ibd/docs/extractionResult__input_id.md b/projects/ibd/docs/extractionResult__input_id.md deleted file mode 100644 index d667d9cc3..000000000 --- a/projects/ibd/docs/extractionResult__input_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_id - - - - -URI: [gocam:extractionResult__input_id](http://w3id.org/ontogpt/gocam/extractionResult__input_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ibd/docs/extractionResult__input_text.md b/projects/ibd/docs/extractionResult__input_text.md deleted file mode 100644 index 5d130aab5..000000000 --- a/projects/ibd/docs/extractionResult__input_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_text - - - - -URI: [gocam:extractionResult__input_text](http://w3id.org/ontogpt/gocam/extractionResult__input_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ibd/docs/extractionResult__input_title.md b/projects/ibd/docs/extractionResult__input_title.md deleted file mode 100644 index 80c0a0585..000000000 --- a/projects/ibd/docs/extractionResult__input_title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_title - - - - -URI: [gocam:extractionResult__input_title](http://w3id.org/ontogpt/gocam/extractionResult__input_title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ibd/docs/extractionResult__named_entities.md b/projects/ibd/docs/extractionResult__named_entities.md deleted file mode 100644 index 6680295e3..000000000 --- a/projects/ibd/docs/extractionResult__named_entities.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: named_entities - - -Named entities extracted from the text - -URI: [gocam:extractionResult__named_entities](http://w3id.org/ontogpt/gocam/extractionResult__named_entities) - - -## Domain and Range - -None → <sub>0..\*</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ibd/docs/extractionResult__prompt.md b/projects/ibd/docs/extractionResult__prompt.md deleted file mode 100644 index 0bc5b4d86..000000000 --- a/projects/ibd/docs/extractionResult__prompt.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: prompt - - - - -URI: [gocam:extractionResult__prompt](http://w3id.org/ontogpt/gocam/extractionResult__prompt) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ibd/docs/extractionResult__raw_completion_output.md b/projects/ibd/docs/extractionResult__raw_completion_output.md deleted file mode 100644 index d5b8ad15b..000000000 --- a/projects/ibd/docs/extractionResult__raw_completion_output.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: raw_completion_output - - - - -URI: [gocam:extractionResult__raw_completion_output](http://w3id.org/ontogpt/gocam/extractionResult__raw_completion_output) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ibd/docs/geneGeneInteraction__gene1.md b/projects/ibd/docs/geneGeneInteraction__gene1.md deleted file mode 100644 index 25ff5d3e1..000000000 --- a/projects/ibd/docs/geneGeneInteraction__gene1.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: gene1 - - - - -URI: [gocam:geneGeneInteraction__gene1](http://w3id.org/ontogpt/gocam/geneGeneInteraction__gene1) - - -## Domain and Range - -None → <sub>0..1</sub> [Gene](Gene.md) - -## Parents - - -## Children - - -## Used by - - * [GeneGeneInteraction](GeneGeneInteraction.md) diff --git a/projects/ibd/docs/geneGeneInteraction__gene2.md b/projects/ibd/docs/geneGeneInteraction__gene2.md deleted file mode 100644 index 8ad830681..000000000 --- a/projects/ibd/docs/geneGeneInteraction__gene2.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: gene2 - - - - -URI: [gocam:geneGeneInteraction__gene2](http://w3id.org/ontogpt/gocam/geneGeneInteraction__gene2) - - -## Domain and Range - -None → <sub>0..1</sub> [Gene](Gene.md) - -## Parents - - -## Children - - -## Used by - - * [GeneGeneInteraction](GeneGeneInteraction.md) diff --git a/projects/ibd/docs/geneMolecularActivityRelationship2__gene.md b/projects/ibd/docs/geneMolecularActivityRelationship2__gene.md deleted file mode 100644 index 29e3876af..000000000 --- a/projects/ibd/docs/geneMolecularActivityRelationship2__gene.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: gene - - - - -URI: [gocam:geneMolecularActivityRelationship2__gene](http://w3id.org/ontogpt/gocam/geneMolecularActivityRelationship2__gene) - - -## Domain and Range - -None → <sub>0..1</sub> [Gene](Gene.md) - -## Parents - - -## Children - - -## Used by - - * [GeneMolecularActivityRelationship2](GeneMolecularActivityRelationship2.md) diff --git a/projects/ibd/docs/geneMolecularActivityRelationship2__molecular_activity.md b/projects/ibd/docs/geneMolecularActivityRelationship2__molecular_activity.md deleted file mode 100644 index db47a4345..000000000 --- a/projects/ibd/docs/geneMolecularActivityRelationship2__molecular_activity.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: molecular_activity - - - - -URI: [gocam:geneMolecularActivityRelationship2__molecular_activity](http://w3id.org/ontogpt/gocam/geneMolecularActivityRelationship2__molecular_activity) - - -## Domain and Range - -None → <sub>0..1</sub> [MolecularActivity](MolecularActivity.md) - -## Parents - - -## Children - - -## Used by - - * [GeneMolecularActivityRelationship2](GeneMolecularActivityRelationship2.md) diff --git a/projects/ibd/docs/geneMolecularActivityRelationship2__target.md b/projects/ibd/docs/geneMolecularActivityRelationship2__target.md deleted file mode 100644 index bb68d8cef..000000000 --- a/projects/ibd/docs/geneMolecularActivityRelationship2__target.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: target - - - - -URI: [gocam:geneMolecularActivityRelationship2__target](http://w3id.org/ontogpt/gocam/geneMolecularActivityRelationship2__target) - - -## Domain and Range - -None → <sub>0..1</sub> [Molecule](Molecule.md) - -## Parents - - -## Children - - -## Used by - - * [GeneMolecularActivityRelationship2](GeneMolecularActivityRelationship2.md) diff --git a/projects/ibd/docs/geneMolecularActivityRelationship__gene.md b/projects/ibd/docs/geneMolecularActivityRelationship__gene.md deleted file mode 100644 index e4df4fa20..000000000 --- a/projects/ibd/docs/geneMolecularActivityRelationship__gene.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: gene - - - - -URI: [gocam:geneMolecularActivityRelationship__gene](http://w3id.org/ontogpt/gocam/geneMolecularActivityRelationship__gene) - - -## Domain and Range - -None → <sub>0..1</sub> [Gene](Gene.md) - -## Parents - - -## Children - - -## Used by - - * [GeneMolecularActivityRelationship](GeneMolecularActivityRelationship.md) diff --git a/projects/ibd/docs/geneMolecularActivityRelationship__molecular_activity.md b/projects/ibd/docs/geneMolecularActivityRelationship__molecular_activity.md deleted file mode 100644 index 42577e0a6..000000000 --- a/projects/ibd/docs/geneMolecularActivityRelationship__molecular_activity.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: molecular_activity - - - - -URI: [gocam:geneMolecularActivityRelationship__molecular_activity](http://w3id.org/ontogpt/gocam/geneMolecularActivityRelationship__molecular_activity) - - -## Domain and Range - -None → <sub>0..1</sub> [MolecularActivity](MolecularActivity.md) - -## Parents - - -## Children - - -## Used by - - * [GeneMolecularActivityRelationship](GeneMolecularActivityRelationship.md) diff --git a/projects/ibd/docs/geneOrganismRelationship__gene.md b/projects/ibd/docs/geneOrganismRelationship__gene.md deleted file mode 100644 index 7071e06cd..000000000 --- a/projects/ibd/docs/geneOrganismRelationship__gene.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: gene - - - - -URI: [gocam:geneOrganismRelationship__gene](http://w3id.org/ontogpt/gocam/geneOrganismRelationship__gene) - - -## Domain and Range - -None → <sub>0..1</sub> [Gene](Gene.md) - -## Parents - - -## Children - - -## Used by - - * [GeneOrganismRelationship](GeneOrganismRelationship.md) diff --git a/projects/ibd/docs/geneOrganismRelationship__organism.md b/projects/ibd/docs/geneOrganismRelationship__organism.md deleted file mode 100644 index 80ad6c95a..000000000 --- a/projects/ibd/docs/geneOrganismRelationship__organism.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: organism - - - - -URI: [gocam:geneOrganismRelationship__organism](http://w3id.org/ontogpt/gocam/geneOrganismRelationship__organism) - - -## Domain and Range - -None → <sub>0..1</sub> [Organism](Organism.md) - -## Parents - - -## Children - - -## Used by - - * [GeneOrganismRelationship](GeneOrganismRelationship.md) diff --git a/projects/ibd/docs/geneSubcellularLocalizationRelationship__gene.md b/projects/ibd/docs/geneSubcellularLocalizationRelationship__gene.md deleted file mode 100644 index 719048841..000000000 --- a/projects/ibd/docs/geneSubcellularLocalizationRelationship__gene.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: gene - - - - -URI: [gocam:geneSubcellularLocalizationRelationship__gene](http://w3id.org/ontogpt/gocam/geneSubcellularLocalizationRelationship__gene) - - -## Domain and Range - -None → <sub>0..1</sub> [Gene](Gene.md) - -## Parents - - -## Children - - -## Used by - - * [GeneSubcellularLocalizationRelationship](GeneSubcellularLocalizationRelationship.md) diff --git a/projects/ibd/docs/geneSubcellularLocalizationRelationship__location.md b/projects/ibd/docs/geneSubcellularLocalizationRelationship__location.md deleted file mode 100644 index c5e53c56a..000000000 --- a/projects/ibd/docs/geneSubcellularLocalizationRelationship__location.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: location - - - - -URI: [gocam:geneSubcellularLocalizationRelationship__location](http://w3id.org/ontogpt/gocam/geneSubcellularLocalizationRelationship__location) - - -## Domain and Range - -None → <sub>0..1</sub> [GeneLocation](GeneLocation.md) - -## Parents - - -## Children - - -## Used by - - * [GeneSubcellularLocalizationRelationship](GeneSubcellularLocalizationRelationship.md) diff --git a/projects/ibd/docs/iBDAnnotations__activities.md b/projects/ibd/docs/iBDAnnotations__activities.md deleted file mode 100644 index e2c0792b4..000000000 --- a/projects/ibd/docs/iBDAnnotations__activities.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: activities - - -semicolon-separated list of molecular activities - -URI: [gocam:iBDAnnotations__activities](http://w3id.org/ontogpt/gocam/iBDAnnotations__activities) - - -## Domain and Range - -None → <sub>0..\*</sub> [MolecularActivity](MolecularActivity.md) - -## Parents - - -## Children - - -## Used by - - * [IBDAnnotations](IBDAnnotations.md) diff --git a/projects/ibd/docs/iBDAnnotations__cellular_processes.md b/projects/ibd/docs/iBDAnnotations__cellular_processes.md deleted file mode 100644 index 13b6e9122..000000000 --- a/projects/ibd/docs/iBDAnnotations__cellular_processes.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: cellular_processes - - -semicolon-separated list of cellular processes - -URI: [gocam:iBDAnnotations__cellular_processes](http://w3id.org/ontogpt/gocam/iBDAnnotations__cellular_processes) - - -## Domain and Range - -None → <sub>0..\*</sub> [CellularProcess](CellularProcess.md) - -## Parents - - -## Children - - -## Used by - - * [IBDAnnotations](IBDAnnotations.md) diff --git a/projects/ibd/docs/iBDAnnotations__gene_functions.md b/projects/ibd/docs/iBDAnnotations__gene_functions.md deleted file mode 100644 index 3d7d3d04e..000000000 --- a/projects/ibd/docs/iBDAnnotations__gene_functions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: gene_functions - - -semicolon-separated list of gene to molecular activity relationships - -URI: [gocam:iBDAnnotations__gene_functions](http://w3id.org/ontogpt/gocam/iBDAnnotations__gene_functions) - - -## Domain and Range - -None → <sub>0..\*</sub> [GeneMolecularActivityRelationship](GeneMolecularActivityRelationship.md) - -## Parents - - -## Children - - -## Used by - - * [IBDAnnotations](IBDAnnotations.md) diff --git a/projects/ibd/docs/iBDAnnotations__gene_gene_interactions.md b/projects/ibd/docs/iBDAnnotations__gene_gene_interactions.md deleted file mode 100644 index c553ca666..000000000 --- a/projects/ibd/docs/iBDAnnotations__gene_gene_interactions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: gene_gene_interactions - - -semicolon-separated list of gene to gene interactions - -URI: [gocam:iBDAnnotations__gene_gene_interactions](http://w3id.org/ontogpt/gocam/iBDAnnotations__gene_gene_interactions) - - -## Domain and Range - -None → <sub>0..\*</sub> [GeneGeneInteraction](GeneGeneInteraction.md) - -## Parents - - -## Children - - -## Used by - - * [IBDAnnotations](IBDAnnotations.md) diff --git a/projects/ibd/docs/iBDAnnotations__gene_localizations.md b/projects/ibd/docs/iBDAnnotations__gene_localizations.md deleted file mode 100644 index 405c87867..000000000 --- a/projects/ibd/docs/iBDAnnotations__gene_localizations.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: gene_localizations - - -semicolon-separated list of genes plus their location in the cell; for example, "gene1 / cytoplasm; gene2 / mitochondrion" - -URI: [gocam:iBDAnnotations__gene_localizations](http://w3id.org/ontogpt/gocam/iBDAnnotations__gene_localizations) - - -## Domain and Range - -None → <sub>0..\*</sub> [GeneSubcellularLocalizationRelationship](GeneSubcellularLocalizationRelationship.md) - -## Parents - - -## Children - - -## Used by - - * [IBDAnnotations](IBDAnnotations.md) diff --git a/projects/ibd/docs/iBDAnnotations__gene_organisms.md b/projects/ibd/docs/iBDAnnotations__gene_organisms.md deleted file mode 100644 index fc53b0518..000000000 --- a/projects/ibd/docs/iBDAnnotations__gene_organisms.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: gene_organisms - - - - -URI: [gocam:iBDAnnotations__gene_organisms](http://w3id.org/ontogpt/gocam/iBDAnnotations__gene_organisms) - - -## Domain and Range - -None → <sub>0..\*</sub> [GeneOrganismRelationship](GeneOrganismRelationship.md) - -## Parents - - -## Children - - -## Used by - - * [IBDAnnotations](IBDAnnotations.md) diff --git a/projects/ibd/docs/iBDAnnotations__genes.md b/projects/ibd/docs/iBDAnnotations__genes.md deleted file mode 100644 index beea5579f..000000000 --- a/projects/ibd/docs/iBDAnnotations__genes.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: genes - - -semicolon-separated list of genes - -URI: [gocam:iBDAnnotations__genes](http://w3id.org/ontogpt/gocam/iBDAnnotations__genes) - - -## Domain and Range - -None → <sub>0..\*</sub> [Gene](Gene.md) - -## Parents - - -## Children - - -## Used by - - * [IBDAnnotations](IBDAnnotations.md) diff --git a/projects/ibd/docs/iBDAnnotations__organisms.md b/projects/ibd/docs/iBDAnnotations__organisms.md deleted file mode 100644 index 60d4434e7..000000000 --- a/projects/ibd/docs/iBDAnnotations__organisms.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: organisms - - -semicolon-separated list of organism taxons - -URI: [gocam:iBDAnnotations__organisms](http://w3id.org/ontogpt/gocam/iBDAnnotations__organisms) - - -## Domain and Range - -None → <sub>0..\*</sub> [Organism](Organism.md) - -## Parents - - -## Children - - -## Used by - - * [IBDAnnotations](IBDAnnotations.md) diff --git a/projects/ibd/docs/iBDAnnotations__pathways.md b/projects/ibd/docs/iBDAnnotations__pathways.md deleted file mode 100644 index 9986dd470..000000000 --- a/projects/ibd/docs/iBDAnnotations__pathways.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: pathways - - -semicolon-separated list of pathways - -URI: [gocam:iBDAnnotations__pathways](http://w3id.org/ontogpt/gocam/iBDAnnotations__pathways) - - -## Domain and Range - -None → <sub>0..\*</sub> [Pathway](Pathway.md) - -## Parents - - -## Children - - -## Used by - - * [IBDAnnotations](IBDAnnotations.md) diff --git a/projects/ibd/docs/ibd.md b/projects/ibd/docs/ibd.md deleted file mode 100644 index 4ecc2e294..000000000 --- a/projects/ibd/docs/ibd.md +++ /dev/null @@ -1,140 +0,0 @@ - -# gocam-template - - -**metamodel version:** 1.7.0 - -**version:** None - - -A template for GO-CAMs - - -### Classes - - * [AnnotatorResult](AnnotatorResult.md) - * [Any](Any.md) - * [CompoundExpression](CompoundExpression.md) - * [GeneGeneInteraction](GeneGeneInteraction.md) - * [GeneMolecularActivityRelationship](GeneMolecularActivityRelationship.md) - * [GeneMolecularActivityRelationship2](GeneMolecularActivityRelationship2.md) - * [GeneOrganismRelationship](GeneOrganismRelationship.md) - * [GeneSubcellularLocalizationRelationship](GeneSubcellularLocalizationRelationship.md) - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - * [ExtractionResult](ExtractionResult.md) - A result of extracting knowledge on text - * [IBDAnnotations](IBDAnnotations.md) - * [NamedEntity](NamedEntity.md) - * [CellularProcess](CellularProcess.md) - * [Gene](Gene.md) - * [GeneLocation](GeneLocation.md) - * [MolecularActivity](MolecularActivity.md) - * [Molecule](Molecule.md) - * [Organism](Organism.md) - * [Pathway](Pathway.md) - * [RelationshipType](RelationshipType.md) - * [Publication](Publication.md) - * [TextWithTriples](TextWithTriples.md) - -### Mixins - - -### Slots - - * [➞object_id](annotatorResult__object_id.md) - * [➞object_text](annotatorResult__object_text.md) - * [➞subject_text](annotatorResult__subject_text.md) - * [➞extracted_object](extractionResult__extracted_object.md) - The complex objects extracted from the text - * [➞input_id](extractionResult__input_id.md) - * [➞input_text](extractionResult__input_text.md) - * [➞input_title](extractionResult__input_title.md) - * [➞named_entities](extractionResult__named_entities.md) - Named entities extracted from the text - * [➞prompt](extractionResult__prompt.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) - * [➞gene1](geneGeneInteraction__gene1.md) - * [➞gene2](geneGeneInteraction__gene2.md) - * [➞gene](geneMolecularActivityRelationship2__gene.md) - * [➞molecular_activity](geneMolecularActivityRelationship2__molecular_activity.md) - * [➞target](geneMolecularActivityRelationship2__target.md) - * [➞gene](geneMolecularActivityRelationship__gene.md) - * [➞molecular_activity](geneMolecularActivityRelationship__molecular_activity.md) - * [➞gene](geneOrganismRelationship__gene.md) - * [➞organism](geneOrganismRelationship__organism.md) - * [➞gene](geneSubcellularLocalizationRelationship__gene.md) - * [➞location](geneSubcellularLocalizationRelationship__location.md) - * [➞activities](iBDAnnotations__activities.md) - semicolon-separated list of molecular activities - * [➞cellular_processes](iBDAnnotations__cellular_processes.md) - semicolon-separated list of cellular processes - * [➞gene_functions](iBDAnnotations__gene_functions.md) - semicolon-separated list of gene to molecular activity relationships - * [➞gene_gene_interactions](iBDAnnotations__gene_gene_interactions.md) - semicolon-separated list of gene to gene interactions - * [➞gene_localizations](iBDAnnotations__gene_localizations.md) - semicolon-separated list of genes plus their location in the cell; for example, "gene1 / cytoplasm; gene2 / mitochondrion" - * [➞gene_organisms](iBDAnnotations__gene_organisms.md) - * [➞genes](iBDAnnotations__genes.md) - semicolon-separated list of genes - * [➞organisms](iBDAnnotations__organisms.md) - semicolon-separated list of organism taxons - * [➞pathways](iBDAnnotations__pathways.md) - semicolon-separated list of pathways - * [➞id](namedEntity__id.md) - A unique identifier for the named entity - * [GeneLocation➞id](GeneLocation_id.md) - * [➞label](namedEntity__label.md) - The label (name) of the named thing - * [➞abstract](publication__abstract.md) - The abstract of the publication - * [➞combined_text](publication__combined_text.md) - * [➞full_text](publication__full_text.md) - The full text of the publication - * [➞id](publication__id.md) - The publication identifier - * [➞title](publication__title.md) - The title of the publication - * [➞publication](textWithTriples__publication.md) - * [➞triples](textWithTriples__triples.md) - * [➞object](triple__object.md) - * [➞object_qualifier](triple__object_qualifier.md) - An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * [➞predicate](triple__predicate.md) - * [➞qualifier](triple__qualifier.md) - A qualifier for the statements, e.g. "NOT" for negation - * [➞subject](triple__subject.md) - * [➞subject_qualifier](triple__subject_qualifier.md) - An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -### Enums - - * [CellType](CellType.md) - * [GOCellComponentType](GOCellComponentType.md) - * [GeneLocationEnum](GeneLocationEnum.md) - * [NullDataOptions](NullDataOptions.md) - -### Subsets - - -### Types - - -#### Built in - - * **Bool** - * **Curie** - * **Decimal** - * **ElementIdentifier** - * **NCName** - * **NodeIdentifier** - * **URI** - * **URIorCURIE** - * **XSDDate** - * **XSDDateTime** - * **XSDTime** - * **float** - * **int** - * **str** - -#### Defined - - * [Boolean](types/Boolean.md) (**Bool**) - A binary (true or false) value - * [Curie](types/Curie.md) (**Curie**) - a compact URI - * [Date](types/Date.md) (**XSDDate**) - a date (year, month and day) in an idealized calendar - * [DateOrDatetime](types/DateOrDatetime.md) (**str**) - Either a date or a datetime - * [Datetime](types/Datetime.md) (**XSDDateTime**) - The combination of a date and time - * [Decimal](types/Decimal.md) (**Decimal**) - A real number with arbitrary precision that conforms to the xsd:decimal specification - * [Double](types/Double.md) (**float**) - A real number that conforms to the xsd:double specification - * [Float](types/Float.md) (**float**) - A real number that conforms to the xsd:float specification - * [Integer](types/Integer.md) (**int**) - An integer - * [Jsonpath](types/Jsonpath.md) (**str**) - A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - * [Jsonpointer](types/Jsonpointer.md) (**str**) - A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - * [Ncname](types/Ncname.md) (**NCName**) - Prefix part of CURIE - * [Nodeidentifier](types/Nodeidentifier.md) (**NodeIdentifier**) - A URI, CURIE or BNODE that represents a node in a model. - * [Objectidentifier](types/Objectidentifier.md) (**ElementIdentifier**) - A URI or CURIE that represents an object in the model. - * [Sparqlpath](types/Sparqlpath.md) (**str**) - A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - * [String](types/String.md) (**str**) - A character string - * [Time](types/Time.md) (**XSDTime**) - A time object represents a (local) time of day, independent of any particular day - * [Uri](types/Uri.md) (**URI**) - a complete URI - * [Uriorcurie](types/Uriorcurie.md) (**URIorCURIE**) - a URI or a CURIE diff --git a/projects/ibd/docs/namedEntity__id.md b/projects/ibd/docs/namedEntity__id.md deleted file mode 100644 index 0555a9f73..000000000 --- a/projects/ibd/docs/namedEntity__id.md +++ /dev/null @@ -1,37 +0,0 @@ - -# Slot: id - - -A unique identifier for the named entity - -URI: [gocam:namedEntity__id](http://w3id.org/ontogpt/gocam/namedEntity__id) - - -## Domain and Range - -None → <sub>1..1</sub> [String](types/String.md) - -## Parents - - -## Children - - * [GeneLocation➞id](GeneLocation_id.md) - -## Used by - - * [CellularProcess](CellularProcess.md) - * [Gene](Gene.md) - * [MolecularActivity](MolecularActivity.md) - * [Molecule](Molecule.md) - * [NamedEntity](NamedEntity.md) - * [Organism](Organism.md) - * [Pathway](Pathway.md) - * [RelationshipType](RelationshipType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | this is populated during the grounding and normalization step | - diff --git a/projects/ibd/docs/namedEntity__label.md b/projects/ibd/docs/namedEntity__label.md deleted file mode 100644 index 2b599b1cc..000000000 --- a/projects/ibd/docs/namedEntity__label.md +++ /dev/null @@ -1,38 +0,0 @@ - -# Slot: label - - -The label (name) of the named thing - -URI: [gocam:namedEntity__label](http://w3id.org/ontogpt/gocam/namedEntity__label) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [CellularProcess](CellularProcess.md) - * [Gene](Gene.md) - * [GeneLocation](GeneLocation.md) - * [MolecularActivity](MolecularActivity.md) - * [Molecule](Molecule.md) - * [NamedEntity](NamedEntity.md) - * [Organism](Organism.md) - * [Pathway](Pathway.md) - * [RelationshipType](RelationshipType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Aliases:** | | name | -| **Mappings:** | | rdfs:label | - diff --git a/projects/ibd/docs/publication__abstract.md b/projects/ibd/docs/publication__abstract.md deleted file mode 100644 index dd434bed1..000000000 --- a/projects/ibd/docs/publication__abstract.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: abstract - - -The abstract of the publication - -URI: [gocam:publication__abstract](http://w3id.org/ontogpt/gocam/publication__abstract) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/ibd/docs/publication__combined_text.md b/projects/ibd/docs/publication__combined_text.md deleted file mode 100644 index 128ca7aed..000000000 --- a/projects/ibd/docs/publication__combined_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: combined_text - - - - -URI: [gocam:publication__combined_text](http://w3id.org/ontogpt/gocam/publication__combined_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/ibd/docs/publication__full_text.md b/projects/ibd/docs/publication__full_text.md deleted file mode 100644 index be255126c..000000000 --- a/projects/ibd/docs/publication__full_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: full_text - - -The full text of the publication - -URI: [gocam:publication__full_text](http://w3id.org/ontogpt/gocam/publication__full_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/ibd/docs/publication__id.md b/projects/ibd/docs/publication__id.md deleted file mode 100644 index 583585698..000000000 --- a/projects/ibd/docs/publication__id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: id - - -The publication identifier - -URI: [gocam:publication__id](http://w3id.org/ontogpt/gocam/publication__id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/ibd/docs/publication__title.md b/projects/ibd/docs/publication__title.md deleted file mode 100644 index af7b52d3f..000000000 --- a/projects/ibd/docs/publication__title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: title - - -The title of the publication - -URI: [gocam:publication__title](http://w3id.org/ontogpt/gocam/publication__title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/ibd/docs/textWithTriples__publication.md b/projects/ibd/docs/textWithTriples__publication.md deleted file mode 100644 index f2480d2c2..000000000 --- a/projects/ibd/docs/textWithTriples__publication.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: publication - - - - -URI: [gocam:textWithTriples__publication](http://w3id.org/ontogpt/gocam/textWithTriples__publication) - - -## Domain and Range - -None → <sub>0..1</sub> [Publication](Publication.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/ibd/docs/textWithTriples__triples.md b/projects/ibd/docs/textWithTriples__triples.md deleted file mode 100644 index 8fe102100..000000000 --- a/projects/ibd/docs/textWithTriples__triples.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: triples - - - - -URI: [gocam:textWithTriples__triples](http://w3id.org/ontogpt/gocam/textWithTriples__triples) - - -## Domain and Range - -None → <sub>0..\*</sub> [Triple](Triple.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/ibd/docs/triple__object.md b/projects/ibd/docs/triple__object.md deleted file mode 100644 index 38e4c4c25..000000000 --- a/projects/ibd/docs/triple__object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object - - - - -URI: [gocam:triple__object](http://w3id.org/ontogpt/gocam/triple__object) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/ibd/docs/triple__object_qualifier.md b/projects/ibd/docs/triple__object_qualifier.md deleted file mode 100644 index 21bae818d..000000000 --- a/projects/ibd/docs/triple__object_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_qualifier - - -An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - -URI: [gocam:triple__object_qualifier](http://w3id.org/ontogpt/gocam/triple__object_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/ibd/docs/triple__predicate.md b/projects/ibd/docs/triple__predicate.md deleted file mode 100644 index 3c7c729c3..000000000 --- a/projects/ibd/docs/triple__predicate.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: predicate - - - - -URI: [gocam:triple__predicate](http://w3id.org/ontogpt/gocam/triple__predicate) - - -## Domain and Range - -None → <sub>0..1</sub> [RelationshipType](RelationshipType.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/ibd/docs/triple__qualifier.md b/projects/ibd/docs/triple__qualifier.md deleted file mode 100644 index 7f62d89e8..000000000 --- a/projects/ibd/docs/triple__qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: qualifier - - -A qualifier for the statements, e.g. "NOT" for negation - -URI: [gocam:triple__qualifier](http://w3id.org/ontogpt/gocam/triple__qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/ibd/docs/triple__subject.md b/projects/ibd/docs/triple__subject.md deleted file mode 100644 index 9b9ece18a..000000000 --- a/projects/ibd/docs/triple__subject.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject - - - - -URI: [gocam:triple__subject](http://w3id.org/ontogpt/gocam/triple__subject) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/ibd/docs/triple__subject_qualifier.md b/projects/ibd/docs/triple__subject_qualifier.md deleted file mode 100644 index 588c54157..000000000 --- a/projects/ibd/docs/triple__subject_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_qualifier - - -An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -URI: [gocam:triple__subject_qualifier](http://w3id.org/ontogpt/gocam/triple__subject_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/ibd/docs/types/Boolean.md b/projects/ibd/docs/types/Boolean.md deleted file mode 100644 index dc83a9c6e..000000000 --- a/projects/ibd/docs/types/Boolean.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: boolean - - -A binary (true or false) value - -URI: [linkml:Boolean](https://w3id.org/linkml/Boolean) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Bool** | -| Representation | | bool | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Boolean | - diff --git a/projects/ibd/docs/types/Curie.md b/projects/ibd/docs/types/Curie.md deleted file mode 100644 index c1803f93f..000000000 --- a/projects/ibd/docs/types/Curie.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: curie - - -a compact URI - -URI: [linkml:Curie](https://w3id.org/linkml/Curie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Curie** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations this MUST be expanded to a URI | -| | | in non-RDF serializations MAY be serialized as the compact representation | - diff --git a/projects/ibd/docs/types/Date.md b/projects/ibd/docs/types/Date.md deleted file mode 100644 index 06948af97..000000000 --- a/projects/ibd/docs/types/Date.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: date - - -a date (year, month and day) in an idealized calendar - -URI: [linkml:Date](https://w3id.org/linkml/Date) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDate** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Date | - diff --git a/projects/ibd/docs/types/DateOrDatetime.md b/projects/ibd/docs/types/DateOrDatetime.md deleted file mode 100644 index ef983898d..000000000 --- a/projects/ibd/docs/types/DateOrDatetime.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: date_or_datetime - - -Either a date or a datetime - -URI: [linkml:DateOrDatetime](https://w3id.org/linkml/DateOrDatetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/ibd/docs/types/Datetime.md b/projects/ibd/docs/types/Datetime.md deleted file mode 100644 index 9510454a8..000000000 --- a/projects/ibd/docs/types/Datetime.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: datetime - - -The combination of a date and time - -URI: [linkml:Datetime](https://w3id.org/linkml/Datetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDateTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:DateTime | - diff --git a/projects/ibd/docs/types/Decimal.md b/projects/ibd/docs/types/Decimal.md deleted file mode 100644 index a7ba14a5d..000000000 --- a/projects/ibd/docs/types/Decimal.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: decimal - - -A real number with arbitrary precision that conforms to the xsd:decimal specification - -URI: [linkml:Decimal](https://w3id.org/linkml/Decimal) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Decimal** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Broad Mappings:** | | schema:Number | - diff --git a/projects/ibd/docs/types/Double.md b/projects/ibd/docs/types/Double.md deleted file mode 100644 index cfe6d71e2..000000000 --- a/projects/ibd/docs/types/Double.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: double - - -A real number that conforms to the xsd:double specification - -URI: [linkml:Double](https://w3id.org/linkml/Double) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Close Mappings:** | | schema:Float | - diff --git a/projects/ibd/docs/types/Float.md b/projects/ibd/docs/types/Float.md deleted file mode 100644 index 7b303f96f..000000000 --- a/projects/ibd/docs/types/Float.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: float - - -A real number that conforms to the xsd:float specification - -URI: [linkml:Float](https://w3id.org/linkml/Float) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Float | - diff --git a/projects/ibd/docs/types/Integer.md b/projects/ibd/docs/types/Integer.md deleted file mode 100644 index 3cfcc66d9..000000000 --- a/projects/ibd/docs/types/Integer.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: integer - - -An integer - -URI: [linkml:Integer](https://w3id.org/linkml/Integer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **int** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Integer | - diff --git a/projects/ibd/docs/types/Jsonpath.md b/projects/ibd/docs/types/Jsonpath.md deleted file mode 100644 index a03a58e67..000000000 --- a/projects/ibd/docs/types/Jsonpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpath - - -A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpath](https://w3id.org/linkml/Jsonpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/ibd/docs/types/Jsonpointer.md b/projects/ibd/docs/types/Jsonpointer.md deleted file mode 100644 index a0e1ac492..000000000 --- a/projects/ibd/docs/types/Jsonpointer.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpointer - - -A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpointer](https://w3id.org/linkml/Jsonpointer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/ibd/docs/types/Ncname.md b/projects/ibd/docs/types/Ncname.md deleted file mode 100644 index 710b0b04a..000000000 --- a/projects/ibd/docs/types/Ncname.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: ncname - - -Prefix part of CURIE - -URI: [linkml:Ncname](https://w3id.org/linkml/Ncname) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NCName** | -| Representation | | str | diff --git a/projects/ibd/docs/types/Nodeidentifier.md b/projects/ibd/docs/types/Nodeidentifier.md deleted file mode 100644 index f0097cdf4..000000000 --- a/projects/ibd/docs/types/Nodeidentifier.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: nodeidentifier - - -A URI, CURIE or BNODE that represents a node in a model. - -URI: [linkml:Nodeidentifier](https://w3id.org/linkml/Nodeidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NodeIdentifier** | -| Representation | | str | diff --git a/projects/ibd/docs/types/Objectidentifier.md b/projects/ibd/docs/types/Objectidentifier.md deleted file mode 100644 index 454ba6be6..000000000 --- a/projects/ibd/docs/types/Objectidentifier.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: objectidentifier - - -A URI or CURIE that represents an object in the model. - -URI: [linkml:Objectidentifier](https://w3id.org/linkml/Objectidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **ElementIdentifier** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | Used for inheritance and type checking | - diff --git a/projects/ibd/docs/types/Sparqlpath.md b/projects/ibd/docs/types/Sparqlpath.md deleted file mode 100644 index fd99a927e..000000000 --- a/projects/ibd/docs/types/Sparqlpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: sparqlpath - - -A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - -URI: [linkml:Sparqlpath](https://w3id.org/linkml/Sparqlpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/ibd/docs/types/String.md b/projects/ibd/docs/types/String.md deleted file mode 100644 index 6e61d7081..000000000 --- a/projects/ibd/docs/types/String.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: string - - -A character string - -URI: [linkml:String](https://w3id.org/linkml/String) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Text | - diff --git a/projects/ibd/docs/types/Time.md b/projects/ibd/docs/types/Time.md deleted file mode 100644 index 2b8652bcd..000000000 --- a/projects/ibd/docs/types/Time.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: time - - -A time object represents a (local) time of day, independent of any particular day - -URI: [linkml:Time](https://w3id.org/linkml/Time) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Time | - diff --git a/projects/ibd/docs/types/Uri.md b/projects/ibd/docs/types/Uri.md deleted file mode 100644 index 343807a5e..000000000 --- a/projects/ibd/docs/types/Uri.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: uri - - -a complete URI - -URI: [linkml:Uri](https://w3id.org/linkml/Uri) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URI** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node | -| **Close Mappings:** | | schema:URL | - diff --git a/projects/ibd/docs/types/Uriorcurie.md b/projects/ibd/docs/types/Uriorcurie.md deleted file mode 100644 index 2f7b65087..000000000 --- a/projects/ibd/docs/types/Uriorcurie.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: uriorcurie - - -a URI or a CURIE - -URI: [linkml:Uriorcurie](https://w3id.org/linkml/Uriorcurie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URIorCURIE** | -| Representation | | str | diff --git a/projects/ibd/excel/ibd.xlsx b/projects/ibd/excel/ibd.xlsx deleted file mode 100644 index 59ed7d971..000000000 Binary files a/projects/ibd/excel/ibd.xlsx and /dev/null differ diff --git a/projects/ibd/graphql/ibd.graphql b/projects/ibd/graphql/ibd.graphql deleted file mode 100644 index 5487f1dad..000000000 --- a/projects/ibd/graphql/ibd.graphql +++ /dev/null @@ -1,149 +0,0 @@ -type AnnotatorResult - { - subjectText: String - objectId: String - objectText: String - } - -type Any - { - } - -type CellularProcess - { - id: String! - label: String - } - -interface CompoundExpression - { - } - -type ExtractionResult - { - inputId: String - inputTitle: String - inputText: String - rawCompletionOutput: String - prompt: String - extractedObject: Any - namedEntities: [Any] - } - -type Gene - { - id: String! - label: String - } - -type GeneGeneInteraction - { - gene1: Gene - gene2: Gene - } - -type GeneLocation - { - label: String - id: String! - } - -type GeneMolecularActivityRelationship - { - gene: Gene - molecularActivity: MolecularActivity - } - -type GeneMolecularActivityRelationship2 - { - gene: Gene - molecularActivity: MolecularActivity - target: Molecule - } - -type GeneOrganismRelationship - { - gene: Gene - organism: Organism - } - -type GeneSubcellularLocalizationRelationship - { - gene: Gene - location: GeneLocation - } - -type IBDAnnotations - { - genes: [Gene] - organisms: [Organism] - geneOrganisms: [GeneOrganismRelationship] - activities: [MolecularActivity] - geneFunctions: [GeneMolecularActivityRelationship] - cellularProcesses: [CellularProcess] - pathways: [Pathway] - geneGeneInteractions: [GeneGeneInteraction] - geneLocalizations: [GeneSubcellularLocalizationRelationship] - } - -type MolecularActivity - { - id: String! - label: String - } - -type Molecule - { - id: String! - label: String - } - -interface NamedEntity - { - id: String! - label: String - } - -type Organism - { - id: String! - label: String - } - -type Pathway - { - id: String! - label: String - } - -type Publication - { - id: String - title: String - abstract: String - combinedText: String - fullText: String - } - -type RelationshipType - { - id: String! - label: String - } - -type TextWithTriples - { - publication: Publication - triples: [Triple] - } - -interface Triple - { - subject: NamedEntity - predicate: RelationshipType - object: NamedEntity - qualifier: String - subjectQualifier: NamedEntity - objectQualifier: NamedEntity - } - diff --git a/projects/ibd/ibd.py b/projects/ibd/ibd.py deleted file mode 100644 index 2e865e160..000000000 --- a/projects/ibd/ibd.py +++ /dev/null @@ -1,794 +0,0 @@ -# Auto generated from ibd.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-08-07T10:54:16 -# Schema: gocam-template -# -# id: http://w3id.org/ontogpt/gocam -# description: A template for GO-CAMs -# license: https://creativecommons.org/publicdomain/zero/1.0/ - -import dataclasses -import sys -import re -from jsonasobj2 import JsonObj, as_dict -from typing import Optional, List, Union, Dict, ClassVar, Any -from dataclasses import dataclass -from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions - -from linkml_runtime.utils.slot import Slot -from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode -from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int -from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs -from linkml_runtime.utils.formatutils import camelcase, underscore, sfx -from linkml_runtime.utils.enumerations import EnumDefinitionImpl -from rdflib import Namespace, URIRef -from linkml_runtime.utils.curienamespace import CurieNamespace -from linkml_runtime.linkml_model.types import String - -metamodel_version = "1.7.0" -version = None - -# Overwrite dataclasses _init_fn to add **kwargs in __init__ -dataclasses._init_fn = dataclasses_init_fn_with_kwargs - -# Namespaces -CHEBI = CurieNamespace('CHEBI', 'http://example.org/UNKNOWN/CHEBI/') -CL = CurieNamespace('CL', 'http://purl.obolibrary.org/obo/CL_') -EFO = CurieNamespace('EFO', 'http://example.org/UNKNOWN/EFO/') -GO = CurieNamespace('GO', 'http://purl.obolibrary.org/obo/GO_') -HGNC = CurieNamespace('HGNC', 'http://example.org/UNKNOWN/HGNC/') -NCBITAXON = CurieNamespace('NCBITaxon', 'http://example.org/UNKNOWN/NCBITaxon/') -PR = CurieNamespace('PR', 'http://example.org/UNKNOWN/PR/') -PW = CurieNamespace('PW', 'http://example.org/UNKNOWN/PW/') -RO = CurieNamespace('RO', 'http://purl.obolibrary.org/obo/RO_') -UBERON = CurieNamespace('UBERON', 'http://example.org/UNKNOWN/UBERON/') -UNIPROTKB = CurieNamespace('UniProtKB', 'http://example.org/UNKNOWN/UniProtKB/') -BIOLINK = CurieNamespace('biolink', 'http://example.org/UNKNOWN/biolink/') -CORE = CurieNamespace('core', 'http://w3id.org/ontogpt/core/') -GOCAM = CurieNamespace('gocam', 'http://w3id.org/ontogpt/gocam/') -LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') -RDFS = CurieNamespace('rdfs', 'http://example.org/UNKNOWN/rdfs/') -DEFAULT_ = GOCAM - - -# Types - -# Class references -class NamedEntityId(extended_str): - pass - - -class GeneId(NamedEntityId): - pass - - -class PathwayId(NamedEntityId): - pass - - -class CellularProcessId(NamedEntityId): - pass - - -class MolecularActivityId(NamedEntityId): - pass - - -class GeneLocationId(NamedEntityId): - pass - - -class OrganismId(NamedEntityId): - pass - - -class MoleculeId(NamedEntityId): - pass - - -class RelationshipTypeId(NamedEntityId): - pass - - -@dataclass -class IBDAnnotations(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = GOCAM.IBDAnnotations - class_class_curie: ClassVar[str] = "gocam:IBDAnnotations" - class_name: ClassVar[str] = "IBDAnnotations" - class_model_uri: ClassVar[URIRef] = GOCAM.IBDAnnotations - - genes: Optional[Union[Union[str, GeneId], List[Union[str, GeneId]]]] = empty_list() - organisms: Optional[Union[Union[str, OrganismId], List[Union[str, OrganismId]]]] = empty_list() - gene_organisms: Optional[Union[Union[dict, "GeneOrganismRelationship"], List[Union[dict, "GeneOrganismRelationship"]]]] = empty_list() - activities: Optional[Union[Union[str, MolecularActivityId], List[Union[str, MolecularActivityId]]]] = empty_list() - gene_functions: Optional[Union[Union[dict, "GeneMolecularActivityRelationship"], List[Union[dict, "GeneMolecularActivityRelationship"]]]] = empty_list() - cellular_processes: Optional[Union[Union[str, CellularProcessId], List[Union[str, CellularProcessId]]]] = empty_list() - pathways: Optional[Union[Union[str, PathwayId], List[Union[str, PathwayId]]]] = empty_list() - gene_gene_interactions: Optional[Union[Union[dict, "GeneGeneInteraction"], List[Union[dict, "GeneGeneInteraction"]]]] = empty_list() - gene_localizations: Optional[Union[Union[dict, "GeneSubcellularLocalizationRelationship"], List[Union[dict, "GeneSubcellularLocalizationRelationship"]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if not isinstance(self.genes, list): - self.genes = [self.genes] if self.genes is not None else [] - self.genes = [v if isinstance(v, GeneId) else GeneId(v) for v in self.genes] - - if not isinstance(self.organisms, list): - self.organisms = [self.organisms] if self.organisms is not None else [] - self.organisms = [v if isinstance(v, OrganismId) else OrganismId(v) for v in self.organisms] - - if not isinstance(self.gene_organisms, list): - self.gene_organisms = [self.gene_organisms] if self.gene_organisms is not None else [] - self.gene_organisms = [v if isinstance(v, GeneOrganismRelationship) else GeneOrganismRelationship(**as_dict(v)) for v in self.gene_organisms] - - if not isinstance(self.activities, list): - self.activities = [self.activities] if self.activities is not None else [] - self.activities = [v if isinstance(v, MolecularActivityId) else MolecularActivityId(v) for v in self.activities] - - if not isinstance(self.gene_functions, list): - self.gene_functions = [self.gene_functions] if self.gene_functions is not None else [] - self.gene_functions = [v if isinstance(v, GeneMolecularActivityRelationship) else GeneMolecularActivityRelationship(**as_dict(v)) for v in self.gene_functions] - - if not isinstance(self.cellular_processes, list): - self.cellular_processes = [self.cellular_processes] if self.cellular_processes is not None else [] - self.cellular_processes = [v if isinstance(v, CellularProcessId) else CellularProcessId(v) for v in self.cellular_processes] - - if not isinstance(self.pathways, list): - self.pathways = [self.pathways] if self.pathways is not None else [] - self.pathways = [v if isinstance(v, PathwayId) else PathwayId(v) for v in self.pathways] - - if not isinstance(self.gene_gene_interactions, list): - self.gene_gene_interactions = [self.gene_gene_interactions] if self.gene_gene_interactions is not None else [] - self.gene_gene_interactions = [v if isinstance(v, GeneGeneInteraction) else GeneGeneInteraction(**as_dict(v)) for v in self.gene_gene_interactions] - - if not isinstance(self.gene_localizations, list): - self.gene_localizations = [self.gene_localizations] if self.gene_localizations is not None else [] - self.gene_localizations = [v if isinstance(v, GeneSubcellularLocalizationRelationship) else GeneSubcellularLocalizationRelationship(**as_dict(v)) for v in self.gene_localizations] - - super().__post_init__(**kwargs) - - -Any = Any - -@dataclass -class ExtractionResult(YAMLRoot): - """ - A result of extracting knowledge on text - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.ExtractionResult - class_class_curie: ClassVar[str] = "core:ExtractionResult" - class_name: ClassVar[str] = "ExtractionResult" - class_model_uri: ClassVar[URIRef] = GOCAM.ExtractionResult - - input_id: Optional[str] = None - input_title: Optional[str] = None - input_text: Optional[str] = None - raw_completion_output: Optional[str] = None - prompt: Optional[str] = None - extracted_object: Optional[Union[dict, Any]] = None - named_entities: Optional[Union[Union[dict, Any], List[Union[dict, Any]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.input_id is not None and not isinstance(self.input_id, str): - self.input_id = str(self.input_id) - - if self.input_title is not None and not isinstance(self.input_title, str): - self.input_title = str(self.input_title) - - if self.input_text is not None and not isinstance(self.input_text, str): - self.input_text = str(self.input_text) - - if self.raw_completion_output is not None and not isinstance(self.raw_completion_output, str): - self.raw_completion_output = str(self.raw_completion_output) - - if self.prompt is not None and not isinstance(self.prompt, str): - self.prompt = str(self.prompt) - - super().__post_init__(**kwargs) - - -@dataclass -class NamedEntity(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.NamedEntity - class_class_curie: ClassVar[str] = "core:NamedEntity" - class_name: ClassVar[str] = "NamedEntity" - class_model_uri: ClassVar[URIRef] = GOCAM.NamedEntity - - id: Union[str, NamedEntityId] = None - label: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, NamedEntityId): - self.id = NamedEntityId(self.id) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - super().__post_init__(**kwargs) - - -@dataclass -class Gene(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = GOCAM.Gene - class_class_curie: ClassVar[str] = "gocam:Gene" - class_name: ClassVar[str] = "Gene" - class_model_uri: ClassVar[URIRef] = GOCAM.Gene - - id: Union[str, GeneId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, GeneId): - self.id = GeneId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Pathway(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = GOCAM.Pathway - class_class_curie: ClassVar[str] = "gocam:Pathway" - class_name: ClassVar[str] = "Pathway" - class_model_uri: ClassVar[URIRef] = GOCAM.Pathway - - id: Union[str, PathwayId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, PathwayId): - self.id = PathwayId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class CellularProcess(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = GOCAM.CellularProcess - class_class_curie: ClassVar[str] = "gocam:CellularProcess" - class_name: ClassVar[str] = "CellularProcess" - class_model_uri: ClassVar[URIRef] = GOCAM.CellularProcess - - id: Union[str, CellularProcessId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, CellularProcessId): - self.id = CellularProcessId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class MolecularActivity(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = GOCAM.MolecularActivity - class_class_curie: ClassVar[str] = "gocam:MolecularActivity" - class_name: ClassVar[str] = "MolecularActivity" - class_model_uri: ClassVar[URIRef] = GOCAM.MolecularActivity - - id: Union[str, MolecularActivityId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, MolecularActivityId): - self.id = MolecularActivityId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class GeneLocation(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = GOCAM.GeneLocation - class_class_curie: ClassVar[str] = "gocam:GeneLocation" - class_name: ClassVar[str] = "GeneLocation" - class_model_uri: ClassVar[URIRef] = GOCAM.GeneLocation - - id: Union[str, GeneLocationId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, GeneLocationId): - self.id = GeneLocationId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Organism(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = GOCAM.Organism - class_class_curie: ClassVar[str] = "gocam:Organism" - class_name: ClassVar[str] = "Organism" - class_model_uri: ClassVar[URIRef] = GOCAM.Organism - - id: Union[str, OrganismId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, OrganismId): - self.id = OrganismId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Molecule(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = GOCAM.Molecule - class_class_curie: ClassVar[str] = "gocam:Molecule" - class_name: ClassVar[str] = "Molecule" - class_model_uri: ClassVar[URIRef] = GOCAM.Molecule - - id: Union[str, MoleculeId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, MoleculeId): - self.id = MoleculeId(self.id) - - super().__post_init__(**kwargs) - - -class CompoundExpression(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.CompoundExpression - class_class_curie: ClassVar[str] = "core:CompoundExpression" - class_name: ClassVar[str] = "CompoundExpression" - class_model_uri: ClassVar[URIRef] = GOCAM.CompoundExpression - - -@dataclass -class GeneOrganismRelationship(CompoundExpression): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = GOCAM.GeneOrganismRelationship - class_class_curie: ClassVar[str] = "gocam:GeneOrganismRelationship" - class_name: ClassVar[str] = "GeneOrganismRelationship" - class_model_uri: ClassVar[URIRef] = GOCAM.GeneOrganismRelationship - - gene: Optional[Union[str, GeneId]] = None - organism: Optional[Union[str, OrganismId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.gene is not None and not isinstance(self.gene, GeneId): - self.gene = GeneId(self.gene) - - if self.organism is not None and not isinstance(self.organism, OrganismId): - self.organism = OrganismId(self.organism) - - super().__post_init__(**kwargs) - - -@dataclass -class GeneMolecularActivityRelationship(CompoundExpression): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = GOCAM.GeneMolecularActivityRelationship - class_class_curie: ClassVar[str] = "gocam:GeneMolecularActivityRelationship" - class_name: ClassVar[str] = "GeneMolecularActivityRelationship" - class_model_uri: ClassVar[URIRef] = GOCAM.GeneMolecularActivityRelationship - - gene: Optional[Union[str, GeneId]] = None - molecular_activity: Optional[Union[str, MolecularActivityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.gene is not None and not isinstance(self.gene, GeneId): - self.gene = GeneId(self.gene) - - if self.molecular_activity is not None and not isinstance(self.molecular_activity, MolecularActivityId): - self.molecular_activity = MolecularActivityId(self.molecular_activity) - - super().__post_init__(**kwargs) - - -@dataclass -class GeneMolecularActivityRelationship2(CompoundExpression): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = GOCAM.GeneMolecularActivityRelationship2 - class_class_curie: ClassVar[str] = "gocam:GeneMolecularActivityRelationship2" - class_name: ClassVar[str] = "GeneMolecularActivityRelationship2" - class_model_uri: ClassVar[URIRef] = GOCAM.GeneMolecularActivityRelationship2 - - gene: Optional[Union[str, GeneId]] = None - molecular_activity: Optional[Union[str, MolecularActivityId]] = None - target: Optional[Union[str, MoleculeId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.gene is not None and not isinstance(self.gene, GeneId): - self.gene = GeneId(self.gene) - - if self.molecular_activity is not None and not isinstance(self.molecular_activity, MolecularActivityId): - self.molecular_activity = MolecularActivityId(self.molecular_activity) - - if self.target is not None and not isinstance(self.target, MoleculeId): - self.target = MoleculeId(self.target) - - super().__post_init__(**kwargs) - - -@dataclass -class GeneSubcellularLocalizationRelationship(CompoundExpression): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = GOCAM.GeneSubcellularLocalizationRelationship - class_class_curie: ClassVar[str] = "gocam:GeneSubcellularLocalizationRelationship" - class_name: ClassVar[str] = "GeneSubcellularLocalizationRelationship" - class_model_uri: ClassVar[URIRef] = GOCAM.GeneSubcellularLocalizationRelationship - - gene: Optional[Union[str, GeneId]] = None - location: Optional[Union[str, GeneLocationId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.gene is not None and not isinstance(self.gene, GeneId): - self.gene = GeneId(self.gene) - - if self.location is not None and not isinstance(self.location, GeneLocationId): - self.location = GeneLocationId(self.location) - - super().__post_init__(**kwargs) - - -@dataclass -class GeneGeneInteraction(CompoundExpression): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = GOCAM.GeneGeneInteraction - class_class_curie: ClassVar[str] = "gocam:GeneGeneInteraction" - class_name: ClassVar[str] = "GeneGeneInteraction" - class_model_uri: ClassVar[URIRef] = GOCAM.GeneGeneInteraction - - gene1: Optional[Union[str, GeneId]] = None - gene2: Optional[Union[str, GeneId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.gene1 is not None and not isinstance(self.gene1, GeneId): - self.gene1 = GeneId(self.gene1) - - if self.gene2 is not None and not isinstance(self.gene2, GeneId): - self.gene2 = GeneId(self.gene2) - - super().__post_init__(**kwargs) - - -@dataclass -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Triple - class_class_curie: ClassVar[str] = "core:Triple" - class_name: ClassVar[str] = "Triple" - class_model_uri: ClassVar[URIRef] = GOCAM.Triple - - subject: Optional[Union[str, NamedEntityId]] = None - predicate: Optional[Union[str, RelationshipTypeId]] = None - object: Optional[Union[str, NamedEntityId]] = None - qualifier: Optional[str] = None - subject_qualifier: Optional[Union[str, NamedEntityId]] = None - object_qualifier: Optional[Union[str, NamedEntityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, NamedEntityId): - self.subject = NamedEntityId(self.subject) - - if self.predicate is not None and not isinstance(self.predicate, RelationshipTypeId): - self.predicate = RelationshipTypeId(self.predicate) - - if self.object is not None and not isinstance(self.object, NamedEntityId): - self.object = NamedEntityId(self.object) - - if self.qualifier is not None and not isinstance(self.qualifier, str): - self.qualifier = str(self.qualifier) - - if self.subject_qualifier is not None and not isinstance(self.subject_qualifier, NamedEntityId): - self.subject_qualifier = NamedEntityId(self.subject_qualifier) - - if self.object_qualifier is not None and not isinstance(self.object_qualifier, NamedEntityId): - self.object_qualifier = NamedEntityId(self.object_qualifier) - - super().__post_init__(**kwargs) - - -@dataclass -class TextWithTriples(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.TextWithTriples - class_class_curie: ClassVar[str] = "core:TextWithTriples" - class_name: ClassVar[str] = "TextWithTriples" - class_model_uri: ClassVar[URIRef] = GOCAM.TextWithTriples - - publication: Optional[Union[dict, "Publication"]] = None - triples: Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.publication is not None and not isinstance(self.publication, Publication): - self.publication = Publication(**as_dict(self.publication)) - - if not isinstance(self.triples, list): - self.triples = [self.triples] if self.triples is not None else [] - self.triples = [v if isinstance(v, Triple) else Triple(**as_dict(v)) for v in self.triples] - - super().__post_init__(**kwargs) - - -@dataclass -class RelationshipType(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.RelationshipType - class_class_curie: ClassVar[str] = "core:RelationshipType" - class_name: ClassVar[str] = "RelationshipType" - class_model_uri: ClassVar[URIRef] = GOCAM.RelationshipType - - id: Union[str, RelationshipTypeId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, RelationshipTypeId): - self.id = RelationshipTypeId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Publication(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Publication - class_class_curie: ClassVar[str] = "core:Publication" - class_name: ClassVar[str] = "Publication" - class_model_uri: ClassVar[URIRef] = GOCAM.Publication - - id: Optional[str] = None - title: Optional[str] = None - abstract: Optional[str] = None - combined_text: Optional[str] = None - full_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.id is not None and not isinstance(self.id, str): - self.id = str(self.id) - - if self.title is not None and not isinstance(self.title, str): - self.title = str(self.title) - - if self.abstract is not None and not isinstance(self.abstract, str): - self.abstract = str(self.abstract) - - if self.combined_text is not None and not isinstance(self.combined_text, str): - self.combined_text = str(self.combined_text) - - if self.full_text is not None and not isinstance(self.full_text, str): - self.full_text = str(self.full_text) - - super().__post_init__(**kwargs) - - -@dataclass -class AnnotatorResult(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.AnnotatorResult - class_class_curie: ClassVar[str] = "core:AnnotatorResult" - class_name: ClassVar[str] = "AnnotatorResult" - class_model_uri: ClassVar[URIRef] = GOCAM.AnnotatorResult - - subject_text: Optional[str] = None - object_id: Optional[str] = None - object_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject_text is not None and not isinstance(self.subject_text, str): - self.subject_text = str(self.subject_text) - - if self.object_id is not None and not isinstance(self.object_id, str): - self.object_id = str(self.object_id) - - if self.object_text is not None and not isinstance(self.object_text, str): - self.object_text = str(self.object_text) - - super().__post_init__(**kwargs) - - -# Enumerations -class GeneLocationEnum(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="GeneLocationEnum", - ) - -class GOCellComponentType(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="GOCellComponentType", - ) - -class CellType(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="CellType", - ) - -class NullDataOptions(EnumDefinitionImpl): - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = PermissibleValue(text="UNSPECIFIED_METHOD_OF_ADMINISTRATION", - meaning=NCIT.C149701) - NOT_APPLICABLE = PermissibleValue(text="NOT_APPLICABLE", - meaning=NCIT.C18902) - NOT_MENTIONED = PermissibleValue(text="NOT_MENTIONED") - - _defn = EnumDefinition( - name="NullDataOptions", - ) - -# Slots -class slots: - pass - -slots.iBDAnnotations__genes = Slot(uri=GOCAM.genes, name="iBDAnnotations__genes", curie=GOCAM.curie('genes'), - model_uri=GOCAM.iBDAnnotations__genes, domain=None, range=Optional[Union[Union[str, GeneId], List[Union[str, GeneId]]]]) - -slots.iBDAnnotations__organisms = Slot(uri=GOCAM.organisms, name="iBDAnnotations__organisms", curie=GOCAM.curie('organisms'), - model_uri=GOCAM.iBDAnnotations__organisms, domain=None, range=Optional[Union[Union[str, OrganismId], List[Union[str, OrganismId]]]]) - -slots.iBDAnnotations__gene_organisms = Slot(uri=GOCAM.gene_organisms, name="iBDAnnotations__gene_organisms", curie=GOCAM.curie('gene_organisms'), - model_uri=GOCAM.iBDAnnotations__gene_organisms, domain=None, range=Optional[Union[Union[dict, GeneOrganismRelationship], List[Union[dict, GeneOrganismRelationship]]]]) - -slots.iBDAnnotations__activities = Slot(uri=GOCAM.activities, name="iBDAnnotations__activities", curie=GOCAM.curie('activities'), - model_uri=GOCAM.iBDAnnotations__activities, domain=None, range=Optional[Union[Union[str, MolecularActivityId], List[Union[str, MolecularActivityId]]]]) - -slots.iBDAnnotations__gene_functions = Slot(uri=GOCAM.gene_functions, name="iBDAnnotations__gene_functions", curie=GOCAM.curie('gene_functions'), - model_uri=GOCAM.iBDAnnotations__gene_functions, domain=None, range=Optional[Union[Union[dict, GeneMolecularActivityRelationship], List[Union[dict, GeneMolecularActivityRelationship]]]]) - -slots.iBDAnnotations__cellular_processes = Slot(uri=GOCAM.cellular_processes, name="iBDAnnotations__cellular_processes", curie=GOCAM.curie('cellular_processes'), - model_uri=GOCAM.iBDAnnotations__cellular_processes, domain=None, range=Optional[Union[Union[str, CellularProcessId], List[Union[str, CellularProcessId]]]]) - -slots.iBDAnnotations__pathways = Slot(uri=GOCAM.pathways, name="iBDAnnotations__pathways", curie=GOCAM.curie('pathways'), - model_uri=GOCAM.iBDAnnotations__pathways, domain=None, range=Optional[Union[Union[str, PathwayId], List[Union[str, PathwayId]]]]) - -slots.iBDAnnotations__gene_gene_interactions = Slot(uri=GOCAM.gene_gene_interactions, name="iBDAnnotations__gene_gene_interactions", curie=GOCAM.curie('gene_gene_interactions'), - model_uri=GOCAM.iBDAnnotations__gene_gene_interactions, domain=None, range=Optional[Union[Union[dict, GeneGeneInteraction], List[Union[dict, GeneGeneInteraction]]]]) - -slots.iBDAnnotations__gene_localizations = Slot(uri=GOCAM.gene_localizations, name="iBDAnnotations__gene_localizations", curie=GOCAM.curie('gene_localizations'), - model_uri=GOCAM.iBDAnnotations__gene_localizations, domain=None, range=Optional[Union[Union[dict, GeneSubcellularLocalizationRelationship], List[Union[dict, GeneSubcellularLocalizationRelationship]]]]) - -slots.geneOrganismRelationship__gene = Slot(uri=GOCAM.gene, name="geneOrganismRelationship__gene", curie=GOCAM.curie('gene'), - model_uri=GOCAM.geneOrganismRelationship__gene, domain=None, range=Optional[Union[str, GeneId]]) - -slots.geneOrganismRelationship__organism = Slot(uri=GOCAM.organism, name="geneOrganismRelationship__organism", curie=GOCAM.curie('organism'), - model_uri=GOCAM.geneOrganismRelationship__organism, domain=None, range=Optional[Union[str, OrganismId]]) - -slots.geneMolecularActivityRelationship__gene = Slot(uri=GOCAM.gene, name="geneMolecularActivityRelationship__gene", curie=GOCAM.curie('gene'), - model_uri=GOCAM.geneMolecularActivityRelationship__gene, domain=None, range=Optional[Union[str, GeneId]]) - -slots.geneMolecularActivityRelationship__molecular_activity = Slot(uri=GOCAM.molecular_activity, name="geneMolecularActivityRelationship__molecular_activity", curie=GOCAM.curie('molecular_activity'), - model_uri=GOCAM.geneMolecularActivityRelationship__molecular_activity, domain=None, range=Optional[Union[str, MolecularActivityId]]) - -slots.geneMolecularActivityRelationship2__gene = Slot(uri=GOCAM.gene, name="geneMolecularActivityRelationship2__gene", curie=GOCAM.curie('gene'), - model_uri=GOCAM.geneMolecularActivityRelationship2__gene, domain=None, range=Optional[Union[str, GeneId]]) - -slots.geneMolecularActivityRelationship2__molecular_activity = Slot(uri=GOCAM.molecular_activity, name="geneMolecularActivityRelationship2__molecular_activity", curie=GOCAM.curie('molecular_activity'), - model_uri=GOCAM.geneMolecularActivityRelationship2__molecular_activity, domain=None, range=Optional[Union[str, MolecularActivityId]]) - -slots.geneMolecularActivityRelationship2__target = Slot(uri=GOCAM.target, name="geneMolecularActivityRelationship2__target", curie=GOCAM.curie('target'), - model_uri=GOCAM.geneMolecularActivityRelationship2__target, domain=None, range=Optional[Union[str, MoleculeId]]) - -slots.geneSubcellularLocalizationRelationship__gene = Slot(uri=GOCAM.gene, name="geneSubcellularLocalizationRelationship__gene", curie=GOCAM.curie('gene'), - model_uri=GOCAM.geneSubcellularLocalizationRelationship__gene, domain=None, range=Optional[Union[str, GeneId]]) - -slots.geneSubcellularLocalizationRelationship__location = Slot(uri=GOCAM.location, name="geneSubcellularLocalizationRelationship__location", curie=GOCAM.curie('location'), - model_uri=GOCAM.geneSubcellularLocalizationRelationship__location, domain=None, range=Optional[Union[str, GeneLocationId]]) - -slots.geneGeneInteraction__gene1 = Slot(uri=GOCAM.gene1, name="geneGeneInteraction__gene1", curie=GOCAM.curie('gene1'), - model_uri=GOCAM.geneGeneInteraction__gene1, domain=None, range=Optional[Union[str, GeneId]]) - -slots.geneGeneInteraction__gene2 = Slot(uri=GOCAM.gene2, name="geneGeneInteraction__gene2", curie=GOCAM.curie('gene2'), - model_uri=GOCAM.geneGeneInteraction__gene2, domain=None, range=Optional[Union[str, GeneId]]) - -slots.extractionResult__input_id = Slot(uri=CORE.input_id, name="extractionResult__input_id", curie=CORE.curie('input_id'), - model_uri=GOCAM.extractionResult__input_id, domain=None, range=Optional[str]) - -slots.extractionResult__input_title = Slot(uri=CORE.input_title, name="extractionResult__input_title", curie=CORE.curie('input_title'), - model_uri=GOCAM.extractionResult__input_title, domain=None, range=Optional[str]) - -slots.extractionResult__input_text = Slot(uri=CORE.input_text, name="extractionResult__input_text", curie=CORE.curie('input_text'), - model_uri=GOCAM.extractionResult__input_text, domain=None, range=Optional[str]) - -slots.extractionResult__raw_completion_output = Slot(uri=CORE.raw_completion_output, name="extractionResult__raw_completion_output", curie=CORE.curie('raw_completion_output'), - model_uri=GOCAM.extractionResult__raw_completion_output, domain=None, range=Optional[str]) - -slots.extractionResult__prompt = Slot(uri=CORE.prompt, name="extractionResult__prompt", curie=CORE.curie('prompt'), - model_uri=GOCAM.extractionResult__prompt, domain=None, range=Optional[str]) - -slots.extractionResult__extracted_object = Slot(uri=CORE.extracted_object, name="extractionResult__extracted_object", curie=CORE.curie('extracted_object'), - model_uri=GOCAM.extractionResult__extracted_object, domain=None, range=Optional[Union[dict, Any]]) - -slots.extractionResult__named_entities = Slot(uri=CORE.named_entities, name="extractionResult__named_entities", curie=CORE.curie('named_entities'), - model_uri=GOCAM.extractionResult__named_entities, domain=None, range=Optional[Union[Union[dict, Any], List[Union[dict, Any]]]]) - -slots.namedEntity__id = Slot(uri=CORE.id, name="namedEntity__id", curie=CORE.curie('id'), - model_uri=GOCAM.namedEntity__id, domain=None, range=URIRef) - -slots.namedEntity__label = Slot(uri=RDFS.label, name="namedEntity__label", curie=RDFS.curie('label'), - model_uri=GOCAM.namedEntity__label, domain=None, range=Optional[str]) - -slots.triple__subject = Slot(uri=CORE.subject, name="triple__subject", curie=CORE.curie('subject'), - model_uri=GOCAM.triple__subject, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__predicate = Slot(uri=CORE.predicate, name="triple__predicate", curie=CORE.curie('predicate'), - model_uri=GOCAM.triple__predicate, domain=None, range=Optional[Union[str, RelationshipTypeId]]) - -slots.triple__object = Slot(uri=CORE.object, name="triple__object", curie=CORE.curie('object'), - model_uri=GOCAM.triple__object, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__qualifier = Slot(uri=CORE.qualifier, name="triple__qualifier", curie=CORE.curie('qualifier'), - model_uri=GOCAM.triple__qualifier, domain=None, range=Optional[str]) - -slots.triple__subject_qualifier = Slot(uri=CORE.subject_qualifier, name="triple__subject_qualifier", curie=CORE.curie('subject_qualifier'), - model_uri=GOCAM.triple__subject_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__object_qualifier = Slot(uri=CORE.object_qualifier, name="triple__object_qualifier", curie=CORE.curie('object_qualifier'), - model_uri=GOCAM.triple__object_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.textWithTriples__publication = Slot(uri=CORE.publication, name="textWithTriples__publication", curie=CORE.curie('publication'), - model_uri=GOCAM.textWithTriples__publication, domain=None, range=Optional[Union[dict, Publication]]) - -slots.textWithTriples__triples = Slot(uri=CORE.triples, name="textWithTriples__triples", curie=CORE.curie('triples'), - model_uri=GOCAM.textWithTriples__triples, domain=None, range=Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]]) - -slots.publication__id = Slot(uri=CORE.id, name="publication__id", curie=CORE.curie('id'), - model_uri=GOCAM.publication__id, domain=None, range=Optional[str]) - -slots.publication__title = Slot(uri=CORE.title, name="publication__title", curie=CORE.curie('title'), - model_uri=GOCAM.publication__title, domain=None, range=Optional[str]) - -slots.publication__abstract = Slot(uri=CORE.abstract, name="publication__abstract", curie=CORE.curie('abstract'), - model_uri=GOCAM.publication__abstract, domain=None, range=Optional[str]) - -slots.publication__combined_text = Slot(uri=CORE.combined_text, name="publication__combined_text", curie=CORE.curie('combined_text'), - model_uri=GOCAM.publication__combined_text, domain=None, range=Optional[str]) - -slots.publication__full_text = Slot(uri=CORE.full_text, name="publication__full_text", curie=CORE.curie('full_text'), - model_uri=GOCAM.publication__full_text, domain=None, range=Optional[str]) - -slots.annotatorResult__subject_text = Slot(uri=CORE.subject_text, name="annotatorResult__subject_text", curie=CORE.curie('subject_text'), - model_uri=GOCAM.annotatorResult__subject_text, domain=None, range=Optional[str]) - -slots.annotatorResult__object_id = Slot(uri=CORE.object_id, name="annotatorResult__object_id", curie=CORE.curie('object_id'), - model_uri=GOCAM.annotatorResult__object_id, domain=None, range=Optional[str]) - -slots.annotatorResult__object_text = Slot(uri=CORE.object_text, name="annotatorResult__object_text", curie=CORE.curie('object_text'), - model_uri=GOCAM.annotatorResult__object_text, domain=None, range=Optional[str]) - -slots.GeneLocation_id = Slot(uri=GOCAM.id, name="GeneLocation_id", curie=GOCAM.curie('id'), - model_uri=GOCAM.GeneLocation_id, domain=GeneLocation, range=Union[str, GeneLocationId]) \ No newline at end of file diff --git a/projects/ibd/jsonld/ibd.context.jsonld b/projects/ibd/jsonld/ibd.context.jsonld deleted file mode 100644 index 32eb76735..000000000 --- a/projects/ibd/jsonld/ibd.context.jsonld +++ /dev/null @@ -1,191 +0,0 @@ -{ - "comments": { - "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2023-08-07T10:54:05", - "source": "ibd.yaml" - }, - "@context": { - "CHEBI": "http://example.org/UNKNOWN/CHEBI/", - "CL": { - "@id": "http://purl.obolibrary.org/obo/CL_", - "@prefix": true - }, - "EFO": "http://example.org/UNKNOWN/EFO/", - "GO": { - "@id": "http://purl.obolibrary.org/obo/GO_", - "@prefix": true - }, - "HGNC": "http://example.org/UNKNOWN/HGNC/", - "NCBITaxon": "http://example.org/UNKNOWN/NCBITaxon/", - "PR": "http://example.org/UNKNOWN/PR/", - "PW": "http://example.org/UNKNOWN/PW/", - "RO": { - "@id": "http://purl.obolibrary.org/obo/RO_", - "@prefix": true - }, - "UBERON": "http://example.org/UNKNOWN/UBERON/", - "UniProtKB": "http://example.org/UNKNOWN/UniProtKB/", - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "gocam": "http://w3id.org/ontogpt/gocam/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "@vocab": "http://w3id.org/ontogpt/gocam/", - "object_id": { - "@id": "core:object_id" - }, - "object_text": { - "@id": "core:object_text" - }, - "subject_text": { - "@id": "core:subject_text" - }, - "extracted_object": { - "@type": "@id", - "@id": "core:extracted_object" - }, - "input_id": { - "@id": "core:input_id" - }, - "input_text": { - "@id": "core:input_text" - }, - "input_title": { - "@id": "core:input_title" - }, - "named_entities": { - "@type": "@id", - "@id": "core:named_entities" - }, - "prompt": { - "@id": "core:prompt" - }, - "raw_completion_output": { - "@id": "core:raw_completion_output" - }, - "gene1": { - "@type": "@id" - }, - "gene2": { - "@type": "@id" - }, - "id": { - "@id": "core:id" - }, - "gene": { - "@type": "@id" - }, - "molecular_activity": { - "@type": "@id" - }, - "target": { - "@type": "@id" - }, - "organism": { - "@type": "@id" - }, - "location": { - "@type": "@id" - }, - "activities": { - "@type": "@id" - }, - "cellular_processes": { - "@type": "@id" - }, - "gene_functions": { - "@type": "@id" - }, - "gene_gene_interactions": { - "@type": "@id" - }, - "gene_localizations": { - "@type": "@id" - }, - "gene_organisms": { - "@type": "@id" - }, - "genes": { - "@type": "@id" - }, - "organisms": { - "@type": "@id" - }, - "pathways": { - "@type": "@id" - }, - "label": { - "@id": "rdfs:label" - }, - "abstract": { - "@id": "core:abstract" - }, - "combined_text": { - "@id": "core:combined_text" - }, - "full_text": { - "@id": "core:full_text" - }, - "title": { - "@id": "core:title" - }, - "publication": { - "@type": "@id", - "@id": "core:publication" - }, - "triples": { - "@type": "@id", - "@id": "core:triples" - }, - "object": { - "@type": "@id", - "@id": "core:object" - }, - "object_qualifier": { - "@type": "@id", - "@id": "core:object_qualifier" - }, - "predicate": { - "@type": "@id", - "@id": "core:predicate" - }, - "qualifier": { - "@id": "core:qualifier" - }, - "subject": { - "@type": "@id", - "@id": "core:subject" - }, - "subject_qualifier": { - "@type": "@id", - "@id": "core:subject_qualifier" - }, - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } - } -} diff --git a/projects/ibd/jsonld/ibd.jsonld b/projects/ibd/jsonld/ibd.jsonld deleted file mode 100644 index 374f60cd9..000000000 --- a/projects/ibd/jsonld/ibd.jsonld +++ /dev/null @@ -1,1767 +0,0 @@ -{ - "name": "gocam-template", - "description": "A template for GO-CAMs", - "title": "GO-CAM Template", - "id": "http://w3id.org/ontogpt/gocam", - "imports": [ - "linkml:types", - "core" - ], - "license": "https://creativecommons.org/publicdomain/zero/1.0/", - "prefixes": [ - { - "prefix_prefix": "linkml", - "prefix_reference": "https://w3id.org/linkml/" - }, - { - "prefix_prefix": "gocam", - "prefix_reference": "http://w3id.org/ontogpt/gocam/" - }, - { - "prefix_prefix": "GO", - "prefix_reference": "http://purl.obolibrary.org/obo/GO_" - }, - { - "prefix_prefix": "CL", - "prefix_reference": "http://purl.obolibrary.org/obo/CL_" - } - ], - "default_prefix": "gocam", - "default_range": "string", - "types": [ - { - "name": "string", - "definition_uri": "https://w3id.org/linkml/String", - "description": "A character string", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Text" - ], - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "@type": "TypeDefinition" - }, - { - "name": "integer", - "definition_uri": "https://w3id.org/linkml/Integer", - "description": "An integer", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Integer" - ], - "base": "int", - "uri": "http://www.w3.org/2001/XMLSchema#integer", - "@type": "TypeDefinition" - }, - { - "name": "boolean", - "definition_uri": "https://w3id.org/linkml/Boolean", - "description": "A binary (true or false) value", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Boolean" - ], - "base": "Bool", - "uri": "http://www.w3.org/2001/XMLSchema#boolean", - "repr": "bool", - "@type": "TypeDefinition" - }, - { - "name": "float", - "definition_uri": "https://w3id.org/linkml/Float", - "description": "A real number that conforms to the xsd:float specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#float", - "@type": "TypeDefinition" - }, - { - "name": "double", - "definition_uri": "https://w3id.org/linkml/Double", - "description": "A real number that conforms to the xsd:double specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#double", - "@type": "TypeDefinition" - }, - { - "name": "decimal", - "definition_uri": "https://w3id.org/linkml/Decimal", - "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "broad_mappings": [ - "schema:Number" - ], - "base": "Decimal", - "uri": "http://www.w3.org/2001/XMLSchema#decimal", - "@type": "TypeDefinition" - }, - { - "name": "time", - "definition_uri": "https://w3id.org/linkml/Time", - "description": "A time object represents a (local) time of day, independent of any particular day", - "notes": [ - "URI is dateTime because OWL reasoners do not work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Time" - ], - "base": "XSDTime", - "uri": "http://www.w3.org/2001/XMLSchema#time", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date", - "definition_uri": "https://w3id.org/linkml/Date", - "description": "a date (year, month and day) in an idealized calendar", - "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Date" - ], - "base": "XSDDate", - "uri": "http://www.w3.org/2001/XMLSchema#date", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "datetime", - "definition_uri": "https://w3id.org/linkml/Datetime", - "description": "The combination of a date and time", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:DateTime" - ], - "base": "XSDDateTime", - "uri": "http://www.w3.org/2001/XMLSchema#dateTime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date_or_datetime", - "definition_uri": "https://w3id.org/linkml/DateOrDatetime", - "description": "Either a date or a datetime", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "https://w3id.org/linkml/DateOrDatetime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uriorcurie", - "definition_uri": "https://w3id.org/linkml/Uriorcurie", - "description": "a URI or a CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "URIorCURIE", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "curie", - "definition_uri": "https://w3id.org/linkml/Curie", - "conforms_to": "https://www.w3.org/TR/curie/", - "description": "a compact URI", - "comments": [ - "in RDF serializations this MUST be expanded to a URI", - "in non-RDF serializations MAY be serialized as the compact representation" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "Curie", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uri", - "definition_uri": "https://w3id.org/linkml/Uri", - "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", - "description": "a complete URI", - "comments": [ - "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:URL" - ], - "base": "URI", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "ncname", - "definition_uri": "https://w3id.org/linkml/Ncname", - "description": "Prefix part of CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NCName", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "objectidentifier", - "definition_uri": "https://w3id.org/linkml/Objectidentifier", - "description": "A URI or CURIE that represents an object in the model.", - "comments": [ - "Used for inheritance and type checking" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "ElementIdentifier", - "uri": "http://www.w3.org/ns/shex#iri", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "nodeidentifier", - "definition_uri": "https://w3id.org/linkml/Nodeidentifier", - "description": "A URI, CURIE or BNODE that represents a node in a model.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NodeIdentifier", - "uri": "http://www.w3.org/ns/shex#nonLiteral", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpointer", - "definition_uri": "https://w3id.org/linkml/Jsonpointer", - "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901", - "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpath", - "definition_uri": "https://w3id.org/linkml/Jsonpath", - "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html", - "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "sparqlpath", - "definition_uri": "https://w3id.org/linkml/Sparqlpath", - "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths", - "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - } - ], - "enums": [ - { - "name": "GeneLocationEnum", - "definition_uri": "http://w3id.org/ontogpt/gocam/GeneLocationEnum", - "from_schema": "http://w3id.org/ontogpt/gocam", - "inherits": [ - "GOCellComponent", - "CellType" - ] - }, - { - "name": "GOCellComponentType", - "definition_uri": "http://w3id.org/ontogpt/gocam/GOCellComponentType", - "from_schema": "http://w3id.org/ontogpt/gocam", - "reachable_from": { - "source_ontology": "obo:go", - "source_nodes": [ - "GO:0005575" - ] - } - }, - { - "name": "CellType", - "definition_uri": "http://w3id.org/ontogpt/gocam/CellType", - "from_schema": "http://w3id.org/ontogpt/gocam", - "reachable_from": { - "source_ontology": "obo:cl", - "source_nodes": [ - "CL:0000000" - ] - } - }, - { - "name": "NullDataOptions", - "definition_uri": "http://w3id.org/ontogpt/core/NullDataOptions", - "from_schema": "http://w3id.org/ontogpt/core", - "permissible_values": [ - { - "text": "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "meaning": "NCIT:C149701" - }, - { - "text": "NOT_APPLICABLE", - "meaning": "NCIT:C18902", - "aliases": [ - "not applicable", - "N/A" - ] - }, - { - "text": "NOT_MENTIONED" - } - ] - } - ], - "slots": [ - { - "name": "iBDAnnotations__genes", - "description": "semicolon-separated list of genes", - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/genes", - "multivalued": true, - "alias": "genes", - "owner": "IBDAnnotations", - "domain_of": [ - "IBDAnnotations" - ], - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "iBDAnnotations__organisms", - "description": "semicolon-separated list of organism taxons", - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/organisms", - "multivalued": true, - "alias": "organisms", - "owner": "IBDAnnotations", - "domain_of": [ - "IBDAnnotations" - ], - "range": "Organism", - "@type": "SlotDefinition" - }, - { - "name": "iBDAnnotations__gene_organisms", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of asterisk separated gene to organism relationships", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/gene_organisms", - "multivalued": true, - "alias": "gene_organisms", - "owner": "IBDAnnotations", - "domain_of": [ - "IBDAnnotations" - ], - "range": "GeneOrganismRelationship", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "iBDAnnotations__activities", - "description": "semicolon-separated list of molecular activities", - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/activities", - "multivalued": true, - "alias": "activities", - "owner": "IBDAnnotations", - "domain_of": [ - "IBDAnnotations" - ], - "range": "MolecularActivity", - "@type": "SlotDefinition" - }, - { - "name": "iBDAnnotations__gene_functions", - "description": "semicolon-separated list of gene to molecular activity relationships", - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/gene_functions", - "multivalued": true, - "alias": "gene_functions", - "owner": "IBDAnnotations", - "domain_of": [ - "IBDAnnotations" - ], - "range": "GeneMolecularActivityRelationship", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "iBDAnnotations__cellular_processes", - "description": "semicolon-separated list of cellular processes", - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/cellular_processes", - "multivalued": true, - "alias": "cellular_processes", - "owner": "IBDAnnotations", - "domain_of": [ - "IBDAnnotations" - ], - "range": "CellularProcess", - "@type": "SlotDefinition" - }, - { - "name": "iBDAnnotations__pathways", - "description": "semicolon-separated list of pathways", - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/pathways", - "multivalued": true, - "alias": "pathways", - "owner": "IBDAnnotations", - "domain_of": [ - "IBDAnnotations" - ], - "range": "Pathway", - "@type": "SlotDefinition" - }, - { - "name": "iBDAnnotations__gene_gene_interactions", - "description": "semicolon-separated list of gene to gene interactions", - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/gene_gene_interactions", - "multivalued": true, - "alias": "gene_gene_interactions", - "owner": "IBDAnnotations", - "domain_of": [ - "IBDAnnotations" - ], - "range": "GeneGeneInteraction", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "iBDAnnotations__gene_localizations", - "description": "semicolon-separated list of genes plus their location in the cell; for example, \"gene1 / cytoplasm; gene2 / mitochondrion\"", - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/gene_localizations", - "multivalued": true, - "alias": "gene_localizations", - "owner": "IBDAnnotations", - "domain_of": [ - "IBDAnnotations" - ], - "range": "GeneSubcellularLocalizationRelationship", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "geneOrganismRelationship__gene", - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/gene", - "alias": "gene", - "owner": "GeneOrganismRelationship", - "domain_of": [ - "GeneOrganismRelationship" - ], - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "geneOrganismRelationship__organism", - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/organism", - "alias": "organism", - "owner": "GeneOrganismRelationship", - "domain_of": [ - "GeneOrganismRelationship" - ], - "range": "Organism", - "@type": "SlotDefinition" - }, - { - "name": "geneMolecularActivityRelationship__gene", - "annotations": [ - { - "tag": "prompt", - "value": "the name of the gene in the pair. This comes first.", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/gene", - "alias": "gene", - "owner": "GeneMolecularActivityRelationship", - "domain_of": [ - "GeneMolecularActivityRelationship" - ], - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "geneMolecularActivityRelationship__molecular_activity", - "annotations": [ - { - "tag": "prompt", - "value": "the name of the molecular function in the pair. This comes second. May be a GO term.", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/molecular_activity", - "alias": "molecular_activity", - "owner": "GeneMolecularActivityRelationship", - "domain_of": [ - "GeneMolecularActivityRelationship" - ], - "range": "MolecularActivity", - "@type": "SlotDefinition" - }, - { - "name": "geneMolecularActivityRelationship2__gene", - "annotations": [ - { - "tag": "prompt", - "value": "the name of the gene.", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/gene", - "alias": "gene", - "owner": "GeneMolecularActivityRelationship2", - "domain_of": [ - "GeneMolecularActivityRelationship2" - ], - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "geneMolecularActivityRelationship2__molecular_activity", - "annotations": [ - { - "tag": "prompt", - "value": "the name of the molecular activity, for example, ubiquitination. May be a GO term.", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/molecular_activity", - "alias": "molecular_activity", - "owner": "GeneMolecularActivityRelationship2", - "domain_of": [ - "GeneMolecularActivityRelationship2" - ], - "range": "MolecularActivity", - "@type": "SlotDefinition" - }, - { - "name": "geneMolecularActivityRelationship2__target", - "annotations": [ - { - "tag": "prompt", - "value": "the name of the molecular entity that is the target of the molecular activity.", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/target", - "alias": "target", - "owner": "GeneMolecularActivityRelationship2", - "domain_of": [ - "GeneMolecularActivityRelationship2" - ], - "range": "Molecule", - "@type": "SlotDefinition" - }, - { - "name": "geneSubcellularLocalizationRelationship__gene", - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/gene", - "alias": "gene", - "owner": "GeneSubcellularLocalizationRelationship", - "domain_of": [ - "GeneSubcellularLocalizationRelationship" - ], - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "geneSubcellularLocalizationRelationship__location", - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/location", - "alias": "location", - "owner": "GeneSubcellularLocalizationRelationship", - "domain_of": [ - "GeneSubcellularLocalizationRelationship" - ], - "range": "GeneLocation", - "@type": "SlotDefinition" - }, - { - "name": "geneGeneInteraction__gene1", - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/gene1", - "alias": "gene1", - "owner": "GeneGeneInteraction", - "domain_of": [ - "GeneGeneInteraction" - ], - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "geneGeneInteraction__gene2", - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/gene2", - "alias": "gene2", - "owner": "GeneGeneInteraction", - "domain_of": [ - "GeneGeneInteraction" - ], - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_id", - "alias": "input_id", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_title", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_title", - "alias": "input_title", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_text", - "alias": "input_text", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__raw_completion_output", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/raw_completion_output", - "alias": "raw_completion_output", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__prompt", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/prompt", - "alias": "prompt", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__extracted_object", - "description": "The complex objects extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/extracted_object", - "alias": "extracted_object", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__named_entities", - "description": "Named entities extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/named_entities", - "multivalued": true, - "alias": "named_entities", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "identifier": true, - "alias": "id", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "required": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "from_schema": "http://w3id.org/ontogpt/core", - "aliases": [ - "name" - ], - "mappings": [ - "http://example.org/UNKNOWN/rdfs/label" - ], - "slot_uri": "http://example.org/UNKNOWN/rdfs/label", - "alias": "label", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject", - "alias": "subject", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__predicate", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/predicate", - "alias": "predicate", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "triple__object", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object", - "alias": "object", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/qualifier", - "alias": "qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_qualifier", - "alias": "subject_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_qualifier", - "alias": "object_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/publication", - "alias": "publication", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__triples", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/triples", - "multivalued": true, - "alias": "triples", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "publication__id", - "description": "The publication identifier", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "alias": "id", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__title", - "description": "The title of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/title", - "alias": "title", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__abstract", - "description": "The abstract of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/abstract", - "alias": "abstract", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__combined_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/combined_text", - "alias": "combined_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__full_text", - "description": "The full text of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/full_text", - "alias": "full_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__subject_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_text", - "alias": "subject_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_id", - "alias": "object_id", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_text", - "alias": "object_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "GeneLocation_id", - "from_schema": "http://w3id.org/ontogpt/gocam", - "is_a": "namedEntity__id", - "values_from": [ - "GOCellComponentType", - "CellType" - ], - "domain": "GeneLocation", - "slot_uri": "http://w3id.org/ontogpt/gocam/id", - "identifier": true, - "alias": "id", - "owner": "GeneLocation", - "domain_of": [ - "GeneLocation" - ], - "is_usage_slot": true, - "usage_slot_name": "id", - "range": "string", - "required": true, - "@type": "SlotDefinition" - } - ], - "classes": [ - { - "name": "IBDAnnotations", - "definition_uri": "http://w3id.org/ontogpt/gocam/IBDAnnotations", - "from_schema": "http://w3id.org/ontogpt/gocam", - "slots": [ - "iBDAnnotations__genes", - "iBDAnnotations__organisms", - "iBDAnnotations__gene_organisms", - "iBDAnnotations__activities", - "iBDAnnotations__gene_functions", - "iBDAnnotations__cellular_processes", - "iBDAnnotations__pathways", - "iBDAnnotations__gene_gene_interactions", - "iBDAnnotations__gene_localizations" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "genes", - "description": "semicolon-separated list of genes", - "multivalued": true, - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "organisms", - "description": "semicolon-separated list of organism taxons", - "multivalued": true, - "range": "Organism", - "@type": "SlotDefinition" - }, - { - "name": "gene_organisms", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of asterisk separated gene to organism relationships", - "@type": "Annotation" - } - ], - "multivalued": true, - "range": "GeneOrganismRelationship", - "@type": "SlotDefinition" - }, - { - "name": "activities", - "description": "semicolon-separated list of molecular activities", - "multivalued": true, - "range": "MolecularActivity", - "@type": "SlotDefinition" - }, - { - "name": "gene_functions", - "description": "semicolon-separated list of gene to molecular activity relationships", - "multivalued": true, - "range": "GeneMolecularActivityRelationship", - "@type": "SlotDefinition" - }, - { - "name": "cellular_processes", - "description": "semicolon-separated list of cellular processes", - "multivalued": true, - "range": "CellularProcess", - "@type": "SlotDefinition" - }, - { - "name": "pathways", - "description": "semicolon-separated list of pathways", - "multivalued": true, - "range": "Pathway", - "@type": "SlotDefinition" - }, - { - "name": "gene_gene_interactions", - "description": "semicolon-separated list of gene to gene interactions", - "multivalued": true, - "range": "GeneGeneInteraction", - "@type": "SlotDefinition" - }, - { - "name": "gene_localizations", - "description": "semicolon-separated list of genes plus their location in the cell; for example, \"gene1 / cytoplasm; gene2 / mitochondrion\"", - "multivalued": true, - "range": "GeneSubcellularLocalizationRelationship", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/gocam/IBDAnnotations", - "tree_root": true, - "@type": "ClassDefinition" - }, - { - "name": "Gene", - "id_prefixes": [ - "HGNC", - "PR", - "UniProtKB" - ], - "definition_uri": "http://w3id.org/ontogpt/gocam/Gene", - "annotations": [ - { - "tag": "annotators", - "value": "gilda:, bioportal:hgnc-nr", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/gocam", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/gocam/Gene", - "@type": "ClassDefinition" - }, - { - "name": "Pathway", - "id_prefixes": [ - "GO", - "PW" - ], - "definition_uri": "http://w3id.org/ontogpt/gocam/Pathway", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:go, sqlite:obo:pw", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/gocam", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/gocam/Pathway", - "@type": "ClassDefinition" - }, - { - "name": "CellularProcess", - "id_prefixes": [ - "GO" - ], - "definition_uri": "http://w3id.org/ontogpt/gocam/CellularProcess", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:go", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/gocam", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/gocam/CellularProcess", - "@type": "ClassDefinition" - }, - { - "name": "MolecularActivity", - "id_prefixes": [ - "GO" - ], - "definition_uri": "http://w3id.org/ontogpt/gocam/MolecularActivity", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:go", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/gocam", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/gocam/MolecularActivity", - "@type": "ClassDefinition" - }, - { - "name": "GeneLocation", - "id_prefixes": [ - "GO", - "CL", - "UBERON" - ], - "definition_uri": "http://w3id.org/ontogpt/gocam/GeneLocation", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:go, sqlite:obo:cl", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/gocam", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__label", - "GeneLocation_id" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/gocam/GeneLocation", - "@type": "ClassDefinition" - }, - { - "name": "Organism", - "id_prefixes": [ - "NCBITaxon", - "EFO" - ], - "definition_uri": "http://w3id.org/ontogpt/gocam/Organism", - "annotations": [ - { - "tag": "annotators", - "value": "gilda:, sqlite:obo:ncbitaxon", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/gocam", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/gocam/Organism", - "@type": "ClassDefinition" - }, - { - "name": "Molecule", - "id_prefixes": [ - "CHEBI", - "PR" - ], - "definition_uri": "http://w3id.org/ontogpt/gocam/Molecule", - "annotations": [ - { - "tag": "annotators", - "value": "gilda:, sqlite:obo:chebi", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/gocam", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/gocam/Molecule", - "@type": "ClassDefinition" - }, - { - "name": "GeneOrganismRelationship", - "definition_uri": "http://w3id.org/ontogpt/gocam/GeneOrganismRelationship", - "from_schema": "http://w3id.org/ontogpt/gocam", - "is_a": "CompoundExpression", - "slots": [ - "geneOrganismRelationship__gene", - "geneOrganismRelationship__organism" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "gene", - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "organism", - "range": "Organism", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/gocam/GeneOrganismRelationship", - "@type": "ClassDefinition" - }, - { - "name": "GeneMolecularActivityRelationship", - "definition_uri": "http://w3id.org/ontogpt/gocam/GeneMolecularActivityRelationship", - "annotations": [ - { - "tag": "prompt.example", - "value": "TODO\n\ngene: HGNC:1234\nmolecular_activity: GO:0003674", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/gocam", - "is_a": "CompoundExpression", - "slots": [ - "geneMolecularActivityRelationship__gene", - "geneMolecularActivityRelationship__molecular_activity" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "gene", - "annotations": [ - { - "tag": "prompt", - "value": "the name of the gene in the pair. This comes first.", - "@type": "Annotation" - } - ], - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "molecular_activity", - "annotations": [ - { - "tag": "prompt", - "value": "the name of the molecular function in the pair. This comes second. May be a GO term.", - "@type": "Annotation" - } - ], - "range": "MolecularActivity", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/gocam/GeneMolecularActivityRelationship", - "@type": "ClassDefinition" - }, - { - "name": "GeneMolecularActivityRelationship2", - "definition_uri": "http://w3id.org/ontogpt/gocam/GeneMolecularActivityRelationship2", - "from_schema": "http://w3id.org/ontogpt/gocam", - "is_a": "CompoundExpression", - "slots": [ - "geneMolecularActivityRelationship2__gene", - "geneMolecularActivityRelationship2__molecular_activity", - "geneMolecularActivityRelationship2__target" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "gene", - "annotations": [ - { - "tag": "prompt", - "value": "the name of the gene.", - "@type": "Annotation" - } - ], - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "molecular_activity", - "annotations": [ - { - "tag": "prompt", - "value": "the name of the molecular activity, for example, ubiquitination. May be a GO term.", - "@type": "Annotation" - } - ], - "range": "MolecularActivity", - "@type": "SlotDefinition" - }, - { - "name": "target", - "annotations": [ - { - "tag": "prompt", - "value": "the name of the molecular entity that is the target of the molecular activity.", - "@type": "Annotation" - } - ], - "range": "Molecule", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/gocam/GeneMolecularActivityRelationship2", - "@type": "ClassDefinition" - }, - { - "name": "GeneSubcellularLocalizationRelationship", - "definition_uri": "http://w3id.org/ontogpt/gocam/GeneSubcellularLocalizationRelationship", - "from_schema": "http://w3id.org/ontogpt/gocam", - "is_a": "CompoundExpression", - "slots": [ - "geneSubcellularLocalizationRelationship__gene", - "geneSubcellularLocalizationRelationship__location" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "gene", - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "location", - "range": "GeneLocation", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/gocam/GeneSubcellularLocalizationRelationship", - "@type": "ClassDefinition" - }, - { - "name": "GeneGeneInteraction", - "definition_uri": "http://w3id.org/ontogpt/gocam/GeneGeneInteraction", - "from_schema": "http://w3id.org/ontogpt/gocam", - "is_a": "CompoundExpression", - "slots": [ - "geneGeneInteraction__gene1", - "geneGeneInteraction__gene2" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "gene1", - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "gene2", - "range": "Gene", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/gocam/GeneGeneInteraction", - "@type": "ClassDefinition" - }, - { - "name": "Any", - "definition_uri": "http://w3id.org/ontogpt/core/Any", - "from_schema": "http://w3id.org/ontogpt/core", - "mappings": [ - "linkml:Any" - ], - "slot_usage": {}, - "class_uri": "https://w3id.org/linkml/Any", - "@type": "ClassDefinition" - }, - { - "name": "ExtractionResult", - "definition_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "description": "A result of extracting knowledge on text", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "extractionResult__input_id", - "extractionResult__input_title", - "extractionResult__input_text", - "extractionResult__raw_completion_output", - "extractionResult__prompt", - "extractionResult__extracted_object", - "extractionResult__named_entities" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "input_id", - "@type": "SlotDefinition" - }, - { - "name": "input_title", - "@type": "SlotDefinition" - }, - { - "name": "input_text", - "@type": "SlotDefinition" - }, - { - "name": "raw_completion_output", - "@type": "SlotDefinition" - }, - { - "name": "prompt", - "@type": "SlotDefinition" - }, - { - "name": "extracted_object", - "description": "The complex objects extracted from the text", - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "named_entities", - "description": "Named entities extracted from the text", - "multivalued": true, - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "@type": "ClassDefinition" - }, - { - "name": "NamedEntity", - "definition_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "identifier": true, - "@type": "SlotDefinition" - }, - { - "name": "label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "aliases": [ - "name" - ], - "slot_uri": "rdfs:label", - "range": "string", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "@type": "ClassDefinition" - }, - { - "name": "CompoundExpression", - "definition_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "@type": "ClassDefinition" - }, - { - "name": "Triple", - "definition_uri": "http://w3id.org/ontogpt/core/Triple", - "description": "Abstract parent for Relation Extraction tasks", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "CompoundExpression", - "abstract": true, - "slots": [ - "triple__subject", - "triple__predicate", - "triple__object", - "triple__qualifier", - "triple__subject_qualifier", - "triple__object_qualifier" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "predicate", - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "object", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Triple", - "@type": "ClassDefinition" - }, - { - "name": "TextWithTriples", - "definition_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "textWithTriples__publication", - "textWithTriples__triples" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "triples", - "multivalued": true, - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "@type": "ClassDefinition" - }, - { - "name": "RelationshipType", - "id_prefixes": [ - "RO", - "biolink" - ], - "definition_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "@type": "ClassDefinition" - }, - { - "name": "Publication", - "definition_uri": "http://w3id.org/ontogpt/core/Publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "publication__id", - "publication__title", - "publication__abstract", - "publication__combined_text", - "publication__full_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "description": "The publication identifier", - "@type": "SlotDefinition" - }, - { - "name": "title", - "description": "The title of the publication", - "@type": "SlotDefinition" - }, - { - "name": "abstract", - "description": "The abstract of the publication", - "@type": "SlotDefinition" - }, - { - "name": "combined_text", - "@type": "SlotDefinition" - }, - { - "name": "full_text", - "description": "The full text of the publication", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Publication", - "@type": "ClassDefinition" - }, - { - "name": "AnnotatorResult", - "definition_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "annotatorResult__subject_text", - "annotatorResult__object_id", - "annotatorResult__object_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject_text", - "@type": "SlotDefinition" - }, - { - "name": "object_id", - "@type": "SlotDefinition" - }, - { - "name": "object_text", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "@type": "ClassDefinition" - } - ], - "metamodel_version": "1.7.0", - "source_file": "ibd.yaml", - "source_file_date": "2023-06-17T15:11:19", - "source_file_size": 4869, - "generation_date": "2023-08-07T10:54:06", - "@type": "SchemaDefinition", - "@context": [ - "projects/ibd/jsonld/ibd.context.jsonld", - "https://w3id.org/linkml/types.context.jsonld", - "core.context.jsonld", - { - "@base": "http://w3id.org/ontogpt/gocam/" - } - ] -} diff --git a/projects/ibd/jsonschema/ibd.schema.json b/projects/ibd/jsonschema/ibd.schema.json deleted file mode 100644 index 8d813645b..000000000 --- a/projects/ibd/jsonschema/ibd.schema.json +++ /dev/null @@ -1,499 +0,0 @@ -{ - "$defs": { - "AnnotatorResult": { - "additionalProperties": false, - "description": "", - "properties": { - "object_id": { - "type": "string" - }, - "object_text": { - "type": "string" - }, - "subject_text": { - "type": "string" - } - }, - "title": "AnnotatorResult", - "type": "object" - }, - "Any": { - "additionalProperties": true, - "description": "", - "title": "Any", - "type": "object" - }, - "CellType": { - "description": "", - "enum": [], - "title": "CellType", - "type": "string" - }, - "CellularProcess": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "CellularProcess", - "type": "object" - }, - "ExtractionResult": { - "additionalProperties": false, - "description": "A result of extracting knowledge on text", - "properties": { - "extracted_object": { - "$ref": "#/$defs/Any", - "description": "The complex objects extracted from the text" - }, - "input_id": { - "type": "string" - }, - "input_text": { - "type": "string" - }, - "input_title": { - "type": "string" - }, - "named_entities": { - "description": "Named entities extracted from the text", - "items": { - "$ref": "#/$defs/Any" - }, - "type": "array" - }, - "prompt": { - "type": "string" - }, - "raw_completion_output": { - "type": "string" - } - }, - "title": "ExtractionResult", - "type": "object" - }, - "GOCellComponentType": { - "description": "", - "enum": [], - "title": "GOCellComponentType", - "type": "string" - }, - "Gene": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Gene", - "type": "object" - }, - "GeneGeneInteraction": { - "additionalProperties": false, - "description": "", - "properties": { - "gene1": { - "type": "string" - }, - "gene2": { - "type": "string" - } - }, - "title": "GeneGeneInteraction", - "type": "object" - }, - "GeneLocation": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "GeneLocation", - "type": "object" - }, - "GeneLocationEnum": { - "description": "", - "enum": [], - "title": "GeneLocationEnum", - "type": "string" - }, - "GeneMolecularActivityRelationship": { - "additionalProperties": false, - "description": "", - "properties": { - "gene": { - "type": "string" - }, - "molecular_activity": { - "type": "string" - } - }, - "title": "GeneMolecularActivityRelationship", - "type": "object" - }, - "GeneMolecularActivityRelationship2": { - "additionalProperties": false, - "description": "", - "properties": { - "gene": { - "type": "string" - }, - "molecular_activity": { - "type": "string" - }, - "target": { - "type": "string" - } - }, - "title": "GeneMolecularActivityRelationship2", - "type": "object" - }, - "GeneOrganismRelationship": { - "additionalProperties": false, - "description": "", - "properties": { - "gene": { - "type": "string" - }, - "organism": { - "type": "string" - } - }, - "title": "GeneOrganismRelationship", - "type": "object" - }, - "GeneSubcellularLocalizationRelationship": { - "additionalProperties": false, - "description": "", - "properties": { - "gene": { - "type": "string" - }, - "location": { - "type": "string" - } - }, - "title": "GeneSubcellularLocalizationRelationship", - "type": "object" - }, - "IBDAnnotations": { - "additionalProperties": false, - "description": "", - "properties": { - "activities": { - "description": "semicolon-separated list of molecular activities", - "items": { - "type": "string" - }, - "type": "array" - }, - "cellular_processes": { - "description": "semicolon-separated list of cellular processes", - "items": { - "type": "string" - }, - "type": "array" - }, - "gene_functions": { - "description": "semicolon-separated list of gene to molecular activity relationships", - "items": { - "$ref": "#/$defs/GeneMolecularActivityRelationship" - }, - "type": "array" - }, - "gene_gene_interactions": { - "description": "semicolon-separated list of gene to gene interactions", - "items": { - "$ref": "#/$defs/GeneGeneInteraction" - }, - "type": "array" - }, - "gene_localizations": { - "description": "semicolon-separated list of genes plus their location in the cell; for example, \"gene1 / cytoplasm; gene2 / mitochondrion\"", - "items": { - "$ref": "#/$defs/GeneSubcellularLocalizationRelationship" - }, - "type": "array" - }, - "gene_organisms": { - "items": { - "$ref": "#/$defs/GeneOrganismRelationship" - }, - "type": "array" - }, - "genes": { - "description": "semicolon-separated list of genes", - "items": { - "type": "string" - }, - "type": "array" - }, - "organisms": { - "description": "semicolon-separated list of organism taxons", - "items": { - "type": "string" - }, - "type": "array" - }, - "pathways": { - "description": "semicolon-separated list of pathways", - "items": { - "type": "string" - }, - "type": "array" - } - }, - "title": "IBDAnnotations", - "type": "object" - }, - "MolecularActivity": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "MolecularActivity", - "type": "object" - }, - "Molecule": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Molecule", - "type": "object" - }, - "NullDataOptions": { - "description": "", - "enum": [ - "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "NOT_APPLICABLE", - "NOT_MENTIONED" - ], - "title": "NullDataOptions", - "type": "string" - }, - "Organism": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Organism", - "type": "object" - }, - "Pathway": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Pathway", - "type": "object" - }, - "Publication": { - "additionalProperties": false, - "description": "", - "properties": { - "abstract": { - "description": "The abstract of the publication", - "type": "string" - }, - "combined_text": { - "type": "string" - }, - "full_text": { - "description": "The full text of the publication", - "type": "string" - }, - "id": { - "description": "The publication identifier", - "type": "string" - }, - "title": { - "description": "The title of the publication", - "type": "string" - } - }, - "title": "Publication", - "type": "object" - }, - "RelationshipType": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "RelationshipType", - "type": "object" - }, - "TextWithTriples": { - "additionalProperties": false, - "description": "", - "properties": { - "publication": { - "$ref": "#/$defs/Publication" - }, - "triples": { - "items": { - "$ref": "#/$defs/Triple" - }, - "type": "array" - } - }, - "title": "TextWithTriples", - "type": "object" - } - }, - "$id": "http://w3id.org/ontogpt/gocam", - "$schema": "http://json-schema.org/draft-07/schema#", - "additionalProperties": true, - "metamodel_version": "1.7.0", - "properties": { - "activities": { - "description": "semicolon-separated list of molecular activities", - "items": { - "type": "string" - }, - "type": "array" - }, - "cellular_processes": { - "description": "semicolon-separated list of cellular processes", - "items": { - "type": "string" - }, - "type": "array" - }, - "gene_functions": { - "description": "semicolon-separated list of gene to molecular activity relationships", - "items": { - "$ref": "#/$defs/GeneMolecularActivityRelationship" - }, - "type": "array" - }, - "gene_gene_interactions": { - "description": "semicolon-separated list of gene to gene interactions", - "items": { - "$ref": "#/$defs/GeneGeneInteraction" - }, - "type": "array" - }, - "gene_localizations": { - "description": "semicolon-separated list of genes plus their location in the cell; for example, \"gene1 / cytoplasm; gene2 / mitochondrion\"", - "items": { - "$ref": "#/$defs/GeneSubcellularLocalizationRelationship" - }, - "type": "array" - }, - "gene_organisms": { - "items": { - "$ref": "#/$defs/GeneOrganismRelationship" - }, - "type": "array" - }, - "genes": { - "description": "semicolon-separated list of genes", - "items": { - "type": "string" - }, - "type": "array" - }, - "organisms": { - "description": "semicolon-separated list of organism taxons", - "items": { - "type": "string" - }, - "type": "array" - }, - "pathways": { - "description": "semicolon-separated list of pathways", - "items": { - "type": "string" - }, - "type": "array" - } - }, - "title": "gocam-template", - "type": "object", - "version": null -} \ No newline at end of file diff --git a/projects/ibd/owl/ibd.owl.ttl b/projects/ibd/owl/ibd.owl.ttl deleted file mode 100644 index 254cfbce4..000000000 --- a/projects/ibd/owl/ibd.owl.ttl +++ /dev/null @@ -1,638 +0,0 @@ -@prefix IAO: <http://purl.obolibrary.org/obo/IAO_> . -@prefix gocam: <http://w3id.org/ontogpt/gocam/> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix owl: <http://www.w3.org/2002/07/owl#> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . -@prefix skos: <http://www.w3.org/2004/02/skos/core#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -<http://w3id.org/ontogpt/gocam> a owl:Ontology ; - rdfs:label "gocam-template" ; - IAO:0000700 <http://w3id.org/ontogpt/core/AnnotatorResult>, - <http://w3id.org/ontogpt/core/Any>, - <http://w3id.org/ontogpt/core/CompoundExpression>, - <http://w3id.org/ontogpt/core/ExtractionResult>, - <http://w3id.org/ontogpt/core/NamedEntity>, - <http://w3id.org/ontogpt/core/Publication>, - <http://w3id.org/ontogpt/core/TextWithTriples>, - gocam:IBDAnnotations ; - linkml:classes "{'IBDAnnotations': ClassDefinition(name='IBDAnnotations', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/gocam/IBDAnnotations', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['iBDAnnotations__genes', 'iBDAnnotations__organisms', 'iBDAnnotations__gene_organisms', 'iBDAnnotations__activities', 'iBDAnnotations__gene_functions', 'iBDAnnotations__cellular_processes', 'iBDAnnotations__pathways', 'iBDAnnotations__gene_gene_interactions', 'iBDAnnotations__gene_localizations'], slot_usage={}, attributes={'genes': SlotDefinition(name='genes', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of genes', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'organisms': SlotDefinition(name='organisms', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of organism taxons', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Organism', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'gene_organisms': SlotDefinition(name='gene_organisms', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of asterisk separated gene to organism relationships', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneOrganismRelationship', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'activities': SlotDefinition(name='activities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of molecular activities', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='MolecularActivity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'gene_functions': SlotDefinition(name='gene_functions', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of gene to molecular activity relationships', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneMolecularActivityRelationship', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'cellular_processes': SlotDefinition(name='cellular_processes', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of cellular processes', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='CellularProcess', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'pathways': SlotDefinition(name='pathways', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of pathways', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Pathway', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'gene_gene_interactions': SlotDefinition(name='gene_gene_interactions', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of gene to gene interactions', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneGeneInteraction', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'gene_localizations': SlotDefinition(name='gene_localizations', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of genes plus their location in the cell; for example, \"gene1 / cytoplasm; gene2 / mitochondrion\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneSubcellularLocalizationRelationship', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='gocam:IBDAnnotations', subclass_of=None, union_of=[], defining_slots=[], tree_root=True, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Gene': ClassDefinition(name='Gene', id_prefixes=['HGNC', 'PR', 'UniProtKB'], definition_uri='http://w3id.org/ontogpt/gocam/Gene', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='gilda:, bioportal:hgnc-nr', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='gocam:Gene', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Pathway': ClassDefinition(name='Pathway', id_prefixes=['GO', 'PW'], definition_uri='http://w3id.org/ontogpt/gocam/Pathway', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:go, sqlite:obo:pw', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='gocam:Pathway', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'CellularProcess': ClassDefinition(name='CellularProcess', id_prefixes=['GO'], definition_uri='http://w3id.org/ontogpt/gocam/CellularProcess', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:go', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='gocam:CellularProcess', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'MolecularActivity': ClassDefinition(name='MolecularActivity', id_prefixes=['GO'], definition_uri='http://w3id.org/ontogpt/gocam/MolecularActivity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:go', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='gocam:MolecularActivity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'GeneLocation': ClassDefinition(name='GeneLocation', id_prefixes=['GO', 'CL', 'UBERON'], definition_uri='http://w3id.org/ontogpt/gocam/GeneLocation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:go, sqlite:obo:cl', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__label', 'GeneLocation_id'], slot_usage={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='namedEntity__id', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=['GOCellComponentType', 'CellType'], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='gocam:GeneLocation', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Organism': ClassDefinition(name='Organism', id_prefixes=['NCBITaxon', 'EFO'], definition_uri='http://w3id.org/ontogpt/gocam/Organism', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='gilda:, sqlite:obo:ncbitaxon', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='gocam:Organism', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Molecule': ClassDefinition(name='Molecule', id_prefixes=['CHEBI', 'PR'], definition_uri='http://w3id.org/ontogpt/gocam/Molecule', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='gilda:, sqlite:obo:chebi', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='gocam:Molecule', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'GeneOrganismRelationship': ClassDefinition(name='GeneOrganismRelationship', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/gocam/GeneOrganismRelationship', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['geneOrganismRelationship__gene', 'geneOrganismRelationship__organism'], slot_usage={}, attributes={'gene': SlotDefinition(name='gene', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'organism': SlotDefinition(name='organism', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Organism', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='gocam:GeneOrganismRelationship', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'GeneMolecularActivityRelationship': ClassDefinition(name='GeneMolecularActivityRelationship', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/gocam/GeneMolecularActivityRelationship', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.example': Annotation(tag='prompt.example', value='TODO\\n\\ngene: HGNC:1234\\nmolecular_activity: GO:0003674', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['geneMolecularActivityRelationship__gene', 'geneMolecularActivityRelationship__molecular_activity'], slot_usage={}, attributes={'gene': SlotDefinition(name='gene', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='the name of the gene in the pair. This comes first.', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'molecular_activity': SlotDefinition(name='molecular_activity', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='the name of the molecular function in the pair. This comes second. May be a GO term.', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='MolecularActivity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='gocam:GeneMolecularActivityRelationship', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'GeneMolecularActivityRelationship2': ClassDefinition(name='GeneMolecularActivityRelationship2', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/gocam/GeneMolecularActivityRelationship2', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['geneMolecularActivityRelationship2__gene', 'geneMolecularActivityRelationship2__molecular_activity', 'geneMolecularActivityRelationship2__target'], slot_usage={}, attributes={'gene': SlotDefinition(name='gene', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='the name of the gene.', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'molecular_activity': SlotDefinition(name='molecular_activity', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='the name of the molecular activity, for example, ubiquitination. May be a GO term.', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='MolecularActivity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'target': SlotDefinition(name='target', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='the name of the molecular entity that is the target of the molecular activity.', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Molecule', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='gocam:GeneMolecularActivityRelationship2', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'GeneSubcellularLocalizationRelationship': ClassDefinition(name='GeneSubcellularLocalizationRelationship', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/gocam/GeneSubcellularLocalizationRelationship', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['geneSubcellularLocalizationRelationship__gene', 'geneSubcellularLocalizationRelationship__location'], slot_usage={}, attributes={'gene': SlotDefinition(name='gene', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'location': SlotDefinition(name='location', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneLocation', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='gocam:GeneSubcellularLocalizationRelationship', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'GeneGeneInteraction': ClassDefinition(name='GeneGeneInteraction', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/gocam/GeneGeneInteraction', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['geneGeneInteraction__gene1', 'geneGeneInteraction__gene2'], slot_usage={}, attributes={'gene1': SlotDefinition(name='gene1', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'gene2': SlotDefinition(name='gene2', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='gocam:GeneGeneInteraction', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Any': ClassDefinition(name='Any', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Any', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=['linkml:Any'], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='linkml:Any', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ExtractionResult': ClassDefinition(name='ExtractionResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/ExtractionResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A result of extracting knowledge on text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['extractionResult__input_id', 'extractionResult__input_title', 'extractionResult__input_text', 'extractionResult__raw_completion_output', 'extractionResult__prompt', 'extractionResult__extracted_object', 'extractionResult__named_entities'], slot_usage={}, attributes={'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:ExtractionResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'NamedEntity': ClassDefinition(name='NamedEntity', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NamedEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:NamedEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'CompoundExpression': ClassDefinition(name='CompoundExpression', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/CompoundExpression', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='core:CompoundExpression', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Triple': ClassDefinition(name='Triple', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Triple', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Abstract parent for Relation Extraction tasks', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['triple__subject', 'triple__predicate', 'triple__object', 'triple__qualifier', 'triple__subject_qualifier', 'triple__object_qualifier'], slot_usage={}, attributes={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Triple', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'TextWithTriples': ClassDefinition(name='TextWithTriples', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/TextWithTriples', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['textWithTriples__publication', 'textWithTriples__triples'], slot_usage={}, attributes={'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:TextWithTriples', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'RelationshipType': ClassDefinition(name='RelationshipType', id_prefixes=['RO', 'biolink'], definition_uri='http://w3id.org/ontogpt/core/RelationshipType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='core:RelationshipType', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Publication': ClassDefinition(name='Publication', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Publication', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['publication__id', 'publication__title', 'publication__abstract', 'publication__combined_text', 'publication__full_text'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Publication', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'AnnotatorResult': ClassDefinition(name='AnnotatorResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/AnnotatorResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['annotatorResult__subject_text', 'annotatorResult__object_id', 'annotatorResult__object_text'], slot_usage={}, attributes={'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:AnnotatorResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={})}" ; - linkml:enums "{'GeneLocationEnum': EnumDefinition(name='GeneLocationEnum', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/gocam/GeneLocationEnum', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={}, include=[], minus=[], inherits=['GOCellComponent', 'CellType'], reachable_from=None, matches=None, concepts=[]), 'GOCellComponentType': EnumDefinition(name='GOCellComponentType', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/gocam/GOCellComponentType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={}, include=[], minus=[], inherits=[], reachable_from=ReachabilityQuery(source_ontology='obo:go', source_nodes=['GO:0005575'], relationship_types=[], is_direct=None, include_self=None, traverse_up=None), matches=None, concepts=[]), 'CellType': EnumDefinition(name='CellType', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/gocam/CellType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={}, include=[], minus=[], inherits=[], reachable_from=ReachabilityQuery(source_ontology='obo:cl', source_nodes=['CL:0000000'], relationship_types=[], is_direct=None, include_self=None, traverse_up=None), matches=None, concepts=[]), 'NullDataOptions': EnumDefinition(name='NullDataOptions', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NullDataOptions', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'UNSPECIFIED_METHOD_OF_ADMINISTRATION': PermissibleValue(text='UNSPECIFIED_METHOD_OF_ADMINISTRATION', description=None, meaning='NCIT:C149701', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_APPLICABLE': PermissibleValue(text='NOT_APPLICABLE', description=None, meaning='NCIT:C18902', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['not applicable', 'N/A'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_MENTIONED': PermissibleValue(text='NOT_MENTIONED', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[])}" ; - linkml:id "http://w3id.org/ontogpt/gocam" ; - linkml:imports "core", - "linkml:types" ; - linkml:types "{'string': TypeDefinition(name='string', id_prefixes=[], definition_uri='https://w3id.org/linkml/String', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A character string', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Text'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'integer': TypeDefinition(name='integer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Integer', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An integer', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Integer'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='int', uri='xsd:integer', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'boolean': TypeDefinition(name='boolean', id_prefixes=[], definition_uri='https://w3id.org/linkml/Boolean', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A binary (true or false) value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Boolean'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Bool', uri='xsd:boolean', repr='bool', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'float': TypeDefinition(name='float', id_prefixes=[], definition_uri='https://w3id.org/linkml/Float', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:float specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Float'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:float', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'double': TypeDefinition(name='double', id_prefixes=[], definition_uri='https://w3id.org/linkml/Double', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:double specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:Float'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:double', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'decimal': TypeDefinition(name='decimal', id_prefixes=[], definition_uri='https://w3id.org/linkml/Decimal', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number with arbitrary precision that conforms to the xsd:decimal specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=['schema:Number'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Decimal', uri='xsd:decimal', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'time': TypeDefinition(name='time', id_prefixes=[], definition_uri='https://w3id.org/linkml/Time', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A time object represents a (local) time of day, independent of any particular day', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=['URI is dateTime because OWL reasoners do not work with straight date or time'], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Time'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDTime', uri='xsd:time', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date': TypeDefinition(name='date', id_prefixes=[], definition_uri='https://w3id.org/linkml/Date', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a date (year, month and day) in an idealized calendar', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[\"URI is dateTime because OWL reasoners don't work with straight date or time\"], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Date'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDate', uri='xsd:date', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'datetime': TypeDefinition(name='datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/Datetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The combination of a date and time', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:DateTime'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDateTime', uri='xsd:dateTime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date_or_datetime': TypeDefinition(name='date_or_datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/DateOrDatetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Either a date or a datetime', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='linkml:DateOrDatetime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uriorcurie': TypeDefinition(name='uriorcurie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uriorcurie', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a URI or a CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URIorCURIE', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'curie': TypeDefinition(name='curie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Curie', local_names={}, conforms_to='https://www.w3.org/TR/curie/', implements=[], extensions={}, annotations={}, description='a compact URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations this MUST be expanded to a URI', 'in non-RDF serializations MAY be serialized as the compact representation'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Curie', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uri': TypeDefinition(name='uri', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uri', local_names={}, conforms_to='https://www.ietf.org/rfc/rfc3987.txt', implements=[], extensions={}, annotations={}, description='a complete URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:URL'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URI', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ncname': TypeDefinition(name='ncname', id_prefixes=[], definition_uri='https://w3id.org/linkml/Ncname', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Prefix part of CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NCName', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'objectidentifier': TypeDefinition(name='objectidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Objectidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI or CURIE that represents an object in the model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['Used for inheritance and type checking'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='ElementIdentifier', uri='shex:iri', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'nodeidentifier': TypeDefinition(name='nodeidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Nodeidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI, CURIE or BNODE that represents a node in a model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NodeIdentifier', uri='shex:nonLiteral', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpointer': TypeDefinition(name='jsonpointer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpointer', local_names={}, conforms_to='https://datatracker.ietf.org/doc/html/rfc6901', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpath': TypeDefinition(name='jsonpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpath', local_names={}, conforms_to='https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sparqlpath': TypeDefinition(name='sparqlpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Sparqlpath', local_names={}, conforms_to='https://www.w3.org/TR/sparql11-query/#propertypaths', implements=[], extensions={}, annotations={}, description='A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -gocam:CellType a owl:Class, - linkml:EnumDefinition ; - rdfs:label "CellType" ; - owl:unionOf [ rdf:rest () ] . - -gocam:GOCellComponentType a owl:Class, - linkml:EnumDefinition ; - rdfs:label "GOCellComponentType" ; - owl:unionOf [ rdf:rest () ] . - -gocam:GeneLocationEnum a owl:Class, - linkml:EnumDefinition ; - rdfs:label "GeneLocationEnum" ; - owl:unionOf [ rdf:rest () ] . - -gocam:GeneMolecularActivityRelationship2 a owl:Class, - linkml:ClassDefinition ; - rdfs:label "GeneMolecularActivityRelationship2" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass gocam:MolecularActivity ; - owl:onProperty gocam:molecular_activity ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass gocam:Gene ; - owl:onProperty gocam:gene ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass gocam:Molecule ; - owl:onProperty gocam:target ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - linkml:attributes "{'gene': SlotDefinition(name='gene', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='the name of the gene.', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'molecular_activity': SlotDefinition(name='molecular_activity', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='the name of the molecular activity, for example, ubiquitination. May be a GO term.', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='MolecularActivity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'target': SlotDefinition(name='target', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='the name of the molecular entity that is the target of the molecular activity.', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Molecule', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -linkml:SubsetDefinition a owl:Class ; - rdfs:label "subset_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" . - -linkml:TypeDefinition a owl:Class ; - rdfs:label "type_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" ; - linkml:mixins "type_expression" . - -linkml:topValue a owl:DatatypeProperty ; - rdfs:label "value" . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "AnnotatorResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_text> ] ; - linkml:attributes "{'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/ExtractionResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ExtractionResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/prompt> ], - [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/named_entities> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/extracted_object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_title> ] ; - skos:definition "A result of extracting knowledge on text" ; - linkml:attributes "{'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/TextWithTriples> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TextWithTriples" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Triple> ; - owl:onProperty <http://w3id.org/ontogpt/core/triples> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Publication> ; - owl:onProperty <http://w3id.org/ontogpt/core/publication> ] ; - linkml:attributes "{'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/abstract> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "abstract" ; - rdfs:range linkml:String ; - skos:definition "The abstract of the publication" . - -<http://w3id.org/ontogpt/core/combined_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "combined_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/extracted_object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "extracted_object" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "The complex objects extracted from the text" . - -<http://w3id.org/ontogpt/core/full_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "full_text" ; - rdfs:range linkml:String ; - skos:definition "The full text of the publication" . - -<http://w3id.org/ontogpt/core/input_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_title" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/named_entities> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "named_entities" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "Named entities extracted from the text" . - -<http://w3id.org/ontogpt/core/object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/object_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/object_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" . - -<http://w3id.org/ontogpt/core/object_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/predicate> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "predicate" ; - rdfs:range <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/prompt> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "prompt" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/publication> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "publication" ; - gocam:prompt.skip "true" ; - rdfs:range <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "qualifier" ; - rdfs:range linkml:String ; - skos:definition "A qualifier for the statements, e.g. \"NOT\" for negation" . - -<http://w3id.org/ontogpt/core/raw_completion_output> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "raw_completion_output" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/subject> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/subject_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" . - -<http://w3id.org/ontogpt/core/subject_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "title" ; - rdfs:range linkml:String ; - skos:definition "The title of the publication" . - -<http://w3id.org/ontogpt/core/triples> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "triples" ; - rdfs:range <http://w3id.org/ontogpt/core/Triple> . - -gocam:IBDAnnotations a owl:Class, - linkml:ClassDefinition ; - rdfs:label "IBDAnnotations" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom gocam:MolecularActivity ; - owl:onProperty gocam:activities ], - [ a owl:Restriction ; - owl:allValuesFrom gocam:GeneOrganismRelationship ; - owl:onProperty gocam:gene_organisms ], - [ a owl:Restriction ; - owl:allValuesFrom gocam:GeneGeneInteraction ; - owl:onProperty gocam:gene_gene_interactions ], - [ a owl:Restriction ; - owl:allValuesFrom gocam:Pathway ; - owl:onProperty gocam:pathways ], - [ a owl:Restriction ; - owl:allValuesFrom gocam:GeneMolecularActivityRelationship ; - owl:onProperty gocam:gene_functions ], - [ a owl:Restriction ; - owl:allValuesFrom gocam:Gene ; - owl:onProperty gocam:genes ], - [ a owl:Restriction ; - owl:allValuesFrom gocam:Organism ; - owl:onProperty gocam:organisms ], - [ a owl:Restriction ; - owl:allValuesFrom gocam:CellularProcess ; - owl:onProperty gocam:cellular_processes ], - [ a owl:Restriction ; - owl:allValuesFrom gocam:GeneSubcellularLocalizationRelationship ; - owl:onProperty gocam:gene_localizations ] ; - linkml:attributes "{'genes': SlotDefinition(name='genes', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of genes', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'organisms': SlotDefinition(name='organisms', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of organism taxons', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Organism', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'gene_organisms': SlotDefinition(name='gene_organisms', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of asterisk separated gene to organism relationships', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneOrganismRelationship', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'activities': SlotDefinition(name='activities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of molecular activities', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='MolecularActivity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'gene_functions': SlotDefinition(name='gene_functions', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of gene to molecular activity relationships', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneMolecularActivityRelationship', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'cellular_processes': SlotDefinition(name='cellular_processes', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of cellular processes', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='CellularProcess', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'pathways': SlotDefinition(name='pathways', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of pathways', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Pathway', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'gene_gene_interactions': SlotDefinition(name='gene_gene_interactions', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of gene to gene interactions', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneGeneInteraction', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'gene_localizations': SlotDefinition(name='gene_localizations', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of genes plus their location in the cell; for example, \"gene1 / cytoplasm; gene2 / mitochondrion\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneSubcellularLocalizationRelationship', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -gocam:activities a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "activities" ; - rdfs:range gocam:MolecularActivity ; - skos:definition "semicolon-separated list of molecular activities" . - -gocam:cellular_processes a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "cellular_processes" ; - rdfs:range gocam:CellularProcess ; - skos:definition "semicolon-separated list of cellular processes" . - -gocam:gene1 a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "gene1" ; - rdfs:range gocam:Gene . - -gocam:gene2 a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "gene2" ; - rdfs:range gocam:Gene . - -gocam:gene_functions a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "gene_functions" ; - rdfs:range gocam:GeneMolecularActivityRelationship ; - skos:definition "semicolon-separated list of gene to molecular activity relationships" . - -gocam:gene_gene_interactions a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "gene_gene_interactions" ; - rdfs:range gocam:GeneGeneInteraction ; - skos:definition "semicolon-separated list of gene to gene interactions" . - -gocam:gene_localizations a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "gene_localizations" ; - rdfs:range gocam:GeneSubcellularLocalizationRelationship ; - skos:definition "semicolon-separated list of genes plus their location in the cell; for example, \"gene1 / cytoplasm; gene2 / mitochondrion\"" . - -gocam:gene_organisms a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "gene_organisms" ; - gocam:prompt "semicolon-separated list of asterisk separated gene to organism relationships" ; - rdfs:range gocam:GeneOrganismRelationship . - -gocam:genes a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "genes" ; - rdfs:range gocam:Gene ; - skos:definition "semicolon-separated list of genes" . - -gocam:id a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "id" ; - rdfs:domain gocam:GeneLocation ; - rdfs:range linkml:String ; - rdfs:subPropertyOf <http://w3id.org/ontogpt/core/id> ; - linkml:is_a "namedEntity__id" . - -gocam:location a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "location" ; - rdfs:range gocam:GeneLocation . - -gocam:organism a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "organism" ; - rdfs:range gocam:Organism . - -gocam:organisms a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "organisms" ; - rdfs:range gocam:Organism ; - skos:definition "semicolon-separated list of organism taxons" . - -gocam:pathways a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "pathways" ; - rdfs:range gocam:Pathway ; - skos:definition "semicolon-separated list of pathways" . - -gocam:target a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "target" ; - gocam:prompt "the name of the molecular entity that is the target of the molecular activity." ; - rdfs:range gocam:Molecule . - -<http://example.org/UNKNOWN/rdfs/label> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "label" ; - gocam:owl "AnnotationProperty, AnnotationAssertion" ; - rdfs:range linkml:String ; - skos:altLabel "name" ; - skos:definition "The label (name) of the named thing" ; - skos:exactMatch <http://example.org/UNKNOWN/rdfs/label> . - -<http://purl.obolibrary.org/obo/NCIT_C149701> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "UNSPECIFIED_METHOD_OF_ADMINISTRATION" . - -<http://purl.obolibrary.org/obo/NCIT_C18902> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_APPLICABLE" . - -<http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_MENTIONED" . - -<http://w3id.org/ontogpt/core/RelationshipType> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "RelationshipType" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/Triple> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Triple" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/RelationshipType> ; - owl:onProperty <http://w3id.org/ontogpt/core/predicate> ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - skos:definition "Abstract parent for Relation Extraction tasks" ; - linkml:attributes "{'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -gocam:CellularProcess a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CellularProcess" ; - gocam:annotators "sqlite:obo:go" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -gocam:GeneGeneInteraction a owl:Class, - linkml:ClassDefinition ; - rdfs:label "GeneGeneInteraction" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass gocam:Gene ; - owl:onProperty gocam:gene1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass gocam:Gene ; - owl:onProperty gocam:gene2 ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - linkml:attributes "{'gene1': SlotDefinition(name='gene1', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'gene2': SlotDefinition(name='gene2', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -gocam:GeneMolecularActivityRelationship a owl:Class, - linkml:ClassDefinition ; - rdfs:label "GeneMolecularActivityRelationship" ; - gocam:prompt.example """TODO - -gene: HGNC:1234 -molecular_activity: GO:0003674""" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass gocam:Gene ; - owl:onProperty gocam:gene ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass gocam:MolecularActivity ; - owl:onProperty gocam:molecular_activity ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - linkml:attributes "{'gene': SlotDefinition(name='gene', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='the name of the gene in the pair. This comes first.', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'molecular_activity': SlotDefinition(name='molecular_activity', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='the name of the molecular function in the pair. This comes second. May be a GO term.', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='MolecularActivity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -gocam:GeneOrganismRelationship a owl:Class, - linkml:ClassDefinition ; - rdfs:label "GeneOrganismRelationship" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass gocam:Organism ; - owl:onProperty gocam:organism ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass gocam:Gene ; - owl:onProperty gocam:gene ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - linkml:attributes "{'gene': SlotDefinition(name='gene', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'organism': SlotDefinition(name='organism', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Organism', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -gocam:GeneSubcellularLocalizationRelationship a owl:Class, - linkml:ClassDefinition ; - rdfs:label "GeneSubcellularLocalizationRelationship" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass gocam:GeneLocation ; - owl:onProperty gocam:location ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass gocam:Gene ; - owl:onProperty gocam:gene ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - linkml:attributes "{'gene': SlotDefinition(name='gene', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'location': SlotDefinition(name='location', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneLocation', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -gocam:Molecule a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Molecule" ; - gocam:annotators "gilda:, sqlite:obo:chebi" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -gocam:Pathway a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Pathway" ; - gocam:annotators "sqlite:obo:go, sqlite:obo:pw" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -gocam:molecular_activity a owl:ObjectProperty, - linkml:SlotDefinition . - -<http://w3id.org/ontogpt/core/NullDataOptions> a owl:Class, - linkml:EnumDefinition ; - rdfs:label "NullDataOptions" ; - owl:unionOf ( <http://purl.obolibrary.org/obo/NCIT_C149701> <http://purl.obolibrary.org/obo/NCIT_C18902> <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> ) ; - linkml:permissible_values <http://purl.obolibrary.org/obo/NCIT_C149701>, - <http://purl.obolibrary.org/obo/NCIT_C18902>, - <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> . - -<http://w3id.org/ontogpt/core/Publication> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Publication" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/abstract> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/combined_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/title> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/full_text> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/id> a owl:ObjectProperty, - linkml:SlotDefinition . - -gocam:GeneLocation a owl:Class, - linkml:ClassDefinition ; - rdfs:label "GeneLocation" ; - gocam:annotators "sqlite:obo:go, sqlite:obo:cl" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty gocam:id ; - owl:qualifiedCardinality 1 ], - <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -gocam:MolecularActivity a owl:Class, - linkml:ClassDefinition ; - rdfs:label "MolecularActivity" ; - gocam:annotators "sqlite:obo:go" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -gocam:Organism a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Organism" ; - gocam:annotators "gilda:, sqlite:obo:ncbitaxon" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -gocam:gene a owl:ObjectProperty, - linkml:SlotDefinition . - -<http://w3id.org/ontogpt/core/Any> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Any" ; - skos:exactMatch linkml:Any ; - linkml:attributes "{}" . - -<http://w3id.org/ontogpt/core/CompoundExpression> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CompoundExpression" ; - linkml:attributes "{}" . - -gocam:Gene a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Gene" ; - gocam:annotators "gilda:, bioportal:hgnc-nr" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/NamedEntity> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "NamedEntity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://example.org/UNKNOWN/rdfs/label> ], - [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ; - owl:qualifiedCardinality 1 ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:ClassDefinition a owl:Class ; - rdfs:label "class_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "class_expression" . - -linkml:SlotDefinition a owl:Class ; - rdfs:label "slot_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "slot_expression" . - - diff --git a/projects/ibd/prefixmap/ibd.yaml b/projects/ibd/prefixmap/ibd.yaml deleted file mode 100644 index e38e646ee..000000000 --- a/projects/ibd/prefixmap/ibd.yaml +++ /dev/null @@ -1,45 +0,0 @@ -{ - "CHEBI": "http://example.org/UNKNOWN/CHEBI/", - "CL": "http://purl.obolibrary.org/obo/CL_", - "EFO": "http://example.org/UNKNOWN/EFO/", - "GO": "http://purl.obolibrary.org/obo/GO_", - "HGNC": "http://example.org/UNKNOWN/HGNC/", - "NCBITaxon": "http://example.org/UNKNOWN/NCBITaxon/", - "PR": "http://example.org/UNKNOWN/PR/", - "PW": "http://example.org/UNKNOWN/PW/", - "RO": "http://purl.obolibrary.org/obo/RO_", - "UBERON": "http://example.org/UNKNOWN/UBERON/", - "UniProtKB": "http://example.org/UNKNOWN/UniProtKB/", - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "gocam": "http://w3id.org/ontogpt/gocam/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } -} diff --git a/projects/ibd/protobuf/ibd.proto b/projects/ibd/protobuf/ibd.proto deleted file mode 100644 index d4e73bcc6..000000000 --- a/projects/ibd/protobuf/ibd.proto +++ /dev/null @@ -1,108 +0,0 @@ -message AnnotatorResult - { - string subjectText = 0 - string objectId = 0 - string objectText = 0 - } -message CellularProcess - { - string id = 0 - string label = 0 - } -// A result of extracting knowledge on text -message ExtractionResult - { - string inputId = 0 - string inputTitle = 0 - string inputText = 0 - string rawCompletionOutput = 0 - string prompt = 0 - any extractedObject = 0 - repeated any namedEntities = 0 - } -message Gene - { - string id = 0 - string label = 0 - } -message GeneGeneInteraction - { - gene gene1 = 0 - gene gene2 = 0 - } -message GeneLocation - { - string label = 0 - string id = 0 - } -message GeneMolecularActivityRelationship - { - gene gene = 0 - molecularActivity molecularActivity = 0 - } -message GeneMolecularActivityRelationship2 - { - gene gene = 0 - molecularActivity molecularActivity = 0 - molecule target = 0 - } -message GeneOrganismRelationship - { - gene gene = 0 - organism organism = 0 - } -message GeneSubcellularLocalizationRelationship - { - gene gene = 0 - geneLocation location = 0 - } -message IBDAnnotations - { - repeated gene genes = 0 - repeated organism organisms = 0 - repeated geneOrganismRelationship geneOrganisms = 0 - repeated molecularActivity activities = 0 - repeated geneMolecularActivityRelationship geneFunctions = 0 - repeated cellularProcess cellularProcesses = 0 - repeated pathway pathways = 0 - repeated geneGeneInteraction geneGeneInteractions = 0 - repeated geneSubcellularLocalizationRelationship geneLocalizations = 0 - } -message MolecularActivity - { - string id = 0 - string label = 0 - } -message Molecule - { - string id = 0 - string label = 0 - } -message Organism - { - string id = 0 - string label = 0 - } -message Pathway - { - string id = 0 - string label = 0 - } -message Publication - { - string id = 0 - string title = 0 - string abstract = 0 - string combinedText = 0 - string fullText = 0 - } -message RelationshipType - { - string id = 0 - string label = 0 - } -message TextWithTriples - { - publication publication = 0 - repeated triple triples = 0 - } diff --git a/projects/ibd/shacl/ibd.shacl.ttl b/projects/ibd/shacl/ibd.shacl.ttl deleted file mode 100644 index 623a2bd88..000000000 --- a/projects/ibd/shacl/ibd.shacl.ttl +++ /dev/null @@ -1,391 +0,0 @@ -@prefix gocam: <http://w3id.org/ontogpt/gocam/> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix sh: <http://www.w3.org/ns/shacl#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject_text> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object_text> ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/object_id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/AnnotatorResult> . - -<http://w3id.org/ontogpt/core/CompoundExpression> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass <http://w3id.org/ontogpt/core/CompoundExpression> . - -<http://w3id.org/ontogpt/core/ExtractionResult> a sh:NodeShape ; - sh:closed true ; - sh:description "A result of extracting knowledge on text" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class linkml:Any ; - sh:description "Named entities extracted from the text" ; - sh:nodeKind sh:BlankNode ; - sh:order 6 ; - sh:path <http://w3id.org/ontogpt/core/named_entities> ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/input_title> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/input_text> ], - [ sh:class linkml:Any ; - sh:description "The complex objects extracted from the text" ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/extracted_object> ], - [ sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/prompt> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/input_id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/ExtractionResult> . - -<http://w3id.org/ontogpt/core/TextWithTriples> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/Triple> ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/triples> ], - [ sh:class <http://w3id.org/ontogpt/core/Publication> ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/publication> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/TextWithTriples> . - -gocam:GeneMolecularActivityRelationship2 a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class gocam:Gene ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path gocam:gene ], - [ sh:class gocam:MolecularActivity ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path gocam:molecular_activity ], - [ sh:class gocam:Molecule ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path gocam:target ] ; - sh:targetClass gocam:GeneMolecularActivityRelationship2 . - -gocam:IBDAnnotations a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class gocam:GeneSubcellularLocalizationRelationship ; - sh:description "semicolon-separated list of genes plus their location in the cell; for example, \"gene1 / cytoplasm; gene2 / mitochondrion\"" ; - sh:nodeKind sh:BlankNode ; - sh:order 8 ; - sh:path gocam:gene_localizations ], - [ sh:class gocam:Gene ; - sh:description "semicolon-separated list of genes" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path gocam:genes ], - [ sh:class gocam:CellularProcess ; - sh:description "semicolon-separated list of cellular processes" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path gocam:cellular_processes ], - [ sh:class gocam:Organism ; - sh:description "semicolon-separated list of organism taxons" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path gocam:organisms ], - [ sh:class gocam:GeneGeneInteraction ; - sh:description "semicolon-separated list of gene to gene interactions" ; - sh:nodeKind sh:BlankNode ; - sh:order 7 ; - sh:path gocam:gene_gene_interactions ], - [ sh:class gocam:Pathway ; - sh:description "semicolon-separated list of pathways" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path gocam:pathways ], - [ sh:class gocam:GeneMolecularActivityRelationship ; - sh:description "semicolon-separated list of gene to molecular activity relationships" ; - sh:nodeKind sh:BlankNode ; - sh:order 4 ; - sh:path gocam:gene_functions ], - [ sh:class gocam:MolecularActivity ; - sh:description "semicolon-separated list of molecular activities" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path gocam:activities ], - [ sh:class gocam:GeneOrganismRelationship ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path gocam:gene_organisms ] ; - sh:targetClass gocam:IBDAnnotations . - -<http://w3id.org/ontogpt/core/Publication> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The title of the publication" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/title> ], - [ sh:description "The abstract of the publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/abstract> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/combined_text> ], - [ sh:description "The full text of the publication" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/full_text> ], - [ sh:description "The publication identifier" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/RelationshipType> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/Triple> a sh:NodeShape ; - sh:closed false ; - sh:description "Abstract parent for Relation Extraction tasks" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A qualifier for the statements, e.g. \"NOT\" for negation" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/object_qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/RelationshipType> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/predicate> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Triple> . - -gocam:CellularProcess a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass gocam:CellularProcess . - -gocam:GeneGeneInteraction a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class gocam:Gene ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path gocam:gene1 ], - [ sh:class gocam:Gene ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path gocam:gene2 ] ; - sh:targetClass gocam:GeneGeneInteraction . - -gocam:GeneLocation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass gocam:GeneLocation . - -gocam:GeneMolecularActivityRelationship a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class gocam:MolecularActivity ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path gocam:molecular_activity ], - [ sh:class gocam:Gene ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path gocam:gene ] ; - sh:targetClass gocam:GeneMolecularActivityRelationship . - -gocam:GeneOrganismRelationship a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class gocam:Organism ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path gocam:organism ], - [ sh:class gocam:Gene ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path gocam:gene ] ; - sh:targetClass gocam:GeneOrganismRelationship . - -gocam:GeneSubcellularLocalizationRelationship a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class gocam:Gene ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path gocam:gene ], - [ sh:class gocam:GeneLocation ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path gocam:location ] ; - sh:targetClass gocam:GeneSubcellularLocalizationRelationship . - -gocam:Molecule a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass gocam:Molecule . - -gocam:Pathway a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass gocam:Pathway . - -gocam:Organism a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass gocam:Organism . - -linkml:Any a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass linkml:Any . - -gocam:MolecularActivity a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass gocam:MolecularActivity . - -<http://w3id.org/ontogpt/core/NamedEntity> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/NamedEntity> . - -gocam:Gene a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass gocam:Gene . - diff --git a/projects/ibd/shex/ibd.shex b/projects/ibd/shex/ibd.shex deleted file mode 100644 index 90266fb11..000000000 --- a/projects/ibd/shex/ibd.shex +++ /dev/null @@ -1,260 +0,0 @@ -BASE <http://w3id.org/ontogpt/gocam/> -PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> -PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> -PREFIX linkml: <https://w3id.org/linkml/> -PREFIX core: <http://w3id.org/ontogpt/core/> -PREFIX rdfs1: <http://example.org/UNKNOWN/rdfs/> - - -linkml:String xsd:string - -linkml:Integer xsd:integer - -linkml:Boolean xsd:boolean - -linkml:Float xsd:float - -linkml:Double xsd:double - -linkml:Decimal xsd:decimal - -linkml:Time xsd:time - -linkml:Date xsd:date - -linkml:Datetime xsd:dateTime - -linkml:DateOrDatetime linkml:DateOrDatetime - -linkml:Uriorcurie IRI - -linkml:Curie xsd:string - -linkml:Uri IRI - -linkml:Ncname xsd:string - -linkml:Objectidentifier IRI - -linkml:Nodeidentifier NONLITERAL - -linkml:Jsonpointer xsd:string - -linkml:Jsonpath xsd:string - -linkml:Sparqlpath xsd:string - -core:AnnotatorResult CLOSED { - ( $core:AnnotatorResult_tes ( core:subject_text @linkml:String ? ; - core:object_id @linkml:String ? ; - core:object_text @linkml:String ? - ) ; - rdf:type [ core:AnnotatorResult ] ? - ) -} - -core:Any CLOSED { - ( $core:Any_tes rdf:type . * ; - rdf:type [ linkml:Any ] ? - ) -} - -<CellularProcess> CLOSED { - ( $<CellularProcess_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <CellularProcess> ] - ) -} - -core:CompoundExpression ( - @<GeneGeneInteraction> OR @<GeneMolecularActivityRelationship> OR @<GeneMolecularActivityRelationship2> OR - @<GeneOrganismRelationship> OR @<GeneSubcellularLocalizationRelationship> OR @core:Triple -) - -core:CompoundExpression_struct { - ( $core:CompoundExpression_tes rdf:type . * ; - rdf:type [ core:CompoundExpression ] ? - ) -} - -core:ExtractionResult CLOSED { - ( $core:ExtractionResult_tes ( core:input_id @linkml:String ? ; - core:input_title @linkml:String ? ; - core:input_text @linkml:String ? ; - core:raw_completion_output @linkml:String ? ; - core:prompt @linkml:String ? ; - core:extracted_object @core:Any ? ; - core:named_entities @core:Any * - ) ; - rdf:type [ core:ExtractionResult ] ? - ) -} - -<Gene> CLOSED { - ( $<Gene_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Gene> ] - ) -} - -<GeneGeneInteraction> CLOSED { - ( $<GeneGeneInteraction_tes> ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - <gene1> @<Gene> ? ; - <gene2> @<Gene> ? - ) ; - rdf:type [ <GeneGeneInteraction> ] ? - ) -} - -<GeneLocation> CLOSED { - ( $<GeneLocation_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <GeneLocation> ] - ) -} - -<GeneMolecularActivityRelationship> CLOSED { - ( $<GeneMolecularActivityRelationship_tes> ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - <gene> @<Gene> ? ; - <molecular_activity> @<MolecularActivity> ? - ) ; - rdf:type [ <GeneMolecularActivityRelationship> ] ? - ) -} - -<GeneMolecularActivityRelationship2> CLOSED { - ( $<GeneMolecularActivityRelationship2_tes> ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - <gene> @<Gene> ? ; - <molecular_activity> @<MolecularActivity> ? ; - <target> @<Molecule> ? - ) ; - rdf:type [ <GeneMolecularActivityRelationship2> ] ? - ) -} - -<GeneOrganismRelationship> CLOSED { - ( $<GeneOrganismRelationship_tes> ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - <gene> @<Gene> ? ; - <organism> @<Organism> ? - ) ; - rdf:type [ <GeneOrganismRelationship> ] ? - ) -} - -<GeneSubcellularLocalizationRelationship> CLOSED { - ( $<GeneSubcellularLocalizationRelationship_tes> ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - <gene> @<Gene> ? ; - <location> @<GeneLocation> ? - ) ; - rdf:type [ <GeneSubcellularLocalizationRelationship> ] ? - ) -} - -<IBDAnnotations> CLOSED { - ( $<IBDAnnotations_tes> ( <genes> @<Gene> * ; - <organisms> @<Organism> * ; - <gene_organisms> @<GeneOrganismRelationship> * ; - <activities> @<MolecularActivity> * ; - <gene_functions> @<GeneMolecularActivityRelationship> * ; - <cellular_processes> @<CellularProcess> * ; - <pathways> @<Pathway> * ; - <gene_gene_interactions> @<GeneGeneInteraction> * ; - <gene_localizations> @<GeneSubcellularLocalizationRelationship> * - ) ; - rdf:type [ <IBDAnnotations> ] ? - ) -} - -<MolecularActivity> CLOSED { - ( $<MolecularActivity_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <MolecularActivity> ] - ) -} - -<Molecule> CLOSED { - ( $<Molecule_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Molecule> ] - ) -} - -core:NamedEntity ( - @<CellularProcess> OR @<Gene> OR @<GeneLocation> OR @<MolecularActivity> OR @<Molecule> OR @<Organism> OR @<Pathway> OR - @core:RelationshipType -) - -core:NamedEntity_struct { - ( $core:NamedEntity_tes rdfs1:label @linkml:String ? ; - rdf:type [ core:NamedEntity ] - ) -} - -<Organism> CLOSED { - ( $<Organism_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Organism> ] - ) -} - -<Pathway> CLOSED { - ( $<Pathway_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Pathway> ] - ) -} - -core:Publication CLOSED { - ( $core:Publication_tes ( core:id @linkml:String ? ; - core:title @linkml:String ? ; - core:abstract @linkml:String ? ; - core:combined_text @linkml:String ? ; - core:full_text @linkml:String ? - ) ; - rdf:type [ core:Publication ] ? - ) -} - -core:RelationshipType CLOSED { - ( $core:RelationshipType_tes ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ core:RelationshipType ] - ) -} - -core:TextWithTriples CLOSED { - ( $core:TextWithTriples_tes ( core:publication @core:Publication ? ; - core:triples @core:Triple * - ) ; - rdf:type [ core:TextWithTriples ] ? - ) -} - -core:Triple { - ( $core:Triple_tes ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - core:subject @core:NamedEntity ? ; - core:predicate @core:RelationshipType ? ; - core:object @core:NamedEntity ? ; - core:qualifier @linkml:String ? ; - core:subject_qualifier @core:NamedEntity ? ; - core:object_qualifier @core:NamedEntity ? - ) ; - rdf:type [ core:Triple ] ? - ) -} - - diff --git a/projects/ibd/sqlschema/ibd.sql b/projects/ibd/sqlschema/ibd.sql deleted file mode 100644 index 6bb0e0191..000000000 --- a/projects/ibd/sqlschema/ibd.sql +++ /dev/null @@ -1,137 +0,0 @@ - - -CREATE TABLE "AnnotatorResult" ( - subject_text TEXT, - object_id TEXT, - object_text TEXT, - PRIMARY KEY (subject_text, object_id, object_text) -); - -CREATE TABLE "CellularProcess" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "ExtractionResult" ( - input_id TEXT, - input_title TEXT, - input_text TEXT, - raw_completion_output TEXT, - prompt TEXT, - extracted_object TEXT, - named_entities TEXT, - PRIMARY KEY (input_id, input_title, input_text, raw_completion_output, prompt, extracted_object, named_entities) -); - -CREATE TABLE "Gene" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "GeneLocation" ( - label TEXT, - id TEXT NOT NULL, - PRIMARY KEY (id) -); - -CREATE TABLE "IBDAnnotations" ( - genes TEXT, - organisms TEXT, - gene_organisms TEXT, - activities TEXT, - gene_functions TEXT, - cellular_processes TEXT, - pathways TEXT, - gene_gene_interactions TEXT, - gene_localizations TEXT, - PRIMARY KEY (genes, organisms, gene_organisms, activities, gene_functions, cellular_processes, pathways, gene_gene_interactions, gene_localizations) -); - -CREATE TABLE "MolecularActivity" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Molecule" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Organism" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Pathway" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Publication" ( - id TEXT, - title TEXT, - abstract TEXT, - combined_text TEXT, - full_text TEXT, - PRIMARY KEY (id, title, abstract, combined_text, full_text) -); - -CREATE TABLE "RelationshipType" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "TextWithTriples" ( - publication TEXT, - triples TEXT, - PRIMARY KEY (publication, triples) -); - -CREATE TABLE "GeneGeneInteraction" ( - gene1 TEXT, - gene2 TEXT, - PRIMARY KEY (gene1, gene2), - FOREIGN KEY(gene1) REFERENCES "Gene" (id), - FOREIGN KEY(gene2) REFERENCES "Gene" (id) -); - -CREATE TABLE "GeneMolecularActivityRelationship" ( - gene TEXT, - molecular_activity TEXT, - PRIMARY KEY (gene, molecular_activity), - FOREIGN KEY(gene) REFERENCES "Gene" (id), - FOREIGN KEY(molecular_activity) REFERENCES "MolecularActivity" (id) -); - -CREATE TABLE "GeneMolecularActivityRelationship2" ( - gene TEXT, - molecular_activity TEXT, - target TEXT, - PRIMARY KEY (gene, molecular_activity, target), - FOREIGN KEY(gene) REFERENCES "Gene" (id), - FOREIGN KEY(molecular_activity) REFERENCES "MolecularActivity" (id), - FOREIGN KEY(target) REFERENCES "Molecule" (id) -); - -CREATE TABLE "GeneOrganismRelationship" ( - gene TEXT, - organism TEXT, - PRIMARY KEY (gene, organism), - FOREIGN KEY(gene) REFERENCES "Gene" (id), - FOREIGN KEY(organism) REFERENCES "Organism" (id) -); - -CREATE TABLE "GeneSubcellularLocalizationRelationship" ( - gene TEXT, - location TEXT, - PRIMARY KEY (gene, location), - FOREIGN KEY(gene) REFERENCES "Gene" (id), - FOREIGN KEY(location) REFERENCES "GeneLocation" (id) -); diff --git a/projects/ibd_literature/docs/AnnotatorResult.md b/projects/ibd_literature/docs/AnnotatorResult.md deleted file mode 100644 index e48de215a..000000000 --- a/projects/ibd_literature/docs/AnnotatorResult.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Class: AnnotatorResult - - - - -URI: [ibdlit:AnnotatorResult](http://w3id.org/ontogpt/ibd_literature/AnnotatorResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F])](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F]) - -## Attributes - - -### Own - - * [➞subject_text](annotatorResult__subject_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_id](annotatorResult__object_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_text](annotatorResult__object_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) diff --git a/projects/ibd_literature/docs/Any.md b/projects/ibd_literature/docs/Any.md deleted file mode 100644 index 59eefc666..000000000 --- a/projects/ibd_literature/docs/Any.md +++ /dev/null @@ -1,25 +0,0 @@ - -# Class: Any - - - - -URI: [ibdlit:Any](http://w3id.org/ontogpt/ibd_literature/Any) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult])](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult]) - -## Referenced by Class - - * **None** *[➞extracted_object](extractionResult__extracted_object.md)* <sub>0..1</sub> **[Any](Any.md)** - * **None** *[➞named_entities](extractionResult__named_entities.md)* <sub>0..\*</sub> **[Any](Any.md)** - -## Attributes - - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | linkml:Any | - diff --git a/projects/ibd_literature/docs/CellularProcess.md b/projects/ibd_literature/docs/CellularProcess.md deleted file mode 100644 index 38723e647..000000000 --- a/projects/ibd_literature/docs/CellularProcess.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: CellularProcess - - - - -URI: [ibdlit:CellularProcess](http://w3id.org/ontogpt/ibd_literature/CellularProcess) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[DiseaseCellularProcessRelationship],[DiseaseCellularProcessRelationship]-%20object%200..1>[CellularProcess|id(i):string;label(i):string%20%3F],[IBDAnnotations]-%20cellular_process%200..*>[CellularProcess],[NamedEntity]^-[CellularProcess],[IBDAnnotations])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[DiseaseCellularProcessRelationship],[DiseaseCellularProcessRelationship]-%20object%200..1>[CellularProcess|id(i):string;label(i):string%20%3F],[IBDAnnotations]-%20cellular_process%200..*>[CellularProcess],[NamedEntity]^-[CellularProcess],[IBDAnnotations]) - -## Identifier prefixes - - * GO - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **[DiseaseCellularProcessRelationship](DiseaseCellularProcessRelationship.md)** *[DiseaseCellularProcessRelationship➞object](DiseaseCellularProcessRelationship_object.md)* <sub>0..1</sub> **[CellularProcess](CellularProcess.md)** - * **None** *[➞cellular_process](iBDAnnotations__cellular_process.md)* <sub>0..\*</sub> **[CellularProcess](CellularProcess.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/ibd_literature/docs/ChemicalExposure.md b/projects/ibd_literature/docs/ChemicalExposure.md deleted file mode 100644 index 72660bf7b..000000000 --- a/projects/ibd_literature/docs/ChemicalExposure.md +++ /dev/null @@ -1,38 +0,0 @@ - -# Class: ChemicalExposure - - - - -URI: [ibdlit:ChemicalExposure](http://w3id.org/ontogpt/ibd_literature/ChemicalExposure) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[GeneExposureRelationship],[GeneExposureRelationship]-%20subject%200..1>[ChemicalExposure|id(i):string;label(i):string%20%3F],[IBDAnnotations]-%20exposures%200..*>[ChemicalExposure],[NamedEntity]^-[ChemicalExposure],[IBDAnnotations])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[GeneExposureRelationship],[GeneExposureRelationship]-%20subject%200..1>[ChemicalExposure|id(i):string;label(i):string%20%3F],[IBDAnnotations]-%20exposures%200..*>[ChemicalExposure],[NamedEntity]^-[ChemicalExposure],[IBDAnnotations]) - -## Identifier prefixes - - * CHEBI - * ECTO - * ExO - * NCIT - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **[GeneExposureRelationship](GeneExposureRelationship.md)** *[GeneExposureRelationship➞subject](GeneExposureRelationship_subject.md)* <sub>0..1</sub> **[ChemicalExposure](ChemicalExposure.md)** - * **None** *[➞exposures](iBDAnnotations__exposures.md)* <sub>0..\*</sub> **[ChemicalExposure](ChemicalExposure.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/ibd_literature/docs/ChemicalExposureToGenePredicate.md b/projects/ibd_literature/docs/ChemicalExposureToGenePredicate.md deleted file mode 100644 index a9803ac2d..000000000 --- a/projects/ibd_literature/docs/ChemicalExposureToGenePredicate.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: ChemicalExposureToGenePredicate - - - - -URI: [ibdlit:ChemicalExposureToGenePredicate](http://w3id.org/ontogpt/ibd_literature/ChemicalExposureToGenePredicate) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[GeneExposureRelationship],[GeneExposureRelationship]-%20predicate%200..1>[ChemicalExposureToGenePredicate|id(i):string;label(i):string%20%3F],[RelationshipType]^-[ChemicalExposureToGenePredicate])](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[GeneExposureRelationship],[GeneExposureRelationship]-%20predicate%200..1>[ChemicalExposureToGenePredicate|id(i):string;label(i):string%20%3F],[RelationshipType]^-[ChemicalExposureToGenePredicate]) - -## Identifier prefixes - - * RO - -## Parents - - * is_a: [RelationshipType](RelationshipType.md) - -## Referenced by Class - - * **[GeneExposureRelationship](GeneExposureRelationship.md)** *[GeneExposureRelationship➞predicate](GeneExposureRelationship_predicate.md)* <sub>0..1</sub> **[ChemicalExposureToGenePredicate](ChemicalExposureToGenePredicate.md)** - -## Attributes - - -### Inherited from RelationshipType: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/ibd_literature/docs/CompoundExpression.md b/projects/ibd_literature/docs/CompoundExpression.md deleted file mode 100644 index ef1ec548e..000000000 --- a/projects/ibd_literature/docs/CompoundExpression.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: CompoundExpression - - - - -URI: [ibdlit:CompoundExpression](http://w3id.org/ontogpt/ibd_literature/CompoundExpression) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[CompoundExpression]^-[Triple])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[CompoundExpression]^-[Triple]) - -## Children - - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - -## Referenced by Class - - -## Attributes - diff --git a/projects/ibd_literature/docs/Disease.md b/projects/ibd_literature/docs/Disease.md deleted file mode 100644 index a04546e69..000000000 --- a/projects/ibd_literature/docs/Disease.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: Disease - - - - -URI: [ibdlit:Disease](http://w3id.org/ontogpt/ibd_literature/Disease) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[DiseaseCellularProcessRelationship],[DiseaseCellularProcessRelationship]-%20subject%200..1>[Disease|id(i):string;label(i):string%20%3F],[IBDAnnotations]-%20diseases%200..*>[Disease],[NamedEntity]^-[Disease],[IBDAnnotations])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[DiseaseCellularProcessRelationship],[DiseaseCellularProcessRelationship]-%20subject%200..1>[Disease|id(i):string;label(i):string%20%3F],[IBDAnnotations]-%20diseases%200..*>[Disease],[NamedEntity]^-[Disease],[IBDAnnotations]) - -## Identifier prefixes - - * MONDO - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **[DiseaseCellularProcessRelationship](DiseaseCellularProcessRelationship.md)** *[DiseaseCellularProcessRelationship➞subject](DiseaseCellularProcessRelationship_subject.md)* <sub>0..1</sub> **[Disease](Disease.md)** - * **None** *[➞diseases](iBDAnnotations__diseases.md)* <sub>0..\*</sub> **[Disease](Disease.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/ibd_literature/docs/DiseaseCellularProcessRelationship.md b/projects/ibd_literature/docs/DiseaseCellularProcessRelationship.md deleted file mode 100644 index 066009c74..000000000 --- a/projects/ibd_literature/docs/DiseaseCellularProcessRelationship.md +++ /dev/null @@ -1,43 +0,0 @@ - -# Class: DiseaseCellularProcessRelationship - - - - -URI: [ibdlit:DiseaseCellularProcessRelationship](http://w3id.org/ontogpt/ibd_literature/DiseaseCellularProcessRelationship) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[NamedEntity],[DiseaseToCellularProcessPredicate],[NamedEntity]<object_qualifier%200..1-%20[DiseaseCellularProcessRelationship|qualifier(i):string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[DiseaseCellularProcessRelationship],[CellularProcess]<object%200..1-%20[DiseaseCellularProcessRelationship],[DiseaseToCellularProcessPredicate]<predicate%200..1-%20[DiseaseCellularProcessRelationship],[Disease]<subject%200..1-%20[DiseaseCellularProcessRelationship],[IBDAnnotations]++-%20disease_cellular_process_relationships%200..*>[DiseaseCellularProcessRelationship],[Triple]^-[DiseaseCellularProcessRelationship],[IBDAnnotations],[Disease],[CellularProcess])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[NamedEntity],[DiseaseToCellularProcessPredicate],[NamedEntity]<object_qualifier%200..1-%20[DiseaseCellularProcessRelationship|qualifier(i):string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[DiseaseCellularProcessRelationship],[CellularProcess]<object%200..1-%20[DiseaseCellularProcessRelationship],[DiseaseToCellularProcessPredicate]<predicate%200..1-%20[DiseaseCellularProcessRelationship],[Disease]<subject%200..1-%20[DiseaseCellularProcessRelationship],[IBDAnnotations]++-%20disease_cellular_process_relationships%200..*>[DiseaseCellularProcessRelationship],[Triple]^-[DiseaseCellularProcessRelationship],[IBDAnnotations],[Disease],[CellularProcess]) - -## Parents - - * is_a: [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - -## Referenced by Class - - * **None** *[➞disease_cellular_process_relationships](iBDAnnotations__disease_cellular_process_relationships.md)* <sub>0..\*</sub> **[DiseaseCellularProcessRelationship](DiseaseCellularProcessRelationship.md)** - -## Attributes - - -### Own - - * [DiseaseCellularProcessRelationship➞subject](DiseaseCellularProcessRelationship_subject.md) <sub>0..1</sub> - * Description: The name of the disease. - * Range: [Disease](Disease.md) - * [DiseaseCellularProcessRelationship➞predicate](DiseaseCellularProcessRelationship_predicate.md) <sub>0..1</sub> - * Description: The name of the type of relationship between a disease and a cellular process. - * Range: [DiseaseToCellularProcessPredicate](DiseaseToCellularProcessPredicate.md) - * [DiseaseCellularProcessRelationship➞object](DiseaseCellularProcessRelationship_object.md) <sub>0..1</sub> - * Description: The name of the cellular process. - * Range: [CellularProcess](CellularProcess.md) - * [DiseaseCellularProcessRelationship➞subject_qualifier](DiseaseCellularProcessRelationship_subject_qualifier.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [DiseaseCellularProcessRelationship➞object_qualifier](DiseaseCellularProcessRelationship_object_qualifier.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - -### Inherited from Triple: - - * [➞qualifier](triple__qualifier.md) <sub>0..1</sub> - * Description: A qualifier for the statements, e.g. "NOT" for negation - * Range: [String](types/String.md) diff --git a/projects/ibd_literature/docs/DiseaseCellularProcessRelationship_object.md b/projects/ibd_literature/docs/DiseaseCellularProcessRelationship_object.md deleted file mode 100644 index 3c273b6d5..000000000 --- a/projects/ibd_literature/docs/DiseaseCellularProcessRelationship_object.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: object - - -The name of the cellular process. - -URI: [ibdlit:DiseaseCellularProcessRelationship_object](http://w3id.org/ontogpt/ibd_literature/DiseaseCellularProcessRelationship_object) - - -## Domain and Range - -[DiseaseCellularProcessRelationship](DiseaseCellularProcessRelationship.md) → <sub>0..1</sub> [CellularProcess](CellularProcess.md) - -## Parents - - * is_a: [➞object](triple__object.md) - -## Children - - -## Used by - - * [DiseaseCellularProcessRelationship](DiseaseCellularProcessRelationship.md) diff --git a/projects/ibd_literature/docs/DiseaseCellularProcessRelationship_object_qualifier.md b/projects/ibd_literature/docs/DiseaseCellularProcessRelationship_object_qualifier.md deleted file mode 100644 index b1f396ac3..000000000 --- a/projects/ibd_literature/docs/DiseaseCellularProcessRelationship_object_qualifier.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: object_qualifier - - - - -URI: [ibdlit:DiseaseCellularProcessRelationship_object_qualifier](http://w3id.org/ontogpt/ibd_literature/DiseaseCellularProcessRelationship_object_qualifier) - - -## Domain and Range - -[DiseaseCellularProcessRelationship](DiseaseCellularProcessRelationship.md) → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - * is_a: [➞object_qualifier](triple__object_qualifier.md) - -## Children - - -## Used by - - * [DiseaseCellularProcessRelationship](DiseaseCellularProcessRelationship.md) diff --git a/projects/ibd_literature/docs/DiseaseCellularProcessRelationship_predicate.md b/projects/ibd_literature/docs/DiseaseCellularProcessRelationship_predicate.md deleted file mode 100644 index 01b2758cf..000000000 --- a/projects/ibd_literature/docs/DiseaseCellularProcessRelationship_predicate.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: predicate - - -The name of the type of relationship between a disease and a cellular process. - -URI: [ibdlit:DiseaseCellularProcessRelationship_predicate](http://w3id.org/ontogpt/ibd_literature/DiseaseCellularProcessRelationship_predicate) - - -## Domain and Range - -[DiseaseCellularProcessRelationship](DiseaseCellularProcessRelationship.md) → <sub>0..1</sub> [DiseaseToCellularProcessPredicate](DiseaseToCellularProcessPredicate.md) - -## Parents - - * is_a: [➞predicate](triple__predicate.md) - -## Children - - -## Used by - - * [DiseaseCellularProcessRelationship](DiseaseCellularProcessRelationship.md) diff --git a/projects/ibd_literature/docs/DiseaseCellularProcessRelationship_subject.md b/projects/ibd_literature/docs/DiseaseCellularProcessRelationship_subject.md deleted file mode 100644 index b0dd129a7..000000000 --- a/projects/ibd_literature/docs/DiseaseCellularProcessRelationship_subject.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: subject - - -The name of the disease. - -URI: [ibdlit:DiseaseCellularProcessRelationship_subject](http://w3id.org/ontogpt/ibd_literature/DiseaseCellularProcessRelationship_subject) - - -## Domain and Range - -[DiseaseCellularProcessRelationship](DiseaseCellularProcessRelationship.md) → <sub>0..1</sub> [Disease](Disease.md) - -## Parents - - * is_a: [➞subject](triple__subject.md) - -## Children - - -## Used by - - * [DiseaseCellularProcessRelationship](DiseaseCellularProcessRelationship.md) diff --git a/projects/ibd_literature/docs/DiseaseCellularProcessRelationship_subject_qualifier.md b/projects/ibd_literature/docs/DiseaseCellularProcessRelationship_subject_qualifier.md deleted file mode 100644 index eea72a153..000000000 --- a/projects/ibd_literature/docs/DiseaseCellularProcessRelationship_subject_qualifier.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: subject_qualifier - - - - -URI: [ibdlit:DiseaseCellularProcessRelationship_subject_qualifier](http://w3id.org/ontogpt/ibd_literature/DiseaseCellularProcessRelationship_subject_qualifier) - - -## Domain and Range - -[DiseaseCellularProcessRelationship](DiseaseCellularProcessRelationship.md) → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - * is_a: [➞subject_qualifier](triple__subject_qualifier.md) - -## Children - - -## Used by - - * [DiseaseCellularProcessRelationship](DiseaseCellularProcessRelationship.md) diff --git a/projects/ibd_literature/docs/DiseaseToCellularProcessPredicate.md b/projects/ibd_literature/docs/DiseaseToCellularProcessPredicate.md deleted file mode 100644 index c35926d70..000000000 --- a/projects/ibd_literature/docs/DiseaseToCellularProcessPredicate.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: DiseaseToCellularProcessPredicate - - - - -URI: [ibdlit:DiseaseToCellularProcessPredicate](http://w3id.org/ontogpt/ibd_literature/DiseaseToCellularProcessPredicate) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[DiseaseCellularProcessRelationship]-%20predicate%200..1>[DiseaseToCellularProcessPredicate|id(i):string;label(i):string%20%3F],[RelationshipType]^-[DiseaseToCellularProcessPredicate],[DiseaseCellularProcessRelationship])](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[DiseaseCellularProcessRelationship]-%20predicate%200..1>[DiseaseToCellularProcessPredicate|id(i):string;label(i):string%20%3F],[RelationshipType]^-[DiseaseToCellularProcessPredicate],[DiseaseCellularProcessRelationship]) - -## Identifier prefixes - - * RO - -## Parents - - * is_a: [RelationshipType](RelationshipType.md) - -## Referenced by Class - - * **[DiseaseCellularProcessRelationship](DiseaseCellularProcessRelationship.md)** *[DiseaseCellularProcessRelationship➞predicate](DiseaseCellularProcessRelationship_predicate.md)* <sub>0..1</sub> **[DiseaseToCellularProcessPredicate](DiseaseToCellularProcessPredicate.md)** - -## Attributes - - -### Inherited from RelationshipType: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/ibd_literature/docs/ExtractionResult.md b/projects/ibd_literature/docs/ExtractionResult.md deleted file mode 100644 index b6fb00ea8..000000000 --- a/projects/ibd_literature/docs/ExtractionResult.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Class: ExtractionResult - - -A result of extracting knowledge on text - -URI: [ibdlit:ExtractionResult](http://w3id.org/ontogpt/ibd_literature/ExtractionResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any])](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any]) - -## Attributes - - -### Own - - * [➞input_id](extractionResult__input_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_title](extractionResult__input_title.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_text](extractionResult__input_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞prompt](extractionResult__prompt.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞extracted_object](extractionResult__extracted_object.md) <sub>0..1</sub> - * Description: The complex objects extracted from the text - * Range: [Any](Any.md) - * [➞named_entities](extractionResult__named_entities.md) <sub>0..\*</sub> - * Description: Named entities extracted from the text - * Range: [Any](Any.md) diff --git a/projects/ibd_literature/docs/Gene.md b/projects/ibd_literature/docs/Gene.md deleted file mode 100644 index 6cfdb829f..000000000 --- a/projects/ibd_literature/docs/Gene.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: Gene - - - - -URI: [ibdlit:Gene](http://w3id.org/ontogpt/ibd_literature/Gene) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[GeneExposureRelationship],[GeneExposureRelationship]-%20object%200..1>[Gene|id(i):string;label(i):string%20%3F],[IBDAnnotations]-%20genes%200..*>[Gene],[NamedEntity]^-[Gene],[IBDAnnotations])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[GeneExposureRelationship],[GeneExposureRelationship]-%20object%200..1>[Gene|id(i):string;label(i):string%20%3F],[IBDAnnotations]-%20genes%200..*>[Gene],[NamedEntity]^-[Gene],[IBDAnnotations]) - -## Identifier prefixes - - * HGNC - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **[GeneExposureRelationship](GeneExposureRelationship.md)** *[GeneExposureRelationship➞object](GeneExposureRelationship_object.md)* <sub>0..1</sub> **[Gene](Gene.md)** - * **None** *[➞genes](iBDAnnotations__genes.md)* <sub>0..\*</sub> **[Gene](Gene.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/ibd_literature/docs/GeneExposureRelationship.md b/projects/ibd_literature/docs/GeneExposureRelationship.md deleted file mode 100644 index b4875649b..000000000 --- a/projects/ibd_literature/docs/GeneExposureRelationship.md +++ /dev/null @@ -1,45 +0,0 @@ - -# Class: GeneExposureRelationship - - - - -URI: [ibdlit:GeneExposureRelationship](http://w3id.org/ontogpt/ibd_literature/GeneExposureRelationship) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[NamedEntity],[NamedEntity]<object_qualifier%200..1-%20[GeneExposureRelationship|qualifier(i):string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[GeneExposureRelationship],[Gene]<object%200..1-%20[GeneExposureRelationship],[ChemicalExposureToGenePredicate]<predicate%200..1-%20[GeneExposureRelationship],[ChemicalExposure]<subject%200..1-%20[GeneExposureRelationship],[IBDAnnotations]++-%20gene_exposures_relationships%200..*>[GeneExposureRelationship],[Triple]^-[GeneExposureRelationship],[IBDAnnotations],[Gene],[ChemicalExposureToGenePredicate],[ChemicalExposure])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[NamedEntity],[NamedEntity]<object_qualifier%200..1-%20[GeneExposureRelationship|qualifier(i):string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[GeneExposureRelationship],[Gene]<object%200..1-%20[GeneExposureRelationship],[ChemicalExposureToGenePredicate]<predicate%200..1-%20[GeneExposureRelationship],[ChemicalExposure]<subject%200..1-%20[GeneExposureRelationship],[IBDAnnotations]++-%20gene_exposures_relationships%200..*>[GeneExposureRelationship],[Triple]^-[GeneExposureRelationship],[IBDAnnotations],[Gene],[ChemicalExposureToGenePredicate],[ChemicalExposure]) - -## Parents - - * is_a: [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - -## Referenced by Class - - * **None** *[➞gene_exposures_relationships](iBDAnnotations__gene_exposures_relationships.md)* <sub>0..\*</sub> **[GeneExposureRelationship](GeneExposureRelationship.md)** - -## Attributes - - -### Own - - * [GeneExposureRelationship➞subject](GeneExposureRelationship_subject.md) <sub>0..1</sub> - * Description: The name of the exposure, such as a exposure to a chemical toxin. - * Range: [ChemicalExposure](ChemicalExposure.md) - * [GeneExposureRelationship➞predicate](GeneExposureRelationship_predicate.md) <sub>0..1</sub> - * Description: The name of the type of relationship between a chemical exposure and a gene. - * Range: [ChemicalExposureToGenePredicate](ChemicalExposureToGenePredicate.md) - * [GeneExposureRelationship➞object](GeneExposureRelationship_object.md) <sub>0..1</sub> - * Description: The name of the gene in the pair. This comes second in the pair. - * Range: [Gene](Gene.md) - * [GeneExposureRelationship➞subject_qualifier](GeneExposureRelationship_subject_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the chemical exposure. - * Range: [NamedEntity](NamedEntity.md) - * [GeneExposureRelationship➞object_qualifier](GeneExposureRelationship_object_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the gene. - * Range: [NamedEntity](NamedEntity.md) - -### Inherited from Triple: - - * [➞qualifier](triple__qualifier.md) <sub>0..1</sub> - * Description: A qualifier for the statements, e.g. "NOT" for negation - * Range: [String](types/String.md) diff --git a/projects/ibd_literature/docs/GeneExposureRelationship_object.md b/projects/ibd_literature/docs/GeneExposureRelationship_object.md deleted file mode 100644 index 89f0b83ae..000000000 --- a/projects/ibd_literature/docs/GeneExposureRelationship_object.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: object - - -The name of the gene in the pair. This comes second in the pair. - -URI: [ibdlit:GeneExposureRelationship_object](http://w3id.org/ontogpt/ibd_literature/GeneExposureRelationship_object) - - -## Domain and Range - -[GeneExposureRelationship](GeneExposureRelationship.md) → <sub>0..1</sub> [Gene](Gene.md) - -## Parents - - * is_a: [➞object](triple__object.md) - -## Children - - -## Used by - - * [GeneExposureRelationship](GeneExposureRelationship.md) diff --git a/projects/ibd_literature/docs/GeneExposureRelationship_object_qualifier.md b/projects/ibd_literature/docs/GeneExposureRelationship_object_qualifier.md deleted file mode 100644 index 05f97900a..000000000 --- a/projects/ibd_literature/docs/GeneExposureRelationship_object_qualifier.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: object_qualifier - - -An optional qualifier or modifier for the gene. - -URI: [ibdlit:GeneExposureRelationship_object_qualifier](http://w3id.org/ontogpt/ibd_literature/GeneExposureRelationship_object_qualifier) - - -## Domain and Range - -[GeneExposureRelationship](GeneExposureRelationship.md) → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - * is_a: [➞object_qualifier](triple__object_qualifier.md) - -## Children - - -## Used by - - * [GeneExposureRelationship](GeneExposureRelationship.md) diff --git a/projects/ibd_literature/docs/GeneExposureRelationship_predicate.md b/projects/ibd_literature/docs/GeneExposureRelationship_predicate.md deleted file mode 100644 index 50e7c9169..000000000 --- a/projects/ibd_literature/docs/GeneExposureRelationship_predicate.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: predicate - - -The name of the type of relationship between a chemical exposure and a gene. - -URI: [ibdlit:GeneExposureRelationship_predicate](http://w3id.org/ontogpt/ibd_literature/GeneExposureRelationship_predicate) - - -## Domain and Range - -[GeneExposureRelationship](GeneExposureRelationship.md) → <sub>0..1</sub> [ChemicalExposureToGenePredicate](ChemicalExposureToGenePredicate.md) - -## Parents - - * is_a: [➞predicate](triple__predicate.md) - -## Children - - -## Used by - - * [GeneExposureRelationship](GeneExposureRelationship.md) diff --git a/projects/ibd_literature/docs/GeneExposureRelationship_subject.md b/projects/ibd_literature/docs/GeneExposureRelationship_subject.md deleted file mode 100644 index af1cf060d..000000000 --- a/projects/ibd_literature/docs/GeneExposureRelationship_subject.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: subject - - -The name of the exposure, such as a exposure to a chemical toxin. - -URI: [ibdlit:GeneExposureRelationship_subject](http://w3id.org/ontogpt/ibd_literature/GeneExposureRelationship_subject) - - -## Domain and Range - -[GeneExposureRelationship](GeneExposureRelationship.md) → <sub>0..1</sub> [ChemicalExposure](ChemicalExposure.md) - -## Parents - - * is_a: [➞subject](triple__subject.md) - -## Children - - -## Used by - - * [GeneExposureRelationship](GeneExposureRelationship.md) diff --git a/projects/ibd_literature/docs/GeneExposureRelationship_subject_qualifier.md b/projects/ibd_literature/docs/GeneExposureRelationship_subject_qualifier.md deleted file mode 100644 index b6dd16f4d..000000000 --- a/projects/ibd_literature/docs/GeneExposureRelationship_subject_qualifier.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: subject_qualifier - - -An optional qualifier or modifier for the chemical exposure. - -URI: [ibdlit:GeneExposureRelationship_subject_qualifier](http://w3id.org/ontogpt/ibd_literature/GeneExposureRelationship_subject_qualifier) - - -## Domain and Range - -[GeneExposureRelationship](GeneExposureRelationship.md) → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - * is_a: [➞subject_qualifier](triple__subject_qualifier.md) - -## Children - - -## Used by - - * [GeneExposureRelationship](GeneExposureRelationship.md) diff --git a/projects/ibd_literature/docs/IBDAnnotations.md b/projects/ibd_literature/docs/IBDAnnotations.md deleted file mode 100644 index 512cc59ce..000000000 --- a/projects/ibd_literature/docs/IBDAnnotations.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: IBDAnnotations - - - - -URI: [ibdlit:IBDAnnotations](http://w3id.org/ontogpt/ibd_literature/IBDAnnotations) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[DiseaseCellularProcessRelationship]<disease_cellular_process_relationships%200..*-++[IBDAnnotations],[CellularProcess]<cellular_process%200..*-%20[IBDAnnotations],[Disease]<diseases%200..*-%20[IBDAnnotations],[GeneExposureRelationship]<gene_exposures_relationships%200..*-++[IBDAnnotations],[ChemicalExposure]<exposures%200..*-%20[IBDAnnotations],[Gene]<genes%200..*-%20[IBDAnnotations],[GeneExposureRelationship],[Gene],[DiseaseCellularProcessRelationship],[Disease],[ChemicalExposure],[CellularProcess])](https://yuml.me/diagram/nofunky;dir:TB/class/[DiseaseCellularProcessRelationship]<disease_cellular_process_relationships%200..*-++[IBDAnnotations],[CellularProcess]<cellular_process%200..*-%20[IBDAnnotations],[Disease]<diseases%200..*-%20[IBDAnnotations],[GeneExposureRelationship]<gene_exposures_relationships%200..*-++[IBDAnnotations],[ChemicalExposure]<exposures%200..*-%20[IBDAnnotations],[Gene]<genes%200..*-%20[IBDAnnotations],[GeneExposureRelationship],[Gene],[DiseaseCellularProcessRelationship],[Disease],[ChemicalExposure],[CellularProcess]) - -## Attributes - - -### Own - - * [➞genes](iBDAnnotations__genes.md) <sub>0..\*</sub> - * Description: semicolon-separated list of genes - * Range: [Gene](Gene.md) - * [➞exposures](iBDAnnotations__exposures.md) <sub>0..\*</sub> - * Description: semicolon-separated list of exposures - * Range: [ChemicalExposure](ChemicalExposure.md) - * [➞gene_exposures_relationships](iBDAnnotations__gene_exposures_relationships.md) <sub>0..\*</sub> - * Description: semicolon-separated list of gene to molecular activity relationships - * Range: [GeneExposureRelationship](GeneExposureRelationship.md) - * [➞diseases](iBDAnnotations__diseases.md) <sub>0..\*</sub> - * Description: semicolon-separated list of diseases - * Range: [Disease](Disease.md) - * [➞cellular_process](iBDAnnotations__cellular_process.md) <sub>0..\*</sub> - * Description: semicolon-separated list of cellular processes - * Range: [CellularProcess](CellularProcess.md) - * [➞disease_cellular_process_relationships](iBDAnnotations__disease_cellular_process_relationships.md) <sub>0..\*</sub> - * Description: semicolon-separated list of disease to cellular process relationships - * Range: [DiseaseCellularProcessRelationship](DiseaseCellularProcessRelationship.md) diff --git a/projects/ibd_literature/docs/NamedEntity.md b/projects/ibd_literature/docs/NamedEntity.md deleted file mode 100644 index 7735e30cf..000000000 --- a/projects/ibd_literature/docs/NamedEntity.md +++ /dev/null @@ -1,41 +0,0 @@ - -# Class: NamedEntity - - - - -URI: [ibdlit:NamedEntity](http://w3id.org/ontogpt/ibd_literature/NamedEntity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[DiseaseCellularProcessRelationship]-%20object_qualifier%200..1>[NamedEntity|id:string;label:string%20%3F],[DiseaseCellularProcessRelationship]-%20subject_qualifier%200..1>[NamedEntity],[GeneExposureRelationship]-%20object_qualifier%200..1>[NamedEntity],[GeneExposureRelationship]-%20subject_qualifier%200..1>[NamedEntity],[Triple]-%20object%200..1>[NamedEntity],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[Gene],[NamedEntity]^-[Disease],[NamedEntity]^-[ChemicalExposure],[NamedEntity]^-[CellularProcess],[Triple],[GeneExposureRelationship],[Gene],[DiseaseCellularProcessRelationship],[Disease],[ChemicalExposure],[CellularProcess])](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[DiseaseCellularProcessRelationship]-%20object_qualifier%200..1>[NamedEntity|id:string;label:string%20%3F],[DiseaseCellularProcessRelationship]-%20subject_qualifier%200..1>[NamedEntity],[GeneExposureRelationship]-%20object_qualifier%200..1>[NamedEntity],[GeneExposureRelationship]-%20subject_qualifier%200..1>[NamedEntity],[Triple]-%20object%200..1>[NamedEntity],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[Gene],[NamedEntity]^-[Disease],[NamedEntity]^-[ChemicalExposure],[NamedEntity]^-[CellularProcess],[Triple],[GeneExposureRelationship],[Gene],[DiseaseCellularProcessRelationship],[Disease],[ChemicalExposure],[CellularProcess]) - -## Children - - * [CellularProcess](CellularProcess.md) - * [ChemicalExposure](ChemicalExposure.md) - * [Disease](Disease.md) - * [Gene](Gene.md) - * [RelationshipType](RelationshipType.md) - -## Referenced by Class - - * **[DiseaseCellularProcessRelationship](DiseaseCellularProcessRelationship.md)** *[DiseaseCellularProcessRelationship➞object_qualifier](DiseaseCellularProcessRelationship_object_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **[DiseaseCellularProcessRelationship](DiseaseCellularProcessRelationship.md)** *[DiseaseCellularProcessRelationship➞subject_qualifier](DiseaseCellularProcessRelationship_subject_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **[GeneExposureRelationship](GeneExposureRelationship.md)** *[GeneExposureRelationship➞object_qualifier](GeneExposureRelationship_object_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **[GeneExposureRelationship](GeneExposureRelationship.md)** *[GeneExposureRelationship➞subject_qualifier](GeneExposureRelationship_subject_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞object](triple__object.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞object_qualifier](triple__object_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject](triple__subject.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject_qualifier](triple__subject_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - -## Attributes - - -### Own - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/ibd_literature/docs/NullDataOptions.md b/projects/ibd_literature/docs/NullDataOptions.md deleted file mode 100644 index 09063060e..000000000 --- a/projects/ibd_literature/docs/NullDataOptions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Enum: NullDataOptions - - - - -URI: [ibdlit:NullDataOptions](http://w3id.org/ontogpt/ibd_literature/NullDataOptions) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | -| UNSPECIFIED_METHOD_OF_ADMINISTRATION | | NCIT:C149701 | | -| NOT_APPLICABLE | | NCIT:C18902 | {'aliases': ['not applicable', 'N/A']} | -| NOT_MENTIONED | | | | - diff --git a/projects/ibd_literature/docs/Publication.md b/projects/ibd_literature/docs/Publication.md deleted file mode 100644 index c5d4a3ac0..000000000 --- a/projects/ibd_literature/docs/Publication.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Publication - - - - -URI: [ibdlit:Publication](http://w3id.org/ontogpt/ibd_literature/Publication) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples])](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples]) - -## Referenced by Class - - * **None** *[➞publication](textWithTriples__publication.md)* <sub>0..1</sub> **[Publication](Publication.md)** - -## Attributes - - -### Own - - * [➞id](publication__id.md) <sub>0..1</sub> - * Description: The publication identifier - * Range: [String](types/String.md) - * [➞title](publication__title.md) <sub>0..1</sub> - * Description: The title of the publication - * Range: [String](types/String.md) - * [➞abstract](publication__abstract.md) <sub>0..1</sub> - * Description: The abstract of the publication - * Range: [String](types/String.md) - * [➞combined_text](publication__combined_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞full_text](publication__full_text.md) <sub>0..1</sub> - * Description: The full text of the publication - * Range: [String](types/String.md) diff --git a/projects/ibd_literature/docs/RelationshipType.md b/projects/ibd_literature/docs/RelationshipType.md deleted file mode 100644 index cdf14db38..000000000 --- a/projects/ibd_literature/docs/RelationshipType.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Class: RelationshipType - - - - -URI: [ibdlit:RelationshipType](http://w3id.org/ontogpt/ibd_literature/RelationshipType) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[RelationshipType]^-[DiseaseToCellularProcessPredicate],[RelationshipType]^-[ChemicalExposureToGenePredicate],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity],[DiseaseToCellularProcessPredicate],[ChemicalExposureToGenePredicate])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[RelationshipType]^-[DiseaseToCellularProcessPredicate],[RelationshipType]^-[ChemicalExposureToGenePredicate],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity],[DiseaseToCellularProcessPredicate],[ChemicalExposureToGenePredicate]) - -## Identifier prefixes - - * RO - * biolink - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Children - - * [ChemicalExposureToGenePredicate](ChemicalExposureToGenePredicate.md) - * [DiseaseToCellularProcessPredicate](DiseaseToCellularProcessPredicate.md) - -## Referenced by Class - - * **None** *[➞predicate](triple__predicate.md)* <sub>0..1</sub> **[RelationshipType](RelationshipType.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/ibd_literature/docs/TextWithTriples.md b/projects/ibd_literature/docs/TextWithTriples.md deleted file mode 100644 index ef6237a45..000000000 --- a/projects/ibd_literature/docs/TextWithTriples.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: TextWithTriples - - - - -URI: [ibdlit:TextWithTriples](http://w3id.org/ontogpt/ibd_literature/TextWithTriples) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication]) - -## Attributes - - -### Own - - * [➞publication](textWithTriples__publication.md) <sub>0..1</sub> - * Range: [Publication](Publication.md) - * [➞triples](textWithTriples__triples.md) <sub>0..\*</sub> - * Range: [Triple](Triple.md) diff --git a/projects/ibd_literature/docs/Triple.md b/projects/ibd_literature/docs/Triple.md deleted file mode 100644 index 46bc252cd..000000000 --- a/projects/ibd_literature/docs/Triple.md +++ /dev/null @@ -1,44 +0,0 @@ - -# Class: Triple - - -Abstract parent for Relation Extraction tasks - -URI: [ibdlit:Triple](http://w3id.org/ontogpt/ibd_literature/Triple) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[Triple]^-[GeneExposureRelationship],[Triple]^-[DiseaseCellularProcessRelationship],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[GeneExposureRelationship],[DiseaseCellularProcessRelationship],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[Triple]^-[GeneExposureRelationship],[Triple]^-[DiseaseCellularProcessRelationship],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[GeneExposureRelationship],[DiseaseCellularProcessRelationship],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Children - - * [DiseaseCellularProcessRelationship](DiseaseCellularProcessRelationship.md) - * [GeneExposureRelationship](GeneExposureRelationship.md) - -## Referenced by Class - - * **None** *[➞triples](textWithTriples__triples.md)* <sub>0..\*</sub> **[Triple](Triple.md)** - -## Attributes - - -### Own - - * [➞subject](triple__subject.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞predicate](triple__predicate.md) <sub>0..1</sub> - * Range: [RelationshipType](RelationshipType.md) - * [➞object](triple__object.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞qualifier](triple__qualifier.md) <sub>0..1</sub> - * Description: A qualifier for the statements, e.g. "NOT" for negation - * Range: [String](types/String.md) - * [➞subject_qualifier](triple__subject_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - * Range: [NamedEntity](NamedEntity.md) - * [➞object_qualifier](triple__object_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * Range: [NamedEntity](NamedEntity.md) diff --git a/projects/ibd_literature/docs/annotatorResult__object_id.md b/projects/ibd_literature/docs/annotatorResult__object_id.md deleted file mode 100644 index 647c4bef4..000000000 --- a/projects/ibd_literature/docs/annotatorResult__object_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_id - - - - -URI: [ibdlit:annotatorResult__object_id](http://w3id.org/ontogpt/ibd_literature/annotatorResult__object_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/ibd_literature/docs/annotatorResult__object_text.md b/projects/ibd_literature/docs/annotatorResult__object_text.md deleted file mode 100644 index a30048036..000000000 --- a/projects/ibd_literature/docs/annotatorResult__object_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_text - - - - -URI: [ibdlit:annotatorResult__object_text](http://w3id.org/ontogpt/ibd_literature/annotatorResult__object_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/ibd_literature/docs/annotatorResult__subject_text.md b/projects/ibd_literature/docs/annotatorResult__subject_text.md deleted file mode 100644 index 2c4f1c51d..000000000 --- a/projects/ibd_literature/docs/annotatorResult__subject_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_text - - - - -URI: [ibdlit:annotatorResult__subject_text](http://w3id.org/ontogpt/ibd_literature/annotatorResult__subject_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/ibd_literature/docs/extractionResult__extracted_object.md b/projects/ibd_literature/docs/extractionResult__extracted_object.md deleted file mode 100644 index 5d30c7a28..000000000 --- a/projects/ibd_literature/docs/extractionResult__extracted_object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: extracted_object - - -The complex objects extracted from the text - -URI: [ibdlit:extractionResult__extracted_object](http://w3id.org/ontogpt/ibd_literature/extractionResult__extracted_object) - - -## Domain and Range - -None → <sub>0..1</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ibd_literature/docs/extractionResult__input_id.md b/projects/ibd_literature/docs/extractionResult__input_id.md deleted file mode 100644 index 9a04136bb..000000000 --- a/projects/ibd_literature/docs/extractionResult__input_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_id - - - - -URI: [ibdlit:extractionResult__input_id](http://w3id.org/ontogpt/ibd_literature/extractionResult__input_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ibd_literature/docs/extractionResult__input_text.md b/projects/ibd_literature/docs/extractionResult__input_text.md deleted file mode 100644 index 599caca0d..000000000 --- a/projects/ibd_literature/docs/extractionResult__input_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_text - - - - -URI: [ibdlit:extractionResult__input_text](http://w3id.org/ontogpt/ibd_literature/extractionResult__input_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ibd_literature/docs/extractionResult__input_title.md b/projects/ibd_literature/docs/extractionResult__input_title.md deleted file mode 100644 index c22ea8d69..000000000 --- a/projects/ibd_literature/docs/extractionResult__input_title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_title - - - - -URI: [ibdlit:extractionResult__input_title](http://w3id.org/ontogpt/ibd_literature/extractionResult__input_title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ibd_literature/docs/extractionResult__named_entities.md b/projects/ibd_literature/docs/extractionResult__named_entities.md deleted file mode 100644 index 0aa94909b..000000000 --- a/projects/ibd_literature/docs/extractionResult__named_entities.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: named_entities - - -Named entities extracted from the text - -URI: [ibdlit:extractionResult__named_entities](http://w3id.org/ontogpt/ibd_literature/extractionResult__named_entities) - - -## Domain and Range - -None → <sub>0..\*</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ibd_literature/docs/extractionResult__prompt.md b/projects/ibd_literature/docs/extractionResult__prompt.md deleted file mode 100644 index 22dde1c30..000000000 --- a/projects/ibd_literature/docs/extractionResult__prompt.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: prompt - - - - -URI: [ibdlit:extractionResult__prompt](http://w3id.org/ontogpt/ibd_literature/extractionResult__prompt) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ibd_literature/docs/extractionResult__raw_completion_output.md b/projects/ibd_literature/docs/extractionResult__raw_completion_output.md deleted file mode 100644 index 3ca6095de..000000000 --- a/projects/ibd_literature/docs/extractionResult__raw_completion_output.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: raw_completion_output - - - - -URI: [ibdlit:extractionResult__raw_completion_output](http://w3id.org/ontogpt/ibd_literature/extractionResult__raw_completion_output) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ibd_literature/docs/iBDAnnotations__cellular_process.md b/projects/ibd_literature/docs/iBDAnnotations__cellular_process.md deleted file mode 100644 index d35161fef..000000000 --- a/projects/ibd_literature/docs/iBDAnnotations__cellular_process.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: cellular_process - - -semicolon-separated list of cellular processes - -URI: [ibdlit:iBDAnnotations__cellular_process](http://w3id.org/ontogpt/ibd_literature/iBDAnnotations__cellular_process) - - -## Domain and Range - -None → <sub>0..\*</sub> [CellularProcess](CellularProcess.md) - -## Parents - - -## Children - - -## Used by - - * [IBDAnnotations](IBDAnnotations.md) diff --git a/projects/ibd_literature/docs/iBDAnnotations__disease_cellular_process_relationships.md b/projects/ibd_literature/docs/iBDAnnotations__disease_cellular_process_relationships.md deleted file mode 100644 index 03eafa9e3..000000000 --- a/projects/ibd_literature/docs/iBDAnnotations__disease_cellular_process_relationships.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: disease_cellular_process_relationships - - -semicolon-separated list of disease to cellular process relationships - -URI: [ibdlit:iBDAnnotations__disease_cellular_process_relationships](http://w3id.org/ontogpt/ibd_literature/iBDAnnotations__disease_cellular_process_relationships) - - -## Domain and Range - -None → <sub>0..\*</sub> [DiseaseCellularProcessRelationship](DiseaseCellularProcessRelationship.md) - -## Parents - - -## Children - - -## Used by - - * [IBDAnnotations](IBDAnnotations.md) diff --git a/projects/ibd_literature/docs/iBDAnnotations__diseases.md b/projects/ibd_literature/docs/iBDAnnotations__diseases.md deleted file mode 100644 index 46e81faa0..000000000 --- a/projects/ibd_literature/docs/iBDAnnotations__diseases.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: diseases - - -semicolon-separated list of diseases - -URI: [ibdlit:iBDAnnotations__diseases](http://w3id.org/ontogpt/ibd_literature/iBDAnnotations__diseases) - - -## Domain and Range - -None → <sub>0..\*</sub> [Disease](Disease.md) - -## Parents - - -## Children - - -## Used by - - * [IBDAnnotations](IBDAnnotations.md) diff --git a/projects/ibd_literature/docs/iBDAnnotations__exposures.md b/projects/ibd_literature/docs/iBDAnnotations__exposures.md deleted file mode 100644 index bfec6310a..000000000 --- a/projects/ibd_literature/docs/iBDAnnotations__exposures.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: exposures - - -semicolon-separated list of exposures - -URI: [ibdlit:iBDAnnotations__exposures](http://w3id.org/ontogpt/ibd_literature/iBDAnnotations__exposures) - - -## Domain and Range - -None → <sub>0..\*</sub> [ChemicalExposure](ChemicalExposure.md) - -## Parents - - -## Children - - -## Used by - - * [IBDAnnotations](IBDAnnotations.md) diff --git a/projects/ibd_literature/docs/iBDAnnotations__gene_exposures_relationships.md b/projects/ibd_literature/docs/iBDAnnotations__gene_exposures_relationships.md deleted file mode 100644 index d51ac65b5..000000000 --- a/projects/ibd_literature/docs/iBDAnnotations__gene_exposures_relationships.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: gene_exposures_relationships - - -semicolon-separated list of gene to molecular activity relationships - -URI: [ibdlit:iBDAnnotations__gene_exposures_relationships](http://w3id.org/ontogpt/ibd_literature/iBDAnnotations__gene_exposures_relationships) - - -## Domain and Range - -None → <sub>0..\*</sub> [GeneExposureRelationship](GeneExposureRelationship.md) - -## Parents - - -## Children - - -## Used by - - * [IBDAnnotations](IBDAnnotations.md) diff --git a/projects/ibd_literature/docs/iBDAnnotations__genes.md b/projects/ibd_literature/docs/iBDAnnotations__genes.md deleted file mode 100644 index 4ae8dc48c..000000000 --- a/projects/ibd_literature/docs/iBDAnnotations__genes.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: genes - - -semicolon-separated list of genes - -URI: [ibdlit:iBDAnnotations__genes](http://w3id.org/ontogpt/ibd_literature/iBDAnnotations__genes) - - -## Domain and Range - -None → <sub>0..\*</sub> [Gene](Gene.md) - -## Parents - - -## Children - - -## Used by - - * [IBDAnnotations](IBDAnnotations.md) diff --git a/projects/ibd_literature/docs/ibd_literature.md b/projects/ibd_literature/docs/ibd_literature.md deleted file mode 100644 index 6b57fc3a7..000000000 --- a/projects/ibd_literature/docs/ibd_literature.md +++ /dev/null @@ -1,128 +0,0 @@ - -# ibd-literature-template - - -**metamodel version:** 1.7.0 - -**version:** None - - -A template for extracting information from IBD literature - - -### Classes - - * [AnnotatorResult](AnnotatorResult.md) - * [Any](Any.md) - * [CompoundExpression](CompoundExpression.md) - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - * [DiseaseCellularProcessRelationship](DiseaseCellularProcessRelationship.md) - * [GeneExposureRelationship](GeneExposureRelationship.md) - * [ExtractionResult](ExtractionResult.md) - A result of extracting knowledge on text - * [IBDAnnotations](IBDAnnotations.md) - * [NamedEntity](NamedEntity.md) - * [CellularProcess](CellularProcess.md) - * [ChemicalExposure](ChemicalExposure.md) - * [Disease](Disease.md) - * [Gene](Gene.md) - * [RelationshipType](RelationshipType.md) - * [ChemicalExposureToGenePredicate](ChemicalExposureToGenePredicate.md) - * [DiseaseToCellularProcessPredicate](DiseaseToCellularProcessPredicate.md) - * [Publication](Publication.md) - * [TextWithTriples](TextWithTriples.md) - -### Mixins - - -### Slots - - * [➞object_id](annotatorResult__object_id.md) - * [➞object_text](annotatorResult__object_text.md) - * [➞subject_text](annotatorResult__subject_text.md) - * [➞extracted_object](extractionResult__extracted_object.md) - The complex objects extracted from the text - * [➞input_id](extractionResult__input_id.md) - * [➞input_text](extractionResult__input_text.md) - * [➞input_title](extractionResult__input_title.md) - * [➞named_entities](extractionResult__named_entities.md) - Named entities extracted from the text - * [➞prompt](extractionResult__prompt.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) - * [➞cellular_process](iBDAnnotations__cellular_process.md) - semicolon-separated list of cellular processes - * [➞disease_cellular_process_relationships](iBDAnnotations__disease_cellular_process_relationships.md) - semicolon-separated list of disease to cellular process relationships - * [➞diseases](iBDAnnotations__diseases.md) - semicolon-separated list of diseases - * [➞exposures](iBDAnnotations__exposures.md) - semicolon-separated list of exposures - * [➞gene_exposures_relationships](iBDAnnotations__gene_exposures_relationships.md) - semicolon-separated list of gene to molecular activity relationships - * [➞genes](iBDAnnotations__genes.md) - semicolon-separated list of genes - * [➞id](namedEntity__id.md) - A unique identifier for the named entity - * [➞label](namedEntity__label.md) - The label (name) of the named thing - * [➞abstract](publication__abstract.md) - The abstract of the publication - * [➞combined_text](publication__combined_text.md) - * [➞full_text](publication__full_text.md) - The full text of the publication - * [➞id](publication__id.md) - The publication identifier - * [➞title](publication__title.md) - The title of the publication - * [➞publication](textWithTriples__publication.md) - * [➞triples](textWithTriples__triples.md) - * [➞object](triple__object.md) - * [DiseaseCellularProcessRelationship➞object](DiseaseCellularProcessRelationship_object.md) - The name of the cellular process. - * [GeneExposureRelationship➞object](GeneExposureRelationship_object.md) - The name of the gene in the pair. This comes second in the pair. - * [➞object_qualifier](triple__object_qualifier.md) - An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * [DiseaseCellularProcessRelationship➞object_qualifier](DiseaseCellularProcessRelationship_object_qualifier.md) - * [GeneExposureRelationship➞object_qualifier](GeneExposureRelationship_object_qualifier.md) - An optional qualifier or modifier for the gene. - * [➞predicate](triple__predicate.md) - * [DiseaseCellularProcessRelationship➞predicate](DiseaseCellularProcessRelationship_predicate.md) - The name of the type of relationship between a disease and a cellular process. - * [GeneExposureRelationship➞predicate](GeneExposureRelationship_predicate.md) - The name of the type of relationship between a chemical exposure and a gene. - * [➞qualifier](triple__qualifier.md) - A qualifier for the statements, e.g. "NOT" for negation - * [➞subject](triple__subject.md) - * [DiseaseCellularProcessRelationship➞subject](DiseaseCellularProcessRelationship_subject.md) - The name of the disease. - * [GeneExposureRelationship➞subject](GeneExposureRelationship_subject.md) - The name of the exposure, such as a exposure to a chemical toxin. - * [➞subject_qualifier](triple__subject_qualifier.md) - An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - * [DiseaseCellularProcessRelationship➞subject_qualifier](DiseaseCellularProcessRelationship_subject_qualifier.md) - * [GeneExposureRelationship➞subject_qualifier](GeneExposureRelationship_subject_qualifier.md) - An optional qualifier or modifier for the chemical exposure. - -### Enums - - * [NullDataOptions](NullDataOptions.md) - -### Subsets - - -### Types - - -#### Built in - - * **Bool** - * **Curie** - * **Decimal** - * **ElementIdentifier** - * **NCName** - * **NodeIdentifier** - * **URI** - * **URIorCURIE** - * **XSDDate** - * **XSDDateTime** - * **XSDTime** - * **float** - * **int** - * **str** - -#### Defined - - * [Boolean](types/Boolean.md) (**Bool**) - A binary (true or false) value - * [Curie](types/Curie.md) (**Curie**) - a compact URI - * [Date](types/Date.md) (**XSDDate**) - a date (year, month and day) in an idealized calendar - * [DateOrDatetime](types/DateOrDatetime.md) (**str**) - Either a date or a datetime - * [Datetime](types/Datetime.md) (**XSDDateTime**) - The combination of a date and time - * [Decimal](types/Decimal.md) (**Decimal**) - A real number with arbitrary precision that conforms to the xsd:decimal specification - * [Double](types/Double.md) (**float**) - A real number that conforms to the xsd:double specification - * [Float](types/Float.md) (**float**) - A real number that conforms to the xsd:float specification - * [Integer](types/Integer.md) (**int**) - An integer - * [Jsonpath](types/Jsonpath.md) (**str**) - A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - * [Jsonpointer](types/Jsonpointer.md) (**str**) - A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - * [Ncname](types/Ncname.md) (**NCName**) - Prefix part of CURIE - * [Nodeidentifier](types/Nodeidentifier.md) (**NodeIdentifier**) - A URI, CURIE or BNODE that represents a node in a model. - * [Objectidentifier](types/Objectidentifier.md) (**ElementIdentifier**) - A URI or CURIE that represents an object in the model. - * [Sparqlpath](types/Sparqlpath.md) (**str**) - A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - * [String](types/String.md) (**str**) - A character string - * [Time](types/Time.md) (**XSDTime**) - A time object represents a (local) time of day, independent of any particular day - * [Uri](types/Uri.md) (**URI**) - a complete URI - * [Uriorcurie](types/Uriorcurie.md) (**URIorCURIE**) - a URI or a CURIE diff --git a/projects/ibd_literature/docs/namedEntity__id.md b/projects/ibd_literature/docs/namedEntity__id.md deleted file mode 100644 index 97e6173e8..000000000 --- a/projects/ibd_literature/docs/namedEntity__id.md +++ /dev/null @@ -1,36 +0,0 @@ - -# Slot: id - - -A unique identifier for the named entity - -URI: [ibdlit:namedEntity__id](http://w3id.org/ontogpt/ibd_literature/namedEntity__id) - - -## Domain and Range - -None → <sub>1..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [CellularProcess](CellularProcess.md) - * [ChemicalExposure](ChemicalExposure.md) - * [ChemicalExposureToGenePredicate](ChemicalExposureToGenePredicate.md) - * [Disease](Disease.md) - * [DiseaseToCellularProcessPredicate](DiseaseToCellularProcessPredicate.md) - * [Gene](Gene.md) - * [NamedEntity](NamedEntity.md) - * [RelationshipType](RelationshipType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | this is populated during the grounding and normalization step | - diff --git a/projects/ibd_literature/docs/namedEntity__label.md b/projects/ibd_literature/docs/namedEntity__label.md deleted file mode 100644 index b9b4b4f60..000000000 --- a/projects/ibd_literature/docs/namedEntity__label.md +++ /dev/null @@ -1,37 +0,0 @@ - -# Slot: label - - -The label (name) of the named thing - -URI: [ibdlit:namedEntity__label](http://w3id.org/ontogpt/ibd_literature/namedEntity__label) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [CellularProcess](CellularProcess.md) - * [ChemicalExposure](ChemicalExposure.md) - * [ChemicalExposureToGenePredicate](ChemicalExposureToGenePredicate.md) - * [Disease](Disease.md) - * [DiseaseToCellularProcessPredicate](DiseaseToCellularProcessPredicate.md) - * [Gene](Gene.md) - * [NamedEntity](NamedEntity.md) - * [RelationshipType](RelationshipType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Aliases:** | | name | -| **Mappings:** | | rdfs:label | - diff --git a/projects/ibd_literature/docs/publication__abstract.md b/projects/ibd_literature/docs/publication__abstract.md deleted file mode 100644 index eaf627af0..000000000 --- a/projects/ibd_literature/docs/publication__abstract.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: abstract - - -The abstract of the publication - -URI: [ibdlit:publication__abstract](http://w3id.org/ontogpt/ibd_literature/publication__abstract) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/ibd_literature/docs/publication__combined_text.md b/projects/ibd_literature/docs/publication__combined_text.md deleted file mode 100644 index a6b2a61f8..000000000 --- a/projects/ibd_literature/docs/publication__combined_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: combined_text - - - - -URI: [ibdlit:publication__combined_text](http://w3id.org/ontogpt/ibd_literature/publication__combined_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/ibd_literature/docs/publication__full_text.md b/projects/ibd_literature/docs/publication__full_text.md deleted file mode 100644 index 76e3d9016..000000000 --- a/projects/ibd_literature/docs/publication__full_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: full_text - - -The full text of the publication - -URI: [ibdlit:publication__full_text](http://w3id.org/ontogpt/ibd_literature/publication__full_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/ibd_literature/docs/publication__id.md b/projects/ibd_literature/docs/publication__id.md deleted file mode 100644 index eb1c6ea60..000000000 --- a/projects/ibd_literature/docs/publication__id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: id - - -The publication identifier - -URI: [ibdlit:publication__id](http://w3id.org/ontogpt/ibd_literature/publication__id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/ibd_literature/docs/publication__title.md b/projects/ibd_literature/docs/publication__title.md deleted file mode 100644 index b0fab18d3..000000000 --- a/projects/ibd_literature/docs/publication__title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: title - - -The title of the publication - -URI: [ibdlit:publication__title](http://w3id.org/ontogpt/ibd_literature/publication__title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/ibd_literature/docs/textWithTriples__publication.md b/projects/ibd_literature/docs/textWithTriples__publication.md deleted file mode 100644 index 504853293..000000000 --- a/projects/ibd_literature/docs/textWithTriples__publication.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: publication - - - - -URI: [ibdlit:textWithTriples__publication](http://w3id.org/ontogpt/ibd_literature/textWithTriples__publication) - - -## Domain and Range - -None → <sub>0..1</sub> [Publication](Publication.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/ibd_literature/docs/textWithTriples__triples.md b/projects/ibd_literature/docs/textWithTriples__triples.md deleted file mode 100644 index 9e55e2553..000000000 --- a/projects/ibd_literature/docs/textWithTriples__triples.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: triples - - - - -URI: [ibdlit:textWithTriples__triples](http://w3id.org/ontogpt/ibd_literature/textWithTriples__triples) - - -## Domain and Range - -None → <sub>0..\*</sub> [Triple](Triple.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/ibd_literature/docs/triple__object.md b/projects/ibd_literature/docs/triple__object.md deleted file mode 100644 index cc10dbac3..000000000 --- a/projects/ibd_literature/docs/triple__object.md +++ /dev/null @@ -1,24 +0,0 @@ - -# Slot: object - - - - -URI: [ibdlit:triple__object](http://w3id.org/ontogpt/ibd_literature/triple__object) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - * [DiseaseCellularProcessRelationship➞object](DiseaseCellularProcessRelationship_object.md) - * [GeneExposureRelationship➞object](GeneExposureRelationship_object.md) - -## Used by - - * [Triple](Triple.md) diff --git a/projects/ibd_literature/docs/triple__object_qualifier.md b/projects/ibd_literature/docs/triple__object_qualifier.md deleted file mode 100644 index 5d4e81ed9..000000000 --- a/projects/ibd_literature/docs/triple__object_qualifier.md +++ /dev/null @@ -1,24 +0,0 @@ - -# Slot: object_qualifier - - -An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - -URI: [ibdlit:triple__object_qualifier](http://w3id.org/ontogpt/ibd_literature/triple__object_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - * [DiseaseCellularProcessRelationship➞object_qualifier](DiseaseCellularProcessRelationship_object_qualifier.md) - * [GeneExposureRelationship➞object_qualifier](GeneExposureRelationship_object_qualifier.md) - -## Used by - - * [Triple](Triple.md) diff --git a/projects/ibd_literature/docs/triple__predicate.md b/projects/ibd_literature/docs/triple__predicate.md deleted file mode 100644 index 87c051c9f..000000000 --- a/projects/ibd_literature/docs/triple__predicate.md +++ /dev/null @@ -1,24 +0,0 @@ - -# Slot: predicate - - - - -URI: [ibdlit:triple__predicate](http://w3id.org/ontogpt/ibd_literature/triple__predicate) - - -## Domain and Range - -None → <sub>0..1</sub> [RelationshipType](RelationshipType.md) - -## Parents - - -## Children - - * [DiseaseCellularProcessRelationship➞predicate](DiseaseCellularProcessRelationship_predicate.md) - * [GeneExposureRelationship➞predicate](GeneExposureRelationship_predicate.md) - -## Used by - - * [Triple](Triple.md) diff --git a/projects/ibd_literature/docs/triple__qualifier.md b/projects/ibd_literature/docs/triple__qualifier.md deleted file mode 100644 index f0f66d196..000000000 --- a/projects/ibd_literature/docs/triple__qualifier.md +++ /dev/null @@ -1,24 +0,0 @@ - -# Slot: qualifier - - -A qualifier for the statements, e.g. "NOT" for negation - -URI: [ibdlit:triple__qualifier](http://w3id.org/ontogpt/ibd_literature/triple__qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [DiseaseCellularProcessRelationship](DiseaseCellularProcessRelationship.md) - * [GeneExposureRelationship](GeneExposureRelationship.md) - * [Triple](Triple.md) diff --git a/projects/ibd_literature/docs/triple__subject.md b/projects/ibd_literature/docs/triple__subject.md deleted file mode 100644 index 1f71e236e..000000000 --- a/projects/ibd_literature/docs/triple__subject.md +++ /dev/null @@ -1,24 +0,0 @@ - -# Slot: subject - - - - -URI: [ibdlit:triple__subject](http://w3id.org/ontogpt/ibd_literature/triple__subject) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - * [DiseaseCellularProcessRelationship➞subject](DiseaseCellularProcessRelationship_subject.md) - * [GeneExposureRelationship➞subject](GeneExposureRelationship_subject.md) - -## Used by - - * [Triple](Triple.md) diff --git a/projects/ibd_literature/docs/triple__subject_qualifier.md b/projects/ibd_literature/docs/triple__subject_qualifier.md deleted file mode 100644 index 146292d1f..000000000 --- a/projects/ibd_literature/docs/triple__subject_qualifier.md +++ /dev/null @@ -1,24 +0,0 @@ - -# Slot: subject_qualifier - - -An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -URI: [ibdlit:triple__subject_qualifier](http://w3id.org/ontogpt/ibd_literature/triple__subject_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - * [DiseaseCellularProcessRelationship➞subject_qualifier](DiseaseCellularProcessRelationship_subject_qualifier.md) - * [GeneExposureRelationship➞subject_qualifier](GeneExposureRelationship_subject_qualifier.md) - -## Used by - - * [Triple](Triple.md) diff --git a/projects/ibd_literature/docs/types/Boolean.md b/projects/ibd_literature/docs/types/Boolean.md deleted file mode 100644 index dc83a9c6e..000000000 --- a/projects/ibd_literature/docs/types/Boolean.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: boolean - - -A binary (true or false) value - -URI: [linkml:Boolean](https://w3id.org/linkml/Boolean) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Bool** | -| Representation | | bool | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Boolean | - diff --git a/projects/ibd_literature/docs/types/Curie.md b/projects/ibd_literature/docs/types/Curie.md deleted file mode 100644 index c1803f93f..000000000 --- a/projects/ibd_literature/docs/types/Curie.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: curie - - -a compact URI - -URI: [linkml:Curie](https://w3id.org/linkml/Curie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Curie** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations this MUST be expanded to a URI | -| | | in non-RDF serializations MAY be serialized as the compact representation | - diff --git a/projects/ibd_literature/docs/types/Date.md b/projects/ibd_literature/docs/types/Date.md deleted file mode 100644 index 06948af97..000000000 --- a/projects/ibd_literature/docs/types/Date.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: date - - -a date (year, month and day) in an idealized calendar - -URI: [linkml:Date](https://w3id.org/linkml/Date) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDate** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Date | - diff --git a/projects/ibd_literature/docs/types/DateOrDatetime.md b/projects/ibd_literature/docs/types/DateOrDatetime.md deleted file mode 100644 index ef983898d..000000000 --- a/projects/ibd_literature/docs/types/DateOrDatetime.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: date_or_datetime - - -Either a date or a datetime - -URI: [linkml:DateOrDatetime](https://w3id.org/linkml/DateOrDatetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/ibd_literature/docs/types/Datetime.md b/projects/ibd_literature/docs/types/Datetime.md deleted file mode 100644 index 9510454a8..000000000 --- a/projects/ibd_literature/docs/types/Datetime.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: datetime - - -The combination of a date and time - -URI: [linkml:Datetime](https://w3id.org/linkml/Datetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDateTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:DateTime | - diff --git a/projects/ibd_literature/docs/types/Decimal.md b/projects/ibd_literature/docs/types/Decimal.md deleted file mode 100644 index a7ba14a5d..000000000 --- a/projects/ibd_literature/docs/types/Decimal.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: decimal - - -A real number with arbitrary precision that conforms to the xsd:decimal specification - -URI: [linkml:Decimal](https://w3id.org/linkml/Decimal) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Decimal** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Broad Mappings:** | | schema:Number | - diff --git a/projects/ibd_literature/docs/types/Double.md b/projects/ibd_literature/docs/types/Double.md deleted file mode 100644 index cfe6d71e2..000000000 --- a/projects/ibd_literature/docs/types/Double.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: double - - -A real number that conforms to the xsd:double specification - -URI: [linkml:Double](https://w3id.org/linkml/Double) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Close Mappings:** | | schema:Float | - diff --git a/projects/ibd_literature/docs/types/Float.md b/projects/ibd_literature/docs/types/Float.md deleted file mode 100644 index 7b303f96f..000000000 --- a/projects/ibd_literature/docs/types/Float.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: float - - -A real number that conforms to the xsd:float specification - -URI: [linkml:Float](https://w3id.org/linkml/Float) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Float | - diff --git a/projects/ibd_literature/docs/types/Integer.md b/projects/ibd_literature/docs/types/Integer.md deleted file mode 100644 index 3cfcc66d9..000000000 --- a/projects/ibd_literature/docs/types/Integer.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: integer - - -An integer - -URI: [linkml:Integer](https://w3id.org/linkml/Integer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **int** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Integer | - diff --git a/projects/ibd_literature/docs/types/Jsonpath.md b/projects/ibd_literature/docs/types/Jsonpath.md deleted file mode 100644 index a03a58e67..000000000 --- a/projects/ibd_literature/docs/types/Jsonpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpath - - -A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpath](https://w3id.org/linkml/Jsonpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/ibd_literature/docs/types/Jsonpointer.md b/projects/ibd_literature/docs/types/Jsonpointer.md deleted file mode 100644 index a0e1ac492..000000000 --- a/projects/ibd_literature/docs/types/Jsonpointer.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpointer - - -A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpointer](https://w3id.org/linkml/Jsonpointer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/ibd_literature/docs/types/Ncname.md b/projects/ibd_literature/docs/types/Ncname.md deleted file mode 100644 index 710b0b04a..000000000 --- a/projects/ibd_literature/docs/types/Ncname.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: ncname - - -Prefix part of CURIE - -URI: [linkml:Ncname](https://w3id.org/linkml/Ncname) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NCName** | -| Representation | | str | diff --git a/projects/ibd_literature/docs/types/Nodeidentifier.md b/projects/ibd_literature/docs/types/Nodeidentifier.md deleted file mode 100644 index f0097cdf4..000000000 --- a/projects/ibd_literature/docs/types/Nodeidentifier.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: nodeidentifier - - -A URI, CURIE or BNODE that represents a node in a model. - -URI: [linkml:Nodeidentifier](https://w3id.org/linkml/Nodeidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NodeIdentifier** | -| Representation | | str | diff --git a/projects/ibd_literature/docs/types/Objectidentifier.md b/projects/ibd_literature/docs/types/Objectidentifier.md deleted file mode 100644 index 454ba6be6..000000000 --- a/projects/ibd_literature/docs/types/Objectidentifier.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: objectidentifier - - -A URI or CURIE that represents an object in the model. - -URI: [linkml:Objectidentifier](https://w3id.org/linkml/Objectidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **ElementIdentifier** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | Used for inheritance and type checking | - diff --git a/projects/ibd_literature/docs/types/Sparqlpath.md b/projects/ibd_literature/docs/types/Sparqlpath.md deleted file mode 100644 index fd99a927e..000000000 --- a/projects/ibd_literature/docs/types/Sparqlpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: sparqlpath - - -A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - -URI: [linkml:Sparqlpath](https://w3id.org/linkml/Sparqlpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/ibd_literature/docs/types/String.md b/projects/ibd_literature/docs/types/String.md deleted file mode 100644 index 6e61d7081..000000000 --- a/projects/ibd_literature/docs/types/String.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: string - - -A character string - -URI: [linkml:String](https://w3id.org/linkml/String) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Text | - diff --git a/projects/ibd_literature/docs/types/Time.md b/projects/ibd_literature/docs/types/Time.md deleted file mode 100644 index 2b8652bcd..000000000 --- a/projects/ibd_literature/docs/types/Time.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: time - - -A time object represents a (local) time of day, independent of any particular day - -URI: [linkml:Time](https://w3id.org/linkml/Time) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Time | - diff --git a/projects/ibd_literature/docs/types/Uri.md b/projects/ibd_literature/docs/types/Uri.md deleted file mode 100644 index 343807a5e..000000000 --- a/projects/ibd_literature/docs/types/Uri.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: uri - - -a complete URI - -URI: [linkml:Uri](https://w3id.org/linkml/Uri) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URI** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node | -| **Close Mappings:** | | schema:URL | - diff --git a/projects/ibd_literature/docs/types/Uriorcurie.md b/projects/ibd_literature/docs/types/Uriorcurie.md deleted file mode 100644 index 2f7b65087..000000000 --- a/projects/ibd_literature/docs/types/Uriorcurie.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: uriorcurie - - -a URI or a CURIE - -URI: [linkml:Uriorcurie](https://w3id.org/linkml/Uriorcurie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URIorCURIE** | -| Representation | | str | diff --git a/projects/ibd_literature/excel/ibd_literature.xlsx b/projects/ibd_literature/excel/ibd_literature.xlsx deleted file mode 100644 index 8fd01e326..000000000 Binary files a/projects/ibd_literature/excel/ibd_literature.xlsx and /dev/null differ diff --git a/projects/ibd_literature/graphql/ibd_literature.graphql b/projects/ibd_literature/graphql/ibd_literature.graphql deleted file mode 100644 index d894e4177..000000000 --- a/projects/ibd_literature/graphql/ibd_literature.graphql +++ /dev/null @@ -1,129 +0,0 @@ -type AnnotatorResult - { - subjectText: String - objectId: String - objectText: String - } - -type Any - { - } - -type CellularProcess - { - id: String! - label: String - } - -type ChemicalExposure - { - id: String! - label: String - } - -type ChemicalExposureToGenePredicate - { - id: String! - label: String - } - -interface CompoundExpression - { - } - -type Disease - { - id: String! - label: String - } - -type DiseaseCellularProcessRelationship - { - qualifier: String - subject: Disease - predicate: DiseaseToCellularProcessPredicate - object: CellularProcess - subjectQualifier: NamedEntity - objectQualifier: NamedEntity - } - -type DiseaseToCellularProcessPredicate - { - id: String! - label: String - } - -type ExtractionResult - { - inputId: String - inputTitle: String - inputText: String - rawCompletionOutput: String - prompt: String - extractedObject: Any - namedEntities: [Any] - } - -type Gene - { - id: String! - label: String - } - -type GeneExposureRelationship - { - qualifier: String - subject: ChemicalExposure - predicate: ChemicalExposureToGenePredicate - object: Gene - subjectQualifier: NamedEntity - objectQualifier: NamedEntity - } - -type IBDAnnotations - { - genes: [Gene] - exposures: [ChemicalExposure] - geneExposuresRelationships: [GeneExposureRelationship] - diseases: [Disease] - cellularProcess: [CellularProcess] - diseaseCellularProcessRelationships: [DiseaseCellularProcessRelationship] - } - -interface NamedEntity - { - id: String! - label: String - } - -type Publication - { - id: String - title: String - abstract: String - combinedText: String - fullText: String - } - -type RelationshipType - { - id: String! - label: String - } - -type TextWithTriples - { - publication: Publication - triples: [Triple] - } - -interface Triple - { - subject: NamedEntity - predicate: RelationshipType - object: NamedEntity - qualifier: String - subjectQualifier: NamedEntity - objectQualifier: NamedEntity - } - diff --git a/projects/ibd_literature/ibd_literature.py b/projects/ibd_literature/ibd_literature.py deleted file mode 100644 index 29ee09d90..000000000 --- a/projects/ibd_literature/ibd_literature.py +++ /dev/null @@ -1,673 +0,0 @@ -# Auto generated from ibd_literature.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-08-07T11:00:44 -# Schema: ibd-literature-template -# -# id: http://w3id.org/ontogpt/ibd_literature -# description: A template for extracting information from IBD literature -# license: https://creativecommons.org/publicdomain/zero/1.0/ - -import dataclasses -import sys -import re -from jsonasobj2 import JsonObj, as_dict -from typing import Optional, List, Union, Dict, ClassVar, Any -from dataclasses import dataclass -from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions - -from linkml_runtime.utils.slot import Slot -from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode -from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int -from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs -from linkml_runtime.utils.formatutils import camelcase, underscore, sfx -from linkml_runtime.utils.enumerations import EnumDefinitionImpl -from rdflib import Namespace, URIRef -from linkml_runtime.utils.curienamespace import CurieNamespace -from linkml_runtime.linkml_model.types import String - -metamodel_version = "1.7.0" -version = None - -# Overwrite dataclasses _init_fn to add **kwargs in __init__ -dataclasses._init_fn = dataclasses_init_fn_with_kwargs - -# Namespaces -CHEBI = CurieNamespace('CHEBI', 'http://purl.obolibrary.org/obo/CHEBI_') -ECTO = CurieNamespace('ECTO', 'http://purl.obolibrary.org/obo/ECTO_') -EXO = CurieNamespace('ExO', 'http://purl.obolibrary.org/obo/ExO_') -GO = CurieNamespace('GO', 'http://example.org/UNKNOWN/GO/') -HGNC = CurieNamespace('HGNC', 'http://identifiers.org/hgnc/') -MONDO = CurieNamespace('MONDO', 'http://example.org/UNKNOWN/MONDO/') -NCIT = CurieNamespace('NCIT', 'http://purl.obolibrary.org/obo/NCIT_') -RO = CurieNamespace('RO', 'http://purl.obolibrary.org/obo/RO_') -BIOLINK = CurieNamespace('biolink', 'http://example.org/UNKNOWN/biolink/') -CORE = CurieNamespace('core', 'http://w3id.org/ontogpt/core/') -IBDLIT = CurieNamespace('ibdlit', 'http://w3id.org/ontogpt/ibd_literature/') -LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') -RDFS = CurieNamespace('rdfs', 'http://example.org/UNKNOWN/rdfs/') -DEFAULT_ = IBDLIT - - -# Types - -# Class references -class NamedEntityId(extended_str): - pass - - -class GeneId(NamedEntityId): - pass - - -class DiseaseId(NamedEntityId): - pass - - -class CellularProcessId(NamedEntityId): - pass - - -class ChemicalExposureId(NamedEntityId): - pass - - -class RelationshipTypeId(NamedEntityId): - pass - - -class DiseaseToCellularProcessPredicateId(RelationshipTypeId): - pass - - -class ChemicalExposureToGenePredicateId(RelationshipTypeId): - pass - - -@dataclass -class IBDAnnotations(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = IBDLIT.IBDAnnotations - class_class_curie: ClassVar[str] = "ibdlit:IBDAnnotations" - class_name: ClassVar[str] = "IBDAnnotations" - class_model_uri: ClassVar[URIRef] = IBDLIT.IBDAnnotations - - genes: Optional[Union[Union[str, GeneId], List[Union[str, GeneId]]]] = empty_list() - exposures: Optional[Union[Union[str, ChemicalExposureId], List[Union[str, ChemicalExposureId]]]] = empty_list() - gene_exposures_relationships: Optional[Union[Union[dict, "GeneExposureRelationship"], List[Union[dict, "GeneExposureRelationship"]]]] = empty_list() - diseases: Optional[Union[Union[str, DiseaseId], List[Union[str, DiseaseId]]]] = empty_list() - cellular_process: Optional[Union[Union[str, CellularProcessId], List[Union[str, CellularProcessId]]]] = empty_list() - disease_cellular_process_relationships: Optional[Union[Union[dict, "DiseaseCellularProcessRelationship"], List[Union[dict, "DiseaseCellularProcessRelationship"]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if not isinstance(self.genes, list): - self.genes = [self.genes] if self.genes is not None else [] - self.genes = [v if isinstance(v, GeneId) else GeneId(v) for v in self.genes] - - if not isinstance(self.exposures, list): - self.exposures = [self.exposures] if self.exposures is not None else [] - self.exposures = [v if isinstance(v, ChemicalExposureId) else ChemicalExposureId(v) for v in self.exposures] - - if not isinstance(self.gene_exposures_relationships, list): - self.gene_exposures_relationships = [self.gene_exposures_relationships] if self.gene_exposures_relationships is not None else [] - self.gene_exposures_relationships = [v if isinstance(v, GeneExposureRelationship) else GeneExposureRelationship(**as_dict(v)) for v in self.gene_exposures_relationships] - - if not isinstance(self.diseases, list): - self.diseases = [self.diseases] if self.diseases is not None else [] - self.diseases = [v if isinstance(v, DiseaseId) else DiseaseId(v) for v in self.diseases] - - if not isinstance(self.cellular_process, list): - self.cellular_process = [self.cellular_process] if self.cellular_process is not None else [] - self.cellular_process = [v if isinstance(v, CellularProcessId) else CellularProcessId(v) for v in self.cellular_process] - - if not isinstance(self.disease_cellular_process_relationships, list): - self.disease_cellular_process_relationships = [self.disease_cellular_process_relationships] if self.disease_cellular_process_relationships is not None else [] - self.disease_cellular_process_relationships = [v if isinstance(v, DiseaseCellularProcessRelationship) else DiseaseCellularProcessRelationship(**as_dict(v)) for v in self.disease_cellular_process_relationships] - - super().__post_init__(**kwargs) - - -Any = Any - -@dataclass -class ExtractionResult(YAMLRoot): - """ - A result of extracting knowledge on text - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.ExtractionResult - class_class_curie: ClassVar[str] = "core:ExtractionResult" - class_name: ClassVar[str] = "ExtractionResult" - class_model_uri: ClassVar[URIRef] = IBDLIT.ExtractionResult - - input_id: Optional[str] = None - input_title: Optional[str] = None - input_text: Optional[str] = None - raw_completion_output: Optional[str] = None - prompt: Optional[str] = None - extracted_object: Optional[Union[dict, Any]] = None - named_entities: Optional[Union[Union[dict, Any], List[Union[dict, Any]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.input_id is not None and not isinstance(self.input_id, str): - self.input_id = str(self.input_id) - - if self.input_title is not None and not isinstance(self.input_title, str): - self.input_title = str(self.input_title) - - if self.input_text is not None and not isinstance(self.input_text, str): - self.input_text = str(self.input_text) - - if self.raw_completion_output is not None and not isinstance(self.raw_completion_output, str): - self.raw_completion_output = str(self.raw_completion_output) - - if self.prompt is not None and not isinstance(self.prompt, str): - self.prompt = str(self.prompt) - - super().__post_init__(**kwargs) - - -@dataclass -class NamedEntity(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.NamedEntity - class_class_curie: ClassVar[str] = "core:NamedEntity" - class_name: ClassVar[str] = "NamedEntity" - class_model_uri: ClassVar[URIRef] = IBDLIT.NamedEntity - - id: Union[str, NamedEntityId] = None - label: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, NamedEntityId): - self.id = NamedEntityId(self.id) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - super().__post_init__(**kwargs) - - -@dataclass -class Gene(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = IBDLIT.Gene - class_class_curie: ClassVar[str] = "ibdlit:Gene" - class_name: ClassVar[str] = "Gene" - class_model_uri: ClassVar[URIRef] = IBDLIT.Gene - - id: Union[str, GeneId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, GeneId): - self.id = GeneId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Disease(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = IBDLIT.Disease - class_class_curie: ClassVar[str] = "ibdlit:Disease" - class_name: ClassVar[str] = "Disease" - class_model_uri: ClassVar[URIRef] = IBDLIT.Disease - - id: Union[str, DiseaseId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, DiseaseId): - self.id = DiseaseId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class CellularProcess(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = IBDLIT.CellularProcess - class_class_curie: ClassVar[str] = "ibdlit:CellularProcess" - class_name: ClassVar[str] = "CellularProcess" - class_model_uri: ClassVar[URIRef] = IBDLIT.CellularProcess - - id: Union[str, CellularProcessId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, CellularProcessId): - self.id = CellularProcessId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class ChemicalExposure(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = IBDLIT.ChemicalExposure - class_class_curie: ClassVar[str] = "ibdlit:ChemicalExposure" - class_name: ClassVar[str] = "ChemicalExposure" - class_model_uri: ClassVar[URIRef] = IBDLIT.ChemicalExposure - - id: Union[str, ChemicalExposureId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, ChemicalExposureId): - self.id = ChemicalExposureId(self.id) - - super().__post_init__(**kwargs) - - -class CompoundExpression(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.CompoundExpression - class_class_curie: ClassVar[str] = "core:CompoundExpression" - class_name: ClassVar[str] = "CompoundExpression" - class_model_uri: ClassVar[URIRef] = IBDLIT.CompoundExpression - - -@dataclass -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Triple - class_class_curie: ClassVar[str] = "core:Triple" - class_name: ClassVar[str] = "Triple" - class_model_uri: ClassVar[URIRef] = IBDLIT.Triple - - subject: Optional[Union[str, NamedEntityId]] = None - predicate: Optional[Union[str, RelationshipTypeId]] = None - object: Optional[Union[str, NamedEntityId]] = None - qualifier: Optional[str] = None - subject_qualifier: Optional[Union[str, NamedEntityId]] = None - object_qualifier: Optional[Union[str, NamedEntityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, NamedEntityId): - self.subject = NamedEntityId(self.subject) - - if self.predicate is not None and not isinstance(self.predicate, RelationshipTypeId): - self.predicate = RelationshipTypeId(self.predicate) - - if self.object is not None and not isinstance(self.object, NamedEntityId): - self.object = NamedEntityId(self.object) - - if self.qualifier is not None and not isinstance(self.qualifier, str): - self.qualifier = str(self.qualifier) - - if self.subject_qualifier is not None and not isinstance(self.subject_qualifier, NamedEntityId): - self.subject_qualifier = NamedEntityId(self.subject_qualifier) - - if self.object_qualifier is not None and not isinstance(self.object_qualifier, NamedEntityId): - self.object_qualifier = NamedEntityId(self.object_qualifier) - - super().__post_init__(**kwargs) - - -@dataclass -class DiseaseCellularProcessRelationship(Triple): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = IBDLIT.DiseaseCellularProcessRelationship - class_class_curie: ClassVar[str] = "ibdlit:DiseaseCellularProcessRelationship" - class_name: ClassVar[str] = "DiseaseCellularProcessRelationship" - class_model_uri: ClassVar[URIRef] = IBDLIT.DiseaseCellularProcessRelationship - - subject: Optional[Union[str, DiseaseId]] = None - predicate: Optional[Union[str, DiseaseToCellularProcessPredicateId]] = None - object: Optional[Union[str, CellularProcessId]] = None - subject_qualifier: Optional[Union[str, NamedEntityId]] = None - object_qualifier: Optional[Union[str, NamedEntityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, DiseaseId): - self.subject = DiseaseId(self.subject) - - if self.predicate is not None and not isinstance(self.predicate, DiseaseToCellularProcessPredicateId): - self.predicate = DiseaseToCellularProcessPredicateId(self.predicate) - - if self.object is not None and not isinstance(self.object, CellularProcessId): - self.object = CellularProcessId(self.object) - - if self.subject_qualifier is not None and not isinstance(self.subject_qualifier, NamedEntityId): - self.subject_qualifier = NamedEntityId(self.subject_qualifier) - - if self.object_qualifier is not None and not isinstance(self.object_qualifier, NamedEntityId): - self.object_qualifier = NamedEntityId(self.object_qualifier) - - super().__post_init__(**kwargs) - - -@dataclass -class GeneExposureRelationship(Triple): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = IBDLIT.GeneExposureRelationship - class_class_curie: ClassVar[str] = "ibdlit:GeneExposureRelationship" - class_name: ClassVar[str] = "GeneExposureRelationship" - class_model_uri: ClassVar[URIRef] = IBDLIT.GeneExposureRelationship - - subject: Optional[Union[str, ChemicalExposureId]] = None - predicate: Optional[Union[str, ChemicalExposureToGenePredicateId]] = None - object: Optional[Union[str, GeneId]] = None - subject_qualifier: Optional[Union[str, NamedEntityId]] = None - object_qualifier: Optional[Union[str, NamedEntityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, ChemicalExposureId): - self.subject = ChemicalExposureId(self.subject) - - if self.predicate is not None and not isinstance(self.predicate, ChemicalExposureToGenePredicateId): - self.predicate = ChemicalExposureToGenePredicateId(self.predicate) - - if self.object is not None and not isinstance(self.object, GeneId): - self.object = GeneId(self.object) - - if self.subject_qualifier is not None and not isinstance(self.subject_qualifier, NamedEntityId): - self.subject_qualifier = NamedEntityId(self.subject_qualifier) - - if self.object_qualifier is not None and not isinstance(self.object_qualifier, NamedEntityId): - self.object_qualifier = NamedEntityId(self.object_qualifier) - - super().__post_init__(**kwargs) - - -@dataclass -class TextWithTriples(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.TextWithTriples - class_class_curie: ClassVar[str] = "core:TextWithTriples" - class_name: ClassVar[str] = "TextWithTriples" - class_model_uri: ClassVar[URIRef] = IBDLIT.TextWithTriples - - publication: Optional[Union[dict, "Publication"]] = None - triples: Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.publication is not None and not isinstance(self.publication, Publication): - self.publication = Publication(**as_dict(self.publication)) - - if not isinstance(self.triples, list): - self.triples = [self.triples] if self.triples is not None else [] - self.triples = [v if isinstance(v, Triple) else Triple(**as_dict(v)) for v in self.triples] - - super().__post_init__(**kwargs) - - -@dataclass -class RelationshipType(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.RelationshipType - class_class_curie: ClassVar[str] = "core:RelationshipType" - class_name: ClassVar[str] = "RelationshipType" - class_model_uri: ClassVar[URIRef] = IBDLIT.RelationshipType - - id: Union[str, RelationshipTypeId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, RelationshipTypeId): - self.id = RelationshipTypeId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class DiseaseToCellularProcessPredicate(RelationshipType): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = IBDLIT.DiseaseToCellularProcessPredicate - class_class_curie: ClassVar[str] = "ibdlit:DiseaseToCellularProcessPredicate" - class_name: ClassVar[str] = "DiseaseToCellularProcessPredicate" - class_model_uri: ClassVar[URIRef] = IBDLIT.DiseaseToCellularProcessPredicate - - id: Union[str, DiseaseToCellularProcessPredicateId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, DiseaseToCellularProcessPredicateId): - self.id = DiseaseToCellularProcessPredicateId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class ChemicalExposureToGenePredicate(RelationshipType): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = IBDLIT.ChemicalExposureToGenePredicate - class_class_curie: ClassVar[str] = "ibdlit:ChemicalExposureToGenePredicate" - class_name: ClassVar[str] = "ChemicalExposureToGenePredicate" - class_model_uri: ClassVar[URIRef] = IBDLIT.ChemicalExposureToGenePredicate - - id: Union[str, ChemicalExposureToGenePredicateId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, ChemicalExposureToGenePredicateId): - self.id = ChemicalExposureToGenePredicateId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Publication(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Publication - class_class_curie: ClassVar[str] = "core:Publication" - class_name: ClassVar[str] = "Publication" - class_model_uri: ClassVar[URIRef] = IBDLIT.Publication - - id: Optional[str] = None - title: Optional[str] = None - abstract: Optional[str] = None - combined_text: Optional[str] = None - full_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.id is not None and not isinstance(self.id, str): - self.id = str(self.id) - - if self.title is not None and not isinstance(self.title, str): - self.title = str(self.title) - - if self.abstract is not None and not isinstance(self.abstract, str): - self.abstract = str(self.abstract) - - if self.combined_text is not None and not isinstance(self.combined_text, str): - self.combined_text = str(self.combined_text) - - if self.full_text is not None and not isinstance(self.full_text, str): - self.full_text = str(self.full_text) - - super().__post_init__(**kwargs) - - -@dataclass -class AnnotatorResult(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.AnnotatorResult - class_class_curie: ClassVar[str] = "core:AnnotatorResult" - class_name: ClassVar[str] = "AnnotatorResult" - class_model_uri: ClassVar[URIRef] = IBDLIT.AnnotatorResult - - subject_text: Optional[str] = None - object_id: Optional[str] = None - object_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject_text is not None and not isinstance(self.subject_text, str): - self.subject_text = str(self.subject_text) - - if self.object_id is not None and not isinstance(self.object_id, str): - self.object_id = str(self.object_id) - - if self.object_text is not None and not isinstance(self.object_text, str): - self.object_text = str(self.object_text) - - super().__post_init__(**kwargs) - - -# Enumerations -class NullDataOptions(EnumDefinitionImpl): - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = PermissibleValue(text="UNSPECIFIED_METHOD_OF_ADMINISTRATION", - meaning=NCIT.C149701) - NOT_APPLICABLE = PermissibleValue(text="NOT_APPLICABLE", - meaning=NCIT.C18902) - NOT_MENTIONED = PermissibleValue(text="NOT_MENTIONED") - - _defn = EnumDefinition( - name="NullDataOptions", - ) - -# Slots -class slots: - pass - -slots.iBDAnnotations__genes = Slot(uri=IBDLIT.genes, name="iBDAnnotations__genes", curie=IBDLIT.curie('genes'), - model_uri=IBDLIT.iBDAnnotations__genes, domain=None, range=Optional[Union[Union[str, GeneId], List[Union[str, GeneId]]]]) - -slots.iBDAnnotations__exposures = Slot(uri=IBDLIT.exposures, name="iBDAnnotations__exposures", curie=IBDLIT.curie('exposures'), - model_uri=IBDLIT.iBDAnnotations__exposures, domain=None, range=Optional[Union[Union[str, ChemicalExposureId], List[Union[str, ChemicalExposureId]]]]) - -slots.iBDAnnotations__gene_exposures_relationships = Slot(uri=IBDLIT.gene_exposures_relationships, name="iBDAnnotations__gene_exposures_relationships", curie=IBDLIT.curie('gene_exposures_relationships'), - model_uri=IBDLIT.iBDAnnotations__gene_exposures_relationships, domain=None, range=Optional[Union[Union[dict, GeneExposureRelationship], List[Union[dict, GeneExposureRelationship]]]]) - -slots.iBDAnnotations__diseases = Slot(uri=IBDLIT.diseases, name="iBDAnnotations__diseases", curie=IBDLIT.curie('diseases'), - model_uri=IBDLIT.iBDAnnotations__diseases, domain=None, range=Optional[Union[Union[str, DiseaseId], List[Union[str, DiseaseId]]]]) - -slots.iBDAnnotations__cellular_process = Slot(uri=IBDLIT.cellular_process, name="iBDAnnotations__cellular_process", curie=IBDLIT.curie('cellular_process'), - model_uri=IBDLIT.iBDAnnotations__cellular_process, domain=None, range=Optional[Union[Union[str, CellularProcessId], List[Union[str, CellularProcessId]]]]) - -slots.iBDAnnotations__disease_cellular_process_relationships = Slot(uri=IBDLIT.disease_cellular_process_relationships, name="iBDAnnotations__disease_cellular_process_relationships", curie=IBDLIT.curie('disease_cellular_process_relationships'), - model_uri=IBDLIT.iBDAnnotations__disease_cellular_process_relationships, domain=None, range=Optional[Union[Union[dict, DiseaseCellularProcessRelationship], List[Union[dict, DiseaseCellularProcessRelationship]]]]) - -slots.extractionResult__input_id = Slot(uri=CORE.input_id, name="extractionResult__input_id", curie=CORE.curie('input_id'), - model_uri=IBDLIT.extractionResult__input_id, domain=None, range=Optional[str]) - -slots.extractionResult__input_title = Slot(uri=CORE.input_title, name="extractionResult__input_title", curie=CORE.curie('input_title'), - model_uri=IBDLIT.extractionResult__input_title, domain=None, range=Optional[str]) - -slots.extractionResult__input_text = Slot(uri=CORE.input_text, name="extractionResult__input_text", curie=CORE.curie('input_text'), - model_uri=IBDLIT.extractionResult__input_text, domain=None, range=Optional[str]) - -slots.extractionResult__raw_completion_output = Slot(uri=CORE.raw_completion_output, name="extractionResult__raw_completion_output", curie=CORE.curie('raw_completion_output'), - model_uri=IBDLIT.extractionResult__raw_completion_output, domain=None, range=Optional[str]) - -slots.extractionResult__prompt = Slot(uri=CORE.prompt, name="extractionResult__prompt", curie=CORE.curie('prompt'), - model_uri=IBDLIT.extractionResult__prompt, domain=None, range=Optional[str]) - -slots.extractionResult__extracted_object = Slot(uri=CORE.extracted_object, name="extractionResult__extracted_object", curie=CORE.curie('extracted_object'), - model_uri=IBDLIT.extractionResult__extracted_object, domain=None, range=Optional[Union[dict, Any]]) - -slots.extractionResult__named_entities = Slot(uri=CORE.named_entities, name="extractionResult__named_entities", curie=CORE.curie('named_entities'), - model_uri=IBDLIT.extractionResult__named_entities, domain=None, range=Optional[Union[Union[dict, Any], List[Union[dict, Any]]]]) - -slots.namedEntity__id = Slot(uri=CORE.id, name="namedEntity__id", curie=CORE.curie('id'), - model_uri=IBDLIT.namedEntity__id, domain=None, range=URIRef) - -slots.namedEntity__label = Slot(uri=RDFS.label, name="namedEntity__label", curie=RDFS.curie('label'), - model_uri=IBDLIT.namedEntity__label, domain=None, range=Optional[str]) - -slots.triple__subject = Slot(uri=CORE.subject, name="triple__subject", curie=CORE.curie('subject'), - model_uri=IBDLIT.triple__subject, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__predicate = Slot(uri=CORE.predicate, name="triple__predicate", curie=CORE.curie('predicate'), - model_uri=IBDLIT.triple__predicate, domain=None, range=Optional[Union[str, RelationshipTypeId]]) - -slots.triple__object = Slot(uri=CORE.object, name="triple__object", curie=CORE.curie('object'), - model_uri=IBDLIT.triple__object, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__qualifier = Slot(uri=CORE.qualifier, name="triple__qualifier", curie=CORE.curie('qualifier'), - model_uri=IBDLIT.triple__qualifier, domain=None, range=Optional[str]) - -slots.triple__subject_qualifier = Slot(uri=CORE.subject_qualifier, name="triple__subject_qualifier", curie=CORE.curie('subject_qualifier'), - model_uri=IBDLIT.triple__subject_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__object_qualifier = Slot(uri=CORE.object_qualifier, name="triple__object_qualifier", curie=CORE.curie('object_qualifier'), - model_uri=IBDLIT.triple__object_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.textWithTriples__publication = Slot(uri=CORE.publication, name="textWithTriples__publication", curie=CORE.curie('publication'), - model_uri=IBDLIT.textWithTriples__publication, domain=None, range=Optional[Union[dict, Publication]]) - -slots.textWithTriples__triples = Slot(uri=CORE.triples, name="textWithTriples__triples", curie=CORE.curie('triples'), - model_uri=IBDLIT.textWithTriples__triples, domain=None, range=Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]]) - -slots.publication__id = Slot(uri=CORE.id, name="publication__id", curie=CORE.curie('id'), - model_uri=IBDLIT.publication__id, domain=None, range=Optional[str]) - -slots.publication__title = Slot(uri=CORE.title, name="publication__title", curie=CORE.curie('title'), - model_uri=IBDLIT.publication__title, domain=None, range=Optional[str]) - -slots.publication__abstract = Slot(uri=CORE.abstract, name="publication__abstract", curie=CORE.curie('abstract'), - model_uri=IBDLIT.publication__abstract, domain=None, range=Optional[str]) - -slots.publication__combined_text = Slot(uri=CORE.combined_text, name="publication__combined_text", curie=CORE.curie('combined_text'), - model_uri=IBDLIT.publication__combined_text, domain=None, range=Optional[str]) - -slots.publication__full_text = Slot(uri=CORE.full_text, name="publication__full_text", curie=CORE.curie('full_text'), - model_uri=IBDLIT.publication__full_text, domain=None, range=Optional[str]) - -slots.annotatorResult__subject_text = Slot(uri=CORE.subject_text, name="annotatorResult__subject_text", curie=CORE.curie('subject_text'), - model_uri=IBDLIT.annotatorResult__subject_text, domain=None, range=Optional[str]) - -slots.annotatorResult__object_id = Slot(uri=CORE.object_id, name="annotatorResult__object_id", curie=CORE.curie('object_id'), - model_uri=IBDLIT.annotatorResult__object_id, domain=None, range=Optional[str]) - -slots.annotatorResult__object_text = Slot(uri=CORE.object_text, name="annotatorResult__object_text", curie=CORE.curie('object_text'), - model_uri=IBDLIT.annotatorResult__object_text, domain=None, range=Optional[str]) - -slots.DiseaseCellularProcessRelationship_subject = Slot(uri=IBDLIT.subject, name="DiseaseCellularProcessRelationship_subject", curie=IBDLIT.curie('subject'), - model_uri=IBDLIT.DiseaseCellularProcessRelationship_subject, domain=DiseaseCellularProcessRelationship, range=Optional[Union[str, DiseaseId]]) - -slots.DiseaseCellularProcessRelationship_predicate = Slot(uri=IBDLIT.predicate, name="DiseaseCellularProcessRelationship_predicate", curie=IBDLIT.curie('predicate'), - model_uri=IBDLIT.DiseaseCellularProcessRelationship_predicate, domain=DiseaseCellularProcessRelationship, range=Optional[Union[str, DiseaseToCellularProcessPredicateId]]) - -slots.DiseaseCellularProcessRelationship_object = Slot(uri=IBDLIT.object, name="DiseaseCellularProcessRelationship_object", curie=IBDLIT.curie('object'), - model_uri=IBDLIT.DiseaseCellularProcessRelationship_object, domain=DiseaseCellularProcessRelationship, range=Optional[Union[str, CellularProcessId]]) - -slots.DiseaseCellularProcessRelationship_subject_qualifier = Slot(uri=IBDLIT.subject_qualifier, name="DiseaseCellularProcessRelationship_subject_qualifier", curie=IBDLIT.curie('subject_qualifier'), - model_uri=IBDLIT.DiseaseCellularProcessRelationship_subject_qualifier, domain=DiseaseCellularProcessRelationship, range=Optional[Union[str, NamedEntityId]]) - -slots.DiseaseCellularProcessRelationship_object_qualifier = Slot(uri=IBDLIT.object_qualifier, name="DiseaseCellularProcessRelationship_object_qualifier", curie=IBDLIT.curie('object_qualifier'), - model_uri=IBDLIT.DiseaseCellularProcessRelationship_object_qualifier, domain=DiseaseCellularProcessRelationship, range=Optional[Union[str, NamedEntityId]]) - -slots.GeneExposureRelationship_subject = Slot(uri=IBDLIT.subject, name="GeneExposureRelationship_subject", curie=IBDLIT.curie('subject'), - model_uri=IBDLIT.GeneExposureRelationship_subject, domain=GeneExposureRelationship, range=Optional[Union[str, ChemicalExposureId]]) - -slots.GeneExposureRelationship_predicate = Slot(uri=IBDLIT.predicate, name="GeneExposureRelationship_predicate", curie=IBDLIT.curie('predicate'), - model_uri=IBDLIT.GeneExposureRelationship_predicate, domain=GeneExposureRelationship, range=Optional[Union[str, ChemicalExposureToGenePredicateId]]) - -slots.GeneExposureRelationship_object = Slot(uri=IBDLIT.object, name="GeneExposureRelationship_object", curie=IBDLIT.curie('object'), - model_uri=IBDLIT.GeneExposureRelationship_object, domain=GeneExposureRelationship, range=Optional[Union[str, GeneId]]) - -slots.GeneExposureRelationship_subject_qualifier = Slot(uri=IBDLIT.subject_qualifier, name="GeneExposureRelationship_subject_qualifier", curie=IBDLIT.curie('subject_qualifier'), - model_uri=IBDLIT.GeneExposureRelationship_subject_qualifier, domain=GeneExposureRelationship, range=Optional[Union[str, NamedEntityId]]) - -slots.GeneExposureRelationship_object_qualifier = Slot(uri=IBDLIT.object_qualifier, name="GeneExposureRelationship_object_qualifier", curie=IBDLIT.curie('object_qualifier'), - model_uri=IBDLIT.GeneExposureRelationship_object_qualifier, domain=GeneExposureRelationship, range=Optional[Union[str, NamedEntityId]]) \ No newline at end of file diff --git a/projects/ibd_literature/jsonld/ibd_literature.context.jsonld b/projects/ibd_literature/jsonld/ibd_literature.context.jsonld deleted file mode 100644 index 867e19231..000000000 --- a/projects/ibd_literature/jsonld/ibd_literature.context.jsonld +++ /dev/null @@ -1,164 +0,0 @@ -{ - "comments": { - "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2023-08-07T11:00:34", - "source": "ibd_literature.yaml" - }, - "@context": { - "CHEBI": { - "@id": "http://purl.obolibrary.org/obo/CHEBI_", - "@prefix": true - }, - "ECTO": { - "@id": "http://purl.obolibrary.org/obo/ECTO_", - "@prefix": true - }, - "ExO": { - "@id": "http://purl.obolibrary.org/obo/ExO_", - "@prefix": true - }, - "GO": "http://example.org/UNKNOWN/GO/", - "HGNC": "http://identifiers.org/hgnc/", - "MONDO": "http://example.org/UNKNOWN/MONDO/", - "NCIT": { - "@id": "http://purl.obolibrary.org/obo/NCIT_", - "@prefix": true - }, - "RO": { - "@id": "http://purl.obolibrary.org/obo/RO_", - "@prefix": true - }, - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "ibdlit": "http://w3id.org/ontogpt/ibd_literature/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "@vocab": "http://w3id.org/ontogpt/ibd_literature/", - "object_id": { - "@id": "core:object_id" - }, - "object_text": { - "@id": "core:object_text" - }, - "subject_text": { - "@id": "core:subject_text" - }, - "extracted_object": { - "@type": "@id", - "@id": "core:extracted_object" - }, - "input_id": { - "@id": "core:input_id" - }, - "input_text": { - "@id": "core:input_text" - }, - "input_title": { - "@id": "core:input_title" - }, - "named_entities": { - "@type": "@id", - "@id": "core:named_entities" - }, - "prompt": { - "@id": "core:prompt" - }, - "raw_completion_output": { - "@id": "core:raw_completion_output" - }, - "cellular_process": { - "@type": "@id" - }, - "disease_cellular_process_relationships": { - "@type": "@id" - }, - "diseases": { - "@type": "@id" - }, - "exposures": { - "@type": "@id" - }, - "gene_exposures_relationships": { - "@type": "@id" - }, - "genes": { - "@type": "@id" - }, - "id": { - "@id": "core:id" - }, - "label": { - "@id": "rdfs:label" - }, - "abstract": { - "@id": "core:abstract" - }, - "combined_text": { - "@id": "core:combined_text" - }, - "full_text": { - "@id": "core:full_text" - }, - "title": { - "@id": "core:title" - }, - "publication": { - "@type": "@id", - "@id": "core:publication" - }, - "triples": { - "@type": "@id", - "@id": "core:triples" - }, - "object": { - "@type": "@id", - "@id": "core:object" - }, - "object_qualifier": { - "@type": "@id", - "@id": "core:object_qualifier" - }, - "predicate": { - "@type": "@id", - "@id": "core:predicate" - }, - "qualifier": { - "@id": "core:qualifier" - }, - "subject": { - "@type": "@id", - "@id": "core:subject" - }, - "subject_qualifier": { - "@type": "@id", - "@id": "core:subject_qualifier" - }, - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } - } -} diff --git a/projects/ibd_literature/jsonld/ibd_literature.jsonld b/projects/ibd_literature/jsonld/ibd_literature.jsonld deleted file mode 100644 index 9e613ceab..000000000 --- a/projects/ibd_literature/jsonld/ibd_literature.jsonld +++ /dev/null @@ -1,1529 +0,0 @@ -{ - "name": "ibd-literature-template", - "description": "A template for extracting information from IBD literature", - "title": "IBD Literature Template", - "id": "http://w3id.org/ontogpt/ibd_literature", - "imports": [ - "linkml:types", - "core" - ], - "license": "https://creativecommons.org/publicdomain/zero/1.0/", - "prefixes": [ - { - "prefix_prefix": "CHEBI", - "prefix_reference": "http://purl.obolibrary.org/obo/CHEBI_" - }, - { - "prefix_prefix": "ECTO", - "prefix_reference": "http://purl.obolibrary.org/obo/ECTO_" - }, - { - "prefix_prefix": "ExO", - "prefix_reference": "http://purl.obolibrary.org/obo/ExO_" - }, - { - "prefix_prefix": "HGNC", - "prefix_reference": "http://identifiers.org/hgnc/" - }, - { - "prefix_prefix": "NCIT", - "prefix_reference": "http://purl.obolibrary.org/obo/NCIT_" - }, - { - "prefix_prefix": "core", - "prefix_reference": "http://w3id.org/ontogpt/core/" - }, - { - "prefix_prefix": "ibdlit", - "prefix_reference": "http://w3id.org/ontogpt/ibd_literature/" - }, - { - "prefix_prefix": "linkml", - "prefix_reference": "https://w3id.org/linkml/" - } - ], - "default_prefix": "ibdlit", - "default_range": "string", - "types": [ - { - "name": "string", - "definition_uri": "https://w3id.org/linkml/String", - "description": "A character string", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Text" - ], - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "@type": "TypeDefinition" - }, - { - "name": "integer", - "definition_uri": "https://w3id.org/linkml/Integer", - "description": "An integer", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Integer" - ], - "base": "int", - "uri": "http://www.w3.org/2001/XMLSchema#integer", - "@type": "TypeDefinition" - }, - { - "name": "boolean", - "definition_uri": "https://w3id.org/linkml/Boolean", - "description": "A binary (true or false) value", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Boolean" - ], - "base": "Bool", - "uri": "http://www.w3.org/2001/XMLSchema#boolean", - "repr": "bool", - "@type": "TypeDefinition" - }, - { - "name": "float", - "definition_uri": "https://w3id.org/linkml/Float", - "description": "A real number that conforms to the xsd:float specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#float", - "@type": "TypeDefinition" - }, - { - "name": "double", - "definition_uri": "https://w3id.org/linkml/Double", - "description": "A real number that conforms to the xsd:double specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#double", - "@type": "TypeDefinition" - }, - { - "name": "decimal", - "definition_uri": "https://w3id.org/linkml/Decimal", - "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "broad_mappings": [ - "schema:Number" - ], - "base": "Decimal", - "uri": "http://www.w3.org/2001/XMLSchema#decimal", - "@type": "TypeDefinition" - }, - { - "name": "time", - "definition_uri": "https://w3id.org/linkml/Time", - "description": "A time object represents a (local) time of day, independent of any particular day", - "notes": [ - "URI is dateTime because OWL reasoners do not work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Time" - ], - "base": "XSDTime", - "uri": "http://www.w3.org/2001/XMLSchema#time", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date", - "definition_uri": "https://w3id.org/linkml/Date", - "description": "a date (year, month and day) in an idealized calendar", - "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Date" - ], - "base": "XSDDate", - "uri": "http://www.w3.org/2001/XMLSchema#date", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "datetime", - "definition_uri": "https://w3id.org/linkml/Datetime", - "description": "The combination of a date and time", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:DateTime" - ], - "base": "XSDDateTime", - "uri": "http://www.w3.org/2001/XMLSchema#dateTime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date_or_datetime", - "definition_uri": "https://w3id.org/linkml/DateOrDatetime", - "description": "Either a date or a datetime", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "https://w3id.org/linkml/DateOrDatetime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uriorcurie", - "definition_uri": "https://w3id.org/linkml/Uriorcurie", - "description": "a URI or a CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "URIorCURIE", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "curie", - "definition_uri": "https://w3id.org/linkml/Curie", - "conforms_to": "https://www.w3.org/TR/curie/", - "description": "a compact URI", - "comments": [ - "in RDF serializations this MUST be expanded to a URI", - "in non-RDF serializations MAY be serialized as the compact representation" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "Curie", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uri", - "definition_uri": "https://w3id.org/linkml/Uri", - "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", - "description": "a complete URI", - "comments": [ - "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:URL" - ], - "base": "URI", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "ncname", - "definition_uri": "https://w3id.org/linkml/Ncname", - "description": "Prefix part of CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NCName", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "objectidentifier", - "definition_uri": "https://w3id.org/linkml/Objectidentifier", - "description": "A URI or CURIE that represents an object in the model.", - "comments": [ - "Used for inheritance and type checking" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "ElementIdentifier", - "uri": "http://www.w3.org/ns/shex#iri", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "nodeidentifier", - "definition_uri": "https://w3id.org/linkml/Nodeidentifier", - "description": "A URI, CURIE or BNODE that represents a node in a model.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NodeIdentifier", - "uri": "http://www.w3.org/ns/shex#nonLiteral", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpointer", - "definition_uri": "https://w3id.org/linkml/Jsonpointer", - "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901", - "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpath", - "definition_uri": "https://w3id.org/linkml/Jsonpath", - "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html", - "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "sparqlpath", - "definition_uri": "https://w3id.org/linkml/Sparqlpath", - "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths", - "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - } - ], - "enums": [ - { - "name": "NullDataOptions", - "definition_uri": "http://w3id.org/ontogpt/core/NullDataOptions", - "from_schema": "http://w3id.org/ontogpt/core", - "permissible_values": [ - { - "text": "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "meaning": "NCIT:C149701" - }, - { - "text": "NOT_APPLICABLE", - "meaning": "NCIT:C18902", - "aliases": [ - "not applicable", - "N/A" - ] - }, - { - "text": "NOT_MENTIONED" - } - ] - } - ], - "slots": [ - { - "name": "iBDAnnotations__genes", - "description": "semicolon-separated list of genes", - "from_schema": "http://w3id.org/ontogpt/ibd_literature", - "slot_uri": "http://w3id.org/ontogpt/ibd_literature/genes", - "multivalued": true, - "alias": "genes", - "owner": "IBDAnnotations", - "domain_of": [ - "IBDAnnotations" - ], - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "iBDAnnotations__exposures", - "annotations": [ - { - "tag": "prompt", - "value": "a chemical or molecule whose direct or indirect effects cause one or more entities to experience biological change", - "@type": "Annotation" - } - ], - "description": "semicolon-separated list of exposures", - "from_schema": "http://w3id.org/ontogpt/ibd_literature", - "slot_uri": "http://w3id.org/ontogpt/ibd_literature/exposures", - "multivalued": true, - "alias": "exposures", - "owner": "IBDAnnotations", - "domain_of": [ - "IBDAnnotations" - ], - "range": "ChemicalExposure", - "@type": "SlotDefinition" - }, - { - "name": "iBDAnnotations__gene_exposures_relationships", - "description": "semicolon-separated list of gene to molecular activity relationships", - "from_schema": "http://w3id.org/ontogpt/ibd_literature", - "slot_uri": "http://w3id.org/ontogpt/ibd_literature/gene_exposures_relationships", - "multivalued": true, - "alias": "gene_exposures_relationships", - "owner": "IBDAnnotations", - "domain_of": [ - "IBDAnnotations" - ], - "range": "GeneExposureRelationship", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "iBDAnnotations__diseases", - "description": "semicolon-separated list of diseases", - "from_schema": "http://w3id.org/ontogpt/ibd_literature", - "slot_uri": "http://w3id.org/ontogpt/ibd_literature/diseases", - "multivalued": true, - "alias": "diseases", - "owner": "IBDAnnotations", - "domain_of": [ - "IBDAnnotations" - ], - "range": "Disease", - "@type": "SlotDefinition" - }, - { - "name": "iBDAnnotations__cellular_process", - "description": "semicolon-separated list of cellular processes", - "from_schema": "http://w3id.org/ontogpt/ibd_literature", - "slot_uri": "http://w3id.org/ontogpt/ibd_literature/cellular_process", - "multivalued": true, - "alias": "cellular_process", - "owner": "IBDAnnotations", - "domain_of": [ - "IBDAnnotations" - ], - "range": "CellularProcess", - "@type": "SlotDefinition" - }, - { - "name": "iBDAnnotations__disease_cellular_process_relationships", - "description": "semicolon-separated list of disease to cellular process relationships", - "from_schema": "http://w3id.org/ontogpt/ibd_literature", - "slot_uri": "http://w3id.org/ontogpt/ibd_literature/disease_cellular_process_relationships", - "multivalued": true, - "alias": "disease_cellular_process_relationships", - "owner": "IBDAnnotations", - "domain_of": [ - "IBDAnnotations" - ], - "range": "DiseaseCellularProcessRelationship", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_id", - "alias": "input_id", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_title", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_title", - "alias": "input_title", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_text", - "alias": "input_text", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__raw_completion_output", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/raw_completion_output", - "alias": "raw_completion_output", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__prompt", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/prompt", - "alias": "prompt", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__extracted_object", - "description": "The complex objects extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/extracted_object", - "alias": "extracted_object", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__named_entities", - "description": "Named entities extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/named_entities", - "multivalued": true, - "alias": "named_entities", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "identifier": true, - "alias": "id", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "required": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "from_schema": "http://w3id.org/ontogpt/core", - "aliases": [ - "name" - ], - "mappings": [ - "http://example.org/UNKNOWN/rdfs/label" - ], - "slot_uri": "http://example.org/UNKNOWN/rdfs/label", - "alias": "label", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject", - "alias": "subject", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__predicate", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/predicate", - "alias": "predicate", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "triple__object", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object", - "alias": "object", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/qualifier", - "alias": "qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_qualifier", - "alias": "subject_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_qualifier", - "alias": "object_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/publication", - "alias": "publication", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__triples", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/triples", - "multivalued": true, - "alias": "triples", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "publication__id", - "description": "The publication identifier", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "alias": "id", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__title", - "description": "The title of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/title", - "alias": "title", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__abstract", - "description": "The abstract of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/abstract", - "alias": "abstract", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__combined_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/combined_text", - "alias": "combined_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__full_text", - "description": "The full text of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/full_text", - "alias": "full_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__subject_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_text", - "alias": "subject_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_id", - "alias": "object_id", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_text", - "alias": "object_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "DiseaseCellularProcessRelationship_subject", - "description": "The name of the disease.", - "from_schema": "http://w3id.org/ontogpt/ibd_literature", - "is_a": "triple__subject", - "domain": "DiseaseCellularProcessRelationship", - "slot_uri": "http://w3id.org/ontogpt/ibd_literature/subject", - "alias": "subject", - "owner": "DiseaseCellularProcessRelationship", - "domain_of": [ - "DiseaseCellularProcessRelationship" - ], - "is_usage_slot": true, - "usage_slot_name": "subject", - "range": "Disease", - "@type": "SlotDefinition" - }, - { - "name": "DiseaseCellularProcessRelationship_predicate", - "description": "The name of the type of relationship between a disease and a cellular process.", - "from_schema": "http://w3id.org/ontogpt/ibd_literature", - "is_a": "triple__predicate", - "domain": "DiseaseCellularProcessRelationship", - "slot_uri": "http://w3id.org/ontogpt/ibd_literature/predicate", - "alias": "predicate", - "owner": "DiseaseCellularProcessRelationship", - "domain_of": [ - "DiseaseCellularProcessRelationship" - ], - "is_usage_slot": true, - "usage_slot_name": "predicate", - "range": "DiseaseToCellularProcessPredicate", - "@type": "SlotDefinition" - }, - { - "name": "DiseaseCellularProcessRelationship_object", - "description": "The name of the cellular process.", - "from_schema": "http://w3id.org/ontogpt/ibd_literature", - "is_a": "triple__object", - "domain": "DiseaseCellularProcessRelationship", - "slot_uri": "http://w3id.org/ontogpt/ibd_literature/object", - "alias": "object", - "owner": "DiseaseCellularProcessRelationship", - "domain_of": [ - "DiseaseCellularProcessRelationship" - ], - "is_usage_slot": true, - "usage_slot_name": "object", - "range": "CellularProcess", - "@type": "SlotDefinition" - }, - { - "name": "DiseaseCellularProcessRelationship_subject_qualifier", - "from_schema": "http://w3id.org/ontogpt/ibd_literature", - "is_a": "triple__subject_qualifier", - "domain": "DiseaseCellularProcessRelationship", - "slot_uri": "http://w3id.org/ontogpt/ibd_literature/subject_qualifier", - "alias": "subject_qualifier", - "owner": "DiseaseCellularProcessRelationship", - "domain_of": [ - "DiseaseCellularProcessRelationship" - ], - "is_usage_slot": true, - "usage_slot_name": "subject_qualifier", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "DiseaseCellularProcessRelationship_object_qualifier", - "from_schema": "http://w3id.org/ontogpt/ibd_literature", - "is_a": "triple__object_qualifier", - "domain": "DiseaseCellularProcessRelationship", - "slot_uri": "http://w3id.org/ontogpt/ibd_literature/object_qualifier", - "alias": "object_qualifier", - "owner": "DiseaseCellularProcessRelationship", - "domain_of": [ - "DiseaseCellularProcessRelationship" - ], - "is_usage_slot": true, - "usage_slot_name": "object_qualifier", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "GeneExposureRelationship_subject", - "description": "The name of the exposure, such as a exposure to a chemical toxin.", - "from_schema": "http://w3id.org/ontogpt/ibd_literature", - "is_a": "triple__subject", - "domain": "GeneExposureRelationship", - "slot_uri": "http://w3id.org/ontogpt/ibd_literature/subject", - "alias": "subject", - "owner": "GeneExposureRelationship", - "domain_of": [ - "GeneExposureRelationship" - ], - "is_usage_slot": true, - "usage_slot_name": "subject", - "range": "ChemicalExposure", - "@type": "SlotDefinition" - }, - { - "name": "GeneExposureRelationship_predicate", - "description": "The name of the type of relationship between a chemical exposure and a gene.", - "from_schema": "http://w3id.org/ontogpt/ibd_literature", - "is_a": "triple__predicate", - "domain": "GeneExposureRelationship", - "slot_uri": "http://w3id.org/ontogpt/ibd_literature/predicate", - "alias": "predicate", - "owner": "GeneExposureRelationship", - "domain_of": [ - "GeneExposureRelationship" - ], - "is_usage_slot": true, - "usage_slot_name": "predicate", - "range": "ChemicalExposureToGenePredicate", - "@type": "SlotDefinition" - }, - { - "name": "GeneExposureRelationship_object", - "description": "The name of the gene in the pair. This comes second in the pair.", - "from_schema": "http://w3id.org/ontogpt/ibd_literature", - "is_a": "triple__object", - "domain": "GeneExposureRelationship", - "slot_uri": "http://w3id.org/ontogpt/ibd_literature/object", - "alias": "object", - "owner": "GeneExposureRelationship", - "domain_of": [ - "GeneExposureRelationship" - ], - "is_usage_slot": true, - "usage_slot_name": "object", - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "GeneExposureRelationship_subject_qualifier", - "description": "An optional qualifier or modifier for the chemical exposure.", - "from_schema": "http://w3id.org/ontogpt/ibd_literature", - "is_a": "triple__subject_qualifier", - "domain": "GeneExposureRelationship", - "slot_uri": "http://w3id.org/ontogpt/ibd_literature/subject_qualifier", - "alias": "subject_qualifier", - "owner": "GeneExposureRelationship", - "domain_of": [ - "GeneExposureRelationship" - ], - "is_usage_slot": true, - "usage_slot_name": "subject_qualifier", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "GeneExposureRelationship_object_qualifier", - "description": "An optional qualifier or modifier for the gene.", - "from_schema": "http://w3id.org/ontogpt/ibd_literature", - "is_a": "triple__object_qualifier", - "domain": "GeneExposureRelationship", - "slot_uri": "http://w3id.org/ontogpt/ibd_literature/object_qualifier", - "alias": "object_qualifier", - "owner": "GeneExposureRelationship", - "domain_of": [ - "GeneExposureRelationship" - ], - "is_usage_slot": true, - "usage_slot_name": "object_qualifier", - "range": "NamedEntity", - "@type": "SlotDefinition" - } - ], - "classes": [ - { - "name": "IBDAnnotations", - "definition_uri": "http://w3id.org/ontogpt/ibd_literature/IBDAnnotations", - "from_schema": "http://w3id.org/ontogpt/ibd_literature", - "slots": [ - "iBDAnnotations__genes", - "iBDAnnotations__exposures", - "iBDAnnotations__gene_exposures_relationships", - "iBDAnnotations__diseases", - "iBDAnnotations__cellular_process", - "iBDAnnotations__disease_cellular_process_relationships" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "genes", - "description": "semicolon-separated list of genes", - "multivalued": true, - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "exposures", - "annotations": [ - { - "tag": "prompt", - "value": "a chemical or molecule whose direct or indirect effects cause one or more entities to experience biological change", - "@type": "Annotation" - } - ], - "description": "semicolon-separated list of exposures", - "multivalued": true, - "range": "ChemicalExposure", - "@type": "SlotDefinition" - }, - { - "name": "gene_exposures_relationships", - "description": "semicolon-separated list of gene to molecular activity relationships", - "multivalued": true, - "range": "GeneExposureRelationship", - "@type": "SlotDefinition" - }, - { - "name": "diseases", - "description": "semicolon-separated list of diseases", - "multivalued": true, - "range": "Disease", - "@type": "SlotDefinition" - }, - { - "name": "cellular_process", - "description": "semicolon-separated list of cellular processes", - "multivalued": true, - "range": "CellularProcess", - "@type": "SlotDefinition" - }, - { - "name": "disease_cellular_process_relationships", - "description": "semicolon-separated list of disease to cellular process relationships", - "multivalued": true, - "range": "DiseaseCellularProcessRelationship", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/ibd_literature/IBDAnnotations", - "tree_root": true, - "@type": "ClassDefinition" - }, - { - "name": "Gene", - "id_prefixes": [ - "HGNC" - ], - "definition_uri": "http://w3id.org/ontogpt/ibd_literature/Gene", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:hgnc, sqlite:obo:pr", - "@type": "Annotation" - }, - { - "tag": "prompt", - "value": "the name of the gene in the pair. This comes second in the pair.", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/ibd_literature", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/ibd_literature/Gene", - "@type": "ClassDefinition" - }, - { - "name": "Disease", - "id_prefixes": [ - "MONDO" - ], - "definition_uri": "http://w3id.org/ontogpt/ibd_literature/Disease", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:mondo", - "@type": "Annotation" - }, - { - "tag": "prompt", - "value": "the name of the disease", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/ibd_literature", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/ibd_literature/Disease", - "@type": "ClassDefinition" - }, - { - "name": "CellularProcess", - "id_prefixes": [ - "GO" - ], - "definition_uri": "http://w3id.org/ontogpt/ibd_literature/CellularProcess", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:go", - "@type": "Annotation" - }, - { - "tag": "prompt", - "value": "the name of the cellular process", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/ibd_literature", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/ibd_literature/CellularProcess", - "@type": "ClassDefinition" - }, - { - "name": "DiseaseToCellularProcessPredicate", - "id_prefixes": [ - "RO" - ], - "definition_uri": "http://w3id.org/ontogpt/ibd_literature/DiseaseToCellularProcessPredicate", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:ro", - "@type": "Annotation" - }, - { - "tag": "prompt", - "value": "the name of the type of relationship between a disease and a cellular process.", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/ibd_literature", - "is_a": "RelationshipType", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/ibd_literature/DiseaseToCellularProcessPredicate", - "@type": "ClassDefinition" - }, - { - "name": "DiseaseCellularProcessRelationship", - "definition_uri": "http://w3id.org/ontogpt/ibd_literature/DiseaseCellularProcessRelationship", - "from_schema": "http://w3id.org/ontogpt/ibd_literature", - "is_a": "Triple", - "slots": [ - "triple__qualifier", - "DiseaseCellularProcessRelationship_subject", - "DiseaseCellularProcessRelationship_predicate", - "DiseaseCellularProcessRelationship_object", - "DiseaseCellularProcessRelationship_subject_qualifier", - "DiseaseCellularProcessRelationship_object_qualifier" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/ibd_literature/DiseaseCellularProcessRelationship", - "@type": "ClassDefinition" - }, - { - "name": "ChemicalExposure", - "id_prefixes": [ - "CHEBI", - "ECTO", - "ExO", - "NCIT" - ], - "definition_uri": "http://w3id.org/ontogpt/ibd_literature/ChemicalExposure", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:ecto, sqlite:obo:chebi", - "@type": "Annotation" - }, - { - "tag": "prompt", - "value": "the name of the exposure, such as a exposure to a chemical toxin. For example, CHEBI:17968 butyrate.", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/ibd_literature", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/ibd_literature/ChemicalExposure", - "@type": "ClassDefinition" - }, - { - "name": "ChemicalExposureToGenePredicate", - "id_prefixes": [ - "RO" - ], - "definition_uri": "http://w3id.org/ontogpt/ibd_literature/ChemicalExposureToGenePredicate", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:ro", - "@type": "Annotation" - }, - { - "tag": "prompt", - "value": "the name of the type of relationship between a chemical exposure and a gene.", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/ibd_literature", - "is_a": "RelationshipType", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/ibd_literature/ChemicalExposureToGenePredicate", - "@type": "ClassDefinition" - }, - { - "name": "GeneExposureRelationship", - "definition_uri": "http://w3id.org/ontogpt/ibd_literature/GeneExposureRelationship", - "from_schema": "http://w3id.org/ontogpt/ibd_literature", - "is_a": "Triple", - "slots": [ - "triple__qualifier", - "GeneExposureRelationship_subject", - "GeneExposureRelationship_predicate", - "GeneExposureRelationship_object", - "GeneExposureRelationship_subject_qualifier", - "GeneExposureRelationship_object_qualifier" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/ibd_literature/GeneExposureRelationship", - "@type": "ClassDefinition" - }, - { - "name": "Any", - "definition_uri": "http://w3id.org/ontogpt/core/Any", - "from_schema": "http://w3id.org/ontogpt/core", - "mappings": [ - "linkml:Any" - ], - "slot_usage": {}, - "class_uri": "https://w3id.org/linkml/Any", - "@type": "ClassDefinition" - }, - { - "name": "ExtractionResult", - "definition_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "description": "A result of extracting knowledge on text", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "extractionResult__input_id", - "extractionResult__input_title", - "extractionResult__input_text", - "extractionResult__raw_completion_output", - "extractionResult__prompt", - "extractionResult__extracted_object", - "extractionResult__named_entities" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "input_id", - "@type": "SlotDefinition" - }, - { - "name": "input_title", - "@type": "SlotDefinition" - }, - { - "name": "input_text", - "@type": "SlotDefinition" - }, - { - "name": "raw_completion_output", - "@type": "SlotDefinition" - }, - { - "name": "prompt", - "@type": "SlotDefinition" - }, - { - "name": "extracted_object", - "description": "The complex objects extracted from the text", - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "named_entities", - "description": "Named entities extracted from the text", - "multivalued": true, - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "@type": "ClassDefinition" - }, - { - "name": "NamedEntity", - "definition_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "identifier": true, - "@type": "SlotDefinition" - }, - { - "name": "label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "aliases": [ - "name" - ], - "slot_uri": "rdfs:label", - "range": "string", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "@type": "ClassDefinition" - }, - { - "name": "CompoundExpression", - "definition_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "@type": "ClassDefinition" - }, - { - "name": "Triple", - "definition_uri": "http://w3id.org/ontogpt/core/Triple", - "description": "Abstract parent for Relation Extraction tasks", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "CompoundExpression", - "abstract": true, - "slots": [ - "triple__subject", - "triple__predicate", - "triple__object", - "triple__qualifier", - "triple__subject_qualifier", - "triple__object_qualifier" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "predicate", - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "object", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Triple", - "@type": "ClassDefinition" - }, - { - "name": "TextWithTriples", - "definition_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "textWithTriples__publication", - "textWithTriples__triples" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "triples", - "multivalued": true, - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "@type": "ClassDefinition" - }, - { - "name": "RelationshipType", - "id_prefixes": [ - "RO", - "biolink" - ], - "definition_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "@type": "ClassDefinition" - }, - { - "name": "Publication", - "definition_uri": "http://w3id.org/ontogpt/core/Publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "publication__id", - "publication__title", - "publication__abstract", - "publication__combined_text", - "publication__full_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "description": "The publication identifier", - "@type": "SlotDefinition" - }, - { - "name": "title", - "description": "The title of the publication", - "@type": "SlotDefinition" - }, - { - "name": "abstract", - "description": "The abstract of the publication", - "@type": "SlotDefinition" - }, - { - "name": "combined_text", - "@type": "SlotDefinition" - }, - { - "name": "full_text", - "description": "The full text of the publication", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Publication", - "@type": "ClassDefinition" - }, - { - "name": "AnnotatorResult", - "definition_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "annotatorResult__subject_text", - "annotatorResult__object_id", - "annotatorResult__object_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject_text", - "@type": "SlotDefinition" - }, - { - "name": "object_id", - "@type": "SlotDefinition" - }, - { - "name": "object_text", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "@type": "ClassDefinition" - } - ], - "metamodel_version": "1.7.0", - "source_file": "ibd_literature.yaml", - "source_file_date": "2023-08-07T11:00:26", - "source_file_size": 4495, - "generation_date": "2023-08-07T11:00:34", - "@type": "SchemaDefinition", - "@context": [ - "projects/ibd_literature/jsonld/ibd_literature.context.jsonld", - "https://w3id.org/linkml/types.context.jsonld", - "core.context.jsonld", - { - "@base": "http://w3id.org/ontogpt/ibd_literature/" - } - ] -} diff --git a/projects/ibd_literature/jsonschema/ibd_literature.schema.json b/projects/ibd_literature/jsonschema/ibd_literature.schema.json deleted file mode 100644 index 76598b5cc..000000000 --- a/projects/ibd_literature/jsonschema/ibd_literature.schema.json +++ /dev/null @@ -1,413 +0,0 @@ -{ - "$defs": { - "AnnotatorResult": { - "additionalProperties": false, - "description": "", - "properties": { - "object_id": { - "type": "string" - }, - "object_text": { - "type": "string" - }, - "subject_text": { - "type": "string" - } - }, - "title": "AnnotatorResult", - "type": "object" - }, - "Any": { - "additionalProperties": true, - "description": "", - "title": "Any", - "type": "object" - }, - "CellularProcess": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "CellularProcess", - "type": "object" - }, - "ChemicalExposure": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "ChemicalExposure", - "type": "object" - }, - "ChemicalExposureToGenePredicate": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "ChemicalExposureToGenePredicate", - "type": "object" - }, - "Disease": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Disease", - "type": "object" - }, - "DiseaseCellularProcessRelationship": { - "additionalProperties": false, - "description": "", - "properties": { - "object": { - "description": "The name of the cellular process.", - "type": "string" - }, - "object_qualifier": { - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "type": "string" - }, - "predicate": { - "description": "The name of the type of relationship between a disease and a cellular process.", - "type": "string" - }, - "qualifier": { - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "type": "string" - }, - "subject": { - "description": "The name of the disease.", - "type": "string" - }, - "subject_qualifier": { - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "type": "string" - } - }, - "title": "DiseaseCellularProcessRelationship", - "type": "object" - }, - "DiseaseToCellularProcessPredicate": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "DiseaseToCellularProcessPredicate", - "type": "object" - }, - "ExtractionResult": { - "additionalProperties": false, - "description": "A result of extracting knowledge on text", - "properties": { - "extracted_object": { - "$ref": "#/$defs/Any", - "description": "The complex objects extracted from the text" - }, - "input_id": { - "type": "string" - }, - "input_text": { - "type": "string" - }, - "input_title": { - "type": "string" - }, - "named_entities": { - "description": "Named entities extracted from the text", - "items": { - "$ref": "#/$defs/Any" - }, - "type": "array" - }, - "prompt": { - "type": "string" - }, - "raw_completion_output": { - "type": "string" - } - }, - "title": "ExtractionResult", - "type": "object" - }, - "Gene": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Gene", - "type": "object" - }, - "GeneExposureRelationship": { - "additionalProperties": false, - "description": "", - "properties": { - "object": { - "description": "The name of the gene in the pair. This comes second in the pair.", - "type": "string" - }, - "object_qualifier": { - "description": "An optional qualifier or modifier for the gene.", - "type": "string" - }, - "predicate": { - "description": "The name of the type of relationship between a chemical exposure and a gene.", - "type": "string" - }, - "qualifier": { - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "type": "string" - }, - "subject": { - "description": "The name of the exposure, such as a exposure to a chemical toxin.", - "type": "string" - }, - "subject_qualifier": { - "description": "An optional qualifier or modifier for the chemical exposure.", - "type": "string" - } - }, - "title": "GeneExposureRelationship", - "type": "object" - }, - "IBDAnnotations": { - "additionalProperties": false, - "description": "", - "properties": { - "cellular_process": { - "description": "semicolon-separated list of cellular processes", - "items": { - "type": "string" - }, - "type": "array" - }, - "disease_cellular_process_relationships": { - "description": "semicolon-separated list of disease to cellular process relationships", - "items": { - "$ref": "#/$defs/DiseaseCellularProcessRelationship" - }, - "type": "array" - }, - "diseases": { - "description": "semicolon-separated list of diseases", - "items": { - "type": "string" - }, - "type": "array" - }, - "exposures": { - "description": "semicolon-separated list of exposures", - "items": { - "type": "string" - }, - "type": "array" - }, - "gene_exposures_relationships": { - "description": "semicolon-separated list of gene to molecular activity relationships", - "items": { - "$ref": "#/$defs/GeneExposureRelationship" - }, - "type": "array" - }, - "genes": { - "description": "semicolon-separated list of genes", - "items": { - "type": "string" - }, - "type": "array" - } - }, - "title": "IBDAnnotations", - "type": "object" - }, - "NullDataOptions": { - "description": "", - "enum": [ - "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "NOT_APPLICABLE", - "NOT_MENTIONED" - ], - "title": "NullDataOptions", - "type": "string" - }, - "Publication": { - "additionalProperties": false, - "description": "", - "properties": { - "abstract": { - "description": "The abstract of the publication", - "type": "string" - }, - "combined_text": { - "type": "string" - }, - "full_text": { - "description": "The full text of the publication", - "type": "string" - }, - "id": { - "description": "The publication identifier", - "type": "string" - }, - "title": { - "description": "The title of the publication", - "type": "string" - } - }, - "title": "Publication", - "type": "object" - }, - "RelationshipType": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "RelationshipType", - "type": "object" - }, - "TextWithTriples": { - "additionalProperties": false, - "description": "", - "properties": { - "publication": { - "$ref": "#/$defs/Publication" - }, - "triples": { - "items": { - "$ref": "#/$defs/Triple" - }, - "type": "array" - } - }, - "title": "TextWithTriples", - "type": "object" - } - }, - "$id": "http://w3id.org/ontogpt/ibd_literature", - "$schema": "http://json-schema.org/draft-07/schema#", - "additionalProperties": true, - "metamodel_version": "1.7.0", - "properties": { - "cellular_process": { - "description": "semicolon-separated list of cellular processes", - "items": { - "type": "string" - }, - "type": "array" - }, - "disease_cellular_process_relationships": { - "description": "semicolon-separated list of disease to cellular process relationships", - "items": { - "$ref": "#/$defs/DiseaseCellularProcessRelationship" - }, - "type": "array" - }, - "diseases": { - "description": "semicolon-separated list of diseases", - "items": { - "type": "string" - }, - "type": "array" - }, - "exposures": { - "description": "semicolon-separated list of exposures", - "items": { - "type": "string" - }, - "type": "array" - }, - "gene_exposures_relationships": { - "description": "semicolon-separated list of gene to molecular activity relationships", - "items": { - "$ref": "#/$defs/GeneExposureRelationship" - }, - "type": "array" - }, - "genes": { - "description": "semicolon-separated list of genes", - "items": { - "type": "string" - }, - "type": "array" - } - }, - "title": "ibd-literature-template", - "type": "object", - "version": null -} \ No newline at end of file diff --git a/projects/ibd_literature/owl/ibd_literature.owl.ttl b/projects/ibd_literature/owl/ibd_literature.owl.ttl deleted file mode 100644 index 18d2c640e..000000000 --- a/projects/ibd_literature/owl/ibd_literature.owl.ttl +++ /dev/null @@ -1,580 +0,0 @@ -@prefix IAO: <http://purl.obolibrary.org/obo/IAO_> . -@prefix NCIT: <http://purl.obolibrary.org/obo/NCIT_> . -@prefix core: <http://w3id.org/ontogpt/core/> . -@prefix ibdlit: <http://w3id.org/ontogpt/ibd_literature/> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix owl: <http://www.w3.org/2002/07/owl#> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . -@prefix skos: <http://www.w3.org/2004/02/skos/core#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -<http://w3id.org/ontogpt/ibd_literature> a owl:Ontology ; - rdfs:label "ibd-literature-template" ; - IAO:0000700 core:AnnotatorResult, - core:Any, - core:CompoundExpression, - core:ExtractionResult, - core:NamedEntity, - core:Publication, - core:TextWithTriples, - ibdlit:IBDAnnotations ; - linkml:classes "{'IBDAnnotations': ClassDefinition(name='IBDAnnotations', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/ibd_literature/IBDAnnotations', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/ibd_literature', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['iBDAnnotations__genes', 'iBDAnnotations__exposures', 'iBDAnnotations__gene_exposures_relationships', 'iBDAnnotations__diseases', 'iBDAnnotations__cellular_process', 'iBDAnnotations__disease_cellular_process_relationships'], slot_usage={}, attributes={'genes': SlotDefinition(name='genes', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of genes', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'exposures': SlotDefinition(name='exposures', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='a chemical or molecule whose direct or indirect effects cause one or more entities to experience biological change', extensions={}, annotations={})}, description='semicolon-separated list of exposures', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ChemicalExposure', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'gene_exposures_relationships': SlotDefinition(name='gene_exposures_relationships', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of gene to molecular activity relationships', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneExposureRelationship', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'diseases': SlotDefinition(name='diseases', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of diseases', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Disease', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'cellular_process': SlotDefinition(name='cellular_process', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of cellular processes', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='CellularProcess', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'disease_cellular_process_relationships': SlotDefinition(name='disease_cellular_process_relationships', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of disease to cellular process relationships', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='DiseaseCellularProcessRelationship', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='ibdlit:IBDAnnotations', subclass_of=None, union_of=[], defining_slots=[], tree_root=True, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Gene': ClassDefinition(name='Gene', id_prefixes=['HGNC'], definition_uri='http://w3id.org/ontogpt/ibd_literature/Gene', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:hgnc, sqlite:obo:pr', extensions={}, annotations={}), 'prompt': Annotation(tag='prompt', value='the name of the gene in the pair. This comes second in the pair.', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/ibd_literature', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='ibdlit:Gene', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Disease': ClassDefinition(name='Disease', id_prefixes=['MONDO'], definition_uri='http://w3id.org/ontogpt/ibd_literature/Disease', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:mondo', extensions={}, annotations={}), 'prompt': Annotation(tag='prompt', value='the name of the disease', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/ibd_literature', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='ibdlit:Disease', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'CellularProcess': ClassDefinition(name='CellularProcess', id_prefixes=['GO'], definition_uri='http://w3id.org/ontogpt/ibd_literature/CellularProcess', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:go', extensions={}, annotations={}), 'prompt': Annotation(tag='prompt', value='the name of the cellular process', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/ibd_literature', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='ibdlit:CellularProcess', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'DiseaseToCellularProcessPredicate': ClassDefinition(name='DiseaseToCellularProcessPredicate', id_prefixes=['RO'], definition_uri='http://w3id.org/ontogpt/ibd_literature/DiseaseToCellularProcessPredicate', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:ro', extensions={}, annotations={}), 'prompt': Annotation(tag='prompt', value='the name of the type of relationship between a disease and a cellular process.', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/ibd_literature', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='RelationshipType', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='ibdlit:DiseaseToCellularProcessPredicate', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'DiseaseCellularProcessRelationship': ClassDefinition(name='DiseaseCellularProcessRelationship', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/ibd_literature/DiseaseCellularProcessRelationship', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/ibd_literature', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='Triple', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['triple__qualifier', 'DiseaseCellularProcessRelationship_subject', 'DiseaseCellularProcessRelationship_predicate', 'DiseaseCellularProcessRelationship_object', 'DiseaseCellularProcessRelationship_subject_qualifier', 'DiseaseCellularProcessRelationship_object_qualifier'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The name of the disease.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='triple__subject', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Disease', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The name of the type of relationship between a disease and a cellular process.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='triple__predicate', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='DiseaseToCellularProcessPredicate', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The name of the cellular process.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='triple__object', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='CellularProcess', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='triple__subject_qualifier', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='triple__object_qualifier', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='ibdlit:DiseaseCellularProcessRelationship', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ChemicalExposure': ClassDefinition(name='ChemicalExposure', id_prefixes=['CHEBI', 'ECTO', 'ExO', 'NCIT'], definition_uri='http://w3id.org/ontogpt/ibd_literature/ChemicalExposure', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:ecto, sqlite:obo:chebi', extensions={}, annotations={}), 'prompt': Annotation(tag='prompt', value='the name of the exposure, such as a exposure to a chemical toxin. For example, CHEBI:17968 butyrate.', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/ibd_literature', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='ibdlit:ChemicalExposure', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ChemicalExposureToGenePredicate': ClassDefinition(name='ChemicalExposureToGenePredicate', id_prefixes=['RO'], definition_uri='http://w3id.org/ontogpt/ibd_literature/ChemicalExposureToGenePredicate', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:ro', extensions={}, annotations={}), 'prompt': Annotation(tag='prompt', value='the name of the type of relationship between a chemical exposure and a gene.', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/ibd_literature', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='RelationshipType', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='ibdlit:ChemicalExposureToGenePredicate', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'GeneExposureRelationship': ClassDefinition(name='GeneExposureRelationship', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/ibd_literature/GeneExposureRelationship', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/ibd_literature', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='Triple', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['triple__qualifier', 'GeneExposureRelationship_subject', 'GeneExposureRelationship_predicate', 'GeneExposureRelationship_object', 'GeneExposureRelationship_subject_qualifier', 'GeneExposureRelationship_object_qualifier'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The name of the exposure, such as a exposure to a chemical toxin.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='triple__subject', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ChemicalExposure', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The name of the type of relationship between a chemical exposure and a gene.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='triple__predicate', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ChemicalExposureToGenePredicate', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The name of the gene in the pair. This comes second in the pair.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='triple__object', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the chemical exposure.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='triple__subject_qualifier', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the gene.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='triple__object_qualifier', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='ibdlit:GeneExposureRelationship', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Any': ClassDefinition(name='Any', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Any', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=['linkml:Any'], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='linkml:Any', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ExtractionResult': ClassDefinition(name='ExtractionResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/ExtractionResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A result of extracting knowledge on text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['extractionResult__input_id', 'extractionResult__input_title', 'extractionResult__input_text', 'extractionResult__raw_completion_output', 'extractionResult__prompt', 'extractionResult__extracted_object', 'extractionResult__named_entities'], slot_usage={}, attributes={'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:ExtractionResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'NamedEntity': ClassDefinition(name='NamedEntity', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NamedEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:NamedEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'CompoundExpression': ClassDefinition(name='CompoundExpression', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/CompoundExpression', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='core:CompoundExpression', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Triple': ClassDefinition(name='Triple', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Triple', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Abstract parent for Relation Extraction tasks', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['triple__subject', 'triple__predicate', 'triple__object', 'triple__qualifier', 'triple__subject_qualifier', 'triple__object_qualifier'], slot_usage={}, attributes={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Triple', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'TextWithTriples': ClassDefinition(name='TextWithTriples', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/TextWithTriples', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['textWithTriples__publication', 'textWithTriples__triples'], slot_usage={}, attributes={'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:TextWithTriples', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'RelationshipType': ClassDefinition(name='RelationshipType', id_prefixes=['RO', 'biolink'], definition_uri='http://w3id.org/ontogpt/core/RelationshipType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='core:RelationshipType', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Publication': ClassDefinition(name='Publication', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Publication', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['publication__id', 'publication__title', 'publication__abstract', 'publication__combined_text', 'publication__full_text'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Publication', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'AnnotatorResult': ClassDefinition(name='AnnotatorResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/AnnotatorResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['annotatorResult__subject_text', 'annotatorResult__object_id', 'annotatorResult__object_text'], slot_usage={}, attributes={'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:AnnotatorResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={})}" ; - linkml:enums "{'NullDataOptions': EnumDefinition(name='NullDataOptions', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NullDataOptions', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'UNSPECIFIED_METHOD_OF_ADMINISTRATION': PermissibleValue(text='UNSPECIFIED_METHOD_OF_ADMINISTRATION', description=None, meaning='NCIT:C149701', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_APPLICABLE': PermissibleValue(text='NOT_APPLICABLE', description=None, meaning='NCIT:C18902', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['not applicable', 'N/A'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_MENTIONED': PermissibleValue(text='NOT_MENTIONED', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[])}" ; - linkml:id "http://w3id.org/ontogpt/ibd_literature" ; - linkml:imports "core", - "linkml:types" ; - linkml:types "{'string': TypeDefinition(name='string', id_prefixes=[], definition_uri='https://w3id.org/linkml/String', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A character string', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Text'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'integer': TypeDefinition(name='integer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Integer', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An integer', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Integer'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='int', uri='xsd:integer', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'boolean': TypeDefinition(name='boolean', id_prefixes=[], definition_uri='https://w3id.org/linkml/Boolean', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A binary (true or false) value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Boolean'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Bool', uri='xsd:boolean', repr='bool', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'float': TypeDefinition(name='float', id_prefixes=[], definition_uri='https://w3id.org/linkml/Float', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:float specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Float'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:float', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'double': TypeDefinition(name='double', id_prefixes=[], definition_uri='https://w3id.org/linkml/Double', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:double specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:Float'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:double', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'decimal': TypeDefinition(name='decimal', id_prefixes=[], definition_uri='https://w3id.org/linkml/Decimal', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number with arbitrary precision that conforms to the xsd:decimal specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=['schema:Number'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Decimal', uri='xsd:decimal', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'time': TypeDefinition(name='time', id_prefixes=[], definition_uri='https://w3id.org/linkml/Time', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A time object represents a (local) time of day, independent of any particular day', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=['URI is dateTime because OWL reasoners do not work with straight date or time'], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Time'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDTime', uri='xsd:time', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date': TypeDefinition(name='date', id_prefixes=[], definition_uri='https://w3id.org/linkml/Date', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a date (year, month and day) in an idealized calendar', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[\"URI is dateTime because OWL reasoners don't work with straight date or time\"], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Date'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDate', uri='xsd:date', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'datetime': TypeDefinition(name='datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/Datetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The combination of a date and time', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:DateTime'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDateTime', uri='xsd:dateTime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date_or_datetime': TypeDefinition(name='date_or_datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/DateOrDatetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Either a date or a datetime', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='linkml:DateOrDatetime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uriorcurie': TypeDefinition(name='uriorcurie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uriorcurie', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a URI or a CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URIorCURIE', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'curie': TypeDefinition(name='curie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Curie', local_names={}, conforms_to='https://www.w3.org/TR/curie/', implements=[], extensions={}, annotations={}, description='a compact URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations this MUST be expanded to a URI', 'in non-RDF serializations MAY be serialized as the compact representation'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Curie', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uri': TypeDefinition(name='uri', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uri', local_names={}, conforms_to='https://www.ietf.org/rfc/rfc3987.txt', implements=[], extensions={}, annotations={}, description='a complete URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:URL'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URI', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ncname': TypeDefinition(name='ncname', id_prefixes=[], definition_uri='https://w3id.org/linkml/Ncname', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Prefix part of CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NCName', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'objectidentifier': TypeDefinition(name='objectidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Objectidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI or CURIE that represents an object in the model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['Used for inheritance and type checking'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='ElementIdentifier', uri='shex:iri', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'nodeidentifier': TypeDefinition(name='nodeidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Nodeidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI, CURIE or BNODE that represents a node in a model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NodeIdentifier', uri='shex:nonLiteral', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpointer': TypeDefinition(name='jsonpointer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpointer', local_names={}, conforms_to='https://datatracker.ietf.org/doc/html/rfc6901', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpath': TypeDefinition(name='jsonpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpath', local_names={}, conforms_to='https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sparqlpath': TypeDefinition(name='sparqlpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Sparqlpath', local_names={}, conforms_to='https://www.w3.org/TR/sparql11-query/#propertypaths', implements=[], extensions={}, annotations={}, description='A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:SubsetDefinition a owl:Class ; - rdfs:label "subset_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" . - -linkml:TypeDefinition a owl:Class ; - rdfs:label "type_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" ; - linkml:mixins "type_expression" . - -linkml:topValue a owl:DatatypeProperty ; - rdfs:label "value" . - -core:AnnotatorResult a owl:Class, - linkml:ClassDefinition ; - rdfs:label "AnnotatorResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty core:object_id ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty core:object_text ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty core:subject_text ] ; - linkml:attributes "{'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -core:ExtractionResult a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ExtractionResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass core:Any ; - owl:onProperty core:extracted_object ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty core:raw_completion_output ], - [ a owl:Restriction ; - owl:allValuesFrom core:Any ; - owl:onProperty core:named_entities ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty core:input_title ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty core:prompt ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty core:input_text ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty core:input_id ] ; - skos:definition "A result of extracting knowledge on text" ; - linkml:attributes "{'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -core:TextWithTriples a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TextWithTriples" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass core:Publication ; - owl:onProperty core:publication ], - [ a owl:Restriction ; - owl:allValuesFrom core:Triple ; - owl:onProperty core:triples ] ; - linkml:attributes "{'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -core:abstract a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "abstract" ; - rdfs:range linkml:String ; - skos:definition "The abstract of the publication" . - -core:combined_text a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "combined_text" ; - rdfs:range linkml:String . - -core:extracted_object a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "extracted_object" ; - rdfs:range core:Any ; - skos:definition "The complex objects extracted from the text" . - -core:full_text a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "full_text" ; - rdfs:range linkml:String ; - skos:definition "The full text of the publication" . - -core:input_id a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_id" ; - rdfs:range linkml:String . - -core:input_text a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_text" ; - rdfs:range linkml:String . - -core:input_title a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_title" ; - rdfs:range linkml:String . - -core:named_entities a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "named_entities" ; - rdfs:range core:Any ; - skos:definition "Named entities extracted from the text" . - -core:object_id a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_id" ; - rdfs:range linkml:String . - -core:object_text a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_text" ; - rdfs:range linkml:String . - -core:prompt a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "prompt" ; - rdfs:range linkml:String . - -core:publication a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "publication" ; - ibdlit:prompt.skip "true" ; - rdfs:range core:Publication . - -core:qualifier a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "qualifier" ; - rdfs:range linkml:String ; - skos:definition "A qualifier for the statements, e.g. \"NOT\" for negation" . - -core:raw_completion_output a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "raw_completion_output" ; - rdfs:range linkml:String . - -core:subject_text a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_text" ; - rdfs:range linkml:String . - -core:title a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "title" ; - rdfs:range linkml:String ; - skos:definition "The title of the publication" . - -core:triples a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "triples" ; - rdfs:range core:Triple . - -ibdlit:IBDAnnotations a owl:Class, - linkml:ClassDefinition ; - rdfs:label "IBDAnnotations" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom ibdlit:ChemicalExposure ; - owl:onProperty ibdlit:exposures ], - [ a owl:Restriction ; - owl:allValuesFrom ibdlit:CellularProcess ; - owl:onProperty ibdlit:cellular_process ], - [ a owl:Restriction ; - owl:allValuesFrom ibdlit:DiseaseCellularProcessRelationship ; - owl:onProperty ibdlit:disease_cellular_process_relationships ], - [ a owl:Restriction ; - owl:allValuesFrom ibdlit:Disease ; - owl:onProperty ibdlit:diseases ], - [ a owl:Restriction ; - owl:allValuesFrom ibdlit:Gene ; - owl:onProperty ibdlit:genes ], - [ a owl:Restriction ; - owl:allValuesFrom ibdlit:GeneExposureRelationship ; - owl:onProperty ibdlit:gene_exposures_relationships ] ; - linkml:attributes "{'genes': SlotDefinition(name='genes', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of genes', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'exposures': SlotDefinition(name='exposures', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='a chemical or molecule whose direct or indirect effects cause one or more entities to experience biological change', extensions={}, annotations={})}, description='semicolon-separated list of exposures', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ChemicalExposure', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'gene_exposures_relationships': SlotDefinition(name='gene_exposures_relationships', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of gene to molecular activity relationships', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneExposureRelationship', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'diseases': SlotDefinition(name='diseases', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of diseases', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Disease', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'cellular_process': SlotDefinition(name='cellular_process', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of cellular processes', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='CellularProcess', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'disease_cellular_process_relationships': SlotDefinition(name='disease_cellular_process_relationships', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of disease to cellular process relationships', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='DiseaseCellularProcessRelationship', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -ibdlit:cellular_process a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "cellular_process" ; - rdfs:range ibdlit:CellularProcess ; - skos:definition "semicolon-separated list of cellular processes" . - -ibdlit:disease_cellular_process_relationships a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "disease_cellular_process_relationships" ; - rdfs:range ibdlit:DiseaseCellularProcessRelationship ; - skos:definition "semicolon-separated list of disease to cellular process relationships" . - -ibdlit:diseases a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "diseases" ; - rdfs:range ibdlit:Disease ; - skos:definition "semicolon-separated list of diseases" . - -ibdlit:exposures a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "exposures" ; - ibdlit:prompt "a chemical or molecule whose direct or indirect effects cause one or more entities to experience biological change" ; - rdfs:range ibdlit:ChemicalExposure ; - skos:definition "semicolon-separated list of exposures" . - -ibdlit:gene_exposures_relationships a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "gene_exposures_relationships" ; - rdfs:range ibdlit:GeneExposureRelationship ; - skos:definition "semicolon-separated list of gene to molecular activity relationships" . - -ibdlit:genes a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "genes" ; - rdfs:range ibdlit:Gene ; - skos:definition "semicolon-separated list of genes" . - -<http://example.org/UNKNOWN/rdfs/label> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "label" ; - ibdlit:owl "AnnotationProperty, AnnotationAssertion" ; - rdfs:range linkml:String ; - skos:altLabel "name" ; - skos:definition "The label (name) of the named thing" ; - skos:exactMatch <http://example.org/UNKNOWN/rdfs/label> . - -NCIT:C149701 a core:NullDataOptions, - owl:Class ; - rdfs:label "UNSPECIFIED_METHOD_OF_ADMINISTRATION" . - -NCIT:C18902 a core:NullDataOptions, - owl:Class ; - rdfs:label "NOT_APPLICABLE" . - -core:CompoundExpression a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CompoundExpression" ; - linkml:attributes "{}" . - -<http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> a core:NullDataOptions, - owl:Class ; - rdfs:label "NOT_MENTIONED" . - -core:id a owl:ObjectProperty, - linkml:SlotDefinition . - -core:object a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object" ; - rdfs:range core:NamedEntity . - -core:object_qualifier a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_qualifier" ; - rdfs:range core:NamedEntity ; - skos:definition "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" . - -core:predicate a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "predicate" ; - rdfs:range core:RelationshipType . - -core:subject a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject" ; - rdfs:range core:NamedEntity . - -core:subject_qualifier a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_qualifier" ; - rdfs:range core:NamedEntity ; - skos:definition "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" . - -ibdlit:ChemicalExposureToGenePredicate a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ChemicalExposureToGenePredicate" ; - ibdlit:annotators "sqlite:obo:ro" ; - ibdlit:prompt "the name of the type of relationship between a chemical exposure and a gene." ; - rdfs:subClassOf core:RelationshipType ; - linkml:attributes "{}" ; - linkml:is_a "RelationshipType" . - -ibdlit:DiseaseToCellularProcessPredicate a owl:Class, - linkml:ClassDefinition ; - rdfs:label "DiseaseToCellularProcessPredicate" ; - ibdlit:annotators "sqlite:obo:ro" ; - ibdlit:prompt "the name of the type of relationship between a disease and a cellular process." ; - rdfs:subClassOf core:RelationshipType ; - linkml:attributes "{}" ; - linkml:is_a "RelationshipType" . - -ibdlit:object a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object" ; - rdfs:domain ibdlit:DiseaseCellularProcessRelationship, - ibdlit:GeneExposureRelationship ; - rdfs:range ibdlit:CellularProcess, - ibdlit:Gene ; - rdfs:subPropertyOf core:object ; - skos:definition "The name of the cellular process.", - "The name of the gene in the pair. This comes second in the pair." ; - linkml:is_a "triple__object" . - -ibdlit:object_qualifier a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_qualifier" ; - rdfs:domain ibdlit:DiseaseCellularProcessRelationship, - ibdlit:GeneExposureRelationship ; - rdfs:range core:NamedEntity ; - rdfs:subPropertyOf core:object_qualifier ; - skos:definition "An optional qualifier or modifier for the gene." ; - linkml:is_a "triple__object_qualifier" . - -ibdlit:predicate a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "predicate" ; - rdfs:domain ibdlit:DiseaseCellularProcessRelationship, - ibdlit:GeneExposureRelationship ; - rdfs:range ibdlit:ChemicalExposureToGenePredicate, - ibdlit:DiseaseToCellularProcessPredicate ; - rdfs:subPropertyOf core:predicate ; - skos:definition "The name of the type of relationship between a chemical exposure and a gene.", - "The name of the type of relationship between a disease and a cellular process." ; - linkml:is_a "triple__predicate" . - -ibdlit:subject a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject" ; - rdfs:domain ibdlit:DiseaseCellularProcessRelationship, - ibdlit:GeneExposureRelationship ; - rdfs:range ibdlit:ChemicalExposure, - ibdlit:Disease ; - rdfs:subPropertyOf core:subject ; - skos:definition "The name of the disease.", - "The name of the exposure, such as a exposure to a chemical toxin." ; - linkml:is_a "triple__subject" . - -ibdlit:subject_qualifier a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_qualifier" ; - rdfs:domain ibdlit:DiseaseCellularProcessRelationship, - ibdlit:GeneExposureRelationship ; - rdfs:range core:NamedEntity ; - rdfs:subPropertyOf core:subject_qualifier ; - skos:definition "An optional qualifier or modifier for the chemical exposure." ; - linkml:is_a "triple__subject_qualifier" . - -core:NullDataOptions a owl:Class, - linkml:EnumDefinition ; - rdfs:label "NullDataOptions" ; - owl:unionOf ( NCIT:C149701 NCIT:C18902 <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> ) ; - linkml:permissible_values NCIT:C149701, - NCIT:C18902, - <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> . - -core:Publication a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Publication" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty core:title ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty core:abstract ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty core:full_text ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty core:id ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty core:combined_text ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -core:RelationshipType a owl:Class, - linkml:ClassDefinition ; - rdfs:label "RelationshipType" ; - rdfs:subClassOf core:NamedEntity ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -core:Triple a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Triple" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass core:NamedEntity ; - owl:onProperty core:object_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass core:NamedEntity ; - owl:onProperty core:subject ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass core:NamedEntity ; - owl:onProperty core:subject_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty core:qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass core:NamedEntity ; - owl:onProperty core:object ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass core:RelationshipType ; - owl:onProperty core:predicate ], - core:CompoundExpression ; - skos:definition "Abstract parent for Relation Extraction tasks" ; - linkml:attributes "{'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -ibdlit:CellularProcess a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CellularProcess" ; - ibdlit:annotators "sqlite:obo:go" ; - ibdlit:prompt "the name of the cellular process" ; - rdfs:subClassOf core:NamedEntity ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -ibdlit:ChemicalExposure a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ChemicalExposure" ; - ibdlit:annotators "sqlite:obo:ecto, sqlite:obo:chebi" ; - ibdlit:prompt "the name of the exposure, such as a exposure to a chemical toxin. For example, CHEBI:17968 butyrate." ; - rdfs:subClassOf core:NamedEntity ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -ibdlit:Disease a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Disease" ; - ibdlit:annotators "sqlite:obo:mondo" ; - ibdlit:prompt "the name of the disease" ; - rdfs:subClassOf core:NamedEntity ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -ibdlit:Gene a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Gene" ; - ibdlit:annotators "sqlite:obo:hgnc, sqlite:obo:pr" ; - ibdlit:prompt "the name of the gene in the pair. This comes second in the pair." ; - rdfs:subClassOf core:NamedEntity ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -core:Any a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Any" ; - skos:exactMatch linkml:Any ; - linkml:attributes "{}" . - -ibdlit:DiseaseCellularProcessRelationship a owl:Class, - linkml:ClassDefinition ; - rdfs:label "DiseaseCellularProcessRelationship" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ibdlit:DiseaseToCellularProcessPredicate ; - owl:onProperty ibdlit:predicate ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass core:NamedEntity ; - owl:onProperty ibdlit:object_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ibdlit:CellularProcess ; - owl:onProperty ibdlit:object ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ibdlit:Disease ; - owl:onProperty ibdlit:subject ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass core:NamedEntity ; - owl:onProperty ibdlit:subject_qualifier ], - core:Triple ; - linkml:attributes "{}" ; - linkml:is_a "Triple" . - -ibdlit:GeneExposureRelationship a owl:Class, - linkml:ClassDefinition ; - rdfs:label "GeneExposureRelationship" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ibdlit:Gene ; - owl:onProperty ibdlit:object ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ibdlit:ChemicalExposureToGenePredicate ; - owl:onProperty ibdlit:predicate ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ibdlit:ChemicalExposure ; - owl:onProperty ibdlit:subject ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass core:NamedEntity ; - owl:onProperty ibdlit:object_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass core:NamedEntity ; - owl:onProperty ibdlit:subject_qualifier ], - core:Triple ; - linkml:attributes "{}" ; - linkml:is_a "Triple" . - -linkml:ClassDefinition a owl:Class ; - rdfs:label "class_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "class_expression" . - -core:NamedEntity a owl:Class, - linkml:ClassDefinition ; - rdfs:label "NamedEntity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty core:id ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://example.org/UNKNOWN/rdfs/label> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:SlotDefinition a owl:Class ; - rdfs:label "slot_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "slot_expression" . - - diff --git a/projects/ibd_literature/prefixmap/ibd_literature.yaml b/projects/ibd_literature/prefixmap/ibd_literature.yaml deleted file mode 100644 index c03580296..000000000 --- a/projects/ibd_literature/prefixmap/ibd_literature.yaml +++ /dev/null @@ -1,42 +0,0 @@ -{ - "CHEBI": "http://purl.obolibrary.org/obo/CHEBI_", - "ECTO": "http://purl.obolibrary.org/obo/ECTO_", - "ExO": "http://purl.obolibrary.org/obo/ExO_", - "GO": "http://example.org/UNKNOWN/GO/", - "HGNC": "http://identifiers.org/hgnc/", - "MONDO": "http://example.org/UNKNOWN/MONDO/", - "NCIT": "http://purl.obolibrary.org/obo/NCIT_", - "RO": "http://purl.obolibrary.org/obo/RO_", - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "ibdlit": "http://w3id.org/ontogpt/ibd_literature/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } -} diff --git a/projects/ibd_literature/protobuf/ibd_literature.proto b/projects/ibd_literature/protobuf/ibd_literature.proto deleted file mode 100644 index 5addfe224..000000000 --- a/projects/ibd_literature/protobuf/ibd_literature.proto +++ /dev/null @@ -1,92 +0,0 @@ -message AnnotatorResult - { - string subjectText = 0 - string objectId = 0 - string objectText = 0 - } -message CellularProcess - { - string id = 0 - string label = 0 - } -message ChemicalExposure - { - string id = 0 - string label = 0 - } -message ChemicalExposureToGenePredicate - { - string id = 0 - string label = 0 - } -message Disease - { - string id = 0 - string label = 0 - } -message DiseaseCellularProcessRelationship - { - string qualifier = 0 - disease subject = 0 - diseaseToCellularProcessPredicate predicate = 0 - cellularProcess object = 0 - namedEntity subjectQualifier = 0 - namedEntity objectQualifier = 0 - } -message DiseaseToCellularProcessPredicate - { - string id = 0 - string label = 0 - } -// A result of extracting knowledge on text -message ExtractionResult - { - string inputId = 0 - string inputTitle = 0 - string inputText = 0 - string rawCompletionOutput = 0 - string prompt = 0 - any extractedObject = 0 - repeated any namedEntities = 0 - } -message Gene - { - string id = 0 - string label = 0 - } -message GeneExposureRelationship - { - string qualifier = 0 - chemicalExposure subject = 0 - chemicalExposureToGenePredicate predicate = 0 - gene object = 0 - namedEntity subjectQualifier = 0 - namedEntity objectQualifier = 0 - } -message IBDAnnotations - { - repeated gene genes = 0 - repeated chemicalExposure exposures = 0 - repeated geneExposureRelationship geneExposuresRelationships = 0 - repeated disease diseases = 0 - repeated cellularProcess cellularProcess = 0 - repeated diseaseCellularProcessRelationship diseaseCellularProcessRelationships = 0 - } -message Publication - { - string id = 0 - string title = 0 - string abstract = 0 - string combinedText = 0 - string fullText = 0 - } -message RelationshipType - { - string id = 0 - string label = 0 - } -message TextWithTriples - { - publication publication = 0 - repeated triple triples = 0 - } diff --git a/projects/ibd_literature/shacl/ibd_literature.shacl.ttl b/projects/ibd_literature/shacl/ibd_literature.shacl.ttl deleted file mode 100644 index 6d8d65e79..000000000 --- a/projects/ibd_literature/shacl/ibd_literature.shacl.ttl +++ /dev/null @@ -1,362 +0,0 @@ -@prefix core: <http://w3id.org/ontogpt/core/> . -@prefix ibdlit: <http://w3id.org/ontogpt/ibd_literature/> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix sh: <http://www.w3.org/ns/shacl#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -core:AnnotatorResult a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 0 ; - sh:path core:subject_text ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path core:object_id ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path core:object_text ] ; - sh:targetClass core:AnnotatorResult . - -core:CompoundExpression a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass core:CompoundExpression . - -core:ExtractionResult a sh:NodeShape ; - sh:closed true ; - sh:description "A result of extracting knowledge on text" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class linkml:Any ; - sh:description "The complex objects extracted from the text" ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path core:extracted_object ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path core:input_id ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path core:input_text ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path core:raw_completion_output ], - [ sh:maxCount 1 ; - sh:order 4 ; - sh:path core:prompt ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path core:input_title ], - [ sh:class linkml:Any ; - sh:description "Named entities extracted from the text" ; - sh:nodeKind sh:BlankNode ; - sh:order 6 ; - sh:path core:named_entities ] ; - sh:targetClass core:ExtractionResult . - -core:TextWithTriples a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class core:Triple ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path core:triples ], - [ sh:class core:Publication ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path core:publication ] ; - sh:targetClass core:TextWithTriples . - -ibdlit:IBDAnnotations a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class ibdlit:GeneExposureRelationship ; - sh:description "semicolon-separated list of gene to molecular activity relationships" ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path ibdlit:gene_exposures_relationships ], - [ sh:class ibdlit:Gene ; - sh:description "semicolon-separated list of genes" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path ibdlit:genes ], - [ sh:class ibdlit:Disease ; - sh:description "semicolon-separated list of diseases" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path ibdlit:diseases ], - [ sh:class ibdlit:ChemicalExposure ; - sh:description "semicolon-separated list of exposures" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path ibdlit:exposures ], - [ sh:class ibdlit:DiseaseCellularProcessRelationship ; - sh:description "semicolon-separated list of disease to cellular process relationships" ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path ibdlit:disease_cellular_process_relationships ], - [ sh:class ibdlit:CellularProcess ; - sh:description "semicolon-separated list of cellular processes" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path ibdlit:cellular_process ] ; - sh:targetClass ibdlit:IBDAnnotations . - -core:Publication a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 3 ; - sh:path core:combined_text ], - [ sh:description "The publication identifier" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path core:id ], - [ sh:description "The title of the publication" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path core:title ], - [ sh:description "The abstract of the publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path core:abstract ], - [ sh:description "The full text of the publication" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path core:full_text ] ; - sh:targetClass core:Publication . - -core:RelationshipType a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path core:id ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass core:RelationshipType . - -core:Triple a sh:NodeShape ; - sh:closed false ; - sh:description "Abstract parent for Relation Extraction tasks" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class core:NamedEntity ; - sh:description "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path core:subject_qualifier ], - [ sh:class core:NamedEntity ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path core:subject ], - [ sh:class core:NamedEntity ; - sh:description "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path core:object_qualifier ], - [ sh:class core:NamedEntity ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path core:object ], - [ sh:description "A qualifier for the statements, e.g. \"NOT\" for negation" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path core:qualifier ], - [ sh:class core:RelationshipType ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path core:predicate ] ; - sh:targetClass core:Triple . - -ibdlit:ChemicalExposureToGenePredicate a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path core:id ] ; - sh:targetClass ibdlit:ChemicalExposureToGenePredicate . - -ibdlit:DiseaseCellularProcessRelationship a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class ibdlit:DiseaseToCellularProcessPredicate ; - sh:description "The name of the type of relationship between a disease and a cellular process." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path core:predicate ], - [ sh:class core:NamedEntity ; - sh:description "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path core:subject_qualifier ], - [ sh:class core:NamedEntity ; - sh:description "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path core:object_qualifier ], - [ sh:description "A qualifier for the statements, e.g. \"NOT\" for negation" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path core:qualifier ], - [ sh:class ibdlit:Disease ; - sh:description "The name of the disease." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path core:subject ], - [ sh:class ibdlit:CellularProcess ; - sh:description "The name of the cellular process." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path core:object ] ; - sh:targetClass ibdlit:DiseaseCellularProcessRelationship . - -ibdlit:DiseaseToCellularProcessPredicate a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path core:id ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass ibdlit:DiseaseToCellularProcessPredicate . - -ibdlit:GeneExposureRelationship a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class ibdlit:Gene ; - sh:description "The name of the gene in the pair. This comes second in the pair." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path core:object ], - [ sh:class ibdlit:ChemicalExposureToGenePredicate ; - sh:description "The name of the type of relationship between a chemical exposure and a gene." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path core:predicate ], - [ sh:description "A qualifier for the statements, e.g. \"NOT\" for negation" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path core:qualifier ], - [ sh:class core:NamedEntity ; - sh:description "An optional qualifier or modifier for the gene." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path core:object_qualifier ], - [ sh:class ibdlit:ChemicalExposure ; - sh:description "The name of the exposure, such as a exposure to a chemical toxin." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path core:subject ], - [ sh:class core:NamedEntity ; - sh:description "An optional qualifier or modifier for the chemical exposure." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path core:subject_qualifier ] ; - sh:targetClass ibdlit:GeneExposureRelationship . - -ibdlit:CellularProcess a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path core:id ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass ibdlit:CellularProcess . - -ibdlit:ChemicalExposure a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path core:id ] ; - sh:targetClass ibdlit:ChemicalExposure . - -ibdlit:Disease a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path core:id ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass ibdlit:Disease . - -ibdlit:Gene a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path core:id ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass ibdlit:Gene . - -linkml:Any a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass linkml:Any . - -core:NamedEntity a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path core:id ] ; - sh:targetClass core:NamedEntity . - diff --git a/projects/ibd_literature/shex/ibd_literature.shex b/projects/ibd_literature/shex/ibd_literature.shex deleted file mode 100644 index 49662bcc2..000000000 --- a/projects/ibd_literature/shex/ibd_literature.shex +++ /dev/null @@ -1,226 +0,0 @@ -BASE <http://w3id.org/ontogpt/ibd_literature/> -PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> -PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> -PREFIX core: <http://w3id.org/ontogpt/core/> -PREFIX linkml: <https://w3id.org/linkml/> -PREFIX rdfs1: <http://example.org/UNKNOWN/rdfs/> - - -linkml:String xsd:string - -linkml:Integer xsd:integer - -linkml:Boolean xsd:boolean - -linkml:Float xsd:float - -linkml:Double xsd:double - -linkml:Decimal xsd:decimal - -linkml:Time xsd:time - -linkml:Date xsd:date - -linkml:Datetime xsd:dateTime - -linkml:DateOrDatetime linkml:DateOrDatetime - -linkml:Uriorcurie IRI - -linkml:Curie xsd:string - -linkml:Uri IRI - -linkml:Ncname xsd:string - -linkml:Objectidentifier IRI - -linkml:Nodeidentifier NONLITERAL - -linkml:Jsonpointer xsd:string - -linkml:Jsonpath xsd:string - -linkml:Sparqlpath xsd:string - -core:AnnotatorResult CLOSED { - ( $core:AnnotatorResult_tes ( core:subject_text @linkml:String ? ; - core:object_id @linkml:String ? ; - core:object_text @linkml:String ? - ) ; - rdf:type [ core:AnnotatorResult ] ? - ) -} - -core:Any CLOSED { - ( $core:Any_tes rdf:type . * ; - rdf:type [ linkml:Any ] ? - ) -} - -<CellularProcess> CLOSED { - ( $<CellularProcess_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <CellularProcess> ] - ) -} - -<ChemicalExposure> CLOSED { - ( $<ChemicalExposure_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <ChemicalExposure> ] - ) -} - -<ChemicalExposureToGenePredicate> CLOSED { - ( $<ChemicalExposureToGenePredicate_tes> ( &core:RelationshipType_tes ; - rdf:type [ core:RelationshipType ] ? - ) ; - rdf:type [ <ChemicalExposureToGenePredicate> ] - ) -} - -core:CompoundExpression ( - { - ( $core:CompoundExpression_tes rdf:type . * ; - rdf:type [ core:CompoundExpression ] ? - ) - } OR @core:Triple -) - -<Disease> CLOSED { - ( $<Disease_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Disease> ] - ) -} - -<DiseaseCellularProcessRelationship> CLOSED { - ( $<DiseaseCellularProcessRelationship_tes> ( &core:Triple_tes ; - rdf:type [ core:Triple ] ? ; - <subject> @<Disease> ? ; - <predicate> @<DiseaseToCellularProcessPredicate> ? ; - <object> @<CellularProcess> ? ; - <subject_qualifier> @core:NamedEntity ? ; - <object_qualifier> @core:NamedEntity ? - ) ; - rdf:type [ <DiseaseCellularProcessRelationship> ] ? - ) -} - -<DiseaseToCellularProcessPredicate> CLOSED { - ( $<DiseaseToCellularProcessPredicate_tes> ( &core:RelationshipType_tes ; - rdf:type [ core:RelationshipType ] ? - ) ; - rdf:type [ <DiseaseToCellularProcessPredicate> ] - ) -} - -core:ExtractionResult CLOSED { - ( $core:ExtractionResult_tes ( core:input_id @linkml:String ? ; - core:input_title @linkml:String ? ; - core:input_text @linkml:String ? ; - core:raw_completion_output @linkml:String ? ; - core:prompt @linkml:String ? ; - core:extracted_object @core:Any ? ; - core:named_entities @core:Any * - ) ; - rdf:type [ core:ExtractionResult ] ? - ) -} - -<Gene> CLOSED { - ( $<Gene_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Gene> ] - ) -} - -<GeneExposureRelationship> CLOSED { - ( $<GeneExposureRelationship_tes> ( &core:Triple_tes ; - rdf:type [ core:Triple ] ? ; - <subject> @<ChemicalExposure> ? ; - <predicate> @<ChemicalExposureToGenePredicate> ? ; - <object> @<Gene> ? ; - <subject_qualifier> @core:NamedEntity ? ; - <object_qualifier> @core:NamedEntity ? - ) ; - rdf:type [ <GeneExposureRelationship> ] ? - ) -} - -<IBDAnnotations> CLOSED { - ( $<IBDAnnotations_tes> ( <genes> @<Gene> * ; - <exposures> @<ChemicalExposure> * ; - <gene_exposures_relationships> @<GeneExposureRelationship> * ; - <diseases> @<Disease> * ; - <cellular_process> @<CellularProcess> * ; - <disease_cellular_process_relationships> @<DiseaseCellularProcessRelationship> * - ) ; - rdf:type [ <IBDAnnotations> ] ? - ) -} - -core:NamedEntity ( - @<CellularProcess> OR @<ChemicalExposure> OR @<Disease> OR @<Gene> OR @core:RelationshipType -) - -core:NamedEntity_struct { - ( $core:NamedEntity_tes rdfs1:label @linkml:String ? ; - rdf:type [ core:NamedEntity ] - ) -} - -core:Publication CLOSED { - ( $core:Publication_tes ( core:id @linkml:String ? ; - core:title @linkml:String ? ; - core:abstract @linkml:String ? ; - core:combined_text @linkml:String ? ; - core:full_text @linkml:String ? - ) ; - rdf:type [ core:Publication ] ? - ) -} - -core:RelationshipType ( - CLOSED { - ( $core:RelationshipType_tes ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ core:RelationshipType ] - ) - } OR @<ChemicalExposureToGenePredicate> OR @<DiseaseToCellularProcessPredicate> -) - -core:TextWithTriples CLOSED { - ( $core:TextWithTriples_tes ( core:publication @core:Publication ? ; - core:triples @core:Triple * - ) ; - rdf:type [ core:TextWithTriples ] ? - ) -} - -core:Triple ( - @<DiseaseCellularProcessRelationship> OR @<GeneExposureRelationship> -) - -core:Triple_struct { - ( $core:Triple_tes ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - core:subject @core:NamedEntity ? ; - core:predicate @core:RelationshipType ? ; - core:object @core:NamedEntity ? ; - core:qualifier @linkml:String ? ; - core:subject_qualifier @core:NamedEntity ? ; - core:object_qualifier @core:NamedEntity ? - ) ; - rdf:type [ core:Triple ] ? - ) -} - - diff --git a/projects/ibd_literature/sqlschema/ibd_literature.sql b/projects/ibd_literature/sqlschema/ibd_literature.sql deleted file mode 100644 index 4d8e2aff9..000000000 --- a/projects/ibd_literature/sqlschema/ibd_literature.sql +++ /dev/null @@ -1,112 +0,0 @@ - - -CREATE TABLE "AnnotatorResult" ( - subject_text TEXT, - object_id TEXT, - object_text TEXT, - PRIMARY KEY (subject_text, object_id, object_text) -); - -CREATE TABLE "CellularProcess" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "ChemicalExposure" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "ChemicalExposureToGenePredicate" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Disease" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "DiseaseToCellularProcessPredicate" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "ExtractionResult" ( - input_id TEXT, - input_title TEXT, - input_text TEXT, - raw_completion_output TEXT, - prompt TEXT, - extracted_object TEXT, - named_entities TEXT, - PRIMARY KEY (input_id, input_title, input_text, raw_completion_output, prompt, extracted_object, named_entities) -); - -CREATE TABLE "Gene" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "IBDAnnotations" ( - genes TEXT, - exposures TEXT, - gene_exposures_relationships TEXT, - diseases TEXT, - cellular_process TEXT, - disease_cellular_process_relationships TEXT, - PRIMARY KEY (genes, exposures, gene_exposures_relationships, diseases, cellular_process, disease_cellular_process_relationships) -); - -CREATE TABLE "Publication" ( - id TEXT, - title TEXT, - abstract TEXT, - combined_text TEXT, - full_text TEXT, - PRIMARY KEY (id, title, abstract, combined_text, full_text) -); - -CREATE TABLE "RelationshipType" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "TextWithTriples" ( - publication TEXT, - triples TEXT, - PRIMARY KEY (publication, triples) -); - -CREATE TABLE "DiseaseCellularProcessRelationship" ( - qualifier TEXT, - subject TEXT, - predicate TEXT, - object TEXT, - subject_qualifier TEXT, - object_qualifier TEXT, - PRIMARY KEY (qualifier, subject, predicate, object, subject_qualifier, object_qualifier), - FOREIGN KEY(subject) REFERENCES "Disease" (id), - FOREIGN KEY(predicate) REFERENCES "DiseaseToCellularProcessPredicate" (id), - FOREIGN KEY(object) REFERENCES "CellularProcess" (id) -); - -CREATE TABLE "GeneExposureRelationship" ( - qualifier TEXT, - subject TEXT, - predicate TEXT, - object TEXT, - subject_qualifier TEXT, - object_qualifier TEXT, - PRIMARY KEY (qualifier, subject, predicate, object, subject_qualifier, object_qualifier), - FOREIGN KEY(subject) REFERENCES "ChemicalExposure" (id), - FOREIGN KEY(predicate) REFERENCES "ChemicalExposureToGenePredicate" (id), - FOREIGN KEY(object) REFERENCES "Gene" (id) -); diff --git a/projects/mendelian_disease/docs/AnnotatorResult.md b/projects/mendelian_disease/docs/AnnotatorResult.md deleted file mode 100644 index ba2647512..000000000 --- a/projects/mendelian_disease/docs/AnnotatorResult.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Class: AnnotatorResult - - - - -URI: [mendelian_disease:AnnotatorResult](http://w3id.org/ontogpt/mendelian_disease/AnnotatorResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F])](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F]) - -## Attributes - - -### Own - - * [➞subject_text](annotatorResult__subject_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_id](annotatorResult__object_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_text](annotatorResult__object_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) diff --git a/projects/mendelian_disease/docs/Any.md b/projects/mendelian_disease/docs/Any.md deleted file mode 100644 index a944133e1..000000000 --- a/projects/mendelian_disease/docs/Any.md +++ /dev/null @@ -1,25 +0,0 @@ - -# Class: Any - - - - -URI: [mendelian_disease:Any](http://w3id.org/ontogpt/mendelian_disease/Any) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult])](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult]) - -## Referenced by Class - - * **None** *[➞extracted_object](extractionResult__extracted_object.md)* <sub>0..1</sub> **[Any](Any.md)** - * **None** *[➞named_entities](extractionResult__named_entities.md)* <sub>0..\*</sub> **[Any](Any.md)** - -## Attributes - - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | linkml:Any | - diff --git a/projects/mendelian_disease/docs/CompoundExpression.md b/projects/mendelian_disease/docs/CompoundExpression.md deleted file mode 100644 index 02d0ad18b..000000000 --- a/projects/mendelian_disease/docs/CompoundExpression.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: CompoundExpression - - - - -URI: [mendelian_disease:CompoundExpression](http://w3id.org/ontogpt/mendelian_disease/CompoundExpression) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[CompoundExpression]^-[Triple])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[CompoundExpression]^-[Triple]) - -## Children - - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - -## Referenced by Class - - -## Attributes - diff --git a/projects/mendelian_disease/docs/DiseaseCategory.md b/projects/mendelian_disease/docs/DiseaseCategory.md deleted file mode 100644 index 49d9de951..000000000 --- a/projects/mendelian_disease/docs/DiseaseCategory.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: DiseaseCategory - - - - -URI: [mendelian_disease:DiseaseCategory](http://w3id.org/ontogpt/mendelian_disease/DiseaseCategory) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[MendelianDisease]-%20subclass_of%200..*>[DiseaseCategory|id(i):string;label(i):string%20%3F],[NamedEntity]^-[DiseaseCategory],[MendelianDisease])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[MendelianDisease]-%20subclass_of%200..*>[DiseaseCategory|id(i):string;label(i):string%20%3F],[NamedEntity]^-[DiseaseCategory],[MendelianDisease]) - -## Identifier prefixes - - * MONDO - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞subclass_of](mendelianDisease__subclass_of.md)* <sub>0..\*</sub> **[DiseaseCategory](DiseaseCategory.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/mendelian_disease/docs/ExtractionResult.md b/projects/mendelian_disease/docs/ExtractionResult.md deleted file mode 100644 index 51ffa7131..000000000 --- a/projects/mendelian_disease/docs/ExtractionResult.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Class: ExtractionResult - - -A result of extracting knowledge on text - -URI: [mendelian_disease:ExtractionResult](http://w3id.org/ontogpt/mendelian_disease/ExtractionResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any])](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any]) - -## Attributes - - -### Own - - * [➞input_id](extractionResult__input_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_title](extractionResult__input_title.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_text](extractionResult__input_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞prompt](extractionResult__prompt.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞extracted_object](extractionResult__extracted_object.md) <sub>0..1</sub> - * Description: The complex objects extracted from the text - * Range: [Any](Any.md) - * [➞named_entities](extractionResult__named_entities.md) <sub>0..\*</sub> - * Description: Named entities extracted from the text - * Range: [Any](Any.md) diff --git a/projects/mendelian_disease/docs/Gene.md b/projects/mendelian_disease/docs/Gene.md deleted file mode 100644 index 6ce201a82..000000000 --- a/projects/mendelian_disease/docs/Gene.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Gene - - - - -URI: [mendelian_disease:Gene](http://w3id.org/ontogpt/mendelian_disease/Gene) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[MendelianDisease]-%20genes%200..*>[Gene|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Gene],[MendelianDisease])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[MendelianDisease]-%20genes%200..*>[Gene|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Gene],[MendelianDisease]) - -## Identifier prefixes - - * HGNC - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞genes](mendelianDisease__genes.md)* <sub>0..\*</sub> **[Gene](Gene.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/mendelian_disease/docs/Inheritance.md b/projects/mendelian_disease/docs/Inheritance.md deleted file mode 100644 index a07f579a7..000000000 --- a/projects/mendelian_disease/docs/Inheritance.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Class: Inheritance - - - - -URI: [mendelian_disease:Inheritance](http://w3id.org/ontogpt/mendelian_disease/Inheritance) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[MendelianDisease]-%20inheritance%200..1>[Inheritance|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Inheritance],[MendelianDisease])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[MendelianDisease]-%20inheritance%200..1>[Inheritance|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Inheritance],[MendelianDisease]) - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞inheritance](mendelianDisease__inheritance.md)* <sub>0..1</sub> **[Inheritance](Inheritance.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/mendelian_disease/docs/MendelianDisease.md b/projects/mendelian_disease/docs/MendelianDisease.md deleted file mode 100644 index 37cc914f5..000000000 --- a/projects/mendelian_disease/docs/MendelianDisease.md +++ /dev/null @@ -1,61 +0,0 @@ - -# Class: MendelianDisease - - - - -URI: [mendelian_disease:MendelianDisease](http://w3id.org/ontogpt/mendelian_disease/MendelianDisease) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Symptom],[Publication],[Onset],[NamedEntity],[Publication]<publications%200..*-++[MendelianDisease|name:string%20%3F;description:string%20%3F;synonyms:string%20*;id(i):string;label(i):string%20%3F],[Onset]<disease_onsets%200..*-%20[MendelianDisease],[Gene]<genes%200..*-%20[MendelianDisease],[Inheritance]<inheritance%200..1-%20[MendelianDisease],[Symptom]<symptoms%200..*-%20[MendelianDisease],[DiseaseCategory]<subclass_of%200..*-%20[MendelianDisease],[NamedEntity]^-[MendelianDisease],[Inheritance],[Gene],[DiseaseCategory])](https://yuml.me/diagram/nofunky;dir:TB/class/[Symptom],[Publication],[Onset],[NamedEntity],[Publication]<publications%200..*-++[MendelianDisease|name:string%20%3F;description:string%20%3F;synonyms:string%20*;id(i):string;label(i):string%20%3F],[Onset]<disease_onsets%200..*-%20[MendelianDisease],[Gene]<genes%200..*-%20[MendelianDisease],[Inheritance]<inheritance%200..1-%20[MendelianDisease],[Symptom]<symptoms%200..*-%20[MendelianDisease],[DiseaseCategory]<subclass_of%200..*-%20[MendelianDisease],[NamedEntity]^-[MendelianDisease],[Inheritance],[Gene],[DiseaseCategory]) - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Attributes - - -### Own - - * [➞name](mendelianDisease__name.md) <sub>0..1</sub> - * Description: the name of the disease - * Range: [String](types/String.md) - * Example: peroxisome biogenesis disorder None - * [➞description](mendelianDisease__description.md) <sub>0..1</sub> - * Description: a description of the disease - * Range: [String](types/String.md) - * Example: Peroxisome biogenesis disorders, Zellweger syndrome spectrum (PBD-ZSS) is a group of autosomal recessive disorders affecting the formation of functional peroxisomes, characterized by sensorineural hearing loss, pigmentary retinal degeneration, multiple organ dysfunction and psychomotor impairment None - * [➞synonyms](mendelianDisease__synonyms.md) <sub>0..\*</sub> - * Range: [String](types/String.md) - * Example: Zellweger syndrome spectrum None - * Example: PBD-ZSS None - * [➞subclass_of](mendelianDisease__subclass_of.md) <sub>0..\*</sub> - * Range: [DiseaseCategory](DiseaseCategory.md) - * Example: lysosomal disease None - * Example: autosomal recessive disorder None - * [➞symptoms](mendelianDisease__symptoms.md) <sub>0..\*</sub> - * Range: [Symptom](Symptom.md) - * Example: sensorineural hearing loss None - * Example: pigmentary retinal degeneration None - * [➞inheritance](mendelianDisease__inheritance.md) <sub>0..1</sub> - * Range: [Inheritance](Inheritance.md) - * Example: autosomal recessive None - * [➞genes](mendelianDisease__genes.md) <sub>0..\*</sub> - * Range: [Gene](Gene.md) - * Example: PEX1 None - * Example: PEX2 None - * Example: PEX3 None - * [➞disease_onsets](mendelianDisease__disease_onsets.md) <sub>0..\*</sub> - * Range: [Onset](Onset.md) - * [➞publications](mendelianDisease__publications.md) <sub>0..\*</sub> - * Range: [Publication](Publication.md) - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/mendelian_disease/docs/NamedEntity.md b/projects/mendelian_disease/docs/NamedEntity.md deleted file mode 100644 index c9f06fce8..000000000 --- a/projects/mendelian_disease/docs/NamedEntity.md +++ /dev/null @@ -1,39 +0,0 @@ - -# Class: NamedEntity - - - - -URI: [mendelian_disease:NamedEntity](http://w3id.org/ontogpt/mendelian_disease/NamedEntity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Symptom],[RelationshipType],[Onset],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[Symptom],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[Onset],[NamedEntity]^-[MendelianDisease],[NamedEntity]^-[Inheritance],[NamedEntity]^-[Gene],[NamedEntity]^-[DiseaseCategory],[Triple],[MendelianDisease],[Inheritance],[Gene],[DiseaseCategory])](https://yuml.me/diagram/nofunky;dir:TB/class/[Symptom],[RelationshipType],[Onset],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[Symptom],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[Onset],[NamedEntity]^-[MendelianDisease],[NamedEntity]^-[Inheritance],[NamedEntity]^-[Gene],[NamedEntity]^-[DiseaseCategory],[Triple],[MendelianDisease],[Inheritance],[Gene],[DiseaseCategory]) - -## Children - - * [DiseaseCategory](DiseaseCategory.md) - * [Gene](Gene.md) - * [Inheritance](Inheritance.md) - * [MendelianDisease](MendelianDisease.md) - * [Onset](Onset.md) - * [RelationshipType](RelationshipType.md) - * [Symptom](Symptom.md) - -## Referenced by Class - - * **None** *[➞object](triple__object.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞object_qualifier](triple__object_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject](triple__subject.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject_qualifier](triple__subject_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - -## Attributes - - -### Own - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/mendelian_disease/docs/NullDataOptions.md b/projects/mendelian_disease/docs/NullDataOptions.md deleted file mode 100644 index 45d64908d..000000000 --- a/projects/mendelian_disease/docs/NullDataOptions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Enum: NullDataOptions - - - - -URI: [mendelian_disease:NullDataOptions](http://w3id.org/ontogpt/mendelian_disease/NullDataOptions) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | -| UNSPECIFIED_METHOD_OF_ADMINISTRATION | | NCIT:C149701 | | -| NOT_APPLICABLE | | NCIT:C18902 | {'aliases': ['not applicable', 'N/A']} | -| NOT_MENTIONED | | | | - diff --git a/projects/mendelian_disease/docs/Onset.md b/projects/mendelian_disease/docs/Onset.md deleted file mode 100644 index 71a6c2a4b..000000000 --- a/projects/mendelian_disease/docs/Onset.md +++ /dev/null @@ -1,44 +0,0 @@ - -# Class: Onset - - - - -URI: [mendelian_disease:Onset](http://w3id.org/ontogpt/mendelian_disease/Onset) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[MendelianDisease]-%20disease_onsets%200..*>[Onset|years_old:string%20%3F;decades:string%20*;juvenile_or_adult:string%20%3F;id(i):string;label(i):string%20%3F],[Symptom]-%20onset_of_symptom%200..1>[Onset],[NamedEntity]^-[Onset],[Symptom],[NamedEntity],[MendelianDisease])](https://yuml.me/diagram/nofunky;dir:TB/class/[MendelianDisease]-%20disease_onsets%200..*>[Onset|years_old:string%20%3F;decades:string%20*;juvenile_or_adult:string%20%3F;id(i):string;label(i):string%20%3F],[Symptom]-%20onset_of_symptom%200..1>[Onset],[NamedEntity]^-[Onset],[Symptom],[NamedEntity],[MendelianDisease]) - -## Identifier prefixes - - * HP - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞disease_onsets](mendelianDisease__disease_onsets.md)* <sub>0..\*</sub> **[Onset](Onset.md)** - * **None** *[➞onset_of_symptom](symptom__onset_of_symptom.md)* <sub>0..1</sub> **[Onset](Onset.md)** - -## Attributes - - -### Own - - * [➞years_old](onset__years_old.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞decades](onset__decades.md) <sub>0..\*</sub> - * Range: [String](types/String.md) - * [➞juvenile_or_adult](onset__juvenile_or_adult.md) <sub>0..1</sub> - * Range: [String](types/String.md) - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/mendelian_disease/docs/Publication.md b/projects/mendelian_disease/docs/Publication.md deleted file mode 100644 index d88dd3c5d..000000000 --- a/projects/mendelian_disease/docs/Publication.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: Publication - - - - -URI: [mendelian_disease:Publication](http://w3id.org/ontogpt/mendelian_disease/Publication) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[MendelianDisease]++-%20publications%200..*>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples]++-%20publication%200..1>[Publication],[TextWithTriples],[MendelianDisease])](https://yuml.me/diagram/nofunky;dir:TB/class/[MendelianDisease]++-%20publications%200..*>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples]++-%20publication%200..1>[Publication],[TextWithTriples],[MendelianDisease]) - -## Referenced by Class - - * **None** *[➞publications](mendelianDisease__publications.md)* <sub>0..\*</sub> **[Publication](Publication.md)** - * **None** *[➞publication](textWithTriples__publication.md)* <sub>0..1</sub> **[Publication](Publication.md)** - -## Attributes - - -### Own - - * [➞id](publication__id.md) <sub>0..1</sub> - * Description: The publication identifier - * Range: [String](types/String.md) - * [➞title](publication__title.md) <sub>0..1</sub> - * Description: The title of the publication - * Range: [String](types/String.md) - * [➞abstract](publication__abstract.md) <sub>0..1</sub> - * Description: The abstract of the publication - * Range: [String](types/String.md) - * [➞combined_text](publication__combined_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞full_text](publication__full_text.md) <sub>0..1</sub> - * Description: The full text of the publication - * Range: [String](types/String.md) diff --git a/projects/mendelian_disease/docs/RelationshipType.md b/projects/mendelian_disease/docs/RelationshipType.md deleted file mode 100644 index 5b5a029d2..000000000 --- a/projects/mendelian_disease/docs/RelationshipType.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: RelationshipType - - - - -URI: [mendelian_disease:RelationshipType](http://w3id.org/ontogpt/mendelian_disease/RelationshipType) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity]) - -## Identifier prefixes - - * RO - * biolink - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞predicate](triple__predicate.md)* <sub>0..1</sub> **[RelationshipType](RelationshipType.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/mendelian_disease/docs/Symptom.md b/projects/mendelian_disease/docs/Symptom.md deleted file mode 100644 index 76bc00661..000000000 --- a/projects/mendelian_disease/docs/Symptom.md +++ /dev/null @@ -1,45 +0,0 @@ - -# Class: Symptom - - - - -URI: [mendelian_disease:Symptom](http://w3id.org/ontogpt/mendelian_disease/Symptom) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Onset]<onset_of_symptom%200..1-%20[Symptom|characteristic:string%20%3F;affects:string%20%3F;severity:string%20%3F;id(i):string;label(i):string%20%3F],[MendelianDisease]-%20symptoms%200..*>[Symptom],[NamedEntity]^-[Symptom],[Onset],[NamedEntity],[MendelianDisease])](https://yuml.me/diagram/nofunky;dir:TB/class/[Onset]<onset_of_symptom%200..1-%20[Symptom|characteristic:string%20%3F;affects:string%20%3F;severity:string%20%3F;id(i):string;label(i):string%20%3F],[MendelianDisease]-%20symptoms%200..*>[Symptom],[NamedEntity]^-[Symptom],[Onset],[NamedEntity],[MendelianDisease]) - -## Identifier prefixes - - * HP - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞symptoms](mendelianDisease__symptoms.md)* <sub>0..\*</sub> **[Symptom](Symptom.md)** - -## Attributes - - -### Own - - * [➞characteristic](symptom__characteristic.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞affects](symptom__affects.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞severity](symptom__severity.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞onset_of_symptom](symptom__onset_of_symptom.md) <sub>0..1</sub> - * Range: [Onset](Onset.md) - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/mendelian_disease/docs/TextWithTriples.md b/projects/mendelian_disease/docs/TextWithTriples.md deleted file mode 100644 index a6ad6b5eb..000000000 --- a/projects/mendelian_disease/docs/TextWithTriples.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: TextWithTriples - - - - -URI: [mendelian_disease:TextWithTriples](http://w3id.org/ontogpt/mendelian_disease/TextWithTriples) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication]) - -## Attributes - - -### Own - - * [➞publication](textWithTriples__publication.md) <sub>0..1</sub> - * Range: [Publication](Publication.md) - * [➞triples](textWithTriples__triples.md) <sub>0..\*</sub> - * Range: [Triple](Triple.md) diff --git a/projects/mendelian_disease/docs/Triple.md b/projects/mendelian_disease/docs/Triple.md deleted file mode 100644 index 777bd9538..000000000 --- a/projects/mendelian_disease/docs/Triple.md +++ /dev/null @@ -1,39 +0,0 @@ - -# Class: Triple - - -Abstract parent for Relation Extraction tasks - -URI: [mendelian_disease:Triple](http://w3id.org/ontogpt/mendelian_disease/Triple) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞triples](textWithTriples__triples.md)* <sub>0..\*</sub> **[Triple](Triple.md)** - -## Attributes - - -### Own - - * [➞subject](triple__subject.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞predicate](triple__predicate.md) <sub>0..1</sub> - * Range: [RelationshipType](RelationshipType.md) - * [➞object](triple__object.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞qualifier](triple__qualifier.md) <sub>0..1</sub> - * Description: A qualifier for the statements, e.g. "NOT" for negation - * Range: [String](types/String.md) - * [➞subject_qualifier](triple__subject_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - * Range: [NamedEntity](NamedEntity.md) - * [➞object_qualifier](triple__object_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * Range: [NamedEntity](NamedEntity.md) diff --git a/projects/mendelian_disease/docs/annotatorResult__object_id.md b/projects/mendelian_disease/docs/annotatorResult__object_id.md deleted file mode 100644 index fa20bb770..000000000 --- a/projects/mendelian_disease/docs/annotatorResult__object_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_id - - - - -URI: [mendelian_disease:annotatorResult__object_id](http://w3id.org/ontogpt/mendelian_disease/annotatorResult__object_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/mendelian_disease/docs/annotatorResult__object_text.md b/projects/mendelian_disease/docs/annotatorResult__object_text.md deleted file mode 100644 index 49f40997d..000000000 --- a/projects/mendelian_disease/docs/annotatorResult__object_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_text - - - - -URI: [mendelian_disease:annotatorResult__object_text](http://w3id.org/ontogpt/mendelian_disease/annotatorResult__object_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/mendelian_disease/docs/annotatorResult__subject_text.md b/projects/mendelian_disease/docs/annotatorResult__subject_text.md deleted file mode 100644 index 4ee88b4ce..000000000 --- a/projects/mendelian_disease/docs/annotatorResult__subject_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_text - - - - -URI: [mendelian_disease:annotatorResult__subject_text](http://w3id.org/ontogpt/mendelian_disease/annotatorResult__subject_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/mendelian_disease/docs/extractionResult__extracted_object.md b/projects/mendelian_disease/docs/extractionResult__extracted_object.md deleted file mode 100644 index 62a9b3631..000000000 --- a/projects/mendelian_disease/docs/extractionResult__extracted_object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: extracted_object - - -The complex objects extracted from the text - -URI: [mendelian_disease:extractionResult__extracted_object](http://w3id.org/ontogpt/mendelian_disease/extractionResult__extracted_object) - - -## Domain and Range - -None → <sub>0..1</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/mendelian_disease/docs/extractionResult__input_id.md b/projects/mendelian_disease/docs/extractionResult__input_id.md deleted file mode 100644 index 953c258c2..000000000 --- a/projects/mendelian_disease/docs/extractionResult__input_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_id - - - - -URI: [mendelian_disease:extractionResult__input_id](http://w3id.org/ontogpt/mendelian_disease/extractionResult__input_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/mendelian_disease/docs/extractionResult__input_text.md b/projects/mendelian_disease/docs/extractionResult__input_text.md deleted file mode 100644 index fb3e5306e..000000000 --- a/projects/mendelian_disease/docs/extractionResult__input_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_text - - - - -URI: [mendelian_disease:extractionResult__input_text](http://w3id.org/ontogpt/mendelian_disease/extractionResult__input_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/mendelian_disease/docs/extractionResult__input_title.md b/projects/mendelian_disease/docs/extractionResult__input_title.md deleted file mode 100644 index a87e4958f..000000000 --- a/projects/mendelian_disease/docs/extractionResult__input_title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_title - - - - -URI: [mendelian_disease:extractionResult__input_title](http://w3id.org/ontogpt/mendelian_disease/extractionResult__input_title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/mendelian_disease/docs/extractionResult__named_entities.md b/projects/mendelian_disease/docs/extractionResult__named_entities.md deleted file mode 100644 index 471ab53d5..000000000 --- a/projects/mendelian_disease/docs/extractionResult__named_entities.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: named_entities - - -Named entities extracted from the text - -URI: [mendelian_disease:extractionResult__named_entities](http://w3id.org/ontogpt/mendelian_disease/extractionResult__named_entities) - - -## Domain and Range - -None → <sub>0..\*</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/mendelian_disease/docs/extractionResult__prompt.md b/projects/mendelian_disease/docs/extractionResult__prompt.md deleted file mode 100644 index ef8d93525..000000000 --- a/projects/mendelian_disease/docs/extractionResult__prompt.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: prompt - - - - -URI: [mendelian_disease:extractionResult__prompt](http://w3id.org/ontogpt/mendelian_disease/extractionResult__prompt) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/mendelian_disease/docs/extractionResult__raw_completion_output.md b/projects/mendelian_disease/docs/extractionResult__raw_completion_output.md deleted file mode 100644 index ea64ea51b..000000000 --- a/projects/mendelian_disease/docs/extractionResult__raw_completion_output.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: raw_completion_output - - - - -URI: [mendelian_disease:extractionResult__raw_completion_output](http://w3id.org/ontogpt/mendelian_disease/extractionResult__raw_completion_output) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/mendelian_disease/docs/mendelianDisease__description.md b/projects/mendelian_disease/docs/mendelianDisease__description.md deleted file mode 100644 index ac56dd5e3..000000000 --- a/projects/mendelian_disease/docs/mendelianDisease__description.md +++ /dev/null @@ -1,29 +0,0 @@ - -# Slot: description - - -a description of the disease - -URI: [mendelian_disease:mendelianDisease__description](http://w3id.org/ontogpt/mendelian_disease/mendelianDisease__description) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [MendelianDisease](MendelianDisease.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Examples:** | | Example(value='Peroxisome biogenesis disorders, Zellweger syndrome spectrum (PBD-ZSS) is a group of autosomal recessive disorders affecting the formation of functional peroxisomes, characterized by sensorineural hearing loss, pigmentary retinal degeneration, multiple organ dysfunction and psychomotor impairment', description=None, object=None) | - diff --git a/projects/mendelian_disease/docs/mendelianDisease__disease_onsets.md b/projects/mendelian_disease/docs/mendelianDisease__disease_onsets.md deleted file mode 100644 index d756e8639..000000000 --- a/projects/mendelian_disease/docs/mendelianDisease__disease_onsets.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: disease_onsets - - - - -URI: [mendelian_disease:mendelianDisease__disease_onsets](http://w3id.org/ontogpt/mendelian_disease/mendelianDisease__disease_onsets) - - -## Domain and Range - -None → <sub>0..\*</sub> [Onset](Onset.md) - -## Parents - - -## Children - - -## Used by - - * [MendelianDisease](MendelianDisease.md) diff --git a/projects/mendelian_disease/docs/mendelianDisease__genes.md b/projects/mendelian_disease/docs/mendelianDisease__genes.md deleted file mode 100644 index 5d9a9256b..000000000 --- a/projects/mendelian_disease/docs/mendelianDisease__genes.md +++ /dev/null @@ -1,31 +0,0 @@ - -# Slot: genes - - - - -URI: [mendelian_disease:mendelianDisease__genes](http://w3id.org/ontogpt/mendelian_disease/mendelianDisease__genes) - - -## Domain and Range - -None → <sub>0..\*</sub> [Gene](Gene.md) - -## Parents - - -## Children - - -## Used by - - * [MendelianDisease](MendelianDisease.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Examples:** | | Example(value='PEX1', description=None, object=None) | -| | | Example(value='PEX2', description=None, object=None) | -| | | Example(value='PEX3', description=None, object=None) | - diff --git a/projects/mendelian_disease/docs/mendelianDisease__inheritance.md b/projects/mendelian_disease/docs/mendelianDisease__inheritance.md deleted file mode 100644 index c27806f64..000000000 --- a/projects/mendelian_disease/docs/mendelianDisease__inheritance.md +++ /dev/null @@ -1,29 +0,0 @@ - -# Slot: inheritance - - - - -URI: [mendelian_disease:mendelianDisease__inheritance](http://w3id.org/ontogpt/mendelian_disease/mendelianDisease__inheritance) - - -## Domain and Range - -None → <sub>0..1</sub> [Inheritance](Inheritance.md) - -## Parents - - -## Children - - -## Used by - - * [MendelianDisease](MendelianDisease.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Examples:** | | Example(value='autosomal recessive', description=None, object=None) | - diff --git a/projects/mendelian_disease/docs/mendelianDisease__name.md b/projects/mendelian_disease/docs/mendelianDisease__name.md deleted file mode 100644 index 817f2b785..000000000 --- a/projects/mendelian_disease/docs/mendelianDisease__name.md +++ /dev/null @@ -1,29 +0,0 @@ - -# Slot: name - - -the name of the disease - -URI: [mendelian_disease:mendelianDisease__name](http://w3id.org/ontogpt/mendelian_disease/mendelianDisease__name) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [MendelianDisease](MendelianDisease.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Examples:** | | Example(value='peroxisome biogenesis disorder', description=None, object=None) | - diff --git a/projects/mendelian_disease/docs/mendelianDisease__publications.md b/projects/mendelian_disease/docs/mendelianDisease__publications.md deleted file mode 100644 index 5904270c5..000000000 --- a/projects/mendelian_disease/docs/mendelianDisease__publications.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: publications - - - - -URI: [mendelian_disease:mendelianDisease__publications](http://w3id.org/ontogpt/mendelian_disease/mendelianDisease__publications) - - -## Domain and Range - -None → <sub>0..\*</sub> [Publication](Publication.md) - -## Parents - - -## Children - - -## Used by - - * [MendelianDisease](MendelianDisease.md) diff --git a/projects/mendelian_disease/docs/mendelianDisease__subclass_of.md b/projects/mendelian_disease/docs/mendelianDisease__subclass_of.md deleted file mode 100644 index 7e0188197..000000000 --- a/projects/mendelian_disease/docs/mendelianDisease__subclass_of.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Slot: subclass_of - - - - -URI: [mendelian_disease:mendelianDisease__subclass_of](http://w3id.org/ontogpt/mendelian_disease/mendelianDisease__subclass_of) - - -## Domain and Range - -None → <sub>0..\*</sub> [DiseaseCategory](DiseaseCategory.md) - -## Parents - - -## Children - - -## Used by - - * [MendelianDisease](MendelianDisease.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Examples:** | | Example(value='lysosomal disease', description=None, object=None) | -| | | Example(value='autosomal recessive disorder', description=None, object=None) | - diff --git a/projects/mendelian_disease/docs/mendelianDisease__symptoms.md b/projects/mendelian_disease/docs/mendelianDisease__symptoms.md deleted file mode 100644 index 5cab05997..000000000 --- a/projects/mendelian_disease/docs/mendelianDisease__symptoms.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Slot: symptoms - - - - -URI: [mendelian_disease:mendelianDisease__symptoms](http://w3id.org/ontogpt/mendelian_disease/mendelianDisease__symptoms) - - -## Domain and Range - -None → <sub>0..\*</sub> [Symptom](Symptom.md) - -## Parents - - -## Children - - -## Used by - - * [MendelianDisease](MendelianDisease.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Examples:** | | Example(value='sensorineural hearing loss', description=None, object=None) | -| | | Example(value='pigmentary retinal degeneration', description=None, object=None) | - diff --git a/projects/mendelian_disease/docs/mendelianDisease__synonyms.md b/projects/mendelian_disease/docs/mendelianDisease__synonyms.md deleted file mode 100644 index 56e200782..000000000 --- a/projects/mendelian_disease/docs/mendelianDisease__synonyms.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Slot: synonyms - - - - -URI: [mendelian_disease:mendelianDisease__synonyms](http://w3id.org/ontogpt/mendelian_disease/mendelianDisease__synonyms) - - -## Domain and Range - -None → <sub>0..\*</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [MendelianDisease](MendelianDisease.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Examples:** | | Example(value='Zellweger syndrome spectrum', description=None, object=None) | -| | | Example(value='PBD-ZSS', description=None, object=None) | - diff --git a/projects/mendelian_disease/docs/mendelian_disease.md b/projects/mendelian_disease/docs/mendelian_disease.md deleted file mode 100644 index 3cd230682..000000000 --- a/projects/mendelian_disease/docs/mendelian_disease.md +++ /dev/null @@ -1,125 +0,0 @@ - -# mendelian_disease-template - - -**metamodel version:** 1.7.0 - -**version:** None - - -A template for GO-CAMs - - -### Classes - - * [AnnotatorResult](AnnotatorResult.md) - * [Any](Any.md) - * [CompoundExpression](CompoundExpression.md) - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - * [ExtractionResult](ExtractionResult.md) - A result of extracting knowledge on text - * [NamedEntity](NamedEntity.md) - * [DiseaseCategory](DiseaseCategory.md) - * [Gene](Gene.md) - * [Inheritance](Inheritance.md) - * [MendelianDisease](MendelianDisease.md) - * [Onset](Onset.md) - * [RelationshipType](RelationshipType.md) - * [Symptom](Symptom.md) - * [Publication](Publication.md) - * [TextWithTriples](TextWithTriples.md) - -### Mixins - - -### Slots - - * [➞object_id](annotatorResult__object_id.md) - * [➞object_text](annotatorResult__object_text.md) - * [➞subject_text](annotatorResult__subject_text.md) - * [➞extracted_object](extractionResult__extracted_object.md) - The complex objects extracted from the text - * [➞input_id](extractionResult__input_id.md) - * [➞input_text](extractionResult__input_text.md) - * [➞input_title](extractionResult__input_title.md) - * [➞named_entities](extractionResult__named_entities.md) - Named entities extracted from the text - * [➞prompt](extractionResult__prompt.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) - * [➞description](mendelianDisease__description.md) - a description of the disease - * [➞disease_onsets](mendelianDisease__disease_onsets.md) - * [➞genes](mendelianDisease__genes.md) - * [➞inheritance](mendelianDisease__inheritance.md) - * [➞name](mendelianDisease__name.md) - the name of the disease - * [➞publications](mendelianDisease__publications.md) - * [➞subclass_of](mendelianDisease__subclass_of.md) - * [➞symptoms](mendelianDisease__symptoms.md) - * [➞synonyms](mendelianDisease__synonyms.md) - * [➞id](namedEntity__id.md) - A unique identifier for the named entity - * [➞label](namedEntity__label.md) - The label (name) of the named thing - * [➞decades](onset__decades.md) - * [➞juvenile_or_adult](onset__juvenile_or_adult.md) - * [➞years_old](onset__years_old.md) - * [➞abstract](publication__abstract.md) - The abstract of the publication - * [➞combined_text](publication__combined_text.md) - * [➞full_text](publication__full_text.md) - The full text of the publication - * [➞id](publication__id.md) - The publication identifier - * [➞title](publication__title.md) - The title of the publication - * [➞affects](symptom__affects.md) - * [➞characteristic](symptom__characteristic.md) - * [➞onset_of_symptom](symptom__onset_of_symptom.md) - * [➞severity](symptom__severity.md) - * [➞publication](textWithTriples__publication.md) - * [➞triples](textWithTriples__triples.md) - * [➞object](triple__object.md) - * [➞object_qualifier](triple__object_qualifier.md) - An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * [➞predicate](triple__predicate.md) - * [➞qualifier](triple__qualifier.md) - A qualifier for the statements, e.g. "NOT" for negation - * [➞subject](triple__subject.md) - * [➞subject_qualifier](triple__subject_qualifier.md) - An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -### Enums - - * [NullDataOptions](NullDataOptions.md) - -### Subsets - - -### Types - - -#### Built in - - * **Bool** - * **Curie** - * **Decimal** - * **ElementIdentifier** - * **NCName** - * **NodeIdentifier** - * **URI** - * **URIorCURIE** - * **XSDDate** - * **XSDDateTime** - * **XSDTime** - * **float** - * **int** - * **str** - -#### Defined - - * [Boolean](types/Boolean.md) (**Bool**) - A binary (true or false) value - * [Curie](types/Curie.md) (**Curie**) - a compact URI - * [Date](types/Date.md) (**XSDDate**) - a date (year, month and day) in an idealized calendar - * [DateOrDatetime](types/DateOrDatetime.md) (**str**) - Either a date or a datetime - * [Datetime](types/Datetime.md) (**XSDDateTime**) - The combination of a date and time - * [Decimal](types/Decimal.md) (**Decimal**) - A real number with arbitrary precision that conforms to the xsd:decimal specification - * [Double](types/Double.md) (**float**) - A real number that conforms to the xsd:double specification - * [Float](types/Float.md) (**float**) - A real number that conforms to the xsd:float specification - * [Integer](types/Integer.md) (**int**) - An integer - * [Jsonpath](types/Jsonpath.md) (**str**) - A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - * [Jsonpointer](types/Jsonpointer.md) (**str**) - A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - * [Ncname](types/Ncname.md) (**NCName**) - Prefix part of CURIE - * [Nodeidentifier](types/Nodeidentifier.md) (**NodeIdentifier**) - A URI, CURIE or BNODE that represents a node in a model. - * [Objectidentifier](types/Objectidentifier.md) (**ElementIdentifier**) - A URI or CURIE that represents an object in the model. - * [Sparqlpath](types/Sparqlpath.md) (**str**) - A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - * [String](types/String.md) (**str**) - A character string - * [Time](types/Time.md) (**XSDTime**) - A time object represents a (local) time of day, independent of any particular day - * [Uri](types/Uri.md) (**URI**) - a complete URI - * [Uriorcurie](types/Uriorcurie.md) (**URIorCURIE**) - a URI or a CURIE diff --git a/projects/mendelian_disease/docs/namedEntity__id.md b/projects/mendelian_disease/docs/namedEntity__id.md deleted file mode 100644 index 3c8c9e09c..000000000 --- a/projects/mendelian_disease/docs/namedEntity__id.md +++ /dev/null @@ -1,36 +0,0 @@ - -# Slot: id - - -A unique identifier for the named entity - -URI: [mendelian_disease:namedEntity__id](http://w3id.org/ontogpt/mendelian_disease/namedEntity__id) - - -## Domain and Range - -None → <sub>1..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [DiseaseCategory](DiseaseCategory.md) - * [Gene](Gene.md) - * [Inheritance](Inheritance.md) - * [MendelianDisease](MendelianDisease.md) - * [NamedEntity](NamedEntity.md) - * [Onset](Onset.md) - * [RelationshipType](RelationshipType.md) - * [Symptom](Symptom.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | this is populated during the grounding and normalization step | - diff --git a/projects/mendelian_disease/docs/namedEntity__label.md b/projects/mendelian_disease/docs/namedEntity__label.md deleted file mode 100644 index 1a0187c2e..000000000 --- a/projects/mendelian_disease/docs/namedEntity__label.md +++ /dev/null @@ -1,37 +0,0 @@ - -# Slot: label - - -The label (name) of the named thing - -URI: [mendelian_disease:namedEntity__label](http://w3id.org/ontogpt/mendelian_disease/namedEntity__label) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [DiseaseCategory](DiseaseCategory.md) - * [Gene](Gene.md) - * [Inheritance](Inheritance.md) - * [MendelianDisease](MendelianDisease.md) - * [NamedEntity](NamedEntity.md) - * [Onset](Onset.md) - * [RelationshipType](RelationshipType.md) - * [Symptom](Symptom.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Aliases:** | | name | -| **Mappings:** | | rdfs:label | - diff --git a/projects/mendelian_disease/docs/onset__decades.md b/projects/mendelian_disease/docs/onset__decades.md deleted file mode 100644 index 248672244..000000000 --- a/projects/mendelian_disease/docs/onset__decades.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: decades - - - - -URI: [mendelian_disease:onset__decades](http://w3id.org/ontogpt/mendelian_disease/onset__decades) - - -## Domain and Range - -None → <sub>0..\*</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Onset](Onset.md) diff --git a/projects/mendelian_disease/docs/onset__juvenile_or_adult.md b/projects/mendelian_disease/docs/onset__juvenile_or_adult.md deleted file mode 100644 index fed7fbd8d..000000000 --- a/projects/mendelian_disease/docs/onset__juvenile_or_adult.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: juvenile_or_adult - - - - -URI: [mendelian_disease:onset__juvenile_or_adult](http://w3id.org/ontogpt/mendelian_disease/onset__juvenile_or_adult) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Onset](Onset.md) diff --git a/projects/mendelian_disease/docs/onset__years_old.md b/projects/mendelian_disease/docs/onset__years_old.md deleted file mode 100644 index 535fb9ae2..000000000 --- a/projects/mendelian_disease/docs/onset__years_old.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: years_old - - - - -URI: [mendelian_disease:onset__years_old](http://w3id.org/ontogpt/mendelian_disease/onset__years_old) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Onset](Onset.md) diff --git a/projects/mendelian_disease/docs/publication__abstract.md b/projects/mendelian_disease/docs/publication__abstract.md deleted file mode 100644 index e3fbd0afc..000000000 --- a/projects/mendelian_disease/docs/publication__abstract.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: abstract - - -The abstract of the publication - -URI: [mendelian_disease:publication__abstract](http://w3id.org/ontogpt/mendelian_disease/publication__abstract) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/mendelian_disease/docs/publication__combined_text.md b/projects/mendelian_disease/docs/publication__combined_text.md deleted file mode 100644 index 81ebab273..000000000 --- a/projects/mendelian_disease/docs/publication__combined_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: combined_text - - - - -URI: [mendelian_disease:publication__combined_text](http://w3id.org/ontogpt/mendelian_disease/publication__combined_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/mendelian_disease/docs/publication__full_text.md b/projects/mendelian_disease/docs/publication__full_text.md deleted file mode 100644 index c7afbf3e3..000000000 --- a/projects/mendelian_disease/docs/publication__full_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: full_text - - -The full text of the publication - -URI: [mendelian_disease:publication__full_text](http://w3id.org/ontogpt/mendelian_disease/publication__full_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/mendelian_disease/docs/publication__id.md b/projects/mendelian_disease/docs/publication__id.md deleted file mode 100644 index 3d49da17b..000000000 --- a/projects/mendelian_disease/docs/publication__id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: id - - -The publication identifier - -URI: [mendelian_disease:publication__id](http://w3id.org/ontogpt/mendelian_disease/publication__id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/mendelian_disease/docs/publication__title.md b/projects/mendelian_disease/docs/publication__title.md deleted file mode 100644 index 6fe7c20e6..000000000 --- a/projects/mendelian_disease/docs/publication__title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: title - - -The title of the publication - -URI: [mendelian_disease:publication__title](http://w3id.org/ontogpt/mendelian_disease/publication__title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/mendelian_disease/docs/symptom__affects.md b/projects/mendelian_disease/docs/symptom__affects.md deleted file mode 100644 index 8fc9d6785..000000000 --- a/projects/mendelian_disease/docs/symptom__affects.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: affects - - - - -URI: [mendelian_disease:symptom__affects](http://w3id.org/ontogpt/mendelian_disease/symptom__affects) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Symptom](Symptom.md) diff --git a/projects/mendelian_disease/docs/symptom__characteristic.md b/projects/mendelian_disease/docs/symptom__characteristic.md deleted file mode 100644 index cc13b16bb..000000000 --- a/projects/mendelian_disease/docs/symptom__characteristic.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: characteristic - - - - -URI: [mendelian_disease:symptom__characteristic](http://w3id.org/ontogpt/mendelian_disease/symptom__characteristic) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Symptom](Symptom.md) diff --git a/projects/mendelian_disease/docs/symptom__onset_of_symptom.md b/projects/mendelian_disease/docs/symptom__onset_of_symptom.md deleted file mode 100644 index 4eaa246e0..000000000 --- a/projects/mendelian_disease/docs/symptom__onset_of_symptom.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: onset_of_symptom - - - - -URI: [mendelian_disease:symptom__onset_of_symptom](http://w3id.org/ontogpt/mendelian_disease/symptom__onset_of_symptom) - - -## Domain and Range - -None → <sub>0..1</sub> [Onset](Onset.md) - -## Parents - - -## Children - - -## Used by - - * [Symptom](Symptom.md) diff --git a/projects/mendelian_disease/docs/symptom__severity.md b/projects/mendelian_disease/docs/symptom__severity.md deleted file mode 100644 index 662a68cc5..000000000 --- a/projects/mendelian_disease/docs/symptom__severity.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: severity - - - - -URI: [mendelian_disease:symptom__severity](http://w3id.org/ontogpt/mendelian_disease/symptom__severity) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Symptom](Symptom.md) diff --git a/projects/mendelian_disease/docs/textWithTriples__publication.md b/projects/mendelian_disease/docs/textWithTriples__publication.md deleted file mode 100644 index 1a85fb332..000000000 --- a/projects/mendelian_disease/docs/textWithTriples__publication.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: publication - - - - -URI: [mendelian_disease:textWithTriples__publication](http://w3id.org/ontogpt/mendelian_disease/textWithTriples__publication) - - -## Domain and Range - -None → <sub>0..1</sub> [Publication](Publication.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/mendelian_disease/docs/textWithTriples__triples.md b/projects/mendelian_disease/docs/textWithTriples__triples.md deleted file mode 100644 index 46f8fbe3b..000000000 --- a/projects/mendelian_disease/docs/textWithTriples__triples.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: triples - - - - -URI: [mendelian_disease:textWithTriples__triples](http://w3id.org/ontogpt/mendelian_disease/textWithTriples__triples) - - -## Domain and Range - -None → <sub>0..\*</sub> [Triple](Triple.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/mendelian_disease/docs/triple__object.md b/projects/mendelian_disease/docs/triple__object.md deleted file mode 100644 index 5c3842d75..000000000 --- a/projects/mendelian_disease/docs/triple__object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object - - - - -URI: [mendelian_disease:triple__object](http://w3id.org/ontogpt/mendelian_disease/triple__object) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/mendelian_disease/docs/triple__object_qualifier.md b/projects/mendelian_disease/docs/triple__object_qualifier.md deleted file mode 100644 index f7592b8d8..000000000 --- a/projects/mendelian_disease/docs/triple__object_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_qualifier - - -An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - -URI: [mendelian_disease:triple__object_qualifier](http://w3id.org/ontogpt/mendelian_disease/triple__object_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/mendelian_disease/docs/triple__predicate.md b/projects/mendelian_disease/docs/triple__predicate.md deleted file mode 100644 index 9816518d1..000000000 --- a/projects/mendelian_disease/docs/triple__predicate.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: predicate - - - - -URI: [mendelian_disease:triple__predicate](http://w3id.org/ontogpt/mendelian_disease/triple__predicate) - - -## Domain and Range - -None → <sub>0..1</sub> [RelationshipType](RelationshipType.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/mendelian_disease/docs/triple__qualifier.md b/projects/mendelian_disease/docs/triple__qualifier.md deleted file mode 100644 index cbe90e2a1..000000000 --- a/projects/mendelian_disease/docs/triple__qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: qualifier - - -A qualifier for the statements, e.g. "NOT" for negation - -URI: [mendelian_disease:triple__qualifier](http://w3id.org/ontogpt/mendelian_disease/triple__qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/mendelian_disease/docs/triple__subject.md b/projects/mendelian_disease/docs/triple__subject.md deleted file mode 100644 index 2843678c0..000000000 --- a/projects/mendelian_disease/docs/triple__subject.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject - - - - -URI: [mendelian_disease:triple__subject](http://w3id.org/ontogpt/mendelian_disease/triple__subject) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/mendelian_disease/docs/triple__subject_qualifier.md b/projects/mendelian_disease/docs/triple__subject_qualifier.md deleted file mode 100644 index c0a7f56a3..000000000 --- a/projects/mendelian_disease/docs/triple__subject_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_qualifier - - -An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -URI: [mendelian_disease:triple__subject_qualifier](http://w3id.org/ontogpt/mendelian_disease/triple__subject_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/mendelian_disease/docs/types/Boolean.md b/projects/mendelian_disease/docs/types/Boolean.md deleted file mode 100644 index dc83a9c6e..000000000 --- a/projects/mendelian_disease/docs/types/Boolean.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: boolean - - -A binary (true or false) value - -URI: [linkml:Boolean](https://w3id.org/linkml/Boolean) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Bool** | -| Representation | | bool | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Boolean | - diff --git a/projects/mendelian_disease/docs/types/Curie.md b/projects/mendelian_disease/docs/types/Curie.md deleted file mode 100644 index c1803f93f..000000000 --- a/projects/mendelian_disease/docs/types/Curie.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: curie - - -a compact URI - -URI: [linkml:Curie](https://w3id.org/linkml/Curie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Curie** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations this MUST be expanded to a URI | -| | | in non-RDF serializations MAY be serialized as the compact representation | - diff --git a/projects/mendelian_disease/docs/types/Date.md b/projects/mendelian_disease/docs/types/Date.md deleted file mode 100644 index 06948af97..000000000 --- a/projects/mendelian_disease/docs/types/Date.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: date - - -a date (year, month and day) in an idealized calendar - -URI: [linkml:Date](https://w3id.org/linkml/Date) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDate** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Date | - diff --git a/projects/mendelian_disease/docs/types/DateOrDatetime.md b/projects/mendelian_disease/docs/types/DateOrDatetime.md deleted file mode 100644 index ef983898d..000000000 --- a/projects/mendelian_disease/docs/types/DateOrDatetime.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: date_or_datetime - - -Either a date or a datetime - -URI: [linkml:DateOrDatetime](https://w3id.org/linkml/DateOrDatetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/mendelian_disease/docs/types/Datetime.md b/projects/mendelian_disease/docs/types/Datetime.md deleted file mode 100644 index 9510454a8..000000000 --- a/projects/mendelian_disease/docs/types/Datetime.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: datetime - - -The combination of a date and time - -URI: [linkml:Datetime](https://w3id.org/linkml/Datetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDateTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:DateTime | - diff --git a/projects/mendelian_disease/docs/types/Decimal.md b/projects/mendelian_disease/docs/types/Decimal.md deleted file mode 100644 index a7ba14a5d..000000000 --- a/projects/mendelian_disease/docs/types/Decimal.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: decimal - - -A real number with arbitrary precision that conforms to the xsd:decimal specification - -URI: [linkml:Decimal](https://w3id.org/linkml/Decimal) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Decimal** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Broad Mappings:** | | schema:Number | - diff --git a/projects/mendelian_disease/docs/types/Double.md b/projects/mendelian_disease/docs/types/Double.md deleted file mode 100644 index cfe6d71e2..000000000 --- a/projects/mendelian_disease/docs/types/Double.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: double - - -A real number that conforms to the xsd:double specification - -URI: [linkml:Double](https://w3id.org/linkml/Double) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Close Mappings:** | | schema:Float | - diff --git a/projects/mendelian_disease/docs/types/Float.md b/projects/mendelian_disease/docs/types/Float.md deleted file mode 100644 index 7b303f96f..000000000 --- a/projects/mendelian_disease/docs/types/Float.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: float - - -A real number that conforms to the xsd:float specification - -URI: [linkml:Float](https://w3id.org/linkml/Float) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Float | - diff --git a/projects/mendelian_disease/docs/types/Integer.md b/projects/mendelian_disease/docs/types/Integer.md deleted file mode 100644 index 3cfcc66d9..000000000 --- a/projects/mendelian_disease/docs/types/Integer.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: integer - - -An integer - -URI: [linkml:Integer](https://w3id.org/linkml/Integer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **int** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Integer | - diff --git a/projects/mendelian_disease/docs/types/Jsonpath.md b/projects/mendelian_disease/docs/types/Jsonpath.md deleted file mode 100644 index a03a58e67..000000000 --- a/projects/mendelian_disease/docs/types/Jsonpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpath - - -A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpath](https://w3id.org/linkml/Jsonpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/mendelian_disease/docs/types/Jsonpointer.md b/projects/mendelian_disease/docs/types/Jsonpointer.md deleted file mode 100644 index a0e1ac492..000000000 --- a/projects/mendelian_disease/docs/types/Jsonpointer.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpointer - - -A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpointer](https://w3id.org/linkml/Jsonpointer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/mendelian_disease/docs/types/Ncname.md b/projects/mendelian_disease/docs/types/Ncname.md deleted file mode 100644 index 710b0b04a..000000000 --- a/projects/mendelian_disease/docs/types/Ncname.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: ncname - - -Prefix part of CURIE - -URI: [linkml:Ncname](https://w3id.org/linkml/Ncname) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NCName** | -| Representation | | str | diff --git a/projects/mendelian_disease/docs/types/Nodeidentifier.md b/projects/mendelian_disease/docs/types/Nodeidentifier.md deleted file mode 100644 index f0097cdf4..000000000 --- a/projects/mendelian_disease/docs/types/Nodeidentifier.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: nodeidentifier - - -A URI, CURIE or BNODE that represents a node in a model. - -URI: [linkml:Nodeidentifier](https://w3id.org/linkml/Nodeidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NodeIdentifier** | -| Representation | | str | diff --git a/projects/mendelian_disease/docs/types/Objectidentifier.md b/projects/mendelian_disease/docs/types/Objectidentifier.md deleted file mode 100644 index 454ba6be6..000000000 --- a/projects/mendelian_disease/docs/types/Objectidentifier.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: objectidentifier - - -A URI or CURIE that represents an object in the model. - -URI: [linkml:Objectidentifier](https://w3id.org/linkml/Objectidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **ElementIdentifier** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | Used for inheritance and type checking | - diff --git a/projects/mendelian_disease/docs/types/Sparqlpath.md b/projects/mendelian_disease/docs/types/Sparqlpath.md deleted file mode 100644 index fd99a927e..000000000 --- a/projects/mendelian_disease/docs/types/Sparqlpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: sparqlpath - - -A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - -URI: [linkml:Sparqlpath](https://w3id.org/linkml/Sparqlpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/mendelian_disease/docs/types/String.md b/projects/mendelian_disease/docs/types/String.md deleted file mode 100644 index 6e61d7081..000000000 --- a/projects/mendelian_disease/docs/types/String.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: string - - -A character string - -URI: [linkml:String](https://w3id.org/linkml/String) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Text | - diff --git a/projects/mendelian_disease/docs/types/Time.md b/projects/mendelian_disease/docs/types/Time.md deleted file mode 100644 index 2b8652bcd..000000000 --- a/projects/mendelian_disease/docs/types/Time.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: time - - -A time object represents a (local) time of day, independent of any particular day - -URI: [linkml:Time](https://w3id.org/linkml/Time) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Time | - diff --git a/projects/mendelian_disease/docs/types/Uri.md b/projects/mendelian_disease/docs/types/Uri.md deleted file mode 100644 index 343807a5e..000000000 --- a/projects/mendelian_disease/docs/types/Uri.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: uri - - -a complete URI - -URI: [linkml:Uri](https://w3id.org/linkml/Uri) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URI** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node | -| **Close Mappings:** | | schema:URL | - diff --git a/projects/mendelian_disease/docs/types/Uriorcurie.md b/projects/mendelian_disease/docs/types/Uriorcurie.md deleted file mode 100644 index 2f7b65087..000000000 --- a/projects/mendelian_disease/docs/types/Uriorcurie.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: uriorcurie - - -a URI or a CURIE - -URI: [linkml:Uriorcurie](https://w3id.org/linkml/Uriorcurie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URIorCURIE** | -| Representation | | str | diff --git a/projects/mendelian_disease/excel/mendelian_disease.xlsx b/projects/mendelian_disease/excel/mendelian_disease.xlsx deleted file mode 100644 index ced006d5b..000000000 Binary files a/projects/mendelian_disease/excel/mendelian_disease.xlsx and /dev/null differ diff --git a/projects/mendelian_disease/graphql/mendelian_disease.graphql b/projects/mendelian_disease/graphql/mendelian_disease.graphql deleted file mode 100644 index 97e9b2c37..000000000 --- a/projects/mendelian_disease/graphql/mendelian_disease.graphql +++ /dev/null @@ -1,115 +0,0 @@ -type AnnotatorResult - { - subjectText: String - objectId: String - objectText: String - } - -type Any - { - } - -interface CompoundExpression - { - } - -type DiseaseCategory - { - id: String! - label: String - } - -type ExtractionResult - { - inputId: String - inputTitle: String - inputText: String - rawCompletionOutput: String - prompt: String - extractedObject: Any - namedEntities: [Any] - } - -type Gene - { - id: String! - label: String - } - -type Inheritance - { - id: String! - label: String - } - -type MendelianDisease - { - id: String! - label: String - name: String - description: String - synonyms: [String] - subclassOf: [DiseaseCategory] - symptoms: [Symptom] - inheritance: Inheritance - genes: [Gene] - diseaseOnsets: [Onset] - publications: [Publication] - } - -interface NamedEntity - { - id: String! - label: String - } - -type Onset - { - id: String! - label: String - yearsOld: String - decades: [String] - juvenileOrAdult: String - } - -type Publication - { - id: String - title: String - abstract: String - combinedText: String - fullText: String - } - -type RelationshipType - { - id: String! - label: String - } - -type Symptom - { - id: String! - label: String - characteristic: String - affects: String - severity: String - onsetOfSymptom: Onset - } - -type TextWithTriples - { - publication: Publication - triples: [Triple] - } - -interface Triple - { - subject: NamedEntity - predicate: RelationshipType - object: NamedEntity - qualifier: String - subjectQualifier: NamedEntity - objectQualifier: NamedEntity - } - diff --git a/projects/mendelian_disease/jsonld/mendelian_disease.context.jsonld b/projects/mendelian_disease/jsonld/mendelian_disease.context.jsonld deleted file mode 100644 index 27f1ab073..000000000 --- a/projects/mendelian_disease/jsonld/mendelian_disease.context.jsonld +++ /dev/null @@ -1,151 +0,0 @@ -{ - "comments": { - "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2023-08-07T10:54:35", - "source": "mendelian_disease.yaml" - }, - "@context": { - "HGNC": "http://example.org/UNKNOWN/HGNC/", - "HP": "http://example.org/UNKNOWN/HP/", - "MONDO": "http://example.org/UNKNOWN/MONDO/", - "RO": { - "@id": "http://purl.obolibrary.org/obo/RO_", - "@prefix": true - }, - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "linkml": "https://w3id.org/linkml/", - "mendelian_disease": "http://w3id.org/ontogpt/mendelian_disease/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "@vocab": "http://w3id.org/ontogpt/mendelian_disease/", - "object_id": { - "@id": "core:object_id" - }, - "object_text": { - "@id": "core:object_text" - }, - "subject_text": { - "@id": "core:subject_text" - }, - "extracted_object": { - "@type": "@id", - "@id": "core:extracted_object" - }, - "input_id": { - "@id": "core:input_id" - }, - "input_text": { - "@id": "core:input_text" - }, - "input_title": { - "@id": "core:input_title" - }, - "named_entities": { - "@type": "@id", - "@id": "core:named_entities" - }, - "prompt": { - "@id": "core:prompt" - }, - "raw_completion_output": { - "@id": "core:raw_completion_output" - }, - "disease_onsets": { - "@type": "@id" - }, - "genes": { - "@type": "@id" - }, - "inheritance": { - "@type": "@id" - }, - "publications": { - "@type": "@id" - }, - "subclass_of": { - "@type": "@id" - }, - "symptoms": { - "@type": "@id" - }, - "id": { - "@id": "core:id" - }, - "label": { - "@id": "rdfs:label" - }, - "abstract": { - "@id": "core:abstract" - }, - "combined_text": { - "@id": "core:combined_text" - }, - "full_text": { - "@id": "core:full_text" - }, - "title": { - "@id": "core:title" - }, - "onset_of_symptom": { - "@type": "@id" - }, - "publication": { - "@type": "@id", - "@id": "core:publication" - }, - "triples": { - "@type": "@id", - "@id": "core:triples" - }, - "object": { - "@type": "@id", - "@id": "core:object" - }, - "object_qualifier": { - "@type": "@id", - "@id": "core:object_qualifier" - }, - "predicate": { - "@type": "@id", - "@id": "core:predicate" - }, - "qualifier": { - "@id": "core:qualifier" - }, - "subject": { - "@type": "@id", - "@id": "core:subject" - }, - "subject_qualifier": { - "@type": "@id", - "@id": "core:subject_qualifier" - }, - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } - } -} diff --git a/projects/mendelian_disease/jsonld/mendelian_disease.jsonld b/projects/mendelian_disease/jsonld/mendelian_disease.jsonld deleted file mode 100644 index 1b839aac1..000000000 --- a/projects/mendelian_disease/jsonld/mendelian_disease.jsonld +++ /dev/null @@ -1,1566 +0,0 @@ -{ - "name": "mendelian_disease-template", - "description": "A template for GO-CAMs", - "title": "GO-CAM Template", - "id": "http://w3id.org/ontogpt/mendelian_disease", - "imports": [ - "linkml:types", - "core" - ], - "license": "https://creativecommons.org/publicdomain/zero/1.0/", - "prefixes": [ - { - "prefix_prefix": "linkml", - "prefix_reference": "https://w3id.org/linkml/" - }, - { - "prefix_prefix": "mendelian_disease", - "prefix_reference": "http://w3id.org/ontogpt/mendelian_disease/" - } - ], - "default_prefix": "mendelian_disease", - "default_range": "string", - "types": [ - { - "name": "string", - "definition_uri": "https://w3id.org/linkml/String", - "description": "A character string", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Text" - ], - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "@type": "TypeDefinition" - }, - { - "name": "integer", - "definition_uri": "https://w3id.org/linkml/Integer", - "description": "An integer", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Integer" - ], - "base": "int", - "uri": "http://www.w3.org/2001/XMLSchema#integer", - "@type": "TypeDefinition" - }, - { - "name": "boolean", - "definition_uri": "https://w3id.org/linkml/Boolean", - "description": "A binary (true or false) value", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Boolean" - ], - "base": "Bool", - "uri": "http://www.w3.org/2001/XMLSchema#boolean", - "repr": "bool", - "@type": "TypeDefinition" - }, - { - "name": "float", - "definition_uri": "https://w3id.org/linkml/Float", - "description": "A real number that conforms to the xsd:float specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#float", - "@type": "TypeDefinition" - }, - { - "name": "double", - "definition_uri": "https://w3id.org/linkml/Double", - "description": "A real number that conforms to the xsd:double specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#double", - "@type": "TypeDefinition" - }, - { - "name": "decimal", - "definition_uri": "https://w3id.org/linkml/Decimal", - "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "broad_mappings": [ - "schema:Number" - ], - "base": "Decimal", - "uri": "http://www.w3.org/2001/XMLSchema#decimal", - "@type": "TypeDefinition" - }, - { - "name": "time", - "definition_uri": "https://w3id.org/linkml/Time", - "description": "A time object represents a (local) time of day, independent of any particular day", - "notes": [ - "URI is dateTime because OWL reasoners do not work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Time" - ], - "base": "XSDTime", - "uri": "http://www.w3.org/2001/XMLSchema#time", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date", - "definition_uri": "https://w3id.org/linkml/Date", - "description": "a date (year, month and day) in an idealized calendar", - "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Date" - ], - "base": "XSDDate", - "uri": "http://www.w3.org/2001/XMLSchema#date", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "datetime", - "definition_uri": "https://w3id.org/linkml/Datetime", - "description": "The combination of a date and time", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:DateTime" - ], - "base": "XSDDateTime", - "uri": "http://www.w3.org/2001/XMLSchema#dateTime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date_or_datetime", - "definition_uri": "https://w3id.org/linkml/DateOrDatetime", - "description": "Either a date or a datetime", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "https://w3id.org/linkml/DateOrDatetime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uriorcurie", - "definition_uri": "https://w3id.org/linkml/Uriorcurie", - "description": "a URI or a CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "URIorCURIE", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "curie", - "definition_uri": "https://w3id.org/linkml/Curie", - "conforms_to": "https://www.w3.org/TR/curie/", - "description": "a compact URI", - "comments": [ - "in RDF serializations this MUST be expanded to a URI", - "in non-RDF serializations MAY be serialized as the compact representation" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "Curie", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uri", - "definition_uri": "https://w3id.org/linkml/Uri", - "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", - "description": "a complete URI", - "comments": [ - "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:URL" - ], - "base": "URI", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "ncname", - "definition_uri": "https://w3id.org/linkml/Ncname", - "description": "Prefix part of CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NCName", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "objectidentifier", - "definition_uri": "https://w3id.org/linkml/Objectidentifier", - "description": "A URI or CURIE that represents an object in the model.", - "comments": [ - "Used for inheritance and type checking" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "ElementIdentifier", - "uri": "http://www.w3.org/ns/shex#iri", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "nodeidentifier", - "definition_uri": "https://w3id.org/linkml/Nodeidentifier", - "description": "A URI, CURIE or BNODE that represents a node in a model.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NodeIdentifier", - "uri": "http://www.w3.org/ns/shex#nonLiteral", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpointer", - "definition_uri": "https://w3id.org/linkml/Jsonpointer", - "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901", - "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpath", - "definition_uri": "https://w3id.org/linkml/Jsonpath", - "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html", - "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "sparqlpath", - "definition_uri": "https://w3id.org/linkml/Sparqlpath", - "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths", - "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - } - ], - "enums": [ - { - "name": "NullDataOptions", - "definition_uri": "http://w3id.org/ontogpt/core/NullDataOptions", - "from_schema": "http://w3id.org/ontogpt/core", - "permissible_values": [ - { - "text": "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "meaning": "NCIT:C149701" - }, - { - "text": "NOT_APPLICABLE", - "meaning": "NCIT:C18902", - "aliases": [ - "not applicable", - "N/A" - ] - }, - { - "text": "NOT_MENTIONED" - } - ] - } - ], - "slots": [ - { - "name": "mendelianDisease__name", - "description": "the name of the disease", - "examples": [ - { - "value": "peroxisome biogenesis disorder", - "@type": "Example" - } - ], - "from_schema": "http://w3id.org/ontogpt/mendelian_disease", - "slot_uri": "http://w3id.org/ontogpt/mendelian_disease/name", - "alias": "name", - "owner": "MendelianDisease", - "domain_of": [ - "MendelianDisease" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "mendelianDisease__description", - "description": "a description of the disease", - "examples": [ - { - "value": "Peroxisome biogenesis disorders, Zellweger syndrome spectrum (PBD-ZSS) is a group of autosomal recessive disorders affecting the formation of functional peroxisomes, characterized by sensorineural hearing loss, pigmentary retinal degeneration, multiple organ dysfunction and psychomotor impairment", - "@type": "Example" - } - ], - "from_schema": "http://w3id.org/ontogpt/mendelian_disease", - "slot_uri": "http://w3id.org/ontogpt/mendelian_disease/description", - "alias": "description", - "owner": "MendelianDisease", - "domain_of": [ - "MendelianDisease" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "mendelianDisease__synonyms", - "examples": [ - { - "value": "Zellweger syndrome spectrum", - "@type": "Example" - }, - { - "value": "PBD-ZSS", - "@type": "Example" - } - ], - "from_schema": "http://w3id.org/ontogpt/mendelian_disease", - "slot_uri": "http://w3id.org/ontogpt/mendelian_disease/synonyms", - "multivalued": true, - "alias": "synonyms", - "owner": "MendelianDisease", - "domain_of": [ - "MendelianDisease" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "mendelianDisease__subclass_of", - "examples": [ - { - "value": "lysosomal disease", - "@type": "Example" - }, - { - "value": "autosomal recessive disorder", - "@type": "Example" - } - ], - "from_schema": "http://w3id.org/ontogpt/mendelian_disease", - "slot_uri": "http://w3id.org/ontogpt/mendelian_disease/subclass_of", - "multivalued": true, - "alias": "subclass_of", - "owner": "MendelianDisease", - "domain_of": [ - "MendelianDisease" - ], - "range": "DiseaseCategory", - "@type": "SlotDefinition" - }, - { - "name": "mendelianDisease__symptoms", - "examples": [ - { - "value": "sensorineural hearing loss", - "@type": "Example" - }, - { - "value": "pigmentary retinal degeneration", - "@type": "Example" - } - ], - "from_schema": "http://w3id.org/ontogpt/mendelian_disease", - "slot_uri": "http://w3id.org/ontogpt/mendelian_disease/symptoms", - "multivalued": true, - "alias": "symptoms", - "owner": "MendelianDisease", - "domain_of": [ - "MendelianDisease" - ], - "range": "Symptom", - "@type": "SlotDefinition" - }, - { - "name": "mendelianDisease__inheritance", - "examples": [ - { - "value": "autosomal recessive", - "@type": "Example" - } - ], - "from_schema": "http://w3id.org/ontogpt/mendelian_disease", - "slot_uri": "http://w3id.org/ontogpt/mendelian_disease/inheritance", - "alias": "inheritance", - "owner": "MendelianDisease", - "domain_of": [ - "MendelianDisease" - ], - "range": "Inheritance", - "@type": "SlotDefinition" - }, - { - "name": "mendelianDisease__genes", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon separated list of gene symbols; for example: PEX1; PEX2; PEX3", - "@type": "Annotation" - } - ], - "examples": [ - { - "value": "PEX1", - "@type": "Example" - }, - { - "value": "PEX2", - "@type": "Example" - }, - { - "value": "PEX3", - "@type": "Example" - } - ], - "from_schema": "http://w3id.org/ontogpt/mendelian_disease", - "slot_uri": "http://w3id.org/ontogpt/mendelian_disease/genes", - "multivalued": true, - "alias": "genes", - "owner": "MendelianDisease", - "domain_of": [ - "MendelianDisease" - ], - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "mendelianDisease__disease_onsets", - "annotations": [ - { - "tag": "prompt", - "value": "semi-colon separated list of onsets at which the disease occurs, for example: adult; juvenile; first decade", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/mendelian_disease", - "slot_uri": "http://w3id.org/ontogpt/mendelian_disease/disease_onsets", - "multivalued": true, - "alias": "disease_onsets", - "owner": "MendelianDisease", - "domain_of": [ - "MendelianDisease" - ], - "range": "Onset", - "@type": "SlotDefinition" - }, - { - "name": "mendelianDisease__publications", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/mendelian_disease", - "slot_uri": "http://w3id.org/ontogpt/mendelian_disease/publications", - "multivalued": true, - "alias": "publications", - "owner": "MendelianDisease", - "domain_of": [ - "MendelianDisease" - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "symptom__characteristic", - "from_schema": "http://w3id.org/ontogpt/mendelian_disease", - "slot_uri": "http://w3id.org/ontogpt/mendelian_disease/characteristic", - "alias": "characteristic", - "owner": "Symptom", - "domain_of": [ - "Symptom" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "symptom__affects", - "from_schema": "http://w3id.org/ontogpt/mendelian_disease", - "slot_uri": "http://w3id.org/ontogpt/mendelian_disease/affects", - "alias": "affects", - "owner": "Symptom", - "domain_of": [ - "Symptom" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "symptom__severity", - "from_schema": "http://w3id.org/ontogpt/mendelian_disease", - "slot_uri": "http://w3id.org/ontogpt/mendelian_disease/severity", - "alias": "severity", - "owner": "Symptom", - "domain_of": [ - "Symptom" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "symptom__onset_of_symptom", - "from_schema": "http://w3id.org/ontogpt/mendelian_disease", - "slot_uri": "http://w3id.org/ontogpt/mendelian_disease/onset_of_symptom", - "alias": "onset_of_symptom", - "owner": "Symptom", - "domain_of": [ - "Symptom" - ], - "range": "Onset", - "@type": "SlotDefinition" - }, - { - "name": "onset__years_old", - "from_schema": "http://w3id.org/ontogpt/mendelian_disease", - "slot_uri": "http://w3id.org/ontogpt/mendelian_disease/years_old", - "alias": "years_old", - "owner": "Onset", - "domain_of": [ - "Onset" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "onset__decades", - "from_schema": "http://w3id.org/ontogpt/mendelian_disease", - "slot_uri": "http://w3id.org/ontogpt/mendelian_disease/decades", - "multivalued": true, - "alias": "decades", - "owner": "Onset", - "domain_of": [ - "Onset" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "onset__juvenile_or_adult", - "from_schema": "http://w3id.org/ontogpt/mendelian_disease", - "slot_uri": "http://w3id.org/ontogpt/mendelian_disease/juvenile_or_adult", - "alias": "juvenile_or_adult", - "owner": "Onset", - "domain_of": [ - "Onset" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_id", - "alias": "input_id", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_title", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_title", - "alias": "input_title", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_text", - "alias": "input_text", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__raw_completion_output", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/raw_completion_output", - "alias": "raw_completion_output", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__prompt", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/prompt", - "alias": "prompt", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__extracted_object", - "description": "The complex objects extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/extracted_object", - "alias": "extracted_object", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__named_entities", - "description": "Named entities extracted from the text", - "from_schema": 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"definition_uri": "http://w3id.org/ontogpt/core/Publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "publication__id", - "publication__title", - "publication__abstract", - "publication__combined_text", - "publication__full_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "description": "The publication identifier", - "@type": "SlotDefinition" - }, - { - "name": "title", - "description": "The title of the publication", - "@type": "SlotDefinition" - }, - { - "name": "abstract", - "description": "The abstract of the publication", - "@type": "SlotDefinition" - }, - { - "name": "combined_text", - "@type": "SlotDefinition" - }, - { - "name": "full_text", - "description": "The full text of the publication", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Publication", - "@type": "ClassDefinition" - }, - { - "name": "AnnotatorResult", - "definition_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "annotatorResult__subject_text", - "annotatorResult__object_id", - "annotatorResult__object_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject_text", - "@type": "SlotDefinition" - }, - { - "name": "object_id", - "@type": "SlotDefinition" - }, - { - "name": "object_text", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "@type": "ClassDefinition" - } - ], - "metamodel_version": "1.7.0", - "source_file": "mendelian_disease.yaml", - "source_file_date": "2023-06-17T15:11:19", - "source_file_size": 3130, - "generation_date": "2023-08-07T10:54:36", - "@type": "SchemaDefinition", - "@context": [ - "projects/mendelian_disease/jsonld/mendelian_disease.context.jsonld", - "https://w3id.org/linkml/types.context.jsonld", - "core.context.jsonld", - { - "@base": "http://w3id.org/ontogpt/mendelian_disease/" - } - ] -} diff --git a/projects/mendelian_disease/jsonschema/mendelian_disease.schema.json b/projects/mendelian_disease/jsonschema/mendelian_disease.schema.json deleted file mode 100644 index beda78946..000000000 --- a/projects/mendelian_disease/jsonschema/mendelian_disease.schema.json +++ /dev/null @@ -1,326 +0,0 @@ -{ - "$defs": { - "AnnotatorResult": { - "additionalProperties": false, - "description": "", - "properties": { - "object_id": { - "type": "string" - }, - "object_text": { - "type": "string" - }, - "subject_text": { - "type": "string" - } - }, - "title": "AnnotatorResult", - "type": "object" - }, - "Any": { - "additionalProperties": true, - "description": "", - "title": "Any", - "type": "object" - }, - "DiseaseCategory": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "DiseaseCategory", - "type": "object" - }, - "ExtractionResult": { - "additionalProperties": false, - "description": "A result of extracting knowledge on text", - "properties": { - "extracted_object": { - "$ref": "#/$defs/Any", - "description": "The complex objects extracted from the text" - }, - "input_id": { - "type": "string" - }, - "input_text": { - "type": "string" - }, - "input_title": { - "type": "string" - }, - "named_entities": { - "description": "Named entities extracted from the text", - "items": { - "$ref": "#/$defs/Any" - }, - "type": "array" - }, - "prompt": { - "type": "string" - }, - "raw_completion_output": { - "type": "string" - } - }, - "title": "ExtractionResult", - "type": "object" - }, - "Gene": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Gene", - "type": "object" - }, - "Inheritance": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Inheritance", - "type": "object" - }, - "MendelianDisease": { - "additionalProperties": false, - "description": "", - "properties": { - "description": { - "description": "a description of the disease", - "type": "string" - }, - "disease_onsets": { - "items": { - "type": "string" - }, - "type": "array" - }, - "genes": { - "items": { - "type": "string" - }, - "type": "array" - }, - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "inheritance": { - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - }, - "name": { - "description": "the name of the disease", - "type": "string" - }, - "publications": { - "items": { - "$ref": "#/$defs/Publication" - }, - "type": "array" - }, - "subclass_of": { - "items": { - "type": "string" - }, - "type": "array" - }, - "symptoms": { - "items": { - "type": "string" - }, - "type": "array" - }, - "synonyms": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "required": [ - "id" - ], - "title": "MendelianDisease", - "type": "object" - }, - "NullDataOptions": { - "description": "", - "enum": [ - "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "NOT_APPLICABLE", - "NOT_MENTIONED" - ], - "title": "NullDataOptions", - "type": "string" - }, - "Onset": { - "additionalProperties": false, - "description": "", - "properties": { - "decades": { - "items": { - "type": "string" - }, - "type": "array" - }, - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "juvenile_or_adult": { - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - }, - "years_old": { - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Onset", - "type": "object" - }, - "Publication": { - "additionalProperties": false, - "description": "", - "properties": { - "abstract": { - "description": "The abstract of the publication", - "type": "string" - }, - "combined_text": { - "type": "string" - }, - "full_text": { - "description": "The full text of the publication", - "type": "string" - }, - "id": { - "description": "The publication identifier", - "type": "string" - }, - "title": { - "description": "The title of the publication", - "type": "string" - } - }, - "title": "Publication", - "type": "object" - }, - "RelationshipType": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "RelationshipType", - "type": "object" - }, - "Symptom": { - "additionalProperties": false, - "description": "", - "properties": { - "affects": { - "type": "string" - }, - "characteristic": { - "type": "string" - }, - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - }, - "onset_of_symptom": { - "type": "string" - }, - "severity": { - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Symptom", - "type": "object" - }, - "TextWithTriples": { - "additionalProperties": false, - "description": "", - "properties": { - "publication": { - "$ref": "#/$defs/Publication" - }, - "triples": { - "items": { - "$ref": "#/$defs/Triple" - }, - "type": "array" - } - }, - "title": "TextWithTriples", - "type": "object" - } - }, - "$id": "http://w3id.org/ontogpt/mendelian_disease", - "$schema": "http://json-schema.org/draft-07/schema#", - "additionalProperties": true, - "metamodel_version": "1.7.0", - "title": "mendelian_disease-template", - "type": "object", - "version": null -} \ No newline at end of file diff --git a/projects/mendelian_disease/mendelian_disease.py b/projects/mendelian_disease/mendelian_disease.py deleted file mode 100644 index 277925b8b..000000000 --- a/projects/mendelian_disease/mendelian_disease.py +++ /dev/null @@ -1,628 +0,0 @@ -# Auto generated from mendelian_disease.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-08-07T10:54:43 -# Schema: mendelian_disease-template -# -# id: http://w3id.org/ontogpt/mendelian_disease -# description: A template for GO-CAMs -# license: https://creativecommons.org/publicdomain/zero/1.0/ - -import dataclasses -import sys -import re -from jsonasobj2 import JsonObj, as_dict -from typing import Optional, List, Union, Dict, ClassVar, Any -from dataclasses import dataclass -from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions - -from linkml_runtime.utils.slot import Slot -from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode -from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int -from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs -from linkml_runtime.utils.formatutils import camelcase, underscore, sfx -from linkml_runtime.utils.enumerations import EnumDefinitionImpl -from rdflib import Namespace, URIRef -from linkml_runtime.utils.curienamespace import CurieNamespace -from linkml_runtime.linkml_model.types import String - -metamodel_version = "1.7.0" -version = None - -# Overwrite dataclasses _init_fn to add **kwargs in __init__ -dataclasses._init_fn = dataclasses_init_fn_with_kwargs - -# Namespaces -HGNC = CurieNamespace('HGNC', 'http://example.org/UNKNOWN/HGNC/') -HP = CurieNamespace('HP', 'http://example.org/UNKNOWN/HP/') -MONDO = CurieNamespace('MONDO', 'http://example.org/UNKNOWN/MONDO/') -RO = CurieNamespace('RO', 'http://purl.obolibrary.org/obo/RO_') -BIOLINK = CurieNamespace('biolink', 'http://example.org/UNKNOWN/biolink/') -CORE = CurieNamespace('core', 'http://w3id.org/ontogpt/core/') -LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') -MENDELIAN_DISEASE = CurieNamespace('mendelian_disease', 'http://w3id.org/ontogpt/mendelian_disease/') -RDFS = CurieNamespace('rdfs', 'http://example.org/UNKNOWN/rdfs/') -DEFAULT_ = MENDELIAN_DISEASE - - -# Types - -# Class references -class NamedEntityId(extended_str): - pass - - -class MendelianDiseaseId(NamedEntityId): - pass - - -class DiseaseCategoryId(NamedEntityId): - pass - - -class GeneId(NamedEntityId): - pass - - -class SymptomId(NamedEntityId): - pass - - -class OnsetId(NamedEntityId): - pass - - -class InheritanceId(NamedEntityId): - pass - - -class RelationshipTypeId(NamedEntityId): - pass - - -Any = Any - -@dataclass -class ExtractionResult(YAMLRoot): - """ - A result of extracting knowledge on text - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.ExtractionResult - class_class_curie: ClassVar[str] = "core:ExtractionResult" - class_name: ClassVar[str] = "ExtractionResult" - class_model_uri: ClassVar[URIRef] = MENDELIAN_DISEASE.ExtractionResult - - input_id: Optional[str] = None - input_title: Optional[str] = None - input_text: Optional[str] = None - raw_completion_output: Optional[str] = None - prompt: Optional[str] = None - extracted_object: Optional[Union[dict, Any]] = None - named_entities: Optional[Union[Union[dict, Any], List[Union[dict, Any]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.input_id is not None and not isinstance(self.input_id, str): - self.input_id = str(self.input_id) - - if self.input_title is not None and not isinstance(self.input_title, str): - self.input_title = str(self.input_title) - - if self.input_text is not None and not isinstance(self.input_text, str): - self.input_text = str(self.input_text) - - if self.raw_completion_output is not None and not isinstance(self.raw_completion_output, str): - self.raw_completion_output = str(self.raw_completion_output) - - if self.prompt is not None and not isinstance(self.prompt, str): - self.prompt = str(self.prompt) - - super().__post_init__(**kwargs) - - -@dataclass -class NamedEntity(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.NamedEntity - class_class_curie: ClassVar[str] = "core:NamedEntity" - class_name: ClassVar[str] = "NamedEntity" - class_model_uri: ClassVar[URIRef] = MENDELIAN_DISEASE.NamedEntity - - id: Union[str, NamedEntityId] = None - label: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, NamedEntityId): - self.id = NamedEntityId(self.id) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - super().__post_init__(**kwargs) - - -@dataclass -class MendelianDisease(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = MENDELIAN_DISEASE.MendelianDisease - class_class_curie: ClassVar[str] = "mendelian_disease:MendelianDisease" - class_name: ClassVar[str] = "MendelianDisease" - class_model_uri: ClassVar[URIRef] = MENDELIAN_DISEASE.MendelianDisease - - id: Union[str, MendelianDiseaseId] = None - name: Optional[str] = None - description: Optional[str] = None - synonyms: Optional[Union[str, List[str]]] = empty_list() - subclass_of: Optional[Union[Union[str, DiseaseCategoryId], List[Union[str, DiseaseCategoryId]]]] = empty_list() - symptoms: Optional[Union[Union[str, SymptomId], List[Union[str, SymptomId]]]] = empty_list() - inheritance: Optional[Union[str, InheritanceId]] = None - genes: Optional[Union[Union[str, GeneId], List[Union[str, GeneId]]]] = empty_list() - disease_onsets: Optional[Union[Union[str, OnsetId], List[Union[str, OnsetId]]]] = empty_list() - publications: Optional[Union[Union[dict, "Publication"], List[Union[dict, "Publication"]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, MendelianDiseaseId): - self.id = MendelianDiseaseId(self.id) - - if self.name is not None and not isinstance(self.name, str): - self.name = str(self.name) - - if self.description is not None and not isinstance(self.description, str): - self.description = str(self.description) - - if not isinstance(self.synonyms, list): - self.synonyms = [self.synonyms] if self.synonyms is not None else [] - self.synonyms = [v if isinstance(v, str) else str(v) for v in self.synonyms] - - if not isinstance(self.subclass_of, list): - self.subclass_of = [self.subclass_of] if self.subclass_of is not None else [] - self.subclass_of = [v if isinstance(v, DiseaseCategoryId) else DiseaseCategoryId(v) for v in self.subclass_of] - - if not isinstance(self.symptoms, list): - self.symptoms = [self.symptoms] if self.symptoms is not None else [] - self.symptoms = [v if isinstance(v, SymptomId) else SymptomId(v) for v in self.symptoms] - - if self.inheritance is not None and not isinstance(self.inheritance, InheritanceId): - self.inheritance = InheritanceId(self.inheritance) - - if not isinstance(self.genes, list): - self.genes = [self.genes] if self.genes is not None else [] - self.genes = [v if isinstance(v, GeneId) else GeneId(v) for v in self.genes] - - if not isinstance(self.disease_onsets, list): - self.disease_onsets = [self.disease_onsets] if self.disease_onsets is not None else [] - self.disease_onsets = [v if isinstance(v, OnsetId) else OnsetId(v) for v in self.disease_onsets] - - if not isinstance(self.publications, list): - self.publications = [self.publications] if self.publications is not None else [] - self.publications = [v if isinstance(v, Publication) else Publication(**as_dict(v)) for v in self.publications] - - super().__post_init__(**kwargs) - - -@dataclass -class DiseaseCategory(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = MENDELIAN_DISEASE.DiseaseCategory - class_class_curie: ClassVar[str] = "mendelian_disease:DiseaseCategory" - class_name: ClassVar[str] = "DiseaseCategory" - class_model_uri: ClassVar[URIRef] = MENDELIAN_DISEASE.DiseaseCategory - - id: Union[str, DiseaseCategoryId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, DiseaseCategoryId): - self.id = DiseaseCategoryId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Gene(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = MENDELIAN_DISEASE.Gene - class_class_curie: ClassVar[str] = "mendelian_disease:Gene" - class_name: ClassVar[str] = "Gene" - class_model_uri: ClassVar[URIRef] = MENDELIAN_DISEASE.Gene - - id: Union[str, GeneId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, GeneId): - self.id = GeneId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Symptom(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = MENDELIAN_DISEASE.Symptom - class_class_curie: ClassVar[str] = "mendelian_disease:Symptom" - class_name: ClassVar[str] = "Symptom" - class_model_uri: ClassVar[URIRef] = MENDELIAN_DISEASE.Symptom - - id: Union[str, SymptomId] = None - characteristic: Optional[str] = None - affects: Optional[str] = None - severity: Optional[str] = None - onset_of_symptom: Optional[Union[str, OnsetId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, SymptomId): - self.id = SymptomId(self.id) - - if self.characteristic is not None and not isinstance(self.characteristic, str): - self.characteristic = str(self.characteristic) - - if self.affects is not None and not isinstance(self.affects, str): - self.affects = str(self.affects) - - if self.severity is not None and not isinstance(self.severity, str): - self.severity = str(self.severity) - - if self.onset_of_symptom is not None and not isinstance(self.onset_of_symptom, OnsetId): - self.onset_of_symptom = OnsetId(self.onset_of_symptom) - - super().__post_init__(**kwargs) - - -@dataclass -class Onset(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = MENDELIAN_DISEASE.Onset - class_class_curie: ClassVar[str] = "mendelian_disease:Onset" - class_name: ClassVar[str] = "Onset" - class_model_uri: ClassVar[URIRef] = MENDELIAN_DISEASE.Onset - - id: Union[str, OnsetId] = None - years_old: Optional[str] = None - decades: Optional[Union[str, List[str]]] = empty_list() - juvenile_or_adult: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, OnsetId): - self.id = OnsetId(self.id) - - if self.years_old is not None and not isinstance(self.years_old, str): - self.years_old = str(self.years_old) - - if not isinstance(self.decades, list): - self.decades = [self.decades] if self.decades is not None else [] - self.decades = [v if isinstance(v, str) else str(v) for v in self.decades] - - if self.juvenile_or_adult is not None and not isinstance(self.juvenile_or_adult, str): - self.juvenile_or_adult = str(self.juvenile_or_adult) - - super().__post_init__(**kwargs) - - -@dataclass -class Inheritance(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = MENDELIAN_DISEASE.Inheritance - class_class_curie: ClassVar[str] = "mendelian_disease:Inheritance" - class_name: ClassVar[str] = "Inheritance" - class_model_uri: ClassVar[URIRef] = MENDELIAN_DISEASE.Inheritance - - id: Union[str, InheritanceId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, InheritanceId): - self.id = InheritanceId(self.id) - - super().__post_init__(**kwargs) - - -class CompoundExpression(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.CompoundExpression - class_class_curie: ClassVar[str] = "core:CompoundExpression" - class_name: ClassVar[str] = "CompoundExpression" - class_model_uri: ClassVar[URIRef] = MENDELIAN_DISEASE.CompoundExpression - - -@dataclass -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Triple - class_class_curie: ClassVar[str] = "core:Triple" - class_name: ClassVar[str] = "Triple" - class_model_uri: ClassVar[URIRef] = MENDELIAN_DISEASE.Triple - - subject: Optional[Union[str, NamedEntityId]] = None - predicate: Optional[Union[str, RelationshipTypeId]] = None - object: Optional[Union[str, NamedEntityId]] = None - qualifier: Optional[str] = None - subject_qualifier: Optional[Union[str, NamedEntityId]] = None - object_qualifier: Optional[Union[str, NamedEntityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, NamedEntityId): - self.subject = NamedEntityId(self.subject) - - if self.predicate is not None and not isinstance(self.predicate, RelationshipTypeId): - self.predicate = RelationshipTypeId(self.predicate) - - if self.object is not None and not isinstance(self.object, NamedEntityId): - self.object = NamedEntityId(self.object) - - if self.qualifier is not None and not isinstance(self.qualifier, str): - self.qualifier = str(self.qualifier) - - if self.subject_qualifier is not None and not isinstance(self.subject_qualifier, NamedEntityId): - self.subject_qualifier = NamedEntityId(self.subject_qualifier) - - if self.object_qualifier is not None and not isinstance(self.object_qualifier, NamedEntityId): - self.object_qualifier = NamedEntityId(self.object_qualifier) - - super().__post_init__(**kwargs) - - -@dataclass -class TextWithTriples(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.TextWithTriples - class_class_curie: ClassVar[str] = "core:TextWithTriples" - class_name: ClassVar[str] = "TextWithTriples" - class_model_uri: ClassVar[URIRef] = MENDELIAN_DISEASE.TextWithTriples - - publication: Optional[Union[dict, "Publication"]] = None - triples: Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.publication is not None and not isinstance(self.publication, Publication): - self.publication = Publication(**as_dict(self.publication)) - - if not isinstance(self.triples, list): - self.triples = [self.triples] if self.triples is not None else [] - self.triples = [v if isinstance(v, Triple) else Triple(**as_dict(v)) for v in self.triples] - - super().__post_init__(**kwargs) - - -@dataclass -class RelationshipType(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.RelationshipType - class_class_curie: ClassVar[str] = "core:RelationshipType" - class_name: ClassVar[str] = "RelationshipType" - class_model_uri: ClassVar[URIRef] = MENDELIAN_DISEASE.RelationshipType - - id: Union[str, RelationshipTypeId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, RelationshipTypeId): - self.id = RelationshipTypeId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Publication(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Publication - class_class_curie: ClassVar[str] = "core:Publication" - class_name: ClassVar[str] = "Publication" - class_model_uri: ClassVar[URIRef] = MENDELIAN_DISEASE.Publication - - id: Optional[str] = None - title: Optional[str] = None - abstract: Optional[str] = None - combined_text: Optional[str] = None - full_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.id is not None and not isinstance(self.id, str): - self.id = str(self.id) - - if self.title is not None and not isinstance(self.title, str): - self.title = str(self.title) - - if self.abstract is not None and not isinstance(self.abstract, str): - self.abstract = str(self.abstract) - - if self.combined_text is not None and not isinstance(self.combined_text, str): - self.combined_text = str(self.combined_text) - - if self.full_text is not None and not isinstance(self.full_text, str): - self.full_text = str(self.full_text) - - super().__post_init__(**kwargs) - - -@dataclass -class AnnotatorResult(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.AnnotatorResult - class_class_curie: ClassVar[str] = "core:AnnotatorResult" - class_name: ClassVar[str] = "AnnotatorResult" - class_model_uri: ClassVar[URIRef] = MENDELIAN_DISEASE.AnnotatorResult - - subject_text: Optional[str] = None - object_id: Optional[str] = None - object_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject_text is not None and not isinstance(self.subject_text, str): - self.subject_text = str(self.subject_text) - - if self.object_id is not None and not isinstance(self.object_id, str): - self.object_id = str(self.object_id) - - if self.object_text is not None and not isinstance(self.object_text, str): - self.object_text = str(self.object_text) - - super().__post_init__(**kwargs) - - -# Enumerations -class NullDataOptions(EnumDefinitionImpl): - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = PermissibleValue(text="UNSPECIFIED_METHOD_OF_ADMINISTRATION", - meaning=NCIT.C149701) - NOT_APPLICABLE = PermissibleValue(text="NOT_APPLICABLE", - meaning=NCIT.C18902) - NOT_MENTIONED = PermissibleValue(text="NOT_MENTIONED") - - _defn = EnumDefinition( - name="NullDataOptions", - ) - -# Slots -class slots: - pass - -slots.mendelianDisease__name = Slot(uri=MENDELIAN_DISEASE.name, name="mendelianDisease__name", curie=MENDELIAN_DISEASE.curie('name'), - model_uri=MENDELIAN_DISEASE.mendelianDisease__name, domain=None, range=Optional[str]) - -slots.mendelianDisease__description = Slot(uri=MENDELIAN_DISEASE.description, name="mendelianDisease__description", curie=MENDELIAN_DISEASE.curie('description'), - model_uri=MENDELIAN_DISEASE.mendelianDisease__description, domain=None, range=Optional[str]) - -slots.mendelianDisease__synonyms = Slot(uri=MENDELIAN_DISEASE.synonyms, name="mendelianDisease__synonyms", curie=MENDELIAN_DISEASE.curie('synonyms'), - model_uri=MENDELIAN_DISEASE.mendelianDisease__synonyms, domain=None, range=Optional[Union[str, List[str]]]) - -slots.mendelianDisease__subclass_of = Slot(uri=MENDELIAN_DISEASE.subclass_of, name="mendelianDisease__subclass_of", curie=MENDELIAN_DISEASE.curie('subclass_of'), - model_uri=MENDELIAN_DISEASE.mendelianDisease__subclass_of, domain=None, range=Optional[Union[Union[str, DiseaseCategoryId], List[Union[str, DiseaseCategoryId]]]]) - -slots.mendelianDisease__symptoms = Slot(uri=MENDELIAN_DISEASE.symptoms, name="mendelianDisease__symptoms", curie=MENDELIAN_DISEASE.curie('symptoms'), - model_uri=MENDELIAN_DISEASE.mendelianDisease__symptoms, domain=None, range=Optional[Union[Union[str, SymptomId], List[Union[str, SymptomId]]]]) - -slots.mendelianDisease__inheritance = Slot(uri=MENDELIAN_DISEASE.inheritance, name="mendelianDisease__inheritance", curie=MENDELIAN_DISEASE.curie('inheritance'), - model_uri=MENDELIAN_DISEASE.mendelianDisease__inheritance, domain=None, range=Optional[Union[str, InheritanceId]]) - -slots.mendelianDisease__genes = Slot(uri=MENDELIAN_DISEASE.genes, name="mendelianDisease__genes", curie=MENDELIAN_DISEASE.curie('genes'), - model_uri=MENDELIAN_DISEASE.mendelianDisease__genes, domain=None, range=Optional[Union[Union[str, GeneId], List[Union[str, GeneId]]]]) - -slots.mendelianDisease__disease_onsets = Slot(uri=MENDELIAN_DISEASE.disease_onsets, name="mendelianDisease__disease_onsets", curie=MENDELIAN_DISEASE.curie('disease_onsets'), - model_uri=MENDELIAN_DISEASE.mendelianDisease__disease_onsets, domain=None, range=Optional[Union[Union[str, OnsetId], List[Union[str, OnsetId]]]]) - -slots.mendelianDisease__publications = Slot(uri=MENDELIAN_DISEASE.publications, name="mendelianDisease__publications", curie=MENDELIAN_DISEASE.curie('publications'), - model_uri=MENDELIAN_DISEASE.mendelianDisease__publications, domain=None, range=Optional[Union[Union[dict, Publication], List[Union[dict, Publication]]]]) - -slots.symptom__characteristic = Slot(uri=MENDELIAN_DISEASE.characteristic, name="symptom__characteristic", curie=MENDELIAN_DISEASE.curie('characteristic'), - model_uri=MENDELIAN_DISEASE.symptom__characteristic, domain=None, range=Optional[str]) - -slots.symptom__affects = Slot(uri=MENDELIAN_DISEASE.affects, name="symptom__affects", curie=MENDELIAN_DISEASE.curie('affects'), - model_uri=MENDELIAN_DISEASE.symptom__affects, domain=None, range=Optional[str]) - -slots.symptom__severity = Slot(uri=MENDELIAN_DISEASE.severity, name="symptom__severity", curie=MENDELIAN_DISEASE.curie('severity'), - model_uri=MENDELIAN_DISEASE.symptom__severity, domain=None, range=Optional[str]) - -slots.symptom__onset_of_symptom = Slot(uri=MENDELIAN_DISEASE.onset_of_symptom, name="symptom__onset_of_symptom", curie=MENDELIAN_DISEASE.curie('onset_of_symptom'), - model_uri=MENDELIAN_DISEASE.symptom__onset_of_symptom, domain=None, range=Optional[Union[str, OnsetId]]) - -slots.onset__years_old = Slot(uri=MENDELIAN_DISEASE.years_old, name="onset__years_old", curie=MENDELIAN_DISEASE.curie('years_old'), - model_uri=MENDELIAN_DISEASE.onset__years_old, domain=None, range=Optional[str]) - -slots.onset__decades = Slot(uri=MENDELIAN_DISEASE.decades, name="onset__decades", curie=MENDELIAN_DISEASE.curie('decades'), - model_uri=MENDELIAN_DISEASE.onset__decades, domain=None, range=Optional[Union[str, List[str]]]) - -slots.onset__juvenile_or_adult = Slot(uri=MENDELIAN_DISEASE.juvenile_or_adult, name="onset__juvenile_or_adult", curie=MENDELIAN_DISEASE.curie('juvenile_or_adult'), - model_uri=MENDELIAN_DISEASE.onset__juvenile_or_adult, domain=None, range=Optional[str]) - -slots.extractionResult__input_id = Slot(uri=CORE.input_id, name="extractionResult__input_id", curie=CORE.curie('input_id'), - model_uri=MENDELIAN_DISEASE.extractionResult__input_id, domain=None, range=Optional[str]) - -slots.extractionResult__input_title = Slot(uri=CORE.input_title, name="extractionResult__input_title", curie=CORE.curie('input_title'), - model_uri=MENDELIAN_DISEASE.extractionResult__input_title, domain=None, range=Optional[str]) - -slots.extractionResult__input_text = Slot(uri=CORE.input_text, name="extractionResult__input_text", curie=CORE.curie('input_text'), - model_uri=MENDELIAN_DISEASE.extractionResult__input_text, domain=None, range=Optional[str]) - -slots.extractionResult__raw_completion_output = Slot(uri=CORE.raw_completion_output, name="extractionResult__raw_completion_output", curie=CORE.curie('raw_completion_output'), - model_uri=MENDELIAN_DISEASE.extractionResult__raw_completion_output, domain=None, range=Optional[str]) - -slots.extractionResult__prompt = Slot(uri=CORE.prompt, name="extractionResult__prompt", curie=CORE.curie('prompt'), - model_uri=MENDELIAN_DISEASE.extractionResult__prompt, domain=None, range=Optional[str]) - -slots.extractionResult__extracted_object = Slot(uri=CORE.extracted_object, name="extractionResult__extracted_object", curie=CORE.curie('extracted_object'), - model_uri=MENDELIAN_DISEASE.extractionResult__extracted_object, domain=None, range=Optional[Union[dict, Any]]) - -slots.extractionResult__named_entities = Slot(uri=CORE.named_entities, name="extractionResult__named_entities", curie=CORE.curie('named_entities'), - model_uri=MENDELIAN_DISEASE.extractionResult__named_entities, domain=None, range=Optional[Union[Union[dict, Any], List[Union[dict, Any]]]]) - -slots.namedEntity__id = Slot(uri=CORE.id, name="namedEntity__id", curie=CORE.curie('id'), - model_uri=MENDELIAN_DISEASE.namedEntity__id, domain=None, range=URIRef) - -slots.namedEntity__label = Slot(uri=RDFS.label, name="namedEntity__label", curie=RDFS.curie('label'), - model_uri=MENDELIAN_DISEASE.namedEntity__label, domain=None, range=Optional[str]) - -slots.triple__subject = Slot(uri=CORE.subject, name="triple__subject", curie=CORE.curie('subject'), - model_uri=MENDELIAN_DISEASE.triple__subject, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__predicate = Slot(uri=CORE.predicate, name="triple__predicate", curie=CORE.curie('predicate'), - model_uri=MENDELIAN_DISEASE.triple__predicate, domain=None, range=Optional[Union[str, RelationshipTypeId]]) - -slots.triple__object = Slot(uri=CORE.object, name="triple__object", curie=CORE.curie('object'), - model_uri=MENDELIAN_DISEASE.triple__object, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__qualifier = Slot(uri=CORE.qualifier, name="triple__qualifier", curie=CORE.curie('qualifier'), - model_uri=MENDELIAN_DISEASE.triple__qualifier, domain=None, range=Optional[str]) - -slots.triple__subject_qualifier = Slot(uri=CORE.subject_qualifier, name="triple__subject_qualifier", curie=CORE.curie('subject_qualifier'), - model_uri=MENDELIAN_DISEASE.triple__subject_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__object_qualifier = Slot(uri=CORE.object_qualifier, name="triple__object_qualifier", curie=CORE.curie('object_qualifier'), - model_uri=MENDELIAN_DISEASE.triple__object_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.textWithTriples__publication = Slot(uri=CORE.publication, name="textWithTriples__publication", curie=CORE.curie('publication'), - model_uri=MENDELIAN_DISEASE.textWithTriples__publication, domain=None, range=Optional[Union[dict, Publication]]) - -slots.textWithTriples__triples = Slot(uri=CORE.triples, name="textWithTriples__triples", curie=CORE.curie('triples'), - model_uri=MENDELIAN_DISEASE.textWithTriples__triples, domain=None, range=Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]]) - -slots.publication__id = Slot(uri=CORE.id, name="publication__id", curie=CORE.curie('id'), - model_uri=MENDELIAN_DISEASE.publication__id, domain=None, range=Optional[str]) - -slots.publication__title = Slot(uri=CORE.title, name="publication__title", curie=CORE.curie('title'), - model_uri=MENDELIAN_DISEASE.publication__title, domain=None, range=Optional[str]) - -slots.publication__abstract = Slot(uri=CORE.abstract, name="publication__abstract", curie=CORE.curie('abstract'), - model_uri=MENDELIAN_DISEASE.publication__abstract, domain=None, range=Optional[str]) - -slots.publication__combined_text = Slot(uri=CORE.combined_text, name="publication__combined_text", curie=CORE.curie('combined_text'), - model_uri=MENDELIAN_DISEASE.publication__combined_text, domain=None, range=Optional[str]) - -slots.publication__full_text = Slot(uri=CORE.full_text, name="publication__full_text", curie=CORE.curie('full_text'), - model_uri=MENDELIAN_DISEASE.publication__full_text, domain=None, range=Optional[str]) - -slots.annotatorResult__subject_text = Slot(uri=CORE.subject_text, name="annotatorResult__subject_text", curie=CORE.curie('subject_text'), - model_uri=MENDELIAN_DISEASE.annotatorResult__subject_text, domain=None, range=Optional[str]) - -slots.annotatorResult__object_id = Slot(uri=CORE.object_id, name="annotatorResult__object_id", curie=CORE.curie('object_id'), - model_uri=MENDELIAN_DISEASE.annotatorResult__object_id, domain=None, range=Optional[str]) - -slots.annotatorResult__object_text = Slot(uri=CORE.object_text, name="annotatorResult__object_text", curie=CORE.curie('object_text'), - model_uri=MENDELIAN_DISEASE.annotatorResult__object_text, domain=None, range=Optional[str]) \ No newline at end of file diff --git a/projects/mendelian_disease/owl/mendelian_disease.owl.ttl b/projects/mendelian_disease/owl/mendelian_disease.owl.ttl deleted file mode 100644 index 48a74b2a0..000000000 --- a/projects/mendelian_disease/owl/mendelian_disease.owl.ttl +++ /dev/null @@ -1,542 +0,0 @@ -@prefix IAO: <http://purl.obolibrary.org/obo/IAO_> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix mendelian_disease: <http://w3id.org/ontogpt/mendelian_disease/> . -@prefix owl: <http://www.w3.org/2002/07/owl#> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . -@prefix skos: <http://www.w3.org/2004/02/skos/core#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -<http://w3id.org/ontogpt/mendelian_disease> a owl:Ontology ; - rdfs:label "mendelian_disease-template" ; - IAO:0000700 <http://w3id.org/ontogpt/core/AnnotatorResult>, - <http://w3id.org/ontogpt/core/Any>, - <http://w3id.org/ontogpt/core/CompoundExpression>, - <http://w3id.org/ontogpt/core/ExtractionResult>, - <http://w3id.org/ontogpt/core/NamedEntity>, - <http://w3id.org/ontogpt/core/Publication>, - <http://w3id.org/ontogpt/core/TextWithTriples> ; - linkml:classes "{'MendelianDisease': ClassDefinition(name='MendelianDisease', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/mendelian_disease/MendelianDisease', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/mendelian_disease', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label', 'mendelianDisease__name', 'mendelianDisease__description', 'mendelianDisease__synonyms', 'mendelianDisease__subclass_of', 'mendelianDisease__symptoms', 'mendelianDisease__inheritance', 'mendelianDisease__genes', 'mendelianDisease__disease_onsets', 'mendelianDisease__publications'], slot_usage={}, attributes={'name': SlotDefinition(name='name', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the name of the disease', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[Example(value='peroxisome biogenesis disorder', description=None, object=None)], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'description': SlotDefinition(name='description', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a description of the disease', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[Example(value='Peroxisome biogenesis disorders, Zellweger syndrome spectrum (PBD-ZSS) is a group of autosomal recessive disorders affecting the formation of functional peroxisomes, characterized by sensorineural hearing loss, pigmentary retinal degeneration, multiple organ dysfunction and psychomotor impairment', description=None, object=None)], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'synonyms': SlotDefinition(name='synonyms', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[Example(value='Zellweger syndrome spectrum', description=None, object=None), Example(value='PBD-ZSS', description=None, object=None)], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subclass_of': SlotDefinition(name='subclass_of', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[Example(value='lysosomal disease', description=None, object=None), Example(value='autosomal recessive disorder', description=None, object=None)], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='DiseaseCategory', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'symptoms': SlotDefinition(name='symptoms', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[Example(value='sensorineural hearing loss', description=None, object=None), Example(value='pigmentary retinal degeneration', description=None, object=None)], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Symptom', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'inheritance': SlotDefinition(name='inheritance', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[Example(value='autosomal recessive', description=None, object=None)], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Inheritance', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'genes': SlotDefinition(name='genes', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon separated list of gene symbols; for example: PEX1; PEX2; PEX3', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[Example(value='PEX1', description=None, object=None), Example(value='PEX2', description=None, object=None), Example(value='PEX3', description=None, object=None)], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'disease_onsets': SlotDefinition(name='disease_onsets', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semi-colon separated list of onsets at which the disease occurs, for example: adult; juvenile; first decade', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Onset', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'publications': SlotDefinition(name='publications', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='mendelian_disease:MendelianDisease', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'DiseaseCategory': ClassDefinition(name='DiseaseCategory', id_prefixes=['MONDO'], definition_uri='http://w3id.org/ontogpt/mendelian_disease/DiseaseCategory', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:mondo', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/mendelian_disease', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='mendelian_disease:DiseaseCategory', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Gene': ClassDefinition(name='Gene', id_prefixes=['HGNC'], definition_uri='http://w3id.org/ontogpt/mendelian_disease/Gene', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='gilda:, bioportal:hgnc-nr, sqlite:obo:pr', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/mendelian_disease', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='mendelian_disease:Gene', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Symptom': ClassDefinition(name='Symptom', id_prefixes=['HP'], definition_uri='http://w3id.org/ontogpt/mendelian_disease/Symptom', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:hp, sqlite:obo:mondo', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/mendelian_disease', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label', 'symptom__characteristic', 'symptom__affects', 'symptom__severity', 'symptom__onset_of_symptom'], slot_usage={}, attributes={'characteristic': SlotDefinition(name='characteristic', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'affects': SlotDefinition(name='affects', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'severity': SlotDefinition(name='severity', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'onset_of_symptom': SlotDefinition(name='onset_of_symptom', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Onset', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='mendelian_disease:Symptom', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Onset': ClassDefinition(name='Onset', id_prefixes=['HP'], definition_uri='http://w3id.org/ontogpt/mendelian_disease/Onset', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:hp, sqlite:obo:hsapdv', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/mendelian_disease', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label', 'onset__years_old', 'onset__decades', 'onset__juvenile_or_adult'], slot_usage={}, attributes={'years_old': SlotDefinition(name='years_old', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'decades': SlotDefinition(name='decades', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'juvenile_or_adult': SlotDefinition(name='juvenile_or_adult', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='mendelian_disease:Onset', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Inheritance': ClassDefinition(name='Inheritance', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/mendelian_disease/Inheritance', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:hp, sqlite:obo:geno', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/mendelian_disease', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='mendelian_disease:Inheritance', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Any': ClassDefinition(name='Any', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Any', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=['linkml:Any'], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='linkml:Any', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ExtractionResult': ClassDefinition(name='ExtractionResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/ExtractionResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A result of extracting knowledge on text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['extractionResult__input_id', 'extractionResult__input_title', 'extractionResult__input_text', 'extractionResult__raw_completion_output', 'extractionResult__prompt', 'extractionResult__extracted_object', 'extractionResult__named_entities'], slot_usage={}, attributes={'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:ExtractionResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'NamedEntity': ClassDefinition(name='NamedEntity', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NamedEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:NamedEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'CompoundExpression': ClassDefinition(name='CompoundExpression', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/CompoundExpression', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='core:CompoundExpression', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Triple': ClassDefinition(name='Triple', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Triple', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Abstract parent for Relation Extraction tasks', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['triple__subject', 'triple__predicate', 'triple__object', 'triple__qualifier', 'triple__subject_qualifier', 'triple__object_qualifier'], slot_usage={}, attributes={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Triple', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'TextWithTriples': ClassDefinition(name='TextWithTriples', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/TextWithTriples', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['textWithTriples__publication', 'textWithTriples__triples'], slot_usage={}, attributes={'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:TextWithTriples', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'RelationshipType': ClassDefinition(name='RelationshipType', id_prefixes=['RO', 'biolink'], definition_uri='http://w3id.org/ontogpt/core/RelationshipType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='core:RelationshipType', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Publication': ClassDefinition(name='Publication', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Publication', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['publication__id', 'publication__title', 'publication__abstract', 'publication__combined_text', 'publication__full_text'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Publication', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'AnnotatorResult': ClassDefinition(name='AnnotatorResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/AnnotatorResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['annotatorResult__subject_text', 'annotatorResult__object_id', 'annotatorResult__object_text'], slot_usage={}, attributes={'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:AnnotatorResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={})}" ; - linkml:enums "{'NullDataOptions': EnumDefinition(name='NullDataOptions', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NullDataOptions', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'UNSPECIFIED_METHOD_OF_ADMINISTRATION': PermissibleValue(text='UNSPECIFIED_METHOD_OF_ADMINISTRATION', description=None, meaning='NCIT:C149701', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_APPLICABLE': PermissibleValue(text='NOT_APPLICABLE', description=None, meaning='NCIT:C18902', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['not applicable', 'N/A'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_MENTIONED': PermissibleValue(text='NOT_MENTIONED', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[])}" ; - linkml:id "http://w3id.org/ontogpt/mendelian_disease" ; - linkml:imports "core", - "linkml:types" ; - linkml:types "{'string': TypeDefinition(name='string', id_prefixes=[], definition_uri='https://w3id.org/linkml/String', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A character string', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Text'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'integer': TypeDefinition(name='integer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Integer', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An integer', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Integer'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='int', uri='xsd:integer', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'boolean': TypeDefinition(name='boolean', id_prefixes=[], definition_uri='https://w3id.org/linkml/Boolean', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A binary (true or false) value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Boolean'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Bool', uri='xsd:boolean', repr='bool', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'float': TypeDefinition(name='float', id_prefixes=[], definition_uri='https://w3id.org/linkml/Float', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:float specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Float'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:float', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'double': TypeDefinition(name='double', id_prefixes=[], definition_uri='https://w3id.org/linkml/Double', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:double specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:Float'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:double', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'decimal': TypeDefinition(name='decimal', id_prefixes=[], definition_uri='https://w3id.org/linkml/Decimal', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number with arbitrary precision that conforms to the xsd:decimal specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=['schema:Number'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Decimal', uri='xsd:decimal', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'time': TypeDefinition(name='time', id_prefixes=[], definition_uri='https://w3id.org/linkml/Time', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A time object represents a (local) time of day, independent of any particular day', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=['URI is dateTime because OWL reasoners do not work with straight date or time'], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Time'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDTime', uri='xsd:time', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date': TypeDefinition(name='date', id_prefixes=[], definition_uri='https://w3id.org/linkml/Date', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a date (year, month and day) in an idealized calendar', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[\"URI is dateTime because OWL reasoners don't work with straight date or time\"], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Date'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDate', uri='xsd:date', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'datetime': TypeDefinition(name='datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/Datetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The combination of a date and time', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:DateTime'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDateTime', uri='xsd:dateTime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date_or_datetime': TypeDefinition(name='date_or_datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/DateOrDatetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Either a date or a datetime', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='linkml:DateOrDatetime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uriorcurie': TypeDefinition(name='uriorcurie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uriorcurie', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a URI or a CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URIorCURIE', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'curie': TypeDefinition(name='curie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Curie', local_names={}, conforms_to='https://www.w3.org/TR/curie/', implements=[], extensions={}, annotations={}, description='a compact URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations this MUST be expanded to a URI', 'in non-RDF serializations MAY be serialized as the compact representation'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Curie', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uri': TypeDefinition(name='uri', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uri', local_names={}, conforms_to='https://www.ietf.org/rfc/rfc3987.txt', implements=[], extensions={}, annotations={}, description='a complete URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:URL'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URI', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ncname': TypeDefinition(name='ncname', id_prefixes=[], definition_uri='https://w3id.org/linkml/Ncname', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Prefix part of CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NCName', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'objectidentifier': TypeDefinition(name='objectidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Objectidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI or CURIE that represents an object in the model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['Used for inheritance and type checking'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='ElementIdentifier', uri='shex:iri', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'nodeidentifier': TypeDefinition(name='nodeidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Nodeidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI, CURIE or BNODE that represents a node in a model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NodeIdentifier', uri='shex:nonLiteral', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpointer': TypeDefinition(name='jsonpointer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpointer', local_names={}, conforms_to='https://datatracker.ietf.org/doc/html/rfc6901', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpath': TypeDefinition(name='jsonpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpath', local_names={}, conforms_to='https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sparqlpath': TypeDefinition(name='sparqlpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Sparqlpath', local_names={}, conforms_to='https://www.w3.org/TR/sparql11-query/#propertypaths', implements=[], extensions={}, annotations={}, description='A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -mendelian_disease:MendelianDisease a owl:Class, - linkml:ClassDefinition ; - rdfs:label "MendelianDisease" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom mendelian_disease:DiseaseCategory ; - owl:onProperty mendelian_disease:subclass_of ], - [ a owl:Restriction ; - owl:allValuesFrom mendelian_disease:Gene ; - owl:onProperty mendelian_disease:genes ], - [ a owl:Restriction ; - owl:allValuesFrom mendelian_disease:Onset ; - owl:onProperty mendelian_disease:disease_onsets ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty mendelian_disease:name ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty mendelian_disease:description ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass mendelian_disease:Inheritance ; - owl:onProperty mendelian_disease:inheritance ], - [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Publication> ; - owl:onProperty mendelian_disease:publications ], - [ a owl:Restriction ; - owl:allValuesFrom mendelian_disease:Symptom ; - owl:onProperty mendelian_disease:symptoms ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty mendelian_disease:synonyms ], - <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{'name': SlotDefinition(name='name', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the name of the disease', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[Example(value='peroxisome biogenesis disorder', description=None, object=None)], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'description': SlotDefinition(name='description', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a description of the disease', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[Example(value='Peroxisome biogenesis disorders, Zellweger syndrome spectrum (PBD-ZSS) is a group of autosomal recessive disorders affecting the formation of functional peroxisomes, characterized by sensorineural hearing loss, pigmentary retinal degeneration, multiple organ dysfunction and psychomotor impairment', description=None, object=None)], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'synonyms': SlotDefinition(name='synonyms', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[Example(value='Zellweger syndrome spectrum', description=None, object=None), Example(value='PBD-ZSS', description=None, object=None)], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subclass_of': SlotDefinition(name='subclass_of', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[Example(value='lysosomal disease', description=None, object=None), Example(value='autosomal recessive disorder', description=None, object=None)], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='DiseaseCategory', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'symptoms': SlotDefinition(name='symptoms', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[Example(value='sensorineural hearing loss', description=None, object=None), Example(value='pigmentary retinal degeneration', description=None, object=None)], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Symptom', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'inheritance': SlotDefinition(name='inheritance', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[Example(value='autosomal recessive', description=None, object=None)], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Inheritance', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'genes': SlotDefinition(name='genes', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon separated list of gene symbols; for example: PEX1; PEX2; PEX3', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[Example(value='PEX1', description=None, object=None), Example(value='PEX2', description=None, object=None), Example(value='PEX3', description=None, object=None)], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'disease_onsets': SlotDefinition(name='disease_onsets', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semi-colon separated list of onsets at which the disease occurs, for example: adult; juvenile; first decade', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Onset', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'publications': SlotDefinition(name='publications', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "NamedEntity" . - -linkml:SubsetDefinition a owl:Class ; - rdfs:label "subset_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" . - -linkml:TypeDefinition a owl:Class ; - rdfs:label "type_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" ; - linkml:mixins "type_expression" . - -linkml:topValue a owl:DatatypeProperty ; - rdfs:label "value" . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "AnnotatorResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_id> ] ; - linkml:attributes "{'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/ExtractionResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ExtractionResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_id> ], - [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/named_entities> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_title> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/prompt> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/extracted_object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_text> ] ; - skos:definition "A result of extracting knowledge on text" ; - linkml:attributes "{'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/TextWithTriples> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TextWithTriples" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Triple> ; - owl:onProperty <http://w3id.org/ontogpt/core/triples> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Publication> ; - owl:onProperty <http://w3id.org/ontogpt/core/publication> ] ; - linkml:attributes "{'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/abstract> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "abstract" ; - rdfs:range linkml:String ; - skos:definition "The abstract of the publication" . - -<http://w3id.org/ontogpt/core/combined_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "combined_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/extracted_object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "extracted_object" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "The complex objects extracted from the text" . - -<http://w3id.org/ontogpt/core/full_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "full_text" ; - rdfs:range linkml:String ; - skos:definition "The full text of the publication" . - -<http://w3id.org/ontogpt/core/input_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_title" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/named_entities> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "named_entities" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "Named entities extracted from the text" . - -<http://w3id.org/ontogpt/core/object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/object_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/object_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" . - -<http://w3id.org/ontogpt/core/object_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/predicate> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "predicate" ; - rdfs:range <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/prompt> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "prompt" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/publication> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "publication" ; - mendelian_disease:prompt.skip "true" ; - rdfs:range <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "qualifier" ; - rdfs:range linkml:String ; - skos:definition "A qualifier for the statements, e.g. \"NOT\" for negation" . - -<http://w3id.org/ontogpt/core/raw_completion_output> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "raw_completion_output" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/subject> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/subject_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" . - -<http://w3id.org/ontogpt/core/subject_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "title" ; - rdfs:range linkml:String ; - skos:definition "The title of the publication" . - -<http://w3id.org/ontogpt/core/triples> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "triples" ; - rdfs:range <http://w3id.org/ontogpt/core/Triple> . - -mendelian_disease:affects a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "affects" ; - rdfs:range linkml:String . - -mendelian_disease:characteristic a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "characteristic" ; - rdfs:range linkml:String . - -mendelian_disease:decades a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "decades" ; - rdfs:range linkml:String . - -mendelian_disease:description a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "description" ; - rdfs:range linkml:String ; - skos:definition "a description of the disease" . - -mendelian_disease:disease_onsets a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "disease_onsets" ; - mendelian_disease:prompt "semi-colon separated list of onsets at which the disease occurs, for example: adult; juvenile; first decade" ; - rdfs:range mendelian_disease:Onset . - -mendelian_disease:genes a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "genes" ; - mendelian_disease:prompt "semicolon separated list of gene symbols; for example: PEX1; PEX2; PEX3" ; - rdfs:range mendelian_disease:Gene . - -mendelian_disease:inheritance a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "inheritance" ; - rdfs:range mendelian_disease:Inheritance . - -mendelian_disease:juvenile_or_adult a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "juvenile_or_adult" ; - rdfs:range linkml:String . - -mendelian_disease:name a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "name" ; - rdfs:range linkml:String ; - skos:definition "the name of the disease" . - -mendelian_disease:onset_of_symptom a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "onset_of_symptom" ; - rdfs:range mendelian_disease:Onset . - -mendelian_disease:publications a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "publications" ; - mendelian_disease:prompt.skip "true" ; - rdfs:range <http://w3id.org/ontogpt/core/Publication> . - -mendelian_disease:severity a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "severity" ; - rdfs:range linkml:String . - -mendelian_disease:subclass_of a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subclass_of" ; - rdfs:range mendelian_disease:DiseaseCategory . - -mendelian_disease:symptoms a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "symptoms" ; - rdfs:range mendelian_disease:Symptom . - -mendelian_disease:synonyms a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "synonyms" ; - rdfs:range linkml:String . - -mendelian_disease:years_old a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "years_old" ; - rdfs:range linkml:String . - -<http://example.org/UNKNOWN/rdfs/label> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "label" ; - mendelian_disease:owl "AnnotationProperty, AnnotationAssertion" ; - rdfs:range linkml:String ; - skos:altLabel "name" ; - skos:definition "The label (name) of the named thing" ; - skos:exactMatch <http://example.org/UNKNOWN/rdfs/label> . - -<http://purl.obolibrary.org/obo/NCIT_C149701> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "UNSPECIFIED_METHOD_OF_ADMINISTRATION" . - -<http://purl.obolibrary.org/obo/NCIT_C18902> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_APPLICABLE" . - -<http://w3id.org/ontogpt/core/CompoundExpression> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CompoundExpression" ; - linkml:attributes "{}" . - -<http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_MENTIONED" . - -<http://w3id.org/ontogpt/core/RelationshipType> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "RelationshipType" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/Triple> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Triple" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/RelationshipType> ; - owl:onProperty <http://w3id.org/ontogpt/core/predicate> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject> ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - skos:definition "Abstract parent for Relation Extraction tasks" ; - linkml:attributes "{'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -<http://w3id.org/ontogpt/core/id> a owl:ObjectProperty, - linkml:SlotDefinition . - -mendelian_disease:DiseaseCategory a owl:Class, - linkml:ClassDefinition ; - rdfs:label "DiseaseCategory" ; - mendelian_disease:annotators "sqlite:obo:mondo" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -mendelian_disease:Gene a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Gene" ; - mendelian_disease:annotators "gilda:, bioportal:hgnc-nr, sqlite:obo:pr" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -mendelian_disease:Inheritance a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Inheritance" ; - mendelian_disease:annotators "sqlite:obo:hp, sqlite:obo:geno" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -mendelian_disease:Symptom a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Symptom" ; - mendelian_disease:annotators "sqlite:obo:hp, sqlite:obo:mondo" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty mendelian_disease:severity ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty mendelian_disease:characteristic ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass mendelian_disease:Onset ; - owl:onProperty mendelian_disease:onset_of_symptom ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty mendelian_disease:affects ], - <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{'characteristic': SlotDefinition(name='characteristic', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'affects': SlotDefinition(name='affects', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'severity': SlotDefinition(name='severity', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'onset_of_symptom': SlotDefinition(name='onset_of_symptom', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Onset', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/NullDataOptions> a owl:Class, - linkml:EnumDefinition ; - rdfs:label "NullDataOptions" ; - owl:unionOf ( <http://purl.obolibrary.org/obo/NCIT_C149701> <http://purl.obolibrary.org/obo/NCIT_C18902> <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> ) ; - linkml:permissible_values <http://purl.obolibrary.org/obo/NCIT_C149701>, - <http://purl.obolibrary.org/obo/NCIT_C18902>, - <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> . - -mendelian_disease:Onset a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Onset" ; - mendelian_disease:annotators "sqlite:obo:hp, sqlite:obo:hsapdv" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty mendelian_disease:decades ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty mendelian_disease:years_old ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty mendelian_disease:juvenile_or_adult ], - <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{'years_old': SlotDefinition(name='years_old', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'decades': SlotDefinition(name='decades', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'juvenile_or_adult': SlotDefinition(name='juvenile_or_adult', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/Any> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Any" ; - skos:exactMatch linkml:Any ; - linkml:attributes "{}" . - -<http://w3id.org/ontogpt/core/Publication> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Publication" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/title> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/full_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/abstract> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/combined_text> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:ClassDefinition a owl:Class ; - rdfs:label "class_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "class_expression" . - -<http://w3id.org/ontogpt/core/NamedEntity> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "NamedEntity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://example.org/UNKNOWN/rdfs/label> ], - [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ; - owl:qualifiedCardinality 1 ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:SlotDefinition a owl:Class ; - rdfs:label "slot_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "slot_expression" . - - diff --git a/projects/mendelian_disease/prefixmap/mendelian_disease.yaml b/projects/mendelian_disease/prefixmap/mendelian_disease.yaml deleted file mode 100644 index 5e93eefe8..000000000 --- a/projects/mendelian_disease/prefixmap/mendelian_disease.yaml +++ /dev/null @@ -1,38 +0,0 @@ -{ - "HGNC": "http://example.org/UNKNOWN/HGNC/", - "HP": "http://example.org/UNKNOWN/HP/", - "MONDO": "http://example.org/UNKNOWN/MONDO/", - "RO": "http://purl.obolibrary.org/obo/RO_", - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "linkml": "https://w3id.org/linkml/", - "mendelian_disease": "http://w3id.org/ontogpt/mendelian_disease/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } -} diff --git a/projects/mendelian_disease/protobuf/mendelian_disease.proto b/projects/mendelian_disease/protobuf/mendelian_disease.proto deleted file mode 100644 index 8f5aa1ee5..000000000 --- a/projects/mendelian_disease/protobuf/mendelian_disease.proto +++ /dev/null @@ -1,81 +0,0 @@ -message AnnotatorResult - { - string subjectText = 0 - string objectId = 0 - string objectText = 0 - } -message DiseaseCategory - { - string id = 0 - string label = 0 - } -// A result of extracting knowledge on text -message ExtractionResult - { - string inputId = 0 - string inputTitle = 0 - string inputText = 0 - string rawCompletionOutput = 0 - string prompt = 0 - any extractedObject = 0 - repeated any namedEntities = 0 - } -message Gene - { - string id = 0 - string label = 0 - } -message Inheritance - { - string id = 0 - string label = 0 - } -message MendelianDisease - { - string id = 0 - string label = 0 - string name = 0 - string description = 0 - repeated string synonyms = 0 - repeated diseaseCategory subclassOf = 0 - repeated symptom symptoms = 0 - inheritance inheritance = 0 - repeated gene genes = 0 - repeated onset diseaseOnsets = 0 - repeated publication publications = 0 - } -message Onset - { - string id = 0 - string label = 0 - string yearsOld = 0 - repeated string decades = 0 - string juvenileOrAdult = 0 - } -message Publication - { - string id = 0 - string title = 0 - string abstract = 0 - string combinedText = 0 - string fullText = 0 - } -message RelationshipType - { - string id = 0 - string label = 0 - } -message Symptom - { - string id = 0 - string label = 0 - string characteristic = 0 - string affects = 0 - string severity = 0 - onset onsetOfSymptom = 0 - } -message TextWithTriples - { - publication publication = 0 - repeated triple triples = 0 - } diff --git a/projects/mendelian_disease/shacl/mendelian_disease.shacl.ttl b/projects/mendelian_disease/shacl/mendelian_disease.shacl.ttl deleted file mode 100644 index 2768d35bc..000000000 --- a/projects/mendelian_disease/shacl/mendelian_disease.shacl.ttl +++ /dev/null @@ -1,305 +0,0 @@ -@prefix linkml: <https://w3id.org/linkml/> . -@prefix mendelian_disease: <http://w3id.org/ontogpt/mendelian_disease/> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix sh: <http://www.w3.org/ns/shacl#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject_text> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object_text> ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/object_id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/AnnotatorResult> . - -<http://w3id.org/ontogpt/core/CompoundExpression> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass <http://w3id.org/ontogpt/core/CompoundExpression> . - -<http://w3id.org/ontogpt/core/ExtractionResult> a sh:NodeShape ; - sh:closed true ; - sh:description "A result of extracting knowledge on text" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class linkml:Any ; - sh:description "The complex objects extracted from the text" ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/extracted_object> ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/input_title> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/prompt> ], - [ sh:class linkml:Any ; - sh:description "Named entities extracted from the text" ; - sh:nodeKind sh:BlankNode ; - sh:order 6 ; - sh:path <http://w3id.org/ontogpt/core/named_entities> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/input_text> ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/input_id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/ExtractionResult> . - -<http://w3id.org/ontogpt/core/TextWithTriples> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/Publication> ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/publication> ], - [ sh:class <http://w3id.org/ontogpt/core/Triple> ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/triples> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/TextWithTriples> . - -mendelian_disease:MendelianDisease a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/Publication> ; - sh:nodeKind sh:BlankNode ; - sh:order 8 ; - sh:path mendelian_disease:publications ], - [ sh:class mendelian_disease:Gene ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path mendelian_disease:genes ], - [ sh:class mendelian_disease:Inheritance ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path mendelian_disease:inheritance ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path <rdfs:label> ], - [ sh:description "a description of the disease" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path mendelian_disease:description ], - [ sh:class mendelian_disease:Onset ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path mendelian_disease:disease_onsets ], - [ sh:class mendelian_disease:Symptom ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path mendelian_disease:symptoms ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:order 2 ; - sh:path mendelian_disease:synonyms ], - [ sh:class mendelian_disease:DiseaseCategory ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path mendelian_disease:subclass_of ], - [ sh:description "the name of the disease" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path mendelian_disease:name ] ; - sh:targetClass mendelian_disease:MendelianDisease . - -<http://w3id.org/ontogpt/core/RelationshipType> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/Triple> a sh:NodeShape ; - sh:closed false ; - sh:description "Abstract parent for Relation Extraction tasks" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/RelationshipType> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/predicate> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/object_qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ sh:description "A qualifier for the statements, e.g. \"NOT\" for negation" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/qualifier> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Triple> . - -mendelian_disease:DiseaseCategory a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass mendelian_disease:DiseaseCategory . - -mendelian_disease:Gene a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass mendelian_disease:Gene . - -mendelian_disease:Inheritance a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass mendelian_disease:Inheritance . - -mendelian_disease:Symptom a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path <rdfs:label> ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path mendelian_disease:affects ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path mendelian_disease:characteristic ], - [ sh:class mendelian_disease:Onset ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path mendelian_disease:onset_of_symptom ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path mendelian_disease:severity ] ; - sh:targetClass mendelian_disease:Symptom . - -<http://w3id.org/ontogpt/core/Publication> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The title of the publication" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/title> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/combined_text> ], - [ sh:description "The full text of the publication" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/full_text> ], - [ sh:description "The abstract of the publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/abstract> ], - [ sh:description "The publication identifier" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Publication> . - -mendelian_disease:Onset a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:order 1 ; - sh:path mendelian_disease:decades ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path <rdfs:label> ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path mendelian_disease:years_old ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path mendelian_disease:juvenile_or_adult ] ; - sh:targetClass mendelian_disease:Onset . - -linkml:Any a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass linkml:Any . - -<http://w3id.org/ontogpt/core/NamedEntity> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/NamedEntity> . - diff --git a/projects/mendelian_disease/shex/mendelian_disease.shex b/projects/mendelian_disease/shex/mendelian_disease.shex deleted file mode 100644 index 6fe919d0a..000000000 --- a/projects/mendelian_disease/shex/mendelian_disease.shex +++ /dev/null @@ -1,198 +0,0 @@ -BASE <http://w3id.org/ontogpt/mendelian_disease/> -PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> -PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> -PREFIX linkml: <https://w3id.org/linkml/> -PREFIX core: <http://w3id.org/ontogpt/core/> -PREFIX rdfs1: <http://example.org/UNKNOWN/rdfs/> - - -linkml:String xsd:string - -linkml:Integer xsd:integer - -linkml:Boolean xsd:boolean - -linkml:Float xsd:float - -linkml:Double xsd:double - -linkml:Decimal xsd:decimal - -linkml:Time xsd:time - -linkml:Date xsd:date - -linkml:Datetime xsd:dateTime - -linkml:DateOrDatetime linkml:DateOrDatetime - -linkml:Uriorcurie IRI - -linkml:Curie xsd:string - -linkml:Uri IRI - -linkml:Ncname xsd:string - -linkml:Objectidentifier IRI - -linkml:Nodeidentifier NONLITERAL - -linkml:Jsonpointer xsd:string - -linkml:Jsonpath xsd:string - -linkml:Sparqlpath xsd:string - -core:AnnotatorResult CLOSED { - ( $core:AnnotatorResult_tes ( core:subject_text @linkml:String ? ; - core:object_id @linkml:String ? ; - core:object_text @linkml:String ? - ) ; - rdf:type [ core:AnnotatorResult ] ? - ) -} - -core:Any CLOSED { - ( $core:Any_tes rdf:type . * ; - rdf:type [ linkml:Any ] ? - ) -} - -core:CompoundExpression ( - { - ( $core:CompoundExpression_tes rdf:type . * ; - rdf:type [ core:CompoundExpression ] ? - ) - } OR @core:Triple -) - -<DiseaseCategory> CLOSED { - ( $<DiseaseCategory_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <DiseaseCategory> ] - ) -} - -core:ExtractionResult CLOSED { - ( $core:ExtractionResult_tes ( core:input_id @linkml:String ? ; - core:input_title @linkml:String ? ; - core:input_text @linkml:String ? ; - core:raw_completion_output @linkml:String ? ; - core:prompt @linkml:String ? ; - core:extracted_object @core:Any ? ; - core:named_entities @core:Any * - ) ; - rdf:type [ core:ExtractionResult ] ? - ) -} - -<Gene> CLOSED { - ( $<Gene_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Gene> ] - ) -} - -<Inheritance> CLOSED { - ( $<Inheritance_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Inheritance> ] - ) -} - -<MendelianDisease> CLOSED { - ( $<MendelianDisease_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? ; - <name> @linkml:String ? ; - <description> @linkml:String ? ; - <synonyms> @linkml:String * ; - <subclass_of> @<DiseaseCategory> * ; - <symptoms> @<Symptom> * ; - <inheritance> @<Inheritance> ? ; - <genes> @<Gene> * ; - <disease_onsets> @<Onset> * ; - <publications> @core:Publication * - ) ; - rdf:type [ <MendelianDisease> ] - ) -} - -core:NamedEntity ( - @<DiseaseCategory> OR @<Gene> OR @<Inheritance> OR @<MendelianDisease> OR @<Onset> OR @core:RelationshipType OR @<Symptom> -) - -core:NamedEntity_struct { - ( $core:NamedEntity_tes rdfs1:label @linkml:String ? ; - rdf:type [ core:NamedEntity ] - ) -} - -<Onset> CLOSED { - ( $<Onset_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? ; - <years_old> @linkml:String ? ; - <decades> @linkml:String * ; - <juvenile_or_adult> @linkml:String ? - ) ; - rdf:type [ <Onset> ] - ) -} - -core:Publication CLOSED { - ( $core:Publication_tes ( core:id @linkml:String ? ; - core:title @linkml:String ? ; - core:abstract @linkml:String ? ; - core:combined_text @linkml:String ? ; - core:full_text @linkml:String ? - ) ; - rdf:type [ core:Publication ] ? - ) -} - -core:RelationshipType CLOSED { - ( $core:RelationshipType_tes ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ core:RelationshipType ] - ) -} - -<Symptom> CLOSED { - ( $<Symptom_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? ; - <characteristic> @linkml:String ? ; - <affects> @linkml:String ? ; - <severity> @linkml:String ? ; - <onset_of_symptom> @<Onset> ? - ) ; - rdf:type [ <Symptom> ] - ) -} - -core:TextWithTriples CLOSED { - ( $core:TextWithTriples_tes ( core:publication @core:Publication ? ; - core:triples @core:Triple * - ) ; - rdf:type [ core:TextWithTriples ] ? - ) -} - -core:Triple { - ( $core:Triple_tes ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - core:subject @core:NamedEntity ? ; - core:predicate @core:RelationshipType ? ; - core:object @core:NamedEntity ? ; - core:qualifier @linkml:String ? ; - core:subject_qualifier @core:NamedEntity ? ; - core:object_qualifier @core:NamedEntity ? - ) ; - rdf:type [ core:Triple ] ? - ) -} - - diff --git a/projects/mendelian_disease/sqlschema/mendelian_disease.sql b/projects/mendelian_disease/sqlschema/mendelian_disease.sql deleted file mode 100644 index 260e51602..000000000 --- a/projects/mendelian_disease/sqlschema/mendelian_disease.sql +++ /dev/null @@ -1,109 +0,0 @@ - - -CREATE TABLE "AnnotatorResult" ( - subject_text TEXT, - object_id TEXT, - object_text TEXT, - PRIMARY KEY (subject_text, object_id, object_text) -); - -CREATE TABLE "ExtractionResult" ( - input_id TEXT, - input_title TEXT, - input_text TEXT, - raw_completion_output TEXT, - prompt TEXT, - extracted_object TEXT, - named_entities TEXT, - PRIMARY KEY (input_id, input_title, input_text, raw_completion_output, prompt, extracted_object, named_entities) -); - -CREATE TABLE "Inheritance" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Onset" ( - id TEXT NOT NULL, - label TEXT, - years_old TEXT, - juvenile_or_adult TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Publication" ( - id TEXT, - title TEXT, - abstract TEXT, - combined_text TEXT, - full_text TEXT, - PRIMARY KEY (id, title, abstract, combined_text, full_text) -); - -CREATE TABLE "RelationshipType" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "TextWithTriples" ( - publication TEXT, - triples TEXT, - PRIMARY KEY (publication, triples) -); - -CREATE TABLE "MendelianDisease" ( - id TEXT NOT NULL, - label TEXT, - name TEXT, - description TEXT, - inheritance TEXT, - disease_onsets TEXT, - publications TEXT, - PRIMARY KEY (id), - FOREIGN KEY(inheritance) REFERENCES "Inheritance" (id) -); - -CREATE TABLE "Onset_decades" ( - backref_id TEXT, - decades TEXT, - PRIMARY KEY (backref_id, decades), - FOREIGN KEY(backref_id) REFERENCES "Onset" (id) -); - -CREATE TABLE "DiseaseCategory" ( - id TEXT NOT NULL, - label TEXT, - "MendelianDisease_id" TEXT, - PRIMARY KEY (id), - FOREIGN KEY("MendelianDisease_id") REFERENCES "MendelianDisease" (id) -); - -CREATE TABLE "Gene" ( - id TEXT NOT NULL, - label TEXT, - "MendelianDisease_id" TEXT, - PRIMARY KEY (id), - FOREIGN KEY("MendelianDisease_id") REFERENCES "MendelianDisease" (id) -); - -CREATE TABLE "Symptom" ( - id TEXT NOT NULL, - label TEXT, - characteristic TEXT, - affects TEXT, - severity TEXT, - onset_of_symptom TEXT, - "MendelianDisease_id" TEXT, - PRIMARY KEY (id), - FOREIGN KEY(onset_of_symptom) REFERENCES "Onset" (id), - FOREIGN KEY("MendelianDisease_id") REFERENCES "MendelianDisease" (id) -); - -CREATE TABLE "MendelianDisease_synonyms" ( - backref_id TEXT, - synonyms TEXT, - PRIMARY KEY (backref_id, synonyms), - FOREIGN KEY(backref_id) REFERENCES "MendelianDisease" (id) -); diff --git a/projects/metabolic_process/docs/AnnotatorResult.md b/projects/metabolic_process/docs/AnnotatorResult.md deleted file mode 100644 index 8d5a8c586..000000000 --- a/projects/metabolic_process/docs/AnnotatorResult.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Class: AnnotatorResult - - - - -URI: [bp:AnnotatorResult](http://w3id.org/ontogpt/metabolic-process-templateAnnotatorResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F])](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F]) - -## Attributes - - -### Own - - * [➞subject_text](annotatorResult__subject_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_id](annotatorResult__object_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_text](annotatorResult__object_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) diff --git a/projects/metabolic_process/docs/Any.md b/projects/metabolic_process/docs/Any.md deleted file mode 100644 index e5c3dde82..000000000 --- a/projects/metabolic_process/docs/Any.md +++ /dev/null @@ -1,25 +0,0 @@ - -# Class: Any - - - - -URI: [bp:Any](http://w3id.org/ontogpt/metabolic-process-templateAny) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult])](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult]) - -## Referenced by Class - - * **None** *[➞extracted_object](extractionResult__extracted_object.md)* <sub>0..1</sub> **[Any](Any.md)** - * **None** *[➞named_entities](extractionResult__named_entities.md)* <sub>0..\*</sub> **[Any](Any.md)** - -## Attributes - - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | linkml:Any | - diff --git a/projects/metabolic_process/docs/ChemicalEntity.md b/projects/metabolic_process/docs/ChemicalEntity.md deleted file mode 100644 index a8f5e0622..000000000 --- a/projects/metabolic_process/docs/ChemicalEntity.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: ChemicalEntity - - - - -URI: [bp:ChemicalEntity](http://w3id.org/ontogpt/metabolic-process-templateChemicalEntity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[MetabolicProcess]-%20inputs%200..*>[ChemicalEntity|id(i):string;label(i):string%20%3F],[MetabolicProcess]-%20outputs%200..*>[ChemicalEntity],[NamedEntity]^-[ChemicalEntity],[MetabolicProcess])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[MetabolicProcess]-%20inputs%200..*>[ChemicalEntity|id(i):string;label(i):string%20%3F],[MetabolicProcess]-%20outputs%200..*>[ChemicalEntity],[NamedEntity]^-[ChemicalEntity],[MetabolicProcess]) - -## Identifier prefixes - - * CHEBI - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞inputs](metabolicProcess__inputs.md)* <sub>0..\*</sub> **[ChemicalEntity](ChemicalEntity.md)** - * **None** *[➞outputs](metabolicProcess__outputs.md)* <sub>0..\*</sub> **[ChemicalEntity](ChemicalEntity.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/metabolic_process/docs/CompoundExpression.md b/projects/metabolic_process/docs/CompoundExpression.md deleted file mode 100644 index b0af5e420..000000000 --- a/projects/metabolic_process/docs/CompoundExpression.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: CompoundExpression - - - - -URI: [bp:CompoundExpression](http://w3id.org/ontogpt/metabolic-process-templateCompoundExpression) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[CompoundExpression]^-[Triple])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[CompoundExpression]^-[Triple]) - -## Children - - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - -## Referenced by Class - - -## Attributes - diff --git a/projects/metabolic_process/docs/ExtractionResult.md b/projects/metabolic_process/docs/ExtractionResult.md deleted file mode 100644 index 71ffeafef..000000000 --- a/projects/metabolic_process/docs/ExtractionResult.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Class: ExtractionResult - - -A result of extracting knowledge on text - -URI: [bp:ExtractionResult](http://w3id.org/ontogpt/metabolic-process-templateExtractionResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any])](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any]) - -## Attributes - - -### Own - - * [➞input_id](extractionResult__input_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_title](extractionResult__input_title.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_text](extractionResult__input_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞prompt](extractionResult__prompt.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞extracted_object](extractionResult__extracted_object.md) <sub>0..1</sub> - * Description: The complex objects extracted from the text - * Range: [Any](Any.md) - * [➞named_entities](extractionResult__named_entities.md) <sub>0..\*</sub> - * Description: Named entities extracted from the text - * Range: [Any](Any.md) diff --git a/projects/metabolic_process/docs/MetabolicProcess.md b/projects/metabolic_process/docs/MetabolicProcess.md deleted file mode 100644 index abcdacc70..000000000 --- a/projects/metabolic_process/docs/MetabolicProcess.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Class: MetabolicProcess - - - - -URI: [bp:MetabolicProcess](http://w3id.org/ontogpt/metabolic-process-templateMetabolicProcess) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[MetabolicProcessCategory],[ChemicalEntity]<outputs%200..*-%20[MetabolicProcess|label:string%20%3F;description:string%20%3F;synonyms:string%20*;id(i):string],[ChemicalEntity]<inputs%200..*-%20[MetabolicProcess],[MetabolicProcessCategory]<category%200..1-%20[MetabolicProcess],[MetabolicProcessCategory]<subclass_of%200..*-%20[MetabolicProcess],[NamedEntity]^-[MetabolicProcess],[ChemicalEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[MetabolicProcessCategory],[ChemicalEntity]<outputs%200..*-%20[MetabolicProcess|label:string%20%3F;description:string%20%3F;synonyms:string%20*;id(i):string],[ChemicalEntity]<inputs%200..*-%20[MetabolicProcess],[MetabolicProcessCategory]<category%200..1-%20[MetabolicProcess],[MetabolicProcessCategory]<subclass_of%200..*-%20[MetabolicProcess],[NamedEntity]^-[MetabolicProcess],[ChemicalEntity]) - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Attributes - - -### Own - - * [➞label](metabolicProcess__label.md) <sub>0..1</sub> - * Description: the name of the metabolic process - * Range: [String](types/String.md) - * [➞description](metabolicProcess__description.md) <sub>0..1</sub> - * Description: a textual description of the metabolic process - * Range: [String](types/String.md) - * [➞synonyms](metabolicProcess__synonyms.md) <sub>0..\*</sub> - * Description: alternative names of the metabolic process - * Range: [String](types/String.md) - * [➞subclass_of](metabolicProcess__subclass_of.md) <sub>0..\*</sub> - * Description: a semicolon separated list of broader metabolic processes which this is a subclass of - * Range: [MetabolicProcessCategory](MetabolicProcessCategory.md) - * [➞category](metabolicProcess__category.md) <sub>0..1</sub> - * Description: the category of metabolic process, e.g metabolic process, catabolic process, biosynthetic process, small molecule sensor activity - * Range: [MetabolicProcessCategory](MetabolicProcessCategory.md) - * [➞inputs](metabolicProcess__inputs.md) <sub>0..\*</sub> - * Description: the inputs of the metabolic process - * Range: [ChemicalEntity](ChemicalEntity.md) - * [➞outputs](metabolicProcess__outputs.md) <sub>0..\*</sub> - * Description: the outputs of the metabolic process - * Range: [ChemicalEntity](ChemicalEntity.md) - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) diff --git a/projects/metabolic_process/docs/MetabolicProcessCategory.md b/projects/metabolic_process/docs/MetabolicProcessCategory.md deleted file mode 100644 index 12c2b0a05..000000000 --- a/projects/metabolic_process/docs/MetabolicProcessCategory.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: MetabolicProcessCategory - - - - -URI: [bp:MetabolicProcessCategory](http://w3id.org/ontogpt/metabolic-process-templateMetabolicProcessCategory) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[MetabolicProcess]-%20category%200..1>[MetabolicProcessCategory|id(i):string;label(i):string%20%3F],[MetabolicProcess]-%20subclass_of%200..*>[MetabolicProcessCategory],[NamedEntity]^-[MetabolicProcessCategory],[MetabolicProcess])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[MetabolicProcess]-%20category%200..1>[MetabolicProcessCategory|id(i):string;label(i):string%20%3F],[MetabolicProcess]-%20subclass_of%200..*>[MetabolicProcessCategory],[NamedEntity]^-[MetabolicProcessCategory],[MetabolicProcess]) - -## Identifier prefixes - - * GO - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞category](metabolicProcess__category.md)* <sub>0..1</sub> **[MetabolicProcessCategory](MetabolicProcessCategory.md)** - * **None** *[➞subclass_of](metabolicProcess__subclass_of.md)* <sub>0..\*</sub> **[MetabolicProcessCategory](MetabolicProcessCategory.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/metabolic_process/docs/NamedEntity.md b/projects/metabolic_process/docs/NamedEntity.md deleted file mode 100644 index 331cb7183..000000000 --- a/projects/metabolic_process/docs/NamedEntity.md +++ /dev/null @@ -1,36 +0,0 @@ - -# Class: NamedEntity - - - - -URI: [bp:NamedEntity](http://w3id.org/ontogpt/metabolic-process-templateNamedEntity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[MetabolicProcessCategory],[NamedEntity]^-[MetabolicProcess],[NamedEntity]^-[ChemicalEntity],[Triple],[MetabolicProcessCategory],[MetabolicProcess],[ChemicalEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[MetabolicProcessCategory],[NamedEntity]^-[MetabolicProcess],[NamedEntity]^-[ChemicalEntity],[Triple],[MetabolicProcessCategory],[MetabolicProcess],[ChemicalEntity]) - -## Children - - * [ChemicalEntity](ChemicalEntity.md) - * [MetabolicProcess](MetabolicProcess.md) - * [MetabolicProcessCategory](MetabolicProcessCategory.md) - * [RelationshipType](RelationshipType.md) - -## Referenced by Class - - * **None** *[➞object](triple__object.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞object_qualifier](triple__object_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject](triple__subject.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject_qualifier](triple__subject_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - -## Attributes - - -### Own - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/metabolic_process/docs/NullDataOptions.md b/projects/metabolic_process/docs/NullDataOptions.md deleted file mode 100644 index 3edea6d1c..000000000 --- a/projects/metabolic_process/docs/NullDataOptions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Enum: NullDataOptions - - - - -URI: [bp:NullDataOptions](http://w3id.org/ontogpt/metabolic-process-templateNullDataOptions) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | -| UNSPECIFIED_METHOD_OF_ADMINISTRATION | | NCIT:C149701 | | -| NOT_APPLICABLE | | NCIT:C18902 | {'aliases': ['not applicable', 'N/A']} | -| NOT_MENTIONED | | | | - diff --git a/projects/metabolic_process/docs/Publication.md b/projects/metabolic_process/docs/Publication.md deleted file mode 100644 index 76e1d2fb7..000000000 --- a/projects/metabolic_process/docs/Publication.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Publication - - - - -URI: [bp:Publication](http://w3id.org/ontogpt/metabolic-process-templatePublication) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples])](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples]) - -## Referenced by Class - - * **None** *[➞publication](textWithTriples__publication.md)* <sub>0..1</sub> **[Publication](Publication.md)** - -## Attributes - - -### Own - - * [➞id](publication__id.md) <sub>0..1</sub> - * Description: The publication identifier - * Range: [String](types/String.md) - * [➞title](publication__title.md) <sub>0..1</sub> - * Description: The title of the publication - * Range: [String](types/String.md) - * [➞abstract](publication__abstract.md) <sub>0..1</sub> - * Description: The abstract of the publication - * Range: [String](types/String.md) - * [➞combined_text](publication__combined_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞full_text](publication__full_text.md) <sub>0..1</sub> - * Description: The full text of the publication - * Range: [String](types/String.md) diff --git a/projects/metabolic_process/docs/RelationshipType.md b/projects/metabolic_process/docs/RelationshipType.md deleted file mode 100644 index 36a6d4172..000000000 --- a/projects/metabolic_process/docs/RelationshipType.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: RelationshipType - - - - -URI: [bp:RelationshipType](http://w3id.org/ontogpt/metabolic-process-templateRelationshipType) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity]) - -## Identifier prefixes - - * RO - * biolink - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞predicate](triple__predicate.md)* <sub>0..1</sub> **[RelationshipType](RelationshipType.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/metabolic_process/docs/TextWithTriples.md b/projects/metabolic_process/docs/TextWithTriples.md deleted file mode 100644 index e6131d139..000000000 --- a/projects/metabolic_process/docs/TextWithTriples.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: TextWithTriples - - - - -URI: [bp:TextWithTriples](http://w3id.org/ontogpt/metabolic-process-templateTextWithTriples) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication]) - -## Attributes - - -### Own - - * [➞publication](textWithTriples__publication.md) <sub>0..1</sub> - * Range: [Publication](Publication.md) - * [➞triples](textWithTriples__triples.md) <sub>0..\*</sub> - * Range: [Triple](Triple.md) diff --git a/projects/metabolic_process/docs/Triple.md b/projects/metabolic_process/docs/Triple.md deleted file mode 100644 index 157ba54c5..000000000 --- a/projects/metabolic_process/docs/Triple.md +++ /dev/null @@ -1,39 +0,0 @@ - -# Class: Triple - - -Abstract parent for Relation Extraction tasks - -URI: [bp:Triple](http://w3id.org/ontogpt/metabolic-process-templateTriple) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞triples](textWithTriples__triples.md)* <sub>0..\*</sub> **[Triple](Triple.md)** - -## Attributes - - -### Own - - * [➞subject](triple__subject.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞predicate](triple__predicate.md) <sub>0..1</sub> - * Range: [RelationshipType](RelationshipType.md) - * [➞object](triple__object.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞qualifier](triple__qualifier.md) <sub>0..1</sub> - * Description: A qualifier for the statements, e.g. "NOT" for negation - * Range: [String](types/String.md) - * [➞subject_qualifier](triple__subject_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - * Range: [NamedEntity](NamedEntity.md) - * [➞object_qualifier](triple__object_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * Range: [NamedEntity](NamedEntity.md) diff --git a/projects/metabolic_process/docs/annotatorResult__object_id.md b/projects/metabolic_process/docs/annotatorResult__object_id.md deleted file mode 100644 index 0ed3b4a01..000000000 --- a/projects/metabolic_process/docs/annotatorResult__object_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_id - - - - -URI: [bp:annotatorResult__object_id](http://w3id.org/ontogpt/metabolic-process-templateannotatorResult__object_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/metabolic_process/docs/annotatorResult__object_text.md b/projects/metabolic_process/docs/annotatorResult__object_text.md deleted file mode 100644 index 077cd93fc..000000000 --- a/projects/metabolic_process/docs/annotatorResult__object_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_text - - - - -URI: [bp:annotatorResult__object_text](http://w3id.org/ontogpt/metabolic-process-templateannotatorResult__object_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/metabolic_process/docs/annotatorResult__subject_text.md b/projects/metabolic_process/docs/annotatorResult__subject_text.md deleted file mode 100644 index 8f258d90c..000000000 --- a/projects/metabolic_process/docs/annotatorResult__subject_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_text - - - - -URI: [bp:annotatorResult__subject_text](http://w3id.org/ontogpt/metabolic-process-templateannotatorResult__subject_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/metabolic_process/docs/extractionResult__extracted_object.md b/projects/metabolic_process/docs/extractionResult__extracted_object.md deleted file mode 100644 index 054936032..000000000 --- a/projects/metabolic_process/docs/extractionResult__extracted_object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: extracted_object - - -The complex objects extracted from the text - -URI: [bp:extractionResult__extracted_object](http://w3id.org/ontogpt/metabolic-process-templateextractionResult__extracted_object) - - -## Domain and Range - -None → <sub>0..1</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/metabolic_process/docs/extractionResult__input_id.md b/projects/metabolic_process/docs/extractionResult__input_id.md deleted file mode 100644 index ed6f1bc59..000000000 --- a/projects/metabolic_process/docs/extractionResult__input_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_id - - - - -URI: [bp:extractionResult__input_id](http://w3id.org/ontogpt/metabolic-process-templateextractionResult__input_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/metabolic_process/docs/extractionResult__input_text.md b/projects/metabolic_process/docs/extractionResult__input_text.md deleted file mode 100644 index 8f76b8a42..000000000 --- a/projects/metabolic_process/docs/extractionResult__input_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_text - - - - -URI: [bp:extractionResult__input_text](http://w3id.org/ontogpt/metabolic-process-templateextractionResult__input_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/metabolic_process/docs/extractionResult__input_title.md b/projects/metabolic_process/docs/extractionResult__input_title.md deleted file mode 100644 index bc462f4a2..000000000 --- a/projects/metabolic_process/docs/extractionResult__input_title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_title - - - - -URI: [bp:extractionResult__input_title](http://w3id.org/ontogpt/metabolic-process-templateextractionResult__input_title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/metabolic_process/docs/extractionResult__named_entities.md b/projects/metabolic_process/docs/extractionResult__named_entities.md deleted file mode 100644 index 2af9f84a2..000000000 --- a/projects/metabolic_process/docs/extractionResult__named_entities.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: named_entities - - -Named entities extracted from the text - -URI: [bp:extractionResult__named_entities](http://w3id.org/ontogpt/metabolic-process-templateextractionResult__named_entities) - - -## Domain and Range - -None → <sub>0..\*</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/metabolic_process/docs/extractionResult__prompt.md b/projects/metabolic_process/docs/extractionResult__prompt.md deleted file mode 100644 index 815243606..000000000 --- a/projects/metabolic_process/docs/extractionResult__prompt.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: prompt - - - - -URI: [bp:extractionResult__prompt](http://w3id.org/ontogpt/metabolic-process-templateextractionResult__prompt) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/metabolic_process/docs/extractionResult__raw_completion_output.md b/projects/metabolic_process/docs/extractionResult__raw_completion_output.md deleted file mode 100644 index 31fd1e0d9..000000000 --- a/projects/metabolic_process/docs/extractionResult__raw_completion_output.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: raw_completion_output - - - - -URI: [bp:extractionResult__raw_completion_output](http://w3id.org/ontogpt/metabolic-process-templateextractionResult__raw_completion_output) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/metabolic_process/docs/metabolicProcess__category.md b/projects/metabolic_process/docs/metabolicProcess__category.md deleted file mode 100644 index f33c38406..000000000 --- a/projects/metabolic_process/docs/metabolicProcess__category.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: category - - -the category of metabolic process, e.g metabolic process, catabolic process, biosynthetic process, small molecule sensor activity - -URI: [bp:metabolicProcess__category](http://w3id.org/ontogpt/metabolic-process-templatemetabolicProcess__category) - - -## Domain and Range - -None → <sub>0..1</sub> [MetabolicProcessCategory](MetabolicProcessCategory.md) - -## Parents - - -## Children - - -## Used by - - * [MetabolicProcess](MetabolicProcess.md) diff --git a/projects/metabolic_process/docs/metabolicProcess__description.md b/projects/metabolic_process/docs/metabolicProcess__description.md deleted file mode 100644 index cb5beec0b..000000000 --- a/projects/metabolic_process/docs/metabolicProcess__description.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: description - - -a textual description of the metabolic process - -URI: [bp:metabolicProcess__description](http://w3id.org/ontogpt/metabolic-process-templatemetabolicProcess__description) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [MetabolicProcess](MetabolicProcess.md) diff --git a/projects/metabolic_process/docs/metabolicProcess__inputs.md b/projects/metabolic_process/docs/metabolicProcess__inputs.md deleted file mode 100644 index 83efb9168..000000000 --- a/projects/metabolic_process/docs/metabolicProcess__inputs.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: inputs - - -the inputs of the metabolic process - -URI: [bp:metabolicProcess__inputs](http://w3id.org/ontogpt/metabolic-process-templatemetabolicProcess__inputs) - - -## Domain and Range - -None → <sub>0..\*</sub> [ChemicalEntity](ChemicalEntity.md) - -## Parents - - -## Children - - -## Used by - - * [MetabolicProcess](MetabolicProcess.md) diff --git a/projects/metabolic_process/docs/metabolicProcess__label.md b/projects/metabolic_process/docs/metabolicProcess__label.md deleted file mode 100644 index 69ec93d09..000000000 --- a/projects/metabolic_process/docs/metabolicProcess__label.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: label - - -the name of the metabolic process - -URI: [bp:metabolicProcess__label](http://w3id.org/ontogpt/metabolic-process-templatemetabolicProcess__label) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [MetabolicProcess](MetabolicProcess.md) diff --git a/projects/metabolic_process/docs/metabolicProcess__outputs.md b/projects/metabolic_process/docs/metabolicProcess__outputs.md deleted file mode 100644 index 8fd1808fe..000000000 --- a/projects/metabolic_process/docs/metabolicProcess__outputs.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: outputs - - -the outputs of the metabolic process - -URI: [bp:metabolicProcess__outputs](http://w3id.org/ontogpt/metabolic-process-templatemetabolicProcess__outputs) - - -## Domain and Range - -None → <sub>0..\*</sub> [ChemicalEntity](ChemicalEntity.md) - -## Parents - - -## Children - - -## Used by - - * [MetabolicProcess](MetabolicProcess.md) diff --git a/projects/metabolic_process/docs/metabolicProcess__subclass_of.md b/projects/metabolic_process/docs/metabolicProcess__subclass_of.md deleted file mode 100644 index 3995a93e5..000000000 --- a/projects/metabolic_process/docs/metabolicProcess__subclass_of.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subclass_of - - -a semicolon separated list of broader metabolic processes which this is a subclass of - -URI: [bp:metabolicProcess__subclass_of](http://w3id.org/ontogpt/metabolic-process-templatemetabolicProcess__subclass_of) - - -## Domain and Range - -None → <sub>0..\*</sub> [MetabolicProcessCategory](MetabolicProcessCategory.md) - -## Parents - - -## Children - - -## Used by - - * [MetabolicProcess](MetabolicProcess.md) diff --git a/projects/metabolic_process/docs/metabolicProcess__synonyms.md b/projects/metabolic_process/docs/metabolicProcess__synonyms.md deleted file mode 100644 index bd9819ea2..000000000 --- a/projects/metabolic_process/docs/metabolicProcess__synonyms.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: synonyms - - -alternative names of the metabolic process - -URI: [bp:metabolicProcess__synonyms](http://w3id.org/ontogpt/metabolic-process-templatemetabolicProcess__synonyms) - - -## Domain and Range - -None → <sub>0..\*</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [MetabolicProcess](MetabolicProcess.md) diff --git a/projects/metabolic_process/docs/metabolic_process.md b/projects/metabolic_process/docs/metabolic_process.md deleted file mode 100644 index 2244dfb4c..000000000 --- a/projects/metabolic_process/docs/metabolic_process.md +++ /dev/null @@ -1,113 +0,0 @@ - -# metabolic-process-template - - -**metamodel version:** 1.7.0 - -**version:** None - - -A template for GO-CAMs - - -### Classes - - * [AnnotatorResult](AnnotatorResult.md) - * [Any](Any.md) - * [CompoundExpression](CompoundExpression.md) - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - * [ExtractionResult](ExtractionResult.md) - A result of extracting knowledge on text - * [NamedEntity](NamedEntity.md) - * [ChemicalEntity](ChemicalEntity.md) - * [MetabolicProcess](MetabolicProcess.md) - * [MetabolicProcessCategory](MetabolicProcessCategory.md) - * [RelationshipType](RelationshipType.md) - * [Publication](Publication.md) - * [TextWithTriples](TextWithTriples.md) - -### Mixins - - -### Slots - - * [➞object_id](annotatorResult__object_id.md) - * [➞object_text](annotatorResult__object_text.md) - * [➞subject_text](annotatorResult__subject_text.md) - * [➞extracted_object](extractionResult__extracted_object.md) - The complex objects extracted from the text - * [➞input_id](extractionResult__input_id.md) - * [➞input_text](extractionResult__input_text.md) - * [➞input_title](extractionResult__input_title.md) - * [➞named_entities](extractionResult__named_entities.md) - Named entities extracted from the text - * [➞prompt](extractionResult__prompt.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) - * [➞category](metabolicProcess__category.md) - the category of metabolic process, e.g metabolic process, catabolic process, biosynthetic process, small molecule sensor activity - * [➞description](metabolicProcess__description.md) - a textual description of the metabolic process - * [➞inputs](metabolicProcess__inputs.md) - the inputs of the metabolic process - * [➞label](metabolicProcess__label.md) - the name of the metabolic process - * [➞outputs](metabolicProcess__outputs.md) - the outputs of the metabolic process - * [➞subclass_of](metabolicProcess__subclass_of.md) - a semicolon separated list of broader metabolic processes which this is a subclass of - * [➞synonyms](metabolicProcess__synonyms.md) - alternative names of the metabolic process - * [➞id](namedEntity__id.md) - A unique identifier for the named entity - * [➞label](namedEntity__label.md) - The label (name) of the named thing - * [➞abstract](publication__abstract.md) - The abstract of the publication - * [➞combined_text](publication__combined_text.md) - * [➞full_text](publication__full_text.md) - The full text of the publication - * [➞id](publication__id.md) - The publication identifier - * [➞title](publication__title.md) - The title of the publication - * [➞publication](textWithTriples__publication.md) - * [➞triples](textWithTriples__triples.md) - * [➞object](triple__object.md) - * [➞object_qualifier](triple__object_qualifier.md) - An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * [➞predicate](triple__predicate.md) - * [➞qualifier](triple__qualifier.md) - A qualifier for the statements, e.g. "NOT" for negation - * [➞subject](triple__subject.md) - * [➞subject_qualifier](triple__subject_qualifier.md) - An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -### Enums - - * [NullDataOptions](NullDataOptions.md) - -### Subsets - - -### Types - - -#### Built in - - * **Bool** - * **Curie** - * **Decimal** - * **ElementIdentifier** - * **NCName** - * **NodeIdentifier** - * **URI** - * **URIorCURIE** - * **XSDDate** - * **XSDDateTime** - * **XSDTime** - * **float** - * **int** - * **str** - -#### Defined - - * [Boolean](types/Boolean.md) (**Bool**) - A binary (true or false) value - * [Curie](types/Curie.md) (**Curie**) - a compact URI - * [Date](types/Date.md) (**XSDDate**) - a date (year, month and day) in an idealized calendar - * [DateOrDatetime](types/DateOrDatetime.md) (**str**) - Either a date or a datetime - * [Datetime](types/Datetime.md) (**XSDDateTime**) - The combination of a date and time - * [Decimal](types/Decimal.md) (**Decimal**) - A real number with arbitrary precision that conforms to the xsd:decimal specification - * [Double](types/Double.md) (**float**) - A real number that conforms to the xsd:double specification - * [Float](types/Float.md) (**float**) - A real number that conforms to the xsd:float specification - * [Integer](types/Integer.md) (**int**) - An integer - * [Jsonpath](types/Jsonpath.md) (**str**) - A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - * [Jsonpointer](types/Jsonpointer.md) (**str**) - A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - * [Ncname](types/Ncname.md) (**NCName**) - Prefix part of CURIE - * [Nodeidentifier](types/Nodeidentifier.md) (**NodeIdentifier**) - A URI, CURIE or BNODE that represents a node in a model. - * [Objectidentifier](types/Objectidentifier.md) (**ElementIdentifier**) - A URI or CURIE that represents an object in the model. - * [Sparqlpath](types/Sparqlpath.md) (**str**) - A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - * [String](types/String.md) (**str**) - A character string - * [Time](types/Time.md) (**XSDTime**) - A time object represents a (local) time of day, independent of any particular day - * [Uri](types/Uri.md) (**URI**) - a complete URI - * [Uriorcurie](types/Uriorcurie.md) (**URIorCURIE**) - a URI or a CURIE diff --git a/projects/metabolic_process/docs/namedEntity__id.md b/projects/metabolic_process/docs/namedEntity__id.md deleted file mode 100644 index 7d07dc170..000000000 --- a/projects/metabolic_process/docs/namedEntity__id.md +++ /dev/null @@ -1,33 +0,0 @@ - -# Slot: id - - -A unique identifier for the named entity - -URI: [bp:namedEntity__id](http://w3id.org/ontogpt/metabolic-process-templatenamedEntity__id) - - -## Domain and Range - -None → <sub>1..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ChemicalEntity](ChemicalEntity.md) - * [MetabolicProcess](MetabolicProcess.md) - * [MetabolicProcessCategory](MetabolicProcessCategory.md) - * [NamedEntity](NamedEntity.md) - * [RelationshipType](RelationshipType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | this is populated during the grounding and normalization step | - diff --git a/projects/metabolic_process/docs/namedEntity__label.md b/projects/metabolic_process/docs/namedEntity__label.md deleted file mode 100644 index 3921b7438..000000000 --- a/projects/metabolic_process/docs/namedEntity__label.md +++ /dev/null @@ -1,33 +0,0 @@ - -# Slot: label - - -The label (name) of the named thing - -URI: [bp:namedEntity__label](http://w3id.org/ontogpt/metabolic-process-templatenamedEntity__label) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ChemicalEntity](ChemicalEntity.md) - * [MetabolicProcessCategory](MetabolicProcessCategory.md) - * [NamedEntity](NamedEntity.md) - * [RelationshipType](RelationshipType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Aliases:** | | name | -| **Mappings:** | | rdfs:label | - diff --git a/projects/metabolic_process/docs/publication__abstract.md b/projects/metabolic_process/docs/publication__abstract.md deleted file mode 100644 index d95c3bb6e..000000000 --- a/projects/metabolic_process/docs/publication__abstract.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: abstract - - -The abstract of the publication - -URI: [bp:publication__abstract](http://w3id.org/ontogpt/metabolic-process-templatepublication__abstract) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/metabolic_process/docs/publication__combined_text.md b/projects/metabolic_process/docs/publication__combined_text.md deleted file mode 100644 index cea215db8..000000000 --- a/projects/metabolic_process/docs/publication__combined_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: combined_text - - - - -URI: [bp:publication__combined_text](http://w3id.org/ontogpt/metabolic-process-templatepublication__combined_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/metabolic_process/docs/publication__full_text.md b/projects/metabolic_process/docs/publication__full_text.md deleted file mode 100644 index c5baca387..000000000 --- a/projects/metabolic_process/docs/publication__full_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: full_text - - -The full text of the publication - -URI: [bp:publication__full_text](http://w3id.org/ontogpt/metabolic-process-templatepublication__full_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/metabolic_process/docs/publication__id.md b/projects/metabolic_process/docs/publication__id.md deleted file mode 100644 index 41e717748..000000000 --- a/projects/metabolic_process/docs/publication__id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: id - - -The publication identifier - -URI: [bp:publication__id](http://w3id.org/ontogpt/metabolic-process-templatepublication__id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/metabolic_process/docs/publication__title.md b/projects/metabolic_process/docs/publication__title.md deleted file mode 100644 index 3f1cac98a..000000000 --- a/projects/metabolic_process/docs/publication__title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: title - - -The title of the publication - -URI: [bp:publication__title](http://w3id.org/ontogpt/metabolic-process-templatepublication__title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/metabolic_process/docs/textWithTriples__publication.md b/projects/metabolic_process/docs/textWithTriples__publication.md deleted file mode 100644 index f488281e7..000000000 --- a/projects/metabolic_process/docs/textWithTriples__publication.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: publication - - - - -URI: [bp:textWithTriples__publication](http://w3id.org/ontogpt/metabolic-process-templatetextWithTriples__publication) - - -## Domain and Range - -None → <sub>0..1</sub> [Publication](Publication.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/metabolic_process/docs/textWithTriples__triples.md b/projects/metabolic_process/docs/textWithTriples__triples.md deleted file mode 100644 index 3be3a12b5..000000000 --- a/projects/metabolic_process/docs/textWithTriples__triples.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: triples - - - - -URI: [bp:textWithTriples__triples](http://w3id.org/ontogpt/metabolic-process-templatetextWithTriples__triples) - - -## Domain and Range - -None → <sub>0..\*</sub> [Triple](Triple.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/metabolic_process/docs/triple__object.md b/projects/metabolic_process/docs/triple__object.md deleted file mode 100644 index 5cb142a08..000000000 --- a/projects/metabolic_process/docs/triple__object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object - - - - -URI: [bp:triple__object](http://w3id.org/ontogpt/metabolic-process-templatetriple__object) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/metabolic_process/docs/triple__object_qualifier.md b/projects/metabolic_process/docs/triple__object_qualifier.md deleted file mode 100644 index 17474aa33..000000000 --- a/projects/metabolic_process/docs/triple__object_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_qualifier - - -An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - -URI: [bp:triple__object_qualifier](http://w3id.org/ontogpt/metabolic-process-templatetriple__object_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/metabolic_process/docs/triple__predicate.md b/projects/metabolic_process/docs/triple__predicate.md deleted file mode 100644 index 65d5544da..000000000 --- a/projects/metabolic_process/docs/triple__predicate.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: predicate - - - - -URI: [bp:triple__predicate](http://w3id.org/ontogpt/metabolic-process-templatetriple__predicate) - - -## Domain and Range - -None → <sub>0..1</sub> [RelationshipType](RelationshipType.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/metabolic_process/docs/triple__qualifier.md b/projects/metabolic_process/docs/triple__qualifier.md deleted file mode 100644 index f1a43c11a..000000000 --- a/projects/metabolic_process/docs/triple__qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: qualifier - - -A qualifier for the statements, e.g. "NOT" for negation - -URI: [bp:triple__qualifier](http://w3id.org/ontogpt/metabolic-process-templatetriple__qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/metabolic_process/docs/triple__subject.md b/projects/metabolic_process/docs/triple__subject.md deleted file mode 100644 index 28e17194c..000000000 --- a/projects/metabolic_process/docs/triple__subject.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject - - - - -URI: [bp:triple__subject](http://w3id.org/ontogpt/metabolic-process-templatetriple__subject) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/metabolic_process/docs/triple__subject_qualifier.md b/projects/metabolic_process/docs/triple__subject_qualifier.md deleted file mode 100644 index 3880349e6..000000000 --- a/projects/metabolic_process/docs/triple__subject_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_qualifier - - -An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -URI: [bp:triple__subject_qualifier](http://w3id.org/ontogpt/metabolic-process-templatetriple__subject_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/metabolic_process/docs/types/Boolean.md b/projects/metabolic_process/docs/types/Boolean.md deleted file mode 100644 index dc83a9c6e..000000000 --- a/projects/metabolic_process/docs/types/Boolean.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: boolean - - -A binary (true or false) value - -URI: [linkml:Boolean](https://w3id.org/linkml/Boolean) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Bool** | -| Representation | | bool | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Boolean | - diff --git a/projects/metabolic_process/docs/types/Curie.md b/projects/metabolic_process/docs/types/Curie.md deleted file mode 100644 index c1803f93f..000000000 --- a/projects/metabolic_process/docs/types/Curie.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: curie - - -a compact URI - -URI: [linkml:Curie](https://w3id.org/linkml/Curie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Curie** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations this MUST be expanded to a URI | -| | | in non-RDF serializations MAY be serialized as the compact representation | - diff --git a/projects/metabolic_process/docs/types/Date.md b/projects/metabolic_process/docs/types/Date.md deleted file mode 100644 index 06948af97..000000000 --- a/projects/metabolic_process/docs/types/Date.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: date - - -a date (year, month and day) in an idealized calendar - -URI: [linkml:Date](https://w3id.org/linkml/Date) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDate** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Date | - diff --git a/projects/metabolic_process/docs/types/DateOrDatetime.md b/projects/metabolic_process/docs/types/DateOrDatetime.md deleted file mode 100644 index ef983898d..000000000 --- a/projects/metabolic_process/docs/types/DateOrDatetime.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: date_or_datetime - - -Either a date or a datetime - -URI: [linkml:DateOrDatetime](https://w3id.org/linkml/DateOrDatetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/metabolic_process/docs/types/Datetime.md b/projects/metabolic_process/docs/types/Datetime.md deleted file mode 100644 index 9510454a8..000000000 --- a/projects/metabolic_process/docs/types/Datetime.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: datetime - - -The combination of a date and time - -URI: [linkml:Datetime](https://w3id.org/linkml/Datetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDateTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:DateTime | - diff --git a/projects/metabolic_process/docs/types/Decimal.md b/projects/metabolic_process/docs/types/Decimal.md deleted file mode 100644 index a7ba14a5d..000000000 --- a/projects/metabolic_process/docs/types/Decimal.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: decimal - - -A real number with arbitrary precision that conforms to the xsd:decimal specification - -URI: [linkml:Decimal](https://w3id.org/linkml/Decimal) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Decimal** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Broad Mappings:** | | schema:Number | - diff --git a/projects/metabolic_process/docs/types/Double.md b/projects/metabolic_process/docs/types/Double.md deleted file mode 100644 index cfe6d71e2..000000000 --- a/projects/metabolic_process/docs/types/Double.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: double - - -A real number that conforms to the xsd:double specification - -URI: [linkml:Double](https://w3id.org/linkml/Double) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Close Mappings:** | | schema:Float | - diff --git a/projects/metabolic_process/docs/types/Float.md b/projects/metabolic_process/docs/types/Float.md deleted file mode 100644 index 7b303f96f..000000000 --- a/projects/metabolic_process/docs/types/Float.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: float - - -A real number that conforms to the xsd:float specification - -URI: [linkml:Float](https://w3id.org/linkml/Float) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Float | - diff --git a/projects/metabolic_process/docs/types/Integer.md b/projects/metabolic_process/docs/types/Integer.md deleted file mode 100644 index 3cfcc66d9..000000000 --- a/projects/metabolic_process/docs/types/Integer.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: integer - - -An integer - -URI: [linkml:Integer](https://w3id.org/linkml/Integer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **int** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Integer | - diff --git a/projects/metabolic_process/docs/types/Jsonpath.md b/projects/metabolic_process/docs/types/Jsonpath.md deleted file mode 100644 index a03a58e67..000000000 --- a/projects/metabolic_process/docs/types/Jsonpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpath - - -A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpath](https://w3id.org/linkml/Jsonpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/metabolic_process/docs/types/Jsonpointer.md b/projects/metabolic_process/docs/types/Jsonpointer.md deleted file mode 100644 index a0e1ac492..000000000 --- a/projects/metabolic_process/docs/types/Jsonpointer.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpointer - - -A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpointer](https://w3id.org/linkml/Jsonpointer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/metabolic_process/docs/types/Ncname.md b/projects/metabolic_process/docs/types/Ncname.md deleted file mode 100644 index 710b0b04a..000000000 --- a/projects/metabolic_process/docs/types/Ncname.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: ncname - - -Prefix part of CURIE - -URI: [linkml:Ncname](https://w3id.org/linkml/Ncname) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NCName** | -| Representation | | str | diff --git a/projects/metabolic_process/docs/types/Nodeidentifier.md b/projects/metabolic_process/docs/types/Nodeidentifier.md deleted file mode 100644 index f0097cdf4..000000000 --- a/projects/metabolic_process/docs/types/Nodeidentifier.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: nodeidentifier - - -A URI, CURIE or BNODE that represents a node in a model. - -URI: [linkml:Nodeidentifier](https://w3id.org/linkml/Nodeidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NodeIdentifier** | -| Representation | | str | diff --git a/projects/metabolic_process/docs/types/Objectidentifier.md b/projects/metabolic_process/docs/types/Objectidentifier.md deleted file mode 100644 index 454ba6be6..000000000 --- a/projects/metabolic_process/docs/types/Objectidentifier.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: objectidentifier - - -A URI or CURIE that represents an object in the model. - -URI: [linkml:Objectidentifier](https://w3id.org/linkml/Objectidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **ElementIdentifier** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | Used for inheritance and type checking | - diff --git a/projects/metabolic_process/docs/types/Sparqlpath.md b/projects/metabolic_process/docs/types/Sparqlpath.md deleted file mode 100644 index fd99a927e..000000000 --- a/projects/metabolic_process/docs/types/Sparqlpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: sparqlpath - - -A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - -URI: [linkml:Sparqlpath](https://w3id.org/linkml/Sparqlpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/metabolic_process/docs/types/String.md b/projects/metabolic_process/docs/types/String.md deleted file mode 100644 index 6e61d7081..000000000 --- a/projects/metabolic_process/docs/types/String.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: string - - -A character string - -URI: [linkml:String](https://w3id.org/linkml/String) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Text | - diff --git a/projects/metabolic_process/docs/types/Time.md b/projects/metabolic_process/docs/types/Time.md deleted file mode 100644 index 2b8652bcd..000000000 --- a/projects/metabolic_process/docs/types/Time.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: time - - -A time object represents a (local) time of day, independent of any particular day - -URI: [linkml:Time](https://w3id.org/linkml/Time) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Time | - diff --git a/projects/metabolic_process/docs/types/Uri.md b/projects/metabolic_process/docs/types/Uri.md deleted file mode 100644 index 343807a5e..000000000 --- a/projects/metabolic_process/docs/types/Uri.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: uri - - -a complete URI - -URI: [linkml:Uri](https://w3id.org/linkml/Uri) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URI** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node | -| **Close Mappings:** | | schema:URL | - diff --git a/projects/metabolic_process/docs/types/Uriorcurie.md b/projects/metabolic_process/docs/types/Uriorcurie.md deleted file mode 100644 index 2f7b65087..000000000 --- a/projects/metabolic_process/docs/types/Uriorcurie.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: uriorcurie - - -a URI or a CURIE - -URI: [linkml:Uriorcurie](https://w3id.org/linkml/Uriorcurie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URIorCURIE** | -| Representation | | str | diff --git a/projects/metabolic_process/excel/metabolic_process.xlsx b/projects/metabolic_process/excel/metabolic_process.xlsx deleted file mode 100644 index 3e2f8fd73..000000000 Binary files a/projects/metabolic_process/excel/metabolic_process.xlsx and /dev/null differ diff --git a/projects/metabolic_process/graphql/metabolic_process.graphql b/projects/metabolic_process/graphql/metabolic_process.graphql deleted file mode 100644 index 8a719ba33..000000000 --- a/projects/metabolic_process/graphql/metabolic_process.graphql +++ /dev/null @@ -1,87 +0,0 @@ -type AnnotatorResult - { - subjectText: String - objectId: String - objectText: String - } - -type Any - { - } - -type ChemicalEntity - { - id: String! - label: String - } - -interface CompoundExpression - { - } - -type ExtractionResult - { - inputId: String - inputTitle: String - inputText: String - rawCompletionOutput: String - prompt: String - extractedObject: Any - namedEntities: [Any] - } - -type MetabolicProcess - { - id: String! - label: String - description: String - synonyms: [String] - subclassOf: [MetabolicProcessCategory] - category: MetabolicProcessCategory - inputs: [ChemicalEntity] - outputs: [ChemicalEntity] - } - -type MetabolicProcessCategory - { - id: String! - label: String - } - -interface NamedEntity - { - id: String! - label: String - } - -type Publication - { - id: String - title: String - abstract: String - combinedText: String - fullText: String - } - -type RelationshipType - { - id: String! - label: String - } - -type TextWithTriples - { - publication: Publication - triples: [Triple] - } - -interface Triple - { - subject: NamedEntity - predicate: RelationshipType - object: NamedEntity - qualifier: String - subjectQualifier: NamedEntity - objectQualifier: NamedEntity - } - diff --git a/projects/metabolic_process/jsonld/metabolic_process.context.jsonld b/projects/metabolic_process/jsonld/metabolic_process.context.jsonld deleted file mode 100644 index 6f0736682..000000000 --- a/projects/metabolic_process/jsonld/metabolic_process.context.jsonld +++ /dev/null @@ -1,144 +0,0 @@ -{ - "comments": { - "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2023-08-07T10:54:48", - "source": "metabolic_process.yaml" - }, - "@context": { - "CHEBI": "http://example.org/UNKNOWN/CHEBI/", - "GO": "http://example.org/UNKNOWN/GO/", - "RO": { - "@id": "http://purl.obolibrary.org/obo/RO_", - "@prefix": true - }, - "biolink": "http://example.org/UNKNOWN/biolink/", - "bp": { - "@id": "http://w3id.org/ontogpt/metabolic-process-template", - "@prefix": true - }, - "core": "http://w3id.org/ontogpt/core/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "@vocab": "http://w3id.org/ontogpt/metabolic-process-template", - "object_id": { - "@id": "core:object_id" - }, - "object_text": { - "@id": "core:object_text" - }, - "subject_text": { - "@id": "core:subject_text" - }, - "extracted_object": { - "@type": "@id", - "@id": "core:extracted_object" - }, - "input_id": { - "@id": "core:input_id" - }, - "input_text": { - "@id": "core:input_text" - }, - "input_title": { - "@id": "core:input_title" - }, - "named_entities": { - "@type": "@id", - "@id": "core:named_entities" - }, - "prompt": { - "@id": "core:prompt" - }, - "raw_completion_output": { - "@id": "core:raw_completion_output" - }, - "category": { - "@type": "@id" - }, - "inputs": { - "@type": "@id" - }, - "outputs": { - "@type": "@id" - }, - "subclass_of": { - "@type": "@id" - }, - "id": { - "@id": "core:id" - }, - "label": { - "@id": "rdfs:label" - }, - "abstract": { - "@id": "core:abstract" - }, - "combined_text": { - "@id": "core:combined_text" - }, - "full_text": { - "@id": "core:full_text" - }, - "title": { - "@id": "core:title" - }, - "publication": { - "@type": "@id", - "@id": "core:publication" - }, - "triples": { - "@type": "@id", - "@id": "core:triples" - }, - "object": { - "@type": "@id", - "@id": "core:object" - }, - "object_qualifier": { - "@type": "@id", - "@id": "core:object_qualifier" - }, - "predicate": { - "@type": "@id", - "@id": "core:predicate" - }, - "qualifier": { - "@id": "core:qualifier" - }, - "subject": { - "@type": "@id", - "@id": "core:subject" - }, - "subject_qualifier": { - "@type": "@id", - "@id": "core:subject_qualifier" - }, - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } - } -} diff --git a/projects/metabolic_process/jsonld/metabolic_process.jsonld b/projects/metabolic_process/jsonld/metabolic_process.jsonld deleted file mode 100644 index 4612d8f3c..000000000 --- a/projects/metabolic_process/jsonld/metabolic_process.jsonld +++ /dev/null @@ -1,1176 +0,0 @@ -{ - "name": "metabolic-process-template", - "description": "A template for GO-CAMs", - "title": "metabolic Process Template", - "id": "https://w3id.org/ontogpt/metabolic_process", - "imports": [ - "linkml:types", - "core" - ], - "license": "https://creativecommons.org/publicdomain/zero/1.0/", - "prefixes": [ - { - "prefix_prefix": "linkml", - "prefix_reference": "https://w3id.org/linkml/" - }, - { - "prefix_prefix": "bp", - "prefix_reference": "http://w3id.org/ontogpt/metabolic-process-template" - } - ], - "default_prefix": "bp", - "default_range": "string", - "types": [ - { - "name": "string", - "definition_uri": "https://w3id.org/linkml/String", - "description": "A character string", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Text" - ], - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "@type": "TypeDefinition" - }, - { - "name": "integer", - "definition_uri": "https://w3id.org/linkml/Integer", - "description": "An integer", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Integer" - ], - "base": "int", - "uri": "http://www.w3.org/2001/XMLSchema#integer", - "@type": "TypeDefinition" - }, - { - "name": "boolean", - "definition_uri": "https://w3id.org/linkml/Boolean", - "description": "A binary (true or false) value", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Boolean" - ], - "base": "Bool", - "uri": "http://www.w3.org/2001/XMLSchema#boolean", - "repr": "bool", - "@type": "TypeDefinition" - }, - { - "name": "float", - "definition_uri": "https://w3id.org/linkml/Float", - "description": "A real number that conforms to the xsd:float specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#float", - "@type": "TypeDefinition" - }, - { - "name": "double", - "definition_uri": "https://w3id.org/linkml/Double", - "description": "A real number that conforms to the xsd:double specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#double", - "@type": "TypeDefinition" - }, - { - "name": "decimal", - "definition_uri": "https://w3id.org/linkml/Decimal", - "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "broad_mappings": [ - "schema:Number" - ], - "base": "Decimal", - "uri": "http://www.w3.org/2001/XMLSchema#decimal", - "@type": "TypeDefinition" - }, - { - "name": "time", - "definition_uri": "https://w3id.org/linkml/Time", - "description": "A time object represents a (local) time of day, independent of any particular day", - "notes": [ - "URI is dateTime because OWL reasoners do not work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Time" - ], - "base": "XSDTime", - "uri": "http://www.w3.org/2001/XMLSchema#time", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date", - "definition_uri": "https://w3id.org/linkml/Date", - "description": "a date (year, month and day) in an idealized calendar", - "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Date" - ], - "base": "XSDDate", - "uri": "http://www.w3.org/2001/XMLSchema#date", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "datetime", - "definition_uri": "https://w3id.org/linkml/Datetime", - "description": "The combination of a date and time", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:DateTime" - ], - "base": "XSDDateTime", - "uri": "http://www.w3.org/2001/XMLSchema#dateTime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date_or_datetime", - "definition_uri": "https://w3id.org/linkml/DateOrDatetime", - "description": "Either a date or a datetime", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "https://w3id.org/linkml/DateOrDatetime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uriorcurie", - "definition_uri": "https://w3id.org/linkml/Uriorcurie", - "description": "a URI or a CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "URIorCURIE", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "curie", - "definition_uri": "https://w3id.org/linkml/Curie", - "conforms_to": "https://www.w3.org/TR/curie/", - "description": "a compact URI", - "comments": [ - "in RDF serializations this MUST be expanded to a URI", - "in non-RDF serializations MAY be serialized as the compact representation" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "Curie", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uri", - "definition_uri": "https://w3id.org/linkml/Uri", - "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", - "description": "a complete URI", - "comments": [ - "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:URL" - ], - "base": "URI", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "ncname", - "definition_uri": "https://w3id.org/linkml/Ncname", - "description": "Prefix part of CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NCName", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "objectidentifier", - "definition_uri": "https://w3id.org/linkml/Objectidentifier", - "description": "A URI or CURIE that represents an object in the model.", - "comments": [ - "Used for inheritance and type checking" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "ElementIdentifier", - "uri": "http://www.w3.org/ns/shex#iri", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "nodeidentifier", - "definition_uri": "https://w3id.org/linkml/Nodeidentifier", - "description": "A URI, CURIE or BNODE that represents a node in a model.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NodeIdentifier", - "uri": "http://www.w3.org/ns/shex#nonLiteral", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpointer", - "definition_uri": "https://w3id.org/linkml/Jsonpointer", - "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901", - "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpath", - "definition_uri": "https://w3id.org/linkml/Jsonpath", - "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html", - "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "sparqlpath", - "definition_uri": "https://w3id.org/linkml/Sparqlpath", - "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths", - "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - } - ], - "enums": [ - { - "name": "NullDataOptions", - "definition_uri": "http://w3id.org/ontogpt/core/NullDataOptions", - "from_schema": "http://w3id.org/ontogpt/core", - "permissible_values": [ - { - "text": "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "meaning": "NCIT:C149701" - }, - { - "text": "NOT_APPLICABLE", - "meaning": "NCIT:C18902", - "aliases": [ - "not applicable", - "N/A" - ] - }, - { - "text": "NOT_MENTIONED" - } - ] - } - ], - "slots": [ - { - "name": "metabolicProcess__label", - "description": "the name of the metabolic process", - "from_schema": "https://w3id.org/ontogpt/metabolic_process", - "slot_uri": "http://w3id.org/ontogpt/metabolic-process-templatelabel", - "alias": "label", - "owner": "MetabolicProcess", - "domain_of": [ - "MetabolicProcess" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "metabolicProcess__description", - "description": "a textual description of the metabolic process", - "from_schema": "https://w3id.org/ontogpt/metabolic_process", - "slot_uri": "http://w3id.org/ontogpt/metabolic-process-templatedescription", - "alias": "description", - "owner": "MetabolicProcess", - "domain_of": [ - "MetabolicProcess" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "metabolicProcess__synonyms", - "description": "alternative names of the metabolic process", - "from_schema": "https://w3id.org/ontogpt/metabolic_process", - "slot_uri": "http://w3id.org/ontogpt/metabolic-process-templatesynonyms", - "multivalued": true, - "alias": "synonyms", - "owner": "MetabolicProcess", - "domain_of": [ - "MetabolicProcess" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "metabolicProcess__subclass_of", - "description": "a semicolon separated list of broader metabolic processes which this is a subclass of", - "from_schema": "https://w3id.org/ontogpt/metabolic_process", - "slot_uri": "http://w3id.org/ontogpt/metabolic-process-templatesubclass_of", - "multivalued": true, - "alias": "subclass_of", - "owner": "MetabolicProcess", - "domain_of": [ - "MetabolicProcess" - ], - "range": "MetabolicProcessCategory", - "@type": "SlotDefinition" - }, - { - "name": "metabolicProcess__category", - "description": "the category of metabolic process, e.g metabolic process, catabolic process, biosynthetic process, small molecule sensor activity", - "from_schema": "https://w3id.org/ontogpt/metabolic_process", - "slot_uri": "http://w3id.org/ontogpt/metabolic-process-templatecategory", - "alias": "category", - "owner": "MetabolicProcess", - "domain_of": [ - "MetabolicProcess" - ], - "range": "MetabolicProcessCategory", - "@type": "SlotDefinition" - }, - { - "name": "metabolicProcess__inputs", - "description": "the inputs of the metabolic process", - "from_schema": "https://w3id.org/ontogpt/metabolic_process", - "slot_uri": "http://w3id.org/ontogpt/metabolic-process-templateinputs", - "multivalued": true, - "alias": "inputs", - "owner": "MetabolicProcess", - "domain_of": [ - "MetabolicProcess" - ], - "range": "ChemicalEntity", - "@type": "SlotDefinition" - }, - { - "name": "metabolicProcess__outputs", - "description": "the outputs of the metabolic process", - "from_schema": "https://w3id.org/ontogpt/metabolic_process", - "slot_uri": "http://w3id.org/ontogpt/metabolic-process-templateoutputs", - "multivalued": true, - "alias": "outputs", - "owner": "MetabolicProcess", - "domain_of": [ - "MetabolicProcess" - ], - "range": "ChemicalEntity", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_id", - "alias": "input_id", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_title", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_title", - "alias": "input_title", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_text", - "alias": "input_text", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__raw_completion_output", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/raw_completion_output", - "alias": "raw_completion_output", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__prompt", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/prompt", - "alias": "prompt", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__extracted_object", - "description": "The complex objects extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/extracted_object", - "alias": "extracted_object", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__named_entities", - "description": "Named entities extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/named_entities", - "multivalued": true, - "alias": "named_entities", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "identifier": true, - "alias": "id", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "required": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "from_schema": "http://w3id.org/ontogpt/core", - "aliases": [ - "name" - ], - "mappings": [ - "http://example.org/UNKNOWN/rdfs/label" - ], - "slot_uri": "http://example.org/UNKNOWN/rdfs/label", - "alias": "label", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject", - "alias": "subject", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__predicate", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/predicate", - "alias": "predicate", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "triple__object", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object", - "alias": "object", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/qualifier", - "alias": "qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_qualifier", - "alias": "subject_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_qualifier", - "alias": "object_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/publication", - "alias": "publication", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__triples", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/triples", - "multivalued": true, - "alias": "triples", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "publication__id", - "description": "The publication identifier", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "alias": "id", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__title", - "description": "The title of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/title", - "alias": "title", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__abstract", - "description": "The abstract of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/abstract", - "alias": "abstract", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__combined_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/combined_text", - "alias": "combined_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__full_text", - "description": "The full text of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/full_text", - "alias": "full_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__subject_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_text", - "alias": "subject_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_id", - "alias": "object_id", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_text", - "alias": "object_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - } - ], - "classes": [ - { - "name": "MetabolicProcess", - "definition_uri": "http://w3id.org/ontogpt/metabolic-process-templateMetabolicProcess", - "from_schema": "https://w3id.org/ontogpt/metabolic_process", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "metabolicProcess__label", - "metabolicProcess__description", - "metabolicProcess__synonyms", - "metabolicProcess__subclass_of", - "metabolicProcess__category", - "metabolicProcess__inputs", - "metabolicProcess__outputs" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "label", - "description": "the name of the metabolic process", - "@type": "SlotDefinition" - }, - { - "name": "description", - "description": "a textual description of the metabolic process", - "@type": "SlotDefinition" - }, - { - "name": "synonyms", - "description": "alternative names of the metabolic process", - "multivalued": true, - "@type": "SlotDefinition" - }, - { - "name": "subclass_of", - "description": "a semicolon separated list of broader metabolic processes which this is a subclass of", - "multivalued": true, - "range": "MetabolicProcessCategory", - "@type": "SlotDefinition" - }, - { - "name": "category", - "description": "the category of metabolic process, e.g metabolic process, catabolic process, biosynthetic process, small molecule sensor activity", - "range": "MetabolicProcessCategory", - "@type": "SlotDefinition" - }, - { - "name": "inputs", - "description": "the inputs of the metabolic process", - "multivalued": true, - "range": "ChemicalEntity", - "@type": "SlotDefinition" - }, - { - "name": "outputs", - "description": "the outputs of the metabolic process", - "multivalued": true, - "range": "ChemicalEntity", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/metabolic-process-templateMetabolicProcess", - "@type": "ClassDefinition" - }, - { - "name": "MetabolicProcessCategory", - "id_prefixes": [ - "GO" - ], - "definition_uri": "http://w3id.org/ontogpt/metabolic-process-templateMetabolicProcessCategory", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:go", - "@type": "Annotation" - } - ], - "from_schema": "https://w3id.org/ontogpt/metabolic_process", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/metabolic-process-templateMetabolicProcessCategory", - "@type": "ClassDefinition" - }, - { - "name": "ChemicalEntity", - "id_prefixes": [ - "CHEBI" - ], - "definition_uri": "http://w3id.org/ontogpt/metabolic-process-templateChemicalEntity", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:chebi", - "@type": "Annotation" - } - ], - "from_schema": "https://w3id.org/ontogpt/metabolic_process", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/metabolic-process-templateChemicalEntity", - "@type": "ClassDefinition" - }, - { - "name": "Any", - "definition_uri": "http://w3id.org/ontogpt/core/Any", - "from_schema": "http://w3id.org/ontogpt/core", - "mappings": [ - "linkml:Any" - ], - "slot_usage": {}, - "class_uri": "https://w3id.org/linkml/Any", - "@type": "ClassDefinition" - }, - { - "name": "ExtractionResult", - "definition_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "description": "A result of extracting knowledge on text", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "extractionResult__input_id", - "extractionResult__input_title", - "extractionResult__input_text", - "extractionResult__raw_completion_output", - "extractionResult__prompt", - "extractionResult__extracted_object", - "extractionResult__named_entities" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "input_id", - "@type": "SlotDefinition" - }, - { - "name": "input_title", - "@type": "SlotDefinition" - }, - { - "name": "input_text", - "@type": "SlotDefinition" - }, - { - "name": "raw_completion_output", - "@type": "SlotDefinition" - }, - { - "name": "prompt", - "@type": "SlotDefinition" - }, - { - "name": "extracted_object", - "description": "The complex objects extracted from the text", - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "named_entities", - "description": "Named entities extracted from the text", - "multivalued": true, - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "@type": "ClassDefinition" - }, - { - "name": "NamedEntity", - "definition_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "identifier": true, - "@type": "SlotDefinition" - }, - { - "name": "label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "aliases": [ - "name" - ], - "slot_uri": "rdfs:label", - "range": "string", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "@type": "ClassDefinition" - }, - { - "name": "CompoundExpression", - "definition_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "@type": "ClassDefinition" - }, - { - "name": "Triple", - "definition_uri": "http://w3id.org/ontogpt/core/Triple", - "description": "Abstract parent for Relation Extraction tasks", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "CompoundExpression", - "abstract": true, - "slots": [ - "triple__subject", - "triple__predicate", - "triple__object", - "triple__qualifier", - "triple__subject_qualifier", - "triple__object_qualifier" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "predicate", - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "object", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Triple", - "@type": "ClassDefinition" - }, - { - "name": "TextWithTriples", - "definition_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "textWithTriples__publication", - "textWithTriples__triples" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "triples", - "multivalued": true, - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "@type": "ClassDefinition" - }, - { - "name": "RelationshipType", - "id_prefixes": [ - "RO", - "biolink" - ], - "definition_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "@type": "ClassDefinition" - }, - { - "name": "Publication", - "definition_uri": "http://w3id.org/ontogpt/core/Publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "publication__id", - "publication__title", - "publication__abstract", - "publication__combined_text", - "publication__full_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "description": "The publication identifier", - "@type": "SlotDefinition" - }, - { - "name": "title", - "description": "The title of the publication", - "@type": "SlotDefinition" - }, - { - "name": "abstract", - "description": "The abstract of the publication", - "@type": "SlotDefinition" - }, - { - "name": "combined_text", - "@type": "SlotDefinition" - }, - { - "name": "full_text", - "description": "The full text of the publication", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Publication", - "@type": "ClassDefinition" - }, - { - "name": "AnnotatorResult", - "definition_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "annotatorResult__subject_text", - "annotatorResult__object_id", - "annotatorResult__object_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject_text", - "@type": "SlotDefinition" - }, - { - "name": "object_id", - "@type": "SlotDefinition" - }, - { - "name": "object_text", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "@type": "ClassDefinition" - } - ], - "metamodel_version": "1.7.0", - "source_file": "metabolic_process.yaml", - "source_file_date": "2023-06-17T15:11:19", - "source_file_size": 1633, - "generation_date": "2023-08-07T10:54:49", - "@type": "SchemaDefinition", - "@context": [ - "projects/metabolic_process/jsonld/metabolic_process.context.jsonld", - "https://w3id.org/linkml/types.context.jsonld", - "core.context.jsonld", - { - "@base": "http://w3id.org/ontogpt/metabolic-process-template" - } - ] -} diff --git a/projects/metabolic_process/jsonschema/metabolic_process.schema.json b/projects/metabolic_process/jsonschema/metabolic_process.schema.json deleted file mode 100644 index f29a0837e..000000000 --- a/projects/metabolic_process/jsonschema/metabolic_process.schema.json +++ /dev/null @@ -1,234 +0,0 @@ -{ - "$defs": { - "AnnotatorResult": { - "additionalProperties": false, - "description": "", - "properties": { - "object_id": { - "type": "string" - }, - "object_text": { - "type": "string" - }, - "subject_text": { - "type": "string" - } - }, - "title": "AnnotatorResult", - "type": "object" - }, - "Any": { - "additionalProperties": true, - "description": "", - "title": "Any", - "type": "object" - }, - "ChemicalEntity": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "ChemicalEntity", - "type": "object" - }, - "ExtractionResult": { - "additionalProperties": false, - "description": "A result of extracting knowledge on text", - "properties": { - "extracted_object": { - "$ref": "#/$defs/Any", - "description": "The complex objects extracted from the text" - }, - "input_id": { - "type": "string" - }, - "input_text": { - "type": "string" - }, - "input_title": { - "type": "string" - }, - "named_entities": { - "description": "Named entities extracted from the text", - "items": { - "$ref": "#/$defs/Any" - }, - "type": "array" - }, - "prompt": { - "type": "string" - }, - "raw_completion_output": { - "type": "string" - } - }, - "title": "ExtractionResult", - "type": "object" - }, - "MetabolicProcess": { - "additionalProperties": false, - "description": "", - "properties": { - "category": { - "description": "the category of metabolic process, e.g metabolic process, catabolic process, biosynthetic process, small molecule sensor activity", - "type": "string" - }, - "description": { - "description": "a textual description of the metabolic process", - "type": "string" - }, - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "inputs": { - "description": "the inputs of the metabolic process", - "items": { - "type": "string" - }, - "type": "array" - }, - "label": { - "description": "the name of the metabolic process", - "type": "string" - }, - "outputs": { - "description": "the outputs of the metabolic process", - "items": { - "type": "string" - }, - "type": "array" - }, - "subclass_of": { - "description": "a semicolon separated list of broader metabolic processes which this is a subclass of", - "items": { - "type": "string" - }, - "type": "array" - }, - "synonyms": { - "description": "alternative names of the metabolic process", - "items": { - "type": "string" - }, - "type": "array" - } - }, - "required": [ - "id" - ], - "title": "MetabolicProcess", - "type": "object" - }, - "MetabolicProcessCategory": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "MetabolicProcessCategory", - "type": "object" - }, - "NullDataOptions": { - "description": "", - "enum": [ - "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "NOT_APPLICABLE", - "NOT_MENTIONED" - ], - "title": "NullDataOptions", - "type": "string" - }, - "Publication": { - "additionalProperties": false, - "description": "", - "properties": { - "abstract": { - "description": "The abstract of the publication", - "type": "string" - }, - "combined_text": { - "type": "string" - }, - "full_text": { - "description": "The full text of the publication", - "type": "string" - }, - "id": { - "description": "The publication identifier", - "type": "string" - }, - "title": { - "description": "The title of the publication", - "type": "string" - } - }, - "title": "Publication", - "type": "object" - }, - "RelationshipType": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "RelationshipType", - "type": "object" - }, - "TextWithTriples": { - "additionalProperties": false, - "description": "", - "properties": { - "publication": { - "$ref": "#/$defs/Publication" - }, - "triples": { - "items": { - "$ref": "#/$defs/Triple" - }, - "type": "array" - } - }, - "title": "TextWithTriples", - "type": "object" - } - }, - "$id": "https://w3id.org/ontogpt/metabolic_process", - "$schema": "http://json-schema.org/draft-07/schema#", - "additionalProperties": true, - "metamodel_version": "1.7.0", - "title": "metabolic-process-template", - "type": "object", - "version": null -} \ No newline at end of file diff --git a/projects/metabolic_process/metabolic_process.py b/projects/metabolic_process/metabolic_process.py deleted file mode 100644 index fbbb06585..000000000 --- a/projects/metabolic_process/metabolic_process.py +++ /dev/null @@ -1,489 +0,0 @@ -# Auto generated from metabolic_process.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-08-07T10:54:56 -# Schema: metabolic-process-template -# -# id: https://w3id.org/ontogpt/metabolic_process -# description: A template for GO-CAMs -# license: https://creativecommons.org/publicdomain/zero/1.0/ - -import dataclasses -import sys -import re -from jsonasobj2 import JsonObj, as_dict -from typing import Optional, List, Union, Dict, ClassVar, Any -from dataclasses import dataclass -from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions - -from linkml_runtime.utils.slot import Slot -from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode -from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int -from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs -from linkml_runtime.utils.formatutils import camelcase, underscore, sfx -from linkml_runtime.utils.enumerations import EnumDefinitionImpl -from rdflib import Namespace, URIRef -from linkml_runtime.utils.curienamespace import CurieNamespace -from linkml_runtime.linkml_model.types import String - -metamodel_version = "1.7.0" -version = None - -# Overwrite dataclasses _init_fn to add **kwargs in __init__ -dataclasses._init_fn = dataclasses_init_fn_with_kwargs - -# Namespaces -CHEBI = CurieNamespace('CHEBI', 'http://example.org/UNKNOWN/CHEBI/') -GO = CurieNamespace('GO', 'http://example.org/UNKNOWN/GO/') -RO = CurieNamespace('RO', 'http://purl.obolibrary.org/obo/RO_') -BIOLINK = CurieNamespace('biolink', 'http://example.org/UNKNOWN/biolink/') -BP = CurieNamespace('bp', 'http://w3id.org/ontogpt/metabolic-process-template') -CORE = CurieNamespace('core', 'http://w3id.org/ontogpt/core/') -LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') -RDFS = CurieNamespace('rdfs', 'http://example.org/UNKNOWN/rdfs/') -DEFAULT_ = BP - - -# Types - -# Class references -class NamedEntityId(extended_str): - pass - - -class MetabolicProcessId(NamedEntityId): - pass - - -class MetabolicProcessCategoryId(NamedEntityId): - pass - - -class ChemicalEntityId(NamedEntityId): - pass - - -class RelationshipTypeId(NamedEntityId): - pass - - -Any = Any - -@dataclass -class ExtractionResult(YAMLRoot): - """ - A result of extracting knowledge on text - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.ExtractionResult - class_class_curie: ClassVar[str] = "core:ExtractionResult" - class_name: ClassVar[str] = "ExtractionResult" - class_model_uri: ClassVar[URIRef] = BP.ExtractionResult - - input_id: Optional[str] = None - input_title: Optional[str] = None - input_text: Optional[str] = None - raw_completion_output: Optional[str] = None - prompt: Optional[str] = None - extracted_object: Optional[Union[dict, Any]] = None - named_entities: Optional[Union[Union[dict, Any], List[Union[dict, Any]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.input_id is not None and not isinstance(self.input_id, str): - self.input_id = str(self.input_id) - - if self.input_title is not None and not isinstance(self.input_title, str): - self.input_title = str(self.input_title) - - if self.input_text is not None and not isinstance(self.input_text, str): - self.input_text = str(self.input_text) - - if self.raw_completion_output is not None and not isinstance(self.raw_completion_output, str): - self.raw_completion_output = str(self.raw_completion_output) - - if self.prompt is not None and not isinstance(self.prompt, str): - self.prompt = str(self.prompt) - - super().__post_init__(**kwargs) - - -@dataclass -class NamedEntity(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.NamedEntity - class_class_curie: ClassVar[str] = "core:NamedEntity" - class_name: ClassVar[str] = "NamedEntity" - class_model_uri: ClassVar[URIRef] = BP.NamedEntity - - id: Union[str, NamedEntityId] = None - label: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, NamedEntityId): - self.id = NamedEntityId(self.id) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - super().__post_init__(**kwargs) - - -@dataclass -class MetabolicProcess(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = BP.MetabolicProcess - class_class_curie: ClassVar[str] = "bp:MetabolicProcess" - class_name: ClassVar[str] = "MetabolicProcess" - class_model_uri: ClassVar[URIRef] = BP.MetabolicProcess - - id: Union[str, MetabolicProcessId] = None - label: Optional[str] = None - description: Optional[str] = None - synonyms: Optional[Union[str, List[str]]] = empty_list() - subclass_of: Optional[Union[Union[str, MetabolicProcessCategoryId], List[Union[str, MetabolicProcessCategoryId]]]] = empty_list() - category: Optional[Union[str, MetabolicProcessCategoryId]] = None - inputs: Optional[Union[Union[str, ChemicalEntityId], List[Union[str, ChemicalEntityId]]]] = empty_list() - outputs: Optional[Union[Union[str, ChemicalEntityId], List[Union[str, ChemicalEntityId]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, MetabolicProcessId): - self.id = MetabolicProcessId(self.id) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - if self.description is not None and not isinstance(self.description, str): - self.description = str(self.description) - - if not isinstance(self.synonyms, list): - self.synonyms = [self.synonyms] if self.synonyms is not None else [] - self.synonyms = [v if isinstance(v, str) else str(v) for v in self.synonyms] - - if not isinstance(self.subclass_of, list): - self.subclass_of = [self.subclass_of] if self.subclass_of is not None else [] - self.subclass_of = [v if isinstance(v, MetabolicProcessCategoryId) else MetabolicProcessCategoryId(v) for v in self.subclass_of] - - if self.category is not None and not isinstance(self.category, MetabolicProcessCategoryId): - self.category = MetabolicProcessCategoryId(self.category) - - if not isinstance(self.inputs, list): - self.inputs = [self.inputs] if self.inputs is not None else [] - self.inputs = [v if isinstance(v, ChemicalEntityId) else ChemicalEntityId(v) for v in self.inputs] - - if not isinstance(self.outputs, list): - self.outputs = [self.outputs] if self.outputs is not None else [] - self.outputs = [v if isinstance(v, ChemicalEntityId) else ChemicalEntityId(v) for v in self.outputs] - - super().__post_init__(**kwargs) - - -@dataclass -class MetabolicProcessCategory(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = BP.MetabolicProcessCategory - class_class_curie: ClassVar[str] = "bp:MetabolicProcessCategory" - class_name: ClassVar[str] = "MetabolicProcessCategory" - class_model_uri: ClassVar[URIRef] = BP.MetabolicProcessCategory - - id: Union[str, MetabolicProcessCategoryId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, MetabolicProcessCategoryId): - self.id = MetabolicProcessCategoryId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class ChemicalEntity(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = BP.ChemicalEntity - class_class_curie: ClassVar[str] = "bp:ChemicalEntity" - class_name: ClassVar[str] = "ChemicalEntity" - class_model_uri: ClassVar[URIRef] = BP.ChemicalEntity - - id: Union[str, ChemicalEntityId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, ChemicalEntityId): - self.id = ChemicalEntityId(self.id) - - super().__post_init__(**kwargs) - - -class CompoundExpression(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.CompoundExpression - class_class_curie: ClassVar[str] = "core:CompoundExpression" - class_name: ClassVar[str] = "CompoundExpression" - class_model_uri: ClassVar[URIRef] = BP.CompoundExpression - - -@dataclass -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Triple - class_class_curie: ClassVar[str] = "core:Triple" - class_name: ClassVar[str] = "Triple" - class_model_uri: ClassVar[URIRef] = BP.Triple - - subject: Optional[Union[str, NamedEntityId]] = None - predicate: Optional[Union[str, RelationshipTypeId]] = None - object: Optional[Union[str, NamedEntityId]] = None - qualifier: Optional[str] = None - subject_qualifier: Optional[Union[str, NamedEntityId]] = None - object_qualifier: Optional[Union[str, NamedEntityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, NamedEntityId): - self.subject = NamedEntityId(self.subject) - - if self.predicate is not None and not isinstance(self.predicate, RelationshipTypeId): - self.predicate = RelationshipTypeId(self.predicate) - - if self.object is not None and not isinstance(self.object, NamedEntityId): - self.object = NamedEntityId(self.object) - - if self.qualifier is not None and not isinstance(self.qualifier, str): - self.qualifier = str(self.qualifier) - - if self.subject_qualifier is not None and not isinstance(self.subject_qualifier, NamedEntityId): - self.subject_qualifier = NamedEntityId(self.subject_qualifier) - - if self.object_qualifier is not None and not isinstance(self.object_qualifier, NamedEntityId): - self.object_qualifier = NamedEntityId(self.object_qualifier) - - super().__post_init__(**kwargs) - - -@dataclass -class TextWithTriples(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.TextWithTriples - class_class_curie: ClassVar[str] = "core:TextWithTriples" - class_name: ClassVar[str] = "TextWithTriples" - class_model_uri: ClassVar[URIRef] = BP.TextWithTriples - - publication: Optional[Union[dict, "Publication"]] = None - triples: Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.publication is not None and not isinstance(self.publication, Publication): - self.publication = Publication(**as_dict(self.publication)) - - if not isinstance(self.triples, list): - self.triples = [self.triples] if self.triples is not None else [] - self.triples = [v if isinstance(v, Triple) else Triple(**as_dict(v)) for v in self.triples] - - super().__post_init__(**kwargs) - - -@dataclass -class RelationshipType(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.RelationshipType - class_class_curie: ClassVar[str] = "core:RelationshipType" - class_name: ClassVar[str] = "RelationshipType" - class_model_uri: ClassVar[URIRef] = BP.RelationshipType - - id: Union[str, RelationshipTypeId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, RelationshipTypeId): - self.id = RelationshipTypeId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Publication(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Publication - class_class_curie: ClassVar[str] = "core:Publication" - class_name: ClassVar[str] = "Publication" - class_model_uri: ClassVar[URIRef] = BP.Publication - - id: Optional[str] = None - title: Optional[str] = None - abstract: Optional[str] = None - combined_text: Optional[str] = None - full_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.id is not None and not isinstance(self.id, str): - self.id = str(self.id) - - if self.title is not None and not isinstance(self.title, str): - self.title = str(self.title) - - if self.abstract is not None and not isinstance(self.abstract, str): - self.abstract = str(self.abstract) - - if self.combined_text is not None and not isinstance(self.combined_text, str): - self.combined_text = str(self.combined_text) - - if self.full_text is not None and not isinstance(self.full_text, str): - self.full_text = str(self.full_text) - - super().__post_init__(**kwargs) - - -@dataclass -class AnnotatorResult(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.AnnotatorResult - class_class_curie: ClassVar[str] = "core:AnnotatorResult" - class_name: ClassVar[str] = "AnnotatorResult" - class_model_uri: ClassVar[URIRef] = BP.AnnotatorResult - - subject_text: Optional[str] = None - object_id: Optional[str] = None - object_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject_text is not None and not isinstance(self.subject_text, str): - self.subject_text = str(self.subject_text) - - if self.object_id is not None and not isinstance(self.object_id, str): - self.object_id = str(self.object_id) - - if self.object_text is not None and not isinstance(self.object_text, str): - self.object_text = str(self.object_text) - - super().__post_init__(**kwargs) - - -# Enumerations -class NullDataOptions(EnumDefinitionImpl): - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = PermissibleValue(text="UNSPECIFIED_METHOD_OF_ADMINISTRATION", - meaning=NCIT.C149701) - NOT_APPLICABLE = PermissibleValue(text="NOT_APPLICABLE", - meaning=NCIT.C18902) - NOT_MENTIONED = PermissibleValue(text="NOT_MENTIONED") - - _defn = EnumDefinition( - name="NullDataOptions", - ) - -# Slots -class slots: - pass - -slots.metabolicProcess__label = Slot(uri=BP.label, name="metabolicProcess__label", curie=BP.curie('label'), - model_uri=BP.metabolicProcess__label, domain=None, range=Optional[str]) - -slots.metabolicProcess__description = Slot(uri=BP.description, name="metabolicProcess__description", curie=BP.curie('description'), - model_uri=BP.metabolicProcess__description, domain=None, range=Optional[str]) - -slots.metabolicProcess__synonyms = Slot(uri=BP.synonyms, name="metabolicProcess__synonyms", curie=BP.curie('synonyms'), - model_uri=BP.metabolicProcess__synonyms, domain=None, range=Optional[Union[str, List[str]]]) - -slots.metabolicProcess__subclass_of = Slot(uri=BP.subclass_of, name="metabolicProcess__subclass_of", curie=BP.curie('subclass_of'), - model_uri=BP.metabolicProcess__subclass_of, domain=None, range=Optional[Union[Union[str, MetabolicProcessCategoryId], List[Union[str, MetabolicProcessCategoryId]]]]) - -slots.metabolicProcess__category = Slot(uri=BP.category, name="metabolicProcess__category", curie=BP.curie('category'), - model_uri=BP.metabolicProcess__category, domain=None, range=Optional[Union[str, MetabolicProcessCategoryId]]) - -slots.metabolicProcess__inputs = Slot(uri=BP.inputs, name="metabolicProcess__inputs", curie=BP.curie('inputs'), - model_uri=BP.metabolicProcess__inputs, domain=None, range=Optional[Union[Union[str, ChemicalEntityId], List[Union[str, ChemicalEntityId]]]]) - -slots.metabolicProcess__outputs = Slot(uri=BP.outputs, name="metabolicProcess__outputs", curie=BP.curie('outputs'), - model_uri=BP.metabolicProcess__outputs, domain=None, range=Optional[Union[Union[str, ChemicalEntityId], List[Union[str, ChemicalEntityId]]]]) - -slots.extractionResult__input_id = Slot(uri=CORE.input_id, name="extractionResult__input_id", curie=CORE.curie('input_id'), - model_uri=BP.extractionResult__input_id, domain=None, range=Optional[str]) - -slots.extractionResult__input_title = Slot(uri=CORE.input_title, name="extractionResult__input_title", curie=CORE.curie('input_title'), - model_uri=BP.extractionResult__input_title, domain=None, range=Optional[str]) - -slots.extractionResult__input_text = Slot(uri=CORE.input_text, name="extractionResult__input_text", curie=CORE.curie('input_text'), - model_uri=BP.extractionResult__input_text, domain=None, range=Optional[str]) - -slots.extractionResult__raw_completion_output = Slot(uri=CORE.raw_completion_output, name="extractionResult__raw_completion_output", curie=CORE.curie('raw_completion_output'), - model_uri=BP.extractionResult__raw_completion_output, domain=None, range=Optional[str]) - -slots.extractionResult__prompt = Slot(uri=CORE.prompt, name="extractionResult__prompt", curie=CORE.curie('prompt'), - model_uri=BP.extractionResult__prompt, domain=None, range=Optional[str]) - -slots.extractionResult__extracted_object = Slot(uri=CORE.extracted_object, name="extractionResult__extracted_object", curie=CORE.curie('extracted_object'), - model_uri=BP.extractionResult__extracted_object, domain=None, range=Optional[Union[dict, Any]]) - -slots.extractionResult__named_entities = Slot(uri=CORE.named_entities, name="extractionResult__named_entities", curie=CORE.curie('named_entities'), - model_uri=BP.extractionResult__named_entities, domain=None, range=Optional[Union[Union[dict, Any], List[Union[dict, Any]]]]) - -slots.namedEntity__id = Slot(uri=CORE.id, name="namedEntity__id", curie=CORE.curie('id'), - model_uri=BP.namedEntity__id, domain=None, range=URIRef) - -slots.namedEntity__label = Slot(uri=RDFS.label, name="namedEntity__label", curie=RDFS.curie('label'), - model_uri=BP.namedEntity__label, domain=None, range=Optional[str]) - -slots.triple__subject = Slot(uri=CORE.subject, name="triple__subject", curie=CORE.curie('subject'), - model_uri=BP.triple__subject, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__predicate = Slot(uri=CORE.predicate, name="triple__predicate", curie=CORE.curie('predicate'), - model_uri=BP.triple__predicate, domain=None, range=Optional[Union[str, RelationshipTypeId]]) - -slots.triple__object = Slot(uri=CORE.object, name="triple__object", curie=CORE.curie('object'), - model_uri=BP.triple__object, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__qualifier = Slot(uri=CORE.qualifier, name="triple__qualifier", curie=CORE.curie('qualifier'), - model_uri=BP.triple__qualifier, domain=None, range=Optional[str]) - -slots.triple__subject_qualifier = Slot(uri=CORE.subject_qualifier, name="triple__subject_qualifier", curie=CORE.curie('subject_qualifier'), - model_uri=BP.triple__subject_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__object_qualifier = Slot(uri=CORE.object_qualifier, name="triple__object_qualifier", curie=CORE.curie('object_qualifier'), - model_uri=BP.triple__object_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.textWithTriples__publication = Slot(uri=CORE.publication, name="textWithTriples__publication", curie=CORE.curie('publication'), - model_uri=BP.textWithTriples__publication, domain=None, range=Optional[Union[dict, Publication]]) - -slots.textWithTriples__triples = Slot(uri=CORE.triples, name="textWithTriples__triples", curie=CORE.curie('triples'), - model_uri=BP.textWithTriples__triples, domain=None, range=Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]]) - -slots.publication__id = Slot(uri=CORE.id, name="publication__id", curie=CORE.curie('id'), - model_uri=BP.publication__id, domain=None, range=Optional[str]) - -slots.publication__title = Slot(uri=CORE.title, name="publication__title", curie=CORE.curie('title'), - model_uri=BP.publication__title, domain=None, range=Optional[str]) - -slots.publication__abstract = Slot(uri=CORE.abstract, name="publication__abstract", curie=CORE.curie('abstract'), - model_uri=BP.publication__abstract, domain=None, range=Optional[str]) - -slots.publication__combined_text = Slot(uri=CORE.combined_text, name="publication__combined_text", curie=CORE.curie('combined_text'), - model_uri=BP.publication__combined_text, domain=None, range=Optional[str]) - -slots.publication__full_text = Slot(uri=CORE.full_text, name="publication__full_text", curie=CORE.curie('full_text'), - model_uri=BP.publication__full_text, domain=None, range=Optional[str]) - -slots.annotatorResult__subject_text = Slot(uri=CORE.subject_text, name="annotatorResult__subject_text", curie=CORE.curie('subject_text'), - model_uri=BP.annotatorResult__subject_text, domain=None, range=Optional[str]) - -slots.annotatorResult__object_id = Slot(uri=CORE.object_id, name="annotatorResult__object_id", curie=CORE.curie('object_id'), - model_uri=BP.annotatorResult__object_id, domain=None, range=Optional[str]) - -slots.annotatorResult__object_text = Slot(uri=CORE.object_text, name="annotatorResult__object_text", curie=CORE.curie('object_text'), - model_uri=BP.annotatorResult__object_text, domain=None, range=Optional[str]) \ No newline at end of file diff --git a/projects/metabolic_process/owl/metabolic_process.owl.ttl b/projects/metabolic_process/owl/metabolic_process.owl.ttl deleted file mode 100644 index 57f4124a0..000000000 --- a/projects/metabolic_process/owl/metabolic_process.owl.ttl +++ /dev/null @@ -1,442 +0,0 @@ -@prefix IAO: <http://purl.obolibrary.org/obo/IAO_> . -@prefix bp: <http://w3id.org/ontogpt/metabolic-process-template> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix owl: <http://www.w3.org/2002/07/owl#> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . -@prefix skos: <http://www.w3.org/2004/02/skos/core#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -bp:MetabolicProcess a owl:Class, - linkml:ClassDefinition ; - rdfs:label "MetabolicProcess" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty bp:synonyms ], - [ a owl:Restriction ; - owl:allValuesFrom bp:MetabolicProcessCategory ; - owl:onProperty bp:subclass_of ], - [ a owl:Restriction ; - owl:allValuesFrom bp:ChemicalEntity ; - owl:onProperty bp:inputs ], - [ a owl:Restriction ; - owl:allValuesFrom bp:ChemicalEntity ; - owl:onProperty bp:outputs ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass bp:MetabolicProcessCategory ; - owl:onProperty bp:category ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty bp:label ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty bp:description ], - <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the name of the metabolic process', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'description': SlotDefinition(name='description', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a textual description of the metabolic process', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'synonyms': SlotDefinition(name='synonyms', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='alternative names of the metabolic process', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subclass_of': SlotDefinition(name='subclass_of', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a semicolon separated list of broader metabolic processes which this is a subclass of', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='MetabolicProcessCategory', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'category': SlotDefinition(name='category', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the category of metabolic process, e.g metabolic process, catabolic process, biosynthetic process, small molecule sensor activity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='MetabolicProcessCategory', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'inputs': SlotDefinition(name='inputs', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the inputs of the metabolic process', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ChemicalEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'outputs': SlotDefinition(name='outputs', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the outputs of the metabolic process', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ChemicalEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "NamedEntity" . - -linkml:SubsetDefinition a owl:Class ; - rdfs:label "subset_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" . - -linkml:TypeDefinition a owl:Class ; - rdfs:label "type_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" ; - linkml:mixins "type_expression" . - -linkml:topValue a owl:DatatypeProperty ; - rdfs:label "value" . - -<https://w3id.org/ontogpt/metabolic_process> a owl:Ontology ; - rdfs:label "metabolic-process-template" ; - IAO:0000700 <http://w3id.org/ontogpt/core/AnnotatorResult>, - <http://w3id.org/ontogpt/core/Any>, - <http://w3id.org/ontogpt/core/CompoundExpression>, - <http://w3id.org/ontogpt/core/ExtractionResult>, - <http://w3id.org/ontogpt/core/NamedEntity>, - <http://w3id.org/ontogpt/core/Publication>, - <http://w3id.org/ontogpt/core/TextWithTriples> ; - linkml:classes "{'MetabolicProcess': ClassDefinition(name='MetabolicProcess', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/metabolic-process-templateMetabolicProcess', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/metabolic_process', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'metabolicProcess__label', 'metabolicProcess__description', 'metabolicProcess__synonyms', 'metabolicProcess__subclass_of', 'metabolicProcess__category', 'metabolicProcess__inputs', 'metabolicProcess__outputs'], slot_usage={}, attributes={'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the name of the metabolic process', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'description': SlotDefinition(name='description', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a textual description of the metabolic process', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'synonyms': SlotDefinition(name='synonyms', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='alternative names of the metabolic process', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subclass_of': SlotDefinition(name='subclass_of', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a semicolon separated list of broader metabolic processes which this is a subclass of', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='MetabolicProcessCategory', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'category': SlotDefinition(name='category', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the category of metabolic process, e.g metabolic process, catabolic process, biosynthetic process, small molecule sensor activity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='MetabolicProcessCategory', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'inputs': SlotDefinition(name='inputs', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the inputs of the metabolic process', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ChemicalEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'outputs': SlotDefinition(name='outputs', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the outputs of the metabolic process', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ChemicalEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='bp:MetabolicProcess', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'MetabolicProcessCategory': ClassDefinition(name='MetabolicProcessCategory', id_prefixes=['GO'], definition_uri='http://w3id.org/ontogpt/metabolic-process-templateMetabolicProcessCategory', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:go', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/metabolic_process', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='bp:MetabolicProcessCategory', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ChemicalEntity': ClassDefinition(name='ChemicalEntity', id_prefixes=['CHEBI'], definition_uri='http://w3id.org/ontogpt/metabolic-process-templateChemicalEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:chebi', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/metabolic_process', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='bp:ChemicalEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Any': ClassDefinition(name='Any', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Any', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=['linkml:Any'], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='linkml:Any', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ExtractionResult': ClassDefinition(name='ExtractionResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/ExtractionResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A result of extracting knowledge on text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['extractionResult__input_id', 'extractionResult__input_title', 'extractionResult__input_text', 'extractionResult__raw_completion_output', 'extractionResult__prompt', 'extractionResult__extracted_object', 'extractionResult__named_entities'], slot_usage={}, attributes={'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:ExtractionResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'NamedEntity': ClassDefinition(name='NamedEntity', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NamedEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:NamedEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'CompoundExpression': ClassDefinition(name='CompoundExpression', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/CompoundExpression', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='core:CompoundExpression', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Triple': ClassDefinition(name='Triple', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Triple', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Abstract parent for Relation Extraction tasks', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['triple__subject', 'triple__predicate', 'triple__object', 'triple__qualifier', 'triple__subject_qualifier', 'triple__object_qualifier'], slot_usage={}, attributes={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Triple', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'TextWithTriples': ClassDefinition(name='TextWithTriples', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/TextWithTriples', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['textWithTriples__publication', 'textWithTriples__triples'], slot_usage={}, attributes={'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:TextWithTriples', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'RelationshipType': ClassDefinition(name='RelationshipType', id_prefixes=['RO', 'biolink'], definition_uri='http://w3id.org/ontogpt/core/RelationshipType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='core:RelationshipType', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Publication': ClassDefinition(name='Publication', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Publication', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['publication__id', 'publication__title', 'publication__abstract', 'publication__combined_text', 'publication__full_text'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Publication', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'AnnotatorResult': ClassDefinition(name='AnnotatorResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/AnnotatorResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['annotatorResult__subject_text', 'annotatorResult__object_id', 'annotatorResult__object_text'], slot_usage={}, attributes={'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:AnnotatorResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={})}" ; - linkml:enums "{'NullDataOptions': EnumDefinition(name='NullDataOptions', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NullDataOptions', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'UNSPECIFIED_METHOD_OF_ADMINISTRATION': PermissibleValue(text='UNSPECIFIED_METHOD_OF_ADMINISTRATION', description=None, meaning='NCIT:C149701', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_APPLICABLE': PermissibleValue(text='NOT_APPLICABLE', description=None, meaning='NCIT:C18902', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['not applicable', 'N/A'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_MENTIONED': PermissibleValue(text='NOT_MENTIONED', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[])}" ; - linkml:id "https://w3id.org/ontogpt/metabolic_process" ; - linkml:imports "core", - "linkml:types" ; - linkml:types "{'string': TypeDefinition(name='string', id_prefixes=[], definition_uri='https://w3id.org/linkml/String', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A character string', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Text'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'integer': TypeDefinition(name='integer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Integer', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An integer', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Integer'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='int', uri='xsd:integer', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'boolean': TypeDefinition(name='boolean', id_prefixes=[], definition_uri='https://w3id.org/linkml/Boolean', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A binary (true or false) value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Boolean'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Bool', uri='xsd:boolean', repr='bool', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'float': TypeDefinition(name='float', id_prefixes=[], definition_uri='https://w3id.org/linkml/Float', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:float specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Float'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:float', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'double': TypeDefinition(name='double', id_prefixes=[], definition_uri='https://w3id.org/linkml/Double', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:double specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:Float'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:double', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'decimal': TypeDefinition(name='decimal', id_prefixes=[], definition_uri='https://w3id.org/linkml/Decimal', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number with arbitrary precision that conforms to the xsd:decimal specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=['schema:Number'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Decimal', uri='xsd:decimal', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'time': TypeDefinition(name='time', id_prefixes=[], definition_uri='https://w3id.org/linkml/Time', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A time object represents a (local) time of day, independent of any particular day', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=['URI is dateTime because OWL reasoners do not work with straight date or time'], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Time'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDTime', uri='xsd:time', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date': TypeDefinition(name='date', id_prefixes=[], definition_uri='https://w3id.org/linkml/Date', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a date (year, month and day) in an idealized calendar', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[\"URI is dateTime because OWL reasoners don't work with straight date or time\"], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Date'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDate', uri='xsd:date', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'datetime': TypeDefinition(name='datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/Datetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The combination of a date and time', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:DateTime'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDateTime', uri='xsd:dateTime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date_or_datetime': TypeDefinition(name='date_or_datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/DateOrDatetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Either a date or a datetime', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='linkml:DateOrDatetime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uriorcurie': TypeDefinition(name='uriorcurie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uriorcurie', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a URI or a CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URIorCURIE', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'curie': TypeDefinition(name='curie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Curie', local_names={}, conforms_to='https://www.w3.org/TR/curie/', implements=[], extensions={}, annotations={}, description='a compact URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations this MUST be expanded to a URI', 'in non-RDF serializations MAY be serialized as the compact representation'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Curie', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uri': TypeDefinition(name='uri', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uri', local_names={}, conforms_to='https://www.ietf.org/rfc/rfc3987.txt', implements=[], extensions={}, annotations={}, description='a complete URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:URL'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URI', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ncname': TypeDefinition(name='ncname', id_prefixes=[], definition_uri='https://w3id.org/linkml/Ncname', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Prefix part of CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NCName', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'objectidentifier': TypeDefinition(name='objectidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Objectidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI or CURIE that represents an object in the model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['Used for inheritance and type checking'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='ElementIdentifier', uri='shex:iri', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'nodeidentifier': TypeDefinition(name='nodeidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Nodeidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI, CURIE or BNODE that represents a node in a model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NodeIdentifier', uri='shex:nonLiteral', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpointer': TypeDefinition(name='jsonpointer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpointer', local_names={}, conforms_to='https://datatracker.ietf.org/doc/html/rfc6901', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpath': TypeDefinition(name='jsonpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpath', local_names={}, conforms_to='https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sparqlpath': TypeDefinition(name='sparqlpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Sparqlpath', local_names={}, conforms_to='https://www.w3.org/TR/sparql11-query/#propertypaths', implements=[], extensions={}, annotations={}, description='A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "AnnotatorResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_text> ] ; - linkml:attributes "{'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/ExtractionResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ExtractionResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_title> ], - [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/named_entities> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/extracted_object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/prompt> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_text> ] ; - skos:definition "A result of extracting knowledge on text" ; - linkml:attributes "{'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/TextWithTriples> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TextWithTriples" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Triple> ; - owl:onProperty <http://w3id.org/ontogpt/core/triples> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Publication> ; - owl:onProperty <http://w3id.org/ontogpt/core/publication> ] ; - linkml:attributes "{'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/abstract> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "abstract" ; - rdfs:range linkml:String ; - skos:definition "The abstract of the publication" . - -<http://w3id.org/ontogpt/core/combined_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "combined_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/extracted_object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "extracted_object" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "The complex objects extracted from the text" . - -<http://w3id.org/ontogpt/core/full_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "full_text" ; - rdfs:range linkml:String ; - skos:definition "The full text of the publication" . - -<http://w3id.org/ontogpt/core/input_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_title" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/named_entities> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "named_entities" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "Named entities extracted from the text" . - -<http://w3id.org/ontogpt/core/object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/object_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/object_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" . - -<http://w3id.org/ontogpt/core/object_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/predicate> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "predicate" ; - rdfs:range <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/prompt> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "prompt" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/publication> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "publication" ; - bp:prompt.skip "true" ; - rdfs:range <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "qualifier" ; - rdfs:range linkml:String ; - skos:definition "A qualifier for the statements, e.g. \"NOT\" for negation" . - -<http://w3id.org/ontogpt/core/raw_completion_output> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "raw_completion_output" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/subject> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/subject_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" . - -<http://w3id.org/ontogpt/core/subject_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "title" ; - rdfs:range linkml:String ; - skos:definition "The title of the publication" . - -<http://w3id.org/ontogpt/core/triples> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "triples" ; - rdfs:range <http://w3id.org/ontogpt/core/Triple> . - -bp:category a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "category" ; - rdfs:range bp:MetabolicProcessCategory ; - skos:definition "the category of metabolic process, e.g metabolic process, catabolic process, biosynthetic process, small molecule sensor activity" . - -bp:description a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "description" ; - rdfs:range linkml:String ; - skos:definition "a textual description of the metabolic process" . - -bp:inputs a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "inputs" ; - rdfs:range bp:ChemicalEntity ; - skos:definition "the inputs of the metabolic process" . - -bp:label a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "label" ; - rdfs:range linkml:String ; - skos:definition "the name of the metabolic process" . - -bp:outputs a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "outputs" ; - rdfs:range bp:ChemicalEntity ; - skos:definition "the outputs of the metabolic process" . - -bp:subclass_of a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subclass_of" ; - rdfs:range bp:MetabolicProcessCategory ; - skos:definition "a semicolon separated list of broader metabolic processes which this is a subclass of" . - -bp:synonyms a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "synonyms" ; - rdfs:range linkml:String ; - skos:definition "alternative names of the metabolic process" . - -<http://example.org/UNKNOWN/rdfs/label> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "label" ; - bp:owl "AnnotationProperty, AnnotationAssertion" ; - rdfs:range linkml:String ; - skos:altLabel "name" ; - skos:definition "The label (name) of the named thing" ; - skos:exactMatch <http://example.org/UNKNOWN/rdfs/label> . - -<http://purl.obolibrary.org/obo/NCIT_C149701> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "UNSPECIFIED_METHOD_OF_ADMINISTRATION" . - -<http://purl.obolibrary.org/obo/NCIT_C18902> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_APPLICABLE" . - -<http://w3id.org/ontogpt/core/CompoundExpression> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CompoundExpression" ; - linkml:attributes "{}" . - -<http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_MENTIONED" . - -<http://w3id.org/ontogpt/core/RelationshipType> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "RelationshipType" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/Triple> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Triple" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/RelationshipType> ; - owl:onProperty <http://w3id.org/ontogpt/core/predicate> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object_qualifier> ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - skos:definition "Abstract parent for Relation Extraction tasks" ; - linkml:attributes "{'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -<http://w3id.org/ontogpt/core/id> a owl:ObjectProperty, - linkml:SlotDefinition . - -<http://w3id.org/ontogpt/core/NullDataOptions> a owl:Class, - linkml:EnumDefinition ; - rdfs:label "NullDataOptions" ; - owl:unionOf ( <http://purl.obolibrary.org/obo/NCIT_C149701> <http://purl.obolibrary.org/obo/NCIT_C18902> <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> ) ; - linkml:permissible_values <http://purl.obolibrary.org/obo/NCIT_C149701>, - <http://purl.obolibrary.org/obo/NCIT_C18902>, - <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> . - -<http://w3id.org/ontogpt/core/Publication> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Publication" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/full_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/title> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/combined_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/abstract> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -bp:ChemicalEntity a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ChemicalEntity" ; - bp:annotators "sqlite:obo:chebi" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -bp:MetabolicProcessCategory a owl:Class, - linkml:ClassDefinition ; - rdfs:label "MetabolicProcessCategory" ; - bp:annotators "sqlite:obo:go" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/Any> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Any" ; - skos:exactMatch linkml:Any ; - linkml:attributes "{}" . - -linkml:ClassDefinition a owl:Class ; - rdfs:label "class_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "class_expression" . - -<http://w3id.org/ontogpt/core/NamedEntity> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "NamedEntity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://example.org/UNKNOWN/rdfs/label> ], - [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ; - owl:qualifiedCardinality 1 ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:SlotDefinition a owl:Class ; - rdfs:label "slot_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "slot_expression" . - - diff --git a/projects/metabolic_process/prefixmap/metabolic_process.yaml b/projects/metabolic_process/prefixmap/metabolic_process.yaml deleted file mode 100644 index 84f0bc643..000000000 --- a/projects/metabolic_process/prefixmap/metabolic_process.yaml +++ /dev/null @@ -1,37 +0,0 @@ -{ - "CHEBI": "http://example.org/UNKNOWN/CHEBI/", - "GO": "http://example.org/UNKNOWN/GO/", - "RO": "http://purl.obolibrary.org/obo/RO_", - "biolink": "http://example.org/UNKNOWN/biolink/", - "bp": "http://w3id.org/ontogpt/metabolic-process-template", - "core": "http://w3id.org/ontogpt/core/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } -} diff --git a/projects/metabolic_process/protobuf/metabolic_process.proto b/projects/metabolic_process/protobuf/metabolic_process.proto deleted file mode 100644 index cd8577a6e..000000000 --- a/projects/metabolic_process/protobuf/metabolic_process.proto +++ /dev/null @@ -1,56 +0,0 @@ -message AnnotatorResult - { - string subjectText = 0 - string objectId = 0 - string objectText = 0 - } -message ChemicalEntity - { - string id = 0 - string label = 0 - } -// A result of extracting knowledge on text -message ExtractionResult - { - string inputId = 0 - string inputTitle = 0 - string inputText = 0 - string rawCompletionOutput = 0 - string prompt = 0 - any extractedObject = 0 - repeated any namedEntities = 0 - } -message MetabolicProcess - { - string id = 0 - string label = 0 - string description = 0 - repeated string synonyms = 0 - repeated metabolicProcessCategory subclassOf = 0 - metabolicProcessCategory category = 0 - repeated chemicalEntity inputs = 0 - repeated chemicalEntity outputs = 0 - } -message MetabolicProcessCategory - { - string id = 0 - string label = 0 - } -message Publication - { - string id = 0 - string title = 0 - string abstract = 0 - string combinedText = 0 - string fullText = 0 - } -message RelationshipType - { - string id = 0 - string label = 0 - } -message TextWithTriples - { - publication publication = 0 - repeated triple triples = 0 - } diff --git a/projects/metabolic_process/shacl/metabolic_process.shacl.ttl b/projects/metabolic_process/shacl/metabolic_process.shacl.ttl deleted file mode 100644 index a914f49c1..000000000 --- a/projects/metabolic_process/shacl/metabolic_process.shacl.ttl +++ /dev/null @@ -1,234 +0,0 @@ -@prefix bp: <http://w3id.org/ontogpt/metabolic-process-template> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix sh: <http://www.w3.org/ns/shacl#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object_text> ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject_text> ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/object_id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/AnnotatorResult> . - -<http://w3id.org/ontogpt/core/CompoundExpression> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass <http://w3id.org/ontogpt/core/CompoundExpression> . - -<http://w3id.org/ontogpt/core/ExtractionResult> a sh:NodeShape ; - sh:closed true ; - sh:description "A result of extracting knowledge on text" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/input_id> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/input_text> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/input_title> ], - [ sh:class linkml:Any ; - sh:description "Named entities extracted from the text" ; - sh:nodeKind sh:BlankNode ; - sh:order 6 ; - sh:path <http://w3id.org/ontogpt/core/named_entities> ], - [ sh:class linkml:Any ; - sh:description "The complex objects extracted from the text" ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/extracted_object> ], - [ sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/prompt> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/ExtractionResult> . - -<http://w3id.org/ontogpt/core/TextWithTriples> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/Triple> ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/triples> ], - [ sh:class <http://w3id.org/ontogpt/core/Publication> ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/publication> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/TextWithTriples> . - -bp:MetabolicProcess a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class bp:MetabolicProcessCategory ; - sh:description "a semicolon separated list of broader metabolic processes which this is a subclass of" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path bp:subclass_of ], - [ sh:description "alternative names of the metabolic process" ; - sh:order 2 ; - sh:path bp:synonyms ], - [ sh:class bp:MetabolicProcessCategory ; - sh:description "the category of metabolic process, e.g metabolic process, catabolic process, biosynthetic process, small molecule sensor activity" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path bp:category ], - [ sh:description "the name of the metabolic process" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path bp:label ], - [ sh:class bp:ChemicalEntity ; - sh:description "the outputs of the metabolic process" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path bp:outputs ], - [ sh:class bp:ChemicalEntity ; - sh:description "the inputs of the metabolic process" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path bp:inputs ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "a textual description of the metabolic process" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path bp:description ] ; - sh:targetClass bp:MetabolicProcess . - -<http://w3id.org/ontogpt/core/Publication> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The title of the publication" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/title> ], - [ sh:description "The full text of the publication" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/full_text> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/combined_text> ], - [ sh:description "The abstract of the publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/abstract> ], - [ sh:description "The publication identifier" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/RelationshipType> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/Triple> a sh:NodeShape ; - sh:closed false ; - sh:description "Abstract parent for Relation Extraction tasks" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/RelationshipType> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/predicate> ], - [ sh:description "A qualifier for the statements, e.g. \"NOT\" for negation" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/object_qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Triple> . - -bp:ChemicalEntity a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass bp:ChemicalEntity . - -bp:MetabolicProcessCategory a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass bp:MetabolicProcessCategory . - -linkml:Any a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass linkml:Any . - -<http://w3id.org/ontogpt/core/NamedEntity> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/NamedEntity> . - diff --git a/projects/metabolic_process/shex/metabolic_process.shex b/projects/metabolic_process/shex/metabolic_process.shex deleted file mode 100644 index c78e8eb49..000000000 --- a/projects/metabolic_process/shex/metabolic_process.shex +++ /dev/null @@ -1,171 +0,0 @@ -BASE <http://w3id.org/ontogpt/metabolic-process-template/> -PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> -PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> -PREFIX linkml: <https://w3id.org/linkml/> -PREFIX core: <http://w3id.org/ontogpt/core/> -PREFIX rdfs1: <http://example.org/UNKNOWN/rdfs/> - - -linkml:String xsd:string - -linkml:Integer xsd:integer - -linkml:Boolean xsd:boolean - -linkml:Float xsd:float - -linkml:Double xsd:double - -linkml:Decimal xsd:decimal - -linkml:Time xsd:time - -linkml:Date xsd:date - -linkml:Datetime xsd:dateTime - -linkml:DateOrDatetime linkml:DateOrDatetime - -linkml:Uriorcurie IRI - -linkml:Curie xsd:string - -linkml:Uri IRI - -linkml:Ncname xsd:string - -linkml:Objectidentifier IRI - -linkml:Nodeidentifier NONLITERAL - -linkml:Jsonpointer xsd:string - -linkml:Jsonpath xsd:string - -linkml:Sparqlpath xsd:string - -core:AnnotatorResult CLOSED { - ( $core:AnnotatorResult_tes ( core:subject_text @linkml:String ? ; - core:object_id @linkml:String ? ; - core:object_text @linkml:String ? - ) ; - rdf:type [ core:AnnotatorResult ] ? - ) -} - -core:Any CLOSED { - ( $core:Any_tes rdf:type . * ; - rdf:type [ linkml:Any ] ? - ) -} - -<http://w3id.org/ontogpt/metabolic-process-templateChemicalEntity> CLOSED { - ( $<http://w3id.org/ontogpt/metabolic-process-templateChemicalEntity_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <http://w3id.org/ontogpt/metabolic-process-templateChemicalEntity> ] - ) -} - -core:CompoundExpression ( - { - ( $core:CompoundExpression_tes rdf:type . * ; - rdf:type [ core:CompoundExpression ] ? - ) - } OR @core:Triple -) - -core:ExtractionResult CLOSED { - ( $core:ExtractionResult_tes ( core:input_id @linkml:String ? ; - core:input_title @linkml:String ? ; - core:input_text @linkml:String ? ; - core:raw_completion_output @linkml:String ? ; - core:prompt @linkml:String ? ; - core:extracted_object @core:Any ? ; - core:named_entities @core:Any * - ) ; - rdf:type [ core:ExtractionResult ] ? - ) -} - -<http://w3id.org/ontogpt/metabolic-process-templateMetabolicProcess> CLOSED { - ( $<http://w3id.org/ontogpt/metabolic-process-templateMetabolicProcess_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? ; - <http://w3id.org/ontogpt/metabolic-process-templatelabel> @linkml:String ? ; - <http://w3id.org/ontogpt/metabolic-process-templatedescription> @linkml:String ? ; - <http://w3id.org/ontogpt/metabolic-process-templatesynonyms> @linkml:String * ; - <http://w3id.org/ontogpt/metabolic-process-templatesubclass_of> - @<http://w3id.org/ontogpt/metabolic-process-templateMetabolicProcessCategory> * ; - <http://w3id.org/ontogpt/metabolic-process-templatecategory> - @<http://w3id.org/ontogpt/metabolic-process-templateMetabolicProcessCategory> ? ; - <http://w3id.org/ontogpt/metabolic-process-templateinputs> - @<http://w3id.org/ontogpt/metabolic-process-templateChemicalEntity> * ; - <http://w3id.org/ontogpt/metabolic-process-templateoutputs> - @<http://w3id.org/ontogpt/metabolic-process-templateChemicalEntity> * - ) ; - rdf:type [ <http://w3id.org/ontogpt/metabolic-process-templateMetabolicProcess> ] - ) -} - -<http://w3id.org/ontogpt/metabolic-process-templateMetabolicProcessCategory> CLOSED { - ( $<http://w3id.org/ontogpt/metabolic-process-templateMetabolicProcessCategory_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <http://w3id.org/ontogpt/metabolic-process-templateMetabolicProcessCategory> ] - ) -} - -core:NamedEntity ( - @<http://w3id.org/ontogpt/metabolic-process-templateChemicalEntity> OR - @<http://w3id.org/ontogpt/metabolic-process-templateMetabolicProcess> OR - @<http://w3id.org/ontogpt/metabolic-process-templateMetabolicProcessCategory> OR @core:RelationshipType -) - -core:NamedEntity_struct { - ( $core:NamedEntity_tes rdfs1:label @linkml:String ? ; - rdf:type [ core:NamedEntity ] - ) -} - -core:Publication CLOSED { - ( $core:Publication_tes ( core:id @linkml:String ? ; - core:title @linkml:String ? ; - core:abstract @linkml:String ? ; - core:combined_text @linkml:String ? ; - core:full_text @linkml:String ? - ) ; - rdf:type [ core:Publication ] ? - ) -} - -core:RelationshipType CLOSED { - ( $core:RelationshipType_tes ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ core:RelationshipType ] - ) -} - -core:TextWithTriples CLOSED { - ( $core:TextWithTriples_tes ( core:publication @core:Publication ? ; - core:triples @core:Triple * - ) ; - rdf:type [ core:TextWithTriples ] ? - ) -} - -core:Triple { - ( $core:Triple_tes ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - core:subject @core:NamedEntity ? ; - core:predicate @core:RelationshipType ? ; - core:object @core:NamedEntity ? ; - core:qualifier @linkml:String ? ; - core:subject_qualifier @core:NamedEntity ? ; - core:object_qualifier @core:NamedEntity ? - ) ; - rdf:type [ core:Triple ] ? - ) -} - - diff --git a/projects/metabolic_process/sqlschema/metabolic_process.sql b/projects/metabolic_process/sqlschema/metabolic_process.sql deleted file mode 100644 index 397869126..000000000 --- a/projects/metabolic_process/sqlschema/metabolic_process.sql +++ /dev/null @@ -1,71 +0,0 @@ - - -CREATE TABLE "AnnotatorResult" ( - subject_text TEXT, - object_id TEXT, - object_text TEXT, - PRIMARY KEY (subject_text, object_id, object_text) -); - -CREATE TABLE "ChemicalEntity" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "ExtractionResult" ( - input_id TEXT, - input_title TEXT, - input_text TEXT, - raw_completion_output TEXT, - prompt TEXT, - extracted_object TEXT, - named_entities TEXT, - PRIMARY KEY (input_id, input_title, input_text, raw_completion_output, prompt, extracted_object, named_entities) -); - -CREATE TABLE "MetabolicProcessCategory" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Publication" ( - id TEXT, - title TEXT, - abstract TEXT, - combined_text TEXT, - full_text TEXT, - PRIMARY KEY (id, title, abstract, combined_text, full_text) -); - -CREATE TABLE "RelationshipType" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "TextWithTriples" ( - publication TEXT, - triples TEXT, - PRIMARY KEY (publication, triples) -); - -CREATE TABLE "MetabolicProcess" ( - id TEXT NOT NULL, - label TEXT, - description TEXT, - subclass_of TEXT, - category TEXT, - inputs TEXT, - outputs TEXT, - PRIMARY KEY (id), - FOREIGN KEY(category) REFERENCES "MetabolicProcessCategory" (id) -); - -CREATE TABLE "MetabolicProcess_synonyms" ( - backref_id TEXT, - synonyms TEXT, - PRIMARY KEY (backref_id, synonyms), - FOREIGN KEY(backref_id) REFERENCES "MetabolicProcess" (id) -); diff --git a/projects/metagenome_study/docs/AnnotatorResult.md b/projects/metagenome_study/docs/AnnotatorResult.md deleted file mode 100644 index 9dc26200c..000000000 --- a/projects/metagenome_study/docs/AnnotatorResult.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Class: AnnotatorResult - - - - -URI: [eg:AnnotatorResult](http://w3id.org/ontogpt/environmental-metagenome/AnnotatorResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F])](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F]) - -## Attributes - - -### Own - - * [➞subject_text](annotatorResult__subject_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_id](annotatorResult__object_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_text](annotatorResult__object_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) diff --git a/projects/metagenome_study/docs/Any.md b/projects/metagenome_study/docs/Any.md deleted file mode 100644 index a7f410b04..000000000 --- a/projects/metagenome_study/docs/Any.md +++ /dev/null @@ -1,25 +0,0 @@ - -# Class: Any - - - - -URI: [eg:Any](http://w3id.org/ontogpt/environmental-metagenome/Any) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult])](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult]) - -## Referenced by Class - - * **None** *[➞extracted_object](extractionResult__extracted_object.md)* <sub>0..1</sub> **[Any](Any.md)** - * **None** *[➞named_entities](extractionResult__named_entities.md)* <sub>0..\*</sub> **[Any](Any.md)** - -## Attributes - - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | linkml:Any | - diff --git a/projects/metagenome_study/docs/CausalRelationship.md b/projects/metagenome_study/docs/CausalRelationship.md deleted file mode 100644 index 653c41417..000000000 --- a/projects/metagenome_study/docs/CausalRelationship.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Class: CausalRelationship - - - - -URI: [eg:CausalRelationship](http://w3id.org/ontogpt/environmental-metagenome/CausalRelationship) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Variable],[CompoundExpression],[Variable]<effect%200..1-%20[CausalRelationship],[Variable]<cause%200..1-%20[CausalRelationship],[Study]++-%20causal_relationships%200..*>[CausalRelationship],[CompoundExpression]^-[CausalRelationship],[Study])](https://yuml.me/diagram/nofunky;dir:TB/class/[Variable],[CompoundExpression],[Variable]<effect%200..1-%20[CausalRelationship],[Variable]<cause%200..1-%20[CausalRelationship],[Study]++-%20causal_relationships%200..*>[CausalRelationship],[CompoundExpression]^-[CausalRelationship],[Study]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞causal_relationships](study__causal_relationships.md)* <sub>0..\*</sub> **[CausalRelationship](CausalRelationship.md)** - -## Attributes - - -### Own - - * [➞cause](causalRelationship__cause.md) <sub>0..1</sub> - * Description: the variable that is the cause of the effect - * Range: [Variable](Variable.md) - * [➞effect](causalRelationship__effect.md) <sub>0..1</sub> - * Description: the things that is affected - * Range: [Variable](Variable.md) diff --git a/projects/metagenome_study/docs/CompoundExpression.md b/projects/metagenome_study/docs/CompoundExpression.md deleted file mode 100644 index 3d2bbfc4e..000000000 --- a/projects/metagenome_study/docs/CompoundExpression.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Class: CompoundExpression - - - - -URI: [eg:CompoundExpression](http://w3id.org/ontogpt/environmental-metagenome/CompoundExpression) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Measurement],[CompoundExpression]^-[Triple],[CompoundExpression]^-[Measurement],[CompoundExpression]^-[CausalRelationship],[CausalRelationship])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Measurement],[CompoundExpression]^-[Triple],[CompoundExpression]^-[Measurement],[CompoundExpression]^-[CausalRelationship],[CausalRelationship]) - -## Children - - * [CausalRelationship](CausalRelationship.md) - * [Measurement](Measurement.md) - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - -## Referenced by Class - - -## Attributes - diff --git a/projects/metagenome_study/docs/Environment.md b/projects/metagenome_study/docs/Environment.md deleted file mode 100644 index 180eb7508..000000000 --- a/projects/metagenome_study/docs/Environment.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Environment - - - - -URI: [eg:Environment](http://w3id.org/ontogpt/environmental-metagenome/Environment) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[Study]-%20environments%200..*>[Environment|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Environment],[Study])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[Study]-%20environments%200..*>[Environment|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Environment],[Study]) - -## Identifier prefixes - - * ENVO - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞environments](study__environments.md)* <sub>0..\*</sub> **[Environment](Environment.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/metagenome_study/docs/EnvironmentalMaterial.md b/projects/metagenome_study/docs/EnvironmentalMaterial.md deleted file mode 100644 index dc8833c98..000000000 --- a/projects/metagenome_study/docs/EnvironmentalMaterial.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: EnvironmentalMaterial - - - - -URI: [eg:EnvironmentalMaterial](http://w3id.org/ontogpt/environmental-metagenome/EnvironmentalMaterial) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[Study]-%20environmental_material%200..*>[EnvironmentalMaterial|id(i):string;label(i):string%20%3F],[NamedEntity]^-[EnvironmentalMaterial],[Study])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[Study]-%20environmental_material%200..*>[EnvironmentalMaterial|id(i):string;label(i):string%20%3F],[NamedEntity]^-[EnvironmentalMaterial],[Study]) - -## Identifier prefixes - - * ENVO - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞environmental_material](study__environmental_material.md)* <sub>0..\*</sub> **[EnvironmentalMaterial](EnvironmentalMaterial.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/metagenome_study/docs/ExtractionResult.md b/projects/metagenome_study/docs/ExtractionResult.md deleted file mode 100644 index 021686661..000000000 --- a/projects/metagenome_study/docs/ExtractionResult.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Class: ExtractionResult - - -A result of extracting knowledge on text - -URI: [eg:ExtractionResult](http://w3id.org/ontogpt/environmental-metagenome/ExtractionResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any])](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any]) - -## Attributes - - -### Own - - * [➞input_id](extractionResult__input_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_title](extractionResult__input_title.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_text](extractionResult__input_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞prompt](extractionResult__prompt.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞extracted_object](extractionResult__extracted_object.md) <sub>0..1</sub> - * Description: The complex objects extracted from the text - * Range: [Any](Any.md) - * [➞named_entities](extractionResult__named_entities.md) <sub>0..\*</sub> - * Description: Named entities extracted from the text - * Range: [Any](Any.md) diff --git a/projects/metagenome_study/docs/Location.md b/projects/metagenome_study/docs/Location.md deleted file mode 100644 index e958632fc..000000000 --- a/projects/metagenome_study/docs/Location.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: Location - - - - -URI: [eg:Location](http://w3id.org/ontogpt/environmental-metagenome/Location) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[Study]-%20location%200..*>[Location|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Location],[Study])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[Study]-%20location%200..*>[Location|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Location],[Study]) - -## Identifier prefixes - - * ENVO - * GAZ - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞location](study__location.md)* <sub>0..\*</sub> **[Location](Location.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/metagenome_study/docs/Measurement.md b/projects/metagenome_study/docs/Measurement.md deleted file mode 100644 index df61443ac..000000000 --- a/projects/metagenome_study/docs/Measurement.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Class: Measurement - - - - -URI: [eg:Measurement](http://w3id.org/ontogpt/environmental-metagenome/Measurement) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Unit],[Unit]<unit%200..1-%20[Measurement|value:string%20%3F],[Study]++-%20measurements%200..*>[Measurement],[CompoundExpression]^-[Measurement],[Study],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[Unit],[Unit]<unit%200..1-%20[Measurement|value:string%20%3F],[Study]++-%20measurements%200..*>[Measurement],[CompoundExpression]^-[Measurement],[Study],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞measurements](study__measurements.md)* <sub>0..\*</sub> **[Measurement](Measurement.md)** - -## Attributes - - -### Own - - * [➞value](measurement__value.md) <sub>0..1</sub> - * Description: the value of the measurement - * Range: [String](types/String.md) - * [➞unit](measurement__unit.md) <sub>0..1</sub> - * Description: the unit of the measurement - * Range: [Unit](Unit.md) diff --git a/projects/metagenome_study/docs/NamedEntity.md b/projects/metagenome_study/docs/NamedEntity.md deleted file mode 100644 index 5cd831b59..000000000 --- a/projects/metagenome_study/docs/NamedEntity.md +++ /dev/null @@ -1,41 +0,0 @@ - -# Class: NamedEntity - - - - -URI: [eg:NamedEntity](http://w3id.org/ontogpt/environmental-metagenome/NamedEntity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Variable],[Unit],[Treatment],[SequencingTechnology],[RelationshipType],[Organism],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[Variable],[NamedEntity]^-[Unit],[NamedEntity]^-[Treatment],[NamedEntity]^-[SequencingTechnology],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[Organism],[NamedEntity]^-[Location],[NamedEntity]^-[EnvironmentalMaterial],[NamedEntity]^-[Environment],[Triple],[Location],[EnvironmentalMaterial],[Environment])](https://yuml.me/diagram/nofunky;dir:TB/class/[Variable],[Unit],[Treatment],[SequencingTechnology],[RelationshipType],[Organism],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[Variable],[NamedEntity]^-[Unit],[NamedEntity]^-[Treatment],[NamedEntity]^-[SequencingTechnology],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[Organism],[NamedEntity]^-[Location],[NamedEntity]^-[EnvironmentalMaterial],[NamedEntity]^-[Environment],[Triple],[Location],[EnvironmentalMaterial],[Environment]) - -## Children - - * [Environment](Environment.md) - * [EnvironmentalMaterial](EnvironmentalMaterial.md) - * [Location](Location.md) - * [Organism](Organism.md) - * [RelationshipType](RelationshipType.md) - * [SequencingTechnology](SequencingTechnology.md) - * [Treatment](Treatment.md) - * [Unit](Unit.md) - * [Variable](Variable.md) - -## Referenced by Class - - * **None** *[➞object](triple__object.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞object_qualifier](triple__object_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject](triple__subject.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject_qualifier](triple__subject_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - -## Attributes - - -### Own - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/metagenome_study/docs/NullDataOptions.md b/projects/metagenome_study/docs/NullDataOptions.md deleted file mode 100644 index 3765a62e3..000000000 --- a/projects/metagenome_study/docs/NullDataOptions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Enum: NullDataOptions - - - - -URI: [eg:NullDataOptions](http://w3id.org/ontogpt/environmental-metagenome/NullDataOptions) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | -| UNSPECIFIED_METHOD_OF_ADMINISTRATION | | NCIT:C149701 | | -| NOT_APPLICABLE | | NCIT:C18902 | {'aliases': ['not applicable', 'N/A']} | -| NOT_MENTIONED | | | | - diff --git a/projects/metagenome_study/docs/Organism.md b/projects/metagenome_study/docs/Organism.md deleted file mode 100644 index d1f86c38d..000000000 --- a/projects/metagenome_study/docs/Organism.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Organism - - - - -URI: [eg:Organism](http://w3id.org/ontogpt/environmental-metagenome/Organism) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Study]-%20organisms%200..*>[Organism|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Organism],[Study],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Study]-%20organisms%200..*>[Organism|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Organism],[Study],[NamedEntity]) - -## Identifier prefixes - - * NCBITaxon - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞organisms](study__organisms.md)* <sub>0..\*</sub> **[Organism](Organism.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/metagenome_study/docs/Publication.md b/projects/metagenome_study/docs/Publication.md deleted file mode 100644 index 69f8ed1b9..000000000 --- a/projects/metagenome_study/docs/Publication.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Publication - - - - -URI: [eg:Publication](http://w3id.org/ontogpt/environmental-metagenome/Publication) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples])](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples]) - -## Referenced by Class - - * **None** *[➞publication](textWithTriples__publication.md)* <sub>0..1</sub> **[Publication](Publication.md)** - -## Attributes - - -### Own - - * [➞id](publication__id.md) <sub>0..1</sub> - * Description: The publication identifier - * Range: [String](types/String.md) - * [➞title](publication__title.md) <sub>0..1</sub> - * Description: The title of the publication - * Range: [String](types/String.md) - * [➞abstract](publication__abstract.md) <sub>0..1</sub> - * Description: The abstract of the publication - * Range: [String](types/String.md) - * [➞combined_text](publication__combined_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞full_text](publication__full_text.md) <sub>0..1</sub> - * Description: The full text of the publication - * Range: [String](types/String.md) diff --git a/projects/metagenome_study/docs/RelationshipType.md b/projects/metagenome_study/docs/RelationshipType.md deleted file mode 100644 index babb8ef3d..000000000 --- a/projects/metagenome_study/docs/RelationshipType.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: RelationshipType - - - - -URI: [eg:RelationshipType](http://w3id.org/ontogpt/environmental-metagenome/RelationshipType) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity]) - -## Identifier prefixes - - * RO - * biolink - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞predicate](triple__predicate.md)* <sub>0..1</sub> **[RelationshipType](RelationshipType.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/metagenome_study/docs/SequencingTechnology.md b/projects/metagenome_study/docs/SequencingTechnology.md deleted file mode 100644 index fd63dd4c0..000000000 --- a/projects/metagenome_study/docs/SequencingTechnology.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: SequencingTechnology - - - - -URI: [eg:SequencingTechnology](http://w3id.org/ontogpt/environmental-metagenome/SequencingTechnology) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Study]-%20sequencing_technologies%200..1>[SequencingTechnology|id(i):string;label(i):string%20%3F],[NamedEntity]^-[SequencingTechnology],[Study],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Study]-%20sequencing_technologies%200..1>[SequencingTechnology|id(i):string;label(i):string%20%3F],[NamedEntity]^-[SequencingTechnology],[Study],[NamedEntity]) - -## Identifier prefixes - - * IDO - * EFO - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞sequencing_technologies](study__sequencing_technologies.md)* <sub>0..1</sub> **[SequencingTechnology](SequencingTechnology.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/metagenome_study/docs/Study.md b/projects/metagenome_study/docs/Study.md deleted file mode 100644 index 9a3076adc..000000000 --- a/projects/metagenome_study/docs/Study.md +++ /dev/null @@ -1,37 +0,0 @@ - -# Class: Study - - - - -URI: [eg:Study](http://w3id.org/ontogpt/environmental-metagenome/Study) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Variable],[Treatment],[Organism]<organisms%200..*-%20[Study],[SequencingTechnology]<sequencing_technologies%200..1-%20[Study],[EnvironmentalMaterial]<environmental_material%200..*-%20[Study],[Location]<location%200..*-%20[Study],[Measurement]<measurements%200..*-++[Study],[Treatment]<treatments%200..*-%20[Study],[Variable]<variables%200..*-%20[Study],[CausalRelationship]<causal_relationships%200..*-++[Study],[Environment]<environments%200..*-%20[Study],[SequencingTechnology],[Organism],[Measurement],[Location],[EnvironmentalMaterial],[Environment],[CausalRelationship])](https://yuml.me/diagram/nofunky;dir:TB/class/[Variable],[Treatment],[Organism]<organisms%200..*-%20[Study],[SequencingTechnology]<sequencing_technologies%200..1-%20[Study],[EnvironmentalMaterial]<environmental_material%200..*-%20[Study],[Location]<location%200..*-%20[Study],[Measurement]<measurements%200..*-++[Study],[Treatment]<treatments%200..*-%20[Study],[Variable]<variables%200..*-%20[Study],[CausalRelationship]<causal_relationships%200..*-++[Study],[Environment]<environments%200..*-%20[Study],[SequencingTechnology],[Organism],[Measurement],[Location],[EnvironmentalMaterial],[Environment],[CausalRelationship]) - -## Attributes - - -### Own - - * [➞environments](study__environments.md) <sub>0..\*</sub> - * Range: [Environment](Environment.md) - * [➞causal_relationships](study__causal_relationships.md) <sub>0..\*</sub> - * Range: [CausalRelationship](CausalRelationship.md) - * [➞variables](study__variables.md) <sub>0..\*</sub> - * Range: [Variable](Variable.md) - * [➞treatments](study__treatments.md) <sub>0..\*</sub> - * Range: [Treatment](Treatment.md) - * [➞measurements](study__measurements.md) <sub>0..\*</sub> - * Range: [Measurement](Measurement.md) - * [➞location](study__location.md) <sub>0..\*</sub> - * Description: the sites at which the study was conducted - * Range: [Location](Location.md) - * [➞environmental_material](study__environmental_material.md) <sub>0..\*</sub> - * Description: the environmental material that was sampled - * Range: [EnvironmentalMaterial](EnvironmentalMaterial.md) - * [➞sequencing_technologies](study__sequencing_technologies.md) <sub>0..1</sub> - * Range: [SequencingTechnology](SequencingTechnology.md) - * [➞organisms](study__organisms.md) <sub>0..\*</sub> - * Description: semicolon-separated list of all studied organism taxons - * Range: [Organism](Organism.md) diff --git a/projects/metagenome_study/docs/TextWithTriples.md b/projects/metagenome_study/docs/TextWithTriples.md deleted file mode 100644 index a01d0e6b2..000000000 --- a/projects/metagenome_study/docs/TextWithTriples.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: TextWithTriples - - - - -URI: [eg:TextWithTriples](http://w3id.org/ontogpt/environmental-metagenome/TextWithTriples) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication]) - -## Attributes - - -### Own - - * [➞publication](textWithTriples__publication.md) <sub>0..1</sub> - * Range: [Publication](Publication.md) - * [➞triples](textWithTriples__triples.md) <sub>0..\*</sub> - * Range: [Triple](Triple.md) diff --git a/projects/metagenome_study/docs/Treatment.md b/projects/metagenome_study/docs/Treatment.md deleted file mode 100644 index 4031646ac..000000000 --- a/projects/metagenome_study/docs/Treatment.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: Treatment - - - - -URI: [eg:Treatment](http://w3id.org/ontogpt/environmental-metagenome/Treatment) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Study]-%20treatments%200..*>[Treatment|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Treatment],[Study],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Study]-%20treatments%200..*>[Treatment|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Treatment],[Study],[NamedEntity]) - -## Identifier prefixes - - * PECO - * OBI - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞treatments](study__treatments.md)* <sub>0..\*</sub> **[Treatment](Treatment.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/metagenome_study/docs/Triple.md b/projects/metagenome_study/docs/Triple.md deleted file mode 100644 index 7cf604a34..000000000 --- a/projects/metagenome_study/docs/Triple.md +++ /dev/null @@ -1,39 +0,0 @@ - -# Class: Triple - - -Abstract parent for Relation Extraction tasks - -URI: [eg:Triple](http://w3id.org/ontogpt/environmental-metagenome/Triple) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞triples](textWithTriples__triples.md)* <sub>0..\*</sub> **[Triple](Triple.md)** - -## Attributes - - -### Own - - * [➞subject](triple__subject.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞predicate](triple__predicate.md) <sub>0..1</sub> - * Range: [RelationshipType](RelationshipType.md) - * [➞object](triple__object.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞qualifier](triple__qualifier.md) <sub>0..1</sub> - * Description: A qualifier for the statements, e.g. "NOT" for negation - * Range: [String](types/String.md) - * [➞subject_qualifier](triple__subject_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - * Range: [NamedEntity](NamedEntity.md) - * [➞object_qualifier](triple__object_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * Range: [NamedEntity](NamedEntity.md) diff --git a/projects/metagenome_study/docs/Unit.md b/projects/metagenome_study/docs/Unit.md deleted file mode 100644 index 23f385687..000000000 --- a/projects/metagenome_study/docs/Unit.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: Unit - - - - -URI: [eg:Unit](http://w3id.org/ontogpt/environmental-metagenome/Unit) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Measurement]-%20unit%200..1>[Unit|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Unit],[NamedEntity],[Measurement])](https://yuml.me/diagram/nofunky;dir:TB/class/[Measurement]-%20unit%200..1>[Unit|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Unit],[NamedEntity],[Measurement]) - -## Identifier prefixes - - * UO - * NCIT - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞unit](measurement__unit.md)* <sub>0..1</sub> **[Unit](Unit.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/metagenome_study/docs/Variable.md b/projects/metagenome_study/docs/Variable.md deleted file mode 100644 index f2743a207..000000000 --- a/projects/metagenome_study/docs/Variable.md +++ /dev/null @@ -1,38 +0,0 @@ - -# Class: Variable - - - - -URI: [eg:Variable](http://w3id.org/ontogpt/environmental-metagenome/Variable) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[CausalRelationship]-%20cause%200..1>[Variable|id(i):string;label(i):string%20%3F],[CausalRelationship]-%20effect%200..1>[Variable],[Study]-%20variables%200..*>[Variable],[NamedEntity]^-[Variable],[Study],[NamedEntity],[CausalRelationship])](https://yuml.me/diagram/nofunky;dir:TB/class/[CausalRelationship]-%20cause%200..1>[Variable|id(i):string;label(i):string%20%3F],[CausalRelationship]-%20effect%200..1>[Variable],[Study]-%20variables%200..*>[Variable],[NamedEntity]^-[Variable],[Study],[NamedEntity],[CausalRelationship]) - -## Identifier prefixes - - * ENVO - * MIXS - * PATO - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞cause](causalRelationship__cause.md)* <sub>0..1</sub> **[Variable](Variable.md)** - * **None** *[➞effect](causalRelationship__effect.md)* <sub>0..1</sub> **[Variable](Variable.md)** - * **None** *[➞variables](study__variables.md)* <sub>0..\*</sub> **[Variable](Variable.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/metagenome_study/docs/annotatorResult__object_id.md b/projects/metagenome_study/docs/annotatorResult__object_id.md deleted file mode 100644 index 0f0f256f6..000000000 --- a/projects/metagenome_study/docs/annotatorResult__object_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_id - - - - -URI: [eg:annotatorResult__object_id](http://w3id.org/ontogpt/environmental-metagenome/annotatorResult__object_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/metagenome_study/docs/annotatorResult__object_text.md b/projects/metagenome_study/docs/annotatorResult__object_text.md deleted file mode 100644 index d130fdc6c..000000000 --- a/projects/metagenome_study/docs/annotatorResult__object_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_text - - - - -URI: [eg:annotatorResult__object_text](http://w3id.org/ontogpt/environmental-metagenome/annotatorResult__object_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/metagenome_study/docs/annotatorResult__subject_text.md b/projects/metagenome_study/docs/annotatorResult__subject_text.md deleted file mode 100644 index 6a6856736..000000000 --- a/projects/metagenome_study/docs/annotatorResult__subject_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_text - - - - -URI: [eg:annotatorResult__subject_text](http://w3id.org/ontogpt/environmental-metagenome/annotatorResult__subject_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/metagenome_study/docs/causalRelationship__cause.md b/projects/metagenome_study/docs/causalRelationship__cause.md deleted file mode 100644 index 911b27c2f..000000000 --- a/projects/metagenome_study/docs/causalRelationship__cause.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: cause - - -the variable that is the cause of the effect - -URI: [eg:causalRelationship__cause](http://w3id.org/ontogpt/environmental-metagenome/causalRelationship__cause) - - -## Domain and Range - -None → <sub>0..1</sub> [Variable](Variable.md) - -## Parents - - -## Children - - -## Used by - - * [CausalRelationship](CausalRelationship.md) diff --git a/projects/metagenome_study/docs/causalRelationship__effect.md b/projects/metagenome_study/docs/causalRelationship__effect.md deleted file mode 100644 index f2c270a5c..000000000 --- a/projects/metagenome_study/docs/causalRelationship__effect.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: effect - - -the things that is affected - -URI: [eg:causalRelationship__effect](http://w3id.org/ontogpt/environmental-metagenome/causalRelationship__effect) - - -## Domain and Range - -None → <sub>0..1</sub> [Variable](Variable.md) - -## Parents - - -## Children - - -## Used by - - * [CausalRelationship](CausalRelationship.md) diff --git a/projects/metagenome_study/docs/extractionResult__extracted_object.md b/projects/metagenome_study/docs/extractionResult__extracted_object.md deleted file mode 100644 index 3bce16ba9..000000000 --- a/projects/metagenome_study/docs/extractionResult__extracted_object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: extracted_object - - -The complex objects extracted from the text - -URI: [eg:extractionResult__extracted_object](http://w3id.org/ontogpt/environmental-metagenome/extractionResult__extracted_object) - - -## Domain and Range - -None → <sub>0..1</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/metagenome_study/docs/extractionResult__input_id.md b/projects/metagenome_study/docs/extractionResult__input_id.md deleted file mode 100644 index e7771714f..000000000 --- a/projects/metagenome_study/docs/extractionResult__input_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_id - - - - -URI: [eg:extractionResult__input_id](http://w3id.org/ontogpt/environmental-metagenome/extractionResult__input_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/metagenome_study/docs/extractionResult__input_text.md b/projects/metagenome_study/docs/extractionResult__input_text.md deleted file mode 100644 index 0b6ee764d..000000000 --- a/projects/metagenome_study/docs/extractionResult__input_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_text - - - - -URI: [eg:extractionResult__input_text](http://w3id.org/ontogpt/environmental-metagenome/extractionResult__input_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/metagenome_study/docs/extractionResult__input_title.md b/projects/metagenome_study/docs/extractionResult__input_title.md deleted file mode 100644 index 9c6974b16..000000000 --- a/projects/metagenome_study/docs/extractionResult__input_title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_title - - - - -URI: [eg:extractionResult__input_title](http://w3id.org/ontogpt/environmental-metagenome/extractionResult__input_title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/metagenome_study/docs/extractionResult__named_entities.md b/projects/metagenome_study/docs/extractionResult__named_entities.md deleted file mode 100644 index 9e1058b1d..000000000 --- a/projects/metagenome_study/docs/extractionResult__named_entities.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: named_entities - - -Named entities extracted from the text - -URI: [eg:extractionResult__named_entities](http://w3id.org/ontogpt/environmental-metagenome/extractionResult__named_entities) - - -## Domain and Range - -None → <sub>0..\*</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/metagenome_study/docs/extractionResult__prompt.md b/projects/metagenome_study/docs/extractionResult__prompt.md deleted file mode 100644 index 92f9fd7f9..000000000 --- a/projects/metagenome_study/docs/extractionResult__prompt.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: prompt - - - - -URI: [eg:extractionResult__prompt](http://w3id.org/ontogpt/environmental-metagenome/extractionResult__prompt) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/metagenome_study/docs/extractionResult__raw_completion_output.md b/projects/metagenome_study/docs/extractionResult__raw_completion_output.md deleted file mode 100644 index 8b9ce4d67..000000000 --- a/projects/metagenome_study/docs/extractionResult__raw_completion_output.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: raw_completion_output - - - - -URI: [eg:extractionResult__raw_completion_output](http://w3id.org/ontogpt/environmental-metagenome/extractionResult__raw_completion_output) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/metagenome_study/docs/measurement__unit.md b/projects/metagenome_study/docs/measurement__unit.md deleted file mode 100644 index cc1ddbfbf..000000000 --- a/projects/metagenome_study/docs/measurement__unit.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: unit - - -the unit of the measurement - -URI: [eg:measurement__unit](http://w3id.org/ontogpt/environmental-metagenome/measurement__unit) - - -## Domain and Range - -None → <sub>0..1</sub> [Unit](Unit.md) - -## Parents - - -## Children - - -## Used by - - * [Measurement](Measurement.md) diff --git a/projects/metagenome_study/docs/measurement__value.md b/projects/metagenome_study/docs/measurement__value.md deleted file mode 100644 index 0f5c56d54..000000000 --- a/projects/metagenome_study/docs/measurement__value.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: value - - -the value of the measurement - -URI: [eg:measurement__value](http://w3id.org/ontogpt/environmental-metagenome/measurement__value) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Measurement](Measurement.md) diff --git a/projects/metagenome_study/docs/metagenome_study.md b/projects/metagenome_study/docs/metagenome_study.md deleted file mode 100644 index d3006b5fc..000000000 --- a/projects/metagenome_study/docs/metagenome_study.md +++ /dev/null @@ -1,127 +0,0 @@ - -# environmental-metagenome - - -**metamodel version:** 1.7.0 - -**version:** None - - -A template for Environmental Metagenome Studies - - -### Classes - - * [AnnotatorResult](AnnotatorResult.md) - * [Any](Any.md) - * [CompoundExpression](CompoundExpression.md) - * [CausalRelationship](CausalRelationship.md) - * [Measurement](Measurement.md) - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - * [ExtractionResult](ExtractionResult.md) - A result of extracting knowledge on text - * [NamedEntity](NamedEntity.md) - * [Environment](Environment.md) - * [EnvironmentalMaterial](EnvironmentalMaterial.md) - * [Location](Location.md) - * [Organism](Organism.md) - * [RelationshipType](RelationshipType.md) - * [SequencingTechnology](SequencingTechnology.md) - * [Treatment](Treatment.md) - * [Unit](Unit.md) - * [Variable](Variable.md) - * [Publication](Publication.md) - * [Study](Study.md) - * [TextWithTriples](TextWithTriples.md) - -### Mixins - - -### Slots - - * [➞object_id](annotatorResult__object_id.md) - * [➞object_text](annotatorResult__object_text.md) - * [➞subject_text](annotatorResult__subject_text.md) - * [➞cause](causalRelationship__cause.md) - the variable that is the cause of the effect - * [➞effect](causalRelationship__effect.md) - the things that is affected - * [➞extracted_object](extractionResult__extracted_object.md) - The complex objects extracted from the text - * [➞input_id](extractionResult__input_id.md) - * [➞input_text](extractionResult__input_text.md) - * [➞input_title](extractionResult__input_title.md) - * [➞named_entities](extractionResult__named_entities.md) - Named entities extracted from the text - * [➞prompt](extractionResult__prompt.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) - * [➞unit](measurement__unit.md) - the unit of the measurement - * [➞value](measurement__value.md) - the value of the measurement - * [➞id](namedEntity__id.md) - A unique identifier for the named entity - * [➞label](namedEntity__label.md) - The label (name) of the named thing - * [➞abstract](publication__abstract.md) - The abstract of the publication - * [➞combined_text](publication__combined_text.md) - * [➞full_text](publication__full_text.md) - The full text of the publication - * [➞id](publication__id.md) - The publication identifier - * [➞title](publication__title.md) - The title of the publication - * [➞causal_relationships](study__causal_relationships.md) - * [➞environmental_material](study__environmental_material.md) - the environmental material that was sampled - * [➞environments](study__environments.md) - * [➞location](study__location.md) - the sites at which the study was conducted - * [➞measurements](study__measurements.md) - * [➞organisms](study__organisms.md) - semicolon-separated list of all studied organism taxons - * [➞sequencing_technologies](study__sequencing_technologies.md) - * [➞treatments](study__treatments.md) - * [➞variables](study__variables.md) - * [➞publication](textWithTriples__publication.md) - * [➞triples](textWithTriples__triples.md) - * [➞object](triple__object.md) - * [➞object_qualifier](triple__object_qualifier.md) - An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * [➞predicate](triple__predicate.md) - * [➞qualifier](triple__qualifier.md) - A qualifier for the statements, e.g. "NOT" for negation - * [➞subject](triple__subject.md) - * [➞subject_qualifier](triple__subject_qualifier.md) - An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -### Enums - - * [NullDataOptions](NullDataOptions.md) - -### Subsets - - -### Types - - -#### Built in - - * **Bool** - * **Curie** - * **Decimal** - * **ElementIdentifier** - * **NCName** - * **NodeIdentifier** - * **URI** - * **URIorCURIE** - * **XSDDate** - * **XSDDateTime** - * **XSDTime** - * **float** - * **int** - * **str** - -#### Defined - - * [Boolean](types/Boolean.md) (**Bool**) - A binary (true or false) value - * [Curie](types/Curie.md) (**Curie**) - a compact URI - * [Date](types/Date.md) (**XSDDate**) - a date (year, month and day) in an idealized calendar - * [DateOrDatetime](types/DateOrDatetime.md) (**str**) - Either a date or a datetime - * [Datetime](types/Datetime.md) (**XSDDateTime**) - The combination of a date and time - * [Decimal](types/Decimal.md) (**Decimal**) - A real number with arbitrary precision that conforms to the xsd:decimal specification - * [Double](types/Double.md) (**float**) - A real number that conforms to the xsd:double specification - * [Float](types/Float.md) (**float**) - A real number that conforms to the xsd:float specification - * [Integer](types/Integer.md) (**int**) - An integer - * [Jsonpath](types/Jsonpath.md) (**str**) - A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - * [Jsonpointer](types/Jsonpointer.md) (**str**) - A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - * [Ncname](types/Ncname.md) (**NCName**) - Prefix part of CURIE - * [Nodeidentifier](types/Nodeidentifier.md) (**NodeIdentifier**) - A URI, CURIE or BNODE that represents a node in a model. - * [Objectidentifier](types/Objectidentifier.md) (**ElementIdentifier**) - A URI or CURIE that represents an object in the model. - * [Sparqlpath](types/Sparqlpath.md) (**str**) - A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - * [String](types/String.md) (**str**) - A character string - * [Time](types/Time.md) (**XSDTime**) - A time object represents a (local) time of day, independent of any particular day - * [Uri](types/Uri.md) (**URI**) - a complete URI - * [Uriorcurie](types/Uriorcurie.md) (**URIorCURIE**) - a URI or a CURIE diff --git a/projects/metagenome_study/docs/namedEntity__id.md b/projects/metagenome_study/docs/namedEntity__id.md deleted file mode 100644 index e286fa5da..000000000 --- a/projects/metagenome_study/docs/namedEntity__id.md +++ /dev/null @@ -1,38 +0,0 @@ - -# Slot: id - - -A unique identifier for the named entity - -URI: [eg:namedEntity__id](http://w3id.org/ontogpt/environmental-metagenome/namedEntity__id) - - -## Domain and Range - -None → <sub>1..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Environment](Environment.md) - * [EnvironmentalMaterial](EnvironmentalMaterial.md) - * [Location](Location.md) - * [NamedEntity](NamedEntity.md) - * [Organism](Organism.md) - * [RelationshipType](RelationshipType.md) - * [SequencingTechnology](SequencingTechnology.md) - * [Treatment](Treatment.md) - * [Unit](Unit.md) - * [Variable](Variable.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | this is populated during the grounding and normalization step | - diff --git a/projects/metagenome_study/docs/namedEntity__label.md b/projects/metagenome_study/docs/namedEntity__label.md deleted file mode 100644 index 91f1700d0..000000000 --- a/projects/metagenome_study/docs/namedEntity__label.md +++ /dev/null @@ -1,39 +0,0 @@ - -# Slot: label - - -The label (name) of the named thing - -URI: [eg:namedEntity__label](http://w3id.org/ontogpt/environmental-metagenome/namedEntity__label) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Environment](Environment.md) - * [EnvironmentalMaterial](EnvironmentalMaterial.md) - * [Location](Location.md) - * [NamedEntity](NamedEntity.md) - * [Organism](Organism.md) - * [RelationshipType](RelationshipType.md) - * [SequencingTechnology](SequencingTechnology.md) - * [Treatment](Treatment.md) - * [Unit](Unit.md) - * [Variable](Variable.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Aliases:** | | name | -| **Mappings:** | | rdfs:label | - diff --git a/projects/metagenome_study/docs/publication__abstract.md b/projects/metagenome_study/docs/publication__abstract.md deleted file mode 100644 index ea3b03594..000000000 --- a/projects/metagenome_study/docs/publication__abstract.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: abstract - - -The abstract of the publication - -URI: [eg:publication__abstract](http://w3id.org/ontogpt/environmental-metagenome/publication__abstract) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/metagenome_study/docs/publication__combined_text.md b/projects/metagenome_study/docs/publication__combined_text.md deleted file mode 100644 index 3a3660515..000000000 --- a/projects/metagenome_study/docs/publication__combined_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: combined_text - - - - -URI: [eg:publication__combined_text](http://w3id.org/ontogpt/environmental-metagenome/publication__combined_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/metagenome_study/docs/publication__full_text.md b/projects/metagenome_study/docs/publication__full_text.md deleted file mode 100644 index 851f27ec7..000000000 --- a/projects/metagenome_study/docs/publication__full_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: full_text - - -The full text of the publication - -URI: [eg:publication__full_text](http://w3id.org/ontogpt/environmental-metagenome/publication__full_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/metagenome_study/docs/publication__id.md b/projects/metagenome_study/docs/publication__id.md deleted file mode 100644 index 4510a8bb1..000000000 --- a/projects/metagenome_study/docs/publication__id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: id - - -The publication identifier - -URI: [eg:publication__id](http://w3id.org/ontogpt/environmental-metagenome/publication__id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/metagenome_study/docs/publication__title.md b/projects/metagenome_study/docs/publication__title.md deleted file mode 100644 index 454b784fe..000000000 --- a/projects/metagenome_study/docs/publication__title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: title - - -The title of the publication - -URI: [eg:publication__title](http://w3id.org/ontogpt/environmental-metagenome/publication__title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/metagenome_study/docs/study__causal_relationships.md b/projects/metagenome_study/docs/study__causal_relationships.md deleted file mode 100644 index 445f65367..000000000 --- a/projects/metagenome_study/docs/study__causal_relationships.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: causal_relationships - - - - -URI: [eg:study__causal_relationships](http://w3id.org/ontogpt/environmental-metagenome/study__causal_relationships) - - -## Domain and Range - -None → <sub>0..\*</sub> [CausalRelationship](CausalRelationship.md) - -## Parents - - -## Children - - -## Used by - - * [Study](Study.md) diff --git a/projects/metagenome_study/docs/study__environmental_material.md b/projects/metagenome_study/docs/study__environmental_material.md deleted file mode 100644 index 74ada8ff9..000000000 --- a/projects/metagenome_study/docs/study__environmental_material.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: environmental_material - - -the environmental material that was sampled - -URI: [eg:study__environmental_material](http://w3id.org/ontogpt/environmental-metagenome/study__environmental_material) - - -## Domain and Range - -None → <sub>0..\*</sub> [EnvironmentalMaterial](EnvironmentalMaterial.md) - -## Parents - - -## Children - - -## Used by - - * [Study](Study.md) diff --git a/projects/metagenome_study/docs/study__environments.md b/projects/metagenome_study/docs/study__environments.md deleted file mode 100644 index 647846758..000000000 --- a/projects/metagenome_study/docs/study__environments.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: environments - - - - -URI: [eg:study__environments](http://w3id.org/ontogpt/environmental-metagenome/study__environments) - - -## Domain and Range - -None → <sub>0..\*</sub> [Environment](Environment.md) - -## Parents - - -## Children - - -## Used by - - * [Study](Study.md) diff --git a/projects/metagenome_study/docs/study__location.md b/projects/metagenome_study/docs/study__location.md deleted file mode 100644 index f0b5d7a61..000000000 --- a/projects/metagenome_study/docs/study__location.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: location - - -the sites at which the study was conducted - -URI: [eg:study__location](http://w3id.org/ontogpt/environmental-metagenome/study__location) - - -## Domain and Range - -None → <sub>0..\*</sub> [Location](Location.md) - -## Parents - - -## Children - - -## Used by - - * [Study](Study.md) diff --git a/projects/metagenome_study/docs/study__measurements.md b/projects/metagenome_study/docs/study__measurements.md deleted file mode 100644 index 4d04c0d93..000000000 --- a/projects/metagenome_study/docs/study__measurements.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: measurements - - - - -URI: [eg:study__measurements](http://w3id.org/ontogpt/environmental-metagenome/study__measurements) - - -## Domain and Range - -None → <sub>0..\*</sub> [Measurement](Measurement.md) - -## Parents - - -## Children - - -## Used by - - * [Study](Study.md) diff --git a/projects/metagenome_study/docs/study__organisms.md b/projects/metagenome_study/docs/study__organisms.md deleted file mode 100644 index 1ce915868..000000000 --- a/projects/metagenome_study/docs/study__organisms.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: organisms - - -semicolon-separated list of all studied organism taxons - -URI: [eg:study__organisms](http://w3id.org/ontogpt/environmental-metagenome/study__organisms) - - -## Domain and Range - -None → <sub>0..\*</sub> [Organism](Organism.md) - -## Parents - - -## Children - - -## Used by - - * [Study](Study.md) diff --git a/projects/metagenome_study/docs/study__sequencing_technologies.md b/projects/metagenome_study/docs/study__sequencing_technologies.md deleted file mode 100644 index 27bdef22a..000000000 --- a/projects/metagenome_study/docs/study__sequencing_technologies.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: sequencing_technologies - - - - -URI: [eg:study__sequencing_technologies](http://w3id.org/ontogpt/environmental-metagenome/study__sequencing_technologies) - - -## Domain and Range - -None → <sub>0..1</sub> [SequencingTechnology](SequencingTechnology.md) - -## Parents - - -## Children - - -## Used by - - * [Study](Study.md) diff --git a/projects/metagenome_study/docs/study__treatments.md b/projects/metagenome_study/docs/study__treatments.md deleted file mode 100644 index e33275db8..000000000 --- a/projects/metagenome_study/docs/study__treatments.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: treatments - - - - -URI: [eg:study__treatments](http://w3id.org/ontogpt/environmental-metagenome/study__treatments) - - -## Domain and Range - -None → <sub>0..\*</sub> [Treatment](Treatment.md) - -## Parents - - -## Children - - -## Used by - - * [Study](Study.md) diff --git a/projects/metagenome_study/docs/study__variables.md b/projects/metagenome_study/docs/study__variables.md deleted file mode 100644 index 33f78519b..000000000 --- a/projects/metagenome_study/docs/study__variables.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: variables - - - - -URI: [eg:study__variables](http://w3id.org/ontogpt/environmental-metagenome/study__variables) - - -## Domain and Range - -None → <sub>0..\*</sub> [Variable](Variable.md) - -## Parents - - -## Children - - -## Used by - - * [Study](Study.md) diff --git a/projects/metagenome_study/docs/textWithTriples__publication.md b/projects/metagenome_study/docs/textWithTriples__publication.md deleted file mode 100644 index 6e8a399ac..000000000 --- a/projects/metagenome_study/docs/textWithTriples__publication.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: publication - - - - -URI: [eg:textWithTriples__publication](http://w3id.org/ontogpt/environmental-metagenome/textWithTriples__publication) - - -## Domain and Range - -None → <sub>0..1</sub> [Publication](Publication.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/metagenome_study/docs/textWithTriples__triples.md b/projects/metagenome_study/docs/textWithTriples__triples.md deleted file mode 100644 index ed815e562..000000000 --- a/projects/metagenome_study/docs/textWithTriples__triples.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: triples - - - - -URI: [eg:textWithTriples__triples](http://w3id.org/ontogpt/environmental-metagenome/textWithTriples__triples) - - -## Domain and Range - -None → <sub>0..\*</sub> [Triple](Triple.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/metagenome_study/docs/triple__object.md b/projects/metagenome_study/docs/triple__object.md deleted file mode 100644 index a619f13a0..000000000 --- a/projects/metagenome_study/docs/triple__object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object - - - - -URI: [eg:triple__object](http://w3id.org/ontogpt/environmental-metagenome/triple__object) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/metagenome_study/docs/triple__object_qualifier.md b/projects/metagenome_study/docs/triple__object_qualifier.md deleted file mode 100644 index aa5e45562..000000000 --- a/projects/metagenome_study/docs/triple__object_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_qualifier - - -An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - -URI: [eg:triple__object_qualifier](http://w3id.org/ontogpt/environmental-metagenome/triple__object_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/metagenome_study/docs/triple__predicate.md b/projects/metagenome_study/docs/triple__predicate.md deleted file mode 100644 index c9ae7609a..000000000 --- a/projects/metagenome_study/docs/triple__predicate.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: predicate - - - - -URI: [eg:triple__predicate](http://w3id.org/ontogpt/environmental-metagenome/triple__predicate) - - -## Domain and Range - -None → <sub>0..1</sub> [RelationshipType](RelationshipType.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/metagenome_study/docs/triple__qualifier.md b/projects/metagenome_study/docs/triple__qualifier.md deleted file mode 100644 index 3acc8ce50..000000000 --- a/projects/metagenome_study/docs/triple__qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: qualifier - - -A qualifier for the statements, e.g. "NOT" for negation - -URI: [eg:triple__qualifier](http://w3id.org/ontogpt/environmental-metagenome/triple__qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/metagenome_study/docs/triple__subject.md b/projects/metagenome_study/docs/triple__subject.md deleted file mode 100644 index 29f69ea83..000000000 --- a/projects/metagenome_study/docs/triple__subject.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject - - - - -URI: [eg:triple__subject](http://w3id.org/ontogpt/environmental-metagenome/triple__subject) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/metagenome_study/docs/triple__subject_qualifier.md b/projects/metagenome_study/docs/triple__subject_qualifier.md deleted file mode 100644 index 882b9d5e4..000000000 --- a/projects/metagenome_study/docs/triple__subject_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_qualifier - - -An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -URI: [eg:triple__subject_qualifier](http://w3id.org/ontogpt/environmental-metagenome/triple__subject_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/metagenome_study/docs/types/Boolean.md b/projects/metagenome_study/docs/types/Boolean.md deleted file mode 100644 index dc83a9c6e..000000000 --- a/projects/metagenome_study/docs/types/Boolean.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: boolean - - -A binary (true or false) value - -URI: [linkml:Boolean](https://w3id.org/linkml/Boolean) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Bool** | -| Representation | | bool | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Boolean | - diff --git a/projects/metagenome_study/docs/types/Curie.md b/projects/metagenome_study/docs/types/Curie.md deleted file mode 100644 index c1803f93f..000000000 --- a/projects/metagenome_study/docs/types/Curie.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: curie - - -a compact URI - -URI: [linkml:Curie](https://w3id.org/linkml/Curie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Curie** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations this MUST be expanded to a URI | -| | | in non-RDF serializations MAY be serialized as the compact representation | - diff --git a/projects/metagenome_study/docs/types/Date.md b/projects/metagenome_study/docs/types/Date.md deleted file mode 100644 index 06948af97..000000000 --- a/projects/metagenome_study/docs/types/Date.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: date - - -a date (year, month and day) in an idealized calendar - -URI: [linkml:Date](https://w3id.org/linkml/Date) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDate** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Date | - diff --git a/projects/metagenome_study/docs/types/DateOrDatetime.md b/projects/metagenome_study/docs/types/DateOrDatetime.md deleted file mode 100644 index ef983898d..000000000 --- a/projects/metagenome_study/docs/types/DateOrDatetime.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: date_or_datetime - - -Either a date or a datetime - -URI: [linkml:DateOrDatetime](https://w3id.org/linkml/DateOrDatetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/metagenome_study/docs/types/Datetime.md b/projects/metagenome_study/docs/types/Datetime.md deleted file mode 100644 index 9510454a8..000000000 --- a/projects/metagenome_study/docs/types/Datetime.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: datetime - - -The combination of a date and time - -URI: [linkml:Datetime](https://w3id.org/linkml/Datetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDateTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:DateTime | - diff --git a/projects/metagenome_study/docs/types/Decimal.md b/projects/metagenome_study/docs/types/Decimal.md deleted file mode 100644 index a7ba14a5d..000000000 --- a/projects/metagenome_study/docs/types/Decimal.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: decimal - - -A real number with arbitrary precision that conforms to the xsd:decimal specification - -URI: [linkml:Decimal](https://w3id.org/linkml/Decimal) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Decimal** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Broad Mappings:** | | schema:Number | - diff --git a/projects/metagenome_study/docs/types/Double.md b/projects/metagenome_study/docs/types/Double.md deleted file mode 100644 index cfe6d71e2..000000000 --- a/projects/metagenome_study/docs/types/Double.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: double - - -A real number that conforms to the xsd:double specification - -URI: [linkml:Double](https://w3id.org/linkml/Double) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Close Mappings:** | | schema:Float | - diff --git a/projects/metagenome_study/docs/types/Float.md b/projects/metagenome_study/docs/types/Float.md deleted file mode 100644 index 7b303f96f..000000000 --- a/projects/metagenome_study/docs/types/Float.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: float - - -A real number that conforms to the xsd:float specification - -URI: [linkml:Float](https://w3id.org/linkml/Float) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Float | - diff --git a/projects/metagenome_study/docs/types/Integer.md b/projects/metagenome_study/docs/types/Integer.md deleted file mode 100644 index 3cfcc66d9..000000000 --- a/projects/metagenome_study/docs/types/Integer.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: integer - - -An integer - -URI: [linkml:Integer](https://w3id.org/linkml/Integer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **int** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Integer | - diff --git a/projects/metagenome_study/docs/types/Jsonpath.md b/projects/metagenome_study/docs/types/Jsonpath.md deleted file mode 100644 index a03a58e67..000000000 --- a/projects/metagenome_study/docs/types/Jsonpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpath - - -A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpath](https://w3id.org/linkml/Jsonpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/metagenome_study/docs/types/Jsonpointer.md b/projects/metagenome_study/docs/types/Jsonpointer.md deleted file mode 100644 index a0e1ac492..000000000 --- a/projects/metagenome_study/docs/types/Jsonpointer.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpointer - - -A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpointer](https://w3id.org/linkml/Jsonpointer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/metagenome_study/docs/types/Ncname.md b/projects/metagenome_study/docs/types/Ncname.md deleted file mode 100644 index 710b0b04a..000000000 --- a/projects/metagenome_study/docs/types/Ncname.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: ncname - - -Prefix part of CURIE - -URI: [linkml:Ncname](https://w3id.org/linkml/Ncname) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NCName** | -| Representation | | str | diff --git a/projects/metagenome_study/docs/types/Nodeidentifier.md b/projects/metagenome_study/docs/types/Nodeidentifier.md deleted file mode 100644 index f0097cdf4..000000000 --- a/projects/metagenome_study/docs/types/Nodeidentifier.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: nodeidentifier - - -A URI, CURIE or BNODE that represents a node in a model. - -URI: [linkml:Nodeidentifier](https://w3id.org/linkml/Nodeidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NodeIdentifier** | -| Representation | | str | diff --git a/projects/metagenome_study/docs/types/Objectidentifier.md b/projects/metagenome_study/docs/types/Objectidentifier.md deleted file mode 100644 index 454ba6be6..000000000 --- a/projects/metagenome_study/docs/types/Objectidentifier.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: objectidentifier - - -A URI or CURIE that represents an object in the model. - -URI: [linkml:Objectidentifier](https://w3id.org/linkml/Objectidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **ElementIdentifier** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | Used for inheritance and type checking | - diff --git a/projects/metagenome_study/docs/types/Sparqlpath.md b/projects/metagenome_study/docs/types/Sparqlpath.md deleted file mode 100644 index fd99a927e..000000000 --- a/projects/metagenome_study/docs/types/Sparqlpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: sparqlpath - - -A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - -URI: [linkml:Sparqlpath](https://w3id.org/linkml/Sparqlpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/metagenome_study/docs/types/String.md b/projects/metagenome_study/docs/types/String.md deleted file mode 100644 index 6e61d7081..000000000 --- a/projects/metagenome_study/docs/types/String.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: string - - -A character string - -URI: [linkml:String](https://w3id.org/linkml/String) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Text | - diff --git a/projects/metagenome_study/docs/types/Time.md b/projects/metagenome_study/docs/types/Time.md deleted file mode 100644 index 2b8652bcd..000000000 --- a/projects/metagenome_study/docs/types/Time.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: time - - -A time object represents a (local) time of day, independent of any particular day - -URI: [linkml:Time](https://w3id.org/linkml/Time) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Time | - diff --git a/projects/metagenome_study/docs/types/Uri.md b/projects/metagenome_study/docs/types/Uri.md deleted file mode 100644 index 343807a5e..000000000 --- a/projects/metagenome_study/docs/types/Uri.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: uri - - -a complete URI - -URI: [linkml:Uri](https://w3id.org/linkml/Uri) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URI** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node | -| **Close Mappings:** | | schema:URL | - diff --git a/projects/metagenome_study/docs/types/Uriorcurie.md b/projects/metagenome_study/docs/types/Uriorcurie.md deleted file mode 100644 index 2f7b65087..000000000 --- a/projects/metagenome_study/docs/types/Uriorcurie.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: uriorcurie - - -a URI or a CURIE - -URI: [linkml:Uriorcurie](https://w3id.org/linkml/Uriorcurie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URIorCURIE** | -| Representation | | str | diff --git a/projects/metagenome_study/excel/metagenome_study.xlsx b/projects/metagenome_study/excel/metagenome_study.xlsx deleted file mode 100644 index 4b57ab418..000000000 Binary files a/projects/metagenome_study/excel/metagenome_study.xlsx and /dev/null differ diff --git a/projects/metagenome_study/graphql/metagenome_study.graphql b/projects/metagenome_study/graphql/metagenome_study.graphql deleted file mode 100644 index d52f84ffd..000000000 --- a/projects/metagenome_study/graphql/metagenome_study.graphql +++ /dev/null @@ -1,136 +0,0 @@ -type AnnotatorResult - { - subjectText: String - objectId: String - objectText: String - } - -type Any - { - } - -type CausalRelationship - { - cause: Variable - effect: Variable - } - -interface CompoundExpression - { - } - -type Environment - { - id: String! - label: String - } - -type EnvironmentalMaterial - { - id: String! - label: String - } - -type ExtractionResult - { - inputId: String - inputTitle: String - inputText: String - rawCompletionOutput: String - prompt: String - extractedObject: Any - namedEntities: [Any] - } - -type Location - { - id: String! - label: String - } - -type Measurement - { - value: String - unit: Unit - } - -interface NamedEntity - { - id: String! - label: String - } - -type Organism - { - id: String! - label: String - } - -type Publication - { - id: String - title: String - abstract: String - combinedText: String - fullText: String - } - -type RelationshipType - { - id: String! - label: String - } - -type SequencingTechnology - { - id: String! - label: String - } - -type Study - { - environments: [Environment] - causalRelationships: [CausalRelationship] - variables: [Variable] - treatments: [Treatment] - measurements: [Measurement] - location: [Location] - environmentalMaterial: [EnvironmentalMaterial] - sequencingTechnologies: SequencingTechnology - organisms: [Organism] - } - -type TextWithTriples - { - publication: Publication - triples: [Triple] - } - -type Treatment - { - id: String! - label: String - } - -interface Triple - { - subject: NamedEntity - predicate: RelationshipType - object: NamedEntity - qualifier: String - subjectQualifier: NamedEntity - objectQualifier: NamedEntity - } - -type Unit - { - id: String! - label: String - } - -type Variable - { - id: String! - label: String - } - diff --git a/projects/metagenome_study/jsonld/metagenome_study.context.jsonld b/projects/metagenome_study/jsonld/metagenome_study.context.jsonld deleted file mode 100644 index 4c7981d7a..000000000 --- a/projects/metagenome_study/jsonld/metagenome_study.context.jsonld +++ /dev/null @@ -1,177 +0,0 @@ -{ - "comments": { - "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2023-08-07T10:55:00", - "source": "metagenome_study.yaml" - }, - "@context": { - "EFO": "http://example.org/UNKNOWN/EFO/", - "ENVO": "http://example.org/UNKNOWN/ENVO/", - "GAZ": "http://example.org/UNKNOWN/GAZ/", - "IDO": "http://example.org/UNKNOWN/IDO/", - "MIXS": "http://example.org/UNKNOWN/MIXS/", - "NCBITaxon": "http://example.org/UNKNOWN/NCBITaxon/", - "NCIT": { - "@id": "http://purl.obolibrary.org/obo/NCIT_", - "@prefix": true - }, - "OBI": "http://example.org/UNKNOWN/OBI/", - "PATO": "http://example.org/UNKNOWN/PATO/", - "PECO": "http://example.org/UNKNOWN/PECO/", - "RO": { - "@id": "http://purl.obolibrary.org/obo/RO_", - "@prefix": true - }, - "UO": "http://example.org/UNKNOWN/UO/", - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "eg": "http://w3id.org/ontogpt/environmental-metagenome/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "@vocab": "http://w3id.org/ontogpt/environmental-metagenome/", - "object_id": { - "@id": "core:object_id" - }, - "object_text": { - "@id": "core:object_text" - }, - "subject_text": { - "@id": "core:subject_text" - }, - "cause": { - "@type": "@id" - }, - "effect": { - "@type": "@id" - }, - "extracted_object": { - "@type": "@id", - "@id": "core:extracted_object" - }, - "input_id": { - "@id": "core:input_id" - }, - "input_text": { - "@id": "core:input_text" - }, - "input_title": { - "@id": "core:input_title" - }, - "named_entities": { - "@type": "@id", - "@id": "core:named_entities" - }, - "prompt": { - "@id": "core:prompt" - }, - "raw_completion_output": { - "@id": "core:raw_completion_output" - }, - "unit": { - "@type": "@id" - }, - "id": { - "@id": "core:id" - }, - "label": { - "@id": "rdfs:label" - }, - "abstract": { - "@id": "core:abstract" - }, - "combined_text": { - "@id": "core:combined_text" - }, - "full_text": { - "@id": "core:full_text" - }, - "title": { - "@id": "core:title" - }, - "causal_relationships": { - "@type": "@id" - }, - "environmental_material": { - "@type": "@id" - }, - "environments": { - "@type": "@id" - }, - "location": { - "@type": "@id" - }, - "measurements": { - "@type": "@id" - }, - "organisms": { - "@type": "@id" - }, - "sequencing_technologies": { - "@type": "@id" - }, - "treatments": { - "@type": "@id" - }, - "variables": { - "@type": "@id" - }, - "publication": { - "@type": "@id", - "@id": "core:publication" - }, - "triples": { - "@type": "@id", - "@id": "core:triples" - }, - "object": { - "@type": "@id", - "@id": "core:object" - }, - "object_qualifier": { - "@type": "@id", - "@id": "core:object_qualifier" - }, - "predicate": { - "@type": "@id", - "@id": "core:predicate" - }, - "qualifier": { - "@id": "core:qualifier" - }, - "subject": { - "@type": "@id", - "@id": "core:subject" - }, - "subject_qualifier": { - "@type": "@id", - "@id": "core:subject_qualifier" - }, - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } - } -} diff --git a/projects/metagenome_study/jsonld/metagenome_study.jsonld b/projects/metagenome_study/jsonld/metagenome_study.jsonld deleted file mode 100644 index a964918f1..000000000 --- a/projects/metagenome_study/jsonld/metagenome_study.jsonld +++ /dev/null @@ -1,1576 +0,0 @@ -{ - "name": "environmental-metagenome", - "description": "A template for Environmental Metagenome Studies", - "title": "Environmental Metagenome Template", - "id": "http://w3id.org/ontogpt/metagenome", - "imports": [ - "linkml:types", - "core" - ], - "license": "https://creativecommons.org/publicdomain/zero/1.0/", - "prefixes": [ - { - "prefix_prefix": "linkml", - "prefix_reference": "https://w3id.org/linkml/" - }, - { - "prefix_prefix": "eg", - "prefix_reference": "http://w3id.org/ontogpt/environmental-metagenome/" - } - ], - "default_prefix": "eg", - "default_range": "string", - "types": [ - { - "name": "string", - "definition_uri": "https://w3id.org/linkml/String", - "description": "A character string", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Text" - ], - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "@type": "TypeDefinition" - }, - { - "name": "integer", - "definition_uri": "https://w3id.org/linkml/Integer", - "description": "An integer", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Integer" - ], - "base": "int", - "uri": "http://www.w3.org/2001/XMLSchema#integer", - "@type": "TypeDefinition" - }, - { - "name": "boolean", - "definition_uri": "https://w3id.org/linkml/Boolean", - "description": "A binary (true or false) value", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Boolean" - ], - "base": "Bool", - "uri": "http://www.w3.org/2001/XMLSchema#boolean", - "repr": "bool", - "@type": "TypeDefinition" - }, - { - "name": "float", - "definition_uri": "https://w3id.org/linkml/Float", - "description": "A real number that conforms to the xsd:float specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#float", - "@type": "TypeDefinition" - }, - { - "name": "double", - "definition_uri": "https://w3id.org/linkml/Double", - "description": "A real number that conforms to the xsd:double specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#double", - "@type": "TypeDefinition" - }, - { - "name": "decimal", - "definition_uri": "https://w3id.org/linkml/Decimal", - "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "broad_mappings": [ - "schema:Number" - ], - "base": "Decimal", - "uri": "http://www.w3.org/2001/XMLSchema#decimal", - "@type": "TypeDefinition" - }, - { - "name": "time", - "definition_uri": "https://w3id.org/linkml/Time", - "description": "A time object represents a (local) time of day, independent of any particular day", - "notes": [ - "URI is dateTime because OWL reasoners do not work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Time" - ], - "base": "XSDTime", - "uri": "http://www.w3.org/2001/XMLSchema#time", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date", - "definition_uri": "https://w3id.org/linkml/Date", - "description": "a date (year, month and day) in an idealized calendar", - "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Date" - ], - "base": "XSDDate", - "uri": "http://www.w3.org/2001/XMLSchema#date", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "datetime", - "definition_uri": "https://w3id.org/linkml/Datetime", - "description": "The combination of a date and time", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:DateTime" - ], - "base": "XSDDateTime", - "uri": "http://www.w3.org/2001/XMLSchema#dateTime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date_or_datetime", - "definition_uri": "https://w3id.org/linkml/DateOrDatetime", - "description": "Either a date or a datetime", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "https://w3id.org/linkml/DateOrDatetime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uriorcurie", - "definition_uri": "https://w3id.org/linkml/Uriorcurie", - "description": "a URI or a CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "URIorCURIE", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "curie", - "definition_uri": "https://w3id.org/linkml/Curie", - "conforms_to": "https://www.w3.org/TR/curie/", - "description": "a compact URI", - "comments": [ - "in RDF serializations this MUST be expanded to a URI", - "in non-RDF serializations MAY be serialized as the compact representation" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "Curie", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uri", - "definition_uri": "https://w3id.org/linkml/Uri", - "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", - "description": "a complete URI", - "comments": [ - "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:URL" - ], - "base": "URI", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "ncname", - "definition_uri": "https://w3id.org/linkml/Ncname", - "description": "Prefix part of CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NCName", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "objectidentifier", - "definition_uri": "https://w3id.org/linkml/Objectidentifier", - "description": "A URI or CURIE that represents an object in the model.", - "comments": [ - "Used for inheritance and type checking" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "ElementIdentifier", - "uri": "http://www.w3.org/ns/shex#iri", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "nodeidentifier", - "definition_uri": "https://w3id.org/linkml/Nodeidentifier", - "description": "A URI, CURIE or BNODE that represents a node in a model.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NodeIdentifier", - "uri": "http://www.w3.org/ns/shex#nonLiteral", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpointer", - "definition_uri": "https://w3id.org/linkml/Jsonpointer", - "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901", - "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpath", - "definition_uri": "https://w3id.org/linkml/Jsonpath", - "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html", - "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "sparqlpath", - "definition_uri": "https://w3id.org/linkml/Sparqlpath", - "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths", - "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - } - ], - "enums": [ - { - "name": "NullDataOptions", - "definition_uri": "http://w3id.org/ontogpt/core/NullDataOptions", - "from_schema": "http://w3id.org/ontogpt/core", - "permissible_values": [ - { - "text": "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "meaning": "NCIT:C149701" - }, - { - "text": "NOT_APPLICABLE", - "meaning": "NCIT:C18902", - "aliases": [ - "not applicable", - "N/A" - ] - }, - { - "text": "NOT_MENTIONED" - } - ] - } - ], - "slots": [ - { - "name": "study__environments", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of environmental systems or biomes in which the study was conducted", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/metagenome", - "slot_uri": "http://w3id.org/ontogpt/environmental-metagenome/environments", - "multivalued": true, - "alias": "environments", - "owner": "Study", - "domain_of": [ - "Study" - ], - "range": "Environment", - "@type": "SlotDefinition" - }, - { - "name": "study__causal_relationships", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of cause-effect pairs, for example, effect of temperature on growth", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/metagenome", - "slot_uri": "http://w3id.org/ontogpt/environmental-metagenome/causal_relationships", - "multivalued": true, - "alias": "causal_relationships", - "owner": "Study", - "domain_of": [ - "Study" - ], - "range": "CausalRelationship", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "study__variables", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of environmental variables which are studies. E.g. temperature, pH, salinity", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/metagenome", - "slot_uri": "http://w3id.org/ontogpt/environmental-metagenome/variables", - "multivalued": true, - "alias": "variables", - "owner": "Study", - "domain_of": [ - "Study" - ], - "range": "Variable", - "@type": "SlotDefinition" - }, - { - "name": "study__treatments", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of treatments that are applied", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/metagenome", - "slot_uri": "http://w3id.org/ontogpt/environmental-metagenome/treatments", - "multivalued": true, - "alias": "treatments", - "owner": "Study", - "domain_of": [ - "Study" - ], - "range": "Treatment", - "@type": "SlotDefinition" - }, - { - "name": "study__measurements", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of value-measurement pairs", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/metagenome", - "slot_uri": "http://w3id.org/ontogpt/environmental-metagenome/measurements", - "multivalued": true, - "alias": "measurements", - "owner": "Study", - "domain_of": [ - "Study" - ], - "range": "Measurement", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "study__location", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of sites at which the study was conducted", - "@type": "Annotation" - } - ], - "description": "the sites at which the study was conducted", - "from_schema": "http://w3id.org/ontogpt/metagenome", - "slot_uri": "http://w3id.org/ontogpt/environmental-metagenome/location", - "multivalued": true, - "alias": "location", - "owner": "Study", - "domain_of": [ - "Study" - ], - "range": "Location", - "@type": "SlotDefinition" - }, - { - "name": "study__environmental_material", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of environmental materials", - "@type": "Annotation" - } - ], - "description": "the environmental material that was sampled", - "from_schema": "http://w3id.org/ontogpt/metagenome", - "slot_uri": "http://w3id.org/ontogpt/environmental-metagenome/environmental_material", - "multivalued": true, - "alias": "environmental_material", - "owner": "Study", - "domain_of": [ - "Study" - ], - "range": "EnvironmentalMaterial", - "@type": "SlotDefinition" - }, - { - "name": "study__sequencing_technologies", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of sequencing technologies used in the project", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/metagenome", - "slot_uri": "http://w3id.org/ontogpt/environmental-metagenome/sequencing_technologies", - "alias": "sequencing_technologies", - "owner": "Study", - "domain_of": [ - "Study" - ], - "range": "SequencingTechnology", - "@type": "SlotDefinition" - }, - { - "name": "study__organisms", - "description": "semicolon-separated list of all studied organism taxons", - "from_schema": "http://w3id.org/ontogpt/metagenome", - "slot_uri": "http://w3id.org/ontogpt/environmental-metagenome/organisms", - "multivalued": true, - "alias": "organisms", - "owner": "Study", - "domain_of": [ - "Study" - ], - "range": "Organism", - "@type": "SlotDefinition" - }, - { - "name": "measurement__value", - "description": "the value of the measurement", - "from_schema": "http://w3id.org/ontogpt/metagenome", - "slot_uri": "http://w3id.org/ontogpt/environmental-metagenome/value", - "alias": "value", - "owner": "Measurement", - "domain_of": [ - "Measurement" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "measurement__unit", - "description": "the unit of the measurement", - "from_schema": "http://w3id.org/ontogpt/metagenome", - "slot_uri": "http://w3id.org/ontogpt/environmental-metagenome/unit", - "alias": "unit", - "owner": "Measurement", - "domain_of": [ - "Measurement" - ], - "range": "Unit", - "@type": "SlotDefinition" - }, - { - "name": "causalRelationship__cause", - "description": "the variable that is the cause of the effect", - "from_schema": "http://w3id.org/ontogpt/metagenome", - "slot_uri": "http://w3id.org/ontogpt/environmental-metagenome/cause", - "alias": "cause", - "owner": "CausalRelationship", - "domain_of": [ - "CausalRelationship" - ], - "range": "Variable", - "@type": "SlotDefinition" - }, - { - "name": "causalRelationship__effect", - "description": "the things that is affected", - "from_schema": "http://w3id.org/ontogpt/metagenome", - "slot_uri": "http://w3id.org/ontogpt/environmental-metagenome/effect", - "alias": "effect", - "owner": "CausalRelationship", - "domain_of": [ - "CausalRelationship" - ], - "range": "Variable", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_id", - "alias": "input_id", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_title", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_title", - "alias": "input_title", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_text", - "alias": "input_text", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__raw_completion_output", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/raw_completion_output", - "alias": "raw_completion_output", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__prompt", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/prompt", - "alias": "prompt", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__extracted_object", - "description": "The complex objects extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/extracted_object", - "alias": "extracted_object", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__named_entities", - "description": "Named entities extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/named_entities", - "multivalued": true, - "alias": "named_entities", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "identifier": true, - "alias": "id", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "required": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "from_schema": "http://w3id.org/ontogpt/core", - "aliases": [ - "name" - ], - "mappings": [ - "http://example.org/UNKNOWN/rdfs/label" - ], - "slot_uri": "http://example.org/UNKNOWN/rdfs/label", - "alias": "label", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject", - "alias": "subject", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__predicate", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/predicate", - "alias": "predicate", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "triple__object", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object", - "alias": "object", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/qualifier", - "alias": "qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_qualifier", - "alias": "subject_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_qualifier", - "alias": "object_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/publication", - "alias": "publication", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__triples", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/triples", - "multivalued": true, - "alias": "triples", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "publication__id", - "description": "The publication identifier", - "from_schema": "http://w3id.org/ontogpt/core", - 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"ClassDefinition" - }, - { - "name": "Environment", - "id_prefixes": [ - "ENVO" - ], - "definition_uri": "http://w3id.org/ontogpt/environmental-metagenome/Environment", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:envo", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/metagenome", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/environmental-metagenome/Environment", - "@type": "ClassDefinition" - }, - { - "name": "Variable", - "id_prefixes": [ - "ENVO", - "MIXS", - "PATO" - ], - "definition_uri": "http://w3id.org/ontogpt/environmental-metagenome/Variable", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:envo, bioportal:bero", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/metagenome", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/environmental-metagenome/Variable", - "@type": "ClassDefinition" - }, - { - "name": "Unit", - "id_prefixes": [ - "UO", - "NCIT" - ], - "definition_uri": "http://w3id.org/ontogpt/environmental-metagenome/Unit", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:uo, bioportal:ncit", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/metagenome", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/environmental-metagenome/Unit", - "@type": "ClassDefinition" - }, - { - "name": "Measurement", - "definition_uri": "http://w3id.org/ontogpt/environmental-metagenome/Measurement", - "from_schema": "http://w3id.org/ontogpt/metagenome", - "is_a": "CompoundExpression", - "slots": [ - "measurement__value", - "measurement__unit" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "value", - "description": "the value of the 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"ClassDefinition" - }, - { - "name": "SequencingTechnology", - "id_prefixes": [ - "IDO", - "EFO" - ], - "definition_uri": "http://w3id.org/ontogpt/environmental-metagenome/SequencingTechnology", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:obi, sqlite:obo:efo, bioportal:bero", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/metagenome", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/environmental-metagenome/SequencingTechnology", - "@type": "ClassDefinition" - }, - { - "name": "Treatment", - "id_prefixes": [ - "PECO", - "OBI" - ], - "definition_uri": "http://w3id.org/ontogpt/environmental-metagenome/Treatment", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:peco, sqlite:obo:obi, bioportal:bero", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/metagenome", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/environmental-metagenome/Treatment", - "@type": "ClassDefinition" - }, - { - "name": "Organism", - "id_prefixes": [ - "NCBITaxon" - ], - "definition_uri": "http://w3id.org/ontogpt/environmental-metagenome/Organism", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:ncbitaxon, gilda:", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/metagenome", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/environmental-metagenome/Organism", - "@type": "ClassDefinition" - }, - { - "name": "Any", - "definition_uri": "http://w3id.org/ontogpt/core/Any", - "from_schema": "http://w3id.org/ontogpt/core", - "mappings": [ - "linkml:Any" - ], - "slot_usage": {}, - "class_uri": "https://w3id.org/linkml/Any", - "@type": "ClassDefinition" - }, - { - "name": "ExtractionResult", - "definition_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "description": "A result of extracting knowledge on text", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "extractionResult__input_id", - "extractionResult__input_title", - "extractionResult__input_text", - "extractionResult__raw_completion_output", - "extractionResult__prompt", - "extractionResult__extracted_object", - "extractionResult__named_entities" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "input_id", - "@type": "SlotDefinition" - }, - { - "name": "input_title", - "@type": "SlotDefinition" - }, - { - "name": "input_text", - "@type": "SlotDefinition" - }, - { - "name": "raw_completion_output", - "@type": "SlotDefinition" - }, - { - "name": "prompt", - "@type": "SlotDefinition" - }, - { - "name": "extracted_object", - "description": "The complex objects extracted from the text", - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "named_entities", - "description": "Named entities extracted from the text", - "multivalued": true, - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "@type": "ClassDefinition" - }, - { - "name": "NamedEntity", - "definition_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "identifier": true, - "@type": "SlotDefinition" - }, - { - "name": "label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, 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"@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Publication", - "@type": "ClassDefinition" - }, - { - "name": "AnnotatorResult", - "definition_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "annotatorResult__subject_text", - "annotatorResult__object_id", - "annotatorResult__object_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject_text", - "@type": "SlotDefinition" - }, - { - "name": "object_id", - "@type": "SlotDefinition" - }, - { - "name": "object_text", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "@type": "ClassDefinition" - } - ], - "metamodel_version": "1.7.0", - "source_file": "metagenome_study.yaml", - "source_file_date": "2023-06-17T15:11:19", - "source_file_size": 3910, - "generation_date": "2023-08-07T10:55:01", - "@type": "SchemaDefinition", - "@context": [ - "projects/metagenome_study/jsonld/metagenome_study.context.jsonld", - "https://w3id.org/linkml/types.context.jsonld", - "core.context.jsonld", - { - "@base": "http://w3id.org/ontogpt/environmental-metagenome/" - } - ] -} diff --git a/projects/metagenome_study/jsonschema/metagenome_study.schema.json b/projects/metagenome_study/jsonschema/metagenome_study.schema.json deleted file mode 100644 index f38bd53fc..000000000 --- a/projects/metagenome_study/jsonschema/metagenome_study.schema.json +++ /dev/null @@ -1,387 +0,0 @@ -{ - "$defs": { - "AnnotatorResult": { - "additionalProperties": false, - "description": "", - "properties": { - "object_id": { - "type": "string" - }, - "object_text": { - "type": "string" - }, - "subject_text": { - "type": "string" - } - }, - "title": "AnnotatorResult", - "type": "object" - }, - "Any": { - "additionalProperties": true, - "description": "", - "title": "Any", - "type": "object" - }, - "CausalRelationship": { - "additionalProperties": false, - "description": "", - "properties": { - "cause": { - "description": "the variable that is the cause of the effect", - "type": "string" - }, - "effect": { - "description": "the things that is affected", - "type": "string" - } - }, - "title": "CausalRelationship", - "type": "object" - }, - "Environment": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Environment", - "type": "object" - }, - "EnvironmentalMaterial": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "EnvironmentalMaterial", - "type": "object" - }, - "ExtractionResult": { - "additionalProperties": false, - "description": "A result of extracting knowledge on text", - "properties": { - "extracted_object": { - "$ref": "#/$defs/Any", - "description": "The complex objects extracted from the text" - }, - "input_id": { - "type": "string" - }, - "input_text": { - "type": "string" - }, - "input_title": { - "type": "string" - }, - "named_entities": { - "description": "Named entities extracted from the text", - "items": { - "$ref": "#/$defs/Any" - }, - "type": "array" - }, - "prompt": { - "type": "string" - }, - "raw_completion_output": { - "type": "string" - } - }, - "title": "ExtractionResult", - "type": "object" - }, - "Location": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Location", - "type": "object" - }, - "Measurement": { - "additionalProperties": false, - "description": "", - "properties": { - "unit": { - "description": "the unit of the measurement", - "type": "string" - }, - "value": { - "description": "the value of the measurement", - "type": "string" - } - }, - "title": "Measurement", - "type": "object" - }, - "NullDataOptions": { - "description": "", - "enum": [ - "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "NOT_APPLICABLE", - "NOT_MENTIONED" - ], - "title": "NullDataOptions", - "type": "string" - }, - "Organism": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Organism", - "type": "object" - }, - "Publication": { - "additionalProperties": false, - "description": "", - "properties": { - "abstract": { - "description": "The abstract of the publication", - "type": "string" - }, - "combined_text": { - "type": "string" - }, - "full_text": { - "description": "The full text of the publication", - "type": "string" - }, - "id": { - "description": "The publication identifier", - "type": "string" - }, - "title": { - "description": "The title of the publication", - "type": "string" - } - }, - "title": "Publication", - "type": "object" - }, - "RelationshipType": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "RelationshipType", - "type": "object" - }, - "SequencingTechnology": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "SequencingTechnology", - "type": "object" - }, - "Study": { - "additionalProperties": false, - "description": "", - "properties": { - "causal_relationships": { - "items": { - "$ref": "#/$defs/CausalRelationship" - }, - "type": "array" - }, - "environmental_material": { - "description": "the environmental material that was sampled", - "items": { - "type": "string" - }, - "type": "array" - }, - "environments": { - "items": { - "type": "string" - }, - "type": "array" - }, - "location": { - "description": "the sites at which the study was conducted", - "items": { - "type": "string" - }, - "type": "array" - }, - "measurements": { - "items": { - "$ref": "#/$defs/Measurement" - }, - "type": "array" - }, - "organisms": { - "description": "semicolon-separated list of all studied organism taxons", - "items": { - "type": "string" - }, - "type": "array" - }, - "sequencing_technologies": { - "type": "string" - }, - "treatments": { - "items": { - "type": "string" - }, - "type": "array" - }, - "variables": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "title": "Study", - "type": "object" - }, - "TextWithTriples": { - "additionalProperties": false, - "description": "", - "properties": { - "publication": { - "$ref": "#/$defs/Publication" - }, - "triples": { - "items": { - "$ref": "#/$defs/Triple" - }, - "type": "array" - } - }, - "title": "TextWithTriples", - "type": "object" - }, - "Treatment": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Treatment", - "type": "object" - }, - "Unit": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Unit", - "type": "object" - }, - "Variable": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Variable", - "type": "object" - } - }, - "$id": "http://w3id.org/ontogpt/metagenome", - "$schema": "http://json-schema.org/draft-07/schema#", - "additionalProperties": true, - "metamodel_version": "1.7.0", - "title": "environmental-metagenome", - "type": "object", - "version": null -} \ No newline at end of file diff --git a/projects/metagenome_study/metagenome_study.py b/projects/metagenome_study/metagenome_study.py deleted file mode 100644 index 27425570e..000000000 --- a/projects/metagenome_study/metagenome_study.py +++ /dev/null @@ -1,706 +0,0 @@ -# Auto generated from metagenome_study.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-08-07T10:55:11 -# Schema: environmental-metagenome -# -# id: http://w3id.org/ontogpt/metagenome -# description: A template for Environmental Metagenome Studies -# license: https://creativecommons.org/publicdomain/zero/1.0/ - -import dataclasses -import sys -import re -from jsonasobj2 import JsonObj, as_dict -from typing import Optional, List, Union, Dict, ClassVar, Any -from dataclasses import dataclass -from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions - -from linkml_runtime.utils.slot import Slot -from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode -from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int -from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs -from linkml_runtime.utils.formatutils import camelcase, underscore, sfx -from linkml_runtime.utils.enumerations import EnumDefinitionImpl -from rdflib import Namespace, URIRef -from linkml_runtime.utils.curienamespace import CurieNamespace -from linkml_runtime.linkml_model.types import String - -metamodel_version = "1.7.0" -version = None - -# Overwrite dataclasses _init_fn to add **kwargs in __init__ -dataclasses._init_fn = dataclasses_init_fn_with_kwargs - -# Namespaces -EFO = CurieNamespace('EFO', 'http://example.org/UNKNOWN/EFO/') -ENVO = CurieNamespace('ENVO', 'http://example.org/UNKNOWN/ENVO/') -GAZ = CurieNamespace('GAZ', 'http://example.org/UNKNOWN/GAZ/') -IDO = CurieNamespace('IDO', 'http://example.org/UNKNOWN/IDO/') -MIXS = CurieNamespace('MIXS', 'http://example.org/UNKNOWN/MIXS/') -NCBITAXON = CurieNamespace('NCBITaxon', 'http://example.org/UNKNOWN/NCBITaxon/') -NCIT = CurieNamespace('NCIT', 'http://purl.obolibrary.org/obo/NCIT_') -OBI = CurieNamespace('OBI', 'http://example.org/UNKNOWN/OBI/') -PATO = CurieNamespace('PATO', 'http://example.org/UNKNOWN/PATO/') -PECO = CurieNamespace('PECO', 'http://example.org/UNKNOWN/PECO/') -RO = CurieNamespace('RO', 'http://purl.obolibrary.org/obo/RO_') -UO = CurieNamespace('UO', 'http://example.org/UNKNOWN/UO/') -BIOLINK = CurieNamespace('biolink', 'http://example.org/UNKNOWN/biolink/') -CORE = CurieNamespace('core', 'http://w3id.org/ontogpt/core/') -EG = CurieNamespace('eg', 'http://w3id.org/ontogpt/environmental-metagenome/') -LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') -RDFS = CurieNamespace('rdfs', 'http://example.org/UNKNOWN/rdfs/') -DEFAULT_ = EG - - -# Types - -# Class references -class NamedEntityId(extended_str): - pass - - -class LocationId(NamedEntityId): - pass - - -class EnvironmentalMaterialId(NamedEntityId): - pass - - -class EnvironmentId(NamedEntityId): - pass - - -class VariableId(NamedEntityId): - pass - - -class UnitId(NamedEntityId): - pass - - -class SequencingTechnologyId(NamedEntityId): - pass - - -class TreatmentId(NamedEntityId): - pass - - -class OrganismId(NamedEntityId): - pass - - -class RelationshipTypeId(NamedEntityId): - pass - - -@dataclass -class Study(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = EG.Study - class_class_curie: ClassVar[str] = "eg:Study" - class_name: ClassVar[str] = "Study" - class_model_uri: ClassVar[URIRef] = EG.Study - - environments: Optional[Union[Union[str, EnvironmentId], List[Union[str, EnvironmentId]]]] = empty_list() - causal_relationships: Optional[Union[Union[dict, "CausalRelationship"], List[Union[dict, "CausalRelationship"]]]] = empty_list() - variables: Optional[Union[Union[str, VariableId], List[Union[str, VariableId]]]] = empty_list() - treatments: Optional[Union[Union[str, TreatmentId], List[Union[str, TreatmentId]]]] = empty_list() - measurements: Optional[Union[Union[dict, "Measurement"], List[Union[dict, "Measurement"]]]] = empty_list() - location: Optional[Union[Union[str, LocationId], List[Union[str, LocationId]]]] = empty_list() - environmental_material: Optional[Union[Union[str, EnvironmentalMaterialId], List[Union[str, EnvironmentalMaterialId]]]] = empty_list() - sequencing_technologies: Optional[Union[str, SequencingTechnologyId]] = None - organisms: Optional[Union[Union[str, OrganismId], List[Union[str, OrganismId]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if not isinstance(self.environments, list): - self.environments = [self.environments] if self.environments is not None else [] - self.environments = [v if isinstance(v, EnvironmentId) else EnvironmentId(v) for v in self.environments] - - if not isinstance(self.causal_relationships, list): - self.causal_relationships = [self.causal_relationships] if self.causal_relationships is not None else [] - self.causal_relationships = [v if isinstance(v, CausalRelationship) else CausalRelationship(**as_dict(v)) for v in self.causal_relationships] - - if not isinstance(self.variables, list): - self.variables = [self.variables] if self.variables is not None else [] - self.variables = [v if isinstance(v, VariableId) else VariableId(v) for v in self.variables] - - if not isinstance(self.treatments, list): - self.treatments = [self.treatments] if self.treatments is not None else [] - self.treatments = [v if isinstance(v, TreatmentId) else TreatmentId(v) for v in self.treatments] - - if not isinstance(self.measurements, list): - self.measurements = [self.measurements] if self.measurements is not None else [] - self.measurements = [v if isinstance(v, Measurement) else Measurement(**as_dict(v)) for v in self.measurements] - - if not isinstance(self.location, list): - self.location = [self.location] if self.location is not None else [] - self.location = [v if isinstance(v, LocationId) else LocationId(v) for v in self.location] - - if not isinstance(self.environmental_material, list): - self.environmental_material = [self.environmental_material] if self.environmental_material is not None else [] - self.environmental_material = [v if isinstance(v, EnvironmentalMaterialId) else EnvironmentalMaterialId(v) for v in self.environmental_material] - - if self.sequencing_technologies is not None and not isinstance(self.sequencing_technologies, SequencingTechnologyId): - self.sequencing_technologies = SequencingTechnologyId(self.sequencing_technologies) - - if not isinstance(self.organisms, list): - self.organisms = [self.organisms] if self.organisms is not None else [] - self.organisms = [v if isinstance(v, OrganismId) else OrganismId(v) for v in self.organisms] - - super().__post_init__(**kwargs) - - -Any = Any - -@dataclass -class ExtractionResult(YAMLRoot): - """ - A result of extracting knowledge on text - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.ExtractionResult - class_class_curie: ClassVar[str] = "core:ExtractionResult" - class_name: ClassVar[str] = "ExtractionResult" - class_model_uri: ClassVar[URIRef] = EG.ExtractionResult - - input_id: Optional[str] = None - input_title: Optional[str] = None - input_text: Optional[str] = None - raw_completion_output: Optional[str] = None - prompt: Optional[str] = None - extracted_object: Optional[Union[dict, Any]] = None - named_entities: Optional[Union[Union[dict, Any], List[Union[dict, Any]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.input_id is not None and not isinstance(self.input_id, str): - self.input_id = str(self.input_id) - - if self.input_title is not None and not isinstance(self.input_title, str): - self.input_title = str(self.input_title) - - if self.input_text is not None and not isinstance(self.input_text, str): - self.input_text = str(self.input_text) - - if self.raw_completion_output is not None and not isinstance(self.raw_completion_output, str): - self.raw_completion_output = str(self.raw_completion_output) - - if self.prompt is not None and not isinstance(self.prompt, str): - self.prompt = str(self.prompt) - - super().__post_init__(**kwargs) - - -@dataclass -class NamedEntity(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.NamedEntity - class_class_curie: ClassVar[str] = "core:NamedEntity" - class_name: ClassVar[str] = "NamedEntity" - class_model_uri: ClassVar[URIRef] = EG.NamedEntity - - id: Union[str, NamedEntityId] = None - label: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, NamedEntityId): - self.id = NamedEntityId(self.id) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - super().__post_init__(**kwargs) - - -@dataclass -class Location(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = EG.Location - class_class_curie: ClassVar[str] = "eg:Location" - class_name: ClassVar[str] = "Location" - class_model_uri: ClassVar[URIRef] = EG.Location - - id: Union[str, LocationId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, LocationId): - self.id = LocationId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class EnvironmentalMaterial(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = EG.EnvironmentalMaterial - class_class_curie: ClassVar[str] = "eg:EnvironmentalMaterial" - class_name: ClassVar[str] = "EnvironmentalMaterial" - class_model_uri: ClassVar[URIRef] = EG.EnvironmentalMaterial - - id: Union[str, EnvironmentalMaterialId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, EnvironmentalMaterialId): - self.id = EnvironmentalMaterialId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Environment(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = EG.Environment - class_class_curie: ClassVar[str] = "eg:Environment" - class_name: ClassVar[str] = "Environment" - class_model_uri: ClassVar[URIRef] = EG.Environment - - id: Union[str, EnvironmentId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, EnvironmentId): - self.id = EnvironmentId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Variable(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = EG.Variable - class_class_curie: ClassVar[str] = "eg:Variable" - class_name: ClassVar[str] = "Variable" - class_model_uri: ClassVar[URIRef] = EG.Variable - - id: Union[str, VariableId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, VariableId): - self.id = VariableId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Unit(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = EG.Unit - class_class_curie: ClassVar[str] = "eg:Unit" - class_name: ClassVar[str] = "Unit" - class_model_uri: ClassVar[URIRef] = EG.Unit - - id: Union[str, UnitId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, UnitId): - self.id = UnitId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class SequencingTechnology(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = EG.SequencingTechnology - class_class_curie: ClassVar[str] = "eg:SequencingTechnology" - class_name: ClassVar[str] = "SequencingTechnology" - class_model_uri: ClassVar[URIRef] = EG.SequencingTechnology - - id: Union[str, SequencingTechnologyId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, SequencingTechnologyId): - self.id = SequencingTechnologyId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Treatment(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = EG.Treatment - class_class_curie: ClassVar[str] = "eg:Treatment" - class_name: ClassVar[str] = "Treatment" - class_model_uri: ClassVar[URIRef] = EG.Treatment - - id: Union[str, TreatmentId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, TreatmentId): - self.id = TreatmentId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Organism(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = EG.Organism - class_class_curie: ClassVar[str] = "eg:Organism" - class_name: ClassVar[str] = "Organism" - class_model_uri: ClassVar[URIRef] = EG.Organism - - id: Union[str, OrganismId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, OrganismId): - self.id = OrganismId(self.id) - - super().__post_init__(**kwargs) - - -class CompoundExpression(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.CompoundExpression - class_class_curie: ClassVar[str] = "core:CompoundExpression" - class_name: ClassVar[str] = "CompoundExpression" - class_model_uri: ClassVar[URIRef] = EG.CompoundExpression - - -@dataclass -class Measurement(CompoundExpression): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = EG.Measurement - class_class_curie: ClassVar[str] = "eg:Measurement" - class_name: ClassVar[str] = "Measurement" - class_model_uri: ClassVar[URIRef] = EG.Measurement - - value: Optional[str] = None - unit: Optional[Union[str, UnitId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.value is not None and not isinstance(self.value, str): - self.value = str(self.value) - - if self.unit is not None and not isinstance(self.unit, UnitId): - self.unit = UnitId(self.unit) - - super().__post_init__(**kwargs) - - -@dataclass -class CausalRelationship(CompoundExpression): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = EG.CausalRelationship - class_class_curie: ClassVar[str] = "eg:CausalRelationship" - class_name: ClassVar[str] = "CausalRelationship" - class_model_uri: ClassVar[URIRef] = EG.CausalRelationship - - cause: Optional[Union[str, VariableId]] = None - effect: Optional[Union[str, VariableId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.cause is not None and not isinstance(self.cause, VariableId): - self.cause = VariableId(self.cause) - - if self.effect is not None and not isinstance(self.effect, VariableId): - self.effect = VariableId(self.effect) - - super().__post_init__(**kwargs) - - -@dataclass -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Triple - class_class_curie: ClassVar[str] = "core:Triple" - class_name: ClassVar[str] = "Triple" - class_model_uri: ClassVar[URIRef] = EG.Triple - - subject: Optional[Union[str, NamedEntityId]] = None - predicate: Optional[Union[str, RelationshipTypeId]] = None - object: Optional[Union[str, NamedEntityId]] = None - qualifier: Optional[str] = None - subject_qualifier: Optional[Union[str, NamedEntityId]] = None - object_qualifier: Optional[Union[str, NamedEntityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, NamedEntityId): - self.subject = NamedEntityId(self.subject) - - if self.predicate is not None and not isinstance(self.predicate, RelationshipTypeId): - self.predicate = RelationshipTypeId(self.predicate) - - if self.object is not None and not isinstance(self.object, NamedEntityId): - self.object = NamedEntityId(self.object) - - if self.qualifier is not None and not isinstance(self.qualifier, str): - self.qualifier = str(self.qualifier) - - if self.subject_qualifier is not None and not isinstance(self.subject_qualifier, NamedEntityId): - self.subject_qualifier = NamedEntityId(self.subject_qualifier) - - if self.object_qualifier is not None and not isinstance(self.object_qualifier, NamedEntityId): - self.object_qualifier = NamedEntityId(self.object_qualifier) - - super().__post_init__(**kwargs) - - -@dataclass -class TextWithTriples(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.TextWithTriples - class_class_curie: ClassVar[str] = "core:TextWithTriples" - class_name: ClassVar[str] = "TextWithTriples" - class_model_uri: ClassVar[URIRef] = EG.TextWithTriples - - publication: Optional[Union[dict, "Publication"]] = None - triples: Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.publication is not None and not isinstance(self.publication, Publication): - self.publication = Publication(**as_dict(self.publication)) - - if not isinstance(self.triples, list): - self.triples = [self.triples] if self.triples is not None else [] - self.triples = [v if isinstance(v, Triple) else Triple(**as_dict(v)) for v in self.triples] - - super().__post_init__(**kwargs) - - -@dataclass -class RelationshipType(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.RelationshipType - class_class_curie: ClassVar[str] = "core:RelationshipType" - class_name: ClassVar[str] = "RelationshipType" - class_model_uri: ClassVar[URIRef] = EG.RelationshipType - - id: Union[str, RelationshipTypeId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, RelationshipTypeId): - self.id = RelationshipTypeId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Publication(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Publication - class_class_curie: ClassVar[str] = "core:Publication" - class_name: ClassVar[str] = "Publication" - class_model_uri: ClassVar[URIRef] = EG.Publication - - id: Optional[str] = None - title: Optional[str] = None - abstract: Optional[str] = None - combined_text: Optional[str] = None - full_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.id is not None and not isinstance(self.id, str): - self.id = str(self.id) - - if self.title is not None and not isinstance(self.title, str): - self.title = str(self.title) - - if self.abstract is not None and not isinstance(self.abstract, str): - self.abstract = str(self.abstract) - - if self.combined_text is not None and not isinstance(self.combined_text, str): - self.combined_text = str(self.combined_text) - - if self.full_text is not None and not isinstance(self.full_text, str): - self.full_text = str(self.full_text) - - super().__post_init__(**kwargs) - - -@dataclass -class AnnotatorResult(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.AnnotatorResult - class_class_curie: ClassVar[str] = "core:AnnotatorResult" - class_name: ClassVar[str] = "AnnotatorResult" - class_model_uri: ClassVar[URIRef] = EG.AnnotatorResult - - subject_text: Optional[str] = None - object_id: Optional[str] = None - object_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject_text is not None and not isinstance(self.subject_text, str): - self.subject_text = str(self.subject_text) - - if self.object_id is not None and not isinstance(self.object_id, str): - self.object_id = str(self.object_id) - - if self.object_text is not None and not isinstance(self.object_text, str): - self.object_text = str(self.object_text) - - super().__post_init__(**kwargs) - - -# Enumerations -class NullDataOptions(EnumDefinitionImpl): - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = PermissibleValue(text="UNSPECIFIED_METHOD_OF_ADMINISTRATION", - meaning=NCIT.C149701) - NOT_APPLICABLE = PermissibleValue(text="NOT_APPLICABLE", - meaning=NCIT.C18902) - NOT_MENTIONED = PermissibleValue(text="NOT_MENTIONED") - - _defn = EnumDefinition( - name="NullDataOptions", - ) - -# Slots -class slots: - pass - -slots.study__environments = Slot(uri=EG.environments, name="study__environments", curie=EG.curie('environments'), - model_uri=EG.study__environments, domain=None, range=Optional[Union[Union[str, EnvironmentId], List[Union[str, EnvironmentId]]]]) - -slots.study__causal_relationships = Slot(uri=EG.causal_relationships, name="study__causal_relationships", curie=EG.curie('causal_relationships'), - model_uri=EG.study__causal_relationships, domain=None, range=Optional[Union[Union[dict, CausalRelationship], List[Union[dict, CausalRelationship]]]]) - -slots.study__variables = Slot(uri=EG.variables, name="study__variables", curie=EG.curie('variables'), - model_uri=EG.study__variables, domain=None, range=Optional[Union[Union[str, VariableId], List[Union[str, VariableId]]]]) - -slots.study__treatments = Slot(uri=EG.treatments, name="study__treatments", curie=EG.curie('treatments'), - model_uri=EG.study__treatments, domain=None, range=Optional[Union[Union[str, TreatmentId], List[Union[str, TreatmentId]]]]) - -slots.study__measurements = Slot(uri=EG.measurements, name="study__measurements", curie=EG.curie('measurements'), - model_uri=EG.study__measurements, domain=None, range=Optional[Union[Union[dict, Measurement], List[Union[dict, Measurement]]]]) - -slots.study__location = Slot(uri=EG.location, name="study__location", curie=EG.curie('location'), - model_uri=EG.study__location, domain=None, range=Optional[Union[Union[str, LocationId], List[Union[str, LocationId]]]]) - -slots.study__environmental_material = Slot(uri=EG.environmental_material, name="study__environmental_material", curie=EG.curie('environmental_material'), - model_uri=EG.study__environmental_material, domain=None, range=Optional[Union[Union[str, EnvironmentalMaterialId], List[Union[str, EnvironmentalMaterialId]]]]) - -slots.study__sequencing_technologies = Slot(uri=EG.sequencing_technologies, name="study__sequencing_technologies", curie=EG.curie('sequencing_technologies'), - model_uri=EG.study__sequencing_technologies, domain=None, range=Optional[Union[str, SequencingTechnologyId]]) - -slots.study__organisms = Slot(uri=EG.organisms, name="study__organisms", curie=EG.curie('organisms'), - model_uri=EG.study__organisms, domain=None, range=Optional[Union[Union[str, OrganismId], List[Union[str, OrganismId]]]]) - -slots.measurement__value = Slot(uri=EG.value, name="measurement__value", curie=EG.curie('value'), - model_uri=EG.measurement__value, domain=None, range=Optional[str]) - -slots.measurement__unit = Slot(uri=EG.unit, name="measurement__unit", curie=EG.curie('unit'), - model_uri=EG.measurement__unit, domain=None, range=Optional[Union[str, UnitId]]) - -slots.causalRelationship__cause = Slot(uri=EG.cause, name="causalRelationship__cause", curie=EG.curie('cause'), - model_uri=EG.causalRelationship__cause, domain=None, range=Optional[Union[str, VariableId]]) - -slots.causalRelationship__effect = Slot(uri=EG.effect, name="causalRelationship__effect", curie=EG.curie('effect'), - model_uri=EG.causalRelationship__effect, domain=None, range=Optional[Union[str, VariableId]]) - -slots.extractionResult__input_id = Slot(uri=CORE.input_id, name="extractionResult__input_id", curie=CORE.curie('input_id'), - model_uri=EG.extractionResult__input_id, domain=None, range=Optional[str]) - -slots.extractionResult__input_title = Slot(uri=CORE.input_title, name="extractionResult__input_title", curie=CORE.curie('input_title'), - model_uri=EG.extractionResult__input_title, domain=None, range=Optional[str]) - -slots.extractionResult__input_text = Slot(uri=CORE.input_text, name="extractionResult__input_text", curie=CORE.curie('input_text'), - model_uri=EG.extractionResult__input_text, domain=None, range=Optional[str]) - -slots.extractionResult__raw_completion_output = Slot(uri=CORE.raw_completion_output, name="extractionResult__raw_completion_output", curie=CORE.curie('raw_completion_output'), - model_uri=EG.extractionResult__raw_completion_output, domain=None, range=Optional[str]) - -slots.extractionResult__prompt = Slot(uri=CORE.prompt, name="extractionResult__prompt", curie=CORE.curie('prompt'), - model_uri=EG.extractionResult__prompt, domain=None, range=Optional[str]) - -slots.extractionResult__extracted_object = Slot(uri=CORE.extracted_object, name="extractionResult__extracted_object", curie=CORE.curie('extracted_object'), - model_uri=EG.extractionResult__extracted_object, domain=None, range=Optional[Union[dict, Any]]) - -slots.extractionResult__named_entities = Slot(uri=CORE.named_entities, name="extractionResult__named_entities", curie=CORE.curie('named_entities'), - model_uri=EG.extractionResult__named_entities, domain=None, range=Optional[Union[Union[dict, Any], List[Union[dict, Any]]]]) - -slots.namedEntity__id = Slot(uri=CORE.id, name="namedEntity__id", curie=CORE.curie('id'), - model_uri=EG.namedEntity__id, domain=None, range=URIRef) - -slots.namedEntity__label = Slot(uri=RDFS.label, name="namedEntity__label", curie=RDFS.curie('label'), - model_uri=EG.namedEntity__label, domain=None, range=Optional[str]) - -slots.triple__subject = Slot(uri=CORE.subject, name="triple__subject", curie=CORE.curie('subject'), - model_uri=EG.triple__subject, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__predicate = Slot(uri=CORE.predicate, name="triple__predicate", curie=CORE.curie('predicate'), - model_uri=EG.triple__predicate, domain=None, range=Optional[Union[str, RelationshipTypeId]]) - -slots.triple__object = Slot(uri=CORE.object, name="triple__object", curie=CORE.curie('object'), - model_uri=EG.triple__object, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__qualifier = Slot(uri=CORE.qualifier, name="triple__qualifier", curie=CORE.curie('qualifier'), - model_uri=EG.triple__qualifier, domain=None, range=Optional[str]) - -slots.triple__subject_qualifier = Slot(uri=CORE.subject_qualifier, name="triple__subject_qualifier", curie=CORE.curie('subject_qualifier'), - model_uri=EG.triple__subject_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__object_qualifier = Slot(uri=CORE.object_qualifier, name="triple__object_qualifier", curie=CORE.curie('object_qualifier'), - model_uri=EG.triple__object_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.textWithTriples__publication = Slot(uri=CORE.publication, name="textWithTriples__publication", curie=CORE.curie('publication'), - model_uri=EG.textWithTriples__publication, domain=None, range=Optional[Union[dict, Publication]]) - -slots.textWithTriples__triples = Slot(uri=CORE.triples, name="textWithTriples__triples", curie=CORE.curie('triples'), - model_uri=EG.textWithTriples__triples, domain=None, range=Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]]) - -slots.publication__id = Slot(uri=CORE.id, name="publication__id", curie=CORE.curie('id'), - model_uri=EG.publication__id, domain=None, range=Optional[str]) - -slots.publication__title = Slot(uri=CORE.title, name="publication__title", curie=CORE.curie('title'), - model_uri=EG.publication__title, domain=None, range=Optional[str]) - -slots.publication__abstract = Slot(uri=CORE.abstract, name="publication__abstract", curie=CORE.curie('abstract'), - model_uri=EG.publication__abstract, domain=None, range=Optional[str]) - -slots.publication__combined_text = Slot(uri=CORE.combined_text, name="publication__combined_text", curie=CORE.curie('combined_text'), - model_uri=EG.publication__combined_text, domain=None, range=Optional[str]) - -slots.publication__full_text = Slot(uri=CORE.full_text, name="publication__full_text", curie=CORE.curie('full_text'), - model_uri=EG.publication__full_text, domain=None, range=Optional[str]) - -slots.annotatorResult__subject_text = Slot(uri=CORE.subject_text, name="annotatorResult__subject_text", curie=CORE.curie('subject_text'), - model_uri=EG.annotatorResult__subject_text, domain=None, range=Optional[str]) - -slots.annotatorResult__object_id = Slot(uri=CORE.object_id, name="annotatorResult__object_id", curie=CORE.curie('object_id'), - model_uri=EG.annotatorResult__object_id, domain=None, range=Optional[str]) - -slots.annotatorResult__object_text = Slot(uri=CORE.object_text, name="annotatorResult__object_text", curie=CORE.curie('object_text'), - model_uri=EG.annotatorResult__object_text, domain=None, range=Optional[str]) \ No newline at end of file diff --git a/projects/metagenome_study/owl/metagenome_study.owl.ttl b/projects/metagenome_study/owl/metagenome_study.owl.ttl deleted file mode 100644 index 8d048afce..000000000 --- a/projects/metagenome_study/owl/metagenome_study.owl.ttl +++ /dev/null @@ -1,561 +0,0 @@ -@prefix IAO: <http://purl.obolibrary.org/obo/IAO_> . -@prefix eg: <http://w3id.org/ontogpt/environmental-metagenome/> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix owl: <http://www.w3.org/2002/07/owl#> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . -@prefix skos: <http://www.w3.org/2004/02/skos/core#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -<http://w3id.org/ontogpt/metagenome> a owl:Ontology ; - rdfs:label "environmental-metagenome" ; - IAO:0000700 <http://w3id.org/ontogpt/core/AnnotatorResult>, - <http://w3id.org/ontogpt/core/Any>, - <http://w3id.org/ontogpt/core/CompoundExpression>, - <http://w3id.org/ontogpt/core/ExtractionResult>, - <http://w3id.org/ontogpt/core/NamedEntity>, - <http://w3id.org/ontogpt/core/Publication>, - <http://w3id.org/ontogpt/core/TextWithTriples>, - eg:Study ; - linkml:classes "{'Study': ClassDefinition(name='Study', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/environmental-metagenome/Study', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/metagenome', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['study__environments', 'study__causal_relationships', 'study__variables', 'study__treatments', 'study__measurements', 'study__location', 'study__environmental_material', 'study__sequencing_technologies', 'study__organisms'], slot_usage={}, attributes={'environments': SlotDefinition(name='environments', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of environmental systems or biomes in which the study was conducted', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Environment', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'causal_relationships': SlotDefinition(name='causal_relationships', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of cause-effect pairs, for example, effect of temperature on growth', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='CausalRelationship', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'variables': SlotDefinition(name='variables', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of environmental variables which are studies. E.g. temperature, pH, salinity', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Variable', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'treatments': SlotDefinition(name='treatments', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of treatments that are applied', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Treatment', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'measurements': SlotDefinition(name='measurements', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of value-measurement pairs', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Measurement', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'location': SlotDefinition(name='location', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of sites at which the study was conducted', extensions={}, annotations={})}, description='the sites at which the study was conducted', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Location', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'environmental_material': SlotDefinition(name='environmental_material', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of environmental materials', extensions={}, annotations={})}, description='the environmental material that was sampled', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='EnvironmentalMaterial', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sequencing_technologies': SlotDefinition(name='sequencing_technologies', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of sequencing technologies used in the project', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='SequencingTechnology', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'organisms': SlotDefinition(name='organisms', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of all studied organism taxons', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Organism', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='eg:Study', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Location': ClassDefinition(name='Location', id_prefixes=['ENVO', 'GAZ'], definition_uri='http://w3id.org/ontogpt/environmental-metagenome/Location', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:envo, bioportal:gaz', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/metagenome', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='eg:Location', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'EnvironmentalMaterial': ClassDefinition(name='EnvironmentalMaterial', id_prefixes=['ENVO'], definition_uri='http://w3id.org/ontogpt/environmental-metagenome/EnvironmentalMaterial', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:envo', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/metagenome', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='eg:EnvironmentalMaterial', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Environment': ClassDefinition(name='Environment', id_prefixes=['ENVO'], definition_uri='http://w3id.org/ontogpt/environmental-metagenome/Environment', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:envo', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/metagenome', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='eg:Environment', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Variable': ClassDefinition(name='Variable', id_prefixes=['ENVO', 'MIXS', 'PATO'], definition_uri='http://w3id.org/ontogpt/environmental-metagenome/Variable', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:envo, bioportal:bero', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/metagenome', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='eg:Variable', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Unit': ClassDefinition(name='Unit', id_prefixes=['UO', 'NCIT'], definition_uri='http://w3id.org/ontogpt/environmental-metagenome/Unit', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:uo, bioportal:ncit', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/metagenome', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='eg:Unit', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Measurement': ClassDefinition(name='Measurement', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/environmental-metagenome/Measurement', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/metagenome', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['measurement__value', 'measurement__unit'], slot_usage={}, attributes={'value': SlotDefinition(name='value', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the value of the measurement', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'unit': SlotDefinition(name='unit', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the unit of the measurement', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Unit', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='eg:Measurement', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'CausalRelationship': ClassDefinition(name='CausalRelationship', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/environmental-metagenome/CausalRelationship', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/metagenome', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['causalRelationship__cause', 'causalRelationship__effect'], slot_usage={}, attributes={'cause': SlotDefinition(name='cause', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the variable that is the cause of the effect', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Variable', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'effect': SlotDefinition(name='effect', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the things that is affected', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Variable', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='eg:CausalRelationship', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'SequencingTechnology': ClassDefinition(name='SequencingTechnology', id_prefixes=['IDO', 'EFO'], definition_uri='http://w3id.org/ontogpt/environmental-metagenome/SequencingTechnology', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:obi, sqlite:obo:efo, bioportal:bero', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/metagenome', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='eg:SequencingTechnology', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Treatment': ClassDefinition(name='Treatment', id_prefixes=['PECO', 'OBI'], definition_uri='http://w3id.org/ontogpt/environmental-metagenome/Treatment', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:peco, sqlite:obo:obi, bioportal:bero', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/metagenome', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='eg:Treatment', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Organism': ClassDefinition(name='Organism', id_prefixes=['NCBITaxon'], definition_uri='http://w3id.org/ontogpt/environmental-metagenome/Organism', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:ncbitaxon, gilda:', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/metagenome', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='eg:Organism', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Any': ClassDefinition(name='Any', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Any', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=['linkml:Any'], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='linkml:Any', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ExtractionResult': ClassDefinition(name='ExtractionResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/ExtractionResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A result of extracting knowledge on text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['extractionResult__input_id', 'extractionResult__input_title', 'extractionResult__input_text', 'extractionResult__raw_completion_output', 'extractionResult__prompt', 'extractionResult__extracted_object', 'extractionResult__named_entities'], slot_usage={}, attributes={'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:ExtractionResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'NamedEntity': ClassDefinition(name='NamedEntity', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NamedEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:NamedEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'CompoundExpression': ClassDefinition(name='CompoundExpression', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/CompoundExpression', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='core:CompoundExpression', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Triple': ClassDefinition(name='Triple', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Triple', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Abstract parent for Relation Extraction tasks', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['triple__subject', 'triple__predicate', 'triple__object', 'triple__qualifier', 'triple__subject_qualifier', 'triple__object_qualifier'], slot_usage={}, attributes={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Triple', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'TextWithTriples': ClassDefinition(name='TextWithTriples', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/TextWithTriples', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['textWithTriples__publication', 'textWithTriples__triples'], slot_usage={}, attributes={'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:TextWithTriples', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'RelationshipType': ClassDefinition(name='RelationshipType', id_prefixes=['RO', 'biolink'], definition_uri='http://w3id.org/ontogpt/core/RelationshipType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='core:RelationshipType', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Publication': ClassDefinition(name='Publication', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Publication', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['publication__id', 'publication__title', 'publication__abstract', 'publication__combined_text', 'publication__full_text'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Publication', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'AnnotatorResult': ClassDefinition(name='AnnotatorResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/AnnotatorResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['annotatorResult__subject_text', 'annotatorResult__object_id', 'annotatorResult__object_text'], slot_usage={}, attributes={'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:AnnotatorResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={})}" ; - linkml:enums "{'NullDataOptions': EnumDefinition(name='NullDataOptions', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NullDataOptions', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'UNSPECIFIED_METHOD_OF_ADMINISTRATION': PermissibleValue(text='UNSPECIFIED_METHOD_OF_ADMINISTRATION', description=None, meaning='NCIT:C149701', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_APPLICABLE': PermissibleValue(text='NOT_APPLICABLE', description=None, meaning='NCIT:C18902', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['not applicable', 'N/A'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_MENTIONED': PermissibleValue(text='NOT_MENTIONED', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[])}" ; - linkml:id "http://w3id.org/ontogpt/metagenome" ; - linkml:imports "core", - "linkml:types" ; - linkml:types "{'string': TypeDefinition(name='string', id_prefixes=[], definition_uri='https://w3id.org/linkml/String', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A character string', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Text'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'integer': TypeDefinition(name='integer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Integer', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An integer', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Integer'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='int', uri='xsd:integer', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'boolean': TypeDefinition(name='boolean', id_prefixes=[], definition_uri='https://w3id.org/linkml/Boolean', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A binary (true or false) value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Boolean'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Bool', uri='xsd:boolean', repr='bool', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'float': TypeDefinition(name='float', id_prefixes=[], definition_uri='https://w3id.org/linkml/Float', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:float specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Float'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:float', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'double': TypeDefinition(name='double', id_prefixes=[], definition_uri='https://w3id.org/linkml/Double', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:double specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:Float'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:double', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'decimal': TypeDefinition(name='decimal', id_prefixes=[], definition_uri='https://w3id.org/linkml/Decimal', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number with arbitrary precision that conforms to the xsd:decimal specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=['schema:Number'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Decimal', uri='xsd:decimal', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'time': TypeDefinition(name='time', id_prefixes=[], definition_uri='https://w3id.org/linkml/Time', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A time object represents a (local) time of day, independent of any particular day', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=['URI is dateTime because OWL reasoners do not work with straight date or time'], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Time'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDTime', uri='xsd:time', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date': TypeDefinition(name='date', id_prefixes=[], definition_uri='https://w3id.org/linkml/Date', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a date (year, month and day) in an idealized calendar', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[\"URI is dateTime because OWL reasoners don't work with straight date or time\"], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Date'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDate', uri='xsd:date', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'datetime': TypeDefinition(name='datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/Datetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The combination of a date and time', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:DateTime'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDateTime', uri='xsd:dateTime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date_or_datetime': TypeDefinition(name='date_or_datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/DateOrDatetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Either a date or a datetime', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='linkml:DateOrDatetime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uriorcurie': TypeDefinition(name='uriorcurie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uriorcurie', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a URI or a CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URIorCURIE', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'curie': TypeDefinition(name='curie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Curie', local_names={}, conforms_to='https://www.w3.org/TR/curie/', implements=[], extensions={}, annotations={}, description='a compact URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations this MUST be expanded to a URI', 'in non-RDF serializations MAY be serialized as the compact representation'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Curie', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uri': TypeDefinition(name='uri', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uri', local_names={}, conforms_to='https://www.ietf.org/rfc/rfc3987.txt', implements=[], extensions={}, annotations={}, description='a complete URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:URL'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URI', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ncname': TypeDefinition(name='ncname', id_prefixes=[], definition_uri='https://w3id.org/linkml/Ncname', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Prefix part of CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NCName', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'objectidentifier': TypeDefinition(name='objectidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Objectidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI or CURIE that represents an object in the model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['Used for inheritance and type checking'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='ElementIdentifier', uri='shex:iri', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'nodeidentifier': TypeDefinition(name='nodeidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Nodeidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI, CURIE or BNODE that represents a node in a model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NodeIdentifier', uri='shex:nonLiteral', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpointer': TypeDefinition(name='jsonpointer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpointer', local_names={}, conforms_to='https://datatracker.ietf.org/doc/html/rfc6901', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpath': TypeDefinition(name='jsonpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpath', local_names={}, conforms_to='https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sparqlpath': TypeDefinition(name='sparqlpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Sparqlpath', local_names={}, conforms_to='https://www.w3.org/TR/sparql11-query/#propertypaths', implements=[], extensions={}, annotations={}, description='A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:SubsetDefinition a owl:Class ; - rdfs:label "subset_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" . - -linkml:TypeDefinition a owl:Class ; - rdfs:label "type_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" ; - linkml:mixins "type_expression" . - -linkml:topValue a owl:DatatypeProperty ; - rdfs:label "value" . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "AnnotatorResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_text> ] ; - linkml:attributes "{'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/ExtractionResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ExtractionResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/named_entities> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/extracted_object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/prompt> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_title> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_text> ] ; - skos:definition "A result of extracting knowledge on text" ; - linkml:attributes "{'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/TextWithTriples> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TextWithTriples" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Publication> ; - owl:onProperty <http://w3id.org/ontogpt/core/publication> ], - [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Triple> ; - owl:onProperty <http://w3id.org/ontogpt/core/triples> ] ; - linkml:attributes "{'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/abstract> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "abstract" ; - rdfs:range linkml:String ; - skos:definition "The abstract of the publication" . - -<http://w3id.org/ontogpt/core/combined_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "combined_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/extracted_object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "extracted_object" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "The complex objects extracted from the text" . - -<http://w3id.org/ontogpt/core/full_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "full_text" ; - rdfs:range linkml:String ; - skos:definition "The full text of the publication" . - -<http://w3id.org/ontogpt/core/input_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_title" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/named_entities> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "named_entities" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "Named entities extracted from the text" . - -<http://w3id.org/ontogpt/core/object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/object_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/object_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" . - -<http://w3id.org/ontogpt/core/object_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/predicate> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "predicate" ; - rdfs:range <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/prompt> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "prompt" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/publication> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "publication" ; - eg:prompt.skip "true" ; - rdfs:range <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "qualifier" ; - rdfs:range linkml:String ; - skos:definition "A qualifier for the statements, e.g. \"NOT\" for negation" . - -<http://w3id.org/ontogpt/core/raw_completion_output> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "raw_completion_output" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/subject> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/subject_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" . - -<http://w3id.org/ontogpt/core/subject_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "title" ; - rdfs:range linkml:String ; - skos:definition "The title of the publication" . - -<http://w3id.org/ontogpt/core/triples> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "triples" ; - rdfs:range <http://w3id.org/ontogpt/core/Triple> . - -eg:Study a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Study" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom eg:Organism ; - owl:onProperty eg:organisms ], - [ a owl:Restriction ; - owl:allValuesFrom eg:Measurement ; - owl:onProperty eg:measurements ], - [ a owl:Restriction ; - owl:allValuesFrom eg:Environment ; - owl:onProperty eg:environments ], - [ a owl:Restriction ; - owl:allValuesFrom eg:CausalRelationship ; - owl:onProperty eg:causal_relationships ], - [ a owl:Restriction ; - owl:allValuesFrom eg:Variable ; - owl:onProperty eg:variables ], - [ a owl:Restriction ; - owl:allValuesFrom eg:EnvironmentalMaterial ; - owl:onProperty eg:environmental_material ], - [ a owl:Restriction ; - owl:allValuesFrom eg:Location ; - owl:onProperty eg:location ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass eg:SequencingTechnology ; - owl:onProperty eg:sequencing_technologies ], - [ a owl:Restriction ; - owl:allValuesFrom eg:Treatment ; - owl:onProperty eg:treatments ] ; - linkml:attributes "{'environments': SlotDefinition(name='environments', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of environmental systems or biomes in which the study was conducted', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Environment', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'causal_relationships': SlotDefinition(name='causal_relationships', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of cause-effect pairs, for example, effect of temperature on growth', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='CausalRelationship', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'variables': SlotDefinition(name='variables', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of environmental variables which are studies. E.g. temperature, pH, salinity', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Variable', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'treatments': SlotDefinition(name='treatments', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of treatments that are applied', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Treatment', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'measurements': SlotDefinition(name='measurements', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of value-measurement pairs', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Measurement', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'location': SlotDefinition(name='location', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of sites at which the study was conducted', extensions={}, annotations={})}, description='the sites at which the study was conducted', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Location', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'environmental_material': SlotDefinition(name='environmental_material', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of environmental materials', extensions={}, annotations={})}, description='the environmental material that was sampled', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='EnvironmentalMaterial', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sequencing_technologies': SlotDefinition(name='sequencing_technologies', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of sequencing technologies used in the project', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='SequencingTechnology', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'organisms': SlotDefinition(name='organisms', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of all studied organism taxons', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Organism', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -eg:causal_relationships a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "causal_relationships" ; - eg:prompt "semicolon-separated list of cause-effect pairs, for example, effect of temperature on growth" ; - rdfs:range eg:CausalRelationship . - -eg:cause a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "cause" ; - rdfs:range eg:Variable ; - skos:definition "the variable that is the cause of the effect" . - -eg:effect a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "effect" ; - rdfs:range eg:Variable ; - skos:definition "the things that is affected" . - -eg:environmental_material a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "environmental_material" ; - eg:prompt "semicolon-separated list of environmental materials" ; - rdfs:range eg:EnvironmentalMaterial ; - skos:definition "the environmental material that was sampled" . - -eg:environments a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "environments" ; - eg:prompt "semicolon-separated list of environmental systems or biomes in which the study was conducted" ; - rdfs:range eg:Environment . - -eg:location a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "location" ; - eg:prompt "semicolon-separated list of sites at which the study was conducted" ; - rdfs:range eg:Location ; - skos:definition "the sites at which the study was conducted" . - -eg:measurements a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "measurements" ; - eg:prompt "semicolon-separated list of value-measurement pairs" ; - rdfs:range eg:Measurement . - -eg:organisms a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "organisms" ; - rdfs:range eg:Organism ; - skos:definition "semicolon-separated list of all studied organism taxons" . - -eg:sequencing_technologies a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "sequencing_technologies" ; - eg:prompt "semicolon-separated list of sequencing technologies used in the project" ; - rdfs:range eg:SequencingTechnology . - -eg:treatments a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "treatments" ; - eg:prompt "semicolon-separated list of treatments that are applied" ; - rdfs:range eg:Treatment . - -eg:unit a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "unit" ; - rdfs:range eg:Unit ; - skos:definition "the unit of the measurement" . - -eg:value a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "value" ; - rdfs:range linkml:String ; - skos:definition "the value of the measurement" . - -eg:variables a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "variables" ; - eg:prompt "semicolon-separated list of environmental variables which are studies. E.g. temperature, pH, salinity" ; - rdfs:range eg:Variable . - -<http://example.org/UNKNOWN/rdfs/label> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "label" ; - eg:owl "AnnotationProperty, AnnotationAssertion" ; - rdfs:range linkml:String ; - skos:altLabel "name" ; - skos:definition "The label (name) of the named thing" ; - skos:exactMatch <http://example.org/UNKNOWN/rdfs/label> . - -<http://purl.obolibrary.org/obo/NCIT_C149701> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "UNSPECIFIED_METHOD_OF_ADMINISTRATION" . - -<http://purl.obolibrary.org/obo/NCIT_C18902> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_APPLICABLE" . - -<http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_MENTIONED" . - -<http://w3id.org/ontogpt/core/RelationshipType> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "RelationshipType" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/Triple> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Triple" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/RelationshipType> ; - owl:onProperty <http://w3id.org/ontogpt/core/predicate> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/qualifier> ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - skos:definition "Abstract parent for Relation Extraction tasks" ; - linkml:attributes "{'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -<http://w3id.org/ontogpt/core/id> a owl:ObjectProperty, - linkml:SlotDefinition . - -eg:CausalRelationship a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CausalRelationship" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass eg:Variable ; - owl:onProperty eg:cause ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass eg:Variable ; - owl:onProperty eg:effect ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - linkml:attributes "{'cause': SlotDefinition(name='cause', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the variable that is the cause of the effect', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Variable', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'effect': SlotDefinition(name='effect', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the things that is affected', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Variable', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -eg:Environment a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Environment" ; - eg:annotators "sqlite:obo:envo" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -eg:EnvironmentalMaterial a owl:Class, - linkml:ClassDefinition ; - rdfs:label "EnvironmentalMaterial" ; - eg:annotators "sqlite:obo:envo" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -eg:Location a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Location" ; - eg:annotators "sqlite:obo:envo, bioportal:gaz" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -eg:Measurement a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Measurement" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty eg:value ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass eg:Unit ; - owl:onProperty eg:unit ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - linkml:attributes "{'value': SlotDefinition(name='value', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the value of the measurement', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'unit': SlotDefinition(name='unit', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the unit of the measurement', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Unit', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -eg:Organism a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Organism" ; - eg:annotators "sqlite:obo:ncbitaxon, gilda:" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -eg:SequencingTechnology a owl:Class, - linkml:ClassDefinition ; - rdfs:label "SequencingTechnology" ; - eg:annotators "sqlite:obo:obi, sqlite:obo:efo, bioportal:bero" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -eg:Treatment a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Treatment" ; - eg:annotators "sqlite:obo:peco, sqlite:obo:obi, bioportal:bero" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -eg:Unit a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Unit" ; - eg:annotators "sqlite:obo:uo, bioportal:ncit" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/NullDataOptions> a owl:Class, - linkml:EnumDefinition ; - rdfs:label "NullDataOptions" ; - owl:unionOf ( <http://purl.obolibrary.org/obo/NCIT_C149701> <http://purl.obolibrary.org/obo/NCIT_C18902> <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> ) ; - linkml:permissible_values <http://purl.obolibrary.org/obo/NCIT_C149701>, - <http://purl.obolibrary.org/obo/NCIT_C18902>, - <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> . - -<http://w3id.org/ontogpt/core/Publication> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Publication" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/title> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/abstract> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/full_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/combined_text> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/CompoundExpression> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CompoundExpression" ; - linkml:attributes "{}" . - -<http://w3id.org/ontogpt/core/Any> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Any" ; - skos:exactMatch linkml:Any ; - linkml:attributes "{}" . - -eg:Variable a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Variable" ; - eg:annotators "sqlite:obo:envo, bioportal:bero" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/NamedEntity> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "NamedEntity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://example.org/UNKNOWN/rdfs/label> ], - [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ; - owl:qualifiedCardinality 1 ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:ClassDefinition a owl:Class ; - rdfs:label "class_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "class_expression" . - -linkml:SlotDefinition a owl:Class ; - rdfs:label "slot_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "slot_expression" . - - diff --git a/projects/metagenome_study/prefixmap/metagenome_study.yaml b/projects/metagenome_study/prefixmap/metagenome_study.yaml deleted file mode 100644 index 9a8b2c830..000000000 --- a/projects/metagenome_study/prefixmap/metagenome_study.yaml +++ /dev/null @@ -1,46 +0,0 @@ -{ - "EFO": "http://example.org/UNKNOWN/EFO/", - "ENVO": "http://example.org/UNKNOWN/ENVO/", - "GAZ": "http://example.org/UNKNOWN/GAZ/", - "IDO": "http://example.org/UNKNOWN/IDO/", - "MIXS": "http://example.org/UNKNOWN/MIXS/", - "NCBITaxon": "http://example.org/UNKNOWN/NCBITaxon/", - "NCIT": "http://purl.obolibrary.org/obo/NCIT_", - "OBI": "http://example.org/UNKNOWN/OBI/", - "PATO": "http://example.org/UNKNOWN/PATO/", - "PECO": "http://example.org/UNKNOWN/PECO/", - "RO": "http://purl.obolibrary.org/obo/RO_", - "UO": "http://example.org/UNKNOWN/UO/", - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "eg": "http://w3id.org/ontogpt/environmental-metagenome/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } -} diff --git a/projects/metagenome_study/protobuf/metagenome_study.proto b/projects/metagenome_study/protobuf/metagenome_study.proto deleted file mode 100644 index 21a5b3771..000000000 --- a/projects/metagenome_study/protobuf/metagenome_study.proto +++ /dev/null @@ -1,97 +0,0 @@ -message AnnotatorResult - { - string subjectText = 0 - string objectId = 0 - string objectText = 0 - } -message CausalRelationship - { - variable cause = 0 - variable effect = 0 - } -message Environment - { - string id = 0 - string label = 0 - } -message EnvironmentalMaterial - { - string id = 0 - string label = 0 - } -// A result of extracting knowledge on text -message ExtractionResult - { - string inputId = 0 - string inputTitle = 0 - string inputText = 0 - string rawCompletionOutput = 0 - string prompt = 0 - any extractedObject = 0 - repeated any namedEntities = 0 - } -message Location - { - string id = 0 - string label = 0 - } -message Measurement - { - string value = 0 - unit unit = 0 - } -message Organism - { - string id = 0 - string label = 0 - } -message Publication - { - string id = 0 - string title = 0 - string abstract = 0 - string combinedText = 0 - string fullText = 0 - } -message RelationshipType - { - string id = 0 - string label = 0 - } -message SequencingTechnology - { - string id = 0 - string label = 0 - } -message Study - { - repeated environment environments = 0 - repeated causalRelationship causalRelationships = 0 - repeated variable variables = 0 - repeated treatment treatments = 0 - repeated measurement measurements = 0 - repeated location location = 0 - repeated environmentalMaterial environmentalMaterial = 0 - sequencingTechnology sequencingTechnologies = 0 - repeated organism organisms = 0 - } -message TextWithTriples - { - publication publication = 0 - repeated triple triples = 0 - } -message Treatment - { - string id = 0 - string label = 0 - } -message Unit - { - string id = 0 - string label = 0 - } -message Variable - { - string id = 0 - string label = 0 - } diff --git a/projects/metagenome_study/shacl/metagenome_study.shacl.ttl b/projects/metagenome_study/shacl/metagenome_study.shacl.ttl deleted file mode 100644 index c7ad1630c..000000000 --- a/projects/metagenome_study/shacl/metagenome_study.shacl.ttl +++ /dev/null @@ -1,353 +0,0 @@ -@prefix eg: <http://w3id.org/ontogpt/environmental-metagenome/> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix sh: <http://www.w3.org/ns/shacl#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject_text> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object_text> ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/object_id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/AnnotatorResult> . - -<http://w3id.org/ontogpt/core/CompoundExpression> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass <http://w3id.org/ontogpt/core/CompoundExpression> . - -<http://w3id.org/ontogpt/core/ExtractionResult> a sh:NodeShape ; - sh:closed true ; - sh:description "A result of extracting knowledge on text" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/input_text> ], - [ sh:class linkml:Any ; - sh:description "Named entities extracted from the text" ; - sh:nodeKind sh:BlankNode ; - sh:order 6 ; - sh:path <http://w3id.org/ontogpt/core/named_entities> ], - [ sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/prompt> ], - [ sh:class linkml:Any ; - sh:description "The complex objects extracted from the text" ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/extracted_object> ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/input_title> ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/input_id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/ExtractionResult> . - -<http://w3id.org/ontogpt/core/TextWithTriples> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/Triple> ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/triples> ], - [ sh:class <http://w3id.org/ontogpt/core/Publication> ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/publication> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/TextWithTriples> . - -eg:Study a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class eg:Measurement ; - sh:nodeKind sh:BlankNode ; - sh:order 4 ; - sh:path eg:measurements ], - [ sh:class eg:CausalRelationship ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path eg:causal_relationships ], - [ sh:class eg:EnvironmentalMaterial ; - sh:description "the environmental material that was sampled" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path eg:environmental_material ], - [ sh:class eg:Organism ; - sh:description "semicolon-separated list of all studied organism taxons" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path eg:organisms ], - [ sh:class eg:Environment ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path eg:environments ], - [ sh:class eg:Variable ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path eg:variables ], - [ sh:class eg:SequencingTechnology ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path eg:sequencing_technologies ], - [ sh:class eg:Location ; - sh:description "the sites at which the study was conducted" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path eg:location ], - [ sh:class eg:Treatment ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path eg:treatments ] ; - sh:targetClass eg:Study . - -<http://w3id.org/ontogpt/core/Publication> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The title of the publication" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/title> ], - [ sh:description "The full text of the publication" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/full_text> ], - [ sh:description "The abstract of the publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/abstract> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/combined_text> ], - [ sh:description "The publication identifier" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/RelationshipType> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/Triple> a sh:NodeShape ; - sh:closed false ; - sh:description "Abstract parent for Relation Extraction tasks" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject> ], - [ sh:description "A qualifier for the statements, e.g. \"NOT\" for negation" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object> ], - [ sh:class <http://w3id.org/ontogpt/core/RelationshipType> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/predicate> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/object_qualifier> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Triple> . - -eg:CausalRelationship a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class eg:Variable ; - sh:description "the things that is affected" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path eg:effect ], - [ sh:class eg:Variable ; - sh:description "the variable that is the cause of the effect" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path eg:cause ] ; - sh:targetClass eg:CausalRelationship . - -eg:Environment a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass eg:Environment . - -eg:EnvironmentalMaterial a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass eg:EnvironmentalMaterial . - -eg:Location a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass eg:Location . - -eg:Measurement a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class eg:Unit ; - sh:description "the unit of the measurement" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path eg:unit ], - [ sh:description "the value of the measurement" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path eg:value ] ; - sh:targetClass eg:Measurement . - -eg:Organism a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass eg:Organism . - -eg:SequencingTechnology a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass eg:SequencingTechnology . - -eg:Treatment a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass eg:Treatment . - -eg:Unit a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass eg:Unit . - -linkml:Any a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass linkml:Any . - -eg:Variable a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass eg:Variable . - -<http://w3id.org/ontogpt/core/NamedEntity> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/NamedEntity> . - diff --git a/projects/metagenome_study/shex/metagenome_study.shex b/projects/metagenome_study/shex/metagenome_study.shex deleted file mode 100644 index 786fb6e1c..000000000 --- a/projects/metagenome_study/shex/metagenome_study.shex +++ /dev/null @@ -1,236 +0,0 @@ -BASE <http://w3id.org/ontogpt/environmental-metagenome/> -PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> -PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> -PREFIX linkml: <https://w3id.org/linkml/> -PREFIX core: <http://w3id.org/ontogpt/core/> -PREFIX rdfs1: <http://example.org/UNKNOWN/rdfs/> - - -linkml:String xsd:string - -linkml:Integer xsd:integer - -linkml:Boolean xsd:boolean - -linkml:Float xsd:float - -linkml:Double xsd:double - -linkml:Decimal xsd:decimal - -linkml:Time xsd:time - -linkml:Date xsd:date - -linkml:Datetime xsd:dateTime - -linkml:DateOrDatetime linkml:DateOrDatetime - -linkml:Uriorcurie IRI - -linkml:Curie xsd:string - -linkml:Uri IRI - -linkml:Ncname xsd:string - -linkml:Objectidentifier IRI - -linkml:Nodeidentifier NONLITERAL - -linkml:Jsonpointer xsd:string - -linkml:Jsonpath xsd:string - -linkml:Sparqlpath xsd:string - -core:AnnotatorResult CLOSED { - ( $core:AnnotatorResult_tes ( core:subject_text @linkml:String ? ; - core:object_id @linkml:String ? ; - core:object_text @linkml:String ? - ) ; - rdf:type [ core:AnnotatorResult ] ? - ) -} - -core:Any CLOSED { - ( $core:Any_tes rdf:type . * ; - rdf:type [ linkml:Any ] ? - ) -} - -<CausalRelationship> CLOSED { - ( $<CausalRelationship_tes> ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - <cause> @<Variable> ? ; - <effect> @<Variable> ? - ) ; - rdf:type [ <CausalRelationship> ] ? - ) -} - -core:CompoundExpression ( - @<CausalRelationship> OR @<Measurement> OR @core:Triple -) - -core:CompoundExpression_struct { - ( $core:CompoundExpression_tes rdf:type . * ; - rdf:type [ core:CompoundExpression ] ? - ) -} - -<Environment> CLOSED { - ( $<Environment_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Environment> ] - ) -} - -<EnvironmentalMaterial> CLOSED { - ( $<EnvironmentalMaterial_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <EnvironmentalMaterial> ] - ) -} - -core:ExtractionResult CLOSED { - ( $core:ExtractionResult_tes ( core:input_id @linkml:String ? ; - core:input_title @linkml:String ? ; - core:input_text @linkml:String ? ; - core:raw_completion_output @linkml:String ? ; - core:prompt @linkml:String ? ; - core:extracted_object @core:Any ? ; - core:named_entities @core:Any * - ) ; - rdf:type [ core:ExtractionResult ] ? - ) -} - -<Location> CLOSED { - ( $<Location_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Location> ] - ) -} - -<Measurement> CLOSED { - ( $<Measurement_tes> ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - <value> @linkml:String ? ; - <unit> @<Unit> ? - ) ; - rdf:type [ <Measurement> ] ? - ) -} - -core:NamedEntity ( - @<Environment> OR @<EnvironmentalMaterial> OR @<Location> OR @<Organism> OR @core:RelationshipType OR @<SequencingTechnology> - OR @<Treatment> OR @<Unit> OR @<Variable> -) - -core:NamedEntity_struct { - ( $core:NamedEntity_tes rdfs1:label @linkml:String ? ; - rdf:type [ core:NamedEntity ] - ) -} - -<Organism> CLOSED { - ( $<Organism_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Organism> ] - ) -} - -core:Publication CLOSED { - ( $core:Publication_tes ( core:id @linkml:String ? ; - core:title @linkml:String ? ; - core:abstract @linkml:String ? ; - core:combined_text @linkml:String ? ; - core:full_text @linkml:String ? - ) ; - rdf:type [ core:Publication ] ? - ) -} - -core:RelationshipType CLOSED { - ( $core:RelationshipType_tes ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ core:RelationshipType ] - ) -} - -<SequencingTechnology> CLOSED { - ( $<SequencingTechnology_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <SequencingTechnology> ] - ) -} - -<Study> CLOSED { - ( $<Study_tes> ( <environments> @<Environment> * ; - <causal_relationships> @<CausalRelationship> * ; - <variables> @<Variable> * ; - <treatments> @<Treatment> * ; - <measurements> @<Measurement> * ; - <location> @<Location> * ; - <environmental_material> @<EnvironmentalMaterial> * ; - <sequencing_technologies> @<SequencingTechnology> ? ; - <organisms> @<Organism> * - ) ; - rdf:type [ <Study> ] ? - ) -} - -core:TextWithTriples CLOSED { - ( $core:TextWithTriples_tes ( core:publication @core:Publication ? ; - core:triples @core:Triple * - ) ; - rdf:type [ core:TextWithTriples ] ? - ) -} - -<Treatment> CLOSED { - ( $<Treatment_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Treatment> ] - ) -} - -core:Triple { - ( $core:Triple_tes ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - core:subject @core:NamedEntity ? ; - core:predicate @core:RelationshipType ? ; - core:object @core:NamedEntity ? ; - core:qualifier @linkml:String ? ; - core:subject_qualifier @core:NamedEntity ? ; - core:object_qualifier @core:NamedEntity ? - ) ; - rdf:type [ core:Triple ] ? - ) -} - -<Unit> CLOSED { - ( $<Unit_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Unit> ] - ) -} - -<Variable> CLOSED { - ( $<Variable_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Variable> ] - ) -} - - diff --git a/projects/metagenome_study/sqlschema/metagenome_study.sql b/projects/metagenome_study/sqlschema/metagenome_study.sql deleted file mode 100644 index 8c84a1f13..000000000 --- a/projects/metagenome_study/sqlschema/metagenome_study.sql +++ /dev/null @@ -1,117 +0,0 @@ - - -CREATE TABLE "AnnotatorResult" ( - subject_text TEXT, - object_id TEXT, - object_text TEXT, - PRIMARY KEY (subject_text, object_id, object_text) -); - -CREATE TABLE "Environment" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "EnvironmentalMaterial" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "ExtractionResult" ( - input_id TEXT, - input_title TEXT, - input_text TEXT, - raw_completion_output TEXT, - prompt TEXT, - extracted_object TEXT, - named_entities TEXT, - PRIMARY KEY (input_id, input_title, input_text, raw_completion_output, prompt, extracted_object, named_entities) -); - -CREATE TABLE "Location" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Organism" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Publication" ( - id TEXT, - title TEXT, - abstract TEXT, - combined_text TEXT, - full_text TEXT, - PRIMARY KEY (id, title, abstract, combined_text, full_text) -); - -CREATE TABLE "RelationshipType" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "SequencingTechnology" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "TextWithTriples" ( - publication TEXT, - triples TEXT, - PRIMARY KEY (publication, triples) -); - -CREATE TABLE "Treatment" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Unit" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Variable" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "CausalRelationship" ( - cause TEXT, - effect TEXT, - PRIMARY KEY (cause, effect), - FOREIGN KEY(cause) REFERENCES "Variable" (id), - FOREIGN KEY(effect) REFERENCES "Variable" (id) -); - -CREATE TABLE "Measurement" ( - value TEXT, - unit TEXT, - PRIMARY KEY (value, unit), - FOREIGN KEY(unit) REFERENCES "Unit" (id) -); - -CREATE TABLE "Study" ( - environments TEXT, - causal_relationships TEXT, - variables TEXT, - treatments TEXT, - measurements TEXT, - location TEXT, - environmental_material TEXT, - sequencing_technologies TEXT, - organisms TEXT, - PRIMARY KEY (environments, causal_relationships, variables, treatments, measurements, location, environmental_material, sequencing_technologies, organisms), - FOREIGN KEY(sequencing_technologies) REFERENCES "SequencingTechnology" (id) -); diff --git a/projects/ontology_class/docs/AnnotatorResult.md b/projects/ontology_class/docs/AnnotatorResult.md deleted file mode 100644 index 4f189092b..000000000 --- a/projects/ontology_class/docs/AnnotatorResult.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Class: AnnotatorResult - - - - -URI: [oc:AnnotatorResult](http://w3id.org/ontogpt/ontology-class-templateAnnotatorResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F])](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F]) - -## Attributes - - -### Own - - * [➞subject_text](annotatorResult__subject_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_id](annotatorResult__object_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_text](annotatorResult__object_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) diff --git a/projects/ontology_class/docs/Any.md b/projects/ontology_class/docs/Any.md deleted file mode 100644 index 75c20f2f8..000000000 --- a/projects/ontology_class/docs/Any.md +++ /dev/null @@ -1,25 +0,0 @@ - -# Class: Any - - - - -URI: [oc:Any](http://w3id.org/ontogpt/ontology-class-templateAny) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult])](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult]) - -## Referenced by Class - - * **None** *[➞extracted_object](extractionResult__extracted_object.md)* <sub>0..1</sub> **[Any](Any.md)** - * **None** *[➞named_entities](extractionResult__named_entities.md)* <sub>0..\*</sub> **[Any](Any.md)** - -## Attributes - - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | linkml:Any | - diff --git a/projects/ontology_class/docs/CompoundExpression.md b/projects/ontology_class/docs/CompoundExpression.md deleted file mode 100644 index 35fe2b15a..000000000 --- a/projects/ontology_class/docs/CompoundExpression.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: CompoundExpression - - - - -URI: [oc:CompoundExpression](http://w3id.org/ontogpt/ontology-class-templateCompoundExpression) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[CompoundExpression]^-[Triple])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[CompoundExpression]^-[Triple]) - -## Children - - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - -## Referenced by Class - - -## Attributes - diff --git a/projects/ontology_class/docs/ExtractionResult.md b/projects/ontology_class/docs/ExtractionResult.md deleted file mode 100644 index fe7d19bb9..000000000 --- a/projects/ontology_class/docs/ExtractionResult.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Class: ExtractionResult - - -A result of extracting knowledge on text - -URI: [oc:ExtractionResult](http://w3id.org/ontogpt/ontology-class-templateExtractionResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any])](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any]) - -## Attributes - - -### Own - - * [➞input_id](extractionResult__input_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_title](extractionResult__input_title.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_text](extractionResult__input_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞prompt](extractionResult__prompt.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞extracted_object](extractionResult__extracted_object.md) <sub>0..1</sub> - * Description: The complex objects extracted from the text - * Range: [Any](Any.md) - * [➞named_entities](extractionResult__named_entities.md) <sub>0..\*</sub> - * Description: Named entities extracted from the text - * Range: [Any](Any.md) diff --git a/projects/ontology_class/docs/LogicalDefinition.md b/projects/ontology_class/docs/LogicalDefinition.md deleted file mode 100644 index be5a7b0ae..000000000 --- a/projects/ontology_class/docs/LogicalDefinition.md +++ /dev/null @@ -1,26 +0,0 @@ - -# Class: LogicalDefinition - - - - -URI: [oc:LogicalDefinition](http://w3id.org/ontogpt/ontology-class-templateLogicalDefinition) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Relation],[OntologyClass],[OntologyClass]<differentiating_characteristic_parents%200..*-%20[LogicalDefinition],[Relation]<differentiating_characteristic_relationship%200..1-%20[LogicalDefinition],[OntologyClass]<genus%200..*-%20[LogicalDefinition],[OntologyClass]++-%20logical_definition%200..1>[LogicalDefinition])](https://yuml.me/diagram/nofunky;dir:TB/class/[Relation],[OntologyClass],[OntologyClass]<differentiating_characteristic_parents%200..*-%20[LogicalDefinition],[Relation]<differentiating_characteristic_relationship%200..1-%20[LogicalDefinition],[OntologyClass]<genus%200..*-%20[LogicalDefinition],[OntologyClass]++-%20logical_definition%200..1>[LogicalDefinition]) - -## Referenced by Class - - * **None** *[➞logical_definition](ontologyClass__logical_definition.md)* <sub>0..1</sub> **[LogicalDefinition](LogicalDefinition.md)** - -## Attributes - - -### Own - - * [➞genus](logicalDefinition__genus.md) <sub>0..\*</sub> - * Range: [OntologyClass](OntologyClass.md) - * [➞differentiating_characteristic_relationship](logicalDefinition__differentiating_characteristic_relationship.md) <sub>0..1</sub> - * Range: [Relation](Relation.md) - * [➞differentiating_characteristic_parents](logicalDefinition__differentiating_characteristic_parents.md) <sub>0..\*</sub> - * Range: [OntologyClass](OntologyClass.md) diff --git a/projects/ontology_class/docs/NamedEntity.md b/projects/ontology_class/docs/NamedEntity.md deleted file mode 100644 index fba1cadc9..000000000 --- a/projects/ontology_class/docs/NamedEntity.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: NamedEntity - - - - -URI: [oc:NamedEntity](http://w3id.org/ontogpt/ontology-class-templateNamedEntity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[Relation],[OntologyClass],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[Relation],[NamedEntity]^-[OntologyClass],[Triple])](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[Relation],[OntologyClass],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[Relation],[NamedEntity]^-[OntologyClass],[Triple]) - -## Children - - * [OntologyClass](OntologyClass.md) - * [Relation](Relation.md) - * [RelationshipType](RelationshipType.md) - -## Referenced by Class - - * **None** *[➞object](triple__object.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞object_qualifier](triple__object_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject](triple__subject.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject_qualifier](triple__subject_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - -## Attributes - - -### Own - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/ontology_class/docs/NullDataOptions.md b/projects/ontology_class/docs/NullDataOptions.md deleted file mode 100644 index 4b9a6758e..000000000 --- a/projects/ontology_class/docs/NullDataOptions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Enum: NullDataOptions - - - - -URI: [oc:NullDataOptions](http://w3id.org/ontogpt/ontology-class-templateNullDataOptions) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | -| UNSPECIFIED_METHOD_OF_ADMINISTRATION | | NCIT:C149701 | | -| NOT_APPLICABLE | | NCIT:C18902 | {'aliases': ['not applicable', 'N/A']} | -| NOT_MENTIONED | | | | - diff --git a/projects/ontology_class/docs/OntologyClass.md b/projects/ontology_class/docs/OntologyClass.md deleted file mode 100644 index 2c94cf787..000000000 --- a/projects/ontology_class/docs/OntologyClass.md +++ /dev/null @@ -1,50 +0,0 @@ - -# Class: OntologyClass - - - - -URI: [oc:OntologyClass](http://w3id.org/ontogpt/ontology-class-templateOntologyClass) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[LogicalDefinition]<logical_definition%200..1-++[OntologyClass|label:string%20%3F;description:string%20%3F;synonyms:string%20*;id(i):string],[OntologyClass]<subclass_of%200..*-%20[OntologyClass],[OntologyClass]<categories%200..*-%20[OntologyClass],[LogicalDefinition]-%20differentiating_characteristic_parents%200..*>[OntologyClass],[LogicalDefinition]-%20genus%200..*>[OntologyClass],[NamedEntity]^-[OntologyClass],[NamedEntity],[LogicalDefinition])](https://yuml.me/diagram/nofunky;dir:TB/class/[LogicalDefinition]<logical_definition%200..1-++[OntologyClass|label:string%20%3F;description:string%20%3F;synonyms:string%20*;id(i):string],[OntologyClass]<subclass_of%200..*-%20[OntologyClass],[OntologyClass]<categories%200..*-%20[OntologyClass],[LogicalDefinition]-%20differentiating_characteristic_parents%200..*>[OntologyClass],[LogicalDefinition]-%20genus%200..*>[OntologyClass],[NamedEntity]^-[OntologyClass],[NamedEntity],[LogicalDefinition]) - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞differentiating_characteristic_parents](logicalDefinition__differentiating_characteristic_parents.md)* <sub>0..\*</sub> **[OntologyClass](OntologyClass.md)** - * **None** *[➞genus](logicalDefinition__genus.md)* <sub>0..\*</sub> **[OntologyClass](OntologyClass.md)** - * **None** *[➞categories](ontologyClass__categories.md)* <sub>0..\*</sub> **[OntologyClass](OntologyClass.md)** - * **None** *[➞subclass_of](ontologyClass__subclass_of.md)* <sub>0..\*</sub> **[OntologyClass](OntologyClass.md)** - -## Attributes - - -### Own - - * [➞label](ontologyClass__label.md) <sub>0..1</sub> - * Description: the name of the main entity being defined - * Range: [String](types/String.md) - * [➞description](ontologyClass__description.md) <sub>0..1</sub> - * Description: a textual description of the entity - * Range: [String](types/String.md) - * [➞synonyms](ontologyClass__synonyms.md) <sub>0..\*</sub> - * Description: alternative names of the entity - * Range: [String](types/String.md) - * [➞categories](ontologyClass__categories.md) <sub>0..\*</sub> - * Description: the categories to which this entity belongs. - * Range: [OntologyClass](OntologyClass.md) - * [➞subclass_of](ontologyClass__subclass_of.md) <sub>0..\*</sub> - * Range: [OntologyClass](OntologyClass.md) - * [➞logical_definition](ontologyClass__logical_definition.md) <sub>0..1</sub> - * Description: the necessary and sufficient conditions for this entity to be an instance of this class - * Range: [LogicalDefinition](LogicalDefinition.md) - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) diff --git a/projects/ontology_class/docs/Publication.md b/projects/ontology_class/docs/Publication.md deleted file mode 100644 index a55c2f8cc..000000000 --- a/projects/ontology_class/docs/Publication.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Publication - - - - -URI: [oc:Publication](http://w3id.org/ontogpt/ontology-class-templatePublication) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples])](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples]) - -## Referenced by Class - - * **None** *[➞publication](textWithTriples__publication.md)* <sub>0..1</sub> **[Publication](Publication.md)** - -## Attributes - - -### Own - - * [➞id](publication__id.md) <sub>0..1</sub> - * Description: The publication identifier - * Range: [String](types/String.md) - * [➞title](publication__title.md) <sub>0..1</sub> - * Description: The title of the publication - * Range: [String](types/String.md) - * [➞abstract](publication__abstract.md) <sub>0..1</sub> - * Description: The abstract of the publication - * Range: [String](types/String.md) - * [➞combined_text](publication__combined_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞full_text](publication__full_text.md) <sub>0..1</sub> - * Description: The full text of the publication - * Range: [String](types/String.md) diff --git a/projects/ontology_class/docs/Relation.md b/projects/ontology_class/docs/Relation.md deleted file mode 100644 index d0d40a80d..000000000 --- a/projects/ontology_class/docs/Relation.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Relation - - - - -URI: [oc:Relation](http://w3id.org/ontogpt/ontology-class-templateRelation) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[LogicalDefinition]-%20differentiating_characteristic_relationship%200..1>[Relation|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Relation],[NamedEntity],[LogicalDefinition])](https://yuml.me/diagram/nofunky;dir:TB/class/[LogicalDefinition]-%20differentiating_characteristic_relationship%200..1>[Relation|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Relation],[NamedEntity],[LogicalDefinition]) - -## Identifier prefixes - - * RO - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞differentiating_characteristic_relationship](logicalDefinition__differentiating_characteristic_relationship.md)* <sub>0..1</sub> **[Relation](Relation.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/ontology_class/docs/RelationshipType.md b/projects/ontology_class/docs/RelationshipType.md deleted file mode 100644 index 4adecdef0..000000000 --- a/projects/ontology_class/docs/RelationshipType.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: RelationshipType - - - - -URI: [oc:RelationshipType](http://w3id.org/ontogpt/ontology-class-templateRelationshipType) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity]) - -## Identifier prefixes - - * RO - * biolink - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞predicate](triple__predicate.md)* <sub>0..1</sub> **[RelationshipType](RelationshipType.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/ontology_class/docs/TextWithTriples.md b/projects/ontology_class/docs/TextWithTriples.md deleted file mode 100644 index e94121934..000000000 --- a/projects/ontology_class/docs/TextWithTriples.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: TextWithTriples - - - - -URI: [oc:TextWithTriples](http://w3id.org/ontogpt/ontology-class-templateTextWithTriples) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication]) - -## Attributes - - -### Own - - * [➞publication](textWithTriples__publication.md) <sub>0..1</sub> - * Range: [Publication](Publication.md) - * [➞triples](textWithTriples__triples.md) <sub>0..\*</sub> - * Range: [Triple](Triple.md) diff --git a/projects/ontology_class/docs/Triple.md b/projects/ontology_class/docs/Triple.md deleted file mode 100644 index 5a0ca3d43..000000000 --- a/projects/ontology_class/docs/Triple.md +++ /dev/null @@ -1,39 +0,0 @@ - -# Class: Triple - - -Abstract parent for Relation Extraction tasks - -URI: [oc:Triple](http://w3id.org/ontogpt/ontology-class-templateTriple) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞triples](textWithTriples__triples.md)* <sub>0..\*</sub> **[Triple](Triple.md)** - -## Attributes - - -### Own - - * [➞subject](triple__subject.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞predicate](triple__predicate.md) <sub>0..1</sub> - * Range: [RelationshipType](RelationshipType.md) - * [➞object](triple__object.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞qualifier](triple__qualifier.md) <sub>0..1</sub> - * Description: A qualifier for the statements, e.g. "NOT" for negation - * Range: [String](types/String.md) - * [➞subject_qualifier](triple__subject_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - * Range: [NamedEntity](NamedEntity.md) - * [➞object_qualifier](triple__object_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * Range: [NamedEntity](NamedEntity.md) diff --git a/projects/ontology_class/docs/annotatorResult__object_id.md b/projects/ontology_class/docs/annotatorResult__object_id.md deleted file mode 100644 index be14e5b97..000000000 --- a/projects/ontology_class/docs/annotatorResult__object_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_id - - - - -URI: [oc:annotatorResult__object_id](http://w3id.org/ontogpt/ontology-class-templateannotatorResult__object_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/ontology_class/docs/annotatorResult__object_text.md b/projects/ontology_class/docs/annotatorResult__object_text.md deleted file mode 100644 index fbf16b458..000000000 --- a/projects/ontology_class/docs/annotatorResult__object_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_text - - - - -URI: [oc:annotatorResult__object_text](http://w3id.org/ontogpt/ontology-class-templateannotatorResult__object_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/ontology_class/docs/annotatorResult__subject_text.md b/projects/ontology_class/docs/annotatorResult__subject_text.md deleted file mode 100644 index 1525bf843..000000000 --- a/projects/ontology_class/docs/annotatorResult__subject_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_text - - - - -URI: [oc:annotatorResult__subject_text](http://w3id.org/ontogpt/ontology-class-templateannotatorResult__subject_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/ontology_class/docs/extractionResult__extracted_object.md b/projects/ontology_class/docs/extractionResult__extracted_object.md deleted file mode 100644 index b1bc7ddff..000000000 --- a/projects/ontology_class/docs/extractionResult__extracted_object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: extracted_object - - -The complex objects extracted from the text - -URI: [oc:extractionResult__extracted_object](http://w3id.org/ontogpt/ontology-class-templateextractionResult__extracted_object) - - -## Domain and Range - -None → <sub>0..1</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ontology_class/docs/extractionResult__input_id.md b/projects/ontology_class/docs/extractionResult__input_id.md deleted file mode 100644 index 06eab71c1..000000000 --- a/projects/ontology_class/docs/extractionResult__input_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_id - - - - -URI: [oc:extractionResult__input_id](http://w3id.org/ontogpt/ontology-class-templateextractionResult__input_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ontology_class/docs/extractionResult__input_text.md b/projects/ontology_class/docs/extractionResult__input_text.md deleted file mode 100644 index 1dc6a7221..000000000 --- a/projects/ontology_class/docs/extractionResult__input_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_text - - - - -URI: [oc:extractionResult__input_text](http://w3id.org/ontogpt/ontology-class-templateextractionResult__input_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ontology_class/docs/extractionResult__input_title.md b/projects/ontology_class/docs/extractionResult__input_title.md deleted file mode 100644 index 2d7893d36..000000000 --- a/projects/ontology_class/docs/extractionResult__input_title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_title - - - - -URI: [oc:extractionResult__input_title](http://w3id.org/ontogpt/ontology-class-templateextractionResult__input_title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ontology_class/docs/extractionResult__named_entities.md b/projects/ontology_class/docs/extractionResult__named_entities.md deleted file mode 100644 index 37772a93c..000000000 --- a/projects/ontology_class/docs/extractionResult__named_entities.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: named_entities - - -Named entities extracted from the text - -URI: [oc:extractionResult__named_entities](http://w3id.org/ontogpt/ontology-class-templateextractionResult__named_entities) - - -## Domain and Range - -None → <sub>0..\*</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ontology_class/docs/extractionResult__prompt.md b/projects/ontology_class/docs/extractionResult__prompt.md deleted file mode 100644 index 8ba0ddcab..000000000 --- a/projects/ontology_class/docs/extractionResult__prompt.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: prompt - - - - -URI: [oc:extractionResult__prompt](http://w3id.org/ontogpt/ontology-class-templateextractionResult__prompt) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ontology_class/docs/extractionResult__raw_completion_output.md b/projects/ontology_class/docs/extractionResult__raw_completion_output.md deleted file mode 100644 index ec9df2512..000000000 --- a/projects/ontology_class/docs/extractionResult__raw_completion_output.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: raw_completion_output - - - - -URI: [oc:extractionResult__raw_completion_output](http://w3id.org/ontogpt/ontology-class-templateextractionResult__raw_completion_output) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ontology_class/docs/logicalDefinition__differentiating_characteristic_parents.md b/projects/ontology_class/docs/logicalDefinition__differentiating_characteristic_parents.md deleted file mode 100644 index c973bd6c1..000000000 --- a/projects/ontology_class/docs/logicalDefinition__differentiating_characteristic_parents.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: differentiating_characteristic_parents - - - - -URI: [oc:logicalDefinition__differentiating_characteristic_parents](http://w3id.org/ontogpt/ontology-class-templatelogicalDefinition__differentiating_characteristic_parents) - - -## Domain and Range - -None → <sub>0..\*</sub> [OntologyClass](OntologyClass.md) - -## Parents - - -## Children - - -## Used by - - * [LogicalDefinition](LogicalDefinition.md) diff --git a/projects/ontology_class/docs/logicalDefinition__differentiating_characteristic_relationship.md b/projects/ontology_class/docs/logicalDefinition__differentiating_characteristic_relationship.md deleted file mode 100644 index c638fdcf7..000000000 --- a/projects/ontology_class/docs/logicalDefinition__differentiating_characteristic_relationship.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: differentiating_characteristic_relationship - - - - -URI: [oc:logicalDefinition__differentiating_characteristic_relationship](http://w3id.org/ontogpt/ontology-class-templatelogicalDefinition__differentiating_characteristic_relationship) - - -## Domain and Range - -None → <sub>0..1</sub> [Relation](Relation.md) - -## Parents - - -## Children - - -## Used by - - * [LogicalDefinition](LogicalDefinition.md) diff --git a/projects/ontology_class/docs/logicalDefinition__genus.md b/projects/ontology_class/docs/logicalDefinition__genus.md deleted file mode 100644 index 07eb934cd..000000000 --- a/projects/ontology_class/docs/logicalDefinition__genus.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: genus - - - - -URI: [oc:logicalDefinition__genus](http://w3id.org/ontogpt/ontology-class-templatelogicalDefinition__genus) - - -## Domain and Range - -None → <sub>0..\*</sub> [OntologyClass](OntologyClass.md) - -## Parents - - -## Children - - -## Used by - - * [LogicalDefinition](LogicalDefinition.md) diff --git a/projects/ontology_class/docs/namedEntity__id.md b/projects/ontology_class/docs/namedEntity__id.md deleted file mode 100644 index 6fad481c7..000000000 --- a/projects/ontology_class/docs/namedEntity__id.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Slot: id - - -A unique identifier for the named entity - -URI: [oc:namedEntity__id](http://w3id.org/ontogpt/ontology-class-templatenamedEntity__id) - - -## Domain and Range - -None → <sub>1..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [NamedEntity](NamedEntity.md) - * [OntologyClass](OntologyClass.md) - * [Relation](Relation.md) - * [RelationshipType](RelationshipType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | this is populated during the grounding and normalization step | - diff --git a/projects/ontology_class/docs/namedEntity__label.md b/projects/ontology_class/docs/namedEntity__label.md deleted file mode 100644 index 32c673a9d..000000000 --- a/projects/ontology_class/docs/namedEntity__label.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Slot: label - - -The label (name) of the named thing - -URI: [oc:namedEntity__label](http://w3id.org/ontogpt/ontology-class-templatenamedEntity__label) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [NamedEntity](NamedEntity.md) - * [Relation](Relation.md) - * [RelationshipType](RelationshipType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Aliases:** | | name | -| **Mappings:** | | rdfs:label | - diff --git a/projects/ontology_class/docs/ontologyClass__categories.md b/projects/ontology_class/docs/ontologyClass__categories.md deleted file mode 100644 index 22d9e3e95..000000000 --- a/projects/ontology_class/docs/ontologyClass__categories.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: categories - - -the categories to which this entity belongs. - -URI: [oc:ontologyClass__categories](http://w3id.org/ontogpt/ontology-class-templateontologyClass__categories) - - -## Domain and Range - -None → <sub>0..\*</sub> [OntologyClass](OntologyClass.md) - -## Parents - - -## Children - - -## Used by - - * [OntologyClass](OntologyClass.md) diff --git a/projects/ontology_class/docs/ontologyClass__description.md b/projects/ontology_class/docs/ontologyClass__description.md deleted file mode 100644 index 01eeb1a88..000000000 --- a/projects/ontology_class/docs/ontologyClass__description.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: description - - -a textual description of the entity - -URI: [oc:ontologyClass__description](http://w3id.org/ontogpt/ontology-class-templateontologyClass__description) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [OntologyClass](OntologyClass.md) diff --git a/projects/ontology_class/docs/ontologyClass__label.md b/projects/ontology_class/docs/ontologyClass__label.md deleted file mode 100644 index d62bfa3ca..000000000 --- a/projects/ontology_class/docs/ontologyClass__label.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: label - - -the name of the main entity being defined - -URI: [oc:ontologyClass__label](http://w3id.org/ontogpt/ontology-class-templateontologyClass__label) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [OntologyClass](OntologyClass.md) diff --git a/projects/ontology_class/docs/ontologyClass__logical_definition.md b/projects/ontology_class/docs/ontologyClass__logical_definition.md deleted file mode 100644 index d617d2a2d..000000000 --- a/projects/ontology_class/docs/ontologyClass__logical_definition.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: logical_definition - - -the necessary and sufficient conditions for this entity to be an instance of this class - -URI: [oc:ontologyClass__logical_definition](http://w3id.org/ontogpt/ontology-class-templateontologyClass__logical_definition) - - -## Domain and Range - -None → <sub>0..1</sub> [LogicalDefinition](LogicalDefinition.md) - -## Parents - - -## Children - - -## Used by - - * [OntologyClass](OntologyClass.md) diff --git a/projects/ontology_class/docs/ontologyClass__subclass_of.md b/projects/ontology_class/docs/ontologyClass__subclass_of.md deleted file mode 100644 index f648d140c..000000000 --- a/projects/ontology_class/docs/ontologyClass__subclass_of.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subclass_of - - - - -URI: [oc:ontologyClass__subclass_of](http://w3id.org/ontogpt/ontology-class-templateontologyClass__subclass_of) - - -## Domain and Range - -None → <sub>0..\*</sub> [OntologyClass](OntologyClass.md) - -## Parents - - -## Children - - -## Used by - - * [OntologyClass](OntologyClass.md) diff --git a/projects/ontology_class/docs/ontologyClass__synonyms.md b/projects/ontology_class/docs/ontologyClass__synonyms.md deleted file mode 100644 index fa56183b1..000000000 --- a/projects/ontology_class/docs/ontologyClass__synonyms.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: synonyms - - -alternative names of the entity - -URI: [oc:ontologyClass__synonyms](http://w3id.org/ontogpt/ontology-class-templateontologyClass__synonyms) - - -## Domain and Range - -None → <sub>0..\*</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [OntologyClass](OntologyClass.md) diff --git a/projects/ontology_class/docs/ontology_class.md b/projects/ontology_class/docs/ontology_class.md deleted file mode 100644 index af1279bea..000000000 --- a/projects/ontology_class/docs/ontology_class.md +++ /dev/null @@ -1,115 +0,0 @@ - -# ontology-class - - -**metamodel version:** 1.7.0 - -**version:** None - - -A template for Ontology Classes - - -### Classes - - * [AnnotatorResult](AnnotatorResult.md) - * [Any](Any.md) - * [CompoundExpression](CompoundExpression.md) - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - * [ExtractionResult](ExtractionResult.md) - A result of extracting knowledge on text - * [LogicalDefinition](LogicalDefinition.md) - * [NamedEntity](NamedEntity.md) - * [OntologyClass](OntologyClass.md) - * [Relation](Relation.md) - * [RelationshipType](RelationshipType.md) - * [Publication](Publication.md) - * [TextWithTriples](TextWithTriples.md) - -### Mixins - - -### Slots - - * [➞object_id](annotatorResult__object_id.md) - * [➞object_text](annotatorResult__object_text.md) - * [➞subject_text](annotatorResult__subject_text.md) - * [➞extracted_object](extractionResult__extracted_object.md) - The complex objects extracted from the text - * [➞input_id](extractionResult__input_id.md) - * [➞input_text](extractionResult__input_text.md) - * [➞input_title](extractionResult__input_title.md) - * [➞named_entities](extractionResult__named_entities.md) - Named entities extracted from the text - * [➞prompt](extractionResult__prompt.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) - * [➞differentiating_characteristic_parents](logicalDefinition__differentiating_characteristic_parents.md) - * [➞differentiating_characteristic_relationship](logicalDefinition__differentiating_characteristic_relationship.md) - * [➞genus](logicalDefinition__genus.md) - * [➞id](namedEntity__id.md) - A unique identifier for the named entity - * [➞label](namedEntity__label.md) - The label (name) of the named thing - * [➞categories](ontologyClass__categories.md) - the categories to which this entity belongs. - * [➞description](ontologyClass__description.md) - a textual description of the entity - * [➞label](ontologyClass__label.md) - the name of the main entity being defined - * [➞logical_definition](ontologyClass__logical_definition.md) - the necessary and sufficient conditions for this entity to be an instance of this class - * [➞subclass_of](ontologyClass__subclass_of.md) - * [➞synonyms](ontologyClass__synonyms.md) - alternative names of the entity - * [➞abstract](publication__abstract.md) - The abstract of the publication - * [➞combined_text](publication__combined_text.md) - * [➞full_text](publication__full_text.md) - The full text of the publication - * [➞id](publication__id.md) - The publication identifier - * [➞title](publication__title.md) - The title of the publication - * [➞publication](textWithTriples__publication.md) - * [➞triples](textWithTriples__triples.md) - * [➞object](triple__object.md) - * [➞object_qualifier](triple__object_qualifier.md) - An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * [➞predicate](triple__predicate.md) - * [➞qualifier](triple__qualifier.md) - A qualifier for the statements, e.g. "NOT" for negation - * [➞subject](triple__subject.md) - * [➞subject_qualifier](triple__subject_qualifier.md) - An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -### Enums - - * [NullDataOptions](NullDataOptions.md) - -### Subsets - - -### Types - - -#### Built in - - * **Bool** - * **Curie** - * **Decimal** - * **ElementIdentifier** - * **NCName** - * **NodeIdentifier** - * **URI** - * **URIorCURIE** - * **XSDDate** - * **XSDDateTime** - * **XSDTime** - * **float** - * **int** - * **str** - -#### Defined - - * [Boolean](types/Boolean.md) (**Bool**) - A binary (true or false) value - * [Curie](types/Curie.md) (**Curie**) - a compact URI - * [Date](types/Date.md) (**XSDDate**) - a date (year, month and day) in an idealized calendar - * [DateOrDatetime](types/DateOrDatetime.md) (**str**) - Either a date or a datetime - * [Datetime](types/Datetime.md) (**XSDDateTime**) - The combination of a date and time - * [Decimal](types/Decimal.md) (**Decimal**) - A real number with arbitrary precision that conforms to the xsd:decimal specification - * [Double](types/Double.md) (**float**) - A real number that conforms to the xsd:double specification - * [Float](types/Float.md) (**float**) - A real number that conforms to the xsd:float specification - * [Integer](types/Integer.md) (**int**) - An integer - * [Jsonpath](types/Jsonpath.md) (**str**) - A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - * [Jsonpointer](types/Jsonpointer.md) (**str**) - A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - * [Ncname](types/Ncname.md) (**NCName**) - Prefix part of CURIE - * [Nodeidentifier](types/Nodeidentifier.md) (**NodeIdentifier**) - A URI, CURIE or BNODE that represents a node in a model. - * [Objectidentifier](types/Objectidentifier.md) (**ElementIdentifier**) - A URI or CURIE that represents an object in the model. - * [Sparqlpath](types/Sparqlpath.md) (**str**) - A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - * [String](types/String.md) (**str**) - A character string - * [Time](types/Time.md) (**XSDTime**) - A time object represents a (local) time of day, independent of any particular day - * [Uri](types/Uri.md) (**URI**) - a complete URI - * [Uriorcurie](types/Uriorcurie.md) (**URIorCURIE**) - a URI or a CURIE diff --git a/projects/ontology_class/docs/publication__abstract.md b/projects/ontology_class/docs/publication__abstract.md deleted file mode 100644 index 7e1c7ff37..000000000 --- a/projects/ontology_class/docs/publication__abstract.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: abstract - - -The abstract of the publication - -URI: [oc:publication__abstract](http://w3id.org/ontogpt/ontology-class-templatepublication__abstract) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/ontology_class/docs/publication__combined_text.md b/projects/ontology_class/docs/publication__combined_text.md deleted file mode 100644 index de03f19fd..000000000 --- a/projects/ontology_class/docs/publication__combined_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: combined_text - - - - -URI: [oc:publication__combined_text](http://w3id.org/ontogpt/ontology-class-templatepublication__combined_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/ontology_class/docs/publication__full_text.md b/projects/ontology_class/docs/publication__full_text.md deleted file mode 100644 index ae02a60d4..000000000 --- a/projects/ontology_class/docs/publication__full_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: full_text - - -The full text of the publication - -URI: [oc:publication__full_text](http://w3id.org/ontogpt/ontology-class-templatepublication__full_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/ontology_class/docs/publication__id.md b/projects/ontology_class/docs/publication__id.md deleted file mode 100644 index 3fbcffacd..000000000 --- a/projects/ontology_class/docs/publication__id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: id - - -The publication identifier - -URI: [oc:publication__id](http://w3id.org/ontogpt/ontology-class-templatepublication__id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/ontology_class/docs/publication__title.md b/projects/ontology_class/docs/publication__title.md deleted file mode 100644 index 5f9f7ed69..000000000 --- a/projects/ontology_class/docs/publication__title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: title - - -The title of the publication - -URI: [oc:publication__title](http://w3id.org/ontogpt/ontology-class-templatepublication__title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/ontology_class/docs/textWithTriples__publication.md b/projects/ontology_class/docs/textWithTriples__publication.md deleted file mode 100644 index 27b0af18d..000000000 --- a/projects/ontology_class/docs/textWithTriples__publication.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: publication - - - - -URI: [oc:textWithTriples__publication](http://w3id.org/ontogpt/ontology-class-templatetextWithTriples__publication) - - -## Domain and Range - -None → <sub>0..1</sub> [Publication](Publication.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/ontology_class/docs/textWithTriples__triples.md b/projects/ontology_class/docs/textWithTriples__triples.md deleted file mode 100644 index d3a729b64..000000000 --- a/projects/ontology_class/docs/textWithTriples__triples.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: triples - - - - -URI: [oc:textWithTriples__triples](http://w3id.org/ontogpt/ontology-class-templatetextWithTriples__triples) - - -## Domain and Range - -None → <sub>0..\*</sub> [Triple](Triple.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/ontology_class/docs/triple__object.md b/projects/ontology_class/docs/triple__object.md deleted file mode 100644 index 19c663552..000000000 --- a/projects/ontology_class/docs/triple__object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object - - - - -URI: [oc:triple__object](http://w3id.org/ontogpt/ontology-class-templatetriple__object) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/ontology_class/docs/triple__object_qualifier.md b/projects/ontology_class/docs/triple__object_qualifier.md deleted file mode 100644 index bead5d4a5..000000000 --- a/projects/ontology_class/docs/triple__object_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_qualifier - - -An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - -URI: [oc:triple__object_qualifier](http://w3id.org/ontogpt/ontology-class-templatetriple__object_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/ontology_class/docs/triple__predicate.md b/projects/ontology_class/docs/triple__predicate.md deleted file mode 100644 index 425642196..000000000 --- a/projects/ontology_class/docs/triple__predicate.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: predicate - - - - -URI: [oc:triple__predicate](http://w3id.org/ontogpt/ontology-class-templatetriple__predicate) - - -## Domain and Range - -None → <sub>0..1</sub> [RelationshipType](RelationshipType.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/ontology_class/docs/triple__qualifier.md b/projects/ontology_class/docs/triple__qualifier.md deleted file mode 100644 index 9277dabfe..000000000 --- a/projects/ontology_class/docs/triple__qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: qualifier - - -A qualifier for the statements, e.g. "NOT" for negation - -URI: [oc:triple__qualifier](http://w3id.org/ontogpt/ontology-class-templatetriple__qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/ontology_class/docs/triple__subject.md b/projects/ontology_class/docs/triple__subject.md deleted file mode 100644 index 89487785e..000000000 --- a/projects/ontology_class/docs/triple__subject.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject - - - - -URI: [oc:triple__subject](http://w3id.org/ontogpt/ontology-class-templatetriple__subject) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/ontology_class/docs/triple__subject_qualifier.md b/projects/ontology_class/docs/triple__subject_qualifier.md deleted file mode 100644 index e63c6bbd8..000000000 --- a/projects/ontology_class/docs/triple__subject_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_qualifier - - -An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -URI: [oc:triple__subject_qualifier](http://w3id.org/ontogpt/ontology-class-templatetriple__subject_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/ontology_class/docs/types/Boolean.md b/projects/ontology_class/docs/types/Boolean.md deleted file mode 100644 index dc83a9c6e..000000000 --- a/projects/ontology_class/docs/types/Boolean.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: boolean - - -A binary (true or false) value - -URI: [linkml:Boolean](https://w3id.org/linkml/Boolean) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Bool** | -| Representation | | bool | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Boolean | - diff --git a/projects/ontology_class/docs/types/Curie.md b/projects/ontology_class/docs/types/Curie.md deleted file mode 100644 index c1803f93f..000000000 --- a/projects/ontology_class/docs/types/Curie.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: curie - - -a compact URI - -URI: [linkml:Curie](https://w3id.org/linkml/Curie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Curie** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations this MUST be expanded to a URI | -| | | in non-RDF serializations MAY be serialized as the compact representation | - diff --git a/projects/ontology_class/docs/types/Date.md b/projects/ontology_class/docs/types/Date.md deleted file mode 100644 index 06948af97..000000000 --- a/projects/ontology_class/docs/types/Date.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: date - - -a date (year, month and day) in an idealized calendar - -URI: [linkml:Date](https://w3id.org/linkml/Date) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDate** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Date | - diff --git a/projects/ontology_class/docs/types/DateOrDatetime.md b/projects/ontology_class/docs/types/DateOrDatetime.md deleted file mode 100644 index ef983898d..000000000 --- a/projects/ontology_class/docs/types/DateOrDatetime.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: date_or_datetime - - -Either a date or a datetime - -URI: [linkml:DateOrDatetime](https://w3id.org/linkml/DateOrDatetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/ontology_class/docs/types/Datetime.md b/projects/ontology_class/docs/types/Datetime.md deleted file mode 100644 index 9510454a8..000000000 --- a/projects/ontology_class/docs/types/Datetime.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: datetime - - -The combination of a date and time - -URI: [linkml:Datetime](https://w3id.org/linkml/Datetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDateTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:DateTime | - diff --git a/projects/ontology_class/docs/types/Decimal.md b/projects/ontology_class/docs/types/Decimal.md deleted file mode 100644 index a7ba14a5d..000000000 --- a/projects/ontology_class/docs/types/Decimal.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: decimal - - -A real number with arbitrary precision that conforms to the xsd:decimal specification - -URI: [linkml:Decimal](https://w3id.org/linkml/Decimal) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Decimal** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Broad Mappings:** | | schema:Number | - diff --git a/projects/ontology_class/docs/types/Double.md b/projects/ontology_class/docs/types/Double.md deleted file mode 100644 index cfe6d71e2..000000000 --- a/projects/ontology_class/docs/types/Double.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: double - - -A real number that conforms to the xsd:double specification - -URI: [linkml:Double](https://w3id.org/linkml/Double) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Close Mappings:** | | schema:Float | - diff --git a/projects/ontology_class/docs/types/Float.md b/projects/ontology_class/docs/types/Float.md deleted file mode 100644 index 7b303f96f..000000000 --- a/projects/ontology_class/docs/types/Float.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: float - - -A real number that conforms to the xsd:float specification - -URI: [linkml:Float](https://w3id.org/linkml/Float) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Float | - diff --git a/projects/ontology_class/docs/types/Integer.md b/projects/ontology_class/docs/types/Integer.md deleted file mode 100644 index 3cfcc66d9..000000000 --- a/projects/ontology_class/docs/types/Integer.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: integer - - -An integer - -URI: [linkml:Integer](https://w3id.org/linkml/Integer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **int** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Integer | - diff --git a/projects/ontology_class/docs/types/Jsonpath.md b/projects/ontology_class/docs/types/Jsonpath.md deleted file mode 100644 index a03a58e67..000000000 --- a/projects/ontology_class/docs/types/Jsonpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpath - - -A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpath](https://w3id.org/linkml/Jsonpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/ontology_class/docs/types/Jsonpointer.md b/projects/ontology_class/docs/types/Jsonpointer.md deleted file mode 100644 index a0e1ac492..000000000 --- a/projects/ontology_class/docs/types/Jsonpointer.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpointer - - -A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpointer](https://w3id.org/linkml/Jsonpointer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/ontology_class/docs/types/Ncname.md b/projects/ontology_class/docs/types/Ncname.md deleted file mode 100644 index 710b0b04a..000000000 --- a/projects/ontology_class/docs/types/Ncname.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: ncname - - -Prefix part of CURIE - -URI: [linkml:Ncname](https://w3id.org/linkml/Ncname) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NCName** | -| Representation | | str | diff --git a/projects/ontology_class/docs/types/Nodeidentifier.md b/projects/ontology_class/docs/types/Nodeidentifier.md deleted file mode 100644 index f0097cdf4..000000000 --- a/projects/ontology_class/docs/types/Nodeidentifier.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: nodeidentifier - - -A URI, CURIE or BNODE that represents a node in a model. - -URI: [linkml:Nodeidentifier](https://w3id.org/linkml/Nodeidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NodeIdentifier** | -| Representation | | str | diff --git a/projects/ontology_class/docs/types/Objectidentifier.md b/projects/ontology_class/docs/types/Objectidentifier.md deleted file mode 100644 index 454ba6be6..000000000 --- a/projects/ontology_class/docs/types/Objectidentifier.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: objectidentifier - - -A URI or CURIE that represents an object in the model. - -URI: [linkml:Objectidentifier](https://w3id.org/linkml/Objectidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **ElementIdentifier** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | Used for inheritance and type checking | - diff --git a/projects/ontology_class/docs/types/Sparqlpath.md b/projects/ontology_class/docs/types/Sparqlpath.md deleted file mode 100644 index fd99a927e..000000000 --- a/projects/ontology_class/docs/types/Sparqlpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: sparqlpath - - -A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - -URI: [linkml:Sparqlpath](https://w3id.org/linkml/Sparqlpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/ontology_class/docs/types/String.md b/projects/ontology_class/docs/types/String.md deleted file mode 100644 index 6e61d7081..000000000 --- a/projects/ontology_class/docs/types/String.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: string - - -A character string - -URI: [linkml:String](https://w3id.org/linkml/String) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Text | - diff --git a/projects/ontology_class/docs/types/Time.md b/projects/ontology_class/docs/types/Time.md deleted file mode 100644 index 2b8652bcd..000000000 --- a/projects/ontology_class/docs/types/Time.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: time - - -A time object represents a (local) time of day, independent of any particular day - -URI: [linkml:Time](https://w3id.org/linkml/Time) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Time | - diff --git a/projects/ontology_class/docs/types/Uri.md b/projects/ontology_class/docs/types/Uri.md deleted file mode 100644 index 343807a5e..000000000 --- a/projects/ontology_class/docs/types/Uri.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: uri - - -a complete URI - -URI: [linkml:Uri](https://w3id.org/linkml/Uri) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URI** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node | -| **Close Mappings:** | | schema:URL | - diff --git a/projects/ontology_class/docs/types/Uriorcurie.md b/projects/ontology_class/docs/types/Uriorcurie.md deleted file mode 100644 index 2f7b65087..000000000 --- a/projects/ontology_class/docs/types/Uriorcurie.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: uriorcurie - - -a URI or a CURIE - -URI: [linkml:Uriorcurie](https://w3id.org/linkml/Uriorcurie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URIorCURIE** | -| Representation | | str | diff --git a/projects/ontology_class/excel/ontology_class.xlsx b/projects/ontology_class/excel/ontology_class.xlsx deleted file mode 100644 index 134f42bc1..000000000 Binary files a/projects/ontology_class/excel/ontology_class.xlsx and /dev/null differ diff --git a/projects/ontology_class/graphql/ontology_class.graphql b/projects/ontology_class/graphql/ontology_class.graphql deleted file mode 100644 index 657e48175..000000000 --- a/projects/ontology_class/graphql/ontology_class.graphql +++ /dev/null @@ -1,87 +0,0 @@ -type AnnotatorResult - { - subjectText: String - objectId: String - objectText: String - } - -type Any - { - } - -interface CompoundExpression - { - } - -type ExtractionResult - { - inputId: String - inputTitle: String - inputText: String - rawCompletionOutput: String - prompt: String - extractedObject: Any - namedEntities: [Any] - } - -type LogicalDefinition - { - genus: [OntologyClass] - differentiatingCharacteristicRelationship: Relation - differentiatingCharacteristicParents: [OntologyClass] - } - -interface NamedEntity - { - id: String! - label: String - } - -type OntologyClass - { - id: String! - label: String - description: String - synonyms: [String] - categories: [OntologyClass] - subclassOf: [OntologyClass] - logicalDefinition: LogicalDefinition - } - -type Publication - { - id: String - title: String - abstract: String - combinedText: String - fullText: String - } - -type Relation - { - id: String! - label: String - } - -type RelationshipType - { - id: String! - label: String - } - -type TextWithTriples - { - publication: Publication - triples: [Triple] - } - -interface Triple - { - subject: NamedEntity - predicate: RelationshipType - object: NamedEntity - qualifier: String - subjectQualifier: NamedEntity - objectQualifier: NamedEntity - } - diff --git a/projects/ontology_class/jsonld/ontology_class.context.jsonld b/projects/ontology_class/jsonld/ontology_class.context.jsonld deleted file mode 100644 index 1508d1715..000000000 --- a/projects/ontology_class/jsonld/ontology_class.context.jsonld +++ /dev/null @@ -1,148 +0,0 @@ -{ - "comments": { - "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2023-08-07T10:55:16", - "source": "ontology_class.yaml" - }, - "@context": { - "RO": { - "@id": "http://purl.obolibrary.org/obo/RO_", - "@prefix": true - }, - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "linkml": "https://w3id.org/linkml/", - "oc": { - "@id": "http://w3id.org/ontogpt/ontology-class-template", - "@prefix": true - }, - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "@vocab": "http://w3id.org/ontogpt/ontology-class-template", - "object_id": { - "@id": "core:object_id" - }, - "object_text": { - "@id": "core:object_text" - }, - "subject_text": { - "@id": "core:subject_text" - }, - "extracted_object": { - "@type": "@id", - "@id": "core:extracted_object" - }, - "input_id": { - "@id": "core:input_id" - }, - "input_text": { - "@id": "core:input_text" - }, - "input_title": { - "@id": "core:input_title" - }, - "named_entities": { - "@type": "@id", - "@id": "core:named_entities" - }, - "prompt": { - "@id": "core:prompt" - }, - "raw_completion_output": { - "@id": "core:raw_completion_output" - }, - "differentiating_characteristic_parents": { - "@type": "@id" - }, - "differentiating_characteristic_relationship": { - "@type": "@id" - }, - "genus": { - "@type": "@id" - }, - "id": { - "@id": "core:id" - }, - "label": { - "@id": "rdfs:label" - }, - "categories": { - "@type": "@id" - }, - "logical_definition": { - "@type": "@id" - }, - "subclass_of": { - "@type": "@id" - }, - "abstract": { - "@id": "core:abstract" - }, - "combined_text": { - "@id": "core:combined_text" - }, - "full_text": { - "@id": "core:full_text" - }, - "title": { - "@id": "core:title" - }, - "publication": { - "@type": "@id", - "@id": "core:publication" - }, - "triples": { - "@type": "@id", - "@id": "core:triples" - }, - "object": { - "@type": "@id", - "@id": "core:object" - }, - "object_qualifier": { - "@type": "@id", - "@id": "core:object_qualifier" - }, - "predicate": { - "@type": "@id", - "@id": "core:predicate" - }, - "qualifier": { - "@id": "core:qualifier" - }, - "subject": { - "@type": "@id", - "@id": "core:subject" - }, - "subject_qualifier": { - "@type": "@id", - "@id": "core:subject_qualifier" - }, - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } - } -} diff --git a/projects/ontology_class/jsonld/ontology_class.jsonld b/projects/ontology_class/jsonld/ontology_class.jsonld deleted file mode 100644 index 09ed16126..000000000 --- a/projects/ontology_class/jsonld/ontology_class.jsonld +++ /dev/null @@ -1,1285 +0,0 @@ -{ - "name": "ontology-class", - "description": "A template for Ontology Classes", - "title": "Ontology Class Template", - "id": "https://w3id.org/ontogpt/ontology_class", - "imports": [ - "linkml:types", - "core" - ], - "license": "https://creativecommons.org/publicdomain/zero/1.0/", - "prefixes": [ - { - "prefix_prefix": "linkml", - "prefix_reference": "https://w3id.org/linkml/" - }, - { - "prefix_prefix": "oc", - "prefix_reference": "http://w3id.org/ontogpt/ontology-class-template" - } - ], - "default_prefix": "oc", - "default_range": "string", - "types": [ - { - "name": "string", - "definition_uri": "https://w3id.org/linkml/String", - "description": "A character string", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Text" - ], - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "@type": "TypeDefinition" - }, - { - "name": "integer", - "definition_uri": "https://w3id.org/linkml/Integer", - "description": "An integer", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Integer" - ], - "base": "int", - "uri": "http://www.w3.org/2001/XMLSchema#integer", - "@type": "TypeDefinition" - }, - { - "name": "boolean", - "definition_uri": "https://w3id.org/linkml/Boolean", - "description": "A binary (true or false) value", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Boolean" - ], - "base": "Bool", - "uri": "http://www.w3.org/2001/XMLSchema#boolean", - "repr": "bool", - "@type": "TypeDefinition" - }, - { - "name": "float", - "definition_uri": "https://w3id.org/linkml/Float", - "description": "A real number that conforms to the xsd:float specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#float", - "@type": "TypeDefinition" - }, - { - "name": "double", - "definition_uri": "https://w3id.org/linkml/Double", - "description": "A real number that conforms to the xsd:double specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#double", - "@type": "TypeDefinition" - }, - { - "name": "decimal", - "definition_uri": "https://w3id.org/linkml/Decimal", - "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "broad_mappings": [ - "schema:Number" - ], - "base": "Decimal", - "uri": "http://www.w3.org/2001/XMLSchema#decimal", - "@type": "TypeDefinition" - }, - { - "name": "time", - "definition_uri": "https://w3id.org/linkml/Time", - "description": "A time object represents a (local) time of day, independent of any particular day", - "notes": [ - "URI is dateTime because OWL reasoners do not work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Time" - ], - "base": "XSDTime", - "uri": "http://www.w3.org/2001/XMLSchema#time", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date", - "definition_uri": "https://w3id.org/linkml/Date", - "description": "a date (year, month and day) in an idealized calendar", - "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Date" - ], - "base": "XSDDate", - "uri": "http://www.w3.org/2001/XMLSchema#date", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "datetime", - "definition_uri": "https://w3id.org/linkml/Datetime", - "description": "The combination of a date and time", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:DateTime" - ], - "base": "XSDDateTime", - "uri": "http://www.w3.org/2001/XMLSchema#dateTime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date_or_datetime", - "definition_uri": "https://w3id.org/linkml/DateOrDatetime", - "description": "Either a date or a datetime", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "https://w3id.org/linkml/DateOrDatetime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uriorcurie", - "definition_uri": "https://w3id.org/linkml/Uriorcurie", - "description": "a URI or a CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "URIorCURIE", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "curie", - "definition_uri": "https://w3id.org/linkml/Curie", - "conforms_to": "https://www.w3.org/TR/curie/", - "description": "a compact URI", - "comments": [ - "in RDF serializations this MUST be expanded to a URI", - "in non-RDF serializations MAY be serialized as the compact representation" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "Curie", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uri", - "definition_uri": "https://w3id.org/linkml/Uri", - "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", - "description": "a complete URI", - "comments": [ - "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:URL" - ], - "base": "URI", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "ncname", - "definition_uri": "https://w3id.org/linkml/Ncname", - "description": "Prefix part of CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NCName", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "objectidentifier", - "definition_uri": "https://w3id.org/linkml/Objectidentifier", - "description": "A URI or CURIE that represents an object in the model.", - "comments": [ - "Used for inheritance and type checking" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "ElementIdentifier", - "uri": "http://www.w3.org/ns/shex#iri", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "nodeidentifier", - "definition_uri": "https://w3id.org/linkml/Nodeidentifier", - "description": "A URI, CURIE or BNODE that represents a node in a model.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NodeIdentifier", - "uri": "http://www.w3.org/ns/shex#nonLiteral", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpointer", - "definition_uri": "https://w3id.org/linkml/Jsonpointer", - "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901", - "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpath", - "definition_uri": "https://w3id.org/linkml/Jsonpath", - "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html", - "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "sparqlpath", - "definition_uri": "https://w3id.org/linkml/Sparqlpath", - "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths", - "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - } - ], - "enums": [ - { - "name": "NullDataOptions", - "definition_uri": "http://w3id.org/ontogpt/core/NullDataOptions", - "from_schema": "http://w3id.org/ontogpt/core", - "permissible_values": [ - { - "text": "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "meaning": "NCIT:C149701" - }, - { - "text": "NOT_APPLICABLE", - "meaning": "NCIT:C18902", - "aliases": [ - "not applicable", - "N/A" - ] - }, - { - "text": "NOT_MENTIONED" - } - ] - } - ], - "slots": [ - { - "name": "ontologyClass__label", - "description": "the name of the main entity being defined", - "from_schema": "https://w3id.org/ontogpt/ontology_class", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templatelabel", - "alias": "label", - "owner": "OntologyClass", - "domain_of": [ - "OntologyClass" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "ontologyClass__description", - "description": "a textual description of the entity", - "from_schema": "https://w3id.org/ontogpt/ontology_class", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templatedescription", - "alias": "description", - "owner": "OntologyClass", - "domain_of": [ - "OntologyClass" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "ontologyClass__synonyms", - "description": "alternative names of the entity", - "from_schema": "https://w3id.org/ontogpt/ontology_class", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templatesynonyms", - "multivalued": true, - "alias": "synonyms", - "owner": "OntologyClass", - "domain_of": [ - "OntologyClass" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "ontologyClass__categories", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of categories to which the entity belongs. These may be taken from an upper level ontology such as COB, BioLink, or UMLS semantic types.", - "@type": "Annotation" - } - ], - "description": "the categories to which this entity belongs.", - "from_schema": "https://w3id.org/ontogpt/ontology_class", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templatecategories", - "multivalued": true, - "alias": "categories", - "owner": "OntologyClass", - "domain_of": [ - "OntologyClass" - ], - "range": "OntologyClass", - "@type": "SlotDefinition" - }, - { - "name": "ontologyClass__subclass_of", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of parent classes, indicating broader concepts. E.g. if the input text is \"a type of bone\", then the parent class is \"bone\"", - "@type": "Annotation" - } - ], - "from_schema": "https://w3id.org/ontogpt/ontology_class", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templatesubclass_of", - "multivalued": true, - "alias": "subclass_of", - "owner": "OntologyClass", - "domain_of": [ - "OntologyClass" - ], - "range": "OntologyClass", - "@type": "SlotDefinition" - }, - { - "name": "ontologyClass__logical_definition", - "annotations": [ - { - "tag": "prompt", - "value": "the necessary and sufficient conditions for this entity to be an instance of this class, written in OWL manchester syntax, e.g. bone and (part_of some 'hand')", - "@type": "Annotation" - } - ], - "description": "the necessary and sufficient conditions for this entity to be an instance of this class", - "from_schema": "https://w3id.org/ontogpt/ontology_class", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templatelogical_definition", - "alias": "logical_definition", - "owner": "OntologyClass", - "domain_of": [ - "OntologyClass" - ], - "range": "LogicalDefinition", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "logicalDefinition__genus", - "annotations": [ - { - "tag": "prompt", - "value": "in a logical definition expression, this is the parent (genus) class, e.g. bone", - "@type": "Annotation" - } - ], - "from_schema": "https://w3id.org/ontogpt/ontology_class", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templategenus", - "multivalued": true, - "alias": "genus", - "owner": "LogicalDefinition", - "domain_of": [ - "LogicalDefinition" - ], - "range": "OntologyClass", - "@type": "SlotDefinition" - }, - { - "name": "logicalDefinition__differentiating_characteristic_relationship", - "annotations": [ - { - "tag": "prompt", - "value": "in a logical definition expression, this is the parent (differentiating characteristic) relationship type, e.g. part of", - "@type": "Annotation" - } - ], - "from_schema": "https://w3id.org/ontogpt/ontology_class", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templatedifferentiating_characteristic_relationship", - "alias": "differentiating_characteristic_relationship", - "owner": "LogicalDefinition", - "domain_of": [ - "LogicalDefinition" - ], - "range": "Relation", - "@type": "SlotDefinition" - }, - { - "name": "logicalDefinition__differentiating_characteristic_parents", - "annotations": [ - { - "tag": "prompt", - "value": "in a logical definition expression, this the parent (differentiating characteristic) class, e.g. hand", - "@type": "Annotation" - } - ], - "from_schema": "https://w3id.org/ontogpt/ontology_class", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templatedifferentiating_characteristic_parents", - "multivalued": true, - "alias": "differentiating_characteristic_parents", - "owner": "LogicalDefinition", - "domain_of": [ - "LogicalDefinition" - ], - "range": "OntologyClass", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_id", - "alias": "input_id", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_title", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_title", - "alias": "input_title", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_text", - "alias": "input_text", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__raw_completion_output", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/raw_completion_output", - "alias": "raw_completion_output", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__prompt", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/prompt", - "alias": "prompt", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__extracted_object", - "description": "The complex objects extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/extracted_object", - "alias": "extracted_object", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__named_entities", - "description": "Named entities extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/named_entities", - "multivalued": true, - "alias": "named_entities", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "identifier": true, - "alias": "id", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "required": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "from_schema": "http://w3id.org/ontogpt/core", - "aliases": [ - "name" - ], - "mappings": [ - "http://example.org/UNKNOWN/rdfs/label" - ], - "slot_uri": "http://example.org/UNKNOWN/rdfs/label", - "alias": "label", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject", - "alias": "subject", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__predicate", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/predicate", - "alias": "predicate", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "triple__object", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object", - "alias": "object", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/qualifier", - "alias": "qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_qualifier", - "alias": "subject_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_qualifier", - "alias": "object_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/publication", - "alias": "publication", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__triples", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/triples", - "multivalued": true, - "alias": "triples", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "publication__id", - "description": "The publication identifier", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "alias": "id", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__title", - "description": "The title of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/title", - "alias": "title", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__abstract", - "description": "The abstract of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/abstract", - "alias": "abstract", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__combined_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/combined_text", - "alias": "combined_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__full_text", - "description": "The full text of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/full_text", - "alias": "full_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__subject_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_text", - "alias": "subject_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_id", - "alias": "object_id", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_text", - "alias": "object_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - } - ], - "classes": [ - { - "name": "OntologyClass", - "definition_uri": "http://w3id.org/ontogpt/ontology-class-templateOntologyClass", - "from_schema": "https://w3id.org/ontogpt/ontology_class", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "ontologyClass__label", - "ontologyClass__description", - "ontologyClass__synonyms", - "ontologyClass__categories", - "ontologyClass__subclass_of", - "ontologyClass__logical_definition" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "label", - "description": "the name of the main entity being defined", - "@type": "SlotDefinition" - }, - { - "name": "description", - "description": "a textual description of the entity", - "@type": "SlotDefinition" - }, - { - "name": "synonyms", - "description": "alternative names of the entity", - "multivalued": true, - "@type": "SlotDefinition" - }, - { - "name": "categories", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of categories to which the entity belongs. These may be taken from an upper level ontology such as COB, BioLink, or UMLS semantic types.", - "@type": "Annotation" - } - ], - "description": "the categories to which this entity belongs.", - "multivalued": true, - "range": "OntologyClass", - "@type": "SlotDefinition" - }, - { - "name": "subclass_of", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of parent classes, indicating broader concepts. E.g. if the input text is \"a type of bone\", then the parent class is \"bone\"", - "@type": "Annotation" - } - ], - "multivalued": true, - "range": "OntologyClass", - "@type": "SlotDefinition" - }, - { - "name": "logical_definition", - "annotations": [ - { - "tag": "prompt", - "value": "the necessary and sufficient conditions for this entity to be an instance of this class, written in OWL manchester syntax, e.g. bone and (part_of some 'hand')", - "@type": "Annotation" - } - ], - "description": "the necessary and sufficient conditions for this entity to be an instance of this class", - "range": "LogicalDefinition", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/ontology-class-templateOntologyClass", - "tree_root": true, - "@type": "ClassDefinition" - }, - { - "name": "LogicalDefinition", - "definition_uri": "http://w3id.org/ontogpt/ontology-class-templateLogicalDefinition", - "from_schema": "https://w3id.org/ontogpt/ontology_class", - "slots": [ - "logicalDefinition__genus", - "logicalDefinition__differentiating_characteristic_relationship", - "logicalDefinition__differentiating_characteristic_parents" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "genus", - "annotations": [ - { - "tag": "prompt", - "value": "in a logical definition expression, this is the parent (genus) class, e.g. bone", - "@type": "Annotation" - } - ], - "multivalued": true, - "range": "OntologyClass", - "@type": "SlotDefinition" - }, - { - "name": "differentiating_characteristic_relationship", - "annotations": [ - { - "tag": "prompt", - "value": "in a logical definition expression, this is the parent (differentiating characteristic) relationship type, e.g. part of", - "@type": "Annotation" - } - ], - "range": "Relation", - "@type": "SlotDefinition" - }, - { - "name": "differentiating_characteristic_parents", - "annotations": [ - { - "tag": "prompt", - "value": "in a logical definition expression, this the parent (differentiating characteristic) class, e.g. hand", - "@type": "Annotation" - } - ], - "multivalued": true, - "range": "OntologyClass", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/ontology-class-templateLogicalDefinition", - "@type": "ClassDefinition" - }, - { - "name": "Relation", - "id_prefixes": [ - "RO" - ], - "definition_uri": "http://w3id.org/ontogpt/ontology-class-templateRelation", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:ro", - "@type": "Annotation" - } - ], - "from_schema": "https://w3id.org/ontogpt/ontology_class", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/ontology-class-templateRelation", - "@type": "ClassDefinition" - }, - { - "name": "Any", - "definition_uri": "http://w3id.org/ontogpt/core/Any", - "from_schema": "http://w3id.org/ontogpt/core", - "mappings": [ - "linkml:Any" - ], - "slot_usage": {}, - "class_uri": "https://w3id.org/linkml/Any", - "@type": "ClassDefinition" - }, - { - "name": "ExtractionResult", - "definition_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "description": "A result of extracting knowledge on text", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "extractionResult__input_id", - "extractionResult__input_title", - "extractionResult__input_text", - "extractionResult__raw_completion_output", - "extractionResult__prompt", - "extractionResult__extracted_object", - "extractionResult__named_entities" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "input_id", - "@type": "SlotDefinition" - }, - { - "name": "input_title", - "@type": "SlotDefinition" - }, - { - "name": "input_text", - "@type": "SlotDefinition" - }, - { - "name": "raw_completion_output", - "@type": "SlotDefinition" - }, - { - "name": "prompt", - "@type": "SlotDefinition" - }, - { - "name": "extracted_object", - "description": "The complex objects extracted from the text", - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "named_entities", - "description": "Named entities extracted from the text", - "multivalued": true, - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "@type": "ClassDefinition" - }, - { - "name": "NamedEntity", - "definition_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "identifier": true, - "@type": "SlotDefinition" - }, - { - "name": "label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "aliases": [ - "name" - ], - "slot_uri": "rdfs:label", - "range": "string", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "@type": "ClassDefinition" - }, - { - "name": "CompoundExpression", - "definition_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "@type": "ClassDefinition" - }, - { - "name": "Triple", - "definition_uri": "http://w3id.org/ontogpt/core/Triple", - "description": "Abstract parent for Relation Extraction tasks", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "CompoundExpression", - "abstract": true, - "slots": [ - "triple__subject", - "triple__predicate", - "triple__object", - "triple__qualifier", - "triple__subject_qualifier", - "triple__object_qualifier" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "predicate", - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "object", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Triple", - "@type": "ClassDefinition" - }, - { - "name": "TextWithTriples", - "definition_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "textWithTriples__publication", - "textWithTriples__triples" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "triples", - "multivalued": true, - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "@type": "ClassDefinition" - }, - { - "name": "RelationshipType", - "id_prefixes": [ - "RO", - "biolink" - ], - "definition_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "@type": "ClassDefinition" - }, - { - "name": "Publication", - "definition_uri": "http://w3id.org/ontogpt/core/Publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "publication__id", - "publication__title", - "publication__abstract", - "publication__combined_text", - "publication__full_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "description": "The publication identifier", - "@type": "SlotDefinition" - }, - { - "name": "title", - "description": "The title of the publication", - "@type": "SlotDefinition" - }, - { - "name": "abstract", - "description": "The abstract of the publication", - "@type": "SlotDefinition" - }, - { - "name": "combined_text", - "@type": "SlotDefinition" - }, - { - "name": "full_text", - "description": "The full text of the publication", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Publication", - "@type": "ClassDefinition" - }, - { - "name": "AnnotatorResult", - "definition_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "annotatorResult__subject_text", - "annotatorResult__object_id", - "annotatorResult__object_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject_text", - "@type": "SlotDefinition" - }, - { - "name": "object_id", - "@type": "SlotDefinition" - }, - { - "name": "object_text", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "@type": "ClassDefinition" - } - ], - "metamodel_version": "1.7.0", - "source_file": "ontology_class.yaml", - "source_file_date": "2023-06-17T15:11:19", - "source_file_size": 2686, - "generation_date": "2023-08-07T10:55:17", - "@type": "SchemaDefinition", - "@context": [ - "projects/ontology_class/jsonld/ontology_class.context.jsonld", - "https://w3id.org/linkml/types.context.jsonld", - "core.context.jsonld", - { - "@base": "http://w3id.org/ontogpt/ontology-class-template" - } - ] -} diff --git a/projects/ontology_class/jsonschema/ontology_class.schema.json b/projects/ontology_class/jsonschema/ontology_class.schema.json deleted file mode 100644 index e721fe8c7..000000000 --- a/projects/ontology_class/jsonschema/ontology_class.schema.json +++ /dev/null @@ -1,271 +0,0 @@ -{ - "$defs": { - "AnnotatorResult": { - "additionalProperties": false, - "description": "", - "properties": { - "object_id": { - "type": "string" - }, - "object_text": { - "type": "string" - }, - "subject_text": { - "type": "string" - } - }, - "title": "AnnotatorResult", - "type": "object" - }, - "Any": { - "additionalProperties": true, - "description": "", - "title": "Any", - "type": "object" - }, - "ExtractionResult": { - "additionalProperties": false, - "description": "A result of extracting knowledge on text", - "properties": { - "extracted_object": { - "$ref": "#/$defs/Any", - "description": "The complex objects extracted from the text" - }, - "input_id": { - "type": "string" - }, - "input_text": { - "type": "string" - }, - "input_title": { - "type": "string" - }, - "named_entities": { - "description": "Named entities extracted from the text", - "items": { - "$ref": "#/$defs/Any" - }, - "type": "array" - }, - "prompt": { - "type": "string" - }, - "raw_completion_output": { - "type": "string" - } - }, - "title": "ExtractionResult", - "type": "object" - }, - "LogicalDefinition": { - "additionalProperties": false, - "description": "", - "properties": { - "differentiating_characteristic_parents": { - "items": { - "type": "string" - }, - "type": "array" - }, - "differentiating_characteristic_relationship": { - "type": "string" - }, - "genus": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "title": "LogicalDefinition", - "type": "object" - }, - "NullDataOptions": { - "description": "", - "enum": [ - "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "NOT_APPLICABLE", - "NOT_MENTIONED" - ], - "title": "NullDataOptions", - "type": "string" - }, - "OntologyClass": { - "additionalProperties": false, - "description": "", - "properties": { - "categories": { - "description": "the categories to which this entity belongs.", - "items": { - "type": "string" - }, - "type": "array" - }, - "description": { - "description": "a textual description of the entity", - "type": "string" - }, - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "the name of the main entity being defined", - "type": "string" - }, - "logical_definition": { - "$ref": "#/$defs/LogicalDefinition", - "description": "the necessary and sufficient conditions for this entity to be an instance of this class" - }, - "subclass_of": { - "items": { - "type": "string" - }, - "type": "array" - }, - "synonyms": { - "description": "alternative names of the entity", - "items": { - "type": "string" - }, - "type": "array" - } - }, - "required": [ - "id" - ], - "title": "OntologyClass", - "type": "object" - }, - "Publication": { - "additionalProperties": false, - "description": "", - "properties": { - "abstract": { - "description": "The abstract of the publication", - "type": "string" - }, - "combined_text": { - "type": "string" - }, - "full_text": { - "description": "The full text of the publication", - "type": "string" - }, - "id": { - "description": "The publication identifier", - "type": "string" - }, - "title": { - "description": "The title of the publication", - "type": "string" - } - }, - "title": "Publication", - "type": "object" - }, - "Relation": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Relation", - "type": "object" - }, - "RelationshipType": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "RelationshipType", - "type": "object" - }, - "TextWithTriples": { - "additionalProperties": false, - "description": "", - "properties": { - "publication": { - "$ref": "#/$defs/Publication" - }, - "triples": { - "items": { - "$ref": "#/$defs/Triple" - }, - "type": "array" - } - }, - "title": "TextWithTriples", - "type": "object" - } - }, - "$id": "https://w3id.org/ontogpt/ontology_class", - "$schema": "http://json-schema.org/draft-07/schema#", - "additionalProperties": true, - "metamodel_version": "1.7.0", - "properties": { - "categories": { - "description": "the categories to which this entity belongs.", - "items": { - "type": "string" - }, - "type": "array" - }, - "description": { - "description": "a textual description of the entity", - "type": "string" - }, - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "the name of the main entity being defined", - "type": "string" - }, - "logical_definition": { - "$ref": "#/$defs/LogicalDefinition", - "description": "the necessary and sufficient conditions for this entity to be an instance of this class" - }, - "subclass_of": { - "items": { - "type": "string" - }, - "type": "array" - }, - "synonyms": { - "description": "alternative names of the entity", - "items": { - "type": "string" - }, - "type": "array" - } - }, - "required": [ - "id" - ], - "title": "ontology-class", - "type": "object", - "version": null -} \ No newline at end of file diff --git a/projects/ontology_class/ontology_class.py b/projects/ontology_class/ontology_class.py deleted file mode 100644 index 3129eb9d1..000000000 --- a/projects/ontology_class/ontology_class.py +++ /dev/null @@ -1,492 +0,0 @@ -# Auto generated from ontology_class.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-08-07T10:55:23 -# Schema: ontology-class -# -# id: https://w3id.org/ontogpt/ontology_class -# description: A template for Ontology Classes -# license: https://creativecommons.org/publicdomain/zero/1.0/ - -import dataclasses -import sys -import re -from jsonasobj2 import JsonObj, as_dict -from typing import Optional, List, Union, Dict, ClassVar, Any -from dataclasses import dataclass -from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions - -from linkml_runtime.utils.slot import Slot -from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode -from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int -from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs -from linkml_runtime.utils.formatutils import camelcase, underscore, sfx -from linkml_runtime.utils.enumerations import EnumDefinitionImpl -from rdflib import Namespace, URIRef -from linkml_runtime.utils.curienamespace import CurieNamespace -from linkml_runtime.linkml_model.types import String - -metamodel_version = "1.7.0" -version = None - -# Overwrite dataclasses _init_fn to add **kwargs in __init__ -dataclasses._init_fn = dataclasses_init_fn_with_kwargs - -# Namespaces -RO = CurieNamespace('RO', 'http://purl.obolibrary.org/obo/RO_') -BIOLINK = CurieNamespace('biolink', 'http://example.org/UNKNOWN/biolink/') -CORE = CurieNamespace('core', 'http://w3id.org/ontogpt/core/') -LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') -OC = CurieNamespace('oc', 'http://w3id.org/ontogpt/ontology-class-template') -RDFS = CurieNamespace('rdfs', 'http://example.org/UNKNOWN/rdfs/') -DEFAULT_ = OC - - -# Types - -# Class references -class NamedEntityId(extended_str): - pass - - -class OntologyClassId(NamedEntityId): - pass - - -class RelationId(NamedEntityId): - pass - - -class RelationshipTypeId(NamedEntityId): - pass - - -@dataclass -class LogicalDefinition(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = OC.LogicalDefinition - class_class_curie: ClassVar[str] = "oc:LogicalDefinition" - class_name: ClassVar[str] = "LogicalDefinition" - class_model_uri: ClassVar[URIRef] = OC.LogicalDefinition - - genus: Optional[Union[Union[str, OntologyClassId], List[Union[str, OntologyClassId]]]] = empty_list() - differentiating_characteristic_relationship: Optional[Union[str, RelationId]] = None - differentiating_characteristic_parents: Optional[Union[Union[str, OntologyClassId], List[Union[str, OntologyClassId]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if not isinstance(self.genus, list): - self.genus = [self.genus] if self.genus is not None else [] - self.genus = [v if isinstance(v, OntologyClassId) else OntologyClassId(v) for v in self.genus] - - if self.differentiating_characteristic_relationship is not None and not isinstance(self.differentiating_characteristic_relationship, RelationId): - self.differentiating_characteristic_relationship = RelationId(self.differentiating_characteristic_relationship) - - if not isinstance(self.differentiating_characteristic_parents, list): - self.differentiating_characteristic_parents = [self.differentiating_characteristic_parents] if self.differentiating_characteristic_parents is not None else [] - self.differentiating_characteristic_parents = [v if isinstance(v, OntologyClassId) else OntologyClassId(v) for v in self.differentiating_characteristic_parents] - - super().__post_init__(**kwargs) - - -Any = Any - -@dataclass -class ExtractionResult(YAMLRoot): - """ - A result of extracting knowledge on text - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.ExtractionResult - class_class_curie: ClassVar[str] = "core:ExtractionResult" - class_name: ClassVar[str] = "ExtractionResult" - class_model_uri: ClassVar[URIRef] = OC.ExtractionResult - - input_id: Optional[str] = None - input_title: Optional[str] = None - input_text: Optional[str] = None - raw_completion_output: Optional[str] = None - prompt: Optional[str] = None - extracted_object: Optional[Union[dict, Any]] = None - named_entities: Optional[Union[Union[dict, Any], List[Union[dict, Any]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.input_id is not None and not isinstance(self.input_id, str): - self.input_id = str(self.input_id) - - if self.input_title is not None and not isinstance(self.input_title, str): - self.input_title = str(self.input_title) - - if self.input_text is not None and not isinstance(self.input_text, str): - self.input_text = str(self.input_text) - - if self.raw_completion_output is not None and not isinstance(self.raw_completion_output, str): - self.raw_completion_output = str(self.raw_completion_output) - - if self.prompt is not None and not isinstance(self.prompt, str): - self.prompt = str(self.prompt) - - super().__post_init__(**kwargs) - - -@dataclass -class NamedEntity(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.NamedEntity - class_class_curie: ClassVar[str] = "core:NamedEntity" - class_name: ClassVar[str] = "NamedEntity" - class_model_uri: ClassVar[URIRef] = OC.NamedEntity - - id: Union[str, NamedEntityId] = None - label: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, NamedEntityId): - self.id = NamedEntityId(self.id) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - super().__post_init__(**kwargs) - - -@dataclass -class OntologyClass(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = OC.OntologyClass - class_class_curie: ClassVar[str] = "oc:OntologyClass" - class_name: ClassVar[str] = "OntologyClass" - class_model_uri: ClassVar[URIRef] = OC.OntologyClass - - id: Union[str, OntologyClassId] = None - label: Optional[str] = None - description: Optional[str] = None - synonyms: Optional[Union[str, List[str]]] = empty_list() - categories: Optional[Union[Union[str, OntologyClassId], List[Union[str, OntologyClassId]]]] = empty_list() - subclass_of: Optional[Union[Union[str, OntologyClassId], List[Union[str, OntologyClassId]]]] = empty_list() - logical_definition: Optional[Union[dict, "LogicalDefinition"]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, OntologyClassId): - self.id = OntologyClassId(self.id) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - if self.description is not None and not isinstance(self.description, str): - self.description = str(self.description) - - if not isinstance(self.synonyms, list): - self.synonyms = [self.synonyms] if self.synonyms is not None else [] - self.synonyms = [v if isinstance(v, str) else str(v) for v in self.synonyms] - - if not isinstance(self.categories, list): - self.categories = [self.categories] if self.categories is not None else [] - self.categories = [v if isinstance(v, OntologyClassId) else OntologyClassId(v) for v in self.categories] - - if not isinstance(self.subclass_of, list): - self.subclass_of = [self.subclass_of] if self.subclass_of is not None else [] - self.subclass_of = [v if isinstance(v, OntologyClassId) else OntologyClassId(v) for v in self.subclass_of] - - if self.logical_definition is not None and not isinstance(self.logical_definition, LogicalDefinition): - self.logical_definition = LogicalDefinition(**as_dict(self.logical_definition)) - - super().__post_init__(**kwargs) - - -@dataclass -class Relation(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = OC.Relation - class_class_curie: ClassVar[str] = "oc:Relation" - class_name: ClassVar[str] = "Relation" - class_model_uri: ClassVar[URIRef] = OC.Relation - - id: Union[str, RelationId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, RelationId): - self.id = RelationId(self.id) - - super().__post_init__(**kwargs) - - -class CompoundExpression(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.CompoundExpression - class_class_curie: ClassVar[str] = "core:CompoundExpression" - class_name: ClassVar[str] = "CompoundExpression" - class_model_uri: ClassVar[URIRef] = OC.CompoundExpression - - -@dataclass -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Triple - class_class_curie: ClassVar[str] = "core:Triple" - class_name: ClassVar[str] = "Triple" - class_model_uri: ClassVar[URIRef] = OC.Triple - - subject: Optional[Union[str, NamedEntityId]] = None - predicate: Optional[Union[str, RelationshipTypeId]] = None - object: Optional[Union[str, NamedEntityId]] = None - qualifier: Optional[str] = None - subject_qualifier: Optional[Union[str, NamedEntityId]] = None - object_qualifier: Optional[Union[str, NamedEntityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, NamedEntityId): - self.subject = NamedEntityId(self.subject) - - if self.predicate is not None and not isinstance(self.predicate, RelationshipTypeId): - self.predicate = RelationshipTypeId(self.predicate) - - if self.object is not None and not isinstance(self.object, NamedEntityId): - self.object = NamedEntityId(self.object) - - if self.qualifier is not None and not isinstance(self.qualifier, str): - self.qualifier = str(self.qualifier) - - if self.subject_qualifier is not None and not isinstance(self.subject_qualifier, NamedEntityId): - self.subject_qualifier = NamedEntityId(self.subject_qualifier) - - if self.object_qualifier is not None and not isinstance(self.object_qualifier, NamedEntityId): - self.object_qualifier = NamedEntityId(self.object_qualifier) - - super().__post_init__(**kwargs) - - -@dataclass -class TextWithTriples(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.TextWithTriples - class_class_curie: ClassVar[str] = "core:TextWithTriples" - class_name: ClassVar[str] = "TextWithTriples" - class_model_uri: ClassVar[URIRef] = OC.TextWithTriples - - publication: Optional[Union[dict, "Publication"]] = None - triples: Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.publication is not None and not isinstance(self.publication, Publication): - self.publication = Publication(**as_dict(self.publication)) - - if not isinstance(self.triples, list): - self.triples = [self.triples] if self.triples is not None else [] - self.triples = [v if isinstance(v, Triple) else Triple(**as_dict(v)) for v in self.triples] - - super().__post_init__(**kwargs) - - -@dataclass -class RelationshipType(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.RelationshipType - class_class_curie: ClassVar[str] = "core:RelationshipType" - class_name: ClassVar[str] = "RelationshipType" - class_model_uri: ClassVar[URIRef] = OC.RelationshipType - - id: Union[str, RelationshipTypeId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, RelationshipTypeId): - self.id = RelationshipTypeId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Publication(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Publication - class_class_curie: ClassVar[str] = "core:Publication" - class_name: ClassVar[str] = "Publication" - class_model_uri: ClassVar[URIRef] = OC.Publication - - id: Optional[str] = None - title: Optional[str] = None - abstract: Optional[str] = None - combined_text: Optional[str] = None - full_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.id is not None and not isinstance(self.id, str): - self.id = str(self.id) - - if self.title is not None and not isinstance(self.title, str): - self.title = str(self.title) - - if self.abstract is not None and not isinstance(self.abstract, str): - self.abstract = str(self.abstract) - - if self.combined_text is not None and not isinstance(self.combined_text, str): - self.combined_text = str(self.combined_text) - - if self.full_text is not None and not isinstance(self.full_text, str): - self.full_text = str(self.full_text) - - super().__post_init__(**kwargs) - - -@dataclass -class AnnotatorResult(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.AnnotatorResult - class_class_curie: ClassVar[str] = "core:AnnotatorResult" - class_name: ClassVar[str] = "AnnotatorResult" - class_model_uri: ClassVar[URIRef] = OC.AnnotatorResult - - subject_text: Optional[str] = None - object_id: Optional[str] = None - object_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject_text is not None and not isinstance(self.subject_text, str): - self.subject_text = str(self.subject_text) - - if self.object_id is not None and not isinstance(self.object_id, str): - self.object_id = str(self.object_id) - - if self.object_text is not None and not isinstance(self.object_text, str): - self.object_text = str(self.object_text) - - super().__post_init__(**kwargs) - - -# Enumerations -class NullDataOptions(EnumDefinitionImpl): - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = PermissibleValue(text="UNSPECIFIED_METHOD_OF_ADMINISTRATION", - meaning=NCIT.C149701) - NOT_APPLICABLE = PermissibleValue(text="NOT_APPLICABLE", - meaning=NCIT.C18902) - NOT_MENTIONED = PermissibleValue(text="NOT_MENTIONED") - - _defn = EnumDefinition( - name="NullDataOptions", - ) - -# Slots -class slots: - pass - -slots.ontologyClass__label = Slot(uri=OC.label, name="ontologyClass__label", curie=OC.curie('label'), - model_uri=OC.ontologyClass__label, domain=None, range=Optional[str]) - -slots.ontologyClass__description = Slot(uri=OC.description, name="ontologyClass__description", curie=OC.curie('description'), - model_uri=OC.ontologyClass__description, domain=None, range=Optional[str]) - -slots.ontologyClass__synonyms = Slot(uri=OC.synonyms, name="ontologyClass__synonyms", curie=OC.curie('synonyms'), - model_uri=OC.ontologyClass__synonyms, domain=None, range=Optional[Union[str, List[str]]]) - -slots.ontologyClass__categories = Slot(uri=OC.categories, name="ontologyClass__categories", curie=OC.curie('categories'), - model_uri=OC.ontologyClass__categories, domain=None, range=Optional[Union[Union[str, OntologyClassId], List[Union[str, OntologyClassId]]]]) - -slots.ontologyClass__subclass_of = Slot(uri=OC.subclass_of, name="ontologyClass__subclass_of", curie=OC.curie('subclass_of'), - model_uri=OC.ontologyClass__subclass_of, domain=None, range=Optional[Union[Union[str, OntologyClassId], List[Union[str, OntologyClassId]]]]) - -slots.ontologyClass__logical_definition = Slot(uri=OC.logical_definition, name="ontologyClass__logical_definition", curie=OC.curie('logical_definition'), - model_uri=OC.ontologyClass__logical_definition, domain=None, range=Optional[Union[dict, LogicalDefinition]]) - -slots.logicalDefinition__genus = Slot(uri=OC.genus, name="logicalDefinition__genus", curie=OC.curie('genus'), - model_uri=OC.logicalDefinition__genus, domain=None, range=Optional[Union[Union[str, OntologyClassId], List[Union[str, OntologyClassId]]]]) - -slots.logicalDefinition__differentiating_characteristic_relationship = Slot(uri=OC.differentiating_characteristic_relationship, name="logicalDefinition__differentiating_characteristic_relationship", curie=OC.curie('differentiating_characteristic_relationship'), - model_uri=OC.logicalDefinition__differentiating_characteristic_relationship, domain=None, range=Optional[Union[str, RelationId]]) - -slots.logicalDefinition__differentiating_characteristic_parents = Slot(uri=OC.differentiating_characteristic_parents, name="logicalDefinition__differentiating_characteristic_parents", curie=OC.curie('differentiating_characteristic_parents'), - model_uri=OC.logicalDefinition__differentiating_characteristic_parents, domain=None, range=Optional[Union[Union[str, OntologyClassId], List[Union[str, OntologyClassId]]]]) - -slots.extractionResult__input_id = Slot(uri=CORE.input_id, name="extractionResult__input_id", curie=CORE.curie('input_id'), - model_uri=OC.extractionResult__input_id, domain=None, range=Optional[str]) - -slots.extractionResult__input_title = Slot(uri=CORE.input_title, name="extractionResult__input_title", curie=CORE.curie('input_title'), - model_uri=OC.extractionResult__input_title, domain=None, range=Optional[str]) - -slots.extractionResult__input_text = Slot(uri=CORE.input_text, name="extractionResult__input_text", curie=CORE.curie('input_text'), - model_uri=OC.extractionResult__input_text, domain=None, range=Optional[str]) - -slots.extractionResult__raw_completion_output = Slot(uri=CORE.raw_completion_output, name="extractionResult__raw_completion_output", curie=CORE.curie('raw_completion_output'), - model_uri=OC.extractionResult__raw_completion_output, domain=None, range=Optional[str]) - -slots.extractionResult__prompt = Slot(uri=CORE.prompt, name="extractionResult__prompt", curie=CORE.curie('prompt'), - model_uri=OC.extractionResult__prompt, domain=None, range=Optional[str]) - -slots.extractionResult__extracted_object = Slot(uri=CORE.extracted_object, name="extractionResult__extracted_object", curie=CORE.curie('extracted_object'), - model_uri=OC.extractionResult__extracted_object, domain=None, range=Optional[Union[dict, Any]]) - -slots.extractionResult__named_entities = Slot(uri=CORE.named_entities, name="extractionResult__named_entities", curie=CORE.curie('named_entities'), - model_uri=OC.extractionResult__named_entities, domain=None, range=Optional[Union[Union[dict, Any], List[Union[dict, Any]]]]) - -slots.namedEntity__id = Slot(uri=CORE.id, name="namedEntity__id", curie=CORE.curie('id'), - model_uri=OC.namedEntity__id, domain=None, range=URIRef) - -slots.namedEntity__label = Slot(uri=RDFS.label, name="namedEntity__label", curie=RDFS.curie('label'), - model_uri=OC.namedEntity__label, domain=None, range=Optional[str]) - -slots.triple__subject = Slot(uri=CORE.subject, name="triple__subject", curie=CORE.curie('subject'), - model_uri=OC.triple__subject, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__predicate = Slot(uri=CORE.predicate, name="triple__predicate", curie=CORE.curie('predicate'), - model_uri=OC.triple__predicate, domain=None, range=Optional[Union[str, RelationshipTypeId]]) - -slots.triple__object = Slot(uri=CORE.object, name="triple__object", curie=CORE.curie('object'), - model_uri=OC.triple__object, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__qualifier = Slot(uri=CORE.qualifier, name="triple__qualifier", curie=CORE.curie('qualifier'), - model_uri=OC.triple__qualifier, domain=None, range=Optional[str]) - -slots.triple__subject_qualifier = Slot(uri=CORE.subject_qualifier, name="triple__subject_qualifier", curie=CORE.curie('subject_qualifier'), - model_uri=OC.triple__subject_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__object_qualifier = Slot(uri=CORE.object_qualifier, name="triple__object_qualifier", curie=CORE.curie('object_qualifier'), - model_uri=OC.triple__object_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.textWithTriples__publication = Slot(uri=CORE.publication, name="textWithTriples__publication", curie=CORE.curie('publication'), - model_uri=OC.textWithTriples__publication, domain=None, range=Optional[Union[dict, Publication]]) - -slots.textWithTriples__triples = Slot(uri=CORE.triples, name="textWithTriples__triples", curie=CORE.curie('triples'), - model_uri=OC.textWithTriples__triples, domain=None, range=Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]]) - -slots.publication__id = Slot(uri=CORE.id, name="publication__id", curie=CORE.curie('id'), - model_uri=OC.publication__id, domain=None, range=Optional[str]) - -slots.publication__title = Slot(uri=CORE.title, name="publication__title", curie=CORE.curie('title'), - model_uri=OC.publication__title, domain=None, range=Optional[str]) - -slots.publication__abstract = Slot(uri=CORE.abstract, name="publication__abstract", curie=CORE.curie('abstract'), - model_uri=OC.publication__abstract, domain=None, range=Optional[str]) - -slots.publication__combined_text = Slot(uri=CORE.combined_text, name="publication__combined_text", curie=CORE.curie('combined_text'), - model_uri=OC.publication__combined_text, domain=None, range=Optional[str]) - -slots.publication__full_text = Slot(uri=CORE.full_text, name="publication__full_text", curie=CORE.curie('full_text'), - model_uri=OC.publication__full_text, domain=None, range=Optional[str]) - -slots.annotatorResult__subject_text = Slot(uri=CORE.subject_text, name="annotatorResult__subject_text", curie=CORE.curie('subject_text'), - model_uri=OC.annotatorResult__subject_text, domain=None, range=Optional[str]) - -slots.annotatorResult__object_id = Slot(uri=CORE.object_id, name="annotatorResult__object_id", curie=CORE.curie('object_id'), - model_uri=OC.annotatorResult__object_id, domain=None, range=Optional[str]) - -slots.annotatorResult__object_text = Slot(uri=CORE.object_text, name="annotatorResult__object_text", curie=CORE.curie('object_text'), - model_uri=OC.annotatorResult__object_text, domain=None, range=Optional[str]) \ No newline at end of file diff --git a/projects/ontology_class/owl/ontology_class.owl.ttl b/projects/ontology_class/owl/ontology_class.owl.ttl deleted file mode 100644 index 00ee6e1e2..000000000 --- a/projects/ontology_class/owl/ontology_class.owl.ttl +++ /dev/null @@ -1,461 +0,0 @@ -@prefix IAO: <http://purl.obolibrary.org/obo/IAO_> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix oc: <http://w3id.org/ontogpt/ontology-class-template> . -@prefix owl: <http://www.w3.org/2002/07/owl#> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . -@prefix skos: <http://www.w3.org/2004/02/skos/core#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -linkml:SubsetDefinition a owl:Class ; - rdfs:label "subset_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" . - -linkml:TypeDefinition a owl:Class ; - rdfs:label "type_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" ; - linkml:mixins "type_expression" . - -linkml:topValue a owl:DatatypeProperty ; - rdfs:label "value" . - -<https://w3id.org/ontogpt/ontology_class> a owl:Ontology ; - rdfs:label "ontology-class" ; - IAO:0000700 <http://w3id.org/ontogpt/core/AnnotatorResult>, - <http://w3id.org/ontogpt/core/Any>, - <http://w3id.org/ontogpt/core/CompoundExpression>, - <http://w3id.org/ontogpt/core/ExtractionResult>, - <http://w3id.org/ontogpt/core/NamedEntity>, - <http://w3id.org/ontogpt/core/Publication>, - <http://w3id.org/ontogpt/core/TextWithTriples>, - oc:LogicalDefinition ; - linkml:classes "{'OntologyClass': ClassDefinition(name='OntologyClass', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/ontology-class-templateOntologyClass', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/ontology_class', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'ontologyClass__label', 'ontologyClass__description', 'ontologyClass__synonyms', 'ontologyClass__categories', 'ontologyClass__subclass_of', 'ontologyClass__logical_definition'], slot_usage={}, attributes={'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the name of the main entity being defined', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'description': SlotDefinition(name='description', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a textual description of the entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'synonyms': SlotDefinition(name='synonyms', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='alternative names of the entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'categories': SlotDefinition(name='categories', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of categories to which the entity belongs. These may be taken from an upper level ontology such as COB, BioLink, or UMLS semantic types.', extensions={}, annotations={})}, description='the categories to which this entity belongs.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='OntologyClass', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subclass_of': SlotDefinition(name='subclass_of', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of parent classes, indicating broader concepts. E.g. if the input text is \"a type of bone\", then the parent class is \"bone\"', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='OntologyClass', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'logical_definition': SlotDefinition(name='logical_definition', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value=\"the necessary and sufficient conditions for this entity to be an instance of this class, written in OWL manchester syntax, e.g. bone and (part_of some 'hand')\", extensions={}, annotations={})}, description='the necessary and sufficient conditions for this entity to be an instance of this class', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='LogicalDefinition', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='oc:OntologyClass', subclass_of=None, union_of=[], defining_slots=[], tree_root=True, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'LogicalDefinition': ClassDefinition(name='LogicalDefinition', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/ontology-class-templateLogicalDefinition', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/ontology_class', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['logicalDefinition__genus', 'logicalDefinition__differentiating_characteristic_relationship', 'logicalDefinition__differentiating_characteristic_parents'], slot_usage={}, attributes={'genus': SlotDefinition(name='genus', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='in a logical definition expression, this is the parent (genus) class, e.g. bone', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='OntologyClass', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'differentiating_characteristic_relationship': SlotDefinition(name='differentiating_characteristic_relationship', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='in a logical definition expression, this is the parent (differentiating characteristic) relationship type, e.g. part of', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Relation', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'differentiating_characteristic_parents': SlotDefinition(name='differentiating_characteristic_parents', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='in a logical definition expression, this the parent (differentiating characteristic) class, e.g. hand', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='OntologyClass', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='oc:LogicalDefinition', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Relation': ClassDefinition(name='Relation', id_prefixes=['RO'], definition_uri='http://w3id.org/ontogpt/ontology-class-templateRelation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:ro', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/ontology_class', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='oc:Relation', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Any': ClassDefinition(name='Any', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Any', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=['linkml:Any'], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='linkml:Any', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ExtractionResult': ClassDefinition(name='ExtractionResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/ExtractionResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A result of extracting knowledge on text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['extractionResult__input_id', 'extractionResult__input_title', 'extractionResult__input_text', 'extractionResult__raw_completion_output', 'extractionResult__prompt', 'extractionResult__extracted_object', 'extractionResult__named_entities'], slot_usage={}, attributes={'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:ExtractionResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'NamedEntity': ClassDefinition(name='NamedEntity', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NamedEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:NamedEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'CompoundExpression': ClassDefinition(name='CompoundExpression', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/CompoundExpression', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='core:CompoundExpression', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Triple': ClassDefinition(name='Triple', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Triple', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Abstract parent for Relation Extraction tasks', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['triple__subject', 'triple__predicate', 'triple__object', 'triple__qualifier', 'triple__subject_qualifier', 'triple__object_qualifier'], slot_usage={}, attributes={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Triple', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'TextWithTriples': ClassDefinition(name='TextWithTriples', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/TextWithTriples', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['textWithTriples__publication', 'textWithTriples__triples'], slot_usage={}, attributes={'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:TextWithTriples', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'RelationshipType': ClassDefinition(name='RelationshipType', id_prefixes=['RO', 'biolink'], definition_uri='http://w3id.org/ontogpt/core/RelationshipType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='core:RelationshipType', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Publication': ClassDefinition(name='Publication', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Publication', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['publication__id', 'publication__title', 'publication__abstract', 'publication__combined_text', 'publication__full_text'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Publication', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'AnnotatorResult': ClassDefinition(name='AnnotatorResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/AnnotatorResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['annotatorResult__subject_text', 'annotatorResult__object_id', 'annotatorResult__object_text'], slot_usage={}, attributes={'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:AnnotatorResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={})}" ; - linkml:enums "{'NullDataOptions': EnumDefinition(name='NullDataOptions', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NullDataOptions', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'UNSPECIFIED_METHOD_OF_ADMINISTRATION': PermissibleValue(text='UNSPECIFIED_METHOD_OF_ADMINISTRATION', description=None, meaning='NCIT:C149701', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_APPLICABLE': PermissibleValue(text='NOT_APPLICABLE', description=None, meaning='NCIT:C18902', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['not applicable', 'N/A'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_MENTIONED': PermissibleValue(text='NOT_MENTIONED', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[])}" ; - linkml:id "https://w3id.org/ontogpt/ontology_class" ; - linkml:imports "core", - "linkml:types" ; - linkml:types "{'string': TypeDefinition(name='string', id_prefixes=[], definition_uri='https://w3id.org/linkml/String', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A character string', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Text'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'integer': TypeDefinition(name='integer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Integer', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An integer', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Integer'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='int', uri='xsd:integer', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'boolean': TypeDefinition(name='boolean', id_prefixes=[], definition_uri='https://w3id.org/linkml/Boolean', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A binary (true or false) value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Boolean'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Bool', uri='xsd:boolean', repr='bool', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'float': TypeDefinition(name='float', id_prefixes=[], definition_uri='https://w3id.org/linkml/Float', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:float specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Float'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:float', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'double': TypeDefinition(name='double', id_prefixes=[], definition_uri='https://w3id.org/linkml/Double', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:double specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:Float'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:double', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'decimal': TypeDefinition(name='decimal', id_prefixes=[], definition_uri='https://w3id.org/linkml/Decimal', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number with arbitrary precision that conforms to the xsd:decimal specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=['schema:Number'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Decimal', uri='xsd:decimal', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'time': TypeDefinition(name='time', id_prefixes=[], definition_uri='https://w3id.org/linkml/Time', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A time object represents a (local) time of day, independent of any particular day', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=['URI is dateTime because OWL reasoners do not work with straight date or time'], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Time'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDTime', uri='xsd:time', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date': TypeDefinition(name='date', id_prefixes=[], definition_uri='https://w3id.org/linkml/Date', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a date (year, month and day) in an idealized calendar', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[\"URI is dateTime because OWL reasoners don't work with straight date or time\"], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Date'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDate', uri='xsd:date', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'datetime': TypeDefinition(name='datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/Datetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The combination of a date and time', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:DateTime'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDateTime', uri='xsd:dateTime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date_or_datetime': TypeDefinition(name='date_or_datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/DateOrDatetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Either a date or a datetime', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='linkml:DateOrDatetime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uriorcurie': TypeDefinition(name='uriorcurie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uriorcurie', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a URI or a CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URIorCURIE', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'curie': TypeDefinition(name='curie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Curie', local_names={}, conforms_to='https://www.w3.org/TR/curie/', implements=[], extensions={}, annotations={}, description='a compact URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations this MUST be expanded to a URI', 'in non-RDF serializations MAY be serialized as the compact representation'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Curie', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uri': TypeDefinition(name='uri', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uri', local_names={}, conforms_to='https://www.ietf.org/rfc/rfc3987.txt', implements=[], extensions={}, annotations={}, description='a complete URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:URL'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URI', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ncname': TypeDefinition(name='ncname', id_prefixes=[], definition_uri='https://w3id.org/linkml/Ncname', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Prefix part of CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NCName', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'objectidentifier': TypeDefinition(name='objectidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Objectidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI or CURIE that represents an object in the model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['Used for inheritance and type checking'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='ElementIdentifier', uri='shex:iri', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'nodeidentifier': TypeDefinition(name='nodeidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Nodeidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI, CURIE or BNODE that represents a node in a model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NodeIdentifier', uri='shex:nonLiteral', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpointer': TypeDefinition(name='jsonpointer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpointer', local_names={}, conforms_to='https://datatracker.ietf.org/doc/html/rfc6901', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpath': TypeDefinition(name='jsonpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpath', local_names={}, conforms_to='https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sparqlpath': TypeDefinition(name='sparqlpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Sparqlpath', local_names={}, conforms_to='https://www.w3.org/TR/sparql11-query/#propertypaths', implements=[], extensions={}, annotations={}, description='A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "AnnotatorResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_text> ] ; - linkml:attributes "{'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/ExtractionResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ExtractionResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_title> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/extracted_object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/prompt> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/named_entities> ] ; - skos:definition "A result of extracting knowledge on text" ; - linkml:attributes "{'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/TextWithTriples> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TextWithTriples" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Triple> ; - owl:onProperty <http://w3id.org/ontogpt/core/triples> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Publication> ; - owl:onProperty <http://w3id.org/ontogpt/core/publication> ] ; - linkml:attributes "{'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/abstract> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "abstract" ; - rdfs:range linkml:String ; - skos:definition "The abstract of the publication" . - -<http://w3id.org/ontogpt/core/combined_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "combined_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/extracted_object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "extracted_object" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "The complex objects extracted from the text" . - -<http://w3id.org/ontogpt/core/full_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "full_text" ; - rdfs:range linkml:String ; - skos:definition "The full text of the publication" . - -<http://w3id.org/ontogpt/core/input_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_title" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/named_entities> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "named_entities" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "Named entities extracted from the text" . - -<http://w3id.org/ontogpt/core/object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/object_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/object_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" . - -<http://w3id.org/ontogpt/core/object_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/predicate> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "predicate" ; - rdfs:range <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/prompt> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "prompt" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/publication> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "publication" ; - oc:prompt.skip "true" ; - rdfs:range <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "qualifier" ; - rdfs:range linkml:String ; - skos:definition "A qualifier for the statements, e.g. \"NOT\" for negation" . - -<http://w3id.org/ontogpt/core/raw_completion_output> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "raw_completion_output" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/subject> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/subject_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" . - -<http://w3id.org/ontogpt/core/subject_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "title" ; - rdfs:range linkml:String ; - skos:definition "The title of the publication" . - -<http://w3id.org/ontogpt/core/triples> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "triples" ; - rdfs:range <http://w3id.org/ontogpt/core/Triple> . - -oc:categories a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "categories" ; - oc:prompt "semicolon-separated list of categories to which the entity belongs. These may be taken from an upper level ontology such as COB, BioLink, or UMLS semantic types." ; - rdfs:range oc:OntologyClass ; - skos:definition "the categories to which this entity belongs." . - -oc:description a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "description" ; - rdfs:range linkml:String ; - skos:definition "a textual description of the entity" . - -oc:differentiating_characteristic_parents a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "differentiating_characteristic_parents" ; - oc:prompt "in a logical definition expression, this the parent (differentiating characteristic) class, e.g. hand" ; - rdfs:range oc:OntologyClass . - -oc:differentiating_characteristic_relationship a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "differentiating_characteristic_relationship" ; - oc:prompt "in a logical definition expression, this is the parent (differentiating characteristic) relationship type, e.g. part of" ; - rdfs:range oc:Relation . - -oc:genus a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "genus" ; - oc:prompt "in a logical definition expression, this is the parent (genus) class, e.g. bone" ; - rdfs:range oc:OntologyClass . - -oc:label a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "label" ; - rdfs:range linkml:String ; - skos:definition "the name of the main entity being defined" . - -oc:logical_definition a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "logical_definition" ; - oc:prompt "the necessary and sufficient conditions for this entity to be an instance of this class, written in OWL manchester syntax, e.g. bone and (part_of some 'hand')" ; - rdfs:range oc:LogicalDefinition ; - skos:definition "the necessary and sufficient conditions for this entity to be an instance of this class" . - -oc:subclass_of a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subclass_of" ; - oc:prompt "semicolon-separated list of parent classes, indicating broader concepts. E.g. if the input text is \"a type of bone\", then the parent class is \"bone\"" ; - rdfs:range oc:OntologyClass . - -oc:synonyms a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "synonyms" ; - rdfs:range linkml:String ; - skos:definition "alternative names of the entity" . - -<http://example.org/UNKNOWN/rdfs/label> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "label" ; - oc:owl "AnnotationProperty, AnnotationAssertion" ; - rdfs:range linkml:String ; - skos:altLabel "name" ; - skos:definition "The label (name) of the named thing" ; - skos:exactMatch <http://example.org/UNKNOWN/rdfs/label> . - -<http://purl.obolibrary.org/obo/NCIT_C149701> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "UNSPECIFIED_METHOD_OF_ADMINISTRATION" . - -<http://purl.obolibrary.org/obo/NCIT_C18902> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_APPLICABLE" . - -<http://w3id.org/ontogpt/core/CompoundExpression> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CompoundExpression" ; - linkml:attributes "{}" . - -<http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_MENTIONED" . - -<http://w3id.org/ontogpt/core/RelationshipType> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "RelationshipType" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/Triple> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Triple" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/RelationshipType> ; - owl:onProperty <http://w3id.org/ontogpt/core/predicate> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject> ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - skos:definition "Abstract parent for Relation Extraction tasks" ; - linkml:attributes "{'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -<http://w3id.org/ontogpt/core/id> a owl:ObjectProperty, - linkml:SlotDefinition . - -oc:Relation a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Relation" ; - oc:annotators "sqlite:obo:ro" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/NullDataOptions> a owl:Class, - linkml:EnumDefinition ; - rdfs:label "NullDataOptions" ; - owl:unionOf ( <http://purl.obolibrary.org/obo/NCIT_C149701> <http://purl.obolibrary.org/obo/NCIT_C18902> <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> ) ; - linkml:permissible_values <http://purl.obolibrary.org/obo/NCIT_C149701>, - <http://purl.obolibrary.org/obo/NCIT_C18902>, - <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> . - -<http://w3id.org/ontogpt/core/Publication> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Publication" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/abstract> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/full_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/combined_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/title> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -oc:LogicalDefinition a owl:Class, - linkml:ClassDefinition ; - rdfs:label "LogicalDefinition" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass oc:Relation ; - owl:onProperty oc:differentiating_characteristic_relationship ], - [ a owl:Restriction ; - owl:allValuesFrom oc:OntologyClass ; - owl:onProperty oc:differentiating_characteristic_parents ], - [ a owl:Restriction ; - owl:allValuesFrom oc:OntologyClass ; - owl:onProperty oc:genus ] ; - linkml:attributes "{'genus': SlotDefinition(name='genus', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='in a logical definition expression, this is the parent (genus) class, e.g. bone', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='OntologyClass', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'differentiating_characteristic_relationship': SlotDefinition(name='differentiating_characteristic_relationship', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='in a logical definition expression, this is the parent (differentiating characteristic) relationship type, e.g. part of', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Relation', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'differentiating_characteristic_parents': SlotDefinition(name='differentiating_characteristic_parents', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='in a logical definition expression, this the parent (differentiating characteristic) class, e.g. hand', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='OntologyClass', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/Any> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Any" ; - skos:exactMatch linkml:Any ; - linkml:attributes "{}" . - -oc:OntologyClass a owl:Class, - linkml:ClassDefinition ; - rdfs:label "OntologyClass" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty oc:description ], - [ a owl:Restriction ; - owl:allValuesFrom oc:OntologyClass ; - owl:onProperty oc:subclass_of ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty oc:label ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty oc:synonyms ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass oc:LogicalDefinition ; - owl:onProperty oc:logical_definition ], - [ a owl:Restriction ; - owl:allValuesFrom oc:OntologyClass ; - owl:onProperty oc:categories ], - <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the name of the main entity being defined', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'description': SlotDefinition(name='description', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a textual description of the entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'synonyms': SlotDefinition(name='synonyms', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='alternative names of the entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'categories': SlotDefinition(name='categories', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of categories to which the entity belongs. These may be taken from an upper level ontology such as COB, BioLink, or UMLS semantic types.', extensions={}, annotations={})}, description='the categories to which this entity belongs.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='OntologyClass', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subclass_of': SlotDefinition(name='subclass_of', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of parent classes, indicating broader concepts. E.g. if the input text is \"a type of bone\", then the parent class is \"bone\"', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='OntologyClass', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'logical_definition': SlotDefinition(name='logical_definition', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value=\"the necessary and sufficient conditions for this entity to be an instance of this class, written in OWL manchester syntax, e.g. bone and (part_of some 'hand')\", extensions={}, annotations={})}, description='the necessary and sufficient conditions for this entity to be an instance of this class', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='LogicalDefinition', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/NamedEntity> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "NamedEntity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://example.org/UNKNOWN/rdfs/label> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:ClassDefinition a owl:Class ; - rdfs:label "class_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "class_expression" . - -linkml:SlotDefinition a owl:Class ; - rdfs:label "slot_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "slot_expression" . - - diff --git a/projects/ontology_class/prefixmap/ontology_class.yaml b/projects/ontology_class/prefixmap/ontology_class.yaml deleted file mode 100644 index d7c94693b..000000000 --- a/projects/ontology_class/prefixmap/ontology_class.yaml +++ /dev/null @@ -1,35 +0,0 @@ -{ - "RO": "http://purl.obolibrary.org/obo/RO_", - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "linkml": "https://w3id.org/linkml/", - "oc": "http://w3id.org/ontogpt/ontology-class-template", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } -} diff --git a/projects/ontology_class/protobuf/ontology_class.proto b/projects/ontology_class/protobuf/ontology_class.proto deleted file mode 100644 index 6a684de6e..000000000 --- a/projects/ontology_class/protobuf/ontology_class.proto +++ /dev/null @@ -1,56 +0,0 @@ -message AnnotatorResult - { - string subjectText = 0 - string objectId = 0 - string objectText = 0 - } -// A result of extracting knowledge on text -message ExtractionResult - { - string inputId = 0 - string inputTitle = 0 - string inputText = 0 - string rawCompletionOutput = 0 - string prompt = 0 - any extractedObject = 0 - repeated any namedEntities = 0 - } -message LogicalDefinition - { - repeated ontologyClass genus = 0 - relation differentiatingCharacteristicRelationship = 0 - repeated ontologyClass differentiatingCharacteristicParents = 0 - } -message OntologyClass - { - string id = 0 - string label = 0 - string description = 0 - repeated string synonyms = 0 - repeated ontologyClass categories = 0 - repeated ontologyClass subclassOf = 0 - logicalDefinition logicalDefinition = 0 - } -message Publication - { - string id = 0 - string title = 0 - string abstract = 0 - string combinedText = 0 - string fullText = 0 - } -message Relation - { - string id = 0 - string label = 0 - } -message RelationshipType - { - string id = 0 - string label = 0 - } -message TextWithTriples - { - publication publication = 0 - repeated triple triples = 0 - } diff --git a/projects/ontology_class/shacl/ontology_class.shacl.ttl b/projects/ontology_class/shacl/ontology_class.shacl.ttl deleted file mode 100644 index d7f6620c4..000000000 --- a/projects/ontology_class/shacl/ontology_class.shacl.ttl +++ /dev/null @@ -1,232 +0,0 @@ -@prefix linkml: <https://w3id.org/linkml/> . -@prefix oc: <http://w3id.org/ontogpt/ontology-class-template> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix sh: <http://www.w3.org/ns/shacl#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/object_id> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object_text> ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject_text> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/AnnotatorResult> . - -<http://w3id.org/ontogpt/core/CompoundExpression> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass <http://w3id.org/ontogpt/core/CompoundExpression> . - -<http://w3id.org/ontogpt/core/ExtractionResult> a sh:NodeShape ; - sh:closed true ; - sh:description "A result of extracting knowledge on text" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/prompt> ], - [ sh:class linkml:Any ; - sh:description "Named entities extracted from the text" ; - sh:nodeKind sh:BlankNode ; - sh:order 6 ; - sh:path <http://w3id.org/ontogpt/core/named_entities> ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/input_id> ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/input_title> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/input_text> ], - [ sh:class linkml:Any ; - sh:description "The complex objects extracted from the text" ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/extracted_object> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/ExtractionResult> . - -<http://w3id.org/ontogpt/core/TextWithTriples> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/Publication> ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/publication> ], - [ sh:class <http://w3id.org/ontogpt/core/Triple> ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/triples> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/TextWithTriples> . - -<http://w3id.org/ontogpt/core/Publication> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/combined_text> ], - [ sh:description "The title of the publication" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/title> ], - [ sh:description "The abstract of the publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/abstract> ], - [ sh:description "The full text of the publication" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/full_text> ], - [ sh:description "The publication identifier" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/RelationshipType> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/Triple> a sh:NodeShape ; - sh:closed false ; - sh:description "Abstract parent for Relation Extraction tasks" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/object_qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject> ], - [ sh:description "A qualifier for the statements, e.g. \"NOT\" for negation" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object> ], - [ sh:class <http://w3id.org/ontogpt/core/RelationshipType> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/predicate> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/subject_qualifier> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Triple> . - -oc:LogicalDefinition a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class oc:OntologyClass ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path oc:differentiating_characteristic_parents ], - [ sh:class oc:OntologyClass ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path oc:genus ], - [ sh:class oc:Relation ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path oc:differentiating_characteristic_relationship ] ; - sh:targetClass oc:LogicalDefinition . - -oc:Relation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass oc:Relation . - -linkml:Any a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass linkml:Any . - -<http://w3id.org/ontogpt/core/NamedEntity> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/NamedEntity> . - -oc:OntologyClass a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class oc:LogicalDefinition ; - sh:description "the necessary and sufficient conditions for this entity to be an instance of this class" ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path oc:logical_definition ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:class oc:OntologyClass ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path oc:subclass_of ], - [ sh:class oc:OntologyClass ; - sh:description "the categories to which this entity belongs." ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path oc:categories ], - [ sh:description "a textual description of the entity" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path oc:description ], - [ sh:description "alternative names of the entity" ; - sh:order 2 ; - sh:path oc:synonyms ], - [ sh:description "the name of the main entity being defined" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path oc:label ] ; - sh:targetClass oc:OntologyClass . - diff --git a/projects/ontology_class/shex/ontology_class.shex b/projects/ontology_class/shex/ontology_class.shex deleted file mode 100644 index d6ebdf44a..000000000 --- a/projects/ontology_class/shex/ontology_class.shex +++ /dev/null @@ -1,173 +0,0 @@ -BASE <http://w3id.org/ontogpt/ontology-class-template/> -PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> -PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> -PREFIX linkml: <https://w3id.org/linkml/> -PREFIX core: <http://w3id.org/ontogpt/core/> -PREFIX rdfs1: <http://example.org/UNKNOWN/rdfs/> - - -linkml:String xsd:string - -linkml:Integer xsd:integer - -linkml:Boolean xsd:boolean - -linkml:Float xsd:float - -linkml:Double xsd:double - -linkml:Decimal xsd:decimal - -linkml:Time xsd:time - -linkml:Date xsd:date - -linkml:Datetime xsd:dateTime - -linkml:DateOrDatetime linkml:DateOrDatetime - -linkml:Uriorcurie IRI - -linkml:Curie xsd:string - -linkml:Uri IRI - -linkml:Ncname xsd:string - -linkml:Objectidentifier IRI - -linkml:Nodeidentifier NONLITERAL - -linkml:Jsonpointer xsd:string - -linkml:Jsonpath xsd:string - -linkml:Sparqlpath xsd:string - -core:AnnotatorResult CLOSED { - ( $core:AnnotatorResult_tes ( core:subject_text @linkml:String ? ; - core:object_id @linkml:String ? ; - core:object_text @linkml:String ? - ) ; - rdf:type [ core:AnnotatorResult ] ? - ) -} - -core:Any CLOSED { - ( $core:Any_tes rdf:type . * ; - rdf:type [ linkml:Any ] ? - ) -} - -core:CompoundExpression ( - { - ( $core:CompoundExpression_tes rdf:type . * ; - rdf:type [ core:CompoundExpression ] ? - ) - } OR @core:Triple -) - -core:ExtractionResult CLOSED { - ( $core:ExtractionResult_tes ( core:input_id @linkml:String ? ; - core:input_title @linkml:String ? ; - core:input_text @linkml:String ? ; - core:raw_completion_output @linkml:String ? ; - core:prompt @linkml:String ? ; - core:extracted_object @core:Any ? ; - core:named_entities @core:Any * - ) ; - rdf:type [ core:ExtractionResult ] ? - ) -} - -<http://w3id.org/ontogpt/ontology-class-templateLogicalDefinition> CLOSED { - ( $<http://w3id.org/ontogpt/ontology-class-templateLogicalDefinition_tes> ( - <http://w3id.org/ontogpt/ontology-class-templategenus> @<http://w3id.org/ontogpt/ontology-class-templateOntologyClass> * - ; - <http://w3id.org/ontogpt/ontology-class-templatedifferentiating_characteristic_relationship> - @<http://w3id.org/ontogpt/ontology-class-templateRelation> ? ; - <http://w3id.org/ontogpt/ontology-class-templatedifferentiating_characteristic_parents> - @<http://w3id.org/ontogpt/ontology-class-templateOntologyClass> * - ) ; - rdf:type [ <http://w3id.org/ontogpt/ontology-class-templateLogicalDefinition> ] ? - ) -} - -core:NamedEntity ( - @<http://w3id.org/ontogpt/ontology-class-templateOntologyClass> OR @<http://w3id.org/ontogpt/ontology-class-templateRelation> - OR @core:RelationshipType -) - -core:NamedEntity_struct { - ( $core:NamedEntity_tes rdfs1:label @linkml:String ? ; - rdf:type [ core:NamedEntity ] - ) -} - -<http://w3id.org/ontogpt/ontology-class-templateOntologyClass> CLOSED { - ( $<http://w3id.org/ontogpt/ontology-class-templateOntologyClass_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? ; - <http://w3id.org/ontogpt/ontology-class-templatelabel> @linkml:String ? ; - <http://w3id.org/ontogpt/ontology-class-templatedescription> @linkml:String ? ; - <http://w3id.org/ontogpt/ontology-class-templatesynonyms> @linkml:String * ; - <http://w3id.org/ontogpt/ontology-class-templatecategories> - @<http://w3id.org/ontogpt/ontology-class-templateOntologyClass> * ; - <http://w3id.org/ontogpt/ontology-class-templatesubclass_of> - @<http://w3id.org/ontogpt/ontology-class-templateOntologyClass> * ; - <http://w3id.org/ontogpt/ontology-class-templatelogical_definition> - @<http://w3id.org/ontogpt/ontology-class-templateLogicalDefinition> ? - ) ; - rdf:type [ <http://w3id.org/ontogpt/ontology-class-templateOntologyClass> ] - ) -} - -core:Publication CLOSED { - ( $core:Publication_tes ( core:id @linkml:String ? ; - core:title @linkml:String ? ; - core:abstract @linkml:String ? ; - core:combined_text @linkml:String ? ; - core:full_text @linkml:String ? - ) ; - rdf:type [ core:Publication ] ? - ) -} - -<http://w3id.org/ontogpt/ontology-class-templateRelation> CLOSED { - ( $<http://w3id.org/ontogpt/ontology-class-templateRelation_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <http://w3id.org/ontogpt/ontology-class-templateRelation> ] - ) -} - -core:RelationshipType CLOSED { - ( $core:RelationshipType_tes ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ core:RelationshipType ] - ) -} - -core:TextWithTriples CLOSED { - ( $core:TextWithTriples_tes ( core:publication @core:Publication ? ; - core:triples @core:Triple * - ) ; - rdf:type [ core:TextWithTriples ] ? - ) -} - -core:Triple { - ( $core:Triple_tes ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - core:subject @core:NamedEntity ? ; - core:predicate @core:RelationshipType ? ; - core:object @core:NamedEntity ? ; - core:qualifier @linkml:String ? ; - core:subject_qualifier @core:NamedEntity ? ; - core:object_qualifier @core:NamedEntity ? - ) ; - rdf:type [ core:Triple ] ? - ) -} - - diff --git a/projects/ontology_class/sqlschema/ontology_class.sql b/projects/ontology_class/sqlschema/ontology_class.sql deleted file mode 100644 index 3fbad0bd3..000000000 --- a/projects/ontology_class/sqlschema/ontology_class.sql +++ /dev/null @@ -1,71 +0,0 @@ - - -CREATE TABLE "AnnotatorResult" ( - subject_text TEXT, - object_id TEXT, - object_text TEXT, - PRIMARY KEY (subject_text, object_id, object_text) -); - -CREATE TABLE "ExtractionResult" ( - input_id TEXT, - input_title TEXT, - input_text TEXT, - raw_completion_output TEXT, - prompt TEXT, - extracted_object TEXT, - named_entities TEXT, - PRIMARY KEY (input_id, input_title, input_text, raw_completion_output, prompt, extracted_object, named_entities) -); - -CREATE TABLE "OntologyClass" ( - id TEXT NOT NULL, - label TEXT, - description TEXT, - categories TEXT, - subclass_of TEXT, - logical_definition TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Publication" ( - id TEXT, - title TEXT, - abstract TEXT, - combined_text TEXT, - full_text TEXT, - PRIMARY KEY (id, title, abstract, combined_text, full_text) -); - -CREATE TABLE "Relation" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "RelationshipType" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "TextWithTriples" ( - publication TEXT, - triples TEXT, - PRIMARY KEY (publication, triples) -); - -CREATE TABLE "LogicalDefinition" ( - genus TEXT, - differentiating_characteristic_relationship TEXT, - differentiating_characteristic_parents TEXT, - PRIMARY KEY (genus, differentiating_characteristic_relationship, differentiating_characteristic_parents), - FOREIGN KEY(differentiating_characteristic_relationship) REFERENCES "Relation" (id) -); - -CREATE TABLE "OntologyClass_synonyms" ( - backref_id TEXT, - synonyms TEXT, - PRIMARY KEY (backref_id, synonyms), - FOREIGN KEY(backref_id) REFERENCES "OntologyClass" (id) -); diff --git a/projects/ontology_issue/docs/AnnotatorResult.md b/projects/ontology_issue/docs/AnnotatorResult.md deleted file mode 100644 index 4f189092b..000000000 --- a/projects/ontology_issue/docs/AnnotatorResult.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Class: AnnotatorResult - - - - -URI: [oc:AnnotatorResult](http://w3id.org/ontogpt/ontology-class-templateAnnotatorResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F])](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F]) - -## Attributes - - -### Own - - * [➞subject_text](annotatorResult__subject_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_id](annotatorResult__object_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_text](annotatorResult__object_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) diff --git a/projects/ontology_issue/docs/Any.md b/projects/ontology_issue/docs/Any.md deleted file mode 100644 index 75c20f2f8..000000000 --- a/projects/ontology_issue/docs/Any.md +++ /dev/null @@ -1,25 +0,0 @@ - -# Class: Any - - - - -URI: [oc:Any](http://w3id.org/ontogpt/ontology-class-templateAny) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult])](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult]) - -## Referenced by Class - - * **None** *[➞extracted_object](extractionResult__extracted_object.md)* <sub>0..1</sub> **[Any](Any.md)** - * **None** *[➞named_entities](extractionResult__named_entities.md)* <sub>0..\*</sub> **[Any](Any.md)** - -## Attributes - - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | linkml:Any | - diff --git a/projects/ontology_issue/docs/ChangeType.md b/projects/ontology_issue/docs/ChangeType.md deleted file mode 100644 index 3ea79df25..000000000 --- a/projects/ontology_issue/docs/ChangeType.md +++ /dev/null @@ -1,24 +0,0 @@ - -# Enum: ChangeType - - - - -URI: [oc:ChangeType](http://w3id.org/ontogpt/ontology-class-templateChangeType) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | -| UNKNOWN | | | | -| CHANGE_DEFINITION | | | | -| CHANGE_LABEL | | | | -| CHANGE_XREF | | | | -| MOVE_TERM | | | | - diff --git a/projects/ontology_issue/docs/CompoundExpression.md b/projects/ontology_issue/docs/CompoundExpression.md deleted file mode 100644 index 1e1d4dd38..000000000 --- a/projects/ontology_issue/docs/CompoundExpression.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Class: CompoundExpression - - - - -URI: [oc:CompoundExpression](http://w3id.org/ontogpt/ontology-class-templateCompoundExpression) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[OntologyProblem],[OntologyChange],[CompoundExpression]^-[Triple],[CompoundExpression]^-[OntologyProblem],[CompoundExpression]^-[OntologyChange])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[OntologyProblem],[OntologyChange],[CompoundExpression]^-[Triple],[CompoundExpression]^-[OntologyProblem],[CompoundExpression]^-[OntologyChange]) - -## Children - - * [OntologyChange](OntologyChange.md) - * [OntologyProblem](OntologyProblem.md) - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - -## Referenced by Class - - -## Attributes - diff --git a/projects/ontology_issue/docs/ExtractionResult.md b/projects/ontology_issue/docs/ExtractionResult.md deleted file mode 100644 index fe7d19bb9..000000000 --- a/projects/ontology_issue/docs/ExtractionResult.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Class: ExtractionResult - - -A result of extracting knowledge on text - -URI: [oc:ExtractionResult](http://w3id.org/ontogpt/ontology-class-templateExtractionResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any])](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any]) - -## Attributes - - -### Own - - * [➞input_id](extractionResult__input_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_title](extractionResult__input_title.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_text](extractionResult__input_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞prompt](extractionResult__prompt.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞extracted_object](extractionResult__extracted_object.md) <sub>0..1</sub> - * Description: The complex objects extracted from the text - * Range: [Any](Any.md) - * [➞named_entities](extractionResult__named_entities.md) <sub>0..\*</sub> - * Description: Named entities extracted from the text - * Range: [Any](Any.md) diff --git a/projects/ontology_issue/docs/NamedEntity.md b/projects/ontology_issue/docs/NamedEntity.md deleted file mode 100644 index a3f5f4d52..000000000 --- a/projects/ontology_issue/docs/NamedEntity.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: NamedEntity - - - - -URI: [oc:NamedEntity](http://w3id.org/ontogpt/ontology-class-templateNamedEntity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[OntologyClass],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[OntologyClass],[Triple])](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[OntologyClass],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[OntologyClass],[Triple]) - -## Children - - * [OntologyClass](OntologyClass.md) - * [RelationshipType](RelationshipType.md) - -## Referenced by Class - - * **None** *[➞object](triple__object.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞object_qualifier](triple__object_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject](triple__subject.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject_qualifier](triple__subject_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - -## Attributes - - -### Own - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/ontology_issue/docs/NullDataOptions.md b/projects/ontology_issue/docs/NullDataOptions.md deleted file mode 100644 index 4b9a6758e..000000000 --- a/projects/ontology_issue/docs/NullDataOptions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Enum: NullDataOptions - - - - -URI: [oc:NullDataOptions](http://w3id.org/ontogpt/ontology-class-templateNullDataOptions) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | -| UNSPECIFIED_METHOD_OF_ADMINISTRATION | | NCIT:C149701 | | -| NOT_APPLICABLE | | NCIT:C18902 | {'aliases': ['not applicable', 'N/A']} | -| NOT_MENTIONED | | | | - diff --git a/projects/ontology_issue/docs/OntologyChange.md b/projects/ontology_issue/docs/OntologyChange.md deleted file mode 100644 index 5797a47ff..000000000 --- a/projects/ontology_issue/docs/OntologyChange.md +++ /dev/null @@ -1,33 +0,0 @@ - -# Class: OntologyChange - - - - -URI: [oc:OntologyChange](http://w3id.org/ontogpt/ontology-class-templateOntologyChange) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[OntologyClass],[OntologyClass]<about%200..*-%20[OntologyChange|description:string%20%3F;category:ChangeType%20%3F],[OntologyIssue]++-%20proposed_changes%200..*>[OntologyChange],[CompoundExpression]^-[OntologyChange],[OntologyIssue],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[OntologyClass],[OntologyClass]<about%200..*-%20[OntologyChange|description:string%20%3F;category:ChangeType%20%3F],[OntologyIssue]++-%20proposed_changes%200..*>[OntologyChange],[CompoundExpression]^-[OntologyChange],[OntologyIssue],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞proposed_changes](ontologyIssue__proposed_changes.md)* <sub>0..\*</sub> **[OntologyChange](OntologyChange.md)** - -## Attributes - - -### Own - - * [➞description](ontologyChange__description.md) <sub>0..1</sub> - * Description: A succinct description of the proposed change - * Range: [String](types/String.md) - * [➞category](ontologyChange__category.md) <sub>0..1</sub> - * Description: What kind of change? - * Range: [ChangeType](ChangeType.md) - * [➞about](ontologyChange__about.md) <sub>0..\*</sub> - * Description: What terms in the ontology will this change affect? - * Range: [OntologyClass](OntologyClass.md) diff --git a/projects/ontology_issue/docs/OntologyClass.md b/projects/ontology_issue/docs/OntologyClass.md deleted file mode 100644 index 57455ae27..000000000 --- a/projects/ontology_issue/docs/OntologyClass.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Class: OntologyClass - - - - -URI: [oc:OntologyClass](http://w3id.org/ontogpt/ontology-class-templateOntologyClass) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[OntologyChange]-%20about%200..*>[OntologyClass|id(i):string;label(i):string%20%3F],[OntologyIssue]-%20domains%200..*>[OntologyClass],[OntologyProblem]-%20about%200..*>[OntologyClass],[NamedEntity]^-[OntologyClass],[OntologyProblem],[OntologyIssue],[OntologyChange],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[OntologyChange]-%20about%200..*>[OntologyClass|id(i):string;label(i):string%20%3F],[OntologyIssue]-%20domains%200..*>[OntologyClass],[OntologyProblem]-%20about%200..*>[OntologyClass],[NamedEntity]^-[OntologyClass],[OntologyProblem],[OntologyIssue],[OntologyChange],[NamedEntity]) - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞about](ontologyChange__about.md)* <sub>0..\*</sub> **[OntologyClass](OntologyClass.md)** - * **None** *[➞domains](ontologyIssue__domains.md)* <sub>0..\*</sub> **[OntologyClass](OntologyClass.md)** - * **None** *[➞about](ontologyProblem__about.md)* <sub>0..\*</sub> **[OntologyClass](OntologyClass.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/ontology_issue/docs/OntologyIssue.md b/projects/ontology_issue/docs/OntologyIssue.md deleted file mode 100644 index 0bcbc9999..000000000 --- a/projects/ontology_issue/docs/OntologyIssue.md +++ /dev/null @@ -1,33 +0,0 @@ - -# Class: OntologyIssue - - - - -URI: [oc:OntologyIssue](http://w3id.org/ontogpt/ontology-class-templateOntologyIssue) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[OntologyProblem],[OntologyChange]<proposed_changes%200..*-++[OntologyIssue|title:string%20%3F;summary:string%20%3F;status:string%20%3F],[OntologyProblem]<problem_list%200..*-++[OntologyIssue],[OntologyClass]<domains%200..*-%20[OntologyIssue],[OntologyClass],[OntologyChange])](https://yuml.me/diagram/nofunky;dir:TB/class/[OntologyProblem],[OntologyChange]<proposed_changes%200..*-++[OntologyIssue|title:string%20%3F;summary:string%20%3F;status:string%20%3F],[OntologyProblem]<problem_list%200..*-++[OntologyIssue],[OntologyClass]<domains%200..*-%20[OntologyIssue],[OntologyClass],[OntologyChange]) - -## Attributes - - -### Own - - * [➞title](ontologyIssue__title.md) <sub>0..1</sub> - * Description: the title of the issue - * Range: [String](types/String.md) - * [➞summary](ontologyIssue__summary.md) <sub>0..1</sub> - * Description: a high level summary - * Range: [String](types/String.md) - * [➞status](ontologyIssue__status.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞domains](ontologyIssue__domains.md) <sub>0..\*</sub> - * Description: What part of the ontology does this pertain to. - * Range: [OntologyClass](OntologyClass.md) - * [➞problem_list](ontologyIssue__problem_list.md) <sub>0..\*</sub> - * Description: A list of problems stated at a high level - * Range: [OntologyProblem](OntologyProblem.md) - * [➞proposed_changes](ontologyIssue__proposed_changes.md) <sub>0..\*</sub> - * Description: What part of the ontology does this pertain to. - * Range: [OntologyChange](OntologyChange.md) diff --git a/projects/ontology_issue/docs/OntologyProblem.md b/projects/ontology_issue/docs/OntologyProblem.md deleted file mode 100644 index 2d0fef019..000000000 --- a/projects/ontology_issue/docs/OntologyProblem.md +++ /dev/null @@ -1,36 +0,0 @@ - -# Class: OntologyProblem - - - - -URI: [oc:OntologyProblem](http://w3id.org/ontogpt/ontology-class-templateOntologyProblem) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[OntologyClass]<about%200..*-%20[OntologyProblem|description:string%20%3F;severity:string%20%3F;category:ProblemType%20%3F],[OntologyIssue]++-%20problem_list%200..*>[OntologyProblem],[CompoundExpression]^-[OntologyProblem],[OntologyIssue],[OntologyClass],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[OntologyClass]<about%200..*-%20[OntologyProblem|description:string%20%3F;severity:string%20%3F;category:ProblemType%20%3F],[OntologyIssue]++-%20problem_list%200..*>[OntologyProblem],[CompoundExpression]^-[OntologyProblem],[OntologyIssue],[OntologyClass],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞problem_list](ontologyIssue__problem_list.md)* <sub>0..\*</sub> **[OntologyProblem](OntologyProblem.md)** - -## Attributes - - -### Own - - * [➞description](ontologyProblem__description.md) <sub>0..1</sub> - * Description: A succinct description of the problem - * Range: [String](types/String.md) - * [➞severity](ontologyProblem__severity.md) <sub>0..1</sub> - * Description: How severe is this problem? - * Range: [String](types/String.md) - * [➞category](ontologyProblem__category.md) <sub>0..1</sub> - * Description: What category does this problem fall into? - * Range: [ProblemType](ProblemType.md) - * [➞about](ontologyProblem__about.md) <sub>0..\*</sub> - * Description: What terms in the ontology is this problem about? - * Range: [OntologyClass](OntologyClass.md) diff --git a/projects/ontology_issue/docs/ProblemType.md b/projects/ontology_issue/docs/ProblemType.md deleted file mode 100644 index 7eb7d154c..000000000 --- a/projects/ontology_issue/docs/ProblemType.md +++ /dev/null @@ -1,26 +0,0 @@ - -# Enum: ProblemType - - - - -URI: [oc:ProblemType](http://w3id.org/ontogpt/ontology-class-templateProblemType) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | -| UNKNOWN | | | | -| TYPO | | | | -| BAD_XREF | | | | -| MISSING_DEFINITION | | | | -| MISSING_PARENT | | | | -| BAD_RELATIONSHIP | | | | -| OTHER | | | | - diff --git a/projects/ontology_issue/docs/Publication.md b/projects/ontology_issue/docs/Publication.md deleted file mode 100644 index a55c2f8cc..000000000 --- a/projects/ontology_issue/docs/Publication.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Publication - - - - -URI: [oc:Publication](http://w3id.org/ontogpt/ontology-class-templatePublication) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples])](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples]) - -## Referenced by Class - - * **None** *[➞publication](textWithTriples__publication.md)* <sub>0..1</sub> **[Publication](Publication.md)** - -## Attributes - - -### Own - - * [➞id](publication__id.md) <sub>0..1</sub> - * Description: The publication identifier - * Range: [String](types/String.md) - * [➞title](publication__title.md) <sub>0..1</sub> - * Description: The title of the publication - * Range: [String](types/String.md) - * [➞abstract](publication__abstract.md) <sub>0..1</sub> - * Description: The abstract of the publication - * Range: [String](types/String.md) - * [➞combined_text](publication__combined_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞full_text](publication__full_text.md) <sub>0..1</sub> - * Description: The full text of the publication - * Range: [String](types/String.md) diff --git a/projects/ontology_issue/docs/RelationshipType.md b/projects/ontology_issue/docs/RelationshipType.md deleted file mode 100644 index 4adecdef0..000000000 --- a/projects/ontology_issue/docs/RelationshipType.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: RelationshipType - - - - -URI: [oc:RelationshipType](http://w3id.org/ontogpt/ontology-class-templateRelationshipType) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity]) - -## Identifier prefixes - - * RO - * biolink - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞predicate](triple__predicate.md)* <sub>0..1</sub> **[RelationshipType](RelationshipType.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/ontology_issue/docs/TextWithTriples.md b/projects/ontology_issue/docs/TextWithTriples.md deleted file mode 100644 index e94121934..000000000 --- a/projects/ontology_issue/docs/TextWithTriples.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: TextWithTriples - - - - -URI: [oc:TextWithTriples](http://w3id.org/ontogpt/ontology-class-templateTextWithTriples) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication]) - -## Attributes - - -### Own - - * [➞publication](textWithTriples__publication.md) <sub>0..1</sub> - * Range: [Publication](Publication.md) - * [➞triples](textWithTriples__triples.md) <sub>0..\*</sub> - * Range: [Triple](Triple.md) diff --git a/projects/ontology_issue/docs/Triple.md b/projects/ontology_issue/docs/Triple.md deleted file mode 100644 index 5a0ca3d43..000000000 --- a/projects/ontology_issue/docs/Triple.md +++ /dev/null @@ -1,39 +0,0 @@ - -# Class: Triple - - -Abstract parent for Relation Extraction tasks - -URI: [oc:Triple](http://w3id.org/ontogpt/ontology-class-templateTriple) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞triples](textWithTriples__triples.md)* <sub>0..\*</sub> **[Triple](Triple.md)** - -## Attributes - - -### Own - - * [➞subject](triple__subject.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞predicate](triple__predicate.md) <sub>0..1</sub> - * Range: [RelationshipType](RelationshipType.md) - * [➞object](triple__object.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞qualifier](triple__qualifier.md) <sub>0..1</sub> - * Description: A qualifier for the statements, e.g. "NOT" for negation - * Range: [String](types/String.md) - * [➞subject_qualifier](triple__subject_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - * Range: [NamedEntity](NamedEntity.md) - * [➞object_qualifier](triple__object_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * Range: [NamedEntity](NamedEntity.md) diff --git a/projects/ontology_issue/docs/annotatorResult__object_id.md b/projects/ontology_issue/docs/annotatorResult__object_id.md deleted file mode 100644 index be14e5b97..000000000 --- a/projects/ontology_issue/docs/annotatorResult__object_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_id - - - - -URI: [oc:annotatorResult__object_id](http://w3id.org/ontogpt/ontology-class-templateannotatorResult__object_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/ontology_issue/docs/annotatorResult__object_text.md b/projects/ontology_issue/docs/annotatorResult__object_text.md deleted file mode 100644 index fbf16b458..000000000 --- a/projects/ontology_issue/docs/annotatorResult__object_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_text - - - - -URI: [oc:annotatorResult__object_text](http://w3id.org/ontogpt/ontology-class-templateannotatorResult__object_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/ontology_issue/docs/annotatorResult__subject_text.md b/projects/ontology_issue/docs/annotatorResult__subject_text.md deleted file mode 100644 index 1525bf843..000000000 --- a/projects/ontology_issue/docs/annotatorResult__subject_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_text - - - - -URI: [oc:annotatorResult__subject_text](http://w3id.org/ontogpt/ontology-class-templateannotatorResult__subject_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/ontology_issue/docs/extractionResult__extracted_object.md b/projects/ontology_issue/docs/extractionResult__extracted_object.md deleted file mode 100644 index b1bc7ddff..000000000 --- a/projects/ontology_issue/docs/extractionResult__extracted_object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: extracted_object - - -The complex objects extracted from the text - -URI: [oc:extractionResult__extracted_object](http://w3id.org/ontogpt/ontology-class-templateextractionResult__extracted_object) - - -## Domain and Range - -None → <sub>0..1</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ontology_issue/docs/extractionResult__input_id.md b/projects/ontology_issue/docs/extractionResult__input_id.md deleted file mode 100644 index 06eab71c1..000000000 --- a/projects/ontology_issue/docs/extractionResult__input_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_id - - - - -URI: [oc:extractionResult__input_id](http://w3id.org/ontogpt/ontology-class-templateextractionResult__input_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ontology_issue/docs/extractionResult__input_text.md b/projects/ontology_issue/docs/extractionResult__input_text.md deleted file mode 100644 index 1dc6a7221..000000000 --- a/projects/ontology_issue/docs/extractionResult__input_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_text - - - - -URI: [oc:extractionResult__input_text](http://w3id.org/ontogpt/ontology-class-templateextractionResult__input_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ontology_issue/docs/extractionResult__input_title.md b/projects/ontology_issue/docs/extractionResult__input_title.md deleted file mode 100644 index 2d7893d36..000000000 --- a/projects/ontology_issue/docs/extractionResult__input_title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_title - - - - -URI: [oc:extractionResult__input_title](http://w3id.org/ontogpt/ontology-class-templateextractionResult__input_title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ontology_issue/docs/extractionResult__named_entities.md b/projects/ontology_issue/docs/extractionResult__named_entities.md deleted file mode 100644 index 37772a93c..000000000 --- a/projects/ontology_issue/docs/extractionResult__named_entities.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: named_entities - - -Named entities extracted from the text - -URI: [oc:extractionResult__named_entities](http://w3id.org/ontogpt/ontology-class-templateextractionResult__named_entities) - - -## Domain and Range - -None → <sub>0..\*</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ontology_issue/docs/extractionResult__prompt.md b/projects/ontology_issue/docs/extractionResult__prompt.md deleted file mode 100644 index 8ba0ddcab..000000000 --- a/projects/ontology_issue/docs/extractionResult__prompt.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: prompt - - - - -URI: [oc:extractionResult__prompt](http://w3id.org/ontogpt/ontology-class-templateextractionResult__prompt) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ontology_issue/docs/extractionResult__raw_completion_output.md b/projects/ontology_issue/docs/extractionResult__raw_completion_output.md deleted file mode 100644 index ec9df2512..000000000 --- a/projects/ontology_issue/docs/extractionResult__raw_completion_output.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: raw_completion_output - - - - -URI: [oc:extractionResult__raw_completion_output](http://w3id.org/ontogpt/ontology-class-templateextractionResult__raw_completion_output) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ontology_issue/docs/namedEntity__id.md b/projects/ontology_issue/docs/namedEntity__id.md deleted file mode 100644 index 4a2cd961b..000000000 --- a/projects/ontology_issue/docs/namedEntity__id.md +++ /dev/null @@ -1,31 +0,0 @@ - -# Slot: id - - -A unique identifier for the named entity - -URI: [oc:namedEntity__id](http://w3id.org/ontogpt/ontology-class-templatenamedEntity__id) - - -## Domain and Range - -None → <sub>1..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [NamedEntity](NamedEntity.md) - * [OntologyClass](OntologyClass.md) - * [RelationshipType](RelationshipType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | this is populated during the grounding and normalization step | - diff --git a/projects/ontology_issue/docs/namedEntity__label.md b/projects/ontology_issue/docs/namedEntity__label.md deleted file mode 100644 index 03552dc0a..000000000 --- a/projects/ontology_issue/docs/namedEntity__label.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Slot: label - - -The label (name) of the named thing - -URI: [oc:namedEntity__label](http://w3id.org/ontogpt/ontology-class-templatenamedEntity__label) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [NamedEntity](NamedEntity.md) - * [OntologyClass](OntologyClass.md) - * [RelationshipType](RelationshipType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Aliases:** | | name | -| **Mappings:** | | rdfs:label | - diff --git a/projects/ontology_issue/docs/ontologyChange__about.md b/projects/ontology_issue/docs/ontologyChange__about.md deleted file mode 100644 index 1f9f75b60..000000000 --- a/projects/ontology_issue/docs/ontologyChange__about.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: about - - -What terms in the ontology will this change affect? - -URI: [oc:ontologyChange__about](http://w3id.org/ontogpt/ontology-class-templateontologyChange__about) - - -## Domain and Range - -None → <sub>0..\*</sub> [OntologyClass](OntologyClass.md) - -## Parents - - -## Children - - -## Used by - - * [OntologyChange](OntologyChange.md) diff --git a/projects/ontology_issue/docs/ontologyChange__category.md b/projects/ontology_issue/docs/ontologyChange__category.md deleted file mode 100644 index 677ce9bc2..000000000 --- a/projects/ontology_issue/docs/ontologyChange__category.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: category - - -What kind of change? - -URI: [oc:ontologyChange__category](http://w3id.org/ontogpt/ontology-class-templateontologyChange__category) - - -## Domain and Range - -None → <sub>0..1</sub> [ChangeType](ChangeType.md) - -## Parents - - -## Children - - -## Used by - - * [OntologyChange](OntologyChange.md) diff --git a/projects/ontology_issue/docs/ontologyChange__description.md b/projects/ontology_issue/docs/ontologyChange__description.md deleted file mode 100644 index 8c815de49..000000000 --- a/projects/ontology_issue/docs/ontologyChange__description.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: description - - -A succinct description of the proposed change - -URI: [oc:ontologyChange__description](http://w3id.org/ontogpt/ontology-class-templateontologyChange__description) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [OntologyChange](OntologyChange.md) diff --git a/projects/ontology_issue/docs/ontologyIssue__domains.md b/projects/ontology_issue/docs/ontologyIssue__domains.md deleted file mode 100644 index ae6a2c436..000000000 --- a/projects/ontology_issue/docs/ontologyIssue__domains.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: domains - - -What part of the ontology does this pertain to. - -URI: [oc:ontologyIssue__domains](http://w3id.org/ontogpt/ontology-class-templateontologyIssue__domains) - - -## Domain and Range - -None → <sub>0..\*</sub> [OntologyClass](OntologyClass.md) - -## Parents - - -## Children - - -## Used by - - * [OntologyIssue](OntologyIssue.md) diff --git a/projects/ontology_issue/docs/ontologyIssue__problem_list.md b/projects/ontology_issue/docs/ontologyIssue__problem_list.md deleted file mode 100644 index a4b1088ab..000000000 --- a/projects/ontology_issue/docs/ontologyIssue__problem_list.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: problem_list - - -A list of problems stated at a high level - -URI: [oc:ontologyIssue__problem_list](http://w3id.org/ontogpt/ontology-class-templateontologyIssue__problem_list) - - -## Domain and Range - -None → <sub>0..\*</sub> [OntologyProblem](OntologyProblem.md) - -## Parents - - -## Children - - -## Used by - - * [OntologyIssue](OntologyIssue.md) diff --git a/projects/ontology_issue/docs/ontologyIssue__proposed_changes.md b/projects/ontology_issue/docs/ontologyIssue__proposed_changes.md deleted file mode 100644 index d74166a67..000000000 --- a/projects/ontology_issue/docs/ontologyIssue__proposed_changes.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: proposed_changes - - -What part of the ontology does this pertain to. - -URI: [oc:ontologyIssue__proposed_changes](http://w3id.org/ontogpt/ontology-class-templateontologyIssue__proposed_changes) - - -## Domain and Range - -None → <sub>0..\*</sub> [OntologyChange](OntologyChange.md) - -## Parents - - -## Children - - -## Used by - - * [OntologyIssue](OntologyIssue.md) diff --git a/projects/ontology_issue/docs/ontologyIssue__status.md b/projects/ontology_issue/docs/ontologyIssue__status.md deleted file mode 100644 index 729aa27de..000000000 --- a/projects/ontology_issue/docs/ontologyIssue__status.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: status - - - - -URI: [oc:ontologyIssue__status](http://w3id.org/ontogpt/ontology-class-templateontologyIssue__status) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [OntologyIssue](OntologyIssue.md) diff --git a/projects/ontology_issue/docs/ontologyIssue__summary.md b/projects/ontology_issue/docs/ontologyIssue__summary.md deleted file mode 100644 index d44e96302..000000000 --- a/projects/ontology_issue/docs/ontologyIssue__summary.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: summary - - -a high level summary - -URI: [oc:ontologyIssue__summary](http://w3id.org/ontogpt/ontology-class-templateontologyIssue__summary) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [OntologyIssue](OntologyIssue.md) diff --git a/projects/ontology_issue/docs/ontologyIssue__title.md b/projects/ontology_issue/docs/ontologyIssue__title.md deleted file mode 100644 index 1841d9231..000000000 --- a/projects/ontology_issue/docs/ontologyIssue__title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: title - - -the title of the issue - -URI: [oc:ontologyIssue__title](http://w3id.org/ontogpt/ontology-class-templateontologyIssue__title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [OntologyIssue](OntologyIssue.md) diff --git a/projects/ontology_issue/docs/ontologyProblem__about.md b/projects/ontology_issue/docs/ontologyProblem__about.md deleted file mode 100644 index d8c6d2a12..000000000 --- a/projects/ontology_issue/docs/ontologyProblem__about.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: about - - -What terms in the ontology is this problem about? - -URI: [oc:ontologyProblem__about](http://w3id.org/ontogpt/ontology-class-templateontologyProblem__about) - - -## Domain and Range - -None → <sub>0..\*</sub> [OntologyClass](OntologyClass.md) - -## Parents - - -## Children - - -## Used by - - * [OntologyProblem](OntologyProblem.md) diff --git a/projects/ontology_issue/docs/ontologyProblem__category.md b/projects/ontology_issue/docs/ontologyProblem__category.md deleted file mode 100644 index 9d2308473..000000000 --- a/projects/ontology_issue/docs/ontologyProblem__category.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: category - - -What category does this problem fall into? - -URI: [oc:ontologyProblem__category](http://w3id.org/ontogpt/ontology-class-templateontologyProblem__category) - - -## Domain and Range - -None → <sub>0..1</sub> [ProblemType](ProblemType.md) - -## Parents - - -## Children - - -## Used by - - * [OntologyProblem](OntologyProblem.md) diff --git a/projects/ontology_issue/docs/ontologyProblem__description.md b/projects/ontology_issue/docs/ontologyProblem__description.md deleted file mode 100644 index b85edbdf7..000000000 --- a/projects/ontology_issue/docs/ontologyProblem__description.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: description - - -A succinct description of the problem - -URI: [oc:ontologyProblem__description](http://w3id.org/ontogpt/ontology-class-templateontologyProblem__description) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [OntologyProblem](OntologyProblem.md) diff --git a/projects/ontology_issue/docs/ontologyProblem__severity.md b/projects/ontology_issue/docs/ontologyProblem__severity.md deleted file mode 100644 index 5148a03dd..000000000 --- a/projects/ontology_issue/docs/ontologyProblem__severity.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: severity - - -How severe is this problem? - -URI: [oc:ontologyProblem__severity](http://w3id.org/ontogpt/ontology-class-templateontologyProblem__severity) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [OntologyProblem](OntologyProblem.md) diff --git a/projects/ontology_issue/docs/ontology_issue.md b/projects/ontology_issue/docs/ontology_issue.md deleted file mode 100644 index 8bcf333ac..000000000 --- a/projects/ontology_issue/docs/ontology_issue.md +++ /dev/null @@ -1,122 +0,0 @@ - -# ontology-issue - - -**metamodel version:** 1.7.0 - -**version:** None - - -A data model for representing the contents of a GitHub issue on an ontology tracker - - -### Classes - - * [AnnotatorResult](AnnotatorResult.md) - * [Any](Any.md) - * [CompoundExpression](CompoundExpression.md) - * [OntologyChange](OntologyChange.md) - * [OntologyProblem](OntologyProblem.md) - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - * [ExtractionResult](ExtractionResult.md) - A result of extracting knowledge on text - * [NamedEntity](NamedEntity.md) - * [OntologyClass](OntologyClass.md) - * [RelationshipType](RelationshipType.md) - * [OntologyIssue](OntologyIssue.md) - * [Publication](Publication.md) - * [TextWithTriples](TextWithTriples.md) - -### Mixins - - -### Slots - - * [➞object_id](annotatorResult__object_id.md) - * [➞object_text](annotatorResult__object_text.md) - * [➞subject_text](annotatorResult__subject_text.md) - * [➞extracted_object](extractionResult__extracted_object.md) - The complex objects extracted from the text - * [➞input_id](extractionResult__input_id.md) - * [➞input_text](extractionResult__input_text.md) - * [➞input_title](extractionResult__input_title.md) - * [➞named_entities](extractionResult__named_entities.md) - Named entities extracted from the text - * [➞prompt](extractionResult__prompt.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) - * [➞id](namedEntity__id.md) - A unique identifier for the named entity - * [➞label](namedEntity__label.md) - The label (name) of the named thing - * [➞about](ontologyChange__about.md) - What terms in the ontology will this change affect? - * [➞category](ontologyChange__category.md) - What kind of change? - * [➞description](ontologyChange__description.md) - A succinct description of the proposed change - * [➞domains](ontologyIssue__domains.md) - What part of the ontology does this pertain to. - * [➞problem_list](ontologyIssue__problem_list.md) - A list of problems stated at a high level - * [➞proposed_changes](ontologyIssue__proposed_changes.md) - What part of the ontology does this pertain to. - * [➞status](ontologyIssue__status.md) - * [➞summary](ontologyIssue__summary.md) - a high level summary - * [➞title](ontologyIssue__title.md) - the title of the issue - * [➞about](ontologyProblem__about.md) - What terms in the ontology is this problem about? - * [➞category](ontologyProblem__category.md) - What category does this problem fall into? - * [➞description](ontologyProblem__description.md) - A succinct description of the problem - * [➞severity](ontologyProblem__severity.md) - How severe is this problem? - * [➞abstract](publication__abstract.md) - The abstract of the publication - * [➞combined_text](publication__combined_text.md) - * [➞full_text](publication__full_text.md) - The full text of the publication - * [➞id](publication__id.md) - The publication identifier - * [➞title](publication__title.md) - The title of the publication - * [➞publication](textWithTriples__publication.md) - * [➞triples](textWithTriples__triples.md) - * [➞object](triple__object.md) - * [➞object_qualifier](triple__object_qualifier.md) - An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * [➞predicate](triple__predicate.md) - * [➞qualifier](triple__qualifier.md) - A qualifier for the statements, e.g. "NOT" for negation - * [➞subject](triple__subject.md) - * [➞subject_qualifier](triple__subject_qualifier.md) - An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -### Enums - - * [ChangeType](ChangeType.md) - * [NullDataOptions](NullDataOptions.md) - * [ProblemType](ProblemType.md) - -### Subsets - - -### Types - - -#### Built in - - * **Bool** - * **Curie** - * **Decimal** - * **ElementIdentifier** - * **NCName** - * **NodeIdentifier** - * **URI** - * **URIorCURIE** - * **XSDDate** - * **XSDDateTime** - * **XSDTime** - * **float** - * **int** - * **str** - -#### Defined - - * [Boolean](types/Boolean.md) (**Bool**) - A binary (true or false) value - * [Curie](types/Curie.md) (**Curie**) - a compact URI - * [Date](types/Date.md) (**XSDDate**) - a date (year, month and day) in an idealized calendar - * [DateOrDatetime](types/DateOrDatetime.md) (**str**) - Either a date or a datetime - * [Datetime](types/Datetime.md) (**XSDDateTime**) - The combination of a date and time - * [Decimal](types/Decimal.md) (**Decimal**) - A real number with arbitrary precision that conforms to the xsd:decimal specification - * [Double](types/Double.md) (**float**) - A real number that conforms to the xsd:double specification - * [Float](types/Float.md) (**float**) - A real number that conforms to the xsd:float specification - * [Integer](types/Integer.md) (**int**) - An integer - * [Jsonpath](types/Jsonpath.md) (**str**) - A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - * [Jsonpointer](types/Jsonpointer.md) (**str**) - A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - * [Ncname](types/Ncname.md) (**NCName**) - Prefix part of CURIE - * [Nodeidentifier](types/Nodeidentifier.md) (**NodeIdentifier**) - A URI, CURIE or BNODE that represents a node in a model. - * [Objectidentifier](types/Objectidentifier.md) (**ElementIdentifier**) - A URI or CURIE that represents an object in the model. - * [Sparqlpath](types/Sparqlpath.md) (**str**) - A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - * [String](types/String.md) (**str**) - A character string - * [Time](types/Time.md) (**XSDTime**) - A time object represents a (local) time of day, independent of any particular day - * [Uri](types/Uri.md) (**URI**) - a complete URI - * [Uriorcurie](types/Uriorcurie.md) (**URIorCURIE**) - a URI or a CURIE diff --git a/projects/ontology_issue/docs/publication__abstract.md b/projects/ontology_issue/docs/publication__abstract.md deleted file mode 100644 index 7e1c7ff37..000000000 --- a/projects/ontology_issue/docs/publication__abstract.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: abstract - - -The abstract of the publication - -URI: [oc:publication__abstract](http://w3id.org/ontogpt/ontology-class-templatepublication__abstract) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/ontology_issue/docs/publication__combined_text.md b/projects/ontology_issue/docs/publication__combined_text.md deleted file mode 100644 index de03f19fd..000000000 --- a/projects/ontology_issue/docs/publication__combined_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: combined_text - - - - -URI: [oc:publication__combined_text](http://w3id.org/ontogpt/ontology-class-templatepublication__combined_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/ontology_issue/docs/publication__full_text.md b/projects/ontology_issue/docs/publication__full_text.md deleted file mode 100644 index ae02a60d4..000000000 --- a/projects/ontology_issue/docs/publication__full_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: full_text - - -The full text of the publication - -URI: [oc:publication__full_text](http://w3id.org/ontogpt/ontology-class-templatepublication__full_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/ontology_issue/docs/publication__id.md b/projects/ontology_issue/docs/publication__id.md deleted file mode 100644 index 3fbcffacd..000000000 --- a/projects/ontology_issue/docs/publication__id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: id - - -The publication identifier - -URI: [oc:publication__id](http://w3id.org/ontogpt/ontology-class-templatepublication__id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/ontology_issue/docs/publication__title.md b/projects/ontology_issue/docs/publication__title.md deleted file mode 100644 index 5f9f7ed69..000000000 --- a/projects/ontology_issue/docs/publication__title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: title - - -The title of the publication - -URI: [oc:publication__title](http://w3id.org/ontogpt/ontology-class-templatepublication__title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/ontology_issue/docs/textWithTriples__publication.md b/projects/ontology_issue/docs/textWithTriples__publication.md deleted file mode 100644 index 27b0af18d..000000000 --- a/projects/ontology_issue/docs/textWithTriples__publication.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: publication - - - - -URI: [oc:textWithTriples__publication](http://w3id.org/ontogpt/ontology-class-templatetextWithTriples__publication) - - -## Domain and Range - -None → <sub>0..1</sub> [Publication](Publication.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/ontology_issue/docs/textWithTriples__triples.md b/projects/ontology_issue/docs/textWithTriples__triples.md deleted file mode 100644 index d3a729b64..000000000 --- a/projects/ontology_issue/docs/textWithTriples__triples.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: triples - - - - -URI: [oc:textWithTriples__triples](http://w3id.org/ontogpt/ontology-class-templatetextWithTriples__triples) - - -## Domain and Range - -None → <sub>0..\*</sub> [Triple](Triple.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/ontology_issue/docs/triple__object.md b/projects/ontology_issue/docs/triple__object.md deleted file mode 100644 index 19c663552..000000000 --- a/projects/ontology_issue/docs/triple__object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object - - - - -URI: [oc:triple__object](http://w3id.org/ontogpt/ontology-class-templatetriple__object) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/ontology_issue/docs/triple__object_qualifier.md b/projects/ontology_issue/docs/triple__object_qualifier.md deleted file mode 100644 index bead5d4a5..000000000 --- a/projects/ontology_issue/docs/triple__object_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_qualifier - - -An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - -URI: [oc:triple__object_qualifier](http://w3id.org/ontogpt/ontology-class-templatetriple__object_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/ontology_issue/docs/triple__predicate.md b/projects/ontology_issue/docs/triple__predicate.md deleted file mode 100644 index 425642196..000000000 --- a/projects/ontology_issue/docs/triple__predicate.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: predicate - - - - -URI: [oc:triple__predicate](http://w3id.org/ontogpt/ontology-class-templatetriple__predicate) - - -## Domain and Range - -None → <sub>0..1</sub> [RelationshipType](RelationshipType.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/ontology_issue/docs/triple__qualifier.md b/projects/ontology_issue/docs/triple__qualifier.md deleted file mode 100644 index 9277dabfe..000000000 --- a/projects/ontology_issue/docs/triple__qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: qualifier - - -A qualifier for the statements, e.g. "NOT" for negation - -URI: [oc:triple__qualifier](http://w3id.org/ontogpt/ontology-class-templatetriple__qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/ontology_issue/docs/triple__subject.md b/projects/ontology_issue/docs/triple__subject.md deleted file mode 100644 index 89487785e..000000000 --- a/projects/ontology_issue/docs/triple__subject.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject - - - - -URI: [oc:triple__subject](http://w3id.org/ontogpt/ontology-class-templatetriple__subject) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/ontology_issue/docs/triple__subject_qualifier.md b/projects/ontology_issue/docs/triple__subject_qualifier.md deleted file mode 100644 index e63c6bbd8..000000000 --- a/projects/ontology_issue/docs/triple__subject_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_qualifier - - -An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -URI: [oc:triple__subject_qualifier](http://w3id.org/ontogpt/ontology-class-templatetriple__subject_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/ontology_issue/docs/types/Boolean.md b/projects/ontology_issue/docs/types/Boolean.md deleted file mode 100644 index dc83a9c6e..000000000 --- a/projects/ontology_issue/docs/types/Boolean.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: boolean - - -A binary (true or false) value - -URI: [linkml:Boolean](https://w3id.org/linkml/Boolean) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Bool** | -| Representation | | bool | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Boolean | - diff --git a/projects/ontology_issue/docs/types/Curie.md b/projects/ontology_issue/docs/types/Curie.md deleted file mode 100644 index c1803f93f..000000000 --- a/projects/ontology_issue/docs/types/Curie.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: curie - - -a compact URI - -URI: [linkml:Curie](https://w3id.org/linkml/Curie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Curie** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations this MUST be expanded to a URI | -| | | in non-RDF serializations MAY be serialized as the compact representation | - diff --git a/projects/ontology_issue/docs/types/Date.md b/projects/ontology_issue/docs/types/Date.md deleted file mode 100644 index 06948af97..000000000 --- a/projects/ontology_issue/docs/types/Date.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: date - - -a date (year, month and day) in an idealized calendar - -URI: [linkml:Date](https://w3id.org/linkml/Date) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDate** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Date | - diff --git a/projects/ontology_issue/docs/types/DateOrDatetime.md b/projects/ontology_issue/docs/types/DateOrDatetime.md deleted file mode 100644 index ef983898d..000000000 --- a/projects/ontology_issue/docs/types/DateOrDatetime.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: date_or_datetime - - -Either a date or a datetime - -URI: [linkml:DateOrDatetime](https://w3id.org/linkml/DateOrDatetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/ontology_issue/docs/types/Datetime.md b/projects/ontology_issue/docs/types/Datetime.md deleted file mode 100644 index 9510454a8..000000000 --- a/projects/ontology_issue/docs/types/Datetime.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: datetime - - -The combination of a date and time - -URI: [linkml:Datetime](https://w3id.org/linkml/Datetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDateTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:DateTime | - diff --git a/projects/ontology_issue/docs/types/Decimal.md b/projects/ontology_issue/docs/types/Decimal.md deleted file mode 100644 index a7ba14a5d..000000000 --- a/projects/ontology_issue/docs/types/Decimal.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: decimal - - -A real number with arbitrary precision that conforms to the xsd:decimal specification - -URI: [linkml:Decimal](https://w3id.org/linkml/Decimal) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Decimal** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Broad Mappings:** | | schema:Number | - diff --git a/projects/ontology_issue/docs/types/Double.md b/projects/ontology_issue/docs/types/Double.md deleted file mode 100644 index cfe6d71e2..000000000 --- a/projects/ontology_issue/docs/types/Double.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: double - - -A real number that conforms to the xsd:double specification - -URI: [linkml:Double](https://w3id.org/linkml/Double) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Close Mappings:** | | schema:Float | - diff --git a/projects/ontology_issue/docs/types/Float.md b/projects/ontology_issue/docs/types/Float.md deleted file mode 100644 index 7b303f96f..000000000 --- a/projects/ontology_issue/docs/types/Float.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: float - - -A real number that conforms to the xsd:float specification - -URI: [linkml:Float](https://w3id.org/linkml/Float) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Float | - diff --git a/projects/ontology_issue/docs/types/Integer.md b/projects/ontology_issue/docs/types/Integer.md deleted file mode 100644 index 3cfcc66d9..000000000 --- a/projects/ontology_issue/docs/types/Integer.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: integer - - -An integer - -URI: [linkml:Integer](https://w3id.org/linkml/Integer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **int** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Integer | - diff --git a/projects/ontology_issue/docs/types/Jsonpath.md b/projects/ontology_issue/docs/types/Jsonpath.md deleted file mode 100644 index a03a58e67..000000000 --- a/projects/ontology_issue/docs/types/Jsonpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpath - - -A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpath](https://w3id.org/linkml/Jsonpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/ontology_issue/docs/types/Jsonpointer.md b/projects/ontology_issue/docs/types/Jsonpointer.md deleted file mode 100644 index a0e1ac492..000000000 --- a/projects/ontology_issue/docs/types/Jsonpointer.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpointer - - -A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpointer](https://w3id.org/linkml/Jsonpointer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/ontology_issue/docs/types/Ncname.md b/projects/ontology_issue/docs/types/Ncname.md deleted file mode 100644 index 710b0b04a..000000000 --- a/projects/ontology_issue/docs/types/Ncname.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: ncname - - -Prefix part of CURIE - -URI: [linkml:Ncname](https://w3id.org/linkml/Ncname) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NCName** | -| Representation | | str | diff --git a/projects/ontology_issue/docs/types/Nodeidentifier.md b/projects/ontology_issue/docs/types/Nodeidentifier.md deleted file mode 100644 index f0097cdf4..000000000 --- a/projects/ontology_issue/docs/types/Nodeidentifier.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: nodeidentifier - - -A URI, CURIE or BNODE that represents a node in a model. - -URI: [linkml:Nodeidentifier](https://w3id.org/linkml/Nodeidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NodeIdentifier** | -| Representation | | str | diff --git a/projects/ontology_issue/docs/types/Objectidentifier.md b/projects/ontology_issue/docs/types/Objectidentifier.md deleted file mode 100644 index 454ba6be6..000000000 --- a/projects/ontology_issue/docs/types/Objectidentifier.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: objectidentifier - - -A URI or CURIE that represents an object in the model. - -URI: [linkml:Objectidentifier](https://w3id.org/linkml/Objectidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **ElementIdentifier** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | Used for inheritance and type checking | - diff --git a/projects/ontology_issue/docs/types/Sparqlpath.md b/projects/ontology_issue/docs/types/Sparqlpath.md deleted file mode 100644 index fd99a927e..000000000 --- a/projects/ontology_issue/docs/types/Sparqlpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: sparqlpath - - -A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - -URI: [linkml:Sparqlpath](https://w3id.org/linkml/Sparqlpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/ontology_issue/docs/types/String.md b/projects/ontology_issue/docs/types/String.md deleted file mode 100644 index 6e61d7081..000000000 --- a/projects/ontology_issue/docs/types/String.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: string - - -A character string - -URI: [linkml:String](https://w3id.org/linkml/String) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Text | - diff --git a/projects/ontology_issue/docs/types/Time.md b/projects/ontology_issue/docs/types/Time.md deleted file mode 100644 index 2b8652bcd..000000000 --- a/projects/ontology_issue/docs/types/Time.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: time - - -A time object represents a (local) time of day, independent of any particular day - -URI: [linkml:Time](https://w3id.org/linkml/Time) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Time | - diff --git a/projects/ontology_issue/docs/types/Uri.md b/projects/ontology_issue/docs/types/Uri.md deleted file mode 100644 index 343807a5e..000000000 --- a/projects/ontology_issue/docs/types/Uri.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: uri - - -a complete URI - -URI: [linkml:Uri](https://w3id.org/linkml/Uri) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URI** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node | -| **Close Mappings:** | | schema:URL | - diff --git a/projects/ontology_issue/docs/types/Uriorcurie.md b/projects/ontology_issue/docs/types/Uriorcurie.md deleted file mode 100644 index 2f7b65087..000000000 --- a/projects/ontology_issue/docs/types/Uriorcurie.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: uriorcurie - - -a URI or a CURIE - -URI: [linkml:Uriorcurie](https://w3id.org/linkml/Uriorcurie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URIorCURIE** | -| Representation | | str | diff --git a/projects/ontology_issue/excel/ontology_issue.xlsx b/projects/ontology_issue/excel/ontology_issue.xlsx deleted file mode 100644 index 0cb00b42a..000000000 Binary files a/projects/ontology_issue/excel/ontology_issue.xlsx and /dev/null differ diff --git a/projects/ontology_issue/graphql/ontology_issue.graphql b/projects/ontology_issue/graphql/ontology_issue.graphql deleted file mode 100644 index 20d44419e..000000000 --- a/projects/ontology_issue/graphql/ontology_issue.graphql +++ /dev/null @@ -1,94 +0,0 @@ -type AnnotatorResult - { - subjectText: String - objectId: String - objectText: String - } - -type Any - { - } - -interface CompoundExpression - { - } - -type ExtractionResult - { - inputId: String - inputTitle: String - inputText: String - rawCompletionOutput: String - prompt: String - extractedObject: Any - namedEntities: [Any] - } - -interface NamedEntity - { - id: String! - label: String - } - -type OntologyChange - { - description: String - category: ChangeType - about: [OntologyClass] - } - -type OntologyClass - { - id: String! - label: String - } - -type OntologyIssue - { - title: String - summary: String - status: String - domains: [OntologyClass] - problemList: [OntologyProblem] - proposedChanges: [OntologyChange] - } - -type OntologyProblem - { - description: String - severity: String - category: ProblemType - about: [OntologyClass] - } - -type Publication - { - id: String - title: String - abstract: String - combinedText: String - fullText: String - } - -type RelationshipType - { - id: String! - label: String - } - -type TextWithTriples - { - publication: Publication - triples: [Triple] - } - -interface Triple - { - subject: NamedEntity - predicate: RelationshipType - object: NamedEntity - qualifier: String - subjectQualifier: NamedEntity - objectQualifier: NamedEntity - } - diff --git a/projects/ontology_issue/jsonld/ontology_issue.context.jsonld b/projects/ontology_issue/jsonld/ontology_issue.context.jsonld deleted file mode 100644 index 3fd4e3438..000000000 --- a/projects/ontology_issue/jsonld/ontology_issue.context.jsonld +++ /dev/null @@ -1,151 +0,0 @@ -{ - "comments": { - "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2023-08-07T10:55:28", - "source": "ontology_issue.yaml" - }, - "@context": { - "RO": { - "@id": "http://purl.obolibrary.org/obo/RO_", - "@prefix": true - }, - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "linkml": "https://w3id.org/linkml/", - "oc": { - "@id": "http://w3id.org/ontogpt/ontology-class-template", - "@prefix": true - }, - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "skos": "http://www.w3.org/2004/02/skos/core#", - "@vocab": "http://w3id.org/ontogpt/ontology-class-template", - "object_id": { - "@id": "core:object_id" - }, - "object_text": { - "@id": "core:object_text" - }, - "subject_text": { - "@id": "core:subject_text" - }, - "extracted_object": { - "@type": "@id", - "@id": "core:extracted_object" - }, - "input_id": { - "@id": "core:input_id" - }, - "input_text": { - "@id": "core:input_text" - }, - "input_title": { - "@id": "core:input_title" - }, - "named_entities": { - "@type": "@id", - "@id": "core:named_entities" - }, - "prompt": { - "@id": "core:prompt" - }, - "raw_completion_output": { - "@id": "core:raw_completion_output" - }, - "id": { - "@id": "core:id" - }, - "label": { - "@id": "rdfs:label" - }, - "about": { - "@type": "@id" - }, - "category": { - "@context": { - "@vocab": "@null", - "text": "skos:notation", - "description": "skos:prefLabel", - "meaning": "@id" - } - }, - "domains": { - "@type": "@id" - }, - "problem_list": { - "@type": "@id" - }, - "proposed_changes": { - "@type": "@id" - }, - "abstract": { - "@id": "core:abstract" - }, - "combined_text": { - "@id": "core:combined_text" - }, - "full_text": { - "@id": "core:full_text" - }, - "title": { - "@id": "core:title" - }, - "publication": { - "@type": "@id", - "@id": "core:publication" - }, - "triples": { - "@type": "@id", - "@id": "core:triples" - }, - "object": { - "@type": "@id", - "@id": "core:object" - }, - "object_qualifier": { - "@type": "@id", - "@id": "core:object_qualifier" - }, - "predicate": { - "@type": "@id", - "@id": "core:predicate" - }, - "qualifier": { - "@id": "core:qualifier" - }, - "subject": { - "@type": "@id", - "@id": "core:subject" - }, - "subject_qualifier": { - "@type": "@id", - "@id": "core:subject_qualifier" - }, - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } - } -} diff --git a/projects/ontology_issue/jsonld/ontology_issue.jsonld b/projects/ontology_issue/jsonld/ontology_issue.jsonld deleted file mode 100644 index 6fc9554aa..000000000 --- a/projects/ontology_issue/jsonld/ontology_issue.jsonld +++ /dev/null @@ -1,1428 +0,0 @@ -{ - "name": "ontology-issue", - "description": "A data model for representing the contents of a GitHub issue on an ontology tracker", - "title": "Ontology Issue Data Model", - "id": "https://w3id.org/ontogpt/ontology_issue", - "imports": [ - "linkml:types", - "core" - ], - "license": "https://creativecommons.org/publicdomain/zero/1.0/", - "prefixes": [ - { - "prefix_prefix": "linkml", - "prefix_reference": "https://w3id.org/linkml/" - }, - { - "prefix_prefix": "oc", - "prefix_reference": "http://w3id.org/ontogpt/ontology-class-template" - } - ], - "default_prefix": "oc", - "default_range": "string", - "types": [ - { - "name": "string", - "definition_uri": "https://w3id.org/linkml/String", - "description": "A character string", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Text" - ], - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "@type": "TypeDefinition" - }, - { - "name": "integer", - "definition_uri": "https://w3id.org/linkml/Integer", - "description": "An integer", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Integer" - ], - "base": "int", - "uri": "http://www.w3.org/2001/XMLSchema#integer", - "@type": "TypeDefinition" - }, - { - "name": "boolean", - "definition_uri": "https://w3id.org/linkml/Boolean", - "description": "A binary (true or false) value", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Boolean" - ], - "base": "Bool", - "uri": "http://www.w3.org/2001/XMLSchema#boolean", - "repr": "bool", - "@type": "TypeDefinition" - }, - { - "name": "float", - "definition_uri": "https://w3id.org/linkml/Float", - "description": "A real number that conforms to the xsd:float specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#float", - "@type": "TypeDefinition" - }, - { - "name": "double", - "definition_uri": "https://w3id.org/linkml/Double", - "description": "A real number that conforms to the xsd:double specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#double", - "@type": "TypeDefinition" - }, - { - "name": "decimal", - "definition_uri": "https://w3id.org/linkml/Decimal", - "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "broad_mappings": [ - "schema:Number" - ], - "base": "Decimal", - "uri": "http://www.w3.org/2001/XMLSchema#decimal", - "@type": "TypeDefinition" - }, - { - "name": "time", - "definition_uri": "https://w3id.org/linkml/Time", - "description": "A time object represents a (local) time of day, independent of any particular day", - "notes": [ - "URI is dateTime because OWL reasoners do not work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Time" - ], - "base": "XSDTime", - "uri": "http://www.w3.org/2001/XMLSchema#time", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date", - "definition_uri": "https://w3id.org/linkml/Date", - "description": "a date (year, month and day) in an idealized calendar", - "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Date" - ], - "base": "XSDDate", - "uri": "http://www.w3.org/2001/XMLSchema#date", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "datetime", - "definition_uri": "https://w3id.org/linkml/Datetime", - "description": "The combination of a date and time", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:DateTime" - ], - "base": "XSDDateTime", - "uri": "http://www.w3.org/2001/XMLSchema#dateTime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date_or_datetime", - "definition_uri": "https://w3id.org/linkml/DateOrDatetime", - "description": "Either a date or a datetime", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "https://w3id.org/linkml/DateOrDatetime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uriorcurie", - "definition_uri": "https://w3id.org/linkml/Uriorcurie", - "description": "a URI or a CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "URIorCURIE", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "curie", - "definition_uri": "https://w3id.org/linkml/Curie", - "conforms_to": "https://www.w3.org/TR/curie/", - "description": "a compact URI", - "comments": [ - "in RDF serializations this MUST be expanded to a URI", - "in non-RDF serializations MAY be serialized as the compact representation" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "Curie", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uri", - "definition_uri": "https://w3id.org/linkml/Uri", - "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", - "description": "a complete URI", - "comments": [ - "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:URL" - ], - "base": "URI", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "ncname", - "definition_uri": "https://w3id.org/linkml/Ncname", - "description": "Prefix part of CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NCName", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "objectidentifier", - "definition_uri": "https://w3id.org/linkml/Objectidentifier", - "description": "A URI or CURIE that represents an object in the model.", - "comments": [ - "Used for inheritance and type checking" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "ElementIdentifier", - "uri": "http://www.w3.org/ns/shex#iri", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "nodeidentifier", - "definition_uri": "https://w3id.org/linkml/Nodeidentifier", - "description": "A URI, CURIE or BNODE that represents a node in a model.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NodeIdentifier", - "uri": "http://www.w3.org/ns/shex#nonLiteral", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpointer", - "definition_uri": "https://w3id.org/linkml/Jsonpointer", - "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901", - "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpath", - "definition_uri": "https://w3id.org/linkml/Jsonpath", - "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html", - "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "sparqlpath", - "definition_uri": "https://w3id.org/linkml/Sparqlpath", - "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths", - "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - } - ], - "enums": [ - { - "name": "ProblemType", - "definition_uri": "http://w3id.org/ontogpt/ontology-class-templateProblemType", - "from_schema": "https://w3id.org/ontogpt/ontology_issue", - "permissible_values": [ - { - "text": "UNKNOWN" - }, - { - "text": "TYPO" - }, - { - "text": "BAD_XREF" - }, - { - "text": "MISSING_DEFINITION" - }, - { - "text": "MISSING_PARENT" - }, - { - "text": "BAD_RELATIONSHIP" - }, - { - "text": "OTHER" - } - ] - }, - { - "name": "ChangeType", - "definition_uri": "http://w3id.org/ontogpt/ontology-class-templateChangeType", - "from_schema": "https://w3id.org/ontogpt/ontology_issue", - "permissible_values": [ - { - "text": "UNKNOWN" - }, - { - "text": "CHANGE_DEFINITION" - }, - { - "text": "CHANGE_LABEL" - }, - { - "text": "CHANGE_XREF" - }, - { - "text": "MOVE_TERM" - } - ] - }, - { - "name": "NullDataOptions", - "definition_uri": "http://w3id.org/ontogpt/core/NullDataOptions", - "from_schema": "http://w3id.org/ontogpt/core", - "permissible_values": [ - { - "text": "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "meaning": "NCIT:C149701" - }, - { - "text": "NOT_APPLICABLE", - "meaning": "NCIT:C18902", - "aliases": [ - "not applicable", - "N/A" - ] - }, - { - "text": "NOT_MENTIONED" - } - ] - } - ], - "slots": [ - { - "name": "ontologyIssue__title", - "description": "the title of the issue", - "from_schema": "https://w3id.org/ontogpt/ontology_issue", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templatetitle", - "alias": "title", - "owner": "OntologyIssue", - "domain_of": [ - "OntologyIssue" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "ontologyIssue__summary", - "annotations": [ - { - "tag": "prompt", - "value": "a high level one or two line summary of the issue, e.g. \"the definition of the class 'bone' is too vague\"", - "@type": "Annotation" - } - ], - "description": "a high level summary", - "from_schema": "https://w3id.org/ontogpt/ontology_issue", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templatesummary", - "alias": "summary", - "owner": "OntologyIssue", - "domain_of": [ - "OntologyIssue" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "ontologyIssue__status", - "from_schema": "https://w3id.org/ontogpt/ontology_issue", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templatestatus", - "alias": "status", - "owner": "OntologyIssue", - "domain_of": [ - "OntologyIssue" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "ontologyIssue__domains", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of grouping terms in the ontology.", - "@type": "Annotation" - } - ], - "description": "What part of the ontology does this pertain to.", - "from_schema": "https://w3id.org/ontogpt/ontology_issue", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templatedomains", - "multivalued": true, - "alias": "domains", - "owner": "OntologyIssue", - "domain_of": [ - "OntologyIssue" - ], - "range": "OntologyClass", - "@type": "SlotDefinition" - }, - { - "name": "ontologyIssue__problem_list", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of problems each written as a simple statement. For example \"T cell is classified in the wrong place\"", - "@type": "Annotation" - } - ], - "description": "A list of problems stated at a high level", - "from_schema": "https://w3id.org/ontogpt/ontology_issue", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templateproblem_list", - "multivalued": true, - "alias": "problem_list", - "owner": "OntologyIssue", - "domain_of": [ - "OntologyIssue" - ], - "range": "OntologyProblem", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "ontologyIssue__proposed_changes", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of grouping terms in the ontology. Example terms will be high level terms in the relevant ontology, e.g. \"skeletal system\" for an anatomy ontology.", - "@type": "Annotation" - } - ], - "description": "What part of the ontology does this pertain to.", - "from_schema": "https://w3id.org/ontogpt/ontology_issue", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templateproposed_changes", - "multivalued": true, - "alias": "proposed_changes", - "owner": "OntologyIssue", - "domain_of": [ - "OntologyIssue" - ], - "range": "OntologyChange", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "ontologyProblem__description", - "description": "A succinct description of the problem", - "from_schema": "https://w3id.org/ontogpt/ontology_issue", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templatedescription", - "alias": "description", - "owner": "OntologyProblem", - "domain_of": [ - "OntologyProblem" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "ontologyProblem__severity", - "description": "How severe is this problem?", - "from_schema": "https://w3id.org/ontogpt/ontology_issue", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templateseverity", - "alias": "severity", - "owner": "OntologyProblem", - "domain_of": [ - "OntologyProblem" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "ontologyProblem__category", - "description": "What category does this problem fall into?", - "from_schema": "https://w3id.org/ontogpt/ontology_issue", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templatecategory", - "alias": "category", - "owner": "OntologyProblem", - "domain_of": [ - "OntologyProblem" - ], - "range": "ProblemType", - "@type": "SlotDefinition" - }, - { - "name": "ontologyProblem__about", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of terms in the ontology that are problematic.", - "@type": "Annotation" - } - ], - "description": "What terms in the ontology is this problem about?", - "from_schema": "https://w3id.org/ontogpt/ontology_issue", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templateabout", - "multivalued": true, - "alias": "about", - "owner": "OntologyProblem", - "domain_of": [ - "OntologyProblem" - ], - "range": "OntologyClass", - "@type": "SlotDefinition" - }, - { - "name": "ontologyChange__description", - "description": "A succinct description of the proposed change", - "from_schema": "https://w3id.org/ontogpt/ontology_issue", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templatedescription", - "alias": "description", - "owner": "OntologyChange", - "domain_of": [ - "OntologyChange" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "ontologyChange__category", - "description": "What kind of change?", - "from_schema": "https://w3id.org/ontogpt/ontology_issue", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templatecategory", - "alias": "category", - "owner": "OntologyChange", - "domain_of": [ - "OntologyChange" - ], - "range": "ChangeType", - "@type": "SlotDefinition" - }, - { - "name": "ontologyChange__about", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of specific terms in the ontology which will be affected by the change.", - "@type": "Annotation" - } - ], - "description": "What terms in the ontology will this change affect?", - "from_schema": "https://w3id.org/ontogpt/ontology_issue", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templateabout", - "multivalued": true, - "alias": "about", - "owner": "OntologyChange", - "domain_of": [ - "OntologyChange" - ], - "range": "OntologyClass", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_id", - "alias": "input_id", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_title", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_title", - "alias": "input_title", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_text", - "alias": "input_text", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__raw_completion_output", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/raw_completion_output", - "alias": "raw_completion_output", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__prompt", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/prompt", - "alias": "prompt", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__extracted_object", - "description": "The complex objects extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/extracted_object", - "alias": "extracted_object", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__named_entities", - "description": "Named entities extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/named_entities", - "multivalued": true, - "alias": "named_entities", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "identifier": true, - "alias": "id", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "required": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "from_schema": "http://w3id.org/ontogpt/core", - "aliases": [ - "name" - ], - "mappings": [ - "http://example.org/UNKNOWN/rdfs/label" - ], - "slot_uri": "http://example.org/UNKNOWN/rdfs/label", - "alias": "label", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject", - "alias": "subject", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__predicate", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/predicate", - "alias": "predicate", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "triple__object", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object", - "alias": "object", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/qualifier", - "alias": "qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_qualifier", - "alias": "subject_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_qualifier", - "alias": "object_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/publication", - "alias": "publication", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__triples", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/triples", - "multivalued": true, - "alias": "triples", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "publication__id", - "description": "The publication identifier", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "alias": "id", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__title", - "description": "The title of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/title", - "alias": "title", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__abstract", - "description": "The abstract of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/abstract", - "alias": "abstract", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__combined_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/combined_text", - "alias": "combined_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__full_text", - "description": "The full text of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/full_text", - "alias": "full_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__subject_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_text", - "alias": "subject_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_id", - "alias": "object_id", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_text", - "alias": "object_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - } - ], - "classes": [ - { - "name": "OntologyIssue", - "definition_uri": "http://w3id.org/ontogpt/ontology-class-templateOntologyIssue", - "from_schema": "https://w3id.org/ontogpt/ontology_issue", - "slots": [ - "ontologyIssue__title", - "ontologyIssue__summary", - "ontologyIssue__status", - "ontologyIssue__domains", - "ontologyIssue__problem_list", - "ontologyIssue__proposed_changes" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "title", - "description": "the title of the issue", - "@type": "SlotDefinition" - }, - { - "name": "summary", - "annotations": [ - { - "tag": "prompt", - "value": "a high level one or two line summary of the issue, e.g. \"the definition of the class 'bone' is too vague\"", - "@type": "Annotation" - } - ], - "description": "a high level summary", - "@type": "SlotDefinition" - }, - { - "name": "status", - "@type": "SlotDefinition" - }, - { - "name": "domains", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of grouping terms in the ontology.", - "@type": "Annotation" - } - ], - "description": "What part of the ontology does this pertain to.", - "multivalued": true, - "range": "OntologyClass", - "@type": "SlotDefinition" - }, - { - "name": "problem_list", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of problems each written as a simple statement. For example \"T cell is classified in the wrong place\"", - "@type": "Annotation" - } - ], - "description": "A list of problems stated at a high level", - "multivalued": true, - "range": "OntologyProblem", - "@type": "SlotDefinition" - }, - { - "name": "proposed_changes", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of grouping terms in the ontology. Example terms will be high level terms in the relevant ontology, e.g. \"skeletal system\" for an anatomy ontology.", - "@type": "Annotation" - } - ], - "description": "What part of the ontology does this pertain to.", - "multivalued": true, - "range": "OntologyChange", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/ontology-class-templateOntologyIssue", - "tree_root": true, - "@type": "ClassDefinition" - }, - { - "name": "OntologyClass", - "definition_uri": "http://w3id.org/ontogpt/ontology-class-templateOntologyClass", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:go", - "@type": "Annotation" - } - ], - "from_schema": "https://w3id.org/ontogpt/ontology_issue", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/ontology-class-templateOntologyClass", - "@type": "ClassDefinition" - }, - { - "name": "OntologyProblem", - "definition_uri": "http://w3id.org/ontogpt/ontology-class-templateOntologyProblem", - "from_schema": "https://w3id.org/ontogpt/ontology_issue", - "is_a": "CompoundExpression", - "slots": [ - "ontologyProblem__description", - "ontologyProblem__severity", - "ontologyProblem__category", - "ontologyProblem__about" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "description", - "description": "A succinct description of the problem", - "@type": "SlotDefinition" - }, - { - "name": "severity", - "description": "How severe is this problem?", - "@type": "SlotDefinition" - }, - { - "name": "category", - "description": "What category does this problem fall into?", - "range": "ProblemType", - "@type": "SlotDefinition" - }, - { - "name": "about", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of terms in the ontology that are problematic.", - "@type": "Annotation" - } - ], - "description": "What terms in the ontology is this problem about?", - "multivalued": true, - "range": "OntologyClass", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/ontology-class-templateOntologyProblem", - "@type": "ClassDefinition" - }, - { - "name": "OntologyChange", - "definition_uri": "http://w3id.org/ontogpt/ontology-class-templateOntologyChange", - "from_schema": "https://w3id.org/ontogpt/ontology_issue", - "is_a": "CompoundExpression", - "slots": [ - "ontologyChange__description", - "ontologyChange__category", - "ontologyChange__about" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "description", - "description": "A succinct description of the proposed change", - "@type": "SlotDefinition" - }, - { - "name": "category", - "description": "What kind of change?", - "range": "ChangeType", - "@type": "SlotDefinition" - }, - { - "name": "about", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of specific terms in the ontology which will be affected by the change.", - "@type": "Annotation" - } - ], - "description": "What terms in the ontology will this change affect?", - "multivalued": true, - "range": "OntologyClass", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/ontology-class-templateOntologyChange", - "@type": "ClassDefinition" - }, - { - "name": "Any", - "definition_uri": "http://w3id.org/ontogpt/core/Any", - "from_schema": "http://w3id.org/ontogpt/core", - "mappings": [ - "linkml:Any" - ], - "slot_usage": {}, - "class_uri": "https://w3id.org/linkml/Any", - "@type": "ClassDefinition" - }, - { - "name": "ExtractionResult", - "definition_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "description": "A result of extracting knowledge on text", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "extractionResult__input_id", - "extractionResult__input_title", - "extractionResult__input_text", - "extractionResult__raw_completion_output", - "extractionResult__prompt", - "extractionResult__extracted_object", - "extractionResult__named_entities" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "input_id", - "@type": "SlotDefinition" - }, - { - "name": "input_title", - "@type": "SlotDefinition" - }, - { - "name": "input_text", - "@type": "SlotDefinition" - }, - { - "name": "raw_completion_output", - "@type": "SlotDefinition" - }, - { - "name": "prompt", - "@type": "SlotDefinition" - }, - { - "name": "extracted_object", - "description": "The complex objects extracted from the text", - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "named_entities", - "description": "Named entities extracted from the text", - "multivalued": true, - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "@type": "ClassDefinition" - }, - { - "name": "NamedEntity", - "definition_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "identifier": true, - "@type": "SlotDefinition" - }, - { - "name": "label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "aliases": [ - "name" - ], - "slot_uri": "rdfs:label", - "range": "string", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "@type": "ClassDefinition" - }, - { - "name": "CompoundExpression", - "definition_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "@type": "ClassDefinition" - }, - { - "name": "Triple", - "definition_uri": "http://w3id.org/ontogpt/core/Triple", - "description": "Abstract parent for Relation Extraction tasks", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "CompoundExpression", - "abstract": true, - "slots": [ - "triple__subject", - "triple__predicate", - "triple__object", - "triple__qualifier", - "triple__subject_qualifier", - "triple__object_qualifier" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "predicate", - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "object", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Triple", - "@type": "ClassDefinition" - }, - { - "name": "TextWithTriples", - "definition_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "textWithTriples__publication", - "textWithTriples__triples" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "triples", - "multivalued": true, - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "@type": "ClassDefinition" - }, - { - "name": "RelationshipType", - "id_prefixes": [ - "RO", - "biolink" - ], - "definition_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "@type": "ClassDefinition" - }, - { - "name": "Publication", - "definition_uri": "http://w3id.org/ontogpt/core/Publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "publication__id", - "publication__title", - "publication__abstract", - "publication__combined_text", - "publication__full_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "description": "The publication identifier", - "@type": "SlotDefinition" - }, - { - "name": "title", - "description": "The title of the publication", - "@type": "SlotDefinition" - }, - { - "name": "abstract", - "description": "The abstract of the publication", - "@type": "SlotDefinition" - }, - { - "name": "combined_text", - "@type": "SlotDefinition" - }, - { - "name": "full_text", - "description": "The full text of the publication", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Publication", - "@type": "ClassDefinition" - }, - { - "name": "AnnotatorResult", - "definition_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "annotatorResult__subject_text", - "annotatorResult__object_id", - "annotatorResult__object_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject_text", - "@type": "SlotDefinition" - }, - { - "name": "object_id", - "@type": "SlotDefinition" - }, - { - "name": "object_text", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "@type": "ClassDefinition" - } - ], - "metamodel_version": "1.7.0", - "source_file": "ontology_issue.yaml", - "source_file_date": "2023-06-17T15:11:19", - "source_file_size": 3383, - "generation_date": "2023-08-07T10:55:29", - "@type": "SchemaDefinition", - "@context": [ - "projects/ontology_issue/jsonld/ontology_issue.context.jsonld", - "https://w3id.org/linkml/types.context.jsonld", - "core.context.jsonld", - { - "@base": "http://w3id.org/ontogpt/ontology-class-template" - } - ] -} diff --git a/projects/ontology_issue/jsonschema/ontology_issue.schema.json b/projects/ontology_issue/jsonschema/ontology_issue.schema.json deleted file mode 100644 index 211e455ba..000000000 --- a/projects/ontology_issue/jsonschema/ontology_issue.schema.json +++ /dev/null @@ -1,310 +0,0 @@ -{ - "$defs": { - "AnnotatorResult": { - "additionalProperties": false, - "description": "", - "properties": { - "object_id": { - "type": "string" - }, - "object_text": { - "type": "string" - }, - "subject_text": { - "type": "string" - } - }, - "title": "AnnotatorResult", - "type": "object" - }, - "Any": { - "additionalProperties": true, - "description": "", - "title": "Any", - "type": "object" - }, - "ChangeType": { - "description": "", - "enum": [ - "UNKNOWN", - "CHANGE_DEFINITION", - "CHANGE_LABEL", - "CHANGE_XREF", - "MOVE_TERM" - ], - "title": "ChangeType", - "type": "string" - }, - "ExtractionResult": { - "additionalProperties": false, - "description": "A result of extracting knowledge on text", - "properties": { - "extracted_object": { - "$ref": "#/$defs/Any", - "description": "The complex objects extracted from the text" - }, - "input_id": { - "type": "string" - }, - "input_text": { - "type": "string" - }, - "input_title": { - "type": "string" - }, - "named_entities": { - "description": "Named entities extracted from the text", - "items": { - "$ref": "#/$defs/Any" - }, - "type": "array" - }, - "prompt": { - "type": "string" - }, - "raw_completion_output": { - "type": "string" - } - }, - "title": "ExtractionResult", - "type": "object" - }, - "NullDataOptions": { - "description": "", - "enum": [ - "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "NOT_APPLICABLE", - "NOT_MENTIONED" - ], - "title": "NullDataOptions", - "type": "string" - }, - "OntologyChange": { - "additionalProperties": false, - "description": "", - "properties": { - "about": { - "description": "What terms in the ontology will this change affect?", - "items": { - "type": "string" - }, - "type": "array" - }, - "category": { - "$ref": "#/$defs/ChangeType", - "description": "What kind of change?" - }, - "description": { - "description": "A succinct description of the proposed change", - "type": "string" - } - }, - "title": "OntologyChange", - "type": "object" - }, - "OntologyClass": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "OntologyClass", - "type": "object" - }, - "OntologyIssue": { - "additionalProperties": false, - "description": "", - "properties": { - "domains": { - "description": "What part of the ontology does this pertain to.", - "items": { - "type": "string" - }, - "type": "array" - }, - "problem_list": { - "description": "A list of problems stated at a high level", - "items": { - "$ref": "#/$defs/OntologyProblem" - }, - "type": "array" - }, - "proposed_changes": { - "description": "What part of the ontology does this pertain to.", - "items": { - "$ref": "#/$defs/OntologyChange" - }, - "type": "array" - }, - "status": { - "type": "string" - }, - "summary": { - "description": "a high level summary", - "type": "string" - }, - "title": { - "description": "the title of the issue", - "type": "string" - } - }, - "title": "OntologyIssue", - "type": "object" - }, - "OntologyProblem": { - "additionalProperties": false, - "description": "", - "properties": { - "about": { - "description": "What terms in the ontology is this problem about?", - "items": { - "type": "string" - }, - "type": "array" - }, - "category": { - "$ref": "#/$defs/ProblemType", - "description": "What category does this problem fall into?" - }, - "description": { - "description": "A succinct description of the problem", - "type": "string" - }, - "severity": { - "description": "How severe is this problem?", - "type": "string" - } - }, - "title": "OntologyProblem", - "type": "object" - }, - "ProblemType": { - "description": "", - "enum": [ - "UNKNOWN", - "TYPO", - "BAD_XREF", - "MISSING_DEFINITION", - "MISSING_PARENT", - "BAD_RELATIONSHIP", - "OTHER" - ], - "title": "ProblemType", - "type": "string" - }, - "Publication": { - "additionalProperties": false, - "description": "", - "properties": { - "abstract": { - "description": "The abstract of the publication", - "type": "string" - }, - "combined_text": { - "type": "string" - }, - "full_text": { - "description": "The full text of the publication", - "type": "string" - }, - "id": { - "description": "The publication identifier", - "type": "string" - }, - "title": { - "description": "The title of the publication", - "type": "string" - } - }, - "title": "Publication", - "type": "object" - }, - "RelationshipType": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "RelationshipType", - "type": "object" - }, - "TextWithTriples": { - "additionalProperties": false, - "description": "", - "properties": { - "publication": { - "$ref": "#/$defs/Publication" - }, - "triples": { - "items": { - "$ref": "#/$defs/Triple" - }, - "type": "array" - } - }, - "title": "TextWithTriples", - "type": "object" - } - }, - "$id": "https://w3id.org/ontogpt/ontology_issue", - "$schema": "http://json-schema.org/draft-07/schema#", - "additionalProperties": true, - "metamodel_version": "1.7.0", - "properties": { - "domains": { - "description": "What part of the ontology does this pertain to.", - "items": { - "type": "string" - }, - "type": "array" - }, - "problem_list": { - "description": "A list of problems stated at a high level", - "items": { - "$ref": "#/$defs/OntologyProblem" - }, - "type": "array" - }, - "proposed_changes": { - "description": "What part of the ontology does this pertain to.", - "items": { - "$ref": "#/$defs/OntologyChange" - }, - "type": "array" - }, - "status": { - "type": "string" - }, - "summary": { - "description": "a high level summary", - "type": "string" - }, - "title": { - "description": "the title of the issue", - "type": "string" - } - }, - "title": "ontology-issue", - "type": "object", - "version": null -} \ No newline at end of file diff --git a/projects/ontology_issue/ontology_issue.py b/projects/ontology_issue/ontology_issue.py deleted file mode 100644 index 13815b537..000000000 --- a/projects/ontology_issue/ontology_issue.py +++ /dev/null @@ -1,550 +0,0 @@ -# Auto generated from ontology_issue.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-08-07T10:55:36 -# Schema: ontology-issue -# -# id: https://w3id.org/ontogpt/ontology_issue -# description: A data model for representing the contents of a GitHub issue on an ontology tracker -# license: https://creativecommons.org/publicdomain/zero/1.0/ - -import dataclasses -import sys -import re -from jsonasobj2 import JsonObj, as_dict -from typing import Optional, List, Union, Dict, ClassVar, Any -from dataclasses import dataclass -from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions - -from linkml_runtime.utils.slot import Slot -from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode -from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int -from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs -from linkml_runtime.utils.formatutils import camelcase, underscore, sfx -from linkml_runtime.utils.enumerations import EnumDefinitionImpl -from rdflib import Namespace, URIRef -from linkml_runtime.utils.curienamespace import CurieNamespace -from linkml_runtime.linkml_model.types import String - -metamodel_version = "1.7.0" -version = None - -# Overwrite dataclasses _init_fn to add **kwargs in __init__ -dataclasses._init_fn = dataclasses_init_fn_with_kwargs - -# Namespaces -RO = CurieNamespace('RO', 'http://purl.obolibrary.org/obo/RO_') -BIOLINK = CurieNamespace('biolink', 'http://example.org/UNKNOWN/biolink/') -CORE = CurieNamespace('core', 'http://w3id.org/ontogpt/core/') -LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') -OC = CurieNamespace('oc', 'http://w3id.org/ontogpt/ontology-class-template') -RDFS = CurieNamespace('rdfs', 'http://example.org/UNKNOWN/rdfs/') -DEFAULT_ = OC - - -# Types - -# Class references -class NamedEntityId(extended_str): - pass - - -class OntologyClassId(NamedEntityId): - pass - - -class RelationshipTypeId(NamedEntityId): - pass - - -@dataclass -class OntologyIssue(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = OC.OntologyIssue - class_class_curie: ClassVar[str] = "oc:OntologyIssue" - class_name: ClassVar[str] = "OntologyIssue" - class_model_uri: ClassVar[URIRef] = OC.OntologyIssue - - title: Optional[str] = None - summary: Optional[str] = None - status: Optional[str] = None - domains: Optional[Union[Union[str, OntologyClassId], List[Union[str, OntologyClassId]]]] = empty_list() - problem_list: Optional[Union[Union[dict, "OntologyProblem"], List[Union[dict, "OntologyProblem"]]]] = empty_list() - proposed_changes: Optional[Union[Union[dict, "OntologyChange"], List[Union[dict, "OntologyChange"]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.title is not None and not isinstance(self.title, str): - self.title = str(self.title) - - if self.summary is not None and not isinstance(self.summary, str): - self.summary = str(self.summary) - - if self.status is not None and not isinstance(self.status, str): - self.status = str(self.status) - - if not isinstance(self.domains, list): - self.domains = [self.domains] if self.domains is not None else [] - self.domains = [v if isinstance(v, OntologyClassId) else OntologyClassId(v) for v in self.domains] - - if not isinstance(self.problem_list, list): - self.problem_list = [self.problem_list] if self.problem_list is not None else [] - self.problem_list = [v if isinstance(v, OntologyProblem) else OntologyProblem(**as_dict(v)) for v in self.problem_list] - - if not isinstance(self.proposed_changes, list): - self.proposed_changes = [self.proposed_changes] if self.proposed_changes is not None else [] - self.proposed_changes = [v if isinstance(v, OntologyChange) else OntologyChange(**as_dict(v)) for v in self.proposed_changes] - - super().__post_init__(**kwargs) - - -Any = Any - -@dataclass -class ExtractionResult(YAMLRoot): - """ - A result of extracting knowledge on text - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.ExtractionResult - class_class_curie: ClassVar[str] = "core:ExtractionResult" - class_name: ClassVar[str] = "ExtractionResult" - class_model_uri: ClassVar[URIRef] = OC.ExtractionResult - - input_id: Optional[str] = None - input_title: Optional[str] = None - input_text: Optional[str] = None - raw_completion_output: Optional[str] = None - prompt: Optional[str] = None - extracted_object: Optional[Union[dict, Any]] = None - named_entities: Optional[Union[Union[dict, Any], List[Union[dict, Any]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.input_id is not None and not isinstance(self.input_id, str): - self.input_id = str(self.input_id) - - if self.input_title is not None and not isinstance(self.input_title, str): - self.input_title = str(self.input_title) - - if self.input_text is not None and not isinstance(self.input_text, str): - self.input_text = str(self.input_text) - - if self.raw_completion_output is not None and not isinstance(self.raw_completion_output, str): - self.raw_completion_output = str(self.raw_completion_output) - - if self.prompt is not None and not isinstance(self.prompt, str): - self.prompt = str(self.prompt) - - super().__post_init__(**kwargs) - - -@dataclass -class NamedEntity(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.NamedEntity - class_class_curie: ClassVar[str] = "core:NamedEntity" - class_name: ClassVar[str] = "NamedEntity" - class_model_uri: ClassVar[URIRef] = OC.NamedEntity - - id: Union[str, NamedEntityId] = None - label: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, NamedEntityId): - self.id = NamedEntityId(self.id) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - super().__post_init__(**kwargs) - - -@dataclass -class OntologyClass(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = OC.OntologyClass - class_class_curie: ClassVar[str] = "oc:OntologyClass" - class_name: ClassVar[str] = "OntologyClass" - class_model_uri: ClassVar[URIRef] = OC.OntologyClass - - id: Union[str, OntologyClassId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, OntologyClassId): - self.id = OntologyClassId(self.id) - - super().__post_init__(**kwargs) - - -class CompoundExpression(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.CompoundExpression - class_class_curie: ClassVar[str] = "core:CompoundExpression" - class_name: ClassVar[str] = "CompoundExpression" - class_model_uri: ClassVar[URIRef] = OC.CompoundExpression - - -@dataclass -class OntologyProblem(CompoundExpression): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = OC.OntologyProblem - class_class_curie: ClassVar[str] = "oc:OntologyProblem" - class_name: ClassVar[str] = "OntologyProblem" - class_model_uri: ClassVar[URIRef] = OC.OntologyProblem - - description: Optional[str] = None - severity: Optional[str] = None - category: Optional[Union[str, "ProblemType"]] = None - about: Optional[Union[Union[str, OntologyClassId], List[Union[str, OntologyClassId]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.description is not None and not isinstance(self.description, str): - self.description = str(self.description) - - if self.severity is not None and not isinstance(self.severity, str): - self.severity = str(self.severity) - - if self.category is not None and not isinstance(self.category, ProblemType): - self.category = ProblemType(self.category) - - if not isinstance(self.about, list): - self.about = [self.about] if self.about is not None else [] - self.about = [v if isinstance(v, OntologyClassId) else OntologyClassId(v) for v in self.about] - - super().__post_init__(**kwargs) - - -@dataclass -class OntologyChange(CompoundExpression): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = OC.OntologyChange - class_class_curie: ClassVar[str] = "oc:OntologyChange" - class_name: ClassVar[str] = "OntologyChange" - class_model_uri: ClassVar[URIRef] = OC.OntologyChange - - description: Optional[str] = None - category: Optional[Union[str, "ChangeType"]] = None - about: Optional[Union[Union[str, OntologyClassId], List[Union[str, OntologyClassId]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.description is not None and not isinstance(self.description, str): - self.description = str(self.description) - - if self.category is not None and not isinstance(self.category, ChangeType): - self.category = ChangeType(self.category) - - if not isinstance(self.about, list): - self.about = [self.about] if self.about is not None else [] - self.about = [v if isinstance(v, OntologyClassId) else OntologyClassId(v) for v in self.about] - - super().__post_init__(**kwargs) - - -@dataclass -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Triple - class_class_curie: ClassVar[str] = "core:Triple" - class_name: ClassVar[str] = "Triple" - class_model_uri: ClassVar[URIRef] = OC.Triple - - subject: Optional[Union[str, NamedEntityId]] = None - predicate: Optional[Union[str, RelationshipTypeId]] = None - object: Optional[Union[str, NamedEntityId]] = None - qualifier: Optional[str] = None - subject_qualifier: Optional[Union[str, NamedEntityId]] = None - object_qualifier: Optional[Union[str, NamedEntityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, NamedEntityId): - self.subject = NamedEntityId(self.subject) - - if self.predicate is not None and not isinstance(self.predicate, RelationshipTypeId): - self.predicate = RelationshipTypeId(self.predicate) - - if self.object is not None and not isinstance(self.object, NamedEntityId): - self.object = NamedEntityId(self.object) - - if self.qualifier is not None and not isinstance(self.qualifier, str): - self.qualifier = str(self.qualifier) - - if self.subject_qualifier is not None and not isinstance(self.subject_qualifier, NamedEntityId): - self.subject_qualifier = NamedEntityId(self.subject_qualifier) - - if self.object_qualifier is not None and not isinstance(self.object_qualifier, NamedEntityId): - self.object_qualifier = NamedEntityId(self.object_qualifier) - - super().__post_init__(**kwargs) - - -@dataclass -class TextWithTriples(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.TextWithTriples - class_class_curie: ClassVar[str] = "core:TextWithTriples" - class_name: ClassVar[str] = "TextWithTriples" - class_model_uri: ClassVar[URIRef] = OC.TextWithTriples - - publication: Optional[Union[dict, "Publication"]] = None - triples: Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.publication is not None and not isinstance(self.publication, Publication): - self.publication = Publication(**as_dict(self.publication)) - - if not isinstance(self.triples, list): - self.triples = [self.triples] if self.triples is not None else [] - self.triples = [v if isinstance(v, Triple) else Triple(**as_dict(v)) for v in self.triples] - - super().__post_init__(**kwargs) - - -@dataclass -class RelationshipType(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.RelationshipType - class_class_curie: ClassVar[str] = "core:RelationshipType" - class_name: ClassVar[str] = "RelationshipType" - class_model_uri: ClassVar[URIRef] = OC.RelationshipType - - id: Union[str, RelationshipTypeId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, RelationshipTypeId): - self.id = RelationshipTypeId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Publication(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Publication - class_class_curie: ClassVar[str] = "core:Publication" - class_name: ClassVar[str] = "Publication" - class_model_uri: ClassVar[URIRef] = OC.Publication - - id: Optional[str] = None - title: Optional[str] = None - abstract: Optional[str] = None - combined_text: Optional[str] = None - full_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.id is not None and not isinstance(self.id, str): - self.id = str(self.id) - - if self.title is not None and not isinstance(self.title, str): - self.title = str(self.title) - - if self.abstract is not None and not isinstance(self.abstract, str): - self.abstract = str(self.abstract) - - if self.combined_text is not None and not isinstance(self.combined_text, str): - self.combined_text = str(self.combined_text) - - if self.full_text is not None and not isinstance(self.full_text, str): - self.full_text = str(self.full_text) - - super().__post_init__(**kwargs) - - -@dataclass -class AnnotatorResult(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.AnnotatorResult - class_class_curie: ClassVar[str] = "core:AnnotatorResult" - class_name: ClassVar[str] = "AnnotatorResult" - class_model_uri: ClassVar[URIRef] = OC.AnnotatorResult - - subject_text: Optional[str] = None - object_id: Optional[str] = None - object_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject_text is not None and not isinstance(self.subject_text, str): - self.subject_text = str(self.subject_text) - - if self.object_id is not None and not isinstance(self.object_id, str): - self.object_id = str(self.object_id) - - if self.object_text is not None and not isinstance(self.object_text, str): - self.object_text = str(self.object_text) - - super().__post_init__(**kwargs) - - -# Enumerations -class ProblemType(EnumDefinitionImpl): - - UNKNOWN = PermissibleValue(text="UNKNOWN") - TYPO = PermissibleValue(text="TYPO") - BAD_XREF = PermissibleValue(text="BAD_XREF") - MISSING_DEFINITION = PermissibleValue(text="MISSING_DEFINITION") - MISSING_PARENT = PermissibleValue(text="MISSING_PARENT") - BAD_RELATIONSHIP = PermissibleValue(text="BAD_RELATIONSHIP") - OTHER = PermissibleValue(text="OTHER") - - _defn = EnumDefinition( - name="ProblemType", - ) - -class ChangeType(EnumDefinitionImpl): - - UNKNOWN = PermissibleValue(text="UNKNOWN") - CHANGE_DEFINITION = PermissibleValue(text="CHANGE_DEFINITION") - CHANGE_LABEL = PermissibleValue(text="CHANGE_LABEL") - CHANGE_XREF = PermissibleValue(text="CHANGE_XREF") - MOVE_TERM = PermissibleValue(text="MOVE_TERM") - - _defn = EnumDefinition( - name="ChangeType", - ) - -class NullDataOptions(EnumDefinitionImpl): - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = PermissibleValue(text="UNSPECIFIED_METHOD_OF_ADMINISTRATION", - meaning=NCIT.C149701) - NOT_APPLICABLE = PermissibleValue(text="NOT_APPLICABLE", - meaning=NCIT.C18902) - NOT_MENTIONED = PermissibleValue(text="NOT_MENTIONED") - - _defn = EnumDefinition( - name="NullDataOptions", - ) - -# Slots -class slots: - pass - -slots.ontologyIssue__title = Slot(uri=OC.title, name="ontologyIssue__title", curie=OC.curie('title'), - model_uri=OC.ontologyIssue__title, domain=None, range=Optional[str]) - -slots.ontologyIssue__summary = Slot(uri=OC.summary, name="ontologyIssue__summary", curie=OC.curie('summary'), - model_uri=OC.ontologyIssue__summary, domain=None, range=Optional[str]) - -slots.ontologyIssue__status = Slot(uri=OC.status, name="ontologyIssue__status", curie=OC.curie('status'), - model_uri=OC.ontologyIssue__status, domain=None, range=Optional[str]) - -slots.ontologyIssue__domains = Slot(uri=OC.domains, name="ontologyIssue__domains", curie=OC.curie('domains'), - model_uri=OC.ontologyIssue__domains, domain=None, range=Optional[Union[Union[str, OntologyClassId], List[Union[str, OntologyClassId]]]]) - -slots.ontologyIssue__problem_list = Slot(uri=OC.problem_list, name="ontologyIssue__problem_list", curie=OC.curie('problem_list'), - model_uri=OC.ontologyIssue__problem_list, domain=None, range=Optional[Union[Union[dict, OntologyProblem], List[Union[dict, OntologyProblem]]]]) - -slots.ontologyIssue__proposed_changes = Slot(uri=OC.proposed_changes, name="ontologyIssue__proposed_changes", curie=OC.curie('proposed_changes'), - model_uri=OC.ontologyIssue__proposed_changes, domain=None, range=Optional[Union[Union[dict, OntologyChange], List[Union[dict, OntologyChange]]]]) - -slots.ontologyProblem__description = Slot(uri=OC.description, name="ontologyProblem__description", curie=OC.curie('description'), - model_uri=OC.ontologyProblem__description, domain=None, range=Optional[str]) - -slots.ontologyProblem__severity = Slot(uri=OC.severity, name="ontologyProblem__severity", curie=OC.curie('severity'), - model_uri=OC.ontologyProblem__severity, domain=None, range=Optional[str]) - -slots.ontologyProblem__category = Slot(uri=OC.category, name="ontologyProblem__category", curie=OC.curie('category'), - model_uri=OC.ontologyProblem__category, domain=None, range=Optional[Union[str, "ProblemType"]]) - -slots.ontologyProblem__about = Slot(uri=OC.about, name="ontologyProblem__about", curie=OC.curie('about'), - model_uri=OC.ontologyProblem__about, domain=None, range=Optional[Union[Union[str, OntologyClassId], List[Union[str, OntologyClassId]]]]) - -slots.ontologyChange__description = Slot(uri=OC.description, name="ontologyChange__description", curie=OC.curie('description'), - model_uri=OC.ontologyChange__description, domain=None, range=Optional[str]) - -slots.ontologyChange__category = Slot(uri=OC.category, name="ontologyChange__category", curie=OC.curie('category'), - model_uri=OC.ontologyChange__category, domain=None, range=Optional[Union[str, "ChangeType"]]) - -slots.ontologyChange__about = Slot(uri=OC.about, name="ontologyChange__about", curie=OC.curie('about'), - model_uri=OC.ontologyChange__about, domain=None, range=Optional[Union[Union[str, OntologyClassId], List[Union[str, OntologyClassId]]]]) - -slots.extractionResult__input_id = Slot(uri=CORE.input_id, name="extractionResult__input_id", curie=CORE.curie('input_id'), - model_uri=OC.extractionResult__input_id, domain=None, range=Optional[str]) - -slots.extractionResult__input_title = Slot(uri=CORE.input_title, name="extractionResult__input_title", curie=CORE.curie('input_title'), - model_uri=OC.extractionResult__input_title, domain=None, range=Optional[str]) - -slots.extractionResult__input_text = Slot(uri=CORE.input_text, name="extractionResult__input_text", curie=CORE.curie('input_text'), - model_uri=OC.extractionResult__input_text, domain=None, range=Optional[str]) - -slots.extractionResult__raw_completion_output = Slot(uri=CORE.raw_completion_output, name="extractionResult__raw_completion_output", curie=CORE.curie('raw_completion_output'), - model_uri=OC.extractionResult__raw_completion_output, domain=None, range=Optional[str]) - -slots.extractionResult__prompt = Slot(uri=CORE.prompt, name="extractionResult__prompt", curie=CORE.curie('prompt'), - model_uri=OC.extractionResult__prompt, domain=None, range=Optional[str]) - -slots.extractionResult__extracted_object = Slot(uri=CORE.extracted_object, name="extractionResult__extracted_object", curie=CORE.curie('extracted_object'), - model_uri=OC.extractionResult__extracted_object, domain=None, range=Optional[Union[dict, Any]]) - -slots.extractionResult__named_entities = Slot(uri=CORE.named_entities, name="extractionResult__named_entities", curie=CORE.curie('named_entities'), - model_uri=OC.extractionResult__named_entities, domain=None, range=Optional[Union[Union[dict, Any], List[Union[dict, Any]]]]) - -slots.namedEntity__id = Slot(uri=CORE.id, name="namedEntity__id", curie=CORE.curie('id'), - model_uri=OC.namedEntity__id, domain=None, range=URIRef) - -slots.namedEntity__label = Slot(uri=RDFS.label, name="namedEntity__label", curie=RDFS.curie('label'), - model_uri=OC.namedEntity__label, domain=None, range=Optional[str]) - -slots.triple__subject = Slot(uri=CORE.subject, name="triple__subject", curie=CORE.curie('subject'), - model_uri=OC.triple__subject, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__predicate = Slot(uri=CORE.predicate, name="triple__predicate", curie=CORE.curie('predicate'), - model_uri=OC.triple__predicate, domain=None, range=Optional[Union[str, RelationshipTypeId]]) - -slots.triple__object = Slot(uri=CORE.object, name="triple__object", curie=CORE.curie('object'), - model_uri=OC.triple__object, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__qualifier = Slot(uri=CORE.qualifier, name="triple__qualifier", curie=CORE.curie('qualifier'), - model_uri=OC.triple__qualifier, domain=None, range=Optional[str]) - -slots.triple__subject_qualifier = Slot(uri=CORE.subject_qualifier, name="triple__subject_qualifier", curie=CORE.curie('subject_qualifier'), - model_uri=OC.triple__subject_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__object_qualifier = Slot(uri=CORE.object_qualifier, name="triple__object_qualifier", curie=CORE.curie('object_qualifier'), - model_uri=OC.triple__object_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.textWithTriples__publication = Slot(uri=CORE.publication, name="textWithTriples__publication", curie=CORE.curie('publication'), - model_uri=OC.textWithTriples__publication, domain=None, range=Optional[Union[dict, Publication]]) - -slots.textWithTriples__triples = Slot(uri=CORE.triples, name="textWithTriples__triples", curie=CORE.curie('triples'), - model_uri=OC.textWithTriples__triples, domain=None, range=Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]]) - -slots.publication__id = Slot(uri=CORE.id, name="publication__id", curie=CORE.curie('id'), - model_uri=OC.publication__id, domain=None, range=Optional[str]) - -slots.publication__title = Slot(uri=CORE.title, name="publication__title", curie=CORE.curie('title'), - model_uri=OC.publication__title, domain=None, range=Optional[str]) - -slots.publication__abstract = Slot(uri=CORE.abstract, name="publication__abstract", curie=CORE.curie('abstract'), - model_uri=OC.publication__abstract, domain=None, range=Optional[str]) - -slots.publication__combined_text = Slot(uri=CORE.combined_text, name="publication__combined_text", curie=CORE.curie('combined_text'), - model_uri=OC.publication__combined_text, domain=None, range=Optional[str]) - -slots.publication__full_text = Slot(uri=CORE.full_text, name="publication__full_text", curie=CORE.curie('full_text'), - model_uri=OC.publication__full_text, domain=None, range=Optional[str]) - -slots.annotatorResult__subject_text = Slot(uri=CORE.subject_text, name="annotatorResult__subject_text", curie=CORE.curie('subject_text'), - model_uri=OC.annotatorResult__subject_text, domain=None, range=Optional[str]) - -slots.annotatorResult__object_id = Slot(uri=CORE.object_id, name="annotatorResult__object_id", curie=CORE.curie('object_id'), - model_uri=OC.annotatorResult__object_id, domain=None, range=Optional[str]) - -slots.annotatorResult__object_text = Slot(uri=CORE.object_text, name="annotatorResult__object_text", curie=CORE.curie('object_text'), - model_uri=OC.annotatorResult__object_text, domain=None, range=Optional[str]) \ No newline at end of file diff --git a/projects/ontology_issue/owl/ontology_issue.owl.ttl b/projects/ontology_issue/owl/ontology_issue.owl.ttl deleted file mode 100644 index a60c4b124..000000000 --- a/projects/ontology_issue/owl/ontology_issue.owl.ttl +++ /dev/null @@ -1,552 +0,0 @@ -@prefix IAO: <http://purl.obolibrary.org/obo/IAO_> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix oc: <http://w3id.org/ontogpt/ontology-class-template> . -@prefix owl: <http://www.w3.org/2002/07/owl#> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . -@prefix skos: <http://www.w3.org/2004/02/skos/core#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -linkml:SubsetDefinition a owl:Class ; - rdfs:label "subset_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" . - -linkml:TypeDefinition a owl:Class ; - rdfs:label "type_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" ; - linkml:mixins "type_expression" . - -linkml:topValue a owl:DatatypeProperty ; - rdfs:label "value" . - -<https://w3id.org/ontogpt/ontology_issue> a owl:Ontology ; - rdfs:label "ontology-issue" ; - IAO:0000700 <http://w3id.org/ontogpt/core/AnnotatorResult>, - <http://w3id.org/ontogpt/core/Any>, - <http://w3id.org/ontogpt/core/CompoundExpression>, - <http://w3id.org/ontogpt/core/ExtractionResult>, - <http://w3id.org/ontogpt/core/NamedEntity>, - <http://w3id.org/ontogpt/core/Publication>, - <http://w3id.org/ontogpt/core/TextWithTriples>, - oc:OntologyIssue ; - linkml:classes "{'OntologyIssue': ClassDefinition(name='OntologyIssue', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/ontology-class-templateOntologyIssue', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/ontology_issue', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['ontologyIssue__title', 'ontologyIssue__summary', 'ontologyIssue__status', 'ontologyIssue__domains', 'ontologyIssue__problem_list', 'ontologyIssue__proposed_changes'], slot_usage={}, attributes={'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the title of the issue', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'summary': SlotDefinition(name='summary', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='a high level one or two line summary of the issue, e.g. \"the definition of the class \\'bone\\' is too vague\"', extensions={}, annotations={})}, description='a high level summary', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'status': SlotDefinition(name='status', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'domains': SlotDefinition(name='domains', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of grouping terms in the ontology.', extensions={}, annotations={})}, description='What part of the ontology does this pertain to.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='OntologyClass', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'problem_list': SlotDefinition(name='problem_list', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of problems each written as a simple statement. For example \"T cell is classified in the wrong place\"', extensions={}, annotations={})}, description='A list of problems stated at a high level', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='OntologyProblem', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'proposed_changes': SlotDefinition(name='proposed_changes', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of grouping terms in the ontology. Example terms will be high level terms in the relevant ontology, e.g. \"skeletal system\" for an anatomy ontology.', extensions={}, annotations={})}, description='What part of the ontology does this pertain to.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='OntologyChange', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='oc:OntologyIssue', subclass_of=None, union_of=[], defining_slots=[], tree_root=True, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'OntologyClass': ClassDefinition(name='OntologyClass', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/ontology-class-templateOntologyClass', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:go', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/ontology_issue', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='oc:OntologyClass', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'OntologyProblem': ClassDefinition(name='OntologyProblem', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/ontology-class-templateOntologyProblem', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/ontology_issue', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['ontologyProblem__description', 'ontologyProblem__severity', 'ontologyProblem__category', 'ontologyProblem__about'], slot_usage={}, attributes={'description': SlotDefinition(name='description', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A succinct description of the problem', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'severity': SlotDefinition(name='severity', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='How severe is this problem?', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'category': SlotDefinition(name='category', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='What category does this problem fall into?', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ProblemType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'about': SlotDefinition(name='about', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of terms in the ontology that are problematic.', extensions={}, annotations={})}, description='What terms in the ontology is this problem about?', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='OntologyClass', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='oc:OntologyProblem', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'OntologyChange': ClassDefinition(name='OntologyChange', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/ontology-class-templateOntologyChange', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/ontology_issue', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['ontologyChange__description', 'ontologyChange__category', 'ontologyChange__about'], slot_usage={}, attributes={'description': SlotDefinition(name='description', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A succinct description of the proposed change', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'category': SlotDefinition(name='category', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='What kind of change?', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ChangeType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'about': SlotDefinition(name='about', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of specific terms in the ontology which will be affected by the change.', extensions={}, annotations={})}, description='What terms in the ontology will this change affect?', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='OntologyClass', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='oc:OntologyChange', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Any': ClassDefinition(name='Any', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Any', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=['linkml:Any'], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='linkml:Any', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ExtractionResult': ClassDefinition(name='ExtractionResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/ExtractionResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A result of extracting knowledge on text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['extractionResult__input_id', 'extractionResult__input_title', 'extractionResult__input_text', 'extractionResult__raw_completion_output', 'extractionResult__prompt', 'extractionResult__extracted_object', 'extractionResult__named_entities'], slot_usage={}, attributes={'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:ExtractionResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'NamedEntity': ClassDefinition(name='NamedEntity', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NamedEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:NamedEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'CompoundExpression': ClassDefinition(name='CompoundExpression', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/CompoundExpression', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='core:CompoundExpression', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Triple': ClassDefinition(name='Triple', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Triple', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Abstract parent for Relation Extraction tasks', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['triple__subject', 'triple__predicate', 'triple__object', 'triple__qualifier', 'triple__subject_qualifier', 'triple__object_qualifier'], slot_usage={}, attributes={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Triple', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'TextWithTriples': ClassDefinition(name='TextWithTriples', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/TextWithTriples', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['textWithTriples__publication', 'textWithTriples__triples'], slot_usage={}, attributes={'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:TextWithTriples', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'RelationshipType': ClassDefinition(name='RelationshipType', id_prefixes=['RO', 'biolink'], definition_uri='http://w3id.org/ontogpt/core/RelationshipType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='core:RelationshipType', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Publication': ClassDefinition(name='Publication', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Publication', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['publication__id', 'publication__title', 'publication__abstract', 'publication__combined_text', 'publication__full_text'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Publication', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'AnnotatorResult': ClassDefinition(name='AnnotatorResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/AnnotatorResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['annotatorResult__subject_text', 'annotatorResult__object_id', 'annotatorResult__object_text'], slot_usage={}, attributes={'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:AnnotatorResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={})}" ; - linkml:enums "{'ProblemType': EnumDefinition(name='ProblemType', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/ontology-class-templateProblemType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/ontology_issue', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'UNKNOWN': PermissibleValue(text='UNKNOWN', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'TYPO': PermissibleValue(text='TYPO', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'BAD_XREF': PermissibleValue(text='BAD_XREF', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'MISSING_DEFINITION': PermissibleValue(text='MISSING_DEFINITION', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'MISSING_PARENT': PermissibleValue(text='MISSING_PARENT', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'BAD_RELATIONSHIP': PermissibleValue(text='BAD_RELATIONSHIP', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'OTHER': PermissibleValue(text='OTHER', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[]), 'ChangeType': EnumDefinition(name='ChangeType', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/ontology-class-templateChangeType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/ontology_issue', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'UNKNOWN': PermissibleValue(text='UNKNOWN', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'CHANGE_DEFINITION': PermissibleValue(text='CHANGE_DEFINITION', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'CHANGE_LABEL': PermissibleValue(text='CHANGE_LABEL', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'CHANGE_XREF': PermissibleValue(text='CHANGE_XREF', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'MOVE_TERM': PermissibleValue(text='MOVE_TERM', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[]), 'NullDataOptions': EnumDefinition(name='NullDataOptions', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NullDataOptions', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'UNSPECIFIED_METHOD_OF_ADMINISTRATION': PermissibleValue(text='UNSPECIFIED_METHOD_OF_ADMINISTRATION', description=None, meaning='NCIT:C149701', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_APPLICABLE': PermissibleValue(text='NOT_APPLICABLE', description=None, meaning='NCIT:C18902', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['not applicable', 'N/A'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_MENTIONED': PermissibleValue(text='NOT_MENTIONED', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[])}" ; - linkml:id "https://w3id.org/ontogpt/ontology_issue" ; - linkml:imports "core", - "linkml:types" ; - linkml:types "{'string': TypeDefinition(name='string', id_prefixes=[], definition_uri='https://w3id.org/linkml/String', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A character string', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Text'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'integer': TypeDefinition(name='integer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Integer', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An integer', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Integer'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='int', uri='xsd:integer', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'boolean': TypeDefinition(name='boolean', id_prefixes=[], definition_uri='https://w3id.org/linkml/Boolean', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A binary (true or false) value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Boolean'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Bool', uri='xsd:boolean', repr='bool', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'float': TypeDefinition(name='float', id_prefixes=[], definition_uri='https://w3id.org/linkml/Float', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:float specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Float'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:float', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'double': TypeDefinition(name='double', id_prefixes=[], definition_uri='https://w3id.org/linkml/Double', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:double specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:Float'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:double', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'decimal': TypeDefinition(name='decimal', id_prefixes=[], definition_uri='https://w3id.org/linkml/Decimal', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number with arbitrary precision that conforms to the xsd:decimal specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=['schema:Number'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Decimal', uri='xsd:decimal', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'time': TypeDefinition(name='time', id_prefixes=[], definition_uri='https://w3id.org/linkml/Time', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A time object represents a (local) time of day, independent of any particular day', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=['URI is dateTime because OWL reasoners do not work with straight date or time'], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Time'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDTime', uri='xsd:time', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date': TypeDefinition(name='date', id_prefixes=[], definition_uri='https://w3id.org/linkml/Date', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a date (year, month and day) in an idealized calendar', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[\"URI is dateTime because OWL reasoners don't work with straight date or time\"], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Date'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDate', uri='xsd:date', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'datetime': TypeDefinition(name='datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/Datetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The combination of a date and time', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:DateTime'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDateTime', uri='xsd:dateTime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date_or_datetime': TypeDefinition(name='date_or_datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/DateOrDatetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Either a date or a datetime', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='linkml:DateOrDatetime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uriorcurie': TypeDefinition(name='uriorcurie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uriorcurie', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a URI or a CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URIorCURIE', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'curie': TypeDefinition(name='curie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Curie', local_names={}, conforms_to='https://www.w3.org/TR/curie/', implements=[], extensions={}, annotations={}, description='a compact URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations this MUST be expanded to a URI', 'in non-RDF serializations MAY be serialized as the compact representation'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Curie', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uri': TypeDefinition(name='uri', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uri', local_names={}, conforms_to='https://www.ietf.org/rfc/rfc3987.txt', implements=[], extensions={}, annotations={}, description='a complete URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:URL'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URI', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ncname': TypeDefinition(name='ncname', id_prefixes=[], definition_uri='https://w3id.org/linkml/Ncname', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Prefix part of CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NCName', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'objectidentifier': TypeDefinition(name='objectidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Objectidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI or CURIE that represents an object in the model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['Used for inheritance and type checking'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='ElementIdentifier', uri='shex:iri', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'nodeidentifier': TypeDefinition(name='nodeidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Nodeidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI, CURIE or BNODE that represents a node in a model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NodeIdentifier', uri='shex:nonLiteral', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpointer': TypeDefinition(name='jsonpointer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpointer', local_names={}, conforms_to='https://datatracker.ietf.org/doc/html/rfc6901', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpath': TypeDefinition(name='jsonpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpath', local_names={}, conforms_to='https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sparqlpath': TypeDefinition(name='sparqlpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Sparqlpath', local_names={}, conforms_to='https://www.w3.org/TR/sparql11-query/#propertypaths', implements=[], extensions={}, annotations={}, description='A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "AnnotatorResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_text> ] ; - linkml:attributes "{'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/ExtractionResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ExtractionResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/prompt> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/extracted_object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_id> ], - [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/named_entities> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_title> ] ; - skos:definition "A result of extracting knowledge on text" ; - linkml:attributes "{'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/TextWithTriples> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TextWithTriples" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Publication> ; - owl:onProperty <http://w3id.org/ontogpt/core/publication> ], - [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Triple> ; - owl:onProperty <http://w3id.org/ontogpt/core/triples> ] ; - linkml:attributes "{'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/abstract> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "abstract" ; - rdfs:range linkml:String ; - skos:definition "The abstract of the publication" . - -<http://w3id.org/ontogpt/core/combined_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "combined_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/extracted_object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "extracted_object" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "The complex objects extracted from the text" . - -<http://w3id.org/ontogpt/core/full_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "full_text" ; - rdfs:range linkml:String ; - skos:definition "The full text of the publication" . - -<http://w3id.org/ontogpt/core/input_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_title" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/named_entities> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "named_entities" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "Named entities extracted from the text" . - -<http://w3id.org/ontogpt/core/object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/object_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/object_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" . - -<http://w3id.org/ontogpt/core/object_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/predicate> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "predicate" ; - rdfs:range <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/prompt> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "prompt" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/publication> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "publication" ; - oc:prompt.skip "true" ; - rdfs:range <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "qualifier" ; - rdfs:range linkml:String ; - skos:definition "A qualifier for the statements, e.g. \"NOT\" for negation" . - -<http://w3id.org/ontogpt/core/raw_completion_output> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "raw_completion_output" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/subject> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/subject_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" . - -<http://w3id.org/ontogpt/core/subject_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "title" ; - rdfs:range linkml:String ; - skos:definition "The title of the publication" . - -<http://w3id.org/ontogpt/core/triples> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "triples" ; - rdfs:range <http://w3id.org/ontogpt/core/Triple> . - -oc:OntologyIssue a owl:Class, - linkml:ClassDefinition ; - rdfs:label "OntologyIssue" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty oc:summary ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty oc:title ], - [ a owl:Restriction ; - owl:allValuesFrom oc:OntologyProblem ; - owl:onProperty oc:problem_list ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty oc:status ], - [ a owl:Restriction ; - owl:allValuesFrom oc:OntologyChange ; - owl:onProperty oc:proposed_changes ], - [ a owl:Restriction ; - owl:allValuesFrom oc:OntologyClass ; - owl:onProperty oc:domains ] ; - linkml:attributes "{'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the title of the issue', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'summary': SlotDefinition(name='summary', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='a high level one or two line summary of the issue, e.g. \"the definition of the class \\'bone\\' is too vague\"', extensions={}, annotations={})}, description='a high level summary', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'status': SlotDefinition(name='status', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'domains': SlotDefinition(name='domains', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of grouping terms in the ontology.', extensions={}, annotations={})}, description='What part of the ontology does this pertain to.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='OntologyClass', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'problem_list': SlotDefinition(name='problem_list', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of problems each written as a simple statement. For example \"T cell is classified in the wrong place\"', extensions={}, annotations={})}, description='A list of problems stated at a high level', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='OntologyProblem', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'proposed_changes': SlotDefinition(name='proposed_changes', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of grouping terms in the ontology. Example terms will be high level terms in the relevant ontology, e.g. \"skeletal system\" for an anatomy ontology.', extensions={}, annotations={})}, description='What part of the ontology does this pertain to.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='OntologyChange', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -oc:domains a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "domains" ; - oc:prompt "semicolon-separated list of grouping terms in the ontology." ; - rdfs:range oc:OntologyClass ; - skos:definition "What part of the ontology does this pertain to." . - -oc:problem_list a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "problem_list" ; - oc:prompt "semicolon-separated list of problems each written as a simple statement. For example \"T cell is classified in the wrong place\"" ; - rdfs:range oc:OntologyProblem ; - skos:definition "A list of problems stated at a high level" . - -oc:proposed_changes a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "proposed_changes" ; - oc:prompt "semicolon-separated list of grouping terms in the ontology. Example terms will be high level terms in the relevant ontology, e.g. \"skeletal system\" for an anatomy ontology." ; - rdfs:range oc:OntologyChange ; - skos:definition "What part of the ontology does this pertain to." . - -oc:severity a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "severity" ; - rdfs:range linkml:String ; - skos:definition "How severe is this problem?" . - -oc:status a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "status" ; - rdfs:range linkml:String . - -oc:summary a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "summary" ; - oc:prompt "a high level one or two line summary of the issue, e.g. \"the definition of the class 'bone' is too vague\"" ; - rdfs:range linkml:String ; - skos:definition "a high level summary" . - -oc:title a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "title" ; - rdfs:range linkml:String ; - skos:definition "the title of the issue" . - -<http://example.org/UNKNOWN/rdfs/label> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "label" ; - oc:owl "AnnotationProperty, AnnotationAssertion" ; - rdfs:range linkml:String ; - skos:altLabel "name" ; - skos:definition "The label (name) of the named thing" ; - skos:exactMatch <http://example.org/UNKNOWN/rdfs/label> . - -<http://purl.obolibrary.org/obo/NCIT_C149701> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "UNSPECIFIED_METHOD_OF_ADMINISTRATION" . - -<http://purl.obolibrary.org/obo/NCIT_C18902> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_APPLICABLE" . - -<http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_MENTIONED" . - -<http://w3id.org/ontogpt/core/RelationshipType> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "RelationshipType" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/Triple> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Triple" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/RelationshipType> ; - owl:onProperty <http://w3id.org/ontogpt/core/predicate> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_qualifier> ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - skos:definition "Abstract parent for Relation Extraction tasks" ; - linkml:attributes "{'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -<http://w3id.org/ontogpt/core/id> a owl:ObjectProperty, - linkml:SlotDefinition . - -<http://w3id.org/ontogpt/ontology-class-templateChangeType#CHANGE_DEFINITION> a oc:ChangeType, - owl:Class ; - rdfs:label "CHANGE_DEFINITION" . - -<http://w3id.org/ontogpt/ontology-class-templateChangeType#CHANGE_LABEL> a oc:ChangeType, - owl:Class ; - rdfs:label "CHANGE_LABEL" . - -<http://w3id.org/ontogpt/ontology-class-templateChangeType#CHANGE_XREF> a oc:ChangeType, - owl:Class ; - rdfs:label "CHANGE_XREF" . - -<http://w3id.org/ontogpt/ontology-class-templateChangeType#MOVE_TERM> a oc:ChangeType, - owl:Class ; - rdfs:label "MOVE_TERM" . - -<http://w3id.org/ontogpt/ontology-class-templateChangeType#UNKNOWN> a oc:ChangeType, - owl:Class ; - rdfs:label "UNKNOWN" . - -oc:OntologyChange a owl:Class, - linkml:ClassDefinition ; - rdfs:label "OntologyChange" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty oc:description ], - [ a owl:Restriction ; - owl:allValuesFrom oc:OntologyClass ; - owl:onProperty oc:about ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass oc:ChangeType ; - owl:onProperty oc:category ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - linkml:attributes "{'description': SlotDefinition(name='description', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A succinct description of the proposed change', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'category': SlotDefinition(name='category', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='What kind of change?', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ChangeType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'about': SlotDefinition(name='about', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of specific terms in the ontology which will be affected by the change.', extensions={}, annotations={})}, description='What terms in the ontology will this change affect?', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='OntologyClass', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -oc:OntologyProblem a owl:Class, - linkml:ClassDefinition ; - rdfs:label "OntologyProblem" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass oc:ProblemType ; - owl:onProperty oc:category ], - [ a owl:Restriction ; - owl:allValuesFrom oc:OntologyClass ; - owl:onProperty oc:about ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty oc:severity ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty oc:description ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - linkml:attributes "{'description': SlotDefinition(name='description', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A succinct description of the problem', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'severity': SlotDefinition(name='severity', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='How severe is this problem?', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'category': SlotDefinition(name='category', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='What category does this problem fall into?', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ProblemType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'about': SlotDefinition(name='about', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of terms in the ontology that are problematic.', extensions={}, annotations={})}, description='What terms in the ontology is this problem about?', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='OntologyClass', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -<http://w3id.org/ontogpt/ontology-class-templateProblemType#BAD_RELATIONSHIP> a oc:ProblemType, - owl:Class ; - rdfs:label "BAD_RELATIONSHIP" . - -<http://w3id.org/ontogpt/ontology-class-templateProblemType#BAD_XREF> a oc:ProblemType, - owl:Class ; - rdfs:label "BAD_XREF" . - -<http://w3id.org/ontogpt/ontology-class-templateProblemType#MISSING_DEFINITION> a oc:ProblemType, - owl:Class ; - rdfs:label "MISSING_DEFINITION" . - -<http://w3id.org/ontogpt/ontology-class-templateProblemType#MISSING_PARENT> a oc:ProblemType, - owl:Class ; - rdfs:label "MISSING_PARENT" . - -<http://w3id.org/ontogpt/ontology-class-templateProblemType#OTHER> a oc:ProblemType, - owl:Class ; - rdfs:label "OTHER" . - -<http://w3id.org/ontogpt/ontology-class-templateProblemType#TYPO> a oc:ProblemType, - owl:Class ; - rdfs:label "TYPO" . - -<http://w3id.org/ontogpt/ontology-class-templateProblemType#UNKNOWN> a oc:ProblemType, - owl:Class ; - rdfs:label "UNKNOWN" . - -oc:about a owl:ObjectProperty, - linkml:SlotDefinition . - -oc:category a owl:ObjectProperty, - linkml:SlotDefinition . - -oc:description a owl:ObjectProperty, - linkml:SlotDefinition . - -<http://w3id.org/ontogpt/core/NullDataOptions> a owl:Class, - linkml:EnumDefinition ; - rdfs:label "NullDataOptions" ; - owl:unionOf ( <http://purl.obolibrary.org/obo/NCIT_C149701> <http://purl.obolibrary.org/obo/NCIT_C18902> <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> ) ; - linkml:permissible_values <http://purl.obolibrary.org/obo/NCIT_C149701>, - <http://purl.obolibrary.org/obo/NCIT_C18902>, - <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> . - -<http://w3id.org/ontogpt/core/Publication> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Publication" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/combined_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/title> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/full_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/abstract> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/CompoundExpression> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CompoundExpression" ; - linkml:attributes "{}" . - -oc:OntologyClass a owl:Class, - linkml:ClassDefinition ; - rdfs:label "OntologyClass" ; - oc:annotators "sqlite:obo:go" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/Any> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Any" ; - skos:exactMatch linkml:Any ; - linkml:attributes "{}" . - -oc:ChangeType a owl:Class, - linkml:EnumDefinition ; - rdfs:label "ChangeType" ; - owl:unionOf ( <http://w3id.org/ontogpt/ontology-class-templateChangeType#UNKNOWN> <http://w3id.org/ontogpt/ontology-class-templateChangeType#CHANGE_DEFINITION> <http://w3id.org/ontogpt/ontology-class-templateChangeType#CHANGE_LABEL> <http://w3id.org/ontogpt/ontology-class-templateChangeType#CHANGE_XREF> <http://w3id.org/ontogpt/ontology-class-templateChangeType#MOVE_TERM> ) ; - linkml:permissible_values <http://w3id.org/ontogpt/ontology-class-templateChangeType#CHANGE_DEFINITION>, - <http://w3id.org/ontogpt/ontology-class-templateChangeType#CHANGE_LABEL>, - <http://w3id.org/ontogpt/ontology-class-templateChangeType#CHANGE_XREF>, - <http://w3id.org/ontogpt/ontology-class-templateChangeType#MOVE_TERM>, - <http://w3id.org/ontogpt/ontology-class-templateChangeType#UNKNOWN> . - -oc:ProblemType a owl:Class, - linkml:EnumDefinition ; - rdfs:label "ProblemType" ; - owl:unionOf ( <http://w3id.org/ontogpt/ontology-class-templateProblemType#UNKNOWN> <http://w3id.org/ontogpt/ontology-class-templateProblemType#TYPO> <http://w3id.org/ontogpt/ontology-class-templateProblemType#BAD_XREF> <http://w3id.org/ontogpt/ontology-class-templateProblemType#MISSING_DEFINITION> <http://w3id.org/ontogpt/ontology-class-templateProblemType#MISSING_PARENT> <http://w3id.org/ontogpt/ontology-class-templateProblemType#BAD_RELATIONSHIP> <http://w3id.org/ontogpt/ontology-class-templateProblemType#OTHER> ) ; - linkml:permissible_values <http://w3id.org/ontogpt/ontology-class-templateProblemType#BAD_RELATIONSHIP>, - <http://w3id.org/ontogpt/ontology-class-templateProblemType#BAD_XREF>, - <http://w3id.org/ontogpt/ontology-class-templateProblemType#MISSING_DEFINITION>, - <http://w3id.org/ontogpt/ontology-class-templateProblemType#MISSING_PARENT>, - <http://w3id.org/ontogpt/ontology-class-templateProblemType#OTHER>, - <http://w3id.org/ontogpt/ontology-class-templateProblemType#TYPO>, - <http://w3id.org/ontogpt/ontology-class-templateProblemType#UNKNOWN> . - -<http://w3id.org/ontogpt/core/NamedEntity> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "NamedEntity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://example.org/UNKNOWN/rdfs/label> ], - [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ; - owl:qualifiedCardinality 1 ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:ClassDefinition a owl:Class ; - rdfs:label "class_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "class_expression" . - -linkml:SlotDefinition a owl:Class ; - rdfs:label "slot_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "slot_expression" . - - diff --git a/projects/ontology_issue/prefixmap/ontology_issue.yaml b/projects/ontology_issue/prefixmap/ontology_issue.yaml deleted file mode 100644 index d7c94693b..000000000 --- a/projects/ontology_issue/prefixmap/ontology_issue.yaml +++ /dev/null @@ -1,35 +0,0 @@ -{ - "RO": "http://purl.obolibrary.org/obo/RO_", - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "linkml": "https://w3id.org/linkml/", - "oc": "http://w3id.org/ontogpt/ontology-class-template", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } -} diff --git a/projects/ontology_issue/protobuf/ontology_issue.proto b/projects/ontology_issue/protobuf/ontology_issue.proto deleted file mode 100644 index 2b363fbed..000000000 --- a/projects/ontology_issue/protobuf/ontology_issue.proto +++ /dev/null @@ -1,62 +0,0 @@ -message AnnotatorResult - { - string subjectText = 0 - string objectId = 0 - string objectText = 0 - } -// A result of extracting knowledge on text -message ExtractionResult - { - string inputId = 0 - string inputTitle = 0 - string inputText = 0 - string rawCompletionOutput = 0 - string prompt = 0 - any extractedObject = 0 - repeated any namedEntities = 0 - } -message OntologyChange - { - string description = 0 - changeType category = 0 - repeated ontologyClass about = 0 - } -message OntologyClass - { - string id = 0 - string label = 0 - } -message OntologyIssue - { - string title = 0 - string summary = 0 - string status = 0 - repeated ontologyClass domains = 0 - repeated ontologyProblem problemList = 0 - repeated ontologyChange proposedChanges = 0 - } -message OntologyProblem - { - string description = 0 - string severity = 0 - problemType category = 0 - repeated ontologyClass about = 0 - } -message Publication - { - string id = 0 - string title = 0 - string abstract = 0 - string combinedText = 0 - string fullText = 0 - } -message RelationshipType - { - string id = 0 - string label = 0 - } -message TextWithTriples - { - publication publication = 0 - repeated triple triples = 0 - } diff --git a/projects/ontology_issue/shacl/ontology_issue.shacl.ttl b/projects/ontology_issue/shacl/ontology_issue.shacl.ttl deleted file mode 100644 index 9b0e18cf4..000000000 --- a/projects/ontology_issue/shacl/ontology_issue.shacl.ttl +++ /dev/null @@ -1,251 +0,0 @@ -@prefix linkml: <https://w3id.org/linkml/> . -@prefix oc: <http://w3id.org/ontogpt/ontology-class-template> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix sh: <http://www.w3.org/ns/shacl#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object_text> ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject_text> ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/object_id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/AnnotatorResult> . - -<http://w3id.org/ontogpt/core/CompoundExpression> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass <http://w3id.org/ontogpt/core/CompoundExpression> . - -<http://w3id.org/ontogpt/core/ExtractionResult> a sh:NodeShape ; - sh:closed true ; - sh:description "A result of extracting knowledge on text" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/input_text> ], - [ sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/prompt> ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/input_id> ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/input_title> ], - [ sh:class linkml:Any ; - sh:description "The complex objects extracted from the text" ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/extracted_object> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ sh:class linkml:Any ; - sh:description "Named entities extracted from the text" ; - sh:nodeKind sh:BlankNode ; - sh:order 6 ; - sh:path <http://w3id.org/ontogpt/core/named_entities> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/ExtractionResult> . - -<http://w3id.org/ontogpt/core/TextWithTriples> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/Triple> ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/triples> ], - [ sh:class <http://w3id.org/ontogpt/core/Publication> ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/publication> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/TextWithTriples> . - -oc:OntologyIssue a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class oc:OntologyChange ; - sh:description "What part of the ontology does this pertain to." ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path oc:proposed_changes ], - [ sh:class oc:OntologyClass ; - sh:description "What part of the ontology does this pertain to." ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path oc:domains ], - [ sh:class oc:OntologyProblem ; - sh:description "A list of problems stated at a high level" ; - sh:nodeKind sh:BlankNode ; - sh:order 4 ; - sh:path oc:problem_list ], - [ sh:description "a high level summary" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path oc:summary ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path oc:status ], - [ sh:description "the title of the issue" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path oc:title ] ; - sh:targetClass oc:OntologyIssue . - -<http://w3id.org/ontogpt/core/Publication> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/combined_text> ], - [ sh:description "The publication identifier" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The title of the publication" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/title> ], - [ sh:description "The full text of the publication" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/full_text> ], - [ sh:description "The abstract of the publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/abstract> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/RelationshipType> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/Triple> a sh:NodeShape ; - sh:closed false ; - sh:description "Abstract parent for Relation Extraction tasks" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/RelationshipType> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/predicate> ], - [ sh:description "A qualifier for the statements, e.g. \"NOT\" for negation" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/object_qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Triple> . - -oc:OntologyChange a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "What kind of change?" ; - sh:in ( "UNKNOWN" "CHANGE_DEFINITION" "CHANGE_LABEL" "CHANGE_XREF" "MOVE_TERM" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path oc:category ], - [ sh:description "A succinct description of the proposed change" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path oc:description ], - [ sh:class oc:OntologyClass ; - sh:description "What terms in the ontology will this change affect?" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path oc:about ] ; - sh:targetClass oc:OntologyChange . - -oc:OntologyProblem a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A succinct description of the problem" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path oc:description ], - [ sh:description "What category does this problem fall into?" ; - sh:in ( "UNKNOWN" "TYPO" "BAD_XREF" "MISSING_DEFINITION" "MISSING_PARENT" "BAD_RELATIONSHIP" "OTHER" ) ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path oc:category ], - [ sh:description "How severe is this problem?" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path oc:severity ], - [ sh:class oc:OntologyClass ; - sh:description "What terms in the ontology is this problem about?" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path oc:about ] ; - sh:targetClass oc:OntologyProblem . - -linkml:Any a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass linkml:Any . - -oc:OntologyClass a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass oc:OntologyClass . - -<http://w3id.org/ontogpt/core/NamedEntity> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/NamedEntity> . - diff --git a/projects/ontology_issue/shex/ontology_issue.shex b/projects/ontology_issue/shex/ontology_issue.shex deleted file mode 100644 index dc5c5fe35..000000000 --- a/projects/ontology_issue/shex/ontology_issue.shex +++ /dev/null @@ -1,186 +0,0 @@ -BASE <http://w3id.org/ontogpt/ontology-class-template/> -PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> -PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> -PREFIX linkml: <https://w3id.org/linkml/> -PREFIX core: <http://w3id.org/ontogpt/core/> -PREFIX rdfs1: <http://example.org/UNKNOWN/rdfs/> - - -linkml:String xsd:string - -linkml:Integer xsd:integer - -linkml:Boolean xsd:boolean - -linkml:Float xsd:float - -linkml:Double xsd:double - -linkml:Decimal xsd:decimal - -linkml:Time xsd:time - -linkml:Date xsd:date - -linkml:Datetime xsd:dateTime - -linkml:DateOrDatetime linkml:DateOrDatetime - -linkml:Uriorcurie IRI - -linkml:Curie xsd:string - -linkml:Uri IRI - -linkml:Ncname xsd:string - -linkml:Objectidentifier IRI - -linkml:Nodeidentifier NONLITERAL - -linkml:Jsonpointer xsd:string - -linkml:Jsonpath xsd:string - -linkml:Sparqlpath xsd:string - -core:AnnotatorResult CLOSED { - ( $core:AnnotatorResult_tes ( core:subject_text @linkml:String ? ; - core:object_id @linkml:String ? ; - core:object_text @linkml:String ? - ) ; - rdf:type [ core:AnnotatorResult ] ? - ) -} - -core:Any CLOSED { - ( $core:Any_tes rdf:type . * ; - rdf:type [ linkml:Any ] ? - ) -} - -core:CompoundExpression ( - @<http://w3id.org/ontogpt/ontology-class-templateOntologyChange> OR - @<http://w3id.org/ontogpt/ontology-class-templateOntologyProblem> OR @core:Triple -) - -core:CompoundExpression_struct { - ( $core:CompoundExpression_tes rdf:type . * ; - rdf:type [ core:CompoundExpression ] ? - ) -} - -core:ExtractionResult CLOSED { - ( $core:ExtractionResult_tes ( core:input_id @linkml:String ? ; - core:input_title @linkml:String ? ; - core:input_text @linkml:String ? ; - core:raw_completion_output @linkml:String ? ; - core:prompt @linkml:String ? ; - core:extracted_object @core:Any ? ; - core:named_entities @core:Any * - ) ; - rdf:type [ core:ExtractionResult ] ? - ) -} - -core:NamedEntity ( - @<http://w3id.org/ontogpt/ontology-class-templateOntologyClass> OR @core:RelationshipType -) - -core:NamedEntity_struct { - ( $core:NamedEntity_tes rdfs1:label @linkml:String ? ; - rdf:type [ core:NamedEntity ] - ) -} - -<http://w3id.org/ontogpt/ontology-class-templateOntologyChange> CLOSED { - ( $<http://w3id.org/ontogpt/ontology-class-templateOntologyChange_tes> ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - <http://w3id.org/ontogpt/ontology-class-templatedescription> @linkml:String ? ; - <http://w3id.org/ontogpt/ontology-class-templatecategory> @<http://w3id.org/ontogpt/ontology-class-templateChangeType> ? - ; - <http://w3id.org/ontogpt/ontology-class-templateabout> @<http://w3id.org/ontogpt/ontology-class-templateOntologyClass> * - ) ; - rdf:type [ <http://w3id.org/ontogpt/ontology-class-templateOntologyChange> ] ? - ) -} - -<http://w3id.org/ontogpt/ontology-class-templateOntologyClass> CLOSED { - ( $<http://w3id.org/ontogpt/ontology-class-templateOntologyClass_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <http://w3id.org/ontogpt/ontology-class-templateOntologyClass> ] - ) -} - -<http://w3id.org/ontogpt/ontology-class-templateOntologyIssue> CLOSED { - ( $<http://w3id.org/ontogpt/ontology-class-templateOntologyIssue_tes> ( - <http://w3id.org/ontogpt/ontology-class-templatetitle> @linkml:String ? ; - <http://w3id.org/ontogpt/ontology-class-templatesummary> @linkml:String ? ; - <http://w3id.org/ontogpt/ontology-class-templatestatus> @linkml:String ? ; - <http://w3id.org/ontogpt/ontology-class-templatedomains> @<http://w3id.org/ontogpt/ontology-class-templateOntologyClass> - * ; - <http://w3id.org/ontogpt/ontology-class-templateproblem_list> - @<http://w3id.org/ontogpt/ontology-class-templateOntologyProblem> * ; - <http://w3id.org/ontogpt/ontology-class-templateproposed_changes> - @<http://w3id.org/ontogpt/ontology-class-templateOntologyChange> * - ) ; - rdf:type [ <http://w3id.org/ontogpt/ontology-class-templateOntologyIssue> ] ? - ) -} - -<http://w3id.org/ontogpt/ontology-class-templateOntologyProblem> CLOSED { - ( $<http://w3id.org/ontogpt/ontology-class-templateOntologyProblem_tes> ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - <http://w3id.org/ontogpt/ontology-class-templatedescription> @linkml:String ? ; - <http://w3id.org/ontogpt/ontology-class-templateseverity> @linkml:String ? ; - <http://w3id.org/ontogpt/ontology-class-templatecategory> @<http://w3id.org/ontogpt/ontology-class-templateProblemType> ? - ; - <http://w3id.org/ontogpt/ontology-class-templateabout> @<http://w3id.org/ontogpt/ontology-class-templateOntologyClass> * - ) ; - rdf:type [ <http://w3id.org/ontogpt/ontology-class-templateOntologyProblem> ] ? - ) -} - -core:Publication CLOSED { - ( $core:Publication_tes ( core:id @linkml:String ? ; - core:title @linkml:String ? ; - core:abstract @linkml:String ? ; - core:combined_text @linkml:String ? ; - core:full_text @linkml:String ? - ) ; - rdf:type [ core:Publication ] ? - ) -} - -core:RelationshipType CLOSED { - ( $core:RelationshipType_tes ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ core:RelationshipType ] - ) -} - -core:TextWithTriples CLOSED { - ( $core:TextWithTriples_tes ( core:publication @core:Publication ? ; - core:triples @core:Triple * - ) ; - rdf:type [ core:TextWithTriples ] ? - ) -} - -core:Triple { - ( $core:Triple_tes ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - core:subject @core:NamedEntity ? ; - core:predicate @core:RelationshipType ? ; - core:object @core:NamedEntity ? ; - core:qualifier @linkml:String ? ; - core:subject_qualifier @core:NamedEntity ? ; - core:object_qualifier @core:NamedEntity ? - ) ; - rdf:type [ core:Triple ] ? - ) -} - - diff --git a/projects/ontology_issue/sqlschema/ontology_issue.sql b/projects/ontology_issue/sqlschema/ontology_issue.sql deleted file mode 100644 index e9ae4ce38..000000000 --- a/projects/ontology_issue/sqlschema/ontology_issue.sql +++ /dev/null @@ -1,71 +0,0 @@ - - -CREATE TABLE "AnnotatorResult" ( - subject_text TEXT, - object_id TEXT, - object_text TEXT, - PRIMARY KEY (subject_text, object_id, object_text) -); - -CREATE TABLE "ExtractionResult" ( - input_id TEXT, - input_title TEXT, - input_text TEXT, - raw_completion_output TEXT, - prompt TEXT, - extracted_object TEXT, - named_entities TEXT, - PRIMARY KEY (input_id, input_title, input_text, raw_completion_output, prompt, extracted_object, named_entities) -); - -CREATE TABLE "OntologyChange" ( - description TEXT, - category VARCHAR(17), - about TEXT, - PRIMARY KEY (description, category, about) -); - -CREATE TABLE "OntologyClass" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "OntologyIssue" ( - title TEXT, - summary TEXT, - status TEXT, - domains TEXT, - problem_list TEXT, - proposed_changes TEXT, - PRIMARY KEY (title, summary, status, domains, problem_list, proposed_changes) -); - -CREATE TABLE "OntologyProblem" ( - description TEXT, - severity TEXT, - category VARCHAR(18), - about TEXT, - PRIMARY KEY (description, severity, category, about) -); - -CREATE TABLE "Publication" ( - id TEXT, - title TEXT, - abstract TEXT, - combined_text TEXT, - full_text TEXT, - PRIMARY KEY (id, title, abstract, combined_text, full_text) -); - -CREATE TABLE "RelationshipType" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "TextWithTriples" ( - publication TEXT, - triples TEXT, - PRIMARY KEY (publication, triples) -); diff --git a/projects/phenotype/docs/AnatomicalEntity.md b/projects/phenotype/docs/AnatomicalEntity.md deleted file mode 100644 index 7fbfa471a..000000000 --- a/projects/phenotype/docs/AnatomicalEntity.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: AnatomicalEntity - - - - -URI: [phenotype:AnatomicalEntity](http://w3id.org/ontogpt/phenotype/AnatomicalEntity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[Trait]-%20anatomical_entity%200..1>[AnatomicalEntity|id(i):string;label(i):string%20%3F],[NamedEntity]^-[AnatomicalEntity],[Trait])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[Trait]-%20anatomical_entity%200..1>[AnatomicalEntity|id(i):string;label(i):string%20%3F],[NamedEntity]^-[AnatomicalEntity],[Trait]) - -## Identifier prefixes - - * UBERON - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞anatomical_entity](trait__anatomical_entity.md)* <sub>0..1</sub> **[AnatomicalEntity](AnatomicalEntity.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/phenotype/docs/AnnotatorResult.md b/projects/phenotype/docs/AnnotatorResult.md deleted file mode 100644 index 87c4ab23c..000000000 --- a/projects/phenotype/docs/AnnotatorResult.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Class: AnnotatorResult - - - - -URI: [phenotype:AnnotatorResult](http://w3id.org/ontogpt/phenotype/AnnotatorResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F])](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F]) - -## Attributes - - -### Own - - * [➞subject_text](annotatorResult__subject_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_id](annotatorResult__object_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_text](annotatorResult__object_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) diff --git a/projects/phenotype/docs/Any.md b/projects/phenotype/docs/Any.md deleted file mode 100644 index 788bc3c44..000000000 --- a/projects/phenotype/docs/Any.md +++ /dev/null @@ -1,25 +0,0 @@ - -# Class: Any - - - - -URI: [phenotype:Any](http://w3id.org/ontogpt/phenotype/Any) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult])](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult]) - -## Referenced by Class - - * **None** *[➞extracted_object](extractionResult__extracted_object.md)* <sub>0..1</sub> **[Any](Any.md)** - * **None** *[➞named_entities](extractionResult__named_entities.md)* <sub>0..\*</sub> **[Any](Any.md)** - -## Attributes - - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | linkml:Any | - diff --git a/projects/phenotype/docs/ChemicalEntity.md b/projects/phenotype/docs/ChemicalEntity.md deleted file mode 100644 index 989d382b6..000000000 --- a/projects/phenotype/docs/ChemicalEntity.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: ChemicalEntity - - - - -URI: [phenotype:ChemicalEntity](http://w3id.org/ontogpt/phenotype/ChemicalEntity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[Trait]-%20chemical_entity%200..1>[ChemicalEntity|id(i):string;label(i):string%20%3F],[NamedEntity]^-[ChemicalEntity],[Trait])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[Trait]-%20chemical_entity%200..1>[ChemicalEntity|id(i):string;label(i):string%20%3F],[NamedEntity]^-[ChemicalEntity],[Trait]) - -## Identifier prefixes - - * CHEBI - * PR - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞chemical_entity](trait__chemical_entity.md)* <sub>0..1</sub> **[ChemicalEntity](ChemicalEntity.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/phenotype/docs/CompoundExpression.md b/projects/phenotype/docs/CompoundExpression.md deleted file mode 100644 index c96367f76..000000000 --- a/projects/phenotype/docs/CompoundExpression.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: CompoundExpression - - - - -URI: [phenotype:CompoundExpression](http://w3id.org/ontogpt/phenotype/CompoundExpression) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[CompoundExpression]^-[Triple])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[CompoundExpression]^-[Triple]) - -## Children - - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - -## Referenced by Class - - -## Attributes - diff --git a/projects/phenotype/docs/ExtractionResult.md b/projects/phenotype/docs/ExtractionResult.md deleted file mode 100644 index 75c3a72ea..000000000 --- a/projects/phenotype/docs/ExtractionResult.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Class: ExtractionResult - - -A result of extracting knowledge on text - -URI: [phenotype:ExtractionResult](http://w3id.org/ontogpt/phenotype/ExtractionResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any])](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any]) - -## Attributes - - -### Own - - * [➞input_id](extractionResult__input_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_title](extractionResult__input_title.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_text](extractionResult__input_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞prompt](extractionResult__prompt.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞extracted_object](extractionResult__extracted_object.md) <sub>0..1</sub> - * Description: The complex objects extracted from the text - * Range: [Any](Any.md) - * [➞named_entities](extractionResult__named_entities.md) <sub>0..\*</sub> - * Description: Named entities extracted from the text - * Range: [Any](Any.md) diff --git a/projects/phenotype/docs/NamedEntity.md b/projects/phenotype/docs/NamedEntity.md deleted file mode 100644 index 037abfb20..000000000 --- a/projects/phenotype/docs/NamedEntity.md +++ /dev/null @@ -1,36 +0,0 @@ - -# Class: NamedEntity - - - - -URI: [phenotype:NamedEntity](http://w3id.org/ontogpt/phenotype/NamedEntity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[Quality],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[Quality],[NamedEntity]^-[ChemicalEntity],[NamedEntity]^-[AnatomicalEntity],[Triple],[ChemicalEntity],[AnatomicalEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[Quality],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[Quality],[NamedEntity]^-[ChemicalEntity],[NamedEntity]^-[AnatomicalEntity],[Triple],[ChemicalEntity],[AnatomicalEntity]) - -## Children - - * [AnatomicalEntity](AnatomicalEntity.md) - * [ChemicalEntity](ChemicalEntity.md) - * [Quality](Quality.md) - * [RelationshipType](RelationshipType.md) - -## Referenced by Class - - * **None** *[➞object](triple__object.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞object_qualifier](triple__object_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject](triple__subject.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject_qualifier](triple__subject_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - -## Attributes - - -### Own - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/phenotype/docs/NullDataOptions.md b/projects/phenotype/docs/NullDataOptions.md deleted file mode 100644 index f0e959e56..000000000 --- a/projects/phenotype/docs/NullDataOptions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Enum: NullDataOptions - - - - -URI: [phenotype:NullDataOptions](http://w3id.org/ontogpt/phenotype/NullDataOptions) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | -| UNSPECIFIED_METHOD_OF_ADMINISTRATION | | NCIT:C149701 | | -| NOT_APPLICABLE | | NCIT:C18902 | {'aliases': ['not applicable', 'N/A']} | -| NOT_MENTIONED | | | | - diff --git a/projects/phenotype/docs/Publication.md b/projects/phenotype/docs/Publication.md deleted file mode 100644 index e7327753c..000000000 --- a/projects/phenotype/docs/Publication.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Publication - - - - -URI: [phenotype:Publication](http://w3id.org/ontogpt/phenotype/Publication) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples])](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples]) - -## Referenced by Class - - * **None** *[➞publication](textWithTriples__publication.md)* <sub>0..1</sub> **[Publication](Publication.md)** - -## Attributes - - -### Own - - * [➞id](publication__id.md) <sub>0..1</sub> - * Description: The publication identifier - * Range: [String](types/String.md) - * [➞title](publication__title.md) <sub>0..1</sub> - * Description: The title of the publication - * Range: [String](types/String.md) - * [➞abstract](publication__abstract.md) <sub>0..1</sub> - * Description: The abstract of the publication - * Range: [String](types/String.md) - * [➞combined_text](publication__combined_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞full_text](publication__full_text.md) <sub>0..1</sub> - * Description: The full text of the publication - * Range: [String](types/String.md) diff --git a/projects/phenotype/docs/Quality.md b/projects/phenotype/docs/Quality.md deleted file mode 100644 index b86d7fab7..000000000 --- a/projects/phenotype/docs/Quality.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Quality - - - - -URI: [phenotype:Quality](http://w3id.org/ontogpt/phenotype/Quality) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Trait]-%20quality%200..1>[Quality|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Quality],[Trait],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Trait]-%20quality%200..1>[Quality|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Quality],[Trait],[NamedEntity]) - -## Identifier prefixes - - * PATO - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞quality](trait__quality.md)* <sub>0..1</sub> **[Quality](Quality.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/phenotype/docs/RelationshipType.md b/projects/phenotype/docs/RelationshipType.md deleted file mode 100644 index 928594936..000000000 --- a/projects/phenotype/docs/RelationshipType.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: RelationshipType - - - - -URI: [phenotype:RelationshipType](http://w3id.org/ontogpt/phenotype/RelationshipType) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity]) - -## Identifier prefixes - - * RO - * biolink - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞predicate](triple__predicate.md)* <sub>0..1</sub> **[RelationshipType](RelationshipType.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/phenotype/docs/TextWithTriples.md b/projects/phenotype/docs/TextWithTriples.md deleted file mode 100644 index a781491ac..000000000 --- a/projects/phenotype/docs/TextWithTriples.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: TextWithTriples - - - - -URI: [phenotype:TextWithTriples](http://w3id.org/ontogpt/phenotype/TextWithTriples) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication]) - -## Attributes - - -### Own - - * [➞publication](textWithTriples__publication.md) <sub>0..1</sub> - * Range: [Publication](Publication.md) - * [➞triples](textWithTriples__triples.md) <sub>0..\*</sub> - * Range: [Triple](Triple.md) diff --git a/projects/phenotype/docs/Trait.md b/projects/phenotype/docs/Trait.md deleted file mode 100644 index f1f31cea9..000000000 --- a/projects/phenotype/docs/Trait.md +++ /dev/null @@ -1,25 +0,0 @@ - -# Class: Trait - - - - -URI: [phenotype:Trait](http://w3id.org/ontogpt/phenotype/Trait) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ChemicalEntity]<chemical_entity%200..1-%20[Trait],[AnatomicalEntity]<anatomical_entity%200..1-%20[Trait],[Quality]<quality%200..1-%20[Trait],[Quality],[ChemicalEntity],[AnatomicalEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[ChemicalEntity]<chemical_entity%200..1-%20[Trait],[AnatomicalEntity]<anatomical_entity%200..1-%20[Trait],[Quality]<quality%200..1-%20[Trait],[Quality],[ChemicalEntity],[AnatomicalEntity]) - -## Attributes - - -### Own - - * [➞quality](trait__quality.md) <sub>0..1</sub> - * Description: The property being measured, or changes in this property, for example, amount, level, increased amount, decreased concentration - * Range: [Quality](Quality.md) - * [➞anatomical_entity](trait__anatomical_entity.md) <sub>0..1</sub> - * Description: The anatomical location that the chemical entity is measured in - * Range: [AnatomicalEntity](AnatomicalEntity.md) - * [➞chemical_entity](trait__chemical_entity.md) <sub>0..1</sub> - * Description: The chemical entity that is being measured - * Range: [ChemicalEntity](ChemicalEntity.md) diff --git a/projects/phenotype/docs/Triple.md b/projects/phenotype/docs/Triple.md deleted file mode 100644 index a4d83f04e..000000000 --- a/projects/phenotype/docs/Triple.md +++ /dev/null @@ -1,39 +0,0 @@ - -# Class: Triple - - -Abstract parent for Relation Extraction tasks - -URI: [phenotype:Triple](http://w3id.org/ontogpt/phenotype/Triple) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞triples](textWithTriples__triples.md)* <sub>0..\*</sub> **[Triple](Triple.md)** - -## Attributes - - -### Own - - * [➞subject](triple__subject.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞predicate](triple__predicate.md) <sub>0..1</sub> - * Range: [RelationshipType](RelationshipType.md) - * [➞object](triple__object.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞qualifier](triple__qualifier.md) <sub>0..1</sub> - * Description: A qualifier for the statements, e.g. "NOT" for negation - * Range: [String](types/String.md) - * [➞subject_qualifier](triple__subject_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - * Range: [NamedEntity](NamedEntity.md) - * [➞object_qualifier](triple__object_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * Range: [NamedEntity](NamedEntity.md) diff --git a/projects/phenotype/docs/annotatorResult__object_id.md b/projects/phenotype/docs/annotatorResult__object_id.md deleted file mode 100644 index 18830848d..000000000 --- a/projects/phenotype/docs/annotatorResult__object_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_id - - - - -URI: [phenotype:annotatorResult__object_id](http://w3id.org/ontogpt/phenotype/annotatorResult__object_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/phenotype/docs/annotatorResult__object_text.md b/projects/phenotype/docs/annotatorResult__object_text.md deleted file mode 100644 index 3fa2e801b..000000000 --- a/projects/phenotype/docs/annotatorResult__object_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_text - - - - -URI: [phenotype:annotatorResult__object_text](http://w3id.org/ontogpt/phenotype/annotatorResult__object_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/phenotype/docs/annotatorResult__subject_text.md b/projects/phenotype/docs/annotatorResult__subject_text.md deleted file mode 100644 index 0ee097512..000000000 --- a/projects/phenotype/docs/annotatorResult__subject_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_text - - - - -URI: [phenotype:annotatorResult__subject_text](http://w3id.org/ontogpt/phenotype/annotatorResult__subject_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/phenotype/docs/extractionResult__extracted_object.md b/projects/phenotype/docs/extractionResult__extracted_object.md deleted file mode 100644 index 98c0ac785..000000000 --- a/projects/phenotype/docs/extractionResult__extracted_object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: extracted_object - - -The complex objects extracted from the text - -URI: [phenotype:extractionResult__extracted_object](http://w3id.org/ontogpt/phenotype/extractionResult__extracted_object) - - -## Domain and Range - -None → <sub>0..1</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/phenotype/docs/extractionResult__input_id.md b/projects/phenotype/docs/extractionResult__input_id.md deleted file mode 100644 index 8c037e889..000000000 --- a/projects/phenotype/docs/extractionResult__input_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_id - - - - -URI: [phenotype:extractionResult__input_id](http://w3id.org/ontogpt/phenotype/extractionResult__input_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/phenotype/docs/extractionResult__input_text.md b/projects/phenotype/docs/extractionResult__input_text.md deleted file mode 100644 index da5b1ca77..000000000 --- a/projects/phenotype/docs/extractionResult__input_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_text - - - - -URI: [phenotype:extractionResult__input_text](http://w3id.org/ontogpt/phenotype/extractionResult__input_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/phenotype/docs/extractionResult__input_title.md b/projects/phenotype/docs/extractionResult__input_title.md deleted file mode 100644 index 41cca82ff..000000000 --- a/projects/phenotype/docs/extractionResult__input_title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_title - - - - -URI: [phenotype:extractionResult__input_title](http://w3id.org/ontogpt/phenotype/extractionResult__input_title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/phenotype/docs/extractionResult__named_entities.md b/projects/phenotype/docs/extractionResult__named_entities.md deleted file mode 100644 index 31d600dbc..000000000 --- a/projects/phenotype/docs/extractionResult__named_entities.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: named_entities - - -Named entities extracted from the text - -URI: [phenotype:extractionResult__named_entities](http://w3id.org/ontogpt/phenotype/extractionResult__named_entities) - - -## Domain and Range - -None → <sub>0..\*</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/phenotype/docs/extractionResult__prompt.md b/projects/phenotype/docs/extractionResult__prompt.md deleted file mode 100644 index d40260a23..000000000 --- a/projects/phenotype/docs/extractionResult__prompt.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: prompt - - - - -URI: [phenotype:extractionResult__prompt](http://w3id.org/ontogpt/phenotype/extractionResult__prompt) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/phenotype/docs/extractionResult__raw_completion_output.md b/projects/phenotype/docs/extractionResult__raw_completion_output.md deleted file mode 100644 index f6079007f..000000000 --- a/projects/phenotype/docs/extractionResult__raw_completion_output.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: raw_completion_output - - - - -URI: [phenotype:extractionResult__raw_completion_output](http://w3id.org/ontogpt/phenotype/extractionResult__raw_completion_output) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/phenotype/docs/namedEntity__id.md b/projects/phenotype/docs/namedEntity__id.md deleted file mode 100644 index cfacc0a73..000000000 --- a/projects/phenotype/docs/namedEntity__id.md +++ /dev/null @@ -1,33 +0,0 @@ - -# Slot: id - - -A unique identifier for the named entity - -URI: [phenotype:namedEntity__id](http://w3id.org/ontogpt/phenotype/namedEntity__id) - - -## Domain and Range - -None → <sub>1..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnatomicalEntity](AnatomicalEntity.md) - * [ChemicalEntity](ChemicalEntity.md) - * [NamedEntity](NamedEntity.md) - * [Quality](Quality.md) - * [RelationshipType](RelationshipType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | this is populated during the grounding and normalization step | - diff --git a/projects/phenotype/docs/namedEntity__label.md b/projects/phenotype/docs/namedEntity__label.md deleted file mode 100644 index 94431ea47..000000000 --- a/projects/phenotype/docs/namedEntity__label.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Slot: label - - -The label (name) of the named thing - -URI: [phenotype:namedEntity__label](http://w3id.org/ontogpt/phenotype/namedEntity__label) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnatomicalEntity](AnatomicalEntity.md) - * [ChemicalEntity](ChemicalEntity.md) - * [NamedEntity](NamedEntity.md) - * [Quality](Quality.md) - * [RelationshipType](RelationshipType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Aliases:** | | name | -| **Mappings:** | | rdfs:label | - diff --git a/projects/phenotype/docs/phenotype.md b/projects/phenotype/docs/phenotype.md deleted file mode 100644 index 92e772248..000000000 --- a/projects/phenotype/docs/phenotype.md +++ /dev/null @@ -1,110 +0,0 @@ - -# eq-template - - -**metamodel version:** 1.7.0 - -**version:** None - - -A template for Computational Phenotypes - - -### Classes - - * [AnnotatorResult](AnnotatorResult.md) - * [Any](Any.md) - * [CompoundExpression](CompoundExpression.md) - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - * [ExtractionResult](ExtractionResult.md) - A result of extracting knowledge on text - * [NamedEntity](NamedEntity.md) - * [AnatomicalEntity](AnatomicalEntity.md) - * [ChemicalEntity](ChemicalEntity.md) - * [Quality](Quality.md) - * [RelationshipType](RelationshipType.md) - * [Publication](Publication.md) - * [TextWithTriples](TextWithTriples.md) - * [Trait](Trait.md) - -### Mixins - - -### Slots - - * [➞object_id](annotatorResult__object_id.md) - * [➞object_text](annotatorResult__object_text.md) - * [➞subject_text](annotatorResult__subject_text.md) - * [➞extracted_object](extractionResult__extracted_object.md) - The complex objects extracted from the text - * [➞input_id](extractionResult__input_id.md) - * [➞input_text](extractionResult__input_text.md) - * [➞input_title](extractionResult__input_title.md) - * [➞named_entities](extractionResult__named_entities.md) - Named entities extracted from the text - * [➞prompt](extractionResult__prompt.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) - * [➞id](namedEntity__id.md) - A unique identifier for the named entity - * [➞label](namedEntity__label.md) - The label (name) of the named thing - * [➞abstract](publication__abstract.md) - The abstract of the publication - * [➞combined_text](publication__combined_text.md) - * [➞full_text](publication__full_text.md) - The full text of the publication - * [➞id](publication__id.md) - The publication identifier - * [➞title](publication__title.md) - The title of the publication - * [➞publication](textWithTriples__publication.md) - * [➞triples](textWithTriples__triples.md) - * [➞anatomical_entity](trait__anatomical_entity.md) - The anatomical location that the chemical entity is measured in - * [➞chemical_entity](trait__chemical_entity.md) - The chemical entity that is being measured - * [➞quality](trait__quality.md) - The property being measured, or changes in this property, for example, amount, level, increased amount, decreased concentration - * [➞object](triple__object.md) - * [➞object_qualifier](triple__object_qualifier.md) - An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * [➞predicate](triple__predicate.md) - * [➞qualifier](triple__qualifier.md) - A qualifier for the statements, e.g. "NOT" for negation - * [➞subject](triple__subject.md) - * [➞subject_qualifier](triple__subject_qualifier.md) - An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -### Enums - - * [NullDataOptions](NullDataOptions.md) - -### Subsets - - -### Types - - -#### Built in - - * **Bool** - * **Curie** - * **Decimal** - * **ElementIdentifier** - * **NCName** - * **NodeIdentifier** - * **URI** - * **URIorCURIE** - * **XSDDate** - * **XSDDateTime** - * **XSDTime** - * **float** - * **int** - * **str** - -#### Defined - - * [Boolean](types/Boolean.md) (**Bool**) - A binary (true or false) value - * [Curie](types/Curie.md) (**Curie**) - a compact URI - * [Date](types/Date.md) (**XSDDate**) - a date (year, month and day) in an idealized calendar - * [DateOrDatetime](types/DateOrDatetime.md) (**str**) - Either a date or a datetime - * [Datetime](types/Datetime.md) (**XSDDateTime**) - The combination of a date and time - * [Decimal](types/Decimal.md) (**Decimal**) - A real number with arbitrary precision that conforms to the xsd:decimal specification - * [Double](types/Double.md) (**float**) - A real number that conforms to the xsd:double specification - * [Float](types/Float.md) (**float**) - A real number that conforms to the xsd:float specification - * [Integer](types/Integer.md) (**int**) - An integer - * [Jsonpath](types/Jsonpath.md) (**str**) - A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - * [Jsonpointer](types/Jsonpointer.md) (**str**) - A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - * [Ncname](types/Ncname.md) (**NCName**) - Prefix part of CURIE - * [Nodeidentifier](types/Nodeidentifier.md) (**NodeIdentifier**) - A URI, CURIE or BNODE that represents a node in a model. - * [Objectidentifier](types/Objectidentifier.md) (**ElementIdentifier**) - A URI or CURIE that represents an object in the model. - * [Sparqlpath](types/Sparqlpath.md) (**str**) - A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - * [String](types/String.md) (**str**) - A character string - * [Time](types/Time.md) (**XSDTime**) - A time object represents a (local) time of day, independent of any particular day - * [Uri](types/Uri.md) (**URI**) - a complete URI - * [Uriorcurie](types/Uriorcurie.md) (**URIorCURIE**) - a URI or a CURIE diff --git a/projects/phenotype/docs/publication__abstract.md b/projects/phenotype/docs/publication__abstract.md deleted file mode 100644 index 3763adb02..000000000 --- a/projects/phenotype/docs/publication__abstract.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: abstract - - -The abstract of the publication - -URI: [phenotype:publication__abstract](http://w3id.org/ontogpt/phenotype/publication__abstract) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/phenotype/docs/publication__combined_text.md b/projects/phenotype/docs/publication__combined_text.md deleted file mode 100644 index 755e14f97..000000000 --- a/projects/phenotype/docs/publication__combined_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: combined_text - - - - -URI: [phenotype:publication__combined_text](http://w3id.org/ontogpt/phenotype/publication__combined_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/phenotype/docs/publication__full_text.md b/projects/phenotype/docs/publication__full_text.md deleted file mode 100644 index ea9f4bbce..000000000 --- a/projects/phenotype/docs/publication__full_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: full_text - - -The full text of the publication - -URI: [phenotype:publication__full_text](http://w3id.org/ontogpt/phenotype/publication__full_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/phenotype/docs/publication__id.md b/projects/phenotype/docs/publication__id.md deleted file mode 100644 index f654e3ccc..000000000 --- a/projects/phenotype/docs/publication__id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: id - - -The publication identifier - -URI: [phenotype:publication__id](http://w3id.org/ontogpt/phenotype/publication__id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/phenotype/docs/publication__title.md b/projects/phenotype/docs/publication__title.md deleted file mode 100644 index 1a050deba..000000000 --- a/projects/phenotype/docs/publication__title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: title - - -The title of the publication - -URI: [phenotype:publication__title](http://w3id.org/ontogpt/phenotype/publication__title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/phenotype/docs/textWithTriples__publication.md b/projects/phenotype/docs/textWithTriples__publication.md deleted file mode 100644 index e3a2918a2..000000000 --- a/projects/phenotype/docs/textWithTriples__publication.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: publication - - - - -URI: [phenotype:textWithTriples__publication](http://w3id.org/ontogpt/phenotype/textWithTriples__publication) - - -## Domain and Range - -None → <sub>0..1</sub> [Publication](Publication.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/phenotype/docs/textWithTriples__triples.md b/projects/phenotype/docs/textWithTriples__triples.md deleted file mode 100644 index 09139f36b..000000000 --- a/projects/phenotype/docs/textWithTriples__triples.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: triples - - - - -URI: [phenotype:textWithTriples__triples](http://w3id.org/ontogpt/phenotype/textWithTriples__triples) - - -## Domain and Range - -None → <sub>0..\*</sub> [Triple](Triple.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/phenotype/docs/trait__anatomical_entity.md b/projects/phenotype/docs/trait__anatomical_entity.md deleted file mode 100644 index a39a90f14..000000000 --- a/projects/phenotype/docs/trait__anatomical_entity.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: anatomical_entity - - -The anatomical location that the chemical entity is measured in - -URI: [phenotype:trait__anatomical_entity](http://w3id.org/ontogpt/phenotype/trait__anatomical_entity) - - -## Domain and Range - -None → <sub>0..1</sub> [AnatomicalEntity](AnatomicalEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Trait](Trait.md) diff --git a/projects/phenotype/docs/trait__chemical_entity.md b/projects/phenotype/docs/trait__chemical_entity.md deleted file mode 100644 index b329a70aa..000000000 --- a/projects/phenotype/docs/trait__chemical_entity.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: chemical_entity - - -The chemical entity that is being measured - -URI: [phenotype:trait__chemical_entity](http://w3id.org/ontogpt/phenotype/trait__chemical_entity) - - -## Domain and Range - -None → <sub>0..1</sub> [ChemicalEntity](ChemicalEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Trait](Trait.md) diff --git a/projects/phenotype/docs/trait__quality.md b/projects/phenotype/docs/trait__quality.md deleted file mode 100644 index 55074a070..000000000 --- a/projects/phenotype/docs/trait__quality.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: quality - - -The property being measured, or changes in this property, for example, amount, level, increased amount, decreased concentration - -URI: [phenotype:trait__quality](http://w3id.org/ontogpt/phenotype/trait__quality) - - -## Domain and Range - -None → <sub>0..1</sub> [Quality](Quality.md) - -## Parents - - -## Children - - -## Used by - - * [Trait](Trait.md) diff --git a/projects/phenotype/docs/triple__object.md b/projects/phenotype/docs/triple__object.md deleted file mode 100644 index 69ce54769..000000000 --- a/projects/phenotype/docs/triple__object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object - - - - -URI: [phenotype:triple__object](http://w3id.org/ontogpt/phenotype/triple__object) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/phenotype/docs/triple__object_qualifier.md b/projects/phenotype/docs/triple__object_qualifier.md deleted file mode 100644 index 3ff07e51b..000000000 --- a/projects/phenotype/docs/triple__object_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_qualifier - - -An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - -URI: [phenotype:triple__object_qualifier](http://w3id.org/ontogpt/phenotype/triple__object_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/phenotype/docs/triple__predicate.md b/projects/phenotype/docs/triple__predicate.md deleted file mode 100644 index 1e69cb7d9..000000000 --- a/projects/phenotype/docs/triple__predicate.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: predicate - - - - -URI: [phenotype:triple__predicate](http://w3id.org/ontogpt/phenotype/triple__predicate) - - -## Domain and Range - -None → <sub>0..1</sub> [RelationshipType](RelationshipType.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/phenotype/docs/triple__qualifier.md b/projects/phenotype/docs/triple__qualifier.md deleted file mode 100644 index 70806ec0e..000000000 --- a/projects/phenotype/docs/triple__qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: qualifier - - -A qualifier for the statements, e.g. "NOT" for negation - -URI: [phenotype:triple__qualifier](http://w3id.org/ontogpt/phenotype/triple__qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/phenotype/docs/triple__subject.md b/projects/phenotype/docs/triple__subject.md deleted file mode 100644 index 69cb37875..000000000 --- a/projects/phenotype/docs/triple__subject.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject - - - - -URI: [phenotype:triple__subject](http://w3id.org/ontogpt/phenotype/triple__subject) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/phenotype/docs/triple__subject_qualifier.md b/projects/phenotype/docs/triple__subject_qualifier.md deleted file mode 100644 index f59fcedfa..000000000 --- a/projects/phenotype/docs/triple__subject_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_qualifier - - -An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -URI: [phenotype:triple__subject_qualifier](http://w3id.org/ontogpt/phenotype/triple__subject_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/phenotype/docs/types/Boolean.md b/projects/phenotype/docs/types/Boolean.md deleted file mode 100644 index dc83a9c6e..000000000 --- a/projects/phenotype/docs/types/Boolean.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: boolean - - -A binary (true or false) value - -URI: [linkml:Boolean](https://w3id.org/linkml/Boolean) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Bool** | -| Representation | | bool | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Boolean | - diff --git a/projects/phenotype/docs/types/Curie.md b/projects/phenotype/docs/types/Curie.md deleted file mode 100644 index c1803f93f..000000000 --- a/projects/phenotype/docs/types/Curie.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: curie - - -a compact URI - -URI: [linkml:Curie](https://w3id.org/linkml/Curie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Curie** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations this MUST be expanded to a URI | -| | | in non-RDF serializations MAY be serialized as the compact representation | - diff --git a/projects/phenotype/docs/types/Date.md b/projects/phenotype/docs/types/Date.md deleted file mode 100644 index 06948af97..000000000 --- a/projects/phenotype/docs/types/Date.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: date - - -a date (year, month and day) in an idealized calendar - -URI: [linkml:Date](https://w3id.org/linkml/Date) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDate** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Date | - diff --git a/projects/phenotype/docs/types/DateOrDatetime.md b/projects/phenotype/docs/types/DateOrDatetime.md deleted file mode 100644 index ef983898d..000000000 --- a/projects/phenotype/docs/types/DateOrDatetime.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: date_or_datetime - - -Either a date or a datetime - -URI: [linkml:DateOrDatetime](https://w3id.org/linkml/DateOrDatetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/phenotype/docs/types/Datetime.md b/projects/phenotype/docs/types/Datetime.md deleted file mode 100644 index 9510454a8..000000000 --- a/projects/phenotype/docs/types/Datetime.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: datetime - - -The combination of a date and time - -URI: [linkml:Datetime](https://w3id.org/linkml/Datetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDateTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:DateTime | - diff --git a/projects/phenotype/docs/types/Decimal.md b/projects/phenotype/docs/types/Decimal.md deleted file mode 100644 index a7ba14a5d..000000000 --- a/projects/phenotype/docs/types/Decimal.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: decimal - - -A real number with arbitrary precision that conforms to the xsd:decimal specification - -URI: [linkml:Decimal](https://w3id.org/linkml/Decimal) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Decimal** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Broad Mappings:** | | schema:Number | - diff --git a/projects/phenotype/docs/types/Double.md b/projects/phenotype/docs/types/Double.md deleted file mode 100644 index cfe6d71e2..000000000 --- a/projects/phenotype/docs/types/Double.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: double - - -A real number that conforms to the xsd:double specification - -URI: [linkml:Double](https://w3id.org/linkml/Double) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Close Mappings:** | | schema:Float | - diff --git a/projects/phenotype/docs/types/Float.md b/projects/phenotype/docs/types/Float.md deleted file mode 100644 index 7b303f96f..000000000 --- a/projects/phenotype/docs/types/Float.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: float - - -A real number that conforms to the xsd:float specification - -URI: [linkml:Float](https://w3id.org/linkml/Float) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Float | - diff --git a/projects/phenotype/docs/types/Integer.md b/projects/phenotype/docs/types/Integer.md deleted file mode 100644 index 3cfcc66d9..000000000 --- a/projects/phenotype/docs/types/Integer.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: integer - - -An integer - -URI: [linkml:Integer](https://w3id.org/linkml/Integer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **int** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Integer | - diff --git a/projects/phenotype/docs/types/Jsonpath.md b/projects/phenotype/docs/types/Jsonpath.md deleted file mode 100644 index a03a58e67..000000000 --- a/projects/phenotype/docs/types/Jsonpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpath - - -A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpath](https://w3id.org/linkml/Jsonpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/phenotype/docs/types/Jsonpointer.md b/projects/phenotype/docs/types/Jsonpointer.md deleted file mode 100644 index a0e1ac492..000000000 --- a/projects/phenotype/docs/types/Jsonpointer.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpointer - - -A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpointer](https://w3id.org/linkml/Jsonpointer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/phenotype/docs/types/Ncname.md b/projects/phenotype/docs/types/Ncname.md deleted file mode 100644 index 710b0b04a..000000000 --- a/projects/phenotype/docs/types/Ncname.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: ncname - - -Prefix part of CURIE - -URI: [linkml:Ncname](https://w3id.org/linkml/Ncname) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NCName** | -| Representation | | str | diff --git a/projects/phenotype/docs/types/Nodeidentifier.md b/projects/phenotype/docs/types/Nodeidentifier.md deleted file mode 100644 index f0097cdf4..000000000 --- a/projects/phenotype/docs/types/Nodeidentifier.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: nodeidentifier - - -A URI, CURIE or BNODE that represents a node in a model. - -URI: [linkml:Nodeidentifier](https://w3id.org/linkml/Nodeidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NodeIdentifier** | -| Representation | | str | diff --git a/projects/phenotype/docs/types/Objectidentifier.md b/projects/phenotype/docs/types/Objectidentifier.md deleted file mode 100644 index 454ba6be6..000000000 --- a/projects/phenotype/docs/types/Objectidentifier.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: objectidentifier - - -A URI or CURIE that represents an object in the model. - -URI: [linkml:Objectidentifier](https://w3id.org/linkml/Objectidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **ElementIdentifier** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | Used for inheritance and type checking | - diff --git a/projects/phenotype/docs/types/Sparqlpath.md b/projects/phenotype/docs/types/Sparqlpath.md deleted file mode 100644 index fd99a927e..000000000 --- a/projects/phenotype/docs/types/Sparqlpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: sparqlpath - - -A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - -URI: [linkml:Sparqlpath](https://w3id.org/linkml/Sparqlpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/phenotype/docs/types/String.md b/projects/phenotype/docs/types/String.md deleted file mode 100644 index 6e61d7081..000000000 --- a/projects/phenotype/docs/types/String.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: string - - -A character string - -URI: [linkml:String](https://w3id.org/linkml/String) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Text | - diff --git a/projects/phenotype/docs/types/Time.md b/projects/phenotype/docs/types/Time.md deleted file mode 100644 index 2b8652bcd..000000000 --- a/projects/phenotype/docs/types/Time.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: time - - -A time object represents a (local) time of day, independent of any particular day - -URI: [linkml:Time](https://w3id.org/linkml/Time) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Time | - diff --git a/projects/phenotype/docs/types/Uri.md b/projects/phenotype/docs/types/Uri.md deleted file mode 100644 index 343807a5e..000000000 --- a/projects/phenotype/docs/types/Uri.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: uri - - -a complete URI - -URI: [linkml:Uri](https://w3id.org/linkml/Uri) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URI** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node | -| **Close Mappings:** | | schema:URL | - diff --git a/projects/phenotype/docs/types/Uriorcurie.md b/projects/phenotype/docs/types/Uriorcurie.md deleted file mode 100644 index 2f7b65087..000000000 --- a/projects/phenotype/docs/types/Uriorcurie.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: uriorcurie - - -a URI or a CURIE - -URI: [linkml:Uriorcurie](https://w3id.org/linkml/Uriorcurie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URIorCURIE** | -| Representation | | str | diff --git a/projects/phenotype/excel/phenotype.xlsx b/projects/phenotype/excel/phenotype.xlsx deleted file mode 100644 index 80bd69cc1..000000000 Binary files a/projects/phenotype/excel/phenotype.xlsx and /dev/null differ diff --git a/projects/phenotype/graphql/phenotype.graphql b/projects/phenotype/graphql/phenotype.graphql deleted file mode 100644 index a6d131dfd..000000000 --- a/projects/phenotype/graphql/phenotype.graphql +++ /dev/null @@ -1,88 +0,0 @@ -type AnatomicalEntity - { - id: String! - label: String - } - -type AnnotatorResult - { - subjectText: String - objectId: String - objectText: String - } - -type Any - { - } - -type ChemicalEntity - { - id: String! - label: String - } - -interface CompoundExpression - { - } - -type ExtractionResult - { - inputId: String - inputTitle: String - inputText: String - rawCompletionOutput: String - prompt: String - extractedObject: Any - namedEntities: [Any] - } - -interface NamedEntity - { - id: String! - label: String - } - -type Publication - { - id: String - title: String - abstract: String - combinedText: String - fullText: String - } - -type Quality - { - id: String! - label: String - } - -type RelationshipType - { - id: String! - label: String - } - -type TextWithTriples - { - publication: Publication - triples: [Triple] - } - -type Trait - { - quality: Quality - anatomicalEntity: AnatomicalEntity - chemicalEntity: ChemicalEntity - } - -interface Triple - { - subject: NamedEntity - predicate: RelationshipType - object: NamedEntity - qualifier: String - subjectQualifier: NamedEntity - objectQualifier: NamedEntity - } - diff --git a/projects/phenotype/jsonld/phenotype.context.jsonld b/projects/phenotype/jsonld/phenotype.context.jsonld deleted file mode 100644 index 553f73430..000000000 --- a/projects/phenotype/jsonld/phenotype.context.jsonld +++ /dev/null @@ -1,140 +0,0 @@ -{ - "comments": { - "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2023-08-07T10:55:41", - "source": "phenotype.yaml" - }, - "@context": { - "CHEBI": "http://example.org/UNKNOWN/CHEBI/", - "PATO": "http://example.org/UNKNOWN/PATO/", - "PR": "http://example.org/UNKNOWN/PR/", - "RO": { - "@id": "http://purl.obolibrary.org/obo/RO_", - "@prefix": true - }, - "UBERON": "http://example.org/UNKNOWN/UBERON/", - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "linkml": "https://w3id.org/linkml/", - "phenotype": "http://w3id.org/ontogpt/phenotype/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "@vocab": "http://w3id.org/ontogpt/phenotype/", - "object_id": { - "@id": "core:object_id" - }, - "object_text": { - "@id": "core:object_text" - }, - "subject_text": { - "@id": "core:subject_text" - }, - "extracted_object": { - "@type": "@id", - "@id": "core:extracted_object" - }, - "input_id": { - "@id": "core:input_id" - }, - "input_text": { - "@id": "core:input_text" - }, - "input_title": { - "@id": "core:input_title" - }, - "named_entities": { - "@type": "@id", - "@id": "core:named_entities" - }, - "prompt": { - "@id": "core:prompt" - }, - "raw_completion_output": { - "@id": "core:raw_completion_output" - }, - "id": { - "@id": "core:id" - }, - "label": { - "@id": "rdfs:label" - }, - "abstract": { - "@id": "core:abstract" - }, - "combined_text": { - "@id": "core:combined_text" - }, - "full_text": { - "@id": "core:full_text" - }, - "title": { - "@id": "core:title" - }, - "publication": { - "@type": "@id", - "@id": "core:publication" - }, - "triples": { - "@type": "@id", - "@id": "core:triples" - }, - "anatomical_entity": { - "@type": "@id" - }, - "chemical_entity": { - "@type": "@id" - }, - "quality": { - "@type": "@id" - }, - "object": { - "@type": "@id", - "@id": "core:object" - }, - "object_qualifier": { - "@type": "@id", - "@id": "core:object_qualifier" - }, - "predicate": { - "@type": "@id", - "@id": "core:predicate" - }, - "qualifier": { - "@id": "core:qualifier" - }, - "subject": { - "@type": "@id", - "@id": "core:subject" - }, - "subject_qualifier": { - "@type": "@id", - "@id": "core:subject_qualifier" - }, - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } - } -} diff --git a/projects/phenotype/jsonld/phenotype.jsonld b/projects/phenotype/jsonld/phenotype.jsonld deleted file mode 100644 index eee2d6a7b..000000000 --- a/projects/phenotype/jsonld/phenotype.jsonld +++ /dev/null @@ -1,1160 +0,0 @@ -{ - "name": "eq-template", - "description": "A template for Computational Phenotypes", - "title": "EQ Template", - "id": "http://w3id.org/ontogpt/eq", - "imports": [ - "linkml:types", - "core" - ], - "license": "https://creativecommons.org/publicdomain/zero/1.0/", - "prefixes": [ - { - "prefix_prefix": "linkml", - "prefix_reference": "https://w3id.org/linkml/" - }, - { - "prefix_prefix": "phenotype", - "prefix_reference": "http://w3id.org/ontogpt/phenotype/" - } - ], - "default_prefix": "phenotype", - "default_range": "string", - "types": [ - { - "name": "string", - "definition_uri": "https://w3id.org/linkml/String", - "description": "A character string", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Text" - ], - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "@type": "TypeDefinition" - }, - { - "name": "integer", - "definition_uri": "https://w3id.org/linkml/Integer", - "description": "An integer", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Integer" - ], - "base": "int", - "uri": "http://www.w3.org/2001/XMLSchema#integer", - "@type": "TypeDefinition" - }, - { - "name": "boolean", - "definition_uri": "https://w3id.org/linkml/Boolean", - "description": "A binary (true or false) value", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Boolean" - ], - "base": "Bool", - "uri": "http://www.w3.org/2001/XMLSchema#boolean", - "repr": "bool", - "@type": "TypeDefinition" - }, - { - "name": "float", - "definition_uri": "https://w3id.org/linkml/Float", - "description": "A real number that conforms to the xsd:float specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#float", - "@type": "TypeDefinition" - }, - { - "name": "double", - "definition_uri": "https://w3id.org/linkml/Double", - "description": "A real number that conforms to the xsd:double specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#double", - "@type": "TypeDefinition" - }, - { - "name": "decimal", - "definition_uri": "https://w3id.org/linkml/Decimal", - "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "broad_mappings": [ - "schema:Number" - ], - "base": "Decimal", - "uri": "http://www.w3.org/2001/XMLSchema#decimal", - "@type": "TypeDefinition" - }, - { - "name": "time", - "definition_uri": "https://w3id.org/linkml/Time", - "description": "A time object represents a (local) time of day, independent of any particular day", - "notes": [ - "URI is dateTime because OWL reasoners do not work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Time" - ], - "base": "XSDTime", - "uri": "http://www.w3.org/2001/XMLSchema#time", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date", - "definition_uri": "https://w3id.org/linkml/Date", - "description": "a date (year, month and day) in an idealized calendar", - "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Date" - ], - "base": "XSDDate", - "uri": "http://www.w3.org/2001/XMLSchema#date", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "datetime", - "definition_uri": "https://w3id.org/linkml/Datetime", - "description": "The combination of a date and time", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:DateTime" - ], - "base": "XSDDateTime", - "uri": "http://www.w3.org/2001/XMLSchema#dateTime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date_or_datetime", - "definition_uri": "https://w3id.org/linkml/DateOrDatetime", - "description": "Either a date or a datetime", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "https://w3id.org/linkml/DateOrDatetime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uriorcurie", - "definition_uri": "https://w3id.org/linkml/Uriorcurie", - "description": "a URI or a CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "URIorCURIE", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "curie", - "definition_uri": "https://w3id.org/linkml/Curie", - "conforms_to": "https://www.w3.org/TR/curie/", - "description": "a compact URI", - "comments": [ - "in RDF serializations this MUST be expanded to a URI", - "in non-RDF serializations MAY be serialized as the compact representation" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "Curie", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uri", - "definition_uri": "https://w3id.org/linkml/Uri", - "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", - "description": "a complete URI", - "comments": [ - "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:URL" - ], - "base": "URI", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "ncname", - "definition_uri": "https://w3id.org/linkml/Ncname", - "description": "Prefix part of CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NCName", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "objectidentifier", - "definition_uri": "https://w3id.org/linkml/Objectidentifier", - "description": "A URI or CURIE that represents an object in the model.", - "comments": [ - "Used for inheritance and type checking" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "ElementIdentifier", - "uri": "http://www.w3.org/ns/shex#iri", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "nodeidentifier", - "definition_uri": "https://w3id.org/linkml/Nodeidentifier", - "description": "A URI, CURIE or BNODE that represents a node in a model.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NodeIdentifier", - "uri": "http://www.w3.org/ns/shex#nonLiteral", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpointer", - "definition_uri": "https://w3id.org/linkml/Jsonpointer", - "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901", - "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpath", - "definition_uri": "https://w3id.org/linkml/Jsonpath", - "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html", - "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "sparqlpath", - "definition_uri": "https://w3id.org/linkml/Sparqlpath", - "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths", - "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - } - ], - "enums": [ - { - "name": "NullDataOptions", - "definition_uri": "http://w3id.org/ontogpt/core/NullDataOptions", - "from_schema": "http://w3id.org/ontogpt/core", - "permissible_values": [ - { - "text": "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "meaning": "NCIT:C149701" - }, - { - "text": "NOT_APPLICABLE", - "meaning": "NCIT:C18902", - "aliases": [ - "not applicable", - "N/A" - ] - }, - { - "text": "NOT_MENTIONED" - } - ] - } - ], - "slots": [ - { - "name": "trait__quality", - "annotations": [ - { - "tag": "prompt.example", - "value": "amount, level, increased amount, decreased concentration", - "@type": "Annotation" - } - ], - "description": "The property being measured, or changes in this property, for example, amount, level, increased amount, decreased concentration", - "from_schema": "http://w3id.org/ontogpt/eq", - "slot_uri": "http://w3id.org/ontogpt/phenotype/quality", - "alias": "quality", - "owner": "Trait", - "domain_of": [ - "Trait" - ], - "range": "Quality", - "@type": "SlotDefinition" - }, - { - "name": "trait__anatomical_entity", - "annotations": [ - { - "tag": "prompt.example", - "value": "liver, heart, brain, finger", - "@type": "Annotation" - } - ], - "description": "The anatomical location that the chemical entity is measured in", - "from_schema": "http://w3id.org/ontogpt/eq", - "slot_uri": "http://w3id.org/ontogpt/phenotype/anatomical_entity", - "alias": "anatomical_entity", - "owner": "Trait", - "domain_of": [ - "Trait" - ], - "range": "AnatomicalEntity", - "@type": "SlotDefinition" - }, - { - "name": "trait__chemical_entity", - "annotations": [ - { - "tag": "prompt.example", - "value": "lysine, metabolite", - "@type": "Annotation" - } - ], - "description": "The chemical entity that is being measured", - "from_schema": "http://w3id.org/ontogpt/eq", - "slot_uri": "http://w3id.org/ontogpt/phenotype/chemical_entity", - "alias": "chemical_entity", - "owner": "Trait", - "domain_of": [ - "Trait" - ], - "range": "ChemicalEntity", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_id", - "alias": "input_id", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_title", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_title", - "alias": "input_title", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_text", - "alias": "input_text", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__raw_completion_output", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/raw_completion_output", - "alias": "raw_completion_output", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__prompt", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/prompt", - "alias": "prompt", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__extracted_object", - "description": "The complex objects extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/extracted_object", - "alias": "extracted_object", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__named_entities", - "description": "Named entities extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/named_entities", - "multivalued": true, - "alias": "named_entities", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "identifier": true, - "alias": "id", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "required": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "from_schema": "http://w3id.org/ontogpt/core", - "aliases": [ - "name" - ], - "mappings": [ - "http://example.org/UNKNOWN/rdfs/label" - ], - "slot_uri": "http://example.org/UNKNOWN/rdfs/label", - "alias": "label", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject", - "alias": "subject", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__predicate", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/predicate", - "alias": "predicate", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "triple__object", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object", - "alias": "object", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/qualifier", - "alias": "qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_qualifier", - "alias": "subject_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_qualifier", - "alias": "object_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/publication", - "alias": "publication", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__triples", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/triples", - "multivalued": true, - "alias": "triples", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "publication__id", - "description": "The publication identifier", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "alias": "id", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__title", - "description": "The title of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/title", - "alias": "title", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__abstract", - "description": "The abstract of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/abstract", - "alias": "abstract", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__combined_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/combined_text", - "alias": "combined_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__full_text", - "description": "The full text of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/full_text", - "alias": "full_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__subject_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_text", - "alias": "subject_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_id", - "alias": "object_id", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_text", - "alias": "object_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - } - ], - "classes": [ - { - "name": "Trait", - "definition_uri": "http://w3id.org/ontogpt/phenotype/Trait", - "from_schema": "http://w3id.org/ontogpt/eq", - "slots": [ - "trait__quality", - "trait__anatomical_entity", - "trait__chemical_entity" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "quality", - "annotations": [ - { - "tag": "prompt.example", - "value": "amount, level, increased amount, decreased concentration", - "@type": "Annotation" - } - ], - "description": "The property being measured, or changes in this property, for example, amount, level, increased amount, decreased concentration", - "range": "Quality", - "@type": "SlotDefinition" - }, - { - "name": "anatomical_entity", - "annotations": [ - { - "tag": "prompt.example", - "value": "liver, heart, brain, finger", - "@type": "Annotation" - } - ], - "description": "The anatomical location that the chemical entity is measured in", - "range": "AnatomicalEntity", - "@type": "SlotDefinition" - }, - { - "name": "chemical_entity", - "annotations": [ - { - "tag": "prompt.example", - "value": "lysine, metabolite", - "@type": "Annotation" - } - ], - "description": "The chemical entity that is being measured", - "range": "ChemicalEntity", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/phenotype/Trait", - "tree_root": true, - "@type": "ClassDefinition" - }, - { - "name": "Quality", - "id_prefixes": [ - "PATO" - ], - "definition_uri": "http://w3id.org/ontogpt/phenotype/Quality", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:pato", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/eq", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/phenotype/Quality", - "@type": "ClassDefinition" - }, - { - "name": "ChemicalEntity", - "id_prefixes": [ - "CHEBI", - "PR" - ], - "definition_uri": "http://w3id.org/ontogpt/phenotype/ChemicalEntity", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:chebi", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/eq", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/phenotype/ChemicalEntity", - "@type": "ClassDefinition" - }, - { - "name": "AnatomicalEntity", - "id_prefixes": [ - "UBERON" - ], - "definition_uri": "http://w3id.org/ontogpt/phenotype/AnatomicalEntity", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:uberon", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/eq", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/phenotype/AnatomicalEntity", - "@type": "ClassDefinition" - }, - { - "name": "Any", - "definition_uri": "http://w3id.org/ontogpt/core/Any", - "from_schema": "http://w3id.org/ontogpt/core", - "mappings": [ - "linkml:Any" - ], - "slot_usage": {}, - "class_uri": "https://w3id.org/linkml/Any", - "@type": "ClassDefinition" - }, - { - "name": "ExtractionResult", - "definition_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "description": "A result of extracting knowledge on text", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "extractionResult__input_id", - "extractionResult__input_title", - "extractionResult__input_text", - "extractionResult__raw_completion_output", - "extractionResult__prompt", - "extractionResult__extracted_object", - "extractionResult__named_entities" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "input_id", - "@type": "SlotDefinition" - }, - { - "name": "input_title", - "@type": "SlotDefinition" - }, - { - "name": "input_text", - "@type": "SlotDefinition" - }, - { - "name": "raw_completion_output", - "@type": "SlotDefinition" - }, - { - "name": "prompt", - "@type": "SlotDefinition" - }, - { - "name": "extracted_object", - "description": "The complex objects extracted from the text", - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "named_entities", - "description": "Named entities extracted from the text", - "multivalued": true, - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "@type": "ClassDefinition" - }, - { - "name": "NamedEntity", - "definition_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "identifier": true, - "@type": "SlotDefinition" - }, - { - "name": "label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "aliases": [ - "name" - ], - "slot_uri": "rdfs:label", - "range": "string", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "@type": "ClassDefinition" - }, - { - "name": "CompoundExpression", - "definition_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "@type": "ClassDefinition" - }, - { - "name": "Triple", - "definition_uri": "http://w3id.org/ontogpt/core/Triple", - "description": "Abstract parent for Relation Extraction tasks", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "CompoundExpression", - "abstract": true, - "slots": [ - "triple__subject", - "triple__predicate", - "triple__object", - "triple__qualifier", - "triple__subject_qualifier", - "triple__object_qualifier" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "predicate", - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "object", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Triple", - "@type": "ClassDefinition" - }, - { - "name": "TextWithTriples", - "definition_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "textWithTriples__publication", - "textWithTriples__triples" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "triples", - "multivalued": true, - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "@type": "ClassDefinition" - }, - { - "name": "RelationshipType", - "id_prefixes": [ - "RO", - "biolink" - ], - "definition_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "@type": "ClassDefinition" - }, - { - "name": "Publication", - "definition_uri": "http://w3id.org/ontogpt/core/Publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "publication__id", - "publication__title", - "publication__abstract", - "publication__combined_text", - "publication__full_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "description": "The publication identifier", - "@type": "SlotDefinition" - }, - { - "name": "title", - "description": "The title of the publication", - "@type": "SlotDefinition" - }, - { - "name": "abstract", - "description": "The abstract of the publication", - "@type": "SlotDefinition" - }, - { - "name": "combined_text", - "@type": "SlotDefinition" - }, - { - "name": "full_text", - "description": "The full text of the publication", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Publication", - "@type": "ClassDefinition" - }, - { - "name": "AnnotatorResult", - "definition_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "annotatorResult__subject_text", - "annotatorResult__object_id", - "annotatorResult__object_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject_text", - "@type": "SlotDefinition" - }, - { - "name": "object_id", - "@type": "SlotDefinition" - }, - { - "name": "object_text", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "@type": "ClassDefinition" - } - ], - "metamodel_version": "1.7.0", - "source_file": "phenotype.yaml", - "source_file_date": "2023-06-17T15:11:19", - "source_file_size": 1532, - "generation_date": "2023-08-07T10:55:42", - "keywords": [ - "phenotype", - "traits" - ], - "@type": "SchemaDefinition", - "@context": [ - "projects/phenotype/jsonld/phenotype.context.jsonld", - "https://w3id.org/linkml/types.context.jsonld", - "core.context.jsonld", - { - "@base": "http://w3id.org/ontogpt/phenotype/" - } - ] -} diff --git a/projects/phenotype/jsonschema/phenotype.schema.json b/projects/phenotype/jsonschema/phenotype.schema.json deleted file mode 100644 index 2917ae1bd..000000000 --- a/projects/phenotype/jsonschema/phenotype.schema.json +++ /dev/null @@ -1,232 +0,0 @@ -{ - "$defs": { - "AnatomicalEntity": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "AnatomicalEntity", - "type": "object" - }, - "AnnotatorResult": { - "additionalProperties": false, - "description": "", - "properties": { - "object_id": { - "type": "string" - }, - "object_text": { - "type": "string" - }, - "subject_text": { - "type": "string" - } - }, - "title": "AnnotatorResult", - "type": "object" - }, - "Any": { - "additionalProperties": true, - "description": "", - "title": "Any", - "type": "object" - }, - "ChemicalEntity": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "ChemicalEntity", - "type": "object" - }, - "ExtractionResult": { - "additionalProperties": false, - "description": "A result of extracting knowledge on text", - "properties": { - "extracted_object": { - "$ref": "#/$defs/Any", - "description": "The complex objects extracted from the text" - }, - "input_id": { - "type": "string" - }, - "input_text": { - "type": "string" - }, - "input_title": { - "type": "string" - }, - "named_entities": { - "description": "Named entities extracted from the text", - "items": { - "$ref": "#/$defs/Any" - }, - "type": "array" - }, - "prompt": { - "type": "string" - }, - "raw_completion_output": { - "type": "string" - } - }, - "title": "ExtractionResult", - "type": "object" - }, - "NullDataOptions": { - "description": "", - "enum": [ - "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "NOT_APPLICABLE", - "NOT_MENTIONED" - ], - "title": "NullDataOptions", - "type": "string" - }, - "Publication": { - "additionalProperties": false, - "description": "", - "properties": { - "abstract": { - "description": "The abstract of the publication", - "type": "string" - }, - "combined_text": { - "type": "string" - }, - "full_text": { - "description": "The full text of the publication", - "type": "string" - }, - "id": { - "description": "The publication identifier", - "type": "string" - }, - "title": { - "description": "The title of the publication", - "type": "string" - } - }, - "title": "Publication", - "type": "object" - }, - "Quality": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Quality", - "type": "object" - }, - "RelationshipType": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "RelationshipType", - "type": "object" - }, - "TextWithTriples": { - "additionalProperties": false, - "description": "", - "properties": { - "publication": { - "$ref": "#/$defs/Publication" - }, - "triples": { - "items": { - "$ref": "#/$defs/Triple" - }, - "type": "array" - } - }, - "title": "TextWithTriples", - "type": "object" - }, - "Trait": { - "additionalProperties": false, - "description": "", - "properties": { - "anatomical_entity": { - "description": "The anatomical location that the chemical entity is measured in", - "type": "string" - }, - "chemical_entity": { - "description": "The chemical entity that is being measured", - "type": "string" - }, - "quality": { - "description": "The property being measured, or changes in this property, for example, amount, level, increased amount, decreased concentration", - "type": "string" - } - }, - "title": "Trait", - "type": "object" - } - }, - "$id": "http://w3id.org/ontogpt/eq", - "$schema": "http://json-schema.org/draft-07/schema#", - "additionalProperties": true, - "metamodel_version": "1.7.0", - "properties": { - "anatomical_entity": { - "description": "The anatomical location that the chemical entity is measured in", - "type": "string" - }, - "chemical_entity": { - "description": "The chemical entity that is being measured", - "type": "string" - }, - "quality": { - "description": "The property being measured, or changes in this property, for example, amount, level, increased amount, decreased concentration", - "type": "string" - } - }, - "title": "eq-template", - "type": "object", - "version": null -} \ No newline at end of file diff --git a/projects/phenotype/owl/phenotype.owl.ttl b/projects/phenotype/owl/phenotype.owl.ttl deleted file mode 100644 index 724513002..000000000 --- a/projects/phenotype/owl/phenotype.owl.ttl +++ /dev/null @@ -1,416 +0,0 @@ -@prefix IAO: <http://purl.obolibrary.org/obo/IAO_> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix owl: <http://www.w3.org/2002/07/owl#> . -@prefix phenotype: <http://w3id.org/ontogpt/phenotype/> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . -@prefix skos: <http://www.w3.org/2004/02/skos/core#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -<http://w3id.org/ontogpt/eq> a owl:Ontology ; - rdfs:label "eq-template" ; - IAO:0000700 <http://w3id.org/ontogpt/core/AnnotatorResult>, - <http://w3id.org/ontogpt/core/Any>, - <http://w3id.org/ontogpt/core/CompoundExpression>, - <http://w3id.org/ontogpt/core/ExtractionResult>, - <http://w3id.org/ontogpt/core/NamedEntity>, - <http://w3id.org/ontogpt/core/Publication>, - <http://w3id.org/ontogpt/core/TextWithTriples>, - phenotype:Trait ; - linkml:classes "{'Trait': ClassDefinition(name='Trait', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/phenotype/Trait', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/eq', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['trait__quality', 'trait__anatomical_entity', 'trait__chemical_entity'], slot_usage={}, attributes={'quality': SlotDefinition(name='quality', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.example': Annotation(tag='prompt.example', value='amount, level, increased amount, decreased concentration', extensions={}, annotations={})}, description='The property being measured, or changes in this property, for example, amount, level, increased amount, decreased concentration', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Quality', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'anatomical_entity': SlotDefinition(name='anatomical_entity', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.example': Annotation(tag='prompt.example', value='liver, heart, brain, finger', extensions={}, annotations={})}, description='The anatomical location that the chemical entity is measured in', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='AnatomicalEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'chemical_entity': SlotDefinition(name='chemical_entity', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.example': Annotation(tag='prompt.example', value='lysine, metabolite', extensions={}, annotations={})}, description='The chemical entity that is being measured', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ChemicalEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='phenotype:Trait', subclass_of=None, union_of=[], defining_slots=[], tree_root=True, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Quality': ClassDefinition(name='Quality', id_prefixes=['PATO'], definition_uri='http://w3id.org/ontogpt/phenotype/Quality', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:pato', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/eq', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='phenotype:Quality', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ChemicalEntity': ClassDefinition(name='ChemicalEntity', id_prefixes=['CHEBI', 'PR'], definition_uri='http://w3id.org/ontogpt/phenotype/ChemicalEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:chebi', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/eq', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='phenotype:ChemicalEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'AnatomicalEntity': ClassDefinition(name='AnatomicalEntity', id_prefixes=['UBERON'], definition_uri='http://w3id.org/ontogpt/phenotype/AnatomicalEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:uberon', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/eq', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='phenotype:AnatomicalEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Any': ClassDefinition(name='Any', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Any', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=['linkml:Any'], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='linkml:Any', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ExtractionResult': ClassDefinition(name='ExtractionResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/ExtractionResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A result of extracting knowledge on text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['extractionResult__input_id', 'extractionResult__input_title', 'extractionResult__input_text', 'extractionResult__raw_completion_output', 'extractionResult__prompt', 'extractionResult__extracted_object', 'extractionResult__named_entities'], slot_usage={}, attributes={'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:ExtractionResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'NamedEntity': ClassDefinition(name='NamedEntity', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NamedEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:NamedEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'CompoundExpression': ClassDefinition(name='CompoundExpression', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/CompoundExpression', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='core:CompoundExpression', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Triple': ClassDefinition(name='Triple', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Triple', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Abstract parent for Relation Extraction tasks', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['triple__subject', 'triple__predicate', 'triple__object', 'triple__qualifier', 'triple__subject_qualifier', 'triple__object_qualifier'], slot_usage={}, attributes={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Triple', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'TextWithTriples': ClassDefinition(name='TextWithTriples', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/TextWithTriples', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['textWithTriples__publication', 'textWithTriples__triples'], slot_usage={}, attributes={'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:TextWithTriples', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'RelationshipType': ClassDefinition(name='RelationshipType', id_prefixes=['RO', 'biolink'], definition_uri='http://w3id.org/ontogpt/core/RelationshipType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='core:RelationshipType', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Publication': ClassDefinition(name='Publication', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Publication', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['publication__id', 'publication__title', 'publication__abstract', 'publication__combined_text', 'publication__full_text'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Publication', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'AnnotatorResult': ClassDefinition(name='AnnotatorResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/AnnotatorResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['annotatorResult__subject_text', 'annotatorResult__object_id', 'annotatorResult__object_text'], slot_usage={}, attributes={'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:AnnotatorResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={})}" ; - linkml:enums "{'NullDataOptions': EnumDefinition(name='NullDataOptions', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NullDataOptions', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'UNSPECIFIED_METHOD_OF_ADMINISTRATION': PermissibleValue(text='UNSPECIFIED_METHOD_OF_ADMINISTRATION', description=None, meaning='NCIT:C149701', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_APPLICABLE': PermissibleValue(text='NOT_APPLICABLE', description=None, meaning='NCIT:C18902', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['not applicable', 'N/A'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_MENTIONED': PermissibleValue(text='NOT_MENTIONED', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[])}" ; - linkml:id "http://w3id.org/ontogpt/eq" ; - linkml:imports "core", - "linkml:types" ; - linkml:types "{'string': TypeDefinition(name='string', id_prefixes=[], definition_uri='https://w3id.org/linkml/String', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A character string', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Text'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'integer': TypeDefinition(name='integer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Integer', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An integer', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Integer'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='int', uri='xsd:integer', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'boolean': TypeDefinition(name='boolean', id_prefixes=[], definition_uri='https://w3id.org/linkml/Boolean', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A binary (true or false) value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Boolean'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Bool', uri='xsd:boolean', repr='bool', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'float': TypeDefinition(name='float', id_prefixes=[], definition_uri='https://w3id.org/linkml/Float', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:float specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Float'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:float', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'double': TypeDefinition(name='double', id_prefixes=[], definition_uri='https://w3id.org/linkml/Double', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:double specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:Float'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:double', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'decimal': TypeDefinition(name='decimal', id_prefixes=[], definition_uri='https://w3id.org/linkml/Decimal', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number with arbitrary precision that conforms to the xsd:decimal specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=['schema:Number'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Decimal', uri='xsd:decimal', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'time': TypeDefinition(name='time', id_prefixes=[], definition_uri='https://w3id.org/linkml/Time', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A time object represents a (local) time of day, independent of any particular day', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=['URI is dateTime because OWL reasoners do not work with straight date or time'], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Time'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDTime', uri='xsd:time', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date': TypeDefinition(name='date', id_prefixes=[], definition_uri='https://w3id.org/linkml/Date', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a date (year, month and day) in an idealized calendar', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[\"URI is dateTime because OWL reasoners don't work with straight date or time\"], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Date'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDate', uri='xsd:date', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'datetime': TypeDefinition(name='datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/Datetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The combination of a date and time', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:DateTime'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDateTime', uri='xsd:dateTime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date_or_datetime': TypeDefinition(name='date_or_datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/DateOrDatetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Either a date or a datetime', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='linkml:DateOrDatetime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uriorcurie': TypeDefinition(name='uriorcurie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uriorcurie', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a URI or a CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URIorCURIE', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'curie': TypeDefinition(name='curie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Curie', local_names={}, conforms_to='https://www.w3.org/TR/curie/', implements=[], extensions={}, annotations={}, description='a compact URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations this MUST be expanded to a URI', 'in non-RDF serializations MAY be serialized as the compact representation'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Curie', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uri': TypeDefinition(name='uri', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uri', local_names={}, conforms_to='https://www.ietf.org/rfc/rfc3987.txt', implements=[], extensions={}, annotations={}, description='a complete URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:URL'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URI', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ncname': TypeDefinition(name='ncname', id_prefixes=[], definition_uri='https://w3id.org/linkml/Ncname', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Prefix part of CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NCName', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'objectidentifier': TypeDefinition(name='objectidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Objectidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI or CURIE that represents an object in the model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['Used for inheritance and type checking'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='ElementIdentifier', uri='shex:iri', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'nodeidentifier': TypeDefinition(name='nodeidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Nodeidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI, CURIE or BNODE that represents a node in a model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NodeIdentifier', uri='shex:nonLiteral', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpointer': TypeDefinition(name='jsonpointer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpointer', local_names={}, conforms_to='https://datatracker.ietf.org/doc/html/rfc6901', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpath': TypeDefinition(name='jsonpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpath', local_names={}, conforms_to='https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sparqlpath': TypeDefinition(name='sparqlpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Sparqlpath', local_names={}, conforms_to='https://www.w3.org/TR/sparql11-query/#propertypaths', implements=[], extensions={}, annotations={}, description='A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:SubsetDefinition a owl:Class ; - rdfs:label "subset_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" . - -linkml:TypeDefinition a owl:Class ; - rdfs:label "type_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" ; - linkml:mixins "type_expression" . - -linkml:topValue a owl:DatatypeProperty ; - rdfs:label "value" . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "AnnotatorResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_text> ] ; - linkml:attributes "{'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/ExtractionResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ExtractionResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/named_entities> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/extracted_object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/prompt> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_title> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/raw_completion_output> ] ; - skos:definition "A result of extracting knowledge on text" ; - linkml:attributes "{'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/TextWithTriples> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TextWithTriples" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Publication> ; - owl:onProperty <http://w3id.org/ontogpt/core/publication> ], - [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Triple> ; - owl:onProperty <http://w3id.org/ontogpt/core/triples> ] ; - linkml:attributes "{'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/abstract> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "abstract" ; - rdfs:range linkml:String ; - skos:definition "The abstract of the publication" . - -<http://w3id.org/ontogpt/core/combined_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "combined_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/extracted_object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "extracted_object" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "The complex objects extracted from the text" . - -<http://w3id.org/ontogpt/core/full_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "full_text" ; - rdfs:range linkml:String ; - skos:definition "The full text of the publication" . - -<http://w3id.org/ontogpt/core/input_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_title" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/named_entities> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "named_entities" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "Named entities extracted from the text" . - -<http://w3id.org/ontogpt/core/object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/object_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/object_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" . - -<http://w3id.org/ontogpt/core/object_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/predicate> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "predicate" ; - rdfs:range <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/prompt> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "prompt" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/publication> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "publication" ; - phenotype:prompt.skip "true" ; - rdfs:range <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "qualifier" ; - rdfs:range linkml:String ; - skos:definition "A qualifier for the statements, e.g. \"NOT\" for negation" . - -<http://w3id.org/ontogpt/core/raw_completion_output> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "raw_completion_output" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/subject> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/subject_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" . - -<http://w3id.org/ontogpt/core/subject_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "title" ; - rdfs:range linkml:String ; - skos:definition "The title of the publication" . - -<http://w3id.org/ontogpt/core/triples> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "triples" ; - rdfs:range <http://w3id.org/ontogpt/core/Triple> . - -phenotype:Trait a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Trait" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass phenotype:Quality ; - owl:onProperty phenotype:quality ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass phenotype:AnatomicalEntity ; - owl:onProperty phenotype:anatomical_entity ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass phenotype:ChemicalEntity ; - owl:onProperty phenotype:chemical_entity ] ; - linkml:attributes "{'quality': SlotDefinition(name='quality', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.example': Annotation(tag='prompt.example', value='amount, level, increased amount, decreased concentration', extensions={}, annotations={})}, description='The property being measured, or changes in this property, for example, amount, level, increased amount, decreased concentration', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Quality', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'anatomical_entity': SlotDefinition(name='anatomical_entity', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.example': Annotation(tag='prompt.example', value='liver, heart, brain, finger', extensions={}, annotations={})}, description='The anatomical location that the chemical entity is measured in', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='AnatomicalEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'chemical_entity': SlotDefinition(name='chemical_entity', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.example': Annotation(tag='prompt.example', value='lysine, metabolite', extensions={}, annotations={})}, description='The chemical entity that is being measured', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ChemicalEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -phenotype:anatomical_entity a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "anatomical_entity" ; - phenotype:prompt.example "liver, heart, brain, finger" ; - rdfs:range phenotype:AnatomicalEntity ; - skos:definition "The anatomical location that the chemical entity is measured in" . - -phenotype:chemical_entity a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "chemical_entity" ; - phenotype:prompt.example "lysine, metabolite" ; - rdfs:range phenotype:ChemicalEntity ; - skos:definition "The chemical entity that is being measured" . - -phenotype:quality a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "quality" ; - phenotype:prompt.example "amount, level, increased amount, decreased concentration" ; - rdfs:range phenotype:Quality ; - skos:definition "The property being measured, or changes in this property, for example, amount, level, increased amount, decreased concentration" . - -<http://example.org/UNKNOWN/rdfs/label> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "label" ; - phenotype:owl "AnnotationProperty, AnnotationAssertion" ; - rdfs:range linkml:String ; - skos:altLabel "name" ; - skos:definition "The label (name) of the named thing" ; - skos:exactMatch <http://example.org/UNKNOWN/rdfs/label> . - -<http://purl.obolibrary.org/obo/NCIT_C149701> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "UNSPECIFIED_METHOD_OF_ADMINISTRATION" . - -<http://purl.obolibrary.org/obo/NCIT_C18902> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_APPLICABLE" . - -<http://w3id.org/ontogpt/core/CompoundExpression> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CompoundExpression" ; - linkml:attributes "{}" . - -<http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_MENTIONED" . - -<http://w3id.org/ontogpt/core/RelationshipType> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "RelationshipType" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/Triple> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Triple" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/RelationshipType> ; - owl:onProperty <http://w3id.org/ontogpt/core/predicate> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_qualifier> ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - skos:definition "Abstract parent for Relation Extraction tasks" ; - linkml:attributes "{'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -<http://w3id.org/ontogpt/core/id> a owl:ObjectProperty, - linkml:SlotDefinition . - -phenotype:AnatomicalEntity a owl:Class, - linkml:ClassDefinition ; - rdfs:label "AnatomicalEntity" ; - phenotype:annotators "sqlite:obo:uberon" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -phenotype:ChemicalEntity a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ChemicalEntity" ; - phenotype:annotators "sqlite:obo:chebi" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -phenotype:Quality a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Quality" ; - phenotype:annotators "sqlite:obo:pato" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/NullDataOptions> a owl:Class, - linkml:EnumDefinition ; - rdfs:label "NullDataOptions" ; - owl:unionOf ( <http://purl.obolibrary.org/obo/NCIT_C149701> <http://purl.obolibrary.org/obo/NCIT_C18902> <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> ) ; - linkml:permissible_values <http://purl.obolibrary.org/obo/NCIT_C149701>, - <http://purl.obolibrary.org/obo/NCIT_C18902>, - <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> . - -<http://w3id.org/ontogpt/core/Publication> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Publication" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/combined_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/title> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/abstract> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/full_text> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/Any> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Any" ; - skos:exactMatch linkml:Any ; - linkml:attributes "{}" . - -<http://w3id.org/ontogpt/core/NamedEntity> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "NamedEntity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://example.org/UNKNOWN/rdfs/label> ], - [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ; - owl:qualifiedCardinality 1 ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:ClassDefinition a owl:Class ; - rdfs:label "class_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "class_expression" . - -linkml:SlotDefinition a owl:Class ; - rdfs:label "slot_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "slot_expression" . - - diff --git a/projects/phenotype/phenotype.py b/projects/phenotype/phenotype.py deleted file mode 100644 index f70864d7d..000000000 --- a/projects/phenotype/phenotype.py +++ /dev/null @@ -1,473 +0,0 @@ -# Auto generated from phenotype.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-08-07T10:55:50 -# Schema: eq-template -# -# id: http://w3id.org/ontogpt/eq -# description: A template for Computational Phenotypes -# license: https://creativecommons.org/publicdomain/zero/1.0/ - -import dataclasses -import sys -import re -from jsonasobj2 import JsonObj, as_dict -from typing import Optional, List, Union, Dict, ClassVar, Any -from dataclasses import dataclass -from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions - -from linkml_runtime.utils.slot import Slot -from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode -from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int -from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs -from linkml_runtime.utils.formatutils import camelcase, underscore, sfx -from linkml_runtime.utils.enumerations import EnumDefinitionImpl -from rdflib import Namespace, URIRef -from linkml_runtime.utils.curienamespace import CurieNamespace -from linkml_runtime.linkml_model.types import String - -metamodel_version = "1.7.0" -version = None - -# Overwrite dataclasses _init_fn to add **kwargs in __init__ -dataclasses._init_fn = dataclasses_init_fn_with_kwargs - -# Namespaces -CHEBI = CurieNamespace('CHEBI', 'http://example.org/UNKNOWN/CHEBI/') -PATO = CurieNamespace('PATO', 'http://example.org/UNKNOWN/PATO/') -PR = CurieNamespace('PR', 'http://example.org/UNKNOWN/PR/') -RO = CurieNamespace('RO', 'http://purl.obolibrary.org/obo/RO_') -UBERON = CurieNamespace('UBERON', 'http://example.org/UNKNOWN/UBERON/') -BIOLINK = CurieNamespace('biolink', 'http://example.org/UNKNOWN/biolink/') -CORE = CurieNamespace('core', 'http://w3id.org/ontogpt/core/') -LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') -PHENOTYPE = CurieNamespace('phenotype', 'http://w3id.org/ontogpt/phenotype/') -RDFS = CurieNamespace('rdfs', 'http://example.org/UNKNOWN/rdfs/') -DEFAULT_ = PHENOTYPE - - -# Types - -# Class references -class NamedEntityId(extended_str): - pass - - -class QualityId(NamedEntityId): - pass - - -class ChemicalEntityId(NamedEntityId): - pass - - -class AnatomicalEntityId(NamedEntityId): - pass - - -class RelationshipTypeId(NamedEntityId): - pass - - -@dataclass -class Trait(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = PHENOTYPE.Trait - class_class_curie: ClassVar[str] = "phenotype:Trait" - class_name: ClassVar[str] = "Trait" - class_model_uri: ClassVar[URIRef] = PHENOTYPE.Trait - - quality: Optional[Union[str, QualityId]] = None - anatomical_entity: Optional[Union[str, AnatomicalEntityId]] = None - chemical_entity: Optional[Union[str, ChemicalEntityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.quality is not None and not isinstance(self.quality, QualityId): - self.quality = QualityId(self.quality) - - if self.anatomical_entity is not None and not isinstance(self.anatomical_entity, AnatomicalEntityId): - self.anatomical_entity = AnatomicalEntityId(self.anatomical_entity) - - if self.chemical_entity is not None and not isinstance(self.chemical_entity, ChemicalEntityId): - self.chemical_entity = ChemicalEntityId(self.chemical_entity) - - super().__post_init__(**kwargs) - - -Any = Any - -@dataclass -class ExtractionResult(YAMLRoot): - """ - A result of extracting knowledge on text - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.ExtractionResult - class_class_curie: ClassVar[str] = "core:ExtractionResult" - class_name: ClassVar[str] = "ExtractionResult" - class_model_uri: ClassVar[URIRef] = PHENOTYPE.ExtractionResult - - input_id: Optional[str] = None - input_title: Optional[str] = None - input_text: Optional[str] = None - raw_completion_output: Optional[str] = None - prompt: Optional[str] = None - extracted_object: Optional[Union[dict, Any]] = None - named_entities: Optional[Union[Union[dict, Any], List[Union[dict, Any]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.input_id is not None and not isinstance(self.input_id, str): - self.input_id = str(self.input_id) - - if self.input_title is not None and not isinstance(self.input_title, str): - self.input_title = str(self.input_title) - - if self.input_text is not None and not isinstance(self.input_text, str): - self.input_text = str(self.input_text) - - if self.raw_completion_output is not None and not isinstance(self.raw_completion_output, str): - self.raw_completion_output = str(self.raw_completion_output) - - if self.prompt is not None and not isinstance(self.prompt, str): - self.prompt = str(self.prompt) - - super().__post_init__(**kwargs) - - -@dataclass -class NamedEntity(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.NamedEntity - class_class_curie: ClassVar[str] = "core:NamedEntity" - class_name: ClassVar[str] = "NamedEntity" - class_model_uri: ClassVar[URIRef] = PHENOTYPE.NamedEntity - - id: Union[str, NamedEntityId] = None - label: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, NamedEntityId): - self.id = NamedEntityId(self.id) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - super().__post_init__(**kwargs) - - -@dataclass -class Quality(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = PHENOTYPE.Quality - class_class_curie: ClassVar[str] = "phenotype:Quality" - class_name: ClassVar[str] = "Quality" - class_model_uri: ClassVar[URIRef] = PHENOTYPE.Quality - - id: Union[str, QualityId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, QualityId): - self.id = QualityId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class ChemicalEntity(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = PHENOTYPE.ChemicalEntity - class_class_curie: ClassVar[str] = "phenotype:ChemicalEntity" - class_name: ClassVar[str] = "ChemicalEntity" - class_model_uri: ClassVar[URIRef] = PHENOTYPE.ChemicalEntity - - id: Union[str, ChemicalEntityId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, ChemicalEntityId): - self.id = ChemicalEntityId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class AnatomicalEntity(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = PHENOTYPE.AnatomicalEntity - class_class_curie: ClassVar[str] = "phenotype:AnatomicalEntity" - class_name: ClassVar[str] = "AnatomicalEntity" - class_model_uri: ClassVar[URIRef] = PHENOTYPE.AnatomicalEntity - - id: Union[str, AnatomicalEntityId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, AnatomicalEntityId): - self.id = AnatomicalEntityId(self.id) - - super().__post_init__(**kwargs) - - -class CompoundExpression(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.CompoundExpression - class_class_curie: ClassVar[str] = "core:CompoundExpression" - class_name: ClassVar[str] = "CompoundExpression" - class_model_uri: ClassVar[URIRef] = PHENOTYPE.CompoundExpression - - -@dataclass -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Triple - class_class_curie: ClassVar[str] = "core:Triple" - class_name: ClassVar[str] = "Triple" - class_model_uri: ClassVar[URIRef] = PHENOTYPE.Triple - - subject: Optional[Union[str, NamedEntityId]] = None - predicate: Optional[Union[str, RelationshipTypeId]] = None - object: Optional[Union[str, NamedEntityId]] = None - qualifier: Optional[str] = None - subject_qualifier: Optional[Union[str, NamedEntityId]] = None - object_qualifier: Optional[Union[str, NamedEntityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, NamedEntityId): - self.subject = NamedEntityId(self.subject) - - if self.predicate is not None and not isinstance(self.predicate, RelationshipTypeId): - self.predicate = RelationshipTypeId(self.predicate) - - if self.object is not None and not isinstance(self.object, NamedEntityId): - self.object = NamedEntityId(self.object) - - if self.qualifier is not None and not isinstance(self.qualifier, str): - self.qualifier = str(self.qualifier) - - if self.subject_qualifier is not None and not isinstance(self.subject_qualifier, NamedEntityId): - self.subject_qualifier = NamedEntityId(self.subject_qualifier) - - if self.object_qualifier is not None and not isinstance(self.object_qualifier, NamedEntityId): - self.object_qualifier = NamedEntityId(self.object_qualifier) - - super().__post_init__(**kwargs) - - -@dataclass -class TextWithTriples(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.TextWithTriples - class_class_curie: ClassVar[str] = "core:TextWithTriples" - class_name: ClassVar[str] = "TextWithTriples" - class_model_uri: ClassVar[URIRef] = PHENOTYPE.TextWithTriples - - publication: Optional[Union[dict, "Publication"]] = None - triples: Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.publication is not None and not isinstance(self.publication, Publication): - self.publication = Publication(**as_dict(self.publication)) - - if not isinstance(self.triples, list): - self.triples = [self.triples] if self.triples is not None else [] - self.triples = [v if isinstance(v, Triple) else Triple(**as_dict(v)) for v in self.triples] - - super().__post_init__(**kwargs) - - -@dataclass -class RelationshipType(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.RelationshipType - class_class_curie: ClassVar[str] = "core:RelationshipType" - class_name: ClassVar[str] = "RelationshipType" - class_model_uri: ClassVar[URIRef] = PHENOTYPE.RelationshipType - - id: Union[str, RelationshipTypeId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, RelationshipTypeId): - self.id = RelationshipTypeId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Publication(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Publication - class_class_curie: ClassVar[str] = "core:Publication" - class_name: ClassVar[str] = "Publication" - class_model_uri: ClassVar[URIRef] = PHENOTYPE.Publication - - id: Optional[str] = None - title: Optional[str] = None - abstract: Optional[str] = None - combined_text: Optional[str] = None - full_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.id is not None and not isinstance(self.id, str): - self.id = str(self.id) - - if self.title is not None and not isinstance(self.title, str): - self.title = str(self.title) - - if self.abstract is not None and not isinstance(self.abstract, str): - self.abstract = str(self.abstract) - - if self.combined_text is not None and not isinstance(self.combined_text, str): - self.combined_text = str(self.combined_text) - - if self.full_text is not None and not isinstance(self.full_text, str): - self.full_text = str(self.full_text) - - super().__post_init__(**kwargs) - - -@dataclass -class AnnotatorResult(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.AnnotatorResult - class_class_curie: ClassVar[str] = "core:AnnotatorResult" - class_name: ClassVar[str] = "AnnotatorResult" - class_model_uri: ClassVar[URIRef] = PHENOTYPE.AnnotatorResult - - subject_text: Optional[str] = None - object_id: Optional[str] = None - object_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject_text is not None and not isinstance(self.subject_text, str): - self.subject_text = str(self.subject_text) - - if self.object_id is not None and not isinstance(self.object_id, str): - self.object_id = str(self.object_id) - - if self.object_text is not None and not isinstance(self.object_text, str): - self.object_text = str(self.object_text) - - super().__post_init__(**kwargs) - - -# Enumerations -class NullDataOptions(EnumDefinitionImpl): - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = PermissibleValue(text="UNSPECIFIED_METHOD_OF_ADMINISTRATION", - meaning=NCIT.C149701) - NOT_APPLICABLE = PermissibleValue(text="NOT_APPLICABLE", - meaning=NCIT.C18902) - NOT_MENTIONED = PermissibleValue(text="NOT_MENTIONED") - - _defn = EnumDefinition( - name="NullDataOptions", - ) - -# Slots -class slots: - pass - -slots.trait__quality = Slot(uri=PHENOTYPE.quality, name="trait__quality", curie=PHENOTYPE.curie('quality'), - model_uri=PHENOTYPE.trait__quality, domain=None, range=Optional[Union[str, QualityId]]) - -slots.trait__anatomical_entity = Slot(uri=PHENOTYPE.anatomical_entity, name="trait__anatomical_entity", curie=PHENOTYPE.curie('anatomical_entity'), - model_uri=PHENOTYPE.trait__anatomical_entity, domain=None, range=Optional[Union[str, AnatomicalEntityId]]) - -slots.trait__chemical_entity = Slot(uri=PHENOTYPE.chemical_entity, name="trait__chemical_entity", curie=PHENOTYPE.curie('chemical_entity'), - model_uri=PHENOTYPE.trait__chemical_entity, domain=None, range=Optional[Union[str, ChemicalEntityId]]) - -slots.extractionResult__input_id = Slot(uri=CORE.input_id, name="extractionResult__input_id", curie=CORE.curie('input_id'), - model_uri=PHENOTYPE.extractionResult__input_id, domain=None, range=Optional[str]) - -slots.extractionResult__input_title = Slot(uri=CORE.input_title, name="extractionResult__input_title", curie=CORE.curie('input_title'), - model_uri=PHENOTYPE.extractionResult__input_title, domain=None, range=Optional[str]) - -slots.extractionResult__input_text = Slot(uri=CORE.input_text, name="extractionResult__input_text", curie=CORE.curie('input_text'), - model_uri=PHENOTYPE.extractionResult__input_text, domain=None, range=Optional[str]) - -slots.extractionResult__raw_completion_output = Slot(uri=CORE.raw_completion_output, name="extractionResult__raw_completion_output", curie=CORE.curie('raw_completion_output'), - model_uri=PHENOTYPE.extractionResult__raw_completion_output, domain=None, range=Optional[str]) - -slots.extractionResult__prompt = Slot(uri=CORE.prompt, name="extractionResult__prompt", curie=CORE.curie('prompt'), - model_uri=PHENOTYPE.extractionResult__prompt, domain=None, range=Optional[str]) - -slots.extractionResult__extracted_object = Slot(uri=CORE.extracted_object, name="extractionResult__extracted_object", curie=CORE.curie('extracted_object'), - model_uri=PHENOTYPE.extractionResult__extracted_object, domain=None, range=Optional[Union[dict, Any]]) - -slots.extractionResult__named_entities = Slot(uri=CORE.named_entities, name="extractionResult__named_entities", curie=CORE.curie('named_entities'), - model_uri=PHENOTYPE.extractionResult__named_entities, domain=None, range=Optional[Union[Union[dict, Any], List[Union[dict, Any]]]]) - -slots.namedEntity__id = Slot(uri=CORE.id, name="namedEntity__id", curie=CORE.curie('id'), - model_uri=PHENOTYPE.namedEntity__id, domain=None, range=URIRef) - -slots.namedEntity__label = Slot(uri=RDFS.label, name="namedEntity__label", curie=RDFS.curie('label'), - model_uri=PHENOTYPE.namedEntity__label, domain=None, range=Optional[str]) - -slots.triple__subject = Slot(uri=CORE.subject, name="triple__subject", curie=CORE.curie('subject'), - model_uri=PHENOTYPE.triple__subject, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__predicate = Slot(uri=CORE.predicate, name="triple__predicate", curie=CORE.curie('predicate'), - model_uri=PHENOTYPE.triple__predicate, domain=None, range=Optional[Union[str, RelationshipTypeId]]) - -slots.triple__object = Slot(uri=CORE.object, name="triple__object", curie=CORE.curie('object'), - model_uri=PHENOTYPE.triple__object, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__qualifier = Slot(uri=CORE.qualifier, name="triple__qualifier", curie=CORE.curie('qualifier'), - model_uri=PHENOTYPE.triple__qualifier, domain=None, range=Optional[str]) - -slots.triple__subject_qualifier = Slot(uri=CORE.subject_qualifier, name="triple__subject_qualifier", curie=CORE.curie('subject_qualifier'), - model_uri=PHENOTYPE.triple__subject_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__object_qualifier = Slot(uri=CORE.object_qualifier, name="triple__object_qualifier", curie=CORE.curie('object_qualifier'), - model_uri=PHENOTYPE.triple__object_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.textWithTriples__publication = Slot(uri=CORE.publication, name="textWithTriples__publication", curie=CORE.curie('publication'), - model_uri=PHENOTYPE.textWithTriples__publication, domain=None, range=Optional[Union[dict, Publication]]) - -slots.textWithTriples__triples = Slot(uri=CORE.triples, name="textWithTriples__triples", curie=CORE.curie('triples'), - model_uri=PHENOTYPE.textWithTriples__triples, domain=None, range=Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]]) - -slots.publication__id = Slot(uri=CORE.id, name="publication__id", curie=CORE.curie('id'), - model_uri=PHENOTYPE.publication__id, domain=None, range=Optional[str]) - -slots.publication__title = Slot(uri=CORE.title, name="publication__title", curie=CORE.curie('title'), - model_uri=PHENOTYPE.publication__title, domain=None, range=Optional[str]) - -slots.publication__abstract = Slot(uri=CORE.abstract, name="publication__abstract", curie=CORE.curie('abstract'), - model_uri=PHENOTYPE.publication__abstract, domain=None, range=Optional[str]) - -slots.publication__combined_text = Slot(uri=CORE.combined_text, name="publication__combined_text", curie=CORE.curie('combined_text'), - model_uri=PHENOTYPE.publication__combined_text, domain=None, range=Optional[str]) - -slots.publication__full_text = Slot(uri=CORE.full_text, name="publication__full_text", curie=CORE.curie('full_text'), - model_uri=PHENOTYPE.publication__full_text, domain=None, range=Optional[str]) - -slots.annotatorResult__subject_text = Slot(uri=CORE.subject_text, name="annotatorResult__subject_text", curie=CORE.curie('subject_text'), - model_uri=PHENOTYPE.annotatorResult__subject_text, domain=None, range=Optional[str]) - -slots.annotatorResult__object_id = Slot(uri=CORE.object_id, name="annotatorResult__object_id", curie=CORE.curie('object_id'), - model_uri=PHENOTYPE.annotatorResult__object_id, domain=None, range=Optional[str]) - -slots.annotatorResult__object_text = Slot(uri=CORE.object_text, name="annotatorResult__object_text", curie=CORE.curie('object_text'), - model_uri=PHENOTYPE.annotatorResult__object_text, domain=None, range=Optional[str]) \ No newline at end of file diff --git a/projects/phenotype/prefixmap/phenotype.yaml b/projects/phenotype/prefixmap/phenotype.yaml deleted file mode 100644 index d12ea9a81..000000000 --- a/projects/phenotype/prefixmap/phenotype.yaml +++ /dev/null @@ -1,39 +0,0 @@ -{ - "CHEBI": "http://example.org/UNKNOWN/CHEBI/", - "PATO": "http://example.org/UNKNOWN/PATO/", - "PR": "http://example.org/UNKNOWN/PR/", - "RO": "http://purl.obolibrary.org/obo/RO_", - "UBERON": "http://example.org/UNKNOWN/UBERON/", - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "linkml": "https://w3id.org/linkml/", - "phenotype": "http://w3id.org/ontogpt/phenotype/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } -} diff --git a/projects/phenotype/protobuf/phenotype.proto b/projects/phenotype/protobuf/phenotype.proto deleted file mode 100644 index f8a704a2b..000000000 --- a/projects/phenotype/protobuf/phenotype.proto +++ /dev/null @@ -1,56 +0,0 @@ -message AnatomicalEntity - { - string id = 0 - string label = 0 - } -message AnnotatorResult - { - string subjectText = 0 - string objectId = 0 - string objectText = 0 - } -message ChemicalEntity - { - string id = 0 - string label = 0 - } -// A result of extracting knowledge on text -message ExtractionResult - { - string inputId = 0 - string inputTitle = 0 - string inputText = 0 - string rawCompletionOutput = 0 - string prompt = 0 - any extractedObject = 0 - repeated any namedEntities = 0 - } -message Publication - { - string id = 0 - string title = 0 - string abstract = 0 - string combinedText = 0 - string fullText = 0 - } -message Quality - { - string id = 0 - string label = 0 - } -message RelationshipType - { - string id = 0 - string label = 0 - } -message TextWithTriples - { - publication publication = 0 - repeated triple triples = 0 - } -message Trait - { - quality quality = 0 - anatomicalEntity anatomicalEntity = 0 - chemicalEntity chemicalEntity = 0 - } diff --git a/projects/phenotype/shacl/phenotype.shacl.ttl b/projects/phenotype/shacl/phenotype.shacl.ttl deleted file mode 100644 index c49528c43..000000000 --- a/projects/phenotype/shacl/phenotype.shacl.ttl +++ /dev/null @@ -1,229 +0,0 @@ -@prefix linkml: <https://w3id.org/linkml/> . -@prefix phenotype: <http://w3id.org/ontogpt/phenotype/> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix sh: <http://www.w3.org/ns/shacl#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/object_id> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object_text> ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject_text> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/AnnotatorResult> . - -<http://w3id.org/ontogpt/core/CompoundExpression> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass <http://w3id.org/ontogpt/core/CompoundExpression> . - -<http://w3id.org/ontogpt/core/ExtractionResult> a sh:NodeShape ; - sh:closed true ; - sh:description "A result of extracting knowledge on text" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class linkml:Any ; - sh:description "Named entities extracted from the text" ; - sh:nodeKind sh:BlankNode ; - sh:order 6 ; - sh:path <http://w3id.org/ontogpt/core/named_entities> ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/input_id> ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/input_title> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/input_text> ], - [ sh:class linkml:Any ; - sh:description "The complex objects extracted from the text" ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/extracted_object> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/prompt> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/ExtractionResult> . - -<http://w3id.org/ontogpt/core/TextWithTriples> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/Triple> ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/triples> ], - [ sh:class <http://w3id.org/ontogpt/core/Publication> ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/publication> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/TextWithTriples> . - -phenotype:Trait a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class phenotype:Quality ; - sh:description "The property being measured, or changes in this property, for example, amount, level, increased amount, decreased concentration" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path phenotype:quality ], - [ sh:class phenotype:AnatomicalEntity ; - sh:description "The anatomical location that the chemical entity is measured in" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path phenotype:anatomical_entity ], - [ sh:class phenotype:ChemicalEntity ; - sh:description "The chemical entity that is being measured" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path phenotype:chemical_entity ] ; - sh:targetClass phenotype:Trait . - -<http://w3id.org/ontogpt/core/Publication> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The title of the publication" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/title> ], - [ sh:description "The full text of the publication" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/full_text> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/combined_text> ], - [ sh:description "The abstract of the publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/abstract> ], - [ sh:description "The publication identifier" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/RelationshipType> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/Triple> a sh:NodeShape ; - sh:closed false ; - sh:description "Abstract parent for Relation Extraction tasks" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject> ], - [ sh:description "A qualifier for the statements, e.g. \"NOT\" for negation" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/RelationshipType> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/predicate> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/object_qualifier> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Triple> . - -phenotype:AnatomicalEntity a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass phenotype:AnatomicalEntity . - -phenotype:ChemicalEntity a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass phenotype:ChemicalEntity . - -phenotype:Quality a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass phenotype:Quality . - -linkml:Any a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass linkml:Any . - -<http://w3id.org/ontogpt/core/NamedEntity> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/NamedEntity> . - diff --git a/projects/phenotype/shex/phenotype.shex b/projects/phenotype/shex/phenotype.shex deleted file mode 100644 index 2c22558ee..000000000 --- a/projects/phenotype/shex/phenotype.shex +++ /dev/null @@ -1,167 +0,0 @@ -BASE <http://w3id.org/ontogpt/phenotype/> -PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> -PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> -PREFIX linkml: <https://w3id.org/linkml/> -PREFIX core: <http://w3id.org/ontogpt/core/> -PREFIX rdfs1: <http://example.org/UNKNOWN/rdfs/> - - -linkml:String xsd:string - -linkml:Integer xsd:integer - -linkml:Boolean xsd:boolean - -linkml:Float xsd:float - -linkml:Double xsd:double - -linkml:Decimal xsd:decimal - -linkml:Time xsd:time - -linkml:Date xsd:date - -linkml:Datetime xsd:dateTime - -linkml:DateOrDatetime linkml:DateOrDatetime - -linkml:Uriorcurie IRI - -linkml:Curie xsd:string - -linkml:Uri IRI - -linkml:Ncname xsd:string - -linkml:Objectidentifier IRI - -linkml:Nodeidentifier NONLITERAL - -linkml:Jsonpointer xsd:string - -linkml:Jsonpath xsd:string - -linkml:Sparqlpath xsd:string - -<AnatomicalEntity> CLOSED { - ( $<AnatomicalEntity_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <AnatomicalEntity> ] - ) -} - -core:AnnotatorResult CLOSED { - ( $core:AnnotatorResult_tes ( core:subject_text @linkml:String ? ; - core:object_id @linkml:String ? ; - core:object_text @linkml:String ? - ) ; - rdf:type [ core:AnnotatorResult ] ? - ) -} - -core:Any CLOSED { - ( $core:Any_tes rdf:type . * ; - rdf:type [ linkml:Any ] ? - ) -} - -<ChemicalEntity> CLOSED { - ( $<ChemicalEntity_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <ChemicalEntity> ] - ) -} - -core:CompoundExpression ( - { - ( $core:CompoundExpression_tes rdf:type . * ; - rdf:type [ core:CompoundExpression ] ? - ) - } OR @core:Triple -) - -core:ExtractionResult CLOSED { - ( $core:ExtractionResult_tes ( core:input_id @linkml:String ? ; - core:input_title @linkml:String ? ; - core:input_text @linkml:String ? ; - core:raw_completion_output @linkml:String ? ; - core:prompt @linkml:String ? ; - core:extracted_object @core:Any ? ; - core:named_entities @core:Any * - ) ; - rdf:type [ core:ExtractionResult ] ? - ) -} - -core:NamedEntity ( - @<AnatomicalEntity> OR @<ChemicalEntity> OR @<Quality> OR @core:RelationshipType -) - -core:NamedEntity_struct { - ( $core:NamedEntity_tes rdfs1:label @linkml:String ? ; - rdf:type [ core:NamedEntity ] - ) -} - -core:Publication CLOSED { - ( $core:Publication_tes ( core:id @linkml:String ? ; - core:title @linkml:String ? ; - core:abstract @linkml:String ? ; - core:combined_text @linkml:String ? ; - core:full_text @linkml:String ? - ) ; - rdf:type [ core:Publication ] ? - ) -} - -<Quality> CLOSED { - ( $<Quality_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Quality> ] - ) -} - -core:RelationshipType CLOSED { - ( $core:RelationshipType_tes ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ core:RelationshipType ] - ) -} - -core:TextWithTriples CLOSED { - ( $core:TextWithTriples_tes ( core:publication @core:Publication ? ; - core:triples @core:Triple * - ) ; - rdf:type [ core:TextWithTriples ] ? - ) -} - -<Trait> CLOSED { - ( $<Trait_tes> ( <quality> @<Quality> ? ; - <anatomical_entity> @<AnatomicalEntity> ? ; - <chemical_entity> @<ChemicalEntity> ? - ) ; - rdf:type [ <Trait> ] ? - ) -} - -core:Triple { - ( $core:Triple_tes ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - core:subject @core:NamedEntity ? ; - core:predicate @core:RelationshipType ? ; - core:object @core:NamedEntity ? ; - core:qualifier @linkml:String ? ; - core:subject_qualifier @core:NamedEntity ? ; - core:object_qualifier @core:NamedEntity ? - ) ; - rdf:type [ core:Triple ] ? - ) -} - - diff --git a/projects/phenotype/sqlschema/phenotype.sql b/projects/phenotype/sqlschema/phenotype.sql deleted file mode 100644 index 7bd14dd68..000000000 --- a/projects/phenotype/sqlschema/phenotype.sql +++ /dev/null @@ -1,68 +0,0 @@ - - -CREATE TABLE "AnatomicalEntity" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "AnnotatorResult" ( - subject_text TEXT, - object_id TEXT, - object_text TEXT, - PRIMARY KEY (subject_text, object_id, object_text) -); - -CREATE TABLE "ChemicalEntity" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "ExtractionResult" ( - input_id TEXT, - input_title TEXT, - input_text TEXT, - raw_completion_output TEXT, - prompt TEXT, - extracted_object TEXT, - named_entities TEXT, - PRIMARY KEY (input_id, input_title, input_text, raw_completion_output, prompt, extracted_object, named_entities) -); - -CREATE TABLE "Publication" ( - id TEXT, - title TEXT, - abstract TEXT, - combined_text TEXT, - full_text TEXT, - PRIMARY KEY (id, title, abstract, combined_text, full_text) -); - -CREATE TABLE "Quality" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "RelationshipType" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "TextWithTriples" ( - publication TEXT, - triples TEXT, - PRIMARY KEY (publication, triples) -); - -CREATE TABLE "Trait" ( - quality TEXT, - anatomical_entity TEXT, - chemical_entity TEXT, - PRIMARY KEY (quality, anatomical_entity, chemical_entity), - FOREIGN KEY(quality) REFERENCES "Quality" (id), - FOREIGN KEY(anatomical_entity) REFERENCES "AnatomicalEntity" (id), - FOREIGN KEY(chemical_entity) REFERENCES "ChemicalEntity" (id) -); diff --git a/projects/reaction/docs/AnnotatorResult.md b/projects/reaction/docs/AnnotatorResult.md deleted file mode 100644 index 630731463..000000000 --- a/projects/reaction/docs/AnnotatorResult.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Class: AnnotatorResult - - - - -URI: [reaction:AnnotatorResult](http://w3id.org/ontogpt/reaction/AnnotatorResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F])](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F]) - -## Attributes - - -### Own - - * [➞subject_text](annotatorResult__subject_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_id](annotatorResult__object_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_text](annotatorResult__object_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) diff --git a/projects/reaction/docs/Any.md b/projects/reaction/docs/Any.md deleted file mode 100644 index b2f19a55a..000000000 --- a/projects/reaction/docs/Any.md +++ /dev/null @@ -1,25 +0,0 @@ - -# Class: Any - - - - -URI: [reaction:Any](http://w3id.org/ontogpt/reaction/Any) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult])](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult]) - -## Referenced by Class - - * **None** *[➞extracted_object](extractionResult__extracted_object.md)* <sub>0..1</sub> **[Any](Any.md)** - * **None** *[➞named_entities](extractionResult__named_entities.md)* <sub>0..\*</sub> **[Any](Any.md)** - -## Attributes - - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | linkml:Any | - diff --git a/projects/reaction/docs/ChemicalEntity.md b/projects/reaction/docs/ChemicalEntity.md deleted file mode 100644 index c36fa7384..000000000 --- a/projects/reaction/docs/ChemicalEntity.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: ChemicalEntity - - - - -URI: [reaction:ChemicalEntity](http://w3id.org/ontogpt/reaction/ChemicalEntity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[Reaction]-%20left_side%200..*>[ChemicalEntity|id(i):string;label(i):string%20%3F],[Reaction]-%20right_side%200..*>[ChemicalEntity],[NamedEntity]^-[ChemicalEntity],[Reaction])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[Reaction]-%20left_side%200..*>[ChemicalEntity|id(i):string;label(i):string%20%3F],[Reaction]-%20right_side%200..*>[ChemicalEntity],[NamedEntity]^-[ChemicalEntity],[Reaction]) - -## Identifier prefixes - - * CHEBI - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞left_side](reaction__left_side.md)* <sub>0..\*</sub> **[ChemicalEntity](ChemicalEntity.md)** - * **None** *[➞right_side](reaction__right_side.md)* <sub>0..\*</sub> **[ChemicalEntity](ChemicalEntity.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/reaction/docs/CompoundExpression.md b/projects/reaction/docs/CompoundExpression.md deleted file mode 100644 index 0e7601850..000000000 --- a/projects/reaction/docs/CompoundExpression.md +++ /dev/null @@ -1,21 +0,0 @@ - -# Class: CompoundExpression - - - - -URI: [reaction:CompoundExpression](http://w3id.org/ontogpt/reaction/CompoundExpression) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[GeneReactionPairing],[CompoundExpression]^-[Triple],[CompoundExpression]^-[GeneReactionPairing])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[GeneReactionPairing],[CompoundExpression]^-[Triple],[CompoundExpression]^-[GeneReactionPairing]) - -## Children - - * [GeneReactionPairing](GeneReactionPairing.md) - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - -## Referenced by Class - - -## Attributes - diff --git a/projects/reaction/docs/Evidence.md b/projects/reaction/docs/Evidence.md deleted file mode 100644 index 13cf7dcda..000000000 --- a/projects/reaction/docs/Evidence.md +++ /dev/null @@ -1,36 +0,0 @@ - -# Class: Evidence - - - - -URI: [reaction:Evidence](http://w3id.org/ontogpt/reaction/Evidence) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[ReactionDocument]-%20has_evidence%200..*>[Evidence|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Evidence],[ReactionDocument])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[ReactionDocument]-%20has_evidence%200..*>[Evidence|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Evidence],[ReactionDocument]) - -## Identifier prefixes - - * OBI - * ECO - * MS - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞has_evidence](reactionDocument__has_evidence.md)* <sub>0..\*</sub> **[Evidence](Evidence.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/reaction/docs/ExtractionResult.md b/projects/reaction/docs/ExtractionResult.md deleted file mode 100644 index f7dbf9d9e..000000000 --- a/projects/reaction/docs/ExtractionResult.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Class: ExtractionResult - - -A result of extracting knowledge on text - -URI: [reaction:ExtractionResult](http://w3id.org/ontogpt/reaction/ExtractionResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any])](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any]) - -## Attributes - - -### Own - - * [➞input_id](extractionResult__input_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_title](extractionResult__input_title.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_text](extractionResult__input_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞prompt](extractionResult__prompt.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞extracted_object](extractionResult__extracted_object.md) <sub>0..1</sub> - * Description: The complex objects extracted from the text - * Range: [Any](Any.md) - * [➞named_entities](extractionResult__named_entities.md) <sub>0..\*</sub> - * Description: Named entities extracted from the text - * Range: [Any](Any.md) diff --git a/projects/reaction/docs/Gene.md b/projects/reaction/docs/Gene.md deleted file mode 100644 index e89406d93..000000000 --- a/projects/reaction/docs/Gene.md +++ /dev/null @@ -1,36 +0,0 @@ - -# Class: Gene - - - - -URI: [reaction:Gene](http://w3id.org/ontogpt/reaction/Gene) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[GeneReactionPairing]-%20gene%200..1>[Gene|id(i):string;label(i):string%20%3F],[GeneToReaction]-%20gene%200..1>[Gene],[ReactionDocument]-%20genes%200..*>[Gene],[NamedEntity]^-[Gene],[ReactionDocument],[GeneToReaction],[GeneReactionPairing])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[GeneReactionPairing]-%20gene%200..1>[Gene|id(i):string;label(i):string%20%3F],[GeneToReaction]-%20gene%200..1>[Gene],[ReactionDocument]-%20genes%200..*>[Gene],[NamedEntity]^-[Gene],[ReactionDocument],[GeneToReaction],[GeneReactionPairing]) - -## Identifier prefixes - - * HGNC - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞gene](geneReactionPairing__gene.md)* <sub>0..1</sub> **[Gene](Gene.md)** - * **None** *[➞gene](geneToReaction__gene.md)* <sub>0..1</sub> **[Gene](Gene.md)** - * **None** *[➞genes](reactionDocument__genes.md)* <sub>0..\*</sub> **[Gene](Gene.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/reaction/docs/GeneReactionPairing.md b/projects/reaction/docs/GeneReactionPairing.md deleted file mode 100644 index 8037a4490..000000000 --- a/projects/reaction/docs/GeneReactionPairing.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Class: GeneReactionPairing - - - - -URI: [reaction:GeneReactionPairing](http://w3id.org/ontogpt/reaction/GeneReactionPairing) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Reaction],[Reaction]<reaction%200..1-%20[GeneReactionPairing],[Gene]<gene%200..1-%20[GeneReactionPairing],[ReactionDocument]++-%20gene_reaction_pairings%200..*>[GeneReactionPairing],[CompoundExpression]^-[GeneReactionPairing],[ReactionDocument],[Gene],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[Reaction],[Reaction]<reaction%200..1-%20[GeneReactionPairing],[Gene]<gene%200..1-%20[GeneReactionPairing],[ReactionDocument]++-%20gene_reaction_pairings%200..*>[GeneReactionPairing],[CompoundExpression]^-[GeneReactionPairing],[ReactionDocument],[Gene],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞gene_reaction_pairings](reactionDocument__gene_reaction_pairings.md)* <sub>0..\*</sub> **[GeneReactionPairing](GeneReactionPairing.md)** - -## Attributes - - -### Own - - * [➞gene](geneReactionPairing__gene.md) <sub>0..1</sub> - * Description: name of the gene that catalyzes the reaction - * Range: [Gene](Gene.md) - * [➞reaction](geneReactionPairing__reaction.md) <sub>0..1</sub> - * Description: equation describing the reaction (e.g. A+B = C+D) catalyzed by the gene - * Range: [Reaction](Reaction.md) diff --git a/projects/reaction/docs/GeneToReaction.md b/projects/reaction/docs/GeneToReaction.md deleted file mode 100644 index 6da2fa107..000000000 --- a/projects/reaction/docs/GeneToReaction.md +++ /dev/null @@ -1,24 +0,0 @@ - -# Class: GeneToReaction - - - - -URI: [reaction:GeneToReaction](http://w3id.org/ontogpt/reaction/GeneToReaction) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Reaction],[Organism],[Organism]<organism%200..1-%20[GeneToReaction],[Reaction]<reactions%200..*-++[GeneToReaction],[Gene]<gene%200..1-%20[GeneToReaction],[Gene])](https://yuml.me/diagram/nofunky;dir:TB/class/[Reaction],[Organism],[Organism]<organism%200..1-%20[GeneToReaction],[Reaction]<reactions%200..*-++[GeneToReaction],[Gene]<gene%200..1-%20[GeneToReaction],[Gene]) - -## Attributes - - -### Own - - * [➞gene](geneToReaction__gene.md) <sub>0..1</sub> - * Description: name of the gene that catalyzes the reaction - * Range: [Gene](Gene.md) - * [➞reactions](geneToReaction__reactions.md) <sub>0..\*</sub> - * Description: semicolon separated list of reaction equations (e.g. A+B = C+D) catalyzed by the gene - * Range: [Reaction](Reaction.md) - * [➞organism](geneToReaction__organism.md) <sub>0..1</sub> - * Range: [Organism](Organism.md) diff --git a/projects/reaction/docs/NamedEntity.md b/projects/reaction/docs/NamedEntity.md deleted file mode 100644 index 2d2b15016..000000000 --- a/projects/reaction/docs/NamedEntity.md +++ /dev/null @@ -1,39 +0,0 @@ - -# Class: NamedEntity - - - - -URI: [reaction:NamedEntity](http://w3id.org/ontogpt/reaction/NamedEntity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[ReactionGrouping],[Reaction],[Organism],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[ReactionGrouping],[NamedEntity]^-[Reaction],[NamedEntity]^-[Organism],[NamedEntity]^-[Gene],[NamedEntity]^-[Evidence],[NamedEntity]^-[ChemicalEntity],[Triple],[Gene],[Evidence],[ChemicalEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[ReactionGrouping],[Reaction],[Organism],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[ReactionGrouping],[NamedEntity]^-[Reaction],[NamedEntity]^-[Organism],[NamedEntity]^-[Gene],[NamedEntity]^-[Evidence],[NamedEntity]^-[ChemicalEntity],[Triple],[Gene],[Evidence],[ChemicalEntity]) - -## Children - - * [ChemicalEntity](ChemicalEntity.md) - * [Evidence](Evidence.md) - * [Gene](Gene.md) - * [Organism](Organism.md) - * [Reaction](Reaction.md) - * [ReactionGrouping](ReactionGrouping.md) - * [RelationshipType](RelationshipType.md) - -## Referenced by Class - - * **None** *[➞object](triple__object.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞object_qualifier](triple__object_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject](triple__subject.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject_qualifier](triple__subject_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - -## Attributes - - -### Own - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/reaction/docs/NullDataOptions.md b/projects/reaction/docs/NullDataOptions.md deleted file mode 100644 index a7dc176a9..000000000 --- a/projects/reaction/docs/NullDataOptions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Enum: NullDataOptions - - - - -URI: [reaction:NullDataOptions](http://w3id.org/ontogpt/reaction/NullDataOptions) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | -| UNSPECIFIED_METHOD_OF_ADMINISTRATION | | NCIT:C149701 | | -| NOT_APPLICABLE | | NCIT:C18902 | {'aliases': ['not applicable', 'N/A']} | -| NOT_MENTIONED | | | | - diff --git a/projects/reaction/docs/Organism.md b/projects/reaction/docs/Organism.md deleted file mode 100644 index 62b7ccf96..000000000 --- a/projects/reaction/docs/Organism.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: Organism - - - - -URI: [reaction:Organism](http://w3id.org/ontogpt/reaction/Organism) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[GeneToReaction]-%20organism%200..1>[Organism|id(i):string;label(i):string%20%3F],[ReactionDocument]-%20organism%200..1>[Organism],[NamedEntity]^-[Organism],[ReactionDocument],[NamedEntity],[GeneToReaction])](https://yuml.me/diagram/nofunky;dir:TB/class/[GeneToReaction]-%20organism%200..1>[Organism|id(i):string;label(i):string%20%3F],[ReactionDocument]-%20organism%200..1>[Organism],[NamedEntity]^-[Organism],[ReactionDocument],[NamedEntity],[GeneToReaction]) - -## Identifier prefixes - - * NCBITaxon - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞organism](geneToReaction__organism.md)* <sub>0..1</sub> **[Organism](Organism.md)** - * **None** *[➞organism](reactionDocument__organism.md)* <sub>0..1</sub> **[Organism](Organism.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/reaction/docs/Publication.md b/projects/reaction/docs/Publication.md deleted file mode 100644 index d0146decc..000000000 --- a/projects/reaction/docs/Publication.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Publication - - - - -URI: [reaction:Publication](http://w3id.org/ontogpt/reaction/Publication) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples])](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples]) - -## Referenced by Class - - * **None** *[➞publication](textWithTriples__publication.md)* <sub>0..1</sub> **[Publication](Publication.md)** - -## Attributes - - -### Own - - * [➞id](publication__id.md) <sub>0..1</sub> - * Description: The publication identifier - * Range: [String](types/String.md) - * [➞title](publication__title.md) <sub>0..1</sub> - * Description: The title of the publication - * Range: [String](types/String.md) - * [➞abstract](publication__abstract.md) <sub>0..1</sub> - * Description: The abstract of the publication - * Range: [String](types/String.md) - * [➞combined_text](publication__combined_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞full_text](publication__full_text.md) <sub>0..1</sub> - * Description: The full text of the publication - * Range: [String](types/String.md) diff --git a/projects/reaction/docs/ReactionDocument.md b/projects/reaction/docs/ReactionDocument.md deleted file mode 100644 index 36a8b24ca..000000000 --- a/projects/reaction/docs/ReactionDocument.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Class: ReactionDocument - - - - -URI: [reaction:ReactionDocument](http://w3id.org/ontogpt/reaction/ReactionDocument) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Evidence]<has_evidence%200..*-%20[ReactionDocument],[Organism]<organism%200..1-%20[ReactionDocument],[GeneReactionPairing]<gene_reaction_pairings%200..*-++[ReactionDocument],[Reaction]<reactions%200..*-++[ReactionDocument],[Gene]<genes%200..*-%20[ReactionDocument],[Reaction],[Organism],[GeneReactionPairing],[Gene],[Evidence])](https://yuml.me/diagram/nofunky;dir:TB/class/[Evidence]<has_evidence%200..*-%20[ReactionDocument],[Organism]<organism%200..1-%20[ReactionDocument],[GeneReactionPairing]<gene_reaction_pairings%200..*-++[ReactionDocument],[Reaction]<reactions%200..*-++[ReactionDocument],[Gene]<genes%200..*-%20[ReactionDocument],[Reaction],[Organism],[GeneReactionPairing],[Gene],[Evidence]) - -## Attributes - - -### Own - - * [➞genes](reactionDocument__genes.md) <sub>0..\*</sub> - * Description: semicolon separated list of genes that catalyzes the mentioned reactions - * Range: [Gene](Gene.md) - * [➞reactions](reactionDocument__reactions.md) <sub>0..\*</sub> - * Description: semicolon separated list of reaction equations (e.g. A+B = C+D) catalyzed by the gene - * Range: [Reaction](Reaction.md) - * [➞gene_reaction_pairings](reactionDocument__gene_reaction_pairings.md) <sub>0..\*</sub> - * Description: semicolon separated list of gene to reaction pairings - * Range: [GeneReactionPairing](GeneReactionPairing.md) - * [➞organism](reactionDocument__organism.md) <sub>0..1</sub> - * Range: [Organism](Organism.md) - * [➞has_evidence](reactionDocument__has_evidence.md) <sub>0..\*</sub> - * Description: evidence for the reaction - * Range: [Evidence](Evidence.md) diff --git a/projects/reaction/docs/ReactionGrouping.md b/projects/reaction/docs/ReactionGrouping.md deleted file mode 100644 index d950c2a36..000000000 --- a/projects/reaction/docs/ReactionGrouping.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: ReactionGrouping - - - - -URI: [reaction:ReactionGrouping](http://w3id.org/ontogpt/reaction/ReactionGrouping) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Reaction]-%20subclass_of%200..1>[ReactionGrouping|id(i):string;label(i):string%20%3F],[NamedEntity]^-[ReactionGrouping],[Reaction],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Reaction]-%20subclass_of%200..1>[ReactionGrouping|id(i):string;label(i):string%20%3F],[NamedEntity]^-[ReactionGrouping],[Reaction],[NamedEntity]) - -## Identifier prefixes - - * GO - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞subclass_of](reaction__subclass_of.md)* <sub>0..1</sub> **[ReactionGrouping](ReactionGrouping.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/reaction/docs/RelationshipType.md b/projects/reaction/docs/RelationshipType.md deleted file mode 100644 index 8756233da..000000000 --- a/projects/reaction/docs/RelationshipType.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: RelationshipType - - - - -URI: [reaction:RelationshipType](http://w3id.org/ontogpt/reaction/RelationshipType) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity]) - -## Identifier prefixes - - * RO - * biolink - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞predicate](triple__predicate.md)* <sub>0..1</sub> **[RelationshipType](RelationshipType.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/reaction/docs/TextWithTriples.md b/projects/reaction/docs/TextWithTriples.md deleted file mode 100644 index 36ff97b7b..000000000 --- a/projects/reaction/docs/TextWithTriples.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: TextWithTriples - - - - -URI: [reaction:TextWithTriples](http://w3id.org/ontogpt/reaction/TextWithTriples) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication]) - -## Attributes - - -### Own - - * [➞publication](textWithTriples__publication.md) <sub>0..1</sub> - * Range: [Publication](Publication.md) - * [➞triples](textWithTriples__triples.md) <sub>0..\*</sub> - * Range: [Triple](Triple.md) diff --git a/projects/reaction/docs/Triple.md b/projects/reaction/docs/Triple.md deleted file mode 100644 index f97c07b58..000000000 --- a/projects/reaction/docs/Triple.md +++ /dev/null @@ -1,39 +0,0 @@ - -# Class: Triple - - -Abstract parent for Relation Extraction tasks - -URI: [reaction:Triple](http://w3id.org/ontogpt/reaction/Triple) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞triples](textWithTriples__triples.md)* <sub>0..\*</sub> **[Triple](Triple.md)** - -## Attributes - - -### Own - - * [➞subject](triple__subject.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞predicate](triple__predicate.md) <sub>0..1</sub> - * Range: [RelationshipType](RelationshipType.md) - * [➞object](triple__object.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞qualifier](triple__qualifier.md) <sub>0..1</sub> - * Description: A qualifier for the statements, e.g. "NOT" for negation - * Range: [String](types/String.md) - * [➞subject_qualifier](triple__subject_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - * Range: [NamedEntity](NamedEntity.md) - * [➞object_qualifier](triple__object_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * Range: [NamedEntity](NamedEntity.md) diff --git a/projects/reaction/docs/annotatorResult__object_id.md b/projects/reaction/docs/annotatorResult__object_id.md deleted file mode 100644 index 3a38819b6..000000000 --- a/projects/reaction/docs/annotatorResult__object_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_id - - - - -URI: [reaction:annotatorResult__object_id](http://w3id.org/ontogpt/reaction/annotatorResult__object_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/reaction/docs/annotatorResult__object_text.md b/projects/reaction/docs/annotatorResult__object_text.md deleted file mode 100644 index e5f9997b9..000000000 --- a/projects/reaction/docs/annotatorResult__object_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_text - - - - -URI: [reaction:annotatorResult__object_text](http://w3id.org/ontogpt/reaction/annotatorResult__object_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/reaction/docs/annotatorResult__subject_text.md b/projects/reaction/docs/annotatorResult__subject_text.md deleted file mode 100644 index ea577a57f..000000000 --- a/projects/reaction/docs/annotatorResult__subject_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_text - - - - -URI: [reaction:annotatorResult__subject_text](http://w3id.org/ontogpt/reaction/annotatorResult__subject_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/reaction/docs/extractionResult__extracted_object.md b/projects/reaction/docs/extractionResult__extracted_object.md deleted file mode 100644 index 444e2017c..000000000 --- a/projects/reaction/docs/extractionResult__extracted_object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: extracted_object - - -The complex objects extracted from the text - -URI: [reaction:extractionResult__extracted_object](http://w3id.org/ontogpt/reaction/extractionResult__extracted_object) - - -## Domain and Range - -None → <sub>0..1</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/reaction/docs/extractionResult__input_id.md b/projects/reaction/docs/extractionResult__input_id.md deleted file mode 100644 index f0ecd78b8..000000000 --- a/projects/reaction/docs/extractionResult__input_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_id - - - - -URI: [reaction:extractionResult__input_id](http://w3id.org/ontogpt/reaction/extractionResult__input_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/reaction/docs/extractionResult__input_text.md b/projects/reaction/docs/extractionResult__input_text.md deleted file mode 100644 index f1a85839c..000000000 --- a/projects/reaction/docs/extractionResult__input_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_text - - - - -URI: [reaction:extractionResult__input_text](http://w3id.org/ontogpt/reaction/extractionResult__input_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/reaction/docs/extractionResult__input_title.md b/projects/reaction/docs/extractionResult__input_title.md deleted file mode 100644 index cba484596..000000000 --- a/projects/reaction/docs/extractionResult__input_title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_title - - - - -URI: [reaction:extractionResult__input_title](http://w3id.org/ontogpt/reaction/extractionResult__input_title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/reaction/docs/extractionResult__named_entities.md b/projects/reaction/docs/extractionResult__named_entities.md deleted file mode 100644 index e7c2aa71d..000000000 --- a/projects/reaction/docs/extractionResult__named_entities.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: named_entities - - -Named entities extracted from the text - -URI: [reaction:extractionResult__named_entities](http://w3id.org/ontogpt/reaction/extractionResult__named_entities) - - -## Domain and Range - -None → <sub>0..\*</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/reaction/docs/extractionResult__prompt.md b/projects/reaction/docs/extractionResult__prompt.md deleted file mode 100644 index fc74bc6c7..000000000 --- a/projects/reaction/docs/extractionResult__prompt.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: prompt - - - - -URI: [reaction:extractionResult__prompt](http://w3id.org/ontogpt/reaction/extractionResult__prompt) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/reaction/docs/extractionResult__raw_completion_output.md b/projects/reaction/docs/extractionResult__raw_completion_output.md deleted file mode 100644 index ceb798b8a..000000000 --- a/projects/reaction/docs/extractionResult__raw_completion_output.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: raw_completion_output - - - - -URI: [reaction:extractionResult__raw_completion_output](http://w3id.org/ontogpt/reaction/extractionResult__raw_completion_output) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/reaction/docs/geneReactionPairing__gene.md b/projects/reaction/docs/geneReactionPairing__gene.md deleted file mode 100644 index 4a6333b14..000000000 --- a/projects/reaction/docs/geneReactionPairing__gene.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: gene - - -name of the gene that catalyzes the reaction - -URI: [reaction:geneReactionPairing__gene](http://w3id.org/ontogpt/reaction/geneReactionPairing__gene) - - -## Domain and Range - -None → <sub>0..1</sub> [Gene](Gene.md) - -## Parents - - -## Children - - -## Used by - - * [GeneReactionPairing](GeneReactionPairing.md) diff --git a/projects/reaction/docs/geneReactionPairing__reaction.md b/projects/reaction/docs/geneReactionPairing__reaction.md deleted file mode 100644 index 1bf183062..000000000 --- a/projects/reaction/docs/geneReactionPairing__reaction.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: reaction - - -equation describing the reaction (e.g. A+B = C+D) catalyzed by the gene - -URI: [reaction:geneReactionPairing__reaction](http://w3id.org/ontogpt/reaction/geneReactionPairing__reaction) - - -## Domain and Range - -None → <sub>0..1</sub> [Reaction](Reaction.md) - -## Parents - - -## Children - - -## Used by - - * [GeneReactionPairing](GeneReactionPairing.md) diff --git a/projects/reaction/docs/geneToReaction__gene.md b/projects/reaction/docs/geneToReaction__gene.md deleted file mode 100644 index 9fcdfb641..000000000 --- a/projects/reaction/docs/geneToReaction__gene.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: gene - - -name of the gene that catalyzes the reaction - -URI: [reaction:geneToReaction__gene](http://w3id.org/ontogpt/reaction/geneToReaction__gene) - - -## Domain and Range - -None → <sub>0..1</sub> [Gene](Gene.md) - -## Parents - - -## Children - - -## Used by - - * [GeneToReaction](GeneToReaction.md) diff --git a/projects/reaction/docs/geneToReaction__organism.md b/projects/reaction/docs/geneToReaction__organism.md deleted file mode 100644 index b2871c56e..000000000 --- a/projects/reaction/docs/geneToReaction__organism.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: organism - - - - -URI: [reaction:geneToReaction__organism](http://w3id.org/ontogpt/reaction/geneToReaction__organism) - - -## Domain and Range - -None → <sub>0..1</sub> [Organism](Organism.md) - -## Parents - - -## Children - - -## Used by - - * [GeneToReaction](GeneToReaction.md) diff --git a/projects/reaction/docs/geneToReaction__reactions.md b/projects/reaction/docs/geneToReaction__reactions.md deleted file mode 100644 index 16aaa476d..000000000 --- a/projects/reaction/docs/geneToReaction__reactions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: reactions - - -semicolon separated list of reaction equations (e.g. A+B = C+D) catalyzed by the gene - -URI: [reaction:geneToReaction__reactions](http://w3id.org/ontogpt/reaction/geneToReaction__reactions) - - -## Domain and Range - -None → <sub>0..\*</sub> [Reaction](Reaction.md) - -## Parents - - -## Children - - -## Used by - - * [GeneToReaction](GeneToReaction.md) diff --git a/projects/reaction/docs/namedEntity__id.md b/projects/reaction/docs/namedEntity__id.md deleted file mode 100644 index 30a77c19e..000000000 --- a/projects/reaction/docs/namedEntity__id.md +++ /dev/null @@ -1,36 +0,0 @@ - -# Slot: id - - -A unique identifier for the named entity - -URI: [reaction:namedEntity__id](http://w3id.org/ontogpt/reaction/namedEntity__id) - - -## Domain and Range - -None → <sub>1..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ChemicalEntity](ChemicalEntity.md) - * [Evidence](Evidence.md) - * [Gene](Gene.md) - * [NamedEntity](NamedEntity.md) - * [Organism](Organism.md) - * [Reaction](Reaction.md) - * [ReactionGrouping](ReactionGrouping.md) - * [RelationshipType](RelationshipType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | this is populated during the grounding and normalization step | - diff --git a/projects/reaction/docs/namedEntity__label.md b/projects/reaction/docs/namedEntity__label.md deleted file mode 100644 index 9bc9ec0da..000000000 --- a/projects/reaction/docs/namedEntity__label.md +++ /dev/null @@ -1,36 +0,0 @@ - -# Slot: label - - -The label (name) of the named thing - -URI: [reaction:namedEntity__label](http://w3id.org/ontogpt/reaction/namedEntity__label) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ChemicalEntity](ChemicalEntity.md) - * [Evidence](Evidence.md) - * [Gene](Gene.md) - * [NamedEntity](NamedEntity.md) - * [Organism](Organism.md) - * [ReactionGrouping](ReactionGrouping.md) - * [RelationshipType](RelationshipType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Aliases:** | | name | -| **Mappings:** | | rdfs:label | - diff --git a/projects/reaction/docs/publication__abstract.md b/projects/reaction/docs/publication__abstract.md deleted file mode 100644 index cac225e17..000000000 --- a/projects/reaction/docs/publication__abstract.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: abstract - - -The abstract of the publication - -URI: [reaction:publication__abstract](http://w3id.org/ontogpt/reaction/publication__abstract) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/reaction/docs/publication__combined_text.md b/projects/reaction/docs/publication__combined_text.md deleted file mode 100644 index 7f78a388a..000000000 --- a/projects/reaction/docs/publication__combined_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: combined_text - - - - -URI: [reaction:publication__combined_text](http://w3id.org/ontogpt/reaction/publication__combined_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/reaction/docs/publication__full_text.md b/projects/reaction/docs/publication__full_text.md deleted file mode 100644 index 63194f9eb..000000000 --- a/projects/reaction/docs/publication__full_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: full_text - - -The full text of the publication - -URI: [reaction:publication__full_text](http://w3id.org/ontogpt/reaction/publication__full_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/reaction/docs/publication__id.md b/projects/reaction/docs/publication__id.md deleted file mode 100644 index f146bb8b1..000000000 --- a/projects/reaction/docs/publication__id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: id - - -The publication identifier - -URI: [reaction:publication__id](http://w3id.org/ontogpt/reaction/publication__id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/reaction/docs/publication__title.md b/projects/reaction/docs/publication__title.md deleted file mode 100644 index 693cac688..000000000 --- a/projects/reaction/docs/publication__title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: title - - -The title of the publication - -URI: [reaction:publication__title](http://w3id.org/ontogpt/reaction/publication__title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/reaction/docs/reaction.md b/projects/reaction/docs/reaction.md deleted file mode 100644 index 38f802435..000000000 --- a/projects/reaction/docs/reaction.md +++ /dev/null @@ -1,50 +0,0 @@ - -# Class: Reaction - - - - -URI: [reaction:Reaction](http://w3id.org/ontogpt/reaction/Reaction) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ReactionGrouping],[ChemicalEntity]<right_side%200..*-%20[Reaction|label:string%20%3F;description:string%20%3F;synonyms:string%20*;id(i):string],[ChemicalEntity]<left_side%200..*-%20[Reaction],[ReactionGrouping]<subclass_of%200..1-%20[Reaction],[GeneReactionPairing]-%20reaction%200..1>[Reaction],[GeneToReaction]++-%20reactions%200..*>[Reaction],[ReactionDocument]++-%20reactions%200..*>[Reaction],[NamedEntity]^-[Reaction],[ReactionDocument],[NamedEntity],[GeneToReaction],[GeneReactionPairing],[ChemicalEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[ReactionGrouping],[ChemicalEntity]<right_side%200..*-%20[Reaction|label:string%20%3F;description:string%20%3F;synonyms:string%20*;id(i):string],[ChemicalEntity]<left_side%200..*-%20[Reaction],[ReactionGrouping]<subclass_of%200..1-%20[Reaction],[GeneReactionPairing]-%20reaction%200..1>[Reaction],[GeneToReaction]++-%20reactions%200..*>[Reaction],[ReactionDocument]++-%20reactions%200..*>[Reaction],[NamedEntity]^-[Reaction],[ReactionDocument],[NamedEntity],[GeneToReaction],[GeneReactionPairing],[ChemicalEntity]) - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞reaction](geneReactionPairing__reaction.md)* <sub>0..1</sub> **[Reaction](Reaction.md)** - * **None** *[➞reactions](geneToReaction__reactions.md)* <sub>0..\*</sub> **[Reaction](Reaction.md)** - * **None** *[➞reactions](reactionDocument__reactions.md)* <sub>0..\*</sub> **[Reaction](Reaction.md)** - -## Attributes - - -### Own - - * [➞label](reaction__label.md) <sub>0..1</sub> - * Description: the name of the reaction - * Range: [String](types/String.md) - * [➞description](reaction__description.md) <sub>0..1</sub> - * Description: a textual description of the reaction - * Range: [String](types/String.md) - * [➞synonyms](reaction__synonyms.md) <sub>0..\*</sub> - * Description: alternative names of the reaction - * Range: [String](types/String.md) - * [➞subclass_of](reaction__subclass_of.md) <sub>0..1</sub> - * Description: the category to which this biological process belongs - * Range: [ReactionGrouping](ReactionGrouping.md) - * [➞left_side](reaction__left_side.md) <sub>0..\*</sub> - * Description: semicolon separated list of chemical entities on the left side - * Range: [ChemicalEntity](ChemicalEntity.md) - * [➞right_side](reaction__right_side.md) <sub>0..\*</sub> - * Description: semicolon separated list of chemical entities on the right side - * Range: [ChemicalEntity](ChemicalEntity.md) - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) diff --git a/projects/reaction/docs/reactionDocument__gene_reaction_pairings.md b/projects/reaction/docs/reactionDocument__gene_reaction_pairings.md deleted file mode 100644 index 82ff4ba6f..000000000 --- a/projects/reaction/docs/reactionDocument__gene_reaction_pairings.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: gene_reaction_pairings - - -semicolon separated list of gene to reaction pairings - -URI: [reaction:reactionDocument__gene_reaction_pairings](http://w3id.org/ontogpt/reaction/reactionDocument__gene_reaction_pairings) - - -## Domain and Range - -None → <sub>0..\*</sub> [GeneReactionPairing](GeneReactionPairing.md) - -## Parents - - -## Children - - -## Used by - - * [ReactionDocument](ReactionDocument.md) diff --git a/projects/reaction/docs/reactionDocument__genes.md b/projects/reaction/docs/reactionDocument__genes.md deleted file mode 100644 index 8ef05a541..000000000 --- a/projects/reaction/docs/reactionDocument__genes.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: genes - - -semicolon separated list of genes that catalyzes the mentioned reactions - -URI: [reaction:reactionDocument__genes](http://w3id.org/ontogpt/reaction/reactionDocument__genes) - - -## Domain and Range - -None → <sub>0..\*</sub> [Gene](Gene.md) - -## Parents - - -## Children - - -## Used by - - * [ReactionDocument](ReactionDocument.md) diff --git a/projects/reaction/docs/reactionDocument__has_evidence.md b/projects/reaction/docs/reactionDocument__has_evidence.md deleted file mode 100644 index 6dccc2d49..000000000 --- a/projects/reaction/docs/reactionDocument__has_evidence.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: has_evidence - - -evidence for the reaction - -URI: [reaction:reactionDocument__has_evidence](http://w3id.org/ontogpt/reaction/reactionDocument__has_evidence) - - -## Domain and Range - -None → <sub>0..\*</sub> [Evidence](Evidence.md) - -## Parents - - -## Children - - -## Used by - - * [ReactionDocument](ReactionDocument.md) diff --git a/projects/reaction/docs/reactionDocument__organism.md b/projects/reaction/docs/reactionDocument__organism.md deleted file mode 100644 index ad238ee3b..000000000 --- a/projects/reaction/docs/reactionDocument__organism.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: organism - - - - -URI: [reaction:reactionDocument__organism](http://w3id.org/ontogpt/reaction/reactionDocument__organism) - - -## Domain and Range - -None → <sub>0..1</sub> [Organism](Organism.md) - -## Parents - - -## Children - - -## Used by - - * [ReactionDocument](ReactionDocument.md) diff --git a/projects/reaction/docs/reactionDocument__reactions.md b/projects/reaction/docs/reactionDocument__reactions.md deleted file mode 100644 index a48382d74..000000000 --- a/projects/reaction/docs/reactionDocument__reactions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: reactions - - -semicolon separated list of reaction equations (e.g. A+B = C+D) catalyzed by the gene - -URI: [reaction:reactionDocument__reactions](http://w3id.org/ontogpt/reaction/reactionDocument__reactions) - - -## Domain and Range - -None → <sub>0..\*</sub> [Reaction](Reaction.md) - -## Parents - - -## Children - - -## Used by - - * [ReactionDocument](ReactionDocument.md) diff --git a/projects/reaction/docs/reaction__description.md b/projects/reaction/docs/reaction__description.md deleted file mode 100644 index 751400873..000000000 --- a/projects/reaction/docs/reaction__description.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: description - - -a textual description of the reaction - -URI: [reaction:reaction__description](http://w3id.org/ontogpt/reaction/reaction__description) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Reaction](Reaction.md) diff --git a/projects/reaction/docs/reaction__label.md b/projects/reaction/docs/reaction__label.md deleted file mode 100644 index b95206713..000000000 --- a/projects/reaction/docs/reaction__label.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: label - - -the name of the reaction - -URI: [reaction:reaction__label](http://w3id.org/ontogpt/reaction/reaction__label) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Reaction](Reaction.md) diff --git a/projects/reaction/docs/reaction__left_side.md b/projects/reaction/docs/reaction__left_side.md deleted file mode 100644 index cef237520..000000000 --- a/projects/reaction/docs/reaction__left_side.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: left_side - - -semicolon separated list of chemical entities on the left side - -URI: [reaction:reaction__left_side](http://w3id.org/ontogpt/reaction/reaction__left_side) - - -## Domain and Range - -None → <sub>0..\*</sub> [ChemicalEntity](ChemicalEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Reaction](Reaction.md) diff --git a/projects/reaction/docs/reaction__right_side.md b/projects/reaction/docs/reaction__right_side.md deleted file mode 100644 index 4752bd01d..000000000 --- a/projects/reaction/docs/reaction__right_side.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: right_side - - -semicolon separated list of chemical entities on the right side - -URI: [reaction:reaction__right_side](http://w3id.org/ontogpt/reaction/reaction__right_side) - - -## Domain and Range - -None → <sub>0..\*</sub> [ChemicalEntity](ChemicalEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Reaction](Reaction.md) diff --git a/projects/reaction/docs/reaction__subclass_of.md b/projects/reaction/docs/reaction__subclass_of.md deleted file mode 100644 index bf5e68de4..000000000 --- a/projects/reaction/docs/reaction__subclass_of.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subclass_of - - -the category to which this biological process belongs - -URI: [reaction:reaction__subclass_of](http://w3id.org/ontogpt/reaction/reaction__subclass_of) - - -## Domain and Range - -None → <sub>0..1</sub> [ReactionGrouping](ReactionGrouping.md) - -## Parents - - -## Children - - -## Used by - - * [Reaction](Reaction.md) diff --git a/projects/reaction/docs/reaction__synonyms.md b/projects/reaction/docs/reaction__synonyms.md deleted file mode 100644 index 96fd7bfc9..000000000 --- a/projects/reaction/docs/reaction__synonyms.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: synonyms - - -alternative names of the reaction - -URI: [reaction:reaction__synonyms](http://w3id.org/ontogpt/reaction/reaction__synonyms) - - -## Domain and Range - -None → <sub>0..\*</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Reaction](Reaction.md) diff --git a/projects/reaction/docs/textWithTriples__publication.md b/projects/reaction/docs/textWithTriples__publication.md deleted file mode 100644 index 4579adbe9..000000000 --- a/projects/reaction/docs/textWithTriples__publication.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: publication - - - - -URI: [reaction:textWithTriples__publication](http://w3id.org/ontogpt/reaction/textWithTriples__publication) - - -## Domain and Range - -None → <sub>0..1</sub> [Publication](Publication.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/reaction/docs/textWithTriples__triples.md b/projects/reaction/docs/textWithTriples__triples.md deleted file mode 100644 index 37be2829b..000000000 --- a/projects/reaction/docs/textWithTriples__triples.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: triples - - - - -URI: [reaction:textWithTriples__triples](http://w3id.org/ontogpt/reaction/textWithTriples__triples) - - -## Domain and Range - -None → <sub>0..\*</sub> [Triple](Triple.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/reaction/docs/triple__object.md b/projects/reaction/docs/triple__object.md deleted file mode 100644 index 8f20b1f4d..000000000 --- a/projects/reaction/docs/triple__object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object - - - - -URI: [reaction:triple__object](http://w3id.org/ontogpt/reaction/triple__object) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/reaction/docs/triple__object_qualifier.md b/projects/reaction/docs/triple__object_qualifier.md deleted file mode 100644 index 1b13239cd..000000000 --- a/projects/reaction/docs/triple__object_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_qualifier - - -An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - -URI: [reaction:triple__object_qualifier](http://w3id.org/ontogpt/reaction/triple__object_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/reaction/docs/triple__predicate.md b/projects/reaction/docs/triple__predicate.md deleted file mode 100644 index 3407b24b1..000000000 --- a/projects/reaction/docs/triple__predicate.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: predicate - - - - -URI: [reaction:triple__predicate](http://w3id.org/ontogpt/reaction/triple__predicate) - - -## Domain and Range - -None → <sub>0..1</sub> [RelationshipType](RelationshipType.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/reaction/docs/triple__qualifier.md b/projects/reaction/docs/triple__qualifier.md deleted file mode 100644 index dcb24101f..000000000 --- a/projects/reaction/docs/triple__qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: qualifier - - -A qualifier for the statements, e.g. "NOT" for negation - -URI: [reaction:triple__qualifier](http://w3id.org/ontogpt/reaction/triple__qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/reaction/docs/triple__subject.md b/projects/reaction/docs/triple__subject.md deleted file mode 100644 index 111983700..000000000 --- a/projects/reaction/docs/triple__subject.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject - - - - -URI: [reaction:triple__subject](http://w3id.org/ontogpt/reaction/triple__subject) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/reaction/docs/triple__subject_qualifier.md b/projects/reaction/docs/triple__subject_qualifier.md deleted file mode 100644 index 03bb6f816..000000000 --- a/projects/reaction/docs/triple__subject_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_qualifier - - -An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -URI: [reaction:triple__subject_qualifier](http://w3id.org/ontogpt/reaction/triple__subject_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/reaction/docs/types/Boolean.md b/projects/reaction/docs/types/Boolean.md deleted file mode 100644 index dc83a9c6e..000000000 --- a/projects/reaction/docs/types/Boolean.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: boolean - - -A binary (true or false) value - -URI: [linkml:Boolean](https://w3id.org/linkml/Boolean) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Bool** | -| Representation | | bool | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Boolean | - diff --git a/projects/reaction/docs/types/Curie.md b/projects/reaction/docs/types/Curie.md deleted file mode 100644 index c1803f93f..000000000 --- a/projects/reaction/docs/types/Curie.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: curie - - -a compact URI - -URI: [linkml:Curie](https://w3id.org/linkml/Curie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Curie** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations this MUST be expanded to a URI | -| | | in non-RDF serializations MAY be serialized as the compact representation | - diff --git a/projects/reaction/docs/types/Date.md b/projects/reaction/docs/types/Date.md deleted file mode 100644 index 06948af97..000000000 --- a/projects/reaction/docs/types/Date.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: date - - -a date (year, month and day) in an idealized calendar - -URI: [linkml:Date](https://w3id.org/linkml/Date) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDate** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Date | - diff --git a/projects/reaction/docs/types/DateOrDatetime.md b/projects/reaction/docs/types/DateOrDatetime.md deleted file mode 100644 index ef983898d..000000000 --- a/projects/reaction/docs/types/DateOrDatetime.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: date_or_datetime - - -Either a date or a datetime - -URI: [linkml:DateOrDatetime](https://w3id.org/linkml/DateOrDatetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/reaction/docs/types/Datetime.md b/projects/reaction/docs/types/Datetime.md deleted file mode 100644 index 9510454a8..000000000 --- a/projects/reaction/docs/types/Datetime.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: datetime - - -The combination of a date and time - -URI: [linkml:Datetime](https://w3id.org/linkml/Datetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDateTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:DateTime | - diff --git a/projects/reaction/docs/types/Decimal.md b/projects/reaction/docs/types/Decimal.md deleted file mode 100644 index a7ba14a5d..000000000 --- a/projects/reaction/docs/types/Decimal.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: decimal - - -A real number with arbitrary precision that conforms to the xsd:decimal specification - -URI: [linkml:Decimal](https://w3id.org/linkml/Decimal) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Decimal** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Broad Mappings:** | | schema:Number | - diff --git a/projects/reaction/docs/types/Double.md b/projects/reaction/docs/types/Double.md deleted file mode 100644 index cfe6d71e2..000000000 --- a/projects/reaction/docs/types/Double.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: double - - -A real number that conforms to the xsd:double specification - -URI: [linkml:Double](https://w3id.org/linkml/Double) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Close Mappings:** | | schema:Float | - diff --git a/projects/reaction/docs/types/Float.md b/projects/reaction/docs/types/Float.md deleted file mode 100644 index 7b303f96f..000000000 --- a/projects/reaction/docs/types/Float.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: float - - -A real number that conforms to the xsd:float specification - -URI: [linkml:Float](https://w3id.org/linkml/Float) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Float | - diff --git a/projects/reaction/docs/types/Integer.md b/projects/reaction/docs/types/Integer.md deleted file mode 100644 index 3cfcc66d9..000000000 --- a/projects/reaction/docs/types/Integer.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: integer - - -An integer - -URI: [linkml:Integer](https://w3id.org/linkml/Integer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **int** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Integer | - diff --git a/projects/reaction/docs/types/Jsonpath.md b/projects/reaction/docs/types/Jsonpath.md deleted file mode 100644 index a03a58e67..000000000 --- a/projects/reaction/docs/types/Jsonpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpath - - -A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpath](https://w3id.org/linkml/Jsonpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/reaction/docs/types/Jsonpointer.md b/projects/reaction/docs/types/Jsonpointer.md deleted file mode 100644 index a0e1ac492..000000000 --- a/projects/reaction/docs/types/Jsonpointer.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpointer - - -A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpointer](https://w3id.org/linkml/Jsonpointer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/reaction/docs/types/Ncname.md b/projects/reaction/docs/types/Ncname.md deleted file mode 100644 index 710b0b04a..000000000 --- a/projects/reaction/docs/types/Ncname.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: ncname - - -Prefix part of CURIE - -URI: [linkml:Ncname](https://w3id.org/linkml/Ncname) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NCName** | -| Representation | | str | diff --git a/projects/reaction/docs/types/Nodeidentifier.md b/projects/reaction/docs/types/Nodeidentifier.md deleted file mode 100644 index f0097cdf4..000000000 --- a/projects/reaction/docs/types/Nodeidentifier.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: nodeidentifier - - -A URI, CURIE or BNODE that represents a node in a model. - -URI: [linkml:Nodeidentifier](https://w3id.org/linkml/Nodeidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NodeIdentifier** | -| Representation | | str | diff --git a/projects/reaction/docs/types/Objectidentifier.md b/projects/reaction/docs/types/Objectidentifier.md deleted file mode 100644 index 454ba6be6..000000000 --- a/projects/reaction/docs/types/Objectidentifier.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: objectidentifier - - -A URI or CURIE that represents an object in the model. - -URI: [linkml:Objectidentifier](https://w3id.org/linkml/Objectidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **ElementIdentifier** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | Used for inheritance and type checking | - diff --git a/projects/reaction/docs/types/Sparqlpath.md b/projects/reaction/docs/types/Sparqlpath.md deleted file mode 100644 index fd99a927e..000000000 --- a/projects/reaction/docs/types/Sparqlpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: sparqlpath - - -A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - -URI: [linkml:Sparqlpath](https://w3id.org/linkml/Sparqlpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/reaction/docs/types/String.md b/projects/reaction/docs/types/String.md deleted file mode 100644 index 6e61d7081..000000000 --- a/projects/reaction/docs/types/String.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: string - - -A character string - -URI: [linkml:String](https://w3id.org/linkml/String) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Text | - diff --git a/projects/reaction/docs/types/Time.md b/projects/reaction/docs/types/Time.md deleted file mode 100644 index 2b8652bcd..000000000 --- a/projects/reaction/docs/types/Time.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: time - - -A time object represents a (local) time of day, independent of any particular day - -URI: [linkml:Time](https://w3id.org/linkml/Time) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Time | - diff --git a/projects/reaction/docs/types/Uri.md b/projects/reaction/docs/types/Uri.md deleted file mode 100644 index 343807a5e..000000000 --- a/projects/reaction/docs/types/Uri.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: uri - - -a complete URI - -URI: [linkml:Uri](https://w3id.org/linkml/Uri) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URI** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node | -| **Close Mappings:** | | schema:URL | - diff --git a/projects/reaction/docs/types/Uriorcurie.md b/projects/reaction/docs/types/Uriorcurie.md deleted file mode 100644 index 2f7b65087..000000000 --- a/projects/reaction/docs/types/Uriorcurie.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: uriorcurie - - -a URI or a CURIE - -URI: [linkml:Uriorcurie](https://w3id.org/linkml/Uriorcurie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URIorCURIE** | -| Representation | | str | diff --git a/projects/reaction/excel/reaction.xlsx b/projects/reaction/excel/reaction.xlsx deleted file mode 100644 index 323404bd6..000000000 Binary files a/projects/reaction/excel/reaction.xlsx and /dev/null differ diff --git a/projects/reaction/graphql/reaction.graphql b/projects/reaction/graphql/reaction.graphql deleted file mode 100644 index ab997884f..000000000 --- a/projects/reaction/graphql/reaction.graphql +++ /dev/null @@ -1,126 +0,0 @@ -type AnnotatorResult - { - subjectText: String - objectId: String - objectText: String - } - -type Any - { - } - -type ChemicalEntity - { - id: String! - label: String - } - -interface CompoundExpression - { - } - -type Evidence - { - id: String! - label: String - } - -type ExtractionResult - { - inputId: String - inputTitle: String - inputText: String - rawCompletionOutput: String - prompt: String - extractedObject: Any - namedEntities: [Any] - } - -type Gene - { - id: String! - label: String - } - -type GeneReactionPairing - { - gene: Gene - reaction: Reaction - } - -type GeneToReaction - { - gene: Gene - reactions: [Reaction] - organism: Organism - } - -interface NamedEntity - { - id: String! - label: String - } - -type Organism - { - id: String! - label: String - } - -type Publication - { - id: String - title: String - abstract: String - combinedText: String - fullText: String - } - -type Reaction - { - id: String! - label: String - description: String - synonyms: [String] - subclassOf: ReactionGrouping - leftSide: [ChemicalEntity] - rightSide: [ChemicalEntity] - } - -type ReactionDocument - { - genes: [Gene] - reactions: [Reaction] - geneReactionPairings: [GeneReactionPairing] - organism: Organism - hasEvidence: [Evidence] - } - -type ReactionGrouping - { - id: String! - label: String - } - -type RelationshipType - { - id: String! - label: String - } - -type TextWithTriples - { - publication: Publication - triples: [Triple] - } - -interface Triple - { - subject: NamedEntity - predicate: RelationshipType - object: NamedEntity - qualifier: String - subjectQualifier: NamedEntity - objectQualifier: NamedEntity - } - diff --git a/projects/reaction/jsonld/reaction.context.jsonld b/projects/reaction/jsonld/reaction.context.jsonld deleted file mode 100644 index fc8c112b7..000000000 --- a/projects/reaction/jsonld/reaction.context.jsonld +++ /dev/null @@ -1,163 +0,0 @@ -{ - "comments": { - "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2023-08-07T10:55:54", - "source": "reaction.yaml" - }, - "@context": { - "CHEBI": "http://example.org/UNKNOWN/CHEBI/", - "ECO": "http://example.org/UNKNOWN/ECO/", - "GO": "http://example.org/UNKNOWN/GO/", - "HGNC": "http://example.org/UNKNOWN/HGNC/", - "MS": "http://example.org/UNKNOWN/MS/", - "NCBITaxon": "http://example.org/UNKNOWN/NCBITaxon/", - "OBI": "http://example.org/UNKNOWN/OBI/", - "RO": { - "@id": "http://purl.obolibrary.org/obo/RO_", - "@prefix": true - }, - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "reaction": { - "@type": "@id" - }, - "@vocab": "http://w3id.org/ontogpt/reaction/", - "object_id": { - "@id": "core:object_id" - }, - "object_text": { - "@id": "core:object_text" - }, - "subject_text": { - "@id": "core:subject_text" - }, - "extracted_object": { - "@type": "@id", - "@id": "core:extracted_object" - }, - "input_id": { - "@id": "core:input_id" - }, - "input_text": { - "@id": "core:input_text" - }, - "input_title": { - "@id": "core:input_title" - }, - "named_entities": { - "@type": "@id", - "@id": "core:named_entities" - }, - "prompt": { - "@id": "core:prompt" - }, - "raw_completion_output": { - "@id": "core:raw_completion_output" - }, - "gene": { - "@type": "@id" - }, - "organism": { - "@type": "@id" - }, - "reactions": { - "@type": "@id" - }, - "id": { - "@id": "core:id" - }, - "label": { - "@id": "rdfs:label" - }, - "abstract": { - "@id": "core:abstract" - }, - "combined_text": { - "@id": "core:combined_text" - }, - "full_text": { - "@id": "core:full_text" - }, - "title": { - "@id": "core:title" - }, - "left_side": { - "@type": "@id" - }, - "right_side": { - "@type": "@id" - }, - "subclass_of": { - "@type": "@id" - }, - "gene_reaction_pairings": { - "@type": "@id" - }, - "genes": { - "@type": "@id" - }, - "has_evidence": { - "@type": "@id" - }, - "publication": { - "@type": "@id", - "@id": "core:publication" - }, - "triples": { - "@type": "@id", - "@id": "core:triples" - }, - "object": { - "@type": "@id", - "@id": "core:object" - }, - "object_qualifier": { - "@type": "@id", - "@id": "core:object_qualifier" - }, - "predicate": { - "@type": "@id", - "@id": "core:predicate" - }, - "qualifier": { - "@id": "core:qualifier" - }, - "subject": { - "@type": "@id", - "@id": "core:subject" - }, - "subject_qualifier": { - "@type": "@id", - "@id": "core:subject_qualifier" - }, - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } - } -} diff --git a/projects/reaction/jsonld/reaction.jsonld b/projects/reaction/jsonld/reaction.jsonld deleted file mode 100644 index aaad0f195..000000000 --- a/projects/reaction/jsonld/reaction.jsonld +++ /dev/null @@ -1,1474 +0,0 @@ -{ - "name": "reaction-template", - "description": "A template for reactions", - "title": "reaction Template", - "id": "https://w3id.org/ontogpt/reaction", - "imports": [ - "linkml:types", - "core" - ], - "license": "https://creativecommons.org/publicdomain/zero/1.0/", - "prefixes": [ - { - "prefix_prefix": "linkml", - "prefix_reference": "https://w3id.org/linkml/" - }, - { - "prefix_prefix": "reaction", - "prefix_reference": "http://w3id.org/ontogpt/reaction/" - } - ], - "default_prefix": "reaction", - "default_range": "string", - "types": [ - { - "name": "string", - "definition_uri": "https://w3id.org/linkml/String", - "description": "A character string", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Text" - ], - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "@type": "TypeDefinition" - }, - { - "name": "integer", - "definition_uri": "https://w3id.org/linkml/Integer", - "description": "An integer", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Integer" - ], - "base": "int", - "uri": "http://www.w3.org/2001/XMLSchema#integer", - "@type": "TypeDefinition" - }, - { - "name": "boolean", - "definition_uri": "https://w3id.org/linkml/Boolean", - "description": "A binary (true or false) value", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Boolean" - ], - "base": "Bool", - "uri": "http://www.w3.org/2001/XMLSchema#boolean", - "repr": "bool", - "@type": "TypeDefinition" - }, - { - "name": "float", - "definition_uri": "https://w3id.org/linkml/Float", - "description": "A real number that conforms to the xsd:float specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#float", - "@type": "TypeDefinition" - }, - { - "name": "double", - "definition_uri": "https://w3id.org/linkml/Double", - "description": "A real number that conforms to the xsd:double specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#double", - "@type": "TypeDefinition" - }, - { - "name": "decimal", - "definition_uri": "https://w3id.org/linkml/Decimal", - "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "broad_mappings": [ - "schema:Number" - ], - "base": "Decimal", - "uri": "http://www.w3.org/2001/XMLSchema#decimal", - "@type": "TypeDefinition" - }, - { - "name": "time", - "definition_uri": "https://w3id.org/linkml/Time", - "description": "A time object represents a (local) time of day, independent of any particular day", - "notes": [ - "URI is dateTime because OWL reasoners do not work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Time" - ], - "base": "XSDTime", - "uri": "http://www.w3.org/2001/XMLSchema#time", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date", - "definition_uri": "https://w3id.org/linkml/Date", - "description": "a date (year, month and day) in an idealized calendar", - "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Date" - ], - "base": "XSDDate", - "uri": "http://www.w3.org/2001/XMLSchema#date", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "datetime", - "definition_uri": "https://w3id.org/linkml/Datetime", - "description": "The combination of a date and time", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:DateTime" - ], - "base": "XSDDateTime", - "uri": "http://www.w3.org/2001/XMLSchema#dateTime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date_or_datetime", - "definition_uri": "https://w3id.org/linkml/DateOrDatetime", - "description": "Either a date or a datetime", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "https://w3id.org/linkml/DateOrDatetime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uriorcurie", - "definition_uri": "https://w3id.org/linkml/Uriorcurie", - "description": "a URI or a CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "URIorCURIE", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "curie", - "definition_uri": "https://w3id.org/linkml/Curie", - "conforms_to": "https://www.w3.org/TR/curie/", - "description": "a compact URI", - "comments": [ - "in RDF serializations this MUST be expanded to a URI", - "in non-RDF serializations MAY be serialized as the compact representation" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "Curie", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uri", - "definition_uri": "https://w3id.org/linkml/Uri", - "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", - "description": "a complete URI", - "comments": [ - "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:URL" - ], - "base": "URI", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "ncname", - "definition_uri": "https://w3id.org/linkml/Ncname", - "description": "Prefix part of CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NCName", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "objectidentifier", - "definition_uri": "https://w3id.org/linkml/Objectidentifier", - "description": "A URI or CURIE that represents an object in the model.", - "comments": [ - "Used for inheritance and type checking" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "ElementIdentifier", - "uri": "http://www.w3.org/ns/shex#iri", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "nodeidentifier", - "definition_uri": "https://w3id.org/linkml/Nodeidentifier", - "description": "A URI, CURIE or BNODE that represents a node in a model.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NodeIdentifier", - "uri": "http://www.w3.org/ns/shex#nonLiteral", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpointer", - "definition_uri": "https://w3id.org/linkml/Jsonpointer", - "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901", - "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpath", - "definition_uri": "https://w3id.org/linkml/Jsonpath", - "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html", - "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "sparqlpath", - "definition_uri": "https://w3id.org/linkml/Sparqlpath", - "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths", - "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - } - ], - "enums": [ - { - "name": "NullDataOptions", - "definition_uri": "http://w3id.org/ontogpt/core/NullDataOptions", - "from_schema": "http://w3id.org/ontogpt/core", - "permissible_values": [ - { - "text": "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "meaning": "NCIT:C149701" - }, - { - "text": "NOT_APPLICABLE", - "meaning": "NCIT:C18902", - "aliases": [ - "not applicable", - "N/A" - ] - }, - { - "text": "NOT_MENTIONED" - } - ] - } - ], - "slots": [ - { - "name": "reaction__label", - "description": "the name of the reaction", - "from_schema": "https://w3id.org/ontogpt/reaction", - "slot_uri": "http://w3id.org/ontogpt/reaction/label", - "alias": "label", - "owner": "Reaction", - "domain_of": [ - "Reaction" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "reaction__description", - "description": "a textual description of the reaction", - "from_schema": "https://w3id.org/ontogpt/reaction", - "slot_uri": "http://w3id.org/ontogpt/reaction/description", - "alias": "description", - "owner": "Reaction", - "domain_of": [ - "Reaction" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "reaction__synonyms", - "description": "alternative names of the reaction", - "from_schema": "https://w3id.org/ontogpt/reaction", - "slot_uri": "http://w3id.org/ontogpt/reaction/synonyms", - "multivalued": true, - "alias": "synonyms", - "owner": "Reaction", - "domain_of": [ - "Reaction" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "reaction__subclass_of", - "description": "the category to which this biological process belongs", - "from_schema": "https://w3id.org/ontogpt/reaction", - "slot_uri": "http://w3id.org/ontogpt/reaction/subclass_of", - "alias": "subclass_of", - "owner": "Reaction", - "domain_of": [ - "Reaction" - ], - "range": "ReactionGrouping", - "@type": "SlotDefinition" - }, - { - "name": "reaction__left_side", - "description": "semicolon separated list of chemical entities on the left side", - "from_schema": "https://w3id.org/ontogpt/reaction", - "slot_uri": "http://w3id.org/ontogpt/reaction/left_side", - "multivalued": true, - "alias": "left_side", - "owner": "Reaction", - "domain_of": [ - "Reaction" - ], - "range": "ChemicalEntity", - "@type": "SlotDefinition" - }, - { - "name": "reaction__right_side", - "description": "semicolon separated list of chemical entities on the right side", - "from_schema": "https://w3id.org/ontogpt/reaction", - "slot_uri": "http://w3id.org/ontogpt/reaction/right_side", - "multivalued": true, - "alias": "right_side", - "owner": "Reaction", - "domain_of": [ - "Reaction" - ], - "range": "ChemicalEntity", - "@type": "SlotDefinition" - }, - { - "name": "geneToReaction__gene", - "description": "name of the gene that catalyzes the reaction", - "from_schema": "https://w3id.org/ontogpt/reaction", - "slot_uri": "http://w3id.org/ontogpt/reaction/gene", - "alias": "gene", - "owner": "GeneToReaction", - "domain_of": [ - "GeneToReaction" - ], - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "geneToReaction__reactions", - "description": "semicolon separated list of reaction equations (e.g. A+B = C+D) catalyzed by the gene", - "from_schema": "https://w3id.org/ontogpt/reaction", - "slot_uri": "http://w3id.org/ontogpt/reaction/reactions", - "multivalued": true, - "alias": "reactions", - "owner": "GeneToReaction", - "domain_of": [ - "GeneToReaction" - ], - "range": "Reaction", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "geneToReaction__organism", - "from_schema": "https://w3id.org/ontogpt/reaction", - "slot_uri": "http://w3id.org/ontogpt/reaction/organism", - "alias": "organism", - "owner": "GeneToReaction", - "domain_of": [ - "GeneToReaction" - ], - "range": "Organism", - "@type": "SlotDefinition" - }, - { - "name": "reactionDocument__genes", - "description": "semicolon separated list of genes that catalyzes the mentioned reactions", - "from_schema": "https://w3id.org/ontogpt/reaction", - "slot_uri": "http://w3id.org/ontogpt/reaction/genes", - "multivalued": true, - "alias": "genes", - "owner": "ReactionDocument", - "domain_of": [ - "ReactionDocument" - ], - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "reactionDocument__reactions", - "description": "semicolon separated list of reaction equations (e.g. A+B = C+D) catalyzed by the gene", - "from_schema": "https://w3id.org/ontogpt/reaction", - "slot_uri": "http://w3id.org/ontogpt/reaction/reactions", - "multivalued": true, - "alias": "reactions", - "owner": "ReactionDocument", - "domain_of": [ - "ReactionDocument" - ], - "range": "Reaction", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "reactionDocument__gene_reaction_pairings", - "description": "semicolon separated list of gene to reaction pairings", - "from_schema": "https://w3id.org/ontogpt/reaction", - "slot_uri": "http://w3id.org/ontogpt/reaction/gene_reaction_pairings", - "multivalued": true, - "alias": "gene_reaction_pairings", - "owner": "ReactionDocument", - "domain_of": [ - "ReactionDocument" - ], - "range": "GeneReactionPairing", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "reactionDocument__organism", - "from_schema": "https://w3id.org/ontogpt/reaction", - "slot_uri": "http://w3id.org/ontogpt/reaction/organism", - "alias": "organism", - "owner": "ReactionDocument", - "domain_of": [ - "ReactionDocument" - ], - "range": "Organism", - "@type": "SlotDefinition" - }, - { - "name": "reactionDocument__has_evidence", - "description": "evidence for the reaction", - "from_schema": "https://w3id.org/ontogpt/reaction", - "slot_uri": "http://w3id.org/ontogpt/reaction/has_evidence", - "multivalued": true, - "alias": "has_evidence", - "owner": "ReactionDocument", - "domain_of": [ - "ReactionDocument" - ], - "range": "Evidence", - "@type": "SlotDefinition" - }, - { - "name": "geneReactionPairing__gene", - "description": "name of the gene that catalyzes the reaction", - "from_schema": "https://w3id.org/ontogpt/reaction", - "slot_uri": "http://w3id.org/ontogpt/reaction/gene", - "alias": "gene", - "owner": "GeneReactionPairing", - "domain_of": [ - "GeneReactionPairing" - ], - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "geneReactionPairing__reaction", - "description": "equation describing the reaction (e.g. A+B = C+D) catalyzed by the gene", - "from_schema": "https://w3id.org/ontogpt/reaction", - "slot_uri": "http://w3id.org/ontogpt/reaction/reaction", - "alias": "reaction", - "owner": "GeneReactionPairing", - "domain_of": [ - "GeneReactionPairing" - ], - "range": "Reaction", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_id", - "alias": "input_id", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_title", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_title", - "alias": "input_title", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_text", - "alias": "input_text", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__raw_completion_output", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/raw_completion_output", - "alias": "raw_completion_output", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__prompt", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/prompt", - "alias": "prompt", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__extracted_object", - "description": "The complex objects extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/extracted_object", - "alias": "extracted_object", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__named_entities", - "description": "Named entities extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/named_entities", - "multivalued": true, - "alias": "named_entities", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "identifier": true, - "alias": "id", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "required": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "from_schema": "http://w3id.org/ontogpt/core", - "aliases": [ - "name" - ], - "mappings": [ - "http://example.org/UNKNOWN/rdfs/label" - ], - "slot_uri": "http://example.org/UNKNOWN/rdfs/label", - "alias": "label", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject", - "alias": "subject", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__predicate", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/predicate", - "alias": "predicate", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "triple__object", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object", - "alias": "object", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/qualifier", - "alias": "qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_qualifier", - "alias": "subject_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_qualifier", - "alias": "object_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/publication", - "alias": "publication", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__triples", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/triples", - "multivalued": true, - "alias": "triples", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "publication__id", - "description": "The publication identifier", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "alias": "id", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__title", - "description": "The title of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/title", - "alias": "title", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__abstract", - "description": "The abstract of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/abstract", - "alias": "abstract", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__combined_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/combined_text", - "alias": "combined_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__full_text", - "description": "The full text of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/full_text", - "alias": "full_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__subject_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_text", - "alias": "subject_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_id", - "alias": "object_id", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_text", - "alias": "object_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - } - ], - "classes": [ - { - "name": "Reaction", - "definition_uri": "http://w3id.org/ontogpt/reaction/Reaction", - "from_schema": "https://w3id.org/ontogpt/reaction", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "reaction__label", - "reaction__description", - "reaction__synonyms", - "reaction__subclass_of", - "reaction__left_side", - "reaction__right_side" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "label", - "description": "the name of the reaction", - "@type": "SlotDefinition" - }, - { - "name": "description", - "description": "a textual description of the reaction", - "@type": "SlotDefinition" - }, - { - "name": "synonyms", - "description": "alternative names of the reaction", - "multivalued": true, - "@type": "SlotDefinition" - }, - { - "name": "subclass_of", - "description": "the category to which this biological process belongs", - "range": "ReactionGrouping", - "@type": "SlotDefinition" - }, - { - "name": "left_side", - "description": "semicolon separated list of chemical entities on the left side", - "multivalued": true, - "range": "ChemicalEntity", - "@type": "SlotDefinition" - }, - { - "name": "right_side", - "description": "semicolon separated list of chemical entities on the right side", - "multivalued": true, - "range": "ChemicalEntity", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/reaction/Reaction", - "@type": "ClassDefinition" - }, - { - "name": "GeneToReaction", - "definition_uri": "http://w3id.org/ontogpt/reaction/GeneToReaction", - "from_schema": "https://w3id.org/ontogpt/reaction", - "slots": [ - "geneToReaction__gene", - "geneToReaction__reactions", - "geneToReaction__organism" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "gene", - "description": "name of the gene that catalyzes the reaction", - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "reactions", - "description": "semicolon separated list of reaction equations (e.g. A+B = C+D) catalyzed by the gene", - "multivalued": true, - "range": "Reaction", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "organism", - "range": "Organism", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/reaction/GeneToReaction", - "@type": "ClassDefinition" - }, - { - "name": "ReactionDocument", - "definition_uri": "http://w3id.org/ontogpt/reaction/ReactionDocument", - "from_schema": "https://w3id.org/ontogpt/reaction", - "slots": [ - "reactionDocument__genes", - "reactionDocument__reactions", - "reactionDocument__gene_reaction_pairings", - "reactionDocument__organism", - "reactionDocument__has_evidence" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "genes", - "description": "semicolon separated list of genes that catalyzes the mentioned reactions", - "multivalued": true, - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "reactions", - "description": "semicolon separated list of reaction equations (e.g. A+B = C+D) catalyzed by the gene", - "multivalued": true, - "range": "Reaction", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "gene_reaction_pairings", - "description": "semicolon separated list of gene to reaction pairings", - "multivalued": true, - "range": "GeneReactionPairing", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "organism", - "range": "Organism", - "@type": "SlotDefinition" - }, - { - "name": "has_evidence", - "description": "evidence for the reaction", - "multivalued": true, - "range": "Evidence", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/reaction/ReactionDocument", - "@type": "ClassDefinition" - }, - { - "name": "GeneReactionPairing", - "definition_uri": "http://w3id.org/ontogpt/reaction/GeneReactionPairing", - "from_schema": "https://w3id.org/ontogpt/reaction", - "is_a": "CompoundExpression", - "slots": [ - "geneReactionPairing__gene", - "geneReactionPairing__reaction" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "gene", - "description": "name of the gene that catalyzes the reaction", - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "reaction", - "description": "equation describing the reaction (e.g. A+B = C+D) catalyzed by the gene", - "range": "Reaction", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/reaction/GeneReactionPairing", - "@type": "ClassDefinition" - }, - { - "name": "ReactionGrouping", - "id_prefixes": [ - "GO" - ], - "definition_uri": "http://w3id.org/ontogpt/reaction/ReactionGrouping", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:go", - "@type": "Annotation" - } - ], - "from_schema": "https://w3id.org/ontogpt/reaction", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/reaction/ReactionGrouping", - "@type": "ClassDefinition" - }, - { - "name": "ChemicalEntity", - "id_prefixes": [ - "CHEBI" - ], - "definition_uri": "http://w3id.org/ontogpt/reaction/ChemicalEntity", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:chebi", - "@type": "Annotation" - } - ], - "from_schema": "https://w3id.org/ontogpt/reaction", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/reaction/ChemicalEntity", - "@type": "ClassDefinition" - }, - { - "name": "Evidence", - "id_prefixes": [ - "OBI", - "ECO", - "MS" - ], - "definition_uri": "http://w3id.org/ontogpt/reaction/Evidence", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:obi, sqlite:obo:eco, sqlite:obo:ms", - "@type": "Annotation" - } - ], - "from_schema": "https://w3id.org/ontogpt/reaction", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/reaction/Evidence", - "@type": "ClassDefinition" - }, - { - "name": "Gene", - "id_prefixes": [ - "HGNC" - ], - "definition_uri": "http://w3id.org/ontogpt/reaction/Gene", - "annotations": [ - { - "tag": "annotators", - "value": "gilda:, bioportal:hgnc-nr, bioportal:pr", - "@type": "Annotation" - } - ], - "from_schema": "https://w3id.org/ontogpt/reaction", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/reaction/Gene", - "@type": "ClassDefinition" - }, - { - "name": "Organism", - "id_prefixes": [ - "NCBITaxon" - ], - "definition_uri": "http://w3id.org/ontogpt/reaction/Organism", - "annotations": [ - { - "tag": "annotators", - "value": "gilda:, sqlite:obo:ncbitaxon", - "@type": "Annotation" - } - ], - "from_schema": "https://w3id.org/ontogpt/reaction", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/reaction/Organism", - "@type": "ClassDefinition" - }, - { - "name": "Any", - "definition_uri": "http://w3id.org/ontogpt/core/Any", - "from_schema": "http://w3id.org/ontogpt/core", - "mappings": [ - "linkml:Any" - ], - "slot_usage": {}, - "class_uri": "https://w3id.org/linkml/Any", - "@type": "ClassDefinition" - }, - { - "name": "ExtractionResult", - "definition_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "description": "A result of extracting knowledge on text", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "extractionResult__input_id", - "extractionResult__input_title", - "extractionResult__input_text", - "extractionResult__raw_completion_output", - "extractionResult__prompt", - "extractionResult__extracted_object", - "extractionResult__named_entities" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "input_id", - "@type": "SlotDefinition" - }, - { - "name": "input_title", - "@type": "SlotDefinition" - }, - { - "name": "input_text", - "@type": "SlotDefinition" - }, - { - "name": "raw_completion_output", - "@type": "SlotDefinition" - }, - { - "name": "prompt", - "@type": "SlotDefinition" - }, - { - "name": "extracted_object", - "description": "The complex objects extracted from the text", - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "named_entities", - "description": "Named entities extracted from the text", - "multivalued": true, - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "@type": "ClassDefinition" - }, - { - "name": "NamedEntity", - "definition_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "identifier": true, - "@type": "SlotDefinition" - }, - { - "name": "label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "aliases": [ - "name" - ], - "slot_uri": "rdfs:label", - "range": "string", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "@type": "ClassDefinition" - }, - { - "name": "CompoundExpression", - "definition_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "@type": "ClassDefinition" - }, - { - "name": "Triple", - "definition_uri": "http://w3id.org/ontogpt/core/Triple", - "description": "Abstract parent for Relation Extraction tasks", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "CompoundExpression", - "abstract": true, - "slots": [ - "triple__subject", - "triple__predicate", - "triple__object", - "triple__qualifier", - "triple__subject_qualifier", - "triple__object_qualifier" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "predicate", - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "object", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Triple", - "@type": "ClassDefinition" - }, - { - "name": "TextWithTriples", - "definition_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "textWithTriples__publication", - "textWithTriples__triples" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "triples", - "multivalued": true, - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "@type": "ClassDefinition" - }, - { - "name": "RelationshipType", - "id_prefixes": [ - "RO", - "biolink" - ], - "definition_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "@type": "ClassDefinition" - }, - { - "name": "Publication", - "definition_uri": "http://w3id.org/ontogpt/core/Publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "publication__id", - "publication__title", - "publication__abstract", - "publication__combined_text", - "publication__full_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "description": "The publication identifier", - "@type": "SlotDefinition" - }, - { - "name": "title", - "description": "The title of the publication", - "@type": "SlotDefinition" - }, - { - "name": "abstract", - "description": "The abstract of the publication", - "@type": "SlotDefinition" - }, - { - "name": "combined_text", - "@type": "SlotDefinition" - }, - { - "name": "full_text", - "description": "The full text of the publication", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Publication", - "@type": "ClassDefinition" - }, - { - "name": "AnnotatorResult", - "definition_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "annotatorResult__subject_text", - "annotatorResult__object_id", - "annotatorResult__object_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject_text", - "@type": "SlotDefinition" - }, - { - "name": "object_id", - "@type": "SlotDefinition" - }, - { - "name": "object_text", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "@type": "ClassDefinition" - } - ], - "metamodel_version": "1.7.0", - "source_file": "reaction.yaml", - "source_file_date": "2023-06-17T15:11:19", - "source_file_size": 3187, - "generation_date": "2023-08-07T10:55:55", - "@type": "SchemaDefinition", - "@context": [ - "projects/reaction/jsonld/reaction.context.jsonld", - "https://w3id.org/linkml/types.context.jsonld", - "core.context.jsonld", - { - "@base": "http://w3id.org/ontogpt/reaction/" - } - ] -} diff --git a/projects/reaction/jsonschema/reaction.schema.json b/projects/reaction/jsonschema/reaction.schema.json deleted file mode 100644 index 412202eba..000000000 --- a/projects/reaction/jsonschema/reaction.schema.json +++ /dev/null @@ -1,407 +0,0 @@ -{ - "$defs": { - "AnnotatorResult": { - "additionalProperties": false, - "description": "", - "properties": { - "object_id": { - "type": "string" - }, - "object_text": { - "type": "string" - }, - "subject_text": { - "type": "string" - } - }, - "title": "AnnotatorResult", - "type": "object" - }, - "Any": { - "additionalProperties": true, - "description": "", - "title": "Any", - "type": "object" - }, - "ChemicalEntity": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "ChemicalEntity", - "type": "object" - }, - "Evidence": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Evidence", - "type": "object" - }, - "ExtractionResult": { - "additionalProperties": false, - "description": "A result of extracting knowledge on text", - "properties": { - "extracted_object": { - "$ref": "#/$defs/Any", - "description": "The complex objects extracted from the text" - }, - "input_id": { - "type": "string" - }, - "input_text": { - "type": "string" - }, - "input_title": { - "type": "string" - }, - "named_entities": { - "description": "Named entities extracted from the text", - "items": { - "$ref": "#/$defs/Any" - }, - "type": "array" - }, - "prompt": { - "type": "string" - }, - "raw_completion_output": { - "type": "string" - } - }, - "title": "ExtractionResult", - "type": "object" - }, - "Gene": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Gene", - "type": "object" - }, - "GeneReactionPairing": { - "additionalProperties": false, - "description": "", - "properties": { - "gene": { - "description": "name of the gene that catalyzes the reaction", - "type": "string" - }, - "reaction": { - "description": "equation describing the reaction (e.g. A+B = C+D) catalyzed by the gene", - "type": "string" - } - }, - "title": "GeneReactionPairing", - "type": "object" - }, - "GeneToReaction": { - "additionalProperties": false, - "description": "", - "properties": { - "gene": { - "description": "name of the gene that catalyzes the reaction", - "type": "string" - }, - "organism": { - "type": "string" - }, - "reactions": { - "additionalProperties": { - "$ref": "#/$defs/Reaction__identifier_optional" - }, - "description": "semicolon separated list of reaction equations (e.g. A+B = C+D) catalyzed by the gene", - "type": "object" - } - }, - "title": "GeneToReaction", - "type": "object" - }, - "NullDataOptions": { - "description": "", - "enum": [ - "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "NOT_APPLICABLE", - "NOT_MENTIONED" - ], - "title": "NullDataOptions", - "type": "string" - }, - "Organism": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Organism", - "type": "object" - }, - "Publication": { - "additionalProperties": false, - "description": "", - "properties": { - "abstract": { - "description": "The abstract of the publication", - "type": "string" - }, - "combined_text": { - "type": "string" - }, - "full_text": { - "description": "The full text of the publication", - "type": "string" - }, - "id": { - "description": "The publication identifier", - "type": "string" - }, - "title": { - "description": "The title of the publication", - "type": "string" - } - }, - "title": "Publication", - "type": "object" - }, - "Reaction": { - "additionalProperties": false, - "description": "", - "properties": { - "description": { - "description": "a textual description of the reaction", - "type": "string" - }, - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "the name of the reaction", - "type": "string" - }, - "left_side": { - "description": "semicolon separated list of chemical entities on the left side", - "items": { - "type": "string" - }, - "type": "array" - }, - "right_side": { - "description": "semicolon separated list of chemical entities on the right side", - "items": { - "type": "string" - }, - "type": "array" - }, - "subclass_of": { - "description": "the category to which this biological process belongs", - "type": "string" - }, - "synonyms": { - "description": "alternative names of the reaction", - "items": { - "type": "string" - }, - "type": "array" - } - }, - "required": [ - "id" - ], - "title": "Reaction", - "type": "object" - }, - "ReactionDocument": { - "additionalProperties": false, - "description": "", - "properties": { - "gene_reaction_pairings": { - "description": "semicolon separated list of gene to reaction pairings", - "items": { - "$ref": "#/$defs/GeneReactionPairing" - }, - "type": "array" - }, - "genes": { - "description": "semicolon separated list of genes that catalyzes the mentioned reactions", - "items": { - "type": "string" - }, - "type": "array" - }, - "has_evidence": { - "description": "evidence for the reaction", - "items": { - "type": "string" - }, - "type": "array" - }, - "organism": { - "type": "string" - }, - "reactions": { - "additionalProperties": { - "$ref": "#/$defs/Reaction__identifier_optional" - }, - "description": "semicolon separated list of reaction equations (e.g. A+B = C+D) catalyzed by the gene", - "type": "object" - } - }, - "title": "ReactionDocument", - "type": "object" - }, - "ReactionGrouping": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "ReactionGrouping", - "type": "object" - }, - "Reaction__identifier_optional": { - "additionalProperties": false, - "description": "", - "properties": { - "description": { - "description": "a textual description of the reaction", - "type": "string" - }, - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "the name of the reaction", - "type": "string" - }, - "left_side": { - "description": "semicolon separated list of chemical entities on the left side", - "items": { - "type": "string" - }, - "type": "array" - }, - "right_side": { - "description": "semicolon separated list of chemical entities on the right side", - "items": { - "type": "string" - }, - "type": "array" - }, - "subclass_of": { - "description": "the category to which this biological process belongs", - "type": "string" - }, - "synonyms": { - "description": "alternative names of the reaction", - "items": { - "type": "string" - }, - "type": "array" - } - }, - "required": [], - "title": "Reaction", - "type": "object" - }, - "RelationshipType": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "RelationshipType", - "type": "object" - }, - "TextWithTriples": { - "additionalProperties": false, - "description": "", - "properties": { - "publication": { - "$ref": "#/$defs/Publication" - }, - "triples": { - "items": { - "$ref": "#/$defs/Triple" - }, - "type": "array" - } - }, - "title": "TextWithTriples", - "type": "object" - } - }, - "$id": "https://w3id.org/ontogpt/reaction", - "$schema": "http://json-schema.org/draft-07/schema#", - "additionalProperties": true, - "metamodel_version": "1.7.0", - "title": "reaction-template", - "type": "object", - "version": null -} \ No newline at end of file diff --git a/projects/reaction/owl/reaction.owl.ttl b/projects/reaction/owl/reaction.owl.ttl deleted file mode 100644 index c50abc2c2..000000000 --- a/projects/reaction/owl/reaction.owl.ttl +++ /dev/null @@ -1,544 +0,0 @@ -@prefix IAO: <http://purl.obolibrary.org/obo/IAO_> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix owl: <http://www.w3.org/2002/07/owl#> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . -@prefix reaction: <http://w3id.org/ontogpt/reaction/> . -@prefix skos: <http://www.w3.org/2004/02/skos/core#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -linkml:SubsetDefinition a owl:Class ; - rdfs:label "subset_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" . - -linkml:TypeDefinition a owl:Class ; - rdfs:label "type_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" ; - linkml:mixins "type_expression" . - -linkml:topValue a owl:DatatypeProperty ; - rdfs:label "value" . - -<https://w3id.org/ontogpt/reaction> a owl:Ontology ; - rdfs:label "reaction-template" ; - IAO:0000700 <http://w3id.org/ontogpt/core/AnnotatorResult>, - <http://w3id.org/ontogpt/core/Any>, - <http://w3id.org/ontogpt/core/CompoundExpression>, - <http://w3id.org/ontogpt/core/ExtractionResult>, - <http://w3id.org/ontogpt/core/NamedEntity>, - <http://w3id.org/ontogpt/core/Publication>, - <http://w3id.org/ontogpt/core/TextWithTriples>, - reaction:GeneToReaction, - reaction:ReactionDocument ; - linkml:classes "{'Reaction': ClassDefinition(name='Reaction', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/reaction/Reaction', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/reaction', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'reaction__label', 'reaction__description', 'reaction__synonyms', 'reaction__subclass_of', 'reaction__left_side', 'reaction__right_side'], slot_usage={}, attributes={'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the name of the reaction', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'description': SlotDefinition(name='description', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a textual description of the reaction', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'synonyms': SlotDefinition(name='synonyms', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='alternative names of the reaction', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subclass_of': SlotDefinition(name='subclass_of', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the category to which this biological process belongs', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ReactionGrouping', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'left_side': SlotDefinition(name='left_side', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon separated list of chemical entities on the left side', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ChemicalEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'right_side': SlotDefinition(name='right_side', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon separated list of chemical entities on the right side', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ChemicalEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='reaction:Reaction', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'GeneToReaction': ClassDefinition(name='GeneToReaction', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/reaction/GeneToReaction', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/reaction', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['geneToReaction__gene', 'geneToReaction__reactions', 'geneToReaction__organism'], slot_usage={}, attributes={'gene': SlotDefinition(name='gene', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='name of the gene that catalyzes the reaction', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'reactions': SlotDefinition(name='reactions', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon separated list of reaction equations (e.g. A+B = C+D) catalyzed by the gene', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Reaction', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'organism': SlotDefinition(name='organism', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Organism', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='reaction:GeneToReaction', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ReactionDocument': ClassDefinition(name='ReactionDocument', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/reaction/ReactionDocument', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/reaction', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['reactionDocument__genes', 'reactionDocument__reactions', 'reactionDocument__gene_reaction_pairings', 'reactionDocument__organism', 'reactionDocument__has_evidence'], slot_usage={}, attributes={'genes': SlotDefinition(name='genes', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon separated list of genes that catalyzes the mentioned reactions', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'reactions': SlotDefinition(name='reactions', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon separated list of reaction equations (e.g. A+B = C+D) catalyzed by the gene', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Reaction', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'gene_reaction_pairings': SlotDefinition(name='gene_reaction_pairings', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon separated list of gene to reaction pairings', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneReactionPairing', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'organism': SlotDefinition(name='organism', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Organism', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'has_evidence': SlotDefinition(name='has_evidence', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='evidence for the reaction', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Evidence', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='reaction:ReactionDocument', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'GeneReactionPairing': ClassDefinition(name='GeneReactionPairing', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/reaction/GeneReactionPairing', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/reaction', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['geneReactionPairing__gene', 'geneReactionPairing__reaction'], slot_usage={}, attributes={'gene': SlotDefinition(name='gene', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='name of the gene that catalyzes the reaction', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'reaction': SlotDefinition(name='reaction', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='equation describing the reaction (e.g. A+B = C+D) catalyzed by the gene', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Reaction', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='reaction:GeneReactionPairing', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ReactionGrouping': ClassDefinition(name='ReactionGrouping', id_prefixes=['GO'], definition_uri='http://w3id.org/ontogpt/reaction/ReactionGrouping', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:go', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/reaction', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='reaction:ReactionGrouping', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ChemicalEntity': ClassDefinition(name='ChemicalEntity', id_prefixes=['CHEBI'], definition_uri='http://w3id.org/ontogpt/reaction/ChemicalEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:chebi', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/reaction', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='reaction:ChemicalEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Evidence': ClassDefinition(name='Evidence', id_prefixes=['OBI', 'ECO', 'MS'], definition_uri='http://w3id.org/ontogpt/reaction/Evidence', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:obi, sqlite:obo:eco, sqlite:obo:ms', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/reaction', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='reaction:Evidence', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Gene': ClassDefinition(name='Gene', id_prefixes=['HGNC'], definition_uri='http://w3id.org/ontogpt/reaction/Gene', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='gilda:, bioportal:hgnc-nr, bioportal:pr', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/reaction', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='reaction:Gene', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Organism': ClassDefinition(name='Organism', id_prefixes=['NCBITaxon'], definition_uri='http://w3id.org/ontogpt/reaction/Organism', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='gilda:, sqlite:obo:ncbitaxon', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/reaction', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='reaction:Organism', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Any': ClassDefinition(name='Any', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Any', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=['linkml:Any'], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='linkml:Any', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ExtractionResult': ClassDefinition(name='ExtractionResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/ExtractionResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A result of extracting knowledge on text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['extractionResult__input_id', 'extractionResult__input_title', 'extractionResult__input_text', 'extractionResult__raw_completion_output', 'extractionResult__prompt', 'extractionResult__extracted_object', 'extractionResult__named_entities'], slot_usage={}, attributes={'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:ExtractionResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'NamedEntity': ClassDefinition(name='NamedEntity', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NamedEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:NamedEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'CompoundExpression': ClassDefinition(name='CompoundExpression', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/CompoundExpression', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='core:CompoundExpression', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Triple': ClassDefinition(name='Triple', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Triple', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Abstract parent for Relation Extraction tasks', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['triple__subject', 'triple__predicate', 'triple__object', 'triple__qualifier', 'triple__subject_qualifier', 'triple__object_qualifier'], slot_usage={}, attributes={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Triple', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'TextWithTriples': ClassDefinition(name='TextWithTriples', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/TextWithTriples', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['textWithTriples__publication', 'textWithTriples__triples'], slot_usage={}, attributes={'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:TextWithTriples', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'RelationshipType': ClassDefinition(name='RelationshipType', id_prefixes=['RO', 'biolink'], definition_uri='http://w3id.org/ontogpt/core/RelationshipType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='core:RelationshipType', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Publication': ClassDefinition(name='Publication', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Publication', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['publication__id', 'publication__title', 'publication__abstract', 'publication__combined_text', 'publication__full_text'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Publication', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'AnnotatorResult': ClassDefinition(name='AnnotatorResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/AnnotatorResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['annotatorResult__subject_text', 'annotatorResult__object_id', 'annotatorResult__object_text'], slot_usage={}, attributes={'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:AnnotatorResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={})}" ; - linkml:enums "{'NullDataOptions': EnumDefinition(name='NullDataOptions', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NullDataOptions', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'UNSPECIFIED_METHOD_OF_ADMINISTRATION': PermissibleValue(text='UNSPECIFIED_METHOD_OF_ADMINISTRATION', description=None, meaning='NCIT:C149701', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_APPLICABLE': PermissibleValue(text='NOT_APPLICABLE', description=None, meaning='NCIT:C18902', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['not applicable', 'N/A'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_MENTIONED': PermissibleValue(text='NOT_MENTIONED', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[])}" ; - linkml:id "https://w3id.org/ontogpt/reaction" ; - linkml:imports "core", - "linkml:types" ; - linkml:types "{'string': TypeDefinition(name='string', id_prefixes=[], definition_uri='https://w3id.org/linkml/String', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A character string', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Text'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'integer': TypeDefinition(name='integer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Integer', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An integer', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Integer'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='int', uri='xsd:integer', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'boolean': TypeDefinition(name='boolean', id_prefixes=[], definition_uri='https://w3id.org/linkml/Boolean', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A binary (true or false) value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Boolean'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Bool', uri='xsd:boolean', repr='bool', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'float': TypeDefinition(name='float', id_prefixes=[], definition_uri='https://w3id.org/linkml/Float', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:float specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Float'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:float', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'double': TypeDefinition(name='double', id_prefixes=[], definition_uri='https://w3id.org/linkml/Double', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:double specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:Float'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:double', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'decimal': TypeDefinition(name='decimal', id_prefixes=[], definition_uri='https://w3id.org/linkml/Decimal', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number with arbitrary precision that conforms to the xsd:decimal specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=['schema:Number'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Decimal', uri='xsd:decimal', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'time': TypeDefinition(name='time', id_prefixes=[], definition_uri='https://w3id.org/linkml/Time', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A time object represents a (local) time of day, independent of any particular day', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=['URI is dateTime because OWL reasoners do not work with straight date or time'], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Time'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDTime', uri='xsd:time', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date': TypeDefinition(name='date', id_prefixes=[], definition_uri='https://w3id.org/linkml/Date', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a date (year, month and day) in an idealized calendar', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[\"URI is dateTime because OWL reasoners don't work with straight date or time\"], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Date'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDate', uri='xsd:date', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'datetime': TypeDefinition(name='datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/Datetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The combination of a date and time', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:DateTime'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDateTime', uri='xsd:dateTime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date_or_datetime': TypeDefinition(name='date_or_datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/DateOrDatetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Either a date or a datetime', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='linkml:DateOrDatetime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uriorcurie': TypeDefinition(name='uriorcurie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uriorcurie', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a URI or a CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URIorCURIE', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'curie': TypeDefinition(name='curie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Curie', local_names={}, conforms_to='https://www.w3.org/TR/curie/', implements=[], extensions={}, annotations={}, description='a compact URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations this MUST be expanded to a URI', 'in non-RDF serializations MAY be serialized as the compact representation'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Curie', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uri': TypeDefinition(name='uri', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uri', local_names={}, conforms_to='https://www.ietf.org/rfc/rfc3987.txt', implements=[], extensions={}, annotations={}, description='a complete URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:URL'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URI', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ncname': TypeDefinition(name='ncname', id_prefixes=[], definition_uri='https://w3id.org/linkml/Ncname', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Prefix part of CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NCName', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'objectidentifier': TypeDefinition(name='objectidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Objectidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI or CURIE that represents an object in the model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['Used for inheritance and type checking'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='ElementIdentifier', uri='shex:iri', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'nodeidentifier': TypeDefinition(name='nodeidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Nodeidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI, CURIE or BNODE that represents a node in a model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NodeIdentifier', uri='shex:nonLiteral', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpointer': TypeDefinition(name='jsonpointer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpointer', local_names={}, conforms_to='https://datatracker.ietf.org/doc/html/rfc6901', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpath': TypeDefinition(name='jsonpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpath', local_names={}, conforms_to='https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sparqlpath': TypeDefinition(name='sparqlpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Sparqlpath', local_names={}, conforms_to='https://www.w3.org/TR/sparql11-query/#propertypaths', implements=[], extensions={}, annotations={}, description='A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "AnnotatorResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_text> ] ; - linkml:attributes "{'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/ExtractionResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ExtractionResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/extracted_object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_id> ], - [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/named_entities> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/prompt> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_title> ] ; - skos:definition "A result of extracting knowledge on text" ; - linkml:attributes "{'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/TextWithTriples> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TextWithTriples" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Publication> ; - owl:onProperty <http://w3id.org/ontogpt/core/publication> ], - [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Triple> ; - owl:onProperty <http://w3id.org/ontogpt/core/triples> ] ; - linkml:attributes "{'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/abstract> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "abstract" ; - rdfs:range linkml:String ; - skos:definition "The abstract of the publication" . - -<http://w3id.org/ontogpt/core/combined_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "combined_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/extracted_object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "extracted_object" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "The complex objects extracted from the text" . - -<http://w3id.org/ontogpt/core/full_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "full_text" ; - rdfs:range linkml:String ; - skos:definition "The full text of the publication" . - -<http://w3id.org/ontogpt/core/input_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_title" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/named_entities> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "named_entities" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "Named entities extracted from the text" . - -<http://w3id.org/ontogpt/core/object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/object_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/object_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" . - -<http://w3id.org/ontogpt/core/object_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/predicate> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "predicate" ; - rdfs:range <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/prompt> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "prompt" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/publication> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "publication" ; - reaction:prompt.skip "true" ; - rdfs:range <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "qualifier" ; - rdfs:range linkml:String ; - skos:definition "A qualifier for the statements, e.g. \"NOT\" for negation" . - -<http://w3id.org/ontogpt/core/raw_completion_output> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "raw_completion_output" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/subject> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/subject_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" . - -<http://w3id.org/ontogpt/core/subject_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "title" ; - rdfs:range linkml:String ; - skos:definition "The title of the publication" . - -<http://w3id.org/ontogpt/core/triples> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "triples" ; - rdfs:range <http://w3id.org/ontogpt/core/Triple> . - -reaction:GeneToReaction a owl:Class, - linkml:ClassDefinition ; - rdfs:label "GeneToReaction" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass reaction:Gene ; - owl:onProperty reaction:gene ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass reaction:Organism ; - owl:onProperty reaction:organism ], - [ a owl:Restriction ; - owl:allValuesFrom reaction:Reaction ; - owl:onProperty reaction:reactions ] ; - linkml:attributes "{'gene': SlotDefinition(name='gene', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='name of the gene that catalyzes the reaction', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'reactions': SlotDefinition(name='reactions', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon separated list of reaction equations (e.g. A+B = C+D) catalyzed by the gene', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Reaction', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'organism': SlotDefinition(name='organism', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Organism', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -reaction:ReactionDocument a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ReactionDocument" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom reaction:GeneReactionPairing ; - owl:onProperty reaction:gene_reaction_pairings ], - [ a owl:Restriction ; - owl:allValuesFrom reaction:Gene ; - owl:onProperty reaction:genes ], - [ a owl:Restriction ; - owl:allValuesFrom reaction:Reaction ; - owl:onProperty reaction:reactions ], - [ a owl:Restriction ; - owl:allValuesFrom reaction:Evidence ; - owl:onProperty reaction:has_evidence ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass reaction:Organism ; - owl:onProperty reaction:organism ] ; - linkml:attributes "{'genes': SlotDefinition(name='genes', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon separated list of genes that catalyzes the mentioned reactions', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'reactions': SlotDefinition(name='reactions', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon separated list of reaction equations (e.g. A+B = C+D) catalyzed by the gene', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Reaction', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'gene_reaction_pairings': SlotDefinition(name='gene_reaction_pairings', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon separated list of gene to reaction pairings', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneReactionPairing', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'organism': SlotDefinition(name='organism', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Organism', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'has_evidence': SlotDefinition(name='has_evidence', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='evidence for the reaction', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Evidence', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -reaction:description a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "description" ; - rdfs:range linkml:String ; - skos:definition "a textual description of the reaction" . - -reaction:gene_reaction_pairings a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "gene_reaction_pairings" ; - rdfs:range reaction:GeneReactionPairing ; - skos:definition "semicolon separated list of gene to reaction pairings" . - -reaction:genes a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "genes" ; - rdfs:range reaction:Gene ; - skos:definition "semicolon separated list of genes that catalyzes the mentioned reactions" . - -reaction:has_evidence a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "has_evidence" ; - rdfs:range reaction:Evidence ; - skos:definition "evidence for the reaction" . - -reaction:label a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "label" ; - rdfs:range linkml:String ; - skos:definition "the name of the reaction" . - -reaction:left_side a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "left_side" ; - rdfs:range reaction:ChemicalEntity ; - skos:definition "semicolon separated list of chemical entities on the left side" . - -reaction:reaction a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "reaction" ; - rdfs:range reaction:Reaction ; - skos:definition "equation describing the reaction (e.g. A+B = C+D) catalyzed by the gene" . - -reaction:right_side a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "right_side" ; - rdfs:range reaction:ChemicalEntity ; - skos:definition "semicolon separated list of chemical entities on the right side" . - -reaction:subclass_of a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subclass_of" ; - rdfs:range reaction:ReactionGrouping ; - skos:definition "the category to which this biological process belongs" . - -reaction:synonyms a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "synonyms" ; - rdfs:range linkml:String ; - skos:definition "alternative names of the reaction" . - -<http://example.org/UNKNOWN/rdfs/label> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "label" ; - reaction:owl "AnnotationProperty, AnnotationAssertion" ; - rdfs:range linkml:String ; - skos:altLabel "name" ; - skos:definition "The label (name) of the named thing" ; - skos:exactMatch <http://example.org/UNKNOWN/rdfs/label> . - -<http://purl.obolibrary.org/obo/NCIT_C149701> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "UNSPECIFIED_METHOD_OF_ADMINISTRATION" . - -<http://purl.obolibrary.org/obo/NCIT_C18902> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_APPLICABLE" . - -<http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_MENTIONED" . - -<http://w3id.org/ontogpt/core/RelationshipType> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "RelationshipType" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/Triple> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Triple" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/RelationshipType> ; - owl:onProperty <http://w3id.org/ontogpt/core/predicate> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_qualifier> ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - skos:definition "Abstract parent for Relation Extraction tasks" ; - linkml:attributes "{'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -<http://w3id.org/ontogpt/core/id> a owl:ObjectProperty, - linkml:SlotDefinition . - -reaction:Evidence a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Evidence" ; - reaction:annotators "sqlite:obo:obi, sqlite:obo:eco, sqlite:obo:ms" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -reaction:GeneReactionPairing a owl:Class, - linkml:ClassDefinition ; - rdfs:label "GeneReactionPairing" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass reaction:Reaction ; - owl:onProperty reaction:reaction ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass reaction:Gene ; - owl:onProperty reaction:gene ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - linkml:attributes "{'gene': SlotDefinition(name='gene', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='name of the gene that catalyzes the reaction', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'reaction': SlotDefinition(name='reaction', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='equation describing the reaction (e.g. A+B = C+D) catalyzed by the gene', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Reaction', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -reaction:Organism a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Organism" ; - reaction:annotators "gilda:, sqlite:obo:ncbitaxon" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -reaction:ReactionGrouping a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ReactionGrouping" ; - reaction:annotators "sqlite:obo:go" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -reaction:gene a owl:ObjectProperty, - linkml:SlotDefinition . - -reaction:organism a owl:ObjectProperty, - linkml:SlotDefinition . - -reaction:reactions a owl:ObjectProperty, - linkml:SlotDefinition . - -<http://w3id.org/ontogpt/core/CompoundExpression> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CompoundExpression" ; - linkml:attributes "{}" . - -<http://w3id.org/ontogpt/core/NullDataOptions> a owl:Class, - linkml:EnumDefinition ; - rdfs:label "NullDataOptions" ; - owl:unionOf ( <http://purl.obolibrary.org/obo/NCIT_C149701> <http://purl.obolibrary.org/obo/NCIT_C18902> <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> ) ; - linkml:permissible_values <http://purl.obolibrary.org/obo/NCIT_C149701>, - <http://purl.obolibrary.org/obo/NCIT_C18902>, - <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> . - -<http://w3id.org/ontogpt/core/Publication> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Publication" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/abstract> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/title> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/full_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/combined_text> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -reaction:ChemicalEntity a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ChemicalEntity" ; - reaction:annotators "sqlite:obo:chebi" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -reaction:Gene a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Gene" ; - reaction:annotators "gilda:, bioportal:hgnc-nr, bioportal:pr" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -reaction:Reaction a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Reaction" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom reaction:ChemicalEntity ; - owl:onProperty reaction:left_side ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty reaction:description ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass reaction:ReactionGrouping ; - owl:onProperty reaction:subclass_of ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty reaction:label ], - [ a owl:Restriction ; - owl:allValuesFrom reaction:ChemicalEntity ; - owl:onProperty reaction:right_side ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty reaction:synonyms ], - <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the name of the reaction', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'description': SlotDefinition(name='description', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a textual description of the reaction', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'synonyms': SlotDefinition(name='synonyms', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='alternative names of the reaction', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subclass_of': SlotDefinition(name='subclass_of', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the category to which this biological process belongs', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ReactionGrouping', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'left_side': SlotDefinition(name='left_side', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon separated list of chemical entities on the left side', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ChemicalEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'right_side': SlotDefinition(name='right_side', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon separated list of chemical entities on the right side', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ChemicalEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/Any> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Any" ; - skos:exactMatch linkml:Any ; - linkml:attributes "{}" . - -<http://w3id.org/ontogpt/core/NamedEntity> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "NamedEntity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://example.org/UNKNOWN/rdfs/label> ], - [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ; - owl:qualifiedCardinality 1 ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:ClassDefinition a owl:Class ; - rdfs:label "class_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "class_expression" . - -linkml:SlotDefinition a owl:Class ; - rdfs:label "slot_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "slot_expression" . - - diff --git a/projects/reaction/prefixmap/reaction.yaml b/projects/reaction/prefixmap/reaction.yaml deleted file mode 100644 index c55f40b7c..000000000 --- a/projects/reaction/prefixmap/reaction.yaml +++ /dev/null @@ -1,42 +0,0 @@ -{ - "CHEBI": "http://example.org/UNKNOWN/CHEBI/", - "ECO": "http://example.org/UNKNOWN/ECO/", - "GO": "http://example.org/UNKNOWN/GO/", - "HGNC": "http://example.org/UNKNOWN/HGNC/", - "MS": "http://example.org/UNKNOWN/MS/", - "NCBITaxon": "http://example.org/UNKNOWN/NCBITaxon/", - "OBI": "http://example.org/UNKNOWN/OBI/", - "RO": "http://purl.obolibrary.org/obo/RO_", - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "reaction": "http://w3id.org/ontogpt/reaction/", - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } -} diff --git a/projects/reaction/protobuf/reaction.proto b/projects/reaction/protobuf/reaction.proto deleted file mode 100644 index 4b4294df0..000000000 --- a/projects/reaction/protobuf/reaction.proto +++ /dev/null @@ -1,89 +0,0 @@ -message AnnotatorResult - { - string subjectText = 0 - string objectId = 0 - string objectText = 0 - } -message ChemicalEntity - { - string id = 0 - string label = 0 - } -message Evidence - { - string id = 0 - string label = 0 - } -// A result of extracting knowledge on text -message ExtractionResult - { - string inputId = 0 - string inputTitle = 0 - string inputText = 0 - string rawCompletionOutput = 0 - string prompt = 0 - any extractedObject = 0 - repeated any namedEntities = 0 - } -message Gene - { - string id = 0 - string label = 0 - } -message GeneReactionPairing - { - gene gene = 0 - reaction reaction = 0 - } -message GeneToReaction - { - gene gene = 0 - repeated reaction reactions = 0 - organism organism = 0 - } -message Organism - { - string id = 0 - string label = 0 - } -message Publication - { - string id = 0 - string title = 0 - string abstract = 0 - string combinedText = 0 - string fullText = 0 - } -message Reaction - { - string id = 0 - string label = 0 - string description = 0 - repeated string synonyms = 0 - reactionGrouping subclassOf = 0 - repeated chemicalEntity leftSide = 0 - repeated chemicalEntity rightSide = 0 - } -message ReactionDocument - { - repeated gene genes = 0 - repeated reaction reactions = 0 - repeated geneReactionPairing geneReactionPairings = 0 - organism organism = 0 - repeated evidence hasEvidence = 0 - } -message ReactionGrouping - { - string id = 0 - string label = 0 - } -message RelationshipType - { - string id = 0 - string label = 0 - } -message TextWithTriples - { - publication publication = 0 - repeated triple triples = 0 - } diff --git a/projects/reaction/reaction.py b/projects/reaction/reaction.py deleted file mode 100644 index a1b30abf3..000000000 --- a/projects/reaction/reaction.py +++ /dev/null @@ -1,671 +0,0 @@ -# Auto generated from reaction.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-08-07T10:56:03 -# Schema: reaction-template -# -# id: https://w3id.org/ontogpt/reaction -# description: A template for reactions -# license: https://creativecommons.org/publicdomain/zero/1.0/ - -import dataclasses -import sys -import re -from jsonasobj2 import JsonObj, as_dict -from typing import Optional, List, Union, Dict, ClassVar, Any -from dataclasses import dataclass -from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions - -from linkml_runtime.utils.slot import Slot -from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode -from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int -from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs -from linkml_runtime.utils.formatutils import camelcase, underscore, sfx -from linkml_runtime.utils.enumerations import EnumDefinitionImpl -from rdflib import Namespace, URIRef -from linkml_runtime.utils.curienamespace import CurieNamespace -from linkml_runtime.linkml_model.types import String - -metamodel_version = "1.7.0" -version = None - -# Overwrite dataclasses _init_fn to add **kwargs in __init__ -dataclasses._init_fn = dataclasses_init_fn_with_kwargs - -# Namespaces -CHEBI = CurieNamespace('CHEBI', 'http://example.org/UNKNOWN/CHEBI/') -ECO = CurieNamespace('ECO', 'http://example.org/UNKNOWN/ECO/') -GO = CurieNamespace('GO', 'http://example.org/UNKNOWN/GO/') -HGNC = CurieNamespace('HGNC', 'http://example.org/UNKNOWN/HGNC/') -MS = CurieNamespace('MS', 'http://example.org/UNKNOWN/MS/') -NCBITAXON = CurieNamespace('NCBITaxon', 'http://example.org/UNKNOWN/NCBITaxon/') -OBI = CurieNamespace('OBI', 'http://example.org/UNKNOWN/OBI/') -RO = CurieNamespace('RO', 'http://purl.obolibrary.org/obo/RO_') -BIOLINK = CurieNamespace('biolink', 'http://example.org/UNKNOWN/biolink/') -CORE = CurieNamespace('core', 'http://w3id.org/ontogpt/core/') -LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') -RDFS = CurieNamespace('rdfs', 'http://example.org/UNKNOWN/rdfs/') -REACTION = CurieNamespace('reaction', 'http://w3id.org/ontogpt/reaction/') -DEFAULT_ = REACTION - - -# Types - -# Class references -class NamedEntityId(extended_str): - pass - - -class ReactionId(NamedEntityId): - pass - - -class ReactionGroupingId(NamedEntityId): - pass - - -class ChemicalEntityId(NamedEntityId): - pass - - -class EvidenceId(NamedEntityId): - pass - - -class GeneId(NamedEntityId): - pass - - -class OrganismId(NamedEntityId): - pass - - -class RelationshipTypeId(NamedEntityId): - pass - - -@dataclass -class GeneToReaction(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = REACTION.GeneToReaction - class_class_curie: ClassVar[str] = "reaction:GeneToReaction" - class_name: ClassVar[str] = "GeneToReaction" - class_model_uri: ClassVar[URIRef] = REACTION.GeneToReaction - - gene: Optional[Union[str, GeneId]] = None - reactions: Optional[Union[Dict[Union[str, ReactionId], Union[dict, Reaction]], List[Union[dict, Reaction]]]] = empty_dict() - organism: Optional[Union[str, OrganismId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.gene is not None and not isinstance(self.gene, GeneId): - self.gene = GeneId(self.gene) - - self._normalize_inlined_as_dict(slot_name="reactions", slot_type=Reaction, key_name="id", keyed=True) - - if self.organism is not None and not isinstance(self.organism, OrganismId): - self.organism = OrganismId(self.organism) - - super().__post_init__(**kwargs) - - -@dataclass -class ReactionDocument(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = REACTION.ReactionDocument - class_class_curie: ClassVar[str] = "reaction:ReactionDocument" - class_name: ClassVar[str] = "ReactionDocument" - class_model_uri: ClassVar[URIRef] = REACTION.ReactionDocument - - genes: Optional[Union[Union[str, GeneId], List[Union[str, GeneId]]]] = empty_list() - reactions: Optional[Union[Dict[Union[str, ReactionId], Union[dict, Reaction]], List[Union[dict, Reaction]]]] = empty_dict() - gene_reaction_pairings: Optional[Union[Union[dict, "GeneReactionPairing"], List[Union[dict, "GeneReactionPairing"]]]] = empty_list() - organism: Optional[Union[str, OrganismId]] = None - has_evidence: Optional[Union[Union[str, EvidenceId], List[Union[str, EvidenceId]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if not isinstance(self.genes, list): - self.genes = [self.genes] if self.genes is not None else [] - self.genes = [v if isinstance(v, GeneId) else GeneId(v) for v in self.genes] - - self._normalize_inlined_as_dict(slot_name="reactions", slot_type=Reaction, key_name="id", keyed=True) - - if not isinstance(self.gene_reaction_pairings, list): - self.gene_reaction_pairings = [self.gene_reaction_pairings] if self.gene_reaction_pairings is not None else [] - self.gene_reaction_pairings = [v if isinstance(v, GeneReactionPairing) else GeneReactionPairing(**as_dict(v)) for v in self.gene_reaction_pairings] - - if self.organism is not None and not isinstance(self.organism, OrganismId): - self.organism = OrganismId(self.organism) - - if not isinstance(self.has_evidence, list): - self.has_evidence = [self.has_evidence] if self.has_evidence is not None else [] - self.has_evidence = [v if isinstance(v, EvidenceId) else EvidenceId(v) for v in self.has_evidence] - - super().__post_init__(**kwargs) - - -Any = Any - -@dataclass -class ExtractionResult(YAMLRoot): - """ - A result of extracting knowledge on text - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.ExtractionResult - class_class_curie: ClassVar[str] = "core:ExtractionResult" - class_name: ClassVar[str] = "ExtractionResult" - class_model_uri: ClassVar[URIRef] = REACTION.ExtractionResult - - input_id: Optional[str] = None - input_title: Optional[str] = None - input_text: Optional[str] = None - raw_completion_output: Optional[str] = None - prompt: Optional[str] = None - extracted_object: Optional[Union[dict, Any]] = None - named_entities: Optional[Union[Union[dict, Any], List[Union[dict, Any]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.input_id is not None and not isinstance(self.input_id, str): - self.input_id = str(self.input_id) - - if self.input_title is not None and not isinstance(self.input_title, str): - self.input_title = str(self.input_title) - - if self.input_text is not None and not isinstance(self.input_text, str): - self.input_text = str(self.input_text) - - if self.raw_completion_output is not None and not isinstance(self.raw_completion_output, str): - self.raw_completion_output = str(self.raw_completion_output) - - if self.prompt is not None and not isinstance(self.prompt, str): - self.prompt = str(self.prompt) - - super().__post_init__(**kwargs) - - -@dataclass -class NamedEntity(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.NamedEntity - class_class_curie: ClassVar[str] = "core:NamedEntity" - class_name: ClassVar[str] = "NamedEntity" - class_model_uri: ClassVar[URIRef] = REACTION.NamedEntity - - id: Union[str, NamedEntityId] = None - label: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, NamedEntityId): - self.id = NamedEntityId(self.id) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - super().__post_init__(**kwargs) - - -@dataclass -class Reaction(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = REACTION.Reaction - class_class_curie: ClassVar[str] = "reaction:Reaction" - class_name: ClassVar[str] = "Reaction" - class_model_uri: ClassVar[URIRef] = REACTION.Reaction - - id: Union[str, ReactionId] = None - label: Optional[str] = None - description: Optional[str] = None - synonyms: Optional[Union[str, List[str]]] = empty_list() - subclass_of: Optional[Union[str, ReactionGroupingId]] = None - left_side: Optional[Union[Union[str, ChemicalEntityId], List[Union[str, ChemicalEntityId]]]] = empty_list() - right_side: Optional[Union[Union[str, ChemicalEntityId], List[Union[str, ChemicalEntityId]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, ReactionId): - self.id = ReactionId(self.id) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - if self.description is not None and not isinstance(self.description, str): - self.description = str(self.description) - - if not isinstance(self.synonyms, list): - self.synonyms = [self.synonyms] if self.synonyms is not None else [] - self.synonyms = [v if isinstance(v, str) else str(v) for v in self.synonyms] - - if self.subclass_of is not None and not isinstance(self.subclass_of, ReactionGroupingId): - self.subclass_of = ReactionGroupingId(self.subclass_of) - - if not isinstance(self.left_side, list): - self.left_side = [self.left_side] if self.left_side is not None else [] - self.left_side = [v if isinstance(v, ChemicalEntityId) else ChemicalEntityId(v) for v in self.left_side] - - if not isinstance(self.right_side, list): - self.right_side = [self.right_side] if self.right_side is not None else [] - self.right_side = [v if isinstance(v, ChemicalEntityId) else ChemicalEntityId(v) for v in self.right_side] - - super().__post_init__(**kwargs) - - -@dataclass -class ReactionGrouping(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = REACTION.ReactionGrouping - class_class_curie: ClassVar[str] = "reaction:ReactionGrouping" - class_name: ClassVar[str] = "ReactionGrouping" - class_model_uri: ClassVar[URIRef] = REACTION.ReactionGrouping - - id: Union[str, ReactionGroupingId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, ReactionGroupingId): - self.id = ReactionGroupingId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class ChemicalEntity(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = REACTION.ChemicalEntity - class_class_curie: ClassVar[str] = "reaction:ChemicalEntity" - class_name: ClassVar[str] = "ChemicalEntity" - class_model_uri: ClassVar[URIRef] = REACTION.ChemicalEntity - - id: Union[str, ChemicalEntityId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, ChemicalEntityId): - self.id = ChemicalEntityId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Evidence(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = REACTION.Evidence - class_class_curie: ClassVar[str] = "reaction:Evidence" - class_name: ClassVar[str] = "Evidence" - class_model_uri: ClassVar[URIRef] = REACTION.Evidence - - id: Union[str, EvidenceId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, EvidenceId): - self.id = EvidenceId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Gene(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = REACTION.Gene - class_class_curie: ClassVar[str] = "reaction:Gene" - class_name: ClassVar[str] = "Gene" - class_model_uri: ClassVar[URIRef] = REACTION.Gene - - id: Union[str, GeneId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, GeneId): - self.id = GeneId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Organism(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = REACTION.Organism - class_class_curie: ClassVar[str] = "reaction:Organism" - class_name: ClassVar[str] = "Organism" - class_model_uri: ClassVar[URIRef] = REACTION.Organism - - id: Union[str, OrganismId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, OrganismId): - self.id = OrganismId(self.id) - - super().__post_init__(**kwargs) - - -class CompoundExpression(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.CompoundExpression - class_class_curie: ClassVar[str] = "core:CompoundExpression" - class_name: ClassVar[str] = "CompoundExpression" - class_model_uri: ClassVar[URIRef] = REACTION.CompoundExpression - - -@dataclass -class GeneReactionPairing(CompoundExpression): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = REACTION.GeneReactionPairing - class_class_curie: ClassVar[str] = "reaction:GeneReactionPairing" - class_name: ClassVar[str] = "GeneReactionPairing" - class_model_uri: ClassVar[URIRef] = REACTION.GeneReactionPairing - - gene: Optional[Union[str, GeneId]] = None - reaction: Optional[Union[str, ReactionId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.gene is not None and not isinstance(self.gene, GeneId): - self.gene = GeneId(self.gene) - - if self.reaction is not None and not isinstance(self.reaction, ReactionId): - self.reaction = ReactionId(self.reaction) - - super().__post_init__(**kwargs) - - -@dataclass -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Triple - class_class_curie: ClassVar[str] = "core:Triple" - class_name: ClassVar[str] = "Triple" - class_model_uri: ClassVar[URIRef] = REACTION.Triple - - subject: Optional[Union[str, NamedEntityId]] = None - predicate: Optional[Union[str, RelationshipTypeId]] = None - object: Optional[Union[str, NamedEntityId]] = None - qualifier: Optional[str] = None - subject_qualifier: Optional[Union[str, NamedEntityId]] = None - object_qualifier: Optional[Union[str, NamedEntityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, NamedEntityId): - self.subject = NamedEntityId(self.subject) - - if self.predicate is not None and not isinstance(self.predicate, RelationshipTypeId): - self.predicate = RelationshipTypeId(self.predicate) - - if self.object is not None and not isinstance(self.object, NamedEntityId): - self.object = NamedEntityId(self.object) - - if self.qualifier is not None and not isinstance(self.qualifier, str): - self.qualifier = str(self.qualifier) - - if self.subject_qualifier is not None and not isinstance(self.subject_qualifier, NamedEntityId): - self.subject_qualifier = NamedEntityId(self.subject_qualifier) - - if self.object_qualifier is not None and not isinstance(self.object_qualifier, NamedEntityId): - self.object_qualifier = NamedEntityId(self.object_qualifier) - - super().__post_init__(**kwargs) - - -@dataclass -class TextWithTriples(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.TextWithTriples - class_class_curie: ClassVar[str] = "core:TextWithTriples" - class_name: ClassVar[str] = "TextWithTriples" - class_model_uri: ClassVar[URIRef] = REACTION.TextWithTriples - - publication: Optional[Union[dict, "Publication"]] = None - triples: Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.publication is not None and not isinstance(self.publication, Publication): - self.publication = Publication(**as_dict(self.publication)) - - if not isinstance(self.triples, list): - self.triples = [self.triples] if self.triples is not None else [] - self.triples = [v if isinstance(v, Triple) else Triple(**as_dict(v)) for v in self.triples] - - super().__post_init__(**kwargs) - - -@dataclass -class RelationshipType(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.RelationshipType - class_class_curie: ClassVar[str] = "core:RelationshipType" - class_name: ClassVar[str] = "RelationshipType" - class_model_uri: ClassVar[URIRef] = REACTION.RelationshipType - - id: Union[str, RelationshipTypeId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, RelationshipTypeId): - self.id = RelationshipTypeId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Publication(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Publication - class_class_curie: ClassVar[str] = "core:Publication" - class_name: ClassVar[str] = "Publication" - class_model_uri: ClassVar[URIRef] = REACTION.Publication - - id: Optional[str] = None - title: Optional[str] = None - abstract: Optional[str] = None - combined_text: Optional[str] = None - full_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.id is not None and not isinstance(self.id, str): - self.id = str(self.id) - - if self.title is not None and not isinstance(self.title, str): - self.title = str(self.title) - - if self.abstract is not None and not isinstance(self.abstract, str): - self.abstract = str(self.abstract) - - if self.combined_text is not None and not isinstance(self.combined_text, str): - self.combined_text = str(self.combined_text) - - if self.full_text is not None and not isinstance(self.full_text, str): - self.full_text = str(self.full_text) - - super().__post_init__(**kwargs) - - -@dataclass -class AnnotatorResult(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.AnnotatorResult - class_class_curie: ClassVar[str] = "core:AnnotatorResult" - class_name: ClassVar[str] = "AnnotatorResult" - class_model_uri: ClassVar[URIRef] = REACTION.AnnotatorResult - - subject_text: Optional[str] = None - object_id: Optional[str] = None - object_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject_text is not None and not isinstance(self.subject_text, str): - self.subject_text = str(self.subject_text) - - if self.object_id is not None and not isinstance(self.object_id, str): - self.object_id = str(self.object_id) - - if self.object_text is not None and not isinstance(self.object_text, str): - self.object_text = str(self.object_text) - - super().__post_init__(**kwargs) - - -# Enumerations -class NullDataOptions(EnumDefinitionImpl): - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = PermissibleValue(text="UNSPECIFIED_METHOD_OF_ADMINISTRATION", - meaning=NCIT.C149701) - NOT_APPLICABLE = PermissibleValue(text="NOT_APPLICABLE", - meaning=NCIT.C18902) - NOT_MENTIONED = PermissibleValue(text="NOT_MENTIONED") - - _defn = EnumDefinition( - name="NullDataOptions", - ) - -# Slots -class slots: - pass - -slots.reaction__label = Slot(uri=REACTION.label, name="reaction__label", curie=REACTION.curie('label'), - model_uri=REACTION.reaction__label, domain=None, range=Optional[str]) - -slots.reaction__description = Slot(uri=REACTION.description, name="reaction__description", curie=REACTION.curie('description'), - model_uri=REACTION.reaction__description, domain=None, range=Optional[str]) - -slots.reaction__synonyms = Slot(uri=REACTION.synonyms, name="reaction__synonyms", curie=REACTION.curie('synonyms'), - model_uri=REACTION.reaction__synonyms, domain=None, range=Optional[Union[str, List[str]]]) - -slots.reaction__subclass_of = Slot(uri=REACTION.subclass_of, name="reaction__subclass_of", curie=REACTION.curie('subclass_of'), - model_uri=REACTION.reaction__subclass_of, domain=None, range=Optional[Union[str, ReactionGroupingId]]) - -slots.reaction__left_side = Slot(uri=REACTION.left_side, name="reaction__left_side", curie=REACTION.curie('left_side'), - model_uri=REACTION.reaction__left_side, domain=None, range=Optional[Union[Union[str, ChemicalEntityId], List[Union[str, ChemicalEntityId]]]]) - -slots.reaction__right_side = Slot(uri=REACTION.right_side, name="reaction__right_side", curie=REACTION.curie('right_side'), - model_uri=REACTION.reaction__right_side, domain=None, range=Optional[Union[Union[str, ChemicalEntityId], List[Union[str, ChemicalEntityId]]]]) - -slots.geneToReaction__gene = Slot(uri=REACTION.gene, name="geneToReaction__gene", curie=REACTION.curie('gene'), - model_uri=REACTION.geneToReaction__gene, domain=None, range=Optional[Union[str, GeneId]]) - -slots.geneToReaction__reactions = Slot(uri=REACTION.reactions, name="geneToReaction__reactions", curie=REACTION.curie('reactions'), - model_uri=REACTION.geneToReaction__reactions, domain=None, range=Optional[Union[Dict[Union[str, ReactionId], Union[dict, Reaction]], List[Union[dict, Reaction]]]]) - -slots.geneToReaction__organism = Slot(uri=REACTION.organism, name="geneToReaction__organism", curie=REACTION.curie('organism'), - model_uri=REACTION.geneToReaction__organism, domain=None, range=Optional[Union[str, OrganismId]]) - -slots.reactionDocument__genes = Slot(uri=REACTION.genes, name="reactionDocument__genes", curie=REACTION.curie('genes'), - model_uri=REACTION.reactionDocument__genes, domain=None, range=Optional[Union[Union[str, GeneId], List[Union[str, GeneId]]]]) - -slots.reactionDocument__reactions = Slot(uri=REACTION.reactions, name="reactionDocument__reactions", curie=REACTION.curie('reactions'), - model_uri=REACTION.reactionDocument__reactions, domain=None, range=Optional[Union[Dict[Union[str, ReactionId], Union[dict, Reaction]], List[Union[dict, Reaction]]]]) - -slots.reactionDocument__gene_reaction_pairings = Slot(uri=REACTION.gene_reaction_pairings, name="reactionDocument__gene_reaction_pairings", curie=REACTION.curie('gene_reaction_pairings'), - model_uri=REACTION.reactionDocument__gene_reaction_pairings, domain=None, range=Optional[Union[Union[dict, GeneReactionPairing], List[Union[dict, GeneReactionPairing]]]]) - -slots.reactionDocument__organism = Slot(uri=REACTION.organism, name="reactionDocument__organism", curie=REACTION.curie('organism'), - model_uri=REACTION.reactionDocument__organism, domain=None, range=Optional[Union[str, OrganismId]]) - -slots.reactionDocument__has_evidence = Slot(uri=REACTION.has_evidence, name="reactionDocument__has_evidence", curie=REACTION.curie('has_evidence'), - model_uri=REACTION.reactionDocument__has_evidence, domain=None, range=Optional[Union[Union[str, EvidenceId], List[Union[str, EvidenceId]]]]) - -slots.geneReactionPairing__gene = Slot(uri=REACTION.gene, name="geneReactionPairing__gene", curie=REACTION.curie('gene'), - model_uri=REACTION.geneReactionPairing__gene, domain=None, range=Optional[Union[str, GeneId]]) - -slots.geneReactionPairing__reaction = Slot(uri=REACTION.reaction, name="geneReactionPairing__reaction", curie=REACTION.curie('reaction'), - model_uri=REACTION.geneReactionPairing__reaction, domain=None, range=Optional[Union[str, ReactionId]]) - -slots.extractionResult__input_id = Slot(uri=CORE.input_id, name="extractionResult__input_id", curie=CORE.curie('input_id'), - model_uri=REACTION.extractionResult__input_id, domain=None, range=Optional[str]) - -slots.extractionResult__input_title = Slot(uri=CORE.input_title, name="extractionResult__input_title", curie=CORE.curie('input_title'), - model_uri=REACTION.extractionResult__input_title, domain=None, range=Optional[str]) - -slots.extractionResult__input_text = Slot(uri=CORE.input_text, name="extractionResult__input_text", curie=CORE.curie('input_text'), - model_uri=REACTION.extractionResult__input_text, domain=None, range=Optional[str]) - -slots.extractionResult__raw_completion_output = Slot(uri=CORE.raw_completion_output, name="extractionResult__raw_completion_output", curie=CORE.curie('raw_completion_output'), - model_uri=REACTION.extractionResult__raw_completion_output, domain=None, range=Optional[str]) - -slots.extractionResult__prompt = Slot(uri=CORE.prompt, name="extractionResult__prompt", curie=CORE.curie('prompt'), - model_uri=REACTION.extractionResult__prompt, domain=None, range=Optional[str]) - -slots.extractionResult__extracted_object = Slot(uri=CORE.extracted_object, name="extractionResult__extracted_object", curie=CORE.curie('extracted_object'), - model_uri=REACTION.extractionResult__extracted_object, domain=None, range=Optional[Union[dict, Any]]) - -slots.extractionResult__named_entities = Slot(uri=CORE.named_entities, name="extractionResult__named_entities", curie=CORE.curie('named_entities'), - model_uri=REACTION.extractionResult__named_entities, domain=None, range=Optional[Union[Union[dict, Any], List[Union[dict, Any]]]]) - -slots.namedEntity__id = Slot(uri=CORE.id, name="namedEntity__id", curie=CORE.curie('id'), - model_uri=REACTION.namedEntity__id, domain=None, range=URIRef) - -slots.namedEntity__label = Slot(uri=RDFS.label, name="namedEntity__label", curie=RDFS.curie('label'), - model_uri=REACTION.namedEntity__label, domain=None, range=Optional[str]) - -slots.triple__subject = Slot(uri=CORE.subject, name="triple__subject", curie=CORE.curie('subject'), - model_uri=REACTION.triple__subject, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__predicate = Slot(uri=CORE.predicate, name="triple__predicate", curie=CORE.curie('predicate'), - model_uri=REACTION.triple__predicate, domain=None, range=Optional[Union[str, RelationshipTypeId]]) - -slots.triple__object = Slot(uri=CORE.object, name="triple__object", curie=CORE.curie('object'), - model_uri=REACTION.triple__object, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__qualifier = Slot(uri=CORE.qualifier, name="triple__qualifier", curie=CORE.curie('qualifier'), - model_uri=REACTION.triple__qualifier, domain=None, range=Optional[str]) - -slots.triple__subject_qualifier = Slot(uri=CORE.subject_qualifier, name="triple__subject_qualifier", curie=CORE.curie('subject_qualifier'), - model_uri=REACTION.triple__subject_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__object_qualifier = Slot(uri=CORE.object_qualifier, name="triple__object_qualifier", curie=CORE.curie('object_qualifier'), - model_uri=REACTION.triple__object_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.textWithTriples__publication = Slot(uri=CORE.publication, name="textWithTriples__publication", curie=CORE.curie('publication'), - model_uri=REACTION.textWithTriples__publication, domain=None, range=Optional[Union[dict, Publication]]) - -slots.textWithTriples__triples = Slot(uri=CORE.triples, name="textWithTriples__triples", curie=CORE.curie('triples'), - model_uri=REACTION.textWithTriples__triples, domain=None, range=Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]]) - -slots.publication__id = Slot(uri=CORE.id, name="publication__id", curie=CORE.curie('id'), - model_uri=REACTION.publication__id, domain=None, range=Optional[str]) - -slots.publication__title = Slot(uri=CORE.title, name="publication__title", curie=CORE.curie('title'), - model_uri=REACTION.publication__title, domain=None, range=Optional[str]) - -slots.publication__abstract = Slot(uri=CORE.abstract, name="publication__abstract", curie=CORE.curie('abstract'), - model_uri=REACTION.publication__abstract, domain=None, range=Optional[str]) - -slots.publication__combined_text = Slot(uri=CORE.combined_text, name="publication__combined_text", curie=CORE.curie('combined_text'), - model_uri=REACTION.publication__combined_text, domain=None, range=Optional[str]) - -slots.publication__full_text = Slot(uri=CORE.full_text, name="publication__full_text", curie=CORE.curie('full_text'), - model_uri=REACTION.publication__full_text, domain=None, range=Optional[str]) - -slots.annotatorResult__subject_text = Slot(uri=CORE.subject_text, name="annotatorResult__subject_text", curie=CORE.curie('subject_text'), - model_uri=REACTION.annotatorResult__subject_text, domain=None, range=Optional[str]) - -slots.annotatorResult__object_id = Slot(uri=CORE.object_id, name="annotatorResult__object_id", curie=CORE.curie('object_id'), - model_uri=REACTION.annotatorResult__object_id, domain=None, range=Optional[str]) - -slots.annotatorResult__object_text = Slot(uri=CORE.object_text, name="annotatorResult__object_text", curie=CORE.curie('object_text'), - model_uri=REACTION.annotatorResult__object_text, domain=None, range=Optional[str]) \ No newline at end of file diff --git a/projects/reaction/shacl/reaction.shacl.ttl b/projects/reaction/shacl/reaction.shacl.ttl deleted file mode 100644 index 7acc24ba3..000000000 --- a/projects/reaction/shacl/reaction.shacl.ttl +++ /dev/null @@ -1,339 +0,0 @@ -@prefix linkml: <https://w3id.org/linkml/> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix reaction: <http://w3id.org/ontogpt/reaction/> . -@prefix sh: <http://www.w3.org/ns/shacl#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject_text> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object_text> ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/object_id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/AnnotatorResult> . - -<http://w3id.org/ontogpt/core/CompoundExpression> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass <http://w3id.org/ontogpt/core/CompoundExpression> . - -<http://w3id.org/ontogpt/core/ExtractionResult> a sh:NodeShape ; - sh:closed true ; - sh:description "A result of extracting knowledge on text" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/input_title> ], - [ sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/prompt> ], - [ sh:class linkml:Any ; - sh:description "The complex objects extracted from the text" ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/extracted_object> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/input_text> ], - [ sh:class linkml:Any ; - sh:description "Named entities extracted from the text" ; - sh:nodeKind sh:BlankNode ; - sh:order 6 ; - sh:path <http://w3id.org/ontogpt/core/named_entities> ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/input_id> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/raw_completion_output> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/ExtractionResult> . - -<http://w3id.org/ontogpt/core/TextWithTriples> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/Triple> ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/triples> ], - [ sh:class <http://w3id.org/ontogpt/core/Publication> ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/publication> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/TextWithTriples> . - -reaction:GeneToReaction a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class reaction:Reaction ; - sh:description "semicolon separated list of reaction equations (e.g. A+B = C+D) catalyzed by the gene" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path reaction:reactions ], - [ sh:class reaction:Gene ; - sh:description "name of the gene that catalyzes the reaction" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path reaction:gene ], - [ sh:class reaction:Organism ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path reaction:organism ] ; - sh:targetClass reaction:GeneToReaction . - -reaction:ReactionDocument a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class reaction:Evidence ; - sh:description "evidence for the reaction" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path reaction:has_evidence ], - [ sh:class reaction:Organism ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path reaction:organism ], - [ sh:class reaction:Gene ; - sh:description "semicolon separated list of genes that catalyzes the mentioned reactions" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path reaction:genes ], - [ sh:class reaction:GeneReactionPairing ; - sh:description "semicolon separated list of gene to reaction pairings" ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path reaction:gene_reaction_pairings ], - [ sh:class reaction:Reaction ; - sh:description "semicolon separated list of reaction equations (e.g. A+B = C+D) catalyzed by the gene" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path reaction:reactions ] ; - sh:targetClass reaction:ReactionDocument . - -<http://w3id.org/ontogpt/core/Publication> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The full text of the publication" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/full_text> ], - [ sh:description "The title of the publication" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/title> ], - [ sh:description "The publication identifier" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The abstract of the publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/abstract> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/combined_text> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/RelationshipType> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/Triple> a sh:NodeShape ; - sh:closed false ; - sh:description "Abstract parent for Relation Extraction tasks" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/object_qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject> ], - [ sh:class <http://w3id.org/ontogpt/core/RelationshipType> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/predicate> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ sh:description "A qualifier for the statements, e.g. \"NOT\" for negation" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/qualifier> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Triple> . - -reaction:Evidence a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass reaction:Evidence . - -reaction:GeneReactionPairing a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class reaction:Reaction ; - sh:description "equation describing the reaction (e.g. A+B = C+D) catalyzed by the gene" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path reaction:reaction ], - [ sh:class reaction:Gene ; - sh:description "name of the gene that catalyzes the reaction" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path reaction:gene ] ; - sh:targetClass reaction:GeneReactionPairing . - -reaction:ReactionGrouping a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass reaction:ReactionGrouping . - -reaction:ChemicalEntity a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass reaction:ChemicalEntity . - -reaction:Organism a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass reaction:Organism . - -linkml:Any a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass linkml:Any . - -reaction:Gene a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass reaction:Gene . - -reaction:Reaction a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class reaction:ReactionGrouping ; - sh:description "the category to which this biological process belongs" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path reaction:subclass_of ], - [ sh:class reaction:ChemicalEntity ; - sh:description "semicolon separated list of chemical entities on the right side" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path reaction:right_side ], - [ sh:description "alternative names of the reaction" ; - sh:order 2 ; - sh:path reaction:synonyms ], - [ sh:class reaction:ChemicalEntity ; - sh:description "semicolon separated list of chemical entities on the left side" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path reaction:left_side ], - [ sh:description "the name of the reaction" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path reaction:label ], - [ sh:description "a textual description of the reaction" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path reaction:description ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass reaction:Reaction . - -<http://w3id.org/ontogpt/core/NamedEntity> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/NamedEntity> . - diff --git a/projects/reaction/shex/reaction.shex b/projects/reaction/shex/reaction.shex deleted file mode 100644 index 636748acd..000000000 --- a/projects/reaction/shex/reaction.shex +++ /dev/null @@ -1,220 +0,0 @@ -BASE <http://w3id.org/ontogpt/reaction/> -PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> -PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> -PREFIX linkml: <https://w3id.org/linkml/> -PREFIX core: <http://w3id.org/ontogpt/core/> -PREFIX rdfs1: <http://example.org/UNKNOWN/rdfs/> - - -linkml:String xsd:string - -linkml:Integer xsd:integer - -linkml:Boolean xsd:boolean - -linkml:Float xsd:float - -linkml:Double xsd:double - -linkml:Decimal xsd:decimal - -linkml:Time xsd:time - -linkml:Date xsd:date - -linkml:Datetime xsd:dateTime - -linkml:DateOrDatetime linkml:DateOrDatetime - -linkml:Uriorcurie IRI - -linkml:Curie xsd:string - -linkml:Uri IRI - -linkml:Ncname xsd:string - -linkml:Objectidentifier IRI - -linkml:Nodeidentifier NONLITERAL - -linkml:Jsonpointer xsd:string - -linkml:Jsonpath xsd:string - -linkml:Sparqlpath xsd:string - -core:AnnotatorResult CLOSED { - ( $core:AnnotatorResult_tes ( core:subject_text @linkml:String ? ; - core:object_id @linkml:String ? ; - core:object_text @linkml:String ? - ) ; - rdf:type [ core:AnnotatorResult ] ? - ) -} - -core:Any CLOSED { - ( $core:Any_tes rdf:type . * ; - rdf:type [ linkml:Any ] ? - ) -} - -<ChemicalEntity> CLOSED { - ( $<ChemicalEntity_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <ChemicalEntity> ] - ) -} - -core:CompoundExpression ( - @<GeneReactionPairing> OR @core:Triple -) - -core:CompoundExpression_struct { - ( $core:CompoundExpression_tes rdf:type . * ; - rdf:type [ core:CompoundExpression ] ? - ) -} - -<Evidence> CLOSED { - ( $<Evidence_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Evidence> ] - ) -} - -core:ExtractionResult CLOSED { - ( $core:ExtractionResult_tes ( core:input_id @linkml:String ? ; - core:input_title @linkml:String ? ; - core:input_text @linkml:String ? ; - core:raw_completion_output @linkml:String ? ; - core:prompt @linkml:String ? ; - core:extracted_object @core:Any ? ; - core:named_entities @core:Any * - ) ; - rdf:type [ core:ExtractionResult ] ? - ) -} - -<Gene> CLOSED { - ( $<Gene_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Gene> ] - ) -} - -<GeneReactionPairing> CLOSED { - ( $<GeneReactionPairing_tes> ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - <gene> @<Gene> ? ; - <reaction> @<Reaction> ? - ) ; - rdf:type [ <GeneReactionPairing> ] ? - ) -} - -<GeneToReaction> CLOSED { - ( $<GeneToReaction_tes> ( <gene> @<Gene> ? ; - <reactions> @<Reaction> * ; - <organism> @<Organism> ? - ) ; - rdf:type [ <GeneToReaction> ] ? - ) -} - -core:NamedEntity ( - @<ChemicalEntity> OR @<Evidence> OR @<Gene> OR @<Organism> OR @<Reaction> OR @<ReactionGrouping> OR @core:RelationshipType -) - -core:NamedEntity_struct { - ( $core:NamedEntity_tes rdfs1:label @linkml:String ? ; - rdf:type [ core:NamedEntity ] - ) -} - -<Organism> CLOSED { - ( $<Organism_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Organism> ] - ) -} - -core:Publication CLOSED { - ( $core:Publication_tes ( core:id @linkml:String ? ; - core:title @linkml:String ? ; - core:abstract @linkml:String ? ; - core:combined_text @linkml:String ? ; - core:full_text @linkml:String ? - ) ; - rdf:type [ core:Publication ] ? - ) -} - -<Reaction> CLOSED { - ( $<Reaction_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? ; - <label> @linkml:String ? ; - <description> @linkml:String ? ; - <synonyms> @linkml:String * ; - <subclass_of> @<ReactionGrouping> ? ; - <left_side> @<ChemicalEntity> * ; - <right_side> @<ChemicalEntity> * - ) ; - rdf:type [ <Reaction> ] - ) -} - -<ReactionDocument> CLOSED { - ( $<ReactionDocument_tes> ( <genes> @<Gene> * ; - <reactions> @<Reaction> * ; - <gene_reaction_pairings> @<GeneReactionPairing> * ; - <organism> @<Organism> ? ; - <has_evidence> @<Evidence> * - ) ; - rdf:type [ <ReactionDocument> ] ? - ) -} - -<ReactionGrouping> CLOSED { - ( $<ReactionGrouping_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <ReactionGrouping> ] - ) -} - -core:RelationshipType CLOSED { - ( $core:RelationshipType_tes ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ core:RelationshipType ] - ) -} - -core:TextWithTriples CLOSED { - ( $core:TextWithTriples_tes ( core:publication @core:Publication ? ; - core:triples @core:Triple * - ) ; - rdf:type [ core:TextWithTriples ] ? - ) -} - -core:Triple { - ( $core:Triple_tes ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - core:subject @core:NamedEntity ? ; - core:predicate @core:RelationshipType ? ; - core:object @core:NamedEntity ? ; - core:qualifier @linkml:String ? ; - core:subject_qualifier @core:NamedEntity ? ; - core:object_qualifier @core:NamedEntity ? - ) ; - rdf:type [ core:Triple ] ? - ) -} - - diff --git a/projects/reaction/sqlschema/reaction.sql b/projects/reaction/sqlschema/reaction.sql deleted file mode 100644 index 8fcc91b84..000000000 --- a/projects/reaction/sqlschema/reaction.sql +++ /dev/null @@ -1,115 +0,0 @@ - - -CREATE TABLE "AnnotatorResult" ( - subject_text TEXT, - object_id TEXT, - object_text TEXT, - PRIMARY KEY (subject_text, object_id, object_text) -); - -CREATE TABLE "ChemicalEntity" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Evidence" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "ExtractionResult" ( - input_id TEXT, - input_title TEXT, - input_text TEXT, - raw_completion_output TEXT, - prompt TEXT, - extracted_object TEXT, - named_entities TEXT, - PRIMARY KEY (input_id, input_title, input_text, raw_completion_output, prompt, extracted_object, named_entities) -); - -CREATE TABLE "Gene" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Organism" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Publication" ( - id TEXT, - title TEXT, - abstract TEXT, - combined_text TEXT, - full_text TEXT, - PRIMARY KEY (id, title, abstract, combined_text, full_text) -); - -CREATE TABLE "ReactionGrouping" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "RelationshipType" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "TextWithTriples" ( - publication TEXT, - triples TEXT, - PRIMARY KEY (publication, triples) -); - -CREATE TABLE "GeneToReaction" ( - gene TEXT, - reactions TEXT, - organism TEXT, - PRIMARY KEY (gene, reactions, organism), - FOREIGN KEY(gene) REFERENCES "Gene" (id), - FOREIGN KEY(organism) REFERENCES "Organism" (id) -); - -CREATE TABLE "Reaction" ( - id TEXT NOT NULL, - label TEXT, - description TEXT, - subclass_of TEXT, - left_side TEXT, - right_side TEXT, - PRIMARY KEY (id), - FOREIGN KEY(subclass_of) REFERENCES "ReactionGrouping" (id) -); - -CREATE TABLE "ReactionDocument" ( - genes TEXT, - reactions TEXT, - gene_reaction_pairings TEXT, - organism TEXT, - has_evidence TEXT, - PRIMARY KEY (genes, reactions, gene_reaction_pairings, organism, has_evidence), - FOREIGN KEY(organism) REFERENCES "Organism" (id) -); - -CREATE TABLE "GeneReactionPairing" ( - gene TEXT, - reaction TEXT, - PRIMARY KEY (gene, reaction), - FOREIGN KEY(gene) REFERENCES "Gene" (id), - FOREIGN KEY(reaction) REFERENCES "Reaction" (id) -); - -CREATE TABLE "Reaction_synonyms" ( - backref_id TEXT, - synonyms TEXT, - PRIMARY KEY (backref_id, synonyms), - FOREIGN KEY(backref_id) REFERENCES "Reaction" (id) -); diff --git a/projects/recipe/docs/Action.md b/projects/recipe/docs/Action.md deleted file mode 100644 index cb73e2e8f..000000000 --- a/projects/recipe/docs/Action.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: Action - - - - -URI: [recipe:Action](http://w3id.org/ontogpt/recipe/Action) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[Step]-%20action%200..1>[Action|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Action],[Step])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[Step]-%20action%200..1>[Action|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Action],[Step]) - -## Identifier prefixes - - * dbpediaont - * FOODON - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞action](step__action.md)* <sub>0..1</sub> **[Action](Action.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/recipe/docs/AnnotatorResult.md b/projects/recipe/docs/AnnotatorResult.md deleted file mode 100644 index 159a54e4b..000000000 --- a/projects/recipe/docs/AnnotatorResult.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Class: AnnotatorResult - - - - -URI: [recipe:AnnotatorResult](http://w3id.org/ontogpt/recipe/AnnotatorResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F])](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F]) - -## Attributes - - -### Own - - * [➞subject_text](annotatorResult__subject_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_id](annotatorResult__object_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_text](annotatorResult__object_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) diff --git a/projects/recipe/docs/Any.md b/projects/recipe/docs/Any.md deleted file mode 100644 index 8c087c31a..000000000 --- a/projects/recipe/docs/Any.md +++ /dev/null @@ -1,25 +0,0 @@ - -# Class: Any - - - - -URI: [recipe:Any](http://w3id.org/ontogpt/recipe/Any) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult])](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult]) - -## Referenced by Class - - * **None** *[➞extracted_object](extractionResult__extracted_object.md)* <sub>0..1</sub> **[Any](Any.md)** - * **None** *[➞named_entities](extractionResult__named_entities.md)* <sub>0..\*</sub> **[Any](Any.md)** - -## Attributes - - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | linkml:Any | - diff --git a/projects/recipe/docs/CompoundExpression.md b/projects/recipe/docs/CompoundExpression.md deleted file mode 100644 index bd3d323a2..000000000 --- a/projects/recipe/docs/CompoundExpression.md +++ /dev/null @@ -1,24 +0,0 @@ - -# Class: CompoundExpression - - - - -URI: [recipe:CompoundExpression](http://w3id.org/ontogpt/recipe/CompoundExpression) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Step],[Quantity],[Ingredient],[FoodItem],[CompoundExpression]^-[Triple],[CompoundExpression]^-[Step],[CompoundExpression]^-[Quantity],[CompoundExpression]^-[Ingredient],[CompoundExpression]^-[FoodItem])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Step],[Quantity],[Ingredient],[FoodItem],[CompoundExpression]^-[Triple],[CompoundExpression]^-[Step],[CompoundExpression]^-[Quantity],[CompoundExpression]^-[Ingredient],[CompoundExpression]^-[FoodItem]) - -## Children - - * [FoodItem](FoodItem.md) - * [Ingredient](Ingredient.md) - * [Quantity](Quantity.md) - * [Step](Step.md) - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - -## Referenced by Class - - -## Attributes - diff --git a/projects/recipe/docs/ExtractionResult.md b/projects/recipe/docs/ExtractionResult.md deleted file mode 100644 index a21dd2caa..000000000 --- a/projects/recipe/docs/ExtractionResult.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Class: ExtractionResult - - -A result of extracting knowledge on text - -URI: [recipe:ExtractionResult](http://w3id.org/ontogpt/recipe/ExtractionResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any])](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any]) - -## Attributes - - -### Own - - * [➞input_id](extractionResult__input_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_title](extractionResult__input_title.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_text](extractionResult__input_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞prompt](extractionResult__prompt.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞extracted_object](extractionResult__extracted_object.md) <sub>0..1</sub> - * Description: The complex objects extracted from the text - * Range: [Any](Any.md) - * [➞named_entities](extractionResult__named_entities.md) <sub>0..\*</sub> - * Description: Named entities extracted from the text - * Range: [Any](Any.md) diff --git a/projects/recipe/docs/FoodItem.md b/projects/recipe/docs/FoodItem.md deleted file mode 100644 index 893fcb8c3..000000000 --- a/projects/recipe/docs/FoodItem.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Class: FoodItem - - - - -URI: [recipe:FoodItem](http://w3id.org/ontogpt/recipe/FoodItem) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[FoodType],[FoodType]<food%200..1-%20[FoodItem|state:string%20%3F],[Ingredient]++-%20food_item%200..1>[FoodItem],[Step]++-%20inputs%200..*>[FoodItem],[Step]++-%20outputs%200..*>[FoodItem],[CompoundExpression]^-[FoodItem],[Step],[Ingredient],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[FoodType],[FoodType]<food%200..1-%20[FoodItem|state:string%20%3F],[Ingredient]++-%20food_item%200..1>[FoodItem],[Step]++-%20inputs%200..*>[FoodItem],[Step]++-%20outputs%200..*>[FoodItem],[CompoundExpression]^-[FoodItem],[Step],[Ingredient],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞food_item](ingredient__food_item.md)* <sub>0..1</sub> **[FoodItem](FoodItem.md)** - * **None** *[➞inputs](step__inputs.md)* <sub>0..\*</sub> **[FoodItem](FoodItem.md)** - * **None** *[➞outputs](step__outputs.md)* <sub>0..\*</sub> **[FoodItem](FoodItem.md)** - -## Attributes - - -### Own - - * [➞food](foodItem__food.md) <sub>0..1</sub> - * Description: the food item - * Range: [FoodType](FoodType.md) - * [➞state](foodItem__state.md) <sub>0..1</sub> - * Description: the state of the food item (e.g. chopped, diced) - * Range: [String](types/String.md) diff --git a/projects/recipe/docs/FoodType.md b/projects/recipe/docs/FoodType.md deleted file mode 100644 index 411873775..000000000 --- a/projects/recipe/docs/FoodType.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: FoodType - - - - -URI: [recipe:FoodType](http://w3id.org/ontogpt/recipe/FoodType) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[FoodItem]-%20food%200..1>[FoodType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[FoodType],[FoodItem])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[FoodItem]-%20food%200..1>[FoodType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[FoodType],[FoodItem]) - -## Identifier prefixes - - * dbpediaont - * FOODON - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞food](foodItem__food.md)* <sub>0..1</sub> **[FoodType](FoodType.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/recipe/docs/Ingredient.md b/projects/recipe/docs/Ingredient.md deleted file mode 100644 index 2abfcf2cf..000000000 --- a/projects/recipe/docs/Ingredient.md +++ /dev/null @@ -1,37 +0,0 @@ - -# Class: Ingredient - - - - -URI: [recipe:Ingredient](http://w3id.org/ontogpt/recipe/Ingredient) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Quantity],[Quantity]<amount%200..1-++[Ingredient],[FoodItem]<food_item%200..1-++[Ingredient],[Recipe]++-%20ingredients%200..*>[Ingredient],[CompoundExpression]^-[Ingredient],[Recipe],[FoodItem],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[Quantity],[Quantity]<amount%200..1-++[Ingredient],[FoodItem]<food_item%200..1-++[Ingredient],[Recipe]++-%20ingredients%200..*>[Ingredient],[CompoundExpression]^-[Ingredient],[Recipe],[FoodItem],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞ingredients](recipe__ingredients.md)* <sub>0..\*</sub> **[Ingredient](Ingredient.md)** - -## Attributes - - -### Own - - * [➞food_item](ingredient__food_item.md) <sub>0..1</sub> - * Description: the food item - * Range: [FoodItem](FoodItem.md) - * [➞amount](ingredient__amount.md) <sub>0..1</sub> - * Description: the quantity of the ingredient, e.g. 2 lbs - * Range: [Quantity](Quantity.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | FOODON:00004085 | - diff --git a/projects/recipe/docs/NamedEntity.md b/projects/recipe/docs/NamedEntity.md deleted file mode 100644 index e8cef3484..000000000 --- a/projects/recipe/docs/NamedEntity.md +++ /dev/null @@ -1,38 +0,0 @@ - -# Class: NamedEntity - - - - -URI: [recipe:NamedEntity](http://w3id.org/ontogpt/recipe/NamedEntity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[UtensilType],[Unit],[RelationshipType],[RecipeCategory],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[UtensilType],[NamedEntity]^-[Unit],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[RecipeCategory],[NamedEntity]^-[FoodType],[NamedEntity]^-[Action],[Triple],[FoodType],[Action])](https://yuml.me/diagram/nofunky;dir:TB/class/[UtensilType],[Unit],[RelationshipType],[RecipeCategory],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[UtensilType],[NamedEntity]^-[Unit],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[RecipeCategory],[NamedEntity]^-[FoodType],[NamedEntity]^-[Action],[Triple],[FoodType],[Action]) - -## Children - - * [Action](Action.md) - * [FoodType](FoodType.md) - * [RecipeCategory](RecipeCategory.md) - * [RelationshipType](RelationshipType.md) - * [Unit](Unit.md) - * [UtensilType](UtensilType.md) - -## Referenced by Class - - * **None** *[➞object](triple__object.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞object_qualifier](triple__object_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject](triple__subject.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject_qualifier](triple__subject_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - -## Attributes - - -### Own - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/recipe/docs/NullDataOptions.md b/projects/recipe/docs/NullDataOptions.md deleted file mode 100644 index e1b6bd1a6..000000000 --- a/projects/recipe/docs/NullDataOptions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Enum: NullDataOptions - - - - -URI: [recipe:NullDataOptions](http://w3id.org/ontogpt/recipe/NullDataOptions) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | -| UNSPECIFIED_METHOD_OF_ADMINISTRATION | | NCIT:C149701 | | -| NOT_APPLICABLE | | NCIT:C18902 | {'aliases': ['not applicable', 'N/A']} | -| NOT_MENTIONED | | | | - diff --git a/projects/recipe/docs/Publication.md b/projects/recipe/docs/Publication.md deleted file mode 100644 index aed8f8d74..000000000 --- a/projects/recipe/docs/Publication.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Publication - - - - -URI: [recipe:Publication](http://w3id.org/ontogpt/recipe/Publication) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples])](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples]) - -## Referenced by Class - - * **None** *[➞publication](textWithTriples__publication.md)* <sub>0..1</sub> **[Publication](Publication.md)** - -## Attributes - - -### Own - - * [➞id](publication__id.md) <sub>0..1</sub> - * Description: The publication identifier - * Range: [String](types/String.md) - * [➞title](publication__title.md) <sub>0..1</sub> - * Description: The title of the publication - * Range: [String](types/String.md) - * [➞abstract](publication__abstract.md) <sub>0..1</sub> - * Description: The abstract of the publication - * Range: [String](types/String.md) - * [➞combined_text](publication__combined_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞full_text](publication__full_text.md) <sub>0..1</sub> - * Description: The full text of the publication - * Range: [String](types/String.md) diff --git a/projects/recipe/docs/Quantity.md b/projects/recipe/docs/Quantity.md deleted file mode 100644 index fd676298c..000000000 --- a/projects/recipe/docs/Quantity.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Class: Quantity - - - - -URI: [recipe:Quantity](http://w3id.org/ontogpt/recipe/Quantity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Unit],[Unit]<unit%200..1-%20[Quantity|value:string%20%3F],[Ingredient]++-%20amount%200..1>[Quantity],[CompoundExpression]^-[Quantity],[Ingredient],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[Unit],[Unit]<unit%200..1-%20[Quantity|value:string%20%3F],[Ingredient]++-%20amount%200..1>[Quantity],[CompoundExpression]^-[Quantity],[Ingredient],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞amount](ingredient__amount.md)* <sub>0..1</sub> **[Quantity](Quantity.md)** - -## Attributes - - -### Own - - * [➞value](quantity__value.md) <sub>0..1</sub> - * Description: the value of the quantity - * Range: [String](types/String.md) - * [➞unit](quantity__unit.md) <sub>0..1</sub> - * Description: the unit of the quantity, e.g. grams, cups, etc. - * Range: [Unit](Unit.md) diff --git a/projects/recipe/docs/RecipeCategory.md b/projects/recipe/docs/RecipeCategory.md deleted file mode 100644 index 3a5ea90cf..000000000 --- a/projects/recipe/docs/RecipeCategory.md +++ /dev/null @@ -1,36 +0,0 @@ - -# Class: RecipeCategory - - - - -URI: [recipe:RecipeCategory](http://w3id.org/ontogpt/recipe/RecipeCategory) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Recipe]-%20categories%200..*>[RecipeCategory|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RecipeCategory],[Recipe],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Recipe]-%20categories%200..*>[RecipeCategory|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RecipeCategory],[Recipe],[NamedEntity]) - -## Identifier prefixes - - * dbpediaont - * FOODON - * HANCESTRO - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞categories](recipe__categories.md)* <sub>0..\*</sub> **[RecipeCategory](RecipeCategory.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/recipe/docs/RelationshipType.md b/projects/recipe/docs/RelationshipType.md deleted file mode 100644 index b73e48c48..000000000 --- a/projects/recipe/docs/RelationshipType.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: RelationshipType - - - - -URI: [recipe:RelationshipType](http://w3id.org/ontogpt/recipe/RelationshipType) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity]) - -## Identifier prefixes - - * RO - * biolink - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞predicate](triple__predicate.md)* <sub>0..1</sub> **[RelationshipType](RelationshipType.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/recipe/docs/Step.md b/projects/recipe/docs/Step.md deleted file mode 100644 index e3c5f94c5..000000000 --- a/projects/recipe/docs/Step.md +++ /dev/null @@ -1,43 +0,0 @@ - -# Class: Step - - - - -URI: [recipe:Step](http://w3id.org/ontogpt/recipe/Step) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[UtensilType],[UtensilType]<utensils%200..*-%20[Step],[FoodItem]<outputs%200..*-++[Step],[FoodItem]<inputs%200..*-++[Step],[Action]<action%200..1-%20[Step],[Recipe]++-%20steps%200..*>[Step],[CompoundExpression]^-[Step],[Recipe],[FoodItem],[CompoundExpression],[Action])](https://yuml.me/diagram/nofunky;dir:TB/class/[UtensilType],[UtensilType]<utensils%200..*-%20[Step],[FoodItem]<outputs%200..*-++[Step],[FoodItem]<inputs%200..*-++[Step],[Action]<action%200..1-%20[Step],[Recipe]++-%20steps%200..*>[Step],[CompoundExpression]^-[Step],[Recipe],[FoodItem],[CompoundExpression],[Action]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞steps](recipe__steps.md)* <sub>0..\*</sub> **[Step](Step.md)** - -## Attributes - - -### Own - - * [➞action](step__action.md) <sub>0..1</sub> - * Description: the action taken in this step (e.g. mix, add) - * Range: [Action](Action.md) - * [➞inputs](step__inputs.md) <sub>0..\*</sub> - * Description: a semicolon separated list of the inputs of this step - * Range: [FoodItem](FoodItem.md) - * [➞outputs](step__outputs.md) <sub>0..\*</sub> - * Description: a semicolon separated list of the outputs of this step - * Range: [FoodItem](FoodItem.md) - * [➞utensils](step__utensils.md) <sub>0..\*</sub> - * Description: the kitchen utensil used in this step (e.g. pan, bowl) - * Range: [UtensilType](UtensilType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | FOODON:00004087 | - diff --git a/projects/recipe/docs/TextWithTriples.md b/projects/recipe/docs/TextWithTriples.md deleted file mode 100644 index 97fc5bae1..000000000 --- a/projects/recipe/docs/TextWithTriples.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: TextWithTriples - - - - -URI: [recipe:TextWithTriples](http://w3id.org/ontogpt/recipe/TextWithTriples) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication]) - -## Attributes - - -### Own - - * [➞publication](textWithTriples__publication.md) <sub>0..1</sub> - * Range: [Publication](Publication.md) - * [➞triples](textWithTriples__triples.md) <sub>0..\*</sub> - * Range: [Triple](Triple.md) diff --git a/projects/recipe/docs/Triple.md b/projects/recipe/docs/Triple.md deleted file mode 100644 index 7f1334410..000000000 --- a/projects/recipe/docs/Triple.md +++ /dev/null @@ -1,39 +0,0 @@ - -# Class: Triple - - -Abstract parent for Relation Extraction tasks - -URI: [recipe:Triple](http://w3id.org/ontogpt/recipe/Triple) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞triples](textWithTriples__triples.md)* <sub>0..\*</sub> **[Triple](Triple.md)** - -## Attributes - - -### Own - - * [➞subject](triple__subject.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞predicate](triple__predicate.md) <sub>0..1</sub> - * Range: [RelationshipType](RelationshipType.md) - * [➞object](triple__object.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞qualifier](triple__qualifier.md) <sub>0..1</sub> - * Description: A qualifier for the statements, e.g. "NOT" for negation - * Range: [String](types/String.md) - * [➞subject_qualifier](triple__subject_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - * Range: [NamedEntity](NamedEntity.md) - * [➞object_qualifier](triple__object_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * Range: [NamedEntity](NamedEntity.md) diff --git a/projects/recipe/docs/Unit.md b/projects/recipe/docs/Unit.md deleted file mode 100644 index 203ea7914..000000000 --- a/projects/recipe/docs/Unit.md +++ /dev/null @@ -1,36 +0,0 @@ - -# Class: Unit - - - - -URI: [recipe:Unit](http://w3id.org/ontogpt/recipe/Unit) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Quantity]-%20unit%200..1>[Unit|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Unit],[Quantity],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Quantity]-%20unit%200..1>[Unit|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Unit],[Quantity],[NamedEntity]) - -## Identifier prefixes - - * UO - * NCIT - * dbpediaont - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞unit](quantity__unit.md)* <sub>0..1</sub> **[Unit](Unit.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/recipe/docs/UtensilType.md b/projects/recipe/docs/UtensilType.md deleted file mode 100644 index 2fcbadd98..000000000 --- a/projects/recipe/docs/UtensilType.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: UtensilType - - - - -URI: [recipe:UtensilType](http://w3id.org/ontogpt/recipe/UtensilType) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Step]-%20utensils%200..*>[UtensilType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[UtensilType],[Step],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Step]-%20utensils%200..*>[UtensilType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[UtensilType],[Step],[NamedEntity]) - -## Identifier prefixes - - * dbpediaont - * FOODON - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞utensils](step__utensils.md)* <sub>0..\*</sub> **[UtensilType](UtensilType.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/recipe/docs/annotatorResult__object_id.md b/projects/recipe/docs/annotatorResult__object_id.md deleted file mode 100644 index 8f36a50fc..000000000 --- a/projects/recipe/docs/annotatorResult__object_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_id - - - - -URI: [recipe:annotatorResult__object_id](http://w3id.org/ontogpt/recipe/annotatorResult__object_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/recipe/docs/annotatorResult__object_text.md b/projects/recipe/docs/annotatorResult__object_text.md deleted file mode 100644 index bbd4f7329..000000000 --- a/projects/recipe/docs/annotatorResult__object_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_text - - - - -URI: [recipe:annotatorResult__object_text](http://w3id.org/ontogpt/recipe/annotatorResult__object_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/recipe/docs/annotatorResult__subject_text.md b/projects/recipe/docs/annotatorResult__subject_text.md deleted file mode 100644 index 90eb59580..000000000 --- a/projects/recipe/docs/annotatorResult__subject_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_text - - - - -URI: [recipe:annotatorResult__subject_text](http://w3id.org/ontogpt/recipe/annotatorResult__subject_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/recipe/docs/extractionResult__extracted_object.md b/projects/recipe/docs/extractionResult__extracted_object.md deleted file mode 100644 index 73539d87c..000000000 --- a/projects/recipe/docs/extractionResult__extracted_object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: extracted_object - - -The complex objects extracted from the text - -URI: [recipe:extractionResult__extracted_object](http://w3id.org/ontogpt/recipe/extractionResult__extracted_object) - - -## Domain and Range - -None → <sub>0..1</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/recipe/docs/extractionResult__input_id.md b/projects/recipe/docs/extractionResult__input_id.md deleted file mode 100644 index 37362b850..000000000 --- a/projects/recipe/docs/extractionResult__input_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_id - - - - -URI: [recipe:extractionResult__input_id](http://w3id.org/ontogpt/recipe/extractionResult__input_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/recipe/docs/extractionResult__input_text.md b/projects/recipe/docs/extractionResult__input_text.md deleted file mode 100644 index 531648c15..000000000 --- a/projects/recipe/docs/extractionResult__input_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_text - - - - -URI: [recipe:extractionResult__input_text](http://w3id.org/ontogpt/recipe/extractionResult__input_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/recipe/docs/extractionResult__input_title.md b/projects/recipe/docs/extractionResult__input_title.md deleted file mode 100644 index 6d2d20ebe..000000000 --- a/projects/recipe/docs/extractionResult__input_title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_title - - - - -URI: [recipe:extractionResult__input_title](http://w3id.org/ontogpt/recipe/extractionResult__input_title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/recipe/docs/extractionResult__named_entities.md b/projects/recipe/docs/extractionResult__named_entities.md deleted file mode 100644 index 1a74a622c..000000000 --- a/projects/recipe/docs/extractionResult__named_entities.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: named_entities - - -Named entities extracted from the text - -URI: [recipe:extractionResult__named_entities](http://w3id.org/ontogpt/recipe/extractionResult__named_entities) - - -## Domain and Range - -None → <sub>0..\*</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/recipe/docs/extractionResult__prompt.md b/projects/recipe/docs/extractionResult__prompt.md deleted file mode 100644 index 7c1a6a917..000000000 --- a/projects/recipe/docs/extractionResult__prompt.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: prompt - - - - -URI: [recipe:extractionResult__prompt](http://w3id.org/ontogpt/recipe/extractionResult__prompt) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/recipe/docs/extractionResult__raw_completion_output.md b/projects/recipe/docs/extractionResult__raw_completion_output.md deleted file mode 100644 index 6a73aaa9b..000000000 --- a/projects/recipe/docs/extractionResult__raw_completion_output.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: raw_completion_output - - - - -URI: [recipe:extractionResult__raw_completion_output](http://w3id.org/ontogpt/recipe/extractionResult__raw_completion_output) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/recipe/docs/foodItem__food.md b/projects/recipe/docs/foodItem__food.md deleted file mode 100644 index 74f5826a7..000000000 --- a/projects/recipe/docs/foodItem__food.md +++ /dev/null @@ -1,29 +0,0 @@ - -# Slot: food - - -the food item - -URI: [recipe:foodItem__food](http://w3id.org/ontogpt/recipe/foodItem__food) - - -## Domain and Range - -None → <sub>0..1</sub> [FoodType](FoodType.md) - -## Parents - - -## Children - - -## Used by - - * [FoodItem](FoodItem.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | BFO:0000051 | - diff --git a/projects/recipe/docs/foodItem__state.md b/projects/recipe/docs/foodItem__state.md deleted file mode 100644 index d09bfc6a6..000000000 --- a/projects/recipe/docs/foodItem__state.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: state - - -the state of the food item (e.g. chopped, diced) - -URI: [recipe:foodItem__state](http://w3id.org/ontogpt/recipe/foodItem__state) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [FoodItem](FoodItem.md) diff --git a/projects/recipe/docs/ingredient__amount.md b/projects/recipe/docs/ingredient__amount.md deleted file mode 100644 index a7e0a01e1..000000000 --- a/projects/recipe/docs/ingredient__amount.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: amount - - -the quantity of the ingredient, e.g. 2 lbs - -URI: [recipe:ingredient__amount](http://w3id.org/ontogpt/recipe/ingredient__amount) - - -## Domain and Range - -None → <sub>0..1</sub> [Quantity](Quantity.md) - -## Parents - - -## Children - - -## Used by - - * [Ingredient](Ingredient.md) diff --git a/projects/recipe/docs/ingredient__food_item.md b/projects/recipe/docs/ingredient__food_item.md deleted file mode 100644 index 5d9ec1c7d..000000000 --- a/projects/recipe/docs/ingredient__food_item.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: food_item - - -the food item - -URI: [recipe:ingredient__food_item](http://w3id.org/ontogpt/recipe/ingredient__food_item) - - -## Domain and Range - -None → <sub>0..1</sub> [FoodItem](FoodItem.md) - -## Parents - - -## Children - - -## Used by - - * [Ingredient](Ingredient.md) diff --git a/projects/recipe/docs/namedEntity__id.md b/projects/recipe/docs/namedEntity__id.md deleted file mode 100644 index d5de30f9b..000000000 --- a/projects/recipe/docs/namedEntity__id.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Slot: id - - -A unique identifier for the named entity - -URI: [recipe:namedEntity__id](http://w3id.org/ontogpt/recipe/namedEntity__id) - - -## Domain and Range - -None → <sub>1..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Action](Action.md) - * [FoodType](FoodType.md) - * [NamedEntity](NamedEntity.md) - * [RecipeCategory](RecipeCategory.md) - * [RelationshipType](RelationshipType.md) - * [Unit](Unit.md) - * [UtensilType](UtensilType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | this is populated during the grounding and normalization step | - diff --git a/projects/recipe/docs/namedEntity__label.md b/projects/recipe/docs/namedEntity__label.md deleted file mode 100644 index 1a4979d25..000000000 --- a/projects/recipe/docs/namedEntity__label.md +++ /dev/null @@ -1,36 +0,0 @@ - -# Slot: label - - -The label (name) of the named thing - -URI: [recipe:namedEntity__label](http://w3id.org/ontogpt/recipe/namedEntity__label) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Action](Action.md) - * [FoodType](FoodType.md) - * [NamedEntity](NamedEntity.md) - * [RecipeCategory](RecipeCategory.md) - * [RelationshipType](RelationshipType.md) - * [Unit](Unit.md) - * [UtensilType](UtensilType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Aliases:** | | name | -| **Mappings:** | | rdfs:label | - diff --git a/projects/recipe/docs/publication__abstract.md b/projects/recipe/docs/publication__abstract.md deleted file mode 100644 index 02fe69c28..000000000 --- a/projects/recipe/docs/publication__abstract.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: abstract - - -The abstract of the publication - -URI: [recipe:publication__abstract](http://w3id.org/ontogpt/recipe/publication__abstract) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/recipe/docs/publication__combined_text.md b/projects/recipe/docs/publication__combined_text.md deleted file mode 100644 index 35f1aae56..000000000 --- a/projects/recipe/docs/publication__combined_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: combined_text - - - - -URI: [recipe:publication__combined_text](http://w3id.org/ontogpt/recipe/publication__combined_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/recipe/docs/publication__full_text.md b/projects/recipe/docs/publication__full_text.md deleted file mode 100644 index 19d1c161a..000000000 --- a/projects/recipe/docs/publication__full_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: full_text - - -The full text of the publication - -URI: [recipe:publication__full_text](http://w3id.org/ontogpt/recipe/publication__full_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/recipe/docs/publication__id.md b/projects/recipe/docs/publication__id.md deleted file mode 100644 index 08c4bc8e2..000000000 --- a/projects/recipe/docs/publication__id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: id - - -The publication identifier - -URI: [recipe:publication__id](http://w3id.org/ontogpt/recipe/publication__id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/recipe/docs/publication__title.md b/projects/recipe/docs/publication__title.md deleted file mode 100644 index 38963c34a..000000000 --- a/projects/recipe/docs/publication__title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: title - - -The title of the publication - -URI: [recipe:publication__title](http://w3id.org/ontogpt/recipe/publication__title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/recipe/docs/quantity__unit.md b/projects/recipe/docs/quantity__unit.md deleted file mode 100644 index e69c68805..000000000 --- a/projects/recipe/docs/quantity__unit.md +++ /dev/null @@ -1,29 +0,0 @@ - -# Slot: unit - - -the unit of the quantity, e.g. grams, cups, etc. - -URI: [recipe:quantity__unit](http://w3id.org/ontogpt/recipe/quantity__unit) - - -## Domain and Range - -None → <sub>0..1</sub> [Unit](Unit.md) - -## Parents - - -## Children - - -## Used by - - * [Quantity](Quantity.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | qudt:unit | - diff --git a/projects/recipe/docs/quantity__value.md b/projects/recipe/docs/quantity__value.md deleted file mode 100644 index 2a5d28a3a..000000000 --- a/projects/recipe/docs/quantity__value.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: value - - -the value of the quantity - -URI: [recipe:quantity__value](http://w3id.org/ontogpt/recipe/quantity__value) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Quantity](Quantity.md) diff --git a/projects/recipe/docs/recipe.md b/projects/recipe/docs/recipe.md deleted file mode 100644 index c9f5c6960..000000000 --- a/projects/recipe/docs/recipe.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Class: Recipe - - - - -URI: [recipe:Recipe](http://w3id.org/ontogpt/recipe/Recipe) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Step],[RecipeCategory],[Step]<steps%200..*-++[Recipe|url:uriorcurie;label:string%20%3F;description:string%20%3F],[Ingredient]<ingredients%200..*-++[Recipe],[RecipeCategory]<categories%200..*-%20[Recipe],[Ingredient])](https://yuml.me/diagram/nofunky;dir:TB/class/[Step],[RecipeCategory],[Step]<steps%200..*-++[Recipe|url:uriorcurie;label:string%20%3F;description:string%20%3F],[Ingredient]<ingredients%200..*-++[Recipe],[RecipeCategory]<categories%200..*-%20[Recipe],[Ingredient]) - -## Attributes - - -### Own - - * [➞url](recipe__url.md) <sub>1..1</sub> - * Range: [Uriorcurie](types/Uriorcurie.md) - * [➞label](recipe__label.md) <sub>0..1</sub> - * Description: the name of the recipe - * Range: [String](types/String.md) - * [➞description](recipe__description.md) <sub>0..1</sub> - * Description: a brief textual description of the recipe - * Range: [String](types/String.md) - * [➞categories](recipe__categories.md) <sub>0..\*</sub> - * Description: a semicolon separated list of the categories to which this recipe belongs - * Range: [RecipeCategory](RecipeCategory.md) - * [➞ingredients](recipe__ingredients.md) <sub>0..\*</sub> - * Description: a semicolon separated list of the ingredients plus quantities of the recipe - * Range: [Ingredient](Ingredient.md) - * [➞steps](recipe__steps.md) <sub>0..\*</sub> - * Description: a semicolon separated list of the individual steps involved in this recipe - * Range: [Step](Step.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Close Mappings:** | | FOODON:00004081 | - diff --git a/projects/recipe/docs/recipe__categories.md b/projects/recipe/docs/recipe__categories.md deleted file mode 100644 index 552d36f1a..000000000 --- a/projects/recipe/docs/recipe__categories.md +++ /dev/null @@ -1,29 +0,0 @@ - -# Slot: categories - - -a semicolon separated list of the categories to which this recipe belongs - -URI: [recipe:recipe__categories](http://w3id.org/ontogpt/recipe/recipe__categories) - - -## Domain and Range - -None → <sub>0..\*</sub> [RecipeCategory](RecipeCategory.md) - -## Parents - - -## Children - - -## Used by - - * [Recipe](Recipe.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | dcterms:subject | - diff --git a/projects/recipe/docs/recipe__description.md b/projects/recipe/docs/recipe__description.md deleted file mode 100644 index 9f8902a2a..000000000 --- a/projects/recipe/docs/recipe__description.md +++ /dev/null @@ -1,29 +0,0 @@ - -# Slot: description - - -a brief textual description of the recipe - -URI: [recipe:recipe__description](http://w3id.org/ontogpt/recipe/recipe__description) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Recipe](Recipe.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | dcterms:description | - diff --git a/projects/recipe/docs/recipe__ingredients.md b/projects/recipe/docs/recipe__ingredients.md deleted file mode 100644 index fd33e366b..000000000 --- a/projects/recipe/docs/recipe__ingredients.md +++ /dev/null @@ -1,29 +0,0 @@ - -# Slot: ingredients - - -a semicolon separated list of the ingredients plus quantities of the recipe - -URI: [recipe:recipe__ingredients](http://w3id.org/ontogpt/recipe/recipe__ingredients) - - -## Domain and Range - -None → <sub>0..\*</sub> [Ingredient](Ingredient.md) - -## Parents - - -## Children - - -## Used by - - * [Recipe](Recipe.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | FOODON:00002420 | - diff --git a/projects/recipe/docs/recipe__label.md b/projects/recipe/docs/recipe__label.md deleted file mode 100644 index dfc9b8edc..000000000 --- a/projects/recipe/docs/recipe__label.md +++ /dev/null @@ -1,29 +0,0 @@ - -# Slot: label - - -the name of the recipe - -URI: [recipe:recipe__label](http://w3id.org/ontogpt/recipe/recipe__label) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Recipe](Recipe.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | rdfs:label | - diff --git a/projects/recipe/docs/recipe__steps.md b/projects/recipe/docs/recipe__steps.md deleted file mode 100644 index eb00df9a4..000000000 --- a/projects/recipe/docs/recipe__steps.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: steps - - -a semicolon separated list of the individual steps involved in this recipe - -URI: [recipe:recipe__steps](http://w3id.org/ontogpt/recipe/recipe__steps) - - -## Domain and Range - -None → <sub>0..\*</sub> [Step](Step.md) - -## Parents - - -## Children - - -## Used by - - * [Recipe](Recipe.md) diff --git a/projects/recipe/docs/recipe__url.md b/projects/recipe/docs/recipe__url.md deleted file mode 100644 index c0f59c5bf..000000000 --- a/projects/recipe/docs/recipe__url.md +++ /dev/null @@ -1,29 +0,0 @@ - -# Slot: url - - - - -URI: [recipe:recipe__url](http://w3id.org/ontogpt/recipe/recipe__url) - - -## Domain and Range - -None → <sub>1..1</sub> [Uriorcurie](types/Uriorcurie.md) - -## Parents - - -## Children - - -## Used by - - * [Recipe](Recipe.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | rdf:Resource | - diff --git a/projects/recipe/docs/step__action.md b/projects/recipe/docs/step__action.md deleted file mode 100644 index cc3e9b6d4..000000000 --- a/projects/recipe/docs/step__action.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: action - - -the action taken in this step (e.g. mix, add) - -URI: [recipe:step__action](http://w3id.org/ontogpt/recipe/step__action) - - -## Domain and Range - -None → <sub>0..1</sub> [Action](Action.md) - -## Parents - - -## Children - - -## Used by - - * [Step](Step.md) diff --git a/projects/recipe/docs/step__inputs.md b/projects/recipe/docs/step__inputs.md deleted file mode 100644 index 938b74117..000000000 --- a/projects/recipe/docs/step__inputs.md +++ /dev/null @@ -1,29 +0,0 @@ - -# Slot: inputs - - -a semicolon separated list of the inputs of this step - -URI: [recipe:step__inputs](http://w3id.org/ontogpt/recipe/step__inputs) - - -## Domain and Range - -None → <sub>0..\*</sub> [FoodItem](FoodItem.md) - -## Parents - - -## Children - - -## Used by - - * [Step](Step.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | RO:0002233 | - diff --git a/projects/recipe/docs/step__outputs.md b/projects/recipe/docs/step__outputs.md deleted file mode 100644 index 4384ff660..000000000 --- a/projects/recipe/docs/step__outputs.md +++ /dev/null @@ -1,29 +0,0 @@ - -# Slot: outputs - - -a semicolon separated list of the outputs of this step - -URI: [recipe:step__outputs](http://w3id.org/ontogpt/recipe/step__outputs) - - -## Domain and Range - -None → <sub>0..\*</sub> [FoodItem](FoodItem.md) - -## Parents - - -## Children - - -## Used by - - * [Step](Step.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | RO:0002234 | - diff --git a/projects/recipe/docs/step__utensils.md b/projects/recipe/docs/step__utensils.md deleted file mode 100644 index 584f6084e..000000000 --- a/projects/recipe/docs/step__utensils.md +++ /dev/null @@ -1,29 +0,0 @@ - -# Slot: utensils - - -the kitchen utensil used in this step (e.g. pan, bowl) - -URI: [recipe:step__utensils](http://w3id.org/ontogpt/recipe/step__utensils) - - -## Domain and Range - -None → <sub>0..\*</sub> [UtensilType](UtensilType.md) - -## Parents - - -## Children - - -## Used by - - * [Step](Step.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | RO:0002500 | - diff --git a/projects/recipe/docs/textWithTriples__publication.md b/projects/recipe/docs/textWithTriples__publication.md deleted file mode 100644 index 2056033ae..000000000 --- a/projects/recipe/docs/textWithTriples__publication.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: publication - - - - -URI: [recipe:textWithTriples__publication](http://w3id.org/ontogpt/recipe/textWithTriples__publication) - - -## Domain and Range - -None → <sub>0..1</sub> [Publication](Publication.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/recipe/docs/textWithTriples__triples.md b/projects/recipe/docs/textWithTriples__triples.md deleted file mode 100644 index acbc04e65..000000000 --- a/projects/recipe/docs/textWithTriples__triples.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: triples - - - - -URI: [recipe:textWithTriples__triples](http://w3id.org/ontogpt/recipe/textWithTriples__triples) - - -## Domain and Range - -None → <sub>0..\*</sub> [Triple](Triple.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/recipe/docs/triple__object.md b/projects/recipe/docs/triple__object.md deleted file mode 100644 index 7669b81f3..000000000 --- a/projects/recipe/docs/triple__object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object - - - - -URI: [recipe:triple__object](http://w3id.org/ontogpt/recipe/triple__object) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/recipe/docs/triple__object_qualifier.md b/projects/recipe/docs/triple__object_qualifier.md deleted file mode 100644 index f2b4a904d..000000000 --- a/projects/recipe/docs/triple__object_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_qualifier - - -An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - -URI: [recipe:triple__object_qualifier](http://w3id.org/ontogpt/recipe/triple__object_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/recipe/docs/triple__predicate.md b/projects/recipe/docs/triple__predicate.md deleted file mode 100644 index d4264ec18..000000000 --- a/projects/recipe/docs/triple__predicate.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: predicate - - - - -URI: [recipe:triple__predicate](http://w3id.org/ontogpt/recipe/triple__predicate) - - -## Domain and Range - -None → <sub>0..1</sub> [RelationshipType](RelationshipType.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/recipe/docs/triple__qualifier.md b/projects/recipe/docs/triple__qualifier.md deleted file mode 100644 index 8f0dcdb4c..000000000 --- a/projects/recipe/docs/triple__qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: qualifier - - -A qualifier for the statements, e.g. "NOT" for negation - -URI: [recipe:triple__qualifier](http://w3id.org/ontogpt/recipe/triple__qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/recipe/docs/triple__subject.md b/projects/recipe/docs/triple__subject.md deleted file mode 100644 index 07ec2df93..000000000 --- a/projects/recipe/docs/triple__subject.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject - - - - -URI: [recipe:triple__subject](http://w3id.org/ontogpt/recipe/triple__subject) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/recipe/docs/triple__subject_qualifier.md b/projects/recipe/docs/triple__subject_qualifier.md deleted file mode 100644 index 9cfc7a442..000000000 --- a/projects/recipe/docs/triple__subject_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_qualifier - - -An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -URI: [recipe:triple__subject_qualifier](http://w3id.org/ontogpt/recipe/triple__subject_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/recipe/docs/types/Boolean.md b/projects/recipe/docs/types/Boolean.md deleted file mode 100644 index dc83a9c6e..000000000 --- a/projects/recipe/docs/types/Boolean.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: boolean - - -A binary (true or false) value - -URI: [linkml:Boolean](https://w3id.org/linkml/Boolean) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Bool** | -| Representation | | bool | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Boolean | - diff --git a/projects/recipe/docs/types/Curie.md b/projects/recipe/docs/types/Curie.md deleted file mode 100644 index c1803f93f..000000000 --- a/projects/recipe/docs/types/Curie.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: curie - - -a compact URI - -URI: [linkml:Curie](https://w3id.org/linkml/Curie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Curie** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations this MUST be expanded to a URI | -| | | in non-RDF serializations MAY be serialized as the compact representation | - diff --git a/projects/recipe/docs/types/Date.md b/projects/recipe/docs/types/Date.md deleted file mode 100644 index 06948af97..000000000 --- a/projects/recipe/docs/types/Date.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: date - - -a date (year, month and day) in an idealized calendar - -URI: [linkml:Date](https://w3id.org/linkml/Date) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDate** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Date | - diff --git a/projects/recipe/docs/types/DateOrDatetime.md b/projects/recipe/docs/types/DateOrDatetime.md deleted file mode 100644 index ef983898d..000000000 --- a/projects/recipe/docs/types/DateOrDatetime.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: date_or_datetime - - -Either a date or a datetime - -URI: [linkml:DateOrDatetime](https://w3id.org/linkml/DateOrDatetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/recipe/docs/types/Datetime.md b/projects/recipe/docs/types/Datetime.md deleted file mode 100644 index 9510454a8..000000000 --- a/projects/recipe/docs/types/Datetime.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: datetime - - -The combination of a date and time - -URI: [linkml:Datetime](https://w3id.org/linkml/Datetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDateTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:DateTime | - diff --git a/projects/recipe/docs/types/Decimal.md b/projects/recipe/docs/types/Decimal.md deleted file mode 100644 index a7ba14a5d..000000000 --- a/projects/recipe/docs/types/Decimal.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: decimal - - -A real number with arbitrary precision that conforms to the xsd:decimal specification - -URI: [linkml:Decimal](https://w3id.org/linkml/Decimal) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Decimal** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Broad Mappings:** | | schema:Number | - diff --git a/projects/recipe/docs/types/Double.md b/projects/recipe/docs/types/Double.md deleted file mode 100644 index cfe6d71e2..000000000 --- a/projects/recipe/docs/types/Double.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: double - - -A real number that conforms to the xsd:double specification - -URI: [linkml:Double](https://w3id.org/linkml/Double) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Close Mappings:** | | schema:Float | - diff --git a/projects/recipe/docs/types/Float.md b/projects/recipe/docs/types/Float.md deleted file mode 100644 index 7b303f96f..000000000 --- a/projects/recipe/docs/types/Float.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: float - - -A real number that conforms to the xsd:float specification - -URI: [linkml:Float](https://w3id.org/linkml/Float) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Float | - diff --git a/projects/recipe/docs/types/Integer.md b/projects/recipe/docs/types/Integer.md deleted file mode 100644 index 3cfcc66d9..000000000 --- a/projects/recipe/docs/types/Integer.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: integer - - -An integer - -URI: [linkml:Integer](https://w3id.org/linkml/Integer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **int** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Integer | - diff --git a/projects/recipe/docs/types/Jsonpath.md b/projects/recipe/docs/types/Jsonpath.md deleted file mode 100644 index a03a58e67..000000000 --- a/projects/recipe/docs/types/Jsonpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpath - - -A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpath](https://w3id.org/linkml/Jsonpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/recipe/docs/types/Jsonpointer.md b/projects/recipe/docs/types/Jsonpointer.md deleted file mode 100644 index a0e1ac492..000000000 --- a/projects/recipe/docs/types/Jsonpointer.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpointer - - -A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpointer](https://w3id.org/linkml/Jsonpointer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/recipe/docs/types/Ncname.md b/projects/recipe/docs/types/Ncname.md deleted file mode 100644 index 710b0b04a..000000000 --- a/projects/recipe/docs/types/Ncname.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: ncname - - -Prefix part of CURIE - -URI: [linkml:Ncname](https://w3id.org/linkml/Ncname) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NCName** | -| Representation | | str | diff --git a/projects/recipe/docs/types/Nodeidentifier.md b/projects/recipe/docs/types/Nodeidentifier.md deleted file mode 100644 index f0097cdf4..000000000 --- a/projects/recipe/docs/types/Nodeidentifier.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: nodeidentifier - - -A URI, CURIE or BNODE that represents a node in a model. - -URI: [linkml:Nodeidentifier](https://w3id.org/linkml/Nodeidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NodeIdentifier** | -| Representation | | str | diff --git a/projects/recipe/docs/types/Objectidentifier.md b/projects/recipe/docs/types/Objectidentifier.md deleted file mode 100644 index 454ba6be6..000000000 --- a/projects/recipe/docs/types/Objectidentifier.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: objectidentifier - - -A URI or CURIE that represents an object in the model. - -URI: [linkml:Objectidentifier](https://w3id.org/linkml/Objectidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **ElementIdentifier** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | Used for inheritance and type checking | - diff --git a/projects/recipe/docs/types/Sparqlpath.md b/projects/recipe/docs/types/Sparqlpath.md deleted file mode 100644 index fd99a927e..000000000 --- a/projects/recipe/docs/types/Sparqlpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: sparqlpath - - -A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - -URI: [linkml:Sparqlpath](https://w3id.org/linkml/Sparqlpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/recipe/docs/types/String.md b/projects/recipe/docs/types/String.md deleted file mode 100644 index 6e61d7081..000000000 --- a/projects/recipe/docs/types/String.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: string - - -A character string - -URI: [linkml:String](https://w3id.org/linkml/String) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Text | - diff --git a/projects/recipe/docs/types/Time.md b/projects/recipe/docs/types/Time.md deleted file mode 100644 index 2b8652bcd..000000000 --- a/projects/recipe/docs/types/Time.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: time - - -A time object represents a (local) time of day, independent of any particular day - -URI: [linkml:Time](https://w3id.org/linkml/Time) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Time | - diff --git a/projects/recipe/docs/types/Uri.md b/projects/recipe/docs/types/Uri.md deleted file mode 100644 index 343807a5e..000000000 --- a/projects/recipe/docs/types/Uri.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: uri - - -a complete URI - -URI: [linkml:Uri](https://w3id.org/linkml/Uri) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URI** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node | -| **Close Mappings:** | | schema:URL | - diff --git a/projects/recipe/docs/types/Uriorcurie.md b/projects/recipe/docs/types/Uriorcurie.md deleted file mode 100644 index 2f7b65087..000000000 --- a/projects/recipe/docs/types/Uriorcurie.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: uriorcurie - - -a URI or a CURIE - -URI: [linkml:Uriorcurie](https://w3id.org/linkml/Uriorcurie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URIorCURIE** | -| Representation | | str | diff --git a/projects/recipe/excel/recipe.xlsx b/projects/recipe/excel/recipe.xlsx deleted file mode 100644 index b3874b666..000000000 Binary files a/projects/recipe/excel/recipe.xlsx and /dev/null differ diff --git a/projects/recipe/graphql/recipe.graphql b/projects/recipe/graphql/recipe.graphql deleted file mode 100644 index f13d1b830..000000000 --- a/projects/recipe/graphql/recipe.graphql +++ /dev/null @@ -1,129 +0,0 @@ -type Action - { - id: String! - label: String - } - -type AnnotatorResult - { - subjectText: String - objectId: String - objectText: String - } - -type Any - { - } - -interface CompoundExpression - { - } - -type ExtractionResult - { - inputId: String - inputTitle: String - inputText: String - rawCompletionOutput: String - prompt: String - extractedObject: Any - namedEntities: [Any] - } - -type FoodItem - { - food: FoodType - state: String - } - -type FoodType - { - id: String! - label: String - } - -type Ingredient - { - foodItem: FoodItem - amount: Quantity - } - -interface NamedEntity - { - id: String! - label: String - } - -type Publication - { - id: String - title: String - abstract: String - combinedText: String - fullText: String - } - -type Quantity - { - value: String - unit: Unit - } - -type Recipe - { - url: Uriorcurie! - label: String - description: String - categories: [RecipeCategory] - ingredients: [Ingredient] - steps: [Step] - } - -type RecipeCategory - { - id: String! - label: String - } - -type RelationshipType - { - id: String! - label: String - } - -type Step - { - action: Action - inputs: [FoodItem] - outputs: [FoodItem] - utensils: [UtensilType] - } - -type TextWithTriples - { - publication: Publication - triples: [Triple] - } - -interface Triple - { - subject: NamedEntity - predicate: RelationshipType - object: NamedEntity - qualifier: String - subjectQualifier: NamedEntity - objectQualifier: NamedEntity - } - -type Unit - { - id: String! - label: String - } - -type UtensilType - { - id: String! - label: String - } - diff --git a/projects/recipe/jsonld/recipe.context.jsonld b/projects/recipe/jsonld/recipe.context.jsonld deleted file mode 100644 index 552c39b04..000000000 --- a/projects/recipe/jsonld/recipe.context.jsonld +++ /dev/null @@ -1,201 +0,0 @@ -{ - "comments": { - "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2023-08-07T10:56:08", - "source": "recipe.yaml" - }, - "@context": { - "AUTO": "http://example.org/auto/", - "BFO": { - "@id": "http://purl.obolibrary.org/obo/BFO_", - "@prefix": true - }, - "FOODON": { - "@id": "http://purl.obolibrary.org/obo/FOODON_", - "@prefix": true - }, - "HANCESTRO": { - "@id": "http://purl.obolibrary.org/obo/HANCESTRO_", - "@prefix": true - }, - "NCIT": { - "@id": "http://purl.obolibrary.org/obo/NCIT_", - "@prefix": true - }, - "RO": { - "@id": "http://purl.obolibrary.org/obo/RO_", - "@prefix": true - }, - "UO": { - "@id": "http://purl.obolibrary.org/obo/UO_", - "@prefix": true - }, - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "dbpediaont": "http://dbpedia.org/ontology/", - "dcterms": "http://purl.org/dc/terms/", - "linkml": "https://w3id.org/linkml/", - "qudt": "http://qudt.org/schema/qudt/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "recipe": "http://w3id.org/ontogpt/recipe/", - "@vocab": "http://w3id.org/ontogpt/recipe/", - "object_id": { - "@id": "core:object_id" - }, - "object_text": { - "@id": "core:object_text" - }, - "subject_text": { - "@id": "core:subject_text" - }, - "extracted_object": { - "@type": "@id", - "@id": "core:extracted_object" - }, - "input_id": { - "@id": "core:input_id" - }, - "input_text": { - "@id": "core:input_text" - }, - "input_title": { - "@id": "core:input_title" - }, - "named_entities": { - "@type": "@id", - "@id": "core:named_entities" - }, - "prompt": { - "@id": "core:prompt" - }, - "raw_completion_output": { - "@id": "core:raw_completion_output" - }, - "food": { - "@type": "@id", - "@id": "BFO:0000051" - }, - "amount": { - "@type": "@id" - }, - "food_item": { - "@type": "@id" - }, - "id": { - "@id": "core:id" - }, - "label": { - "@id": "rdfs:label" - }, - "abstract": { - "@id": "core:abstract" - }, - "combined_text": { - "@id": "core:combined_text" - }, - "full_text": { - "@id": "core:full_text" - }, - "title": { - "@id": "core:title" - }, - "unit": { - "@type": "@id", - "@id": "qudt:unit" - }, - "categories": { - "@type": "@id", - "@id": "dcterms:subject" - }, - "description": { - "@id": "dcterms:description" - }, - "ingredients": { - "@type": "@id", - "@id": "FOODON:00002420" - }, - "steps": { - "@type": "@id" - }, - "url": "@id", - "action": { - "@type": "@id" - }, - "inputs": { - "@type": "@id", - "@id": "RO:0002233" - }, - "outputs": { - "@type": "@id", - "@id": "RO:0002234" - }, - "utensils": { - "@type": "@id", - "@id": "RO:0002500" - }, - "publication": { - "@type": "@id", - "@id": "core:publication" - }, - "triples": { - "@type": "@id", - "@id": "core:triples" - }, - "object": { - "@type": "@id", - "@id": "core:object" - }, - "object_qualifier": { - "@type": "@id", - "@id": "core:object_qualifier" - }, - "predicate": { - "@type": "@id", - "@id": "core:predicate" - }, - "qualifier": { - "@id": "core:qualifier" - }, - "subject": { - "@type": "@id", - "@id": "core:subject" - }, - "subject_qualifier": { - "@type": "@id", - "@id": "core:subject_qualifier" - }, - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "Ingredient": { - "@id": "FOODON:00004085" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "Step": { - "@id": "FOODON:00004087" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } - } -} diff --git a/projects/recipe/jsonld/recipe.jsonld b/projects/recipe/jsonld/recipe.jsonld deleted file mode 100644 index 0ef266f0a..000000000 --- a/projects/recipe/jsonld/recipe.jsonld +++ /dev/null @@ -1,1828 +0,0 @@ -{ - "name": "recipe-template", - "description": "A template for food recipes", - "title": "Food Recipe Template", - "id": "https://w3id.org/ontogpt/recipe", - "imports": [ - "linkml:types", - "core" - ], - "license": "https://creativecommons.org/publicdomain/zero/1.0/", - "prefixes": [ - { - "prefix_prefix": "linkml", - "prefix_reference": "https://w3id.org/linkml/" - }, - { - "prefix_prefix": "recipe", - "prefix_reference": "http://w3id.org/ontogpt/recipe/" - }, - { - "prefix_prefix": "FOODON", - "prefix_reference": "http://purl.obolibrary.org/obo/FOODON_" - }, - { - "prefix_prefix": "UO", - "prefix_reference": "http://purl.obolibrary.org/obo/UO_" - }, - { - "prefix_prefix": "dcterms", - "prefix_reference": "http://purl.org/dc/terms/" - }, - { - "prefix_prefix": "HANCESTRO", - "prefix_reference": "http://purl.obolibrary.org/obo/HANCESTRO_" - }, - { - "prefix_prefix": "BFO", - "prefix_reference": "http://purl.obolibrary.org/obo/BFO_" - }, - { - "prefix_prefix": "AUTO", - "prefix_reference": "http://example.org/auto/" - }, - { - "prefix_prefix": "RO", - "prefix_reference": "http://purl.obolibrary.org/obo/RO_" - }, - { - "prefix_prefix": "qudt", - "prefix_reference": "http://qudt.org/schema/qudt/" - }, - { - "prefix_prefix": "dbpediaont", - "prefix_reference": "http://dbpedia.org/ontology/" - } - ], - "default_prefix": "recipe", - "default_range": "string", - "types": [ - { - "name": "string", - "definition_uri": "https://w3id.org/linkml/String", - "description": "A character string", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Text" - ], - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "@type": "TypeDefinition" - }, - { - "name": "integer", - "definition_uri": "https://w3id.org/linkml/Integer", - "description": "An integer", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Integer" - ], - "base": "int", - "uri": "http://www.w3.org/2001/XMLSchema#integer", - "@type": "TypeDefinition" - }, - { - "name": "boolean", - "definition_uri": "https://w3id.org/linkml/Boolean", - "description": "A binary (true or false) value", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Boolean" - ], - "base": "Bool", - "uri": "http://www.w3.org/2001/XMLSchema#boolean", - "repr": "bool", - "@type": "TypeDefinition" - }, - { - "name": "float", - "definition_uri": "https://w3id.org/linkml/Float", - "description": "A real number that conforms to the xsd:float specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#float", - "@type": "TypeDefinition" - }, - { - "name": "double", - "definition_uri": "https://w3id.org/linkml/Double", - "description": "A real number that conforms to the xsd:double specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#double", - "@type": "TypeDefinition" - }, - { - "name": "decimal", - "definition_uri": "https://w3id.org/linkml/Decimal", - "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "broad_mappings": [ - "schema:Number" - ], - "base": "Decimal", - "uri": "http://www.w3.org/2001/XMLSchema#decimal", - "@type": "TypeDefinition" - }, - { - "name": "time", - "definition_uri": "https://w3id.org/linkml/Time", - "description": "A time object represents a (local) time of day, independent of any particular day", - "notes": [ - "URI is dateTime because OWL reasoners do not work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Time" - ], - "base": "XSDTime", - "uri": "http://www.w3.org/2001/XMLSchema#time", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date", - "definition_uri": "https://w3id.org/linkml/Date", - "description": "a date (year, month and day) in an idealized calendar", - "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Date" - ], - "base": "XSDDate", - "uri": "http://www.w3.org/2001/XMLSchema#date", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "datetime", - "definition_uri": "https://w3id.org/linkml/Datetime", - "description": "The combination of a date and time", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:DateTime" - ], - "base": "XSDDateTime", - "uri": "http://www.w3.org/2001/XMLSchema#dateTime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date_or_datetime", - "definition_uri": "https://w3id.org/linkml/DateOrDatetime", - "description": "Either a date or a datetime", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "https://w3id.org/linkml/DateOrDatetime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uriorcurie", - "definition_uri": "https://w3id.org/linkml/Uriorcurie", - "description": "a URI or a CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "URIorCURIE", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "curie", - "definition_uri": "https://w3id.org/linkml/Curie", - "conforms_to": "https://www.w3.org/TR/curie/", - "description": "a compact URI", - "comments": [ - "in RDF serializations this MUST be expanded to a URI", - "in non-RDF serializations MAY be serialized as the compact representation" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "Curie", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uri", - "definition_uri": "https://w3id.org/linkml/Uri", - "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", - "description": "a complete URI", - "comments": [ - "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:URL" - ], - "base": "URI", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "ncname", - "definition_uri": "https://w3id.org/linkml/Ncname", - "description": "Prefix part of CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NCName", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "objectidentifier", - "definition_uri": "https://w3id.org/linkml/Objectidentifier", - "description": "A URI or CURIE that represents an object in the model.", - "comments": [ - "Used for inheritance and type checking" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "ElementIdentifier", - "uri": "http://www.w3.org/ns/shex#iri", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "nodeidentifier", - "definition_uri": "https://w3id.org/linkml/Nodeidentifier", - "description": "A URI, CURIE or BNODE that represents a node in a model.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NodeIdentifier", - "uri": "http://www.w3.org/ns/shex#nonLiteral", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpointer", - "definition_uri": "https://w3id.org/linkml/Jsonpointer", - "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901", - "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpath", - "definition_uri": "https://w3id.org/linkml/Jsonpath", - "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html", - "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "sparqlpath", - "definition_uri": "https://w3id.org/linkml/Sparqlpath", - "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths", - "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - } - ], - "enums": [ - { - "name": "NullDataOptions", - "definition_uri": "http://w3id.org/ontogpt/core/NullDataOptions", - "from_schema": "http://w3id.org/ontogpt/core", - "permissible_values": [ - { - "text": "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "meaning": "NCIT:C149701" - }, - { - "text": "NOT_APPLICABLE", - "meaning": "NCIT:C18902", - "aliases": [ - "not applicable", - "N/A" - ] - }, - { - "text": "NOT_MENTIONED" - } - ] - } - ], - "slots": [ - { - "name": "recipe__url", - "annotations": [ - { - "tag": "prompt.ignore", - "value": "True", - "@type": "Annotation" - } - ], - "from_schema": "https://w3id.org/ontogpt/recipe", - "mappings": [ - "http://example.org/UNKNOWN/rdf/Resource" - ], - "slot_uri": "http://example.org/UNKNOWN/rdf/Resource", - "identifier": true, - "alias": "url", - "owner": "Recipe", - "domain_of": [ - "Recipe" - ], - "range": "uriorcurie", - "required": true, - "@type": "SlotDefinition" - }, - { - "name": "recipe__label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "the name of the recipe", - "from_schema": "https://w3id.org/ontogpt/recipe", - "mappings": [ - "http://example.org/UNKNOWN/rdfs/label" - ], - "slot_uri": "http://example.org/UNKNOWN/rdfs/label", - "alias": "label", - "owner": "Recipe", - "domain_of": [ - "Recipe" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "recipe__description", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "a brief textual description of the recipe", - "from_schema": "https://w3id.org/ontogpt/recipe", - "mappings": [ - "http://purl.org/dc/terms/description" - ], - "slot_uri": "http://purl.org/dc/terms/description", - "alias": "description", - "owner": "Recipe", - "domain_of": [ - "Recipe" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "recipe__categories", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "a semicolon separated list of the categories to which this recipe belongs", - "from_schema": "https://w3id.org/ontogpt/recipe", - "mappings": [ - "http://purl.org/dc/terms/subject" - ], - "slot_uri": "http://purl.org/dc/terms/subject", - "multivalued": true, - "alias": "categories", - "owner": "Recipe", - "domain_of": [ - "Recipe" - ], - "range": "RecipeCategory", - "@type": "SlotDefinition" - }, - { - "name": "recipe__ingredients", - "annotations": [ - { - "tag": "owl", - "value": "ObjectProperty, ObjectSomeValuesFrom", - "@type": "Annotation" - } - ], - "description": "a semicolon separated list of the ingredients plus quantities of the recipe", - "from_schema": "https://w3id.org/ontogpt/recipe", - "mappings": [ - "http://purl.obolibrary.org/obo/FOODON_00002420" - ], - "slot_uri": "http://purl.obolibrary.org/obo/FOODON_00002420", - "multivalued": true, - "alias": "ingredients", - "owner": "Recipe", - "domain_of": [ - "Recipe" - ], - "range": "Ingredient", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "recipe__steps", - "annotations": [ - { - "tag": "owl", - "value": "ObjectProperty, ObjectSomeValuesFrom", - "@type": "Annotation" - } - ], - "description": "a semicolon separated list of the individual steps involved in this recipe", - "from_schema": "https://w3id.org/ontogpt/recipe", - "slot_uri": "http://w3id.org/ontogpt/recipe/steps", - "multivalued": true, - "alias": "steps", - "owner": "Recipe", - "domain_of": [ - "Recipe" - ], - "range": "Step", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "ingredient__food_item", - "annotations": [ - { - "tag": "owl", - "value": "ObjectProperty, ObjectSomeValuesFrom", - "@type": "Annotation" - } - ], - "description": "the food item", - "from_schema": "https://w3id.org/ontogpt/recipe", - "slot_uri": "http://w3id.org/ontogpt/recipe/food_item", - "alias": "food_item", - "owner": "Ingredient", - "domain_of": [ - "Ingredient" - ], - "range": "FoodItem", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "ingredient__amount", - "annotations": [ - { - "tag": "owl", - "value": "ObjectProperty, ObjectSomeValuesFrom", - "@type": "Annotation" - } - ], - "description": "the quantity of the ingredient, e.g. 2 lbs", - "from_schema": "https://w3id.org/ontogpt/recipe", - "slot_uri": "http://w3id.org/ontogpt/recipe/amount", - "alias": "amount", - "owner": "Ingredient", - "domain_of": [ - "Ingredient" - ], - "range": "Quantity", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "quantity__value", - "annotations": [ - { - "tag": "owl", - "value": "DataProperty, DataHasValue", - "@type": "Annotation" - } - ], - "description": "the value of the quantity", - "from_schema": "https://w3id.org/ontogpt/recipe", - "slot_uri": "http://w3id.org/ontogpt/recipe/value", - "alias": "value", - "owner": "Quantity", - "domain_of": [ - "Quantity" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "quantity__unit", - "annotations": [ - { - "tag": "owl", - "value": "ObjectProperty, ObjectSomeValuesFrom", - "@type": "Annotation" - } - ], - "description": "the unit of the quantity, e.g. grams, cups, etc.", - "from_schema": "https://w3id.org/ontogpt/recipe", - "mappings": [ - "http://qudt.org/schema/qudt/unit" - ], - "slot_uri": "http://qudt.org/schema/qudt/unit", - "alias": "unit", - "owner": "Quantity", - "domain_of": [ - "Quantity" - ], - "range": "Unit", - "@type": "SlotDefinition" - }, - { - "name": "step__action", - "description": "the action taken in this step (e.g. mix, add)", - "from_schema": "https://w3id.org/ontogpt/recipe", - "slot_uri": "http://w3id.org/ontogpt/recipe/action", - "alias": "action", - "owner": "Step", - "domain_of": [ - "Step" - ], - "range": "Action", - "@type": "SlotDefinition" - }, - { - "name": "step__inputs", - "annotations": [ - { - "tag": "owl", - "value": "ObjectProperty, ObjectSomeValuesFrom", - "@type": "Annotation" - } - ], - "description": "a semicolon separated list of the inputs of this step", - "from_schema": "https://w3id.org/ontogpt/recipe", - "mappings": [ - "http://purl.obolibrary.org/obo/RO_0002233" - ], - "slot_uri": "http://purl.obolibrary.org/obo/RO_0002233", - "multivalued": true, - "alias": "inputs", - "owner": "Step", - "domain_of": [ - "Step" - ], - "range": "FoodItem", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "step__outputs", - "annotations": [ - { - "tag": "owl", - "value": "ObjectProperty, ObjectSomeValuesFrom", - "@type": "Annotation" - } - ], - "description": "a semicolon separated list of the outputs of this step", - "from_schema": "https://w3id.org/ontogpt/recipe", - "mappings": [ - "http://purl.obolibrary.org/obo/RO_0002234" - ], - "slot_uri": "http://purl.obolibrary.org/obo/RO_0002234", - "multivalued": true, - "alias": "outputs", - "owner": "Step", - "domain_of": [ - "Step" - ], - "range": "FoodItem", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "step__utensils", - "annotations": [ - { - "tag": "owl", - "value": "ObjectProperty, ObjectSomeValuesFrom", - "@type": "Annotation" - } - ], - "description": "the kitchen utensil used in this step (e.g. pan, bowl)", - "from_schema": "https://w3id.org/ontogpt/recipe", - "mappings": [ - "http://purl.obolibrary.org/obo/RO_0002500" - ], - "slot_uri": "http://purl.obolibrary.org/obo/RO_0002500", - "multivalued": true, - "alias": "utensils", - "owner": "Step", - "domain_of": [ - "Step" - ], - "range": "UtensilType", - "@type": "SlotDefinition" - }, - { - "name": "foodItem__food", - "annotations": [ - { - "tag": "owl", - "value": "ObjectProperty, ObjectSomeValuesFrom", - "@type": "Annotation" - } - ], - "description": "the food item", - "from_schema": "https://w3id.org/ontogpt/recipe", - "mappings": [ - "http://purl.obolibrary.org/obo/BFO_0000051" - ], - "slot_uri": "http://purl.obolibrary.org/obo/BFO_0000051", - "alias": "food", - "owner": "FoodItem", - "domain_of": [ - "FoodItem" - ], - "range": "FoodType", - "@type": "SlotDefinition" - }, - { - "name": "foodItem__state", - "annotations": [ - { - "tag": "owl", - "value": "DataProperty, DataHasValue", - "@type": "Annotation" - } - ], - "description": "the state of the food item (e.g. chopped, diced)", - "from_schema": "https://w3id.org/ontogpt/recipe", - "slot_uri": "http://w3id.org/ontogpt/recipe/state", - "alias": "state", - "owner": "FoodItem", - "domain_of": [ - "FoodItem" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_id", - "alias": "input_id", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_title", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_title", - "alias": "input_title", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_text", - "alias": "input_text", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__raw_completion_output", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/raw_completion_output", - "alias": "raw_completion_output", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__prompt", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/prompt", - "alias": "prompt", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__extracted_object", - "description": "The complex objects extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/extracted_object", - "alias": "extracted_object", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__named_entities", - "description": "Named entities extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/named_entities", - "multivalued": true, - "alias": "named_entities", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "identifier": true, - "alias": "id", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "required": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "from_schema": "http://w3id.org/ontogpt/core", - "aliases": [ - "name" - ], - "mappings": [ - "http://example.org/UNKNOWN/rdfs/label" - ], - "slot_uri": "http://example.org/UNKNOWN/rdfs/label", - "alias": "label", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject", - "alias": "subject", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__predicate", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/predicate", - "alias": "predicate", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "triple__object", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object", - "alias": "object", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/qualifier", - "alias": "qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_qualifier", - "alias": "subject_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_qualifier", - "alias": "object_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/publication", - "alias": "publication", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__triples", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/triples", - "multivalued": true, - "alias": "triples", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "publication__id", - "description": "The publication identifier", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "alias": "id", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__title", - "description": "The title of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/title", - "alias": "title", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__abstract", - "description": "The abstract of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/abstract", - "alias": "abstract", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__combined_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/combined_text", - "alias": "combined_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__full_text", - "description": "The full text of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/full_text", - "alias": "full_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__subject_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_text", - "alias": "subject_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_id", - "alias": "object_id", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_text", - "alias": "object_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - } - ], - "classes": [ - { - "name": "Recipe", - "definition_uri": "http://w3id.org/ontogpt/recipe/Recipe", - "annotations": [ - { - "tag": "owl", - "value": "Class", - "@type": "Annotation" - }, - { - "tag": "owl.template", - "value": "EquivalentClasses(\n {{url}}\n ObjectIntersectionOf(\n recipe:Recipe\n \n {% for step in steps %}\n ObjectSomeValuesFrom(\n recipe:steps\n {{tr(step)}}\n )\n {% endfor %}\n {% for ingredient in ingredients %}\n ObjectSomeValuesFrom(\n FOODON:00002420\n {{tr(ingredient)}}\n )\n {% endfor %}\n )\n)\n", - "@type": "Annotation" - } - ], - "from_schema": "https://w3id.org/ontogpt/recipe", - "close_mappings": [ - "FOODON:00004081" - ], - "slots": [ - "recipe__url", - "recipe__label", - "recipe__description", - "recipe__categories", - "recipe__ingredients", - "recipe__steps" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "url", - "annotations": [ - { - "tag": "prompt.ignore", - "value": "True", - "@type": "Annotation" - } - ], - "slot_uri": "rdf:Resource", - "identifier": true, - "range": "uriorcurie", - "@type": "SlotDefinition" - }, - { - "name": "label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "the name of the recipe", - "slot_uri": "rdfs:label", - "@type": "SlotDefinition" - }, - { - "name": "description", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "a brief textual description of the recipe", - "slot_uri": "dcterms:description", - "@type": "SlotDefinition" - }, - { - "name": "categories", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "a semicolon separated list of the categories to which this recipe belongs", - "slot_uri": "dcterms:subject", - "multivalued": true, - "range": "RecipeCategory", - "@type": "SlotDefinition" - }, - { - "name": "ingredients", - "annotations": [ - { - "tag": "owl", - "value": "ObjectProperty, ObjectSomeValuesFrom", - "@type": "Annotation" - } - ], - "description": "a semicolon separated list of the ingredients plus quantities of the recipe", - "slot_uri": "FOODON:00002420", - "multivalued": true, - "range": "Ingredient", - "@type": "SlotDefinition" - }, - { - "name": "steps", - "annotations": [ - { - "tag": "owl", - "value": "ObjectProperty, ObjectSomeValuesFrom", - "@type": "Annotation" - } - ], - "description": "a semicolon separated list of the individual steps involved in this recipe", - "multivalued": true, - "range": "Step", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/recipe/Recipe", - "tree_root": true, - "@type": "ClassDefinition" - }, - { - "name": "Ingredient", - "definition_uri": "http://w3id.org/ontogpt/recipe/Ingredient", - "annotations": [ - { - "tag": "owl", - "value": "IntersectionOf", - "@type": "Annotation" - } - ], - "from_schema": "https://w3id.org/ontogpt/recipe", - "mappings": [ - "FOODON:00004085" - ], - "is_a": "CompoundExpression", - "slots": [ - "ingredient__food_item", - "ingredient__amount" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "food_item", - "annotations": [ - { - "tag": "owl", - "value": "ObjectProperty, ObjectSomeValuesFrom", - "@type": "Annotation" - } - ], - "description": "the food item", - "range": "FoodItem", - "@type": "SlotDefinition" - }, - { - "name": "amount", - "annotations": [ - { - "tag": "owl", - "value": "ObjectProperty, ObjectSomeValuesFrom", - "@type": "Annotation" - } - ], - "description": "the quantity of the ingredient, e.g. 2 lbs", - "range": "Quantity", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://purl.obolibrary.org/obo/FOODON_00004085", - "@type": "ClassDefinition" - }, - { - "name": "Quantity", - "definition_uri": "http://w3id.org/ontogpt/recipe/Quantity", - "annotations": [ - { - "tag": "owl", - "value": "IntersectionOf", - "@type": "Annotation" - } - ], - "from_schema": "https://w3id.org/ontogpt/recipe", - "is_a": "CompoundExpression", - "slots": [ - "quantity__value", - "quantity__unit" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "value", - "annotations": [ - { - "tag": "owl", - "value": "DataProperty, DataHasValue", - "@type": "Annotation" - } - ], - "description": "the value of the quantity", - "@type": "SlotDefinition" - }, - { - "name": "unit", - "annotations": [ - { - "tag": "owl", - "value": "ObjectProperty, ObjectSomeValuesFrom", - "@type": "Annotation" - } - ], - "description": "the unit of the quantity, e.g. grams, cups, etc.", - "slot_uri": "qudt:unit", - "range": "Unit", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/recipe/Quantity", - "@type": "ClassDefinition" - }, - { - "name": "Step", - "definition_uri": "http://w3id.org/ontogpt/recipe/Step", - "annotations": [ - { - "tag": "owl", - "value": "IntersectionOf", - "@type": "Annotation" - } - ], - "from_schema": "https://w3id.org/ontogpt/recipe", - "mappings": [ - "FOODON:00004087" - ], - "is_a": "CompoundExpression", - "slots": [ - "step__action", - "step__inputs", - "step__outputs", - "step__utensils" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "action", - "description": "the action taken in this step (e.g. mix, add)", - "range": "Action", - "@type": "SlotDefinition" - }, - { - "name": "inputs", - "annotations": [ - { - "tag": "owl", - "value": "ObjectProperty, ObjectSomeValuesFrom", - "@type": "Annotation" - } - ], - "description": "a semicolon separated list of the inputs of this step", - "slot_uri": "RO:0002233", - "multivalued": true, - "range": "FoodItem", - "@type": "SlotDefinition" - }, - { - "name": "outputs", - "annotations": [ - { - "tag": "owl", - "value": "ObjectProperty, ObjectSomeValuesFrom", - "@type": "Annotation" - } - ], - "description": "a semicolon separated list of the outputs of this step", - "slot_uri": "RO:0002234", - "multivalued": true, - "range": "FoodItem", - "@type": "SlotDefinition" - }, - { - "name": "utensils", - "annotations": [ - { - "tag": "owl", - "value": "ObjectProperty, ObjectSomeValuesFrom", - "@type": "Annotation" - } - ], - "description": "the kitchen utensil used in this step (e.g. pan, bowl)", - "slot_uri": "RO:0002500", - "multivalued": true, - "range": "UtensilType", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://purl.obolibrary.org/obo/FOODON_00004087", - "@type": "ClassDefinition" - }, - { - "name": "FoodItem", - "definition_uri": "http://w3id.org/ontogpt/recipe/FoodItem", - "annotations": [ - { - "tag": "owl", - "value": "IntersectionOf", - "@type": "Annotation" - } - ], - "from_schema": "https://w3id.org/ontogpt/recipe", - "is_a": "CompoundExpression", - "slots": [ - "foodItem__food", - "foodItem__state" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "food", - "annotations": [ - { - "tag": "owl", - "value": "ObjectProperty, ObjectSomeValuesFrom", - "@type": "Annotation" - } - ], - "description": "the food item", - "slot_uri": "BFO:0000051", - "range": "FoodType", - "@type": "SlotDefinition" - }, - { - "name": "state", - "annotations": [ - { - "tag": "owl", - "value": "DataProperty, DataHasValue", - "@type": "Annotation" - } - ], - "description": "the state of the food item (e.g. chopped, diced)", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/recipe/FoodItem", - "@type": "ClassDefinition" - }, - { - "name": "FoodType", - "id_prefixes": [ - "dbpediaont", - "FOODON" - ], - "definition_uri": "http://w3id.org/ontogpt/recipe/FoodType", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:foodon, sqlite:obo:dbpediaont", - "@type": "Annotation" - } - ], - "from_schema": "https://w3id.org/ontogpt/recipe", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/recipe/FoodType", - "@type": "ClassDefinition" - }, - { - "name": "RecipeCategory", - "id_prefixes": [ - "dbpediaont", - "FOODON", - "HANCESTRO" - ], - "definition_uri": "http://w3id.org/ontogpt/recipe/RecipeCategory", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:foodon, sqlite:obo:dbpediaont", - "@type": "Annotation" - } - ], - "from_schema": "https://w3id.org/ontogpt/recipe", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/recipe/RecipeCategory", - "@type": "ClassDefinition" - }, - { - "name": "Action", - "id_prefixes": [ - "dbpediaont", - "FOODON" - ], - "definition_uri": "http://w3id.org/ontogpt/recipe/Action", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:dbpediaont, sqlite:obo:foodon", - "@type": "Annotation" - } - ], - "from_schema": "https://w3id.org/ontogpt/recipe", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/recipe/Action", - "@type": "ClassDefinition" - }, - { - "name": "UtensilType", - "id_prefixes": [ - "dbpediaont", - "FOODON" - ], - "definition_uri": "http://w3id.org/ontogpt/recipe/UtensilType", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:dbpediaont, sqlite:obo:foodon", - "@type": "Annotation" - } - ], - "from_schema": "https://w3id.org/ontogpt/recipe", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/recipe/UtensilType", - "@type": "ClassDefinition" - }, - { - "name": "Unit", - "id_prefixes": [ - "UO", - "NCIT", - "dbpediaont" - ], - "definition_uri": "http://w3id.org/ontogpt/recipe/Unit", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:uo, sqlite:obo:dbpediaont, sqlite:obo:foodon", - "@type": "Annotation" - } - ], - "from_schema": "https://w3id.org/ontogpt/recipe", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/recipe/Unit", - "@type": "ClassDefinition" - }, - { - "name": "Any", - "definition_uri": "http://w3id.org/ontogpt/core/Any", - "from_schema": "http://w3id.org/ontogpt/core", - "mappings": [ - "linkml:Any" - ], - "slot_usage": {}, - "class_uri": "https://w3id.org/linkml/Any", - "@type": "ClassDefinition" - }, - { - "name": "ExtractionResult", - "definition_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "description": "A result of extracting knowledge on text", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "extractionResult__input_id", - "extractionResult__input_title", - "extractionResult__input_text", - "extractionResult__raw_completion_output", - "extractionResult__prompt", - "extractionResult__extracted_object", - "extractionResult__named_entities" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "input_id", - "@type": "SlotDefinition" - }, - { - "name": "input_title", - "@type": "SlotDefinition" - }, - { - "name": "input_text", - "@type": "SlotDefinition" - }, - { - "name": "raw_completion_output", - "@type": "SlotDefinition" - }, - { - "name": "prompt", - "@type": "SlotDefinition" - }, - { - "name": "extracted_object", - "description": "The complex objects extracted from the text", - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "named_entities", - "description": "Named entities extracted from the text", - "multivalued": true, - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "@type": "ClassDefinition" - }, - { - "name": "NamedEntity", - "definition_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "identifier": true, - "@type": "SlotDefinition" - }, - { - "name": "label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "aliases": [ - "name" - ], - "slot_uri": "rdfs:label", - "range": "string", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "@type": "ClassDefinition" - }, - { - "name": "CompoundExpression", - "definition_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "@type": "ClassDefinition" - }, - { - "name": "Triple", - "definition_uri": "http://w3id.org/ontogpt/core/Triple", - "description": "Abstract parent for Relation Extraction tasks", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "CompoundExpression", - "abstract": true, - "slots": [ - "triple__subject", - "triple__predicate", - "triple__object", - "triple__qualifier", - "triple__subject_qualifier", - "triple__object_qualifier" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "predicate", - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "object", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Triple", - "@type": "ClassDefinition" - }, - { - "name": "TextWithTriples", - "definition_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "textWithTriples__publication", - "textWithTriples__triples" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "triples", - "multivalued": true, - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "@type": "ClassDefinition" - }, - { - "name": "RelationshipType", - "id_prefixes": [ - "RO", - "biolink" - ], - "definition_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "@type": "ClassDefinition" - }, - { - "name": "Publication", - "definition_uri": "http://w3id.org/ontogpt/core/Publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "publication__id", - "publication__title", - "publication__abstract", - "publication__combined_text", - "publication__full_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "description": "The publication identifier", - "@type": "SlotDefinition" - }, - { - "name": "title", - "description": "The title of the publication", - "@type": "SlotDefinition" - }, - { - "name": "abstract", - "description": "The abstract of the publication", - "@type": "SlotDefinition" - }, - { - "name": "combined_text", - "@type": "SlotDefinition" - }, - { - "name": "full_text", - "description": "The full text of the publication", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Publication", - "@type": "ClassDefinition" - }, - { - "name": "AnnotatorResult", - "definition_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "annotatorResult__subject_text", - "annotatorResult__object_id", - "annotatorResult__object_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject_text", - "@type": "SlotDefinition" - }, - { - "name": "object_id", - "@type": "SlotDefinition" - }, - { - "name": "object_text", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "@type": "ClassDefinition" - } - ], - "metamodel_version": "1.7.0", - "source_file": "recipe.yaml", - "source_file_date": "2023-06-17T15:11:19", - "source_file_size": 5792, - "generation_date": "2023-08-07T10:56:09", - "@type": "SchemaDefinition", - "@context": [ - "projects/recipe/jsonld/recipe.context.jsonld", - "https://w3id.org/linkml/types.context.jsonld", - "core.context.jsonld", - { - "@base": "http://w3id.org/ontogpt/recipe/" - } - ] -} diff --git a/projects/recipe/jsonschema/recipe.schema.json b/projects/recipe/jsonschema/recipe.schema.json deleted file mode 100644 index 6c29c2c57..000000000 --- a/projects/recipe/jsonschema/recipe.schema.json +++ /dev/null @@ -1,397 +0,0 @@ -{ - "$defs": { - "Action": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Action", - "type": "object" - }, - "AnnotatorResult": { - "additionalProperties": false, - "description": "", - "properties": { - "object_id": { - "type": "string" - }, - "object_text": { - "type": "string" - }, - "subject_text": { - "type": "string" - } - }, - "title": "AnnotatorResult", - "type": "object" - }, - "Any": { - "additionalProperties": true, - "description": "", - "title": "Any", - "type": "object" - }, - "ExtractionResult": { - "additionalProperties": false, - "description": "A result of extracting knowledge on text", - "properties": { - "extracted_object": { - "$ref": "#/$defs/Any", - "description": "The complex objects extracted from the text" - }, - "input_id": { - "type": "string" - }, - "input_text": { - "type": "string" - }, - "input_title": { - "type": "string" - }, - "named_entities": { - "description": "Named entities extracted from the text", - "items": { - "$ref": "#/$defs/Any" - }, - "type": "array" - }, - "prompt": { - "type": "string" - }, - "raw_completion_output": { - "type": "string" - } - }, - "title": "ExtractionResult", - "type": "object" - }, - "FoodItem": { - "additionalProperties": false, - "description": "", - "properties": { - "food": { - "description": "the food item", - "type": "string" - }, - "state": { - "description": "the state of the food item (e.g. chopped, diced)", - "type": "string" - } - }, - "title": "FoodItem", - "type": "object" - }, - "FoodType": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "FoodType", - "type": "object" - }, - "Ingredient": { - "additionalProperties": false, - "description": "", - "properties": { - "amount": { - "$ref": "#/$defs/Quantity", - "description": "the quantity of the ingredient, e.g. 2 lbs" - }, - "food_item": { - "$ref": "#/$defs/FoodItem", - "description": "the food item" - } - }, - "title": "Ingredient", - "type": "object" - }, - "NullDataOptions": { - "description": "", - "enum": [ - "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "NOT_APPLICABLE", - "NOT_MENTIONED" - ], - "title": "NullDataOptions", - "type": "string" - }, - "Publication": { - "additionalProperties": false, - "description": "", - "properties": { - "abstract": { - "description": "The abstract of the publication", - "type": "string" - }, - "combined_text": { - "type": "string" - }, - "full_text": { - "description": "The full text of the publication", - "type": "string" - }, - "id": { - "description": "The publication identifier", - "type": "string" - }, - "title": { - "description": "The title of the publication", - "type": "string" - } - }, - "title": "Publication", - "type": "object" - }, - "Quantity": { - "additionalProperties": false, - "description": "", - "properties": { - "unit": { - "description": "the unit of the quantity, e.g. grams, cups, etc.", - "type": "string" - }, - "value": { - "description": "the value of the quantity", - "type": "string" - } - }, - "title": "Quantity", - "type": "object" - }, - "Recipe": { - "additionalProperties": false, - "description": "", - "properties": { - "categories": { - "description": "a semicolon separated list of the categories to which this recipe belongs", - "items": { - "type": "string" - }, - "type": "array" - }, - "description": { - "description": "a brief textual description of the recipe", - "type": "string" - }, - "ingredients": { - "description": "a semicolon separated list of the ingredients plus quantities of the recipe", - "items": { - "$ref": "#/$defs/Ingredient" - }, - "type": "array" - }, - "label": { - "description": "the name of the recipe", - "type": "string" - }, - "steps": { - "description": "a semicolon separated list of the individual steps involved in this recipe", - "items": { - "$ref": "#/$defs/Step" - }, - "type": "array" - }, - "url": { - "type": "string" - } - }, - "required": [ - "url" - ], - "title": "Recipe", - "type": "object" - }, - "RecipeCategory": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "RecipeCategory", - "type": "object" - }, - "RelationshipType": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "RelationshipType", - "type": "object" - }, - "Step": { - "additionalProperties": false, - "description": "", - "properties": { - "action": { - "description": "the action taken in this step (e.g. mix, add)", - "type": "string" - }, - "inputs": { - "description": "a semicolon separated list of the inputs of this step", - "items": { - "$ref": "#/$defs/FoodItem" - }, - "type": "array" - }, - "outputs": { - "description": "a semicolon separated list of the outputs of this step", - "items": { - "$ref": "#/$defs/FoodItem" - }, - "type": "array" - }, - "utensils": { - "description": "the kitchen utensil used in this step (e.g. pan, bowl)", - "items": { - "type": "string" - }, - "type": "array" - } - }, - "title": "Step", - "type": "object" - }, - "TextWithTriples": { - "additionalProperties": false, - "description": "", - "properties": { - "publication": { - "$ref": "#/$defs/Publication" - }, - "triples": { - "items": { - "$ref": "#/$defs/Triple" - }, - "type": "array" - } - }, - "title": "TextWithTriples", - "type": "object" - }, - "Unit": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Unit", - "type": "object" - }, - "UtensilType": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "UtensilType", - "type": "object" - } - }, - "$id": "https://w3id.org/ontogpt/recipe", - "$schema": "http://json-schema.org/draft-07/schema#", - "additionalProperties": true, - "metamodel_version": "1.7.0", - "properties": { - "categories": { - "description": "a semicolon separated list of the categories to which this recipe belongs", - "items": { - "type": "string" - }, - "type": "array" - }, - "description": { - "description": "a brief textual description of the recipe", - "type": "string" - }, - "ingredients": { - "description": "a semicolon separated list of the ingredients plus quantities of the recipe", - "items": { - "$ref": "#/$defs/Ingredient" - }, - "type": "array" - }, - "label": { - "description": "the name of the recipe", - "type": "string" - }, - "steps": { - "description": "a semicolon separated list of the individual steps involved in this recipe", - "items": { - "$ref": "#/$defs/Step" - }, - "type": "array" - }, - "url": { - "type": "string" - } - }, - "required": [ - "url" - ], - "title": "recipe-template", - "type": "object", - "version": null -} \ No newline at end of file diff --git a/projects/recipe/owl/recipe.owl.ttl b/projects/recipe/owl/recipe.owl.ttl deleted file mode 100644 index 6e74a6b37..000000000 --- a/projects/recipe/owl/recipe.owl.ttl +++ /dev/null @@ -1,624 +0,0 @@ -@prefix BFO: <http://purl.obolibrary.org/obo/BFO_> . -@prefix FOODON: <http://purl.obolibrary.org/obo/FOODON_> . -@prefix IAO: <http://purl.obolibrary.org/obo/IAO_> . -@prefix RO: <http://purl.obolibrary.org/obo/RO_> . -@prefix dcterms: <http://purl.org/dc/terms/> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix owl: <http://www.w3.org/2002/07/owl#> . -@prefix qudt: <http://qudt.org/schema/qudt/> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . -@prefix recipe: <http://w3id.org/ontogpt/recipe/> . -@prefix skos: <http://www.w3.org/2004/02/skos/core#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -linkml:SubsetDefinition a owl:Class ; - rdfs:label "subset_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" . - -linkml:TypeDefinition a owl:Class ; - rdfs:label "type_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" ; - linkml:mixins "type_expression" . - -linkml:topValue a owl:DatatypeProperty ; - rdfs:label "value" . - -<https://w3id.org/ontogpt/recipe> a owl:Ontology ; - rdfs:label "recipe-template" ; - IAO:0000700 <http://w3id.org/ontogpt/core/AnnotatorResult>, - <http://w3id.org/ontogpt/core/Any>, - <http://w3id.org/ontogpt/core/CompoundExpression>, - <http://w3id.org/ontogpt/core/ExtractionResult>, - <http://w3id.org/ontogpt/core/NamedEntity>, - <http://w3id.org/ontogpt/core/Publication>, - <http://w3id.org/ontogpt/core/TextWithTriples>, - recipe:Recipe ; - linkml:classes "{'Recipe': ClassDefinition(name='Recipe', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/recipe/Recipe', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='Class', extensions={}, annotations={}), 'owl.template': Annotation(tag='owl.template', value='EquivalentClasses(\\n {{url}}\\n ObjectIntersectionOf(\\n recipe:Recipe\\n \\n {% for step in steps %}\\n ObjectSomeValuesFrom(\\n recipe:steps\\n {{tr(step)}}\\n )\\n {% endfor %}\\n {% for ingredient in ingredients %}\\n ObjectSomeValuesFrom(\\n FOODON:00002420\\n {{tr(ingredient)}}\\n )\\n {% endfor %}\\n )\\n)\\n', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/recipe', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['FOODON:00004081'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['recipe__url', 'recipe__label', 'recipe__description', 'recipe__categories', 'recipe__ingredients', 'recipe__steps'], slot_usage={}, attributes={'url': SlotDefinition(name='url', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.ignore': Annotation(tag='prompt.ignore', value='True', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdf:Resource', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='uriorcurie', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='the name of the recipe', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'description': SlotDefinition(name='description', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='a brief textual description of the recipe', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='dcterms:description', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'categories': SlotDefinition(name='categories', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationAssertion', extensions={}, annotations={})}, description='a semicolon separated list of the categories to which this recipe belongs', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='dcterms:subject', multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RecipeCategory', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ingredients': SlotDefinition(name='ingredients', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='ObjectProperty, ObjectSomeValuesFrom', extensions={}, annotations={})}, description='a semicolon separated list of the ingredients plus quantities of the recipe', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='FOODON:00002420', multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Ingredient', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'steps': SlotDefinition(name='steps', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='ObjectProperty, ObjectSomeValuesFrom', extensions={}, annotations={})}, description='a semicolon separated list of the individual steps involved in this recipe', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Step', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='recipe:Recipe', subclass_of=None, union_of=[], defining_slots=[], tree_root=True, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Ingredient': ClassDefinition(name='Ingredient', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/recipe/Ingredient', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='IntersectionOf', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/recipe', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=['FOODON:00004085'], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['ingredient__food_item', 'ingredient__amount'], slot_usage={}, attributes={'food_item': SlotDefinition(name='food_item', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='ObjectProperty, ObjectSomeValuesFrom', extensions={}, annotations={})}, description='the food item', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='FoodItem', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'amount': SlotDefinition(name='amount', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='ObjectProperty, ObjectSomeValuesFrom', extensions={}, annotations={})}, description='the quantity of the ingredient, e.g. 2 lbs', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Quantity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='FOODON:00004085', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Quantity': ClassDefinition(name='Quantity', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/recipe/Quantity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='IntersectionOf', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/recipe', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['quantity__value', 'quantity__unit'], slot_usage={}, attributes={'value': SlotDefinition(name='value', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='DataProperty, DataHasValue', extensions={}, annotations={})}, description='the value of the quantity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'unit': SlotDefinition(name='unit', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='ObjectProperty, ObjectSomeValuesFrom', extensions={}, annotations={})}, description='the unit of the quantity, e.g. grams, cups, etc.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='qudt:unit', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Unit', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='recipe:Quantity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Step': ClassDefinition(name='Step', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/recipe/Step', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='IntersectionOf', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/recipe', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=['FOODON:00004087'], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['step__action', 'step__inputs', 'step__outputs', 'step__utensils'], slot_usage={}, attributes={'action': SlotDefinition(name='action', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the action taken in this step (e.g. mix, add)', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Action', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'inputs': SlotDefinition(name='inputs', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='ObjectProperty, ObjectSomeValuesFrom', extensions={}, annotations={})}, description='a semicolon separated list of the inputs of this step', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='RO:0002233', multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='FoodItem', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'outputs': SlotDefinition(name='outputs', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='ObjectProperty, ObjectSomeValuesFrom', extensions={}, annotations={})}, description='a semicolon separated list of the outputs of this step', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='RO:0002234', multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='FoodItem', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'utensils': SlotDefinition(name='utensils', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='ObjectProperty, ObjectSomeValuesFrom', extensions={}, annotations={})}, description='the kitchen utensil used in this step (e.g. pan, bowl)', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='RO:0002500', multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='UtensilType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='FOODON:00004087', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'FoodItem': ClassDefinition(name='FoodItem', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/recipe/FoodItem', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='IntersectionOf', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/recipe', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['foodItem__food', 'foodItem__state'], slot_usage={}, attributes={'food': SlotDefinition(name='food', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='ObjectProperty, ObjectSomeValuesFrom', extensions={}, annotations={})}, description='the food item', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='BFO:0000051', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='FoodType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'state': SlotDefinition(name='state', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='DataProperty, DataHasValue', extensions={}, annotations={})}, description='the state of the food item (e.g. chopped, diced)', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='recipe:FoodItem', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'FoodType': ClassDefinition(name='FoodType', id_prefixes=['dbpediaont', 'FOODON'], definition_uri='http://w3id.org/ontogpt/recipe/FoodType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:foodon, sqlite:obo:dbpediaont', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/recipe', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='recipe:FoodType', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'RecipeCategory': ClassDefinition(name='RecipeCategory', id_prefixes=['dbpediaont', 'FOODON', 'HANCESTRO'], definition_uri='http://w3id.org/ontogpt/recipe/RecipeCategory', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:foodon, sqlite:obo:dbpediaont', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/recipe', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='recipe:RecipeCategory', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Action': ClassDefinition(name='Action', id_prefixes=['dbpediaont', 'FOODON'], definition_uri='http://w3id.org/ontogpt/recipe/Action', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:dbpediaont, sqlite:obo:foodon', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/recipe', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='recipe:Action', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'UtensilType': ClassDefinition(name='UtensilType', id_prefixes=['dbpediaont', 'FOODON'], definition_uri='http://w3id.org/ontogpt/recipe/UtensilType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:dbpediaont, sqlite:obo:foodon', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/recipe', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='recipe:UtensilType', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Unit': ClassDefinition(name='Unit', id_prefixes=['UO', 'NCIT', 'dbpediaont'], definition_uri='http://w3id.org/ontogpt/recipe/Unit', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:uo, sqlite:obo:dbpediaont, sqlite:obo:foodon', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/recipe', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='recipe:Unit', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Any': ClassDefinition(name='Any', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Any', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=['linkml:Any'], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='linkml:Any', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ExtractionResult': ClassDefinition(name='ExtractionResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/ExtractionResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A result of extracting knowledge on text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['extractionResult__input_id', 'extractionResult__input_title', 'extractionResult__input_text', 'extractionResult__raw_completion_output', 'extractionResult__prompt', 'extractionResult__extracted_object', 'extractionResult__named_entities'], slot_usage={}, attributes={'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:ExtractionResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'NamedEntity': ClassDefinition(name='NamedEntity', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NamedEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:NamedEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'CompoundExpression': ClassDefinition(name='CompoundExpression', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/CompoundExpression', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='core:CompoundExpression', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Triple': ClassDefinition(name='Triple', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Triple', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Abstract parent for Relation Extraction tasks', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['triple__subject', 'triple__predicate', 'triple__object', 'triple__qualifier', 'triple__subject_qualifier', 'triple__object_qualifier'], slot_usage={}, attributes={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Triple', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'TextWithTriples': ClassDefinition(name='TextWithTriples', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/TextWithTriples', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['textWithTriples__publication', 'textWithTriples__triples'], slot_usage={}, attributes={'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:TextWithTriples', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'RelationshipType': ClassDefinition(name='RelationshipType', id_prefixes=['RO', 'biolink'], definition_uri='http://w3id.org/ontogpt/core/RelationshipType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='core:RelationshipType', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Publication': ClassDefinition(name='Publication', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Publication', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['publication__id', 'publication__title', 'publication__abstract', 'publication__combined_text', 'publication__full_text'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Publication', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'AnnotatorResult': ClassDefinition(name='AnnotatorResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/AnnotatorResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['annotatorResult__subject_text', 'annotatorResult__object_id', 'annotatorResult__object_text'], slot_usage={}, attributes={'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:AnnotatorResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={})}" ; - linkml:enums "{'NullDataOptions': EnumDefinition(name='NullDataOptions', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NullDataOptions', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'UNSPECIFIED_METHOD_OF_ADMINISTRATION': PermissibleValue(text='UNSPECIFIED_METHOD_OF_ADMINISTRATION', description=None, meaning='NCIT:C149701', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_APPLICABLE': PermissibleValue(text='NOT_APPLICABLE', description=None, meaning='NCIT:C18902', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['not applicable', 'N/A'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_MENTIONED': PermissibleValue(text='NOT_MENTIONED', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[])}" ; - linkml:id "https://w3id.org/ontogpt/recipe" ; - linkml:imports "core", - "linkml:types" ; - linkml:types "{'string': TypeDefinition(name='string', id_prefixes=[], definition_uri='https://w3id.org/linkml/String', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A character string', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Text'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'integer': TypeDefinition(name='integer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Integer', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An integer', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Integer'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='int', uri='xsd:integer', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'boolean': TypeDefinition(name='boolean', id_prefixes=[], definition_uri='https://w3id.org/linkml/Boolean', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A binary (true or false) value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Boolean'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Bool', uri='xsd:boolean', repr='bool', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'float': TypeDefinition(name='float', id_prefixes=[], definition_uri='https://w3id.org/linkml/Float', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:float specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Float'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:float', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'double': TypeDefinition(name='double', id_prefixes=[], definition_uri='https://w3id.org/linkml/Double', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:double specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:Float'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:double', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'decimal': TypeDefinition(name='decimal', id_prefixes=[], definition_uri='https://w3id.org/linkml/Decimal', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number with arbitrary precision that conforms to the xsd:decimal specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=['schema:Number'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Decimal', uri='xsd:decimal', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'time': TypeDefinition(name='time', id_prefixes=[], definition_uri='https://w3id.org/linkml/Time', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A time object represents a (local) time of day, independent of any particular day', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=['URI is dateTime because OWL reasoners do not work with straight date or time'], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Time'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDTime', uri='xsd:time', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date': TypeDefinition(name='date', id_prefixes=[], definition_uri='https://w3id.org/linkml/Date', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a date (year, month and day) in an idealized calendar', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[\"URI is dateTime because OWL reasoners don't work with straight date or time\"], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Date'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDate', uri='xsd:date', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'datetime': TypeDefinition(name='datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/Datetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The combination of a date and time', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:DateTime'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDateTime', uri='xsd:dateTime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date_or_datetime': TypeDefinition(name='date_or_datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/DateOrDatetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Either a date or a datetime', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='linkml:DateOrDatetime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uriorcurie': TypeDefinition(name='uriorcurie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uriorcurie', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a URI or a CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URIorCURIE', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'curie': TypeDefinition(name='curie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Curie', local_names={}, conforms_to='https://www.w3.org/TR/curie/', implements=[], extensions={}, annotations={}, description='a compact URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations this MUST be expanded to a URI', 'in non-RDF serializations MAY be serialized as the compact representation'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Curie', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uri': TypeDefinition(name='uri', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uri', local_names={}, conforms_to='https://www.ietf.org/rfc/rfc3987.txt', implements=[], extensions={}, annotations={}, description='a complete URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:URL'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URI', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ncname': TypeDefinition(name='ncname', id_prefixes=[], definition_uri='https://w3id.org/linkml/Ncname', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Prefix part of CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NCName', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'objectidentifier': TypeDefinition(name='objectidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Objectidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI or CURIE that represents an object in the model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['Used for inheritance and type checking'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='ElementIdentifier', uri='shex:iri', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'nodeidentifier': TypeDefinition(name='nodeidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Nodeidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI, CURIE or BNODE that represents a node in a model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NodeIdentifier', uri='shex:nonLiteral', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpointer': TypeDefinition(name='jsonpointer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpointer', local_names={}, conforms_to='https://datatracker.ietf.org/doc/html/rfc6901', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpath': TypeDefinition(name='jsonpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpath', local_names={}, conforms_to='https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sparqlpath': TypeDefinition(name='sparqlpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Sparqlpath', local_names={}, conforms_to='https://www.w3.org/TR/sparql11-query/#propertypaths', implements=[], extensions={}, annotations={}, description='A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "AnnotatorResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_id> ] ; - linkml:attributes "{'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/ExtractionResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ExtractionResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/prompt> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_title> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/named_entities> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/extracted_object> ] ; - skos:definition "A result of extracting knowledge on text" ; - linkml:attributes "{'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/TextWithTriples> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TextWithTriples" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Triple> ; - owl:onProperty <http://w3id.org/ontogpt/core/triples> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Publication> ; - owl:onProperty <http://w3id.org/ontogpt/core/publication> ] ; - linkml:attributes "{'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/abstract> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "abstract" ; - rdfs:range linkml:String ; - skos:definition "The abstract of the publication" . - -<http://w3id.org/ontogpt/core/combined_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "combined_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/extracted_object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "extracted_object" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "The complex objects extracted from the text" . - -<http://w3id.org/ontogpt/core/full_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "full_text" ; - rdfs:range linkml:String ; - skos:definition "The full text of the publication" . - -<http://w3id.org/ontogpt/core/input_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_title" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/named_entities> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "named_entities" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "Named entities extracted from the text" . - -<http://w3id.org/ontogpt/core/object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/object_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/object_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" . - -<http://w3id.org/ontogpt/core/object_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/predicate> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "predicate" ; - rdfs:range <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/prompt> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "prompt" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/publication> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "publication" ; - recipe:prompt.skip "true" ; - rdfs:range <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "qualifier" ; - rdfs:range linkml:String ; - skos:definition "A qualifier for the statements, e.g. \"NOT\" for negation" . - -<http://w3id.org/ontogpt/core/raw_completion_output> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "raw_completion_output" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/subject> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/subject_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" . - -<http://w3id.org/ontogpt/core/subject_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "title" ; - rdfs:range linkml:String ; - skos:definition "The title of the publication" . - -<http://w3id.org/ontogpt/core/triples> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "triples" ; - rdfs:range <http://w3id.org/ontogpt/core/Triple> . - -recipe:Recipe a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Recipe" ; - recipe:owl "Class" ; - recipe:owl.template """EquivalentClasses( - {{url}} - ObjectIntersectionOf( - recipe:Recipe - - {% for step in steps %} - ObjectSomeValuesFrom( - recipe:steps - {{tr(step)}} - ) - {% endfor %} - {% for ingredient in ingredients %} - ObjectSomeValuesFrom( - FOODON:00002420 - {{tr(ingredient)}} - ) - {% endfor %} - ) -) -""" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom recipe:Ingredient ; - owl:onProperty FOODON:00002420 ], - [ a owl:Restriction ; - owl:allValuesFrom recipe:Step ; - owl:onProperty recipe:steps ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty dcterms:description ], - [ a owl:Restriction ; - owl:allValuesFrom recipe:RecipeCategory ; - owl:onProperty dcterms:subject ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://example.org/UNKNOWN/rdfs/label> ], - [ a owl:Restriction ; - owl:onClass linkml:Uriorcurie ; - owl:onProperty <http://example.org/UNKNOWN/rdf/Resource> ; - owl:qualifiedCardinality 1 ] ; - skos:closeMatch FOODON:00004081 ; - linkml:attributes "{'url': SlotDefinition(name='url', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.ignore': Annotation(tag='prompt.ignore', value='True', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdf:Resource', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='uriorcurie', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='the name of the recipe', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'description': SlotDefinition(name='description', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='a brief textual description of the recipe', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='dcterms:description', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'categories': SlotDefinition(name='categories', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationAssertion', extensions={}, annotations={})}, description='a semicolon separated list of the categories to which this recipe belongs', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='dcterms:subject', multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RecipeCategory', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ingredients': SlotDefinition(name='ingredients', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='ObjectProperty, ObjectSomeValuesFrom', extensions={}, annotations={})}, description='a semicolon separated list of the ingredients plus quantities of the recipe', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='FOODON:00002420', multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Ingredient', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'steps': SlotDefinition(name='steps', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='ObjectProperty, ObjectSomeValuesFrom', extensions={}, annotations={})}, description='a semicolon separated list of the individual steps involved in this recipe', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Step', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -recipe:action a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "action" ; - rdfs:range recipe:Action ; - skos:definition "the action taken in this step (e.g. mix, add)" . - -recipe:amount a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "amount" ; - recipe:owl "ObjectProperty, ObjectSomeValuesFrom" ; - rdfs:range recipe:Quantity ; - skos:definition "the quantity of the ingredient, e.g. 2 lbs" . - -recipe:food_item a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "food_item" ; - recipe:owl "ObjectProperty, ObjectSomeValuesFrom" ; - rdfs:range recipe:FoodItem ; - skos:definition "the food item" . - -recipe:state a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "state" ; - recipe:owl "DataProperty, DataHasValue" ; - rdfs:range linkml:String ; - skos:definition "the state of the food item (e.g. chopped, diced)" . - -recipe:steps a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "steps" ; - recipe:owl "ObjectProperty, ObjectSomeValuesFrom" ; - rdfs:range recipe:Step ; - skos:definition "a semicolon separated list of the individual steps involved in this recipe" . - -recipe:value a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "value" ; - recipe:owl "DataProperty, DataHasValue" ; - rdfs:range linkml:String ; - skos:definition "the value of the quantity" . - -<http://example.org/UNKNOWN/rdf/Resource> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "url" ; - recipe:prompt.ignore "True" ; - rdfs:range linkml:Uriorcurie ; - skos:exactMatch <http://example.org/UNKNOWN/rdf/Resource> . - -<http://example.org/UNKNOWN/rdfs/label> a owl:ObjectProperty, - linkml:SlotDefinition . - -BFO:0000051 a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "food" ; - recipe:owl "ObjectProperty, ObjectSomeValuesFrom" ; - rdfs:range recipe:FoodType ; - skos:definition "the food item" ; - skos:exactMatch BFO:0000051 . - -FOODON:00002420 a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "ingredients" ; - recipe:owl "ObjectProperty, ObjectSomeValuesFrom" ; - rdfs:range recipe:Ingredient ; - skos:definition "a semicolon separated list of the ingredients plus quantities of the recipe" ; - skos:exactMatch FOODON:00002420 . - -<http://purl.obolibrary.org/obo/NCIT_C149701> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "UNSPECIFIED_METHOD_OF_ADMINISTRATION" . - -<http://purl.obolibrary.org/obo/NCIT_C18902> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_APPLICABLE" . - -RO:0002233 a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "inputs" ; - recipe:owl "ObjectProperty, ObjectSomeValuesFrom" ; - rdfs:range recipe:FoodItem ; - skos:definition "a semicolon separated list of the inputs of this step" ; - skos:exactMatch RO:0002233 . - -RO:0002234 a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "outputs" ; - recipe:owl "ObjectProperty, ObjectSomeValuesFrom" ; - rdfs:range recipe:FoodItem ; - skos:definition "a semicolon separated list of the outputs of this step" ; - skos:exactMatch RO:0002234 . - -RO:0002500 a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "utensils" ; - recipe:owl "ObjectProperty, ObjectSomeValuesFrom" ; - rdfs:range recipe:UtensilType ; - skos:definition "the kitchen utensil used in this step (e.g. pan, bowl)" ; - skos:exactMatch RO:0002500 . - -dcterms:description a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "description" ; - recipe:owl "AnnotationProperty, AnnotationAssertion" ; - rdfs:range linkml:String ; - skos:definition "a brief textual description of the recipe" ; - skos:exactMatch dcterms:description . - -dcterms:subject a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "categories" ; - recipe:owl "AnnotationAssertion" ; - rdfs:range recipe:RecipeCategory ; - skos:definition "a semicolon separated list of the categories to which this recipe belongs" ; - skos:exactMatch dcterms:subject . - -qudt:unit a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "unit" ; - recipe:owl "ObjectProperty, ObjectSomeValuesFrom" ; - rdfs:range recipe:Unit ; - skos:definition "the unit of the quantity, e.g. grams, cups, etc." ; - skos:exactMatch qudt:unit . - -<http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_MENTIONED" . - -<http://w3id.org/ontogpt/core/RelationshipType> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "RelationshipType" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/Triple> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Triple" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/RelationshipType> ; - owl:onProperty <http://w3id.org/ontogpt/core/predicate> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/qualifier> ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - skos:definition "Abstract parent for Relation Extraction tasks" ; - linkml:attributes "{'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -<http://w3id.org/ontogpt/core/id> a owl:ObjectProperty, - linkml:SlotDefinition . - -recipe:Action a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Action" ; - recipe:annotators "sqlite:obo:dbpediaont, sqlite:obo:foodon" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -recipe:FoodType a owl:Class, - linkml:ClassDefinition ; - rdfs:label "FoodType" ; - recipe:annotators "sqlite:obo:foodon, sqlite:obo:dbpediaont" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -recipe:Ingredient a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Ingredient" ; - recipe:owl "IntersectionOf" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass recipe:Quantity ; - owl:onProperty recipe:amount ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass recipe:FoodItem ; - owl:onProperty recipe:food_item ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - skos:exactMatch FOODON:00004085 ; - linkml:attributes "{'food_item': SlotDefinition(name='food_item', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='ObjectProperty, ObjectSomeValuesFrom', extensions={}, annotations={})}, description='the food item', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='FoodItem', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'amount': SlotDefinition(name='amount', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='ObjectProperty, ObjectSomeValuesFrom', extensions={}, annotations={})}, description='the quantity of the ingredient, e.g. 2 lbs', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Quantity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -recipe:Quantity a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Quantity" ; - recipe:owl "IntersectionOf" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass recipe:Unit ; - owl:onProperty qudt:unit ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty recipe:value ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - linkml:attributes "{'value': SlotDefinition(name='value', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='DataProperty, DataHasValue', extensions={}, annotations={})}, description='the value of the quantity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'unit': SlotDefinition(name='unit', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='ObjectProperty, ObjectSomeValuesFrom', extensions={}, annotations={})}, description='the unit of the quantity, e.g. grams, cups, etc.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='qudt:unit', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Unit', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -recipe:RecipeCategory a owl:Class, - linkml:ClassDefinition ; - rdfs:label "RecipeCategory" ; - recipe:annotators "sqlite:obo:foodon, sqlite:obo:dbpediaont" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -recipe:Step a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Step" ; - recipe:owl "IntersectionOf" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom recipe:UtensilType ; - owl:onProperty RO:0002500 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass recipe:Action ; - owl:onProperty recipe:action ], - [ a owl:Restriction ; - owl:allValuesFrom recipe:FoodItem ; - owl:onProperty RO:0002233 ], - [ a owl:Restriction ; - owl:allValuesFrom recipe:FoodItem ; - owl:onProperty RO:0002234 ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - skos:exactMatch FOODON:00004087 ; - linkml:attributes "{'action': SlotDefinition(name='action', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the action taken in this step (e.g. mix, add)', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Action', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'inputs': SlotDefinition(name='inputs', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='ObjectProperty, ObjectSomeValuesFrom', extensions={}, annotations={})}, description='a semicolon separated list of the inputs of this step', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='RO:0002233', multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='FoodItem', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'outputs': SlotDefinition(name='outputs', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='ObjectProperty, ObjectSomeValuesFrom', extensions={}, annotations={})}, description='a semicolon separated list of the outputs of this step', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='RO:0002234', multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='FoodItem', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'utensils': SlotDefinition(name='utensils', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='ObjectProperty, ObjectSomeValuesFrom', extensions={}, annotations={})}, description='the kitchen utensil used in this step (e.g. pan, bowl)', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='RO:0002500', multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='UtensilType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -recipe:Unit a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Unit" ; - recipe:annotators "sqlite:obo:uo, sqlite:obo:dbpediaont, sqlite:obo:foodon" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -recipe:UtensilType a owl:Class, - linkml:ClassDefinition ; - rdfs:label "UtensilType" ; - recipe:annotators "sqlite:obo:dbpediaont, sqlite:obo:foodon" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/NullDataOptions> a owl:Class, - linkml:EnumDefinition ; - rdfs:label "NullDataOptions" ; - owl:unionOf ( <http://purl.obolibrary.org/obo/NCIT_C149701> <http://purl.obolibrary.org/obo/NCIT_C18902> <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> ) ; - linkml:permissible_values <http://purl.obolibrary.org/obo/NCIT_C149701>, - <http://purl.obolibrary.org/obo/NCIT_C18902>, - <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> . - -<http://w3id.org/ontogpt/core/Publication> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Publication" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/combined_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/abstract> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/title> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/full_text> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/Any> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Any" ; - skos:exactMatch linkml:Any ; - linkml:attributes "{}" . - -<http://w3id.org/ontogpt/core/CompoundExpression> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CompoundExpression" ; - linkml:attributes "{}" . - -recipe:FoodItem a owl:Class, - linkml:ClassDefinition ; - rdfs:label "FoodItem" ; - recipe:owl "IntersectionOf" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass recipe:FoodType ; - owl:onProperty BFO:0000051 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty recipe:state ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - linkml:attributes "{'food': SlotDefinition(name='food', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='ObjectProperty, ObjectSomeValuesFrom', extensions={}, annotations={})}, description='the food item', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='BFO:0000051', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='FoodType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'state': SlotDefinition(name='state', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='DataProperty, DataHasValue', extensions={}, annotations={})}, description='the state of the food item (e.g. chopped, diced)', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -<http://w3id.org/ontogpt/core/NamedEntity> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "NamedEntity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://example.org/UNKNOWN/rdfs/label> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:ClassDefinition a owl:Class ; - rdfs:label "class_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "class_expression" . - -linkml:SlotDefinition a owl:Class ; - rdfs:label "slot_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "slot_expression" . - - diff --git a/projects/recipe/prefixmap/recipe.yaml b/projects/recipe/prefixmap/recipe.yaml deleted file mode 100644 index 81b4e434d..000000000 --- a/projects/recipe/prefixmap/recipe.yaml +++ /dev/null @@ -1,51 +0,0 @@ -{ - "AUTO": "http://example.org/auto/", - "BFO": "http://purl.obolibrary.org/obo/BFO_", - "FOODON": "http://purl.obolibrary.org/obo/FOODON_", - "HANCESTRO": "http://purl.obolibrary.org/obo/HANCESTRO_", - "NCIT": "http://purl.obolibrary.org/obo/NCIT_", - "RO": "http://purl.obolibrary.org/obo/RO_", - "UO": "http://purl.obolibrary.org/obo/UO_", - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "dbpediaont": "http://dbpedia.org/ontology/", - "dcterms": "http://purl.org/dc/terms/", - "linkml": "https://w3id.org/linkml/", - "qudt": "http://qudt.org/schema/qudt/", - "rdf": "http://example.org/UNKNOWN/rdf/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "recipe": "http://w3id.org/ontogpt/recipe/", - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "Ingredient": { - "@id": "FOODON:00004085" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "Step": { - "@id": "FOODON:00004087" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } -} diff --git a/projects/recipe/protobuf/recipe.proto b/projects/recipe/protobuf/recipe.proto deleted file mode 100644 index 9238d8178..000000000 --- a/projects/recipe/protobuf/recipe.proto +++ /dev/null @@ -1,91 +0,0 @@ -message Action - { - string id = 0 - string label = 0 - } -message AnnotatorResult - { - string subjectText = 0 - string objectId = 0 - string objectText = 0 - } -// A result of extracting knowledge on text -message ExtractionResult - { - string inputId = 0 - string inputTitle = 0 - string inputText = 0 - string rawCompletionOutput = 0 - string prompt = 0 - any extractedObject = 0 - repeated any namedEntities = 0 - } -message FoodItem - { - foodType food = 0 - string state = 0 - } -message FoodType - { - string id = 0 - string label = 0 - } -message Ingredient - { - foodItem foodItem = 0 - quantity amount = 0 - } -message Publication - { - string id = 0 - string title = 0 - string abstract = 0 - string combinedText = 0 - string fullText = 0 - } -message Quantity - { - string value = 0 - unit unit = 0 - } -message Recipe - { - uriorcurie url = 0 - string label = 0 - string description = 0 - repeated recipeCategory categories = 0 - repeated ingredient ingredients = 0 - repeated step steps = 0 - } -message RecipeCategory - { - string id = 0 - string label = 0 - } -message RelationshipType - { - string id = 0 - string label = 0 - } -message Step - { - action action = 0 - repeated foodItem inputs = 0 - repeated foodItem outputs = 0 - repeated utensilType utensils = 0 - } -message TextWithTriples - { - publication publication = 0 - repeated triple triples = 0 - } -message Unit - { - string id = 0 - string label = 0 - } -message UtensilType - { - string id = 0 - string label = 0 - } diff --git a/projects/recipe/recipe.py b/projects/recipe/recipe.py deleted file mode 100644 index 0e868f756..000000000 --- a/projects/recipe/recipe.py +++ /dev/null @@ -1,687 +0,0 @@ -# Auto generated from recipe.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-08-07T10:56:18 -# Schema: recipe-template -# -# id: https://w3id.org/ontogpt/recipe -# description: A template for food recipes -# license: https://creativecommons.org/publicdomain/zero/1.0/ - -import dataclasses -import sys -import re -from jsonasobj2 import JsonObj, as_dict -from typing import Optional, List, Union, Dict, ClassVar, Any -from dataclasses import dataclass -from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions - -from linkml_runtime.utils.slot import Slot -from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode -from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int -from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs -from linkml_runtime.utils.formatutils import camelcase, underscore, sfx -from linkml_runtime.utils.enumerations import EnumDefinitionImpl -from rdflib import Namespace, URIRef -from linkml_runtime.utils.curienamespace import CurieNamespace -from linkml_runtime.linkml_model.types import String, Uriorcurie -from linkml_runtime.utils.metamodelcore import URIorCURIE - -metamodel_version = "1.7.0" -version = None - -# Overwrite dataclasses _init_fn to add **kwargs in __init__ -dataclasses._init_fn = dataclasses_init_fn_with_kwargs - -# Namespaces -AUTO = CurieNamespace('AUTO', 'http://example.org/auto/') -BFO = CurieNamespace('BFO', 'http://purl.obolibrary.org/obo/BFO_') -FOODON = CurieNamespace('FOODON', 'http://purl.obolibrary.org/obo/FOODON_') -HANCESTRO = CurieNamespace('HANCESTRO', 'http://purl.obolibrary.org/obo/HANCESTRO_') -NCIT = CurieNamespace('NCIT', 'http://purl.obolibrary.org/obo/NCIT_') -RO = CurieNamespace('RO', 'http://purl.obolibrary.org/obo/RO_') -UO = CurieNamespace('UO', 'http://purl.obolibrary.org/obo/UO_') -BIOLINK = CurieNamespace('biolink', 'http://example.org/UNKNOWN/biolink/') -CORE = CurieNamespace('core', 'http://w3id.org/ontogpt/core/') -DBPEDIAONT = CurieNamespace('dbpediaont', 'http://dbpedia.org/ontology/') -DCTERMS = CurieNamespace('dcterms', 'http://purl.org/dc/terms/') -LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') -QUDT = CurieNamespace('qudt', 'http://qudt.org/schema/qudt/') -RDF = CurieNamespace('rdf', 'http://example.org/UNKNOWN/rdf/') -RDFS = CurieNamespace('rdfs', 'http://example.org/UNKNOWN/rdfs/') -RECIPE = CurieNamespace('recipe', 'http://w3id.org/ontogpt/recipe/') -DEFAULT_ = RECIPE - - -# Types - -# Class references -class RecipeUrl(URIorCURIE): - pass - - -class NamedEntityId(extended_str): - pass - - -class FoodTypeId(NamedEntityId): - pass - - -class RecipeCategoryId(NamedEntityId): - pass - - -class ActionId(NamedEntityId): - pass - - -class UtensilTypeId(NamedEntityId): - pass - - -class UnitId(NamedEntityId): - pass - - -class RelationshipTypeId(NamedEntityId): - pass - - -@dataclass -class Recipe(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = RECIPE.Recipe - class_class_curie: ClassVar[str] = "recipe:Recipe" - class_name: ClassVar[str] = "Recipe" - class_model_uri: ClassVar[URIRef] = RECIPE.Recipe - - url: Union[str, RecipeUrl] = None - label: Optional[str] = None - description: Optional[str] = None - categories: Optional[Union[Union[str, RecipeCategoryId], List[Union[str, RecipeCategoryId]]]] = empty_list() - ingredients: Optional[Union[Union[dict, "Ingredient"], List[Union[dict, "Ingredient"]]]] = empty_list() - steps: Optional[Union[Union[dict, "Step"], List[Union[dict, "Step"]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.url): - self.MissingRequiredField("url") - if not isinstance(self.url, RecipeUrl): - self.url = RecipeUrl(self.url) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - if self.description is not None and not isinstance(self.description, str): - self.description = str(self.description) - - if not isinstance(self.categories, list): - self.categories = [self.categories] if self.categories is not None else [] - self.categories = [v if isinstance(v, RecipeCategoryId) else RecipeCategoryId(v) for v in self.categories] - - if not isinstance(self.ingredients, list): - self.ingredients = [self.ingredients] if self.ingredients is not None else [] - self.ingredients = [v if isinstance(v, Ingredient) else Ingredient(**as_dict(v)) for v in self.ingredients] - - if not isinstance(self.steps, list): - self.steps = [self.steps] if self.steps is not None else [] - self.steps = [v if isinstance(v, Step) else Step(**as_dict(v)) for v in self.steps] - - super().__post_init__(**kwargs) - - -Any = Any - -@dataclass -class ExtractionResult(YAMLRoot): - """ - A result of extracting knowledge on text - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.ExtractionResult - class_class_curie: ClassVar[str] = "core:ExtractionResult" - class_name: ClassVar[str] = "ExtractionResult" - class_model_uri: ClassVar[URIRef] = RECIPE.ExtractionResult - - input_id: Optional[str] = None - input_title: Optional[str] = None - input_text: Optional[str] = None - raw_completion_output: Optional[str] = None - prompt: Optional[str] = None - extracted_object: Optional[Union[dict, Any]] = None - named_entities: Optional[Union[Union[dict, Any], List[Union[dict, Any]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.input_id is not None and not isinstance(self.input_id, str): - self.input_id = str(self.input_id) - - if self.input_title is not None and not isinstance(self.input_title, str): - self.input_title = str(self.input_title) - - if self.input_text is not None and not isinstance(self.input_text, str): - self.input_text = str(self.input_text) - - if self.raw_completion_output is not None and not isinstance(self.raw_completion_output, str): - self.raw_completion_output = str(self.raw_completion_output) - - if self.prompt is not None and not isinstance(self.prompt, str): - self.prompt = str(self.prompt) - - super().__post_init__(**kwargs) - - -@dataclass -class NamedEntity(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.NamedEntity - class_class_curie: ClassVar[str] = "core:NamedEntity" - class_name: ClassVar[str] = "NamedEntity" - class_model_uri: ClassVar[URIRef] = RECIPE.NamedEntity - - id: Union[str, NamedEntityId] = None - label: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, NamedEntityId): - self.id = NamedEntityId(self.id) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - super().__post_init__(**kwargs) - - -@dataclass -class FoodType(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = RECIPE.FoodType - class_class_curie: ClassVar[str] = "recipe:FoodType" - class_name: ClassVar[str] = "FoodType" - class_model_uri: ClassVar[URIRef] = RECIPE.FoodType - - id: Union[str, FoodTypeId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, FoodTypeId): - self.id = FoodTypeId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class RecipeCategory(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = RECIPE.RecipeCategory - class_class_curie: ClassVar[str] = "recipe:RecipeCategory" - class_name: ClassVar[str] = "RecipeCategory" - class_model_uri: ClassVar[URIRef] = RECIPE.RecipeCategory - - id: Union[str, RecipeCategoryId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, RecipeCategoryId): - self.id = RecipeCategoryId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Action(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = RECIPE.Action - class_class_curie: ClassVar[str] = "recipe:Action" - class_name: ClassVar[str] = "Action" - class_model_uri: ClassVar[URIRef] = RECIPE.Action - - id: Union[str, ActionId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, ActionId): - self.id = ActionId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class UtensilType(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = RECIPE.UtensilType - class_class_curie: ClassVar[str] = "recipe:UtensilType" - class_name: ClassVar[str] = "UtensilType" - class_model_uri: ClassVar[URIRef] = RECIPE.UtensilType - - id: Union[str, UtensilTypeId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, UtensilTypeId): - self.id = UtensilTypeId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Unit(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = RECIPE.Unit - class_class_curie: ClassVar[str] = "recipe:Unit" - class_name: ClassVar[str] = "Unit" - class_model_uri: ClassVar[URIRef] = RECIPE.Unit - - id: Union[str, UnitId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, UnitId): - self.id = UnitId(self.id) - - super().__post_init__(**kwargs) - - -class CompoundExpression(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.CompoundExpression - class_class_curie: ClassVar[str] = "core:CompoundExpression" - class_name: ClassVar[str] = "CompoundExpression" - class_model_uri: ClassVar[URIRef] = RECIPE.CompoundExpression - - -@dataclass -class Ingredient(CompoundExpression): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = FOODON["00004085"] - class_class_curie: ClassVar[str] = "FOODON:00004085" - class_name: ClassVar[str] = "Ingredient" - class_model_uri: ClassVar[URIRef] = RECIPE.Ingredient - - food_item: Optional[Union[dict, "FoodItem"]] = None - amount: Optional[Union[dict, "Quantity"]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.food_item is not None and not isinstance(self.food_item, FoodItem): - self.food_item = FoodItem(**as_dict(self.food_item)) - - if self.amount is not None and not isinstance(self.amount, Quantity): - self.amount = Quantity(**as_dict(self.amount)) - - super().__post_init__(**kwargs) - - -@dataclass -class Quantity(CompoundExpression): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = RECIPE.Quantity - class_class_curie: ClassVar[str] = "recipe:Quantity" - class_name: ClassVar[str] = "Quantity" - class_model_uri: ClassVar[URIRef] = RECIPE.Quantity - - value: Optional[str] = None - unit: Optional[Union[str, UnitId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.value is not None and not isinstance(self.value, str): - self.value = str(self.value) - - if self.unit is not None and not isinstance(self.unit, UnitId): - self.unit = UnitId(self.unit) - - super().__post_init__(**kwargs) - - -@dataclass -class Step(CompoundExpression): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = FOODON["00004087"] - class_class_curie: ClassVar[str] = "FOODON:00004087" - class_name: ClassVar[str] = "Step" - class_model_uri: ClassVar[URIRef] = RECIPE.Step - - action: Optional[Union[str, ActionId]] = None - inputs: Optional[Union[Union[dict, "FoodItem"], List[Union[dict, "FoodItem"]]]] = empty_list() - outputs: Optional[Union[Union[dict, "FoodItem"], List[Union[dict, "FoodItem"]]]] = empty_list() - utensils: Optional[Union[Union[str, UtensilTypeId], List[Union[str, UtensilTypeId]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.action is not None and not isinstance(self.action, ActionId): - self.action = ActionId(self.action) - - if not isinstance(self.inputs, list): - self.inputs = [self.inputs] if self.inputs is not None else [] - self.inputs = [v if isinstance(v, FoodItem) else FoodItem(**as_dict(v)) for v in self.inputs] - - if not isinstance(self.outputs, list): - self.outputs = [self.outputs] if self.outputs is not None else [] - self.outputs = [v if isinstance(v, FoodItem) else FoodItem(**as_dict(v)) for v in self.outputs] - - if not isinstance(self.utensils, list): - self.utensils = [self.utensils] if self.utensils is not None else [] - self.utensils = [v if isinstance(v, UtensilTypeId) else UtensilTypeId(v) for v in self.utensils] - - super().__post_init__(**kwargs) - - -@dataclass -class FoodItem(CompoundExpression): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = RECIPE.FoodItem - class_class_curie: ClassVar[str] = "recipe:FoodItem" - class_name: ClassVar[str] = "FoodItem" - class_model_uri: ClassVar[URIRef] = RECIPE.FoodItem - - food: Optional[Union[str, FoodTypeId]] = None - state: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.food is not None and not isinstance(self.food, FoodTypeId): - self.food = FoodTypeId(self.food) - - if self.state is not None and not isinstance(self.state, str): - self.state = str(self.state) - - super().__post_init__(**kwargs) - - -@dataclass -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Triple - class_class_curie: ClassVar[str] = "core:Triple" - class_name: ClassVar[str] = "Triple" - class_model_uri: ClassVar[URIRef] = RECIPE.Triple - - subject: Optional[Union[str, NamedEntityId]] = None - predicate: Optional[Union[str, RelationshipTypeId]] = None - object: Optional[Union[str, NamedEntityId]] = None - qualifier: Optional[str] = None - subject_qualifier: Optional[Union[str, NamedEntityId]] = None - object_qualifier: Optional[Union[str, NamedEntityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, NamedEntityId): - self.subject = NamedEntityId(self.subject) - - if self.predicate is not None and not isinstance(self.predicate, RelationshipTypeId): - self.predicate = RelationshipTypeId(self.predicate) - - if self.object is not None and not isinstance(self.object, NamedEntityId): - self.object = NamedEntityId(self.object) - - if self.qualifier is not None and not isinstance(self.qualifier, str): - self.qualifier = str(self.qualifier) - - if self.subject_qualifier is not None and not isinstance(self.subject_qualifier, NamedEntityId): - self.subject_qualifier = NamedEntityId(self.subject_qualifier) - - if self.object_qualifier is not None and not isinstance(self.object_qualifier, NamedEntityId): - self.object_qualifier = NamedEntityId(self.object_qualifier) - - super().__post_init__(**kwargs) - - -@dataclass -class TextWithTriples(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.TextWithTriples - class_class_curie: ClassVar[str] = "core:TextWithTriples" - class_name: ClassVar[str] = "TextWithTriples" - class_model_uri: ClassVar[URIRef] = RECIPE.TextWithTriples - - publication: Optional[Union[dict, "Publication"]] = None - triples: Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.publication is not None and not isinstance(self.publication, Publication): - self.publication = Publication(**as_dict(self.publication)) - - if not isinstance(self.triples, list): - self.triples = [self.triples] if self.triples is not None else [] - self.triples = [v if isinstance(v, Triple) else Triple(**as_dict(v)) for v in self.triples] - - super().__post_init__(**kwargs) - - -@dataclass -class RelationshipType(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.RelationshipType - class_class_curie: ClassVar[str] = "core:RelationshipType" - class_name: ClassVar[str] = "RelationshipType" - class_model_uri: ClassVar[URIRef] = RECIPE.RelationshipType - - id: Union[str, RelationshipTypeId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, RelationshipTypeId): - self.id = RelationshipTypeId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Publication(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Publication - class_class_curie: ClassVar[str] = "core:Publication" - class_name: ClassVar[str] = "Publication" - class_model_uri: ClassVar[URIRef] = RECIPE.Publication - - id: Optional[str] = None - title: Optional[str] = None - abstract: Optional[str] = None - combined_text: Optional[str] = None - full_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.id is not None and not isinstance(self.id, str): - self.id = str(self.id) - - if self.title is not None and not isinstance(self.title, str): - self.title = str(self.title) - - if self.abstract is not None and not isinstance(self.abstract, str): - self.abstract = str(self.abstract) - - if self.combined_text is not None and not isinstance(self.combined_text, str): - self.combined_text = str(self.combined_text) - - if self.full_text is not None and not isinstance(self.full_text, str): - self.full_text = str(self.full_text) - - super().__post_init__(**kwargs) - - -@dataclass -class AnnotatorResult(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.AnnotatorResult - class_class_curie: ClassVar[str] = "core:AnnotatorResult" - class_name: ClassVar[str] = "AnnotatorResult" - class_model_uri: ClassVar[URIRef] = RECIPE.AnnotatorResult - - subject_text: Optional[str] = None - object_id: Optional[str] = None - object_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject_text is not None and not isinstance(self.subject_text, str): - self.subject_text = str(self.subject_text) - - if self.object_id is not None and not isinstance(self.object_id, str): - self.object_id = str(self.object_id) - - if self.object_text is not None and not isinstance(self.object_text, str): - self.object_text = str(self.object_text) - - super().__post_init__(**kwargs) - - -# Enumerations -class NullDataOptions(EnumDefinitionImpl): - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = PermissibleValue(text="UNSPECIFIED_METHOD_OF_ADMINISTRATION", - meaning=NCIT.C149701) - NOT_APPLICABLE = PermissibleValue(text="NOT_APPLICABLE", - meaning=NCIT.C18902) - NOT_MENTIONED = PermissibleValue(text="NOT_MENTIONED") - - _defn = EnumDefinition( - name="NullDataOptions", - ) - -# Slots -class slots: - pass - -slots.recipe__url = Slot(uri=RDF.Resource, name="recipe__url", curie=RDF.curie('Resource'), - model_uri=RECIPE.recipe__url, domain=None, range=URIRef) - -slots.recipe__label = Slot(uri=RDFS.label, name="recipe__label", curie=RDFS.curie('label'), - model_uri=RECIPE.recipe__label, domain=None, range=Optional[str]) - -slots.recipe__description = Slot(uri=DCTERMS.description, name="recipe__description", curie=DCTERMS.curie('description'), - model_uri=RECIPE.recipe__description, domain=None, range=Optional[str]) - -slots.recipe__categories = Slot(uri=DCTERMS.subject, name="recipe__categories", curie=DCTERMS.curie('subject'), - model_uri=RECIPE.recipe__categories, domain=None, range=Optional[Union[Union[str, RecipeCategoryId], List[Union[str, RecipeCategoryId]]]]) - -slots.recipe__ingredients = Slot(uri=FOODON['00002420'], name="recipe__ingredients", curie=FOODON.curie('00002420'), - model_uri=RECIPE.recipe__ingredients, domain=None, range=Optional[Union[Union[dict, Ingredient], List[Union[dict, Ingredient]]]]) - -slots.recipe__steps = Slot(uri=RECIPE.steps, name="recipe__steps", curie=RECIPE.curie('steps'), - model_uri=RECIPE.recipe__steps, domain=None, range=Optional[Union[Union[dict, Step], List[Union[dict, Step]]]]) - -slots.ingredient__food_item = Slot(uri=RECIPE.food_item, name="ingredient__food_item", curie=RECIPE.curie('food_item'), - model_uri=RECIPE.ingredient__food_item, domain=None, range=Optional[Union[dict, FoodItem]]) - -slots.ingredient__amount = Slot(uri=RECIPE.amount, name="ingredient__amount", curie=RECIPE.curie('amount'), - model_uri=RECIPE.ingredient__amount, domain=None, range=Optional[Union[dict, Quantity]]) - -slots.quantity__value = Slot(uri=RECIPE.value, name="quantity__value", curie=RECIPE.curie('value'), - model_uri=RECIPE.quantity__value, domain=None, range=Optional[str]) - -slots.quantity__unit = Slot(uri=QUDT.unit, name="quantity__unit", curie=QUDT.curie('unit'), - model_uri=RECIPE.quantity__unit, domain=None, range=Optional[Union[str, UnitId]]) - -slots.step__action = Slot(uri=RECIPE.action, name="step__action", curie=RECIPE.curie('action'), - model_uri=RECIPE.step__action, domain=None, range=Optional[Union[str, ActionId]]) - -slots.step__inputs = Slot(uri=RO['0002233'], name="step__inputs", curie=RO.curie('0002233'), - model_uri=RECIPE.step__inputs, domain=None, range=Optional[Union[Union[dict, FoodItem], List[Union[dict, FoodItem]]]]) - -slots.step__outputs = Slot(uri=RO['0002234'], name="step__outputs", curie=RO.curie('0002234'), - model_uri=RECIPE.step__outputs, domain=None, range=Optional[Union[Union[dict, FoodItem], List[Union[dict, FoodItem]]]]) - -slots.step__utensils = Slot(uri=RO['0002500'], name="step__utensils", curie=RO.curie('0002500'), - model_uri=RECIPE.step__utensils, domain=None, range=Optional[Union[Union[str, UtensilTypeId], List[Union[str, UtensilTypeId]]]]) - -slots.foodItem__food = Slot(uri=BFO['0000051'], name="foodItem__food", curie=BFO.curie('0000051'), - model_uri=RECIPE.foodItem__food, domain=None, range=Optional[Union[str, FoodTypeId]]) - -slots.foodItem__state = Slot(uri=RECIPE.state, name="foodItem__state", curie=RECIPE.curie('state'), - model_uri=RECIPE.foodItem__state, domain=None, range=Optional[str]) - -slots.extractionResult__input_id = Slot(uri=CORE.input_id, name="extractionResult__input_id", curie=CORE.curie('input_id'), - model_uri=RECIPE.extractionResult__input_id, domain=None, range=Optional[str]) - -slots.extractionResult__input_title = Slot(uri=CORE.input_title, name="extractionResult__input_title", curie=CORE.curie('input_title'), - model_uri=RECIPE.extractionResult__input_title, domain=None, range=Optional[str]) - -slots.extractionResult__input_text = Slot(uri=CORE.input_text, name="extractionResult__input_text", curie=CORE.curie('input_text'), - model_uri=RECIPE.extractionResult__input_text, domain=None, range=Optional[str]) - -slots.extractionResult__raw_completion_output = Slot(uri=CORE.raw_completion_output, name="extractionResult__raw_completion_output", curie=CORE.curie('raw_completion_output'), - model_uri=RECIPE.extractionResult__raw_completion_output, domain=None, range=Optional[str]) - -slots.extractionResult__prompt = Slot(uri=CORE.prompt, name="extractionResult__prompt", curie=CORE.curie('prompt'), - model_uri=RECIPE.extractionResult__prompt, domain=None, range=Optional[str]) - -slots.extractionResult__extracted_object = Slot(uri=CORE.extracted_object, name="extractionResult__extracted_object", curie=CORE.curie('extracted_object'), - model_uri=RECIPE.extractionResult__extracted_object, domain=None, range=Optional[Union[dict, Any]]) - -slots.extractionResult__named_entities = Slot(uri=CORE.named_entities, name="extractionResult__named_entities", curie=CORE.curie('named_entities'), - model_uri=RECIPE.extractionResult__named_entities, domain=None, range=Optional[Union[Union[dict, Any], List[Union[dict, Any]]]]) - -slots.namedEntity__id = Slot(uri=CORE.id, name="namedEntity__id", curie=CORE.curie('id'), - model_uri=RECIPE.namedEntity__id, domain=None, range=URIRef) - -slots.namedEntity__label = Slot(uri=RDFS.label, name="namedEntity__label", curie=RDFS.curie('label'), - model_uri=RECIPE.namedEntity__label, domain=None, range=Optional[str]) - -slots.triple__subject = Slot(uri=CORE.subject, name="triple__subject", curie=CORE.curie('subject'), - model_uri=RECIPE.triple__subject, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__predicate = Slot(uri=CORE.predicate, name="triple__predicate", curie=CORE.curie('predicate'), - model_uri=RECIPE.triple__predicate, domain=None, range=Optional[Union[str, RelationshipTypeId]]) - -slots.triple__object = Slot(uri=CORE.object, name="triple__object", curie=CORE.curie('object'), - model_uri=RECIPE.triple__object, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__qualifier = Slot(uri=CORE.qualifier, name="triple__qualifier", curie=CORE.curie('qualifier'), - model_uri=RECIPE.triple__qualifier, domain=None, range=Optional[str]) - -slots.triple__subject_qualifier = Slot(uri=CORE.subject_qualifier, name="triple__subject_qualifier", curie=CORE.curie('subject_qualifier'), - model_uri=RECIPE.triple__subject_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__object_qualifier = Slot(uri=CORE.object_qualifier, name="triple__object_qualifier", curie=CORE.curie('object_qualifier'), - model_uri=RECIPE.triple__object_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.textWithTriples__publication = Slot(uri=CORE.publication, name="textWithTriples__publication", curie=CORE.curie('publication'), - model_uri=RECIPE.textWithTriples__publication, domain=None, range=Optional[Union[dict, Publication]]) - -slots.textWithTriples__triples = Slot(uri=CORE.triples, name="textWithTriples__triples", curie=CORE.curie('triples'), - model_uri=RECIPE.textWithTriples__triples, domain=None, range=Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]]) - -slots.publication__id = Slot(uri=CORE.id, name="publication__id", curie=CORE.curie('id'), - model_uri=RECIPE.publication__id, domain=None, range=Optional[str]) - -slots.publication__title = Slot(uri=CORE.title, name="publication__title", curie=CORE.curie('title'), - model_uri=RECIPE.publication__title, domain=None, range=Optional[str]) - -slots.publication__abstract = Slot(uri=CORE.abstract, name="publication__abstract", curie=CORE.curie('abstract'), - model_uri=RECIPE.publication__abstract, domain=None, range=Optional[str]) - -slots.publication__combined_text = Slot(uri=CORE.combined_text, name="publication__combined_text", curie=CORE.curie('combined_text'), - model_uri=RECIPE.publication__combined_text, domain=None, range=Optional[str]) - -slots.publication__full_text = Slot(uri=CORE.full_text, name="publication__full_text", curie=CORE.curie('full_text'), - model_uri=RECIPE.publication__full_text, domain=None, range=Optional[str]) - -slots.annotatorResult__subject_text = Slot(uri=CORE.subject_text, name="annotatorResult__subject_text", curie=CORE.curie('subject_text'), - model_uri=RECIPE.annotatorResult__subject_text, domain=None, range=Optional[str]) - -slots.annotatorResult__object_id = Slot(uri=CORE.object_id, name="annotatorResult__object_id", curie=CORE.curie('object_id'), - model_uri=RECIPE.annotatorResult__object_id, domain=None, range=Optional[str]) - -slots.annotatorResult__object_text = Slot(uri=CORE.object_text, name="annotatorResult__object_text", curie=CORE.curie('object_text'), - model_uri=RECIPE.annotatorResult__object_text, domain=None, range=Optional[str]) \ No newline at end of file diff --git a/projects/recipe/shacl/recipe.shacl.ttl b/projects/recipe/shacl/recipe.shacl.ttl deleted file mode 100644 index bdf47cb6d..000000000 --- a/projects/recipe/shacl/recipe.shacl.ttl +++ /dev/null @@ -1,343 +0,0 @@ -@prefix BFO: <http://purl.obolibrary.org/obo/BFO_> . -@prefix FOODON: <http://purl.obolibrary.org/obo/FOODON_> . -@prefix RO: <http://purl.obolibrary.org/obo/RO_> . -@prefix dcterms: <http://purl.org/dc/terms/> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix qudt: <http://qudt.org/schema/qudt/> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix recipe: <http://w3id.org/ontogpt/recipe/> . -@prefix sh: <http://www.w3.org/ns/shacl#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject_text> ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/object_id> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object_text> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/AnnotatorResult> . - -<http://w3id.org/ontogpt/core/CompoundExpression> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass <http://w3id.org/ontogpt/core/CompoundExpression> . - -<http://w3id.org/ontogpt/core/ExtractionResult> a sh:NodeShape ; - sh:closed true ; - sh:description "A result of extracting knowledge on text" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/input_id> ], - [ sh:class linkml:Any ; - sh:description "Named entities extracted from the text" ; - sh:nodeKind sh:BlankNode ; - sh:order 6 ; - sh:path <http://w3id.org/ontogpt/core/named_entities> ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/input_title> ], - [ sh:class linkml:Any ; - sh:description "The complex objects extracted from the text" ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/extracted_object> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/input_text> ], - [ sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/prompt> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/ExtractionResult> . - -<http://w3id.org/ontogpt/core/TextWithTriples> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/Triple> ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/triples> ], - [ sh:class <http://w3id.org/ontogpt/core/Publication> ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/publication> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/TextWithTriples> . - -recipe:Recipe a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "the name of the recipe" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:class recipe:RecipeCategory ; - sh:description "a semicolon separated list of the categories to which this recipe belongs" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path dcterms:subject ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <rdf:Resource> ], - [ sh:class FOODON:00004085 ; - sh:description "a semicolon separated list of the ingredients plus quantities of the recipe" ; - sh:nodeKind sh:BlankNode ; - sh:order 4 ; - sh:path FOODON:00002420 ], - [ sh:class FOODON:00004087 ; - sh:description "a semicolon separated list of the individual steps involved in this recipe" ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path recipe:steps ], - [ sh:description "a brief textual description of the recipe" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path dcterms:description ] ; - sh:targetClass recipe:Recipe . - -FOODON:00004085 a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class recipe:FoodItem ; - sh:description "the food item" ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path recipe:food_item ], - [ sh:class recipe:Quantity ; - sh:description "the quantity of the ingredient, e.g. 2 lbs" ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path recipe:amount ] ; - sh:targetClass FOODON:00004085 . - -FOODON:00004087 a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class recipe:Action ; - sh:description "the action taken in this step (e.g. mix, add)" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path recipe:action ], - [ sh:class recipe:FoodItem ; - sh:description "a semicolon separated list of the inputs of this step" ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path RO:0002233 ], - [ sh:class recipe:UtensilType ; - sh:description "the kitchen utensil used in this step (e.g. pan, bowl)" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path RO:0002500 ], - [ sh:class recipe:FoodItem ; - sh:description "a semicolon separated list of the outputs of this step" ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path RO:0002234 ] ; - sh:targetClass FOODON:00004087 . - -<http://w3id.org/ontogpt/core/Publication> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The full text of the publication" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/full_text> ], - [ sh:description "The title of the publication" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/title> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/combined_text> ], - [ sh:description "The abstract of the publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/abstract> ], - [ sh:description "The publication identifier" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/RelationshipType> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/Triple> a sh:NodeShape ; - sh:closed false ; - sh:description "Abstract parent for Relation Extraction tasks" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject> ], - [ sh:description "A qualifier for the statements, e.g. \"NOT\" for negation" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/object_qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/RelationshipType> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/predicate> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Triple> . - -recipe:Action a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass recipe:Action . - -recipe:FoodType a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass recipe:FoodType . - -recipe:Quantity a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class recipe:Unit ; - sh:description "the unit of the quantity, e.g. grams, cups, etc." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path qudt:unit ], - [ sh:description "the value of the quantity" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path recipe:value ] ; - sh:targetClass recipe:Quantity . - -recipe:RecipeCategory a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass recipe:RecipeCategory . - -recipe:Unit a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass recipe:Unit . - -recipe:UtensilType a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass recipe:UtensilType . - -linkml:Any a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass linkml:Any . - -recipe:FoodItem a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class recipe:FoodType ; - sh:description "the food item" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path BFO:0000051 ], - [ sh:description "the state of the food item (e.g. chopped, diced)" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path recipe:state ] ; - sh:targetClass recipe:FoodItem . - -<http://w3id.org/ontogpt/core/NamedEntity> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/NamedEntity> . - diff --git a/projects/recipe/shex/recipe.shex b/projects/recipe/shex/recipe.shex deleted file mode 100644 index 1eedc7b1c..000000000 --- a/projects/recipe/shex/recipe.shex +++ /dev/null @@ -1,231 +0,0 @@ -BASE <http://w3id.org/ontogpt/recipe/> -PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> -PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> -PREFIX linkml: <https://w3id.org/linkml/> -PREFIX dcterms: <http://purl.org/dc/terms/> -PREFIX qudt: <http://qudt.org/schema/qudt/> -PREFIX core: <http://w3id.org/ontogpt/core/> -PREFIX rdfs1: <http://example.org/UNKNOWN/rdfs/> - - -linkml:String xsd:string - -linkml:Integer xsd:integer - -linkml:Boolean xsd:boolean - -linkml:Float xsd:float - -linkml:Double xsd:double - -linkml:Decimal xsd:decimal - -linkml:Time xsd:time - -linkml:Date xsd:date - -linkml:Datetime xsd:dateTime - -linkml:DateOrDatetime linkml:DateOrDatetime - -linkml:Uriorcurie IRI - -linkml:Curie xsd:string - -linkml:Uri IRI - -linkml:Ncname xsd:string - -linkml:Objectidentifier IRI - -linkml:Nodeidentifier NONLITERAL - -linkml:Jsonpointer xsd:string - -linkml:Jsonpath xsd:string - -linkml:Sparqlpath xsd:string - -<Action> CLOSED { - ( $<Action_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Action> ] - ) -} - -core:AnnotatorResult CLOSED { - ( $core:AnnotatorResult_tes ( core:subject_text @linkml:String ? ; - core:object_id @linkml:String ? ; - core:object_text @linkml:String ? - ) ; - rdf:type [ core:AnnotatorResult ] ? - ) -} - -core:Any CLOSED { - ( $core:Any_tes rdf:type . * ; - rdf:type [ linkml:Any ] ? - ) -} - -core:CompoundExpression ( - @<FoodItem> OR @<Ingredient> OR @<Quantity> OR @<Step> OR @core:Triple -) - -core:CompoundExpression_struct { - ( $core:CompoundExpression_tes rdf:type . * ; - rdf:type [ core:CompoundExpression ] ? - ) -} - -core:ExtractionResult CLOSED { - ( $core:ExtractionResult_tes ( core:input_id @linkml:String ? ; - core:input_title @linkml:String ? ; - core:input_text @linkml:String ? ; - core:raw_completion_output @linkml:String ? ; - core:prompt @linkml:String ? ; - core:extracted_object @core:Any ? ; - core:named_entities @core:Any * - ) ; - rdf:type [ core:ExtractionResult ] ? - ) -} - -<FoodItem> CLOSED { - ( $<FoodItem_tes> ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - <http://purl.obolibrary.org/obo/BFO_0000051> @<FoodType> ? ; - <state> @linkml:String ? - ) ; - rdf:type [ <FoodItem> ] ? - ) -} - -<FoodType> CLOSED { - ( $<FoodType_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <FoodType> ] - ) -} - -<Ingredient> CLOSED { - ( $<Ingredient_tes> ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - <food_item> @<FoodItem> ? ; - <amount> @<Quantity> ? - ) ; - rdf:type [ <http://purl.obolibrary.org/obo/FOODON_00004085> ] ? - ) -} - -core:NamedEntity ( - @<Action> OR @<FoodType> OR @<RecipeCategory> OR @core:RelationshipType OR @<Unit> OR @<UtensilType> -) - -core:NamedEntity_struct { - ( $core:NamedEntity_tes rdfs1:label @linkml:String ? ; - rdf:type [ core:NamedEntity ] - ) -} - -core:Publication CLOSED { - ( $core:Publication_tes ( core:id @linkml:String ? ; - core:title @linkml:String ? ; - core:abstract @linkml:String ? ; - core:combined_text @linkml:String ? ; - core:full_text @linkml:String ? - ) ; - rdf:type [ core:Publication ] ? - ) -} - -<Quantity> CLOSED { - ( $<Quantity_tes> ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - <value> @linkml:String ? ; - qudt:unit @<Unit> ? - ) ; - rdf:type [ <Quantity> ] ? - ) -} - -<Recipe> CLOSED { - ( $<Recipe_tes> ( rdfs1:label @linkml:String ? ; - dcterms:description @linkml:String ? ; - dcterms:subject @<RecipeCategory> * ; - <http://purl.obolibrary.org/obo/FOODON_00002420> @<Ingredient> * ; - <steps> @<Step> * - ) ; - rdf:type [ <Recipe> ] - ) -} - -<RecipeCategory> CLOSED { - ( $<RecipeCategory_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <RecipeCategory> ] - ) -} - -core:RelationshipType CLOSED { - ( $core:RelationshipType_tes ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ core:RelationshipType ] - ) -} - -<Step> CLOSED { - ( $<Step_tes> ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - <action> @<Action> ? ; - <http://purl.obolibrary.org/obo/RO_0002233> @<FoodItem> * ; - <http://purl.obolibrary.org/obo/RO_0002234> @<FoodItem> * ; - <http://purl.obolibrary.org/obo/RO_0002500> @<UtensilType> * - ) ; - rdf:type [ <http://purl.obolibrary.org/obo/FOODON_00004087> ] ? - ) -} - -core:TextWithTriples CLOSED { - ( $core:TextWithTriples_tes ( core:publication @core:Publication ? ; - core:triples @core:Triple * - ) ; - rdf:type [ core:TextWithTriples ] ? - ) -} - -core:Triple { - ( $core:Triple_tes ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - core:subject @core:NamedEntity ? ; - core:predicate @core:RelationshipType ? ; - core:object @core:NamedEntity ? ; - core:qualifier @linkml:String ? ; - core:subject_qualifier @core:NamedEntity ? ; - core:object_qualifier @core:NamedEntity ? - ) ; - rdf:type [ core:Triple ] ? - ) -} - -<Unit> CLOSED { - ( $<Unit_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Unit> ] - ) -} - -<UtensilType> CLOSED { - ( $<UtensilType_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <UtensilType> ] - ) -} - - diff --git a/projects/recipe/sqlschema/recipe.sql b/projects/recipe/sqlschema/recipe.sql deleted file mode 100644 index 0219330df..000000000 --- a/projects/recipe/sqlschema/recipe.sql +++ /dev/null @@ -1,112 +0,0 @@ - - -CREATE TABLE "Action" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "AnnotatorResult" ( - subject_text TEXT, - object_id TEXT, - object_text TEXT, - PRIMARY KEY (subject_text, object_id, object_text) -); - -CREATE TABLE "ExtractionResult" ( - input_id TEXT, - input_title TEXT, - input_text TEXT, - raw_completion_output TEXT, - prompt TEXT, - extracted_object TEXT, - named_entities TEXT, - PRIMARY KEY (input_id, input_title, input_text, raw_completion_output, prompt, extracted_object, named_entities) -); - -CREATE TABLE "FoodType" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Publication" ( - id TEXT, - title TEXT, - abstract TEXT, - combined_text TEXT, - full_text TEXT, - PRIMARY KEY (id, title, abstract, combined_text, full_text) -); - -CREATE TABLE "Recipe" ( - url TEXT NOT NULL, - label TEXT, - description TEXT, - PRIMARY KEY (url) -); - -CREATE TABLE "RelationshipType" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "TextWithTriples" ( - publication TEXT, - triples TEXT, - PRIMARY KEY (publication, triples) -); - -CREATE TABLE "Unit" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "UtensilType" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "FoodItem" ( - food TEXT, - state TEXT, - PRIMARY KEY (food, state), - FOREIGN KEY(food) REFERENCES "FoodType" (id) -); - -CREATE TABLE "Ingredient" ( - food_item TEXT, - amount TEXT, - "Recipe_url" TEXT, - PRIMARY KEY (food_item, amount, "Recipe_url"), - FOREIGN KEY("Recipe_url") REFERENCES "Recipe" (url) -); - -CREATE TABLE "Quantity" ( - value TEXT, - unit TEXT, - PRIMARY KEY (value, unit), - FOREIGN KEY(unit) REFERENCES "Unit" (id) -); - -CREATE TABLE "RecipeCategory" ( - id TEXT NOT NULL, - label TEXT, - "Recipe_url" TEXT, - PRIMARY KEY (id), - FOREIGN KEY("Recipe_url") REFERENCES "Recipe" (url) -); - -CREATE TABLE "Step" ( - action TEXT, - inputs TEXT, - outputs TEXT, - utensils TEXT, - "Recipe_url" TEXT, - PRIMARY KEY (action, inputs, outputs, utensils, "Recipe_url"), - FOREIGN KEY(action) REFERENCES "Action" (id), - FOREIGN KEY("Recipe_url") REFERENCES "Recipe" (url) -); diff --git a/projects/traits/docs/AnnotatorResult.md b/projects/traits/docs/AnnotatorResult.md deleted file mode 100644 index e10c9d367..000000000 --- a/projects/traits/docs/AnnotatorResult.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Class: AnnotatorResult - - - - -URI: [traits:AnnotatorResult](http://w3id.org/ontogpt/traits/AnnotatorResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F])](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F]) - -## Attributes - - -### Own - - * [➞subject_text](annotatorResult__subject_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_id](annotatorResult__object_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_text](annotatorResult__object_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) diff --git a/projects/traits/docs/Any.md b/projects/traits/docs/Any.md deleted file mode 100644 index 4a2c73eee..000000000 --- a/projects/traits/docs/Any.md +++ /dev/null @@ -1,25 +0,0 @@ - -# Class: Any - - - - -URI: [traits:Any](http://w3id.org/ontogpt/traits/Any) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult])](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult]) - -## Referenced by Class - - * **None** *[➞extracted_object](extractionResult__extracted_object.md)* <sub>0..1</sub> **[Any](Any.md)** - * **None** *[➞named_entities](extractionResult__named_entities.md)* <sub>0..\*</sub> **[Any](Any.md)** - -## Attributes - - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | linkml:Any | - diff --git a/projects/traits/docs/CompoundExpression.md b/projects/traits/docs/CompoundExpression.md deleted file mode 100644 index bb651e01c..000000000 --- a/projects/traits/docs/CompoundExpression.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: CompoundExpression - - - - -URI: [traits:CompoundExpression](http://w3id.org/ontogpt/traits/CompoundExpression) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[CompoundExpression]^-[Triple])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[CompoundExpression]^-[Triple]) - -## Children - - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - -## Referenced by Class - - -## Attributes - diff --git a/projects/traits/docs/ExtractionResult.md b/projects/traits/docs/ExtractionResult.md deleted file mode 100644 index 317422990..000000000 --- a/projects/traits/docs/ExtractionResult.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Class: ExtractionResult - - -A result of extracting knowledge on text - -URI: [traits:ExtractionResult](http://w3id.org/ontogpt/traits/ExtractionResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any])](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any]) - -## Attributes - - -### Own - - * [➞input_id](extractionResult__input_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_title](extractionResult__input_title.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_text](extractionResult__input_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞prompt](extractionResult__prompt.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞extracted_object](extractionResult__extracted_object.md) <sub>0..1</sub> - * Description: The complex objects extracted from the text - * Range: [Any](Any.md) - * [➞named_entities](extractionResult__named_entities.md) <sub>0..\*</sub> - * Description: Named entities extracted from the text - * Range: [Any](Any.md) diff --git a/projects/traits/docs/NamedEntity.md b/projects/traits/docs/NamedEntity.md deleted file mode 100644 index 15f13f911..000000000 --- a/projects/traits/docs/NamedEntity.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: NamedEntity - - - - -URI: [traits:NamedEntity](http://w3id.org/ontogpt/traits/NamedEntity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Trait],[RelationshipType],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[Trait],[NamedEntity]^-[RelationshipType],[Triple])](https://yuml.me/diagram/nofunky;dir:TB/class/[Trait],[RelationshipType],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[Trait],[NamedEntity]^-[RelationshipType],[Triple]) - -## Children - - * [RelationshipType](RelationshipType.md) - * [Trait](Trait.md) - -## Referenced by Class - - * **None** *[➞object](triple__object.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞object_qualifier](triple__object_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject](triple__subject.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject_qualifier](triple__subject_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - -## Attributes - - -### Own - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/traits/docs/NullDataOptions.md b/projects/traits/docs/NullDataOptions.md deleted file mode 100644 index cb9a038f3..000000000 --- a/projects/traits/docs/NullDataOptions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Enum: NullDataOptions - - - - -URI: [traits:NullDataOptions](http://w3id.org/ontogpt/traits/NullDataOptions) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | -| UNSPECIFIED_METHOD_OF_ADMINISTRATION | | NCIT:C149701 | | -| NOT_APPLICABLE | | NCIT:C18902 | {'aliases': ['not applicable', 'N/A']} | -| NOT_MENTIONED | | | | - diff --git a/projects/traits/docs/Publication.md b/projects/traits/docs/Publication.md deleted file mode 100644 index 7299f4469..000000000 --- a/projects/traits/docs/Publication.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Publication - - - - -URI: [traits:Publication](http://w3id.org/ontogpt/traits/Publication) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples])](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples]) - -## Referenced by Class - - * **None** *[➞publication](textWithTriples__publication.md)* <sub>0..1</sub> **[Publication](Publication.md)** - -## Attributes - - -### Own - - * [➞id](publication__id.md) <sub>0..1</sub> - * Description: The publication identifier - * Range: [String](types/String.md) - * [➞title](publication__title.md) <sub>0..1</sub> - * Description: The title of the publication - * Range: [String](types/String.md) - * [➞abstract](publication__abstract.md) <sub>0..1</sub> - * Description: The abstract of the publication - * Range: [String](types/String.md) - * [➞combined_text](publication__combined_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞full_text](publication__full_text.md) <sub>0..1</sub> - * Description: The full text of the publication - * Range: [String](types/String.md) diff --git a/projects/traits/docs/RelationshipType.md b/projects/traits/docs/RelationshipType.md deleted file mode 100644 index 22477ca9b..000000000 --- a/projects/traits/docs/RelationshipType.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: RelationshipType - - - - -URI: [traits:RelationshipType](http://w3id.org/ontogpt/traits/RelationshipType) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity]) - -## Identifier prefixes - - * RO - * biolink - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞predicate](triple__predicate.md)* <sub>0..1</sub> **[RelationshipType](RelationshipType.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/traits/docs/Taxon.md b/projects/traits/docs/Taxon.md deleted file mode 100644 index 682670fd6..000000000 --- a/projects/traits/docs/Taxon.md +++ /dev/null @@ -1,43 +0,0 @@ - -# Class: Taxon - - - - -URI: [traits:Taxon](http://w3id.org/ontogpt/traits/Taxon) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Trait],[Trait]<preferred_environments%200..*-%20[Taxon],[Trait]<phenotypic_plasticiticy_traits%200..*-%20[Taxon],[Trait]<survival_traits%200..*-%20[Taxon],[Trait]<reproductive_traits%200..*-%20[Taxon],[Trait]<ecological_traits%200..*-%20[Taxon],[Trait]<cellular_traits%200..*-%20[Taxon],[Trait]<genetic_traits%200..*-%20[Taxon],[Trait]<morphological_traits%200..*-%20[Taxon],[Trait]<metabolic_traits%200..*-%20[Taxon])](https://yuml.me/diagram/nofunky;dir:TB/class/[Trait],[Trait]<preferred_environments%200..*-%20[Taxon],[Trait]<phenotypic_plasticiticy_traits%200..*-%20[Taxon],[Trait]<survival_traits%200..*-%20[Taxon],[Trait]<reproductive_traits%200..*-%20[Taxon],[Trait]<ecological_traits%200..*-%20[Taxon],[Trait]<cellular_traits%200..*-%20[Taxon],[Trait]<genetic_traits%200..*-%20[Taxon],[Trait]<morphological_traits%200..*-%20[Taxon],[Trait]<metabolic_traits%200..*-%20[Taxon]) - -## Attributes - - -### Own - - * [➞metabolic_traits](taxon__metabolic_traits.md) <sub>0..\*</sub> - * Description: The metabolic traits for the taxon. - * Range: [Trait](Trait.md) - * [➞morphological_traits](taxon__morphological_traits.md) <sub>0..\*</sub> - * Description: The morphological traits for the taxon. - * Range: [Trait](Trait.md) - * [➞genetic_traits](taxon__genetic_traits.md) <sub>0..\*</sub> - * Description: The genetic traits for the taxon. - * Range: [Trait](Trait.md) - * [➞cellular_traits](taxon__cellular_traits.md) <sub>0..\*</sub> - * Description: The cellular traits for the taxon. - * Range: [Trait](Trait.md) - * [➞ecological_traits](taxon__ecological_traits.md) <sub>0..\*</sub> - * Description: The ecological traits for the taxon. - * Range: [Trait](Trait.md) - * [➞reproductive_traits](taxon__reproductive_traits.md) <sub>0..\*</sub> - * Description: The reproductive traits for the taxon. - * Range: [Trait](Trait.md) - * [➞survival_traits](taxon__survival_traits.md) <sub>0..\*</sub> - * Description: The survival traits for the taxon. - * Range: [Trait](Trait.md) - * [➞phenotypic_plasticiticy_traits](taxon__phenotypic_plasticiticy_traits.md) <sub>0..\*</sub> - * Description: The phenotypic plasticiticy traits for the taxon. - * Range: [Trait](Trait.md) - * [➞preferred_environments](taxon__preferred_environments.md) <sub>0..\*</sub> - * Description: The preferred environments for the taxon. - * Range: [Trait](Trait.md) diff --git a/projects/traits/docs/TextWithTriples.md b/projects/traits/docs/TextWithTriples.md deleted file mode 100644 index f8b5b4fce..000000000 --- a/projects/traits/docs/TextWithTriples.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: TextWithTriples - - - - -URI: [traits:TextWithTriples](http://w3id.org/ontogpt/traits/TextWithTriples) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication]) - -## Attributes - - -### Own - - * [➞publication](textWithTriples__publication.md) <sub>0..1</sub> - * Range: [Publication](Publication.md) - * [➞triples](textWithTriples__triples.md) <sub>0..\*</sub> - * Range: [Triple](Triple.md) diff --git a/projects/traits/docs/Trait.md b/projects/traits/docs/Trait.md deleted file mode 100644 index cc2473fff..000000000 --- a/projects/traits/docs/Trait.md +++ /dev/null @@ -1,46 +0,0 @@ - -# Class: Trait - - - - -URI: [traits:Trait](http://w3id.org/ontogpt/traits/Trait) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Taxon]-%20cellular_traits%200..*>[Trait|id(i):string;label(i):string%20%3F],[Taxon]-%20ecological_traits%200..*>[Trait],[Taxon]-%20genetic_traits%200..*>[Trait],[Taxon]-%20metabolic_traits%200..*>[Trait],[Taxon]-%20morphological_traits%200..*>[Trait],[Taxon]-%20phenotypic_plasticiticy_traits%200..*>[Trait],[Taxon]-%20preferred_environments%200..*>[Trait],[Taxon]-%20reproductive_traits%200..*>[Trait],[Taxon]-%20survival_traits%200..*>[Trait],[NamedEntity]^-[Trait],[Taxon],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Taxon]-%20cellular_traits%200..*>[Trait|id(i):string;label(i):string%20%3F],[Taxon]-%20ecological_traits%200..*>[Trait],[Taxon]-%20genetic_traits%200..*>[Trait],[Taxon]-%20metabolic_traits%200..*>[Trait],[Taxon]-%20morphological_traits%200..*>[Trait],[Taxon]-%20phenotypic_plasticiticy_traits%200..*>[Trait],[Taxon]-%20preferred_environments%200..*>[Trait],[Taxon]-%20reproductive_traits%200..*>[Trait],[Taxon]-%20survival_traits%200..*>[Trait],[NamedEntity]^-[Trait],[Taxon],[NamedEntity]) - -## Identifier prefixes - - * ECOCORE - * PATO - * GO - * OBA - * BIODIVTHES - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞cellular_traits](taxon__cellular_traits.md)* <sub>0..\*</sub> **[Trait](Trait.md)** - * **None** *[➞ecological_traits](taxon__ecological_traits.md)* <sub>0..\*</sub> **[Trait](Trait.md)** - * **None** *[➞genetic_traits](taxon__genetic_traits.md)* <sub>0..\*</sub> **[Trait](Trait.md)** - * **None** *[➞metabolic_traits](taxon__metabolic_traits.md)* <sub>0..\*</sub> **[Trait](Trait.md)** - * **None** *[➞morphological_traits](taxon__morphological_traits.md)* <sub>0..\*</sub> **[Trait](Trait.md)** - * **None** *[➞phenotypic_plasticiticy_traits](taxon__phenotypic_plasticiticy_traits.md)* <sub>0..\*</sub> **[Trait](Trait.md)** - * **None** *[➞preferred_environments](taxon__preferred_environments.md)* <sub>0..\*</sub> **[Trait](Trait.md)** - * **None** *[➞reproductive_traits](taxon__reproductive_traits.md)* <sub>0..\*</sub> **[Trait](Trait.md)** - * **None** *[➞survival_traits](taxon__survival_traits.md)* <sub>0..\*</sub> **[Trait](Trait.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/traits/docs/Triple.md b/projects/traits/docs/Triple.md deleted file mode 100644 index ebd00345c..000000000 --- a/projects/traits/docs/Triple.md +++ /dev/null @@ -1,39 +0,0 @@ - -# Class: Triple - - -Abstract parent for Relation Extraction tasks - -URI: [traits:Triple](http://w3id.org/ontogpt/traits/Triple) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞triples](textWithTriples__triples.md)* <sub>0..\*</sub> **[Triple](Triple.md)** - -## Attributes - - -### Own - - * [➞subject](triple__subject.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞predicate](triple__predicate.md) <sub>0..1</sub> - * Range: [RelationshipType](RelationshipType.md) - * [➞object](triple__object.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞qualifier](triple__qualifier.md) <sub>0..1</sub> - * Description: A qualifier for the statements, e.g. "NOT" for negation - * Range: [String](types/String.md) - * [➞subject_qualifier](triple__subject_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - * Range: [NamedEntity](NamedEntity.md) - * [➞object_qualifier](triple__object_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * Range: [NamedEntity](NamedEntity.md) diff --git a/projects/traits/docs/annotatorResult__object_id.md b/projects/traits/docs/annotatorResult__object_id.md deleted file mode 100644 index b026238c9..000000000 --- a/projects/traits/docs/annotatorResult__object_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_id - - - - -URI: [traits:annotatorResult__object_id](http://w3id.org/ontogpt/traits/annotatorResult__object_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/traits/docs/annotatorResult__object_text.md b/projects/traits/docs/annotatorResult__object_text.md deleted file mode 100644 index 4c878a3ca..000000000 --- a/projects/traits/docs/annotatorResult__object_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_text - - - - -URI: [traits:annotatorResult__object_text](http://w3id.org/ontogpt/traits/annotatorResult__object_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/traits/docs/annotatorResult__subject_text.md b/projects/traits/docs/annotatorResult__subject_text.md deleted file mode 100644 index 36c413e76..000000000 --- a/projects/traits/docs/annotatorResult__subject_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_text - - - - -URI: [traits:annotatorResult__subject_text](http://w3id.org/ontogpt/traits/annotatorResult__subject_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/traits/docs/extractionResult__extracted_object.md b/projects/traits/docs/extractionResult__extracted_object.md deleted file mode 100644 index af596bbf2..000000000 --- a/projects/traits/docs/extractionResult__extracted_object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: extracted_object - - -The complex objects extracted from the text - -URI: [traits:extractionResult__extracted_object](http://w3id.org/ontogpt/traits/extractionResult__extracted_object) - - -## Domain and Range - -None → <sub>0..1</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/traits/docs/extractionResult__input_id.md b/projects/traits/docs/extractionResult__input_id.md deleted file mode 100644 index 5841eb865..000000000 --- a/projects/traits/docs/extractionResult__input_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_id - - - - -URI: [traits:extractionResult__input_id](http://w3id.org/ontogpt/traits/extractionResult__input_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/traits/docs/extractionResult__input_text.md b/projects/traits/docs/extractionResult__input_text.md deleted file mode 100644 index 0882e1796..000000000 --- a/projects/traits/docs/extractionResult__input_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_text - - - - -URI: [traits:extractionResult__input_text](http://w3id.org/ontogpt/traits/extractionResult__input_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/traits/docs/extractionResult__input_title.md b/projects/traits/docs/extractionResult__input_title.md deleted file mode 100644 index d0c6251eb..000000000 --- a/projects/traits/docs/extractionResult__input_title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_title - - - - -URI: [traits:extractionResult__input_title](http://w3id.org/ontogpt/traits/extractionResult__input_title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/traits/docs/extractionResult__named_entities.md b/projects/traits/docs/extractionResult__named_entities.md deleted file mode 100644 index fdd763859..000000000 --- a/projects/traits/docs/extractionResult__named_entities.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: named_entities - - -Named entities extracted from the text - -URI: [traits:extractionResult__named_entities](http://w3id.org/ontogpt/traits/extractionResult__named_entities) - - -## Domain and Range - -None → <sub>0..\*</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/traits/docs/extractionResult__prompt.md b/projects/traits/docs/extractionResult__prompt.md deleted file mode 100644 index f637fbce5..000000000 --- a/projects/traits/docs/extractionResult__prompt.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: prompt - - - - -URI: [traits:extractionResult__prompt](http://w3id.org/ontogpt/traits/extractionResult__prompt) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/traits/docs/extractionResult__raw_completion_output.md b/projects/traits/docs/extractionResult__raw_completion_output.md deleted file mode 100644 index 15bfec7a7..000000000 --- a/projects/traits/docs/extractionResult__raw_completion_output.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: raw_completion_output - - - - -URI: [traits:extractionResult__raw_completion_output](http://w3id.org/ontogpt/traits/extractionResult__raw_completion_output) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/traits/docs/namedEntity__id.md b/projects/traits/docs/namedEntity__id.md deleted file mode 100644 index 1c92fed5a..000000000 --- a/projects/traits/docs/namedEntity__id.md +++ /dev/null @@ -1,31 +0,0 @@ - -# Slot: id - - -A unique identifier for the named entity - -URI: [traits:namedEntity__id](http://w3id.org/ontogpt/traits/namedEntity__id) - - -## Domain and Range - -None → <sub>1..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [NamedEntity](NamedEntity.md) - * [RelationshipType](RelationshipType.md) - * [Trait](Trait.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | this is populated during the grounding and normalization step | - diff --git a/projects/traits/docs/namedEntity__label.md b/projects/traits/docs/namedEntity__label.md deleted file mode 100644 index 47b15a216..000000000 --- a/projects/traits/docs/namedEntity__label.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Slot: label - - -The label (name) of the named thing - -URI: [traits:namedEntity__label](http://w3id.org/ontogpt/traits/namedEntity__label) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [NamedEntity](NamedEntity.md) - * [RelationshipType](RelationshipType.md) - * [Trait](Trait.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Aliases:** | | name | -| **Mappings:** | | rdfs:label | - diff --git a/projects/traits/docs/publication__abstract.md b/projects/traits/docs/publication__abstract.md deleted file mode 100644 index f54714106..000000000 --- a/projects/traits/docs/publication__abstract.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: abstract - - -The abstract of the publication - -URI: [traits:publication__abstract](http://w3id.org/ontogpt/traits/publication__abstract) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/traits/docs/publication__combined_text.md b/projects/traits/docs/publication__combined_text.md deleted file mode 100644 index ce6d7aad4..000000000 --- a/projects/traits/docs/publication__combined_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: combined_text - - - - -URI: [traits:publication__combined_text](http://w3id.org/ontogpt/traits/publication__combined_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/traits/docs/publication__full_text.md b/projects/traits/docs/publication__full_text.md deleted file mode 100644 index 54692c4f5..000000000 --- a/projects/traits/docs/publication__full_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: full_text - - -The full text of the publication - -URI: [traits:publication__full_text](http://w3id.org/ontogpt/traits/publication__full_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/traits/docs/publication__id.md b/projects/traits/docs/publication__id.md deleted file mode 100644 index 9676d3df5..000000000 --- a/projects/traits/docs/publication__id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: id - - -The publication identifier - -URI: [traits:publication__id](http://w3id.org/ontogpt/traits/publication__id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/traits/docs/publication__title.md b/projects/traits/docs/publication__title.md deleted file mode 100644 index 194d3364e..000000000 --- a/projects/traits/docs/publication__title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: title - - -The title of the publication - -URI: [traits:publication__title](http://w3id.org/ontogpt/traits/publication__title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/traits/docs/taxon__cellular_traits.md b/projects/traits/docs/taxon__cellular_traits.md deleted file mode 100644 index ef120a5ba..000000000 --- a/projects/traits/docs/taxon__cellular_traits.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: cellular_traits - - -The cellular traits for the taxon. - -URI: [traits:taxon__cellular_traits](http://w3id.org/ontogpt/traits/taxon__cellular_traits) - - -## Domain and Range - -None → <sub>0..\*</sub> [Trait](Trait.md) - -## Parents - - -## Children - - -## Used by - - * [Taxon](Taxon.md) diff --git a/projects/traits/docs/taxon__ecological_traits.md b/projects/traits/docs/taxon__ecological_traits.md deleted file mode 100644 index 309b64561..000000000 --- a/projects/traits/docs/taxon__ecological_traits.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: ecological_traits - - -The ecological traits for the taxon. - -URI: [traits:taxon__ecological_traits](http://w3id.org/ontogpt/traits/taxon__ecological_traits) - - -## Domain and Range - -None → <sub>0..\*</sub> [Trait](Trait.md) - -## Parents - - -## Children - - -## Used by - - * [Taxon](Taxon.md) diff --git a/projects/traits/docs/taxon__genetic_traits.md b/projects/traits/docs/taxon__genetic_traits.md deleted file mode 100644 index b4de8e391..000000000 --- a/projects/traits/docs/taxon__genetic_traits.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: genetic_traits - - -The genetic traits for the taxon. - -URI: [traits:taxon__genetic_traits](http://w3id.org/ontogpt/traits/taxon__genetic_traits) - - -## Domain and Range - -None → <sub>0..\*</sub> [Trait](Trait.md) - -## Parents - - -## Children - - -## Used by - - * [Taxon](Taxon.md) diff --git a/projects/traits/docs/taxon__metabolic_traits.md b/projects/traits/docs/taxon__metabolic_traits.md deleted file mode 100644 index dd3430938..000000000 --- a/projects/traits/docs/taxon__metabolic_traits.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: metabolic_traits - - -The metabolic traits for the taxon. - -URI: [traits:taxon__metabolic_traits](http://w3id.org/ontogpt/traits/taxon__metabolic_traits) - - -## Domain and Range - -None → <sub>0..\*</sub> [Trait](Trait.md) - -## Parents - - -## Children - - -## Used by - - * [Taxon](Taxon.md) diff --git a/projects/traits/docs/taxon__morphological_traits.md b/projects/traits/docs/taxon__morphological_traits.md deleted file mode 100644 index 0da5f0d30..000000000 --- a/projects/traits/docs/taxon__morphological_traits.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: morphological_traits - - -The morphological traits for the taxon. - -URI: [traits:taxon__morphological_traits](http://w3id.org/ontogpt/traits/taxon__morphological_traits) - - -## Domain and Range - -None → <sub>0..\*</sub> [Trait](Trait.md) - -## Parents - - -## Children - - -## Used by - - * [Taxon](Taxon.md) diff --git a/projects/traits/docs/taxon__phenotypic_plasticiticy_traits.md b/projects/traits/docs/taxon__phenotypic_plasticiticy_traits.md deleted file mode 100644 index 25ef50a48..000000000 --- a/projects/traits/docs/taxon__phenotypic_plasticiticy_traits.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: phenotypic_plasticiticy_traits - - -The phenotypic plasticiticy traits for the taxon. - -URI: [traits:taxon__phenotypic_plasticiticy_traits](http://w3id.org/ontogpt/traits/taxon__phenotypic_plasticiticy_traits) - - -## Domain and Range - -None → <sub>0..\*</sub> [Trait](Trait.md) - -## Parents - - -## Children - - -## Used by - - * [Taxon](Taxon.md) diff --git a/projects/traits/docs/taxon__preferred_environments.md b/projects/traits/docs/taxon__preferred_environments.md deleted file mode 100644 index 6f84ea5fb..000000000 --- a/projects/traits/docs/taxon__preferred_environments.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: preferred_environments - - -The preferred environments for the taxon. - -URI: [traits:taxon__preferred_environments](http://w3id.org/ontogpt/traits/taxon__preferred_environments) - - -## Domain and Range - -None → <sub>0..\*</sub> [Trait](Trait.md) - -## Parents - - -## Children - - -## Used by - - * [Taxon](Taxon.md) diff --git a/projects/traits/docs/taxon__reproductive_traits.md b/projects/traits/docs/taxon__reproductive_traits.md deleted file mode 100644 index 6cb428c57..000000000 --- a/projects/traits/docs/taxon__reproductive_traits.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: reproductive_traits - - -The reproductive traits for the taxon. - -URI: [traits:taxon__reproductive_traits](http://w3id.org/ontogpt/traits/taxon__reproductive_traits) - - -## Domain and Range - -None → <sub>0..\*</sub> [Trait](Trait.md) - -## Parents - - -## Children - - -## Used by - - * [Taxon](Taxon.md) diff --git a/projects/traits/docs/taxon__survival_traits.md b/projects/traits/docs/taxon__survival_traits.md deleted file mode 100644 index 6e69f9634..000000000 --- a/projects/traits/docs/taxon__survival_traits.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: survival_traits - - -The survival traits for the taxon. - -URI: [traits:taxon__survival_traits](http://w3id.org/ontogpt/traits/taxon__survival_traits) - - -## Domain and Range - -None → <sub>0..\*</sub> [Trait](Trait.md) - -## Parents - - -## Children - - -## Used by - - * [Taxon](Taxon.md) diff --git a/projects/traits/docs/textWithTriples__publication.md b/projects/traits/docs/textWithTriples__publication.md deleted file mode 100644 index adc637c95..000000000 --- a/projects/traits/docs/textWithTriples__publication.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: publication - - - - -URI: [traits:textWithTriples__publication](http://w3id.org/ontogpt/traits/textWithTriples__publication) - - -## Domain and Range - -None → <sub>0..1</sub> [Publication](Publication.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/traits/docs/textWithTriples__triples.md b/projects/traits/docs/textWithTriples__triples.md deleted file mode 100644 index 5fe3ee468..000000000 --- a/projects/traits/docs/textWithTriples__triples.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: triples - - - - -URI: [traits:textWithTriples__triples](http://w3id.org/ontogpt/traits/textWithTriples__triples) - - -## Domain and Range - -None → <sub>0..\*</sub> [Triple](Triple.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/traits/docs/traits.md b/projects/traits/docs/traits.md deleted file mode 100644 index fa0a3254b..000000000 --- a/projects/traits/docs/traits.md +++ /dev/null @@ -1,114 +0,0 @@ - -# traits - - -**metamodel version:** 1.7.0 - -**version:** None - - -A template for Traits - - -### Classes - - * [AnnotatorResult](AnnotatorResult.md) - * [Any](Any.md) - * [CompoundExpression](CompoundExpression.md) - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - * [ExtractionResult](ExtractionResult.md) - A result of extracting knowledge on text - * [NamedEntity](NamedEntity.md) - * [RelationshipType](RelationshipType.md) - * [Trait](Trait.md) - * [Publication](Publication.md) - * [Taxon](Taxon.md) - * [TextWithTriples](TextWithTriples.md) - -### Mixins - - -### Slots - - * [➞object_id](annotatorResult__object_id.md) - * [➞object_text](annotatorResult__object_text.md) - * [➞subject_text](annotatorResult__subject_text.md) - * [➞extracted_object](extractionResult__extracted_object.md) - The complex objects extracted from the text - * [➞input_id](extractionResult__input_id.md) - * [➞input_text](extractionResult__input_text.md) - * [➞input_title](extractionResult__input_title.md) - * [➞named_entities](extractionResult__named_entities.md) - Named entities extracted from the text - * [➞prompt](extractionResult__prompt.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) - * [➞id](namedEntity__id.md) - A unique identifier for the named entity - * [➞label](namedEntity__label.md) - The label (name) of the named thing - * [➞abstract](publication__abstract.md) - The abstract of the publication - * [➞combined_text](publication__combined_text.md) - * [➞full_text](publication__full_text.md) - The full text of the publication - * [➞id](publication__id.md) - The publication identifier - * [➞title](publication__title.md) - The title of the publication - * [➞cellular_traits](taxon__cellular_traits.md) - The cellular traits for the taxon. - * [➞ecological_traits](taxon__ecological_traits.md) - The ecological traits for the taxon. - * [➞genetic_traits](taxon__genetic_traits.md) - The genetic traits for the taxon. - * [➞metabolic_traits](taxon__metabolic_traits.md) - The metabolic traits for the taxon. - * [➞morphological_traits](taxon__morphological_traits.md) - The morphological traits for the taxon. - * [➞phenotypic_plasticiticy_traits](taxon__phenotypic_plasticiticy_traits.md) - The phenotypic plasticiticy traits for the taxon. - * [➞preferred_environments](taxon__preferred_environments.md) - The preferred environments for the taxon. - * [➞reproductive_traits](taxon__reproductive_traits.md) - The reproductive traits for the taxon. - * [➞survival_traits](taxon__survival_traits.md) - The survival traits for the taxon. - * [➞publication](textWithTriples__publication.md) - * [➞triples](textWithTriples__triples.md) - * [➞object](triple__object.md) - * [➞object_qualifier](triple__object_qualifier.md) - An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * [➞predicate](triple__predicate.md) - * [➞qualifier](triple__qualifier.md) - A qualifier for the statements, e.g. "NOT" for negation - * [➞subject](triple__subject.md) - * [➞subject_qualifier](triple__subject_qualifier.md) - An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -### Enums - - * [NullDataOptions](NullDataOptions.md) - -### Subsets - - -### Types - - -#### Built in - - * **Bool** - * **Curie** - * **Decimal** - * **ElementIdentifier** - * **NCName** - * **NodeIdentifier** - * **URI** - * **URIorCURIE** - * **XSDDate** - * **XSDDateTime** - * **XSDTime** - * **float** - * **int** - * **str** - -#### Defined - - * [Boolean](types/Boolean.md) (**Bool**) - A binary (true or false) value - * [Curie](types/Curie.md) (**Curie**) - a compact URI - * [Date](types/Date.md) (**XSDDate**) - a date (year, month and day) in an idealized calendar - * [DateOrDatetime](types/DateOrDatetime.md) (**str**) - Either a date or a datetime - * [Datetime](types/Datetime.md) (**XSDDateTime**) - The combination of a date and time - * [Decimal](types/Decimal.md) (**Decimal**) - A real number with arbitrary precision that conforms to the xsd:decimal specification - * [Double](types/Double.md) (**float**) - A real number that conforms to the xsd:double specification - * [Float](types/Float.md) (**float**) - A real number that conforms to the xsd:float specification - * [Integer](types/Integer.md) (**int**) - An integer - * [Jsonpath](types/Jsonpath.md) (**str**) - A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - * [Jsonpointer](types/Jsonpointer.md) (**str**) - A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - * [Ncname](types/Ncname.md) (**NCName**) - Prefix part of CURIE - * [Nodeidentifier](types/Nodeidentifier.md) (**NodeIdentifier**) - A URI, CURIE or BNODE that represents a node in a model. - * [Objectidentifier](types/Objectidentifier.md) (**ElementIdentifier**) - A URI or CURIE that represents an object in the model. - * [Sparqlpath](types/Sparqlpath.md) (**str**) - A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - * [String](types/String.md) (**str**) - A character string - * [Time](types/Time.md) (**XSDTime**) - A time object represents a (local) time of day, independent of any particular day - * [Uri](types/Uri.md) (**URI**) - a complete URI - * [Uriorcurie](types/Uriorcurie.md) (**URIorCURIE**) - a URI or a CURIE diff --git a/projects/traits/docs/triple__object.md b/projects/traits/docs/triple__object.md deleted file mode 100644 index 7b2fa004f..000000000 --- a/projects/traits/docs/triple__object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object - - - - -URI: [traits:triple__object](http://w3id.org/ontogpt/traits/triple__object) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/traits/docs/triple__object_qualifier.md b/projects/traits/docs/triple__object_qualifier.md deleted file mode 100644 index bbafc0ff9..000000000 --- a/projects/traits/docs/triple__object_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_qualifier - - -An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - -URI: [traits:triple__object_qualifier](http://w3id.org/ontogpt/traits/triple__object_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/traits/docs/triple__predicate.md b/projects/traits/docs/triple__predicate.md deleted file mode 100644 index 5ba49bb44..000000000 --- a/projects/traits/docs/triple__predicate.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: predicate - - - - -URI: [traits:triple__predicate](http://w3id.org/ontogpt/traits/triple__predicate) - - -## Domain and Range - -None → <sub>0..1</sub> [RelationshipType](RelationshipType.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/traits/docs/triple__qualifier.md b/projects/traits/docs/triple__qualifier.md deleted file mode 100644 index 7acc93a88..000000000 --- a/projects/traits/docs/triple__qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: qualifier - - -A qualifier for the statements, e.g. "NOT" for negation - -URI: [traits:triple__qualifier](http://w3id.org/ontogpt/traits/triple__qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/traits/docs/triple__subject.md b/projects/traits/docs/triple__subject.md deleted file mode 100644 index 3de81a682..000000000 --- a/projects/traits/docs/triple__subject.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject - - - - -URI: [traits:triple__subject](http://w3id.org/ontogpt/traits/triple__subject) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/traits/docs/triple__subject_qualifier.md b/projects/traits/docs/triple__subject_qualifier.md deleted file mode 100644 index d5adf9d53..000000000 --- a/projects/traits/docs/triple__subject_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_qualifier - - -An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -URI: [traits:triple__subject_qualifier](http://w3id.org/ontogpt/traits/triple__subject_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/traits/docs/types/Boolean.md b/projects/traits/docs/types/Boolean.md deleted file mode 100644 index dc83a9c6e..000000000 --- a/projects/traits/docs/types/Boolean.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: boolean - - -A binary (true or false) value - -URI: [linkml:Boolean](https://w3id.org/linkml/Boolean) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Bool** | -| Representation | | bool | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Boolean | - diff --git a/projects/traits/docs/types/Curie.md b/projects/traits/docs/types/Curie.md deleted file mode 100644 index c1803f93f..000000000 --- a/projects/traits/docs/types/Curie.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: curie - - -a compact URI - -URI: [linkml:Curie](https://w3id.org/linkml/Curie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Curie** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations this MUST be expanded to a URI | -| | | in non-RDF serializations MAY be serialized as the compact representation | - diff --git a/projects/traits/docs/types/Date.md b/projects/traits/docs/types/Date.md deleted file mode 100644 index 06948af97..000000000 --- a/projects/traits/docs/types/Date.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: date - - -a date (year, month and day) in an idealized calendar - -URI: [linkml:Date](https://w3id.org/linkml/Date) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDate** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Date | - diff --git a/projects/traits/docs/types/DateOrDatetime.md b/projects/traits/docs/types/DateOrDatetime.md deleted file mode 100644 index ef983898d..000000000 --- a/projects/traits/docs/types/DateOrDatetime.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: date_or_datetime - - -Either a date or a datetime - -URI: [linkml:DateOrDatetime](https://w3id.org/linkml/DateOrDatetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/traits/docs/types/Datetime.md b/projects/traits/docs/types/Datetime.md deleted file mode 100644 index 9510454a8..000000000 --- a/projects/traits/docs/types/Datetime.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: datetime - - -The combination of a date and time - -URI: [linkml:Datetime](https://w3id.org/linkml/Datetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDateTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:DateTime | - diff --git a/projects/traits/docs/types/Decimal.md b/projects/traits/docs/types/Decimal.md deleted file mode 100644 index a7ba14a5d..000000000 --- a/projects/traits/docs/types/Decimal.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: decimal - - -A real number with arbitrary precision that conforms to the xsd:decimal specification - -URI: [linkml:Decimal](https://w3id.org/linkml/Decimal) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Decimal** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Broad Mappings:** | | schema:Number | - diff --git a/projects/traits/docs/types/Double.md b/projects/traits/docs/types/Double.md deleted file mode 100644 index cfe6d71e2..000000000 --- a/projects/traits/docs/types/Double.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: double - - -A real number that conforms to the xsd:double specification - -URI: [linkml:Double](https://w3id.org/linkml/Double) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Close Mappings:** | | schema:Float | - diff --git a/projects/traits/docs/types/Float.md b/projects/traits/docs/types/Float.md deleted file mode 100644 index 7b303f96f..000000000 --- a/projects/traits/docs/types/Float.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: float - - -A real number that conforms to the xsd:float specification - -URI: [linkml:Float](https://w3id.org/linkml/Float) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Float | - diff --git a/projects/traits/docs/types/Integer.md b/projects/traits/docs/types/Integer.md deleted file mode 100644 index 3cfcc66d9..000000000 --- a/projects/traits/docs/types/Integer.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: integer - - -An integer - -URI: [linkml:Integer](https://w3id.org/linkml/Integer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **int** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Integer | - diff --git a/projects/traits/docs/types/Jsonpath.md b/projects/traits/docs/types/Jsonpath.md deleted file mode 100644 index a03a58e67..000000000 --- a/projects/traits/docs/types/Jsonpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpath - - -A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpath](https://w3id.org/linkml/Jsonpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/traits/docs/types/Jsonpointer.md b/projects/traits/docs/types/Jsonpointer.md deleted file mode 100644 index a0e1ac492..000000000 --- a/projects/traits/docs/types/Jsonpointer.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpointer - - -A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpointer](https://w3id.org/linkml/Jsonpointer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/traits/docs/types/Ncname.md b/projects/traits/docs/types/Ncname.md deleted file mode 100644 index 710b0b04a..000000000 --- a/projects/traits/docs/types/Ncname.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: ncname - - -Prefix part of CURIE - -URI: [linkml:Ncname](https://w3id.org/linkml/Ncname) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NCName** | -| Representation | | str | diff --git a/projects/traits/docs/types/Nodeidentifier.md b/projects/traits/docs/types/Nodeidentifier.md deleted file mode 100644 index f0097cdf4..000000000 --- a/projects/traits/docs/types/Nodeidentifier.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: nodeidentifier - - -A URI, CURIE or BNODE that represents a node in a model. - -URI: [linkml:Nodeidentifier](https://w3id.org/linkml/Nodeidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NodeIdentifier** | -| Representation | | str | diff --git a/projects/traits/docs/types/Objectidentifier.md b/projects/traits/docs/types/Objectidentifier.md deleted file mode 100644 index 454ba6be6..000000000 --- a/projects/traits/docs/types/Objectidentifier.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: objectidentifier - - -A URI or CURIE that represents an object in the model. - -URI: [linkml:Objectidentifier](https://w3id.org/linkml/Objectidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **ElementIdentifier** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | Used for inheritance and type checking | - diff --git a/projects/traits/docs/types/Sparqlpath.md b/projects/traits/docs/types/Sparqlpath.md deleted file mode 100644 index fd99a927e..000000000 --- a/projects/traits/docs/types/Sparqlpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: sparqlpath - - -A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - -URI: [linkml:Sparqlpath](https://w3id.org/linkml/Sparqlpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/traits/docs/types/String.md b/projects/traits/docs/types/String.md deleted file mode 100644 index 6e61d7081..000000000 --- a/projects/traits/docs/types/String.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: string - - -A character string - -URI: [linkml:String](https://w3id.org/linkml/String) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Text | - diff --git a/projects/traits/docs/types/Time.md b/projects/traits/docs/types/Time.md deleted file mode 100644 index 2b8652bcd..000000000 --- a/projects/traits/docs/types/Time.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: time - - -A time object represents a (local) time of day, independent of any particular day - -URI: [linkml:Time](https://w3id.org/linkml/Time) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Time | - diff --git a/projects/traits/docs/types/Uri.md b/projects/traits/docs/types/Uri.md deleted file mode 100644 index 343807a5e..000000000 --- a/projects/traits/docs/types/Uri.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: uri - - -a complete URI - -URI: [linkml:Uri](https://w3id.org/linkml/Uri) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URI** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node | -| **Close Mappings:** | | schema:URL | - diff --git a/projects/traits/docs/types/Uriorcurie.md b/projects/traits/docs/types/Uriorcurie.md deleted file mode 100644 index 2f7b65087..000000000 --- a/projects/traits/docs/types/Uriorcurie.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: uriorcurie - - -a URI or a CURIE - -URI: [linkml:Uriorcurie](https://w3id.org/linkml/Uriorcurie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URIorCURIE** | -| Representation | | str | diff --git a/projects/traits/excel/traits.xlsx b/projects/traits/excel/traits.xlsx deleted file mode 100644 index b5f205034..000000000 Binary files a/projects/traits/excel/traits.xlsx and /dev/null differ diff --git a/projects/traits/graphql/traits.graphql b/projects/traits/graphql/traits.graphql deleted file mode 100644 index dd08a8af6..000000000 --- a/projects/traits/graphql/traits.graphql +++ /dev/null @@ -1,82 +0,0 @@ -type AnnotatorResult - { - subjectText: String - objectId: String - objectText: String - } - -type Any - { - } - -interface CompoundExpression - { - } - -type ExtractionResult - { - inputId: String - inputTitle: String - inputText: String - rawCompletionOutput: String - prompt: String - extractedObject: Any - namedEntities: [Any] - } - -interface NamedEntity - { - id: String! - label: String - } - -type Publication - { - id: String - title: String - abstract: String - combinedText: String - fullText: String - } - -type RelationshipType - { - id: String! - label: String - } - -type Taxon - { - metabolicTraits: [Trait] - morphologicalTraits: [Trait] - geneticTraits: [Trait] - cellularTraits: [Trait] - ecologicalTraits: [Trait] - reproductiveTraits: [Trait] - survivalTraits: [Trait] - phenotypicPlasticiticyTraits: [Trait] - preferredEnvironments: [Trait] - } - -type TextWithTriples - { - publication: Publication - triples: [Triple] - } - -type Trait - { - id: String! - label: String - } - -interface Triple - { - subject: NamedEntity - predicate: RelationshipType - object: NamedEntity - qualifier: String - subjectQualifier: NamedEntity - objectQualifier: NamedEntity - } - diff --git a/projects/traits/jsonld/traits.context.jsonld b/projects/traits/jsonld/traits.context.jsonld deleted file mode 100644 index bb4e529fe..000000000 --- a/projects/traits/jsonld/traits.context.jsonld +++ /dev/null @@ -1,159 +0,0 @@ -{ - "comments": { - "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2023-08-07T10:56:23", - "source": "traits.yaml" - }, - "@context": { - "BIODIVTHES": "http://example.org/UNKNOWN/BIODIVTHES/", - "ECOCORE": "http://example.org/UNKNOWN/ECOCORE/", - "GO": "http://example.org/UNKNOWN/GO/", - "OBA": "http://example.org/UNKNOWN/OBA/", - "PATO": "http://example.org/UNKNOWN/PATO/", - "RO": { - "@id": "http://purl.obolibrary.org/obo/RO_", - "@prefix": true - }, - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "traits": "http://w3id.org/ontogpt/traits/", - "@vocab": "http://w3id.org/ontogpt/traits/", - "object_id": { - "@id": "core:object_id" - }, - "object_text": { - "@id": "core:object_text" - }, - "subject_text": { - "@id": "core:subject_text" - }, - "extracted_object": { - "@type": "@id", - "@id": "core:extracted_object" - }, - "input_id": { - "@id": "core:input_id" - }, - "input_text": { - "@id": "core:input_text" - }, - "input_title": { - "@id": "core:input_title" - }, - "named_entities": { - "@type": "@id", - "@id": "core:named_entities" - }, - "prompt": { - "@id": "core:prompt" - }, - "raw_completion_output": { - "@id": "core:raw_completion_output" - }, - "id": { - "@id": "core:id" - }, - "label": { - "@id": "rdfs:label" - }, - "abstract": { - "@id": "core:abstract" - }, - "combined_text": { - "@id": "core:combined_text" - }, - "full_text": { - "@id": "core:full_text" - }, - "title": { - "@id": "core:title" - }, - "cellular_traits": { - "@type": "@id" - }, - "ecological_traits": { - "@type": "@id" - }, - "genetic_traits": { - "@type": "@id" - }, - "metabolic_traits": { - "@type": "@id" - }, - "morphological_traits": { - "@type": "@id" - }, - "phenotypic_plasticiticy_traits": { - "@type": "@id" - }, - "preferred_environments": { - "@type": "@id" - }, - "reproductive_traits": { - "@type": "@id" - }, - "survival_traits": { - "@type": "@id" - }, - "publication": { - "@type": "@id", - "@id": "core:publication" - }, - "triples": { - "@type": "@id", - "@id": "core:triples" - }, - "object": { - "@type": "@id", - "@id": "core:object" - }, - "object_qualifier": { - "@type": "@id", - "@id": "core:object_qualifier" - }, - "predicate": { - "@type": "@id", - "@id": "core:predicate" - }, - "qualifier": { - "@id": "core:qualifier" - }, - "subject": { - "@type": "@id", - "@id": "core:subject" - }, - "subject_qualifier": { - "@type": "@id", - "@id": "core:subject_qualifier" - }, - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } - } -} diff --git a/projects/traits/jsonld/traits.jsonld b/projects/traits/jsonld/traits.jsonld deleted file mode 100644 index 0bd832b53..000000000 --- a/projects/traits/jsonld/traits.jsonld +++ /dev/null @@ -1,1335 +0,0 @@ -{ - "name": "traits", - "description": "A template for Traits", - "title": "Traits Template", - "id": "http://w3id.org/ontogpt/traits", - "imports": [ - "linkml:types", - "core" - ], - "license": "https://creativecommons.org/publicdomain/zero/1.0/", - "prefixes": [ - { - "prefix_prefix": "linkml", - "prefix_reference": "https://w3id.org/linkml/" - }, - { - "prefix_prefix": "traits", - "prefix_reference": "http://w3id.org/ontogpt/traits/" - } - ], - "default_prefix": "traits", - "default_range": "string", - "types": [ - { - "name": "string", - "definition_uri": "https://w3id.org/linkml/String", - "description": "A character string", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Text" - ], - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "@type": "TypeDefinition" - }, - { - "name": "integer", - "definition_uri": "https://w3id.org/linkml/Integer", - "description": "An integer", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Integer" - ], - "base": "int", - "uri": "http://www.w3.org/2001/XMLSchema#integer", - "@type": "TypeDefinition" - }, - { - "name": "boolean", - "definition_uri": "https://w3id.org/linkml/Boolean", - "description": "A binary (true or false) value", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Boolean" - ], - "base": "Bool", - "uri": "http://www.w3.org/2001/XMLSchema#boolean", - "repr": "bool", - "@type": "TypeDefinition" - }, - { - "name": "float", - "definition_uri": "https://w3id.org/linkml/Float", - "description": "A real number that conforms to the xsd:float specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#float", - "@type": "TypeDefinition" - }, - { - "name": "double", - "definition_uri": "https://w3id.org/linkml/Double", - "description": "A real number that conforms to the xsd:double specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#double", - "@type": "TypeDefinition" - }, - { - "name": "decimal", - "definition_uri": "https://w3id.org/linkml/Decimal", - "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "broad_mappings": [ - "schema:Number" - ], - "base": "Decimal", - "uri": "http://www.w3.org/2001/XMLSchema#decimal", - "@type": "TypeDefinition" - }, - { - "name": "time", - "definition_uri": "https://w3id.org/linkml/Time", - "description": "A time object represents a (local) time of day, independent of any particular day", - "notes": [ - "URI is dateTime because OWL reasoners do not work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Time" - ], - "base": "XSDTime", - "uri": "http://www.w3.org/2001/XMLSchema#time", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date", - "definition_uri": "https://w3id.org/linkml/Date", - "description": "a date (year, month and day) in an idealized calendar", - "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Date" - ], - "base": "XSDDate", - "uri": "http://www.w3.org/2001/XMLSchema#date", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "datetime", - "definition_uri": "https://w3id.org/linkml/Datetime", - "description": "The combination of a date and time", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:DateTime" - ], - "base": "XSDDateTime", - "uri": "http://www.w3.org/2001/XMLSchema#dateTime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date_or_datetime", - "definition_uri": "https://w3id.org/linkml/DateOrDatetime", - "description": "Either a date or a datetime", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "https://w3id.org/linkml/DateOrDatetime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uriorcurie", - "definition_uri": "https://w3id.org/linkml/Uriorcurie", - "description": "a URI or a CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "URIorCURIE", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "curie", - "definition_uri": "https://w3id.org/linkml/Curie", - "conforms_to": "https://www.w3.org/TR/curie/", - "description": "a compact URI", - "comments": [ - "in RDF serializations this MUST be expanded to a URI", - "in non-RDF serializations MAY be serialized as the compact representation" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "Curie", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uri", - "definition_uri": "https://w3id.org/linkml/Uri", - "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", - "description": "a complete URI", - "comments": [ - "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:URL" - ], - "base": "URI", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "ncname", - "definition_uri": "https://w3id.org/linkml/Ncname", - "description": "Prefix part of CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NCName", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "objectidentifier", - "definition_uri": "https://w3id.org/linkml/Objectidentifier", - "description": "A URI or CURIE that represents an object in the model.", - "comments": [ - "Used for inheritance and type checking" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "ElementIdentifier", - "uri": "http://www.w3.org/ns/shex#iri", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "nodeidentifier", - "definition_uri": "https://w3id.org/linkml/Nodeidentifier", - "description": "A URI, CURIE or BNODE that represents a node in a model.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NodeIdentifier", - "uri": "http://www.w3.org/ns/shex#nonLiteral", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpointer", - "definition_uri": "https://w3id.org/linkml/Jsonpointer", - "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901", - "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpath", - "definition_uri": "https://w3id.org/linkml/Jsonpath", - "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html", - "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "sparqlpath", - "definition_uri": "https://w3id.org/linkml/Sparqlpath", - "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths", - "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - } - ], - "enums": [ - { - "name": "NullDataOptions", - "definition_uri": "http://w3id.org/ontogpt/core/NullDataOptions", - "from_schema": "http://w3id.org/ontogpt/core", - "permissible_values": [ - { - "text": "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "meaning": "NCIT:C149701" - }, - { - "text": "NOT_APPLICABLE", - "meaning": "NCIT:C18902", - "aliases": [ - "not applicable", - "N/A" - ] - }, - { - "text": "NOT_MENTIONED" - } - ] - } - ], - "slots": [ - { - "name": "taxon__metabolic_traits", - "annotations": [ - { - "tag": "prompt", - "value": "a semicolon separated list of every specific organism metabolic trait", - "@type": "Annotation" - } - ], - "description": "The metabolic traits for the taxon.", - "from_schema": "http://w3id.org/ontogpt/traits", - "slot_uri": "http://w3id.org/ontogpt/traits/metabolic_traits", - "multivalued": true, - "alias": "metabolic_traits", - "owner": "Taxon", - "domain_of": [ - "Taxon" - ], - "range": "Trait", - "@type": "SlotDefinition" - }, - { - "name": "taxon__morphological_traits", - "annotations": [ - { - "tag": "prompt", - "value": "a semicolon separated list of every specific organism morphological trait", - "@type": "Annotation" - } - ], - "description": "The morphological traits for the taxon.", - "from_schema": "http://w3id.org/ontogpt/traits", - "slot_uri": "http://w3id.org/ontogpt/traits/morphological_traits", - "multivalued": true, - "alias": "morphological_traits", - "owner": "Taxon", - "domain_of": [ - "Taxon" - ], - "range": "Trait", - "@type": "SlotDefinition" - }, - { - "name": "taxon__genetic_traits", - "annotations": [ - { - "tag": "prompt", - "value": "a semicolon separated list of every specific organism genetic trait", - "@type": "Annotation" - } - ], - "description": "The genetic traits for the taxon.", - "from_schema": "http://w3id.org/ontogpt/traits", - "slot_uri": "http://w3id.org/ontogpt/traits/genetic_traits", - "multivalued": true, - "alias": "genetic_traits", - "owner": "Taxon", - "domain_of": [ - "Taxon" - ], - "range": "Trait", - "@type": "SlotDefinition" - }, - { - "name": "taxon__cellular_traits", - "annotations": [ - { - "tag": "prompt", - "value": "a semicolon separated list of every specific organism cellular trait", - "@type": "Annotation" - } - ], - "description": "The cellular traits for the taxon.", - "from_schema": "http://w3id.org/ontogpt/traits", - "slot_uri": "http://w3id.org/ontogpt/traits/cellular_traits", - "multivalued": true, - "alias": "cellular_traits", - "owner": "Taxon", - "domain_of": [ - "Taxon" - ], - "range": "Trait", - "@type": "SlotDefinition" - }, - { - "name": "taxon__ecological_traits", - "annotations": [ - { - "tag": "prompt", - "value": "a semicolon separated list of every specific organism ecological trait", - "@type": "Annotation" - } - ], - "description": "The ecological traits for the taxon.", - "from_schema": "http://w3id.org/ontogpt/traits", - "slot_uri": "http://w3id.org/ontogpt/traits/ecological_traits", - "multivalued": true, - "alias": "ecological_traits", - "owner": "Taxon", - "domain_of": [ - "Taxon" - ], - "range": "Trait", - "@type": "SlotDefinition" - }, - { - "name": "taxon__reproductive_traits", - "annotations": [ - { - "tag": "prompt", - "value": "a semicolon separated list of every specific organism reproductive trait", - "@type": "Annotation" - } - ], - "description": "The reproductive traits for the taxon.", - "from_schema": "http://w3id.org/ontogpt/traits", - "slot_uri": "http://w3id.org/ontogpt/traits/reproductive_traits", - "multivalued": true, - "alias": "reproductive_traits", - "owner": "Taxon", - "domain_of": [ - "Taxon" - ], - "range": "Trait", - "@type": "SlotDefinition" - }, - { - "name": "taxon__survival_traits", - "annotations": [ - { - "tag": "prompt", - "value": "a semicolon separated list of every specific organism survival trait", - "@type": "Annotation" - } - ], - "description": "The survival traits for the taxon.", - "from_schema": "http://w3id.org/ontogpt/traits", - "slot_uri": "http://w3id.org/ontogpt/traits/survival_traits", - "multivalued": true, - "alias": "survival_traits", - "owner": "Taxon", - "domain_of": [ - "Taxon" - ], - "range": "Trait", - "@type": "SlotDefinition" - }, - { - "name": "taxon__phenotypic_plasticiticy_traits", - "annotations": [ - { - "tag": "prompt", - "value": "a semicolon separated list of every specific organism phenotypic plasticiticy trait", - "@type": "Annotation" - } - ], - "description": "The phenotypic plasticiticy traits for the taxon.", - "from_schema": "http://w3id.org/ontogpt/traits", - "slot_uri": "http://w3id.org/ontogpt/traits/phenotypic_plasticiticy_traits", - "multivalued": true, - "alias": "phenotypic_plasticiticy_traits", - "owner": "Taxon", - "domain_of": [ - "Taxon" - ], - "range": "Trait", - "@type": "SlotDefinition" - }, - { - "name": "taxon__preferred_environments", - "annotations": [ - { - "tag": "prompt", - "value": "a semicolon separated list of the environments the organism is typically found in or isolated from", - "@type": "Annotation" - } - ], - "description": "The preferred environments for the taxon.", - "from_schema": "http://w3id.org/ontogpt/traits", - "slot_uri": "http://w3id.org/ontogpt/traits/preferred_environments", - "multivalued": true, - "alias": "preferred_environments", - "owner": "Taxon", - "domain_of": [ - "Taxon" - ], - "range": "Trait", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_id", - "alias": "input_id", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_title", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_title", - "alias": "input_title", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_text", - "alias": "input_text", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__raw_completion_output", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/raw_completion_output", - "alias": "raw_completion_output", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__prompt", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/prompt", - "alias": "prompt", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__extracted_object", - "description": "The complex objects extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/extracted_object", - "alias": "extracted_object", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__named_entities", - "description": "Named entities extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/named_entities", - "multivalued": true, - "alias": "named_entities", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "identifier": true, - "alias": "id", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "required": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "from_schema": "http://w3id.org/ontogpt/core", - "aliases": [ - "name" - ], - "mappings": [ - "http://example.org/UNKNOWN/rdfs/label" - ], - "slot_uri": "http://example.org/UNKNOWN/rdfs/label", - "alias": "label", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject", - "alias": "subject", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__predicate", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/predicate", - "alias": "predicate", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "triple__object", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object", - "alias": "object", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/qualifier", - "alias": "qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_qualifier", - "alias": "subject_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_qualifier", - "alias": "object_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/publication", - "alias": "publication", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__triples", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/triples", - "multivalued": true, - "alias": "triples", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "publication__id", - "description": "The publication identifier", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "alias": "id", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__title", - "description": "The title of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/title", - "alias": "title", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__abstract", - "description": "The abstract of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/abstract", - "alias": "abstract", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__combined_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/combined_text", - "alias": "combined_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__full_text", - "description": "The full text of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/full_text", - "alias": "full_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__subject_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_text", - "alias": "subject_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_id", - "alias": "object_id", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_text", - "alias": "object_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - } - ], - "classes": [ - { - "name": "Taxon", - "definition_uri": "http://w3id.org/ontogpt/traits/Taxon", - "from_schema": "http://w3id.org/ontogpt/traits", - "slots": [ - "taxon__metabolic_traits", - "taxon__morphological_traits", - "taxon__genetic_traits", - "taxon__cellular_traits", - "taxon__ecological_traits", - "taxon__reproductive_traits", - "taxon__survival_traits", - "taxon__phenotypic_plasticiticy_traits", - "taxon__preferred_environments" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "metabolic_traits", - "annotations": [ - { - "tag": "prompt", - "value": "a semicolon separated list of every specific organism metabolic trait", - "@type": "Annotation" - } - ], - "description": "The metabolic traits for the taxon.", - "multivalued": true, - "range": "Trait", - "@type": "SlotDefinition" - }, - { - "name": "morphological_traits", - "annotations": [ - { - "tag": "prompt", - "value": "a semicolon separated list of every specific organism morphological trait", - "@type": "Annotation" - } - ], - "description": "The morphological traits for the taxon.", - "multivalued": true, - "range": "Trait", - "@type": "SlotDefinition" - }, - { - "name": "genetic_traits", - "annotations": [ - { - "tag": "prompt", - "value": "a semicolon separated list of every specific organism genetic trait", - "@type": "Annotation" - } - ], - "description": "The genetic traits for the taxon.", - "multivalued": true, - "range": "Trait", - "@type": "SlotDefinition" - }, - { - "name": "cellular_traits", - "annotations": [ - { - "tag": "prompt", - "value": "a semicolon separated list of every specific organism cellular trait", - "@type": "Annotation" - } - ], - "description": "The cellular traits for the taxon.", - "multivalued": true, - "range": "Trait", - "@type": "SlotDefinition" - }, - { - "name": "ecological_traits", - "annotations": [ - { - "tag": "prompt", - "value": "a semicolon separated list of every specific organism ecological trait", - "@type": "Annotation" - } - ], - "description": "The ecological traits for the taxon.", - "multivalued": true, - "range": "Trait", - "@type": "SlotDefinition" - }, - { - "name": "reproductive_traits", - "annotations": [ - { - "tag": "prompt", - "value": "a semicolon separated list of every specific organism reproductive trait", - "@type": "Annotation" - } - ], - "description": "The reproductive traits for the taxon.", - "multivalued": true, - "range": "Trait", - "@type": "SlotDefinition" - }, - { - "name": "survival_traits", - "annotations": [ - { - "tag": "prompt", - "value": "a semicolon separated list of every specific organism survival trait", - "@type": "Annotation" - } - ], - "description": "The survival traits for the taxon.", - "multivalued": true, - "range": "Trait", - "@type": "SlotDefinition" - }, - { - "name": "phenotypic_plasticiticy_traits", - "annotations": [ - { - "tag": "prompt", - "value": "a semicolon separated list of every specific organism phenotypic plasticiticy trait", - "@type": "Annotation" - } - ], - "description": "The phenotypic plasticiticy traits for the taxon.", - "multivalued": true, - "range": "Trait", - "@type": "SlotDefinition" - }, - { - "name": "preferred_environments", - "annotations": [ - { - "tag": "prompt", - "value": "a semicolon separated list of the environments the organism is typically found in or isolated from", - "@type": "Annotation" - } - ], - "description": "The preferred environments for the taxon.", - "multivalued": true, - "range": "Trait", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/traits/Taxon", - "tree_root": true, - "@type": "ClassDefinition" - }, - { - "name": "Trait", - "id_prefixes": [ - "ECOCORE", - "PATO", - "GO", - "OBA", - "BIODIVTHES" - ], - "definition_uri": "http://w3id.org/ontogpt/traits/Trait", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:ecocore, sqlite:obo:pato, sqlite:obo:go, sqlite:obo:oba, bioportal:biodivthes", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/traits", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/traits/Trait", - "@type": "ClassDefinition" - }, - { - "name": "Any", - "definition_uri": "http://w3id.org/ontogpt/core/Any", - "from_schema": "http://w3id.org/ontogpt/core", - "mappings": [ - "linkml:Any" - ], - "slot_usage": {}, - "class_uri": "https://w3id.org/linkml/Any", - "@type": "ClassDefinition" - }, - { - "name": "ExtractionResult", - "definition_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "description": "A result of extracting knowledge on text", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "extractionResult__input_id", - "extractionResult__input_title", - "extractionResult__input_text", - "extractionResult__raw_completion_output", - "extractionResult__prompt", - "extractionResult__extracted_object", - "extractionResult__named_entities" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "input_id", - "@type": "SlotDefinition" - }, - { - "name": "input_title", - "@type": "SlotDefinition" - }, - { - "name": "input_text", - "@type": "SlotDefinition" - }, - { - "name": "raw_completion_output", - "@type": "SlotDefinition" - }, - { - "name": "prompt", - "@type": "SlotDefinition" - }, - { - "name": "extracted_object", - "description": "The complex objects extracted from the text", - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "named_entities", - "description": "Named entities extracted from the text", - "multivalued": true, - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "@type": "ClassDefinition" - }, - { - "name": "NamedEntity", - "definition_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "identifier": true, - "@type": "SlotDefinition" - }, - { - "name": "label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "aliases": [ - "name" - ], - "slot_uri": "rdfs:label", - "range": "string", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "@type": "ClassDefinition" - }, - { - "name": "CompoundExpression", - "definition_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "@type": "ClassDefinition" - }, - { - "name": "Triple", - "definition_uri": "http://w3id.org/ontogpt/core/Triple", - "description": "Abstract parent for Relation Extraction tasks", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "CompoundExpression", - "abstract": true, - "slots": [ - "triple__subject", - "triple__predicate", - "triple__object", - "triple__qualifier", - "triple__subject_qualifier", - "triple__object_qualifier" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "predicate", - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "object", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Triple", - "@type": "ClassDefinition" - }, - { - "name": "TextWithTriples", - "definition_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "textWithTriples__publication", - "textWithTriples__triples" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "triples", - "multivalued": true, - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "@type": "ClassDefinition" - }, - { - "name": "RelationshipType", - "id_prefixes": [ - "RO", - "biolink" - ], - "definition_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "@type": "ClassDefinition" - }, - { - "name": "Publication", - "definition_uri": "http://w3id.org/ontogpt/core/Publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "publication__id", - "publication__title", - "publication__abstract", - "publication__combined_text", - "publication__full_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "description": "The publication identifier", - "@type": "SlotDefinition" - }, - { - "name": "title", - "description": "The title of the publication", - "@type": "SlotDefinition" - }, - { - "name": "abstract", - "description": "The abstract of the publication", - "@type": "SlotDefinition" - }, - { - "name": "combined_text", - "@type": "SlotDefinition" - }, - { - "name": "full_text", - "description": "The full text of the publication", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Publication", - "@type": "ClassDefinition" - }, - { - "name": "AnnotatorResult", - "definition_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "annotatorResult__subject_text", - "annotatorResult__object_id", - "annotatorResult__object_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject_text", - "@type": "SlotDefinition" - }, - { - "name": "object_id", - "@type": "SlotDefinition" - }, - { - "name": "object_text", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "@type": "ClassDefinition" - } - ], - "metamodel_version": "1.7.0", - "source_file": "traits.yaml", - "source_file_date": "2023-06-17T15:11:19", - "source_file_size": 3502, - "generation_date": "2023-08-07T10:56:24", - "@type": "SchemaDefinition", - "@context": [ - "projects/traits/jsonld/traits.context.jsonld", - "https://w3id.org/linkml/types.context.jsonld", - "core.context.jsonld", - { - "@base": "http://w3id.org/ontogpt/traits/" - } - ] -} diff --git a/projects/traits/jsonschema/traits.schema.json b/projects/traits/jsonschema/traits.schema.json deleted file mode 100644 index 088b349a4..000000000 --- a/projects/traits/jsonschema/traits.schema.json +++ /dev/null @@ -1,296 +0,0 @@ -{ - "$defs": { - "AnnotatorResult": { - "additionalProperties": false, - "description": "", - "properties": { - "object_id": { - "type": "string" - }, - "object_text": { - "type": "string" - }, - "subject_text": { - "type": "string" - } - }, - "title": "AnnotatorResult", - "type": "object" - }, - "Any": { - "additionalProperties": true, - "description": "", - "title": "Any", - "type": "object" - }, - "ExtractionResult": { - "additionalProperties": false, - "description": "A result of extracting knowledge on text", - "properties": { - "extracted_object": { - "$ref": "#/$defs/Any", - "description": "The complex objects extracted from the text" - }, - "input_id": { - "type": "string" - }, - "input_text": { - "type": "string" - }, - "input_title": { - "type": "string" - }, - "named_entities": { - "description": "Named entities extracted from the text", - "items": { - "$ref": "#/$defs/Any" - }, - "type": "array" - }, - "prompt": { - "type": "string" - }, - "raw_completion_output": { - "type": "string" - } - }, - "title": "ExtractionResult", - "type": "object" - }, - "NullDataOptions": { - "description": "", - "enum": [ - "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "NOT_APPLICABLE", - "NOT_MENTIONED" - ], - "title": "NullDataOptions", - "type": "string" - }, - "Publication": { - "additionalProperties": false, - "description": "", - "properties": { - "abstract": { - "description": "The abstract of the publication", - "type": "string" - }, - "combined_text": { - "type": "string" - }, - "full_text": { - "description": "The full text of the publication", - "type": "string" - }, - "id": { - "description": "The publication identifier", - "type": "string" - }, - "title": { - "description": "The title of the publication", - "type": "string" - } - }, - "title": "Publication", - "type": "object" - }, - "RelationshipType": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "RelationshipType", - "type": "object" - }, - "Taxon": { - "additionalProperties": false, - "description": "", - "properties": { - "cellular_traits": { - "description": "The cellular traits for the taxon.", - "items": { - "type": "string" - }, - "type": "array" - }, - "ecological_traits": { - "description": "The ecological traits for the taxon.", - "items": { - "type": "string" - }, - "type": "array" - }, - "genetic_traits": { - "description": "The genetic traits for the taxon.", - "items": { - "type": "string" - }, - "type": "array" - }, - "metabolic_traits": { - "description": "The metabolic traits for the taxon.", - "items": { - "type": "string" - }, - "type": "array" - }, - "morphological_traits": { - "description": "The morphological traits for the taxon.", - "items": { - "type": "string" - }, - "type": "array" - }, - "phenotypic_plasticiticy_traits": { - "description": "The phenotypic plasticiticy traits for the taxon.", - "items": { - "type": "string" - }, - "type": "array" - }, - "preferred_environments": { - "description": "The preferred environments for the taxon.", - "items": { - "type": "string" - }, - "type": "array" - }, - "reproductive_traits": { - "description": "The reproductive traits for the taxon.", - "items": { - "type": "string" - }, - "type": "array" - }, - "survival_traits": { - "description": "The survival traits for the taxon.", - "items": { - "type": "string" - }, - "type": "array" - } - }, - "title": "Taxon", - "type": "object" - }, - "TextWithTriples": { - "additionalProperties": false, - "description": "", - "properties": { - "publication": { - "$ref": "#/$defs/Publication" - }, - "triples": { - "items": { - "$ref": "#/$defs/Triple" - }, - "type": "array" - } - }, - "title": "TextWithTriples", - "type": "object" - }, - "Trait": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Trait", - "type": "object" - } - }, - "$id": "http://w3id.org/ontogpt/traits", - "$schema": "http://json-schema.org/draft-07/schema#", - "additionalProperties": true, - "metamodel_version": "1.7.0", - "properties": { - "cellular_traits": { - "description": "The cellular traits for the taxon.", - "items": { - "type": "string" - }, - "type": "array" - }, - "ecological_traits": { - "description": "The ecological traits for the taxon.", - "items": { - "type": "string" - }, - "type": "array" - }, - "genetic_traits": { - "description": "The genetic traits for the taxon.", - "items": { - "type": "string" - }, - "type": "array" - }, - "metabolic_traits": { - "description": "The metabolic traits for the taxon.", - "items": { - "type": "string" - }, - "type": "array" - }, - "morphological_traits": { - "description": "The morphological traits for the taxon.", - "items": { - "type": "string" - }, - "type": "array" - }, - "phenotypic_plasticiticy_traits": { - "description": "The phenotypic plasticiticy traits for the taxon.", - "items": { - "type": "string" - }, - "type": "array" - }, - "preferred_environments": { - "description": "The preferred environments for the taxon.", - "items": { - "type": "string" - }, - "type": "array" - }, - "reproductive_traits": { - "description": "The reproductive traits for the taxon.", - "items": { - "type": "string" - }, - "type": "array" - }, - "survival_traits": { - "description": "The survival traits for the taxon.", - "items": { - "type": "string" - }, - "type": "array" - } - }, - "title": "traits", - "type": "object", - "version": null -} \ No newline at end of file diff --git a/projects/traits/owl/traits.owl.ttl b/projects/traits/owl/traits.owl.ttl deleted file mode 100644 index 1b531ac3a..000000000 --- a/projects/traits/owl/traits.owl.ttl +++ /dev/null @@ -1,457 +0,0 @@ -@prefix IAO: <http://purl.obolibrary.org/obo/IAO_> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix owl: <http://www.w3.org/2002/07/owl#> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . -@prefix skos: <http://www.w3.org/2004/02/skos/core#> . -@prefix traits: <http://w3id.org/ontogpt/traits/> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -<http://w3id.org/ontogpt/traits> a owl:Ontology ; - rdfs:label "traits" ; - IAO:0000700 <http://w3id.org/ontogpt/core/AnnotatorResult>, - <http://w3id.org/ontogpt/core/Any>, - <http://w3id.org/ontogpt/core/CompoundExpression>, - <http://w3id.org/ontogpt/core/ExtractionResult>, - <http://w3id.org/ontogpt/core/NamedEntity>, - <http://w3id.org/ontogpt/core/Publication>, - <http://w3id.org/ontogpt/core/TextWithTriples>, - traits:Taxon ; - linkml:classes "{'Taxon': ClassDefinition(name='Taxon', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/traits/Taxon', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/traits', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['taxon__metabolic_traits', 'taxon__morphological_traits', 'taxon__genetic_traits', 'taxon__cellular_traits', 'taxon__ecological_traits', 'taxon__reproductive_traits', 'taxon__survival_traits', 'taxon__phenotypic_plasticiticy_traits', 'taxon__preferred_environments'], slot_usage={}, attributes={'metabolic_traits': SlotDefinition(name='metabolic_traits', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='a semicolon separated list of every specific organism metabolic trait', extensions={}, annotations={})}, description='The metabolic traits for the taxon.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Trait', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'morphological_traits': SlotDefinition(name='morphological_traits', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='a semicolon separated list of every specific organism morphological trait', extensions={}, annotations={})}, description='The morphological traits for the taxon.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Trait', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'genetic_traits': SlotDefinition(name='genetic_traits', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='a semicolon separated list of every specific organism genetic trait', extensions={}, annotations={})}, description='The genetic traits for the taxon.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Trait', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'cellular_traits': SlotDefinition(name='cellular_traits', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='a semicolon separated list of every specific organism cellular trait', extensions={}, annotations={})}, description='The cellular traits for the taxon.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Trait', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ecological_traits': SlotDefinition(name='ecological_traits', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='a semicolon separated list of every specific organism ecological trait', extensions={}, annotations={})}, description='The ecological traits for the taxon.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Trait', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'reproductive_traits': SlotDefinition(name='reproductive_traits', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='a semicolon separated list of every specific organism reproductive trait', extensions={}, annotations={})}, description='The reproductive traits for the taxon.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Trait', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'survival_traits': SlotDefinition(name='survival_traits', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='a semicolon separated list of every specific organism survival trait', extensions={}, annotations={})}, description='The survival traits for the taxon.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Trait', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'phenotypic_plasticiticy_traits': SlotDefinition(name='phenotypic_plasticiticy_traits', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='a semicolon separated list of every specific organism phenotypic plasticiticy trait', extensions={}, annotations={})}, description='The phenotypic plasticiticy traits for the taxon.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Trait', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'preferred_environments': SlotDefinition(name='preferred_environments', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='a semicolon separated list of the environments the organism is typically found in or isolated from', extensions={}, annotations={})}, description='The preferred environments for the taxon.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Trait', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='traits:Taxon', subclass_of=None, union_of=[], defining_slots=[], tree_root=True, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Trait': ClassDefinition(name='Trait', id_prefixes=['ECOCORE', 'PATO', 'GO', 'OBA', 'BIODIVTHES'], definition_uri='http://w3id.org/ontogpt/traits/Trait', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:ecocore, sqlite:obo:pato, sqlite:obo:go, sqlite:obo:oba, bioportal:biodivthes', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/traits', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='traits:Trait', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Any': ClassDefinition(name='Any', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Any', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=['linkml:Any'], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='linkml:Any', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ExtractionResult': ClassDefinition(name='ExtractionResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/ExtractionResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A result of extracting knowledge on text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['extractionResult__input_id', 'extractionResult__input_title', 'extractionResult__input_text', 'extractionResult__raw_completion_output', 'extractionResult__prompt', 'extractionResult__extracted_object', 'extractionResult__named_entities'], slot_usage={}, attributes={'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:ExtractionResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'NamedEntity': ClassDefinition(name='NamedEntity', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NamedEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:NamedEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'CompoundExpression': ClassDefinition(name='CompoundExpression', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/CompoundExpression', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='core:CompoundExpression', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Triple': ClassDefinition(name='Triple', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Triple', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Abstract parent for Relation Extraction tasks', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['triple__subject', 'triple__predicate', 'triple__object', 'triple__qualifier', 'triple__subject_qualifier', 'triple__object_qualifier'], slot_usage={}, attributes={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Triple', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'TextWithTriples': ClassDefinition(name='TextWithTriples', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/TextWithTriples', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['textWithTriples__publication', 'textWithTriples__triples'], slot_usage={}, attributes={'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:TextWithTriples', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'RelationshipType': ClassDefinition(name='RelationshipType', id_prefixes=['RO', 'biolink'], definition_uri='http://w3id.org/ontogpt/core/RelationshipType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='core:RelationshipType', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Publication': ClassDefinition(name='Publication', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Publication', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['publication__id', 'publication__title', 'publication__abstract', 'publication__combined_text', 'publication__full_text'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Publication', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'AnnotatorResult': ClassDefinition(name='AnnotatorResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/AnnotatorResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['annotatorResult__subject_text', 'annotatorResult__object_id', 'annotatorResult__object_text'], slot_usage={}, attributes={'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:AnnotatorResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={})}" ; - linkml:enums "{'NullDataOptions': EnumDefinition(name='NullDataOptions', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NullDataOptions', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'UNSPECIFIED_METHOD_OF_ADMINISTRATION': PermissibleValue(text='UNSPECIFIED_METHOD_OF_ADMINISTRATION', description=None, meaning='NCIT:C149701', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_APPLICABLE': PermissibleValue(text='NOT_APPLICABLE', description=None, meaning='NCIT:C18902', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['not applicable', 'N/A'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_MENTIONED': PermissibleValue(text='NOT_MENTIONED', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[])}" ; - linkml:id "http://w3id.org/ontogpt/traits" ; - linkml:imports "core", - "linkml:types" ; - linkml:types "{'string': TypeDefinition(name='string', id_prefixes=[], definition_uri='https://w3id.org/linkml/String', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A character string', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Text'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'integer': TypeDefinition(name='integer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Integer', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An integer', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Integer'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='int', uri='xsd:integer', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'boolean': TypeDefinition(name='boolean', id_prefixes=[], definition_uri='https://w3id.org/linkml/Boolean', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A binary (true or false) value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Boolean'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Bool', uri='xsd:boolean', repr='bool', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'float': TypeDefinition(name='float', id_prefixes=[], definition_uri='https://w3id.org/linkml/Float', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:float specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Float'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:float', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'double': TypeDefinition(name='double', id_prefixes=[], definition_uri='https://w3id.org/linkml/Double', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:double specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:Float'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:double', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'decimal': TypeDefinition(name='decimal', id_prefixes=[], definition_uri='https://w3id.org/linkml/Decimal', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number with arbitrary precision that conforms to the xsd:decimal specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=['schema:Number'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Decimal', uri='xsd:decimal', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'time': TypeDefinition(name='time', id_prefixes=[], definition_uri='https://w3id.org/linkml/Time', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A time object represents a (local) time of day, independent of any particular day', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=['URI is dateTime because OWL reasoners do not work with straight date or time'], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Time'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDTime', uri='xsd:time', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date': TypeDefinition(name='date', id_prefixes=[], definition_uri='https://w3id.org/linkml/Date', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a date (year, month and day) in an idealized calendar', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[\"URI is dateTime because OWL reasoners don't work with straight date or time\"], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Date'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDate', uri='xsd:date', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'datetime': TypeDefinition(name='datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/Datetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The combination of a date and time', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:DateTime'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDateTime', uri='xsd:dateTime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date_or_datetime': TypeDefinition(name='date_or_datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/DateOrDatetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Either a date or a datetime', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='linkml:DateOrDatetime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uriorcurie': TypeDefinition(name='uriorcurie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uriorcurie', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a URI or a CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URIorCURIE', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'curie': TypeDefinition(name='curie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Curie', local_names={}, conforms_to='https://www.w3.org/TR/curie/', implements=[], extensions={}, annotations={}, description='a compact URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations this MUST be expanded to a URI', 'in non-RDF serializations MAY be serialized as the compact representation'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Curie', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uri': TypeDefinition(name='uri', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uri', local_names={}, conforms_to='https://www.ietf.org/rfc/rfc3987.txt', implements=[], extensions={}, annotations={}, description='a complete URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:URL'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URI', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ncname': TypeDefinition(name='ncname', id_prefixes=[], definition_uri='https://w3id.org/linkml/Ncname', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Prefix part of CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NCName', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'objectidentifier': TypeDefinition(name='objectidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Objectidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI or CURIE that represents an object in the model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['Used for inheritance and type checking'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='ElementIdentifier', uri='shex:iri', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'nodeidentifier': TypeDefinition(name='nodeidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Nodeidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI, CURIE or BNODE that represents a node in a model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NodeIdentifier', uri='shex:nonLiteral', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpointer': TypeDefinition(name='jsonpointer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpointer', local_names={}, conforms_to='https://datatracker.ietf.org/doc/html/rfc6901', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpath': TypeDefinition(name='jsonpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpath', local_names={}, conforms_to='https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sparqlpath': TypeDefinition(name='sparqlpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Sparqlpath', local_names={}, conforms_to='https://www.w3.org/TR/sparql11-query/#propertypaths', implements=[], extensions={}, annotations={}, description='A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:SubsetDefinition a owl:Class ; - rdfs:label "subset_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" . - -linkml:TypeDefinition a owl:Class ; - rdfs:label "type_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" ; - linkml:mixins "type_expression" . - -linkml:topValue a owl:DatatypeProperty ; - rdfs:label "value" . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "AnnotatorResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_id> ] ; - linkml:attributes "{'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/ExtractionResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ExtractionResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/prompt> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/extracted_object> ], - [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/named_entities> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_title> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_text> ] ; - skos:definition "A result of extracting knowledge on text" ; - linkml:attributes "{'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/TextWithTriples> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TextWithTriples" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Triple> ; - owl:onProperty <http://w3id.org/ontogpt/core/triples> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Publication> ; - owl:onProperty <http://w3id.org/ontogpt/core/publication> ] ; - linkml:attributes "{'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/abstract> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "abstract" ; - rdfs:range linkml:String ; - skos:definition "The abstract of the publication" . - -<http://w3id.org/ontogpt/core/combined_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "combined_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/extracted_object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "extracted_object" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "The complex objects extracted from the text" . - -<http://w3id.org/ontogpt/core/full_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "full_text" ; - rdfs:range linkml:String ; - skos:definition "The full text of the publication" . - -<http://w3id.org/ontogpt/core/input_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_title" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/named_entities> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "named_entities" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "Named entities extracted from the text" . - -<http://w3id.org/ontogpt/core/object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/object_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/object_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" . - -<http://w3id.org/ontogpt/core/object_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/predicate> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "predicate" ; - rdfs:range <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/prompt> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "prompt" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/publication> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "publication" ; - traits:prompt.skip "true" ; - rdfs:range <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "qualifier" ; - rdfs:range linkml:String ; - skos:definition "A qualifier for the statements, e.g. \"NOT\" for negation" . - -<http://w3id.org/ontogpt/core/raw_completion_output> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "raw_completion_output" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/subject> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/subject_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" . - -<http://w3id.org/ontogpt/core/subject_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "title" ; - rdfs:range linkml:String ; - skos:definition "The title of the publication" . - -<http://w3id.org/ontogpt/core/triples> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "triples" ; - rdfs:range <http://w3id.org/ontogpt/core/Triple> . - -traits:Taxon a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Taxon" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom traits:Trait ; - owl:onProperty traits:genetic_traits ], - [ a owl:Restriction ; - owl:allValuesFrom traits:Trait ; - owl:onProperty traits:phenotypic_plasticiticy_traits ], - [ a owl:Restriction ; - owl:allValuesFrom traits:Trait ; - owl:onProperty traits:cellular_traits ], - [ a owl:Restriction ; - owl:allValuesFrom traits:Trait ; - owl:onProperty traits:preferred_environments ], - [ a owl:Restriction ; - owl:allValuesFrom traits:Trait ; - owl:onProperty traits:ecological_traits ], - [ a owl:Restriction ; - owl:allValuesFrom traits:Trait ; - owl:onProperty traits:reproductive_traits ], - [ a owl:Restriction ; - owl:allValuesFrom traits:Trait ; - owl:onProperty traits:survival_traits ], - [ a owl:Restriction ; - owl:allValuesFrom traits:Trait ; - owl:onProperty traits:metabolic_traits ], - [ a owl:Restriction ; - owl:allValuesFrom traits:Trait ; - owl:onProperty traits:morphological_traits ] ; - linkml:attributes "{'metabolic_traits': SlotDefinition(name='metabolic_traits', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='a semicolon separated list of every specific organism metabolic trait', extensions={}, annotations={})}, description='The metabolic traits for the taxon.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Trait', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'morphological_traits': SlotDefinition(name='morphological_traits', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='a semicolon separated list of every specific organism morphological trait', extensions={}, annotations={})}, description='The morphological traits for the taxon.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Trait', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'genetic_traits': SlotDefinition(name='genetic_traits', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='a semicolon separated list of every specific organism genetic trait', extensions={}, annotations={})}, description='The genetic traits for the taxon.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Trait', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'cellular_traits': SlotDefinition(name='cellular_traits', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='a semicolon separated list of every specific organism cellular trait', extensions={}, annotations={})}, description='The cellular traits for the taxon.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Trait', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ecological_traits': SlotDefinition(name='ecological_traits', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='a semicolon separated list of every specific organism ecological trait', extensions={}, annotations={})}, description='The ecological traits for the taxon.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Trait', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'reproductive_traits': SlotDefinition(name='reproductive_traits', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='a semicolon separated list of every specific organism reproductive trait', extensions={}, annotations={})}, description='The reproductive traits for the taxon.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Trait', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'survival_traits': SlotDefinition(name='survival_traits', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='a semicolon separated list of every specific organism survival trait', extensions={}, annotations={})}, description='The survival traits for the taxon.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Trait', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'phenotypic_plasticiticy_traits': SlotDefinition(name='phenotypic_plasticiticy_traits', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='a semicolon separated list of every specific organism phenotypic plasticiticy trait', extensions={}, annotations={})}, description='The phenotypic plasticiticy traits for the taxon.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Trait', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'preferred_environments': SlotDefinition(name='preferred_environments', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='a semicolon separated list of the environments the organism is typically found in or isolated from', extensions={}, annotations={})}, description='The preferred environments for the taxon.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Trait', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -traits:cellular_traits a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "cellular_traits" ; - traits:prompt "a semicolon separated list of every specific organism cellular trait" ; - rdfs:range traits:Trait ; - skos:definition "The cellular traits for the taxon." . - -traits:ecological_traits a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "ecological_traits" ; - traits:prompt "a semicolon separated list of every specific organism ecological trait" ; - rdfs:range traits:Trait ; - skos:definition "The ecological traits for the taxon." . - -traits:genetic_traits a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "genetic_traits" ; - traits:prompt "a semicolon separated list of every specific organism genetic trait" ; - rdfs:range traits:Trait ; - skos:definition "The genetic traits for the taxon." . - -traits:metabolic_traits a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "metabolic_traits" ; - traits:prompt "a semicolon separated list of every specific organism metabolic trait" ; - rdfs:range traits:Trait ; - skos:definition "The metabolic traits for the taxon." . - -traits:morphological_traits a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "morphological_traits" ; - traits:prompt "a semicolon separated list of every specific organism morphological trait" ; - rdfs:range traits:Trait ; - skos:definition "The morphological traits for the taxon." . - -traits:phenotypic_plasticiticy_traits a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "phenotypic_plasticiticy_traits" ; - traits:prompt "a semicolon separated list of every specific organism phenotypic plasticiticy trait" ; - rdfs:range traits:Trait ; - skos:definition "The phenotypic plasticiticy traits for the taxon." . - -traits:preferred_environments a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "preferred_environments" ; - traits:prompt "a semicolon separated list of the environments the organism is typically found in or isolated from" ; - rdfs:range traits:Trait ; - skos:definition "The preferred environments for the taxon." . - -traits:reproductive_traits a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "reproductive_traits" ; - traits:prompt "a semicolon separated list of every specific organism reproductive trait" ; - rdfs:range traits:Trait ; - skos:definition "The reproductive traits for the taxon." . - -traits:survival_traits a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "survival_traits" ; - traits:prompt "a semicolon separated list of every specific organism survival trait" ; - rdfs:range traits:Trait ; - skos:definition "The survival traits for the taxon." . - -<http://example.org/UNKNOWN/rdfs/label> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "label" ; - traits:owl "AnnotationProperty, AnnotationAssertion" ; - rdfs:range linkml:String ; - skos:altLabel "name" ; - skos:definition "The label (name) of the named thing" ; - skos:exactMatch <http://example.org/UNKNOWN/rdfs/label> . - -<http://purl.obolibrary.org/obo/NCIT_C149701> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "UNSPECIFIED_METHOD_OF_ADMINISTRATION" . - -<http://purl.obolibrary.org/obo/NCIT_C18902> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_APPLICABLE" . - -<http://w3id.org/ontogpt/core/CompoundExpression> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CompoundExpression" ; - linkml:attributes "{}" . - -<http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_MENTIONED" . - -<http://w3id.org/ontogpt/core/RelationshipType> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "RelationshipType" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/Triple> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Triple" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/RelationshipType> ; - owl:onProperty <http://w3id.org/ontogpt/core/predicate> ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - skos:definition "Abstract parent for Relation Extraction tasks" ; - linkml:attributes "{'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -<http://w3id.org/ontogpt/core/id> a owl:ObjectProperty, - linkml:SlotDefinition . - -<http://w3id.org/ontogpt/core/NullDataOptions> a owl:Class, - linkml:EnumDefinition ; - rdfs:label "NullDataOptions" ; - owl:unionOf ( <http://purl.obolibrary.org/obo/NCIT_C149701> <http://purl.obolibrary.org/obo/NCIT_C18902> <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> ) ; - linkml:permissible_values <http://purl.obolibrary.org/obo/NCIT_C149701>, - <http://purl.obolibrary.org/obo/NCIT_C18902>, - <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> . - -<http://w3id.org/ontogpt/core/Publication> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Publication" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/title> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/abstract> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/combined_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/full_text> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/Any> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Any" ; - skos:exactMatch linkml:Any ; - linkml:attributes "{}" . - -<http://w3id.org/ontogpt/core/NamedEntity> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "NamedEntity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://example.org/UNKNOWN/rdfs/label> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:ClassDefinition a owl:Class ; - rdfs:label "class_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "class_expression" . - -traits:Trait a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Trait" ; - traits:annotators "sqlite:obo:ecocore, sqlite:obo:pato, sqlite:obo:go, sqlite:obo:oba, bioportal:biodivthes" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -linkml:SlotDefinition a owl:Class ; - rdfs:label "slot_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "slot_expression" . - - diff --git a/projects/traits/prefixmap/traits.yaml b/projects/traits/prefixmap/traits.yaml deleted file mode 100644 index 8b9ce761a..000000000 --- a/projects/traits/prefixmap/traits.yaml +++ /dev/null @@ -1,40 +0,0 @@ -{ - "BIODIVTHES": "http://example.org/UNKNOWN/BIODIVTHES/", - "ECOCORE": "http://example.org/UNKNOWN/ECOCORE/", - "GO": "http://example.org/UNKNOWN/GO/", - "OBA": "http://example.org/UNKNOWN/OBA/", - "PATO": "http://example.org/UNKNOWN/PATO/", - "RO": "http://purl.obolibrary.org/obo/RO_", - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "traits": "http://w3id.org/ontogpt/traits/", - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } -} diff --git a/projects/traits/protobuf/traits.proto b/projects/traits/protobuf/traits.proto deleted file mode 100644 index 8cfeb2c3e..000000000 --- a/projects/traits/protobuf/traits.proto +++ /dev/null @@ -1,52 +0,0 @@ -message AnnotatorResult - { - string subjectText = 0 - string objectId = 0 - string objectText = 0 - } -// A result of extracting knowledge on text -message ExtractionResult - { - string inputId = 0 - string inputTitle = 0 - string inputText = 0 - string rawCompletionOutput = 0 - string prompt = 0 - any extractedObject = 0 - repeated any namedEntities = 0 - } -message Publication - { - string id = 0 - string title = 0 - string abstract = 0 - string combinedText = 0 - string fullText = 0 - } -message RelationshipType - { - string id = 0 - string label = 0 - } -message Taxon - { - repeated trait metabolicTraits = 0 - repeated trait morphologicalTraits = 0 - repeated trait geneticTraits = 0 - repeated trait cellularTraits = 0 - repeated trait ecologicalTraits = 0 - repeated trait reproductiveTraits = 0 - repeated trait survivalTraits = 0 - repeated trait phenotypicPlasticiticyTraits = 0 - repeated trait preferredEnvironments = 0 - } -message TextWithTriples - { - publication publication = 0 - repeated triple triples = 0 - } -message Trait - { - string id = 0 - string label = 0 - } diff --git a/projects/traits/shacl/traits.shacl.ttl b/projects/traits/shacl/traits.shacl.ttl deleted file mode 100644 index 89f18885e..000000000 --- a/projects/traits/shacl/traits.shacl.ttl +++ /dev/null @@ -1,228 +0,0 @@ -@prefix linkml: <https://w3id.org/linkml/> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix sh: <http://www.w3.org/ns/shacl#> . -@prefix traits: <http://w3id.org/ontogpt/traits/> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/object_id> ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject_text> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object_text> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/AnnotatorResult> . - -<http://w3id.org/ontogpt/core/CompoundExpression> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass <http://w3id.org/ontogpt/core/CompoundExpression> . - -<http://w3id.org/ontogpt/core/ExtractionResult> a sh:NodeShape ; - sh:closed true ; - sh:description "A result of extracting knowledge on text" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class linkml:Any ; - sh:description "The complex objects extracted from the text" ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/extracted_object> ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/input_id> ], - [ sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/prompt> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/input_text> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/input_title> ], - [ sh:class linkml:Any ; - sh:description "Named entities extracted from the text" ; - sh:nodeKind sh:BlankNode ; - sh:order 6 ; - sh:path <http://w3id.org/ontogpt/core/named_entities> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/ExtractionResult> . - -<http://w3id.org/ontogpt/core/TextWithTriples> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/Triple> ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/triples> ], - [ sh:class <http://w3id.org/ontogpt/core/Publication> ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/publication> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/TextWithTriples> . - -traits:Taxon a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class traits:Trait ; - sh:description "The cellular traits for the taxon." ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path traits:cellular_traits ], - [ sh:class traits:Trait ; - sh:description "The survival traits for the taxon." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path traits:survival_traits ], - [ sh:class traits:Trait ; - sh:description "The genetic traits for the taxon." ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path traits:genetic_traits ], - [ sh:class traits:Trait ; - sh:description "The reproductive traits for the taxon." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path traits:reproductive_traits ], - [ sh:class traits:Trait ; - sh:description "The preferred environments for the taxon." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path traits:preferred_environments ], - [ sh:class traits:Trait ; - sh:description "The ecological traits for the taxon." ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path traits:ecological_traits ], - [ sh:class traits:Trait ; - sh:description "The morphological traits for the taxon." ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path traits:morphological_traits ], - [ sh:class traits:Trait ; - sh:description "The phenotypic plasticiticy traits for the taxon." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path traits:phenotypic_plasticiticy_traits ], - [ sh:class traits:Trait ; - sh:description "The metabolic traits for the taxon." ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path traits:metabolic_traits ] ; - sh:targetClass traits:Taxon . - -<http://w3id.org/ontogpt/core/Publication> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The full text of the publication" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/full_text> ], - [ sh:description "The publication identifier" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The abstract of the publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/abstract> ], - [ sh:description "The title of the publication" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/title> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/combined_text> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/RelationshipType> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/Triple> a sh:NodeShape ; - sh:closed false ; - sh:description "Abstract parent for Relation Extraction tasks" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject> ], - [ sh:description "A qualifier for the statements, e.g. \"NOT\" for negation" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/RelationshipType> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/predicate> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/object_qualifier> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Triple> . - -linkml:Any a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass linkml:Any . - -<http://w3id.org/ontogpt/core/NamedEntity> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/NamedEntity> . - -traits:Trait a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass traits:Trait . - diff --git a/projects/traits/shex/traits.shex b/projects/traits/shex/traits.shex deleted file mode 100644 index 12c6ec8da..000000000 --- a/projects/traits/shex/traits.shex +++ /dev/null @@ -1,157 +0,0 @@ -BASE <http://w3id.org/ontogpt/traits/> -PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> -PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> -PREFIX linkml: <https://w3id.org/linkml/> -PREFIX core: <http://w3id.org/ontogpt/core/> -PREFIX rdfs1: <http://example.org/UNKNOWN/rdfs/> - - -linkml:String xsd:string - -linkml:Integer xsd:integer - -linkml:Boolean xsd:boolean - -linkml:Float xsd:float - -linkml:Double xsd:double - -linkml:Decimal xsd:decimal - -linkml:Time xsd:time - -linkml:Date xsd:date - -linkml:Datetime xsd:dateTime - -linkml:DateOrDatetime linkml:DateOrDatetime - -linkml:Uriorcurie IRI - -linkml:Curie xsd:string - -linkml:Uri IRI - -linkml:Ncname xsd:string - -linkml:Objectidentifier IRI - -linkml:Nodeidentifier NONLITERAL - -linkml:Jsonpointer xsd:string - -linkml:Jsonpath xsd:string - -linkml:Sparqlpath xsd:string - -core:AnnotatorResult CLOSED { - ( $core:AnnotatorResult_tes ( core:subject_text @linkml:String ? ; - core:object_id @linkml:String ? ; - core:object_text @linkml:String ? - ) ; - rdf:type [ core:AnnotatorResult ] ? - ) -} - -core:Any CLOSED { - ( $core:Any_tes rdf:type . * ; - rdf:type [ linkml:Any ] ? - ) -} - -core:CompoundExpression ( - { - ( $core:CompoundExpression_tes rdf:type . * ; - rdf:type [ core:CompoundExpression ] ? - ) - } OR @core:Triple -) - -core:ExtractionResult CLOSED { - ( $core:ExtractionResult_tes ( core:input_id @linkml:String ? ; - core:input_title @linkml:String ? ; - core:input_text @linkml:String ? ; - core:raw_completion_output @linkml:String ? ; - core:prompt @linkml:String ? ; - core:extracted_object @core:Any ? ; - core:named_entities @core:Any * - ) ; - rdf:type [ core:ExtractionResult ] ? - ) -} - -core:NamedEntity ( - @core:RelationshipType OR @<Trait> -) - -core:NamedEntity_struct { - ( $core:NamedEntity_tes rdfs1:label @linkml:String ? ; - rdf:type [ core:NamedEntity ] - ) -} - -core:Publication CLOSED { - ( $core:Publication_tes ( core:id @linkml:String ? ; - core:title @linkml:String ? ; - core:abstract @linkml:String ? ; - core:combined_text @linkml:String ? ; - core:full_text @linkml:String ? - ) ; - rdf:type [ core:Publication ] ? - ) -} - -core:RelationshipType CLOSED { - ( $core:RelationshipType_tes ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ core:RelationshipType ] - ) -} - -<Taxon> CLOSED { - ( $<Taxon_tes> ( <metabolic_traits> @<Trait> * ; - <morphological_traits> @<Trait> * ; - <genetic_traits> @<Trait> * ; - <cellular_traits> @<Trait> * ; - <ecological_traits> @<Trait> * ; - <reproductive_traits> @<Trait> * ; - <survival_traits> @<Trait> * ; - <phenotypic_plasticiticy_traits> @<Trait> * ; - <preferred_environments> @<Trait> * - ) ; - rdf:type [ <Taxon> ] ? - ) -} - -core:TextWithTriples CLOSED { - ( $core:TextWithTriples_tes ( core:publication @core:Publication ? ; - core:triples @core:Triple * - ) ; - rdf:type [ core:TextWithTriples ] ? - ) -} - -<Trait> CLOSED { - ( $<Trait_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Trait> ] - ) -} - -core:Triple { - ( $core:Triple_tes ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - core:subject @core:NamedEntity ? ; - core:predicate @core:RelationshipType ? ; - core:object @core:NamedEntity ? ; - core:qualifier @linkml:String ? ; - core:subject_qualifier @core:NamedEntity ? ; - core:object_qualifier @core:NamedEntity ? - ) ; - rdf:type [ core:Triple ] ? - ) -} - - diff --git a/projects/traits/sqlschema/traits.sql b/projects/traits/sqlschema/traits.sql deleted file mode 100644 index 36ce87d04..000000000 --- a/projects/traits/sqlschema/traits.sql +++ /dev/null @@ -1,59 +0,0 @@ - - -CREATE TABLE "AnnotatorResult" ( - subject_text TEXT, - object_id TEXT, - object_text TEXT, - PRIMARY KEY (subject_text, object_id, object_text) -); - -CREATE TABLE "ExtractionResult" ( - input_id TEXT, - input_title TEXT, - input_text TEXT, - raw_completion_output TEXT, - prompt TEXT, - extracted_object TEXT, - named_entities TEXT, - PRIMARY KEY (input_id, input_title, input_text, raw_completion_output, prompt, extracted_object, named_entities) -); - -CREATE TABLE "Publication" ( - id TEXT, - title TEXT, - abstract TEXT, - combined_text TEXT, - full_text TEXT, - PRIMARY KEY (id, title, abstract, combined_text, full_text) -); - -CREATE TABLE "RelationshipType" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Taxon" ( - metabolic_traits TEXT, - morphological_traits TEXT, - genetic_traits TEXT, - cellular_traits TEXT, - ecological_traits TEXT, - reproductive_traits TEXT, - survival_traits TEXT, - phenotypic_plasticiticy_traits TEXT, - preferred_environments TEXT, - PRIMARY KEY (metabolic_traits, morphological_traits, genetic_traits, cellular_traits, ecological_traits, reproductive_traits, survival_traits, phenotypic_plasticiticy_traits, preferred_environments) -); - -CREATE TABLE "TextWithTriples" ( - publication TEXT, - triples TEXT, - PRIMARY KEY (publication, triples) -); - -CREATE TABLE "Trait" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); diff --git a/projects/traits/traits.py b/projects/traits/traits.py deleted file mode 100644 index 1719ab9f9..000000000 --- a/projects/traits/traits.py +++ /dev/null @@ -1,477 +0,0 @@ -# Auto generated from traits.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-08-07T10:56:31 -# Schema: traits -# -# id: http://w3id.org/ontogpt/traits -# description: A template for Traits -# license: https://creativecommons.org/publicdomain/zero/1.0/ - -import dataclasses -import sys -import re -from jsonasobj2 import JsonObj, as_dict -from typing import Optional, List, Union, Dict, ClassVar, Any -from dataclasses import dataclass -from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions - -from linkml_runtime.utils.slot import Slot -from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode -from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int -from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs -from linkml_runtime.utils.formatutils import camelcase, underscore, sfx -from linkml_runtime.utils.enumerations import EnumDefinitionImpl -from rdflib import Namespace, URIRef -from linkml_runtime.utils.curienamespace import CurieNamespace -from linkml_runtime.linkml_model.types import String - -metamodel_version = "1.7.0" -version = None - -# Overwrite dataclasses _init_fn to add **kwargs in __init__ -dataclasses._init_fn = dataclasses_init_fn_with_kwargs - -# Namespaces -BIODIVTHES = CurieNamespace('BIODIVTHES', 'http://example.org/UNKNOWN/BIODIVTHES/') -ECOCORE = CurieNamespace('ECOCORE', 'http://example.org/UNKNOWN/ECOCORE/') -GO = CurieNamespace('GO', 'http://example.org/UNKNOWN/GO/') -OBA = CurieNamespace('OBA', 'http://example.org/UNKNOWN/OBA/') -PATO = CurieNamespace('PATO', 'http://example.org/UNKNOWN/PATO/') -RO = CurieNamespace('RO', 'http://purl.obolibrary.org/obo/RO_') -BIOLINK = CurieNamespace('biolink', 'http://example.org/UNKNOWN/biolink/') -CORE = CurieNamespace('core', 'http://w3id.org/ontogpt/core/') -LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') -RDFS = CurieNamespace('rdfs', 'http://example.org/UNKNOWN/rdfs/') -TRAITS = CurieNamespace('traits', 'http://w3id.org/ontogpt/traits/') -DEFAULT_ = TRAITS - - -# Types - -# Class references -class NamedEntityId(extended_str): - pass - - -class TraitId(NamedEntityId): - pass - - -class RelationshipTypeId(NamedEntityId): - pass - - -@dataclass -class Taxon(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = TRAITS.Taxon - class_class_curie: ClassVar[str] = "traits:Taxon" - class_name: ClassVar[str] = "Taxon" - class_model_uri: ClassVar[URIRef] = TRAITS.Taxon - - metabolic_traits: Optional[Union[Union[str, TraitId], List[Union[str, TraitId]]]] = empty_list() - morphological_traits: Optional[Union[Union[str, TraitId], List[Union[str, TraitId]]]] = empty_list() - genetic_traits: Optional[Union[Union[str, TraitId], List[Union[str, TraitId]]]] = empty_list() - cellular_traits: Optional[Union[Union[str, TraitId], List[Union[str, TraitId]]]] = empty_list() - ecological_traits: Optional[Union[Union[str, TraitId], List[Union[str, TraitId]]]] = empty_list() - reproductive_traits: Optional[Union[Union[str, TraitId], List[Union[str, TraitId]]]] = empty_list() - survival_traits: Optional[Union[Union[str, TraitId], List[Union[str, TraitId]]]] = empty_list() - phenotypic_plasticiticy_traits: Optional[Union[Union[str, TraitId], List[Union[str, TraitId]]]] = empty_list() - preferred_environments: Optional[Union[Union[str, TraitId], List[Union[str, TraitId]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if not isinstance(self.metabolic_traits, list): - self.metabolic_traits = [self.metabolic_traits] if self.metabolic_traits is not None else [] - self.metabolic_traits = [v if isinstance(v, TraitId) else TraitId(v) for v in self.metabolic_traits] - - if not isinstance(self.morphological_traits, list): - self.morphological_traits = [self.morphological_traits] if self.morphological_traits is not None else [] - self.morphological_traits = [v if isinstance(v, TraitId) else TraitId(v) for v in self.morphological_traits] - - if not isinstance(self.genetic_traits, list): - self.genetic_traits = [self.genetic_traits] if self.genetic_traits is not None else [] - self.genetic_traits = [v if isinstance(v, TraitId) else TraitId(v) for v in self.genetic_traits] - - if not isinstance(self.cellular_traits, list): - self.cellular_traits = [self.cellular_traits] if self.cellular_traits is not None else [] - self.cellular_traits = [v if isinstance(v, TraitId) else TraitId(v) for v in self.cellular_traits] - - if not isinstance(self.ecological_traits, list): - self.ecological_traits = [self.ecological_traits] if self.ecological_traits is not None else [] - self.ecological_traits = [v if isinstance(v, TraitId) else TraitId(v) for v in self.ecological_traits] - - if not isinstance(self.reproductive_traits, list): - self.reproductive_traits = [self.reproductive_traits] if self.reproductive_traits is not None else [] - self.reproductive_traits = [v if isinstance(v, TraitId) else TraitId(v) for v in self.reproductive_traits] - - if not isinstance(self.survival_traits, list): - self.survival_traits = [self.survival_traits] if self.survival_traits is not None else [] - self.survival_traits = [v if isinstance(v, TraitId) else TraitId(v) for v in self.survival_traits] - - if not isinstance(self.phenotypic_plasticiticy_traits, list): - self.phenotypic_plasticiticy_traits = [self.phenotypic_plasticiticy_traits] if self.phenotypic_plasticiticy_traits is not None else [] - self.phenotypic_plasticiticy_traits = [v if isinstance(v, TraitId) else TraitId(v) for v in self.phenotypic_plasticiticy_traits] - - if not isinstance(self.preferred_environments, list): - self.preferred_environments = [self.preferred_environments] if self.preferred_environments is not None else [] - self.preferred_environments = [v if isinstance(v, TraitId) else TraitId(v) for v in self.preferred_environments] - - super().__post_init__(**kwargs) - - -Any = Any - -@dataclass -class ExtractionResult(YAMLRoot): - """ - A result of extracting knowledge on text - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.ExtractionResult - class_class_curie: ClassVar[str] = "core:ExtractionResult" - class_name: ClassVar[str] = "ExtractionResult" - class_model_uri: ClassVar[URIRef] = TRAITS.ExtractionResult - - input_id: Optional[str] = None - input_title: Optional[str] = None - input_text: Optional[str] = None - raw_completion_output: Optional[str] = None - prompt: Optional[str] = None - extracted_object: Optional[Union[dict, Any]] = None - named_entities: Optional[Union[Union[dict, Any], List[Union[dict, Any]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.input_id is not None and not isinstance(self.input_id, str): - self.input_id = str(self.input_id) - - if self.input_title is not None and not isinstance(self.input_title, str): - self.input_title = str(self.input_title) - - if self.input_text is not None and not isinstance(self.input_text, str): - self.input_text = str(self.input_text) - - if self.raw_completion_output is not None and not isinstance(self.raw_completion_output, str): - self.raw_completion_output = str(self.raw_completion_output) - - if self.prompt is not None and not isinstance(self.prompt, str): - self.prompt = str(self.prompt) - - super().__post_init__(**kwargs) - - -@dataclass -class NamedEntity(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.NamedEntity - class_class_curie: ClassVar[str] = "core:NamedEntity" - class_name: ClassVar[str] = "NamedEntity" - class_model_uri: ClassVar[URIRef] = TRAITS.NamedEntity - - id: Union[str, NamedEntityId] = None - label: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, NamedEntityId): - self.id = NamedEntityId(self.id) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - super().__post_init__(**kwargs) - - -@dataclass -class Trait(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = TRAITS.Trait - class_class_curie: ClassVar[str] = "traits:Trait" - class_name: ClassVar[str] = "Trait" - class_model_uri: ClassVar[URIRef] = TRAITS.Trait - - id: Union[str, TraitId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, TraitId): - self.id = TraitId(self.id) - - super().__post_init__(**kwargs) - - -class CompoundExpression(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.CompoundExpression - class_class_curie: ClassVar[str] = "core:CompoundExpression" - class_name: ClassVar[str] = "CompoundExpression" - class_model_uri: ClassVar[URIRef] = TRAITS.CompoundExpression - - -@dataclass -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Triple - class_class_curie: ClassVar[str] = "core:Triple" - class_name: ClassVar[str] = "Triple" - class_model_uri: ClassVar[URIRef] = TRAITS.Triple - - subject: Optional[Union[str, NamedEntityId]] = None - predicate: Optional[Union[str, RelationshipTypeId]] = None - object: Optional[Union[str, NamedEntityId]] = None - qualifier: Optional[str] = None - subject_qualifier: Optional[Union[str, NamedEntityId]] = None - object_qualifier: Optional[Union[str, NamedEntityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, NamedEntityId): - self.subject = NamedEntityId(self.subject) - - if self.predicate is not None and not isinstance(self.predicate, RelationshipTypeId): - self.predicate = RelationshipTypeId(self.predicate) - - if self.object is not None and not isinstance(self.object, NamedEntityId): - self.object = NamedEntityId(self.object) - - if self.qualifier is not None and not isinstance(self.qualifier, str): - self.qualifier = str(self.qualifier) - - if self.subject_qualifier is not None and not isinstance(self.subject_qualifier, NamedEntityId): - self.subject_qualifier = NamedEntityId(self.subject_qualifier) - - if self.object_qualifier is not None and not isinstance(self.object_qualifier, NamedEntityId): - self.object_qualifier = NamedEntityId(self.object_qualifier) - - super().__post_init__(**kwargs) - - -@dataclass -class TextWithTriples(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.TextWithTriples - class_class_curie: ClassVar[str] = "core:TextWithTriples" - class_name: ClassVar[str] = "TextWithTriples" - class_model_uri: ClassVar[URIRef] = TRAITS.TextWithTriples - - publication: Optional[Union[dict, "Publication"]] = None - triples: Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.publication is not None and not isinstance(self.publication, Publication): - self.publication = Publication(**as_dict(self.publication)) - - if not isinstance(self.triples, list): - self.triples = [self.triples] if self.triples is not None else [] - self.triples = [v if isinstance(v, Triple) else Triple(**as_dict(v)) for v in self.triples] - - super().__post_init__(**kwargs) - - -@dataclass -class RelationshipType(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.RelationshipType - class_class_curie: ClassVar[str] = "core:RelationshipType" - class_name: ClassVar[str] = "RelationshipType" - class_model_uri: ClassVar[URIRef] = TRAITS.RelationshipType - - id: Union[str, RelationshipTypeId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, RelationshipTypeId): - self.id = RelationshipTypeId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Publication(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Publication - class_class_curie: ClassVar[str] = "core:Publication" - class_name: ClassVar[str] = "Publication" - class_model_uri: ClassVar[URIRef] = TRAITS.Publication - - id: Optional[str] = None - title: Optional[str] = None - abstract: Optional[str] = None - combined_text: Optional[str] = None - full_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.id is not None and not isinstance(self.id, str): - self.id = str(self.id) - - if self.title is not None and not isinstance(self.title, str): - self.title = str(self.title) - - if self.abstract is not None and not isinstance(self.abstract, str): - self.abstract = str(self.abstract) - - if self.combined_text is not None and not isinstance(self.combined_text, str): - self.combined_text = str(self.combined_text) - - if self.full_text is not None and not isinstance(self.full_text, str): - self.full_text = str(self.full_text) - - super().__post_init__(**kwargs) - - -@dataclass -class AnnotatorResult(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.AnnotatorResult - class_class_curie: ClassVar[str] = "core:AnnotatorResult" - class_name: ClassVar[str] = "AnnotatorResult" - class_model_uri: ClassVar[URIRef] = TRAITS.AnnotatorResult - - subject_text: Optional[str] = None - object_id: Optional[str] = None - object_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject_text is not None and not isinstance(self.subject_text, str): - self.subject_text = str(self.subject_text) - - if self.object_id is not None and not isinstance(self.object_id, str): - self.object_id = str(self.object_id) - - if self.object_text is not None and not isinstance(self.object_text, str): - self.object_text = str(self.object_text) - - super().__post_init__(**kwargs) - - -# Enumerations -class NullDataOptions(EnumDefinitionImpl): - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = PermissibleValue(text="UNSPECIFIED_METHOD_OF_ADMINISTRATION", - meaning=NCIT.C149701) - NOT_APPLICABLE = PermissibleValue(text="NOT_APPLICABLE", - meaning=NCIT.C18902) - NOT_MENTIONED = PermissibleValue(text="NOT_MENTIONED") - - _defn = EnumDefinition( - name="NullDataOptions", - ) - -# Slots -class slots: - pass - -slots.taxon__metabolic_traits = Slot(uri=TRAITS.metabolic_traits, name="taxon__metabolic_traits", curie=TRAITS.curie('metabolic_traits'), - model_uri=TRAITS.taxon__metabolic_traits, domain=None, range=Optional[Union[Union[str, TraitId], List[Union[str, TraitId]]]]) - -slots.taxon__morphological_traits = Slot(uri=TRAITS.morphological_traits, name="taxon__morphological_traits", curie=TRAITS.curie('morphological_traits'), - model_uri=TRAITS.taxon__morphological_traits, domain=None, range=Optional[Union[Union[str, TraitId], List[Union[str, TraitId]]]]) - -slots.taxon__genetic_traits = Slot(uri=TRAITS.genetic_traits, name="taxon__genetic_traits", curie=TRAITS.curie('genetic_traits'), - model_uri=TRAITS.taxon__genetic_traits, domain=None, range=Optional[Union[Union[str, TraitId], List[Union[str, TraitId]]]]) - -slots.taxon__cellular_traits = Slot(uri=TRAITS.cellular_traits, name="taxon__cellular_traits", curie=TRAITS.curie('cellular_traits'), - model_uri=TRAITS.taxon__cellular_traits, domain=None, range=Optional[Union[Union[str, TraitId], List[Union[str, TraitId]]]]) - -slots.taxon__ecological_traits = Slot(uri=TRAITS.ecological_traits, name="taxon__ecological_traits", curie=TRAITS.curie('ecological_traits'), - model_uri=TRAITS.taxon__ecological_traits, domain=None, range=Optional[Union[Union[str, TraitId], List[Union[str, TraitId]]]]) - -slots.taxon__reproductive_traits = Slot(uri=TRAITS.reproductive_traits, name="taxon__reproductive_traits", curie=TRAITS.curie('reproductive_traits'), - model_uri=TRAITS.taxon__reproductive_traits, domain=None, range=Optional[Union[Union[str, TraitId], List[Union[str, TraitId]]]]) - -slots.taxon__survival_traits = Slot(uri=TRAITS.survival_traits, name="taxon__survival_traits", curie=TRAITS.curie('survival_traits'), - model_uri=TRAITS.taxon__survival_traits, domain=None, range=Optional[Union[Union[str, TraitId], List[Union[str, TraitId]]]]) - -slots.taxon__phenotypic_plasticiticy_traits = Slot(uri=TRAITS.phenotypic_plasticiticy_traits, name="taxon__phenotypic_plasticiticy_traits", curie=TRAITS.curie('phenotypic_plasticiticy_traits'), - model_uri=TRAITS.taxon__phenotypic_plasticiticy_traits, domain=None, range=Optional[Union[Union[str, TraitId], List[Union[str, TraitId]]]]) - -slots.taxon__preferred_environments = Slot(uri=TRAITS.preferred_environments, name="taxon__preferred_environments", curie=TRAITS.curie('preferred_environments'), - model_uri=TRAITS.taxon__preferred_environments, domain=None, range=Optional[Union[Union[str, TraitId], List[Union[str, TraitId]]]]) - -slots.extractionResult__input_id = Slot(uri=CORE.input_id, name="extractionResult__input_id", curie=CORE.curie('input_id'), - model_uri=TRAITS.extractionResult__input_id, domain=None, range=Optional[str]) - -slots.extractionResult__input_title = Slot(uri=CORE.input_title, name="extractionResult__input_title", curie=CORE.curie('input_title'), - model_uri=TRAITS.extractionResult__input_title, domain=None, range=Optional[str]) - -slots.extractionResult__input_text = Slot(uri=CORE.input_text, name="extractionResult__input_text", curie=CORE.curie('input_text'), - model_uri=TRAITS.extractionResult__input_text, domain=None, range=Optional[str]) - -slots.extractionResult__raw_completion_output = Slot(uri=CORE.raw_completion_output, name="extractionResult__raw_completion_output", curie=CORE.curie('raw_completion_output'), - model_uri=TRAITS.extractionResult__raw_completion_output, domain=None, range=Optional[str]) - -slots.extractionResult__prompt = Slot(uri=CORE.prompt, name="extractionResult__prompt", curie=CORE.curie('prompt'), - model_uri=TRAITS.extractionResult__prompt, domain=None, range=Optional[str]) - -slots.extractionResult__extracted_object = Slot(uri=CORE.extracted_object, name="extractionResult__extracted_object", curie=CORE.curie('extracted_object'), - model_uri=TRAITS.extractionResult__extracted_object, domain=None, range=Optional[Union[dict, Any]]) - -slots.extractionResult__named_entities = Slot(uri=CORE.named_entities, name="extractionResult__named_entities", curie=CORE.curie('named_entities'), - model_uri=TRAITS.extractionResult__named_entities, domain=None, range=Optional[Union[Union[dict, Any], List[Union[dict, Any]]]]) - -slots.namedEntity__id = Slot(uri=CORE.id, name="namedEntity__id", curie=CORE.curie('id'), - model_uri=TRAITS.namedEntity__id, domain=None, range=URIRef) - -slots.namedEntity__label = Slot(uri=RDFS.label, name="namedEntity__label", curie=RDFS.curie('label'), - model_uri=TRAITS.namedEntity__label, domain=None, range=Optional[str]) - -slots.triple__subject = Slot(uri=CORE.subject, name="triple__subject", curie=CORE.curie('subject'), - model_uri=TRAITS.triple__subject, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__predicate = Slot(uri=CORE.predicate, name="triple__predicate", curie=CORE.curie('predicate'), - model_uri=TRAITS.triple__predicate, domain=None, range=Optional[Union[str, RelationshipTypeId]]) - -slots.triple__object = Slot(uri=CORE.object, name="triple__object", curie=CORE.curie('object'), - model_uri=TRAITS.triple__object, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__qualifier = Slot(uri=CORE.qualifier, name="triple__qualifier", curie=CORE.curie('qualifier'), - model_uri=TRAITS.triple__qualifier, domain=None, range=Optional[str]) - -slots.triple__subject_qualifier = Slot(uri=CORE.subject_qualifier, name="triple__subject_qualifier", curie=CORE.curie('subject_qualifier'), - model_uri=TRAITS.triple__subject_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__object_qualifier = Slot(uri=CORE.object_qualifier, name="triple__object_qualifier", curie=CORE.curie('object_qualifier'), - model_uri=TRAITS.triple__object_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.textWithTriples__publication = Slot(uri=CORE.publication, name="textWithTriples__publication", curie=CORE.curie('publication'), - model_uri=TRAITS.textWithTriples__publication, domain=None, range=Optional[Union[dict, Publication]]) - -slots.textWithTriples__triples = Slot(uri=CORE.triples, name="textWithTriples__triples", curie=CORE.curie('triples'), - model_uri=TRAITS.textWithTriples__triples, domain=None, range=Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]]) - -slots.publication__id = Slot(uri=CORE.id, name="publication__id", curie=CORE.curie('id'), - model_uri=TRAITS.publication__id, domain=None, range=Optional[str]) - -slots.publication__title = Slot(uri=CORE.title, name="publication__title", curie=CORE.curie('title'), - model_uri=TRAITS.publication__title, domain=None, range=Optional[str]) - -slots.publication__abstract = Slot(uri=CORE.abstract, name="publication__abstract", curie=CORE.curie('abstract'), - model_uri=TRAITS.publication__abstract, domain=None, range=Optional[str]) - -slots.publication__combined_text = Slot(uri=CORE.combined_text, name="publication__combined_text", curie=CORE.curie('combined_text'), - model_uri=TRAITS.publication__combined_text, domain=None, range=Optional[str]) - -slots.publication__full_text = Slot(uri=CORE.full_text, name="publication__full_text", curie=CORE.curie('full_text'), - model_uri=TRAITS.publication__full_text, domain=None, range=Optional[str]) - -slots.annotatorResult__subject_text = Slot(uri=CORE.subject_text, name="annotatorResult__subject_text", curie=CORE.curie('subject_text'), - model_uri=TRAITS.annotatorResult__subject_text, domain=None, range=Optional[str]) - -slots.annotatorResult__object_id = Slot(uri=CORE.object_id, name="annotatorResult__object_id", curie=CORE.curie('object_id'), - model_uri=TRAITS.annotatorResult__object_id, domain=None, range=Optional[str]) - -slots.annotatorResult__object_text = Slot(uri=CORE.object_text, name="annotatorResult__object_text", curie=CORE.curie('object_text'), - model_uri=TRAITS.annotatorResult__object_text, domain=None, range=Optional[str]) \ No newline at end of file diff --git a/projects/treatment/docs/AdverseEffect.md b/projects/treatment/docs/AdverseEffect.md deleted file mode 100644 index 8242cd541..000000000 --- a/projects/treatment/docs/AdverseEffect.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Class: AdverseEffect - - - - -URI: [treatment:AdverseEffect](http://w3id.org/ontogpt/treatments/AdverseEffect) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[TreatmentAdverseEffect]-%20adverse_effects%200..*>[AdverseEffect|id(i):string;label(i):string%20%3F],[NamedEntity]^-[AdverseEffect],[TreatmentAdverseEffect])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[TreatmentAdverseEffect]-%20adverse_effects%200..*>[AdverseEffect|id(i):string;label(i):string%20%3F],[NamedEntity]^-[AdverseEffect],[TreatmentAdverseEffect]) - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞adverse_effects](treatmentAdverseEffect__adverse_effects.md)* <sub>0..\*</sub> **[AdverseEffect](AdverseEffect.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/treatment/docs/AnnotatorResult.md b/projects/treatment/docs/AnnotatorResult.md deleted file mode 100644 index bc9629fcf..000000000 --- a/projects/treatment/docs/AnnotatorResult.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Class: AnnotatorResult - - - - -URI: [treatment:AnnotatorResult](http://w3id.org/ontogpt/treatments/AnnotatorResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F])](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F]) - -## Attributes - - -### Own - - * [➞subject_text](annotatorResult__subject_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_id](annotatorResult__object_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_text](annotatorResult__object_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) diff --git a/projects/treatment/docs/Any.md b/projects/treatment/docs/Any.md deleted file mode 100644 index 9abde1382..000000000 --- a/projects/treatment/docs/Any.md +++ /dev/null @@ -1,25 +0,0 @@ - -# Class: Any - - - - -URI: [treatment:Any](http://w3id.org/ontogpt/treatments/Any) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult])](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult]) - -## Referenced by Class - - * **None** *[➞extracted_object](extractionResult__extracted_object.md)* <sub>0..1</sub> **[Any](Any.md)** - * **None** *[➞named_entities](extractionResult__named_entities.md)* <sub>0..\*</sub> **[Any](Any.md)** - -## Attributes - - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | linkml:Any | - diff --git a/projects/treatment/docs/CHEBIDrugType.md b/projects/treatment/docs/CHEBIDrugType.md deleted file mode 100644 index a3ad7a5ad..000000000 --- a/projects/treatment/docs/CHEBIDrugType.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Enum: CHEBIDrugType - - - - -URI: [treatment:CHEBIDrugType](http://w3id.org/ontogpt/treatments/CHEBIDrugType) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | - diff --git a/projects/treatment/docs/CompoundExpression.md b/projects/treatment/docs/CompoundExpression.md deleted file mode 100644 index f4039af7f..000000000 --- a/projects/treatment/docs/CompoundExpression.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Class: CompoundExpression - - - - -URI: [treatment:CompoundExpression](http://w3id.org/ontogpt/treatments/CompoundExpression) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[TreatmentMechanism],[TreatmentEfficacy],[TreatmentAdverseEffect],[CompoundExpression]^-[Triple],[CompoundExpression]^-[TreatmentMechanism],[CompoundExpression]^-[TreatmentEfficacy],[CompoundExpression]^-[TreatmentAdverseEffect])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[TreatmentMechanism],[TreatmentEfficacy],[TreatmentAdverseEffect],[CompoundExpression]^-[Triple],[CompoundExpression]^-[TreatmentMechanism],[CompoundExpression]^-[TreatmentEfficacy],[CompoundExpression]^-[TreatmentAdverseEffect]) - -## Children - - * [TreatmentAdverseEffect](TreatmentAdverseEffect.md) - * [TreatmentEfficacy](TreatmentEfficacy.md) - * [TreatmentMechanism](TreatmentMechanism.md) - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - -## Referenced by Class - - -## Attributes - diff --git a/projects/treatment/docs/Disease.md b/projects/treatment/docs/Disease.md deleted file mode 100644 index 4b0212050..000000000 --- a/projects/treatment/docs/Disease.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Class: Disease - - - - -URI: [treatment:Disease](http://w3id.org/ontogpt/treatments/Disease) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[DiseaseTreatmentSummary]-%20disease%200..1>[Disease|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Disease],[DiseaseTreatmentSummary])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[DiseaseTreatmentSummary]-%20disease%200..1>[Disease|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Disease],[DiseaseTreatmentSummary]) - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞disease](diseaseTreatmentSummary__disease.md)* <sub>0..1</sub> **[Disease](Disease.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/treatment/docs/DiseaseTreatmentSummary.md b/projects/treatment/docs/DiseaseTreatmentSummary.md deleted file mode 100644 index 7291c8464..000000000 --- a/projects/treatment/docs/DiseaseTreatmentSummary.md +++ /dev/null @@ -1,37 +0,0 @@ - -# Class: DiseaseTreatmentSummary - - - - -URI: [treatment:DiseaseTreatmentSummary](http://w3id.org/ontogpt/treatments/DiseaseTreatmentSummary) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[TreatmentMechanism],[TreatmentEfficacy],[TreatmentAdverseEffect],[Treatment],[Drug],[TreatmentAdverseEffect]<treatment_adverse_effects%200..*-++[DiseaseTreatmentSummary],[TreatmentEfficacy]<treatment_efficacies%200..*-++[DiseaseTreatmentSummary],[TreatmentMechanism]<treatment_mechanisms%200..*-++[DiseaseTreatmentSummary],[Treatment]<contraindications%200..*-%20[DiseaseTreatmentSummary],[Treatment]<treatments%200..*-%20[DiseaseTreatmentSummary],[Drug]<drugs%200..*-%20[DiseaseTreatmentSummary],[Disease]<disease%200..1-%20[DiseaseTreatmentSummary],[Disease])](https://yuml.me/diagram/nofunky;dir:TB/class/[TreatmentMechanism],[TreatmentEfficacy],[TreatmentAdverseEffect],[Treatment],[Drug],[TreatmentAdverseEffect]<treatment_adverse_effects%200..*-++[DiseaseTreatmentSummary],[TreatmentEfficacy]<treatment_efficacies%200..*-++[DiseaseTreatmentSummary],[TreatmentMechanism]<treatment_mechanisms%200..*-++[DiseaseTreatmentSummary],[Treatment]<contraindications%200..*-%20[DiseaseTreatmentSummary],[Treatment]<treatments%200..*-%20[DiseaseTreatmentSummary],[Drug]<drugs%200..*-%20[DiseaseTreatmentSummary],[Disease]<disease%200..1-%20[DiseaseTreatmentSummary],[Disease]) - -## Attributes - - -### Own - - * [➞disease](diseaseTreatmentSummary__disease.md) <sub>0..1</sub> - * Description: the name of the disease that is treated. - * Range: [Disease](Disease.md) - * [➞drugs](diseaseTreatmentSummary__drugs.md) <sub>0..\*</sub> - * Description: semicolon-separated list of named small molecule drugs - * Range: [Drug](Drug.md) - * [➞treatments](diseaseTreatmentSummary__treatments.md) <sub>0..\*</sub> - * Description: semicolon-separated list of therapies and treatments are indicated for treating the disease. - * Range: [Treatment](Treatment.md) - * [➞contraindications](diseaseTreatmentSummary__contraindications.md) <sub>0..\*</sub> - * Description: semicolon-separated list of therapies and treatments that are contra-indicated for the disease, and should not be used, due to risk of adverse effects. - * Range: [Treatment](Treatment.md) - * [➞treatment_mechanisms](diseaseTreatmentSummary__treatment_mechanisms.md) <sub>0..\*</sub> - * Description: semicolon-separated list of treatment to asterisk-separated mechanism associations - * Range: [TreatmentMechanism](TreatmentMechanism.md) - * [➞treatment_efficacies](diseaseTreatmentSummary__treatment_efficacies.md) <sub>0..\*</sub> - * Description: semicolon-separated list of treatment to efficacy associations, e.g. Imatinib*effective - * Range: [TreatmentEfficacy](TreatmentEfficacy.md) - * [➞treatment_adverse_effects](diseaseTreatmentSummary__treatment_adverse_effects.md) <sub>0..\*</sub> - * Description: semicolon-separated list of treatment to adverse effect associations, e.g. Imatinib*nausea - * Range: [TreatmentAdverseEffect](TreatmentAdverseEffect.md) diff --git a/projects/treatment/docs/Drug.md b/projects/treatment/docs/Drug.md deleted file mode 100644 index 3bed19e60..000000000 --- a/projects/treatment/docs/Drug.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Class: Drug - - - - -URI: [treatment:Drug](http://w3id.org/ontogpt/treatments/Drug) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[DiseaseTreatmentSummary]-%20drugs%200..*>[Drug|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Drug],[DiseaseTreatmentSummary])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[DiseaseTreatmentSummary]-%20drugs%200..*>[Drug|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Drug],[DiseaseTreatmentSummary]) - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞drugs](diseaseTreatmentSummary__drugs.md)* <sub>0..\*</sub> **[Drug](Drug.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/treatment/docs/ExtractionResult.md b/projects/treatment/docs/ExtractionResult.md deleted file mode 100644 index 5a9073b6d..000000000 --- a/projects/treatment/docs/ExtractionResult.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Class: ExtractionResult - - -A result of extracting knowledge on text - -URI: [treatment:ExtractionResult](http://w3id.org/ontogpt/treatments/ExtractionResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any])](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any]) - -## Attributes - - -### Own - - * [➞input_id](extractionResult__input_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_title](extractionResult__input_title.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_text](extractionResult__input_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞prompt](extractionResult__prompt.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞extracted_object](extractionResult__extracted_object.md) <sub>0..1</sub> - * Description: The complex objects extracted from the text - * Range: [Any](Any.md) - * [➞named_entities](extractionResult__named_entities.md) <sub>0..\*</sub> - * Description: Named entities extracted from the text - * Range: [Any](Any.md) diff --git a/projects/treatment/docs/Gene.md b/projects/treatment/docs/Gene.md deleted file mode 100644 index 25de630ea..000000000 --- a/projects/treatment/docs/Gene.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Class: Gene - - - - -URI: [treatment:Gene](http://w3id.org/ontogpt/treatments/Gene) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[NamedEntity]^-[Gene|id(i):string;label(i):string%20%3F])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[NamedEntity]^-[Gene|id(i):string;label(i):string%20%3F]) - -## Identifier prefixes - - * HGNC - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/treatment/docs/MAXOActionType.md b/projects/treatment/docs/MAXOActionType.md deleted file mode 100644 index 2b0fe096b..000000000 --- a/projects/treatment/docs/MAXOActionType.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Enum: MAXOActionType - - - - -URI: [treatment:MAXOActionType](http://w3id.org/ontogpt/treatments/MAXOActionType) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | - diff --git a/projects/treatment/docs/MESHTherapeuticType.md b/projects/treatment/docs/MESHTherapeuticType.md deleted file mode 100644 index 0854fbe8a..000000000 --- a/projects/treatment/docs/MESHTherapeuticType.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Enum: MESHTherapeuticType - - - - -URI: [treatment:MESHTherapeuticType](http://w3id.org/ontogpt/treatments/MESHTherapeuticType) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | - diff --git a/projects/treatment/docs/Mechanism.md b/projects/treatment/docs/Mechanism.md deleted file mode 100644 index 9f5b3b682..000000000 --- a/projects/treatment/docs/Mechanism.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Class: Mechanism - - - - -URI: [treatment:Mechanism](http://w3id.org/ontogpt/treatments/Mechanism) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[TreatmentMechanism]-%20mechanism%200..1>[Mechanism|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Mechanism],[TreatmentMechanism])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[TreatmentMechanism]-%20mechanism%200..1>[Mechanism|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Mechanism],[TreatmentMechanism]) - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞mechanism](treatmentMechanism__mechanism.md)* <sub>0..1</sub> **[Mechanism](Mechanism.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/treatment/docs/NCITDrugType.md b/projects/treatment/docs/NCITDrugType.md deleted file mode 100644 index 207ca34fc..000000000 --- a/projects/treatment/docs/NCITDrugType.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Enum: NCITDrugType - - - - -URI: [treatment:NCITDrugType](http://w3id.org/ontogpt/treatments/NCITDrugType) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | - diff --git a/projects/treatment/docs/NCITTActivityType.md b/projects/treatment/docs/NCITTActivityType.md deleted file mode 100644 index 137a51225..000000000 --- a/projects/treatment/docs/NCITTActivityType.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Enum: NCITTActivityType - - - - -URI: [treatment:NCITTActivityType](http://w3id.org/ontogpt/treatments/NCITTActivityType) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | - diff --git a/projects/treatment/docs/NCITTreatmentType.md b/projects/treatment/docs/NCITTreatmentType.md deleted file mode 100644 index 9c3f64e51..000000000 --- a/projects/treatment/docs/NCITTreatmentType.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Enum: NCITTreatmentType - - - - -URI: [treatment:NCITTreatmentType](http://w3id.org/ontogpt/treatments/NCITTreatmentType) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | - diff --git a/projects/treatment/docs/NamedEntity.md b/projects/treatment/docs/NamedEntity.md deleted file mode 100644 index 14298c0fa..000000000 --- a/projects/treatment/docs/NamedEntity.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Class: NamedEntity - - - - -URI: [treatment:NamedEntity](http://w3id.org/ontogpt/treatments/NamedEntity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Treatment],[Symptom],[RelationshipType],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[Treatment],[NamedEntity]^-[Symptom],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[Mechanism],[NamedEntity]^-[Gene],[NamedEntity]^-[Drug],[NamedEntity]^-[Disease],[NamedEntity]^-[AdverseEffect],[Triple],[Mechanism],[Gene],[Drug],[Disease],[AdverseEffect])](https://yuml.me/diagram/nofunky;dir:TB/class/[Treatment],[Symptom],[RelationshipType],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[Treatment],[NamedEntity]^-[Symptom],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[Mechanism],[NamedEntity]^-[Gene],[NamedEntity]^-[Drug],[NamedEntity]^-[Disease],[NamedEntity]^-[AdverseEffect],[Triple],[Mechanism],[Gene],[Drug],[Disease],[AdverseEffect]) - -## Children - - * [AdverseEffect](AdverseEffect.md) - * [Disease](Disease.md) - * [Drug](Drug.md) - * [Gene](Gene.md) - * [Mechanism](Mechanism.md) - * [RelationshipType](RelationshipType.md) - * [Symptom](Symptom.md) - * [Treatment](Treatment.md) - -## Referenced by Class - - * **None** *[➞object](triple__object.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞object_qualifier](triple__object_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject](triple__subject.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject_qualifier](triple__subject_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - -## Attributes - - -### Own - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/treatment/docs/NullDataOptions.md b/projects/treatment/docs/NullDataOptions.md deleted file mode 100644 index e1042633c..000000000 --- a/projects/treatment/docs/NullDataOptions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Enum: NullDataOptions - - - - -URI: [treatment:NullDataOptions](http://w3id.org/ontogpt/treatments/NullDataOptions) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | -| UNSPECIFIED_METHOD_OF_ADMINISTRATION | | NCIT:C149701 | | -| NOT_APPLICABLE | | NCIT:C18902 | {'aliases': ['not applicable', 'N/A']} | -| NOT_MENTIONED | | | | - diff --git a/projects/treatment/docs/Publication.md b/projects/treatment/docs/Publication.md deleted file mode 100644 index e32646674..000000000 --- a/projects/treatment/docs/Publication.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Publication - - - - -URI: [treatment:Publication](http://w3id.org/ontogpt/treatments/Publication) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples])](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples]) - -## Referenced by Class - - * **None** *[➞publication](textWithTriples__publication.md)* <sub>0..1</sub> **[Publication](Publication.md)** - -## Attributes - - -### Own - - * [➞id](publication__id.md) <sub>0..1</sub> - * Description: The publication identifier - * Range: [String](types/String.md) - * [➞title](publication__title.md) <sub>0..1</sub> - * Description: The title of the publication - * Range: [String](types/String.md) - * [➞abstract](publication__abstract.md) <sub>0..1</sub> - * Description: The abstract of the publication - * Range: [String](types/String.md) - * [➞combined_text](publication__combined_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞full_text](publication__full_text.md) <sub>0..1</sub> - * Description: The full text of the publication - * Range: [String](types/String.md) diff --git a/projects/treatment/docs/RelationshipType.md b/projects/treatment/docs/RelationshipType.md deleted file mode 100644 index aa95855a1..000000000 --- a/projects/treatment/docs/RelationshipType.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: RelationshipType - - - - -URI: [treatment:RelationshipType](http://w3id.org/ontogpt/treatments/RelationshipType) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity]) - -## Identifier prefixes - - * RO - * biolink - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞predicate](triple__predicate.md)* <sub>0..1</sub> **[RelationshipType](RelationshipType.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/treatment/docs/Symptom.md b/projects/treatment/docs/Symptom.md deleted file mode 100644 index 05d3d1aba..000000000 --- a/projects/treatment/docs/Symptom.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Class: Symptom - - - - -URI: [treatment:Symptom](http://w3id.org/ontogpt/treatments/Symptom) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]^-[Symptom|id(i):string;label(i):string%20%3F],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]^-[Symptom|id(i):string;label(i):string%20%3F],[NamedEntity]) - -## Identifier prefixes - - * HP - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/treatment/docs/TextWithTriples.md b/projects/treatment/docs/TextWithTriples.md deleted file mode 100644 index ac1a41b02..000000000 --- a/projects/treatment/docs/TextWithTriples.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: TextWithTriples - - - - -URI: [treatment:TextWithTriples](http://w3id.org/ontogpt/treatments/TextWithTriples) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication]) - -## Attributes - - -### Own - - * [➞publication](textWithTriples__publication.md) <sub>0..1</sub> - * Range: [Publication](Publication.md) - * [➞triples](textWithTriples__triples.md) <sub>0..\*</sub> - * Range: [Triple](Triple.md) diff --git a/projects/treatment/docs/TreatmentAdverseEffect.md b/projects/treatment/docs/TreatmentAdverseEffect.md deleted file mode 100644 index 566edd21d..000000000 --- a/projects/treatment/docs/TreatmentAdverseEffect.md +++ /dev/null @@ -1,28 +0,0 @@ - -# Class: TreatmentAdverseEffect - - - - -URI: [treatment:TreatmentAdverseEffect](http://w3id.org/ontogpt/treatments/TreatmentAdverseEffect) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[AdverseEffect]<adverse_effects%200..*-%20[TreatmentAdverseEffect],[Treatment]<treatment%200..1-%20[TreatmentAdverseEffect],[DiseaseTreatmentSummary]++-%20treatment_adverse_effects%200..*>[TreatmentAdverseEffect],[CompoundExpression]^-[TreatmentAdverseEffect],[Treatment],[DiseaseTreatmentSummary],[CompoundExpression],[AdverseEffect])](https://yuml.me/diagram/nofunky;dir:TB/class/[AdverseEffect]<adverse_effects%200..*-%20[TreatmentAdverseEffect],[Treatment]<treatment%200..1-%20[TreatmentAdverseEffect],[DiseaseTreatmentSummary]++-%20treatment_adverse_effects%200..*>[TreatmentAdverseEffect],[CompoundExpression]^-[TreatmentAdverseEffect],[Treatment],[DiseaseTreatmentSummary],[CompoundExpression],[AdverseEffect]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞treatment_adverse_effects](diseaseTreatmentSummary__treatment_adverse_effects.md)* <sub>0..\*</sub> **[TreatmentAdverseEffect](TreatmentAdverseEffect.md)** - -## Attributes - - -### Own - - * [➞treatment](treatmentAdverseEffect__treatment.md) <sub>0..1</sub> - * Range: [Treatment](Treatment.md) - * [➞adverse_effects](treatmentAdverseEffect__adverse_effects.md) <sub>0..\*</sub> - * Range: [AdverseEffect](AdverseEffect.md) diff --git a/projects/treatment/docs/TreatmentEfficacy.md b/projects/treatment/docs/TreatmentEfficacy.md deleted file mode 100644 index f1e9c8c46..000000000 --- a/projects/treatment/docs/TreatmentEfficacy.md +++ /dev/null @@ -1,28 +0,0 @@ - -# Class: TreatmentEfficacy - - - - -URI: [treatment:TreatmentEfficacy](http://w3id.org/ontogpt/treatments/TreatmentEfficacy) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Treatment]<treatment%200..1-%20[TreatmentEfficacy|efficacy:string%20%3F],[DiseaseTreatmentSummary]++-%20treatment_efficacies%200..*>[TreatmentEfficacy],[CompoundExpression]^-[TreatmentEfficacy],[Treatment],[DiseaseTreatmentSummary],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[Treatment]<treatment%200..1-%20[TreatmentEfficacy|efficacy:string%20%3F],[DiseaseTreatmentSummary]++-%20treatment_efficacies%200..*>[TreatmentEfficacy],[CompoundExpression]^-[TreatmentEfficacy],[Treatment],[DiseaseTreatmentSummary],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞treatment_efficacies](diseaseTreatmentSummary__treatment_efficacies.md)* <sub>0..\*</sub> **[TreatmentEfficacy](TreatmentEfficacy.md)** - -## Attributes - - -### Own - - * [➞treatment](treatmentEfficacy__treatment.md) <sub>0..1</sub> - * Range: [Treatment](Treatment.md) - * [➞efficacy](treatmentEfficacy__efficacy.md) <sub>0..1</sub> - * Range: [String](types/String.md) diff --git a/projects/treatment/docs/TreatmentMechanism.md b/projects/treatment/docs/TreatmentMechanism.md deleted file mode 100644 index f679702fc..000000000 --- a/projects/treatment/docs/TreatmentMechanism.md +++ /dev/null @@ -1,28 +0,0 @@ - -# Class: TreatmentMechanism - - - - -URI: [treatment:TreatmentMechanism](http://w3id.org/ontogpt/treatments/TreatmentMechanism) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Mechanism]<mechanism%200..1-%20[TreatmentMechanism],[Treatment]<treatment%200..1-%20[TreatmentMechanism],[DiseaseTreatmentSummary]++-%20treatment_mechanisms%200..*>[TreatmentMechanism],[CompoundExpression]^-[TreatmentMechanism],[Treatment],[Mechanism],[DiseaseTreatmentSummary],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[Mechanism]<mechanism%200..1-%20[TreatmentMechanism],[Treatment]<treatment%200..1-%20[TreatmentMechanism],[DiseaseTreatmentSummary]++-%20treatment_mechanisms%200..*>[TreatmentMechanism],[CompoundExpression]^-[TreatmentMechanism],[Treatment],[Mechanism],[DiseaseTreatmentSummary],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞treatment_mechanisms](diseaseTreatmentSummary__treatment_mechanisms.md)* <sub>0..\*</sub> **[TreatmentMechanism](TreatmentMechanism.md)** - -## Attributes - - -### Own - - * [➞treatment](treatmentMechanism__treatment.md) <sub>0..1</sub> - * Range: [Treatment](Treatment.md) - * [➞mechanism](treatmentMechanism__mechanism.md) <sub>0..1</sub> - * Range: [Mechanism](Mechanism.md) diff --git a/projects/treatment/docs/Triple.md b/projects/treatment/docs/Triple.md deleted file mode 100644 index 758d9b45c..000000000 --- a/projects/treatment/docs/Triple.md +++ /dev/null @@ -1,39 +0,0 @@ - -# Class: Triple - - -Abstract parent for Relation Extraction tasks - -URI: [treatment:Triple](http://w3id.org/ontogpt/treatments/Triple) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞triples](textWithTriples__triples.md)* <sub>0..\*</sub> **[Triple](Triple.md)** - -## Attributes - - -### Own - - * [➞subject](triple__subject.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞predicate](triple__predicate.md) <sub>0..1</sub> - * Range: [RelationshipType](RelationshipType.md) - * [➞object](triple__object.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞qualifier](triple__qualifier.md) <sub>0..1</sub> - * Description: A qualifier for the statements, e.g. "NOT" for negation - * Range: [String](types/String.md) - * [➞subject_qualifier](triple__subject_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - * Range: [NamedEntity](NamedEntity.md) - * [➞object_qualifier](triple__object_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * Range: [NamedEntity](NamedEntity.md) diff --git a/projects/treatment/docs/annotatorResult__object_id.md b/projects/treatment/docs/annotatorResult__object_id.md deleted file mode 100644 index 02bcff799..000000000 --- a/projects/treatment/docs/annotatorResult__object_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_id - - - - -URI: [treatment:annotatorResult__object_id](http://w3id.org/ontogpt/treatments/annotatorResult__object_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/treatment/docs/annotatorResult__object_text.md b/projects/treatment/docs/annotatorResult__object_text.md deleted file mode 100644 index a318994e9..000000000 --- a/projects/treatment/docs/annotatorResult__object_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_text - - - - -URI: [treatment:annotatorResult__object_text](http://w3id.org/ontogpt/treatments/annotatorResult__object_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/treatment/docs/annotatorResult__subject_text.md b/projects/treatment/docs/annotatorResult__subject_text.md deleted file mode 100644 index b04025e26..000000000 --- a/projects/treatment/docs/annotatorResult__subject_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_text - - - - -URI: [treatment:annotatorResult__subject_text](http://w3id.org/ontogpt/treatments/annotatorResult__subject_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/treatment/docs/diseaseTreatmentSummary__contraindications.md b/projects/treatment/docs/diseaseTreatmentSummary__contraindications.md deleted file mode 100644 index 4c67b2b00..000000000 --- a/projects/treatment/docs/diseaseTreatmentSummary__contraindications.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: contraindications - - -semicolon-separated list of therapies and treatments that are contra-indicated for the disease, and should not be used, due to risk of adverse effects. - -URI: [treatment:diseaseTreatmentSummary__contraindications](http://w3id.org/ontogpt/treatments/diseaseTreatmentSummary__contraindications) - - -## Domain and Range - -None → <sub>0..\*</sub> [Treatment](Treatment.md) - -## Parents - - -## Children - - -## Used by - - * [DiseaseTreatmentSummary](DiseaseTreatmentSummary.md) diff --git a/projects/treatment/docs/diseaseTreatmentSummary__disease.md b/projects/treatment/docs/diseaseTreatmentSummary__disease.md deleted file mode 100644 index c5fb326eb..000000000 --- a/projects/treatment/docs/diseaseTreatmentSummary__disease.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: disease - - -the name of the disease that is treated. - -URI: [treatment:diseaseTreatmentSummary__disease](http://w3id.org/ontogpt/treatments/diseaseTreatmentSummary__disease) - - -## Domain and Range - -None → <sub>0..1</sub> [Disease](Disease.md) - -## Parents - - -## Children - - -## Used by - - * [DiseaseTreatmentSummary](DiseaseTreatmentSummary.md) diff --git a/projects/treatment/docs/diseaseTreatmentSummary__drugs.md b/projects/treatment/docs/diseaseTreatmentSummary__drugs.md deleted file mode 100644 index a7e766a23..000000000 --- a/projects/treatment/docs/diseaseTreatmentSummary__drugs.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: drugs - - -semicolon-separated list of named small molecule drugs - -URI: [treatment:diseaseTreatmentSummary__drugs](http://w3id.org/ontogpt/treatments/diseaseTreatmentSummary__drugs) - - -## Domain and Range - -None → <sub>0..\*</sub> [Drug](Drug.md) - -## Parents - - -## Children - - -## Used by - - * [DiseaseTreatmentSummary](DiseaseTreatmentSummary.md) diff --git a/projects/treatment/docs/diseaseTreatmentSummary__treatment_adverse_effects.md b/projects/treatment/docs/diseaseTreatmentSummary__treatment_adverse_effects.md deleted file mode 100644 index 1171a5eb4..000000000 --- a/projects/treatment/docs/diseaseTreatmentSummary__treatment_adverse_effects.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: treatment_adverse_effects - - -semicolon-separated list of treatment to adverse effect associations, e.g. Imatinib*nausea - -URI: [treatment:diseaseTreatmentSummary__treatment_adverse_effects](http://w3id.org/ontogpt/treatments/diseaseTreatmentSummary__treatment_adverse_effects) - - -## Domain and Range - -None → <sub>0..\*</sub> [TreatmentAdverseEffect](TreatmentAdverseEffect.md) - -## Parents - - -## Children - - -## Used by - - * [DiseaseTreatmentSummary](DiseaseTreatmentSummary.md) diff --git a/projects/treatment/docs/diseaseTreatmentSummary__treatment_efficacies.md b/projects/treatment/docs/diseaseTreatmentSummary__treatment_efficacies.md deleted file mode 100644 index 9da50e227..000000000 --- a/projects/treatment/docs/diseaseTreatmentSummary__treatment_efficacies.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: treatment_efficacies - - -semicolon-separated list of treatment to efficacy associations, e.g. Imatinib*effective - -URI: [treatment:diseaseTreatmentSummary__treatment_efficacies](http://w3id.org/ontogpt/treatments/diseaseTreatmentSummary__treatment_efficacies) - - -## Domain and Range - -None → <sub>0..\*</sub> [TreatmentEfficacy](TreatmentEfficacy.md) - -## Parents - - -## Children - - -## Used by - - * [DiseaseTreatmentSummary](DiseaseTreatmentSummary.md) diff --git a/projects/treatment/docs/diseaseTreatmentSummary__treatment_mechanisms.md b/projects/treatment/docs/diseaseTreatmentSummary__treatment_mechanisms.md deleted file mode 100644 index 4e152c17d..000000000 --- a/projects/treatment/docs/diseaseTreatmentSummary__treatment_mechanisms.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: treatment_mechanisms - - -semicolon-separated list of treatment to asterisk-separated mechanism associations - -URI: [treatment:diseaseTreatmentSummary__treatment_mechanisms](http://w3id.org/ontogpt/treatments/diseaseTreatmentSummary__treatment_mechanisms) - - -## Domain and Range - -None → <sub>0..\*</sub> [TreatmentMechanism](TreatmentMechanism.md) - -## Parents - - -## Children - - -## Used by - - * [DiseaseTreatmentSummary](DiseaseTreatmentSummary.md) diff --git a/projects/treatment/docs/diseaseTreatmentSummary__treatments.md b/projects/treatment/docs/diseaseTreatmentSummary__treatments.md deleted file mode 100644 index ec1002dfb..000000000 --- a/projects/treatment/docs/diseaseTreatmentSummary__treatments.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: treatments - - -semicolon-separated list of therapies and treatments are indicated for treating the disease. - -URI: [treatment:diseaseTreatmentSummary__treatments](http://w3id.org/ontogpt/treatments/diseaseTreatmentSummary__treatments) - - -## Domain and Range - -None → <sub>0..\*</sub> [Treatment](Treatment.md) - -## Parents - - -## Children - - -## Used by - - * [DiseaseTreatmentSummary](DiseaseTreatmentSummary.md) diff --git a/projects/treatment/docs/extractionResult__extracted_object.md b/projects/treatment/docs/extractionResult__extracted_object.md deleted file mode 100644 index 455833d35..000000000 --- a/projects/treatment/docs/extractionResult__extracted_object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: extracted_object - - -The complex objects extracted from the text - -URI: [treatment:extractionResult__extracted_object](http://w3id.org/ontogpt/treatments/extractionResult__extracted_object) - - -## Domain and Range - -None → <sub>0..1</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/treatment/docs/extractionResult__input_id.md b/projects/treatment/docs/extractionResult__input_id.md deleted file mode 100644 index 31fd80560..000000000 --- a/projects/treatment/docs/extractionResult__input_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_id - - - - -URI: [treatment:extractionResult__input_id](http://w3id.org/ontogpt/treatments/extractionResult__input_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/treatment/docs/extractionResult__input_text.md b/projects/treatment/docs/extractionResult__input_text.md deleted file mode 100644 index 50cc4f58e..000000000 --- a/projects/treatment/docs/extractionResult__input_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_text - - - - -URI: [treatment:extractionResult__input_text](http://w3id.org/ontogpt/treatments/extractionResult__input_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/treatment/docs/extractionResult__input_title.md b/projects/treatment/docs/extractionResult__input_title.md deleted file mode 100644 index c2c211e2e..000000000 --- a/projects/treatment/docs/extractionResult__input_title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_title - - - - -URI: [treatment:extractionResult__input_title](http://w3id.org/ontogpt/treatments/extractionResult__input_title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/treatment/docs/extractionResult__named_entities.md b/projects/treatment/docs/extractionResult__named_entities.md deleted file mode 100644 index 7394e2a73..000000000 --- a/projects/treatment/docs/extractionResult__named_entities.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: named_entities - - -Named entities extracted from the text - -URI: [treatment:extractionResult__named_entities](http://w3id.org/ontogpt/treatments/extractionResult__named_entities) - - -## Domain and Range - -None → <sub>0..\*</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/treatment/docs/extractionResult__prompt.md b/projects/treatment/docs/extractionResult__prompt.md deleted file mode 100644 index 6212791e0..000000000 --- a/projects/treatment/docs/extractionResult__prompt.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: prompt - - - - -URI: [treatment:extractionResult__prompt](http://w3id.org/ontogpt/treatments/extractionResult__prompt) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/treatment/docs/extractionResult__raw_completion_output.md b/projects/treatment/docs/extractionResult__raw_completion_output.md deleted file mode 100644 index 2948d0656..000000000 --- a/projects/treatment/docs/extractionResult__raw_completion_output.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: raw_completion_output - - - - -URI: [treatment:extractionResult__raw_completion_output](http://w3id.org/ontogpt/treatments/extractionResult__raw_completion_output) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/treatment/docs/namedEntity__id.md b/projects/treatment/docs/namedEntity__id.md deleted file mode 100644 index d15dd9322..000000000 --- a/projects/treatment/docs/namedEntity__id.md +++ /dev/null @@ -1,37 +0,0 @@ - -# Slot: id - - -A unique identifier for the named entity - -URI: [treatment:namedEntity__id](http://w3id.org/ontogpt/treatments/namedEntity__id) - - -## Domain and Range - -None → <sub>1..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AdverseEffect](AdverseEffect.md) - * [Disease](Disease.md) - * [Drug](Drug.md) - * [Gene](Gene.md) - * [Mechanism](Mechanism.md) - * [NamedEntity](NamedEntity.md) - * [RelationshipType](RelationshipType.md) - * [Symptom](Symptom.md) - * [Treatment](Treatment.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | this is populated during the grounding and normalization step | - diff --git a/projects/treatment/docs/namedEntity__label.md b/projects/treatment/docs/namedEntity__label.md deleted file mode 100644 index 2cb998313..000000000 --- a/projects/treatment/docs/namedEntity__label.md +++ /dev/null @@ -1,38 +0,0 @@ - -# Slot: label - - -The label (name) of the named thing - -URI: [treatment:namedEntity__label](http://w3id.org/ontogpt/treatments/namedEntity__label) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AdverseEffect](AdverseEffect.md) - * [Disease](Disease.md) - * [Drug](Drug.md) - * [Gene](Gene.md) - * [Mechanism](Mechanism.md) - * [NamedEntity](NamedEntity.md) - * [RelationshipType](RelationshipType.md) - * [Symptom](Symptom.md) - * [Treatment](Treatment.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Aliases:** | | name | -| **Mappings:** | | rdfs:label | - diff --git a/projects/treatment/docs/publication__abstract.md b/projects/treatment/docs/publication__abstract.md deleted file mode 100644 index f406354ef..000000000 --- a/projects/treatment/docs/publication__abstract.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: abstract - - -The abstract of the publication - -URI: [treatment:publication__abstract](http://w3id.org/ontogpt/treatments/publication__abstract) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/treatment/docs/publication__combined_text.md b/projects/treatment/docs/publication__combined_text.md deleted file mode 100644 index 6d29fcece..000000000 --- a/projects/treatment/docs/publication__combined_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: combined_text - - - - -URI: [treatment:publication__combined_text](http://w3id.org/ontogpt/treatments/publication__combined_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/treatment/docs/publication__full_text.md b/projects/treatment/docs/publication__full_text.md deleted file mode 100644 index 5761cb8f8..000000000 --- a/projects/treatment/docs/publication__full_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: full_text - - -The full text of the publication - -URI: [treatment:publication__full_text](http://w3id.org/ontogpt/treatments/publication__full_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/treatment/docs/publication__id.md b/projects/treatment/docs/publication__id.md deleted file mode 100644 index 8f426fe8a..000000000 --- a/projects/treatment/docs/publication__id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: id - - -The publication identifier - -URI: [treatment:publication__id](http://w3id.org/ontogpt/treatments/publication__id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/treatment/docs/publication__title.md b/projects/treatment/docs/publication__title.md deleted file mode 100644 index 562b800b5..000000000 --- a/projects/treatment/docs/publication__title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: title - - -The title of the publication - -URI: [treatment:publication__title](http://w3id.org/ontogpt/treatments/publication__title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/treatment/docs/textWithTriples__publication.md b/projects/treatment/docs/textWithTriples__publication.md deleted file mode 100644 index c30861d98..000000000 --- a/projects/treatment/docs/textWithTriples__publication.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: publication - - - - -URI: [treatment:textWithTriples__publication](http://w3id.org/ontogpt/treatments/textWithTriples__publication) - - -## Domain and Range - -None → <sub>0..1</sub> [Publication](Publication.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/treatment/docs/textWithTriples__triples.md b/projects/treatment/docs/textWithTriples__triples.md deleted file mode 100644 index 95ed30315..000000000 --- a/projects/treatment/docs/textWithTriples__triples.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: triples - - - - -URI: [treatment:textWithTriples__triples](http://w3id.org/ontogpt/treatments/textWithTriples__triples) - - -## Domain and Range - -None → <sub>0..\*</sub> [Triple](Triple.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/treatment/docs/treatment.md b/projects/treatment/docs/treatment.md deleted file mode 100644 index 97abd9181..000000000 --- a/projects/treatment/docs/treatment.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Treatment - - - - -URI: [treatment:Treatment](http://w3id.org/ontogpt/treatments/Treatment) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[DiseaseTreatmentSummary]-%20contraindications%200..*>[Treatment|id(i):string;label(i):string%20%3F],[DiseaseTreatmentSummary]-%20treatments%200..*>[Treatment],[TreatmentAdverseEffect]-%20treatment%200..1>[Treatment],[TreatmentEfficacy]-%20treatment%200..1>[Treatment],[TreatmentMechanism]-%20treatment%200..1>[Treatment],[NamedEntity]^-[Treatment],[TreatmentMechanism],[TreatmentEfficacy],[TreatmentAdverseEffect],[NamedEntity],[DiseaseTreatmentSummary])](https://yuml.me/diagram/nofunky;dir:TB/class/[DiseaseTreatmentSummary]-%20contraindications%200..*>[Treatment|id(i):string;label(i):string%20%3F],[DiseaseTreatmentSummary]-%20treatments%200..*>[Treatment],[TreatmentAdverseEffect]-%20treatment%200..1>[Treatment],[TreatmentEfficacy]-%20treatment%200..1>[Treatment],[TreatmentMechanism]-%20treatment%200..1>[Treatment],[NamedEntity]^-[Treatment],[TreatmentMechanism],[TreatmentEfficacy],[TreatmentAdverseEffect],[NamedEntity],[DiseaseTreatmentSummary]) - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞contraindications](diseaseTreatmentSummary__contraindications.md)* <sub>0..\*</sub> **[Treatment](Treatment.md)** - * **None** *[➞treatments](diseaseTreatmentSummary__treatments.md)* <sub>0..\*</sub> **[Treatment](Treatment.md)** - * **None** *[➞treatment](treatmentAdverseEffect__treatment.md)* <sub>0..1</sub> **[Treatment](Treatment.md)** - * **None** *[➞treatment](treatmentEfficacy__treatment.md)* <sub>0..1</sub> **[Treatment](Treatment.md)** - * **None** *[➞treatment](treatmentMechanism__treatment.md)* <sub>0..1</sub> **[Treatment](Treatment.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/treatment/docs/treatmentAdverseEffect__adverse_effects.md b/projects/treatment/docs/treatmentAdverseEffect__adverse_effects.md deleted file mode 100644 index 63a57698c..000000000 --- a/projects/treatment/docs/treatmentAdverseEffect__adverse_effects.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: adverse_effects - - - - -URI: [treatment:treatmentAdverseEffect__adverse_effects](http://w3id.org/ontogpt/treatments/treatmentAdverseEffect__adverse_effects) - - -## Domain and Range - -None → <sub>0..\*</sub> [AdverseEffect](AdverseEffect.md) - -## Parents - - -## Children - - -## Used by - - * [TreatmentAdverseEffect](TreatmentAdverseEffect.md) diff --git a/projects/treatment/docs/treatmentAdverseEffect__treatment.md b/projects/treatment/docs/treatmentAdverseEffect__treatment.md deleted file mode 100644 index 5f377383a..000000000 --- a/projects/treatment/docs/treatmentAdverseEffect__treatment.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: treatment - - - - -URI: [treatment:treatmentAdverseEffect__treatment](http://w3id.org/ontogpt/treatments/treatmentAdverseEffect__treatment) - - -## Domain and Range - -None → <sub>0..1</sub> [Treatment](Treatment.md) - -## Parents - - -## Children - - -## Used by - - * [TreatmentAdverseEffect](TreatmentAdverseEffect.md) diff --git a/projects/treatment/docs/treatmentEfficacy__efficacy.md b/projects/treatment/docs/treatmentEfficacy__efficacy.md deleted file mode 100644 index 51f902c15..000000000 --- a/projects/treatment/docs/treatmentEfficacy__efficacy.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: efficacy - - - - -URI: [treatment:treatmentEfficacy__efficacy](http://w3id.org/ontogpt/treatments/treatmentEfficacy__efficacy) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [TreatmentEfficacy](TreatmentEfficacy.md) diff --git a/projects/treatment/docs/treatmentEfficacy__treatment.md b/projects/treatment/docs/treatmentEfficacy__treatment.md deleted file mode 100644 index fab6d5f8f..000000000 --- a/projects/treatment/docs/treatmentEfficacy__treatment.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: treatment - - - - -URI: [treatment:treatmentEfficacy__treatment](http://w3id.org/ontogpt/treatments/treatmentEfficacy__treatment) - - -## Domain and Range - -None → <sub>0..1</sub> [Treatment](Treatment.md) - -## Parents - - -## Children - - -## Used by - - * [TreatmentEfficacy](TreatmentEfficacy.md) diff --git a/projects/treatment/docs/treatmentMechanism__mechanism.md b/projects/treatment/docs/treatmentMechanism__mechanism.md deleted file mode 100644 index bd063cfbe..000000000 --- a/projects/treatment/docs/treatmentMechanism__mechanism.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: mechanism - - - - -URI: [treatment:treatmentMechanism__mechanism](http://w3id.org/ontogpt/treatments/treatmentMechanism__mechanism) - - -## Domain and Range - -None → <sub>0..1</sub> [Mechanism](Mechanism.md) - -## Parents - - -## Children - - -## Used by - - * [TreatmentMechanism](TreatmentMechanism.md) diff --git a/projects/treatment/docs/treatmentMechanism__treatment.md b/projects/treatment/docs/treatmentMechanism__treatment.md deleted file mode 100644 index b721b4cd8..000000000 --- a/projects/treatment/docs/treatmentMechanism__treatment.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: treatment - - - - -URI: [treatment:treatmentMechanism__treatment](http://w3id.org/ontogpt/treatments/treatmentMechanism__treatment) - - -## Domain and Range - -None → <sub>0..1</sub> [Treatment](Treatment.md) - -## Parents - - -## Children - - -## Used by - - * [TreatmentMechanism](TreatmentMechanism.md) diff --git a/projects/treatment/docs/triple__object.md b/projects/treatment/docs/triple__object.md deleted file mode 100644 index ad7e70bd2..000000000 --- a/projects/treatment/docs/triple__object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object - - - - -URI: [treatment:triple__object](http://w3id.org/ontogpt/treatments/triple__object) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/treatment/docs/triple__object_qualifier.md b/projects/treatment/docs/triple__object_qualifier.md deleted file mode 100644 index a649d636d..000000000 --- a/projects/treatment/docs/triple__object_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_qualifier - - -An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - -URI: [treatment:triple__object_qualifier](http://w3id.org/ontogpt/treatments/triple__object_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/treatment/docs/triple__predicate.md b/projects/treatment/docs/triple__predicate.md deleted file mode 100644 index 6d05e896f..000000000 --- a/projects/treatment/docs/triple__predicate.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: predicate - - - - -URI: [treatment:triple__predicate](http://w3id.org/ontogpt/treatments/triple__predicate) - - -## Domain and Range - -None → <sub>0..1</sub> [RelationshipType](RelationshipType.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/treatment/docs/triple__qualifier.md b/projects/treatment/docs/triple__qualifier.md deleted file mode 100644 index bdc6c1e95..000000000 --- a/projects/treatment/docs/triple__qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: qualifier - - -A qualifier for the statements, e.g. "NOT" for negation - -URI: [treatment:triple__qualifier](http://w3id.org/ontogpt/treatments/triple__qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/treatment/docs/triple__subject.md b/projects/treatment/docs/triple__subject.md deleted file mode 100644 index 6675a6fab..000000000 --- a/projects/treatment/docs/triple__subject.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject - - - - -URI: [treatment:triple__subject](http://w3id.org/ontogpt/treatments/triple__subject) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/treatment/docs/triple__subject_qualifier.md b/projects/treatment/docs/triple__subject_qualifier.md deleted file mode 100644 index ec2f79e2d..000000000 --- a/projects/treatment/docs/triple__subject_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_qualifier - - -An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -URI: [treatment:triple__subject_qualifier](http://w3id.org/ontogpt/treatments/triple__subject_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/treatment/docs/types/Boolean.md b/projects/treatment/docs/types/Boolean.md deleted file mode 100644 index dc83a9c6e..000000000 --- a/projects/treatment/docs/types/Boolean.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: boolean - - -A binary (true or false) value - -URI: [linkml:Boolean](https://w3id.org/linkml/Boolean) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Bool** | -| Representation | | bool | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Boolean | - diff --git a/projects/treatment/docs/types/Curie.md b/projects/treatment/docs/types/Curie.md deleted file mode 100644 index c1803f93f..000000000 --- a/projects/treatment/docs/types/Curie.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: curie - - -a compact URI - -URI: [linkml:Curie](https://w3id.org/linkml/Curie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Curie** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations this MUST be expanded to a URI | -| | | in non-RDF serializations MAY be serialized as the compact representation | - diff --git a/projects/treatment/docs/types/Date.md b/projects/treatment/docs/types/Date.md deleted file mode 100644 index 06948af97..000000000 --- a/projects/treatment/docs/types/Date.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: date - - -a date (year, month and day) in an idealized calendar - -URI: [linkml:Date](https://w3id.org/linkml/Date) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDate** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Date | - diff --git a/projects/treatment/docs/types/DateOrDatetime.md b/projects/treatment/docs/types/DateOrDatetime.md deleted file mode 100644 index ef983898d..000000000 --- a/projects/treatment/docs/types/DateOrDatetime.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: date_or_datetime - - -Either a date or a datetime - -URI: [linkml:DateOrDatetime](https://w3id.org/linkml/DateOrDatetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/treatment/docs/types/Datetime.md b/projects/treatment/docs/types/Datetime.md deleted file mode 100644 index 9510454a8..000000000 --- a/projects/treatment/docs/types/Datetime.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: datetime - - -The combination of a date and time - -URI: [linkml:Datetime](https://w3id.org/linkml/Datetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDateTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:DateTime | - diff --git a/projects/treatment/docs/types/Decimal.md b/projects/treatment/docs/types/Decimal.md deleted file mode 100644 index a7ba14a5d..000000000 --- a/projects/treatment/docs/types/Decimal.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: decimal - - -A real number with arbitrary precision that conforms to the xsd:decimal specification - -URI: [linkml:Decimal](https://w3id.org/linkml/Decimal) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Decimal** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Broad Mappings:** | | schema:Number | - diff --git a/projects/treatment/docs/types/Double.md b/projects/treatment/docs/types/Double.md deleted file mode 100644 index cfe6d71e2..000000000 --- a/projects/treatment/docs/types/Double.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: double - - -A real number that conforms to the xsd:double specification - -URI: [linkml:Double](https://w3id.org/linkml/Double) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Close Mappings:** | | schema:Float | - diff --git a/projects/treatment/docs/types/Float.md b/projects/treatment/docs/types/Float.md deleted file mode 100644 index 7b303f96f..000000000 --- a/projects/treatment/docs/types/Float.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: float - - -A real number that conforms to the xsd:float specification - -URI: [linkml:Float](https://w3id.org/linkml/Float) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Float | - diff --git a/projects/treatment/docs/types/Integer.md b/projects/treatment/docs/types/Integer.md deleted file mode 100644 index 3cfcc66d9..000000000 --- a/projects/treatment/docs/types/Integer.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: integer - - -An integer - -URI: [linkml:Integer](https://w3id.org/linkml/Integer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **int** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Integer | - diff --git a/projects/treatment/docs/types/Jsonpath.md b/projects/treatment/docs/types/Jsonpath.md deleted file mode 100644 index a03a58e67..000000000 --- a/projects/treatment/docs/types/Jsonpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpath - - -A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpath](https://w3id.org/linkml/Jsonpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/treatment/docs/types/Jsonpointer.md b/projects/treatment/docs/types/Jsonpointer.md deleted file mode 100644 index a0e1ac492..000000000 --- a/projects/treatment/docs/types/Jsonpointer.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpointer - - -A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpointer](https://w3id.org/linkml/Jsonpointer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/treatment/docs/types/Ncname.md b/projects/treatment/docs/types/Ncname.md deleted file mode 100644 index 710b0b04a..000000000 --- a/projects/treatment/docs/types/Ncname.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: ncname - - -Prefix part of CURIE - -URI: [linkml:Ncname](https://w3id.org/linkml/Ncname) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NCName** | -| Representation | | str | diff --git a/projects/treatment/docs/types/Nodeidentifier.md b/projects/treatment/docs/types/Nodeidentifier.md deleted file mode 100644 index f0097cdf4..000000000 --- a/projects/treatment/docs/types/Nodeidentifier.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: nodeidentifier - - -A URI, CURIE or BNODE that represents a node in a model. - -URI: [linkml:Nodeidentifier](https://w3id.org/linkml/Nodeidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NodeIdentifier** | -| Representation | | str | diff --git a/projects/treatment/docs/types/Objectidentifier.md b/projects/treatment/docs/types/Objectidentifier.md deleted file mode 100644 index 454ba6be6..000000000 --- a/projects/treatment/docs/types/Objectidentifier.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: objectidentifier - - -A URI or CURIE that represents an object in the model. - -URI: [linkml:Objectidentifier](https://w3id.org/linkml/Objectidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **ElementIdentifier** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | Used for inheritance and type checking | - diff --git a/projects/treatment/docs/types/Sparqlpath.md b/projects/treatment/docs/types/Sparqlpath.md deleted file mode 100644 index fd99a927e..000000000 --- a/projects/treatment/docs/types/Sparqlpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: sparqlpath - - -A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - -URI: [linkml:Sparqlpath](https://w3id.org/linkml/Sparqlpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/treatment/docs/types/String.md b/projects/treatment/docs/types/String.md deleted file mode 100644 index 6e61d7081..000000000 --- a/projects/treatment/docs/types/String.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: string - - -A character string - -URI: [linkml:String](https://w3id.org/linkml/String) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Text | - diff --git a/projects/treatment/docs/types/Time.md b/projects/treatment/docs/types/Time.md deleted file mode 100644 index 2b8652bcd..000000000 --- a/projects/treatment/docs/types/Time.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: time - - -A time object represents a (local) time of day, independent of any particular day - -URI: [linkml:Time](https://w3id.org/linkml/Time) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Time | - diff --git a/projects/treatment/docs/types/Uri.md b/projects/treatment/docs/types/Uri.md deleted file mode 100644 index 343807a5e..000000000 --- a/projects/treatment/docs/types/Uri.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: uri - - -a complete URI - -URI: [linkml:Uri](https://w3id.org/linkml/Uri) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URI** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node | -| **Close Mappings:** | | schema:URL | - diff --git a/projects/treatment/docs/types/Uriorcurie.md b/projects/treatment/docs/types/Uriorcurie.md deleted file mode 100644 index 2f7b65087..000000000 --- a/projects/treatment/docs/types/Uriorcurie.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: uriorcurie - - -a URI or a CURIE - -URI: [linkml:Uriorcurie](https://w3id.org/linkml/Uriorcurie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URIorCURIE** | -| Representation | | str | diff --git a/projects/treatment/excel/treatment.xlsx b/projects/treatment/excel/treatment.xlsx deleted file mode 100644 index 733b78318..000000000 Binary files a/projects/treatment/excel/treatment.xlsx and /dev/null differ diff --git a/projects/treatment/graphql/treatment.graphql b/projects/treatment/graphql/treatment.graphql deleted file mode 100644 index cc70eff10..000000000 --- a/projects/treatment/graphql/treatment.graphql +++ /dev/null @@ -1,134 +0,0 @@ -type AdverseEffect - { - id: String! - label: String - } - -type AnnotatorResult - { - subjectText: String - objectId: String - objectText: String - } - -type Any - { - } - -interface CompoundExpression - { - } - -type Disease - { - id: String! - label: String - } - -type DiseaseTreatmentSummary - { - disease: Disease - drugs: [Drug] - treatments: [Treatment] - contraindications: [Treatment] - treatmentMechanisms: [TreatmentMechanism] - treatmentEfficacies: [TreatmentEfficacy] - treatmentAdverseEffects: [TreatmentAdverseEffect] - } - -type Drug - { - id: String! - label: String - } - -type ExtractionResult - { - inputId: String - inputTitle: String - inputText: String - rawCompletionOutput: String - prompt: String - extractedObject: Any - namedEntities: [Any] - } - -type Gene - { - id: String! - label: String - } - -type Mechanism - { - id: String! - label: String - } - -interface NamedEntity - { - id: String! - label: String - } - -type Publication - { - id: String - title: String - abstract: String - combinedText: String - fullText: String - } - -type RelationshipType - { - id: String! - label: String - } - -type Symptom - { - id: String! - label: String - } - -type TextWithTriples - { - publication: Publication - triples: [Triple] - } - -type Treatment - { - id: String! - label: String - } - -type TreatmentAdverseEffect - { - treatment: Treatment - adverseEffects: [AdverseEffect] - } - -type TreatmentEfficacy - { - treatment: Treatment - efficacy: String - } - -type TreatmentMechanism - { - treatment: Treatment - mechanism: Mechanism - } - -interface Triple - { - subject: NamedEntity - predicate: RelationshipType - object: NamedEntity - qualifier: String - subjectQualifier: NamedEntity - objectQualifier: NamedEntity - } - diff --git a/projects/treatment/jsonld/treatment.context.jsonld b/projects/treatment/jsonld/treatment.context.jsonld deleted file mode 100644 index b71dfde88..000000000 --- a/projects/treatment/jsonld/treatment.context.jsonld +++ /dev/null @@ -1,158 +0,0 @@ -{ - "comments": { - "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2023-08-07T10:56:36", - "source": "treatment.yaml" - }, - "@context": { - "HGNC": "http://example.org/UNKNOWN/HGNC/", - "HP": "http://example.org/UNKNOWN/HP/", - "RO": { - "@id": "http://purl.obolibrary.org/obo/RO_", - "@prefix": true - }, - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "treatment": { - "@type": "@id" - }, - "@vocab": "http://w3id.org/ontogpt/treatments/", - "object_id": { - "@id": "core:object_id" - }, - "object_text": { - "@id": "core:object_text" - }, - "subject_text": { - "@id": "core:subject_text" - }, - "contraindications": { - "@type": "@id" - }, - "disease": { - "@type": "@id" - }, - "drugs": { - "@type": "@id" - }, - "treatment_adverse_effects": { - "@type": "@id" - }, - "treatment_efficacies": { - "@type": "@id" - }, - "treatment_mechanisms": { - "@type": "@id" - }, - "treatments": { - "@type": "@id" - }, - "extracted_object": { - "@type": "@id", - "@id": "core:extracted_object" - }, - "input_id": { - "@id": "core:input_id" - }, - "input_text": { - "@id": "core:input_text" - }, - "input_title": { - "@id": "core:input_title" - }, - "named_entities": { - "@type": "@id", - "@id": "core:named_entities" - }, - "prompt": { - "@id": "core:prompt" - }, - "raw_completion_output": { - "@id": "core:raw_completion_output" - }, - "id": { - "@id": "core:id" - }, - "label": { - "@id": "rdfs:label" - }, - "abstract": { - "@id": "core:abstract" - }, - "combined_text": { - "@id": "core:combined_text" - }, - "full_text": { - "@id": "core:full_text" - }, - "title": { - "@id": "core:title" - }, - "publication": { - "@type": "@id", - "@id": "core:publication" - }, - "triples": { - "@type": "@id", - "@id": "core:triples" - }, - "adverse_effects": { - "@type": "@id" - }, - "mechanism": { - "@type": "@id" - }, - "object": { - "@type": "@id", - "@id": "core:object" - }, - "object_qualifier": { - "@type": "@id", - "@id": "core:object_qualifier" - }, - "predicate": { - "@type": "@id", - "@id": "core:predicate" - }, - "qualifier": { - "@id": "core:qualifier" - }, - "subject": { - "@type": "@id", - "@id": "core:subject" - }, - "subject_qualifier": { - "@type": "@id", - "@id": "core:subject_qualifier" - }, - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } - } -} diff --git a/projects/treatment/jsonld/treatment.jsonld b/projects/treatment/jsonld/treatment.jsonld deleted file mode 100644 index 79f6be1a5..000000000 --- a/projects/treatment/jsonld/treatment.jsonld +++ /dev/null @@ -1,1587 +0,0 @@ -{ - "name": "treatment-template", - "description": "A template for MAXO treatments", - "title": "MAXO treatment Template", - "id": "http://w3id.org/ontogpt/treatment", - "imports": [ - "linkml:types", - "core" - ], - "license": "https://creativecommons.org/publicdomain/zero/1.0/", - "prefixes": [ - { - "prefix_prefix": "linkml", - "prefix_reference": "https://w3id.org/linkml/" - }, - { - "prefix_prefix": "treatment", - "prefix_reference": "http://w3id.org/ontogpt/treatments/" - } - ], - "default_prefix": "treatment", - "default_range": "string", - "types": [ - { - "name": "string", - "definition_uri": "https://w3id.org/linkml/String", - "description": "A character string", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Text" - ], - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "@type": "TypeDefinition" - }, - { - "name": "integer", - "definition_uri": "https://w3id.org/linkml/Integer", - "description": "An integer", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Integer" - ], - "base": "int", - "uri": "http://www.w3.org/2001/XMLSchema#integer", - "@type": "TypeDefinition" - }, - { - "name": "boolean", - "definition_uri": "https://w3id.org/linkml/Boolean", - "description": "A binary (true or false) value", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Boolean" - ], - "base": "Bool", - "uri": "http://www.w3.org/2001/XMLSchema#boolean", - "repr": "bool", - "@type": "TypeDefinition" - }, - { - "name": "float", - "definition_uri": "https://w3id.org/linkml/Float", - "description": "A real number that conforms to the xsd:float specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#float", - "@type": "TypeDefinition" - }, - { - "name": "double", - "definition_uri": "https://w3id.org/linkml/Double", - "description": "A real number that conforms to the xsd:double specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#double", - "@type": "TypeDefinition" - }, - { - "name": "decimal", - "definition_uri": "https://w3id.org/linkml/Decimal", - "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "broad_mappings": [ - "schema:Number" - ], - "base": "Decimal", - "uri": "http://www.w3.org/2001/XMLSchema#decimal", - "@type": "TypeDefinition" - }, - { - "name": "time", - "definition_uri": "https://w3id.org/linkml/Time", - "description": "A time object represents a (local) time of day, independent of any particular day", - "notes": [ - "URI is dateTime because OWL reasoners do not work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Time" - ], - "base": "XSDTime", - "uri": "http://www.w3.org/2001/XMLSchema#time", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date", - "definition_uri": "https://w3id.org/linkml/Date", - "description": "a date (year, month and day) in an idealized calendar", - "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Date" - ], - "base": "XSDDate", - "uri": "http://www.w3.org/2001/XMLSchema#date", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "datetime", - "definition_uri": "https://w3id.org/linkml/Datetime", - "description": "The combination of a date and time", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:DateTime" - ], - "base": "XSDDateTime", - "uri": "http://www.w3.org/2001/XMLSchema#dateTime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date_or_datetime", - "definition_uri": "https://w3id.org/linkml/DateOrDatetime", - "description": "Either a date or a datetime", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "https://w3id.org/linkml/DateOrDatetime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uriorcurie", - "definition_uri": "https://w3id.org/linkml/Uriorcurie", - "description": "a URI or a CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "URIorCURIE", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "curie", - "definition_uri": "https://w3id.org/linkml/Curie", - "conforms_to": "https://www.w3.org/TR/curie/", - "description": "a compact URI", - "comments": [ - "in RDF serializations this MUST be expanded to a URI", - "in non-RDF serializations MAY be serialized as the compact representation" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "Curie", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uri", - "definition_uri": "https://w3id.org/linkml/Uri", - "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", - "description": "a complete URI", - "comments": [ - "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:URL" - ], - "base": "URI", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "ncname", - "definition_uri": "https://w3id.org/linkml/Ncname", - "description": "Prefix part of CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NCName", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "objectidentifier", - "definition_uri": "https://w3id.org/linkml/Objectidentifier", - "description": "A URI or CURIE that represents an object in the model.", - "comments": [ - "Used for inheritance and type checking" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "ElementIdentifier", - "uri": "http://www.w3.org/ns/shex#iri", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "nodeidentifier", - "definition_uri": "https://w3id.org/linkml/Nodeidentifier", - "description": "A URI, CURIE or BNODE that represents a node in a model.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NodeIdentifier", - "uri": "http://www.w3.org/ns/shex#nonLiteral", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpointer", - "definition_uri": "https://w3id.org/linkml/Jsonpointer", - "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901", - "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpath", - "definition_uri": "https://w3id.org/linkml/Jsonpath", - "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html", - "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "sparqlpath", - "definition_uri": "https://w3id.org/linkml/Sparqlpath", - "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths", - "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - } - ], - "enums": [ - { - "name": "NCITDrugType", - "definition_uri": "http://w3id.org/ontogpt/treatments/NCITDrugType", - "from_schema": "http://w3id.org/ontogpt/treatment", - "reachable_from": { - "source_ontology": "obo:ncit", - "source_nodes": [ - "NCIT:C1908" - ] - } - }, - { - "name": "NCITTreatmentType", - "definition_uri": "http://w3id.org/ontogpt/treatments/NCITTreatmentType", - "from_schema": "http://w3id.org/ontogpt/treatment", - "reachable_from": { - "source_ontology": "obo:ncit", - "source_nodes": [ - "NCIT:C25218" - ] - } - }, - { - "name": "NCITTActivityType", - "definition_uri": "http://w3id.org/ontogpt/treatments/NCITTActivityType", - "from_schema": "http://w3id.org/ontogpt/treatment", - "reachable_from": { - "source_ontology": "obo:ncit", - "source_nodes": [ - "NCIT:C43431" - ] - } - }, - { - "name": "MAXOActionType", - "definition_uri": "http://w3id.org/ontogpt/treatments/MAXOActionType", - "from_schema": "http://w3id.org/ontogpt/treatment", - "reachable_from": { - "source_ontology": "obo:maxo", - "source_nodes": [ - "MAXO:0000001" - ] - } - }, - { - "name": "MESHTherapeuticType", - "definition_uri": "http://w3id.org/ontogpt/treatments/MESHTherapeuticType", - "from_schema": "http://w3id.org/ontogpt/treatment", - "reachable_from": { - "source_ontology": "obo:mesh", - "source_nodes": [ - "MESH:D013812" - ] - } - }, - { - "name": "CHEBIDrugType", - "definition_uri": "http://w3id.org/ontogpt/treatments/CHEBIDrugType", - "from_schema": "http://w3id.org/ontogpt/treatment", - "reachable_from": { - "source_ontology": "obo:chebi", - "source_nodes": [ - "CHEBI:23888" - ], - "relationship_types": [ - "rdfs:subClassOf", - "RO:0000087" - ] - } - }, - { - "name": "NullDataOptions", - "definition_uri": "http://w3id.org/ontogpt/core/NullDataOptions", - "from_schema": "http://w3id.org/ontogpt/core", - "permissible_values": [ - { - "text": "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "meaning": "NCIT:C149701" - }, - { - "text": "NOT_APPLICABLE", - "meaning": "NCIT:C18902", - "aliases": [ - "not applicable", - "N/A" - ] - }, - { - "text": "NOT_MENTIONED" - } - ] - } - ], - "slots": [ - { - "name": "diseaseTreatmentSummary__disease", - "description": "the name of the disease that is treated.", - "from_schema": "http://w3id.org/ontogpt/treatment", - "slot_uri": "http://w3id.org/ontogpt/treatments/disease", - "alias": "disease", - "owner": "DiseaseTreatmentSummary", - "domain_of": [ - "DiseaseTreatmentSummary" - ], - "range": "Disease", - "@type": "SlotDefinition" - }, - { - "name": "diseaseTreatmentSummary__drugs", - "description": "semicolon-separated list of named small molecule drugs", - "from_schema": "http://w3id.org/ontogpt/treatment", - "slot_uri": "http://w3id.org/ontogpt/treatments/drugs", - "multivalued": true, - "alias": "drugs", - "owner": "DiseaseTreatmentSummary", - "domain_of": [ - "DiseaseTreatmentSummary" - ], - "range": "Drug", - "@type": "SlotDefinition" - }, - { - "name": "diseaseTreatmentSummary__treatments", - "annotations": [ - { - "tag": "prompt.examples", - "value": "Imatinib, exercise, surgery", - "@type": "Annotation" - } - ], - "description": "semicolon-separated list of therapies and treatments are indicated for treating the disease.", - "from_schema": "http://w3id.org/ontogpt/treatment", - "slot_uri": "http://w3id.org/ontogpt/treatments/treatments", - "multivalued": true, - "alias": "treatments", - "owner": "DiseaseTreatmentSummary", - "domain_of": [ - "DiseaseTreatmentSummary" - ], - "range": "Treatment", - "@type": "SlotDefinition" - }, - { - "name": "diseaseTreatmentSummary__contraindications", - "annotations": [ - { - "tag": "prompt.examples", - "value": "Beta-blockers, exercise, surgery", - "@type": "Annotation" - } - ], - "description": "semicolon-separated list of therapies and treatments that are contra-indicated for the disease, and should not be used, due to risk of adverse effects.", - "from_schema": "http://w3id.org/ontogpt/treatment", - "slot_uri": "http://w3id.org/ontogpt/treatments/contraindications", - "multivalued": true, - "alias": "contraindications", - "owner": "DiseaseTreatmentSummary", - "domain_of": [ - "DiseaseTreatmentSummary" - ], - "range": "Treatment", - "@type": "SlotDefinition" - }, - { - "name": "diseaseTreatmentSummary__treatment_mechanisms", - "annotations": [ - { - "tag": "prompt.separator", - "value": "*", - "@type": "Annotation" - } - ], - "description": "semicolon-separated list of treatment to asterisk-separated mechanism associations", - "from_schema": "http://w3id.org/ontogpt/treatment", - "slot_uri": "http://w3id.org/ontogpt/treatments/treatment_mechanisms", - "multivalued": true, - "alias": "treatment_mechanisms", - "owner": "DiseaseTreatmentSummary", - "domain_of": [ - "DiseaseTreatmentSummary" - ], - "range": "TreatmentMechanism", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "diseaseTreatmentSummary__treatment_efficacies", - "annotations": [ - { - "tag": "prompt.separator", - "value": "*", - "@type": "Annotation" - } - ], - "description": "semicolon-separated list of treatment to efficacy associations, e.g. Imatinib*effective", - "from_schema": "http://w3id.org/ontogpt/treatment", - "slot_uri": "http://w3id.org/ontogpt/treatments/treatment_efficacies", - "multivalued": true, - "alias": "treatment_efficacies", - "owner": "DiseaseTreatmentSummary", - "domain_of": [ - "DiseaseTreatmentSummary" - ], - "range": "TreatmentEfficacy", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "diseaseTreatmentSummary__treatment_adverse_effects", - "annotations": [ - { - "tag": "prompt.separator", - "value": "*", - "@type": "Annotation" - } - ], - "description": "semicolon-separated list of treatment to adverse effect associations, e.g. Imatinib*nausea", - "from_schema": "http://w3id.org/ontogpt/treatment", - "slot_uri": "http://w3id.org/ontogpt/treatments/treatment_adverse_effects", - "multivalued": true, - "alias": "treatment_adverse_effects", - "owner": "DiseaseTreatmentSummary", - "domain_of": [ - "DiseaseTreatmentSummary" - ], - "range": "TreatmentAdverseEffect", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "treatmentMechanism__treatment", - "from_schema": "http://w3id.org/ontogpt/treatment", - "slot_uri": "http://w3id.org/ontogpt/treatments/treatment", - "alias": "treatment", - "owner": "TreatmentMechanism", - "domain_of": [ - "TreatmentMechanism" - ], - "range": "Treatment", - "@type": "SlotDefinition" - }, - { - "name": "treatmentMechanism__mechanism", - "from_schema": "http://w3id.org/ontogpt/treatment", - "slot_uri": "http://w3id.org/ontogpt/treatments/mechanism", - "alias": "mechanism", - "owner": "TreatmentMechanism", - "domain_of": [ - "TreatmentMechanism" - ], - "range": "Mechanism", - "@type": "SlotDefinition" - }, - { - "name": "treatmentAdverseEffect__treatment", - "from_schema": "http://w3id.org/ontogpt/treatment", - "slot_uri": "http://w3id.org/ontogpt/treatments/treatment", - "alias": "treatment", - "owner": "TreatmentAdverseEffect", - "domain_of": [ - "TreatmentAdverseEffect" - ], - "range": "Treatment", - "@type": "SlotDefinition" - }, - { - "name": "treatmentAdverseEffect__adverse_effects", - "from_schema": "http://w3id.org/ontogpt/treatment", - "slot_uri": "http://w3id.org/ontogpt/treatments/adverse_effects", - "multivalued": true, - "alias": "adverse_effects", - "owner": "TreatmentAdverseEffect", - "domain_of": [ - "TreatmentAdverseEffect" - ], - "range": "AdverseEffect", - "@type": "SlotDefinition" - }, - { - "name": "treatmentEfficacy__treatment", - "from_schema": "http://w3id.org/ontogpt/treatment", - "slot_uri": "http://w3id.org/ontogpt/treatments/treatment", - "alias": "treatment", - "owner": "TreatmentEfficacy", - "domain_of": [ - "TreatmentEfficacy" - ], - "range": "Treatment", - "@type": "SlotDefinition" - }, - { - "name": "treatmentEfficacy__efficacy", - "from_schema": "http://w3id.org/ontogpt/treatment", - "slot_uri": "http://w3id.org/ontogpt/treatments/efficacy", - "alias": "efficacy", - "owner": "TreatmentEfficacy", - "domain_of": [ - "TreatmentEfficacy" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_id", - "alias": "input_id", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_title", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_title", - "alias": "input_title", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_text", - "alias": "input_text", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__raw_completion_output", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/raw_completion_output", - "alias": "raw_completion_output", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__prompt", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/prompt", - "alias": "prompt", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__extracted_object", - "description": "The complex objects extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/extracted_object", - "alias": "extracted_object", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__named_entities", - "description": "Named entities extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/named_entities", - "multivalued": true, - "alias": "named_entities", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "identifier": true, - "alias": "id", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "required": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "from_schema": "http://w3id.org/ontogpt/core", - "aliases": [ - "name" - ], - "mappings": [ - "http://example.org/UNKNOWN/rdfs/label" - ], - "slot_uri": "http://example.org/UNKNOWN/rdfs/label", - "alias": "label", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject", - "alias": "subject", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__predicate", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/predicate", - "alias": "predicate", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "triple__object", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object", - "alias": "object", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/qualifier", - "alias": "qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_qualifier", - "alias": "subject_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_qualifier", - "alias": "object_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/publication", - "alias": "publication", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__triples", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/triples", - "multivalued": true, - "alias": "triples", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "publication__id", - "description": "The publication identifier", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "alias": "id", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__title", - "description": "The title of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/title", - "alias": "title", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__abstract", - "description": "The abstract of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/abstract", - "alias": "abstract", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__combined_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/combined_text", - "alias": "combined_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__full_text", - "description": "The full text of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/full_text", - "alias": "full_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__subject_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_text", - "alias": "subject_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_id", - "alias": "object_id", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_text", - "alias": "object_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - } - ], - "classes": [ - { - "name": "DiseaseTreatmentSummary", - "definition_uri": "http://w3id.org/ontogpt/treatments/DiseaseTreatmentSummary", - "from_schema": "http://w3id.org/ontogpt/treatment", - "slots": [ - "diseaseTreatmentSummary__disease", - "diseaseTreatmentSummary__drugs", - "diseaseTreatmentSummary__treatments", - "diseaseTreatmentSummary__contraindications", - "diseaseTreatmentSummary__treatment_mechanisms", - "diseaseTreatmentSummary__treatment_efficacies", - "diseaseTreatmentSummary__treatment_adverse_effects" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "disease", - "description": "the name of the disease that is treated.", - "range": "Disease", - "@type": "SlotDefinition" - }, - { - "name": "drugs", - "description": "semicolon-separated list of named small molecule drugs", - "multivalued": true, - "range": "Drug", - "@type": "SlotDefinition" - }, - { - "name": "treatments", - "annotations": [ - { - "tag": "prompt.examples", - "value": "Imatinib, exercise, surgery", - "@type": "Annotation" - } - ], - "description": "semicolon-separated list of therapies and treatments are indicated for treating the disease.", - "multivalued": true, - "range": "Treatment", - "@type": "SlotDefinition" - }, - { - "name": "contraindications", - "annotations": [ - { - "tag": "prompt.examples", - "value": "Beta-blockers, exercise, surgery", - "@type": "Annotation" - } - ], - "description": 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"value": "*", - "@type": "Annotation" - } - ], - "description": "semicolon-separated list of treatment to adverse effect associations, e.g. Imatinib*nausea", - "multivalued": true, - "range": "TreatmentAdverseEffect", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/treatments/DiseaseTreatmentSummary", - "tree_root": true, - "@type": "ClassDefinition" - }, - { - "name": "Gene", - "id_prefixes": [ - "HGNC" - ], - "definition_uri": "http://w3id.org/ontogpt/treatments/Gene", - "annotations": [ - { - "tag": "annotators", - "value": "gilda:, obo:sql:hgnc, bioportal:hgnc-nr", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/treatment", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/treatments/Gene", - "@type": "ClassDefinition" - }, - { - "name": "Symptom", - "id_prefixes": [ - "HP" - ], - "definition_uri": "http://w3id.org/ontogpt/treatments/Symptom", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:hp", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/treatment", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/treatments/Symptom", - "@type": "ClassDefinition" - }, - { - "name": "Disease", - "definition_uri": "http://w3id.org/ontogpt/treatments/Disease", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:mondo", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/treatment", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/treatments/Disease", - "@type": "ClassDefinition" - }, - { - "name": "AdverseEffect", - "definition_uri": "http://w3id.org/ontogpt/treatments/AdverseEffect", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:hp, sqlite:obo:ncit", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/treatment", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/treatments/AdverseEffect", - "@type": "ClassDefinition" - }, - { - "name": "Treatment", - "definition_uri": "http://w3id.org/ontogpt/treatments/Treatment", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:maxo, sqlite:obo:ncit, sqlite:obo:mesh, sqlite:obo:chebi", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/treatment", - "is_a": "NamedEntity", - "values_from": [ - "NCITDrugType", - "NCITTreatmentType", - "NCITActivityType", - "MAXOTreatmentType", - "MESHTherapeuticType", - "CHEBIDrugType" - ], - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/treatments/Treatment", - "@type": "ClassDefinition" - }, - { - "name": "Mechanism", - "definition_uri": "http://w3id.org/ontogpt/treatments/Mechanism", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:go, sqlite:obo:ncit, sqlite:obo:mesh", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/treatment", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/treatments/Mechanism", - "@type": "ClassDefinition" - }, - { - "name": "Drug", - "definition_uri": "http://w3id.org/ontogpt/treatments/Drug", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:chebi, sqlite:obo:drugbank", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/treatment", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/treatments/Drug", - "@type": "ClassDefinition" - }, - { - "name": "TreatmentMechanism", - "definition_uri": "http://w3id.org/ontogpt/treatments/TreatmentMechanism", - "from_schema": "http://w3id.org/ontogpt/treatment", - "is_a": "CompoundExpression", - "slots": [ - "treatmentMechanism__treatment", - "treatmentMechanism__mechanism" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "treatment", - "range": "Treatment", - "@type": "SlotDefinition" - }, - { - "name": "mechanism", - "range": "Mechanism", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/treatments/TreatmentMechanism", - "@type": "ClassDefinition" - }, - { - "name": "TreatmentAdverseEffect", - "definition_uri": "http://w3id.org/ontogpt/treatments/TreatmentAdverseEffect", - "from_schema": "http://w3id.org/ontogpt/treatment", - "is_a": "CompoundExpression", - "slots": [ - "treatmentAdverseEffect__treatment", - "treatmentAdverseEffect__adverse_effects" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "treatment", - "range": "Treatment", - "@type": "SlotDefinition" - }, - { - "name": "adverse_effects", - "multivalued": true, - "range": "AdverseEffect", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/treatments/TreatmentAdverseEffect", - "@type": "ClassDefinition" - }, - { - "name": "TreatmentEfficacy", - "definition_uri": "http://w3id.org/ontogpt/treatments/TreatmentEfficacy", - "from_schema": "http://w3id.org/ontogpt/treatment", - "is_a": "CompoundExpression", - "slots": [ - "treatmentEfficacy__treatment", - "treatmentEfficacy__efficacy" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "treatment", - "range": "Treatment", - "@type": "SlotDefinition" - }, - { - "name": "efficacy", - "range": "string", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/treatments/TreatmentEfficacy", - "@type": "ClassDefinition" - }, - { - "name": "Any", - "definition_uri": "http://w3id.org/ontogpt/core/Any", - "from_schema": "http://w3id.org/ontogpt/core", - "mappings": [ - "linkml:Any" - ], - "slot_usage": {}, - "class_uri": "https://w3id.org/linkml/Any", - "@type": "ClassDefinition" - }, - { - "name": "ExtractionResult", - "definition_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "description": "A result of extracting knowledge on text", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "extractionResult__input_id", - "extractionResult__input_title", - "extractionResult__input_text", - "extractionResult__raw_completion_output", - "extractionResult__prompt", - "extractionResult__extracted_object", - "extractionResult__named_entities" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "input_id", - "@type": "SlotDefinition" - }, - { - "name": "input_title", - "@type": "SlotDefinition" - }, - { - "name": "input_text", - "@type": "SlotDefinition" - }, - { - "name": "raw_completion_output", - "@type": "SlotDefinition" - }, - { - "name": "prompt", - "@type": "SlotDefinition" - }, - { - "name": "extracted_object", - "description": "The complex objects extracted from the text", - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "named_entities", - "description": "Named entities extracted from the text", - "multivalued": true, - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "@type": "ClassDefinition" - }, - { - "name": "NamedEntity", - "definition_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "identifier": true, - "@type": "SlotDefinition" - }, - { - "name": "label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "aliases": [ - "name" - ], - "slot_uri": "rdfs:label", - "range": "string", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "@type": "ClassDefinition" - }, - { - "name": "CompoundExpression", - "definition_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "@type": "ClassDefinition" - }, - { - "name": "Triple", - "definition_uri": "http://w3id.org/ontogpt/core/Triple", - "description": "Abstract parent for Relation Extraction tasks", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "CompoundExpression", - "abstract": true, - "slots": [ - "triple__subject", - "triple__predicate", - "triple__object", - "triple__qualifier", - "triple__subject_qualifier", - "triple__object_qualifier" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "predicate", - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "object", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Triple", - "@type": "ClassDefinition" - }, - { - "name": "TextWithTriples", - "definition_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "textWithTriples__publication", - "textWithTriples__triples" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "triples", - "multivalued": true, - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "@type": "ClassDefinition" - }, - { - "name": "RelationshipType", - "id_prefixes": [ - "RO", - "biolink" - ], - "definition_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "@type": "ClassDefinition" - }, - { - "name": "Publication", - "definition_uri": "http://w3id.org/ontogpt/core/Publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "publication__id", - "publication__title", - "publication__abstract", - "publication__combined_text", - "publication__full_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "description": "The publication identifier", - "@type": "SlotDefinition" - }, - { - "name": "title", - "description": "The title of the publication", - "@type": "SlotDefinition" - }, - { - "name": "abstract", - "description": "The abstract of the publication", - "@type": "SlotDefinition" - }, - { - "name": "combined_text", - "@type": "SlotDefinition" - }, - { - "name": "full_text", - "description": "The full text of the publication", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Publication", - "@type": "ClassDefinition" - }, - { - "name": "AnnotatorResult", - "definition_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "annotatorResult__subject_text", - "annotatorResult__object_id", - "annotatorResult__object_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject_text", - "@type": "SlotDefinition" - }, - { - "name": "object_id", - "@type": "SlotDefinition" - }, - { - "name": "object_text", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "@type": "ClassDefinition" - } - ], - "metamodel_version": "1.7.0", - "source_file": "treatment.yaml", - "source_file_date": "2023-06-17T15:11:19", - "source_file_size": 4485, - "generation_date": "2023-08-07T10:56:36", - "keywords": [ - "treatments", - "drugs", - "therapies" - ], - "@type": "SchemaDefinition", - "@context": [ - "projects/treatment/jsonld/treatment.context.jsonld", - "https://w3id.org/linkml/types.context.jsonld", - "core.context.jsonld", - { - "@base": "http://w3id.org/ontogpt/treatments/" - } - ] -} diff --git a/projects/treatment/jsonschema/treatment.schema.json b/projects/treatment/jsonschema/treatment.schema.json deleted file mode 100644 index d63296511..000000000 --- a/projects/treatment/jsonschema/treatment.schema.json +++ /dev/null @@ -1,457 +0,0 @@ -{ - "$defs": { - "AdverseEffect": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "AdverseEffect", - "type": "object" - }, - "AnnotatorResult": { - "additionalProperties": false, - "description": "", - "properties": { - "object_id": { - "type": "string" - }, - "object_text": { - "type": "string" - }, - "subject_text": { - "type": "string" - } - }, - "title": "AnnotatorResult", - "type": "object" - }, - "Any": { - "additionalProperties": true, - "description": "", - "title": "Any", - "type": "object" - }, - "CHEBIDrugType": { - "description": "", - "enum": [], - "title": "CHEBIDrugType", - "type": "string" - }, - "Disease": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Disease", - "type": "object" - }, - "DiseaseTreatmentSummary": { - "additionalProperties": false, - "description": "", - "properties": { - "contraindications": { - "description": "semicolon-separated list of therapies and treatments that are contra-indicated for the disease, and should not be used, due to risk of adverse effects.", - "items": { - "type": "string" - }, - "type": "array" - }, - "disease": { - "description": "the name of the disease that is treated.", - "type": "string" - }, - "drugs": { - "description": "semicolon-separated list of named small molecule drugs", - "items": { - "type": "string" - }, - "type": "array" - }, - "treatment_adverse_effects": { - "description": "semicolon-separated list of treatment to adverse effect associations, e.g. Imatinib*nausea", - "items": { - "$ref": "#/$defs/TreatmentAdverseEffect" - }, - "type": "array" - }, - "treatment_efficacies": { - "description": "semicolon-separated list of treatment to efficacy associations, e.g. Imatinib*effective", - "items": { - "$ref": "#/$defs/TreatmentEfficacy" - }, - "type": "array" - }, - "treatment_mechanisms": { - "description": "semicolon-separated list of treatment to asterisk-separated mechanism associations", - "items": { - "$ref": "#/$defs/TreatmentMechanism" - }, - "type": "array" - }, - "treatments": { - "description": "semicolon-separated list of therapies and treatments are indicated for treating the disease.", - "items": { - "type": "string" - }, - "type": "array" - } - }, - "title": "DiseaseTreatmentSummary", - "type": "object" - }, - "Drug": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Drug", - "type": "object" - }, - "ExtractionResult": { - "additionalProperties": false, - "description": "A result of extracting knowledge on text", - "properties": { - "extracted_object": { - "$ref": "#/$defs/Any", - "description": "The complex objects extracted from the text" - }, - "input_id": { - "type": "string" - }, - "input_text": { - "type": "string" - }, - "input_title": { - "type": "string" - }, - "named_entities": { - "description": "Named entities extracted from the text", - "items": { - "$ref": "#/$defs/Any" - }, - "type": "array" - }, - "prompt": { - "type": "string" - }, - "raw_completion_output": { - "type": "string" - } - }, - "title": "ExtractionResult", - "type": "object" - }, - "Gene": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Gene", - "type": "object" - }, - "MAXOActionType": { - "description": "", - "enum": [], - "title": "MAXOActionType", - "type": "string" - }, - "MESHTherapeuticType": { - "description": "", - "enum": [], - "title": "MESHTherapeuticType", - "type": "string" - }, - "Mechanism": { - "additionalProperties": 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publication", - "type": "string" - }, - "combined_text": { - "type": "string" - }, - "full_text": { - "description": "The full text of the publication", - "type": "string" - }, - "id": { - "description": "The publication identifier", - "type": "string" - }, - "title": { - "description": "The title of the publication", - "type": "string" - } - }, - "title": "Publication", - "type": "object" - }, - "RelationshipType": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "RelationshipType", - "type": "object" - }, - "Symptom": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Symptom", - "type": "object" - }, - "TextWithTriples": { - "additionalProperties": false, - "description": "", - "properties": { - "publication": { - "$ref": "#/$defs/Publication" - }, - "triples": { - "items": { - "$ref": "#/$defs/Triple" - }, - "type": "array" - } - }, - "title": "TextWithTriples", - "type": "object" - }, - "Treatment": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Treatment", - "type": "object" - }, - "TreatmentAdverseEffect": { - "additionalProperties": false, - "description": "", - "properties": { - "adverse_effects": { - "items": { - "type": "string" - }, - "type": "array" - }, - "treatment": { - "type": "string" - } - }, - "title": "TreatmentAdverseEffect", - "type": "object" - }, - "TreatmentEfficacy": { - "additionalProperties": false, - "description": "", - "properties": { - "efficacy": { - "type": "string" - }, - "treatment": { - "type": "string" - } - }, - "title": "TreatmentEfficacy", - "type": "object" - }, - "TreatmentMechanism": { - "additionalProperties": false, - "description": "", - "properties": { - "mechanism": { - "type": "string" - }, - "treatment": { - "type": "string" - } - }, - "title": "TreatmentMechanism", - "type": "object" - } - }, - "$id": "http://w3id.org/ontogpt/treatment", - "$schema": "http://json-schema.org/draft-07/schema#", - "additionalProperties": true, - "metamodel_version": "1.7.0", - "properties": { - "contraindications": { - "description": "semicolon-separated list of therapies and treatments that are contra-indicated for the disease, and should not be used, due to risk of adverse effects.", - "items": { - "type": "string" - }, - "type": "array" - }, - "disease": { - "description": "the name of the disease that is treated.", - "type": "string" - }, - "drugs": { - "description": "semicolon-separated list of named small molecule drugs", - "items": { - "type": "string" - }, - "type": "array" - }, - "treatment_adverse_effects": { - "description": "semicolon-separated list of treatment to adverse effect associations, e.g. Imatinib*nausea", - "items": { - "$ref": "#/$defs/TreatmentAdverseEffect" - }, - "type": "array" - }, - "treatment_efficacies": { - "description": "semicolon-separated list of treatment to efficacy associations, e.g. Imatinib*effective", - "items": { - "$ref": "#/$defs/TreatmentEfficacy" - }, - "type": "array" - }, - "treatment_mechanisms": { - "description": "semicolon-separated list of treatment to asterisk-separated mechanism associations", - "items": { - "$ref": "#/$defs/TreatmentMechanism" - }, - "type": "array" - }, - "treatments": { - "description": "semicolon-separated list of therapies and treatments are indicated for treating the disease.", - "items": { - "type": "string" - }, - "type": "array" - } - }, - "title": "treatment-template", - "type": "object", - "version": null -} \ No newline at end of file diff --git a/projects/treatment/owl/treatment.owl.ttl b/projects/treatment/owl/treatment.owl.ttl deleted file mode 100644 index 3ed1f1492..000000000 --- a/projects/treatment/owl/treatment.owl.ttl +++ /dev/null @@ -1,576 +0,0 @@ -@prefix IAO: <http://purl.obolibrary.org/obo/IAO_> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix owl: <http://www.w3.org/2002/07/owl#> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . -@prefix skos: <http://www.w3.org/2004/02/skos/core#> . -@prefix treatment: <http://w3id.org/ontogpt/treatments/> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -<http://w3id.org/ontogpt/treatment> a owl:Ontology ; - rdfs:label "treatment-template" ; - IAO:0000700 <http://w3id.org/ontogpt/core/AnnotatorResult>, - <http://w3id.org/ontogpt/core/Any>, - <http://w3id.org/ontogpt/core/CompoundExpression>, - <http://w3id.org/ontogpt/core/ExtractionResult>, - <http://w3id.org/ontogpt/core/NamedEntity>, - <http://w3id.org/ontogpt/core/Publication>, - <http://w3id.org/ontogpt/core/TextWithTriples>, - treatment:DiseaseTreatmentSummary ; - linkml:classes "{'DiseaseTreatmentSummary': ClassDefinition(name='DiseaseTreatmentSummary', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/treatments/DiseaseTreatmentSummary', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/treatment', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['diseaseTreatmentSummary__disease', 'diseaseTreatmentSummary__drugs', 'diseaseTreatmentSummary__treatments', 'diseaseTreatmentSummary__contraindications', 'diseaseTreatmentSummary__treatment_mechanisms', 'diseaseTreatmentSummary__treatment_efficacies', 'diseaseTreatmentSummary__treatment_adverse_effects'], slot_usage={}, attributes={'disease': SlotDefinition(name='disease', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the name of the disease that is treated.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Disease', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'drugs': SlotDefinition(name='drugs', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of named small molecule drugs', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Drug', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'treatments': SlotDefinition(name='treatments', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.examples': Annotation(tag='prompt.examples', value='Imatinib, exercise, surgery', extensions={}, annotations={})}, description='semicolon-separated list of therapies and treatments are indicated for treating the disease.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Treatment', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'contraindications': SlotDefinition(name='contraindications', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.examples': Annotation(tag='prompt.examples', value='Beta-blockers, exercise, surgery', extensions={}, annotations={})}, description='semicolon-separated list of therapies and treatments that are contra-indicated for the disease, and should not be used, due to risk of adverse effects.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Treatment', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'treatment_mechanisms': SlotDefinition(name='treatment_mechanisms', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.separator': Annotation(tag='prompt.separator', value='*', extensions={}, annotations={})}, description='semicolon-separated list of treatment to asterisk-separated mechanism associations', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='TreatmentMechanism', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'treatment_efficacies': SlotDefinition(name='treatment_efficacies', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.separator': Annotation(tag='prompt.separator', value='*', extensions={}, annotations={})}, description='semicolon-separated list of treatment to efficacy associations, e.g. Imatinib*effective', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='TreatmentEfficacy', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'treatment_adverse_effects': SlotDefinition(name='treatment_adverse_effects', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.separator': Annotation(tag='prompt.separator', value='*', extensions={}, annotations={})}, description='semicolon-separated list of treatment to adverse effect associations, e.g. Imatinib*nausea', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='TreatmentAdverseEffect', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='treatment:DiseaseTreatmentSummary', subclass_of=None, union_of=[], defining_slots=[], tree_root=True, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Gene': ClassDefinition(name='Gene', id_prefixes=['HGNC'], definition_uri='http://w3id.org/ontogpt/treatments/Gene', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='gilda:, obo:sql:hgnc, bioportal:hgnc-nr', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/treatment', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='treatment:Gene', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Symptom': ClassDefinition(name='Symptom', id_prefixes=['HP'], definition_uri='http://w3id.org/ontogpt/treatments/Symptom', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:hp', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/treatment', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='treatment:Symptom', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Disease': ClassDefinition(name='Disease', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/treatments/Disease', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:mondo', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/treatment', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='treatment:Disease', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'AdverseEffect': ClassDefinition(name='AdverseEffect', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/treatments/AdverseEffect', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:hp, sqlite:obo:ncit', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/treatment', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='treatment:AdverseEffect', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Treatment': ClassDefinition(name='Treatment', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/treatments/Treatment', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:maxo, sqlite:obo:ncit, sqlite:obo:mesh, sqlite:obo:chebi', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/treatment', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=['NCITDrugType', 'NCITTreatmentType', 'NCITActivityType', 'MAXOTreatmentType', 'MESHTherapeuticType', 'CHEBIDrugType'], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='treatment:Treatment', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Mechanism': ClassDefinition(name='Mechanism', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/treatments/Mechanism', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:go, sqlite:obo:ncit, sqlite:obo:mesh', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/treatment', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='treatment:Mechanism', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Drug': ClassDefinition(name='Drug', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/treatments/Drug', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:chebi, sqlite:obo:drugbank', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/treatment', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='treatment:Drug', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'TreatmentMechanism': ClassDefinition(name='TreatmentMechanism', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/treatments/TreatmentMechanism', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/treatment', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['treatmentMechanism__treatment', 'treatmentMechanism__mechanism'], slot_usage={}, attributes={'treatment': SlotDefinition(name='treatment', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Treatment', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'mechanism': SlotDefinition(name='mechanism', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Mechanism', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='treatment:TreatmentMechanism', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'TreatmentAdverseEffect': ClassDefinition(name='TreatmentAdverseEffect', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/treatments/TreatmentAdverseEffect', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/treatment', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['treatmentAdverseEffect__treatment', 'treatmentAdverseEffect__adverse_effects'], slot_usage={}, attributes={'treatment': SlotDefinition(name='treatment', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Treatment', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'adverse_effects': SlotDefinition(name='adverse_effects', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='AdverseEffect', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='treatment:TreatmentAdverseEffect', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'TreatmentEfficacy': ClassDefinition(name='TreatmentEfficacy', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/treatments/TreatmentEfficacy', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/treatment', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['treatmentEfficacy__treatment', 'treatmentEfficacy__efficacy'], slot_usage={}, attributes={'treatment': SlotDefinition(name='treatment', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Treatment', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'efficacy': SlotDefinition(name='efficacy', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='treatment:TreatmentEfficacy', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Any': ClassDefinition(name='Any', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Any', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=['linkml:Any'], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='linkml:Any', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ExtractionResult': ClassDefinition(name='ExtractionResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/ExtractionResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A result of extracting knowledge on text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['extractionResult__input_id', 'extractionResult__input_title', 'extractionResult__input_text', 'extractionResult__raw_completion_output', 'extractionResult__prompt', 'extractionResult__extracted_object', 'extractionResult__named_entities'], slot_usage={}, attributes={'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:ExtractionResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'NamedEntity': ClassDefinition(name='NamedEntity', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NamedEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:NamedEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'CompoundExpression': ClassDefinition(name='CompoundExpression', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/CompoundExpression', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='core:CompoundExpression', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Triple': ClassDefinition(name='Triple', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Triple', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Abstract parent for Relation Extraction tasks', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['triple__subject', 'triple__predicate', 'triple__object', 'triple__qualifier', 'triple__subject_qualifier', 'triple__object_qualifier'], slot_usage={}, attributes={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Triple', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'TextWithTriples': ClassDefinition(name='TextWithTriples', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/TextWithTriples', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['textWithTriples__publication', 'textWithTriples__triples'], slot_usage={}, attributes={'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:TextWithTriples', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'RelationshipType': ClassDefinition(name='RelationshipType', id_prefixes=['RO', 'biolink'], definition_uri='http://w3id.org/ontogpt/core/RelationshipType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='core:RelationshipType', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Publication': ClassDefinition(name='Publication', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Publication', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['publication__id', 'publication__title', 'publication__abstract', 'publication__combined_text', 'publication__full_text'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Publication', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'AnnotatorResult': ClassDefinition(name='AnnotatorResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/AnnotatorResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['annotatorResult__subject_text', 'annotatorResult__object_id', 'annotatorResult__object_text'], slot_usage={}, attributes={'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:AnnotatorResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={})}" ; - linkml:enums "{'NCITDrugType': EnumDefinition(name='NCITDrugType', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/treatments/NCITDrugType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/treatment', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={}, include=[], minus=[], inherits=[], reachable_from=ReachabilityQuery(source_ontology='obo:ncit', source_nodes=['NCIT:C1908'], relationship_types=[], is_direct=None, include_self=None, traverse_up=None), matches=None, concepts=[]), 'NCITTreatmentType': EnumDefinition(name='NCITTreatmentType', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/treatments/NCITTreatmentType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/treatment', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={}, include=[], minus=[], inherits=[], reachable_from=ReachabilityQuery(source_ontology='obo:ncit', source_nodes=['NCIT:C25218'], relationship_types=[], is_direct=None, include_self=None, traverse_up=None), matches=None, concepts=[]), 'NCITTActivityType': EnumDefinition(name='NCITTActivityType', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/treatments/NCITTActivityType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/treatment', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={}, include=[], minus=[], inherits=[], reachable_from=ReachabilityQuery(source_ontology='obo:ncit', source_nodes=['NCIT:C43431'], relationship_types=[], is_direct=None, include_self=None, traverse_up=None), matches=None, concepts=[]), 'MAXOActionType': EnumDefinition(name='MAXOActionType', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/treatments/MAXOActionType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/treatment', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={}, include=[], minus=[], inherits=[], reachable_from=ReachabilityQuery(source_ontology='obo:maxo', source_nodes=['MAXO:0000001'], relationship_types=[], is_direct=None, include_self=None, traverse_up=None), matches=None, concepts=[]), 'MESHTherapeuticType': EnumDefinition(name='MESHTherapeuticType', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/treatments/MESHTherapeuticType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/treatment', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={}, include=[], minus=[], inherits=[], reachable_from=ReachabilityQuery(source_ontology='obo:mesh', source_nodes=['MESH:D013812'], relationship_types=[], is_direct=None, include_self=None, traverse_up=None), matches=None, concepts=[]), 'CHEBIDrugType': EnumDefinition(name='CHEBIDrugType', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/treatments/CHEBIDrugType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/treatment', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={}, include=[], minus=[], inherits=[], reachable_from=ReachabilityQuery(source_ontology='obo:chebi', source_nodes=['CHEBI:23888'], relationship_types=['rdfs:subClassOf', 'RO:0000087'], is_direct=None, include_self=None, traverse_up=None), matches=None, concepts=[]), 'NullDataOptions': EnumDefinition(name='NullDataOptions', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NullDataOptions', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'UNSPECIFIED_METHOD_OF_ADMINISTRATION': PermissibleValue(text='UNSPECIFIED_METHOD_OF_ADMINISTRATION', description=None, meaning='NCIT:C149701', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_APPLICABLE': PermissibleValue(text='NOT_APPLICABLE', description=None, meaning='NCIT:C18902', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['not applicable', 'N/A'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_MENTIONED': PermissibleValue(text='NOT_MENTIONED', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[])}" ; - linkml:id "http://w3id.org/ontogpt/treatment" ; - linkml:imports "core", - "linkml:types" ; - linkml:types "{'string': TypeDefinition(name='string', id_prefixes=[], definition_uri='https://w3id.org/linkml/String', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A character string', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Text'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'integer': TypeDefinition(name='integer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Integer', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An integer', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Integer'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='int', uri='xsd:integer', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'boolean': TypeDefinition(name='boolean', id_prefixes=[], definition_uri='https://w3id.org/linkml/Boolean', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A binary (true or false) value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Boolean'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Bool', uri='xsd:boolean', repr='bool', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'float': TypeDefinition(name='float', id_prefixes=[], definition_uri='https://w3id.org/linkml/Float', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:float specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Float'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:float', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'double': TypeDefinition(name='double', id_prefixes=[], definition_uri='https://w3id.org/linkml/Double', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:double specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:Float'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:double', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'decimal': TypeDefinition(name='decimal', id_prefixes=[], definition_uri='https://w3id.org/linkml/Decimal', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number with arbitrary precision that conforms to the xsd:decimal specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=['schema:Number'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Decimal', uri='xsd:decimal', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'time': TypeDefinition(name='time', id_prefixes=[], definition_uri='https://w3id.org/linkml/Time', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A time object represents a (local) time of day, independent of any particular day', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=['URI is dateTime because OWL reasoners do not work with straight date or time'], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Time'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDTime', uri='xsd:time', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date': TypeDefinition(name='date', id_prefixes=[], definition_uri='https://w3id.org/linkml/Date', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a date (year, month and day) in an idealized calendar', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[\"URI is dateTime because OWL reasoners don't work with straight date or time\"], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Date'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDate', uri='xsd:date', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'datetime': TypeDefinition(name='datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/Datetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The combination of a date and time', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:DateTime'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDateTime', uri='xsd:dateTime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date_or_datetime': TypeDefinition(name='date_or_datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/DateOrDatetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Either a date or a datetime', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='linkml:DateOrDatetime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uriorcurie': TypeDefinition(name='uriorcurie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uriorcurie', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a URI or a CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URIorCURIE', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'curie': TypeDefinition(name='curie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Curie', local_names={}, conforms_to='https://www.w3.org/TR/curie/', implements=[], extensions={}, annotations={}, description='a compact URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations this MUST be expanded to a URI', 'in non-RDF serializations MAY be serialized as the compact representation'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Curie', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uri': TypeDefinition(name='uri', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uri', local_names={}, conforms_to='https://www.ietf.org/rfc/rfc3987.txt', implements=[], extensions={}, annotations={}, description='a complete URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:URL'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URI', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ncname': TypeDefinition(name='ncname', id_prefixes=[], definition_uri='https://w3id.org/linkml/Ncname', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Prefix part of CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NCName', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'objectidentifier': TypeDefinition(name='objectidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Objectidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI or CURIE that represents an object in the model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['Used for inheritance and type checking'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='ElementIdentifier', uri='shex:iri', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'nodeidentifier': TypeDefinition(name='nodeidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Nodeidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI, CURIE or BNODE that represents a node in a model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NodeIdentifier', uri='shex:nonLiteral', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpointer': TypeDefinition(name='jsonpointer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpointer', local_names={}, conforms_to='https://datatracker.ietf.org/doc/html/rfc6901', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpath': TypeDefinition(name='jsonpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpath', local_names={}, conforms_to='https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sparqlpath': TypeDefinition(name='sparqlpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Sparqlpath', local_names={}, conforms_to='https://www.w3.org/TR/sparql11-query/#propertypaths', implements=[], extensions={}, annotations={}, description='A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -treatment:CHEBIDrugType a owl:Class, - linkml:EnumDefinition ; - rdfs:label "CHEBIDrugType" ; - owl:unionOf [ rdf:rest () ] . - -treatment:Gene a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Gene" ; - treatment:annotators "gilda:, obo:sql:hgnc, bioportal:hgnc-nr" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -treatment:MAXOActionType a owl:Class, - linkml:EnumDefinition ; - rdfs:label "MAXOActionType" ; - owl:unionOf [ rdf:rest () ] . - -treatment:MESHTherapeuticType a owl:Class, - linkml:EnumDefinition ; - rdfs:label "MESHTherapeuticType" ; - owl:unionOf [ rdf:rest () ] . - -treatment:NCITDrugType a owl:Class, - linkml:EnumDefinition ; - rdfs:label "NCITDrugType" ; - owl:unionOf [ rdf:rest () ] . - -treatment:NCITTActivityType a owl:Class, - linkml:EnumDefinition ; - rdfs:label "NCITTActivityType" ; - owl:unionOf [ rdf:rest () ] . - -treatment:NCITTreatmentType a owl:Class, - linkml:EnumDefinition ; - rdfs:label "NCITTreatmentType" ; - owl:unionOf [ rdf:rest () ] . - -treatment:Symptom a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Symptom" ; - treatment:annotators "sqlite:obo:hp" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -linkml:SubsetDefinition a owl:Class ; - rdfs:label "subset_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" . - -linkml:TypeDefinition a owl:Class ; - rdfs:label "type_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" ; - linkml:mixins "type_expression" . - -linkml:topValue a owl:DatatypeProperty ; - rdfs:label "value" . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "AnnotatorResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_text> ] ; - linkml:attributes "{'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/ExtractionResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ExtractionResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/prompt> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_text> ], - [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/named_entities> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/extracted_object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_title> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_id> ] ; - skos:definition "A result of extracting knowledge on text" ; - linkml:attributes "{'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/TextWithTriples> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TextWithTriples" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Triple> ; - owl:onProperty <http://w3id.org/ontogpt/core/triples> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Publication> ; - owl:onProperty <http://w3id.org/ontogpt/core/publication> ] ; - linkml:attributes "{'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/abstract> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "abstract" ; - rdfs:range linkml:String ; - skos:definition "The abstract of the publication" . - -<http://w3id.org/ontogpt/core/combined_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "combined_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/extracted_object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "extracted_object" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "The complex objects extracted from the text" . - -<http://w3id.org/ontogpt/core/full_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "full_text" ; - rdfs:range linkml:String ; - skos:definition "The full text of the publication" . - -<http://w3id.org/ontogpt/core/input_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_title" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/named_entities> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "named_entities" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "Named entities extracted from the text" . - -<http://w3id.org/ontogpt/core/object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/object_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/object_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" . - -<http://w3id.org/ontogpt/core/object_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/predicate> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "predicate" ; - rdfs:range <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/prompt> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "prompt" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/publication> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "publication" ; - treatment:prompt.skip "true" ; - rdfs:range <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "qualifier" ; - rdfs:range linkml:String ; - skos:definition "A qualifier for the statements, e.g. \"NOT\" for negation" . - -<http://w3id.org/ontogpt/core/raw_completion_output> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "raw_completion_output" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/subject> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/subject_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" . - -<http://w3id.org/ontogpt/core/subject_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "title" ; - rdfs:range linkml:String ; - skos:definition "The title of the publication" . - -<http://w3id.org/ontogpt/core/triples> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "triples" ; - rdfs:range <http://w3id.org/ontogpt/core/Triple> . - -treatment:DiseaseTreatmentSummary a owl:Class, - linkml:ClassDefinition ; - rdfs:label "DiseaseTreatmentSummary" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom treatment:TreatmentMechanism ; - owl:onProperty treatment:treatment_mechanisms ], - [ a owl:Restriction ; - owl:allValuesFrom treatment:TreatmentAdverseEffect ; - owl:onProperty treatment:treatment_adverse_effects ], - [ a owl:Restriction ; - owl:allValuesFrom treatment:TreatmentEfficacy ; - owl:onProperty treatment:treatment_efficacies ], - [ a owl:Restriction ; - owl:allValuesFrom treatment:Drug ; - owl:onProperty treatment:drugs ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass treatment:Disease ; - owl:onProperty treatment:disease ], - [ a owl:Restriction ; - owl:allValuesFrom treatment:Treatment ; - owl:onProperty treatment:treatments ], - [ a owl:Restriction ; - owl:allValuesFrom treatment:Treatment ; - owl:onProperty treatment:contraindications ] ; - linkml:attributes "{'disease': SlotDefinition(name='disease', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the name of the disease that is treated.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Disease', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'drugs': SlotDefinition(name='drugs', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of named small molecule drugs', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Drug', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'treatments': SlotDefinition(name='treatments', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.examples': Annotation(tag='prompt.examples', value='Imatinib, exercise, surgery', extensions={}, annotations={})}, description='semicolon-separated list of therapies and treatments are indicated for treating the disease.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Treatment', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'contraindications': SlotDefinition(name='contraindications', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.examples': Annotation(tag='prompt.examples', value='Beta-blockers, exercise, surgery', extensions={}, annotations={})}, description='semicolon-separated list of therapies and treatments that are contra-indicated for the disease, and should not be used, due to risk of adverse effects.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Treatment', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'treatment_mechanisms': SlotDefinition(name='treatment_mechanisms', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.separator': Annotation(tag='prompt.separator', value='*', extensions={}, annotations={})}, description='semicolon-separated list of treatment to asterisk-separated mechanism associations', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='TreatmentMechanism', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'treatment_efficacies': SlotDefinition(name='treatment_efficacies', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.separator': Annotation(tag='prompt.separator', value='*', extensions={}, annotations={})}, description='semicolon-separated list of treatment to efficacy associations, e.g. Imatinib*effective', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='TreatmentEfficacy', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'treatment_adverse_effects': SlotDefinition(name='treatment_adverse_effects', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.separator': Annotation(tag='prompt.separator', value='*', extensions={}, annotations={})}, description='semicolon-separated list of treatment to adverse effect associations, e.g. Imatinib*nausea', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='TreatmentAdverseEffect', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -treatment:adverse_effects a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "adverse_effects" ; - rdfs:range treatment:AdverseEffect . - -treatment:contraindications a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "contraindications" ; - treatment:prompt.examples "Beta-blockers, exercise, surgery" ; - rdfs:range treatment:Treatment ; - skos:definition "semicolon-separated list of therapies and treatments that are contra-indicated for the disease, and should not be used, due to risk of adverse effects." . - -treatment:disease a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "disease" ; - rdfs:range treatment:Disease ; - skos:definition "the name of the disease that is treated." . - -treatment:drugs a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "drugs" ; - rdfs:range treatment:Drug ; - skos:definition "semicolon-separated list of named small molecule drugs" . - -treatment:efficacy a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "efficacy" ; - rdfs:range linkml:String . - -treatment:mechanism a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "mechanism" ; - rdfs:range treatment:Mechanism . - -treatment:treatment_adverse_effects a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "treatment_adverse_effects" ; - treatment:prompt.separator "*" ; - rdfs:range treatment:TreatmentAdverseEffect ; - skos:definition "semicolon-separated list of treatment to adverse effect associations, e.g. Imatinib*nausea" . - -treatment:treatment_efficacies a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "treatment_efficacies" ; - treatment:prompt.separator "*" ; - rdfs:range treatment:TreatmentEfficacy ; - skos:definition "semicolon-separated list of treatment to efficacy associations, e.g. Imatinib*effective" . - -treatment:treatment_mechanisms a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "treatment_mechanisms" ; - treatment:prompt.separator "*" ; - rdfs:range treatment:TreatmentMechanism ; - skos:definition "semicolon-separated list of treatment to asterisk-separated mechanism associations" . - -treatment:treatments a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "treatments" ; - treatment:prompt.examples "Imatinib, exercise, surgery" ; - rdfs:range treatment:Treatment ; - skos:definition "semicolon-separated list of therapies and treatments are indicated for treating the disease." . - -<http://example.org/UNKNOWN/rdfs/label> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "label" ; - treatment:owl "AnnotationProperty, AnnotationAssertion" ; - rdfs:range linkml:String ; - skos:altLabel "name" ; - skos:definition "The label (name) of the named thing" ; - skos:exactMatch <http://example.org/UNKNOWN/rdfs/label> . - -<http://purl.obolibrary.org/obo/NCIT_C149701> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "UNSPECIFIED_METHOD_OF_ADMINISTRATION" . - -<http://purl.obolibrary.org/obo/NCIT_C18902> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_APPLICABLE" . - -<http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_MENTIONED" . - -<http://w3id.org/ontogpt/core/RelationshipType> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "RelationshipType" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/Triple> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Triple" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/RelationshipType> ; - owl:onProperty <http://w3id.org/ontogpt/core/predicate> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_qualifier> ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - skos:definition "Abstract parent for Relation Extraction tasks" ; - linkml:attributes "{'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -<http://w3id.org/ontogpt/core/id> a owl:ObjectProperty, - linkml:SlotDefinition . - -treatment:AdverseEffect a owl:Class, - linkml:ClassDefinition ; - rdfs:label "AdverseEffect" ; - treatment:annotators "sqlite:obo:hp, sqlite:obo:ncit" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -treatment:Disease a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Disease" ; - treatment:annotators "sqlite:obo:mondo" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -treatment:Drug a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Drug" ; - treatment:annotators "sqlite:obo:chebi, sqlite:obo:drugbank" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -treatment:Mechanism a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Mechanism" ; - treatment:annotators "sqlite:obo:go, sqlite:obo:ncit, sqlite:obo:mesh" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -treatment:TreatmentAdverseEffect a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TreatmentAdverseEffect" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass treatment:Treatment ; - owl:onProperty treatment:treatment ], - [ a owl:Restriction ; - owl:allValuesFrom treatment:AdverseEffect ; - owl:onProperty treatment:adverse_effects ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - linkml:attributes "{'treatment': SlotDefinition(name='treatment', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Treatment', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'adverse_effects': SlotDefinition(name='adverse_effects', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='AdverseEffect', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -treatment:TreatmentEfficacy a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TreatmentEfficacy" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass treatment:Treatment ; - owl:onProperty treatment:treatment ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty treatment:efficacy ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - linkml:attributes "{'treatment': SlotDefinition(name='treatment', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Treatment', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'efficacy': SlotDefinition(name='efficacy', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -treatment:TreatmentMechanism a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TreatmentMechanism" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass treatment:Mechanism ; - owl:onProperty treatment:mechanism ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass treatment:Treatment ; - owl:onProperty treatment:treatment ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - linkml:attributes "{'treatment': SlotDefinition(name='treatment', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Treatment', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'mechanism': SlotDefinition(name='mechanism', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Mechanism', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -<http://w3id.org/ontogpt/core/NullDataOptions> a owl:Class, - linkml:EnumDefinition ; - rdfs:label "NullDataOptions" ; - owl:unionOf ( <http://purl.obolibrary.org/obo/NCIT_C149701> <http://purl.obolibrary.org/obo/NCIT_C18902> <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> ) ; - linkml:permissible_values <http://purl.obolibrary.org/obo/NCIT_C149701>, - <http://purl.obolibrary.org/obo/NCIT_C18902>, - <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> . - -<http://w3id.org/ontogpt/core/Publication> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Publication" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/combined_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/title> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/full_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/abstract> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -treatment:treatment a owl:ObjectProperty, - linkml:SlotDefinition . - -<http://w3id.org/ontogpt/core/Any> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Any" ; - skos:exactMatch linkml:Any ; - linkml:attributes "{}" . - -<http://w3id.org/ontogpt/core/CompoundExpression> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CompoundExpression" ; - linkml:attributes "{}" . - -treatment:Treatment a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Treatment" ; - treatment:annotators "sqlite:obo:maxo, sqlite:obo:ncit, sqlite:obo:mesh, sqlite:obo:chebi" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/NamedEntity> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "NamedEntity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://example.org/UNKNOWN/rdfs/label> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:ClassDefinition a owl:Class ; - rdfs:label "class_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "class_expression" . - -linkml:SlotDefinition a owl:Class ; - rdfs:label "slot_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "slot_expression" . - - diff --git a/projects/treatment/prefixmap/treatment.yaml b/projects/treatment/prefixmap/treatment.yaml deleted file mode 100644 index c0137da11..000000000 --- a/projects/treatment/prefixmap/treatment.yaml +++ /dev/null @@ -1,37 +0,0 @@ -{ - "HGNC": "http://example.org/UNKNOWN/HGNC/", - "HP": "http://example.org/UNKNOWN/HP/", - "RO": "http://purl.obolibrary.org/obo/RO_", - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "treatment": "http://w3id.org/ontogpt/treatments/", - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } -} diff --git a/projects/treatment/protobuf/treatment.proto b/projects/treatment/protobuf/treatment.proto deleted file mode 100644 index f6abf4613..000000000 --- a/projects/treatment/protobuf/treatment.proto +++ /dev/null @@ -1,95 +0,0 @@ -message AdverseEffect - { - string id = 0 - string label = 0 - } -message AnnotatorResult - { - string subjectText = 0 - string objectId = 0 - string objectText = 0 - } -message Disease - { - string id = 0 - string label = 0 - } -message DiseaseTreatmentSummary - { - disease disease = 0 - repeated drug drugs = 0 - repeated treatment treatments = 0 - repeated treatment contraindications = 0 - repeated treatmentMechanism treatmentMechanisms = 0 - repeated treatmentEfficacy treatmentEfficacies = 0 - repeated treatmentAdverseEffect treatmentAdverseEffects = 0 - } -message Drug - { - string id = 0 - string label = 0 - } -// A result of extracting knowledge on text -message ExtractionResult - { - string inputId = 0 - string inputTitle = 0 - string inputText = 0 - string rawCompletionOutput = 0 - string prompt = 0 - any extractedObject = 0 - repeated any namedEntities = 0 - } -message Gene - { - string id = 0 - string label = 0 - } -message Mechanism - { - string id = 0 - string label = 0 - } -message Publication - { - string id = 0 - string title = 0 - string abstract = 0 - string combinedText = 0 - string fullText = 0 - } -message RelationshipType - { - string id = 0 - string label = 0 - } -message Symptom - { - string id = 0 - string label = 0 - } -message TextWithTriples - { - publication publication = 0 - repeated triple triples = 0 - } -message Treatment - { - string id = 0 - string label = 0 - } -message TreatmentAdverseEffect - { - treatment treatment = 0 - repeated adverseEffect adverseEffects = 0 - } -message TreatmentEfficacy - { - treatment treatment = 0 - string efficacy = 0 - } -message TreatmentMechanism - { - treatment treatment = 0 - mechanism mechanism = 0 - } diff --git a/projects/treatment/shacl/treatment.shacl.ttl b/projects/treatment/shacl/treatment.shacl.ttl deleted file mode 100644 index db93ed7d9..000000000 --- a/projects/treatment/shacl/treatment.shacl.ttl +++ /dev/null @@ -1,345 +0,0 @@ -@prefix linkml: <https://w3id.org/linkml/> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix sh: <http://www.w3.org/ns/shacl#> . -@prefix treatment: <http://w3id.org/ontogpt/treatments/> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object_text> ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/object_id> ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject_text> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/AnnotatorResult> . - -<http://w3id.org/ontogpt/core/CompoundExpression> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass <http://w3id.org/ontogpt/core/CompoundExpression> . - -<http://w3id.org/ontogpt/core/ExtractionResult> a sh:NodeShape ; - sh:closed true ; - sh:description "A result of extracting knowledge on text" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/input_title> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/input_id> ], - [ sh:class linkml:Any ; - sh:description "Named entities extracted from the text" ; - sh:nodeKind sh:BlankNode ; - sh:order 6 ; - sh:path <http://w3id.org/ontogpt/core/named_entities> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/input_text> ], - [ sh:class linkml:Any ; - sh:description "The complex objects extracted from the text" ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/extracted_object> ], - [ sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/prompt> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/ExtractionResult> . - -<http://w3id.org/ontogpt/core/TextWithTriples> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/Triple> ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/triples> ], - [ sh:class <http://w3id.org/ontogpt/core/Publication> ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/publication> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/TextWithTriples> . - -treatment:DiseaseTreatmentSummary a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class treatment:TreatmentMechanism ; - sh:description "semicolon-separated list of treatment to asterisk-separated mechanism associations" ; - sh:nodeKind sh:BlankNode ; - sh:order 4 ; - sh:path treatment:treatment_mechanisms ], - [ sh:class treatment:Disease ; - sh:description "the name of the disease that is treated." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path treatment:disease ], - [ sh:class treatment:TreatmentEfficacy ; - sh:description "semicolon-separated list of treatment to efficacy associations, e.g. Imatinib*effective" ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path treatment:treatment_efficacies ], - [ sh:class treatment:Drug ; - sh:description "semicolon-separated list of named small molecule drugs" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path treatment:drugs ], - [ sh:class treatment:Treatment ; - sh:description "semicolon-separated list of therapies and treatments that are contra-indicated for the disease, and should not be used, due to risk of adverse effects." ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path treatment:contraindications ], - [ sh:class treatment:Treatment ; - sh:description "semicolon-separated list of therapies and treatments are indicated for treating the disease." ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path treatment:treatments ], - [ sh:class treatment:TreatmentAdverseEffect ; - sh:description "semicolon-separated list of treatment to adverse effect associations, e.g. Imatinib*nausea" ; - sh:nodeKind sh:BlankNode ; - sh:order 6 ; - sh:path treatment:treatment_adverse_effects ] ; - sh:targetClass treatment:DiseaseTreatmentSummary . - -treatment:Gene a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass treatment:Gene . - -treatment:Symptom a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass treatment:Symptom . - -<http://w3id.org/ontogpt/core/Publication> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The title of the publication" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/title> ], - [ sh:description "The publication identifier" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The full text of the publication" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/full_text> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/combined_text> ], - [ sh:description "The abstract of the publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/abstract> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/RelationshipType> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/Triple> a sh:NodeShape ; - sh:closed false ; - sh:description "Abstract parent for Relation Extraction tasks" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object> ], - [ sh:class <http://w3id.org/ontogpt/core/RelationshipType> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/predicate> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/object_qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ sh:description "A qualifier for the statements, e.g. \"NOT\" for negation" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Triple> . - -treatment:AdverseEffect a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass treatment:AdverseEffect . - -treatment:Disease a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass treatment:Disease . - -treatment:Drug a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass treatment:Drug . - -treatment:Mechanism a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass treatment:Mechanism . - -treatment:TreatmentAdverseEffect a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class treatment:Treatment ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path treatment:treatment ], - [ sh:class treatment:AdverseEffect ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path treatment:adverse_effects ] ; - sh:targetClass treatment:TreatmentAdverseEffect . - -treatment:TreatmentEfficacy a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 1 ; - sh:path treatment:efficacy ], - [ sh:class treatment:Treatment ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path treatment:treatment ] ; - sh:targetClass treatment:TreatmentEfficacy . - -treatment:TreatmentMechanism a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class treatment:Treatment ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path treatment:treatment ], - [ sh:class treatment:Mechanism ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path treatment:mechanism ] ; - sh:targetClass treatment:TreatmentMechanism . - -linkml:Any a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass linkml:Any . - -<http://w3id.org/ontogpt/core/NamedEntity> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/NamedEntity> . - -treatment:Treatment a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass treatment:Treatment . - diff --git a/projects/treatment/shex/treatment.shex b/projects/treatment/shex/treatment.shex deleted file mode 100644 index 894306fd7..000000000 --- a/projects/treatment/shex/treatment.shex +++ /dev/null @@ -1,235 +0,0 @@ -BASE <http://w3id.org/ontogpt/treatments/> -PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> -PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> -PREFIX linkml: <https://w3id.org/linkml/> -PREFIX core: <http://w3id.org/ontogpt/core/> -PREFIX rdfs1: <http://example.org/UNKNOWN/rdfs/> - - -linkml:String xsd:string - -linkml:Integer xsd:integer - -linkml:Boolean xsd:boolean - -linkml:Float xsd:float - -linkml:Double xsd:double - -linkml:Decimal xsd:decimal - -linkml:Time xsd:time - -linkml:Date xsd:date - -linkml:Datetime xsd:dateTime - -linkml:DateOrDatetime linkml:DateOrDatetime - -linkml:Uriorcurie IRI - -linkml:Curie xsd:string - -linkml:Uri IRI - -linkml:Ncname xsd:string - -linkml:Objectidentifier IRI - -linkml:Nodeidentifier NONLITERAL - -linkml:Jsonpointer xsd:string - -linkml:Jsonpath xsd:string - -linkml:Sparqlpath xsd:string - -<AdverseEffect> CLOSED { - ( $<AdverseEffect_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <AdverseEffect> ] - ) -} - -core:AnnotatorResult CLOSED { - ( $core:AnnotatorResult_tes ( core:subject_text @linkml:String ? ; - core:object_id @linkml:String ? ; - core:object_text @linkml:String ? - ) ; - rdf:type [ core:AnnotatorResult ] ? - ) -} - -core:Any CLOSED { - ( $core:Any_tes rdf:type . * ; - rdf:type [ linkml:Any ] ? - ) -} - -core:CompoundExpression ( - @<TreatmentAdverseEffect> OR @<TreatmentEfficacy> OR @<TreatmentMechanism> OR @core:Triple -) - -core:CompoundExpression_struct { - ( $core:CompoundExpression_tes rdf:type . * ; - rdf:type [ core:CompoundExpression ] ? - ) -} - -<Disease> CLOSED { - ( $<Disease_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Disease> ] - ) -} - -<DiseaseTreatmentSummary> CLOSED { - ( $<DiseaseTreatmentSummary_tes> ( <disease> @<Disease> ? ; - <drugs> @<Drug> * ; - <treatments> @<Treatment> * ; - <contraindications> @<Treatment> * ; - <treatment_mechanisms> @<TreatmentMechanism> * ; - <treatment_efficacies> @<TreatmentEfficacy> * ; - <treatment_adverse_effects> @<TreatmentAdverseEffect> * - ) ; - rdf:type [ <DiseaseTreatmentSummary> ] ? - ) -} - -<Drug> CLOSED { - ( $<Drug_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Drug> ] - ) -} - -core:ExtractionResult CLOSED { - ( $core:ExtractionResult_tes ( core:input_id @linkml:String ? ; - core:input_title @linkml:String ? ; - core:input_text @linkml:String ? ; - core:raw_completion_output @linkml:String ? ; - core:prompt @linkml:String ? ; - core:extracted_object @core:Any ? ; - core:named_entities @core:Any * - ) ; - rdf:type [ core:ExtractionResult ] ? - ) -} - -<Gene> CLOSED { - ( $<Gene_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Gene> ] - ) -} - -<Mechanism> CLOSED { - ( $<Mechanism_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Mechanism> ] - ) -} - -core:NamedEntity ( - @<AdverseEffect> OR @<Disease> OR @<Drug> OR @<Gene> OR @<Mechanism> OR @core:RelationshipType OR @<Symptom> OR @<Treatment> -) - -core:NamedEntity_struct { - ( $core:NamedEntity_tes rdfs1:label @linkml:String ? ; - rdf:type [ core:NamedEntity ] - ) -} - -core:Publication CLOSED { - ( $core:Publication_tes ( core:id @linkml:String ? ; - core:title @linkml:String ? ; - core:abstract @linkml:String ? ; - core:combined_text @linkml:String ? ; - core:full_text @linkml:String ? - ) ; - rdf:type [ core:Publication ] ? - ) -} - -core:RelationshipType CLOSED { - ( $core:RelationshipType_tes ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ core:RelationshipType ] - ) -} - -<Symptom> CLOSED { - ( $<Symptom_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Symptom> ] - ) -} - -core:TextWithTriples CLOSED { - ( $core:TextWithTriples_tes ( core:publication @core:Publication ? ; - core:triples @core:Triple * - ) ; - rdf:type [ core:TextWithTriples ] ? - ) -} - -<Treatment> CLOSED { - ( $<Treatment_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Treatment> ] - ) -} - -<TreatmentAdverseEffect> CLOSED { - ( $<TreatmentAdverseEffect_tes> ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - <treatment> @<Treatment> ? ; - <adverse_effects> @<AdverseEffect> * - ) ; - rdf:type [ <TreatmentAdverseEffect> ] ? - ) -} - -<TreatmentEfficacy> CLOSED { - ( $<TreatmentEfficacy_tes> ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - <treatment> @<Treatment> ? ; - <efficacy> @linkml:String ? - ) ; - rdf:type [ <TreatmentEfficacy> ] ? - ) -} - -<TreatmentMechanism> CLOSED { - ( $<TreatmentMechanism_tes> ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - <treatment> @<Treatment> ? ; - <mechanism> @<Mechanism> ? - ) ; - rdf:type [ <TreatmentMechanism> ] ? - ) -} - -core:Triple { - ( $core:Triple_tes ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - core:subject @core:NamedEntity ? ; - core:predicate @core:RelationshipType ? ; - core:object @core:NamedEntity ? ; - core:qualifier @linkml:String ? ; - core:subject_qualifier @core:NamedEntity ? ; - core:object_qualifier @core:NamedEntity ? - ) ; - rdf:type [ core:Triple ] ? - ) -} - - diff --git a/projects/treatment/sqlschema/treatment.sql b/projects/treatment/sqlschema/treatment.sql deleted file mode 100644 index ab4c20588..000000000 --- a/projects/treatment/sqlschema/treatment.sql +++ /dev/null @@ -1,116 +0,0 @@ - - -CREATE TABLE "AdverseEffect" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "AnnotatorResult" ( - subject_text TEXT, - object_id TEXT, - object_text TEXT, - PRIMARY KEY (subject_text, object_id, object_text) -); - -CREATE TABLE "Disease" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Drug" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "ExtractionResult" ( - input_id TEXT, - input_title TEXT, - input_text TEXT, - raw_completion_output TEXT, - prompt TEXT, - extracted_object TEXT, - named_entities TEXT, - PRIMARY KEY (input_id, input_title, input_text, raw_completion_output, prompt, extracted_object, named_entities) -); - -CREATE TABLE "Gene" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Mechanism" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Publication" ( - id TEXT, - title TEXT, - abstract TEXT, - combined_text TEXT, - full_text TEXT, - PRIMARY KEY (id, title, abstract, combined_text, full_text) -); - -CREATE TABLE "RelationshipType" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Symptom" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "TextWithTriples" ( - publication TEXT, - triples TEXT, - PRIMARY KEY (publication, triples) -); - -CREATE TABLE "Treatment" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "DiseaseTreatmentSummary" ( - disease TEXT, - drugs TEXT, - treatments TEXT, - contraindications TEXT, - treatment_mechanisms TEXT, - treatment_efficacies TEXT, - treatment_adverse_effects TEXT, - PRIMARY KEY (disease, drugs, treatments, contraindications, treatment_mechanisms, treatment_efficacies, treatment_adverse_effects), - FOREIGN KEY(disease) REFERENCES "Disease" (id) -); - -CREATE TABLE "TreatmentAdverseEffect" ( - treatment TEXT, - adverse_effects TEXT, - PRIMARY KEY (treatment, adverse_effects), - FOREIGN KEY(treatment) REFERENCES "Treatment" (id) -); - -CREATE TABLE "TreatmentEfficacy" ( - treatment TEXT, - efficacy TEXT, - PRIMARY KEY (treatment, efficacy), - FOREIGN KEY(treatment) REFERENCES "Treatment" (id) -); - -CREATE TABLE "TreatmentMechanism" ( - treatment TEXT, - mechanism TEXT, - PRIMARY KEY (treatment, mechanism), - FOREIGN KEY(treatment) REFERENCES "Treatment" (id), - FOREIGN KEY(mechanism) REFERENCES "Mechanism" (id) -); diff --git a/projects/treatment/treatment.py b/projects/treatment/treatment.py deleted file mode 100644 index 03f70ef31..000000000 --- a/projects/treatment/treatment.py +++ /dev/null @@ -1,722 +0,0 @@ -# Auto generated from treatment.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-08-07T10:56:46 -# Schema: treatment-template -# -# id: http://w3id.org/ontogpt/treatment -# description: A template for MAXO treatments -# license: https://creativecommons.org/publicdomain/zero/1.0/ - -import dataclasses -import sys -import re -from jsonasobj2 import JsonObj, as_dict -from typing import Optional, List, Union, Dict, ClassVar, Any -from dataclasses import dataclass -from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions - -from linkml_runtime.utils.slot import Slot -from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode -from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int -from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs -from linkml_runtime.utils.formatutils import camelcase, underscore, sfx -from linkml_runtime.utils.enumerations import EnumDefinitionImpl -from rdflib import Namespace, URIRef -from linkml_runtime.utils.curienamespace import CurieNamespace -from linkml_runtime.linkml_model.types import String - -metamodel_version = "1.7.0" -version = None - -# Overwrite dataclasses _init_fn to add **kwargs in __init__ -dataclasses._init_fn = dataclasses_init_fn_with_kwargs - -# Namespaces -HGNC = CurieNamespace('HGNC', 'http://example.org/UNKNOWN/HGNC/') -HP = CurieNamespace('HP', 'http://example.org/UNKNOWN/HP/') -RO = CurieNamespace('RO', 'http://purl.obolibrary.org/obo/RO_') -BIOLINK = CurieNamespace('biolink', 'http://example.org/UNKNOWN/biolink/') -CORE = CurieNamespace('core', 'http://w3id.org/ontogpt/core/') -LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') -RDFS = CurieNamespace('rdfs', 'http://example.org/UNKNOWN/rdfs/') -TREATMENT = CurieNamespace('treatment', 'http://w3id.org/ontogpt/treatments/') -DEFAULT_ = TREATMENT - - -# Types - -# Class references -class NamedEntityId(extended_str): - pass - - -class GeneId(NamedEntityId): - pass - - -class SymptomId(NamedEntityId): - pass - - -class DiseaseId(NamedEntityId): - pass - - -class AdverseEffectId(NamedEntityId): - pass - - -class TreatmentId(NamedEntityId): - pass - - -class MechanismId(NamedEntityId): - pass - - -class DrugId(NamedEntityId): - pass - - -class RelationshipTypeId(NamedEntityId): - pass - - -@dataclass -class DiseaseTreatmentSummary(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = TREATMENT.DiseaseTreatmentSummary - class_class_curie: ClassVar[str] = "treatment:DiseaseTreatmentSummary" - class_name: ClassVar[str] = "DiseaseTreatmentSummary" - class_model_uri: ClassVar[URIRef] = TREATMENT.DiseaseTreatmentSummary - - disease: Optional[Union[str, DiseaseId]] = None - drugs: Optional[Union[Union[str, DrugId], List[Union[str, DrugId]]]] = empty_list() - treatments: Optional[Union[Union[str, TreatmentId], List[Union[str, TreatmentId]]]] = empty_list() - contraindications: Optional[Union[Union[str, TreatmentId], List[Union[str, TreatmentId]]]] = empty_list() - treatment_mechanisms: Optional[Union[Union[dict, "TreatmentMechanism"], List[Union[dict, "TreatmentMechanism"]]]] = empty_list() - treatment_efficacies: Optional[Union[Union[dict, "TreatmentEfficacy"], List[Union[dict, "TreatmentEfficacy"]]]] = empty_list() - treatment_adverse_effects: Optional[Union[Union[dict, "TreatmentAdverseEffect"], List[Union[dict, "TreatmentAdverseEffect"]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.disease is not None and not isinstance(self.disease, DiseaseId): - self.disease = DiseaseId(self.disease) - - if not isinstance(self.drugs, list): - self.drugs = [self.drugs] if self.drugs is not None else [] - self.drugs = [v if isinstance(v, DrugId) else DrugId(v) for v in self.drugs] - - if not isinstance(self.treatments, list): - self.treatments = [self.treatments] if self.treatments is not None else [] - self.treatments = [v if isinstance(v, TreatmentId) else TreatmentId(v) for v in self.treatments] - - if not isinstance(self.contraindications, list): - self.contraindications = [self.contraindications] if self.contraindications is not None else [] - self.contraindications = [v if isinstance(v, TreatmentId) else TreatmentId(v) for v in self.contraindications] - - if not isinstance(self.treatment_mechanisms, list): - self.treatment_mechanisms = [self.treatment_mechanisms] if self.treatment_mechanisms is not None else [] - self.treatment_mechanisms = [v if isinstance(v, TreatmentMechanism) else TreatmentMechanism(**as_dict(v)) for v in self.treatment_mechanisms] - - if not isinstance(self.treatment_efficacies, list): - self.treatment_efficacies = [self.treatment_efficacies] if self.treatment_efficacies is not None else [] - self.treatment_efficacies = [v if isinstance(v, TreatmentEfficacy) else TreatmentEfficacy(**as_dict(v)) for v in self.treatment_efficacies] - - if not isinstance(self.treatment_adverse_effects, list): - self.treatment_adverse_effects = [self.treatment_adverse_effects] if self.treatment_adverse_effects is not None else [] - self.treatment_adverse_effects = [v if isinstance(v, TreatmentAdverseEffect) else TreatmentAdverseEffect(**as_dict(v)) for v in self.treatment_adverse_effects] - - super().__post_init__(**kwargs) - - -Any = Any - -@dataclass -class ExtractionResult(YAMLRoot): - """ - A result of extracting knowledge on text - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.ExtractionResult - class_class_curie: ClassVar[str] = "core:ExtractionResult" - class_name: ClassVar[str] = "ExtractionResult" - class_model_uri: ClassVar[URIRef] = TREATMENT.ExtractionResult - - input_id: Optional[str] = None - input_title: Optional[str] = None - input_text: Optional[str] = None - raw_completion_output: Optional[str] = None - prompt: Optional[str] = None - extracted_object: Optional[Union[dict, Any]] = None - named_entities: Optional[Union[Union[dict, Any], List[Union[dict, Any]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.input_id is not None and not isinstance(self.input_id, str): - self.input_id = str(self.input_id) - - if self.input_title is not None and not isinstance(self.input_title, str): - self.input_title = str(self.input_title) - - if self.input_text is not None and not isinstance(self.input_text, str): - self.input_text = str(self.input_text) - - if self.raw_completion_output is not None and not isinstance(self.raw_completion_output, str): - self.raw_completion_output = str(self.raw_completion_output) - - if self.prompt is not None and not isinstance(self.prompt, str): - self.prompt = str(self.prompt) - - super().__post_init__(**kwargs) - - -@dataclass -class NamedEntity(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.NamedEntity - class_class_curie: ClassVar[str] = "core:NamedEntity" - class_name: ClassVar[str] = "NamedEntity" - class_model_uri: ClassVar[URIRef] = TREATMENT.NamedEntity - - id: Union[str, NamedEntityId] = None - label: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, NamedEntityId): - self.id = NamedEntityId(self.id) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - super().__post_init__(**kwargs) - - -@dataclass -class Gene(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = TREATMENT.Gene - class_class_curie: ClassVar[str] = "treatment:Gene" - class_name: ClassVar[str] = "Gene" - class_model_uri: ClassVar[URIRef] = TREATMENT.Gene - - id: Union[str, GeneId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, GeneId): - self.id = GeneId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Symptom(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = TREATMENT.Symptom - class_class_curie: ClassVar[str] = "treatment:Symptom" - class_name: ClassVar[str] = "Symptom" - class_model_uri: ClassVar[URIRef] = TREATMENT.Symptom - - id: Union[str, SymptomId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, SymptomId): - self.id = SymptomId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Disease(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = TREATMENT.Disease - class_class_curie: ClassVar[str] = "treatment:Disease" - class_name: ClassVar[str] = "Disease" - class_model_uri: ClassVar[URIRef] = TREATMENT.Disease - - id: Union[str, DiseaseId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, DiseaseId): - self.id = DiseaseId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class AdverseEffect(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = TREATMENT.AdverseEffect - class_class_curie: ClassVar[str] = "treatment:AdverseEffect" - class_name: ClassVar[str] = "AdverseEffect" - class_model_uri: ClassVar[URIRef] = TREATMENT.AdverseEffect - - id: Union[str, AdverseEffectId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, AdverseEffectId): - self.id = AdverseEffectId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Treatment(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = TREATMENT.Treatment - class_class_curie: ClassVar[str] = "treatment:Treatment" - class_name: ClassVar[str] = "Treatment" - class_model_uri: ClassVar[URIRef] = TREATMENT.Treatment - - id: Union[str, TreatmentId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, TreatmentId): - self.id = TreatmentId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Mechanism(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = TREATMENT.Mechanism - class_class_curie: ClassVar[str] = "treatment:Mechanism" - class_name: ClassVar[str] = "Mechanism" - class_model_uri: ClassVar[URIRef] = TREATMENT.Mechanism - - id: Union[str, MechanismId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, MechanismId): - self.id = MechanismId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Drug(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = TREATMENT.Drug - class_class_curie: ClassVar[str] = "treatment:Drug" - class_name: ClassVar[str] = "Drug" - class_model_uri: ClassVar[URIRef] = TREATMENT.Drug - - id: Union[str, DrugId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, DrugId): - self.id = DrugId(self.id) - - super().__post_init__(**kwargs) - - -class CompoundExpression(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.CompoundExpression - class_class_curie: ClassVar[str] = "core:CompoundExpression" - class_name: ClassVar[str] = "CompoundExpression" - class_model_uri: ClassVar[URIRef] = TREATMENT.CompoundExpression - - -@dataclass -class TreatmentMechanism(CompoundExpression): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = TREATMENT.TreatmentMechanism - class_class_curie: ClassVar[str] = "treatment:TreatmentMechanism" - class_name: ClassVar[str] = "TreatmentMechanism" - class_model_uri: ClassVar[URIRef] = TREATMENT.TreatmentMechanism - - treatment: Optional[Union[str, TreatmentId]] = None - mechanism: Optional[Union[str, MechanismId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.treatment is not None and not isinstance(self.treatment, TreatmentId): - self.treatment = TreatmentId(self.treatment) - - if self.mechanism is not None and not isinstance(self.mechanism, MechanismId): - self.mechanism = MechanismId(self.mechanism) - - super().__post_init__(**kwargs) - - -@dataclass -class TreatmentAdverseEffect(CompoundExpression): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = TREATMENT.TreatmentAdverseEffect - class_class_curie: ClassVar[str] = "treatment:TreatmentAdverseEffect" - class_name: ClassVar[str] = "TreatmentAdverseEffect" - class_model_uri: ClassVar[URIRef] = TREATMENT.TreatmentAdverseEffect - - treatment: Optional[Union[str, TreatmentId]] = None - adverse_effects: Optional[Union[Union[str, AdverseEffectId], List[Union[str, AdverseEffectId]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.treatment is not None and not isinstance(self.treatment, TreatmentId): - self.treatment = TreatmentId(self.treatment) - - if not isinstance(self.adverse_effects, list): - self.adverse_effects = [self.adverse_effects] if self.adverse_effects is not None else [] - self.adverse_effects = [v if isinstance(v, AdverseEffectId) else AdverseEffectId(v) for v in self.adverse_effects] - - super().__post_init__(**kwargs) - - -@dataclass -class TreatmentEfficacy(CompoundExpression): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = TREATMENT.TreatmentEfficacy - class_class_curie: ClassVar[str] = "treatment:TreatmentEfficacy" - class_name: ClassVar[str] = "TreatmentEfficacy" - class_model_uri: ClassVar[URIRef] = TREATMENT.TreatmentEfficacy - - treatment: Optional[Union[str, TreatmentId]] = None - efficacy: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.treatment is not None and not isinstance(self.treatment, TreatmentId): - self.treatment = TreatmentId(self.treatment) - - if self.efficacy is not None and not isinstance(self.efficacy, str): - self.efficacy = str(self.efficacy) - - super().__post_init__(**kwargs) - - -@dataclass -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Triple - class_class_curie: ClassVar[str] = "core:Triple" - class_name: ClassVar[str] = "Triple" - class_model_uri: ClassVar[URIRef] = TREATMENT.Triple - - subject: Optional[Union[str, NamedEntityId]] = None - predicate: Optional[Union[str, RelationshipTypeId]] = None - object: Optional[Union[str, NamedEntityId]] = None - qualifier: Optional[str] = None - subject_qualifier: Optional[Union[str, NamedEntityId]] = None - object_qualifier: Optional[Union[str, NamedEntityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, NamedEntityId): - self.subject = NamedEntityId(self.subject) - - if self.predicate is not None and not isinstance(self.predicate, RelationshipTypeId): - self.predicate = RelationshipTypeId(self.predicate) - - if self.object is not None and not isinstance(self.object, NamedEntityId): - self.object = NamedEntityId(self.object) - - if self.qualifier is not None and not isinstance(self.qualifier, str): - self.qualifier = str(self.qualifier) - - if self.subject_qualifier is not None and not isinstance(self.subject_qualifier, NamedEntityId): - self.subject_qualifier = NamedEntityId(self.subject_qualifier) - - if self.object_qualifier is not None and not isinstance(self.object_qualifier, NamedEntityId): - self.object_qualifier = NamedEntityId(self.object_qualifier) - - super().__post_init__(**kwargs) - - -@dataclass -class TextWithTriples(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.TextWithTriples - class_class_curie: ClassVar[str] = "core:TextWithTriples" - class_name: ClassVar[str] = "TextWithTriples" - class_model_uri: ClassVar[URIRef] = TREATMENT.TextWithTriples - - publication: Optional[Union[dict, "Publication"]] = None - triples: Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.publication is not None and not isinstance(self.publication, Publication): - self.publication = Publication(**as_dict(self.publication)) - - if not isinstance(self.triples, list): - self.triples = [self.triples] if self.triples is not None else [] - self.triples = [v if isinstance(v, Triple) else Triple(**as_dict(v)) for v in self.triples] - - super().__post_init__(**kwargs) - - -@dataclass -class RelationshipType(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.RelationshipType - class_class_curie: ClassVar[str] = "core:RelationshipType" - class_name: ClassVar[str] = "RelationshipType" - class_model_uri: ClassVar[URIRef] = TREATMENT.RelationshipType - - id: Union[str, RelationshipTypeId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, RelationshipTypeId): - self.id = RelationshipTypeId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Publication(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Publication - class_class_curie: ClassVar[str] = "core:Publication" - class_name: ClassVar[str] = "Publication" - class_model_uri: ClassVar[URIRef] = TREATMENT.Publication - - id: Optional[str] = None - title: Optional[str] = None - abstract: Optional[str] = None - combined_text: Optional[str] = None - full_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.id is not None and not isinstance(self.id, str): - self.id = str(self.id) - - if self.title is not None and not isinstance(self.title, str): - self.title = str(self.title) - - if self.abstract is not None and not isinstance(self.abstract, str): - self.abstract = str(self.abstract) - - if self.combined_text is not None and not isinstance(self.combined_text, str): - self.combined_text = str(self.combined_text) - - if self.full_text is not None and not isinstance(self.full_text, str): - self.full_text = str(self.full_text) - - super().__post_init__(**kwargs) - - -@dataclass -class AnnotatorResult(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.AnnotatorResult - class_class_curie: ClassVar[str] = "core:AnnotatorResult" - class_name: ClassVar[str] = "AnnotatorResult" - class_model_uri: ClassVar[URIRef] = TREATMENT.AnnotatorResult - - subject_text: Optional[str] = None - object_id: Optional[str] = None - object_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject_text is not None and not isinstance(self.subject_text, str): - self.subject_text = str(self.subject_text) - - if self.object_id is not None and not isinstance(self.object_id, str): - self.object_id = str(self.object_id) - - if self.object_text is not None and not isinstance(self.object_text, str): - self.object_text = str(self.object_text) - - super().__post_init__(**kwargs) - - -# Enumerations -class NCITDrugType(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="NCITDrugType", - ) - -class NCITTreatmentType(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="NCITTreatmentType", - ) - -class NCITTActivityType(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="NCITTActivityType", - ) - -class MAXOActionType(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="MAXOActionType", - ) - -class MESHTherapeuticType(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="MESHTherapeuticType", - ) - -class CHEBIDrugType(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="CHEBIDrugType", - ) - -class NullDataOptions(EnumDefinitionImpl): - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = PermissibleValue(text="UNSPECIFIED_METHOD_OF_ADMINISTRATION", - meaning=NCIT.C149701) - NOT_APPLICABLE = PermissibleValue(text="NOT_APPLICABLE", - meaning=NCIT.C18902) - NOT_MENTIONED = PermissibleValue(text="NOT_MENTIONED") - - _defn = EnumDefinition( - name="NullDataOptions", - ) - -# Slots -class slots: - pass - -slots.diseaseTreatmentSummary__disease = Slot(uri=TREATMENT.disease, name="diseaseTreatmentSummary__disease", curie=TREATMENT.curie('disease'), - model_uri=TREATMENT.diseaseTreatmentSummary__disease, domain=None, range=Optional[Union[str, DiseaseId]]) - -slots.diseaseTreatmentSummary__drugs = Slot(uri=TREATMENT.drugs, name="diseaseTreatmentSummary__drugs", curie=TREATMENT.curie('drugs'), - model_uri=TREATMENT.diseaseTreatmentSummary__drugs, domain=None, range=Optional[Union[Union[str, DrugId], List[Union[str, DrugId]]]]) - -slots.diseaseTreatmentSummary__treatments = Slot(uri=TREATMENT.treatments, name="diseaseTreatmentSummary__treatments", curie=TREATMENT.curie('treatments'), - model_uri=TREATMENT.diseaseTreatmentSummary__treatments, domain=None, range=Optional[Union[Union[str, TreatmentId], List[Union[str, TreatmentId]]]]) - -slots.diseaseTreatmentSummary__contraindications = Slot(uri=TREATMENT.contraindications, name="diseaseTreatmentSummary__contraindications", curie=TREATMENT.curie('contraindications'), - model_uri=TREATMENT.diseaseTreatmentSummary__contraindications, domain=None, range=Optional[Union[Union[str, TreatmentId], List[Union[str, TreatmentId]]]]) - -slots.diseaseTreatmentSummary__treatment_mechanisms = Slot(uri=TREATMENT.treatment_mechanisms, name="diseaseTreatmentSummary__treatment_mechanisms", curie=TREATMENT.curie('treatment_mechanisms'), - model_uri=TREATMENT.diseaseTreatmentSummary__treatment_mechanisms, domain=None, range=Optional[Union[Union[dict, TreatmentMechanism], List[Union[dict, TreatmentMechanism]]]]) - -slots.diseaseTreatmentSummary__treatment_efficacies = Slot(uri=TREATMENT.treatment_efficacies, name="diseaseTreatmentSummary__treatment_efficacies", curie=TREATMENT.curie('treatment_efficacies'), - model_uri=TREATMENT.diseaseTreatmentSummary__treatment_efficacies, domain=None, range=Optional[Union[Union[dict, TreatmentEfficacy], List[Union[dict, TreatmentEfficacy]]]]) - -slots.diseaseTreatmentSummary__treatment_adverse_effects = Slot(uri=TREATMENT.treatment_adverse_effects, name="diseaseTreatmentSummary__treatment_adverse_effects", curie=TREATMENT.curie('treatment_adverse_effects'), - model_uri=TREATMENT.diseaseTreatmentSummary__treatment_adverse_effects, domain=None, range=Optional[Union[Union[dict, TreatmentAdverseEffect], List[Union[dict, TreatmentAdverseEffect]]]]) - -slots.treatmentMechanism__treatment = Slot(uri=TREATMENT.treatment, name="treatmentMechanism__treatment", curie=TREATMENT.curie('treatment'), - model_uri=TREATMENT.treatmentMechanism__treatment, domain=None, range=Optional[Union[str, TreatmentId]]) - -slots.treatmentMechanism__mechanism = Slot(uri=TREATMENT.mechanism, name="treatmentMechanism__mechanism", curie=TREATMENT.curie('mechanism'), - model_uri=TREATMENT.treatmentMechanism__mechanism, domain=None, range=Optional[Union[str, MechanismId]]) - -slots.treatmentAdverseEffect__treatment = Slot(uri=TREATMENT.treatment, name="treatmentAdverseEffect__treatment", curie=TREATMENT.curie('treatment'), - model_uri=TREATMENT.treatmentAdverseEffect__treatment, domain=None, range=Optional[Union[str, TreatmentId]]) - -slots.treatmentAdverseEffect__adverse_effects = Slot(uri=TREATMENT.adverse_effects, name="treatmentAdverseEffect__adverse_effects", curie=TREATMENT.curie('adverse_effects'), - model_uri=TREATMENT.treatmentAdverseEffect__adverse_effects, domain=None, range=Optional[Union[Union[str, AdverseEffectId], List[Union[str, AdverseEffectId]]]]) - -slots.treatmentEfficacy__treatment = Slot(uri=TREATMENT.treatment, name="treatmentEfficacy__treatment", curie=TREATMENT.curie('treatment'), - model_uri=TREATMENT.treatmentEfficacy__treatment, domain=None, range=Optional[Union[str, TreatmentId]]) - -slots.treatmentEfficacy__efficacy = Slot(uri=TREATMENT.efficacy, name="treatmentEfficacy__efficacy", curie=TREATMENT.curie('efficacy'), - model_uri=TREATMENT.treatmentEfficacy__efficacy, domain=None, range=Optional[str]) - -slots.extractionResult__input_id = Slot(uri=CORE.input_id, name="extractionResult__input_id", curie=CORE.curie('input_id'), - model_uri=TREATMENT.extractionResult__input_id, domain=None, range=Optional[str]) - -slots.extractionResult__input_title = Slot(uri=CORE.input_title, name="extractionResult__input_title", curie=CORE.curie('input_title'), - model_uri=TREATMENT.extractionResult__input_title, domain=None, range=Optional[str]) - -slots.extractionResult__input_text = Slot(uri=CORE.input_text, name="extractionResult__input_text", curie=CORE.curie('input_text'), - model_uri=TREATMENT.extractionResult__input_text, domain=None, range=Optional[str]) - -slots.extractionResult__raw_completion_output = Slot(uri=CORE.raw_completion_output, name="extractionResult__raw_completion_output", curie=CORE.curie('raw_completion_output'), - model_uri=TREATMENT.extractionResult__raw_completion_output, domain=None, range=Optional[str]) - -slots.extractionResult__prompt = Slot(uri=CORE.prompt, name="extractionResult__prompt", curie=CORE.curie('prompt'), - model_uri=TREATMENT.extractionResult__prompt, domain=None, range=Optional[str]) - -slots.extractionResult__extracted_object = Slot(uri=CORE.extracted_object, name="extractionResult__extracted_object", curie=CORE.curie('extracted_object'), - model_uri=TREATMENT.extractionResult__extracted_object, domain=None, range=Optional[Union[dict, Any]]) - -slots.extractionResult__named_entities = Slot(uri=CORE.named_entities, name="extractionResult__named_entities", curie=CORE.curie('named_entities'), - model_uri=TREATMENT.extractionResult__named_entities, domain=None, range=Optional[Union[Union[dict, Any], List[Union[dict, Any]]]]) - -slots.namedEntity__id = Slot(uri=CORE.id, name="namedEntity__id", curie=CORE.curie('id'), - model_uri=TREATMENT.namedEntity__id, domain=None, range=URIRef) - -slots.namedEntity__label = Slot(uri=RDFS.label, name="namedEntity__label", curie=RDFS.curie('label'), - model_uri=TREATMENT.namedEntity__label, domain=None, range=Optional[str]) - -slots.triple__subject = Slot(uri=CORE.subject, name="triple__subject", curie=CORE.curie('subject'), - model_uri=TREATMENT.triple__subject, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__predicate = Slot(uri=CORE.predicate, name="triple__predicate", curie=CORE.curie('predicate'), - model_uri=TREATMENT.triple__predicate, domain=None, range=Optional[Union[str, RelationshipTypeId]]) - -slots.triple__object = Slot(uri=CORE.object, name="triple__object", curie=CORE.curie('object'), - model_uri=TREATMENT.triple__object, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__qualifier = Slot(uri=CORE.qualifier, name="triple__qualifier", curie=CORE.curie('qualifier'), - model_uri=TREATMENT.triple__qualifier, domain=None, range=Optional[str]) - -slots.triple__subject_qualifier = Slot(uri=CORE.subject_qualifier, name="triple__subject_qualifier", curie=CORE.curie('subject_qualifier'), - model_uri=TREATMENT.triple__subject_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__object_qualifier = Slot(uri=CORE.object_qualifier, name="triple__object_qualifier", curie=CORE.curie('object_qualifier'), - model_uri=TREATMENT.triple__object_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.textWithTriples__publication = Slot(uri=CORE.publication, name="textWithTriples__publication", curie=CORE.curie('publication'), - model_uri=TREATMENT.textWithTriples__publication, domain=None, range=Optional[Union[dict, Publication]]) - -slots.textWithTriples__triples = Slot(uri=CORE.triples, name="textWithTriples__triples", curie=CORE.curie('triples'), - model_uri=TREATMENT.textWithTriples__triples, domain=None, range=Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]]) - -slots.publication__id = Slot(uri=CORE.id, name="publication__id", curie=CORE.curie('id'), - model_uri=TREATMENT.publication__id, domain=None, range=Optional[str]) - -slots.publication__title = Slot(uri=CORE.title, name="publication__title", curie=CORE.curie('title'), - model_uri=TREATMENT.publication__title, domain=None, range=Optional[str]) - -slots.publication__abstract = Slot(uri=CORE.abstract, name="publication__abstract", curie=CORE.curie('abstract'), - model_uri=TREATMENT.publication__abstract, domain=None, range=Optional[str]) - -slots.publication__combined_text = Slot(uri=CORE.combined_text, name="publication__combined_text", curie=CORE.curie('combined_text'), - model_uri=TREATMENT.publication__combined_text, domain=None, range=Optional[str]) - -slots.publication__full_text = Slot(uri=CORE.full_text, name="publication__full_text", curie=CORE.curie('full_text'), - model_uri=TREATMENT.publication__full_text, domain=None, range=Optional[str]) - -slots.annotatorResult__subject_text = Slot(uri=CORE.subject_text, name="annotatorResult__subject_text", curie=CORE.curie('subject_text'), - model_uri=TREATMENT.annotatorResult__subject_text, domain=None, range=Optional[str]) - -slots.annotatorResult__object_id = Slot(uri=CORE.object_id, name="annotatorResult__object_id", curie=CORE.curie('object_id'), - model_uri=TREATMENT.annotatorResult__object_id, domain=None, range=Optional[str]) - -slots.annotatorResult__object_text = Slot(uri=CORE.object_text, name="annotatorResult__object_text", curie=CORE.curie('object_text'), - model_uri=TREATMENT.annotatorResult__object_text, domain=None, range=Optional[str]) \ No newline at end of file diff --git a/pyproject.toml b/pyproject.toml index 99180175f..5f2e11e9e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,56 +1,14 @@ [tool.poetry] -name = "ontogpt" -version = "0.3.6" -description = "OntoGPT" -authors = ["Chris Mungall <cjmungall@lbl.gov>"] +name = "talisman" +version = "0.0.1" +description = "TALISMAN" +authors = ["Marcin Joachimiak"] license = "BSD-3" readme = "README.md" [tool.poetry.dependencies] python = ">=3.9,<3.9.7 || >3.9.7,<4.0" -"ruamel.yaml" = ">=0.17.31" -Jinja2 = {version = ">=3.1.2", optional = true} -aiohttp = ">=3.8.4" -airium = ">=0.2.5" -beautifulsoup4 = ">=4.11.1" -bioc = ">=2.0.post5" -cachier = ">=2.1.0" -class-resolver = ">=0.4.2" -click = ">=8.1.3" -eutils = ">=0.6.0" -fastapi = {version = ">=0.88.0", optional = true} -gilda = ">=1.0.0" -gpt4 = ">=0.0.1" -gpt4all = {version = "1.0.8", extras = ["gpt4all"], optional = true} -httpx = ">=0.23.3" -huggingface_hub = {version = ">=0.15.1", extras = ["huggingface"], optional = true} -inflect = ">=6.0.2" -inflection = ">=0.5.1" -jsonlines = ">=3.1.0" -linkml = "^1.5.7" -linkml-owl = "^0.3.0" -llm = ">=0.8" -llm-gpt4all = {version = "^0.1.1", extras = ["gpt4all"], optional = true} -myst-parser = {version = ">=0.18.1", extras = ["docs"], optional = true} -nlpcloud = ">=1.0.39" -oaklib = ">=0.5.15" -openai = ">=0.27.8, <1.0" -pydantic = ">=2.4.0" -pystow = "^0.5.0" -python-multipart = "^0.0.5" -recipe-scrapers = {version = ">=14.35.0", extras = ["recipes"], optional = true} -requests = "^2.31.0" -requests-cache = ">=1.0.1" -sphinx = {version = ">=5.3.0", extras = ["docs"], optional = true} -sphinx-autodoc-typehints = {version = ">=1.19.4", extras = ["docs"], optional = true} -sphinx-click = {version = ">=4.3.0", extras = ["docs"], optional = true} -sphinx-rtd-theme = {version = ">=1.0.0", extras = ["docs"], optional = true} -streamlit = ">=1.22.0" -textract = {version = "*", extras = ["textract"], optional = true} -tiktoken = ">=0.3.3" -uvicorn = {version = ">=0.20.0", optional = true} -wikipedia = ">=1.4.0" -wikipedia-api = ">=0.5.8" +ontogpt = ">=0.3.6" [tool.poetry.dev-dependencies] pytest = ">=7.1.2" @@ -59,8 +17,7 @@ tox = ">=3.25.1" mkdocs-mermaid2-plugin = ">=0.6.0" [tool.poetry.scripts] -ontogpt = "ontogpt.cli:main" -web-ontogpt = "ontogpt.webapp.main:start" +talisman = "talisman.cli:main" [tool.poetry.extras] docs = [ @@ -70,24 +27,6 @@ docs = [ "sphinx-click", "myst-parser" ] -web = [ - "fastapi", - "uvicorn", - "Jinja2" -] -recipes = [ - "recipe-scrapers" -] -gpt4all = [ - "gpt4all", - "llm-gpt4all" -] -textract = [ - "textract" -] -huggingface = [ - "huggingface_hub" -] [tool.poetry.group.dev.dependencies] jupyter = "^1.0.0" diff --git a/src/ontogpt/__init__.py b/src/ontogpt/__init__.py deleted file mode 100644 index 49e2d1cda..000000000 --- a/src/ontogpt/__init__.py +++ /dev/null @@ -1,23 +0,0 @@ -"""ontogpt package.""" -from importlib import metadata -from pathlib import Path - -from yaml import safe_load - -# Load the model list and define the default model -rel_path = Path(__file__).resolve() -models_path = rel_path.parent / "models.yaml" - -with open(models_path, "r") as models_file: - MODELS = (safe_load(models_file))["models"] -for model in MODELS: - if "is_default" in model: - DEFAULT_MODEL_DETAILS = model - DEFAULT_MODEL = model["alternative_names"][0] - break - -try: - __version__ = metadata.version(__name__) -except metadata.PackageNotFoundError: - # package is not installed - __version__ = "0.0.0" # pragma: no cover diff --git a/src/ontogpt/cli.py b/src/ontogpt/cli.py deleted file mode 100644 index c36775890..000000000 --- a/src/ontogpt/cli.py +++ /dev/null @@ -1,1749 +0,0 @@ -"""Command line interface for ontogpt.""" -import codecs -import json -import logging -import pickle -import sys -from copy import copy, deepcopy -from dataclasses import dataclass -from io import BytesIO, TextIOWrapper -from pathlib import Path -from typing import List, Optional, Union - -import click -import jsonlines -import openai -import yaml -from oaklib import get_adapter -from oaklib.cli import query_terms_iterator -from oaklib.interfaces import OboGraphInterface -from oaklib.io.streaming_csv_writer import StreamingCsvWriter -from sssom.parsers import parse_sssom_table, to_mapping_set_document -from sssom.util import to_mapping_set_dataframe - -import ontogpt.ontex.extractor as extractor -from ontogpt import DEFAULT_MODEL, DEFAULT_MODEL_DETAILS, MODELS, __version__ -from ontogpt.clients import OpenAIClient -from ontogpt.clients.pubmed_client import PubmedClient -from ontogpt.clients.soup_client import SoupClient -from ontogpt.clients.wikipedia_client import WikipediaClient -from ontogpt.engines import create_engine -from ontogpt.engines.embedding_similarity_engine import SimilarityEngine -from ontogpt.engines.enrichment import EnrichmentEngine -from ontogpt.engines.generic_engine import GenericEngine, QuestionCollection -from ontogpt.engines.gpt4all_engine import GPT4AllEngine # type: ignore -from ontogpt.engines.halo_engine import HALOEngine # type: ignore - -# from ontogpt.engines.hfhub_engine import HFHubEngine -from ontogpt.engines.knowledge_engine import KnowledgeEngine -from ontogpt.engines.mapping_engine import MappingEngine -from ontogpt.engines.pheno_engine import PhenoEngine -from ontogpt.engines.reasoner_engine import ReasonerEngine -from ontogpt.engines.spires_engine import SPIRESEngine -from ontogpt.engines.synonym_engine import SynonymEngine -from ontogpt.evaluation.enrichment.eval_enrichment import EvalEnrichment -from ontogpt.evaluation.resolver import create_evaluator -from ontogpt.io.csv_wrapper import output_parser, write_obj_as_csv -from ontogpt.io.html_exporter import HTMLExporter -from ontogpt.io.markdown_exporter import MarkdownExporter -from ontogpt.utils.gene_set_utils import ( - GeneSet, - _is_human, - fill_missing_gene_set_values, - parse_gene_set, -) -from ontogpt.utils.gpt4all_runner import chain_gpt4all_model, set_up_gpt4all_model - -__all__ = [ - "main", -] - -from ontogpt.io.owl_exporter import OWLExporter -from ontogpt.io.rdf_exporter import RDFExporter -from ontogpt.io.yaml_wrapper import dump_minimal_yaml -from ontogpt.templates.core import ExtractionResult - - -@dataclass -class Settings: - """Global command line settings.""" - - cache_db: Optional[str] = None - skip_annotators: Optional[List[str]] = None - - -settings = Settings() - - -def _as_text_writer(f): - if isinstance(f, TextIOWrapper): - return f - else: - return codecs.getwriter("utf-8")(f) - - -def write_extraction( - results: ExtractionResult, - output: BytesIO, - output_format: str, - knowledge_engine: KnowledgeEngine, -): - """Write results of extraction to a given output stream.""" - # Check if this result contains anything writable first - if results.extracted_object: - exporter: Union[MarkdownExporter, HTMLExporter, RDFExporter, OWLExporter] - - if output_format not in ["pickle"]: - output = _as_text_writer(output) - - if output_format == "pickle": - output.write(pickle.dumps(results)) - elif output_format == "md": - exporter = MarkdownExporter() - exporter.export(results, output) - elif output_format == "html": - exporter = HTMLExporter(output=output) - exporter.export(results, output) - elif output_format == "yaml": - output.write("---\n") # type: ignore - output.write(dump_minimal_yaml(results)) # type: ignore - elif output_format == "turtle": - exporter = RDFExporter() - exporter.export(results, output, knowledge_engine.schemaview) - elif output_format == "owl": - exporter = OWLExporter() - exporter.export(results, output, knowledge_engine.schemaview) - elif output_format == "kgx": - # output.write(write_obj_as_csv(results)) - output.write(dump_minimal_yaml(results)) # type: ignore - with open("output.kgx.tsv") as secondoutput: - for line in output_parser(obj=results, file=output): - secondoutput.write(line) - else: - output.write("---\n") # type: ignore - output.write(dump_minimal_yaml(results)) # type: ignore - - -def get_model_by_name(modelname: str): - """Retrieve a model name and metadata from those available. - - Returns a dict describing the selected model. - """ - found = False - for knownmodel in MODELS: - if modelname in knownmodel["alternative_names"] or modelname == knownmodel["name"]: - selectmodel = knownmodel - found = True - logging.info( - f"Found model: {selectmodel['name']}, provided by {selectmodel['provider']}." - ) - if "not_implemented" in selectmodel or "deprecated" in selectmodel: - logging.error(f"Model {selectmodel['name']} not implemented or is deprecated.") - raise NotImplementedError - break - if not found: - logging.warning( - f"""Model name not recognized or not supported yet. Using default, {DEFAULT_MODEL}. - See all models with `ontogpt list-models`""" - ) - selectmodel = DEFAULT_MODEL_DETAILS - - return selectmodel - - -inputfile_option = click.option("-i", "--inputfile", help="Path to a file containing input text.") -template_option = click.option("-t", "--template", required=True, help="Template to use.") -target_class_option = click.option( - "-T", "--target-class", help="Target class (if not already root)." -) -interactive_option = click.option( - "--interactive/--no-interactive", - default=False, - show_default=True, - help="Interactive mode - rather than call the LLM API it will prompt you do this.", -) -model_option = click.option( - "-m", - "--model", - help="Model name to use, e.g. orca-mini-7b or gpt-4." - " See all model names with ontogpt list-models.", -) -prompt_template_option = click.option( - "--prompt-template", help="Path to a file containing the prompt." -) -recurse_option = click.option( - "--recurse/--no-recurse", default=True, show_default=True, help="Recursively parse structures." -) -use_textract_options = click.option( - "--use-textract/--no-use-textract", - default=False, - show_default=True, - help="Use textract to extract text.", -) -output_option_wb = click.option( - "-o", "--output", type=click.File(mode="wb"), default=sys.stdout, help="Output file." -) -output_option_txt = click.option( - "-o", "--output", type=click.File(mode="w"), default=sys.stdout, help="Output file." -) -output_format_options = click.option( - "-O", - "--output-format", - type=click.Choice(["json", "yaml", "pickle", "md", "html", "owl", "turtle", "jsonl"]), - default="yaml", - help="Output format.", -) -auto_prefix_option = click.option( - "--auto-prefix", - default="AUTO", - help="Prefix to use for auto-generated classes. Default is AUTO.", -) -show_prompt_option = click.option( - "--show-prompt/--no-show-prompt", - default=False, - show_default=True, - help="If set, show all prompts passed to model through an API. Use with verbose setting.", -) - - -@click.group() -@click.option("-v", "--verbose", count=True) -@click.option("-q", "--quiet") -@click.option("--cache-db", help="Path to sqlite database to cache prompt-completion results") -@click.option( - "--skip-annotator", - multiple=True, - help="Skip one or more annotators (e.g. --skip-annotator gilda)", -) -@click.version_option(__version__) -def main(verbose: int, quiet: bool, cache_db: str, skip_annotator): - """CLI for ontogpt. - - :param verbose: Verbosity while running. - :param quiet: Boolean to be quiet or verbose. - """ - logger = logging.getLogger() - if verbose >= 2: - logger.setLevel(level=logging.DEBUG) - elif verbose == 1: - logger.setLevel(level=logging.INFO) - else: - logger.setLevel(level=logging.WARNING) - if quiet: - logger.setLevel(level=logging.ERROR) - logger.info(f"Logger {logger.name} set to level {logger.level}") - if cache_db: - settings.cache_db = cache_db - if skip_annotator: - settings.skip_annotators = list(skip_annotator) - - -@main.command() -@inputfile_option -@template_option -@target_class_option -@model_option -@recurse_option -@output_option_wb -@click.option("--dictionary") -@output_format_options -@use_textract_options -@auto_prefix_option -@show_prompt_option -@click.option( - "--set-slot-value", - "-S", - multiple=True, - help="Set slot value, e.g. --set-slot-value has_participant=protein", -) -@click.argument("input", required=False) -def extract( - inputfile, - template, - target_class, - dictionary, - input, - output, - output_format, - set_slot_value, - use_textract, - model, - show_prompt, - **kwargs, -): - """Extract knowledge from text guided by schema, using SPIRES engine. - - Example: - - ontogpt extract -t gocam.GoCamAnnotations -i gocam-27929086.txt - - The input argument may be: - A file path, - A directory, - or a string. - Use the -i/--input-file option followed by the path to the input file - or directory. - If the input is a directory, all files with the .txt extension will be read. - This is not recursive. - Otherwise, the input is assumed to be a string to be read as input. - - You can also use fragments of existing schemas, use the --target-class option (-T) to - specify an alternative Container/root class. - - Example: - - ontogpt extract -t gocam.GoCamAnnotations -T GeneOrganismRelationship "the mouse Shh gene" - - """ - logging.info(f"Creating for {template}") - - # Choose model based on input, or use the default - if not model: - model = DEFAULT_MODEL - selectmodel = get_model_by_name(model) - model_source = selectmodel["provider"] - model_name = selectmodel["alternative_names"][0] - - inputlist = [] - - if not inputfile or inputfile == "-": - text = sys.stdin.read() - inputlist.append(text) - elif inputfile and Path(inputfile).is_dir(): - logging.info(f"Input file directory: {inputfile}") - inputfiles = Path(inputfile).glob("*.txt") - inputlist = [open(f, "r").read() for f in inputfiles if f.is_file()] - logging.info(f"Found {len(inputlist)} input files here.") - elif inputfile and Path(inputfile).exists(): - logging.info(f"Input file: {inputfile}") - if use_textract: - import textract - - text = textract.process(inputfile).decode("utf-8") - else: - text = open(inputfile, "r").read() - logging.info(f"Input text: {text}") - inputlist.append(text) - elif inputfile and not Path(inputfile).exists(): - raise FileNotFoundError(f"Cannot find input file {inputfile}") - - if model_source == "OpenAI": - ke = SPIRESEngine(template=template, model=model_name, **kwargs) - if settings.cache_db: - ke.client.cache_db_path = settings.cache_db - if settings.skip_annotators: - ke.client.skip_annotators = settings.skip_annotators - - elif model_source == "GPT4All": - ke = GPT4AllEngine(template=template, model=model_name, **kwargs) - - elif model_source == "HuggingFace Hub": - raise NotImplementedError("HF Hub support temporarily disabled. Sorry!") - # hf_repo_name = selectmodel["hf_repo_name"] - # ke = HFHubEngine(template=template, local_model=hf_repo_name, **kwargs) - - if dictionary: - ke.load_dictionary(dictionary) - if target_class: - target_class_def = ke.schemaview.get_class(target_class) - else: - target_class_def = None - - i = 0 - for input_entry in inputlist: - if len(inputlist) > 1: - i = i + 1 - logging.info(f"Now extracting from file {i} of {len(inputlist)}") - results = ke.extract_from_text( - text=input_entry, cls=target_class_def, show_prompt=show_prompt - ) - if set_slot_value: - for slot_value in set_slot_value: - slot, value = slot_value.split("=") - setattr(results.extracted_object, slot, value) - write_extraction(results, output, output_format, ke) - - -@main.command() -@template_option -@model_option -@recurse_option -@output_option_wb -@output_format_options -@auto_prefix_option -@show_prompt_option -@click.argument("entity") -def generate_extract(model, entity, template, output, output_format, show_prompt, **kwargs): - """Generate text and then extract knowledge from it.""" - logging.info(f"Creating for {template}") - - if not model: - model = DEFAULT_MODEL - selectmodel = get_model_by_name(model) - model_source = selectmodel["provider"] - - if model_source == "OpenAI": - ke = SPIRESEngine(template, **kwargs) - if settings.cache_db: - ke.client.cache_db_path = settings.cache_db - if settings.skip_annotators: - ke.skip_annotators = settings.skip_annotators - - elif model_source == "GPT4All": - model_name = selectmodel["alternative_names"][0] - ke = GPT4AllEngine(template=template, model=model_name, **kwargs) - - logging.debug(f"Input entity: {entity}") - results = ke.generate_and_extract( - entity=entity, prompt_template=template, show_prompt=show_prompt - ) - write_extraction(results, output, output_format, ke) - - -@main.command() -@template_option -@model_option -@recurse_option -@output_option_wb -@output_format_options -@auto_prefix_option -@show_prompt_option -@click.option("--ontology", "-r", help="Ontology to use; use oaklib selector path") -@click.option("--max-iterations", "-M", default=10, type=click.INT) -@click.option("--iteration-slot", "-I", multiple=True, help="Slots to iterate over") -@click.option("--db", "-D", help="Where the resulting yaml database is stored") -@click.option( - "--clear/--no-clear", default=False, show_default=True, help="Clear the db before starting" -) -@click.argument("entity") -def iteratively_generate_extract( - model, - entity, - template, - output, - output_format, - db, - iteration_slot, - max_iterations, - clear, - ontology, - show_prompt, - **kwargs, -): - """Iterate through generate-extract.""" - logging.info(f"Creating for {template}") - - if not model: - model = DEFAULT_MODEL - selectmodel = get_model_by_name(model) - model_source = selectmodel["provider"] - - if model_source == "OpenAI": - ke = SPIRESEngine(template, **kwargs) - if settings.cache_db: - ke.client.cache_db_path = settings.cache_db - if settings.skip_annotators: - ke.skip_annotators = settings.skip_annotators - - elif model_source == "GPT4All": - model_name = selectmodel["alternative_names"][0] - ke = GPT4AllEngine(template=template, model=model_name, **kwargs) - - logging.debug(f"Input entity: {entity}") - adapter = get_adapter(ontology) - for results in ke.iteratively_generate_and_extract( - entity, - db, - show_prompt=show_prompt, - iteration_slots=list(iteration_slot), - max_iterations=max_iterations, - adapter=adapter, - clear=clear, - ): - write_extraction(results, output, output_format, ke) - - -# TODO: combine this command with pubmed_annotate - they are converging -@main.command() -@template_option -@model_option -@recurse_option -@output_option_wb -@output_format_options -@show_prompt_option -@click.option( - "--get-pmc/--no-get-pmc", - default=False, - help="Attempt to parse PubMed Central full text(s) instead of abstract(s) alone.", -) -@click.argument("pmid") -def pubmed_extract(model, pmid, template, output, output_format, get_pmc, show_prompt, **kwargs): - """Extract knowledge from a single PubMed ID.""" - logging.info(f"Creating for {template}") - - if not model: - model = DEFAULT_MODEL - selectmodel = get_model_by_name(model) - model_source = selectmodel["provider"] - - if model_source == "OpenAI": - ke = SPIRESEngine(template, **kwargs) - if settings.cache_db: - ke.client.cache_db_path = settings.cache_db - if settings.skip_annotators: - ke.skip_annotators = settings.skip_annotators - - elif model_source == "GPT4All": - model_name = selectmodel["alternative_names"][0] - ke = GPT4AllEngine(template=template, model=model_name, **kwargs) - - pmc = PubmedClient() - if get_pmc: - logging.info(f"Will try to retrieve PubMed Central text for {pmid}.") - textlist = pmc.text(pmid, pubmedcental=True) - else: - textlist = pmc.text(pmid) - for text in textlist: - logging.debug(f"Input text: {text}") - results = ke.extract_from_text(text=text, show_prompt=show_prompt) - write_extraction(results, output, output_format) - - -@main.command() -@template_option -@model_option -@recurse_option -@output_option_wb -@output_format_options -@show_prompt_option -@click.option( - "--limit", - default=20, - help="Total number of citation records to return.", -) -@click.option( - "--get-pmc/--no-get-pmc", - default=False, - help="Attempt to parse PubMed Central full text(s) instead of abstract(s) alone.", -) -@click.argument("search") -def pubmed_annotate( - model, search, template, output, output_format, limit, get_pmc, show_prompt, **kwargs -): - """Retrieve a collection of PubMed IDs for a search term; annotate them using a template. - - Example: - ontogpt pubmed-annotate -t phenotype "Takotsubo Cardiomyopathy: A Brief Review" - --get-pmc --model gpt-3.5-turbo-16k --limit 3 - """ - logging.info(f"Creating for {template}") - - if not model: - model = DEFAULT_MODEL - selectmodel = get_model_by_name(model) - model_source = selectmodel["provider"] - - if model_source == "OpenAI": - ke = SPIRESEngine(template, **kwargs) - if settings.cache_db: - ke.client.cache_db_path = settings.cache_db - if settings.skip_annotators: - ke.skip_annotators = settings.skip_annotators - - elif model_source == "GPT4All": - model_name = selectmodel["alternative_names"][0] - ke = GPT4AllEngine(template=template, model=model_name, **kwargs) - - pubmed_annotate_limit = limit - pmc = PubmedClient() - pmids = pmc.get_pmids(search) - if get_pmc: - logging.info("Will try to retrieve PubMed Central texts.") - textlist = pmc.text(pmids[: pubmed_annotate_limit + 1], pubmedcental=True) - else: - textlist = pmc.text(pmids[: pubmed_annotate_limit + 1]) - for text in textlist: - logging.debug(f"Input text: {text}") - results = ke.extract_from_text(text=text, show_prompt=show_prompt) - write_extraction(results, output, output_format, ke) - - -@main.command() -@template_option -@model_option -@recurse_option -@output_option_wb -@output_format_options -@show_prompt_option -@click.option("--auto-prefix", default="AUTO", help="Prefix to use for auto-generated classes.") -@click.argument("article") -def wikipedia_extract(model, article, template, output, output_format, show_prompt, **kwargs): - """Extract knowledge from a Wikipedia page.""" - if not model: - model = DEFAULT_MODEL - selectmodel = get_model_by_name(model) - model_source = selectmodel["provider"] - - if model_source == "OpenAI": - ke = SPIRESEngine(template=template, model=model, **kwargs) - if settings.cache_db: - ke.client.cache_db_path = settings.cache_db - if settings.skip_annotators: - ke.skip_annotators = settings.skip_annotators - - elif model_source == "GPT4All": - model_name = selectmodel["alternative_names"][0] - ke = GPT4AllEngine(template=template, model=model_name, **kwargs) - - logging.info(f"Creating for {template} => {article}") - client = WikipediaClient() - text = client.text(article) - - logging.debug(f"Input text: {text}") - results = ke.extract_from_text(text=text, show_prompt=show_prompt) - write_extraction(results, output, output_format, ke) - - -@main.command() -@template_option -@model_option -@recurse_option -@output_option_wb -@output_format_options -@show_prompt_option -@click.option( - "--keyword", - "-k", - multiple=True, - help="Keyword to search for (e.g. --keyword therapy). Also obtained from schema", -) -@click.argument("topic") -def wikipedia_search(model, topic, keyword, template, output, output_format, show_prompt, **kwargs): - """Extract knowledge from a Wikipedia page.""" - if not model: - model = DEFAULT_MODEL - selectmodel = get_model_by_name(model) - model_source = selectmodel["provider"] - - if model_source == "OpenAI": - ke = SPIRESEngine(template=template, model=model, **kwargs) - - elif model_source == "GPT4All": - model_name = selectmodel["alternative_names"][0] - ke = GPT4AllEngine(template=template, model=model_name, **kwargs) - - logging.info(f"Creating for {template} => {topic}") - client = WikipediaClient() - keywords = list(keyword) if keyword else [] - logging.info(f"KW={keywords}") - - keywords.extend(ke.schemaview.schema.keywords) - search_term = f"{topic + ' ' + ' '.join(keywords)}" - print(f"Searching for {search_term}") - search_results = client.search_wikipedia_articles(search_term) - for _index, result in enumerate(search_results, start=1): - title = result["title"] - text = client.text(title) - logging.debug(f"Input text: {text}") - if len(text) > 4000: - # TODO - expand this to fit context limits better - # or add as cli option - text = text[:4000] - results = ke.extract_from_text(text=text, show_prompt=show_prompt) - write_extraction(results, output, output_format, ke) - break - - -@main.command() -@template_option -@model_option -@recurse_option -@output_option_wb -@output_format_options -@show_prompt_option -@click.option( - "--keyword", - "-k", - multiple=True, - help="Keyword to search for (e.g. --keyword therapy). Also obtained from schema", -) -@click.argument("term_tokens", nargs=-1) -def search_and_extract( - model, term_tokens, keyword, template, output, output_format, show_prompt, **kwargs -): - """Search for relevant literature and extract knowledge from it.""" - if not model: - model = DEFAULT_MODEL - selectmodel = get_model_by_name(model) - model_source = selectmodel["provider"] - - if model_source == "OpenAI": - ke = SPIRESEngine(template, **kwargs) - - elif model_source == "GPT4All": - model_name = selectmodel["alternative_names"][0] - ke = GPT4AllEngine(template=template, model=model_name, **kwargs) - - term = " ".join(term_tokens) - logging.info(f"Creating for {template}; search={term} kw={keyword}") - - logging.info(f"Creating PubMed client for {template}; search={term}") - pmc = PubmedClient() - logging.info("Got client") - keywords = list(keyword) if keyword else [] - logging.info(f"KW={keywords}") - keywords.extend(ke.schemaview.schema.keywords) - logging.info(f"Keywords={keywords}") - if not keywords: - raise ValueError("No keywords specified; use --keyword or annotate schema with keywords") - pmids = list(pmc.search(term, keywords)) - logging.info(f"PMIDs={pmids}") - pmid = pmids[0] - logging.info(f"PMID={pmid}") - text = pmc.text(pmid) - logging.info(f"Input text: {text}") - results = ke.extract_from_text(text=text, show_prompt=show_prompt) - write_extraction(results, output, output_format, ke) - - -@main.command() -@template_option -@model_option -@recurse_option -@output_option_wb -@output_format_options -@show_prompt_option -@click.argument("url") -def web_extract(model, template, url, output, output_format, show_prompt, **kwargs): - """Extract knowledge from web page.""" - logging.info(f"Creating for {template}") - - if not model: - model = DEFAULT_MODEL - selectmodel = get_model_by_name(model) - model_source = selectmodel["provider"] - - if model_source == "OpenAI": - ke = SPIRESEngine(template=template, model=model, **kwargs) - if settings.cache_db: - ke.client.cache_db_path = settings.cache_db - if settings.skip_annotators: - ke.skip_annotators = settings.skip_annotators - - elif model_source == "GPT4All": - model_name = selectmodel["alternative_names"][0] - ke = GPT4AllEngine(template=template, model=model_name, **kwargs) - - web_client = SoupClient() - text = web_client.text(url) - - logging.debug(f"Input text: {text}") - results = ke.extract_from_text(text=text, show_prompt=show_prompt) - write_extraction(results, output, output_format, ke) - - -@main.command() -@output_option_wb -@click.option("--dictionary") -@output_format_options -@click.option( - "--recipes-urls-file", - "-R", - help="File with URLs to recipes to use for extraction", -) -@click.option("--auto-prefix", default="AUTO", help="Prefix to use for auto-generated classes.") -@model_option -@show_prompt_option -@click.argument("url") -def recipe_extract( - model, url, recipes_urls_file, dictionary, output, output_format, show_prompt, **kwargs -): - """Extract from recipe on the web.""" - try: - from recipe_scrapers import scrape_me - except ModuleNotFoundError as e: - logging.error( - f"Did not find recipe_scrapers. Try: poetry install extras=recipes. Error: {e}" - ) - - template = "recipe" - - if not model: - model = DEFAULT_MODEL - selectmodel = get_model_by_name(model) - model_source = selectmodel["provider"] - - if model_source == "OpenAI": - ke = SPIRESEngine(template, **kwargs) - if settings.cache_db: - ke.client.cache_db_path = settings.cache_db - if settings.skip_annotators: - ke.skip_annotators = settings.skip_annotators - - elif model_source == "GPT4All": - model_name = selectmodel["alternative_names"][0] - ke = GPT4AllEngine(template=template, model=model_name, **kwargs) - - if recipes_urls_file: - with open(recipes_urls_file, "r") as f: - urls = [line.strip() for line in f.readlines() if url in line] - if len(urls) != 1: - raise ValueError(f"Found {len(urls)} URLs in {recipes_urls_file}") - url = urls[0] - scraper = scrape_me(url) - - logging.info(f"Creating for {template}") - - if dictionary: - ke.load_dictionary(dictionary) - ingredients = "\n".join(scraper.ingredients()) - instructions = "\n".join(scraper.instructions_list()) - text = f""" - Recipe: {scraper.title()} - Ingredients:\n{ingredients} - Instructions:\n{instructions} - """ - logging.info(f"Input text: {text}") - results = ke.extract_from_text(text=text, show_prompt=show_prompt) - logging.debug(f"Results: {results}") - results.extracted_object.url = url - write_extraction(results, output, output_format, ke) - - -@main.command() -@model_option -@template_option -@output_option_wb -@output_format_options -@click.argument("input") -def convert(model, template, input, output, output_format, **kwargs): - """Convert output format.""" - logging.info(f"Creating for {template}") - - if not model: - model = DEFAULT_MODEL - selectmodel = get_model_by_name(model) - model_source = selectmodel["provider"] - - if model_source == "OpenAI": - ke = SPIRESEngine(template, **kwargs) - - elif model_source == "GPT4All": - model_name = selectmodel["alternative_names"][0] - ke = GPT4AllEngine(template=template, model=model_name, **kwargs) - - cls = ke.template_pyclass - with open(input, "r") as f: - data = yaml.safe_load(f) - obj = cls(**data["extracted_object"]) - results = ExtractionResult(extracted_object=obj) - write_extraction(results, output, output_format, ke) - - -@main.command() -@model_option -@output_option_txt -@output_format_options -@click.option( - "-C", "--context", required=True, help="domain e.g. anatomy, industry, health-related" -) -@click.argument("term") -def synonyms(model, term, context, output, output_format, **kwargs): - """Extract synonyms.""" - logging.info(f"Creating for {term}") - - if model: - selectmodel = get_model_by_name(model) - model_source = selectmodel["provider"] - - if model_source != "OpenAI": - raise NotImplementedError("Model not yet supported for this function.") - - ke = SynonymEngine() - out = str(ke.synonyms(term, context)) - output.write(out) - - -@main.command() -@output_option_txt -@output_format_options -@click.option( - "--annotation-path", - "-A", - required=True, -) -@click.argument("term") -def create_gene_set(term, output, output_format, annotation_path, **kwargs): - """Create a gene set.""" - logging.info(f"Creating for {term}") - evaluator = EvalEnrichment() - evaluator.load_annotations(annotation_path) - gene_set = evaluator.create_gene_set_from_term(term) - print(yaml.dump(gene_set.dict(), sort_keys=False)) - - -@main.command() -@output_option_txt -@output_format_options -@click.option("--fill/--no-fill", default=False) -@click.option( - "--input-file", - "-U", - help="File with gene IDs to enrich (if not passed as arguments)", -) -def convert_geneset(input_file, output, output_format, fill, **kwargs): - """Convert gene set to YAML.""" - gene_set = parse_gene_set(input_file) - if fill: - fill_missing_gene_set_values(gene_set) - output.write(dump_minimal_yaml(gene_set.dict())) - - -@main.command() -@output_option_txt -@output_format_options -@model_option -@show_prompt_option -@click.option( - "--resolver", "-r", help="OAK selector for the gene ID resolver. E.g. sqlite:obo:hgnc" -) -@click.option( - "-C", - "--context", - help="domain e.g. anatomy, industry, health-related (NOT IMPLEMENTED - currently gene only)", -) -@click.option( - "--strict/--no-strict", - default=True, - show_default=True, - help="If set, there must be a unique mappings from labels to IDs", -) -@click.option( - "--input-file", - "-U", - help="File with gene IDs to enrich (if not passed as arguments)", -) -@click.option( - "--randomize-gene-descriptions-using-file", - help="FOR EVALUATION ONLY. Swap out gene descriptions with genes from this gene set filefile", -) -@click.option( - "--ontological-synopsis/--no-ontological-synopsis", - default=True, - show_default=True, - help="If set, use automated rather than manual gene descriptions", -) -@click.option( - "--combined-synopsis/--no-combined-synopsis", - default=False, - show_default=True, - help="If set, both gene descriptions", -) -@click.option( - "--end-marker", - help="For testing minor variants of prompts", -) -@click.option( - "--annotations/--no-annotations", - default=True, - show_default=True, - help="If set, include annotations in the prompt", -) -@prompt_template_option -@interactive_option -@click.argument("genes", nargs=-1) -def enrichment( - genes, - context, - input_file, - resolver, - output, - model, - show_prompt, - interactive, - end_marker, - output_format, - randomize_gene_descriptions_using_file, - **kwargs, -): - """Gene class summary enriching (SPINDOCTOR). - - Algorithm: - - 1. Map gene symbols to IDs using the resolver (unless IDs specified) - 2. Fetch gene descriptions using Alliance API - 3. Create a prompt using descriptions - - Limitations: - - It is very easy to exceed the max token length with GPT-3 models. - - Usage: - - ontogpt enrichment -r sqlite:obo:hgnc -U tests/input/genesets/dopamine.yaml - - Usage: - - ontogpt enrichment -r sqlite:obo:hgnc -U tests/input/genesets/dopamine.yaml - """ - if model: - selectmodel = get_model_by_name(model) - model_source = selectmodel["provider"] - - if model_source != "OpenAI": - raise NotImplementedError( - "Model not yet supported for gene enrichment or enrichment evaluation." - ) - - if not genes and not input_file: - raise ValueError("Either genes or input file must be passed") - if genes: - gene_set = GeneSet(name="TEMP", gene_symbols=genes) - if input_file: - if genes: - raise ValueError("Either genes or input file must be passed") - gene_set = parse_gene_set(input_file) - if not gene_set: - raise ValueError("No genes passed") - ke = create_engine(None, EnrichmentEngine, model=model) - if end_marker: - ke.end_marker = end_marker - if interactive: - ke.client.interactive = True - if settings.cache_db: - ke.client.cache_db_path = settings.cache_db - if not isinstance(ke, EnrichmentEngine): - raise ValueError(f"Expected EnrichmentEngine, got {type(ke)}") - if resolver: - ke.add_resolver(resolver) - if randomize_gene_descriptions_using_file: - print("WARNING!! Randomly spiking gene descriptions") - spike_gene_set = parse_gene_set(randomize_gene_descriptions_using_file) - aliases = {} - if not spike_gene_set.gene_symbols: - raise ValueError("No gene symbols for spike set") - syms = copy(gene_set.gene_symbols) - if len(spike_gene_set.gene_symbols) < len(gene_set.gene_symbols): - raise ValueError("Not enough genes in spike set") - for sym in spike_gene_set.gene_symbols: - if not syms: - break - aliases[sym] = syms.pop() - results = ke.summarize( - spike_gene_set, normalize=resolver is not None, gene_aliases=aliases, **kwargs - ) - else: - results = ke.summarize(gene_set, normalize=resolver is not None, **kwargs) - if results.truncation_factor is not None and results.truncation_factor < 1.0: - logging.warning(f"Text was truncated; factor = {results.truncation_factor}") - output = _as_text_writer(output) - if show_prompt: - print(results.prompt) - output.write(dump_minimal_yaml(results)) - - -@main.command() -@output_option_txt -@output_format_options -@model_option -@click.option( - "-C", - "--context", - help="domain e.g. anatomy, industry, health-related (NOT IMPLEMENTED - currently gene only)", -) -@click.argument("text", nargs=-1) -def embed(text, context, output, model, output_format, **kwargs): - """Embed text. - - Not currently supported for open models. - """ - if model: - selectmodel = get_model_by_name(model) - model_source = selectmodel["provider"] - - if model_source != "OpenAI": - raise NotImplementedError("Model not yet supported for embeddings.") - else: - model = "text-embedding-ada-002" - - if not text: - raise ValueError("Text must be passed") - - client = OpenAIClient(model=model) - resp = client.embeddings(text) - print(resp) - - -@main.command() -@output_option_txt -@output_format_options -@model_option -@click.option( - "-C", - "--context", - help="domain e.g. anatomy, industry, health-related (NOT IMPLEMENTED - currently gene only)", -) -@click.argument("text", nargs=-1) -def text_similarity(text, context, output, model, output_format, **kwargs): - """Embed text. - - Not currently supported for open models. - """ - if model: - selectmodel = get_model_by_name(model) - model_source = selectmodel["provider"] - - if model_source != "OpenAI": - raise NotImplementedError("Model not yet supported for embeddings.") - else: - model = "text-embedding-ada-002" - - if not text: - raise ValueError("Text must be passed") - text = list(text) - if "@" not in text: - raise ValueError("Text must contain @") - ix = text.index("@") - text1 = " ".join(text[:ix]) - text2 = " ".join(text[ix + 1 :]) - print(text1) - print(text2) - - client = OpenAIClient(model=model) - sim = client.similarity(text1, text2, model=model) - print(sim) - - -@main.command() -@output_option_txt -@output_format_options -@model_option -@click.option( - "-C", - "--context", - help="domain e.g. anatomy, industry, health-related (NOT IMPLEMENTED - currently gene only)", -) -@click.argument("text", nargs=-1) -def text_distance(text, context, output, model, output_format, **kwargs): - """Embed text and calculate euclidian distance between embeddings. - - Not currently supported for open models. - """ - if model: - selectmodel = get_model_by_name(model) - model_source = selectmodel["provider"] - - if model_source != "OpenAI": - raise NotImplementedError("Model not yet supported for embeddings.") - else: - model = "text-embedding-ada-002" - - if not text: - raise ValueError("Text must be passed") - text = list(text) - if "@" not in text: - raise ValueError("Text must contain @") - ix = text.index("@") - text1 = " ".join(text[:ix]) - text2 = " ".join(text[ix + 1 :]) - print(text1) - print(text2) - - client = OpenAIClient(model=model) - sim = client.euclidian_distance(text1, text2, model=model) - print(sim) - - -@main.command() -@output_option_txt -@output_format_options -@model_option -@click.option("--ontology", "-r", help="Ontology to use") -@click.option( - "--definitions/--no-definitions", - default=True, - show_default=True, - help="Include text definitions in the text to embed", -) -@click.option( - "--parents/--no-parents", - default=True, - show_default=True, - help="Include is-a parent terms in the text to embed", -) -@click.option( - "--ancestors/--no-ancestors", - default=True, - show_default=True, - help="Include all ancestors in the text to embed", -) -@click.option( - "--logical-definitions/--no-logical-definitions", - default=True, - show_default=True, - help="Include logical definitions in the text to embed", -) -@click.option( - "--autolabel/--no-autolabel", - default=True, - show_default=True, - help="Add subj/obj labels to report objects", -) -@click.option( - "--synonyms/--no-synonyms", - default=True, - show_default=True, - help="Include synonyms in the text to embed", -) -@click.argument("terms", nargs=-1) -def entity_similarity(terms, ontology, output, model, output_format, **kwargs): - """Embed text. - - Not currently supported for open models. - """ - if model: - selectmodel = get_model_by_name(model) - model_source = selectmodel["provider"] - - if model_source != "OpenAI": - raise NotImplementedError("Model not yet supported for embeddings.") - - if not terms: - raise ValueError("terms must be passed") - terms = list(terms) - if "@" not in terms: - logging.info("No @ found, assuming all by all") - terms1 = list(terms) - terms2 = list(terms) - else: - ix = terms.index("@") - terms1 = terms[:ix] - terms2 = terms[ix + 1 :] - adapter = get_adapter(ontology) - entities1 = list(query_terms_iterator(terms1, adapter)) - entities2 = list(query_terms_iterator(terms2, adapter)) - - engine = SimilarityEngine(model=model, adapter=adapter, **kwargs) - writer = StreamingCsvWriter(output, heterogeneous_keys=False) - - for e1 in entities1: - sims = engine.search(e1, entities2) - for sim in sims: - writer.emit(sim) - - -@main.command() -@inputfile_option -@output_option_txt -@model_option -@click.option("--task-file") -@click.option("--task-type") -@click.option("--tsv-output") -@click.option("--all-methods/--no-all-methods", default=False) -@click.option("--explain/--no-explain", default=False) -@click.option("--evaluate/--no-evaluate", default=False) -@click.argument("terms", nargs=-1) -def reason( - terms, - inputfile, - model, - task_file, - explain, - task_type, - output, - tsv_output, - all_methods, - evaluate, - **kwargs, -): - """Reason.""" - reasoner = ReasonerEngine(model=model) - if task_file: - tc = extractor.TaskCollection.load(task_file) - else: - adapter = get_adapter(inputfile) - if not isinstance(adapter, OboGraphInterface): - raise ValueError("Only OBO graphs supported") - ex = extractor.OntologyExtractor(adapter=adapter) - # ex.use_identifiers = True - task = ex.create_task(task_type=task_type, parameters=list(terms)) - tc = extractor.TaskCollection(tasks=[task]) - if all_methods: - tasks = [] - print(f"Cloning {len(tc.tasks)} tasks") - for core_task in tc.tasks: - for m in extractor.GPTReasonMethodType: - print(f"Cloning {m}") - task = deepcopy(core_task) - task.method = m - task.init_method() - tasks.append(task) - tc.tasks = tasks - print(f"New {len(tc.tasks)} tasks") - else: - for task in tc.tasks: - task.include_explanations = explain - resultset = reasoner.reason_multiple(tc, evaluate=evaluate) - dump_minimal_yaml(resultset.dict(), file=output) - if tsv_output: - write_obj_as_csv(resultset.results, tsv_output) - - -@main.command() -@output_option_txt -@model_option -@click.argument("phenopacket_files", nargs=-1) -def diagnose( - phenopacket_files, - model, - output, - **kwargs, -): - """Diagnose a clinical case represented as one or more Phenopackets.""" - phenopackets = [json.load(open(f)) for f in phenopacket_files] - engine = PhenoEngine(model=model) - results = engine.evaluate(phenopackets) - print(dump_minimal_yaml(results)) - write_obj_as_csv(results, output) - - -@main.command() -@inputfile_option -@output_option_txt -@model_option -@click.option("--tsv-output") -@click.option("--template-path") -def answer( - inputfile, - model, - template_path, - output, - tsv_output, - **kwargs, -): - """Answer a set of questions defined in YAML.""" - qc = QuestionCollection(**yaml.safe_load(open(inputfile))) - engine = GenericEngine(model=model) - qs = [] - for q in engine.run(qc, template_path=template_path): - print(dump_minimal_yaml(q)) - qs.append(q) - qc.questions = qs - output.write(dump_minimal_yaml(qs)) - if tsv_output: - write_obj_as_csv(qs, tsv_output) - - -@main.command() -@inputfile_option -@output_option_txt -@model_option -@click.option("--task-file") -@click.option("--task-type") -@click.option("--tsv-output") -@click.option("--yaml-output") -@click.option("--all-methods/--no-all-methods", default=False) -@click.option("--explain/--no-explain", default=False) -@click.option("--evaluate/--no-evaluate", default=False) -def categorize_mappings( - inputfile, - model, - task_file, - explain, - task_type, - output, - tsv_output, - yaml_output, - all_methods, - evaluate, - **kwargs, -): - """Categorize a collection of SSSOM mappings.""" - mapper = MappingEngine(model=model) - if tsv_output: - tc = mapper.from_sssom(inputfile) - for cm in mapper.run_tasks(tc, evaluate=evaluate): - print(dump_minimal_yaml(cm.dict())) - # dump_minimal_yaml(cm.dict(), file=output) - # write_obj_as_csv(resultset.results, tsv_output) - else: - import sssom.writers as sssom_writers - - msdf = parse_sssom_table(inputfile) - msd = to_mapping_set_document(msdf) - mappings = [] - cms = [] - done = [] - for mapping in msd.mapping_set.mappings: - pair = mapping.subject_id, mapping.object_id - if pair in done: - continue - mapping, cm = mapper.categorize_sssom_mapping(mapping) - mappings.append(mapping) - cms.append(cm.dict()) - done.append(pair) - msd.mapping_set.mappings = mappings - msdf = to_mapping_set_dataframe(msd) - sssom_writers.write_table(msdf, output) - if yaml_output: - with open(yaml_output, "w") as file: - dump_minimal_yaml(cms, file=file) - - -@main.command() -@output_option_txt -@click.option( - "--strict/--no-strict", - default=True, - show_default=True, - help="If set, there must be a unique mappings from labels to IDs", -) -@click.option( - "--input-file", - "-U", - help="File with gene IDs to enrich (if not passed as arguments)", -) -@click.option( - "--ontological-synopsis/--no-ontological-synopsis", - default=True, - show_default=True, - help="If set, use automated rather than manual gene descriptions", -) -@click.option( - "--combined-synopsis/--no-combined-synopsis", - default=False, - show_default=True, - help="If set, both gene descriptions", -) -@click.option( - "--annotations/--no-annotations", - default=True, - show_default=True, - help="If set, include annotations in the prompt", -) -@click.option( - "--number-to-drop", - "-n", - type=click.types.INT, - default=1, - help="Max number of genes to drop", -) -# @click.option( -# "--randomize-gene-descriptions/--no-randomize-gene-descriptions", -# help="DO NOT USE EXCEPT FOR EVALUATION PUPOSES." -# ) -@click.option( - "--annotations-path", - "-A", - help="Path to annotations", -) -@model_option -@click.argument("genes", nargs=-1) -def eval_enrichment(genes, input_file, number_to_drop, annotations_path, model, output, **kwargs): - """Run enrichment using multiple methods.""" - if model: - selectmodel = get_model_by_name(model) - model_source = selectmodel["provider"] - - if model_source != "OpenAI": - raise NotImplementedError( - "Model not yet supported for gene enrichment or enrichment evaluation." - ) - - if not genes and not input_file: - raise ValueError("Either genes or input file must be passed") - if genes: - gene_set = GeneSet(name="TEMP", gene_symbols=genes) - if input_file: - if genes: - raise ValueError("Either genes or input file must be passed") - gene_set = parse_gene_set(input_file) - if not gene_set: - raise ValueError("No genes passed") - fill_missing_gene_set_values(gene_set) - if not annotations_path: - if not _is_human(gene_set): - raise ValueError("No annotations path passed") - annotations_path = "tests/input/genes2go.tsv.gz" - eval_engine = EvalEnrichment(model=model) - eval_engine.load_annotations(annotations_path) - comps = eval_engine.evaluate_methods_on_gene_set(gene_set, n=number_to_drop, **kwargs) - output.write(dump_minimal_yaml(comps)) - - -@main.command() -@recurse_option -@model_option -@output_option_txt -@click.option( - "--num-tests", - type=click.INT, - default=5, - show_default=True, - help="number of iterations to cycle through.", -) -@click.option( - "--chunking/--no-chunking", - default=False, - show_default=True, - help="If set, chunk input text, then prepare a separate prompt for each chunk." - " Otherwise the full input text is passed.", -) -@click.argument("evaluator") -def eval(evaluator, num_tests, output, chunking, model, **kwargs): - """Evaluate an extractor.""" - logging.info(f"Creating for {evaluator}") - - if model: - selectmodel = get_model_by_name(model) - modelname = selectmodel["alternative_names"][0] - else: - modelname = DEFAULT_MODEL - - evaluator = create_evaluator( - name=evaluator, num_tests=num_tests, chunking=chunking, model=modelname - ) - eos = evaluator.eval() - output.write(dump_minimal_yaml(eos, minimize=False)) - - -@main.command() -@template_option -@model_option -@click.option("-E", "--examples", type=click.File("r"), help="File of example objects.") -@recurse_option -@output_option_wb -@output_format_options -@show_prompt_option -@click.argument("object") -def fill(model, template, object: str, examples, output, output_format, show_prompt, **kwargs): - """Fill in missing values.""" - logging.info(f"Creating for {template}") - - ke: KnowledgeEngine - - # Choose model based on input, or use the default - if not model: - model = DEFAULT_MODEL - selectmodel = get_model_by_name(model) - model_source = selectmodel["provider"] - - if model_source == "OpenAI": - ke = SPIRESEngine(template=template, **kwargs) - else: - model_name = selectmodel["alternative_names"][0] - ke = GPT4AllEngine(template=template, model=model_name, **kwargs) - - object = yaml.safe_load(object) - logging.info(f"Object to fill = {object}") - logging.info(f"Loading {examples}") - examples = yaml.safe_load(examples) - logging.debug(f"Input object: {object}") - results = ke.generalize(object=object, examples=examples, show_prompt=show_prompt) - - output.write(yaml.dump(results.dict())) - - -@main.command() -def openai_models(**kwargs): - """List OpenAI models for prompt completion.""" - ai = OpenAIClient() - for model in openai.Model.list(): - print(model) - - -@main.command() -@model_option -@output_option_txt -@output_format_options -@show_prompt_option -@click.argument("input") -def complete(model, input, output, output_format, show_prompt, **kwargs): - """Prompt completion.""" - if not model: - model = DEFAULT_MODEL - selectmodel = get_model_by_name(model) - model_source = selectmodel["provider"] - model_name = selectmodel["alternative_names"][0] - - text = open(input).read() - - if model_source == "OpenAI": - c = OpenAIClient(model=model_name) - results = c.complete(prompt=text, show_prompt=show_prompt) - - elif model_source == "GPT4All": - c = set_up_gpt4all_model(modelname=model_name) - results = chain_gpt4all_model(model=c, prompt_text=text) - - output.write(results) - - -@main.command() -@template_option -@click.option("--input", "-i", type=click.File("r"), default=sys.stdin, help="Input file") -def parse(template, input): - """Parse OpenAI results.""" - logging.info(f"Creating for {template}") - ke = SPIRESEngine(template) - text = input.read() - logging.debug(f"Input text: {text}") - # ke.annotator = BioPortalImplementation() - results = ke.parse_completion_payload(text) - print(yaml.dump(results)) - - -@main.command() -@click.option("-o", "--output", type=click.File(mode="w"), default=sys.stdout, help="Output file.") -@output_format_options -@model_option -@click.option("-m", "match", help="Match string to use for filtering.") -@click.option("-D", "database", help="Path to sqlite database.") -def dump_completions(model, match, database, output, output_format): - """Dump cached completions.""" - if model: - raise NotImplementedError("Caching not currently enabled for this model.") - else: - client = OpenAIClient() - - if database: - client.cache_db_path = database - if output_format == "jsonl": - writer = jsonlines.Writer(output) - for _engine, prompt, completion in client.cached_completions(match): - writer.write(dict(engine=model, prompt=prompt, completion=completion)) - elif output_format == "yaml": - for _engine, prompt, completion in client.cached_completions(match): - output.write( - dump_minimal_yaml(dict(engine=model, prompt=prompt, completion=completion)) - ) - else: - output.write("# Cached Completions:\n") - for engine, prompt, completion in client.cached_completions(match): - output.write("## Entry\n") - output.write(f"### Engine: {engine}\n") - output.write(f"### Prompt:\n\n {prompt}\n\n") - output.write(f"### Completion:\n\n {completion}\n\n") - - -@main.command() -@click.option("-o", "--output", type=click.File(mode="w"), default=sys.stdout, help="Output file.") -@click.argument("input", type=click.File("r")) -def convert_examples(input, output): - """Convert training examples from YAML.""" - logging.info(f"Creating examples for {input}") - example_doc = yaml.safe_load(input) - writer = jsonlines.Writer(output) - for example in example_doc["examples"]: - prompt = example["prompt"] - completion = yaml.dump(example["completion"], sort_keys=False) - writer.write(dict(prompt=prompt, completion=completion)) - - -@main.command() -@model_option -@click.option("-o", "--output", type=click.File(mode="w"), default=sys.stdout, help="Output file.") -@click.option("-i", "--input", help="Input ontology.") -@click.option("-c", "--context", help="Context.") -@click.option( - "--num-iterations", - type=click.INT, - default=5, - show_default=True, - help="number of iterations to cycle through.", -) -@click.argument("terms", nargs=-1) -def halo(model, input, context, terms, output, **kwargs): - """Run HALO over inputs.""" - if model: - raise NotImplementedError("HALO not currently supported for this model.") - - engine = HALOEngine() - engine.seed_from_file(input) - if context is None: - context = engine.ontology.elements[0].context - engine.fixed_slot_values = {"context": context} - engine.hallucinate(terms, **kwargs) - output.write(dump_minimal_yaml(engine.ontology)) - - -@main.command() -@model_option -@output_option_wb -@output_format_options -@show_prompt_option -@click.option( - "-d", - "--description", - help="domain e.g. anatomy, industry, health-related (NOT IMPLEMENTED - currently gene only)", -) -@click.option( - "--sections", multiple=True, help="sections to include e.g. medications, vital signs, etc." -) -def clinical_notes( - description, - sections, - output, - model, - show_prompt, - output_format, - **kwargs, -): - """Create mock clinical notes. - - Example: - - ontogpt clinical-notes -d "middle-aged female patient with diabetes" - ontogpt clinical-notes --description "middle-aged female patient with diabetes"\ - --sections medications --sections "vital signs" - - """ - prompt = "create mock clinical notes for a patient like this: " + description - if sections: - prompt += " including sections: " + ", ".join(sections) - - if not model: - model = DEFAULT_MODEL - selectmodel = get_model_by_name(model) - model_source = selectmodel["provider"] - model_name = selectmodel["alternative_names"][0] - - if model_source == "OpenAI": - c = OpenAIClient(model=model_name) - results = c.complete(prompt=prompt, show_prompt=show_prompt) - - elif model_source == "GPT4All": - c = set_up_gpt4all_model(modelname=model_name) - results = chain_gpt4all_model(model=c, prompt_text=prompt) - - output.write(results) - - -@main.command() -def list_templates(): - """List the templates.""" - print("TODO") - - -@main.command() -def list_models(): - """List all available models.""" - print("Model Name\tProvider\tAlternative Names\tStatus\tDisk Space\tSystem Memory") - for model in MODELS: - primary_name = model["name"] - provider = model["provider"] - alternative_names = ( - " ".join(model["alternative_names"]) if model["alternative_names"] else "" - ) - if "not_implemented" in model or "deprecated" in model: - status = "Not Implemented" - else: - status = "Implemented" - disk = model["requirements"]["diskspace"] - memory = model["requirements"]["memory"] - - print(f"{primary_name}\t{provider}\t{alternative_names}\t{status}\t{disk}\t{memory}") - - -if __name__ == "__main__": - main() diff --git a/src/ontogpt/clients/__init__.py b/src/ontogpt/clients/__init__.py deleted file mode 100644 index f8310d5d9..000000000 --- a/src/ontogpt/clients/__init__.py +++ /dev/null @@ -1,4 +0,0 @@ -"""Clients for accessing different APIs.""" -from ontogpt.clients.openai_client import OpenAIClient # noqa:F401 -from ontogpt.clients.pubmed_client import PubmedClient # noqa:F401 -from ontogpt.clients.soup_client import SoupClient # noqa:F401 diff --git a/src/ontogpt/clients/hfhub_client.py b/src/ontogpt/clients/hfhub_client.py deleted file mode 100644 index 161d0611f..000000000 --- a/src/ontogpt/clients/hfhub_client.py +++ /dev/null @@ -1,53 +0,0 @@ -"""HuggingFace Hub Client.""" -import logging -from dataclasses import dataclass - -from langchain import HuggingFaceHub, LLMChain, PromptTemplate -from oaklib.utilities.apikey_manager import get_apikey_value - -# Note: See https://huggingface.co/models?pipeline_tag=text-generation&sort=downloads -# for all relevant models - - -@dataclass -class HFHubClient: - """A client for the HuggingFace Hub API.""" - - try: - api_key = get_apikey_value("hfhub-key") - except ValueError: - logging.error("HuggingFace Hub API key not found. See README.") - - def get_model(self, modelname: str) -> HuggingFaceHub: - """Retreive a model from the Hub, given its repository name. - - Returns a model object of type - langchain.llms.huggingface_hub.HuggingFaceHub - """ - model = HuggingFaceHub( - repo_id=modelname, - verbose=True, - model_kwargs={"temperature": 0.2, "max_length": 500}, - huggingfacehub_api_token=self.api_key, - task="text-generation", - ) - - return model - - def query_hf_model(self, llm, prompt_text): - """Interact with a GPT4All model.""" - logging.info(f"Complete: prompt[{len(prompt_text)}]={prompt_text[0:100]}...") - - template = """{prompt_text}""" - - prompt = PromptTemplate(template=template, input_variables=["prompt_text"]) - - llm_chain = LLMChain(prompt=prompt, llm=llm) - - try: - raw_output = llm_chain.run({"prompt_text": prompt_text}) - except ValueError as e: - logging.error(e) - raw_output = "" - - return raw_output diff --git a/src/ontogpt/clients/openai_client.py b/src/ontogpt/clients/openai_client.py deleted file mode 100644 index 92bfccfdf..000000000 --- a/src/ontogpt/clients/openai_client.py +++ /dev/null @@ -1,189 +0,0 @@ -"""OpenAI client.""" -import ast -import logging -import sqlite3 -import sys -from dataclasses import dataclass, field -from pathlib import Path -from time import sleep -from typing import Iterator, Optional, Tuple - -import numpy as np -import openai -from oaklib.utilities.apikey_manager import get_apikey_value - -logger = logging.getLogger(__name__) -NUM_RETRIES = 3 - - -@dataclass -class OpenAIClient: - # max_tokens: int = field(default_factory=lambda: 3000) - model: str = field(default_factory=lambda: "gpt-3.5-turbo") - cache_db_path: str = "" - api_key: str = "" - interactive: Optional[bool] = None - - def __post_init__(self): - if not self.api_key: - self.api_key = get_apikey_value("openai") - openai.api_key = self.api_key - - def complete(self, prompt, max_tokens=3000, show_prompt: bool = False, **kwargs) -> str: - engine = self.model - logger.info(f"Complete: engine={engine}, prompt[{len(prompt)}]={prompt[0:100]}...") - if show_prompt: - logger.info(f" SENDING PROMPT:\n{prompt}") - cur = self.db_connection() - res = cur.execute("SELECT payload FROM cache WHERE prompt=? AND engine=?", (prompt, engine)) - payload = res.fetchone() - if payload: - prompt_peek = str(prompt)[0:80].replace("\n", "\\n") - logger.info(f"Using cached payload for prompt: {prompt_peek}...") - return payload[0] - response = None - i = 0 - while not response: - i += 1 - logger.debug(f"Calling OpenAI API (attempt {i})...") - try: - if self.interactive: - response = self._interactive_completion(prompt, engine, max_tokens, **kwargs) - elif self._must_use_chat_api(): - response = openai.ChatCompletion.create( - model=engine, - messages=[ - { - "role": "user", - "content": prompt, - }, - ], - max_tokens=max_tokens, - **kwargs, - ) - else: - response = openai.Completion.create( - engine=engine, - prompt=prompt, - max_tokens=max_tokens, - ) - break - except Exception as e: - logger.error(f"OpenAI API connection error: {e}") - if i >= NUM_RETRIES: - raise e - sleep_time = 4**i - logger.info(f"Retrying {i} of {NUM_RETRIES} after {sleep_time} seconds...") - sleep(sleep_time) - - if self.interactive: - payload = response - elif self._must_use_chat_api(): - payload = response["choices"][0]["message"]["content"] - else: - payload = response["choices"][0]["text"] - logger.info(f"Storing payload of len: {len(payload)}") - cur.execute( - "INSERT INTO cache (prompt, engine, payload) VALUES (?, ?, ?)", - (prompt, engine, payload), - ) - cur.connection.commit() - return payload - - def db_connection(self): - if not self.cache_db_path: - self.cache_db_path = ".openai_cache.db" - logger.info(f"Caching OpenAI responses to {Path(self.cache_db_path).absolute()}") - create = not Path(self.cache_db_path).exists() - con = sqlite3.connect(self.cache_db_path) - cur = con.cursor() - if create: - cur.execute("CREATE TABLE cache (prompt, engine, payload)") - return cur - - def _interactive_completion( - self, prompt: str, engine: str, max_tokens: Optional[int], **kwargs - ): - print("Please use the ChatGPT interface to complete the following prompt:") - print(f"IMPORTANT: make sure model == {engine}") - print(f"Note: max_tokens == {max_tokens}") - print("Prompt:") - print(prompt) - print("Paste in the response here, then ctrl-d to continue:") - response = sys.stdin.read() - print("OK? (y/n)") - ok = input() - if ok == "y": - print("Thank you! This will now be cached.") - print("Please be patient for the rest of the process to finish...") - return response - else: - return self._interactive_completion(prompt, engine, max_tokens, **kwargs) - - def cached_completions( - self, search_term: str = "", engine: str = "" - ) -> Iterator[Tuple[str, str, str]]: - if search_term: - search_term = search_term.lower() - cur = self.db_connection() - res = cur.execute("SELECT engine, prompt, payload FROM cache") - for row in res: - if ( - search_term - and search_term not in row[1].lower() - and search_term not in row[2].lower() - ): - continue - if engine and engine != row[0]: - continue - yield row - - def _must_use_chat_api(self) -> bool: - """Return True if the model requires the chat API, False otherwise.""" - if self.model.startswith("text-davinci"): - return False - return True - - def embeddings(self, text: str, model: str = ""): - text = str(text) - - if model == "": - model = "text-embedding-ada-002" - cur = self.db_connection() - try: - logger.info("creating embeddings cache") - cur.execute("CREATE TABLE embeddings_cache (text, engine, vector_as_string)") - except sqlite3.OperationalError: - logger.info("Embeddings cache table already exists") - pass - res = cur.execute( - "SELECT vector_as_string FROM embeddings_cache WHERE text=? AND engine=?", (text, model) - ) - payload = res.fetchone() - if payload: - logger.info(f"Using cached embeddings for {model} {text[0:80]}...") - return ast.literal_eval(payload[0]) - logger.info(f"querying OpenAI for {model} {text[0:80]}...") - response = openai.Embedding.create( - model=model, - input=text, - ) - v = response.data[0]["embedding"] - logger.info(f"Storing embeddings of len: {len(v)}") - cur.execute( - "INSERT INTO embeddings_cache (text, engine, vector_as_string) VALUES (?, ?, ?)", - (text, model, str(v)), - ) - cur.connection.commit() - return v - - def similarity(self, text1: str, text2: str, **kwargs): - a1 = self.embeddings(text1, **kwargs) - a2 = self.embeddings(text2, **kwargs) - logger.debug(f"similarity: {a1[0:10]}... x {a2[0:10]}... // ({len(a1)} x {len(a2)})") - return np.dot(a1, a2) / (np.linalg.norm(a1) * np.linalg.norm(a2)) - - def euclidian_distance(self, text1: str, text2: str, **kwargs): - a1 = self.embeddings(text1, **kwargs) - a2 = self.embeddings(text2, **kwargs) - return np.linalg.norm(np.array(a1) - np.array(a2)) diff --git a/src/ontogpt/clients/pubmed_client.py b/src/ontogpt/clients/pubmed_client.py deleted file mode 100644 index de35ecacd..000000000 --- a/src/ontogpt/clients/pubmed_client.py +++ /dev/null @@ -1,525 +0,0 @@ -"""Pubmed Client.""" -import logging -import time -from dataclasses import dataclass -from typing import Generator, List, Tuple, Union -from urllib import parse - -import inflection -import requests -from bs4 import BeautifulSoup -from oaklib.utilities.apikey_manager import get_apikey_value - -PMID = str -TITLE_WEIGHT = 5 -MAX_PMIDS = 50 -RETRY_MAX = 2 - -PUBMED = "pubmed" -EUTILS_URL = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/" - - -def _normalize(s: str) -> str: - return inflection.singularize(s).lower() - - -def _score_paper(paper: str, keywords: List[str]) -> Tuple[PMID, int]: - """Assign a quality score to a PubMed entry. - - Input needs to be XML so it can be parsed by component. - :param paper: string, the text of the paper, as XML - :param keywords: list of keywords to use in scoring - :return: tuple of article ID (PMID) and score - """ - # Parse the paper by component first - soup = BeautifulSoup(paper, "xml") - for pa in soup.find_all(["PubmedArticle", "PubmedBookArticle"]): # This should be one exactly - ti = pa.find("ArticleTitle").text - pmid = pa.find("ArticleId", IdType="pubmed").text - if pa.find("Abstract"): # Document may not have abstract - ab = pa.find("Abstract").text - else: - ab = "" - - title_score = _score_text(ti, keywords) - abstract_score = _score_text(ab, keywords) - logging.info(f"Scored {pmid} {ti} with TS={title_score} AS={abstract_score} ") - score = title_score * TITLE_WEIGHT + abstract_score - return (pmid, score) - - -def _score_text(text: str, keywords: List[str]) -> int: - """Assign a quality score to a text entry. - - A text entry not mentioning any of its keywords has a score of zero. - Score increases by one for each keyword mentioned in the text. - :param text: The text to assign the score to - :param keywords: The keywords to use in scoring - """ - text = text.lower() - if not text: - return -100 - score = 0 - for kw in keywords: - if kw in text: - score += 1 - return score - - -def clean_pmids(ids: list[PMID]) -> list[PMID]: - """Remove prefixes from a list of PMIDs, returning the new list.""" - clean_ids = [id.replace("PMID:", "", 1) for id in ids] - return clean_ids - - -@dataclass -class PubmedClient: - """A client for the Pubmed API. - - This class is a wrapper around the Entrez API. - """ - - # TODO: this doesn't need to be hardcoded - # and may vary based on the model in use - max_text_length = 3000 - - try: - email = get_apikey_value("ncbi-email") - except ValueError: - email = None - logging.info("Email for NCBI API not found.") - - try: - ncbi_key = get_apikey_value("ncbi-key") - except ValueError: - ncbi_key = None - logging.info("NCBI API key not found. Will use no key.") - - def get_pmids(self, term: str) -> List[str]: - """Search PubMed and retrieve a list of PMIDs matching the search term. - - :param term: The search term to query PubMed. - :return: A list of PMIDs matching the search term. - """ - pmids = [] - - batch_size = 5000 - - search_url = EUTILS_URL + "esearch.fcgi" - - logging.info(f"Finding count of PMIDs matching search term {term}...") - # If retmax==0, we get only the size of the search result in count of PMIDs - if self.email and self.ncbi_key: - params = { - "db": PUBMED, - "term": term, - "retmode": "json", - "retmax": 0, - "email": self.email, - "api_key": self.ncbi_key, - } - else: - params = {"db": PUBMED, "term": term, "retmode": "json", "retmax": 0} - - # We are explicit with the delimiters in this query, - # no percent encoding allowed. This mostly just makes it more human readable - response = requests.get(search_url, params=parse.urlencode(params, safe=",")) - - if response.status_code == 200: - data = response.json() - resultcount = int(data["esearchresult"]["count"]) - logging.info(f"Search returned {resultcount} PMIDs matching search term {term}") - elif response.status_code == 429: - logging.error("Too many requests to NCBI API. Try again later, or use API key.") - else: - logging.error("Encountered error in searching PubMed:", response.status_code) - - if resultcount > 9999: - logging.warning("PubMed limits search results to 9999 records.") - resultcount = 9999 - - # Now we get the list of PMIDs, iterating as needed - logging.info(f"Retrieving PMIDs matching search term {term}...") - for retstart in range(0, resultcount, batch_size): - params["retstart"] = retstart - params["retmax"] = batch_size - - response = requests.get(search_url, params=parse.urlencode(params, safe=",")) - - trying = True - try_count = 0 - while trying: - if response.status_code == 200: - data = response.json(strict=False) - try: - these_ids = data["esearchresult"]["idlist"] - pmids.extend(these_ids) - except KeyError: # Likely an error message. - errortext = data["esearchresult"]["ERROR"] - logging.error(f"Response: {errortext}") - trying = False - else: - logging.error(f"Encountered error in searching PubMed: {response.status_code}") - try_count = try_count + 1 - if try_count < RETRY_MAX: - logging.info("Trying again...") - time.sleep(1) - else: - logging.info(f"Giving up - last status code {response.status_code}") - trying = False - logging.info("Retrieved all PMIDs.") - - return pmids - - def text( - self, ids: Union[list[PMID], PMID], raw=False, autoformat=True, pubmedcental=False - ) -> Union[list[str], str]: - """Get the text of one or more papers from their PMIDs. - - :param ids: List of PubMed IDs, or string with single PMID - :param raw: if True, do not parse the xml, just return the raw output with tags - :param autoformat: if True include title and abstract concatenated - :param pubmedcentral: if True, retreive text from PubMed Central where possible - :return: the text of a single entry, or a list of strings for text of multiple entries - """ - batch_size = 200 - - # Check if the PMID(s) can be parsed - # and remove prefix if present - if isinstance(ids, PMID): # If it's a single PMID - ids = [ids] - singledoc = True - else: - singledoc = False - clean_ids = clean_pmids(ids) - ids = clean_ids - - # this will store the document data - xml_data = "" - - # Check if we have enough IDs to require epost - # This is stated as being 10000 - # But in practice, the API won't even accept more than ~2500 - # chars worth of IDs, or about 280 to 320 PMIDs. - # So instead, we iterate. - use_post = False - if len(ids) > 275: - use_post = True - - fetch_url = EUTILS_URL + "efetch.fcgi" - - if not use_post: - if self.email and self.ncbi_key: - params = { - "db": PUBMED, - "id": ",".join(ids), - "rettype": "xml", - "retmode": "xml", - "email": self.email, - "api_key": self.ncbi_key, - } - else: - params = {"db": PUBMED, "id": ",".join(ids), "rettype": "xml", "retmode": "xml"} - - for retstart in range(0, len(ids), batch_size): - params["retstart"] = retstart - params["retmax"] = batch_size - - response = requests.get(fetch_url, params=parse.urlencode(params, safe=",")) - - trying = True - try_count = 0 - while trying: - if response.status_code == 200: - xml_data = xml_data + "\n" + response.text - trying = False - else: - logging.error( - f"Encountered error in fetching from PubMed: {response.status_code}" - ) - try_count = try_count + 1 - if try_count < RETRY_MAX: - logging.info("Trying again...") - time.sleep(1) - else: - logging.info(f"Giving up - last status code {response.status_code}") - trying = False - logging.info("Retrieved document data.") - - else: - # Do post request first, iterating as needed - post_url = EUTILS_URL + "epost.fcgi" - if self.email and self.ncbi_key: - params = { - "db": PUBMED, - "id": "", - "email": self.email, - "api_key": self.ncbi_key, - "WebEnv": "", - } - else: - params = {"db": PUBMED, "id": ",".join(ids), "WebEnv": ""} - - query_keys = [] - - # Need to batch the IDs manually for this endpoint - id_batches = [ids[pmid : pmid + batch_size] for pmid in range(0, len(ids), batch_size)] - - for batch in id_batches: - params["id"] = ",".join(batch) - - response = requests.post(post_url, params=parse.urlencode(params, safe=",")) - - # Get a webenv the first time, then reuse on subsequent requests - # import pdb; pdb.set_trace() - if params["WebEnv"] == "": - webenv = response.text.split("<WebEnv>")[1].split("</WebEnv>")[0] - params["WebEnv"] = webenv - querykey = response.text.split("<QueryKey>")[1].split("</QueryKey>")[0] - query_keys.append(querykey) - - trying = True - try_count = 0 - while trying: - if response.status_code == 200: - trying = False - else: - logging.error( - f"Encountered error in posting IDs to PubMed: {response.status_code}" - ) - try_count = try_count + 1 - if try_count < RETRY_MAX: - logging.info("Trying again...") - time.sleep(0.5) - else: - logging.info(f"Giving up - last status code {response.status_code}") - trying = False - logging.info(f"Posted PMIDs to WebEnv:{webenv}.") - - # Now do the fetch - params = { - "db": PUBMED, - "query_key": "", - "WebEnv": webenv, - "rettype": "xml", - } - - # Iterate through the query keys we have - for this_key in query_keys: - params["query_key"] = this_key - - response = requests.get(fetch_url, params=parse.urlencode(params, safe=",")) - - trying = True - try_count = 0 - while trying: - if response.status_code == 200: - xml_data = xml_data + "\n" + response.text - trying = False - else: - logging.error( - f"Encountered error in fetching from PubMed: {response.status_code}" - ) - try_count = try_count + 1 - if try_count < RETRY_MAX: - logging.info("Trying again...") - time.sleep(0.5) - else: - logging.info(f"Giving up - last status code {response.status_code}") - trying = False - logging.info("Retrieved document data.") - - # Parse that xml - this returns a list of strings - # if raw is True, the tags are kept, but we still get a list of docs - # and we don't truncate them - these_docs = self.parse_pmxml( - xml=xml_data, raw=raw, autoformat=autoformat, pubmedcentral=pubmedcental - ) - - txt = [] - onetxt = "" - for doc in these_docs: - if len(doc) > self.max_text_length and not raw: - logging.warning( - f'Truncating entry beginning "{doc[:50]}" to {str(self.max_text_length)} chars' - ) - shortdoc = doc[0 : self.max_text_length] - txt.append(shortdoc) - else: - txt.append(doc) - if singledoc and not pubmedcental: - onetxt = txt[0] - - if len(onetxt) > 0: - return onetxt - else: - return txt - - def pmc_text(self, pmc_id: str) -> str: - """Get the text of one PubMed Central entry. - - Don't parse further here - just get the raw response. - :param pmc_id: List of PubMed IDs, or string with single PMID - :return: the text of a single entry as XML - """ - xml_data = "" - - fetch_url = EUTILS_URL + "efetch.fcgi" - - if self.email and self.ncbi_key: - params = { - "db": "pmc", - "id": pmc_id, - "rettype": "xml", - "retmode": "xml", - "email": self.email, - "api_key": self.ncbi_key, - } - else: - params = {"db": "pmc", "id": pmc_id, "rettype": "xml", "retmode": "xml"} - - response = requests.get(fetch_url, params=parse.urlencode(params, safe=",")) - - trying = True - try_count = 0 - while trying: - if response.status_code == 200: - xml_data = response.text - trying = False - else: - logging.error( - f"Encountered error in fetching from PubMed Central: {response.status_code}" - ) - try_count = try_count + 1 - if try_count < RETRY_MAX: - logging.info("Trying again...") - time.sleep(1) - else: - logging.info(f"Giving up - last status code {response.status_code}") - trying = False - logging.info(f"Retrieved PubMed Central document data for {pmc_id}.") - - return xml_data - - def search(self, term: str, keywords: List[str]) -> Generator[PMID, None, None]: - """Get the quality-scored text of PubMed papers relating to a search term and keywords. - - This generator yields PMIDs. Note this uses the MAX_PMIDS value - to determine how many documents to collect. - :param term: search term, a string - :param keywords: keywords, a list of strings - :return: PMIDs corresponding to the search term and keywords - """ - if keywords: - keywords = [_normalize(kw) for kw in keywords] - term = f"({term}) AND ({' OR '.join(keywords)})" - else: - keywords = [] - - logging.info(f"Searching for {term}...") - - esr = self.get_pmids(term=term) - - paset = self.text(ids=esr[0:MAX_PMIDS], raw=True) - - scored_papers = [(_score_paper(paper, keywords), paper) for paper in paset] - scored_papers.sort(key=lambda x: x[1][0], reverse=True) - - for id_and_score, _paper in scored_papers: - pmid = id_and_score[0] - score = id_and_score[1] - logging.debug(f"Yielding {pmid} with score {score} ") - yield f"{pmid}" - - def parse_pmxml(self, xml: str, raw: bool, autoformat: bool, pubmedcentral: bool) -> List[str]: - """Extract structured text from PubMed and PubMed Central XML. - - :param xml: One or more xml entries, as string - :param raw: if True, do not parse the xml beyond separating documents - :param autoformat: if True include title and abstract concatenated - Otherwise the output will include ALL text contents besides XML tags - :param pubmedcentral: if True replace abstract with PubMed Central text - If there isn't a PMC ID, just use the abstract. - If there is a PMC ID, use the abstract AND chunk the body text. - This means the same ID may have multiple entries and may require multiple - queries to the LLM. - :return: a list of strings, one per entry - """ - docs = [] - - # Preprocess the string to ensure it's valid xml - if not raw: - logging.info("Preprocessing all xml entries...") - header = "\n".join(xml.split("\n", 3)[0:3]) - pmas_opener = "<PubmedArticleSet>" - pmas_closer = "</PubmedArticleSet>" - for remove_string in [header, pmas_opener, pmas_closer]: - xml = xml.replace(remove_string, "\n") - xml = pmas_opener + xml + pmas_closer - - soup = BeautifulSoup(xml, "xml") - - logging.info("Parsing all xml entries...") - for pa in soup.find_all(["PubmedArticle", "PubmedBookArticle"]): - # First check the PMID, and if requested, any PMC ID - pmid = "" - if pa.find("PMID"): # If this is missing something has gone Wrong - pmid = pa.find("PMID").text - pmc_id = "" - has_pmc_id = False - try: # There's a chance that this entry is missing one or more fields below - if ( - pa.find("PubmedData").find("ArticleIdList").find("ArticleId", {"IdType": "pmc"}) - and pubmedcentral - ): - pmc_id = ( - pa.find("PubmedData") - .find("ArticleIdList") - .find("ArticleId", {"IdType": "pmc"}) - .text - ) - has_pmc_id = True - except AttributeError: - logging.info(f"PubMed entry {pmid} is missing the expected PubMedData fields.") - if autoformat and not raw and not has_pmc_id: # No PMC ID - just use title+abstract - ti = "" - if pa.find("ArticleTitle"): - ti = pa.find("ArticleTitle").text - ab = "" - if pa.find("Abstract"): # Document may not have abstract - ab = pa.find("Abstract").text - kw = [""] - if pa.find("KeywordList"): # Document may not have MeSH terms or keywords - kw = [tag.text for tag in pa.find_all("Keyword")] - txt = f"Title: {ti}\nKeywords: {'; '.join(kw)}\nPMID: {pmid}\nAbstract: {ab}" - docs.append(txt) - elif autoformat and not raw and has_pmc_id: # PMC ID - get and use that text instead - fulltext = self.pmc_text(pmc_id) - fullsoup = BeautifulSoup(fulltext, "xml") - body = "" - if fullsoup.find("pmc-articleset").find("article").find("body"): - body = fullsoup.find("pmc-articleset").find("article").find("body").text - body = body.replace("\n", " ") - ti = "" - if pa.find("ArticleTitle"): - ti = pa.find("ArticleTitle").text - if pa.find("Abstract"): # Document may not have abstract - body = pa.find("Abstract").text + body - kw = [""] - if pa.find("KeywordList"): # Document may not have MeSH terms or keywords - kw = [tag.text for tag in pa.find_all("Keyword")] - - id_txt = f"Title: {ti}\nKeywords: {'; '.join(kw)}\nPMID: {pmid}\nPMCID: {pmc_id}\n" - full_max_len = self.max_text_length - len(id_txt) - chunktxt = [body[i : i + full_max_len] for i in range(0, len(body), full_max_len)] - for txt in chunktxt: - docs.append(id_txt + txt) - logging.warning( - f'Truncating entry containing "{txt[:50]}" to {self.max_text_length} chars' - ) - elif raw: - docs.append(str(pa)) - else: - docs.append(soup.get_text()) - - return docs diff --git a/src/ontogpt/clients/soup_client.py b/src/ontogpt/clients/soup_client.py deleted file mode 100644 index 64101c3fd..000000000 --- a/src/ontogpt/clients/soup_client.py +++ /dev/null @@ -1,25 +0,0 @@ -"""Soup client.""" -from dataclasses import dataclass - -import requests -from bs4 import BeautifulSoup - -PMID = str - - -@dataclass -class SoupClient: - """A client for the Beautiful Soup API.""" - - def text(self, url: str) -> str: - """Get the text of a paper from its PMID. - - :param id: - :param autoformat: if True include title and abstract concatenated - :return: - """ - result = requests.get(url) - if result.status_code != 200: - raise Exception(f"Error fetching {url}: {result.status_code}") - soup = BeautifulSoup(result.text) - return soup.text diff --git a/src/ontogpt/clients/wikipedia_client.py b/src/ontogpt/clients/wikipedia_client.py deleted file mode 100644 index 565e2702e..000000000 --- a/src/ontogpt/clients/wikipedia_client.py +++ /dev/null @@ -1,41 +0,0 @@ -"""Pubmed Client.""" -from dataclasses import dataclass - -import requests -import wikipediaapi - - -@dataclass -class WikipediaClient: - """A client for Wikipedia articles.""" - - language: str = "en" - - def text(self, title: str) -> str: - """Get the text of a an article.""" - wiki = wikipediaapi.Wikipedia("ontogpt", self.language) - page = wiki.page(title) - - if page.exists(): - return page.text - else: - raise ValueError(f"Page {title} does not exist.") - - def search_wikipedia_articles(self, topic, results=10): - base_url = f"https://{self.language}.wikipedia.org/w/api.php" - params = { - "action": "query", - "list": "search", - "format": "json", - "srsearch": topic, - "srprop": "size|wordcount", - "srlimit": results, - "srinfo": "totalhits", - } - response = requests.get(base_url, params=params) - data = response.json() - - if data and "query" in data and "search" in data["query"]: - return data["query"]["search"] - else: - return [] diff --git a/src/ontogpt/conf/synonymizer-conf.yaml b/src/ontogpt/conf/synonymizer-conf.yaml deleted file mode 100644 index 6d4428df5..000000000 --- a/src/ontogpt/conf/synonymizer-conf.yaml +++ /dev/null @@ -1,25 +0,0 @@ -rules: - - type: NewSynonym - description: adding X as synonym for X-activity in GO - see_also: - - https://github.com/geneontology/go-ontology/issues/21978 - branches: - - molecular_function - match: "(.*)(activity)" - match_scope: "*" - replacement: "\\1" - tests: - - input: "ChS ABC lyase activity" - output: "ChS ABC lyase" - ontology: GO - - synonymizer: - the_rule: Remove parentheses bound info from the label. - match: r'\([^)]*\)' - match_scope: "*" - replacement: "" - - synonymizer: - the_rule: Synonymize foodon food products - match: "(.*) food product" - match_scope: "FOODON" - replacement: "\\1" - diff --git a/src/ontogpt/converters/__init__.py b/src/ontogpt/converters/__init__.py deleted file mode 100644 index f7c8b449a..000000000 --- a/src/ontogpt/converters/__init__.py +++ /dev/null @@ -1 +0,0 @@ -from ontogpt.converters.ontology_converter import OntologyConverter # noqa:F401 diff --git a/src/ontogpt/converters/ontology_converter.py b/src/ontogpt/converters/ontology_converter.py deleted file mode 100644 index 5efc4287c..000000000 --- a/src/ontogpt/converters/ontology_converter.py +++ /dev/null @@ -1,143 +0,0 @@ -"""Ontology converter.""" -import logging -from dataclasses import dataclass, field -from pathlib import Path -from typing import Dict, List, Optional - -from linkml_runtime import SchemaView -from linkml_runtime.utils.formatutils import camelcase -from oaklib.datamodels.obograph import Graph -from oaklib.datamodels.vocabulary import IS_A -from oaklib.interfaces.obograph_interface import OboGraphInterface - -from ontogpt.templates.halo import Ontology, OntologyElement - -this_path = Path(__file__).parent -logger = logging.getLogger(__name__) - - -@dataclass -class OntologyConverter: - """Converts an OAK ontology to an OntoGPT schema.""" - - adapter: OboGraphInterface = None - schemaview: SchemaView = None - fixed_slot_values: Dict[str, str] = field(default_factory=lambda: {}) - - def __post_init__(self): - templates_path = this_path.parent / "templates" - path_to_template = str(templates_path / "halo.yaml") - self.schemaview = SchemaView(path_to_template) - - def extract_seed_ontology(self, seeds: List[str], predicates: List[str]) -> Ontology: - """Extract an ontology from a given text. - - :param text: - :return: - """ - ancestors = list(set(list(self.adapter.ancestors(seeds, predicates, reflexive=True)))) - seed_graph = self.adapter.extract_graph(ancestors, predicates, dangling=False) - logger.info(len(seed_graph.nodes)) - seed_ontology = self.from_obograph(seed_graph) - return seed_ontology - - def from_adapter(self) -> Ontology: - """Convert an OAK adapter to an Ontology. - - :param adapter: - :return: - """ - graph = self.adapter.as_obograph() - return self.from_obograph(graph) - - def from_obograph(self, graph: Graph) -> Ontology: - """Convert an OBO Graph to an Ontology. - - :param graph: - :return: - """ - adapter = self.adapter - ontology = Ontology() - element_index = {} - node_to_element_name = {} - id2slot = {} - inverses = {} - for slot in self.schemaview.class_induced_slots(OntologyElement.__name__): - if slot.inverse: - inverses[slot.name] = slot.inverse - inverses[slot.inverse] = slot.name - if slot.slot_uri: - id2slot[slot.slot_uri] = slot - logger.info(list(id2slot.keys())) - logger.info(inverses) - for node in graph.nodes: - meta = node.meta - if not node.lbl: - continue - if not meta: - # logger.warning(f"Node {node.id} has no meta") - continue - element = OntologyElement( - name=self.node_to_name(node.id, node.lbl), - synonyms=[synonym.val for synonym in meta.synonyms], - description=meta.definition.val if meta.definition else None, - ) - for k, v in self.fixed_slot_values.items(): - setattr(element, k, v) - element_index[element.name] = element - node_to_element_name[node.id] = element.name - for edge in graph.edges: - if edge.pred == "is_a": - pred = IS_A - else: - try: - pred = adapter.uri_to_curie(edge.pred) - except: - pred = edge.pred - if pred not in id2slot: - continue - if edge.sub not in node_to_element_name: - continue - if edge.obj not in node_to_element_name: - continue - subject = node_to_element_name[edge.sub] - object = node_to_element_name[edge.obj] - slot = id2slot[pred] - getattr(element_index[subject], slot.name).append(object) - if slot.name in inverses: - inverse = inverses[slot.name] - getattr(element_index[object], inverse).append(subject) - for ldef in adapter.logical_definitions([node.id for node in graph.nodes]): - if ldef.definedClassId in node_to_element_name: - element = element_index[node_to_element_name[ldef.definedClassId]] - if not ldef.genusIds: - continue - if not ldef.restrictions: - continue - genus_elts = [node_to_element_name[g] for g in ldef.genusIds] - differentia = [ - f"{adapter.label(r.propertyId)} some {self.node_to_name(r.fillerId)}" - for r in ldef.restrictions - ] - element.equivalent_to = ( - f"{' and '.join(genus_elts)} and {' and '.join(differentia)}" - ) - logging.info(f"Equiv[{element.name}] = {element.equivalent_to}") - if ontology.elements is not None: - for element in element_index.values(): - ontology.elements.append(element) - return ontology - - def node_to_name(self, curie: str, label: Optional[str] = None) -> str: - """Convert a node to a name. - - :param curie: - :param label: - :return: - """ - if label is None: - label = self.adapter.label(curie) - if label is None: - logger.warning(f"Node {curie} has no label") - label = curie - return camelcase(label) diff --git a/src/ontogpt/engines/__init__.py b/src/ontogpt/engines/__init__.py deleted file mode 100644 index 989f83784..000000000 --- a/src/ontogpt/engines/__init__.py +++ /dev/null @@ -1 +0,0 @@ -from ontogpt.engines.resolver import create_engine # noqa diff --git a/src/ontogpt/engines/embedding_similarity_engine.py b/src/ontogpt/engines/embedding_similarity_engine.py deleted file mode 100644 index dee151eac..000000000 --- a/src/ontogpt/engines/embedding_similarity_engine.py +++ /dev/null @@ -1,100 +0,0 @@ -"""Similarity engine.""" -import logging -from dataclasses import dataclass -from typing import Iterable, List - -from oaklib import BasicOntologyInterface -from oaklib.datamodels.vocabulary import IS_A - -from ontogpt.clients import OpenAIClient -from ontogpt.engines.knowledge_engine import KnowledgeEngine - -logger = logging.getLogger(__name__) - - -@dataclass -class EmbeddingSimilarity: - subject_id: str = "" - subject_label: str = "" - object_id: str = "" - object_label: str = "" - embedding_cosine_similarity: float = None - object_rank_for_subject: int = None - - -@dataclass -class SimilarityEngine(KnowledgeEngine): - """Engine for generating synonyms.""" - - adapter: BasicOntologyInterface = None - autolabel: bool = True - definitions: bool = True - parents: bool = True - ancestors: bool = True - synonyms: bool = True - logical_definitions: bool = False - - def similarity(self, entity1: str, entity2: str) -> EmbeddingSimilarity: - """Get similarity.""" - t1 = self.entity_text(entity1) - t2 = self.entity_text(entity2) - client = OpenAIClient() - score = client.similarity(t1, t2) - obj = EmbeddingSimilarity( - subject_id=entity1, object_id=entity2, embedding_cosine_similarity=score - ) - if self.autolabel: - obj.subject_label = self.adapter.label(entity1) - obj.object_label = self.adapter.label(entity2) - return obj - - def search(self, entity1: str, entities: List[str]) -> Iterable[EmbeddingSimilarity]: - """Get similarity.""" - client = OpenAIClient() - t1 = self.entity_text(entity1) - sims = [] - for entity2 in entities: - t2 = self.entity_text(entity2) - score = client.similarity(t1, t2) - sim = EmbeddingSimilarity( - subject_id=entity1, object_id=entity2, embedding_cosine_similarity=score - ) - if self.autolabel: - sim.subject_label = self.adapter.label(entity1) - sim.object_label = self.adapter.label(entity2) - sims.append(sim) - sims = sorted(sims, key=lambda x: x.embedding_cosine_similarity, reverse=True) - for i, sim in enumerate(sims): - sim.object_rank_for_subject = i - yield from sims - - def entity_text(self, entity: str) -> str: - """Get text for an entity.""" - adapter = self.adapter - s = f"{adapter.label(entity)}" - if self.definitions: - s += f"\ndefinition: {adapter.definition(entity)}" - if self.parents: - parent_labels = [ - adapter.label(o) for _s, _p, o in adapter.relationships([entity], [IS_A]) - ] - s += f"\nparents: {'; '.join(parent_labels)}" - if self.ancestors: - ancestor_labels = [ - adapter.label(a) for a in adapter.ancestors([entity], [IS_A], reflexive=False) - ] - s += f"\nancestors: {'; '.join(ancestor_labels)}" - if self.synonyms: - s += f"\nsynonyms: {'; '.join(adapter.entity_aliases(entity))}" - if self.logical_definitions: - for ldef in adapter.logical_definitions(entity): - genus_labels = [adapter.label(g) for g in ldef.genusIds] - restriction_labels = [ - f"{adapter.label(r.propertyId)} {adapter.label(r.valueId)}" - for r in ldef.restrictions - ] - s += f"\nlogical definition: A {', '.join(genus_labels)} that\ - {' and '.join(restriction_labels)}" - s += f"\nlogical definitions: {'; '.join(adapter.logical_definitions(entity))}" - logger.info(f"Entity text for {entity}: {s}") - return s diff --git a/src/ontogpt/engines/generic_engine.py b/src/ontogpt/engines/generic_engine.py deleted file mode 100644 index 9c4d3eb05..000000000 --- a/src/ontogpt/engines/generic_engine.py +++ /dev/null @@ -1,74 +0,0 @@ -"""Synonym engine.""" -import logging -from copy import deepcopy -from dataclasses import dataclass -from pathlib import Path -from typing import Iterator, List, Union - -from jinja2 import Template -from pydantic import BaseModel - -from ontogpt.engines.knowledge_engine import KnowledgeEngine -from ontogpt.prompts.qa import GENERIC_QA_PROMPT - -logger = logging.getLogger(__name__) - -MAX_TOKENS = 300 - - -class Question(BaseModel): - name: str - question: str - original_question: str = "" - answer: str = "" - accepted_answer: str = "" - iteration: int = 0 - instructions: str = "" - prompt: str = "" - model: str = "" - - -class Instruction(BaseModel): - name: str - text: str = "" - template: str = "" - - -class QuestionCollection(BaseModel): - url: str = "" - questions: List[Question] = [] - instructions: List[Instruction] = [] - - -@dataclass -class GenericEngine(KnowledgeEngine): - def run( - self, - question_collection: QuestionCollection, - template_path: Union[str, Path] = "", - ) -> Iterator[Question]: - if template_path is None: - template_path = GENERIC_QA_PROMPT - if isinstance(template_path, Path): - template_path = str(template_path) - if isinstance(template_path, str): - # create a Jinja2 template object - with open(template_path) as file: - template_txt = file.read() - main_template = Template(template_txt) - for question in question_collection.questions: - for instruction in question_collection.instructions: - template = main_template - if instruction.template is not None: - template = Template(instruction.template) - prompt = template.render( - question=question.question, - instructions=instruction.text, - ) - payload = self.client.complete(prompt, max_tokens=MAX_TOKENS) - question_with_answer = deepcopy(question) - question_with_answer.answer = payload - question_with_answer.instructions = instruction.name - question_with_answer.prompt = prompt - question_with_answer.model = self.model - yield question_with_answer diff --git a/src/ontogpt/engines/gpt4all_engine.py b/src/ontogpt/engines/gpt4all_engine.py deleted file mode 100644 index 5df901c60..000000000 --- a/src/ontogpt/engines/gpt4all_engine.py +++ /dev/null @@ -1,601 +0,0 @@ -# type: ignore -""" -gpt4all-based knowledge extractor class. - -Like the SPIRES implementation seen in spires_engine.py, -this process constructs prompt-completions in which -a pseudo-YAML structure is requested and the YAML -structure corresponds to a template class. - -This class is intended for use with models -such as those released by GPT4All (https://gpt4all.io/). -""" -import logging -import re -from dataclasses import dataclass -from pathlib import Path -from typing import Any, Dict, Iterator, List, Optional, Tuple, Union - -import pydantic -import yaml -from linkml_runtime.linkml_model import ClassDefinition, SlotDefinition -from oaklib import BasicOntologyInterface - -from ontogpt.engines.knowledge_engine import ( - ANNOTATION_KEY_PROMPT, - ANNOTATION_KEY_PROMPT_SKIP, - EXAMPLE, - FIELD, - OBJECT, - KnowledgeEngine, - chunk_text, -) -from ontogpt.templates.core import ExtractionResult -from ontogpt.utils.gpt4all_runner import chain_gpt4all_model, set_up_gpt4all_model - -this_path = Path(__file__).parent - - -RESPONSE_ATOM = Union[str, "ResponseAtom"] -RESPONSE_DICT = Dict[FIELD, Union[RESPONSE_ATOM, List[RESPONSE_ATOM]]] - - -@dataclass -class GPT4AllEngine(KnowledgeEngine): - """Knowledge extractor for GGML chat models.""" - - sentences_per_window: Optional[int] = None - """If set, this will split the text into chains of sentences, - where this determines the maximum number of sentences per chain. - The results are then merged together.""" - - recurse: bool = True - """If true, then complex non-named entity objects are always recursively parsed. - If this is false AND the complex object is a pair, then token-based splitting is - instead used.""" - - loaded_model = None - """Loaded model object.""" - - def __post_init__(self): - self.loaded_model = set_up_gpt4all_model(self.model) - if self.template: - self.template_class = self._get_template_class(self.template) - if self.template_class: - logging.info(f"Using template {self.template_class.name}") - - def extract_from_text( - self, - text: str, - show_prompt: bool = False, - cls: ClassDefinition = None, - object: OBJECT = None, - ) -> ExtractionResult: - """ - Extract annotations from the given text. - - :param text: - :param cls: - :param object: optional stub object - :return: - """ - if self.sentences_per_window: - chunks = chunk_text(text, self.sentences_per_window) - extracted_object = None - for chunk in chunks: - raw_text = self._raw_extract(chunk, cls=cls, object=object) - logging.info(f"RAW TEXT: {raw_text}") - if show_prompt: - logging.info(f" PROVIDED PROMPT:\n{self.last_prompt}") - next_object = self.parse_completion_payload(raw_text, cls, object=object) - if extracted_object is None: - extracted_object = next_object - else: - for k, v in next_object.items(): - if isinstance(v, list): - extracted_object[k] += v - else: - if k not in extracted_object: - extracted_object[k] = v - else: - extracted_object[k] = v - else: - raw_text = self._raw_extract(text=text, cls=cls, object=object) - logging.info(f"RAW TEXT: {raw_text}") - if show_prompt: - logging.info(f" PROVIDED PROMPT:\n{self.last_prompt}") - extracted_object = self.parse_completion_payload(raw_text, cls=cls, object=object) - return ExtractionResult( - input_text=text, - raw_completion_output=raw_text, - prompt=self.last_prompt, - extracted_object=extracted_object, - named_entities=self.named_entities, - ) - - def _extract_from_text_to_dict(self, text: str, cls: ClassDefinition = None) -> RESPONSE_DICT: - raw_text = self._raw_extract(text=text, cls=cls) - return self._parse_response_to_dict(raw_text, cls) - - def iteratively_generate_and_extract( - self, - entity: str, - cache_path: Union[str, Path], - iteration_slots: List[str], - adapter: BasicOntologyInterface = None, - clear=False, - max_iterations=10, - prompt_template=None, - **kwargs, - ) -> Iterator[ExtractionResult]: - def _remove_parenthetical_context(s: str): - return re.sub(r"\(.*\)", "", s) - - iteration = 0 - if isinstance(cache_path, str): - cache_path = Path(cache_path) - if cache_path.exists() and not clear: - db = yaml.safe_load(cache_path.open()) - if "entities_in_queue" not in db: - db["entities_in_queue"] = [] - else: - db = {"processed_entities": [], "entities_in_queue": [], "results": []} - if entity not in db["processed_entities"]: - db["entities_in_queue"].append(entity) - if prompt_template is None: - prompt_template = ( - "Generate a comprehensive description of {entity}. " - + "The description should include the information on" - + " and ".join(iteration_slots) - + ".\n" - ) - while db["entities_in_queue"] and iteration < max_iterations: - iteration += 1 - next_entity = db["entities_in_queue"].pop(0) - logging.info(f"ITERATION {iteration}, entity={next_entity}") - # check if entity matches a curie pattern using re - if re.match(r"^[A-Z]+:[A-Z0-9]+$", next_entity): - curie = next_entity - next_entity = adapter.label(next_entity) - else: - curie = None - result = self.generate_and_extract( - next_entity, prompt_template=prompt_template, **kwargs - ) - if curie: - if result.extracted_object: - result.extracted_object.id = curie - db["results"].append(result) - db["processed_entities"].append(next_entity) - yield result - for s in iteration_slots: - # if s not in result.extracted_object: - # raise ValueError(f"Slot {s} not found in {result.extracted_object}") - vals = getattr(result.extracted_object, s, []) - if not vals: - logging.info("dead-end: no values found for slot") - continue - if not isinstance(vals, list): - vals = [vals] - for val in vals: - entity = val - - for ne in result.named_entities: - if ne.id == val: - entity = ne.label - if ne.id.startswith("AUTO"): - # Sometimes the value of some slots will lack - context = next_entity - context = re.sub(r"\(.*\)", "", context) - entity = f"{entity} ({context})" - else: - entity = ne.id - break - queue_deparenthesized = [ - _remove_parenthetical_context(e) for e in db["entities_in_queue"] - ] - if ( - entity not in db["processed_entities"] - and entity not in db["entities_in_queue"] - and _remove_parenthetical_context(entity) not in queue_deparenthesized - ): - db["entities_in_queue"].append(entity) - with open(cache_path, "w") as f: - # TODO: consider a more robust backend e.g. mongo - f.write(dump_minimal_yaml(db)) - - def generalize( - self, object: Union[pydantic.BaseModel, dict], examples: List[EXAMPLE] - ) -> ExtractionResult: - """ - Generalize the given examples. - - :param object: - :param examples: - :return: - """ - cls = self.template_class - sv = self.schemaview - prompt = "example:\n" - for example in examples: - prompt += f"{self.serialize_object(example)}\n\n" - prompt += "\n\n===\n\n" - if isinstance(object, pydantic.BaseModel): - object = object.dict() - for k, v in object.items(): - if v: - slot = sv.induced_slot(k, cls.name) - prompt += f"{k}: {self._serialize_value(v, slot)}\n" - logging.debug(f"PROMPT: {prompt}") - payload = self.client.complete(prompt) - prediction = self.parse_completion_payload(payload, object=object) - return ExtractionResult( - input_text=prompt, - raw_completion_output=payload, - # prompt=self.last_prompt, - results=[prediction], - named_entities=self.named_entities, - ) - - def map_terms(self, terms: List[str], ontology: str) -> Dict[str, List[str]]: - """ - Map the given terms to the given ontology. - - EXPERIMENTAL - - currently GPT-3 does not do so well with this task. - - :param terms: - :param ontology: - :return: - """ - # TODO: make a separate config - examples = { - "go": { - "nucleui": "nucleus", - "mitochondrial": "mitochondrion", - "signaling": "signaling pathway", - "cysteine biosynthesis": "cysteine biosynthetic process", - "alcohol dehydrogenase": "alcohol dehydrogenase activity", - }, - "uberon": { - "feet": "pes", - "forelimb, left": "left forelimb", - "hippocampus": "Ammons horn", - }, - } - ontology = ontology.lower() - if ontology in examples: - example = examples[ontology] - else: - example = examples["uberon"] - prompt = "Normalize the following semicolon separated\ - list of terms to the {ontology.upper()} ontology\n\n" - prompt += "For example:\n\n" - for k, v in example.items(): - prompt += f"{k}: {v}\n" - prompt += "===\n\nTerms:" - prompt += "; ".join(terms) - prompt += "===\n\n" - payload = self.client.complete(prompt) - # outer parse - for sep in ["\n", "; "]: - results = payload.split(sep) - if len(results) > len(best_results): - best_results = results - - def normalize(s: str) -> str: - s = s.strip() - s.replace("_", " ") - return s.lower() - - mappings = {} - for result in best_results: - if ":" not in result: - logging.error(f"Count not parse result: {result}") - continue - k, v = result.strip().split(":", 1) - k = k.strip() - v = v.strip() - for t in terms: - if normalize(t) == normalize(k): - mappings[t] = v - break - for t in terms: - if t not in mappings: - logging.warning(f"Could not map term: {t}") - return mappings - - def serialize_object(self, example: EXAMPLE, cls: ClassDefinition = None) -> str: - if cls is None: - cls = self.template_class - if isinstance(example, str): - return example - if isinstance(example, pydantic.BaseModel): - example = example.dict() - lines = [] - sv = self.schemaview - for k, v in example.items(): - if not v: - continue - slot = sv.induced_slot(k, cls.name) - v_serialized = self._serialize_value(v, slot) - lines.append(f"{k}: {v_serialized}") - return "\n".join(lines) - - def _serialize_value(self, val: Any, slot: SlotDefinition) -> str: - if val is None: - return "" - if isinstance(val, list): - return "; ".join([self._serialize_value(v, slot) for v in val if v]) - if isinstance(val, dict): - return " - ".join([self._serialize_value(v, slot) for v in val.values() if v]) - sv = self.schemaview - if slot.range in sv.all_classes(): - if self.labelers: - labelers = list(self.labelers) - else: - labelers = [] - labelers += self.get_annotators(sv.get_class(slot.range)) - if labelers: - for labeler in labelers: - label = labeler.label(val) - if label: - return label - return val - - def _raw_extract(self, text, cls: ClassDefinition = None, object: OBJECT = None) -> str: - """ - Extract annotations from the given text. - - :param text: - :return: - """ - prompt = self.get_completion_prompt(cls, text, object=object) - self.last_prompt = prompt - payload = chain_gpt4all_model(self.loaded_model, prompt) - return payload - - def get_completion_prompt( - self, cls: ClassDefinition = None, text: str = "", object: OBJECT = None - ) -> str: - """Get the prompt for the given template.""" - if cls is None: - cls = self.template_class - if not text or ("\n" in text or len(text) > 60): - prompt = ( - "From the text below, extract the following entities in the following format:\n\n" - ) - else: - prompt = "Split the following piece of text into fields in the following format:\n\n" - for slot in self.schemaview.class_induced_slots(cls.name): - if ANNOTATION_KEY_PROMPT_SKIP in slot.annotations: - continue - if ANNOTATION_KEY_PROMPT in slot.annotations: - slot_prompt = slot.annotations[ANNOTATION_KEY_PROMPT].value - elif slot.description: - slot_prompt = slot.description - else: - if slot.multivalued: - slot_prompt = f"semicolon-separated list of {slot.name}s" - else: - slot_prompt = f"the value for {slot.name}" - if slot.range in self.schemaview.all_enums(): - enum_def = self.schemaview.get_enum(slot.range) - pvs = [str(k) for k in enum_def.permissible_values.keys()] - slot_prompt += f"Must be one of: {', '.join(pvs)}" - prompt += f"{slot.name}: <{slot_prompt}>\n" - # prompt += "Do not answer if you don't know\n\n" - prompt = f"{prompt}\n\nText:\n{text}\n\n===\n\n" - if object: - if cls is None: - cls = self.template_class - if isinstance(object, pydantic.BaseModel): - object = object.dict() - for k, v in object.items(): - if v: - slot = self.schemaview.induced_slot(k, cls.name) - prompt += f"{k}: {self._serialize_value(v, slot)}\n" - return prompt - - def _parse_response_to_dict( - self, results: str, cls: ClassDefinition = None - ) -> Optional[RESPONSE_DICT]: - """ - Parse the pseudo-YAML response from OpenAI into a dictionary object. - - E.g. - - foo: a; b; c - - becomes - - {"foo": ["a", "b", "c"]} - - :param results: - :return: - """ - lines = results.splitlines() - ann = {} - promptable_slots = self.promptable_slots(cls) - for line in lines: - line = line.strip() - if not line: - continue - if ":" not in line: - if len(promptable_slots) == 1: - slot = promptable_slots[0] - logging.warning( - f"Coercing to YAML-like with key {slot.name}: Original line: {line}" - ) - line = f"{slot.name}: {line}" - else: - logging.error(f"Line '{line}' does not contain a colon; ignoring") - return - r = self._parse_line_to_dict(line, cls) - if r is not None: - field, val = r - ann[field] = val - return ann - - def _parse_line_to_dict( - self, line: str, cls: ClassDefinition = None - ) -> Optional[Tuple[FIELD, RESPONSE_ATOM]]: - if cls is None: - cls = self.template_class - sv = self.schemaview - # each line is a key-value pair - logging.info(f"PARSING LINE: {line}") - field, val = line.split(":", 1) - # Field nornalization: - # The LLML may mutate the output format somewhat, - # randomly pluralizing or replacing spaces with underscores - field = field.lower().replace(" ", "_") - cls_slots = sv.class_slots(cls.name) - slot = None - if field in cls_slots: - slot = sv.induced_slot(field, cls.name) - else: - if field.endswith("s"): - field = field[:-1] - if field in cls_slots: - slot = sv.induced_slot(field, cls.name) - if not slot: - logging.error(f"Cannot find slot for {field} in {line}") - # raise ValueError(f"Cannot find slot for {field} in {line}") - return - if not val: - msg = f"Empty value in key-value line: {line}" - if slot.required: - raise ValueError(msg) - if slot.recommended: - logging.warning(msg) - return - inlined = slot.inlined - slot_range = sv.get_class(slot.range) - if not inlined: - if slot.range in sv.all_classes(): - inlined = sv.get_identifier_slot(slot_range.name) is None - val = val.strip() - if slot.multivalued: - vals = [v.strip() for v in val.split(";")] - else: - vals = [val] - vals = [val for val in vals if val] - logging.debug(f"SLOT: {slot.name} INL: {inlined} VALS: {vals}") - if inlined: - transformed = False - slots_of_range = sv.class_slots(slot_range.name) - if self.recurse or len(slots_of_range) > 2: - vals = [self._extract_from_text_to_dict(v, slot_range) for v in vals] - else: - for sep in [" - ", ":", "/", "*", "-"]: - if all([sep in v for v in vals]): - vals = [dict(zip(slots_of_range, v.split(sep, 1))) for v in vals] - for v in vals: - for k in v.keys(): - v[k] = v[k].strip() - transformed = True - break - if not transformed: - logging.warning(f"Did not find separator in {vals} for line {line}") - return - # transform back from list to single value if not multivalued - if slot.multivalued: - final_val = vals - else: - if len(vals) != 1: - logging.error(f"Expected 1 value for {slot.name} in '{line}' but got {vals}") - final_val = vals[0] - return field, final_val - - def parse_completion_payload( - self, results: str, cls: ClassDefinition = None, object: dict = None - ) -> pydantic.BaseModel: - """ - Parse the completion payload into a pydantic class. - - :param results: - :param cls: - :param object: stub object - :return: - """ - raw = self._parse_response_to_dict(results, cls) - logging.debug(f"RAW: {raw}") - if object: - raw = {**object, **raw} - return self.ground_annotation_object(raw, cls) - - def ground_annotation_object( - self, ann: RESPONSE_DICT, cls: ClassDefinition = None - ) -> Optional[pydantic.BaseModel]: - """Ground the direct parse of the OpenAI payload. - - The raw openAI payload is a YAML-like string, which is parsed to - a response dictionary. - - This dictionary is then grounded, using this method - - :param ann: Raw annotation object - :param cls: schema class the ground object should instantiate - :return: Grounded annotation object - """ - logging.debug(f"Grounding annotation object {ann}") - if cls is None: - cls = self.template_class - sv = self.schemaview - new_ann = {} - if ann is None: - logging.error(f"Cannot ground None annotation, cls={cls.name}") - return - for field, vals in ann.items(): - if isinstance(vals, list): - multivalued = True - else: - multivalued = False - vals = [vals] - slot = sv.induced_slot(field, cls.name) - rng_cls = sv.get_class(slot.range) - enum_def = None - if slot.range: - if slot.range in self.schemaview.all_enums(): - enum_def = self.schemaview.get_enum(slot.range) - new_ann[field] = [] - for val in vals: - if not val: - continue - if isinstance(val, tuple): - # special case for pairs - sub_slots = sv.class_induced_slots(rng_cls.name) - obj = {} - for i in range(0, len(val)): - sub_slot = sub_slots[i] - sub_rng = sv.get_class(sub_slot.range) - if not sub_rng: - logging.error(f"Cannot find range for {sub_slot.name}") - result = self.normalize_named_entity(val[i], sub_slot.range) - obj[sub_slot.name] = result - elif isinstance(val, dict): - # recurse - obj = self.ground_annotation_object(val, rng_cls) - else: - obj = self.normalize_named_entity(val, slot.range) - if enum_def: - found = False - logging.info(f"Looking for {obj} in {enum_def.name}") - for k, _pv in enum_def.permissible_values.items(): - if obj.lower() == k.lower(): - obj = k - found = True - break - if not found: - logging.info(f"Cannot find enum value for {obj} in {enum_def.name}") - obj = None - if multivalued: - new_ann[field].append(obj) - else: - new_ann[field] = obj - logging.debug(f"Creating object from dict {new_ann}") - logging.info(new_ann) - py_cls = self.template_module.__dict__[cls.name] - return py_cls(**new_ann) diff --git a/src/ontogpt/engines/halo_engine.py b/src/ontogpt/engines/halo_engine.py deleted file mode 100644 index a84b91b7b..000000000 --- a/src/ontogpt/engines/halo_engine.py +++ /dev/null @@ -1,524 +0,0 @@ -# type: ignore -""" -HALO. - -Originally used code-davinci-002, which has since been supplanted by -gpt chat models. - -""" -import logging -from dataclasses import dataclass, field -from pathlib import Path -from typing import Any, Dict, List, Optional, Set - -import openai -import pydantic -import tiktoken -import yaml -from linkml.utils.schema_fixer import uncamel -from linkml_runtime.utils.formatutils import camelcase -from oaklib.datamodels.obograph import Graph -from oaklib.datamodels.vocabulary import IS_A -from oaklib.interfaces.obograph_interface import OboGraphInterface -from tiktoken import Encoding - -from ontogpt.clients import OpenAIClient -from ontogpt.engines.knowledge_engine import FIELD, KnowledgeEngine -from ontogpt.io.yaml_wrapper import dump_minimal_yaml -from ontogpt.templates.halo import Ontology, OntologyElement - -this_path = Path(__file__).parent -logger = logging.getLogger(__name__) - - -ELEMENT_NAME = str - -INSTRUCTIONS = """ -## Instructions: -## Add an additional element to the YAML below, which is for elements -## in an industrial ontology. Complete as far as possible the following -## fields: -""" - -# TODO: Needs rewrite - or consider this a different variation in its -# own right, as CurateGPT is the reference implementation of HALO - - -class StructuredPrompt(pydantic.BaseModel): - header: str = "" - body: str = "" - main_prompt: str = "" - - @property - def text(self) -> str: - return f"{self.header}\n{self.body}\n{self.main_prompt}" - - -@dataclass -class HALOEngine(KnowledgeEngine): - """Engine for Hallucinating Latent Ontologies.""" - - engine: str = "gpt-3.5-turbo" - ontology: Ontology = None - traverse_slots: List[FIELD] = field( - default_factory=lambda: ["subtypes", "parts", "subclass_of", "part_of"] - ) - fixed_slot_values: Optional[Dict[str, str]] = None - adapter: OboGraphInterface = None - visited: Set[ELEMENT_NAME] = field(default_factory=lambda: set()) - candidates: List[ELEMENT_NAME] = None - always_extend: bool = False - expand_horizon: bool = False - - element_scores: Dict[ELEMENT_NAME, float] = field(default_factory=lambda: {}) - """Ranks each element by estimated informativeness for training.""" - - tokenizer_encoding: Encoding = field( - default_factory=lambda: tiktoken.get_encoding("cl100k_base") - ) - - def __post_init__(self): - self.template_class = self._get_template_class("halo.OntologyElement") - self.client = OpenAIClient(model=self.engine) - self.api_key = self._get_openai_api_key() - openai.api_key = self.api_key - - def seed(self, seed_ontology: Ontology): - """Seed the engine with an initial ontology. - - :param seed_ontology: - :return: - """ - self.ontology = seed_ontology - if not self.expand_horizon: - self.visited = {x.name for x in self.ontology.elements} - - def seed_from_file(self, file_path: str) -> Ontology: - """Seed the engine with an initial ontology from a file. - - :param file_path: - :return: - """ - ontology = Ontology(**yaml.safe_load(open(file_path))) - self.seed(ontology) - logger.info(f"Seeded with {len(ontology.elements)} elements") - return ontology - - def hallucinate( - self, seed_elements: List[ELEMENT_NAME] = None, num_iterations=10 - ) -> List[OntologyElement]: - """Run the HALO engine for a given number of iterations. - - Each iteration will expand the initial seed ontology. - - :param num_iterations: - :return: - """ - added = [] - if seed_elements: - for e in seed_elements: - added.append(self.hallucinate_element(e)) - for i in range(num_iterations): - logger.info(f"Running HALO iteration {i}") - elt = self.hallucinate_once() - if elt: - added.append(elt) - else: - break - return added - - def hallucinate_once(self) -> Optional[OntologyElement]: - """Run the HALO engine once. - - Finds a candidate element to expand, - then runs HALO on that element by generating - a prompt for it. - - :return: - """ - candidate_elements = self.get_candidate_elements() - logger.info(f"Found {len(candidate_elements)} candidate elements") - logger.info(f"Candidate elements: {candidate_elements} // visited={self.visited}") - if not candidate_elements: - return None - element = candidate_elements[0] - logger.info(f"Selected element {element}") - return self.hallucinate_element(element) - - def get_candidate_elements(self) -> List[ELEMENT_NAME]: - """Get candidate elements to expand. - - Has side effect of removing candidate cache if visited - :return: - """ - if self.candidates is None: - # TODO: exclude seed set that is not on the horizon - self.candidates = [x.name for x in self.ontology.elements] - self.candidates = [c for c in self.candidates if c not in self.visited] - return self.candidates - - def extend_candidates(self, elements: List[ELEMENT_NAME]) -> List[ELEMENT_NAME]: - """Extend candidates by all entities in the signature of the specified elements. - - :return: - """ - visited = self.visited - if not self.traverse_slots: - raise ValueError("No slots to traverse") - for element_name in elements: - visited.add(element_name) - logger.info(f"Extending candidates for {element_name}; visited={visited}") - element = self.get_element(element_name) - for slot_name in self.traverse_slots: - refs = getattr(element, slot_name) - for ref in refs: - if ref not in visited: - if not self.candidates: - self.candidates = [] - self.candidates.append(ref) - logger.info(f" -- Added {ref} to candidates") - return self.candidates - - def get_element(self, element_name: ELEMENT_NAME) -> Optional[OntologyElement]: - """Get an element by name. - - :param element_name: - :return: - """ - for e in self.ontology.elements: - if e.name == element_name: - return e - - def old_get_candidate_elements(self) -> List[ELEMENT_NAME]: - """Get candidate elements for HALO. - - :return: - """ - candidate_elements = set() - visited = self.visited - if not self.traverse_slots: - raise ValueError("No slots to traverse") - for element in self.ontology.elements: - all_slots_have_refs = True - for slot_name in self.traverse_slots: - refs = getattr(element, slot_name) - if len(refs) == 0 and element.name not in visited: - candidate_elements.add(element.name) - all_slots_have_refs = False - for ref in refs: - if ref not in visited: - candidate_elements.add(ref) - visited.add(ref) - if all_slots_have_refs and not self.always_extend: - visited.add(element.name) - return list(candidate_elements) - - def hallucinate_element(self, element: ELEMENT_NAME) -> OntologyElement: - """Generate an ontology element based on its name. - - :param element: example: LeftDigit1OfHand - :return: - """ - logger.info(f"Hallucinating element {element}") - example_elements = self.get_example_elements(element) - example_element_names = [x.name for x in example_elements] - logger.info(f"Found {len(example_elements)} example elements: {example_element_names}") - # TODO: set bound dynamically - prompt = self.generate_prompt(element, example_elements[0:10]) - # logger.info(f"Generated prompt: {prompt}") - payload = self.client.complete(prompt.text) - objs = self.integrate_payload(prompt, payload) - logger.info(f"Integrated {len(objs)} objects") - obj = objs[0] - self.extend_candidates([obj.name]) - return obj - - def get_example_elements(self, element: ELEMENT_NAME) -> List[OntologyElement]: - """Get example elements for HALO. - - :param element: - :return: - """ - name = uncamel(element) - toks = set(self.tokenizer_encoding.encode(name)) - score_element_pairs = [(self.get_element_score(e, toks), e) for e in self.ontology.elements] - score_element_pairs.sort(key=lambda x: x[0], reverse=True) - logger.info(f"Scores[{element}: {[x for x, _ in score_element_pairs]}") - logger.info(f"Sorted elements: {score_element_pairs}") - return [x for _, x in score_element_pairs] - - def get_element_score(self, element: OntologyElement, tokens: Set[int]) -> float: - """Calculate a score for an element based on how informative it is for few-shot learning. - - :param element: - :param tokens: tokenized form of the element name - :return: - """ - element_name = element.name - if element_name in self.element_scores: - score = self.element_scores[element_name] - else: - score = 0 - for _, v in element.dict().items(): - if v: - score += 1 - self.element_scores[element_name] = score - element_tokens = set(self.tokenizer_encoding.encode(element_name)) - jaccard = len(tokens.intersection(element_tokens)) / len(tokens.union(element_tokens)) - return score / 100 + jaccard - - def generate_prompt( - self, seed_element: ELEMENT_NAME, example_elements: List[OntologyElement] - ) -> StructuredPrompt: - """Generate a prompt for HALO. - - :param seed_element: - :param example_elements: - :return: - """ - prompt = StructuredPrompt() - prompt.header = INSTRUCTIONS - for slot in self.schemaview.class_induced_slots("OntologyElement"): - desc = slot.description - if not desc: - logger.warning(f"No description for slot {slot.name}") - desc = "" - prompt.header += f"## {slot.name}: {desc}\n" - prompt.body = "\n## Examples:\n" - for element in example_elements: - prompt.body += dump_minimal_yaml(element) - stub_object = { - "name": seed_element, - } - for k, v in self.fixed_slot_values.items(): - stub_object[k] = v - prompt.main_prompt = yaml.dump([stub_object]) - logger.info( - f"Generated prompt: {len(prompt.text)} = {len(prompt.header)} +\ - {len(prompt.body)} + {len(prompt.main_prompt)}" - ) - return prompt - - def integrate_payload( - self, prompt: StructuredPrompt, payload: Dict[str, Any] - ) -> List[OntologyElement]: - """Integrate the payload from HALO into the ontology. - - :param payload: - :param element: - :return: - """ - effective_payload = prompt.main_prompt + payload - # logger.info(f"## EFFECTIVE: {effective_payload}") - try: - objs = yaml.safe_load(effective_payload) - except: - # codex does not give reliable YAML - objs = self.parse_what_you_can(effective_payload) - logger.info(f"## PARSED: {len(objs)}") - elt = self.integrate_object(objs[0]) - logger.info(f" * INTEGRATED: {elt}") - return [elt] - - def integrate_object(self, obj: Dict[str, Any], strict=True) -> Optional[OntologyElement]: - obj = self.repair_dict(obj) - try: - elt = OntologyElement(**obj) - except pydantic.ValidationError as e: - logger.warning(f"## COULD NOT PARSE: {obj} /// {e}") - if strict: - raise e - return None - self.add_element(elt) - return elt - - def repair_dict(self, obj: dict) -> dict: - slots = self.schemaview.class_slots("OntologyElement") - nu_obj = {} - for k, v in obj.items(): - if k not in slots: - logger.warning(f"Could not find slot {k} in slots") - continue - slot = self.schemaview.induced_slot(k, "OntologyElement") - if slot.multivalued and not isinstance(v, list): - logger.warning(f"Coercing {v} to list") - v = [v] - elif not slot.multivalued and isinstance(v, list): - logger.warning(f"Coercing {v} len {len(v)} to single value") - v = v[0] - nu_obj[k] = v - return nu_obj - - def old_integrate_payload(self, prompt: StructuredPrompt, payload: Dict[str, Any]): - """Integrate the payload from HALO into the ontology. - - :param payload: - :param element: - :return: - """ - allowed_slots = self.schemaview.class_slots("OntologyElement") - effective_payload = prompt.main_prompt + payload - # logger.info(f"## EFFECTIVE: {effective_payload}") - try: - objs = yaml.safe_load(effective_payload) - except: - # codex does not give reliable YAML - objs = self.parse_what_you_can(effective_payload) - logger.info(f"## PARSED: {len(objs)}") - added = [] - n = 0 - for obj in objs: - n += 1 - slots_populated = [k for k, v in obj.items() if v] - diff = set(slots_populated).difference(allowed_slots) - if diff: - logger.info(f"## SKIPPING SLOTS {diff}") - obj = {k: v for k, v in obj.items() if k in allowed_slots} - try: - elt = OntologyElement(**obj) - except pydantic.ValidationError as e: - logger.info(f"## COULD NOT PARSE: {obj} /// {e}") - return added - logger.info(f"Elt: {elt.name} // {slots_populated} // {obj}") - if self.add_element(elt): - logger.info(f" - Added {elt.name}") - added.append(elt) - else: - logger.info(f" - already got {elt.name}") - if n == 1: - logger.error(f"Failed to add first element {elt.name}") - logger.info(f"Added {len(added)} elements") - return added - - def parse_what_you_can(self, yaml_str: str) -> List[Dict[str, Any]]: - """Parse as much of the YAML as possible. - - :param yaml_str: - :return: - """ - objs = None - chunk = "" - for line in yaml_str.split("\n"): - chunk += line + "\n" - try: - objs = yaml.safe_load(chunk) - except: - pass - if objs is None: - raise ValueError(f"Could not parse YAML {yaml_str}") - return objs - - def add_element(self, element: OntologyElement) -> bool: - """Add an element to the ontology. - - :param obj: - :return: - """ - existing = self.get_element(element.name) - if existing: - return False - self.ontology.elements.append(element) - return True - - def xxextract_seed_ontology(self, seeds: List[str], predicates: List[str]) -> Ontology: - """Extract an ontology from a given text. - - :param text: - :return: - """ - ancestors = list(set(list(self.adapter.ancestors(seeds, predicates, reflexive=True)))) - seed_graph = self.adapter.extract_graph(ancestors, predicates, dangling=False) - logger.info(len(seed_graph.nodes)) - seed_ontology = self.ontology_from_obograph(seed_graph) - return seed_ontology - - def xxontology_from_obograph(self, graph: Graph) -> Ontology: - """Convert an OBO Graph to an Ontology. - - :param graph: - :return: - """ - adapter = self.adapter - ontology = Ontology() - element_index = {} - node_to_element_name = {} - id2slot = {} - inverses = {} - for slot in self.schemaview.class_induced_slots(OntologyElement.__name__): - if slot.inverse: - inverses[slot.name] = slot.inverse - inverses[slot.inverse] = slot.name - if slot.slot_uri: - id2slot[slot.slot_uri] = slot - logger.info(list(id2slot.keys())) - logger.info(inverses) - for node in graph.nodes: - meta = node.meta - if not node.lbl: - continue - if not meta: - # logger.warning(f"Node {node.id} has no meta") - continue - element = OntologyElement( - name=self.node_to_name(node.id, node.lbl), - synonyms=[synonym.val for synonym in meta.synonyms], - description=meta.definition.val if meta.definition else None, - ) - for k, v in self.fixed_slot_values.items(): - setattr(element, k, v) - element_index[element.name] = element - node_to_element_name[node.id] = element.name - for edge in graph.edges: - if edge.pred == "is_a": - pred = IS_A - else: - try: - pred = adapter.uri_to_curie(edge.pred) - except: - pred = edge.pred - if pred not in id2slot: - continue - if edge.sub not in node_to_element_name: - continue - if edge.obj not in node_to_element_name: - continue - subject = node_to_element_name[edge.sub] - object = node_to_element_name[edge.obj] - slot = id2slot[pred] - getattr(element_index[subject], slot.name).append(object) - if slot.name in inverses: - inverse = inverses[slot.name] - getattr(element_index[object], inverse).append(subject) - for ldef in adapter.logical_definitions([node.id for node in graph.nodes]): - if ldef.definedClassId in node_to_element_name: - element = element_index[node_to_element_name[ldef.definedClassId]] - if not ldef.genusIds: - continue - if not ldef.restrictions: - continue - genus_elts = [node_to_element_name[g] for g in ldef.genusIds] - differentia = [ - f"{adapter.label(r.propertyId)} some {self.node_to_name(r.fillerId)}" - for r in ldef.restrictions - ] - element.equivalent_to = ( - f"{' and '.join(genus_elts)} and {' and '.join(differentia)}" - ) - logger.info(f"Equiv[{element.name}] = {element.equivalent_to}") - for element in element_index.values(): - ontology.elements.append(element) - return ontology - - def xxnode_to_name(self, curie: str, label: Optional[str] = None) -> str: - """Convert a node to a name. - - :param curie: - :param label: - :return: - """ - if label is None: - label = self.adapter.label(curie) - if label is None: - logger.warning(f"Node {curie} has no label") - label = curie - return camelcase(label) diff --git a/src/ontogpt/engines/hfhub_engine.py b/src/ontogpt/engines/hfhub_engine.py deleted file mode 100644 index 7cccb3c94..000000000 --- a/src/ontogpt/engines/hfhub_engine.py +++ /dev/null @@ -1,509 +0,0 @@ -# type: ignore -""" -HuggingFace Hub-based knowledge extractor class. - -Like the SPIRES implementation seen in spires_engine.py, -this process constructs prompt-completions in which -a pseudo-YAML structure is requested and the YAML -structure corresponds to a template class. - -This class is intended for use with HuggingFace Hub -models, specifically text-generation models. -Find them here: -https://huggingface.co/models?pipeline_tag=text-generation -""" -import logging -from dataclasses import dataclass -from pathlib import Path -from typing import Any, Dict, List, Optional, Tuple, Union - -import pydantic -from linkml_runtime.linkml_model import ClassDefinition, SlotDefinition - -from ontogpt.clients.hfhub_client import HFHubClient -from ontogpt.engines.knowledge_engine import ( - ANNOTATION_KEY_PROMPT, - ANNOTATION_KEY_PROMPT_SKIP, - EXAMPLE, - FIELD, - OBJECT, - KnowledgeEngine, - chunk_text, -) -from ontogpt.templates.core import ExtractionResult - -this_path = Path(__file__).parent - - -RESPONSE_ATOM = Union[str, "ResponseAtom"] -RESPONSE_DICT = Dict[FIELD, Union[RESPONSE_ATOM, List[RESPONSE_ATOM]]] - - -@dataclass -class HFHubEngine(KnowledgeEngine): - """Knowledge extractor for HuggingFace Hub models.""" - - sentences_per_window: Optional[int] = None - """If set, this will split the text into chains of sentences, - where this determines the maximum number of sentences per chain. - The results are then merged together.""" - - recurse: bool = True - """If true, then complex non-named entity objects are always recursively parsed. - If this is false AND the complex object is a pair, then token-based splitting is - instead used.""" - - api_client = HFHubClient() - """API client for HF Hub.""" - - local_model = None - """The name of the HF Hub model as per its repo, e.g., gpt2 or databricks/dolly-v2-3b""" - - loaded_model = None - """Langchain loaded model object.""" - - def __post_init__(self, local_model): - self.local_model = local_model - logging.info(f"Using HuggingFace model {self.local_model}") - self.loaded_model = self.api_client.get_model(self.local_model) - if self.template: - self.template_class = self._get_template_class(self.template) - if self.template_class: - logging.info(f"Using template {self.template_class.name}") - - def extract_from_text( - self, text: str, cls: ClassDefinition = None, object: OBJECT = None - ) -> ExtractionResult: - """ - Extract annotations from the given text. - - :param text: - :param cls: - :param object: optional stub object - :return: - """ - if self.sentences_per_window: - chunks = chunk_text(text, self.sentences_per_window) - extracted_object = None - for chunk in chunks: - raw_text = self._raw_extract(chunk, cls, object=object) - logging.info(f"RAW TEXT: {raw_text}") - next_object = self.parse_completion_payload(raw_text, cls, object=object) - if extracted_object is None: - extracted_object = next_object - else: - for k, v in next_object.items(): - if isinstance(v, list): - extracted_object[k] += v - else: - if k not in extracted_object: - extracted_object[k] = v - else: - extracted_object[k] = v - else: - raw_text = self._raw_extract(text, cls, object=object) - logging.info(f"RAW TEXT: {raw_text}") - extracted_object = self.parse_completion_payload(raw_text, cls, object=object) - return ExtractionResult( - input_text=text, - raw_completion_output=raw_text, - prompt=self.last_prompt, - extracted_object=extracted_object, - named_entities=self.named_entities, - ) - - def _extract_from_text_to_dict(self, text: str, cls: ClassDefinition = None) -> RESPONSE_DICT: - raw_text = self._raw_extract(text, cls) - return self._parse_response_to_dict(raw_text, cls) - - def generalize( - self, object: Union[pydantic.BaseModel, dict], examples: List[EXAMPLE] - ) -> ExtractionResult: - """ - Generalize the given examples. - - :param object: - :param examples: - :return: - """ - cls = self.template_class - sv = self.schemaview - prompt = "example:\n" - for example in examples: - prompt += f"{self.serialize_object(example)}\n\n" - prompt += "\n\n===\n\n" - if isinstance(object, pydantic.BaseModel): - object = object.dict() - for k, v in object.items(): - if v: - slot = sv.induced_slot(k, cls.name) - prompt += f"{k}: {self._serialize_value(v, slot)}\n" - logging.debug(f"PROMPT: {prompt}") - payload = self.client.complete(prompt) - prediction = self.parse_completion_payload(payload, object=object) - return ExtractionResult( - input_text=prompt, - raw_completion_output=payload, - # prompt=self.last_prompt, - results=[prediction], - named_entities=self.named_entities, - ) - - def map_terms(self, terms: List[str], ontology: str) -> Dict[str, List[str]]: - """ - Map the given terms to the given ontology. - - :param terms: - :param ontology: - :return: - """ - # TODO: make a separate config - examples = { - "go": { - "nucleui": "nucleus", - "mitochondrial": "mitochondrion", - "signaling": "signaling pathway", - "cysteine biosynthesis": "cysteine biosynthetic process", - "alcohol dehydrogenase": "alcohol dehydrogenase activity", - }, - "uberon": { - "feet": "pes", - "forelimb, left": "left forelimb", - "hippocampus": "Ammons horn", - }, - } - ontology = ontology.lower() - if ontology in examples: - example = examples[ontology] - else: - example = examples["uberon"] - prompt = "Normalize the following semicolon separated\ - list of terms to the {ontology.upper()} ontology\n\n" - prompt += "For example:\n\n" - for k, v in example.items(): - prompt += f"{k}: {v}\n" - prompt += "===\n\nTerms:" - prompt += "; ".join(terms) - prompt += "===\n\n" - payload = self.client.complete(prompt) - # outer parse - for sep in ["\n", "; "]: - results = payload.split(sep) - if len(results) > len(best_results): - best_results = results - - def normalize(s: str) -> str: - s = s.strip() - s.replace("_", " ") - return s.lower() - - mappings = {} - for result in best_results: - if ":" not in result: - logging.error(f"Count not parse result: {result}") - continue - k, v = result.strip().split(":", 1) - k = k.strip() - v = v.strip() - for t in terms: - if normalize(t) == normalize(k): - mappings[t] = v - break - for t in terms: - if t not in mappings: - logging.warning(f"Could not map term: {t}") - return mappings - - def serialize_object(self, example: EXAMPLE, cls: ClassDefinition = None) -> str: - if cls is None: - cls = self.template_class - if isinstance(example, str): - return example - if isinstance(example, pydantic.BaseModel): - example = example.dict() - lines = [] - sv = self.schemaview - for k, v in example.items(): - if not v: - continue - slot = sv.induced_slot(k, cls.name) - v_serialized = self._serialize_value(v, slot) - lines.append(f"{k}: {v_serialized}") - return "\n".join(lines) - - def _serialize_value(self, val: Any, slot: SlotDefinition) -> str: - if val is None: - return "" - if isinstance(val, list): - return "; ".join([self._serialize_value(v, slot) for v in val if v]) - if isinstance(val, dict): - return " - ".join([self._serialize_value(v, slot) for v in val.values() if v]) - sv = self.schemaview - if slot.range in sv.all_classes(): - if self.labelers: - labelers = list(self.labelers) - else: - labelers = [] - labelers += self.get_annotators(sv.get_class(slot.range)) - if labelers: - for labeler in labelers: - label = labeler.label(val) - if label: - return label - return val - - def _raw_extract(self, text, cls: ClassDefinition = None, object: OBJECT = None) -> str: - """ - Extract annotations from the given text. - - :param text: - :return: - """ - prompt = self.get_completion_prompt(cls, text, object=object) - self.last_prompt = prompt - payload = self.api_client.query_hf_model(self.loaded_model, prompt) - return payload - - def get_completion_prompt( - self, cls: ClassDefinition = None, text: str = "", object: OBJECT = None - ) -> str: - """Get the prompt for the given template.""" - if cls is None: - cls = self.template_class - if not text or ("\n" in text or len(text) > 60): - prompt = ( - "From the text below, extract the following entities in the following format:\n\n" - ) - else: - prompt = "Split the following piece of text into fields in the following format:\n\n" - for slot in self.schemaview.class_induced_slots(cls.name): - if ANNOTATION_KEY_PROMPT_SKIP in slot.annotations: - continue - if ANNOTATION_KEY_PROMPT in slot.annotations: - slot_prompt = slot.annotations[ANNOTATION_KEY_PROMPT].value - elif slot.description: - slot_prompt = slot.description - else: - if slot.multivalued: - slot_prompt = f"semicolon-separated list of {slot.name}s" - else: - slot_prompt = f"the value for {slot.name}" - if slot.range in self.schemaview.all_enums(): - enum_def = self.schemaview.get_enum(slot.range) - pvs = [str(k) for k in enum_def.permissible_values.keys()] - slot_prompt += f"Must be one of: {', '.join(pvs)}" - prompt += f"{slot.name}: <{slot_prompt}>\n" - # prompt += "Do not answer if you don't know\n\n" - prompt = f"{prompt}\n\nText:\n{text}\n\n===\n\n" - if object: - if cls is None: - cls = self.template_class - if isinstance(object, pydantic.BaseModel): - object = object.dict() - for k, v in object.items(): - if v: - slot = self.schemaview.induced_slot(k, cls.name) - prompt += f"{k}: {self._serialize_value(v, slot)}\n" - return prompt - - def _parse_response_to_dict( - self, results: str, cls: ClassDefinition = None - ) -> Optional[RESPONSE_DICT]: - """ - Parse the pseudo-YAML response from OpenAI into a dictionary object. - - E.g. - - foo: a; b; c - - becomes - - {"foo": ["a", "b", "c"]} - - :param results: - :return: - """ - lines = results.splitlines() - ann = {} - promptable_slots = self.promptable_slots(cls) - for line in lines: - line = line.strip() - if not line: - continue - if ":" not in line: - if len(promptable_slots) == 1: - slot = promptable_slots[0] - logging.warning( - f"Coercing to YAML-like with key {slot.name}: Original line: {line}" - ) - line = f"{slot.name}: {line}" - else: - logging.error(f"Line '{line}' does not contain a colon; ignoring") - return - r = self._parse_line_to_dict(line, cls) - if r is not None: - field, val = r - ann[field] = val - return ann - - def _parse_line_to_dict( - self, line: str, cls: ClassDefinition = None - ) -> Optional[Tuple[FIELD, RESPONSE_ATOM]]: - if cls is None: - cls = self.template_class - sv = self.schemaview - # each line is a key-value pair - logging.info(f"PARSING LINE: {line}") - field, val = line.split(":", 1) - # Field nornalization: - # The LLML may mutate the output format somewhat, - # randomly pluralizing or replacing spaces with underscores - field = field.lower().replace(" ", "_") - cls_slots = sv.class_slots(cls.name) - slot = None - if field in cls_slots: - slot = sv.induced_slot(field, cls.name) - else: - if field.endswith("s"): - field = field[:-1] - if field in cls_slots: - slot = sv.induced_slot(field, cls.name) - if not slot: - logging.error(f"Cannot find slot for {field} in {line}") - # raise ValueError(f"Cannot find slot for {field} in {line}") - return - if not val: - msg = f"Empty value in key-value line: {line}" - if slot.required: - raise ValueError(msg) - if slot.recommended: - logging.warning(msg) - return - inlined = slot.inlined - slot_range = sv.get_class(slot.range) - if not inlined: - if slot.range in sv.all_classes(): - inlined = sv.get_identifier_slot(slot_range.name) is None - val = val.strip() - if slot.multivalued: - vals = [v.strip() for v in val.split(";")] - else: - vals = [val] - vals = [val for val in vals if val] - logging.debug(f"SLOT: {slot.name} INL: {inlined} VALS: {vals}") - if inlined: - transformed = False - slots_of_range = sv.class_slots(slot_range.name) - if self.recurse or len(slots_of_range) > 2: - vals = [self._extract_from_text_to_dict(v, slot_range) for v in vals] - else: - for sep in [" - ", ":", "/", "*", "-"]: - if all([sep in v for v in vals]): - vals = [dict(zip(slots_of_range, v.split(sep, 1))) for v in vals] - for v in vals: - for k in v.keys(): - v[k] = v[k].strip() - transformed = True - break - if not transformed: - logging.warning(f"Did not find separator in {vals} for line {line}") - return - # transform back from list to single value if not multivalued - if slot.multivalued: - final_val = vals - else: - if len(vals) != 1: - logging.error(f"Expected 1 value for {slot.name} in '{line}' but got {vals}") - final_val = vals[0] - return field, final_val - - def parse_completion_payload( - self, results: str, cls: ClassDefinition = None, object: dict = None - ) -> pydantic.BaseModel: - """ - Parse the completion payload into a pydantic class. - - :param results: - :param cls: - :param object: stub object - :return: - """ - raw = self._parse_response_to_dict(results, cls) - logging.debug(f"RAW: {raw}") - if object: - raw = {**object, **raw} - return self.ground_annotation_object(raw, cls) - - def ground_annotation_object( - self, ann: RESPONSE_DICT, cls: ClassDefinition = None - ) -> Optional[pydantic.BaseModel]: - """Ground the direct parse of the OpenAI payload. - - The raw openAI payload is a YAML-like string, which is parsed to - a response dictionary. - - This dictionary is then grounded, using this method - - :param ann: Raw annotation object - :param cls: schema class the ground object should instantiate - :return: Grounded annotation object - """ - logging.debug(f"Grounding annotation object {ann}") - if cls is None: - cls = self.template_class - sv = self.schemaview - new_ann = {} - if ann is None: - logging.error(f"Cannot ground None annotation, cls={cls.name}") - return - for field, vals in ann.items(): - if isinstance(vals, list): - multivalued = True - else: - multivalued = False - vals = [vals] - slot = sv.induced_slot(field, cls.name) - rng_cls = sv.get_class(slot.range) - enum_def = None - if slot.range: - if slot.range in self.schemaview.all_enums(): - enum_def = self.schemaview.get_enum(slot.range) - new_ann[field] = [] - for val in vals: - if not val: - continue - if isinstance(val, tuple): - # special case for pairs - sub_slots = sv.class_induced_slots(rng_cls.name) - obj = {} - for i in range(0, len(val)): - sub_slot = sub_slots[i] - sub_rng = sv.get_class(sub_slot.range) - if not sub_rng: - logging.error(f"Cannot find range for {sub_slot.name}") - result = self.normalize_named_entity(val[i], sub_slot.range) - obj[sub_slot.name] = result - elif isinstance(val, dict): - # recurse - obj = self.ground_annotation_object(val, rng_cls) - else: - obj = self.normalize_named_entity(val, slot.range) - if enum_def: - found = False - logging.info(f"Looking for {obj} in {enum_def.name}") - for k, _pv in enum_def.permissible_values.items(): - if obj.lower() == k.lower(): - obj = k - found = True - break - if not found: - logging.info(f"Cannot find enum value for {obj} in {enum_def.name}") - obj = None - if multivalued: - new_ann[field].append(obj) - else: - new_ann[field] = obj - logging.debug(f"Creating object from dict {new_ann}") - logging.info(new_ann) - py_cls = self.template_module.__dict__[cls.name] - return py_cls(**new_ann) diff --git a/src/ontogpt/engines/pheno_engine.py b/src/ontogpt/engines/pheno_engine.py deleted file mode 100644 index 0efd07e57..000000000 --- a/src/ontogpt/engines/pheno_engine.py +++ /dev/null @@ -1,128 +0,0 @@ -"""Reasoner engine.""" -import json -import logging -from dataclasses import dataclass -from pathlib import Path -from typing import Any, Dict, List, Optional, Union - -from jinja2 import Template -from oaklib import get_adapter -from oaklib.datamodels.text_annotator import TextAnnotationConfiguration -from oaklib.interfaces import MappingProviderInterface, TextAnnotatorInterface -from pydantic import BaseModel - -from ontogpt.engines.knowledge_engine import KnowledgeEngine -from ontogpt.io.yaml_wrapper import dump_minimal_yaml -from ontogpt.prompts.phenopacket import DEFAULT_PHENOPACKET_PROMPT - -logger = logging.getLogger(__name__) - - -# TODO: use phenopacket python datamodel -PHENOPACKET = Dict[str, Any] -DIAGNOSIS = Dict[str, Any] - - -class DiagnosisPrediction(BaseModel): - case_id: str - validated_disease_ids: Optional[List[str]] = None - validated_disease_labels: Optional[List[str]] = None - validated_mondo_disease_ids: Optional[List[str]] = None - validated_mondo_disease_labels: Optional[List[str]] = None - predicted_disease_ids: Optional[List[str]] = None - predicted_disease_labels: Optional[List[str]] = None - matching_disease_ids: Optional[List[str]] = None - rank: Optional[int] = None - model: Optional[str] = None - prompt: Optional[str] = None - - -@dataclass -class PhenoEngine(KnowledgeEngine): - completion_length = 850 - _mondo: TextAnnotatorInterface = None - - @property - def mondo(self): - if not self._mondo: - self._mondo = get_adapter("sqlite:obo:mondo") - return self._mondo - - def predict_disease( - self, phenopacket: PHENOPACKET, template_path: Optional[Union[str, Path]] = None - ) -> List[DIAGNOSIS]: - if template_path is None: - template_path = DEFAULT_PHENOPACKET_PROMPT - if isinstance(template_path, Path): - template_path = str(template_path) - if isinstance(template_path, str): - # create a Jinja2 template object - with open(template_path) as file: - template_txt = file.read() - template = Template(template_txt) - prompt = template.render( - phenopacket=phenopacket, - ) - payload = self.client.complete(prompt, max_tokens=self.completion_length) - print(payload) - try: - obj = json.loads(payload) - except json.JSONDecodeError as e: - logger.error(f"Error decoding JSON: {e}") - logger.error(f"Payload: {payload}") - obj = [] - self.enhance_payload(obj) - return obj - - def evaluate(self, phenopackets: List[PHENOPACKET]) -> List[DiagnosisPrediction]: - mondo = self.mondo - if not isinstance(mondo, MappingProviderInterface): - raise TypeError("Mondo adapter must implement MappingProviderInterface") - - results = [] - for phenopacket in phenopackets: - dp = DiagnosisPrediction(case_id=phenopacket["id"], model=self.model) - validated_disease_ids = {disease["term"]["id"] for disease in phenopacket["diseases"]} - dp.validated_disease_ids = list(validated_disease_ids) - dp.validated_disease_labels = [ - disease["term"]["label"] for disease in phenopacket["diseases"] - ] - dp.validated_mondo_disease_ids = [] - dp.validated_mondo_disease_labels = [] - for disease_id in validated_disease_ids: - mondo_id = mondo.normalize(disease_id, target_prefixes=["MONDO"]) - if mondo_id: - dp.validated_mondo_disease_ids.append(mondo_id) - dp.validated_mondo_disease_labels.append(mondo.label(mondo_id)) - else: - logger.warning(f"Could not normalize {disease_id} to MONDO") - diagnoses = self.predict_disease(phenopacket) - dp.predicted_disease_ids = [] - dp.predicted_disease_labels = [] - dp.rank = 999 - for i, diagnosis in enumerate(diagnoses): - predicted_disease_ids = diagnosis["disease_ids"] - dp.predicted_disease_ids.append(";".join(predicted_disease_ids)) - dp.predicted_disease_labels.append(diagnosis["disease"]) - matches = set(dp.validated_mondo_disease_ids).intersection(predicted_disease_ids) - if matches: - print("Found match at index", i) - dp.rank = i - dp.matching_disease_ids = list(matches) - break - print(dump_minimal_yaml(dp.dict())) - results.append(dp) - return results - - def enhance_payload(self, diagnoses: List[DIAGNOSIS]) -> List[DIAGNOSIS]: - """Enhance payload with additional information.""" - mondo = self.mondo - config = TextAnnotationConfiguration(matches_whole_text=True) - if not isinstance(mondo, TextAnnotatorInterface): - raise ValueError("Mondo adapter must implement TextAnnotatorInterface") - for diagnosis in diagnoses: - disease_label = diagnosis["disease"] - anns = list(mondo.annotate_text(disease_label, config)) - # print(anns) - diagnosis["disease_ids"] = [ann.object_id for ann in anns] - return diagnoses diff --git a/src/ontogpt/engines/reasoner_engine.py b/src/ontogpt/engines/reasoner_engine.py deleted file mode 100644 index 940ba8e06..000000000 --- a/src/ontogpt/engines/reasoner_engine.py +++ /dev/null @@ -1,302 +0,0 @@ -"""Reasoner engine.""" -import logging -import re -from dataclasses import dataclass -from pathlib import Path -from typing import List, Optional, Union - -from jinja2 import Template -from pydantic import BaseModel - -from ontogpt import MODELS -from ontogpt.engines.knowledge_engine import KnowledgeEngine -from ontogpt.ontex.extractor import ( - Answer, - Axiom, - Explanation, - GPTReasonMethodType, - Task, - TaskCollection, -) -from ontogpt.prompts.reasoning import DEFAULT_REASONING_PROMPT -from ontogpt.utils.parse_utils import split_on_one_of - -logger = logging.getLogger(__name__) - - -MODEL_GPT_4_NAMES = [ - model["alternative_names"][0] for model in MODELS if model["name"] == "MODEL_GPT_4" -][0] - - -def flatten_list(lst): - flat_list = [] - for item in lst: - if isinstance(item, list): - flat_list.extend(flatten_list(item)) - else: - flat_list.append(item) - return flat_list - - -class ReasonerResult(BaseModel): - """The result of a reason query.""" - - name: Optional[str] = None - completed: Optional[bool] = True - task_name: Optional[str] = None - task_type: Optional[str] = None - task_obfuscated: Optional[bool] = None - method: Optional[GPTReasonMethodType] = None - model: Optional[str] = None - description: Optional[str] = None - answers: Optional[List[Answer]] = None - prompt: Optional[str] = None - completion: Optional[str] = None - jaccard_score: Optional[float] = 0.0 - false_positives: Optional[List[str]] = None - false_negatives: Optional[List[str]] = None - num_false_positives: Optional[int] = None - num_false_negatives: Optional[int] = None - num_true_positives: Optional[int] = None - num_true_negatives: Optional[int] = None - precision: Optional[float] = 0.0 - recall: Optional[float] = None - f1_score: Optional[float] = None - len_shortest_explanation: Optional[int] = None - - class Config: - """Pydantic config.""" - - use_enum_values = True - - -class ReasonerResultSet(BaseModel): - name: str = "" - results: List[ReasonerResult] - - -@dataclass -class ReasonerEngine(KnowledgeEngine): - """Engine for performing reasoning using GPT. - - This engine takes as input an Ontology, and a query Task, - and then translates this to a GPT prompt that asks GPT to - perform the task over the ontology after reasoning over it. - - The Task is typically a query such as finding superclasses of - a given class. - - This is intended primarily for investigation purposes. For practical - scenarios, it is recommended to use a dedicated OWL reasoner. The goal - of this engine is to evaluate the extent to which GPT can perform - reasoning-like tasks, including deduction and abduction (explanation). - - Due to token-length constraints on GPT models, it is usually necessary - to extract a submodule prior to reasoning. This can be done using the - OntologyExtractor: - - >>> from oaklib import get_adapter - >>> from ontogpt.ontex.extractor import OntologyExtractor, Task - >>> adapter = get_adapter("sqlite:obo:go") - >>> extractor = OntologyExtractor(adapter=adapter) - >>> task = extractor.extract_indirect_superclasses_task( - ... subclass="GO:0005634", siblings=["GO:0005773"], roots=["GO:0043226"] - ... ) - - The extractor will actually perform the intended reasoning task, and include - the expected answer in the Task object. This may seem a little circular, but - the goal here is to evaluate. - - The task can then be passed to the reasoner engine: - - >>> from ontogpt.engines.reasoner_engine import ReasonerEngine - >>> reasoner = ReasonerEngine() - >>> result = reasoner.reason(task) - - We can expand on this: - - >>> for answer in result.answers: - ... print(f"PARENT: {answer.text}") - <BLANKLINE> - PARENT: MembraneBoundedOrganelle - ... - PARENT: IntracellularOrganelle - - We can also ask for explanations: - - >>> task.include_explanations = True - >>> result = reasoner.reason(task) - >>> for answer in result.answers: - ... print(f"PARENT: {answer.text}") - ... if answer.explanations: - ... print(" EXPLANATION:") - ... for e in answer.explanations: - ... for axiom in e.axioms: - ... print(f" AXIOM: {axiom.text}") - <BLANKLINE> - ... - PARENT: IntracellularOrganelle - EXPLANATION: - AXIOM: Nucleus SubClassOf IntracellularMembraneBoundedOrganelle - AXIOM: IntracellularMembraneBoundedOrganelle SubClassOf IntracellularOrganelle - - """ - - completion_length = 250 - - def reason( - self, task: Task, template_path=None, strict=False, evaluate: bool = None - ) -> ReasonerResult: - """Reason over axioms and query entailments.""" - if template_path is None: - template_path = DEFAULT_REASONING_PROMPT - if isinstance(template_path, Path): - template_path = str(template_path) - if isinstance(template_path, str): - # create a Jinja2 template object - with open(template_path) as file: - template_txt = file.read() - template = Template(template_txt) - prompt = template.render( - task=task, - ontology=task.ontology, - query=task.query, - examples=task.examples, - ) - completion_length = self.completion_length - if task.method == GPTReasonMethodType.EXPLANATION: - completion_length *= 2 - elif task.method == GPTReasonMethodType.CHAIN_OF_THOUGHT: - completion_length *= 2 - logger.info(f"Prompt: {prompt}") - if self.encoding is not None: - prompt_length = len(self.encoding.encode(prompt)) + 10 - else: - prompt_length = len(prompt) - max_len_total = 4097 - if self.model in MODEL_GPT_4_NAMES: - max_len_total = 8193 - max_len = max_len_total - completion_length - completed = True - logger.info(f"PROMPT LENGTH: {prompt_length} [max={max_len}]") - if prompt_length > max_len: - if strict: - raise ValueError(f"Prompt length ({prompt_length}) exceeds maximum ({max_len})") - logger.warning(f"Prompt length ({prompt_length}) exceeds maximum ({max_len})") - answers = [] - completed = False - payload = "" - else: - payload = self.client.complete(prompt, max_tokens=completion_length) - if task.has_multiple_answers: - elements = payload.split("- ") - answers = [self._parse_single_answer(e, task) for e in elements] - else: - answers = [self._parse_single_answer(payload, task)] - answers = [a for a in flatten_list(answers) if a is not None] - result = ReasonerResult( - completed=completed, - task_name=task.name, - task_type=task.type, - task_obfuscated=task.obfuscated, - method=task.method, - len_shortest_explanation=task.len_shortest_explanation, - model=self.model, - prompt=prompt, - completion=payload, - ) - # TODO: determine which it doesn't work to initialize with this - result.answers = answers # type: ignore - logger.debug(f"Answers: {task.answers} // {answers}") - result.name = f"{task.name}-{task.method.value}-{self.model}" - if not task.answers and evaluate: - raise ValueError(f"Cannot evaluate without expected answers: {task}") - if task.answers is not None: - self.evaluate(result, task) - return result - - def reason_multiple(self, task_collection: TaskCollection, **kwargs) -> ReasonerResultSet: - """ - Reason over multiple tasks. - - :param task_collection: - :param kwargs: - :return: - """ - results = [self.reason(task, **kwargs) for task in task_collection.tasks] - return ReasonerResultSet(results=results) - - def _parse_single_answer( - self, payload: str, task: Task - ) -> Optional[Union[Answer, List[Answer]]]: - """Parse single answer from payload. - - In some cases for COT reasoning the model may compress multiple - answers into a single answer line. - """ - payload = payload.strip() - if not payload: - return None - payload = payload.replace("\n", " ") - if task.chain_of_thought: - pattern = r"^REASONING:\s*\[\s*(.*?)\s*\]\s*CONCLUSION:\s*(.*?)$" - match = re.match(pattern, payload) - print(f"CHAIN OF THOUGHT: {payload}") - if match: - print(f"MATCH: {match.groups()}") - explanation = match.group(1) - text = match.group(2) - # rest = match.group(3) - axioms = [x.strip() for x in split_on_one_of(explanation, [";", ","])] - explanation = Explanation(axioms=[Axiom(text=a) for a in axioms if a]) - axiom_texts = split_on_one_of(text, [";", ","]) - if len(axiom_texts) == 1: - return Answer(text=text, explanations=[explanation]) - else: - return [ - Answer(text=axiom_text, explanations=[explanation]) - for axiom_text in axiom_texts - ] - pattern = r"^(.*?)\s*\[\s*(.*?)\s*\]\s*(.*?)$" - match = re.match(pattern, payload) - if match: - text = match.group(1) - explanation = match.group(2) - rest = match.group(3) - axioms = [x.strip() for x in split_on_one_of(explanation, [";", ","])] - explanation = Explanation(axioms=[Axiom(text=a) for a in axioms if a]) - if rest: - explanation.comments = [rest] - return Answer(text=text, explanations=[explanation]) - else: - return Answer(text=payload) - - def evaluate(self, result: ReasonerResult, task: Task): - """Evaluate result against task.""" - logger.debug(f"Evaluating result: {result}") - positives = {t.text for t in task.answers} - result_answer_texts = {a.text for a in result.answers} - ixn = positives.intersection(result_answer_texts) - all_texts = positives.union(result_answer_texts) - result.false_positives = list(result_answer_texts - positives) - result.false_negatives = list(positives - result_answer_texts) - result.num_false_positives = len(result.false_positives) - result.num_false_negatives = len(result.false_negatives) - result.num_true_positives = len(ixn) - tp_plus_tn = result.num_true_positives + result.num_false_positives - if tp_plus_tn == 0: - result.precision = 0.0 - else: - result.precision = result.num_true_positives / tp_plus_tn - result.recall = result.num_true_positives / len(positives) - if len(all_texts) == 0: - result.jaccard_score = 0.0 - else: - result.jaccard_score = len(ixn) / len(all_texts) - if result.num_true_positives == 0: - result.f1_score = 0.0 - else: - result.f1_score = ( - 2 * (result.precision * result.recall) / (result.precision + result.recall) - ) diff --git a/src/ontogpt/engines/resolver.py b/src/ontogpt/engines/resolver.py deleted file mode 100644 index ae330bd92..000000000 --- a/src/ontogpt/engines/resolver.py +++ /dev/null @@ -1,25 +0,0 @@ -"""Resolver engine.""" -from typing import Optional, Type, Union - -from class_resolver import ClassResolver - -from ontogpt.engines.enrichment import EnrichmentEngine -from ontogpt.engines.halo_engine import HALOEngine # type: ignore -from ontogpt.engines.knowledge_engine import KnowledgeEngine -from ontogpt.engines.spires_engine import SPIRESEngine - -resolver = ClassResolver([SPIRESEngine, HALOEngine, EnrichmentEngine], base=KnowledgeEngine) - - -def create_engine( - template: str, engine: Optional[Union[str, Type]] = None, **kwargs -) -> Union[KnowledgeEngine, SPIRESEngine]: - """Create a knowledge engine.""" - if engine is None: - engine = SPIRESEngine - if isinstance(engine, str): - engine = resolver.get_class(engine)(**kwargs) - if engine is not None and not isinstance(engine, str): - return engine(template, **kwargs) - else: - return SPIRESEngine # type: ignore diff --git a/src/ontogpt/engines/spires_engine.py b/src/ontogpt/engines/spires_engine.py deleted file mode 100644 index 22d563e6f..000000000 --- a/src/ontogpt/engines/spires_engine.py +++ /dev/null @@ -1,654 +0,0 @@ -""" -Main Knowledge Extractor class. - -This works by recursively constructing structured prompt-completions where -a pseudo-YAML structure is requested, where the YAML -structure corresponds to a template class. - -Describe in the SPIRES manuscript -TODO: add link -""" -import logging -import re -import uuid -from dataclasses import dataclass -from pathlib import Path -from typing import Any, Dict, Iterator, List, Optional, Tuple, Union - -import pydantic -import yaml -from linkml_runtime.linkml_model import ClassDefinition, SlotDefinition -from oaklib import BasicOntologyInterface - -from ontogpt.engines.knowledge_engine import ( - ANNOTATION_KEY_PROMPT, - ANNOTATION_KEY_PROMPT_SKIP, - EXAMPLE, - FIELD, - OBJECT, - KnowledgeEngine, - chunk_text, -) -from ontogpt.io.yaml_wrapper import dump_minimal_yaml -from ontogpt.templates.core import ExtractionResult - -this_path = Path(__file__).parent - - -RESPONSE_ATOM = Union[str, "ResponseAtom"] # type: ignore -RESPONSE_DICT = Dict[FIELD, Union[RESPONSE_ATOM, List[RESPONSE_ATOM]]] - - -@dataclass -class SPIRESEngine(KnowledgeEngine): - """Knowledge extractor.""" - - engine: str = None - """The engine name.""" - - recurse: bool = True - """If true, then complex non-named entity objects are always recursively parsed. - If this is false AND the complex object is a pair, then token-based splitting is - instead used. - TODO: deprecate this, it's not clear that token-based splitting is better, due to - the inability to control which tokens GPT will use""" - - sentences_per_window: Optional[int] = None - """If set, this will split the text into chains of sentences, - where this determines the maximum number of sentences per chain. - The results are then merged together.""" - - def extract_from_text( - self, - text: str, - cls: ClassDefinition = None, - object: OBJECT = None, - show_prompt: bool = False, - ) -> ExtractionResult: - """ - Extract annotations from the given text. - - :param text: - :param cls: - :param object: optional stub object - :return: - """ - if self.sentences_per_window: - chunks = chunk_text(text, self.sentences_per_window) - extracted_object = None - for chunk in chunks: - raw_text = self._raw_extract(chunk, cls=cls, object=object, show_prompt=show_prompt) - logging.info(f"RAW TEXT: {raw_text}") - next_object = self.parse_completion_payload( - raw_text, cls, object=object # type: ignore - ) - if extracted_object is None: - extracted_object = next_object - else: - for k, v in next_object.items(): - if isinstance(v, list): - extracted_object[k] += v - else: - if k not in extracted_object: - extracted_object[k] = v - else: - extracted_object[k] = v - else: - raw_text = self._raw_extract(text=text, cls=cls, object=object, show_prompt=show_prompt) - logging.info(f"RAW TEXT: {raw_text}") - extracted_object = self.parse_completion_payload( - raw_text, cls, object=object # type: ignore - ) - return ExtractionResult( - input_text=text, - raw_completion_output=raw_text, - prompt=self.last_prompt, - extracted_object=extracted_object, - named_entities=self.named_entities, - ) - - def _extract_from_text_to_dict(self, text: str, cls: ClassDefinition = None) -> RESPONSE_DICT: - raw_text = self._raw_extract(text=text, cls=cls) - return self._parse_response_to_dict(raw_text, cls) - - def generate_and_extract( - self, entity: str, prompt_template: str = "", show_prompt: bool = False, **kwargs - ) -> ExtractionResult: - """ - Generate a description using GPT and then extract from it using SPIRES. - - :param entity: - :param kwargs: - :return: - """ - if prompt_template == "": - prompt_template = "Generate a comprehensive description of {entity}.\n" - prompt = prompt_template.format(entity=entity) - if self.client is not None: - payload = self.client.complete(prompt=prompt, show_prompt=show_prompt) - else: - payload = "" - return self.extract_from_text(payload, **kwargs) - - def iteratively_generate_and_extract( - self, - entity: str, - cache_path: Union[str, Path], - iteration_slots: List[str], - adapter: BasicOntologyInterface = None, - clear=False, - max_iterations=10, - prompt_template=None, - show_prompt: bool = False, - **kwargs, - ) -> Iterator[ExtractionResult]: - def _remove_parenthetical_context(s: str): - return re.sub(r"\(.*\)", "", s) - - iteration = 0 - if isinstance(cache_path, str): - cache_path = Path(cache_path) - if cache_path: - if cache_path.exists() and not clear: - db = yaml.safe_load(cache_path.open()) - if "entities_in_queue" not in db: - db["entities_in_queue"] = [] - else: - db = {"processed_entities": [], "entities_in_queue": [], "results": []} - if entity not in db["processed_entities"]: - db["entities_in_queue"].append(entity) - if prompt_template is None: - prompt_template = ( - "Generate a comprehensive description of {entity}. " - + "The description should include the information on" - + " and ".join(iteration_slots) - + ".\n" - ) - while db["entities_in_queue"] and iteration < max_iterations: - iteration += 1 - next_entity = db["entities_in_queue"].pop(0) - logging.info(f"ITERATION {iteration}, entity={next_entity}") - # check if entity matches a curie pattern using re - if re.match(r"^[A-Z]+:[A-Z0-9]+$", next_entity): - curie = next_entity - next_entity = adapter.label(next_entity) - else: - curie = None - result = self.generate_and_extract( - next_entity, prompt_template=prompt_template, show_prompt=show_prompt, **kwargs - ) - if curie: - if result.extracted_object: - result.extracted_object.id = curie - db["results"].append(result) - db["processed_entities"].append(next_entity) - yield result - for s in iteration_slots: - # if s not in result.extracted_object: - # raise ValueError(f"Slot {s} not found in {result.extracted_object}") - vals = getattr(result.extracted_object, s, []) - if not vals: - logging.info("dead-end: no values found for slot") - continue - if not isinstance(vals, list): - vals = [vals] - for val in vals: - entity = val - if result.named_entities is not None: - for ne in result.named_entities: - if ne.id == val: - entity = ne.label - if ne.id.startswith("AUTO"): - # Sometimes the value of some slots will lack - context = next_entity - context = re.sub(r"\(.*\)", "", context) - entity = f"{entity} ({context})" - else: - entity = ne.id - break - queue_deparenthesized = [ - _remove_parenthetical_context(e) for e in db["entities_in_queue"] - ] - if ( - entity not in db["processed_entities"] - and entity not in db["entities_in_queue"] - and _remove_parenthetical_context(entity) not in queue_deparenthesized - ): - db["entities_in_queue"].append(entity) - with open(cache_path, "w") as f: - # TODO: consider a more robust backend e.g. mongo - f.write(dump_minimal_yaml(db)) - - def generalize( - self, - object: Union[pydantic.BaseModel, dict], - examples: List[EXAMPLE], - show_prompt: bool = False, - ) -> ExtractionResult: - """ - Generalize the given examples. - - :param object: - :param examples: - :return: - """ - cls = self.template_class - sv = self.schemaview - prompt = "example:\n" - for example in examples: - prompt += f"{self.serialize_object(example)}\n\n" - prompt += "\n\n===\n\n" - if isinstance(object, pydantic.BaseModel): - object = object.dict() - for k, v in object.items(): - if v: - slot = sv.induced_slot(k, cls.name) - prompt += f"{k}: {self._serialize_value(v, slot)}\n" - logging.debug(f"PROMPT: {prompt}") - payload = self.client.complete(prompt, show_prompt) - prediction = self.parse_completion_payload(payload, object=object) - return ExtractionResult( - input_text=prompt, - raw_completion_output=payload, - # prompt=self.last_prompt, - results=[prediction], - named_entities=self.named_entities, - ) - - def map_terms( - self, terms: List[str], ontology: str, show_prompt: bool = False - ) -> Dict[str, str]: - """ - Map the given terms to the given ontology. - - EXPERIMENTAL - - currently GPT-3 does not do so well with this task. - - :param terms: - :param ontology: - :return: - """ - # TODO: make a separate config - examples = { - "go": { - "nucleui": "nucleus", - "mitochondrial": "mitochondrion", - "signaling": "signaling pathway", - "cysteine biosynthesis": "cysteine biosynthetic process", - "alcohol dehydrogenase": "alcohol dehydrogenase activity", - }, - "uberon": { - "feet": "pes", - "forelimb, left": "left forelimb", - "hippocampus": "Ammons horn", - }, - } - ontology = ontology.lower() - if ontology in examples: - example = examples[ontology] - else: - example = examples["uberon"] - prompt = "Normalize the following semicolon separated\ - list of terms to the {ontology.upper()} ontology\n\n" - prompt += "For example:\n\n" - for k, v in example.items(): - prompt += f"{k}: {v}\n" - prompt += "===\n\nTerms:" - prompt += "; ".join(terms) - prompt += "===\n\n" - payload = self.client.complete(prompt, show_prompt) - # outer parse - best_results: List[str] = [] - for sep in ["\n", "; "]: - results = payload.split(sep) - if len(results) > len(best_results): - best_results = results - - def normalize(s: str) -> str: - s = s.strip() - s.replace("_", " ") - return s.lower() - - mappings = {} - for result in best_results: - if ":" not in result: - logging.error(f"Count not parse result: {result}") - continue - k, v = result.strip().split(":", 1) - k = k.strip() - v = v.strip() - for t in terms: - if normalize(t) == normalize(k): - mappings[t] = v - break - for t in terms: - if t not in mappings: - logging.warning(f"Could not map term: {t}") - return mappings - - def serialize_object(self, example: EXAMPLE, cls: ClassDefinition = None) -> str: - if cls is None: - cls = self.template_class - if isinstance(example, str): - return example - if isinstance(example, pydantic.BaseModel): - example = example.dict() - lines = [] - sv = self.schemaview - for k, v in example.items(): - if not v: - continue - slot = sv.induced_slot(k, cls.name) - v_serialized = self._serialize_value(v, slot) - lines.append(f"{k}: {v_serialized}") - return "\n".join(lines) - - def _serialize_value(self, val: Any, slot: SlotDefinition) -> str: - if val is None: - return "" - if isinstance(val, list): - return "; ".join([self._serialize_value(v, slot) for v in val if v]) - if isinstance(val, dict): - return " - ".join([self._serialize_value(v, slot) for v in val.values() if v]) - sv = self.schemaview - if slot.range in sv.all_classes(): - if self.labelers: - labelers = list(self.labelers) - else: - labelers = [] - labelers += self.get_annotators(sv.get_class(slot.range)) - if labelers: - for labeler in labelers: - label = labeler.label(val) - if label: - return label - return val - - def _raw_extract( - self, - text, - cls: ClassDefinition = None, - object: OBJECT = None, - show_prompt: bool = False, - ) -> str: - """ - Extract annotations from the given text. - - :param text: - :return: - """ - prompt = self.get_completion_prompt(cls=cls, text=text, object=object) - self.last_prompt = prompt - payload = self.client.complete(prompt=prompt, show_prompt=show_prompt) - return payload - - def get_completion_prompt( - self, cls: ClassDefinition = None, text: str = "", object: OBJECT = None - ) -> str: - """Get the prompt for the given template.""" - if cls is None: - cls = self.template_class - if not text or ("\n" in text or len(text) > 60): - prompt = ( - "From the text below, extract the following entities in the following format:\n\n" - ) - else: - prompt = "Split the following piece of text into fields in the following format:\n\n" - for slot in self.schemaview.class_induced_slots(cls.name): - if ANNOTATION_KEY_PROMPT_SKIP in slot.annotations: - continue - if ANNOTATION_KEY_PROMPT in slot.annotations: - slot_prompt = slot.annotations[ANNOTATION_KEY_PROMPT].value - elif slot.description: - slot_prompt = slot.description - else: - if slot.multivalued: - slot_prompt = f"semicolon-separated list of {slot.name}s" - else: - slot_prompt = f"the value for {slot.name}" - if slot.range in self.schemaview.all_enums(): - enum_def = self.schemaview.get_enum(slot.range) - pvs = [str(k) for k in enum_def.permissible_values.keys()] - slot_prompt += f"Must be one of: {', '.join(pvs)}" - prompt += f"{slot.name}: <{slot_prompt}>\n" - # prompt += "Do not answer if you don't know\n\n" - prompt = f"{prompt}\n\nText:\n{text}\n\n===\n\n" - if object: - if cls is None: - cls = self.template_class - if isinstance(object, pydantic.BaseModel): - object = object.dict() - for k, v in object.items(): - if v: - slot = self.schemaview.induced_slot(k, cls.name) - prompt += f"{k}: {self._serialize_value(v, slot)}\n" - return prompt - - def _parse_response_to_dict( - self, results: str, cls: ClassDefinition = None - ) -> Optional[RESPONSE_DICT]: - """ - Parse the pseudo-YAML response from OpenAI into a dictionary object. - - E.g. - - foo: a; b; c - - becomes - - {"foo": ["a", "b", "c"]} - - :param results: - :return: - """ - lines = results.splitlines() - ann = {} - promptable_slots = self.promptable_slots(cls) - for line in lines: - line = line.strip() - if not line: - continue - if ":" not in line: - if len(promptable_slots) == 1: - slot = promptable_slots[0] - logging.warning( - f"Coercing to YAML-like with key {slot.name}: Original line: {line}" - ) - line = f"{slot.name}: {line}" - else: - logging.error(f"Line '{line}' does not contain a colon; ignoring") - return None - r = self._parse_line_to_dict(line, cls) - if r is not None: - field, val = r - ann[field] = val - return ann - - def _parse_line_to_dict( - self, line: str, cls: ClassDefinition = None - ) -> Optional[Tuple[FIELD, RESPONSE_ATOM]]: - if cls is None: - cls = self.template_class - sv = self.schemaview - # each line is a key-value pair - logging.info(f"PARSING LINE: {line}") - field, val = line.split(":", 1) - # Field nornalization: - # The LLML may mutate the output format somewhat, - # randomly pluralizing or replacing spaces with underscores - field = field.lower().replace(" ", "_") - logging.debug(f" FIELD: {field}") - cls_slots = sv.class_slots(cls.name) - slot = None - if field in cls_slots: - slot = sv.induced_slot(field, cls.name) - else: - # TODO: check this - if field.endswith("s"): - field = field[:-1] - if field in cls_slots: - slot = sv.induced_slot(field, cls.name) - if not slot: - logging.error(f"Cannot find slot for {field} in {line}") - # raise ValueError(f"Cannot find slot for {field} in {line}") - return None - if not val: - msg = f"Empty value in key-value line: {line}" - if slot.required: - raise ValueError(msg) - if slot.recommended: - logging.warning(msg) - return None - inlined = slot.inlined - slot_range = sv.get_class(slot.range) - if not inlined: - if slot.range in sv.all_classes(): - inlined = sv.get_identifier_slot(slot_range.name) is None - val = val.strip() - if slot.multivalued: - vals = [v.strip() for v in val.split(";")] - else: - vals = [val] - vals = [val for val in vals if val] - logging.debug(f"SLOT: {slot.name} INL: {inlined} VALS: {vals}") - if inlined: - transformed = False - slots_of_range = sv.class_slots(slot_range.name) - if self.recurse or len(slots_of_range) > 2: - logging.debug(f" RECURSING ON SLOT: {slot.name}, range={slot_range.name}") - vals = [ - self._extract_from_text_to_dict(v, slot_range) for v in vals # type: ignore - ] - else: - for sep in [" - ", ":", "/", "*", "-"]: - if all([sep in v for v in vals]): - vals = [ - dict(zip(slots_of_range, v.split(sep, 1))) for v in vals # type: ignore - ] - for v in vals: - for k in v.keys(): # type: ignore - v[k] = v[k].strip() # type: ignore - transformed = True - break - if not transformed: - logging.warning(f"Did not find separator in {vals} for line {line}") - return None - # transform back from list to single value if not multivalued - if slot.multivalued: - final_val = vals - else: - if len(vals) != 1: - logging.error(f"Expected 1 value for {slot.name} in '{line}' but got {vals}") - final_val = vals[0] # type: ignore - return field, final_val - - def parse_completion_payload( - self, results: str, cls: ClassDefinition = None, object: dict = None - ) -> pydantic.BaseModel: - """ - Parse the completion payload into a pydantic class. - - :param results: - :param cls: - :param object: stub object - :return: - """ - raw = self._parse_response_to_dict(results, cls) - logging.debug(f"RAW: {raw}") - if object: - raw = {**object, **raw} - self._auto_add_ids(raw, cls) - return self.ground_annotation_object(raw, cls) - - def _auto_add_ids(self, ann: RESPONSE_DICT, cls: ClassDefinition = None) -> None: - if ann is None: - return - if cls is None: - cls = self.template_class - for slot in self.schemaview.class_induced_slots(cls.name): - if slot.identifier: - if slot.name not in ann: - auto_id = str(uuid.uuid4()) - auto_prefix = self.auto_prefix - if slot.range == "uriorcurie" or slot.range == "uri": - ann[slot.name] = f"{auto_prefix}:{auto_id}" - else: - ann[slot.name] = auto_id - - def ground_annotation_object( - self, ann: RESPONSE_DICT, cls: ClassDefinition = None - ) -> Optional[pydantic.BaseModel]: - """Ground the direct parse of the OpenAI payload. - - The raw openAI payload is a YAML-like string, which is parsed to - a response dictionary. - - This dictionary is then grounded, using this method - - :param ann: Raw annotation object - :param cls: schema class the ground object should instantiate - :return: Grounded annotation object - """ - logging.debug(f"Grounding annotation object {ann}") - if cls is None: - cls = self.template_class - sv = self.schemaview - new_ann: Dict[str, Any] = {} - if ann is None: - logging.error(f"Cannot ground None annotation, cls={cls.name}") - return None - for field, vals in ann.items(): - if isinstance(vals, list): - multivalued = True - else: - multivalued = False - vals = [vals] - slot = sv.induced_slot(field, cls.name) - rng_cls = sv.get_class(slot.range) - enum_def = None - if slot.range: - if slot.range in self.schemaview.all_enums(): - enum_def = self.schemaview.get_enum(slot.range) - new_ann[field] = [] - logging.debug(f"FIELD: {field} SLOT: {slot.name}") - for val in vals: - if not val: - continue - logging.debug(f" VAL: {val}") - if isinstance(val, tuple): - # special case for pairs - sub_slots = sv.class_induced_slots(rng_cls.name) - obj = {} - for i in range(0, len(val)): - sub_slot = sub_slots[i] - sub_rng = sv.get_class(sub_slot.range) - if not sub_rng: - logging.error(f"Cannot find range for {sub_slot.name}") - result = self.normalize_named_entity(val[i], sub_slot.range) - obj[sub_slot.name] = result - elif isinstance(val, dict): - # recurse - obj = self.ground_annotation_object(val, rng_cls) - else: - obj = self.normalize_named_entity(val, slot.range) # type: ignore - if enum_def: - found = False - logging.info(f"Looking for {obj} in {enum_def.name}") - for k, _pv in enum_def.permissible_values.items(): - if type(obj) is str and type(k) is str: - if obj.lower() == k.lower(): # type: ignore - obj = k # type: ignore - found = True - break - if not found: - logging.info(f"Cannot find enum value for {obj} in {enum_def.name}") - obj = None - if multivalued: - new_ann[field].append(obj) - else: - new_ann[field] = obj - logging.debug(f"Creating object from dict {new_ann}") - logging.info(new_ann) - py_cls = self.template_module.__dict__[cls.name] - return py_cls(**new_ann) diff --git a/src/ontogpt/engines/synonym_engine.py b/src/ontogpt/engines/synonym_engine.py deleted file mode 100644 index b55bffa9f..000000000 --- a/src/ontogpt/engines/synonym_engine.py +++ /dev/null @@ -1,20 +0,0 @@ -"""Synonym engine.""" -from dataclasses import dataclass -from typing import List - -from ontogpt.engines.knowledge_engine import KnowledgeEngine - - -@dataclass -class SynonymEngine(KnowledgeEngine): - """Engine for generating synonyms.""" - - engine: str = "gpt-3.5-turbo-instruct" - - def synonyms(self, named_entity: str, domain: str) -> List[str]: - """Get synonyms for a given text.""" - prompt = f"List the example formal scientific\ - synonyms for the {domain} concept {named_entity} as a semi-colon separated list." - prompt += " Only include terms with identical meaning, not more specific or general terms." - payload = self.client.complete(prompt) - return payload.split("; ") diff --git a/src/ontogpt/evaluation/__init__.py b/src/ontogpt/evaluation/__init__.py deleted file mode 100644 index 059c59d49..000000000 --- a/src/ontogpt/evaluation/__init__.py +++ /dev/null @@ -1 +0,0 @@ -from ontogpt.evaluation.resolver import create_evaluator # noqa:F401 diff --git a/src/ontogpt/io/csv_wrapper.py b/src/ontogpt/io/csv_wrapper.py deleted file mode 100644 index 86855f103..000000000 --- a/src/ontogpt/io/csv_wrapper.py +++ /dev/null @@ -1,135 +0,0 @@ -"""Utilities for CSVs and TSVs.""" -import csv -import logging -from pathlib import Path -from typing import Any, List - -from oaklib import get_adapter -from pydantic import BaseModel - -logger = logging.getLogger(__name__) - - -def output_parser(obj: Any, file) -> List[str]: - # Declare initial variables - NULL_VALS = [ - "", - "Not mentioned", - "none mentioned", - "Not mentioned in the text", - "Not mentioned in the provided text.", - "No exposures mentioned in the text.", - "No exposures mentioned in the text.", - "None mentioned in the text.", - "None mentioned in the text", - "Not mentioned in the text.", - "None relevant", - "No gene to molecular activity relationships mentioned in the text.", - "No genes mentioned", - "No genes mentioned in the text.", - "None", - "N/A", - ] - lines = [] - output_file = file - - # Extract all 'subject', 'predicate', and 'object' output lines - with open(output_file, "r") as file: - to_print = False - perpetuators = tuple([" subject:", " predicate:", " object:", " "]) - for line in file: - line = line.strip("\n") - if line.startswith("extracted_object:"): - to_print = True - elif not line.startswith(perpetuators): - to_print = False - if to_print: - lines.append(line) - - # Clean & strip lines - lines = list(filter(lambda elem: not (elem.isspace()), lines)) - cleaned_lines = [x for x in lines if x.strip()] - cleaned_lines = [x for x in cleaned_lines if x != "extracted_object: {}"] - i = 1 - while i < len(cleaned_lines): - if cleaned_lines[i].startswith(" "): - cleaned_lines[i - 1] += " " - cleaned_lines[i - 1] += cleaned_lines[i][4:] - del cleaned_lines[i] - else: - i += 1 - # Remove any underdeveloped extracted objects - i = 0 - while i < len(cleaned_lines): - if cleaned_lines[i].startswith("extracted_object"): - for index, elem in enumerate(cleaned_lines[i + 1 : i + 4]): - if elem.startswith("extracted_object"): - next_index = i + 1 + index - del cleaned_lines[i:next_index] - i -= 1 - i += 1 - - # Separate extracted values into indexed items in dictionary of lists - grouped_lines = [cleaned_lines[n : n + 4] for n in range(0, len(cleaned_lines), 4)] - trimmed_dict: dict = {"genes": [], "relationships": [], "exposures": []} - for group in grouped_lines: - group.pop(0) - for group in grouped_lines: - gene = group[0].split(":", 1)[1].strip() - relation = group[1].split(":", 1)[1].strip() - exposure = group[2].split(":", 1)[1].strip() - trimmed_dict["genes"].append(gene) - trimmed_dict["relationships"].append(relation) - trimmed_dict["exposures"].append(exposure) - - # Remove all null values - for _, value in trimmed_dict.copy().items(): - for i, elem in enumerate(value): - if elem.lower() in (val.lower() for val in NULL_VALS): - for _, value in trimmed_dict.items(): - del value[i] - - # Find names for all ID entries in OBO Foundry - for key, value in trimmed_dict.copy().items(): - for index, elem in enumerate(value): - if ":" in elem: - try: - prefix = elem[: (elem.index(":"))] - adapter_str = "sqlite:obo:" + str(prefix) - curr_adapter = get_adapter(adapter_str) - trimmed_dict[key][index] = curr_adapter.label(elem) - except KeyError: - continue - - return lines - - -def write_obj_as_csv(obj: Any, file, minimize=True, index_field=None) -> None: - if isinstance(obj, BaseModel): - obj = obj.dict() - if isinstance(obj, list): - rows = obj - elif not isinstance(obj, dict): - if not index_field: - index_fields = [k for k, v in obj.items() if v and isinstance(v, list)] - if len(index_fields) == 1: - index_field = index_fields[0] - logger.warning(f"Using {index_field} as index field") - rows = obj[index_field] - else: - raise ValueError(f"Cannot dump {obj} as CSV") - if isinstance(file, Path) or isinstance(file, str): - file = open(file, "w", encoding="utf-8") - rows = [row.dict() if isinstance(row, BaseModel) else row for row in rows] - writer = csv.DictWriter(file, fieldnames=rows[0].keys(), delimiter="\t") - writer.writeheader() - for row in rows: - - def _str(s): - if s is None: - return "" - return str(s) - - # row = {k: v for k, v in row.items() if "\n" not in str(v)} - row = {k: _str(v).replace("\n", r"\n").replace("\t", " ") for k, v in row.items()} - writer.writerow(row) diff --git a/src/ontogpt/io/exporter.py b/src/ontogpt/io/exporter.py deleted file mode 100644 index 36b79b437..000000000 --- a/src/ontogpt/io/exporter.py +++ /dev/null @@ -1,24 +0,0 @@ -"""Exporter.""" -from dataclasses import dataclass -from io import BytesIO -from pathlib import Path -from typing import Optional, TextIO, Union - -from linkml_runtime import SchemaView - -from ontogpt.templates.core import ExtractionResult - - -def is_curie(s: str) -> bool: - return ":" in s and " " not in s - - -@dataclass -class Exporter: - def export( - self, - extraction_output: ExtractionResult, - output: Union[str, Path, TextIO, BytesIO], - schemaview: Optional[SchemaView], - ): - raise NotImplementedError diff --git a/src/ontogpt/io/html_exporter.py b/src/ontogpt/io/html_exporter.py deleted file mode 100644 index 0d841047f..000000000 --- a/src/ontogpt/io/html_exporter.py +++ /dev/null @@ -1,150 +0,0 @@ -"""HTML Exporter.""" -import html -from dataclasses import dataclass -from io import BytesIO, StringIO, TextIOWrapper -from pathlib import Path -from typing import Any, Optional, TextIO, Union - -import pydantic -import yaml -from linkml_runtime import SchemaView - -from ontogpt.io.exporter import Exporter, is_curie -from ontogpt.templates.core import ExtractionResult - - -@dataclass -class HTMLExporter(Exporter): - """ - An exporter that will generate HTML for extraction results. - - TODO: rewrite to use bootstrap - """ - - output: Optional[Union[BytesIO, TextIO]] - - def export( - self, - extraction_output: ExtractionResult, - output: Union[str, Path, TextIO, BytesIO], - schemaview: Optional[SchemaView] = None, - ): # type: ignore - if isinstance(output, Path): - output = open(str(output), "w", encoding="utf-8") - if isinstance(output, str): - output = StringIO(output) - self.output = output - self.export_metadata(extraction_output) - self.export_results(extraction_output.extracted_object, extraction_output) - self.h2("YAML Object") - self.details(yaml.dump(extraction_output.dict()), output, code="yaml") - self.h2("Prompt") - self.details(extraction_output.prompt, output) - self.h2("Completion") - self.details(extraction_output.raw_completion_output, output) - - def export_metadata(self, extraction_output: ExtractionResult): - output = self.output - self.h1(f"Results: {extraction_output.input_id}\n\n") - self.h2("Input") - self.i(extraction_output.input_text) - - def export_results(self, obj: Any, extraction_output: ExtractionResult): - self.h2("Results") - self.export_object(obj, extraction_output, -1) - - def export_object( - self, obj: pydantic.BaseModel, extraction_output: ExtractionResult, indent: int - ): - self.open_div() - if indent >= 0: - self.open_ul() - for field_name, _field in obj.model_fields.items(): - if indent < 0: - self.h3(field_name) - else: - self.li(f"<i>{field_name}</i>: ") - value = getattr(obj, field_name) - if isinstance(value, pydantic.BaseModel): - self.export_object(value, extraction_output, indent + 1) - elif isinstance(value, list): - self.open_ul() - n = 1 - for item in value: - self.li(f"<b>item: {n}</b>: ") - n += 1 - if isinstance(item, pydantic.BaseModel): - self.export_object( - item, extraction_output=extraction_output, indent=indent + 1 - ) - else: - self.export_atom(item, extraction_output, indent + 1) - self.close_ul() - else: - self.export_atom(value, extraction_output, indent + 1) - if indent >= 0: - self.open_ul() - self.close_div() - - def export_atom(self, value, extraction_output: ExtractionResult, indent: int): - output = self.output - matches = [ - ne for ne in extraction_output.named_entities if ne.id == value and is_curie(ne.id) - ] - if isinstance(output, BytesIO): - output = TextIOWrapper(output, encoding="utf-8") - if matches: - match = matches[0] - output.write(f"{match.label} {self.link(match.id)}") - else: - output.write(str(value)) - output.write("\n") - - def details(self, text: Optional[str], output: Union[BytesIO, TextIO], code: str = ""): - if isinstance(output, BytesIO): - output = TextIOWrapper(output, encoding="utf-8") - output.write("<details>\n") - output.write("<pre>\n") - self.w(text) - output.write("\n</pre>\n") - output.write("\n</details>\n") - - def link(self, curie: str) -> str: - return f'<a href="https://bioregistry.io/{curie}">{curie}</a>' - - def open_ul(self): - self.output.write("<ul>\n") - - def close_ul(self): - self.output.write("</ul>\n") - - def open_div(self): - self.output.write("<div>\n") - - def close_div(self): - self.output.write("</div>\n") - - def li(self, text: str = ""): - self.tag("li", text) - - def h1(self, text: str): - self.tag("h1", text) - - def h2(self, text: str): - self.tag("h1", text) - - def h3(self, text: str): - self.tag("h3", text) - - def i(self, text: Optional[str]): - self.tag("i", html.escape(text)) - - def tag(self, tag: str, text: str): - if isinstance(self.output, BytesIO): - self.output = TextIOWrapper(self.output, encoding="utf-8") - self.output.write(f"<{tag}>{text}</{tag}>\n") - - def w(self, text: str): - if isinstance(self.output, BytesIO): - self.output = TextIOWrapper(self.output, encoding="utf-8") - self.output.write(html.escape(text)) diff --git a/src/ontogpt/io/markdown_exporter.py b/src/ontogpt/io/markdown_exporter.py deleted file mode 100644 index 55a217001..000000000 --- a/src/ontogpt/io/markdown_exporter.py +++ /dev/null @@ -1,93 +0,0 @@ -"""Markdown exporter.""" -from dataclasses import dataclass -from io import BytesIO, StringIO, TextIOWrapper -from pathlib import Path -from typing import Optional, TextIO, Union - -import pydantic -import yaml -from linkml_runtime import SchemaView - -from ontogpt.io.exporter import Exporter, is_curie -from ontogpt.templates.core import ExtractionResult - - -@dataclass -class MarkdownExporter(Exporter): - def export( - self, - extraction_output: ExtractionResult, - output: Union[str, Path, TextIO, BytesIO], - schemaview: Optional[SchemaView] = None, - ): # type: ignore - if isinstance(output, Path): - output = open(str(output), "w", encoding="utf-8") - if isinstance(output, str): - output = StringIO(output) - if isinstance(output, BytesIO): - output = TextIOWrapper(output, encoding="utf-8") - output.write(f"# {extraction_output.input_id}\n\n") - output.write("## Input\n\n") - for block in extraction_output.input_text.split("\n"): - output.write(f"_{block.replace('_', '')}_\n\n") - output.write("## Results\n\n") - obj = extraction_output.extracted_object - self.export_object(obj, extraction_output, output, -1) - output.write("\n\nYAML:\n\n") - self.details(yaml.dump(extraction_output.dict()), output, code="yaml") - output.write("\n\nPrompt:\n\n") - self.details(extraction_output.prompt, output) - output.write("\n\nCompletion:\n\n") - self.details(extraction_output.raw_completion_output, output) - - def export_object( - self, - obj: pydantic.BaseModel, - extraction_output: ExtractionResult, - output: TextIO, - indent: int, - ): - for field in obj.__fields__.values(): - if indent < 0: - output.write(f"\n\n### {field.name}\n\n") - else: - output.write(f"\n{' ' * indent}- {field.name}:") - value = getattr(obj, field.name) - if isinstance(value, pydantic.BaseModel): - self.export_object(value, extraction_output, output, indent + 1) - elif isinstance(value, list): - for item in value: - if isinstance(item, pydantic.BaseModel): - self.export_object( - item, - extraction_output=extraction_output, - output=output, - indent=indent + 1, - ) - else: - self.export_atom(item, extraction_output, output, indent + 1) - else: - self.export_atom(value, extraction_output, output, indent + 1) - output.write("\n") - - def export_atom(self, value, extraction_output: ExtractionResult, output: TextIO, indent: int): - matches = [ - ne for ne in extraction_output.named_entities if ne.id == value and is_curie(ne.id) - ] - output.write(f"\n{' ' * indent}- ") - if matches: - match = matches[0] - output.write(f"{match.label} {self.link(match.id)}") - else: - output.write(f"{value}") - output.write("\n") - - def details(self, text: str, output: TextIO, code: str = ""): - output.write("<details>\n") - output.write(f"```{code}\n") - output.write(text) - output.write("\n```\n") - output.write("\n</details>\n") - - def link(self, curie: str) -> str: - return f"[{curie}](https://bioregistry.io/{curie})" diff --git a/src/ontogpt/io/owl_exporter.py b/src/ontogpt/io/owl_exporter.py deleted file mode 100644 index bbb13490e..000000000 --- a/src/ontogpt/io/owl_exporter.py +++ /dev/null @@ -1,60 +0,0 @@ -"""OWL convertor.""" -from dataclasses import dataclass -from io import BytesIO -from pathlib import Path -from typing import TextIO, Union - -import pydantic -from linkml.generators.pythongen import PythonGenerator -from linkml_owl.dumpers.owl_dumper import OWLDumper -from linkml_runtime import SchemaView - -from ontogpt.io.exporter import Exporter -from ontogpt.templates.core import ExtractionResult - - -@dataclass -class OWLExporter(Exporter): - def export( - self, - extraction_output: ExtractionResult, - output: Union[str, Path, TextIO, BytesIO], - schemaview: SchemaView, - id_value=None, - ): - if isinstance(output, Path): - output = str(output) - if isinstance(output, str): - output = open(str(output), "w", encoding="utf-8") - dumper = OWLDumper() - element = extraction_output.extracted_object - cls_name = type(element).__name__ - id_slot = schemaview.get_identifier_slot(cls_name) - if id_slot is not None: - id_slot_name = id_slot.name - if id_value is not None: - setattr(element, id_slot_name, "AUTO:_ROOT") - else: - id_value = getattr(element, id_slot_name, None) - print(f"Setting {id_slot_name} [{id_value}] to AUTO:_ROOT for {cls_name}") - if id_value is None: - setattr(element, id_slot_name, "AUTO:_ROOT") - axioms = [] - if extraction_output.named_entities is not None: - for named_entity in extraction_output.named_entities: - ne_as_dc = self._as_dataclass_object(named_entity, schemaview) - doc = dumper.to_ontology_document(ne_as_dc, schemaview.schema) - axioms.extend(doc.ontology.axioms) - element_as_dataclass = self._as_dataclass_object(element, schemaview) - doc = dumper.to_ontology_document(element_as_dataclass, schemaview.schema) - doc.ontology.axioms.extend(axioms) - output.write(str(doc).encode("utf-8")) # type: ignore - - def _as_dataclass_object(self, element: pydantic.BaseModel, schemaview: SchemaView): - cls_name = type(element).__name__ - schemaview.merge_imports() - element_dict = element.dict() - dataclasses_module = PythonGenerator(schemaview.schema).compile_module() - target_class_py = dataclasses_module.__dict__[cls_name] - element_as_dataclass = target_class_py(**element_dict) - return element_as_dataclass diff --git a/src/ontogpt/io/rdf_exporter.py b/src/ontogpt/io/rdf_exporter.py deleted file mode 100644 index e7c0f4c9c..000000000 --- a/src/ontogpt/io/rdf_exporter.py +++ /dev/null @@ -1,51 +0,0 @@ -"""RDF convertor.""" -import logging -from dataclasses import dataclass -from io import BytesIO -from pathlib import Path -from typing import TextIO, Union - -from linkml.generators.pythongen import PythonGenerator -from linkml_runtime import SchemaView -from linkml_runtime.dumpers import rdflib_dumper - -from ontogpt.io.exporter import Exporter -from ontogpt.templates.core import ExtractionResult - -# TODO: get URI prefixes from bioregistry - - -@dataclass -class RDFExporter(Exporter): - def export( - self, - extraction_output: ExtractionResult, - output: Union[str, Path, TextIO, BytesIO], - schemaview: SchemaView, - id_value=None, - ): - if isinstance(output, Path): - output = str(output) - if isinstance(output, str): - output = open(str(output), "w", encoding="utf-8") - element = extraction_output.extracted_object - cls_name = type(element).__name__ - element_dict_obj = element.dict() - dc_mod = self._dataclass_model(schemaview) - dc_cls = dc_mod.__dict__[cls_name] - dc_obj = dc_cls(**element_dict_obj) - pm = {"_base": "http://example.org/NOPREFIX/"} - if "AUTO" not in schemaview.schema.prefixes: - pm["AUTO"] = "http://example.org/AUTO/" - try: - dmp = rdflib_dumper.dumps(dc_obj, schemaview=schemaview, prefix_map=pm) - output.write(dmp) - except Exception as e: - # Don't really like catching base Exception here, - # but that's what rdflib raises. - # Otherwise, catch ValueError - logging.error(e) - - def _dataclass_model(self, schemaview: SchemaView): - schemaview.merge_imports() - return PythonGenerator(schemaview.schema).compile_module() diff --git a/src/ontogpt/io/yaml_wrapper.py b/src/ontogpt/io/yaml_wrapper.py deleted file mode 100644 index 4a3c4aadf..000000000 --- a/src/ontogpt/io/yaml_wrapper.py +++ /dev/null @@ -1,54 +0,0 @@ -"""YAML Wrapper.""" -import io -import logging -from typing import Any, Optional, TextIO - -import pydantic -from ruamel.yaml import YAML, RoundTripRepresenter - -# import yaml -# from yaml import SafeDumper - -logger = logging.getLogger(__name__) - - -def eliminate_empty(obj: Any, preserve=False) -> Any: - """Eliminate empty lists and dicts from an object.""" - if isinstance(obj, list): - return [eliminate_empty(x, preserve) for x in obj if x or preserve] - elif isinstance(obj, dict): - return {k: eliminate_empty(v, preserve) for k, v in obj.items() if v or preserve} - elif isinstance(obj, pydantic.BaseModel): - return eliminate_empty(obj.model_dump(), preserve) - elif isinstance(obj, tuple): - return [eliminate_empty(x, preserve) for x in obj] - elif isinstance(obj, str): - return str(obj) - else: - return obj - - -# SafeDumper.add_representer(str, -# lambda dumper, value: dumper.represent_scalar('tag:yaml.org,2002:str', value, style='|') -# ) - - -def repr_str(dumper: RoundTripRepresenter, data: str): - if "\n" in data: - return dumper.represent_scalar("tag:yaml.org,2002:str", data, style="|") - return dumper.represent_scalar("tag:yaml.org,2002:str", data) - - -def dump_minimal_yaml(obj: Any, minimize=True, file: Optional[TextIO] = None) -> str: - """Dump a YAML string, but eliminating Nones and empty lists and dicts.""" - yaml = YAML() - yaml.representer.add_representer(str, repr_str) - yaml.default_flow_style = False - yaml.indent(sequence=4, offset=2) - if not file: - file = io.StringIO() - yaml.dump(eliminate_empty(obj, not minimize), file) - return file.getvalue() - else: - yaml.dump(eliminate_empty(obj, not minimize), file) - return "" diff --git a/src/ontogpt/models.yaml b/src/ontogpt/models.yaml deleted file mode 100644 index 51815ba1a..000000000 --- a/src/ontogpt/models.yaml +++ /dev/null @@ -1,342 +0,0 @@ -models: - - name: MODEL_GPT_3_5_TURBO - alternative_names: - - "gpt-3.5-turbo" - - "openai-gpt-3.5-turbo" - provider: OpenAI - creators: - - OpenAI - requirements: - diskspace: "N/A" - memory: "N/A" - is_default: true - - - name: MODEL_GPT_3_5_TURBO_16K - alternative_names: - - "gpt-3.5-turbo-16k" - - "openai-gpt-3.5-turbo-16k" - provider: OpenAI - creators: - - OpenAI - requirements: - diskspace: "N/A" - memory: "N/A" - - - name: MODEL_GPT_4 - alternative_names: - - "gpt-4" - - "openai-gpt-4" - provider: OpenAI - creators: - - OpenAI - requirements: - diskspace: "N/A" - memory: "N/A" - - - name: MODEL_GPT_4_32K - alternative_names: - - "gpt-4-32k" - - "openai-gpt-4-32k" - provider: OpenAI - creators: - - OpenAI - requirements: - diskspace: "N/A" - memory: "N/A" - - - name: MODEL_GPT_4_1106_PREVIEW - alternative_names: - - "gpt-4-1106-preview" - - "openai-gpt-4-1106-preview" - provider: OpenAI - creators: - - OpenAI - requirements: - diskspace: "N/A" - memory: "N/A" - - - name: MODEL_GPT_3_5_TURBO_INSTRUCT - alternative_names: - - "gpt-3.5-turbo-instruct" - - "openai-gpt-3.5-turbo-instruct" - provider: OpenAI - creators: - - OpenAI - requirements: - diskspace: "N/A" - memory: "N/A" - - - name: MODEL_TEXT_DAVINCI_003 - alternative_names: - - "text-davinci-003" - - "openai-text-davinci-003" - provider: OpenAI - creators: - - OpenAI - requirements: - diskspace: "N/A" - memory: "N/A" - deprecated: true - - - name: MODEL_CODE_DAVINCI_002 - alternative_names: - - "code-davinci-002" - - "openai-code-davinci-002" - provider: OpenAI - creators: - - OpenAI - requirements: - diskspace: "N/A" - memory: "N/A" - deprecated: true - - - name: ORCA_MINI_3B - alternative_names: - - orca-mini-3b - provider: GPT4All - creators: - - "Subhabrata Mukherjee" - - "Arindam Mitra" - - "Ganesh Jawahar" - - "Sahaj Agarwal" - - "Hamid Palangi" - - "Ahmed Awadallah" - requirements: - diskspace: "1.80 GB" - memory: "4 GB" - - - name: GGML_ALL_MINILM_L6_V2_F16 - alternative_names: - - ggml-all-MiniLM-L6-v2-f16 - provider: GPT4All - creators: - - "Google" - requirements: - diskspace: "43.41 MB" - memory: "1 GB" - - - name: GGML_GPT4ALL_J_V1 - alternative_names: - - ggml-gpt4all-j-v1 - provider: GPT4All - creators: - - "Nomic AI" - requirements: - diskspace: "3.53 GB" - memory: "8 GB" - - - name: LLAMA_2_7B_CHAT - alternative_names: - - llama-2-7b-chat - provider: GPT4All - creators: - - "Meta AI" - requirements: - diskspace: "3.53 GB" - memory: "8 GB" - - - name: ORCA_MINI_7B - alternative_names: - - orca-mini-7b - provider: GPT4All - creators: - - "Subhabrata Mukherjee" - - "Arindam Mitra" - - "Ganesh Jawahar" - - "Sahaj Agarwal" - - "Hamid Palangi" - - "Ahmed Awadallah" - requirements: - diskspace: "3.53 GB" - memory: "8 GB" - - - name: GGML_MODEL_GPT4ALL_FALCON_Q4_0 - alternative_names: - - ggml-model-gpt4all-falcon-q4_0 - provider: GPT4All - creators: - - "Technology Innovation Institute" - - "Nomic AI" - requirements: - diskspace: "3.78 GB" - memory: "8 GB" - - - name: GGML_VICUNA_7B_1 - alternative_names: - - ggml-vicuna-7b-1 - provider: GPT4All - creators: - - "UC Berkeley" - - "Carnegie Mellon University" - - "Stanford University" - - "Mohamed bin Zayed University of Artificial Intelligence" - - "UC San Diego" - requirements: - diskspace: "3.92 GB" - memory: "8 GB" - - - name: GGML_WIZARDLM_7B - alternative_names: - - ggml-wizardLM-7B - provider: GPT4All - creators: - - "Microsoft Corporation" - - "Peking University" - requirements: - diskspace: "3.92 GB" - memory: "8 GB" - - - name: GGML_MPT_7B_BASE - alternative_names: - - ggml-mpt-7b-base - provider: GPT4All - creators: - - "Mosaic ML" - requirements: - diskspace: "4.52 GB" - memory: "8 GB" - - - name: GGML_MPT_7B_INSTRUCT - alternative_names: - - ggml-mpt-7b-instruct - provider: GPT4All - creators: - - "Mosaic ML" - requirements: - diskspace: "4.52 GB" - memory: "8 GB" - - - name: GGML_MPT_7B_CHAT - alternative_names: - - ggml-mpt-7b-chat - provider: GPT4All - creators: - - "Mosaic ML" - requirements: - diskspace: "4.52 GB" - memory: "8 GB" - - - name: GGML_REPLIT_CODE_V1_3B - alternative_names: - - ggml-replit-code-v1-3b - provider: GPT4All - creators: - - "Replit Inc." - - "Mosaic ML" - requirements: - diskspace: "4.84 GB" - memory: "4 GB" - - - name: WIZARDLM_13B_V1 - alternative_names: - - wizardlm-13b-v1 - provider: GPT4All - creators: - - "Microsoft Corporation" - - "Peking University" - requirements: - diskspace: "6.82 GB" - memory: "16 GB" - - - name: ORCA_MINI_13B - alternative_names: - - orca-mini-13b - provider: GPT4All - creators: - - "Subhabrata Mukherjee" - - "Arindam Mitra" - - "Ganesh Jawahar" - - "Sahaj Agarwal" - - "Hamid Palangi" - - "Ahmed Awadallah" - requirements: - diskspace: "6.82 GB" - memory: "16 GB" - - - name: STARCODERBASE-3B-GGML - alternative_names: - - starcoderbase-3b-ggml - provider: GPT4All - creators: - - "BigCode" - requirements: - diskspace: "6.99 GB" - memory: "8 GB" - - - name: GPT4ALL_13B_SNOOZY - alternative_names: - - GPT4All-13B-snoozy - provider: GPT4All - creators: - - "Nomic AI" - requirements: - diskspace: "7.58 GB" - memory: "16 GB" - - - name: GGML_VICUNA_13B_1 - alternative_names: - - ggml-vicuna-13b-1 - provider: GPT4All - creators: - - "UC Berkeley" - - "Carnegie Mellon University" - - "Stanford University" - - "Mohamed bin Zayed University of Artificial Intelligence" - - "UC San Diego" - requirements: - diskspace: "7.58 GB" - memory: "16 GB" - - - name: GGML_NOUS_GPT4_VICUNA_13B - alternative_names: - - ggml-nous-gpt4-vicuna-13b - provider: GPT4All - creators: - - "UC Berkeley" - - "Carnegie Mellon University" - - "Stanford University" - - "Mohamed bin Zayed University of Artificial Intelligence" - - "UC San Diego" - - "Nous Research" - requirements: - diskspace: "7.58 GB" - memory: "16 GB" - - - name: GGML_STABLE_VICUNA_13B - alternative_names: - - ggml-stable-vicuna-13B - provider: GPT4All - creators: - - "UC Berkeley" - - "Carnegie Mellon University" - - "Stanford University" - - "Mohamed bin Zayed University of Artificial Intelligence" - - "UC San Diego" - requirements: - diskspace: "7.58 GB" - memory: "16 GB" - - - name: NOUS_HERMES_13B - alternative_names: - - nous-hermes-13b - provider: GPT4All - creators: - - "Nous Research" - - "Teknium" - - "Karan4" - - "Huemin Art" - - "Redmond AI" - requirements: - diskspace: "7.58 GB" - memory: "16 GB" - - - name: WIZARDLM_13B_UNCENSORED - alternative_names: - - wizardLM-13B-Uncensored - provider: GPT4All - creators: - - "Microsoft Corporation" - - "Peking University" - requirements: - diskspace: "7.58 GB" - memory: "16 GB" diff --git a/src/ontogpt/ontex/extractor.py b/src/ontogpt/ontex/extractor.py deleted file mode 100644 index e2c514e4d..000000000 --- a/src/ontogpt/ontex/extractor.py +++ /dev/null @@ -1,1711 +0,0 @@ -"""Tools to extract sub-ontologies and reasoner tasks.""" -import base64 -import logging -import random -import re -import sys -import uuid -from collections import defaultdict -from dataclasses import dataclass, field -from enum import Enum -from pathlib import Path -from typing import ( - Any, - ClassVar, - Iterable, - List, - Literal, - Mapping, - Optional, - TextIO, - Tuple, - Type, - Union, -) - -import inflection -import yaml -from oaklib.datamodels.taxon_constraints import SubjectTerm, Taxon, TaxonConstraint -from oaklib.datamodels.vocabulary import ( - DISJOINT_WITH, - IN_TAXON, - INVERSE_OF, - IS_A, - NEVER_IN_TAXON, - ONLY_IN_TAXON, - OWL_CLASS, - OWL_NAMED_INDIVIDUAL, - OWL_SYMMETRIC_PROPERTY, - OWL_TRANSITIVE_PROPERTY, - PART_OF, - SUBPROPERTY_OF, -) -from oaklib.implementations import SqlImplementation -from oaklib.interfaces import OboGraphInterface -from oaklib.interfaces.basic_ontology_interface import RELATIONSHIP -from oaklib.interfaces.obograph_interface import GraphTraversalMethod -from oaklib.interfaces.semsim_interface import SemanticSimilarityInterface -from oaklib.interfaces.taxon_constraint_interface import TAXON_PREDICATES, TaxonConstraintInterface -from oaklib.types import CURIE, PRED_CURIE -from oaklib.utilities.obograph_utils import shortest_paths -from pydantic import BaseModel, Field -from semsql.sqla.semsql import RdfListMemberStatement, RdfTypeStatement, Statements - -logger = logging.getLogger(__name__) - - -OBFUSCATED_ID = "str" - - -class Axiom(BaseModel): - """Represents an individual logical axiom.""" - - text: str = "" - """Textual representation of the axiom, e.g A SubClassOf B""" - - obfuscated_text: Optional[str] = None - """Textual representation of the axiom, with obfuscated terms""" - - abox: bool = False - """Whether the axiom is an ABox axiom.""" - - edge: Optional[RELATIONSHIP] = None - """The relationship between the two terms in the axiom.""" - - -class Ontology(BaseModel): - """An ontology is a collection of axioms.""" - - name: Optional[str] = None - axioms: List[Axiom] - """All axioms in the ontology""" - - terms: List[CURIE] = [""] - predicates: List[PRED_CURIE] = [""] - - comments: Optional[List[str]] = None - - -class Query(BaseModel): - """Query.""" - - text: Optional[str] = None - """Text representation of the query.""" - - parameters: Optional[List[str]] = None - """Parameters to the query. - E.g for a query of the form 'what is the superclass of X', - there is one parameter X, for the subclass.""" - - -class Explanation(BaseModel): - """A set of axioms that entail some explained axiom.""" - - axioms: List[Axiom] = [] - text: Optional[str] = None - comments: Optional[List[str]] = None - - -class Answer(BaseModel): - """Individual answer to a query.""" - - _value_domain: ClassVar[str] - """Class variable indicating answer types.""" - - text: str - """Textual representation of the answer.""" - - explanations: Optional[List[Explanation]] = None - """All explanations for the answer.""" - - def shortest_explanation(self) -> Explanation: - """Return the shortest explanation for the answer.""" - if not self.explanations: - return Explanation(axioms=[Axiom(text="No explanation found")]) - shortest = min(self.explanations, key=lambda x: len(x.axioms)) - return shortest - - -class ObjectAnswer(Answer): - """Answer that is an object, e.g class.""" - - _value_domain = "The name of the object." - - -class ClassAnswer(Answer): - """Answer that is an OWL class.""" - - _value_domain = "The name of the class." - - -class InstanceAnswer(Answer): - """Answer that is an OWL individual.""" - - _value_domain = "The name of the individual." - - -class BooleanAnswer(Answer): - """Answer that is a boolean, e.g. true or false.""" - - _value_domain = "Either TRUE or FALSE." - - -class AxiomAnswer(Answer): - """Answer that is a axiom.""" - - _value_domain = "An axiom written in Manchester syntax." - - -class ExampleQueryAnswers(BaseModel): - """An example query, plus all expected answers.""" - - query: Query - answers: Optional[List[Answer]] = None - - -class Example(BaseModel): - """An example of a query plus answers, in the context of an ontology.""" - - ontology: Ontology - query_answers: Optional[List[ExampleQueryAnswers]] = None - - -class GPTReasonMethodType(str, Enum): - BASIC = "basic" - EXPLANATION = "explanation" - CHAIN_OF_THOUGHT = "chain_of_thought" - - -class Task(BaseModel): - """ - A task is a query on an ontology that has a set of defined answers. - - For example, a task group might be to determine if an ontology is consistent. - """ - - _query_format: ClassVar[str] - - type: Literal["Task"] = Field("Task") - _code: ClassVar[str] - - has_multiple_answers: ClassVar[bool] = True - - ontology: Ontology - name: Optional[str] = None - description: Optional[str] = None - query: Optional[Query] = None - answers: Optional[List[Answer]] = None - examples: Optional[List[Example]] = None - obfuscated: Optional[bool] = False - - method: Optional[GPTReasonMethodType] = None - - include_explanations: Optional[bool] = False - """If true then completing the task must involve providing explanations for each answer.""" - - chain_of_thought: Optional[bool] = False - """If true explanations come first, providing chain of thought reasoning.""" - - abductive: Optional[bool] = False - """If true then the task is to find explanations for answers that are given.""" - - shortest_explanation: Optional[Explanation] = None - - len_shortest_explanation: Optional[int] = None - - class Config: - """Pydantic configuration.""" - - use_enum_values = True - - def populate(self) -> None: - qf = self._query_format - for example in self.examples: - for query_answer in example.query_answers: - if not query_answer.query.text: - query_answer.query.text = qf.format(params=query_answer.query.parameters) - if self.query is not None: - if not self.query.text: - self.query.text = qf.format(params=self.query.parameters) - if self.answers is not None: - if len(self.answers) == 0: - self.shortest_explanation = None - self.len_shortest_explanation = 0 - else: - most_complex_answer = max( - self.answers, key=lambda x: len(x.shortest_explanation().axioms) - ) - if self.shortest_explanation is not None: - self.shortest_explanation = most_complex_answer.shortest_explanation() - self.len_shortest_explanation = len(self.shortest_explanation.axioms) - if not self.name: - self.name = f"{self.type}-{uuid.uuid4()}" - self.init_method() - - def init_method(self): - if self.method: - logger.info(f"Initializing method for {self.name}") - if not isinstance(self.method, GPTReasonMethodType): - self.method = GPTReasonMethodType(self.method) - if self.method == GPTReasonMethodType.EXPLANATION: - self.include_explanations = True - elif self.method == GPTReasonMethodType.CHAIN_OF_THOUGHT: - self.chain_of_thought = True - else: - if self.include_explanations: - self.method = GPTReasonMethodType.EXPLANATION - elif self.chain_of_thought: - self.method = GPTReasonMethodType.CHAIN_OF_THOUGHT - else: - self.method = GPTReasonMethodType.BASIC - - -class OntologyCoherencyTask(Task): - """ - A task to determine if an ontology is coherent. - - There should be a single answer, which is a boolean. - """ - - _query_format = """ - What are the unsatisfiable classes in the ontology? - A class X is unsatisfiable if X is a subclass of DC1 and also a subclass of DC2, - where there is an axiom DC1 DisjointWith DC2. - Here, SubClassOf can mean either direct or indirect subclass, entailed - through the transitivity of SubClassOf. - List all unsatisfiable classes that can be found with this rule. - If there are no unsatisfiable classes, just write NONE.""" - - type: Literal["OntologyCoherencyTask"] = Field("OntologyCoherencyTask") # type: ignore - _code: str = "sat" # type: ignore - - has_multiple_answers = False - answers: Optional[List[ClassAnswer]] = None - - examples: Optional[List[Example]] = [ - Example( - ontology=Ontology( - axioms=[ - Axiom(text="B SubClassOf A"), - Axiom(text="C SubClassOf A"), - Axiom(text="D SubClassOf B"), - Axiom(text="D SubClassOf C"), - Axiom(text="B DisjointWith C"), - ] - ), - query_answers=[ - ExampleQueryAnswers( - query=Query(), - answers=[ - ClassAnswer( - text="D", - explanations=[ - Explanation( - text="""D is unsatisfiable because it is a subclass - of two disjoint classes (B and C).""", - axioms=[ - Axiom(text="D SubClassOf B"), - Axiom(text="D SubClassOf C"), - Axiom(text="B DisjointWith C"), - ], - ) - ], - ) - ], - ), - ], - ), - Example( - ontology=Ontology( - axioms=[ - Axiom(text="B SubClassOf A"), - Axiom(text="C SubClassOf A"), - Axiom(text="D SubClassOf B"), - Axiom(text="B DisjointWith A"), - ] - ), - query_answers=[ - ExampleQueryAnswers( - query=Query(), - answers=[ - ClassAnswer( - text="NONE", - explanations=[ - Explanation( - text="""There is only one Disjointness Axiom (B DisjointWith A), - and B and A do not share either direct - or indirect subclasses.""", - axioms=[], - ) - ], - ) - ], - ), - ], - ), - ] - - -class EntailedIndirectSuperClassTask(Task): - """A task to determine the indirect superclasses of a class.""" - - _query_format = """ - What are the indirect entailed superclasses of {params[0]}? - Include answers entailed by the transitivity of SubClassOf. - Do not include direct (one-hop) superclasses. - """ - - type: Literal["EntailedIndirectSuperClassTask"] = Field( - "EntailedIndirectSuperClassTask" - ) # type: ignore - _code: str = "indirect" # type: ignore - - answers: Optional[List[ClassAnswer]] = None - - examples: Optional[List[Example]] = [ - Example( - ontology=Ontology( - axioms=[ - Axiom(text="E2 SubClassOf E"), - Axiom(text="E SubClassOf B"), - Axiom(text="B SubClassOf A"), - Axiom(text="C SubClassOf A"), - Axiom(text="D SubClassOf B"), - ] - ), - query_answers=[ - ExampleQueryAnswers( - query=Query(parameters=["E"]), - answers=[ - ClassAnswer( - text="A", - explanations=[ - Explanation( - text="""A is an indirect entailed superclass of E because - E SubClassOf B, and B SubClassOf A, and SubClassOf is - transitive.""", - axioms=[ - Axiom(text="E SubClassOf B"), - Axiom(text="B SubClassOf A"), - ], - ) - ], - ), - ], - ), - ExampleQueryAnswers( - query=Query(parameters=["E2"]), - answers=[ - ClassAnswer( - text="A", - explanations=[ - Explanation( - text="""A is an indirect entailed superclass of E2 because - E2 SubClassOf E, and E SubClassOf B, and B SubClassOf A, - and because SubClassOf is transitive.""", - axioms=[ - Axiom(text="E2 SubClassOf E"), - Axiom(text="E SubClassOf B"), - Axiom(text="B SubClassOf A"), - ], - ) - ], - ), - ClassAnswer( - text="B", - explanations=[ - Explanation( - text="""B is an indirect entailed superclass of E2 because - E2 SubClassOf E, and E SubClassOf B, and because SubClassOf - is transitive.""", - axioms=[ - Axiom(text="E SubClassOf B"), - Axiom(text="E2 SubClassOf E"), - ], - ) - ], - ), - ], - ), - ], - ) - ] - - -class EntailedTransitiveSuperClassTask(Task): - """A task to determine the all transitive superclasses of a class.""" - - _query_format = """ - What are the transitive superclasses of {params[0]}? - Include answers entailed by the transitivity of SubClassOf. - Also direct (one-hop) superclasses. - """ - - type: Literal["EntailedTransitiveSuperClassTask"] = Field( - "EntailedTransitiveSuperClassTask" - ) # type: ignore - _code: str = "superc" # type: ignore - - answers: Optional[List[ClassAnswer]] = None - - examples: Optional[List[Example]] = [ - Example( - ontology=Ontology( - axioms=[ - Axiom(text="E2 SubClassOf E"), - Axiom(text="E SubClassOf B"), - Axiom(text="B SubClassOf A"), - Axiom(text="C SubClassOf A"), - Axiom(text="D SubClassOf B"), - ] - ), - query_answers=[ - ExampleQueryAnswers( - query=Query(parameters=["E"]), - answers=[ - ClassAnswer( - text="A", - explanations=[ - Explanation( - text="""A is an entailed superclass of E because - E SubClassOf B, and B SubClassOf A, and SubClassOf is - transitive.""", - axioms=[ - Axiom(text="E SubClassOf B"), - Axiom(text="B SubClassOf A"), - ], - ) - ], - ), - ClassAnswer( - text="B", - explanations=[ - Explanation( - text="""B is an indirect entailed superclass of E because - it is already asserted.""", - axioms=[ - Axiom(text="B SubClassOf A"), - ], - ) - ], - ), - ], - ), - ExampleQueryAnswers( - query=Query(parameters=["E2"]), - answers=[ - ClassAnswer( - text="A", - explanations=[ - Explanation( - text="""A is an indirect entailed superclass of E2 because - E2 SubClassOf E, and E SubClassOf B, and B SubClassOf A, - and because SubClassOf is transitive.""", - axioms=[ - Axiom(text="E2 SubClassOf E"), - Axiom(text="E SubClassOf B"), - Axiom(text="B SubClassOf A"), - ], - ) - ], - ), - ClassAnswer( - text="B", - explanations=[ - Explanation( - text="""B is an entailed superclass of E2 because - E2 SubClassOf E, and E SubClassOf B, and because SubClassOf - is transitive.""", - axioms=[ - Axiom(text="E SubClassOf B"), - Axiom(text="E2 SubClassOf E"), - ], - ) - ], - ), - ClassAnswer( - text="E", - explanations=[ - Explanation( - text="""E is an entailed superclass of E2 because - it is directly asserted.""", - axioms=[ - Axiom(text="E2 SubClassOf E"), - ], - ) - ], - ), - ], - ), - ], - ) - ] - - -class EntailedSubClassOfExpressionTask(Task): - """A task to determine the subclasses of a class expression.""" - - _query_format = """ - What are the entailed subclasses of the expression {params[0]} Some {params[1]}? - Include indirect (transitive) descendants. - """ - - type: Literal["EntailedSubClassOfExpressionTask"] = Field( - "EntailedSubClassOfExpressionTask" - ) # type: ignore - _code: str = "expr" # type: ignore - - answers: Optional[List[ClassAnswer]] = None - - examples: Optional[List[Example]] = [ - Example( - ontology=Ontology( - axioms=[ - Axiom(text="P type TransitiveProperty"), - Axiom(text="E2 SubClassOf P some E"), - Axiom(text="E SubClassOf B"), - Axiom(text="B SubClassOf P some A"), - Axiom(text="C SubClassOf A"), - Axiom(text="D SubClassOf Q some B"), - ] - ), - query_answers=[ - ExampleQueryAnswers( - query=Query(parameters=["P", "A"]), - answers=[ - ClassAnswer( - text="B", - explanations=[ - Explanation( - text="""B is an entailed subclass of P some A because - it is directly asserted in the ontology.""", - axioms=[ - Axiom(text="B SubClassOf P some A"), - ], - ) - ], - ), - ClassAnswer( - text="E", - explanations=[ - Explanation( - text="""E is an entailed subclass of P some A because - E SubClassOf B and B SubClassOf P some A - (i.e. every B stands in relation P to some A)""", - axioms=[ - Axiom(text="E SubClassOf B"), - Axiom(text="B SubClassOf P some A"), - ], - ) - ], - ), - ClassAnswer( - text="E2", - explanations=[ - Explanation( - text="""E2 is an entailed subclass of P some A because - E2 SubClassOf E and E SubClassOf B and B SubClassOf P some A - (i.e. every B stands in relation P to some A)""", - axioms=[ - Axiom(text="B SubClassOf P some A"), - Axiom(text="E SubClassOf B"), - Axiom(text="E2 SubClassOf P some E"), - ], - ) - ], - ), - ], - ), - ExampleQueryAnswers( - query=Query(parameters=["Q", "B"]), - answers=[ - ClassAnswer( - text="D", - explanations=[ - Explanation( - text="""D is an entailed subclass of Q some B because - it is directly asserted in the ontology. This is the only - answer because Q is not declared transitive.""", - axioms=[ - Axiom(text="D SubClassOf Q some B"), - ], - ) - ], - ), - ], - ), - ], - ) - ] - - -class EntailedDirectSuperClassTask(Task): - """ - A task to determine the direct superclasses of a class. - - Includes those entailed by other axioms, e.g. equivalence axioms. - - Context: a standard pattern in bio-ontologies is to infer the structure - of one ontology from another - e.g. the metabolic process branch in GO - may be entailed by GO equivalence axioms plus the IS_A links in CHEBI. - """ - - _query_format = """ - What are the direct entailed superclasses of {params[0]}?. - Make use of all axioms in the provided ontology. - """ - - type: Literal["EntailedDirectSuperClassTask"] = Field( - "EntailedDirectSuperClassTask" - ) # type: ignore - _code: str = "dir-sup" # type: ignore - - answers: Optional[List[ClassAnswer]] = None - - # TODO: examples - - -class MostRecentCommonSubsumerTask(Task): - """A task to determine the most specific common ancestors.""" - - _query_format = """ - What are the most specific common entailed superclasses of {params[0]} and {params[1]}?. - """ - - type: Literal["MostRecentCommonSubsumerTask"] = Field( - "MostRecentCommonSubsumerTask" - ) # type: ignore - _code: str = "mrca" # type: ignore - - answers: Optional[List[ClassAnswer]] = None - - examples: Optional[List[Example]] = [ - Example( - ontology=Ontology( - axioms=[ - Axiom(text="E2 SubClassOf E"), - Axiom(text="E SubClassOf B"), - Axiom(text="B SubClassOf A"), - Axiom(text="C SubClassOf A"), - Axiom(text="D SubClassOf B"), - ] - ), - query_answers=[ - ExampleQueryAnswers( - query=Query(parameters=["E2", "D"]), - answers=[ - ClassAnswer( - text="B", - explanations=[ - Explanation( - text="""B is the most specific common entailed superclass - of E2 and D because E2 is a SubClassOf B via E, and D is - a direct SubClassOf B, and there are no more specific common - ancestors.""", - axioms=[ - Axiom(text="E2 SubClassOf E"), - Axiom(text="E SubClassOf B"), - Axiom(text="D SubClassOf B"), - ], - ) - ], - ), - ], - ), - ExampleQueryAnswers( - query=Query(parameters=["E2", "C"]), - answers=[ - ClassAnswer( - text="A", - explanations=[ - Explanation( - text="""A is the most specific common entailed superclass - of E2 and C because E2 is a SubClassOf A via E then B, and C is - a SubClassOf A via B, and there are no more specific common - ancestors.""", - axioms=[ - Axiom(text="E2 SubClassOf E"), - Axiom(text="E SubClassOf B"), - Axiom(text="B SubClassOf A"), - Axiom(text="C SubClassOf B"), - Axiom(text="B SubClassOf A"), - ], - ) - ], - ), - ], - ), - ExampleQueryAnswers( - query=Query(parameters=["E2", "E"]), - answers=[ - ClassAnswer( - text="E", - explanations=[ - Explanation( - text="""E is the most specific common entailed superclass of E2 and E because - trivially E2 SubClassOf E""", - axioms=[ - Axiom(text="E2 SubClassOf E"), - ], - ) - ], - ), - ], - ), - ], - ) - ] - - -class TaxonConstraintTask(Task): - """A task to determine inapplicable classes by taxon.""" - - _query_format = """ - Is the term {params[0]} applicable for the taxon {params[1]}?. - Make use of subclass and part of axioms. - subclass is transitive: if A subClassOf B and B subClassOf C, then A subClassOf C. - part of is transitive: if A subClassOf part_of some B, and B subClassOf part_of some C, - then A subClassOf part_of some C. - subclass and part of chain: if A subClassOf B and B subClassOf part_of some C, - then A subClassOf part_of some C. - part of and subclass chain: if A subClassOf part_of some B and B subClassOf C, - then A subClassOf part_of some C. - only_in_taxon restricts a term to a taxon: if A only_in_taxon T, - and T DisjointWith T2, then A is INVALID for T2. - never_in_taxon restricts a term to a taxon: if A never_in_taxon T, - then A is INVALID for T. - only_in_taxon propagates up subClassOf: if A only_in_taxon T, and T subClassOf T2, - then A only_in_taxon T2. - never_in_taxon propagates down subClassOf: if A only_in_taxon T, and T2 subClassOf T, - then A never_in_taxon T2. - """ - - type: Literal["TaxonConstraintTask"] = Field("TaxonConstraintTask") # type: ignore - _code: str = "tc" # type: ignore - - answers: Optional[List[ClassAnswer]] = None - - examples: Optional[List[Example]] = [ - Example( - ontology=Ontology( - axioms=[ - Axiom(text="E2 SubClassOf part_of some E"), - Axiom(text="E SubClassOf B"), - Axiom(text="B SubClassOf A"), - Axiom(text="C SubClassOf A"), - Axiom(text="D SubClassOf B"), - Axiom(text="D1 SubClassOf D"), - Axiom(text="D2 SubClassOf D"), - Axiom(text="Tax1 SubClassOf Tax1Root"), - Axiom(text="Tax2 SubClassOf Tax1Root"), - Axiom(text="Tax1 DisjointWith Tax2"), - Axiom(text="Tax1x SubClassOf Tax1"), - Axiom(text="Tax1y SubClassOf Tax1"), - Axiom(text="Tax1x DisjointWith Tax1y"), - Axiom(text="Tax1xF SubClassOf Tax1x"), - Axiom(text="Tax1xG SubClassOf Tax1x"), - Axiom(text="Tax1xF DisjointWith Tax1xG"), - Axiom(text="Tax1yJ SubClassOf Tax1y"), - Axiom(text="Tax1yK SubClassOf Tax1y"), - Axiom(text="Tax1yJ DisjointWith Tax1yK"), - Axiom(text="E only_in_taxon Tax1"), - Axiom(text="E never_in_taxon Tax1x"), - Axiom(text="D only_in_taxon Tax1y"), - ] - ), - query_answers=[ - ExampleQueryAnswers( - query=Query(parameters=["E2", "Tax2"]), - answers=[ - ClassAnswer( - text="INVALID", - explanations=[ - Explanation( - text="""Every E2 is part of some E, - and E is only found in Tax1, - and Tax1 is disjoint with Tax2, - therefore E2 is invalid for Tax2""", - axioms=[ - Axiom(text="E2 SubClassOf part_of some E"), - Axiom(text="E only_in_taxon Tax1"), - Axiom(text="Tax1 DisjointWith Tax2"), - ], - ) - ], - ), - ], - ), - ExampleQueryAnswers( - query=Query(parameters=["E2", "Tax1y"]), - answers=[ - ClassAnswer( - text="VALID", - explanations=[ - Explanation( - text="""Every E2 is part of some E, - E SubClassOf B, B SubClassOf A, - and there are no conflicting taxon - constraints for E2, E, B, or A, - therefore E2 is valid for Tax1y""", - axioms=[ - Axiom(text="E2 SubClassOf part_of some E"), - Axiom(text="E SubClassOf B"), - Axiom(text="B SubClassOf A"), - ], - ) - ], - ), - ], - ), - ExampleQueryAnswers( - query=Query(parameters=["D", "Tax1y"]), - answers=[ - ClassAnswer( - text="VALID", - explanations=[ - Explanation( - text="""Every D is part of some B, B SubClassOf A, - and there are no conflicting taxon - constraints for D, B, or A, - therefore D is valid for Tax1y""", - axioms=[ - Axiom(text="D SubClassOf part_of some B"), - Axiom(text="B SubClassOf A"), - ], - ) - ], - ), - ], - ), - ExampleQueryAnswers( - query=Query(parameters=["E2", "Tax1xF"]), - answers=[ - ClassAnswer( - text="INVALID", - explanations=[ - Explanation( - text="""Every E2 is part of some E, and E is never - found in Tax1x, - Tax1xF is a subclass of Tax1x, - therefore E2 is invalid for Tax1xF""", - axioms=[ - Axiom(text="E2 SubClassOf part_of some E"), - Axiom(text="E never_in_taxon Tax1x"), - Axiom(text="Tax1xF SubClassOf Tax1x"), - ], - ) - ], - ), - ], - ), - ], - ) - ] - - -class ABoxTask(Task): - """A task to infer assertions over property chains and transitvity in aboxes.""" - - _query_format = """ - What instances <I> satisfy {params[0]} {params[1]} <I> ?. - Make use of property chain axioms of the form - PROPERTY1 o PROPERTY2 SubPropertyOf PROPERTY3. - This means that if x PROPERTY1 y and y PROPERTY2 z then x PROPERTY3 z. - Also make use of transitivity axioms of the form - PROPERTY type TransitiveProperty. - This means that if x PROPERTY y and y PROPERTY z then x PROPERTY z. - """ - - type: Literal["ABoxTask"] = Field("ABoxTask") # type: ignore - _code: str = "abox" # type: ignore - - answers: Optional[List[InstanceAnswer]] = None - - # TODO: examples - - examples: Optional[List[Example]] = [ - Example( - ontology=Ontology( - axioms=[ - Axiom(text="p1 o p2 SubPropertyOf p3"), - Axiom(text="p1 type TransitiveProperty"), - Axiom(text="i0 p1 i1"), - Axiom(text="i1 p1 i2"), - Axiom(text="i2 p2 i3"), - Axiom(text="i3 p1 i4"), - ], - comments=["""a chain of two transitive properties followed by a property chain."""], - ), - query_answers=[ - ExampleQueryAnswers( - query=Query(parameters=["i0", "p3"]), - answers=[ - InstanceAnswer( - text="i3", - explanations=[ - Explanation( - text="""i0 p3 i3 because - i0 p1 i1 and i1 p1 i2 and p1 is transitive, so i0 p1 i2. - i2 p2 i3 and p1 o p2 SubPropertyOf p3, so i0 p3 i3""", - axioms=[ - Axiom(text="i0 p1 i1"), - Axiom(text="i1 p1 i2"), - Axiom(text="p1 type TransitiveProperty"), - Axiom(text="i2 p2 i3"), - Axiom(text="p1 o p2 SubPropertyOf p3"), - ], - ) - ], - ), - InstanceAnswer( - text="i2", - explanations=[ - Explanation( - text="""i0 p3 i2 because - i0 p1 i1 and i1 p1 i2 and p1 is transitive, so i0 p1 i2.""", - axioms=[ - Axiom(text="i0 p1 i1"), - Axiom(text="i1 p1 i2"), - Axiom(text="p1 type TransitiveProperty"), - ], - ) - ], - ), - ], - ), - ExampleQueryAnswers( - query=Query(parameters=["i1", "p3"]), - answers=[ - InstanceAnswer( - text="i3", - explanations=[ - Explanation( - text="""i1 p3 i3 because - i1 p1 i2 and - i2 p2 i3 and p1 o p2 SubPropertyOf p3, so i1 p3 i3""", - axioms=[ - Axiom(text="i1 p1 i2"), - Axiom(text="i2 p2 i3"), - Axiom(text="p1 o p2 SubPropertyOf p3"), - ], - ) - ], - ), - ], - ), - ExampleQueryAnswers( - query=Query(parameters=["i0", "p1"]), - answers=[ - InstanceAnswer( - text="i1", - explanations=[ - Explanation( - text="""i0 p1 i1 is directly asserted""", - axioms=[ - Axiom(text="i0 p1 i1"), - ], - ) - ], - ), - InstanceAnswer( - text="i2", - explanations=[ - Explanation( - text="""i0 p1 i2 because - i0 p1 i1 and i1 p1 i2 and p1 is transitive, - so i0 p1 i2.""", - axioms=[ - Axiom(text="i0 p1 i1"), - Axiom(text="i1 p1 i2"), - Axiom(text="p1 type TransitiveProperty"), - ], - ) - ], - ), - ], - ), - ], - ) - ] - - -class TaskCollection(BaseModel): - name: Optional[str] = None - tasks: List[Task] = None - obfuscated_curie_map: Optional[Mapping[str, str]] = None - name_map: Optional[Mapping[str, str]] = None - - @staticmethod - def load(file_or_object: Union[dict, str, Path, TextIO]): - if isinstance(file_or_object, Path): - file_or_object = str(file_or_object) - if isinstance(file_or_object, str): - with open(file_or_object) as f: - tc_dict = yaml.safe_load(f) - else: - tc_dict = yaml.safe_load(str(file_or_object)) - current_module = sys.modules[__name__] - tasks = [] - for task_dict in tc_dict["tasks"]: - typ = task_dict["type"] - cls = current_module.__dict__[typ] - task = cls(**task_dict) - if not isinstance(task.method, GPTReasonMethodType): - # TODO: figure how to get pydantic to do this - task.method = GPTReasonMethodType(task.method) - tasks.append(task) - tc_dict["tasks"] = tasks - return TaskCollection(**tc_dict) - - -@dataclass -class OntologyExtractor: - """ - Ontology extractor. - - This will extract Task objects from an ontology. These Task objects - can be used by a ReasonerEngine object as queries or evaluation tests. - - Examples of types of Task objects include: - - - OntologyCoherencyTask: determine if an ontology is coherent - - EntailedIndirectSuperClassTask: determine the indirect superclasses of a class - - The extraction process is guided by seed classes or objects, and the resulting Task - object contains a minimal ontology (similar to a SLME module) that should be sufficient - to answer the query, as well as a specification of the task. - """ - - adapter: OboGraphInterface - additional_axioms: Optional[List[Axiom]] = None - query_predicates: Optional[List[PRED_CURIE]] = None - - use_identifiers: bool = False - name_map: Optional[Mapping[str, str]] = field(default_factory=lambda: {}) # type: ignore - obfuscate: bool = False - obfuscated_curie_map: Optional[Mapping[str, str]] = field( - default_factory=lambda: {} # type: ignore - ) - - def create_task( - self, task_type: Union[str, Type[Task]], parameters: Optional[List[Any]] = None, **kwargs - ) -> Task: - terms = list(self.adapter.entities(filter_obsoletes=True, owl_type=OWL_CLASS)) - ontology = self.extract_ontology(terms) - if isinstance(task_type, str): - task_type = globals()[task_type] - if not isinstance(task_type, str): # Just to be sure! - task = task_type(ontology=ontology, query=Query(parameters=parameters)) - task.populate() - return task - - def create_random_tasks( - self, - num_tasks_per_type: int = 10, - methods: List = None, - abox=False, - ) -> TaskCollection: - if methods is None: - if abox: - methods = [ - self.extract_abox_task, - ] - else: - methods = [ - self.extract_taxon_constraint_task, - self.extract_indirect_superclasses_task, - self.extract_transitive_superclasses_task, - self.extract_most_recent_common_subsumers_task, - self.extract_subclass_of_expression_task, - self.extract_incoherent_ontology_task, - ] - objs = [] - for method in methods: - for _n in range(num_tasks_per_type): - task = method(select_random=True) - task.obfuscated = self.obfuscate - objs.append(task) - logger.info(f" {task.name}") - tc = TaskCollection(tasks=objs) - if self.obfuscated_curie_map: - tc.obfuscated_curie_map = self.obfuscated_curie_map - tc.name_map = self.name_map - return tc - - def extract_ontology( - self, - terms: List[CURIE], - roots: Optional[List[CURIE]] = None, - predicates: Optional[List[PRED_CURIE]] = None, - include_abox=False, - ) -> Ontology: - """ - Extract an ontology module following specified terms up the hierarchy. - - :param terms: leaf nodes to traverse up from - :param roots: optional root nodes to stop at - :param predicates: defaults to IS_A - :return: - """ - if predicates is None and not include_abox: - predicates = [IS_A] - adapter = self.adapter - onts = list(adapter.ontologies()) - ancs = list( - adapter.ancestors(terms, predicates=predicates, method=GraphTraversalMethod.HOP) - ) - if NEVER_IN_TAXON in predicates: - tax_ancs = list(adapter.ancestors(ancs, predicates=[IS_A])) - ancs.extend(tax_ancs) - if roots: - roots_set = set(roots) - ancs = [ - t - for t in ancs - if roots_set.intersection(adapter.ancestors(t, predicates=predicates)) - ] - axioms = [] - already_have = set() - terms_set = set(terms) - used_predicates = set() - if not ancs: - raise ValueError(f"No ancestors found for {terms} over {predicates}") - for t in ancs: - for rel in adapter.relationships([t], predicates=predicates, include_abox=include_abox): - if rel in already_have: - continue - s, p, o = rel - terms_set.add(s) - terms_set.add(o) - used_predicates.add(p) - if roots and not set(adapter.ancestors(o, predicates=predicates)).intersection( - roots - ): - continue - axioms.append(self._axiom(rel, tbox=not include_abox)) - already_have.add(rel) - if not axioms: - raise ValueError( - f"No axioms found for ancestors {ancs} over {predicates} (roots={roots})" - ) - - ontology = Ontology( - name="-".join(onts), axioms=axioms, terms=list(terms_set), predicates=used_predicates - ) - if include_abox: - ontology.axioms.extend(list(self.extract_rbox())) - if self.additional_axioms: - ontology.axioms.extend(self.additional_axioms) - return ontology - - def extract_indirect_superclasses_task( - self, - subclass: Optional[CURIE] = None, - siblings: Optional[List[CURIE]] = None, - roots: Optional[List[CURIE]] = None, - predicates: Optional[List[PRED_CURIE]] = None, - select_random=False, - **kwargs, - ) -> EntailedIndirectSuperClassTask: - """ - Extract a task for finding all indirect superclasses of a class. - - >>> from oaklib import get_adapter - >>> from ontogpt.ontex.extractor import OntologyExtractor - >>> adapter = get_adapter("sqlite:obo:go") - >>> extractor = OntologyExtractor(adapter=adapter) - >>> task = extractor.extract_indirect_superclasses_task( - ... subclass="GO:0005634", siblings=["GO:0005773"], roots=["GO:0043226"] - ... ) - - :param subclass: the main focus of the query - :param siblings: other terms to include (to make the task harder) - :param roots: only include descendants of these terms - :return: An EntailedIndirectSuperClassTask - """ - if predicates is None: - predicates = [IS_A] - adapter = self.adapter - if select_random: - all_classes = list(adapter.entities(filter_obsoletes=True, owl_type=OWL_CLASS)) - subclass = random.choice(all_classes) - siblings = random.sample(all_classes, 3) - subclass_ancestors = list(adapter.ancestors(subclass, predicates=predicates)) - terms = [subclass] + siblings - ontology = self.extract_ontology(terms, roots) - if roots is not None: - roots_set = set(roots) - subclass_parents = {r[2] for r in adapter.relationships([subclass], predicates=predicates)} - - def _filter(anc: CURIE) -> bool: - if anc == subclass: - return True - if anc in subclass_parents: - return True - if roots is not None: - if not roots_set.intersection(adapter.ancestors(anc, predicates=predicates)): - return True - - filtered_ancestors = [anc for anc in subclass_ancestors if not _filter(anc)] - answers = self._answers_from_ancestors(subclass, filtered_ancestors, predicates=predicates) - task = EntailedIndirectSuperClassTask( - ontology=ontology, - query=Query(parameters=[self._name(subclass)]), - answers=answers, - **kwargs, - ) - task.populate() - - return task - - def _answers_from_ancestors( - self, start: CURIE, ends: List[CURIE], predicates: List[PRED_CURIE] - ) -> List[ClassAnswer]: - graph = self.adapter.ancestor_graph([start], predicates=predicates) - answer_map = defaultdict(list) - for _s, end, path in shortest_paths(graph, [start], ends, directed=True): - axioms = [] - for i in range(len(path) - 1): - axioms.append(self._axiom((path[i], IS_A, path[i + 1]))) - answer_map[end].append(Explanation(axioms=axioms)) - return [ClassAnswer(text=self._name(end), explanations=answer_map[end]) for end in ends] - - def extract_transitive_superclasses_task( - self, - subclass: CURIE = None, - siblings: List[CURIE] = None, - roots: Optional[List[CURIE]] = None, - predicates: Optional[List[PRED_CURIE]] = None, - select_random=False, - **kwargs, - ) -> EntailedTransitiveSuperClassTask: - """ - Extract a task for finding all transitive superclasses of a class. - - >>> from oaklib import get_adapter - >>> from ontogpt.ontex.extractor import OntologyExtractor - >>> adapter = get_adapter("sqlite:obo:go") - >>> extractor = OntologyExtractor(adapter=adapter) - >>> task = extractor.extract_transitive_superclasses_task( - ... subclass="GO:0005634", siblings=["GO:0005773"], roots=["GO:0043226"] - ... ) - - :param subclass: the main focus of the query - :param siblings: other terms to include (to make the task harder) - :param roots: only include descendants of these terms - :return: An EntailedIndirectSuperClassTask - """ - if predicates is None: - predicates = [IS_A] - adapter = self.adapter - if select_random: - all_classes = list(adapter.entities(filter_obsoletes=True, owl_type=OWL_CLASS)) - subclass = random.choice(all_classes) - siblings = random.sample(all_classes, 3) - subclass_ancestors = list(adapter.ancestors(subclass, predicates=predicates)) - terms = [subclass] + siblings - ontology = self.extract_ontology(terms, roots) - answers = [] - if roots is not None: - roots = list(set(roots)) - - def _filter(anc: CURIE) -> bool: - if anc == subclass: - return True - if roots is not None: - roots_set = set(roots) - if not roots_set.intersection(adapter.ancestors(anc, predicates=predicates)): - return True - - filtered_ancestors = [anc for anc in subclass_ancestors if not _filter(anc)] - answers = self._answers_from_ancestors(subclass, filtered_ancestors, predicates=predicates) - task = EntailedTransitiveSuperClassTask( - ontology=ontology, - query=Query(parameters=[self._name(subclass)]), - answers=answers, - **kwargs, - ) - task.populate() - return task - - def extract_abox_task( - self, - subject: CURIE = None, - siblings: List[CURIE] = None, - predicate: PRED_CURIE = None, - select_random=False, - **kwargs, - ) -> ABoxTask: - """Extract a task for finding all entailed edges.""" - adapter = self.adapter - # TODO: this is currently necessary to get all entailed abox relationships - include_tbox = True - if select_random: - all_entities = list( - adapter.entities(filter_obsoletes=True, owl_type=OWL_NAMED_INDIVIDUAL) - ) - all_direct_rels = list( - adapter.relationships( - include_abox=True, include_tbox=include_tbox, include_entailed=False - ) - ) - all_rels = list( - adapter.relationships( - include_abox=True, include_tbox=include_tbox, include_entailed=True - ) - ) - all_rels = [r for r in all_rels if r[2] in all_entities] - if self.query_predicates: - all_rels = [r for r in all_rels if r[1] in self.query_predicates] - # for r in all_rels: - # print(r) - all_indirect_rels = [r for r in all_rels if r not in all_direct_rels] - candidate_rel = random.choice(all_indirect_rels) - subject = candidate_rel[0] - predicate = candidate_rel[1] - siblings = random.sample(all_entities, 3) - predicates = [predicate] - relationships = list( - adapter.relationships( - [subject], - predicates=predicates, - include_abox=True, - include_tbox=include_tbox, - include_entailed=True, - ) - ) - terms = [subject] + siblings - # note: we need to extract over all predicates - ontology = self.extract_ontology(terms, predicates=None, include_abox=True) - # exclude reflexive - ancestors = [r[2] for r in relationships if r[2] != subject] - answers = self._answers_from_ancestors(subject, ancestors, predicates=predicates) - task = ABoxTask( - ontology=ontology, - query=Query(parameters=[self._name(subject), self._name(predicate)]), - answers=answers, - **kwargs, - ) - task.populate() - return task - - def extract_most_recent_common_subsumers_task( - self, - subclass1: CURIE = None, - subclass2: CURIE = None, - siblings: List[CURIE] = None, - roots: Optional[List[CURIE]] = None, - predicates: Optional[List[PRED_CURIE]] = None, - select_random=False, - **kwargs, - ) -> MostRecentCommonSubsumerTask: - """Extract a task for finding all MRCAs of a pair of classes.""" - if predicates is None: - predicates = [IS_A] - adapter = self.adapter - if select_random: - all_classes = list(adapter.entities(filter_obsoletes=True, owl_type=OWL_CLASS)) - subclass1 = random.choice(all_classes) - subclass2 = random.choice(all_classes) - siblings = random.sample(all_classes, 2) - terms = [subclass1, subclass2] + siblings - ontology = self.extract_ontology(terms, roots) - answers = [] - if not isinstance(adapter, SemanticSimilarityInterface): - raise ValueError("Adapter must implement SemanticSimilarityInterface") - mrcas = list( - adapter.most_recent_common_ancestors(subclass1, subclass2, predicates=predicates) - ) - for mrca in mrcas: - explanations = [ - Explanation( - axioms=[ - self._axiom((mrca, IS_A, subclass1)), - self._axiom((mrca, IS_A, subclass2)), - ] - ) - ] - answers.append(ClassAnswer(text=self._name(mrca), explanations=explanations)) - task = MostRecentCommonSubsumerTask( - ontology=ontology, - query=Query(parameters=[self._name(subclass1), self._name(subclass2)]), - answers=answers, - **kwargs, - ) - task.populate() - return task - - def extract_subclass_of_expression_task( - self, - superclass: CURIE = None, - predicate: PRED_CURIE = None, - siblings: List[CURIE] = None, - predicates: Optional[List[PRED_CURIE]] = None, - select_random=False, - **kwargs, - ) -> EntailedSubClassOfExpressionTask: - adapter = self.adapter - if predicate is None: - predicate = PART_OF - if not predicates: - predicates = [IS_A, predicate] - if select_random: - all_classes = list(adapter.entities(filter_obsoletes=True, owl_type=OWL_CLASS)) - siblings = random.sample(all_classes, 2) - n = 0 - while True: - superclass = random.choice(all_classes) - descendants = list(adapter.descendants(superclass, predicates=predicates)) - isa_descendants = list(adapter.descendants(superclass, predicates=[IS_A])) - if ( - len(descendants) < 15 - and len(descendants) > 0 - and len(descendants) != len(isa_descendants) - ): - break - n += 1 - if n > 100: - raise ValueError( - f"Could not find suitable parent (ontology MUST have {predicate}" - ) - logger.info(f"Extracting subclass of expression task for {superclass}, preds={predicates}") - descendants = list(adapter.descendants(superclass, predicates=predicates)) - isa_descendants = list(adapter.descendants(superclass, predicates=[IS_A])) - terms = descendants + siblings - roots = [superclass] + siblings - ontology = self.extract_ontology(terms, roots, predicates=predicates) - answers = [] - if roots is not None: - roots = list(set(roots)) - for desc in descendants: - if desc == superclass: - continue - if desc in isa_descendants: - # TODO: Reflexive scenario - continue - # if desc not in ontology.terms: - # continue - explanations: List[str] = [] - answers.append(ClassAnswer(text=self._name(desc), explanations=explanations)) - task = EntailedSubClassOfExpressionTask( - ontology=ontology, - query=Query(parameters=[self._name(predicate), self._name(superclass)]), - answers=answers, - **kwargs, - ) - task.populate() - return task - - def extract_incoherent_ontology_task( - self, - incoherents: List[CURIE] = None, - siblings: List[CURIE] = None, - disjoints: List[Tuple[CURIE, CURIE]] = None, - spiked_relationships: List[RELATIONSHIP] = None, - roots: Optional[List[CURIE]] = None, - select_random=False, - **kwargs, - ) -> OntologyCoherencyTask: - """ - Extract task for testing ability to find incoherencies based on disjointness axioms. - - :param incoherents: expected incoherent classes - :param siblings: - :param disjoints: pairs of disjoint classes - :param spiked_relationships: edges to insert into ontology - :param roots: - :return: - """ - adapter = self.adapter - if select_random: - all_classes = list(adapter.entities(filter_obsoletes=True, owl_type=OWL_CLASS)) - siblings = random.sample(all_classes, 2) - candidates = [] - for c in all_classes: - parents = {rel[2] for rel in adapter.relationships(subjects=[c], predicates=[IS_A])} - if len(parents) > 1: - candidates.append((c, parents)) - if len(candidates) == 0: - raise ValueError("No suitable candidates") - root_incoherent, parents = random.choice(candidates) - incoherents = [ - random.choice(list(adapter.descendants(root_incoherent, predicates=[IS_A]))) - ] - parents_list = list(parents) - random.shuffle(parents_list) - disjoints = [(parents_list[0], parents_list[1])] - if not incoherents or not siblings or not disjoints: - raise ValueError("Must specify incoherents, siblings, and disjoints") - if not spiked_relationships: - spiked_relationships = [] - terms = incoherents + siblings - for s, _p, o in spiked_relationships: - terms += [s, o] - terms = list(set(terms)) - ontology = self.extract_ontology(terms, roots) - for s, p, o in spiked_relationships: - ontology.axioms.append(self._axiom((s, p, o))) - for s, o in disjoints: - ontology.axioms.append(self._axiom((s, DISJOINT_WITH, o))) - # for s, p, o in spiked_relationships: - # if not isinstance(adapter, PatcherInterface): - # raise ValueError("Cannot patch ontology") - # adapter.apply_patch(kgcl.EdgeCreation(id='tmp', subject=s, predicate=p, object=o)) - answers = [] - if roots is not None: - roots = list(set(roots)) - for incoherent in incoherents: - ancestors = list( - adapter.ancestors(incoherent, predicates=[IS_A], method=GraphTraversalMethod.HOP) - ) - explanations = [] - # TODO: - for s, o in disjoints: - if s in ancestors and o in ancestors: - explanation = Explanation( - axioms=[ - self._axiom((incoherent, IS_A, s)), - self._axiom((incoherent, IS_A, o)), - ] - ) - explanations.append(explanation) - if not explanations: - explanations = [ - Explanation(axioms=[self._axiom(rel) for rel in spiked_relationships]) - ] - answers.append(ClassAnswer(text=self._name(incoherent), explanations=explanations)) - task = OntologyCoherencyTask( - ontology=ontology, - query=Query(), - answers=answers, - **kwargs, - ) - task.populate() - return task - - def extract_taxon_constraint_task( - self, - term: CURIE = None, - taxon: CURIE = None, - siblings: List[CURIE] = None, - never_in=False, - select_random=False, - **kwargs, - ) -> TaxonConstraintTask: - adapter = self.adapter - taxa = list(adapter.descendants("NCBITaxon:1", predicates=[IS_A])) - all_terms = [ - t for t in adapter.entities(filter_obsoletes=True, owl_type=OWL_CLASS) if t not in taxa - ] - true_taxa = [t for t in taxa if "Union" not in t] - relationships = list(adapter.relationships(predicates=TAXON_PREDICATES)) - never_in = [rel for rel in relationships if rel[1] == NEVER_IN_TAXON] - if not never_in: - raise ValueError("No never in taxon relationships") - if select_random: - if never_in or random.choice([True, False]): - anc_term, p, direct_taxon = random.choice(never_in) - else: - anc_term, p, direct_taxon = random.choice( - [r for r in relationships if r[1] != NEVER_IN_TAXON] - ) - candidates = list(adapter.descendants(anc_term)) - candidate_taxa = list(adapter.descendants(direct_taxon)) - candidate_taxa = [t for t in candidate_taxa if t in true_taxa] - term = random.choice(candidates) - taxon = random.choice(candidate_taxa) - remaining = list(set(candidates) - set(all_terms)) - siblings = random.sample(remaining, min(2, len(remaining))) - if not term or not taxon: - raise ValueError("Must specify term and taxon") - terms = true_taxa + [term] + siblings - ontology = self.extract_ontology(terms, predicates=TAXON_PREDICATES + [IS_A, PART_OF]) - for t in true_taxa: - children = {rel[0] for rel in adapter.relationships(objects=[t], predicates=[IS_A])} - children_list = [c for c in children if c in true_taxa] - if len(children_list) > 1: - for i in range(len(children_list)): - for j in range(i + 1, len(children_list)): - ontology.axioms.append( - self._axiom((children_list[i], DISJOINT_WITH, children_list[j])) - ) - if not isinstance(adapter, TaxonConstraintInterface): - raise ValueError("Cannot evaluate taxon constraints") - st = SubjectTerm(term, label=adapter.label(term)) - st.present_in.append(TaxonConstraint(taxon=Taxon(taxon))) - st = adapter.eval_candidate_taxon_constraint(st, predicates=[IS_A, PART_OF]) - if st.unsatisfiable: - validity = "INVALID" - else: - validity = "VALID" - answers = [] - answers.append(ClassAnswer(text=validity, explanations=[])) - task = TaxonConstraintTask( - ontology=ontology, - query=Query(parameters=[self._name(term), self._name(taxon)]), - answers=answers, - **kwargs, - ) - task.populate() - return task - - def _axiom(self, rel: RELATIONSHIP, tbox=True) -> Axiom: - s, p, o = rel - s_n, p_n, o_n = self._name(s), self._name(p), self._name(o) - if p == IS_A: - return Axiom(text=f"{s_n} SubClassOf {o_n}") - elif p == DISJOINT_WITH: - return Axiom(text=f"{s_n} DisjointWith {o_n}") - elif p == NEVER_IN_TAXON: - return Axiom(text=f"{s_n} never_in_taxon {o_n}") - elif p in [IN_TAXON, ONLY_IN_TAXON]: - return Axiom(text=f"{s_n} only_in_taxon {o_n}") - elif tbox: - return Axiom(text=f"{s_n} SubClassOf {p_n} Some {o_n}") - else: - return Axiom(text=f"{s_n} {p_n} {o_n}") - - def _name(self, curie: CURIE) -> str: - lbl = self.adapter.label(curie) - if lbl is None: - return curie - else: - lbl = re.sub(r"\W+", "_", lbl) - lbl = inflection.camelize(lbl) - self.name_map[curie] = lbl # type: ignore - if self.use_identifiers: - return curie - elif self.obfuscate: - obfuscated = base64.b64encode(curie.encode("utf-8")).decode("utf-8") - self.obfuscated_curie_map[obfuscated] = curie # type: ignore - return obfuscated - else: - return lbl - - def extract_rbox(self) -> Iterable[Axiom]: - if not isinstance(self.adapter, SqlImplementation): - raise ValueError("Only SQL adapters supported") - session = self.adapter.session - for name, curie in [ - ("TransitiveProperty", OWL_TRANSITIVE_PROPERTY), - ("SymmetricProperty", OWL_SYMMETRIC_PROPERTY), - ]: - q = session.query(RdfTypeStatement).filter(RdfTypeStatement.object == curie) - for row in q: - yield Axiom(text=f"{self._name(row.subject)} type {name}") - for row in session.query(Statements).filter(Statements.predicate == SUBPROPERTY_OF): - yield Axiom(text=f"{self._name(row.subject)} SubPropertyOf {self._name(row.object)}") - for row in session.query(Statements).filter(Statements.predicate == INVERSE_OF): - yield Axiom(text=f"{self._name(row.subject)} SubPropertyOf {self._name(row.object)}") - for row in session.query(Statements).filter( - Statements.predicate == "owl:propertyChainAxiom" - ): - entailed_pred = row.subject - bnode = row.object - chain = [] - for inner_row in session.query(RdfListMemberStatement.object).filter( - RdfListMemberStatement.subject == bnode - ): - chain.append(inner_row[0]) - expr = " o ".join(self._name(p) for p in chain) - yield Axiom(text=f"{expr} SubPropertyOf {self._name(entailed_pred)}") diff --git a/src/ontogpt/prompts/__init__.py b/src/ontogpt/prompts/__init__.py deleted file mode 100644 index e69de29bb..000000000 diff --git a/src/ontogpt/prompts/mapping/__init__.py b/src/ontogpt/prompts/mapping/__init__.py deleted file mode 100644 index 9261fa3fd..000000000 --- a/src/ontogpt/prompts/mapping/__init__.py +++ /dev/null @@ -1,4 +0,0 @@ -from pathlib import Path - -MAPPING_PROMPT_DIR_PATH = Path(__file__).parent -DEFAULT_MAPPING_EVAL_PROMPT = MAPPING_PROMPT_DIR_PATH / "eval-mapping.jinja2" diff --git a/src/ontogpt/prompts/mapping/eval-mapping.jinja2 b/src/ontogpt/prompts/mapping/eval-mapping.jinja2 deleted file mode 100644 index 6244f0124..000000000 --- a/src/ontogpt/prompts/mapping/eval-mapping.jinja2 +++ /dev/null @@ -1,118 +0,0 @@ -What is the relationship between the two specified concepts? - -Give your answer in the form: - -category: <one of: EXACT_MATCH, BROADER_THAN, NARROWER_THAN, RELATED_TO, DIFFERENT> -confidence: <one of: LOW, HIGH, MEDIUM> -similarities: <semicolon-separated list of similarities> -differences: <semicolon-separated list of differences> - -Make use of all provided information, including the concept names, definitions, and relationships. - -Examples: - ---- - -[Concept A] -id: FOO:123 -name: car -def: a vehicle with four wheels -is_a: Vehicle - -[Concept B] -id: BAR:456 -name: automobile -def: A motorized 4-wheeled vehicle -is_a: MotorizedVehicle - -category: EXACT_MATCH -confidence: HIGH -similarities: same concept; vehicle; number of wheels -differences: B mentions motorized; name - ---- - -[Concept A] -id: FOO:123 -name: car -def: a vehicle with four wheels -is_a: Vehicle -relationship: has_part Wheel - -[Concept B] -id: BAR:457 -name: car -synonyms: caboose; railroad car -def: A railway vehicle that forms part of a train -is_a: Vehicle -relationship: part_of Train - -category: RELATED_TO -confidence: MEDIUM -similarities: vehicle; function -differences: B is a railway car - ---- - -[Concept A] -id: FOO:125 -name: wing -def: part of a bird that is flapped to enable flight -is_a: Limb -relationship: part_of Bird -relationship: has_part Feather - -[Concept B] -id: BAR:458 -name: wing -relationship: part_of Aeroplane - -category: DIFFERENT -confidence: HIGH -similarities: function -differences: A is an anatomical part; B is a part of a vehicle - ---- - -[Concept A] -id: BAZ:789 -name: head -def: part of the body that has the brain -is_a: Appendage -relationship: part_of Body - -[Concept B] -id: XYZ:123 -name: head -def: the toilet in a ship - -category: DIFFERENT -confidence: HIGH -similarities: NONE -differences: A is an anatomical part; B is a lavatory - ---- - -Here are the two concepts: - -{% macro write_concept(concept, role) -%} -[Concept {{ role }}] -id: {{concept.id}} -name: {{concept.label}} -{% if concept.definition -%} -def: {{concept.definition}} -{%- endif %} -{% if concept.synonyms -%} -synonyms: {% for synonym in concept.synonyms %} {{synonym}} ; {% endfor %} -{%- endif %} -{% if concept.parents -%} -is_a: {% for parent in concept.parents %} {{parent}} ; {% endfor %} -{%- endif %} -{% for rel in concept.relationships -%} -relationship: {{rel.predicate_label}} {{rel.object_label}} -{% endfor -%} -{%- endmacro %} - -{{ write_concept(subject, 'A') }} -{{ write_concept(object, 'B') }} - diff --git a/src/ontogpt/prompts/phenopacket/__init__.py b/src/ontogpt/prompts/phenopacket/__init__.py deleted file mode 100644 index 03299ce2b..000000000 --- a/src/ontogpt/prompts/phenopacket/__init__.py +++ /dev/null @@ -1,4 +0,0 @@ -from pathlib import Path - -PHENOPACKET_PROMPT_DIR_PATH = Path(__file__).parent -DEFAULT_PHENOPACKET_PROMPT = PHENOPACKET_PROMPT_DIR_PATH / "phenopacket.jinja2" diff --git a/src/ontogpt/prompts/phenopacket/phenopacket.jinja2 b/src/ontogpt/prompts/phenopacket/phenopacket.jinja2 deleted file mode 100644 index ff169a7e8..000000000 --- a/src/ontogpt/prompts/phenopacket/phenopacket.jinja2 +++ /dev/null @@ -1,24 +0,0 @@ -I will provide a list of phenotypes. Predict the underlying disease. -The case is a {{ phenopacket.subject.sex }} of age {{ phenopacket.subject.ageAtCollection.age }}. - -Case Phenotypes: - -{% for pf in phenopacket.phenotypicFeatures -%} -* {{pf.type.label}} -{% endfor -%} - -Provide ranked list of diseases. For each disease list the phenotypes in common with the case. Provide the -output in JSON. For example - -[ - {"disease": "<Disease1>", - "score": 0.9, - "phenotypes": ["<phenotype1>", "<phenotype2>"] - }, - {"disease": "<Disease2>", - "score": 0.8, - "phenotypes": ["<phenotype1>", "<phenotype2>", ""] - } -] - -Provide the JSON here: \ No newline at end of file diff --git a/src/ontogpt/prompts/qa/__init__.py b/src/ontogpt/prompts/qa/__init__.py deleted file mode 100644 index 0a3620d38..000000000 --- a/src/ontogpt/prompts/qa/__init__.py +++ /dev/null @@ -1,4 +0,0 @@ -from pathlib import Path - -QA_PROMPT_DIR_PATH = Path(__file__).parent -GENERIC_QA_PROMPT = QA_PROMPT_DIR_PATH / "generic.jinja2" diff --git a/src/ontogpt/prompts/qa/generic.jinja2 b/src/ontogpt/prompts/qa/generic.jinja2 deleted file mode 100644 index 4dfbdcf56..000000000 --- a/src/ontogpt/prompts/qa/generic.jinja2 +++ /dev/null @@ -1,2 +0,0 @@ -{{question}}. -{{instructions}} diff --git a/src/ontogpt/prompts/reasoning/__init__.py b/src/ontogpt/prompts/reasoning/__init__.py deleted file mode 100644 index 467e76843..000000000 --- a/src/ontogpt/prompts/reasoning/__init__.py +++ /dev/null @@ -1,4 +0,0 @@ -from pathlib import Path - -REASONING_PROMPT_DIR_PATH = Path(__file__).parent -DEFAULT_REASONING_PROMPT = REASONING_PROMPT_DIR_PATH / "reasoning.jinja2" diff --git a/src/ontogpt/prompts/reasoning/reasoning.jinja2 b/src/ontogpt/prompts/reasoning/reasoning.jinja2 deleted file mode 100644 index 5c2edfd6b..000000000 --- a/src/ontogpt/prompts/reasoning/reasoning.jinja2 +++ /dev/null @@ -1,50 +0,0 @@ -{% macro write_axiom(axiom) %}{{ axiom.text }}{% endmacro %} -{% macro write_explanation_as_axioms(explanation) -%} -{% for axiom in explanation.axioms %} {{ write_axiom(axiom) }} ; {% endfor %} -{%- endmacro %} - -I will provide an ontology as a list of axioms using OWL syntax. -I will then ask a question about the ontology. -Answer the question, after performing reasoning over the ontology. -If there are multiple answers, list them all each on a separate line starting with the minus symbol ("-"), -like a markdown list. -{%- if task.include_explanations %} include explanations with each answer. -Each explanation must be an OWL axiom. Do not include narrative text. -{% endif -%} - -{% if examples %} -Here are some examples: - -{% for example in examples %} -## EXAMPLE ONTOLOGY: -{% for axiom in example.ontology.axioms %} -- {{ axiom.text }} -{%- endfor %} - -{% for qa in example.query_answers %} -QUERY: {{ qa.query.text }} -ANSWERS: -{% for answer in qa.answers -%} -{% if task.chain_of_thought -%} -- REASONING: [ {% for e in answer.explanations %}{{ e.text }}{% endfor %} ] CONCLUSION: {{ answer.text }} -{% elif task.include_explanations -%} -- {{ answer.text }} [ {% for e in answer.explanations %}{{ write_explanation_as_axioms(e) }}{% endfor %}] -{% else -%} -- {{ answer.text }} -{%- endif %} -{%- endfor %} -{% endfor %} - -{% endfor %} -{% endif %} - ---- -Here is the actual ontology: - -{% for axiom in ontology.axioms %} -- {{ axiom.text }} -{%- endfor %} - -QUERY: {{ query.text }} - -ANSWERS: \ No newline at end of file diff --git a/src/ontogpt/prompts/similarity/connections.jinja2 b/src/ontogpt/prompts/similarity/connections.jinja2 deleted file mode 100644 index c859b29ac..000000000 --- a/src/ontogpt/prompts/similarity/connections.jinja2 +++ /dev/null @@ -1,22 +0,0 @@ -I will give you a list of genes and descriptions of those genes. -I will then give a list of phenotypes for a patient with a disease. - -Return a ranked list of candidate genes for that disease, together with confidence, and an explanations - -Results should be in the format - -- <gene1> <confidence1> <explanation1> -- <gene2> <confidence2> <explanation2> -- ... - -Here are the gene descriptions: - -{% for gd in gene_descriptions %} -{{ gd[0] }}: {{ gd[1] }} -{% endfor % - -Here are the patient phenotypes: - -{% for phenotype in phenotypes %} -{{ phenotype }} ; -{% endfor %} \ No newline at end of file diff --git a/src/ontogpt/templates/__init__.py b/src/ontogpt/templates/__init__.py deleted file mode 100644 index 388be6a3a..000000000 --- a/src/ontogpt/templates/__init__.py +++ /dev/null @@ -1,3 +0,0 @@ -from pathlib import Path - -PATH_TO_TEMPLATES = Path(__file__).parent \ No newline at end of file diff --git a/src/ontogpt/templates/biological_process.py b/src/ontogpt/templates/biological_process.py deleted file mode 100644 index fbbe579f0..000000000 --- a/src/ontogpt/templates/biological_process.py +++ /dev/null @@ -1,188 +0,0 @@ -from __future__ import annotations -from datetime import datetime, date -from enum import Enum -from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, ConfigDict, Field, field_validator -import re -import sys -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal - - -metamodel_version = "None" -version = "None" - -class ConfiguredBaseModel(BaseModel): - model_config = ConfigDict( - validate_assignment=True, - validate_default=True, - extra = 'forbid', - arbitrary_types_allowed=True, - use_enum_values = True) - - -class NullDataOptions(str, Enum): - - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = "UNSPECIFIED_METHOD_OF_ADMINISTRATION" - - NOT_APPLICABLE = "NOT_APPLICABLE" - - NOT_MENTIONED = "NOT_MENTIONED" - - - -class GeneMolecularActivityRelationship(ConfiguredBaseModel): - - gene: Optional[str] = Field(None) - molecular_activity: Optional[str] = Field(None) - - - -class ExtractionResult(ConfiguredBaseModel): - """ - A result of extracting knowledge on text - """ - input_id: Optional[str] = Field(None) - input_title: Optional[str] = Field(None) - input_text: Optional[str] = Field(None) - raw_completion_output: Optional[str] = Field(None) - prompt: Optional[str] = Field(None) - extracted_object: Optional[Any] = Field(None, description="""The complex objects extracted from the text""") - named_entities: Optional[List[Any]] = Field(default_factory=list, description="""Named entities extracted from the text""") - - - -class NamedEntity(ConfiguredBaseModel): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class BiologicalProcess(NamedEntity): - - label: Optional[str] = Field(None, description="""the name of the biological process""") - description: Optional[str] = Field(None, description="""a textual description of the biological process""") - synonyms: Optional[List[str]] = Field(default_factory=list, description="""alternative names of the biological process""") - subclass_of: Optional[str] = Field(None, description="""the category to which this biological process belongs""") - inputs: Optional[List[str]] = Field(default_factory=list, description="""the inputs of the biological process""") - outputs: Optional[List[str]] = Field(default_factory=list, description="""the outputs of the biological process""") - steps: Optional[List[str]] = Field(default_factory=list, description="""the steps involved in this biological process""") - genes: Optional[List[str]] = Field(default_factory=list) - gene_activities: Optional[List[GeneMolecularActivityRelationship]] = Field(default_factory=list, description="""semicolon-separated list of gene to molecular activity relationships""") - id: str = Field(..., description="""A unique identifier for the named entity""") - - - -class Gene(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class CellType(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class MolecularActivity(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class ChemicalEntity(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class CompoundExpression(ConfiguredBaseModel): - - None - - - -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - subject: Optional[str] = Field(None) - predicate: Optional[str] = Field(None) - object: Optional[str] = Field(None) - qualifier: Optional[str] = Field(None, description="""A qualifier for the statements, e.g. \"NOT\" for negation""") - subject_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"""") - object_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"""") - - - -class TextWithTriples(ConfiguredBaseModel): - """ - A text containing one or more relations of the Triple type. - """ - publication: Optional[Publication] = Field(None) - triples: Optional[List[Triple]] = Field(default_factory=list) - - - -class TextWithEntity(ConfiguredBaseModel): - """ - A text containing one or more instances of a single type of entity. - """ - publication: Optional[Publication] = Field(None) - entities: Optional[List[str]] = Field(default_factory=list) - - - -class RelationshipType(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Publication(ConfiguredBaseModel): - - id: Optional[str] = Field(None, description="""The publication identifier""") - title: Optional[str] = Field(None, description="""The title of the publication""") - abstract: Optional[str] = Field(None, description="""The abstract of the publication""") - combined_text: Optional[str] = Field(None) - full_text: Optional[str] = Field(None, description="""The full text of the publication""") - - - -class AnnotatorResult(ConfiguredBaseModel): - - subject_text: Optional[str] = Field(None) - object_id: Optional[str] = Field(None) - object_text: Optional[str] = Field(None) - - - - -# Model rebuild -# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model -GeneMolecularActivityRelationship.model_rebuild() -ExtractionResult.model_rebuild() -NamedEntity.model_rebuild() -BiologicalProcess.model_rebuild() -Gene.model_rebuild() -CellType.model_rebuild() -MolecularActivity.model_rebuild() -ChemicalEntity.model_rebuild() -CompoundExpression.model_rebuild() -Triple.model_rebuild() -TextWithTriples.model_rebuild() -TextWithEntity.model_rebuild() -RelationshipType.model_rebuild() -Publication.model_rebuild() -AnnotatorResult.model_rebuild() - diff --git a/src/ontogpt/templates/biological_process.yaml b/src/ontogpt/templates/biological_process.yaml deleted file mode 100644 index bfa442a7b..000000000 --- a/src/ontogpt/templates/biological_process.yaml +++ /dev/null @@ -1,87 +0,0 @@ -id: https://w3id.org/ontogpt/biological_process -name: biological-process-template -title: Biological Process Template -description: >- - A template for GO-CAMs -license: https://creativecommons.org/publicdomain/zero/1.0/ -prefixes: - linkml: https://w3id.org/linkml/ - bp: http://w3id.org/ontogpt/biological-process-template - -default_prefix: bp -default_range: string - -imports: - - linkml:types - - core - -classes: - BiologicalProcess: - tree_root: true - is_a: NamedEntity - attributes: - label: - description: the name of the biological process - description: - description: a textual description of the biological process - synonyms: - description: alternative names of the biological process - multivalued: true - subclass_of: - description: the category to which this biological process belongs - range: BiologicalProcess - inputs: - description: the inputs of the biological process - multivalued: true - range: ChemicalEntity - outputs: - description: the outputs of the biological process - multivalued: true - range: ChemicalEntity - steps: - description: the steps involved in this biological process - multivalued: true - range: MolecularActivity - genes: - range: Gene - multivalued: true - gene_activities: - description: semicolon-separated list of gene to molecular activity relationships - multivalued: true - range: GeneMolecularActivityRelationship - - Gene: - is_a: NamedEntity - id_prefixes: - - HGNC - annotations: - annotators: sqlite:obo:hgnc - - CellType: - is_a: NamedEntity - id_prefixes: - - CL - annotations: - annotators: sqlite:obo:cl - - MolecularActivity: - is_a: NamedEntity - id_prefixes: - - GO - annotations: - annotators: sqlite:obo:go - - ChemicalEntity: - is_a: NamedEntity - id_prefixes: - - CHEBI - annotations: - annotators: sqlite:obo:chebi - - GeneMolecularActivityRelationship: - attributes: - gene: - range: Gene - molecular_activity: - range: MolecularActivity - diff --git a/src/ontogpt/templates/biotic_interaction.py b/src/ontogpt/templates/biotic_interaction.py deleted file mode 100644 index 93ff8a619..000000000 --- a/src/ontogpt/templates/biotic_interaction.py +++ /dev/null @@ -1,164 +0,0 @@ -from __future__ import annotations -from datetime import datetime, date -from enum import Enum -from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, ConfigDict, Field, field_validator -import re -import sys -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal - - -metamodel_version = "None" -version = "None" - -class ConfiguredBaseModel(BaseModel): - model_config = ConfigDict( - validate_assignment=True, - validate_default=True, - extra = 'forbid', - arbitrary_types_allowed=True, - use_enum_values = True) - - -class NullDataOptions(str, Enum): - - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = "UNSPECIFIED_METHOD_OF_ADMINISTRATION" - - NOT_APPLICABLE = "NOT_APPLICABLE" - - NOT_MENTIONED = "NOT_MENTIONED" - - - -class Container(ConfiguredBaseModel): - - interactions: Optional[List[BioticInteraction]] = Field(default_factory=list) - - - -class BioticInteraction(ConfiguredBaseModel): - - source_taxon: Optional[str] = Field(None, description="""the taxon that is the subject of the interaction""") - target_taxon: Optional[str] = Field(None, description="""the taxon that is the object of the interaction""") - interaction_type: Optional[str] = Field(None, description="""the type of interaction""") - - - -class ExtractionResult(ConfiguredBaseModel): - """ - A result of extracting knowledge on text - """ - input_id: Optional[str] = Field(None) - input_title: Optional[str] = Field(None) - input_text: Optional[str] = Field(None) - raw_completion_output: Optional[str] = Field(None) - prompt: Optional[str] = Field(None) - extracted_object: Optional[Any] = Field(None, description="""The complex objects extracted from the text""") - named_entities: Optional[List[Any]] = Field(default_factory=list, description="""Named entities extracted from the text""") - - - -class NamedEntity(ConfiguredBaseModel): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Taxon(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class InteractionType(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class CompoundExpression(ConfiguredBaseModel): - - None - - - -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - subject: Optional[str] = Field(None) - predicate: Optional[str] = Field(None) - object: Optional[str] = Field(None) - qualifier: Optional[str] = Field(None, description="""A qualifier for the statements, e.g. \"NOT\" for negation""") - subject_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"""") - object_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"""") - - - -class TextWithTriples(ConfiguredBaseModel): - """ - A text containing one or more relations of the Triple type. - """ - publication: Optional[Publication] = Field(None) - triples: Optional[List[Triple]] = Field(default_factory=list) - - - -class TextWithEntity(ConfiguredBaseModel): - """ - A text containing one or more instances of a single type of entity. - """ - publication: Optional[Publication] = Field(None) - entities: Optional[List[str]] = Field(default_factory=list) - - - -class RelationshipType(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Publication(ConfiguredBaseModel): - - id: Optional[str] = Field(None, description="""The publication identifier""") - title: Optional[str] = Field(None, description="""The title of the publication""") - abstract: Optional[str] = Field(None, description="""The abstract of the publication""") - combined_text: Optional[str] = Field(None) - full_text: Optional[str] = Field(None, description="""The full text of the publication""") - - - -class AnnotatorResult(ConfiguredBaseModel): - - subject_text: Optional[str] = Field(None) - object_id: Optional[str] = Field(None) - object_text: Optional[str] = Field(None) - - - - -# Model rebuild -# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model -Container.model_rebuild() -BioticInteraction.model_rebuild() -ExtractionResult.model_rebuild() -NamedEntity.model_rebuild() -Taxon.model_rebuild() -InteractionType.model_rebuild() -CompoundExpression.model_rebuild() -Triple.model_rebuild() -TextWithTriples.model_rebuild() -TextWithEntity.model_rebuild() -RelationshipType.model_rebuild() -Publication.model_rebuild() -AnnotatorResult.model_rebuild() - diff --git a/src/ontogpt/templates/biotic_interaction.yaml b/src/ontogpt/templates/biotic_interaction.yaml deleted file mode 100644 index 1810be266..000000000 --- a/src/ontogpt/templates/biotic_interaction.yaml +++ /dev/null @@ -1,64 +0,0 @@ -id: https://w3id.org/ontogpt/biotic_interaction -name: biotic-interaction-template -title: Biotic Interaction Template -description: >- - A template for biotic interactions -license: https://creativecommons.org/publicdomain/zero/1.0/ -prefixes: - linkml: https://w3id.org/linkml/ - bp: http://w3id.org/ontogpt/biotic-interaction-template - NCBITaxon: http://purl.obolibrary.org/obo/NCBITAXON_ - col: https://www.catalogueoflife.org/data/taxon/ - itis: https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value= - gbif: https://www.gbif.org/species/ - -default_prefix: bp -default_range: string - -imports: - - linkml:types - - core - -classes: - Container: - tree_root: true - attributes: - interactions: - range: BioticInteraction - multivalued: true - inlined_as_list: true - - BioticInteraction: - attributes: - source_taxon: - description: the taxon that is the subject of the interaction - range: Taxon - target_taxon: - description: the taxon that is the object of the interaction - range: Taxon - interaction_type: - description: the type of interaction - range: InteractionType - annotations: - prompt: A semi-colon separated list of taxon to taxon relationships - prompt.example: Carcharodon carcharias eats elephant seal; Pandarus sinuatus parasitizes Carcharodon carcharias; orca eats Carcharodon carcharias - - Taxon: - is_a: NamedEntity - id_prefixes: - - NCBITaxon - - SNOMEDCT - annotations: - annotators: sqlite:obo:ncbitaxon, bioportal:SNOMEDCT - #prompt.example: shark, Carcharodon carcharias, elephant seal, Pandarus sinuatus, orca, Panthera leo, lion, ungulates - - InteractionType: - is_a: NamedEntity - id_prefixes: - - RO - - MESH - - ECOCORE - - NCIT - annotations: - annotators: sqlite:obo:go, sqlite:obo:ro, sqlite:obo:bero - #prompt.example: eat, competes with, parasitizes, subsist on a diet, kill, compete, prey consists, hunting, killed by, compete for, dominate, competitors diff --git a/src/ontogpt/templates/cell_type.py b/src/ontogpt/templates/cell_type.py deleted file mode 100644 index bdc731f03..000000000 --- a/src/ontogpt/templates/cell_type.py +++ /dev/null @@ -1,304 +0,0 @@ -from __future__ import annotations -from datetime import datetime, date -from enum import Enum -from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, ConfigDict, Field, field_validator -import re -import sys -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal - - -metamodel_version = "None" -version = "None" - -class ConfiguredBaseModel(BaseModel): - model_config = ConfigDict( - validate_assignment=True, - validate_default=True, - extra = 'forbid', - arbitrary_types_allowed=True, - use_enum_values = True) - - -class BrainRegionIdentifier(str): - """ - Brain region (or for now, any nervous system part) - """ - - dummy = "dummy" - - -class NeurotransmitterIdentifier(str): - - - dummy = "dummy" - - -class NullDataOptions(str, Enum): - - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = "UNSPECIFIED_METHOD_OF_ADMINISTRATION" - - NOT_APPLICABLE = "NOT_APPLICABLE" - - NOT_MENTIONED = "NOT_MENTIONED" - - - -class CellType(ConfiguredBaseModel): - """ - Represents a cell type - """ - id: str = Field(...) - label: Optional[str] = Field(None, description="""the concise name of the cell type""") - equivalent_to: Optional[str] = Field(None, description="""the the cell type described""") - definition: Optional[str] = Field(None) - parents: Optional[List[str]] = Field(default_factory=list, description="""categorization""") - subtypes: Optional[List[str]] = Field(default_factory=list) - localizations: Optional[List[str]] = Field(default_factory=list) - genes: Optional[List[str]] = Field(default_factory=list) - diseases: Optional[List[str]] = Field(default_factory=list) - roles: Optional[List[str]] = Field(default_factory=list) - - - -class ImmuneCell(CellType): - - has_surface_markers: Optional[List[str]] = Field(default_factory=list) - id: str = Field(...) - label: Optional[str] = Field(None, description="""the concise name of the cell type""") - equivalent_to: Optional[str] = Field(None, description="""the the cell type described""") - definition: Optional[str] = Field(None) - parents: Optional[List[str]] = Field(default_factory=list, description="""categorization""") - subtypes: Optional[List[str]] = Field(default_factory=list) - localizations: Optional[List[str]] = Field(default_factory=list) - genes: Optional[List[str]] = Field(default_factory=list) - diseases: Optional[List[str]] = Field(default_factory=list) - roles: Optional[List[str]] = Field(default_factory=list) - - - -class Neuron(CellType): - - releases_neurotransitter: Optional[List[str]] = Field(default_factory=list) - id: str = Field(...) - label: Optional[str] = Field(None, description="""the concise name of the cell type""") - equivalent_to: Optional[str] = Field(None, description="""the the cell type described""") - definition: Optional[str] = Field(None) - parents: Optional[List[str]] = Field(default_factory=list, description="""categorization""") - subtypes: Optional[List[str]] = Field(default_factory=list) - localizations: Optional[List[str]] = Field(default_factory=list) - genes: Optional[List[str]] = Field(default_factory=list) - diseases: Optional[List[str]] = Field(default_factory=list) - roles: Optional[List[str]] = Field(default_factory=list) - - - -class Interneuron(Neuron): - - projects_to_or_from: Optional[List[str]] = Field(default_factory=list, description="""Brain structures from which this cell type projects into or receives projections from""") - releases_neurotransitter: Optional[List[str]] = Field(default_factory=list) - id: str = Field(...) - label: Optional[str] = Field(None, description="""the concise name of the cell type""") - equivalent_to: Optional[str] = Field(None, description="""the the cell type described""") - definition: Optional[str] = Field(None) - parents: Optional[List[str]] = Field(default_factory=list, description="""categorization""") - subtypes: Optional[List[str]] = Field(default_factory=list) - localizations: Optional[List[str]] = Field(default_factory=list) - genes: Optional[List[str]] = Field(default_factory=list) - diseases: Optional[List[str]] = Field(default_factory=list) - roles: Optional[List[str]] = Field(default_factory=list) - - - -class ExtractionResult(ConfiguredBaseModel): - """ - A result of extracting knowledge on text - """ - input_id: Optional[str] = Field(None) - input_title: Optional[str] = Field(None) - input_text: Optional[str] = Field(None) - raw_completion_output: Optional[str] = Field(None) - prompt: Optional[str] = Field(None) - extracted_object: Optional[Any] = Field(None, description="""The complex objects extracted from the text""") - named_entities: Optional[List[Any]] = Field(default_factory=list, description="""Named entities extracted from the text""") - - - -class NamedEntity(ConfiguredBaseModel): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Gene(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class ProteinOrComplex(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class BiologicalProcess(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Pathway(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class AnatomicalStructure(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class ChemicalEntity(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Neurotransmitter(ChemicalEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class BrainRegion(AnatomicalStructure): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class CellOntologyTerm(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Disease(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Drug(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class CompoundExpression(ConfiguredBaseModel): - - None - - - -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - subject: Optional[str] = Field(None) - predicate: Optional[str] = Field(None) - object: Optional[str] = Field(None) - qualifier: Optional[str] = Field(None, description="""A qualifier for the statements, e.g. \"NOT\" for negation""") - subject_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"""") - object_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"""") - - - -class TextWithTriples(ConfiguredBaseModel): - """ - A text containing one or more relations of the Triple type. - """ - publication: Optional[Publication] = Field(None) - triples: Optional[List[Triple]] = Field(default_factory=list) - - - -class TextWithEntity(ConfiguredBaseModel): - """ - A text containing one or more instances of a single type of entity. - """ - publication: Optional[Publication] = Field(None) - entities: Optional[List[str]] = Field(default_factory=list) - - - -class RelationshipType(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Publication(ConfiguredBaseModel): - - id: Optional[str] = Field(None, description="""The publication identifier""") - title: Optional[str] = Field(None, description="""The title of the publication""") - abstract: Optional[str] = Field(None, description="""The abstract of the publication""") - combined_text: Optional[str] = Field(None) - full_text: Optional[str] = Field(None, description="""The full text of the publication""") - - - -class AnnotatorResult(ConfiguredBaseModel): - - subject_text: Optional[str] = Field(None) - object_id: Optional[str] = Field(None) - object_text: Optional[str] = Field(None) - - - - -# Model rebuild -# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model -CellType.model_rebuild() -ImmuneCell.model_rebuild() -Neuron.model_rebuild() -Interneuron.model_rebuild() -ExtractionResult.model_rebuild() -NamedEntity.model_rebuild() -Gene.model_rebuild() -ProteinOrComplex.model_rebuild() -BiologicalProcess.model_rebuild() -Pathway.model_rebuild() -AnatomicalStructure.model_rebuild() -ChemicalEntity.model_rebuild() -Neurotransmitter.model_rebuild() -BrainRegion.model_rebuild() -CellOntologyTerm.model_rebuild() -Disease.model_rebuild() -Drug.model_rebuild() -CompoundExpression.model_rebuild() -Triple.model_rebuild() -TextWithTriples.model_rebuild() -TextWithEntity.model_rebuild() -RelationshipType.model_rebuild() -Publication.model_rebuild() -AnnotatorResult.model_rebuild() - diff --git a/src/ontogpt/templates/cell_type.yaml b/src/ontogpt/templates/cell_type.yaml deleted file mode 100644 index df9b65076..000000000 --- a/src/ontogpt/templates/cell_type.yaml +++ /dev/null @@ -1,304 +0,0 @@ -id: http://w3id.org/ontogpt/cell_type -name: cell_type -title: Composite Disease -description: >- - A template for representing cell types -license: https://creativecommons.org/publicdomain/zero/1.0/ -prefixes: - linkml: https://w3id.org/linkml/ - cell_type: http://w3id.org/ontogpt/cell_type/ - NCIT: http://purl.obolibrary.org/obo/NCIT_ - RO: http://purl.obolibrary.org/obo/RO_ - MONDO: http://purl.obolibrary.org/obo/MONDO_ - HP: http://purl.obolibrary.org/obo/HP_ - GO: http://purl.obolibrary.org/obo/GO_ - UBERON: http://purl.obolibrary.org/obo/UBERON_ - FBbt: http://purl.obolibrary.org/obo/FBbt_ - HGNC: http://identifiers.org/hgnc/ - CL: http://purl.obolibrary.org/obo/CL_ - IAO: http://purl.obolibrary.org/obo/IAO_ - BFO: http://purl.obolibrary.org/obo/BFO_ - AUTO: http://w3id.org/ontogpt/auto/ - PW: http://purl.obolibrary.org/obo/PW_ - CHEBI: http://purl.obolibrary.org/obo/CHEBI_ - skos: http://www.w3.org/2004/02/skos/core# -keywords: - - disease - - indication - -default_prefix: cell_type -default_range: string - -imports: - - linkml:types - - core - -classes: - CellType: - description: Represents a cell type - tree_root: true - attributes: - id: - identifier: true - range: uriorcurie - slot_uri: rdf:Resource - annotations: - prompt.skip: true - - label: - range: string - description: the concise name of the cell type - slot_uri: rdfs:label - annotations: - owl: AnnotationAssertion - - equivalent_to: - description: the the cell type described - range: CellOntologyTerm - annotations: - prompt: the cell type described in the text - #owl: EquivalentClasses - owl: AnnotationAssertion - slot_uri: skos:exactMatch - - definition: - annotations: - prompt: >- - A concise textual definition in genus-differentia form, i.e - 'A <genus> that <differentiating characteristics>' - owl: AnnotationProperty, AnnotationAssertion - slot_uri: IAO:0000115 - - parents: - description: categorization - annotations: - prompt: semicolon-separated list of parent (broader) cell types - owl: SubClassOf - multivalued: true - range: CellOntologyTerm - - subtypes: - annotations: - prompt: >- - semicolon-separated list of the subtypes (subclasses) of this cell type. - Use concise terms, and separate elements in a list using semicolon (;) - owl.template: | - {% for subtype in subtypes %} - SubClassOf( {{ tr(subtype) }} {{ id }} ) - {% endfor %} - multivalued: true - range: CellOntologyTerm - - localizations: - annotations: - prompt: semicolon-separated list of anatomical structures in which this cell type is localized - owl: SubClassOf, ObjectSomeValuesFrom - slot_uri: BFO:0000050 - multivalued: true - range: AnatomicalStructure - - genes: - annotations: - prompt: semicolon-separated list of genes expressed in cells of this type - owl: SubClassOf, ObjectSomeValuesFrom - slot_uri: RO:0002292 - multivalued: true - range: Gene - - diseases: - annotations: - prompt: semicolon-separated list of diseases in which this cell type is implicated - owl.template: | - {% for disease in diseases %} - SubClassOf( {{ tr(disease) }} ObjectSomeValuesFrom( RO:0004026 {{ id }} )) - {% endfor %} - multivalued: true - range: Disease - - roles: - annotations: - prompt: >- - semicolon-separated list of roles (e.g. biological processes) that this cell type plays. - These should be short descriptive terms corresponding to ontology terms in the GO biological process - hierarchy. - owl: SubClassOf, ObjectSomeValuesFrom - slot_uri: RO:0002215 - multivalued: true - range: BiologicalProcess - - - ImmuneCell: - is_a: CellType - - attributes: - has_surface_markers: - annotations: - prompt: semicolon-separated list of proteins or complexes expressed on the surface of the cell - owl: SubClassOf, ObjectSomeValuesFrom - multivalued: true - range: ProteinOrComplex - - Neuron: - is_a: CellType - - attributes: - releases_neurotransitter: - annotations: - prompt: named of chemical entity that this neuron releases - owl: SubClassOf, ObjectSomeValuesFrom - multivalued: true - range: Neurotransmitter - slot_uri: RO:0002111 - - - Interneuron: - is_a: Neuron - attributes: - projects_to_or_from: - description: Brain structures from which this cell type projects into or receives projections from - annotations: - prompt: semicolon-separated list of anatomical structures from which this cell type projects from or into - multivalued: true - range: BrainRegion - slot_uri: RO:0002170 - - Gene: - is_a: NamedEntity - id_prefixes: - - HGNC - - MGI - - PR - - UniProtKB - annotations: - annotators: sqlite:obo:hgnc, bioportal:hgnc-nr - - ProteinOrComplex: - is_a: NamedEntity - id_prefixes: - - HGNC - - MGI - - PR - - UniProtKB - - GO - annotations: - annotators: sqlite:obo:hgnc, bioportal:hgnc-nr, sqlite:obo:go, sqlite:obo:pr - - - BiologicalProcess: - is_a: NamedEntity - id_prefixes: - - GO - annotations: - annotators: sqlite:obo:go - - Pathway: - is_a: NamedEntity - id_prefixes: - - GO - - PW - annotations: - annotators: sqlite:obo:go, sqlite:obo:pw - - AnatomicalStructure: - is_a: NamedEntity - id_prefixes: - - UBERON - - FBbt - - WBbt - annotations: - annotators: sqlite:obo:uberon, sqlite:obo:fbbt, sqlite:obo:wbbt - - ChemicalEntity: - is_a: NamedEntity - id_prefixes: - - CHEBI - annotations: - annotators: - sqlite:obo:chebi - - Neurotransmitter: - is_a: ChemicalEntity - id_prefixes: - - CHEBI - annotations: - annotators: - sqlite:obo:chebi - slot_usage: - id: - values_from: - - NeurotransmitterIdentifier - identifier: true - - BrainRegion: - is_a: AnatomicalStructure - id_prefixes: - - UBERON - - FBbt - - WBbt - annotations: - annotators: sqlite:obo:uberon, sqlite:obo:fbbt, sqlite:obo:wbbt - slot_usage: - id: - values_from: - - BrainRegionIdentifier - identifier: true - - CellOntologyTerm: - is_a: NamedEntity - id_prefixes: - - CL - - FBbt - - WBbt - annotations: - annotators: sqlite:obo:cl, sqlite:obo:fbbt, sqlite:obo:wbbt - - Disease: - is_a: NamedEntity - id_prefixes: - - MONDO - - HP - annotations: - annotators: sqlite:obo:mondo, sqlite:obo:hp - - Drug: - is_a: NamedEntity - annotations: - annotators: sqlite:obo:chebi, sqlite:obo:drugbank - -enums: - - BrainRegionIdentifier: - description: Brain region (or for now, any nervous system part) - comments: - - consider adding brain atlases here - include: - - reachable_from: - source_ontology: obo:uberon - relationship_types: - - rdfs:subClassOf - - BFO:0000050 - source_nodes: - - UBERON:0001016 ## nervous system - - reachable_from: - source_ontology: obo:fbbt - relationship_types: - - rdfs:subClassOf - - BFO:0000050 - source_nodes: - - FBbt:00005093 ## nervous system - - reachable_from: - source_ontology: obo:wbbt - relationship_types: - - rdfs:subClassOf - - BFO:0000050 - source_nodes: - - WBbt:0005735 ## nervous system - - NeurotransmitterIdentifier: - reachable_from: - source_ontology: obo:chebi - relationship_types: - - rdfs:subClassOf - - RO:0000087 - source_nodes: - - CHEBI:35942 ## neurotransmitter agent diff --git a/src/ontogpt/templates/class_enrichment.py b/src/ontogpt/templates/class_enrichment.py deleted file mode 100644 index 9034b9356..000000000 --- a/src/ontogpt/templates/class_enrichment.py +++ /dev/null @@ -1,80 +0,0 @@ -from __future__ import annotations -from datetime import datetime, date -from enum import Enum -from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, ConfigDict, Field, field_validator -import re -import sys -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal - - -metamodel_version = "None" -version = "None" - -class ConfiguredBaseModel(BaseModel): - model_config = ConfigDict( - validate_assignment=True, - validate_default=True, - extra = 'forbid', - arbitrary_types_allowed=True, - use_enum_values = True) - - -class SortFieldEnum(str, Enum): - """ - The field to sort by - """ - - ANY = "ANY" - - P_VALUE = "P_VALUE" - - - -class ClassEnrichmentConfiguration(ConfiguredBaseModel): - """ - configuration for search - """ - p_value_cutoff: float = Field(..., description="""p-value cutoff for enrichment""") - - - -class ClassEnrichmentResultSet(ConfiguredBaseModel): - """ - A collection of enrichemt results - """ - results: Optional[List[ClassEnrichmentResult]] = Field(default_factory=list, description="""The enrichment results""") - - - -class ClassEnrichmentResult(ConfiguredBaseModel): - """ - A single enrichment result - """ - class_id: str = Field(..., description="""The class id""") - class_label: Optional[str] = Field(None, description="""The class label""") - rank: Optional[int] = Field(None, description="""The rank of this result""") - p_value: float = Field(..., description="""The p-value""") - p_value_adjusted: Optional[float] = Field(None, description="""The adjusted p-value""") - false_discovery_rate: Optional[float] = Field(None, description="""The false discovery rate""") - fold_enrichment: Optional[float] = Field(None, description="""The fold enrichment""") - probability: Optional[float] = Field(None, description="""The probability, as estimated by model-based approaches""", ge=0, le=1) - sample_count: Optional[int] = Field(None, description="""The number of entities in the sample with this class""") - sample_total: Optional[int] = Field(None, description="""The total number of entities in the sample""") - background_count: Optional[int] = Field(None, description="""The background count""") - background_total: Optional[int] = Field(None, description="""The background total""") - ancestor_of_more_informative_result: Optional[bool] = Field(None, description="""This term is more general than a previously reported result""") - descendant_of_more_informative_result: Optional[bool] = Field(None, description="""This term is more specific than a previously reported result""") - - - - -# Model rebuild -# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model -ClassEnrichmentConfiguration.model_rebuild() -ClassEnrichmentResultSet.model_rebuild() -ClassEnrichmentResult.model_rebuild() - diff --git a/src/ontogpt/templates/class_enrichment.yaml b/src/ontogpt/templates/class_enrichment.yaml deleted file mode 100644 index a8a2e1e88..000000000 --- a/src/ontogpt/templates/class_enrichment.yaml +++ /dev/null @@ -1,118 +0,0 @@ -id: https://w3id.org/oak/class-enrichment -title: Class Enrichment Datamodel -name: class-enrichment -description: >- - A datamodel for representing the results of class enrichment on gene sets -license: https://creativecommons.org/publicdomain/zero/1.0/ - -prefixes: - linkml: https://w3id.org/linkml/ - ontoenrich: https://w3id.org/oak/class-enrichment/ - skos: http://www.w3.org/2004/02/skos/core# - pav: http://purl.org/pav/ - schema: http://schema.org/ - sh: https://w3id.org/shacl/ - prov: http://www.w3.org/ns/prov# - sssom: http://w3id.org/sssom/ - bpa: https://bioportal.bioontology.org/annotator/ - oa: http://www.w3.org/ns/oa# - STATO: http://purl.obolibrary.org/obo/STATO_ - OBI: http://purl.obolibrary.org/obo/OBI_ - -default_prefix: ontoenrich -default_range: string - -default_curi_maps: - - semweb_context - -emit_prefixes: - - linkml - - rdf - - rdfs - - xsd - - owl - -imports: - - linkml:types - -types: - Position: - typeof: integer - -#================================== -# Classes # -#================================== -classes: - ClassEnrichmentConfiguration: - description: configuration for search - attributes: - p_value_cutoff: - description: p-value cutoff for enrichment - range: float - required: true - - ClassEnrichmentResultSet: - description: A collection of enrichemt results - attributes: - results: - description: The enrichment results - range: ClassEnrichmentResult - multivalued: true - - ClassEnrichmentResult: - description: A single enrichment result - attributes: - class_id: - description: The class id - range: uriorcurie - required: true - class_label: - description: The class label - range: string - rank: - description: The rank of this result - range: integer - p_value: - slot_uri: OBI:0000175 - description: The p-value - range: float - required: true - p_value_adjusted: - description: The adjusted p-value - range: float - false_discovery_rate: - description: The false discovery rate - range: float - fold_enrichment: - description: The fold enrichment - range: float - probability: - description: The probability, as estimated by model-based approaches - range: float - minimum_value: 0 - maximum_value: 1 - sample_count: - description: The number of entities in the sample with this class - range: integer - sample_total: - description: The total number of entities in the sample - range: integer - background_count: - description: The background count - range: integer - background_total: - description: The background total - range: integer - ancestor_of_more_informative_result: - description: This term is more general than a previously reported result - range: boolean - descendant_of_more_informative_result: - description: This term is more specific than a previously reported result - range: boolean - -enums: - SortFieldEnum: - description: The field to sort by - permissible_values: - ANY: - P_VALUE: diff --git a/src/ontogpt/templates/composite_disease.py b/src/ontogpt/templates/composite_disease.py deleted file mode 100644 index b723fd310..000000000 --- a/src/ontogpt/templates/composite_disease.py +++ /dev/null @@ -1,261 +0,0 @@ -from __future__ import annotations -from datetime import datetime, date -from enum import Enum -from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, ConfigDict, Field, field_validator -import re -import sys -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal - - -metamodel_version = "None" -version = "None" - -class ConfiguredBaseModel(BaseModel): - model_config = ConfigDict( - validate_assignment=True, - validate_default=True, - extra = 'forbid', - arbitrary_types_allowed=True, - use_enum_values = True) - - -class NCITDrugType(str): - - - dummy = "dummy" - - -class NCITTreatmentType(str): - - - dummy = "dummy" - - -class NCITTActivityType(str): - - - dummy = "dummy" - - -class MAXOActionType(str): - - - dummy = "dummy" - - -class MESHTherapeuticType(str): - - - dummy = "dummy" - - -class CHEBIDrugType(str): - - - dummy = "dummy" - - -class NullDataOptions(str, Enum): - - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = "UNSPECIFIED_METHOD_OF_ADMINISTRATION" - - NOT_APPLICABLE = "NOT_APPLICABLE" - - NOT_MENTIONED = "NOT_MENTIONED" - - - -class CompositeDisease(ConfiguredBaseModel): - - main_disease: Optional[str] = Field(None, description="""the name of the disease that is treated.""") - drugs: Optional[List[str]] = Field(default_factory=list, description="""semicolon-separated list of named small molecule drugs""") - treatments: Optional[List[str]] = Field(default_factory=list, description="""semicolon-separated list of therapies and treatments are indicated for treating the disease.""") - contraindications: Optional[List[str]] = Field(default_factory=list, description="""semicolon-separated list of therapies and treatments that are contra-indicated for the disease, and should not be used, due to risk of adverse effects.""") - treatment_mechanisms: Optional[List[TreatmentMechanism]] = Field(default_factory=list, description="""semicolon-separated list of treatment to asterisk-separated mechanism associations""") - treatment_efficacies: Optional[List[TreatmentEfficacy]] = Field(default_factory=list, description="""semicolon-separated list of treatment to efficacy associations, e.g. Imatinib*effective""") - treatment_adverse_effects: Optional[List[TreatmentAdverseEffect]] = Field(default_factory=list, description="""semicolon-separated list of treatment to adverse effect associations, e.g. Imatinib*nausea""") - - - -class ExtractionResult(ConfiguredBaseModel): - """ - A result of extracting knowledge on text - """ - input_id: Optional[str] = Field(None) - input_title: Optional[str] = Field(None) - input_text: Optional[str] = Field(None) - raw_completion_output: Optional[str] = Field(None) - prompt: Optional[str] = Field(None) - extracted_object: Optional[Any] = Field(None, description="""The complex objects extracted from the text""") - named_entities: Optional[List[Any]] = Field(default_factory=list, description="""Named entities extracted from the text""") - - - -class NamedEntity(ConfiguredBaseModel): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Gene(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Symptom(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Disease(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class AdverseEffect(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Treatment(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Mechanism(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Drug(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class CompoundExpression(ConfiguredBaseModel): - - None - - - -class TreatmentMechanism(CompoundExpression): - - treatment: Optional[str] = Field(None) - mechanism: Optional[str] = Field(None) - - - -class TreatmentAdverseEffect(CompoundExpression): - - treatment: Optional[str] = Field(None) - adverse_effects: Optional[List[str]] = Field(default_factory=list) - - - -class TreatmentEfficacy(CompoundExpression): - - treatment: Optional[str] = Field(None) - efficacy: Optional[str] = Field(None) - - - -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - subject: Optional[str] = Field(None) - predicate: Optional[str] = Field(None) - object: Optional[str] = Field(None) - qualifier: Optional[str] = Field(None, description="""A qualifier for the statements, e.g. \"NOT\" for negation""") - subject_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"""") - object_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"""") - - - -class TextWithTriples(ConfiguredBaseModel): - """ - A text containing one or more relations of the Triple type. - """ - publication: Optional[Publication] = Field(None) - triples: Optional[List[Triple]] = Field(default_factory=list) - - - -class TextWithEntity(ConfiguredBaseModel): - """ - A text containing one or more instances of a single type of entity. - """ - publication: Optional[Publication] = Field(None) - entities: Optional[List[str]] = Field(default_factory=list) - - - -class RelationshipType(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Publication(ConfiguredBaseModel): - - id: Optional[str] = Field(None, description="""The publication identifier""") - title: Optional[str] = Field(None, description="""The title of the publication""") - abstract: Optional[str] = Field(None, description="""The abstract of the publication""") - combined_text: Optional[str] = Field(None) - full_text: Optional[str] = Field(None, description="""The full text of the publication""") - - - -class AnnotatorResult(ConfiguredBaseModel): - - subject_text: Optional[str] = Field(None) - object_id: Optional[str] = Field(None) - object_text: Optional[str] = Field(None) - - - - -# Model rebuild -# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model -CompositeDisease.model_rebuild() -ExtractionResult.model_rebuild() -NamedEntity.model_rebuild() -Gene.model_rebuild() -Symptom.model_rebuild() -Disease.model_rebuild() -AdverseEffect.model_rebuild() -Treatment.model_rebuild() -Mechanism.model_rebuild() -Drug.model_rebuild() -CompoundExpression.model_rebuild() -TreatmentMechanism.model_rebuild() -TreatmentAdverseEffect.model_rebuild() -TreatmentEfficacy.model_rebuild() -Triple.model_rebuild() -TextWithTriples.model_rebuild() -TextWithEntity.model_rebuild() -RelationshipType.model_rebuild() -Publication.model_rebuild() -AnnotatorResult.model_rebuild() - diff --git a/src/ontogpt/templates/composite_disease.yaml b/src/ontogpt/templates/composite_disease.yaml deleted file mode 100644 index 6c816de46..000000000 --- a/src/ontogpt/templates/composite_disease.yaml +++ /dev/null @@ -1,182 +0,0 @@ -id: http://w3id.org/ontogpt/composite_disease -name: composite_disease -title: Composite Disease -description: >- - A template for representing composite disease concepts -license: https://creativecommons.org/publicdomain/zero/1.0/ -prefixes: - linkml: https://w3id.org/linkml/ - composite_disease: http://w3id.org/ontogpt/composite_disease/ -keywords: - - disease - - indication - -default_prefix: composite_disease -default_range: string - -imports: - - linkml:types - - core - -classes: - CompositeDisease: - tree_root: true - attributes: - main_disease: - description: the name of the disease that is treated. - range: Disease - - drugs: - description: semicolon-separated list of named small molecule drugs - multivalued: true - range: Drug - - treatments: - description: >- - semicolon-separated list of therapies and treatments are indicated for treating the disease. - annotations: - prompt.examples: Imatinib, exercise, surgery - multivalued: true - range: Treatment - - contraindications: - description: >- - semicolon-separated list of therapies and treatments that are contra-indicated for the disease, - and should not be used, due to risk of adverse effects. - annotations: - prompt.examples: Beta-blockers, exercise, surgery - multivalued: true - range: Treatment - - treatment_mechanisms: - description: semicolon-separated list of treatment to asterisk-separated mechanism associations - multivalued: true - range: TreatmentMechanism - annotations: - prompt.separator: "*" - - treatment_efficacies: - description: semicolon-separated list of treatment to efficacy associations, e.g. Imatinib*effective - multivalued: true - range: TreatmentEfficacy - annotations: - prompt.separator: "*" - - treatment_adverse_effects: - description: semicolon-separated list of treatment to adverse effect associations, e.g. Imatinib*nausea - multivalued: true - range: TreatmentAdverseEffect - annotations: - prompt.separator: "*" - - Gene: - is_a: NamedEntity - id_prefixes: - - HGNC - annotations: - annotators: gilda:, obo:sql:hgnc, bioportal:hgnc-nr - - Symptom: - is_a: NamedEntity - id_prefixes: - - HP - annotations: - annotators: sqlite:obo:hp - - Disease: - is_a: NamedEntity - annotations: - annotators: sqlite:obo:mondo - - AdverseEffect: - is_a: NamedEntity - annotations: - annotators: sqlite:obo:hp, sqlite:obo:ncit - - Treatment: - is_a: NamedEntity - annotations: - annotators: sqlite:obo:maxo, sqlite:obo:ncit, sqlite:obo:mesh, sqlite:obo:chebi - values_from: - - NCITDrugType - - NCITTreatmentType - - NCITActivityType - - MAXOTreatmentType - - MESHTherapeuticType - - CHEBIDrugType - - Mechanism: - is_a: NamedEntity - annotations: - annotators: sqlite:obo:go, sqlite:obo:ncit, sqlite:obo:mesh - - Drug: - is_a: NamedEntity - annotations: - annotators: sqlite:obo:chebi, sqlite:obo:drugbank - - TreatmentMechanism: - is_a: CompoundExpression - attributes: - treatment: - range: Treatment - mechanism: - range: Mechanism - - TreatmentAdverseEffect: - is_a: CompoundExpression - attributes: - treatment: - range: Treatment - adverse_effects: - range: AdverseEffect - multivalued: true - - TreatmentEfficacy: - is_a: CompoundExpression - attributes: - treatment: - range: Treatment - efficacy: - range: string - -enums: - - NCITDrugType: - reachable_from: - source_ontology: obo:ncit - source_nodes: - - NCIT:C1908 ## Drug, Food, Chemical or Biomedical Material - - NCITTreatmentType: - reachable_from: - source_ontology: obo:ncit - source_nodes: - - NCIT:C25218 ## Intervention or Procedure - - NCITTActivityType: - reachable_from: - source_ontology: obo:ncit - source_nodes: - - NCIT:C43431 ## Activity - - MAXOActionType: - reachable_from: - source_ontology: obo:maxo - source_nodes: - - MAXO:0000001 ## Medical Action - - MESHTherapeuticType: - reachable_from: - source_ontology: obo:mesh - source_nodes: - - MESH:D013812 ## Therapeutics - - CHEBIDrugType: - reachable_from: - source_ontology: obo:chebi - source_nodes: - - CHEBI:23888 ## drug - relationship_types: - - rdfs:subClassOf - - RO:0000087 \ No newline at end of file diff --git a/src/ontogpt/templates/core.py b/src/ontogpt/templates/core.py deleted file mode 100644 index d17845d12..000000000 --- a/src/ontogpt/templates/core.py +++ /dev/null @@ -1,132 +0,0 @@ -from __future__ import annotations -from datetime import datetime, date -from enum import Enum -from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, ConfigDict, Field, field_validator -import re -import sys -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal - - -metamodel_version = "None" -version = "None" - -class ConfiguredBaseModel(BaseModel): - model_config = ConfigDict( - validate_assignment=True, - validate_default=True, - extra = 'forbid', - arbitrary_types_allowed=True, - use_enum_values = True) - - -class NullDataOptions(str, Enum): - - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = "UNSPECIFIED_METHOD_OF_ADMINISTRATION" - - NOT_APPLICABLE = "NOT_APPLICABLE" - - NOT_MENTIONED = "NOT_MENTIONED" - - - -class ExtractionResult(ConfiguredBaseModel): - """ - A result of extracting knowledge on text - """ - input_id: Optional[str] = Field(None) - input_title: Optional[str] = Field(None) - input_text: Optional[str] = Field(None) - raw_completion_output: Optional[str] = Field(None) - prompt: Optional[str] = Field(None) - extracted_object: Optional[Any] = Field(None, description="""The complex objects extracted from the text""") - named_entities: Optional[List[Any]] = Field(default_factory=list, description="""Named entities extracted from the text""") - - - -class NamedEntity(ConfiguredBaseModel): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class CompoundExpression(ConfiguredBaseModel): - - None - - - -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - subject: Optional[str] = Field(None) - predicate: Optional[str] = Field(None) - object: Optional[str] = Field(None) - qualifier: Optional[str] = Field(None, description="""A qualifier for the statements, e.g. \"NOT\" for negation""") - subject_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"""") - object_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"""") - - - -class TextWithTriples(ConfiguredBaseModel): - """ - A text containing one or more relations of the Triple type. - """ - publication: Optional[Publication] = Field(None) - triples: Optional[List[Triple]] = Field(default_factory=list) - - - -class TextWithEntity(ConfiguredBaseModel): - """ - A text containing one or more instances of a single type of entity. - """ - publication: Optional[Publication] = Field(None) - entities: Optional[List[str]] = Field(default_factory=list) - - - -class RelationshipType(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Publication(ConfiguredBaseModel): - - id: Optional[str] = Field(None, description="""The publication identifier""") - title: Optional[str] = Field(None, description="""The title of the publication""") - abstract: Optional[str] = Field(None, description="""The abstract of the publication""") - combined_text: Optional[str] = Field(None) - full_text: Optional[str] = Field(None, description="""The full text of the publication""") - - - -class AnnotatorResult(ConfiguredBaseModel): - - subject_text: Optional[str] = Field(None) - object_id: Optional[str] = Field(None) - object_text: Optional[str] = Field(None) - - - - -# Model rebuild -# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model -ExtractionResult.model_rebuild() -NamedEntity.model_rebuild() -CompoundExpression.model_rebuild() -Triple.model_rebuild() -TextWithTriples.model_rebuild() -TextWithEntity.model_rebuild() -RelationshipType.model_rebuild() -Publication.model_rebuild() -AnnotatorResult.model_rebuild() - diff --git a/src/ontogpt/templates/core.yaml b/src/ontogpt/templates/core.yaml deleted file mode 100644 index cc7367b7a..000000000 --- a/src/ontogpt/templates/core.yaml +++ /dev/null @@ -1,157 +0,0 @@ -id: http://w3id.org/ontogpt/core -name: core -title: AI core Template -license: https://creativecommons.org/publicdomain/zero/1.0/ -prefixes: - linkml: https://w3id.org/linkml/ - core: http://w3id.org/ontogpt/core/ - NCIT: http://purl.obolibrary.org/obo/NCIT_ - RO: http://purl.obolibrary.org/obo/RO_ -description: Core upper level - -default_prefix: core -default_range: string - -imports: - - linkml:types - -classes: - Any: - class_uri: linkml:Any - - ExtractionResult: - description: >- - A result of extracting knowledge on text - attributes: - input_id: - input_title: - input_text: - raw_completion_output: - prompt: - extracted_object: - description: >- - The complex objects extracted from the text - range: Any - inlined: true - named_entities: - description: >- - Named entities extracted from the text - range: Any - multivalued: true - inlined: true - inlined_as_list: true - - NamedEntity: - abstract: true - attributes: - id: - description: >- - A unique identifier for the named entity - comments: - - this is populated during the grounding and normalization step - identifier: true - annotations: - prompt.skip: "true" - label: - aliases: - - name - description: >- - The label (name) of the named thing - range: string - slot_uri: rdfs:label - annotations: - owl: AnnotationProperty, AnnotationAssertion - - CompoundExpression: - abstract: true - - Triple: - abstract: true - description: Abstract parent for Relation Extraction tasks - is_a: CompoundExpression - attributes: - subject: - range: NamedEntity - predicate: - range: RelationshipType - object: - range: NamedEntity - qualifier: - range: string - description: >- - A qualifier for the statements, e.g. "NOT" for negation - subject_qualifier: - range: NamedEntity - description: >- - An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - object_qualifier: - range: NamedEntity - description: >- - An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - - TextWithTriples: - description: A text containing one or more relations of the Triple type. - attributes: - publication: - range: Publication - inlined: true - annotations: - prompt.skip: "true" - triples: - range: Triple - multivalued: true - inlined: true - inlined_as_list: true - - TextWithEntity: - description: A text containing one or more instances of a single type of entity. - attributes: - publication: - range: Publication - inlined: true - annotations: - prompt.skip: "true" - entities: - range: NamedEntity - multivalued: true - - RelationshipType: - is_a: NamedEntity - id_prefixes: - - RO - - biolink - - Publication: - attributes: - id: - description: >- - The publication identifier - title: - description: >- - The title of the publication - abstract: - description: >- - The abstract of the publication - combined_text: - full_text: - description: >- - The full text of the publication - - AnnotatorResult: - attributes: - subject_text: - object_id: - object_text: - -enums: - - NullDataOptions: - permissible_values: - UNSPECIFIED_METHOD_OF_ADMINISTRATION: - meaning: NCIT:C149701 - NOT_APPLICABLE: - meaning: NCIT:C18902 - aliases: - - "not applicable" - - "N/A" - NOT_MENTIONED: diff --git a/src/ontogpt/templates/ctd.py b/src/ontogpt/templates/ctd.py deleted file mode 100644 index f0e5f8085..000000000 --- a/src/ontogpt/templates/ctd.py +++ /dev/null @@ -1,218 +0,0 @@ -from __future__ import annotations -from datetime import datetime, date -from enum import Enum -from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, ConfigDict, Field, field_validator -import re -import sys -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal - - -metamodel_version = "None" -version = "None" - -class ConfiguredBaseModel(BaseModel): - model_config = ConfigDict( - validate_assignment=True, - validate_default=True, - extra = 'forbid', - arbitrary_types_allowed=True, - use_enum_values = True) - - -class MeshChemicalIdentifier(str): - - - dummy = "dummy" - - -class MeshDiseaseIdentifier(str): - - - dummy = "dummy" - - -class NullDataOptions(str, Enum): - - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = "UNSPECIFIED_METHOD_OF_ADMINISTRATION" - - NOT_APPLICABLE = "NOT_APPLICABLE" - - NOT_MENTIONED = "NOT_MENTIONED" - - - -class ExtractionResult(ConfiguredBaseModel): - """ - A result of extracting knowledge on text - """ - input_id: Optional[str] = Field(None) - input_title: Optional[str] = Field(None) - input_text: Optional[str] = Field(None) - raw_completion_output: Optional[str] = Field(None) - prompt: Optional[str] = Field(None) - extracted_object: Optional[Any] = Field(None, description="""The complex objects extracted from the text""") - named_entities: Optional[List[Any]] = Field(default_factory=list, description="""Named entities extracted from the text""") - - - -class NamedEntity(ConfiguredBaseModel): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Disease(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - @field_validator('id') - def pattern_id(cls, v): - pattern=re.compile(r"^MESH:[CD][0-9]{6}$") - if isinstance(v,list): - for element in v: - if not pattern.match(element): - raise ValueError(f"Invalid id format: {element}") - elif isinstance(v,str): - if not pattern.match(v): - raise ValueError(f"Invalid id format: {v}") - return v - - -class Chemical(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - @field_validator('id') - def pattern_id(cls, v): - pattern=re.compile(r"^MESH:[CD][0-9]{6}$") - if isinstance(v,list): - for element in v: - if not pattern.match(element): - raise ValueError(f"Invalid id format: {element}") - elif isinstance(v,str): - if not pattern.match(v): - raise ValueError(f"Invalid id format: {v}") - return v - - -class CompoundExpression(ConfiguredBaseModel): - - None - - - -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - subject: Optional[str] = Field(None) - predicate: Optional[str] = Field(None) - object: Optional[str] = Field(None) - qualifier: Optional[str] = Field(None, description="""A qualifier for the statements, e.g. \"NOT\" for negation""") - subject_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"""") - object_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"""") - - - -class ChemicalToDiseaseRelationship(Triple): - """ - A triple where the subject is a chemical and the object is a disease. - """ - subject: Optional[str] = Field(None, description="""The chemical substance, drug, or small molecule. For example: Lidocaine, Monosodium Glutamate, Imatinib.""") - predicate: Optional[str] = Field(None, description="""The relationship type, e.g. INDUCES, TREATS.""") - object: Optional[str] = Field(None, description="""The disease or condition that is being treated or induced by the chemical. For example, asthma, cancer, covid-19, cardiac asystole, Hypotension, Headache.""") - qualifier: Optional[str] = Field(None, description="""A qualifier for the statements, e.g. \"NOT\" for negation""") - subject_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the chemical, e.g. \"high dose\" or \"intravenously administered\"""") - object_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the disease, e.g. \"severe\" or \"with additional complications\"""") - - - -class TextWithTriples(ConfiguredBaseModel): - """ - A text containing one or more relations of the Triple type. - """ - publication: Optional[Publication] = Field(None) - triples: Optional[List[Triple]] = Field(default_factory=list) - - - -class ChemicalToDiseaseDocument(TextWithTriples): - """ - A document that contains chemical to disease relations. - """ - publication: Optional[Publication] = Field(None) - triples: Optional[List[ChemicalToDiseaseRelationship]] = Field(default_factory=list) - - - -class TextWithEntity(ConfiguredBaseModel): - """ - A text containing one or more instances of a single type of entity. - """ - publication: Optional[Publication] = Field(None) - entities: Optional[List[str]] = Field(default_factory=list) - - - -class RelationshipType(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class ChemicalToDiseasePredicate(RelationshipType): - """ - A predicate for chemical to disease relationships - """ - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Publication(ConfiguredBaseModel): - - id: Optional[str] = Field(None, description="""The publication identifier""") - title: Optional[str] = Field(None, description="""The title of the publication""") - abstract: Optional[str] = Field(None, description="""The abstract of the publication""") - combined_text: Optional[str] = Field(None) - full_text: Optional[str] = Field(None, description="""The full text of the publication""") - - - -class AnnotatorResult(ConfiguredBaseModel): - - subject_text: Optional[str] = Field(None) - object_id: Optional[str] = Field(None) - object_text: Optional[str] = Field(None) - - - - -# Model rebuild -# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model -ExtractionResult.model_rebuild() -NamedEntity.model_rebuild() -Disease.model_rebuild() -Chemical.model_rebuild() -CompoundExpression.model_rebuild() -Triple.model_rebuild() -ChemicalToDiseaseRelationship.model_rebuild() -TextWithTriples.model_rebuild() -ChemicalToDiseaseDocument.model_rebuild() -TextWithEntity.model_rebuild() -RelationshipType.model_rebuild() -ChemicalToDiseasePredicate.model_rebuild() -Publication.model_rebuild() -AnnotatorResult.model_rebuild() - diff --git a/src/ontogpt/templates/ctd.yaml b/src/ontogpt/templates/ctd.yaml deleted file mode 100644 index 135036dc4..000000000 --- a/src/ontogpt/templates/ctd.yaml +++ /dev/null @@ -1,161 +0,0 @@ -id: http://w3id.org/ontogpt/ctd -name: ctd -title: Chemical to Disease Template -description: >- - A template for Chemical to Disease associations. - - This template is intended to represent associations between chemicals and diseases, - and for evaluating Semantic Llama against BioCreative V Chemical Disease - Relation (CDR) Task (BC5CDR). -see_also: - - https://biocreative.bioinformatics.udel.edu/media/store/files/2015/BC5CDR_overview.final.pdf - - https://academic.oup.com/database/article/doi/10.1093/database/baw068/2630414 -source: https://biocreative.bioinformatics.udel.edu/tasks/biocreative-v/track-3-cdr/ -license: https://creativecommons.org/publicdomain/zero/1.0/ -prefixes: - linkml: https://w3id.org/linkml/ - drug: http://w3id.org/ontogpt/drug/ - -default_prefix: drug -default_range: string - -imports: - - linkml:types - - core - -classes: - - ChemicalToDiseaseDocument: - description: A document that contains chemical to disease relations. - is_a: TextWithTriples - slot_usage: - triples: - range: ChemicalToDiseaseRelationship - annotations: - prompt: >- - A semi-colon separated list of chemical to disease relationships, where the relationship is either INDUCES - or TREATS. - for example: Lidocaine INDUCES cardiac asystole; - Hydroxychloroquine NOT TREATS COVID-19; - Methyldopa INDUCES Hypotension; - Monosodium Glutamate NOT INDUCES Headache; - Imatinib TREATS cancer - exclude: Lidocaine, cardiac asystole, Hydroxychloroquine, COVID-19, Methyldopa, Headache, Imatinib, cancer - - - ChemicalToDiseaseRelationship: - is_a: Triple - description: A triple where the subject is a chemical and the object is a disease. - slot_usage: - subject: - range: Chemical - description: >- - The chemical substance, drug, or small molecule. - For example: Lidocaine, Monosodium Glutamate, Imatinib. - object: - range: Disease - description: >- - The disease or condition that is being treated or induced by the chemical. - For example, asthma, cancer, covid-19, cardiac asystole, Hypotension, Headache. - predicate: - range: ChemicalToDiseasePredicate - description: The relationship type, e.g. INDUCES, TREATS. - subject_qualifier: - range: NamedEntity - description: >- - An optional qualifier or modifier for the chemical, e.g. "high dose" or "intravenously administered" - object_qualifier: - range: NamedEntity - description: >- - An optional qualifier or modifier for the disease, e.g. "severe" or "with additional complications" - - Disease: - is_a: NamedEntity - annotations: - annotators: "sqlite:obo:mesh, sqlite:obo:mondo, sqlite:obo:hp, sqlite:obo:ncit, sqlite:obo:doid, bioportal:meddra" - prompt.examples: cardiac asystole, COVID-19, Headache, cancer - # For the purposes of evaluating against BC5CDR, we force normalization to MESH - id_prefixes: - - MESH - slot_usage: - id: - pattern: "^MESH:[CD][0-9]{6}$" - values_from: - - MeshDiseaseIdentifier - - Chemical: - is_a: NamedEntity - annotations: - # https://data.bioontology.org/ontologies/MDM: The Mapping of Drug Names and MeSH 2022 (MDM) provides owl:sameAs relationships as well as owl:equivalentClass of similar concepts for Drug Names from the DrugBank vocabulary (released 2022-01-03 under version 5.1.9: https://go.drugbank.com/releases/latest#open-data) and the Medical Subject Headings (2022 version: http://id.nlm.nih.gov/mesh/). - annotators: "sqlite:obo:mesh, sqlite:obo:chebi, sqlite:obo:ncit, bioportal:mdm, sqlite:obo:drugbank, gilda:" - prompt.examples: Lidocaine, Hydroxychloroquine, Methyldopa, Imatinib - # For the purposes of evaluating against BC5CDR, we force normalization to MESH - id_prefixes: - - MESH - slot_usage: - id: - pattern: "^MESH:[CD][0-9]{6}$" - values_from: - - MeshChemicalIdentifier - - - - ChemicalToDiseasePredicate: - is_a: RelationshipType - description: >- - A predicate for chemical to disease relationships - comments: - - for the purposes of evaluation against BC5CDR, any predicate other than INDUCES is ignored. - -enums: - - MeshChemicalIdentifier: - reachable_from: - source_ontology: obo:mesh - source_nodes: - - MESH:D000602 ## Amino Acids, Peptides, and Proteins - - MESH:D001685 ## Biological Factors - - MESH:D002241 ## Carbohydrates - - MESH:D004364 ## Pharmaceutical Preparations - - MESH:D006571 ## Heterocyclic Compounds - - MESH:D007287 ## Inorganic Chemicals - - MESH:D008055 ## Lipids - - MESH:D009706 ## Nucleic Acids, Nucleotides, and Nucleosides - - MESH:D009930 ## Organic Chemicals - - MESH:D011083 ## Polycyclic Compounds - - MESH:D013812 ## Therapeutics - - MESH:D019602 ## Food and Beverages - - MESH:D045424 ## Complex Mixtures - - MESH:D045762 ## Enzymes and Coenzymes - - MESH:D046911 ## Macromolecular Substances - MeshDiseaseIdentifier: - reachable_from: - source_ontology: obo:mesh - source_nodes: - - MESH:D001423 ## Bacterial Infections and Mycoses - - MESH:D001523 ## Mental Disorders - - MESH:D002318 ## Cardiovascular Diseases - - MESH:D002943 ## Circulatory and Respiratory Physiological Phenomena - - MESH:D004066 ## Digestive System Diseases - - MESH:D004700 ## Endocrine System Diseases - - MESH:D005128 ## Eye Diseases - - MESH:D005261 ## Female Urogenital Diseases and Pregnancy Complications - - MESH:D006425 ## Hemic and Lymphatic Diseases - - MESH:D007154 ## Immune System Diseases - - MESH:D007280 ## Disorders of Environmental Origin - - MESH:D009057 ## Stomatognathic Diseases - - MESH:D009140 ## Musculoskeletal Diseases - - MESH:D009358 ## Congenital, Hereditary, and Neonatal Diseases and Abnormalities - - MESH:D009369 ## Neoplasms - - MESH:D009422 ## Nervous System Diseases - - MESH:D009750 ## Nutritional and Metabolic Diseases - - MESH:D009784 ## Occupational Diseases - - MESH:D010038 ## Otorhinolaryngologic Diseases - - MESH:D010272 ## Parasitic Diseases - - MESH:D012140 ## Respiratory Tract Diseases - - MESH:D013568 ## Pathological Conditions, Signs and Symptoms - - MESH:D014777 ## Virus Diseases - - MESH:D014947 ## Wounds and Injuries - - MESH:D017437 ## Skin and Connective Tissue Diseases - - MESH:D052801 ## Male Urogenital Diseases - - MESH:D064419 ## Chemically-Induced Disorders diff --git a/src/ontogpt/templates/ctd_ner.py b/src/ontogpt/templates/ctd_ner.py deleted file mode 100644 index 576ffccb2..000000000 --- a/src/ontogpt/templates/ctd_ner.py +++ /dev/null @@ -1,196 +0,0 @@ -from __future__ import annotations -from datetime import datetime, date -from enum import Enum -from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, ConfigDict, Field, field_validator -import re -import sys -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal - - -metamodel_version = "None" -version = "None" - -class ConfiguredBaseModel(BaseModel): - model_config = ConfigDict( - validate_assignment=True, - validate_default=True, - extra = 'forbid', - arbitrary_types_allowed=True, - use_enum_values = True) - - -class MeshChemicalIdentifier(str): - - - dummy = "dummy" - - -class MeshDiseaseIdentifier(str): - - - dummy = "dummy" - - -class NullDataOptions(str, Enum): - - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = "UNSPECIFIED_METHOD_OF_ADMINISTRATION" - - NOT_APPLICABLE = "NOT_APPLICABLE" - - NOT_MENTIONED = "NOT_MENTIONED" - - - -class ExtractionResult(ConfiguredBaseModel): - """ - A result of extracting knowledge on text - """ - input_id: Optional[str] = Field(None) - input_title: Optional[str] = Field(None) - input_text: Optional[str] = Field(None) - raw_completion_output: Optional[str] = Field(None) - prompt: Optional[str] = Field(None) - extracted_object: Optional[Any] = Field(None, description="""The complex objects extracted from the text""") - named_entities: Optional[List[Any]] = Field(default_factory=list, description="""Named entities extracted from the text""") - - - -class NamedEntity(ConfiguredBaseModel): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Chemical(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - @field_validator('id') - def pattern_id(cls, v): - pattern=re.compile(r"^MESH:[CD][0-9]{6}$") - if isinstance(v,list): - for element in v: - if not pattern.match(element): - raise ValueError(f"Invalid id format: {element}") - elif isinstance(v,str): - if not pattern.match(v): - raise ValueError(f"Invalid id format: {v}") - return v - - -class Disease(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - @field_validator('id') - def pattern_id(cls, v): - pattern=re.compile(r"^MESH:[CD][0-9]{6}$") - if isinstance(v,list): - for element in v: - if not pattern.match(element): - raise ValueError(f"Invalid id format: {element}") - elif isinstance(v,str): - if not pattern.match(v): - raise ValueError(f"Invalid id format: {v}") - return v - - -class CompoundExpression(ConfiguredBaseModel): - - None - - - -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - subject: Optional[str] = Field(None) - predicate: Optional[str] = Field(None) - object: Optional[str] = Field(None) - qualifier: Optional[str] = Field(None, description="""A qualifier for the statements, e.g. \"NOT\" for negation""") - subject_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"""") - object_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"""") - - - -class TextWithTriples(ConfiguredBaseModel): - """ - A text containing one or more relations of the Triple type. - """ - publication: Optional[Publication] = Field(None) - triples: Optional[List[Triple]] = Field(default_factory=list) - - - -class TextWithEntity(ConfiguredBaseModel): - """ - A text containing one or more instances of a single type of entity. - """ - publication: Optional[Publication] = Field(None) - entities: Optional[List[str]] = Field(default_factory=list) - - - -class ChemicalToDiseaseDocument(TextWithEntity): - """ - A document that contains chemical and disease entities. - """ - chemicals: Optional[List[str]] = Field(default_factory=list, description="""One or more chemical substances, drugs, or small molecules.""") - diseases: Optional[List[str]] = Field(default_factory=list, description="""One or more diseases or conditions.""") - publication: Optional[Publication] = Field(None) - entities: Optional[List[str]] = Field(default_factory=list) - - - -class RelationshipType(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Publication(ConfiguredBaseModel): - - id: Optional[str] = Field(None, description="""The publication identifier""") - title: Optional[str] = Field(None, description="""The title of the publication""") - abstract: Optional[str] = Field(None, description="""The abstract of the publication""") - combined_text: Optional[str] = Field(None) - full_text: Optional[str] = Field(None, description="""The full text of the publication""") - - - -class AnnotatorResult(ConfiguredBaseModel): - - subject_text: Optional[str] = Field(None) - object_id: Optional[str] = Field(None) - object_text: Optional[str] = Field(None) - - - - -# Model rebuild -# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model -ExtractionResult.model_rebuild() -NamedEntity.model_rebuild() -Chemical.model_rebuild() -Disease.model_rebuild() -CompoundExpression.model_rebuild() -Triple.model_rebuild() -TextWithTriples.model_rebuild() -TextWithEntity.model_rebuild() -ChemicalToDiseaseDocument.model_rebuild() -RelationshipType.model_rebuild() -Publication.model_rebuild() -AnnotatorResult.model_rebuild() - diff --git a/src/ontogpt/templates/ctd_ner.yaml b/src/ontogpt/templates/ctd_ner.yaml deleted file mode 100644 index 7d4a36c52..000000000 --- a/src/ontogpt/templates/ctd_ner.yaml +++ /dev/null @@ -1,130 +0,0 @@ -id: http://w3id.org/ontogpt/ctd_ner -name: ctd_ner -title: Chemical and Disease Entity Recognition Template -description: >- - A template for Chemical and Disease named entity recognition. - - This template is intended to represent entities (chemicals and diseases), - and for evaluating SPIRES against the BioCreative V Disease Named Entity - Recognition (DNER) results. As the test set also contains chemical names, - it is also appropriate to use this template for evaluating chemical NER. -see_also: - - https://biocreative.bioinformatics.udel.edu/media/store/files/2015/BC5CDR_overview.final.pdf - - https://academic.oup.com/database/article/doi/10.1093/database/baw068/2630414 -source: >- - https://biocreative.bioinformatics.udel.edu/tasks/biocreative-v/track-3-cdr/ -license: https://creativecommons.org/publicdomain/zero/1.0/ -prefixes: - linkml: https://w3id.org/linkml/ - ctdner: http://w3id.org/ontogpt/ctd_ner - -default_prefix: ctdner -default_range: string - -imports: - - linkml:types - - core - -classes: - - ChemicalToDiseaseDocument: - description: A document that contains chemical and disease entities. - is_a: TextWithEntity - attributes: - chemicals: - range: Chemical - multivalued: true - description: One or more chemical substances, drugs, or small molecules. - annotations: - prompt: >- - A semi-colon separated list of chemical names, for example: Lidocaine; - Hydroxychloroquine; Methyldopa; Monosodium Glutamate; Imatinib - diseases: - range: Disease - multivalued: true - description: One or more diseases or conditions. - annotations: - prompt: >- - A semi-colon separated list of disease names, for example: cardiac - asystole; COVID-19; Hypotension; Headache; cancer - - Chemical: - is_a: NamedEntity - annotations: - annotators: "sqlite:obo:mesh, sqlite:obo:chebi, sqlite:obo:ncit, bioportal:mdm, sqlite:obo:drugbank, gilda:" - prompt.examples: Lidocaine, Hydroxychloroquine, Methyldopa, Imatinib - # For the purposes of evaluating against BC5CDR, we force normalization to MESH - id_prefixes: - - MESH - slot_usage: - id: - pattern: "^MESH:[CD][0-9]{6}$" - values_from: - - MeshChemicalIdentifier - - Disease: - is_a: NamedEntity - annotations: - annotators: "sqlite:obo:mesh, sqlite:obo:mondo, sqlite:obo:hp, sqlite:obo:ncit, sqlite:obo:doid, bioportal:meddra" - prompt.examples: cardiac asystole, COVID-19, Headache, cancer - # For the purposes of evaluating against BC5CDR, we force normalization to MESH - id_prefixes: - - MESH - slot_usage: - id: - pattern: "^MESH:[CD][0-9]{6}$" - values_from: - - MeshDiseaseIdentifier - -enums: - - MeshChemicalIdentifier: - reachable_from: - source_ontology: obo:mesh - source_nodes: - - MESH:D000602 ## Amino Acids, Peptides, and Proteins - - MESH:D001685 ## Biological Factors - - MESH:D002241 ## Carbohydrates - - MESH:D004364 ## Pharmaceutical Preparations - - MESH:D006571 ## Heterocyclic Compounds - - MESH:D007287 ## Inorganic Chemicals - - MESH:D008055 ## Lipids - - MESH:D009706 ## Nucleic Acids, Nucleotides, and Nucleosides - - MESH:D009930 ## Organic Chemicals - - MESH:D011083 ## Polycyclic Compounds - - MESH:D013812 ## Therapeutics - - MESH:D019602 ## Food and Beverages - - MESH:D045424 ## Complex Mixtures - - MESH:D045762 ## Enzymes and Coenzymes - - MESH:D046911 ## Macromolecular Substances - MeshDiseaseIdentifier: - reachable_from: - source_ontology: obo:mesh - source_nodes: - - MESH:D001423 ## Bacterial Infections and Mycoses - - MESH:D001523 ## Mental Disorders - - MESH:D002318 ## Cardiovascular Diseases - - MESH:D002943 ## Circulatory and Respiratory Physiological Phenomena - - MESH:D004066 ## Digestive System Diseases - - MESH:D004700 ## Endocrine System Diseases - - MESH:D005128 ## Eye Diseases - - MESH:D005261 ## Female Urogenital Diseases and Pregnancy Complications - - MESH:D006425 ## Hemic and Lymphatic Diseases - - MESH:D007154 ## Immune System Diseases - - MESH:D007280 ## Disorders of Environmental Origin - - MESH:D009057 ## Stomatognathic Diseases - - MESH:D009140 ## Musculoskeletal Diseases - - MESH:D009358 ## Congenital, Hereditary, and Neonatal Diseases and Abnormalities - - MESH:D009369 ## Neoplasms - - MESH:D009422 ## Nervous System Diseases - - MESH:D009750 ## Nutritional and Metabolic Diseases - - MESH:D009784 ## Occupational Diseases - - MESH:D010038 ## Otorhinolaryngologic Diseases - - MESH:D010272 ## Parasitic Diseases - - MESH:D012140 ## Respiratory Tract Diseases - - MESH:D013568 ## Pathological Conditions, Signs and Symptoms - - MESH:D014777 ## Virus Diseases - - MESH:D014947 ## Wounds and Injuries - - MESH:D017437 ## Skin and Connective Tissue Diseases - - MESH:D052801 ## Male Urogenital Diseases - - MESH:D064419 ## Chemically-Induced Disorders diff --git a/src/ontogpt/templates/datasheet.py b/src/ontogpt/templates/datasheet.py deleted file mode 100644 index 015348f36..000000000 --- a/src/ontogpt/templates/datasheet.py +++ /dev/null @@ -1,160 +0,0 @@ -from __future__ import annotations -from datetime import datetime, date -from enum import Enum -from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, ConfigDict, Field, field_validator -import re -import sys -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal - - -metamodel_version = "None" -version = "None" - -class ConfiguredBaseModel(BaseModel): - model_config = ConfigDict( - validate_assignment=True, - validate_default=True, - extra = 'forbid', - arbitrary_types_allowed=True, - use_enum_values = True) - - -class NullDataOptions(str, Enum): - - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = "UNSPECIFIED_METHOD_OF_ADMINISTRATION" - - NOT_APPLICABLE = "NOT_APPLICABLE" - - NOT_MENTIONED = "NOT_MENTIONED" - - - -class ExtractionResult(ConfiguredBaseModel): - """ - A result of extracting knowledge on text - """ - input_id: Optional[str] = Field(None) - input_title: Optional[str] = Field(None) - input_text: Optional[str] = Field(None) - raw_completion_output: Optional[str] = Field(None) - prompt: Optional[str] = Field(None) - extracted_object: Optional[Any] = Field(None, description="""The complex objects extracted from the text""") - named_entities: Optional[List[Any]] = Field(default_factory=list, description="""Named entities extracted from the text""") - - - -class NamedEntity(ConfiguredBaseModel): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Dataset(NamedEntity): - """ - A document that contains a description of a dataset. - """ - name: Optional[str] = Field(None, description="""The name of the dataset.""") - subsets: Optional[List[str]] = Field(default_factory=list, description="""Semicolon-separated list of names of any subsets of the dataset.""") - authors: Optional[List[str]] = Field(default_factory=list, description="""Semicolon-separated list of names of creators of the dataset.""") - funding_organization: Optional[List[str]] = Field(default_factory=list, description="""Semicolon-separated list of organizations supporting creation of the dataset.""") - funding_identifiers: Optional[List[str]] = Field(default_factory=list, description="""Semicolon-separated list of names, numbers, or other identifiers for grants supporting creation of the dataset.""") - purpose: Optional[str] = Field(None, description="""The stated purpose of the dataset. This should be no more than 1 sentence.""") - limitations: Optional[str] = Field(None, description="""Known limitations of the dataset. This should be no more than 1 sentence.""") - warnings: Optional[str] = Field(None, description="""Warnings regarding content or application of the dataset.""") - references: Optional[List[str]] = Field(default_factory=list, description="""Semicolon-separated list of publications describing the data or the process used to produce it.""") - license: Optional[str] = Field(None, description="""The set of rules defining the rights of the developer and the users of the dataset, for example, BSD-3 or CC0.""") - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Organization(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class CompoundExpression(ConfiguredBaseModel): - - None - - - -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - subject: Optional[str] = Field(None) - predicate: Optional[str] = Field(None) - object: Optional[str] = Field(None) - qualifier: Optional[str] = Field(None, description="""A qualifier for the statements, e.g. \"NOT\" for negation""") - subject_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"""") - object_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"""") - - - -class TextWithTriples(ConfiguredBaseModel): - """ - A text containing one or more relations of the Triple type. - """ - publication: Optional[Publication] = Field(None) - triples: Optional[List[Triple]] = Field(default_factory=list) - - - -class TextWithEntity(ConfiguredBaseModel): - """ - A text containing one or more instances of a single type of entity. - """ - publication: Optional[Publication] = Field(None) - entities: Optional[List[str]] = Field(default_factory=list) - - - -class RelationshipType(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Publication(ConfiguredBaseModel): - - id: Optional[str] = Field(None, description="""The publication identifier""") - title: Optional[str] = Field(None, description="""The title of the publication""") - abstract: Optional[str] = Field(None, description="""The abstract of the publication""") - combined_text: Optional[str] = Field(None) - full_text: Optional[str] = Field(None, description="""The full text of the publication""") - - - -class AnnotatorResult(ConfiguredBaseModel): - - subject_text: Optional[str] = Field(None) - object_id: Optional[str] = Field(None) - object_text: Optional[str] = Field(None) - - - - -# Model rebuild -# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model -ExtractionResult.model_rebuild() -NamedEntity.model_rebuild() -Dataset.model_rebuild() -Organization.model_rebuild() -CompoundExpression.model_rebuild() -Triple.model_rebuild() -TextWithTriples.model_rebuild() -TextWithEntity.model_rebuild() -RelationshipType.model_rebuild() -Publication.model_rebuild() -AnnotatorResult.model_rebuild() - diff --git a/src/ontogpt/templates/datasheet.yaml b/src/ontogpt/templates/datasheet.yaml deleted file mode 100644 index 9f0a7776c..000000000 --- a/src/ontogpt/templates/datasheet.yaml +++ /dev/null @@ -1,81 +0,0 @@ -id: http://w3id.org/ontogpt/datasheet -name: datasheet -title: Datasheet Extraction Template -description: >- - A template for extracting metadata about a dataset, - as defined by the Datasheets for Datasets model - (see https://github.com/bridge2ai/data-sheets-schema), - itself based on Gebru et al. (2021) - (https://cacm.acm.org/magazines/2021/12/256932-datasheets-for-datasets/abstract) - -license: https://creativecommons.org/publicdomain/zero/1.0/ -prefixes: - linkml: https://w3id.org/linkml/ - d4d: http://w3id.org/ontogpt/datasheet - -default_prefix: d4d -default_range: string - -imports: - - linkml:types - - core - -classes: - - Dataset: - description: A document that contains a description of a dataset. - tree_root: true - is_a: NamedEntity - attributes: - name: - description: The name of the dataset. - subsets: - description: >- - Semicolon-separated list of names of any subsets of the dataset. - multivalued: true - authors: - description: >- - Semicolon-separated list of names of creators of the dataset. - multivalued: true - funding_organization: - description: >- - Semicolon-separated list of organizations supporting - creation of the dataset. - multivalued: true - range: Organization - funding_identifiers: - description: >- - Semicolon-separated list of names, numbers, or other - identifiers for grants supporting creation of the dataset. - multivalued: true - purpose: - description: >- - The stated purpose of the dataset. This should be no more than 1 - sentence. - limitations: - description: >- - Known limitations of the dataset. This should be no more than 1 - sentence. - warnings: - description: >- - Warnings regarding content or application of the dataset. - references: - description: >- - Semicolon-separated list of publications describing the data or the - process used to produce it. - multivalued: true - license: - description: >- - The set of rules defining the rights of the developer and the users - of the dataset, for example, BSD-3 or CC0. - - # Using wikidata as an annotator can be problematic due to ambiguity - # e.g., "stability" is the name of a company and the concept of robustness - # (wikidata:Q403605) - Organization: - is_a: NamedEntity - id_prefixes: - - wikidata - - NCIT - annotations: - annotators: "wikidata:, sqlite:obo:ncit" diff --git a/src/ontogpt/templates/desiccation.py b/src/ontogpt/templates/desiccation.py deleted file mode 100644 index ca92d9d16..000000000 --- a/src/ontogpt/templates/desiccation.py +++ /dev/null @@ -1,167 +0,0 @@ -from __future__ import annotations -from datetime import datetime, date -from enum import Enum -from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, ConfigDict, Field, field_validator -import re -import sys -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal - - -metamodel_version = "None" -version = "None" - -class ConfiguredBaseModel(BaseModel): - model_config = ConfigDict( - validate_assignment=True, - validate_default=True, - extra = 'forbid', - arbitrary_types_allowed=True, - use_enum_values = True) - - -class NullDataOptions(str, Enum): - - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = "UNSPECIFIED_METHOD_OF_ADMINISTRATION" - - NOT_APPLICABLE = "NOT_APPLICABLE" - - NOT_MENTIONED = "NOT_MENTIONED" - - - -class ExtractionResult(ConfiguredBaseModel): - """ - A result of extracting knowledge on text - """ - input_id: Optional[str] = Field(None) - input_title: Optional[str] = Field(None) - input_text: Optional[str] = Field(None) - raw_completion_output: Optional[str] = Field(None) - prompt: Optional[str] = Field(None) - extracted_object: Optional[Any] = Field(None, description="""The complex objects extracted from the text""") - named_entities: Optional[List[Any]] = Field(default_factory=list, description="""Named entities extracted from the text""") - - - -class NamedEntity(ConfiguredBaseModel): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class EntityContainingDocument(NamedEntity): - - environmental_conditions: Optional[List[str]] = Field(default_factory=list, description="""A semicolon-separated list of environmental terms.""") - taxa: Optional[List[str]] = Field(default_factory=list, description="""A semicolon-separated list of taxonomic terms of living things.""") - traits: Optional[List[str]] = Field(default_factory=list, description="""A semicolon-separated list of plant traits.""") - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class EnvironmentalCondition(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Taxon(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Trait(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class CompoundExpression(ConfiguredBaseModel): - - None - - - -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - subject: Optional[str] = Field(None) - predicate: Optional[str] = Field(None) - object: Optional[str] = Field(None) - qualifier: Optional[str] = Field(None, description="""A qualifier for the statements, e.g. \"NOT\" for negation""") - subject_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"""") - object_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"""") - - - -class TextWithTriples(ConfiguredBaseModel): - """ - A text containing one or more relations of the Triple type. - """ - publication: Optional[Publication] = Field(None) - triples: Optional[List[Triple]] = Field(default_factory=list) - - - -class TextWithEntity(ConfiguredBaseModel): - """ - A text containing one or more instances of a single type of entity. - """ - publication: Optional[Publication] = Field(None) - entities: Optional[List[str]] = Field(default_factory=list) - - - -class RelationshipType(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Publication(ConfiguredBaseModel): - - id: Optional[str] = Field(None, description="""The publication identifier""") - title: Optional[str] = Field(None, description="""The title of the publication""") - abstract: Optional[str] = Field(None, description="""The abstract of the publication""") - combined_text: Optional[str] = Field(None) - full_text: Optional[str] = Field(None, description="""The full text of the publication""") - - - -class AnnotatorResult(ConfiguredBaseModel): - - subject_text: Optional[str] = Field(None) - object_id: Optional[str] = Field(None) - object_text: Optional[str] = Field(None) - - - - -# Model rebuild -# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model -ExtractionResult.model_rebuild() -NamedEntity.model_rebuild() -EntityContainingDocument.model_rebuild() -EnvironmentalCondition.model_rebuild() -Taxon.model_rebuild() -Trait.model_rebuild() -CompoundExpression.model_rebuild() -Triple.model_rebuild() -TextWithTriples.model_rebuild() -TextWithEntity.model_rebuild() -RelationshipType.model_rebuild() -Publication.model_rebuild() -AnnotatorResult.model_rebuild() - diff --git a/src/ontogpt/templates/desiccation.yaml b/src/ontogpt/templates/desiccation.yaml deleted file mode 100644 index 88f78e2b4..000000000 --- a/src/ontogpt/templates/desiccation.yaml +++ /dev/null @@ -1,67 +0,0 @@ -id: http://w3id.org/ontogpt/desiccation -name: desiccation -title: desiccationTemplate -description: >- - A template for extracting ChEBI, GO, NCBITAXON, PO, TO, PECO -license: https://creativecommons.org/publicdomain/zero/1.0/ -prefixes: - linkml: https://w3id.org/linkml/ - desiccation: http://w3id.org/ontogpt/desiccation - -default_prefix: desiccation -default_range: string - -imports: - - linkml:types - - core - -classes: - EntityContainingDocument: - tree_root: true - is_a: NamedEntity - attributes: - environmental_conditions: - range: EnvironmentalCondition - multivalued: true - description: >- - A semicolon-separated list of environmental terms. - taxa: - range: Taxon - multivalued: true - description: >- - A semicolon-separated list of taxonomic terms of living things. - traits: - range: Trait - multivalued: true - description: >- - A semicolon-separated list of plant traits. - - EnvironmentalCondition: - is_a: NamedEntity - id_prefixes: - - PECO - annotations: - annotators: sqlite:obo:peco - prompt: >- - the name of an environmental treatment. - Examples are drought, salt stress, cold tolerance. - - Taxon: - is_a: NamedEntity - id_prefixes: - - NCBITaxon - annotations: - annotators: sqlite:obo:ncbitaxon - prompt: >- - the name of a taxonomic name or species. - Examples are Bacillus subtilus, Bos taurus, blue whale. - - Trait: - is_a: NamedEntity - id_prefixes: - - TO - annotations: - annotators: sqlite:obo:to - prompt: >- - the description of a plant trait. - Examples of trait categories are germination ratio, fruit hollowness, arid region exposure. \ No newline at end of file diff --git a/src/ontogpt/templates/diagnostic_procedure.py b/src/ontogpt/templates/diagnostic_procedure.py deleted file mode 100644 index f4adaff0c..000000000 --- a/src/ontogpt/templates/diagnostic_procedure.py +++ /dev/null @@ -1,221 +0,0 @@ -from __future__ import annotations -from datetime import datetime, date -from enum import Enum -from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, ConfigDict, Field, field_validator -import re -import sys -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal - - -metamodel_version = "None" -version = "None" - -class ConfiguredBaseModel(BaseModel): - model_config = ConfigDict( - validate_assignment=True, - validate_default=True, - extra = 'forbid', - arbitrary_types_allowed=True, - use_enum_values = True) - - -class NullDataOptions(str, Enum): - - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = "UNSPECIFIED_METHOD_OF_ADMINISTRATION" - - NOT_APPLICABLE = "NOT_APPLICABLE" - - NOT_MENTIONED = "NOT_MENTIONED" - - - -class ExtractionResult(ConfiguredBaseModel): - """ - A result of extracting knowledge on text - """ - input_id: Optional[str] = Field(None) - input_title: Optional[str] = Field(None) - input_text: Optional[str] = Field(None) - raw_completion_output: Optional[str] = Field(None) - prompt: Optional[str] = Field(None) - extracted_object: Optional[Any] = Field(None, description="""The complex objects extracted from the text""") - named_entities: Optional[List[Any]] = Field(default_factory=list, description="""Named entities extracted from the text""") - - - -class NamedEntity(ConfiguredBaseModel): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class DiagnosticProcedure(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Phenotype(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class ClinicalAttribute(NamedEntity): - - unit: Optional[str] = Field(None, description="""the unit used to measure the attribute""") - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Quality(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Unit(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class CompoundExpression(ConfiguredBaseModel): - - None - - - -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - subject: Optional[str] = Field(None) - predicate: Optional[str] = Field(None) - object: Optional[str] = Field(None) - qualifier: Optional[str] = Field(None, description="""A qualifier for the statements, e.g. \"NOT\" for negation""") - subject_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"""") - object_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"""") - - - -class DiagnosticProceduretoPhenotypeAssociation(Triple): - """ - A triple representing a relationship between a diagnostic procedure and an associated phenotype, e.g., \"blood pressure measurement\" is associated with \"high blood pressure\". - """ - subject: Optional[str] = Field(None, description="""A diagnostic procedure yielding a result, which in turn may be interpreted as a phenotype. Procedures include \"heart rate measurement\", \"blood pressure measurement\", \"oxygen saturation measurement\", etc. In practice, procedures may be named based on what they measure, with the \"measurement\" part left implicit.""") - predicate: Optional[str] = Field(None, description="""The relationship type, e.g. RELATED_TO""") - object: Optional[List[str]] = Field(default_factory=list, description="""The observable physical or biochemical characteristics of a patient. Not equivalent to a disease state, but may contribute to a diagnosis.""") - qualifier: Optional[str] = Field(None, description="""A qualifier for the statements, e.g. \"NOT\" for negation""") - subject_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the procedure.""") - object_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the phenotype.""") - - - -class DiagnosticProceduretoAttributeAssociation(Triple): - """ - A triple representing a relationship between a diagnostic procedure and a measured attribute, e.g., \"blood pressure measurement\" is associated with \"blood pressure\" (or in OBA, something like OBA:VT0000183, \"blood pressure trait\"). - """ - subject: Optional[str] = Field(None, description="""A diagnostic procedure yielding a result, which in turn may be interpreted as a phenotype. Procedures include \"heart rate measurement\", \"blood pressure measurement\", \"oxygen saturation measurement\", etc. In practice, procedures may be named based on what they measure, with the \"measurement\" part left implicit.""") - predicate: Optional[str] = Field(None, description="""The relationship type, e.g. RELATED_TO""") - object: Optional[List[str]] = Field(default_factory=list, description="""Any measurable clinical attribute.""") - qualifier: Optional[str] = Field(None, description="""A qualifier for the statements, e.g. \"NOT\" for negation""") - subject_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the procedure.""") - object_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the phenotype.""") - - - -class TextWithTriples(ConfiguredBaseModel): - """ - A text containing one or more relations of the Triple type. - """ - publication: Optional[Publication] = Field(None) - triples: Optional[List[Triple]] = Field(default_factory=list) - - - -class TextWithEntity(ConfiguredBaseModel): - """ - A text containing one or more instances of a single type of entity. - """ - publication: Optional[Publication] = Field(None) - entities: Optional[List[str]] = Field(default_factory=list) - - - -class RelationshipType(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class ProcedureToPhenotypePredicate(RelationshipType): - """ - A predicate for procedure to phenotype relationships, defining \"this procedure is intended to provide support for/against this phenotype\". - """ - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class ProcedureToAttributePredicate(RelationshipType): - """ - A predicate for procedure to attribute relationships, defining \"this procedure is a measurement of this attribute\". - """ - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Publication(ConfiguredBaseModel): - - id: Optional[str] = Field(None, description="""The publication identifier""") - title: Optional[str] = Field(None, description="""The title of the publication""") - abstract: Optional[str] = Field(None, description="""The abstract of the publication""") - combined_text: Optional[str] = Field(None) - full_text: Optional[str] = Field(None, description="""The full text of the publication""") - - - -class AnnotatorResult(ConfiguredBaseModel): - - subject_text: Optional[str] = Field(None) - object_id: Optional[str] = Field(None) - object_text: Optional[str] = Field(None) - - - - -# Model rebuild -# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model -ExtractionResult.model_rebuild() -NamedEntity.model_rebuild() -DiagnosticProcedure.model_rebuild() -Phenotype.model_rebuild() -ClinicalAttribute.model_rebuild() -Quality.model_rebuild() -Unit.model_rebuild() -CompoundExpression.model_rebuild() -Triple.model_rebuild() -DiagnosticProceduretoPhenotypeAssociation.model_rebuild() -DiagnosticProceduretoAttributeAssociation.model_rebuild() -TextWithTriples.model_rebuild() -TextWithEntity.model_rebuild() -RelationshipType.model_rebuild() -ProcedureToPhenotypePredicate.model_rebuild() -ProcedureToAttributePredicate.model_rebuild() -Publication.model_rebuild() -AnnotatorResult.model_rebuild() - diff --git a/src/ontogpt/templates/diagnostic_procedure.yaml b/src/ontogpt/templates/diagnostic_procedure.yaml deleted file mode 100644 index a004b974a..000000000 --- a/src/ontogpt/templates/diagnostic_procedure.yaml +++ /dev/null @@ -1,148 +0,0 @@ -id: http://w3id.org/ontogpt/diagnostic_procedure -name: diagnostic_procedure -title: Diagnostic Procedure Template -description: >- - A template for clinical diagnostic procedures and the - phenotypes they may contribute to. -license: https://creativecommons.org/publicdomain/zero/1.0/ -prefixes: - linkml: https://w3id.org/linkml/ - diag: http://w3id.org/ontogpt/diagnostic_procedure/ - LOINC: http://loinc.org/rdf/ - HP: http://purl.obolibrary.org/obo/HP_ - RO: http://purl.obolibrary.org/obo/RO_ - OBA: http://purl.obolibrary.org/obo/OBA_ - PATO: http://purl.obolibrary.org/obo/PATO_ - biolink: https://w3id.org/biolink/vocab/ - -default_prefix: diag -default_range: string - -imports: - - linkml:types - - core - -# TODO: LOINC isn't great for grounding, -# but perhaps a combo of subject, unit, and qualifier would work -# since LOINC names are often like "IgG [Units/volume] in Serum" - -classes: - - DiagnosticProceduretoPhenotypeAssociation: - is_a: Triple - description: >- - A triple representing a relationship between a diagnostic - procedure and an associated phenotype, e.g., "blood pressure measurement" - is associated with "high blood pressure". - slot_usage: - subject: - range: DiagnosticProcedure - description: >- - A diagnostic procedure yielding a result, which in turn - may be interpreted as a phenotype. - Procedures include "heart rate measurement", "blood pressure measurement", - "oxygen saturation measurement", etc. In practice, procedures may be - named based on what they measure, with the "measurement" part left implicit. - object: - range: Phenotype - multivalued: true - description: >- - The observable physical or biochemical characteristics of a patient. - Not equivalent to a disease state, but may contribute to a diagnosis. - predicate: - range: ProcedureToPhenotypePredicate - description: The relationship type, e.g. RELATED_TO - subject_qualifier: - range: NamedEntity - description: >- - An optional qualifier or modifier for the procedure. - object_qualifier: - range: NamedEntity - description: >- - An optional qualifier or modifier for the phenotype. - - DiagnosticProceduretoAttributeAssociation: - is_a: Triple - description: >- - A triple representing a relationship between a diagnostic - procedure and a measured attribute, e.g., "blood pressure measurement" - is associated with "blood pressure" (or in OBA, something like - OBA:VT0000183, "blood pressure trait"). - slot_usage: - subject: - range: DiagnosticProcedure - description: >- - A diagnostic procedure yielding a result, which in turn - may be interpreted as a phenotype. - Procedures include "heart rate measurement", "blood pressure measurement", - "oxygen saturation measurement", etc. In practice, procedures may be - named based on what they measure, with the "measurement" part left implicit. - object: - range: ClinicalAttribute - multivalued: true - description: >- - Any measurable clinical attribute. - predicate: - range: ProcedureToAttributePredicate - description: The relationship type, e.g. RELATED_TO - subject_qualifier: - range: NamedEntity - description: >- - An optional qualifier or modifier for the procedure. - object_qualifier: - range: Quality - description: >- - An optional qualifier or modifier for the phenotype. - - DiagnosticProcedure: - is_a: NamedEntity - annotations: - annotators: bioportal:loinc, sqlite:obo:ncit - id_prefixes: - - LOINC - - Phenotype: - is_a: NamedEntity - annotations: - annotators: sqlite:obo:hp - id_prefixes: - - HP - - ClinicalAttribute: - is_a: NamedEntity - attributes: - unit: - description: the unit used to measure the attribute - range: Unit - annotations: - annotators: sqlite:obo:oba, sqlite:obo:ncit - id_prefixes: - - OBA - - Quality: - is_a: NamedEntity - annotations: - annotators: sqlite:obo:pato - id_prefixes: - - PATO - - ProcedureToPhenotypePredicate: - is_a: RelationshipType - description: >- - A predicate for procedure to phenotype relationships, - defining "this procedure is intended to provide support - for/against this phenotype". - - ProcedureToAttributePredicate: - is_a: RelationshipType - description: >- - A predicate for procedure to attribute relationships, - defining "this procedure is a measurement of this - attribute". - - Unit: - is_a: NamedEntity - id_prefixes: - - UO - annotations: - annotators: sqlite:obo:uo diff --git a/src/ontogpt/templates/dietician_notes.py b/src/ontogpt/templates/dietician_notes.py deleted file mode 100644 index b3bf67f05..000000000 --- a/src/ontogpt/templates/dietician_notes.py +++ /dev/null @@ -1,210 +0,0 @@ -from __future__ import annotations -from datetime import datetime, date -from enum import Enum -from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, ConfigDict, Field, field_validator -import re -import sys -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal - - -metamodel_version = "None" -version = "None" - -class ConfiguredBaseModel(BaseModel): - model_config = ConfigDict( - validate_assignment=True, - validate_default=True, - extra = 'forbid', - arbitrary_types_allowed=True, - use_enum_values = True) - - -class NullDataOptions(str, Enum): - - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = "UNSPECIFIED_METHOD_OF_ADMINISTRATION" - - NOT_APPLICABLE = "NOT_APPLICABLE" - - NOT_MENTIONED = "NOT_MENTIONED" - - - -class ClinicalObservationSet(ConfiguredBaseModel): - """ - A set of sets of clinical observations. - """ - observations: Optional[List[str]] = Field(default_factory=list) - - - -class MalnutritionObservations(ConfiguredBaseModel): - - malnutrition_presence: Optional[str] = Field(None, description="""True if the patient is malnourished, False otherwise.""") - severity: Optional[str] = Field(None, description="""The severity of the patient's malnutrition, if present.""") - diagnosis: Optional[str] = Field(None, description="""The patient's malnutrition diagnosis, if present.""") - - - -class ExtractionResult(ConfiguredBaseModel): - """ - A result of extracting knowledge on text - """ - input_id: Optional[str] = Field(None) - input_title: Optional[str] = Field(None) - input_text: Optional[str] = Field(None) - raw_completion_output: Optional[str] = Field(None) - prompt: Optional[str] = Field(None) - extracted_object: Optional[Any] = Field(None, description="""The complex objects extracted from the text""") - named_entities: Optional[List[Any]] = Field(default_factory=list, description="""Named entities extracted from the text""") - - - -class NamedEntity(ConfiguredBaseModel): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class ClinicalObservations(NamedEntity): - """ - A set of clinical observations about a single patient at a single time. - """ - is_pediatric: Optional[str] = Field(None) - patient_height: Optional[QuantitativeValue] = Field(None) - patient_weight: Optional[QuantitativeValue] = Field(None) - malnutrition_status: Optional[MalnutritionObservations] = Field(None) - diet_supplementation: Optional[List[str]] = Field(default_factory=list, description="""A semicolon-separated list of the patient's diet supplementation therapies.""") - nutrition_support: Optional[List[str]] = Field(default_factory=list, description="""A semicolon-separated list of the patient's nutrition support therapies, usually enteral or parenteral nutrition.""") - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class DietSupplementation(NamedEntity): - """ - A diet supplementation therapy. - """ - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class NutritionSupport(NamedEntity): - """ - A nutrition support therapy used to treat or prevent malnutrition. - """ - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Disease(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Unit(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class CompoundExpression(ConfiguredBaseModel): - - None - - - -class QuantitativeValue(CompoundExpression): - - value: Optional[float] = Field(None, description="""The value of the quantity.""") - unit: Optional[str] = Field(None, description="""The unit of the quantity.""") - - - -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - subject: Optional[str] = Field(None) - predicate: Optional[str] = Field(None) - object: Optional[str] = Field(None) - qualifier: Optional[str] = Field(None, description="""A qualifier for the statements, e.g. \"NOT\" for negation""") - subject_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"""") - object_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"""") - - - -class TextWithTriples(ConfiguredBaseModel): - """ - A text containing one or more relations of the Triple type. - """ - publication: Optional[Publication] = Field(None) - triples: Optional[List[Triple]] = Field(default_factory=list) - - - -class TextWithEntity(ConfiguredBaseModel): - """ - A text containing one or more instances of a single type of entity. - """ - publication: Optional[Publication] = Field(None) - entities: Optional[List[str]] = Field(default_factory=list) - - - -class RelationshipType(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Publication(ConfiguredBaseModel): - - id: Optional[str] = Field(None, description="""The publication identifier""") - title: Optional[str] = Field(None, description="""The title of the publication""") - abstract: Optional[str] = Field(None, description="""The abstract of the publication""") - combined_text: Optional[str] = Field(None) - full_text: Optional[str] = Field(None, description="""The full text of the publication""") - - - -class AnnotatorResult(ConfiguredBaseModel): - - subject_text: Optional[str] = Field(None) - object_id: Optional[str] = Field(None) - object_text: Optional[str] = Field(None) - - - - -# Model rebuild -# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model -ClinicalObservationSet.model_rebuild() -MalnutritionObservations.model_rebuild() -ExtractionResult.model_rebuild() -NamedEntity.model_rebuild() -ClinicalObservations.model_rebuild() -DietSupplementation.model_rebuild() -NutritionSupport.model_rebuild() -Disease.model_rebuild() -Unit.model_rebuild() -CompoundExpression.model_rebuild() -QuantitativeValue.model_rebuild() -Triple.model_rebuild() -TextWithTriples.model_rebuild() -TextWithEntity.model_rebuild() -RelationshipType.model_rebuild() -Publication.model_rebuild() -AnnotatorResult.model_rebuild() - diff --git a/src/ontogpt/templates/dietician_notes.yaml b/src/ontogpt/templates/dietician_notes.yaml deleted file mode 100644 index 4c5a6ef89..000000000 --- a/src/ontogpt/templates/dietician_notes.yaml +++ /dev/null @@ -1,145 +0,0 @@ -id: http://w3id.org/ontogpt/dietician_notes -name: dietician_notes -title: Dietician Notes Extraction Template -description: >- - A template for extracting clinical observations from dietician notes -license: https://creativecommons.org/publicdomain/zero/1.0/ -prefixes: - linkml: https://w3id.org/linkml/ - dietician_notes: http://w3id.org/ontogpt/dietician_notes - HP: http://purl.obolibrary.org/obo/HP_ - -default_prefix: dietician_notes -default_range: string - -imports: - - linkml:types - - core - -classes: - ClinicalObservationSet: - description: >- - A set of sets of clinical observations. - attributes: - observations: - range: ClinicalObservations - multivalued: true - - ClinicalObservations: - tree_root: true - description: >- - A set of clinical observations about a single patient at a single time. - is_a: NamedEntity - attributes: - is_pediatric: - annotations: - prompt: >- - True if the patient is a child, False otherwise. - range: string - patient_height: - annotations: - prompt: >- - The value and units of the patient's height. - range: QuantitativeValue - patient_weight: - annotations: - prompt: >- - The value and units of the patient's weight. - range: QuantitativeValue - malnutrition_status: - annotations: - prompt: >- - Observations of the patient's malnutrition status. - range: MalnutritionObservations - diet_supplementation: - description: >- - A semicolon-separated list of the patient's diet supplementation - therapies. - range: DietSupplementation - multivalued: true - nutrition_support: - description: >- - A semicolon-separated list of the patient's nutrition support - therapies, usually enteral or parenteral nutrition. - range: NutritionSupport - multivalued: true - - # TODO: Resolve validation errors if the values can't be parsed as floats - # This may happen if no value is provided. - QuantitativeValue: - is_a: CompoundExpression - annotations: - owl: IntersectionOf - attributes: - value: - description: The value of the quantity. - range: float - annotations: - owl: DataProperty, DataHasValue - unit: - description: The unit of the quantity. - range: Unit - slot_uri: qudt:unit - annotations: - owl: ObjectProperty, ObjectSomeValuesFrom - - MalnutritionObservations: - attributes: - malnutrition_presence: - description: True if the patient is malnourished, False otherwise. - range: string - severity: - description: >- - The severity of the patient's malnutrition, if present. - range: string - diagnosis: - description: >- - The patient's malnutrition diagnosis, if present. - range: Disease - - # TODO: distinguish whether this is currently active therapy - # or a reccomendation for future therapy (but not yet started) - DietSupplementation: - description: >- - A diet supplementation therapy. - is_a: NamedEntity - id_prefixes: - - FOODON - - MAXO - annotations: - annotators: "sqlite:obo:foodon, sqlite:obo:chebi, sqlite:obo:maxo" - prompt.examples: >- - single vitamin supplement, ginkgo biloba supplement, - multi-mineral supplement, biotin supplementation, - glucosamine supplement - - # TODO: consider limiting to children of MAXO:0000009 - # or a more specific group of terms - NutritionSupport: - description: >- - A nutrition support therapy used to treat or prevent malnutrition. - is_a: NamedEntity - id_prefixes: - - MAXO - annotations: - annotators: sqlite:obo:maxo - prompt.examples: >- - enteral nutrition intake, gavage nutrition intake, - parenteral nutrition intake, partial parenteral nutrition intake - - Disease: - is_a: NamedEntity - id_prefixes: - - MONDO - annotations: - annotators: sqlite:obo:mondo - prompt.examples: cardiac asystole, COVID-19, Headache, cancer - - Unit: - is_a: NamedEntity - id_prefixes: - - UO - - NCIT - - dbpediaont - annotations: - annotators: sqlite:obo:uo, sqlite:obo:dbpediaont, sqlite:obo:foodon diff --git a/src/ontogpt/templates/drug.py b/src/ontogpt/templates/drug.py deleted file mode 100644 index 4f18d6d7d..000000000 --- a/src/ontogpt/templates/drug.py +++ /dev/null @@ -1,184 +0,0 @@ -from __future__ import annotations -from datetime import datetime, date -from enum import Enum -from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, ConfigDict, Field, field_validator -import re -import sys -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal - - -metamodel_version = "None" -version = "None" - -class ConfiguredBaseModel(BaseModel): - model_config = ConfigDict( - validate_assignment=True, - validate_default=True, - extra = 'forbid', - arbitrary_types_allowed=True, - use_enum_values = True) - - -class NullDataOptions(str, Enum): - - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = "UNSPECIFIED_METHOD_OF_ADMINISTRATION" - - NOT_APPLICABLE = "NOT_APPLICABLE" - - NOT_MENTIONED = "NOT_MENTIONED" - - - -class DrugMechanism(ConfiguredBaseModel): - - disease: Optional[str] = Field(None, description="""the name of the disease that is treated""") - drug: Optional[str] = Field(None, description="""the name of the drug that treats the disease""") - mechanism_links: Optional[List[MechanismLink]] = Field(default_factory=list, description="""semicolon-separated list of links, where each link is a triple connecting two entities via a relationship type""") - references: Optional[List[str]] = Field(default_factory=list) - source_text: Optional[str] = Field(None) - - - -class ExtractionResult(ConfiguredBaseModel): - """ - A result of extracting knowledge on text - """ - input_id: Optional[str] = Field(None) - input_title: Optional[str] = Field(None) - input_text: Optional[str] = Field(None) - raw_completion_output: Optional[str] = Field(None) - prompt: Optional[str] = Field(None) - extracted_object: Optional[Any] = Field(None, description="""The complex objects extracted from the text""") - named_entities: Optional[List[Any]] = Field(default_factory=list, description="""Named entities extracted from the text""") - - - -class NamedEntity(ConfiguredBaseModel): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class MechanismElement(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Disease(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Drug(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Predicate(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class CompoundExpression(ConfiguredBaseModel): - - None - - - -class MechanismLink(CompoundExpression): - - subject: Optional[str] = Field(None) - predicate: Optional[str] = Field(None) - object: Optional[str] = Field(None) - - - -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - subject: Optional[str] = Field(None) - predicate: Optional[str] = Field(None) - object: Optional[str] = Field(None) - qualifier: Optional[str] = Field(None, description="""A qualifier for the statements, e.g. \"NOT\" for negation""") - subject_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"""") - object_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"""") - - - -class TextWithTriples(ConfiguredBaseModel): - """ - A text containing one or more relations of the Triple type. - """ - publication: Optional[Publication] = Field(None) - triples: Optional[List[Triple]] = Field(default_factory=list) - - - -class TextWithEntity(ConfiguredBaseModel): - """ - A text containing one or more instances of a single type of entity. - """ - publication: Optional[Publication] = Field(None) - entities: Optional[List[str]] = Field(default_factory=list) - - - -class RelationshipType(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Publication(ConfiguredBaseModel): - - id: Optional[str] = Field(None, description="""The publication identifier""") - title: Optional[str] = Field(None, description="""The title of the publication""") - abstract: Optional[str] = Field(None, description="""The abstract of the publication""") - combined_text: Optional[str] = Field(None) - full_text: Optional[str] = Field(None, description="""The full text of the publication""") - - - -class AnnotatorResult(ConfiguredBaseModel): - - subject_text: Optional[str] = Field(None) - object_id: Optional[str] = Field(None) - object_text: Optional[str] = Field(None) - - - - -# Model rebuild -# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model -DrugMechanism.model_rebuild() -ExtractionResult.model_rebuild() -NamedEntity.model_rebuild() -MechanismElement.model_rebuild() -Disease.model_rebuild() -Drug.model_rebuild() -Predicate.model_rebuild() -CompoundExpression.model_rebuild() -MechanismLink.model_rebuild() -Triple.model_rebuild() -TextWithTriples.model_rebuild() -TextWithEntity.model_rebuild() -RelationshipType.model_rebuild() -Publication.model_rebuild() -AnnotatorResult.model_rebuild() - diff --git a/src/ontogpt/templates/drug.yaml b/src/ontogpt/templates/drug.yaml deleted file mode 100644 index ad1630469..000000000 --- a/src/ontogpt/templates/drug.yaml +++ /dev/null @@ -1,75 +0,0 @@ -id: http://w3id.org/ontogpt/drug -name: drug -title: Drug Template -description: >- - A template for Drugs and drug mechanism -license: https://creativecommons.org/publicdomain/zero/1.0/ -prefixes: - linkml: https://w3id.org/linkml/ - drug: http://w3id.org/ontogpt/drug/ - -default_prefix: drug -default_range: string - -imports: - - linkml:types - - core - -classes: - DrugMechanism: - tree_root: true - attributes: - disease: - description: the name of the disease that is treated - range: Disease - drug: - description: the name of the drug that treats the disease - range: Drug - mechanism_links: - description: semicolon-separated list of links, where each link is a triple connecting two entities via a relationship type - multivalued: true - range: MechanismLink - references: - multivalued: true - range: string - annotations: - prompt.skip: "true" - source_text: - range: string - annotations: - prompt.skip: "true" - - MechanismElement: - is_a: NamedEntity - id_prefixes: - - HGNC - - MESH - annotations: - annotators: sqlite:obo:go, sqlite:obo:mesh, sqlite:obo:uberon, sqlite:obo:pr, sqlite:obo:ncbitaxon, sqlite:obo:cl - - Disease: - is_a: NamedEntity - # TODO: make mondo primary; we use mesh for now for evaluating drugmechdb - annotations: - annotators: sqlite:obo:mesh, sqlite:obo:mondo - - Drug: - is_a: NamedEntity - annotations: - annotators: sqlite:obo:drugbank, sqlite:obo:chebi, sqlite:obo:mesh - - Predicate: - is_a: NamedEntity - annotations: - annotators: sqlite:obo:biolink, sqlite:obo:ro - - MechanismLink: - is_a: CompoundExpression - attributes: - subject: - range: MechanismElement - predicate: - range: Predicate - object: - range: MechanismElement - diff --git a/src/ontogpt/templates/emapa_simple.py b/src/ontogpt/templates/emapa_simple.py deleted file mode 100644 index 8b4337c9d..000000000 --- a/src/ontogpt/templates/emapa_simple.py +++ /dev/null @@ -1,149 +0,0 @@ -from __future__ import annotations -from datetime import datetime, date -from enum import Enum -from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, ConfigDict, Field, field_validator -import re -import sys -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal - - -metamodel_version = "None" -version = "None" - -class ConfiguredBaseModel(BaseModel): - model_config = ConfigDict( - validate_assignment=True, - validate_default=True, - extra = 'forbid', - arbitrary_types_allowed=True, - use_enum_values = True) - - -class NullDataOptions(str, Enum): - - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = "UNSPECIFIED_METHOD_OF_ADMINISTRATION" - - NOT_APPLICABLE = "NOT_APPLICABLE" - - NOT_MENTIONED = "NOT_MENTIONED" - - - -class ExtractionResult(ConfiguredBaseModel): - """ - A result of extracting knowledge on text - """ - input_id: Optional[str] = Field(None) - input_title: Optional[str] = Field(None) - input_text: Optional[str] = Field(None) - raw_completion_output: Optional[str] = Field(None) - prompt: Optional[str] = Field(None) - extracted_object: Optional[Any] = Field(None, description="""The complex objects extracted from the text""") - named_entities: Optional[List[Any]] = Field(default_factory=list, description="""Named entities extracted from the text""") - - - -class NamedEntity(ConfiguredBaseModel): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class OntologyTermSet(NamedEntity): - - terms: Optional[List[str]] = Field(default_factory=list, description="""A semicolon-separated list of any Mouse Developmental Anatomy Ontology terms.""") - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class OntologyTerm(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class CompoundExpression(ConfiguredBaseModel): - - None - - - -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - subject: Optional[str] = Field(None) - predicate: Optional[str] = Field(None) - object: Optional[str] = Field(None) - qualifier: Optional[str] = Field(None, description="""A qualifier for the statements, e.g. \"NOT\" for negation""") - subject_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"""") - object_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"""") - - - -class TextWithTriples(ConfiguredBaseModel): - """ - A text containing one or more relations of the Triple type. - """ - publication: Optional[Publication] = Field(None) - triples: Optional[List[Triple]] = Field(default_factory=list) - - - -class TextWithEntity(ConfiguredBaseModel): - """ - A text containing one or more instances of a single type of entity. - """ - publication: Optional[Publication] = Field(None) - entities: Optional[List[str]] = Field(default_factory=list) - - - -class RelationshipType(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Publication(ConfiguredBaseModel): - - id: Optional[str] = Field(None, description="""The publication identifier""") - title: Optional[str] = Field(None, description="""The title of the publication""") - abstract: Optional[str] = Field(None, description="""The abstract of the publication""") - combined_text: Optional[str] = Field(None) - full_text: Optional[str] = Field(None, description="""The full text of the publication""") - - - -class AnnotatorResult(ConfiguredBaseModel): - - subject_text: Optional[str] = Field(None) - object_id: Optional[str] = Field(None) - object_text: Optional[str] = Field(None) - - - - -# Model rebuild -# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model -ExtractionResult.model_rebuild() -NamedEntity.model_rebuild() -OntologyTermSet.model_rebuild() -OntologyTerm.model_rebuild() -CompoundExpression.model_rebuild() -Triple.model_rebuild() -TextWithTriples.model_rebuild() -TextWithEntity.model_rebuild() -RelationshipType.model_rebuild() -Publication.model_rebuild() -AnnotatorResult.model_rebuild() - diff --git a/src/ontogpt/templates/emapa_simple.yaml b/src/ontogpt/templates/emapa_simple.yaml deleted file mode 100644 index 327b3a7f7..000000000 --- a/src/ontogpt/templates/emapa_simple.yaml +++ /dev/null @@ -1,42 +0,0 @@ -id: http://w3id.org/ontogpt/emapa_simple -name: emapa_simple -title: Simple EMAPA Extraction Template -description: >- - Simple Mouse Developmental Anatomy Ontology Extraction Template -license: https://creativecommons.org/publicdomain/zero/1.0/ -prefixes: - linkml: https://w3id.org/linkml/ - emapa_simple: http://w3id.org/ontogpt/emapa_simple - GO: http://purl.obolibrary.org/obo/GO_ - -default_prefix: emapa_simple -default_range: string - -imports: - - linkml:types - - core - -classes: - OntologyTermSet: - tree_root: true - is_a: NamedEntity - attributes: - terms: - range: OntologyTerm - multivalued: true - description: >- - A semicolon-separated list of any Mouse Developmental Anatomy - Ontology terms. - - OntologyTerm: - is_a: NamedEntity - id_prefixes: - - EMAPA - annotations: - annotators: sqlite:obo:emapa - prompt: >- - The name of a Mouse Developmental Anatomy Ontology term. - Examples include: common carotid artery, - cerebellum anterior vermis, tailgut, - gastro-esophageal junction mesentery, - hindlimb digit 3 phalanx diff --git a/src/ontogpt/templates/environmental_metadata.py b/src/ontogpt/templates/environmental_metadata.py deleted file mode 100644 index dbc136283..000000000 --- a/src/ontogpt/templates/environmental_metadata.py +++ /dev/null @@ -1,184 +0,0 @@ -from __future__ import annotations -from datetime import datetime, date -from enum import Enum -from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, ConfigDict, Field, field_validator -import re -import sys -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal - - -metamodel_version = "None" -version = "None" - -class ConfiguredBaseModel(BaseModel): - model_config = ConfigDict( - validate_assignment=True, - validate_default=True, - extra = 'forbid', - arbitrary_types_allowed=True, - use_enum_values = True) - - -class NullDataOptions(str, Enum): - - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = "UNSPECIFIED_METHOD_OF_ADMINISTRATION" - - NOT_APPLICABLE = "NOT_APPLICABLE" - - NOT_MENTIONED = "NOT_MENTIONED" - - - -class Dataset(ConfiguredBaseModel): - - packageid: Optional[str] = Field(None, description="""The internal identifier for the dataset""") - topic: Optional[List[str]] = Field(default_factory=list, description="""the general scientific area of study concerning the sample(s)""") - location: Optional[List[str]] = Field(default_factory=list, description="""the geographic location where the sample was isolated""") - environmental_material: Optional[List[str]] = Field(default_factory=list, description="""the environmental material that was sampled""") - environments: Optional[List[str]] = Field(default_factory=list, description="""the environmental context in which the study was conducted""") - methods: Optional[List[str]] = Field(default_factory=list) - - - -class ExtractionResult(ConfiguredBaseModel): - """ - A result of extracting knowledge on text - """ - input_id: Optional[str] = Field(None) - input_title: Optional[str] = Field(None) - input_text: Optional[str] = Field(None) - raw_completion_output: Optional[str] = Field(None) - prompt: Optional[str] = Field(None) - extracted_object: Optional[Any] = Field(None, description="""The complex objects extracted from the text""") - named_entities: Optional[List[Any]] = Field(default_factory=list, description="""Named entities extracted from the text""") - - - -class NamedEntity(ConfiguredBaseModel): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Topic(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Location(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class EnvironmentalMaterial(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Environment(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Method(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class CompoundExpression(ConfiguredBaseModel): - - None - - - -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - subject: Optional[str] = Field(None) - predicate: Optional[str] = Field(None) - object: Optional[str] = Field(None) - qualifier: Optional[str] = Field(None, description="""A qualifier for the statements, e.g. \"NOT\" for negation""") - subject_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"""") - object_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"""") - - - -class TextWithTriples(ConfiguredBaseModel): - """ - A text containing one or more relations of the Triple type. - """ - publication: Optional[Publication] = Field(None) - triples: Optional[List[Triple]] = Field(default_factory=list) - - - -class TextWithEntity(ConfiguredBaseModel): - """ - A text containing one or more instances of a single type of entity. - """ - publication: Optional[Publication] = Field(None) - entities: Optional[List[str]] = Field(default_factory=list) - - - -class RelationshipType(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Publication(ConfiguredBaseModel): - - id: Optional[str] = Field(None, description="""The publication identifier""") - title: Optional[str] = Field(None, description="""The title of the publication""") - abstract: Optional[str] = Field(None, description="""The abstract of the publication""") - combined_text: Optional[str] = Field(None) - full_text: Optional[str] = Field(None, description="""The full text of the publication""") - - - -class AnnotatorResult(ConfiguredBaseModel): - - subject_text: Optional[str] = Field(None) - object_id: Optional[str] = Field(None) - object_text: Optional[str] = Field(None) - - - - -# Model rebuild -# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model -Dataset.model_rebuild() -ExtractionResult.model_rebuild() -NamedEntity.model_rebuild() -Topic.model_rebuild() -Location.model_rebuild() -EnvironmentalMaterial.model_rebuild() -Environment.model_rebuild() -Method.model_rebuild() -CompoundExpression.model_rebuild() -Triple.model_rebuild() -TextWithTriples.model_rebuild() -TextWithEntity.model_rebuild() -RelationshipType.model_rebuild() -Publication.model_rebuild() -AnnotatorResult.model_rebuild() - diff --git a/src/ontogpt/templates/environmental_metadata.yaml b/src/ontogpt/templates/environmental_metadata.yaml deleted file mode 100644 index 6a21e06e4..000000000 --- a/src/ontogpt/templates/environmental_metadata.yaml +++ /dev/null @@ -1,100 +0,0 @@ -id: http://w3id.org/ontogpt/environmental-metadata -name: environmental-metadata -title: Environmental sample metadata -description: >- - A template for categorizing Environmental Data Initiative - data entries. See https://github.com/EDIorg/EDIorg-repository-index -license: https://creativecommons.org/publicdomain/zero/1.0/ -prefixes: - linkml: https://w3id.org/linkml/ - envmd: http://w3id.org/ontogpt/environmental-metadata - -default_prefix: envmd -default_range: string - -imports: - - linkml:types - - core - -classes: - Dataset: - tree_root: true - attributes: - packageid: - description: The internal identifier for the dataset - annotations: - prompt: single unique identifier for the dataset - range: string - multivalued: false - - topic: - description: the general scientific area of study concerning the sample(s) - annotations: - prompt: semicolon-separated list of scientific areas of study concerning the sample(s) - range: Topic - multivalued: true - - location: - description: the geographic location where the sample was isolated - annotations: - prompt: semicolon-separated list of geographic locations of sample isolations - range: Location - multivalued: true - - environmental_material: - description: the environmental material that was sampled - annotations: - prompt: semicolon-separated list of environmental materials - range: EnvironmentalMaterial - multivalued: true - - environments: - description: the environmental context in which the study was conducted - annotations: - prompt: semicolon-separated list of environmental contexts in which the study was conducted - range: Environment - multivalued: true - - methods: - annotations: - prompt: semicolon-separated list of methods used in measuring sample variables - range: Method - multivalued: true - - Topic: - is_a: NamedEntity - id_prefixes: - - ENVTHES - annotations: - annotators: bioportal:ENVTHES - - Location: - is_a: NamedEntity - id_prefixes: - - ENVO - - GAZ - annotations: - annotators: sqlite:obo:envo, bioportal:GAZ - - EnvironmentalMaterial: - is_a: NamedEntity - id_prefixes: - - ENVO - - ENVTHES - annotations: - annotators: sqlite:obo:envo, bioportal:ENVTHES - - Environment: - is_a: NamedEntity - id_prefixes: - - ENVO - - ENVTHES - annotations: - annotators: sqlite:obo:envo, bioportal:ENVTHES - - Method: - is_a: NamedEntity - id_prefixes: - - ENVTHES - annotations: - annotators: bioportal:ENVTHES diff --git a/src/ontogpt/templates/environmental_sample.py b/src/ontogpt/templates/environmental_sample.py deleted file mode 100644 index f92ca1a24..000000000 --- a/src/ontogpt/templates/environmental_sample.py +++ /dev/null @@ -1,200 +0,0 @@ -from __future__ import annotations -from datetime import datetime, date -from enum import Enum -from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, ConfigDict, Field, field_validator -import re -import sys -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal - - -metamodel_version = "None" -version = "None" - -class ConfiguredBaseModel(BaseModel): - model_config = ConfigDict( - validate_assignment=True, - validate_default=True, - extra = 'forbid', - arbitrary_types_allowed=True, - use_enum_values = True) - - -class NullDataOptions(str, Enum): - - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = "UNSPECIFIED_METHOD_OF_ADMINISTRATION" - - NOT_APPLICABLE = "NOT_APPLICABLE" - - NOT_MENTIONED = "NOT_MENTIONED" - - - -class Study(ConfiguredBaseModel): - - location: Optional[List[str]] = Field(default_factory=list, description="""the sites at which the study was conducted""") - environmental_material: Optional[List[str]] = Field(default_factory=list, description="""the environmental material that was sampled""") - environments: Optional[List[str]] = Field(default_factory=list) - causal_relationships: Optional[List[CausalRelationship]] = Field(default_factory=list) - variables: Optional[List[str]] = Field(default_factory=list) - measurements: Optional[List[Measurement]] = Field(default_factory=list) - - - -class ExtractionResult(ConfiguredBaseModel): - """ - A result of extracting knowledge on text - """ - input_id: Optional[str] = Field(None) - input_title: Optional[str] = Field(None) - input_text: Optional[str] = Field(None) - raw_completion_output: Optional[str] = Field(None) - prompt: Optional[str] = Field(None) - extracted_object: Optional[Any] = Field(None, description="""The complex objects extracted from the text""") - named_entities: Optional[List[Any]] = Field(default_factory=list, description="""Named entities extracted from the text""") - - - -class NamedEntity(ConfiguredBaseModel): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Location(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class EnvironmentalMaterial(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Environment(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Variable(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Unit(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class CompoundExpression(ConfiguredBaseModel): - - None - - - -class Measurement(CompoundExpression): - - value: Optional[str] = Field(None, description="""the value of the measurement""") - unit: Optional[str] = Field(None, description="""the unit of the measurement""") - - - -class CausalRelationship(CompoundExpression): - - cause: Optional[str] = Field(None, description="""the variable that is the cause of the effect""") - effect: Optional[str] = Field(None, description="""the things that is affected""") - - - -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - subject: Optional[str] = Field(None) - predicate: Optional[str] = Field(None) - object: Optional[str] = Field(None) - qualifier: Optional[str] = Field(None, description="""A qualifier for the statements, e.g. \"NOT\" for negation""") - subject_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"""") - object_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"""") - - - -class TextWithTriples(ConfiguredBaseModel): - """ - A text containing one or more relations of the Triple type. - """ - publication: Optional[Publication] = Field(None) - triples: Optional[List[Triple]] = Field(default_factory=list) - - - -class TextWithEntity(ConfiguredBaseModel): - """ - A text containing one or more instances of a single type of entity. - """ - publication: Optional[Publication] = Field(None) - entities: Optional[List[str]] = Field(default_factory=list) - - - -class RelationshipType(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Publication(ConfiguredBaseModel): - - id: Optional[str] = Field(None, description="""The publication identifier""") - title: Optional[str] = Field(None, description="""The title of the publication""") - abstract: Optional[str] = Field(None, description="""The abstract of the publication""") - combined_text: Optional[str] = Field(None) - full_text: Optional[str] = Field(None, description="""The full text of the publication""") - - - -class AnnotatorResult(ConfiguredBaseModel): - - subject_text: Optional[str] = Field(None) - object_id: Optional[str] = Field(None) - object_text: Optional[str] = Field(None) - - - - -# Model rebuild -# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model -Study.model_rebuild() -ExtractionResult.model_rebuild() -NamedEntity.model_rebuild() -Location.model_rebuild() -EnvironmentalMaterial.model_rebuild() -Environment.model_rebuild() -Variable.model_rebuild() -Unit.model_rebuild() -CompoundExpression.model_rebuild() -Measurement.model_rebuild() -CausalRelationship.model_rebuild() -Triple.model_rebuild() -TextWithTriples.model_rebuild() -TextWithEntity.model_rebuild() -RelationshipType.model_rebuild() -Publication.model_rebuild() -AnnotatorResult.model_rebuild() - diff --git a/src/ontogpt/templates/environmental_sample.yaml b/src/ontogpt/templates/environmental_sample.yaml deleted file mode 100644 index 8c5a6fcee..000000000 --- a/src/ontogpt/templates/environmental_sample.yaml +++ /dev/null @@ -1,122 +0,0 @@ -id: http://w3id.org/ontogpt/environmental-sample -name: environmental-sample -title: Environmental Sample Template -description: >- - A template for Environmental Samples -license: https://creativecommons.org/publicdomain/zero/1.0/ -prefixes: - linkml: https://w3id.org/linkml/ - sample: http://w3id.org/ontogpt/environmental-sample/ - -default_prefix: sample -default_range: string - -imports: - - linkml:types - - core - -classes: - Study: - tree_root: true - attributes: - location: - description: the sites at which the study was conducted - annotations: - prompt: semicolon-separated list of sites at which the study was conducted. give specific place names. if you cannot find a specific place name leave the field as empty. - range: Location - multivalued: true - - environmental_material: - description: the environmental material that was sampled - annotations: - prompt: semicolon-separated list of environmental materials - range: EnvironmentalMaterial - multivalued: true - - environments: - annotations: - prompt: semicolon-separated list of environment terms for the location in which the study was conducted - multivalued: true - range: Environment - - causal_relationships: - annotations: - prompt: semicolon-separated list of cause-effect pairs, for example, effect of temperature on growth - range: CausalRelationship - multivalued: true - - variables: - annotations: - prompt: semicolon-separated list of study variables - range: Variable - multivalued: true - - measurements: - annotations: - prompt: semicolon-separated list of value-measurement pairs - range: Measurement - multivalued: true - - Location: - is_a: NamedEntity - id_prefixes: - - ENVO - - GAZ - - ENVTHES - annotations: - annotators: sqlite:obo:envo, bioportal:gaz, bioportal:envthes - - EnvironmentalMaterial: - is_a: NamedEntity - id_prefixes: - - ENVO - - ENVTHES - annotations: - annotators: sqlite:obo:envo, bioportal:envthes - - Environment: - is_a: NamedEntity - id_prefixes: - - ENVO - - ENVTHES - annotations: - annotators: sqlite:obo:envo, bioportal:envthes - - Variable: - is_a: NamedEntity - id_prefixes: - - ENVO - - MIXS - - PATO - - ENVTHES - annotations: - annotators: sqlite:obo:envo, bioportal:bero, bioportal:envthes - - Unit: - is_a: NamedEntity - id_prefixes: - - UO - - NCIT - annotations: - annotators: sqlite:obo:uo, bioportal:ncit - - Measurement: - is_a: CompoundExpression - attributes: - value: - description: the value of the measurement - #range: float - unit: - description: the unit of the measurement - range: Unit - #variable: - - CausalRelationship: - is_a: CompoundExpression - attributes: - cause: - description: the variable that is the cause of the effect - range: Variable - effect: - description: the things that is affected - range: Variable diff --git a/src/ontogpt/templates/figure.py b/src/ontogpt/templates/figure.py deleted file mode 100644 index 6c3eaa644..000000000 --- a/src/ontogpt/templates/figure.py +++ /dev/null @@ -1,153 +0,0 @@ -from __future__ import annotations -from datetime import datetime, date -from enum import Enum -from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, ConfigDict, Field, field_validator -import re -import sys -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal - - -metamodel_version = "None" -version = "None" - -class ConfiguredBaseModel(BaseModel): - model_config = ConfigDict( - validate_assignment=True, - validate_default=True, - extra = 'forbid', - arbitrary_types_allowed=True, - use_enum_values = True) - - -class NullDataOptions(str, Enum): - - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = "UNSPECIFIED_METHOD_OF_ADMINISTRATION" - - NOT_APPLICABLE = "NOT_APPLICABLE" - - NOT_MENTIONED = "NOT_MENTIONED" - - - -class FigureCaption(ConfiguredBaseModel): - """ - A caption for a figure from a scientific paper. The caption may contain multiple subpanel descriptions. - """ - title: Optional[str] = Field(None, description="""the overall title of the figure caption""") - subpanel: Optional[List[SubPanel]] = Field(default_factory=list, description="""a subpanel of the figure""") - - - -class SubPanel(ConfiguredBaseModel): - """ - A subcomponent of the overall figure caption. - """ - id: Optional[str] = Field(None, description="""The identifier for this figure subpanel""") - text: Optional[str] = Field(None, description="""The text associated with this figure subpanel""") - info: Optional[str] = Field(None, description="""any information from the overall figure caption that applies to that subpanel (which may be duplicated across other subpanels).""") - - - -class ExtractionResult(ConfiguredBaseModel): - """ - A result of extracting knowledge on text - """ - input_id: Optional[str] = Field(None) - input_title: Optional[str] = Field(None) - input_text: Optional[str] = Field(None) - raw_completion_output: Optional[str] = Field(None) - prompt: Optional[str] = Field(None) - extracted_object: Optional[Any] = Field(None, description="""The complex objects extracted from the text""") - named_entities: Optional[List[Any]] = Field(default_factory=list, description="""Named entities extracted from the text""") - - - -class NamedEntity(ConfiguredBaseModel): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class CompoundExpression(ConfiguredBaseModel): - - None - - - -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - subject: Optional[str] = Field(None) - predicate: Optional[str] = Field(None) - object: Optional[str] = Field(None) - qualifier: Optional[str] = Field(None, description="""A qualifier for the statements, e.g. \"NOT\" for negation""") - subject_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"""") - object_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"""") - - - -class TextWithTriples(ConfiguredBaseModel): - """ - A text containing one or more relations of the Triple type. - """ - publication: Optional[Publication] = Field(None) - triples: Optional[List[Triple]] = Field(default_factory=list) - - - -class TextWithEntity(ConfiguredBaseModel): - """ - A text containing one or more instances of a single type of entity. - """ - publication: Optional[Publication] = Field(None) - entities: Optional[List[str]] = Field(default_factory=list) - - - -class RelationshipType(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Publication(ConfiguredBaseModel): - - id: Optional[str] = Field(None, description="""The publication identifier""") - title: Optional[str] = Field(None, description="""The title of the publication""") - abstract: Optional[str] = Field(None, description="""The abstract of the publication""") - combined_text: Optional[str] = Field(None) - full_text: Optional[str] = Field(None, description="""The full text of the publication""") - - - -class AnnotatorResult(ConfiguredBaseModel): - - subject_text: Optional[str] = Field(None) - object_id: Optional[str] = Field(None) - object_text: Optional[str] = Field(None) - - - - -# Model rebuild -# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model -FigureCaption.model_rebuild() -SubPanel.model_rebuild() -ExtractionResult.model_rebuild() -NamedEntity.model_rebuild() -CompoundExpression.model_rebuild() -Triple.model_rebuild() -TextWithTriples.model_rebuild() -TextWithEntity.model_rebuild() -RelationshipType.model_rebuild() -Publication.model_rebuild() -AnnotatorResult.model_rebuild() - diff --git a/src/ontogpt/templates/figure.yaml b/src/ontogpt/templates/figure.yaml deleted file mode 100644 index 24976ca50..000000000 --- a/src/ontogpt/templates/figure.yaml +++ /dev/null @@ -1,44 +0,0 @@ -id: https://w3id.org/ontogpt/figure -name: figure-template -title: Plazi Figure Template -description: >- - A template for Plazi figures and sub-parts -license: https://creativecommons.org/publicdomain/zero/1.0/ -prefixes: - linkml: https://w3id.org/linkml/ - fig: http://w3id.org/ontogpt/figure-template - -default_prefix: fig -default_range: string - -imports: - - linkml:types - - core - -classes: - FigureCaption: - tree_root: true - description: A caption for a figure from a scientific paper. The caption may contain multiple subpanel descriptions. - attributes: - title: - description: the overall title of the figure caption - subpanel: - description: a subpanel of the figure - annotations: - prompt: >- - a semicolon separated list of descriptions of every panel in the text. Keep the panel id and text together. - for example: "1A: A side view of the foo; 1B: A frontal view of the foo" - multivalued: true - range: SubPanel - - SubPanel: - description: A subcomponent of the overall figure caption. - attributes: - id: - description: The identifier for this figure subpanel - annotations: - prompt.example: 1, 2, A, B, I, II - text: - description: The text associated with this figure subpanel - info: - description: any information from the overall figure caption that applies to that subpanel (which may be duplicated across other subpanels). diff --git a/src/ontogpt/templates/gene_description_term.py b/src/ontogpt/templates/gene_description_term.py deleted file mode 100644 index 6312a4828..000000000 --- a/src/ontogpt/templates/gene_description_term.py +++ /dev/null @@ -1,159 +0,0 @@ -from __future__ import annotations -from datetime import datetime, date -from enum import Enum -from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, ConfigDict, Field, field_validator -import re -import sys -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal - - -metamodel_version = "None" -version = "None" - -class ConfiguredBaseModel(BaseModel): - model_config = ConfigDict( - validate_assignment=True, - validate_default=True, - extra = 'forbid', - arbitrary_types_allowed=True, - use_enum_values = True) - - -class NullDataOptions(str, Enum): - - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = "UNSPECIFIED_METHOD_OF_ADMINISTRATION" - - NOT_APPLICABLE = "NOT_APPLICABLE" - - NOT_MENTIONED = "NOT_MENTIONED" - - - -class GeneDescription(ConfiguredBaseModel): - """ - A summarization of an individual gene - """ - about: Optional[str] = Field(None, description="""The official symbol of the gene that is described. For example \"TP53\". Do not include the word \"gene\" in the answer.""") - narrative_summary: Optional[str] = Field(None, description="""A free text summary describing the function of the gene""") - terms: Optional[List[str]] = Field(default_factory=list, description="""A semicolon separated list of controlled terms drawn from the Gene Ontology that describe the function of the gene""") - - - -class ExtractionResult(ConfiguredBaseModel): - """ - A result of extracting knowledge on text - """ - input_id: Optional[str] = Field(None) - input_title: Optional[str] = Field(None) - input_text: Optional[str] = Field(None) - raw_completion_output: Optional[str] = Field(None) - prompt: Optional[str] = Field(None) - extracted_object: Optional[Any] = Field(None, description="""The complex objects extracted from the text""") - named_entities: Optional[List[Any]] = Field(default_factory=list, description="""Named entities extracted from the text""") - - - -class NamedEntity(ConfiguredBaseModel): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Gene(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class GeneDescriptionTerm(NamedEntity): - - label: Optional[str] = Field(None, description="""the name of the GO term""") - id: str = Field(..., description="""A unique identifier for the named entity""") - - - -class CompoundExpression(ConfiguredBaseModel): - - None - - - -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - subject: Optional[str] = Field(None) - predicate: Optional[str] = Field(None) - object: Optional[str] = Field(None) - qualifier: Optional[str] = Field(None, description="""A qualifier for the statements, e.g. \"NOT\" for negation""") - subject_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"""") - object_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"""") - - - -class TextWithTriples(ConfiguredBaseModel): - """ - A text containing one or more relations of the Triple type. - """ - publication: Optional[Publication] = Field(None) - triples: Optional[List[Triple]] = Field(default_factory=list) - - - -class TextWithEntity(ConfiguredBaseModel): - """ - A text containing one or more instances of a single type of entity. - """ - publication: Optional[Publication] = Field(None) - entities: Optional[List[str]] = Field(default_factory=list) - - - -class RelationshipType(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Publication(ConfiguredBaseModel): - - id: Optional[str] = Field(None, description="""The publication identifier""") - title: Optional[str] = Field(None, description="""The title of the publication""") - abstract: Optional[str] = Field(None, description="""The abstract of the publication""") - combined_text: Optional[str] = Field(None) - full_text: Optional[str] = Field(None, description="""The full text of the publication""") - - - -class AnnotatorResult(ConfiguredBaseModel): - - subject_text: Optional[str] = Field(None) - object_id: Optional[str] = Field(None) - object_text: Optional[str] = Field(None) - - - - -# Model rebuild -# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model -GeneDescription.model_rebuild() -ExtractionResult.model_rebuild() -NamedEntity.model_rebuild() -Gene.model_rebuild() -GeneDescriptionTerm.model_rebuild() -CompoundExpression.model_rebuild() -Triple.model_rebuild() -TextWithTriples.model_rebuild() -TextWithEntity.model_rebuild() -RelationshipType.model_rebuild() -Publication.model_rebuild() -AnnotatorResult.model_rebuild() - diff --git a/src/ontogpt/templates/gene_description_term.yaml b/src/ontogpt/templates/gene_description_term.yaml deleted file mode 100644 index aa58edc25..000000000 --- a/src/ontogpt/templates/gene_description_term.yaml +++ /dev/null @@ -1,58 +0,0 @@ -id: https://w3id.org/ontogpt/go_term -name: go-term-template -title: GO Term Template -description: >- - A simple GO term template for NER -license: https://creativecommons.org/publicdomain/zero/1.0/ -prefixes: - linkml: https://w3id.org/linkml/ - bp: http://w3id.org/ontogpt/biological-process-template - HGNC: http://identifiers.org/hgnc/ - GO: http://purl.obolibrary.org/obo/GO_ - MONDO: http://purl.obolibrary.org/obo/MONDO_ - MESH: http://identifiers.org/mesh/ - -default_prefix: bp -default_range: string - -imports: - - linkml:types - - core - -classes: - Gene: - is_a: NamedEntity - id_prefixes: - - HGNC - annotations: - annotators: sqlite:obo:hgnc - GeneDescription: - description: >- - A summarization of an individual gene - attributes: - about: - range: Gene - description: >- - The official symbol of the gene that is described. For example "TP53". Do not include the word "gene" in the answer. - narrative_summary: - description: >- - A free text summary describing the function of the gene - range: string - terms: - range: GeneDescriptionTerm - multivalued: true - description: >- - A semicolon separated list of controlled terms drawn from the Gene Ontology that describe the function of the gene - GeneDescriptionTerm: - tree_root: true - is_a: NamedEntity - attributes: - label: - description: the name of the GO term - annotations: - annotators: sqlite:obo:go, sqlite:obo:mondo, sqlite:obo:uberon, sqlite:obo:mesh - id_prefixes: - - GO - - MONDO - - UBERON - - MESH \ No newline at end of file diff --git a/src/ontogpt/templates/genesummary.py b/src/ontogpt/templates/genesummary.py deleted file mode 100644 index ca21c9ffc..000000000 --- a/src/ontogpt/templates/genesummary.py +++ /dev/null @@ -1,140 +0,0 @@ -from __future__ import annotations -from datetime import datetime, date -from enum import Enum -from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, ConfigDict, Field, field_validator -import re -import sys -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal - - -metamodel_version = "None" -version = "None" - -class ConfiguredBaseModel(BaseModel): - model_config = ConfigDict( - validate_assignment=True, - validate_default=True, - extra = 'forbid', - arbitrary_types_allowed=True, - use_enum_values = True) - - -class NullDataOptions(str, Enum): - - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = "UNSPECIFIED_METHOD_OF_ADMINISTRATION" - - NOT_APPLICABLE = "NOT_APPLICABLE" - - NOT_MENTIONED = "NOT_MENTIONED" - - - -class ExtractionResult(ConfiguredBaseModel): - """ - A result of extracting knowledge on text - """ - input_id: Optional[str] = Field(None) - input_title: Optional[str] = Field(None) - input_text: Optional[str] = Field(None) - raw_completion_output: Optional[str] = Field(None) - prompt: Optional[str] = Field(None) - extracted_object: Optional[Any] = Field(None, description="""The complex objects extracted from the text""") - named_entities: Optional[List[Any]] = Field(default_factory=list, description="""Named entities extracted from the text""") - - - -class NamedEntity(ConfiguredBaseModel): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Gene(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class CompoundExpression(ConfiguredBaseModel): - - None - - - -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - subject: Optional[str] = Field(None) - predicate: Optional[str] = Field(None) - object: Optional[str] = Field(None) - qualifier: Optional[str] = Field(None, description="""A qualifier for the statements, e.g. \"NOT\" for negation""") - subject_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"""") - object_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"""") - - - -class TextWithTriples(ConfiguredBaseModel): - """ - A text containing one or more relations of the Triple type. - """ - publication: Optional[Publication] = Field(None) - triples: Optional[List[Triple]] = Field(default_factory=list) - - - -class TextWithEntity(ConfiguredBaseModel): - """ - A text containing one or more instances of a single type of entity. - """ - publication: Optional[Publication] = Field(None) - entities: Optional[List[str]] = Field(default_factory=list) - - - -class RelationshipType(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Publication(ConfiguredBaseModel): - - id: Optional[str] = Field(None, description="""The publication identifier""") - title: Optional[str] = Field(None, description="""The title of the publication""") - abstract: Optional[str] = Field(None, description="""The abstract of the publication""") - combined_text: Optional[str] = Field(None) - full_text: Optional[str] = Field(None, description="""The full text of the publication""") - - - -class AnnotatorResult(ConfiguredBaseModel): - - subject_text: Optional[str] = Field(None) - object_id: Optional[str] = Field(None) - object_text: Optional[str] = Field(None) - - - - -# Model rebuild -# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model -ExtractionResult.model_rebuild() -NamedEntity.model_rebuild() -Gene.model_rebuild() -CompoundExpression.model_rebuild() -Triple.model_rebuild() -TextWithTriples.model_rebuild() -TextWithEntity.model_rebuild() -RelationshipType.model_rebuild() -Publication.model_rebuild() -AnnotatorResult.model_rebuild() - diff --git a/src/ontogpt/templates/genesummary.yaml b/src/ontogpt/templates/genesummary.yaml deleted file mode 100644 index 5f1359ca5..000000000 --- a/src/ontogpt/templates/genesummary.yaml +++ /dev/null @@ -1,45 +0,0 @@ -id: http://w3id.org/ontogpt/gocam -name: genesummary-template -title: genesummary Template -description: >- - A template for genesummary -license: https://creativecommons.org/publicdomain/zero/1.0/ -prefixes: - linkml: https://w3id.org/linkml/ - genesummary: http://w3id.org/ontogpt/genesummary/ - GO: http://purl.obolibrary.org/obo/GO_ - CL: http://purl.obolibrary.org/obo/CL_ - -default_prefix: genesummary -default_range: string - -imports: - - linkml:types - - core - -classes: - Gene: - is_a: NamedEntity - id_prefixes: - - HGNC - - PR - - UniProtKB - annotations: - annotators: gilda:, bioportal:hgnc-nr - slots: - - id - -slots: - summary_text: - description: >- - A summary of the abstract in a few sentences - range: string - required: true - multivalued: false - inlined: true - id: - description: >- - A unique identifier for the named entity - comments: - - this is populated during the grounding and normalization step - identifier: true \ No newline at end of file diff --git a/src/ontogpt/templates/go_simple.py b/src/ontogpt/templates/go_simple.py deleted file mode 100644 index 47a0f6e3d..000000000 --- a/src/ontogpt/templates/go_simple.py +++ /dev/null @@ -1,149 +0,0 @@ -from __future__ import annotations -from datetime import datetime, date -from enum import Enum -from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, ConfigDict, Field, field_validator -import re -import sys -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal - - -metamodel_version = "None" -version = "None" - -class ConfiguredBaseModel(BaseModel): - model_config = ConfigDict( - validate_assignment=True, - validate_default=True, - extra = 'forbid', - arbitrary_types_allowed=True, - use_enum_values = True) - - -class NullDataOptions(str, Enum): - - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = "UNSPECIFIED_METHOD_OF_ADMINISTRATION" - - NOT_APPLICABLE = "NOT_APPLICABLE" - - NOT_MENTIONED = "NOT_MENTIONED" - - - -class ExtractionResult(ConfiguredBaseModel): - """ - A result of extracting knowledge on text - """ - input_id: Optional[str] = Field(None) - input_title: Optional[str] = Field(None) - input_text: Optional[str] = Field(None) - raw_completion_output: Optional[str] = Field(None) - prompt: Optional[str] = Field(None) - extracted_object: Optional[Any] = Field(None, description="""The complex objects extracted from the text""") - named_entities: Optional[List[Any]] = Field(default_factory=list, description="""Named entities extracted from the text""") - - - -class NamedEntity(ConfiguredBaseModel): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class OntologyTermSet(NamedEntity): - - terms: Optional[List[str]] = Field(default_factory=list, description="""A semicolon-separated list of any Gene Ontology terms.""") - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class OntologyTerm(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class CompoundExpression(ConfiguredBaseModel): - - None - - - -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - subject: Optional[str] = Field(None) - predicate: Optional[str] = Field(None) - object: Optional[str] = Field(None) - qualifier: Optional[str] = Field(None, description="""A qualifier for the statements, e.g. \"NOT\" for negation""") - subject_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"""") - object_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"""") - - - -class TextWithTriples(ConfiguredBaseModel): - """ - A text containing one or more relations of the Triple type. - """ - publication: Optional[Publication] = Field(None) - triples: Optional[List[Triple]] = Field(default_factory=list) - - - -class TextWithEntity(ConfiguredBaseModel): - """ - A text containing one or more instances of a single type of entity. - """ - publication: Optional[Publication] = Field(None) - entities: Optional[List[str]] = Field(default_factory=list) - - - -class RelationshipType(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Publication(ConfiguredBaseModel): - - id: Optional[str] = Field(None, description="""The publication identifier""") - title: Optional[str] = Field(None, description="""The title of the publication""") - abstract: Optional[str] = Field(None, description="""The abstract of the publication""") - combined_text: Optional[str] = Field(None) - full_text: Optional[str] = Field(None, description="""The full text of the publication""") - - - -class AnnotatorResult(ConfiguredBaseModel): - - subject_text: Optional[str] = Field(None) - object_id: Optional[str] = Field(None) - object_text: Optional[str] = Field(None) - - - - -# Model rebuild -# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model -ExtractionResult.model_rebuild() -NamedEntity.model_rebuild() -OntologyTermSet.model_rebuild() -OntologyTerm.model_rebuild() -CompoundExpression.model_rebuild() -Triple.model_rebuild() -TextWithTriples.model_rebuild() -TextWithEntity.model_rebuild() -RelationshipType.model_rebuild() -Publication.model_rebuild() -AnnotatorResult.model_rebuild() - diff --git a/src/ontogpt/templates/go_simple.yaml b/src/ontogpt/templates/go_simple.yaml deleted file mode 100644 index bb1a2ccf0..000000000 --- a/src/ontogpt/templates/go_simple.yaml +++ /dev/null @@ -1,41 +0,0 @@ -id: http://w3id.org/ontogpt/go_simple -name: go_simple -title: Simple Gene Ontology Extraction Template -description: >- - Simple Gene Ontology Extraction Template -license: https://creativecommons.org/publicdomain/zero/1.0/ -prefixes: - linkml: https://w3id.org/linkml/ - go_simple: http://w3id.org/ontogpt/go_simple - GO: http://purl.obolibrary.org/obo/GO_ - -default_prefix: go_simple -default_range: string - -imports: - - linkml:types - - core - -classes: - OntologyTermSet: - tree_root: true - is_a: NamedEntity - attributes: - terms: - range: OntologyTerm - multivalued: true - description: >- - A semicolon-separated list of any Gene Ontology terms. - - OntologyTerm: - is_a: NamedEntity - id_prefixes: - - GO - annotations: - annotators: sqlite:obo:go - prompt: >- - The name of a Gene Ontology term. - Examples include: regulation of dehydroepiandrosterone secretion, - lignan metabolic process, ITP catabolic process, - determination of imaginal disc primordium, - kinetoplast diff --git a/src/ontogpt/templates/go_terms.py b/src/ontogpt/templates/go_terms.py deleted file mode 100644 index e3714a0f2..000000000 --- a/src/ontogpt/templates/go_terms.py +++ /dev/null @@ -1,187 +0,0 @@ -from __future__ import annotations -from datetime import datetime, date -from enum import Enum -from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, ConfigDict, Field, field_validator -import re -import sys -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal - - -metamodel_version = "None" -version = "None" - -class ConfiguredBaseModel(BaseModel): - model_config = ConfigDict( - validate_assignment=True, - validate_default=True, - extra = 'forbid', - arbitrary_types_allowed=True, - use_enum_values = True) - - -class GOBiologicalProcessType(str): - - - dummy = "dummy" - - -class GOCellComponentType(str): - - - dummy = "dummy" - - -class GOMolecularFunctionType(str): - - - dummy = "dummy" - - -class NullDataOptions(str, Enum): - - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = "UNSPECIFIED_METHOD_OF_ADMINISTRATION" - - NOT_APPLICABLE = "NOT_APPLICABLE" - - NOT_MENTIONED = "NOT_MENTIONED" - - - -class ExtractionResult(ConfiguredBaseModel): - """ - A result of extracting knowledge on text - """ - input_id: Optional[str] = Field(None) - input_title: Optional[str] = Field(None) - input_text: Optional[str] = Field(None) - raw_completion_output: Optional[str] = Field(None) - prompt: Optional[str] = Field(None) - extracted_object: Optional[Any] = Field(None, description="""The complex objects extracted from the text""") - named_entities: Optional[List[Any]] = Field(default_factory=list, description="""Named entities extracted from the text""") - - - -class NamedEntity(ConfiguredBaseModel): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class BiologicalProcess(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class CellularComponent(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class MolecularFunction(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class CompoundExpression(ConfiguredBaseModel): - - None - - - -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - subject: Optional[str] = Field(None) - predicate: Optional[str] = Field(None) - object: Optional[str] = Field(None) - qualifier: Optional[str] = Field(None, description="""A qualifier for the statements, e.g. \"NOT\" for negation""") - subject_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"""") - object_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"""") - - - -class TextWithTriples(ConfiguredBaseModel): - """ - A text containing one or more relations of the Triple type. - """ - publication: Optional[Publication] = Field(None) - triples: Optional[List[Triple]] = Field(default_factory=list) - - - -class TextWithEntity(ConfiguredBaseModel): - """ - A text containing one or more instances of a single type of entity. - """ - publication: Optional[Publication] = Field(None) - entities: Optional[List[str]] = Field(default_factory=list) - - - -class Document(TextWithEntity): - """ - A document that contains biological or biomedical concepts. - """ - biologicalprocesses: Optional[List[str]] = Field(default_factory=list, description="""One or more biological processes, as defined by the Gene Ontology.""") - cellularcomponents: Optional[List[str]] = Field(default_factory=list, description="""One or more cellular components, as defined by the Gene Ontology.""") - molecularfunctions: Optional[List[str]] = Field(default_factory=list, description="""One or more molecular functions, as defined by the Gene Ontology.""") - publication: Optional[Publication] = Field(None) - entities: Optional[List[str]] = Field(default_factory=list) - - - -class RelationshipType(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Publication(ConfiguredBaseModel): - - id: Optional[str] = Field(None, description="""The publication identifier""") - title: Optional[str] = Field(None, description="""The title of the publication""") - abstract: Optional[str] = Field(None, description="""The abstract of the publication""") - combined_text: Optional[str] = Field(None) - full_text: Optional[str] = Field(None, description="""The full text of the publication""") - - - -class AnnotatorResult(ConfiguredBaseModel): - - subject_text: Optional[str] = Field(None) - object_id: Optional[str] = Field(None) - object_text: Optional[str] = Field(None) - - - - -# Model rebuild -# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model -ExtractionResult.model_rebuild() -NamedEntity.model_rebuild() -BiologicalProcess.model_rebuild() -CellularComponent.model_rebuild() -MolecularFunction.model_rebuild() -CompoundExpression.model_rebuild() -Triple.model_rebuild() -TextWithTriples.model_rebuild() -TextWithEntity.model_rebuild() -Document.model_rebuild() -RelationshipType.model_rebuild() -Publication.model_rebuild() -AnnotatorResult.model_rebuild() - diff --git a/src/ontogpt/templates/go_terms.yaml b/src/ontogpt/templates/go_terms.yaml deleted file mode 100644 index e45c5f01b..000000000 --- a/src/ontogpt/templates/go_terms.yaml +++ /dev/null @@ -1,119 +0,0 @@ -id: http://w3id.org/ontogpt/go_terms -name: go_terms -title: Gene Ontology Term and CURIE Extraction -description: >- - A template for GO Term and ID extraction. -license: https://creativecommons.org/publicdomain/zero/1.0/ -prefixes: - linkml: https://w3id.org/linkml/ - go_terms: http://w3id.org/ontogpt/go_terms - -default_prefix: go_terms -default_range: string - -imports: - - linkml:types - - core - -classes: - Document: - tree_root: true - description: A document that contains biological or biomedical concepts. - is_a: TextWithEntity - attributes: - biologicalprocesses: - range: BiologicalProcess - multivalued: true - description: >- - One or more biological processes, as defined by the Gene Ontology. - annotations: - prompt: >- - A semi-colon separated list of biological processes, for - example: nuclear axial expansion; intracellular transport; - medial surface of mandible; ribosomal subunit export from nucleus; - pole cell development - cellularcomponents: - range: CellularComponent - multivalued: true - description: >- - One or more cellular components, as defined by the Gene Ontology. - annotations: - prompt: >- - A semi-colon separated list of cellular components and structures, - for example: tubulin complex; proteasome complex; - cytoplasm; keratohyalin granule; nucleus - molecularfunctions: - range: MolecularFunction - multivalued: true - description: >- - One or more molecular functions, as defined by the Gene Ontology. - annotations: - prompt: >- - A semi-colon separated list of molecular functions, - for example: catalytic activity; amine binding; - peptide receptor activity; oxygen carrier activity; - structural constituent of cytoskeleton - - BiologicalProcess: - is_a: NamedEntity - annotations: - annotators: "sqlite:obo:go" - prompt.examples: >- - nuclear axial expansion, intracellular transport, - medial surface of mandible, ribosomal subunit export from nucleus, - pole cell development - id_prefixes: - - GO - slot_usage: - id: - values_from: - - GOBiologicalProcessType - - CellularComponent: - is_a: NamedEntity - annotations: - annotators: "sqlite:obo:go" - prompt.examples: >- - tubulin complex, proteasome complex, cytoplasm, keratohyalin granule, - nucleus - id_prefixes: - - GO - slot_usage: - id: - values_from: - - GOCellComponentType - - MolecularFunction: - is_a: NamedEntity - annotations: - annotators: "sqlite:obo:go" - prompt.examples: >- - catalytic activity, amine binding, - peptide receptor activity, oxygen carrier activity, - structural constituent of cytoskeleton - id_prefixes: - - GO - slot_usage: - id: - values_from: - - GOMolecularFunctionType - -enums: - - GOBiologicalProcessType: - reachable_from: - source_ontology: obo:go - source_nodes: - - GO:0008150 # biological_process - - GOCellComponentType: - reachable_from: - source_ontology: obo:go - source_nodes: - - GO:0005575 # cellular_component - - GOMolecularFunctionType: - reachable_from: - source_ontology: obo:go - source_nodes: - - GO:0003674 # molecular_function diff --git a/src/ontogpt/templates/go_terms_relational.py b/src/ontogpt/templates/go_terms_relational.py deleted file mode 100644 index c5fbf8501..000000000 --- a/src/ontogpt/templates/go_terms_relational.py +++ /dev/null @@ -1,182 +0,0 @@ -from __future__ import annotations -from datetime import datetime, date -from enum import Enum -from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, ConfigDict, Field, field_validator -import re -import sys -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal - - -metamodel_version = "None" -version = "None" - -class ConfiguredBaseModel(BaseModel): - model_config = ConfigDict( - validate_assignment=True, - validate_default=True, - extra = 'forbid', - arbitrary_types_allowed=True, - use_enum_values = True) - - -class NullDataOptions(str, Enum): - - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = "UNSPECIFIED_METHOD_OF_ADMINISTRATION" - - NOT_APPLICABLE = "NOT_APPLICABLE" - - NOT_MENTIONED = "NOT_MENTIONED" - - - -class ExtractionResult(ConfiguredBaseModel): - """ - A result of extracting knowledge on text - """ - input_id: Optional[str] = Field(None) - input_title: Optional[str] = Field(None) - input_text: Optional[str] = Field(None) - raw_completion_output: Optional[str] = Field(None) - prompt: Optional[str] = Field(None) - extracted_object: Optional[Any] = Field(None, description="""The complex objects extracted from the text""") - named_entities: Optional[List[Any]] = Field(default_factory=list, description="""Named entities extracted from the text""") - - - -class NamedEntity(ConfiguredBaseModel): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Protein(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class GOTerm(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class CompoundExpression(ConfiguredBaseModel): - - None - - - -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - subject: Optional[str] = Field(None) - predicate: Optional[str] = Field(None) - object: Optional[str] = Field(None) - qualifier: Optional[str] = Field(None, description="""A qualifier for the statements, e.g. \"NOT\" for negation""") - subject_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"""") - object_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"""") - - - -class ProteinToGORelationship(Triple): - """ - A triple where the subject is a protein and the object is a GO term. - """ - subject: Optional[str] = Field(None, description="""The protein participating in the relationship, for example: Klp61F, GATA binding protein 3, S-formylglutathione hydrolase""") - predicate: Optional[str] = Field(None, description="""The relationship type, usually HAS ANNOTATION.""") - object: Optional[str] = Field(None, description="""The Gene Ontology term participating in the relationship, for example: cytosol, plasma cell differentiation, small-subunit processome""") - qualifier: Optional[str] = Field(None, description="""A qualifier for the statements, e.g. \"NOT\" for negation""") - subject_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the protein.""") - object_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the GO term.""") - - - -class TextWithTriples(ConfiguredBaseModel): - """ - A text containing one or more relations of the Triple type. - """ - publication: Optional[Publication] = Field(None) - triples: Optional[List[Triple]] = Field(default_factory=list) - - - -class Document(TextWithTriples): - """ - A document that contains biological or biomedical concepts. - """ - publication: Optional[Publication] = Field(None) - triples: Optional[List[ProteinToGORelationship]] = Field(default_factory=list) - - - -class TextWithEntity(ConfiguredBaseModel): - """ - A text containing one or more instances of a single type of entity. - """ - publication: Optional[Publication] = Field(None) - entities: Optional[List[str]] = Field(default_factory=list) - - - -class RelationshipType(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class ProteinToGOPredicate(RelationshipType): - """ - A predicate for protein to GO term relationships. - """ - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Publication(ConfiguredBaseModel): - - id: Optional[str] = Field(None, description="""The publication identifier""") - title: Optional[str] = Field(None, description="""The title of the publication""") - abstract: Optional[str] = Field(None, description="""The abstract of the publication""") - combined_text: Optional[str] = Field(None) - full_text: Optional[str] = Field(None, description="""The full text of the publication""") - - - -class AnnotatorResult(ConfiguredBaseModel): - - subject_text: Optional[str] = Field(None) - object_id: Optional[str] = Field(None) - object_text: Optional[str] = Field(None) - - - - -# Model rebuild -# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model -ExtractionResult.model_rebuild() -NamedEntity.model_rebuild() -Protein.model_rebuild() -GOTerm.model_rebuild() -CompoundExpression.model_rebuild() -Triple.model_rebuild() -ProteinToGORelationship.model_rebuild() -TextWithTriples.model_rebuild() -Document.model_rebuild() -TextWithEntity.model_rebuild() -RelationshipType.model_rebuild() -ProteinToGOPredicate.model_rebuild() -Publication.model_rebuild() -AnnotatorResult.model_rebuild() - diff --git a/src/ontogpt/templates/go_terms_relational.yaml b/src/ontogpt/templates/go_terms_relational.yaml deleted file mode 100644 index d037e949e..000000000 --- a/src/ontogpt/templates/go_terms_relational.yaml +++ /dev/null @@ -1,98 +0,0 @@ -id: http://w3id.org/ontogpt/go_terms_relational -name: go_terms_relational -title: Gene Ontology Relation and CURIE Extraction -description: >- - A template for GO Term and ID extraction, - as relations involving specific proteins. - Note this does not make a distinction between - GO term types. -license: https://creativecommons.org/publicdomain/zero/1.0/ -prefixes: - linkml: https://w3id.org/linkml/ - go_terms_relational: http://w3id.org/ontogpt/go_terms_relational - -default_prefix: go_terms_relational -default_range: string - -imports: - - linkml:types - - core - -classes: - Document: - tree_root: true - description: A document that contains biological or biomedical concepts. - is_a: TextWithTriples - slot_usage: - triples: - range: ProteinToGORelationship - annotations: - prompt: >- - A semi-colon separated list of protein to GO term relationships, - where the relationship is HAS ANNOTATION, - for example: - RPS7B HAS ANNOTATION structural constituent of ribosome; - granzyme M HAS ANNOTATION endopeptidase activity; - Mknk1 HAS ANNOTATION nucleoplasm - - ProteinToGORelationship: - is_a: Triple - description: >- - A triple where the subject is a protein and the object is a GO term. - slot_usage: - subject: - range: Protein - description: >- - The protein participating in the relationship, - for example: Klp61F, GATA binding protein 3, S-formylglutathione - hydrolase - object: - range: GOTerm - description: >- - The Gene Ontology term participating in the relationship, - for example: cytosol, plasma cell differentiation, small-subunit - processome - predicate: - range: ProteinToGOPredicate - description: The relationship type, usually HAS ANNOTATION. - subject_qualifier: - range: NamedEntity - description: >- - An optional qualifier or modifier for the protein. - object_qualifier: - range: NamedEntity - description: >- - An optional qualifier or modifier for the GO term. - - Protein: - is_a: NamedEntity - annotations: - annotators: "gilda:, bioportal:hgnc-nr, sqlite:obo:pr" - id_prefixes: - - PR - - HGNC - comments: - - Technically gene or protein - - Can also be UniProt accession, etc - - GOTerm: - is_a: NamedEntity - annotations: - annotators: "sqlite:obo:go" - prompt.examples: >- - nuclear axial expansion, intracellular transport, - medial surface of mandible, ribosomal subunit export from nucleus, - pole cell development, tubulin complex, proteasome complex, cytoplasm, - keratohyalin granule, catalytic activity, amine binding, - peptide receptor activity, oxygen carrier activity, - structural constituent of cytoskeleton - id_prefixes: - - GO - - ProteinToGOPredicate: - is_a: RelationshipType - description: >- - A predicate for protein to GO term relationships. - comments: - - This may be changed to a more specific type, like RO - - Any changes should be reflected for the triples slot in Document diff --git a/src/ontogpt/templates/gocam.py b/src/ontogpt/templates/gocam.py deleted file mode 100644 index c1ebd5ea3..000000000 --- a/src/ontogpt/templates/gocam.py +++ /dev/null @@ -1,262 +0,0 @@ -from __future__ import annotations -from datetime import datetime, date -from enum import Enum -from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, ConfigDict, Field, field_validator -import re -import sys -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal - - -metamodel_version = "None" -version = "None" - -class ConfiguredBaseModel(BaseModel): - model_config = ConfigDict( - validate_assignment=True, - validate_default=True, - extra = 'forbid', - arbitrary_types_allowed=True, - use_enum_values = True) - - -class GeneLocationEnum(str): - - - dummy = "dummy" - - -class GOCellComponentType(str): - - - dummy = "dummy" - - -class CellType(str): - - - dummy = "dummy" - - -class NullDataOptions(str, Enum): - - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = "UNSPECIFIED_METHOD_OF_ADMINISTRATION" - - NOT_APPLICABLE = "NOT_APPLICABLE" - - NOT_MENTIONED = "NOT_MENTIONED" - - - -class GoCamAnnotations(ConfiguredBaseModel): - - genes: Optional[List[str]] = Field(default_factory=list, description="""semicolon-separated list of genes""") - organisms: Optional[List[str]] = Field(default_factory=list, description="""semicolon-separated list of organism taxons""") - gene_organisms: Optional[List[GeneOrganismRelationship]] = Field(default_factory=list) - activities: Optional[List[str]] = Field(default_factory=list, description="""semicolon-separated list of molecular activities""") - gene_functions: Optional[List[GeneMolecularActivityRelationship]] = Field(default_factory=list, description="""semicolon-separated list of gene to molecular activity relationships""") - cellular_processes: Optional[List[str]] = Field(default_factory=list, description="""semicolon-separated list of cellular processes""") - pathways: Optional[List[str]] = Field(default_factory=list, description="""semicolon-separated list of pathways""") - gene_gene_interactions: Optional[List[GeneGeneInteraction]] = Field(default_factory=list, description="""semicolon-separated list of gene to gene interactions""") - gene_localizations: Optional[List[GeneSubcellularLocalizationRelationship]] = Field(default_factory=list, description="""semicolon-separated list of genes plus their location in the cell; for example, \"gene1 / cytoplasm; gene2 / mitochondrion\"""") - - - -class ExtractionResult(ConfiguredBaseModel): - """ - A result of extracting knowledge on text - """ - input_id: Optional[str] = Field(None) - input_title: Optional[str] = Field(None) - input_text: Optional[str] = Field(None) - raw_completion_output: Optional[str] = Field(None) - prompt: Optional[str] = Field(None) - extracted_object: Optional[Any] = Field(None, description="""The complex objects extracted from the text""") - named_entities: Optional[List[Any]] = Field(default_factory=list, description="""Named entities extracted from the text""") - - - -class NamedEntity(ConfiguredBaseModel): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Gene(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Pathway(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class CellularProcess(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class MolecularActivity(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class GeneLocation(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Organism(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Molecule(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class CompoundExpression(ConfiguredBaseModel): - - None - - - -class GeneOrganismRelationship(CompoundExpression): - - gene: Optional[str] = Field(None) - organism: Optional[str] = Field(None) - - - -class GeneMolecularActivityRelationship(CompoundExpression): - - gene: Optional[str] = Field(None) - molecular_activity: Optional[str] = Field(None) - - - -class GeneMolecularActivityRelationship2(CompoundExpression): - - gene: Optional[str] = Field(None) - molecular_activity: Optional[str] = Field(None) - target: Optional[str] = Field(None) - - - -class GeneSubcellularLocalizationRelationship(CompoundExpression): - - gene: Optional[str] = Field(None) - location: Optional[str] = Field(None) - - - -class GeneGeneInteraction(CompoundExpression): - - gene1: Optional[str] = Field(None) - gene2: Optional[str] = Field(None) - - - -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - subject: Optional[str] = Field(None) - predicate: Optional[str] = Field(None) - object: Optional[str] = Field(None) - qualifier: Optional[str] = Field(None, description="""A qualifier for the statements, e.g. \"NOT\" for negation""") - subject_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"""") - object_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"""") - - - -class TextWithTriples(ConfiguredBaseModel): - """ - A text containing one or more relations of the Triple type. - """ - publication: Optional[Publication] = Field(None) - triples: Optional[List[Triple]] = Field(default_factory=list) - - - -class TextWithEntity(ConfiguredBaseModel): - """ - A text containing one or more instances of a single type of entity. - """ - publication: Optional[Publication] = Field(None) - entities: Optional[List[str]] = Field(default_factory=list) - - - -class RelationshipType(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Publication(ConfiguredBaseModel): - - id: Optional[str] = Field(None, description="""The publication identifier""") - title: Optional[str] = Field(None, description="""The title of the publication""") - abstract: Optional[str] = Field(None, description="""The abstract of the publication""") - combined_text: Optional[str] = Field(None) - full_text: Optional[str] = Field(None, description="""The full text of the publication""") - - - -class AnnotatorResult(ConfiguredBaseModel): - - subject_text: Optional[str] = Field(None) - object_id: Optional[str] = Field(None) - object_text: Optional[str] = Field(None) - - - - -# Model rebuild -# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model -GoCamAnnotations.model_rebuild() -ExtractionResult.model_rebuild() -NamedEntity.model_rebuild() -Gene.model_rebuild() -Pathway.model_rebuild() -CellularProcess.model_rebuild() -MolecularActivity.model_rebuild() -GeneLocation.model_rebuild() -Organism.model_rebuild() -Molecule.model_rebuild() -CompoundExpression.model_rebuild() -GeneOrganismRelationship.model_rebuild() -GeneMolecularActivityRelationship.model_rebuild() -GeneMolecularActivityRelationship2.model_rebuild() -GeneSubcellularLocalizationRelationship.model_rebuild() -GeneGeneInteraction.model_rebuild() -Triple.model_rebuild() -TextWithTriples.model_rebuild() -TextWithEntity.model_rebuild() -RelationshipType.model_rebuild() -Publication.model_rebuild() -AnnotatorResult.model_rebuild() - diff --git a/src/ontogpt/templates/gocam.yaml b/src/ontogpt/templates/gocam.yaml deleted file mode 100644 index 936352628..000000000 --- a/src/ontogpt/templates/gocam.yaml +++ /dev/null @@ -1,193 +0,0 @@ -id: http://w3id.org/ontogpt/gocam -name: gocam-template -title: GO-CAM Template -description: >- - A template for GO-CAMs -license: https://creativecommons.org/publicdomain/zero/1.0/ -prefixes: - linkml: https://w3id.org/linkml/ - gocam: http://w3id.org/ontogpt/gocam/ - GO: http://purl.obolibrary.org/obo/GO_ - CL: http://purl.obolibrary.org/obo/CL_ - -default_prefix: gocam -default_range: string - -imports: - - linkml:types - - core - -classes: - GoCamAnnotations: - tree_root: true - attributes: - genes: - description: semicolon-separated list of genes - multivalued: true - range: Gene - organisms: - description: semicolon-separated list of organism taxons - multivalued: true - range: Organism - gene_organisms: - annotations: - prompt: semicolon-separated list of asterisk separated gene to organism relationships - multivalued: true - range: GeneOrganismRelationship - activities: - description: semicolon-separated list of molecular activities - multivalued: true - range: MolecularActivity - gene_functions: - description: semicolon-separated list of gene to molecular activity relationships - multivalued: true - range: GeneMolecularActivityRelationship - cellular_processes: - description: semicolon-separated list of cellular processes - multivalued: true - range: CellularProcess - pathways: - description: semicolon-separated list of pathways - multivalued: true - range: Pathway - gene_gene_interactions: - description: semicolon-separated list of gene to gene interactions - multivalued: true - range: GeneGeneInteraction - gene_localizations: - description: >- - semicolon-separated list of genes plus their location in the cell; - for example, "gene1 / cytoplasm; gene2 / mitochondrion" - multivalued: true - range: GeneSubcellularLocalizationRelationship - - Gene: - is_a: NamedEntity - id_prefixes: - - HGNC - - PR - - UniProtKB - annotations: - annotators: gilda:, bioportal:hgnc-nr - Pathway: - is_a: NamedEntity - id_prefixes: - - GO - - PW - annotations: - annotators: sqlite:obo:go, sqlite:obo:pw - CellularProcess: - is_a: NamedEntity - id_prefixes: - - GO - annotations: - annotators: sqlite:obo:go - MolecularActivity: - is_a: NamedEntity - id_prefixes: - - GO - annotations: - annotators: sqlite:obo:go - GeneLocation: - is_a: NamedEntity - id_prefixes: - - GO - - CL - - UBERON - annotations: - annotators: "sqlite:obo:go, sqlite:obo:cl" - slot_usage: - id: - values_from: - - GOCellComponentType - - CellType - Organism: - is_a: NamedEntity - id_prefixes: - - NCBITaxon - - EFO - annotations: - annotators: gilda:, sqlite:obo:ncbitaxon - Molecule: - is_a: NamedEntity - id_prefixes: - - CHEBI - - PR - annotations: - annotators: gilda:, sqlite:obo:chebi - - GeneOrganismRelationship: - is_a: CompoundExpression - attributes: - gene: - range: Gene - organism: - range: Organism - - GeneMolecularActivityRelationship: - is_a: CompoundExpression - attributes: - gene: - range: Gene - annotations: - prompt: the name of the gene in the pair. This comes first. - molecular_activity: - range: MolecularActivity - annotations: - prompt: the name of the molecular function in the pair. This comes second. May be a GO term. - annotations: - prompt.example: |- - TODO - - gene: HGNC:1234 - molecular_activity: GO:0003674 - - GeneMolecularActivityRelationship2: - is_a: CompoundExpression - attributes: - gene: - range: Gene - annotations: - prompt: the name of the gene. - molecular_activity: - range: MolecularActivity - annotations: - prompt: the name of the molecular activity, for example, ubiquitination. May be a GO term. - target: - range: Molecule - annotations: - prompt: the name of the molecular entity that is the target of the molecular activity. - - GeneSubcellularLocalizationRelationship: - is_a: CompoundExpression - attributes: - gene: - range: Gene - location: - range: GeneLocation - - GeneGeneInteraction: - is_a: CompoundExpression - attributes: - gene1: - range: Gene - gene2: - range: Gene - -enums: - - GeneLocationEnum: - inherits: - - GOCellComponent - - CellType - - GOCellComponentType: - reachable_from: - source_ontology: obo:go - source_nodes: - - GO:0005575 ## cellular_component - CellType: - reachable_from: - source_ontology: obo:cl - source_nodes: - - CL:0000000 ## cell \ No newline at end of file diff --git a/src/ontogpt/templates/halo.py b/src/ontogpt/templates/halo.py deleted file mode 100644 index 505a08053..000000000 --- a/src/ontogpt/templates/halo.py +++ /dev/null @@ -1,171 +0,0 @@ -from __future__ import annotations -from datetime import datetime, date -from enum import Enum -from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, ConfigDict, Field, field_validator -import re -import sys -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal - - -metamodel_version = "None" -version = "None" - -class ConfiguredBaseModel(BaseModel): - model_config = ConfigDict( - validate_assignment=True, - validate_default=True, - extra = 'forbid', - arbitrary_types_allowed=True, - use_enum_values = True) - - -class NullDataOptions(str, Enum): - - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = "UNSPECIFIED_METHOD_OF_ADMINISTRATION" - - NOT_APPLICABLE = "NOT_APPLICABLE" - - NOT_MENTIONED = "NOT_MENTIONED" - - - -class Ontology(ConfiguredBaseModel): - - elements: Optional[List[OntologyElement]] = Field(default_factory=list) - - - -class OntologyElement(ConfiguredBaseModel): - - name: str = Field(..., description="""the name of the entity""") - context: Optional[str] = Field(None, description="""the ontology to which this belongs (single-valued)""") - description: Optional[str] = Field(None, description="""a textual description of the entity (single-valued)""") - synonyms: Optional[List[str]] = Field(default_factory=list, description="""a list of alternative names of the entity""") - categories: Optional[List[str]] = Field(default_factory=list, description="""a list of the categories to which this entity belongs""") - subclass_of: Optional[List[str]] = Field(default_factory=list, description="""a list of parent class (superclasses) of this entity""") - part_of: Optional[List[str]] = Field(default_factory=list, description="""a list of things this element is part of""") - subtypes: Optional[List[str]] = Field(default_factory=list, description="""a list of child classes (subclasses) of this entity""") - parts: Optional[List[str]] = Field(default_factory=list, description="""a list of names of things this element has as parts (components)""") - equivalent_to: Optional[str] = Field(None, description="""an OWL class expression with the necessary and sufficient conditions for this entity to be an instance of this class""") - - - -class Category(OntologyElement): - - name: str = Field(..., description="""the name of the entity""") - context: Optional[str] = Field(None, description="""the ontology to which this belongs (single-valued)""") - description: Optional[str] = Field(None, description="""a textual description of the entity (single-valued)""") - synonyms: Optional[List[str]] = Field(default_factory=list, description="""a list of alternative names of the entity""") - categories: Optional[List[str]] = Field(default_factory=list, description="""a list of the categories to which this entity belongs""") - subclass_of: Optional[List[str]] = Field(default_factory=list, description="""a list of parent class (superclasses) of this entity""") - part_of: Optional[List[str]] = Field(default_factory=list, description="""a list of things this element is part of""") - subtypes: Optional[List[str]] = Field(default_factory=list, description="""a list of child classes (subclasses) of this entity""") - parts: Optional[List[str]] = Field(default_factory=list, description="""a list of names of things this element has as parts (components)""") - equivalent_to: Optional[str] = Field(None, description="""an OWL class expression with the necessary and sufficient conditions for this entity to be an instance of this class""") - - - -class ExtractionResult(ConfiguredBaseModel): - """ - A result of extracting knowledge on text - """ - input_id: Optional[str] = Field(None) - input_title: Optional[str] = Field(None) - input_text: Optional[str] = Field(None) - raw_completion_output: Optional[str] = Field(None) - prompt: Optional[str] = Field(None) - extracted_object: Optional[Any] = Field(None, description="""The complex objects extracted from the text""") - named_entities: Optional[List[Any]] = Field(default_factory=list, description="""Named entities extracted from the text""") - - - -class NamedEntity(ConfiguredBaseModel): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class CompoundExpression(ConfiguredBaseModel): - - None - - - -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - subject: Optional[str] = Field(None) - predicate: Optional[str] = Field(None) - object: Optional[str] = Field(None) - qualifier: Optional[str] = Field(None, description="""A qualifier for the statements, e.g. \"NOT\" for negation""") - subject_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"""") - object_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"""") - - - -class TextWithTriples(ConfiguredBaseModel): - """ - A text containing one or more relations of the Triple type. - """ - publication: Optional[Publication] = Field(None) - triples: Optional[List[Triple]] = Field(default_factory=list) - - - -class TextWithEntity(ConfiguredBaseModel): - """ - A text containing one or more instances of a single type of entity. - """ - publication: Optional[Publication] = Field(None) - entities: Optional[List[str]] = Field(default_factory=list) - - - -class RelationshipType(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Publication(ConfiguredBaseModel): - - id: Optional[str] = Field(None, description="""The publication identifier""") - title: Optional[str] = Field(None, description="""The title of the publication""") - abstract: Optional[str] = Field(None, description="""The abstract of the publication""") - combined_text: Optional[str] = Field(None) - full_text: Optional[str] = Field(None, description="""The full text of the publication""") - - - -class AnnotatorResult(ConfiguredBaseModel): - - subject_text: Optional[str] = Field(None) - object_id: Optional[str] = Field(None) - object_text: Optional[str] = Field(None) - - - - -# Model rebuild -# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model -Ontology.model_rebuild() -OntologyElement.model_rebuild() -Category.model_rebuild() -ExtractionResult.model_rebuild() -NamedEntity.model_rebuild() -CompoundExpression.model_rebuild() -Triple.model_rebuild() -TextWithTriples.model_rebuild() -TextWithEntity.model_rebuild() -RelationshipType.model_rebuild() -Publication.model_rebuild() -AnnotatorResult.model_rebuild() - diff --git a/src/ontogpt/templates/halo.yaml b/src/ontogpt/templates/halo.yaml deleted file mode 100644 index ccdd66649..000000000 --- a/src/ontogpt/templates/halo.yaml +++ /dev/null @@ -1,81 +0,0 @@ -id: https://w3id.org/ontogpt/halo -name: ontology-class -title: Ontology Class Template -description: >- - A template for Ontology Classes -license: https://creativecommons.org/publicdomain/zero/1.0/ -prefixes: - linkml: https://w3id.org/linkml/ - oc: http://w3id.org/ontogpt/ontology-class-template - BFO: http://purl.obolibrary.org/obo/BFO_ - -default_prefix: oc -default_range: string - -imports: - - linkml:types - - core - -classes: - Ontology: - attributes: - elements: - range: OntologyElement - multivalued: true - inlined: true - inlined_as_list: true - - OntologyElement: - attributes: - name: - identifier: true - description: the name of the entity - context: - description: the ontology to which this belongs (single-valued) - description: - description: a textual description of the entity (single-valued) - synonyms: - description: a list of alternative names of the entity - multivalued: true - categories: - description: a list of the categories to which this entity belongs - range: Category - multivalued: true - subclass_of: - range: OntologyElement - description: a list of parent class (superclasses) of this entity - multivalued: true - slot_uri: rdfs:subClassOf - part_of: - range: OntologyElement - multivalued: true - slot_uri: BFO:0000050 - description: a list of things this element is part of - subtypes: - range: OntologyElement - multivalued: true - inverse: subclass_of - description: a list of child classes (subclasses) of this entity - parts: - range: OntologyElement - multivalued: true - inverse: part_of - description: a list of names of things this element has as parts (components) - equivalent_to: - description: an OWL class expression with the necessary and sufficient conditions for this entity to be an instance of this class - range: string - - Category: - is_a: OntologyElement - -slots: - subclass_of: - range: OntologyElement - description: a list of parent class (superclasses) of this entity - multivalued: true - slot_uri: rdfs:subClassOf - part_of: - range: OntologyElement - multivalued: true - slot_uri: BFO:0000050 - description: a list of things this element is part of \ No newline at end of file diff --git a/src/ontogpt/templates/human_phenotype.py b/src/ontogpt/templates/human_phenotype.py deleted file mode 100644 index 3170dad2e..000000000 --- a/src/ontogpt/templates/human_phenotype.py +++ /dev/null @@ -1,149 +0,0 @@ -from __future__ import annotations -from datetime import datetime, date -from enum import Enum -from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, ConfigDict, Field, field_validator -import re -import sys -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal - - -metamodel_version = "None" -version = "None" - -class ConfiguredBaseModel(BaseModel): - model_config = ConfigDict( - validate_assignment=True, - validate_default=True, - extra = 'forbid', - arbitrary_types_allowed=True, - use_enum_values = True) - - -class NullDataOptions(str, Enum): - - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = "UNSPECIFIED_METHOD_OF_ADMINISTRATION" - - NOT_APPLICABLE = "NOT_APPLICABLE" - - NOT_MENTIONED = "NOT_MENTIONED" - - - -class ExtractionResult(ConfiguredBaseModel): - """ - A result of extracting knowledge on text - """ - input_id: Optional[str] = Field(None) - input_title: Optional[str] = Field(None) - input_text: Optional[str] = Field(None) - raw_completion_output: Optional[str] = Field(None) - prompt: Optional[str] = Field(None) - extracted_object: Optional[Any] = Field(None, description="""The complex objects extracted from the text""") - named_entities: Optional[List[Any]] = Field(default_factory=list, description="""Named entities extracted from the text""") - - - -class NamedEntity(ConfiguredBaseModel): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class HumanPhenotypeSet(NamedEntity): - - phenotypes: Optional[List[str]] = Field(default_factory=list, description="""A semicolon-separated list of human phenotypes, including symptoms of disease. It must be semicolon-separated. Labels containing the word 'with' should be split into multiple phenotypes.""") - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class HumanPhenotype(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class CompoundExpression(ConfiguredBaseModel): - - None - - - -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - subject: Optional[str] = Field(None) - predicate: Optional[str] = Field(None) - object: Optional[str] = Field(None) - qualifier: Optional[str] = Field(None, description="""A qualifier for the statements, e.g. \"NOT\" for negation""") - subject_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"""") - object_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"""") - - - -class TextWithTriples(ConfiguredBaseModel): - """ - A text containing one or more relations of the Triple type. - """ - publication: Optional[Publication] = Field(None) - triples: Optional[List[Triple]] = Field(default_factory=list) - - - -class TextWithEntity(ConfiguredBaseModel): - """ - A text containing one or more instances of a single type of entity. - """ - publication: Optional[Publication] = Field(None) - entities: Optional[List[str]] = Field(default_factory=list) - - - -class RelationshipType(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Publication(ConfiguredBaseModel): - - id: Optional[str] = Field(None, description="""The publication identifier""") - title: Optional[str] = Field(None, description="""The title of the publication""") - abstract: Optional[str] = Field(None, description="""The abstract of the publication""") - combined_text: Optional[str] = Field(None) - full_text: Optional[str] = Field(None, description="""The full text of the publication""") - - - -class AnnotatorResult(ConfiguredBaseModel): - - subject_text: Optional[str] = Field(None) - object_id: Optional[str] = Field(None) - object_text: Optional[str] = Field(None) - - - - -# Model rebuild -# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model -ExtractionResult.model_rebuild() -NamedEntity.model_rebuild() -HumanPhenotypeSet.model_rebuild() -HumanPhenotype.model_rebuild() -CompoundExpression.model_rebuild() -Triple.model_rebuild() -TextWithTriples.model_rebuild() -TextWithEntity.model_rebuild() -RelationshipType.model_rebuild() -Publication.model_rebuild() -AnnotatorResult.model_rebuild() - diff --git a/src/ontogpt/templates/human_phenotype.yaml b/src/ontogpt/templates/human_phenotype.yaml deleted file mode 100644 index 7035d74fb..000000000 --- a/src/ontogpt/templates/human_phenotype.yaml +++ /dev/null @@ -1,40 +0,0 @@ -id: http://w3id.org/ontogpt/human_phenotype -name: human_phenotype-template -title: Human Phenotype Extraction Template -description: >- - A template for extracting human phenotypes to HPO terms -license: https://creativecommons.org/publicdomain/zero/1.0/ -prefixes: - linkml: https://w3id.org/linkml/ - human_phenotype: http://w3id.org/ontogpt/human_phenotype - HP: http://purl.obolibrary.org/obo/HP_ - -default_prefix: human_phenotype -default_range: string - -imports: - - linkml:types - - core - -classes: - HumanPhenotypeSet: - tree_root: true - is_a: NamedEntity - attributes: - phenotypes: - range: HumanPhenotype - multivalued: true - description: >- - A semicolon-separated list of human phenotypes, including symptoms of disease. - It must be semicolon-separated. - Labels containing the word 'with' should be split into multiple phenotypes. - - HumanPhenotype: - is_a: NamedEntity - id_prefixes: - - HP - annotations: - annotators: sqlite:obo:hp, sqlite:obo:mondo, sqlite:obo:mesh, sqlite:obo:ncit - prompt: >- - the name of a human phenotype or symptom. - Examples are ascites, fever, pain, seizure, increased intracranial pressure, lactic acidosis. diff --git a/src/ontogpt/templates/ibd.py b/src/ontogpt/templates/ibd.py deleted file mode 100644 index c3f18f7d1..000000000 --- a/src/ontogpt/templates/ibd.py +++ /dev/null @@ -1,262 +0,0 @@ -from __future__ import annotations -from datetime import datetime, date -from enum import Enum -from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, ConfigDict, Field, field_validator -import re -import sys -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal - - -metamodel_version = "None" -version = "None" - -class ConfiguredBaseModel(BaseModel): - model_config = ConfigDict( - validate_assignment=True, - validate_default=True, - extra = 'forbid', - arbitrary_types_allowed=True, - use_enum_values = True) - - -class GeneLocationEnum(str): - - - dummy = "dummy" - - -class GOCellComponentType(str): - - - dummy = "dummy" - - -class CellType(str): - - - dummy = "dummy" - - -class NullDataOptions(str, Enum): - - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = "UNSPECIFIED_METHOD_OF_ADMINISTRATION" - - NOT_APPLICABLE = "NOT_APPLICABLE" - - NOT_MENTIONED = "NOT_MENTIONED" - - - -class IBDAnnotations(ConfiguredBaseModel): - - genes: Optional[List[str]] = Field(default_factory=list, description="""semicolon-separated list of genes""") - organisms: Optional[List[str]] = Field(default_factory=list, description="""semicolon-separated list of organism taxons""") - gene_organisms: Optional[List[GeneOrganismRelationship]] = Field(default_factory=list) - activities: Optional[List[str]] = Field(default_factory=list, description="""semicolon-separated list of molecular activities""") - gene_functions: Optional[List[GeneMolecularActivityRelationship]] = Field(default_factory=list, description="""semicolon-separated list of gene to molecular activity relationships""") - cellular_processes: Optional[List[str]] = Field(default_factory=list, description="""semicolon-separated list of cellular processes""") - pathways: Optional[List[str]] = Field(default_factory=list, description="""semicolon-separated list of pathways""") - gene_gene_interactions: Optional[List[GeneGeneInteraction]] = Field(default_factory=list, description="""semicolon-separated list of gene to gene interactions""") - gene_localizations: Optional[List[GeneSubcellularLocalizationRelationship]] = Field(default_factory=list, description="""semicolon-separated list of genes plus their location in the cell; for example, \"gene1 / cytoplasm; gene2 / mitochondrion\"""") - - - -class ExtractionResult(ConfiguredBaseModel): - """ - A result of extracting knowledge on text - """ - input_id: Optional[str] = Field(None) - input_title: Optional[str] = Field(None) - input_text: Optional[str] = Field(None) - raw_completion_output: Optional[str] = Field(None) - prompt: Optional[str] = Field(None) - extracted_object: Optional[Any] = Field(None, description="""The complex objects extracted from the text""") - named_entities: Optional[List[Any]] = Field(default_factory=list, description="""Named entities extracted from the text""") - - - -class NamedEntity(ConfiguredBaseModel): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Gene(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Pathway(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class CellularProcess(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class MolecularActivity(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class GeneLocation(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Organism(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Molecule(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class CompoundExpression(ConfiguredBaseModel): - - None - - - -class GeneOrganismRelationship(CompoundExpression): - - gene: Optional[str] = Field(None) - organism: Optional[str] = Field(None) - - - -class GeneMolecularActivityRelationship(CompoundExpression): - - gene: Optional[str] = Field(None) - molecular_activity: Optional[str] = Field(None) - - - -class GeneMolecularActivityRelationship2(CompoundExpression): - - gene: Optional[str] = Field(None) - molecular_activity: Optional[str] = Field(None) - target: Optional[str] = Field(None) - - - -class GeneSubcellularLocalizationRelationship(CompoundExpression): - - gene: Optional[str] = Field(None) - location: Optional[str] = Field(None) - - - -class GeneGeneInteraction(CompoundExpression): - - gene1: Optional[str] = Field(None) - gene2: Optional[str] = Field(None) - - - -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - subject: Optional[str] = Field(None) - predicate: Optional[str] = Field(None) - object: Optional[str] = Field(None) - qualifier: Optional[str] = Field(None, description="""A qualifier for the statements, e.g. \"NOT\" for negation""") - subject_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"""") - object_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"""") - - - -class TextWithTriples(ConfiguredBaseModel): - """ - A text containing one or more relations of the Triple type. - """ - publication: Optional[Publication] = Field(None) - triples: Optional[List[Triple]] = Field(default_factory=list) - - - -class TextWithEntity(ConfiguredBaseModel): - """ - A text containing one or more instances of a single type of entity. - """ - publication: Optional[Publication] = Field(None) - entities: Optional[List[str]] = Field(default_factory=list) - - - -class RelationshipType(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Publication(ConfiguredBaseModel): - - id: Optional[str] = Field(None, description="""The publication identifier""") - title: Optional[str] = Field(None, description="""The title of the publication""") - abstract: Optional[str] = Field(None, description="""The abstract of the publication""") - combined_text: Optional[str] = Field(None) - full_text: Optional[str] = Field(None, description="""The full text of the publication""") - - - -class AnnotatorResult(ConfiguredBaseModel): - - subject_text: Optional[str] = Field(None) - object_id: Optional[str] = Field(None) - object_text: Optional[str] = Field(None) - - - - -# Model rebuild -# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model -IBDAnnotations.model_rebuild() -ExtractionResult.model_rebuild() -NamedEntity.model_rebuild() -Gene.model_rebuild() -Pathway.model_rebuild() -CellularProcess.model_rebuild() -MolecularActivity.model_rebuild() -GeneLocation.model_rebuild() -Organism.model_rebuild() -Molecule.model_rebuild() -CompoundExpression.model_rebuild() -GeneOrganismRelationship.model_rebuild() -GeneMolecularActivityRelationship.model_rebuild() -GeneMolecularActivityRelationship2.model_rebuild() -GeneSubcellularLocalizationRelationship.model_rebuild() -GeneGeneInteraction.model_rebuild() -Triple.model_rebuild() -TextWithTriples.model_rebuild() -TextWithEntity.model_rebuild() -RelationshipType.model_rebuild() -Publication.model_rebuild() -AnnotatorResult.model_rebuild() - diff --git a/src/ontogpt/templates/ibd.yaml b/src/ontogpt/templates/ibd.yaml deleted file mode 100644 index 0b4d2482a..000000000 --- a/src/ontogpt/templates/ibd.yaml +++ /dev/null @@ -1,193 +0,0 @@ -id: http://w3id.org/ontogpt/gocam -name: gocam-template -title: GO-CAM Template -description: >- - A template for GO-CAMs -license: https://creativecommons.org/publicdomain/zero/1.0/ -prefixes: - linkml: https://w3id.org/linkml/ - gocam: http://w3id.org/ontogpt/gocam/ - GO: http://purl.obolibrary.org/obo/GO_ - CL: http://purl.obolibrary.org/obo/CL_ - -default_prefix: gocam -default_range: string - -imports: - - linkml:types - - core - -classes: - IBDAnnotations: - tree_root: true - attributes: - genes: - description: semicolon-separated list of genes - multivalued: true - range: Gene - organisms: - description: semicolon-separated list of organism taxons - multivalued: true - range: Organism - gene_organisms: - annotations: - prompt: semicolon-separated list of asterisk separated gene to organism relationships - multivalued: true - range: GeneOrganismRelationship - activities: - description: semicolon-separated list of molecular activities - multivalued: true - range: MolecularActivity - gene_functions: - description: semicolon-separated list of gene to molecular activity relationships - multivalued: true - range: GeneMolecularActivityRelationship - cellular_processes: - description: semicolon-separated list of cellular processes - multivalued: true - range: CellularProcess - pathways: - description: semicolon-separated list of pathways - multivalued: true - range: Pathway - gene_gene_interactions: - description: semicolon-separated list of gene to gene interactions - multivalued: true - range: GeneGeneInteraction - gene_localizations: - description: >- - semicolon-separated list of genes plus their location in the cell; - for example, "gene1 / cytoplasm; gene2 / mitochondrion" - multivalued: true - range: GeneSubcellularLocalizationRelationship - - Gene: - is_a: NamedEntity - id_prefixes: - - HGNC - - PR - - UniProtKB - annotations: - annotators: gilda:, bioportal:hgnc-nr - Pathway: - is_a: NamedEntity - id_prefixes: - - GO - - PW - annotations: - annotators: sqlite:obo:go, sqlite:obo:pw - CellularProcess: - is_a: NamedEntity - id_prefixes: - - GO - annotations: - annotators: sqlite:obo:go - MolecularActivity: - is_a: NamedEntity - id_prefixes: - - GO - annotations: - annotators: sqlite:obo:go - GeneLocation: - is_a: NamedEntity - id_prefixes: - - GO - - CL - - UBERON - annotations: - annotators: "sqlite:obo:go, sqlite:obo:cl" - slot_usage: - id: - values_from: - - GOCellComponentType - - CellType - Organism: - is_a: NamedEntity - id_prefixes: - - NCBITaxon - - EFO - annotations: - annotators: gilda:, sqlite:obo:ncbitaxon - Molecule: - is_a: NamedEntity - id_prefixes: - - CHEBI - - PR - annotations: - annotators: gilda:, sqlite:obo:chebi - - GeneOrganismRelationship: - is_a: CompoundExpression - attributes: - gene: - range: Gene - organism: - range: Organism - - GeneMolecularActivityRelationship: - is_a: CompoundExpression - attributes: - gene: - range: Gene - annotations: - prompt: the name of the gene in the pair. This comes first. - molecular_activity: - range: MolecularActivity - annotations: - prompt: the name of the molecular function in the pair. This comes second. May be a GO term. - annotations: - prompt.example: |- - TODO - - gene: HGNC:1234 - molecular_activity: GO:0003674 - - GeneMolecularActivityRelationship2: - is_a: CompoundExpression - attributes: - gene: - range: Gene - annotations: - prompt: the name of the gene. - molecular_activity: - range: MolecularActivity - annotations: - prompt: the name of the molecular activity, for example, ubiquitination. May be a GO term. - target: - range: Molecule - annotations: - prompt: the name of the molecular entity that is the target of the molecular activity. - - GeneSubcellularLocalizationRelationship: - is_a: CompoundExpression - attributes: - gene: - range: Gene - location: - range: GeneLocation - - GeneGeneInteraction: - is_a: CompoundExpression - attributes: - gene1: - range: Gene - gene2: - range: Gene - -enums: - - GeneLocationEnum: - inherits: - - GOCellComponent - - CellType - - GOCellComponentType: - reachable_from: - source_ontology: obo:go - source_nodes: - - GO:0005575 ## cellular_component - CellType: - reachable_from: - source_ontology: obo:cl - source_nodes: - - CL:0000000 ## cell \ No newline at end of file diff --git a/src/ontogpt/templates/ibd_literature.py b/src/ontogpt/templates/ibd_literature.py deleted file mode 100644 index 2a54f0e32..000000000 --- a/src/ontogpt/templates/ibd_literature.py +++ /dev/null @@ -1,214 +0,0 @@ -from __future__ import annotations -from datetime import datetime, date -from enum import Enum -from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, ConfigDict, Field, field_validator -import re -import sys -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal - - -metamodel_version = "None" -version = "None" - -class ConfiguredBaseModel(BaseModel): - model_config = ConfigDict( - validate_assignment=True, - validate_default=True, - extra = 'forbid', - arbitrary_types_allowed=True, - use_enum_values = True) - - -class NullDataOptions(str, Enum): - - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = "UNSPECIFIED_METHOD_OF_ADMINISTRATION" - - NOT_APPLICABLE = "NOT_APPLICABLE" - - NOT_MENTIONED = "NOT_MENTIONED" - - - -class IBDAnnotations(ConfiguredBaseModel): - - genes: Optional[List[str]] = Field(default_factory=list, description="""semicolon-separated list of genes""") - exposures: Optional[List[str]] = Field(default_factory=list, description="""semicolon-separated list of exposures""") - gene_exposures_relationships: Optional[List[GeneExposureRelationship]] = Field(default_factory=list, description="""semicolon-separated list of gene to molecular activity relationships""") - diseases: Optional[List[str]] = Field(default_factory=list, description="""semicolon-separated list of diseases""") - cellular_process: Optional[List[str]] = Field(default_factory=list, description="""semicolon-separated list of cellular processes""") - disease_cellular_process_relationships: Optional[List[DiseaseCellularProcessRelationship]] = Field(default_factory=list, description="""semicolon-separated list of disease to cellular process relationships""") - - - -class ExtractionResult(ConfiguredBaseModel): - """ - A result of extracting knowledge on text - """ - input_id: Optional[str] = Field(None) - input_title: Optional[str] = Field(None) - input_text: Optional[str] = Field(None) - raw_completion_output: Optional[str] = Field(None) - prompt: Optional[str] = Field(None) - extracted_object: Optional[Any] = Field(None, description="""The complex objects extracted from the text""") - named_entities: Optional[List[Any]] = Field(default_factory=list, description="""Named entities extracted from the text""") - - - -class NamedEntity(ConfiguredBaseModel): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Gene(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class ChemicalExposure(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class ChemicalExposureToGenePredicate(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Disease(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class CellularProcess(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class DiseaseToCellularProcessPredicate(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class CompoundExpression(ConfiguredBaseModel): - - None - - - -class GeneExposureRelationship(CompoundExpression): - - subject: Optional[str] = Field(None, description="""The name of the exposure, such as a exposure to a chemical toxin.""") - predicate: Optional[str] = Field(None, description="""The name of the type of relationship between a chemical exposure and a gene.""") - object: Optional[str] = Field(None, description="""The name of the gene in the pair. This comes second in the pair.""") - subject_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the chemical exposure.""") - object_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the gene.""") - - - -class DiseaseCellularProcessRelationship(CompoundExpression): - - subject: Optional[str] = Field(None, description="""The name of the disease.""") - predicate: Optional[str] = Field(None, description="""The name of the type of relationship between a disease and a cellular process.""") - object: Optional[str] = Field(None, description="""The name of the cellular process.""") - subject_qualifier: Optional[str] = Field(None) - object_qualifier: Optional[str] = Field(None) - - - -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - subject: Optional[str] = Field(None) - predicate: Optional[str] = Field(None) - object: Optional[str] = Field(None) - qualifier: Optional[str] = Field(None, description="""A qualifier for the statements, e.g. \"NOT\" for negation""") - subject_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"""") - object_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"""") - - - -class TextWithTriples(ConfiguredBaseModel): - """ - A text containing one or more relations of the Triple type. - """ - publication: Optional[Publication] = Field(None) - triples: Optional[List[Triple]] = Field(default_factory=list) - - - -class TextWithEntity(ConfiguredBaseModel): - """ - A text containing one or more instances of a single type of entity. - """ - publication: Optional[Publication] = Field(None) - entities: Optional[List[str]] = Field(default_factory=list) - - - -class RelationshipType(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Publication(ConfiguredBaseModel): - - id: Optional[str] = Field(None, description="""The publication identifier""") - title: Optional[str] = Field(None, description="""The title of the publication""") - abstract: Optional[str] = Field(None, description="""The abstract of the publication""") - combined_text: Optional[str] = Field(None) - full_text: Optional[str] = Field(None, description="""The full text of the publication""") - - - -class AnnotatorResult(ConfiguredBaseModel): - - subject_text: Optional[str] = Field(None) - object_id: Optional[str] = Field(None) - object_text: Optional[str] = Field(None) - - - - -# Model rebuild -# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model -IBDAnnotations.model_rebuild() -ExtractionResult.model_rebuild() -NamedEntity.model_rebuild() -Gene.model_rebuild() -ChemicalExposure.model_rebuild() -ChemicalExposureToGenePredicate.model_rebuild() -Disease.model_rebuild() -CellularProcess.model_rebuild() -DiseaseToCellularProcessPredicate.model_rebuild() -CompoundExpression.model_rebuild() -GeneExposureRelationship.model_rebuild() -DiseaseCellularProcessRelationship.model_rebuild() -Triple.model_rebuild() -TextWithTriples.model_rebuild() -TextWithEntity.model_rebuild() -RelationshipType.model_rebuild() -Publication.model_rebuild() -AnnotatorResult.model_rebuild() - diff --git a/src/ontogpt/templates/ibd_literature.yaml b/src/ontogpt/templates/ibd_literature.yaml deleted file mode 100644 index fc4966348..000000000 --- a/src/ontogpt/templates/ibd_literature.yaml +++ /dev/null @@ -1,157 +0,0 @@ -id: http://w3id.org/ontogpt/ibd_literature -name: ibd-literature-template -title: IBD Literature Template -description: >- - A template for extracting information from IBD literature -license: https://creativecommons.org/publicdomain/zero/1.0/ -prefixes: - CHEBI: http://purl.obolibrary.org/obo/CHEBI_ - ECTO: http://purl.obolibrary.org/obo/ECTO_ - ExO: http://purl.obolibrary.org/obo/ExO_ - HGNC: http://identifiers.org/hgnc/ - NCIT: http://purl.obolibrary.org/obo/NCIT_ - MONDO: http://purl.obolibrary.org/obo/MONDO_ - GO: http://purl.obolibrary.org/obo/GO_ - core: http://w3id.org/ontogpt/core/ - ibdlit: http://w3id.org/ontogpt/ibd_literature/ - linkml: https://w3id.org/linkml/ - -default_prefix: ibdlit -default_range: string - -imports: - - linkml:types - - core - -classes: - IBDAnnotations: - tree_root: true - attributes: - genes: - description: semicolon-separated list of genes - multivalued: true - range: Gene - exposures: - description: semicolon-separated list of exposures - annotations: - # prompt.example - prompt: a chemical or molecule whose direct or indirect effects cause one or more entities to experience biological change - multivalued: true - range: ChemicalExposure - gene_exposures_relationships: - description: semicolon-separated list of gene to molecular activity relationships - multivalued: true - range: GeneExposureRelationship - diseases: - description: semicolon-separated list of diseases - multivalued: true - range: Disease - cellular_process: - description: semicolon-separated list of cellular processes - multivalued: true - range: CellularProcess - disease_cellular_process_relationships: - description: semicolon-separated list of disease to cellular process relationships - multivalued: true - range: DiseaseCellularProcessRelationship - - Gene: - is_a: NamedEntity - id_prefixes: - - HGNC - annotations: - annotators: sqlite:obo:hgnc, sqlite:obo:pr - prompt: the name of the gene in the pair. This comes second in the pair. - - ChemicalExposure: - is_a: NamedEntity - id_prefixes: - - CHEBI - - ECTO - - ExO - - NCIT - annotations: - annotators: sqlite:obo:ecto, sqlite:obo:chebi - prompt: the name of the exposure, such as a exposure to a chemical toxin. For example, CHEBI:17968 butyrate. - - ChemicalExposureToGenePredicate: - # is_a: RelationshipType - is_a: NamedEntity - id_prefixes: - - RO - annotations: - annotators: sqlite:obo:ro - prompt: the name of the type of relationship between a chemical exposure and a gene. - - GeneExposureRelationship: - # is_a: Triple - is_a: CompoundExpression - attributes: - # slot_usage: - subject: - range: ChemicalExposure - description: >- - The name of the exposure, such as a exposure to a chemical toxin. - predicate: - range: ChemicalExposureToGenePredicate - description: >- - The name of the type of relationship between a chemical exposure and a gene. - object: - range: Gene - description: >- - The name of the gene in the pair. This comes second in the pair. - subject_qualifier: - range: NamedEntity - description: >- - An optional qualifier or modifier for the chemical exposure. - object_qualifier: - range: NamedEntity - description: >- - An optional qualifier or modifier for the gene. - - Disease: - is_a: NamedEntity - id_prefixes: - - MONDO - annotations: - annotators: sqlite:obo:mondo - prompt: the name of the disease - - CellularProcess: - is_a: NamedEntity - id_prefixes: - - GO - annotations: - annotators: sqlite:obo:go - prompt: the name of the cellular process - - DiseaseToCellularProcessPredicate: - # is_a: RelationshipType - is_a: NamedEntity - id_prefixes: - - RO - annotations: - annotators: sqlite:obo:ro - prompt: the name of the type of relationship between a disease and a cellular process. - - DiseaseCellularProcessRelationship: - # is_a: Triple - is_a: CompoundExpression - attributes: - # slot_usage: - subject: - range: Disease - description: >- - The name of the disease. - predicate: - range: DiseaseToCellularProcessPredicate - description: >- - The name of the type of relationship between a disease and a cellular process. - object: - range: CellularProcess - description: >- - The name of the cellular process. - subject_qualifier: - range: NamedEntity - object_qualifier: - range: NamedEntity \ No newline at end of file diff --git a/src/ontogpt/templates/kidney.py b/src/ontogpt/templates/kidney.py deleted file mode 100644 index d56fade94..000000000 --- a/src/ontogpt/templates/kidney.py +++ /dev/null @@ -1,156 +0,0 @@ -from __future__ import annotations -from datetime import datetime, date -from enum import Enum -from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, ConfigDict, Field, field_validator -import re -import sys -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal - - -metamodel_version = "None" -version = "None" - -class ConfiguredBaseModel(BaseModel): - model_config = ConfigDict( - validate_assignment=True, - validate_default=True, - extra = 'forbid', - arbitrary_types_allowed=True, - use_enum_values = True) - - -class NullDataOptions(str, Enum): - - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = "UNSPECIFIED_METHOD_OF_ADMINISTRATION" - - NOT_APPLICABLE = "NOT_APPLICABLE" - - NOT_MENTIONED = "NOT_MENTIONED" - - - -class KidneyAnnotations(ConfiguredBaseModel): - - cell_type: Optional[List[str]] = Field(default_factory=list) - gene: Optional[List[str]] = Field(default_factory=list, description="""A gene""") - - - -class ExtractionResult(ConfiguredBaseModel): - """ - A result of extracting knowledge on text - """ - input_id: Optional[str] = Field(None) - input_title: Optional[str] = Field(None) - input_text: Optional[str] = Field(None) - raw_completion_output: Optional[str] = Field(None) - prompt: Optional[str] = Field(None) - extracted_object: Optional[Any] = Field(None, description="""The complex objects extracted from the text""") - named_entities: Optional[List[Any]] = Field(default_factory=list, description="""Named entities extracted from the text""") - - - -class NamedEntity(ConfiguredBaseModel): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class CellType(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Gene(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class CompoundExpression(ConfiguredBaseModel): - - None - - - -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - subject: Optional[str] = Field(None) - predicate: Optional[str] = Field(None) - object: Optional[str] = Field(None) - qualifier: Optional[str] = Field(None, description="""A qualifier for the statements, e.g. \"NOT\" for negation""") - subject_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"""") - object_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"""") - - - -class TextWithTriples(ConfiguredBaseModel): - """ - A text containing one or more relations of the Triple type. - """ - publication: Optional[Publication] = Field(None) - triples: Optional[List[Triple]] = Field(default_factory=list) - - - -class TextWithEntity(ConfiguredBaseModel): - """ - A text containing one or more instances of a single type of entity. - """ - publication: Optional[Publication] = Field(None) - entities: Optional[List[str]] = Field(default_factory=list) - - - -class RelationshipType(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Publication(ConfiguredBaseModel): - - id: Optional[str] = Field(None, description="""The publication identifier""") - title: Optional[str] = Field(None, description="""The title of the publication""") - abstract: Optional[str] = Field(None, description="""The abstract of the publication""") - combined_text: Optional[str] = Field(None) - full_text: Optional[str] = Field(None, description="""The full text of the publication""") - - - -class AnnotatorResult(ConfiguredBaseModel): - - subject_text: Optional[str] = Field(None) - object_id: Optional[str] = Field(None) - object_text: Optional[str] = Field(None) - - - - -# Model rebuild -# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model -KidneyAnnotations.model_rebuild() -ExtractionResult.model_rebuild() -NamedEntity.model_rebuild() -CellType.model_rebuild() -Gene.model_rebuild() -CompoundExpression.model_rebuild() -Triple.model_rebuild() -TextWithTriples.model_rebuild() -TextWithEntity.model_rebuild() -RelationshipType.model_rebuild() -Publication.model_rebuild() -AnnotatorResult.model_rebuild() - diff --git a/src/ontogpt/templates/kidney.yaml b/src/ontogpt/templates/kidney.yaml deleted file mode 100644 index 73b5693dd..000000000 --- a/src/ontogpt/templates/kidney.yaml +++ /dev/null @@ -1,46 +0,0 @@ -id: https://w3id.org/ontogpt/biological_process -name: kidney-template -title: kidney-template -description: >- - A template for extracting kidney info from literature -license: https://creativecommons.org/publicdomain/zero/1.0/ -prefixes: - linkml: https://w3id.org/linkml/ - kidney: http://w3id.org/ontogpt/kidney-template - -default_prefix: kidney -default_range: string - -imports: - - linkml:types - - core - -classes: - KidneyAnnotations: - tree_root: true - attributes: - cell_type: - range: CellType - multivalued: true - gene: - description: >- - A gene - range: Gene - multivalued: true - CellType: - is_a: NamedEntity - id_prefixes: - - CL - - UBERON - annotations: - annotators: sqlite:obo:cl, sqlite:obo:uberon - prompt.examples: | - tubule epithelial cell, macula densa cell, glomerular endothelial cell, - podocyte, mesangial cell, parietal epithelial cell - - Gene: - is_a: NamedEntity - id_prefixes: - - HGNC - annotations: - annotators: sqlite:obo:hgnc diff --git a/src/ontogpt/templates/maxo.py b/src/ontogpt/templates/maxo.py deleted file mode 100644 index f803d26c1..000000000 --- a/src/ontogpt/templates/maxo.py +++ /dev/null @@ -1,203 +0,0 @@ -from __future__ import annotations -from datetime import datetime, date -from enum import Enum -from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, ConfigDict, Field, field_validator -import re -import sys -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal - - -metamodel_version = "None" -version = "None" - -class ConfiguredBaseModel(BaseModel): - model_config = ConfigDict( - validate_assignment=True, - validate_default=True, - extra = 'forbid', - arbitrary_types_allowed=True, - use_enum_values = True) - - -class NullDataOptions(str, Enum): - - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = "UNSPECIFIED_METHOD_OF_ADMINISTRATION" - - NOT_APPLICABLE = "NOT_APPLICABLE" - - NOT_MENTIONED = "NOT_MENTIONED" - - - -class ExtractionResult(ConfiguredBaseModel): - """ - A result of extracting knowledge on text - """ - input_id: Optional[str] = Field(None) - input_title: Optional[str] = Field(None) - input_text: Optional[str] = Field(None) - raw_completion_output: Optional[str] = Field(None) - prompt: Optional[str] = Field(None) - extracted_object: Optional[Any] = Field(None, description="""The complex objects extracted from the text""") - named_entities: Optional[List[Any]] = Field(default_factory=list, description="""Named entities extracted from the text""") - - - -class NamedEntity(ConfiguredBaseModel): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Action(NamedEntity): - """ - A clinically prescribed procedure, therapy, intervention, or recommendation. - """ - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Disease(NamedEntity): - """ - A disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. - """ - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Symptom(NamedEntity): - """ - A condition or phenotype resulting from an abnormal health state. - """ - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class CompoundExpression(ConfiguredBaseModel): - - None - - - -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - subject: Optional[str] = Field(None) - predicate: Optional[str] = Field(None) - object: Optional[str] = Field(None) - qualifier: Optional[str] = Field(None, description="""A qualifier for the statements, e.g. \"NOT\" for negation""") - subject_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"""") - object_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"""") - - - -class ActionToDiseaseRelationship(Triple): - """ - A triple representing a relationship between a medical action (A clinically prescribed procedure, therapy, intervention, or recommendation) and a disease, for example, radiation therapy TREATS cancer, or PET scan IS USED TO DIAGNOSE myocarditis. - """ - subject: Optional[str] = Field(None) - predicate: Optional[str] = Field(None, description="""The relationship type, usually TREATS or IS USED TO DIAGNOSE""") - object: Optional[List[str]] = Field(default_factory=list) - qualifier: Optional[str] = Field(None, description="""A qualifier for the statements, e.g. \"NOT\" for negation""") - subject_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the medical action.""") - object_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the disease.""") - - - -class ActionToSymptomRelationship(Triple): - """ - A triple representing a relationship between a medical action (A clinically prescribed procedure, therapy, intervention, or recommendation) and a symptom, for example, a chest X-ray IS USED TO DIAGNOSE pleural effusion. - """ - subject: Optional[str] = Field(None) - predicate: Optional[str] = Field(None, description="""The relationship type, usually IS USED TO DIAGNOSE""") - object: Optional[List[str]] = Field(default_factory=list) - qualifier: Optional[str] = Field(None, description="""A qualifier for the statements, e.g. \"NOT\" for negation""") - subject_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the medical action.""") - object_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the symptom.""") - - - -class TextWithTriples(ConfiguredBaseModel): - """ - A text containing one or more relations of the Triple type. - """ - publication: Optional[Publication] = Field(None) - triples: Optional[List[Triple]] = Field(default_factory=list) - - - -class MaxoAnnotations(TextWithTriples): - - action: Optional[List[str]] = Field(default_factory=list, description="""Semicolon-separated list of medical actions.""") - disease: Optional[List[str]] = Field(default_factory=list, description="""Semicolon-separated list of diseases.""") - symptom: Optional[List[str]] = Field(default_factory=list, description="""Semicolon-separated list of symptoms.""") - action_to_disease: Optional[List[ActionToDiseaseRelationship]] = Field(default_factory=list) - action_to_symptom: Optional[List[ActionToSymptomRelationship]] = Field(default_factory=list) - publication: Optional[Publication] = Field(None) - triples: Optional[List[Triple]] = Field(default_factory=list) - - - -class TextWithEntity(ConfiguredBaseModel): - """ - A text containing one or more instances of a single type of entity. - """ - publication: Optional[Publication] = Field(None) - entities: Optional[List[str]] = Field(default_factory=list) - - - -class RelationshipType(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Publication(ConfiguredBaseModel): - - id: Optional[str] = Field(None, description="""The publication identifier""") - title: Optional[str] = Field(None, description="""The title of the publication""") - abstract: Optional[str] = Field(None, description="""The abstract of the publication""") - combined_text: Optional[str] = Field(None) - full_text: Optional[str] = Field(None, description="""The full text of the publication""") - - - -class AnnotatorResult(ConfiguredBaseModel): - - subject_text: Optional[str] = Field(None) - object_id: Optional[str] = Field(None) - object_text: Optional[str] = Field(None) - - - - -# Model rebuild -# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model -ExtractionResult.model_rebuild() -NamedEntity.model_rebuild() -Action.model_rebuild() -Disease.model_rebuild() -Symptom.model_rebuild() -CompoundExpression.model_rebuild() -Triple.model_rebuild() -ActionToDiseaseRelationship.model_rebuild() -ActionToSymptomRelationship.model_rebuild() -TextWithTriples.model_rebuild() -MaxoAnnotations.model_rebuild() -TextWithEntity.model_rebuild() -RelationshipType.model_rebuild() -Publication.model_rebuild() -AnnotatorResult.model_rebuild() - diff --git a/src/ontogpt/templates/maxo.yaml b/src/ontogpt/templates/maxo.yaml deleted file mode 100644 index 944547db9..000000000 --- a/src/ontogpt/templates/maxo.yaml +++ /dev/null @@ -1,143 +0,0 @@ -id: http://w3id.org/ontogpt/maxo -name: maxo -title: Template for Medical Action Extraction -description: >- - A template for extracting relationships relevant to the - MAXO medical action ontology. -license: https://creativecommons.org/publicdomain/zero/1.0/ -prefixes: - linkml: https://w3id.org/linkml/ - maxo_extract: http://w3id.org/ontogpt/maxo - MAXO: http://purl.obolibrary.org/obo/MAXO_ - MONDO: http://purl.obolibrary.org/obo/MONDO_ - HP: http://purl.obolibrary.org/obo/HP_ - RO: http://purl.obolibrary.org/obo/RO_ - OBA: http://purl.obolibrary.org/obo/OBA_ - PATO: http://purl.obolibrary.org/obo/PATO_ - biolink: https://w3id.org/biolink/vocab/ - -default_prefix: maxo_extract -default_range: string - -imports: - - linkml:types - - core - -classes: - - MaxoAnnotations: - tree_root: true - is_a: TextWithTriples - attributes: - action: - annotations: - prompt: >- - Semicolon-separated list of medical actions, where each is a - clinically prescribed procedure, therapy, intervention, or recommendation. - description: Semicolon-separated list of medical actions. - multivalued: true - range: Action - disease: - description: Semicolon-separated list of diseases. - multivalued: true - range: Disease - symptom: - description: Semicolon-separated list of symptoms. - multivalued: true - range: Symptom - action_to_disease: - annotations: - prompt: >- - Semicolon-separated list of medical action to disease relationships, where - each is a triple representing a relationship between a medical action - and a disease, for example, radiation therapy TREATS cancer, - or PET scan IS USED TO DIAGNOSE myocarditis. - multivalued: true - range: ActionToDiseaseRelationship - action_to_symptom: - annotations: - prompt: >- - A triple representing a relationship between a medical action - (A clinically prescribed procedure, therapy, intervention, or recommendation) - and a symptom, for example, - a chest X-ray IS USED TO DIAGNOSE pleural effusion. - multivalued: true - range: ActionToSymptomRelationship - - ActionToDiseaseRelationship: - is_a: Triple - description: >- - A triple representing a relationship between a medical action - (A clinically prescribed procedure, therapy, intervention, or recommendation) - and a disease, for example, radiation therapy TREATS cancer, - or PET scan IS USED TO DIAGNOSE myocarditis. - slot_usage: - subject: - range: Action - object: - range: Disease - multivalued: true - predicate: - range: NamedEntity - description: The relationship type, usually TREATS or IS USED TO DIAGNOSE - subject_qualifier: - range: NamedEntity - description: >- - An optional qualifier or modifier for the medical action. - object_qualifier: - range: NamedEntity - description: >- - An optional qualifier or modifier for the disease. - - ActionToSymptomRelationship: - is_a: Triple - description: >- - A triple representing a relationship between a medical action - (A clinically prescribed procedure, therapy, intervention, or recommendation) - and a symptom, for example, - a chest X-ray IS USED TO DIAGNOSE pleural effusion. - slot_usage: - subject: - range: Action - object: - range: Symptom - multivalued: true - predicate: - range: NamedEntity - description: The relationship type, usually IS USED TO DIAGNOSE - subject_qualifier: - range: NamedEntity - description: >- - An optional qualifier or modifier for the medical action. - object_qualifier: - range: NamedEntity - description: >- - An optional qualifier or modifier for the symptom. - - Action: - is_a: NamedEntity - description: >- - A clinically prescribed procedure, therapy, intervention, or recommendation. - annotations: - annotators: sqlite:obo:maxo, sqlite:obo:ogms, sqlite:obo:ncit - id_prefixes: - - MAXO - - Disease: - is_a: NamedEntity - description: >- - A disposition to undergo pathological processes that exists in an organism - because of one or more disorders in that organism. - annotations: - annotators: sqlite:obo:mondo - id_prefixes: - - MONDO - - Symptom: - is_a: NamedEntity - description: >- - A condition or phenotype resulting from an abnormal health state. - annotations: - annotators: sqlite:obo:hp - id_prefixes: - - HP \ No newline at end of file diff --git a/src/ontogpt/templates/mendelian_disease.py b/src/ontogpt/templates/mendelian_disease.py deleted file mode 100644 index da2ff02d3..000000000 --- a/src/ontogpt/templates/mendelian_disease.py +++ /dev/null @@ -1,196 +0,0 @@ -from __future__ import annotations -from datetime import datetime, date -from enum import Enum -from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, ConfigDict, Field, field_validator -import re -import sys -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal - - -metamodel_version = "None" -version = "None" - -class ConfiguredBaseModel(BaseModel): - model_config = ConfigDict( - validate_assignment=True, - validate_default=True, - extra = 'forbid', - arbitrary_types_allowed=True, - use_enum_values = True) - - -class NullDataOptions(str, Enum): - - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = "UNSPECIFIED_METHOD_OF_ADMINISTRATION" - - NOT_APPLICABLE = "NOT_APPLICABLE" - - NOT_MENTIONED = "NOT_MENTIONED" - - - -class ExtractionResult(ConfiguredBaseModel): - """ - A result of extracting knowledge on text - """ - input_id: Optional[str] = Field(None) - input_title: Optional[str] = Field(None) - input_text: Optional[str] = Field(None) - raw_completion_output: Optional[str] = Field(None) - prompt: Optional[str] = Field(None) - extracted_object: Optional[Any] = Field(None, description="""The complex objects extracted from the text""") - named_entities: Optional[List[Any]] = Field(default_factory=list, description="""Named entities extracted from the text""") - - - -class NamedEntity(ConfiguredBaseModel): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class MendelianDisease(NamedEntity): - - name: Optional[str] = Field(None, description="""the name of the disease""") - description: Optional[str] = Field(None, description="""a description of the disease""") - synonyms: Optional[List[str]] = Field(default_factory=list) - subclass_of: Optional[List[str]] = Field(default_factory=list) - symptoms: Optional[List[str]] = Field(default_factory=list) - inheritance: Optional[str] = Field(None) - genes: Optional[List[str]] = Field(default_factory=list) - disease_onsets: Optional[List[str]] = Field(default_factory=list) - publications: Optional[List[Publication]] = Field(default_factory=list) - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class DiseaseCategory(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Gene(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Symptom(NamedEntity): - - characteristic: Optional[str] = Field(None) - affects: Optional[str] = Field(None) - severity: Optional[str] = Field(None) - onset_of_symptom: Optional[str] = Field(None) - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Onset(NamedEntity): - - years_old: Optional[str] = Field(None) - decades: Optional[List[str]] = Field(default_factory=list) - juvenile_or_adult: Optional[str] = Field(None) - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Inheritance(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class CompoundExpression(ConfiguredBaseModel): - - None - - - -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - subject: Optional[str] = Field(None) - predicate: Optional[str] = Field(None) - object: Optional[str] = Field(None) - qualifier: Optional[str] = Field(None, description="""A qualifier for the statements, e.g. \"NOT\" for negation""") - subject_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"""") - object_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"""") - - - -class TextWithTriples(ConfiguredBaseModel): - """ - A text containing one or more relations of the Triple type. - """ - publication: Optional[Publication] = Field(None) - triples: Optional[List[Triple]] = Field(default_factory=list) - - - -class TextWithEntity(ConfiguredBaseModel): - """ - A text containing one or more instances of a single type of entity. - """ - publication: Optional[Publication] = Field(None) - entities: Optional[List[str]] = Field(default_factory=list) - - - -class RelationshipType(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Publication(ConfiguredBaseModel): - - id: Optional[str] = Field(None, description="""The publication identifier""") - title: Optional[str] = Field(None, description="""The title of the publication""") - abstract: Optional[str] = Field(None, description="""The abstract of the publication""") - combined_text: Optional[str] = Field(None) - full_text: Optional[str] = Field(None, description="""The full text of the publication""") - - - -class AnnotatorResult(ConfiguredBaseModel): - - subject_text: Optional[str] = Field(None) - object_id: Optional[str] = Field(None) - object_text: Optional[str] = Field(None) - - - - -# Model rebuild -# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model -ExtractionResult.model_rebuild() -NamedEntity.model_rebuild() -MendelianDisease.model_rebuild() -DiseaseCategory.model_rebuild() -Gene.model_rebuild() -Symptom.model_rebuild() -Onset.model_rebuild() -Inheritance.model_rebuild() -CompoundExpression.model_rebuild() -Triple.model_rebuild() -TextWithTriples.model_rebuild() -TextWithEntity.model_rebuild() -RelationshipType.model_rebuild() -Publication.model_rebuild() -AnnotatorResult.model_rebuild() - diff --git a/src/ontogpt/templates/mendelian_disease.yaml b/src/ontogpt/templates/mendelian_disease.yaml deleted file mode 100644 index e3622d92d..000000000 --- a/src/ontogpt/templates/mendelian_disease.yaml +++ /dev/null @@ -1,118 +0,0 @@ -id: http://w3id.org/ontogpt/mendelian_disease -name: mendelian_disease-template -title: GO-CAM Template -description: >- - A template for GO-CAMs -license: https://creativecommons.org/publicdomain/zero/1.0/ -prefixes: - linkml: https://w3id.org/linkml/ - mendelian_disease: http://w3id.org/ontogpt/mendelian_disease/ - -default_prefix: mendelian_disease -default_range: string - -imports: - - linkml:types - - core - -classes: - MendelianDisease: - is_a: NamedEntity - attributes: - name: - description: the name of the disease - examples: - - value: peroxisome biogenesis disorder - #identifier: true ## needed for inlining - description: - description: a description of the disease - examples: - - value: >- - Peroxisome biogenesis disorders, Zellweger syndrome spectrum (PBD-ZSS) is a group of autosomal recessive disorders affecting the formation of functional peroxisomes, characterized by sensorineural hearing loss, pigmentary retinal degeneration, multiple organ dysfunction and psychomotor impairment - synonyms: - multivalued: true - examples: - - value: Zellweger syndrome spectrum - - value: PBD-ZSS - subclass_of: - multivalued: true - range: DiseaseCategory - examples: - - value: lysosomal disease - - value: autosomal recessive disorder - symptoms: - range: Symptom - multivalued: true - examples: - - value: sensorineural hearing loss - - value: pigmentary retinal degeneration - inheritance: - range: Inheritance - examples: - - value: autosomal recessive - genes: - range: Gene - multivalued: true - examples: - - value: PEX1 - - value: PEX2 - - value: PEX3 - annotations: - prompt: >- - semicolon separated list of gene symbols; for example: PEX1; PEX2; PEX3 - disease_onsets: - range: Onset - multivalued: true - annotations: - prompt: >- - semi-colon separated list of onsets at which the disease occurs, for example: adult; juvenile; first decade - publications: - range: Publication - multivalued: true - annotations: - prompt.skip: "true" - - DiseaseCategory: - is_a: NamedEntity - id_prefixes: - - MONDO - annotations: - annotators: sqlite:obo:mondo - - Gene: - is_a: NamedEntity - id_prefixes: - - HGNC - annotations: - annotators: gilda:, bioportal:hgnc-nr, sqlite:obo:pr - - Symptom: - is_a: NamedEntity - id_prefixes: - - HP - annotations: - annotators: sqlite:obo:hp, sqlite:obo:mondo - attributes: - characteristic: - affects: - severity: - onset_of_symptom: - range: Onset - - Onset: - is_a: NamedEntity - id_prefixes: - - HP - annotations: - annotators: sqlite:obo:hp, sqlite:obo:hsapdv - attributes: - years_old: - decades: - multivalued: true - juvenile_or_adult: - - - Inheritance: - is_a: NamedEntity - annotations: - annotators: sqlite:obo:hp, sqlite:obo:geno \ No newline at end of file diff --git a/src/ontogpt/templates/metabolic_process.py b/src/ontogpt/templates/metabolic_process.py deleted file mode 100644 index d6c39c015..000000000 --- a/src/ontogpt/templates/metabolic_process.py +++ /dev/null @@ -1,162 +0,0 @@ -from __future__ import annotations -from datetime import datetime, date -from enum import Enum -from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, ConfigDict, Field, field_validator -import re -import sys -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal - - -metamodel_version = "None" -version = "None" - -class ConfiguredBaseModel(BaseModel): - model_config = ConfigDict( - validate_assignment=True, - validate_default=True, - extra = 'forbid', - arbitrary_types_allowed=True, - use_enum_values = True) - - -class NullDataOptions(str, Enum): - - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = "UNSPECIFIED_METHOD_OF_ADMINISTRATION" - - NOT_APPLICABLE = "NOT_APPLICABLE" - - NOT_MENTIONED = "NOT_MENTIONED" - - - -class ExtractionResult(ConfiguredBaseModel): - """ - A result of extracting knowledge on text - """ - input_id: Optional[str] = Field(None) - input_title: Optional[str] = Field(None) - input_text: Optional[str] = Field(None) - raw_completion_output: Optional[str] = Field(None) - prompt: Optional[str] = Field(None) - extracted_object: Optional[Any] = Field(None, description="""The complex objects extracted from the text""") - named_entities: Optional[List[Any]] = Field(default_factory=list, description="""Named entities extracted from the text""") - - - -class NamedEntity(ConfiguredBaseModel): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class MetabolicProcess(NamedEntity): - - label: Optional[str] = Field(None, description="""the name of the metabolic process""") - description: Optional[str] = Field(None, description="""a textual description of the metabolic process""") - synonyms: Optional[List[str]] = Field(default_factory=list, description="""alternative names of the metabolic process""") - subclass_of: Optional[List[str]] = Field(default_factory=list, description="""a semicolon separated list of broader metabolic processes which this is a subclass of""") - category: Optional[str] = Field(None, description="""the category of metabolic process, e.g metabolic process, catabolic process, biosynthetic process, small molecule sensor activity""") - inputs: Optional[List[str]] = Field(default_factory=list, description="""the inputs of the metabolic process""") - outputs: Optional[List[str]] = Field(default_factory=list, description="""the outputs of the metabolic process""") - id: str = Field(..., description="""A unique identifier for the named entity""") - - - -class MetabolicProcessCategory(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class ChemicalEntity(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class CompoundExpression(ConfiguredBaseModel): - - None - - - -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - subject: Optional[str] = Field(None) - predicate: Optional[str] = Field(None) - object: Optional[str] = Field(None) - qualifier: Optional[str] = Field(None, description="""A qualifier for the statements, e.g. \"NOT\" for negation""") - subject_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"""") - object_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"""") - - - -class TextWithTriples(ConfiguredBaseModel): - """ - A text containing one or more relations of the Triple type. - """ - publication: Optional[Publication] = Field(None) - triples: Optional[List[Triple]] = Field(default_factory=list) - - - -class TextWithEntity(ConfiguredBaseModel): - """ - A text containing one or more instances of a single type of entity. - """ - publication: Optional[Publication] = Field(None) - entities: Optional[List[str]] = Field(default_factory=list) - - - -class RelationshipType(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Publication(ConfiguredBaseModel): - - id: Optional[str] = Field(None, description="""The publication identifier""") - title: Optional[str] = Field(None, description="""The title of the publication""") - abstract: Optional[str] = Field(None, description="""The abstract of the publication""") - combined_text: Optional[str] = Field(None) - full_text: Optional[str] = Field(None, description="""The full text of the publication""") - - - -class AnnotatorResult(ConfiguredBaseModel): - - subject_text: Optional[str] = Field(None) - object_id: Optional[str] = Field(None) - object_text: Optional[str] = Field(None) - - - - -# Model rebuild -# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model -ExtractionResult.model_rebuild() -NamedEntity.model_rebuild() -MetabolicProcess.model_rebuild() -MetabolicProcessCategory.model_rebuild() -ChemicalEntity.model_rebuild() -CompoundExpression.model_rebuild() -Triple.model_rebuild() -TextWithTriples.model_rebuild() -TextWithEntity.model_rebuild() -RelationshipType.model_rebuild() -Publication.model_rebuild() -AnnotatorResult.model_rebuild() - diff --git a/src/ontogpt/templates/metabolic_process.yaml b/src/ontogpt/templates/metabolic_process.yaml deleted file mode 100644 index 98b5656a4..000000000 --- a/src/ontogpt/templates/metabolic_process.yaml +++ /dev/null @@ -1,59 +0,0 @@ -id: https://w3id.org/ontogpt/metabolic_process -name: metabolic-process-template -title: metabolic Process Template -description: >- - A template for GO-CAMs -license: https://creativecommons.org/publicdomain/zero/1.0/ -prefixes: - linkml: https://w3id.org/linkml/ - bp: http://w3id.org/ontogpt/metabolic-process-template - -default_prefix: bp -default_range: string - -imports: - - linkml:types - - core - -classes: - MetabolicProcess: - is_a: NamedEntity - attributes: - label: - description: the name of the metabolic process - description: - description: a textual description of the metabolic process - synonyms: - description: alternative names of the metabolic process - multivalued: true - subclass_of: - description: a semicolon separated list of broader metabolic processes which this is a subclass of - range: MetabolicProcessCategory - multivalued: true - category: - range: MetabolicProcessCategory - description: the category of metabolic process, e.g metabolic process, catabolic process, biosynthetic process, small molecule sensor activity - inputs: - description: the inputs of the metabolic process - multivalued: true - range: ChemicalEntity - outputs: - description: the outputs of the metabolic process - multivalued: true - range: ChemicalEntity - - MetabolicProcessCategory: - is_a: NamedEntity - id_prefixes: - - GO - annotations: - annotators: sqlite:obo:go - - ChemicalEntity: - is_a: NamedEntity - id_prefixes: - - CHEBI - annotations: - annotators: sqlite:obo:chebi - - diff --git a/src/ontogpt/templates/metagenome_study.py b/src/ontogpt/templates/metagenome_study.py deleted file mode 100644 index e8a6d76dd..000000000 --- a/src/ontogpt/templates/metagenome_study.py +++ /dev/null @@ -1,227 +0,0 @@ -from __future__ import annotations -from datetime import datetime, date -from enum import Enum -from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, ConfigDict, Field, field_validator -import re -import sys -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal - - -metamodel_version = "None" -version = "None" - -class ConfiguredBaseModel(BaseModel): - model_config = ConfigDict( - validate_assignment=True, - validate_default=True, - extra = 'forbid', - arbitrary_types_allowed=True, - use_enum_values = True) - - -class NullDataOptions(str, Enum): - - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = "UNSPECIFIED_METHOD_OF_ADMINISTRATION" - - NOT_APPLICABLE = "NOT_APPLICABLE" - - NOT_MENTIONED = "NOT_MENTIONED" - - - -class Study(ConfiguredBaseModel): - - environments: Optional[List[str]] = Field(default_factory=list) - causal_relationships: Optional[List[CausalRelationship]] = Field(default_factory=list) - variables: Optional[List[str]] = Field(default_factory=list) - treatments: Optional[List[str]] = Field(default_factory=list) - measurements: Optional[List[Measurement]] = Field(default_factory=list) - location: Optional[List[str]] = Field(default_factory=list, description="""the sites at which the study was conducted""") - environmental_material: Optional[List[str]] = Field(default_factory=list, description="""the environmental material that was sampled""") - sequencing_technologies: Optional[str] = Field(None) - organisms: Optional[List[str]] = Field(default_factory=list, description="""semicolon-separated list of all studied organism taxons""") - - - -class ExtractionResult(ConfiguredBaseModel): - """ - A result of extracting knowledge on text - """ - input_id: Optional[str] = Field(None) - input_title: Optional[str] = Field(None) - input_text: Optional[str] = Field(None) - raw_completion_output: Optional[str] = Field(None) - prompt: Optional[str] = Field(None) - extracted_object: Optional[Any] = Field(None, description="""The complex objects extracted from the text""") - named_entities: Optional[List[Any]] = Field(default_factory=list, description="""Named entities extracted from the text""") - - - -class NamedEntity(ConfiguredBaseModel): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Location(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class EnvironmentalMaterial(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Environment(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Variable(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Unit(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class SequencingTechnology(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Treatment(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Organism(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class CompoundExpression(ConfiguredBaseModel): - - None - - - -class Measurement(CompoundExpression): - - value: Optional[str] = Field(None, description="""the value of the measurement""") - unit: Optional[str] = Field(None, description="""the unit of the measurement""") - - - -class CausalRelationship(CompoundExpression): - - cause: Optional[str] = Field(None, description="""the variable that is the cause of the effect""") - effect: Optional[str] = Field(None, description="""the things that is affected""") - - - -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - subject: Optional[str] = Field(None) - predicate: Optional[str] = Field(None) - object: Optional[str] = Field(None) - qualifier: Optional[str] = Field(None, description="""A qualifier for the statements, e.g. \"NOT\" for negation""") - subject_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"""") - object_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"""") - - - -class TextWithTriples(ConfiguredBaseModel): - """ - A text containing one or more relations of the Triple type. - """ - publication: Optional[Publication] = Field(None) - triples: Optional[List[Triple]] = Field(default_factory=list) - - - -class TextWithEntity(ConfiguredBaseModel): - """ - A text containing one or more instances of a single type of entity. - """ - publication: Optional[Publication] = Field(None) - entities: Optional[List[str]] = Field(default_factory=list) - - - -class RelationshipType(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Publication(ConfiguredBaseModel): - - id: Optional[str] = Field(None, description="""The publication identifier""") - title: Optional[str] = Field(None, description="""The title of the publication""") - abstract: Optional[str] = Field(None, description="""The abstract of the publication""") - combined_text: Optional[str] = Field(None) - full_text: Optional[str] = Field(None, description="""The full text of the publication""") - - - -class AnnotatorResult(ConfiguredBaseModel): - - subject_text: Optional[str] = Field(None) - object_id: Optional[str] = Field(None) - object_text: Optional[str] = Field(None) - - - - -# Model rebuild -# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model -Study.model_rebuild() -ExtractionResult.model_rebuild() -NamedEntity.model_rebuild() -Location.model_rebuild() -EnvironmentalMaterial.model_rebuild() -Environment.model_rebuild() -Variable.model_rebuild() -Unit.model_rebuild() -SequencingTechnology.model_rebuild() -Treatment.model_rebuild() -Organism.model_rebuild() -CompoundExpression.model_rebuild() -Measurement.model_rebuild() -CausalRelationship.model_rebuild() -Triple.model_rebuild() -TextWithTriples.model_rebuild() -TextWithEntity.model_rebuild() -RelationshipType.model_rebuild() -Publication.model_rebuild() -AnnotatorResult.model_rebuild() - diff --git a/src/ontogpt/templates/metagenome_study.yaml b/src/ontogpt/templates/metagenome_study.yaml deleted file mode 100644 index b5ee43292..000000000 --- a/src/ontogpt/templates/metagenome_study.yaml +++ /dev/null @@ -1,157 +0,0 @@ -id: http://w3id.org/ontogpt/metagenome -name: environmental-metagenome -title: Environmental Metagenome Template -description: >- - A template for Environmental Metagenome Studies -license: https://creativecommons.org/publicdomain/zero/1.0/ -prefixes: - linkml: https://w3id.org/linkml/ - eg: http://w3id.org/ontogpt/environmental-metagenome/ - -default_prefix: eg -default_range: string - -imports: - - linkml:types - - core - -classes: - Study: - attributes: - - environments: - annotations: - prompt: semicolon-separated list of environmental systems or biomes in which the study was conducted - multivalued: true - range: Environment - - causal_relationships: - annotations: - prompt: semicolon-separated list of cause-effect pairs, for example, effect of temperature on growth - range: CausalRelationship - multivalued: true - - variables: - annotations: - prompt: semicolon-separated list of environmental variables which are studies. E.g. temperature, pH, salinity - range: Variable - multivalued: true - - treatments: - annotations: - prompt: semicolon-separated list of treatments that are applied - range: Treatment - multivalued: true - - measurements: - annotations: - prompt: semicolon-separated list of value-measurement pairs - range: Measurement - multivalued: true - - location: - description: the sites at which the study was conducted - annotations: - prompt: semicolon-separated list of sites at which the study was conducted - range: Location - multivalued: true - - environmental_material: - description: the environmental material that was sampled - annotations: - prompt: semicolon-separated list of environmental materials - range: EnvironmentalMaterial - multivalued: true - - sequencing_technologies: - annotations: - prompt: semicolon-separated list of sequencing technologies used in the project - range: SequencingTechnology - - organisms: - description: semicolon-separated list of all studied organism taxons - multivalued: true - range: Organism - - Location: - is_a: NamedEntity - id_prefixes: - - ENVO - - GAZ - annotations: - annotators: sqlite:obo:envo, bioportal:gaz - - EnvironmentalMaterial: - is_a: NamedEntity - id_prefixes: - - ENVO - annotations: - annotators: sqlite:obo:envo - - Environment: - is_a: NamedEntity - id_prefixes: - - ENVO - annotations: - annotators: sqlite:obo:envo - - Variable: - is_a: NamedEntity - id_prefixes: - - ENVO - - MIXS - - PATO - annotations: - annotators: sqlite:obo:envo, bioportal:bero - - Unit: - is_a: NamedEntity - id_prefixes: - - UO - - NCIT - annotations: - annotators: sqlite:obo:uo, bioportal:ncit - - Measurement: - is_a: CompoundExpression - attributes: - value: - description: the value of the measurement - #range: float - unit: - description: the unit of the measurement - range: Unit - #variable: - - CausalRelationship: - is_a: CompoundExpression - attributes: - cause: - description: the variable that is the cause of the effect - range: Variable - effect: - description: the things that is affected - range: Variable - - SequencingTechnology: - is_a: NamedEntity - id_prefixes: - - IDO - - EFO - annotations: - annotators: sqlite:obo:obi, sqlite:obo:efo, bioportal:bero - - Treatment: - is_a: NamedEntity - id_prefixes: - - PECO - - OBI - annotations: - annotators: sqlite:obo:peco, sqlite:obo:obi, bioportal:bero - - Organism: - is_a: NamedEntity - id_prefixes: - - NCBITaxon - annotations: - annotators: "sqlite:obo:ncbitaxon, gilda:" diff --git a/src/ontogpt/templates/mondo_simple.py b/src/ontogpt/templates/mondo_simple.py deleted file mode 100644 index 3e892a986..000000000 --- a/src/ontogpt/templates/mondo_simple.py +++ /dev/null @@ -1,149 +0,0 @@ -from __future__ import annotations -from datetime import datetime, date -from enum import Enum -from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, ConfigDict, Field, field_validator -import re -import sys -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal - - -metamodel_version = "None" -version = "None" - -class ConfiguredBaseModel(BaseModel): - model_config = ConfigDict( - validate_assignment=True, - validate_default=True, - extra = 'forbid', - arbitrary_types_allowed=True, - use_enum_values = True) - - -class NullDataOptions(str, Enum): - - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = "UNSPECIFIED_METHOD_OF_ADMINISTRATION" - - NOT_APPLICABLE = "NOT_APPLICABLE" - - NOT_MENTIONED = "NOT_MENTIONED" - - - -class ExtractionResult(ConfiguredBaseModel): - """ - A result of extracting knowledge on text - """ - input_id: Optional[str] = Field(None) - input_title: Optional[str] = Field(None) - input_text: Optional[str] = Field(None) - raw_completion_output: Optional[str] = Field(None) - prompt: Optional[str] = Field(None) - extracted_object: Optional[Any] = Field(None, description="""The complex objects extracted from the text""") - named_entities: Optional[List[Any]] = Field(default_factory=list, description="""Named entities extracted from the text""") - - - -class NamedEntity(ConfiguredBaseModel): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class OntologyTermSet(NamedEntity): - - terms: Optional[List[str]] = Field(default_factory=list, description="""A semicolon-separated list of any MONDO Disease Ontology terms.""") - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class OntologyTerm(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class CompoundExpression(ConfiguredBaseModel): - - None - - - -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - subject: Optional[str] = Field(None) - predicate: Optional[str] = Field(None) - object: Optional[str] = Field(None) - qualifier: Optional[str] = Field(None, description="""A qualifier for the statements, e.g. \"NOT\" for negation""") - subject_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"""") - object_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"""") - - - -class TextWithTriples(ConfiguredBaseModel): - """ - A text containing one or more relations of the Triple type. - """ - publication: Optional[Publication] = Field(None) - triples: Optional[List[Triple]] = Field(default_factory=list) - - - -class TextWithEntity(ConfiguredBaseModel): - """ - A text containing one or more instances of a single type of entity. - """ - publication: Optional[Publication] = Field(None) - entities: Optional[List[str]] = Field(default_factory=list) - - - -class RelationshipType(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Publication(ConfiguredBaseModel): - - id: Optional[str] = Field(None, description="""The publication identifier""") - title: Optional[str] = Field(None, description="""The title of the publication""") - abstract: Optional[str] = Field(None, description="""The abstract of the publication""") - combined_text: Optional[str] = Field(None) - full_text: Optional[str] = Field(None, description="""The full text of the publication""") - - - -class AnnotatorResult(ConfiguredBaseModel): - - subject_text: Optional[str] = Field(None) - object_id: Optional[str] = Field(None) - object_text: Optional[str] = Field(None) - - - - -# Model rebuild -# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model -ExtractionResult.model_rebuild() -NamedEntity.model_rebuild() -OntologyTermSet.model_rebuild() -OntologyTerm.model_rebuild() -CompoundExpression.model_rebuild() -Triple.model_rebuild() -TextWithTriples.model_rebuild() -TextWithEntity.model_rebuild() -RelationshipType.model_rebuild() -Publication.model_rebuild() -AnnotatorResult.model_rebuild() - diff --git a/src/ontogpt/templates/mondo_simple.yaml b/src/ontogpt/templates/mondo_simple.yaml deleted file mode 100644 index d86f87886..000000000 --- a/src/ontogpt/templates/mondo_simple.yaml +++ /dev/null @@ -1,38 +0,0 @@ -id: http://w3id.org/ontogpt/mondo_simple -name: mondo_simple -title: Simple MONDO Extraction Template -description: >- - Simple MONDO Disease Ontology Extraction Template -license: https://creativecommons.org/publicdomain/zero/1.0/ -prefixes: - linkml: https://w3id.org/linkml/ - mondo_simple: http://w3id.org/ontogpt/emapa_simple - -default_prefix: mondo_simple -default_range: string - -imports: - - linkml:types - - core - -classes: - OntologyTermSet: - tree_root: true - is_a: NamedEntity - attributes: - terms: - range: OntologyTerm - multivalued: true - description: >- - A semicolon-separated list of any MONDO Disease Ontology terms. - OntologyTerm: - is_a: NamedEntity - id_prefixes: - - MONDO - annotations: - annotators: sqlite:obo:mondo - prompt: >- - The name of a MONDO Disease Ontology term. - Examples include: neurothekoma, retinal vasculitis, - chicken monocytic leukemia, neoplasm of spinal cord, - moyamoya disease 3 diff --git a/src/ontogpt/templates/nmdc_schema_data.py b/src/ontogpt/templates/nmdc_schema_data.py deleted file mode 100644 index 42172a68a..000000000 --- a/src/ontogpt/templates/nmdc_schema_data.py +++ /dev/null @@ -1,157 +0,0 @@ -from __future__ import annotations -from datetime import datetime, date -from enum import Enum -from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, ConfigDict, Field, field_validator -import re -import sys -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal - - -metamodel_version = "None" -version = "None" - -class ConfiguredBaseModel(BaseModel): - model_config = ConfigDict( - validate_assignment=True, - validate_default=True, - extra = 'forbid', - arbitrary_types_allowed=True, - use_enum_values = True) - - -class NullDataOptions(str, Enum): - - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = "UNSPECIFIED_METHOD_OF_ADMINISTRATION" - - NOT_APPLICABLE = "NOT_APPLICABLE" - - NOT_MENTIONED = "NOT_MENTIONED" - - - -class Dataset(ConfiguredBaseModel): - - packageid: Optional[str] = Field(None, description="""The internal identifier for the dataset""") - environmental_material: Optional[List[str]] = Field(default_factory=list, description="""the environmental material that was sampled""") - environments: Optional[List[str]] = Field(default_factory=list, description="""the environmental context in which the study was conducted""") - - - -class ExtractionResult(ConfiguredBaseModel): - """ - A result of extracting knowledge on text - """ - input_id: Optional[str] = Field(None) - input_title: Optional[str] = Field(None) - input_text: Optional[str] = Field(None) - raw_completion_output: Optional[str] = Field(None) - prompt: Optional[str] = Field(None) - extracted_object: Optional[Any] = Field(None, description="""The complex objects extracted from the text""") - named_entities: Optional[List[Any]] = Field(default_factory=list, description="""Named entities extracted from the text""") - - - -class NamedEntity(ConfiguredBaseModel): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class EnvironmentalMaterial(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Environment(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class CompoundExpression(ConfiguredBaseModel): - - None - - - -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - subject: Optional[str] = Field(None) - predicate: Optional[str] = Field(None) - object: Optional[str] = Field(None) - qualifier: Optional[str] = Field(None, description="""A qualifier for the statements, e.g. \"NOT\" for negation""") - subject_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"""") - object_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"""") - - - -class TextWithTriples(ConfiguredBaseModel): - """ - A text containing one or more relations of the Triple type. - """ - publication: Optional[Publication] = Field(None) - triples: Optional[List[Triple]] = Field(default_factory=list) - - - -class TextWithEntity(ConfiguredBaseModel): - """ - A text containing one or more instances of a single type of entity. - """ - publication: Optional[Publication] = Field(None) - entities: Optional[List[str]] = Field(default_factory=list) - - - -class RelationshipType(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Publication(ConfiguredBaseModel): - - id: Optional[str] = Field(None, description="""The publication identifier""") - title: Optional[str] = Field(None, description="""The title of the publication""") - abstract: Optional[str] = Field(None, description="""The abstract of the publication""") - combined_text: Optional[str] = Field(None) - full_text: Optional[str] = Field(None, description="""The full text of the publication""") - - - -class AnnotatorResult(ConfiguredBaseModel): - - subject_text: Optional[str] = Field(None) - object_id: Optional[str] = Field(None) - object_text: Optional[str] = Field(None) - - - - -# Model rebuild -# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model -Dataset.model_rebuild() -ExtractionResult.model_rebuild() -NamedEntity.model_rebuild() -EnvironmentalMaterial.model_rebuild() -Environment.model_rebuild() -CompoundExpression.model_rebuild() -Triple.model_rebuild() -TextWithTriples.model_rebuild() -TextWithEntity.model_rebuild() -RelationshipType.model_rebuild() -Publication.model_rebuild() -AnnotatorResult.model_rebuild() - diff --git a/src/ontogpt/templates/nmdc_schema_data.yaml b/src/ontogpt/templates/nmdc_schema_data.yaml deleted file mode 100644 index 6793d8673..000000000 --- a/src/ontogpt/templates/nmdc_schema_data.yaml +++ /dev/null @@ -1,58 +0,0 @@ -id: http://w3id.org/ontogpt/nmdc-schema-data -name: nmdc-schema-data -title: nmdc-schema-data -description: >- - A template for populating nmdc-schema required slots - from data entries. Primarily, this involves three different - levels corresponding to ENVO terms, as well as conversion - of NLCD values and FAO soil taxonomy classes to ENVO. -license: https://creativecommons.org/publicdomain/zero/1.0/ -prefixes: - linkml: https://w3id.org/linkml/ - nmdcsd: http://w3id.org/ontogpt/nmdc-schema-data - -default_prefix: nmdcsd -default_range: string - -imports: - - linkml:types - - core - -classes: - Dataset: - tree_root: true - attributes: - packageid: - description: The internal identifier for the dataset - annotations: - prompt: single unique identifier for the dataset - range: string - multivalued: false - - environmental_material: - description: the environmental material that was sampled - annotations: - prompt: semicolon-separated list of environmental materials - range: EnvironmentalMaterial - multivalued: true - - environments: - description: the environmental context in which the study was conducted - annotations: - prompt: semicolon-separated list of environmental contexts in which the study was conducted - range: Environment - multivalued: true - - EnvironmentalMaterial: - is_a: NamedEntity - id_prefixes: - - ENVO - annotations: - annotators: sqlite:obo:envo - - Environment: - is_a: NamedEntity - id_prefixes: - - ENVO - annotations: - annotators: sqlite:obo:envo diff --git a/src/ontogpt/templates/ontology_class.py b/src/ontogpt/templates/ontology_class.py deleted file mode 100644 index 588529fcd..000000000 --- a/src/ontogpt/templates/ontology_class.py +++ /dev/null @@ -1,162 +0,0 @@ -from __future__ import annotations -from datetime import datetime, date -from enum import Enum -from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, ConfigDict, Field, field_validator -import re -import sys -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal - - -metamodel_version = "None" -version = "None" - -class ConfiguredBaseModel(BaseModel): - model_config = ConfigDict( - validate_assignment=True, - validate_default=True, - extra = 'forbid', - arbitrary_types_allowed=True, - use_enum_values = True) - - -class NullDataOptions(str, Enum): - - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = "UNSPECIFIED_METHOD_OF_ADMINISTRATION" - - NOT_APPLICABLE = "NOT_APPLICABLE" - - NOT_MENTIONED = "NOT_MENTIONED" - - - -class LogicalDefinition(ConfiguredBaseModel): - - genus: Optional[List[str]] = Field(default_factory=list) - differentiating_characteristic_relationship: Optional[str] = Field(None) - differentiating_characteristic_parents: Optional[List[str]] = Field(default_factory=list) - - - -class ExtractionResult(ConfiguredBaseModel): - """ - A result of extracting knowledge on text - """ - input_id: Optional[str] = Field(None) - input_title: Optional[str] = Field(None) - input_text: Optional[str] = Field(None) - raw_completion_output: Optional[str] = Field(None) - prompt: Optional[str] = Field(None) - extracted_object: Optional[Any] = Field(None, description="""The complex objects extracted from the text""") - named_entities: Optional[List[Any]] = Field(default_factory=list, description="""Named entities extracted from the text""") - - - -class NamedEntity(ConfiguredBaseModel): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class OntologyClass(NamedEntity): - - label: Optional[str] = Field(None, description="""the name of the main entity being defined""") - description: Optional[str] = Field(None, description="""a textual description of the entity""") - synonyms: Optional[List[str]] = Field(default_factory=list, description="""alternative names of the entity""") - categories: Optional[List[str]] = Field(default_factory=list, description="""the categories to which this entity belongs.""") - subclass_of: Optional[List[str]] = Field(default_factory=list) - logical_definition: Optional[LogicalDefinition] = Field(None, description="""the necessary and sufficient conditions for this entity to be an instance of this class""") - id: str = Field(..., description="""A unique identifier for the named entity""") - - - -class Relation(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class CompoundExpression(ConfiguredBaseModel): - - None - - - -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - subject: Optional[str] = Field(None) - predicate: Optional[str] = Field(None) - object: Optional[str] = Field(None) - qualifier: Optional[str] = Field(None, description="""A qualifier for the statements, e.g. \"NOT\" for negation""") - subject_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"""") - object_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"""") - - - -class TextWithTriples(ConfiguredBaseModel): - """ - A text containing one or more relations of the Triple type. - """ - publication: Optional[Publication] = Field(None) - triples: Optional[List[Triple]] = Field(default_factory=list) - - - -class TextWithEntity(ConfiguredBaseModel): - """ - A text containing one or more instances of a single type of entity. - """ - publication: Optional[Publication] = Field(None) - entities: Optional[List[str]] = Field(default_factory=list) - - - -class RelationshipType(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Publication(ConfiguredBaseModel): - - id: Optional[str] = Field(None, description="""The publication identifier""") - title: Optional[str] = Field(None, description="""The title of the publication""") - abstract: Optional[str] = Field(None, description="""The abstract of the publication""") - combined_text: Optional[str] = Field(None) - full_text: Optional[str] = Field(None, description="""The full text of the publication""") - - - -class AnnotatorResult(ConfiguredBaseModel): - - subject_text: Optional[str] = Field(None) - object_id: Optional[str] = Field(None) - object_text: Optional[str] = Field(None) - - - - -# Model rebuild -# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model -LogicalDefinition.model_rebuild() -ExtractionResult.model_rebuild() -NamedEntity.model_rebuild() -OntologyClass.model_rebuild() -Relation.model_rebuild() -CompoundExpression.model_rebuild() -Triple.model_rebuild() -TextWithTriples.model_rebuild() -TextWithEntity.model_rebuild() -RelationshipType.model_rebuild() -Publication.model_rebuild() -AnnotatorResult.model_rebuild() - diff --git a/src/ontogpt/templates/ontology_class.yaml b/src/ontogpt/templates/ontology_class.yaml deleted file mode 100644 index 246f4f59e..000000000 --- a/src/ontogpt/templates/ontology_class.yaml +++ /dev/null @@ -1,84 +0,0 @@ -id: https://w3id.org/ontogpt/ontology_class -name: ontology-class -title: Ontology Class Template -description: >- - A template for Ontology Classes -license: https://creativecommons.org/publicdomain/zero/1.0/ -prefixes: - linkml: https://w3id.org/linkml/ - oc: http://w3id.org/ontogpt/ontology-class-template - -default_prefix: oc -default_range: string - -imports: - - linkml:types - - core - -classes: - OntologyClass: - tree_root: true - is_a: NamedEntity - attributes: - label: - description: the name of the main entity being defined - description: - description: a textual description of the entity - synonyms: - description: alternative names of the entity - multivalued: true - categories: - description: >- - the categories to which this entity belongs. - annotations: - prompt: >- - semicolon-separated list of categories to which the entity belongs. - These may be taken from an upper - level ontology such as COB, BioLink, or UMLS semantic types. - range: OntologyClass - multivalued: true - subclass_of: - annotations: - prompt: >- - semicolon-separated list of parent classes, indicating broader concepts. - E.g. if the input text is "a type of bone", then the parent class is "bone" - range: OntologyClass - multivalued: true - logical_definition: - description: the necessary and sufficient conditions for this entity to be an instance of this class - annotations: - prompt: >- - the necessary and sufficient conditions for this entity to be an instance of this class, - written in OWL manchester syntax, e.g. bone and (part_of some 'hand') - range: LogicalDefinition - - LogicalDefinition: - attributes: - genus: - range: OntologyClass - multivalued: true - annotations: - prompt: >- - in a logical definition expression, this is the parent (genus) class, - e.g. bone - differentiating_characteristic_relationship: - range: Relation - annotations: - prompt: >- - in a logical definition expression, this is the parent (differentiating characteristic) relationship type, - e.g. part of - differentiating_characteristic_parents: - range: OntologyClass - multivalued: true - annotations: - prompt: >- - in a logical definition expression, this the parent (differentiating characteristic) class, - e.g. hand - - Relation: - is_a: NamedEntity - id_prefixes: - - RO - annotations: - annotators: sqlite:obo:ro - diff --git a/src/ontogpt/templates/ontology_issue.py b/src/ontogpt/templates/ontology_issue.py deleted file mode 100644 index 3f3319e2e..000000000 --- a/src/ontogpt/templates/ontology_issue.py +++ /dev/null @@ -1,205 +0,0 @@ -from __future__ import annotations -from datetime import datetime, date -from enum import Enum -from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, ConfigDict, Field, field_validator -import re -import sys -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal - - -metamodel_version = "None" -version = "None" - -class ConfiguredBaseModel(BaseModel): - model_config = ConfigDict( - validate_assignment=True, - validate_default=True, - extra = 'forbid', - arbitrary_types_allowed=True, - use_enum_values = True) - - -class ProblemType(str, Enum): - - - UNKNOWN = "UNKNOWN" - - TYPO = "TYPO" - - BAD_XREF = "BAD_XREF" - - MISSING_DEFINITION = "MISSING_DEFINITION" - - MISSING_PARENT = "MISSING_PARENT" - - BAD_RELATIONSHIP = "BAD_RELATIONSHIP" - - OTHER = "OTHER" - - - -class ChangeType(str, Enum): - - - UNKNOWN = "UNKNOWN" - - CHANGE_DEFINITION = "CHANGE_DEFINITION" - - CHANGE_LABEL = "CHANGE_LABEL" - - CHANGE_XREF = "CHANGE_XREF" - - MOVE_TERM = "MOVE_TERM" - - - -class NullDataOptions(str, Enum): - - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = "UNSPECIFIED_METHOD_OF_ADMINISTRATION" - - NOT_APPLICABLE = "NOT_APPLICABLE" - - NOT_MENTIONED = "NOT_MENTIONED" - - - -class OntologyIssue(ConfiguredBaseModel): - - title: Optional[str] = Field(None, description="""the title of the issue""") - summary: Optional[str] = Field(None, description="""a high level summary""") - status: Optional[str] = Field(None) - domains: Optional[List[str]] = Field(default_factory=list, description="""What part of the ontology does this pertain to.""") - problem_list: Optional[List[OntologyProblem]] = Field(default_factory=list, description="""A list of problems stated at a high level""") - proposed_changes: Optional[List[OntologyChange]] = Field(default_factory=list, description="""What part of the ontology does this pertain to.""") - - - -class ExtractionResult(ConfiguredBaseModel): - """ - A result of extracting knowledge on text - """ - input_id: Optional[str] = Field(None) - input_title: Optional[str] = Field(None) - input_text: Optional[str] = Field(None) - raw_completion_output: Optional[str] = Field(None) - prompt: Optional[str] = Field(None) - extracted_object: Optional[Any] = Field(None, description="""The complex objects extracted from the text""") - named_entities: Optional[List[Any]] = Field(default_factory=list, description="""Named entities extracted from the text""") - - - -class NamedEntity(ConfiguredBaseModel): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class OntologyClass(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class CompoundExpression(ConfiguredBaseModel): - - None - - - -class OntologyProblem(CompoundExpression): - - description: Optional[str] = Field(None, description="""A succinct description of the problem""") - severity: Optional[str] = Field(None, description="""How severe is this problem?""") - category: Optional[ProblemType] = Field(None, description="""What category does this problem fall into?""") - about: Optional[List[str]] = Field(default_factory=list, description="""What terms in the ontology is this problem about?""") - - - -class OntologyChange(CompoundExpression): - - description: Optional[str] = Field(None, description="""A succinct description of the proposed change""") - category: Optional[ChangeType] = Field(None, description="""What kind of change?""") - about: Optional[List[str]] = Field(default_factory=list, description="""What terms in the ontology will this change affect?""") - - - -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - subject: Optional[str] = Field(None) - predicate: Optional[str] = Field(None) - object: Optional[str] = Field(None) - qualifier: Optional[str] = Field(None, description="""A qualifier for the statements, e.g. \"NOT\" for negation""") - subject_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"""") - object_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"""") - - - -class TextWithTriples(ConfiguredBaseModel): - """ - A text containing one or more relations of the Triple type. - """ - publication: Optional[Publication] = Field(None) - triples: Optional[List[Triple]] = Field(default_factory=list) - - - -class TextWithEntity(ConfiguredBaseModel): - """ - A text containing one or more instances of a single type of entity. - """ - publication: Optional[Publication] = Field(None) - entities: Optional[List[str]] = Field(default_factory=list) - - - -class RelationshipType(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Publication(ConfiguredBaseModel): - - id: Optional[str] = Field(None, description="""The publication identifier""") - title: Optional[str] = Field(None, description="""The title of the publication""") - abstract: Optional[str] = Field(None, description="""The abstract of the publication""") - combined_text: Optional[str] = Field(None) - full_text: Optional[str] = Field(None, description="""The full text of the publication""") - - - -class AnnotatorResult(ConfiguredBaseModel): - - subject_text: Optional[str] = Field(None) - object_id: Optional[str] = Field(None) - object_text: Optional[str] = Field(None) - - - - -# Model rebuild -# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model -OntologyIssue.model_rebuild() -ExtractionResult.model_rebuild() -NamedEntity.model_rebuild() -OntologyClass.model_rebuild() -CompoundExpression.model_rebuild() -OntologyProblem.model_rebuild() -OntologyChange.model_rebuild() -Triple.model_rebuild() -TextWithTriples.model_rebuild() -TextWithEntity.model_rebuild() -RelationshipType.model_rebuild() -Publication.model_rebuild() -AnnotatorResult.model_rebuild() - diff --git a/src/ontogpt/templates/ontology_issue.yaml b/src/ontogpt/templates/ontology_issue.yaml deleted file mode 100644 index 1c875c5a1..000000000 --- a/src/ontogpt/templates/ontology_issue.yaml +++ /dev/null @@ -1,118 +0,0 @@ -id: https://w3id.org/ontogpt/ontology_issue -name: ontology-issue -title: Ontology Issue Data Model -description: >- - A data model for representing the contents of a GitHub issue on an ontology tracker -license: https://creativecommons.org/publicdomain/zero/1.0/ -prefixes: - linkml: https://w3id.org/linkml/ - oc: http://w3id.org/ontogpt/ontology-class-template - -default_prefix: oc -default_range: string - -imports: - - linkml:types - - core - -classes: - OntologyIssue: - tree_root: true - attributes: - title: - description: the title of the issue - summary: - description: a high level summary - annotations: - prompt: >- - a high level one or two line summary of the issue, e.g. "the definition of the class 'bone' is too vague" - status: - domains: - description: >- - What part of the ontology does this pertain to. - annotations: - prompt: >- - semicolon-separated list of grouping terms in the ontology. - range: OntologyClass - multivalued: true - problem_list: - description: A list of problems stated at a high level - annotations: - prompt: >- - semicolon-separated list of problems each written as a simple statement. - For example "T cell is classified in the wrong place" - multivalued: true - range: OntologyProblem - proposed_changes: - description: >- - What part of the ontology does this pertain to. - annotations: - prompt: >- - semicolon-separated list of grouping terms in the ontology. Example terms will be high level - terms in the relevant ontology, e.g. "skeletal system" for an anatomy ontology. - multivalued: true - range: OntologyChange - - OntologyClass: - is_a: NamedEntity - annotations: - annotators: sqlite:obo:go - - OntologyProblem: - is_a: CompoundExpression - attributes: - description: - description: >- - A succinct description of the problem - severity: - description: >- - How severe is this problem? - category: - description: >- - What category does this problem fall into? - range: ProblemType - about: - description: >- - What terms in the ontology is this problem about? - annotations: - prompt: >- - semicolon-separated list of terms in the ontology that are problematic. - range: OntologyClass - multivalued: true - - OntologyChange: - is_a: CompoundExpression - attributes: - description: - description: >- - A succinct description of the proposed change - category: - description: >- - What kind of change? - range: ChangeType - about: - description: >- - What terms in the ontology will this change affect? - annotations: - prompt: >- - semicolon-separated list of specific terms in the ontology which will be affected by the change. - range: OntologyClass - multivalued: true - -enums: - ProblemType: - permissible_values: - UNKNOWN: - TYPO: - BAD_XREF: - MISSING_DEFINITION: - MISSING_PARENT: - BAD_RELATIONSHIP: - OTHER: - ChangeType: - permissible_values: - UNKNOWN: - CHANGE_DEFINITION: - CHANGE_LABEL: - CHANGE_XREF: - MOVE_TERM: diff --git a/src/ontogpt/templates/phenotype.py b/src/ontogpt/templates/phenotype.py deleted file mode 100644 index 45e8cb1bf..000000000 --- a/src/ontogpt/templates/phenotype.py +++ /dev/null @@ -1,165 +0,0 @@ -from __future__ import annotations -from datetime import datetime, date -from enum import Enum -from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, ConfigDict, Field, field_validator -import re -import sys -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal - - -metamodel_version = "None" -version = "None" - -class ConfiguredBaseModel(BaseModel): - model_config = ConfigDict( - validate_assignment=True, - validate_default=True, - extra = 'forbid', - arbitrary_types_allowed=True, - use_enum_values = True) - - -class NullDataOptions(str, Enum): - - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = "UNSPECIFIED_METHOD_OF_ADMINISTRATION" - - NOT_APPLICABLE = "NOT_APPLICABLE" - - NOT_MENTIONED = "NOT_MENTIONED" - - - -class Trait(ConfiguredBaseModel): - - quality: Optional[str] = Field(None, description="""The property being measured, or changes in this property, for example, amount, level, increased amount, decreased concentration""") - anatomical_entity: Optional[str] = Field(None, description="""The anatomical location that the chemical entity is measured in""") - chemical_entity: Optional[str] = Field(None, description="""The chemical entity that is being measured""") - - - -class ExtractionResult(ConfiguredBaseModel): - """ - A result of extracting knowledge on text - """ - input_id: Optional[str] = Field(None) - input_title: Optional[str] = Field(None) - input_text: Optional[str] = Field(None) - raw_completion_output: Optional[str] = Field(None) - prompt: Optional[str] = Field(None) - extracted_object: Optional[Any] = Field(None, description="""The complex objects extracted from the text""") - named_entities: Optional[List[Any]] = Field(default_factory=list, description="""Named entities extracted from the text""") - - - -class NamedEntity(ConfiguredBaseModel): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Quality(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class ChemicalEntity(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class AnatomicalEntity(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class CompoundExpression(ConfiguredBaseModel): - - None - - - -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - subject: Optional[str] = Field(None) - predicate: Optional[str] = Field(None) - object: Optional[str] = Field(None) - qualifier: Optional[str] = Field(None, description="""A qualifier for the statements, e.g. \"NOT\" for negation""") - subject_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"""") - object_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"""") - - - -class TextWithTriples(ConfiguredBaseModel): - """ - A text containing one or more relations of the Triple type. - """ - publication: Optional[Publication] = Field(None) - triples: Optional[List[Triple]] = Field(default_factory=list) - - - -class TextWithEntity(ConfiguredBaseModel): - """ - A text containing one or more instances of a single type of entity. - """ - publication: Optional[Publication] = Field(None) - entities: Optional[List[str]] = Field(default_factory=list) - - - -class RelationshipType(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Publication(ConfiguredBaseModel): - - id: Optional[str] = Field(None, description="""The publication identifier""") - title: Optional[str] = Field(None, description="""The title of the publication""") - abstract: Optional[str] = Field(None, description="""The abstract of the publication""") - combined_text: Optional[str] = Field(None) - full_text: Optional[str] = Field(None, description="""The full text of the publication""") - - - -class AnnotatorResult(ConfiguredBaseModel): - - subject_text: Optional[str] = Field(None) - object_id: Optional[str] = Field(None) - object_text: Optional[str] = Field(None) - - - - -# Model rebuild -# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model -Trait.model_rebuild() -ExtractionResult.model_rebuild() -NamedEntity.model_rebuild() -Quality.model_rebuild() -ChemicalEntity.model_rebuild() -AnatomicalEntity.model_rebuild() -CompoundExpression.model_rebuild() -Triple.model_rebuild() -TextWithTriples.model_rebuild() -TextWithEntity.model_rebuild() -RelationshipType.model_rebuild() -Publication.model_rebuild() -AnnotatorResult.model_rebuild() - diff --git a/src/ontogpt/templates/phenotype.yaml b/src/ontogpt/templates/phenotype.yaml deleted file mode 100644 index 1448cc98f..000000000 --- a/src/ontogpt/templates/phenotype.yaml +++ /dev/null @@ -1,66 +0,0 @@ -id: http://w3id.org/ontogpt/eq -name: eq-template -title: EQ Template -description: >- - A template for Computational Phenotypes -license: https://creativecommons.org/publicdomain/zero/1.0/ -prefixes: - linkml: https://w3id.org/linkml/ - phenotype: http://w3id.org/ontogpt/phenotype/ -keywords: - - phenotype - - traits - -default_prefix: phenotype -default_range: string - -imports: - - linkml:types - - core - -classes: - Trait: - tree_root: true - attributes: - - quality: - description: The property being measured, or changes in this property, for example, amount, level, increased amount, decreased concentration - annotations: - prompt.example: amount, level, increased amount, decreased concentration - range: Quality - - anatomical_entity: - description: The anatomical location that the chemical entity is measured in - range: AnatomicalEntity - annotations: - prompt.example: liver, heart, brain, finger - - chemical_entity: - description: The chemical entity that is being measured - range: ChemicalEntity - annotations: - prompt.example: lysine, metabolite - - - Quality: - is_a: NamedEntity - id_prefixes: - - PATO - annotations: - annotators: sqlite:obo:pato - - ChemicalEntity: - is_a: NamedEntity - id_prefixes: - - CHEBI - - PR - annotations: - annotators: sqlite:obo:chebi - - AnatomicalEntity: - is_a: NamedEntity - id_prefixes: - - UBERON - annotations: - annotators: sqlite:obo:uberon - diff --git a/src/ontogpt/templates/reaction.py b/src/ontogpt/templates/reaction.py deleted file mode 100644 index f836ecc97..000000000 --- a/src/ontogpt/templates/reaction.py +++ /dev/null @@ -1,213 +0,0 @@ -from __future__ import annotations -from datetime import datetime, date -from enum import Enum -from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, ConfigDict, Field, field_validator -import re -import sys -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal - - -metamodel_version = "None" -version = "None" - -class ConfiguredBaseModel(BaseModel): - model_config = ConfigDict( - validate_assignment=True, - validate_default=True, - extra = 'forbid', - arbitrary_types_allowed=True, - use_enum_values = True) - - -class NullDataOptions(str, Enum): - - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = "UNSPECIFIED_METHOD_OF_ADMINISTRATION" - - NOT_APPLICABLE = "NOT_APPLICABLE" - - NOT_MENTIONED = "NOT_MENTIONED" - - - -class GeneToReaction(ConfiguredBaseModel): - - gene: Optional[str] = Field(None, description="""name of the gene that catalyzes the reaction""") - reactions: Optional[Dict[str, Reaction]] = Field(default_factory=dict, description="""semicolon separated list of reaction equations (e.g. A+B = C+D) catalyzed by the gene""") - organism: Optional[str] = Field(None) - - - -class ReactionDocument(ConfiguredBaseModel): - - genes: Optional[List[str]] = Field(default_factory=list, description="""semicolon separated list of genes that catalyzes the mentioned reactions""") - reactions: Optional[Dict[str, Reaction]] = Field(default_factory=dict, description="""semicolon separated list of reaction equations (e.g. A+B = C+D) catalyzed by the gene""") - gene_reaction_pairings: Optional[List[GeneReactionPairing]] = Field(default_factory=list, description="""semicolon separated list of gene to reaction pairings""") - organism: Optional[str] = Field(None) - has_evidence: Optional[List[str]] = Field(default_factory=list, description="""evidence for the reaction""") - - - -class ExtractionResult(ConfiguredBaseModel): - """ - A result of extracting knowledge on text - """ - input_id: Optional[str] = Field(None) - input_title: Optional[str] = Field(None) - input_text: Optional[str] = Field(None) - raw_completion_output: Optional[str] = Field(None) - prompt: Optional[str] = Field(None) - extracted_object: Optional[Any] = Field(None, description="""The complex objects extracted from the text""") - named_entities: Optional[List[Any]] = Field(default_factory=list, description="""Named entities extracted from the text""") - - - -class NamedEntity(ConfiguredBaseModel): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Reaction(NamedEntity): - - label: Optional[str] = Field(None, description="""the name of the reaction""") - description: Optional[str] = Field(None, description="""a textual description of the reaction""") - synonyms: Optional[List[str]] = Field(default_factory=list, description="""alternative names of the reaction""") - subclass_of: Optional[str] = Field(None, description="""the category to which this biological process belongs""") - left_side: Optional[List[str]] = Field(default_factory=list, description="""semicolon separated list of chemical entities on the left side""") - right_side: Optional[List[str]] = Field(default_factory=list, description="""semicolon separated list of chemical entities on the right side""") - id: str = Field(..., description="""A unique identifier for the named entity""") - - - -class ReactionGrouping(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class ChemicalEntity(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Evidence(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Gene(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Organism(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class CompoundExpression(ConfiguredBaseModel): - - None - - - -class GeneReactionPairing(CompoundExpression): - - gene: Optional[str] = Field(None, description="""name of the gene that catalyzes the reaction""") - reaction: Optional[str] = Field(None, description="""equation describing the reaction (e.g. A+B = C+D) catalyzed by the gene""") - - - -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - subject: Optional[str] = Field(None) - predicate: Optional[str] = Field(None) - object: Optional[str] = Field(None) - qualifier: Optional[str] = Field(None, description="""A qualifier for the statements, e.g. \"NOT\" for negation""") - subject_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"""") - object_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"""") - - - -class TextWithTriples(ConfiguredBaseModel): - """ - A text containing one or more relations of the Triple type. - """ - publication: Optional[Publication] = Field(None) - triples: Optional[List[Triple]] = Field(default_factory=list) - - - -class TextWithEntity(ConfiguredBaseModel): - """ - A text containing one or more instances of a single type of entity. - """ - publication: Optional[Publication] = Field(None) - entities: Optional[List[str]] = Field(default_factory=list) - - - -class RelationshipType(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Publication(ConfiguredBaseModel): - - id: Optional[str] = Field(None, description="""The publication identifier""") - title: Optional[str] = Field(None, description="""The title of the publication""") - abstract: Optional[str] = Field(None, description="""The abstract of the publication""") - combined_text: Optional[str] = Field(None) - full_text: Optional[str] = Field(None, description="""The full text of the publication""") - - - -class AnnotatorResult(ConfiguredBaseModel): - - subject_text: Optional[str] = Field(None) - object_id: Optional[str] = Field(None) - object_text: Optional[str] = Field(None) - - - - -# Model rebuild -# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model -GeneToReaction.model_rebuild() -ReactionDocument.model_rebuild() -ExtractionResult.model_rebuild() -NamedEntity.model_rebuild() -Reaction.model_rebuild() -ReactionGrouping.model_rebuild() -ChemicalEntity.model_rebuild() -Evidence.model_rebuild() -Gene.model_rebuild() -Organism.model_rebuild() -CompoundExpression.model_rebuild() -GeneReactionPairing.model_rebuild() -Triple.model_rebuild() -TextWithTriples.model_rebuild() -TextWithEntity.model_rebuild() -RelationshipType.model_rebuild() -Publication.model_rebuild() -AnnotatorResult.model_rebuild() - diff --git a/src/ontogpt/templates/reaction.yaml b/src/ontogpt/templates/reaction.yaml deleted file mode 100644 index 9d1cd0eca..000000000 --- a/src/ontogpt/templates/reaction.yaml +++ /dev/null @@ -1,124 +0,0 @@ -id: https://w3id.org/ontogpt/reaction -name: reaction-template -title: reaction Template -description: >- - A template for reactions -license: https://creativecommons.org/publicdomain/zero/1.0/ -prefixes: - linkml: https://w3id.org/linkml/ - reaction: http://w3id.org/ontogpt/reaction/ - -default_prefix: reaction -default_range: string - -imports: - - linkml:types - - core - -classes: - Reaction: - is_a: NamedEntity - attributes: - label: - description: the name of the reaction - description: - description: a textual description of the reaction - synonyms: - description: alternative names of the reaction - multivalued: true - subclass_of: - description: the category to which this biological process belongs - range: ReactionGrouping - left_side: - description: semicolon separated list of chemical entities on the left side - multivalued: true - range: ChemicalEntity - right_side: - description: semicolon separated list of chemical entities on the right side - multivalued: true - range: ChemicalEntity - - GeneToReaction: - attributes: - gene: - range: Gene - description: name of the gene that catalyzes the reaction - reactions: - range: Reaction - description: semicolon separated list of reaction equations (e.g. A+B = C+D) catalyzed by the gene - multivalued: true - inlined: true - organism: - range: Organism - - ReactionDocument: - attributes: - genes: - range: Gene - description: semicolon separated list of genes that catalyzes the mentioned reactions - multivalued: true - reactions: - range: Reaction - description: semicolon separated list of reaction equations (e.g. A+B = C+D) catalyzed by the gene - multivalued: true - inlined: true - gene_reaction_pairings: - range: GeneReactionPairing - description: semicolon separated list of gene to reaction pairings - multivalued: true - inlined: true - organism: - range: Organism - has_evidence: - range: Evidence - description: evidence for the reaction - multivalued: true - - GeneReactionPairing: - is_a: CompoundExpression - attributes: - gene: - range: Gene - description: name of the gene that catalyzes the reaction - reaction: - range: Reaction - description: equation describing the reaction (e.g. A+B = C+D) catalyzed by the gene - - ReactionGrouping: - is_a: NamedEntity - id_prefixes: - - GO - annotations: - annotators: sqlite:obo:go - - ChemicalEntity: - is_a: NamedEntity - id_prefixes: - - CHEBI - annotations: - annotators: sqlite:obo:chebi - - Evidence: - is_a: NamedEntity - id_prefixes: - - OBI - - ECO - - MS - annotations: - annotators: sqlite:obo:obi, sqlite:obo:eco, sqlite:obo:ms - - Gene: - is_a: NamedEntity - id_prefixes: - - HGNC - annotations: - annotators: gilda:, bioportal:hgnc-nr, bioportal:pr - - Organism: - is_a: NamedEntity - id_prefixes: - - NCBITaxon - annotations: - annotators: gilda:, sqlite:obo:ncbitaxon - - diff --git a/src/ontogpt/templates/recipe.py b/src/ontogpt/templates/recipe.py deleted file mode 100644 index 394e17304..000000000 --- a/src/ontogpt/templates/recipe.py +++ /dev/null @@ -1,218 +0,0 @@ -from __future__ import annotations -from datetime import datetime, date -from enum import Enum -from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, ConfigDict, Field, field_validator -import re -import sys -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal - - -metamodel_version = "None" -version = "None" - -class ConfiguredBaseModel(BaseModel): - model_config = ConfigDict( - validate_assignment=True, - validate_default=True, - extra = 'forbid', - arbitrary_types_allowed=True, - use_enum_values = True) - - -class NullDataOptions(str, Enum): - - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = "UNSPECIFIED_METHOD_OF_ADMINISTRATION" - - NOT_APPLICABLE = "NOT_APPLICABLE" - - NOT_MENTIONED = "NOT_MENTIONED" - - - -class Recipe(ConfiguredBaseModel): - - url: str = Field(...) - label: Optional[str] = Field(None, description="""the name of the recipe""") - description: Optional[str] = Field(None, description="""a brief textual description of the recipe""") - categories: Optional[List[str]] = Field(default_factory=list, description="""a semicolon separated list of the categories to which this recipe belongs""") - ingredients: Optional[List[Ingredient]] = Field(default_factory=list, description="""a semicolon separated list of the ingredients plus quantities of the recipe""") - steps: Optional[List[Step]] = Field(default_factory=list, description="""a semicolon separated list of the individual steps involved in this recipe""") - - - -class ExtractionResult(ConfiguredBaseModel): - """ - A result of extracting knowledge on text - """ - input_id: Optional[str] = Field(None) - input_title: Optional[str] = Field(None) - input_text: Optional[str] = Field(None) - raw_completion_output: Optional[str] = Field(None) - prompt: Optional[str] = Field(None) - extracted_object: Optional[Any] = Field(None, description="""The complex objects extracted from the text""") - named_entities: Optional[List[Any]] = Field(default_factory=list, description="""Named entities extracted from the text""") - - - -class NamedEntity(ConfiguredBaseModel): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class FoodType(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class RecipeCategory(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Action(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class UtensilType(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Unit(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class CompoundExpression(ConfiguredBaseModel): - - None - - - -class Ingredient(CompoundExpression): - - food_item: Optional[FoodItem] = Field(None, description="""the food item""") - amount: Optional[Quantity] = Field(None, description="""the quantity of the ingredient, e.g. 2 lbs""") - - - -class Quantity(CompoundExpression): - - value: Optional[str] = Field(None, description="""the value of the quantity""") - unit: Optional[str] = Field(None, description="""the unit of the quantity, e.g. grams, cups, etc.""") - - - -class Step(CompoundExpression): - - action: Optional[str] = Field(None, description="""the action taken in this step (e.g. mix, add)""") - inputs: Optional[List[FoodItem]] = Field(default_factory=list, description="""a semicolon separated list of the inputs of this step""") - outputs: Optional[List[FoodItem]] = Field(default_factory=list, description="""a semicolon separated list of the outputs of this step""") - utensils: Optional[List[str]] = Field(default_factory=list, description="""the kitchen utensil used in this step (e.g. pan, bowl)""") - - - -class FoodItem(CompoundExpression): - - food: Optional[str] = Field(None, description="""the food item""") - state: Optional[str] = Field(None, description="""the state of the food item (e.g. chopped, diced)""") - - - -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - subject: Optional[str] = Field(None) - predicate: Optional[str] = Field(None) - object: Optional[str] = Field(None) - qualifier: Optional[str] = Field(None, description="""A qualifier for the statements, e.g. \"NOT\" for negation""") - subject_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"""") - object_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"""") - - - -class TextWithTriples(ConfiguredBaseModel): - """ - A text containing one or more relations of the Triple type. - """ - publication: Optional[Publication] = Field(None) - triples: Optional[List[Triple]] = Field(default_factory=list) - - - -class TextWithEntity(ConfiguredBaseModel): - """ - A text containing one or more instances of a single type of entity. - """ - publication: Optional[Publication] = Field(None) - entities: Optional[List[str]] = Field(default_factory=list) - - - -class RelationshipType(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Publication(ConfiguredBaseModel): - - id: Optional[str] = Field(None, description="""The publication identifier""") - title: Optional[str] = Field(None, description="""The title of the publication""") - abstract: Optional[str] = Field(None, description="""The abstract of the publication""") - combined_text: Optional[str] = Field(None) - full_text: Optional[str] = Field(None, description="""The full text of the publication""") - - - -class AnnotatorResult(ConfiguredBaseModel): - - subject_text: Optional[str] = Field(None) - object_id: Optional[str] = Field(None) - object_text: Optional[str] = Field(None) - - - - -# Model rebuild -# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model -Recipe.model_rebuild() -ExtractionResult.model_rebuild() -NamedEntity.model_rebuild() -FoodType.model_rebuild() -RecipeCategory.model_rebuild() -Action.model_rebuild() -UtensilType.model_rebuild() -Unit.model_rebuild() -CompoundExpression.model_rebuild() -Ingredient.model_rebuild() -Quantity.model_rebuild() -Step.model_rebuild() -FoodItem.model_rebuild() -Triple.model_rebuild() -TextWithTriples.model_rebuild() -TextWithEntity.model_rebuild() -RelationshipType.model_rebuild() -Publication.model_rebuild() -AnnotatorResult.model_rebuild() - diff --git a/src/ontogpt/templates/recipe.yaml b/src/ontogpt/templates/recipe.yaml deleted file mode 100644 index 6f1c55165..000000000 --- a/src/ontogpt/templates/recipe.yaml +++ /dev/null @@ -1,217 +0,0 @@ -id: https://w3id.org/ontogpt/recipe -name: recipe-template -title: Food Recipe Template -description: >- - A template for food recipes -license: https://creativecommons.org/publicdomain/zero/1.0/ -prefixes: - linkml: https://w3id.org/linkml/ - recipe: http://w3id.org/ontogpt/recipe/ - FOODON: http://purl.obolibrary.org/obo/FOODON_ - UO: http://purl.obolibrary.org/obo/UO_ - dcterms: http://purl.org/dc/terms/ - HANCESTRO: http://purl.obolibrary.org/obo/HANCESTRO_ - BFO: http://purl.obolibrary.org/obo/BFO_ - AUTO: http://example.org/auto/ - RO: http://purl.obolibrary.org/obo/RO_ - qudt: http://qudt.org/schema/qudt/ - dbpediaont: http://dbpedia.org/ontology/ - -# This template incorportates syntax from -# linkml-owl to define OWL interpretations -# and enable advanced functionality. -# https://linkml.io/linkml-owl/templates/ - -default_prefix: recipe -default_range: string - -imports: - - linkml:types - - core - -classes: - Recipe: - tree_root: true - close_mappings: - - FOODON:00004081 # food recipe - attributes: - url: - identifier: true - range: uriorcurie - slot_uri: rdf:Resource - annotations: - prompt.skip: true - label: - description: the name of the recipe - slot_uri: rdfs:label - annotations: - owl: AnnotationProperty, AnnotationAssertion - description: - description: a brief textual description of the recipe - slot_uri: dcterms:description - annotations: - owl: AnnotationProperty, AnnotationAssertion - categories: - description: a semicolon separated list of the categories to which this recipe belongs - range: RecipeCategory - multivalued: true - slot_uri: dcterms:subject - annotations: - owl: AnnotationAssertion - ingredients: - description: a semicolon separated list of the ingredients plus quantities of the recipe - multivalued: true - range: Ingredient - slot_uri: FOODON:00002420 - annotations: - owl: ObjectProperty, ObjectSomeValuesFrom - steps: - description: a semicolon separated list of the individual steps involved in this recipe - multivalued: true - range: Step - annotations: - owl: ObjectProperty, ObjectSomeValuesFrom - annotations: - owl: Class - owl.template: | - EquivalentClasses( - {{url}} - ObjectIntersectionOf( - recipe:Recipe - - {% for step in steps %} - ObjectSomeValuesFrom( - recipe:steps - {{tr(step)}} - ) - {% endfor %} - {% for ingredient in ingredients %} - ObjectSomeValuesFrom( - FOODON:00002420 - {{tr(ingredient)}} - ) - {% endfor %} - ) - ) - Ingredient: - is_a: CompoundExpression - class_uri: FOODON:00004085 - annotations: - owl: IntersectionOf - attributes: - food_item: - description: the food item - range: FoodItem - annotations: - owl: ObjectProperty, ObjectSomeValuesFrom - amount: - description: the quantity of the ingredient, e.g. 2 lbs - range: Quantity - annotations: - owl: ObjectProperty, ObjectSomeValuesFrom - - Quantity: - is_a: CompoundExpression - annotations: - owl: IntersectionOf - attributes: - value: - description: the value of the quantity - #range: float - annotations: - owl: DataProperty, DataHasValue - unit: - description: the unit of the quantity, e.g. grams, cups, etc. - range: Unit - slot_uri: qudt:unit - annotations: - owl: ObjectProperty, ObjectSomeValuesFrom - - Step: - is_a: CompoundExpression - class_uri: FOODON:00004087 - annotations: - owl: IntersectionOf - attributes: - action: - description: the action taken in this step (e.g. mix, add) - range: Action - inputs: - description: a semicolon separated list of the inputs of this step - range: FoodItem - multivalued: true - slot_uri: RO:0002233 - annotations: - owl: ObjectProperty, ObjectSomeValuesFrom - outputs: - description: a semicolon separated list of the outputs of this step - range: FoodItem - multivalued: true - slot_uri: RO:0002234 - annotations: - owl: ObjectProperty, ObjectSomeValuesFrom - utensils: - description: the kitchen utensil used in this step (e.g. pan, bowl) - range: UtensilType - multivalued: true - slot_uri: RO:0002500 - annotations: - owl: ObjectProperty, ObjectSomeValuesFrom - - FoodItem: - is_a: CompoundExpression - annotations: - owl: IntersectionOf - attributes: - food: - description: the food item - range: FoodType - slot_uri: BFO:0000051 - annotations: - owl: ObjectProperty, ObjectSomeValuesFrom - state: - description: the state of the food item (e.g. chopped, diced) - annotations: - owl: DataProperty, DataHasValue - - FoodType: - is_a: NamedEntity - id_prefixes: - - dbpediaont - - FOODON - annotations: - annotators: sqlite:obo:foodon, sqlite:obo:dbpediaont - - RecipeCategory: - is_a: NamedEntity - id_prefixes: - - dbpediaont - - FOODON - - HANCESTRO - annotations: - annotators: sqlite:obo:foodon, sqlite:obo:dbpediaont - - Action: - is_a: NamedEntity - id_prefixes: - - dbpediaont - - FOODON - annotations: - annotators: sqlite:obo:dbpediaont, sqlite:obo:foodon - - UtensilType: - is_a: NamedEntity - id_prefixes: - - dbpediaont - - FOODON - annotations: - annotators: sqlite:obo:dbpediaont, sqlite:obo:foodon - - Unit: - is_a: NamedEntity - id_prefixes: - - UO - - NCIT - - dbpediaont - annotations: - annotators: sqlite:obo:uo, sqlite:obo:dbpediaont, sqlite:obo:foodon diff --git a/src/ontogpt/templates/traits.py b/src/ontogpt/templates/traits.py deleted file mode 100644 index 37fc7d712..000000000 --- a/src/ontogpt/templates/traits.py +++ /dev/null @@ -1,155 +0,0 @@ -from __future__ import annotations -from datetime import datetime, date -from enum import Enum -from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, ConfigDict, Field, field_validator -import re -import sys -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal - - -metamodel_version = "None" -version = "None" - -class ConfiguredBaseModel(BaseModel): - model_config = ConfigDict( - validate_assignment=True, - validate_default=True, - extra = 'forbid', - arbitrary_types_allowed=True, - use_enum_values = True) - - -class NullDataOptions(str, Enum): - - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = "UNSPECIFIED_METHOD_OF_ADMINISTRATION" - - NOT_APPLICABLE = "NOT_APPLICABLE" - - NOT_MENTIONED = "NOT_MENTIONED" - - - -class Taxon(ConfiguredBaseModel): - - metabolic_traits: Optional[List[str]] = Field(default_factory=list, description="""The metabolic traits for the taxon.""") - morphological_traits: Optional[List[str]] = Field(default_factory=list, description="""The morphological traits for the taxon.""") - genetic_traits: Optional[List[str]] = Field(default_factory=list, description="""The genetic traits for the taxon.""") - cellular_traits: Optional[List[str]] = Field(default_factory=list, description="""The cellular traits for the taxon.""") - ecological_traits: Optional[List[str]] = Field(default_factory=list, description="""The ecological traits for the taxon.""") - reproductive_traits: Optional[List[str]] = Field(default_factory=list, description="""The reproductive traits for the taxon.""") - survival_traits: Optional[List[str]] = Field(default_factory=list, description="""The survival traits for the taxon.""") - phenotypic_plasticiticy_traits: Optional[List[str]] = Field(default_factory=list, description="""The phenotypic plasticiticy traits for the taxon.""") - preferred_environments: Optional[List[str]] = Field(default_factory=list, description="""The preferred environments for the taxon.""") - - - -class ExtractionResult(ConfiguredBaseModel): - """ - A result of extracting knowledge on text - """ - input_id: Optional[str] = Field(None) - input_title: Optional[str] = Field(None) - input_text: Optional[str] = Field(None) - raw_completion_output: Optional[str] = Field(None) - prompt: Optional[str] = Field(None) - extracted_object: Optional[Any] = Field(None, description="""The complex objects extracted from the text""") - named_entities: Optional[List[Any]] = Field(default_factory=list, description="""Named entities extracted from the text""") - - - -class NamedEntity(ConfiguredBaseModel): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Trait(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class CompoundExpression(ConfiguredBaseModel): - - None - - - -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - subject: Optional[str] = Field(None) - predicate: Optional[str] = Field(None) - object: Optional[str] = Field(None) - qualifier: Optional[str] = Field(None, description="""A qualifier for the statements, e.g. \"NOT\" for negation""") - subject_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"""") - object_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"""") - - - -class TextWithTriples(ConfiguredBaseModel): - """ - A text containing one or more relations of the Triple type. - """ - publication: Optional[Publication] = Field(None) - triples: Optional[List[Triple]] = Field(default_factory=list) - - - -class TextWithEntity(ConfiguredBaseModel): - """ - A text containing one or more instances of a single type of entity. - """ - publication: Optional[Publication] = Field(None) - entities: Optional[List[str]] = Field(default_factory=list) - - - -class RelationshipType(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Publication(ConfiguredBaseModel): - - id: Optional[str] = Field(None, description="""The publication identifier""") - title: Optional[str] = Field(None, description="""The title of the publication""") - abstract: Optional[str] = Field(None, description="""The abstract of the publication""") - combined_text: Optional[str] = Field(None) - full_text: Optional[str] = Field(None, description="""The full text of the publication""") - - - -class AnnotatorResult(ConfiguredBaseModel): - - subject_text: Optional[str] = Field(None) - object_id: Optional[str] = Field(None) - object_text: Optional[str] = Field(None) - - - - -# Model rebuild -# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model -Taxon.model_rebuild() -ExtractionResult.model_rebuild() -NamedEntity.model_rebuild() -Trait.model_rebuild() -CompoundExpression.model_rebuild() -Triple.model_rebuild() -TextWithTriples.model_rebuild() -TextWithEntity.model_rebuild() -RelationshipType.model_rebuild() -Publication.model_rebuild() -AnnotatorResult.model_rebuild() - diff --git a/src/ontogpt/templates/traits.yaml b/src/ontogpt/templates/traits.yaml deleted file mode 100644 index 4bf068a2d..000000000 --- a/src/ontogpt/templates/traits.yaml +++ /dev/null @@ -1,101 +0,0 @@ -id: http://w3id.org/ontogpt/traits -name: traits -title: Traits Template -description: >- - A template for Traits -license: https://creativecommons.org/publicdomain/zero/1.0/ -prefixes: - linkml: https://w3id.org/linkml/ - traits: http://w3id.org/ontogpt/traits/ - -default_prefix: traits -default_range: string - -imports: - - linkml:types - - core - -classes: - Taxon: - tree_root: true - attributes: - # name: - # description: The name of the taxon. - # annotations: - # prompt: The name of the taxon. - # range: string - #traits: - # description: The traits for the taxon. - # annotations: - # prompt: a semicolon separated list of every specific organism characteristic such as metabolic or cellular - # prompt: List every specific characteristic measured of the target organism by the described research. Include both common and novel microbial traits. A semicolon separated list. - # range: Trait - # multivalued: true - metabolic_traits: - description: The metabolic traits for the taxon. - annotations: - prompt: a semicolon separated list of every specific organism metabolic trait - range: Trait - multivalued: true - morphological_traits: - description: The morphological traits for the taxon. - annotations: - prompt: a semicolon separated list of every specific organism morphological trait - range: Trait - multivalued: true - genetic_traits: - description: The genetic traits for the taxon. - annotations: - prompt: a semicolon separated list of every specific organism genetic trait - range: Trait - multivalued: true - cellular_traits: - description: The cellular traits for the taxon. - annotations: - prompt: a semicolon separated list of every specific organism cellular trait - range: Trait - multivalued: true - ecological_traits: - description: The ecological traits for the taxon. - annotations: - prompt: a semicolon separated list of every specific organism ecological trait - range: Trait - multivalued: true - reproductive_traits: - description: The reproductive traits for the taxon. - annotations: - prompt: a semicolon separated list of every specific organism reproductive trait - range: Trait - multivalued: true - survival_traits: - description: The survival traits for the taxon. - annotations: - prompt: a semicolon separated list of every specific organism survival trait - range: Trait - multivalued: true - phenotypic_plasticiticy_traits: - description: The phenotypic plasticiticy traits for the taxon. - annotations: - prompt: a semicolon separated list of every specific organism phenotypic plasticiticy trait - range: Trait - multivalued: true - preferred_environments: - description: The preferred environments for the taxon. - annotations: - prompt: a semicolon separated list of the environments the organism is typically found in or isolated from - range: Trait - multivalued: true - - - Trait: - is_a: NamedEntity - id_prefixes: - - ECOCORE - - PATO - - GO - #- ENVTHES - - OBA - - BIODIVTHES - annotations: - annotators: sqlite:obo:ecocore, sqlite:obo:pato, sqlite:obo:go, sqlite:obo:oba, bioportal:biodivthes - #bioportal:envthes, \ No newline at end of file diff --git a/src/ontogpt/templates/treatment.py b/src/ontogpt/templates/treatment.py deleted file mode 100644 index 6644eeac4..000000000 --- a/src/ontogpt/templates/treatment.py +++ /dev/null @@ -1,261 +0,0 @@ -from __future__ import annotations -from datetime import datetime, date -from enum import Enum -from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, ConfigDict, Field, field_validator -import re -import sys -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal - - -metamodel_version = "None" -version = "None" - -class ConfiguredBaseModel(BaseModel): - model_config = ConfigDict( - validate_assignment=True, - validate_default=True, - extra = 'forbid', - arbitrary_types_allowed=True, - use_enum_values = True) - - -class NCITDrugType(str): - - - dummy = "dummy" - - -class NCITTreatmentType(str): - - - dummy = "dummy" - - -class NCITTActivityType(str): - - - dummy = "dummy" - - -class MAXOActionType(str): - - - dummy = "dummy" - - -class MESHTherapeuticType(str): - - - dummy = "dummy" - - -class CHEBIDrugType(str): - - - dummy = "dummy" - - -class NullDataOptions(str, Enum): - - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = "UNSPECIFIED_METHOD_OF_ADMINISTRATION" - - NOT_APPLICABLE = "NOT_APPLICABLE" - - NOT_MENTIONED = "NOT_MENTIONED" - - - -class DiseaseTreatmentSummary(ConfiguredBaseModel): - - disease: Optional[str] = Field(None, description="""the name of the disease that is treated.""") - drugs: Optional[List[str]] = Field(default_factory=list, description="""semicolon-separated list of named small molecule drugs""") - treatments: Optional[List[str]] = Field(default_factory=list, description="""semicolon-separated list of therapies and treatments are indicated for treating the disease.""") - contraindications: Optional[List[str]] = Field(default_factory=list, description="""semicolon-separated list of therapies and treatments that are contra-indicated for the disease, and should not be used, due to risk of adverse effects.""") - treatment_mechanisms: Optional[List[TreatmentMechanism]] = Field(default_factory=list, description="""semicolon-separated list of treatment to asterisk-separated mechanism associations""") - treatment_efficacies: Optional[List[TreatmentEfficacy]] = Field(default_factory=list, description="""semicolon-separated list of treatment to efficacy associations, e.g. Imatinib*effective""") - treatment_adverse_effects: Optional[List[TreatmentAdverseEffect]] = Field(default_factory=list, description="""semicolon-separated list of treatment to adverse effect associations, e.g. Imatinib*nausea""") - - - -class ExtractionResult(ConfiguredBaseModel): - """ - A result of extracting knowledge on text - """ - input_id: Optional[str] = Field(None) - input_title: Optional[str] = Field(None) - input_text: Optional[str] = Field(None) - raw_completion_output: Optional[str] = Field(None) - prompt: Optional[str] = Field(None) - extracted_object: Optional[Any] = Field(None, description="""The complex objects extracted from the text""") - named_entities: Optional[List[Any]] = Field(default_factory=list, description="""Named entities extracted from the text""") - - - -class NamedEntity(ConfiguredBaseModel): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Gene(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Symptom(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Disease(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class AdverseEffect(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Treatment(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Mechanism(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Drug(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class CompoundExpression(ConfiguredBaseModel): - - None - - - -class TreatmentMechanism(CompoundExpression): - - treatment: Optional[str] = Field(None) - mechanism: Optional[str] = Field(None) - - - -class TreatmentAdverseEffect(CompoundExpression): - - treatment: Optional[str] = Field(None) - adverse_effects: Optional[List[str]] = Field(default_factory=list) - - - -class TreatmentEfficacy(CompoundExpression): - - treatment: Optional[str] = Field(None) - efficacy: Optional[str] = Field(None) - - - -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - subject: Optional[str] = Field(None) - predicate: Optional[str] = Field(None) - object: Optional[str] = Field(None) - qualifier: Optional[str] = Field(None, description="""A qualifier for the statements, e.g. \"NOT\" for negation""") - subject_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"""") - object_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"""") - - - -class TextWithTriples(ConfiguredBaseModel): - """ - A text containing one or more relations of the Triple type. - """ - publication: Optional[Publication] = Field(None) - triples: Optional[List[Triple]] = Field(default_factory=list) - - - -class TextWithEntity(ConfiguredBaseModel): - """ - A text containing one or more instances of a single type of entity. - """ - publication: Optional[Publication] = Field(None) - entities: Optional[List[str]] = Field(default_factory=list) - - - -class RelationshipType(NamedEntity): - - id: str = Field(..., description="""A unique identifier for the named entity""") - label: Optional[str] = Field(None, description="""The label (name) of the named thing""") - - - -class Publication(ConfiguredBaseModel): - - id: Optional[str] = Field(None, description="""The publication identifier""") - title: Optional[str] = Field(None, description="""The title of the publication""") - abstract: Optional[str] = Field(None, description="""The abstract of the publication""") - combined_text: Optional[str] = Field(None) - full_text: Optional[str] = Field(None, description="""The full text of the publication""") - - - -class AnnotatorResult(ConfiguredBaseModel): - - subject_text: Optional[str] = Field(None) - object_id: Optional[str] = Field(None) - object_text: Optional[str] = Field(None) - - - - -# Model rebuild -# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model -DiseaseTreatmentSummary.model_rebuild() -ExtractionResult.model_rebuild() -NamedEntity.model_rebuild() -Gene.model_rebuild() -Symptom.model_rebuild() -Disease.model_rebuild() -AdverseEffect.model_rebuild() -Treatment.model_rebuild() -Mechanism.model_rebuild() -Drug.model_rebuild() -CompoundExpression.model_rebuild() -TreatmentMechanism.model_rebuild() -TreatmentAdverseEffect.model_rebuild() -TreatmentEfficacy.model_rebuild() -Triple.model_rebuild() -TextWithTriples.model_rebuild() -TextWithEntity.model_rebuild() -RelationshipType.model_rebuild() -Publication.model_rebuild() -AnnotatorResult.model_rebuild() - diff --git a/src/ontogpt/templates/treatment.yaml b/src/ontogpt/templates/treatment.yaml deleted file mode 100644 index 959f6acc0..000000000 --- a/src/ontogpt/templates/treatment.yaml +++ /dev/null @@ -1,183 +0,0 @@ -id: http://w3id.org/ontogpt/treatment -name: treatment-template -title: MAXO treatment Template -description: >- - A template for MAXO treatments -license: https://creativecommons.org/publicdomain/zero/1.0/ -prefixes: - linkml: https://w3id.org/linkml/ - treatment: http://w3id.org/ontogpt/treatments/ -keywords: - - treatments - - drugs - - therapies - -default_prefix: treatment -default_range: string - -imports: - - linkml:types - - core - -classes: - DiseaseTreatmentSummary: - tree_root: true - attributes: - disease: - description: the name of the disease that is treated. - range: Disease - - drugs: - description: semicolon-separated list of named small molecule drugs - multivalued: true - range: Drug - - treatments: - description: >- - semicolon-separated list of therapies and treatments are indicated for treating the disease. - annotations: - prompt.examples: Imatinib, exercise, surgery - multivalued: true - range: Treatment - - contraindications: - description: >- - semicolon-separated list of therapies and treatments that are contra-indicated for the disease, - and should not be used, due to risk of adverse effects. - annotations: - prompt.examples: Beta-blockers, exercise, surgery - multivalued: true - range: Treatment - - treatment_mechanisms: - description: semicolon-separated list of treatment to asterisk-separated mechanism associations - multivalued: true - range: TreatmentMechanism - annotations: - prompt.separator: "*" - - treatment_efficacies: - description: semicolon-separated list of treatment to efficacy associations, e.g. Imatinib*effective - multivalued: true - range: TreatmentEfficacy - annotations: - prompt.separator: "*" - - treatment_adverse_effects: - description: semicolon-separated list of treatment to adverse effect associations, e.g. Imatinib*nausea - multivalued: true - range: TreatmentAdverseEffect - annotations: - prompt.separator: "*" - - Gene: - is_a: NamedEntity - id_prefixes: - - HGNC - annotations: - annotators: gilda:, obo:sql:hgnc, bioportal:hgnc-nr - - Symptom: - is_a: NamedEntity - id_prefixes: - - HP - annotations: - annotators: sqlite:obo:hp - - Disease: - is_a: NamedEntity - annotations: - annotators: sqlite:obo:mondo - - AdverseEffect: - is_a: NamedEntity - annotations: - annotators: sqlite:obo:hp, sqlite:obo:ncit - - Treatment: - is_a: NamedEntity - annotations: - annotators: sqlite:obo:maxo, sqlite:obo:ncit, sqlite:obo:mesh, sqlite:obo:chebi - values_from: - - NCITDrugType - - NCITTreatmentType - - NCITActivityType - - MAXOTreatmentType - - MESHTherapeuticType - - CHEBIDrugType - - Mechanism: - is_a: NamedEntity - annotations: - annotators: sqlite:obo:go, sqlite:obo:ncit, sqlite:obo:mesh - - Drug: - is_a: NamedEntity - annotations: - annotators: sqlite:obo:chebi, sqlite:obo:drugbank - - TreatmentMechanism: - is_a: CompoundExpression - attributes: - treatment: - range: Treatment - mechanism: - range: Mechanism - - TreatmentAdverseEffect: - is_a: CompoundExpression - attributes: - treatment: - range: Treatment - adverse_effects: - range: AdverseEffect - multivalued: true - - TreatmentEfficacy: - is_a: CompoundExpression - attributes: - treatment: - range: Treatment - efficacy: - range: string - -enums: - - NCITDrugType: - reachable_from: - source_ontology: obo:ncit - source_nodes: - - NCIT:C1908 ## Drug, Food, Chemical or Biomedical Material - - NCITTreatmentType: - reachable_from: - source_ontology: obo:ncit - source_nodes: - - NCIT:C25218 ## Intervention or Procedure - - NCITTActivityType: - reachable_from: - source_ontology: obo:ncit - source_nodes: - - NCIT:C43431 ## Activity - - MAXOActionType: - reachable_from: - source_ontology: obo:maxo - source_nodes: - - MAXO:0000001 ## Medical Action - - MESHTherapeuticType: - reachable_from: - source_ontology: obo:mesh - source_nodes: - - MESH:D013812 ## Therapeutics - - CHEBIDrugType: - reachable_from: - source_ontology: obo:chebi - source_nodes: - - CHEBI:23888 ## drug - relationship_types: - - rdfs:subClassOf - - RO:0000087 \ No newline at end of file diff --git a/src/ontogpt/utils/__init__.py b/src/ontogpt/utils/__init__.py deleted file mode 100644 index e69de29bb..000000000 diff --git a/src/ontogpt/utils/gpt4all_runner.py b/src/ontogpt/utils/gpt4all_runner.py deleted file mode 100644 index 264b3bd4b..000000000 --- a/src/ontogpt/utils/gpt4all_runner.py +++ /dev/null @@ -1,21 +0,0 @@ -"""Tools for loading and working with GPT4All models.""" - -import logging - -import llm - - -def set_up_gpt4all_model(modelname): - """Prepare a GPT4All model for LLM interaction.""" - logging.info(f"Preparing {modelname}...") - - model = llm.get_model(modelname) - - return model - - -def chain_gpt4all_model(model, prompt_text): - """Interact with a GPT4All model.""" - raw_output = model.prompt(prompt_text) - - return raw_output.text() diff --git a/src/ontogpt/utils/model_utils.py b/src/ontogpt/utils/model_utils.py deleted file mode 100644 index e0aabe726..000000000 --- a/src/ontogpt/utils/model_utils.py +++ /dev/null @@ -1,21 +0,0 @@ -"""Utilities for retrieving and applying prebuild models.""" - -import logging -from pathlib import PosixPath - -import pystow - -ONTOGPT_MODULE = pystow.module("ontogpt") - - -def get_model(url: str) -> PosixPath: - """Retrieve a model from a given URL. - - Returns the Path for the retrieved file, - or the path to where it already exists. - """ - logging.info(f"Retrieving model from {url} if needed...") - mod_path = ONTOGPT_MODULE.ensure(url=url, force=False, download_kwargs={"backend": "requests"}) - logging.info(f"Model now at {mod_path}") - - return mod_path diff --git a/src/ontogpt/utils/parse_utils.py b/src/ontogpt/utils/parse_utils.py deleted file mode 100644 index cd043d7ae..000000000 --- a/src/ontogpt/utils/parse_utils.py +++ /dev/null @@ -1,10 +0,0 @@ -"""Utilities for parsing text.""" -from typing import List - - -def split_on_one_of(text: str, separators: List[str]) -> List[str]: - """Split text on the first separator found.""" - for sep in separators: - if sep in text: - return text.split(sep) - return [text] diff --git a/src/ontogpt/webapp/__init__.py b/src/ontogpt/webapp/__init__.py deleted file mode 100644 index e69de29bb..000000000 diff --git a/src/ontogpt/webapp/html/form.html b/src/ontogpt/webapp/html/form.html deleted file mode 100644 index fafa0541f..000000000 --- a/src/ontogpt/webapp/html/form.html +++ /dev/null @@ -1,40 +0,0 @@ -<!DOCTYPE html> -<html lang="en"> -<head> - <meta charset="UTF-8"> - <title>OntoGPT SPIRES: Enter text - - -
-
-
- Select Schema: - -
- -
- -
- -
- -
- -
-
-

Powered by OntoGPT

-
- - diff --git a/src/ontogpt/webapp/html/results.html b/src/ontogpt/webapp/html/results.html deleted file mode 100644 index 92f4b0dd9..000000000 --- a/src/ontogpt/webapp/html/results.html +++ /dev/null @@ -1,15 +0,0 @@ - - - - - SPIRES: Results - - - - -{{ inner_html|safe }} - - - diff --git a/src/ontogpt/webapp/html/spindoctor/form.html b/src/ontogpt/webapp/html/spindoctor/form.html deleted file mode 100644 index 28d39826a..000000000 --- a/src/ontogpt/webapp/html/spindoctor/form.html +++ /dev/null @@ -1,32 +0,0 @@ - - - - - OntoGPT SPINDOCTOR: Enter genes - - -
-
-
- Select Model: - -
-
- -
- -
- -
- -
-
-

Powered by OntoGPT

-
- - diff --git a/src/ontogpt/webapp/html/spindoctor/results.html b/src/ontogpt/webapp/html/spindoctor/results.html deleted file mode 100644 index 8df392d76..000000000 --- a/src/ontogpt/webapp/html/spindoctor/results.html +++ /dev/null @@ -1,15 +0,0 @@ - - - - - SPINDOCTOR: Results - - - - -{{ inner_html|safe }} - - - diff --git a/src/ontogpt/webapp/main.py b/src/ontogpt/webapp/main.py deleted file mode 100644 index 4503bde15..000000000 --- a/src/ontogpt/webapp/main.py +++ /dev/null @@ -1,92 +0,0 @@ -"""Webapp main function.""" -from io import StringIO -from pathlib import Path -from typing import Dict - -import uvicorn -from fastapi import FastAPI, Form, Request -from pydantic import BaseModel -from starlette.staticfiles import StaticFiles -from starlette.templating import Jinja2Templates - -from ontogpt import MODELS -from ontogpt.engines.enrichment import EnrichmentEngine -from ontogpt.engines.knowledge_engine import DATAMODELS -from ontogpt.engines.spires_engine import SPIRESEngine -from ontogpt.io.html_exporter import HTMLExporter -from ontogpt.utils.gene_set_utils import GeneSet - -this_path = Path(__file__).parent -static_dir = this_path / "static" -html_dir = this_path / "html" - - -class Query(BaseModel): - text: str - datamodel: str - model: str - - -app = FastAPI() -static_dir.mkdir(parents=True, exist_ok=True) -app.mount("/static", StaticFiles(directory=str(static_dir)), name="static") -templates = Jinja2Templates(directory=str(html_dir)) - -html_exporter = HTMLExporter(output=None) -engines: Dict[str, SPIRESEngine] = {} - - -def get_engine(datamodel: str): - if datamodel not in engines: - engines[datamodel] = SPIRESEngine(datamodel) - return engines[datamodel] - - -@app.get("/") -def read_root(request: Request): - return templates.TemplateResponse( - "form.html", context={"request": request, "datamodels": DATAMODELS} - ) - - -@app.post("/") -def form_post(request: Request, datamodel: str = Form(...), text: str = Form(...)): - print(f"Received request with schema {datamodel}") - print(f"Received request with text {text}") - engine = get_engine(datamodel) - ann = engine.extract_from_text(text) - print(f"Got {ann}") - output = StringIO() - html_exporter.export(extraction_output=ann, output=output) - return templates.TemplateResponse( - "results.html", context={"request": request, "inner_html": output.getvalue()} - ) - - -@app.get("/spindoctor") -def sd_read_root(request: Request): - all_models = [modelname for model in MODELS for modelname in model["alternative_names"]] - return templates.TemplateResponse( - "spindoctor/form.html", context={"request": request, "models": all_models} - ) - - -@app.post("/spindoctor") -def sd_form_post(request: Request, model: str = Form(...), text: str = Form(...)): - print(f"Received request with model {model}") - print(f"Received request with text {text}") - symbols = [s.strip() for s in text.split("\n")] - engine = EnrichmentEngine(model=model) - gene_set = GeneSet(name="TEMP", gene_symbols=symbols) - ann = engine.summarize(gene_set) - print(f"Got {ann}") - output = StringIO() - html_exporter.export(ann, output) - return templates.TemplateResponse( - "spindoctor/results.html", context={"request": request, "inner_html": output.getvalue()} - ) - - -def start(): - """Launch with `poetry run start` at root level.""" - uvicorn.run("ontogpt.webapp.main:app", host="127.0.0.1", port=8000, reload=True) diff --git a/src/talisman/__init__.py b/src/talisman/__init__.py new file mode 100644 index 000000000..687e1a9a9 --- /dev/null +++ b/src/talisman/__init__.py @@ -0,0 +1 @@ +"""TALISMAN package.""" diff --git a/src/talisman/cli.py b/src/talisman/cli.py new file mode 100644 index 000000000..d535f7b75 --- /dev/null +++ b/src/talisman/cli.py @@ -0,0 +1,511 @@ +"""Command line interface for TALISMAN.""" +import codecs +import logging +import pickle +import sys +from copy import copy +from dataclasses import dataclass +from io import BytesIO, TextIOWrapper +from pathlib import Path +from typing import List, Optional, Union + +import click +import yaml + +from ontogpt import DEFAULT_MODEL, DEFAULT_MODEL_DETAILS, MODELS, __version__ +from ontogpt.engines import create_engine +from ontogpt.engines.knowledge_engine import KnowledgeEngine +from ontogpt.evaluation.enrichment.eval_enrichment import EvalEnrichment +from ontogpt.evaluation.resolver import create_evaluator +from ontogpt.io.csv_wrapper import output_parser +from ontogpt.io.html_exporter import HTMLExporter +from ontogpt.io.markdown_exporter import MarkdownExporter +from ontogpt.io.owl_exporter import OWLExporter +from ontogpt.io.rdf_exporter import RDFExporter +from ontogpt.io.yaml_wrapper import dump_minimal_yaml +from ontogpt.templates.core import ExtractionResult + +from talisman.engines.enrichment import EnrichmentEngine +from talisman.utils.gene_set_utils import ( + GeneSet, + _is_human, + fill_missing_gene_set_values, + parse_gene_set, +) + +__all__ = [ + "main", +] + + +@dataclass +class Settings: + """Global command line settings.""" + + cache_db: Optional[str] = None + skip_annotators: Optional[List[str]] = None + + +settings = Settings() + + +def _as_text_writer(f): + if isinstance(f, TextIOWrapper): + return f + else: + return codecs.getwriter("utf-8")(f) + + +def write_extraction( + results: ExtractionResult, + output: BytesIO, + output_format: str, + knowledge_engine: KnowledgeEngine, +): + """Write results of extraction to a given output stream.""" + # Check if this result contains anything writable first + if results.extracted_object: + exporter: Union[MarkdownExporter, HTMLExporter, RDFExporter, OWLExporter] + + if output_format not in ["pickle"]: + output = _as_text_writer(output) + + if output_format == "pickle": + output.write(pickle.dumps(results)) + elif output_format == "md": + exporter = MarkdownExporter() + exporter.export(results, output) + elif output_format == "html": + exporter = HTMLExporter(output=output) + exporter.export(results, output) + elif output_format == "yaml": + output.write("---\n") # type: ignore + output.write(dump_minimal_yaml(results)) # type: ignore + elif output_format == "turtle": + exporter = RDFExporter() + exporter.export(results, output, knowledge_engine.schemaview) + elif output_format == "owl": + exporter = OWLExporter() + exporter.export(results, output, knowledge_engine.schemaview) + elif output_format == "kgx": + # output.write(write_obj_as_csv(results)) + output.write(dump_minimal_yaml(results)) # type: ignore + with open("output.kgx.tsv") as secondoutput: + for line in output_parser(obj=results, file=output): + secondoutput.write(line) + else: + output.write("---\n") # type: ignore + output.write(dump_minimal_yaml(results)) # type: ignore + + +def get_model_by_name(modelname: str): + """Retrieve a model name and metadata from those available. + + Returns a dict describing the selected model. + """ + found = False + for knownmodel in MODELS: + if modelname in knownmodel["alternative_names"] or modelname == knownmodel["name"]: + selectmodel = knownmodel + found = True + logging.info( + f"Found model: {selectmodel['name']}, provided by {selectmodel['provider']}." + ) + if "not_implemented" in selectmodel or "deprecated" in selectmodel: + logging.error(f"Model {selectmodel['name']} not implemented or is deprecated.") + raise NotImplementedError + break + if not found: + logging.warning( + f"""Model name not recognized or not supported yet. Using default, {DEFAULT_MODEL}. + See all models with `ontogpt list-models`""" + ) + selectmodel = DEFAULT_MODEL_DETAILS + + return selectmodel + + +inputfile_option = click.option("-i", "--inputfile", help="Path to a file containing input text.") +template_option = click.option("-t", "--template", required=True, help="Template to use.") +target_class_option = click.option( + "-T", "--target-class", help="Target class (if not already root)." +) +interactive_option = click.option( + "--interactive/--no-interactive", + default=False, + show_default=True, + help="Interactive mode - rather than call the LLM API it will prompt you do this.", +) +model_option = click.option( + "-m", + "--model", + help="Model name to use, e.g. orca-mini-7b or gpt-4." + " See all model names with ontogpt list-models.", +) +prompt_template_option = click.option( + "--prompt-template", help="Path to a file containing the prompt." +) +recurse_option = click.option( + "--recurse/--no-recurse", default=True, show_default=True, help="Recursively parse structures." +) +use_textract_options = click.option( + "--use-textract/--no-use-textract", + default=False, + show_default=True, + help="Use textract to extract text.", +) +output_option_wb = click.option( + "-o", "--output", type=click.File(mode="wb"), default=sys.stdout, help="Output file." +) +output_option_txt = click.option( + "-o", "--output", type=click.File(mode="w"), default=sys.stdout, help="Output file." +) +output_format_options = click.option( + "-O", + "--output-format", + type=click.Choice(["json", "yaml", "pickle", "md", "html", "owl", "turtle", "jsonl"]), + default="yaml", + help="Output format.", +) +auto_prefix_option = click.option( + "--auto-prefix", + default="AUTO", + help="Prefix to use for auto-generated classes. Default is AUTO.", +) +show_prompt_option = click.option( + "--show-prompt/--no-show-prompt", + default=False, + show_default=True, + help="If set, show all prompts passed to model through an API. Use with verbose setting.", +) + + +@click.group() +@click.option("-v", "--verbose", count=True) +@click.option("-q", "--quiet") +@click.option("--cache-db", help="Path to sqlite database to cache prompt-completion results") +@click.option( + "--skip-annotator", + multiple=True, + help="Skip one or more annotators (e.g. --skip-annotator gilda)", +) +@click.version_option(__version__) +def main(verbose: int, quiet: bool, cache_db: str, skip_annotator): + """CLI for TALISMAN. + + :param verbose: Verbosity while running. + :param quiet: Boolean to be quiet or verbose. + """ + logger = logging.getLogger() + if verbose >= 2: + logger.setLevel(level=logging.DEBUG) + elif verbose == 1: + logger.setLevel(level=logging.INFO) + else: + logger.setLevel(level=logging.WARNING) + if quiet: + logger.setLevel(level=logging.ERROR) + logger.info(f"Logger {logger.name} set to level {logger.level}") + if cache_db: + settings.cache_db = cache_db + if skip_annotator: + settings.skip_annotators = list(skip_annotator) + + +@main.command() +@output_option_txt +@output_format_options +@click.option( + "--annotation-path", + "-A", + required=True, +) +@click.argument("term") +def create_gene_set(term, output, output_format, annotation_path, **kwargs): + """Create a gene set.""" + logging.info(f"Creating for {term}") + evaluator = EvalEnrichment() + evaluator.load_annotations(annotation_path) + gene_set = evaluator.create_gene_set_from_term(term) + print(yaml.dump(gene_set.dict(), sort_keys=False)) + + +@main.command() +@output_option_txt +@output_format_options +@click.option("--fill/--no-fill", default=False) +@click.option( + "--input-file", + "-U", + help="File with gene IDs to enrich (if not passed as arguments)", +) +def convert_geneset(input_file, output, output_format, fill, **kwargs): + """Convert gene set to YAML.""" + gene_set = parse_gene_set(input_file) + if fill: + fill_missing_gene_set_values(gene_set) + output.write(dump_minimal_yaml(gene_set.dict())) + + +@main.command() +@output_option_txt +@output_format_options +@model_option +@show_prompt_option +@click.option( + "--resolver", "-r", help="OAK selector for the gene ID resolver. E.g. sqlite:obo:hgnc" +) +@click.option( + "-C", + "--context", + help="domain e.g. anatomy, industry, health-related (NOT IMPLEMENTED - currently gene only)", +) +@click.option( + "--strict/--no-strict", + default=True, + show_default=True, + help="If set, there must be a unique mappings from labels to IDs", +) +@click.option( + "--input-file", + "-U", + help="File with gene IDs to enrich (if not passed as arguments)", +) +@click.option( + "--randomize-gene-descriptions-using-file", + help="FOR EVALUATION ONLY. Swap out gene descriptions with genes from this gene set filefile", +) +@click.option( + "--ontological-synopsis/--no-ontological-synopsis", + default=True, + show_default=True, + help="If set, use automated rather than manual gene descriptions", +) +@click.option( + "--combined-synopsis/--no-combined-synopsis", + default=False, + show_default=True, + help="If set, both gene descriptions", +) +@click.option( + "--end-marker", + help="For testing minor variants of prompts", +) +@click.option( + "--annotations/--no-annotations", + default=True, + show_default=True, + help="If set, include annotations in the prompt", +) +@prompt_template_option +@interactive_option +@click.argument("genes", nargs=-1) +def enrichment( + genes, + context, + input_file, + resolver, + output, + model, + show_prompt, + interactive, + end_marker, + output_format, + randomize_gene_descriptions_using_file, + **kwargs, +): + """Gene class summary enriching (TALISMAN). + + Algorithm: + + 1. Map gene symbols to IDs using the resolver (unless IDs specified) + 2. Fetch gene descriptions using Alliance API + 3. Create a prompt using descriptions + + Limitations: + + It is very easy to exceed the max token length with GPT-3 models. + + Usage: + + ontogpt enrichment -r sqlite:obo:hgnc -U tests/input/genesets/dopamine.yaml + + Usage: + + ontogpt enrichment -r sqlite:obo:hgnc -U tests/input/genesets/dopamine.yaml + """ + if model: + selectmodel = get_model_by_name(model) + model_source = selectmodel["provider"] + + if model_source != "OpenAI": + raise NotImplementedError( + "Model not yet supported for gene enrichment or enrichment evaluation." + ) + + if not genes and not input_file: + raise ValueError("Either genes or input file must be passed") + if genes: + gene_set = GeneSet(name="TEMP", gene_symbols=genes) + if input_file: + if genes: + raise ValueError("Either genes or input file must be passed") + gene_set = parse_gene_set(input_file) + if not gene_set: + raise ValueError("No genes passed") + ke = create_engine(None, EnrichmentEngine, model=model) + if end_marker: + ke.end_marker = end_marker + if interactive: + ke.client.interactive = True + if settings.cache_db: + ke.client.cache_db_path = settings.cache_db + if not isinstance(ke, EnrichmentEngine): + raise ValueError(f"Expected EnrichmentEngine, got {type(ke)}") + if resolver: + ke.add_resolver(resolver) + if randomize_gene_descriptions_using_file: + print("WARNING!! Randomly spiking gene descriptions") + spike_gene_set = parse_gene_set(randomize_gene_descriptions_using_file) + aliases = {} + if not spike_gene_set.gene_symbols: + raise ValueError("No gene symbols for spike set") + syms = copy(gene_set.gene_symbols) + if len(spike_gene_set.gene_symbols) < len(gene_set.gene_symbols): + raise ValueError("Not enough genes in spike set") + for sym in spike_gene_set.gene_symbols: + if not syms: + break + aliases[sym] = syms.pop() + results = ke.summarize( + spike_gene_set, normalize=resolver is not None, gene_aliases=aliases, **kwargs + ) + else: + results = ke.summarize(gene_set, normalize=resolver is not None, **kwargs) + if results.truncation_factor is not None and results.truncation_factor < 1.0: + logging.warning(f"Text was truncated; factor = {results.truncation_factor}") + output = _as_text_writer(output) + if show_prompt: + print(results.prompt) + output.write(dump_minimal_yaml(results)) + + +@main.command() +@output_option_txt +@click.option( + "--strict/--no-strict", + default=True, + show_default=True, + help="If set, there must be a unique mappings from labels to IDs", +) +@click.option( + "--input-file", + "-U", + help="File with gene IDs to enrich (if not passed as arguments)", +) +@click.option( + "--ontological-synopsis/--no-ontological-synopsis", + default=True, + show_default=True, + help="If set, use automated rather than manual gene descriptions", +) +@click.option( + "--combined-synopsis/--no-combined-synopsis", + default=False, + show_default=True, + help="If set, both gene descriptions", +) +@click.option( + "--annotations/--no-annotations", + default=True, + show_default=True, + help="If set, include annotations in the prompt", +) +@click.option( + "--number-to-drop", + "-n", + type=click.types.INT, + default=1, + help="Max number of genes to drop", +) +# @click.option( +# "--randomize-gene-descriptions/--no-randomize-gene-descriptions", +# help="DO NOT USE EXCEPT FOR EVALUATION PUPOSES." +# ) +@click.option( + "--annotations-path", + "-A", + help="Path to annotations", +) +@model_option +@click.argument("genes", nargs=-1) +def eval_enrichment(genes, input_file, number_to_drop, annotations_path, model, output, **kwargs): + """Run enrichment using multiple methods.""" + if model: + selectmodel = get_model_by_name(model) + model_source = selectmodel["provider"] + + if model_source != "OpenAI": + raise NotImplementedError( + "Model not yet supported for gene enrichment or enrichment evaluation." + ) + + if not genes and not input_file: + raise ValueError("Either genes or input file must be passed") + if genes: + gene_set = GeneSet(name="TEMP", gene_symbols=genes) + if input_file: + if genes: + raise ValueError("Either genes or input file must be passed") + gene_set = parse_gene_set(input_file) + if not gene_set: + raise ValueError("No genes passed") + fill_missing_gene_set_values(gene_set) + if not annotations_path: + if not _is_human(gene_set): + raise ValueError("No annotations path passed") + annotations_path = "tests/input/genes2go.tsv.gz" + eval_engine = EvalEnrichment(model=model) + eval_engine.load_annotations(annotations_path) + comps = eval_engine.evaluate_methods_on_gene_set(gene_set, n=number_to_drop, **kwargs) + output.write(dump_minimal_yaml(comps)) + + +@main.command() +@recurse_option +@model_option +@output_option_txt +@click.option( + "--num-tests", + type=click.INT, + default=5, + show_default=True, + help="number of iterations to cycle through.", +) +@click.option( + "--chunking/--no-chunking", + default=False, + show_default=True, + help="If set, chunk input text, then prepare a separate prompt for each chunk." + " Otherwise the full input text is passed.", +) +@click.argument("evaluator") +def eval(evaluator, num_tests, output, chunking, model, **kwargs): + """Evaluate an extractor.""" + logging.info(f"Creating for {evaluator}") + + if model: + selectmodel = get_model_by_name(model) + modelname = selectmodel["alternative_names"][0] + else: + modelname = DEFAULT_MODEL + + evaluator = create_evaluator( + name=evaluator, num_tests=num_tests, chunking=chunking, model=modelname + ) + eos = evaluator.eval() + output.write(dump_minimal_yaml(eos, minimize=False)) + + +if __name__ == "__main__": + main() diff --git a/src/ontogpt/engines/enrichment.py b/src/talisman/engines/enrichment.py similarity index 99% rename from src/ontogpt/engines/enrichment.py rename to src/talisman/engines/enrichment.py index 7e02bbc06..a73616010 100644 --- a/src/ontogpt/engines/enrichment.py +++ b/src/talisman/engines/enrichment.py @@ -16,7 +16,8 @@ from ontogpt.prompts.enrichment import DEFAULT_ENRICHMENT_PROMPT from ontogpt.templates.class_enrichment import ClassEnrichmentResult from ontogpt.templates.gene_description_term import GeneDescriptionTerm -from ontogpt.utils.gene_set_utils import ( + +from talisman.utils.gene_set_utils import ( ENTITY_ID, GENE_TUPLE, GeneSet, diff --git a/src/ontogpt/engines/knowledge_engine.py b/src/talisman/engines/knowledge_engine.py similarity index 99% rename from src/ontogpt/engines/knowledge_engine.py rename to src/talisman/engines/knowledge_engine.py index cb6da8e74..04177196a 100644 --- a/src/ontogpt/engines/knowledge_engine.py +++ b/src/talisman/engines/knowledge_engine.py @@ -24,9 +24,9 @@ from oaklib.utilities.subsets.value_set_expander import ValueSetExpander from requests.exceptions import ConnectionError, HTTPError, ProxyError -from ontogpt import DEFAULT_MODEL -from ontogpt.clients import OpenAIClient -from ontogpt.templates.core import ExtractionResult, NamedEntity +from talisman import DEFAULT_MODEL +from talisman.clients import OpenAIClient +from talisman.templates.core import ExtractionResult, NamedEntity this_path = Path(__file__).parent logger = logging.getLogger(__name__) diff --git a/src/ontogpt/engines/mapping_engine.py b/src/talisman/engines/mapping_engine.py similarity index 98% rename from src/ontogpt/engines/mapping_engine.py rename to src/talisman/engines/mapping_engine.py index 883c20c54..93536a2b2 100644 --- a/src/ontogpt/engines/mapping_engine.py +++ b/src/talisman/engines/mapping_engine.py @@ -15,8 +15,8 @@ from sssom.parsers import parse_sssom_table, to_mapping_set_document from sssom_schema import Mapping -from ontogpt.engines.knowledge_engine import KnowledgeEngine -from ontogpt.prompts.mapping import DEFAULT_MAPPING_EVAL_PROMPT +from talisman.engines.knowledge_engine import KnowledgeEngine +from talisman.prompts.mapping import DEFAULT_MAPPING_EVAL_PROMPT logger = logging.getLogger(__name__) diff --git a/src/talisman/evaluation/__init__.py b/src/talisman/evaluation/__init__.py new file mode 100644 index 000000000..666bb2303 --- /dev/null +++ b/src/talisman/evaluation/__init__.py @@ -0,0 +1 @@ +from talisman.evaluation.resolver import create_evaluator # noqa:F401 diff --git a/src/ontogpt/evaluation/ctd/__init__.py b/src/talisman/evaluation/ctd/__init__.py similarity index 100% rename from src/ontogpt/evaluation/ctd/__init__.py rename to src/talisman/evaluation/ctd/__init__.py diff --git a/src/ontogpt/evaluation/ctd/database/CDR_TestSet.BioC.xml.gz b/src/talisman/evaluation/ctd/database/CDR_TestSet.BioC.xml.gz similarity index 100% rename from src/ontogpt/evaluation/ctd/database/CDR_TestSet.BioC.xml.gz rename to src/talisman/evaluation/ctd/database/CDR_TestSet.BioC.xml.gz diff --git a/src/ontogpt/evaluation/ctd/database/CDR_TrainSet.BioC.xml.gz b/src/talisman/evaluation/ctd/database/CDR_TrainSet.BioC.xml.gz similarity index 100% rename from src/ontogpt/evaluation/ctd/database/CDR_TrainSet.BioC.xml.gz rename to src/talisman/evaluation/ctd/database/CDR_TrainSet.BioC.xml.gz diff --git a/src/ontogpt/evaluation/ctd/database/synonyms.yaml b/src/talisman/evaluation/ctd/database/synonyms.yaml similarity index 100% rename from src/ontogpt/evaluation/ctd/database/synonyms.yaml rename to src/talisman/evaluation/ctd/database/synonyms.yaml diff --git a/src/ontogpt/evaluation/ctd/eval_ctd.py b/src/talisman/evaluation/ctd/eval_ctd.py similarity index 97% rename from src/ontogpt/evaluation/ctd/eval_ctd.py rename to src/talisman/evaluation/ctd/eval_ctd.py index 10766905c..42b16815a 100644 --- a/src/ontogpt/evaluation/ctd/eval_ctd.py +++ b/src/talisman/evaluation/ctd/eval_ctd.py @@ -32,10 +32,10 @@ from oaklib import BasicOntologyInterface, get_adapter from pydantic import BaseModel -from ontogpt.engines.knowledge_engine import chunk_text -from ontogpt.engines.spires_engine import SPIRESEngine -from ontogpt.evaluation.evaluation_engine import SimilarityScore, SPIRESEvaluationEngine -from ontogpt.templates.ctd import ( +from talisman.engines.knowledge_engine import chunk_text +from talisman.engines.spires_engine import SPIRESEngine +from talisman.evaluation.evaluation_engine import SimilarityScore, SPIRESEvaluationEngine +from talisman.templates.ctd import ( ChemicalToDiseaseDocument, ChemicalToDiseaseRelationship, Publication, diff --git a/src/ontogpt/evaluation/ctd/eval_ctd_ner.py b/src/talisman/evaluation/ctd/eval_ctd_ner.py similarity index 98% rename from src/ontogpt/evaluation/ctd/eval_ctd_ner.py rename to src/talisman/evaluation/ctd/eval_ctd_ner.py index 11c0d8067..e61bfd3aa 100644 --- a/src/ontogpt/evaluation/ctd/eval_ctd_ner.py +++ b/src/talisman/evaluation/ctd/eval_ctd_ner.py @@ -36,10 +36,10 @@ from oaklib import BasicOntologyInterface, get_adapter from pydantic import BaseModel -from ontogpt.engines.knowledge_engine import chunk_text -from ontogpt.engines.spires_engine import SPIRESEngine -from ontogpt.evaluation.evaluation_engine import SimilarityScore, SPIRESEvaluationEngine -from ontogpt.templates.ctd_ner import ( +from talisman.engines.knowledge_engine import chunk_text +from talisman.engines.spires_engine import SPIRESEngine +from talisman.evaluation.evaluation_engine import SimilarityScore, SPIRESEvaluationEngine +from talisman.templates.ctd_ner import ( ChemicalToDiseaseDocument, Chemical, Disease, diff --git a/src/ontogpt/evaluation/drugmechdb/__init__.py b/src/talisman/evaluation/drugmechdb/__init__.py similarity index 100% rename from src/ontogpt/evaluation/drugmechdb/__init__.py rename to src/talisman/evaluation/drugmechdb/__init__.py diff --git a/src/ontogpt/evaluation/drugmechdb/datamodel/drugmechdb.py b/src/talisman/evaluation/drugmechdb/datamodel/drugmechdb.py similarity index 100% rename from src/ontogpt/evaluation/drugmechdb/datamodel/drugmechdb.py rename to src/talisman/evaluation/drugmechdb/datamodel/drugmechdb.py diff --git a/src/ontogpt/evaluation/drugmechdb/datamodel/drugmechdb.yaml b/src/talisman/evaluation/drugmechdb/datamodel/drugmechdb.yaml similarity index 100% rename from src/ontogpt/evaluation/drugmechdb/datamodel/drugmechdb.yaml rename to src/talisman/evaluation/drugmechdb/datamodel/drugmechdb.yaml diff --git a/src/ontogpt/evaluation/drugmechdb/eval_drugmechdb.py b/src/talisman/evaluation/drugmechdb/eval_drugmechdb.py similarity index 97% rename from src/ontogpt/evaluation/drugmechdb/eval_drugmechdb.py rename to src/talisman/evaluation/drugmechdb/eval_drugmechdb.py index 65cc23753..2e51eb694 100644 --- a/src/ontogpt/evaluation/drugmechdb/eval_drugmechdb.py +++ b/src/talisman/evaluation/drugmechdb/eval_drugmechdb.py @@ -16,10 +16,10 @@ from oaklib import get_implementation_from_shorthand from pydantic import BaseModel -import ontogpt.evaluation.drugmechdb.datamodel.drugmechdb as source_datamodel -import ontogpt.templates.drug as target_datamodel -from ontogpt.engines.spires_engine import SPIRESEngine -from ontogpt.evaluation.evaluation_engine import SimilarityScore, SPIRESEvaluationEngine +import talisman.evaluation.drugmechdb.datamodel.drugmechdb as source_datamodel +import talisman.templates.drug as target_datamodel +from talisman.engines.spires_engine import SPIRESEngine +from talisman.evaluation.evaluation_engine import SimilarityScore, SPIRESEvaluationEngine THIS_DIR = Path(__file__).parent DATABASE_DIR = Path(__file__).parent / "database" diff --git a/src/ontogpt/evaluation/enrichment/__init__.py b/src/talisman/evaluation/enrichment/__init__.py similarity index 100% rename from src/ontogpt/evaluation/enrichment/__init__.py rename to src/talisman/evaluation/enrichment/__init__.py diff --git a/src/ontogpt/evaluation/enrichment/eval_enrichment.py b/src/talisman/evaluation/enrichment/eval_enrichment.py similarity index 96% rename from src/ontogpt/evaluation/enrichment/eval_enrichment.py rename to src/talisman/evaluation/enrichment/eval_enrichment.py index bfd860aa7..388aca402 100644 --- a/src/ontogpt/evaluation/enrichment/eval_enrichment.py +++ b/src/talisman/evaluation/enrichment/eval_enrichment.py @@ -23,13 +23,13 @@ from pydantic import BaseModel from tiktoken import Encoding -from ontogpt import MODELS -from ontogpt.engines import create_engine -from ontogpt.engines.enrichment import ENTITY_ID, EnrichmentEngine, EnrichmentPayload -from ontogpt.engines.knowledge_engine import MODEL_NAME -from ontogpt.evaluation.evaluation_engine import EvaluationEngine -from ontogpt.templates.class_enrichment import ClassEnrichmentResult -from ontogpt.utils.gene_set_utils import SYMBOL, GeneSet, drop_genes_from_gene_set, gene_info +from talisman import MODELS +from talisman.engines import create_engine +from talisman.engines.enrichment import ENTITY_ID, EnrichmentEngine, EnrichmentPayload +from talisman.engines.knowledge_engine import MODEL_NAME +from talisman.evaluation.evaluation_engine import EvaluationEngine +from talisman.templates.class_enrichment import ClassEnrichmentResult +from talisman.utils.gene_set_utils import SYMBOL, GeneSet, drop_genes_from_gene_set, gene_info THIS_DIR = Path(__file__).parent DATABASE_DIR = Path(__file__).parent / "database" diff --git a/src/ontogpt/evaluation/evaluation_engine.py b/src/talisman/evaluation/evaluation_engine.py similarity index 98% rename from src/ontogpt/evaluation/evaluation_engine.py rename to src/talisman/evaluation/evaluation_engine.py index 7dafddc2b..5ffbc8f07 100644 --- a/src/ontogpt/evaluation/evaluation_engine.py +++ b/src/talisman/evaluation/evaluation_engine.py @@ -16,7 +16,7 @@ from oaklib import BasicOntologyInterface from pydantic import BaseModel -from ontogpt.engines.spires_engine import SPIRESEngine +from talisman.engines.spires_engine import SPIRESEngine def jaccard_index(a: Set, b: Set): diff --git a/src/ontogpt/evaluation/go/eval_go.py b/src/talisman/evaluation/go/eval_go.py similarity index 96% rename from src/ontogpt/evaluation/go/eval_go.py rename to src/talisman/evaluation/go/eval_go.py index 7e4846455..e5b2e6c0f 100644 --- a/src/ontogpt/evaluation/go/eval_go.py +++ b/src/talisman/evaluation/go/eval_go.py @@ -11,9 +11,9 @@ from oaklib.interfaces.obograph_interface import OboGraphInterface from pydantic import BaseModel -from ontogpt.engines.spires_engine import SPIRESEngine -from ontogpt.evaluation.evaluation_engine import SimilarityScore, SPIRESEvaluationEngine -from ontogpt.templates.metabolic_process import MetabolicProcess +from talisman.engines.spires_engine import SPIRESEngine +from talisman.evaluation.evaluation_engine import SimilarityScore, SPIRESEvaluationEngine +from talisman.templates.metabolic_process import MetabolicProcess TEST_CASES_DIR = Path(__file__).parent / "test_cases" diff --git a/src/ontogpt/evaluation/hpoa/__init__.py b/src/talisman/evaluation/hpoa/__init__.py similarity index 100% rename from src/ontogpt/evaluation/hpoa/__init__.py rename to src/talisman/evaluation/hpoa/__init__.py diff --git a/src/ontogpt/evaluation/hpoa/eval_hpoa.py b/src/talisman/evaluation/hpoa/eval_hpoa.py similarity index 97% rename from src/ontogpt/evaluation/hpoa/eval_hpoa.py rename to src/talisman/evaluation/hpoa/eval_hpoa.py index 72c3eb676..c184c4906 100644 --- a/src/ontogpt/evaluation/hpoa/eval_hpoa.py +++ b/src/talisman/evaluation/hpoa/eval_hpoa.py @@ -13,10 +13,10 @@ from oaklib.interfaces import SearchInterface from pydantic import BaseModel -from ontogpt.clients.pubmed_client import PubmedClient -from ontogpt.engines.spires_engine import SPIRESEngine -from ontogpt.evaluation.evaluation_engine import SimilarityScore, SPIRESEvaluationEngine -from ontogpt.templates.mendelian_disease import MendelianDisease +from talisman.clients.pubmed_client import PubmedClient +from talisman.engines.spires_engine import SPIRESEngine +from talisman.evaluation.evaluation_engine import SimilarityScore, SPIRESEvaluationEngine +from talisman.templates.mendelian_disease import MendelianDisease DATABASE_DIR = Path(__file__).parent / "database" TEST_CASES_DIR = Path("tests").joinpath("input") diff --git a/src/ontogpt/evaluation/ibd/Abstracts/10338374.txt b/src/talisman/evaluation/ibd/Abstracts/10338374.txt similarity index 100% rename from src/ontogpt/evaluation/ibd/Abstracts/10338374.txt rename to src/talisman/evaluation/ibd/Abstracts/10338374.txt diff --git a/src/ontogpt/evaluation/ibd/Abstracts/17653185.txt b/src/talisman/evaluation/ibd/Abstracts/17653185.txt similarity index 100% rename from src/ontogpt/evaluation/ibd/Abstracts/17653185.txt rename to src/talisman/evaluation/ibd/Abstracts/17653185.txt diff --git a/src/ontogpt/evaluation/ibd/Abstracts/18253950.txt b/src/talisman/evaluation/ibd/Abstracts/18253950.txt similarity index 100% rename from src/ontogpt/evaluation/ibd/Abstracts/18253950.txt rename to src/talisman/evaluation/ibd/Abstracts/18253950.txt diff --git a/src/ontogpt/evaluation/ibd/Abstracts/24104886.txt b/src/talisman/evaluation/ibd/Abstracts/24104886.txt similarity index 100% rename from src/ontogpt/evaluation/ibd/Abstracts/24104886.txt rename to src/talisman/evaluation/ibd/Abstracts/24104886.txt diff --git a/src/ontogpt/evaluation/ibd/Abstracts/28846760.txt b/src/talisman/evaluation/ibd/Abstracts/28846760.txt similarity index 100% rename from src/ontogpt/evaluation/ibd/Abstracts/28846760.txt rename to src/talisman/evaluation/ibd/Abstracts/28846760.txt diff --git a/src/ontogpt/evaluation/ibd/Abstracts/29285689.txt b/src/talisman/evaluation/ibd/Abstracts/29285689.txt similarity index 100% rename from src/ontogpt/evaluation/ibd/Abstracts/29285689.txt rename to src/talisman/evaluation/ibd/Abstracts/29285689.txt diff --git a/src/ontogpt/evaluation/ibd/Abstracts/29441064.txt b/src/talisman/evaluation/ibd/Abstracts/29441064.txt similarity index 100% rename from src/ontogpt/evaluation/ibd/Abstracts/29441064.txt rename to src/talisman/evaluation/ibd/Abstracts/29441064.txt diff --git a/src/ontogpt/evaluation/ibd/Abstracts/31767987.txt b/src/talisman/evaluation/ibd/Abstracts/31767987.txt similarity index 100% rename from src/ontogpt/evaluation/ibd/Abstracts/31767987.txt rename to src/talisman/evaluation/ibd/Abstracts/31767987.txt diff --git a/src/ontogpt/evaluation/ibd/Abstracts/PMC4961083.txt b/src/talisman/evaluation/ibd/Abstracts/PMC4961083.txt similarity index 100% rename from src/ontogpt/evaluation/ibd/Abstracts/PMC4961083.txt rename to src/talisman/evaluation/ibd/Abstracts/PMC4961083.txt diff --git a/src/ontogpt/evaluation/ibd/Abstracts/PMC6386158.txt b/src/talisman/evaluation/ibd/Abstracts/PMC6386158.txt similarity index 100% rename from src/ontogpt/evaluation/ibd/Abstracts/PMC6386158.txt rename to src/talisman/evaluation/ibd/Abstracts/PMC6386158.txt diff --git a/src/ontogpt/evaluation/ibd/Abstracts/PMC7003169.txt b/src/talisman/evaluation/ibd/Abstracts/PMC7003169.txt similarity index 100% rename from src/ontogpt/evaluation/ibd/Abstracts/PMC7003169.txt rename to src/talisman/evaluation/ibd/Abstracts/PMC7003169.txt diff --git a/src/ontogpt/evaluation/ibd/PMC6386158_fig2_legend.txt~ b/src/talisman/evaluation/ibd/PMC6386158_fig2_legend.txt~ similarity index 100% rename from src/ontogpt/evaluation/ibd/PMC6386158_fig2_legend.txt~ rename to src/talisman/evaluation/ibd/PMC6386158_fig2_legend.txt~ diff --git a/src/ontogpt/evaluation/ibd/run.sh b/src/talisman/evaluation/ibd/run.sh similarity index 100% rename from src/ontogpt/evaluation/ibd/run.sh rename to src/talisman/evaluation/ibd/run.sh diff --git a/src/ontogpt/evaluation/ibd/run.sh~ b/src/talisman/evaluation/ibd/run.sh~ similarity index 100% rename from src/ontogpt/evaluation/ibd/run.sh~ rename to src/talisman/evaluation/ibd/run.sh~ diff --git a/src/ontogpt/evaluation/ibd/text_data/10338374_smoking.txt b/src/talisman/evaluation/ibd/text_data/10338374_smoking.txt similarity index 100% rename from src/ontogpt/evaluation/ibd/text_data/10338374_smoking.txt rename to src/talisman/evaluation/ibd/text_data/10338374_smoking.txt diff --git a/src/ontogpt/evaluation/ibd/text_data/PMC6386158_review.txt b/src/talisman/evaluation/ibd/text_data/PMC6386158_review.txt similarity index 100% rename from src/ontogpt/evaluation/ibd/text_data/PMC6386158_review.txt rename to src/talisman/evaluation/ibd/text_data/PMC6386158_review.txt diff --git a/src/ontogpt/evaluation/ibd/text_data/PMC6386158_review_fig2_legend.txt b/src/talisman/evaluation/ibd/text_data/PMC6386158_review_fig2_legend.txt similarity index 100% rename from src/ontogpt/evaluation/ibd/text_data/PMC6386158_review_fig2_legend.txt rename to src/talisman/evaluation/ibd/text_data/PMC6386158_review_fig2_legend.txt diff --git a/src/ontogpt/evaluation/ibd/text_data/PMC6386158_review_fig2_legend.yaml b/src/talisman/evaluation/ibd/text_data/PMC6386158_review_fig2_legend.yaml similarity index 100% rename from src/ontogpt/evaluation/ibd/text_data/PMC6386158_review_fig2_legend.yaml rename to src/talisman/evaluation/ibd/text_data/PMC6386158_review_fig2_legend.yaml diff --git a/src/ontogpt/evaluation/kidney/test.txt b/src/talisman/evaluation/kidney/test.txt similarity index 100% rename from src/ontogpt/evaluation/kidney/test.txt rename to src/talisman/evaluation/kidney/test.txt diff --git a/src/ontogpt/evaluation/kidney/test2.txt b/src/talisman/evaluation/kidney/test2.txt similarity index 100% rename from src/ontogpt/evaluation/kidney/test2.txt rename to src/talisman/evaluation/kidney/test2.txt diff --git a/src/ontogpt/evaluation/kidney/test3.txt b/src/talisman/evaluation/kidney/test3.txt similarity index 100% rename from src/ontogpt/evaluation/kidney/test3.txt rename to src/talisman/evaluation/kidney/test3.txt diff --git a/src/ontogpt/evaluation/maxo/__init__.py b/src/talisman/evaluation/maxo/__init__.py similarity index 100% rename from src/ontogpt/evaluation/maxo/__init__.py rename to src/talisman/evaluation/maxo/__init__.py diff --git a/src/ontogpt/evaluation/maxo/eval_maxo.py b/src/talisman/evaluation/maxo/eval_maxo.py similarity index 97% rename from src/ontogpt/evaluation/maxo/eval_maxo.py rename to src/talisman/evaluation/maxo/eval_maxo.py index b4709141a..cb8ff0c9a 100644 --- a/src/ontogpt/evaluation/maxo/eval_maxo.py +++ b/src/talisman/evaluation/maxo/eval_maxo.py @@ -39,10 +39,10 @@ from oaklib import BasicOntologyInterface, get_adapter from pydantic import BaseModel -from ontogpt.engines.knowledge_engine import chunk_text -from ontogpt.engines.spires_engine import SPIRESEngine -from ontogpt.evaluation.evaluation_engine import SimilarityScore, SPIRESEvaluationEngine -from ontogpt.templates.maxo import MaxoAnnotations, ActionToSymptomRelationship, Publication +from talisman.engines.knowledge_engine import chunk_text +from talisman.engines.spires_engine import SPIRESEngine +from talisman.evaluation.evaluation_engine import SimilarityScore, SPIRESEvaluationEngine +from talisman.templates.maxo import MaxoAnnotations, ActionToSymptomRelationship, Publication THIS_DIR = Path(__file__).parent DATABASE_DIR = Path(__file__).parent / "test_cases" diff --git a/src/ontogpt/evaluation/maxo/test_cases/maxo_case_12958596.yaml b/src/talisman/evaluation/maxo/test_cases/maxo_case_12958596.yaml similarity index 100% rename from src/ontogpt/evaluation/maxo/test_cases/maxo_case_12958596.yaml rename to src/talisman/evaluation/maxo/test_cases/maxo_case_12958596.yaml diff --git a/src/ontogpt/evaluation/maxo/test_cases/maxo_case_20301368.yaml b/src/talisman/evaluation/maxo/test_cases/maxo_case_20301368.yaml similarity index 100% rename from src/ontogpt/evaluation/maxo/test_cases/maxo_case_20301368.yaml rename to src/talisman/evaluation/maxo/test_cases/maxo_case_20301368.yaml diff --git a/src/ontogpt/evaluation/maxo/test_cases/maxo_case_20301450.yaml b/src/talisman/evaluation/maxo/test_cases/maxo_case_20301450.yaml similarity index 100% rename from src/ontogpt/evaluation/maxo/test_cases/maxo_case_20301450.yaml rename to src/talisman/evaluation/maxo/test_cases/maxo_case_20301450.yaml diff --git a/src/ontogpt/evaluation/maxo/test_cases/maxo_case_20301519.yaml b/src/talisman/evaluation/maxo/test_cases/maxo_case_20301519.yaml similarity index 100% rename from src/ontogpt/evaluation/maxo/test_cases/maxo_case_20301519.yaml rename to src/talisman/evaluation/maxo/test_cases/maxo_case_20301519.yaml diff --git a/src/ontogpt/evaluation/maxo/test_cases/maxo_case_20301527.yaml b/src/talisman/evaluation/maxo/test_cases/maxo_case_20301527.yaml similarity index 100% rename from src/ontogpt/evaluation/maxo/test_cases/maxo_case_20301527.yaml rename to src/talisman/evaluation/maxo/test_cases/maxo_case_20301527.yaml diff --git a/src/ontogpt/evaluation/maxo/test_cases/maxo_case_20301572.yaml b/src/talisman/evaluation/maxo/test_cases/maxo_case_20301572.yaml similarity index 100% rename from src/ontogpt/evaluation/maxo/test_cases/maxo_case_20301572.yaml rename to src/talisman/evaluation/maxo/test_cases/maxo_case_20301572.yaml diff --git a/src/ontogpt/evaluation/maxo/test_cases/maxo_case_20301644.yaml b/src/talisman/evaluation/maxo/test_cases/maxo_case_20301644.yaml similarity index 100% rename from src/ontogpt/evaluation/maxo/test_cases/maxo_case_20301644.yaml rename to src/talisman/evaluation/maxo/test_cases/maxo_case_20301644.yaml diff --git a/src/ontogpt/evaluation/maxo/test_cases/maxo_case_20301675.yaml b/src/talisman/evaluation/maxo/test_cases/maxo_case_20301675.yaml similarity index 100% rename from src/ontogpt/evaluation/maxo/test_cases/maxo_case_20301675.yaml rename to src/talisman/evaluation/maxo/test_cases/maxo_case_20301675.yaml diff --git a/src/ontogpt/evaluation/maxo/test_cases/maxo_case_20301765.yaml b/src/talisman/evaluation/maxo/test_cases/maxo_case_20301765.yaml similarity index 100% rename from src/ontogpt/evaluation/maxo/test_cases/maxo_case_20301765.yaml rename to src/talisman/evaluation/maxo/test_cases/maxo_case_20301765.yaml diff --git a/src/ontogpt/evaluation/maxo/test_cases/maxo_case_2063868.yaml b/src/talisman/evaluation/maxo/test_cases/maxo_case_2063868.yaml similarity index 100% rename from src/ontogpt/evaluation/maxo/test_cases/maxo_case_2063868.yaml rename to src/talisman/evaluation/maxo/test_cases/maxo_case_2063868.yaml diff --git a/src/ontogpt/evaluation/maxo/test_cases/maxo_case_26110198.yaml b/src/talisman/evaluation/maxo/test_cases/maxo_case_26110198.yaml similarity index 100% rename from src/ontogpt/evaluation/maxo/test_cases/maxo_case_26110198.yaml rename to src/talisman/evaluation/maxo/test_cases/maxo_case_26110198.yaml diff --git a/src/ontogpt/evaluation/maxo/test_cases/maxo_case_27077170.yaml b/src/talisman/evaluation/maxo/test_cases/maxo_case_27077170.yaml similarity index 100% rename from src/ontogpt/evaluation/maxo/test_cases/maxo_case_27077170.yaml rename to src/talisman/evaluation/maxo/test_cases/maxo_case_27077170.yaml diff --git a/src/ontogpt/evaluation/maxo/test_cases/maxo_case_28406602.yaml b/src/talisman/evaluation/maxo/test_cases/maxo_case_28406602.yaml similarity index 100% rename from src/ontogpt/evaluation/maxo/test_cases/maxo_case_28406602.yaml rename to src/talisman/evaluation/maxo/test_cases/maxo_case_28406602.yaml diff --git a/src/ontogpt/evaluation/maxo/test_cases/maxo_case_29478819.yaml b/src/talisman/evaluation/maxo/test_cases/maxo_case_29478819.yaml similarity index 100% rename from src/ontogpt/evaluation/maxo/test_cases/maxo_case_29478819.yaml rename to src/talisman/evaluation/maxo/test_cases/maxo_case_29478819.yaml diff --git a/src/ontogpt/evaluation/maxo/test_cases/maxo_case_30488337.yaml b/src/talisman/evaluation/maxo/test_cases/maxo_case_30488337.yaml similarity index 100% rename from src/ontogpt/evaluation/maxo/test_cases/maxo_case_30488337.yaml rename to src/talisman/evaluation/maxo/test_cases/maxo_case_30488337.yaml diff --git a/src/ontogpt/evaluation/maxo/test_cases/maxo_case_36977302.yaml b/src/talisman/evaluation/maxo/test_cases/maxo_case_36977302.yaml similarity index 100% rename from src/ontogpt/evaluation/maxo/test_cases/maxo_case_36977302.yaml rename to src/talisman/evaluation/maxo/test_cases/maxo_case_36977302.yaml diff --git a/src/ontogpt/evaluation/maxo/test_cases/maxo_case_9543069.yaml b/src/talisman/evaluation/maxo/test_cases/maxo_case_9543069.yaml similarity index 100% rename from src/ontogpt/evaluation/maxo/test_cases/maxo_case_9543069.yaml rename to src/talisman/evaluation/maxo/test_cases/maxo_case_9543069.yaml diff --git a/src/ontogpt/evaluation/resolver.py b/src/talisman/evaluation/resolver.py similarity index 75% rename from src/ontogpt/evaluation/resolver.py rename to src/talisman/evaluation/resolver.py index 023035394..04a5b5bf1 100644 --- a/src/ontogpt/evaluation/resolver.py +++ b/src/talisman/evaluation/resolver.py @@ -3,10 +3,10 @@ from class_resolver import ClassResolver -from ontogpt.evaluation.ctd.eval_ctd import EvalCTD -from ontogpt.evaluation.ctd.eval_ctd_ner import EvalCTDNER -from ontogpt.evaluation.maxo.eval_maxo import EvalMAXO -from ontogpt.evaluation.evaluation_engine import SPIRESEvaluationEngine +from talisman.evaluation.ctd.eval_ctd import EvalCTD +from talisman.evaluation.ctd.eval_ctd_ner import EvalCTDNER +from talisman.evaluation.maxo.eval_maxo import EvalMAXO +from talisman.evaluation.evaluation_engine import SPIRESEvaluationEngine resolver = ClassResolver([EvalCTD, EvalCTDNER, EvalMAXO], base=SPIRESEvaluationEngine) diff --git a/src/ontogpt/io/__init__.py b/src/talisman/prompts/__init__.py similarity index 100% rename from src/ontogpt/io/__init__.py rename to src/talisman/prompts/__init__.py diff --git a/src/ontogpt/prompts/enrichment/__init__.py b/src/talisman/prompts/enrichment/__init__.py similarity index 100% rename from src/ontogpt/prompts/enrichment/__init__.py rename to src/talisman/prompts/enrichment/__init__.py diff --git a/src/ontogpt/prompts/enrichment/gene_set_summarization.jinja2 b/src/talisman/prompts/enrichment/gene_set_summarization.jinja2 similarity index 100% rename from src/ontogpt/prompts/enrichment/gene_set_summarization.jinja2 rename to src/talisman/prompts/enrichment/gene_set_summarization.jinja2 diff --git a/src/ontogpt/prompts/enrichment/gene_set_summarization_with_p_values.jinja2 b/src/talisman/prompts/enrichment/gene_set_summarization_with_p_values.jinja2 similarity index 100% rename from src/ontogpt/prompts/enrichment/gene_set_summarization_with_p_values.jinja2 rename to src/talisman/prompts/enrichment/gene_set_summarization_with_p_values.jinja2 diff --git a/src/ontogpt/prompts/enrichment/gene_set_summarization_with_p_values_0.jinja2 b/src/talisman/prompts/enrichment/gene_set_summarization_with_p_values_0.jinja2 similarity index 100% rename from src/ontogpt/prompts/enrichment/gene_set_summarization_with_p_values_0.jinja2 rename to src/talisman/prompts/enrichment/gene_set_summarization_with_p_values_0.jinja2 diff --git a/src/ontogpt/prompts/enrichment/gene_set_summarization_with_p_values_1.jinja2 b/src/talisman/prompts/enrichment/gene_set_summarization_with_p_values_1.jinja2 similarity index 100% rename from src/ontogpt/prompts/enrichment/gene_set_summarization_with_p_values_1.jinja2 rename to src/talisman/prompts/enrichment/gene_set_summarization_with_p_values_1.jinja2 diff --git a/src/ontogpt/prompts/enrichment/gene_set_summarization_with_p_values_2.jinja2 b/src/talisman/prompts/enrichment/gene_set_summarization_with_p_values_2.jinja2 similarity index 100% rename from src/ontogpt/prompts/enrichment/gene_set_summarization_with_p_values_2.jinja2 rename to src/talisman/prompts/enrichment/gene_set_summarization_with_p_values_2.jinja2 diff --git a/src/ontogpt/streamlit/spindoctor.py b/src/talisman/streamlit/talisman.py similarity index 90% rename from src/ontogpt/streamlit/spindoctor.py rename to src/talisman/streamlit/talisman.py index f7c388d25..95f7d7576 100644 --- a/src/ontogpt/streamlit/spindoctor.py +++ b/src/talisman/streamlit/talisman.py @@ -1,13 +1,13 @@ -"""Streamlist web app for spindoctor.""" +"""Streamlist web app for TALISMAN.""" # Import necessary libraries import re import streamlit as st from oaklib import get_adapter -from ontogpt.engines import create_engine -from ontogpt.engines.enrichment import EnrichmentEngine, GeneDescriptionSource -from ontogpt.utils.gene_set_utils import GeneSet +from talisman.engines import create_engine +from talisman.engines.enrichment import EnrichmentEngine, GeneDescriptionSource +from talisman.utils.gene_set_utils import GeneSet MODEL_GPT_3_5_TURBO = "gpt-3.5-turbo" MODEL_GPT_3_5_TURBO_INSTRUCT = "gpt-3.5-turbo-instruct" @@ -16,7 +16,7 @@ go = get_adapter("sqlite:obo:go") # Title of the app -st.title("SPINDOCTOR") +st.title("TALISMAN") st.caption("A tool for summarizing gene sets using GPT") col1, col2 = st.columns(2) diff --git a/src/ontogpt/ontex/__init__.py b/src/talisman/utils/__init__.py similarity index 100% rename from src/ontogpt/ontex/__init__.py rename to src/talisman/utils/__init__.py diff --git a/src/ontogpt/utils/gene_set_utils.py b/src/talisman/utils/gene_set_utils.py similarity index 100% rename from src/ontogpt/utils/gene_set_utils.py rename to src/talisman/utils/gene_set_utils.py diff --git a/tests/__init__.py b/tests/__init__.py index a22fd7b22..4ac1d1468 100644 --- a/tests/__init__.py +++ b/tests/__init__.py @@ -1,4 +1,4 @@ -"""Tests for ontogpt.""" +"""Tests for TALISMAN.""" import logging import os from pathlib import Path diff --git a/tests/input/Guo-2017-EXTL3-Patient_1.json b/tests/input/Guo-2017-EXTL3-Patient_1.json deleted file mode 100644 index 03ed6005e..000000000 --- a/tests/input/Guo-2017-EXTL3-Patient_1.json +++ /dev/null @@ -1,837 +0,0 @@ -{ - "id": "PMID:28331220-Guo-2017-EXTL3-Patient_1", - "subject": { - "id": "Patient 1", - "ageAtCollection": { - "age": "P2Y" - }, - "sex": "FEMALE", - "taxonomy": { - "id": "NCBITaxon:9606", - "label": "Homo sapiens" - } - }, - "phenotypicFeatures": [{ - "type": { - "id": "HP:0003196", - "label": "Short nose" - }, - "evidence": [{ - "evidenceCode": { - "id": "ECO:0000033", - "label": "author statement supported by traceable reference" - }, - "reference": { - "id": "PMID:28331220", - "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia" - } - }] - }, { - "type": { - "id": "HP:0002176", - "label": "Spinal cord compression" - }, - "evidence": [{ - "evidenceCode": { - "id": "ECO:0000033", - "label": "author statement supported by traceable reference" - }, - "reference": { - "id": "PMID:28331220", - "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia" - } - }] - }, { - "type": { - "id": "HP:0003265", - "label": "Neonatal hyperbilirubinemia" - }, - "evidence": [{ - "evidenceCode": { - "id": "ECO:0000033", - "label": "author statement supported by traceable reference" - }, - "reference": { - "id": "PMID:28331220", - "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia" - } - }] - }, { - "type": { - "id": "HP:0005280", - "label": "Depressed nasal bridge" - }, - "evidence": [{ - "evidenceCode": { - "id": "ECO:0000033", - "label": "author statement supported by traceable reference" - }, - "reference": { - "id": "PMID:28331220", - "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia" - } - }] - }, { - "type": { - "id": "HP:0002090", - "label": "Pneumonia" - }, - "evidence": [{ - "evidenceCode": { - "id": "ECO:0000033", - "label": "author statement supported by traceable reference" - }, - "reference": { - "id": "PMID:28331220", - "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia" - } - }] - }, { - "type": { - "id": "HP:0003016", - "label": "Metaphyseal widening" - }, - "evidence": [{ - "evidenceCode": { - "id": "ECO:0000033", - "label": "author statement supported by traceable reference" - }, - "reference": { - "id": "PMID:28331220", - "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia" - } - }] - }, { - "type": { - "id": "HP:0008936", - "label": "Muscular hypotonia of the trunk" - }, - "evidence": [{ - "evidenceCode": { - "id": "ECO:0000033", - "label": "author statement supported by traceable reference" - }, - "reference": { - "id": "PMID:28331220", - "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia" - } - }] - }, { - "type": { - "id": "HP:0000463", - "label": "Anteverted nares" - }, - "evidence": [{ - "evidenceCode": { - "id": "ECO:0000033", - "label": "author statement supported by traceable reference" - }, - "reference": { - "id": "PMID:28331220", - "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia" - } - }] - }, { - "type": { - "id": "HP:0000212", - "label": "Gingival overgrowth" - }, - "evidence": [{ - "evidenceCode": { - "id": "ECO:0000033", - "label": "author statement supported by traceable reference" - }, - "reference": { - "id": "PMID:28331220", - "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia" - } - }] - }, { - "type": { - "id": "HP:0005306", - "label": "Capillary hemangioma" - }, - "evidence": [{ - "evidenceCode": { - "id": "ECO:0000033", - "label": "author statement supported by traceable reference" - }, - "reference": { - "id": "PMID:28331220", - "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia" - } - }] - }, { - "type": { - "id": "HP:0001270", - "label": "Motor delay" - }, - "evidence": [{ - "evidenceCode": { - "id": "ECO:0000033", - "label": "author statement supported by traceable reference" - }, - "reference": { - "id": "PMID:28331220", - "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia" - } - }] - }, { - "type": { - "id": "HP:0100625", - "label": "Enlarged thorax" - }, - "evidence": [{ - "evidenceCode": { - "id": "ECO:0000033", - "label": "author statement supported by traceable reference" - }, - "reference": { - "id": "PMID:28331220", - "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia" - } - }] - }, { - "type": { - "id": "HP:0001028", - "label": "Hemangioma" - }, - "evidence": [{ - "evidenceCode": { - "id": "ECO:0000033", - "label": "author statement supported by traceable reference" - }, - "reference": { - "id": "PMID:28331220", - "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia" - } - }] - }, { - "type": { - "id": "HP:0003307", - "label": "Hyperlordosis" - }, - "evidence": [{ - "evidenceCode": { - "id": "ECO:0000033", - "label": "author statement supported by traceable reference" - }, - "reference": { - "id": "PMID:28331220", - "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia" - } - }] - }, { - "type": { - "id": "HP:0000960", - "label": "Sacral dimple" - }, - "evidence": [{ - "evidenceCode": { - "id": "ECO:0000033", - "label": "author statement supported by traceable reference" - }, - "reference": { - "id": "PMID:28331220", - "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia" - } - }] - }, { - "type": { - "id": "HP:0002063", - "label": "Rigidity" - }, - "evidence": [{ - "evidenceCode": { - "id": "ECO:0000033", - "label": "author statement supported by traceable reference" - }, - "reference": { - "id": "PMID:28331220", - "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia" - } - }] - }, { - "type": { - "id": "HP:0000252", - "label": "Microcephaly" - }, - "evidence": [{ - "evidenceCode": { - "id": "ECO:0000033", - "label": "author statement supported by traceable reference" - }, - "reference": { - "id": "PMID:28331220", - "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia" - } - }] - }, { - "type": { - "id": "HP:0100865", - "label": "Broad ischia" - }, - "evidence": [{ - "evidenceCode": { - "id": "ECO:0000033", - "label": "author statement supported by traceable reference" - }, - "reference": { - "id": "PMID:28331220", - "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia" - } - }] - }, { - "type": { - "id": "HP:0000347", - "label": "Micrognathia" - }, - "evidence": [{ - "evidenceCode": { - "id": "ECO:0000033", - "label": "author statement supported by traceable reference" - }, - "reference": { - "id": "PMID:28331220", - "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia" - } - }] - }, { - "type": { - "id": "HP:0003690", - "label": "Limb muscle weakness" - }, - "evidence": [{ - "evidenceCode": { - "id": "ECO:0000033", - "label": "author statement supported by traceable reference" - }, - "reference": { - "id": "PMID:28331220", - "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia" - } - }] - }, { - "type": { - "id": "HP:0001156", - "label": "Brachydactyly" - }, - "evidence": [{ - "evidenceCode": { - "id": "ECO:0000033", - "label": "author statement supported by traceable reference" - }, - "reference": { - "id": "PMID:28331220", - "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia" - } - }] - }, { - "type": { - "id": "HP:0002867", - "label": "Abnormality of the ilium" - }, - "evidence": [{ - "evidenceCode": { - "id": "ECO:0000033", - "label": "author statement supported by traceable reference" - }, - "reference": { - "id": "PMID:28331220", - "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia" - } - }] - }, { - "type": { - "id": "HP:0001265", - "label": "Hyporeflexia" - }, - "evidence": [{ - "evidenceCode": { - "id": "ECO:0000033", - "label": "author statement supported by traceable reference" - }, - "reference": { - "id": "PMID:28331220", - "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia" - } - }] - }, { - "type": { - "id": "HP:0002240", - "label": "Hepatomegaly" - }, - "evidence": [{ - "evidenceCode": { - "id": "ECO:0000033", - "label": "author statement supported by traceable reference" - }, - "reference": { - "id": "PMID:28331220", - "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia" - } - }] - }, { - "type": { - "id": "HP:0001324", - "label": "Muscle weakness" - }, - "evidence": [{ - "evidenceCode": { - "id": "ECO:0000033", - "label": "author statement supported by traceable reference" - }, - "reference": { - "id": "PMID:28331220", - "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia" - } - }] - }, { - "type": { - "id": "HP:0004565", - "label": "Severe platyspondyly" - }, - "evidence": [{ - "evidenceCode": { - "id": "ECO:0000033", - "label": "author statement supported by traceable reference" - }, - "reference": { - "id": "PMID:28331220", - "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia" - } - }] - }, { - "type": { - "id": "HP:0002007", - "label": "Frontal bossing" - }, - "evidence": [{ - "evidenceCode": { - "id": "ECO:0000033", - "label": "author statement supported by traceable reference" - }, - "reference": { - "id": "PMID:28331220", - "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia" - } - }] - }, { - "type": { - "id": "HP:0005193", - "label": "Restricted large joint movement" - }, - "evidence": [{ - "evidenceCode": { - "id": "ECO:0000033", - "label": "author statement supported by traceable reference" - }, - "reference": { - "id": "PMID:28331220", - "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia" - } - }] - }, { - "type": { - "id": "HP:0002808", - "label": "Kyphosis" - }, - "evidence": [{ - "evidenceCode": { - "id": "ECO:0000033", - "label": "author statement supported by traceable reference" - }, - "reference": { - "id": "PMID:28331220", - "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia" - } - }] - }, { - "type": { - "id": "HP:0002850", - "label": "Decreased circulating total IgM" - }, - "evidence": [{ - "evidenceCode": { - "id": "ECO:0000033", - "label": "author statement supported by traceable reference" - }, - "reference": { - "id": "PMID:28331220", - "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia" - } - }] - }, { - "type": { - "id": "HP:0001508", - "label": "Failure to thrive" - }, - "evidence": [{ - "evidenceCode": { - "id": "ECO:0000033", - "label": "author statement supported by traceable reference" - }, - "reference": { - "id": "PMID:28331220", - "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia" - } - }] - }, { - "type": { - "id": "HP:0000924", - "label": "Abnormality of the skeletal system" - }, - "evidence": [{ - "evidenceCode": { - "id": "ECO:0000033", - "label": "author statement supported by traceable reference" - }, - "reference": { - "id": "PMID:28331220", - "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia" - } - }] - }, { - "type": { - "id": "HP:0004060", - "label": "Trident hand" - }, - "evidence": [{ - "evidenceCode": { - "id": "ECO:0000033", - "label": "author statement supported by traceable reference" - }, - "reference": { - "id": "PMID:28331220", - "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia" - } - }] - }, { - "type": { - "id": "HP:0002904", - "label": "Hyperbilirubinemia" - }, - "evidence": [{ - "evidenceCode": { - "id": "ECO:0000033", - "label": "author statement supported by traceable reference" - }, - "reference": { - "id": "PMID:28331220", - "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia" - } - }] - }, { - "type": { - "id": "HP:0007340", - "label": "Lower limb muscle weakness" - }, - "evidence": [{ - "evidenceCode": { - "id": "ECO:0000033", - "label": "author statement supported by traceable reference" - }, - "reference": { - "id": "PMID:28331220", - "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia" - } - }] - }, { - "type": { - "id": "HP:0001407", - "label": "Hepatic cysts" - }, - "evidence": [{ - "evidenceCode": { - "id": "ECO:0000033", - "label": "author statement supported by traceable reference" - }, - "reference": { - "id": "PMID:28331220", - "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia" - } - }] - }, { - "type": { - "id": "HP:0000670", - "label": "Carious teeth" - }, - "evidence": [{ - "evidenceCode": { - "id": "ECO:0000033", - "label": "author statement supported by traceable reference" - }, - "reference": { - "id": "PMID:28331220", - "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia" - } - }] - }, { - "type": { - "id": "HP:0003416", - "label": "Spinal canal stenosis" - }, - "evidence": [{ - "evidenceCode": { - "id": "ECO:0000033", - "label": "author statement supported by traceable reference" - }, - "reference": { - "id": "PMID:28331220", - "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia" - } - }] - }, { - "type": { - "id": "HP:0001252", - "label": "Muscular hypotonia" - }, - "evidence": [{ - "evidenceCode": { - "id": "ECO:0000033", - "label": "author statement supported by traceable reference" - }, - "reference": { - "id": "PMID:28331220", - "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia" - } - }] - }, { - "type": { - "id": "HP:0000253", - "label": "Progressive microcephaly" - }, - "evidence": [{ - "evidenceCode": { - "id": "ECO:0000033", - "label": "author statement supported by traceable reference" - }, - "reference": { - "id": "PMID:28331220", - "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia" - } - }] - }, { - "type": { - "id": "HP:0004315", - "label": "Decreased circulating IgG level" - }, - "evidence": [{ - "evidenceCode": { - "id": "ECO:0000033", - "label": "author statement supported by traceable reference" - }, - "reference": { - "id": "PMID:28331220", - "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia" - } - }] - }, { - "type": { - "id": "HP:0100543", - "label": "Cognitive impairment" - }, - "evidence": [{ - "evidenceCode": { - "id": "ECO:0000033", - "label": "author statement supported by traceable reference" - }, - "reference": { - "id": "PMID:28331220", - "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia" - } - }] - }, { - "type": { - "id": "HP:0009826", - "label": "Limb undergrowth" - }, - "evidence": [{ - "evidenceCode": { - "id": "ECO:0000033", - "label": "author statement supported by traceable reference" - }, - "reference": { - "id": "PMID:28331220", - "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia" - } - }] - }, { - "type": { - "id": "HP:0000520", - "label": "Proptosis" - }, - "evidence": [{ - "evidenceCode": { - "id": "ECO:0000033", - "label": "author statement supported by traceable reference" - }, - "reference": { - "id": "PMID:28331220", - "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia" - } - }] - }, { - "type": { - "id": "HP:0001561", - "label": "Polyhydramnios" - }, - "evidence": [{ - "evidenceCode": { - "id": "ECO:0000033", - "label": "author statement supported by traceable reference" - }, - "reference": { - "id": "PMID:28331220", - "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia" - } - }] - }, { - "type": { - "id": "HP:0005619", - "label": "Thoracolumbar kyphosis" - }, - "evidence": [{ - "evidenceCode": { - "id": "ECO:0000033", - "label": "author statement supported by traceable reference" - }, - "reference": { - "id": "PMID:28331220", - "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia" - } - }] - }, { - "type": { - "id": "HP:0006532", - "label": "Recurrent pneumonia" - }, - "evidence": [{ - "evidenceCode": { - "id": "ECO:0000033", - "label": "author statement supported by traceable reference" - }, - "reference": { - "id": "PMID:28331220", - "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia" - } - }] - }, { - "type": { - "id": "HP:0001548", - "label": "Overgrowth" - }, - "evidence": [{ - "evidenceCode": { - "id": "ECO:0000033", - "label": "author statement supported by traceable reference" - }, - "reference": { - "id": "PMID:28331220", - "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia" - } - }] - }, { - "type": { - "id": "HP:0001290", - "label": "Generalized hypotonia" - }, - "evidence": [{ - "evidenceCode": { - "id": "ECO:0000033", - "label": "author statement supported by traceable reference" - }, - "reference": { - "id": "PMID:28331220", - "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia" - } - }] - }, { - "type": { - "id": "HP:0002938", - "label": "Lumbar hyperlordosis" - }, - "evidence": [{ - "evidenceCode": { - "id": "ECO:0000033", - "label": "author statement supported by traceable reference" - }, - "reference": { - "id": "PMID:28331220", - "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia" - } - }] - }], - "genes": [{ - "id": "NCBIGene:2137", - "symbol": "EXTL3" - }], - "variants": [{ - "vcfAllele": { - "genomeAssembly": "GRCh37", - "chr": "8", - "pos": 28574529, - "ref": "C", - "alt": "T" - }, - "zygosity": { - "id": "GENO:0000136", - "label": "homozygous" - } - }], - "diseases": [{ - "term": { - "id": "OMIM:617425", - "label": "Immunoskeletal dysplasia with neurodevelopmental abnormalities" - } - }], - "metaData": { - "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT", - "submittedBy": "UNC:biocuration", - "resources": [{ - "id": "hp", - "name": "human phenotype ontology", - "url": "http://purl.obolibrary.org/obo/hp.owl", - "version": "2018-03-08", - "namespacePrefix": "HP", - "iriPrefix": "http://purl.obolibrary.org/obo/HP_" - }, { - "id": "pato", - "name": "Phenotype And Trait Ontology", - "url": "http://purl.obolibrary.org/obo/pato.owl", - "version": "2018-03-28", - "namespacePrefix": "PATO", - "iriPrefix": "http://purl.obolibrary.org/obo/PATO_" - }, { - "id": "geno", - "name": "Genotype Ontology", - "url": "http://purl.obolibrary.org/obo/geno.owl", - "version": "19-03-2018", - "namespacePrefix": "GENO", - "iriPrefix": "http://purl.obolibrary.org/obo/GENO_" - }, { - "id": "ncbitaxon", - "name": "NCBI organismal classification", - "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl", - "version": "2018-03-02", - "namespacePrefix": "NCBITaxon" - }, { - "id": "eco", - "name": "Evidence and Conclusion Ontology", - "url": "http://purl.obolibrary.org/obo/eco.owl", - "version": "2018-11-10", - "namespacePrefix": "ECO", - "iriPrefix": "http://purl.obolibrary.org/obo/ECO_" - }, { - "id": "omim", - "name": "Online Mendelian Inheritance in Man", - "url": "https://www.omim.org", - "namespacePrefix": "OMIM" - }], - "phenopacketSchemaVersion": "1.0.0-RC3", - "externalReferences": [{ - "id": "PMID:28331220", - "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia" - }] - } -} \ No newline at end of file diff --git a/tests/input/cases/amphibian_skin.txt b/tests/input/cases/amphibian_skin.txt deleted file mode 100644 index 9eaba48a7..000000000 --- a/tests/input/cases/amphibian_skin.txt +++ /dev/null @@ -1,2 +0,0 @@ -Abstract -Host-microbe symbioses rely on the successful transmission or acquisition of symbionts in each new generation. Amphibians host a diverse cutaneous microbiota, and many of these symbionts appear to be mutualistic and may limit infection by the chytrid fungus, Batrachochytrium dendrobatidis, which has caused global amphibian population declines and extinctions in recent decades. Using bar-coded 454 pyrosequencing of the 16S rRNA gene, we addressed the question of symbiont transmission by examining variation in amphibian skin microbiota across species and sites and in direct relation to environmental microbes. Although acquisition of environmental microbes occurs in some host-symbiont systems, this has not been extensively examined in free-living vertebrate-microbe symbioses. Juvenile bullfrogs (Rana catesbeiana), adult red-spotted newts (Notophthalmus viridescens), pond water and pond substrate were sampled at a single pond to examine host-specificity and potential environmental transmission of microbiota. To assess population level variation in skin microbiota, adult newts from two additional sites were also sampled. Cohabiting bullfrogs and newts had distinct microbial communities, as did newts across the three sites. The microbial communities of amphibians and the environment were distinct; there was very little overlap in the amphibians’ core microbes and the most abundant environmental microbes, and the relative abundances of OTUs that were shared by amphibians and the environment were inversely related. These results suggest that, in a host species-specific manner, amphibian skin may select for microbes that are generally in low abundance in the environment. diff --git a/tests/input/cases/biotic_interaction-001.txt b/tests/input/cases/biotic_interaction-001.txt deleted file mode 100644 index 394d2d6f1..000000000 --- a/tests/input/cases/biotic_interaction-001.txt +++ /dev/null @@ -1,6 +0,0 @@ -Great white sharks are apex predators, meaning they have a large affect on the populations of their prey including elephant seals and sea lions. Great white sharks are hosts to parasites such as copepods (Pandarus sinuatus and Pandarus smithii). - -Commensal/Parasitic Species: - -Pandarus sinuatus -Pandarus smithii \ No newline at end of file diff --git a/tests/input/cases/biotic_interaction-002.txt b/tests/input/cases/biotic_interaction-002.txt deleted file mode 100644 index 626ad9efd..000000000 --- a/tests/input/cases/biotic_interaction-002.txt +++ /dev/null @@ -1,5 +0,0 @@ -Young great white sharks typically feed on smaller species such as squid and stingrays, as well as other small sharks (McGrouther, 2008). As these fish mature their appetites change. The diet of adults consists primarily of seals, sealions, dolphins, and whale carcasses (McGrouther, 2008). One of the most frequent prey animals of great white sharks are elephant seals (MarineBio, 2009). Sometimes they feed on turtles and various sea birds (McGrouther, 2008). Great white sharks may attack with different strategies depending on the size of their prey. The most common attack method used by great white sharks involves the shark positioning itself directly below its prey and then swimming vertically into an attack (MarineBio, 2009). These sharks collide into their prey and then bite them. Prey often die from blood loss, decapitation or severance of vital appendages such as fins. Great white sharks have been reported to attack humans but there have been as few as 311 verified deaths from great white shark attacks (Burnie and Wilson, 2001). - -Animal Foods: birds; mammals; reptiles; fish; mollusks; other marine invertebrates - -Primary Diet: carnivore (Eats terrestrial vertebrates, Piscivore , Molluscivore ) \ No newline at end of file diff --git a/tests/input/cases/biotic_interaction-003.txt b/tests/input/cases/biotic_interaction-003.txt deleted file mode 100644 index 8e17213c6..000000000 --- a/tests/input/cases/biotic_interaction-003.txt +++ /dev/null @@ -1 +0,0 @@ -Great white sharks are apex predators; they are at the top of the food chain. Occasionally great white sharks will encounter a killer whale or another shark of comparable size (Martins and Knickle, 2009). These species pose a small threat to great white sharks. \ No newline at end of file diff --git a/tests/input/cases/biotic_interaction-004.txt b/tests/input/cases/biotic_interaction-004.txt deleted file mode 100644 index 3fd41a61c..000000000 --- a/tests/input/cases/biotic_interaction-004.txt +++ /dev/null @@ -1 +0,0 @@ -Great white sharks prey upon halibut, salmon, tuna, rays, other sharks, dolphins, porpoises, whales, hair seals, fur seals, elephant seals, sea lions, sea turtles, sea otters, seabirds and invetebrates. As they become adult and get larger, great white sharks take large prey and more marine mammals. Large great white sharks have been observed taking beluga whales in Cook Inlet; they may take walruses in the Bering Sea and Arctic Ocean. \ No newline at end of file diff --git a/tests/input/cases/biotic_interaction-005.txt b/tests/input/cases/biotic_interaction-005.txt deleted file mode 100644 index baa2aa711..000000000 --- a/tests/input/cases/biotic_interaction-005.txt +++ /dev/null @@ -1 +0,0 @@ -Known to feed on mammals (Ref. 247). Anthosoma crassum, Dinemoura latifolia and Pandarus sinuatua (copepods) are known to be parasites of the species (Ref. 5951). Also in Ref. 9137. \ No newline at end of file diff --git a/tests/input/cases/biotic_interaction-006.txt b/tests/input/cases/biotic_interaction-006.txt deleted file mode 100644 index 7a5fec44b..000000000 --- a/tests/input/cases/biotic_interaction-006.txt +++ /dev/null @@ -1,15 +0,0 @@ -Great white sharks are carnivorous and prey upon fish (e.g. tuna, rays, other sharks),[107] cetaceans (i.e., dolphins, porpoises, whales), pinnipeds (e.g. seals, fur seals,[107] and sea lions), sea turtles,[107] sea otters (Enhydra lutris) and seabirds.[108] Great whites have also been known to eat objects that they are unable to digest. Juvenile white sharks predominantly prey on fish, including other elasmobranchs, as their jaws are not strong enough to withstand the forces required to attack larger prey such as pinnipeds and cetaceans until they reach a length of 3 m (9.8 ft) or more, at which point their jaw cartilage mineralizes enough to withstand the impact of biting into larger prey species.[109] Upon approaching a length of nearly 4 m (13 ft), great white sharks begin to target predominantly marine mammals for food, though individual sharks seem to specialize in different types of prey depending on their preferences.[110][111] They seem to be highly opportunistic.[112][113] These sharks prefer prey with a high content of energy-rich fat. Shark expert Peter Klimley used a rod-and-reel rig and trolled carcasses of a seal, a pig, and a sheep from his boat in the South Farallons. The sharks attacked all three baits but rejected the sheep carcass.[114] - -Off of Seal Island, False Bay in South Africa, the sharks ambush brown fur seals (Arctocephalus pusillus) from below at high speeds, hitting the seal mid-body. They achieve high speeds that allow them to completely breach the surface of the water. The peak burst speed is estimated to be above 40 km/h (25 mph).[115] They have also been observed chasing prey after a missed attack. Prey is usually attacked at the surface.[116] Shark attacks occur most often in the morning, within two hours of sunrise, when visibility is poor. Their success rate is 55% in the first two hours, falling to 40% in late morning after which hunting stops.[107] - -Off California, sharks immobilize northern elephant seals (Mirounga angustirostris) with a large bite to the hindquarters (which is the main source of the seal's mobility) and wait for the seal to bleed to death. This technique is especially used on adult male elephant seals, which are typically larger than the shark, ranging between 1,500 and 2,000 kg (3,300 and 4,400 lb), and are potentially dangerous adversaries.[117][118] Most commonly though, juvenile elephant seals are the most frequently eaten at elephant seal colonies.[119] Prey is normally attacked sub-surface. Harbor seals (Phoca vitulina) are taken from the surface and dragged down until they stop struggling. They are then eaten near the bottom. California sea lions (Zalophus californianus) are ambushed from below and struck mid-body before being dragged and eaten.[120] - -In the Northwest Atlantic mature great whites are known to feed on both harbor and grey seals.[50] Unlike adults, juvenile white sharks in the area feed on smaller fish species until they are large enough to prey on marine mammals such as seals.[121] - -White sharks also attack dolphins and porpoises from above, behind or below to avoid being detected by their echolocation. Targeted species include dusky dolphins (Sagmatias obscurus),[67] Risso's dolphins (Grampus griseus),[67] bottlenose dolphins (Tursiops ssp.),[67][122] humpback dolphins (Sousa ssp.),[122] harbour porpoises (Phocoena phocoena),[67] and Dall's porpoises (Phocoenoides dalli).[67] Groups of dolphins have occasionally been observed defending themselves from sharks with mobbing behaviour.[122] White shark predation on other species of small cetacean has also been observed. In August 1989, a 1.8 m (5.9 ft) juvenile male pygmy sperm whale (Kogia breviceps) was found stranded in central California with a bite mark on its caudal peduncle from a great white shark.[123] In addition, white sharks attack and prey upon beaked whales.[67][122] Cases where an adult Stejneger's beaked whale (Mesoplodon stejnegeri), with a mean mass of around 1,100 kg (2,400 lb),[124] and a juvenile Cuvier's beaked whale (Ziphius cavirostris), an individual estimated at 3 m (9.8 ft), were hunted and killed by great white sharks have also been observed.[125] When hunting sea turtles, they appear to simply bite through the carapace around a flipper, immobilizing the turtle. The heaviest species of bony fish, the oceanic sunfish (Mola mola), has been found in great white shark stomachs.[112] - -Whale carcasses comprise an important part of the diet of white sharks. However, this has rarely been observed due to whales dying in remote areas. It has been estimated that 30 kg (66 lb) of whale blubber could feed a 4.5 m (15 ft) white shark for 1.5 months. Detailed observations were made of four whale carcasses in False Bay between 2000 and 2010. Sharks were drawn to the carcass by chemical and odour detection, spread by strong winds. After initially feeding on the whale caudal peduncle and fluke, the sharks would investigate the carcass by slowly swimming around it and mouthing several parts before selecting a blubber-rich area. During feeding bouts of 15–20 seconds the sharks removed flesh with lateral headshakes, without the protective ocular rotation they employ when attacking live prey. The sharks were frequently observed regurgitating chunks of blubber and immediately returning to feed, possibly in order to replace low energy yield pieces with high energy yield pieces, using their teeth as mechanoreceptors to distinguish them. After feeding for several hours, the sharks appeared to become lethargic, no longer swimming to the surface; they were observed mouthing the carcass but apparently unable to bite hard enough to remove flesh, they would instead bounce off and slowly sink. Up to eight sharks were observed feeding simultaneously, bumping into each other without showing any signs of aggression; on one occasion a shark accidentally bit the head of a neighbouring shark, leaving two teeth embedded, but both continued to feed unperturbed. Smaller individuals hovered around the carcass eating chunks that drifted away. Unusually for the area, large numbers of sharks over five metres long were observed, suggesting that the largest sharks change their behaviour to search for whales as they lose the manoeuvrability required to hunt seals. The investigating team concluded that the importance of whale carcasses, particularly for the largest white sharks, has been underestimated.[126] - -In another documented incident, white sharks were observed scavenging on a whale carcass alongside tiger sharks.[127] In 2020, marine biologists Sasha Dines and Enrico Gennari published a documented incident in the journal Marine and Freshwater Research of a group of great white sharks exhibiting pack-like behaviour, successfully attacking and killing a live juvenile 7 m (23 ft) humpback whale. The sharks utilized the classic attack strategy used on pinnipeds when attacking the whale, even utilizing the bite-and-spit tactic they employ on smaller prey items. The whale was an entangled individual, heavily emaciated and thus more vulnerable to the sharks' attacks. The incident is the first known documentation of great whites actively killing a large baleen whale.[128][129] A second incident regarding great white sharks killing humpback whales involving a single large female great white nicknamed Helen was documented off the coast of South Africa. Working alone, the shark attacked a 33 ft (10 m) emaciated and entangled humpback whale by attacking the whale's tail to cripple it before she managed to drown the whale by biting onto its head and pulling it underwater. The attack was witnessed via aerial drone by marine biologist Ryan Johnson, who said the attack went on for roughly 50 minutes before the shark successfully killed the whale. Johnson suggested that the shark may have strategized its attack in order to kill such a large animal.[130][131] - -Stomach contents of great whites also indicates that whale sharks both juvenile and adult may also be included on the animal's menu, though whether this is active hunting or scavenging is not known at present.[132] \ No newline at end of file diff --git a/tests/input/cases/biotic_interaction-007.txt b/tests/input/cases/biotic_interaction-007.txt deleted file mode 100644 index b9c254dbf..000000000 --- a/tests/input/cases/biotic_interaction-007.txt +++ /dev/null @@ -1,3 +0,0 @@ -Interspecific competition between the great white shark and the orca is probable in regions where dietary preferences of both species may overlap.[122] An incident was documented on 4 October 1997, in the Farallon Islands off California in the United States. An estimated 4.7–5.3 m (15–17 ft) female orca immobilized an estimated 3–4 m (9.8–13.1 ft) great white shark.[143] The orca held the shark upside down to induce tonic immobility and kept the shark still for fifteen minutes, causing it to suffocate. The orca then proceeded to eat the dead shark's liver.[122][143][144] It is believed that the scent of the slain shark's carcass caused all the great whites in the region to flee, forfeiting an opportunity for a great seasonal feed.[145] Another similar attack apparently occurred there in 2000, but its outcome is not clear.[146] After both attacks, the local population of about 100 great whites vanished.[144][146] Following the 2000 incident, a great white with a satellite tag was found to have immediately submerged to a depth of 500 m (1,600 ft) and swum to Hawaii.[146] - -In 2015, a pod of orcas was recorded to have killed a great white shark off South Australia.[147] In 2017, three great whites were found washed ashore near Gansbaai, South Africa, with their body cavities torn open and the livers removed by what is likely to have been orcas.[148] Orcas also generally impact great white distribution. Studies published in 2019 of orca and great white shark distribution and interactions around the Farallon Islands indicate that the cetaceans impact the sharks negatively, with brief appearances by orcas causing the sharks to seek out new feeding areas until the next season.[149] Occasionally, however, some great whites have been seen to swim near orcas without fear.[150] \ No newline at end of file diff --git a/tests/input/cases/biotic_interaction-008.txt b/tests/input/cases/biotic_interaction-008.txt deleted file mode 100644 index bdc9b8f12..000000000 --- a/tests/input/cases/biotic_interaction-008.txt +++ /dev/null @@ -1 +0,0 @@ -Bony fishes such as salmon, hake, halibut, mackerel and tunas. As well, other sharks, sea turtles, seabirds and marine mammals are eaten. \ No newline at end of file diff --git a/tests/input/cases/biotic_interaction-009.txt b/tests/input/cases/biotic_interaction-009.txt deleted file mode 100644 index 8d2bcbdde..000000000 --- a/tests/input/cases/biotic_interaction-009.txt +++ /dev/null @@ -1,11 +0,0 @@ -Lions are predatory carnivores. They usually hunt in groups, but the actual killing is done by an individual lion. They frequently bring down prey much bigger than they are themselves. Showy males have more difficulty hunting than females because of their conspicuousness, therefore females in a pride do the majority of hunting. Males are still more aggressive during feeding than are females, even though they are less likely to have killed the prey. - -African lions eat the most common large ungulates in the area (Thompson's gazelles Eudorcas thomsonii, zebras Equus burchellii, impalas Aepyceros melampus, and wildebeests Connochaetes taurinus). Individual prides tend to have their own eating preferences. Some prides tend to target large prey such as cape buffalo Syncerus caffer and giraffe Giraffa camelopardalis. Lions that are not able to capture large prey will eat birds, rodents, fish, ostrich eggs, amphibians and reptiles. Lions also actively scavenge, taking cues from hyenas and vultures. - -In Tanzania's Serengeti National Park, local lions subsist on a diet comprized mainly of 7 species: zebras Equus burchellii, wildebeests Connochaetes taurinus, Thompson's gazelles Eudorcas thomsonii, buffalos Syncerus caffer, warthogs Phacochoerus aethiopicus, hartebeests Alcelaphus buselaphus, and topis Damaliscus lunatus provide 90% of their diet. - -Hunting effectiveness is increased by hunting in groups. Serengeti research has shown that individual lions succeed in their hunting 17% of the time, whereas group hunts succeed 30% of the time. - -Animal Foods: birds; mammals; amphibians; reptiles; fish; eggs; carrion - -Primary Diet: carnivore (Eats terrestrial vertebrates) \ No newline at end of file diff --git a/tests/input/cases/biotic_interaction-010.txt b/tests/input/cases/biotic_interaction-010.txt deleted file mode 100644 index 66ba947bd..000000000 --- a/tests/input/cases/biotic_interaction-010.txt +++ /dev/null @@ -1,10 +0,0 @@ -Adult lions have no natural predators, excepting persecution by humans. Lions often kill and/or compete with other predators (leopards Panthera pardus and cheetahs Acinonyx jubatus). Spotted hyenas Crocuta crocuta defend kills or scavenged food from immature and female lions, but typically leave the food to a big male lion. Hyenas are known to kill lion cubs, juveniles, or weak and sick adult lions. - -Lion cubs, if left alone, can be vulnerable to other large predators. However, infanticide is the primary threat to cubs. - -Human poaching is a problem for lions. These animals are poached with wire snares, rifles, and arrows. Since lions are scavengers, they are particularly vulnerable to intentionally poisoned carcasses. There are still poachers that operate within some national parks in Africa. It has been estimated that in the 1960's, poachers were responsible for approximately 20,000 lion deaths per year in Serengeti National Park. Trophy hunting is allowed in 6 African countries. - -Known Predators: - -spotted hyenas (Crocuta crocuta) -humans (Homo sapiens) \ No newline at end of file diff --git a/tests/input/cases/biotic_interaction-011.txt b/tests/input/cases/biotic_interaction-011.txt deleted file mode 100644 index d3afd23cc..000000000 --- a/tests/input/cases/biotic_interaction-011.txt +++ /dev/null @@ -1,9 +0,0 @@ -The lion is a generalist hypercarnivore and is considered to be both an apex and keystone predator due to its wide prey spectrum.[100][101] Its prey consists mainly of mammals, particularly ungulates weighing 190–550 kg (420–1,210 lb) with a preference for blue wildebeest, plains zebra, African buffalo, gemsbok and giraffe. Lions also hunt common warthog depending on availability, although the species is below the preferred weight range.[102] In India, sambar deer and chital are the most commonly recorded wild prey,[46][102][103] while domestic livestock may contribute significantly to their diet.[103] They usually avoid fully grown adult elephants, rhinoceroses and hippopotamus and small prey like dik-dik, hyrax, hare and monkey.[102][104] Unusual prey include porcupines and small reptiles. Lions kill other predators such as leopard, cheetah and spotted hyena but seldom consume them.[105] - -Young lions first display stalking behaviour at around three months of age, although they do not participate in hunting until they are almost a year old and begin to hunt effectively when nearing the age of two.[106] Single lions are capable of bringing down zebra and wildebeest, while larger prey like buffalo and giraffe are riskier.[90] In Chobe National Park, large prides have been observed hunting African bush elephants up to around 15 years old in exceptional cases, with the victims being calves, juveniles, and even subadults.[107][108] In typical hunts, each lioness has a favoured position in the group, either stalking prey on the "wing", then attacking, or moving a smaller distance in the centre of the group and capturing prey fleeing from other lionesses. Males attached to prides do not usually participate in group hunting.[109] Some evidence suggests, however, that males are just as successful as females; they are typically solo hunters who ambush prey in small bushland.[110] - -Lions are not particularly known for their stamina; for instance, a lioness' heart comprises only 0.57% of her body weight and a male's is about 0.45% of his body weight, whereas a hyena's heart comprises almost 1% of its body weight.[111] Thus, lions run quickly only in short bursts at about 48–59 km/h (30–37 mph) and need to be close to their prey before starting the attack.[112] One study in 2018 recorded a lion running at a top speed of 74.1 km/h (46.0 mph).[113] They take advantage of factors that reduce visibility; many kills take place near some form of cover or at night.[114] The lion's attack is short and powerful; they attempt to catch prey with a fast rush and final leap. They usually pull it down by the rump and kill by a strangling bite to the throat. They also kill prey by enclosing its muzzle in their jaws.[115] - -Lions typically consume prey at the location of the hunt but sometimes drag large prey into cover.[116] They tend to squabble over kills, particularly the males. Cubs suffer most when food is scarce but otherwise all pride members eat their fill, including old and crippled lions, which can live on leftovers.[90] Large kills are shared more widely among pride members.[117] An adult lioness requires an average of about 5 kg (11 lb) of meat per day while males require about 7 kg (15 lb).[118] Lions gorge themselves and eat up to 30 kg (66 lb) in one session;[80] if it is unable to consume all of the kill, it rests for a few hours before continuing to eat. On hot days, the pride retreats to shade with one or two males standing guard.[116] Lions defend their kills from scavengers such as vultures and hyenas.[90] - -Lions scavenge on carrion when the opportunity arises; they scavenge animals dead from natural causes such as disease or those that were killed by other predators. Scavenging lions keep a constant lookout for circling vultures, which indicate the death or distress of an animal.[119] Most carrion on which both hyenas and lions feed upon are killed by hyenas rather than lions.[56] Carrion is thought to provide a large part of lion diet.[120] \ No newline at end of file diff --git a/tests/input/cases/biotic_interaction-012.txt b/tests/input/cases/biotic_interaction-012.txt deleted file mode 100644 index 2f9dc9c57..000000000 --- a/tests/input/cases/biotic_interaction-012.txt +++ /dev/null @@ -1,7 +0,0 @@ -Lions and spotted hyenas occupy a similar ecological niche and where they coexist they compete for prey and carrion; a review of data across several studies indicates a dietary overlap of 58.6%.[121] Lions typically ignore spotted hyenas unless the lions are on a kill or are being harassed by the hyenas, while the latter tend to visibly react to the presence of lions, with or without the presence of food. Lions seize the kills of spotted hyenas; in the Ngorongoro crater it is common for lions to subsist largely on kills stolen from hyenas, causing the hyenas to increase their kill rate.[122] In Botswana's Chobe National Park, the situation is reversed; hyenas frequently challenge lions and steal their kills, obtaining food from 63% of all lion kills.[123] When confronted on a kill by lions, spotted hyenas may either leave or wait patiently at a distance of 30–100 m (100–330 ft) until the lions have finished.[124] - -Hyenas are bold enough to feed alongside lions and to force the lions off a kill. The two species attack one another even when there is no food involved for no apparent reason.[125][126] Lion predation can account for up to 71% of hyena deaths in Etosha National Park. Spotted hyenas have adapted by frequently mobbing lions that enter their territories.[127] When the lion population in Kenya's Masai Mara National Reserve declined, the spotted hyena population increased rapidly.[128] Experiments on captive spotted hyenas show that specimens without prior experience with lions act indifferently to the sight of them, but will react fearfully to lion scent.[122] - -Lions tend to dominate cheetahs and leopards, steal their kills and kill their cubs and even adults when given the chance.[129] Cheetahs in particular often lose their kills to lions or other predators.[130] A study in the Serengeti ecosystem revealed that lions killed at least 17 of 125 cheetah cubs born between 1987 and 1990.[131] Cheetahs avoid their competitors by using different temporal and habitat niches.[132] Leopards are able to take refuge in trees; lionesses, however, occasionally attempt to climb up and retrieve leopard kills from that height.[133] - -Lions similarly dominate African wild dogs, taking their kills and preying on young and rarely adult dogs. Population densities of wild dogs are low in areas where lions are more abundant.[134] However, there are a few reported cases of old and wounded lions falling prey to wild dogs.[135][136] Lions also charge at Nile crocodiles; depending on the size of the crocodile and the lion, either animal can lose their kills to the other. Lions have been observed killing crocodiles that ventured onto land.[137] Crocodiles may also kill and eat lions, evidenced by the occasional lion claw found in crocodile stomachs.[138] \ No newline at end of file diff --git a/tests/input/cases/cell-type-salivary-acinar.txt b/tests/input/cases/cell-type-salivary-acinar.txt deleted file mode 100644 index fadf89f2d..000000000 --- a/tests/input/cases/cell-type-salivary-acinar.txt +++ /dev/null @@ -1,5 +0,0 @@ -Acinar cells of the salivary gland are a critical part of the oral physiology and the digestive mechanism. These specialized cells are concentrated towards the terminal ends of the salivary glands, where they form sac-like acini or clusters, giving them their name. They are amphicrine in nature, which means they play both secretory and endocrine roles. - -The primary function of the acinar cells of the salivary gland is to manufacture and secrete saliva. This substance, comprised mainly of water, electrolytes, mucins, and enzymes, is vital for the initial stages of digestion and for the regular maintenance of oral health. The acinar cells produce the two main types of saliva: serous and mucinous. The serous type, predominantly produced by the parotid gland, contains the enzyme amylase responsible for the initial breakdown of complex carbohydrates. The mucinous type, more common in the submandibular and sublingual glands, contains mucin that aids in lubrication, facilitating the process of mastication and bolus formation. - -Moreover, acinar cells also express and respond to various endocrine, paracrine, and autocrine hormones that govern the quantity and composition of the saliva produced. This implies sensitivity and modulation according to the internal and external environment, dietary habits, and even circadian rhythms. Impairment of acinar cells, whether due to damage or related to a systemic condition such as Sjögren's Syndrome, could disrupt the optimal functioning of the oral and digestive systems. In conclusion, acinar cells of the salivary gland, despite their diminutive size, have a substantial role in oral health and overall homeostasis. diff --git a/tests/input/cases/dental-restoration-material-ceramic-1.txt b/tests/input/cases/dental-restoration-material-ceramic-1.txt deleted file mode 100644 index 86fe5f48d..000000000 --- a/tests/input/cases/dental-restoration-material-ceramic-1.txt +++ /dev/null @@ -1,3 +0,0 @@ -AIM: This study assessed the effect of pretreatment of hybrid and glass ceramics using a self-etching primer on the shear bond strength (SBS) and surface topography, in comparison to pretreatment with hydrofluoric acid and silane. -METHODS: 40 rectangular discs from each ceramic material (IPS e.max CAD;EM, Vita Mark II;VM, Vita Enamic;VE), were equally divided (n=10) and assigned to one of four surface pretreatment methods; etching with 4.8% hydrofluoric acid followed by Monobond plus (HFMP), Monobond etch & prime (Ivoclar Vivadent) (MEP), No treatment (NT) as negative control and Monobond plus (Ivoclar Vivadent) with no etching (MP) as positive control. SBS of resin cement (Multilink-N, Ivoclar Vivadent) to ceramic surfaces was tested following a standard protocol. Surface roughness was evaluated using an Atomic force microscope (AFM). Surface topography and elemental analysis were analyzed using SEM/EDX. Data were analyzed with two-way analysis of variance (ANOVA) and post-hoc Bonferroni test at a significance level of α=0.05. -RESULTS: Pretreatment with HFMP resulted in higher SBS and increased surface roughness in comparison to MEP and MP. Regardless the method of surface pretreatment, the mean SBS values of EM ceramic was significantly higher (p<0.05) than those recorded for VM and VE, except when VE was treated with MEP, where the difference was statistically insignificant. Traces of fluoride ion were detected when MEP was used with VE and VM. CONCLUSION: Under limited conditions, using MEP resulted in comparable SBS results to HFMP; meanwhile HFMP remains the gold standard for pretreatment of glass ceramics for resin-luting cementation. diff --git a/tests/input/cases/dental-restoration-material-ceramic-2.txt b/tests/input/cases/dental-restoration-material-ceramic-2.txt deleted file mode 100644 index 37781ee70..000000000 --- a/tests/input/cases/dental-restoration-material-ceramic-2.txt +++ /dev/null @@ -1,3 +0,0 @@ - BACKGROUND: The aim of this study was to evaluate the biomechanical response of the peri-implant bone to standard, short-wide, and double mini implants replacing missing molar supporting either hybrid ceramic crowns (Lava Ultimate restorative) or full-metal crowns under two different loading conditions (axial and off-axial loading) using strain gauge analysis. - METHODS: Three single-molar implant designs, (1) single, 3.8-mm (regular) diameter implant, (2) single, 5.8-mm (wide) diameter implant, and (3) two 2.5-mm diameter (double) implants connected through a single-molar crown, were embedded in epoxy resin by the aid of a surveyor to ensure their parallelism. Each implant supported full-metal crowns made of Ni-Cr alloy and hybrid ceramic with standardized dimensions. Epoxy resin casts were prepared to receive 4 strain gauges around each implant design, on the buccal, lingual, mesial, and distal surfaces. Results were analyzed statistically. RESULTS: Results showed that implant design has statistically significant effect on peri-implant microstrains, where the standard implant showed the highest mean microstrain values followed by double mini implants, while the short-wide implant showed the lowest mean microstrain values. Concerning the superstructure material, implants supporting Lava Ultimate crowns had statistically significant higher mean microstrain values than those supporting full-metal crowns. Concerning the load direction, off-axial loading caused uneven distribution of load with statistically significant higher microstrain values on the site of off-axial loading (distal surface) than the axial loading. - CONCLUSIONS: Implant design, superstructure material, and load direction significantly affect peri-implant microstrains. diff --git a/tests/input/cases/dental-restoration-material-ceramic-composite-1.txt b/tests/input/cases/dental-restoration-material-ceramic-composite-1.txt deleted file mode 100644 index 87e14d1c4..000000000 --- a/tests/input/cases/dental-restoration-material-ceramic-composite-1.txt +++ /dev/null @@ -1 +0,0 @@ - Computer-aided design/computer-aided manufacturing (CAD/CAM) technology was developed to ensure the sufficient strength of tooth restorations, to improve esthetic restorations with a natural appearance and to make the techniques easier, faster and more accurate. In the view of the limited research on the surface treatments of the CAD/CAM materials and the need to evaluate the ideal surface characteristics of a material to achieve the best adhesion to tooth tissues, this study aimed to investigate the surface roughness and morphology of four different CAD/CAM materials using four different surface treatments. The CAD/CAM materials used in this study were three composites (Shofu Block HC, Lava Ultimate and Brilliant Crios) and a hybrid ceramic (Enamic). The surface of the specimens of each material received one of the following treatments: no surface treatment, sandblasting with 29 μm Al(2)O(3) particles, 9% hydrofluoric acid etching and silane application, and the tribochemical method using CoJet System. Surface roughness was evaluated using optical profilometry, and surface morphology was observed by means of scanning electron microscopy. All surface treatments resulted in higher surface roughness values compared to the control group. Different treatments affected the surface properties of the materials, presumably due to discrepancies in their composition and structure. diff --git a/tests/input/cases/dental-restoration-material-ceramic-composite-polymer-1.txt b/tests/input/cases/dental-restoration-material-ceramic-composite-polymer-1.txt deleted file mode 100644 index cb4fd79bf..000000000 --- a/tests/input/cases/dental-restoration-material-ceramic-composite-polymer-1.txt +++ /dev/null @@ -1,5 +0,0 @@ - OBJECTIVES: To prospectively evaluate the One-step No-prep treatment of full mouth-worn dentition, a minimally invasive and multidisciplinary approach using PICN CAD-CAM composite restorations without provisional phase. - METHODS: Seven patients (n = 192 restorations) with severe tooth wear were included. Patient data were recorded, and an occlusal analysis and a tissue-guided wax-up were realized. After replacement of old fillings, no-prep Vita Enamic restorations (posterior restorations and palatal veneers) were bonded within 24 h. Direct composites were performed to mask the buccal joint on anterior teeth. Maxillo-facial physiotherapy was performed. Restorations were evaluated following World Dental Federation criteria. Treatment influence on Oral-Health-Impact-Profile-49 (OHIP-49) score was assessed. - RESULTS: Tooth wear etiology was related to soft drink consumption and bruxism. Mean VDO increase was 5.09 ± 0.85 mm on the incisal pin. The mean restoration thickness on molars was 0.55 ± 0.21 mm, and the lowest was 0.11 mm. 2-year survival rate of restorations was 100 % and success rate was 93.5 %, with 11 minor chippings and one debonding. A significant improvement of the global OHIP-49 score was observed. - CONCLUSIONS: In this clinical study on high risk patients, PICN restorations, applied in a minimally invasive way, showed high survival and success rates after two years, while minor chipping of very thin occlusal borders constituted the most frequent complication. Moreover, the patient acceptance was good according to OHIP-49 in this multidisciplinary approach. - CLINICAL SIGNIFICANCE: The use of PICNs allows the development of no prep and simple treatment protocols of worn dentition. The absence of provisionals did not engender any problem, on the basis of the realization of an occlusal analysis, the support of a maxillo-facial physiotherapist, and the use of an easy-to-adjust restorative material. diff --git a/tests/input/cases/dental-restoration-material-ceramic-composite-polymer-2.txt b/tests/input/cases/dental-restoration-material-ceramic-composite-polymer-2.txt deleted file mode 100644 index 2e766ce1c..000000000 --- a/tests/input/cases/dental-restoration-material-ceramic-composite-polymer-2.txt +++ /dev/null @@ -1 +0,0 @@ - The aim of this study was to investigate the relationship between the microstructure of a CAD/CAM composite and the silanization effect on adhesive bonding, using surface free energy (SFE) analysis. Six commercial CAD/CAM composites, as well as control samples of two glass-ceramics and a resin, were investigated. The samples were characterized by morphological observations and SFE analysis. The bonding characteristics of the samples with the resin-cement were evaluated according to the silanization effect, which was determined from the ratio between the shear-bond strengths for the sample groups, with and without a silane-primer application. The composites were classified into two groups in terms of their microstructure; ENAMIC exhibits a polymer-infiltrated-ceramic-network (PICN) structure, while the other composites have a dispersed-filler (DF) structure. The dispersive component of the SFE was significantly lower in the PICN composite than in the DF composites. On the other hand, the polar component of the SFE was significantly higher in the PICN composite than in the DF composites. These SFE components were similar to those of glass-ceramics for the PICN composite and to those of the resin for the DF composites. The silanization effect increased linearly with the polar component or with a decrease in the dispersive component. Additionally, the silanization effect increased with the inorganic content. As a result, the silanization effect was found to be the highest for the PICN structure of ENAMIC. The results revealed that the silanization effect on the adhesive bonding is more effective for a PICN composite than for a DF composite. diff --git a/tests/input/cases/dental-restoration-material-ceramic-composite-polymer-resin-1.txt b/tests/input/cases/dental-restoration-material-ceramic-composite-polymer-resin-1.txt deleted file mode 100644 index 52c28b4e6..000000000 --- a/tests/input/cases/dental-restoration-material-ceramic-composite-polymer-resin-1.txt +++ /dev/null @@ -1,4 +0,0 @@ - BACKGROUND: Polymer infiltrated ceramics and nano-ceramic resins are the new restorative materials which have been developed in order to enhance the adverse properties of glass-matrix ceramics and resin composites. The aim of the present in vitro study was to evaluate the characteristics of various CAD/CAM materials through mechanical, microstructural, and SEM analysis. - METHODS: Five test groups (n = 22) were formed by using the indicated CAD/CAM blocks: VITA Enamic (VITA Zahnfabrik), Lava Ultimate (3 M ESPE), IPS e.max CAD (Ivoclar Vivadent), IPS Empress CAD (Ivoclar Vivadent), and VITA Mark II (VITA Zahnfabrik). Two specimens from each test group were used for XRD and EDS analysis. Remaining samples were divided into two subgroups (n = 10). One subgroup specimens were thermocycled (5 °C to 55 °C, 30s, 10,000 cycles) whereas the other were not. All of the specimens were evaluated in terms of flexural strength, Vickers hardness, and fracture toughness. - Results were statistically analyzed using two-way ANOVA, one-way ANOVA, Tukey's HSD, and Student's t tests (α = .05). Fractured specimens were evaluated using SEM. RESULTS: The highest Vickers microhardness value was found for VITA Mark II (p < .001), however flexural strength and fracture toughness results were lowest conversely (p < .05). IPS e.max CAD was found to have the highest flexural strength (p < .001). Fracture toughness of IPS e.max CAD was also higher than other tested block materials (p < .001). Lava Ultimate and VITA Enamic's mechanical properties were affected negatively from thermocycling (p < .05). Microhardness, flexural strength, and fracture toughness values of Lava Ultimate and VITA Enamic were found to be similar to VITA Mark II and IPS Empress CAD groups. - CONCLUSIONS: It should be realised that simulated aging process seem to affect ceramic-polymer composite materials more significantly than glass ceramics. diff --git a/tests/input/cases/dental-restoration-material-ceramic-composite-polymer-resin-2.txt b/tests/input/cases/dental-restoration-material-ceramic-composite-polymer-resin-2.txt deleted file mode 100644 index e90473380..000000000 --- a/tests/input/cases/dental-restoration-material-ceramic-composite-polymer-resin-2.txt +++ /dev/null @@ -1,4 +0,0 @@ - OBJECTIVES: The present study aimed to evaluate the effect of restoration thickness, CAD/CAM material, and 6 months of artificial saliva storage on the fracture resistance of occlusal veneers. MATERIALS AND - METHODS: A total of 84 intact maxillary molars were sectioned 4.0 mm occlusal to the cementoenamel junction to expose the dentine. The teeth were assigned into 3 main groups according to the type of restorative material (e.max CAD, Vita Enamic, and Lava Ultimate). In each group, the teeth were allocated into 2 subgroups (n = 14) according to restoration thickness (1.0 and 1.5 mm). The veneers were adhesively bonded using dual-cure self-adhesive luting agent. A total of 42 specimens comprising half the tested subgroups were stored in distilled water for 24-h before the test. The remaining half was stored in artificial saliva at 37 ± 1 °C in an incubator for 6 months. All specimens (n = 84) were subjected to 5000 thermal cycles between 5 and 55 °C ± 2 before the fracture resistance test. The maximum force at fracture was recorded in Newton. Failure mode was analyzed using a stereomicroscope. The results were analyzed using a parametric Three-way ANOVA test. - RESULTS: The results of the Three-way ANOVA test revealed that material type and restoration thickness significantly affected fracture resistance values (p < 0.5), while 6 months of storage in artificial saliva had no significant effect on mean fracture resistance values (p˃0.5). The most common failure patterns in CAD/CAM resin composite and polymer-infiltrated ceramics were scores I and score II. For glass ceramic groups, score IV and III were more dominant. - CONCLUSIONS: All the tested CAD/CAM restorations in both thicknesses exhibited fracture resistance values exceeding normal and parafunctional bite forces. Polymer-infiltrated ceramics and CAD/CAM resin composite veneers showed more favorable fracture patterns. diff --git a/tests/input/cases/dental-restoration-material-ceramic-composite-resin-1.txt b/tests/input/cases/dental-restoration-material-ceramic-composite-resin-1.txt deleted file mode 100644 index d8e699492..000000000 --- a/tests/input/cases/dental-restoration-material-ceramic-composite-resin-1.txt +++ /dev/null @@ -1,4 +0,0 @@ - PURPOSE: To evaluate the effect of surface conditioning methods and aging on the repair bond strength between resin composite and nanoceramic CAD/CAM resin. - MATERIALS AND METHODS: Twenty-four blocks of nanoceramic CAD/CAM resin (NCR) (Lava Ultimate, 3M Oral Care) (10 x 5 x 2 mm3) and resin composite (Filtek Z350, 3M Oral Care) (RC) were made, embedded in acrylic resin, polished (#600, #800, #1200) and randomly divided into 8 groups (n = 12 each) according to surface conditioning methods (air abrasion with 30-μm CoJet [CJ] or air abrasion with 50-μm Al2O3 [AB]) and aging prior to repair (without aging, 24 h in water at 37°C; with aging 6 months in water at 37°C). The blocks were air abraded (20 s, 2.5 bar, 10 mm) using a standardized device. A layer of adhesive resin (Scotchbond Universal) was applied (20 s) and photopolymerized for 20 s. RC cylinders (Ø = 2 mm; h = 2 mm) were then bonded to the NCR substrates using a Teflon matrix and photopolymerized for 40 s. All specimens were thermocycled (10,000 cycles, 5°C-55°C) and submitted to the shear bond test (50 kgf, 0.5 mm/min) to measure repair strength. Data (MPa) were analyzed using 3-way ANOVA and Tukey's test (α = 0.05). Failure analysis was performed using stereomicroscopy (20X). - RESULTS: ANOVA revealed a significant effect of only the "material" factor (p = 0.00). The group NCR6mCJ presented bond strengths (29.37 ± 5.41) which were significantly higher than those of the NCR24hCJ (20.88 ± 5.74) and RC groups (p < 0.05). The group RC24hCJ (19.71 ± 4.21) presented the lowest shear bond strength (p < 0.05). Failure analysis revealed predominantly type B mixed failures (adhesive+cohesive in the substrate material) except for the groups NCR24hCJ and NCR6mAB, where mainly type C failure (adhesive+cohesive at the RC) was observed. - CONCLUSION: Air abrasion with Al2O3 particles or silicatization with CoJet followed by adhesive resin application are effective surface conditioning methods for the repair of nanoceramic CAD/CAM resin with resin composite. diff --git a/tests/input/cases/dental-restoration-material-composite-1.txt b/tests/input/cases/dental-restoration-material-composite-1.txt deleted file mode 100644 index be284a7d0..000000000 --- a/tests/input/cases/dental-restoration-material-composite-1.txt +++ /dev/null @@ -1,4 +0,0 @@ - AIMS: To evaluate the effect of two composite restorative techniques (direct bulk fill vs indirect CAD/CAM) on the fracture resistance and mode of fracture of extended mesio-occlusal-distal (MOD) cavity preparations. - METHODS: Fifty-one sound human mandibular third molars were divided into three groups (n=17). Extended bucco-lingual MOD cavities were prepared. Teeth in group 1 were restored with a bulk-fill resin composite (Filtek Bulk-Fill Posterior Restorative), teeth in group 2 were restored with composite computer-aided design/computer-aided manufacturing (CAD/CAM) inlays (Lava Ultimate), and teeth in group 3 served as control and remained intact. All specimens were submitted to thermocycling, and a fracture resistance test was performed using a Universal testing machine (0.5 mm/min). Mode of fracture was classified into five types. One-way analysis of variance and the Duncan test were used to analyze the fracture load data at a significance level of α = 0.05. A chi-square test was used for the analysis of fracture mode between the restorative groups. - RESULTS: Statistical analysis showed significant differences in fracture resistance among the experimental groups. The teeth restored with the bulk-fill composite exhibited lower fracture resistance (1285.3±655.0 N) when compared to the teeth restored with the composite CAD/CAM inlays (1869.8±529.4 N) (p<0.05). Mode of fracture showed the same distribution between the restorative groups. - CONCLUSIONS: Although both types of restorations failed at loads larger than those found in the oral cavity, the CAD/CAM composite inlays increased the fracture resistance of teeth with large MOD cavities when compared to direct bulk-fill composite restorations. The majority of fracture types were intraorally repairable for both restorative techniques. diff --git a/tests/input/cases/dental-restoration-material-composite-2.txt b/tests/input/cases/dental-restoration-material-composite-2.txt deleted file mode 100644 index 79c38db20..000000000 --- a/tests/input/cases/dental-restoration-material-composite-2.txt +++ /dev/null @@ -1 +0,0 @@ - Endocrowns represent a conservative and esthetic restorative alternative to full coverage crowns. They can be constructed using various CAD/CAM materials that can provide a modulus of elasticity similar to that of teeth. The ability to use of such materials in composite blocks that can be easily repaired is also an advantage, provided appropriate bonding performance is ensured. This study, therefore, evaluated the marginal gap and fracture resistance of two CAD/CAM endocrown materials using two bonding protocols. Thirty-two mandibular molars were evaluated in two groups based on the material type: a Cerasmart group (GC America Inc; n = 16) acting as the control and a Ceramill COMP group (Amann Girrbach, Germany; n = 16). These groups were then classified according to the bonding protocol used: a total-etch bonding protocol (n = 8) and a self-etch bonding protocol (n = 8) implemented using RelyX ultimate adhesive resin cement (3M ESPE). The samples were then subjected to aging by simulating a 1-year thermo-mechanical process. The marginal gap results were statistically insignificant across the material and bonding protocol groups before thermo-mechanical aging. Thermo-mechanical aging significantly reduced the marginal gap distance for Ceramill COMP endocrowns cemented using the total-etch protocol (p = 0.002). No statistically significant difference was recorded for the fracture resistance in either the material or bonding protocol groups (p ≥ 0.05). Both materials and bonding protocols can, therefore, be used in the posterior region providing conservative treatment, adequate marginal gap and fracture resistance. diff --git a/tests/input/cases/dental-restoration-material-composite-polymer-1.txt b/tests/input/cases/dental-restoration-material-composite-polymer-1.txt deleted file mode 100644 index 97347e89c..000000000 --- a/tests/input/cases/dental-restoration-material-composite-polymer-1.txt +++ /dev/null @@ -1,5 +0,0 @@ - OBJECTIVES: This study aims to investigate the influence of thermocycling on the physical properties of different CAD/CAM restorative materials and assess their ability to maintain energy dissipation capacities and damping effects. - MATERIALS AND METHODS: The results of a 3-point bending test were used to calculate flexural strength (FS), modulus of elasticity (ME), modulus of toughness (MT) and elastic recovery (ER) for three ceramic, twelve composite and five polymer-based materials. Specimens (n = 10, 4.0 × 1.5 × 17.0 mm(3)) were loaded until rupture after water storage (24 h; 37.0 ± 1.0 °C) or thermocycling (5000 cycles; 5-55 °C). Statistical data analysis was performed using parametric statistics (p = 0.05). - RESULTS: Thermocycling had no significant influence on any investigated properties of ceramic materials (p > 0.05). Hybrid composites showed significant differences between water storage and thermocycling (p < 0.05), with the exception of FS of Tetric CAD. Similarly, ME with AMBARINO High-Class, CERASMART, Tetric CAD and Vita Enamic and MT and ER with Paradigm and Tetric CAD were not affected. For polymer-based materials, significant differences were found with the exceptions of FS (PEEK-OPTIMA, Telio CAD), ME (M-PM Disc, PEEK-OPTIMA, Telio CAD, Vita CAD-Temp), MT (Telio CAD) and ER (Telio CAD). - CONCLUSIONS: The material properties of composite and polymer-based CAD/CAM materials were susceptible to degradation processes induced by thermocycling. Only Telio CAD and Tetric CAD showed no significant effects like all ceramic materials, thus preserving their inherent ability to elastically and plastically dissipate energy. - CLINICAL RELEVANCE: A careful material selection is advisable when planning CAD/CAM restorations as remarkable differences may exist in the durability of physical characteristics through the impact of water. diff --git a/tests/input/cases/dental-restoration-material-composite-resin-1.txt b/tests/input/cases/dental-restoration-material-composite-resin-1.txt deleted file mode 100644 index 43fb67cf3..000000000 --- a/tests/input/cases/dental-restoration-material-composite-resin-1.txt +++ /dev/null @@ -1 +0,0 @@ -To compare the 1-year clinical performance of lithium disilicate and resin composite CAD/CAM onlay restorations. Twenty patients that required two restorations in posterior teeth, with at least one cusp to be covered, received two onlays. One was made with IPS e.max CAD (Ivoclar-Vivadent) and the other with Lava Ultimate (3M Oral Care). Two blind observers evaluated the restorations at baseline and 1 year after the onlays were cemented, according to FDI criteria. At each recall, digital photographs, bite-wing radiographs and impressions of the restorations were taken for SEM evaluation of the interface. Results were analyzed by Mann-Whitney U and Wilcoxon tests (p < 0.05). At baseline and in the 1-year recall, both CAD/CAM materials exhibited excellent results in most criteria with similar esthetic, functional and biological properties (p > 0.05). However, deterioration in surface lustre (p = 0.020) and color match/translucency (p = 0.039) were detected for IPS e.max CAD onlays after 1-year. Under SEM evaluation, there were no statistically differences in micromorphological criteria at baseline nor after a year between IPS e.max CAD and Lava Ultimate onlays. Conclusion: After 1 year of clinical service IPS e.max CAD and Lava Ultimate onlays showed a similar clinical performance that needs to be confirmed in long-term evaluations. diff --git a/tests/input/cases/dental-restoration-material-polymer-1.txt b/tests/input/cases/dental-restoration-material-polymer-1.txt deleted file mode 100644 index e0ebe70eb..000000000 --- a/tests/input/cases/dental-restoration-material-polymer-1.txt +++ /dev/null @@ -1,4 +0,0 @@ - OBJECTIVES: CAD/CAM-fabricated long-term temporary restorations from high-density polymers can be applied for a wide range of indications. Milled from monolithic, mono-colored polymer blocks, the translucency of the material plays an important role for an esthetically acceptable result. The aim of this study was to compare the transmittance through visible light and blue light of CAD CAM polymers to a glass-ceramic material of the same color. - MATERIALS AND METHODS: Ambarino High-Class (AM), Telio-CAD (TC), Zenotec PMMA (ZT), Cercon base PMMA (CB), CAD Temp (CT), Artbloc Temp (AT), Polycon ae (PS), New Outline CAD (NC), QUATTRO DISK Eco PMMA (GQ), Lava Ultimate (LU), and Paradigm MZ 100 (PA) were employed in this study using the feldspathic glass-ceramic Vita Mark II (MK) as control group. Using a spectrophotometer, the overall light transmittance was measured for each material (n = 40) and was calculated as the integration (t (c) (λ) dλ [10(-5)]) of all t (c) values for the wavelengths of blue light (360-540 nm). Results were compared to previous data of the authors for visible light (400 to 700 nm). RESULTS: Wilcoxon test showed significant differences between the light transmittance of visible and blue light for all materials. - CONCLUSION: CAD/CAM polymers showed different translucency for blue and visible light. This means clinicians may not conclude from the visible translucency of a material to its permeability for blue light. This influences considerations regarding light curing. - CLINICAL RELEVANCE: CAD/CAM polymers need to be luted adhesively; therefore, clinicians should be aware about the amount of blue light passing through a restoration. diff --git a/tests/input/cases/dental-restoration-material-polymer-2.txt b/tests/input/cases/dental-restoration-material-polymer-2.txt deleted file mode 100644 index cabef3596..000000000 --- a/tests/input/cases/dental-restoration-material-polymer-2.txt +++ /dev/null @@ -1,4 +0,0 @@ - PURPOSE: Concurrently with the growing interest in CAD-CAM systems, several new materials of different chemical nature have become available. As an alternative to ceramics, numerous polymer-based materials have recently been proposed for permanent prosthetic restorations. Aim of this study was to test the CAD-CAM polymer-based materials available on the market, comparing mean flexural strength, Weibull characteristic strength and Weibull modulus. - METHODS: Seven types of polymer-based blocks were tested: Lava Ultimate, 3M; Brilliant Crios, Coltene; Cerasmart, GC; Block HC, Shofu; Katana Avencia, Noritake; Grandio Blocs, Voco; Tetric CAD, and Ivoclar-Vivadent. Specimens were cut out from blocks, finished, polished, and tested in a three-point bending test apparatus until failure (n=30). Flexural strength, Weibull characteristic strength, and Weibull modulus were calculated. Flexural strength data were statistically analyzed. ANOVA on Ranks was applied, followed by the Dunn's test for post hoc comparisons (P= 0.05). - RESULTS: Flexural strength values (MPa) were measured (mean±standard deviation). Different letters in parentheses label statistically significant differences: Grandio Blocs 266±24(a), Brilliant Crios 259±21(ab); Tetric CAD 254±15(ab); Katana Avencia 241±29(bc); Cerasmart 221±24(cd); Lava Ultimate 196±23(de); Block HC 139±10(e). All the tested materials had flexural strengths greater than 100 MPa, thereby satisfying the requirements of ISO standards for polymer-based materials. For all the tested materials the Weibull characteristic strength was greater than 100 MPa. Weibull modulus ranged between 21.20 (Tetric CAD) and 9.09 (Katana Avencia). - CLINICAL SIGNIFICANCE: Even though all the CAD-CAM polymer-based materials marketed in blocks tested in the present study satisfy the requirements of ISO standard for polymer-based materials, their flexural resistance differs significantly. The data presented in the study may be helpful to clinicians for selecting the most appropriate materials for each clinical case. diff --git a/tests/input/cases/dental-restoration-material-resin-1.txt b/tests/input/cases/dental-restoration-material-resin-1.txt deleted file mode 100644 index 0152315a0..000000000 --- a/tests/input/cases/dental-restoration-material-resin-1.txt +++ /dev/null @@ -1,4 +0,0 @@ - OBJECTIVE: The present study aimed to identify and quantify the elution of monomers of five different resin-based CAD/CAM blocks (RCBs) using HPLC. - METHODS: Five different RCBs were used in the study: GC Cerasmart (CS), Voco Grandio blocs (GR), 3M Lava Ultimate (LU), Shofu Block (SB), and Vita Enamic (VE). Fifteen samples from each material were prepared using a low-speed precision diamond saw (ISOMET Buehler, Lake Bluff, IL, USA) at 5 × 5 × 4 mm size. After the preparation of samples, an extraction solution was mixed with %75/%25 ethanol/water. The samples were stored in the amber-colored bottles during three different immersed periods as 1 h, 24 h, and 90 days (n = 5). After immersion, 0.5 ml solutions were taken from each bottle and analyzed using HPLC. RESULTS: A total of 16.7 μg/ml of monomers from SB, 13.4 μg/ml of monomers from GR, 13.2 μg/ml of monomers from CS, and 6.7 μg/ml of monomers from LU were found after 3-m immersion. TEGDMA after 3-m of immersion was only released from the SB group, and also BisEMA was released from the CS group. Among the specimens immersed for 1 h, UDMA was released the least from the LU group and the most from the GR group (p < 0.05). Correspondingly, 24 h and 3 m after immersion, the highest release of monomers was found in the GR (p < 0.05). - CONCLUSIONS: When the monomer release from RCBs was evaluated, it was shown that these materials released methacrylate-based monomers except VE, especially if they were kept in a solvent solution for a long time such as 3 m. - CLINICAL SIGNIFICANCE: The novel resin-based CAD/CAM blocks might monomer release, which may cause cytotoxic effects. But, the detected amount of monomer release is below the estimated daily limit. diff --git a/tests/input/cases/dental-restoration-material-resin-2.txt b/tests/input/cases/dental-restoration-material-resin-2.txt deleted file mode 100644 index 0e269bb12..000000000 --- a/tests/input/cases/dental-restoration-material-resin-2.txt +++ /dev/null @@ -1,4 +0,0 @@ - OBJECTIVE: To compare mechanical performance and enamel-crack propensity of direct, semi-direct, and CAD/CAM approaches for large MOD composite-resin restorations. - METHODS: 45 extracted maxillary molars underwent standardized slot-type preparation (5-mm depth and bucco-palatal width) including immediate dentin sealing (Optibond FL) for the inlays (30 teeth). Short-fiber reinforced composite-resin (EverX Posterior covered by Gradia Direct Posterior) was used for the direct approach, Gradia Direct Posterior for the semi-direct, and Cerasmart composite resin blocks for CAD/CAM inlays. All inlays were adhesively luted with light-curing composite-resin (preheated Gradia Direct Posterior). Shrinkage-induced enamel cracks were tracked by transillumination photography. Cyclic axial isometric chewing (5-Hz) was simulated, starting with a load of 200N (5000 cycles), followed by stages of 400, 600, 800, 1000, 1200, and 1400N (maximum 30,000 cycles each) until fracture or to a maximum of 185,000 cycles. Survived specimens were subjected to cyclic-load-to-failure test at 30-degree angle on the palatal cusp. - RESULTS: Only small shrinkage-induced cracks were found in 47% of the direct restorations compared to 7% and 13% of semi-direct and CAD/CAM inlays, respectively. Survival to accelerated fatigue was similar for all three groups (Kaplan-Meier p>.05) and ranged between 87% (direct) and 93% (semi-direct and CAD/CAM). Cyclic-load-to-failure tests did not yield significant differences either (Life Table analysis, p>.05) with median values of 1675N for CAD/CAM inlays, 1775N for fiber-reinforced direct restorations and 1900N for semi-direct inlays. - SIGNIFICANCE: All three restorative techniques yielded excellent mechanical performance above physiological masticatory loads. Direct restorations performed as good as inlays when a short-fiber reinforced composite-resin base was used. diff --git a/tests/input/cases/drug-DB00316-moa.txt b/tests/input/cases/drug-DB00316-moa.txt deleted file mode 100644 index 2b5244dc4..000000000 --- a/tests/input/cases/drug-DB00316-moa.txt +++ /dev/null @@ -1,3 +0,0 @@ -According to its FDA labeling, acetaminophen's exact mechanism of action has not been fully establishedLabel - despite this, it is often categorized alongside NSAIDs (nonsteroidal anti-inflammatory drugs) due to its ability to inhibit the cyclooxygenase (COX) pathways.14 It is thought to exert central actions which ultimately lead to the alleviation of pain symptoms.14 - -One theory is that acetaminophen increases the pain threshold by inhibiting two isoforms of cyclooxygenase, COX-1 and COX-2, which are involved in prostaglandin (PG) synthesis. Prostaglandins are responsible for eliciting pain sensations.13 Acetaminophen does not inhibit cyclooxygenase in peripheral tissues and, therefore, has no peripheral anti-inflammatory effects. Though acetylsalicylic acid (aspirin) is an irreversible inhibitor of COX and directly blocks the active site of this enzyme, studies have shown that acetaminophen (paracetamol) blocks COX indirectly.24 Studies also suggest that acetaminophen selectively blocks a variant type of the COX enzyme that is unique from the known variants COX-1 and COX-2.6 This enzyme has been referred to as COX-3. The antipyretic actions of acetaminophen are likely attributed to direct action on heat-regulating centers in the brain, resulting in peripheral vasodilation, sweating, and loss of body heat.24 The exact mechanism of action of this drug is not fully understood at this time, but future research may contribute to deeper knowledge \ No newline at end of file diff --git a/tests/input/cases/environmental-metadata-1.txt b/tests/input/cases/environmental-metadata-1.txt deleted file mode 100644 index b37e436e3..000000000 --- a/tests/input/cases/environmental-metadata-1.txt +++ /dev/null @@ -1,22 +0,0 @@ -"edi.1","Long-term studies of secondary succession and community assembly in the prairie-forest -ecotone of eastern Kansas, Old-field succession experiment","LTREB,NSF,plant community,succession,fertilization"," Local and regional-scale processes interact to govern the assembly, diversity and -functioning of ecological communities. Evaluating the interplay of these differently-scaled -processes in the regulation of ecological systems is a challenging problem, but is crucial -towards understanding and predicting the potential effects of accelerated human activity on -biological diversity and ecosystem sustainability. Since 2000, two long-term field -experiments have been underway in grasslands of eastern Kansas to investigate the interplay -of soil resource availability, species interactions and regional processes governing plant -secondary succession, community assembly, biodiversity, and ecosystem functioning. Both -experiments involve manipulations of soil nutrients in permanent grassland study plots and -employ multi-species seed addition treatments to evaluate the contribution of dispersal -limitation and regional constraints on local species pools to the regulation of plant -community dynamics. Old-field succession experiment, previously funded by the National Science Foundation, -was initiated in 2001 in a section of the abandoned hay field that was sprayed with -herbicide, plowed and disked prior to the start of the study to investigate plant community -dynamics in the context of old-field succession initiated on bare soil. The experimental -design involves factorial experimental gradients of nitrogen (N) supply (four levels of N -fertilization), phosphorus (P) supply (two levels of P fertilization) and plant propagule -input achieved by adding seeds of 50+ native and naturalized species to half of the study -plots. With annual sampling this experiment allows us to examine old-field succession and -community assembly unfolding along gradients of N and P fertilization and under conditions -of ambient and experimentally-enriched species pools. " diff --git a/tests/input/cases/environmental-metadata-2.txt b/tests/input/cases/environmental-metadata-2.txt deleted file mode 100644 index 2b4006142..000000000 --- a/tests/input/cases/environmental-metadata-2.txt +++ /dev/null @@ -1,11 +0,0 @@ -"edi.1004","Soil nitrous oxide (N2O) and carbon dioxide (CO2) flux from a Central Iowa crop field and accompanying soil edaphic and climatic variables.","Nitrous Oxide,Carbon Dioxide,N2O,CO2,Greenhouse Gas,Iowa,Central Iowa,Agriculture,Corn,Zea mays,Soy,Glycine max,Soil,Nitrogen,Soil Carbon,Soil Moisture,Prairie Pothole,Trace Gas Emissions,Denitrification,Soil Drainage"," -To quantify the magnitude of soil nitrous oxide flux and the drivers -of nitrous oxide emissions in a representative central Iowa -corn-soybean agricultural system, we measured greenhouse gas -emissions (N2O and -CO2) from 2017 to 2019 (primarily using -custom automated chambers) along with soil chemical and physical -parameters across a topographic gradient in a typically managed -agricultural field near Ames, Iowa, USA. More details can be found -in the associated manuscript, Lawrence et al. (2021). -" diff --git a/tests/input/cases/environmental-metadata-3.txt b/tests/input/cases/environmental-metadata-3.txt deleted file mode 100644 index 1b9b0005f..000000000 --- a/tests/input/cases/environmental-metadata-3.txt +++ /dev/null @@ -1,9 +0,0 @@ -"knb-lter-hbr.155","Fine Root Data at the Hubbard Brook Experimental Forest, 1998 and 2013 collections","calcium,fine roots,forests,HBEF Watershed 1,HBEF Bear Brook Watershed,HBR,Hubbard Brook LTER,roots,root biomass,watersheds,primary production","We restored calcium to soils of a forested watershed at -Hubbard Brook and measured the response of fine root biomass fourteen years after treatment. -Fine root samples were collected in Watershed 1 and the Bear Brook Watershed reference forest, located to the west -of Watershed 6, in 1998 (pre-Ca treatment) and in 2013. In this northern hardwood forest fine root -(< 1 mm diameter) biomass declined significantly in the Ca addition treatment relative to pretreatment and -reference forest conditions. The decline was greatest in the high-elevation hardwood zone of the watershed where soils are -thinnest and most base poor. In that zone fine roots were distributed more shallowly after -treatment than for reference conditions. We suggest that relatively higher tree C allocation to roots contributes to -depressed aboveground productivity in acidified northern hardwood forest ecosystems." \ No newline at end of file diff --git a/tests/input/cases/environmental-sample-hyporheic.txt b/tests/input/cases/environmental-sample-hyporheic.txt deleted file mode 100644 index 7bf3e01ee..000000000 --- a/tests/input/cases/environmental-sample-hyporheic.txt +++ /dev/null @@ -1 +0,0 @@ -Sediment communities from the hyporheic zone of the Columbia River along the Hanford Reach were sampled from April 30, 2014 to November 25, 2014, using sand packs deployed at three equivalent hyporheic zone locations approximately 100m apart along the river (T2, T3, and T4) for six weeks at a time [22]. Water chemistry data taken in parallel at the three sites showed similar, yet not identical temporal patterns. A mid-year shift in hydraulic regime was observed, with higher influx of surface water in the spring resulting in higher levels of dissolved organic carbon (measured as non-purgeable organic carbon) (NPOC) (0.8–1.0 mg/L) (Fig 2A) and low levels of nitrate (10–15 μM) (Fig 2B), transitioning to a more groundwater-influenced condition in the fall, increasing the nitrate concentrations (up to 300 μM) and decreasing NPOC concentration (down to <0.4 mg/L). Because the groundwater in this system is oxic, the DO concentration was fairly constant for the duration of sampling, ranging from ~60–100% saturation (Fig 2C). The water temperature followed expected seasonal trends, warming in the summer and cooling in the fall (Fig 2D). Sampling times were categorized as early (Apr 30 through Jul 22) or late (Sep 2 through Nov 30), based on these observations. diff --git a/tests/input/cases/gocam-27929086.txt b/tests/input/cases/gocam-27929086.txt deleted file mode 100644 index 30a51499b..000000000 --- a/tests/input/cases/gocam-27929086.txt +++ /dev/null @@ -1,31 +0,0 @@ -Title: The E3 ubiquitin ligase TRIM31 attenuates NLRP3 inflammasome -activation by promoting proteasomal degradation of NLRP3 - -Abstract: The NLRP3 inflammasome has a fundamental role in host -defence against microbial pathogens and its deregulation may cause -diverse inflammatory diseases. NLRP3 protein expression is a -rate-limiting step for inflammasome activation, thus its expression -must be tightly controlled to maintain immune homeostasis and avoid -detrimental effects. However, how NLRP3 expression is regulated -remains largely unknown. In this study, we identify E3 ubiquitin -ligase TRIM31 as a feedback suppressor of NLRP3 inflammasome. TRIM31 -directly binds to NLRP3, promotes K48-linked polyubiquitination and -proteasomal degradation of NLRP3. Consequently, TRIM31 deficiency -enhances NLRP3 inflammasome activation and aggravates alum-induced -peritonitis in vivo. Furthermore, TRIM31 deficiency attenuates the -severity of dextran sodium sulfate (DSS)-induced colitis, an -inflammatory bowel diseases model in which NLRP3 possesses protective -roles. Thus, our research describes a mechanism by which TRIM31 limits -NLRP3 inflammasome activity under physiological conditions and -suggests TRIM31 as a potential therapeutic target for the intervention -of NLRP3 inflammasome related diseases. - -Figure 1: TRIM31 specifically inhibits NLRP3 inflammasome activation -Figure 2. TRIM31 promotes proteasomal degradation of NLRP3 -Figure 3. TRIM31 interacts with NLRP3 -Figure 4. TRIM31 promotes K48-linked polyubiquitination of NLRP3. -Figure 5. IL-1β and LPS induce TRIM31 expression -Figure 6. TRIM31 deficiency enhances IL-1β secretion and aggravates -Alum-induced peritonitis in vivo -Figure 7. TRIM31 deficiency ameliorates DSS-induced colitis -Figure 8. Working model for TRIM31 inhibiting NLRP3 inflammasome activation. diff --git a/tests/input/cases/gocam-33246504.txt b/tests/input/cases/gocam-33246504.txt deleted file mode 100644 index 1eea93b8c..000000000 --- a/tests/input/cases/gocam-33246504.txt +++ /dev/null @@ -1,13 +0,0 @@ -Text: An allosteric interleukin-1 receptor modulator mitigates -inflammation and photoreceptor toxicity in a model of retinal -degeneration - -Background: Inflammation and particularly interleukin-1β (IL-1β), a pro-inflammatory cytokine highly secreted by activated immune cells during early AMD pathological events, contribute significantly to retinal neurodegeneration. Here, we identify specific cell types that generate IL-1β and harbor the IL-1 receptor (IL-1R) and pharmacologically validate IL-1β's contribution to neuro-retinal degeneration using the IL-1R allosteric modulator composed of the amino acid sequence rytvela (as well as the orthosteric antagonist, Kineret) in a model of blue light-induced retinal degeneration. - -Methods: Mice were exposed to blue light for 6 h and sacrificed 3 days later. Mice were intraperitoneally injected with rytvela, Kineret, or vehicle twice daily for 3 days. The inflammatory markers F4/80, NLRP3, caspase-1, and IL-1β were assessed in the retinas. Single-cell RNA sequencing was used to determine the cell-specific expression patterns of retinal Il1b and Il1r1. Macrophage-induced photoreceptor death was assessed ex vivo using retinal explants co-cultured with LPS-activated bone marrow-derived macrophages. Photoreceptor cell death was evaluated by the TUNEL assay. Retinal function was assessed by flash electroretinography. - -Results: Blue light markedly increased the mononuclear phagocyte recruitment and levels of inflammatory markers associated with photoreceptor death. Co-localization of NLRP3, caspase-1, and IL-1β with F4/80+ mononuclear phagocytes was clearly detected in the subretinal space, suggesting that these inflammatory cells are the main source of IL-1β. Single-cell RNA sequencing confirmed the immune-specific expression of Il1b and notably perivascular macrophages in light-challenged mice, while Il1r1 expression was found primarily in astrocytes, bipolar, and vascular cells. Retinal explants co-cultured with LPS/ATP-activated bone marrow-derived macrophages displayed a high number of TUNEL-positive photoreceptors, which was abrogated by rytvela treatment. IL-1R antagonism significantly mitigated the inflammatory response triggered in vivo by blue light exposure, and rytvela was superior to Kineret in preserving photoreceptor density and retinal function. - -Conclusion: These findings substantiate the importance of IL-1β in neuro-retinal degeneration and revealed specific sources of Il1b from perivascular MPs, with its receptor Ilr1 being separately expressed on surrounding neuro-vascular and astroglial cells. They also validate the efficacy of rytvela-induced IL-1R modulation in suppressing detrimental inflammatory responses and preserving photoreceptor density and function in these conditions, reinforcing the rationale for clinical translation. - -Keywords: Inflammasome; Inflammation; Interleukin-1; Interleukin-1 receptor; Photoreceptors; Retinal degeneration; Rytvela; cell death. diff --git a/tests/input/cases/gocam-betacat.txt b/tests/input/cases/gocam-betacat.txt deleted file mode 100644 index 6f28e3cac..000000000 --- a/tests/input/cases/gocam-betacat.txt +++ /dev/null @@ -1,36 +0,0 @@ -Title: β-Catenin Is Required for the cGAS/STING Signaling Pathway but Antagonized by the Herpes Simplex Virus 1 US3 Protein -Text: -The cGAS/STING-mediated DNA-sensing signaling pathway is crucial -for interferon (IFN) production and host antiviral -responses. Herpes simplex virus I (HSV-1) is a DNA virus that has -evolved multiple strategies to evade host immune responses. Here, -we demonstrate that the highly conserved β-catenin protein in the -Wnt signaling pathway is an important factor to enhance the -transcription of type I interferon (IFN-I) in the cGAS/STING -signaling pathway, and the production of IFN-I mediated by -β-catenin was antagonized by HSV-1 US3 protein via its kinase -activity. Infection by US3-deficienct HSV-1 and its kinase-dead -variants failed to downregulate IFN-I and IFN-stimulated -gene (ISG) production induced by β-catenin. Consistent with this, -absence of β-catenin enhanced the replication of US3-deficienct -HSV-1, but not wild-type HSV-1. The underlying mechanism was the -interaction of US3 with β-catenin and its hyperphosphorylation of -β-catenin at Thr556 to block its nuclear translocation. For the -first time, HSV-1 US3 has been shown to inhibit IFN-I production -through hyperphosphorylation of β-catenin and to subvert host -antiviral innate immunity.IMPORTANCE Although increasing evidence -has demonstrated that HSV-1 subverts host immune responses and -establishes lifelong latent infection, the molecular mechanisms -by which HSV-1 interrupts antiviral innate immunity, especially -the cGAS/STING-mediated cellular DNA-sensing signaling pathway, -have not been fully explored. Here, we show that β-catenin -promotes cGAS/STING-mediated activation of the IFN pathway, which -is important for cellular innate immune responses and intrinsic -resistance to DNA virus infection. The protein kinase US3 -antagonizes the production of IFN by targeting β-catenin via its -kinase activity. The findings in this study reveal a novel -mechanism for HSV-1 to evade host antiviral immunity and add new -knowledge to help in understanding the interaction between the -host and HSV-1 infection. - -Keywords: HSV-1; US3; type I IFN; β-catenin. \ No newline at end of file diff --git a/tests/input/cases/human_smoking_China.txt b/tests/input/cases/human_smoking_China.txt deleted file mode 100644 index 782ef1453..000000000 --- a/tests/input/cases/human_smoking_China.txt +++ /dev/null @@ -1,35 +0,0 @@ -Title -Smoking related environmental microbes affecting the pulmonary microbiome in Chinese population - -Highlights -• -Smoking may change the environmental microbes and then the lung microbiome. - -• -Our study subjects were Chinese. - -• -NGS was used to analyze the sample's sequence in this study. - - -Abstract -Background -Smoking is a serious public health problem that affects human health conditions. Although there is evidence that microorganisms are associated with smoking-related lung diseases, the relationship between the rich lung microbiome of upper respiratory tract groups and smoking has not been studied. - -Objective -In this study, we investigated the effects of smoking on environmental microbes and lung microbiome in the Chinese population and provided clues for the role of smoking in the development of respiratory disease. - -Methods -Bronchoalveolar lavage fluid samples were collected from 55 individuals with a history of smoking. Microbial gene sequencing was carried out through NGS technology. We analyzed and compared the diversity, community structure, and species abundance of bronchoalveolar lavage microbiome between smokers and nonsmokers, to speculate the effects of smoking on the lung microbiome. - -Results -Smoking hardly affected the α diversity of microbial groups of bronchoalveolar lavage, but it had a huge influence on the microbiome composition. The relative abundance of Rothia, Actinomycetes, Haemophilus, Porphyrins, Neisseria, Acinetobacter, and Streptococcus genera had a remarkable increase in the smoking group. On the other hand, the relative abundance of Plusella and Veronella decreased significantly. - -Conclusion -Smoking may change the environmental microbes and then alter the structure of the lung microbiome, which may lead to smoking-related diseases. - -Graphical abstract -Smoking might change the environmental microbes and then alter the structure of the lung microbiome, which may lead to smoking-related diseases. - -Keywords -Smoking Lung microbiome, Next-generation sequencing technology (NGS technology), Lung diseases diff --git a/tests/input/cases/human_urban_green_space.txt b/tests/input/cases/human_urban_green_space.txt deleted file mode 100644 index ac7a0db19..000000000 --- a/tests/input/cases/human_urban_green_space.txt +++ /dev/null @@ -1,29 +0,0 @@ -Title -Transfer of environmental microbes to the skin and respiratory tract of humans after urban green space exposure - -Highlights -• -Microbes from urban green spaces may help to shape the human microbiome. - -• -After urban green space exposure, skin and nasal microbial diversity increased. - -• -Skin and nasal microbial composition became more similar to environmental sources. - -• -Nasal microbiota are more variable between sites and individuals than skin microbiota. - - -Abstract -Background -In industrialized countries, non-communicable diseases have been increasing in prevalence since the middle of the 20th century. While the causal mechanisms remain poorly understood, increased population density, pollution, sedentary behavior, smoking, changes in diet, and limited outdoor exposure have all been proposed as significant contributors. Several hypotheses (e.g. Hygiene, Old Friends, and Biodiversity Hypotheses) also suggest that limited environmental microbial exposures may underpin part of this rise in non-communicable diseases. In response, the Microbiome Rewilding Hypothesis proposes that adequate environmental microbial exposures could be achieved by restoring urban green spaces and could potentially decrease the prevalence of non-communicable diseases. However, the microbial interactions between humans and their surrounding environment and the passaging of microbes between both entities remains poorly understood, especially within an urban context. - -Results -Here, we survey human skin (n = 90 swabs) and nasal (n = 90 swabs) microbiota of three subjects that were exposed to air (n = 15), soil (n = 15), and leaves (n = 15) from different urban green space environments in three different cities across different continents (Adelaide, Australia; Bournemouth, United Kingdom; New Delhi, India). Using 16S ribosomal RNA metabarcoding, we examined baseline controls (pre-exposure) of both skin (n = 16) and nasal (n = 16) swabs and tracked microbiota transfer from the environment to the human body after exposure events. Microbial richness and phylogenetic diversity increased after urban green space exposure in skin and nasal samples collected in two of the three locations. The microbial composition of skin samples also became more similar to soil microbiota after exposure, while nasal samples became more similar to air samples. Nasal samples were more variable between sites and individuals than skin samples. - -Conclusions -We show that exposure to urban green spaces can increase skin and nasal microbial diversity and alter human microbiota composition. Our study improves our understanding of human-environmental microbial interactions and suggests that increased exposure to diverse outdoor environments may increase the microbial diversity, which could lead to positive health outcomes for non-communicable diseases. - -Keywords -Microbiota, Biodiversity, Rewilding, Non-communicable diseases, Allergies, Urban green space diff --git a/tests/input/cases/mendelian-disease-cmt2e-summary.txt b/tests/input/cases/mendelian-disease-cmt2e-summary.txt deleted file mode 100644 index f9521de04..000000000 --- a/tests/input/cases/mendelian-disease-cmt2e-summary.txt +++ /dev/null @@ -1,54 +0,0 @@ -CHARCOT-MARIE-TOOTH DISEASE, AXONAL, TYPE 2E; CMT2E - -INHERITANCE -- Autosomal dominant -HEAD & NECK -Face -- Facial muscle weakness (in some patients) -Eyes -- Ptosis (in some patients) -Mouth -- High-arched palate (in some patients) -SKELETAL -- Joint contractures -Spine -- Scoliosis (in some patients) -Hands -- Claw hand deformities (in severe cases) -Feet -- Pes cavus -- Hammer toes -- Foot deformities -MUSCLE, SOFT TISSUES -- Shoulder muscle weakness (in some patients) -- Hypotrophy of the small hand muscles -- Fiber-type predominance seen on muscle biopsy (in some patients) -- Fiber size variation (in some patients) -- Internal nuclei (in some patients) -- Increased connective tissue (in some patients) -- Nemaline rods (in some patients) -- Group fiber atrophy (in some patients) -- Angular fibers (in some patients) -- EMG consistent with chronic neurogenic disorder -NEUROLOGIC -Central Nervous System -- Delayed motor development (in some patients) -Peripheral Nervous System -- Distal limb muscle weakness due to peripheral neuropathy -- Distal limb muscle atrophy due to peripheral neuropathy -- 'Steppage' gait -- Foot drop -- Distal sensory impairment -- Hyporeflexia -- Areflexia -- Normal or mildly decreased motor nerve conduction velocity (NCV) (greater than 38 m/s) -- Axonopathy seen on nerve biopsy -- Giant axons with accumulation of disorganized neurofilaments -MISCELLANEOUS -- Variable age of onset (range first to third decade) -- Usually begins in feet and legs (peroneal distribution) -- Upper limb involvement occurs later -- Variable severity -- Some patients may become wheelchair-bound -MOLECULAR BASIS -- Caused by mutation in the light polypeptide neurofilament protein gene (NEFL, 162280.0001) diff --git a/tests/input/cases/mendelian-disease-cmt2e.txt b/tests/input/cases/mendelian-disease-cmt2e.txt deleted file mode 100644 index d91e785e4..000000000 --- a/tests/input/cases/mendelian-disease-cmt2e.txt +++ /dev/null @@ -1,7 +0,0 @@ -Mersiyanova et al. (2000) reported a large 6-generation family from Russia with autosomal dominant CMT2. Onset was in the second and third decade, characterized by difficulty in walking and weakness and atrophy of the distal lower limb muscles and a variable degree of deformity of the feet (pes cavus). Affected individuals did not exhibit enlarged nerves, ulcerated feet, hearing impairment, or paralysis of the vocal cords. Several patients had hyperkeratosis, although the association, if any, between the 2 disorders was not clear. The authors suggested the designation CMT2E for this disorder. - -Georgiou et al. (2002) described a large 5-generation Slovenian family with autosomal dominant CMT type 2E. Disease onset in most patients was in the first decade of life. The presenting symptoms were difficulty in walking or running, due to a slowly progressive distal weakness and wasting of the lower limbs. A steppage gait, pes cavus, and hammertoes were typically present. Over a period of 20 years after disease onset, two-thirds of patients developed upper limb involvement resulting in claw hands. All patients were ambulatory 20 to 30 years after onset. - -Fabrizi et al. (2004) reported a large kindred from southern Italy with autosomal dominant CMT2E spanning 5 generations and caused by mutation in the NEFL gene (162280.0002). An affected woman and her 2 affected sons had steppage gait, ataxic gait, peroneal muscular atrophy, decreased vibration sense with stocking and glove distribution, and hypotrophy of the hand muscles. One of the sons had claw hand deformities. Motor nerve conduction velocities (NCV) were decreased, consistent with a demyelinating neuropathy, but sural nerve biopsy of the mother showed a primary axonopathy characterized by giant axons containing disorganized neurofilaments. - -Miltenberger-Miltenyi et al. (2007) reported a large Austrian family in which at least 4 members had CMT2E confirmed by genetic analysis (162880.0006). Disease onset was in the second decade of life with pes cavus, progressive plantar extensor weakness, and distal lower limb atrophy and weakness. Two patients became wheelchair-bound. Affected members of a second Austrian family, with a different NEFL mutation (162280.0003), had disease onset before age 15 years in all but 1 patient. The disorder was slowly progressive but resulted in a severe and disabling phenotype. Electrophysiologic studies of both families showed intermediate motor nerve conduction velocities consistent with axonal pathology. diff --git a/tests/input/cases/mendelian-disease-marfan.txt b/tests/input/cases/mendelian-disease-marfan.txt deleted file mode 100644 index 542066a41..000000000 --- a/tests/input/cases/mendelian-disease-marfan.txt +++ /dev/null @@ -1 +0,0 @@ -Marfan syndrome is a genetic disorder that affects connective tissue, which is the material between cells of the body that gives the tissues form and strength. Connective tissue is found all over the body and multiple organ systems may be affected in individuals with Marfan syndrome. The heart and blood vessels (cardiovascular), skeletal, and eye (ocular) systems are most often affected. Major symptoms include overgrowth of the long bones of the arms and legs, abnormal side-to-side curvature of the spine (scoliosis), indentation or protrusion of the chest wall (pectus deformity), dislocation of the lenses of the eyes (ectopia lentis), nearsightedness (myopia), widening (aneurysm) and tear (dissection) of the main artery that carries blood away from the heart (aorta), floppiness of the mitral valve (mitral valve prolapse) and backward flow of blood through the aortic and mitral valves (aortic and mitral regurgitation). The specific symptoms and the severity of Marfan syndrome vary greatly from person to person. Marfan syndrome is inherited as an autosomal dominant trait, meaning that only one abnormal copy of the Marfan gene inherited from one parent is sufficient to have the condition. Defects or deletions (pathogenic variants) of the fibrillin-1 (FBN1) gene have been shown to cause Marfan syndrome. \ No newline at end of file diff --git a/tests/input/cases/mendelian-disease-sly.txt b/tests/input/cases/mendelian-disease-sly.txt deleted file mode 100644 index 6ce146322..000000000 --- a/tests/input/cases/mendelian-disease-sly.txt +++ /dev/null @@ -1 +0,0 @@ -Sly syndrome, also called mucopolysaccharidosis type VII (MPS-VII), is an autosomal recessive lysosomal storage disease caused by a deficiency of the enzyme β-glucuronidase. This enzyme is responsible for breaking down large sugar molecules called glycosaminoglycans (AKA GAGs, or mucopolysaccharides). The inability to break down GAGs leads to a buildup in many tissues and organs of the body. The severity of the disease can vary widely. diff --git a/tests/input/cases/omim-608716.txt b/tests/input/cases/omim-608716.txt deleted file mode 100644 index 9634bfa39..000000000 --- a/tests/input/cases/omim-608716.txt +++ /dev/null @@ -1 +0,0 @@ -Autosomal recessive primary microcephaly-5 (MCPH5) is characterized by decreased occipitofrontal circumference (OFC), usually less than 3 standard deviations (SD) of the mean, present at birth and associated with mental retardation and speech delay. Other features may include short stature or mild seizures. MCPH5 is associated with a simplification of the cerebral cortical gyral pattern in some cases, which is considered within the phenotypic spectrum of primary microcephaly (review by Woods et al., 2005; Saadi et al., 2009; Passemard et al., 2009). \ No newline at end of file diff --git a/tests/input/cases/omim-619428.txt b/tests/input/cases/omim-619428.txt deleted file mode 100644 index 1d5a329dd..000000000 --- a/tests/input/cases/omim-619428.txt +++ /dev/null @@ -1 +0,0 @@ -Focal segmental glomerulosclerosis and neurodevelopmental syndrome (FSGSNEDS) is characterized by global developmental delay and renal dysfunction manifest as proteinuria and nephrotic syndrome apparent from infancy or early childhood. Some patients present with renal disease, whereas others present with developmental delay and develop renal disease later in childhood. Renal biopsy shows focal segmental glomerulosclerosis (FSGS), but the course of the disease is variable: some patients have transient proteinuria and others require renal transplant. Neurodevelopmental features are also variable, with some patients having only mildly impaired intellectual development, and others having a severe developmental disorder associated with early-onset refractory seizures or epileptic encephalopathy. Additional features, including feeding difficulties, poor overall growth, and nonspecific dysmorphic facial features, are commonly observed (summary by Assoum et al., 2018 and Weng et al., 2021). \ No newline at end of file diff --git a/tests/input/cases/omim-620038.txt b/tests/input/cases/omim-620038.txt deleted file mode 100644 index 9e5752289..000000000 --- a/tests/input/cases/omim-620038.txt +++ /dev/null @@ -1 +0,0 @@ -Neurodevelopmental disorder with microcephaly, hypotonia, and absent language (NEDMHAL) is a severe autosomal recessive disorder characterized by the constellation of these features. Behavioral problems and hearing loss are also present (Ansar et al., 2020). \ No newline at end of file diff --git a/tests/input/cases/reaction-20657015.txt b/tests/input/cases/reaction-20657015.txt deleted file mode 100644 index b4deed0be..000000000 --- a/tests/input/cases/reaction-20657015.txt +++ /dev/null @@ -1,4 +0,0 @@ -Title: Molecular identification of N-acetylaspartylglutamate synthase and beta-citrylglutamate synthase - -Abstract -The purpose of the present work was to determine the identity of the enzymes that synthesize N-acetylaspartylglutamate (NAAG), the most abundant dipeptide present in vertebrate central nervous system (CNS), and β-citrylglutamate, a structural analogue of NAAG present in testis and immature brain. Previous evidence suggests that NAAG is not synthesized on ribosomes but presumably is synthesized by a ligase. As attempts to detect this ligase in brain extracts failed, we searched the mammalian genomes for putative enzymes that could catalyze this type of reaction. Mammalian genomes were found to encode two putative ligases homologous to Escherichia coli RIMK, which ligates glutamates to the C terminus of ribosomal protein S6. One of them, named RIMKLA, is almost exclusively expressed in the CNS, whereas RIMKLB, which shares 65% sequence identity with RIMKLA, is expressed in CNS and testis. Both proteins were expressed in bacteria or HEK293T cells and purified. RIMKLA catalyzed the ATP-dependent synthesis of N-acetylaspartylglutamate from N-acetylaspartate and l-glutamate. RIMKLB catalyzed this reaction as well as the synthesis of β-citrylglutamate. The nature of the reaction products was confirmed by mass spectrometry and NMR. RIMKLA was shown to produce stoichiometric amounts of NAAG and ADP, in agreement with its belonging to the ATP-grasp family of ligases. The molecular identification of these two enzymes will facilitate progress in the understanding of the function of NAAG and β-citrylglutamate. \ No newline at end of file diff --git a/tests/input/cases/reaction-21290071.txt b/tests/input/cases/reaction-21290071.txt deleted file mode 100644 index 9a8b237f4..000000000 --- a/tests/input/cases/reaction-21290071.txt +++ /dev/null @@ -1,6 +0,0 @@ -Title: Substrate specificity of Rv3378c, an enzyme from Mycobacterium -tuberculosis, and the inhibitory activity of the bicyclic diterpenoids -against macrophage phagocytosis - -Abstract -The Rv3378c gene product from Mycobacterium tuberculosis encodes a diterpene synthase to produce tuberculosinol (3), 13R-isotuberculosinol (4a), and 13S-isotuberculosinol (4b) from tuberculosinyl diphosphate (2). The product distribution ratios are 1 : 1 for 3 to 4 and 1 : 3 for 4a to 4b. The substrate specificity of the Rv3378c-encoded enzyme was examined. The 3 labdadienyl diphosphates, copalyl diphosphate (CDP) (7), ent-CDP (8), and syn-CDP (9), underwent the conversion reaction, with good yields (67-78%). Copalol (23) and manool (24) were produced from 7, ent-copalol (25) and ent-manool (26) from 8, and syn-copalol (27) and vitexifolin A (28) from 9. The ratio of 23 to 24 was 40 : 27, that of 25:26 was 22 : 50, and that of 27:28 was 16 : 62. Analysis on a GC-MS chromatograph equipped with a chiral column revealed that 24, 26, and 28 consisted of a mixture of 13R- (a) and 13S-stereoisomers (b) in the following ratio: ca. 1 : 1 for 24a to 24b, ca. 1 : 5 for 26a to 26b, and ca. 1 : 19 for 28a to 28b. The structures of these products indicate that the reactions of the 3 CDPs proceeded in the same fashion as that of 2. This is the first report on the enzymatic synthesis of natural diterpenes manool, ent-manool, and vitexifolin A. Both Rv3377c and Rv3378c genes are found in virulent Mycobacterium species, but not in avirulent species. We found that 3 and 4 inhibited the phagocytosis of opsonized zymosan particles by human macrophage-like cells. Interestingly, the inhibitory activity was synergistically increased by the coexistence of 3 and 4b. Other labdane-related diterpenes, 13-16 and 23-28, had little or no inhibitory activity. This synergistic inhibition by 3 and 4 may provide further advantage to the impairment of phagocyte function, which might contribute to pathogenicity of M. tuberculosis. diff --git a/tests/input/cases/recipe-egg-noodles.txt b/tests/input/cases/recipe-egg-noodles.txt deleted file mode 100644 index 52569b484..000000000 --- a/tests/input/cases/recipe-egg-noodles.txt +++ /dev/null @@ -1,35 +0,0 @@ -Homemade Egg Noodles - -Gather the ingredients. - -Combine the flour and salt in a large shallow bowl or on a clean work surface. Make a well in the center, almost like a "bowl" of flour, to hold the eggs. Crack the eggs into it. - -Flour with eggs cracked into the well in the center -Use a fork to beat the eggs and then gradually start incorporating the flour into the eggs. As you beat them, they will slowly but surely take up some flour from the edges. - -Eggs beat with a fork in a well in the center of flour -Keep stirring and pulling in more flour until a solid dough forms. The dough will be sticky. Don't worry; you'll be working in more flour in a moment. Add too much flour now, and the extra flour needed to roll out the noodles will lead to a dry rather than tender noodle. - -Mixed egg and flour kneaded together to form a shaggy dough -Turn the dough out onto a well-floured work surface. With well-floured hands, knead the dough, incorporating more flour as necessary to keep it from sticking to either the work surface or your hands, until the dough is smooth and firm and no longer sticky. This takes roughly 5 to 10 minutes. - -Formed dough ball for egg pasta -Wrap the dough with plastic wrap and chill it for at least 30 minutes and up to overnight. - -Ball of egg pasta dough in glass bowl covered with plastic wrap -Divide the chilled dough into 2 pieces and work with one half of the dough at a time. - -Ball of egg pasta dough cut in half with a knife -On a well-floured surface, roll out the dough to the desired thickness (anywhere from 1/4 inch to paper-thin, depending on your preference). Be sure to rotate or otherwise move the dough between each pass of the rolling pin to keep the dough from sticking to the work surface underneath. Sprinkle everything with flour—including the work surface when you lift the dough—as necessary to keep the dough from sticking. - -Egg pasta dough rolled out with wooden rolling pin -Use a sharp knife or pizza cutting wheel to cut the noodles. You can make them as narrow or wide as you like. Be sure to cut them as evenly as possible to ensure a uniform cooking time. If you fold the dough to cut, make sure it is floured so it does not stick together. - -Fresh pasta cut into noodles with a knife -Lay the noodles on a cooling or drying rack and let them sit until ready to cook. Repeat rolling and cutting with the remaining half of the dough. - -Fresh homemade egg pasta noodles on a marble counter -Boil the noodles in well-salted water until tender to the bite (2 to 10 minutes for fresh noodles depending on the thickness). Drain and use in your favorite recipe. Enjoy! - -Egg pasta noodles with pesto and Parmesan cheese on a plate - diff --git a/tests/input/cases/recipe-spaghetti.txt b/tests/input/cases/recipe-spaghetti.txt deleted file mode 100644 index d4f38eaac..000000000 --- a/tests/input/cases/recipe-spaghetti.txt +++ /dev/null @@ -1,30 +0,0 @@ -SIMPLE SPAGHETTI - -DIRECTIONS -On medium heat melt the butter and sautee the onion and bell peppers. -Add the hamburger meat and cook until meat is well done. -Add the tomato sauce, salt, pepper and garlic powder. -Salt, pepper and garlic powder can be adjusted to your own tastes. -Cook noodles as directed. -Mix the sauce and noodles if you like, I keep them separated. - -INGREDIENTS -UNITS: US -1 -small onion (chopped) -1 -bell pepper (chopped) -2 -tablespoons garlic powder -3 -tablespoons butter -1 -teaspoon salt -1 -teaspoon pepper -2 -(15 ounce) cans tomato sauce -1 -(16 ounce) box spaghetti noodles -1 - 1 1⁄2 -lb hamburger meat. diff --git a/tests/input/cases/recipe-tortilla-soup.txt b/tests/input/cases/recipe-tortilla-soup.txt deleted file mode 100644 index d2aa1f320..000000000 --- a/tests/input/cases/recipe-tortilla-soup.txt +++ /dev/null @@ -1,31 +0,0 @@ -Tortilla Soup - -Ingredients -1 rotisserie chicken or 3-4 cups poached chicken -1 (15 oz) can fire roasted tomatoes, diced -1 (10 oz) can red enchilada sauce, mild -1 small onion, chopped -1 medium zucchini, sliced into 1/4-inch half circles -1 (4 oz) can green chilies -4 cloves garlic, minced -4 cups chicken broth -1 (14.5 oz) can creamed corn, undrained (can sub with 1 can sweet corn, drained) -1 tsp ground cumin -1 tsp chili powder -1 tsp sea salt -1/4 tsp freshly ground black pepper -3 bay leaves - -Garnish -4 Tbsp chopped cilantro -1 lime cut into wedges -sour cream -cheese, shredded (cheddar, mozzarella, Mexican blend) -1 large avocado, sliced -Tortilla chips, crushed - -Method -While rotisserie chicken is still warm, pick all meat of the bones, discard skin. Place the chicken meat in a large stock pot. Discard bones, or save if you like to make homemade stock. -Add to the pot the tomatoes, enchilada sauce, chicken broth, onion, zucchini, chilis, garlic, corn, cumin, chili powder, salt, pepper and bay leaves. Stir to combine and turn the heat to high. -As soon as soup begins to boil, turn the heat to medium-low heat and continue to cook, uncovered, until the onions are translucent and zucchini is tender, about 30 minutes. -Serve the soup topped with chopped cilantro, a squeeze of fresh lime juice, sour cream, cheese, avocado and corn chips. diff --git a/tests/input/cases/traits-dinoflagellate.txt b/tests/input/cases/traits-dinoflagellate.txt deleted file mode 100644 index 097968e35..000000000 --- a/tests/input/cases/traits-dinoflagellate.txt +++ /dev/null @@ -1,2 +0,0 @@ -Abstract -We have examined the inter- and intra-group seasonal succession of 113 diatom and dinoflagellate taxa, as surveyed by the Continuous Plankton Recorder (CPR) in the North Atlantic, by grouping taxa according to two key functional traits: cell size (µg C cell−1) and trophic strategy (photoautotrophy, mixotrophy, or heterotrophy). Mixotrophic dinoflagellates follow photoautotrophic diatoms but precede their obligate heterotrophic counterparts in the succession because of the relative advantages afforded by photosynthesizing when light and nutrients are available in spring. The mean cell size of the sampled diatoms is smallest in the summer, likely because of the higher specific nutrient affinity of smaller relative to larger cells. Contrastingly, we hypothesize that mixotrophy diminishes the size selection based on nutrient limitation and accounts for the lack of a seasonal size shift among surveyed dinoflagellates. Relatively small, heterotrophic dinoflagellates (µg C cell−1 < 10−3) peak after other, larger dinoflagellates, in part because of the increased abundance of their small prey during nutrient-deplete summer months. The largest surveyed diatoms (µg C cell−1 > 10−2) bloom later than others, and we hypothesize that this may be because of their relatively slow maximum potential growth rates and high internal nutrient storage, as well as to the slower predation of these larger cells. The new trait database and analysis presented here helps translate the taxonomic information of the CPR survey into metrics that can be directly compared with trait-based models.. diff --git a/tests/input/cases/traits-patescibacteria.txt b/tests/input/cases/traits-patescibacteria.txt deleted file mode 100644 index cc9a8537f..000000000 --- a/tests/input/cases/traits-patescibacteria.txt +++ /dev/null @@ -1,9 +0,0 @@ -Abstract -Background -The newly defined superphylum Patescibacteria such as Parcubacteria (OD1) and Microgenomates (OP11) has been found to be prevalent in groundwater, sediment, lake, and other aquifer environments. Recently increasing attention has been paid to this diverse superphylum including > 20 candidate phyla (a large part of the candidate phylum radiation, CPR) because it refreshed our view of the tree of life. However, adaptive traits contributing to its prevalence are still not well known. - -Results -Here, we investigated the genomic features and metabolic pathways of Patescibacteria in groundwater through genome-resolved metagenomics analysis of > 600 Gbp sequence data. We observed that, while the members of Patescibacteria have reduced genomes (~ 1 Mbp) exclusively, functions essential to growth and reproduction such as genetic information processing were retained. Surprisingly, they have sharply reduced redundant and nonessential functions, including specific metabolic activities and stress response systems. The Patescibacteria have ultra-small cells and simplified membrane structures, including flagellar assembly, transporters, and two-component systems. Despite the lack of CRISPR viral defense, the bacteria may evade predation through deletion of common membrane phage receptors and other alternative strategies, which may explain the low representation of prophage proteins in their genomes and lack of CRISPR. By establishing the linkages between bacterial features and the groundwater environmental conditions, our results provide important insights into the functions and evolution of this CPR group. - -Conclusions -We found that Patescibacteria has streamlined many functions while acquiring advantages such as avoiding phage invasion, to adapt to the groundwater environment. The unique features of small genome size, ultra-small cell size, and lacking CRISPR of this large lineage are bringing new understandings on life of Bacteria. Our results provide important insights into the mechanisms for adaptation of the superphylum in the groundwater environments, and demonstrate a case where less is more, and small is mighty.. diff --git a/tests/input/cases/treatment-eds.txt b/tests/input/cases/treatment-eds.txt deleted file mode 100644 index c82f20f2f..000000000 --- a/tests/input/cases/treatment-eds.txt +++ /dev/null @@ -1,5 +0,0 @@ -Disease: Ehlers Danlos Syndrome -Treatment: -The care of patients with EDS is generally focused on implementing preventative measures against serious or life-threatening complications. The primary complications seen in EDS involve the skin, musculoskeletal, and cardiovascular systems. Patient skin is velvety thin, loose, and stretchable. This predisposes patients to difficulties with wound healing. For both accidental and surgical wounds, deep stiches are applied generously. Superficial stiches are placed to carefully realign the skin to prevent scarring. Stiches are also left in for extended periods of time to allow best strengthening of the forming scar tissue. Ascorbic acid (Vitamin C) may be recommended to help reduce the easy bruising that accompanies EDS. Hypermobile joints easily dislocate. With each dislocation, subsequent dislocations are increasingly likely, therefore prevention is particularly important for quality of life. Heavy sports, lifting, and other strenuous efforts should be avoided due to the risk of inciting trauma. Blood vessel fragility increases the risk for serious bleeds and dissections. High blood pressure (hypertension) puts additional strain on the fragile vasculature and increases the risk for complications. Regular screening for hypertension and arterial disease should be conducted and treatment should be initiated early on. The best approaches to screening are by non-invasive technology: ultrasound, MRI, or CT. Arteriography, colonoscopy, and other similarly invasive screening procedures should be considered carefully for benefit versus risk. Surgery for non-life threatening conditions should also be carefully considered. Pregnancies should be followed by obstetricians that are well trained in dealing with high-risk pregnancies. Delivery can progress very quickly in EDS patients and it is yet unclear if there is an advantage to mothers to deliver by vaginal or cesarean routes. Expectant mothers with known aortic root dilations should have echocardiograms each trimester to observe for possible exacerbation. All EDS-affected individuals should seek immediate medical attention for any sudden or unexplained pains and consider wearing a MedicAlert bracelet to communicate their status as a patient with EDS should they lose consciousness. - -hEDS patients may especially benefit from physical therapy, low-resistance exercise, and assistive devices like braces, wheelchairs, and scooters. Comfortable writing utensils and a low-stress mattress serve an important role in reducing musculoskeletal pain. Pain management is tailored to the individual. Gastrointestinal and psychological complications are likewise managed per an individual’s needs. In addition to physical therapy and low-resistance exercise, calcium and vitamin D can help maximize bone density. DEXA bone density scans should be conducted every other year. kEDS patients should have routine eye exams as they are at risk for globus rupture, retinal detachment and glaucoma. dEDS patients may benefit from protective bandages over exposed areas such as the skin of the elbows and knees. diff --git a/tests/input/cases/treatment-marfan.txt b/tests/input/cases/treatment-marfan.txt deleted file mode 100644 index 06beadd66..000000000 --- a/tests/input/cases/treatment-marfan.txt +++ /dev/null @@ -1,7 +0,0 @@ -The treatment of Marfan syndrome is directed toward the specific symptoms that are apparent in each individual. Treatment may require the coordinated efforts of a team of specialists including geneticists, surgeons, cardiologists, dental specialists, eye specialists (ophthalmologists), orthopedists, and other healthcare professionals. - -Individuals with Marfan syndrome are encouraged to avoid competitive and contact sports, heavy lifting and any exercise that increases the strain on the aorta produced by rapid or vigorous beating of the heart or increased blood pressure. Restriction of such activities can slow the rate of the widening of the aorta (aortic dilatation) and decrease the tendency for aortic tear (dissection). In general, moving types of exercises performed in moderation are thought to be good for people with Marfan syndrome. Such exercises, performed regularly, will naturally lower heart rate and blood pressure. - -Beta-adrenergic receptor blocking drugs (β-blockers) such as propranalol or atenolol are often used in treating the cardiovascular problems associated with Marfan syndrome. Such drugs help to reduce the strength and frequency of the contractions of the heart. In doing so, they may reduce the strain on the walls of the aorta. Beta-blockers may delay the need for heart surgery. The dosage needs to be adjusted to the individual patient’s needs, and therapy should be closely monitored. Some individuals may not be able to tolerate these drugs and others such as those with asthma or depession may not be able to take them (contraindicated). - -A second class of blood pressure medication called angiotensin receptor blockers (ARBs) is commonly used in the treatment of cardiovascular problems associated with Marfan syndrome. This includes medications such as losartan or irbesatan. There is experimental evidence that ARBs can help by both lowering blood pressure and by blocking TGF-β activity. In animal models of Marfan syndrome the protective effects of ARBs was superior to that seen with β-blockers. In clinical trials, ARBs have variably been shown to be either better than or as good as β-blockers in suppressing aneurysm growth, but this may not be true for all patients or in all circumstances. In the largest trial performed to date, young patients receiving β-blockers (at high dosing) or ARBs (at standard dosing) had a comparable decline in the deviation of the aortic root size from that expected for age and body size (decreasing aortic root z-score). While both treatments were well tolerated in this study, in general, ARBs are thought to be better tolerated than β-blockers. It is the stated position of the Marfan Foundation that the choice of treatment should be guided by the particular circumstances. A combination of β-blocker and ARB therapy can be considered in circumstances where one or the other type of medication does not achieve an adequate response. diff --git a/tests/input/cases/treatment-schiz.txt b/tests/input/cases/treatment-schiz.txt deleted file mode 100644 index bd1a7d34c..000000000 --- a/tests/input/cases/treatment-schiz.txt +++ /dev/null @@ -1,3 +0,0 @@ -According to the American Psychiatric Association, second-generation (atypical) antipsychotics (SGAs)—with the exception of clozapine—are the agents of choice for first-line treatment of schizophrenia.16,25 Clozapine is not recommended because of its risk of agranulocytosis.2 SGAs are usually preferred over first-generation (typical) antipsychotics (FGAs) because they are associated with fewer extrapyramidal symptoms.2 However, SGAs tend to have metabolic side effects, such as weight gain, hyperlipidemia, and diabetes mellitus.26 These adverse effects can contribute to the increased risk of cardiovascular mortality observed in schizophrenia patients.26 - -The Texas Medication Algorithm Project (TMAP) has provided a six-stage pharmacotherapeutic algorithm for the treatment of schizophrenia. Stage 1 is first-line monotherapy with an SGA. If the patient shows little or no response, he or she should proceed to stage 2, which consists of monotherapy with either another SGA or an FGA. If there is still no response, the patient should move to stage 3, which consists of clozapine monotherapy with monitoring of the white blood cell (WBC) count.24 If agranulocytosis occurs, clozapine should be discontinued. If stage-3 therapy fails to elicit a response, the patient should proceed to stage 4, which combines clozapine with an FGA, an SGA, or electroconvulsive therapy (ECT).24 If the patient still shows no response to treatment, stage 5 calls for monotherapy with an FGA or an SGA that has not been tried.24 Finally, if stage 5 treatment is unsuccessful, stage 6 consists of combination therapy with an SGA, an FGA, ECT, and/or a mood stabilizer. \ No newline at end of file diff --git a/tests/input/dentin.txt b/tests/input/dentin.txt deleted file mode 100644 index a8491ab22..000000000 --- a/tests/input/dentin.txt +++ /dev/null @@ -1,15 +0,0 @@ -Dentin is a major component of teeth that protects dental pulp and maintains tooth health. Bone morphogenetic protein -(BMP) signaling is required for the formation of dentin. Mice lacking a BMP type I receptor, activin A receptor type -1 (ACVR1), in the neural crest display a deformed mandible. Acvr1 is known to be expressed in the dental mesenchyme. -However, little is known about how BMP signaling mediated by ACVR1 regulates dentinogenesis. To explore the role of -ACVR1 in dentin formation in molars and incisors in mice, Acvr1 was conditionally disrupted in Osterix-expressing -cells (designated as cKO). We found that loss of Acvr1 in the dental mesenchyme led to dentin dysplasia in molars and -osteodentin formation in incisors. Specifically, the cKO mice exhibited remarkable tooth phenotypes characterized by -thinner dentin and thicker predentin, as well as compromised differentiation of odontoblasts in molars. We also found -osteodentin formation in the coronal part of the cKO mandibular incisors, which was associated with a reduction in -the expression of odontogenic gene Dsp and an increase in the expression of osteogenic gene Bsp, leading to an -alteration of cell fate from odontoblasts to osteoblasts. In addition, the expressions of WNT antagonists, Dkk1 and -Sost, were downregulated and B-catenin was up-regulated in the cKO incisors, while the expression levels were not -changed in the cKO molars, compared with the corresponding controls. Our results indicate the distinct and critical -roles of ACVR1 between incisors and molars, which is associated with alterations in the WNT signaling related -molecules. This study demonstrates for the first time the physiological roles of ACVR1 during dentinogenesis. diff --git a/tests/input/drug-mech-db-example.yaml b/tests/input/drug-mech-db-example.yaml deleted file mode 100644 index 819935618..000000000 --- a/tests/input/drug-mech-db-example.yaml +++ /dev/null @@ -1,751 +0,0 @@ -- directed: true - graph: - _id: DB00619_MESH_D015464_1 - disease: CML (ph+) - disease_mesh: MESH:D015464 - drug: imatinib - drug_mesh: MESH:D000068877 - drugbank: DB:DB00619 - links: - - key: decreases activity of - source: MESH:D000068877 - target: UniProt:P00519 - - key: causes - source: UniProt:P00519 - target: MESH:D015464 - multigraph: true - nodes: - - id: MESH:D000068877 - label: Drug - name: imatinib - - id: UniProt:P00519 - label: Protein - name: BCR/ABL - - id: MESH:D015464 - label: Disease - name: CML (ph+) -- directed: true - graph: - _id: DB00619_MESH_D034721_1 - disease: Systemic mast cell disease - disease_mesh: MESH:D034721 - drug: imatinib - drug_mesh: MESH:D000068877 - drugbank: DB:DB00619 - links: - - key: decreases activity of - source: MESH:D000068877 - target: UniProt:P10721 - - key: decreases activity of - source: MESH:D000068877 - target: UniProt:P16234 - - key: positively regulates - source: UniProt:P10721 - target: GO:0008283 - - key: positively regulates - source: UniProt:P16234 - target: GO:0008283 - - key: causes - source: GO:0008283 - target: MESH:D034721 - multigraph: true - nodes: - - id: MESH:D000068877 - label: Drug - name: imatinib - - id: UniProt:P10721 - label: Protein - name: c-Kit - - id: UniProt:P16234 - label: Protein - name: Pdgf - - id: GO:0008283 - label: BiologicalProcess - name: Cellular proliferation - - id: MESH:D034721 - label: Disease - name: Systemic mast cell disease -- directed: true - graph: - _id: DB00316_MESH_D010146_1 - disease: Pain - disease_mesh: MESH:D010146 - drug: Acetaminophen - drug_mesh: MESH:D000082 - drugbank: DB:DB00316 - links: - - key: decreases activity of - source: MESH:D000082 - target: UniProt:P23219 - - key: decreases activity of - source: MESH:D000082 - target: UniProt:P35354 - - key: decreases activity of - source: MESH:D000082 - target: UniProt:Q15185 - - key: positively regulates - source: UniProt:P23219 - target: GO:0001516 - - key: positively regulates - source: UniProt:P35354 - target: GO:0001516 - - key: positively regulates - source: UniProt:Q15185 - target: GO:0001516 - - key: increases abundance of - source: GO:0001516 - target: MESH:D011453 - - key: positively correlated with - source: MESH:D011453 - target: MESH:D010146 - multigraph: true - nodes: - - id: MESH:D000082 - label: Drug - name: Acetaminophen - - id: UniProt:P23219 - label: Protein - name: Prostaglandin G/H synthase 1 - - id: UniProt:P35354 - label: Protein - name: Prostaglandin G/H synthase 2 - - id: UniProt:Q15185 - label: Protein - name: Prostaglandin E synthase 3 - - id: GO:0001516 - label: BiologicalProcess - name: prostaglandin biosynthetic process - - id: MESH:D011453 - label: ChemicalSubstance - name: Prostaglandins - - id: MESH:D010146 - label: Disease - name: Pain - reference: - - https://go.drugbank.com/drugs/DB00316#mechanism-of-action - - https://www.uniprot.org/uniprot/P23219#function - - https://www.uniprot.org/uniprot/P35354#function - - https://www.uniprot.org/uniprot/Q15185#function - - https://en.wikipedia.org/wiki/Pain -- directed: true - graph: - _id: DB00316_MESH_D005334_1 - disease: Fever - disease_mesh: MESH:D005334 - drug: acetaminophen - drug_mesh: MESH:D000082 - drugbank: DB:DB00316 - links: - - key: negatively regulates - source: MESH:D000082 - target: REACT:R-HSA-2162123 - - key: occurs in - source: REACT:R-HSA-2162123 - target: UBERON:0000955 - - key: location of - source: UBERON:0000955 - target: GO:0001659 - - key: negatively correlated with - source: GO:0001659 - target: MESH:D005334 - multigraph: true - nodes: - - id: MESH:D000082 - label: Drug - name: acetaminophen - - id: REACT:R-HSA-2162123 - label: Pathway - name: cycloxygenaze pathways - - id: UBERON:0000955 - label: GrossAnatomicalStructure - name: Brain - - id: GO:0001659 - label: BiologicalProcess - name: Temperature Homeostasis - - id: MESH:D005334 - label: Disease - name: Fever -- directed: true - graph: - _id: DB00945_MESH_D010146_1 - disease: Pain - disease_mesh: MESH:D010146 - drug: acetylsalicylic acid - drug_mesh: MESH:D001241 - drugbank: DB:DB00945 - links: - - key: decreases activity of - source: MESH:D001241 - target: UniProt:P23219 - - key: decreases activity of - source: MESH:D001241 - target: UniProt:P35354 - - key: increases abundance of - source: UniProt:P23219 - target: MESH:D011453 - - key: increases abundance of - source: UniProt:P35354 - target: MESH:D011453 - - key: causes - source: MESH:D011453 - target: MESH:D010146 - multigraph: true - nodes: - - id: MESH:D001241 - label: Drug - name: acetylsalicylic acid - - id: UniProt:P23219 - label: Protein - name: Cox-1 - - id: UniProt:P35354 - label: Protein - name: Cox-2 - - id: MESH:D011453 - label: ChemicalSubstance - name: Prostaglandins - - id: MESH:D010146 - label: Disease - name: Pain -- directed: true - graph: - _id: DB00945_MESH_D013927_1 - disease: Thrombosis - disease_mesh: MESH:D013927 - drug: acetylsalicylic acid - drug_mesh: MESH:D001241 - drugbank: DB:DB00945 - links: - - key: decreases activity of - source: MESH:D001241 - target: UniProt:P23219 - - key: participates in - source: UniProt:P23219 - target: REACT:R-HSA-2162123 - - key: participates in - source: UniProt:P23219 - target: GO:0007596 - - key: has output - source: REACT:R-HSA-2162123 - target: MESH:D013928 - - key: participates in - source: MESH:D013928 - target: GO:0007596 - - key: causes - source: GO:0007596 - target: MESH:D013927 - multigraph: true - nodes: - - id: MESH:D001241 - label: Drug - name: acetylsalicylic acid - - id: UniProt:P23219 - label: Protein - name: COX - - id: REACT:R-HSA-2162123 - label: Pathway - name: Synthesis of Prostaglandins and Thromboxanes - - id: MESH:D013928 - label: ChemicalSubstance - name: Thromboxane A2 - - id: GO:0007596 - label: BiologicalProcess - name: Platelet Activiation / Blood Coagulation - - id: MESH:D013927 - label: Disease - name: Thrombosis -- directed: true - graph: - _id: DB00788_MESH_D010146_1 - disease: Pain - disease_mesh: MESH:D010146 - drug: naproxen - drug_mesh: MESH:D009288 - drugbank: DB:DB00788 - links: - - key: decreases activity of - source: MESH:D009288 - target: UniProt:P35354 - - key: increases abundance of - source: UniProt:P35354 - target: MESH:D011453 - - key: participates in - source: MESH:D011453 - target: GO:0006954 - - key: causes - source: GO:0006954 - target: MESH:D010146 - multigraph: true - nodes: - - id: MESH:D009288 - label: Drug - name: naproxen - - id: UniProt:P35354 - label: Protein - name: Cox-2 - - id: MESH:D011453 - label: ChemicalSubstance - name: Prostaglandins - - id: GO:0006954 - label: BiologicalProcess - name: Inflammation - - id: MESH:D010146 - label: Disease - name: Pain -- directed: true - graph: - _id: DB01059_MESH_D004405_1 - disease: Shigellosis - disease_mesh: MESH:D004405 - drug: norfloxacin - drug_mesh: MESH:D009643 - drugbank: DB:DB01059 - links: - - key: decreases activity of - source: MESH:D009643 - target: UniProt:P43702 - - key: negatively regulates - source: MESH:D009643 - target: GO:0003746 - - key: participates in - source: UniProt:P43702 - target: GO:0006260 - - key: precedes - source: GO:0003746 - target: GO:0006412 - - key: occurs in - source: GO:0006260 - target: NCBITaxon:622 - - key: occurs in - source: GO:0006412 - target: NCBITaxon:622 - - key: causes - source: NCBITaxon:622 - target: MESH:D004405 - multigraph: true - nodes: - - id: MESH:D009643 - label: Drug - name: norfloxacin - - id: UniProt:P43702 - label: Protein - name: topoisomerases II, IV - - id: GO:0003746 - label: MolecularActivity - name: Translocation of EF-G - - id: GO:0006260 - label: BiologicalProcess - name: Bacterial DNA replication - - id: GO:0006412 - label: BiologicalProcess - name: Bacterial Protein Synthesis - - id: NCBITaxon:622 - label: OrganismTaxon - name: Shigella dysenteriae - - id: MESH:D004405 - label: Disease - name: Shigellosis -- directed: true - graph: - _id: DB01380_MESH_D007634_1 - disease: Keratitis - disease_mesh: MESH:D007634 - drug: cortisone acetate - drug_mesh: MESH:D003348 - drugbank: DB:DB01380 - links: - - key: increases activity of - source: MESH:D003348 - target: UniProt:P04150 - - key: increases abundance of - source: MESH:D003348 - target: UniProt:P04083 - - key: decreases abundance of - source: MESH:D003348 - target: UniProt:P23219 - - key: increases abundance of - source: UniProt:P04150 - target: UniProt:P04083 - - key: decreases abundance of - source: UniProt:P04150 - target: UniProt:P23219 - - key: increases abundance of - source: UniProt:P23219 - target: MESH:D011453 - - key: negatively regulates - source: UniProt:P04083 - target: GO:0050900 - - key: negatively regulates - source: UniProt:P04083 - target: REACT:R-HSA-2162123 - - key: participates in - source: REACT:R-HSA-2162123 - target: GO:0006954 - - key: participates in - source: MESH:D011453 - target: GO:0006954 - - key: positively regulates - source: GO:0050900 - target: GO:0006954 - - key: positively regulates - source: REACT:R-HSA-2162123 - target: GO:0006954 - - key: causes - source: GO:0006954 - target: MESH:D007634 - multigraph: true - nodes: - - id: MESH:D003348 - label: Drug - name: cortisone acetate - - id: UniProt:P04150 - label: Protein - name: Glucocorticoid receptor - - id: UniProt:P23219 - label: Protein - name: COX Genes - - id: UniProt:P04083 - label: Protein - name: lipocortin-1 - - id: REACT:R-HSA-2162123 - label: Pathway - name: Prostaglandin Synthesis - - id: MESH:D011453 - label: ChemicalSubstance - name: Prostaglandins - - id: GO:0050900 - label: BiologicalProcess - name: Immune Cell Funciton - - id: GO:0006954 - label: BiologicalProcess - name: Inflammation - - id: MESH:D007634 - label: Disease - name: Keratitis -- directed: true - graph: - _id: DB01610_MESH_D003586_1 - disease: CMV infection - disease_mesh: MESH:D003586 - drug: valganciclovir - drug_mesh: MESH:D000077562 - drugbank: DB:DB01610 - links: - - key: increases abundance of - source: MESH:D000077562 - target: MESH:D015774 - - key: negatively regulates - source: MESH:D015774 - target: GO:0039693 - - key: occurs in - source: GO:0039693 - target: NCBITaxon:10358 - - key: causes - source: NCBITaxon:10358 - target: MESH:D003586 - multigraph: true - nodes: - - id: MESH:D000077562 - label: Drug - name: valganciclovir - - id: MESH:D015774 - label: ChemicalSubstance - name: ganciclovir - - id: GO:0039693 - label: BiologicalProcess - name: viral DNA replication - - id: NCBITaxon:10358 - label: OrganismTaxon - name: Cytomegalovirus - - id: MESH:D003586 - label: Disease - name: CMV infection -- directed: true - graph: - _id: DB00916_MESH_D018805_1 - disease: Bacterial septicemia - disease_mesh: MESH:D018805 - drug: metronidazole - drug_mesh: MESH:D008795 - drugbank: DB:DB00916 - links: - - key: increases abundance of - source: MESH:D008795 - target: MESH:C029371 - - key: negatively regulates - source: MESH:C029371 - target: GO:0003676 - - key: occurs in - source: GO:0003676 - target: NCBITaxon:2 - - key: causes - source: NCBITaxon:2 - target: MESH:D018805 - multigraph: true - nodes: - - id: MESH:D008795 - label: Drug - name: metronidazole - - id: MESH:C029371 - label: ChemicalSubstance - name: hydroxyethyl oxamic acid - - id: GO:0003676 - label: BiologicalProcess - name: bacterial Nucleic Acid synthesis - - id: NCBITaxon:2 - label: OrganismTaxon - name: Bacteria - - id: MESH:D018805 - label: Disease - name: Bacterial septicemia -- directed: true - graph: - _id: DB00618_MESH_D000073605_1 - disease: Rickettsialpox - disease_mesh: MESH:D000073605 - drug: demeclocycline - drug_mesh: MESH:D003707 - drugbank: DB:DB00618 - links: - - key: decreases activity of - source: MESH:D003707 - target: UniProt:P0A7S3 - - key: decreases activity of - source: MESH:D003707 - target: UniProt:P0A7J3 - - key: participates in - source: UniProt:P0A7S3 - target: GO:0006412 - - key: participates in - source: UniProt:P0A7J3 - target: GO:0006412 - - key: occurs in - source: GO:0006412 - target: NCBITaxon:786 - - key: causes - source: NCBITaxon:786 - target: MESH:D000073605 - multigraph: true - nodes: - - id: MESH:D003707 - label: Drug - name: demeclocycline - - id: UniProt:P0A7S3 - label: Protein - name: 30S Ribosomal Subunit - - id: UniProt:P0A7J3 - label: Protein - name: 50S Ribosomal Subunit - - id: GO:0006412 - label: BiologicalProcess - name: Bacterial Translation - - id: NCBITaxon:786 - label: OrganismTaxon - name: Rickettsia akari - - id: MESH:D000073605 - label: Disease - name: Rickettsialpox -- directed: true - graph: - _id: DB01060_MESH_D014069_1 - disease: Streptococcal tonsillitis - disease_mesh: MESH:D014069 - drug: amoxicillin - drug_mesh: MESH:D000658 - drugbank: DB:DB01060 - links: - - key: decreases activity of - source: MESH:D000658 - target: TIGR:02074 - - key: participates in - source: TIGR:02074 - target: GO:0009252 - - key: occurs in - source: GO:0009252 - target: NCBITaxon:1314 - - key: causes - source: NCBITaxon:1314 - target: MESH:D014069 - multigraph: true - nodes: - - id: MESH:D000658 - label: Drug - name: amoxicillin - - id: TIGR:02074 - label: GeneFamily - name: Penicillin-binding proteins 1A - - id: GO:0009252 - label: BiologicalProcess - name: Peptidoglycan Biosyntheic Process - - id: NCBITaxon:1314 - label: OrganismTaxon - name: Streptococcus pyogenes - - id: MESH:D014069 - label: Disease - name: Streptococcal tonsillitis -- directed: true - graph: - _id: DB09335_MESH_D011023_1 - disease: Staphylococcal pneumonia - disease_mesh: MESH:D011023 - drug: alatrofloxacin - drug_mesh: MESH:C106856 - drugbank: DB:DB09335 - links: - - key: decreases activity of - source: MESH:C106856 - target: UniProt:P0C1U9 - - key: decreases activity of - source: MESH:C106856 - target: UniProt:P20831 - - key: participates in - source: UniProt:P0C1U9 - target: GO:0006260 - - key: participates in - source: UniProt:P20831 - target: GO:0006260 - - key: occurs in - source: GO:0006260 - target: NCBITaxon:1280 - - key: causes - source: NCBITaxon:1280 - target: MESH:D011023 - multigraph: true - nodes: - - id: MESH:C106856 - label: Drug - name: alatrofloxacin - - id: UniProt:P0C1U9 - label: Protein - name: Topoisomeraze 4 - - id: UniProt:P20831 - label: Protein - name: DNA gyrase - - id: GO:0006260 - label: BiologicalProcess - name: Bacterial DNA replication - - id: NCBITaxon:1280 - label: OrganismTaxon - name: Staphylococcus aureus - - id: MESH:D011023 - label: Disease - name: Staphylococcal pneumonia -- directed: true - graph: - _id: DB00479_MESH_D016920_1 - disease: Bacterial meningitis - disease_mesh: MESH:D016920 - drug: amikacin - drug_mesh: MESH:D000583 - drugbank: DB:DB00479 - links: - - key: decreases activity of - source: MESH:D000583 - target: UniProt:P0A7S3 - - key: participates in - source: UniProt:P0A7S3 - target: GO:0006412 - - key: occurs in - source: GO:0006412 - target: NCBITaxon:2 - - key: causes - source: NCBITaxon:2 - target: MESH:D016920 - multigraph: true - nodes: - - id: MESH:D000583 - label: Drug - name: amikacin - - id: UniProt:P0A7S3 - label: Protein - name: 30S Ribosomal Subunit - - id: GO:0006412 - label: BiologicalProcess - name: Bacterial Translation - - id: NCBITaxon:2 - label: OrganismTaxon - name: Bacteria - - id: MESH:D016920 - label: Disease - name: Bacterial meningitis -- directed: true - graph: - _id: DB01234_MESH_D013717_1 - disease: Tenosynovitis - disease_mesh: MESH:D013717 - drug: dexamethasone - drug_mesh: MESH:D003907 - drugbank: DB:DB01234 - links: - - key: increases activity of - source: MESH:D003907 - target: UniProt:P04150 - - key: increases abundance of - source: UniProt:P04150 - target: UniProt:P04083 - - key: negatively regulates - source: UniProt:P04083 - target: REACT:R-HSA-2162123 - - key: positively regulates - source: REACT:R-HSA-2162123 - target: GO:0006954 - - key: causes - source: GO:0006954 - target: MESH:D013717 - multigraph: true - nodes: - - id: MESH:D003907 - label: Drug - name: dexamethasone - - id: UniProt:P04150 - label: Protein - name: Glucocorticoid receptor - - id: UniProt:P04083 - label: Protein - name: Annexin A1 - - id: REACT:R-HSA-2162123 - label: Pathway - name: Prostaglandin Synthesis - - id: GO:0006954 - label: BiologicalProcess - name: Inflammation - - id: MESH:D013717 - label: Disease - name: Tenosynovitis -- directed: true - graph: - _id: DB00438_MESH_D014552_1 - disease: Bacterial urinary infection - disease_mesh: MESH:D014552 - drug: ceftazidime - drug_mesh: MESH:D002442 - drugbank: DB:DB00438 - links: - - key: decreases activity of - source: MESH:D002442 - target: TIGR:02074 - - key: participates in - source: TIGR:02074 - target: GO:0009252 - - key: occurs in - source: GO:0009252 - target: NCBITaxon:562 - - key: causes - source: NCBITaxon:562 - target: MESH:D014552 - multigraph: true - nodes: - - id: MESH:D002442 - label: Drug - name: ceftazidime - - id: TIGR:02074 - label: GeneFamily - name: Penicillin-binding protein 1A - - id: GO:0009252 - label: BiologicalProcess - name: Bacterial Cell Wall Synthesis - - id: NCBITaxon:562 - label: OrganismTaxon - name: Escherichia coli - - id: MESH:D014552 - label: Disease - name: Bacterial urinary infection diff --git a/tests/input/eds-output.pickle b/tests/input/eds-output.pickle deleted file mode 100644 index df3b7d0b3..000000000 Binary files a/tests/input/eds-output.pickle and /dev/null differ diff --git a/tests/input/eds-output.yaml b/tests/input/eds-output.yaml deleted file mode 100644 index 6f503b98f..000000000 --- a/tests/input/eds-output.yaml +++ /dev/null @@ -1,196 +0,0 @@ -Caching OpenAI responses to .openai_cache.db -Using cached payload for prompt: From the text below, extract the following entities in the following format: - -disease: -drugs: -treatments: -treatment_mechanisms: -treatment_efficacies: - - -Text: -Disease: Ehlers Danlos Syndrome -Treatment: -The care of patients with EDS is generally focused on implementing preventative measures against serious or life-threatening complications. The primary complications seen in EDS involve the skin, musculoskeletal, and cardiovascular systems. Patient skin is velvety thin, loose, and stretchable. This predisposes patients to difficulties with wound healing. For both accidental and surgical wounds, deep stiches are applied generously. Superficial stiches are placed to carefully realign the skin to prevent scarring. Stiches are also left in for extended periods of time to allow best strengthening of the forming scar tissue. Ascorbic acid (Vitamin C) may be recommended to help reduce the easy bruising that accompanies EDS. Hypermobile joints easily dislocate. With each dislocation, subsequent dislocations are increasingly likely, therefore prevention is particularly important for quality of life. Heavy sports, lifting, and other strenuous efforts should be avoided due to the risk of inciting trauma. Blood vessel fragility increases the risk for serious bleeds and dissections. High blood pressure (hypertension) puts additional strain on the fragile vasculature and increases the risk for complications. Regular screening for hypertension and arterial disease should be conducted and treatment should be initiated early on. The best approaches to screening are by non-invasive technology: ultrasound, MRI, or CT. Arteriography, colonoscopy, and other similarly invasive screening procedures should be considered carefully for benefit versus risk. Surgery for non-life threatening conditions should also be carefully considered. Pregnancies should be followed by obstetricians that are well trained in dealing with high-risk pregnancies. Delivery can progress very quickly in EDS patients and it is yet unclear if there is an advantage to mothers to deliver by vaginal or cesarean routes. Expectant mothers with known aortic root dilations should have echocardiograms each trimester to observe for possible exacerbation. All EDS-affected individuals should seek immediate medical attention for any sudden or unexplained pains and consider wearing a MedicAlert bracelet to communicate their status as a patient with EDS should they lose consciousness. - -hEDS patients may especially benefit from physical therapy, low-resistance exercise, and assistive devices like braces, wheelchairs, and scooters. Comfortable writing utensils and a low-stress mattress serve an important role in reducing musculoskeletal pain. Pain management is tailored to the individual. Gastrointestinal and psychological complications are likewise managed per an individual’s needs. In addition to physical therapy and low-resistance exercise, calcium and vitamin D can help maximize bone density. DEXA bone density scans should be conducted every other year. kEDS patients should have routine eye exams as they are at risk for globus rupture, retinal detachment and glaucoma. dEDS patients may benefit from protective bandages over exposed areas such as the skin of the elbows and knees. - - -=== - - -RAW: {'disease': 'Ehlers Danlos Syndrome;', 'drugs': ['Ascorbic Acid (Vitamin C)'], 'treatments': ['Superficial stiches', 'Preventative measures', 'Exercise', 'Physical therapy', 'Assitive devices', 'Bandages', 'Calcium', 'Vitamin D', 'DEXA bone density scans', 'Eye exams'], 'treatment_mechanisms': [{'treatment': 'Superficial stiches', 'mechanism': 'wound healing'}, {'treatment': 'Preventative measures', 'mechanism': 'life threatening complications'}, {'treatment': 'Exercise', 'mechanism': 'dislocations'}, {'treatment': 'Physical therapy', 'mechanism': 'musculoskeletal pain'}, {'treatment': 'Assistive devices', 'mechanism': 'quality of life'}, {'treatment': 'Bandages', 'mechanism': 'skin protection'}, {'treatment': 'Calcium', 'mechanism': 'bone density'}, {'treatment': 'Vitamin D', 'mechanism': 'bone density'}, {'treatment': 'DEXA bone density scans', 'mechanism': 'screening'}, {'treatment': 'Eye exams', 'mechanism': 'glaucoma'}], 'treatment_efficacies': [{'treatment': 'Superficial stiches', 'efficacy': 'effective'}, {'treatment': 'Preventative measures', 'efficacy': 'effective'}, {'treatment': 'Exercise', 'efficacy': 'preventive'}, {'treatment': 'Physical therapy', 'efficacy': 'pain management'}, {'treatment': 'Assistive devices', 'efficacy': 'pain management'}, {'treatment': 'Bandages', 'efficacy': 'skin protection'}, {'treatment': 'Calcium', 'efficacy': 'bone density maximization'}, {'treatment': 'Vitamin D', 'efficacy': 'bone density maximization'}, {'treatment': 'DEXA bone density scans', 'efficacy': 'screening'}, {'treatment': 'Eye exams', 'efficacy': 'screening.'}]} -{'treatment': 'Superficial stiches', 'mechanism': 'GO:0042060'} -{'treatment': 'Preventative measures', 'mechanism': 'life threatening complications'} -{'treatment': 'NCIT:C16567', 'mechanism': 'dislocations'} -{'treatment': 'MAXO:0000011', 'mechanism': 'NCIT:C3244'} -{'treatment': 'NCIT:C157792', 'mechanism': 'NCIT:C17047'} -{'treatment': 'Bandages', 'mechanism': 'skin protection'} -{'treatment': 'CHEBI:22984', 'mechanism': 'NCIT:C61545'} -{'treatment': 'CHEBI:27300', 'mechanism': 'NCIT:C61545'} -{'treatment': 'DEXA bone density scans', 'mechanism': 'NCIT:C48261'} -{'treatment': 'Eye exams', 'mechanism': 'NCIT:C26782'} -{'treatment': 'Superficial stiches', 'efficacy': 'effective'} -{'treatment': 'Preventative measures', 'efficacy': 'effective'} -{'treatment': 'NCIT:C16567', 'efficacy': 'preventive'} -{'treatment': 'MAXO:0000011', 'efficacy': 'pain management'} -{'treatment': 'NCIT:C157792', 'efficacy': 'pain management'} -{'treatment': 'Bandages', 'efficacy': 'skin protection'} -{'treatment': 'CHEBI:22984', 'efficacy': 'bone density maximization'} -{'treatment': 'CHEBI:27300', 'efficacy': 'bone density maximization'} -{'treatment': 'DEXA bone density scans', 'efficacy': 'screening'} -{'treatment': 'Eye exams', 'efficacy': 'screening.'} -{'disease': 'Ehlers Danlos Syndrome;', 'drugs': ['Ascorbic Acid (Vitamin C)'], 'treatments': ['Superficial stiches', 'Preventative measures', 'NCIT:C16567', 'MAXO:0000011', 'Assitive devices', 'Bandages', 'CHEBI:22984', 'CHEBI:27300', 'DEXA bone density scans', 'Eye exams'], 'treatment_mechanisms': [TreatmentMechanism(treatment='Superficial stiches', mechanism='GO:0042060'), TreatmentMechanism(treatment='Preventative measures', mechanism='life threatening complications'), TreatmentMechanism(treatment='NCIT:C16567', mechanism='dislocations'), TreatmentMechanism(treatment='MAXO:0000011', mechanism='NCIT:C3244'), TreatmentMechanism(treatment='NCIT:C157792', mechanism='NCIT:C17047'), TreatmentMechanism(treatment='Bandages', mechanism='skin protection'), TreatmentMechanism(treatment='CHEBI:22984', mechanism='NCIT:C61545'), TreatmentMechanism(treatment='CHEBI:27300', mechanism='NCIT:C61545'), TreatmentMechanism(treatment='DEXA bone density scans', mechanism='NCIT:C48261'), TreatmentMechanism(treatment='Eye exams', mechanism='NCIT:C26782')], 'treatment_efficacies': [TreatmentEfficacy(treatment='Superficial stiches', efficacy='effective'), TreatmentEfficacy(treatment='Preventative measures', efficacy='effective'), TreatmentEfficacy(treatment='NCIT:C16567', efficacy='preventive'), TreatmentEfficacy(treatment='MAXO:0000011', efficacy='pain management'), TreatmentEfficacy(treatment='NCIT:C157792', efficacy='pain management'), TreatmentEfficacy(treatment='Bandages', efficacy='skin protection'), TreatmentEfficacy(treatment='CHEBI:22984', efficacy='bone density maximization'), TreatmentEfficacy(treatment='CHEBI:27300', efficacy='bone density maximization'), TreatmentEfficacy(treatment='DEXA bone density scans', efficacy='screening'), TreatmentEfficacy(treatment='Eye exams', efficacy='screening.')]} -input_id: null -input_text: "Disease: Ehlers Danlos Syndrome\nTreatment:\nThe care of patients with\ - \ EDS is generally focused on implementing preventative measures against serious\ - \ or life-threatening complications. The primary complications seen in EDS involve\ - \ the skin, musculoskeletal, and cardiovascular systems. Patient skin is velvety\ - \ thin, loose, and stretchable. This predisposes patients to difficulties with wound\ - \ healing. For both accidental and surgical wounds, deep stiches are applied generously.\ - \ Superficial stiches are placed to carefully realign the skin to prevent scarring.\ - \ Stiches are also left in for extended periods of time to allow best strengthening\ - \ of the forming scar tissue. Ascorbic acid (Vitamin C) may be recommended to help\ - \ reduce the easy bruising that accompanies EDS. Hypermobile joints easily dislocate.\ - \ With each dislocation, subsequent dislocations are increasingly likely, therefore\ - \ prevention is particularly important for quality of life. Heavy sports, lifting,\ - \ and other strenuous efforts should be avoided due to the risk of inciting trauma.\ - \ Blood vessel fragility increases the risk for serious bleeds and dissections.\ - \ High blood pressure (hypertension) puts additional strain on the fragile vasculature\ - \ and increases the risk for complications. Regular screening for hypertension and\ - \ arterial disease should be conducted and treatment should be initiated early on.\ - \ The best approaches to screening are by non-invasive technology: ultrasound, MRI,\ - \ or CT. Arteriography, colonoscopy, and other similarly invasive screening procedures\ - \ should be considered carefully for benefit versus risk. Surgery for non-life threatening\ - \ conditions should also be carefully considered. Pregnancies should be followed\ - \ by obstetricians that are well trained in dealing with high-risk pregnancies.\ - \ Delivery can progress very quickly in EDS patients and it is yet unclear if there\ - \ is an advantage to mothers to deliver by vaginal or cesarean routes. Expectant\ - \ mothers with known aortic root dilations should have echocardiograms each trimester\ - \ to observe for possible exacerbation. All EDS-affected individuals should seek\ - \ immediate medical attention for any sudden or unexplained pains and consider wearing\ - \ a MedicAlert bracelet to communicate their status as a patient with EDS should\ - \ they lose consciousness.\n\nhEDS patients may especially benefit from physical\ - \ therapy, low-resistance exercise, and assistive devices like braces, wheelchairs,\ - \ and scooters. Comfortable writing utensils and a low-stress mattress serve an\ - \ important role in reducing musculoskeletal pain. Pain management is tailored to\ - \ the individual. Gastrointestinal and psychological complications are likewise\ - \ managed per an individual\u2019s needs. In addition to physical therapy and low-resistance\ - \ exercise, calcium and vitamin D can help maximize bone density. DEXA bone density\ - \ scans should be conducted every other year. kEDS patients should have routine\ - \ eye exams as they are at risk for globus rupture, retinal detachment and glaucoma.\ - \ dEDS patients may benefit from protective bandages over exposed areas such as\ - \ the skin of the elbows and knees.\n" -input_title: null -named_entities: -- id: NCIT:C16567 - label: Exercise -- id: MAXO:0000011 - label: Physical therapy -- id: CHEBI:22984 - label: Calcium -- id: CHEBI:27300 - label: Vitamin D -- id: GO:0042060 - label: wound healing -- id: NCIT:C16567 - label: Exercise -- id: MAXO:0000011 - label: Physical therapy -- id: NCIT:C3244 - label: musculoskeletal pain -- id: NCIT:C157792 - label: Assistive devices -- id: NCIT:C17047 - label: quality of life -- id: CHEBI:22984 - label: Calcium -- id: NCIT:C61545 - label: bone density -- id: CHEBI:27300 - label: Vitamin D -- id: NCIT:C61545 - label: bone density -- id: NCIT:C48261 - label: screening -- id: NCIT:C26782 - label: glaucoma -- id: NCIT:C16567 - label: Exercise -- id: MAXO:0000011 - label: Physical therapy -- id: NCIT:C157792 - label: Assistive devices -- id: CHEBI:22984 - label: Calcium -- id: CHEBI:27300 - label: Vitamin D -raw_completion_output: "\nDisease: Ehlers Danlos Syndrome; \nDrugs: Ascorbic Acid\ - \ (Vitamin C); \nTreatments: Superficial stiches; Preventative measures; Exercise;\ - \ Physical therapy; Assitive devices; Bandages; Calcium; Vitamin D; DEXA bone density\ - \ scans; Eye exams; \nTreatment_mechanisms: Superficial stiches*wound healing; Preventative\ - \ measures*life threatening complications; Exercise*dislocations; Physical therapy*musculoskeletal\ - \ pain; Assistive devices*quality of life; Bandages*skin protection; Calcium*bone\ - \ density; Vitamin D*bone density; DEXA bone density scans*screening; Eye exams*glaucoma;\n\ - \nTreatment_efficacies: Superficial stiches*effective; Preventative measures*effective;\ - \ Exercise*preventive; Physical therapy*pain management; Assistive devices*pain\ - \ management; Bandages*skin protection; Calcium*bone density maximization; Vitamin\ - \ D*bone density maximization; DEXA bone density scans*screening; Eye exams*screening." -results: - disease: Ehlers Danlos Syndrome; - drugs: - - Ascorbic Acid (Vitamin C) - treatment_efficacies: - - efficacy: effective - treatment: Superficial stiches - - efficacy: effective - treatment: Preventative measures - - efficacy: preventive - treatment: NCIT:C16567 - - efficacy: pain management - treatment: MAXO:0000011 - - efficacy: pain management - treatment: NCIT:C157792 - - efficacy: skin protection - treatment: Bandages - - efficacy: bone density maximization - treatment: CHEBI:22984 - - efficacy: bone density maximization - treatment: CHEBI:27300 - - efficacy: screening - treatment: DEXA bone density scans - - efficacy: screening. - treatment: Eye exams - treatment_mechanisms: - - mechanism: GO:0042060 - treatment: Superficial stiches - - mechanism: life threatening complications - treatment: Preventative measures - - mechanism: dislocations - treatment: NCIT:C16567 - - mechanism: NCIT:C3244 - treatment: MAXO:0000011 - - mechanism: NCIT:C17047 - treatment: NCIT:C157792 - - mechanism: skin protection - treatment: Bandages - - mechanism: NCIT:C61545 - treatment: CHEBI:22984 - - mechanism: NCIT:C61545 - treatment: CHEBI:27300 - - mechanism: NCIT:C48261 - treatment: DEXA bone density scans - - mechanism: NCIT:C26782 - treatment: Eye exams - treatments: - - Superficial stiches - - Preventative measures - - NCIT:C16567 - - MAXO:0000011 - - Assitive devices - - Bandages - - CHEBI:22984 - - CHEBI:27300 - - DEXA bone density scans - - Eye exams - diff --git a/tests/input/example-raw-output.txt b/tests/input/example-raw-output.txt deleted file mode 100644 index 5aa06e5e4..000000000 --- a/tests/input/example-raw-output.txt +++ /dev/null @@ -1,9 +0,0 @@ -genes: β-Catenin; cGAS; STING; US3; IFN; ISG -organisms: Herpes Simplex Virus I (HSV-1); -gene_organisms: β-Catenin:host; cGAS:host; STING:host; US3:HSV-1; IFN:host; ISG:host -activities: production of type I IFN; transcription of type I IFN; replication of HSV-1; nuclear translocation of β-catenin -gene_functions: β-catenin:enhance the transcription of type I IFN; US3:antagonize the production of IFN; β-catenin:block nuclear translocation -cellular_processes: cGAS/STING-mediated DNA-sensing signaling; activation of IFN pathway -pathways: IFN pathway; Wnt signalling pathway -gene_gene_interactions: US3:β-catenin -gene_localizations: US3:host; β-catenin:host diff --git a/tests/input/fhkb.db b/tests/input/fhkb.db deleted file mode 100644 index 6ce1964ce..000000000 Binary files a/tests/input/fhkb.db and /dev/null differ diff --git a/tests/input/fhkb.owl b/tests/input/fhkb.owl deleted file mode 100644 index 3da571af4..000000000 --- a/tests/input/fhkb.owl +++ /dev/null @@ -1,625 +0,0 @@ - - - - - - - -]> - - - - - - - - http://mowl-power.cs.man.ac.uk/fhkbtutorial/1.1/ontology/fhkb_chapter_9.owl - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/tests/input/genes2go.tsv.gz b/tests/input/genes2go.tsv.gz deleted file mode 100644 index b4fdfa075..000000000 Binary files a/tests/input/genes2go.tsv.gz and /dev/null differ diff --git a/tests/input/industry-ontology-seed.yaml b/tests/input/industry-ontology-seed.yaml deleted file mode 100644 index 66fd07c6a..000000000 --- a/tests/input/industry-ontology-seed.yaml +++ /dev/null @@ -1,64 +0,0 @@ -elements: - - name: Building - context: IndustrialOntology - subtypes: - - House - - OfficeBlock - - Warehouse - parts: - - BuildingEntrance - - Window - - name: Vehicle - context: IndustrialOntology - subtypes: - - Car - - Bicycle - - Truck - - Motorcycle - - Train - - Boat - parts: - - Wheel - - name: Car - context: IndustrialOntology - description: a vehicle with four wheels - equivalent_to: MotorVehicle and has_part exactly 4 Wheel - synonyms: - - automobile - subtypes: - - Sedan - - SUV - - Coupe - parts: - - CarEngine - - CarDoor - - Wheel - - Frame - - name: CarDoor - context: IndustrialOntology - description: a door that is part of a car - parts: - - DoorHandle - - DoorLock - equivalent_to: Door and part_of some Car - - name: Transportation - context: IndustrialOntology - description: the act of moving people or goods from one place to another - synonyms: - - transport - subtypes: - - Shipping - - Trucking - - TransportByTrain - parts: - - Loading - - Unloading - - name: TransportByTrain - context: IndustrialOntology - description: the act of moving people or goods by train - synonyms: - - train transport - subtypes: - - TransportBySubway - - TransportByHighSpeedRail - equivalent_to: Transport and utilizes some Train \ No newline at end of file diff --git a/tests/input/instances/biological-process-cysteine-biosynthesis.yaml b/tests/input/instances/biological-process-cysteine-biosynthesis.yaml deleted file mode 100644 index cb9e35c8a..000000000 --- a/tests/input/instances/biological-process-cysteine-biosynthesis.yaml +++ /dev/null @@ -1,6 +0,0 @@ -id: xx -name: cysteine biosynthetic process -description: The chemical reactions and pathways resulting in the formation of cysteine from other compounds, including serine -outputs: - - cysteine -subclass_of: amino acid cysteine biosynthetic process \ No newline at end of file diff --git a/tests/input/instances/drug-mechanisms-001.yaml b/tests/input/instances/drug-mechanisms-001.yaml deleted file mode 100644 index c8408788c..000000000 --- a/tests/input/instances/drug-mechanisms-001.yaml +++ /dev/null @@ -1,69 +0,0 @@ -- disease: MESH:D015464 - drug: drugbank:DB00619 - mechanism_links: - - object: PR:P00519 - predicate: decreases activity of - subject: MESH:D000068877 - - object: MESH:D015464 - predicate: causes - subject: PR:P00519 -- disease: MESH:D034721 - drug: drugbank:DB00619 - mechanism_links: - - object: PR:P10721 - predicate: decreases activity of - subject: MESH:D000068877 - - object: PR:P16234 - predicate: decreases activity of - subject: MESH:D000068877 - - object: GO:0008283 - predicate: positively regulates - subject: PR:P10721 - - object: GO:0008283 - predicate: positively regulates - subject: PR:P16234 - - object: MESH:D034721 - predicate: causes - subject: GO:0008283 -- disease: MESH:D010146 - drug: drugbank:DB00316 - mechanism_links: - - object: PR:P23219 - predicate: decreases activity of - subject: MESH:D000082 - - object: PR:P35354 - predicate: decreases activity of - subject: MESH:D000082 - - object: PR:Q15185 - predicate: decreases activity of - subject: MESH:D000082 - - object: GO:0001516 - predicate: positively regulates - subject: PR:P23219 - - object: GO:0001516 - predicate: positively regulates - subject: PR:P35354 - - object: GO:0001516 - predicate: positively regulates - subject: PR:Q15185 - - object: MESH:D011453 - predicate: increases abundance of - subject: GO:0001516 - - object: MESH:D010146 - predicate: positively correlated with - subject: MESH:D011453 -- disease: MESH:D005334 - drug: drugbank:DB00316 - mechanism_links: - - object: REACT:R-HSA-2162123 - predicate: negatively regulates - subject: MESH:D000082 - - object: UBERON:0000955 - predicate: occurs in - subject: REACT:R-HSA-2162123 - - object: GO:0001659 - predicate: location of - subject: UBERON:0000955 - - object: MESH:D005334 - predicate: negatively correlated with - subject: GO:0001659 \ No newline at end of file diff --git a/tests/input/instances/ontology-class-ncit-001.yaml b/tests/input/instances/ontology-class-ncit-001.yaml deleted file mode 100644 index b6a6fff33..000000000 --- a/tests/input/instances/ontology-class-ncit-001.yaml +++ /dev/null @@ -1,36 +0,0 @@ -- label: glioblastoma - description: >- - A carcinoma that arises from a glial cell in the nervous system - subclass_of: - - nervous system cancer - - glioma - logical_definition: - genus: - - carcinoma - differentiating_characteristic_relationship: arises from - differentiating_characteristic_parents: - - glial cell -- label: Langerhans cell sarcoma - description: >- - A neoplastic proliferation of Langerhans cells with overtly malignant cytologic features. - subclass_of: - - dendritic cell tumor - - sarcoma - logical_definition: - genus: - - sarcoma - differentiating_characteristic_relationship: arises from - differentiating_characteristic_parents: - - Langerhans -- label: lung cancer - description: >- - A malignant neoplasm of the lung. - subclass_of: - - cancer - - lung neoplasm - logical_definition: - genus: - - cancer - differentiating_characteristic_relationship: part of - differentiating_characteristic_parents: - - lung diff --git a/tests/input/instances/reactions-001.yaml b/tests/input/instances/reactions-001.yaml deleted file mode 100644 index bd5cfd957..000000000 --- a/tests/input/instances/reactions-001.yaml +++ /dev/null @@ -1,36 +0,0 @@ -- label: trans-hexaprenyltranstransferase activity - description: >- - Catalysis of the reaction: - (2E,6E)-farnesyl diphosphate + 4 isopentenyl diphosphate = - 4 diphosphate + all-trans-heptaprenyl diphosphate. - subclass_of: - - prenyltransferase activity - left_side: - - (2E,6E)-farnesyl diphosphate - - 4 isopentenyl diphosphate - right_side: - - 4 diphosphate - - all-trans-heptaprenyl diphosphate -- label: dihydroorotate dehydrogenase (fumarate) activity - description: >- - Catalysis of the reaction: (S)-dihydroorotate + fumarate = orotate + succinate. - subclass_of: - - dihydroorotate dehydrogenase activity - left_side: - - (S)-dihydroorotate - - fumarate - right_side: - - orotate - - succinate -- label: butanol dehydrogenase activity - description: >- - Catalysis of the reaction: butanal + NADH + H+ => n-butanol + NAD+. - subclass_of: - - alcohol dehydrogenase (NAD+) activity - left_side: - - butanal - - NADPH - - H+ - right_side: - - butanol - - NAD+ diff --git a/tests/input/inter-organism.yaml b/tests/input/inter-organism.yaml deleted file mode 100644 index 6b836635a..000000000 --- a/tests/input/inter-organism.yaml +++ /dev/null @@ -1,114 +0,0 @@ -- - publication: - title: "β-Catenin Is Required for the cGAS/STING Signaling Pathway but Antagonized by the Herpes Simplex Virus 1 US3 Protein" >- - abstract: >- - The cGAS/STING-mediated DNA-sensing signaling pathway is crucial for interferon (IFN) production and host antiviral responses. Herpes simplex virus I (HSV-1) is a DNA virus that has evolved multiple strategies to evade host immune responses. Here, we demonstrate that the highly conserved β-catenin protein in the Wnt signaling pathway is an important factor to enhance the transcription of type I interferon (IFN-I) in the cGAS/STING signaling pathway, and the production of IFN-I mediated by β-catenin was antagonized by HSV-1 US3 protein via its kinase activity. Infection by US3-deficienct HSV-1 and its kinase-dead variants failed to downregulate IFN-I and IFN-stimulated gene (ISG) production induced by β-catenin. Consistent with this, absence of β-catenin enhanced the replication of US3-deficienct HSV-1, but not wild-type HSV-1. The underlying mechanism was the interaction of US3 with β-catenin and its hyperphosphorylation of β-catenin at Thr556 to block its nuclear translocation. For the first time, HSV-1 US3 has been shown to inhibit IFN-I production through hyperphosphorylation of β-catenin and to subvert host antiviral innate immunity.IMPORTANCE Although increasing evidence has demonstrated that HSV-1 subverts host immune responses and establishes lifelong latent infection, the molecular mechanisms by which HSV-1 interrupts antiviral innate immunity, especially the cGAS/STING-mediated cellular DNA-sensing signaling pathway, have not been fully explored. Here, we show that β-catenin promotes cGAS/STING-mediated activation of the IFN pathway, which is important for cellular innate immune responses and intrinsic resistance to DNA virus infection. The protein kinase US3 antagonizes the production of IFN by targeting β-catenin via its kinase activity. The findings in this study reveal a novel mechanism for HSV-1 to evade host antiviral immunity and add new knowledge to help in understanding the interaction between the host and HSV-1 infection. - keywords: "HSV-1; US3; type I IFN; β-catenin." - genes: - - cGAS - - STING - - β-catenin - gene_organism_pairs: - - gene: cGAS - organism: Human - - gene: STING - organism: Human - - gene: β-catenin - organism: Human - - gene: US3 - organism: HSV-1 - functions: - - DNA-sensing signaling pathway - - interferon production - - host antiviral responses - gene_function_pairs: - - gene: cGAS - function: DNA-sensing signaling pathway - - gene: STING - function: DNA-sensing signaling pathway - - gene: β-catenin - function: interferon production - - gene: US3 - function: host antiviral responses - processes: - - cellular DNA-sensing signaling pathway - - cellular innate immune responses - - intrinsic resistance to DNA virus infection - pathways: - - Wnt signaling pathway - - cGAS/STING-mediated cellular DNA-sensing signaling pathway - - type I interferon production - gene_gene_interactions: - - gene1: cGAS - gene2: STING - - gene1: β-catenin - gene2: US3 - gene_localization_pairs: - - gene: β-catenin - localization: nucleus - - gene: US3 - localization: nucleus -- - publication: - title: The interferon-inducible ubiquitin-protein isopeptide ligase (E3) EFP also functions as an ISG15 E3 ligase - abstract: The expression of the ubiquitin-like protein ISG15 and protein modification by ISG15 (ISGylation) are strongly activated by interferons. Accordingly, ISG15 expression and protein ISGylation are strongly activated upon viral and bacterial infections and during other stress conditions, suggesting important roles for the ISG15 system in innate immune responses. Here, we report the identification of the ubiquitin-protein isopeptide ligase (E3) EFP (estrogen-responsive finger protein) as the ISG15 E3 ligase for 14-3-3sigma protein. Like other known components of the protein ISGylation system (ISG15, UBE1L, UBP43, and UBC8), EFP is also an interferon-inducible protein. Expression of EFP small interfering RNA decreased the ISGylation of 14-3-3sigma in the 293T cell ISGylation system as well as in MCF-7 cells upon interferon treatment. Furthermore, the ISGylation enzyme activity of EFP was RING domain-dependent. These findings indicate that EFP is an ISG15 E3 ligase for 14-3-3sigma in vivo. The fact that both UBC8 and EFP are common components in the ubiquitin and ISG15 conjugation pathways suggests a mechanism whereby a limited set of enzymes accomplishes diverse post-translational modifications of their substrates in response to changes in environmental stimulations. - keywords: "ISG15; EFP; 14-3-3sigma; ISGylation; ubiquitination." - genes: - - EFP - - ISG15 - - UBE1L - - UBP43 - - UBC8 - - 14-3-3sigma - gene_organism_pairs: - - gene: EFP - organism: Human - - gene: ISG15 - organism: Human - - gene: UBE1L - organism: Human - - gene: UBP43 - organism: Human - - gene: UBC8 - organism: Human - - gene: 14-3-3sigma - organism: Human - functions: - - ubiquitin-protein isopeptide ligase - - ISG15 E3 ligase - - ISGylation - - ubiquitination - gene_function_pairs: - - gene: EFP - function: ubiquitin-protein isopeptide ligase - - gene: ISG15 - function: ISG15 E3 ligase - - gene: UBE1L - function: ISG15 E3 ligase - - gene: UBP43 - function: ISG15 E3 ligase - - gene: UBC8 - function: ISG15 E3 ligase - - gene: 14-3-3sigma - function: ISGylation - processes: - - protein ISGylation - - protein ubiquitination - pathways: - - ubiquitin-dependent protein catabolic process - - ISGylation - - ubiquitination - gene_localization_pairs: - - gene: EFP - localization: cytoplasm - - gene: ISG15 - localization: cytoplasm - - gene: UBE1L - localization: cytoplasm - - gene: UBP43 - localization: cytoplasm - - gene: UBC8 - localization: cytoplasm - - gene: 14-3-3sigma - localization: cytoplasm - diff --git a/tests/input/mondo-exact-ncit.sssom.tsv b/tests/input/mondo-exact-ncit.sssom.tsv deleted file mode 100644 index 5c2b71850..000000000 --- a/tests/input/mondo-exact-ncit.sssom.tsv +++ /dev/null @@ -1,40 +0,0 @@ -# curie_map: -# MONDO: http://purl.obolibrary.org/obo/MONDO_ -# NCIT: http://purl.obolibrary.org/obo/NCIT_ -# owl: http://www.w3.org/2002/07/owl# -# rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns# -# rdfs: http://www.w3.org/2000/01/rdf-schema# -# semapv: https://w3id.org/semapv/ -# skos: http://www.w3.org/2004/02/skos/core# -# sssom: https://w3id.org/sssom/ -# license: https://creativecommons.org/publicdomain/zero/1.0/ -# mapping_date: '2018-06-14' -# mapping_set_id: http://purl.obolibrary.org/obo/mondo/mappings/mondo_exactmatch_ncit.sssom.tsv -# mapping_set_version: http://purl.obolibrary.org/obo/mondo/releases/2023-05-01/mappings/mondo_exactmatch_ncit.sssom.tsv -# object_source: http://purl.obolibrary.org/obo/ncit.owl -# object_source_version: http://purl.obolibrary.org/obo/ncit/releases/2018-06-14/ncit.owl -# subject_source: http://purl.obolibrary.org/obo/mondo.owl -subject_id subject_label predicate_id object_id object_label mapping_justification -MONDO:0000001 disease skos:exactMatch NCIT:C2991 Disease or Disorder semapv:ManualMappingCuration -MONDO:0000004 adrenocortical insufficiency skos:exactMatch NCIT:C26691 Adrenocortical Insufficiency semapv:ManualMappingCuration -MONDO:0000022 nocturnal enuresis skos:exactMatch NCIT:C118172 Nocturnal Enuresis semapv:ManualMappingCuration -MONDO:0000087 polymicrogyria skos:exactMatch NCIT:C116936 Polymicrogyria semapv:ManualMappingCuration -MONDO:0000088 precocious puberty skos:exactMatch NCIT:C79704 Precocious Puberty semapv:ManualMappingCuration -MONDO:0000115 Chiari malformation skos:exactMatch NCIT:C84570 Arnold-Chiari Malformation semapv:ManualMappingCuration -MONDO:0000128 giant axonal neuropathy skos:exactMatch NCIT:C84728 Giant Axonal Neuropathy semapv:ManualMappingCuration -MONDO:0000141 mosaic variegated aneuploidy syndrome skos:exactMatch NCIT:C128192 Mosaic Variegated Aneuploidy Syndrome 1 semapv:ManualMappingCuration -MONDO:0000147 polyposis skos:exactMatch NCIT:C4089 Polyposis semapv:ManualMappingCuration -MONDO:0000153 transposition of the great arteries skos:exactMatch NCIT:C84742 Transposition of Great Vessels semapv:ManualMappingCuration -MONDO:0000159 bone marrow failure syndrome skos:exactMatch NCIT:C165614 Bone Marrow Failure Syndrome semapv:ManualMappingCuration -MONDO:0000171 muscular dystrophy-dystroglycanopathy, type A skos:exactMatch NCIT:C99109 Walker-Warburg Syndrome semapv:ManualMappingCuration -MONDO:0000179 Neu-Laxova syndrome skos:exactMatch NCIT:C14089 Nuclear Localization Signal semapv:ManualMappingCuration -MONDO:0000190 ventricular fibrillation skos:exactMatch NCIT:C50799 Ventricular Fibrillation semapv:ManualMappingCuration -MONDO:0000212 hypercalcemia, infantile skos:exactMatch NCIT:C129734 Autosomal Recessive Infantile Hypercalcemia semapv:ManualMappingCuration -MONDO:0000297 baylisascariasis skos:exactMatch NCIT:C128397 Baylisascariasis semapv:ManualMappingCuration -MONDO:0000313 hypophosphatemia skos:exactMatch NCIT:C37977 Hypophosphatemia semapv:ManualMappingCuration -MONDO:0000327 Buruli ulcer disease skos:exactMatch NCIT:C84604 Buruli Ulcer semapv:ManualMappingCuration -MONDO:0000330 endemic typhus skos:exactMatch NCIT:C84688 Endemic Typhus Fever semapv:ManualMappingCuration -MONDO:0000334 multinodular goiter skos:exactMatch NCIT:C131438 Multinodular Goiter semapv:ManualMappingCuration -MONDO:0000337 exanthema subitum skos:exactMatch NCIT:C128420 Roseola Infantum semapv:ManualMappingCuration -MONDO:0000355 Ullrich congenital muscular dystrophy skos:exactMatch NCIT:C123438 Ullrich Congenital Muscular Dystrophy semapv:ManualMappingCuration -MONDO:0000359 spondylocostal dysostosis skos:exactMatch NCIT:C125598 Spondylocostal Dysostosis semapv:ManualMappingCuration diff --git a/tests/input/queries/terms.rq b/tests/input/queries/terms.rq deleted file mode 100644 index 4a1020a5d..000000000 --- a/tests/input/queries/terms.rq +++ /dev/null @@ -1 +0,0 @@ -SELECT ?s WHERE { ?s ?p ?o } \ No newline at end of file diff --git a/tests/input/recipe-spaghetti.pickle b/tests/input/recipe-spaghetti.pickle deleted file mode 100644 index 880285f6d..000000000 Binary files a/tests/input/recipe-spaghetti.pickle and /dev/null differ diff --git a/tests/input/recipe-urls.csv b/tests/input/recipe-urls.csv deleted file mode 100644 index 0c0d10583..000000000 --- a/tests/input/recipe-urls.csv +++ /dev/null @@ -1,17 +0,0 @@ -https://www.allrecipes.com/recipe/158968/spinach-and-feta-turkey-burgers/ -https://www.allrecipes.com/recipe/246198/easy-french-toast-waffles/ -https://www.feastingathome.com/tomato-risotto/ -https://www.allrecipes.com/recipe/220903/shrimp-and-cheesy-grits-with-bacon/ -https://www.allrecipes.com/recipe/256164/easy-palak-paneer/ -https://www.allrecipes.com/recipe/87872/sweet-chili-thai-sauce/ -https://www.allrecipes.com/recipe/17445/grilled-asparagus/ -https://www.allrecipes.com/recipe/8538309/sauteed-lacinato-kale/ -https://www.epicurious.com/recipes/food/views/ba-syn-quick-pickled-onions/ -https://www.epicurious.com/recipes/food/views/deviled-eggs-106562 -https://www.allrecipes.com/recipe/187448/sweet-and-spicy-pork-and-napa-cabbage-stir-fry-with-spicy-noodles/ -https://www.thekitchn.com/corn-dog-recipe-23043903 -https://www.allrecipes.com/recipe/257938/spicy-thai-basil-chicken-pad-krapow-gai/ -https://www.bonappetit.com/recipe/marinated-summer-squash-with-hazelnuts-and-ricotta -https://en.wikibooks.org/wiki/Cookbook:Waldorf_Salad -https://www.vegrecipesofindia.com/rajma-pulao-recipe/ -https://cooking.nytimes.com/recipes/1016062-red-lentil-soup diff --git a/tests/input/test.hpoa.tsv b/tests/input/test.hpoa.tsv deleted file mode 100644 index 84adc3c44..000000000 --- a/tests/input/test.hpoa.tsv +++ /dev/null @@ -1,1585 +0,0 @@ -OMIM:301040 Alpha-Thalassemia/mental retardation syndrome, X-linked HP:0000252 OMIM:301040 IEA P HPO:iea[2009-02-17] -OMIM:616239 Combined oxidative phosphorylation deficiency 24 HP:0000252 OMIM:616239 TAS P HPO:skoehler[2015-03-22] -OMIM:300475 Deafness, dystonia, and cerebral hypomyelination HP:0000252 OMIM:300475 TAS P HPO:skoehler[2013-11-18] -OMIM:605039 Bohring-Opitz syndrome HP:0000252 PMID:21706002 PCS 7/7 P HPO:iea[2009-02-17];HPO:probinson[2022-08-27] -OMIM:600093 Spondyloepiphyseal dysplasia tarda with characteristic facies HP:0000252 OMIM:600093 IEA P HPO:iea[2009-02-17] -OMIM:612389 Pontocerebellar hypoplasia, type 2B HP:0000252 PMID:18711368;PMID:23562994 PCS 2/2 P HPO:skoehler[2015-02-22];HPO:probinson[2022-09-12];HPO:probinson[2022-09-12] -OMIM:616734 Skin creases, congenital symmetric circumferential, 2 HP:0000252 PMID:26637975 PCS 1/4 P HPO:skoehler[2015-12-30];HPO:probinson[2022-10-23] -OMIM:615419 Hypotonia, infantile, with psychomotor retardation and characteristic facies 1 HP:0000252 OMIM:615419 TAS P HPO:skoehler[2013-09-30] -OMIM:311400 Paine syndrome HP:0000252 OMIM:311400 IEA P HPO:iea[2009-02-17] -OMIM:619869 Neurocardiofaciodigital syndrome HP:0000252 PMID:33442026 PCS 2/3 P HPO:probinson[2022-08-07] -OMIM:617391 Epileptic encephalopathy, early infantile, 54 HP:0000252 OMIM:617391 TAS P HPO:skoehler[2017-07-13] -OMIM:601701 Arthrogryposis and ectodermal dysplasia HP:0000252 OMIM:601701 IEA P HPO:iea[2009-02-17] -OMIM:604804 Microcephaly 3, primary, autosomal recessive HP:0000252 OMIM:604804 TAS P HPO:skoehler[2009-02-17] -OMIM:620033 Developmental and epileptic encephalopathy 107 HP:0000252 PMID:28097321 PCS 1/1 P HPO:probinson[2022-10-03] -OMIM:614558 Epileptic encephalopathy, early infantile, 13 HP:0000252 PMID:25239001 PCS HP:0011463 1/1 P HPO:skoehler[2015-01-04];HPO:probinson[2022-06-04] -OMIM:242840 Vici syndrome HP:0000252 PMID:25331754 PCS 14/27 P HPO:iea[2009-02-17];HPO:probinson[2022-11-08] -OMIM:615574 Asparagine synthetase deficiency HP:0000252 PMID:24139043 PCS 8/8 P HPO:skoehler[2014-01-28];HPO:probinson[2022-12-14] -OMIM:617752 Mental retardation, autosomal dominant 49 HP:0000252 PMID:27848077;PMID:28251352 PCS 2/17 P HPO:probinson[2022-07-20] -OMIM:617162 Epileptic encephalopathy, early infantile, 46 HP:0000252 OMIM:617162 TAS P HPO:skoehler[2017-07-13] -OMIM:609049 Pierson syndrome HP:0000252 PMID:17256789 PCS 3/4 P HPO:probinson[2022-03-20];HPO:probinson[2022-03-20] -OMIM:612447 Skeletal defects, genital hypoplasia, and mental retardation HP:0000252 OMIM:612447 TAS P HPO:skoehler[2010-06-19] -OMIM:201550 Adducted thumbs syndrome HP:0000252 OMIM:201550 IEA P HPO:iea[2009-02-17] -OMIM:300884 Epileptic encephalopathy, early infantile, 36 HP:0000252 PMID:22492991 PCS 1/1 P HPO:skoehler[2012-11-25];HPO:probinson[2022-05-30] -OMIM:205100 Amyotrophic lateral sclerosis 2, juvenile HP:0000252 PMID:24562058 PCS 2/3 P HPO:probinson[2022-08-16] -OMIM:251240 Microcephaly with chemotactic defect and transient hypogammaglobulinemia HP:0000252 OMIM:251240 IEA P HPO:iea[2009-02-17] -OMIM:618572 Neurodevelopmental disorder with cerebellar hypoplasia and spasticity HP:0000252 PMID:28542170 PCS 3/3 P HPO:probinson[2020-07-10];HPO:probinson[2020-07-10] -OMIM:614129 Perrault syndrome 3 HP:0000252 OMIM:614129 TAS HP:0040283 P HPO:skoehler[2013-10-06] -OMIM:619286 Neurodevelopmental disorder with spasticity, cataracts, and cerebellar hypoplasia HP:0000252 PMID:33443317 PCS 4/14 P HPO:probinson[2021-06-14] -OMIM:609053 Fanconi anemia, complementation group I HP:0000252 OMIM:609053 IEA P HPO:skoehler[2019-04-18] -OMIM:620024 Neurodevelopmental disorder with seizures, microcephaly, and brain abnormalities HP:0000252 PMID:35830857 PCS 15/16 P HPO:probinson[2022-09-05] -OMIM:235550 Hepatic venoocclusive disease with immunodeficiency HP:0000252 OMIM:235550 IEA P HPO:iea[2009-02-17] -OMIM:617284 Dystonia 28, childhood-onset HP:0000252 PMID:27839873 PCS 4/6 P HPO:skoehler[2017-07-13];HPO:probinson[2022-08-23] -OMIM:224230 Dyskeratosis congenita, autosomal recessive 1 HP:0000252 OMIM:224230 IEA P HPO:iea[2009-02-17] -OMIM:617481 Neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies HP:0000252 PMID:28334956 PCS 15/15 P HPO:skoehler[2018-10-08];HPO:probinson[2022-11-26] -OMIM:614485 Trigonocephaly 2 HP:0000252 OMIM:614485 TAS HP:0040283 P HPO:skoehler[2012-11-18] -OMIM:300712 Craniofacioskeletal syndrome HP:0000252 OMIM:300712 IEA P HPO:skoehler[2010-06-20] -OMIM:616910 Immunodeficiency-Centromeric instability-facial anomalies syndrome 3 HP:0000252 PMID:26216346 PCS P HPO:probinson[2017-06-26] -OMIM:614407 Microcephaly, cerebellar hypoplasia, and cardiac conduction defect syndrome HP:0000252 OMIM:614407 TAS P HPO:skoehler[2013-01-22] -OMIM:612731 Faciocardiomelic syndrome HP:0000252 OMIM:612731 IEA P HPO:skoehler[2010-06-19] -OMIM:615328 Shaheen syndrome HP:0000252 OMIM:615328 TAS HP:0040283 P HPO:skoehler[2013-09-10] -OMIM:614104 Mental retardation, autosomal dominant 7 HP:0000252 PMID:23099646;PMID:25167861;PMID:25920557 PCS 17/17 P HPO:probinson[2013-08-10];HP:probinson[2019-02-24];HP:probinson[2019-02-24] -OMIM:190440 Trigonocephaly 1 HP:0000252 OMIM:190440 IEA P HPO:iea[2009-02-17] -OMIM:618877 Leukoencephalopathy, developmental delay, and episodic neurologic regression syndrome HP:0000252 PMID:32197074 PCS 2/9 P HPO:probinson[2020-06-23] -OMIM:268250 Rhizomelic syndrome HP:0000252 OMIM:268250 IEA P HPO:iea[2009-02-17] -OMIM:617864 Neurodevelopmental disorder with or without seizures and gait abnormalities HP:0000252 OMIM:617864 IEA P HPO:skoehler[2019-04-18] -OMIM:607330 Lathosterolosis HP:0000252 PMID:12812989;PMID:17853487 PCS 3/3 P HPO:iea[2012-04-24] -OMIM:615338 Epileptic encephalopathy, early infantile, 16 HP:0000252 OMIM:615338 TAS HP:0040283 P HPO:skoehler[2013-10-06] -OMIM:600001 Pancreatic agenesis and congenital heart defects HP:0000252 OMIM:600001 TAS HP:0040283 P HPO:skoehler[2012-11-18] -OMIM:174300 Orofaciodigital syndrome V HP:0000252 PMID:28711741 PCS 3/3 P HPO:probinson[2022-03-21] -OMIM:618889 Liberfarb syndrome HP:0000252 PMID:31263216 PCS P HPO:probinson[2020-07-24] -OMIM:618736 Structural brain anomalies with impaired intellectual development and craniosynostosis HP:0000252 PMID:26340333 PCS 3/9 P HPO:probinson[2020-05-20] -OMIM:614098 Keppen-Lubinsky syndrome HP:0000252 OMIM:614098 TAS P HPO:skoehler[2015-04-05] -OMIM:616402 Microcephaly 14, primary, autosomal recessive HP:0000252 OMIM:616402 TAS P HPO:skoehler[2015-06-22] -OMIM:610756 Cerebrooculofacioskeletal syndrome 2 HP:0000252 PMID:11443545 PCS 1/1 P HPO:probinson[2013-04-01];HPO:probinson[2022-04-05] -OMIM:604317 Microcephaly 2, primary, autosomal recessive, with or without cortical malformations HP:0000252 PMID:20729831;PMID:20890279 PCS 38/38 P HPO:probinson[2022-10-07];HPO:skoehler[2013-06-12];HPO:probinson[2022-10-07] -OMIM:615356 Muscular dystrophy, limb-girdle, autosomal recessive 18 HP:0000252 OMIM:615356 TAS P HPO:skoehler[2013-10-06] -OMIM:619955 Dworschak-Punetha neurodevelopmental syndrome HP:0000252 PMID:34054129 PCS 1/7 P HPO:probinson[2022-08-23];HPO:probinson[2022-08-23] -OMIM:613627 Brachydactyly, type A1, with short stature, scoliosis, microcephaly,ptosis, hearing loss, and mental retardation HP:0000252 OMIM:613627 TAS P HPO:skoehler[2012-10-17] -OMIM:619026 Neurodevelopmental disorder with progressive spasticity and brain white matter abnormalities HP:0000252 PMID:32707086 PCS 9/12 P HPO:probinson[2020-11-29] -DECIPHER:92 Recurrent 16p12.1 microdeletion (neurodevelopmental susceptibility locus) HP:0000252 DECIPHER:92 IEA P HPO:skoehler[2013-05-29] -OMIM:618012 Epileptic encephalopathy, infantile or early childhood, 3 HP:0000252 OMIM:618012 IEA HP:0040284 P HPO:skoehler[2019-04-18] -OMIM:619522 Neurodevelopmental-craniofacial syndrome with variable renal and cardiac abnormalities HP:0000252 PMID:32891193 PCS 4/19 P HP:probinson[2021-10-27] -OMIM:618644 Osteogenesis imperfecta, type XX HP:0000252 PMID:31564437 PCS 3/5 P HPO:probinson[2020-07-20] -OMIM:609945 Brachyphalangy, polydactyly, and tibial aplasia/hypoplasia HP:0000252 OMIM:609945 IEA P HPO:iea[2009-02-17] -OMIM:619721 Bryant-Li-Bhoj neurodevelopmental syndrome 2 HP:0000252 PMID:33268356 PCS 8/13 P HPO:probinson[2022-05-09] -OMIM:300523 Allan-Herndon-Dudley syndrome HP:0000252 OMIM:300523 TAS P HPO:iea[2018-03-07] -OMIM:613402 Microcephaly, seizures, and developmental delay HP:0000252 PMID:20118933;PMID:23224214 PCS 13/13 P HPO:probinson[2020-12-14] -OMIM:617985 Microcephaly 23, primary, autosomal recessive HP:0000252 PMID:27737959 PCS 1/1 P HPO:skoehler[2019-04-18];HPO:probinson[2022-03-26] -OMIM:618603 Neurodevelopmental disorder with hypotonia and variable intellectual and behavioral abnormalities HP:0000252 PMID:31353023 PCS 5/16 P HPO:probinson[2020-07-22] -OMIM:216400 Cockayne syndrome A HP:0000252 PMID:32160415;PMID:16865293 PCS 9/10 P HPO:iea[2009-02-17];HPO:probinson[2022-04-05];HPO:probinson[2022-04-05] -OMIM:247990 Macdermot-Winter syndrome HP:0000252 OMIM:247990 IEA P HPO:iea[2009-02-17] -OMIM:616632 Seizures, cortical blindness, and microcephaly syndrome HP:0000252 OMIM:616632 TAS P HPO:skoehler[2015-11-15] -OMIM:608097 Periventricular heterotopia with microcephaly, autosomal recessive HP:0000252 OMIM:608097 TAS P HPO:skoehler[2014-01-28] -OMIM:219100 Cutis laxa, autosomal recessive, type IA HP:0000252 OMIM:219100 TAS P HPO:skoehler[2014-11-26] -OMIM:612621 Intellectual developmental disorder, autosomal dominant 5 HP:0000252 PMID:21237447 PCS 1/3 P HPO:skoehler[2013-10-06];HPO:probinson[2022-06-18] -OMIM:619322 Marbach-Rustad progeroid syndrome HP:0000252 PMID:30905398 PCS 2/2 P HPO:probinson[2021-07-04] -OMIM:609981 Immunodeficiency 54 HP:0000252 PMID:22354167 PCS 3/4 P HPO:skoehler[2012-12-02];HPO:probinson[2021-05-30] -OMIM:610758 Cerebrooculofacioskeletal syndrome 4 HP:0000252 PMID:23623389;PMID:17273966 PCS 2/2 P HPO:probinson[2022-04-05];HPO:skoehler[2013-01-09];HPO:probinson[2022-04-05] -OMIM:613804 Meier-Gorlin syndrome 4 HP:0000252 PMID:21358632 PCS 2/7 P HPO:skoehler[2012-10-17];HPO:probinson[2022-03-26] -OMIM:616878 Metabolic encephalomyopathic crises, recurrent, with rhabdomyolysis, cardiac arrhythmias, and neurodegeneration HP:0000252 OMIM:616878 TAS HP:0040283 P HPO:skoehler[2017-07-13] -OMIM:608393 Microcephaly, primary autosomal recessive, 6 HP:0000252 PMID:22775483 PCS 3/3 P HPO:iea[2009-02-17];HPO:probinson[2022-09-02] -OMIM:617984 Microcephaly 22, primary, autosomal recessive HP:0000252 PMID:27737959 PCS 2/2 P HPO:skoehler[2019-04-18];HPO:probinson[2023-01-18] -OMIM:615493 Mental retardation, autosomal recessive 37 HP:0000252 PMID:29302074 IEA 0/2 P HPO:probinson[2022-06-15] -OMIM:616154 Peroxisomal fatty acyl-CoA reductase 1 disorder HP:0000252 PMID:25439727 PCS 3/3 P HPO:skoehler[2015-01-28];HPO:probinson[2021-07-01] -OMIM:608432 Craniosynostosis, calcification of basal ganglia, and facial dysmorphism HP:0000252 OMIM:608432 IEA P HPO:iea[2009-02-17] -OMIM:618493 Hypotonia, hypoventilation, impaired intellectual development, dysautonomia, epilepsy, and eye abnormalities HP:0000252 OMIM:618493 IEA HP:0040284 P HPO:skoehler[2019-09-07] -OMIM:618050 Mental retardation, autosomal dominant 57 HP:0000252 OMIM:618050 IEA P HPO:skoehler[2019-04-18] -OMIM:617661 Vertebral, cardiac, renal, and limb defects syndrome 2 HP:0000252 PMID:28792876 PCS 1/2 P HPO:skoehler[2018-10-08];HPO:probinson[2022-08-23] -OMIM:619453 Microcephaly 28, primary, autosomal recessive HP:0000252 PMID:33199730 PCS HP:0003577 8/8 HP:0012828 P HPO:probinson[2021-08-20] -OMIM:616672 Combined oxidative phosphorylation deficiency 27 HP:0000252 OMIM:616672 TAS P HPO:skoehler[2015-12-30] -OMIM:615160 Mitochondrial complex III deficiency, nuclear type 5 HP:0000252 PMID:23281071 PCS 1/3 P HPO:probinson[2021-07-08] -OMIM:615273 Congenital disorder of deglycosylation 1 HP:0000252 PMID:24651605 PCS 6/8 P HPO:probinson[2017-06-19] -OMIM:618906 Intellectual developmental disorder with autistic features and language delay, with or without seizures HP:0000252 PMID:31616000 PCS 3/18 P HPO:probinson[2020-08-13] -OMIM:251250 Microcephaly with cervical spine fusion anomalies HP:0000252 OMIM:251250 IEA P HPO:iea[2009-02-17] -OMIM:615541 Mental retardation, autosomal recessive 39 HP:0000252 PMID:23956177 PCS 3/3 P HPO:skoehler[2013-11-28];HPO:probinson[2022-02-24] -OMIM:618342 Intellectual developmental disorder with abnormal behavior, microcephaly, and short stature HP:0000252 PMID:30526862;PMID:30778726 PCS 7/8 P HPO:probinson[2022-06-19];HPO:skoehler[2019-04-18];HPO:probinson[2022-06-19] -OMIM:618741 Neurodevelopmental disorder with epilepsy, spasticity, and brain atrophy HP:0000252 PMID:31794024 PCS 7/7 P HPO:probinson[2020-05-08] -OMIM:619310 Leukodystrophy, hypomyelinating, 21 HP:0000252 PMID:30584594 PCS 2/2 P HPO:probinson[2021-07-03] -OMIM:613658 Rajab interstitial lung disease with brain calcifications HP:0000252 PMID:19161147 PCS 8/8 P HPO:skoehler[2012-10-17];HP:probinson[2019-02-19] -OMIM:610181 Aicardi-Goutieres syndrome 2 HP:0000252 OMIM:610181 TAS HP:0040283 P HPO:skoehler[2015-01-04] -OMIM:616393 Intellectual developmental disorder, autosomal dominant 38 HP:0000252 PMID:24697219 PCS 2/2 P HPO:probinson[2022-06-19] -OMIM:603585 Congenital disorder of glycosylation, type IIf HP:0000252 OMIM:603585 IEA P HPO:skoehler[2018-10-08] -OMIM:618874 Chromosome 17q11.2 duplication syndrome, 1.4-Mb HP:0000252 PMID:22241097 PCS 1/7 P HPO:probinson[2021-08-19] -OMIM:251190 Microcephalic primordial dwarfism, Toriello type HP:0000252 OMIM:251190 IEA P HPO:iea[2009-02-17] -OMIM:617635 Intellectual developmental disorder, autosomal dominant 47 HP:0000252 PMID:28119487 PCS 3/17 P HPO:skoehler[2019-04-18];HPO:probinson[2022-06-08] -OMIM:601453 Trichodental dysplasia HP:0000252 OMIM:601453 TAS HP:0012827 P HPO:probinson[2009-02-17] -OMIM:272440 Filippi syndrome HP:0000252 OMIM:272440 IEA P HPO:iea[2009-02-17] -OMIM:614749 Hyperphosphatasia with mental retardation syndrome 2 HP:0000252 PMID:22683086 PCS 1/3 P HPO:skoehler[2012-11-18];HPO:probinson[2021-09-08] -OMIM:615715 Bone marrow failure syndrome 2 HP:0000252 OMIM:615715 TAS P HPO:skoehler[2014-04-13] -OMIM:300915 Microphthalmia, syndromic 13 HP:0000252 OMIM:300915 TAS P HPO:skoehler[2014-02-06] -OMIM:616045 Combined oxidative phosphorylation deficiency 22 HP:0000252 OMIM:616045 TAS P HPO:skoehler[2014-11-26] -OMIM:617281 Epileptic encephalopathy, early infantile, 49 HP:0000252 OMIM:617281 IEA P HPO:skoehler[2019-04-18] -OMIM:617008 Cerebral palsy, spastic quadriplegic, 3 HP:0000252 PMID:23836506 PCS 4/4 P HPO:skoehler[2017-07-13];HPO:probinson[2021-09-20] -OMIM:500007 Cyclic vomiting syndrome HP:0000252 OMIM:500007 IEA P HPO:iea[2009-02-17] -OMIM:617709 Neurodevelopmental disorder with microcephaly, ataxia, and seizures HP:0000252 PMID:28236339 PCS 4/4 P HPO:skoehler[2019-04-18];HPO:probinson[2022-08-21] -OMIM:210730 Microcephalic osteodysplastic primordial dwarfism, type III HP:0000252 OMIM:210730 IEA P HPO:iea[2009-02-17] -OMIM:613676 Seckel syndrome 4 HP:0000252 OMIM:613676 TAS P HPO:skoehler[2012-10-17] -OMIM:616171 Microcephaly and chorioretinopathy, autosomal recessive, 2 HP:0000252 OMIM:616171 TAS P HPO:skoehler[2015-02-22] -OMIM:617751 Intellectual developmental disorder, autosomal dominant 48 HP:0000252 PMID:28886345 PCS 4/7 P HPO:probinson[2018-05-23] -OMIM:600118 Warburg micro syndrome 1 HP:0000252 OMIM:600118 IEA P HPO:iea[2009-02-17] -OMIM:216550 Cohen syndrome HP:0000252 OMIM:216550 IEA P HPO:iea[2009-02-17] -OMIM:615119 Mitochondrial complex IV deficiency, nuclear type 6 HP:0000252 OMIM:615119 TAS P HPO:skoehler[2013-05-03] -OMIM:613638 Chromosome 19p13.13 deletion syndrome HP:0000252 PMID:20613546 PCS P HPO:probinson[2017-06-23] -OMIM:616271 3-Methylglutaconic aciduria with cataracts, neurologic involvement, and neutropenia HP:0000252 PMID:25597511;PMID:25597510 PCS 10/19 P HPO:skoehler[2015-05-31];HPO:probinson[2022-06-04];HPO:probinson[2022-06-04] -OMIM:616647 Epileptic encephalopathy, early infantile, 35 HP:0000252 PMID:26224535 PCS 5/7 P HPO:probinson[2017-06-17] -OMIM:614114 Mosaic variegated aneuploidy syndrome 2 HP:0000252 PMID:21552266 PCS 2/4 P HPO:skoehler[2012-10-17];HPO:probinson[2021-02-18] -OMIM:610443 Koolen-De Vries syndrome HP:0000252 PMID:18628315 PCS 1/22 P HPO:iea[2010-09-08];HPO:probinson[2020-08-02] -OMIM:607872 Chromosome 1p36 deletion syndrome HP:0000252 PMID:18245432;PMID:12687501 PCS 57/90 P HPO:probinson[2021-07-03];HPO:probinson[2009-02-17] -OMIM:145290 HYPERREFLEXIA HP:0000252 OMIM:145290 TAS HP:0040283 P HPO:probinson[2009-02-17] -OMIM:200450 Achalasia-Microcephaly syndrome HP:0000252 OMIM:200450 IEA P HPO:iea[2009-02-17] -OMIM:617883 Fanconi anemia, complementation group S HP:0000252 OMIM:617883 IEA P HPO:skoehler[2019-04-18] -OMIM:618557 Epileptic encephalopathy, early infantile, 78 HP:0000252 PMID:31032849;PMID:29961870 PCS 11/15 P HPO:probinson[2020-06-28] -OMIM:601355 Microcephaly, congenital heart disease, unilateral renal agenesis,and hyposegmented lungs HP:0000252 OMIM:601355 IEA P HPO:iea[2009-02-17] -OMIM:617873 Combined oxidative phosphorylation deficiency 35 HP:0000252 PMID:24901367 PCS 1/1 P HPO:skoehler[2019-04-18];HPO:probinson[2022-11-27] -OMIM:615802 Neurodevelopmental disorder with dysmorphic features, spasticity, and brain abnormalities HP:0000252 PMID:24784135;PMID:26050939 PCS 3/4 P HPO:skoehler[2017-07-13];HPO:probinson[2021-06-27];HPO:probinson[2021-06-27] -OMIM:612015 Congenital disorder of glycosylation, type IN HP:0000252 OMIM:612015 TAS P HPO:skoehler[2015-08-16] -OMIM:618482 Generalized epilepsy with febrile seizures plus, type 10 HP:0000252 PMID:30351409 PCS 2/19 P HPO:probinson[2019-07-06] -OMIM:614886 Peroxisome biogenesis disorder 12A (Zellweger) HP:0000252 OMIM:614886 TAS P HPO:skoehler[2017-07-13] -OMIM:617988 Jaberi-Elahi syndrome HP:0000252 PMID:29449720 PCS 3/3 P HPO:skoehler[2019-04-18];HPO:probinson[2022-09-07] -OMIM:616682 Seizures, scoliosis, and macrocephaly/microcephaly syndrome HP:0000252 OMIM:616682 IEA P HPO:skoehler[2019-09-07] -OMIM:606242 Mental retardation, microcephaly, growth retardation, joint contractures,and facial dysmorphism HP:0000252 OMIM:606242 IEA P HPO:iea[2009-02-17] -OMIM:620062 Developmental delay with short stature, dysmorphic facial features, and sparse hair 2 HP:0000252 PMID:32576952 PCS 2/3 P HPO:probinson[2022-10-02] -OMIM:272300 SULFOCYSTEINURIA HP:0000252 PMID:15952210;PMID:31127934 PCS 2/2 P HPO:probinson[2022-03-13] -OMIM:613885 Meckel syndrome, type 8 HP:0000252 PMID:21462283 PCS 1/5 P HPO:skoehler[2015-04-26];HPO:probinson[2022-10-30] -OMIM:617613 Multiple mitochondrial dysfunctions syndrome 5 HP:0000252 OMIM:617613 IEA HP:0040284 P HPO:skoehler[2019-04-18] -OMIM:300471 Cubitus valgus with mental retardation and unusual facies HP:0000252 OMIM:300471 IEA P HPO:iea[2009-02-17] -OMIM:208870 Ataxia-Microcephaly-Cataract syndrome HP:0000252 OMIM:208870 IEA P HPO:iea[2009-02-17] -OMIM:618724 Heyn-Sproul-Jackson syndrome HP:0000252 PMID:30478443 PCS 3/3 HP:0012828 P HPO:probinson[2020-05-11];HPO:probinson[2020-05-11] -OMIM:614067 Spastic paraplegia 52, autosomal recessive HP:0000252 OMIM:614067 TAS P HPO:skoehler[2012-10-17] -OMIM:615350 MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY (CONGENITAL WITH BRAIN AND EYE ANOMALIES), TYPE A, 14 HP:0000252 OMIM:615350 TAS P HPO:skoehler[2013-10-06] -OMIM:300882 Cornelia de Lange syndrome 5 HP:0000252 OMIM:300882 TAS P HPO:skoehler[2017-07-13] -OMIM:225700 Encephalomalacia, multilocular HP:0000252 OMIM:225700 IEA P HPO:iea[2009-02-17] -OMIM:606744 Seckel syndrome 2 HP:0000252 PMID:21998596 PCS P HPO:probinson[2013-02-24] -OMIM:212080 Cardiac lipidosis, familial HP:0000252 OMIM:212080 IEA P HPO:iea[2009-02-17] -OMIM:616033 Microcephaly, short stature, and impaired glucose metabolism 1 HP:0000252 PMID:24204302 PCS 3/3 P HPO:skoehler[2014-10-06];HPO:probinson[2022-09-08] -OMIM:248800 Marinesco-Sjogren syndrome HP:0000252 OMIM:248800 IEA P HPO:iea[2009-02-17] -OMIM:301006 Galloway-Mowat syndrome 2, X-linked HP:0000252 OMIM:301006 IEA P HPO:skoehler[2019-04-18] -OMIM:618065 Pontocerebellar hypoplasia, type 1D HP:0000252 PMID:29727687 PCS 1/3 P HPO:skoehler[2018-10-08];HPO:probinson[2022-06-26] -OMIM:223800 Dyggve-Melchior-Clausen disease HP:0000252 OMIM:223800 TAS P HPO:probinson[2009-02-17] -OMIM:618973 Neurodegeneration, infantile-onset, biotin-responsive HP:0000252 PMID:27904971;PMID:31754459 PCS 3/3 P HPO:probinson[2020-09-11] -OMIM:113620 Branchiooculofacial syndrome HP:0000252 OMIM:113620 TAS P HPO:iea[2009-02-17] -OMIM:618862 Neurodevelopmental disorder with hypotonia, microcephaly, and seizures HP:0000252 PMID:32220291 PCS HP:0011461 1/4 P HPO:probinson[2020-09-03];HPO:probinson[2020-09-03] -OMIM:618862 Neurodevelopmental disorder with hypotonia, microcephaly, and seizures HP:0000252 PMID:32220291 PCS 4/4 P HPO:probinson[2020-09-03] -OMIM:613406 Witteveen-Kolk syndrome HP:0000252 PMID:33437032;PMID:27399968 PCS 19/41 P HPO:iea[2012-04-24];HPO:probinson[2022-08-27];HPO:probinson[2022-08-27] -OMIM:617228 Combined oxidative phosphorylation deficiency 31 HP:0000252 OMIM:617228 TAS HP:0040283 P HPO:skoehler[2017-07-13] -OMIM:225750 Aicardi-Goutieres syndrome 1 HP:0000252 PMID:17357087;PMID:20799324 PCS 2/2 P HPO:probinson[2021-09-05];HPO:probinson[2020-11-27] -OMIM:619184 Short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies HP:0000252 PMID:33308444 PCS 9/13 P HPO:probinson[2021-04-27] -OMIM:614814 Adams-Oliver syndrome 3 HP:0000252 PMID:22883147 PCS 2/6 P HPO:skoehler[2012-10-17];HPO:probinson[2022-09-11] -OMIM:613805 Meier-Gorlin syndrome 5 HP:0000252 PMID:21358632 PCS 1/1 P HPO:skoehler[2012-10-17];HPO:probinson[2022-03-26] -OMIM:300352 Cerebral creatine deficiency syndrome 1 HP:0000252 PMID:27408820 PCS 2/3 P HPO:iea[2009-02-17];HPO:probinson[2022-03-09] -OMIM:618470 Intellectual developmental disorder with severe speech and ambulation defects HP:0000252 PMID:31031012 PCS 2/10 P HPO:skoehler[2019-09-07];HPO:probinson[2022-11-09] -OMIM:301043 Holoprosencephaly 13, X-linked HP:0000252 PMID:31334757 PCS 8/11 P HPO:probinson[2020-09-02] -OMIM:257910 Oculopalatocerebral syndrome HP:0000252 OMIM:257910 IEA P HPO:iea[2009-02-17] -OMIM:617302 Optic atrophy 11 HP:0000252 OMIM:617302 TAS P HPO:skoehler[2017-07-13] -OMIM:617520 Microcephaly 18, primary, autosomal dominant HP:0000252 OMIM:617520 TAS P HPO:nvasilevsky[2019-02-25] -OMIM:615966 Immunodeficiency 26 with or without neurologic abnormalities HP:0000252 OMIM:615966 TAS P HPO:skoehler[2014-11-26] -OMIM:609056 Salt and pepper developmental regression syndrome HP:0000252 OMIM:609056 TAS HP:0040283 P HPO:skoehler[2014-08-24] -OMIM:617050 Hermansky-Pudlak syndrome 10 HP:0000252 PMID:26744459 PCS HP:0003577 1/1 P HPO:skoehler[2017-07-13];HPO:probinson[2020-10-28] -OMIM:308830 Keratosis follicularis, dwarfism, and cerebral atrophy HP:0000252 OMIM:308830 PCS P HPO:probinson[2009-02-17] -OMIM:206900 Microphthalmia, syndromic 3 HP:0000252 OMIM:206900 IEA P HPO:iea[2009-02-17] -OMIM:617052 Bone marrow failure syndrome 3 HP:0000252 OMIM:617052 TAS HP:0040283 P HPO:skoehler[2017-07-13] -OMIM:278730 Xeroderma pigmentosum, complementation group D HP:0000252 OMIM:278730 IEA P HPO:iea[2009-02-17] -OMIM:618665 Intellectual developmental disorder, autosomal recessive 72 HP:0000252 PMID:31564433 PCS 7/7 P HPO:probinson[2020-06-25] -OMIM:618336 Intrauterine growth retardation, metaphyseal dysplasia, adrenal hypoplasia congenita, genital anomalies, and immunodeficiency HP:0000252 OMIM:618336 IEA P HPO:skoehler[2019-04-18] -OMIM:618622 Neurodevelopmental disorder with microcephaly, arthrogryposis, and structural brain anomalies HP:0000252 PMID:31495489 PCS 15/21 P HPO:probinson[2020-06-27] -OMIM:301900 Borjeson-Forssman-Lehmann syndrome HP:0000252 OMIM:301900 IEA P HPO:iea[2009-02-17] -OMIM:300966 Mental retardation, X-linked, syndromic 33 HP:0000252 PMID:26637982 PCS 7/11 P HPO:probinson[2017-06-17] -OMIM:608093 Congenital disorder of glycosylation, type Ij HP:0000252 OMIM:608093 IEA P HPO:iea[2009-02-17] -OMIM:602342 Pierpont syndrome HP:0000252 OMIM:602342 TAS P HPO:skoehler[2012-10-16] -OMIM:619576 Cerebellar ataxia, brain abnormalities, and cardiac conduction defects HP:0000252 PMID:34089229 PCS 2/2 P HPO:probinson[2021-11-27] -OMIM:309500 Renpenning syndrome HP:0000252 PMID:15782410 PCS 38/44 P HPO:iea[2009-02-17];HPO:probinson[2020-08-09] -OMIM:616462 Acrofacial dysostosis, Cincinnati type HP:0000252 PMID:25913037 PCS 1/3 P HPO:skoehler[2015-08-16];HPO:probinson[2022-09-24] -OMIM:619517 Neurodevelopmental disorder with seizures and brain abnormalities HP:0000252 PMID:34186028 PCS 4/4 P HPO:probinson[2021-10-31] -OMIM:618718 Neurodevelopmental disorder with behavioral abnormalities, absent speech, and hypotonia HP:0000252 PMID:31668703 PCS 5/14 P HPO:probinson[2020-05-11] -OMIM:133540 Cockayne syndrome, type B HP:0000252 PMID:18446857 PCS 3/3 P HPO:iea[2009-02-17];HPO:probinson[2022-04-05] -OMIM:620028 Developmental and epileptic encephalopathy 106 HP:0000252 PMID:33473208 PCS 2/8 P HPO:probinson[2022-10-03] -OMIM:615471 Mitochondrial DNA depletion syndrome 13 (encephalomyopathic type) HP:0000252 OMIM:615471 TAS HP:0040283 P HPO:skoehler[2013-11-18] -OMIM:253280 Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 3 HP:0000252 OMIM:253280 TAS P HPO:skoehler[2012-10-17] -OMIM:600901 Fanconi anemia, complementation group E HP:0000252 OMIM:600901 IEA P HPO:iea[2009-02-17] -OMIM:148050 KBG syndrome HP:0000252 OMIM:148050 IEA P HPO:iea[2009-02-17] -OMIM:613451 Frontonasal dysplasia 2 HP:0000252 PMID:19692347 PCS 1/2 P HPO:skoehler[2015-07-26];HPO:probinson[2022-05-08] -OMIM:614105 Methylmalonate semialdehyde dehydrogenase deficiency HP:0000252 OMIM:614105 TAS P HPO:skoehler[2015-08-16] -OMIM:314580 Wieacker-Wolff syndrome HP:0000252 PMID:31206972 PCS P HPO:skoehler[2017-07-13];HPO:probinson[2020-07-25] -OMIM:619680 Marbach-Schaaf neurodevelopmental syndrome HP:0000252 PMID:33833410 PCS 1/6 P HPO:probinson[2022-02-19] -OMIM:609654 Short stature and facioauriculothoracic malformations HP:0000252 OMIM:609654 IEA P HPO:iea[2009-02-17] -OMIM:300519 Mental retardation, X-linked, syndromic, Martin-Probst type HP:0000252 PMID:11073537 PCS 2/3 P HPO:skoehler[2012-10-14];HPO:probinson[2020-10-20] -OMIM:192430 Velocardiofacial syndrome HP:0000252 OMIM:192430 IEA P HPO:iea[2009-02-17] -OMIM:617804 Neurodevelopmental disorder with severe motor impairment and absent language HP:0000252 PMID:29100085 PCS P HPO:skoehler[2019-04-18];HPO:probinson[2022-12-17] -OMIM:613684 Rubinstein-Taybi syndrome 2 HP:0000252 PMID:17220215 PCS 3/3 P HPO:skoehler[2012-10-17];HPO:probinson[2022-10-13] -DECIPHER:1 Wolf-Hirschhorn syndrome HP:0000252 DECIPHER:1 IEA P HPO:skoehler[2013-05-29] -DECIPHER:45 Xq28 (MECP2) duplication HP:0000252 PMID:17088400 PCS male P HPO:iea[2010-09-15] -OMIM:619321 Growth restriction, hypoplastic kidneys, alopecia, and distinctive facies HP:0000252 PMID:29851065 PCS 4/4 P HPO:probinson[2021-07-03] -OMIM:617694 Al Kaissi syndrome HP:0000252 OMIM:617694 IEA P HPO:skoehler[2019-04-18] -OMIM:604273 Mitochondrial complex V (ATP synthase) deficiency, nuclear type 1 HP:0000252 OMIM:604273 IEA 1/1 P HPO:skoehler[2010-06-19];HPO:probinson[2022-08-21] -OMIM:618165 Bone marrow failure syndrome 5 HP:0000252 PMID:30146126 PCS 2/2 P HPO:skoehler[2019-04-18];HPO:probinson[2022-12-22] -OMIM:616202 Cerebellofaciodental syndrome HP:0000252 PMID:25561519 PCS 6/6 P HPO:skoehler[2015-02-22];HPO:probinson[2022-05-08] -OMIM:249000 Meckel syndrome 1 HP:0000252 OMIM:249000 IEA P HPO:iea[2009-02-17] -OMIM:202900 Alaninuria with microcephaly, dwarfism, enamel hypoplasia, and diabetes mellitus HP:0000252 OMIM:202900 IEA P HPO:iea[2009-02-17] -OMIM:618596 Epilepsy, idiopathic generalized, susceptibility to, 16 HP:0000252 PMID:29330545 PCS 1/2 P HPO:probinson[2020-07-11];HPO:probinson[2020-07-11] -OMIM:608716 Microcephaly 5, primary, autosomal recessive HP:0000252 PMID:16673149 PCS 6/6 P HPO:probinson[2009-02-17];HPO:probinson[2022-06-23] -OMIM:619648 Zaki syndrome HP:0000252 PMID:34587386 PCS 9/9 P HPO:probinson[2022-02-20] -OMIM:217980 Corpus callosum, agenesis of, with facial anomalies and Robin sequence HP:0000252 OMIM:217980 TAS P HPO:skoehler[2015-12-30] -OMIM:620005 Primordial dwarfism-immunodeficiency-lipodystrophy syndrome HP:0000252 PMID:33060134 PCS 5/5 P HPO:probinson[2022-08-28] -OMIM:138770 Gms syndrome HP:0000252 OMIM:138770 IEA P HPO:iea[2009-02-17] -OMIM:606232 Phelan-Mcdermid syndrome HP:0000252 PMID:20301377 PCS HP:0040284 P HPO:iea[2012-04-24];HPO:probinson[2019-11-28] -OMIM:619475 Developmental delay, impaired speech, and behavioral abnormalities HP:0000252 PMID:34211179 PCS 5/21 P HPO:probinson[2021-10-05] -OMIM:164220 Schilbach-Rott syndrome HP:0000252 OMIM:164220 TAS P HPO:skoehler[2012-10-17] -OMIM:616311 Intellectual developmental disorder, autosomal dominant 33 HP:0000252 PMID:23832105 PCS HP:0003577 6/6 P HPO:skoehler[2015-09-16];HPO:probinson[2020-07-22] -OMIM:608540 Congenital disorder of glycosylation, type Ik HP:0000252 OMIM:608540 IEA P HPO:iea[2009-02-17] -OMIM:241800 Hypothalamic hamartomascongenital hypothalamic hamartoma syndrome, included HP:0000252 PMID:30497210 PCS 1/2 P HPO:probinson[2022-10-24] -OMIM:611890 Congenital arthrogryposis with anterior horn cell disease HP:0000252 OMIM:611890 IEA HP:0040284 P HPO:skoehler[2019-04-18] -OMIM:615599 Neurodevelopmental disorder with feeding difficulties, thin corpus callosum, and foot deformity HP:0000252 PMID:21937992 PCS 2/2 P HPO:skoehler[2014-02-06];HPO:probinson[2022-03-15] -OMIM:619743 Combined oxidative phosphorylation deficiency 55 HP:0000252 PMID:33602924 PCS 2/8 P HPO:probinson[2022-04-19] -OMIM:309800 Microphthalmia, syndromic 1 HP:0000252 OMIM:309800 IEA P HPO:iea[2009-02-17] -OMIM:236795 3-hydroxyisobutyric aciduria HP:0000252 OMIM:236795 IEA P HPO:iea[2009-02-17] -OMIM:309555 Mental retardation with optic atrophy, deafness, and seizures HP:0000252 OMIM:309555 IEA P HPO:iea[2009-02-17] -OMIM:246450 3-Hydroxy-3-Methylglutaryl-Coa lyase deficiency HP:0000252 OMIM:246450 IEA HP:0040284 P HPO:skoehler[2019-04-18] -OMIM:615440 Combined oxidative phosphorylation deficiency 17 HP:0000252 OMIM:615440 TAS HP:0040283 P HPO:skoehler[2013-10-22] -OMIM:188400 Digeorge syndrome HP:0000252 PMID:16208694 PCS 5/78 P HPO:probinson[2022-03-17] -OMIM:619981 Braddock-Carey syndrome 2 HP:0000252 PMID:28150392 PCS 1/1 P HPO:probinson[2022-08-17] -OMIM:619244 Neurodevelopmental disorder with cerebral atrophy and variable facial dysmorphism HP:0000252 PMID:32439809 PCS 6/11 P HPO:probinson[2022-02-27] -OMIM:607906 Congenital disorder of glycosylation, type Ii HP:0000252 PMID:33644825 PCS 2/3 P HPO:probinson[2022-06-15] -OMIM:617660 Vertebral, cardiac, renal, and limb defects syndrome 1 HP:0000252 PMID:28792876 PCS 2/2 P HPO:skoehler[2019-04-18];HPO:probinson[2022-08-23] -OMIM:266265 Congenital disorder of glycosylation, type IIc HP:0000252 OMIM:266265 IEA P HPO:iea[2009-02-17] -OMIM:615352 Muscular dystrophy-dystroglycanopathy (limb-girdle), type C, 14 HP:0000252 PMID:23768512 PCS 2/3 P HPO:skoehler[2013-10-06];HPO:probinson[2022-12-13] -OMIM:614607 Coffin-Siris syndrome 2 HP:0000252 PMID:22426308 PCS 1/3 P HPO:probinson[2022-07-02];HPO:probinson[2022-07-02] -OMIM:614563 Intellectual developmental disorder, autosomal dominant 13 HP:0000252 PMID:21076407 PCS 3/8 P HPO:skoehler[2013-10-06];HPO:probinson[2022-05-30] -OMIM:613078 Nijmegen breakage syndrome-like disorder HP:0000252 PMID:19409520 PCS HP:0003577 1/1 P HPO:probinson[2013-01-09];HPO:probinson[2020-07-21] -OMIM:278250 Wrinkly skin syndrome HP:0000252 OMIM:278250 IEA P HPO:iea[2009-02-17] -OMIM:603467 Fanconi anemia, complementation group F HP:0000252 PMID:31288759;PMID:27714961 PCS 2/4 P HPO:probinson[2021-07-05];HPO:probinson[2020-07-22];HPO:probinson[2020-07-22] -OMIM:615673 Myopathy with extrapyramidal signs HP:0000252 PMID:24336167 PCS 5/15 P HPO:skoehler[2017-07-13];HPO:probinson[2021-10-18] -OMIM:617938 Developmental and epileptic encephalopathy 62 HP:0000252 PMID:29466837 PCS 1/6 P HPO:skoehler[2019-04-18];HPO:probinson[2021-02-18] -OMIM:616541 Short stature, microcephaly, and endocrine dysfunction HP:0000252 PMID:25728776 PCS HP:0003577 5/5 P HPO:skoehler[2015-12-30];HPO:probinson[2020-09-12] -OMIM:107480 Townes-Brocks syndrome 1 HP:0000252 OMIM:107480 IEA P HPO:iea[2009-02-17] -OMIM:610204 Pontocerebellar hypoplasia, type 5 HP:0000252 OMIM:610204 TAS P HPO:skoehler[2009-02-17] -OMIM:612952 Aicardi-Goutieres syndrome 5 HP:0000252 OMIM:612952 TAS HP:0040283 P HPO:skoehler[2017-07-13] -OMIM:608363 Chromosome 22q11.2 duplication syndrome HP:0000252 OMIM:608363 IEA P HPO:skoehler[2010-06-19] -OMIM:615905 Epileptic encephalopathy, early infantile, 25, with amelogenesis imperfecta HP:0000252 OMIM:615905 TAS P HPO:skoehler[2015-12-30] -OMIM:117650 Cerebrocostomandibular syndrome HP:0000252 OMIM:117650 TAS P HPO:probinson[2009-02-17] -OMIM:187395 Teratocarcinoma-Derived growth factor 1 HP:0000252 PMID:12073012 IEA P HPO:probinson[2015-05-08] -OMIM:305000 Dyskeratosis congenita, X-linked HP:0000252 OMIM:305000 TAS P HPO:skoehler[2013-09-30] -OMIM:616920 Heart and brain malformation syndrome HP:0000252 PMID:27018474 PCS 1/2 P HPO:skoehler[2017-07-13];HPO:probinson[2022-08-27] -OMIM:615010 Aicardi-Goutieres syndrome 6 HP:0000252 PMID:23001123 PCS 5/14 P HPO:skoehler[2014-05-04];HPO:probinson[2022-12-10] -OMIM:220120 D-glyceric aciduria HP:0000252 PMID:20949620 PCS 1/3 P HPO:skoehler[2012-10-17];HPO:probinson[2022-09-25] -OMIM:614852 Microcephaly 9, primary, autosomal recessive HP:0000252 PMID:20598275;PMID:22775483 PCS 5/5 P HPO:probinson[2022-10-08];HPO:skoehler[2013-06-12];HPO:probinson[2022-10-08] -OMIM:619055 Mitochondrial complex IV deficiency, nuclear type 12 HP:0000252 PMID:24462369 PCS 1/10 P HPO:probinson[2020-12-06] -OMIM:600252 Lowry-Maclean syndrome HP:0000252 OMIM:600252 IEA P HPO:iea[2009-02-17] -OMIM:611523 Pontocerebellar hypoplasia, type 6 HP:0000252 PMID:17847012 PCS 1/3 P HPO:skoehler[2012-11-20];HPO:probinson[2022-10-21] -OMIM:619025 Combined oxidative phosphorylation deficiency 50 HP:0000252 PMID:31039582 PCS 1/1 P HPO:probinson[2020-11-30] -OMIM:610442 Spondyloepimetaphyseal dysplasia, Genevieve type HP:0000252 OMIM:610442 IEA P HPO:iea[2009-02-17] -OMIM:619487 Aicardi-Goutieres syndrome 9 HP:0000252 PMID:33230297 PCS 3/16 P HP:probinson[2021-10-17] -OMIM:615412 Cortical dysplasia, complex, with other brain malformations 4 HP:0000252 PMID:23603762 PCS 2/3 P HPO:skoehler[2013-10-06];HPO:probinson[2022-09-08] -OMIM:610883 Potocki-Lupski syndrome HP:0000252 PMID:17357070 PCS P HPO:iea[2010-09-09] -OMIM:615597 Congenital disorder of glycosylation, type Ix HP:0000252 PMID:23842455 PCS 1/1 P HPO:skoehler[2014-02-06];HPO:probinson[2022-03-27] -OMIM:243800 Johanson-Blizzard syndrome HP:0000252 OMIM:243800 PCS P HPO:iea[2009-02-17] -OMIM:614959 Epileptic encephalopathy, early infantile, 14 HP:0000252 OMIM:614959 TAS P HPO:skoehler[2012-12-30] -OMIM:619092 Neurodevelopmental disorder with microcephaly, impaired language, epilepsy, and gait abnormalities, autosomal dominant HP:0000252 PMID:32738225 PCS 6/8 P HPO:probinson[2020-12-22] -OMIM:616486 Neurodevelopmental disorder with progressive microcephaly, spasticity, and brain abnormalities HP:0000252 PMID:26005868 PCS 3/3 P HPO:skoehler[2015-12-30];HPO:probinson[2022-08-27] -OMIM:614458 Thiamine metabolism dysfunction syndrome 5 (episodic encephalopathy type) HP:0000252 PMID:22152682 PCS 1/5 P HPO:probinson[2022-08-27] -OMIM:613612 Congenital disorder of glycosylation, type IIi HP:0000252 PMID:23228021 PCS 6/7 P HPO:probinson[2020-08-11] -OMIM:613603 Chromosome 4q32.1-q32.2 triplication syndrome HP:0000252 PMID:19764020 PCS 0/4 P HPO:probinson[2022-11-06] -OMIM:617935 Epilepsy, familial focal, with variable foci 4 HP:0000252 PMID:24157691;PMID:28235671 PCS 1/5 P HPO:skoehler[2019-04-18];HPO:probinson[2022-10-02];HPO:probinson[2022-10-02];HPO:probinson[2022-10-02] -OMIM:300534 Intellectual developmental disorder, X-linked syndromic, Claes-Jensen type HP:0000252 PMID:18697827;PMID:19826449;PMID:31419599;PMID:21575681 PCS 7/20 P HPO:probinson[2012-04-25];HPO:probinson[2021-09-25];HPO:probinson[2022-08-23];HPO:probinson[2022-08-23] -OMIM:210710 Microcephalic osteodysplastic primordial dwarfism, type I HP:0000252 PMID:21474761 PCS 10/10 P HPO:probinson[2009-02-17];HPO:probinson[2022-12-04] -OMIM:616364 White-Sutton syndrome HP:0000252 PMID:26739615;PMID:26942287 PCS 14/29 P HPO:skoehler[2017-07-13];HPO:probinson[2022-04-12];HPO:probinson[2022-04-12] -OMIM:600987 Cleft palate, cardiac defects, and mental retardation HP:0000252 OMIM:600987 IEA P HPO:iea[2009-02-17] -OMIM:615411 Cortical dysplasia, complex, with other brain malformations 3 HP:0000252 OMIM:615411 TAS P HPO:skoehler[2013-10-06] -OMIM:619602 Fetal akinesia, respiratory insufficiency, microcephaly, polymicrogyria, and dysmorphic facies HP:0000252 PMID:31608932 PCS 4/4 P HPO:probinson[2022-02-03] -OMIM:121070 Arthrogryposis, distal, type 2E HP:0000252 OMIM:121070 TAS HP:0012825 P HPO:probinson[2010-06-20] -OMIM:617800 Microcephaly 19, primary, autosomal recessive HP:0000252 PMID:29036432 PCS 2/2 P HPO:nvasilevsky[2019-02-25];HPO:probinson[2022-06-22] -OMIM:248760 Marfanoid habitus with microcephaly and glomerulonephritis HP:0000252 OMIM:248760 IEA P HPO:iea[2009-02-17] -OMIM:614347 Mental retardation, autosomal recessive 28 HP:0000252 OMIM:614347 TAS P HPO:skoehler[2017-07-13] -OMIM:619228 Developmental delay with dysmorphic facies and dental anomalies HP:0000252 PMID:33513338 PCS 7/31 P HPO:probinson[2021-05-14] -OMIM:614576 Congenital disorder of glycosylation, type IIl HP:0000252 PMID:26260076 PCS 7/8 P HPO:skoehler[2014-01-28];HPO:probinson[2020-09-12] -OMIM:212720 Martsolf syndrome 1 HP:0000252 PMID:17515302;PMID:16532399 PCS 3/4 P HPO:probinson[2022-04-22];HPO:skoehler[2009-02-17];HPO:probinson[2021-07-10] -OMIM:300957 Mental retardation, X-linked 12/35 HP:0000252 PMID:32116545 PCS 13/38 P HPO:skoehler[2015-11-15];HPO:probinson[2020-08-02] -OMIM:614701 Cornelia de Lange syndrome 4 HP:0000252 PMID:31334757;PMID:22633399 PCS 4/4 P HPO:probinson[2021-10-19];HPO:skoehler[2012-10-17];HPO:probinson[2021-10-19] -OMIM:612541 Neutropenia, severe congenital, 4, autosomal recessive HP:0000252 PMID:19118303 PCS 2/12 P HPO:skoehler[2010-06-20];HPO:probinson[2022-07-11] -DECIPHER:4 Angelman syndrome (Type 1) HP:0000252 DECIPHER:4 IEA P HPO:skoehler[2013-05-29] -DECIPHER:62 1q21.1 recurrent microdeletion (susceptibility locus for neurodevelopmental disorders) HP:0000252 DECIPHER:62 IEA P HPO:skoehler[2013-05-29] -OMIM:618103 Intellectual developmental disorder, autosomal recessive 64 HP:0000252 PMID:28837161 PCS 4/5 P HPO:skoehler[2019-04-18];HPO:probinson[2022-06-18] -OMIM:610543 Chromosome 16p13.3 deletion syndrome HP:0000252 PMID:16783566;PMID:17855048 PCS P HPO:iea[2012-04-24] -OMIM:257300 Mosaic variegated aneuploidy syndrome 1 HP:0000252 PMID:15475955 PCS 9/9 HP:0012828 P HPO:probinson[2009-02-17];HPO:probinson[2022-11-01] -OMIM:619151 AMED syndrome, digenic HP:0000252 PMID:33355142 PCS 6/7 P HPO:probinson[2021-03-05] -OMIM:303600 Coffin-Lowry syndrome HP:0000252 OMIM:303600 IEA P HPO:iea[2009-02-17] -OMIM:301056 Multiple congenital anomalies-neurodevelopmental syndrome, X-linked HP:0000252 PMID:33523931 PCS 5/10 P HPO:probinson[2021-05-02];HPO:probinson[2021-05-02] -OMIM:252010 Mitochondrial complex I deficiency, nuclear type 1 HP:0000252 PMID:10944442 PCS 1/2 P HPO:skoehler[2019-04-18];HPO:probinson[2021-08-18] -OMIM:308205 IFAP syndrome with or without BRESHECK syndrome HP:0000252 PMID:19361614 PCS 1/13 MALE P HPO:probinson[2012-07-15] -OMIM:235730 Mowat-Wilson syndrome HP:0000252 PMID:17958891;PMID:29300384 PCS 379/480 P HPO:lccarmody[2018-09-27];HPO:lccarmody[2018-09-27];HPO:lccarmody[2018-09-27];HPO:iea[2009-02-17] -OMIM:211910 Camptodactyly syndrome, guadalajara, type I HP:0000252 OMIM:211910 IEA P HPO:iea[2009-02-17] -OMIM:300934 Congenital disorder of glycosylation, type Iy HP:0000252 PMID:26264460 PCS 9/9 P HPO:skoehler[2015-01-04];HPO:probinson[2021-02-25] -OMIM:217990 Corpus callosum, agenesis of HP:0000252 OMIM:217990 IEA P HPO:iea[2009-02-17] -OMIM:615917 Combined oxidative phosphorylation deficiency 20 HP:0000252 OMIM:615917 TAS P HPO:skoehler[2014-08-24] -OMIM:618371 Turnpenny-Fry syndrome HP:0000252 OMIM:618371 IEA P HPO:skoehler[2019-09-07] -OMIM:616579 Intellectual developmental disorder, autosomal dominant 40 HP:0000252 PMID:26340335 PCS 2/5 P HPO:skoehler[2015-11-15];HPO:probinson[2022-06-09] -OMIM:618004 Epileptic encephalopathy, early infantile, 64 HP:0000252 OMIM:618004 IEA HP:0040284 P HPO:skoehler[2019-04-18] -OMIM:312080 Pelizaeus-Merzbacher disease HP:0000252 PMID:29486744 PCS 1/1 P HPO:iea[2009-02-17];HPO:probinson[2022-03-23] -OMIM:614249 Mental retardation, autosomal recessive 18 HP:0000252 PMID:21868677 PCS 0/5 P HPO:probinson[2022-04-04] -OMIM:614739 3-Methylglutaconic aciduria with deafness, encephalopathy, and leigh-like syndrome HP:0000252 OMIM:614739 TAS HP:0040283 P HPO:skoehler[2017-07-13] -OMIM:619418 Infantile-onset multisystem neurologic, endocrine, and pancreatic disease 2 HP:0000252 PMID:30304524 PCS 7/7 P HPO:probinson[2021-08-22] -OMIM:611943 Riddle syndrome HP:0000252 OMIM:611943 TAS HP:0040283 P HPO:skoehler[2014-08-24] -OMIM:252160 Molybdenum cofactor deficiency, complementation group B HP:0000252 PMID:16021469 PCS 1/1 P HPO:skoehler[2014-01-28];HPO:probinson[2022-11-08] -OMIM:617188 Mental retardation, autosomal recessive 57 HP:0000252 PMID:27616480 PCS 3/16 P HPO:skoehler[2017-07-13];HPO:probinson[2022-03-03] -OMIM:617090 Microcephaly 17, primary, autosomal recessive HP:0000252 OMIM:617090 TAS P HPO:skoehler[2017-07-13] -OMIM:612079 Alopecia, neurologic defects, and endocrinopathy syndrome HP:0000252 PMID:18439547 PCS 3/5 P HPO:skoehler[2010-06-19];HPO:probinson[2022-11-12] -OMIM:613398 Warsaw breakage syndrome HP:0000252 OMIM:613398 TAS P HPO:skoehler[2012-10-17] -OMIM:620071 Neurodevelopmental disorder with poor growth, spastic tetraplegia, and hearing loss HP:0000252 PMID:35861243 PCS 3/3 HP:0012827 P HPO:probinson[2022-12-04] -OMIM:618347 Galloway-Mowat syndrome 6 HP:0000252 PMID:28617965;PMID:29597095;PMID:30079490 PCS 7/7 P HPO:probinson[2022-03-11];HPO:skoehler[2019-04-18];HPO:probinson[2022-03-11] -OMIM:530000 Kearns-Sayre syndrome HP:0000252 OMIM:530000 IEA P HPO:iea[2009-02-17] -OMIM:619072 Neurodevelopmental disorder with seizures and brain atrophy HP:0000252 PMID:32103185 PCS 2/8 P HPO:probinson[2021-01-01];HPO:probinson[2021-01-01] -OMIM:260600 Leukodystrophy, hypomyelinating, 3 HP:0000252 OMIM:260600 TAS P HPO:skoehler[2012-10-17] -OMIM:613661 Congenital disorder of glycosylation, type Ip HP:0000252 PMID:20080937 PCS 1/2 P HPO:skoehler[2015-07-26];HPO:probinson[2023-01-26] -OMIM:249630 Mental retardation, buenos Aires type HP:0000252 OMIM:249630 IEA P HPO:iea[2009-02-17] -OMIM:241410 Hypoparathyroidism-retardation-dysmorphism syndrome HP:0000252 OMIM:241410 IEA P HPO:iea[2009-02-17] -OMIM:619595 Developmental delay, hypotonia, musculoskeletal defects, and behavioral abnormalities HP:0000252 PMID:33909990 PCS 1/29 P HPO:probinson[2022-02-04];HPO:probinson[2022-02-04] -OMIM:617903 Neurodevelopmental disorder with poor language and loss of hand skills HP:0000252 OMIM:617903 IEA P HPO:skoehler[2018-10-08] -OMIM:618116 Bone marrow failure syndrome 4 HP:0000252 OMIM:618116 IEA HP:0040284 P HPO:skoehler[2019-04-18] -OMIM:182212 Shprintzen-Goldberg craniosynostosis syndrome HP:0000252 PMID:15884042 PCS 6/37 P HPO:iea[2009-02-17] -OMIM:266920 Short-rib thoracic dysplasia 9 with or without polydactyly HP:0000252 PMID:22503633 PCS 3/11 P HPO:skoehler[2012-11-18];HPO:probinson[2022-05-28] -OMIM:272950 Teebi-Shaltout syndrome HP:0000252 OMIM:272950 TAS HP:0040283 P HPO:skoehler[2017-07-13] -OMIM:245348 Pyruvate dehydrogenase E2 deficiency HP:0000252 OMIM:245348 IEA P HPO:iea[2009-02-17] -OMIM:613823 Seckel syndrome 5 HP:0000252 PMID:21131973 PCS P HPO:probinson[2013-08-10] -OMIM:133750 Extrasystoles, multiform ventricular, with short stature, hyperpigmentationand microcephaly HP:0000252 OMIM:133750 IEA P HPO:iea[2009-02-17] -OMIM:612940 Cutis laxa, autosomal recessive, type IIB HP:0000252 PMID:19576563 PCS 4/4 P HPO:skoehler[2010-06-19];HPO:probinson[2022-08-10] -OMIM:602398 DESMOSTEROLOSIS HP:0000252 PMID:12457401 PCS 1/2 P HPO:iea[2012-04-24] -OMIM:618569 Neurodevelopmental disorder with ataxia, hypotonia, and microcephaly HP:0000252 PMID:31363758 PCS P HPO:probinson[2020-06-14] -OMIM:619356 Onychodystrophy, osteodystrophy, impaired intellectual development, and seizures syndrome HP:0000252 PMID:33386993 PCS 1/2 P HPO:probinson[2021-08-20] -OMIM:615919 Ataxia-Telangiectasia-Like disorder 2 HP:0000252 OMIM:615919 TAS HP:0040283 P HPO:skoehler[2014-08-24] -OMIM:617260 Global developmental delay, absent or hypoplastic corpus callosum, and dysmorphic facies HP:0000252 PMID:27964749 PCS 2/4 P HPO:skoehler[2017-07-13];HPO:probinson[2022-09-26] -OMIM:616603 Cutis laxa, autosomal dominant 3 HP:0000252 OMIM:616603 TAS P HPO:skoehler[2015-11-15] -OMIM:300867 Kabuki syndrome 2 HP:0000252 PMID:23913813 PCS 2/4 P HPO:skoehler[2012-10-16];HP:probinson[2019-01-20] -OMIM:305600 Focal dermal hypoplasia HP:0000252 OMIM:305600 IEA P HPO:iea[2009-02-17] -OMIM:213980 Craniofacial dysmorphism, skeletal anomalies, and mental retardation syndrome HP:0000252 OMIM:213980 TAS HP:0040283 P HPO:skoehler[2014-06-24] -OMIM:212540 Cataract, microcephaly, failure to thrive, kyphoscoliosis syndrome HP:0000252 OMIM:212540 IEA P HPO:iea[2009-02-17] -OMIM:611107 Intellectual developmental disorder, autosomal recessive 4 HP:0000252 OMIM:611107 TAS P HPO:skoehler[2017-07-13] -OMIM:618356 Neurodevelopmental disorder with central and peripheral motor dysfunction HP:0000252 OMIM:618356 IEA HP:0040284 P HPO:skoehler[2019-04-18] -OMIM:609029 Emanuel syndrome HP:0000252 OMIM:609029 IEA P HPO:iea[2009-02-17] -OMIM:608747 Insulin-Like growth factor I deficiency HP:0000252 PMID:8857020 PCS 1/1 P HPO:iea[2009-02-17];HPO:probinson[2022-11-25] -OMIM:300578 Chromosome xp11.3 deletion syndrome HP:0000252 PMID:7977353 PCS P HPO:iea[2009-02-17];HPO:probinson[2022-04-10] -OMIM:616368 CHOPS syndrome HP:0000252 PMID:25730767 PCS 1/3 P HPO:probinson[2022-09-22] -OMIM:619827 Intellectual developmental disorder, autosomal recessive 75, with neuropsychiatric features and variant lissencephaly HP:0000252 PMID:33414379 PCS 1/12 P HPO:probinson[2022-07-17] -OMIM:619934 Intellectual developmental disorder, autosomal dominant 68 HP:0000252 PMID:33150406;PMID:29276005 PCS 7/8 P HPO:probinson[2022-08-20] -OMIM:618890 Neurodevelopmental disorder and structural brain anomalies with or without seizures and spasticity HP:0000252 PMID:29090338 PCS 1/1 P HPO:probinson[2020-08-13];HPO:probinson[2020-08-13] -OMIM:617093 Growth retardation, impaired intellectual development, hypotonia, and hepatopathy HP:0000252 OMIM:617093 TAS P HPO:skoehler[2017-07-13] -OMIM:618379 Developmental and epileptic encephalopathy 73 HP:0000252 PMID:30595371 PCS P HPO:skoehler[2019-04-18];HPO:probinson[2021-02-16] -OMIM:300978 Tonne-Kalscheuer syndrome HP:0000252 OMIM:300978 TAS P HPO:skoehler[2017-07-13] -OMIM:241000 Hypogonadism with low-grade mental deficiency and microcephaly HP:0000252 OMIM:241000 TAS P HPO:probinson[2009-02-17] -OMIM:152950 Microcephaly with or without chorioretinopathy, lymphedema, or mental retardation HP:0000252 OMIM:152950 IEA P HPO:iea[2009-02-17] -OMIM:617493 Neurodevelopmental disorder with involuntary movements HP:0000252 OMIM:617493 IEA HP:0040284 P HPO:skoehler[2018-10-08] -OMIM:611726 Epilepsy, progressive myoclonic 3, with or without intracellular inclusions HP:0000252 PMID:22748208 PCS 2/2 P HPO:skoehler[2012-12-03];HPO:probinson[2021-06-26] -OMIM:208400 Aspartylglucosaminuria HP:0000252 OMIM:208400 IEA P HPO:iea[2009-02-17] -OMIM:257320 Lissencephaly 2 HP:0000252 PMID:10973257 PCS P HPO:iea[2009-02-17];HP:probinson[2019-04-09] -OMIM:617899 Leukodystrophy, hypomyelinating, 14 HP:0000252 OMIM:617899 IEA P HPO:skoehler[2019-04-18] -OMIM:619489 Short stature, Dauber-Argente type HP:0000252 PMID:26902202;PMID:34272725 PCS 7/7 P HPO:probinson[2021-10-04];HPO:probinson[2021-10-04];HPO:probinson[2021-10-04] -OMIM:606220 Intellectual developmental disorder with short stature, facial anomalies, and speech defects HP:0000252 PMID:30481285 PCS 1/6 P HPO:skoehler[2019-09-07];HPO:probinson[2022-09-11] -OMIM:618426 Encephalopathy, acute, infection-induced, susceptibility to, 9 HP:0000252 PMID:30758658 PCS 3/3 P HPO:skoehler[2019-09-07];HPO:probinson[2022-12-20] -OMIM:612947 Microcephaly, growth retardation, cataract, hearing loss, and unusual appearance HP:0000252 OMIM:612947 IEA P HPO:skoehler[2010-06-19] -OMIM:304100 Corpus callosum, partial agenesis of, X-linked HP:0000252 OMIM:304100 IEA P HPO:iea[2009-02-17] -OMIM:619227 Vertebral, cardiac, tracheoesophageal, renal, and limb defects HP:0000252 PMID:33276377 PCS 1/9 P HPO:probinson[2021-05-27];HPO:probinson[2021-05-27] -OMIM:616281 Neurodevelopmental disorder with microcephaly and spastic paraplegia HP:0000252 PMID:27601654;PMID:25758935 PCS 16/17 P HPO:probinson[2022-04-12];HPO:skoehler[2015-09-16];HPO:probinson[2022-04-12] -OMIM:614342 Mental retardation, autosomal recessive 30 HP:0000252 OMIM:614342 TAS P HPO:skoehler[2017-07-13] -OMIM:616756 Spastic paraplegia and psychomotor retardation with or without seizures HP:0000252 OMIM:616756 TAS HP:0040283 P HPO:skoehler[2017-07-13] -OMIM:114100 Basal ganglia calcification, idiopathic, childhood-onset HP:0000252 OMIM:114100 IEA P HPO:iea[2009-02-17] -OMIM:226980 Epiphyseal dysplasia, multiple, with early-onset diabetes mellitus HP:0000252 OMIM:226980 TAS P HPO:probinson[2009-02-17] -OMIM:277400 Methylmalonic aciduria and homocystinuria, Cblc type HP:0000252 OMIM:277400 IEA P HPO:iea[2009-02-17] -OMIM:618266 Pontocerebellar hypoplasia, type 12 HP:0000252 OMIM:618266 IEA P HPO:skoehler[2019-04-18] -OMIM:620038 Neurodevelopmental disorder with microcephaly, hypotonia, and absent language HP:0000252 PMID:32129449 PCS 2/2 P HPO:probinson[2022-10-03] -OMIM:616834 Microcephaly, congenital cataract, and psoriasiform dermatitis HP:0000252 PMID:21285510 PCS 1/1 P HPO:probinson[2017-06-17];HPO:probinson[2022-03-08] -OMIM:227646 Fanconi anemia, complementation group D2 HP:0000252 PMID:17436244 PCS 25/28 P HPO:iea[2009-02-17];HPO:probinson[2020-11-28] -OMIM:617982 Ververi-Brady syndrome HP:0000252 PMID:28692176 PCS 1/3 P HPO:skoehler[2019-04-18];HPO:probinson[2021-06-27] -OMIM:233270 Gombo syndrome HP:0000252 OMIM:233270 IEA P HPO:iea[2009-02-17] -OMIM:618325 Lissencephaly 9 with complex brainstem malformation HP:0000252 PMID:30471716 PCS 2/8 P HPO:skoehler[2019-04-18];HPO:probinson[2022-11-10] -OMIM:618766 Arthrogryposis multiplex congenita, neurogenic, with agenesis of the corpus callosum HP:0000252 PMID:31960134 PCS 4/5 P HPO:probinson[2020-05-11] -OMIM:244450 Kaufman oculocerebrofacial syndrome HP:0000252 PMID:23200864 PCS P HPO:iea[2009-02-17] -OMIM:135900 Coffin-Siris syndrome 1 HP:0000252 OMIM:135900 IEA P HPO:iea[2009-02-17] -OMIM:615330 Multiple mitochondrial dysfunctions syndrome 3 HP:0000252 OMIM:615330 TAS P HPO:skoehler[2013-09-10] -OMIM:618142 Microcephaly, facial dysmorphism, renal agenesis, and ambiguous genitalia syndrome HP:0000252 PMID:26633546 PCS 3/3 P HPO:skoehler[2019-02-15];HPO:probinson[2022-09-28] -OMIM:312170 Pyruvate dehydrogenase e1-alpha deficiency HP:0000252 OMIM:312170 IEA P HPO:iea[2009-02-17] -OMIM:616651 Roifman syndrome HP:0000252 PMID:26522830 PCS 5/6 P HPO:skoehler[2015-12-30] -OMIM:234250 Hall-Riggs mental retardation syndrome HP:0000252 OMIM:234250 IEA P HPO:iea[2009-02-17] -OMIM:257920 3mc syndrome 1 HP:0000252 OMIM:257920 IEA P HPO:iea[2009-02-17] -OMIM:616263 Neurologic, endocrine, and pancreatic disease, multisystem, infantile-onset HP:0000252 OMIM:616263 TAS P HPO:skoehler[2015-04-05] -OMIM:612626 Chromosome 15q26-qter deletion syndrome HP:0000252 OMIM:612626 IEA P HPO:skoehler[2010-06-19] -OMIM:618170 Neurodegeneration, childhood-onset, stress-induced, with variable ataxia and seizures HP:0000252 PMID:30401461 PCS 3/5 P HPO:probinson[2022-03-21] -OMIM:616549 Klippel-Feil syndrome 4, autosomal recessive, with myopathy and facial dysmorphism HP:0000252 PMID:25748484 PCS 2/2 P HPO:skoehler[2015-12-30];HPO:probinson[2020-09-12] -OMIM:606812 Fumarase deficiency HP:0000252 OMIM:606812 IEA P HPO:iea[2009-02-17] -OMIM:616817 Microcephaly, short stature, and impaired glucose metabolism 2 HP:0000252 PMID:26159176 PCS P HPO:probinson[2017-06-17] -OMIM:619218 ENDOVE syndrome, limb-brain type HP:0000252 PMID:33568816 PCS 1/1 P HPO:probinson[2021-05-18] -OMIM:618268 Trichohepatoneurodevelopmental syndrome HP:0000252 OMIM:618268 IEA P HPO:skoehler[2019-02-15] -OMIM:156580 Microcephaly, autosomal dominant HP:0000252 OMIM:156580 TAS P HPO:probinson[2012-05-01] -OMIM:616777 Seckel syndrome 9 HP:0000252 PMID:26595769 PCS 3/3 P HPO:probinson[2016-07-03] -OMIM:617977 Neurodevelopmental disorder with spastic quadriplegia and brain abnormalities with or without seizures HP:0000252 PMID:28503735 PCS 4/12 P HPO:skoehler[2019-04-18];HPO:probinson[2022-10-30];HPO:probinson[2022-10-30] -OMIM:616835 Meier-Gorlin syndrome 6 HP:0000252 OMIM:616835 IEA P HPO:skoehler[2019-04-18] -OMIM:309400 Menkes disease HP:0000252 OMIM:309400 IEA P HPO:iea[2009-02-17] -OMIM:619087 Noonan syndrome 13 HP:0000252 PMID:32721402 PCS 1/7 P HPO:probinson[2020-12-21] -OMIM:608670 Robin sequence, distinctive facial appearance, and brachydactyly HP:0000252 PMID:15057987 PCS 1/2 P HP:probinson[2022-02-09] -OMIM:601811 Premature aging syndrome, Okamoto type HP:0000252 OMIM:601811 IEA P HPO:iea[2009-02-17] -OMIM:616681 Microcephaly 16, primary, autosomal recessive HP:0000252 OMIM:616681 TAS P HPO:skoehler[2015-12-30] -OMIM:617768 Kleefstra syndrome 2 HP:0000252 OMIM:617768 IEA P HPO:skoehler[2019-04-18] -OMIM:100300 Adams-Oliver syndrome 1 HP:0000252 OMIM:100300 IEA P HPO:iea[2009-02-17] -OMIM:617796 Intellectual developmental disorder, autosomal dominant 52 HP:0000252 PMID:28394464 PCS 1/1 P HPO:probinson[2022-06-03] -OMIM:246900 Dihydrolipoamide dehydrogenase deficiency HP:0000252 OMIM:246900 TAS P HPO:skoehler[2013-04-02] -OMIM:616553 Dyskeratosis congenita, autosomal dominant 6 HP:0000252 OMIM:616553 TAS P HPO:skoehler[2015-10-05] -OMIM:271109 Spinal muscular atrophy with mental retardation HP:0000252 OMIM:271109 IEA P HPO:iea[2009-02-17] -OMIM:610377 Mevalonic aciduria HP:0000252 PMID:8352861 PCS 2/3 P HPO:iea[2009-02-17];HPO:probinson[2020-11-01] -OMIM:607326 Smith-Mccort dysplasia 1 HP:0000252 OMIM:607326 IEA P HPO:iea[2009-02-17] -OMIM:609060 Combined oxidative phosphorylation deficiency 1 HP:0000252 PMID:15537906 PCS 1/2 HP:0012825 P HPO:probinson[2012-04-17];HPO:probinson[2021-07-12] -OMIM:611603 Lissencephaly 3 HP:0000252 OMIM:611603 IEA P HPO:iea[2009-02-17] -OMIM:268850 Richieri-Costa/guion-Almeida syndrome HP:0000252 OMIM:268850 TAS P HPO:probinson[2012-05-01] -OMIM:620040 Dyskeratosis congenita, digenic HP:0000252 PMID:35931051 PCS 1/10 P HPO:probinson[2022-10-02] -OMIM:301030 Van Esch-O'Driscoll syndrome HP:0000252 PMID:31006512 PCS 9/9 P HPO:skoehler[2019-09-07];HPO:probinson[2022-08-28] -OMIM:610965 XFE progeroid syndrome HP:0000252 PMID:29105242;PMID:17183314 PCS 2/2 P HPO:probinson[2013-01-09];HPO:probinson[2022-03-15];HPO:probinson[2022-03-15] -OMIM:261630 Hyperphenylalaninemia, bh4-deficient, C HP:0000252 OMIM:261630 IEA P HPO:skoehler[2010-06-18] -OMIM:618792 Epileptic encephalopathy, early infantile, 84 HP:0000252 PMID:32001716 PCS 3/30 P HPO:probinson[2020-05-08] -OMIM:611719 Combined oxidative phosphorylation deficiency 5 HP:0000252 OMIM:611719 TAS P HPO:skoehler[2012-10-17] -OMIM:615190 Dyskeratosis congenita, autosomal recessive 5 HP:0000252 OMIM:615190 TAS P HPO:skoehler[2013-06-05] -OMIM:103050 Adenylosuccinase deficiency HP:0000252 OMIM:103050 PCS HP:0040283 P HPO:probinson[2012-03-12] -OMIM:617303 Mucopolysaccharidosis-Plus syndrome HP:0000252 PMID:27547915 PCS 1/2 P HPO:probinson[2021-02-19] -OMIM:616080 Microcephaly 12, primary, autosomal recessive HP:0000252 OMIM:616080 TAS P HPO:skoehler[2014-11-26] -OMIM:251280 Microcephaly, seizures, spasticity, and brain calcifications HP:0000252 OMIM:251280 IEA P HPO:iea[2009-02-17] -OMIM:311200 Orofaciodigital syndrome I HP:0000252 OMIM:311200 TAS P HPO:skoehler[2012-10-17] -OMIM:606170 Genitopatellar syndrome HP:0000252 OMIM:606170 IEA P HPO:iea[2009-02-17] -OMIM:613477 Epileptic encephalopathy, early infantile, 5 HP:0000252 PMID:20493457 PCS 3/3 P HPO:skoehler[2013-01-21];HPO:probinson[2022-10-24] -OMIM:614205 3-M syndrome 3 HP:0000252 PMID:21737058 PCS 1/3 P HPO:probinson[2021-07-07] -OMIM:619580 Neurodevelopmental disorder with impaired language and ataxia and with or without seizures HP:0000252 PMID:28180184 PCS 1/1 P HPO:probinson[2021-11-10] -OMIM:619272 Mitochondrial complex I deficiency, nuclear type 37 HP:0000252 PMID:32385911 PCS 1/1 P HPO:probinson[2021-06-02] -OMIM:618768 Spastic paraplegia 81, autosomal recessive HP:0000252 PMID:28052917 PCS 2/4 P HPO:probinson[2020-05-07] -OMIM:618891 Microcephaly, developmental delay, and brittle hair syndrome HP:0000252 PMID:30824121 PCS 2/4 P HPO:probinson[2020-08-12] -OMIM:612951 Leukoencephalopathy, cystic, without megalencephaly HP:0000252 PMID:19525954 PCS 2/7 P HPO:probinson[2012-04-11];HPO:probinson[2022-11-06] -OMIM:613457 Chromosome 14q11-q22 deletion syndrome HP:0000252 OMIM:613457 TAS P HPO:skoehler[2012-10-17] -OMIM:620023 Neurodevelopmental disorder with microcephaly, movement abnormalities, and seizures HP:0000252 PMID:35202461 PCS 6/6 P HPO:probinson[2022-10-07] -OMIM:300998 Mental retardation, X-linked, syndromic, 35 HP:0000252 PMID:25316788;PMID:25846674 PCS 5/7 P HPO:probinson[2021-10-02];HPO:probinson[2021-10-02];HPO:probinson[2021-10-02] -OMIM:618276 Neurodegeneration, childhood-onset, with cerebellar atrophy HP:0000252 PMID:30420557 PCS 8/13 P HPO:skoehler[2019-04-18];HPO:probinson[2022-06-25] -OMIM:619556 Intellectual developmental disorder with hypotonia, impaired speech, and dysmorphic facies HP:0000252 PMID:34314705 PCS 5/15 P HPO:probinson[2022-01-23] -OMIM:302000 Bullous dystrophy, hereditary Macular type HP:0000252 OMIM:302000 IEA P HPO:iea[2009-02-17] -OMIM:619420 Martsolf syndrome 2 HP:0000252 PMID:30730599;PMID:23420520 PCS 3/3 P HPO:probinson[2021-08-22] -OMIM:608233 Hermansky-Pudlak syndrome 2 HP:0000252 PMID:8042664 PCS P HPO:iea[2009-02-17];HPO:probinson[2020-11-02] -OMIM:614254 Neurodevelopmental disorder with or without hyperkinetic movements and seizures, autosomal dominant HP:0000252 PMID:25864721 PCS 2/4 P HPO:skoehler[2019-04-18];HPO:probinson[2023-01-17] -OMIM:616570 Cerebrooculofacioskeletal syndrome 3 HP:0000252 PMID:24700531 PCS 5/5 P HPO:skoehler[2015-10-16];HPO:probinson[2022-11-27] -OMIM:615249 Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 12 HP:0000252 OMIM:615249 TAS P HPO:skoehler[2014-07-11] -OMIM:618950 Suleiman-El-Hattab syndrome HP:0000252 PMID:31209944 PCS 4/4 P HPO:probinson[2020-08-26] -OMIM:251260 Nijmegen breakage syndrome HP:0000252 PMID:22373003 PCS HP:0003577 P HPO:iea[2009-02-17];HPO:probinson[2022-10-12] -OMIM:614066 Spastic paraplegia 47, autosomal recessive HP:0000252 OMIM:614066 TAS P HPO:skoehler[2012-10-17] -OMIM:618402 Intellectual developmental disorder, autosomal recessive 70 HP:0000252 PMID:29522154 PCS 1/5 P HPO:probinson[2022-04-10] -OMIM:619877 Dentici-Novelli neurodevelopmental syndrome HP:0000252 PMID:33397746 PCS 5/5 P HPO:probinson[2022-08-13] -OMIM:615948 Orofaciodigital syndrome XIV HP:0000252 OMIM:615948 TAS P HPO:skoehler[2014-10-06] -OMIM:618397 Combined oxidative phosphorylation deficiency 39 HP:0000252 OMIM:618397 IEA HP:0040284 P HPO:skoehler[2019-09-07] -OMIM:618295 Intellectual developmental disorder, autosomal recessive 67 HP:0000252 PMID:33736665 PCS 6/19 P HPO:probinson[2022-08-12] -OMIM:223540 Dwarfism, mental retardation, and eye abnormality HP:0000252 OMIM:223540 TAS P HPO:skoehler[2015-07-26] -OMIM:259775 Raine syndrome HP:0000252 OMIM:259775 TAS P HPO:probinson[2009-02-17] -OMIM:300896 Congenital disorder of glycosylation, type IIm HP:0000252 PMID:23561849 PCS 2/3 P HPO:skoehler[2013-06-04];HPO:probinson[2021-06-15] -OMIM:170390 Andersen cardiodysrhythmic periodic paralysis HP:0000252 OMIM:170390 IEA P HPO:iea[2009-02-17] -OMIM:615583 Verheij syndrome HP:0000252 OMIM:615583 TAS P HPO:skoehler[2014-02-06] -OMIM:278760 Xeroderma pigmentosum, complementation group F HP:0000252 OMIM:278760 TAS HP:0040283 P HPO:skoehler[2013-07-17] -OMIM:612438 Leukodystrophy, hypomyelinating, 6 HP:0000252 OMIM:612438 IEA P HPO:skoehler[2010-06-19] -OMIM:618922 Neurodevelopmental disorder with seizures, hypotonia, and brain imaging abnormalities HP:0000252 PMID:32286009 PCS 8/8 P HPO:probinson[2020-08-31] -OMIM:612716 Dystonia, dopa-responsive, due to sepiapterin reductase deficiency HP:0000252 OMIM:612716 IEA P HPO:skoehler[2010-06-19] -OMIM:615182 Combined d-2- and l-2-hydroxyglutaric aciduria HP:0000252 OMIM:615182 TAS HP:0040283 P HPO:skoehler[2013-05-03] -OMIM:619609 Galloway-Mowat syndrome 10 HP:0000252 PMID:31481669 PCS 3/3 P HPO:probinson[2022-02-01] -OMIM:619179 Microcephaly 26, primary, autosomal dominant HP:0000252 PMID:33033404;PMID:32910914 PCS 13/13 P HPO:probinson[2021-03-14] -OMIM:609625 Chromosome 10Q26 deletion syndrome HP:0000252 OMIM:609625 IEA P HPO:iea[2009-02-17] -OMIM:181180 Say syndrome HP:0000252 OMIM:181180 IEA P HPO:iea[2009-02-17] -OMIM:609180 Congenital disorder of glycosylation, type IF HP:0000252 OMIM:609180 TAS P HPO:skoehler[2015-08-16] -OMIM:616949 Spinocerebellar ataxia, autosomal recessive 23 HP:0000252 OMIM:616949 IEA P HPO:skoehler[2019-04-18] -OMIM:239800 Hypertelorism, microtia, facial clefting syndrome HP:0000252 OMIM:239800 IEA P HPO:iea[2009-02-17] -OMIM:614437 Cutis laxa, autosomal recessive, type IB HP:0000252 OMIM:614437 TAS HP:0040283 P HPO:skoehler[2013-08-18] -OMIM:617432 Intellectual developmental disorder, autosomal recessive 60 HP:0000252 PMID:28257693 PCS 4/4 P HPO:skoehler[2017-07-13];HPO:probinson[2022-08-13] -OMIM:301072 Neurodevelopmental disorder with epilepsy and hemochromatosis HP:0000252 PMID:24259288 PCS 2/3 P HPO:probinson[2022-08-13] -OMIM:614673 Microcephaly 8, primary, autosomal recessive HP:0000252 OMIM:614673 TAS HP:0012828 P HPO:skoehler[2013-06-12] -OMIM:251270 Microcephaly and chorioretinopathy, autosomal recessive, 1 HP:0000252 OMIM:251270 IEA P HPO:iea[2009-02-17] -OMIM:271900 Canavan disease HP:0000252 PMID:34446995 PCS 2/12 P HPO:probinson[2022-04-30] -OMIM:249310 Megalocornea-Mental retardation syndrome HP:0000252 OMIM:249310 TAS P HPO:skoehler[2012-10-17] -OMIM:615596 Congenital disorder of glycosylation, type Iw HP:0000252 PMID:23842455 PCS 2/2 P HPO:skoehler[2014-02-06];HPO:probinson[2022-03-27] -OMIM:309585 Wilson-Turner syndrome HP:0000252 PMID:1746601 PCS 2/14 P HPO:skoehler[2012-12-03];HPO:probinson[2021-09-28] -OMIM:617664 Combined oxidative phosphorylation deficiency 32 HP:0000252 PMID:28777931 PCS 3/6 P HPO:skoehler[2019-04-18];HPO:probinson[2022-10-31] -OMIM:231070 Geroderma osteodysplasticum HP:0000252 PMID:18348262 PCS 3/8 P HPO:skoehler[2015-02-22];HPO:probinson[2022-08-04] -OMIM:618910 Epileptic encephalopathy, early infantile, 86 HP:0000252 PMID:32427860 PCS 1/2 P HPO:probinson[2020-08-13] -OMIM:619512 Neurodevelopmental disorder with hypotonia and brain abnormalities HP:0000252 PMID:34186028 PCS 2/9 P HPO:probinson[2021-10-31] -DECIPHER:66 15q24 recurrent microdeletion syndrome HP:0000252 DECIPHER:66 IEA P HPO:skoehler[2013-05-29] -OMIM:615803 Pontocerebellar hypoplasia, type 10 HP:0000252 OMIM:615803 TAS P HPO:skoehler[2014-06-24] -OMIM:617397 Pseudo-Torch syndrome 2 HP:0000252 PMID:27325888 PCS 1/5 P HPO:skoehler[2017-07-13];HPO:probinson[2022-03-23] -OMIM:263210 Gillessen-Kaesbach-Nishimura syndrome HP:0000252 PMID:25966638 PCS 9/11 P HPO:probinson[2012-05-01];HP:probinson[2019-02-02] -OMIM:248700 Marden-Walker syndrome HP:0000252 OMIM:248700 IEA P HPO:iea[2009-02-17] -OMIM:211750 C syndrome HP:0000252 OMIM:211750 IEA P HPO:iea[2009-02-17] -OMIM:613951 Fanconi anemia, complementation group P HP:0000252 OMIM:613951 TAS HP:0040283 P HPO:skoehler[2012-11-18] -OMIM:216340 Yunis-Varon syndrome HP:0000252 PMID:8411078;PMID:23623387 PCS 13/25 P HPO:probinson[2022-01-22];HPO:iea[2009-02-17];HPO:probinson[2022-01-22] -OMIM:617668 Encephalopathy, neonatal severe, with lactic acidosis and brain abnormalities HP:0000252 PMID:28757203 PCS 1/3 P HPO:skoehler[2019-04-18];HPO:probinson[2022-10-07] -OMIM:213300 Joubert syndrome 1 HP:0000252 PMID:19668216 PCS 1/7 P HPO:probinson[2021-01-30] -OMIM:619278 Microcephaly, epilepsy, and diabetes syndrome 2 HP:0000252 PMID:33164986 PCS 6/6 HP:0012828 P HPO:probinson[2021-05-31] -OMIM:220500 Doors syndrome HP:0000252 PMID:17994565 PCS 7/26 P HPO:skoehler[2012-10-17];HPO:probinson[2020-09-19] -OMIM:617914 Microcephaly 20, primary, autosomal recessive HP:0000252 PMID:29343805 PCS 7/9 P HPO:skoehler[2019-04-18];HPO:probinson[2023-01-26] -OMIM:615286 Neurodevelopmental disorder with brain abnormalities, poor growth, and dysmorphic facies HP:0000252 PMID:23620220 PCS 11/24 P HPO:skoehler[2013-09-10];HPO:probinson[2022-11-26] -OMIM:614498 Rigidity and multifocal seizure syndrome, lethal neonatal HP:0000252 OMIM:614498 TAS P HPO:skoehler[2015-02-22] -OMIM:243310 Baraitser-Winter syndrome 1 HP:0000252 OMIM:243310 IEA P HPO:iea[2009-02-17] -OMIM:619428 Focal segmental glomerulosclerosis and neurodevelopmental syndrome HP:0000252 PMID:27346735 PCS 1/1 P HPO:probinson[2021-10-21] -OMIM:300055 Mental retardation, X-linked, syndromic 13 HP:0000252 PMID:11007980 PCS 2/2 FEMALE P HPO:probinson[2021-09-28] -OMIM:300055 Mental retardation, X-linked, syndromic 13 HP:0000252 PMID:11007980 PCS 0/4 MALE P HPO:probinson[2021-09-28] -OMIM:300055 Mental retardation, X-linked, syndromic 13 HP:0000252 PMID:12615169 PCS 1/1 P HPO:iea[2009-02-17] -OMIM:612313 Glass syndrome HP:0000252 OMIM:612313 TAS P HPO:skoehler[2012-10-17] -OMIM:608013 Gaucher disease, perinatal lethal HP:0000252 OMIM:608013 IEA P HPO:iea[2009-02-17] -OMIM:617798 Intellectual developmental disorder, autosomal dominant 53 HP:0000252 PMID:29100089 PCS 1/14 P HPO:probinson[2022-06-16] -OMIM:608836 Carnitine palmitoyltransferase II deficiency, lethal neonatal HP:0000252 OMIM:608836 IEA P HPO:iea[2009-02-17] -OMIM:611134 Meckel syndrome, type 4 HP:0000252 OMIM:611134 TAS HP:0040283 P HPO:skoehler[2015-04-26] -OMIM:618186 Neuropathy, congenital hypomyelinating, 3 HP:0000252 OMIM:618186 IEA P HPO:skoehler[2019-02-15] -OMIM:615834 Intellectual developmental disorder, autosomal dominant 26 HP:0000252 PMID:23332918;PMID:25205402 PCS 16/22 P HPO:probinson[2022-04-11];HPO:skoehler[2015-09-14];HPO:probinson[2022-04-11] -OMIM:615438 Infantile liver failure syndrome 1 HP:0000252 OMIM:615438 TAS P HPO:skoehler[2015-08-02] -OMIM:617243 Fanconi anemia, complementation group V HP:0000252 PMID:27500492 PCS 1/1 P HPO:skoehler[2017-07-13];HPO:probinson[2022-09-27] -OMIM:270400 Smith-Lemli-Opitz syndrome HP:0000252 PMID:10807690;PMID:30674241 PCS 11/11 P HPO:probinson[2012-04-24];HPO:probinson[2022-08-23] -OMIM:616211 Epileptic encephalopathy, early infantile, 28 HP:0000252 OMIM:616211 TAS HP:0040283 P HPO:skoehler[2015-02-22] -OMIM:147920 Kabuki syndrome 1 HP:0000252 OMIM:147920 IEA P HPO:iea[2009-02-17] -OMIM:615817 Intellectual developmental disorder, autosomal recessive 43 HP:0000252 PMID:34599609 PCS 1/2 P HPO:probinson[2022-03-11] -OMIM:617412 Brachycephaly, trichomegaly, and developmental delay HP:0000252 PMID:28257692 PCS 2/2 P HPO:skoehler[2017-07-13];HPO:probinson[2021-04-25] -OMIM:219200 Cutis laxa, autosomal recessive, type IIA HP:0000252 OMIM:219200 IEA P HPO:skoehler[2010-06-18] -OMIM:615282 Cortical dysplasia, complex, with other brain malformations 2 HP:0000252 PMID:23603762 PCS HP:0003577 1/1 P HPO:skoehler[2013-09-30];HPO:probinson[2021-05-04] -OMIM:618008 Developmental and epileptic encephalopathy 65 HP:0000252 PMID:29534297 PCS 3/4 P HPO:probinson[2021-02-18] -OMIM:617360 Congenital heart defects, dysmorphic facial features, and intellectual developmental disorder HP:0000252 PMID:27479907 PCS 3/7 P HPO:skoehler[2017-07-13];HPO:probinson[2022-09-25] -OMIM:608776 Congenital disorder of glycosylation, type Il HP:0000252 OMIM:608776 IEA P HPO:skoehler[2018-10-08] -OMIM:107500 Aortic arch anomaly with peculiar facies and mental retardation HP:0000252 OMIM:107500 IEA P HPO:iea[2009-02-17] -OMIM:618731 Neurodevelopmental disorder with brain anomalies and with or without vertebral or cardiac anomalies HP:0000252 PMID:31256877 PCS 1/5 P HPO:probinson[2020-05-11] -OMIM:609425 Chromosome 3q29 deletion syndrome HP:0000252 PMID:15918153 PCS P HPO:iea[2010-09-13] -OMIM:306990 Holoprosencephaly with fetal akinesia/hypokinesia sequence HP:0000252 OMIM:306990 IEA P HPO:iea[2009-02-17] -OMIM:618744 Epileptic encephalopathy, early infantile, 83 HP:0000252 PMID:31820119 PCS 12/18 P HPO:probinson[2020-04-13] -OMIM:300558 Mental retardation, X-linked 30 HP:0000252 PMID:17853471;PMID:18523455 PCS 4/7 P HPO:iea[2009-02-17];HPO:probinson[2021-09-25];HPO:probinson[2021-09-25] -OMIM:122470 Cornelia de Lange syndrome 1 HP:0000252 OMIM:122470 TAS P HPO:probinson[2009-02-17] -OMIM:617729 Galloway-Mowat syndrome 3 HP:0000252 OMIM:617729 IEA P HPO:skoehler[2019-04-18] -OMIM:309548 Mental retardation, X-linked, associated with fragile site fraxe HP:0000252 PMID:8651274 PCS 1/4 P HPO:probinson[2021-10-02] -OMIM:602249 Progeroid facial appearance with hand anomalies HP:0000252 OMIM:602249 IEA P HPO:iea[2009-02-17] -OMIM:619059 Mitochondrial complex IV deficiency, nuclear type 15 HP:0000252 PMID:26685157 PCS HP:0003593 1/1 P HPO:probinson[2020-12-06] -OMIM:614608 Coffin-Siris syndrome 3 HP:0000252 PMID:22426308 PCS 2/3 P HPO:probinson[2013-08-10];HPO:probinson[2022-12-11] -OMIM:617062 Okur-Chung neurodevelopmental syndrome HP:0000252 OMIM:617062 TAS P HPO:skoehler[2017-07-13] -OMIM:617182 Language delay and attention deficit-hyperactivity disorder/cognitive impairment with or without cardiac arrhythmia HP:0000252 PMID:27677260 PCS 0/3 P HPO:probinson[2022-10-11] -OMIM:619304 Pontocerebellar hypoplasia, type 1F HP:0000252 PMID:33463720 PCS 1/1 P HPO:probinson[2021-07-06] -OMIM:600325 Aminopterin syndrome sine aminopterin HP:0000252 OMIM:600325 TAS P HPO:skoehler[2012-10-17] -OMIM:615807 Seckel syndrome 8 HP:0000252 OMIM:615807 TAS P HPO:skoehler[2014-06-24] -OMIM:614322 Spinocerebellar ataxia, autosomal recessive 12 HP:0000252 OMIM:614322 TAS P HPO:skoehler[2014-03-24] -OMIM:234050 Trichothiodystrophy 4, nonphotosensitive HP:0000252 OMIM:234050 TAS P HPO:skoehler[2014-10-06] -OMIM:610651 Xeroderma pigmentosum, complementation group B HP:0000252 OMIM:610651 IEA P HPO:iea[2009-02-17] -OMIM:616683 Leukodystrophy, hypomyelinating, 12 HP:0000252 PMID:27120463 PCS P HPO:probinson[2017-06-17] -OMIM:614082 Fanconi anemia, complementation group G HP:0000252 PMID:11093276 PCS 14/22 P HPO:probinson[2013-08-10] -OMIM:611936 Chromosome 3q29 duplication syndrome HP:0000252 PMID:18241066 PCS 4/5 P HPO:iea[2010-09-14] -OMIM:193700 Arthrogryposis, distal, type 2A HP:0000252 OMIM:193700 IEA P HPO:iea[2009-02-17] -OMIM:214800 Charge syndrome HP:0000252 OMIM:214800 IEA P HPO:iea[2009-02-17] -OMIM:123450 Cri-Du-Chat syndrome HP:0000252 ISBN-13:978-0721606156 PCS P HPO:iea[2012-04-24] -OMIM:248910 Cutaneous mastocytosis, conductive hearing loss, and microtia HP:0000252 PMID:19764024 PCS 3/3 P HPO:iea[2009-02-17];HPO:probinson[2020-10-20] -OMIM:218900 Crome syndrome HP:0000252 PMID:14065995 PCS 2/2 P HPO:probinson[2020-02-23] -OMIM:616577 Epilepsy, hearing loss, and mental retardation syndrome HP:0000252 PMID:26299366 PCS 12/13 P HPO:skoehler[2015-11-15];HPO:probinson[2022-03-15] -OMIM:612530 Chromosome 1q41-q42 deletion syndrome HP:0000252 PMID:17873649 PCS 3/7 P HPO:skoehler[2012-10-17];HPO:probinson[2022-05-30] -OMIM:619881 Developmental and epileptic encephalopathy 102 HP:0000252 PMID:34605855 PCS 8/10 P HPO:probinson[2022-08-13];HPO:probinson[2022-08-13] -OMIM:615553 Arthrogryposis, mental retardation, and seizures HP:0000252 PMID:24031089 PCS P HPO:skoehler[2014-01-28];HPO:probinson[2022-03-26] -OMIM:601358 Nicolaides-Baraitser syndrome HP:0000252 PMID:22366787;PMID:22822383 PCS 20/38 P HPO:skoehler[2012-11-18];HPO:probinson[2022-09-28];HPO:probinson[2022-09-28] -OMIM:616739 Mental retardation, autosomal recessive 51 HP:0000252 OMIM:616739 TAS P HPO:skoehler[2017-07-13] -OMIM:605724 Fanconi anemia, complementation group D1 HP:0000252 PMID:15070707 PCS 3/7 P HPO:probinson[2013-03-24] -OMIM:618005 Congenital disorder of glycosylation with defective fucosylation 1 HP:0000252 OMIM:618005 IEA P HPO:skoehler[2019-04-18] -OMIM:617669 Encephalopathy, progressive, early-onset, with brain atrophy and spasticity HP:0000252 OMIM:617669 IEA P HPO:skoehler[2019-04-18] -OMIM:613151 Muscular dystrophy-dystroglycanopathy (congenital with mental retardation), type B, 3 HP:0000252 OMIM:613151 TAS P HPO:skoehler[2012-10-17] -OMIM:619268 Alzahrani-Kuwahara syndrome HP:0000252 PMID:33242396 PCS 7/9 P HPO:probinson[2021-05-31] -OMIM:614947 Combined oxidative phosphorylation deficiency 15 HP:0000252 OMIM:614947 TAS HP:0040283 P HPO:skoehler[2014-07-11] -OMIM:610127 Ceroid lipofuscinosis, neuronal, 10 HP:0000252 PMID:16670177 PCS 3/4 P HPO:iea[2009-02-17];HPO:probinson[2021-10-23] -OMIM:613800 Meier-Gorlin syndrome 2 HP:0000252 PMID:21358632 PCS 2/3 P HPO:skoehler[2012-10-17];HPO:probinson[2022-03-26] -OMIM:619229 Kohlschutter-Tonz syndrome-like HP:0000252 PMID:33513338 PCS 4/25 P HPO:probinson[2021-06-20];HPO:probinson[2021-06-20] -OMIM:200130 Absent eyebrows and eyelashes with mental retardation HP:0000252 OMIM:200130 PCS 2/2 P HPO:probinson[2009-02-17] -OMIM:211369 Brachydactyly, type A2, with microcephaly HP:0000252 OMIM:211369 IEA P HPO:iea[2009-02-17] -OMIM:259770 Osteoporosis-pseudoglioma syndrome HP:0000252 OMIM:259770 IEA P HPO:iea[2009-02-17] -OMIM:614226 Holoprosencephaly 11 HP:0000252 PMID:21802063 PCS P HPO:probinson[2013-03-12] -OMIM:300953 Trichothiodystrophy 5, nonphotosensitive HP:0000252 OMIM:300953 TAS P HPO:skoehler[2015-06-22];HPO:probinson[2023-01-20] -OMIM:619720 Bryant-Li-Bhoj neurodevelopmental syndrome 1 HP:0000252 PMID:33268356 PCS 8/33 P HPO:probinson[2022-05-09] -OMIM:613150 Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 2 HP:0000252 OMIM:613150 TAS P HPO:skoehler[2012-10-17] -OMIM:619876 Neurodevelopmental disorder with microcephaly, hypotonia, nystagmus, and seizures HP:0000252 PMID:35121750 PCS 7/8 P HPO:probinson[2022-07-20] -OMIM:259720 Osteopetrosis, autosomal recessive 5 HP:0000252 PMID:16813530;PMID:23772242 PCS 2/4 P HPO:probinson[2022-07-01];HPO:skoehler[2019-02-22];HPO:probinson[2022-02-19] -OMIM:603736 Ohdo syndrome, Say-Barber-Biesecker-Young-Simpson variant HP:0000252 OMIM:603736 IEA P HPO:skoehler[2018-10-08] -OMIM:250800 Methemoglobinemia due to deficiency of methemoglobin reductase HP:0000252 OMIM:250800 IEA P HPO:iea[2009-02-17] -OMIM:615789 Short stature with microcephaly and distinctive facies HP:0000252 PMID:24389050 TAS 2/2 P HPO:probinson[2015-05-08] -OMIM:616139 Developmental and epileptic encephalopathy 27 HP:0000252 OMIM:616139 IEA HP:0040284 P HPO:skoehler[2019-04-18] -OMIM:616606 Ring chromosome 14 syndrome HP:0000252 OMIM:616606 TAS P HPO:skoehler[2015-11-15] -OMIM:618985 Growth hormone insensitivity with immune dysregulation 2, autosomal dominant HP:0000252 PMID:29844444 PCS 3/9 P HPO:probinson[2020-09-10] -OMIM:617193 Encephalopathy, progressive, early-onset, with brain atrophy and thin corpus callosum HP:0000252 PMID:27666370 PCS 4/7 P HPO:probinson[2021-05-04] -OMIM:616801 Hypotonia, infantile, with psychomotor retardation and characteristic facies 2 HP:0000252 PMID:26708753 PCS 3/6 P HPO:probinson[2017-06-18] -OMIM:270450 Insulin-Like growth factor I, resistance to HP:0000252 OMIM:270450 IEA P HPO:iea[2009-02-17] -OMIM:610474 Camptodactyly, tall stature, and hearing loss syndrome HP:0000252 PMID:17033969 PCS P HPO:iea[2009-02-17];HPO:probinson[2023-01-17] -OMIM:614231 Microcephaly, epilepsy, and diabetes syndrome HP:0000252 OMIM:614231 TAS P HPO:skoehler[2013-01-22] -OMIM:226960 Lowry-Wood syndrome HP:0000252 PMID:29265708;PMID:30368667 PCS 5/5 P HPO:probinson[2009-02-17];HPO:probinson[2020-09-15];HPO:probinson[2020-09-15] -OMIM:619742 Charcot-Marie-Tooth disease, demyelinating, type 1I HP:0000252 PMID:33417887 PCS 1/6 P HPO:probinson[2022-04-19] -OMIM:616353 Dyskeratosis congenita, autosomal recessive 6 HP:0000252 PMID:25893599 PCS 4/4 P HPO:skoehler[2015-05-31];HPO:probinson[2022-09-26] -OMIM:614833 Microcephaly, short stature, and polymicrogyria with or without seizures HP:0000252 PMID:26608784 PCS 6/6 P HPO:skoehler[2012-11-21];HP:probinson[2019-03-02] -OMIM:212065 Congenital disorder of glycosylation, type Ia HP:0000252 OMIM:212065 IEA P HPO:skoehler[2009-02-17] -OMIM:618006 Leukodystrophy, hypomyelinating, 17 HP:0000252 PMID:29215095 PCS 4/4 P HPO:skoehler[2019-04-18];HPO:probinson[2022-10-01] -OMIM:618346 Microcephaly, growth deficiency, seizures, and brain malformations HP:0000252 PMID:26416026 PCS 2/2 P HPO:skoehler[2019-04-18];HPO:probinson[2022-04-08] -OMIM:245450 LACTIC ACIDURIA DUE TO D-LACTIC ACID HP:0000252 OMIM:245450 IEA P HPO:iea[2009-02-17] -OMIM:122900 Craniofacial dysostosis with diaphyseal hyperplasia HP:0000252 OMIM:122900 TAS P HPO:skoehler[2015-07-26] -OMIM:239710 Acrofrontofacionasal dysostosis 2 HP:0000252 OMIM:239710 TAS P HPO:probinson[2012-05-01] -DECIPHER:54 Angelman syndrome (Type 2) HP:0000252 DECIPHER:54 IEA P HPO:skoehler[2013-05-29] -OMIM:302950 Chondrodysplasia punctata 1, X-linked recessive HP:0000252 OMIM:302950 IEA P HPO:iea[2009-02-17] -OMIM:617575 Nephrotic syndrome, type 14 HP:0000252 OMIM:617575 IEA P HPO:skoehler[2019-04-18] -OMIM:301041 Wieacker-Wolff syndrome, female-restricted HP:0000252 PMID:31206972 PCS P HPO:probinson[2020-07-25] -OMIM:618354 Neurodevelopmental disorder and language delay with or without structural brain abnormalities HP:0000252 OMIM:618354 IEA HP:0040284 P HPO:skoehler[2019-04-18] -OMIM:616954 You-Hoover-Fong syndrome HP:0000252 OMIM:616954 TAS P HPO:skoehler[2017-07-13] -OMIM:613990 Dyskeratosis congenita, autosomal dominant 3 HP:0000252 OMIM:613990 TAS P HPO:skoehler[2012-10-17] -OMIM:606612 MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY (CONGENITAL WITH OR WITHOUTMENTAL RETARDATION), TYPE B, 5 HP:0000252 OMIM:606612 IEA P HPO:iea[2009-02-17] -OMIM:619273 Cimdag syndrome HP:0000252 PMID:33186545 PCS 6/6 P HPO:probinson[2021-06-19] -OMIM:616339 Epileptic encephalopathy, early infantile, 29 HP:0000252 PMID:25817015 PCS 3/3 P HPO:skoehler[2015-06-22];HPO:probinson[2022-03-24] -OMIM:619157 Neurodevelopmental disorder with or without early-onset generalized epilepsy HP:0000252 PMID:30269351 PCS 3/24 P HPO:probinson[2021-03-06] -OMIM:618056 Neurodevelopmental disorder with cerebellar atrophy and with or without seizures HP:0000252 OMIM:618056 IEA P HPO:skoehler[2018-10-08] -OMIM:614462 Hyperglycinemia, lactic acidosis, and seizures HP:0000252 OMIM:614462 TAS P HPO:skoehler[2012-10-17] -OMIM:278700 Xeroderma pigmentosum, complementation group A HP:0000252 OMIM:278700 IEA P HPO:iea[2009-02-17] -OMIM:619950 Tessadori-van Haaften neurodevelopmental syndrome 3 HP:0000252 PMID:35202563 PCS 1/17 P HPO:probinson[2022-08-21] -OMIM:309541 Methylmalonic acidemia and homocysteinemia, Cblx type HP:0000252 OMIM:309541 TAS P HPO:skoehler[2013-11-18] -OMIM:616716 Rhizomelic chondrodysplasia punctata, type 5 HP:0000252 PMID:26220973 PCS 4/4 P HPO:skoehler[2015-12-30];HPO:probinson[2021-07-05] -DECIPHER:21 Miller-Dieker syndrome (MDS) HP:0000252 DECIPHER:21 IEA P HPO:skoehler[2013-05-29] -OMIM:618143 Glycosylphosphatidylinositol biosynthesis defect 18 HP:0000252 PMID:33410539;PMID:30269814 PCS 8/10 P HPO:lccarmody[2018-12-18];HPO:lccarmody[2018-12-18];HPO:probinson[2021-06-27] -OMIM:154400 Acrofacial dysostosis 1, Nager type HP:0000252 OMIM:154400 IEA P HPO:iea[2009-02-17] -OMIM:620001 Neurodevelopmental disorder with spasticity, seizures, and brain abnormalities HP:0000252 PMID:34385670 PCS 5/6 P HPO:probinson[2022-08-28] -OMIM:614609 Coffin-Siris syndrome 4 HP:0000252 OMIM:614609 TAS 4/5 P HPO:probinson[2013-08-10] -OMIM:619012 Combined oxidative phosphorylation deficiency 48 HP:0000252 PMID:27356879 PCS 1/1 P HPO:probinson[2022-03-04] -OMIM:613355 Chromosome 17q23.1-q23.2 deletion syndrome HP:0000252 OMIM:613355 IEA P HPO:skoehler[2010-06-19] -OMIM:619880 Neurodevelopmental disorder with poor growth and skeletal anomalies HP:0000252 PMID:34244665 PCS 12/19 P HPO:probinson[2022-08-14] -OMIM:617784 Fanconi anemia, complementation group W HP:0000252 PMID:28691929 PCS 1/1 P HPO:probinson[2018-04-13] -OMIM:613161 Beta-ureidopropionase deficiency HP:0000252 OMIM:613161 TAS P HPO:skoehler[2010-06-20];HPO:probinson[2022-11-28] -OMIM:619243 Global developmental delay with speech and behavioral abnormalities HP:0000252 PMID:32152250 PCS 3/17 P HPO:probinson[2021-05-11] -OMIM:615683 Spastic paraplegia 64, autosomal recessive HP:0000252 PMID:24482476 PCS 2/4 P HPO:probinson[2015-05-10] -OMIM:615777 Desbuquois dysplasia 2 HP:0000252 OMIM:615777 IEA P HPO:skoehler[2019-04-18] -OMIM:618798 Beck-Fahrner syndrome HP:0000252 PMID:31928709 PCS 1/11 P HPO:probinson[2020-05-18] -DECIPHER:52 9q subtelomeric deletion syndrome HP:0000252 DECIPHER:52 IEA P HPO:skoehler[2013-05-29] -OMIM:601808 Chromosome 18Q deletion syndrome HP:0000252 OMIM:601808 IEA P HPO:iea[2009-02-17] -OMIM:300855 Ogden syndrome HP:0000252 OMIM:300855 TAS P HPO:skoehler[2015-12-30] -OMIM:601675 Trichothiodystrophy 1, photosensitive HP:0000252 PMID:9758621 PCS P HPO:iea[2009-02-17];HPO:probinson[2022-03-26] -OMIM:616657 Spastic tetraplegia, thin corpus callosum, and progressive microcephaly HP:0000252 PMID:25930971 PCS 1/2 P HPO:skoehler[2015-12-30];HPO:probinson[2022-09-25] -OMIM:616977 Intellectual developmental disorder, autosomal dominant 43 HP:0000252 PMID:26153216 PCS 1/3 P HPO:skoehler[2017-07-13];HPO:probinson[2022-06-09] -OMIM:278780 Xeroderma pigmentosum, complementation group G HP:0000252 PMID:23255472;PMID:11228268 PCS 1/3 P HPO:skoehler[2015-11-15];HPO:probinson[2022-03-15];HPO:probinson[2022-03-15] -OMIM:615485 Bainbridge-Ropers syndrome HP:0000252 PMID:26647312;PMID:24044690;PMID:23383720 PCS 3/8 P HPO:skoehler[2018-10-08];HPO:probinson[2021-10-03];HPO:probinson[2021-10-03] -OMIM:301044 Developmental and epileptic encephalopathy 85, with or without midline brain defects HP:0000252 PMID:26358754;PMID:23863341 PCS 2/2 P HPO:probinson[2021-01-24] -OMIM:227645 Fanconi anemia, complementation group C HP:0000252 OMIM:227645 IEA P HPO:iea[2009-02-17] -OMIM:178110 Contractures, pterygia, and spondylocarpostarsal fusion syndrome 1A HP:0000252 OMIM:178110 IEA HP:0040284 P HPO:skoehler[2019-09-07] -OMIM:619641 Hengel-Maroofian-Schols syndrome HP:0000252 PMID:34022130 PCS 11/13 P HPO:probinson[2022-02-12] -OMIM:300114 Raynaud-Claes syndrome HP:0000252 PMID:23647072 PCS 1/1 P HPO:probinson[2022-11-25] -OMIM:618730 Neurodevelopmental disorder with microcephaly, cortical malformations, and spasticity HP:0000252 PMID:31586943;PMID:31735293 PCS 19/21 P HPO:probinson[2020-04-29] -OMIM:614207 Hyperphosphatasia with mental retardation syndrome 3 HP:0000252 OMIM:614207 TAS HP:0040283 P HPO:skoehler[2013-06-04] -OMIM:613026 Chromosome 19q13.11 deletion syndrome, distal HP:0000252 PMID:19126570 PCS 3/3 P HPO:skoehler[2010-06-19];HPO:probinson[2021-07-06] -OMIM:618500 Holoprosencephaly 12 with or without pancreatic agenesis HP:0000252 OMIM:618500 IEA P HPO:skoehler[2019-09-07] -OMIM:113477 Brachymorphism-Onychodysplasia-Dysphalangism syndrome HP:0000252 OMIM:113477 IEA P HPO:iea[2009-02-17] -OMIM:300590 Cornelia de Lange syndrome 2 HP:0000252 PMID:20358602 PCS P HPO:probinson[2013-02-17] -OMIM:619123 Cardiofacioneurodevelopmental syndrome HP:0000252 PMID:32307552 PCS 2/2 P HPO:probinson[2021-02-14] -OMIM:617164 Short stature, rhizomelic, with microcephaly, micrognathia, and developmental delay HP:0000252 PMID:27476655 PCS 3/4 P HPO:skoehler[2017-07-13];HPO:probinson[2022-11-06] -OMIM:236100 Holoprosencephaly 1 HP:0000252 OMIM:236100 TAS P HPO:skoehler[2017-07-13] -OMIM:615284 Charcot-Marie-Tooth disease, type 4B3 HP:0000252 OMIM:615284 TAS P HPO:skoehler[2015-02-22] -OMIM:617604 Microcephaly, short stature, and limb abnormalities HP:0000252 OMIM:617604 IEA P HPO:skoehler[2019-04-18] -OMIM:619343 Chromosome 1p36 deletion syndrome, proximal HP:0000252 PMID:17850629 PCS 4/5 P HPO:probinson[2022-02-20] -OMIM:618367 Neurodevelopmental disorder with microcephaly, epilepsy, and hypomyelination HP:0000252 OMIM:618367 IEA P HPO:skoehler[2019-04-18] -OMIM:619895 Holoprosencephaly 14 HP:0000252 PMID:33820834 PCS 1/4 P HPO:probinson[2022-06-26] -OMIM:616342 Lissencephaly 7 with cerebellar hypoplasia HP:0000252 PMID:25560765 PCS P HPO:skoehler[2015-07-26];HPO:probinson[2022-09-23] -OMIM:147791 Jacobsen syndrome HP:0000252 OMIM:147791 IEA P HPO:iea[2009-02-17] -OMIM:243605 Stromme syndrome HP:0000252 OMIM:243605 IEA P HPO:skoehler[2019-04-18] -OMIM:251880 Mitochondrial DNA depletion syndrome 3 (hepatocerebral type) HP:0000252 OMIM:251880 IEA P HPO:iea[2009-02-17] -OMIM:278800 De Sanctis-Cacchione syndrome HP:0000252 PMID:1372469 PCS 2/2 P HPO:iea[2009-02-17];HPO:probinson[2022-04-10] -OMIM:612390 Pontocerebellar hypoplasia, type 2C HP:0000252 PMID:18711368 PCS P HPO:probinson[2013-04-14] -OMIM:255995 Myopathy, congenital, bailey-bloch HP:0000252 OMIM:255995 IEA P HPO:skoehler[2019-02-22] -OMIM:616420 Leukodystrophy, hypomyelinating, 10 HP:0000252 OMIM:616420 TAS P HPO:skoehler[2015-07-05] -OMIM:619234 Short stature, oligodontia, dysmorphic facies, and motor delay HP:0000252 PMID:31089205 PCS 1/3 P HPO:probinson[2021-05-30] -DECIPHER:2 Cri du Chat Syndrome (5p deletion) HP:0000252 DECIPHER:2 IEA P HPO:skoehler[2013-05-29] -OMIM:619841 Chilton-Okur-Chung neurodevelopmental syndrome HP:0000252 PMID:32031333 PCS 1/12 P HPO:probinson[2022-06-25] -OMIM:300958 Intellectual developmental disorder, X-linked, syndrome, snijders Blok type HP:0000252 PMID:26235985 PCS 12/38 FEMALE P HPO:skoehler[2015-10-05];HPO:probinson[2020-09-02] -OMIM:300958 Intellectual developmental disorder, X-linked, syndrome, snijders Blok type HP:0000252 PMID:26235985 PCS 2/5 MALE P HPO:probinson[2020-09-02] -OMIM:619814 Developmental and epileptic encephalopathy 101 HP:0000252 PMID:27164704 PCS 1/3 P HPO:probinson[2022-05-14] -OMIM:616602 Craniosynostosis 6 HP:0000252 OMIM:616602 TAS HP:0040283 P HPO:skoehler[2015-11-29] -OMIM:245552 Lambotte syndrome HP:0000252 OMIM:245552 IEA P HPO:iea[2009-02-17] -OMIM:618383 Intellectual developmental disorder, autosomal recessive 69 HP:0000252 PMID:29893856 PCS 5/9 P HPO:skoehler[2019-04-18];HPO:probinson[2022-12-14] -OMIM:615465 Hartsfield syndrome HP:0000252 OMIM:615465 TAS P HPO:skoehler[2013-10-22] -OMIM:618179 Microcephaly 24, primary, autosomal recessive HP:0000252 OMIM:618179 IEA P HPO:skoehler[2019-04-18] -OMIM:615846 Aicardi-Goutieres syndrome 7 HP:0000252 PMID:24686847 PCS 2/5 P HPO:skoehler[2014-06-24];HPO:probinson[2022-05-26] -OMIM:148820 Waardenburg syndrome, type 3 HP:0000252 OMIM:148820 IEA P HPO:iea[2009-02-17] -OMIM:619103 Neurodevelopmental disorder wtih dysmorphic facies, sleep disturbance, and brain abnormalities HP:0000252 PMID:32822602 PCS 2/3 P HPO:probinson[2021-02-14] -OMIM:300997 Mental retardation, X-linked 106 HP:0000252 PMID:28584052;PMID:28302723 PCS 2/5 P HPO:probinson[2021-09-28];HPO:skoehler[2019-04-18];HPO:probinson[2021-09-28] -OMIM:614063 N-ACETYLASPARTATE DEFICIENCY HP:0000252 OMIM:614063 TAS P HPO:probinson[2013-08-10] -OMIM:617941 Shwachman-Diamond syndrome 2 HP:0000252 PMID:28331068 PCS 4/6 P HPO:skoehler[2019-04-18];HPO:probinson[2022-06-15] -OMIM:252650 Mucolipidosis IV HP:0000252 OMIM:252650 IEA P HPO:iea[2009-02-17] -OMIM:619255 Baralle-Macken syndrome HP:0000252 PMID:33632302 PCS 5/6 P HPO:probinson[2021-06-20] -OMIM:616586 Spastic paraplegia 9B, autosomal recessive HP:0000252 PMID:26026163 PCS 4/6 P HPO:skoehler[2015-11-15];HPO:probinson[2022-12-13] -OMIM:300004 Corpus callosum, agenesis of, with abnormal genitalia HP:0000252 OMIM:300004 TAS P HPO:skoehler[2010-06-18] -OMIM:609069 Pancreatic and cerebellar agenesis HP:0000252 OMIM:609069 TAS P HPO:skoehler[2014-08-24] -OMIM:271110 Spinal muscular atrophy with microcephaly and mental subnormality HP:0000252 OMIM:271110 IEA P HPO:iea[2009-02-17] -OMIM:607596 Pontocerebellar hypoplasia type 1A HP:0000252 PMID:19646678 PCS 2/2 P HPO:probinson[2022-05-14] -OMIM:218650 Craniosynostosis-Mental retardation-clefting syndrome HP:0000252 OMIM:218650 IEA P HPO:iea[2009-02-17] -OMIM:300434 Stocco dos santos X-linked mental retardation syndrome HP:0000252 OMIM:300434 TAS P HPO:skoehler[2017-07-13] -OMIM:618702 Short stature and microcephaly with genital anomalies HP:0000252 PMID:29228025 IEA 2/2 P HPO:probinson[2020-07-21] -OMIM:615760 Microcephaly, progressive, with seizures and cerebral and cerebellar atrophy HP:0000252 OMIM:615760 TAS P HPO:skoehler[2014-10-06] -OMIM:617255 Lissencephaly 8 HP:0000252 PMID:27773428 PCS 2/7 P HPO:skoehler[2017-07-13];HPO:probinson[2022-10-01] -OMIM:617244 Fanconi anemia, complementation group R HP:0000252 OMIM:617244 TAS P HPO:skoehler[2017-07-13] -OMIM:613680 Beaulieu-Boycott-Innes syndrome HP:0000252 PMID:23621916 PCS 4/4 P HPO:skoehler[2012-10-17];HPO:probinson[2022-09-08] -OMIM:618808 Intellectual developmental disorder with poor growth and with or without seizures or ataxia HP:0000252 PMID:29302074 PCS 1/3 P HPO:probinson[2020-05-12] -OMIM:614023 Phosphoserine phosphatase deficiency HP:0000252 OMIM:614023 TAS HP:0040283 P HPO:skoehler[2015-04-19] -OMIM:300260 Mental retardation, x-linked syndromic, Lubs type HP:0000252 PMID:17172942 PCS 1/7 P HPO:iea[2009-02-17];HPO:probinson[2021-05-10] -OMIM:605376 Heterotaxy, visceral, 2, autosomal HP:0000252 PMID:11062482 PCS 1/3 P HPO:probinson[2022-10-07] -OMIM:215100 Rhizomelic chondrodysplasia punctata, type 1 HP:0000252 OMIM:215100 IEA P HPO:iea[2009-02-17] -OMIM:303350 MASA syndrome HP:0000252 OMIM:303350 IEA P HPO:iea[2009-02-17] -OMIM:112370 Brachmann-De lange-like facial changes with microcephaly, metatarsusadductus, and developmental delay HP:0000252 OMIM:112370 IEA P HPO:iea[2009-02-17] -OMIM:619989 Neurodevelopmental disorder with speech delay and variable ocular anomalies HP:0000252 PMID:35196516 PCS 4/10 P HPO:probinson[2022-08-28] -OMIM:600384 Aphalangia, partial, with syndactyly and duplication of metatarsaliv HP:0000252 OMIM:600384 IEA P HPO:iea[2009-02-17] -OMIM:618468 Epileptic encephalopathy, early infantile, 76 HP:0000252 PMID:31031012 PCS 6/11 P HPO:probinson[2020-05-15];HPO:probinson[2020-05-15] -OMIM:618606 Pontocerebellar hypoplasia, type 13 HP:0000252 PMID:30624672;PMID:31207318 PCS 11/11 P HPO:probinson[2020-07-15];HPO:probinson[2020-07-15];HPO:probinson[2020-07-15] -OMIM:618709 Neurodevelopmental disorder with nonspecific brain abnormalities and with or without seizures HP:0000252 PMID:31353024 PCS 2/15 P HPO:probinson[2020-07-07] -OMIM:236250 Homocystinuria due to deficiency of n(5,10)-methylenetetrahydrofolatereductase activity HP:0000252 OMIM:236250 IEA P HPO:iea[2009-02-17] -OMIM:609460 Goldberg-Shprintzen syndrome HP:0000252 OMIM:609460 IEA P HPO:iea[2009-02-17] -OMIM:619714 Congenital disorder of glycosylation, type Iw, autosomal dominant HP:0000252 PMID:34653363 PCS 1/16 P HPO:probinson[2022-03-18] -OMIM:619188 Intellectual developmental disorder, autosomal dominant 64 HP:0000252 PMID:31723249 PCS 4/28 P HPO:probinson[2021-04-27] -OMIM:254940 Carey-Fineman-Ziter syndrome HP:0000252 OMIM:254940 TAS P HPO:skoehler[2017-07-13] -OMIM:617364 Congenital heart defects and ectodermal dysplasia HP:0000252 PMID:27479907 PCS 2/3 P HPO:skoehler[2017-07-13];HPO:probinson[2022-12-18] -OMIM:618506 Coffin-Siris syndrome 10 HP:0000252 OMIM:618506 IEA P HPO:skoehler[2019-09-07] -OMIM:614388 Encephalopathy due to defective mitochondrial and peroxisomal fission 1 HP:0000252 PMID:17460227 PCS 1/1 P HPO:skoehler[2012-10-17];HPO:probinson[2022-08-07] -OMIM:601420 Microcephaly, corpus callosum dysgenesis, and cleft lip/palate HP:0000252 OMIM:601420 IEA P HPO:iea[2009-02-17] -OMIM:620012 Developmental delay, hypotonia, and impaired language HP:0000252 PMID:35395208 PCS 2/35 P HPO:probinson[2022-09-04] -OMIM:618443 Neurodevelopmental disorder with or without variable brain abnormalities HP:0000252 PMID:30612693 PCS 3/13 P HPO:skoehler[2019-09-07];HPO:probinson[2022-09-30] -OMIM:618302 Intellectual developmental disorder, autosomal recessive 68 HP:0000252 PMID:30289604 PCS HP:0003577 3/4 P HPO:skoehler[2019-04-18];HPO:probinson[2022-03-11] -OMIM:614457 Ichthyosis, spastic quadriplegia, and mental retardation HP:0000252 OMIM:614457 TAS HP:0040283 P HPO:skoehler[2012-11-18] -OMIM:619091 Neurodevelopmental disorder with microcephaly, impaired language, and gait abnormalities, autosomal recessive HP:0000252 PMID:32738225 PCS 24/24 P HPO:probinson[2020-12-22] -OMIM:612337 Intellectual developmental disorder, autosomal dominant 22 HP:0000252 PMID:24193349 PCS 1/1 P HPO:skoehler[2012-10-17];HPO:probinson[2022-06-11] -OMIM:618089 Intellectual developmental disorder with dysmorphic facies and behavioral abnormalities HP:0000252 PMID:30057029 PCS 5/20 P HPO:skoehler[2018-10-08];HPO:probinson[2022-11-09] -OMIM:610031 Cortical dysplasia, complex, with other brain malformations 7 HP:0000252 OMIM:610031 IEA P HPO:skoehler[2010-06-18] -OMIM:613155 Muscular dystrophy-dystroglycanopathy (congenital with impaired intellectual development), type B, 1 HP:0000252 PMID:16575835 PCS 5/5 P HPO:skoehler[2012-10-17];HPO:probinson[2022-11-04] -OMIM:620066 Neurodevelopmental disorder with microcephaly, cerebral atrophy, and visual impairment HP:0000252 PMID:35858628 PCS 5/5 P HPO:probinson[2022-10-02] -OMIM:619150 Intellectual developmental disorder with paroxysmal dyskinesia or seizures HP:0000252 PMID:32196122 PCS 1/2 P HPO:probinson[2021-03-05] -OMIM:617695 Pontocerebellar hypoplasia, type 11 HP:0000252 OMIM:617695 IEA P HPO:skoehler[2019-04-18] -OMIM:617276 Developmental and epileptic encephalopathy 48 HP:0000252 PMID:27889060 PCS 9/12 P HPO:skoehler[2017-07-13];HPO:probinson[2021-02-13] -OMIM:610006 2-Methylbutyryl-Coa dehydrogenase deficiency HP:0000252 OMIM:610006 IEA P HPO:iea[2009-02-17] -OMIM:617827 Immunodeficiency 55 HP:0000252 PMID:28414293 PCS 2/5 P HPO:skoehler[2019-04-18];HPO:probinson[2022-09-25] -OMIM:617013 Hypermanganesemia with dystonia 2 HP:0000252 PMID:27231142 PCS 1/9 P HP:probinson[2022-02-27] -OMIM:610832 Fanconi anemia, complementation group N HP:0000252 OMIM:610832 TAS P HPO:probinson[2013-04-01] -OMIM:251220 MICROCEPHALY-CARDIOMYOPATHY HP:0000252 OMIM:251220 IEA P HPO:iea[2009-02-17] -OMIM:616362 Mental retardation, autosomal dominant 36 HP:0000252 PMID:26168268 PCS 2/5 P HPO:skoehler[2015-11-15];HPO:probinson[2022-04-12] -OMIM:309801 Linear skin defects with multiple congenital anomalies 1 HP:0000252 PMID:16059943 PCS 1/8 P HPO:iea[2009-02-17];HPO:probinson[2022-06-25] -OMIM:619606 Developmental and epileptic encephalopathy 99 HP:0000252 PMID:33880529 PCS 8/16 P HPO:probinson[2022-02-26] -OMIM:614946 Combined oxidative phosphorylation deficiency 14 HP:0000252 PMID:22833457 PCS 2/2 P HPO:skoehler[2012-12-30];HPO:probinson[2022-11-11] -OMIM:601352 Mental retardation, microcephaly, epilepsy, and coarse face HP:0000252 OMIM:601352 IEA P HPO:iea[2009-02-17] -OMIM:619851 Leukodystrophy, hypomyelinating, 24 HP:0000252 PMID:34403372 PCS 1/1 P HPO:probinson[2022-06-12] -OMIM:617247 FANCONI ANEMIA, COMPLEMENTATION GROUP U HP:0000252 PMID:22232082 PCS 1/1 P HPO:skoehler[2017-07-13];HPO:probinson[2022-03-15] -OMIM:261640 Hyperphenylalaninemia, BH4-deficient, A HP:0000252 OMIM:261640 IEA P HPO:skoehler[2010-06-18] -OMIM:619090 Developmental delay, impaired growth, dysmorphic facies, and axonal neuropathy HP:0000252 PMID:32693025 PCS 15/20 P HPO:probinson[2021-03-08] -OMIM:611093 Intellectual developmental disorder, autosomal recessive 7 HP:0000252 PMID:18452889 PCS 0/7 P HPO:probinson[2022-06-14] -OMIM:618653 Intellectual developmental disorder with impaired language and dysmorphic facies HP:0000252 PMID:31422817 PCS 2/4 P HPO:probinson[2020-07-17] -OMIM:615031 Spastic paraplegia 49, autosomal recessive HP:0000252 OMIM:615031 TAS P HPO:skoehler[2013-03-08] -OMIM:619076 Neurodevelopmental disorder with microcephaly, seizures, and brain atrophy HP:0000252 PMID:32103185 PCS 3/3 P HPO:probinson[2020-12-13] -OMIM:601349 Microphthalmia, syndromic 8 HP:0000252 OMIM:601349 IEA P HPO:skoehler[2010-06-20] -OMIM:300868 Multiple congenital anomalies-hypotonia-seizures syndrome 2 HP:0000252 OMIM:300868 TAS HP:0040283 P HPO:skoehler[2014-06-24] -OMIM:619616 Neurodevelopmental disorder with hearing loss and spasticity HP:0000252 PMID:34626583 PCS 13/25 P HPO:probinson[2022-01-29] -OMIM:216100 Cleft lip/palate with abnormal thumbs and microcephaly HP:0000252 OMIM:216100 IEA P HPO:iea[2009-02-17] -OMIM:612946 Hadziselimovic syndrome HP:0000252 OMIM:612946 IEA P HPO:skoehler[2010-06-19] -OMIM:610954 Pitt-Hopkins syndrome HP:0000252 PMID:17436255 PCS 4/6 P HPO:skoehler[2010-06-19];HPO:probinson[2022-09-11] -OMIM:619980 Braddock-Carey syndrome 1 HP:0000252 PMID:27549381 PCS 2/2 P HPO:probinson[2022-08-17] -OMIM:225790 Proliferative vasculopathy and hydranencephaly-hydrocephaly syndrome HP:0000252 OMIM:225790 IEA P HPO:skoehler[2019-04-18] -OMIM:615414 Microcephaly 11, primary, autosomal recessive HP:0000252 OMIM:615414 TAS P HPO:skoehler[2013-09-30] -OMIM:613404 Arthrogryposis, renal dysfunction, and cholestasis 2 HP:0000252 OMIM:613404 TAS P HPO:skoehler[2012-10-17] -OMIM:619472 VISS syndrome HP:0000252 PMID:33875846 PCS 1/9 P HPO:probinson[2021-10-10] -OMIM:618918 Periventricular nodular heterotopia 9 HP:0000252 PMID:31317654 PCS 1/1 P HPO:probinson[2020-08-11] -OMIM:140350 Hawkinsinuria HP:0000252 PMID:11073718 PCS 1/3 P HPO:probinson[2022-12-18];HPO:probinson[2022-12-18] -OMIM:219000 Fraser syndrome HP:0000252 OMIM:219000 IEA P HPO:iea[2009-02-17] -OMIM:617253 Seckel syndrome 10 HP:0000252 OMIM:617253 TAS P HPO:skoehler[2017-07-13] -OMIM:613330 Spondylo-megaepiphyseal-metaphyseal dysplasia HP:0000252 PMID:20004766 PCS 1/3 P HPO:probinson[2022-12-14] -OMIM:618454 Developmental delay with or without dysmorphic facies and autism HP:0000252 PMID:30827496 PCS 7/24 P HPO:skoehler[2019-09-07];HPO:probinson[2022-10-31] -OMIM:300148 Mehmo syndrome HP:0000252 PMID:28055140 PCS 9/9 male P HP:probinson[2018-04-15] -OMIM:616897 Osteochondrodysplasia, complex lethal, Symoens-Barnes-Gistelinck type HP:0000252 PMID:26365339 PCS P HPO:probinson[2017-06-26] -OMIM:617802 Neurodevelopmental disorder with microcephaly, seizures, and cortical atrophy HP:0000252 PMID:30275004;PMID:29691655;PMID:26539891 PCS 7/7 P HPO:probinson[2022-08-14];HPO:probinson[2022-08-14];HPO:probinson[2022-08-14] -OMIM:618939 Treacher-Collins syndrome 4 HP:0000252 PMID:31649276 PCS 1/6 P HPO:probinson[2020-08-31] -OMIM:611182 Congenital disorder of glycosylation, type IIh HP:0000252 PMID:28619360 PCS HP:0011463 1/1 P HPO:probinson[2019-07-06] -OMIM:616418 Hypomagnesemia, seizures, and mental retardation HP:0000252 OMIM:616418 TAS P HPO:skoehler[2015-07-05] -OMIM:615926 Webb-Dattani syndrome HP:0000252 OMIM:615926 TAS P HPO:skoehler[2014-08-24] -OMIM:619701 Yoon-Bellen neurodevelopmental syndrome HP:0000252 PMID:28017472 PCS 1/1 P HPO:probinson[2022-03-19] -OMIM:251300 Galloway-mowat syndrome 1 HP:0000252 PMID:26123727 PCS 13/15 P HPO:iea[2009-02-17] -OMIM:617807 Neurodevelopmental disorder with ataxic gait, absent speech, and decreased cortical white matter HP:0000252 OMIM:617807 IEA P HPO:skoehler[2019-04-18] -OMIM:616034 2,4-Dienoyl-Coa reductase deficiency HP:0000252 OMIM:616034 TAS P HPO:skoehler[2015-01-04] -OMIM:616460 Mental retardation, autosomal recessive 50 HP:0000252 OMIM:616460 TAS P HPO:skoehler[2015-08-02] -OMIM:151050 Lenz-Majewski hyperostotic dwarfism HP:0000252 OMIM:151050 TAS HP:0040283 P HPO:skoehler[2014-02-25] -OMIM:277470 Pontocerebellar hypoplasia, type 2A HP:0000252 PMID:18711368 PCS P HPO:iea[2009-02-17];HPO:probinson[2022-09-24] -DECIPHER:70 2p15-16.1 microdeletion syndrome HP:0000252 DECIPHER:70 IEA P HPO:skoehler[2013-05-29] -OMIM:614255 Mental retardation, autosomal dominant 9 HP:0000252 OMIM:614255 TAS P HPO:skoehler[2015-10-05] -OMIM:617930 Chromosome 1p35 deletion syndrome HP:0000252 OMIM:617930 IEA HP:0040284 P HPO:skoehler[2019-04-18] -OMIM:614813 Short stature, onychodysplasia, facial dysmorphism, and hypotrichosis HP:0000252 OMIM:614813 TAS HP:0003581 P HPO:skoehler[2012-11-16];HPO:probinson[2021-10-20] -OMIM:616212 Lissencephaly 6, with microcephaly HP:0000252 PMID:25521379 PCS 5/5 P HPO:skoehler[2015-02-22];HPO:probinson[2021-05-11] -OMIM:614559 Infantile cerebellar-retinal degeneration HP:0000252 PMID:22405087 PCS 4/8 P HPO:probinson[2021-06-25] -OMIM:301950 Branchial arch syndrome, X-linked HP:0000252 OMIM:301950 IEA P HPO:iea[2009-02-17] -OMIM:608278 Growth failure, microcephaly, mental retardation, cataracts, largejoint contractures, osteoporosis, cortical dysplasia, and cerebellaratrophy HP:0000252 OMIM:608278 IEA P HPO:iea[2009-02-17] -OMIM:613989 Dyskeratosis congenita, autosomal dominant 2 HP:0000252 OMIM:613989 TAS P HPO:skoehler[2012-11-18] -OMIM:231550 Achalasia-Addisonianism-Alacrima syndrome HP:0000252 OMIM:231550 IEA P HPO:iea[2009-02-17] -OMIM:619725 Neurodevelopmental disorder with or without variable movement or behavioral abnormalities HP:0000252 PMID:33242881 PCS 1/10 P HPO:probinson[2022-03-05] -OMIM:618201 Epileptic encephalopathy, early infantile, 68 HP:0000252 OMIM:618201 IEA HP:0040284 P HPO:skoehler[2019-04-18] -OMIM:616938 Coffin-Siris syndrome 5 HP:0000252 OMIM:616938 TAS P HPO:skoehler[2017-07-13] -OMIM:619884 Osteoporosis, childhood- or juvenile-onset, with developmental delay HP:0000252 PMID:34450031 PCS 4/6 P HPO:probinson[2022-08-14] -OMIM:618348 Galloway-Mowat syndrome 7 HP:0000252 PMID:28280135;PMID:28117080 PCS 8/8 P HPO:skoehler[2019-04-18];HPO:probinson[2021-07-10];HPO:probinson[2021-07-10] -OMIM:600462 Myopathy, lactic acidosis, and sideroblastic anemia 1 HP:0000252 OMIM:600462 IEA P HPO:iea[2009-02-17] -OMIM:617452 Intellectual developmental disorder with dysmorphic facies, seizures, and distal limb anomalies HP:0000252 PMID:28343629 PCS HP:0003593 9/12 P HPO:skoehler[2017-07-13];HP:probinson[2019-05-03] -OMIM:264480 Pseudotrisomy 13 syndrome HP:0000252 OMIM:264480 IEA P HPO:iea[2009-02-17] -OMIM:616051 Microcephaly 13, primary, autosomal recessive HP:0000252 PMID:24748105 PCS 2/2 P HPO:skoehler[2014-11-26];HPO:probinson[2022-03-26] -OMIM:616038 Neu-Laxova syndrome 2 HP:0000252 PMID:25152457 PCS 12/12 P HPO:skoehler[2014-11-26];HPO:probinson[2022-09-27] -OMIM:157170 Holoprosencephaly 2 HP:0000252 PMID:10369266 PCS 2/4 P HPO:iea[2009-02-17];HPO:probinson[2022-09-02] -OMIM:225753 Pontocerebellar hypoplasia, type 4 HP:0000252 OMIM:225753 IEA P HPO:iea[2009-02-17] -OMIM:618087 Spinocerebellar ataxia 42, early-onset, severe, with neurodevelopmental deficits HP:0000252 OMIM:618087 IEA HP:0040284 P HPO:skoehler[2019-04-18] -OMIM:610680 Holoprosencephaly, recurrent infections, and monocytosis HP:0000252 OMIM:610680 IEA P HPO:iea[2009-02-17] -OMIM:234100 Hallermann-Streiff syndrome HP:0000252 OMIM:234100 IEA P HPO:probinson[2009-02-17] -OMIM:617105 Epileptic encephalopathy, early infantile, 41 HP:0000252 PMID:27476654 PCS 1/3 P HPO:skoehler[2017-07-13];HPO:probinson[2022-12-13] -OMIM:619318 Oculogastrointestinal neurodevelopmental syndrome HP:0000252 PMID:32885237 PCS 1/5 P HPO:probinson[2021-07-06] -OMIM:613792 Chromosome 3pter-p25 deletion syndrome HP:0000252 PMID:3443553 PCS 14/19 P HPO:skoehler[2012-10-17];HPO:probinson[2022-06-25] -OMIM:617126 Alazami-Yuan syndrome HP:0000252 PMID:25574841 PCS 1/4 P HPO:skoehler[2017-07-13];HPO:probinson[2022-11-27] -OMIM:308300 Incontinentia pigmenti HP:0000252 OMIM:308300 IEA P HPO:iea[2009-02-17] -OMIM:300166 Microphthalmia, syndromic 2 HP:0000252 PMID:15004558 PCS 1/11 P HPO:skoehler[2015-02-22];HPO:probinson[2020-10-13] -OMIM:620086 Intellectual developmental disorder with ocular anomalies and distinctive facial features HP:0000252 PMID:36067766 PCS 2/5 P HPO:probinson[2022-12-04];HPO:probinson[2022-12-04] -OMIM:247200 Miller-Dieker lissencephaly syndrome HP:0000252 PMID:1671808 PCS 17/25 P HPO:iea[2009-02-17] -OMIM:211180 Bowen-Conradi syndrome HP:0000252 OMIM:211180 IEA P HPO:iea[2009-02-17] -OMIM:619013 Rajab interstitial lung disease with brain calcifications 2 HP:0000252 PMID:31355908 PCS 1/1 P HPO:probinson[2020-12-04] -OMIM:617599 Epileptic encephalopathy, early infantile, 55 HP:0000252 OMIM:617599 IEA P HPO:skoehler[2019-04-18] -OMIM:304050 Aicardi syndrome HP:0000252 OMIM:304050 IEA P HPO:iea[2009-02-17] -OMIM:245349 Pyruvate dehydrogenase e3-binding protein deficiency HP:0000252 OMIM:245349 IEA P HPO:iea[2009-02-17] -OMIM:300000 Opitz GBBB syndrome HP:0000252 PMID:15121778 PCS 2/7 P HPO:probinson[2022-04-28] -OMIM:617755 Neurodevelopmental disorder with dysmorphic facies and distal limb anomalies HP:0000252 PMID:28942966 PCS 7/9 P HPO:skoehler[2019-04-18];HPO:probinson[2020-10-13] -OMIM:278750 Xeroderma pigmentosum, Variant type NOT HP:0000252 OMIM:278750 TAS P HPO:probinson[2012-08-01] -OMIM:618229 Mitochondrial complex I deficiency, nuclear type 7 HP:0000252 OMIM:618229 IEA P HPO:skoehler[2019-04-18] -OMIM:615866 Coffin-Siris syndrome 9 HP:0000252 PMID:24886874 PCS 2/2 P HPO:skoehler[2015-09-14];HPO:probinson[2022-04-12] -OMIM:614222 Warburg micro syndrome 3 HP:0000252 OMIM:614222 TAS P HPO:probinson[2013-08-10] -OMIM:607317 Spinocerebellar ataxia, autosomal recessive 4 HP:0000252 OMIM:607317 IEA HP:0040284 P HPO:skoehler[2019-04-18] -OMIM:619325 Coffin-Siris syndrome 12 HP:0000252 PMID:33232675 PCS 3/12 P HPO:probinson[2021-06-24] -OMIM:615502 Intellectual developmental disorder, autosomal dominant 21 HP:0000252 PMID:23746550 PCS 3/4 P HPO:skoehler[2013-11-18];HPO:probinson[2019-09-04] -OMIM:619470 Neurodevelopmental disorder with motor and speech delay and behavioral abnormalities HP:0000252 PMID:33824500 PCS 8/17 P HPO:probinson[2021-10-16] -OMIM:617598 Mosaic variegated aneuploidy syndrome 3 HP:0000252 PMID:28553959 PCS 3/6 P HPO:skoehler[2019-04-18];HPO:probinson[2022-11-27] -OMIM:615071 Alazami syndrome HP:0000252 PMID:22865833 PCS 4/9 P HPO:skoehler[2013-06-12];HPO:probinson[2023-01-21] -OMIM:608885 Stomatin-Deficient cryohydrocytosis with neurologic defects HP:0000252 OMIM:608885 TAS P HPO:skoehler[2015-12-30] -OMIM:615351 Muscular dystrophy-dystroglycanopathy (congenital with impaired intellectual development), type B, 14 HP:0000252 PMID:23768512 PCS 1/4 P HPO:skoehler[2013-10-06];HPO:probinson[2022-11-05] -OMIM:300749 Mental retardation and microcephaly with pontine and cerebellar hypoplasia HP:0000252 PMID:19165920 PCS 5/5 P HPO:skoehler[2012-10-14];HPO:probinson[2021-09-06] -OMIM:619224 Mitochondrial complex II deficiency, nuclear type 4 HP:0000252 PMID:27159321 PCS 1/5 P HPO:probinson[2022-04-04] -OMIM:150230 Trichorhinophalangeal syndrome, type II HP:0000252 PMID:23913778 PCS 1/4 P HPO:iea[2009-02-17];HPO:probinson[2022-04-19] -OMIM:614541 Chromosome 16q22 deletion syndrome HP:0000252 PMID:8230159 IEA 3/6 P HPO:probinson[2021-06-26] -OMIM:614748 Interstitial lung disease, nephrotic syndrome, and epidermolysis bullosa, congenital HP:0000252 OMIM:614748 TAS P HPO:skoehler[2015-08-16] -OMIM:214150 Cerebrooculofacioskeletal syndrome 1 HP:0000252 PMID:10739753 PCS 3/3 P HPO:iea[2009-02-17];HPO:probinson[2022-05-06] -OMIM:619847 Neurodegeneration, childhood-onset, with progressive microcephaly HP:0000252 PMID:34918187 PCS 1/2 P HPO:probinson[2022-06-01] -OMIM:619504 Chopra-Amiel-Gordon syndrome HP:0000252 PMID:33909992 PCS 7/31 P HPO:probinson[2021-09-18] -OMIM:615084 Mitochondrial DNA depletion syndrome 11 HP:0000252 PMID:23313956 PCS 2/6 P HPO:skoehler[2013-02-25];HPO:probinson[2022-11-09] -OMIM:618492 Neurodevelopmental disorder with microcephaly and structural brain anomalies HP:0000252 PMID:31079899 PCS HP:0003577 5/5 P HPO:probinson[2019-07-07] -OMIM:600092 Nivelon-Nivelon-Mabille syndrome HP:0000252 PMID:24784881;PMID:30912300 PCS 4/4 P HP:probinson[2021-10-16];HPO:iea[2009-02-17];HPO:probinson[2021-02-18] -OMIM:614340 Mental retardation, autosomal recessive 27 HP:0000252 PMID:21937992 PCS 4/4 P HPO:skoehler[2014-05-04];HPO:probinson[2022-02-24] -OMIM:617333 Intellectual developmental disorder with dysmorphic facies and ptosis HP:0000252 OMIM:617333 TAS HP:0040283 P HPO:skoehler[2017-07-13] -OMIM:105650 Diamond-Blackfan anemia 1 HP:0000252 PMID:10590074 PCS 1/55 P HPO:skoehler[2010-06-18];HPO:probinson[2019-07-18] -OMIM:619125 Kaya-Barakat-Masson syndrome HP:0000252 PMID:32006098 PCS 5/6 P HPO:probinson[2021-01-07] -OMIM:617061 Mental retardation, autosomal dominant 44 HP:0000252 PMID:26721934;PMID:32109419 PCS 13/19 P HPO:skoehler[2017-07-13];HPO:probinson[2022-03-28];HPO:probinson[2022-04-02] -OMIM:267430 Renal tubular dysgenesis HP:0000252 OMIM:267430 IEA P HPO:iea[2009-02-17] -OMIM:619488 DEGCAGS syndrome HP:0000252 PMID:33875846 PCS 6/13 P HPO:probinson[2021-10-04] -OMIM:617913 Neurodevelopmental disorder with microcephaly, cataracts, and renal abnormalities HP:0000252 PMID:25558065 PCS 3/3 P HPO:skoehler[2019-04-18];HPO:probinson[2022-11-28] -OMIM:180870 Ruvalcaba syndrome HP:0000252 OMIM:180870 IEA P HPO:iea[2009-02-17] -OMIM:156610 Skin creases, congenital symmetric circumferential, 1 HP:0000252 OMIM:156610 TAS P HPO:skoehler[2015-12-30] -OMIM:300243 Mental retardation, x-linked syndromic, Christianson type HP:0000252 PMID:18342287 PCS 10/11 P HPO:iea[2009-02-17];HPO:probinson[2020-12-10] -OMIM:616723 Spondyloepimetaphyseal dysplasia, Faden-Alkuraya type HP:0000252 OMIM:616723 TAS P HPO:skoehler[2015-12-30] -OMIM:259410 Osteogenesis imperfecta congenita, microcephaly, and cataracts HP:0000252 OMIM:259410 IEA P HPO:iea[2009-02-17] -OMIM:210720 Microcephalic osteodysplastic primordial dwarfism, type II HP:0000252 OMIM:210720 TAS P HPO:probinson[2009-02-17] -OMIM:619170 Mitochondrial complex I deficiency, nuclear type 36 HP:0000252 PMID:32969598 PCS 1/3 P HPO:probinson[2021-02-19] -OMIM:270750 Spastic paraplegia 23 HP:0000252 PMID:14681889 PCS 2/4 P HPO:iea[2009-02-17];HPO:probinson[2022-12-03] -OMIM:185480 Suprabulbar paresis, congenital HP:0000252 OMIM:185480 IEA P HPO:iea[2009-02-17] -OMIM:602541 Muscular dystrophy, congenital, Megaconial type HP:0000252 OMIM:602541 TAS P HPO:skoehler[2012-10-17] -OMIM:611091 Intellectual developmental disorder, autosomal recessive 5 HP:0000252 PMID:22541559 PCS 8/10 P HPO:skoehler[2012-10-17];HPO:probinson[2022-06-18] -OMIM:613489 Congenital disorder of glycosylation, type IIj HP:0000252 OMIM:613489 TAS HP:0040283 P HPO:skoehler[2012-11-18] -OMIM:147250 Solitary median maxillary central incisor HP:0000252 OMIM:147250;PMID:11471164 PCS 8/24 P HPO:iea[2009-10-30];HPO:iea[2009-02-17] -OMIM:614225 Warburg micro syndrome 2 HP:0000252 PMID:20967465 PCS 1/1 P HPO:probinson[2013-08-10];HPO:probinson[2022-12-14] -OMIM:616763 Leukodystrophy and acquired microcephaly with or without dystonia HP:0000252 PMID:26573021 PCS 5/5 P HPO:probinson[2017-06-17] -OMIM:617051 Neurodevelopmental disorder with microcephaly and gray sclerae HP:0000252 PMID:27055666 PCS 2/3 P HPO:skoehler[2017-07-13];HPO:probinson[2021-02-16] -OMIM:619297 KINSSHIP syndrome HP:0000252 PMID:33961779 PCS 11/18 P HPO:probinson[2021-07-05] -OMIM:309590 Mental retardation, x-linked syndromic, Turner type HP:0000252 OMIM:309590 IEA P HPO:skoehler[2019-09-07] -OMIM:614219 Adams-Oliver syndrome 2 HP:0000252 OMIM:614219 TAS P HPO:skoehler[2012-10-17] -OMIM:617235 Myoclonus, intractable, neonatal HP:0000252 OMIM:617235 TAS P HPO:skoehler[2017-07-13] -OMIM:613606 Forsythe-Wakeling syndrome HP:0000252 OMIM:613606 TAS P HPO:skoehler[2012-10-17] -OMIM:609308 Muscular dystrophy-dystroglycanopathy (limb-girdle), type C, 1 HP:0000252 OMIM:609308 IEA P HPO:iea[2009-02-17] -OMIM:164280 Feingold syndrome 1 HP:0000252 OMIM:164280 IEA P HPO:iea[2009-02-17] -OMIM:180849 Rubinstein-Taybi syndrome 1 HP:0000252 PMID:35464843;PMID:10573006 PCS 7/9 P HPO:iea[2009-02-17];HPO:probinson[2022-05-06];HPO:probinson[2022-05-06];HPO:probinson[2022-05-06] -OMIM:268300 Roberts syndrome HP:0000252 OMIM:268300 IEA P HPO:iea[2009-02-17] -OMIM:301022 Neurodevelopmental disorder, X-linked, with craniofacial abnormalities HP:0000252 OMIM:301022 IEA P HPO:skoehler[2019-04-18] -OMIM:619694 Developmental delay with variable neurologic and brain abnormalities HP:0000252 PMID:32820033 PCS 7/10 P HPO:probinson[2022-03-20] -OMIM:613803 Meier-Gorlin syndrome 3 HP:0000252 PMID:21358632 PCS 2/3 P HPO:skoehler[2012-10-17];HPO:probinson[2022-03-26] -OMIM:267750 Knobloch syndrome, type 1 HP:0000252 PMID:17546652 PCS 1/1 P HP:probinson[2022-03-12];HPO:probinson[2022-03-12] -OMIM:613544 Chromosome 6q11-q14 deletion syndrome HP:0000252 PMID:20685673 PCS 0/4 P HPO:probinson[2022-11-02] -OMIM:164200 Oculodentodigital dysplasia HP:0000252 OMIM:164200 IEA P HPO:probinson[2009-02-17] -OMIM:618284 Microcephaly, cataracts, impaired intellectual development, and dystonia with abnormal striatum HP:0000252 OMIM:618284 IEA P HPO:skoehler[2019-04-18] -OMIM:613744 Spastic paraplegia 51, autosomal recessive HP:0000252 OMIM:613744 TAS P HPO:skoehler[2012-10-17] -OMIM:607932 Microphthalmia, syndromic 6 HP:0000252 PMID:18252212 PCS P HPO:iea[2012-04-24];HPO:probinson[2022-02-17] -OMIM:617951 Leukodystrophy, hypomyelinating, 15 HP:0000252 PMID:29576217 PCS 1/4 P HPO:skoehler[2019-04-18];HPO:probinson[2022-05-26] -OMIM:618840 Alopecia-mental retardation syndrome 4 HP:0000252 PMID:30723320 PCS 3/11 P HPO:probinson[2020-07-23] -OMIM:617799 Intellectual developmental disorder, autosomal dominant 54 HP:0000252 PMID:29100089 PCS 5/10 P HPO:skoehler[2019-04-18];HPO:probinson[2022-06-03] -OMIM:618106 Intellectual developmental disorder, autosomal dominant 58 HP:0000252 OMIM:618106 IEA P HPO:skoehler[2018-10-08] -OMIM:616335 Microcephaly and chorioretinopathy, autosomal recessive, 3 HP:0000252 OMIM:616335 TAS P HPO:skoehler[2015-06-22] -OMIM:251290 Band-Like calcification with simplified gyration and polymicrogyria HP:0000252 OMIM:251290 IEA P HPO:skoehler[2010-06-20] -OMIM:618298 Developmental and epileptic encephalopathy 70 HP:0000252 PMID:23033978 PCS 1/1 P HPO:skoehler[2019-04-18];HPO:probinson[2021-04-25] -OMIM:204750 Alpha-aminoadipic and alpha-ketoadipic aciduria HP:0000252 PMID:23141293 PCS 1/2 P HPO:skoehler[2014-11-26];HPO:probinson[2021-05-30] -OMIM:150260 Laryngeal abductor paralysis HP:0000252 OMIM:150260 IEA P HPO:iea[2009-02-17] -OMIM:208085 Arthrogryposis, renal dysfunction, and cholestasis 1 HP:0000252 OMIM:208085 IEA P HPO:skoehler[2010-06-18] -OMIM:139210 Myhre syndrome HP:0000252 OMIM:139210 IEA P HPO:iea[2009-02-17] -OMIM:616140 Leukodystrophy, hypomyelinating, 9 HP:0000252 OMIM:616140 TAS P HPO:skoehler[2015-01-04] -OMIM:619121 Neurodevelopmental disorder with cardiomyopathy, spasticity, and brain abnormalities HP:0000252 PMID:33015733 PCS 5/5 P HPO:probinson[2021-02-01] -OMIM:269000 Sc phocomelia syndrome HP:0000252 OMIM:269000 IEA P HPO:iea[2009-02-17] -OMIM:617119 Bardet-Biedl syndrome 22 HP:0000252 PMID:27486776 PCS 1/1 P HPO:skoehler[2017-07-13];HPO:probinson[2021-09-09] -OMIM:618160 Isolated growth hormone deficiency, type V HP:0000252 OMIM:618160 IEA P HPO:skoehler[2019-04-18] -OMIM:194190 Wolf-Hirschhorn syndrome HP:0000252 http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=gene&part=whs TAS HP:0040282 P HPO:iea[2009-02-17] -OMIM:612474 Chromosome 1q21.1 deletion syndrome, 1.35-mb HP:0000252 PMID:18784092 PCS 14/21 P HPO:skoehler[2012-11-16];HPO:probinson[2022-11-08] -OMIM:617330 Hypotonia, ataxia, and delayed development syndrome HP:0000252 PMID:28017370 PCS 2/8 P HPO:skoehler[2017-07-13];HPO:probinson[2020-10-09] -OMIM:615716 Hyperphosphatasia with impaired intellectual development syndrome 4 HP:0000252 PMID:24439110 PCS 3/5 P HPO:skoehler[2014-08-24];HPO:probinson[2023-01-15] -OMIM:619603 Galloway-Mowat syndrome 9 HP:0000252 PMID:31481669 PCS 11/11 P HPO:probinson[2022-02-01] -OMIM:600546 Intrauterine growth retardation with increased mitomycin C sensitivity HP:0000252 OMIM:600546 PCS P HPO:probinson[2012-03-16] -OMIM:620072 Diamond-Blackfan anemia 21 HP:0000252 PMID:35213692 PCS 1/6 P HPO:probinson[2022-11-24] -OMIM:236670 Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 1 HP:0000252 PMID:15637732 PCS 1/2 P HPO:iea[2009-02-17];HPO:probinson[2021-05-09] -OMIM:610678 Combined oxidative phosphorylation deficiency 4 HP:0000252 PMID:17160893 TAS P HPO:probinson[2013-04-01] -OMIM:619539 Neuroocular syndrome HP:0000252 PMID:29556724 PCS 2/3 P HPO:probinson[2021-10-23] -OMIM:101805 Acrofacial dysostosis, Catania type HP:0000252 OMIM:101805 TAS P HPO:skoehler[2017-07-13] -OMIM:227650 Fanconi anemia HP:0000252 OMIM:227650 IEA P HPO:iea[2009-02-17] -OMIM:147770 Johnson neuroectodermal syndrome HP:0000252 OMIM:147770 TAS HP:0040283 P HPO:skoehler[2015-05-31] -OMIM:615851 Pontocerebellar hypoplasia, type 2E HP:0000252 PMID:24577744 PCS P HPO:skoehler[2014-06-24];HPO:probinson[2020-12-13] -OMIM:619833 Neurodevelopmental disorder with neuromuscular and skeletal abnormalities HP:0000252 PMID:35108495 PCS 3/6 P HPO:probinson[2022-07-03] -OMIM:618349 Galloway-Mowat syndrome 8 HP:0000252 PMID:30427554 PCS 1/4 P HPO:skoehler[2019-04-18];HPO:probinson[2022-12-21] -OMIM:300831 Ck syndrome HP:0000252 OMIM:300831 TAS P HPO:skoehler[2012-10-14] -OMIM:251200 Microcephaly, primary autosomal recessive, 1 HP:0000252 OMIM:251200 IEA P HPO:iea[2009-02-17] -OMIM:619147 Leukoencephalopathy, progressive, infantile-onset, with or without deafness HP:0000252 PMID:21427441 PCS 1/1 P HPO:probinson[2021-05-30];HPO:probinson[2021-05-30] -OMIM:616449 Basel-Vanagaite-Smirin-Yosef syndrome HP:0000252 OMIM:616449 TAS P HPO:skoehler[2015-07-26] -OMIM:604314 Blepharophimosis with facial and genital anomalies and mental retardation HP:0000252 OMIM:604314 IEA P HPO:skoehler[2018-10-08] -OMIM:612936 Spastic paraplegia 50, autosomal recessive HP:0000252 OMIM:612936 IEA P HPO:skoehler[2010-06-19] -OMIM:605013 MICROHYDRANENCEPHALY HP:0000252 PMID:22526350 PCS 2/2 P HPO:iea[2009-02-17];HPO:probinson[2022-08-07] -OMIM:190420 Triglyceride storage disease, type I HP:0000252 OMIM:190420 TAS P HPO:probinson[2009-02-17] -OMIM:606593 Lig4 syndrome HP:0000252 OMIM:606593 IEA P HPO:skoehler[2019-04-18] -OMIM:212066 Congenital disorder of glycosylation, type IIa HP:0000252 OMIM:212066 TAS P HPO:skoehler[2012-10-17] -OMIM:618947 Arthrogryposis multiplex congenita 5 HP:0000252 PMID:30244176 PCS 1/1 P HPO:probinson[2020-08-14];HPO:probinson[2020-08-14] -OMIM:618687 Intellectual developmental disorder with short stature and behavioral abnormalities HP:0000252 PMID:31607425 PCS 2/5 P HPO:probinson[2020-06-27];HPO:probinson[2020-06-27] -OMIM:300263 Siderius X-linked mental retardation syndrome HP:0000252 PMID:17594395 PCS 1/1 P HPO:probinson[2021-09-30] -OMIM:620027 Neurodevelopmental disorder with microcephaly, short stature, and speech delay HP:0000252 PMID:35298461 PCS 7/8 P HPO:probinson[2022-10-05] -OMIM:156200 Mental retardation, autosomal dominant 1 HP:0000252 OMIM:156200 TAS P HPO:skoehler[2012-11-18] -OMIM:616268 Arboleda-Tham syndrome HP:0000252 PMID:32041641 PCS 5/5 P HPO:skoehler[2015-05-31];HPO:probinson[2020-08-02] -OMIM:619695 Rauch-Steindl syndrome HP:0000252 PMID:29760529;PMID:29892088;PMID:31171569 PCS 6/6 P HPO:probinson[2022-03-01];HPO:probinson[2022-03-01];HPO:probinson[2022-03-01] -OMIM:619312 Radio-Tartaglia syndrome HP:0000252 PMID:33596411 PCS 4/32 P HPO:probinson[2021-07-06] -OMIM:609037 Mental retardation with optic atrophy, facial dysmorphism, microcephaly,and short stature HP:0000252 PMID:12522796 PCS 2/2 P HPO:iea[2009-02-17];HPO:probinson[2022-09-06] -OMIM:613156 Muscular dystrophy-dystroglycanopathy (congenital with impaired intellectual development), type B, 2 HP:0000252 PMID:17634419 PCS 4/4 P HPO:skoehler[2012-10-17];HPO:probinson[2023-01-26] -OMIM:617595 Birk-Landau-Perez syndrome HP:0000252 PMID:34716203 PCS 1/1 P HPO:probinson[2022-07-16] -OMIM:616975 Neurodevelopmental disorder with or without anomalies of the brain, eye, or heart HP:0000252 PMID:27087320 PCS 2/9 P HPO:probinson[2019-08-29] -OMIM:308350 Developmental and epileptic encephalopathy 1 HP:0000252 PMID:21108397;PMID:11889467;OMIM:308350 PCS 13/13 P HPO:iea[2009-02-17];HPO:probinson[2022-06-22];HPO:probinson[2021-06-23] -OMIM:617101 Intellectual developmental disorder with persistence of fetal hemoglobin HP:0000252 OMIM:617101 TAS P HPO:skoehler[2017-07-13] -OMIM:222765 Rhizomelic chondrodysplasia punctata, type 2 HP:0000252 OMIM:222765 IEA P HPO:iea[2009-02-17] -OMIM:617157 Short stature, brachydactyly, intellectual developmental disability, and seizures HP:0000252 OMIM:617157 TAS P HPO:skoehler[2017-07-13] -OMIM:616459 Al-Raqad syndrome HP:0000252 OMIM:616459 TAS P HPO:skoehler[2015-08-02] -OMIM:601110 Congenital disorder of glycosylation, type Id HP:0000252 PMID:10581255 PCS 1/1 P HPO:iea[2009-02-17];HPO:probinson[2023-01-26] -OMIM:619239 Neurodevelopmental disorder with or without autism or seizures HP:0000252 PMID:30311385 PCS 1/1 P HPO:probinson[2021-05-11] -OMIM:612289 Fontaine progeroid syndrome HP:0000252 PMID:29100093 PCS 3/5 P HP:probinson[2018-04-29] -OMIM:129900 Ectrodactyly, ectodermal dysplasia, and cleft lip/palate syndrome1 HP:0000252 OMIM:129900 IEA P HPO:iea[2009-02-17] -OMIM:612513 Chromosome 2p16.1-p15 deletion syndrome HP:0000252 OMIM:612513 IEA P HPO:skoehler[2010-06-19] -OMIM:614345 Intellectual developmental disorder, autosomal recessive 24 HP:0000252 OMIM:614345 TAS P HPO:skoehler[2017-07-13] -OMIM:309580 Intellectual disability-hypotonic facies syndrome, X-linked HP:0000252 OMIM:309580 IEA P HPO:iea[2009-02-17] -OMIM:617404 Muscular dystrophy, congenital, with cataracts and intellectual disability HP:0000252 OMIM:617404 TAS 2/12 P HPO:skoehler[2017-07-13];HPO:probinson[2022-11-27] -OMIM:300387 Mental retardation, X-linked 63 HP:0000252 PMID:11889465 PCS 1/8 P HPO:skoehler[2017-07-13];HPO:probinson[2021-08-30] -OMIM:300887 Linear skin defects with multiple congenital anomalies 2 HP:0000252 OMIM:300887 IEA HP:0040280 P HPO:skoehler[2013-01-11] -OMIM:300337 Hypomelanosis of ito HP:0000252 OMIM:300337 IEA P HPO:iea[2009-02-17] -OMIM:261540 Peters-Plus syndrome HP:0000252 OMIM:261540 IEA P HPO:iea[2009-02-17] -OMIM:618885 Congenital disorder of glycosylation, type IIt HP:0000252 PMID:32293671 PCS 2/7 P HPO:probinson[2020-06-23];HPO:probinson[2020-06-23] -OMIM:261600 Phenylketonuria HP:0000252 OMIM:261600 IEA P HPO:iea[2009-02-17] -OMIM:201475 Very long-chain acyl-CoA dehydrogenase deficiency HP:0000252 PMID:4022672 PCS 2/3 P HPO:probinson[2021-07-03] -OMIM:610253 Kleefstra syndrome HP:0000252 PMID:19264732 PCS 8/22 P HPO:sdoelken[2009-02-17] -OMIM:616811 Combined oxidative phosphorylation deficiency 29 HP:0000252 PMID:26626369 PCS P HPO:probinson[2017-06-18] -OMIM:251230 Microcephaly-Micromelia syndrome HP:0000252 OMIM:251230 IEA P HPO:iea[2009-02-17] -OMIM:619148 Chromosome 13q33-q34 deletion syndrome HP:0000252 PMID:19363806 PCS 8/11 P HPO:probinson[2021-03-13] -OMIM:201750 Antley-Bixler syndrome with genital anomalies and disordered steroidogenesis HP:0000252 OMIM:201750 IEA P HPO:iea[2009-02-17] -OMIM:614039 Cortical dysplasia, complex, with other brain malformations 1 HP:0000252 PMID:20829227 PCS 1/9 P HPO:skoehler[2012-11-21];HPO:probinson[2022-02-15] -OMIM:616943 Trichothiodystrophy 6, nonphotosensitive HP:0000252 OMIM:616943 TAS P HPO:skoehler[2017-07-13] -OMIM:208900 Ataxia-telangiectasia HP:0000252 PMID:22563157 PCS 1/2 P HPO:probinson[2022-05-09] -OMIM:609637 Holoprosencephaly 5 HP:0000252 OMIM:609637 TAS P PATOC:GVG[2012-04-24]; PATOC:PS[2012-04-24] -OMIM:223370 Dubowitz syndrome HP:0000252 PMID:18990984 PCS 1/1 P HPO:iea[2009-02-17];HPO:probinson[2022-09-12] -OMIM:258865 Orofaciodigital syndrome IX HP:0000252 OMIM:258865 IEA P HPO:skoehler[2019-04-18] -OMIM:620083 Neurodevelopmental disorder with craniofacial dysmorphism and skeletal defects HP:0000252 PMID:29938792 PCS 1/1 P HPO:probinson[2022-12-04] -OMIM:620141 Developmental delay, language impairment, and ocular abnormalities HP:0000252 PMID:35047857 PCS 6/7 P HPO:probinson[2022-12-12] -OMIM:614851 Seckel syndrome 7 HP:0000252 OMIM:614851 TAS P HPO:skoehler[2012-12-06] -OMIM:616900 Hypotonia, infantile, with psychomotor retardation and characteristic facies 3 NOT HP:0000252 PMID:27040692 PCS P HPO:probinson[2017-06-24] -OMIM:617478 Structural heart defects and renal anomalies syndrome HP:0000252 PMID:28318500 PCS HP:0003623 1/4 P HPO:skoehler[2017-07-13];HPO:probinson[2019-09-03] -OMIM:610829 Holoprosencephaly 9 HP:0000252 PMID:14581620 PCS P HPO:iea[2012-04-24] -OMIM:617301 Glycine encephalopathy with normal serum glycine HP:0000252 OMIM:617301 TAS HP:0040283 P HPO:skoehler[2017-07-13] -OMIM:615272 Fanconi anemia, complementation group Q HP:0000252 PMID:23623386 PCS 1/2 P HPO:skoehler[2013-08-18];HPO:probinson[2022-03-15] -OMIM:614037 Leukotriene C4 synthase deficiency HP:0000252 PMID:9820300 PCS P HPO:probinson[2013-12-15] -OMIM:618097 Microcephaly, growth restriction, and increased sister chromatid exchange 2 HP:0000252 PMID:30057030 PCS 10/10 P HPO:skoehler[2019-04-18];HPO:probinson[2022-11-07] -OMIM:617082 Congenital disorder of glycosylation, type IAA HP:0000252 OMIM:617082 TAS P HPO:skoehler[2017-07-13] -OMIM:619758 Tessadori-van Haaften neurodevelopmental syndrome 1 HP:0000252 PMID:28920961 PCS 3/3 P HPO:probinson[2022-04-17] -OMIM:224690 Meier-Gorlin syndrome 1 HP:0000252 OMIM:224690 IEA P HPO:iea[2009-02-17] -OMIM:610536 Mandibulofacial dysostosis, Guion-Almeida type HP:0000252 OMIM:610536 IEA P HPO:iea[2009-02-17] -OMIM:274270 Dihydropyrimidine dehydrogenase deficiency HP:0000252 PMID:10071185 PCS 3/22 P HPO:skoehler[2010-06-18];HPO:probinson[2022-06-11] -OMIM:142945 Holoprosencephaly 3 HP:0000252 OMIM:142945 IEA P HPO:skoehler[2019-09-07] -OMIM:618076 Neurodevelopmental disorder with spasticity and poor growth HP:0000252 OMIM:618076 IEA P HPO:skoehler[2019-04-18] -OMIM:613970 Intellectual developmental disorder, autosomal dominant 6, with or without seizures HP:0000252 PMID:20890276 PCS 1/6 P HPO:skoehler[2019-04-18];HPO:probinson[2022-06-16] -OMIM:210600 Seckel syndrome 1 HP:0000252 OMIM:210600 IEA P HPO:iea[2009-02-17] -OMIM:618958 Combined oxidative phosphorylation deficiency 47 HP:0000252 PMID:30566640 PCS 1/1 P HPO:probinson[2020-08-27] -OMIM:618479 Cerebellar, ocular, craniofacial, and genital syndrome HP:0000252 OMIM:618479 IEA HP:0040284 P HPO:skoehler[2019-09-07] -OMIM:252150 Molybdenum cofactor deficiency, complementation group A HP:0000252 OMIM:252150 TAS P HPO:skoehler[2014-01-28] -OMIM:618460 Khan-Khan-Katsanis syndrome HP:0000252 OMIM:618460 IEA P HPO:skoehler[2019-09-07] -OMIM:210900 Bloom syndrome HP:0000252 OMIM:210900 IEA P HPO:iea[2009-02-17] -OMIM:616258 Meckel syndrome 12 HP:0000252 OMIM:616258 TAS P HPO:skoehler[2015-03-22] -ORPHA:395 Homocystinuria due to methylene tetrahydrofolate reductase deficiency HP:0000252 ORPHA:395 TAS HP:0040284 P ORPHA:orphadata[2023-01-27] -ORPHA:199318 15q13.3 microdeletion syndrome HP:0000252 ORPHA:199318 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:2719 Oculocerebral hypopigmentation syndrome, Cross type HP:0000252 ORPHA:2719 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:2728 Blepharophimosis-intellectual disability syndrome, Ohdo type HP:0000252 ORPHA:2728 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:2729 Okamoto syndrome HP:0000252 ORPHA:2729 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:2714 Oculo-palato-cerebral syndrome HP:0000252 ORPHA:2714 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:97297 Bohring-Opitz syndrome HP:0000252 ORPHA:97297 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:438216 PURA-related severe neonatal hypotonia-seizures-encephalopathy syndrome due to a point mutation HP:0000252 ORPHA:438216 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:2707 Oculocerebrofacial syndrome, Kaufman type HP:0000252 ORPHA:2707 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:101070 Bilateral frontoparietal polymicrogyria HP:0000252 ORPHA:101070 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:73273 Growth delay due to insulin-like growth factor I resistance HP:0000252 ORPHA:73273 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:73272 Growth delay due to insulin-like growth factor type 1 deficiency HP:0000252 ORPHA:73272 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:26 Methylmalonic acidemia with homocystinuria HP:0000252 ORPHA:26 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:20 3-hydroxy-3-methylglutaric aciduria HP:0000252 ORPHA:20 TAS HP:0040284 P ORPHA:orphadata[2023-01-27] -ORPHA:29 Mevalonic aciduria HP:0000252 ORPHA:29 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:444077 Cognitive impairment-coarse facies-heart defects-obesity-pulmonary involvement-short stature-skeletal dysplasia syndrome HP:0000252 ORPHA:444077 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:444072 Cerebellar-facial-dental syndrome HP:0000252 ORPHA:444072 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:370968 Congenital muscular dystrophy with intellectual disability HP:0000252 ORPHA:370968 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:40366 Acitretin/etretinate embryopathy HP:0000252 ORPHA:40366 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:457351 Microcephaly-intellectual disability-sensorineural hearing loss-epilepsy-abnormal muscle tone syndrome HP:0000252 ORPHA:457351 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:73246 Visceral neuropathy-brain anomalies-facial dysmorphism-developmental delay syndrome HP:0000252 ORPHA:73246 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:322 Exstrophy-epispadias complex HP:0000252 ORPHA:322 TAS HP:0040284 P ORPHA:orphadata[2023-01-27] -ORPHA:101000 Autosomal recessive spastic paraplegia type 20 HP:0000252 ORPHA:101000 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:11 Pentasomy X HP:0000252 ORPHA:11 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:17 Fatal infantile lactic acidosis with methylmalonic aciduria HP:0000252 ORPHA:17 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:370980 Congenital muscular dystrophy without intellectual disability HP:0000252 ORPHA:370980 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:317 Erythrokeratodermia variabilis HP:0000252 ORPHA:317 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:3199 Stimmler syndrome HP:0000252 ORPHA:3199 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:3186 Holoprosencephaly-radial heart renal anomalies syndrome HP:0000252 ORPHA:3186 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:370959 Congenital muscular dystrophy with cerebellar involvement HP:0000252 ORPHA:370959 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:3173 Infantile spasms-broad thumbs syndrome HP:0000252 ORPHA:3173 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:280195 Septopreoptic holoprosencephaly HP:0000252 ORPHA:280195 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:85293 X-linked intellectual disability, Cabezas type HP:0000252 ORPHA:85293 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:85290 X-linked intellectual disability, Wilson type HP:0000252 ORPHA:85290 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:370924 STT3B-CDG HP:0000252 ORPHA:370924 TAS HP:0040280 P ORPHA:orphadata[2023-01-27] -ORPHA:370927 SSR4-CDG HP:0000252 ORPHA:370927 TAS HP:0040280 P ORPHA:orphadata[2023-01-27] -ORPHA:85278 Christianson syndrome HP:0000252 ORPHA:85278 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:85279 KDM5C-related syndromic X-linked intellectual disability HP:0000252 ORPHA:85279 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:85284 BRESEK syndrome HP:0000252 ORPHA:85284 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:457395 Progressive spondyloepimetaphyseal dysplasia-short stature-short fourth metatarsals-intellectual disability syndrome HP:0000252 ORPHA:457395 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:85280 X-linked intellectual disability-cubitus valgus-dysmorphism syndrome HP:0000252 ORPHA:85280 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:85282 MEHMO syndrome HP:0000252 ORPHA:85282 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:370930 XYLT1-CDG HP:0000252 ORPHA:370930 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:85273 X-linked intellectual disability, Abidi type HP:0000252 ORPHA:85273 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:63862 Schisis association HP:0000252 ORPHA:63862 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:99812 LIG4 syndrome HP:0000252 ORPHA:99812 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:3265 Humero-radial synostosis HP:0000252 ORPHA:3265 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:3268 Radioulnar synostosis-microcephaly-scoliosis syndrome HP:0000252 ORPHA:3268 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:263516 Progressive myoclonic epilepsy type 3 HP:0000252 ORPHA:263516 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:447980 19p13.3 microduplication syndrome HP:0000252 ORPHA:447980 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:83472 CAMOS syndrome HP:0000252 ORPHA:83472 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:3255 Filippi syndrome HP:0000252 ORPHA:3255 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:263501 COG4-CDG HP:0000252 ORPHA:263501 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:3242 Renpenning syndrome HP:0000252 ORPHA:3242 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:84 Fanconi anemia HP:0000252 ORPHA:84 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:401768 Proximal myopathy with extrapyramidal signs HP:0000252 ORPHA:401768 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:85201 Genitopatellar syndrome HP:0000252 ORPHA:85201 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:72 Angelman syndrome HP:0000252 ORPHA:72 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:99843 Leukocyte adhesion deficiency type II HP:0000252 ORPHA:99843 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:46 Adenylosuccinate lyase deficiency HP:0000252 ORPHA:46 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:3207 White matter hypoplasia-corpus callosum agenesis-intellectual disability syndrome HP:0000252 ORPHA:3207 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:3201 Ventricular extrasystoles with syncopal episodes-perodactyly-Robin sequence syndrome HP:0000252 ORPHA:3201 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:59 Allan-Herndon-Dudley syndrome HP:0000252 ORPHA:59 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:1497 X-linked complicated corpus callosum dysgenesis HP:0000252 ORPHA:1497 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:1496 Corpus callosum agenesis-neuronopathy syndrome HP:0000252 ORPHA:1496 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:1495 Intellectual disability-hypoplastic corpus callosum-preauricular tag syndrome HP:0000252 ORPHA:1495 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:50 Aicardi syndrome HP:0000252 ORPHA:50 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:51 Aicardi-Goutières syndrome HP:0000252 ORPHA:51 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:1466 COFS syndrome HP:0000252 ORPHA:1466 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:1465 Coffin-Siris syndrome HP:0000252 ORPHA:1465 TAS HP:0040284 P ORPHA:orphadata[2023-01-27] -ORPHA:79350 3-phosphoserine phosphatase deficiency, infantile/juvenile form HP:0000252 ORPHA:79350 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:79351 3-phosphoglycerate dehydrogenase deficiency, infantile/juvenile form HP:0000252 ORPHA:79351 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:177907 Prader-Willi syndrome due to translocation HP:0000252 ORPHA:177907 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:2787 Osteoporosis-macrocephaly-blindness-joint hyperlaxity syndrome HP:0000252 ORPHA:2787 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:1445 Ring chromosome 21 syndrome HP:0000252 ORPHA:1445 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:2772 Congenital osteogenesis imperfecta-microcephaly-cataracts syndrome HP:0000252 ORPHA:2772 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:1449 Ring chromosome 7 syndrome HP:0000252 ORPHA:1449 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:1448 Ring chromosome 6 syndrome HP:0000252 ORPHA:1448 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:1446 Ring chromosome 22 syndrome HP:0000252 ORPHA:1446 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:435938 X-linked microcephaly-growth retardation-prognathism-cryptorchidism syndrome HP:0000252 ORPHA:435938 TAS HP:0040280 P ORPHA:orphadata[2023-01-27] -ORPHA:1439 Ring chromosome 12 syndrome HP:0000252 ORPHA:1439 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:1437 Ring chromosome 1 syndrome HP:0000252 ORPHA:1437 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:1422 Chondrodysplasia-disorder of sex development syndrome HP:0000252 ORPHA:1422 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:220386 Semilobar holoprosencephaly HP:0000252 ORPHA:220386 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:2753 Orofaciodigital syndrome type 4 HP:0000252 ORPHA:2753 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:2745 Opitz GBBB syndrome HP:0000252 ORPHA:2745 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:508533 Skeletal dysplasia-T-cell immunodeficiency-developmental delay syndrome HP:0000252 ORPHA:508533 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:1520 Craniofrontonasal dysplasia HP:0000252 ORPHA:1520 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:1528 Craniotelencephalic dysplasia HP:0000252 ORPHA:1528 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:2850 Alopecia-intellectual disability syndrome HP:0000252 ORPHA:2850 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:488613 Global developmental delay-neuro-ophthalmological abnormalities-seizures-intellectual disability syndrome NOT HP:0000252 ORPHA:488613 TAS P ORPHA:orphadata[2023-01-27] -ORPHA:280200 Microform holoprosencephaly HP:0000252 ORPHA:280200 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:96097 Distal trisomy 5q HP:0000252 ORPHA:96097 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:291 Congenital varicella syndrome HP:0000252 ORPHA:291 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:290 Congenital rubella syndrome HP:0000252 ORPHA:290 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:293 Congenital herpes simplex virus infection HP:0000252 ORPHA:293 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:363958 17q21.31 microdeletion syndrome HP:0000252 ORPHA:363958 TAS HP:0040284 P ORPHA:orphadata[2023-01-27] -ORPHA:244310 RFT1-CDG HP:0000252 ORPHA:244310 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:2836 PEHO syndrome HP:0000252 ORPHA:2836 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:280 Wolf-Hirschhorn syndrome HP:0000252 ORPHA:280 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:281 Monosomy 5p HP:0000252 ORPHA:281 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:488632 TBCK-related intellectual disability syndrome HP:0000252 ORPHA:488632 TAS HP:0040284 P ORPHA:orphadata[2023-01-27] -ORPHA:233 Duane retraction syndrome HP:0000252 ORPHA:233 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:235 Dubowitz syndrome HP:0000252 ORPHA:235 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:226 Dihydropteridine reductase deficiency HP:0000252 ORPHA:226 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:178303 8q22.1 microdeletion syndrome HP:0000252 ORPHA:178303 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:33364 Trichothiodystrophy HP:0000252 ORPHA:33364 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:243 46,XX gonadal dysgenesis HP:0000252 ORPHA:243 TAS HP:0040284 P ORPHA:orphadata[2023-01-27] -ORPHA:357225 Primary non-essential cutis verticis gyrata HP:0000252 ORPHA:357225 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:236 Trisomy 9p HP:0000252 ORPHA:236 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:239 Dyggve-Melchior-Clausen disease HP:0000252 ORPHA:239 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:263487 COG5-CDG HP:0000252 ORPHA:263487 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:79500 DOORS syndrome HP:0000252 ORPHA:79500 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:3380 Trisomy 18 HP:0000252 ORPHA:3380 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:2052 Fraser syndrome HP:0000252 ORPHA:2052 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:2058 Fryns-Smeets-Thiry syndrome HP:0000252 ORPHA:2058 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:502434 STAG1-related intellectual disability-facial dysmorphism-gastroesophageal reflux syndrome HP:0000252 ORPHA:502434 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:36367 Distal monosomy 1q HP:0000252 ORPHA:36367 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:3379 Distal trisomy 17q HP:0000252 ORPHA:3379 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:209905 Brain-lung-thyroid syndrome HP:0000252 ORPHA:209905 TAS HP:0040284 P ORPHA:orphadata[2023-01-27] -ORPHA:352490 Autism spectrum disorder due to AUTS2 deficiency HP:0000252 ORPHA:352490 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:2013 Cleft palate-large ears-small head syndrome HP:0000252 ORPHA:2013 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:352447 Progressive external ophthalmoplegia-myopathy-emaciation syndrome HP:0000252 ORPHA:352447 TAS HP:0040284 P ORPHA:orphadata[2023-01-27] -ORPHA:85329 X-linked intellectual disability-hypotonia-facial dysmorphism-aggressive behavior syndrome HP:0000252 ORPHA:85329 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:261652 Kleefstra syndrome due to a point mutation HP:0000252 ORPHA:261652 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:85321 Deafness-intellectual disability syndrome, Martin-Probst type HP:0000252 ORPHA:85321 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:85323 X-linked intellectual disability, Seemanova type HP:0000252 ORPHA:85323 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:85324 X-linked intellectual disability, Shrimpton type HP:0000252 ORPHA:85324 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:171680 Lissencephaly due to TUBA1A mutation HP:0000252 ORPHA:171680 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:250989 1q21.1 microdeletion syndrome HP:0000252 ORPHA:250989 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:3322 Hoyeraal-Hreidarsson syndrome HP:0000252 ORPHA:3322 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:289504 Combined malonic and methylmalonic acidemia HP:0000252 ORPHA:289504 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:329228 Microcephalic primordial dwarfism due to ZNF335 deficiency HP:0000252 ORPHA:329228 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:329224 Intellectual disability-craniofacial dysmorphism-cryptorchidism syndrome HP:0000252 ORPHA:329224 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:3305 Tetraploidy HP:0000252 ORPHA:3305 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:3306 Inverted duplicated chromosome 15 syndrome HP:0000252 ORPHA:3306 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:3307 Tetrasomy 18p HP:0000252 ORPHA:3307 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:3304 Fallot complex-intellectual disability-growth delay syndrome HP:0000252 ORPHA:3304 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:289522 Microtriplication 11q24.1 HP:0000252 ORPHA:289522 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:1590 Distal monosomy 13q HP:0000252 ORPHA:1590 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:1598 Monosomy 18p HP:0000252 ORPHA:1598 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:1597 Distal monosomy 17q HP:0000252 ORPHA:1597 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:1596 Distal monosomy 15q HP:0000252 ORPHA:1596 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:1580 Distal monosomy 10p HP:0000252 ORPHA:1580 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:544254 SYNGAP1-related developmental and epileptic encephalopathy HP:0000252 ORPHA:544254 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:1587 Monosomy 13q14 HP:0000252 ORPHA:1587 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:401810 Autosomal recessive spastic paraplegia type 64 HP:0000252 ORPHA:401810 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:2898 X-linked intellectual disability-plagiocephaly syndrome HP:0000252 ORPHA:2898 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:2896 Pitt-Hopkins syndrome HP:0000252 ORPHA:2896 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:363965 Koolen-De Vries syndrome due to a point mutation HP:0000252 ORPHA:363965 TAS HP:0040284 P ORPHA:orphadata[2023-01-27] -ORPHA:220295 Xeroderma pigmentosum-Cockayne syndrome complex HP:0000252 ORPHA:220295 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:2884 Piebaldism HP:0000252 ORPHA:2884 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:93950 X-linked intellectual disability, Sutherland-Haan type HP:0000252 ORPHA:93950 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:313781 20p13 microdeletion syndrome HP:0000252 ORPHA:313781 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:93946 Hamel cerebro-palato-cardiac syndrome HP:0000252 ORPHA:93946 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:93947 X-linked intellectual disability, Golabi-Ito-Hall type HP:0000252 ORPHA:93947 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:138 CHARGE syndrome HP:0000252 ORPHA:138 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:177 Rhizomelic chondrodysplasia punctata HP:0000252 ORPHA:177 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:464738 Basel-Vanagaite-Smirin-Yosef syndrome HP:0000252 ORPHA:464738 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:93926 Midline interhemispheric variant of holoprosencephaly HP:0000252 ORPHA:93926 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:93924 Lobar holoprosencephaly HP:0000252 ORPHA:93924 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:93925 Alobar holoprosencephaly HP:0000252 ORPHA:93925 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:159 Carnitine-acylcarnitine translocase deficiency HP:0000252 ORPHA:159 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:135 CACH syndrome HP:0000252 ORPHA:135 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:127 Borjeson-Forssman-Lehmann syndrome HP:0000252 ORPHA:127 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:124 Blackfan-Diamond anemia HP:0000252 ORPHA:124 TAS HP:0040284 P ORPHA:orphadata[2023-01-27] -ORPHA:96148 Distal monosomy 10q HP:0000252 ORPHA:96148 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:96147 Kleefstra syndrome due to 9q34 microdeletion HP:0000252 ORPHA:96147 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:251383 CK syndrome HP:0000252 ORPHA:251383 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:96149 Distal monosomy 12q HP:0000252 ORPHA:96149 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:98791 Alpha-thalassemia-intellectual disability syndrome linked to chromosome 16 HP:0000252 ORPHA:98791 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:541423 Growth delay-intellectual disability-hepatopathy syndrome HP:0000252 ORPHA:541423 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:96123 Monosomy 22 HP:0000252 ORPHA:96123 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:991 PAGOD syndrome HP:0000252 ORPHA:991 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:96170 Emanuel syndrome HP:0000252 ORPHA:96170 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:96176 Ring chromosome 13 syndrome HP:0000252 ORPHA:96176 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:495875 Congenital labioscrotal agenesis-cerebellar malformation-corneal dystrophy-facial dysmorphism syndrome HP:0000252 ORPHA:495875 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:96169 Koolen-De Vries syndrome HP:0000252 ORPHA:96169 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:96168 Monosomy 13q34 HP:0000252 ORPHA:96168 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:544503 RNF13-related severe early-onset epileptic encephalopathy HP:0000252 ORPHA:544503 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:999 Ermine phenotype HP:0000252 ORPHA:999 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:356961 SLC35A2-CDG HP:0000252 ORPHA:356961 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:364577 Intellectual disability-brachydactyly-Pierre Robin syndrome HP:0000252 ORPHA:364577 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:52503 X-linked creatine transporter deficiency HP:0000252 ORPHA:52503 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:513456 Intellectual disability-seizures-abnormal gait-facial dysmorphism syndrome HP:0000252 ORPHA:513456 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:352596 Progressive myoclonic epilepsy with dystonia HP:0000252 ORPHA:352596 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:495818 9q33.3q34.11 microdeletion syndrome HP:0000252 ORPHA:495818 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:1292 Brachymorphism-onychodysplasia-dysphalangism syndrome HP:0000252 ORPHA:1292 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:1299 Branchioskeletogenital syndrome HP:0000252 ORPHA:1299 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:1270 Bowen-Conradi syndrome HP:0000252 ORPHA:1270 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:163971 X-linked intellectual disability, Cilliers type HP:0000252 ORPHA:163971 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:163976 X-linked intellectual disability, Van Esch type HP:0000252 ORPHA:163976 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:1261 Bonnemann-Meinecke-Reich syndrome HP:0000252 ORPHA:1261 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:163937 X-linked intellectual disability, Najm type HP:0000252 ORPHA:163937 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:2598 Mitochondrial myopathy and sideroblastic anemia HP:0000252 ORPHA:2598 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:261519 Maternal uniparental disomy of chromosome X HP:0000252 ORPHA:261519 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:2585 Ataxia-pancytopenia syndrome HP:0000252 ORPHA:2585 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:352577 Bainbridge-Ropers syndrome HP:0000252 ORPHA:352577 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:2570 Lethal intrauterine growth restriction-cortical malformation-congenital contractures syndrome HP:0000252 ORPHA:2570 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:2574 Moynahan syndrome HP:0000252 ORPHA:2574 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:1236 Severe microbrachycephaly-intellectual disability-athetoid cerebral palsy syndrome HP:0000252 ORPHA:1236 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:1234 Bartsocas-Papas syndrome HP:0000252 ORPHA:1234 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:83617 Agammaglobulinemia-microcephaly-craniosynostosis-severe dermatitis syndrome HP:0000252 ORPHA:83617 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:163979 X-linked intellectual disability-craniofacioskeletal syndrome HP:0000252 ORPHA:163979 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:2557 Mietens syndrome HP:0000252 ORPHA:2557 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:1229 Congenital intrauterine infection-like syndrome HP:0000252 ORPHA:1229 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:2554 Ear-patella-short stature syndrome HP:0000252 ORPHA:2554 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:1227 Bangstad syndrome HP:0000252 ORPHA:1227 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:2556 Microphthalmia with linear skin defects syndrome HP:0000252 ORPHA:2556 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:352530 Intellectual disability-obesity-brain malformations-facial dysmorphism syndrome HP:0000252 ORPHA:352530 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:199 Cornelia de Lange syndrome HP:0000252 ORPHA:199 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:192 Coffin-Lowry syndrome HP:0000252 ORPHA:192 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:193 Cohen syndrome HP:0000252 ORPHA:193 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:2533 Microcephaly-deafness-intellectual disability syndrome HP:0000252 ORPHA:2533 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:500180 Childhood-onset motor and cognitive regression syndrome with extrapyramidal movement disorder HP:0000252 ORPHA:500180 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:35107 Desmosterolosis HP:0000252 ORPHA:35107 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:139444 Leukoencephalopathy with bilateral anterior temporal lobe cysts HP:0000252 ORPHA:139444 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:2526 Microcephaly-lymphedema-chorioretinopathy syndrome HP:0000252 ORPHA:2526 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:2528 Microcephaly-microcornea syndrome, Seemanova type HP:0000252 ORPHA:2528 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:2521 Microcephaly-cleft palate-abnormal retinal pigmentation syndrome HP:0000252 ORPHA:2521 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:2522 Microcephaly-cervical spine fusion anomalies syndrome HP:0000252 ORPHA:2522 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:2523 Microcephaly-brain defect-spasticity-hypernatremia syndrome HP:0000252 ORPHA:2523 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:139471 Microphthalmia with brain and digit anomalies HP:0000252 ORPHA:139471 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:139474 17q11.2 microduplication syndrome HP:0000252 ORPHA:139474 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:2513 Microcephaly-albinism-digital anomalies syndrome HP:0000252 ORPHA:2513 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:2514 Autosomal dominant primary microcephaly HP:0000252 ORPHA:2514 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:2515 Microcephaly-cardiomyopathy syndrome HP:0000252 ORPHA:2515 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:2516 Microcephaly-cardiac defect-lung malsegmentation syndrome HP:0000252 ORPHA:2516 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:500159 Microcephaly-corpus callosum and cerebellar vermis hypoplasia-facial dysmorphism-intellectual disability syndrom HP:0000252 ORPHA:500159 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:2518 Autosomal recessive chorioretinopathy-microcephaly syndrome HP:0000252 ORPHA:2518 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:2519 Microcephaly-seizures-intellectual disability-heart disease syndrome HP:0000252 ORPHA:2519 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:2510 Micro syndrome HP:0000252 ORPHA:2510 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:2511 Microbrachycephaly-ptosis-cleft lip syndrome HP:0000252 ORPHA:2511 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:2512 Autosomal recessive primary microcephaly HP:0000252 ORPHA:2512 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:2505 Multiple benign circumferential skin creases on limbs HP:0000252 ORPHA:2505 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:2508 Corpus callosum agenesis-abnormal genitalia syndrome HP:0000252 ORPHA:2508 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:2609 Isolated complex I deficiency HP:0000252 ORPHA:2609 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:2617 Microcephalic primordial dwarfism, Montreal type HP:0000252 ORPHA:2617 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:2604 Familial visceral myopathy HP:0000252 ORPHA:2604 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:254351 Distal 7q11.23 microdeletion syndrome HP:0000252 ORPHA:254351 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:319199 Autosomal recessive spastic paraplegia type 53 HP:0000252 ORPHA:319199 TAS HP:0040284 P ORPHA:orphadata[2023-01-27] -ORPHA:300573 Polymicrogyria due to TUBB2B mutation HP:0000252 ORPHA:300573 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:480907 X-linked intellectual disability-global development delay-facial dysmorphism-sacral caudal remnant syndrome HP:0000252 ORPHA:480907 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:254346 19p13.12 microdeletion syndrome HP:0000252 ORPHA:254346 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:319182 Wiedemann-Steiner syndrome HP:0000252 ORPHA:319182 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:208441 Bilateral parasagittal parieto-occipital polymicrogyria HP:0000252 ORPHA:208441 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:544469 PRUNE1-related neurological syndrome HP:0000252 ORPHA:544469 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:208447 Bilateral generalized polymicrogyria HP:0000252 ORPHA:208447 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:217346 19q13.11 microdeletion syndrome HP:0000252 ORPHA:217346 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:217340 17q21.31 microduplication syndrome HP:0000252 ORPHA:217340 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:3098 Rhizomelic syndrome, Urbach type HP:0000252 ORPHA:3098 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:896 Waardenburg syndrome type 3 HP:0000252 ORPHA:896 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:899 Walker-Warburg syndrome HP:0000252 ORPHA:899 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:88618 S-adenosylhomocysteine hydrolase deficiency HP:0000252 ORPHA:88618 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:3078 Severe X-linked intellectual disability, Gustavson type HP:0000252 ORPHA:3078 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:3079 Intellectual disability, Buenos-Aires type HP:0000252 ORPHA:3079 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:391307 Severe intellectual disability-short stature-behavioral abnormalities-facial dysmorphism syndrome HP:0000252 ORPHA:391307 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:319171 Distal 17p13.1 microdeletion syndrome HP:0000252 ORPHA:319171 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:434179 Orofaciodigital syndrome type 14 HP:0000252 ORPHA:434179 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:3068 Intellectual disability-myopathy-short stature-endocrine defect syndrome HP:0000252 ORPHA:3068 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:869 Triple A syndrome HP:0000252 ORPHA:869 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:3051 Nicolaides-Baraitser syndrome HP:0000252 ORPHA:3051 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:261494 Kleefstra syndrome HP:0000252 ORPHA:261494 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:858 Congenital toxoplasmosis HP:0000252 ORPHA:858 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:893 WAGR syndrome HP:0000252 ORPHA:893 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:891 Familial exudative vitreoretinopathy HP:0000252 ORPHA:891 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:3047 Blepharophimosis-intellectual disability syndrome, SBBYS type HP:0000252 ORPHA:3047 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:3033 Renal tubular dysgenesis HP:0000252 ORPHA:3033 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:309854 Cirrhosis-dystonia-polycythemia-hypermanganesemia syndrome HP:0000252 ORPHA:309854 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:949 Acrocraniofacial dysostosis HP:0000252 ORPHA:949 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:941 D-glyceric aciduria HP:0000252 ORPHA:941 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:3130 Satoyoshi syndrome HP:0000252 ORPHA:3130 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:939 3-hydroxyisobutyric aciduria HP:0000252 ORPHA:939 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:3132 Say-Barber-Miller syndrome HP:0000252 ORPHA:3132 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:3121 Ruvalcaba syndrome HP:0000252 ORPHA:3121 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:904 Williams syndrome HP:0000252 ORPHA:904 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:98889 Bilateral perisylvian polymicrogyria HP:0000252 ORPHA:98889 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:3103 Roberts syndrome HP:0000252 ORPHA:3103 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:300605 Juvenile amyotrophic lateral sclerosis HP:0000252 ORPHA:300605 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:1393 Cerebrocostomandibular syndrome HP:0000252 ORPHA:1393 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:1398 Isolated cerebellar agenesis HP:0000252 ORPHA:1398 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:276413 10q22.3q23.3 microdeletion syndrome HP:0000252 ORPHA:276413 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:1387 Cataract-intellectual disability-hypogonadism syndrome HP:0000252 ORPHA:1387 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:927 Hyperammonemia due to N-acetylglutamate synthase deficiency HP:0000252 ORPHA:927 TAS HP:0040284 P ORPHA:orphadata[2023-01-27] -ORPHA:929 Achalasia-microcephaly syndrome HP:0000252 ORPHA:929 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:276422 10q22.3q23.3 microduplication syndrome HP:0000252 ORPHA:276422 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:912 Zellweger syndrome HP:0000252 ORPHA:912 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:910 Xeroderma pigmentosum HP:0000252 ORPHA:910 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:1352 Atrioventricular defect-blepharophimosis-radial and anal defect syndrome HP:0000252 ORPHA:1352 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:1358 Carey-Fineman-Ziter syndrome HP:0000252 ORPHA:1358 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:50812 Zellweger-like syndrome without peroxisomal anomalies HP:0000252 ORPHA:50812 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:50817 Duane anomaly-myopathy-scoliosis syndrome HP:0000252 ORPHA:50817 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:2671 Neu-Laxova syndrome HP:0000252 ORPHA:2671 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:352665 Neurodevelopmental disorder-craniofacial dysmorphism-cardiac defect-skeletal anomalies syndrome due to 9q21.3 microdeletion HP:0000252 ORPHA:352665 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:480864 Recurrent metabolic encephalomyopathic crises-rhabdomyolysis-cardiac arrhythmia-intellectual disability syndrome HP:0000252 ORPHA:480864 TAS HP:0040284 P ORPHA:orphadata[2023-01-27] -ORPHA:86822 Lissencephaly type 3-metacarpal bone dysplasia syndrome HP:0000252 ORPHA:86822 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:500055 16p13.2 microdeletion syndrome HP:0000252 ORPHA:500055 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:1327 Camptodactyly syndrome, Guadalajara type 1 HP:0000252 ORPHA:1327 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:1326 Camptodactyly syndrome, Guadalajara type 2 HP:0000252 ORPHA:1326 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:86812 POMT1-related limb-girdle muscular dystrophy R11 HP:0000252 ORPHA:86812 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:2643 Microcephalic primordial dwarfism, Toriello type HP:0000252 ORPHA:2643 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:1314 Symmetrical thalamic calcifications HP:0000252 ORPHA:1314 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:2636 Microcephalic osteodysplastic primordial dwarfism types I and III HP:0000252 ORPHA:2636 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:2637 Microcephalic osteodysplastic primordial dwarfism type II HP:0000252 ORPHA:2637 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:1308 C syndrome HP:0000252 ORPHA:1308 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:314389 Xq12-q13.3 duplication syndrome HP:0000252 ORPHA:314389 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:1305 Feingold syndrome HP:0000252 ORPHA:1305 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:404448 ADNP syndrome HP:0000252 ORPHA:404448 TAS HP:0040284 P ORPHA:orphadata[2023-01-27] -ORPHA:1867 Hereditary bullous dystrophy, macular type HP:0000252 ORPHA:1867 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:1865 Dyssegmental dysplasia, Silverman-Handmaker type HP:0000252 ORPHA:1865 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:404473 Severe intellectual disability-progressive spastic diplegia syndrome HP:0000252 ORPHA:404473 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:157954 ANE syndrome HP:0000252 ORPHA:157954 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:543470 Optic atrophy-ataxia-peripheral neuropathy-global developmental delay syndrome HP:0000252 ORPHA:543470 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:1832 Lethal osteosclerotic bone dysplasia HP:0000252 ORPHA:1832 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:1824 Lowry-Wood syndrome HP:0000252 ORPHA:1824 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:65286 3q29 microdeletion syndrome HP:0000252 ORPHA:65286 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:264450 Trisomy 8p HP:0000252 ORPHA:264450 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:783 Rubinstein-Taybi syndrome HP:0000252 ORPHA:783 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:467166 Tubulinopathy-associated dysgyria HP:0000252 ORPHA:467166 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:565624 Combined oxidative phosphorylation defect type 39 HP:0000252 ORPHA:565624 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:391417 HSD10 disease HP:0000252 ORPHA:391417 TAS HP:0040284 P ORPHA:orphadata[2023-01-27] -ORPHA:391428 HSD10 disease, infantile type HP:0000252 ORPHA:391428 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:589618 Dystonia 28 HP:0000252 ORPHA:589618 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:391408 Primary microcephaly-mild intellectual disability-young-onset diabetes syndrome HP:0000252 ORPHA:391408 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:765 Pyruvate dehydrogenase deficiency HP:0000252 ORPHA:765 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:261349 2p15p16.1 microdeletion syndrome HP:0000252 ORPHA:261349 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:46059 Lathosterolosis HP:0000252 ORPHA:46059 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:1083 Microlissencephaly HP:0000252 ORPHA:1083 TAS HP:0040280 P ORPHA:orphadata[2023-01-27] -ORPHA:261337 Distal 22q11.2 microduplication syndrome HP:0000252 ORPHA:261337 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:261330 Distal 22q11.2 microdeletion syndrome HP:0000252 ORPHA:261330 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:816 Sjögren-Larsson syndrome HP:0000252 ORPHA:816 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:819 Smith-Magenis syndrome HP:0000252 ORPHA:819 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:818 Smith-Lemli-Opitz syndrome HP:0000252 ORPHA:818 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:261323 21q22.11q22.12 microdeletion syndrome HP:0000252 ORPHA:261323 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:2394 Pyruvate dehydrogenase E3 deficiency HP:0000252 ORPHA:2394 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:2399 Nasopalpebral lipoma-coloboma syndrome HP:0000252 ORPHA:2399 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:847 Alpha-thalassemia-X-linked intellectual disability syndrome HP:0000252 ORPHA:847 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:1052 Mosaic variegated aneuploidy syndrome HP:0000252 ORPHA:1052 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:833 Encephalopathy due to sulfite oxidase deficiency HP:0000252 ORPHA:833 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:261304 Paternal 20q13.2q13.3 microdeletion syndrome HP:0000252 ORPHA:261304 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:1046 Lethal hemolytic anemia-genital anomalies syndrome HP:0000252 ORPHA:1046 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:64754 Nevus comedonicus syndrome HP:0000252 ORPHA:64754 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:2375 Laryngeal abductor paralysis-intellectual disability syndrome HP:0000252 ORPHA:2375 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:319332 Autosomal recessive myogenic arthrogryposis multiplex congenita NOT HP:0000252 ORPHA:319332 TAS P ORPHA:orphadata[2023-01-27] -ORPHA:96334 Kagami-Ogata syndrome due to paternal uniparental disomy of chromosome 14 HP:0000252 ORPHA:96334 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:808 Seckel syndrome HP:0000252 ORPHA:808 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:800 Schwartz-Jampel syndrome HP:0000252 ORPHA:800 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:2346 Angioosteohypertrophic syndrome HP:0000252 ORPHA:2346 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:1005 Alopecia-contractures-dwarfism-intellectual disability syndrome HP:0000252 ORPHA:1005 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:1001 2q37 microdeletion syndrome HP:0000252 ORPHA:1001 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:2332 KBG syndrome HP:0000252 ORPHA:2332 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:284180 Xp22.13p22.2 duplication syndrome HP:0000252 ORPHA:284180 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:268943 Unilateral polymicrogyria HP:0000252 ORPHA:268943 TAS HP:0040284 P ORPHA:orphadata[2023-01-27] -ORPHA:2339 Keratosis follicularis-dwarfism-cerebral atrophy syndrome HP:0000252 ORPHA:2339 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:2323 Sanjad-Sakati syndrome HP:0000252 ORPHA:2323 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:2322 Kabuki syndrome HP:0000252 ORPHA:2322 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:2321 Jung syndrome HP:0000252 ORPHA:2321 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:169079 Cernunnos-XLF deficiency HP:0000252 ORPHA:169079 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:2311 Autosomal recessive spondylocostal dysostosis HP:0000252 ORPHA:2311 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:2319 Juberg-Hayward syndrome HP:0000252 ORPHA:2319 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:2316 Johnson neuroectodermal syndrome HP:0000252 ORPHA:2316 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:2315 Johanson-Blizzard syndrome HP:0000252 ORPHA:2315 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:2306 Isotretinoin-like syndrome HP:0000252 ORPHA:2306 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:293939 Distal Xq28 microduplication syndrome HP:0000252 ORPHA:293939 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:70594 Dopa-responsive dystonia due to sepiapterin reductase deficiency HP:0000252 ORPHA:70594 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:466688 Severe intellectual disability-corpus callosum agenesis-facial dysmorphism-cerebellar ataxia syndrome HP:0000252 ORPHA:466688 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:506353 Autosomal recessive complex spastic paraplegia due to Kennedy pathway dysfunction HP:0000252 ORPHA:506353 TAS HP:0040280 P ORPHA:orphadata[2023-01-27] -ORPHA:453504 Neurodevelopmental disorder-craniofacial dysmorphism-cardiac defect-skeletal anomalies syndrome due to a point mutation HP:0000252 ORPHA:453504 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:293967 Hypogonadotropic hypogonadism-severe microcephaly-sensorineural hearing loss-dysmorphism syndrome HP:0000252 ORPHA:293967 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:1980 Bilateral striopallidodentate calcinosis HP:0000252 ORPHA:1980 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:90308 Klippel-Trénaunay syndrome HP:0000252 ORPHA:90308 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:251071 8p23.1 microdeletion syndrome HP:0000252 ORPHA:251071 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:442835 Non-specific early-onset epileptic encephalopathy HP:0000252 ORPHA:442835 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:251066 8p11.2 deletion syndrome HP:0000252 ORPHA:251066 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:1964 Extrasystoles-short stature-hyperpigmentation-microcephaly syndrome HP:0000252 ORPHA:1964 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:251056 6q25 microdeletion syndrome HP:0000252 ORPHA:251056 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:699 Pearson syndrome HP:0000252 ORPHA:699 TAS HP:0040284 P ORPHA:orphadata[2023-01-27] -ORPHA:90348 Autosomal dominant cutis laxa HP:0000252 ORPHA:90348 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:90349 Autosomal recessive cutis laxa type 1 NOT HP:0000252 ORPHA:90349 TAS P ORPHA:orphadata[2023-01-27] -ORPHA:1948 Epilepsy-microcephaly-skeletal dysplasia syndrome HP:0000252 ORPHA:1948 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:1942 Myoclonic-astatic epilepsy HP:0000252 ORPHA:1942 TAS HP:0040284 P ORPHA:orphadata[2023-01-27] -ORPHA:251038 3q29 microduplication syndrome HP:0000252 ORPHA:251038 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:1934 Early infantile epileptic encephalopathy HP:0000252 ORPHA:1934 TAS HP:0040284 P ORPHA:orphadata[2023-01-27] -ORPHA:1933 Mitochondrial DNA depletion syndrome, encephalomyopathic form with methylmalonic aciduria HP:0000252 ORPHA:1933 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:1919 Phenobarbital embryopathy HP:0000252 ORPHA:1919 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:1917 Fetal methylmercury syndrome HP:0000252 ORPHA:1917 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:251028 SATB2-associated syndrome due to a chromosomal rearrangement HP:0000252 ORPHA:251028 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:353298 Roifman syndrome HP:0000252 ORPHA:353298 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:1926 Diabetic embryopathy HP:0000252 ORPHA:1926 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:1920 Toluene embryopathy HP:0000252 ORPHA:1920 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:1908 Aminopterin/methotrexate embryofetopathy HP:0000252 ORPHA:1908 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:66631 CEDNIK syndrome HP:0000252 ORPHA:66631 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:261290 Trisomy 17p HP:0000252 ORPHA:261290 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:251019 2q32q33 microdeletion syndrome HP:0000252 ORPHA:251019 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:251014 2q31.1 microdeletion syndrome HP:0000252 ORPHA:251014 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:1915 Fetal alcohol syndrome HP:0000252 ORPHA:1915 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:66629 Goldberg-Shprintzen megacolon syndrome HP:0000252 ORPHA:66629 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:1913 Fetal trimethadione syndrome HP:0000252 ORPHA:1913 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:1912 Fetal hydantoin syndrome HP:0000252 ORPHA:1912 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:398189 Focal facial dermal dysplasia type IV HP:0000252 ORPHA:398189 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:28378 Tyrosinemia type 2 HP:0000252 ORPHA:28378 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:261279 17q23.1q23.2 microdeletion syndrome HP:0000252 ORPHA:261279 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:168577 Hereditary cryohydrocytosis with reduced stomatin HP:0000252 ORPHA:168577 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:621 Hereditary methemoglobinemia HP:0000252 ORPHA:621 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:398156 Oculoauriculofrontonasal syndrome HP:0000252 ORPHA:398156 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:320385 Hereditary sensory and autonomic neuropathy due to TECPR2 mutation HP:0000252 ORPHA:320385 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:647 Nijmegen breakage syndrome HP:0000252 ORPHA:647 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:649 Norrie disease HP:0000252 ORPHA:649 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:77300 Auricular abnormalities-cleft lip with or without cleft palate-ocular abnormalities syndrome HP:0000252 ORPHA:77300 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:261236 16p13.11 microdeletion syndrome HP:0000252 ORPHA:261236 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:1094 Anonychia-microcephaly syndrome HP:0000252 ORPHA:1094 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:435628 Keppen-Lubinsky syndrome HP:0000252 ORPHA:435628 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:709 Peters plus syndrome HP:0000252 ORPHA:709 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:702 Pelizaeus-Merzbacher disease HP:0000252 ORPHA:702 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:1194 TMEM70-related mitochondrial encephalo-cardio-myopathy HP:0000252 ORPHA:1194 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:79096 Pyridoxal phosphate-responsive seizures HP:0000252 ORPHA:79096 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:261204 16p11.2p12.2 microduplication syndrome HP:0000252 ORPHA:261204 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:726 Alpers-Huttenlocher syndrome HP:0000252 ORPHA:726 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:168486 Congenital neuronal ceroid lipofuscinosis HP:0000252 ORPHA:168486 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:2491 Müllerian duct anomalies-limb anomalies syndrome HP:0000252 ORPHA:2491 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:1166 Congenital unilateral hypoplasia of depressor anguli oris HP:0000252 ORPHA:1166 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:2479 Megalocornea-intellectual disability syndrome HP:0000252 ORPHA:2479 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:1131 X-linked mandibulofacial dysostosis HP:0000252 ORPHA:1131 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:2462 Shprintzen-Goldberg syndrome HP:0000252 ORPHA:2462 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:2461 Marden-Walker syndrome HP:0000252 ORPHA:2461 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:530983 Lamb-Shaffer syndrome HP:0000252 ORPHA:530983 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:67046 3-methylglutaconic aciduria type 1 HP:0000252 ORPHA:67046 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:363528 Intellectual disability-strabismus syndrome HP:0000252 ORPHA:363528 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:67048 3-methylglutaconic aciduria type 4 HP:0000252 ORPHA:67048 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:1113 Aphalangy-syndactyly-microcephaly syndrome HP:0000252 ORPHA:1113 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:466768 Autosomal dominant Charcot-Marie-Tooth disease type 2Z HP:0000252 ORPHA:466768 TAS HP:0040284 P ORPHA:orphadata[2023-01-27] -ORPHA:1110 Aortic arch anomaly-facial dysmorphism-intellectual disability syndrome HP:0000252 ORPHA:1110 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:77299 Microphthalmia-brain atrophy syndrome HP:0000252 ORPHA:77299 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:2435 Hypo- and hypermelanotic cutaneous macules-retarded growth-intellectual disability syndrome HP:0000252 ORPHA:2435 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:453499 Neurodevelopmental disorder-craniofacial dysmorphism-cardiac defect-skeletal anomalies syndrome HP:0000252 ORPHA:453499 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:2409 Lowry-MacLean syndrome HP:0000252 ORPHA:2409 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:420561 Temple-Baraitser syndrome HP:0000252 ORPHA:420561 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:280763 Severe intellectual disability and progressive spastic paraplegia HP:0000252 ORPHA:280763 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:93324 Autosomal recessive Kenny-Caffey syndrome HP:0000252 ORPHA:93324 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:466934 VPS11-related autosomal recessive hypomyelinating leukodystrophy HP:0000252 ORPHA:466934 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:2968 Leukocyte adhesion deficiency HP:0000252 ORPHA:2968 TAS HP:0040284 P ORPHA:orphadata[2023-01-27] -ORPHA:466926 Seizures-scoliosis-macrocephaly syndrome HP:0000252 ORPHA:466926 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:1636 Distal monosomy 7q36 HP:0000252 ORPHA:1636 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:1620 Distal monosomy 3p HP:0000252 ORPHA:1620 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:457193 Autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome HP:0000252 ORPHA:457193 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:2959 Progeria-short stature-pigmented nevi syndrome HP:0000252 ORPHA:2959 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:314621 Duplication of the pituitary gland HP:0000252 ORPHA:314621 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:1606 1p36 deletion syndrome HP:0000252 ORPHA:1606 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:464311 Intellectual disability syndrome due to a DYRK1A point mutation HP:0000252 ORPHA:464311 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:1600 Monosomy 18q HP:0000252 ORPHA:1600 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:585 Multiple sulfatase deficiency HP:0000252 ORPHA:585 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:2919 Orofaciodigital syndrome type 5 HP:0000252 ORPHA:2919 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:2920 Oliver syndrome HP:0000252 ORPHA:2920 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:464306 DYRK1A-related intellectual disability syndrome HP:0000252 ORPHA:464306 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:314679 Cerebrofacioarticular syndrome HP:0000252 ORPHA:314679 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:578 Mucolipidosis type IV HP:0000252 ORPHA:578 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:2911 Poland syndrome HP:0000252 ORPHA:2911 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:261190 15q14 microdeletion syndrome HP:0000252 ORPHA:261190 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:420741 RIDDLE syndrome HP:0000252 ORPHA:420741 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:508498 Intellectual disability-cardiac anomalies-short stature-joint laxity syndrome HP:0000252 ORPHA:508498 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:268261 DYRK1A-related intellectual disability syndrome due to 21q22.13q22.2 microdeletion HP:0000252 ORPHA:268261 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:261183 15q11.2 microdeletion syndrome HP:0000252 ORPHA:261183 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:500545 Severe neurodevelopmental disorder with feeding difficulties-stereotypic hand movement-bilateral cataract HP:0000252 ORPHA:500545 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:567 22q11.2 deletion syndrome HP:0000252 ORPHA:567 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:568 Microphthalmia, Lenz type HP:0000252 ORPHA:568 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:565 Menkes disease HP:0000252 ORPHA:565 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:564 Meckel syndrome HP:0000252 ORPHA:564 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:521445 Microcephaly-facial dysmorphism-ocular anomalies-multiple congenital anomalies syndrome HP:0000252 ORPHA:521445 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:42775 PHACE syndrome HP:0000252 ORPHA:42775 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:559 Marinesco-Sjögren syndrome HP:0000252 ORPHA:559 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:391641 Feingold syndrome type 1 HP:0000252 ORPHA:391641 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:261144 FOXG1 syndrome due to 14q12 microdeletion HP:0000252 ORPHA:261144 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:2090 GMS syndrome HP:0000252 ORPHA:2090 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:508 Leprechaunism HP:0000252 ORPHA:508 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:502 Trichorhinophalangeal syndrome type 2 HP:0000252 ORPHA:502 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:2083 Prominent glabella-microcephaly-hypogenitalism syndrome HP:0000252 ORPHA:2083 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:521426 PLAA-associated neurodevelopmental disorder HP:0000252 ORPHA:521426 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:391646 Feingold syndrome type 2 HP:0000252 ORPHA:391646 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:448237 Zika virus disease HP:0000252 ORPHA:448237 TAS HP:0040284 P ORPHA:orphadata[2023-01-27] -ORPHA:2075 Genitopalatocardiac syndrome HP:0000252 ORPHA:2075 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:261112 Monosomy 9p HP:0000252 ORPHA:261112 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:284339 Pontocerebellar hypoplasia type 7 HP:0000252 ORPHA:284339 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:2065 Galloway-Mowat syndrome HP:0000252 ORPHA:2065 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:468678 White-Sutton syndrome HP:0000252 ORPHA:468678 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:2163 Holoprosencephaly-craniosynostosis syndrome HP:0000252 ORPHA:2163 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:2162 Holoprosencephaly HP:0000252 ORPHA:2162 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:2169 Methylcobalamin deficiency type cblE HP:0000252 ORPHA:2169 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:2166 Holoprosencephaly-postaxial polydactyly syndrome HP:0000252 ORPHA:2166 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:2165 Holoprosencephaly-caudal dysgenesis syndrome HP:0000252 ORPHA:2165 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:2152 Mowat-Wilson syndrome HP:0000252 ORPHA:2152 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:464282 Spastic paraplegia-severe developmental delay-epilepsy syndrome HP:0000252 ORPHA:464282 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:464288 Short stature-brachydactyly-obesity-global developmental delay syndrome HP:0000252 ORPHA:464288 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:238769 1q44 microdeletion syndrome HP:0000252 ORPHA:238769 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:86309 DPAGT1-CDG HP:0000252 ORPHA:86309 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:2135 Hennekam-Beemer syndrome HP:0000252 ORPHA:2135 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:181393 Growth hormone insensitivity syndrome HP:0000252 ORPHA:181393 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:3465 Worster-Drought syndrome HP:0000252 ORPHA:3465 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:3469 XK aprosencephaly syndrome HP:0000252 ORPHA:3469 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:447788 Cerebral visual impairment HP:0000252 ORPHA:447788 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:3448 Weaver-Williams syndrome HP:0000252 ORPHA:3448 TAS HP:0040280 P ORPHA:orphadata[2023-01-27] -ORPHA:2115 Harrod syndrome HP:0000252 ORPHA:2115 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:447760 Autosomal recessive spastic paraplegia type 9B HP:0000252 ORPHA:447760 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:3433 Microcephaly-brachydactyly-kyphoscoliosis syndrome HP:0000252 ORPHA:3433 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:2108 Hallermann-Streiff syndrome HP:0000252 ORPHA:2108 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:3434 MMEP syndrome HP:0000252 ORPHA:3434 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:2107 Hall-Riggs syndrome HP:0000252 ORPHA:2107 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:363659 20q11.2 microduplication syndrome HP:0000252 ORPHA:363659 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:79124 Hepatic veno-occlusive disease-immunodeficiency syndrome HP:0000252 ORPHA:79124 TAS HP:0040284 P ORPHA:orphadata[2023-01-27] -ORPHA:1695 Non-distal trisomy 10q HP:0000252 ORPHA:1695 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:363611 CTCF-related neurodevelopmental disorder HP:0000252 ORPHA:363611 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:487796 Macrothrombocytopenia-lymphedema-developmental delay-facial dysmorphism-camptodactyly syndrome HP:0000252 ORPHA:487796 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:468631 Microcephalic cortical malformations-short stature due to RTTN deficiency HP:0000252 ORPHA:468631 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:1675 Dihydropyrimidine dehydrogenase deficiency HP:0000252 ORPHA:1675 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:468620 Intellectual disability-epilepsy-extrapyramidal syndrome HP:0000252 ORPHA:468620 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:1665 Sporadic fetal brain disruption sequence HP:0000252 ORPHA:1665 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:431361 Progressive encephalopathy with leukodystrophy due to DECR deficiency HP:0000252 ORPHA:431361 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:2990 Autosomal recessive multiple pterygium syndrome HP:0000252 ORPHA:2990 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:2994 Short stature-craniofacial anomalies-genital hypoplasia syndrome HP:0000252 ORPHA:2994 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:1667 Wolcott-Rallison syndrome HP:0000252 ORPHA:1667 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:2995 Baraitser-Winter cerebrofrontofacial syndrome HP:0000252 ORPHA:2995 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:363623 GMPPB-related limb-girdle muscular dystrophy R19 HP:0000252 ORPHA:363623 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:2980 Acrootoocular syndrome HP:0000252 ORPHA:2980 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:2985 Pseudoprogeria syndrome HP:0000252 ORPHA:2985 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:397946 Autosomal spastic paraplegia type 58 HP:0000252 ORPHA:397946 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:438114 RARS-related autosomal recessive hypomyelinating leukodystrophy HP:0000252 ORPHA:438114 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:485350 CLCN4-related X-linked intellectual disability syndrome HP:0000252 ORPHA:485350 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:1738 Trisomy 4p HP:0000252 ORPHA:1738 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:1727 22q11.2 duplication syndrome HP:0000252 ORPHA:1727 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:459070 X-linked intellectual disability-cerebellar hypoplasia-spondylo-epiphyseal dysplasia syndrome HP:0000252 ORPHA:459070 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:79326 ALG2-CDG HP:0000252 ORPHA:79326 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:505237 Early-onset seizures-distal limb anomalies-facial dysmorphism-global developmental delay syndrome HP:0000252 ORPHA:505237 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:1707 Distal trisomy 15q HP:0000252 ORPHA:1707 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:1715 Trisomy 18p HP:0000252 ORPHA:1715 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:1713 17p11.2 microduplication syndrome HP:0000252 ORPHA:1713 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:79321 ALG3-CDG HP:0000252 ORPHA:79321 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:1702 Non-distal trisomy 13q HP:0000252 ORPHA:1702 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:438134 PCNA-related progressive neurodegenerative photosensitivity syndrome HP:0000252 ORPHA:438134 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:99776 Mosaic trisomy 9 HP:0000252 ORPHA:99776 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:457260 X-linked intellectual disability-hypotonia-movement disorder syndrome HP:0000252 ORPHA:457260 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:452 X-linked lissencephaly with abnormal genitalia HP:0000252 ORPHA:452 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:94065 15q24 microdeletion syndrome HP:0000252 ORPHA:94065 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:94063 12q14 microdeletion syndrome HP:0000252 ORPHA:94063 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:457240 X-linked intellectual disability-short stature-overweight syndrome HP:0000252 ORPHA:457240 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:99742 Amish lethal microcephaly HP:0000252 ORPHA:99742 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:280071 ALG11-CDG HP:0000252 ORPHA:280071 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:85172 Microcephalic osteodysplastic dysplasia, Saul-Wilson type HP:0000252 ORPHA:85172 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:85165 Severe achondroplasia-developmental delay-acanthosis nigricans syndrome HP:0000252 ORPHA:85165 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:369840 TRAPPC11-related limb-girdle muscular dystrophy R18 HP:0000252 ORPHA:369840 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:228402 2q23.1 microdeletion syndrome HP:0000252 ORPHA:228402 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:2282 Dysmorphism-short stature-deafness-disorder of sex development syndrome HP:0000252 ORPHA:2282 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:228415 5q35 microduplication syndrome HP:0000252 ORPHA:228415 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:370921 STT3A-CDG HP:0000252 ORPHA:370921 TAS HP:0040280 P ORPHA:orphadata[2023-01-27] -ORPHA:2273 Ichthyosis follicularis-alopecia-photophobia syndrome HP:0000252 ORPHA:2273 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:2271 Congenital ichthyosis-microcephalus-tetraplegia syndrome HP:0000252 ORPHA:2271 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:369939 Severe motor and intellectual disabilities-sensorineural deafness-dystonia syndrome HP:0000252 ORPHA:369939 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:2261 Hypospadias-intellectual disability, Goldblatt type syndrome HP:0000252 ORPHA:2261 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:2257 Primary pulmonary hypoplasia HP:0000252 ORPHA:2257 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:2232 Primary hypergonadotropic hypogonadism-partial alopecia syndrome HP:0000252 ORPHA:2232 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:525731 Pediatric-onset Graves disease HP:0000252 ORPHA:525731 TAS HP:0040284 P ORPHA:orphadata[2023-01-27] -ORPHA:319675 Microcephalic primordial dwarfism, Dauber type HP:0000252 ORPHA:319675 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:2220 Hypertrichosis cubiti HP:0000252 ORPHA:2220 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:2213 Hypertelorism-microtia-facial clefting syndrome HP:0000252 ORPHA:2213 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:370079 Proximal 16p11.2 microduplication syndrome HP:0000252 ORPHA:370079 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:255182 Pyruvate dehydrogenase E3-binding protein deficiency HP:0000252 ORPHA:255182 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:2216 Maternal hyperthermia-induced birth defects HP:0000252 ORPHA:2216 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:2204 Dysplastic cortical hyperostosis HP:0000252 ORPHA:2204 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:2203 Hyperlysinemia HP:0000252 ORPHA:2203 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:79254 Classic phenylketonuria HP:0000252 ORPHA:79254 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:2209 Maternal phenylketonuria HP:0000252 ORPHA:2209 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:79243 Pyruvate dehydrogenase E1-alpha deficiency HP:0000252 ORPHA:79243 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:79244 Pyruvate dehydrogenase E2 deficiency HP:0000252 ORPHA:79244 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:79237 Galactokinase deficiency HP:0000252 ORPHA:79237 TAS HP:0040284 P ORPHA:orphadata[2023-01-27] -ORPHA:371364 Hypotonia-speech impairment-severe cognitive delay syndrome HP:0000252 ORPHA:371364 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:1797 Autosomal dominant spondylocostal dysostosis HP:0000252 ORPHA:1797 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:1798 Dysostosis, Stanescu type HP:0000252 ORPHA:1798 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:1786 Acrofacial dysostosis, Catania type HP:0000252 ORPHA:1786 TAS HP:0040281 P ORPHA:orphadata[2023-01-27] -ORPHA:79282 Methylmalonic acidemia with homocystinuria, type cblC HP:0000252 ORPHA:79282 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:370010 Intellectual disability-facial dysmorphism-hand anomalies syndrome HP:0000252 ORPHA:370010 TAS HP:0040283 P ORPHA:orphadata[2023-01-27] -ORPHA:477673 Postnatal microcephaly-infantile hypotonia-spastic diplegia-dysarthria-intellectual disability syndrome HP:0000252 ORPHA:477673 TAS HP:0040282 P ORPHA:orphadata[2023-01-27] -ORPHA:26792 Short chain acyl-CoA dehydrogenase deficiency HP:0000252 ORPHA:26792 TAS HP:0040284 P ORPHA:orphadata[2023-01-27] diff --git a/tests/input/test_sample.hpoa.tsv b/tests/input/test_sample.hpoa.tsv deleted file mode 100644 index 4674d60c2..000000000 --- a/tests/input/test_sample.hpoa.tsv +++ /dev/null @@ -1,100 +0,0 @@ -OMIM:620038 Neurodevelopmental disorder with microcephaly, hypotonia, and absent language HP:0000252 PMID:32129449 PCS 2/2 P HPO:probinson[2022-10-03] -OMIM:608716 Microcephaly 5, primary, autosomal recessive HP:0000252 PMID:16673149 PCS 6/6 P HPO:probinson[2009-02-17];HPO:probinson[2022-06-23] -OMIM:619428 Focal segmental glomerulosclerosis and neurodevelopmental syndrome HP:0000252 PMID:27346735 PCS 1/1 P HPO:probinson[2021-10-21] -OMIM:251250 Microcephaly with cervical spine fusion anomalies HP:0000252 OMIM:251250 IEA P HPO:iea[2009-02-17] -OMIM:612626 Chromosome 15q26-qter deletion syndrome HP:0000252 OMIM:612626 IEA P HPO:skoehler[2010-06-19] -OMIM:309580 Intellectual disability-hypotonic facies syndrome, X-linked HP:0000252 OMIM:309580 IEA P HPO:iea[2009-02-17] -OMIM:614558 Epileptic encephalopathy, early infantile, 13 HP:0000252 PMID:25239001 PCS HP:0011463 1/1 P HPO:skoehler[2015-01-04];HPO:probinson[2022-06-04] -OMIM:616140 Leukodystrophy, hypomyelinating, 9 HP:0000252 OMIM:616140 TAS P HPO:skoehler[2015-01-04] -OMIM:617397 Pseudo-Torch syndrome 2 HP:0000252 PMID:27325888 PCS 1/5 P HPO:skoehler[2017-07-13];HPO:probinson[2022-03-23] -OMIM:309500 Renpenning syndrome HP:0000252 PMID:15782410 PCS 38/44 P HPO:iea[2009-02-17];HPO:probinson[2020-08-09] -OMIM:180870 Ruvalcaba syndrome HP:0000252 OMIM:180870 IEA P HPO:iea[2009-02-17] -OMIM:609460 Goldberg-Shprintzen syndrome HP:0000252 OMIM:609460 IEA P HPO:iea[2009-02-17] -OMIM:615599 Neurodevelopmental disorder with feeding difficulties, thin corpus callosum, and foot deformity HP:0000252 PMID:21937992 PCS 2/2 P HPO:skoehler[2014-02-06];HPO:probinson[2022-03-15] -OMIM:609654 Short stature and facioauriculothoracic malformations HP:0000252 OMIM:609654 IEA P HPO:iea[2009-02-17] -OMIM:608885 Stomatin-Deficient cryohydrocytosis with neurologic defects HP:0000252 OMIM:608885 TAS P HPO:skoehler[2015-12-30] -OMIM:620027 Neurodevelopmental disorder with microcephaly, short stature, and speech delay HP:0000252 PMID:35298461 PCS 7/8 P HPO:probinson[2022-10-05] -OMIM:600001 Pancreatic agenesis and congenital heart defects HP:0000252 OMIM:600001 TAS HP:0040283 P HPO:skoehler[2012-11-18] -OMIM:619304 Pontocerebellar hypoplasia, type 1F HP:0000252 PMID:33463720 PCS 1/1 P HPO:probinson[2021-07-06] -OMIM:619814 Developmental and epileptic encephalopathy 101 HP:0000252 PMID:27164704 PCS 1/3 P HPO:probinson[2022-05-14] -OMIM:617938 Developmental and epileptic encephalopathy 62 HP:0000252 PMID:29466837 PCS 1/6 P HPO:skoehler[2019-04-18];HPO:probinson[2021-02-18] -OMIM:608670 Robin sequence, distinctive facial appearance, and brachydactyly HP:0000252 PMID:15057987 PCS 1/2 P HP:probinson[2022-02-09] -OMIM:308350 Developmental and epileptic encephalopathy 1 HP:0000252 PMID:21108397;PMID:11889467;OMIM:308350 PCS 13/13 P HPO:iea[2009-02-17];HPO:probinson[2022-06-22];HPO:probinson[2021-06-23] -OMIM:615284 Charcot-Marie-Tooth disease, type 4B3 HP:0000252 OMIM:615284 TAS P HPO:skoehler[2015-02-22] -OMIM:312170 Pyruvate dehydrogenase e1-alpha deficiency HP:0000252 OMIM:312170 IEA P HPO:iea[2009-02-17] -OMIM:164280 Feingold syndrome 1 HP:0000252 OMIM:164280 IEA P HPO:iea[2009-02-17] -OMIM:611134 Meckel syndrome, type 4 HP:0000252 OMIM:611134 TAS HP:0040283 P HPO:skoehler[2015-04-26] -OMIM:617827 Immunodeficiency 55 HP:0000252 PMID:28414293 PCS 2/5 P HPO:skoehler[2019-04-18];HPO:probinson[2022-09-25] -OMIM:615673 Myopathy with extrapyramidal signs HP:0000252 PMID:24336167 PCS 5/15 P HPO:skoehler[2017-07-13];HPO:probinson[2021-10-18] -OMIM:618890 Neurodevelopmental disorder and structural brain anomalies with or without seizures and spasticity HP:0000252 PMID:29090338 PCS 1/1 P HPO:probinson[2020-08-13];HPO:probinson[2020-08-13] -OMIM:619243 Global developmental delay with speech and behavioral abnormalities HP:0000252 PMID:32152250 PCS 3/17 P HPO:probinson[2021-05-11] -OMIM:530000 Kearns-Sayre syndrome HP:0000252 OMIM:530000 IEA P HPO:iea[2009-02-17] -OMIM:614541 Chromosome 16q22 deletion syndrome HP:0000252 PMID:8230159 IEA 3/6 P HPO:probinson[2021-06-26] -OMIM:223540 Dwarfism, mental retardation, and eye abnormality HP:0000252 OMIM:223540 TAS P HPO:skoehler[2015-07-26] -OMIM:617061 Mental retardation, autosomal dominant 44 HP:0000252 PMID:26721934;PMID:32109419 PCS 13/19 P HPO:skoehler[2017-07-13];HPO:probinson[2022-03-28];HPO:probinson[2022-04-02] -OMIM:615272 Fanconi anemia, complementation group Q HP:0000252 PMID:23623386 PCS 1/2 P HPO:skoehler[2013-08-18];HPO:probinson[2022-03-15] -OMIM:617101 Intellectual developmental disorder with persistence of fetal hemoglobin HP:0000252 OMIM:617101 TAS P HPO:skoehler[2017-07-13] -OMIM:620023 Neurodevelopmental disorder with microcephaly, movement abnormalities, and seizures HP:0000252 PMID:35202461 PCS 6/6 P HPO:probinson[2022-10-07] -OMIM:612947 Microcephaly, growth retardation, cataract, hearing loss, and unusual appearance HP:0000252 OMIM:612947 IEA P HPO:skoehler[2010-06-19] -OMIM:613680 Beaulieu-Boycott-Innes syndrome HP:0000252 PMID:23621916 PCS 4/4 P HPO:skoehler[2012-10-17];HPO:probinson[2022-09-08] -OMIM:603467 Fanconi anemia, complementation group F HP:0000252 PMID:31288759;PMID:27714961 PCS 2/4 P HPO:probinson[2021-07-05];HPO:probinson[2020-07-22];HPO:probinson[2020-07-22] -OMIM:619148 Chromosome 13q33-q34 deletion syndrome HP:0000252 PMID:19363806 PCS 8/11 P HPO:probinson[2021-03-13] -OMIM:608540 Congenital disorder of glycosylation, type Ik HP:0000252 OMIM:608540 IEA P HPO:iea[2009-02-17] -OMIM:613489 Congenital disorder of glycosylation, type IIj HP:0000252 OMIM:613489 TAS HP:0040283 P HPO:skoehler[2012-11-18] -OMIM:601349 Microphthalmia, syndromic 8 HP:0000252 OMIM:601349 IEA P HPO:skoehler[2010-06-20] -OMIM:618798 Beck-Fahrner syndrome HP:0000252 PMID:31928709 PCS 1/11 P HPO:probinson[2020-05-18] -OMIM:618889 Liberfarb syndrome HP:0000252 PMID:31263216 PCS P HPO:probinson[2020-07-24] -OMIM:617303 Mucopolysaccharidosis-Plus syndrome HP:0000252 PMID:27547915 PCS 1/2 P HPO:probinson[2021-02-19] -OMIM:609625 Chromosome 10Q26 deletion syndrome HP:0000252 OMIM:609625 IEA P HPO:iea[2009-02-17] -OMIM:614485 Trigonocephaly 2 HP:0000252 OMIM:614485 TAS HP:0040283 P HPO:skoehler[2012-11-18] -OMIM:609056 Salt and pepper developmental regression syndrome HP:0000252 OMIM:609056 TAS HP:0040283 P HPO:skoehler[2014-08-24] -OMIM:619218 ENDOVE syndrome, limb-brain type HP:0000252 PMID:33568816 PCS 1/1 P HPO:probinson[2021-05-18] -OMIM:619151 AMED syndrome, digenic HP:0000252 PMID:33355142 PCS 6/7 P HPO:probinson[2021-03-05] -OMIM:271110 Spinal muscular atrophy with microcephaly and mental subnormality HP:0000252 OMIM:271110 IEA P HPO:iea[2009-02-17] -OMIM:616651 Roifman syndrome HP:0000252 PMID:26522830 PCS 5/6 P HPO:skoehler[2015-12-30] -OMIM:244450 Kaufman oculocerebrofacial syndrome HP:0000252 PMID:23200864 PCS P HPO:iea[2009-02-17] -OMIM:301056 Multiple congenital anomalies-neurodevelopmental syndrome, X-linked HP:0000252 PMID:33523931 PCS 5/10 P HPO:probinson[2021-05-02];HPO:probinson[2021-05-02] -OMIM:614886 Peroxisome biogenesis disorder 12A (Zellweger) HP:0000252 OMIM:614886 TAS P HPO:skoehler[2017-07-13] -OMIM:619268 Alzahrani-Kuwahara syndrome HP:0000252 PMID:33242396 PCS 7/9 P HPO:probinson[2021-05-31] -OMIM:615419 Hypotonia, infantile, with psychomotor retardation and characteristic facies 1 HP:0000252 OMIM:615419 TAS P HPO:skoehler[2013-09-30] -OMIM:613612 Congenital disorder of glycosylation, type IIi HP:0000252 PMID:23228021 PCS 6/7 P HPO:probinson[2020-08-11] -OMIM:618470 Intellectual developmental disorder with severe speech and ambulation defects HP:0000252 PMID:31031012 PCS 2/10 P HPO:skoehler[2019-09-07];HPO:probinson[2022-11-09] -OMIM:614231 Microcephaly, epilepsy, and diabetes syndrome HP:0000252 OMIM:614231 TAS P HPO:skoehler[2013-01-22] -OMIM:606232 Phelan-Mcdermid syndrome HP:0000252 PMID:20301377 PCS HP:0040284 P HPO:iea[2012-04-24];HPO:probinson[2019-11-28] -OMIM:156200 Mental retardation, autosomal dominant 1 HP:0000252 OMIM:156200 TAS P HPO:skoehler[2012-11-18] -OMIM:607326 Smith-Mccort dysplasia 1 HP:0000252 OMIM:607326 IEA P HPO:iea[2009-02-17] -OMIM:615352 Muscular dystrophy-dystroglycanopathy (limb-girdle), type C, 14 HP:0000252 PMID:23768512 PCS 2/3 P HPO:skoehler[2013-10-06];HPO:probinson[2022-12-13] -OMIM:617243 Fanconi anemia, complementation group V HP:0000252 PMID:27500492 PCS 1/1 P HPO:skoehler[2017-07-13];HPO:probinson[2022-09-27] -OMIM:614254 Neurodevelopmental disorder with or without hyperkinetic movements and seizures, autosomal dominant HP:0000252 PMID:25864721 PCS 2/4 P HPO:skoehler[2019-04-18];HPO:probinson[2023-01-17] -OMIM:617404 Muscular dystrophy, congenital, with cataracts and intellectual disability HP:0000252 OMIM:617404 TAS 2/12 P HPO:skoehler[2017-07-13];HPO:probinson[2022-11-27] -OMIM:619321 Growth restriction, hypoplastic kidneys, alopecia, and distinctive facies HP:0000252 PMID:29851065 PCS 4/4 P HPO:probinson[2021-07-03] -OMIM:224230 Dyskeratosis congenita, autosomal recessive 1 HP:0000252 OMIM:224230 IEA P HPO:iea[2009-02-17] -OMIM:614462 Hyperglycinemia, lactic acidosis, and seizures HP:0000252 OMIM:614462 TAS P HPO:skoehler[2012-10-17] -OMIM:600901 Fanconi anemia, complementation group E HP:0000252 OMIM:600901 IEA P HPO:iea[2009-02-17] -OMIM:617276 Developmental and epileptic encephalopathy 48 HP:0000252 PMID:27889060 PCS 9/12 P HPO:skoehler[2017-07-13];HPO:probinson[2021-02-13] -OMIM:614813 Short stature, onychodysplasia, facial dysmorphism, and hypotrichosis HP:0000252 OMIM:614813 TAS HP:0003581 P HPO:skoehler[2012-11-16];HPO:probinson[2021-10-20] -OMIM:164200 Oculodentodigital dysplasia HP:0000252 OMIM:164200 IEA P HPO:probinson[2009-02-17] -OMIM:117650 Cerebrocostomandibular syndrome HP:0000252 OMIM:117650 TAS P HPO:probinson[2009-02-17] -OMIM:245349 Pyruvate dehydrogenase e3-binding protein deficiency HP:0000252 OMIM:245349 IEA P HPO:iea[2009-02-17] -OMIM:619087 Noonan syndrome 13 HP:0000252 PMID:32721402 PCS 1/7 P HPO:probinson[2020-12-21] -OMIM:617988 Jaberi-Elahi syndrome HP:0000252 PMID:29449720 PCS 3/3 P HPO:skoehler[2019-04-18];HPO:probinson[2022-09-07] -OMIM:613026 Chromosome 19q13.11 deletion syndrome, distal HP:0000252 PMID:19126570 PCS 3/3 P HPO:skoehler[2010-06-19];HPO:probinson[2021-07-06] -OMIM:618736 Structural brain anomalies with impaired intellectual development and craniosynostosis HP:0000252 PMID:26340333 PCS 3/9 P HPO:probinson[2020-05-20] -OMIM:612952 Aicardi-Goutieres syndrome 5 HP:0000252 OMIM:612952 TAS HP:0040283 P HPO:skoehler[2017-07-13] -OMIM:616603 Cutis laxa, autosomal dominant 3 HP:0000252 OMIM:616603 TAS P HPO:skoehler[2015-11-15] -OMIM:272440 Filippi syndrome HP:0000252 OMIM:272440 IEA P HPO:iea[2009-02-17] -OMIM:300884 Epileptic encephalopathy, early infantile, 36 HP:0000252 PMID:22492991 PCS 1/1 P HPO:skoehler[2012-11-25];HPO:probinson[2022-05-30] -OMIM:252160 Molybdenum cofactor deficiency, complementation group B HP:0000252 PMID:16021469 PCS 1/1 P HPO:skoehler[2014-01-28];HPO:probinson[2022-11-08] -OMIM:619470 Neurodevelopmental disorder with motor and speech delay and behavioral abnormalities HP:0000252 PMID:33824500 PCS 8/17 P HPO:probinson[2021-10-16] -OMIM:615851 Pontocerebellar hypoplasia, type 2E HP:0000252 PMID:24577744 PCS P HPO:skoehler[2014-06-24];HPO:probinson[2020-12-13] -OMIM:613155 Muscular dystrophy-dystroglycanopathy (congenital with impaired intellectual development), type B, 1 HP:0000252 PMID:16575835 PCS 5/5 P HPO:skoehler[2012-10-17];HPO:probinson[2022-11-04] -OMIM:112370 Brachmann-De lange-like facial changes with microcephaly, metatarsusadductus, and developmental delay HP:0000252 OMIM:112370 IEA P HPO:iea[2009-02-17] -OMIM:618482 Generalized epilepsy with febrile seizures plus, type 10 HP:0000252 PMID:30351409 PCS 2/19 P HPO:probinson[2019-07-06] -OMIM:309800 Microphthalmia, syndromic 1 HP:0000252 OMIM:309800 IEA P HPO:iea[2009-02-17] -OMIM:613451 Frontonasal dysplasia 2 HP:0000252 PMID:19692347 PCS 1/2 P HPO:skoehler[2015-07-26];HPO:probinson[2022-05-08] -OMIM:304100 Corpus callosum, partial agenesis of, X-linked HP:0000252 OMIM:304100 IEA P HPO:iea[2009-02-17] -OMIM:618468 Epileptic encephalopathy, early infantile, 76 HP:0000252 PMID:31031012 PCS 6/11 P HPO:probinson[2020-05-15];HPO:probinson[2020-05-15] -OMIM:618325 Lissencephaly 9 with complex brainstem malformation HP:0000252 PMID:30471716 PCS 2/8 P HPO:skoehler[2019-04-18];HPO:probinson[2022-11-10] -OMIM:615596 Congenital disorder of glycosylation, type Iw HP:0000252 PMID:23842455 PCS 2/2 P HPO:skoehler[2014-02-06];HPO:probinson[2022-03-27] -OMIM:609425 Chromosome 3q29 deletion syndrome HP:0000252 PMID:15918153 PCS P HPO:iea[2010-09-13] -OMIM:271109 Spinal muscular atrophy with mental retardation HP:0000252 OMIM:271109 IEA P HPO:iea[2009-02-17] diff --git a/tests/input/training/training-ctd-001.yaml b/tests/input/training/training-ctd-001.yaml deleted file mode 100644 index 821bafa0d..000000000 --- a/tests/input/training/training-ctd-001.yaml +++ /dev/null @@ -1,18 +0,0 @@ -base_model: text-davinci-003 -prompt_header: | - From the text below, extract the following entities in the following format: - triples: - Text: -prompt_footer: | - === -examples: -- completion: | - Cocaine INDUCES myocardial injury - prompt: | - Electrocardiographic evidence of myocardial injury in psychiatrically hospitalized cocaine abusers. -- completion: | - Sulpiride INDUCES tardive dystonia; Sulpiride treats Pyschosis - prompt: | - Sulpiride is a selective D2-receptor antagonist with antipsychotic and antidepressant properties. Although initially thought to be free of extrapyramidal side effects, sulpiride-induced tardive dyskinesia and parkinsonism have been reported occasionally. We studied a 37-year-old man who developed persistent segmental dystonia within 2 months after starting sulpiride therapy. We could not find any previous reports of sulpiride-induced tardive dystonia - - diff --git a/tests/input/training/training-drugmechdb-001.jsonl b/tests/input/training/training-drugmechdb-001.jsonl deleted file mode 100644 index 6d62c72fb..000000000 --- a/tests/input/training/training-drugmechdb-001.jsonl +++ /dev/null @@ -1,100 +0,0 @@ -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\n Bendamustine is a bifunctional mechlorethamine derivative capable of forming electrophilic alkyl groups that covalently bond to other molecules. Through this function as an alkylating agent, bendamustine causes intra- and inter-strand crosslinks between DNA bases resulting in cell death. It is active against both active and quiescent cells, although the exact mechanism of action is unknown.\n\n===\n\ndisease: Leukemia, Lymphocytic, Chronic, B-Cell\ndrug: Bendamustine\n", "completion": "'disease: Leukemia, Lymphocytic, Chronic, B-Cell\n\n drug: Bendamustine\n\n mechanism_links: Bendamustine Hydrochloride - disrupts - DNA; DNA - participates\n in - DNA replication; DNA replication - precedes - lymphocyte proliferation; lymphocyte\n proliferation - positively correlated with - Leukemia, Lymphocytic, Chronic, B-Cell'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nThe bactericidal activity of cefmetazole results from the inhibition of cell wall synthesis via affinity for penicillin-binding proteins (PBPs).\n\n===\n\ndisease: Pneumonia, Staphylococcal\ndrug: Cefmetazole\n", "completion": "'disease: Pneumonia, Staphylococcal\n\n drug: Cefmetazole\n\n mechanism_links: Cefmetazole - decreases activity of - InterPro:IPR005311; InterPro:IPR005311\n - positively regulates - peptidoglycan biosynthetic process; peptidoglycan biosynthetic\n process - positively regulates - peptidoglycan-based cell wall biogenesis; peptidoglycan-based\n cell wall biogenesis - positively correlated with - cell division; cell division\n - in taxon - Staphylococcus aureus; Staphylococcus aureus - causes - Pneumonia,\n Staphylococcal'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nFusidic acid works by interfering with bacterial protein synthesis, specifically by preventing the translocation of the elongation factor G (EF-G) from the ribosome. It also can inhibit chloramphenicol acetyltransferase enzymes.\n\n===\n\ndisease: Pharyngitis\ndrug: Fusidic acid\n", "completion": "'disease: Pharyngitis\n\n drug: Fusidic acid\n\n mechanism_links: Fusidic Acid - decreases activity of - PR:A2RCI2; PR:A2RCI2 - positively\n regulates - translation; translation - occurs in - NCBITaxon:1314; NCBITaxon:1314\n - causes - Pharyngitis'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nFentanyl binds to opioid receptors, especially the mu opioid receptor, which are coupled to G-proteins.[A179533] Activation of opioid receptors causes GTP to be exchanged for GDP on the G-proteins which in turn down regulates adenylate cyclase, reducing concentrations of cAMP.[A179533] Reduced cAMP decreases cAMP dependant influx of calcium ions into the cell.[A179533] The exchange of GTP for GDP results in hyperpolarization of the cell and inhibition of nerve activity.[A179533]\n\n===\n\ndisease: Pain\ndrug: Fentanyl\n", "completion": "'disease: Pain\n\n drug: Fentanyl\n\n mechanism_links: Fentanyl - increases activity of - mu-type opioid receptor (human);\n Fentanyl - increases activity of - delta-type opioid receptor (human); mu-type opioid\n receptor (human) - positively regulates - REACT:R-HSA-372790; delta-type opioid\n receptor (human) - positively regulates - REACT:R-HSA-372790; REACT:R-HSA-372790\n - decreases activity of - PR:B7Z2C7; PR:B7Z2C7 - increases abundance of - 3'',5''-cyclic\n AMP; 3'',5''-cyclic AMP - negatively regulates - ATP-sensitive inward rectifier\n potassium channel 11 (human); 3'',5''-cyclic AMP - positively correlated with -\n calcium ion import; ATP-sensitive inward rectifier potassium channel 11 (human)\n - participates in - membrane hyperpolarization; calcium ion import - positively\n regulates - substance P secretion, neurotransmission; calcium ion import - positively\n regulates - glutamate secretion, neurotransmission; membrane hyperpolarization -\n negatively regulates - action potential initiation; substance P secretion, neurotransmission\n - located in - pain receptor cell; glutamate secretion, neurotransmission - located\n in - pain receptor cell; action potential initiation - positively regulates - pain\n receptor cell; pain receptor cell - positively correlated with - Pain'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nBenzocaine binds to sodium channels and reversibly stabilizes the neuronal membrane which decreases its permeability to sodium ions. Depolarization of the neuronal membrane is inhibited thereby blocking the initiation and conduction of nerve impulses.\n\n===\n\ndisease: Cough\ndrug: Benzocaine\n", "completion": "'disease: Cough\n\n drug: Benzocaine\n\n mechanism_links: Benzocaine - decreases activity of - sodium channel protein type\n 10 subunit alpha (human); sodium channel protein type 10 subunit alpha (human) -\n participates in - voltage-gated sodium channel activity; voltage-gated sodium channel\n activity - increases transport of - Sodium; Sodium - positively correlated with\n - membrane depolarization; membrane depolarization - positively regulates - neuronal\n action potential; neuronal action potential - occurs in - pain receptor cell; pain\n receptor cell - participates in - sensory perception of pain; sensory perception\n of pain - occurs in - Cough'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nCortisone acetate binds to the cytosolic glucocorticoid receptor. After binding the receptor the newly formed receptor-ligand complex translocates itself into the cell nucleus, where it binds to many glucocorticoid response elements (GRE) in the promoter region of the target genes. The DNA bound receptor then interacts with basic transcription factors, causing the increase in expression of specific target genes. The anti-inflammatory actions of corticosteroids are thought to involve lipocortins, phospholipase A2 inhibitory proteins which, through inhibition arachidonic acid, control the biosynthesis of prostaglandins and leukotrienes. Specifically glucocorticoids induce lipocortin-1 (annexin-1) synthesis, which then binds to cell membranes preventing the phospholipase A2 from coming into contact with its substrate arachidonic acid. This leads to diminished eicosanoid production. The cyclooxygenase (both COX-1 and COX-2) expression is also suppressed, potentiating the effect. In other words, the two main products in inflammation Prostaglandins and Leukotrienes are inhibited by the action of Glucocorticoids. Glucocorticoids also stimulate the lipocortin-1 escaping to the extracellular space, where it binds to the leukocyte membrane receptors and inhibits various inflammatory events: epithelial adhesion, emigration, chemotaxis, phagocytosis, respiratory burst and the release of various inflammatory mediators (lysosomal enzymes, cytokines, tissue plasminogen activator, chemokines etc.) from neutrophils, macrophages and mastocytes. Additionally the immune system is suppressed by corticosteroids due to a decrease in the function of the lymphatic system, a reduction in immunoglobulin and complement concentrations, the precipitation of lymphocytopenia, and interference with antigen-antibody binding.\n\n===\n\ndisease: Anemia, Diamond-Blackfan\ndrug: Cortisone acetate\n", "completion": "'disease: Anemia, Diamond-Blackfan\n\n drug: Cortisone acetate\n\n mechanism_links: Cortisone - increases activity of - glucocorticoid receptor (human);\n glucocorticoid receptor (human) - increases activity of - annexin A1 (human); glucocorticoid\n receptor (human) - decreases activity of - prostaglandin G/H synthase 1 (human);\n glucocorticoid receptor (human) - decreases activity of - prostaglandin G/H synthase\n 2 (human); annexin A1 (human) - decreases activity of - cytosolic phospholipase\n A2 (human); prostaglandin G/H synthase 1 (human) - positively regulates - prostaglandin\n biosynthetic process; prostaglandin G/H synthase 2 (human) - positively regulates\n - prostaglandin biosynthetic process; cytosolic phospholipase A2 (human) - positively\n regulates - leukotriene biosynthetic process; cytosolic phospholipase A2 (human)\n - positively regulates - prostaglandin biosynthetic process; leukotriene biosynthetic\n process - positively correlated with - inflammatory response; prostaglandin biosynthetic\n process - positively correlated with - inflammatory response; inflammatory response\n - positively correlated with - HP:0001908; HP:0001908 - manifestation of - Anemia,\n Diamond-Blackfan'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nDione anticonvulsants such as paramethadione reduce T-type calcium currents in thalamic neurons (including thalamic relay neurons). This inhibits corticothalamic transmission and raises the threshold for repetitive activity in the thalamus. This results in a dampening of the abnormal thalamocortical rhythmicity proposed to underlie the 3-Hz spike-and-wave discharge seen on electroencephalogram (EEG) during absence seizures.\n\n===\n\ndisease: Epilepsy, Absence\ndrug: Paramethadione\n", "completion": "'disease: Epilepsy, Absence\n\n drug: Paramethadione\n\n mechanism_links: paramethadione - decreases activity of - voltage-dependent T-type\n calcium channel subunit alpha-1G (human); paramethadione - decreases activity of\n - voltage-dependent T-type calcium channel subunit alpha-1H (human); paramethadione\n - decreases activity of - voltage-dependent T-type calcium channel subunit alpha-1I\n (human); voltage-dependent T-type calcium channel subunit alpha-1G (human) - positively\n regulates - voltage-gated calcium channel activity; voltage-dependent T-type calcium\n channel subunit alpha-1H (human) - positively regulates - voltage-gated calcium\n channel activity; voltage-dependent T-type calcium channel subunit alpha-1I (human)\n - positively regulates - voltage-gated calcium channel activity; voltage-gated calcium\n channel activity - positively regulates - neuronal action potential; neuronal action\n potential - positively regulates - neuronal signal transduction; neuronal signal\n transduction - positively correlated with - Epilepsy, Absence'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nFlumethasone is a glucocorticoid receptor agonist. This complex binds to the nucleus causing a variety of genetic activation and repressions. The antiinflammatory actions of corticosteroids are thought to involve lipocortins, phospholipase A2 inhibitory proteins which, through inhibition arachidonic acid, control the biosynthesis of prostaglandins and leukotrienes. The immune system is suppressed by corticosteroids due to a decrease in the function of the lymphatic system, a reduction in immunoglobulin and complement concentrations, the precipitation of lymphocytopenia, and interference with antigen-antibody binding. Flumethasone binds to plasma transcortin, and it becomes active when it is not bound to transcortin.\n\n===\n\ndisease: Pruritus Ani\ndrug: Flumethasone\n", "completion": "'disease: Pruritus Ani\n\n drug: Flumethasone\n\n mechanism_links: Flumethasone - increases activity of - glucocorticoid receptor\n (human); glucocorticoid receptor (human) - increases activity of - annexin A1 (human);\n annexin A1 (human) - decreases activity of - cytosolic phospholipase A2 (human);\n annexin A1 (human) - negatively regulates - prostaglandin G/H synthase 2 (human);\n cytosolic phospholipase A2 (human) - increases abundance of - Prostaglandins; prostaglandin\n G/H synthase 2 (human) - increases abundance of - Prostaglandins; Prostaglandins\n - positively regulates - inflammatory response; inflammatory response - has phenotype\n - HP:0000989; HP:0000989 - manifestation of - Pruritus Ani'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nThe bactericidal action of gemifloxacin results from inhibition of the enzymes topoisomerase II (DNA gyrase) and topoisomerase IV, which are required for bacterial DNA replication, transcription, repair, and recombination.\n\n===\n\ndisease: Pneumonia, Bacterial\ndrug: Gemifloxacin\n", "completion": "'disease: Pneumonia, Bacterial\n\n drug: Gemifloxacin\n\n mechanism_links: MESH:D000077735 - decreases activity of - DNA topoisomerase 4 subunit\n A (Streptococcus pneumoniae TIGR4); DNA topoisomerase 4 subunit A (Streptococcus\n pneumoniae TIGR4) - participates in - DNA replication; DNA replication - occurs\n in - Streptococcus pneumoniae; Streptococcus pneumoniae - causes - Pneumonia, Bacterial'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nTobramycin binds irreversibly to one of two aminoglycoside binding sites on the 30 S ribosomal subunit, inhibiting bacterial protein synthesis. Tobramycin may also destabilize bacterial memebrane by binding to 16 S 16 S r-RNA. An active transport mechanism for aminoglycoside uptake is necessary in the bacteria in order to attain a significant intracellular concentration of tobramycin.\n\n===\n\ndisease: Escherichia coli Infections\ndrug: Tobramycin\n", "completion": "'disease: Escherichia coli Infections\n\n drug: Tobramycin\n\n mechanism_links: Tobramycin - negatively regulates - RNA, Ribosomal, 16S; Tobramycin\n - negatively regulates - RNA, Ribosomal, 23S; RNA, Ribosomal, 16S - located in -\n ribosome; RNA, Ribosomal, 23S - located in - ribosome; ribosome - positively regulates\n - translation; translation - occurs in - Escherichia coli; Escherichia coli - causes\n - Escherichia coli Infections'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nThe mechanism by which felbamate exerts its anticonvulsant activity is unknown, but in animal test systems designed to detect anticonvulsant activity, felbamate has properties in common with other marketed anticonvulsants. <i>In vitro</i> receptor binding studies suggest that felbamate may be an antagonist at the strychnine-insensitive glycine-recognition site of the N-methyl-D-aspartate (NMDA) receptor-ionophore complex. Antagonism of the NMDA receptor glycine binding site may block the effects of the excitatory amino acids and suppress seizure activity. Animal studies indicate that felbamate may increase the seizure threshold and may decrease seizure spread. It is also indicated that felbamate has weak inhibitory effects on GABA-receptor binding, benzodiazepine receptor binding.\n\n===\n\ndisease: Epilepsy\ndrug: Felbamate\n", "completion": "'disease: Epilepsy\n\n drug: Felbamate\n\n mechanism_links: felbamate - decreases activity of - glutamate receptor ionotropic,\n NMDA 2B (human); felbamate - decreases activity of - glutamate receptor ionotropic,\n NMDA 2A (human); glutamate receptor ionotropic, NMDA 2B (human) - positively correlated\n with - HP:0001250; glutamate receptor ionotropic, NMDA 2A (human) - positively correlated\n with - HP:0001250; HP:0001250 - manifestation of - Epilepsy'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nCorticosteroids like triamcinolone inhibit phospholipase A2 on cell membranes, preventing the breakdown of lysosomal membranes of leukocytes, which in turn prevent the formation of arachidonic acid, which decrease expression of cyclooxygenase and lipoxygenase, inhibiting synthesis of prostaglandins and leukotrienes.[A184463] Anti-inflammatory activity occurs via reversal of vascular dilation and reducing permeability, which prevents macrophage and leukocyte migration.[A184463] Triamcinolone also inhibits nuclear factor kappa-B, which decreases the production of pro-inflammatory signals such as interleukin-6, interleukin-8, and monocyte chemoattractant protein-1.[A184463]\n\n===\n\ndisease: Angioedema\ndrug: Triamcinolone\n", "completion": "'disease: Angioedema\n\n drug: Triamcinolone\n\n mechanism_links: Triamcinolone - increases activity of - glucocorticoid receptor\n (human); glucocorticoid receptor (human) - increases activity of - annexin A1 (human);\n glucocorticoid receptor (human) - decreases activity of - prostaglandin G/H synthase\n 1 (human); glucocorticoid receptor (human) - decreases activity of - prostaglandin\n G/H synthase 2 (human); annexin A1 (human) - decreases activity of - cytosolic phospholipase\n A2 (human); prostaglandin G/H synthase 1 (human) - positively regulates - prostaglandin\n biosynthetic process; prostaglandin G/H synthase 2 (human) - positively regulates\n - prostaglandin biosynthetic process; cytosolic phospholipase A2 (human) - positively\n regulates - leukotriene biosynthetic process; cytosolic phospholipase A2 (human)\n - positively regulates - prostaglandin biosynthetic process; leukotriene biosynthetic\n process - positively correlated with - inflammatory response; prostaglandin biosynthetic\n process - positively correlated with - inflammatory response; inflammatory response\n - located in - dermis; dermis - location of - Angioedema'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nAntihistamines such as phenindamine appear to compete with histamine for histamine H1- receptor sites on effector cells. The antihistamines antagonize those pharmacological effects of histamine which are mediated through activation of H1- receptor sites and thereby reduce the intensity of allergic reactions and tissue injury response involving histamine release.\n\n===\n\ndisease: Rhinitis, Vasomotor\ndrug: Phenindamine\n", "completion": "'disease: Rhinitis, Vasomotor\n\n drug: Phenindamine\n\n mechanism_links: phenindamine - decreases activity of - histamine H1 receptor (human);\n histamine H1 receptor (human) - positively correlated with - Histamine; Histamine\n - causes - hypersensitivity; hypersensitivity - correlated with - Rhinitis, Vasomotor'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nAmphotericin B is fungistatic or fungicidal depending on the concentration obtained in body fluids and the susceptibility of the fungus. The drug acts by binding to sterols (ergosterol) in the cell membrane of susceptible fungi. This creates a transmembrane channel, and the resultant change in membrane permeability allowing leakage of intracellular components. Ergosterol, the principal sterol in the fungal cytoplasmic membrane, is the target site of action of amphotericin B and the azoles. Amphotericin B, a polyene, binds irreversibly to ergosterol, resulting in disruption of membrane integrity and ultimately cell death.\n\n===\n\ndisease: Intraabdominal Infections\ndrug: Amphotericin B\n", "completion": "'disease: Intraabdominal Infections\n\n drug: Amphotericin B\n\n mechanism_links: Amphotericin B - negatively regulates - Ergosterol; Ergosterol\n - positively regulates - fungal-type cell wall; fungal-type cell wall - in taxon\n - Candida albicans; Candida albicans - causes - Intraabdominal Infections'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nBy binding to specific penicillin-binding proteins (PBPs) located inside the bacterial cell wall, Ampicillin inhibits the third and last stage of bacterial cell wall synthesis. Cell lysis is then mediated by bacterial cell wall autolytic enzymes such as autolysins; it is possible that Ampicillin interferes with an autolysin inhibitor.\n\n===\n\ndisease: Escherichia coli Infections\ndrug: Ampicillin\n", "completion": "'disease: Escherichia coli Infections\n\n drug: Ampicillin\n\n mechanism_links: Ampicillin - negatively regulates - Pfam:PF00905; Pfam:PF00905\n - positively regulates - peptidoglycan biosynthetic process; peptidoglycan biosynthetic\n process - positively correlated with - peptidoglycan-based cell wall biogenesis;\n peptidoglycan-based cell wall biogenesis - in taxon - Escherichia coli; Escherichia\n coli - causes - Escherichia coli Infections'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nSalicylic acid directly irreversibly inhibits COX-1 and COX-2 to decrease conversion of arachidonic acid to precursors of prostaglandins and thromboxanes. Salicylate's use in rheumatic diseases is due to it's analgesic and anti-inflammatory activity. Salicylic acid is a key ingredient in many skin-care products for the treatment of acne, psoriasis, calluses, corns, keratosis pilaris, and warts. Salicylic acid allows cells of the epidermis to more readily slough off. Because of its effect on skin cells, salicylic acid is used in several shampoos used to treat dandruff. Salicylic acid is also used as an active ingredient in gels which remove verrucas (plantar warts). Salicylic acid competitively inhibits oxidation of uridine-5-diphosphoglucose (UDPG) with nicotinamide adenosine dinucleotide (NAD) and noncompetitively with UDPG. It also competitively inhibits the transferring of the glucuronyl group of uridine-5-phosphoglucuronic acid (UDPGA) to a phenolic acceptor. Inhibition of mucopoly saccharide synthesis is likely responsible for the slowing of wound healing with salicylates.\n\n===\n\ndisease: Fever\ndrug: Salicylic acid\n", "completion": "'disease: Fever\n\n drug: Salicylic acid\n\n mechanism_links: Salicylic Acid - decreases activity of - prostaglandin G/H synthase\n 1 (human); Salicylic Acid - decreases activity of - prostaglandin G/H synthase 2\n (human); prostaglandin G/H synthase 1 (human) - positively regulates - prostaglandin\n biosynthetic process; prostaglandin G/H synthase 2 (human) - positively regulates\n - prostaglandin biosynthetic process; prostaglandin biosynthetic process - positively\n correlated with - inflammatory response; inflammatory response - positively correlated\n with - Fever'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nFusidic acid works by interfering with bacterial protein synthesis, specifically by preventing the translocation of the elongation factor G (EF-G) from the ribosome. It also can inhibit chloramphenicol acetyltransferase enzymes.\n\n===\n\ndisease: Anthrax\ndrug: Fusidic acid\n", "completion": "'disease: Anthrax\n\n drug: Fusidic acid\n\n mechanism_links: Fusidic Acid - decreases activity of - PR:Q81VT3; PR:Q81VT3 - positively\n regulates - translation; translation - occurs in - Bacillus anthracis; Bacillus\n anthracis - causes - Anthrax'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nAntagonism at D2 receptors is believed to relieve the positive symptoms of schizophrenia such as delusions, hallucinations, and thought disorders. Perospirone targets the mesolimbic patway to reverse the overactivity of the dopaminergic signalling via D2 receptors [T28]. 5-HT2A antagonism is thought to allevaite the negative symptoms and cognitive impairments of schizophrenia. These receptors are Gi/Go coupled receptors that lead to decreased neurotransmitter release and neuronal inhibition when activated, thus play a role in dopamine release regulation. Perospirone targets these receptors in the nigrostriatal pathway to reduce dopamine release and function. In contrast, 5-HT2A receptor antagonism may improve the negative symptoms by enhancing dopamine and glutamate release in the mesocortical pathway [T28]. 5-HT1A receptor activation further inhibits the release of 5-HT into the synaptic cleft.\n\n===\n\ndisease: Schizophrenia\ndrug: Perospirone\n", "completion": "'disease: Schizophrenia\n\n drug: Perospirone\n\n mechanism_links: perospirone - increases activity of - 5-hydroxytryptamine receptor\n 1A (human); perospirone - decreases activity of - D(2) dopamine receptor (human);\n perospirone - decreases activity of - 5-hydroxytryptamine receptor 2A (human); 5-hydroxytryptamine\n receptor 1A (human) - negatively correlated with - HP:0000739; 5-hydroxytryptamine\n receptor 2A (human) - positively regulates - dopamine secretion; 5-hydroxytryptamine\n receptor 2A (human) - positively regulates - glutamate secretion; glutamate secretion\n - positively correlated with - dopamine neurotransmitter receptor activity; dopamine\n neurotransmitter receptor activity - positively correlated with - HP:0000709; D(2)\n dopamine receptor (human) - positively regulates - dopamine secretion; dopamine\n secretion - increases abundance of - dopamine; dopamine - located in - medial forebrain\n bundle; medial forebrain bundle - correlated with - HP:0000709; HP:0000709 - positively\n correlated with - Schizophrenia; dopamine - located in - dorsolateral prefrontal\n cortex; dorsolateral prefrontal cortex - correlated with - HP:0100543; dorsolateral\n prefrontal cortex - correlated with - HP:0030213; dorsolateral prefrontal cortex\n - correlated with - HP:0012154; dorsolateral prefrontal cortex - correlated with\n - HP:0002465; dorsolateral prefrontal cortex - correlated with - HP:0000741; HP:0100543\n - manifestation of - Schizophrenia; HP:0030213 - manifestation of - Schizophrenia;\n HP:0012154 - manifestation of - Schizophrenia; HP:0002465 - manifestation of - Schizophrenia;\n HP:0000741 - manifestation of - Schizophrenia; HP:0000739 - manifestation of - Schizophrenia'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nFluocinonide is a potent glucocorticoid steroid used topically as anti-inflammatory agent for the treatment of skin disorders such as eczema. Fluocinonide binds to the cytosolic glucocorticoid receptor. After binding the receptor the newly formed receptor-ligand complex translocates itself into the cell nucleus, where it binds to many glucocorticoid response elements (GRE) in the promoter region of the target genes. The DNA bound receptor then interacts with basic transcription factors, causing the increase in expression of specific target genes. The anti-inflammatory actions of corticosteroids are thought to involve lipocortins, phospholipase A2 inhibitory proteins which, through inhibition arachidonic acid, control the biosynthesis of prostaglandins and leukotrienes. Specifically glucocorticoids induce lipocortin-1 (annexin-1) synthesis, which then binds to cell membranes preventing the phospholipase A2 from coming into contact with its substrate arachidonic acid. This leads to diminished eicosanoid production. Cyclooxygenase (both COX-1 and COX-2) expression is also suppressed, potentiating the effect. In another words, the two main products in inflammation Prostaglandins and Leukotrienes are inhibited by the action of Glucocorticoids. Glucocorticoids also stimulate the lipocortin-1 escaping to the extracellular space, where it binds to the leukocyte membrane receptors and inhibits various inflammatory events: epithelial adhesion, emigration, chemotaxis, phagocytosis, respiratory burst and the release of various inflammatory mediators (lysosomal enzymes, cytokines, tissue plasminogen activator, chemokines etc.) from neutrophils, macrophages and mastocytes. Additionally the immune system is suppressed by corticosteroids due to a decrease in the function of the lymphatic system, a reduction in immunoglobulin and complement concentrations, the precipitation of lymphocytopenia, and interference with antigen-antibody binding. Like other glucocorticoid agents Fluocinolone acetonide acts as a physiological antagonist to insulin by decreasing glycogenesis (formation of glycogen). It also promotes the breakdown of lipids (lipolysis), and proteins, leading to the mobilization of extrahepatic amino acids and ketone bodies. This leads to increased circulating glucose concentrations (in the blood). There is also decreased glycogen formation in the liver.\n\n===\n\ndisease: Lymphoma, T-Cell, Cutaneous\ndrug: Fluocinonide\n", "completion": "'disease: Lymphoma, T-Cell, Cutaneous\n\n drug: Fluocinonide\n\n mechanism_links: Fluocinonide - increases activity of - glucocorticoid receptor\n (human); glucocorticoid receptor (human) - increases activity of - annexin A1 (human);\n annexin A1 (human) - decreases activity of - cytosolic phospholipase A2 (human);\n annexin A1 (human) - decreases activity of - prostaglandin G/H synthase 2 (human);\n cytosolic phospholipase A2 (human) - increases abundance of - Prostaglandins; prostaglandin\n G/H synthase 2 (human) - increases abundance of - Prostaglandins; Prostaglandins\n - positively regulates - inflammatory response; inflammatory response - has phenotype\n - HP:0000989; inflammatory response - has phenotype - HP:0000988; HP:0000989 - manifestation\n of - Lymphoma, T-Cell, Cutaneous; HP:0000988 - manifestation of - Lymphoma, T-Cell,\n Cutaneous'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nCeftriaxone works by inhibiting the mucopeptide synthesis in the bacterial cell wall.[T324,L15082] The beta-lactam moiety of ceftriaxone binds to carboxypeptidases, endopeptidases, and transpeptidases in the bacterial cytoplasmic membrane. These enzymes are involved in cell-wall synthesis and cell division. Binding of ceftriaxone to these enzymes causes the enzyme to lose activity; therefore, the bacteria produce defective cell walls, causing cell death.\n\n===\n\ndisease: Rhinoscleroma\ndrug: Ceftriaxone\n", "completion": "'disease: Rhinoscleroma\n\n drug: Ceftriaxone\n\n mechanism_links: Ceftriaxone - decreases activity of - InterPro:IPR017790; InterPro:IPR017790\n - participates in - peptidoglycan biosynthetic process; peptidoglycan biosynthetic\n process - positively regulates - peptidoglycan-based cell wall biogenesis; peptidoglycan-based\n cell wall biogenesis - occurs in - NCBITaxon:39831; NCBITaxon:39831 - causes - Rhinoscleroma'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nThe antitumor activity of Vincristine is thought to be due primarily to inhibition of mitosis at metaphase through its interaction with tubulin. Like other vinca alkaloids, Vincristine may also interfere with: 1) amino acid, cyclic AMP, and glutathione metabolism, 2) calmodulin-dependent Ca<sup>2+</sup>-transport ATPase activity, 3) cellular respiration, and 4) nucleic acid and lipid biosynthesis.\n\n===\n\ndisease: Lymphoma, Large B-Cell, Diffuse\ndrug: Vincristine\n", "completion": "'disease: Lymphoma, Large B-Cell, Diffuse\n\n drug: Vincristine\n\n mechanism_links: Vincristine - decreases activity of - tubulin beta chain (human);\n tubulin beta chain (human) - part of - microtubule cytoskeleton organization involved\n in mitosis; microtubule cytoskeleton organization involved in mitosis - positively\n regulates - mitotic nuclear division; mitotic nuclear division - positively regulates\n - cell population proliferation; cell population proliferation - positively correlated\n with - Lymphoma, Large B-Cell, Diffuse'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nAmphotericin B is fungistatic or fungicidal depending on the concentration obtained in body fluids and the susceptibility of the fungus. The drug acts by binding to sterols (ergosterol) in the cell membrane of susceptible fungi. This creates a transmembrane channel, and the resultant change in membrane permeability allowing leakage of intracellular components. Ergosterol, the principal sterol in the fungal cytoplasmic membrane, is the target site of action of amphotericin B and the azoles. Amphotericin B, a polyene, binds irreversibly to ergosterol, resulting in disruption of membrane integrity and ultimately cell death.\n\n===\n\ndisease: Histoplasmosis\ndrug: Amphotericin B\n", "completion": "'disease: Histoplasmosis\n\n drug: Amphotericin B\n\n mechanism_links: Amphotericin B - negatively regulates - Ergosterol; Ergosterol\n - positively regulates - fungal-type cell wall; fungal-type cell wall - in taxon\n - NCBITaxon:5036; NCBITaxon:5036 - causes - Histoplasmosis'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nIn bacterial replication, an interaction that is important for translation initiation of proteins occurs at the 3′ end of the 16S rRNA, found on the ribosome on the 30S subunit [A174046], [A19429], [A174070]. The 30S subunit is the smaller subunit of the ribosome of prokaryotes, including bacteria[F3073]. Tetracyclines such as doxycycline are thought to inhibit translation by binding to the 16S rRNA portion of the ribosome [A174040], preventing binding of tRNA to the RNA-30S bacterial ribosomal subunit, which is necessary for the delivery of amino acids for protein synthesis. As a result of the above actions, the initiation of protein synthesis by polyribosome formation is blocked. This stops the replication of bacteria and produces a bacteriostatic effect [F3052].\n\n===\n\ndisease: Lymphogranuloma Venereum\ndrug: Doxycycline\n", "completion": "'disease: Lymphogranuloma Venereum\n\n drug: Doxycycline\n\n mechanism_links: Doxycycline - negatively regulates - RNA, Ribosomal, 16S; RNA,\n Ribosomal, 16S - located in - small ribosomal subunit; small ribosomal subunit -\n participates in - translation; translation - occurs in - Chlamydia trachomatis;\n Chlamydia trachomatis - causes - Lymphogranuloma Venereum'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nAfter a meal, the hormone gastrin, produced by cells in the lining of the stomach, stimulates the release of histamine, which then binds to histamine H2 receptors, leading to the secretion of gastric acid. Ranitidine reduces the secretion of gastric acid by reversible binding to histamine (H2) receptors, which are found on gastric parietal cells. This process leads to the inhibition of histamine binding to this receptor, causing the reduction of gastric acid secretion. The relief of gastric-acid related symptoms can occur as soon as 60 minutes after administration of a single dose, and the effects can last from 4-10 hours, providing fast and effective symptomatic relief.[A176774,T533,L10818]\n\n===\n\ndisease: Dyspepsia\ndrug: Ranitidine\n", "completion": "'disease: Dyspepsia\n\n drug: Ranitidine\n\n mechanism_links: Ranitidine - decreases activity of - histamine H2 receptor (human);\n histamine H2 receptor (human) - positively regulates - gastric acid secretion; gastric\n acid secretion - increases abundance of - Gastric Acid; Gastric Acid - contributes\n to - Heartburn; Heartburn - manifestation of - Dyspepsia'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nLevocetirizine selectively inhibits histamine H<sub>1</sub> receptors.[L7694] This action prevents histamine from activating this receptor and causing effects like smooth muscle contraction, increased permeability of vascular endothelium, histidine uptake in basophils, stimulation of cough receptors, and stimulation of flare responses in the nervous system.[A181790]\n\n===\n\ndisease: Rhinitis, Allergic, Seasonal\ndrug: Levocetirizine\n", "completion": "'disease: Rhinitis, Allergic, Seasonal\n\n drug: Levocetirizine\n\n mechanism_links: levocetirizine - decreases activity of - histamine H1 receptor\n (human); histamine H1 receptor (human) - positively regulates - histamine receptor\n activity; histamine receptor activity - participates in - cellular response to histamine;\n cellular response to histamine - positively correlated with - inflammatory response;\n inflammatory response - has phenotype - HP:0031417; HP:0031417 - manifestation of\n - Rhinitis, Allergic, Seasonal'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nCeftizoxime is an aminothiazolyl cephalosporin with an extended spectrum of activity against many gram-negative, nosocomially acquired pathogens. It has excellent beta-lactamase stability, with good in vitro activity against Haemophilus influenzae, Neisseria gonorrhoeae and Klebsiella pneumoniae. Ceftizoxime, like the penicillins, is a beta-lactam antibiotic. By binding to specific penicillin-binding proteins (PBPs) located inside the bacterial cell wall, it inhibits the third and last stage of bacterial cell wall synthesis. Cell lysis is then mediated by bacterial cell wall autolytic enzymes such as autolysins; it is possible that ceftizoxime interferes with an autolysin inhibitor.\n\n===\n\ndisease: Enterobacteriaceae Infections\ndrug: Ceftizoxime\n", "completion": "'disease: Enterobacteriaceae Infections\n\n drug: Ceftizoxime\n\n mechanism_links: Ceftizoxime - decreases activity of - InterPro:IPR001460; InterPro:IPR001460\n - participates in - peptidoglycan biosynthetic process; peptidoglycan biosynthetic\n process - positively regulates - peptidoglycan-based cell wall biogenesis; peptidoglycan-based\n cell wall biogenesis - occurs in - Enterobacteriaceae; Enterobacteriaceae - causes\n - Enterobacteriaceae Infections'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nThe mechanism of the anti-inflammatory activity of the topical steroids, in general, is unclear. However, corticosteroids are thought to act by the induction of phospholipase A<sub>2</sub> inhibitory proteins, collectively called lipocortins. It is postulated that these proteins control the biosynthesis of potent mediators of inflammation such as prostaglandins and leukotrienes by inhibiting the release of their common precursor, arachidonic acid. Arachidonic acid is released from membrane phospholipids by phospholipase A<sub>2</sub>. Alclometasone initially binds the corticosteroid receptor. This complex migrates to the nucleus where it binds to different glucocorticoid response elements on the DNA. This in turn enhances and represses various genes, especially those involved in inflammatory pathways.\n\n===\n\ndisease: Lupus Erythematosus, Discoid\ndrug: Alclometasone\n", "completion": "'disease: Lupus Erythematosus, Discoid\n\n drug: Alclometasone\n\n mechanism_links: alclometasone dipropionate - positively regulates - glucocorticoid\n receptor (human); alclometasone dipropionate - negatively correlated with - InterPro:SSF50353;\n alclometasone dipropionate - negatively correlated with - histamine; InterPro:SSF50353\n - positively correlated with - inflammatory response; histamine - positively correlated\n with - inflammatory response; glucocorticoid receptor (human) - increases abundance\n of - InterPro:IPR001464; InterPro:IPR001464 - negatively regulates - InterPro:IPR001211;\n InterPro:IPR001211 - positively correlated with - leukotriene; leukotriene - positively\n correlated with - inflammatory response; inflammatory response - positively correlated\n with - HP:0000969; inflammatory response - positively correlated with - HP:0010783;\n inflammatory response - positively correlated with - HP:0040189; inflammatory response\n - positively correlated with - HP:0032152; inflammatory response - positively correlated\n with - HP:0004334; HP:0000969 - manifestation of - Lupus Erythematosus, Discoid;\n HP:0010783 - manifestation of - Lupus Erythematosus, Discoid; HP:0040189 - manifestation\n of - Lupus Erythematosus, Discoid; HP:0032152 - manifestation of - Lupus Erythematosus,\n Discoid; HP:0004334 - manifestation of - Lupus Erythematosus, Discoid'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nPseudoephedrine acts mainly as an agonist of alpha adrenergic receptors[A189381] and less strongly as an agonist of beta adrenergic receptors.[A10896] This agonism of adrenergic receptors produces vasoconstriction which is used as a decongestant[A188823,L11031,L11037,L11040,L11046,L11052,L11058,L11061] and as a treatment of priapism.[A189384] Pseudoephedrine is also an inhibitor of norepinephrine, dopamine, and serotonin transporters.[A17168,A17169] The sympathomimetic effects of pseudoephedrine include an increase in mean arterial pressure, heart rate, and chronotropic response of the right atria.[A17197] Pseudoephedrine is also a partial agonist of the anococcygeal muscle.[A17197] Pseudoephedrine also inhibits NF-kappa-B, NFAT, and AP-1.[A18244]\n\n===\n\ndisease: Common Cold\ndrug: Pseudoephedrine\n", "completion": "'disease: Common Cold\n\n drug: Pseudoephedrine\n\n mechanism_links: Pseudoephedrine - increases activity of - alpha-1A adrenergic receptor\n (human); Pseudoephedrine - increases activity of - beta-2 adrenergic receptor (human);\n beta-2 adrenergic receptor (human) - negatively correlated with - HP:4000007; HP:4000007\n - positively correlated with - Common Cold; alpha-1A adrenergic receptor (human)\n - positively regulates - vasoconstriction; vasoconstriction - negatively correlated\n with - mucus secretion; mucus secretion - positively correlated with - Common Cold'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nPromalidomide is an immunomodulatory agent with antineoplastic activity. It is shown to inhibit the proliferation and induce apoptosis of various tumour cells. Furthermore, promalidomide enhances T cell and natural killer (NK) cell-mediated immunity and inhibited the production of pro-inflammatory cytokines, like TNF-alpha or IL-6, by monocytes. The primary target of promalidomide is thought to be the protein cereblon. It binds to this target and inhibits ubiquitin ligase activity. It is also a transcriptional inhibitor of COX2.\n\n===\n\ndisease: Multiple Myeloma\ndrug: Pomalidomide\n", "completion": "'disease: Multiple Myeloma\n\n drug: Pomalidomide\n\n mechanism_links: pomalidomide - positively regulates - natural killer cell; natural\n killer cell - positively regulates - natural killer cell mediated immune response\n to tumor cell; natural killer cell mediated immune response to tumor cell - negatively\n correlated with - Multiple Myeloma; pomalidomide - decreases activity of - prostaglandin\n G/H synthase 2 (human); prostaglandin G/H synthase 2 (human) - increases abundance\n of - Prostaglandins; Prostaglandins - positively regulates - inflammatory response;\n inflammatory response - positively correlated with - Multiple Myeloma; pomalidomide\n - decreases activity of - tumor necrosis factor (human); tumor necrosis factor (human)\n - participates in - REACT:R-HSA-75893; REACT:R-HSA-75893 - positively regulates\n - inflammatory response; pomalidomide - negatively regulates - osteoclast; osteoclast\n - positively regulates - bone resorption; bone resorption - occurs in - Multiple\n Myeloma; pomalidomide - negatively regulates - vascular endothelial growth factor\n production; vascular endothelial growth factor production - positively regulates\n - angiogenesis; pomalidomide - negatively regulates - InterPro:IPR001321; InterPro:IPR001321\n - positively regulates - angiogenesis; angiogenesis - positively correlated with\n - Multiple Myeloma'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nFusidic acid works by interfering with bacterial protein synthesis, specifically by preventing the translocation of the elongation factor G (EF-G) from the ribosome. It also can inhibit chloramphenicol acetyltransferase enzymes.\n\n===\n\ndisease: Psittacosis\ndrug: Fusidic acid\n", "completion": "'disease: Psittacosis\n\n drug: Fusidic acid\n\n mechanism_links: Fusidic Acid - decreases activity of - PR:S7JCG1; PR:S7JCG1 - positively\n regulates - translation; translation - occurs in - Chlamydia psittaci; Chlamydia\n psittaci - causes - Psittacosis'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nFoscarnet exerts its antiviral activity by a selective inhibition at the pyrophosphate binding site on virus-specific DNA polymerases at concentrations that do not affect cellular DNA polymerases.\n\n===\n\ndisease: Cytomegalovirus Retinitis\ndrug: Foscarnet\n", "completion": "'disease: Cytomegalovirus Retinitis\n\n drug: Foscarnet\n\n mechanism_links: Foscarnet - decreases activity of - PR:P08546; PR:P08546 - participates\n in - viral DNA genome replication; viral DNA genome replication - occurs in - NCBITaxon:10358;\n NCBITaxon:10358 - causes - Cytomegalovirus Retinitis'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nIt acts by providing a physical barrier to prevent skin irritation and help heal damaged skin.\n\n===\n\ndisease: Tinea Versicolor\ndrug: Zinc oxide\n", "completion": "'disease: Tinea Versicolor\n\n drug: Zinc oxide\n\n mechanism_links: Zinc Oxide - decreases abundance of - Fungi; Zinc Oxide - negatively\n regulates - inflammatory response; Fungi - causes - Tinea Versicolor; inflammatory\n response - occurs in - Tinea Versicolor'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nPemirolast binds to the histamine H<sub>1</sub> receptor. This blocks the action of endogenous histamine, which subsequently leads to temporary relief of the negative symptoms brought on by histamine. Pemirolast has also been observed to inhibit antigen-stimulated calcium ion influx into mast cells through the blockage of calcium channels. Pemirolast inhibits the chemotaxis of eosinophils into ocular tissue, and prevents inflammatory mediator release from human eosinophils.\n\n===\n\ndisease: Asthma\ndrug: Pemirolast\n", "completion": "'disease: Asthma\n\n drug: Pemirolast\n\n mechanism_links: pemirolast - decreases activity of - histamine H1 receptor (human);\n pemirolast - negatively regulates - mast cell degranulation; mast cell degranulation\n - increases abundance of - Histamine; Histamine - causes - cellular response to\n histamine; histamine H1 receptor (human) - participates in - histamine receptor\n activity; histamine receptor activity - participates in - cellular response to histamine;\n cellular response to histamine - positively correlated with - inflammatory response;\n inflammatory response - causes - Asthma'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nClotrimazole acts primarily by damaging the permeability barrier in the cell membrane of fungi. Clotrimazole causes inhibition of ergosterol biosynthesis, an essential constituent of fungal cell membranes. If ergosterol synthesis is either completely or partially inhibited, the cell is no longer able to construct an intact and functional cell membrane [F3088],[F3100]. Because ergosterol directly promotes the growth of fungal cells in a hormone‐like fashion, rapid onset of the above events leads to dose-dependent inhibition of fungal growth [A174094]. Though decreased ergosterol, due to the inhibition of lanosterol 14-demethylase (also known as _CYP51_) [A174094] is accepted to be primarily responsible for the antimycotic properties of clotrimazole, this drug also shows other pharmacological effects. These include the inhibition of sarcoplasmic reticulum Ca2+‐ATPase, depletion of intracellular calcium, and blocking of calcium‐dependent potassium channels and voltage‐dependent calcium channels [A174094]. The action of clotrimazole on these targets accounts for other effects of this drug that are separate from its antimycotic activities [A174094].\n\n===\n\ndisease: Tinea Pedis\ndrug: Clotrimazole\n", "completion": "'disease: Tinea Pedis\n\n drug: Clotrimazole\n\n mechanism_links: Clotrimazole - disrupts - ergosterol; ergosterol - located in -\n yeast-form cell wall; yeast-form cell wall - in taxon - Candida albicans SC5314;\n Candida albicans SC5314 - causes - Tinea Pedis'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nTwo theories have been proposed to explain the efficacy of 5-HT<sub>1D</sub> receptor agonists in migraine: 1) activation of 5-HT<sub>1D</sub> receptors located on intracranial blood vessels, including those on arterio-venous anastomoses, leads to vasoconstriction, which correlates with the relief of migraine headache and 2) activation of 5-HT<sub>1D</sub> receptors on sensory nerve endings of the trigeminal system results in the inhibition of pro-inflammatory neuropeptide release.\n\n===\n\ndisease: Cluster Headache\ndrug: Dihydroergotamine\n", "completion": "'disease: Cluster Headache\n\n drug: Dihydroergotamine\n\n mechanism_links: Dihydroergotamine - increases activity of - 5-hydroxytryptamine\n receptor 1D (human); Dihydroergotamine - increases activity of - 5-hydroxytryptamine\n receptor 1B (human); 5-hydroxytryptamine receptor 1D (human) - positively regulates\n - vasoconstriction; 5-hydroxytryptamine receptor 1B (human) - positively regulates\n - vasoconstriction; 5-hydroxytryptamine receptor 1B (human) - negatively regulates\n - substance P secretion, neurotransmission; 5-hydroxytryptamine receptor 1D (human)\n - negatively regulates - substance P secretion, neurotransmission; vasoconstriction\n - treats - Cluster Headache; substance P secretion, neurotransmission - positively\n correlated with - Pain; Pain - positively correlated with - Cluster Headache'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nDigoxin exerts hemodynamic, electrophysiologic, and neurohormonal effects on the cardiovascular system.[A178234] It reversibly inhibits the Na-K ATPase enzyme, leading to various beneficial effects. The Na-K ATPase enzyme functions to maintain the intracellular environment by regulating the entry and exit of sodium, potassium, and calcium (indirectly). Na-K ATPase is also known as the _sodium pump_[L9143]. The inhibition of the sodium pump by digoxin increases intracellular sodium and increases the calcium level in the myocardial cells, causing an increased contractile force of the heart.[L9143,A178264] This improves the left ventricular ejection fraction (EF), an important measure of cardiac function.[A178234,T613] Digoxin also stimulates the parasympathetic nervous system via the vagus nerve[T607] leading to sinoatrial (SA) and atrioventricular (AV) node effects, decreasing the heart rate.[L9143,A178234] Part of the pathophysiology of heart failure includes neurohormonal activation, leading to an increase in norepinephrine. Digoxin helps to decrease norepinephrine levels through activation of the parasympathetic nervous system.[A178234]\n\n===\n\ndisease: Atrial Fibrillation\ndrug: Digoxin\n", "completion": "'disease: Atrial Fibrillation\n\n drug: Digoxin\n\n mechanism_links: Digoxin - negatively regulates - sodium/potassium-transporting\n ATPase subunit alpha-1 (human); sodium/potassium-transporting ATPase subunit alpha-1\n (human) - positively regulates - sodium ion transport; sodium ion transport - negatively\n correlated with - calcium ion import into cytosol; calcium ion import into cytosol\n - negatively correlated with - heart contraction; heart contraction - correlated\n with - Atrial Fibrillation'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nIn bacterial replication, an interaction that is important for translation initiation of proteins occurs at the 3′ end of the 16S rRNA, found on the ribosome on the 30S subunit [A174046], [A19429], [A174070]. The 30S subunit is the smaller subunit of the ribosome of prokaryotes, including bacteria[F3073]. Tetracyclines such as doxycycline are thought to inhibit translation by binding to the 16S rRNA portion of the ribosome [A174040], preventing binding of tRNA to the RNA-30S bacterial ribosomal subunit, which is necessary for the delivery of amino acids for protein synthesis. As a result of the above actions, the initiation of protein synthesis by polyribosome formation is blocked. This stops the replication of bacteria and produces a bacteriostatic effect [F3052].\n\n===\n\ndisease: Scrub Typhus\ndrug: Doxycycline\n", "completion": "'disease: Scrub Typhus\n\n drug: Doxycycline\n\n mechanism_links: Doxycycline - negatively regulates - RNA, Ribosomal, 16S; RNA,\n Ribosomal, 16S - located in - small ribosomal subunit; small ribosomal subunit -\n participates in - translation; translation - occurs in - NCBITaxon:784; NCBITaxon:784\n - causes - Scrub Typhus'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nAs a diagnostic aid (adrenocortical function), corticotropin combines with a specific receptor on the adrenal cell plasma membrane. In patients with normal adrenocortical function, it stimulates the initial reaction involved in the synthesis of adrenal steroids (including cortisol, cortisone, weak androgenic substances, and a limited quantity of aldosterone) from cholesterol by increasing the quantity of cholesterol within the mitochondria. Corticotropin does not significantly increase serum cortisol concentrations in patients with primary adrenocortical insufficiency (Addison's disease). The mechanism of action of corticotropin in the treatment of infantile myoclonic seizures is unknown.\n\n===\n\ndisease: Spasms, Infantile\ndrug: Corticotropin\n", "completion": "'disease: Spasms, Infantile\n\n drug: Corticotropin\n\n mechanism_links: Corticotropin - positively regulates - adrenocorticotropic hormone\n receptor (human); adrenocorticotropic hormone receptor (human) - decreases expression\n of - CHEBI:65312; CHEBI:65312 - positively correlated with - HP:0001250; adrenocorticotropic\n hormone receptor (human) - negatively correlated with - HP:0012469; HP:0001250 -\n manifestation of - Spasms, Infantile; HP:0012469 - manifestation of - Spasms, Infantile'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nElbasvir is an inhibitor of the HCV non-structural protein 5A. While the precise role of this protein is unknown, it is essential to viral replication and virion assembly.[synthesis] Potential modes of action of NS5A inhibitors like elbasvir include blocking signaling interactions, redistribution of NS5A from the endoplasmic reticulum to the surface of lipid droplets, and modification of the HCV replication complex.[A19593] Computational target-based _in silico_ research suggests that elbasvir may carry activity at several proteins required for replication of SARS-CoV-2 - namely RNA-dependent RNA polymerase, helicase, and papain-like proteinase - although specific activity has yet to be affirmed by follow-up clinical studies.[A193257]\n\n===\n\ndisease: Hepatitis C, Chronic\ndrug: Elbasvir\n", "completion": "'disease: Hepatitis C, Chronic\n\n drug: Elbasvir\n\n mechanism_links: 2-(pyrrolidin-2-yl)-5-(2-(4-(5-(pyrrolidin-2-yl)-1H-imidazol-2-yl)phenyl)benzofuran-5-yl)-1H-imidazole\n - decreases activity of - PR:Q5L478; PR:Q5L478 - negatively regulates - virion assembly;\n virion assembly - in taxon - NCBITaxon:11103; NCBITaxon:11103 - causes - Hepatitis\n C, Chronic'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nVerapamil inhibits L-type calcium channels by binding to a specific area of their alpha-1 subunit,[L10478]Cav1.2, which is highly expressed on L-type calcium channels in vascular smooth muscle and myocardial tissue where these channels are responsible for the control of peripheral vascular resistance and heart contractility.[A175396] Calcium influx through these channels allows for the propagation of action potentials necessary for the contraction of muscle tissue and the heart's electrical pacemaker activity. Verapamil binds to these channels in a voltage- and frequency-dependent manner, meaning affinity is increased 1) as vascular smooth muscle membrane potential is reduced, and 2) with excessive depolarizing stimulus.[L10478] Verapamil is known to interact with other targets, including other calcium channels,[A188490,A13984,A188502,A15331] potassium channels,[A188496,A13985,A13983] and adrenergic receptors.[A20291,A31755]\n\n===\n\ndisease: Hypertension\ndrug: Verapamil\n", "completion": "'disease: Hypertension\n\n drug: Verapamil\n\n mechanism_links: Verapamil - decreases activity of - InterPro:IPR005446; InterPro:IPR005446\n - positively regulates - calcium ion transport into cytosol; calcium ion transport\n into cytosol - positively correlated with - vasoconstriction; vasoconstriction -\n positively correlated with - HP:0033533; HP:0033533 - positively correlated with\n - HP:0032263; HP:0032263 - manifestation of - Hypertension'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nThe short term effects of corticosteroids are decreased vasodilation and permeability of capillaries, as well as decreased leukocyte migration to sites of inflammation.[A187463] Corticosteroids binding to the glucocorticoid receptor mediates changes in gene expression that lead to multiple downstream effects over hours to days.[A187463] Lower doses of corticosteroids provide an anti-inflammatory effect, while higher doses are immunosuppressive.[A187463] High doses of glucocorticoids for an extended period bind to the mineralocorticoid receptor, raising sodium levels and decreasing potassium levels.[A187463]\n\n===\n\ndisease: Crohn Disease\ndrug: Methylprednisolone\n", "completion": "'disease: Crohn Disease\n\n drug: Methylprednisolone\n\n mechanism_links: Methylprednisolone - increases activity of - glucocorticoid receptor\n (human); glucocorticoid receptor (human) - increases activity of - annexin A1 (human);\n glucocorticoid receptor (human) - decreases activity of - prostaglandin G/H synthase\n 1 (human); glucocorticoid receptor (human) - decreases activity of - prostaglandin\n G/H synthase 2 (human); annexin A1 (human) - decreases activity of - cytosolic phospholipase\n A2 (human); prostaglandin G/H synthase 1 (human) - positively regulates - prostaglandin\n biosynthetic process; prostaglandin G/H synthase 2 (human) - positively regulates\n - prostaglandin biosynthetic process; cytosolic phospholipase A2 (human) - positively\n regulates - leukotriene biosynthetic process; cytosolic phospholipase A2 (human)\n - positively regulates - prostaglandin biosynthetic process; leukotriene biosynthetic\n process - positively correlated with - inflammatory response; prostaglandin biosynthetic\n process - positively correlated with - inflammatory response; inflammatory response\n - located in - digestive tract; digestive tract - location of - Crohn Disease'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nSecnidazole enters the bacterial cell as a prodrug without an antimicrobial activity. The drug is converted to an active form via reduction of nitro groups to radical anions by bacterial enzymes. The radical anions are thought to interfere with bacterial DNA synthesis of susceptible isolates [FDA Label].\n\n===\n\ndisease: Vaginosis, Bacterial\ndrug: Secnidazole\n", "completion": "'disease: Vaginosis, Bacterial\n\n drug: Secnidazole\n\n mechanism_links: secnidazole - positively regulates - response to oxygen radical;\n response to oxygen radical - disrupts - DNA; DNA - in taxon - Bacteria; Bacteria\n - causes - Vaginosis, Bacterial'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nAnakinra binds competitively to the Interleukin-1 type I receptor (IL-1RI), thereby inhibiting the action of elevated levels IL-1 which normally can lead to cartilage degradation and bone resorption.\n\n===\n\ndisease: Cryopyrin-Associated Periodic Syndromes\ndrug: Anakinra\n", "completion": "'disease: Cryopyrin-Associated Periodic Syndromes\n\n drug: Anakinra\n\n mechanism_links: Interleukin 1 Receptor Antagonist Protein - decreases activity\n of - interleukin-1 receptor type 1 (human); interleukin-1 receptor type 1 (human)\n - participates in - interleukin-1 receptor activity; interleukin-1 receptor activity\n - positively regulates - inflammatory response; inflammatory response - causes -\n Cryopyrin-Associated Periodic Syndromes'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nAntifungals in the triazole class, such as isavuconazonium, target and inhibit the sterol 14-α-demethylase (Erg11p) which is a key player in the demethylation step of the ergosterol biosynthetic pathway. This inhibition results in a halt in production of ergosterol, a molecule typically found in the membranes of fungi such as Aspergillus, Candida, and Mucorales that plays a role in regulation of membrane integrity, fluidity and permeability. The inhibition of Erg11p also causes the buildup of ergosterol precursors, which are toxic and cause cell death.\n\n===\n\ndisease: Mucormycosis\ndrug: Isavuconazonium\n", "completion": "'disease: Mucormycosis\n\n drug: Isavuconazonium\n\n mechanism_links: isavuconazole - decreases activity of - Pfam:PF00067; Pfam:PF00067\n - positively regulates - sterol 14-demethylase activity; Pfam:PF00067 - positively\n regulates - ergosterol biosynthetic process; sterol 14-demethylase activity - positively\n correlated with - ergosterol; ergosterol biosynthetic process - increases abundance\n of - ergosterol; sterol 14-demethylase activity - negatively correlated with - lanosterol;\n ergosterol biosynthetic process - decreases abundance of - lanosterol; lanosterol\n - negatively correlated with - fungal-type cell wall; ergosterol - contributes to\n - fungal-type cell wall; fungal-type cell wall - in taxon - NCBITaxon:4827; NCBITaxon:4827\n - causes - Mucormycosis'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nChlorpromazine acts as an antagonist (blocking agent) on different postsysnaptic receptors -on dopaminergic-receptors (subtypes D1, D2, D3 and D4 - different antipsychotic properties on productive and unproductive symptoms), on serotonergic-receptors (5-HT1 and 5-HT2, with anxiolytic, antidepressive and antiaggressive properties as well as an attenuation of extrapypramidal side-effects, but also leading to weight gain, fall in blood pressure, sedation and ejaculation difficulties), on histaminergic-receptors (H1-receptors, sedation, antiemesis, vertigo, fall in blood pressure and weight gain), alpha1/alpha2-receptors (antisympathomimetic properties, lowering of blood pressure, reflex tachycardia, vertigo, sedation, hypersalivation and incontinence as well as sexual dysfunction, but may also attenuate pseudoparkinsonism - controversial) and finally on muscarinic (cholinergic) M1/M2-receptors (causing anticholinergic symptoms like dry mouth, blurred vision, obstipation, difficulty/inability to urinate, sinus tachycardia, ECG-changes and loss of memory, but the anticholinergic action may attenuate extrapyramidal side-effects). Additionally, Chlorpromazine is a weak presynaptic inhibitor of Dopamine reuptake, which may lead to (mild) antidepressive and antiparkinsonian effects. This action could also account for psychomotor agitation and amplification of psychosis (very rarely noted in clinical use).\n\n===\n\ndisease: Schizophrenia\ndrug: Chlorpromazine\n", "completion": "'disease: Schizophrenia\n\n drug: Chlorpromazine\n\n mechanism_links: Chlorpromazine - decreases activity of - D(2) dopamine receptor\n (human); D(2) dopamine receptor (human) - positively correlated with - dopamine;\n dopamine - correlated with - regulation of synaptic transmission, dopaminergic;\n regulation of synaptic transmission, dopaminergic - located in - central nervous\n system; central nervous system - prevents - HP:0008760; HP:0008760 - correlated\n with - Schizophrenia'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nThe antacid potential of potassium bicarbonate is attained by increasing the gastrointestinal pH by neutralizing hydrochloric acid.[T144] The increase in pH results in suppression of the action of pepsin which is the enzyme that exacerbates ulceration due to the presence of acid.[T143]\n\n===\n\ndisease: Peptic Ulcer\ndrug: Potassium bicarbonate\n", "completion": "'disease: Peptic Ulcer\n\n drug: Potassium bicarbonate\n\n mechanism_links: potassium bicarbonate - negatively regulates - Gastric Acid; Gastric\n Acid - positively regulates - InterPro:IPR034162; InterPro:IPR034162 - positively\n correlated with - Peptic Ulcer'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nFenofibrate activates peroxisome proliferator activated receptor alpha (PPARα), increasing lipolysis, activating lipoprotein lipase, and reducing apoprotein C-III.[A186002,L8588,L8591] PPARα is a nuclear receptor and its activation alters lipid, glucose, and amino acid homeostasis.[A186002] Activation of PPARα activates transcription of gene transcription and translation that generates peroxisomes filled with hydrogen peroxide, reactive oxygen species, and hydroxyl radicals that also participate in lipolysis.[A186005] This mechanism of increased lipid metabolism is also associated with increased oxidative stress on the liver.[A186005] In rare cases this stress can lead to cirrhosis and chronic active hepatitis.[A186002,L8588,L8591]\n\n===\n\ndisease: Hypoalphalipoproteinemias\ndrug: Fenofibrate\n", "completion": "'disease: Hypoalphalipoproteinemias\n\n drug: Fenofibrate\n\n mechanism_links: Fenofibrate - has metabolite - fenofibric acid; fenofibric acid\n - increases activity of - peroxisome proliferator-activated receptor alpha (human);\n peroxisome proliferator-activated receptor alpha (human) - increases abundance of\n - Lipoproteins, HDL; Lipoproteins, HDL - negatively correlated with - Hypoalphalipoproteinemias'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nPhysostigmine inhibits acetylcholinesterase, the enzyme responsible for the breakdown of used acetylcholine. By interfering with the metabolism of acetylcholine, physostigmine indirectly stimulates both nicotinic and muscarinic receptors due to the consequential increase in available acetylcholine at the synapse.\n\n===\n\ndisease: Glaucoma, Open-Angle\ndrug: Physostigmine\n", "completion": "'disease: Glaucoma, Open-Angle\n\n drug: Physostigmine\n\n mechanism_links: Physostigmine - decreases activity of - acetylcholinesterase (human);\n acetylcholinesterase (human) - increases abundance of - Acetylcholine; Acetylcholine\n - located in - synapse; synapse - increases activity of - InterPro:IPR002394; InterPro:IPR002394\n - treats - Glaucoma, Open-Angle'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nFluoxymesterone is a synthetic androgenic anabolic steroid and is approximately 5 times as potent as natural methyltestosterone. Like testosterone and other androgenic hormones, fluoxymesterone binds to the androgen receptor. It produces retention of nitrogen, sodium, potassium, and phosphorus; increases protein anabolism; decreases amino acid catabolism and decreased urinary excretion of calcium. The antitumour activity of fluoxymesterone appears related to reduction or competitive inhibition of prolactin receptors or estrogen receptors or production.\n\n===\n\ndisease: Puberty, Delayed\ndrug: Fluoxymesterone\n", "completion": "'disease: Puberty, Delayed\n\n drug: Fluoxymesterone\n\n mechanism_links: Fluoxymesterone - increases activity of - androgen receptor (human);\n androgen receptor (human) - positively regulates - androgen receptor signaling pathway;\n androgen receptor signaling pathway - positively correlated with - development of\n secondary sexual characteristics; development of secondary sexual characteristics\n - negatively correlated with - Puberty, Delayed'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nAlthough the mechanism of action of brexpiprazole in the treatment of MDD and schizophrenia is unclear, the efficacy of brexpiprazole may be attributed to partial agonist activity at serotonin 1A and dopamine D2 receptors, and antagonist activity at serotonin 2A receptors.\n\n===\n\ndisease: Schizophrenia\ndrug: Brexpiprazole\n", "completion": "'disease: Schizophrenia\n\n drug: Brexpiprazole\n\n mechanism_links: brexpiprazole - regulates - 5-hydroxytryptamine receptor 1A (human);\n brexpiprazole - regulates - D(2) dopamine receptor (human); brexpiprazole - decreases\n activity of - 5-hydroxytryptamine receptor 2A (human); 5-hydroxytryptamine receptor\n 1A (human) - positively correlated with - Serotonin; D(2) dopamine receptor (human)\n - positively correlated with - Dopamine; 5-hydroxytryptamine receptor 2A (human)\n - positively correlated with - HP:0000716; Serotonin - positively correlated with\n - serotonin secretion, neurotransmission; Dopamine - positively correlated with\n - dopamine secretion, neurotransmission; HP:0000716 - manifestation of - Schizophrenia;\n serotonin secretion, neurotransmission - disrupted by - Schizophrenia; dopamine\n secretion, neurotransmission - disrupted by - Schizophrenia'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nBenzyl alcohol inhibits lice from closing their respiratory spiracles, allowing the vehicle to obstruct the spiracles and causing the lice to asphyxiate.\n\n===\n\ndisease: Pruritus\ndrug: Benzyl alcohol\n", "completion": "'disease: Pruritus\n\n drug: Benzyl alcohol\n\n mechanism_links: Benzyl Alcohol - decreases abundance of - NCBITaxon:52283; NCBITaxon:52283\n - causes - Pruritus'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nMecamylamine is a ganglionic blocker which prevents stimulation of postsynaptic receptors by acetylcholine released from presynaptic nerve endings. The hypotensive effect of Mecamylamine is attributed to reduction in sympathetic tone, vasodilation, and reduced cardiac output, and is primarily postural.\n\n===\n\ndisease: Hypertension\ndrug: Mecamylamine\n", "completion": "'disease: Hypertension\n\n drug: Mecamylamine\n\n mechanism_links: Mecamylamine - decreases activity of - InterPro:IPR002394; InterPro:IPR002394\n - positively regulates - synaptic transmission, cholinergic; synaptic transmission,\n cholinergic - positively correlated with - smooth muscle contraction; smooth muscle\n contraction - positively correlated with - vasoconstriction; vasoconstriction -\n positively correlated with - HP:0032263; HP:0032263 - manifestation of - Hypertension'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nThe androgen receptor exists in the cytoplasm bound to the heat shock proteins HSP90, HSP70, and other chaperones.[A187114] After binding to an androgen, the androgen receptor dissociates from HSP90 and undergoes a conformational change to slow the rate of dissociation from the androgen receptor.[A187114] The androgen-receptor complex is transported into the nucleus where it binds to DNA and recruits other transcriptional regulators to form a pre-initiation complex and eventually induce expression of specific genes.[A187114] Antagonism of the androgen receptor is also responsible for the development of secondary sexual characteristics including facial and body hair, enlargement of the larynx, thickening of the vocal cords, and changes in muscle and fat distribution.[A187111,L8983,L8935,L8938,L8986,L8989,L8992,L8995]\n\n===\n\ndisease: Puberty, Delayed\ndrug: Testosterone\n", "completion": "'disease: Puberty, Delayed\n\n drug: Testosterone\n\n mechanism_links: Testosterone - increases activity of - androgen receptor (human);\n androgen receptor (human) - positively regulates - androgen receptor signaling pathway;\n androgen receptor signaling pathway - positively regulates - developmental process\n involved in reproduction; developmental process involved in reproduction - negatively\n correlated with - Puberty, Delayed'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nThe actions of metolazone result from interference with the renal tubular mechanism of electrolyte reabsorption. Metolazone acts primarily to inhibit sodium reabsorption at the cortical diluting site and to a lesser extent in the proximal convoluted tubule. Sodium and chloride ions are excreted in approximately equivalent amounts. The increased delivery of sodium to the distal tubular exchange site results in increased potassium excretion. Metolazone does not inhibit carbonic anhydrase. The antihypertensive mechanism of action of metolazone is not fully understood but is presumed to be related to its saluretic and diuretic properties.\n\n===\n\ndisease: Hypertension\ndrug: Metolazone\n", "completion": "'disease: Hypertension\n\n drug: Metolazone\n\n mechanism_links: Metolazone - decreases activity of - solute carrier family 12 member\n 3 (human); solute carrier family 12 member 3 (human) - participates in - renal sodium\n ion absorption; renal sodium ion absorption - positively correlated with - renal\n water retention; renal water retention - contributes to - HP:0011104; HP:0011104\n - contributes to - positive regulation of blood pressure; positive regulation of\n blood pressure - affects risk for - Hypertension'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nTolnaftate is a topical fungicide. Though its exact mechanism unknown, it is believed to prevent ergosterol biosynthesis by inhibiting squalene epoxidase. It has also been reported to distort the hyphae and to stunt mycelial growth in susceptible organisms.\n\n===\n\ndisease: Tinea Capitis\ndrug: Tolnaftate\n", "completion": "'disease: Tinea Capitis\n\n drug: Tolnaftate\n\n mechanism_links: Tolnaftate - decreases activity of - InterPro:IPR040125; InterPro:IPR040125\n - positively regulates - ergosterol biosynthetic process; ergosterol biosynthetic\n process - increases abundance of - ergosterol; ergosterol - located in - yeast-form\n cell wall; yeast-form cell wall - in taxon - NCBITaxon:5550; NCBITaxon:5550 - causes\n - Tinea Capitis'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nHistamine acts directly on the blood vessels to dilate arteries and capillaries; this action is mediated by both H 1- and H 2-receptors. Capillary dilatation may produce flushing of the face, a decrease in systemic blood pressure, and gastric gland secretion, causing an increased secretion of gastric juice of high acidity. Increased capillary permeability accompanies capillary dilatation, producing an outward passage of plasma protein and fluid into the extracellular spaces, an increase in lymph flow and protein content, and the formation of edema. In addition, histamine has a direct stimulant action on smooth muscle, producing contraction if H 1-receptors are activated, or mostly relaxation if H 2-receptors are activated. Also in humans, the stimulant effect of histamine may cause contraction of the intestinal muscle. However, little effect is noticed on the uterus, bladder, or gallbladder. Histamine has some stimulant effect on duodenal, salivary, pancreatic, bronchial, and lacrimal glands. Histamine also can bind to H3 and H4 receptors which are involved in the CNS/PNS neurotransmitter release and immune system chemotaxis, respectively.\n\n===\n\ndisease: Leukemia, Myeloid, Acute\ndrug: Histamine\n", "completion": "'disease: Leukemia, Myeloid, Acute\n\n drug: Histamine\n\n mechanism_links: Histamine - increases activity of - interleukin-2 (human); interleukin-2\n (human) - increases activity of - interleukin-2 receptor subunit alpha (human);\n interleukin-2 (human) - increases activity of - interleukin-2 receptor subunit beta\n (human); interleukin-2 (human) - increases activity of - cytokine receptor common\n subunit gamma (human); interleukin-2 receptor subunit alpha (human) - positively\n regulates - REACT:R-HSA-9020558; interleukin-2 receptor subunit beta (human) - positively\n regulates - REACT:R-HSA-9020558; cytokine receptor common subunit gamma (human)\n - positively regulates - REACT:R-HSA-9020558; REACT:R-HSA-9020558 - positively regulates\n - cytotoxic T cell differentiation; REACT:R-HSA-9020558 - positively regulates -\n natural killer cell activation; cytotoxic T cell differentiation - negatively correlated\n with - Leukemia, Myeloid, Acute; natural killer cell activation - negatively correlated\n with - Leukemia, Myeloid, Acute'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nCetirizine, a metabolite of _hydroxyzine_, is an antihistamine drug. Its main effects are achieved through selective inhibition of peripheral H1 receptors. The antihistamine activity of cetirizine has been shown in a variety of animal and human models. _In vivo_ and _ex vivo_ animal models have shown insignificant anticholinergic and antiserotonergic effects. In clinical studies, however, dry mouth was found to be more frequent with cetirizine than with a placebo. In vitro receptor binding studies have demonstrated no detectable affinity of cetirizine for histamine receptors other than the H1 receptors. Studies with radiolabeled cetirizine administration in the rat have demonstrated insignificant penetration into the brain. _Ex vivo_ studies in the mouse have shown that systemically administered cetirizine does not occupy cerebral H1 receptors significantly [FDA label].\n\n===\n\ndisease: Rhinitis, Allergic, Seasonal\ndrug: Cetirizine\n", "completion": "'disease: Rhinitis, Allergic, Seasonal\n\n drug: Cetirizine\n\n mechanism_links: Cetirizine - decreases activity of - histamine H1 receptor (human);\n histamine H1 receptor (human) - positively regulates - histamine receptor activity;\n histamine receptor activity - participates in - cellular response to histamine;\n cellular response to histamine - positively correlated with - inflammatory response;\n inflammatory response - has phenotype - HP:0031417; HP:0031417 - manifestation of\n - Rhinitis, Allergic, Seasonal'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nPrednisone is first metabolized in the liver to its active form, prednisolone, a glucocorticoid agonist corticosteroid.[L10502] Lower doses of corticosteroids provide an anti-inflammatory effect, while higher doses are immunosuppressive.[A187463] High doses of glucocorticoids for an extended period bind to the mineralocorticoid receptor, raising sodium levels and decreasing potassium levels.[A187463]\n\n===\n\ndisease: Thyroiditis\ndrug: Prednisone\n", "completion": "'disease: Thyroiditis\n\n drug: Prednisone\n\n mechanism_links: Prednisone - has metabolite - Prednisolone; Prednisolone - increases\n activity of - glucocorticoid receptor (human); glucocorticoid receptor (human) -\n increases activity of - annexin A1 (human); glucocorticoid receptor (human) - decreases\n activity of - prostaglandin G/H synthase 1 (human); glucocorticoid receptor (human)\n - decreases activity of - prostaglandin G/H synthase 2 (human); annexin A1 (human)\n - decreases activity of - cytosolic phospholipase A2 (human); prostaglandin G/H\n synthase 1 (human) - positively regulates - prostaglandin biosynthetic process;\n prostaglandin G/H synthase 2 (human) - positively regulates - prostaglandin biosynthetic\n process; cytosolic phospholipase A2 (human) - positively regulates - leukotriene\n biosynthetic process; cytosolic phospholipase A2 (human) - positively regulates\n - prostaglandin biosynthetic process; leukotriene biosynthetic process - positively\n correlated with - inflammatory response; prostaglandin biosynthetic process - positively\n correlated with - inflammatory response; inflammatory response - located in - thyroid\n gland; thyroid gland - location of - Thyroiditis'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nThe short term effects of corticosteroids are decreased vasodilation and permeability of capillaries, as well as decreased leukocyte migration to sites of inflammation.[A187463] Corticosteroids binding to the glucocorticoid receptor mediates changes in gene expression that lead to multiple downstream effects over hours to days.[A187463] Lower doses of corticosteroids provide an anti-inflammatory effect, while higher doses are immunosuppressive.[A187463] High doses of glucocorticoids for an extended period bind to the mineralocorticoid receptor, raising sodium levels and decreasing potassium levels.[A187463]\n\n===\n\ndisease: Conjunctivitis, Allergic\ndrug: Hydrocortisone\n", "completion": "'disease: Conjunctivitis, Allergic\n\n drug: Hydrocortisone\n\n mechanism_links: Hydrocortisone - increases activity of - glucocorticoid receptor\n (human); glucocorticoid receptor (human) - increases activity of - annexin A1 (human);\n glucocorticoid receptor (human) - decreases activity of - prostaglandin G/H synthase\n 1 (human); glucocorticoid receptor (human) - decreases activity of - prostaglandin\n G/H synthase 2 (human); annexin A1 (human) - decreases activity of - cytosolic phospholipase\n A2 (human); prostaglandin G/H synthase 1 (human) - positively regulates - prostaglandin\n biosynthetic process; prostaglandin G/H synthase 2 (human) - positively regulates\n - prostaglandin biosynthetic process; cytosolic phospholipase A2 (human) - positively\n regulates - leukotriene biosynthetic process; cytosolic phospholipase A2 (human)\n - positively regulates - prostaglandin biosynthetic process; leukotriene biosynthetic\n process - positively correlated with - inflammatory response; prostaglandin biosynthetic\n process - positively correlated with - inflammatory response; inflammatory response\n - located in - conjunctiva; conjunctiva - location of - Conjunctivitis, Allergic'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nThe short term effects of corticosteroids are decreased vasodilation and permeability of capillaries, as well as decreased leukocyte migration to sites of inflammation.[A187463] Corticosteroids binding to the glucocorticoid receptor mediates changes in gene expression that lead to multiple downstream effects over hours to days.[A187463] Lower doses of corticosteroids provide an anti-inflammatory effect, while higher doses are immunosuppressive.[A187463] High doses of glucocorticoids for an extended period bind to the mineralocorticoid receptor, raising sodium levels and decreasing potassium levels.[A187463]\n\n===\n\ndisease: Berylliosis\ndrug: Methylprednisolone\n", "completion": "'disease: Berylliosis\n\n drug: Methylprednisolone\n\n mechanism_links: Methylprednisolone - increases activity of - glucocorticoid receptor\n (human); glucocorticoid receptor (human) - increases activity of - annexin A1 (human);\n glucocorticoid receptor (human) - decreases activity of - prostaglandin G/H synthase\n 1 (human); glucocorticoid receptor (human) - decreases activity of - prostaglandin\n G/H synthase 2 (human); annexin A1 (human) - decreases activity of - cytosolic phospholipase\n A2 (human); prostaglandin G/H synthase 1 (human) - positively regulates - prostaglandin\n biosynthetic process; prostaglandin G/H synthase 2 (human) - positively regulates\n - prostaglandin biosynthetic process; cytosolic phospholipase A2 (human) - positively\n regulates - leukotriene biosynthetic process; cytosolic phospholipase A2 (human)\n - positively regulates - prostaglandin biosynthetic process; leukotriene biosynthetic\n process - positively correlated with - inflammatory response; prostaglandin biosynthetic\n process - positively correlated with - inflammatory response; inflammatory response\n - located in - bronchus; bronchus - location of - Berylliosis'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nThe bactericidal action of Norfloxacin results from inhibition of the enzymes topoisomerase II (DNA gyrase) and topoisomerase IV, which are required for bacterial DNA replication, transcription, repair, and recombination. Norfloxacin is a broad-spectrum antibiotic agent that is shown to be effective against various Gram-positive and Gram-negative bacterial species. The fluorine atom at the 6 position increases potency against gram-negative organisms, and the piperazine moiety at the 7 position is responsible for anti-pseudomonal activity\n\n===\n\ndisease: Klebsiella Infections\ndrug: Norfloxacin\n", "completion": "'disease: Klebsiella Infections\n\n drug: Norfloxacin\n\n mechanism_links: Norfloxacin - decreases activity of - PR:W1DID1; Norfloxacin -\n decreases activity of - PR:W1DEE8; PR:W1DID1 - positively regulates - DNA replication;\n PR:W1DEE8 - positively regulates - DNA replication; DNA replication - occurs in\n - NCBITaxon:570; NCBITaxon:570 - causes - Klebsiella Infections'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nChloramphenicol succinate is hydrolyzed into the active chloramphenicol.[A204047] Chloramphenicol resembles uridine-5'-phosphate.[A204071] It binds to the residues A2451 and A2452 in the 23S rRNA of the 50S ribosomal subunit of _E. coli_, which prevents translation.[A204077]\n\n===\n\ndisease: Typhoid Fever\ndrug: Chloramphenicol succinate\n", "completion": "'disease: Typhoid Fever\n\n drug: Chloramphenicol succinate\n\n mechanism_links: chloramphenicol succinate - has metabolite - Chloramphenicol; Chloramphenicol\n - decreases activity of - PR:Q8XET6; PR:Q8XET6 - positively regulates - translation;\n translation - in taxon - Salmonella enterica subsp. enterica serovar Typhi; Salmonella\n enterica subsp. enterica serovar Typhi - causes - Typhoid Fever'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nCitrate chelates free calcium ions preventing them from forming a complex with tissue factor and coagulation factor VIIa to promote the activation of coagulation factor X [A19410] [A19411]. This inhibits the extrinsic initiation of the coagulation cascade. Citrate may also exert an anticoagulant effect via a so far unknown mechanism as restoration of calcium concentration does not fully reverse the effect of citrate [A19410]. Citrate is a weak base and so reacts with hydrochloric acid in the stomach to raise the pH. It it further metabolized to bicarbonate which then acts as a systemic alkalizing agent, raising the pH of the blood and urine [L790]. It also acts as a diuretic and increases the urinary excretion of calcium.\n\n===\n\ndisease: Heartburn\ndrug: Sodium citrate\n", "completion": "'disease: Heartburn\n\n drug: Sodium citrate\n\n mechanism_links: Sodium citrate - negatively regulates - Gastric Acid; Gastric Acid\n - positively correlated with - Heartburn'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nGuanfacine is a selective alpha-2A adrenergic receptor agonist, which reduces the effects of the sympathetic nervous system on the heart and circulatory system.[L11277] The link between guanfacine’s molecular mechanism and it’s effect on the treatment of ADHD has not been determined.[L11277]\n\n===\n\ndisease: Attention Deficit Disorder with Hyperactivity\ndrug: Guanfacine\n", "completion": "'disease: Attention Deficit Disorder with Hyperactivity\n\n drug: Guanfacine\n\n mechanism_links: Guanfacine - increases activity of - alpha-2A adrenergic receptor\n (human); alpha-2A adrenergic receptor (human) - treats - Attention Deficit Disorder\n with Hyperactivity'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nRisedronatic acid binds to bone hydroxyapatite[FDA Label]. Bone resorption causes local acidification, releasing risedronic acid which is that taken into osteoclasts by fluid-phase endocytosis[A959]. Endocytic vesicles are acidified, releasing risedronic acid to the cytosol of osteoclasts where they induce apoptosis through inhbition of farnesyl pyrophosphate synthase[A959]. Inhibition of osteoclasts results in decreased bone resorption[A959].\n\n===\n\ndisease: Osteoporosis, Postmenopausal\ndrug: Risedronic acid\n", "completion": "'disease: Osteoporosis, Postmenopausal\n\n drug: Risedronic acid\n\n mechanism_links: Risedronate Sodium - negatively correlated with - obsolete ATP\n hydrolysis activity; obsolete ATP hydrolysis activity - increases activity of -\n osteoclast; Risedronate Sodium - negatively regulates - V-type proton ATPase catalytic\n subunit A (human); V-type proton ATPase catalytic subunit A (human) - positively\n regulates - proton transmembrane transport; proton transmembrane transport - positively\n correlated with - bone resorption; Risedronate Sodium - positively regulates - apoptotic\n process; apoptotic process - decreases abundance of - osteoclast; osteoclast - positively\n regulates - bone resorption; bone resorption - positively correlated with - Osteoporosis,\n Postmenopausal; Risedronate Sodium - molecularly interacts with - hydroxylapatite;\n hydroxylapatite - positively correlated with - ossification; hydroxylapatite - positively\n correlated with - bone regeneration; bone regeneration - negatively correlated with\n - Osteoporosis, Postmenopausal; ossification - negatively correlated with - Osteoporosis,\n Postmenopausal'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nChlorpheniramine binds to the histamine H1 receptor. This blocks the action of endogenous histamine, which subsequently leads to temporary relief of the negative symptoms brought on by histamine.\n\n===\n\ndisease: Rhinitis, Vasomotor\ndrug: Chlorpheniramine\n", "completion": "'disease: Rhinitis, Vasomotor\n\n drug: Chlorpheniramine\n\n mechanism_links: Chlorpheniramine - negatively regulates - histamine H1 receptor\n (human); histamine H1 receptor (human) - positively correlated with - Histamine;\n Histamine - increases abundance of - Substance P; Substance P - participates in\n - Neurogenic Inflammation; Neurogenic Inflammation - contributes to - Rhinitis,\n Vasomotor'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nCiprofloxacin acts on bacterial topoisomerase II (DNA gyrase) and topoisomerase IV.[A178885] Ciprofloxacin's targeting of the alpha subunits of DNA gyrase prevents it from supercoiling the bacterial DNA which prevents DNA replication.[A178876,A178882]\n\n===\n\ndisease: Rhinoscleroma\ndrug: Ciprofloxacin\n", "completion": "'disease: Rhinoscleroma\n\n drug: Ciprofloxacin\n\n mechanism_links: Ciprofloxacin - decreases activity of - PR:R4Y7H5; Ciprofloxacin\n - decreases activity of - PR:R4YE07; PR:R4Y7H5 - positively regulates - DNA replication;\n PR:R4YE07 - positively regulates - DNA replication; DNA replication - occurs in\n - NCBITaxon:39831; NCBITaxon:39831 - causes - Rhinoscleroma'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nAs a tetracycline, meclocycline likely works by reversably associating with the 30s subint of the bacterial ribosome [A19429]. A likely binding site for tetracyclines has been identified on protein S7 of this subunit. This association blocks the association of aminoacyl-tRNA with the ribosome, inhibiting protein synthesis. Ultimately this inhibits bacterial growth due to a lack of proteins necessary for reproduction.\n\n===\n\ndisease: Q Fever\ndrug: Meclocycline\n", "completion": "'disease: Q Fever\n\n drug: Meclocycline\n\n mechanism_links: meclocycline - decreases activity of - InterPro:IPR000235; InterPro:IPR000235\n - positively regulates - tRNA aminoacylation; tRNA aminoacylation - participates\n in - translation; translation - in taxon - Coxiella burnetii; Coxiella burnetii\n - causes - Q Fever'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nAlthough the exact mechanism of action is not known, studies have shown that masoprocol is a potent 5-lipoxygenase inhibitor and has antiproliferative activity against keratinocytes in tissue culture, but the relationship between this activity and its effectiveness in actinic keratoses is unknown. Masoprocol also inhibits prostaglandins but the significance of this action is not yet known.\n\n===\n\ndisease: Keratosis, Actinic\ndrug: Masoprocol\n", "completion": "'disease: Keratosis, Actinic\n\n drug: Masoprocol\n\n mechanism_links: Masoprocol - decreases activity of - serine/threonine-protein kinase\n mTOR (human); serine/threonine-protein kinase mTOR (human) - positively regulates\n - REACT:R-HSA-166208; REACT:R-HSA-166208 - positively correlated with - HP:0031377;\n HP:0031377 - causes - Keratosis, Actinic'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nThe bactericidal action of moxifloxacin results from inhibition of the enzymes topoisomerase II (DNA gyrase) and topoisomerase IV. DNA gyrase is an essential enzyme that is involved in the replication, transcription and repair of bacterial DNA. Topoisomerase IV is an enzyme known to play a key role in the partitioning of the chromosomal DNA during bacterial cell division.\n\n===\n\ndisease: Streptococcal Infections\ndrug: Moxifloxacin\n", "completion": "'disease: Streptococcal Infections\n\n drug: Moxifloxacin\n\n mechanism_links: MESH:D000077266 - decreases activity of - PR:Q9L7Q5; MESH:D000077266\n - decreases activity of - PR:Q9L7Q4; PR:Q9L7Q5 - positively regulates - DNA replication;\n PR:Q9L7Q4 - positively regulates - DNA replication; DNA replication - occurs in\n - NCBITaxon:1314; NCBITaxon:1314 - causes - Streptococcal Infections'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nAcetylsalicylic acid (ASA) blocks prostaglandin synthesis. It is non-selective for COX-1 and COX-2 enzymes [A177241, A10989, A32682]. Inhibition of COX-1 results in the inhibition of platelet aggregation for about 7-10 days (average platelet lifespan). The acetyl group of acetylsalicylic acid binds with a serine residue of the cyclooxygenase-1 (COX-1) enzyme, leading to irreversible inhibition. This prevents the production of pain-causing prostaglandins. This process also stops the conversion of arachidonic acid to thromboxane A2 (TXA2), which is a potent inducer of platelet aggregation [FDA label]. Platelet aggregation can result in clots and harmful venous and arterial thromboembolism, leading to conditions such as pulmonary embolism and stroke. It is important to note that there is 60% homology between the protein structures of COX-1 and COX-2. ASA binds to serine 516 residue on the active site of COX-2 in the same fashion as its binding to the serine 530 residue located on the active site of COX-1. The active site of COX-2 is, however, slightly larger than the active site of COX-1, so that arachidonic acid (which later becomes prostaglandins) manages to bypass the aspirin molecule inactivating COX-2 [A32682, A177256]. ASA, therefore, exerts more action on the COX-1 receptor rather than on the COX-2 receptor [A177268]. A higher dose of acetylsalicylic acid is required for COX-2 inhibition [A177325].\n\n===\n\ndisease: Myocardial Infarction\ndrug: Acetylsalicylic acid\n", "completion": "'disease: Myocardial Infarction\n\n drug: Acetylsalicylic acid\n\n mechanism_links: Aspirin - decreases activity of - prostaglandin G/H synthase 1\n (human); prostaglandin G/H synthase 1 (human) - negatively regulates - prostaglandin\n biosynthetic process; Aspirin - decreases activity of - prostaglandin G/H synthase\n 2 (human); prostaglandin G/H synthase 2 (human) - negatively regulates - prostaglandin\n biosynthetic process; prostaglandin biosynthetic process - decreases abundance of\n - Thromboxane A2; Thromboxane A2 - decreases activity of - platelet aggregation;\n platelet aggregation - prevents - blood coagulation; blood coagulation - causes\n - Myocardial Infarction'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nAminoglycosides like Streptomycin \"irreversibly\" bind to specific 30S-subunit proteins and 16S rRNA. Specifically Streptomycin binds to four nucleotides of 16S rRNA and a single amino acid of protein S12. This interferes with decoding site in the vicinity of nucleotide 1400 in 16S rRNA of 30S subunit. This region interacts with the wobble base in the anticodon of tRNA. This leads to interference with the initiation complex, misreading of mRNA so incorrect amino acids are inserted into the polypeptide leading to nonfunctional or toxic peptides and the breakup of polysomes into nonfunctional monosomes.\n\n===\n\ndisease: Tularemia\ndrug: Streptomycin\n", "completion": "'disease: Tularemia\n\n drug: Streptomycin\n\n mechanism_links: Streptomycin - molecularly interacts with - 30S ribosomal protein\n S2; 30S ribosomal protein S2 - disrupts - translation; translation - in taxon -\n NCBITaxon:263; NCBITaxon:263 - causes - Tularemia'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nAvanafil is a selective phosphodiesterase 5 (PDE5) enzyme inhibitor used for the treatment of erectile dysfunction caused by diabetes, age induced oxidative stress or other complications. Avanafil inhibits the cGMP specific phosphodiesterase type 5 (PDE5) which is responsible for degradation of cGMP in the corpus cavernosum located around the penis. Penile erection during sexual stimulation is caused by increased penile blood flow resulting from the relaxation of penile arteries and corpus cavernosal smooth muscle. This response is mediated by the release of nitric oxide (NO) from nerve terminals and endothelial cells, which stimulates the synthesis of cGMP in smooth muscle cells. Cyclic GMP causes smooth muscle relaxation and increased blood flow into the corpus cavernosum. The inhibition of phosphodiesterase type 5 (PDE5) by avanafil enhances erectile function by increasing the amount of cGMP.\n\n===\n\ndisease: Erectile Dysfunction\ndrug: Avanafil\n", "completion": "'disease: Erectile Dysfunction\n\n drug: Avanafil\n\n mechanism_links: avanafil - decreases activity of - cGMP-specific 3'',5''-cyclic\n phosphodiesterase (human); cGMP-specific 3'',5''-cyclic phosphodiesterase (human)\n - increases abundance of - Cyclic GMP; Cyclic GMP - causes - relaxation of smooth\n muscle; relaxation of smooth muscle - positively regulates - blood circulation;\n blood circulation - located in - corpus cavernosum penis; corpus cavernosum penis\n - participates in - Erectile Dysfunction'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nProcaine benzylpenicillin is hydrolyzed into penicillin G once it is released from the injection site. Penicillin G attaches to the penicillin-binding proteins on bacterial cell wall and inhibit the transpeptidation enzyme that crosslinks the peptide chains attached to the backbone of the peptidoglycan. The final bactericidal event involves the inactivation of an inhibitor of autolytic enzymes in the cell wall, leading to lysis of the bacterium [T33].\n\n===\n\ndisease: Neurosyphilis\ndrug: Procaine benzylpenicillin\n", "completion": "'disease: Neurosyphilis\n\n drug: Procaine benzylpenicillin\n\n mechanism_links: Penicillin G Procaine - produces - Benzylpenicillin; Benzylpenicillin\n - negatively regulates - Pfam:PF00905; Pfam:PF00905 - positively regulates - peptidoglycan\n biosynthetic process; peptidoglycan biosynthetic process - positively correlated\n with - peptidoglycan-based cell wall biogenesis; peptidoglycan-based cell wall biogenesis\n - in taxon - NCBITaxon:160; NCBITaxon:160 - causes - Neurosyphilis'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nAs a tetracycline, meclocycline likely works by reversably associating with the 30s subint of the bacterial ribosome [A19429]. A likely binding site for tetracyclines has been identified on protein S7 of this subunit. This association blocks the association of aminoacyl-tRNA with the ribosome, inhibiting protein synthesis. Ultimately this inhibits bacterial growth due to a lack of proteins necessary for reproduction.\n\n===\n\ndisease: MESH:D000073605\ndrug: Meclocycline\n", "completion": "'disease: MESH:D000073605\n\n drug: Meclocycline\n\n mechanism_links: meclocycline - decreases activity of - InterPro:IPR000235; InterPro:IPR000235\n - positively regulates - tRNA aminoacylation; tRNA aminoacylation - participates\n in - translation; translation - in taxon - NCBITaxon:786; NCBITaxon:786 - causes\n - MESH:D000073605'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nBeclomethasone dipropionate is a corticosteroid and prodrug that is rapidly activated by hydrolysis to the active monoester, 17 monopropionate (17-BMP), which mediates anti-inflammatory actions. 17-BMP has been shown _in vitro_ to exhibit a binding affinity for the human glucocorticoid receptor which is approximately 13 times that of dexamethasone and 25 times that of beclomethasone dipropionate.[L6871] Upon binding of the ligand, the glucocorticoid receptors dimerize and translocate into the nucleus, where they subsequently bind to glucocorticoid response elements (GRE) on glucocorticoid-responsive genes, leading to changes in transcription. There are several proposed mechanisms for the anti-inflammatory action of corticosteroids. Corticosteroids may work by increasing the transcription of genes coding for anti-inflammatory proteins, including lipocortin-1 and interleukin-10.[A179875] Corticosteroids were also shown to inhibit the expression of multiple genes that encode pro-inflammatory factors, such as cytokines, chemokines, and adhesion molecules, that are activated during the chronic inflammatory process.[A31449] This is thought to be due to the direct inhibitory interaction between activated glucocorticoid receptors and activated pro-inflammatory transcription factors, such as nuclear factor-kappa B and activator protein-1.[A179875] Chronic inflammation is often characterized by enhanced expression of these transcription factors that bind to and activate coactivator molecules, which then acetylate core histones to switch on gene transcription to further amplify the inflammatory process.[A31449] Corticosteroids suppress the multiple inflammatory gene expression by promoting histone deacetylation, resulting in tighter coiling of DNA and reduced access of transcription factors to their binding sites.[A179875]\n\n===\n\ndisease: Nasal Polyps\ndrug: Beclomethasone dipropionate\n", "completion": "'disease: Nasal Polyps\n\n drug: Beclomethasone dipropionate\n\n mechanism_links: Beclomethasone dipropionate - has metabolite - CHEBI:3001; CHEBI:3001\n - positively regulates - glucocorticoid receptor (human); glucocorticoid receptor\n (human) - negatively regulates - inflammatory response; inflammatory response -\n positively correlated with - Nasal Polyps'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nFusidic acid works by interfering with bacterial protein synthesis, specifically by preventing the translocation of the elongation factor G (EF-G) from the ribosome. It also can inhibit chloramphenicol acetyltransferase enzymes.\n\n===\n\ndisease: Gastrointestinal anthrax\ndrug: Fusidic acid\n", "completion": "'disease: Gastrointestinal anthrax\n\n drug: Fusidic acid\n\n mechanism_links: Fusidic Acid - decreases activity of - PR:Q81VT3; PR:Q81VT3 - positively\n regulates - translation; translation - occurs in - Bacillus anthracis; Bacillus\n anthracis - causes - Gastrointestinal anthrax'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nMethdilazine binds to the histamine H<sub>1</sub> receptor. This blocks the action of endogenous histamine, which subsequently leads to temporary relief of the negative symptoms brought on by histamine.\n\n===\n\ndisease: Rhinitis, Allergic\ndrug: Methdilazine\n", "completion": "'disease: Rhinitis, Allergic\n\n drug: Methdilazine\n\n mechanism_links: methdilazine - decreases activity of - histamine H1 receptor (human);\n histamine H1 receptor (human) - positively regulates - histamine receptor activity;\n histamine receptor activity - participates in - histamine secretion involved in\n inflammatory response; histamine secretion involved in inflammatory response - positively\n correlated with - Rhinitis, Allergic'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nAccording to its FDA labeling, acetaminophen's exact mechanism of action has not been fully established[Label] - despite this, it is often categorized alongside NSAIDs (nonsteroidal anti-inflammatory drugs) due to its ability to inhibit the cyclooxygenase (COX) pathways.[T518] It is thought to exert central actions which ultimately lead to the alleviation of pain symptoms.[T518] One theory is that acetaminophen increases the pain threshold by inhibiting two isoforms of cyclooxygenase, COX-1 and COX-2, which are involved in prostaglandin (PG) synthesis. Prostaglandins are responsible for eliciting pain sensations.[A176366] Acetaminophen does not inhibit cyclooxygenase in peripheral tissues and, therefore, has no peripheral anti-inflammatory effects. Though acetylsalicylic acid (aspirin) is an irreversible inhibitor of COX and directly blocks the active site of this enzyme, studies have shown that acetaminophen (paracetamol) blocks COX indirectly.[F4133] Studies also suggest that acetaminophen selectively blocks a variant type of the COX enzyme that is unique from the known variants COX-1 and COX-2.[A468] This enzyme has been referred to as _COX-3_. The antipyretic actions of acetaminophen are likely attributed to direct action on heat-regulating centers in the brain, resulting in peripheral vasodilation, sweating, and loss of body heat.[F4133] The exact mechanism of action of this drug is not fully understood at this time, but future research may contribute to deeper knowledge.[F4133]\n\n===\n\ndisease: Rhinitis, Allergic\ndrug: Acetaminophen\n", "completion": "'disease: Rhinitis, Allergic\n\n drug: Acetaminophen\n\n mechanism_links: Acetaminophen - decreases activity of - prostaglandin G/H synthase\n 1 (human); Acetaminophen - decreases activity of - prostaglandin G/H synthase 2\n (human); Acetaminophen - decreases activity of - prostaglandin E synthase 3 (human);\n prostaglandin G/H synthase 1 (human) - positively regulates - prostaglandin biosynthetic\n process; prostaglandin G/H synthase 2 (human) - positively regulates - prostaglandin\n biosynthetic process; prostaglandin E synthase 3 (human) - positively regulates\n - prostaglandin biosynthetic process; prostaglandin biosynthetic process - increases\n abundance of - Prostaglandins; Prostaglandins - positively correlated with - Rhinitis,\n Allergic'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nBy binding to specific penicillin-binding proteins (PBPs) located inside the bacterial cell wall, penicillin G inhibits the third and last stage of bacterial cell wall synthesis. Cell lysis is then mediated by bacterial cell wall autolytic enzymes such as autolysins; it is possible that penicillin G interferes with an autolysin inhibitor.\n\n===\n\ndisease: Streptococcal Infections\ndrug: Benzylpenicillin\n", "completion": "'disease: Streptococcal Infections\n\n drug: Benzylpenicillin\n\n mechanism_links: Penicillin G - decreases activity of - InterPro:IPR001460; InterPro:IPR001460\n - participates in - peptidoglycan biosynthetic process; peptidoglycan biosynthetic\n process - positively regulates - peptidoglycan-based cell wall biogenesis; peptidoglycan-based\n cell wall biogenesis - occurs in - Streptococcus; Streptococcus - causes - Streptococcal\n Infections'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nBy binding to specific penicillin-binding proteins (PBPs) located inside the bacterial cell wall, Ampicillin inhibits the third and last stage of bacterial cell wall synthesis. Cell lysis is then mediated by bacterial cell wall autolytic enzymes such as autolysins; it is possible that Ampicillin interferes with an autolysin inhibitor.\n\n===\n\ndisease: Meningitis, Bacterial\ndrug: Ampicillin\n", "completion": "'disease: Meningitis, Bacterial\n\n drug: Ampicillin\n\n mechanism_links: Ampicillin - negatively regulates - Pfam:PF00905; Pfam:PF00905\n - positively regulates - peptidoglycan biosynthetic process; peptidoglycan biosynthetic\n process - positively correlated with - peptidoglycan-based cell wall biogenesis;\n peptidoglycan-based cell wall biogenesis - in taxon - Neisseria meningitidis; Neisseria\n meningitidis - causes - Meningitis, Bacterial'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nTopotecan has the same mechanism of action as irinotecan and is believed to exert its cytotoxic effects during the S-phase of DNA synthesis. Topoisomerase I relieves torsional strain in DNA by inducing reversible single strand breaks. Topotecan binds to the topoisomerase I-DNA complex and prevents religation of these single strand breaks. This ternary complex interferes with the moving replication fork, which leads to the induction of replication arrest and lethal double-stranded breaks in DNA. As mammalian cells cannot efficiently repair these double strand breaks, the formation of this ternary complex eventually leads to apoptosis (programmed cell death). Topotecan mimics a DNA base pair and binds at the site of DNA cleavage by intercalating between the upstream (−1) and downstream (+1) base pairs. Intercalation displaces the downstream DNA, thus preventing religation of the cleaved strand. By specifically binding to the enzyme–substrate complex, Topotecan acts as an uncompetitive inhibitor.\n\n===\n\ndisease: Small Cell Lung Carcinoma\ndrug: Topotecan\n", "completion": "'disease: Small Cell Lung Carcinoma\n\n drug: Topotecan\n\n mechanism_links: Topotecan - decreases activity of - DNA topoisomerase 1 (human);\n DNA topoisomerase 1 (human) - positively regulates - DNA binding; DNA binding -\n correlated with - DNA replication; DNA replication - positively correlated with\n - neoplastic cell; neoplastic cell - positively correlated with - Small Cell Lung\n Carcinoma'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nIn the CNS, there exist strychnine-sensitive glycine binding sites as well as strychnine-insensitive glycine binding sites. The strychnine-insensitive glycine-binding site is located on the NMDA receptor complex. The strychnine-sensitive glycine receptor complex is comprised of a chloride channel and is a member of the ligand-gated ion channel superfamily. The putative antispastic activity of supplemental glycine could be mediated by glycine's binding to strychnine-sensitive binding sites in the spinal cord. This would result in increased chloride conductance and consequent enhancement of inhibitory neurotransmission. The ability of glycine to potentiate NMDA receptor-mediated neurotransmission raised the possibility of its use in the management of neuroleptic-resistant negative symptoms in schizophrenia. <br/>Animal studies indicate that supplemental glycine protects against endotoxin-induced lethality, hypoxia-reperfusion injury after liver transplantation, and D-galactosamine-mediated liver injury. Neutrophils are thought to participate in these pathologic processes via invasion of tissue and releasing such reactive oxygen species as superoxide. In vitro studies have shown that neutrophils contain a glycine-gated chloride channel that can attenuate increases in intracellular calcium and diminsh neutrophil oxidant production. This research is ealy-stage, but suggests that supplementary glycine may turn out to be useful in processes where neutrophil infiltration contributes to toxicity, such as ARDS.\n\n===\n\ndisease: Common Cold\ndrug: Glycine\n", "completion": "'disease: Common Cold\n\n drug: Glycine\n\n mechanism_links: Glycine - treats - Common Cold'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nLoxoprofen itself is a prodrug and carries little-to-no pharmacological activity - it is rapidly metabolized to its trans-alcohol form, which is a potent and non-selective inhibitor of cyclooxygenase.[A27797] Cyclooxygenase (COX) is present in 2 forms, COX-1 and COX-2, with each serving different functions. COX-1 is present in human cells and is constitutively released, performing cellular housekeeping functions such as mucus production and platelet aggregation.[L1228] COX-2 is induced in human cells post-injury or due to other stimuli, is triggered to appear in large quantities at the sites of injury/stimuli, and is ultimately responsible for the mediation of inflammation and pain.[L1228] Loxoprofen's active metabolite inhibits both COX isoforms, resulting in reduced expression of several mediators of pain, inflammation, and fever (e.g. prostaglandins, prostacyclin, thromboxane, etc).[L1228]\n\n===\n\ndisease: Arthritis, Rheumatoid\ndrug: Loxoprofen\n", "completion": "'disease: Arthritis, Rheumatoid\n\n drug: Loxoprofen\n\n mechanism_links: loxoprofen - decreases activity of - prostaglandin G/H synthase\n 1 (human); loxoprofen - decreases activity of - prostaglandin G/H synthase 2 (human);\n prostaglandin G/H synthase 1 (human) - participates in - REACT:R-HSA-2162123; prostaglandin\n G/H synthase 2 (human) - participates in - REACT:R-HSA-2162123; REACT:R-HSA-2162123\n - increases abundance of - Prostaglandins; Prostaglandins - positively correlated\n with - HP:0002829; Prostaglandins - positively correlated with - HP:0001386; HP:0001386\n - positively correlated with - Arthritis, Rheumatoid; HP:0002829 - positively correlated\n with - Arthritis, Rheumatoid'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nThe precise mechanism of the antiinflammatory activity of topical steroids in the treatment of steroid-responsive dermatoses, in general, is uncertain. However, corticosteroids are thought to act by the induction of phospholipase A<sub>2</sub> inhibitory proteins, collectively called lipocortins. This is achieved first by the drug binding to the glucocorticoid receptors which then translocates into the nucleus and binds to DNA causing various activations and repressions of genes. It is postulated that these proteins control the biosynthesis of potent mediators of inflammation such as prostaglandins and leukotrienes by inhibiting the release of their common precursor arachidonic acid. Arachidonic acid is released from membrane phospholipids by phospholipase A<sub>2</sub>.\n\n===\n\ndisease: Pruritus Ani\ndrug: Desoximetasone\n", "completion": "'disease: Pruritus Ani\n\n drug: Desoximetasone\n\n mechanism_links: Desoximetasone - increases activity of - glucocorticoid receptor\n (human); glucocorticoid receptor (human) - increases abundance of - annexin A1 (human);\n annexin A1 (human) - negatively regulates - REACT:R-HSA-2162123; REACT:R-HSA-2162123\n - positively regulates - inflammatory response; inflammatory response - contributes\n to - HP:0000989; HP:0000989 - manifestation of - Pruritus Ani'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nPiperazine is a GABA receptor agonist. Piperzine binds directly and selectively to muscle membrane GABA receptors, presumably causing hyperpolarization of nerve endings, resulting in flaccid paralysis of the worm. While the worm is paralyzed, it is dislodged from the intestinal lumen and expelled live from the body by normal intestinal peristalsis.\n\n===\n\ndisease: Enterobiasis\ndrug: Piperazine\n", "completion": "'disease: Enterobiasis\n\n drug: Piperazine\n\n mechanism_links: Piperazine - increases activity of - gamma-aminobutyric acid receptor\n subunit beta-3 (human); gamma-aminobutyric acid receptor subunit beta-3 (human)\n - positively correlated with - chloride channel activity; gamma-aminobutyric acid\n receptor subunit beta-3 (human) - decreases abundance of - Acetylcholine; Acetylcholine\n - occurs in - membrane hyperpolarization; chloride channel activity - occurs in\n - membrane hyperpolarization; membrane hyperpolarization - has phenotype - HP:0003470;\n HP:0003470 - increases activity of - defense response to other organism; defense\n response to other organism - in taxon - NCBITaxon:51028; NCBITaxon:51028 - causes\n - Enterobiasis'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nGonadotropin-releasing hormone (GnRH) is a naturally occurring decapeptide that modulates the hypothalamic-pituitary-gonadal (HPG) axis. GnRH binds to corresponding receptors (GnRHRs) on the anterior pituitary gonadotropes, which in turn release luteinizing hormone (LH) and follicle-stimulating hormone (FSH); these, in turn, affect the downstream synthesis and release of the sex hormones testosterone, dihydrotestosterone, estrone, and estradiol.[A203126, A203132] Despite the variety of conditions indicated for treatment with leuprolide, the mechanism of action underlying efficacy is the same in all cases. As a GnRHR agonist, leuprolide binds to and initially activates downstream LH and FSH release; this initial spike in gonadotropin levels is responsible for some of the adverse effects associated with treatment. After 2-4 weeks of treatment, continuous stimulation of GnRHR results in feedback inhibition and significant downregulation of LH, FSH, and their corresponding downstream effects, producing a therapeutic benefit. These effects are reversible upon treatment discontinuation.[A203126, A203129, A203132, A203222, L10310, L13781, L13784, L13787, L13790, L13814]\n\n===\n\ndisease: Puberty, Precocious\ndrug: Leuprolide\n", "completion": "'disease: Puberty, Precocious\n\n drug: Leuprolide\n\n mechanism_links: Leuprolide - increases activity of - gonadotropin-releasing hormone\n receptor (human); gonadotropin-releasing hormone receptor (human) - positively regulates\n - gonadotropin hormone-releasing hormone activity; gonadotropin hormone-releasing\n hormone activity - regulates - estrogen biosynthetic process; gonadotropin hormone-releasing\n hormone activity - regulates - androgen biosynthetic process; gonadotropin hormone-releasing\n hormone activity - regulates - progesterone biosynthetic process; estrogen biosynthetic\n process - negatively correlated with - Puberty, Precocious; androgen biosynthetic\n process - negatively correlated with - Puberty, Precocious; progesterone biosynthetic\n process - negatively correlated with - Puberty, Precocious'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nThe mechanism of its antiparkinsonic effect is not fully understood, but it appears to be releasing dopamine from the nerve endings of the brain cells, together with stimulation of norepinephrine response. It also has NMDA receptor antagonistic effects. The antiviral mechanism seems to be unrelated. The drug interferes with a viral protein, M2 (an ion channel), which is needed for the viral particle to become \"uncoated\" once it is taken inside the cell by endocytosis.\n\n===\n\ndisease: Parkinson Disease\ndrug: Amantadine\n", "completion": "'disease: Parkinson Disease\n\n drug: Amantadine\n\n mechanism_links: Amantadine - increases activity of - D(2) dopamine receptor (human);\n D(2) dopamine receptor (human) - positively correlated with - Dopamine; Dopamine\n - positively correlated with - dopamine secretion, neurotransmission; dopamine secretion,\n neurotransmission - occurs in - substantia nigra; substantia nigra - disrupted by\n - Parkinson Disease'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nTriprolidine binds to the histamine H1 receptor. This blocks the action of endogenous histamine, which subsequently leads to temporary relief of the negative symptoms brought on by histamine.\n\n===\n\ndisease: Rhinitis, Allergic\ndrug: Triprolidine\n", "completion": "'disease: Rhinitis, Allergic\n\n drug: Triprolidine\n\n mechanism_links: Triprolidine - decreases activity of - histamine H1 receptor (human);\n histamine H1 receptor (human) - positively regulates - histamine receptor activity;\n histamine receptor activity - positively correlated with - histamine secretion involved\n in inflammatory response; histamine secretion involved in inflammatory response\n - positively correlated with - Rhinitis, Allergic'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nMedroxyprogesterone acetate (MPA) inhibits the production of gonadotropin, preventing follicular maturation and ovulation, which is responsible for it’s ability to prevent pregnancy.[L8660] This action also thins the endometrium.[L8660] MPA reduces nuclear estrogen receptors and DNA synthesis in epithelial cells of the endometrium.[L8660] MPA can also induce p53 dependant apoptosis in certain cancer cell lines,[A186134] and inhibit GABA-A receptors.[A186140]\n\n===\n\ndisease: Hot Flashes\ndrug: Medroxyprogesterone acetate\n", "completion": "'disease: Hot Flashes\n\n drug: Medroxyprogesterone acetate\n\n mechanism_links: Medroxyprogesterone - increases activity of - progesterone receptor\n (human); progesterone receptor (human) - positively regulates - progesterone receptor\n signaling pathway; progesterone receptor signaling pathway - treats - Hot Flashes;\n Medroxyprogesterone - increases activity of - estrogen receptor (human); estrogen\n receptor (human) - positively regulates - intracellular estrogen receptor signaling\n pathway; intracellular estrogen receptor signaling pathway - treats - Hot Flashes'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nIndapamide acts on the nephron, specifically at the proximal segment of the distal convoluted tubule where it inhibits the Na+/Cl- cotransporter, leading to reduced sodium reabsorption.[A203519,A16729] As a result, sodium and water are retained in the lumen of the nephron for urinary excretion.[A185180] The effects that follow include reduced plasma volume, reduced venous return, lower cardiac output, and ultimately decreased blood pressure.[A16729] Some studies have suggested that indapamide may decrease responsiveness to pressor agents while others have suggested it can decrease peripheral resistance.[A203627] Although it is clear that diuresis contributes to the antihypertensive effects of indapamide, further studies are needed to investigate the medication’s ability to decrease peripheral vascular resistance and relax vascular smooth muscle.[A203627]\n\n===\n\ndisease: Hypertension\ndrug: Indapamide\n", "completion": "'disease: Hypertension\n\n drug: Indapamide\n\n mechanism_links: Indapamide - decreases activity of - solute carrier family 12 member\n 3 (human); solute carrier family 12 member 3 (human) - participates in - renal sodium\n ion absorption; renal sodium ion absorption - positively correlated with - renal\n water retention; renal water retention - contributes to - HP:0011104; HP:0011104\n - contributes to - positive regulation of blood pressure; positive regulation of\n blood pressure - affects risk for - Hypertension'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nThe precise mechanism of action of deutetrabenazine in mediating its anti-chorea effects is not fully elucidated. Deutetrabenazine reversibly depletes the levels of monoamines, such as dopamine, serotonin, norepinephrine, and histamine, from nerve terminals via its active metabolites. The major circulating metabolites are α-dihydrotetrabenazine [HTBZ] and β-HTBZ that act as reversible inhibitors of VMAT2. Inhibition of VMAT2 results in decreased uptake of monoamines into synaptic terminal and depletion of monoamine stores from nerve terminals [FDA Label]. Deutetrabenazine contains the molecule deuterium, which is a naturally-occurring, nontoxic hydrogen isotope but with an increased mass relative to hydrogen [A32046]. Placed at key positions, deuterium forms a stronger hydrogen bond with carbon that requires more energy for cleavage, thus attenuating CYP2D6-mediated metabolism without having any effect on the therapeutic target [A32046].\n\n===\n\ndisease: Tardive Dyskinesia\ndrug: Deutetrabenazine\n", "completion": "'disease: Tardive Dyskinesia\n\n drug: Deutetrabenazine\n\n mechanism_links: deutetrabenazine - has metabolite - Tetrabenazine; Tetrabenazine\n - decreases activity of - synaptic vesicular amine transporter (human); synaptic\n vesicular amine transporter (human) - positively regulates - aminergic neurotransmitter\n loading into synaptic vesicle; aminergic neurotransmitter loading into synaptic\n vesicle - prevents - dopamine catabolic process; dopamine catabolic process - negatively\n regulates - dopamine secretion, neurotransmission; dopamine secretion, neurotransmission\n - correlated with - Tardive Dyskinesia'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nParitaprevir is a potent inhibitor of the NS3/4A serine protease of Hepatitis C Virus (HCV) [FDA Label]. Following viral replication of HCV genetic material and translation into a single polypeptide, Nonstructural Protein 3 (NS3) and its activating cofactor Nonstructural Protein 4A (NS4A) are responsible for cleaving it into the following structural and nonstructural proteins required for assembly into mature virus: NS3, NS4A, NS4B, NS5A, and NS5B. By inhibiting viral protease NS3/4A, paritaprevir therefore prevents viral replication and function.\n\n===\n\ndisease: Hepatitis C, Chronic\ndrug: Paritaprevir\n", "completion": "'disease: Hepatitis C, Chronic\n\n drug: Paritaprevir\n\n mechanism_links: ABT-450 - negatively regulates - PR:P27958; PR:P27958 - positively\n regulates - viral RNA genome replication; viral RNA genome replication - in taxon\n - NCBITaxon:11103; NCBITaxon:11103 - causes - Hepatitis C, Chronic'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nCrizotinib is a tyrosine kinase receptor inhibitor. More specifically, it inhibits anaplastic lymphoma kinase (ALK), hepatocyte growth factor receptor (HGFR, c-MET), and Recepteur d'Origine Nantais (RON). Abnormalities in the ALK gene caused by mutations or translocations may lead to expression of oncogenic fusion proteins. In patients with NSCLC, they have the EML4-ALK gene. Crizotinib inhibits ALK tyrosine kinase which ultimately results in decreased proliferation of cells that carry the genetic mutation and tumour survivability.\n\n===\n\ndisease: Carcinoma, Non-Small-Cell Lung\ndrug: Crizotinib\n", "completion": "'disease: Carcinoma, Non-Small-Cell Lung\n\n drug: Crizotinib\n\n mechanism_links: crizotinib - decreases activity of - hepatocyte growth factor receptor\n (human); hepatocyte growth factor receptor (human) - negatively regulates - cell\n population proliferation; cell population proliferation - contributes to - Carcinoma,\n Non-Small-Cell Lung'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nCiprofloxacin acts on bacterial topoisomerase II (DNA gyrase) and topoisomerase IV.[A178885] Ciprofloxacin's targeting of the alpha subunits of DNA gyrase prevents it from supercoiling the bacterial DNA which prevents DNA replication.[A178876,A178882]\n\n===\n\ndisease: Prostatitis\ndrug: Ciprofloxacin\n", "completion": "'disease: Prostatitis\n\n drug: Ciprofloxacin\n\n mechanism_links: Ciprofloxacin - decreases activity of - DNA gyrase subunit A (Escherichia\n coli K-12); Ciprofloxacin - decreases activity of - DNA topoisomerase 4 subunit\n A (Escherichia coli K-12); DNA gyrase subunit A (Escherichia coli K-12) - positively\n regulates - DNA replication; DNA topoisomerase 4 subunit A (Escherichia coli K-12)\n - positively regulates - DNA replication; DNA replication - occurs in - Escherichia\n coli; Escherichia coli - causes - Prostatitis'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nAlendronic acid binds to bone hydroxyapatite[FDA Label]. Bone resorption causes local acidification, releasing alendronic acid which is that taken into osteoclasts by fluid-phase endocytosis[A959]. Endocytic vesicles are acidified, releasing alendronic acid to the cytosol of osteoclasts where they induce apoptosis[A959]. Inhibition of osteoclasts results in decreased bone resorption which is shown through decreased urinary calcium, deoxypyridinoline and cross-linked N-telopeptidases of type I collagen[FDA Label].\n\n===\n\ndisease: Osteoporosis, Postmenopausal\ndrug: Alendronic acid\n", "completion": "'disease: Osteoporosis, Postmenopausal\n\n drug: Alendronic acid\n\n mechanism_links: Alendronate - positively regulates - apoptotic process; apoptotic\n process - located in - osteoclast; osteoclast - participates in - bone resorption;\n bone resorption - causes - Osteoporosis, Postmenopausal'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nSulindac's exact mechanism of action is unknown. Its antiinflammatory effects are believed to be due to inhibition of both COX-1 and COX-2 which leads to the inhibition of prostaglandin synthesis. Antipyretic effects may be due to action on the hypothalamus, resulting in an increased peripheral blood flow, vasodilation, and subsequent heat dissipation.\n\n===\n\ndisease: Tendinopathy\ndrug: Sulindac\n", "completion": "'disease: Tendinopathy\n\n drug: Sulindac\n\n mechanism_links: Sulindac - decreases activity of - prostaglandin G/H synthase 1\n (human); Sulindac - decreases activity of - prostaglandin G/H synthase 2 (human);\n prostaglandin G/H synthase 1 (human) - increases abundance of - Prostaglandins;\n prostaglandin G/H synthase 2 (human) - increases abundance of - Prostaglandins;\n Prostaglandins - participates in - inflammatory response; inflammatory response\n - contributes to - Pain; Pain - manifestation of - Tendinopathy'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nBy binding to specific penicillin-binding proteins (PBPs) located inside the bacterial cell wall, penicillin G inhibits the third and last stage of bacterial cell wall synthesis. Cell lysis is then mediated by bacterial cell wall autolytic enzymes such as autolysins; it is possible that penicillin G interferes with an autolysin inhibitor.\n\n===\n\ndisease: Pneumonia, Aspiration\ndrug: Benzylpenicillin\n", "completion": "'disease: Pneumonia, Aspiration\n\n drug: Benzylpenicillin\n\n mechanism_links: Penicillin G - decreases activity of - InterPro:IPR001460; InterPro:IPR001460\n - participates in - peptidoglycan biosynthetic process; peptidoglycan biosynthetic\n process - positively regulates - peptidoglycan-based cell wall biogenesis; peptidoglycan-based\n cell wall biogenesis - occurs in - Bacteria; Bacteria - causes - Pneumonia, Aspiration'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nUmeclidinium is a long-acting, antimuscarinic agent, which is often referred to as an anticholinergic. It has similar affinity to the subtypes of muscarinic receptors M1 to M5. In the airways, it exhibits pharmacological effects through the inhibition of M3 receptor at the smooth muscle leading to bronchodilation.\n\n===\n\ndisease: Pulmonary Disease, Chronic Obstructive\ndrug: Umeclidinium\n", "completion": "'disease: Pulmonary Disease, Chronic Obstructive\n\n drug: Umeclidinium\n\n mechanism_links: GSK573719 - decreases activity of - muscarinic acetylcholine receptor\n M2 (human); GSK573719 - decreases activity of - muscarinic acetylcholine receptor\n M3 (human); muscarinic acetylcholine receptor M2 (human) - participates in - response\n to acetylcholine; muscarinic acetylcholine receptor M3 (human) - participates in\n - response to acetylcholine; response to acetylcholine - positively regulates -\n smooth muscle contraction; smooth muscle contraction - located in - bronchus; bronchus\n - location of - inflammatory response; inflammatory response - causes - Pulmonary\n Disease, Chronic Obstructive'\n"} -{"prompt": "From the text below, extract the following entities in the following format:\n\ndisease: \ndrug: \nmechanism_links: \n\n\nText:\nThe short term effects of corticosteroids are decreased vasodilation and permeability of capillaries, as well as decreased leukocyte migration to sites of inflammation.[A187463] Corticosteroids binding to the glucocorticoid receptor mediates changes in gene expression that lead to multiple downstream effects over hours to days.[A187463] Lower doses of corticosteroids provide an anti-inflammatory effect, while higher doses are immunosuppressive.[A187463] High doses of glucocorticoids for an extended period bind to the mineralocorticoid receptor, raising sodium levels and decreasing potassium levels.[A187463]\n\n===\n\ndisease: Psoriasis\ndrug: Methylprednisolone\n", "completion": "'disease: Psoriasis\n\n drug: Methylprednisolone\n\n mechanism_links: Methylprednisolone - increases activity of - glucocorticoid receptor\n (human); glucocorticoid receptor (human) - increases activity of - annexin A1 (human);\n glucocorticoid receptor (human) - decreases activity of - prostaglandin G/H synthase\n 1 (human); glucocorticoid receptor (human) - decreases activity of - prostaglandin\n G/H synthase 2 (human); annexin A1 (human) - decreases activity of - cytosolic phospholipase\n A2 (human); prostaglandin G/H synthase 1 (human) - positively regulates - prostaglandin\n biosynthetic process; prostaglandin G/H synthase 2 (human) - positively regulates\n - prostaglandin biosynthetic process; cytosolic phospholipase A2 (human) - positively\n regulates - leukotriene biosynthetic process; cytosolic phospholipase A2 (human)\n - positively regulates - prostaglandin biosynthetic process; leukotriene biosynthetic\n process - positively correlated with - inflammatory response; prostaglandin biosynthetic\n process - positively correlated with - inflammatory response; inflammatory response\n - positively correlated with - HP:0011123; HP:0011123 - positively correlated with\n - Psoriasis'\n"} diff --git a/tests/input/training/training-drugmechdb-001.yaml b/tests/input/training/training-drugmechdb-001.yaml deleted file mode 100644 index c4b264172..000000000 --- a/tests/input/training/training-drugmechdb-001.yaml +++ /dev/null @@ -1,4023 +0,0 @@ -base_model: text-davinci-003 -examples: -- completion: 'disease: Leukemia, Lymphocytic, Chronic, B-Cell - - drug: Bendamustine - - mechanism_links: Bendamustine Hydrochloride - disrupts - DNA; DNA - participates - in - DNA replication; DNA replication - precedes - lymphocyte proliferation; lymphocyte - proliferation - positively correlated with - Leukemia, Lymphocytic, Chronic, B-Cell' - prompt: "From the text below, extract the following entities in the following format:\n\ - \ndisease: \ndrug: \nmechanism_links: \n\ - \n\nText:\n Bendamustine is a bifunctional mechlorethamine derivative capable\ - \ of forming electrophilic alkyl groups that covalently bond to other molecules.\ - \ Through this function as an alkylating agent, bendamustine causes intra- and\ - \ inter-strand crosslinks between DNA bases resulting in cell death. It is active\ - \ against both active and quiescent cells, although the exact mechanism of action\ - \ is unknown.\n\n===\n\ndisease: Leukemia, Lymphocytic, Chronic, B-Cell\ndrug:\ - \ Bendamustine\n" -- completion: 'disease: Pneumonia, Staphylococcal - - drug: Cefmetazole - - mechanism_links: Cefmetazole - decreases activity of - InterPro:IPR005311; InterPro:IPR005311 - - positively regulates - peptidoglycan biosynthetic process; peptidoglycan biosynthetic - process - positively regulates - peptidoglycan-based cell wall biogenesis; peptidoglycan-based - cell wall biogenesis - positively correlated with - cell division; cell division - - in taxon - Staphylococcus aureus; Staphylococcus aureus - causes - Pneumonia, - Staphylococcal' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - The bactericidal activity of cefmetazole results from the inhibition of cell wall - synthesis via affinity for penicillin-binding proteins (PBPs). - - - === - - - disease: Pneumonia, Staphylococcal - - drug: Cefmetazole - - ' -- completion: 'disease: Pharyngitis - - drug: Fusidic acid - - mechanism_links: Fusidic Acid - decreases activity of - PR:A2RCI2; PR:A2RCI2 - - positively regulates - translation; translation - occurs in - NCBITaxon:1314; - NCBITaxon:1314 - causes - Pharyngitis' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Fusidic acid works by interfering with bacterial protein synthesis, specifically - by preventing the translocation of the elongation factor G (EF-G) from the ribosome. - It also can inhibit chloramphenicol acetyltransferase enzymes. - - - === - - - disease: Pharyngitis - - drug: Fusidic acid - - ' -- completion: 'disease: Pain - - drug: Fentanyl - - mechanism_links: Fentanyl - increases activity of - mu-type opioid receptor (human); - Fentanyl - increases activity of - delta-type opioid receptor (human); mu-type - opioid receptor (human) - positively regulates - REACT:R-HSA-372790; delta-type - opioid receptor (human) - positively regulates - REACT:R-HSA-372790; REACT:R-HSA-372790 - - decreases activity of - PR:B7Z2C7; PR:B7Z2C7 - increases abundance of - 3'',5''-cyclic - AMP; 3'',5''-cyclic AMP - negatively regulates - ATP-sensitive inward rectifier - potassium channel 11 (human); 3'',5''-cyclic AMP - positively correlated with - - calcium ion import; ATP-sensitive inward rectifier potassium channel 11 (human) - - participates in - membrane hyperpolarization; calcium ion import - positively - regulates - substance P secretion, neurotransmission; calcium ion import - positively - regulates - glutamate secretion, neurotransmission; membrane hyperpolarization - - negatively regulates - action potential initiation; substance P secretion, neurotransmission - - located in - pain receptor cell; glutamate secretion, neurotransmission - located - in - pain receptor cell; action potential initiation - positively regulates - - pain receptor cell; pain receptor cell - positively correlated with - Pain' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Fentanyl binds to opioid receptors, especially the mu opioid receptor, which are - coupled to G-proteins.[A179533] Activation of opioid receptors causes GTP to be - exchanged for GDP on the G-proteins which in turn down regulates adenylate cyclase, - reducing concentrations of cAMP.[A179533] Reduced cAMP decreases cAMP dependant - influx of calcium ions into the cell.[A179533] The exchange of GTP for GDP results - in hyperpolarization of the cell and inhibition of nerve activity.[A179533] - - - === - - - disease: Pain - - drug: Fentanyl - - ' -- completion: 'disease: Cough - - drug: Benzocaine - - mechanism_links: Benzocaine - decreases activity of - sodium channel protein type - 10 subunit alpha (human); sodium channel protein type 10 subunit alpha (human) - - participates in - voltage-gated sodium channel activity; voltage-gated sodium - channel activity - increases transport of - Sodium; Sodium - positively correlated - with - membrane depolarization; membrane depolarization - positively regulates - - neuronal action potential; neuronal action potential - occurs in - pain receptor - cell; pain receptor cell - participates in - sensory perception of pain; sensory - perception of pain - occurs in - Cough' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Benzocaine binds to sodium channels and reversibly stabilizes the neuronal membrane - which decreases its permeability to sodium ions. Depolarization of the neuronal - membrane is inhibited thereby blocking the initiation and conduction of nerve - impulses. - - - === - - - disease: Cough - - drug: Benzocaine - - ' -- completion: 'disease: Anemia, Diamond-Blackfan - - drug: Cortisone acetate - - mechanism_links: Cortisone - increases activity of - glucocorticoid receptor (human); - glucocorticoid receptor (human) - increases activity of - annexin A1 (human); - glucocorticoid receptor (human) - decreases activity of - prostaglandin G/H synthase - 1 (human); glucocorticoid receptor (human) - decreases activity of - prostaglandin - G/H synthase 2 (human); annexin A1 (human) - decreases activity of - cytosolic - phospholipase A2 (human); prostaglandin G/H synthase 1 (human) - positively regulates - - prostaglandin biosynthetic process; prostaglandin G/H synthase 2 (human) - positively - regulates - prostaglandin biosynthetic process; cytosolic phospholipase A2 (human) - - positively regulates - leukotriene biosynthetic process; cytosolic phospholipase - A2 (human) - positively regulates - prostaglandin biosynthetic process; leukotriene - biosynthetic process - positively correlated with - inflammatory response; prostaglandin - biosynthetic process - positively correlated with - inflammatory response; inflammatory - response - positively correlated with - HP:0001908; HP:0001908 - manifestation - of - Anemia, Diamond-Blackfan' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Cortisone acetate binds to the cytosolic glucocorticoid receptor. After binding - the receptor the newly formed receptor-ligand complex translocates itself into - the cell nucleus, where it binds to many glucocorticoid response elements (GRE) - in the promoter region of the target genes. The DNA bound receptor then interacts - with basic transcription factors, causing the increase in expression of specific - target genes. The anti-inflammatory actions of corticosteroids are thought to - involve lipocortins, phospholipase A2 inhibitory proteins which, through inhibition - arachidonic acid, control the biosynthesis of prostaglandins and leukotrienes. - Specifically glucocorticoids induce lipocortin-1 (annexin-1) synthesis, which - then binds to cell membranes preventing the phospholipase A2 from coming into - contact with its substrate arachidonic acid. This leads to diminished eicosanoid - production. The cyclooxygenase (both COX-1 and COX-2) expression is also suppressed, - potentiating the effect. In other words, the two main products in inflammation - Prostaglandins and Leukotrienes are inhibited by the action of Glucocorticoids. - Glucocorticoids also stimulate the lipocortin-1 escaping to the extracellular - space, where it binds to the leukocyte membrane receptors and inhibits various - inflammatory events: epithelial adhesion, emigration, chemotaxis, phagocytosis, - respiratory burst and the release of various inflammatory mediators (lysosomal - enzymes, cytokines, tissue plasminogen activator, chemokines etc.) from neutrophils, - macrophages and mastocytes. Additionally the immune system is suppressed by corticosteroids - due to a decrease in the function of the lymphatic system, a reduction in immunoglobulin - and complement concentrations, the precipitation of lymphocytopenia, and interference - with antigen-antibody binding. - - - === - - - disease: Anemia, Diamond-Blackfan - - drug: Cortisone acetate - - ' -- completion: 'disease: Epilepsy, Absence - - drug: Paramethadione - - mechanism_links: paramethadione - decreases activity of - voltage-dependent T-type - calcium channel subunit alpha-1G (human); paramethadione - decreases activity - of - voltage-dependent T-type calcium channel subunit alpha-1H (human); paramethadione - - decreases activity of - voltage-dependent T-type calcium channel subunit alpha-1I - (human); voltage-dependent T-type calcium channel subunit alpha-1G (human) - positively - regulates - voltage-gated calcium channel activity; voltage-dependent T-type calcium - channel subunit alpha-1H (human) - positively regulates - voltage-gated calcium - channel activity; voltage-dependent T-type calcium channel subunit alpha-1I (human) - - positively regulates - voltage-gated calcium channel activity; voltage-gated - calcium channel activity - positively regulates - neuronal action potential; neuronal - action potential - positively regulates - neuronal signal transduction; neuronal - signal transduction - positively correlated with - Epilepsy, Absence' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Dione anticonvulsants such as paramethadione reduce T-type calcium currents in - thalamic neurons (including thalamic relay neurons). This inhibits corticothalamic - transmission and raises the threshold for repetitive activity in the thalamus. - This results in a dampening of the abnormal thalamocortical rhythmicity proposed - to underlie the 3-Hz spike-and-wave discharge seen on electroencephalogram (EEG) - during absence seizures. - - - === - - - disease: Epilepsy, Absence - - drug: Paramethadione - - ' -- completion: 'disease: Pruritus Ani - - drug: Flumethasone - - mechanism_links: Flumethasone - increases activity of - glucocorticoid receptor - (human); glucocorticoid receptor (human) - increases activity of - annexin A1 - (human); annexin A1 (human) - decreases activity of - cytosolic phospholipase - A2 (human); annexin A1 (human) - negatively regulates - prostaglandin G/H synthase - 2 (human); cytosolic phospholipase A2 (human) - increases abundance of - Prostaglandins; - prostaglandin G/H synthase 2 (human) - increases abundance of - Prostaglandins; - Prostaglandins - positively regulates - inflammatory response; inflammatory response - - has phenotype - HP:0000989; HP:0000989 - manifestation of - Pruritus Ani' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Flumethasone is a glucocorticoid receptor agonist. This complex binds to the nucleus - causing a variety of genetic activation and repressions. The antiinflammatory - actions of corticosteroids are thought to involve lipocortins, phospholipase A2 - inhibitory proteins which, through inhibition arachidonic acid, control the biosynthesis - of prostaglandins and leukotrienes. The immune system is suppressed by corticosteroids - due to a decrease in the function of the lymphatic system, a reduction in immunoglobulin - and complement concentrations, the precipitation of lymphocytopenia, and interference - with antigen-antibody binding. Flumethasone binds to plasma transcortin, and it - becomes active when it is not bound to transcortin. - - - === - - - disease: Pruritus Ani - - drug: Flumethasone - - ' -- completion: 'disease: Pneumonia, Bacterial - - drug: Gemifloxacin - - mechanism_links: MESH:D000077735 - decreases activity of - DNA topoisomerase 4 - subunit A (Streptococcus pneumoniae TIGR4); DNA topoisomerase 4 subunit A (Streptococcus - pneumoniae TIGR4) - participates in - DNA replication; DNA replication - occurs - in - Streptococcus pneumoniae; Streptococcus pneumoniae - causes - Pneumonia, - Bacterial' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - The bactericidal action of gemifloxacin results from inhibition of the enzymes - topoisomerase II (DNA gyrase) and topoisomerase IV, which are required for bacterial - DNA replication, transcription, repair, and recombination. - - - === - - - disease: Pneumonia, Bacterial - - drug: Gemifloxacin - - ' -- completion: 'disease: Escherichia coli Infections - - drug: Tobramycin - - mechanism_links: Tobramycin - negatively regulates - RNA, Ribosomal, 16S; Tobramycin - - negatively regulates - RNA, Ribosomal, 23S; RNA, Ribosomal, 16S - located in - - ribosome; RNA, Ribosomal, 23S - located in - ribosome; ribosome - positively - regulates - translation; translation - occurs in - Escherichia coli; Escherichia - coli - causes - Escherichia coli Infections' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Tobramycin binds irreversibly to one of two aminoglycoside binding sites on the - 30 S ribosomal subunit, inhibiting bacterial protein synthesis. Tobramycin may - also destabilize bacterial memebrane by binding to 16 S 16 S r-RNA. An active - transport mechanism for aminoglycoside uptake is necessary in the bacteria in - order to attain a significant intracellular concentration of tobramycin. - - - === - - - disease: Escherichia coli Infections - - drug: Tobramycin - - ' -- completion: 'disease: Epilepsy - - drug: Felbamate - - mechanism_links: felbamate - decreases activity of - glutamate receptor ionotropic, - NMDA 2B (human); felbamate - decreases activity of - glutamate receptor ionotropic, - NMDA 2A (human); glutamate receptor ionotropic, NMDA 2B (human) - positively correlated - with - HP:0001250; glutamate receptor ionotropic, NMDA 2A (human) - positively - correlated with - HP:0001250; HP:0001250 - manifestation of - Epilepsy' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - The mechanism by which felbamate exerts its anticonvulsant activity is unknown, - but in animal test systems designed to detect anticonvulsant activity, felbamate - has properties in common with other marketed anticonvulsants. <i>In vitro</i> - receptor binding studies suggest that felbamate may be an antagonist at the strychnine-insensitive - glycine-recognition site of the N-methyl-D-aspartate (NMDA) receptor-ionophore - complex. Antagonism of the NMDA receptor glycine binding site may block the effects - of the excitatory amino acids and suppress seizure activity. Animal studies indicate - that felbamate may increase the seizure threshold and may decrease seizure spread. - It is also indicated that felbamate has weak inhibitory effects on GABA-receptor - binding, benzodiazepine receptor binding. - - - === - - - disease: Epilepsy - - drug: Felbamate - - ' -- completion: 'disease: Angioedema - - drug: Triamcinolone - - mechanism_links: Triamcinolone - increases activity of - glucocorticoid receptor - (human); glucocorticoid receptor (human) - increases activity of - annexin A1 - (human); glucocorticoid receptor (human) - decreases activity of - prostaglandin - G/H synthase 1 (human); glucocorticoid receptor (human) - decreases activity of - - prostaglandin G/H synthase 2 (human); annexin A1 (human) - decreases activity - of - cytosolic phospholipase A2 (human); prostaglandin G/H synthase 1 (human) - - positively regulates - prostaglandin biosynthetic process; prostaglandin G/H - synthase 2 (human) - positively regulates - prostaglandin biosynthetic process; - cytosolic phospholipase A2 (human) - positively regulates - leukotriene biosynthetic - process; cytosolic phospholipase A2 (human) - positively regulates - prostaglandin - biosynthetic process; leukotriene biosynthetic process - positively correlated - with - inflammatory response; prostaglandin biosynthetic process - positively - correlated with - inflammatory response; inflammatory response - located in - - dermis; dermis - location of - Angioedema' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Corticosteroids like triamcinolone inhibit phospholipase A2 on cell membranes, - preventing the breakdown of lysosomal membranes of leukocytes, which in turn prevent - the formation of arachidonic acid, which decrease expression of cyclooxygenase - and lipoxygenase, inhibiting synthesis of prostaglandins and leukotrienes.[A184463] - Anti-inflammatory activity occurs via reversal of vascular dilation and reducing - permeability, which prevents macrophage and leukocyte migration.[A184463] Triamcinolone - also inhibits nuclear factor kappa-B, which decreases the production of pro-inflammatory - signals such as interleukin-6, interleukin-8, and monocyte chemoattractant protein-1.[A184463] - - - === - - - disease: Angioedema - - drug: Triamcinolone - - ' -- completion: 'disease: Rhinitis, Vasomotor - - drug: Phenindamine - - mechanism_links: phenindamine - decreases activity of - histamine H1 receptor - (human); histamine H1 receptor (human) - positively correlated with - Histamine; - Histamine - causes - hypersensitivity; hypersensitivity - correlated with - Rhinitis, - Vasomotor' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Antihistamines such as phenindamine appear to compete with histamine for histamine - H1- receptor sites on effector cells. The antihistamines antagonize those pharmacological - effects of histamine which are mediated through activation of H1- receptor sites - and thereby reduce the intensity of allergic reactions and tissue injury response - involving histamine release. - - - === - - - disease: Rhinitis, Vasomotor - - drug: Phenindamine - - ' -- completion: 'disease: Intraabdominal Infections - - drug: Amphotericin B - - mechanism_links: Amphotericin B - negatively regulates - Ergosterol; Ergosterol - - positively regulates - fungal-type cell wall; fungal-type cell wall - in taxon - - Candida albicans; Candida albicans - causes - Intraabdominal Infections' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Amphotericin B is fungistatic or fungicidal depending on the concentration obtained - in body fluids and the susceptibility of the fungus. The drug acts by binding - to sterols (ergosterol) in the cell membrane of susceptible fungi. This creates - a transmembrane channel, and the resultant change in membrane permeability allowing - leakage of intracellular components. Ergosterol, the principal sterol in the fungal - cytoplasmic membrane, is the target site of action of amphotericin B and the azoles. - Amphotericin B, a polyene, binds irreversibly to ergosterol, resulting in disruption - of membrane integrity and ultimately cell death. - - - === - - - disease: Intraabdominal Infections - - drug: Amphotericin B - - ' -- completion: 'disease: Escherichia coli Infections - - drug: Ampicillin - - mechanism_links: Ampicillin - negatively regulates - Pfam:PF00905; Pfam:PF00905 - - positively regulates - peptidoglycan biosynthetic process; peptidoglycan biosynthetic - process - positively correlated with - peptidoglycan-based cell wall biogenesis; - peptidoglycan-based cell wall biogenesis - in taxon - Escherichia coli; Escherichia - coli - causes - Escherichia coli Infections' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - By binding to specific penicillin-binding proteins (PBPs) located inside the bacterial - cell wall, Ampicillin inhibits the third and last stage of bacterial cell wall - synthesis. Cell lysis is then mediated by bacterial cell wall autolytic enzymes - such as autolysins; it is possible that Ampicillin interferes with an autolysin - inhibitor. - - - === - - - disease: Escherichia coli Infections - - drug: Ampicillin - - ' -- completion: 'disease: Fever - - drug: Salicylic acid - - mechanism_links: Salicylic Acid - decreases activity of - prostaglandin G/H synthase - 1 (human); Salicylic Acid - decreases activity of - prostaglandin G/H synthase - 2 (human); prostaglandin G/H synthase 1 (human) - positively regulates - prostaglandin - biosynthetic process; prostaglandin G/H synthase 2 (human) - positively regulates - - prostaglandin biosynthetic process; prostaglandin biosynthetic process - positively - correlated with - inflammatory response; inflammatory response - positively correlated - with - Fever' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Salicylic acid directly irreversibly inhibits COX-1 and COX-2 to decrease conversion - of arachidonic acid to precursors of prostaglandins and thromboxanes. Salicylate''s - use in rheumatic diseases is due to it''s analgesic and anti-inflammatory activity. - Salicylic acid is a key ingredient in many skin-care products for the treatment - of acne, psoriasis, calluses, corns, keratosis pilaris, and warts. Salicylic acid - allows cells of the epidermis to more readily slough off. Because of its effect - on skin cells, salicylic acid is used in several shampoos used to treat dandruff. - Salicylic acid is also used as an active ingredient in gels which remove verrucas - (plantar warts). Salicylic acid competitively inhibits oxidation of uridine-5-diphosphoglucose - (UDPG) with nicotinamide adenosine dinucleotide (NAD) and noncompetitively with - UDPG. It also competitively inhibits the transferring of the glucuronyl group - of uridine-5-phosphoglucuronic acid (UDPGA) to a phenolic acceptor. Inhibition - of mucopoly saccharide synthesis is likely responsible for the slowing of wound - healing with salicylates. - - - === - - - disease: Fever - - drug: Salicylic acid - - ' -- completion: 'disease: Anthrax - - drug: Fusidic acid - - mechanism_links: Fusidic Acid - decreases activity of - PR:Q81VT3; PR:Q81VT3 - - positively regulates - translation; translation - occurs in - Bacillus anthracis; - Bacillus anthracis - causes - Anthrax' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Fusidic acid works by interfering with bacterial protein synthesis, specifically - by preventing the translocation of the elongation factor G (EF-G) from the ribosome. - It also can inhibit chloramphenicol acetyltransferase enzymes. - - - === - - - disease: Anthrax - - drug: Fusidic acid - - ' -- completion: 'disease: Schizophrenia - - drug: Perospirone - - mechanism_links: perospirone - increases activity of - 5-hydroxytryptamine receptor - 1A (human); perospirone - decreases activity of - D(2) dopamine receptor (human); - perospirone - decreases activity of - 5-hydroxytryptamine receptor 2A (human); - 5-hydroxytryptamine receptor 1A (human) - negatively correlated with - HP:0000739; - 5-hydroxytryptamine receptor 2A (human) - positively regulates - dopamine secretion; - 5-hydroxytryptamine receptor 2A (human) - positively regulates - glutamate secretion; - glutamate secretion - positively correlated with - dopamine neurotransmitter receptor - activity; dopamine neurotransmitter receptor activity - positively correlated - with - HP:0000709; D(2) dopamine receptor (human) - positively regulates - dopamine - secretion; dopamine secretion - increases abundance of - dopamine; dopamine - - located in - medial forebrain bundle; medial forebrain bundle - correlated with - - HP:0000709; HP:0000709 - positively correlated with - Schizophrenia; dopamine - - located in - dorsolateral prefrontal cortex; dorsolateral prefrontal cortex - - correlated with - HP:0100543; dorsolateral prefrontal cortex - correlated with - - HP:0030213; dorsolateral prefrontal cortex - correlated with - HP:0012154; dorsolateral - prefrontal cortex - correlated with - HP:0002465; dorsolateral prefrontal cortex - - correlated with - HP:0000741; HP:0100543 - manifestation of - Schizophrenia; - HP:0030213 - manifestation of - Schizophrenia; HP:0012154 - manifestation of - - Schizophrenia; HP:0002465 - manifestation of - Schizophrenia; HP:0000741 - manifestation - of - Schizophrenia; HP:0000739 - manifestation of - Schizophrenia' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Antagonism at D2 receptors is believed to relieve the positive symptoms of schizophrenia - such as delusions, hallucinations, and thought disorders. Perospirone targets - the mesolimbic patway to reverse the overactivity of the dopaminergic signalling - via D2 receptors [T28]. 5-HT2A antagonism is thought to allevaite the negative - symptoms and cognitive impairments of schizophrenia. These receptors are Gi/Go - coupled receptors that lead to decreased neurotransmitter release and neuronal - inhibition when activated, thus play a role in dopamine release regulation. Perospirone - targets these receptors in the nigrostriatal pathway to reduce dopamine release - and function. In contrast, 5-HT2A receptor antagonism may improve the negative - symptoms by enhancing dopamine and glutamate release in the mesocortical pathway - [T28]. 5-HT1A receptor activation further inhibits the release of 5-HT into the - synaptic cleft. - - - === - - - disease: Schizophrenia - - drug: Perospirone - - ' -- completion: 'disease: Lymphoma, T-Cell, Cutaneous - - drug: Fluocinonide - - mechanism_links: Fluocinonide - increases activity of - glucocorticoid receptor - (human); glucocorticoid receptor (human) - increases activity of - annexin A1 - (human); annexin A1 (human) - decreases activity of - cytosolic phospholipase - A2 (human); annexin A1 (human) - decreases activity of - prostaglandin G/H synthase - 2 (human); cytosolic phospholipase A2 (human) - increases abundance of - Prostaglandins; - prostaglandin G/H synthase 2 (human) - increases abundance of - Prostaglandins; - Prostaglandins - positively regulates - inflammatory response; inflammatory response - - has phenotype - HP:0000989; inflammatory response - has phenotype - HP:0000988; - HP:0000989 - manifestation of - Lymphoma, T-Cell, Cutaneous; HP:0000988 - manifestation - of - Lymphoma, T-Cell, Cutaneous' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Fluocinonide is a potent glucocorticoid steroid used topically as anti-inflammatory - agent for the treatment of skin disorders such as eczema. Fluocinonide binds to - the cytosolic glucocorticoid receptor. After binding the receptor the newly formed - receptor-ligand complex translocates itself into the cell nucleus, where it binds - to many glucocorticoid response elements (GRE) in the promoter region of the target - genes. The DNA bound receptor then interacts with basic transcription factors, - causing the increase in expression of specific target genes. The anti-inflammatory - actions of corticosteroids are thought to involve lipocortins, phospholipase A2 - inhibitory proteins which, through inhibition arachidonic acid, control the biosynthesis - of prostaglandins and leukotrienes. Specifically glucocorticoids induce lipocortin-1 - (annexin-1) synthesis, which then binds to cell membranes preventing the phospholipase - A2 from coming into contact with its substrate arachidonic acid. This leads to - diminished eicosanoid production. Cyclooxygenase (both COX-1 and COX-2) expression - is also suppressed, potentiating the effect. In another words, the two main products - in inflammation Prostaglandins and Leukotrienes are inhibited by the action of - Glucocorticoids. Glucocorticoids also stimulate the lipocortin-1 escaping to the - extracellular space, where it binds to the leukocyte membrane receptors and inhibits - various inflammatory events: epithelial adhesion, emigration, chemotaxis, phagocytosis, - respiratory burst and the release of various inflammatory mediators (lysosomal - enzymes, cytokines, tissue plasminogen activator, chemokines etc.) from neutrophils, - macrophages and mastocytes. Additionally the immune system is suppressed by corticosteroids - due to a decrease in the function of the lymphatic system, a reduction in immunoglobulin - and complement concentrations, the precipitation of lymphocytopenia, and interference - with antigen-antibody binding. Like other glucocorticoid agents Fluocinolone - acetonide acts as a physiological antagonist to insulin by decreasing glycogenesis - (formation of glycogen). It also promotes the breakdown of lipids (lipolysis), - and proteins, leading to the mobilization of extrahepatic amino acids and ketone - bodies. This leads to increased circulating glucose concentrations (in the blood). - There is also decreased glycogen formation in the liver. - - - === - - - disease: Lymphoma, T-Cell, Cutaneous - - drug: Fluocinonide - - ' -- completion: 'disease: Rhinoscleroma - - drug: Ceftriaxone - - mechanism_links: Ceftriaxone - decreases activity of - InterPro:IPR017790; InterPro:IPR017790 - - participates in - peptidoglycan biosynthetic process; peptidoglycan biosynthetic - process - positively regulates - peptidoglycan-based cell wall biogenesis; peptidoglycan-based - cell wall biogenesis - occurs in - NCBITaxon:39831; NCBITaxon:39831 - causes - - Rhinoscleroma' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Ceftriaxone works by inhibiting the mucopeptide synthesis in the bacterial cell - wall.[T324,L15082] The beta-lactam moiety of ceftriaxone binds to carboxypeptidases, - endopeptidases, and transpeptidases in the bacterial cytoplasmic membrane. These - enzymes are involved in cell-wall synthesis and cell division. Binding of ceftriaxone - to these enzymes causes the enzyme to lose activity; therefore, the bacteria produce - defective cell walls, causing cell death. - - - === - - - disease: Rhinoscleroma - - drug: Ceftriaxone - - ' -- completion: 'disease: Lymphoma, Large B-Cell, Diffuse - - drug: Vincristine - - mechanism_links: Vincristine - decreases activity of - tubulin beta chain (human); - tubulin beta chain (human) - part of - microtubule cytoskeleton organization involved - in mitosis; microtubule cytoskeleton organization involved in mitosis - positively - regulates - mitotic nuclear division; mitotic nuclear division - positively regulates - - cell population proliferation; cell population proliferation - positively correlated - with - Lymphoma, Large B-Cell, Diffuse' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - The antitumor activity of Vincristine is thought to be due primarily to inhibition - of mitosis at metaphase through its interaction with tubulin. Like other vinca - alkaloids, Vincristine may also interfere with: 1) amino acid, cyclic AMP, and - glutathione metabolism, 2) calmodulin-dependent Ca<sup>2+</sup>-transport - ATPase activity, 3) cellular respiration, and 4) nucleic acid and lipid biosynthesis. - - - === - - - disease: Lymphoma, Large B-Cell, Diffuse - - drug: Vincristine - - ' -- completion: 'disease: Histoplasmosis - - drug: Amphotericin B - - mechanism_links: Amphotericin B - negatively regulates - Ergosterol; Ergosterol - - positively regulates - fungal-type cell wall; fungal-type cell wall - in taxon - - NCBITaxon:5036; NCBITaxon:5036 - causes - Histoplasmosis' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Amphotericin B is fungistatic or fungicidal depending on the concentration obtained - in body fluids and the susceptibility of the fungus. The drug acts by binding - to sterols (ergosterol) in the cell membrane of susceptible fungi. This creates - a transmembrane channel, and the resultant change in membrane permeability allowing - leakage of intracellular components. Ergosterol, the principal sterol in the fungal - cytoplasmic membrane, is the target site of action of amphotericin B and the azoles. - Amphotericin B, a polyene, binds irreversibly to ergosterol, resulting in disruption - of membrane integrity and ultimately cell death. - - - === - - - disease: Histoplasmosis - - drug: Amphotericin B - - ' -- completion: 'disease: Lymphogranuloma Venereum - - drug: Doxycycline - - mechanism_links: Doxycycline - negatively regulates - RNA, Ribosomal, 16S; RNA, - Ribosomal, 16S - located in - small ribosomal subunit; small ribosomal subunit - - participates in - translation; translation - occurs in - Chlamydia trachomatis; - Chlamydia trachomatis - causes - Lymphogranuloma Venereum' - prompt: "From the text below, extract the following entities in the following format:\n\ - \ndisease: \ndrug: \nmechanism_links: \n\ - \n\nText:\nIn bacterial replication, an interaction that is important for translation\ - \ initiation of proteins occurs at the 3\u2032 end of the 16S rRNA, found on the\ - \ ribosome on the 30S subunit [A174046], [A19429], [A174070]. The 30S subunit\ - \ is the smaller subunit of the ribosome of prokaryotes, including bacteria[F3073].\ - \ Tetracyclines such as doxycycline are thought to inhibit translation by binding\ - \ to the 16S rRNA portion of the ribosome [A174040], preventing binding of tRNA\ - \ to the RNA-30S bacterial ribosomal subunit, which is necessary for the delivery\ - \ of amino acids for protein synthesis. As a result of the above actions, the\ - \ initiation of protein synthesis by polyribosome formation is blocked. This stops\ - \ the replication of bacteria and produces a bacteriostatic effect [F3052].\n\ - \n===\n\ndisease: Lymphogranuloma Venereum\ndrug: Doxycycline\n" -- completion: 'disease: Dyspepsia - - drug: Ranitidine - - mechanism_links: Ranitidine - decreases activity of - histamine H2 receptor (human); - histamine H2 receptor (human) - positively regulates - gastric acid secretion; - gastric acid secretion - increases abundance of - Gastric Acid; Gastric Acid - - contributes to - Heartburn; Heartburn - manifestation of - Dyspepsia' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - After a meal, the hormone gastrin, produced by cells in the lining of the stomach, - stimulates the release of histamine, which then binds to histamine H2 receptors, - leading to the secretion of gastric acid. Ranitidine reduces the secretion of - gastric acid by reversible binding to histamine (H2) receptors, which are found - on gastric parietal cells. This process leads to the inhibition of histamine binding - to this receptor, causing the reduction of gastric acid secretion. The relief - of gastric-acid related symptoms can occur as soon as 60 minutes after administration - of a single dose, and the effects can last from 4-10 hours, providing fast and - effective symptomatic relief.[A176774,T533,L10818] - - - === - - - disease: Dyspepsia - - drug: Ranitidine - - ' -- completion: 'disease: Rhinitis, Allergic, Seasonal - - drug: Levocetirizine - - mechanism_links: levocetirizine - decreases activity of - histamine H1 receptor - (human); histamine H1 receptor (human) - positively regulates - histamine receptor - activity; histamine receptor activity - participates in - cellular response to - histamine; cellular response to histamine - positively correlated with - inflammatory - response; inflammatory response - has phenotype - HP:0031417; HP:0031417 - manifestation - of - Rhinitis, Allergic, Seasonal' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Levocetirizine selectively inhibits histamine H<sub>1</sub> receptors.[L7694] - This action prevents histamine from activating this receptor and causing effects - like smooth muscle contraction, increased permeability of vascular endothelium, - histidine uptake in basophils, stimulation of cough receptors, and stimulation - of flare responses in the nervous system.[A181790] - - - === - - - disease: Rhinitis, Allergic, Seasonal - - drug: Levocetirizine - - ' -- completion: 'disease: Enterobacteriaceae Infections - - drug: Ceftizoxime - - mechanism_links: Ceftizoxime - decreases activity of - InterPro:IPR001460; InterPro:IPR001460 - - participates in - peptidoglycan biosynthetic process; peptidoglycan biosynthetic - process - positively regulates - peptidoglycan-based cell wall biogenesis; peptidoglycan-based - cell wall biogenesis - occurs in - Enterobacteriaceae; Enterobacteriaceae - causes - - Enterobacteriaceae Infections' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Ceftizoxime is an aminothiazolyl cephalosporin with an extended spectrum of activity - against many gram-negative, nosocomially acquired pathogens. It has excellent - beta-lactamase stability, with good in vitro activity against Haemophilus influenzae, - Neisseria gonorrhoeae and Klebsiella pneumoniae. Ceftizoxime, like the penicillins, - is a beta-lactam antibiotic. By binding to specific penicillin-binding proteins - (PBPs) located inside the bacterial cell wall, it inhibits the third and last - stage of bacterial cell wall synthesis. Cell lysis is then mediated by bacterial - cell wall autolytic enzymes such as autolysins; it is possible that ceftizoxime - interferes with an autolysin inhibitor. - - - === - - - disease: Enterobacteriaceae Infections - - drug: Ceftizoxime - - ' -- completion: 'disease: Lupus Erythematosus, Discoid - - drug: Alclometasone - - mechanism_links: alclometasone dipropionate - positively regulates - glucocorticoid - receptor (human); alclometasone dipropionate - negatively correlated with - InterPro:SSF50353; - alclometasone dipropionate - negatively correlated with - histamine; InterPro:SSF50353 - - positively correlated with - inflammatory response; histamine - positively correlated - with - inflammatory response; glucocorticoid receptor (human) - increases abundance - of - InterPro:IPR001464; InterPro:IPR001464 - negatively regulates - InterPro:IPR001211; - InterPro:IPR001211 - positively correlated with - leukotriene; leukotriene - positively - correlated with - inflammatory response; inflammatory response - positively correlated - with - HP:0000969; inflammatory response - positively correlated with - HP:0010783; - inflammatory response - positively correlated with - HP:0040189; inflammatory - response - positively correlated with - HP:0032152; inflammatory response - positively - correlated with - HP:0004334; HP:0000969 - manifestation of - Lupus Erythematosus, - Discoid; HP:0010783 - manifestation of - Lupus Erythematosus, Discoid; HP:0040189 - - manifestation of - Lupus Erythematosus, Discoid; HP:0032152 - manifestation - of - Lupus Erythematosus, Discoid; HP:0004334 - manifestation of - Lupus Erythematosus, - Discoid' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - The mechanism of the anti-inflammatory activity of the topical steroids, in general, - is unclear. However, corticosteroids are thought to act by the induction of phospholipase - A<sub>2</sub> inhibitory proteins, collectively called lipocortins. - It is postulated that these proteins control the biosynthesis of potent mediators - of inflammation such as prostaglandins and leukotrienes by inhibiting the release - of their common precursor, arachidonic acid. Arachidonic acid is released from - membrane phospholipids by phospholipase A<sub>2</sub>. Alclometasone - initially binds the corticosteroid receptor. This complex migrates to the nucleus - where it binds to different glucocorticoid response elements on the DNA. This - in turn enhances and represses various genes, especially those involved in inflammatory - pathways. - - - === - - - disease: Lupus Erythematosus, Discoid - - drug: Alclometasone - - ' -- completion: 'disease: Common Cold - - drug: Pseudoephedrine - - mechanism_links: Pseudoephedrine - increases activity of - alpha-1A adrenergic - receptor (human); Pseudoephedrine - increases activity of - beta-2 adrenergic - receptor (human); beta-2 adrenergic receptor (human) - negatively correlated with - - HP:4000007; HP:4000007 - positively correlated with - Common Cold; alpha-1A - adrenergic receptor (human) - positively regulates - vasoconstriction; vasoconstriction - - negatively correlated with - mucus secretion; mucus secretion - positively correlated - with - Common Cold' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Pseudoephedrine acts mainly as an agonist of alpha adrenergic receptors[A189381] - and less strongly as an agonist of beta adrenergic receptors.[A10896] This agonism - of adrenergic receptors produces vasoconstriction which is used as a decongestant[A188823,L11031,L11037,L11040,L11046,L11052,L11058,L11061] - and as a treatment of priapism.[A189384] Pseudoephedrine is also an inhibitor - of norepinephrine, dopamine, and serotonin transporters.[A17168,A17169] The sympathomimetic - effects of pseudoephedrine include an increase in mean arterial pressure, heart - rate, and chronotropic response of the right atria.[A17197] Pseudoephedrine is - also a partial agonist of the anococcygeal muscle.[A17197] Pseudoephedrine also - inhibits NF-kappa-B, NFAT, and AP-1.[A18244] - - - === - - - disease: Common Cold - - drug: Pseudoephedrine - - ' -- completion: 'disease: Multiple Myeloma - - drug: Pomalidomide - - mechanism_links: pomalidomide - positively regulates - natural killer cell; natural - killer cell - positively regulates - natural killer cell mediated immune response - to tumor cell; natural killer cell mediated immune response to tumor cell - negatively - correlated with - Multiple Myeloma; pomalidomide - decreases activity of - prostaglandin - G/H synthase 2 (human); prostaglandin G/H synthase 2 (human) - increases abundance - of - Prostaglandins; Prostaglandins - positively regulates - inflammatory response; - inflammatory response - positively correlated with - Multiple Myeloma; pomalidomide - - decreases activity of - tumor necrosis factor (human); tumor necrosis factor - (human) - participates in - REACT:R-HSA-75893; REACT:R-HSA-75893 - positively - regulates - inflammatory response; pomalidomide - negatively regulates - osteoclast; - osteoclast - positively regulates - bone resorption; bone resorption - occurs - in - Multiple Myeloma; pomalidomide - negatively regulates - vascular endothelial - growth factor production; vascular endothelial growth factor production - positively - regulates - angiogenesis; pomalidomide - negatively regulates - InterPro:IPR001321; - InterPro:IPR001321 - positively regulates - angiogenesis; angiogenesis - positively - correlated with - Multiple Myeloma' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Promalidomide is an immunomodulatory agent with antineoplastic activity. It is - shown to inhibit the proliferation and induce apoptosis of various tumour cells. - Furthermore, promalidomide enhances T cell and natural killer (NK) cell-mediated - immunity and inhibited the production of pro-inflammatory cytokines, like TNF-alpha - or IL-6, by monocytes. The primary target of promalidomide is thought to be the - protein cereblon. It binds to this target and inhibits ubiquitin ligase activity. - It is also a transcriptional inhibitor of COX2. - - - === - - - disease: Multiple Myeloma - - drug: Pomalidomide - - ' -- completion: 'disease: Psittacosis - - drug: Fusidic acid - - mechanism_links: Fusidic Acid - decreases activity of - PR:S7JCG1; PR:S7JCG1 - - positively regulates - translation; translation - occurs in - Chlamydia psittaci; - Chlamydia psittaci - causes - Psittacosis' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Fusidic acid works by interfering with bacterial protein synthesis, specifically - by preventing the translocation of the elongation factor G (EF-G) from the ribosome. - It also can inhibit chloramphenicol acetyltransferase enzymes. - - - === - - - disease: Psittacosis - - drug: Fusidic acid - - ' -- completion: 'disease: Cytomegalovirus Retinitis - - drug: Foscarnet - - mechanism_links: Foscarnet - decreases activity of - PR:P08546; PR:P08546 - participates - in - viral DNA genome replication; viral DNA genome replication - occurs in - - NCBITaxon:10358; NCBITaxon:10358 - causes - Cytomegalovirus Retinitis' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Foscarnet exerts its antiviral activity by a selective inhibition at the pyrophosphate - binding site on virus-specific DNA polymerases at concentrations that do not affect - cellular DNA polymerases. - - - === - - - disease: Cytomegalovirus Retinitis - - drug: Foscarnet - - ' -- completion: 'disease: Tinea Versicolor - - drug: Zinc oxide - - mechanism_links: Zinc Oxide - decreases abundance of - Fungi; Zinc Oxide - negatively - regulates - inflammatory response; Fungi - causes - Tinea Versicolor; inflammatory - response - occurs in - Tinea Versicolor' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - It acts by providing a physical barrier to prevent skin irritation and help heal - damaged skin. - - - === - - - disease: Tinea Versicolor - - drug: Zinc oxide - - ' -- completion: 'disease: Asthma - - drug: Pemirolast - - mechanism_links: pemirolast - decreases activity of - histamine H1 receptor (human); - pemirolast - negatively regulates - mast cell degranulation; mast cell degranulation - - increases abundance of - Histamine; Histamine - causes - cellular response to - histamine; histamine H1 receptor (human) - participates in - histamine receptor - activity; histamine receptor activity - participates in - cellular response to - histamine; cellular response to histamine - positively correlated with - inflammatory - response; inflammatory response - causes - Asthma' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Pemirolast binds to the histamine H<sub>1</sub> receptor. This blocks - the action of endogenous histamine, which subsequently leads to temporary relief - of the negative symptoms brought on by histamine. Pemirolast has also been observed - to inhibit antigen-stimulated calcium ion influx into mast cells through the blockage - of calcium channels. Pemirolast inhibits the chemotaxis of eosinophils into ocular - tissue, and prevents inflammatory mediator release from human eosinophils. - - - === - - - disease: Asthma - - drug: Pemirolast - - ' -- completion: 'disease: Tinea Pedis - - drug: Clotrimazole - - mechanism_links: Clotrimazole - disrupts - ergosterol; ergosterol - located in - - yeast-form cell wall; yeast-form cell wall - in taxon - Candida albicans SC5314; - Candida albicans SC5314 - causes - Tinea Pedis' - prompt: "From the text below, extract the following entities in the following format:\n\ - \ndisease: \ndrug: \nmechanism_links: \n\ - \n\nText:\nClotrimazole acts primarily by damaging the permeability barrier in\ - \ the cell membrane of fungi. Clotrimazole causes inhibition of ergosterol biosynthesis,\ - \ an essential constituent of fungal cell membranes. If ergosterol synthesis is\ - \ either completely or partially inhibited, the cell is no longer able to construct\ - \ an intact and functional cell membrane [F3088],[F3100]. Because ergosterol directly\ - \ promotes the growth of fungal cells in a hormone\u2010like fashion, rapid onset\ - \ of the above events leads to dose-dependent inhibition of fungal growth [A174094].\ - \ Though decreased ergosterol, due to the inhibition of lanosterol 14-demethylase\ - \ (also known as _CYP51_) [A174094] is accepted to be primarily responsible for\ - \ the antimycotic properties of clotrimazole, this drug also shows other pharmacological\ - \ effects. These include the inhibition of sarcoplasmic reticulum Ca2+\u2010ATPase,\ - \ depletion of intracellular calcium, and blocking of calcium\u2010dependent\ - \ potassium channels and voltage\u2010dependent calcium channels [A174094]. The\ - \ action of clotrimazole on these targets accounts for other effects of this drug\ - \ that are separate from its antimycotic activities [A174094].\n\n===\n\ndisease:\ - \ Tinea Pedis\ndrug: Clotrimazole\n" -- completion: 'disease: Cluster Headache - - drug: Dihydroergotamine - - mechanism_links: Dihydroergotamine - increases activity of - 5-hydroxytryptamine - receptor 1D (human); Dihydroergotamine - increases activity of - 5-hydroxytryptamine - receptor 1B (human); 5-hydroxytryptamine receptor 1D (human) - positively regulates - - vasoconstriction; 5-hydroxytryptamine receptor 1B (human) - positively regulates - - vasoconstriction; 5-hydroxytryptamine receptor 1B (human) - negatively regulates - - substance P secretion, neurotransmission; 5-hydroxytryptamine receptor 1D (human) - - negatively regulates - substance P secretion, neurotransmission; vasoconstriction - - treats - Cluster Headache; substance P secretion, neurotransmission - positively - correlated with - Pain; Pain - positively correlated with - Cluster Headache' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Two theories have been proposed to explain the efficacy of 5-HT<sub>1D</sub> - receptor agonists in migraine: 1) activation of 5-HT<sub>1D</sub> - receptors located on intracranial blood vessels, including those on arterio-venous - anastomoses, leads to vasoconstriction, which correlates with the relief of migraine - headache and 2) activation of 5-HT<sub>1D</sub> receptors on sensory - nerve endings of the trigeminal system results in the inhibition of pro-inflammatory - neuropeptide release. - - - === - - - disease: Cluster Headache - - drug: Dihydroergotamine - - ' -- completion: 'disease: Atrial Fibrillation - - drug: Digoxin - - mechanism_links: Digoxin - negatively regulates - sodium/potassium-transporting - ATPase subunit alpha-1 (human); sodium/potassium-transporting ATPase subunit alpha-1 - (human) - positively regulates - sodium ion transport; sodium ion transport - - negatively correlated with - calcium ion import into cytosol; calcium ion import - into cytosol - negatively correlated with - heart contraction; heart contraction - - correlated with - Atrial Fibrillation' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Digoxin exerts hemodynamic, electrophysiologic, and neurohormonal effects on the - cardiovascular system.[A178234] It reversibly inhibits the Na-K ATPase enzyme, - leading to various beneficial effects. The Na-K ATPase enzyme functions to maintain - the intracellular environment by regulating the entry and exit of sodium, potassium, - and calcium (indirectly). Na-K ATPase is also known as the _sodium pump_[L9143]. - The inhibition of the sodium pump by digoxin increases intracellular sodium and - increases the calcium level in the myocardial cells, causing an increased contractile - force of the heart.[L9143,A178264] This improves the left ventricular ejection - fraction (EF), an important measure of cardiac function.[A178234,T613] Digoxin - also stimulates the parasympathetic nervous system via the vagus nerve[T607] leading - to sinoatrial (SA) and atrioventricular (AV) node effects, decreasing the heart - rate.[L9143,A178234] Part of the pathophysiology of heart failure includes neurohormonal - activation, leading to an increase in norepinephrine. Digoxin helps to decrease - norepinephrine levels through activation of the parasympathetic nervous system.[A178234] - - - === - - - disease: Atrial Fibrillation - - drug: Digoxin - - ' -- completion: 'disease: Scrub Typhus - - drug: Doxycycline - - mechanism_links: Doxycycline - negatively regulates - RNA, Ribosomal, 16S; RNA, - Ribosomal, 16S - located in - small ribosomal subunit; small ribosomal subunit - - participates in - translation; translation - occurs in - NCBITaxon:784; NCBITaxon:784 - - causes - Scrub Typhus' - prompt: "From the text below, extract the following entities in the following format:\n\ - \ndisease: \ndrug: \nmechanism_links: \n\ - \n\nText:\nIn bacterial replication, an interaction that is important for translation\ - \ initiation of proteins occurs at the 3\u2032 end of the 16S rRNA, found on the\ - \ ribosome on the 30S subunit [A174046], [A19429], [A174070]. The 30S subunit\ - \ is the smaller subunit of the ribosome of prokaryotes, including bacteria[F3073].\ - \ Tetracyclines such as doxycycline are thought to inhibit translation by binding\ - \ to the 16S rRNA portion of the ribosome [A174040], preventing binding of tRNA\ - \ to the RNA-30S bacterial ribosomal subunit, which is necessary for the delivery\ - \ of amino acids for protein synthesis. As a result of the above actions, the\ - \ initiation of protein synthesis by polyribosome formation is blocked. This stops\ - \ the replication of bacteria and produces a bacteriostatic effect [F3052].\n\ - \n===\n\ndisease: Scrub Typhus\ndrug: Doxycycline\n" -- completion: 'disease: Spasms, Infantile - - drug: Corticotropin - - mechanism_links: Corticotropin - positively regulates - adrenocorticotropic hormone - receptor (human); adrenocorticotropic hormone receptor (human) - decreases expression - of - CHEBI:65312; CHEBI:65312 - positively correlated with - HP:0001250; adrenocorticotropic - hormone receptor (human) - negatively correlated with - HP:0012469; HP:0001250 - - manifestation of - Spasms, Infantile; HP:0012469 - manifestation of - Spasms, - Infantile' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - As a diagnostic aid (adrenocortical function), corticotropin combines with a specific - receptor on the adrenal cell plasma membrane. In patients with normal adrenocortical - function, it stimulates the initial reaction involved in the synthesis of adrenal - steroids (including cortisol, cortisone, weak androgenic substances, and a limited - quantity of aldosterone) from cholesterol by increasing the quantity of cholesterol - within the mitochondria. Corticotropin does not significantly increase serum cortisol - concentrations in patients with primary adrenocortical insufficiency (Addison''s - disease). The mechanism of action of corticotropin in the treatment of infantile - myoclonic seizures is unknown. - - - === - - - disease: Spasms, Infantile - - drug: Corticotropin - - ' -- completion: 'disease: Hepatitis C, Chronic - - drug: Elbasvir - - mechanism_links: 2-(pyrrolidin-2-yl)-5-(2-(4-(5-(pyrrolidin-2-yl)-1H-imidazol-2-yl)phenyl)benzofuran-5-yl)-1H-imidazole - - decreases activity of - PR:Q5L478; PR:Q5L478 - negatively regulates - virion - assembly; virion assembly - in taxon - NCBITaxon:11103; NCBITaxon:11103 - causes - - Hepatitis C, Chronic' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Elbasvir is an inhibitor of the HCV non-structural protein 5A. While the precise - role of this protein is unknown, it is essential to viral replication and virion - assembly.[synthesis] Potential modes of action of NS5A inhibitors like elbasvir - include blocking signaling interactions, redistribution of NS5A from the endoplasmic - reticulum to the surface of lipid droplets, and modification of the HCV replication - complex.[A19593] Computational target-based _in silico_ research suggests that - elbasvir may carry activity at several proteins required for replication of SARS-CoV-2 - - namely RNA-dependent RNA polymerase, helicase, and papain-like proteinase - - although specific activity has yet to be affirmed by follow-up clinical studies.[A193257] - - - === - - - disease: Hepatitis C, Chronic - - drug: Elbasvir - - ' -- completion: 'disease: Hypertension - - drug: Verapamil - - mechanism_links: Verapamil - decreases activity of - InterPro:IPR005446; InterPro:IPR005446 - - positively regulates - calcium ion transport into cytosol; calcium ion transport - into cytosol - positively correlated with - vasoconstriction; vasoconstriction - - positively correlated with - HP:0033533; HP:0033533 - positively correlated - with - HP:0032263; HP:0032263 - manifestation of - Hypertension' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Verapamil inhibits L-type calcium channels by binding to a specific area of their - alpha-1 subunit,[L10478]Cav1.2, which is highly expressed on L-type calcium channels - in vascular smooth muscle and myocardial tissue where these channels are responsible - for the control of peripheral vascular resistance and heart contractility.[A175396] - Calcium influx through these channels allows for the propagation of action potentials - necessary for the contraction of muscle tissue and the heart''s electrical pacemaker - activity. Verapamil binds to these channels in a voltage- and frequency-dependent - manner, meaning affinity is increased 1) as vascular smooth muscle membrane potential - is reduced, and 2) with excessive depolarizing stimulus.[L10478] Verapamil is - known to interact with other targets, including other calcium channels,[A188490,A13984,A188502,A15331] - potassium channels,[A188496,A13985,A13983] and adrenergic receptors.[A20291,A31755] - - - === - - - disease: Hypertension - - drug: Verapamil - - ' -- completion: 'disease: Crohn Disease - - drug: Methylprednisolone - - mechanism_links: Methylprednisolone - increases activity of - glucocorticoid receptor - (human); glucocorticoid receptor (human) - increases activity of - annexin A1 - (human); glucocorticoid receptor (human) - decreases activity of - prostaglandin - G/H synthase 1 (human); glucocorticoid receptor (human) - decreases activity of - - prostaglandin G/H synthase 2 (human); annexin A1 (human) - decreases activity - of - cytosolic phospholipase A2 (human); prostaglandin G/H synthase 1 (human) - - positively regulates - prostaglandin biosynthetic process; prostaglandin G/H - synthase 2 (human) - positively regulates - prostaglandin biosynthetic process; - cytosolic phospholipase A2 (human) - positively regulates - leukotriene biosynthetic - process; cytosolic phospholipase A2 (human) - positively regulates - prostaglandin - biosynthetic process; leukotriene biosynthetic process - positively correlated - with - inflammatory response; prostaglandin biosynthetic process - positively - correlated with - inflammatory response; inflammatory response - located in - - digestive tract; digestive tract - location of - Crohn Disease' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - The short term effects of corticosteroids are decreased vasodilation and permeability - of capillaries, as well as decreased leukocyte migration to sites of inflammation.[A187463] - Corticosteroids binding to the glucocorticoid receptor mediates changes in gene - expression that lead to multiple downstream effects over hours to days.[A187463] - Lower doses of corticosteroids provide an anti-inflammatory effect, while higher - doses are immunosuppressive.[A187463] High doses of glucocorticoids for an extended - period bind to the mineralocorticoid receptor, raising sodium levels and decreasing - potassium levels.[A187463] - - - === - - - disease: Crohn Disease - - drug: Methylprednisolone - - ' -- completion: 'disease: Vaginosis, Bacterial - - drug: Secnidazole - - mechanism_links: secnidazole - positively regulates - response to oxygen radical; - response to oxygen radical - disrupts - DNA; DNA - in taxon - Bacteria; Bacteria - - causes - Vaginosis, Bacterial' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Secnidazole enters the bacterial cell as a prodrug without an antimicrobial activity. - The drug is converted to an active form via reduction of nitro groups to radical - anions by bacterial enzymes. The radical anions are thought to interfere with - bacterial DNA synthesis of susceptible isolates [FDA Label]. - - - === - - - disease: Vaginosis, Bacterial - - drug: Secnidazole - - ' -- completion: 'disease: Cryopyrin-Associated Periodic Syndromes - - drug: Anakinra - - mechanism_links: Interleukin 1 Receptor Antagonist Protein - decreases activity - of - interleukin-1 receptor type 1 (human); interleukin-1 receptor type 1 (human) - - participates in - interleukin-1 receptor activity; interleukin-1 receptor activity - - positively regulates - inflammatory response; inflammatory response - causes - - Cryopyrin-Associated Periodic Syndromes' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Anakinra binds competitively to the Interleukin-1 type I receptor (IL-1RI), thereby - inhibiting the action of elevated levels IL-1 which normally can lead to cartilage - degradation and bone resorption. - - - === - - - disease: Cryopyrin-Associated Periodic Syndromes - - drug: Anakinra - - ' -- completion: 'disease: Mucormycosis - - drug: Isavuconazonium - - mechanism_links: isavuconazole - decreases activity of - Pfam:PF00067; Pfam:PF00067 - - positively regulates - sterol 14-demethylase activity; Pfam:PF00067 - positively - regulates - ergosterol biosynthetic process; sterol 14-demethylase activity - - positively correlated with - ergosterol; ergosterol biosynthetic process - increases - abundance of - ergosterol; sterol 14-demethylase activity - negatively correlated - with - lanosterol; ergosterol biosynthetic process - decreases abundance of - - lanosterol; lanosterol - negatively correlated with - fungal-type cell wall; ergosterol - - contributes to - fungal-type cell wall; fungal-type cell wall - in taxon - NCBITaxon:4827; - NCBITaxon:4827 - causes - Mucormycosis' - prompt: "From the text below, extract the following entities in the following format:\n\ - \ndisease: \ndrug: \nmechanism_links: \n\ - \n\nText:\nAntifungals in the triazole class, such as isavuconazonium, target\ - \ and inhibit the sterol 14-\u03B1-demethylase (Erg11p) which is a key player\ - \ in the demethylation step of the ergosterol biosynthetic pathway. This inhibition\ - \ results in a halt in production of ergosterol, a molecule typically found in\ - \ the membranes of fungi such as Aspergillus, Candida, and Mucorales that plays\ - \ a role in regulation of membrane integrity, fluidity and permeability. The inhibition\ - \ of Erg11p also causes the buildup of ergosterol precursors, which are toxic\ - \ and cause cell death.\n\n===\n\ndisease: Mucormycosis\ndrug: Isavuconazonium\n" -- completion: 'disease: Schizophrenia - - drug: Chlorpromazine - - mechanism_links: Chlorpromazine - decreases activity of - D(2) dopamine receptor - (human); D(2) dopamine receptor (human) - positively correlated with - dopamine; - dopamine - correlated with - regulation of synaptic transmission, dopaminergic; - regulation of synaptic transmission, dopaminergic - located in - central nervous - system; central nervous system - prevents - HP:0008760; HP:0008760 - correlated - with - Schizophrenia' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Chlorpromazine acts as an antagonist (blocking agent) on different postsysnaptic - receptors -on dopaminergic-receptors (subtypes D1, D2, D3 and D4 - different antipsychotic - properties on productive and unproductive symptoms), on serotonergic-receptors - (5-HT1 and 5-HT2, with anxiolytic, antidepressive and antiaggressive properties - as well as an attenuation of extrapypramidal side-effects, but also leading to - weight gain, fall in blood pressure, sedation and ejaculation difficulties), on - histaminergic-receptors (H1-receptors, sedation, antiemesis, vertigo, fall in - blood pressure and weight gain), alpha1/alpha2-receptors (antisympathomimetic - properties, lowering of blood pressure, reflex tachycardia, vertigo, sedation, - hypersalivation and incontinence as well as sexual dysfunction, but may also attenuate - pseudoparkinsonism - controversial) and finally on muscarinic (cholinergic) M1/M2-receptors - (causing anticholinergic symptoms like dry mouth, blurred vision, obstipation, - difficulty/inability to urinate, sinus tachycardia, ECG-changes and loss of memory, - but the anticholinergic action may attenuate extrapyramidal side-effects). Additionally, - Chlorpromazine is a weak presynaptic inhibitor of Dopamine reuptake, which may - lead to (mild) antidepressive and antiparkinsonian effects. This action could - also account for psychomotor agitation and amplification of psychosis (very rarely - noted in clinical use). - - - === - - - disease: Schizophrenia - - drug: Chlorpromazine - - ' -- completion: 'disease: Peptic Ulcer - - drug: Potassium bicarbonate - - mechanism_links: potassium bicarbonate - negatively regulates - Gastric Acid; - Gastric Acid - positively regulates - InterPro:IPR034162; InterPro:IPR034162 - - positively correlated with - Peptic Ulcer' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - The antacid potential of potassium bicarbonate is attained by increasing the gastrointestinal - pH by neutralizing hydrochloric acid.[T144] The increase in pH results in suppression - of the action of pepsin which is the enzyme that exacerbates ulceration due to - the presence of acid.[T143] - - - === - - - disease: Peptic Ulcer - - drug: Potassium bicarbonate - - ' -- completion: 'disease: Hypoalphalipoproteinemias - - drug: Fenofibrate - - mechanism_links: Fenofibrate - has metabolite - fenofibric acid; fenofibric acid - - increases activity of - peroxisome proliferator-activated receptor alpha (human); - peroxisome proliferator-activated receptor alpha (human) - increases abundance - of - Lipoproteins, HDL; Lipoproteins, HDL - negatively correlated with - Hypoalphalipoproteinemias' - prompt: "From the text below, extract the following entities in the following format:\n\ - \ndisease: \ndrug: \nmechanism_links: \n\ - \n\nText:\nFenofibrate activates peroxisome proliferator activated receptor alpha\ - \ (PPAR\u03B1), increasing lipolysis, activating lipoprotein lipase, and reducing\ - \ apoprotein C-III.[A186002,L8588,L8591] PPAR\u03B1 is a nuclear receptor and\ - \ its activation alters lipid, glucose, and amino acid homeostasis.[A186002] Activation\ - \ of PPAR\u03B1 activates transcription of gene transcription and translation\ - \ that generates peroxisomes filled with hydrogen peroxide, reactive oxygen species,\ - \ and hydroxyl radicals that also participate in lipolysis.[A186005] This mechanism\ - \ of increased lipid metabolism is also associated with increased oxidative stress\ - \ on the liver.[A186005] In rare cases this stress can lead to cirrhosis and chronic\ - \ active hepatitis.[A186002,L8588,L8591]\n\n===\n\ndisease: Hypoalphalipoproteinemias\n\ - drug: Fenofibrate\n" -- completion: 'disease: Glaucoma, Open-Angle - - drug: Physostigmine - - mechanism_links: Physostigmine - decreases activity of - acetylcholinesterase - (human); acetylcholinesterase (human) - increases abundance of - Acetylcholine; - Acetylcholine - located in - synapse; synapse - increases activity of - InterPro:IPR002394; - InterPro:IPR002394 - treats - Glaucoma, Open-Angle' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Physostigmine inhibits acetylcholinesterase, the enzyme responsible for the breakdown - of used acetylcholine. By interfering with the metabolism of acetylcholine, physostigmine - indirectly stimulates both nicotinic and muscarinic receptors due to the consequential - increase in available acetylcholine at the synapse. - - - === - - - disease: Glaucoma, Open-Angle - - drug: Physostigmine - - ' -- completion: 'disease: Puberty, Delayed - - drug: Fluoxymesterone - - mechanism_links: Fluoxymesterone - increases activity of - androgen receptor (human); - androgen receptor (human) - positively regulates - androgen receptor signaling - pathway; androgen receptor signaling pathway - positively correlated with - development - of secondary sexual characteristics; development of secondary sexual characteristics - - negatively correlated with - Puberty, Delayed' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Fluoxymesterone is a synthetic androgenic anabolic steroid and is approximately - 5 times as potent as natural methyltestosterone. Like testosterone and other androgenic - hormones, fluoxymesterone binds to the androgen receptor. It produces retention - of nitrogen, sodium, potassium, and phosphorus; increases protein anabolism; decreases - amino acid catabolism and decreased urinary excretion of calcium. The antitumour - activity of fluoxymesterone appears related to reduction or competitive inhibition - of prolactin receptors or estrogen receptors or production. - - - === - - - disease: Puberty, Delayed - - drug: Fluoxymesterone - - ' -- completion: 'disease: Schizophrenia - - drug: Brexpiprazole - - mechanism_links: brexpiprazole - regulates - 5-hydroxytryptamine receptor 1A (human); - brexpiprazole - regulates - D(2) dopamine receptor (human); brexpiprazole - decreases - activity of - 5-hydroxytryptamine receptor 2A (human); 5-hydroxytryptamine receptor - 1A (human) - positively correlated with - Serotonin; D(2) dopamine receptor (human) - - positively correlated with - Dopamine; 5-hydroxytryptamine receptor 2A (human) - - positively correlated with - HP:0000716; Serotonin - positively correlated with - - serotonin secretion, neurotransmission; Dopamine - positively correlated with - - dopamine secretion, neurotransmission; HP:0000716 - manifestation of - Schizophrenia; - serotonin secretion, neurotransmission - disrupted by - Schizophrenia; dopamine - secretion, neurotransmission - disrupted by - Schizophrenia' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Although the mechanism of action of brexpiprazole in the treatment of MDD and - schizophrenia is unclear, the efficacy of brexpiprazole may be attributed to partial - agonist activity at serotonin 1A and dopamine D2 receptors, and antagonist activity - at serotonin 2A receptors. - - - === - - - disease: Schizophrenia - - drug: Brexpiprazole - - ' -- completion: 'disease: Pruritus - - drug: Benzyl alcohol - - mechanism_links: Benzyl Alcohol - decreases abundance of - NCBITaxon:52283; NCBITaxon:52283 - - causes - Pruritus' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Benzyl alcohol inhibits lice from closing their respiratory spiracles, allowing - the vehicle to obstruct the spiracles and causing the lice to asphyxiate. - - - === - - - disease: Pruritus - - drug: Benzyl alcohol - - ' -- completion: 'disease: Hypertension - - drug: Mecamylamine - - mechanism_links: Mecamylamine - decreases activity of - InterPro:IPR002394; InterPro:IPR002394 - - positively regulates - synaptic transmission, cholinergic; synaptic transmission, - cholinergic - positively correlated with - smooth muscle contraction; smooth muscle - contraction - positively correlated with - vasoconstriction; vasoconstriction - - positively correlated with - HP:0032263; HP:0032263 - manifestation of - Hypertension' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Mecamylamine is a ganglionic blocker which prevents stimulation of postsynaptic - receptors by acetylcholine released from presynaptic nerve endings. The hypotensive - effect of Mecamylamine is attributed to reduction in sympathetic tone, vasodilation, - and reduced cardiac output, and is primarily postural. - - - === - - - disease: Hypertension - - drug: Mecamylamine - - ' -- completion: 'disease: Puberty, Delayed - - drug: Testosterone - - mechanism_links: Testosterone - increases activity of - androgen receptor (human); - androgen receptor (human) - positively regulates - androgen receptor signaling - pathway; androgen receptor signaling pathway - positively regulates - developmental - process involved in reproduction; developmental process involved in reproduction - - negatively correlated with - Puberty, Delayed' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - The androgen receptor exists in the cytoplasm bound to the heat shock proteins - HSP90, HSP70, and other chaperones.[A187114] After binding to an androgen, the - androgen receptor dissociates from HSP90 and undergoes a conformational change - to slow the rate of dissociation from the androgen receptor.[A187114] The androgen-receptor - complex is transported into the nucleus where it binds to DNA and recruits other - transcriptional regulators to form a pre-initiation complex and eventually induce - expression of specific genes.[A187114] Antagonism of the androgen receptor is - also responsible for the development of secondary sexual characteristics including - facial and body hair, enlargement of the larynx, thickening of the vocal cords, - and changes in muscle and fat distribution.[A187111,L8983,L8935,L8938,L8986,L8989,L8992,L8995] - - - === - - - disease: Puberty, Delayed - - drug: Testosterone - - ' -- completion: 'disease: Hypertension - - drug: Metolazone - - mechanism_links: Metolazone - decreases activity of - solute carrier family 12 - member 3 (human); solute carrier family 12 member 3 (human) - participates in - - renal sodium ion absorption; renal sodium ion absorption - positively correlated - with - renal water retention; renal water retention - contributes to - HP:0011104; - HP:0011104 - contributes to - positive regulation of blood pressure; positive - regulation of blood pressure - affects risk for - Hypertension' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - The actions of metolazone result from interference with the renal tubular mechanism - of electrolyte reabsorption. Metolazone acts primarily to inhibit sodium reabsorption - at the cortical diluting site and to a lesser extent in the proximal convoluted - tubule. Sodium and chloride ions are excreted in approximately equivalent amounts. - The increased delivery of sodium to the distal tubular exchange site results in - increased potassium excretion. Metolazone does not inhibit carbonic anhydrase. - The antihypertensive mechanism of action of metolazone is not fully understood - but is presumed to be related to its saluretic and diuretic properties. - - - === - - - disease: Hypertension - - drug: Metolazone - - ' -- completion: 'disease: Tinea Capitis - - drug: Tolnaftate - - mechanism_links: Tolnaftate - decreases activity of - InterPro:IPR040125; InterPro:IPR040125 - - positively regulates - ergosterol biosynthetic process; ergosterol biosynthetic - process - increases abundance of - ergosterol; ergosterol - located in - yeast-form - cell wall; yeast-form cell wall - in taxon - NCBITaxon:5550; NCBITaxon:5550 - - causes - Tinea Capitis' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Tolnaftate is a topical fungicide. Though its exact mechanism unknown, it is believed - to prevent ergosterol biosynthesis by inhibiting squalene epoxidase. It has also - been reported to distort the hyphae and to stunt mycelial growth in susceptible - organisms. - - - === - - - disease: Tinea Capitis - - drug: Tolnaftate - - ' -- completion: 'disease: Leukemia, Myeloid, Acute - - drug: Histamine - - mechanism_links: Histamine - increases activity of - interleukin-2 (human); interleukin-2 - (human) - increases activity of - interleukin-2 receptor subunit alpha (human); - interleukin-2 (human) - increases activity of - interleukin-2 receptor subunit - beta (human); interleukin-2 (human) - increases activity of - cytokine receptor - common subunit gamma (human); interleukin-2 receptor subunit alpha (human) - positively - regulates - REACT:R-HSA-9020558; interleukin-2 receptor subunit beta (human) - - positively regulates - REACT:R-HSA-9020558; cytokine receptor common subunit gamma - (human) - positively regulates - REACT:R-HSA-9020558; REACT:R-HSA-9020558 - positively - regulates - cytotoxic T cell differentiation; REACT:R-HSA-9020558 - positively - regulates - natural killer cell activation; cytotoxic T cell differentiation - - negatively correlated with - Leukemia, Myeloid, Acute; natural killer cell activation - - negatively correlated with - Leukemia, Myeloid, Acute' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Histamine acts directly on the blood vessels to dilate arteries and capillaries; - this action is mediated by both H 1- and H 2-receptors. Capillary dilatation may - produce flushing of the face, a decrease in systemic blood pressure, and gastric - gland secretion, causing an increased secretion of gastric juice of high acidity. - Increased capillary permeability accompanies capillary dilatation, producing an - outward passage of plasma protein and fluid into the extracellular spaces, an - increase in lymph flow and protein content, and the formation of edema. In addition, - histamine has a direct stimulant action on smooth muscle, producing contraction - if H 1-receptors are activated, or mostly relaxation if H 2-receptors are activated. - Also in humans, the stimulant effect of histamine may cause contraction of the - intestinal muscle. However, little effect is noticed on the uterus, bladder, or - gallbladder. Histamine has some stimulant effect on duodenal, salivary, pancreatic, - bronchial, and lacrimal glands. Histamine also can bind to H3 and H4 receptors - which are involved in the CNS/PNS neurotransmitter release and immune system chemotaxis, - respectively. - - - === - - - disease: Leukemia, Myeloid, Acute - - drug: Histamine - - ' -- completion: 'disease: Rhinitis, Allergic, Seasonal - - drug: Cetirizine - - mechanism_links: Cetirizine - decreases activity of - histamine H1 receptor (human); - histamine H1 receptor (human) - positively regulates - histamine receptor activity; - histamine receptor activity - participates in - cellular response to histamine; - cellular response to histamine - positively correlated with - inflammatory response; - inflammatory response - has phenotype - HP:0031417; HP:0031417 - manifestation - of - Rhinitis, Allergic, Seasonal' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Cetirizine, a metabolite of _hydroxyzine_, is an antihistamine drug. Its main - effects are achieved through selective inhibition of peripheral H1 receptors. - The antihistamine activity of cetirizine has been shown in a variety of animal - and human models. _In vivo_ and _ex vivo_ animal models have shown insignificant - anticholinergic and antiserotonergic effects. In clinical studies, however, dry - mouth was found to be more frequent with cetirizine than with a placebo. In vitro - receptor binding studies have demonstrated no detectable affinity of cetirizine - for histamine receptors other than the H1 receptors. Studies with radiolabeled - cetirizine administration in the rat have demonstrated insignificant penetration - into the brain. _Ex vivo_ studies in the mouse have shown that systemically administered - cetirizine does not occupy cerebral H1 receptors significantly [FDA label]. - - - === - - - disease: Rhinitis, Allergic, Seasonal - - drug: Cetirizine - - ' -- completion: 'disease: Thyroiditis - - drug: Prednisone - - mechanism_links: Prednisone - has metabolite - Prednisolone; Prednisolone - increases - activity of - glucocorticoid receptor (human); glucocorticoid receptor (human) - - increases activity of - annexin A1 (human); glucocorticoid receptor (human) - - decreases activity of - prostaglandin G/H synthase 1 (human); glucocorticoid - receptor (human) - decreases activity of - prostaglandin G/H synthase 2 (human); - annexin A1 (human) - decreases activity of - cytosolic phospholipase A2 (human); - prostaglandin G/H synthase 1 (human) - positively regulates - prostaglandin biosynthetic - process; prostaglandin G/H synthase 2 (human) - positively regulates - prostaglandin - biosynthetic process; cytosolic phospholipase A2 (human) - positively regulates - - leukotriene biosynthetic process; cytosolic phospholipase A2 (human) - positively - regulates - prostaglandin biosynthetic process; leukotriene biosynthetic process - - positively correlated with - inflammatory response; prostaglandin biosynthetic - process - positively correlated with - inflammatory response; inflammatory response - - located in - thyroid gland; thyroid gland - location of - Thyroiditis' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Prednisone is first metabolized in the liver to its active form, prednisolone, - a glucocorticoid agonist corticosteroid.[L10502] Lower doses of corticosteroids - provide an anti-inflammatory effect, while higher doses are immunosuppressive.[A187463] - High doses of glucocorticoids for an extended period bind to the mineralocorticoid - receptor, raising sodium levels and decreasing potassium levels.[A187463] - - - === - - - disease: Thyroiditis - - drug: Prednisone - - ' -- completion: 'disease: Conjunctivitis, Allergic - - drug: Hydrocortisone - - mechanism_links: Hydrocortisone - increases activity of - glucocorticoid receptor - (human); glucocorticoid receptor (human) - increases activity of - annexin A1 - (human); glucocorticoid receptor (human) - decreases activity of - prostaglandin - G/H synthase 1 (human); glucocorticoid receptor (human) - decreases activity of - - prostaglandin G/H synthase 2 (human); annexin A1 (human) - decreases activity - of - cytosolic phospholipase A2 (human); prostaglandin G/H synthase 1 (human) - - positively regulates - prostaglandin biosynthetic process; prostaglandin G/H - synthase 2 (human) - positively regulates - prostaglandin biosynthetic process; - cytosolic phospholipase A2 (human) - positively regulates - leukotriene biosynthetic - process; cytosolic phospholipase A2 (human) - positively regulates - prostaglandin - biosynthetic process; leukotriene biosynthetic process - positively correlated - with - inflammatory response; prostaglandin biosynthetic process - positively - correlated with - inflammatory response; inflammatory response - located in - - conjunctiva; conjunctiva - location of - Conjunctivitis, Allergic' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - The short term effects of corticosteroids are decreased vasodilation and permeability - of capillaries, as well as decreased leukocyte migration to sites of inflammation.[A187463] - Corticosteroids binding to the glucocorticoid receptor mediates changes in gene - expression that lead to multiple downstream effects over hours to days.[A187463] - Lower doses of corticosteroids provide an anti-inflammatory effect, while higher - doses are immunosuppressive.[A187463] High doses of glucocorticoids for an extended - period bind to the mineralocorticoid receptor, raising sodium levels and decreasing - potassium levels.[A187463] - - - === - - - disease: Conjunctivitis, Allergic - - drug: Hydrocortisone - - ' -- completion: 'disease: Berylliosis - - drug: Methylprednisolone - - mechanism_links: Methylprednisolone - increases activity of - glucocorticoid receptor - (human); glucocorticoid receptor (human) - increases activity of - annexin A1 - (human); glucocorticoid receptor (human) - decreases activity of - prostaglandin - G/H synthase 1 (human); glucocorticoid receptor (human) - decreases activity of - - prostaglandin G/H synthase 2 (human); annexin A1 (human) - decreases activity - of - cytosolic phospholipase A2 (human); prostaglandin G/H synthase 1 (human) - - positively regulates - prostaglandin biosynthetic process; prostaglandin G/H - synthase 2 (human) - positively regulates - prostaglandin biosynthetic process; - cytosolic phospholipase A2 (human) - positively regulates - leukotriene biosynthetic - process; cytosolic phospholipase A2 (human) - positively regulates - prostaglandin - biosynthetic process; leukotriene biosynthetic process - positively correlated - with - inflammatory response; prostaglandin biosynthetic process - positively - correlated with - inflammatory response; inflammatory response - located in - - bronchus; bronchus - location of - Berylliosis' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - The short term effects of corticosteroids are decreased vasodilation and permeability - of capillaries, as well as decreased leukocyte migration to sites of inflammation.[A187463] - Corticosteroids binding to the glucocorticoid receptor mediates changes in gene - expression that lead to multiple downstream effects over hours to days.[A187463] - Lower doses of corticosteroids provide an anti-inflammatory effect, while higher - doses are immunosuppressive.[A187463] High doses of glucocorticoids for an extended - period bind to the mineralocorticoid receptor, raising sodium levels and decreasing - potassium levels.[A187463] - - - === - - - disease: Berylliosis - - drug: Methylprednisolone - - ' -- completion: 'disease: Klebsiella Infections - - drug: Norfloxacin - - mechanism_links: Norfloxacin - decreases activity of - PR:W1DID1; Norfloxacin - - decreases activity of - PR:W1DEE8; PR:W1DID1 - positively regulates - DNA replication; - PR:W1DEE8 - positively regulates - DNA replication; DNA replication - occurs in - - NCBITaxon:570; NCBITaxon:570 - causes - Klebsiella Infections' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - The bactericidal action of Norfloxacin results from inhibition of the enzymes - topoisomerase II (DNA gyrase) and topoisomerase IV, which are required for bacterial - DNA replication, transcription, repair, and recombination. Norfloxacin is a broad-spectrum - antibiotic agent that is shown to be effective against various Gram-positive and - Gram-negative bacterial species. The fluorine atom at the 6 position increases - potency against gram-negative organisms, and the piperazine moiety at the 7 position - is responsible for anti-pseudomonal activity - - - === - - - disease: Klebsiella Infections - - drug: Norfloxacin - - ' -- completion: 'disease: Typhoid Fever - - drug: Chloramphenicol succinate - - mechanism_links: chloramphenicol succinate - has metabolite - Chloramphenicol; - Chloramphenicol - decreases activity of - PR:Q8XET6; PR:Q8XET6 - positively regulates - - translation; translation - in taxon - Salmonella enterica subsp. enterica serovar - Typhi; Salmonella enterica subsp. enterica serovar Typhi - causes - Typhoid Fever' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Chloramphenicol succinate is hydrolyzed into the active chloramphenicol.[A204047] - Chloramphenicol resembles uridine-5''-phosphate.[A204071] It binds to the residues - A2451 and A2452 in the 23S rRNA of the 50S ribosomal subunit of _E. coli_, which - prevents translation.[A204077] - - - === - - - disease: Typhoid Fever - - drug: Chloramphenicol succinate - - ' -- completion: 'disease: Heartburn - - drug: Sodium citrate - - mechanism_links: Sodium citrate - negatively regulates - Gastric Acid; Gastric - Acid - positively correlated with - Heartburn' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Citrate chelates free calcium ions preventing them from forming a complex with - tissue factor and coagulation factor VIIa to promote the activation of coagulation - factor X [A19410] [A19411]. This inhibits the extrinsic initiation of the coagulation - cascade. Citrate may also exert an anticoagulant effect via a so far unknown mechanism - as restoration of calcium concentration does not fully reverse the effect of citrate - [A19410]. Citrate is a weak base and so reacts with hydrochloric acid in the stomach - to raise the pH. It it further metabolized to bicarbonate which then acts as a - systemic alkalizing agent, raising the pH of the blood and urine [L790]. It also - acts as a diuretic and increases the urinary excretion of calcium. - - - === - - - disease: Heartburn - - drug: Sodium citrate - - ' -- completion: 'disease: Attention Deficit Disorder with Hyperactivity - - drug: Guanfacine - - mechanism_links: Guanfacine - increases activity of - alpha-2A adrenergic receptor - (human); alpha-2A adrenergic receptor (human) - treats - Attention Deficit Disorder - with Hyperactivity' - prompt: "From the text below, extract the following entities in the following format:\n\ - \ndisease: \ndrug: \nmechanism_links: \n\ - \n\nText:\nGuanfacine is a selective alpha-2A adrenergic receptor agonist, which\ - \ reduces the effects of the sympathetic nervous system on the heart and circulatory\ - \ system.[L11277] The link between guanfacine\u2019s molecular mechanism and it\u2019\ - s effect on the treatment of ADHD has not been determined.[L11277]\n\n===\n\n\ - disease: Attention Deficit Disorder with Hyperactivity\ndrug: Guanfacine\n" -- completion: 'disease: Osteoporosis, Postmenopausal - - drug: Risedronic acid - - mechanism_links: Risedronate Sodium - negatively correlated with - obsolete ATP - hydrolysis activity; obsolete ATP hydrolysis activity - increases activity of - - osteoclast; Risedronate Sodium - negatively regulates - V-type proton ATPase - catalytic subunit A (human); V-type proton ATPase catalytic subunit A (human) - - positively regulates - proton transmembrane transport; proton transmembrane - transport - positively correlated with - bone resorption; Risedronate Sodium - - positively regulates - apoptotic process; apoptotic process - decreases abundance - of - osteoclast; osteoclast - positively regulates - bone resorption; bone resorption - - positively correlated with - Osteoporosis, Postmenopausal; Risedronate Sodium - - molecularly interacts with - hydroxylapatite; hydroxylapatite - positively correlated - with - ossification; hydroxylapatite - positively correlated with - bone regeneration; - bone regeneration - negatively correlated with - Osteoporosis, Postmenopausal; - ossification - negatively correlated with - Osteoporosis, Postmenopausal' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Risedronatic acid binds to bone hydroxyapatite[FDA Label]. Bone resorption causes - local acidification, releasing risedronic acid which is that taken into osteoclasts - by fluid-phase endocytosis[A959]. Endocytic vesicles are acidified, releasing - risedronic acid to the cytosol of osteoclasts where they induce apoptosis through - inhbition of farnesyl pyrophosphate synthase[A959]. Inhibition of osteoclasts - results in decreased bone resorption[A959]. - - - === - - - disease: Osteoporosis, Postmenopausal - - drug: Risedronic acid - - ' -- completion: 'disease: Rhinitis, Vasomotor - - drug: Chlorpheniramine - - mechanism_links: Chlorpheniramine - negatively regulates - histamine H1 receptor - (human); histamine H1 receptor (human) - positively correlated with - Histamine; - Histamine - increases abundance of - Substance P; Substance P - participates in - - Neurogenic Inflammation; Neurogenic Inflammation - contributes to - Rhinitis, - Vasomotor' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Chlorpheniramine binds to the histamine H1 receptor. This blocks the action of - endogenous histamine, which subsequently leads to temporary relief of the negative - symptoms brought on by histamine. - - - === - - - disease: Rhinitis, Vasomotor - - drug: Chlorpheniramine - - ' -- completion: 'disease: Rhinoscleroma - - drug: Ciprofloxacin - - mechanism_links: Ciprofloxacin - decreases activity of - PR:R4Y7H5; Ciprofloxacin - - decreases activity of - PR:R4YE07; PR:R4Y7H5 - positively regulates - DNA replication; - PR:R4YE07 - positively regulates - DNA replication; DNA replication - occurs in - - NCBITaxon:39831; NCBITaxon:39831 - causes - Rhinoscleroma' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Ciprofloxacin acts on bacterial topoisomerase II (DNA gyrase) and topoisomerase - IV.[A178885] Ciprofloxacin''s targeting of the alpha subunits of DNA gyrase prevents - it from supercoiling the bacterial DNA which prevents DNA replication.[A178876,A178882] - - - === - - - disease: Rhinoscleroma - - drug: Ciprofloxacin - - ' -- completion: 'disease: Q Fever - - drug: Meclocycline - - mechanism_links: meclocycline - decreases activity of - InterPro:IPR000235; InterPro:IPR000235 - - positively regulates - tRNA aminoacylation; tRNA aminoacylation - participates - in - translation; translation - in taxon - Coxiella burnetii; Coxiella burnetii - - causes - Q Fever' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - As a tetracycline, meclocycline likely works by reversably associating with the - 30s subint of the bacterial ribosome [A19429]. A likely binding site for tetracyclines - has been identified on protein S7 of this subunit. This association blocks the - association of aminoacyl-tRNA with the ribosome, inhibiting protein synthesis. - Ultimately this inhibits bacterial growth due to a lack of proteins necessary - for reproduction. - - - === - - - disease: Q Fever - - drug: Meclocycline - - ' -- completion: 'disease: Keratosis, Actinic - - drug: Masoprocol - - mechanism_links: Masoprocol - decreases activity of - serine/threonine-protein - kinase mTOR (human); serine/threonine-protein kinase mTOR (human) - positively - regulates - REACT:R-HSA-166208; REACT:R-HSA-166208 - positively correlated with - - HP:0031377; HP:0031377 - causes - Keratosis, Actinic' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Although the exact mechanism of action is not known, studies have shown that masoprocol - is a potent 5-lipoxygenase inhibitor and has antiproliferative activity against - keratinocytes in tissue culture, but the relationship between this activity and - its effectiveness in actinic keratoses is unknown. Masoprocol also inhibits prostaglandins - but the significance of this action is not yet known. - - - === - - - disease: Keratosis, Actinic - - drug: Masoprocol - - ' -- completion: 'disease: Streptococcal Infections - - drug: Moxifloxacin - - mechanism_links: MESH:D000077266 - decreases activity of - PR:Q9L7Q5; MESH:D000077266 - - decreases activity of - PR:Q9L7Q4; PR:Q9L7Q5 - positively regulates - DNA replication; - PR:Q9L7Q4 - positively regulates - DNA replication; DNA replication - occurs in - - NCBITaxon:1314; NCBITaxon:1314 - causes - Streptococcal Infections' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - The bactericidal action of moxifloxacin results from inhibition of the enzymes - topoisomerase II (DNA gyrase) and topoisomerase IV. DNA gyrase is an essential - enzyme that is involved in the replication, transcription and repair of bacterial - DNA. Topoisomerase IV is an enzyme known to play a key role in the partitioning - of the chromosomal DNA during bacterial cell division. - - - === - - - disease: Streptococcal Infections - - drug: Moxifloxacin - - ' -- completion: 'disease: Myocardial Infarction - - drug: Acetylsalicylic acid - - mechanism_links: Aspirin - decreases activity of - prostaglandin G/H synthase - 1 (human); prostaglandin G/H synthase 1 (human) - negatively regulates - prostaglandin - biosynthetic process; Aspirin - decreases activity of - prostaglandin G/H synthase - 2 (human); prostaglandin G/H synthase 2 (human) - negatively regulates - prostaglandin - biosynthetic process; prostaglandin biosynthetic process - decreases abundance - of - Thromboxane A2; Thromboxane A2 - decreases activity of - platelet aggregation; - platelet aggregation - prevents - blood coagulation; blood coagulation - causes - - Myocardial Infarction' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Acetylsalicylic acid (ASA) blocks prostaglandin synthesis. It is non-selective - for COX-1 and COX-2 enzymes [A177241, A10989, A32682]. Inhibition of COX-1 results - in the inhibition of platelet aggregation for about 7-10 days (average platelet - lifespan). The acetyl group of acetylsalicylic acid binds with a serine residue - of the cyclooxygenase-1 (COX-1) enzyme, leading to irreversible inhibition. This - prevents the production of pain-causing prostaglandins. This process also stops - the conversion of arachidonic acid to thromboxane A2 (TXA2), which is a potent - inducer of platelet aggregation [FDA label]. Platelet aggregation can result - in clots and harmful venous and arterial thromboembolism, leading to conditions - such as pulmonary embolism and stroke. It is important to note that there is - 60% homology between the protein structures of COX-1 and COX-2. ASA binds to serine - 516 residue on the active site of COX-2 in the same fashion as its binding to - the serine 530 residue located on the active site of COX-1. The active site of - COX-2 is, however, slightly larger than the active site of COX-1, so that arachidonic - acid (which later becomes prostaglandins) manages to bypass the aspirin molecule - inactivating COX-2 [A32682, A177256]. ASA, therefore, exerts more action on the - COX-1 receptor rather than on the COX-2 receptor [A177268]. A higher dose of acetylsalicylic - acid is required for COX-2 inhibition [A177325]. - - - === - - - disease: Myocardial Infarction - - drug: Acetylsalicylic acid - - ' -- completion: 'disease: Tularemia - - drug: Streptomycin - - mechanism_links: Streptomycin - molecularly interacts with - 30S ribosomal protein - S2; 30S ribosomal protein S2 - disrupts - translation; translation - in taxon - - NCBITaxon:263; NCBITaxon:263 - causes - Tularemia' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Aminoglycosides like Streptomycin "irreversibly" bind to specific 30S-subunit - proteins and 16S rRNA. Specifically Streptomycin binds to four nucleotides of - 16S rRNA and a single amino acid of protein S12. This interferes with decoding - site in the vicinity of nucleotide 1400 in 16S rRNA of 30S subunit. This region - interacts with the wobble base in the anticodon of tRNA. This leads to interference - with the initiation complex, misreading of mRNA so incorrect amino acids are inserted - into the polypeptide leading to nonfunctional or toxic peptides and the breakup - of polysomes into nonfunctional monosomes. - - - === - - - disease: Tularemia - - drug: Streptomycin - - ' -- completion: 'disease: Erectile Dysfunction - - drug: Avanafil - - mechanism_links: avanafil - decreases activity of - cGMP-specific 3'',5''-cyclic - phosphodiesterase (human); cGMP-specific 3'',5''-cyclic phosphodiesterase (human) - - increases abundance of - Cyclic GMP; Cyclic GMP - causes - relaxation of smooth - muscle; relaxation of smooth muscle - positively regulates - blood circulation; - blood circulation - located in - corpus cavernosum penis; corpus cavernosum penis - - participates in - Erectile Dysfunction' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Avanafil is a selective phosphodiesterase 5 (PDE5) enzyme inhibitor used for the - treatment of erectile dysfunction caused by diabetes, age induced oxidative stress - or other complications. Avanafil inhibits the cGMP specific phosphodiesterase - type 5 (PDE5) which is responsible for degradation of cGMP in the corpus cavernosum - located around the penis. Penile erection during sexual stimulation is caused - by increased penile blood flow resulting from the relaxation of penile arteries - and corpus cavernosal smooth muscle. This response is mediated by the release - of nitric oxide (NO) from nerve terminals and endothelial cells, which stimulates - the synthesis of cGMP in smooth muscle cells. Cyclic GMP causes smooth muscle - relaxation and increased blood flow into the corpus cavernosum. The inhibition - of phosphodiesterase type 5 (PDE5) by avanafil enhances erectile function by increasing - the amount of cGMP. - - - === - - - disease: Erectile Dysfunction - - drug: Avanafil - - ' -- completion: 'disease: Neurosyphilis - - drug: Procaine benzylpenicillin - - mechanism_links: Penicillin G Procaine - produces - Benzylpenicillin; Benzylpenicillin - - negatively regulates - Pfam:PF00905; Pfam:PF00905 - positively regulates - peptidoglycan - biosynthetic process; peptidoglycan biosynthetic process - positively correlated - with - peptidoglycan-based cell wall biogenesis; peptidoglycan-based cell wall - biogenesis - in taxon - NCBITaxon:160; NCBITaxon:160 - causes - Neurosyphilis' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Procaine benzylpenicillin is hydrolyzed into penicillin G once it is released - from the injection site. Penicillin G attaches to the penicillin-binding proteins - on bacterial cell wall and inhibit the transpeptidation enzyme that crosslinks - the peptide chains attached to the backbone of the peptidoglycan. The final bactericidal - event involves the inactivation of an inhibitor of autolytic enzymes in the cell - wall, leading to lysis of the bacterium [T33]. - - - === - - - disease: Neurosyphilis - - drug: Procaine benzylpenicillin - - ' -- completion: 'disease: MESH:D000073605 - - drug: Meclocycline - - mechanism_links: meclocycline - decreases activity of - InterPro:IPR000235; InterPro:IPR000235 - - positively regulates - tRNA aminoacylation; tRNA aminoacylation - participates - in - translation; translation - in taxon - NCBITaxon:786; NCBITaxon:786 - causes - - MESH:D000073605' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - As a tetracycline, meclocycline likely works by reversably associating with the - 30s subint of the bacterial ribosome [A19429]. A likely binding site for tetracyclines - has been identified on protein S7 of this subunit. This association blocks the - association of aminoacyl-tRNA with the ribosome, inhibiting protein synthesis. - Ultimately this inhibits bacterial growth due to a lack of proteins necessary - for reproduction. - - - === - - - disease: MESH:D000073605 - - drug: Meclocycline - - ' -- completion: 'disease: Nasal Polyps - - drug: Beclomethasone dipropionate - - mechanism_links: Beclomethasone dipropionate - has metabolite - CHEBI:3001; CHEBI:3001 - - positively regulates - glucocorticoid receptor (human); glucocorticoid receptor - (human) - negatively regulates - inflammatory response; inflammatory response - - positively correlated with - Nasal Polyps' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Beclomethasone dipropionate is a corticosteroid and prodrug that is rapidly activated - by hydrolysis to the active monoester, 17 monopropionate (17-BMP), which mediates - anti-inflammatory actions. 17-BMP has been shown _in vitro_ to exhibit a binding - affinity for the human glucocorticoid receptor which is approximately 13 times - that of dexamethasone and 25 times that of beclomethasone dipropionate.[L6871] - Upon binding of the ligand, the glucocorticoid receptors dimerize and translocate - into the nucleus, where they subsequently bind to glucocorticoid response elements - (GRE) on glucocorticoid-responsive genes, leading to changes in transcription. - There are several proposed mechanisms for the anti-inflammatory action of corticosteroids. - Corticosteroids may work by increasing the transcription of genes coding for anti-inflammatory - proteins, including lipocortin-1 and interleukin-10.[A179875] Corticosteroids - were also shown to inhibit the expression of multiple genes that encode pro-inflammatory - factors, such as cytokines, chemokines, and adhesion molecules, that are activated - during the chronic inflammatory process.[A31449] This is thought to be due to - the direct inhibitory interaction between activated glucocorticoid receptors and - activated pro-inflammatory transcription factors, such as nuclear factor-kappa - B and activator protein-1.[A179875] Chronic inflammation is often characterized - by enhanced expression of these transcription factors that bind to and activate - coactivator molecules, which then acetylate core histones to switch on gene transcription - to further amplify the inflammatory process.[A31449] Corticosteroids suppress - the multiple inflammatory gene expression by promoting histone deacetylation, - resulting in tighter coiling of DNA and reduced access of transcription factors - to their binding sites.[A179875] - - - === - - - disease: Nasal Polyps - - drug: Beclomethasone dipropionate - - ' -- completion: 'disease: Gastrointestinal anthrax - - drug: Fusidic acid - - mechanism_links: Fusidic Acid - decreases activity of - PR:Q81VT3; PR:Q81VT3 - - positively regulates - translation; translation - occurs in - Bacillus anthracis; - Bacillus anthracis - causes - Gastrointestinal anthrax' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Fusidic acid works by interfering with bacterial protein synthesis, specifically - by preventing the translocation of the elongation factor G (EF-G) from the ribosome. - It also can inhibit chloramphenicol acetyltransferase enzymes. - - - === - - - disease: Gastrointestinal anthrax - - drug: Fusidic acid - - ' -- completion: 'disease: Rhinitis, Allergic - - drug: Methdilazine - - mechanism_links: methdilazine - decreases activity of - histamine H1 receptor - (human); histamine H1 receptor (human) - positively regulates - histamine receptor - activity; histamine receptor activity - participates in - histamine secretion - involved in inflammatory response; histamine secretion involved in inflammatory - response - positively correlated with - Rhinitis, Allergic' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Methdilazine binds to the histamine H<sub>1</sub> receptor. This blocks - the action of endogenous histamine, which subsequently leads to temporary relief - of the negative symptoms brought on by histamine. - - - === - - - disease: Rhinitis, Allergic - - drug: Methdilazine - - ' -- completion: 'disease: Rhinitis, Allergic - - drug: Acetaminophen - - mechanism_links: Acetaminophen - decreases activity of - prostaglandin G/H synthase - 1 (human); Acetaminophen - decreases activity of - prostaglandin G/H synthase - 2 (human); Acetaminophen - decreases activity of - prostaglandin E synthase 3 - (human); prostaglandin G/H synthase 1 (human) - positively regulates - prostaglandin - biosynthetic process; prostaglandin G/H synthase 2 (human) - positively regulates - - prostaglandin biosynthetic process; prostaglandin E synthase 3 (human) - positively - regulates - prostaglandin biosynthetic process; prostaglandin biosynthetic process - - increases abundance of - Prostaglandins; Prostaglandins - positively correlated - with - Rhinitis, Allergic' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - According to its FDA labeling, acetaminophen''s exact mechanism of action has - not been fully established[Label] - despite this, it is often categorized alongside - NSAIDs (nonsteroidal anti-inflammatory drugs) due to its ability to inhibit the - cyclooxygenase (COX) pathways.[T518] It is thought to exert central actions which - ultimately lead to the alleviation of pain symptoms.[T518] One theory is that - acetaminophen increases the pain threshold by inhibiting two isoforms of cyclooxygenase, - COX-1 and COX-2, which are involved in prostaglandin (PG) synthesis. Prostaglandins - are responsible for eliciting pain sensations.[A176366] Acetaminophen does not - inhibit cyclooxygenase in peripheral tissues and, therefore, has no peripheral - anti-inflammatory effects. Though acetylsalicylic acid (aspirin) is an irreversible - inhibitor of COX and directly blocks the active site of this enzyme, studies have - shown that acetaminophen (paracetamol) blocks COX indirectly.[F4133] Studies also - suggest that acetaminophen selectively blocks a variant type of the COX enzyme - that is unique from the known variants COX-1 and COX-2.[A468] This enzyme has - been referred to as _COX-3_. The antipyretic actions of acetaminophen are likely - attributed to direct action on heat-regulating centers in the brain, resulting - in peripheral vasodilation, sweating, and loss of body heat.[F4133] The exact - mechanism of action of this drug is not fully understood at this time, but future - research may contribute to deeper knowledge.[F4133] - - - === - - - disease: Rhinitis, Allergic - - drug: Acetaminophen - - ' -- completion: 'disease: Streptococcal Infections - - drug: Benzylpenicillin - - mechanism_links: Penicillin G - decreases activity of - InterPro:IPR001460; InterPro:IPR001460 - - participates in - peptidoglycan biosynthetic process; peptidoglycan biosynthetic - process - positively regulates - peptidoglycan-based cell wall biogenesis; peptidoglycan-based - cell wall biogenesis - occurs in - Streptococcus; Streptococcus - causes - Streptococcal - Infections' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - By binding to specific penicillin-binding proteins (PBPs) located inside the bacterial - cell wall, penicillin G inhibits the third and last stage of bacterial cell wall - synthesis. Cell lysis is then mediated by bacterial cell wall autolytic enzymes - such as autolysins; it is possible that penicillin G interferes with an autolysin - inhibitor. - - - === - - - disease: Streptococcal Infections - - drug: Benzylpenicillin - - ' -- completion: 'disease: Meningitis, Bacterial - - drug: Ampicillin - - mechanism_links: Ampicillin - negatively regulates - Pfam:PF00905; Pfam:PF00905 - - positively regulates - peptidoglycan biosynthetic process; peptidoglycan biosynthetic - process - positively correlated with - peptidoglycan-based cell wall biogenesis; - peptidoglycan-based cell wall biogenesis - in taxon - Neisseria meningitidis; - Neisseria meningitidis - causes - Meningitis, Bacterial' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - By binding to specific penicillin-binding proteins (PBPs) located inside the bacterial - cell wall, Ampicillin inhibits the third and last stage of bacterial cell wall - synthesis. Cell lysis is then mediated by bacterial cell wall autolytic enzymes - such as autolysins; it is possible that Ampicillin interferes with an autolysin - inhibitor. - - - === - - - disease: Meningitis, Bacterial - - drug: Ampicillin - - ' -- completion: 'disease: Small Cell Lung Carcinoma - - drug: Topotecan - - mechanism_links: Topotecan - decreases activity of - DNA topoisomerase 1 (human); - DNA topoisomerase 1 (human) - positively regulates - DNA binding; DNA binding - - correlated with - DNA replication; DNA replication - positively correlated with - - neoplastic cell; neoplastic cell - positively correlated with - Small Cell Lung - Carcinoma' - prompt: "From the text below, extract the following entities in the following format:\n\ - \ndisease: \ndrug: \nmechanism_links: \n\ - \n\nText:\nTopotecan has the same mechanism of action as irinotecan and is believed\ - \ to exert its cytotoxic effects during the S-phase of DNA synthesis. Topoisomerase\ - \ I relieves torsional strain in DNA by inducing reversible single strand breaks.\ - \ Topotecan binds to the topoisomerase I-DNA complex and prevents religation of\ - \ these single strand breaks. This ternary complex interferes with the moving\ - \ replication fork, which leads to the induction of replication arrest and lethal\ - \ double-stranded breaks in DNA. As mammalian cells cannot efficiently repair\ - \ these double strand breaks, the formation of this ternary complex eventually\ - \ leads to apoptosis (programmed cell death). Topotecan mimics a DNA base pair\ - \ and binds at the site of DNA cleavage by intercalating between the upstream\ - \ (\u22121) and downstream (+1) base pairs. Intercalation displaces the downstream\ - \ DNA, thus preventing religation of the cleaved strand. By specifically binding\ - \ to the enzyme\u2013substrate complex, Topotecan acts as an uncompetitive inhibitor.\n\ - \n===\n\ndisease: Small Cell Lung Carcinoma\ndrug: Topotecan\n" -- completion: 'disease: Common Cold - - drug: Glycine - - mechanism_links: Glycine - treats - Common Cold' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - In the CNS, there exist strychnine-sensitive glycine binding sites as well as - strychnine-insensitive glycine binding sites. The strychnine-insensitive glycine-binding - site is located on the NMDA receptor complex. The strychnine-sensitive glycine - receptor complex is comprised of a chloride channel and is a member of the ligand-gated - ion channel superfamily. The putative antispastic activity of supplemental glycine - could be mediated by glycine''s binding to strychnine-sensitive binding sites - in the spinal cord. This would result in increased chloride conductance and consequent - enhancement of inhibitory neurotransmission. The ability of glycine to potentiate - NMDA receptor-mediated neurotransmission raised the possibility of its use in - the management of neuroleptic-resistant negative symptoms in schizophrenia. <br/>Animal - studies indicate that supplemental glycine protects against endotoxin-induced - lethality, hypoxia-reperfusion injury after liver transplantation, and D-galactosamine-mediated - liver injury. Neutrophils are thought to participate in these pathologic processes - via invasion of tissue and releasing such reactive oxygen species as superoxide. - In vitro studies have shown that neutrophils contain a glycine-gated chloride - channel that can attenuate increases in intracellular calcium and diminsh neutrophil - oxidant production. This research is ealy-stage, but suggests that supplementary - glycine may turn out to be useful in processes where neutrophil infiltration contributes - to toxicity, such as ARDS. - - - === - - - disease: Common Cold - - drug: Glycine - - ' -- completion: 'disease: Arthritis, Rheumatoid - - drug: Loxoprofen - - mechanism_links: loxoprofen - decreases activity of - prostaglandin G/H synthase - 1 (human); loxoprofen - decreases activity of - prostaglandin G/H synthase 2 (human); - prostaglandin G/H synthase 1 (human) - participates in - REACT:R-HSA-2162123; - prostaglandin G/H synthase 2 (human) - participates in - REACT:R-HSA-2162123; - REACT:R-HSA-2162123 - increases abundance of - Prostaglandins; Prostaglandins - - positively correlated with - HP:0002829; Prostaglandins - positively correlated - with - HP:0001386; HP:0001386 - positively correlated with - Arthritis, Rheumatoid; - HP:0002829 - positively correlated with - Arthritis, Rheumatoid' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Loxoprofen itself is a prodrug and carries little-to-no pharmacological activity - - it is rapidly metabolized to its trans-alcohol form, which is a potent and non-selective - inhibitor of cyclooxygenase.[A27797] Cyclooxygenase (COX) is present in 2 forms, - COX-1 and COX-2, with each serving different functions. COX-1 is present in human - cells and is constitutively released, performing cellular housekeeping functions - such as mucus production and platelet aggregation.[L1228] COX-2 is induced in - human cells post-injury or due to other stimuli, is triggered to appear in large - quantities at the sites of injury/stimuli, and is ultimately responsible for the - mediation of inflammation and pain.[L1228] Loxoprofen''s active metabolite inhibits - both COX isoforms, resulting in reduced expression of several mediators of pain, - inflammation, and fever (e.g. prostaglandins, prostacyclin, thromboxane, etc).[L1228] - - - === - - - disease: Arthritis, Rheumatoid - - drug: Loxoprofen - - ' -- completion: 'disease: Pruritus Ani - - drug: Desoximetasone - - mechanism_links: Desoximetasone - increases activity of - glucocorticoid receptor - (human); glucocorticoid receptor (human) - increases abundance of - annexin A1 - (human); annexin A1 (human) - negatively regulates - REACT:R-HSA-2162123; REACT:R-HSA-2162123 - - positively regulates - inflammatory response; inflammatory response - contributes - to - HP:0000989; HP:0000989 - manifestation of - Pruritus Ani' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - The precise mechanism of the antiinflammatory activity of topical steroids in - the treatment of steroid-responsive dermatoses, in general, is uncertain. However, - corticosteroids are thought to act by the induction of phospholipase A<sub>2</sub> - inhibitory proteins, collectively called lipocortins. This is achieved first by - the drug binding to the glucocorticoid receptors which then translocates into - the nucleus and binds to DNA causing various activations and repressions of genes. - It is postulated that these proteins control the biosynthesis of potent mediators - of inflammation such as prostaglandins and leukotrienes by inhibiting the release - of their common precursor arachidonic acid. Arachidonic acid is released from - membrane phospholipids by phospholipase A<sub>2</sub>. - - - === - - - disease: Pruritus Ani - - drug: Desoximetasone - - ' -- completion: 'disease: Enterobiasis - - drug: Piperazine - - mechanism_links: Piperazine - increases activity of - gamma-aminobutyric acid - receptor subunit beta-3 (human); gamma-aminobutyric acid receptor subunit beta-3 - (human) - positively correlated with - chloride channel activity; gamma-aminobutyric - acid receptor subunit beta-3 (human) - decreases abundance of - Acetylcholine; - Acetylcholine - occurs in - membrane hyperpolarization; chloride channel activity - - occurs in - membrane hyperpolarization; membrane hyperpolarization - has phenotype - - HP:0003470; HP:0003470 - increases activity of - defense response to other organism; - defense response to other organism - in taxon - NCBITaxon:51028; NCBITaxon:51028 - - causes - Enterobiasis' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Piperazine is a GABA receptor agonist. Piperzine binds directly and selectively - to muscle membrane GABA receptors, presumably causing hyperpolarization of nerve - endings, resulting in flaccid paralysis of the worm. While the worm is paralyzed, - it is dislodged from the intestinal lumen and expelled live from the body by normal - intestinal peristalsis. - - - === - - - disease: Enterobiasis - - drug: Piperazine - - ' -- completion: 'disease: Puberty, Precocious - - drug: Leuprolide - - mechanism_links: Leuprolide - increases activity of - gonadotropin-releasing hormone - receptor (human); gonadotropin-releasing hormone receptor (human) - positively - regulates - gonadotropin hormone-releasing hormone activity; gonadotropin hormone-releasing - hormone activity - regulates - estrogen biosynthetic process; gonadotropin hormone-releasing - hormone activity - regulates - androgen biosynthetic process; gonadotropin hormone-releasing - hormone activity - regulates - progesterone biosynthetic process; estrogen biosynthetic - process - negatively correlated with - Puberty, Precocious; androgen biosynthetic - process - negatively correlated with - Puberty, Precocious; progesterone biosynthetic - process - negatively correlated with - Puberty, Precocious' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Gonadotropin-releasing hormone (GnRH) is a naturally occurring decapeptide that - modulates the hypothalamic-pituitary-gonadal (HPG) axis. GnRH binds to corresponding - receptors (GnRHRs) on the anterior pituitary gonadotropes, which in turn release - luteinizing hormone (LH) and follicle-stimulating hormone (FSH); these, in turn, - affect the downstream synthesis and release of the sex hormones testosterone, - dihydrotestosterone, estrone, and estradiol.[A203126, A203132] Despite the variety - of conditions indicated for treatment with leuprolide, the mechanism of action - underlying efficacy is the same in all cases. As a GnRHR agonist, leuprolide binds - to and initially activates downstream LH and FSH release; this initial spike in - gonadotropin levels is responsible for some of the adverse effects associated - with treatment. After 2-4 weeks of treatment, continuous stimulation of GnRHR - results in feedback inhibition and significant downregulation of LH, FSH, and - their corresponding downstream effects, producing a therapeutic benefit. These - effects are reversible upon treatment discontinuation.[A203126, A203129, A203132, - A203222, L10310, L13781, L13784, L13787, L13790, L13814] - - - === - - - disease: Puberty, Precocious - - drug: Leuprolide - - ' -- completion: 'disease: Parkinson Disease - - drug: Amantadine - - mechanism_links: Amantadine - increases activity of - D(2) dopamine receptor (human); - D(2) dopamine receptor (human) - positively correlated with - Dopamine; Dopamine - - positively correlated with - dopamine secretion, neurotransmission; dopamine - secretion, neurotransmission - occurs in - substantia nigra; substantia nigra - - disrupted by - Parkinson Disease' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - The mechanism of its antiparkinsonic effect is not fully understood, but it appears - to be releasing dopamine from the nerve endings of the brain cells, together with - stimulation of norepinephrine response. It also has NMDA receptor antagonistic - effects. The antiviral mechanism seems to be unrelated. The drug interferes with - a viral protein, M2 (an ion channel), which is needed for the viral particle to - become "uncoated" once it is taken inside the cell by endocytosis. - - - === - - - disease: Parkinson Disease - - drug: Amantadine - - ' -- completion: 'disease: Rhinitis, Allergic - - drug: Triprolidine - - mechanism_links: Triprolidine - decreases activity of - histamine H1 receptor - (human); histamine H1 receptor (human) - positively regulates - histamine receptor - activity; histamine receptor activity - positively correlated with - histamine - secretion involved in inflammatory response; histamine secretion involved in inflammatory - response - positively correlated with - Rhinitis, Allergic' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Triprolidine binds to the histamine H1 receptor. This blocks the action of endogenous - histamine, which subsequently leads to temporary relief of the negative symptoms - brought on by histamine. - - - === - - - disease: Rhinitis, Allergic - - drug: Triprolidine - - ' -- completion: 'disease: Hot Flashes - - drug: Medroxyprogesterone acetate - - mechanism_links: Medroxyprogesterone - increases activity of - progesterone receptor - (human); progesterone receptor (human) - positively regulates - progesterone receptor - signaling pathway; progesterone receptor signaling pathway - treats - Hot Flashes; - Medroxyprogesterone - increases activity of - estrogen receptor (human); estrogen - receptor (human) - positively regulates - intracellular estrogen receptor signaling - pathway; intracellular estrogen receptor signaling pathway - treats - Hot Flashes' - prompt: "From the text below, extract the following entities in the following format:\n\ - \ndisease: \ndrug: \nmechanism_links: \n\ - \n\nText:\nMedroxyprogesterone acetate (MPA) inhibits the production of gonadotropin,\ - \ preventing follicular maturation and ovulation, which is responsible for it\u2019\ - s ability to prevent pregnancy.[L8660] This action also thins the endometrium.[L8660]\ - \ MPA reduces nuclear estrogen receptors and DNA synthesis in epithelial cells\ - \ of the endometrium.[L8660] MPA can also induce p53 dependant apoptosis in certain\ - \ cancer cell lines,[A186134] and inhibit GABA-A receptors.[A186140]\n\n===\n\n\ - disease: Hot Flashes\ndrug: Medroxyprogesterone acetate\n" -- completion: 'disease: Hypertension - - drug: Indapamide - - mechanism_links: Indapamide - decreases activity of - solute carrier family 12 - member 3 (human); solute carrier family 12 member 3 (human) - participates in - - renal sodium ion absorption; renal sodium ion absorption - positively correlated - with - renal water retention; renal water retention - contributes to - HP:0011104; - HP:0011104 - contributes to - positive regulation of blood pressure; positive - regulation of blood pressure - affects risk for - Hypertension' - prompt: "From the text below, extract the following entities in the following format:\n\ - \ndisease: \ndrug: \nmechanism_links: \n\ - \n\nText:\nIndapamide acts on the nephron, specifically at the proximal segment\ - \ of the distal convoluted tubule where it inhibits the Na+/Cl- cotransporter,\ - \ leading to reduced sodium reabsorption.[A203519,A16729] As a result, sodium\ - \ and water are retained in the lumen of the nephron for urinary excretion.[A185180]\ - \ The effects that follow include reduced plasma volume, reduced venous return,\ - \ lower cardiac output, and ultimately decreased blood pressure.[A16729] Some\ - \ studies have suggested that indapamide may decrease responsiveness to pressor\ - \ agents while others have suggested it can decrease peripheral resistance.[A203627]\ - \ Although it is clear that diuresis contributes to the antihypertensive effects\ - \ of indapamide, further studies are needed to investigate the medication\u2019\ - s ability to decrease peripheral vascular resistance and relax vascular smooth\ - \ muscle.[A203627]\n\n===\n\ndisease: Hypertension\ndrug: Indapamide\n" -- completion: 'disease: Tardive Dyskinesia - - drug: Deutetrabenazine - - mechanism_links: deutetrabenazine - has metabolite - Tetrabenazine; Tetrabenazine - - decreases activity of - synaptic vesicular amine transporter (human); synaptic - vesicular amine transporter (human) - positively regulates - aminergic neurotransmitter - loading into synaptic vesicle; aminergic neurotransmitter loading into synaptic - vesicle - prevents - dopamine catabolic process; dopamine catabolic process - - negatively regulates - dopamine secretion, neurotransmission; dopamine secretion, - neurotransmission - correlated with - Tardive Dyskinesia' - prompt: "From the text below, extract the following entities in the following format:\n\ - \ndisease: \ndrug: \nmechanism_links: \n\ - \n\nText:\nThe precise mechanism of action of deutetrabenazine in mediating its\ - \ anti-chorea effects is not fully elucidated. Deutetrabenazine reversibly depletes\ - \ the levels of monoamines, such as dopamine, serotonin, norepinephrine, and histamine,\ - \ from nerve terminals via its active metabolites. The major circulating metabolites\ - \ are \u03B1-dihydrotetrabenazine [HTBZ] and \u03B2-HTBZ that act as reversible\ - \ inhibitors of VMAT2. Inhibition of VMAT2 results in decreased uptake of monoamines\ - \ into synaptic terminal and depletion of monoamine stores from nerve terminals\ - \ [FDA Label]. Deutetrabenazine contains the molecule deuterium, which is a naturally-occurring,\ - \ nontoxic hydrogen isotope but with an increased mass relative to hydrogen [A32046].\ - \ Placed at key positions, deuterium forms a stronger hydrogen bond with carbon\ - \ that requires more energy for cleavage, thus attenuating CYP2D6-mediated metabolism\ - \ without having any effect on the therapeutic target [A32046].\n\n===\n\ndisease:\ - \ Tardive Dyskinesia\ndrug: Deutetrabenazine\n" -- completion: 'disease: Hepatitis C, Chronic - - drug: Paritaprevir - - mechanism_links: ABT-450 - negatively regulates - PR:P27958; PR:P27958 - positively - regulates - viral RNA genome replication; viral RNA genome replication - in taxon - - NCBITaxon:11103; NCBITaxon:11103 - causes - Hepatitis C, Chronic' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Paritaprevir is a potent inhibitor of the NS3/4A serine protease of Hepatitis - C Virus (HCV) [FDA Label]. Following viral replication of HCV genetic material - and translation into a single polypeptide, Nonstructural Protein 3 (NS3) and its - activating cofactor Nonstructural Protein 4A (NS4A) are responsible for cleaving - it into the following structural and nonstructural proteins required for assembly - into mature virus: NS3, NS4A, NS4B, NS5A, and NS5B. By inhibiting viral protease - NS3/4A, paritaprevir therefore prevents viral replication and function. - - - === - - - disease: Hepatitis C, Chronic - - drug: Paritaprevir - - ' -- completion: 'disease: Carcinoma, Non-Small-Cell Lung - - drug: Crizotinib - - mechanism_links: crizotinib - decreases activity of - hepatocyte growth factor - receptor (human); hepatocyte growth factor receptor (human) - negatively regulates - - cell population proliferation; cell population proliferation - contributes to - - Carcinoma, Non-Small-Cell Lung' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Crizotinib is a tyrosine kinase receptor inhibitor. More specifically, it inhibits - anaplastic lymphoma kinase (ALK), hepatocyte growth factor receptor (HGFR, c-MET), - and Recepteur d''Origine Nantais (RON). Abnormalities in the ALK gene caused by - mutations or translocations may lead to expression of oncogenic fusion proteins. - In patients with NSCLC, they have the EML4-ALK gene. Crizotinib inhibits ALK tyrosine - kinase which ultimately results in decreased proliferation of cells that carry - the genetic mutation and tumour survivability. - - - === - - - disease: Carcinoma, Non-Small-Cell Lung - - drug: Crizotinib - - ' -- completion: 'disease: Prostatitis - - drug: Ciprofloxacin - - mechanism_links: Ciprofloxacin - decreases activity of - DNA gyrase subunit A - (Escherichia coli K-12); Ciprofloxacin - decreases activity of - DNA topoisomerase - 4 subunit A (Escherichia coli K-12); DNA gyrase subunit A (Escherichia coli K-12) - - positively regulates - DNA replication; DNA topoisomerase 4 subunit A (Escherichia - coli K-12) - positively regulates - DNA replication; DNA replication - occurs - in - Escherichia coli; Escherichia coli - causes - Prostatitis' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Ciprofloxacin acts on bacterial topoisomerase II (DNA gyrase) and topoisomerase - IV.[A178885] Ciprofloxacin''s targeting of the alpha subunits of DNA gyrase prevents - it from supercoiling the bacterial DNA which prevents DNA replication.[A178876,A178882] - - - === - - - disease: Prostatitis - - drug: Ciprofloxacin - - ' -- completion: 'disease: Osteoporosis, Postmenopausal - - drug: Alendronic acid - - mechanism_links: Alendronate - positively regulates - apoptotic process; apoptotic - process - located in - osteoclast; osteoclast - participates in - bone resorption; - bone resorption - causes - Osteoporosis, Postmenopausal' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Alendronic acid binds to bone hydroxyapatite[FDA Label]. Bone resorption causes - local acidification, releasing alendronic acid which is that taken into osteoclasts - by fluid-phase endocytosis[A959]. Endocytic vesicles are acidified, releasing - alendronic acid to the cytosol of osteoclasts where they induce apoptosis[A959]. - Inhibition of osteoclasts results in decreased bone resorption which is shown - through decreased urinary calcium, deoxypyridinoline and cross-linked N-telopeptidases - of type I collagen[FDA Label]. - - - === - - - disease: Osteoporosis, Postmenopausal - - drug: Alendronic acid - - ' -- completion: 'disease: Tendinopathy - - drug: Sulindac - - mechanism_links: Sulindac - decreases activity of - prostaglandin G/H synthase - 1 (human); Sulindac - decreases activity of - prostaglandin G/H synthase 2 (human); - prostaglandin G/H synthase 1 (human) - increases abundance of - Prostaglandins; - prostaglandin G/H synthase 2 (human) - increases abundance of - Prostaglandins; - Prostaglandins - participates in - inflammatory response; inflammatory response - - contributes to - Pain; Pain - manifestation of - Tendinopathy' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Sulindac''s exact mechanism of action is unknown. Its antiinflammatory effects - are believed to be due to inhibition of both COX-1 and COX-2 which leads to the - inhibition of prostaglandin synthesis. Antipyretic effects may be due to action - on the hypothalamus, resulting in an increased peripheral blood flow, vasodilation, - and subsequent heat dissipation. - - - === - - - disease: Tendinopathy - - drug: Sulindac - - ' -- completion: 'disease: Pneumonia, Aspiration - - drug: Benzylpenicillin - - mechanism_links: Penicillin G - decreases activity of - InterPro:IPR001460; InterPro:IPR001460 - - participates in - peptidoglycan biosynthetic process; peptidoglycan biosynthetic - process - positively regulates - peptidoglycan-based cell wall biogenesis; peptidoglycan-based - cell wall biogenesis - occurs in - Bacteria; Bacteria - causes - Pneumonia, Aspiration' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - By binding to specific penicillin-binding proteins (PBPs) located inside the bacterial - cell wall, penicillin G inhibits the third and last stage of bacterial cell wall - synthesis. Cell lysis is then mediated by bacterial cell wall autolytic enzymes - such as autolysins; it is possible that penicillin G interferes with an autolysin - inhibitor. - - - === - - - disease: Pneumonia, Aspiration - - drug: Benzylpenicillin - - ' -- completion: 'disease: Pulmonary Disease, Chronic Obstructive - - drug: Umeclidinium - - mechanism_links: GSK573719 - decreases activity of - muscarinic acetylcholine - receptor M2 (human); GSK573719 - decreases activity of - muscarinic acetylcholine - receptor M3 (human); muscarinic acetylcholine receptor M2 (human) - participates - in - response to acetylcholine; muscarinic acetylcholine receptor M3 (human) - - participates in - response to acetylcholine; response to acetylcholine - positively - regulates - smooth muscle contraction; smooth muscle contraction - located in - - bronchus; bronchus - location of - inflammatory response; inflammatory response - - causes - Pulmonary Disease, Chronic Obstructive' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Umeclidinium is a long-acting, antimuscarinic agent, which is often referred to - as an anticholinergic. It has similar affinity to the subtypes of muscarinic receptors - M1 to M5. In the airways, it exhibits pharmacological effects through the inhibition - of M3 receptor at the smooth muscle leading to bronchodilation. - - - === - - - disease: Pulmonary Disease, Chronic Obstructive - - drug: Umeclidinium - - ' -- completion: 'disease: Psoriasis - - drug: Methylprednisolone - - mechanism_links: Methylprednisolone - increases activity of - glucocorticoid receptor - (human); glucocorticoid receptor (human) - increases activity of - annexin A1 - (human); glucocorticoid receptor (human) - decreases activity of - prostaglandin - G/H synthase 1 (human); glucocorticoid receptor (human) - decreases activity of - - prostaglandin G/H synthase 2 (human); annexin A1 (human) - decreases activity - of - cytosolic phospholipase A2 (human); prostaglandin G/H synthase 1 (human) - - positively regulates - prostaglandin biosynthetic process; prostaglandin G/H - synthase 2 (human) - positively regulates - prostaglandin biosynthetic process; - cytosolic phospholipase A2 (human) - positively regulates - leukotriene biosynthetic - process; cytosolic phospholipase A2 (human) - positively regulates - prostaglandin - biosynthetic process; leukotriene biosynthetic process - positively correlated - with - inflammatory response; prostaglandin biosynthetic process - positively - correlated with - inflammatory response; inflammatory response - positively correlated - with - HP:0011123; HP:0011123 - positively correlated with - Psoriasis' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - The short term effects of corticosteroids are decreased vasodilation and permeability - of capillaries, as well as decreased leukocyte migration to sites of inflammation.[A187463] - Corticosteroids binding to the glucocorticoid receptor mediates changes in gene - expression that lead to multiple downstream effects over hours to days.[A187463] - Lower doses of corticosteroids provide an anti-inflammatory effect, while higher - doses are immunosuppressive.[A187463] High doses of glucocorticoids for an extended - period bind to the mineralocorticoid receptor, raising sodium levels and decreasing - potassium levels.[A187463] - - - === - - - disease: Psoriasis - - drug: Methylprednisolone - - ' -template: drug.DrugMechanism diff --git a/tests/input/training/training-mendelian-disease-001.jsonl b/tests/input/training/training-mendelian-disease-001.jsonl deleted file mode 100644 index d5ee144c6..000000000 --- a/tests/input/training/training-mendelian-disease-001.jsonl +++ /dev/null @@ -1,2 +0,0 @@ -{"prompt": "Amelogenesis imperfecta type 1K (AI1K) is characterized by hypoplastic enamel of all teeth. In some individuals, the pulp chambers may be enlarged and some molars may exhibit taurodontism Amelogenesis imperfecta segregated as an autosomal dominant trait in the family described by Smith et al. amelogenesis imperfecta type IK (AI1K) is caused by heterozygous mutation in the SP6 gene (608613) on chromosome 17q21.", "completion": "name: amelogenesis imperfecta type 1K\nsynonyms:\n- AI1K\nsubclass_of:\n- amelogenesis imperfecta\ngenes:\n- SP6\ninheritance: autosomal dominant\nphenotypes:\n- hypoplastic enamel\n- pulp chamber enlargement\n- taurodontism\n"} -{"prompt": "Familial hemiplegic migraine-2 (FHM-2) is a rare subtype of familial hemiplegic migraine (FHM) characterized by migraine with aura, nystagmus, and progressive cognitive decline. It is caused by mutations in ATP1A2.", "completion": "name: Familial hemiplegic migraine-2\nsynonyms:\n- FHM2\n- Familial hemiplegic migraine type 2\nsubclass_of:\n- familial hemiplegic migraine\ngenes:\n- ATP1A2\ninheritance: autosomal dominant\nphenotypes:\n- migraine with aura\n- nystagmus\n- progressive cognitive impairment\n"} diff --git a/tests/input/training/training-mendelian-disease-001.yaml b/tests/input/training/training-mendelian-disease-001.yaml deleted file mode 100644 index 70b99a6ef..000000000 --- a/tests/input/training/training-mendelian-disease-001.yaml +++ /dev/null @@ -1,65 +0,0 @@ -base_engine: code-davinci-002 -template: mendelian_disease.MendelianDisease -examples: - - prompt: >- - From the text below, extract the following entities in the following YAML:: - - name: - synonyms: - subclass_of: - genes: - inheritance: - phenotypes: - - Text: - Amelogenesis imperfecta type 1K (AI1K) is characterized by hypoplastic enamel of all teeth. In some individuals, the pulp chambers may be enlarged and some molars may exhibit taurodontism - Amelogenesis imperfecta segregated as an autosomal dominant trait in the family described by Smith et al. - amelogenesis imperfecta type IK (AI1K) is caused by heterozygous mutation in the SP6 gene (608613) on chromosome 17q21. - ### - completion: - name: amelogenesis imperfecta type 1K - synonyms: - - AI1K - subclass_of: - - amelogenesis imperfecta - genes: - - SP6 - inheritance: autosomal dominant - phenotypes: - - hypoplastic enamel - - pulp chamber enlargement - - taurodontism - - prompt: >- - From the text below, extract the following entities in the following YAML:: - - name: - synonyms: - subclass_of: - genes: - inheritance: - phenotypes: - - Familial hemiplegic migraine-2 (FHM-2) is a rare subtype of familial hemiplegic migraine (FHM) characterized by migraine with aura, - nystagmus, and progressive cognitive decline. It is caused by mutations in ATP1A2. - ### - completion: - name: Familial hemiplegic migraine-2 - synonyms: - - FHM2 - - Familial hemiplegic migraine type 2 - subclass_of: - - familial hemiplegic migraine - genes: - - ATP1A2 - inheritance: autosomal dominant - phenotypes: - - migraine with aura - - nystagmus - - progressive cognitive impairment -test: - - prompt: >- - neurodevelopmental disorder with eye movement abnormalities and ataxia (NEDEMA) is caused by heterozygous mutation in the FRMD5 gene. - Neurodevelopmental disorder with eye movement abnormalities and ataxia (NEDEMA) is characterized by global developmental delay apparent from infancy. Affected individuals show delayed walking with an unsteady gait, variably impaired intellectual development, learning disabilities, and speech difficulties. Abnormal eye movements, which are often noted in early childhood, include opsoclonus, nystagmus, and strabismus. Some patients have seizures, which may be refractor. - Lu et al. (2022) reported 8 unrelated patients, ranging in age from 3 to 27 years, with a similar neurodevelopmental disorder and de novo heterozygous mutations in the FRMD5 gene. The patients presented in infancy with global developmental delay and showed delayed walking, variably impaired intellectual development, and poor or absent speech. Those that achieved walking had an unsteady gait, and most had hypotonia and ataxia; a few demonstrated spasticity. Some patients had dyslexia or learning disabilities. Six patients had seizures or evidence of seizures, including 2 patients who were diagnosed in infancy with refractory epilepsy and West syndrome. All patients had eye movement abnormalities, ranging from strabismus and intermittent esotropia to opsoclonus and nystagmus. Two were visually impaired and had myopia or hypermetropia. Brain imaging was normal in most patients, but one had pachygyria and another had delayed myelination. A few patients had additional features such as myoclonus, dystonia, dyskinesia, and behavioral problems. - Inheritance: - The heterozygous mutations in the FRMD5 gene that were identified in most patients with NEDEMA by Lu et al. (2022) occurred de novo. diff --git a/tests/integration/test_cli/test_cli.py b/tests/integration/test_cli/test_cli.py index 2452eeddc..c98e17805 100644 --- a/tests/integration/test_cli/test_cli.py +++ b/tests/integration/test_cli/test_cli.py @@ -1,12 +1,10 @@ """Tests the command-line interface.""" import unittest -import inflection from click.testing import CliRunner -import tests.integration.test_knowledge_engines.test_cases as extract_cases -from ontogpt.cli import main -from tests import CASES_DIR, OUTPUT_DIR +from talisman.cli import main +from tests import OUTPUT_DIR from tests.integration.test_knowledge_engines.test_enrichment import PEX CACHE_DB = str(OUTPUT_DIR / "cli_cache.db") @@ -27,86 +25,6 @@ def test_main_help(self): self.assertIn("halo", out) self.assertEqual(0, result.exit_code) - def test_extract(self): - for case in extract_cases.CASES: - template, input_name = case - input_file = str(CASES_DIR / f"{input_name}.txt") - fmts = ["yaml", "html", "md"] - if template == "recipe": - fmts.append("owl") - for fmt in fmts: - output_file = str(CLI_OUTPUT_DIR / f"{input_name}.{fmt}") - cmd = [ - "--cache-db", - CACHE_DB, - "extract", - "-t", - template, - input_file, - "-O", - fmt, - "-o", - output_file, - ] - print(cmd) - result = self.runner.invoke(main, cmd) - self.assertEqual(0, result.exit_code) - out = result.stdout - print(out) - - def test_pubmed_extract(self): - cases = [ - ("PMID:32044947", "treatment.DiseaseTreatmentSummary"), - ] - for pmid, template in cases: - for fmt in ["yaml", "html"]: - output_file = str(CLI_OUTPUT_DIR / f"pmid-{pmid}-{template}.{fmt}") - cmd = [ - "--cache-db", - CACHE_DB, - "pubmed-extract", - "-t", - template, - pmid, - "-O", - fmt, - "-o", - output_file, - ] - print(cmd) - result = self.runner.invoke(main, cmd) - self.assertEqual(0, result.exit_code) - out = result.stdout - print(out) - - def test_search_and_extract(self): - cases = [ - ("treatment.DiseaseTreatmentSummary", "COVID-19", ["review"]), - ] - for template, term, keywords in cases: - for fmt in ["yaml", "html"]: - safe_term = inflection.underscore(term) - output_file = str(CLI_OUTPUT_DIR / f"{template}-search-{safe_term}.{fmt}") - cmd = [ - "--cache-db", - CACHE_DB, - "search-and-extract", - "-t", - template, - term, - "-O", - fmt, - "-o", - output_file, - ] - for kw in keywords: - cmd.extend(["-k", kw]) - print(cmd) - result = self.runner.invoke(main, cmd) - self.assertEqual(0, result.exit_code) - out = result.stdout - print(out) - def test_enrichment(self): ids = [id for id, _ in PEX] cmd = ["enrichment"] + ids diff --git a/tests/integration/test_clients/__init__.py b/tests/integration/test_clients/__init__.py deleted file mode 100644 index e69de29bb..000000000 diff --git a/tests/integration/test_clients/test_openai_client.py b/tests/integration/test_clients/test_openai_client.py deleted file mode 100644 index cdccdac0f..000000000 --- a/tests/integration/test_clients/test_openai_client.py +++ /dev/null @@ -1,222 +0,0 @@ -"""Open AI client tests.""" -import re -import unittest - -import yaml - -from ontogpt.clients.openai_client import OpenAIClient -from tests import PROMPTS_FILE - -PROMPT = """ -example: - -name: ornithine biosynthesis -def: The biological process that results in the output of ornithine, ornithine, - an amino acid only rarely found in proteins, but which is important in living - organisms as an intermediate in the reactions of the urea cycle and in arginine biosynthesis. -parent: biosynthetic process -differentia: - outputs: ornithine - -=== - -name: selenocysteine biosynthesis -""" - -CODE_PROMPT_GENERALIZATION = """ -- name: ornithine biosynthesis - description: The biological process that results in the output of ornithine, - ornithine, an amino acid only rarely found in proteins, but which is important in - living organisms as an intermediate in the reactions of the urea - cycle and in arginine biosynthesis - subclass_of: - - amino acid biosynthetic process - pattern: - - biosynthetic process - outputs: - - ornithine -- name: selenocysteine biosynthesis -""" - -CODE_PROMPT_EXTRACT = """ -- abstract: >- - Amelogenesis imperfecta type 1K (AI1K) is characterized by hypoplastic enamel of all teeth. - In some individuals, the pulp chambers may be enlarged and some molars may exhibit taurodontism - Amelogenesis imperfecta segregated as an autosomal dominant trait in the family described by - Smith et al. - amelogenesis imperfecta type IK (AI1K) is caused by heterozygous mutation in the - SP6 gene (608613) on chromosome 17q21. - - name: amelogenesis imperfecta type 1K - synonyms: - - AI1K - subclass_of: - - amelogenesis imperfecta - genes: - - SP6 - inheritance: autosomal dominant - phenotypes: - - hypoplastic enamel - - pulp chamber enlargement - - taurodontism -- abstract: >- - Familial hemiplegic migraine-2 (FHM-2) is a rare subtype of familial hemiplegic migraine (FHM) - characterized by migraine with aura, - nystagmus, and progressive cognitive decline. It is caused by mutations in ATP1A2. - name: Familial hemiplegic migraine-2 - synonyms: - - FHM2 - - Familial hemiplegic migraine type 2 - subclass_of: - - familial hemiplegic migraine - genes: - - ATP1A2 - inheritance: autosomal dominant - phenotypes: - - migraine with aura - - nystagmus - - progressive cognitive impairment -- abstract: >- - neurodevelopmental disorder with eye movement abnormalities and ataxia (NEDEMA) - is caused by heterozygous mutation in the FRMD5 gene. - Neurodevelopmental disorder with eye movement abnormalities and ataxia (NEDEMA) - is characterized by global developmental delay apparent from infancy. - Affected individuals show delayed walking with an unsteady gait, - variably impaired intellectual development, learning disabilities, - and speech difficulties. Abnormal eye movements, which are often noted in early childhood, - include opsoclonus, nystagmus, and strabismus. Some patients have seizures, - which may be refractor. - Lu et al. (2022) reported 8 unrelated patients, ranging in age from 3 to 27 years, - with a similar neurodevelopmental disorder and de novo heterozygous mutations - in the FRMD5 gene. The patients presented in infancy with global developmental - delay and showed delayed walking, variably impaired intellectual development, - and poor or absent speech. Those that achieved walking had an unsteady gait, - and most had hypotonia and ataxia; a few demonstrated spasticity. - Some patients had dyslexia or learning disabilities. Six patients had seizures - or evidence of seizures, including 2 patients who were diagnosed in infancy - with refractory epilepsy and West syndrome. All patients had eye movement abnormalities, - ranging from strabismus and intermittent esotropia to opsoclonus and nystagmus. - Two were visually impaired and had myopia or hypermetropia. Brain imaging was normal - in most patients, but one had pachygyria and another had delayed myelination. - A few patients had additional features such as myoclonus, dystonia, dyskinesia, - and behavioral problems. - Inheritance: - The heterozygous mutations in the FRMD5 gene that were identified in most - patients with NEDEMA by Lu et al. (2022) occurred de novo. - - name: """ - -TUNED_TEST_PROMPT = """ -From the text below, extract the following entities in the following YAML:: - -name: -synonyms: -subclass_of: -genes: -inheritance: -phenotypes: - -Text: -neurodevelopmental disorder with eye movement abnormalities and ataxia (NEDEMA) -is caused by heterozygous mutation in the FRMD5 gene. -Neurodevelopmental disorder with eye movement abnormalities and ataxia (NEDEMA) -is characterized by global developmental delay apparent from infancy. -Affected individuals show delayed walking with an unsteady gait, variably impaired -intellectual development, learning disabilities, and speech difficulties. -Abnormal eye movements, which are often noted in early childhood, include opsoclonus, -nystagmus, and strabismus. Some patients have seizures, which may be refractor. -Lu et al. (2022) reported 8 unrelated patients, ranging in age from 3 to 27 years, -with a similar neurodevelopmental disorder and de novo heterozygous mutations in the FRMD5 gene. -The patients presented in infancy with global developmental delay and showed delayed walking, -variably impaired intellectual development, and poor or absent speech. -Those that achieved walking had an unsteady gait, and most had hypotonia and ataxia; -a few demonstrated spasticity. Some patients had dyslexia or learning disabilities. -Six patients had seizures or evidence of seizures, including 2 patients who were diagnosed -in infancy with refractory epilepsy and West syndrome. All patients had eye movement -abnormalities, ranging from strabismus and intermittent esotropia to opsoclonus and nystagmus. -Two were visually impaired and had myopia or hypermetropia. Brain imaging was -normal in most patients, but one had pachygyria and another had delayed myelination. -A few patients had additional features such as myoclonus, dystonia, dyskinesia, and -behavioral problems. -Inheritance: -### -""" - - -class TestCompletion(unittest.TestCase): - """Test annotation.""" - - def setUp(self) -> None: - """Set up.""" - self.llm_client = OpenAIClient() - - def test_all_prompts(self): - """Test all prompts.""" - prompt_doc = yaml.safe_load(open(PROMPTS_FILE)) - default_engine = prompt_doc.get("default_engine", "gpt-3.5-turbo-instruct") - for prompt in prompt_doc["prompts"]: - prompt_text = prompt["prompt"] - if not isinstance(prompt_text, str): - prompt_text = yaml.dump(prompt_text) - engine = prompt.get("engine", default_engine) - client = OpenAIClient(model=engine) - pre_prompt = prompt.get("pre_prompt", "") - prompt_text = "".join([pre_prompt, prompt_text]) - print(f"## Testing prompt [{engine}: [{len(prompt_text)}] {prompt_text}") - ann = client.complete(prompt_text) - print(f"## Response: len={len(ann)}") - print(ann) - for expected in prompt.get("expected", []): - self.assertTrue(re.search(expected, ann, re.IGNORECASE)) - - def test_completion(self): - """Tests end to end knowledge extraction.""" - client = self.llm_client - ann = client.complete(PROMPT) - print(ann) - - def test_drug_mech_db(self): - """Test drug mechanism database.""" - client = self.llm_client - ann = client.complete( - """ - Explain the chain of events that relate a drug to a disease as a semi-colon separated list. - - Example: - - cortisone treats keratitis: - - cortisone increases glucocorticoid receptor; glucocorticoid receptor regulates COX; - COX regulates prostaglandin; prostaglandin regulates inflammation; - inflammation cause keratitis - - Text: - - imatinib treats chronic myeloid leukemia: - """ - ) - print(ann) - - def test_code_completion_generalization(self): - """Tests structured responses.""" - engine = "gpt-3.5-turbo" - client = OpenAIClient(model=engine) - print(len(CODE_PROMPT_GENERALIZATION)) - ann = client.complete(CODE_PROMPT_GENERALIZATION) - print(ann) - - def test_extract_via_code_completion(self): - """Tests structured responses.""" - engine = "gpt-3.5-turbo" - client = OpenAIClient(model=engine) - ann = client.complete(CODE_PROMPT_EXTRACT) - print(ann) - - @unittest.skip("Doesn't work well with current OpenAI API") - def test_fine_tuned(self): - engine = ( - "davinci:ft-lawrence-berkeley-national-laboratory:mendelian-disease-2022-12-22-00-53-36" - ) - client = OpenAIClient(model=engine) - ann = client.complete(TUNED_TEST_PROMPT) - print(ann) diff --git a/tests/integration/test_clients/test_pubmed_client.py b/tests/integration/test_clients/test_pubmed_client.py deleted file mode 100644 index bf33938a5..000000000 --- a/tests/integration/test_clients/test_pubmed_client.py +++ /dev/null @@ -1,33 +0,0 @@ -"""PubMed client tests.""" -import unittest - -from ontogpt.clients import PubmedClient - - -class TestCompletion(unittest.TestCase): - """Test annotation.""" - - def setUp(self) -> None: - """Set up.""" - self.client = PubmedClient() - - def test_lookup(self): - """Test PMID lookup.""" - text = self.client.text("PMID:28449677") - print(text) - - def test_multiple_lookup(self): - """Test lookup of multiple PMIDs.""" - text = self.client.text(["25662031", "28449677"]) - print(text) - - def test_malformed_lookup(self): - """Text lookup of invalid PMID.""" - text = self.client.text("jelly") - self.assertFalse(text) - - def test_search(self): - """Test PMID search.""" - print("Testing...") - results = list(self.client.search("Long covid", ["review", "treatment", "therapies"])) - print(results) diff --git a/tests/integration/test_evaluation/test_eval_ctd.py b/tests/integration/test_evaluation/test_eval_ctd.py deleted file mode 100644 index 404cc3650..000000000 --- a/tests/integration/test_evaluation/test_eval_ctd.py +++ /dev/null @@ -1,89 +0,0 @@ -"""Core tests.""" -import logging -import unittest - -from ontogpt.evaluation.ctd import eval_ctd -from ontogpt.evaluation.ctd.eval_ctd import EvalCTD -from ontogpt.io.yaml_wrapper import dump_minimal_yaml -from tests import OUTPUT_DIR - -EXTRACTIONS_OUT = OUTPUT_DIR / "eval-ctd-extractions.yaml" - -ALT_EXAMPLE = """Title: Cocaine induced myocardial ischemia. -Abstract: We report a case of myocardial ischemia induced by cocaine. -The ischemia probably induced by coronary artery spasm was reversed by -nitroglycerin and calcium blocking agents. -""" - -EXAMPLE = """Title: Downbeat nystagmus associated with intravenous patient-controlled -administration of morphine. -Abstract: IMPLICATIONS: This case documents a patient who developed dizziness with -downbeating nystagmus while receiving a relatively large dose of IV patient-controlled -analgesia morphine.Although there have been case reports of epidural morphine with these -symptoms and signs,this has not been previously documented with IV or patient-controlled -analgesia morphine. -""" - -logger = logging.getLogger(eval_ctd.__name__) -logger.setLevel(logging.INFO) - - -class TestCTD(unittest.TestCase): - """Test CTD evaluation.""" - - def setUp(self) -> None: - """Set up all engines in advance.""" - self.engine = EvalCTD() - - def test_load_test_sets(self): - docs = list(self.engine.load_test_cases()) - self.assertGreater(len(docs), 100) - for d in docs: - logger.debug(dump_minimal_yaml(d)) - - def test_eval(self): - evaluator = self.engine - evaluator.num_tests = 1 - eos = evaluator.eval() - with open(EXTRACTIONS_OUT, "w") as f: - f.write(dump_minimal_yaml(eos, minimize=False)) - # yaml.dump(eos.dict(), f) - - def test_individual_case(self): - evaluator = self.engine - ke = evaluator.extractor - r = ke.extract_from_text(EXAMPLE) - print(dump_minimal_yaml(r)) - - def test_is_valid_identifier(self): - evaluator = self.engine - ke = evaluator.extractor - chemical = ke.schemaview.get_class("Chemical") - disease = ke.schemaview.get_class("Disease") - cases = [ - ("MESH:C1", chemical, False, "too short"), - ("MESH:D009020", chemical, True, "valid chemical"), - ("MESH:D000071256", chemical, False, "too long"), - ("CHEBI:12345", chemical, False, "not an requested ID space"), - ("MESH:D054556", chemical, False, "disease"), - ("MESH:D054556", disease, True, "valid disease"), - ] - for case, cls, valid, reason in cases: - self.assertEqual(valid, ke.is_valid_identifier(case, cls), reason) - - def test_normalize_identifier(self): - evaluator = self.engine - ke = evaluator.extractor - chemical = ke.schemaview.get_class("Chemical") - disease = ke.schemaview.get_class("Disease") - cases = [ - ("CHEBI:17303", chemical, ["MESH:D009020"], "via node normalization"), - ("MESH:D009020", chemical, ["MESH:D009020"], "reflexive (chemical)"), - ("MESH:D054556", chemical, [], "disease"), - ("MESH:D054556", disease, ["MESH:D054556"], "reflexive (disease)"), - ("MESH:D009020", disease, [], "disease"), - ] - for case, cls, expected, reason in cases: - normalized = list(ke.normalize_identifier(case, cls)) - print(normalized) - self.assertCountEqual(expected, normalized, reason) diff --git a/tests/integration/test_evaluation/test_eval_drugmechdb.py b/tests/integration/test_evaluation/test_eval_drugmechdb.py deleted file mode 100644 index ffc74d397..000000000 --- a/tests/integration/test_evaluation/test_eval_drugmechdb.py +++ /dev/null @@ -1,178 +0,0 @@ -"""Core tests.""" -import unittest - -import yaml - -from ontogpt.engines.spires_engine import SPIRESEngine -from ontogpt.evaluation.drugmechdb.datamodel.drugmechdb import Graph, Mechanism -from ontogpt.evaluation.drugmechdb.eval_drugmechdb import EvalDrugMechDB, _fix_source_mechanism -from tests import OUTPUT_DIR - -NORMALIZED_OUT = OUTPUT_DIR / "drugmechdb-normalized.yaml" -PREDICTIONS_OUT = OUTPUT_DIR / "eval-drugmechdb-predictions.yaml" -EXTRACTION_OUT = OUTPUT_DIR / "eval-drugmechdb-extraction.yaml" -TRAINING_OUT = OUTPUT_DIR / "training-drugmechdb.yaml" - -EXAMPLE_SOURCE = """ -- directed: true - graph: - _id: DB00316_MESH_D018771_1 - disease: Arthralgia - disease_mesh: MESH:D018771 - drug: Acetaminophen - drug_mesh: MESH:D000082 - drugbank: DB:DB00316 - links: - - key: decreases activity of - source: MESH:D000082 - target: UniProt:P23219 - - key: decreases activity of - source: MESH:D000082 - target: UniProt:P35354 - - key: decreases activity of - source: MESH:D000082 - target: UniProt:Q15185 - - key: positively regulates - source: UniProt:P23219 - target: GO:0001516 - - key: positively regulates - source: UniProt:P35354 - target: GO:0001516 - - key: positively regulates - source: UniProt:Q15185 - target: GO:0001516 - - key: increases abundance of - source: GO:0001516 - target: MESH:D011453 - - key: positively correlated with - source: MESH:D011453 - target: MESH:D018771 - multigraph: true - nodes: - - id: MESH:D000082 - label: Drug - name: Acetaminophen - - id: UniProt:P23219 - label: Protein - name: Prostaglandin G/H synthase 1 - - id: UniProt:P35354 - label: Protein - name: Prostaglandin G/H synthase 2 - - id: UniProt:Q15185 - label: Protein - name: Prostaglandin E synthase 3 - - id: GO:0001516 - label: BiologicalProcess - name: prostaglandin biosynthetic process - - id: MESH:D011453 - label: ChemicalSubstance - name: Prostaglandins - - id: MESH:D018771 - label: Disease - name: Arthralgia - reference: - - https://go.drugbank.com/drugs/DB00316#mechanism-of-action - - https://www.uniprot.org/uniprot/P23219#function - - https://www.uniprot.org/uniprot/P35354#function - - https://www.uniprot.org/uniprot/Q15185#function - - https://en.wikipedia.org/wiki/Arthralgia -""" - - -class TestDrugMechDB(unittest.TestCase): - """Test GO evaluation.""" - - def setUp(self) -> None: - """Set up all engines in advance.""" - self.engine = EvalDrugMechDB() - - def test_data_model(self): - g = Graph(id="x") - m = Mechanism( - directed=True, - graph={ - "id": "DB11888_MESH_D007251_1", - }, - ) - - def test_load_exemplars(self): - mechanisms = self.engine.load_exemplars() - objs = [m.dict() for m in mechanisms] - print(yaml.dump(objs[0:5])) - self.assertGreater(len(mechanisms), 0) - - def test_transform(self): - objs = yaml.safe_load(EXAMPLE_SOURCE) - obj = _fix_source_mechanism(objs[0]) - src_mechanism = Mechanism(**obj) - r = self.engine.transform_mechanism(src_mechanism) - print(yaml.dump(r.dict())) - - def test_load_and_transform_source_database(self): - """ - Tests the ability to translate the source DrugMechDB yaml into Llama model. - - This is currently slow: this test may be skipped. - - If the source YAML changes, then re-run this and copy the file from - the output directory (drugmechdb-normalized.yaml) to - - :return: - """ - mechanisms = self.engine.load_and_transform_source_database() - print(f"Loaded {len(mechanisms)} mechanisms") - objs = [m.dict() for m in mechanisms] - with open(NORMALIZED_OUT, "w") as f: - yaml.dump(objs, f) - print(yaml.dump(objs[0:5])) - self.assertGreater(len(mechanisms), 0) - - def test_load_target_database(self): - mechanisms = self.engine.load_target_database() - print(f"Loaded {len(mechanisms)} mechanisms") - objs = [m.dict() for m in mechanisms[0:5]] - print(yaml.dump(objs)) - self.assertGreater(len(mechanisms), 0) - - def test_drug_to_mechanism_text(self): - self.assertTrue( - self.engine.drug_to_mechanism_text["drugbank:DB00005"].startswith( - "There are two distinct receptors" - ) - ) - - def test_training_set(self): - evaluator = self.engine - ke = evaluator.extractor - training_set = list(evaluator.create_training_set(100)) - t = dict(base_model="gpt-3.5-turbo-instruct", template=ke.template, examples=training_set) - with open(TRAINING_OUT, "w") as f: - yaml.dump(t, f) - # print(yaml.dump(training_set)) - - def test_eval_extraction(self): - evaluator = self.engine - evaluator.num_tests = 100 - eos = evaluator.eval() - with open(EXTRACTION_OUT, "w") as f: - yaml.dump(eos.dict(), f) - - @unittest.skip("Skip this test because it takes a long time and is more expensive") - def test_eval_fine_tuned_extraction(self): - evaluator = EvalDrugMechDB() - ft = "davinci:ft-lawrence-berkeley-national-laboratory:drugmechdb-001-2022-12-22-02-25-40" - evaluator.extractor = SPIRESEngine("drug.DrugMechanism", engine=ft) - evaluator.num_tests = 40 - eos = evaluator.eval() - with open(EXTRACTION_OUT, "w") as f: - yaml.dump(eos.dict(), f) - - def test_eval_generalize(self): - evaluator = self.engine - evaluator.num_tests = 3 - evaluator.num_training = 3 - mechanisms = self.engine.load_exemplars() - evaluator.data = mechanisms - eos = evaluator.eval_path_prediction() - with open(PREDICTIONS_OUT, "w") as f: - yaml.dump(eos.dict(), f) diff --git a/tests/integration/test_evaluation/test_eval_enrichment.py b/tests/integration/test_evaluation/test_eval_enrichment.py index b4e8625e8..8f8c27d22 100644 --- a/tests/integration/test_evaluation/test_eval_enrichment.py +++ b/tests/integration/test_evaluation/test_eval_enrichment.py @@ -5,9 +5,9 @@ import yaml from oaklib import get_adapter -from ontogpt.evaluation.enrichment.eval_enrichment import EvalEnrichment -from ontogpt.io.yaml_wrapper import dump_minimal_yaml -from ontogpt.utils.gene_set_utils import GeneSet, fill_missing_gene_set_values, load_gene_sets +from talisman.evaluation.enrichment.eval_enrichment import EvalEnrichment +from talisman.io.yaml_wrapper import dump_minimal_yaml +from talisman.utils.gene_set_utils import GeneSet, fill_missing_gene_set_values, load_gene_sets from tests import GENE_SETS_DIR, INPUT_DIR, OUTPUT_DIR RESULTS_PATH = OUTPUT_DIR / "enrichment_results" diff --git a/tests/integration/test_evaluation/test_eval_go.py b/tests/integration/test_evaluation/test_eval_go.py deleted file mode 100644 index dc06591c6..000000000 --- a/tests/integration/test_evaluation/test_eval_go.py +++ /dev/null @@ -1,43 +0,0 @@ -"""Core tests.""" -import unittest - -import yaml - -from ontogpt.evaluation.go.eval_go import EvalGO, EvaluationObjectSetGO -from ontogpt.templates.metabolic_process import MetabolicProcess -from tests import OUTPUT_DIR - -EXAMPLES_OUT = OUTPUT_DIR / "eval-go-examples.yaml" -PREDICTIONS_OUT = OUTPUT_DIR / "eval-go-predictions.yaml" - - -class TestEvalGO(unittest.TestCase): - """Test GO evaluation.""" - - def setUp(self) -> None: - """Set up all engines in advance.""" - self.engine = EvalGO() - - def test_dm(self): - mp = MetabolicProcess( - id="GO:0008152", - ) - eos = EvaluationObjectSetGO(test=[mp], training=[]) - print(yaml.dump(eos.dict())) - - def test_create_test_and_training(self): - engine = self.engine - ke = engine.extractor - eos = engine.create_test_and_training() - with open(EXAMPLES_OUT, "w") as f: - yaml.dump(eos.dict(), f) - for t in eos.test: - print(yaml.dump(t.dict())) - ser = ke.serialize_object(t) - print(f"Serialized: {ser}") - - def test_eval_predictions(self): - engine = self.engine - eos = engine.eval() - with open(PREDICTIONS_OUT, "w") as f: - yaml.dump(eos.dict(), f) diff --git a/tests/integration/test_evaluation/test_eval_hpoa.py b/tests/integration/test_evaluation/test_eval_hpoa.py deleted file mode 100644 index bd5574eb6..000000000 --- a/tests/integration/test_evaluation/test_eval_hpoa.py +++ /dev/null @@ -1,67 +0,0 @@ -"""Core tests for Human Phenotype Ontology Annotations (HPOA) evaluation.""" -import unittest - -import yaml - -from ontogpt.evaluation.hpoa.eval_hpoa import EvalHPOA -from tests import OUTPUT_DIR - -NORMALIZED_OUT = OUTPUT_DIR / "hpoa-normalized.yaml" -PREDICTIONS_OMIM_OUT = OUTPUT_DIR / "eval-hpoa-predictions-omim.yaml" -PREDICTIONS_PUBS_OUT = OUTPUT_DIR / "eval-hpoa-predictions-pubs.yaml" -PREDICTIONS_ALL_OUT = OUTPUT_DIR / "eval-hpoa-predictions-all.yaml" - - -class Testhpoa(unittest.TestCase): - """Test HPOA evaluation.""" - - def setUp(self) -> None: - """Set up all engines in advance.""" - self.engine = EvalHPOA() - - def test_load_hpoa(self): - diseases = self.engine.annotations_to_diseases() - objs = [m.model_dump() for m in diseases] - print(yaml.dump(objs[0:3])) - self.assertGreater(len(diseases), 0) - - def test_diseases(self): - diseases = self.engine.diseases() - for test_case in diseases[0:2]: - text = self.engine.disease_text(test_case.id) - self.assertIsNotNone(text) - self.assertGreater(len(text), 100) - objs = [m.model_dump() for m in diseases] - print(yaml.dump(objs[0:3])) - self.assertGreater(len(diseases), 0) - - def test_diseases_by_publication(self): - t2d = self.engine.diseases_by_publication() - t2d_sample = {k: t2d[k] for k in list(t2d)[0:2]} - for k, disease in t2d_sample.items(): - text = self.engine.disease_text(disease.id) - self.assertIsNotNone(text) - self.assertGreater(len(text), 100) - print(f"## {k}: {disease.id} ") - print(yaml.dump(disease.model_dump())) - - def test_eval_pubs(self): - evaluator = self.engine - eos = evaluator.eval("pubs") - with open(PREDICTIONS_PUBS_OUT, "w") as f: - yaml.dump(eos.model_dump(), f) - - @unittest.skip("Need to retrieve more OMIM texts - stochastic") - def test_eval_all(self): - evaluator = self.engine - eos = evaluator.eval("all") - with open(PREDICTIONS_ALL_OUT, "w") as f: - yaml.dump(eos.model_dump(), f) - - @unittest.skip("Need to retrieve more OMIM texts - stochastic") - def test_eval_omim(self): - """Evaluates extraction purely from OMIM texts.""" - evaluator = self.engine - eos = evaluator.eval("omim") - with open(PREDICTIONS_OMIM_OUT, "w") as f: - yaml.dump(eos.model_dump(), f) diff --git a/tests/integration/test_knowledge_engines/test_cases.py b/tests/integration/test_knowledge_engines/test_cases.py deleted file mode 100644 index eec95b86d..000000000 --- a/tests/integration/test_knowledge_engines/test_cases.py +++ /dev/null @@ -1,69 +0,0 @@ -"""Core tests.""" -import pickle -import unittest - -from ontogpt.engines.spires_engine import SPIRESEngine -from ontogpt.io.yaml_wrapper import dump_minimal_yaml -from tests import CASES_DIR, OUTPUT_DIR - -CASES = [ - ("recipe", "recipe-palak-paneer"), - ("treatment", "treatment-schiz"), - ("recipe.Recipe", "recipe-spaghetti"), - ("recipe.Recipe", "recipe-tortilla-soup"), - ("recipe.Recipe", "recipe-egg-noodles"), - ("mendelian_disease.MendelianDisease", "mendelian-disease-cmt2e-summary"), - ("mendelian_disease.MendelianDisease", "mendelian-disease-cmt2e"), - ("drug.DrugMechanism", "drug-DB00316-moa"), - ("metagenome_study.Study", "environment-jgi2"), - ("environmental_sample.Study", "environment-jgi1"), - ("reaction.ReactionDocument", "reaction-20657015"), - ("reaction.GeneToReaction", "reaction-21290071"), - ("gocam.GoCamAnnotations", "gocam-27929086"), - ("gocam.GoCamAnnotations", "gocam-33246504"), - ("gocam.GoCamAnnotations", "gocam-betacat"), - ("environmental_sample.Study", "environmental-sample-hyporheic"), - ("treatment.DiseaseTreatmentSummary", "treatment-marfan"), - ("treatment.DiseaseTreatmentSummary", "treatment-eds"), - ("mendelian_disease.MendelianDisease", "mendelian-disease-sly"), - ("mendelian_disease.MendelianDisease", "mendelian-disease-marfan"), - ("environmental_sample.Study", "amphibian_skin"), - ("environmental_sample.Study", "human_urban_green_space"), - ("environmental_sample.Study", "human_smoking_China"), -] - - -class TestCases(unittest.TestCase): - """Test annotation.""" - - def setUp(self) -> None: - """Set up all engines in advance.""" - ke_map = {} - for template, _ in CASES: - ke_map[template] = SPIRESEngine(template, recurse=True, auto_prefix="AUTO") - self.ke_map = ke_map - - def test_cases(self): - """Tests end to end knowledge extraction.""" - for template, input_name in CASES: - ke = self.ke_map[template] - input_file = CASES_DIR / f"{input_name}.txt" - ann = ke.extract_from_file(input_file) - # print(yaml.dump(ann.dict())) - # for ne in ke.named_entities: - # print(yaml.dump(ne.dict())) - # result_dict = { - # "input_file": str(input_file), - # "text": ke.last_text, - # "results": ann.dict(), - # "named_entities": [ne.dict() for ne in ke.named_entities], - # } - # print(yaml.dump(result_dict)) - output_file = str(OUTPUT_DIR / f"{input_name}.yaml") - print(f"Writing {output_file}") - with open(output_file, "w", encoding="utf-8") as f: - f.write(dump_minimal_yaml(ann)) - pkl_output_file = str(OUTPUT_DIR / f"{input_name}.pickle") - print(f"Writing {pkl_output_file}") - with open(pkl_output_file, "wb") as f: - f.write(pickle.dumps(ann)) diff --git a/tests/integration/test_knowledge_engines/test_enrichment.py b/tests/integration/test_knowledge_engines/test_enrichment.py index 0b6cfb2d9..b35b2d49c 100644 --- a/tests/integration/test_knowledge_engines/test_enrichment.py +++ b/tests/integration/test_knowledge_engines/test_enrichment.py @@ -1,10 +1,10 @@ """Core tests.""" import unittest -from ontogpt.engines import create_engine -from ontogpt.engines.enrichment import EnrichmentEngine -from ontogpt.templates.gene_description_term import GeneDescriptionTerm -from ontogpt.utils.gene_set_utils import GeneSet, gene_info +from talisman.engines import create_engine +from talisman.engines.enrichment import EnrichmentEngine +from talisman.templates.gene_description_term import GeneDescriptionTerm +from talisman.utils.gene_set_utils import GeneSet, gene_info PEX = [ ("HGNC:8850", "PEX1"), diff --git a/tests/integration/test_knowledge_engines/test_generalizations.py b/tests/integration/test_knowledge_engines/test_generalizations.py deleted file mode 100644 index 866f91f86..000000000 --- a/tests/integration/test_knowledge_engines/test_generalizations.py +++ /dev/null @@ -1,89 +0,0 @@ -"""Core tests.""" -import unittest - -import yaml -from oaklib import get_implementation_from_shorthand - -from ontogpt.engines.spires_engine import SPIRESEngine -from tests import INSTANCES_DIR, OUTPUT_DIR - -CASES = [ - ( - "drug.DrugMechanism", - [{"disease": "MESH:D014552", "drug": "drugbank:DB00438"}], - [ - ["disease", "drug"], - ], - [ - "sqlite:obo:mesh", - "sqlite:obo:drugbank", - "sqlite:obo:go", - "sqlite:obo:uberon", - "sqlite:obo:pr", - ], - "drug-mechanisms-001", - ), - ( - "reaction.Reaction", - [ - { - "label": "pseudouridine 5'-phosphatase activity", - "description": "Catalysis of the reaction:\ - pseudouridine 5'-phosphate + H2O = pseudouridine + phosphate.", - }, - { - "label": "L-altrarate dehydratase activity", - "description": "Catalysis of the reaction:\ - L-altrarate = 5-dehydro-4-deoxy-D-glucarate + H2O.", - }, - # rhea:40031 - {"description": "ent-copalyl diphosphate + H2O = diphosphate + ent-manool"}, - ], - [ - ["label"], - ["description"], - ["label", "description"], - ], - [], - "reactions-001", - ), -] - - -class TestGeneralize(unittest.TestCase): - """Test generalization.""" - - def setUp(self) -> None: - """Set up all engines in advance.""" - ke_map = {} - for c in CASES: - template = c[0] - ke_map[template] = SPIRESEngine(template) - self.ke_map = ke_map - - def test_cases(self): - """Tests generalization over all cases.""" - for template, objs, combos, labelers, input_file in CASES: - ke = self.ke_map[template] - ke.labelers = [get_implementation_from_shorthand(labeler) for labeler in labelers] - print(f"Loading {input_file}") - with open(INSTANCES_DIR / f"{input_file}.yaml") as f: - examples = yaml.safe_load(f) - print(examples) - nu_objs = [] - for obj in objs: - for combo in combos: - if any(c not in obj for c in combo): - continue - print(f"Testing {combo}") - test_obj = {k: obj[k] for k in combo} - nu_obj = ke.generalize(test_obj, examples) - print(nu_obj) - nu_obj = nu_obj.dict() - nu_obj["_combo"] = list(combo) - nu_obj["_input"] = test_obj - nu_objs.append(nu_obj) - with open( - str(OUTPUT_DIR / f"generalized-{input_file}.yaml"), "w", encoding="utf-8" - ) as f: - yaml.dump(nu_objs, f) diff --git a/tests/integration/test_knowledge_engines/test_gpt4all_engine.py b/tests/integration/test_knowledge_engines/test_gpt4all_engine.py deleted file mode 100644 index 553324783..000000000 --- a/tests/integration/test_knowledge_engines/test_gpt4all_engine.py +++ /dev/null @@ -1,33 +0,0 @@ -"""Tests for using local GGML models.""" -import unittest - -import yaml - -from ontogpt.engines.gpt4all_engine import GPT4AllEngine - -TEMPLATE = "mendelian_disease.MendelianDisease" - -# This is a small test model. It doesn't really -# do extraction - it's a BERT model for sentence -# embeddings - but it tests functionality. -TEST_MODEL = "ggml-all-MiniLM-L6-v2-f16" - -TEXT_INPUT = "Peanut butter and cheese" - - -class TestCore(unittest.TestCase): - """Test annotation.""" - - def setUp(self) -> None: - """Set up.""" - self.ke = GPT4AllEngine(template=TEMPLATE, model=TEST_MODEL) - - def test_extract(self): - """Tests end to end knowledge extraction.""" - ke = self.ke - ann = ke.extract_from_text(TEXT_INPUT) - print(f"RESULTS={ann}") - print(yaml.dump(ann.dict())) - results = ann.extracted_object - if results is not None: - raise ValueError(f"Unexpected output type, got {type(results)}") diff --git a/tests/integration/test_knowledge_engines/test_halo_engine.py b/tests/integration/test_knowledge_engines/test_halo_engine.py deleted file mode 100644 index e56fb58d2..000000000 --- a/tests/integration/test_knowledge_engines/test_halo_engine.py +++ /dev/null @@ -1,88 +0,0 @@ -"""Core tests.""" -import logging -import unittest - -import yaml -from oaklib import get_implementation_from_shorthand -from oaklib.datamodels.vocabulary import IS_A, PART_OF - -from ontogpt.converters.ontology_converter import OntologyConverter -from ontogpt.engines import halo_engine -from ontogpt.engines.halo_engine import HALOEngine -from ontogpt.io.yaml_wrapper import dump_minimal_yaml -from tests import INPUT_DIR, OUTPUT_DIR - -TEST_ONTOLOGY_OAK = INPUT_DIR / "go-nucleus.db" -TEST_ONTOLOGY_HALO = INPUT_DIR / "go-nucleus.halo.yaml" -TEST_ONTOLOGY_OUTPUT = OUTPUT_DIR / "go-nucleus.halo.yaml" -HALLUCINATED_ONTOLOGY_OUTPUT = OUTPUT_DIR / "go-nucleus.hallucinated.halo.yaml" - -logger = logging.getLogger(halo_engine.__name__) -logger.setLevel(level=logging.INFO) - - -class TestHALO(unittest.TestCase): - """Test annotation.""" - - def setUp(self) -> None: - """Set up.""" - self.ke = HALOEngine( - expand_horizon=False, - fixed_slot_values={"context": "subcellular"}, - ) - self.ke.seed_from_file(TEST_ONTOLOGY_HALO) - adapter = get_implementation_from_shorthand(str(TEST_ONTOLOGY_OAK)) - self.converter = OntologyConverter(adapter) - - @unittest.skip("Algorithm changed") - def test_get_candidate_elements(self): - ke = self.ke - elts = ke.get_candidate_elements() - print(len(elts)) - self.assertGreater(len(elts), 10) - print(elts[0:5]) - - def test_hallucinate_element(self): - ke = self.ke - candidates = set(ke.get_candidate_elements()) - name = "Axon" - elt = ke.hallucinate_element(name) - print("## ELEMENT:") - print(yaml.dump(elt.dict())) - [elt2] = [elt for elt in ke.ontology.elements if elt.name == name] - self.assertEqual(elt, elt2) - self.assertIn(name, ke.visited) - next_candidates = set(ke.get_candidate_elements()) - new_candidates = next_candidates.difference(candidates) - print(f"New candidates={new_candidates}") - self.assertGreater(len(new_candidates), 0) - # ensure that new ones are added to the end - self.assertIn(ke.get_candidate_elements()[-1], new_candidates) - - def test_hallucinate(self): - ke = self.ke - elts = ke.hallucinate(["Axon", "Dendrite"], num_iterations=4) - for e in elts: - print(f"{e.name} {e.description}") - print(f"ELTS: {len(elts)}") - with open(HALLUCINATED_ONTOLOGY_OUTPUT, "w") as f: - f.write(dump_minimal_yaml(ke.ontology)) - - def test_hallucinate_metabolism(self): - ke = HALOEngine( - expand_horizon=False, - fixed_slot_values={"context": "metabolism"}, - ) - preds = [IS_A, PART_OF] - adapter = get_implementation_from_shorthand("sqlite:obo:go") - converter = OntologyConverter(adapter) - ke.ontology = converter.extract_seed_ontology(["GO:0034651", "GO:0034653"], preds) - elts = ke.hallucinate( - ["KetoaldopentoseBiosyntheticProcess", "IsomaltotrioseMetabolicProcess"], - num_iterations=3, - ) - for e in elts: - print(f"{e.name} {e.description}") - print(f"ELTS: {len(elts)}") - with open(str(OUTPUT_DIR / "carbohydrate-metabolism.hallucinated.halo.yaml"), "w") as f: - f.write(dump_minimal_yaml(ke.ontology)) diff --git a/tests/integration/test_knowledge_engines/test_mapping.py b/tests/integration/test_knowledge_engines/test_mapping.py deleted file mode 100644 index a337403a4..000000000 --- a/tests/integration/test_knowledge_engines/test_mapping.py +++ /dev/null @@ -1,157 +0,0 @@ -"""Core tests.""" -import logging -import unittest - -from oaklib import get_adapter -from sssom.parsers import parse_sssom_table, to_mapping_set_document -from sssom_schema import Mapping - -from ontogpt.clients import openai_client -from ontogpt.engines import mapping_engine -from ontogpt.engines.mapping_engine import CategorizedMapping, MappingEngine, MappingTaskCollection -from ontogpt.io.yaml_wrapper import dump_minimal_yaml -from tests import INPUT_DIR - -TEST_ONTOLOGY_OAK = INPUT_DIR / "go-nucleus.db" - -HEART = "UBERON:0000948" -NECK_OF_ORGAN = "UBERON:0001560" -MA_NECK_ORGAN = "MA:0000589" -MA_HEART = "MA:0000072" - -ENVO_MOUTH = "ENVO:00000479" # river mouth -WIKIDATA_MOUTH = "wikidata:Q9635" # anatomical mouth -UBERON_MOUTH = "UBERON:0000165" # anatomical mouth -UBERON_ORAL_OPENING = "UBERON:0000166" - -logger = logging.getLogger(mapping_engine.__name__) -client_logger = logging.getLogger(openai_client.__name__) - -client_logger.setLevel(logging.DEBUG) - - -def _show(mapping_eval: CategorizedMapping): - print(f"{mapping_eval.subject} -> {mapping_eval.object}") - print(mapping_eval.completion) - print(dump_minimal_yaml(mapping_eval.dict())) - - -class TestMapping(unittest.TestCase): - """Test ability to convert from OAK to native HALO form.""" - - def setUp(self) -> None: - """Set up OAK adapter, extractor, and reasoner.""" - subject_adapter = get_adapter("sqlite:obo:uberon") - object_adapter = get_adapter("sqlite:obo:zfa") - self.mapper = MappingEngine(subject_adapter=subject_adapter, object_adapter=object_adapter) - - def test_generate(self): - mapper = self.mapper - subjects = [HEART] - tc = MappingTaskCollection(name="test", subjects=subjects, object_sources=["ZFA"]) - tasks = list(mapper.generate_tasks(tc)) - for task in tasks: - print(dump_minimal_yaml(task.dict())) - tc.tasks = tasks - results = list(mapper.run_tasks(tc)) - for result in results: - print(dump_minimal_yaml(result.dict())) - - def test_from_sssom(self): - mapper = self.mapper - - def _exclude_trivial(m: Mapping) -> bool: - return m.subject_label.lower() == m.object_label.lower() - - tc = mapper.from_sssom( - INPUT_DIR / "mondo-exact-ncit.sssom.tsv", exclude_functions=[_exclude_trivial] - ) - # print(dump_minimal_yaml(tc.dict())) - results = list(mapper.run_tasks(tc)) - for result in results: - print(dump_minimal_yaml(result.dict())) - - def test_from_sssom2(self): - mapper = MappingEngine( - subject_adapter=get_adapter("sqlite:obo:mondo"), - object_adapter=get_adapter("sqlite:obo:ncit"), - ) - - msdf = parse_sssom_table(INPUT_DIR / "mondo-exact-ncit.sssom.tsv") - msd = to_mapping_set_document(msdf) - - def _exclude_trivial(m: Mapping) -> bool: - return m.subject_label.lower() == m.object_label.lower() - - for m in msd.mapping_set.mappings: - if _exclude_trivial(m): - continue - m2 = mapper.categorize_sssom_mapping(m) - print(m2) - - def test_mapping_eval(self): - """Test evaluation of mapping on uberon.""" - mapper = self.mapper - subjects = [HEART] - for meval in mapper.categorize_mappings(subjects, object_sources=["ZFA"]): - _show(meval) - - def test_different_from(self): - mapper = MappingEngine( - subject_adapter=get_adapter("sqlite:obo:uberon"), - object_adapter=get_adapter("sqlite:obo:ma"), - ) - subjects = [NECK_OF_ORGAN] - objects = [MA_NECK_ORGAN] - for subject in subjects: - for object in objects: - meval = mapper.categorize_mapping(subject, object) - _show(meval) - - def test_very_different_from(self): - mapper = MappingEngine( - subject_adapter=get_adapter("sqlite:obo:uberon"), - object_adapter=get_adapter("sqlite:obo:ma"), - ) - subjects = [HEART] - objects = [MA_NECK_ORGAN] - for subject in subjects: - for object in objects: - meval = mapper.categorize_mapping(subject, object) - _show(meval) - - def test_very_different_from2(self): - mapper = MappingEngine( - subject_adapter=get_adapter("sqlite:obo:uberon"), - object_adapter=get_adapter("sqlite:obo:envo"), - ) - subjects = [UBERON_MOUTH, UBERON_ORAL_OPENING] - objects = [ENVO_MOUTH] - for subject in subjects: - for object in objects: - meval = mapper.categorize_mapping(subject, object) - _show(meval) - - def test_species_identical(self): - mapper = MappingEngine( - subject_adapter=get_adapter("sqlite:obo:uberon"), - object_adapter=get_adapter("sqlite:obo:ma"), - ) - subjects = [HEART] - objects = [MA_HEART] - for subject in subjects: - for object in objects: - meval = mapper.categorize_mapping(subject, object) - _show(meval) - - @unittest.skip("Requires new OAK release") - def test_wikidata(self): - mapper = MappingEngine( - subject_adapter=get_adapter("sqlite:obo:envo"), object_adapter=get_adapter("wikidata:") - ) - subjects = [ENVO_MOUTH] - objects = [WIKIDATA_MOUTH] - for subject in subjects: - for object in objects: - meval = mapper.categorize_mapping(subject, object) - _show(meval) diff --git a/tests/integration/test_knowledge_engines/test_pheno.py b/tests/integration/test_knowledge_engines/test_pheno.py deleted file mode 100644 index 80f3769aa..000000000 --- a/tests/integration/test_knowledge_engines/test_pheno.py +++ /dev/null @@ -1,37 +0,0 @@ -"""Core tests.""" -import json -import logging -import unittest - -from oaklib import get_adapter - -from ontogpt.clients import openai_client -from ontogpt.engines import mapping_engine -from ontogpt.engines.pheno_engine import PhenoEngine -from ontogpt.io.yaml_wrapper import dump_minimal_yaml -from tests import INPUT_DIR - -PHENOPACKET_FILE = INPUT_DIR / "Guo-2017-EXTL3-Patient_1.json" - -logger = logging.getLogger(mapping_engine.__name__) -client_logger = logging.getLogger(openai_client.__name__) - -# client_logger.setLevel(logging.DEBUG) - - -class TestPhenopackets(unittest.TestCase): - def setUp(self) -> None: - """Set up OAK adapter, extractor, and reasoner.""" - self.adapter = get_adapter("sqlite:obo:hp") - - def test_diagnose(self): - phenopacket = json.load(open(PHENOPACKET_FILE)) - engine = PhenoEngine() - result = engine.predict_disease(phenopacket) - print(result) - - def test_eval(self): - phenopacket = json.load(open(PHENOPACKET_FILE)) - engine = PhenoEngine() - results = engine.evaluate([phenopacket]) - print(dump_minimal_yaml(results)) diff --git a/tests/integration/test_knowledge_engines/test_reasoning.py b/tests/integration/test_knowledge_engines/test_reasoning.py deleted file mode 100644 index efcfa1527..000000000 --- a/tests/integration/test_knowledge_engines/test_reasoning.py +++ /dev/null @@ -1,188 +0,0 @@ -"""Core tests.""" -import logging -import unittest -from typing import Iterator, List - -import yaml -from oaklib import get_adapter -from oaklib.datamodels.vocabulary import IS_A, PART_OF -from oaklib.interfaces.obograph_interface import OboGraphInterface - -from ontogpt.engines.reasoner_engine import ReasonerEngine, ReasonerResult, ReasonerResultSet -from ontogpt.io.csv_wrapper import write_obj_as_csv -from ontogpt.io.yaml_wrapper import dump_minimal_yaml -from ontogpt.ontex import extractor -from ontogpt.ontex.extractor import OntologyExtractor, Task -from tests import ( - BIOLOGICAL_PROCESS, - CELLULAR_ANATOMICAL_ENTITY, - CELLULAR_ORGANISMS, - ENVELOPE, - FUNGI, - IMBO, - INPUT_DIR, - MAMMALIA, - MEMBRANE, - NUCLEAR_ENVELOPE, - NUCLEAR_MEMBRANE, - NUCLEUS, - ORGANELLE, - OUTPUT_DIR, - PLASMA_MEMBRANE, - VACUOLE, -) - -TEST_ONTOLOGY_OAK = INPUT_DIR / "go-nucleus.db" - - -logger = logging.getLogger(extractor.__name__) -logger.setLevel(level=logging.INFO) - - -class TestReasoning(unittest.TestCase): - """Test ability to convert from OAK to native HALO form.""" - - def setUp(self) -> None: - """Set up OAK adapter, extractor, and reasoner.""" - self.adapter = get_adapter(str(TEST_ONTOLOGY_OAK)) - if not isinstance(self.adapter, OboGraphInterface): - raise ValueError("Not an OboGraphInterface") - self.extractor = OntologyExtractor(adapter=self.adapter) - self.reasoner = ReasonerEngine() - # self.reasoner.client.model = "gpt-4" - - def save(self, results: List[ReasonerResult], name: str): - rset = ReasonerResultSet(name=name, results=results) - model = self.reasoner.client.model - with open(OUTPUT_DIR / f"reasoner-{name}-{model}.yaml", "w") as f: - f.write(dump_minimal_yaml(rset)) - path = str(OUTPUT_DIR / f"reasoner-{name}-{model}.tsv") - write_obj_as_csv(results, path) - - def tasks(self) -> Iterator[Task]: - extractor = self.extractor - # yield extractor.extract_indirect_superclasses_task( - # name="random", - # select_random=True, - # ) - yield extractor.extract_transitive_superclasses_task( - name="transitive-ancestor-nucleus", - subclass=NUCLEUS, - siblings=[VACUOLE], - roots=[ORGANELLE], - ) - yield extractor.extract_indirect_superclasses_task( - name="indirect-ancestor-nucleus", - subclass=NUCLEUS, - siblings=[VACUOLE], - roots=[ORGANELLE], - ) - yield extractor.extract_transitive_superclasses_task( - name="transitive-ancestor-nuclear-membrane", - subclass=IMBO, - siblings=[NUCLEUS], - roots=[ORGANELLE, BIOLOGICAL_PROCESS], - ) - yield extractor.extract_indirect_superclasses_task( - name="indirect-ancestor-nuclear-membrane", - subclass=IMBO, - siblings=[NUCLEUS], - roots=[ORGANELLE, BIOLOGICAL_PROCESS], - ) - yield extractor.extract_indirect_superclasses_task( - name="ancestor-nuclear-envelope", - subclass=NUCLEAR_MEMBRANE, - siblings=[NUCLEAR_ENVELOPE], - roots=[CELLULAR_ANATOMICAL_ENTITY], - ) - yield extractor.extract_indirect_superclasses_task( - name="ancestor-human", - subclass=IMBO, - siblings=[NUCLEUS], - roots=[ORGANELLE, BIOLOGICAL_PROCESS], - ) - yield extractor.extract_most_recent_common_subsumers_task( - name="mrca-nucleus-vacuole", - subclass1=NUCLEUS, - subclass2=VACUOLE, - siblings=[NUCLEAR_MEMBRANE], - roots=[], - ) - yield extractor.extract_subclass_of_expression_task( - name="subclass-of-part-of-nuclear-envelope", - superclass=NUCLEUS, - predicate=PART_OF, - siblings=[VACUOLE], - ) - yield extractor.extract_incoherent_ontology_task( - name="incoherent-nucleus", - incoherents=[NUCLEUS], - siblings=[VACUOLE], - disjoints=[(ORGANELLE, ENVELOPE)], - spiked_relationships=[(NUCLEUS, IS_A, NUCLEAR_MEMBRANE)], - roots=[CELLULAR_ANATOMICAL_ENTITY], - ) - yield extractor.extract_incoherent_ontology_task( - name="incoherent-plasma-membrane", - incoherents=[PLASMA_MEMBRANE], - siblings=[NUCLEUS], - disjoints=[(ORGANELLE, MEMBRANE)], - spiked_relationships=[(PLASMA_MEMBRANE, IS_A, ORGANELLE)], - roots=[CELLULAR_ANATOMICAL_ENTITY], - ) - yield extractor.extract_incoherent_ontology_task( - name="incoherent-ok-organism", - incoherents=[], - siblings=[], - disjoints=[(MAMMALIA, FUNGI)], - spiked_relationships=[], - roots=[CELLULAR_ORGANISMS], - ) - - def test_reason(self): - """Test basic reasoning, no explanations.""" - reasoner = self.reasoner - results = [] - for task in self.tasks(): - result = reasoner.reason(task) - print(yaml.dump(result.dict(), sort_keys=False)) - print(result.prompt) - results.append(result) - ReasonerResultSet(results=[result]) - for result in results: - print( - f"Result: {result.jaccard_score} {result.false_positives} {result.false_negatives}" - ) - self.save(results, "basic") - - def test_reason_with_explanations(self): - """Test reasoning with explanations included.""" - reasoner = self.reasoner - results = [] - for task in self.tasks(): - task.include_explanations = True - result = reasoner.reason(task) - print(result.prompt) - print(yaml.dump(result.dict(), sort_keys=False)) - results.append(result) - for result in results: - print( - f"Result: {result.jaccard_score} {result.false_positives} {result.false_negatives}" - ) - self.save(results, "explanation") - - def test_reason_with_chain_of_thought(self): - """Test reasoning with explicit chain-of-thought trigger.""" - reasoner = self.reasoner - results = [] - for task in self.tasks(): - task.chain_of_thought = True - result = reasoner.reason(task) - print(result.prompt) - print(yaml.dump(result.dict(), sort_keys=False)) - results.append(result) - for result in results: - print( - f"Result: {result.jaccard_score} {result.false_positives} {result.false_negatives}" - ) - self.save(results, "chain-of-thought") diff --git a/tests/integration/test_knowledge_engines/test_spires_engine.py b/tests/integration/test_knowledge_engines/test_spires_engine.py deleted file mode 100644 index e3f026bed..000000000 --- a/tests/integration/test_knowledge_engines/test_spires_engine.py +++ /dev/null @@ -1,448 +0,0 @@ -"""Core tests.""" -import unittest - -import yaml -from linkml_runtime.linkml_model import ClassDefinitionName -from oaklib import get_implementation_from_shorthand - -from ontogpt.clients.pubmed_client import PubmedClient -from ontogpt.engines import create_engine -from ontogpt.engines.knowledge_engine import chunk_text -from ontogpt.engines.spires_engine import SPIRESEngine -from ontogpt.io.yaml_wrapper import dump_minimal_yaml -from ontogpt.templates.biological_process import BiologicalProcess -from ontogpt.templates.gocam import ( - ExtractionResult, - Gene, - GeneLocation, - GeneOrganismRelationship, - GoCamAnnotations, -) - -TEMPLATE = "gocam.GoCamAnnotations" - -PAPER = """ -Title: β-Catenin Is Required for the cGAS/STING Signaling Pathway but - Antagonized by the Herpes Simplex Virus 1 US3 Protein. -Text: -The cGAS/STING-mediated DNA-sensing signaling pathway is crucial -for interferon (IFN) production and host antiviral -responses. Herpes simplex virus I (HSV-1) is a DNA virus that has -evolved multiple strategies to evade host immune responses. Here, -we demonstrate that the highly conserved β-catenin protein in the -Wnt signaling pathway is an important factor to enhance the -transcription of type I interferon (IFN-I) in the cGAS/STING -signaling pathway, and the production of IFN-I mediated by -β-catenin was antagonized by HSV-1 US3 protein via its kinase -activity. Infection by US3-deficienct HSV-1 and its kinase-dead -variants failed to downregulate IFN-I and IFN-stimulated -gene (ISG) production induced by β-catenin. Consistent with this, -absence of β-catenin enhanced the replication of US3-deficienct -HSV-1, but not wild-type HSV-1. The underlying mechanism was the -interaction of US3 with β-catenin and its hyperphosphorylation of -β-catenin at Thr556 to block its nuclear translocation. For the -first time, HSV-1 US3 has been shown to inhibit IFN-I production -through hyperphosphorylation of β-catenin and to subvert host -antiviral innate immunity.IMPORTANCE Although increasing evidence -has demonstrated that HSV-1 subverts host immune responses and -establishes lifelong latent infection, the molecular mechanisms -by which HSV-1 interrupts antiviral innate immunity, especially -the cGAS/STING-mediated cellular DNA-sensing signaling pathway, -have not been fully explored. Here, we show that β-catenin -promotes cGAS/STING-mediated activation of the IFN pathway, which -is important for cellular innate immune responses and intrinsic -resistance to DNA virus infection. The protein kinase US3 -antagonizes the production of IFN by targeting β-catenin via its -kinase activity. The findings in this study reveal a novel -mechanism for HSV-1 to evade host antiviral immunity and add new -knowledge to help in understanding the interaction between the -host and HSV-1 infection. - -Keywords: HSV-1; US3; type I IFN; β-catenin. -""" - -EXAMPLE_RESULTS = """ -genes: β-Catenin; cGAS; STING; US3; IFN; ISG -organisms: Herpes Simplex Virus I (HSV-1); -gene_organisms: β-Catenin:host; cGAS:host; STING:host; US3:HSV-1; IFN:host; ISG:host -activities: production of type I IFN; transcription of type I IFN; replication of HSV-1; -nuclear translocation of β-catenin. -gene_functions: β-catenin:enhance the transcription of type I IFN; US3:antagonize -the production of IFN; β-catenin:block nuclear translocation. -cellular_processes: cGAS/STING-mediated DNA-sensing signaling; activation of IFN pathway -pathways: IFN pathway; Wnt signalling pathway -gene_gene_interactions: US3:β-catenin -gene_localizations: US3:host; β-catenin:host -""" - -EXAMPLE_RESULTS_ALT = """ -genes: β-Catenin; cGAS; STING; US3; IFN; ISG -organisms: Herpes Simplex Virus I (HSV-1); -gene_organisms: β-Catenin - Human; cGAS - Human; STING - Human; -US3 - Human; IFN - Human; ISG - Human. -activities: Transcription; Production; Downregulation; Replication; Nuclear Translocation -gene_functions: β-Catenin - Enhances Transcription; US3 - Antagonizes Production; -US3 - Downregulates IFN-I; US3 - Blocks Nuclear Translocation; β-Catenin - Enhances Production -cellular_processes: DNA-sensing; Interferon Production; Antiviral Innate Immunity; -Host Innate Immune Responses; Interaction with Host; Evade Host Antiviral Immunity -pathways: cGAS/STING-mediated DNA-sensing; Wnt Signaling; IFN pathway -gene_gene_interactions: US3 - β-Catenin; β-Catenin - US3 -gene_localizations: β-Catenin - Nuclear; US3 - Hyperphosphorylation -""" - -TEST_PROCESS = BiologicalProcess( - label="autophagosome assembly", - description="The formation of a double membrane-bounded structure, the autophagosome,\ - that occurs when a specialized membrane sac, called the isolation membrane,\ - starts to enclose a portion of the cytoplasm", - subclass_of="GO:0022607", - outputs=["GO:0005776"], -) - -DIRECT_PARSE = { - "genes": ["β-Catenin", "cGAS", "STING", "US3", "IFN", "ISG"], - "gene_organisms": [ - ("β-Catenin", "host"), - ("cGAS", "host"), - ("STING", "host"), - ("US3", "HSV-1"), - ("IFN", "host"), - ("ISG", "host"), - ], -} - - -class TestCore(unittest.TestCase): - """Test annotation.""" - - def setUp(self) -> None: - """Set up.""" - self.ke = create_engine(TEMPLATE, SPIRESEngine) - - def test_setup(self): - """Tests template and module is loaded.""" - ke = self.ke - pyc = ke.template_pyclass - print(pyc) - obj = pyc(genes=["a"], gene_organisms=[{"gene": "a", "organism": "b"}]) - print(yaml.dump(obj.dict())) - self.assertEqual(obj.genes, ["a"]) - self.assertEqual(obj.gene_organisms[0].gene, "a") - self.assertEqual(obj.gene_organisms[0].organism, "b") - slot = ke.schemaview.induced_slot("genes", "GeneOrganismRelationship") - self.assertEqual(slot.name, "genes") - self.assertEqual(slot.multivalued, True) - self.assertEqual(slot.range, "Gene") - - def test_chunk_text(self): - """Test chunking.""" - text = "Title: foo. Abstract: Sentence 1. Sentence 2.\n Sentence 3. Sentence 4." - chunks = list(chunk_text(text)) - for chunk in chunks: - print(chunk) - self.assertEqual(len(chunks), 4) - self.assertEqual(chunks[0], "Title: foo") - self.assertEqual(chunks[1], "Title: foo. Abstract: Sentence 1") - self.assertEqual(chunks[2], "Title: foo. Abstract: Sentence 1. Sentence 2") - self.assertEqual(chunks[3], "Abstract: Sentence 1. Sentence 2. Sentence 3") - - def test_generalize(self): - """Tests generalization.""" - ke = SPIRESEngine("biological_process.BiologicalProcess") - ke.labelers = [get_implementation_from_shorthand("sqlite:obo:go")] - examples = [ - """ - label: mannose biosynthesis - description: The chemical reactions and pathways resulting - in the formation of mannose, the aldohexose manno-hexose, - the C-2 epimer of glucose. - synonyms: mannose anabolism - subclass_of: hexose biosynthesis - outputs: mannose - """, - """ - label: maltose biosynthesis - description: The chemical reactions and pathways - resulting in the formation of the - disaccharide maltose (4-O-alpha-D-glucopyranosyl-D-glucopyranose) - subclass_of: disaccharide biosynthesis - outputs: maltose - """, - TEST_PROCESS, - ] - label = "beta-D-lyxofuranose biosynthesis" - ann = ke.generalize({"label": label}, examples) - print(f"RESULTS={ann}") - print(yaml.dump(ann.dict())) - self.assertEqual(label, ann.label) - self.assertEqual(["CHEBI:151400"], ann.outputs) - - def test_serialize_example(self): - ke = SPIRESEngine("biological_process.BiologicalProcess") - ke.labelers = [get_implementation_from_shorthand("sqlite:obo:go")] - ser = ke.serialize_object(TEST_PROCESS) - # print(f"SERIALIZED={ser}") - self.assertIn("outputs: autophagosome", ser) - - def test_extract(self): - """Tests end to end knowledge extraction.""" - ke = self.ke - ann = ke.extract_from_text(PAPER) - print(f"RESULTS={ann}") - print(yaml.dump(ann.dict())) - results = ann.extracted_object - if not isinstance(results, GoCamAnnotations): - raise ValueError(f"Expected GoCamAnnotations, got {type(results)}") - self.assertIn("HGNC:2514", results.genes) - - def test_extract_with_stub(self): - """Tests end to end knowledge extraction.""" - ke = self.ke - ann = ke.extract_from_text(PAPER, object={"pathways": ["GO:0140896"]}) - print(f"RESULTS={ann}") - print(yaml.dump(ann.dict())) - results = ann.extracted_object - if not isinstance(results, GoCamAnnotations): - raise ValueError(f"Expected GoCamAnnotations, got {type(results)}") - self.assertIn("HGNC:2514", results.genes) - - def test_subextract(self): - """Tests end to end knowledge extraction.""" - ke = self.ke - cls = ke.schemaview.get_class("GeneMolecularActivityRelationship") - ann = ke.extract_from_text("β-Catenin-Translocation", cls) - print(f"RESULTS={ann}") - print(yaml.dump(ann.dict())) - self.assertEqual({"gene": "HGNC:2514", "molecular_activity": "Translocation"}, ann.dict()) - # try and fool it - ann = ke._extract_from_text_to_dict("foobaz", cls) - print(f"RESULTS={ann}") - self.assertIsNone(ann) - # print(yaml.dump(ann.dict())) - - def test_prompt(self): - """Tests prompt generation. - - Tests that the prompt can be derived from a prompt annotation, - or from description, if no such annotation present - """ - ke = self.ke - prompt = ke.get_completion_prompt() - self.assertIn( - "genes: ", - prompt, - "Expected to derived prompt from description of gene slot", - ) - self.assertIn( - "gene_organisms: ", - prompt, - "Expected to derived prompt from annotations of gene_organisms slot", - ) - - def test_parse_completion_payload(self): - """Tests parsing of textual payload from openai API. - - This involves two steps: - - - parsing the payload into a dict of slot values - - annotating the dict using OAK annotators - - We use a ready-made payload from the API, to avoid - invoking an API call - """ - ke = self.ke - ann = ke.parse_completion_payload(EXAMPLE_RESULTS) - print(f"PARSED={ann}") - print(yaml.dump(ann.dict())) - self.assertIn("HGNC:2514", ann.genes) - self.assertEqual(2, len(ann.pathways)) - - def test_parse_response_to_dict(self): - """Tests parsing of textual payload from openai API.""" - ke = self.ke - ann = ke._parse_response_to_dict(EXAMPLE_RESULTS) - print(f"PARSED={ann}") - print(yaml.dump(ann)) - self.assertIn("STING", ann["genes"]) - self.assertIn({"gene": "β-Catenin", "organism": "host"}, ann["gene_organisms"]) - # test resilience to missing internal separators - ann = ke._parse_response_to_dict("gene_organisms: a ; b ; c\ngenes: g") - self.assertEqual(ann["genes"], ["g"]) - self.assertEqual(["genes"], list(ann.keys())) - # test resilience to multiple internal separators - ann = ke._parse_response_to_dict("gene_organisms: a-b-c") - self.assertEqual(ann["gene_organisms"], [{"gene": "a", "organism": "b-c"}]) - - def test_parse_completion_payload_alt(self): - """Tests parsing of textual payload from openai API. - - This uses a variant of the output, sometimes OpenAI will - use ':' as separators instead of ' - '. - """ - ke = self.ke - ann = ke.parse_completion_payload(EXAMPLE_RESULTS_ALT) - print(f"PARSED={ann}") - print(dump_minimal_yaml(ann)) - - def test_ground_annotation_object(self): - """ - Tests grounding of annotation object. - - E.g. takes - - {'genes': ['β-Catenin', 'cGAS', ...]} - - And produces: - - {'genes': ['HGNC:2514', 'HGNC:21367', ... - """ - ke = self.ke - if not isinstance(ke, SPIRESEngine): - raise ValueError(f"Expected SPIRESEngine, got {type(ke)}") - annotated = ke.ground_annotation_object(DIRECT_PARSE) - print(dump_minimal_yaml(annotated)) - self.assertIn("HGNC:2514", annotated.genes) - expected = GeneOrganismRelationship(gene="HGNC:2514", organism="EFO:0000532") - self.assertIn(expected, annotated.gene_organisms) - - def test_normalize_named_entity(self): - ke = self.ke - normalize_cases = [ - ("β-Catenin", ClassDefinitionName(Gene.__name__), "HGNC:2514"), - ("nucleus", ClassDefinitionName(GeneLocation.__name__), "GO:0005634"), - ( - "transport", - ClassDefinitionName(GeneLocation.__name__), - "transport", - ), # not a location - ("perivascular macrophage", ClassDefinitionName(GeneLocation.__name__), "CL:0000881"), - ("perivascular macrophages", ClassDefinitionName(GeneLocation.__name__), "CL:0000881"), - ("blah blah (nucleus)", ClassDefinitionName(GeneLocation.__name__), "GO:0005634"), - ("nucleus (blah blah)", ClassDefinitionName(GeneLocation.__name__), "GO:0005634"), - ("NUCLEUS (blah blah)", ClassDefinitionName(GeneLocation.__name__), "GO:0005634"), - ] - for text, elt_name, expected in normalize_cases: - result = ke.normalize_named_entity(text, elt_name) - self.assertEqual(expected, result) - - def test_is_valid_identifier(self): - ke = self.ke - value_set_cases = [ - ("HGNC:2514", Gene, True), - ("CL:0000881", GeneLocation, True), - ("GO:0005634", GeneLocation, True), - ("HGNC:2514", GeneLocation, False), - ("GO:0005634", Gene, False), - ("GO:0006810", GeneLocation, False), # wrong hierarchy - ] - for curie, cls, is_valid in value_set_cases: - cls_def = ke.schemaview.get_class(cls.__name__) - result = ke.is_valid_identifier(curie, cls_def) - self.assertEqual( - result, is_valid, f"Expected validity of {curie} for {cls} to be {is_valid}" - ) - - def test_custom_dictionary(self): - ke = create_engine(TEMPLATE, SPIRESEngine) - ke.load_dictionary( - [ - {"synonym": "TING", "id": "HGNC:test1"}, - {"synonym": "sting", "id": "HGNC:test2"}, - {"synonym": "Cat", "id": "HGNC:test3"}, - ] - ) - if not isinstance(ke, SPIRESEngine): - raise ValueError(f"Expected TextModelKnowledgeEngine, got {type(ke)}") - annotated = ke.ground_annotation_object(DIRECT_PARSE) - print(dump_minimal_yaml(annotated)) - self.assertIn("HGNC:test2", annotated.genes) - self.assertNotIn("HGNC:test1", annotated.genes, "longer synonyms should take priority") - self.assertNotIn( - "HGNC:test3", - annotated.genes, - "number of overlapping characters should be beneath threshold", - ) - - def test_mapping(self): - """Tests mapping of annotation object to OAK model.""" - ke = self.ke - cases = [ - ( - "uberon", - [ - "pinky", - "brain", - "cerebellum", - "feet", - "epithelia", - "skin", - "hair", - "lungs", - "pancreatic", - "nerves", - "nostrils", - ], - ), - ( - "go", - [ - "Wnt signaling", - "apoptosis", - "lactase", - "positive regulation of alpha-glucoside transport", - "development of lungs", - ], - ), - ] - for ontology, terms in cases: - ann = ke.map_terms(terms, ontology) - print(yaml.dump(ann)) - - def test_extract_from_pubmed(self): - """Tests end to end knowledge extraction.""" - ke = self.ke - pmc = PubmedClient() - text = pmc.text("PMID:27929086") - print(text) - ann = ke.extract_from_text(PAPER) - print(f"RESULTS={ann}") - print(yaml.dump(ann.dict())) - - def test_merge(self): - bp1 = BiologicalProcess( - label="bp", - description="d1", - synonyms=["s1a", "s1b", "shared"], - inputs=["c1", "c2"], - ) - bp2 = BiologicalProcess( - label="bp", - description="d2", - synonyms=["s2a", "s2b", "shared"], - outputs=["c3", "c4"], - ) - r1 = ExtractionResult(extracted_object=bp1) - r2 = ExtractionResult(extracted_object=bp2) - bp = self.ke.merge_resultsets([r1, r2]).extracted_object - print(yaml.dump(bp.dict())) - self.assertEqual("bp", bp.label) - self.assertEqual("d2", bp.description) - self.assertCountEqual(["s1a", "s1b", "s2a", "s2b", "shared"], bp.synonyms) - self.assertEqual(5, len(bp.synonyms), "Expected 5 distinct synonyms") - self.assertCountEqual(["c1", "c2", "c3", "c4"], bp.inputs + bp.outputs) - self.assertCountEqual(["c1", "c2"], bp.inputs) - self.assertCountEqual(["c3", "c4"], bp.outputs) - - def test_merge_with_pmids(self): - """Tests end to end knowledge extraction.""" - ke = self.ke - pmids = ["32716108", "27929086"] - pmc = PubmedClient() - rsets = [] - for pmid in pmids: - text = pmc.text(f"PMID:{pmid}") - rsets.append(ke.extract_from_text(text)) - print(f"Merging {len(rsets)} results") - merged = ke.merge_resultsets(rsets) - print(yaml.dump(merged.dict())) diff --git a/tests/output/README.md b/tests/output/README.md deleted file mode 100644 index 4460bf088..000000000 --- a/tests/output/README.md +++ /dev/null @@ -1 +0,0 @@ -Test results here diff --git a/tests/output/carbohydrate-metabolism.hallucinated.halo.yaml b/tests/output/carbohydrate-metabolism.hallucinated.halo.yaml deleted file mode 100644 index 42d9a24f5..000000000 --- a/tests/output/carbohydrate-metabolism.hallucinated.halo.yaml +++ /dev/null @@ -1,993 +0,0 @@ -elements: -- name: Fat-solubleVitaminMetabolicProcess - description: The chemical reactions and pathways involving of any of a diverse group - of vitamins that are soluble in organic solvents and relatively insoluble in water. - synonyms: - - fat-soluble vitamin metabolism - subclass_of: - - VitaminMetabolicProcess - subtypes: - - Fat-solubleVitaminCatabolicProcess - equivalent_to: MetabolicProcess and has primary input or output some SubstanceWithFat-solubleVitamin(role)Role -- name: LipidMetabolicProcess - description: The chemical reactions and pathways involving lipids, compounds soluble - in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty - acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols - and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and - sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids. - synonyms: - - lipid metabolism - subclass_of: - - PrimaryMetabolicProcess - - OrganicSubstanceMetabolicProcess - subtypes: - - SteroidMetabolicProcess - - LipidBiosyntheticProcess - - LipidCatabolicProcess - - CellularLipidMetabolicProcess - equivalent_to: MetabolicProcess and has primary input or output some Lipid -- name: OlefinicCompoundMetabolicProcess - description: The chemical reactions and pathways involving an olefinic compound, - any compound which contains a carbon-carbon double bond (aka C=C). - synonyms: - - alkene substituted compound metabolic process - - alkene substituted compound metabolism - subclass_of: - - OrganicSubstanceMetabolicProcess - subtypes: - - CortisolMetabolicProcess - - OlefinicCompoundBiosyntheticProcess - equivalent_to: MetabolicProcess and has primary input or output some OlefinicCompound -- name: TertiaryAlcoholMetabolicProcess - description: The chemical reactions and pathways involving tertiary alcohol. - synonyms: - - tertiary alcohol metabolism - subclass_of: - - AlcoholMetabolicProcess - subtypes: - - CortisolMetabolicProcess - - TertiaryAlcoholBiosyntheticProcess - equivalent_to: MetabolicProcess and has primary input or output some TertiaryAlcohol -- name: OrganicSubstanceBiosyntheticProcess - description: The chemical reactions and pathways resulting in the formation of an - organic substance, any molecular entity containing carbon. - synonyms: - - organic molecular entity anabolism - - organic molecular entity biosynthesis - - organic molecular entity biosynthetic process - - organic molecular entity formation - - organic molecular entity synthesis - - organic substance anabolism - - organic substance biosynthesis - - organic substance formation - - organic substance synthesis - subclass_of: - - BiosyntheticProcess - - OrganicSubstanceMetabolicProcess - subtypes: - - LipidBiosyntheticProcess - - KetoneBiosyntheticProcess - - OlefinicCompoundBiosyntheticProcess - - OrganicCyclicCompoundBiosyntheticProcess - - OrganicHydroxyCompoundBiosyntheticProcess - equivalent_to: BiosyntheticProcess and has primary output some OrganicMolecularEntity -- name: HormoneMetabolicProcess - description: The chemical reactions and pathways involving any hormone, naturally - occurring substances secreted by specialized cells that affects the metabolism - or behavior of other cells possessing functional receptors for the hormone. - synonyms: - - hormone metabolism - - cellular hormone metabolic process - subclass_of: - - MetabolicProcess - - RegulationOfHormoneLevels - subtypes: - - RetinoicAcidMetabolicProcess - equivalent_to: MetabolicProcess and has primary input or output some SubstanceWithHormoneRole -- name: OrganicSubstanceCatabolicProcess - description: The chemical reactions and pathways resulting in the breakdown of an - organic substance, any molecular entity containing carbon. - synonyms: - - organic molecular entity breakdown - - organic molecular entity catabolic process - - organic molecular entity catabolism - - organic molecular entity degradation - - organic substance breakdown - - organic substance catabolism - - organic substance degradation - subclass_of: - - CatabolicProcess - - OrganicSubstanceMetabolicProcess - subtypes: - - LipidCatabolicProcess - - OrganicAcidCatabolicProcess - equivalent_to: CatabolicProcess and has primary input some OrganicMolecularEntity -- name: AlcoholBiosyntheticProcess - description: The chemical reactions and pathways resulting in the formation of alcohols, - any of a class of compounds containing one or more hydroxyl groups attached to - a saturated carbon atom. - synonyms: - - alcohol anabolism - - alcohol biosynthesis - - alcohol formation - - alcohol synthesis - subclass_of: - - AlcoholMetabolicProcess - - SmallMoleculeBiosyntheticProcess - - OrganicHydroxyCompoundBiosyntheticProcess - subtypes: - - PrimaryAlcoholBiosyntheticProcess - - TertiaryAlcoholBiosyntheticProcess - equivalent_to: BiosyntheticProcess and has primary output some Alcohol -- name: CellularKetoneMetabolicProcess - description: The chemical reactions and pathways involving any of a class of organic - compounds that contain the carbonyl group, CO, and in which the carbonyl group - is bonded only to carbon atoms, as carried out by individual cells. The general - formula for a ketone is RCOR, where R and R are alkyl or aryl groups. - synonyms: - - ketone metabolism - subclass_of: - - CellularMetabolicProcess - - SmallMoleculeMetabolicProcess - - OrganicSubstanceMetabolicProcess - subtypes: - - CortisolMetabolicProcess - - KetoneBiosyntheticProcess - equivalent_to: MetabolicProcess and has primary input or output some Ketone -- name: CarboxylicAcidMetabolicProcess - description: The chemical reactions and pathways involving carboxylic acids, any - organic acid containing one or more carboxyl (COOH) groups or anions (COO-). - synonyms: - - carboxylic acid metabolism - subclass_of: - - OxoacidMetabolicProcess - subtypes: - - MonocarboxylicAcidMetabolicProcess - - CarboxylicAcidCatabolicProcess - equivalent_to: MetabolicProcess and has primary input or output some CarboxylicAcidAnion -- name: GlucocorticoidMetabolicProcess - description: The chemical reactions and pathways involving glucocorticoids, hormonal - C21 corticosteroids synthesized from cholesterol. Glucocorticoids act primarily - on carbohydrate and protein metabolism, and have anti-inflammatory effects. - synonyms: - - glucocorticoid metabolism - - glucocorticosteroid metabolic process - - glucocorticosteroid metabolism - subclass_of: - - SteroidMetabolicProcess - subtypes: - - GlucocorticoidBiosyntheticProcess - - CortisolMetabolicProcess - equivalent_to: MetabolicProcess and has primary input or output some Glucocorticoid -- name: CellularLipidMetabolicProcess - description: The chemical reactions and pathways involving lipids, as carried out - by individual cells. - synonyms: - - cellular lipid metabolism - subclass_of: - - LipidMetabolicProcess - - CellularMetabolicProcess - subtypes: - - IsoprenoidMetabolicProcess - - CellularLipidCatabolicProcess -- name: OlefinicCompoundBiosyntheticProcess - description: The chemical reactions and pathways resulting in the formation of an - olefinic compound, any compound which contains a carbon-carbon double bond (aka - C=C). - synonyms: - - alkene substituted compound anabolic process - - alkene substituted compound anabolism - - alkene substituted compound biosynthesis - - alkene substituted compound biosynthetic process - - alkene substituted compound synthesis - subclass_of: - - OlefinicCompoundMetabolicProcess - - OrganicSubstanceBiosyntheticProcess - subtypes: - - CortisolBiosyntheticProcess - equivalent_to: BiosyntheticProcess and has primary output some OlefinicCompound -- name: CellularProcess - description: Any process that is carried out at the cellular level, but not necessarily - restricted to a single cell. For example, cell communication occurs among more - than one cell, but occurs at the cellular level. - synonyms: - - cell physiology - - cellular physiological process - - cell growth and/or maintenance - - single-organism cellular process - subclass_of: - - BiologicalProcess - subtypes: - - CellularMetabolicProcess -- name: LipidBiosyntheticProcess - description: The chemical reactions and pathways resulting in the formation of lipids, - compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. - synonyms: - - lipid anabolism - - lipid biosynthesis - - lipid formation - - lipid synthesis - - lipogenesis - subclass_of: - - LipidMetabolicProcess - - OrganicSubstanceBiosyntheticProcess - subtypes: - - SteroidBiosyntheticProcess - equivalent_to: BiosyntheticProcess and has primary output some Lipid -- name: CellularBiosyntheticProcess - description: The chemical reactions and pathways resulting in the formation of substances, - carried out by individual cells. - synonyms: - - cellular anabolism - - cellular biosynthesis - - cellular formation - - cellular synthesis - subclass_of: - - BiosyntheticProcess - - CellularMetabolicProcess - subtypes: - - KetoneBiosyntheticProcess -- name: SteroidMetabolicProcess - description: The chemical reactions and pathways involving steroids, compounds with - a 1,2,cyclopentanoperhydrophenanthrene nucleus. - synonyms: - - steroid metabolism - subclass_of: - - LipidMetabolicProcess - - OrganicCyclicCompoundMetabolicProcess - subtypes: - - SteroidBiosyntheticProcess - - GlucocorticoidMetabolicProcess - equivalent_to: MetabolicProcess and has primary input or output some Steroid -- name: PrimaryAlcoholBiosyntheticProcess - description: The chemical reactions and pathways resulting in the formation of primary - alcohols. A primary alcohol is any alcohol in which a hydroxy group, -OH, is attached - to a saturated carbon atom which has either three hydrogen atoms attached to it - or only one other carbon atom and two hydrogen atoms attached to it. - synonyms: - - monohydric alcohol biosynthetic process - - primary alcohol anabolism - - primary alcohol biosynthesis - - primary alcohol formation - - primary alcohol synthesis - subclass_of: - - PrimaryAlcoholMetabolicProcess - - AlcoholBiosyntheticProcess - subtypes: - - CortisolBiosyntheticProcess - equivalent_to: BiosyntheticProcess and has primary output some PrimaryAlcohol -- name: KetoneBiosyntheticProcess - description: The chemical reactions and pathways resulting in the formation of ketones, - a class of organic compounds that contain the carbonyl group, CO, and in which - the carbonyl group is bonded only to carbon atoms. The general formula for a ketone - is RCOR, where R and R are alkyl or aryl groups. - synonyms: - - ketone anabolism - - ketone biosynthesis - - ketone formation - - ketone synthesis - subclass_of: - - CellularKetoneMetabolicProcess - - CellularBiosyntheticProcess - - SmallMoleculeBiosyntheticProcess - - OrganicSubstanceBiosyntheticProcess - subtypes: - - CortisolBiosyntheticProcess - equivalent_to: BiosyntheticProcess and has primary output some Ketone -- name: Occurrent - description: An entity that has temporal parts and that happens, unfolds or develops - through time. - subtypes: - - Process -- name: CortisolBiosyntheticProcess - description: The chemical reactions and pathways resulting in the formation of cortisol, - the steroid hormone 11-beta-17,21-trihydroxypregn-4-ene-3,20-dione. Cortisol is - synthesized from cholesterol in the adrenal gland and controls carbohydrate, fat - and protein metabolism and has anti-inflammatory properties. - synonyms: - - cortisol biosynthesis - - cortisol formation - - cortisol synthesis - - cortisol anabolism - subclass_of: - - GlucocorticoidBiosyntheticProcess - - PrimaryAlcoholBiosyntheticProcess - - CortisolMetabolicProcess - - KetoneBiosyntheticProcess - - OlefinicCompoundBiosyntheticProcess - - TertiaryAlcoholBiosyntheticProcess - equivalent_to: BiosyntheticProcess and has primary output some Cortisol -- name: OrganicSubstanceMetabolicProcess - description: The chemical reactions and pathways involving an organic substance, - any molecular entity containing carbon. - synonyms: - - organic molecular entity metabolic process - - organic molecular entity metabolism - - organic substance metabolism - subclass_of: - - MetabolicProcess - subtypes: - - OrganicAcidMetabolicProcess - - LipidMetabolicProcess - - CellularKetoneMetabolicProcess - - OlefinicCompoundMetabolicProcess - - OrganicCyclicCompoundMetabolicProcess - - OrganicSubstanceCatabolicProcess - - OrganicSubstanceBiosyntheticProcess - - OrganicHydroxyCompoundMetabolicProcess - equivalent_to: MetabolicProcess and has primary input or output some OrganicMolecularEntity -- name: OrganicCyclicCompoundBiosyntheticProcess - description: The chemical reactions and pathways resulting in the formation of organic - cyclic compound. - synonyms: - - organic cyclic compound anabolism - - organic cyclic compound biosynthesis - - organic cyclic compound formation - - organic cyclic compound synthesis - subclass_of: - - OrganicCyclicCompoundMetabolicProcess - - OrganicSubstanceBiosyntheticProcess - subtypes: - - SteroidBiosyntheticProcess - equivalent_to: BiosyntheticProcess and has primary output some OrganicCyclicCompound -- name: OrganicHydroxyCompoundMetabolicProcess - description: The chemical reactions and pathways involving organic hydroxy compound. - synonyms: - - organic hydroxy compound metabolism - subclass_of: - - OrganicSubstanceMetabolicProcess - subtypes: - - AlcoholMetabolicProcess - - OrganicHydroxyCompoundBiosyntheticProcess - equivalent_to: MetabolicProcess and has primary input or output some OrganicHydroxyCompound -- name: OrganicHydroxyCompoundBiosyntheticProcess - description: The chemical reactions and pathways resulting in the formation of organic - hydroxy compound. - synonyms: - - organic hydroxy compound anabolism - - organic hydroxy compound biosynthesis - - organic hydroxy compound formation - - organic hydroxy compound synthesis - subclass_of: - - OrganicSubstanceBiosyntheticProcess - - OrganicHydroxyCompoundMetabolicProcess - subtypes: - - AlcoholBiosyntheticProcess - equivalent_to: BiosyntheticProcess and has primary output some OrganicHydroxyCompound -- name: IsoprenoidMetabolicProcess - description: The chemical reactions and pathways involving isoprenoid compounds, - isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked - isoprene (3-methyl-2-butenylene) residues. - synonyms: - - isoprenoid metabolism - - polyisoprenoid metabolic process - - polyisoprenoid metabolism - - polyterpene metabolic process - - polyterpene metabolism - subclass_of: - - CellularLipidMetabolicProcess - subtypes: - - TerpenoidMetabolicProcess - - IsoprenoidCatabolicProcess - equivalent_to: MetabolicProcess and has primary input or output some Isoprenoid -- name: TerpenoidMetabolicProcess - description: The chemical reactions and pathways involving terpenoids, any member - of a class of compounds characterized by an isoprenoid chemical structure and - including derivatives with various functional groups. - synonyms: - - terpenoid metabolism - subclass_of: - - IsoprenoidMetabolicProcess - subtypes: - - DiterpenoidMetabolicProcess - - TerpenoidCatabolicProcess - equivalent_to: MetabolicProcess and has primary input or output some Terpenoid -- name: IsoprenoidCatabolicProcess - description: The chemical reactions and pathways resulting in the breakdown of an - isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing - or derived from linked isoprene (3-methyl-2-butenylene) residues. - synonyms: - - isoprenoid breakdown - - isoprenoid catabolism - - isoprenoid degradation - - polyisoprenoid breakdown - - polyisoprenoid catabolic process - - polyisoprenoid catabolism - - polyisoprenoid degradation - - polyterpene catabolic process - - polyterpene catabolism - subclass_of: - - IsoprenoidMetabolicProcess - - CellularLipidCatabolicProcess - subtypes: - - TerpenoidCatabolicProcess - equivalent_to: CatabolicProcess and has primary input some Isoprenoid -- name: CatabolicProcess - description: The chemical reactions and pathways resulting in the breakdown of substances, - including the breakdown of carbon compounds with the liberation of energy for - use by the cell or organism. - synonyms: - - breakdown - - catabolism - - degradation - - multicellular organismal catabolic process - - single-organism catabolic process - subclass_of: - - MetabolicProcess - subtypes: - - CellularCatabolicProcess - - SmallMoleculeCatabolicProcess - - OrganicSubstanceCatabolicProcess -- name: DiterpenoidCatabolicProcess - description: The chemical reactions and pathways resulting in the breakdown of diterpenoid - compounds, terpenoids with four isoprene units. - synonyms: - - diterpenoid breakdown - - diterpenoid catabolism - - diterpenoid degradation - - diterpene catabolic process - - diterpene catabolism - subclass_of: - - DiterpenoidMetabolicProcess - - TerpenoidCatabolicProcess - subtypes: - - RetinoicAcidCatabolicProcess - equivalent_to: CatabolicProcess and has primary input some Diterpenoid -- name: LipidCatabolicProcess - description: The chemical reactions and pathways resulting in the breakdown of lipids, - compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. - synonyms: - - lipid breakdown - - lipid catabolism - - lipid degradation - - lipolysis - - multicellular organism lipid catabolic process - - multicellular organismal lipid catabolic process - subclass_of: - - LipidMetabolicProcess - - OrganicSubstanceCatabolicProcess - subtypes: - - CellularLipidCatabolicProcess - equivalent_to: CatabolicProcess and has primary input some Lipid -- name: Fat-solubleVitaminCatabolicProcess - description: The chemical reactions and pathways resulting in the breakdown of any - of a diverse group of vitamins that are soluble in organic solvents and relatively - insoluble in water. - synonyms: - - fat-soluble vitamin breakdown - - fat-soluble vitamin catabolism - - fat-soluble vitamin degradation - subclass_of: - - Fat-solubleVitaminMetabolicProcess - - VitaminCatabolicProcess - subtypes: - - RetinoicAcidCatabolicProcess - equivalent_to: CatabolicProcess and has primary input some SubstanceWithFat-solubleVitamin(role)Role -- name: RetinoicAcidMetabolicProcess - description: The chemical reactions and pathways involving retinoic acid, one of - the three components that makes up vitamin A. - synonyms: - - retinoic acid metabolism - - vitamin A1 acid metabolic process - - vitamin A1 acid metabolism - subclass_of: - - RetinoidMetabolicProcess - - MonocarboxylicAcidMetabolicProcess - - HormoneMetabolicProcess - subtypes: - - RetinoicAcidCatabolicProcess - equivalent_to: MetabolicProcess and has primary input or output some Retinoate -- name: OxoacidMetabolicProcess - description: The chemical reactions and pathways involving any oxoacid; an oxoacid - is a compound which contains oxygen, at least one other element, and at least - one hydrogen bound to oxygen, and which produces a conjugate base by loss of positive - hydrogen ion(s) (hydrons). - synonyms: - - keto acid metabolic process - - keto acid metabolism - - ketoacid metabolic process - - ketoacid metabolism - - oxo acid metabolic process - - oxo acid metabolism - - oxoacid metabolism - subclass_of: - - OrganicAcidMetabolicProcess - subtypes: - - CarboxylicAcidMetabolicProcess - equivalent_to: MetabolicProcess and has primary input or output some Oxoanion -- name: MetabolicProcess - description: The chemical reactions and pathways, including anabolism and catabolism, - by which living organisms transform chemical substances. Metabolic processes typically - transform small molecules, but also include macromolecular processes such as DNA - repair and replication, and protein synthesis and degradation. - synonyms: - - metabolism - - metabolic process resulting in cell growth - - metabolism resulting in cell growth - - multicellular organism metabolic process - - single-organism metabolic process - subclass_of: - - BiologicalProcess - subtypes: - - CatabolicProcess - - BiosyntheticProcess - - HormoneMetabolicProcess - - CellularMetabolicProcess - - PrimaryMetabolicProcess - - SmallMoleculeMetabolicProcess - - OrganicSubstanceMetabolicProcess -- name: CarboxylicAcidCatabolicProcess - description: The chemical reactions and pathways resulting in the breakdown of carboxylic - acids, any organic acid containing one or more carboxyl (-COOH) groups. - synonyms: - - carboxylic acid breakdown - - carboxylic acid catabolism - - carboxylic acid degradation - subclass_of: - - OrganicAcidCatabolicProcess - - CarboxylicAcidMetabolicProcess - subtypes: - - MonocarboxylicAcidCatabolicProcess - equivalent_to: CatabolicProcess and has primary input some CarboxylicAcidAnion -- name: SteroidHormoneBiosyntheticProcess - description: The chemical reactions and pathways resulting in the formation of any - steroid hormone, naturally occurring substances secreted by specialized cells - that affects the metabolism or behavior of other cells possessing functional receptors - for the hormone. - subclass_of: - - SteroidBiosyntheticProcess - subtypes: - - GlucocorticoidBiosyntheticProcess - equivalent_to: SteroidBiosyntheticProcess and has output some SteroidHormone -- name: GlucocorticoidBiosyntheticProcess - description: The chemical reactions and pathways resulting in the formation of glucocorticoids, - hormonal C21 corticosteroids synthesized from cholesterol. - synonyms: - - glucocorticoid anabolism - - glucocorticoid biosynthesis - - glucocorticoid formation - - glucocorticoid synthesis - subclass_of: - - GlucocorticoidMetabolicProcess - - SteroidHormoneBiosyntheticProcess - subtypes: - - CortisolBiosyntheticProcess - equivalent_to: BiosyntheticProcess and has primary output some Glucocorticoid -- name: TertiaryAlcoholBiosyntheticProcess - description: The chemical reactions and pathways resulting in the formation of tertiary - alcohol. - synonyms: - - tertiary alcohol anabolism - - tertiary alcohol biosynthesis - - tertiary alcohol formation - - tertiary alcohol synthesis - subclass_of: - - AlcoholBiosyntheticProcess - - TertiaryAlcoholMetabolicProcess - subtypes: - - CortisolBiosyntheticProcess - equivalent_to: BiosyntheticProcess and has primary output some TertiaryAlcohol -- name: VitaminMetabolicProcess - description: The chemical reactions and pathways involving vitamins. Vitamin is - a general term for a number of unrelated organic substances that occur in many - foods in small amounts and that are necessary in trace amounts for the normal - metabolic functioning of the body. Vitamins may be water-soluble or fat-soluble - and usually serve as components of coenzyme systems. - synonyms: - - vitamin metabolism - subclass_of: - - SmallMoleculeMetabolicProcess - subtypes: - - Fat-solubleVitaminMetabolicProcess - - VitaminCatabolicProcess - equivalent_to: MetabolicProcess and has primary input or output some SubstanceWithVitamin(role)Role -- name: SmallMoleculeBiosyntheticProcess - description: The chemical reactions and pathways resulting in the formation of small - molecules, any low molecular weight, monomeric, non-encoded molecule. - synonyms: - - small molecule biosynthesis - subclass_of: - - BiosyntheticProcess - - SmallMoleculeMetabolicProcess - subtypes: - - KetoneBiosyntheticProcess - - AlcoholBiosyntheticProcess -- name: OrganicCyclicCompoundMetabolicProcess - description: The chemical reactions and pathways involving organic cyclic compound. - synonyms: - - organic cyclic compound metabolism - subclass_of: - - OrganicSubstanceMetabolicProcess - subtypes: - - SteroidMetabolicProcess - - OrganicCyclicCompoundBiosyntheticProcess - equivalent_to: MetabolicProcess and has primary input or output some OrganicCyclicCompound -- name: OrganicAcidMetabolicProcess - description: The chemical reactions and pathways involving organic acids, any acidic - compound containing carbon in covalent linkage. - synonyms: - - organic acid metabolism - subclass_of: - - CellularMetabolicProcess - - SmallMoleculeMetabolicProcess - - OrganicSubstanceMetabolicProcess - subtypes: - - OrganicAcidCatabolicProcess - - OxoacidMetabolicProcess - equivalent_to: MetabolicProcess and has primary input or output some OrganicAcid -- name: OrganicAcidCatabolicProcess - description: The chemical reactions and pathways resulting in the breakdown of organic - acids, any acidic compound containing carbon in covalent linkage. - synonyms: - - organic acid breakdown - - organic acid catabolism - - organic acid degradation - subclass_of: - - OrganicAcidMetabolicProcess - - CellularCatabolicProcess - - SmallMoleculeCatabolicProcess - - OrganicSubstanceCatabolicProcess - subtypes: - - CarboxylicAcidCatabolicProcess - equivalent_to: CatabolicProcess and has primary input some OrganicAcid -- name: SmallMoleculeCatabolicProcess - description: The chemical reactions and pathways resulting in the breakdown of small - molecules, any low molecular weight, monomeric, non-encoded molecule. - synonyms: - - small molecule catabolism - subclass_of: - - CatabolicProcess - - SmallMoleculeMetabolicProcess - subtypes: - - VitaminCatabolicProcess - - OrganicAcidCatabolicProcess -- name: RegulationOfBiologicalQuality - description: Any process that modulates a qualitative or quantitative trait of a - biological quality. A biological quality is a measurable attribute of an organism - or part of an organism, such as size, mass, shape, color, etc. - synonyms: - - regulation of biological attribute - - regulation of biological characteristic - subclass_of: - - BiologicalRegulation - subtypes: - - RegulationOfHormoneLevels - equivalent_to: BiologicalRegulation and regulates characteristic some BiologicalAttribute -- name: CellularLipidCatabolicProcess - description: The chemical reactions and pathways resulting in the breakdown of lipids, - as carried out by individual cells. - synonyms: - - cellular lipid breakdown - - cellular lipid catabolism - - cellular lipid degradation - subclass_of: - - LipidCatabolicProcess - - CellularCatabolicProcess - - CellularLipidMetabolicProcess - subtypes: - - IsoprenoidCatabolicProcess -- name: CortisolMetabolicProcess - description: The chemical reactions and pathways involving cortisol, the steroid - hormone 11-beta-17,21-trihydroxypregn-4-ene-3,20-dione. Cortisol is synthesized - from cholesterol in the adrenal gland and controls carbohydrate, fat and protein - metabolism and has anti-inflammatory properties. - synonyms: - - cortisol metabolism - subclass_of: - - GlucocorticoidMetabolicProcess - - PrimaryAlcoholMetabolicProcess - - CellularKetoneMetabolicProcess - - OlefinicCompoundMetabolicProcess - - TertiaryAlcoholMetabolicProcess - subtypes: - - CortisolBiosyntheticProcess - equivalent_to: MetabolicProcess and has primary input or output some Cortisol -- name: BiosyntheticProcess - description: The chemical reactions and pathways resulting in the formation of substances; - typically the energy-requiring part of metabolism in which simpler substances - are transformed into more complex ones. - synonyms: - - formation - - anabolism - - biosynthesis - - synthesis - - multicellular organismal biosynthetic process - - single-organism biosynthetic process - subclass_of: - - MetabolicProcess - subtypes: - - CellularBiosyntheticProcess - - SmallMoleculeBiosyntheticProcess - - OrganicSubstanceBiosyntheticProcess -- name: SteroidBiosyntheticProcess - description: The chemical reactions and pathways resulting in the formation of steroids, - compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus; includes de novo - formation and steroid interconversion by modification. - synonyms: - - steroid anabolism - - steroid biosynthesis - - steroid formation - - steroid synthesis - - steroidogenesis - subclass_of: - - SteroidMetabolicProcess - - LipidBiosyntheticProcess - - OrganicCyclicCompoundBiosyntheticProcess - subtypes: - - SteroidHormoneBiosyntheticProcess - equivalent_to: BiosyntheticProcess and has primary output some Steroid -- name: BiologicalProcess - description: A biological process represents a specific objective that the organism - is genetically programmed to achieve. Biological processes are often described - by their outcome or ending state, e.g., the biological process of cell division - results in the creation of two daughter cells (a divided cell) from a single parent - cell. A biological process is accomplished by a particular set of molecular functions - carried out by specific gene products (or macromolecular complexes), often in - a highly regulated manner and in a particular temporal sequence. - synonyms: - - biological process - - physiological process - - single organism process - - single-organism process - subclass_of: - - Process - subtypes: - - MetabolicProcess - - CellularProcess - - BiologicalRegulation -- name: RetinoidMetabolicProcess - description: The chemical reactions and pathways involving retinoids, any member - of a class of isoprenoids that contain or are derived from four prenyl groups - linked head-to-tail. Retinoids include retinol and retinal and structurally similar - natural derivatives or synthetic compounds, but need not have vitamin A activity. - synonyms: - - retinoid metabolism - subclass_of: - - DiterpenoidMetabolicProcess - subtypes: - - RetinoicAcidMetabolicProcess - equivalent_to: MetabolicProcess and has primary input or output some Retinoid -- name: DiterpenoidMetabolicProcess - description: The chemical reactions and pathways involving diterpenoid compounds, - terpenoids with four isoprene units. - synonyms: - - diterpenoid metabolism - - diterpene metabolic process - - diterpene metabolism - subclass_of: - - TerpenoidMetabolicProcess - subtypes: - - RetinoidMetabolicProcess - - DiterpenoidCatabolicProcess - equivalent_to: MetabolicProcess and has primary input or output some Diterpenoid -- name: AlcoholMetabolicProcess - description: The chemical reactions and pathways involving alcohols, any of a class - of compounds containing one or more hydroxyl groups attached to a saturated carbon - atom. - synonyms: - - alcohol metabolism - subclass_of: - - SmallMoleculeMetabolicProcess - - OrganicHydroxyCompoundMetabolicProcess - subtypes: - - PrimaryAlcoholMetabolicProcess - - AlcoholBiosyntheticProcess - - TertiaryAlcoholMetabolicProcess - equivalent_to: MetabolicProcess and has primary input or output some Alcohol -- name: MonocarboxylicAcidMetabolicProcess - description: The chemical reactions and pathways involving monocarboxylic acids, - any organic acid containing one carboxyl (COOH) group or anion (COO-). - synonyms: - - monocarboxylate metabolic process - - monocarboxylic acid metabolism - subclass_of: - - CarboxylicAcidMetabolicProcess - subtypes: - - RetinoicAcidMetabolicProcess - - MonocarboxylicAcidCatabolicProcess - equivalent_to: MetabolicProcess and has primary input or output some MonocarboxylicAcidAnion -- name: BiologicalRegulation - description: Any process that modulates a measurable attribute of any biological - process, quality or function. - synonyms: - - regulation - subclass_of: - - BiologicalProcess - subtypes: - - RegulationOfBiologicalQuality -- name: CellularCatabolicProcess - description: The chemical reactions and pathways resulting in the breakdown of substances, - carried out by individual cells. - synonyms: - - cellular breakdown - - cellular catabolism - - cellular degradation - subclass_of: - - CatabolicProcess - - CellularMetabolicProcess - subtypes: - - VitaminCatabolicProcess - - OrganicAcidCatabolicProcess - - CellularLipidCatabolicProcess -- name: Process - description: An occurrent that has temporal proper parts and for some time t, p - s-depends_on some material entity at t. - subclass_of: - - Occurrent - subtypes: - - BiologicalProcess -- name: PrimaryAlcoholMetabolicProcess - description: The chemical reactions and pathways involving primary alcohols. A primary - alcohol is any alcohol in which a hydroxy group, -OH, is attached to a saturated - carbon atom which has either three hydrogen atoms attached to it or only one other - carbon atom and two hydrogen atoms attached to it. - synonyms: - - monohydric alcohol metabolic process - - primary alcohol metabolism - subclass_of: - - AlcoholMetabolicProcess - subtypes: - - PrimaryAlcoholBiosyntheticProcess - - CortisolMetabolicProcess - equivalent_to: MetabolicProcess and has primary input or output some PrimaryAlcohol -- name: TerpenoidCatabolicProcess - description: The chemical reactions and pathways resulting in the breakdown of terpenoids, - any member of a class of compounds characterized by an isoprenoid chemical structure. - synonyms: - - terpenoid breakdown - - terpenoid catabolism - - terpenoid degradation - subclass_of: - - TerpenoidMetabolicProcess - - IsoprenoidCatabolicProcess - subtypes: - - DiterpenoidCatabolicProcess - equivalent_to: CatabolicProcess and has primary input some Terpenoid -- name: MonocarboxylicAcidCatabolicProcess - description: The chemical reactions and pathways resulting in the breakdown of monocarboxylic - acids, any organic acid containing one carboxyl (-COOH) group. - subclass_of: - - MonocarboxylicAcidMetabolicProcess - - CarboxylicAcidCatabolicProcess - subtypes: - - RetinoicAcidCatabolicProcess - equivalent_to: CatabolicProcess and has primary input some MonocarboxylicAcidAnion -- name: SmallMoleculeMetabolicProcess - description: The chemical reactions and pathways involving small molecules, any - low molecular weight, monomeric, non-encoded molecule. - synonyms: - - small molecule metabolism - subclass_of: - - MetabolicProcess - subtypes: - - AlcoholMetabolicProcess - - OrganicAcidMetabolicProcess - - VitaminMetabolicProcess - - CellularKetoneMetabolicProcess - - SmallMoleculeCatabolicProcess - - SmallMoleculeBiosyntheticProcess -- name: RegulationOfHormoneLevels - description: Any process that modulates the levels of hormone within an organism - or a tissue. A hormone is any substance formed in very small amounts in one specialized - organ or group of cells and carried (sometimes in the bloodstream) to another - organ or group of cells in the same organism, upon which it has a specific regulatory - action. - subclass_of: - - RegulationOfBiologicalQuality - subtypes: - - HormoneMetabolicProcess - equivalent_to: BiologicalRegulation and regulates characteristic some HormoneLevels -- name: VitaminCatabolicProcess - description: The chemical reactions and pathways resulting in the breakdown of a - vitamin, one of a number of unrelated organic substances that occur in many foods - in small amounts and that are necessary in trace amounts for the normal metabolic - functioning of the body. - synonyms: - - vitamin breakdown - - vitamin catabolism - - vitamin degradation - subclass_of: - - VitaminMetabolicProcess - - CellularCatabolicProcess - - SmallMoleculeCatabolicProcess - subtypes: - - Fat-solubleVitaminCatabolicProcess - equivalent_to: CatabolicProcess and has primary input some SubstanceWithVitamin(role)Role -- name: PrimaryMetabolicProcess - description: The chemical reactions and pathways involving those compounds which - are formed as a part of the normal anabolic and catabolic processes. These processes - take place in most, if not all, cells of the organism. - synonyms: - - primary metabolism - subclass_of: - - MetabolicProcess - subtypes: - - LipidMetabolicProcess -- name: CellularMetabolicProcess - description: The chemical reactions and pathways by which individual cells transform - chemical substances. - synonyms: - - cellular metabolism - - intermediary metabolism - subclass_of: - - MetabolicProcess - - CellularProcess - subtypes: - - OrganicAcidMetabolicProcess - - CellularKetoneMetabolicProcess - - CellularCatabolicProcess - - CellularBiosyntheticProcess - - CellularLipidMetabolicProcess -- name: RetinoicAcidCatabolicProcess - description: The chemical reactions and pathways resulting in the breakdown of retinoic - acid, one of the three components that makes up vitamin A. - synonyms: - - retinoic acid breakdown - - retinoic acid catabolism - - retinoic acid degradation - - vitamin A1 acid catabolic process - subclass_of: - - DiterpenoidCatabolicProcess - - Fat-solubleVitaminCatabolicProcess - - RetinoicAcidMetabolicProcess - - MonocarboxylicAcidCatabolicProcess - equivalent_to: CatabolicProcess and has primary input some Retinoate -- name: KetoaldopentoseBiosyntheticProcess - context: metabolism - description: The chemical reactions and pathways resulting in the formation of ketoaldopentose. -- name: IsomaltotrioseMetabolicProcess - context: metabolism - description: The chemical reactions and pathways involving any isomaltotriose, an - isomeric mixture of 3-alpha, 6-alpha-disaccharide containing an alpha prenyle - group. - synonyms: - - isomaltotriose metabolism - categories: - - metabolism - subtypes: - - IsomaltotrioseBiosyntheticProcess - - IsomaltotrioseCatabolicProcess - equivalent_to: MetabolicProcess and has primary input or output some Isomaltotriose -- name: IsomaltotrioseBiosyntheticProcess - context: metabolism - description: The chemical reactions and pathways resulting in the formation of any - isomaltotriose, an isomeric mixture of 3-alpha, 6-alpha-disaccharide containing - an alpha prenyle group. - synonyms: - - isomaltotriose biosynthesis - - isomaltotriose formation - - isomaltotriose synthesis - - isomaltotriose anabolism - subclass_of: - - AcylglucosideBiosyntheticProcess - - IsomaltotrioseMetabolicProcess - equivalent_to: BiosyntheticProcess and has primary output some Isomaltotriose -- name: IsomaltotrioseCatabolicProcess - context: metabolism - description: The chemical reactions and pathways resulting in the breakdown of an - isomaltotriose, an isomeric mixture of 3-alpha, 6-alpha-disaccharide containing - an alpha prenyle group. - synonyms: - - isomaltotriose breakdown - - isomaltotriose degradation - subclass_of: - - IsomaltotrioseMetabolicProcess - part_of: - - AcylglucosideCatabolicProcess - equivalent_to: CatabolicProcess and has primary input some Isomaltotriose -- name: AcylglucosideBiosyntheticProcess - context: metabolism - synonyms: - - acylglucoside anabolism - - acylglucoside biosynthesis - - acylglucoside biosynthetic process - - acylglucoside formation - - acyl glucoside biosynthetic process - - acyl glucoside formation - - acyl glucoside biosynthesis - - acyl glucoside synthesis - - acylglucoside synthesis - categories: - - AcylglucosideBiosyntheticProcess - - anabolic_process - - organic_substance_biosynthetic_process diff --git a/tests/output/drug-DB00316-moa.pickle b/tests/output/drug-DB00316-moa.pickle deleted file mode 100644 index 4d80fc6dc..000000000 Binary files a/tests/output/drug-DB00316-moa.pickle and /dev/null differ diff --git a/tests/output/drug-DB00316-moa.yaml b/tests/output/drug-DB00316-moa.yaml deleted file mode 100644 index 2be88f394..000000000 --- a/tests/output/drug-DB00316-moa.yaml +++ /dev/null @@ -1,106 +0,0 @@ -input_id: /Users/cjm/repos/ontogpt/tests/input/cases/drug-DB00316-moa.txt -input_text: 'According to its FDA labeling, acetaminophen''s exact mechanism of action - has not been fully establishedLabel - despite this, it is often categorized alongside - NSAIDs (nonsteroidal anti-inflammatory drugs) due to its ability to inhibit the - cyclooxygenase (COX) pathways.14 It is thought to exert central actions which ultimately - lead to the alleviation of pain symptoms.14 - - - One theory is that acetaminophen increases the pain threshold by inhibiting two - isoforms of cyclooxygenase, COX-1 and COX-2, which are involved in prostaglandin - (PG) synthesis. Prostaglandins are responsible for eliciting pain sensations.13 - Acetaminophen does not inhibit cyclooxygenase in peripheral tissues and, therefore, - has no peripheral anti-inflammatory effects. Though acetylsalicylic acid (aspirin) - is an irreversible inhibitor of COX and directly blocks the active site of this - enzyme, studies have shown that acetaminophen (paracetamol) blocks COX indirectly.24 - Studies also suggest that acetaminophen selectively blocks a variant type of the - COX enzyme that is unique from the known variants COX-1 and COX-2.6 This enzyme - has been referred to as COX-3. The antipyretic actions of acetaminophen are likely - attributed to direct action on heat-regulating centers in the brain, resulting in - peripheral vasodilation, sweating, and loss of body heat.24 The exact mechanism - of action of this drug is not fully understood at this time, but future research - may contribute to deeper knowledge' -raw_completion_output: 'Disease: Pain Symptoms; - - Drug: Acetaminophen; - - Mechanism_links: cyclooxygenase (COX)-pain sensations;13; COX-1-acetaminophen;14; - COX-2-acetaminophen;14; COX-3-acetaminophen;6; antipyretic-direct action on heat-regulating - centers;24' -prompt: 'Split the following piece of text into fields in the following format: - - - subject: - - predicate: - - object: - - - - Text: - - 24 - - - === - - - ' -extracted_object: - disease: AUTO:Pain%20Symptoms%3B - drug: AUTO:Acetaminophen%3B - mechanism_links: - - subject: MESH:D011451 - predicate: AUTO:-pain - object: MESH:D012677 - - subject: AUTO:COX-1 - predicate: AUTO:acetaminophen - object: AUTO:- - - subject: AUTO:14 - - subject: AUTO:COX-2 - predicate: - object: MESH:D000082 - - subject: AUTO:14 - - subject: AUTO:COX-3 - predicate: AUTO:acetaminophen - object: AUTO:- - - subject: MESH:D058633 - predicate: AUTO:direct%20action%20on - object: AUTO:heat-regulating%20centers - - subject: AUTO:24 -named_entities: -- id: AUTO:Pain%20Symptoms%3B - label: Pain Symptoms; -- id: AUTO:Acetaminophen%3B - label: Acetaminophen; -- id: MESH:D011451 - label: cyclooxygenase (COX) -- id: AUTO:-pain - label: -pain -- id: MESH:D012677 - label: sensations -- id: AUTO:COX-1 - label: COX-1 -- id: AUTO:acetaminophen - label: acetaminophen -- id: AUTO:- - label: '-' -- id: AUTO:14 - label: '14' -- id: AUTO:COX-2 - label: COX-2 -- id: - label: '-' -- id: MESH:D000082 - label: Acetaminophen -- id: AUTO:COX-3 - label: COX-3 -- id: MESH:D058633 - label: antipyretic -- id: AUTO:direct%20action%20on - label: direct action on -- id: AUTO:heat-regulating%20centers - label: heat-regulating centers -- id: AUTO:24 - label: '24' diff --git a/tests/output/drugmechdb-normalized.yaml.gz b/tests/output/drugmechdb-normalized.yaml.gz deleted file mode 100644 index e417300dc..000000000 Binary files a/tests/output/drugmechdb-normalized.yaml.gz and /dev/null differ diff --git a/tests/output/eds-output.html b/tests/output/eds-output.html deleted file mode 100644 index 5d622bf97..000000000 --- a/tests/output/eds-output.html +++ /dev/null @@ -1,573 +0,0 @@ -

Results: /Users/cjm/repos/semantic-llama/tests/input/cases/treatment-eds.txt - -

-

Input

-Disease: Ehlers Danlos Syndrome -Treatment: -The care of patients with EDS is generally focused on implementing preventative measures against serious or life-threatening complications. The primary complications seen in EDS involve the skin, musculoskeletal, and cardiovascular systems. Patient skin is velvety thin, loose, and stretchable. This predisposes patients to difficulties with wound healing. For both accidental and surgical wounds, deep stiches are applied generously. Superficial stiches are placed to carefully realign the skin to prevent scarring. Stiches are also left in for extended periods of time to allow best strengthening of the forming scar tissue. Ascorbic acid (Vitamin C) may be recommended to help reduce the easy bruising that accompanies EDS. Hypermobile joints easily dislocate. With each dislocation, subsequent dislocations are increasingly likely, therefore prevention is particularly important for quality of life. Heavy sports, lifting, and other strenuous efforts should be avoided due to the risk of inciting trauma. Blood vessel fragility increases the risk for serious bleeds and dissections. High blood pressure (hypertension) puts additional strain on the fragile vasculature and increases the risk for complications. Regular screening for hypertension and arterial disease should be conducted and treatment should be initiated early on. The best approaches to screening are by non-invasive technology: ultrasound, MRI, or CT. Arteriography, colonoscopy, and other similarly invasive screening procedures should be considered carefully for benefit versus risk. Surgery for non-life threatening conditions should also be carefully considered. Pregnancies should be followed by obstetricians that are well trained in dealing with high-risk pregnancies. Delivery can progress very quickly in EDS patients and it is yet unclear if there is an advantage to mothers to deliver by vaginal or cesarean routes. Expectant mothers with known aortic root dilations should have echocardiograms each trimester to observe for possible exacerbation. All EDS-affected individuals should seek immediate medical attention for any sudden or unexplained pains and consider wearing a MedicAlert bracelet to communicate their status as a patient with EDS should they lose consciousness. - -hEDS patients may especially benefit from physical therapy, low-resistance exercise, and assistive devices like braces, wheelchairs, and scooters. Comfortable writing utensils and a low-stress mattress serve an important role in reducing musculoskeletal pain. Pain management is tailored to the individual. Gastrointestinal and psychological complications are likewise managed per an individual’s needs. In addition to physical therapy and low-resistance exercise, calcium and vitamin D can help maximize bone density. DEXA bone density scans should be conducted every other year. kEDS patients should have routine eye exams as they are at risk for globus rupture, retinal detachment and glaucoma. dEDS patients may benefit from protective bandages over exposed areas such as the skin of the elbows and knees. - -

Results

-
-

disease

-Ehlers Danlos Syndrome MONDO:0020066 -

drugs

-
    -
  • item: 1:
    • -Ascorbic Acid (Vitamin C) -
-

treatments

-
    -
  • item: 1:
    • -Preventative measures -
  • item: 2:
    • -Deep stiches -
  • item: 3:
    • -Superficial stiches -
  • item: 4:
    • -Ascorbic Acid (Vitamin C) -
  • item: 5:
    • -Avoidance of heavy sports, lifting, and other strenuous efforts -
  • item: 6:
    • -Screening for hypertension and arterial disease -
  • item: 7:
    • -Non-invasive technology screening -
  • item: 8:
    • -Careful consideration of surgery for non-life threatening conditions -
  • item: 9:
    • -Monitoring during pregnancy -
  • item: 10:
    • -Physical therapy MAXO:0000011 -
  • item: 11:
    • -Low-resistance exercise -
  • item: 12:
    • -Assistive devices NCIT:C157792 -
  • item: 13:
    • -Comfortable writing utensils -
  • item: 14:
    • -Low-stress mattress -
  • item: 15:
    • -Pain management MAXO:0000457 -
  • item: 16:
    • -Calcium and vitamin D -
  • item: 17:
    • -DEXA bone density scans -
  • item: 18:
    • -Routine eye exams -
  • item: 19:
    • -Protective bandages -
-

treatment_mechanisms

-
    -
  • item: 1:
    • -
    -
      -
    • treatment:
      • -Deep stiches -
    • mechanism:
      • -Wound healing GO:0042060 -
        -
    -
  • item: 2:
    • -
    -
      -
    • treatment:
      • -Superficial stiches -
    • mechanism:
      • -scarring NCIT:C34483 -
        -
    -
  • item: 3:
    • -
    -
      -
    • treatment:
      • -Ascorbic Acid (Vitamin C) -
    • mechanism:
      • -bruising NCIT:C143345 -
        -
    -
  • item: 4:
    • -
    -
      -
    • treatment:
      • -Avoidance of heavy sports, lifting, and other strenuous efforts -
    • mechanism:
      • -prevention NCIT:C15405 -
        -
    -
  • item: 5:
    • -
    -
      -
    • treatment:
      • -hypertension HP:0000822 -
    • mechanism:
      • -arterial screening -
        -
    -
  • item: 6:
    • -
    -
      -
    • treatment:
      • -Non-invasive technology -
    • mechanism:
      • -screening*screening -
        -
    -
  • item: 7:
    • -
    -
    -
  • item: 8:
    • -
    -
      -
    • treatment:
      • -Monitoring during pregnancy -
    • mechanism:
      • -screening NCIT:C48261 -
        -
    -
  • item: 9:
    • -
    -
    -
  • item: 10:
    • -
    -
      -
    • treatment:
      • -Low-resistance exercise -
    • mechanism:
      • -musculoskeletal pain NCIT:C3244 -
        -
    -
  • item: 11:
    • -
    -
    -
  • item: 12:
    • -
    -
      -
    • treatment:
      • -writing utensils -
    • mechanism:
      • -musculoskeletal pain NCIT:C3244 -
        -
    -
  • item: 13:
    • -
    -
      -
    • treatment:
      • -Low-stress mattress -
    • mechanism:
      • -musculoskeletal pain NCIT:C3244 -
        -
    -
  • item: 14:
    • -
    -
    -
  • item: 15:
    • -
    -
      -
    • treatment:
      • -Calcium and vitamin D -
    • mechanism:
      • -bone density NCIT:C61545 -
        -
    -
  • item: 16:
    • -
    -
      -
    • treatment:
      • -DEXA bone density scans -
    • mechanism:
      • -bone density NCIT:C61545 -
        -
    -
  • item: 17:
    • -
    -
      -
    • treatment:
      • -Routine eye exams -
    • mechanism:
      • -globus rupture -
        -
    -
  • item: 18:
    • -
    -
      -
    • treatment:
      • -Retinal detachment NCIT:C26874 -
    • mechanism:
      • -None -
        -
    -
  • item: 19:
    • -
    -
    -
  • item: 20:
    • -
    -
      -
    • treatment:
      • -Protective bandages -
    • mechanism:
      • -protection -
        -
    -
-

treatment_efficacies

-
    -
  • item: 1:
    • -
    -
      -
    • treatment:
      • -Ascorbic Acid (Vitamin C) -
    • efficacy:
      • -effective -
        -
    -
  • item: 2:
    • -
    -
      -
    • treatment:
      • -Physical therapy MAXO:0000011 -
    • efficacy:
      • -effective -
        -
    -
  • item: 3:
    • -
    -
      -
    • treatment:
      • -Low-resistance exercise -
    • efficacy:
      • -effective -
        -
    -
  • item: 4:
    • -
    -
      -
    • treatment:
      • -Calcium and vitamin D -
    • efficacy:
      • -effective -
        -
    -
  • item: 5:
    • -
    -
      -
    • treatment:
      • -Routine eye exams -
    • efficacy:
      • -effective -
        -
    -
  • item: 6:
    • -
    -
      -
    • treatment:
      • -Protective bandages -
    • efficacy:
      • -effective -
        -
    -
-
-

YAML Object

-
-
-extracted_object:
-  disease: MONDO:0020066
-  drugs:
-  - Ascorbic Acid (Vitamin C)
-  treatment_efficacies:
-  - efficacy: effective
-    treatment: Ascorbic Acid (Vitamin C)
-  - efficacy: effective
-    treatment: MAXO:0000011
-  - efficacy: effective
-    treatment: Low-resistance exercise
-  - efficacy: effective
-    treatment: Calcium and vitamin D
-  - efficacy: effective
-    treatment: Routine eye exams
-  - efficacy: effective
-    treatment: Protective bandages
-  treatment_mechanisms:
-  - mechanism: GO:0042060
-    treatment: Deep stiches
-  - mechanism: NCIT:C34483
-    treatment: Superficial stiches
-  - mechanism: NCIT:C143345
-    treatment: Ascorbic Acid (Vitamin C)
-  - mechanism: NCIT:C15405
-    treatment: Avoidance of heavy sports, lifting, and other strenuous efforts
-  - mechanism: arterial screening
-    treatment: HP:0000822
-  - mechanism: screening*screening
-    treatment: Non-invasive technology
-  - mechanism: NCIT:C15405
-    treatment: MAXO:0000004
-  - mechanism: NCIT:C48261
-    treatment: Monitoring during pregnancy
-  - mechanism: NCIT:C3244
-    treatment: MAXO:0000011
-  - mechanism: NCIT:C3244
-    treatment: Low-resistance exercise
-  - mechanism: NCIT:C3244
-    treatment: NCIT:C157792
-  - mechanism: NCIT:C3244
-    treatment: writing utensils
-  - mechanism: NCIT:C3244
-    treatment: Low-stress mattress
-  - mechanism: NCIT:C15292
-    treatment: MAXO:0000457
-  - mechanism: NCIT:C61545
-    treatment: Calcium and vitamin D
-  - mechanism: NCIT:C61545
-    treatment: DEXA bone density scans
-  - mechanism: globus rupture
-    treatment: Routine eye exams
-  - mechanism: null
-    treatment: NCIT:C26874
-  - mechanism: NCIT:C18902
-    treatment: NCIT:C26782
-  - mechanism: protection
-    treatment: Protective bandages
-  treatments:
-  - Preventative measures
-  - Deep stiches
-  - Superficial stiches
-  - Ascorbic Acid (Vitamin C)
-  - Avoidance of heavy sports, lifting, and other strenuous efforts
-  - Screening for hypertension and arterial disease
-  - Non-invasive technology screening
-  - Careful consideration of surgery for non-life threatening conditions
-  - Monitoring during pregnancy
-  - MAXO:0000011
-  - Low-resistance exercise
-  - NCIT:C157792
-  - Comfortable writing utensils
-  - Low-stress mattress
-  - MAXO:0000457
-  - Calcium and vitamin D
-  - DEXA bone density scans
-  - Routine eye exams
-  - Protective bandages
-input_id: /Users/cjm/repos/semantic-llama/tests/input/cases/treatment-eds.txt
-input_text: "Disease: Ehlers Danlos Syndrome\nTreatment:\nThe care of patients with\
-  \ EDS is generally focused on implementing preventative measures against serious\
-  \ or life-threatening complications. The primary complications seen in EDS involve\
-  \ the skin, musculoskeletal, and cardiovascular systems. Patient skin is velvety\
-  \ thin, loose, and stretchable. This predisposes patients to difficulties with wound\
-  \ healing. For both accidental and surgical wounds, deep stiches are applied generously.\
-  \ Superficial stiches are placed to carefully realign the skin to prevent scarring.\
-  \ Stiches are also left in for extended periods of time to allow best strengthening\
-  \ of the forming scar tissue. Ascorbic acid (Vitamin C) may be recommended to help\
-  \ reduce the easy bruising that accompanies EDS. Hypermobile joints easily dislocate.\
-  \ With each dislocation, subsequent dislocations are increasingly likely, therefore\
-  \ prevention is particularly important for quality of life. Heavy sports, lifting,\
-  \ and other strenuous efforts should be avoided due to the risk of inciting trauma.\
-  \ Blood vessel fragility increases the risk for serious bleeds and dissections.\
-  \ High blood pressure (hypertension) puts additional strain on the fragile vasculature\
-  \ and increases the risk for complications. Regular screening for hypertension and\
-  \ arterial disease should be conducted and treatment should be initiated early on.\
-  \ The best approaches to screening are by non-invasive technology: ultrasound, MRI,\
-  \ or CT. Arteriography, colonoscopy, and other similarly invasive screening procedures\
-  \ should be considered carefully for benefit versus risk. Surgery for non-life threatening\
-  \ conditions should also be carefully considered. Pregnancies should be followed\
-  \ by obstetricians that are well trained in dealing with high-risk pregnancies.\
-  \ Delivery can progress very quickly in EDS patients and it is yet unclear if there\
-  \ is an advantage to mothers to deliver by vaginal or cesarean routes. Expectant\
-  \ mothers with known aortic root dilations should have echocardiograms each trimester\
-  \ to observe for possible exacerbation. All EDS-affected individuals should seek\
-  \ immediate medical attention for any sudden or unexplained pains and consider wearing\
-  \ a MedicAlert bracelet to communicate their status as a patient with EDS should\
-  \ they lose consciousness.\n\nhEDS patients may especially benefit from physical\
-  \ therapy, low-resistance exercise, and assistive devices like braces, wheelchairs,\
-  \ and scooters. Comfortable writing utensils and a low-stress mattress serve an\
-  \ important role in reducing musculoskeletal pain. Pain management is tailored to\
-  \ the individual. Gastrointestinal and psychological complications are likewise\
-  \ managed per an individual\u2019s needs. In addition to physical therapy and low-resistance\
-  \ exercise, calcium and vitamin D can help maximize bone density. DEXA bone density\
-  \ scans should be conducted every other year. kEDS patients should have routine\
-  \ eye exams as they are at risk for globus rupture, retinal detachment and glaucoma.\
-  \ dEDS patients may benefit from protective bandages over exposed areas such as\
-  \ the skin of the elbows and knees.\n"
-input_title: null
-named_entities:
-- id: MONDO:0007947
-  label: Marfan Syndrome
-- id: CHEBI:8499
-  label: Propranolol
-- id: CHEBI:2904
-  label: Atenolol
-- id: CHEBI:6541
-  label: Losartan
-- id: CHEBI:35530
-  label: Beta-blockers
-- id: NCIT:C66930
-  label: Angiotensin receptor blockers
-- id: NCIT:C16567
-  label: Exercise
-- id: CHEBI:35530
-  label: Beta-blockers
-- id: CHEBI:35530
-  label: Beta-blockers
-- id: MONDO:0020066
-  label: Ehlers Danlos Syndrome
-- id: MAXO:0000011
-  label: Physical therapy
-- id: NCIT:C157792
-  label: Assistive devices
-- id: MAXO:0000457
-  label: Pain management
-- id: GO:0042060
-  label: Wound healing
-- id: NCIT:C34483
-  label: scarring
-- id: NCIT:C143345
-  label: bruising
-- id: NCIT:C15405
-  label: prevention
-- id: HP:0000822
-  label: hypertension
-- id: MAXO:0000004
-  label: surgery
-- id: NCIT:C15405
-  label: prevention
-- id: NCIT:C48261
-  label: screening
-- id: MAXO:0000011
-  label: Physical therapy
-- id: NCIT:C3244
-  label: musculoskeletal pain
-- id: NCIT:C3244
-  label: musculoskeletal pain
-- id: NCIT:C157792
-  label: Assistive devices
-- id: NCIT:C3244
-  label: musculoskeletal pain
-- id: NCIT:C3244
-  label: musculoskeletal pain
-- id: NCIT:C3244
-  label: musculoskeletal pain
-- id: MAXO:0000457
-  label: Pain management
-- id: NCIT:C15292
-  label: Palliative care
-- id: NCIT:C61545
-  label: bone density
-- id: NCIT:C61545
-  label: bone density
-- id: NCIT:C26874
-  label: Retinal detachment
-- id: NCIT:C26782
-  label: Glaucoma
-- id: NCIT:C18902
-  label: N/A
-- id: MAXO:0000011
-  label: Physical therapy
-prompt: 'Split the following piece of text into fields in the following format:
-
-
-  treatment: <the value for treatment>
-
-  efficacy: <the value for efficacy>
-
-
-
-  Text:
-
-  Protective bandages*effective
-
-
-  ===
-
-
-  '
-raw_completion_output: 'Disease: Ehlers Danlos Syndrome
-
-  Drugs: Ascorbic Acid (Vitamin C)
-
-  Treatments: Preventative measures; Deep stiches; Superficial stiches; Ascorbic Acid
-  (Vitamin C); Avoidance of heavy sports, lifting, and other strenuous efforts; Screening
-  for hypertension and arterial disease; Non-invasive technology screening; Careful
-  consideration of surgery for non-life threatening conditions; Monitoring during
-  pregnancy; Physical therapy; Low-resistance exercise; Assistive devices; Comfortable
-  writing utensils; Low-stress mattress; Pain management; Calcium and vitamin D; DEXA
-  bone density scans; Routine eye exams; Protective bandages
-
-  Treatment Mechanisms: Deep stiches*wound healing; Superficial stiches*scarring;
-  Ascorbic Acid (Vitamin C)*bruising; Avoidance of heavy sports, lifting, and other
-  strenuous efforts*prevention; Screening for hypertension and arterial disease*arterial
-  screening; Non-invasive technology screening*screening; Careful consideration of
-  surgery for non-life threatening conditions*prevention; Monitoring during pregnancy*screening;
-  Physical therapy*musculoskeletal pain; Low-resistance exercise*musculoskeletal pain;
-  Assistive devices*musculoskeletal pain; Comfortable writing utensils*musculoskeletal
-  pain; Low-stress mattress*musculoskeletal pain; Pain management*palliative care;
-  Calcium and vitamin D*bone density; DEXA bone density scans*bone density; Routine
-  eye exams*globus rupture; Retinal detachment; Glaucoma; Protective bandages*protection
-
-  Treatment Efficacies: Ascorbic Acid (Vitamin C)*effective; Physical therapy*effective;
-  Low-resistance exercise*effective; Calcium and vitamin D*effective; Routine eye
-  exams*effective; Protective bandages*effective'
-
-
- -
-

Prompt

-
-
-Split the following piece of text into fields in the following format:
-
-treatment: <the value for treatment>
-efficacy: <the value for efficacy>
-
-
-Text:
-Protective bandages*effective
-
-===
-
-
-
- -
-

Completion

-
-
-Disease: Ehlers Danlos Syndrome
-Drugs: Ascorbic Acid (Vitamin C)
-Treatments: Preventative measures; Deep stiches; Superficial stiches; Ascorbic Acid (Vitamin C); Avoidance of heavy sports, lifting, and other strenuous efforts; Screening for hypertension and arterial disease; Non-invasive technology screening; Careful consideration of surgery for non-life threatening conditions; Monitoring during pregnancy; Physical therapy; Low-resistance exercise; Assistive devices; Comfortable writing utensils; Low-stress mattress; Pain management; Calcium and vitamin D; DEXA bone density scans; Routine eye exams; Protective bandages
-Treatment Mechanisms: Deep stiches*wound healing; Superficial stiches*scarring; Ascorbic Acid (Vitamin C)*bruising; Avoidance of heavy sports, lifting, and other strenuous efforts*prevention; Screening for hypertension and arterial disease*arterial screening; Non-invasive technology screening*screening; Careful consideration of surgery for non-life threatening conditions*prevention; Monitoring during pregnancy*screening; Physical therapy*musculoskeletal pain; Low-resistance exercise*musculoskeletal pain; Assistive devices*musculoskeletal pain; Comfortable writing utensils*musculoskeletal pain; Low-stress mattress*musculoskeletal pain; Pain management*palliative care; Calcium and vitamin D*bone density; DEXA bone density scans*bone density; Routine eye exams*globus rupture; Retinal detachment; Glaucoma; Protective bandages*protection
-Treatment Efficacies: Ascorbic Acid (Vitamin C)*effective; Physical therapy*effective; Low-resistance exercise*effective; Calcium and vitamin D*effective; Routine eye exams*effective; Protective bandages*effective
-
- -
diff --git a/tests/output/eds-output.md b/tests/output/eds-output.md deleted file mode 100644 index dcd6c6d0b..000000000 --- a/tests/output/eds-output.md +++ /dev/null @@ -1,76 +0,0 @@ -# /Users/cjm/repos/ontogpt/tests/input/cases/treatment-eds.txt - -## Input - -_Disease: Ehlers Danlos Syndrome_ - -_Treatment:_ - -_The care of patients with EDS is generally focused on implementing preventative measures against serious or life-threatening complications. The primary complications seen in EDS involve the skin, musculoskeletal, and cardiovascular systems. Patient skin is velvety thin, loose, and stretchable. This predisposes patients to difficulties with wound healing. For both accidental and surgical wounds, deep stiches are applied generously. Superficial stiches are placed to carefully realign the skin to prevent scarring. Stiches are also left in for extended periods of time to allow best strengthening of the forming scar tissue. Ascorbic acid (Vitamin C) may be recommended to help reduce the easy bruising that accompanies EDS. Hypermobile joints easily dislocate. With each dislocation, subsequent dislocations are increasingly likely, therefore prevention is particularly important for quality of life. Heavy sports, lifting, and other strenuous efforts should be avoided due to the risk of inciting trauma. Blood vessel fragility increases the risk for serious bleeds and dissections. High blood pressure (hypertension) puts additional strain on the fragile vasculature and increases the risk for complications. Regular screening for hypertension and arterial disease should be conducted and treatment should be initiated early on. The best approaches to screening are by non-invasive technology: ultrasound, MRI, or CT. Arteriography, colonoscopy, and other similarly invasive screening procedures should be considered carefully for benefit versus risk. Surgery for non-life threatening conditions should also be carefully considered. Pregnancies should be followed by obstetricians that are well trained in dealing with high-risk pregnancies. Delivery can progress very quickly in EDS patients and it is yet unclear if there is an advantage to mothers to deliver by vaginal or cesarean routes. Expectant mothers with known aortic root dilations should have echocardiograms each trimester to observe for possible exacerbation. All EDS-affected individuals should seek immediate medical attention for any sudden or unexplained pains and consider wearing a MedicAlert bracelet to communicate their status as a patient with EDS should they lose consciousness._ - -__ - -_hEDS patients may especially benefit from physical therapy, low-resistance exercise, and assistive devices like braces, wheelchairs, and scooters. Comfortable writing utensils and a low-stress mattress serve an important role in reducing musculoskeletal pain. Pain management is tailored to the individual. Gastrointestinal and psychological complications are likewise managed per an individual’s needs. In addition to physical therapy and low-resistance exercise, calcium and vitamin D can help maximize bone density. DEXA bone density scans should be conducted every other year. kEDS patients should have routine eye exams as they are at risk for globus rupture, retinal detachment and glaucoma. dEDS patients may benefit from protective bandages over exposed areas such as the skin of the elbows and knees._ - -__ - -## Results - - - -### disease - - -- Ehlers Danlos Syndrome [MONDO:0020066](https://bioregistry.io/MONDO:0020066) - - -### drugs - - -- AUTO:Ascorbic%20Acid%20%28Vitamin%20C%29 - - -### treatments - - -- AUTO:Preventative%20measures - -- AUTO:Deep%20stiches - -- AUTO:Superficial%20stiches - -- AUTO:Ascorbic%20Acid%20%28Vitamin%20C%29 - -- AUTO:Avoidance%20of%20heavy%20sports%2C%20lifting%2C%20and%20other%20strenuous%20efforts - -- AUTO:Screening%20for%20hypertension%20and%20arterial%20disease - -- AUTO:Non-invasive%20technology%20screening - -- AUTO:Careful%20consideration%20of%20surgery%20for%20non-life%20threatening%20conditions - -- AUTO:Monitoring%20during%20pregnancy - -- Physical therapy [MAXO:0000011](https://bioregistry.io/MAXO:0000011) - -- AUTO:Low-resistance%20exercise - -- Assistive devices [NCIT:C157792](https://bioregistry.io/NCIT:C157792) - -- AUTO:Comfortable%20writing%20utensils - -- AUTO:Low-stress%20mattress - -- Pain management [MAXO:0000457](https://bioregistry.io/MAXO:0000457) - -- AUTO:Calcium%20and%20vitamin%20D - -- AUTO:DEXA%20bone%20density%20scans - -- AUTO:Routine%20eye%20exams - -- AUTO:Protective%20bandages - - -### contraindications - diff --git a/tests/output/gene_requests_cache.db b/tests/output/gene_requests_cache.db deleted file mode 100644 index 751bbb2ee..000000000 Binary files a/tests/output/gene_requests_cache.db and /dev/null differ diff --git a/tests/output/generalized-drug-mechanisms-001.yaml b/tests/output/generalized-drug-mechanisms-001.yaml deleted file mode 100644 index 14d01d8e4..000000000 --- a/tests/output/generalized-drug-mechanisms-001.yaml +++ /dev/null @@ -1,109 +0,0 @@ -- _combo: - - disease - - drug - _input: - disease: MESH:D014552 - drug: drugbank:DB00438 - input_id: null - input_text: 'example: - - disease: Leukemia, Myelogenous, Chronic, BCR-ABL Positive - - drug: Imatinib - - mechanism_links: tyrosine-protein kinase ABL1 (human) - decreases activity of - - Imatinib Mesylate; Leukemia, Myelogenous, Chronic, BCR-ABL Positive - causes - - tyrosine-protein kinase ABL1 (human) - - - disease: Mastocytosis, Systemic - - drug: Imatinib - - mechanism_links: mast/stem cell growth factor receptor Kit (human) - decreases - activity of - Imatinib Mesylate; platelet-derived growth factor receptor alpha - (human) - decreases activity of - Imatinib Mesylate; cell population proliferation - - positively regulates - mast/stem cell growth factor receptor Kit (human); cell - population proliferation - positively regulates - platelet-derived growth factor - receptor alpha (human); Mastocytosis, Systemic - causes - cell population proliferation - - - disease: Pain - - drug: Acetaminophen - - mechanism_links: prostaglandin G/H synthase 1 (human) - decreases activity of - - Acetaminophen; prostaglandin G/H synthase 2 (human) - decreases activity of - - Acetaminophen; prostaglandin E synthase 3 (human) - decreases activity of - - Acetaminophen; prostaglandin biosynthetic process - positively regulates - prostaglandin - G/H synthase 1 (human); prostaglandin biosynthetic process - positively regulates - - prostaglandin G/H synthase 2 (human); prostaglandin biosynthetic process - positively - regulates - prostaglandin E synthase 3 (human); Prostaglandins - increases abundance - of - prostaglandin biosynthetic process; Pain - positively correlated with - Prostaglandins - - - disease: Fever - - drug: Acetaminophen - - mechanism_links: REACT:R-HSA-2162123 - negatively regulates - Acetaminophen; brain - - occurs in - REACT:R-HSA-2162123; temperature homeostasis - location of - brain; - Fever - negatively correlated with - temperature homeostasis - - - - - === - - - disease: Urinary Tract Infections - - drug: Ceftazidime - - ' - input_title: null - named_entities: - - id: MESH:D014552 - label: Urinary Tract Infections - - id: GO:0009273 - label: cell wall biosynthetic process - - id: RO:0002213 - label: positively regulates - - id: GO:0009273 - label: cell envelope biosynthetic process - - id: RO:0002213 - label: positively regulates - - id: MESH:D002442 - label: Ceftazidime - - id: RO:0001019 - label: contains - prompt: 'From the text below, extract the following entities in the following format: - - - subject: - - predicate: - - object: - - ' - raw_completion_output: null - results: - - disease: MESH:D014552 - drug: drugbank:DB00438 - mechanism_links: - - object: MESH:D014552 - predicate: biological process involved in - subject: Gram-negative bacilli - - object: Gram-negative bacilli - predicate: RO:0002213 - subject: GO:0009273 - - object: Gram-negative bacilli - predicate: RO:0002213 - subject: GO:0009273 - - object: MESH:D002442 - predicate: binds to - subject: penicillin binding proteins - - object: penicillin binding proteins - predicate: RO:0001019 - subject: Gram-negative bacilli diff --git a/tests/output/generalized-reactions-001.yaml b/tests/output/generalized-reactions-001.yaml deleted file mode 100644 index 0a0e8aa98..000000000 --- a/tests/output/generalized-reactions-001.yaml +++ /dev/null @@ -1,708 +0,0 @@ -- _combo: - - label - _input: - label: pseudouridine 5'-phosphatase activity - input_id: null - input_text: 'example: - - label: trans-hexaprenyltranstransferase activity - - description: Catalysis of the reaction: (2E,6E)-farnesyl diphosphate + 4 isopentenyl - diphosphate = 4 diphosphate + all-trans-heptaprenyl diphosphate. - - subclass_of: prenyltransferase activity - - left_side: (2E,6E)-farnesyl diphosphate; 4 isopentenyl diphosphate - - right_side: 4 diphosphate; all-trans-heptaprenyl diphosphate - - - label: dihydroorotate dehydrogenase (fumarate) activity - - description: Catalysis of the reaction: (S)-dihydroorotate + fumarate = orotate - + succinate. - - subclass_of: dihydroorotate dehydrogenase activity - - left_side: (S)-dihydroorotate; fumarate - - right_side: orotate; succinate - - - label: butanol dehydrogenase activity - - description: Catalysis of the reaction: butanal + NADH + H+ => n-butanol + NAD+. - - subclass_of: alcohol dehydrogenase (NAD+) activity - - left_side: butanal; NADPH; H+ - - right_side: butanol; NAD+ - - - - - === - - - label: pseudouridine 5''-phosphatase activity - - ' - input_title: null - named_entities: - - id: CHEBI:18116 - label: pseudouridine 5'-phosphate - - id: CHEBI:15377 - label: H2O - - id: CHEBI:17802 - label: pseudouridine - - id: CHEBI:26020 - label: phosphate - prompt: null - raw_completion_output: null - results: - - description: 'Catalysis of the reaction: pseudouridine 5''-phosphate + H2O = pseudouridine - + phosphate.' - id: null - label: pseudouridine 5'-phosphatase activity - left_side: - - CHEBI:18116 - - CHEBI:15377 - right_side: - - CHEBI:17802 - - CHEBI:26020 - subclass_of: nucleoside 5'-phosphatase activity - synonyms: [] -- _combo: - - description - _input: - description: 'Catalysis of the reaction: pseudouridine 5''-phosphate + H2O = pseudouridine - + phosphate.' - input_id: null - input_text: 'example: - - label: trans-hexaprenyltranstransferase activity - - description: Catalysis of the reaction: (2E,6E)-farnesyl diphosphate + 4 isopentenyl - diphosphate = 4 diphosphate + all-trans-heptaprenyl diphosphate. - - subclass_of: prenyltransferase activity - - left_side: (2E,6E)-farnesyl diphosphate; 4 isopentenyl diphosphate - - right_side: 4 diphosphate; all-trans-heptaprenyl diphosphate - - - label: dihydroorotate dehydrogenase (fumarate) activity - - description: Catalysis of the reaction: (S)-dihydroorotate + fumarate = orotate - + succinate. - - subclass_of: dihydroorotate dehydrogenase activity - - left_side: (S)-dihydroorotate; fumarate - - right_side: orotate; succinate - - - label: butanol dehydrogenase activity - - description: Catalysis of the reaction: butanal + NADH + H+ => n-butanol + NAD+. - - subclass_of: alcohol dehydrogenase (NAD+) activity - - left_side: butanal; NADPH; H+ - - right_side: butanol; NAD+ - - - - - === - - - description: Catalysis of the reaction: pseudouridine 5''-phosphate + H2O = pseudouridine - + phosphate. - - ' - input_title: null - named_entities: - - id: CHEBI:18116 - label: pseudouridine 5'-phosphate - - id: CHEBI:15377 - label: H2O - - id: CHEBI:17802 - label: pseudouridine - - id: CHEBI:26020 - label: phosphate - - id: CHEBI:18116 - label: pseudouridine 5'-phosphate - - id: CHEBI:15377 - label: H2O - - id: CHEBI:17802 - label: pseudouridine - - id: CHEBI:26020 - label: phosphate - prompt: null - raw_completion_output: null - results: - - description: 'Catalysis of the reaction: pseudouridine 5''-phosphate + H2O = pseudouridine - + phosphate.' - id: null - label: null - left_side: - - CHEBI:18116 - - CHEBI:15377 - right_side: - - CHEBI:17802 - - CHEBI:26020 - subclass_of: pseudouridine 5'-phosphate phosphohydrolase activity - synonyms: [] -- _combo: - - label - - description - _input: - description: 'Catalysis of the reaction: pseudouridine 5''-phosphate + H2O = pseudouridine - + phosphate.' - label: pseudouridine 5'-phosphatase activity - input_id: null - input_text: 'example: - - label: trans-hexaprenyltranstransferase activity - - description: Catalysis of the reaction: (2E,6E)-farnesyl diphosphate + 4 isopentenyl - diphosphate = 4 diphosphate + all-trans-heptaprenyl diphosphate. - - subclass_of: prenyltransferase activity - - left_side: (2E,6E)-farnesyl diphosphate; 4 isopentenyl diphosphate - - right_side: 4 diphosphate; all-trans-heptaprenyl diphosphate - - - label: dihydroorotate dehydrogenase (fumarate) activity - - description: Catalysis of the reaction: (S)-dihydroorotate + fumarate = orotate - + succinate. - - subclass_of: dihydroorotate dehydrogenase activity - - left_side: (S)-dihydroorotate; fumarate - - right_side: orotate; succinate - - - label: butanol dehydrogenase activity - - description: Catalysis of the reaction: butanal + NADH + H+ => n-butanol + NAD+. - - subclass_of: alcohol dehydrogenase (NAD+) activity - - left_side: butanal; NADPH; H+ - - right_side: butanol; NAD+ - - - - - === - - - label: pseudouridine 5''-phosphatase activity - - description: Catalysis of the reaction: pseudouridine 5''-phosphate + H2O = pseudouridine - + phosphate. - - ' - input_title: null - named_entities: - - id: CHEBI:18116 - label: pseudouridine 5'-phosphate - - id: CHEBI:15377 - label: H2O - - id: CHEBI:17802 - label: pseudouridine - - id: CHEBI:26020 - label: phosphate - - id: CHEBI:18116 - label: pseudouridine 5'-phosphate - - id: CHEBI:15377 - label: H2O - - id: CHEBI:17802 - label: pseudouridine - - id: CHEBI:26020 - label: phosphate - - id: GO:0016791 - label: phosphatase activity - - id: CHEBI:18116 - label: pseudouridine 5'-phosphate - - id: CHEBI:15377 - label: H2O - - id: CHEBI:17802 - label: pseudouridine - - id: CHEBI:26020 - label: phosphate - prompt: null - raw_completion_output: null - results: - - description: 'Catalysis of the reaction: pseudouridine 5''-phosphate + H2O = pseudouridine - + phosphate.' - id: null - label: pseudouridine 5'-phosphatase activity - left_side: - - CHEBI:18116 - - CHEBI:15377 - right_side: - - CHEBI:17802 - - CHEBI:26020 - subclass_of: GO:0016791 - synonyms: [] -- _combo: - - label - _input: - label: L-altrarate dehydratase activity - input_id: null - input_text: 'example: - - label: trans-hexaprenyltranstransferase activity - - description: Catalysis of the reaction: (2E,6E)-farnesyl diphosphate + 4 isopentenyl - diphosphate = 4 diphosphate + all-trans-heptaprenyl diphosphate. - - subclass_of: prenyltransferase activity - - left_side: (2E,6E)-farnesyl diphosphate; 4 isopentenyl diphosphate - - right_side: 4 diphosphate; all-trans-heptaprenyl diphosphate - - - label: dihydroorotate dehydrogenase (fumarate) activity - - description: Catalysis of the reaction: (S)-dihydroorotate + fumarate = orotate - + succinate. - - subclass_of: dihydroorotate dehydrogenase activity - - left_side: (S)-dihydroorotate; fumarate - - right_side: orotate; succinate - - - label: butanol dehydrogenase activity - - description: Catalysis of the reaction: butanal + NADH + H+ => n-butanol + NAD+. - - subclass_of: alcohol dehydrogenase (NAD+) activity - - left_side: butanal; NADPH; H+ - - right_side: butanol; NAD+ - - - - - === - - - label: L-altrarate dehydratase activity - - ' - input_title: null - named_entities: - - id: CHEBI:18116 - label: pseudouridine 5'-phosphate - - id: CHEBI:15377 - label: H2O - - id: CHEBI:17802 - label: pseudouridine - - id: CHEBI:26020 - label: phosphate - - id: CHEBI:18116 - label: pseudouridine 5'-phosphate - - id: CHEBI:15377 - label: H2O - - id: CHEBI:17802 - label: pseudouridine - - id: CHEBI:26020 - label: phosphate - - id: GO:0016791 - label: phosphatase activity - - id: CHEBI:18116 - label: pseudouridine 5'-phosphate - - id: CHEBI:15377 - label: H2O - - id: CHEBI:17802 - label: pseudouridine - - id: CHEBI:26020 - label: phosphate - - id: CHEBI:37547 - label: L-altrarate - - id: CHEBI:15377 - label: H2O - - id: CHEBI:18276 - label: H2 - prompt: null - raw_completion_output: null - results: - - description: 'Catalysis of the reaction: L-altrarate + H2O = 2-dehydro-3-deoxy-L-altronate - + H2.' - id: null - label: L-altrarate dehydratase activity - left_side: - - CHEBI:37547 - - CHEBI:15377 - right_side: - - 2-dehydro-3-deoxy-L-altronate - - CHEBI:18276 - subclass_of: amino acid dehydratase activity - synonyms: [] -- _combo: - - description - _input: - description: 'Catalysis of the reaction: L-altrarate = 5-dehydro-4-deoxy-D-glucarate - + H2O.' - input_id: null - input_text: 'example: - - label: trans-hexaprenyltranstransferase activity - - description: Catalysis of the reaction: (2E,6E)-farnesyl diphosphate + 4 isopentenyl - diphosphate = 4 diphosphate + all-trans-heptaprenyl diphosphate. - - subclass_of: prenyltransferase activity - - left_side: (2E,6E)-farnesyl diphosphate; 4 isopentenyl diphosphate - - right_side: 4 diphosphate; all-trans-heptaprenyl diphosphate - - - label: dihydroorotate dehydrogenase (fumarate) activity - - description: Catalysis of the reaction: (S)-dihydroorotate + fumarate = orotate - + succinate. - - subclass_of: dihydroorotate dehydrogenase activity - - left_side: (S)-dihydroorotate; fumarate - - right_side: orotate; succinate - - - label: butanol dehydrogenase activity - - description: Catalysis of the reaction: butanal + NADH + H+ => n-butanol + NAD+. - - subclass_of: alcohol dehydrogenase (NAD+) activity - - left_side: butanal; NADPH; H+ - - right_side: butanol; NAD+ - - - - - === - - - description: Catalysis of the reaction: L-altrarate = 5-dehydro-4-deoxy-D-glucarate - + H2O. - - ' - input_title: null - named_entities: - - id: CHEBI:18116 - label: pseudouridine 5'-phosphate - - id: CHEBI:15377 - label: H2O - - id: CHEBI:17802 - label: pseudouridine - - id: CHEBI:26020 - label: phosphate - - id: CHEBI:18116 - label: pseudouridine 5'-phosphate - - id: CHEBI:15377 - label: H2O - - id: CHEBI:17802 - label: pseudouridine - - id: CHEBI:26020 - label: phosphate - - id: GO:0016791 - label: phosphatase activity - - id: CHEBI:18116 - label: pseudouridine 5'-phosphate - - id: CHEBI:15377 - label: H2O - - id: CHEBI:17802 - label: pseudouridine - - id: CHEBI:26020 - label: phosphate - - id: CHEBI:37547 - label: L-altrarate - - id: CHEBI:15377 - label: H2O - - id: CHEBI:18276 - label: H2 - - id: GO:0016491 - label: oxidoreductase activity - - id: CHEBI:37547 - label: L-altrarate - - id: CHEBI:16369 - label: 5-dehydro-4-deoxy-D-glucarate - - id: CHEBI:15377 - label: H2O - prompt: null - raw_completion_output: null - results: - - description: 'Catalysis of the reaction: L-altrarate = 5-dehydro-4-deoxy-D-glucarate - + H2O.' - id: null - label: null - left_side: - - CHEBI:37547 - right_side: - - CHEBI:16369 - - CHEBI:15377 - subclass_of: GO:0016491 - synonyms: [] -- _combo: - - label - - description - _input: - description: 'Catalysis of the reaction: L-altrarate = 5-dehydro-4-deoxy-D-glucarate - + H2O.' - label: L-altrarate dehydratase activity - input_id: null - input_text: 'example: - - label: trans-hexaprenyltranstransferase activity - - description: Catalysis of the reaction: (2E,6E)-farnesyl diphosphate + 4 isopentenyl - diphosphate = 4 diphosphate + all-trans-heptaprenyl diphosphate. - - subclass_of: prenyltransferase activity - - left_side: (2E,6E)-farnesyl diphosphate; 4 isopentenyl diphosphate - - right_side: 4 diphosphate; all-trans-heptaprenyl diphosphate - - - label: dihydroorotate dehydrogenase (fumarate) activity - - description: Catalysis of the reaction: (S)-dihydroorotate + fumarate = orotate - + succinate. - - subclass_of: dihydroorotate dehydrogenase activity - - left_side: (S)-dihydroorotate; fumarate - - right_side: orotate; succinate - - - label: butanol dehydrogenase activity - - description: Catalysis of the reaction: butanal + NADH + H+ => n-butanol + NAD+. - - subclass_of: alcohol dehydrogenase (NAD+) activity - - left_side: butanal; NADPH; H+ - - right_side: butanol; NAD+ - - - - - === - - - label: L-altrarate dehydratase activity - - description: Catalysis of the reaction: L-altrarate = 5-dehydro-4-deoxy-D-glucarate - + H2O. - - ' - input_title: null - named_entities: - - id: CHEBI:18116 - label: pseudouridine 5'-phosphate - - id: CHEBI:15377 - label: H2O - - id: CHEBI:17802 - label: pseudouridine - - id: CHEBI:26020 - label: phosphate - - id: CHEBI:18116 - label: pseudouridine 5'-phosphate - - id: CHEBI:15377 - label: H2O - - id: CHEBI:17802 - label: pseudouridine - - id: CHEBI:26020 - label: phosphate - - id: GO:0016791 - label: phosphatase activity - - id: CHEBI:18116 - label: pseudouridine 5'-phosphate - - id: CHEBI:15377 - label: H2O - - id: CHEBI:17802 - label: pseudouridine - - id: CHEBI:26020 - label: phosphate - - id: CHEBI:37547 - label: L-altrarate - - id: CHEBI:15377 - label: H2O - - id: CHEBI:18276 - label: H2 - - id: GO:0016491 - label: oxidoreductase activity - - id: CHEBI:37547 - label: L-altrarate - - id: CHEBI:16369 - label: 5-dehydro-4-deoxy-D-glucarate - - id: CHEBI:15377 - label: H2O - - id: GO:0016829 - label: lyase activity - - id: CHEBI:37547 - label: L-altrarate - - id: CHEBI:16369 - label: 5-dehydro-4-deoxy-D-glucarate - - id: CHEBI:15377 - label: H2O - prompt: null - raw_completion_output: null - results: - - description: 'Catalysis of the reaction: L-altrarate = 5-dehydro-4-deoxy-D-glucarate - + H2O.' - id: null - label: L-altrarate dehydratase activity - left_side: - - CHEBI:37547 - right_side: - - CHEBI:16369 - - CHEBI:15377 - subclass_of: GO:0016829 - synonyms: [] -- _combo: - - description - _input: - description: ent-copalyl diphosphate + H2O = diphosphate + ent-manool - input_id: null - input_text: 'example: - - label: trans-hexaprenyltranstransferase activity - - description: Catalysis of the reaction: (2E,6E)-farnesyl diphosphate + 4 isopentenyl - diphosphate = 4 diphosphate + all-trans-heptaprenyl diphosphate. - - subclass_of: prenyltransferase activity - - left_side: (2E,6E)-farnesyl diphosphate; 4 isopentenyl diphosphate - - right_side: 4 diphosphate; all-trans-heptaprenyl diphosphate - - - label: dihydroorotate dehydrogenase (fumarate) activity - - description: Catalysis of the reaction: (S)-dihydroorotate + fumarate = orotate - + succinate. - - subclass_of: dihydroorotate dehydrogenase activity - - left_side: (S)-dihydroorotate; fumarate - - right_side: orotate; succinate - - - label: butanol dehydrogenase activity - - description: Catalysis of the reaction: butanal + NADH + H+ => n-butanol + NAD+. - - subclass_of: alcohol dehydrogenase (NAD+) activity - - left_side: butanal; NADPH; H+ - - right_side: butanol; NAD+ - - - - - === - - - description: ent-copalyl diphosphate + H2O = diphosphate + ent-manool - - ' - input_title: null - named_entities: - - id: CHEBI:18116 - label: pseudouridine 5'-phosphate - - id: CHEBI:15377 - label: H2O - - id: CHEBI:17802 - label: pseudouridine - - id: CHEBI:26020 - label: phosphate - - id: CHEBI:18116 - label: pseudouridine 5'-phosphate - - id: CHEBI:15377 - label: H2O - - id: CHEBI:17802 - label: pseudouridine - - id: CHEBI:26020 - label: phosphate - - id: GO:0016791 - label: phosphatase activity - - id: CHEBI:18116 - label: pseudouridine 5'-phosphate - - id: CHEBI:15377 - label: H2O - - id: CHEBI:17802 - label: pseudouridine - - id: CHEBI:26020 - label: phosphate - - id: CHEBI:37547 - label: L-altrarate - - id: CHEBI:15377 - label: H2O - - id: CHEBI:18276 - label: H2 - - id: GO:0016491 - label: oxidoreductase activity - - id: CHEBI:37547 - label: L-altrarate - - id: CHEBI:16369 - label: 5-dehydro-4-deoxy-D-glucarate - - id: CHEBI:15377 - label: H2O - - id: GO:0016829 - label: lyase activity - - id: CHEBI:37547 - label: L-altrarate - - id: CHEBI:16369 - label: 5-dehydro-4-deoxy-D-glucarate - - id: CHEBI:15377 - label: H2O - - id: GO:0016787 - label: hydrolase activity - - id: CHEBI:15377 - label: H2O - - id: CHEBI:18361 - label: diphosphate - - id: CHEBI:76948 - label: ent-manool - prompt: null - raw_completion_output: null - results: - - description: ent-copalyl diphosphate + H2O = diphosphate + ent-manool - id: null - label: Ent-copalyl-diphosphate DD-hydrolase activity - left_side: - - ent-copalyl-diphosphate - - CHEBI:15377 - right_side: - - CHEBI:18361 - - CHEBI:76948 - subclass_of: GO:0016787 - synonyms: [] diff --git a/tests/output/go-nucleus.hallucinated.halo.yaml b/tests/output/go-nucleus.hallucinated.halo.yaml deleted file mode 100644 index f36cf9d4f..000000000 --- a/tests/output/go-nucleus.hallucinated.halo.yaml +++ /dev/null @@ -1,408 +0,0 @@ -elements: -- name: Cell - context: subcellular - description: A material entity of anatomical origin (part of or deriving from an - organism) that has as its parts a maximally connected cell compartment surrounded - by a plasma membrane. - subclass_of: - - ConnectedAnatomicalStructure - parts: - - IntracellularAnatomicalStructure - - EndomembraneSystem - - Envelope -- name: Occurrent - context: subcellular - description: An entity that has temporal parts and that happens, unfolds or develops - through time. - subtypes: - - Process -- name: Membrane-boundedOrganelle - context: subcellular - description: Organized structure of distinctive morphology and function, bounded - by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, - plastids, vacuoles, and vesicles. Excludes the plasma membrane. - synonyms: - - membrane-enclosed organelle - subclass_of: - - Organelle - subtypes: - - IntracellularMembrane-boundedOrganelle - parts: - - OrganelleMembrane - - OrganelleEnvelope - equivalent_to: Organelle and has part some Membrane -- name: MetabolicProcess - context: subcellular - description: The chemical reactions and pathways, including anabolism and catabolism, - by which living organisms transform chemical substances. Metabolic processes typically - transform small molecules, but also include macromolecular processes such as DNA - repair and replication, and protein synthesis and degradation. - synonyms: - - metabolism - - metabolic process resulting in cell growth - - metabolism resulting in cell growth - - multicellular organism metabolic process - - single-organism metabolic process - subclass_of: - - BiologicalProcess - subtypes: - - CellularMetabolicProcess -- name: NuclearMembrane - context: subcellular - description: Either of the lipid bilayers that surround the nucleus and form the - nuclear envelope; excludes the intermembrane space. - subclass_of: - - OrganelleMembrane - part_of: - - Nucleus - - NuclearEnvelope - equivalent_to: Membrane and part of some Nucleus -- name: Process - context: subcellular - description: An occurrent that has temporal proper parts and for some time t, p - s-depends_on some material entity at t. - subclass_of: - - Occurrent - subtypes: - - BiologicalProcess -- name: CellularComponent - context: subcellular - description: 'A location, relative to cellular compartments and structures, occupied - by a macromolecular machine when it carries out a molecular function. There are - two ways in which the gene ontology describes locations of gene products: (1) - relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or - compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes - of which they are parts (e.g., the ribosome).' - synonyms: - - cell or subcellular entity - - cellular component - - subcellular entity - subclass_of: - - MaterialEntity - subtypes: - - CellularAnatomicalEntity -- name: PhosphorusMetabolicProcess - context: subcellular - description: The chemical reactions and pathways involving the nonmetallic element - phosphorus or compounds that contain phosphorus, usually in the form of a phosphate - group (PO4). - synonyms: - - phosphorus metabolism - subclass_of: - - CellularMetabolicProcess - equivalent_to: MetabolicProcess and has primary input or output some PhosphorusMolecularEntity -- name: BiologicalEntity - context: subcellular - subclass_of: - - IndependentContinuant - subtypes: - - AnatomicalEntity -- name: IntracellularMembrane-boundedOrganelle - context: subcellular - description: Organized structure of distinctive morphology and function, bounded - by a single or double lipid bilayer membrane and occurring within the cell. Includes - the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma - membrane. - synonyms: - - intracellular membrane-enclosed organelle - subclass_of: - - Membrane-boundedOrganelle - - IntracellularOrganelle - part_of: - - IntracellularAnatomicalStructure - subtypes: - - Nucleus - equivalent_to: Membrane-boundedOrganelle and part of some IntracellularAnatomicalStructure -- name: Membrane - context: subcellular - description: A lipid bilayer along with all the proteins and protein complexes embedded - in it an attached to it. - synonyms: - - membrane region - - region of membrane - - whole membrane - subclass_of: - - CellularAnatomicalEntity - subtypes: - - OrganelleMembrane -- name: BiologicalProcess - context: subcellular - description: A biological process represents a specific objective that the organism - is genetically programmed to achieve. Biological processes are often described - by their outcome or ending state, e.g., the biological process of cell division - results in the creation of two daughter cells (a divided cell) from a single parent - cell. A biological process is accomplished by a particular set of molecular functions - carried out by specific gene products (or macromolecular complexes), often in - a highly regulated manner and in a particular temporal sequence. - synonyms: - - biological process - - physiological process - - single organism process - - single-organism process - subclass_of: - - Process - subtypes: - - MetabolicProcess - - CellularProcess -- name: MaterialAnatomicalEntity - context: subcellular - subclass_of: - - MaterialEntity - - AnatomicalEntity - subtypes: - - ConnectedAnatomicalStructure -- name: IntracellularAnatomicalStructure - context: subcellular - description: A component of a cell contained within (but not including) the plasma - membrane. In eukaryotes it includes the nucleus and cytoplasm. - synonyms: - - internal to cell - - intracellular - - protoplasm - - nucleocytoplasm - - protoplast - subclass_of: - - CellularAnatomicalEntity - part_of: - - Cell - parts: - - IntracellularOrganelle - - IntracellularMembrane-boundedOrganelle -- name: CellularMetabolicProcess - context: subcellular - description: The chemical reactions and pathways by which individual cells transform - chemical substances. - synonyms: - - cellular metabolism - - intermediary metabolism - subclass_of: - - MetabolicProcess - - CellularProcess - subtypes: - - PhosphorusMetabolicProcess -- name: Organelle - context: subcellular - description: Organized structure of distinctive morphology and function. Includes - the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, - and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes - the plasma membrane. - subclass_of: - - CellularAnatomicalEntity - subtypes: - - Membrane-boundedOrganelle - - IntracellularOrganelle -- name: Envelope - context: subcellular - description: A multilayered structure surrounding all or part of a cell; encompasses - one or more lipid bilayers, and may include a cell wall layer; also includes the - space between layers. - subclass_of: - - CellularAnatomicalEntity - part_of: - - Cell - subtypes: - - OrganelleEnvelope -- name: EndomembraneSystem - context: subcellular - description: A collection of membranous structures involved in transport within - the cell. The main components of the endomembrane system are endoplasmic reticulum, - Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane - system pass materials through each other or though the use of vesicles. - subclass_of: - - CellularAnatomicalEntity - part_of: - - Cell - parts: - - NuclearEnvelope -- name: Nucleus - context: subcellular - description: A membrane-bounded organelle of eukaryotic cells in which chromosomes - are housed and replicated. In most cells, the nucleus contains all of the cell's - chromosomes except the organellar chromosomes, and is the site of RNA synthesis - and processing. In some species, or in specialized cell types, RNA metabolism - or DNA replication may be absent. - synonyms: - - cell nucleus - - horsetail nucleus - subclass_of: - - IntracellularMembrane-boundedOrganelle - parts: - - NuclearEnvelope - - NuclearMembrane -- name: MaterialEntity - context: subcellular - description: An independent continuant that is spatially extended whose identity - is independent of that of other entities and can be maintained through time. - subclass_of: - - IndependentContinuant - subtypes: - - MaterialAnatomicalEntity - - CellularComponent -- name: OrganelleMembrane - context: subcellular - description: A membrane that is one of the two lipid bilayers of an organelle envelope - or the outermost membrane of single membrane bound organelle. - synonyms: - - intracellular membrane - subclass_of: - - Membrane - part_of: - - Membrane-boundedOrganelle - subtypes: - - NuclearMembrane - equivalent_to: Membrane and part of some Membrane-boundedOrganelle -- name: IntracellularOrganelle - context: subcellular - description: Organized structure of distinctive morphology and function, occurring - within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, - ribosomes and the cytoskeleton. Excludes the plasma membrane. - subclass_of: - - Organelle - part_of: - - IntracellularAnatomicalStructure - subtypes: - - IntracellularMembrane-boundedOrganelle - parts: - - OrganelleEnvelope - equivalent_to: Organelle and part of some IntracellularAnatomicalStructure -- name: NuclearEnvelope - context: subcellular - description: The double lipid bilayer enclosing the nucleus and separating its contents - from the rest of the cytoplasm; includes the intermembrane space, a gap of width - 20-40 nm (also called the perinuclear space). - subclass_of: - - OrganelleEnvelope - part_of: - - Nucleus - - EndomembraneSystem - parts: - - NuclearMembrane -- name: OrganelleEnvelope - context: subcellular - description: A double membrane structure enclosing an organelle, including two lipid - bilayers and the region between them. In some cases, an organelle envelope may - have more than two membranes. - subclass_of: - - Envelope - part_of: - - Membrane-boundedOrganelle - - IntracellularOrganelle - subtypes: - - NuclearEnvelope -- name: AnatomicalEntity - context: subcellular - subclass_of: - - BiologicalEntity - subtypes: - - MaterialAnatomicalEntity - - CellularAnatomicalEntity -- name: CellularAnatomicalEntity - context: subcellular - description: A part of a cellular organism that is either an immaterial entity or - a material entity with granularity above the level of a protein complex but below - that of an anatomical system. Or, a substance produced by a cellular organism - with granularity above the level of a protein complex. - subclass_of: - - AnatomicalEntity - - CellularComponent - subtypes: - - IntracellularAnatomicalStructure - - EndomembraneSystem - - Membrane - - Envelope - - Organelle -- name: Continuant - context: subcellular - description: An entity that exists in full at any time in which it exists at all, - persists through time while maintaining its identity and has no temporal parts. - subtypes: - - IndependentContinuant -- name: IndependentContinuant - context: subcellular - description: A continuant that is a bearer of quality and realizable entity entities, - in which other entities inhere and which itself cannot inhere in anything. - subclass_of: - - Continuant - subtypes: - - MaterialEntity - - BiologicalEntity -- name: CellularProcess - context: subcellular - description: Any process that is carried out at the cellular level, but not necessarily - restricted to a single cell. For example, cell communication occurs among more - than one cell, but occurs at the cellular level. - synonyms: - - cell physiology - - cellular physiological process - - cell growth and/or maintenance - - single-organism cellular process - subclass_of: - - BiologicalProcess - subtypes: - - CellularMetabolicProcess -- name: ConnectedAnatomicalStructure - context: subcellular - subclass_of: - - MaterialAnatomicalEntity - subtypes: - - Cell -- name: Axon - context: subcellular - description: The long process of a neuron that conducts nerve impulses, usually - away from the cell body to the terminals and varicosities, which are sites of - storage and release of neurotransmitter. - synonyms: - - process of Anaxonic cell - - process of neuron cell - subclass_of: - - PartOfSensorimotorSystem - - AnaxonicCellProcess - - Neuron - equivalent_to: Neuron and has part some '(process of Anaxonic cell) or (process - of neuron cell)' -- name: Dendrite - context: subcellular - description: a neuron's branched extension that conducts the reflex impulses to - the cell body - synonyms: - - ecdysone receptor - subclass_of: - - Axon - subtypes: - - Autograph - - Encephalograph - - Telegraph - - Timeograph - - Xylograph -- name: PartOfSensorimotorSystem - context: subcellular - subclass_of: - - NeurologicalTissue - - MobileAnatomicalStructure - part_of: - - WholeSensorimotorSystem - subtypes: - - AfferentNerve - - EfferentNerve - - Ganglion - - MotorSystem - - SensoryReceptor - - SomaticCentralNervousSystemCell - equivalent_to: NeuralTissue and part of some MobileAnatomicalStructure -- name: AnaxonicCellProcess - context: subcellular - part_of: - - CellProcess - - AnatomicalStructureProcess - - BiologicalProcess -- name: Neuron - context: subcellular - subtypes: - - CentralNervousSystemNeuron - - DorsalRootGangliaNeuron -- name: Segment - context: subcellular - description: Describes how we visually represent the context, that is what is written. - subtypes: - - Autinem, Automeme, Autoradic, Autoflume - equivalent_to: isWriteContextOf diff --git a/tests/output/go-nucleus.halo.yaml b/tests/output/go-nucleus.halo.yaml deleted file mode 100644 index 20386acda..000000000 --- a/tests/output/go-nucleus.halo.yaml +++ /dev/null @@ -1,318 +0,0 @@ -elements: -- name: PhosphorusMetabolicProcess - description: The chemical reactions and pathways involving the nonmetallic element - phosphorus or compounds that contain phosphorus, usually in the form of a phosphate - group (PO4). - synonyms: - - phosphorus metabolism - subclass_of: - - CellularMetabolicProcess - equivalent_to: MetabolicProcess and has primary input or output some PhosphorusMolecularEntity -- name: OrganelleMembrane - description: A membrane that is one of the two lipid bilayers of an organelle envelope - or the outermost membrane of single membrane bound organelle. - synonyms: - - intracellular membrane - subclass_of: - - Membrane - part_of: - - Membrane-boundedOrganelle - subtypes: - - NuclearMembrane - equivalent_to: Membrane and part of some Membrane-boundedOrganelle -- name: AnatomicalEntity - subclass_of: - - BiologicalEntity - subtypes: - - MaterialAnatomicalEntity - - CellularAnatomicalEntity -- name: NuclearMembrane - description: Either of the lipid bilayers that surround the nucleus and form the - nuclear envelope; excludes the intermembrane space. - subclass_of: - - OrganelleMembrane - part_of: - - Nucleus - - NuclearEnvelope - equivalent_to: Membrane and part of some Nucleus -- name: CellularAnatomicalEntity - description: A part of a cellular organism that is either an immaterial entity or - a material entity with granularity above the level of a protein complex but below - that of an anatomical system. Or, a substance produced by a cellular organism - with granularity above the level of a protein complex. - subclass_of: - - AnatomicalEntity - - CellularComponent - subtypes: - - IntracellularAnatomicalStructure - - EndomembraneSystem - - Membrane - - Envelope - - Organelle -- name: Cell - description: A material entity of anatomical origin (part of or deriving from an - organism) that has as its parts a maximally connected cell compartment surrounded - by a plasma membrane. - subclass_of: - - ConnectedAnatomicalStructure - parts: - - IntracellularAnatomicalStructure - - EndomembraneSystem - - Envelope -- name: CellularComponent - description: 'A location, relative to cellular compartments and structures, occupied - by a macromolecular machine when it carries out a molecular function. There are - two ways in which the gene ontology describes locations of gene products: (1) - relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or - compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes - of which they are parts (e.g., the ribosome).' - synonyms: - - cell or subcellular entity - - cellular component - - subcellular entity - subclass_of: - - MaterialEntity - subtypes: - - CellularAnatomicalEntity -- name: EndomembraneSystem - description: A collection of membranous structures involved in transport within - the cell. The main components of the endomembrane system are endoplasmic reticulum, - Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane - system pass materials through each other or though the use of vesicles. - subclass_of: - - CellularAnatomicalEntity - part_of: - - Cell - parts: - - NuclearEnvelope -- name: IndependentContinuant - description: A continuant that is a bearer of quality and realizable entity entities, - in which other entities inhere and which itself cannot inhere in anything. - subclass_of: - - Continuant - subtypes: - - MaterialEntity - - BiologicalEntity -- name: IntracellularOrganelle - description: Organized structure of distinctive morphology and function, occurring - within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, - ribosomes and the cytoskeleton. Excludes the plasma membrane. - subclass_of: - - Organelle - part_of: - - IntracellularAnatomicalStructure - subtypes: - - IntracellularMembrane-boundedOrganelle - parts: - - OrganelleEnvelope - equivalent_to: Organelle and part of some IntracellularAnatomicalStructure -- name: Process - description: An occurrent that has temporal proper parts and for some time t, p - s-depends_on some material entity at t. - subclass_of: - - Occurrent - subtypes: - - BiologicalProcess -- name: OrganelleEnvelope - description: A double membrane structure enclosing an organelle, including two lipid - bilayers and the region between them. In some cases, an organelle envelope may - have more than two membranes. - subclass_of: - - Envelope - part_of: - - Membrane-boundedOrganelle - - IntracellularOrganelle - subtypes: - - NuclearEnvelope -- name: IntracellularAnatomicalStructure - description: A component of a cell contained within (but not including) the plasma - membrane. In eukaryotes it includes the nucleus and cytoplasm. - synonyms: - - internal to cell - - intracellular - - protoplasm - - nucleocytoplasm - - protoplast - subclass_of: - - CellularAnatomicalEntity - part_of: - - Cell - parts: - - IntracellularOrganelle - - IntracellularMembrane-boundedOrganelle -- name: Organelle - description: Organized structure of distinctive morphology and function. Includes - the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, - and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes - the plasma membrane. - subclass_of: - - CellularAnatomicalEntity - subtypes: - - Membrane-boundedOrganelle - - IntracellularOrganelle -- name: MaterialAnatomicalEntity - subclass_of: - - MaterialEntity - - AnatomicalEntity - subtypes: - - ConnectedAnatomicalStructure -- name: ConnectedAnatomicalStructure - subclass_of: - - MaterialAnatomicalEntity - subtypes: - - Cell -- name: Membrane-boundedOrganelle - description: Organized structure of distinctive morphology and function, bounded - by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, - plastids, vacuoles, and vesicles. Excludes the plasma membrane. - synonyms: - - membrane-enclosed organelle - subclass_of: - - Organelle - subtypes: - - IntracellularMembrane-boundedOrganelle - parts: - - OrganelleMembrane - - OrganelleEnvelope - equivalent_to: Organelle and has part some Membrane -- name: Membrane - description: A lipid bilayer along with all the proteins and protein complexes embedded - in it an attached to it. - synonyms: - - membrane region - - region of membrane - - whole membrane - subclass_of: - - CellularAnatomicalEntity - subtypes: - - OrganelleMembrane -- name: Continuant - description: An entity that exists in full at any time in which it exists at all, - persists through time while maintaining its identity and has no temporal parts. - subtypes: - - IndependentContinuant -- name: Nucleus - description: A membrane-bounded organelle of eukaryotic cells in which chromosomes - are housed and replicated. In most cells, the nucleus contains all of the cell's - chromosomes except the organellar chromosomes, and is the site of RNA synthesis - and processing. In some species, or in specialized cell types, RNA metabolism - or DNA replication may be absent. - synonyms: - - cell nucleus - - horsetail nucleus - subclass_of: - - IntracellularMembrane-boundedOrganelle - parts: - - NuclearEnvelope - - NuclearMembrane -- name: MetabolicProcess - description: The chemical reactions and pathways, including anabolism and catabolism, - by which living organisms transform chemical substances. Metabolic processes typically - transform small molecules, but also include macromolecular processes such as DNA - repair and replication, and protein synthesis and degradation. - synonyms: - - metabolism - - metabolic process resulting in cell growth - - metabolism resulting in cell growth - - multicellular organism metabolic process - - single-organism metabolic process - subclass_of: - - BiologicalProcess - subtypes: - - CellularMetabolicProcess -- name: BiologicalProcess - description: A biological process represents a specific objective that the organism - is genetically programmed to achieve. Biological processes are often described - by their outcome or ending state, e.g., the biological process of cell division - results in the creation of two daughter cells (a divided cell) from a single parent - cell. A biological process is accomplished by a particular set of molecular functions - carried out by specific gene products (or macromolecular complexes), often in - a highly regulated manner and in a particular temporal sequence. - synonyms: - - biological process - - physiological process - - single organism process - - single-organism process - subclass_of: - - Process - subtypes: - - MetabolicProcess - - CellularProcess -- name: Envelope - description: A multilayered structure surrounding all or part of a cell; encompasses - one or more lipid bilayers, and may include a cell wall layer; also includes the - space between layers. - subclass_of: - - CellularAnatomicalEntity - part_of: - - Cell - subtypes: - - OrganelleEnvelope -- name: CellularProcess - description: Any process that is carried out at the cellular level, but not necessarily - restricted to a single cell. For example, cell communication occurs among more - than one cell, but occurs at the cellular level. - synonyms: - - cell physiology - - cellular physiological process - - cell growth and/or maintenance - - single-organism cellular process - subclass_of: - - BiologicalProcess - subtypes: - - CellularMetabolicProcess -- name: CellularMetabolicProcess - description: The chemical reactions and pathways by which individual cells transform - chemical substances. - synonyms: - - cellular metabolism - - intermediary metabolism - subclass_of: - - MetabolicProcess - - CellularProcess - subtypes: - - PhosphorusMetabolicProcess -- name: Occurrent - description: An entity that has temporal parts and that happens, unfolds or develops - through time. - subtypes: - - Process -- name: MaterialEntity - description: An independent continuant that is spatially extended whose identity - is independent of that of other entities and can be maintained through time. - subclass_of: - - IndependentContinuant - subtypes: - - MaterialAnatomicalEntity - - CellularComponent -- name: BiologicalEntity - subclass_of: - - IndependentContinuant - subtypes: - - AnatomicalEntity -- name: NuclearEnvelope - description: The double lipid bilayer enclosing the nucleus and separating its contents - from the rest of the cytoplasm; includes the intermembrane space, a gap of width - 20-40 nm (also called the perinuclear space). - subclass_of: - - OrganelleEnvelope - part_of: - - Nucleus - - EndomembraneSystem - parts: - - NuclearMembrane -- name: IntracellularMembrane-boundedOrganelle - description: Organized structure of distinctive morphology and function, bounded - by a single or double lipid bilayer membrane and occurring within the cell. Includes - the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma - membrane. - synonyms: - - intracellular membrane-enclosed organelle - subclass_of: - - Membrane-boundedOrganelle - - IntracellularOrganelle - part_of: - - IntracellularAnatomicalStructure - subtypes: - - Nucleus - equivalent_to: Membrane-boundedOrganelle and part of some IntracellularAnatomicalStructure diff --git a/tests/output/gocam-27929086.pickle b/tests/output/gocam-27929086.pickle deleted file mode 100644 index 5834cd89e..000000000 Binary files a/tests/output/gocam-27929086.pickle and /dev/null differ diff --git a/tests/output/gocam-27929086.yaml b/tests/output/gocam-27929086.yaml deleted file mode 100644 index 48ce6b4cb..000000000 --- a/tests/output/gocam-27929086.yaml +++ /dev/null @@ -1,137 +0,0 @@ -input_id: /Users/cjm/repos/ontogpt/tests/input/cases/gocam-27929086.txt -input_text: "Title: The E3 ubiquitin ligase TRIM31 attenuates NLRP3 inflammasome\n\ - activation by promoting proteasomal degradation of NLRP3\n\nAbstract: The NLRP3\ - \ inflammasome has a fundamental role in host\ndefence against microbial pathogens\ - \ and its deregulation may cause\ndiverse inflammatory diseases. NLRP3 protein expression\ - \ is a\nrate-limiting step for inflammasome activation, thus its expression\nmust\ - \ be tightly controlled to maintain immune homeostasis and avoid\ndetrimental effects.\ - \ However, how NLRP3 expression is regulated\nremains largely unknown. In this study,\ - \ we identify E3 ubiquitin\nligase TRIM31 as a feedback suppressor of NLRP3 inflammasome.\ - \ TRIM31\ndirectly binds to NLRP3, promotes K48-linked polyubiquitination and\n\ - proteasomal degradation of NLRP3. Consequently, TRIM31 deficiency\nenhances NLRP3\ - \ inflammasome activation and aggravates alum-induced\nperitonitis in vivo. Furthermore,\ - \ TRIM31 deficiency attenuates the\nseverity of dextran sodium sulfate (DSS)-induced\ - \ colitis, an\ninflammatory bowel diseases model in which NLRP3 possesses protective\n\ - roles. Thus, our research describes a mechanism by which TRIM31 limits\nNLRP3 inflammasome\ - \ activity under physiological conditions and\nsuggests TRIM31 as a potential therapeutic\ - \ target for the intervention\nof NLRP3 inflammasome related diseases.\n\nFigure\ - \ 1: TRIM31 specifically inhibits NLRP3 inflammasome activation\nFigure 2. TRIM31\ - \ promotes proteasomal degradation of NLRP3\nFigure 3. TRIM31 interacts with NLRP3\n\ - Figure 4. TRIM31 promotes K48-linked polyubiquitination of NLRP3.\nFigure 5. IL-1\u03B2\ - \ and LPS induce TRIM31 expression\nFigure 6. TRIM31 deficiency enhances IL-1\u03B2\ - \ secretion and aggravates\nAlum-induced peritonitis in vivo\nFigure 7. TRIM31 deficiency\ - \ ameliorates DSS-induced colitis\nFigure 8. Working model for TRIM31 inhibiting\ - \ NLRP3 inflammasome activation.\n" -raw_completion_output: "\ngenes: TRIM31; NLRP3; IL-1\u03B2; LPS\norganisms: Homo sapiens;\ - \ Mus musculus\ngene_organisms: TRIM31*:Homo sapiens; NLRP3*:Homo sapiens; IL-1\u03B2\ - *:Homo sapiens; LPS*:Homo sapiens\nactivities: binding; K48-linked polyubiquitination;\ - \ proteasomal degradation; expression; secrection\ngene_functions: TRIM31*:binding;\ - \ TRIM31*:K48-linked polyubiquitination; TRIM31*:proteasomal degradation; NLRP3*:expression;\ - \ IL-1\u03B2*:secretion\ncellular_processes: inflammasome activation; immune homeostasis\n\ - pathways: NLRP3 inflammasome\ngene_gene_interactions: TRIM31*:NLRP3; IL-1\u03B2\ - *:LPS\ngene_localizations: TRIM31*/cytoplasm; NLRP3*/mitochondrion" -prompt: 'Split the following piece of text into fields in the following format: - - - gene: - - location: - - - - Text: - - NLRP3*/mitochondrion - - - === - - - ' -extracted_object: - genes: - - HGNC:16289 - - HGNC:16400 - - HGNC:5992 - - HGNC:6121 - organisms: - - NCBITaxon:9606 - - NCBITaxon:10090 - gene_organisms: - - gene: AUTO:TRIM31%2A - organism: NCBITaxon:9606 - - gene: AUTO:NLRP3%2A - organism: NCBITaxon:9606 - - gene: AUTO:IL-1%CE%B2%2A - organism: NCBITaxon:9606 - - gene: AUTO:LPS%2A - organism: NCBITaxon:9606 - activities: - - GO:0005488 - - AUTO:K48-linked%20polyubiquitination - - AUTO:proteasomal%20degradation - - AUTO:expression - - AUTO:secrection - gene_functions: - - gene: AUTO:TRIM31%2A - molecular_activity: GO:0005488 - - gene: AUTO:TRIM31%2A - molecular_activity: AUTO:K48-linked%20polyubiquitination - - gene: AUTO:TRIM31%2A - molecular_activity: AUTO:proteasomal%20degradation - - gene: AUTO:NLRP3%2A - molecular_activity: AUTO:Expression - - gene: AUTO:IL-1%CE%B2%2A - molecular_activity: GO:0046903 - cellular_processes: - - AUTO:inflammasome%20activation - - AUTO:immune%20homeostasis - pathways: - - AUTO:NLRP3%20inflammasome - gene_gene_interactions: - - gene1: AUTO:TRIM31%2A - gene2: HGNC:16400 - - gene1: AUTO:IL-1%CE%B2%2A - gene2: HGNC:6121 - gene_localizations: - - gene: AUTO:TRIM31%2A - location: GO:0005737 - - gene: HGNC:16400 - location: GO:0005739 -named_entities: -- id: HGNC:16289 - label: TRIM31 -- id: HGNC:16400 - label: NLRP3 -- id: HGNC:5992 - label: "IL-1\u03B2" -- id: HGNC:6121 - label: LPS -- id: MESH:D006801 - label: Homo sapiens -- id: NCBITaxon:10090 - label: Mus musculus -- id: MESH:D006801 - label: Homo sapiens -- id: MESH:D006801 - label: Homo sapiens -- id: MESH:D006801 - label: Homo sapiens -- id: MESH:D006801 - label: Homo sapiens -- id: GO:0005488 - label: binding -- id: GO:0005488 - label: binding -- id: GO:0046903 - label: secretion -- id: HGNC:16400 - label: NLRP3 -- id: HGNC:6121 - label: LPS -- id: GO:0005737 - label: cytoplasm -- id: HGNC:16400 - label: NLRP3 -- id: GO:0005739 - label: mitochondrion diff --git a/tests/output/gocam-33246504.pickle b/tests/output/gocam-33246504.pickle deleted file mode 100644 index c18082890..000000000 Binary files a/tests/output/gocam-33246504.pickle and /dev/null differ diff --git a/tests/output/gocam-33246504.yaml b/tests/output/gocam-33246504.yaml deleted file mode 100644 index f741fcc99..000000000 --- a/tests/output/gocam-33246504.yaml +++ /dev/null @@ -1,216 +0,0 @@ -input_id: /Users/cjm/repos/ontogpt/tests/input/cases/gocam-33246504.txt -input_text: "Text: An allosteric interleukin-1 receptor modulator mitigates\ninflammation\ - \ and photoreceptor toxicity in a model of retinal\ndegeneration\n\nBackground:\ - \ Inflammation and particularly interleukin-1\u03B2 (IL-1\u03B2), a pro-inflammatory\ - \ cytokine highly secreted by activated immune cells during early AMD pathological\ - \ events, contribute significantly to retinal neurodegeneration. Here, we identify\ - \ specific cell types that generate IL-1\u03B2 and harbor the IL-1 receptor (IL-1R)\ - \ and pharmacologically validate IL-1\u03B2's contribution to neuro-retinal degeneration\ - \ using the IL-1R allosteric modulator composed of the amino acid sequence rytvela\ - \ (as well as the orthosteric antagonist, Kineret) in a model of blue light-induced\ - \ retinal degeneration.\n\nMethods: Mice were exposed to blue light for 6 h and\ - \ sacrificed 3 days later. Mice were intraperitoneally injected with rytvela, Kineret,\ - \ or vehicle twice daily for 3 days. The inflammatory markers F4/80, NLRP3, caspase-1,\ - \ and IL-1\u03B2 were assessed in the retinas. Single-cell RNA sequencing was used\ - \ to determine the cell-specific expression patterns of retinal Il1b and Il1r1.\ - \ Macrophage-induced photoreceptor death was assessed ex vivo using retinal explants\ - \ co-cultured with LPS-activated bone marrow-derived macrophages. Photoreceptor\ - \ cell death was evaluated by the TUNEL assay. Retinal function was assessed by\ - \ flash electroretinography.\n\nResults: Blue light markedly increased the mononuclear\ - \ phagocyte recruitment and levels of inflammatory markers associated with photoreceptor\ - \ death. Co-localization of NLRP3, caspase-1, and IL-1\u03B2 with F4/80+ mononuclear\ - \ phagocytes was clearly detected in the subretinal space, suggesting that these\ - \ inflammatory cells are the main source of IL-1\u03B2. Single-cell RNA sequencing\ - \ confirmed the immune-specific expression of Il1b and notably perivascular macrophages\ - \ in light-challenged mice, while Il1r1 expression was found primarily in astrocytes,\ - \ bipolar, and vascular cells. Retinal explants co-cultured with LPS/ATP-activated\ - \ bone marrow-derived macrophages displayed a high number of TUNEL-positive photoreceptors,\ - \ which was abrogated by rytvela treatment. IL-1R antagonism significantly mitigated\ - \ the inflammatory response triggered in vivo by blue light exposure, and rytvela\ - \ was superior to Kineret in preserving photoreceptor density and retinal function.\n\ - \nConclusion: These findings substantiate the importance of IL-1\u03B2 in neuro-retinal\ - \ degeneration and revealed specific sources of Il1b from perivascular MPs, with\ - \ its receptor Ilr1 being separately expressed on surrounding neuro-vascular and\ - \ astroglial cells. They also validate the efficacy of rytvela-induced IL-1R modulation\ - \ in suppressing detrimental inflammatory responses and preserving photoreceptor\ - \ density and function in these conditions, reinforcing the rationale for clinical\ - \ translation.\n\nKeywords: Inflammasome; Inflammation; Interleukin-1; Interleukin-1\ - \ receptor; Photoreceptors; Retinal degeneration; Rytvela; cell death.\n" -raw_completion_output: "\ngenes: Il1b; Il1r1; NLRP3; caspase-1; F4/80;\norganisms:\ - \ Mus Musculus;\ngene_organisms: Il1b / Mus Musculus; Il1r1 / Mus Musculus; NLRP3\ - \ / Mus Musculus; caspase-1 / Mus Musculus; F4/80 / Mus Musculus; \nactivities:\ - \ targeting; suppressing; validating;\ngene_functions: Il1b / targeting; Il1r1 /\ - \ targeting; NLRP3 / targeting; caspase-1 / targeting; F4/80 / targeting; rytvela\ - \ / suppressing; Kineret / suppressing;\ncellular_processes: neuro-retinal degeneration;\ - \ neuronal ativation; macrophage-induced photoreceptor death;\npathways: interleukin-1\ - \ pathway;\ngene_gene_interactions: Il1b and Il1r1; NLRP3 and caspase-1;\ngene_localizations:\ - \ Il1b / perivascular macrophages; Il1r1 / astrocytes, bipolar, and vascular cells;\ - \ NLRP3 / subretinal space; caspase-1 / subretinal space; F4/80 / mononuclear phagocytes." -prompt: 'Split the following piece of text into fields in the following format: - - - gene: - - location: - - - - Text: - - F4/80 / mononuclear phagocytes. - - - === - - - ' -extracted_object: - genes: - - HGNC:5992 - - HGNC:5993 - - HGNC:16400 - - HGNC:1499 - - AUTO:F4/80 - organisms: - - NCBITaxon:10090 - gene_organisms: - - gene: HGNC:5992 - organism: NCBITaxon:10090 - - gene: HGNC:5993 - organism: NCBITaxon:10090 - - gene: HGNC:16400 - organism: NCBITaxon:10090 - - gene: HGNC:1499 - organism: NCBITaxon:10090 - - gene: AUTO:F4/80 - organism: NCBITaxon:10090 - activities: - - AUTO:targeting - - AUTO:suppressing - - AUTO:validating - gene_functions: - - gene: HGNC:5992 - molecular_activity: AUTO:targeting - - gene: HGNC:5993 - molecular_activity: AUTO:targeting - - gene: HGNC:16400 - molecular_activity: AUTO:targeting - - gene: HGNC:1499 - molecular_activity: AUTO:targeting - - gene: AUTO:F4/80 - molecular_activity: AUTO:Targeting - - gene: AUTO:rytvela - molecular_activity: AUTO:suppressing - - gene: AUTO:Kineret - molecular_activity: AUTO:suppressing - cellular_processes: - - AUTO:neuro-retinal%20degeneration - - AUTO:neuronal%20ativation - - AUTO:macrophage-induced%20photoreceptor%20death - pathways: - - AUTO:interleukin-1%20pathway - gene_gene_interactions: - - gene1: HGNC:5992 - gene2: HGNC:5993 - - gene1: HGNC:16400 - gene2: HGNC:1499 - gene_localizations: - - gene: HGNC:5992 - location: AUTO:Perivascular%20Macrophages - - gene: HGNC:5993 - location: AUTO:astrocytes%2C%20bipolar%2C%20and%20vascular%20cells - - gene: HGNC:16400 - location: AUTO:subretinal%20space - - gene: HGNC:1499 - location: AUTO:subretinal%20space - - gene: AUTO:F4/80 - location: AUTO:mononuclear%20phagocytes -named_entities: -- id: HGNC:16289 - label: TRIM31 -- id: HGNC:16400 - label: NLRP3 -- id: HGNC:5992 - label: "IL-1\u03B2" -- id: HGNC:6121 - label: LPS -- id: MESH:D006801 - label: Homo sapiens -- id: NCBITaxon:10090 - label: Mus musculus -- id: MESH:D006801 - label: Homo sapiens -- id: MESH:D006801 - label: Homo sapiens -- id: MESH:D006801 - label: Homo sapiens -- id: MESH:D006801 - label: Homo sapiens -- id: GO:0005488 - label: binding -- id: GO:0005488 - label: binding -- id: GO:0046903 - label: secretion -- id: HGNC:16400 - label: NLRP3 -- id: HGNC:6121 - label: LPS -- id: GO:0005737 - label: cytoplasm -- id: HGNC:16400 - label: NLRP3 -- id: GO:0005739 - label: mitochondrion -- id: HGNC:5992 - label: Il1b -- id: HGNC:5993 - label: Il1r1 -- id: HGNC:16400 - label: NLRP3 -- id: HGNC:1499 - label: caspase-1 -- id: NCBITaxon:10090 - label: Mus Musculus -- id: HGNC:5992 - label: Il1b -- id: NCBITaxon:10090 - label: Mus Musculus -- id: HGNC:5993 - label: Il1r1 -- id: NCBITaxon:10090 - label: Mus Musculus -- id: HGNC:16400 - label: NLRP3 -- id: NCBITaxon:10090 - label: Mus Musculus -- id: HGNC:1499 - label: caspase-1 -- id: NCBITaxon:10090 - label: Mus Musculus -- id: NCBITaxon:10090 - label: Mus Musculus -- id: HGNC:5992 - label: Il1b -- id: HGNC:5993 - label: Il1r1 -- id: HGNC:16400 - label: NLRP3 -- id: HGNC:1499 - label: caspase-1 -- id: HGNC:5992 - label: Il1b -- id: HGNC:5993 - label: Il1r1 -- id: HGNC:16400 - label: NLRP3 -- id: HGNC:1499 - label: caspase-1 -- id: HGNC:5992 - label: Il1b -- id: HGNC:5993 - label: Il1r1 -- id: HGNC:16400 - label: NLRP3 -- id: HGNC:1499 - label: caspase-1 diff --git a/tests/output/gocam-betacat.pickle b/tests/output/gocam-betacat.pickle deleted file mode 100644 index 1615c136c..000000000 Binary files a/tests/output/gocam-betacat.pickle and /dev/null differ diff --git a/tests/output/gocam-betacat.yaml b/tests/output/gocam-betacat.yaml deleted file mode 100644 index f93759905..000000000 --- a/tests/output/gocam-betacat.yaml +++ /dev/null @@ -1,279 +0,0 @@ -input_id: /Users/cjm/repos/ontogpt/tests/input/cases/gocam-betacat.txt -input_text: "Title: \u03B2-Catenin Is Required for the cGAS/STING Signaling Pathway\ - \ but Antagonized by the Herpes Simplex Virus 1 US3 Protein\nText:\nThe cGAS/STING-mediated\ - \ DNA-sensing signaling pathway is crucial\nfor interferon (IFN) production and\ - \ host antiviral\nresponses. Herpes simplex virus I (HSV-1) is a DNA virus that\ - \ has\nevolved multiple strategies to evade host immune responses. Here,\nwe demonstrate\ - \ that the highly conserved \u03B2-catenin protein in the\nWnt signaling pathway\ - \ is an important factor to enhance the\ntranscription of type I interferon (IFN-I)\ - \ in the cGAS/STING\nsignaling pathway, and the production of IFN-I mediated by\n\ - \u03B2-catenin was antagonized by HSV-1 US3 protein via its kinase\nactivity. Infection\ - \ by US3-deficienct HSV-1 and its kinase-dead\nvariants failed to downregulate IFN-I\ - \ and IFN-stimulated\ngene (ISG) production induced by \u03B2-catenin. Consistent\ - \ with this,\nabsence of \u03B2-catenin enhanced the replication of US3-deficienct\n\ - HSV-1, but not wild-type HSV-1. The underlying mechanism was the\ninteraction of\ - \ US3 with \u03B2-catenin and its hyperphosphorylation of\n\u03B2-catenin at Thr556\ - \ to block its nuclear translocation. For the\nfirst time, HSV-1 US3 has been shown\ - \ to inhibit IFN-I production\nthrough hyperphosphorylation of \u03B2-catenin and\ - \ to subvert host\nantiviral innate immunity.IMPORTANCE Although increasing evidence\n\ - has demonstrated that HSV-1 subverts host immune responses and\nestablishes lifelong\ - \ latent infection, the molecular mechanisms\nby which HSV-1 interrupts antiviral\ - \ innate immunity, especially\nthe cGAS/STING-mediated cellular DNA-sensing signaling\ - \ pathway,\nhave not been fully explored. Here, we show that \u03B2-catenin\npromotes\ - \ cGAS/STING-mediated activation of the IFN pathway, which\nis important for cellular\ - \ innate immune responses and intrinsic\nresistance to DNA virus infection. The\ - \ protein kinase US3\nantagonizes the production of IFN by targeting \u03B2-catenin\ - \ via its\nkinase activity. The findings in this study reveal a novel\nmechanism\ - \ for HSV-1 to evade host antiviral immunity and add new\nknowledge to help in understanding\ - \ the interaction between the\nhost and HSV-1 infection.\n\nKeywords: HSV-1; US3;\ - \ type I IFN; \u03B2-catenin." -raw_completion_output: "genes: cGAS; STING; \u03B2-catenin; US3; IFN; ISG; Thr556\n\ - organisms: Homo sapiens; Herpes simplex virus I\ngene_organisms: cGAS/Homo sapiens;\ - \ STING/Homo sapiens; \u03B2-catenin/Homo sapiens; US3/Herpes simplex virus I; IFN/Homo\ - \ sapiens; ISG/Homo sapiens; Thr556/Homo sapiens\nactivities: transcription; replication;\ - \ production; nuclear translocation\ngene_functions: cGAS/activate type I IFN; STING/activate\ - \ type I IFN; \u03B2-catenin/enhance transcription of type I IFN; US3/antagonize\ - \ production of IFN; IFN/produce type I IFN; ISG/produce type I IFN; Thr556/block\ - \ nuclear translocation\ncellular_processes: DNA-sensing; interferon production;\ - \ host antiviral responses; Wnt signaling; hyperphosphorylation\npathways: cGAS/STING\ - \ signaling; Wnt signaling\ngene_gene_interactions: US3/\u03B2-catenin\ngene_localizations:\ - \ cGAS/--; STING/--; \u03B2-catenin/nuclear; US3/--; IFN/--; ISG/--; Thr556/--" -prompt: 'Split the following piece of text into fields in the following format: - - - gene: - - location: - - - - Text: - - Thr556/-- - - - === - - - ' -extracted_object: - genes: - - HGNC:21367 - - HGNC:27962 - - HGNC:2514 - - AUTO:US3 - - HGNC:5417 - - AUTO:ISG - - AUTO:Thr556 - organisms: - - NCBITaxon:9606 - - NCBITaxon:10298 - gene_organisms: - - gene: HGNC:21367 - organism: NCBITaxon:9606 - - gene: HGNC:27962 - organism: NCBITaxon:9606 - - gene: HGNC:2514 - organism: NCBITaxon:9606 - - gene: AUTO:US3 - organism: NCBITaxon:10298 - - gene: HGNC:5417 - organism: NCBITaxon:9606 - - gene: AUTO:ISG - organism: NCBITaxon:9606 - - gene: AUTO:Thr556 - organism: NCBITaxon:9606 - activities: - - GO:0006351 - - AUTO:replication - - AUTO:production - - AUTO:nuclear%20translocation - gene_functions: - - gene: HGNC:21367 - molecular_activity: AUTO:activate%20type%20I%20IFN - - gene: HGNC:27962 - molecular_activity: AUTO:activate%20type%20I%20IFN - - gene: HGNC:2514 - molecular_activity: AUTO:enhance%20transcription%20of%20type%20I%20IFN - - gene: AUTO:US3 - molecular_activity: AUTO:antagonize%20production%20of%20IFN - - gene: HGNC:5417 - molecular_activity: AUTO:produce%20type%20I%20IFN - - gene: AUTO:ISG - molecular_activity: AUTO:produce%20type%20I%20IFN - - gene: AUTO:Thr556 - molecular_activity: AUTO:block%20nuclear%20translocation - cellular_processes: - - AUTO:DNA-sensing - - GO:0001816 - - AUTO:host%20antiviral%20responses - - AUTO:Wnt%20signaling - - GO:0048151 - pathways: - - AUTO:cGAS/STING%20signaling - - AUTO:Wnt%20signaling - gene_gene_interactions: - - gene1: AUTO:US3 - gene2: HGNC:2514 - gene_localizations: - - gene: HGNC:21367 - location: AUTO:-- - - gene: HGNC:27962 - location: AUTO:-- - - gene: HGNC:2514 - location: AUTO:nuclear - - gene: AUTO:US3 - location: AUTO:-- - - gene: HGNC:5417 - location: AUTO:-- - - gene: AUTO:ISG - location: AUTO:-- - - gene: AUTO:Thr556 - location: AUTO:-- -named_entities: -- id: HGNC:16289 - label: TRIM31 -- id: HGNC:16400 - label: NLRP3 -- id: HGNC:5992 - label: "IL-1\u03B2" -- id: HGNC:6121 - label: LPS -- id: MESH:D006801 - label: Homo sapiens -- id: NCBITaxon:10090 - label: Mus musculus -- id: MESH:D006801 - label: Homo sapiens -- id: MESH:D006801 - label: Homo sapiens -- id: MESH:D006801 - label: Homo sapiens -- id: MESH:D006801 - label: Homo sapiens -- id: GO:0005488 - label: binding -- id: GO:0005488 - label: binding -- id: GO:0046903 - label: secretion -- id: HGNC:16400 - label: NLRP3 -- id: HGNC:6121 - label: LPS -- id: GO:0005737 - label: cytoplasm -- id: HGNC:16400 - label: NLRP3 -- id: GO:0005739 - label: mitochondrion -- id: HGNC:5992 - label: Il1b -- id: HGNC:5993 - label: Il1r1 -- id: HGNC:16400 - label: NLRP3 -- id: HGNC:1499 - label: caspase-1 -- id: NCBITaxon:10090 - label: Mus Musculus -- id: HGNC:5992 - label: Il1b -- id: NCBITaxon:10090 - label: Mus Musculus -- id: HGNC:5993 - label: Il1r1 -- id: NCBITaxon:10090 - label: Mus Musculus -- id: HGNC:16400 - label: NLRP3 -- id: NCBITaxon:10090 - label: Mus Musculus -- id: HGNC:1499 - label: caspase-1 -- id: NCBITaxon:10090 - label: Mus Musculus -- id: NCBITaxon:10090 - label: Mus Musculus -- id: HGNC:5992 - label: Il1b -- id: HGNC:5993 - label: Il1r1 -- id: HGNC:16400 - label: NLRP3 -- id: HGNC:1499 - label: caspase-1 -- id: HGNC:5992 - label: Il1b -- id: HGNC:5993 - label: Il1r1 -- id: HGNC:16400 - label: NLRP3 -- id: HGNC:1499 - label: caspase-1 -- id: HGNC:5992 - label: Il1b -- id: HGNC:5993 - label: Il1r1 -- id: HGNC:16400 - label: NLRP3 -- id: HGNC:1499 - label: caspase-1 -- id: HGNC:21367 - label: cGAS -- id: HGNC:27962 - label: STING -- id: HGNC:2514 - label: "\u03B2-catenin" -- id: HGNC:5417 - label: IFN -- id: MESH:D006801 - label: Homo sapiens -- id: MESH:D018259 - label: Herpes simplex virus I -- id: HGNC:21367 - label: cGAS -- id: MESH:D006801 - label: Homo sapiens -- id: HGNC:27962 - label: STING -- id: MESH:D006801 - label: Homo sapiens -- id: HGNC:2514 - label: "\u03B2-catenin" -- id: MESH:D006801 - label: Homo sapiens -- id: MESH:D018259 - label: Herpes simplex virus I -- id: HGNC:5417 - label: IFN -- id: MESH:D006801 - label: Homo sapiens -- id: MESH:D006801 - label: Homo sapiens -- id: MESH:D006801 - label: Homo sapiens -- id: GO:0006351 - label: transcription -- id: HGNC:21367 - label: cGAS -- id: HGNC:27962 - label: STING -- id: HGNC:2514 - label: "\u03B2-catenin" -- id: HGNC:5417 - label: IFN -- id: GO:0001816 - label: interferon production -- id: GO:0048151 - label: hyperphosphorylation -- id: HGNC:2514 - label: "\u03B2-catenin" -- id: HGNC:21367 - label: cGAS -- id: HGNC:27962 - label: STING -- id: HGNC:2514 - label: "\u03B2-catenin" -- id: HGNC:5417 - label: IFN diff --git a/tests/output/mendelian-disease-cmt2e-summary.pickle b/tests/output/mendelian-disease-cmt2e-summary.pickle deleted file mode 100644 index 458f3be2e..000000000 Binary files a/tests/output/mendelian-disease-cmt2e-summary.pickle and /dev/null differ diff --git a/tests/output/mendelian-disease-cmt2e-summary.yaml b/tests/output/mendelian-disease-cmt2e-summary.yaml deleted file mode 100644 index 47dc67651..000000000 --- a/tests/output/mendelian-disease-cmt2e-summary.yaml +++ /dev/null @@ -1,63 +0,0 @@ -input_id: /Users/cjm/repos/ontogpt/tests/input/cases/mendelian-disease-cmt2e-summary.txt -input_text: "CHARCOT-MARIE-TOOTH DISEASE, AXONAL, TYPE 2E; CMT2E\n\nINHERITANCE\n\ - - Autosomal dominant\nHEAD & NECK\nFace\n- Facial muscle weakness (in some patients)\n\ - Eyes\n- Ptosis (in some patients) \nMouth\n- High-arched palate (in some patients)\n\ - SKELETAL\n- Joint contractures\nSpine\n- Scoliosis (in some patients)\nHands\n-\ - \ Claw hand deformities (in severe cases)\nFeet\n- Pes cavus \n- Hammer toes\n-\ - \ Foot deformities\nMUSCLE, SOFT TISSUES\n- Shoulder muscle weakness (in some patients)\n\ - - Hypotrophy of the small hand muscles\n- Fiber-type predominance seen on muscle\ - \ biopsy (in some patients)\n- Fiber size variation (in some patients)\n- Internal\ - \ nuclei (in some patients)\n- Increased connective tissue (in some patients)\n\ - - Nemaline rods (in some patients)\n- Group fiber atrophy (in some patients)\n-\ - \ Angular fibers (in some patients)\n- EMG consistent with chronic neurogenic disorder\n\ - NEUROLOGIC\nCentral Nervous System\n- Delayed motor development (in some patients)\n\ - Peripheral Nervous System\n- Distal limb muscle weakness due to peripheral neuropathy\n\ - - Distal limb muscle atrophy due to peripheral neuropathy\n- 'Steppage' gait\n-\ - \ Foot drop\n- Distal sensory impairment\n- Hyporeflexia\n- Areflexia\n- Normal\ - \ or mildly decreased motor nerve conduction velocity (NCV) (greater than 38 m/s)\n\ - - Axonopathy seen on nerve biopsy\n- Giant axons with accumulation of disorganized\ - \ neurofilaments\nMISCELLANEOUS\n- Variable age of onset (range first to third decade)\n\ - - Usually begins in feet and legs (peroneal distribution)\n- Upper limb involvement\ - \ occurs later\n- Variable severity\n- Some patients may become wheelchair-bound\n\ - MOLECULAR BASIS\n- Caused by mutation in the light polypeptide neurofilament protein\ - \ gene (NEFL, 162280.0001)\n" -raw_completion_output: "name: Charcot-Marie-Tooth Disease, Axonal, Type 2E \ndescription:\ - \ A peripheral neuropathy characterized by distal limb muscle weakness and atrophy,\ - \ 'steppage' gait, foot drop, distal sensory impairment, hyporeflexia, areflexia,\ - \ and normal or mildly decreased motor nerve conduction velocity \nsynonyms: CMT2E\n\ - subclass_of; Charcot-Marie-Tooth Disease\nsymptoms: Facial muscle weakness; Ptosis;\ - \ High-arched palate; Joint contractures; Scoliosis; Claw hand deformities; Pes\ - \ cavus; Hammer toes; Foot deformities; Shoulder muscle weakness; Hypotrophy of\ - \ the small hand muscles; Delayed motor development\ninheritance: Autosomal dominant\n\ - genes: NEFL\ndisease_onsets: Adult; Juvenile; First decade\nlabel: Charcot-Marie-Tooth\ - \ Disease, Axonal, Type 2E" -prompt: "From the text below, extract the following entities in the following format:\n\ - \nname: \ndescription: \n\ - synonyms: \nsubclass_of: \nsymptoms: \ninheritance:\ - \ \ngenes: \ndisease_onsets: \n\ - label: \n\n\nText:\nCHARCOT-MARIE-TOOTH DISEASE,\ - \ AXONAL, TYPE 2E; CMT2E\n\nINHERITANCE\n- Autosomal dominant\nHEAD & NECK\nFace\n\ - - Facial muscle weakness (in some patients)\nEyes\n- Ptosis (in some patients) \n\ - Mouth\n- High-arched palate (in some patients)\nSKELETAL\n- Joint contractures\n\ - Spine\n- Scoliosis (in some patients)\nHands\n- Claw hand deformities (in severe\ - \ cases)\nFeet\n- Pes cavus \n- Hammer toes\n- Foot deformities\nMUSCLE, SOFT TISSUES\n\ - - Shoulder muscle weakness (in some patients)\n- Hypotrophy of the small hand muscles\n\ - - Fiber-type predominance seen on muscle biopsy (in some patients)\n- Fiber size\ - \ variation (in some patients)\n- Internal nuclei (in some patients)\n- Increased\ - \ connective tissue (in some patients)\n- Nemaline rods (in some patients)\n- Group\ - \ fiber atrophy (in some patients)\n- Angular fibers (in some patients)\n- EMG consistent\ - \ with chronic neurogenic disorder\nNEUROLOGIC\nCentral Nervous System\n- Delayed\ - \ motor development (in some patients)\nPeripheral Nervous System\n- Distal limb\ - \ muscle weakness due to peripheral neuropathy\n- Distal limb muscle atrophy due\ - \ to peripheral neuropathy\n- 'Steppage' gait\n- Foot drop\n- Distal sensory impairment\n\ - - Hyporeflexia\n- Areflexia\n- Normal or mildly decreased motor nerve conduction\ - \ velocity (NCV) (greater than 38 m/s)\n- Axonopathy seen on nerve biopsy\n- Giant\ - \ axons with accumulation of disorganized neurofilaments\nMISCELLANEOUS\n- Variable\ - \ age of onset (range first to third decade)\n- Usually begins in feet and legs\ - \ (peroneal distribution)\n- Upper limb involvement occurs later\n- Variable severity\n\ - - Some patients may become wheelchair-bound\nMOLECULAR BASIS\n- Caused by mutation\ - \ in the light polypeptide neurofilament protein gene (NEFL, 162280.0001)\n\n\n\ - ===\n\n" diff --git a/tests/output/mendelian-disease-cmt2e.pickle b/tests/output/mendelian-disease-cmt2e.pickle deleted file mode 100644 index d95ed2f1f..000000000 Binary files a/tests/output/mendelian-disease-cmt2e.pickle and /dev/null differ diff --git a/tests/output/mendelian-disease-cmt2e.yaml b/tests/output/mendelian-disease-cmt2e.yaml deleted file mode 100644 index 11186dee1..000000000 --- a/tests/output/mendelian-disease-cmt2e.yaml +++ /dev/null @@ -1,146 +0,0 @@ -input_id: /Users/cjm/repos/ontogpt/tests/input/cases/mendelian-disease-cmt2e.txt -input_text: "Mersiyanova et al. (2000) reported a large 6-generation family from Russia\ - \ with autosomal dominant CMT2. Onset was in the second and third decade, characterized\ - \ by difficulty in walking and weakness and atrophy of the distal lower limb muscles\ - \ and a variable degree of deformity of the feet (pes cavus). Affected individuals\ - \ did not exhibit enlarged nerves, ulcerated feet, hearing impairment, or paralysis\ - \ of the vocal cords. Several patients had hyperkeratosis, although the association,\ - \ if any, between the 2 disorders was not clear. The authors suggested the designation\ - \ CMT2E for this disorder. \n\nGeorgiou et al. (2002) described a large 5-generation\ - \ Slovenian family with autosomal dominant CMT type 2E. Disease onset in most patients\ - \ was in the first decade of life. The presenting symptoms were difficulty in walking\ - \ or running, due to a slowly progressive distal weakness and wasting of the lower\ - \ limbs. A steppage gait, pes cavus, and hammertoes were typically present. Over\ - \ a period of 20 years after disease onset, two-thirds of patients developed upper\ - \ limb involvement resulting in claw hands. All patients were ambulatory 20 to 30\ - \ years after onset. \n\nFabrizi et al. (2004) reported a large kindred from southern\ - \ Italy with autosomal dominant CMT2E spanning 5 generations and caused by mutation\ - \ in the NEFL gene (162280.0002). An affected woman and her 2 affected sons had\ - \ steppage gait, ataxic gait, peroneal muscular atrophy, decreased vibration sense\ - \ with stocking and glove distribution, and hypotrophy of the hand muscles. One\ - \ of the sons had claw hand deformities. Motor nerve conduction velocities (NCV)\ - \ were decreased, consistent with a demyelinating neuropathy, but sural nerve biopsy\ - \ of the mother showed a primary axonopathy characterized by giant axons containing\ - \ disorganized neurofilaments. \n\nMiltenberger-Miltenyi et al. (2007) reported\ - \ a large Austrian family in which at least 4 members had CMT2E confirmed by genetic\ - \ analysis (162880.0006). Disease onset was in the second decade of life with pes\ - \ cavus, progressive plantar extensor weakness, and distal lower limb atrophy and\ - \ weakness. Two patients became wheelchair-bound. Affected members of a second Austrian\ - \ family, with a different NEFL mutation (162280.0003), had disease onset before\ - \ age 15 years in all but 1 patient. The disorder was slowly progressive but resulted\ - \ in a severe and disabling phenotype. Electrophysiologic studies of both families\ - \ showed intermediate motor nerve conduction velocities consistent with axonal pathology.\n" -raw_completion_output: "Name: CMT2\nDescription: A hereditary motor and sensory neuropathy\ - \ characterized by slowly progressive distal lower limb muscle weakness.\nSynonyms:\ - \ Charcot-Marie-Tooth disease type 2; Hereditary Motor and Sensory Neuropathy Type\ - \ 2; CMT2E\nSubclass_of: Charcot-Marie-Tooth Disease\nSymptoms: Difficulty in walking;\ - \ Steppage gait; Pes cavus; Hammertoes; Claw hands; Decreased vibration sense with\ - \ stocking and glove distribution; Hypotrophy of hand muscles\nInheritance: Autosomal\ - \ dominant\nGenes: NEFL; 162280.0002; 162880.0006; 162280.0003\nDisease_Onsets:\ - \ Second and third decade; First decade; Adult; Juvenile; First decade \nLabel:\ - \ Charcot-Marie-Tooth Disease Type 2" -prompt: "From the text below, extract the following entities in the following format:\n\ - \nname: \ndescription: \n\ - synonyms: \nsubclass_of: \nsymptoms: \ninheritance:\ - \ \ngenes: \ndisease_onsets: \n\ - label: \n\n\nText:\nMersiyanova et al. (2000)\ - \ reported a large 6-generation family from Russia with autosomal dominant CMT2.\ - \ Onset was in the second and third decade, characterized by difficulty in walking\ - \ and weakness and atrophy of the distal lower limb muscles and a variable degree\ - \ of deformity of the feet (pes cavus). Affected individuals did not exhibit enlarged\ - \ nerves, ulcerated feet, hearing impairment, or paralysis of the vocal cords. Several\ - \ patients had hyperkeratosis, although the association, if any, between the 2 disorders\ - \ was not clear. The authors suggested the designation CMT2E for this disorder.\ - \ \n\nGeorgiou et al. (2002) described a large 5-generation Slovenian family with\ - \ autosomal dominant CMT type 2E. Disease onset in most patients was in the first\ - \ decade of life. The presenting symptoms were difficulty in walking or running,\ - \ due to a slowly progressive distal weakness and wasting of the lower limbs. A\ - \ steppage gait, pes cavus, and hammertoes were typically present. Over a period\ - \ of 20 years after disease onset, two-thirds of patients developed upper limb involvement\ - \ resulting in claw hands. All patients were ambulatory 20 to 30 years after onset.\ - \ \n\nFabrizi et al. (2004) reported a large kindred from southern Italy with autosomal\ - \ dominant CMT2E spanning 5 generations and caused by mutation in the NEFL gene\ - \ (162280.0002). An affected woman and her 2 affected sons had steppage gait, ataxic\ - \ gait, peroneal muscular atrophy, decreased vibration sense with stocking and glove\ - \ distribution, and hypotrophy of the hand muscles. One of the sons had claw hand\ - \ deformities. Motor nerve conduction velocities (NCV) were decreased, consistent\ - \ with a demyelinating neuropathy, but sural nerve biopsy of the mother showed a\ - \ primary axonopathy characterized by giant axons containing disorganized neurofilaments.\ - \ \n\nMiltenberger-Miltenyi et al. (2007) reported a large Austrian family in which\ - \ at least 4 members had CMT2E confirmed by genetic analysis (162880.0006). Disease\ - \ onset was in the second decade of life with pes cavus, progressive plantar extensor\ - \ weakness, and distal lower limb atrophy and weakness. Two patients became wheelchair-bound.\ - \ Affected members of a second Austrian family, with a different NEFL mutation (162280.0003),\ - \ had disease onset before age 15 years in all but 1 patient. The disorder was slowly\ - \ progressive but resulted in a severe and disabling phenotype. Electrophysiologic\ - \ studies of both families showed intermediate motor nerve conduction velocities\ - \ consistent with axonal pathology.\n\n\n===\n\n" -extracted_object: - label: Charcot-Marie-Tooth Disease Type 2 - name: CMT2 - description: A hereditary motor and sensory neuropathy characterized by slowly progressive - distal lower limb muscle weakness. - synonyms: - - Charcot-Marie-Tooth disease type 2 - - Hereditary Motor and Sensory Neuropathy Type 2 - - CMT2E - subclass_of: - - MONDO:0015626 - symptoms: - - HP:0002355 - - HP:0003376 - - HP:0001761 - - HP:0001765 - - AUTO:Claw%20hands - - AUTO:Decreased%20vibration%20sense%20with%20stocking%20and%20glove%20distribution - - AUTO:Hypotrophy%20of%20hand%20muscles - inheritance: HP:0000006 - genes: - - HGNC:7739 - - AUTO:162280.0002 - - AUTO:162880.0006 - - AUTO:162280.0003 - disease_onsets: - - AUTO:Second%20and%20third%20decade - - AUTO:First%20decade - - AUTO:Adult - - AUTO:Juvenile - - AUTO:First%20decade -named_entities: -- id: MONDO:0015626 - label: Charcot-Marie-Tooth Disease -- id: HP:0002355 - label: Difficulty in walking -- id: HP:0003376 - label: Steppage gait -- id: HP:0001761 - label: Pes cavus -- id: HP:0001765 - label: Hammertoes -- id: AUTO:Claw%20hands - label: Claw hands -- id: AUTO:Decreased%20vibration%20sense%20with%20stocking%20and%20glove%20distribution - label: Decreased vibration sense with stocking and glove distribution -- id: AUTO:Hypotrophy%20of%20hand%20muscles - label: Hypotrophy of hand muscles -- id: HP:0000006 - label: Autosomal dominant -- id: HGNC:7739 - label: NEFL -- id: AUTO:162280.0002 - label: '162280.0002' -- id: AUTO:162880.0006 - label: '162880.0006' -- id: AUTO:162280.0003 - label: '162280.0003' -- id: AUTO:Second%20and%20third%20decade - label: Second and third decade -- id: AUTO:First%20decade - label: First decade -- id: AUTO:Adult - label: Adult -- id: AUTO:Juvenile - label: Juvenile diff --git a/tests/output/mendelian-disease-marfan.pickle b/tests/output/mendelian-disease-marfan.pickle deleted file mode 100644 index 94541bc43..000000000 Binary files a/tests/output/mendelian-disease-marfan.pickle and /dev/null differ diff --git a/tests/output/mendelian-disease-marfan.yaml b/tests/output/mendelian-disease-marfan.yaml deleted file mode 100644 index c4bd19191..000000000 --- a/tests/output/mendelian-disease-marfan.yaml +++ /dev/null @@ -1,159 +0,0 @@ -input_id: /Users/cjm/repos/ontogpt/tests/input/cases/mendelian-disease-marfan.txt -input_text: Marfan syndrome is a genetic disorder that affects connective tissue, - which is the material between cells of the body that gives the tissues form and - strength. Connective tissue is found all over the body and multiple organ systems - may be affected in individuals with Marfan syndrome. The heart and blood vessels - (cardiovascular), skeletal, and eye (ocular) systems are most often affected. Major - symptoms include overgrowth of the long bones of the arms and legs, abnormal side-to-side - curvature of the spine (scoliosis), indentation or protrusion of the chest wall - (pectus deformity), dislocation of the lenses of the eyes (ectopia lentis), nearsightedness - (myopia), widening (aneurysm) and tear (dissection) of the main artery that carries - blood away from the heart (aorta), floppiness of the mitral valve (mitral valve - prolapse) and backward flow of blood through the aortic and mitral valves (aortic - and mitral regurgitation). The specific symptoms and the severity of Marfan syndrome - vary greatly from person to person. Marfan syndrome is inherited as an autosomal - dominant trait, meaning that only one abnormal copy of the Marfan gene inherited - from one parent is sufficient to have the condition. Defects or deletions (pathogenic - variants) of the fibrillin-1 (FBN1) gene have been shown to cause Marfan syndrome. -raw_completion_output: "Name: Marfan syndrome \nDescription: A genetic disorder that\ - \ affects connective tissue, which is the material between cells of the body that\ - \ gives the tissues form and strength \nSynonyms: Marfan\u2019s Syndrome; Marie\u2013\ - Strumpell disease; Ochronotic arthropathy; Dysfibrillinosis \nSubclass_of: N/A\n\ - Symptoms: Overgrowth of the long bones of the arms and legs; abnormal side-to-side\ - \ curvature of the spine (scoliosis); indentation or protrusion of the chest wall\ - \ (pectus deformity); dislocation of the lenses of the eyes (ectopia lentis); nearsightedness\ - \ (myopia); widening (aneurysm); tear (dissection) of the main artery that carries\ - \ blood away from the heart (aorta); floppiness of the mitral valve (mitral valve\ - \ prolapse); backward flow of blood through the aortic and mitral valves (aortic\ - \ and mitral regurgitation)\nInheritance: Autosomal Dominant \nGenes: FBN1 \nDisease_Onsets:\ - \ Adult; Juvenile; First Decade \nLabel: Marfan Syndrome" -prompt: 'From the text below, extract the following entities in the following format: - - - name: - - description: - - synonyms: - - subclass_of: - - symptoms: - - inheritance: - - genes: - - disease_onsets: - - label: - - - - Text: - - Marfan syndrome is a genetic disorder that affects connective tissue, which is the - material between cells of the body that gives the tissues form and strength. Connective - tissue is found all over the body and multiple organ systems may be affected in - individuals with Marfan syndrome. The heart and blood vessels (cardiovascular), - skeletal, and eye (ocular) systems are most often affected. Major symptoms include - overgrowth of the long bones of the arms and legs, abnormal side-to-side curvature - of the spine (scoliosis), indentation or protrusion of the chest wall (pectus deformity), - dislocation of the lenses of the eyes (ectopia lentis), nearsightedness (myopia), - widening (aneurysm) and tear (dissection) of the main artery that carries blood - away from the heart (aorta), floppiness of the mitral valve (mitral valve prolapse) - and backward flow of blood through the aortic and mitral valves (aortic and mitral - regurgitation). The specific symptoms and the severity of Marfan syndrome vary greatly - from person to person. Marfan syndrome is inherited as an autosomal dominant trait, - meaning that only one abnormal copy of the Marfan gene inherited from one parent - is sufficient to have the condition. Defects or deletions (pathogenic variants) - of the fibrillin-1 (FBN1) gene have been shown to cause Marfan syndrome. - - - === - - - ' -extracted_object: - label: Marfan Syndrome - name: Marfan syndrome - description: A genetic disorder that affects connective tissue, which is the material - between cells of the body that gives the tissues form and strength - synonyms: - - "Marfan\u2019s Syndrome" - - "Marie\u2013Strumpell disease" - - Ochronotic arthropathy - - Dysfibrillinosis - subclass_of: - - AUTO:N/A - symptoms: - - AUTO:Overgrowth%20of%20the%20long%20bones%20of%20the%20arms%20and%20legs - - AUTO:abnormal%20side-to-side%20curvature%20of%20the%20spine%20%28scoliosis%29 - - AUTO:indentation%20or%20protrusion%20of%20the%20chest%20wall%20%28pectus%20deformity%29 - - AUTO:dislocation%20of%20the%20lenses%20of%20the%20eyes%20%28ectopia%20lentis%29 - - AUTO:nearsightedness%20%28myopia%29 - - AUTO:widening%20%28aneurysm%29 - - AUTO:tear%20%28dissection%29%20of%20the%20main%20artery%20that%20carries%20blood%20away%20from%20the%20heart%20%28aorta%29 - - AUTO:floppiness%20of%20the%20mitral%20valve%20%28mitral%20valve%20prolapse%29 - - AUTO:backward%20flow%20of%20blood%20through%20the%20aortic%20and%20mitral%20valves%20%28aortic%20and%20mitral%20regurgitation%29 - inheritance: HP:0000006 - genes: - - HGNC:3603 - disease_onsets: - - AUTO:Adult - - AUTO:Juvenile - - AUTO:First%20Decade -named_entities: -- id: HP:0009830 - label: Peripheral Neuropathy -- id: HP:0001371 - label: Joint contractures -- id: HP:0001761 - label: Pes cavus -- id: HP:0001760 - label: Foot deformities -- id: HP:0006006 - label: Hypotrophy of the small hand muscles -- id: HP:0002460 - label: Distal limb muscle weakness due to peripheral neuropathy -- id: HP:0009027 - label: Foot drop -- id: HP:0002936 - label: Distal sensory impairment -- id: HP:0001265 - label: Hyporeflexia -- id: HP:0001284 - label: Areflexia -- id: HP:0000006 - label: Autosomal dominant -- id: HGNC:7739 - label: NEFL -- id: MONDO:0030433 - label: Charcot-Marie-Tooth Neuropathy -- id: MONDO:0015626 - label: Peroneal Muscular Atrophy -- id: HP:0003376 - label: steppage gait -- id: HP:0001761 - label: pes cavus -- id: HP:0001765 - label: hammertoes -- id: HP:0000006 - label: autosomal dominant -- id: HGNC:7739 - label: NEFL -- id: HGNC:8850 - label: PEX1 -- id: HGNC:9717 - label: PEX2 -- id: HGNC:8858 - label: PEX3 -- id: HP:0000007 - label: Autosomal recessive -- id: HGNC:4696 - label: "\u03B2-glucuronidase" -- id: HP:0000006 - label: Autosomal Dominant -- id: HGNC:3603 - label: FBN1 diff --git a/tests/output/mendelian-disease-sly.pickle b/tests/output/mendelian-disease-sly.pickle deleted file mode 100644 index b12c4fa03..000000000 Binary files a/tests/output/mendelian-disease-sly.pickle and /dev/null differ diff --git a/tests/output/mendelian-disease-sly.yaml b/tests/output/mendelian-disease-sly.yaml deleted file mode 100644 index e2040fd59..000000000 --- a/tests/output/mendelian-disease-sly.yaml +++ /dev/null @@ -1,92 +0,0 @@ -input_id: /Users/cjm/repos/ontogpt/tests/input/cases/mendelian-disease-sly.txt -input_text: "Sly syndrome, also called mucopolysaccharidosis type VII (MPS-VII), is\ - \ an autosomal recessive lysosomal storage disease caused by a deficiency of the\ - \ enzyme \u03B2-glucuronidase. This enzyme is responsible for breaking down large\ - \ sugar molecules called glycosaminoglycans (AKA GAGs, or mucopolysaccharides).\ - \ The inability to break down GAGs leads to a buildup in many tissues and organs\ - \ of the body. The severity of the disease can vary widely.\n" -raw_completion_output: "Name: Sly Syndrome\nDescription: Autosomal recessive lysosomal\ - \ storage disease caused by a deficiency of the enzyme \u03B2-glucuronidase\nSynonyms:\ - \ Mucopolysaccharidosis type VII (MPS-VII)\nSubclass_of: None\nSymptoms: Buildup\ - \ in many tissues and organs of the body, Severity of the disease can vary widely\n\ - Inheritance: Autosomal recessive\nGenes: \u03B2-glucuronidase \nDisease_Onsets:\ - \ None\nLabel: Sly Syndrome" -prompt: "From the text below, extract the following entities in the following format:\n\ - \nname: \ndescription: \n\ - synonyms: \nsubclass_of: \nsymptoms: \ninheritance:\ - \ \ngenes: \ndisease_onsets: \n\ - label: \n\n\nText:\nSly syndrome, also called\ - \ mucopolysaccharidosis type VII (MPS-VII), is an autosomal recessive lysosomal\ - \ storage disease caused by a deficiency of the enzyme \u03B2-glucuronidase. This\ - \ enzyme is responsible for breaking down large sugar molecules called glycosaminoglycans\ - \ (AKA GAGs, or mucopolysaccharides). The inability to break down GAGs leads to\ - \ a buildup in many tissues and organs of the body. The severity of the disease\ - \ can vary widely.\n\n\n===\n\n" -extracted_object: - label: Sly Syndrome - name: Sly Syndrome - description: "Autosomal recessive lysosomal storage disease caused by a deficiency\ - \ of the enzyme \u03B2-glucuronidase" - synonyms: - - Mucopolysaccharidosis type VII (MPS-VII) - subclass_of: - - AUTO:None - symptoms: - - AUTO:Buildup%20in%20many%20tissues%20and%20organs%20of%20the%20body%2C%20Severity%20of%20the%20disease%20can%20vary%20widely - inheritance: HP:0000007 - genes: - - HGNC:4696 - disease_onsets: - - AUTO:None -named_entities: -- id: HP:0009830 - label: Peripheral Neuropathy -- id: HP:0001371 - label: Joint contractures -- id: HP:0001761 - label: Pes cavus -- id: HP:0001760 - label: Foot deformities -- id: HP:0006006 - label: Hypotrophy of the small hand muscles -- id: HP:0002460 - label: Distal limb muscle weakness due to peripheral neuropathy -- id: HP:0009027 - label: Foot drop -- id: HP:0002936 - label: Distal sensory impairment -- id: HP:0001265 - label: Hyporeflexia -- id: HP:0001284 - label: Areflexia -- id: HP:0000006 - label: Autosomal dominant -- id: HGNC:7739 - label: NEFL -- id: MONDO:0030433 - label: Charcot-Marie-Tooth Neuropathy -- id: MONDO:0015626 - label: Peroneal Muscular Atrophy -- id: HP:0003376 - label: steppage gait -- id: HP:0001761 - label: pes cavus -- id: HP:0001765 - label: hammertoes -- id: HP:0000006 - label: autosomal dominant -- id: HGNC:7739 - label: NEFL -- id: HGNC:8850 - label: PEX1 -- id: HGNC:9717 - label: PEX2 -- id: HGNC:8858 - label: PEX3 -- id: HP:0000007 - label: Autosomal recessive -- id: HGNC:4696 - label: "\u03B2-glucuronidase" diff --git a/tests/output/owl/merged/recipe-all-merged.owl b/tests/output/owl/merged/recipe-all-merged.owl deleted file mode 100644 index bec3952d9..000000000 --- a/tests/output/owl/merged/recipe-all-merged.owl +++ /dev/null @@ -1,54490 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - is part of - a core relation that holds between a part and its whole - - part of - part of - part_of - - - - - - - - - - has part - a core relation that holds between a whole and its part - - - has part - has part - has_part - - - - - - - - - has food substance analog - - - - - - - - - A defining ingredient defines what a food is principally categorized as, rather than an ingredient listed by percentage of weight or volume. A food may have more than one defining ingredient. - Damion Dooley - FoodOn - For example, 'bean soup' has a defining ingredient of some 'bean (whole)'. Similarly, spicy chicken wings require a defining ingredient of (usually minute) amounts of chilli. - -A soup may 'has ingredient' some bean, but that doesn't make it a 'bean soup', i.e. there should be no inference to that category. However, some classes may have that simple ingredient "necessary and sufficient" equivalency. - has defining ingredient - - - - - - - - - - - A relation attaching between a food material and another food material that has been added to it at some point in its history. - Damion Dooley - FoodOn - has ingredient - - - - - - - - - - has_specified_output - has_specified_output - - The inverse property of is_specified_output_of - - has_specified_output - - - - - - - - participates in - a relation between a continuant and a process, in which the continuant is somehow involved in the process - - - participates in - participates_in - - - - - - - - has participant - a relation between a process and a continuant, in which the continuant is somehow involved in the process - - has participant - has_participant - - - - - - - - a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence - - has quality - - - - - - - - a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence - - has role - - - - - - - - - a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity - - derives from - - - - - - - - - x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. - - - - in taxon - - - - - - - - - develops from - develops from - develops_from - - - - - - - - - p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. - - has input - - - - - - - - - p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. - - has output - - - - - - - - - An organism that is a member of a population of organisms - is member of is a mereological relation between a item and a collection. - is member of - member part of - SIO - - - member of - - - - - - - - - has member is a mereological relation between a collection and an item. - SIO - - has member - - - - - - - - inverse of has output - - output of - - - - - - - - x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. - - - composed primarily of - - - - - - - - - - - - - - - a produced_by b iff some process that occurs_in b has_output a. - - produced by - - - - - - - - - - "has substance added" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time. - Damion Dooley - - has substance added - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Place - - - - - - - - - Add - - - - - - - - - Bacon - - - - - - - - - Bowl - - - - - - - - - Can - - - - - - - - - Cilantro - - - - - - - - - Combine - - - - - - - - - Cook - - - - - - - - - Cool - - - - - - - - - Cooled - - - - - - - - - Dip - - - - - - - - - Drain - - - - - - - - - Drizzle - - - - - - - - - Form - - - - - - - - - Fry - - - - - - - - - Golden - - - - - - - - - Heat - - - - - - - - - Insert - - - - - - - - - Knife. - - - - - - - - - Mix - - - - - - - - - Mixture - - - - - - - - - NA - - - - - - - - - None - - - - - - - - - None. - - - - - - - - - Oven - - - - - - - - - Pan - - - - - - - - - Paprika - - - - - - - - - Pot - - - - - - - - - Pour - - - - - - - - - Preheat - - - - - - - - - Repeat - - - - - - - - - Return - - - - - - - - - Ricotta - - - - - - - - - Salt - - - - - - - - - Saute - - - - - - - - - Serve - - - - - - - - - Simmer - - - - - - - - - Soup - - - - - - - - - Spoon - - - - - - - - - Spray - - - - - - - - - Stir - - - - - - - - - Tbsp - - - - - - - - - Tbsp. - - - - - - - - - Transfer - - - - - - - - - Well - - - - - - - - - Whisk - - - - - - - - - a - - - - - - - - - add - - - - - - - - - bacon - - - - - - - - - blender - - - - - - - - - bowl - - - - - - - - - bowl. - - - - - - - - - bread - - - - - - - - - brioche - - - - - - - - - bunch - - - - - - - - - buttermilk - - - - - - - - - cayenne - - - - - - - - - charred - - - - - - - - - chilies - - - - - - - - - chill - - - - - - - - - chopped - - - - - - - - - cilantro - - - - - - - - - colander - - - - - - - - - combine - - - - - - - - - cook - - - - - - - - - coriander - - - - - - - - - corn - - - - - - - - - cornstarch - - - - - - - - - covered - - - - - - - - - crisp - - - - - - - - - cup - - - - - - - - - cups - - - - - - - - - diced - - - - - - - - - dry - - - - - - - - - feta - - - - - - - - - first - - - - - - - - - fork - - - - - - - - - fork. - - - - - - - - - fragrant - - - - - - - - - g - - - - - - - - - golden - - - - - - - - - grill. - - - - - - - - - hands. - - - - - - - - - heat - - - - - - - - - iron - - - - - - - - - knife. - - - - - - - - - large - - - - - - - - - lbs - - - - - - - - - meat - - - - - - - - - medium - - - - - - - - - minced - - - - - - - - - mix - - - - - - - - - mixture - - - - - - - - - mustard - - - - - - - - - none - - - - - - - - - none. - - - - - - - - - oz - - - - - - - - - pan - - - - - - - - - pan. - - - - - - - - - pieces - - - - - - - - - pinch - - - - - - - - - plate - - - - - - - - - platter - - - - - - - - - pot - - - - - - - - - pot. - - - - - - - - - remove - - - - - - - - - ribbons - - - - - - - - - rolling - - - - - - - - - room - - - - - - - - - salt - - - - - - - - - saucepan - - - - - - - - - saucepan. - - - - - - - - - serve - - - - - - - - - simmer - - - - - - - - - skillet - - - - - - - - - skillet. - - - - - - - - - sliced - - - - - - - - - small - - - - - - - - - smock - - - - - - - - - smooth - - - - - - - - - soup - - - - - - - - - spoon - - - - - - - - - sticks - - - - - - - - - stir - - - - - - - - - stir-fry - - - - - - - - - stove - - - - - - - - - thermometer - - - - - - - - - thick - - - - - - - - - to - - - - - - - - - tsp - - - - - - - - - tsp. - - - - - - - - - whisk - - - - - - - - - whisk. - - - - - - - - - wok - - - - - - - - - (15 ounce) cans - - - - - - - - - <N/A> - - - - - - - - - - - - - - - - - - - 1 cup - - - - - - - - - 1 (15 oz) can fire roasted tomatoes - - - - - - - - - 1 (16 ounce) box spaghetti noodles - - - - - - - - - 1 (4 oz) can green chilies - - - - - - - - - 1 large egg - - - - - - - - - 1/2 cup soy sauce - - - - - - - - - 10 ounce packages - - - - - - - - - 2 large eggs - - - - - - - - - 3 to 5 minutes - - - - - - - - - 300° - - - - - - - - - Add; - - - - - - - - - Add; Continue cooking - - - - - - - - - Add; stir fry - - - - - - - - - Baking sheet. - - - - - - - - - Beat; incorporate - - - - - - - - - Boil; Drain - - - - - - - - - Boiled Water - - - - - - - - - Chopped fresh chives - - - - - - - - - Cook; Stir - - - - - - - - - Cook; stir - - - - - - - - - Cover; Chill - - - - - - - - - Crushed red pepper flakes - - - - - - - - - Cut; - - - - - - - - - Dijon mustard - - - - - - - - - Dip; press - - - - - - - - - Discarded ribs - - - - - - - - - Do Ahead - - - - - - - - - Drizzle; Add - - - - - - - - - Fill; pipe - - - - - - - - - Flaky sea salt - - - - - - - - - Freshly ground black pepper - - - - - - - - - Fried corn dogs - - - - - - - - - Gather; - - - - - - - - - Good Olive Oil - - - - - - - - - Heat; - - - - - - - - - Hot dish - - - - - - - - - Immersion blender - - - - - - - - - Insert; - - - - - - - - - Large eggs - - - - - - - - - Let sit - - - - - - - - - Make; let - - - - - - - - - Melt; Sauté - - - - - - - - - Mix; - - - - - - - - - N/A - - - - - - - - - N/A. - - - - - - - - - Pastry bag - - - - - - - - - Peel; Halve - - - - - - - - - Pick; - - - - - - - - - Place; - - - - - - - - - Pour; - - - - - - - - - Preheat; - - - - - - - - - Purée; add - - - - - - - - - Puréed soup - - - - - - - - - Read; - - - - - - - - - Red onion - - - - - - - - - Red Delicious apple - - - - - - - - - Red wine vinegar - - - - - - - - - Remove from heat - - - - - - - - - Remove; Cool - - - - - - - - - Serve; - - - - - - - - - Serving dish - - - - - - - - - Set up - - - - - - - - - Shredded Cheddar cheese - - - - - - - - - Slice; Place - - - - - - - - - Spread; - - - - - - - - - Stir; - - - - - - - - - Stir; sauté - - - - - - - - - Thai chilies - - - - - - - - - Toasted country-style bread - - - - - - - - - Toss; - - - - - - - - - Toss; Serve - - - - - - - - - Transfer; Cover - - - - - - - - - Wilted Kale - - - - - - - - - Work surface - - - - - - - - - Wrap; Chill - - - - - - - - - add; - - - - - - - - - add; cook - - - - - - - - - add; mix - - - - - - - - - add; stir - - - - - - - - - add; sauté - - - - - - - - - adjust; - - - - - - - - - all-purpose flour - - - - - - - - - apple cider vinegar - - - - - - - - - asparagus spears - - - - - - - - - bacon drippings - - - - - - - - - baking soda - - - - - - - - - bay leaves - - - - - - - - - blanched hazelnuts - - - - - - - - - blended mixture - - - - - - - - - both sides - - - - - - - - - bottom of the pan - - - - - - - - - bring to a rolling boil - - - - - - - - - bring to a simmer; - - - - - - - - - bring; - - - - - - - - - caramelized sauce - - - - - - - - - cayenne pepper - - - - - - - - - cloves garlic - - - - - - - - - coat; - - - - - - - - - coated noodles - - - - - - - - - cold water - - - - - - - - - combined mixture - - - - - - - - - cook and stir; - - - - - - - - - cook; - - - - - - - - - cook; stir - - - - - - - - - cooking spray - - - - - - - - - covered pan - - - - - - - - - creamed corn - - - - - - - - - crushed red pepper - - - - - - - - - crushed red pepper flakes - - - - - - - - - cubed paneer - - - - - - - - - cut; toss - - - - - - - - - cutting board - - - - - - - - - divide; roll out - - - - - - - - - drizzle; sprinkle - - - - - - - - - dry Chinese noodles - - - - - - - - - dry hot dogs - - - - - - - - - extra-virgin olive oil - - - - - - - - - food processor - - - - - - - - - fresh ricotta - - - - - - - - - fresh basil leaves - - - - - - - - - fresh ginger root - - - - - - - - - fresh lime juice - - - - - - - - - freshly ground black pepper - - - - - - - - - frozen chopped spinach - - - - - - - - - garam masala - - - - - - - - - garlic cloves - - - - - - - - - glazed meat - - - - - - - - - granulated sugar - - - - - - - - - grated fresh ginger root - - - - - - - - - ground coriander - - - - - - - - - ground cumin - - - - - - - - - ground turmeric - - - - - - - - - heat; - - - - - - - - - heated cooking oil - - - - - - - - - hot chile pepper - - - - - - - - - hot cooked rice - - - - - - - - - inch thick pieces - - - - - - - - - jumbo or regular - - - - - - - - - knead; - - - - - - - - - kosher salt - - - - - - - - - large carrot - - - - - - - - - large pot - - - - - - - - - large saucepan - - - - - - - - - large skillet - - - - - - - - - large leaves of lettuce - - - - - - - - - large stock pot - - - - - - - - - large, chopped - - - - - - - - - large, sliced - - - - - - - - - large, deep skillet - - - - - - - - - lemon, more to taste - - - - - - - - - let cool; - - - - - - - - - let sit; - - - - - - - - - let stand; - - - - - - - - - lift; add - - - - - - - - - mash; - - - - - - - - - medium, sliced into 1/4-inch half circles - - - - - - - - - mint sprigs - - - - - - - - - mix; - - - - - - - - - mixed ingredients - - - - - - - - - n/a - - - - - - - - - napa cabbage - - - - - - - - - none; - - - - - - - - - outdoor grill - - - - - - - - - paper towels. - - - - - - - - - pastry bag - - - - - - - - - pat; dust - - - - - - - - - peanut or vegetable oil - - - - - - - - - peeled and diced - - - - - - - - - place; - - - - - - - - - pluck out - - - - - - - - - plumped raisins - - - - - - - - - poached chicken - - - - - - - - - popsicle sticks - - - - - - - - - pre-cooked chicken - - - - - - - - - preheat; - - - - - - - - - quick-cooking grits - - - - - - - - - red enchilada sauce - - - - - - - - - red pepper flakes - - - - - - - - - red wine vinegar - - - - - - - - - reduce; add - - - - - - - - - reduce; stir; simmer - - - - - - - - - regular blender - - - - - - - - - reserved dressing - - - - - - - - - return to a boil; - - - - - - - - - rimmed baking sheet - - - - - - - - - sauce mixture - - - - - - - - - scatter; - - - - - - - - - sea salt - - - - - - - - - season; - - - - - - - - - serve; - - - - - - - - - set aside - - - - - - - - - skinless, boneless chicken thighs - - - - - - - - - slice; - - - - - - - - - sliced carrots - - - - - - - - - slotted spatula - - - - - - - - - slotted spoon. - - - - - - - - - slotted spoon, bowl - - - - - - - - - small bowl - - - - - - - - - small (chopped) - - - - - - - - - small bunch mint - - - - - - - - - soak; - - - - - - - - - soft lentils - - - - - - - - - spread; - - - - - - - - - stir; - - - - - - - - - stirring utensil. - - - - - - - - - sweet chili sauce - - - - - - - - - tablespoons, plus more for drizzling - - - - - - - - - tastier dish - - - - - - - - - top; dress - - - - - - - - - topping; - - - - - - - - - toss and saute; - - - - - - - - - toss; - - - - - - - - - transfer; - - - - - - - - - transfer; blend - - - - - - - - - two salads - - - - - - - - - two large plates - - - - - - - - - two pieces of dough - - - - - - - - - uncooked medium shrimp - - - - - - - - - vanilla extract - - - - - - - - - waffle iron - - - - - - - - - waffle iron. - - - - - - - - - well done - - - - - - - - - whisk; - - - - - - - - - white wine vinegar - - - - - - - - - yellow cornmeal - - - - - - - - - yolk mixture - - - - - - - - - entity - Entity - Julius Caesar - Verdi’s Requiem - the Second World War - your body mass index - BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 - Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf - - - - - - An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) - - entity - entity - - - - - Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf - - per discussion with Barry Smith - - - - - - An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) - - - - - - - - - - - - - - - - - continuant - Continuant - continuant - An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. - An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. - BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 - Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants - - - - - A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) - if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) - if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) - if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) - (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] - (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] - (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] - (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] - - continuant - continuant - - - - - (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] - - - - - - (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] - - - - - - (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] - - - - - - Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants - - - - - - A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) - - - - - - if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) - - - - - - if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) - - - - - - if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) - - - - - - (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] - - - - - - - - - - occurrent - Occurrent - An entity that has temporal parts and that happens, unfolds or develops through time. - An entity that has temporal parts and that happens, unfolds or develops through time. - BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region - BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. - Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. - Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. - - - - - An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) - Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) - b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) - (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] - (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] - - occurrent - occurrent - - - - - Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. - - per discussion with Barry Smith - - - - - Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. - - - - - - An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) - - - - - - Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) - - - - - - b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) - - - - - - (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] - - - - - - (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] - - - - - - - - - - - - - - - - - - ic - IndependentContinuant - a chair - a heart - a leg - a molecule - a spatial region - an atom - an orchestra. - an organism - the bottom right portion of a human torso - the interior of your mouth - A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. - A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) - - - - - For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) - For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) - (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] - (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] - (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] - - independent continuant - independent continuant - - - - - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) - - - - - - For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) - - - - - - For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) - - - - - - (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] - - - - - - (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] - - - - - - (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] - - - - - - - - - - - t-region - TemporalRegion - Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional - A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) - All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) - Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) - (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] - (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] - (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] - - temporal region - - - - - Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional - - per discussion with Barry Smith - - - - - A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) - - - - - - All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) - - - - - - Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) - - - - - - (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] - - - - - - (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] - - - - - - (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] - - - - - - - - - - process - Process - a process of cell-division, \ a beating of the heart - a process of meiosis - a process of sleeping - the course of a disease - the flight of a bird - the life of an organism - your process of aging. - An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. - An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. - p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) - p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) - BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) - - - - - - (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] - - process - process - - - - - p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) - - - - - - (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] - - - - - - - - - - sdc - SpecificallyDependentContinuant - Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key - of one-sided specifically dependent continuants: the mass of this tomato - of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. - the disposition of this fish to decay - the function of this heart: to pump blood - the mutual dependence of proton donors and acceptors in chemical reactions [79 - the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction - the pink color of a medium rare piece of grilled filet mignon at its center - the role of being a doctor - the shape of this hole. - the smell of this portion of mozzarella - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. - (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] - - specifically dependent continuant - - - - - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - - - - - - Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. - - per discussion with Barry Smith - - - - - (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] - - - - - - - - - - fiat-object-part - FiatObjectPart - or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29 - the FMA:regional parts of an intact human body. - the Western hemisphere of the Earth - the division of the brain into regions - the division of the planet into hemispheres - the dorsal and ventral surfaces of the body - the upper and lower lobes of the left lung - BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions - - b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) - (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] - - fiat object - fiat object part - - - - - b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) - - - - - - (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] - - - - - - - - - - object-aggregate - ObjectAggregate - a collection of cells in a blood biobank. - a swarm of bees is an aggregate of members who are linked together through natural bonds - a symphony orchestra - an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team) - defined by fiat: the aggregate of members of an organization - defined through physical attachment: the aggregate of atoms in a lump of granite - defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container - defined via attributive delimitations such as: the patients in this hospital - the aggregate of bearings in a constant velocity axle joint - the aggregate of blood cells in your body - the nitrogen atoms in the atmosphere - the restaurants in Palo Alto - your collection of Meissen ceramic plates. - An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects - BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee). - ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. - b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) - (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] - - object aggregate - - - - - An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects - - - - - - An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects - - - - - - ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. - - - - - - b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) - - - - - - (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] - - - - - - - - - - gdc - GenericallyDependentContinuant - The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. - the pdf file on your laptop, the pdf file that is a copy thereof on my laptop - the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - - (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] - - generically dependent continuant - - - - - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - - - - - - (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] - - - - - - - - - - 1d-t-region - OneDimensionalTemporalRegion - the temporal region during which a process occurs. - BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks). - A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) - (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] - - one-dimensional temporal region - - - - - A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) - - - - - - (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] - - - - - - - - - - material - MaterialEntity - material entity - material entity - a flame - a forest fire - a human being - a hurricane - a photon - a puff of smoke - a sea wave - a tornado - an aggregate of human beings. - an energy wave - an epidemic - the undetached arm of a human being - An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. - BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 - BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. - BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. - - - - - A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) - Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) - every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) - (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] - bfo - BFO:0000040 - - material entity - material entity - - - - - A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) - - - - - - Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) - - - - - - every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) - - - - - - (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] - - - - - - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] - - - - - - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] - - - - - - - - - - A peduncle arising at or beneath the surface of the ground in an acaulescent plant (as the tulip); broadly: a flower stalk. - - BrendaTissueOBO - BTO:0001217 - scape - - - - - - - - - A material entity that is ingested and contributes to survival, growth and development - - dietary chemical component - - - - - - - - - Carbohydrates that are absorbed in the small intestine and provide carbohydrate for metabolism in monogastric animals. - - digestible carbohydrate - available carbohydrate - - - - - - - - - Available carbohydrate in monosaccharide and disaccharide form - - free sugar - - - - - - - - - - - Any member of the class of organooxygen compounds that is a polyhydroxy-aldehyde or -ketone or a lactol resulting from their intramolecular condensation (monosaccharides); substances derived from these by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom; and polymeric products arising by intermolecular acetal formation between two or more such molecules (disaccharides, polysaccharides and oligosaccharides). Carbohydrates contain only carbon, hydrogen and oxygen atoms; prior to any oxidation or reduction, most have the empirical formula Cm(H2O)n. Compounds obtained from carbohydrates by substitution, etc., are known as carbohydrate derivatives and may contain other elements. Cyclitols are generally not regarded as carbohydrates. - - - CHEBI:15131 - CHEBI:23008 - CHEBI:9318 - Wikipedia:Carbohydrate - carbohydrate - carbohydrates - chebi_ontology - Kohlenhydrat - Kohlenhydrate - a carbohydrate - carbohidrato - carbohidratos - glucide - glucides - glucido - glucidos - hydrates de carbone - saccharide - saccharides - saccharidum - CHEBI:16646 - - carbohydrate - carbohydrate - - - - - - - - - Any oligosaccharide, polysaccharide or their derivatives consisting of monosaccharides or monosaccharide derivatives linked by glycosidic bonds. See also http://www.ontobee.org/ontology/GNO?iri=http://purl.obolibrary.org/obo/GNO_00000001. - - glycan - - - - - - - - - - - A glycosyl glycoside formed by glucose and fructose units joined by an acetal oxygen bridge from hemiacetal of glucose to the hemiketal of the fructose. - - - 0 - C12H22O11 - InChI=1S/C12H22O11/c13-1-4-6(16)8(18)9(19)11(21-4)23-12(3-15)10(20)7(17)5(2-14)22-12/h4-11,13-20H,1-3H2/t4-,5-,6-,7-,8+,9-,10+,11-,12+/m1/s1 - CZMRCDWAGMRECN-UGDNZRGBSA-N - 342.29650 - 342.11621 - OC[C@H]1O[C@H](O[C@]2(CO)O[C@H](CO)[C@@H](O)[C@@H]2O)[C@H](O)[C@@H](O)[C@@H]1O - CHEBI:15128 - CHEBI:26812 - CHEBI:45795 - CHEBI:9314 - Beilstein:90825 - CAS:57-50-1 - DrugBank:DB02772 - Drug_Central:4610 - Gmelin:97695 - HMDB:HMDB0000258 - KEGG:C00089 - KEGG:D00025 - KEGG:D06533 - KEGG:G00370 - KNApSAcK:C00001151 - MetaCyc:SUCROSE - PDBeChem:SUC - PMID:11021636 - PMID:11093712 - PMID:11111003 - PMID:12065720 - PMID:12706980 - PMID:13508893 - PMID:15291457 - PMID:15660210 - PMID:15792978 - PMID:15845855 - PMID:16228482 - PMID:16304615 - PMID:16313996 - PMID:16525719 - PMID:16660545 - PMID:16663947 - PMID:16665852 - PMID:17233733 - PMID:17439666 - PMID:17597061 - PMID:18625236 - PMID:19199566 - PMID:19726178 - PMID:21703290 - PMID:21972845 - PMID:22085755 - PMID:22311778 - PMID:22404833 - PMID:22751876 - Reaxys:1435311 - Reaxys:90825 - SUBSET_SIREN:F15176 - Wikipedia:Sucrose - http://www.langual.org/langual_thesaurus.asp?termid=C0210 - http://www.langual.org/langual_thesaurus.asp?termid=H0136 - http://www.langual.org/langual_thesaurus.asp?termid=H0158 - SUCROSE - Sucrose - beta-D-fructofuranosyl alpha-D-glucopyranoside - sucrose - chebi_ontology - 1-alpha-D-Glucopyranosyl-2-beta-D-fructofuranoside - Cane sugar - Saccharose - Sacharose - White sugar - beta-D-Fruf-(2<->1)-alpha-D-Glcp - sacarosa - table sugar - CHEBI:17992 - - subset_siren - LanguaL term definition: Used when sucrose (e.g., cane sugar or beet sugar) is the major ingredient. Note: on a product label or in a recipe, 'sugar' means sucrose. - sucrose - sucrose - - - - - - - - - - 'Lipids' is a loosely defined term for substances of biological origin that are soluble in nonpolar solvents. They consist of saponifiable lipids, such as glycerides (fats and oils) and phospholipids, as well as nonsaponifiable lipids, principally steroids. - - - CHEBI:14517 - CHEBI:25054 - CHEBI:6486 - KEGG:C01356 - Lipid - lipids - chebi_ontology - CHEBI:18059 - - lipid - - - - - - - - - Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. - - molecular entity - - - - - - - - - Any disaccharide in which the two monosaccharide components are connected by a glycosidic linkage between their anomeric centres. - - glycosyl glycoside - - - - - - - - - A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances. - - chemical entity - - - - - - - - - A role played by the molecular entity or part thereof within a biological context. - - biological role - - - - - - - - - - oxygen molecular entity - - - - - - - - - A heteroorganic entity is an organic molecular entity in which carbon atoms or organic groups are bonded directly to one or more heteroatoms. - - heteroorganic entity - - - - - - - - - food role - A physiological role played by any substance of either plant, animal or artificial origin which contains essential body nutrients that can be ingested by an organism to provide energy, promote growth, and maintain the processes of life. - - food - - - - - - - - - Any p-block molecular entity containing a chalcogen. - - chalcogen molecular entity - - - - - - - - - A molecular entity containing one or more atoms from any of groups 1, 2, 13, 14, 15, 16, 17, and 18 of the periodic table. - - main group molecular entity - - - - - - - - - - carbon group molecular entity - - - - - - - - - A main group molecular entity that contains one or more atoms of a p-block element. - - p-block molecular entity - - - - - - - - - A compound in which two monosaccharides are joined by a glycosidic bond. - - - CHEBI:23844 - CHEBI:4654 - KEGG:C01911 - Disaccharide - disaccharides - chebi_ontology - Disaccharid - Disacharid - disacarido - disacaridos - CHEBI:36233 - - disaccharide - disaccharide - - - - - - - - - - An organochalcogen compound is a compound containing at least one carbon-chalcogen bond. - - organochalcogen compound - - - - - - - - - - An organochalcogen compound containing at least one carbon-oxygen bond. - - organooxygen compound - - - - - - - - - - A compound in which monosaccharide units are joined by glycosidic linkages. The term is commonly used to refer to a defined structure as opposed to a polymer of unspecified length or a homologous mixture. When the linkages are of other types the compounds are regarded as oligosaccharide analogues. - oligosaccharide - - - http://langual.org - CHEBI:25679 - CHEBI:35319 - CHEBI:7758 - KEGG:C00930 - http://www.langual.org/langual_thesaurus.asp?termid=C0226 - Oligosaccharide - oligosaccharides - chebi_ontology - O-glycosylglycoside - O-glycosylglycosides - oligosacarido - oligosacaridos - CHEBI:50699 - - LanguaL term definition: Complex carbohydrate with molecules composed of three to ten saccharide units (specifically dextrin). May be slightly sweet to the taste. - oligosaccharide - - - - - - - - - Any molecular entity that contains carbon. - - organic molecular entity - - - - - - - - - role (CHEBI) - A role is particular behaviour which a material entity may exhibit. - - role - - - - - - - - - - physiological role - - - - - - - - - A chemical substance is a portion of matter of constant composition, composed of molecular entities of the same type or of different types. - - chemical substance - - - - - - - - - A mixture is a chemical substance composed of multiple molecules, at least two of which are of a different kind. - - mixture - - - - - - - - - Any organooxygen compound that is a polyhydroxy-aldehyde or -ketone, or a compound derived from one. Carbohydrates contain only carbon, hydrogen and oxygen and usually have an empirical formula Cm(H2O)n; carbohydrate derivatives may contain other elements by substitution or condensation. - - carbohydrates and carbohydrate derivatives - - - - - - - - - - - - - - - - - - A mixture of sugar (fructose, glucose, sucrose) and carbohydrate components that is a by-product from sugar refinery. - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=H0156 - LANGUAL:C0207 - LanguaL term definition: Liquid product remaining after crystallization of sugar from sugar syrup; most molasses is made from sugar cane. - molasses - - - - - - - - - An environmental material primarily composed of dihydrogen oxide in its liquid form. - - liquid water - - - - - - - - - Water which has a low concentration of dissolved solutes, particularly that of sodium chloride. - - fresh water - - - - - - - - - A portion of environmental material is a fiat object part which forms the medium or part of the medium of an environmental system. - - environmental - environmental material - - - - - - - - - An environmental material which is in a liquid state. - - liquid environmental material - - - - - - - - - A liquid or a gas. - - fluid environmental material - - - - - - - - - A process of cutting food into smaller pieces, chunks or slices. - Damion Dooley - food cutting process - - - - - - - - - Food material for humans and animals which is processed with the intention that it be consumable as a whole or added to other food products. - Damion Dooley - Foodon product type - https://en.wikipedia.org/wiki/Food - The FoodOn "food product" class is provided as a branch under which new food product categories and food products themselves can be placed. Here classes are provided to differentiate a food product by its food composition, processing and/or consumption characteristics. This avoids brand name products but it may include generic food dish categories. It has a much greater depth and polyhierarchy than other agency product type schemes have in an effort to group related products together. The upper level basis of this tree originated in the environment ontology (ENVO) and from the US Code of Federal Regulations. - food product - - - - - - - - - - - - - - - - - - - - - - A food product made of meat, the skeletal muscle and associated fat, and other edible tissues such as organs, livers, skin, brains, bone marrow, kidneys, or lungs, of mammals. - - SUBSET_SIREN:F17332 - mammalian meat food product - - - - - - - - - A processed meat food product that is made from a sausage. - - 2022-10-28T11:02:42Z - sausage food product - - - - - - - - - - A hot dog is a moist sausage of soft, even texture and flavor, often made from advanced meat recovery or meat slurry. Most types are fully cooked, cured or smoked. It is often placed hot in a special purpose soft, sliced hot dog bun. - Damion Dooley - - - hotdog - frankfurter - hot dog - hot dogs - - - - - - - - - - - - - - - - - - - - - - - - - - - - - processed meat food product - - - - - - - - - - - - - - - - Cheese is a food derived from milk that is produced in a wide range of flavors, textures, and forms by coagulation of the milk protein casein. - SUBSET_SIREN:F1076 - https://en.wikipedia.org/wiki/Cheese - cheese - cheese - cheese food product - - - - - - - - - - - - - - - - - - - - - - - - - - - - - This class includes food products which are derived from or produced by a plant. - plant food product - - - - - - - - - - - - - - - - - - - - - - - - - - - A food product made from domestic pig meat (Sus domesticus or Sus scrofa scrofa). - Damion Dooley - http://en.wikipedia.org/wiki/Pork - pork - Pork - pork meat food product - - - - - - - - - - - - - - - - - - - - - - - - - chicken meat food product - - - - - - - - - - - - - - - - - - - - - - - - - - Meat from bovines, especially domestic cattle (cows). - beef food product - - - - - Meat from bovines, especially domestic cattle (cows). - http://en.wikipedia.org/wiki/Beef - - - - - - - - - - - - - - - - A seafood product is a vertebrate or invertibrate organism from an aquatic environment. - Some of the subclasses are currently freshwater organisms. - Damion Dooley - animal seafood product - - - - - - - - - - - - - - - - - - fermented dairy food product - - - - - - - - - - - - - - - - - - - - - - - - - - - - - fermented fish or seafood food product - - - - - - - - - - sea water fish food product - - - - - - - - - A fine powder made from cereals or other starchy food sources. - Damion Dooley - Wikipedia:Flour - http://www.langual.org/langual_thesaurus.asp?termid=H0152 - flour added - flour food product - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A food product derived from plant fruit. - plant fruit food product - - - - - - - - - - - - - - - - - - - Apple juice is a fruit juice made by the maceration and pressing of an apple. - https://en.wikipedia.org/wiki/Apple_juice - http://langual.org - SUBSET_SIREN:F1419 - apple juice - subset_siren - apple juice - - - - - - - - - - - - - - - - - - - - - - - - - - fermented fruit food product - - - - - - - - - - - - - - - - A liquid produced from the fermentation of ethanol in a process that yields its key ingredient, acetic acid. - vinegar food product - - - - - A liquid produced from the fermentation of ethanol in a process that yields its key ingredient, acetic acid. - Wikipedia:Vinegar - - - - - - - - - - - - - - - - - - - - - - - - - - - A food preserved by soaking and storing it in vinegar or brine. - - SUBSET_SIREN:F1302 - SUBSET_SIREN:F16510 - pickled - subset_siren - subset_siren - SIREN DB annotation: -* has quality 'solid' (http://purl.obolibrary.org/obo/FOODON_03430151) -* formed as a result of 'pickling process' (http://purl.obolibrary.org/obo/FOODON_03460190) - food (pickled) - - - - - - - - - - - - - - - - - - - - - - - - - - sugar condiment - - - - - - - - - - - A lipid material derived from plants. Physically, oils are liquid at room temperature. - Damion Dooley - - vegetable oil food product - - - - - - - - - - - - - - - - - - - - - corn flour food product - - - - - - - - - - - - - - - - - - - - - - - - - - - A food product which is derived from or produced by an animal that has a vertibrae. - Damion Dooley - vertebrate animal food product - - - - - - - - - - - - - - - - - - - - - - - - - - cereal grain food product - - - - - - - - - - - - - - - - - - Damion Dooley - http://langual.org - 2019-06-11T07:25:19Z - SUBSET_SIREN:F5644 - alcoholic beverage - subset_siren - SIREN DB annotation: -* has quality 'liquid' (http://purl.obolibrary.org/obo/FOODON_03430130) -* formed as a result of 'microbial/enzymatic modification process' (http://purl.obolibrary.org/obo/FOODON_03460119) -* formed as a result of 'curing or aging process' (http://purl.obolibrary.org/obo/FOODON_03460253) - - fermented beverage - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A food product made from an avian egg. - avian egg food product - - - - - - - - - bovine dairy food product - - - - - - - - - - - - - - - cattle dairy food product - - - - - - - - - bovine cheese food product - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cow milk cheese - - - - - - - - - - - - - - - - - - - - - - - - - - - A food product made from domesticated bird meat. - Damion Dooley - - poultry meat food product - - - - - - - - - - - - - - - - - - - - - - - - - - - Suidae is a family of artiodactyl mammals which are commonly called pigs, hogs or boars. In addition to numerous fossil species, 17 extant species are currently recognized (or 18 counting domestic pigs and wild boars separately), classified into between four and eight genera. The family includes the domestic pig, Sus scrofa domesticus or Sus domesticus, in addition to numerous species of wild pig, such as babirusas and warthogs. All suids, or swine, are native to the Old World, ranging from Asia to Europe and Africa. - Damion Dooley - https://en.wikipedia.org/wiki/Suidae - porcine meat - swine food product - - - - - - - - - - - - - - - A relish, sauce, or seasoning added to food to impart a particular flavour or to complement the dish. - Damion Dooley - https://en.wikipedia.org/wiki/Condiment - condiment - condiment food product - - - - - - - - - - - - - - - - - - - - - - - - - - bovine meat food product - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - fruit juice food product - - - - - - - - - - - - - - - wheat food product - - - - - - - - - - - - - - - - - - - - - - - - - - A food product deriving primarily from corn (maize). - Damion Dooley - - maize food product - maize (corn) food product - - - - - - - - - A food product derived from or produced by a plant root. - plant root food product - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A citrus fruit is botanically classified as a type of berry called a hesperidium that has a thick, leathery rind, with numerous oil glands, and a large flesh portion composed of several wedge-shaped sections. Unlike pome fruit, such as the apple, the citrus fruit is derived from a superior ovary, an ovary completely separate from the calyx. - Damion Dooley - https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/hesperidium - citrus - citrus fruit food product - - - - - - - - - - - - - - - - - - citrus fruit juice - - - - - - - - - - - - - - - - - - - - - - - - - - pomes - pomaceous fruit food product - - - - - - - - - - solanaceous fruit food product - - - - - - - - - - - - - - - - A food product deriving from one or more tomatoes. - tomato food product - - - - - - - - - solanaceous food product - - - - - - - - - cruciferous food product - - - - - - - - - - - - - - - - - - - - - - - - - - grape berry food product - - - - - - - - - - - - - - - - - - - - - - - The default nut product is a whole, raw nut - meaning that the kernel is whole, and moderately or significantly dried, but not baked. Minimal references to nuts often leave ambiguous whether the shell is on or off. "I ate a peanut" doesn't clarify whether I ate a shell-off nut or whether I did the shelling. - Damion Dooley - SUBSET_SIREN:F16972 - nut food product - - - - - - - - - - - - - - - - - - - - - - - - - - plant seed food product - - - - - - - - - - plant lipid food product - - - - - - - - - plant stem food product - - - - - - - - - - - - - - - - - - - - - - - - - - invertebrate animal food product - - - - - - - - - - - - - - - Food product that is 1) ready or nearly ready for consumption; 2) usually a composite of several foods or ingredients that often belong to distinct product types; 3) usually formulated, mixed and partially or fully cooked. - - prepared - prepared food product - - - - - - - - - - - - - - - - - - - - - - Damion Dooley - cooked - food (cooked) - - - - - - - - - - - - - - - - bread food product - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - rice food product - - - - - - - - - - wheat flour food product - - - - - - - - - - A dairy product that is composed of the higher-butterfat layer skimmed from the top of milk before homogenization. - LANGUAL:C0195 - sweet cream - cream food product - - - - - A dairy product that is composed of the higher-butterfat layer skimmed from the top of milk before homogenization. - http://en.wikipedia.org/wiki/Cream - - - - - - - - - - - - - - - - - - - - - - A sausage made with fresh meats, and then fully cooked. - Damion Dooley - - sausage (cooked) - - - - - - - - - A salad dressing that is usually mayonnaise-based, but which may also contain yogurt, sour cream, or creme fraiche. - creamy salad dressing - - - - - A salad dressing that is usually mayonnaise-based, but which may also contain yogurt, sour cream, or creme fraiche. - http://en.wikipedia.org/wiki/Salad_dressing#Dressings - - - - - - - - - - - - - - - A stable emulsion of oil, and vinegar or lemon juice, with many options for embellishment with other herbs and spices. Egg yolk is the traditional emulsifier. - mayonnaise food product - - - - - A stable emulsion of oil, and vinegar or lemon juice, with many options for embellishment with other herbs and spices. Egg yolk is the traditional emulsifier. - http://en.wikipedia.org/wiki/Mayonnaise - - - - - - - - - - - - - - - - - - processed pork meat food product - - - - - - - - - - - - - - - - - A vegetable product such as leaves, flowers, seeds and roots that is rich in essential oils and aromatic principles. Used mainly a a condiment. - Damion Dooley - http://www.fao.org/WAICENT/faoinfo/economic/faodef/fdef10e.htm#1.01 - http://www.langual.org/langual_thesaurus.asp?termid=H0151 - herb and spice - herb or spice - spice or herb - - - - - - - - - - animal lipid food product - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A fish food product includes products made from any fish species (aquatic vertebrate with gills and fins). - Damion Dooley - - fish food product - - - - - - - - - avian food product - - - - - - - - - - plant derived beverage - - - - - - - - - - - - - - - - - - plant derived fermented beverage - - - - - - - - - nonfermented plant derived beverage product - - - - - - - - - - - - - - - - - - - - - - A dairy food product has mammilian milk or a milk component as an ingredient. - Damion Dooley - http://www.langual.org/langual_thesaurus.asp?termid=H0242 - dairy product - milk product - dairy food product - - - - - - - - - milk or milk based food product - - - - - - - - - - - - - - - - - - Are all fermented foods considered preserved to some extent? - Damion Dooley - food (fermented) - - - - - - - - - - - - - - - - - - - - - Any plant food product which, typically, is constituted by intact parts from one or more annual plants cultivated as field and garden crops in the open and under glass, and used almost exclusively for food. - - vegetable food product - - - - - - - - - Mature ovary of a plant, with a fleshy part of the carpel that develops with the seed to attract animals for aid in dispersal. Botanically, nuts are considered fruits. - botanical fruit food product - - - - - Mature ovary of a plant, with a fleshy part of the carpel that develops with the seed to attract animals for aid in dispersal. Botanically, nuts are considered fruits. - http://eurovoc.europa.eu/drupal/?q=request&amp;uri=http://eurovoc.europa.eu/1115 - http://oek1.fao.org/skosmos/agrovoc/en/page/c_3119 - http://www.fao.org/pollination/resources/glossary/en/ - https://en.wikipedia.org/wiki/Fruit - - - - - - - - - A one-celled fruit (pod) usually dehiscing down both sutures, and having the seed attached along a ventral suture. (Roubik 1995) - http://www.fao.org/pollination/resources/glossary/en/ - legume - http://purl.obolibrary.org/obo/FOODON_03411338 - http://purl.obolibrary.org/obo/FOODON_03411254 - legume food product - - - - - - - - - - - - - - - A food consisting of a round or oval body laid by the female of many animals, consisting of an ovum surrounded by layers of membranes and an outer casing, which acts to nourish and protect a developing embryo and its nutrient reserves. - Regarding American regulatory aspects of egg products, see this summary: -https://www.politico.com/agenda/story/2016/03/crazy-us-chicken-egg-regulation-graphic-000077 - egg food product - - - - - A food consisting of a round or oval body laid by the female of many animals, consisting of an ovum surrounded by layers of membranes and an outer casing, which acts to nourish and protect a developing embryo and its nutrient reserves. - Wikipedia:Egg_%28food%29 - - - - - - - - - - - - - - - - - - - - - - - - - - - A hen egg food product is any food product consisting mainly of hen eggs or derivatives. - https://en.wikipedia.org/wiki/Egg_as_food - SUBSET_SIREN:F1074 - hen egg food product - - - - - - - - - - A ground beef product is made of beef that has been finely chopped with a knife or a meat grinder (American English) or mincing machine (British English). Ground beef is used in many recipes including hamburgers and spaghetti Bolognese. - - - beef mince - beef mince - ground beef - hamburger meat - minced beef - ground beef food product - hamburger meat - - - - - - - - - - - - - - - - A food product from a category of domestic birds kept for meat, eggs, and feathers including fowl such as chickens, turkeys, and waterfowls such as domestic ducks and geese and other meat birds such as pigeons and doves and games birds including pheasants. - Damion Dooley - - poultry food product - - - - - - - - - - - - - - - - - - - - - - - - - - - A turkey meat food product is any food product made predominantly of turkey parts. - Damion Dooley - turkey meat food product - - - - - - - - - - - - - - - - A sauce for a salad. - http://en.wikipedia.org/wiki/Salad_dressing#Dressings - salad dressing - - - - - - - - - - - - - - - - - - - - - - - - - - oyster food product - - - - - - - - - - - - - - - - - - - - - - - - - - - - shellfish food product - - - - - - - - - - - - - - - - A fermentation process in which either carbohydrates, proteins or fats are modified through microbial, enzymatic and/or other biological process. - Damion Dooley - food fermentation - - - - - - - - - - - - - - - - - - - - - - - - - - - Fermented meat product is any product made primarily of meat subjected to a fermentation process. - Damion Dooley - fermented meat product - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Food trimmings are the parts removed from the culinary trimming of unwanted or inedible parts (i.e. sinews, skin, fat etc.) from meat, fish poultry or vegetables. Trimmings are used for making stocks, soups and sauces. - Gregory Harhay - http://en.foodlexicon.org/p0000380.php - trim - trimmings - food trimming - - - - - - - - - - - - - - - animal product sandwich - - - - - - - - - - - - - - - - - - - - - - - - - - apple condiment - - - - - - - - - - - - - - - - - - - - - - - - - - apple food product - - - - - - - - - - - - - - - - - - - apple vinegar food product - - - - - - - - - - - - - - - - - - - - - - - - - - asparagus vegetable food product - - - - - - - - - - - - - - - - A food product deriving from one or more avocados. - avocado food product - - - - - - - - - - - - - - - bakery food product - - - - - - - - - - - - - - - - - - - - - - - - - - berry food product - - - - - - - - - pepper - Pepper - black or white pepper product - pepper - - - - - - - - - - - - - - - black pepper food product - - - - - - - - - - - - - - - - - - carrot juice food product - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - carrot food product - - - - - - - - - - - - - - - cattle sandwich - - - - - - - - - - - - - - - - - - - - - - - - - - A plant food product derived from a celery plant (Apium graveolens) - - celery food product - - - - - - - - - - - - - - - - - - - - - cheese product analog - - - - - - - - - A food product which normally exists as an ingredient to another food product, rather than eaten on its own, and is more complex than a chemical food component. - food product component - - - - - - - - - - - - - - - A food product deriving from one or more cherries. - cherry food product - - - - - - - - - - condiment sauce - - - - - - - - - - - - - - - - - - - - - - - - - - coriander food product - - - - - - - - - - - - - - - - corn snack - - - - - - - - - - - - - - - - - - - - - - - - - - - - vegetable corn food product - - - - - - - - - - - - - - - - - - - - - - - - - - - cow milk based food product - - - - - - - - - cow milk butter food product - - - - - - - - - - cow milk cream food product - - - - - - - - - - - - - - - cow milk hard cheese food product - - - - - - - - - - - - - - - - - - - - - - - - - - crustacean food product - - - - - - - - - - - - - - - - - - - - - - - - - - - A pickled cucumber (commonly known as a pickle in the United States and Canada or generically as gherkins in the United Kingdom, Ireland, Australia, and New Zealand) is a cucumber that has been pickled in a brine, vinegar, or other solution and left to ferment for a period of time, by either immersing the cucumbers in an acidic solution or through souring by lacto-fermentation. - Damion Dooley - https://en.wikipedia.org/wiki/Pickled_cucumber - cucumber or gherkin pickle food product - - - - - - - - - - - - - - - A food product deriving from one or more cucumbers. - cucumber food product - - - - - - - - - SUBSET_SIREN:F1442 - dairy product analog - - - - - - - - - - - - - - - - - - - - - - Damion Dooley - egg substitute - egg product analog - - - - - - - - - - - - - - - - - - - - - - - - - - fermented cereal beverage - - - - - - - - - - - - - - - - - - - - - field corn based bakery food product - - - - - - - - - - - - - - - - - - - - - - - - - - - A product made from the North American term for maize (Zea mays) grown for livestock fodder (silage), ethanol, cereal and processed food products. The principal field corn varieties are dent corn, flint corn, flour corn (also known as soft corn) which includes blue corn (Zea mays amylacea), and waxy corn. - Damion Dooley - - dry corn food product - dry corn - field corn food product - - - - - - - - - - - - - - - field corn snack food product - - - - - - - - - - - - - - - - - - - - - - - - - - - field corn sweetener product - - - - - - - - - - - - - - - food flavoring or seasoning product - - - - - - - - - food dressing product - - - - - - - - - food product analog - - - - - - - - - - - - - - - - - - - - - - - - - - - garlic food product - - - - - - - - - - - - - - - - - - - - - - - - - - ginger - ginger - ginger food product - - - - - - - - - - - - - - - - - - - - - grain based bakery food product - - - - - - - - - - - - - - - - - - - - - - - - - - grain based vinegar food product - - - - - - - - - - - - - - - gravy or sauce - - - - - - - - - - - - - - - - - - - - - - - - - - green bell pepper food product - - - - - - - - - - hot pepper spice food product - - - - - - - - - - - - - - - - - - - - - - - - - - red pepper - hot pepper food product - - - - - - - - - imitation food product - - - - - - - - - - - - - - - - - - - - - - - - - - - - A food product made from a kale plant. - - kale food product - - - - - - - - - - - - - - - - - - - - - - - - - - lemon food product - - - - - - - - - - - - - - - - - - - - - - - - - - lentil vegetable food product - - - - - - - - - - - - - - - - - - - - - - - - - - - A lettuce vegetable food product is the head, stem or leaf portion of a lettuce plant. - Damion Dooley - 2019-06-27T13:30:10Z - lettuce - lettuce - lettuce head food product - - - - - - - - - - - - - - - - - macaroni or noodle food product - - - - - - - - - - - - - - - - - - - - - - - - - - milk based gravy or sauce food product - - - - - - - - - - - - - - - - - - - - - - - - - - mollusk food product - mollusc food product - - - - - - - - - nonalcoholic beverage - - - - - - - - - - - - - - - olive fat or oil refined food product - - - - - - - - - - - - - - - - - - - - - onion flavouring food product - - - - - - - - - - - - - - - - - - - - - - - - - - onion food product - - - - - - - - - - - - - - - pancake or waffle food product - - - - - - - - - - - - - - - - - - green or red pepper pickle food product - - - - - - - - - - - - - - - A food product deriving from one or more sweet or hot peppers. - pepper vegetable food product - - - - - - - - - - - - - - - - - - plant based bakery food product - - - - - - - - - - - - - - - - - - - - - plant based refined or partially-refined food product - - - - - - - - - - - - - - - - - An edible plant fat or oil product with characteristics that consumers desire such as bland flavour and odour, clear appearance, light colour, stability to oxidation and suitability for frying, and which is the result of a refining process that removes free fatty acids. - Damion Dooley - plant fat or oil refined food product - - - - - - - - - - - - - - - - A plant fruit food product which is labeled (in common language or by regulation) as a vegetable food product. - plant fruit as vegetable food product - - - - - - - - - plant head vegetable food product - - - - - - - - - - - - - - - - - - - - - - - - - - plant leaf vegetable food product - - - - - - - - - - - - - - - - - - plant product dressing - - - - - - - - - - - - - - - - - - - - - - - - - - - - A food product harvested from underground plant parts. - plant root vegetable food product - - - - - - - - - - - - - - - - - - plant seed based bakery food product - - - - - - - - - - - - - - - - - - - - - - - - - - - - plant seed vegetable food product - - - - - - - - - - - - - - - - - - plant stem or spear vegetable food product - - - - - - - - - plant sweetener - - - - - - - - - - Damion Dooley - preserved - food (preserved) - - - - - - - - - - - - - - - - - - - A prepared hen egg product is a product predominantly made of hen egg that has been cooked and may only require defrosting or reheating for consumption. - Damion Dooley - prepared hen egg product - - - - - - - - - - - - - - - - - - - - - - - - - - - red bell pepper food product - - - - - - - - - refined or partially-refined food product - - - - - - - - - - - - - - - salad food product - - - - - - - - - - - - - - - - - - - - - - A sandwich food product is a food product used to create a sandwich. This includes bread as a container, and sandwich ingredients and spreads. - Damion Dooley - sandwich food product - - - - - - - - - - - - - - - - - - - - - - - - - - - sesame food product - - - - - - - - - - - - - - - - - - - - - - - - - - shallot food product - - - - - - - - - - - - - - - - - - - - - - - - - - shrimp food product - - - - - - - - - - - - - - - - Damion Dooley notes: We can't say all soups are cooked there are many chilled soup recipes. - soup food product - - - - - - - - - - - - - - - A food product deriving from one or more squashes. - squash food product - - - - - - - - - stone fruit food product - - - - - - - - - - - - - - - - - - - - - sugar based vinegar food product - - - - - - - - - - - - - - - - - - - - - - - - - - - sugar cane food product - - - - - - - - - sugar maple sweetener food product - - - - - - - - - - http://www.langual.org/langual_thesaurus.asp?termid=H0202 - sweetener food product - - - - - - - - - tomato condiment - - - - - - - - - - - - - - - - - - tomato juice food product - - - - - - - - - - - - - - - - - - - - - - - - - - Curcuma - turmeric food product - - - - - - - - - uncured cheese food product - - - - - - - - - uncured cow milk cheese food product - - - - - - - - - - - - - - - multi-component corn food product - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - vegetable pickle food product - - - - - - - - - - - - - - - A food product derived from one or more walnuts. - walnut food product - - - - - - - - - - - - - - - - - - - - - - A water food product is a food product derived from H20 (water) in its liquid form. - https://en.wikipedia.org/wiki/Water - SUBSET_SIREN:F10414 - water - subset_siren - SIREN DB annotation: -* has quality 'liquid, low viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430123) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) - Water - water - water food product - - - - - - - - - - - - - - - - - - - - - - - - - - wheat based bakery food product - - - - - - - - - - - - - - - wheat based pastry food product - - - - - - - - - wheat bread food product - - - - - - - - - - - - - - - - - - - - - - - - - - white pepper food product - - - - - - - - - - A meal type is the name of an eating occasion that may have location, food type, or other customary contextual features. (Damion's 1st draft definition) - Damion Dooley - food product by meal type - - - - - - - - - food seasoning product - - - - - - - - - - - - - - - A food product consisting of food material derived primarily from a single organism. - Damion Dooley - food product by organism - - - - - - - - - baking supply product - - - - - - - - - - - - - - - - - - - - - - - - - - Any substance that can be consumed by an organism to satisfy nutritional or other health needs, or to provide a social or organoleptic food experience - - - food - foodstuff - nourishment - sustenance - This class is the top of FOODON's main food product hierarchy which is described in the https://www.foodon.org website, and can be searched in lookup services like https://www.ebi.ac.uk/ols/ - food material - - - - - - - - - - - - - - - - - - - - - - - - - - - A product derived from any variety of mint plant. - Damion Dooley - mint - American Corn Mint, Brook Mint, Canadian Mint, Chinese Mint, Corn Mint, Cornmint Oil, Field Mint Oil, Huile de Menthe, Huile de Menthe des Champs, Japanese Oil of Peppermint, Menta Japonesa, Mentha Arvensis Aetheroleum, Mentha arvensis var. piperascens, Mentha canadensis, Menthe du Canada, Menthe des Champs, Menthe Japonaise, Mint Oil, Minzol, Poleo, Pudina, Putiha. [source: https://www.webmd.com/vitamins-supplements/ingredientmono-616-japanese%20mint.aspx?activeingredientid=616&activeingredientname=japanese%20mint] - mint - mint food product - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A zucchini food product is a food product deriving from either golden or green zucchini plant cultivars. - Damion Dooley - zucchini food product - - - - - - - - - - - - - - - requires discussion - A process involving the physical transformation of a food source or food product into some derived organic material or food product - Damion Dooley - food transformation process - - - - - - - - - Familiar examples of invertebrates include arthropods (insects, arachnids, crustaceans, and myriapods), mollusks (chitons, snails, bivalves, squids, and octopuses), annelids (earthworms and leeches), and cnidarians (hydras, jellyfishes, sea anemones, and corals).[wikipedia] - - Invertebrates are animals that neither possess nor develop a vertebral column (commonly known as a backbone or spine), derived from the notochord. This includes all animals apart from the subphylum Vertebrata. - Damion Dooley - https://en.wikipedia.org/wiki/Invertebrate - animal - invertebrate animal - - - - - - - - - - - - - - - - - - Raw apple is apple that has not been subject to cooking or other preservation processes other than by cold storage. - apple (raw) - - - - - - - - - - A class which contains food product categories qualified by a quality such as granularity or temperature, which is useful for tasks like food inspection where little prior knowledge of how the food came to be is available. Some terms like "food (frozen)" are both a quality descriptor and the output of a process. - Damion Dooley - food product by quality - - - - - - - - - - - - - - - - - - - - - baked - baked food product - food (baked) - - - - - - - - - - - - - - - - - - - - - - - - - - lime fruit food product - - - - - - - - - - A physical object quality which can describe an attribute of a food item or related to a food product. - http://orcid.org/0000-0001-8008-8249 - food object quality - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A pome fruit of an apple tree (Malus domestica). - http://orcid.org/0000-0002-8844-9165 - apple - A whole apple may include a stem. - Apples - apple (whole) - https://www-atlasobscura-com.cdn.ampproject.org/c/s/www.atlasobscura.com/articles/heritage-appalachian-apples.amp - - - - - - - - - cherry (whole or parts) - - - - - - - - - carrot root (whole or parts) - - - - - - - - - - - - - - - - - - - - - - A food product consisting of food material derived from ingredients sourced from multiple organisms. - Damion Dooley - 2019-01-23T22:40:32Z - multi-ingredient - The definition of this is being discussed in issue: https://github.com/FoodOntology/foodon/issues/57 - -Namely, how to characterize the threshold of ingredients that make for multi-component classification? Salt, pepper, spices wouldn't normally make a food multi-component? - multi-component food product - - - - - - - - - - Dairy cattle are a type of cattle bred for the ability to produce large quantities of milk, from which dairy products are made. This class covers both male and female members of a dairy breed. - Damion Dooley - https://en.wikipedia.org/wiki/Dairy_cattle - 2019-01-26T22:49:27Z - dairy cattle - https://en.wikipedia.org/wiki/List_of_dairy_cattle_breeds - - - - - - - - - - Taurine cattle (Bos taurus taurus), also called European cattle, are a subspecies of domesticated cattle originating in the Near East. Both taurine cattle and indicine cattle (zebus) are descended from the aurochs. Taurine cattle were originally considered a distinct species, but are now typically grouped with zebus and aurochs into one species, Bos taurus. Most modern breeds of cattle are taurine cattle. - Damion Dooley - https://en.wikipedia.org/wiki/Taurine_cattle - 2019-01-28T02:41:04Z - http://www.langual.org/langual_thesaurus.asp?termid=B5186 - taurine cattle - - - - - - - - - - Pork loin is a cut of meat from a pig, created from the tissue along the dorsal side of the rib cage. - Damion Dooley - https://en.wikipedia.org/wiki/Pork_loin - 2019-04-13T18:58:46Z - pork loin - pork loin - - - - - - - - - - An aquatic invertebrate may live entirely beneath the water, or may live upon its surface or on the plants surrounding it. Some breathe air, others breathe water. To move, they may walk, swim, float, skate, fly or glide on their bellies—or they may not move much at all. - Because snails are members of gastropod, a subclass of molluscs, ... leading to aquatic invertebrates, we can't make aquatic invertebrates disjoint with terrestrial invertebrates. - Damion Dooley - https://nature.mdc.mo.gov/discover-nature/general-species-information/aquatic-invertebrate-facts - 2019-04-29T19:23:38Z - aquatic invertebrate - - - - - - - - - - - - - - - Damion Dooley - 2019-05-21T22:37:06Z - Aves - avian - bird - avian animal - - - - - - - - - - A food product organized by the process which it results from. - Damion Dooley - 2019-05-23T23:02:07Z - food product by process - - - - - - - - - - The largest and main meal of the day, taken either around midday or in the evening. - - Damion Dooley - https://en.wikipedia.org/wiki/Dinner - 2019-05-25T05:03:08Z - dinner - main meal - supper - Main Meal - dinner food - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Damion Dooley - 2019-05-25T06:38:12Z - pasteurized - food (pasteurized) - - - - - - - - - Damion Dooley - 2019-06-14T04:23:35Z - pork food product - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A lipid food product is a food product made primarily of plant or animal fat or oil - Damion Dooley - 2019-06-11T09:18:41Z - fats and oils - oils and fats - lipid food product - - - - - - - - - - A food product made of ground or minced turkey meat - Damion Dooley - 2019-06-28T04:44:34Z - ground turkey - minced turkey - ground turkey - turkey (ground or minced) - - - - - - - - - Damion Dooley - 2019-06-28T00:25:22Z - ginger - ginger root - - - - - - - - - - - - - - - - - A hamburger (short: burger) is a sandwich consisting of one or more cooked patties of ground meat, usually beef, placed inside a sliced bread roll or bun. The patty may be pan fried, grilled, or flame broiled. - Damion Dooley - https://en.wikipedia.org/wiki/Hamburger - 2019-06-28T07:39:11Z - burger - hamburger - Burgers - beef hamburger (dish) - - - - - - - - - - - - - - - - - - - - - - - Food material chopped into roughly bite-sized pieces. - Damion Dooley - 2019-07-09T20:59:57Z - chopped - cut - Cut - food (chopped) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Damion Dooley - 2019-07-10T17:35:07Z - SUBSET_SIREN:F4839 - turkey egg - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'egg' (http://purl.obolibrary.org/obo/FOODON_03420194) - turkey egg (whole, shell on, raw) - - - - - - - - - - A whole turkey food product consists of the plucked carcass of a turkey with head and entrails removed and with organ meats and neck severed and possibly included in body cavity. - Damion Dooley - 2019-07-10T19:28:58Z - turkey - turkey - turkey (whole, raw) - https://www.nwtf.org/hunt/article/how-to-clean-wild-turkey - - - - - - - - - - The Granny Smith is a tip-bearing apple cultivar, which originated in Australia in 1868. The tree is thought to be a hybrid of Malus sylvestris, the European wild apple, with the North American apple Malus pumila as the polleniser. - - - 2019-08-07T19:29:34Z - Granny Smith apple tree - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A pome fruit of a Granny Smith apple tree cultivar. - - Damion Dooley - - https://en.wikipedia.org/wiki/Granny_Smith - 2019-08-07T19:34:52 - - granny smith apple - Granny Smith apple - Granny Smith apple (whole) - - - - - - - - - - - - - - - - - - - - - - - - - - A hazelnut food product is a food product that derives from hazelnuts - - 2019-08-09T22:59:15Z - hazelnut food product - - - - - - - - - - The hazelnut is the nut of the hazel and therefore includes any of the nuts deriving from species of the genus Corylus, especially the nuts of the species Corylus avellana. It also is known as cobnut or filbert nut according to species. - - Emma Griffiths - - 2019-08-09T23:07:38Z - cobnut - Hazelnuts - hazelnut - - - - - - - - - - - A patty, in American, Canadian, South African, Australian and New Zealand English, is a flattened, usually round, serving of ground food, often meat or meat alternatives. The food is compacted and shaped into the patty, then cooked, and served. - - Emma Griffiths - - 2019-08-11T05:07:26Z - pattie - patties - patty - - - - - - - - - - Gnetum africanum is a vine gymnosperm species found natively throughout tropical Africa. It is grown in various countries across Africa, including: Cameroon. - - Emma Griffiths - - 2019-08-11T22:22:09Z - Gnetum africanum - KoKo - afang - eru - fumbua - m’fumbua - okok - ukase - wild spinach - African jointfir plant - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A leaf of an okazi plant (Gnetum africanum). - - - - https://pfaf.org/user/Plant.aspx?LatinName=Gnetum+africanum - 2019-08-11T22:28:35 - spinach - Gnetum africanum leaf - afang leaf - african jointfir leaf - eru leaf - fumbua leaf - okazi leaf - okok leaf - ukazi leaf - wild spinach leaf - Okazi leaves, often referred to as wild spinach, are used as a leafy vegetable for soups and stews, commonly called eru soup or afang soup, or eaten raw. The leaves may further be used as a remedy for nausea, sore throats, or as a dressing for warts. - okazi leaf (whole) - spinach - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A tuber of an okazi plant (Gnetum africanum). - - - https://pfaf.org/user/Plant.aspx?LatinName=Gnetum+africanum - 2019-08-11T22:31:04 - Gnetum africanum tuber - afang tuber - african jointfir tuber - eru tuber - gnetum africanum tuber - okazi root tuber - ukazi tuber - The okazi root tuber may be used as a source of famine food, and is similar to that of a yam. - okazi tuber - - - - - - - - - - - - - - - - - - - - - - - - - - - The poblano (Capsicum annuum) is a mild chili pepper originating in the state of Puebla, Mexico. Dried, it is called ancho or chile ancho, from the Spanish word ancho ("wide"). - - Emma Griffiths - 2019-08-13T04:55:19Z - ancho - ancho pepper - chile ancho - poblano - ancho pepper - - - - - - - - - - A multicellular eukaryotic heterotrophic organism within the kingdom Animalia. - - - 2019-08-14T18:02:36Z - - animal - - - - - - - - - - A pickled cucumber (commonly known as a pickle in the United States and Canada and a gherkin in Britain, Ireland, Australia, South Africa and New Zealand) is a cucumber that has been pickled in a brine, vinegar, or other solution and left to ferment for a period of time, by either immersing the cucumbers in an acidic solution or through souring by lacto-fermentation. - - - 2019-08-20T19:10:28Z - - gherkin - pickle - Pickles - pickled cucumber - - - - - - - - - - - - - - - - - - - - - - - - - - - A bell pepper is a fruits in different colours - including red, yellow, orange, green, white, and purple - from a bell pepper plant cultivar. Bell peppers are sometimes grouped with less pungent pepper varieties as "sweet peppers". - - - 2019-08-22T18:01:49Z - - pepper - bell pepper food product - - - - - - - Kham Tran - www.khamtran.com - - - - - - - - - - Golden zucchini is a modern hybrid summer squash (Cucurbita pepo). - - - 2019-08-22T19:52:25Z - gold gush zucchini - golden delight zucchini - goldfinger zucchini - yellow zucchini - golden zucchini plant - - - - - - - - - - - - - - - - - - - - - - - - - - A golden or yellow zucchini is a summer squash harvested from the golden zucchini cultivar. - - 2019-08-22T20:36:52Z - golden zucchini - yellow zucchini - golden zucchini squash (whole) - - - - - - - - - - - - - - - - - - - Sunburst squash is a summer squash (species *Cucurbita pepo*) notable for its small size, round and shallow shape, and scalloped edges, somewhat resembling a small toy top, or flying saucer. - - - 2019-08-22T21:11:29Z - cibleme - pattypan squash - scallopini - sunburst squash - white squash - yellow squash - pattypan squash - pattypan squash (whole, raw) - - - - - - - - - - A shallot is the bulb part of a shallot plant - - 2019-08-22T23:45:59Z - shallot - shallot (whole, raw) - shallots - - - - - - - - - - Damion Dooley - http://langual.org - 2019-08-23T00:37:18Z - SUBSET_SIREN:F11872 - cumin - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'seed (anatomical part)' (http://purl.obolibrary.org/obo/FOODON_03420155) -* formed as a result of 'water removal process' (http://purl.obolibrary.org/obo/FOODON_03460138) -* formed as a result of 'preservation by dehydration or drying' (http://purl.obolibrary.org/obo/FOODON_03470116) - - cumin - cumin seed (whole, dried) - - - - - - - - - - 2019-08-24T15:46:35Z - basil - basil - basil food product - - - - - - - - - - A dish made from boiled cornmeal. - - - 2019-08-24T17:49:54Z - corn grits - Grits - grits - - - - - - - - - - - - - - - Malus is a genus of about 30–55 species[3] of small deciduous trees or shrubs in the family Rosaceae, including the domesticated orchard apple (M. pumila syn. M. domestica) – also known as the eating apple, cooking apple, or culinary apple. The other species are commonly known as crabapples, crab apples, crabtrees or wild apples - - 2019-08-25T15:37:56Z - Malus group - - - - - - - - - - A poultry sandwich contains chicken, turkey or other poultry meat. - - Damion Dooley - 2019-08-26T18:45:16Z - poultry sandwich - - - - - - - - - - A variety of kale with a long tradition in Italian cuisine, especially that of Tuscany. - - - 2019-09-11T00:21:19Z - Cavolo nero - Lacinato - Tuscan kale - black Tuscan palm - black cabbage - dinosaur kale - flat back cabbage - palm tree kale - Lacinato kale - lacinato kale - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A food product not including meat and animal tissue products (such as gelatin or animal-derived rennet). - - https://en.wikipedia.org/wiki/Vegetarian_cuisine - 2019-09-11T21:12:43Z - vegetarian food - vegetarian food product - - - - - - - - - - - - - - - - - - - - An adult female chicken. - - 2019-11-15T20:12:48Z - - hen - - - - - - - - - - A food product made from black, white, pink or similar peppercorns. - - 2019-11-15T23:03:24Z - peppercorn food product - - - - - - - - - - 2019-11-15T23:19:38Z - multi-component meat product - - - - - - - - - - - - - - - - - - - - - - - - - - - 2020-01-08T00:20:27Z - echinoderm food product - - - - - - - - - A lemon, whole or in pieces, for eating or other food processing. - - 2020-03-28T23:38:10Z - lemon (whole or parts) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A hesperidium fruit of a citrus plant (Citrus). - - https://orcid.org/0000-0001-5275-8866 - 2020-10-20T06:54:39 - citrus fruit - citrus fruit (whole) - - - - - - - - - - - - - - - - - - - - - - A genus of plants in the mustard family (Brassicaceae). The members of the genus are informally known as cruciferous vegetables, cabbages, or mustard plants. - - bok choy vegetable food product - bomdong vegetable food product - broccolini vegetable food product - chinese cabbage vegetable food product - choy sum vegetable food product - collard greens vegetable food product - gai lan vegetable food product - komatsuna vegetable food product - mizuna vegetable food product - rutabaga vegetable food product - savoy cabbage vegetable food product - tatsoi vegetable food product - cole crop vegetable food product - cruciferous vegetable food product - brassica food product - - - - - - - - - - Food contact materials are materials that are intended to be in contact with food. These can be things that are quite obvious like a glass or a can for soft drinks as well as machinery in a food factory or a coffee machine. - - - 2020-07-31T17:07:09Z - food contact material - - - - - - - - - - - - - - - - 2020-09-06T15:59:54Z - multi-component wheat food product - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A seed of a cumin plant (Cuminum cyminum). - - https://en.wikipedia.org/wiki/Cumin - 2020-09-06T16:35:13 - cumin - cumin seed (whole) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A primary root of a carrot plant (Daucus carota). - http://orcid.org/0000-0002-8844-9165 - 2020-09-09T07:27:10 - carrot - carrot - carrot root (whole) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A petiole of a celery plant (Apium graveolens Dulce Group). - http://orcid.org/0000-0002-8844-9165 - 2020-09-09T07:43:45 - celery stalk - celery stalk (whole) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A pepo fruit of a cucumber plant (Cucumis sativus). - http://orcid.org/0000-0002-8844-9165 - 2020-09-09T14:18:28 - cucumber (whole) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A berry fruit of a grape plant. - http://orcid.org/0000-0002-8844-9165 - 2020-09-09T14:38:33 - de-stemmed grape - grape - grape (whole) - - - - - - - - - - - - - - - - 2020-09-09T19:28:43Z - Maize plant - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A stem of an asparagus plant (Asparagus officinalis) - - https://orcid.org/0000-0001-5275-8866 - 2020-10-13T05:48:32 - asaparagus - asparagus spear (whole) - - - - - - - - - A food product which has been separated into pieces. - - 2020-10-12T07:07:16Z - food (pieces) - - - - - - - - - - - - - - - - - - - - - - - - - An edible drupe fruit of a cherry plant. - - https://orcid.org/0000-0001-5275-8866 - 2020-10-13T05:48:32 - cherry - cherries - cherry (whole) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A ripened red colored berry fruit of a bell pepper plant cultivar. - - https://orcid.org/0000-0001-5275-8866 - 2020-10-14T12:37:01 - bell pepper - capsicum - pepper - sweet pepper - sweet red bell pepper - Bell pepper - bell pepper - sweet red bell pepper (whole) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A berry fruit of a pepper plant (Capsicum) - - https://orcid.org/0000-0001-5275-8866 - https://www.britannica.com/plant/pepper-plant-Capsicum-genus - 2020-10-14T02:39:11 - pepper - peppers - pepper (whole) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A juicy, rounded, brightly colored fruit without a stone or pit, though pips or seeds may be present. - - https://orcid.org/0000-0001-5275-8866 - https://en.wikipedia.org/wiki/Berry - 2020-10-23T09:28:05 - berry - common berry - berry (whole) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A pepo fruit varietal of a squash plant (Cucurbita). - - https://orcid.org/0000-0001-5275-8866 - https://en.wikipedia.org/wiki/Cucurbita - 2020-10-20T12:01:59 - squash - squash - squash (whole) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A berry fruit in the Grossum cultivar group of a bell pepper plant. - - 2020-11-19T01:08:58Z - bell pepper - capsicum - pepper - sweet pepper - bell pepper (whole) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An immature green colored berry fruit of a bell pepper plant cultivar. - - https://orcid.org/0000-0001-5275-8866 - 2020-10-14T07:08:14 - bell pepper - capsicum - pepper - sweet green pepper - sweet pepper - sweet green bell pepper (whole) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A mature yellow colored berry fruit of a bell pepper plant cultivar. - - 2020-11-19T01:24:18Z - bell pepper - capsicum - pepper - sweet pepper - sweet yellow pepper - sweet yellow bell pepper (whole) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A bulb of a garlic plant (Allium sativum) - - https://en.wikipedia.org/wiki/Garlic - 2020-11-30T04:49:32 - garlic - garlic - garlic bulb - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An immature flower stalk of a garlic plant. - - https://en.wikipedia.org/wiki/Garlic - 2020-12-16T22:45:47 - garlic spear - garlic stem - garlic top - garlic scape - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A berry fruit of an avocado plant (Persea americana) - - https://en.wikipedia.org/wiki/Avocado - 2021-02-10T22:52:57 - avocado - avocado - avocado (whole) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A leaf of a celery plant (Apium graveolens Dulce Group). - - https://en.wikipedia.org/wiki/Celery - 2021-02-11T02:01:06 - celery leaf - celery leaf (whole) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A bunch of a raw celery leaves. - - https://en.wikipedia.org/wiki/Celery - 2021-02-11T02:01:46 - celery bunch - celery bunch - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A leaf of a grape plant. - - 2021-02-11T02:02:32 - grape leaf - grape leaf (whole) - - - - - - - - - - - - - - - - - - - - - - - - - - - A leaf of a vegetable-producing plant. - - 2021-02-11T02:40:22 - vegetable leaf (whole) - - - - - - - - - - - - - - - - - - - - - - - - - - - A hesperidium fruit of a lime plant. - - https://en.wikipedia.org/wiki/Lime_(fruit) - 2021-02-11T02:57:03 - lime - lime - lime (whole) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A pepo fruit of a pattypan squash plant, a varietal of summer squash. - - https://en.wikipedia.org/wiki/Pattypan_squash - 2021-02-11T16:45:15 - button squash - custard squash - pattypan squash - scallop squash - scallopini squash - pattypan squash (whole) - - - - - - - - - - - - - - - - - - - - - - - A pepo fruit of a summer squash plant. - - https://en.wikipedia.org/wiki/Summer_squash - 2021-02-11T16:47:21 - summer squash - summer squash (whole) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A root of a ginger plant (Zingiber officinale) - - https://en.wikipedia.org/wiki/Ginger - 2021-02-11T17:33:19 - elephant ginger - elephant ginger root - ginger - ginger root - ginger root (whole) - - - - - - - - - - A berry fruit of a chili pepper plant. - - https://en.wikipedia.org/wiki/Chili_pepper - 2021-02-11T21:40:27 - chile pepper - chili - chili pepper - chili pod - chilli - chilli pepper - chile pepper - chili pepper (whole) - - - - - - - - - - - - - - - - - - - - - - - - - - - A bulb of a shallot plant (Allium cepa var. aggregatum) - - https://en.wikipedia.org/wiki/Shallot - 2021-02-11T21:44:21 - shallot - shallot (whole) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A root of a turmeric plant (Curcuma longa) - - https://en.wikipedia.org/wiki/Turmeric - 2021-02-11T22:31:47 - indian saffron - turmeric - yellow ginger - turmeric - turmeric root (whole) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A riped berry fruit of a white pepper plant. - - https://en.wikipedia.org/wiki/Black_pepper - 2021-02-11T23:07:09 - white pepper - white peppercorn - white peppercorn (whole) - - - - - - - - - - An anatomical part of a plant that is consumed by humans or other animals as food. - - https://en.wikipedia.org/wiki/Vegetable - 2021-02-12T18:49:32 - vegetable (whole) - - - - - - - - - - A sausage (usually a hot dog) on a stick that has been coated in a thick layer of cornmeal batter and deep fried. - - https://en.wikipedia.org/wiki/Corn_dog - - 2021-07-19T11:58:23Z - corndog - Corn dogs - corn dog - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A pepo fruit of a winter squash plant harvested in the fall. - - https://orcid.org/0000-0002-7463-6306 - https://en.wikipedia.org/wiki/Winter_squash - 2021-07-22T17:39:12 - winter squash - winter squash (whole) - - - - - - - - - - A food product made from feta cheese. - - 2022-01-06T22:23:57Z - feta cheese food product - - - - - - - - - - - A celery food product derived from an Apium graveolens Dulce Group plant. - 2022-01-31T07:44:24Z - celery (Dulce Group) food product - - - - - - - - - A food product deriving from one or more animals. - - 2022-09-01T16:31:09Z - animal food product - - - - - - - - - - A processed material which is referenced in an ingredient specification. - This term could probably go in the COB ontology. - - 2022-08-12T04:23:10Z - ingredient - ingredients - - - - - - - - - - Chickens, turkeys, quail, ducks, and geese are only called poultry if they aren't reared in the wild. - A domesticated bird that is kept by humans for its eggs, meat or feathers. - - 2022-08-25T10:01:00Z - - poultry - - - - - - - - - An unshelled lentil with a brown seed coat and an orange-red cotyledon. - https://orcid.org/0000-0001-5275-8866 - https://en.wikipedia.org/wiki/Lentil - 2022-03-28T16:12:32Z - masoor daal - orange lentil - red lentil - pink lentil (whole) - red lentils - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A leaf of a ginger plant (Zingiber officinale). - ginger leaf (whole) - - - - - - - - - - - - - - - - - - - - - - - - - - - - A whole ginger leaf or some substance made from a processed ginger leaf. - https://orcid.org/0000-0001-5275-8866 - https://en.wikipedia.org/wiki/Ginger - 2022-04-13T09:40:25Z - ginger leaf - ginger leaf (whole or parts) - - - - - - - - - - - - - - - - - - - - - - - - - - - - A whole ginger root or some substance made from a processed ginger root. - https://orcid.org/0000-0001-5275-8866 - https://en.wikipedia.org/wiki/Ginger - ginger - ginger root - ginger root (whole or parts) - - - - - - - - - - - - - - - - - - - - - - - - - - - - A whole tomato or some substance made from a processed tomato. - https://orcid.org/0000-0001-5275-8866 - https://en.wikipedia.org/wiki/Tomato - 2022-04-13T12:27:40Z - tomato - tomato - tomato (whole or parts) - tomatoes - - - - - - - - - - - - - - - - - - - - - - - - - - - - A whole cucumber or some substance made from a processed cucumber. - https://orcid.org/0000-0001-5275-8866 - cucumber - cucumber (whole or parts) - - - - - - - - - - - - - - - - - - - - - - - Whole kale or some substance made from processed kale. - https://orcid.org/0000-0001-5275-8866 - https://en.wikipedia.org/wiki/Kale - 2022-04-13T09:55:24Z - kale - kale - kale (whole or parts) - - - - - - - - - - - - - - - - - - - - - - - A whole black pepper or some substance made from processed black pepper. - https://orcid.org/0000-0001-5275-8866 - black pepper - black pepper - black pepper (whole or parts) - - - - - - - - - - - - - - - - - - - - - - - - - - - - A whole squash or some substance made from a processed squash. - squash (whole or parts) - - - - - - - - - - http://langual.org - SUBSET_SIREN:F1073 - subset_siren - SIREN DB annotation: -* has quality 'crystal' (http://purl.obolibrary.org/obo/FOODON_03430143) -* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) -* derives from 'sugar' (http://purl.obolibrary.org/obo/FOODON_03420108) -* formed as a result of 'water removal process' (http://purl.obolibrary.org/obo/FOODON_03460138) -* formed as a result of 'preservation by dehydration or drying' (http://purl.obolibrary.org/obo/FOODON_03470116) - - sugar (granulated) - - - - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F1115 - subset_siren - SIREN DB annotation: -* has quality 'liquid, low viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430123) -* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) -* derives from 'seed (anatomical part)' (http://purl.obolibrary.org/obo/FOODON_03420155) -* formed as a result of 'proteolytic fermentation process' (http://purl.obolibrary.org/obo/FOODON_03460102) - - soy sauce - soy sauce - - - - - - - - - - - - - - - - http://langual.org - flour - SUBSET_SIREN:F1116 - subset_siren - SIREN DB annotation: -* has quality 'finely ground' (http://purl.obolibrary.org/obo/FOODON_03430106) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'seed, skin removed, germ removed (endosperm)' (http://purl.obolibrary.org/obo/FOODON_03420208) -* formed as a result of 'water removal process' (http://purl.obolibrary.org/obo/FOODON_03460138) -* formed as a result of 'preservation by dehydration or drying' (http://purl.obolibrary.org/obo/FOODON_03470116) - - Flour - wheat flour - - - - - - - - - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F1146 - SUBSET_SIREN:F1404 - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* has quality 'partially heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440018) -* derives from 'fruit, peel present, core, pit or seed present' (http://purl.obolibrary.org/obo/FOODON_03420140) -* formed as a result of 'pickling process' (http://purl.obolibrary.org/obo/FOODON_03460190) -* formed as a result of 'acidified' (http://purl.obolibrary.org/obo/FOODON_03460200) -* immersed in 'packed in salt brine' (http://purl.obolibrary.org/obo/FOODON_03480018) - - cucumber pickle - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F1256 - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* derives from 'fruit, peel present, core, pit or seed removed' (http://purl.obolibrary.org/obo/FOODON_03420139) -* has substance added 'flavoring or spice extract or concentrate added' (http://purl.obolibrary.org/obo/FOODON_03460100) -* has substance added 'sugar or sugar syrup added' (http://purl.obolibrary.org/obo/FOODON_03460136) - - maraschino cherries - maraschino cherry - - - - - - - - - - http://langual.org - SUBSET_SIREN:F1283 - raisin - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* derives from 'fruit, peel present' (http://purl.obolibrary.org/obo/FOODON_03420137) -* formed as a result of 'water removal process' (http://purl.obolibrary.org/obo/FOODON_03460138) -* formed as a result of 'preservation by dehydration or drying' (http://purl.obolibrary.org/obo/FOODON_03470116) - - raisin (whole) - raisins - - - - - - - - - - http://langual.org - SUBSET_SIREN:F1304 - subset_siren - SIREN DB annotation: -* has quality 'semiliquid' (http://purl.obolibrary.org/obo/FOODON_03430103) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* has substance added 'grain added' (http://purl.obolibrary.org/obo/FOODON_03460152) - - Batter - batter - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F1337 - citrus fruit - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'fruit, peel present, core, pit or seed present' (http://purl.obolibrary.org/obo/FOODON_03420140) - - citrus fruit (whole, raw) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A drupe fruit from a walnut tree (Juglans). - https://en.wikipedia.org/wiki/Walnut - http://langual.org - SUBSET_SIREN:F1364 - walnut - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* derives from 'seed (anatomical part)' (http://purl.obolibrary.org/obo/FOODON_03420155) -* formed as a result of 'water removal process' (http://purl.obolibrary.org/obo/FOODON_03460138) -* formed as a result of 'preservation by dehydration or drying' (http://purl.obolibrary.org/obo/FOODON_03470116) - - walnut (whole) - walnuts - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F1440 - subset_siren - SIREN DB annotation: -* has quality 'semisolid with smooth consistency' (http://purl.obolibrary.org/obo/FOODON_03430119) -* has quality 'partially heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440018) -* derives from 'fat or oil' (http://purl.obolibrary.org/obo/FOODON_03420190) -* formed as a result of 'acidified' (http://purl.obolibrary.org/obo/FOODON_03460200) -* has substance added 'spice or herb added' (http://purl.obolibrary.org/obo/FOODON_03460151) -* has substance added http://purl.obolibrary.org/obo/FOODON_03460185 - - mayonnaise - mayonnaise - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F1441 - lemon - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'fruit, peel present, core, pit or seed present' (http://purl.obolibrary.org/obo/FOODON_03420140) - - lemon - lemon (whole, raw) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F1444 - subset_siren - SIREN DB annotation: -* has quality 'liquid' (http://purl.obolibrary.org/obo/FOODON_03430130) -* derives from 'part of plant' (http://purl.obolibrary.org/obo/FOODON_03420174) - - vegetable juice food product - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A berry fruit of a tomato plant (Solanum lycopersicum). - http://orcid.org/0000-0002-8844-9165 - http://langual.org - SUBSET_SIREN:F1453 - tomato - subset_siren - tomato (whole) - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F1460 - Ketchup - subset_siren - SIREN DB annotation: -* has quality 'semiliquid with smooth consistency' (http://purl.obolibrary.org/obo/FOODON_03430135) -* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) -* derives from 'fruit, peel present, core, pit or seed present' (http://purl.obolibrary.org/obo/FOODON_03420140) -* formed as a result of 'acidified' (http://purl.obolibrary.org/obo/FOODON_03460200) -* has substance added 'sugar or sugar syrup added' (http://purl.obolibrary.org/obo/FOODON_03460136) -* has substance added 'flavoring, spice or herb added' (http://purl.obolibrary.org/obo/FOODON_03460227) - - ketchup - tomato catsup - - - - - - - - - - A concentrated cow milk product is obtained through partial water removal, yeilding milk that has less than the approximate 88% water content that fresh whole milk has. - Damion Dooley - https://www.uoguelph.ca/foodscience/book-page/concentrated-and-dried-dairy-products - http://langual.org - SUBSET_SIREN:F1503 - condensed milk - subset_siren - SIREN DB annotation: -* has quality 'liquid, high viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430139) -* has quality 'partially heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440018) -* derives from 'milk (mammary secretion)' (http://purl.obolibrary.org/obo/UBERON_0001913) -* formed as a result of 'water removal process' (http://purl.obolibrary.org/obo/FOODON_03460138) -* formed as a result of 'pasteurization by heating' (http://purl.obolibrary.org/obo/FOODON_03470135) - - cow milk (concentrated) - - - - - - - - - - http://langual.org - SUBSET_SIREN:F1505 - subset_siren - SIREN DB annotation: -* has quality 'liquid, high viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430139) -* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) -* derives from 'milk (mammary secretion)' (http://purl.obolibrary.org/obo/UBERON_0001913) -* formed as a result of 'water removal process' (http://purl.obolibrary.org/obo/FOODON_03460138) -* formed as a result of 'food homogenization or emulsification process' (http://purl.obolibrary.org/obo/FOODON_03460306) -* formed as a result of 'sterilization by heating' (http://purl.obolibrary.org/obo/FOODON_03470123) -* has substance added 'vitamin D' (http://purl.obolibrary.org/obo/CHEBI_27300) -* has substance added 'nutrient or dietary substance added' (http://purl.obolibrary.org/obo/FOODON_03460194) - - evaporated milk - evaporated milk - - - - - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F1545 - cucumber - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'fruit, peel present, core, pit or seed present' (http://purl.obolibrary.org/obo/FOODON_03420140) - - cucumber (whole, raw) - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F1570 - carrot - carrot root - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'root, tuber or bulb' (http://purl.obolibrary.org/obo/FOODON_03420238) - - carrot root (whole, raw) - - - - - - - - - - http://langual.org - SUBSET_SIREN:F1577 - squash - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'fruit, peel present, core, pit or seed present' (http://purl.obolibrary.org/obo/FOODON_03420140) - - squash (whole, raw) - - - - - - - - - - A rice food product consisting of hulled rice kernels. - http://langual.org - SUBSET_SIREN:F1641 - rice - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* derives from 'seed (anatomical part)' (http://purl.obolibrary.org/obo/FOODON_03420155) -* formed as a result of 'water removal process' (http://purl.obolibrary.org/obo/FOODON_03460138) -* formed as a result of 'preservation by dehydration or drying' (http://purl.obolibrary.org/obo/FOODON_03470116) - - rice - rice kernel food product - - - - - - - - - - http://langual.org - SUBSET_SIREN:F1704 - onion - subset_siren - SIREN DB annotation: -* has quality 'solid' (http://purl.obolibrary.org/obo/FOODON_03430151) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'root, tuber or bulb, with peel' (http://purl.obolibrary.org/obo/FOODON_03420239) - - onion - onion (whole, raw) - onions - - - - - - - - - - http://langual.org - SUBSET_SIREN:F1705 - subset_siren - SIREN DB annotation: -* has quality 'liquid, low viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430123) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* formed as a result of 'alcohol-acetic acid fermentation process' (http://purl.obolibrary.org/obo/FOODON_03460123) -* formed as a result of 'curing or aging process' (http://purl.obolibrary.org/obo/FOODON_03460253) -* formed as a result of 'preservation by heat treatment' (http://purl.obolibrary.org/obo/FOODON_03470120) - - vinegar - vinegar - - - - - - - - - - - - - - - - - - - - A whole raw apple is an apple harvested from an apple tree. It may include a stem. It has not been subject to cooking or preservation processes other than cold storage or waxing. - Damion Dooley - http://langual.org - SUBSET_SIREN:F1710 - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'fruit, peel present, core, pit or seed present' (http://purl.obolibrary.org/obo/FOODON_03420140) - - apple (whole, raw) - - - - - - - - - - http://langual.org - SUBSET_SIREN:F1727 - celery - celery stalk - subset_siren - SIREN DB annotation: -* has quality 'solid' (http://purl.obolibrary.org/obo/FOODON_03430151) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'stem or stalk (without leaves)' (http://purl.obolibrary.org/obo/FOODON_03420101) - - celery - celery stalk (whole, raw) - - - - - - - - - - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F1774 - subset_siren - asparagus (raw) - - - - - - - - - - http://langual.org - SUBSET_SIREN:F1826 - subset_siren - SIREN DB annotation: -* has quality 'liquid, high viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430139) -* derives from 'fat or oil' (http://purl.obolibrary.org/obo/FOODON_03420190) - - olive oil - olive oil - https://static.oliveoiltimes.com/library/ioc-olive-oil-standard.pdf - - - - - - - - - - - - - - - - A spice mixture that is made from finely ground spices and is used for making curry. - http://langual.org - SUBSET_SIREN:F1842 - subset_siren - SIREN DB annotation: -* has quality 'finely ground' (http://purl.obolibrary.org/obo/FOODON_03430106) -* derives from 'fruit part' (http://purl.obolibrary.org/obo/FOODON_03420167) -* formed as a result of 'water removal process' (http://purl.obolibrary.org/obo/FOODON_03460138) -* formed as a result of 'preservation by dehydration or drying' (http://purl.obolibrary.org/obo/FOODON_03470116) -* has substance added 'flavoring, spice or herb added' (http://purl.obolibrary.org/obo/FOODON_03460227) - - curry powder - curry powder - - - - - - - - - - - A seasoning made from dried garlic flake that has been ground into a powder. - http://langual.org - - SUBSET_SIREN:F1844 - subset_siren - SIREN DB annotation: -* has quality 'finely ground' (http://purl.obolibrary.org/obo/FOODON_03430106) -* derives from 'root, tuber or bulb, without peel' (http://purl.obolibrary.org/obo/FOODON_03420240) -* formed as a result of 'water removal process' (http://purl.obolibrary.org/obo/FOODON_03460138) -* formed as a result of 'preservation by dehydration or drying' (http://purl.obolibrary.org/obo/FOODON_03470116) - - garlic powder - garlic powder - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F1848 - subset_siren - SIREN DB annotation: -* has quality 'liquid, high viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430139) -* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) -* derives from 'sugar syrup or syrup solids' (http://purl.obolibrary.org/obo/FOODON_03420271) -* formed as a result of 'water removal process' (http://purl.obolibrary.org/obo/FOODON_03460138) - - maple syrup - maple syrup - - - - - - - - - - - - - - - - - - - - http://langual.org - 2019-08-26T14:29:56Z - SUBSET_SIREN:F1886 - SUBSET_SIREN:F5599 - raw beef hamburger - subset_siren - SIREN DB annotation: -* has quality 'divided or disintegrated' (http://purl.obolibrary.org/obo/FOODON_03430122) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'skeletal meat part, without bone, without skin' (http://purl.obolibrary.org/obo/FOODON_03420268) - - ground beef (raw) - - - - - - - - - - A sandwich is a food typically consisting of vegetables, sliced cheese or meat, placed on or between slices of bread, or more generally any dish wherein two or more pieces of bread serve as a container or wrapper for another food type. - - http://langual.org - SUBSET_SIREN:F1906 - subset_siren - SIREN DB annotation: -* has quality 'whole, shape achieved by forming, thickness 1.5-7 cm.' (http://purl.obolibrary.org/obo/FOODON_03430105) -* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) -* formed as a result of 'food filling process' (http://purl.obolibrary.org/obo/FOODON_03460207) -* formed as a result of 'carbohydrate fermentation process' (http://purl.obolibrary.org/obo/FOODON_03460256) -* has substance added 'grain added' (http://purl.obolibrary.org/obo/FOODON_03460152) - - sandwich - - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F1924 - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) -* derives from 'fruit, peel present, core, pit or seed removed' (http://purl.obolibrary.org/obo/FOODON_03420139) -* formed as a result of 'food baking process' (http://purl.obolibrary.org/obo/FOODON_03450005) -* has substance added 'spice or herb added' (http://purl.obolibrary.org/obo/FOODON_03460151) -* has substance added 'sucrose added' (http://purl.obolibrary.org/obo/FOODON_03460158) - - apple (baked) - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F1940 - subset_siren - SIREN DB annotation: -* has quality 'finely ground' (http://purl.obolibrary.org/obo/FOODON_03430106) - - baking powder - baking powder - - - - - - - - - - - - - - - - A liquid prepared for consumption, or a product that can be combined with water or milk to make one. - Damion Dooley - http://langual.org - 2019-09-12T00:00:00 - beverage food product - - - - - - - - - - - - - - - - - - - - - - Fruit which has not been subjected to heat treatment, but which may have other mechanical processes such as slicing applied to it. - http://langual.org - SUBSET_SIREN:F2007 - subset_siren - SIREN DB annotation: -* has quality 'solid' (http://purl.obolibrary.org/obo/FOODON_03430151) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'fruit part' (http://purl.obolibrary.org/obo/FOODON_03420167) - - fruit (raw) - - - - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F2008 - subset_siren - SIREN DB annotation: -* has quality 'solid' (http://purl.obolibrary.org/obo/FOODON_03430151) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'part of plant' (http://purl.obolibrary.org/obo/FOODON_03420174) - - vegetable (raw) - - - - - - - - - - http://langual.org - SUBSET_SIREN:F2030 - subset_siren - SIREN DB annotation: -* has quality 'finely ground' (http://purl.obolibrary.org/obo/FOODON_03430106) -* derives from 'pod or seed' (http://purl.obolibrary.org/obo/FOODON_03420158) -* formed as a result of 'water removal process' (http://purl.obolibrary.org/obo/FOODON_03460138) -* formed as a result of 'preservation by dehydration or drying' (http://purl.obolibrary.org/obo/FOODON_03470116) - - chili powder - chili powder - - - - - - - - - - http://langual.org - SUBSET_SIREN:F2052 - subset_siren - SIREN DB annotation: -* has quality 'whole, shape achieved by forming, thickness <0.3 cm.' (http://purl.obolibrary.org/obo/FOODON_03430153) -* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) -* derives from 'seed (anatomical part)' (http://purl.obolibrary.org/obo/FOODON_03420155) -* formed as a result of 'salted' (http://purl.obolibrary.org/obo/FOODON_03460173) -* has substance added 'fat or oil added' (http://purl.obolibrary.org/obo/FOODON_03460221) - - corn chip - corn chips - - - - - - - - - - - http://langual.org - milk - SUBSET_SIREN:F2116 - cow milk - subset_siren - SIREN DB annotation: -* has quality 'liquid, low viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430123) -* derives from 'milk (mammary secretion)' (http://purl.obolibrary.org/obo/UBERON_0001913) - - cow milk (liquid) - milk - - - - - - - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F2386 - subset_siren - SIREN DB annotation: -* has quality 'liquid' (http://purl.obolibrary.org/obo/FOODON_03430130) -* derives from 'fruit, peel present, core, pit or seed present' (http://purl.obolibrary.org/obo/FOODON_03420140) - - lemon beverage - - - - - - - - - - http://langual.org - SUBSET_SIREN:F2458 - subset_siren - SIREN DB annotation: -* has quality 'solid' (http://purl.obolibrary.org/obo/FOODON_03430151) -* derives from 'curd' (http://purl.obolibrary.org/obo/FOODON_03420245) -* formed as a result of 'curing or aging process' (http://purl.obolibrary.org/obo/FOODON_03460253) -* formed as a result of 'interior bacteria curing process' (http://purl.obolibrary.org/obo/FOODON_03460328) - - Cheddar cheese - cheddar cheese - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F2515 - subset_siren - SIREN DB annotation: -* has quality 'semisolid with smooth consistency' (http://purl.obolibrary.org/obo/FOODON_03430119) -* has quality 'partially heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440018) -* derives from 'cream food product' (http://purl.obolibrary.org/obo/FOODON_00001216) -* formed as a result of 'lactic acid fermentation process' (http://purl.obolibrary.org/obo/FOODON_03460101) -* formed as a result of 'food homogenization or emulsification process' (http://purl.obolibrary.org/obo/FOODON_03460306) -* formed as a result of 'pasteurization by heating' (http://purl.obolibrary.org/obo/FOODON_03470135) - - sour cream - sour cream - - - - - - - - - - http://langual.org - SUBSET_SIREN:F2653 - subset_siren - SIREN DB annotation: -* has quality 'liquid, high viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430139) -* derives from 'fat or oil' (http://purl.obolibrary.org/obo/FOODON_03420190) - - cooking oil - cooking oil - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F2676 - subset_siren - SIREN DB annotation: -* has quality 'liquid, high viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430139) -* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) -* derives from 'sugar' (http://purl.obolibrary.org/obo/FOODON_03420108) -* has substance added 'flavoring or taste ingredient added' (http://purl.obolibrary.org/obo/FOODON_03460117) - - imitation maple sweetener - - - - - - - - - - http://langual.org - SUBSET_SIREN:F2695 - subset_siren - SIREN DB annotation: -* has quality 'sliced, thick, between 0.5 and 1.5 cm.' (http://purl.obolibrary.org/obo/FOODON_03430124) -* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) -* derives from 'seed, skin removed, germ removed (endosperm)' (http://purl.obolibrary.org/obo/FOODON_03420208) -* formed as a result of 'griddle cooking' (http://purl.obolibrary.org/obo/FOODON_03450008) -* formed as a result of 'carbohydrate fermentation process' (http://purl.obolibrary.org/obo/FOODON_03460256) -* has substance added http://purl.obolibrary.org/obo/FOODON_03460184 -* has substance added http://purl.obolibrary.org/obo/FOODON_03460186 -* has substance added 'flavoring, spice or herb added' (http://purl.obolibrary.org/obo/FOODON_03460227) - - French Toast - french toast - - - - - - - - - - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F2726 - subset_siren - SIREN DB annotation: -* has quality 'liquid, high viscosity' (http://purl.obolibrary.org/obo/FOODON_03430102) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'fat or oil' (http://purl.obolibrary.org/obo/FOODON_03420190) - - chili seed oil - - - - - - - - - - http://langual.org - SUBSET_SIREN:F2735 - subset_siren - SIREN DB annotation: -* has quality 'solid' (http://purl.obolibrary.org/obo/FOODON_03430151) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'skeletal meat part' (http://purl.obolibrary.org/obo/FOODON_03420175) - - pork (raw) - - - - - - - - - - - - - - - - A seed, fruit, root, bark, or other plant substance that is primarily used for flavouring or colouring food. - https://en.wikipedia.org/wiki/Spice - http://langual.org - SUBSET_SIREN:F3380 - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'part of plant' (http://purl.obolibrary.org/obo/FOODON_03420174) - - spice - - - - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F4007 - subset_siren - SIREN DB annotation: -* has quality 'liquid, high viscosity, with small particles' (http://purl.obolibrary.org/obo/FOODON_03430121) -* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) -* derives from 'fruit, peel present, core, pit or seed present' (http://purl.obolibrary.org/obo/FOODON_03420140) -* has substance added 'flavoring, spice or herb added' (http://purl.obolibrary.org/obo/FOODON_03460227) -* has substance added 'animal fat or oil added' (http://purl.obolibrary.org/obo/FOODON_03460262) - - enchilada sauce - enchilada sauce - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F4152 - subset_siren - SIREN DB annotation: -* has quality 'liquid, high viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430139) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'fat or oil' (http://purl.obolibrary.org/obo/FOODON_03420190) - - sesame oil - sesame oil - - - - - - - - - - A spice product which is a mixture of more than one spice. - https://en.wikipedia.org/wiki/Spice_mix - http://langual.org - https://orcid.org/0000-0001-8008-8249 - https://orcid.org/0000-0002-8844-9165 - https://orcid.org/0000-0002-9578-0788 - SUBSET_SIREN:F4292 - spice blend - spice mix - subset_siren - Spice mixes can be whole or in parts, but are most commonly blended spices or herbs. - -SIREN DB annotation: -* has quality 'whole and pieces' (http://purl.obolibrary.org/obo/FOODON_03430104) -* has substance added 'flavoring, spice or herb added' (http://purl.obolibrary.org/obo/FOODON_03460227) - spice mixture (whole or parts) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F4497 - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* derives from 'seed (anatomical part)' (http://purl.obolibrary.org/obo/FOODON_03420155) - - edible seed food product - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F4583 - subset_siren - SIREN DB annotation: -* has quality 'semiliquid with smooth consistency' (http://purl.obolibrary.org/obo/FOODON_03430135) -* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) -* derives from 'fruit, peel present, core, pit or seed present' (http://purl.obolibrary.org/obo/FOODON_03420140) -* formed as a result of 'acidified' (http://purl.obolibrary.org/obo/FOODON_03460200) -* has substance added 'spice or herb added' (http://purl.obolibrary.org/obo/FOODON_03460151) - - chili sauce - chili sauce - - - - - - - - - - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F4616 - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'shelled egg' (http://purl.obolibrary.org/obo/UBERON_0007379) - - hen egg (whole, shell on, raw) - - - - - - - - - - - - - - - - - - - Note that this allows for several kinds of fruit in one sample, e.g. "some fruit (whole,raw)" allows "apple (whole, raw)" and "orange (whole, raw)". - Damion Dooley - http://langual.org - SUBSET_SIREN:F4644 - fruit - fruits - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'fruit part' (http://purl.obolibrary.org/obo/FOODON_03420167) - - Fruit - fruit (whole, raw) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F4706 - subset_siren - SIREN DB annotation: -* has quality 'liquid, high viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430139) -* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) -* derives from 'sugar syrup or syrup solids' (http://purl.obolibrary.org/obo/FOODON_03420271) -* has substance added 'flavoring or taste ingredient added' (http://purl.obolibrary.org/obo/FOODON_03460117) - - imitation maple syrup - - - - - - - - - - - - - - - - - - - - - - - - - - - A food product derived from one or more turkey eggs. - Damion Dooley - http://langual.org - turkey egg food product - - - - - - - - - - - - - - - - http://langual.org - egg white - SUBSET_SIREN:F4840 - egg albumen food product - subset_siren - SIREN DB annotation: -* has quality 'liquid, high viscosity' (http://purl.obolibrary.org/obo/FOODON_03430102) -* derives from 'albumen' (http://purl.obolibrary.org/obo/UBERON_0008944) - - egg whites - hen egg white food product - - - - - - - - - - http://langual.org - SUBSET_SIREN:F5086 - lime - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'fruit, peel present, core, pit or seed present' (http://purl.obolibrary.org/obo/FOODON_03420140) - - lime (whole, raw) - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F5146 - subset_siren - SIREN DB annotation: -* has quality 'whole, shape achieved by forming, thickness 1.5-7 cm.' (http://purl.obolibrary.org/obo/FOODON_03430105) -* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) -* derives from 'fruit part' (http://purl.obolibrary.org/obo/FOODON_03420167) -* has substance added 'sugar or sugar syrup added' (http://purl.obolibrary.org/obo/FOODON_03460136) -* has substance added 'color added' (http://purl.obolibrary.org/obo/FOODON_03460150) -* immersed in 'packed in heavily sweetened liquid' (http://purl.obolibrary.org/obo/FOODON_03480012) - - imitation maraschino cherry - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F5263 - subset_siren - SIREN DB annotation: -* has quality 'liquid, high viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430139) -* derives from 'fat or oil' (http://purl.obolibrary.org/obo/FOODON_03420190) - - vegetable oil - vegetable oil - - - - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F5364 - subset_siren - SIREN DB annotation: -* formed as a result of 'sterilization by irradiation' (http://purl.obolibrary.org/obo/FOODON_03470113) - - food (irradiated) - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F5428 - subset_siren - SIREN DB annotation: -* has quality 'liquid, low viscosity' (http://purl.obolibrary.org/obo/FOODON_03430109) -* derives from 'fruit, peel present, core, pit or seed present' (http://purl.obolibrary.org/obo/FOODON_03420140) - - Lemon juice - lemon juice - lemon juice - - - - - - - - - - An hors d'oeuvre (French: hors-d'œuvre), appetizer or starter is a small dish served before a meal in European cuisine. Typically smaller than a main dish, an hors d'oeuvre is often designed to be eaten by hand. - Damion Dooley - https://en.wikipedia.org/wiki/Hors_d%27oeuvre - http://langual.org - SUBSET_SIREN:F5516 - appetizer - canapé - subset_siren - Appetizer - Appetizers - hors d'oeuvre - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F5609 - subset_siren - SIREN DB annotation: -* has quality 'liquid, low viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430123) -* has quality 'partially heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440018) -* derives from 'milk (mammary secretion)' (http://purl.obolibrary.org/obo/UBERON_0001913) -* formed as a result of 'pasteurization by heating' (http://purl.obolibrary.org/obo/FOODON_03470135) - - cow milk (pasteurized) - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F6160 - subset_siren - SIREN DB annotation: -* has quality 'liquid, low viscosity' (http://purl.obolibrary.org/obo/FOODON_03430109) -* derives from 'fruit, peel present, core, pit or seed present' (http://purl.obolibrary.org/obo/FOODON_03420140) - - lime juice - - - - - - - - - - http://langual.org - SUBSET_SIREN:F6255 - subset_siren - SIREN DB annotation: -* has quality 'sliced, thick, between 0.5 and 1.5 cm.' (http://purl.obolibrary.org/obo/FOODON_03430124) -* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) -* derives from 'seed (anatomical part)' (http://purl.obolibrary.org/obo/FOODON_03420155) -* formed as a result of 'food toasting process' (http://purl.obolibrary.org/obo/FOODON_03450010) -* formed as a result of 'water removal process' (http://purl.obolibrary.org/obo/FOODON_03460138) -* formed as a result of 'carbohydrate fermentation process' (http://purl.obolibrary.org/obo/FOODON_03460256) - - toast - toast - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F6347 - subset_siren - SIREN DB annotation: -* has quality 'whole, shape achieved by forming, thickness <0.3 cm.' (http://purl.obolibrary.org/obo/FOODON_03430153) -* derives from 'seed (anatomical part)' (http://purl.obolibrary.org/obo/FOODON_03420155) - - Pasta - pasta - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Damion Dooley - http://langual.org - 2019-06-15T02:12:40Z - SUBSET_SIREN:F16329 - SUBSET_SIREN:F6409 - subset_siren - SIREN DB annotation: -* has quality 'semisolid with smooth consistency' (http://purl.obolibrary.org/obo/FOODON_03430119) -* has quality 'partially heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440018) -* derives from 'fat or oil' (http://purl.obolibrary.org/obo/FOODON_03420190) -* formed as a result of 'acidified' (http://purl.obolibrary.org/obo/FOODON_03460200) -* formed as a result of 'food homogenization or emulsification process' (http://purl.obolibrary.org/obo/FOODON_03460306) - mayonnaise analog - - - - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F6429 - subset_siren - SIREN DB annotation: -* has quality 'solid' (http://purl.obolibrary.org/obo/FOODON_03430151) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'skeletal meat part' (http://purl.obolibrary.org/obo/FOODON_03420175) - - meat (raw) - - - - - - - - - - http://langual.org - SUBSET_SIREN:F6581 - subset_siren - SIREN DB annotation: -* has quality 'liquid, low viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430123) -* has quality 'partially heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440018) -* derives from 'milk (mammary secretion)' (http://purl.obolibrary.org/obo/UBERON_0001913) -* formed as a result of 'pasteurization by heating' (http://purl.obolibrary.org/obo/FOODON_03470135) - - cow whole milk (pasteurized) - - - - - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F6667 - subset_siren - SIREN DB annotation: -* has quality 'semisolid with smooth consistency' (http://purl.obolibrary.org/obo/FOODON_03430119) -* derives from 'fructose' (http://purl.obolibrary.org/obo/CHEBI_28757) -* has substance added 'nonnutritive sweetener added' (http://purl.obolibrary.org/obo/FOODON_03460108) -* has substance added 'flavoring or taste ingredient added' (http://purl.obolibrary.org/obo/FOODON_03460117) -* has consumer 'energy special claim or use' (http://purl.obolibrary.org/obo/FOODON_03510045) - - imitation maple syrup (artificially sweetened) - - - - - - - - - - http://langual.org - SUBSET_SIREN:F6726 - green bell pepper - green pepper - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* has quality 'unripe or immature' (http://purl.obolibrary.org/obo/FOODON_03530051) -* derives from 'pod containing small, immature seed' (http://purl.obolibrary.org/obo/FOODON_03420169) - - green bell pepper - sweet green pepper (whole, raw) - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F6944 - subset_siren - SIREN DB annotation: -* has quality 'whole, shape achieved by forming, thickness <0.3 cm.' (http://purl.obolibrary.org/obo/FOODON_03430153) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'seed, skin removed, germ removed (endosperm)' (http://purl.obolibrary.org/obo/FOODON_03420208) -* formed as a result of 'water removal process' (http://purl.obolibrary.org/obo/FOODON_03460138) -* formed as a result of 'preservation by dehydration or drying' (http://purl.obolibrary.org/obo/FOODON_03470116) -* has substance added http://purl.obolibrary.org/obo/FOODON_03460186 - - Noodles - noodle - noodles - - - - - - - - - - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F6952 - subset_siren - SIREN DB annotation: -* has quality 'whole, shape achieved by forming, thickness <0.3 cm.' (http://purl.obolibrary.org/obo/FOODON_03430153) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'seed, skin removed, germ removed (endosperm)' (http://purl.obolibrary.org/obo/FOODON_03420208) -* formed as a result of 'water removal process' (http://purl.obolibrary.org/obo/FOODON_03460138) -* formed as a result of 'preservation by dehydration or drying' (http://purl.obolibrary.org/obo/FOODON_03470116) - - imitation noodle - - - - - - - - - - - A Greek brined curd white cheese made from sheep's milk or from a mixture of sheep and goat's milk. - - http://langual.org - SUBSET_SIREN:F7280 - subset_siren - SIREN DB annotation: -* has quality 'solid' (http://purl.obolibrary.org/obo/FOODON_03430151) -* derives from 'curd' (http://purl.obolibrary.org/obo/FOODON_03420245) -* formed as a result of 'lactic acid-other agent fermentation process' (http://purl.obolibrary.org/obo/FOODON_03460107) - - feta cheese - feta cheese - - - - - - - - - - http://langual.org - SUBSET_SIREN:F7345 - subset_siren - SIREN DB annotation: -* has quality 'crystal' (http://purl.obolibrary.org/obo/FOODON_03430143) -* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) -* derives from 'white sugar' (http://purl.obolibrary.org/obo/FOODON_03420157) - - sugar (refined) - - - - - - - - - - - - - - - - - - - - - - http://langual.org - raw milk - SUBSET_SIREN:F7455 - milk - subset_siren - SIREN DB annotation: -* has quality 'liquid, low viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430123) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'milk (mammary secretion)' (http://purl.obolibrary.org/obo/UBERON_0001913) -* has consumer 'not pasteurized claim or use' (http://purl.obolibrary.org/obo/FOODON_03510121) - - cow milk (raw) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F7555 - subset_siren - SIREN DB annotation: -* has quality 'finely ground' (http://purl.obolibrary.org/obo/FOODON_03430106) -* derives from 'sugar' (http://purl.obolibrary.org/obo/FOODON_03420108) -* has substance added 'nonnutritive sweetener added' (http://purl.obolibrary.org/obo/FOODON_03460108) -* has consumer 'dietary claim or use' (http://purl.obolibrary.org/obo/FOODON_03510023) - - imitation sugar - - - - - - - - - - http://langual.org - SUBSET_SIREN:F9389 - subset_siren - Note - curators are implementing "whole or pieces" rather than "whole and pieces". -SIREN DB annotation: -* has quality 'whole and pieces' (http://purl.obolibrary.org/obo/FOODON_03430104) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'root, tuber or bulb' (http://purl.obolibrary.org/obo/FOODON_03420238) - carrot root (raw, whole or parts) - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F9462 - subset_siren - SIREN DB annotation: -* has quality 'liquid, low viscosity' (http://purl.obolibrary.org/obo/FOODON_03430109) -* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) -* derives from 'broth or stock' (http://purl.obolibrary.org/obo/FOODON_03420170) - - broth - broth - - - - - - - - - - - - - - - - - - - A meat part that has been cut from a large piece of meat and is too small to be sold individually. - https://www.merriam-webster.com/dictionary/meat%20scrap - http://langual.org - - SUBSET_SIREN:F9475 - meat scrap - meat trim - meat trim - subset_siren - SIREN DB annotation: -* has quality 'finely ground' (http://purl.obolibrary.org/obo/FOODON_03430106) -* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) -* derives from 'animal body or body part' (http://purl.obolibrary.org/obo/FOODON_03420127) -* formed as a result of 'cooking with inherent fat or oil' (http://purl.obolibrary.org/obo/FOODON_03450030) -* formed as a result of 'water removal process' (http://purl.obolibrary.org/obo/FOODON_03460138) -* formed as a result of 'partial fat removal process' (http://purl.obolibrary.org/obo/FOODON_03460247) -* formed as a result of 'preservation by dehydration or drying' (http://purl.obolibrary.org/obo/FOODON_03470116) -* has consumer 'animal as consumer' (http://purl.obolibrary.org/obo/FOODON_03510021) - - meat trimming - - - - - - - - - - - - - - - - - - - definition: Shrimp paste or shrimp sauce is a fermented condiment commonly used in Southeast Asian, Northeastern South Asian and Southern Chinese cuisines. - Need to set languages of synonyms (japanese/thai ?) - http://orcid.org/0000-0002-1816-4260 - - http://langual.org - SUBSET_SIREN:F9823 - shrimp sauce - bagoong alamang - bagoong aramang - belacan - belachan - blachang - hae ko - hom ha - kapi - mắm ruốc - mắm tép - mắm tôm - ngapi - sidol - terasi - subset_siren - SIREN DB annotation: -* has quality 'semisolid' (http://purl.obolibrary.org/obo/FOODON_03430144) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'whole animal or most parts used' (http://purl.obolibrary.org/obo/FOODON_03420173) -* formed as a result of 'fermentation/modification process, multiple component' (http://purl.obolibrary.org/obo/FOODON_03460128) -* formed as a result of 'water removal process' (http://purl.obolibrary.org/obo/FOODON_03460138) -* formed as a result of 'salted' (http://purl.obolibrary.org/obo/FOODON_03460173) -* formed as a result of 'preservation by fermentation' (http://purl.obolibrary.org/obo/FOODON_03470104) - - shrimp paste - - - - - - - - - - http://langual.org - SUBSET_SIREN:F9840 - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'root, tuber or bulb, with peel' (http://purl.obolibrary.org/obo/FOODON_03420239) - - ginger root (whole, raw) - - - - - - - - - - http://langual.org - SUBSET_SIREN:F10351 - subset_siren - SIREN DB annotation: -* has quality 'semisolid with smooth consistency' (http://purl.obolibrary.org/obo/FOODON_03430119) -* has quality 'partially heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440018) -* derives from 'butter' (http://purl.obolibrary.org/obo/FOODON_00001023) -* formed as a result of 'pasteurization by heating' (http://purl.obolibrary.org/obo/FOODON_03470135) - - butter - butter - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F10387 - subset_siren - SIREN DB annotation: -* has quality 'liquid, high viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430139) -* derives from 'fat or oil' (http://purl.obolibrary.org/obo/FOODON_03420190) - - oil - oil - - - - - - - - - - http://langual.org - SUBSET_SIREN:F10490 - ground ginger - subset_siren - SIREN DB annotation: -* has quality 'finely ground' (http://purl.obolibrary.org/obo/FOODON_03430106) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'root, tuber or bulb' (http://purl.obolibrary.org/obo/FOODON_03420238) -* formed as a result of 'water removal process' (http://purl.obolibrary.org/obo/FOODON_03460138) -* formed as a result of 'preservation by dehydration or drying' (http://purl.obolibrary.org/obo/FOODON_03470116) - - ginger (ground) - ground ginger - - - - - - - - - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F10573 - subset_siren - SIREN DB annotation: -* has quality 'whole, shape achieved by forming, thickness 1.5-7 cm.' (http://purl.obolibrary.org/obo/FOODON_03430105) -* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) -* has quality 'meat color, undesignated or unknown (deprecated)' (http://purl.obolibrary.org/obo/FOODON_03530003) -* derives from 'skeletal meat part, without bone, without skin' (http://purl.obolibrary.org/obo/FOODON_03420268) -* formed as a result of 'food baking process' (http://purl.obolibrary.org/obo/FOODON_03450005) -* formed as a result of 'food filling process' (http://purl.obolibrary.org/obo/FOODON_03460207) -* formed as a result of 'carbohydrate fermentation process' (http://purl.obolibrary.org/obo/FOODON_03460256) -* has substance added 'grain added' (http://purl.obolibrary.org/obo/FOODON_03460152) - - turkey sandwich - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A seed of a lentil plant (Lens culinaris). - http://orcid.org/0000-0002-8844-9165 - http://langual.org - SUBSET_SIREN:F10641 - lentil - subset_siren - lentil (whole) - lentils - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A seed of a legume plant in the family Fabaceae. - https://orcid.org/0000-0001-5275-8866 - http://langual.org - 2020-10-21T09:28:28 - SUBSET_SIREN:F10646 - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'seed (anatomical part)' (http://purl.obolibrary.org/obo/FOODON_03420155) - - legume (whole) - - - - - - - - - - http://langual.org - SUBSET_SIREN:F10710 - subset_siren - SIREN DB annotation: -* has quality 'whole, shape achieved by forming, thickness <0.3 cm.' (http://purl.obolibrary.org/obo/FOODON_03430153) -* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) -* derives from 'seed (anatomical part)' (http://purl.obolibrary.org/obo/FOODON_03420155) -* formed as a result of 'salted' (http://purl.obolibrary.org/obo/FOODON_03460173) -* formed as a result of 'food alkalization process' (http://purl.obolibrary.org/obo/FOODON_03460206) -* has substance added 'vegetable fat or oil added' (http://purl.obolibrary.org/obo/FOODON_03460263) - - Tortilla chips - tortilla chip - - - - - - - - - - http://langual.org - SUBSET_SIREN:F10780 - cow whole milk - whole milk - subset_siren - SIREN DB annotation: -* has quality 'liquid, low viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430123) -* has quality 'partially heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440018) -* derives from 'milk (mammary secretion)' (http://purl.obolibrary.org/obo/UBERON_0001913) -* formed as a result of 'pasteurization by heating' (http://purl.obolibrary.org/obo/FOODON_03470135) - - cow whole milk 3.5% fat - whole milk - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F10784 - subset_siren - SIREN DB annotation: -* has quality 'solid' (http://purl.obolibrary.org/obo/FOODON_03430151) -* derives from 'part of plant' (http://purl.obolibrary.org/obo/FOODON_03420174) -* formed as a result of 'microbial/enzymatic modification process' (http://purl.obolibrary.org/obo/FOODON_03460119) - - fermented vegetable food product - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A whole apple or some substance made from processed apple. - Damion Dooley - http://langual.org - SUBSET_SIREN:F10788 - apple - subset_siren - apple (whole or parts) - - - - - - - - - - - - - - - - - - - - - - - - - - - - Damion Dooley - http://langual.org - zucchini - SUBSET_SIREN:F10943 - green zucchini - zucchini squash - courgettes - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'fruit, peel present, core, pit or seed present' (http://purl.obolibrary.org/obo/FOODON_03420140) - - zucchini - zucchini squash (whole) - - - - - - - - - - A food product that has not been cooked. - http://langual.org - SUBSET_SIREN:F11126 - subset_siren - SIREN DB annotation: -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) - - food (raw) - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F11146 - subset_siren - SIREN DB annotation: -* has quality 'liquid' (http://purl.obolibrary.org/obo/FOODON_03430130) - - Sauces - sauce - sauce - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F11349 - asparagus - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'spear or shoot' (http://purl.obolibrary.org/obo/FOODON_03420186) - - asparagus - asparagus spear (whole, raw) - - - - - - - - - - http://langual.org - SUBSET_SIREN:F11353 - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'leaf' (http://purl.obolibrary.org/obo/FOODON_03420200) - - carrot top (raw) - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F11507 - subset_siren - SIREN DB annotation: -* has quality 'divided or disintegrated' (http://purl.obolibrary.org/obo/FOODON_03430122) -* derives from 'animal body or body part' (http://purl.obolibrary.org/obo/FOODON_03420127) - - pork trimming - - - - - - - - - - http://langual.org - SUBSET_SIREN:F11552 - subset_siren - SIREN DB annotation: -* has quality 'semisolid' (http://purl.obolibrary.org/obo/FOODON_03430144) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'part of plant' (http://purl.obolibrary.org/obo/FOODON_03420174) -* has substance added 'grain added' (http://purl.obolibrary.org/obo/FOODON_03460152) - - dough - dough - - - - - - - - - - http://langual.org - SUBSET_SIREN:F11737 - subset_siren - processed food product - - - - - - - - - - - - - - - - - - - - - - - - - - - A cumin food product is derived from the seed of a cumin plant. - Damion Dooley - http://langual.org - cumin - cumin food product - - - - - - - - - - - - - - - - snack - A snack is a small portion of food and generally eaten between meals. - Damion Dooley - - http://langual.org - SUBSET_SIREN:F15013 - subset_siren - snack food - - - - - - - - - - Hen egg substance is food material derived from a hen egg - http://langual.org - SUBSET_SIREN:F15102 - subset_siren - SIREN DB annotation: -* derives from 'egg' (http://purl.obolibrary.org/obo/FOODON_03420194) - - hen egg substance - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A hesperidium fruit of a lemon plant (Citrus limon) - http://langual.org - SUBSET_SIREN:F15104 - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* derives from 'fruit, peel present, core, pit or seed present' (http://purl.obolibrary.org/obo/FOODON_03420140) - - lemon (whole) - - - - - - - - - - http://langual.org - SUBSET_SIREN:F15150 - subset_siren - SIREN DB annotation: -* derives from 'milk (mammary secretion)' (http://purl.obolibrary.org/obo/UBERON_0001913) - - mammalian milk product - - - - - - - - - - A fish product is a home-made or commercially produced or retail or wholesale product containing substantial amounts of freshwater or saltwater fish and/or shellfish flesh. Note that this category should avoid items that mention a particular species of fish or shellfish. - Damion Dooley - http://langual.org - SUBSET_SIREN:F15173 - subset_siren - SIREN DB annotation: -* derives from 'skeletal meat part' (http://purl.obolibrary.org/obo/FOODON_03420175) - - fish product (unspecified species) - https://en.wikipedia.org/wiki/Fish_products - - - - - - - - - - http://langual.org - SUBSET_SIREN:F15259 - subset_siren - SIREN DB annotation: -* has quality 'whole, shape achieved by forming, thickness 0.3-1.5 cm.' (http://purl.obolibrary.org/obo/FOODON_03430140) -* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) -* derives from 'seed, skin removed, germ removed (endosperm)' (http://purl.obolibrary.org/obo/FOODON_03420208) -* formed as a result of 'griddle cooking' (http://purl.obolibrary.org/obo/FOODON_03450008) - - waffle - waffle - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F15272 - subset_siren - SIREN DB annotation: -* has quality 'whole, shape achieved by forming' (http://purl.obolibrary.org/obo/FOODON_03430147) -* derives from 'seed, skin removed, germ removed (endosperm)' (http://purl.obolibrary.org/obo/FOODON_03420208) -* has substance added 'sucrose added' (http://purl.obolibrary.org/obo/FOODON_03460158) - - pastry - pastry - - - - - - - - - - - - - - - - - - - - - - - - - - - - A whole vegetable or some substance made from a processed vegetable. - https://orcid.org/0000-0001-5275-8866 - https://en.wikipedia.org/wiki/Vegetable - 2022-04-13T09:20:12Z - vegetable - Vegetable - Vegetables - vegetable - vegetable (whole or parts) - - - - - - - - - - http://langual.org - SUBSET_SIREN:F15552 - juice - subset_siren - juice beverage - - - - - - - - - - http://langual.org - SUBSET_SIREN:F15614 - subset_siren - SIREN DB annotation: -* derives from 'fruit part' (http://purl.obolibrary.org/obo/FOODON_03420167) - - berry product - - - - - - - - - - http://langual.org - SUBSET_SIREN:F15615 - subset_siren - SIREN DB annotation: -* derives from 'fruit part' (http://purl.obolibrary.org/obo/FOODON_03420167) - - fruit food product - - - - - - - - - - http://langual.org - SUBSET_SIREN:F15708 - subset_siren - Condiments - condiment - - - - - - - - - - - - - - - - http://langual.org - yolk - SUBSET_SIREN:F15772 - subset_siren - SIREN DB annotation: -* derives from 'egg yolk' (http://purl.obolibrary.org/obo/UBERON_0007378) - - hen egg yolk food product - yolks - - - - - - - - - - The chili pepper is the fruit of plants from the genus Capsicum which are members of the nightshade family, Solanaceae. - Damion Dooley - https://en.wikipedia.org/wiki/Chili_pepper - http://langual.org - SUBSET_SIREN:F15873 - chile - chile pepper - chilli - chilli pepper - chīlli - green chili - green chilli pepper - red chili pepper - chili pod - green chilies - subset_siren - The color of the chili can vary depending on its harvest time. - -SIREN DB annotation: -* has quality 'solid' (http://purl.obolibrary.org/obo/FOODON_03430151) -* derives from 'fruit part' (http://purl.obolibrary.org/obo/FOODON_03420167) - chili pepper - - - - - - - - - - Is this red bell pepper entry different from "Sweet red bell pepper"? - http://langual.org - SUBSET_SIREN:F15874 - red bell pepper - subset_siren - SIREN DB annotation: -* has quality 'whole, shape achieved by forming, thickness 0.3-1.5 cm.' (http://purl.obolibrary.org/obo/FOODON_03430140) -* derives from 'pod or seed' (http://purl.obolibrary.org/obo/FOODON_03420158) - - red bell pepper (whole, raw) - red bell peppers - - - - - - - - - - - - - - - A food product that is highly seasoned minced meat and is encased in a skin in the shape of a cylinder. - https://en.wikipedia.org/wiki/Sausage - http://langual.org - - SUBSET_SIREN:F15904 - sausage - subset_siren - SIREN DB annotation: -* has quality 'whole, shape achieved by forming' (http://purl.obolibrary.org/obo/FOODON_03430147) -* derives from 'meat part of animal' (http://purl.obolibrary.org/obo/FOODON_03420103) -* has substance added 'flavoring, spice or herb added' (http://purl.obolibrary.org/obo/FOODON_03460227) - - sausage (whole) - - - - - - - - - - http://langual.org - SUBSET_SIREN:F16042 - subset_siren - Salad - salad - - - - - - - - - - An egg produced by a chicken hen. - http://langual.org - egg - SUBSET_SIREN:F16061 - chicken egg - hen egg - subset_siren - This term is ambiguous about whether shell remains on egg or not, i.e. this encompasses both an uncooked egg in shell, or a boiled peeled egg, or a fried egg. - -SIREN DB annotation: -* derives from 'whole egg' (http://purl.obolibrary.org/obo/FOODON_03420274) - Eggs - eggs - hen egg (whole) - - - - - - - - - - http://langual.org - SUBSET_SIREN:F16133 - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* derives from 'fruit, peel present, core, pit or seed removed' (http://purl.obolibrary.org/obo/FOODON_03420139) -* has substance added 'sugar or sugar syrup added' (http://purl.obolibrary.org/obo/FOODON_03460136) -* has substance added 'color added' (http://purl.obolibrary.org/obo/FOODON_03460150) -* has substance added 'flavoring, spice or herb added' (http://purl.obolibrary.org/obo/FOODON_03460227) - - cocktail cherry - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F16271 - subset_siren - SIREN DB annotation: -* derives from 'sugar' (http://purl.obolibrary.org/obo/FOODON_03420108) - - sugar product - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A bulb of an onion plant (Allium cepa). - https://orcid.org/0000-0001-5275-8866 - http://langual.org - 2020-10-21T05:43:41 - SUBSET_SIREN:F16347 - bulb onion - common onion - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* derives from 'root, tuber or bulb, with peel' (http://purl.obolibrary.org/obo/FOODON_03420239) - - onion (whole) - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F16449 - subset_siren - SIREN DB annotation: - - dough raising agent - - - - - - - - - - http://langual.org - SUBSET_SIREN:F16453 - subset_siren - seasoning substance - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A whole or processed walnut. - https://orcid.org/0000-0001-5275-8866 - https://en.wikipedia.org/wiki/Walnut - http://langual.org - - 2022-04-13T12:47:02Z - SUBSET_SIREN:F16466 - walnut - subset_siren - SIREN DB annotation: -* has quality 'solid' (http://purl.obolibrary.org/obo/FOODON_03430151) -* derives from 'seed (anatomical part)' (http://purl.obolibrary.org/obo/FOODON_03420155) - - walnut (whole or parts) - - - - - - - - - - http://langual.org - SUBSET_SIREN:F16490 - subset_siren - SIREN DB annotation: -* has quality 'finely ground' (http://purl.obolibrary.org/obo/FOODON_03430106) -* formed as a result of 'water removal process' (http://purl.obolibrary.org/obo/FOODON_03460138) -* formed as a result of 'preservation by dehydration or drying' (http://purl.obolibrary.org/obo/FOODON_03470116) - - seasoning, powdered - - - - - - - - - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F16563 - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* derives from 'fruit, peel present, core, pit or seed present' (http://purl.obolibrary.org/obo/FOODON_03420140) -* formed as a result of 'pickling process' (http://purl.obolibrary.org/obo/FOODON_03460190) -* has substance added 'sweetener added' (http://purl.obolibrary.org/obo/FOODON_03460202) - - gherkin pickle - http://www.differencebetween.net/object/comparisons-of-food-items/difference-between-gherkins-and-pickles/ - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F16579 - subset_siren - SIREN DB annotation: -* derives from 'part of plant' (http://purl.obolibrary.org/obo/FOODON_03420174) - - multi-component plant food product - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F16694 - subset_siren - SIREN DB annotation: -* derives from 'fat or oil' (http://purl.obolibrary.org/obo/FOODON_03420190) - - vegetable fat food product - - - - - - - - - - A meat product is a product organized by the form of - or processing done to - its meat component (a skeletal meat part of an animal or crustacean). - http://langual.org - SUBSET_SIREN:F17170 - subset_siren - SIREN DB annotation: -* derives from 'animal body or body part' (http://purl.obolibrary.org/obo/FOODON_03420127) - - meat (whole or parts) - - - - - - - - - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F17238 - subset_siren - SIREN DB annotation: -* has quality 'solid' (http://purl.obolibrary.org/obo/FOODON_03430151) -* derives from 'part of plant' (http://purl.obolibrary.org/obo/FOODON_03420174) - - spice (capsicum-based) - - - - - - - - - - http://langual.org - chili - chilli - SUBSET_SIREN:F17304 - subset_siren - SIREN DB annotation: -* has quality 'semisolid with solid pieces' (http://purl.obolibrary.org/obo/FOODON_03430134) -* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) -* has substance added 'spice or herb added' (http://purl.obolibrary.org/obo/FOODON_03460151) -* has substance added http://purl.obolibrary.org/obo/FOODON_03460191 -* has substance added http://purl.obolibrary.org/obo/FOODON_03460212 - - chili con carne with beans (dish, vegetarian) - chilis - - - - - - - - - - - http://langual.org - 2019-08-26T14:16:46Z - SUBSET_SIREN:F10762 - SUBSET_SIREN:F17336 - SUBSET_SIREN:F17337 - beef hamburger patty - beef patty - beefburger - subset_siren - SIREN DB annotation: -* has quality 'whole, shape achieved by forming' (http://purl.obolibrary.org/obo/FOODON_03430147) -* derives from 'skeletal meat part, without bone, without skin' (http://purl.obolibrary.org/obo/FOODON_03420268) - - ground beef patty - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F17492 - subset_siren - cheese analog, dairy-based - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F17654 - subset_siren - SIREN DB annotation: -* has quality 'liquid, high viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430139) -* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) -* derives from 'whole animal or most parts used' (http://purl.obolibrary.org/obo/FOODON_03420173) -* has substance added 'spice or herb added' (http://purl.obolibrary.org/obo/FOODON_03460151) -* has substance added 'grain added' (http://purl.obolibrary.org/obo/FOODON_03460152) -* has substance added http://purl.obolibrary.org/obo/FOODON_03460184 - - oyster sauce - oyster sauce - - - - - - - - - - Milk modified by adding acid-producing and/or flavor-producing bacteria under controlled conditions. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0101 - milk product, cultured - cultured milk product (us cfr) - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0102 - crepe, dinner - taco, prepared - prepared food product with bakery base or enclosure, unsweetened (us cfr) - - - - - - - - - - Liquid food prepared from fruit (21 CFR 146). Products prepared from fruit juice by thickening with pectin are indexed under *FRUIT JELLY*; those thickened with gelatin are under *FRUIT BUTTER, JELLY, PRESERVE OR RELATED PRODUCT*. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0104 - fruit juice or related product (us cfr) - - - - - - - - - - Seasoned product that contains multiple ingredients and that is used in limited amounts to accompany other foods; excludes flavors, spices and herbs. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0105 - condiment, dressing, gravy or sauce - gravy, condiment, dressing or sauce - sauce, condiment, dressing or gravy - dressing, condiment, gravy or sauce (us cfr) - - - - - - - - - - Food product prepared by drying and/or cooking a mixture of milled grain or non-grain starch with a liquid and usually other ingredients such as sweeteners or fats. Includes sweetened and unsweetened bakery products, macaroni or noodle products and breakfast cereals. Excludes *PUDDING, STARCH*, which is under *CUSTARD OR PUDDING*. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0106 - prepared grain or starch product (us cfr) - - - - - - - - - - Includes breads, crackers, pie or pizza crusts and pretzels. Excludes glazed, filled or frosted bakery products, which fall under *BAKERY PRODUCT, SWEETENED* and unsweetened filled products that fall under *PREPARED FOOD PRODUCT WITH BAKERY BASE OR ENCLOSURE, UNSWEETENED* or the appropriate narrower term. See 21 CFR for description of some subgroups. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0107 - crepe, unfilled - unfilled crepe - unsweetened bakery product - bakery product, unsweetened (us cfr) - - - - - - - - - - - - - - - - Beverage containing no more than 0.5% alcohol; it may be flavored, sweetened or carbonated; includes soft drinks and steeped beverages; excludes milk in all forms, fruit juices, diluted fruit juices and vegetable juices. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0112 - malt beverage, nonalcoholic - nonalcoholic beverage (us cfr) - - - - - - - - - - Aromatic or pungent plant product used whole or ground as a seasoning in food products. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0113 - herb or spice - spice or herb (us cfr) - - - - - - - - - - Natural cheese, cured or uncured, cheese product (which is further processed), or cheese product analog. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0115 - cheese or cheese product (us cfr) - - - - - - - - - - - A substance having greater than 2% of the caloric value of sucrose per equivalent unit of sweetening capacity. For example, the amount of such subtance having the sweetening capacity of 1 teaspoon of sucrose would have more than 0.4 calories (21 CFR 170.3(o)(21)). - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0118 - nutritive carbohydrate sweetener - sweetener, nutritive - nutritive sweetener (us cfr) - - - - - - - - - - Any form of whole or milled grain, prepared grain product or starch containing product derived from non-grain sources. [FDA CFSAN 1995] - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0125 - grain or starch product (us cfr) - - - - - - - - - - The liquid extracted or expressed from mature fruit with or without the application of heat. Includes concentrated juice and single-strength juice. If the single-strength juice is prepared from concentrate, then *WATER ADDED* should be used. Carbonated fruit juices are indexed by *FRUIT JUICE* or *FRUIT JUICE, DILUTED* and *CARBONATED* or the appropriate narrower term. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0127 - juice, fruit - fruit juice (us cfr) - - - - - - - - - - Food product having functional characteristics similar to those of cheese or cheese product; it may be nutritionally equivalent or inferior to the product it purports to resemble. The ingredients may or may not be milk-based. An example is a cheese-like product made from skim milk and vegetable oil. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0128 - cheese substitute - cheese, imitation - imitation cheese - cheese product analog (us cfr) - - - - - - - - - - Extract, concentrate or isolate derived from a food source through one or more refining steps (see *EXTRACT, CONCENTRATE OR ISOLATE OF PLANT OR ANIMAL*) and marketed as such. [FDA CFSAN 1995] - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0129 - refined or partially-refined food product (us cfr) - - - - - - - - - - Product that imparts or helps to impart a taste or aroma in food (21 CFR.170.3(n)(26). [FDA CFSAN 1995] - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0133 - seasoning or flavoring - flavoring or seasoning (us cfr) - - - - - - - - - - Includes cakes, cookies, pies, quick breads, doughnuts and related products, also bakery products that are glazed, frosted or have a sweetened filling. If sugar is not the first ingredient, *SUGAR OR SUGAR SYRUP ADDED* as well as *SWEETENER ADDED* (or the appropriate narrower term under each) should be indexed in *H. TREATMENT APPLIED*. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0135 - crepe, dessert - dessert crepe - sweetened bakery product - bakery product, sweetened (us cfr) - - - - - - - - - - Dressing for which no standards of identity are specified in the CFR. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0136 - nonstandardized dressing (us cfr) - - - - - - - - - - A multiple-component food product typically containing a protein source, a vegetable, and a potato, rice or cereal-based component packaged to be served after heating, either as separate items or courses or mixed as recipe components; see 21 CFR 102.26, 102.28 and 104.47 for nutritional quality guidelines. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0139 - compartmentalized dinner - dinner with components separated in serving containers - dinner, compartmentalized - food packs with separate components - heat and serve dinner - multiple-course dinner - tv dinner - multicomponent meal (us cfr) - - - - - - - - - - Fruit in all forms; includes fruit juices and fruit juice drinks, fruit butters, jellies, preserves, and related products. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0143 - pie filling, fruit - fruit or fruit product (us cfr) - - - - - - - - - - Milk in all forms, milk-based beverage, cultured milk product, or milk or milk product analog. Index infant formula under *MEAL REPLACEMENT*. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0148 - milk or milk product (us cfr) - - - - - - - - - - Food product prepared by milling a grain or by producing flour, meal or grits from a non-grain source such as beans, starchy roots or tubers. Refined starch is indexed under *REFINED OR PARTIALLY REFINED FOOD PRODUCT*. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0149 - milled grain or starch product (us cfr) - - - - - - - - - - Meat (flesh and organs including blood and bone marrow) from mammals. Used for meat in all forms including cured meat, sausage or luncheon meat and meat product analogs. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0150 - meat or meat product (from mammal) (us cfr) - - - - - - - - - - Vegetables in all forms except where a use-related product type descriptior (such as *PREPARED FOOD PRODUCT* or *SNACK FOOD*) takes precedence. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0152 - vegetable or vegetable product (us cfr) - - - - - - - - - - Milk, a product derived from milk, or a dairy product analog; includes cheese and frozen dairy desserts. [FDA CFSAN 1995] - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0164 - dairy product (us cfr) - - - - - - - - - - Natural cheese that is cured; includes cheeses that are normally consumed cured but may be sold in an uncured or very lightly cured stage. The classification of cured cheeses is based on the method of curing, the moisture content, and the milk fat content measured as the proportion of solids. Scope notes given for the general classes give moisture and milkfat proportions that cover the entire range specified in the CFR for the individual cheeses included in a class; the class definition given in the CFR section cited may be more restrictive. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0168 - cheese, cured - cured cheese (us cfr) - - - - - - - - - - Food product that is 1) ready or nearly ready for consumption; 2) usually a composite of several foods or ingredients that often belong to distinct product types; 3) usually formulated, mixed and partially or fully cooked. Prepared foods often undergo several of the processes listed in *F. EXTENT OF HEAT TREATMENT* and *H. TREATMENT APPLIED*; these factors should be carefully considered in indexing. The classification of prepared food products emphasizes consumption characteristics. [FDA CFSAN 1995] - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0172 - prepared dish - prepared food product (us cfr) - - - - - - - - - - Unsweetened bakery product that may be unleavened or yeast-leavened and may be baked in various forms. Excludes pie crust. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0178 - bun, roll, or bread - roll, bun, or bread - bread (us cfr) - - - - - - - - - - Food product that is usually pungent, tart, salty, or spicy and is used to enhance the flavors of other foods; includes catsup, relish, prepared mustard, prepared horseradish, and condiment sauces. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0179 - relish or condiment - condiment or relish (us cfr) - - - - - - - - - - Substance that is added to food or that is used to treat food and that becomes a component of the food or otherwise affects the functional or nutritional characteristics of the food; for purposes of this vocabulary it excludes products that fall under other categories, such as flavors and sweeteners. - Damion Dooley - FDA CFSAN 1995 - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0181 - food additive (us cfr) - - - - - - - - - - - - Natural cheese that is not cured or is cured for less than 7 days. It may undergo some further processing, such as creaming. It is consumed fresh and has a mild acid flavor. Moisture max. 80%. Includes such products as cottage cheese, cream cheese and mozzarella cheese. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0185 - soft cheese - uncured cheese (us cfr) - - - - - - - - - - Cured cheese ripened by bacteria. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0186 - LanguaL curation note: Used for cheeses, which contain not more than 39 percent of moisture, and their solids contain not less than 50 percent of milkfat [21 CFR Ch. I (4-1-99 Edition)] - hard cheese (us cfr) - - - - - - - - - - Cheese made from milk or milk components, such as cream, by the following process: (1) produce curd through coagulation of milk by bacterial action and/or enzymes and/or acidification and draining of whey. (2) For cured cheese only: cure the curd. Excludes products made through further processing, such as comminuting (see *CHEESE PRODUCT*). - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0187 - natural cheese (us cfr) - - - - - - - - - - Prepared grain product made by baking or frying. Includes doughs, batters and mixes. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0191 - bakery product (us cfr) - - - - - - - - - - A thin, sweetened bakery product griddled or cooked in a heated mold. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0194 - waffle or pancake - pancake or waffle (us cfr) - - - - - - - - - - A liquid food made by simmering meat, poultry, seafood or vegetables, being clear or thickened to the consistency of a thin puree or having milk or cream added, and often containing pieces of solid food such as meat, shellfish, pasta or vegetables. Soup takes precedence over other food products. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0198 - soup (us cfr) - - - - - - - - - - Sweetened bakery product consisting of a sweetened or unsweetened pastry shell or enclosure containing a sweetened filling, usually fruit, cheese or custard. Examples would be apple strudel, danish pastry or cream puff. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0202 - pastry, sweetened (us cfr) - - - - - - - - - - A combination of one or more vegetable, fruit, herb, meat, poultry, seafood, egg, cereal or pasta, usually served with some kind of moist dressing; may be molded with a jelling agent. Salad takes precedence over other product types. Examples are egg salad, tuna salad, mixed vegetable salad, jelled fruit salad and macaroni salad. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0208 - salad (us cfr) - - - - - - - - - - Natural or synthetic product, dissolved in a suitable solvent or carried on an appropriate dry base and added to a food product to enhance or impart taste and aroma. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0215 - aroma - flavoring (us cfr) - - - - - - - - - - Products of the flesh of animals. [FDA CFSAN 1995] - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0217 - meat, poultry, seafood or related product (us cfr) - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0218 - LanguaL curation note: Sandwich takes precedent over other product types. Examples: peanut butter and jelly sandwich, tuna sandwich, egg salad sandwich or hamburger on roll. The filling of a sandwich is always indexed as the food source, even if the bread is the same weight or outweighs the filling ingredient(s). The bread would be indexed by *GRAIN ADDED* or the appropriate narrower term. - sandwich (us cfr) - - - - - - - - - - This category includes a wide variety of products made from comminuted or chopped meat (skeletal and/or organ meat) that is usually salted and/or seasoned and often stuffed in an edible or inedible casing. Includes products such as pork sausage, pickle or pimiento loaf, meat spread and pate, and products made by binding meat chunks with gelatin or other binders, such as sectioned and formed ham, beef rolls, and headcheese. Excludes plain ground meat, meat loaf and products made by slicing intact muscle or other tissue, even if packaged and marketed like luncheon meat. Index all processes applied to the product at hand; examples: *FULLY HEAT TREATED*, *CURED FOR 2 MONTHS*, *SMOKED*, *FERMENTED*, *EMULSIFIED OR HOMOGENIZED*. Also consider *PARTICLE SIZE IN SOLID FORMED PRODUCTS* and *TYPEOF SAUSAGE CASING* in *Z. ADJUNCT CHARACTERISTICS OF FOOD*. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0221 - luncheon meat - sausage or luncheon meat (us cfr) - - - - - - - - - - Unsweetened food product marketed for consumption between meals; excludes nuts, edible seeds, and sweetened products such as cakes, puddings and candies. [FDA CFSAN 1995] - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0228 - snack food (us cfr) - - - - - - - - - - - - - - - - - - - - - - - - Alcoholic or nonalcoholic beverage; excludes milk and milk-based beverages, fruit juices and fruit juice drinks, and vegetable juices. [FDA CFSAN 1995] - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0229 - beverage (us cfr) - - - - - - - - - - A product added to a food item to achieve some degree of sweet taste; it may be nutritive or nonnutritive. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0237 - sweetener (us cfr) - - - - - - - - - - A soup in which the liquid phase has low viscosity. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0243 - bouillon - consomme - soup, thin (us cfr) - - - - - - - - - - Fruits and vegetables in all forms. [FDA CFSAN 1995] - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0257 - fruit or vegetable product (us cfr) - - - - - - - - - - Nuts in all forms, including nut butters and pastes. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0260 - nut or nut product (us cfr) - - - - - - - - - - Fresh egg in shell, liquid, frozen, dried egg or egg component, or egg product analog. Includes boiled, poached, scrambled, and fried eggs. Excludes prepared egg dishes, such as omelettes. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0261 - egg or egg product (us cfr) - - - - - - - - - - Pourable condiment that is usually applied after the food is prepared but can also be used in cooking. Examples are soy sauce, pepper sauce or barbeque sauce. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0263 - sauce, condiment - condiment sauce (us cfr) - - - - - - - - - - The liquid extracted or expressed from mature vegetables with or without optional ingredients such as seasoning or salt. Products prepared from vegetable juice by thickening with gelatin or pectin are indexed under the broader term *VEGETABLE OR VEGETABLE PRODUCT*. For part or portion, index the part or the plant from which the juice was extracted, rather than *PLANT EXTRACT, CONCENTRATE, OR ISOLATE*. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0264 - juice, vegetable - vegetable juice (us cfr) - - - - - - - - - - Flesh from fish or shellfish. Includes seafood product analogs and seafood-based sausage or luncheon meat as well as such products as squid ink and clam juice. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0267 - seafood or seafood product (us cfr) - - - - - - - - - - Vegetable product prepared by immersing vegetable in a brine or an acid solution. Often this treatment induces fermentation and/or other changes in the product. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0271 - pickle, vegetable - vegetable pickle (us cfr) - - - - - - - - - - Meat (flesh and organs including blood and bone marrow) from poultry. Used for poultry meat in all forms including poultry product analogs and poultry-based sausage or luncheon meat. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0273 - poultry or poultry product (us cfr) - - - - - - - - - - A prepared grain or starch product made by forming units of dough composed of one or more flours, water and other ingredients. Macaroni, spaghetti and vermicelli may have *EGG WHITE ADDED*, but not egg yolk. Noodles, egg macaroni, egg spaghetti and egg vermicelli have *EGG YOLK ADDED* and should be so indexed. This refers to macaroni or noodles used as ingredients; excludes *PASTA DISH*, which is found under *PREPARED FOOD PRODUCT* (21 CFR 139). - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0275 - macaroni or noodle product (us cfr) - - - - - - - - - - Standardized or nonstandardized mixture of edible fats or oils, acidifying agents and optional ingredients such as sweeteners (nutritive or nonnutritive), starch, egg and seasonings. Used in limited amounts to accompany salads and other foods. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0276 - food dressing - dressing for food (us cfr) - - - - - - - - - - Nonstandardized food product used as a meal accompaniment and consisting of a mixture of fats or oils, starch, liquid and other optional ingredients specified by the recipe; excludes condiment sauce (q.v.) and tomato or spaghetti sauce, which are vegetable products. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0286 - sauce or gravy - gravy or sauce (us cfr) - - - - - - - - - - Food group having common consumption, functional or manufacturing characteristics, e.g. *FRUIT OR VEGETABLE PRODUCT*, *DAIRY PRODUCT*, *CONFECTIONARY*, *PREPARED FOOD PRODUCT*, etc. [FDA CFSAN 1995] - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0289 - LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term. - USA agency food product type - - - - - - - - - - Dressing for which standards of identity are specified in the CFR. Includes french dressing (21 CFR 169.115), mayonnaise (21 CFR 169.140) and salad dressing (21 CFR 169.150). - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0292 - standardized dressing (us cfr) - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0300 - flavor enhancer or flavoring - flavoring or flavor enhancer (us cfr) - - - - - - - - - - An acetic acid-containing liquid. Used as condiment or preservative in cooking, pickling and salad dressing preparation; may be flavored with herbs, vegetables or fruits. Natural vinegar is made by fermenting cider, wine, etc. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0302 - vinegar (us cfr) - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0306 - nut or seed product (us cfr) - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0316 - cheese hardness class (us cfr) - - - - - - - - - - An agency food product type is a class of food product defined by an agency or consortium. - Damion Dooley - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0361 - This class is designed to hold 3rd party food classification schemes which are being mapped to FoodOn classes using the 'has member' relation. The two hierarchies are not melded into a subclass polyhierarchy because of possible logical inconsistencies in the agency schemes. The hierarchies of agency schemes are as true to their agency representation as possible. - agency food product type - - - - - - - - - - Food and Drugs, title 21, Code of Federal Regulations. Original food classification in LanguaL. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A1270 - LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term. - U.S. code of federal regulations, title 21 food product type - https://www.ecfr.gov/cgi-bin/text-idx?SID=87f720ce0d0b6c4548f4bbfd1f8e4c3d&mc=true&tpl=/ecfrbrowse/Title21/21chapterI.tpl - - - - - - - - - Examples of stem vegetables are kohlrabi, celery, fennel and rhubarb. Examples of shoot vegetables are asparagus, hop, bamboo shoots and taugé. - - A vegetable having shoot or stem which can be cooked and eaten. - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1005 - shoot vegetable - spear vegetable - stem or spear vegetable plant - - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1006 - fruit plant used as vegetable - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1009 - polysaccharide-producing plant - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1012 - sugar-producing plant - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1013 - plant used for producing extract or concentrate - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1016 - starch-producing plant - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1017 - oil-producing plant - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1018 - vegetable-producing plant, root, tuber or bulb - - - - - - - - - - - - - - - - - - - An aquatic animal is an animal, either vertebrate or invertebrate, which lives in the water for most or all of its lifetime. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1021 - This is equivalent to: - -'fish (food source)' or 'shellfish (food source)' or 'crustacean (food source)' or 'echinoderm (food source)' or 'coelenterate (food source)' - -However, this disjunction appears to be a burden on reasoners, and so this is currently not implemented. - fish or lower water animal - - - - - - - - - - Any chemical or chemical mixture that exists in a food material or was added to a food material. - http://langual.org - - http://www.langual.org/langual_thesaurus.asp?termid=B1041 - LanguaL curation note: A chemical food component is a food substance derived from a nonliving source (e.g., salt, water or synthesized compounds). - -Note however that the LanguaL category includes additives which may be naturally derived, such as agar. - chemical food component - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1047 - grain or seed-producing plant - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1048 - carbohydrate-producing plant - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1057 - vegetable-producing plant, above-ground parts - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1058 - vegetable-producing plant, most parts - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1062 - temperate-zone nut producing plant - - - - - - - - - - A lime is a hybrid citrus fruit, which is typically round, lime green, 3-6 centimetres (1.2-2.4 in) in diameter, and contains acidic juice vesicles. There are several species of citrus trees whose fruits are called limes, including the Key lime (*Citrus aurantifolia*), Persian lime, kaffir lime, and desert lime. Limes are a rich source of vitamin C, sour and are often used to accent the flavours of foods and beverages. They are grown year-round. Plants with fruit called "limes" have diverse genetic origins; limes do not form a monophyletic group. [https://en.wikipedia.org/wiki/Lime_(fruit)] - http://langual.org - GRIN:10683 - ITIS:506403 - MANSFELD:7576 - PLANTS:CIAU7 - http://eol.org/pages/4414 - http://www.langual.org/langual_thesaurus.asp?termid=B1067 - Citrus aurantiifolia (Christm. & Panz.) Swingle - Citrus aurantiifolia (Christm.) Swingle - Citrus ×aurantiifolia (Christm.) Swingle (pro sp.) - citrus aurantiifolia - citrus medica var. acida - indian lime - key lime - sour lime - lime (citrus) plant - - - - - - - - - - Mammals (from Latin mamma "breast") are vertebrate animals constituting the class Mammalia, and characterized by the presence of mammary glands which in females produce milk for feeding (nursing) their young, a neocortex (a region of the brain), fur or hair, and three middle ear bones. - Damion Dooley - https://en.wikipedia.org/wiki/Mammal - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1134 - mammal - - - - - - - - - - - - - - - - Suidae is a family of artiodactyl mammals which are commonly called pigs, hogs or boars. - Damion Dooley - https://en.wikipedia.org/wiki/Suidae - http://langual.org - In addition to numerous fossil species, 17 extant species are currently recognized (or 18 counting domestic pigs and wild boars separately), classified into between four and eight genera. The family includes the domestic pig, Sus scrofa domesticus or Sus domesticus, in addition to numerous species of wild pig, such as babirusas and warthogs. All suids, or swine, are native to the Old World, ranging from Asia to Europe and Africa. [Wikipedia] - - ITIS:180722 - MSW3:14200054 - http://eol.org/pages/328663 - http://www.langual.org/langual_thesaurus.asp?termid=B1136 - porcine - sus domesticus - sus scrofa - sus scrofa domesticus - Sus scrofa Linnaeus, 1758 - hog - pig - swine - - - - - - - - - - - Rutaceae, commonly known as the rue or citrus family, is a family of flowering plants, usually placed in the order Sapindales. -Citrus is a common term and genus (*Citrus*) of flowering plants in the rue family, *Rutaceae*. Citrus is believed to have originated in the part of Southeast Asia bordered by Northeastern India, Myanmar (Burma) and the Yunnan province of China. Citrus fruit has been cultivated in an ever-widening area since ancient times; the best-known examples are the oranges, lemons, grapefruit, and limes. - WIKIPEDIA:Rutaceae - http://langual.org - http://eol.org/pages/4414 - http://www.langual.org/langual_thesaurus.asp?termid=B1139 - rutaceae - citrus family - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1140 - fruit-producing plant - - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1141 - white pepper - white pepper plant - - - - - - - - - - - - - - - - - - - Aquatic animals other than fish and shellfish - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1142 - aquatic invertebrate animal (excluding shellfish) - - - - - - - - - - A legume is a plant or its fruit or seed in the family *Fabaceae* (or *Leguminosae*). Legumes are grown agriculturally, primarily for their grain seed called pulse, for livestock forage and silage, and as soil-enhancing green manure. Well-known legumes include alfalfa, clover, peas, beans, chickpeas, lentils, lupin bean, mesquite, carob, soybeans, peanuts and tamarind. [https://en.wikipedia.org/wiki/Legume] - http://langual.org - http://eol.org/pages/4277 - http://www.langual.org/langual_thesaurus.asp?termid=B1156 - fabaceae - pod or seed vegetable plant - - - - - - - - - - http://langual.org - GRIN:1227 - MANSFELD:7306 - http://www.langual.org/langual_thesaurus.asp?termid=B1167 - Acer saccharum Marsh. - sugar maple plant - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1174 - edible seed producing plant - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1179 - flavor-producing plant - herb-producing plant - spice or flavor-producing plant - - - - - - - - - - Winter squash is an annual fruit representing several squash species within the genus Cucurbita. It differs from summer squash in that it is harvested and eaten in the mature fruit stage when the seeds within have matured fully and the skin has hardened into a tough rind. At this stage, most varieties of this fruit can be stored for use during the winter. - - http://langual.org - - http://www.langual.org/langual_thesaurus.asp?termid=B1189 - curcurbita - winter squash - Cucurbita moschata - Cucurbita pepo - cucurbita maxima - winter squash plant - - - - - - - - Californiacondor - - - - - - - - - - http://langual.org - GRIN:12606 - MANSFELD:4153 - http://www.langual.org/langual_thesaurus.asp?termid=B1190 - Cucurbita pepo L. - cucurbita pepo - yellow crookneck squash - yellow squash - summer squash plant - - - - - - - - - - http://langual.org - GRIN:28589 - MANSFELD:9964 - http://www.langual.org/langual_thesaurus.asp?termid=B1191 - Piper nigrum L. - black pepper - malabar black pepper - black pepper plant - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1194 - head vegetable plant - - - - - - - - - - - - - - - - - - - - - A dairy cow is an adult female member of a dairy cattle breed - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1201 - cow - domesticated cattle - dairy cow - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1208 - squash plant - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1213 - nut producing plant - - - - - - - - - - - Fish are the gill-bearing aquatic craniate animals that lack limbs with digits. Most fish are ectothermic ("cold-blooded"), allowing their body temperatures to vary as ambient temperatures change, though some of the large active swimmers like white shark and tuna can hold a higher core temperature. - Damion Dooley - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1222 - fish - fish - - - - - - - - - - - Oyster is the common name for a number of different families of salt-water bivalve molluscs that live in marine or brackish habitats. In some species the valves are highly calcified, and many are somewhat irregular in shape. -True oysters are members of the family *Ostreidae*. This family includes the edible oysters, which mainly belong to the genera *Ostrea, Crassostrea, Ostreola, Magallana, Saccostrea*. Pearl oysters are not closely related to true oysters, being members of a distinct family, the feathered oysters (*Pteriidae*). - Damion Dooley - https://en.wikipedia.org/wiki/Oyster - http://langual.org - http://eol.org/pages/2267 - http://www.langual.org/langual_thesaurus.asp?termid=B1224 - ostreidae - crassostrea spp. - ostrea spp. - pteriidae - oyster - - - - - - - - - - - http://langual.org - GRIN:33749 - ITIS:505186 - MANSFELD:10138 - PLANTS:SEOR4 - http://eol.org/pages/4428 - http://www.langual.org/langual_thesaurus.asp?termid=B1226 - simsim - Sesamum indicum L. - Sesamum orientale L. - sesamum indicum - sesamum orientale - sesame plant - - - - - - - - - - A berry is a small, pulpy, and often edible fruit. Berries are typically juicy, rounded, brightly colored, sweet or sour, and do not have a stone or pit, although many pips or seeds may be present. Common examples are strawberries, raspberries, blueberries, red currants, and blackcurrants. - The scientific usage of the term "berry" differs from common usage. In scientific terminology, a berry is a fruit produced from the ovary of a single flower in which the outer layer of the ovary wall develops into an edible fleshy portion (pericarp). The definition includes many fruits that are not commonly known as berries, such as grapes, tomatoes, cucumbers, eggplants (aubergines) and bananas. Fruits excluded by the botanical definition include strawberries, raspberries, and blackberries, which are aggregate fruits, and mulberries, which are multiple fruits. [https://en.wikipedia.org/wiki/Berry] - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1231 - berry plant - - - - - - - - - - - - - - - - - http://langual.org - - GRIN:311987 - ITIS:42269 - MANSFELD:36372 - PLANTS:ZEMA - http://eol.org/pages/1115259 - http://www.langual.org/langual_thesaurus.asp?termid=B1232 - Zea mays L. - maize - zea mays - LanguaL curation note: Use 'field corn' for any breakfast cereals or snack foods having 'corn' as the main ingredient. - Zia mays plant - - - - - - - - - - - - - - - - The turkey is a large bird in the genus Meleagris, which is native to the Americas. Males of both turkey species have a distinctive fleshy wattle or protuberance that hangs from the top of the beak (called a snood). They are among the largest birds in their ranges. As in many galliformes, the male is larger and much more colorful than the female. - - http://langual.org - http://eol.org/pages/18523 - http://www.langual.org/langual_thesaurus.asp?termid=B1236 - turkey - meleagris spp. - turkey (bird) - - - - - - - - - - http://langual.org - http://eol.org/pages/2602479 - http://www.langual.org/langual_thesaurus.asp?termid=B1237 - caridea - crangonidae - palaemondidae - penaeidae - prawn - Shrimp - shrimp - - - - - - - - - - - - - - - - - - - - - - - An apple tree (Malus pumila species in genus Malus), is cultivated worldwide as a fruit tree, providing sweet, edible fruit. Malus pumila encompasses over 7,500 apple cultivars (https://en.wikipedia.org/wiki/List_of_apple_cultivars). - https://en.wikipedia.org/wiki/Apple - http://langual.org - GRIN:104681 - MANSFELD:8860 - http://eol.org/pages/8097 - http://www.langual.org/langual_thesaurus.asp?termid=B1245 - Malus domestica Borkh. - malus communis - malus domestica - pyrus malus - Malus pumila encompasses over 7,500 apple cultivars (https://en.wikipedia.org/wiki/List_of_apple_cultivars). - apple tree - - - - - - - - - - - - The taxonomies given vary widely. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1250 - capsicum - capsicum annuum - green or red pepper plant - - - - - - - - - - *Mentha* is a genus of plants in the family *Lamiaceae* (mint family). It is estimated that 13 to 18 species exist, and the exact distinction between species is still unclear. Hybridization between some of the species occurs naturally. The genus has a subcosmopolitan distribution across Europe, Africa, Asia, Australia, and North America. Mints are aromatic, almost exclusively perennial, rarely annual herbs. [https://en.wikipedia.org/wiki/Mentha] - http://langual.org - GRIN:313210 - PLANTS:MENTH - http://eol.org/pages/4302 - http://www.langual.org/langual_thesaurus.asp?termid=B1267 - Mentha - Mentha L. - Mentha spp. - mentha spp. - mint plant - - - - - - - - - - http://langual.org - GRIN:21739 - MANSFELD:30720 - http://www.langual.org/langual_thesaurus.asp?termid=B1268 - Lens culinaris Medik. - lens culinaris - lentil plant - - - - - - - - - - http://langual.org - GRIN:12617 - MANSFELD:1199 - http://www.langual.org/langual_thesaurus.asp?termid=B1274 - Cuminum cyminum L. - cuminum cyminum - cumin plant - - - - - - - - - - - The lemon, *Citrus limon *(L.) Osbeck, is a species of small evergreen tree in the flowering plant family Rutaceae, native to Asia. The tree's ellipsoidal yellow fruit is used for culinary and non-culinary purposes throughout the world, primarily for its juice, which has both culinary and cleaning uses. The pulp and rind (zest) are also used in cooking and baking. The juice of the lemon is about 5% to 6% citric acid, with a pH of around 2.2, giving it a sour taste. The distinctive sour taste of lemon juice makes it a key ingredient in drinks and foods such as lemonade and lemon meringue pie. [https://en.wikipedia.org/wiki/Lemon] - http://langual.org - GRIN:10732 - ITIS:28885 - MANSFELD:7625 - PLANTS:CILI5 - http://eol.org/pages/4414 - http://www.langual.org/langual_thesaurus.asp?termid=B1275 - Citrus limon (L.) Burm. f. - Citrus limon (L.) Burm. fil. - Citrus ×limon (L.) Burm. f. (pro sp.) - citrus limon - citrus medica var. limonum - lemon plant - - - - - - - - - - - - - - - - - The word "tomato" may refer to the plant (*Solanum lycopersicum*) or the edible, typically red, fruit that it bears. Originating in South America, the tomato was spread around the world following the Spanish colonization of the Americas, and its many varieties are now widely grown, often in greenhouses in cooler climates.See also the list of tomato cultivars - WIKIPEDIA:List_of_tomato_cultivars - http://langual.org - - GRIN:101442 - ITIS:521671 - ITIS:529044 - MANSFELD:6054 - PLANTS:SOLY2 - http://eol.org/pages/392557 - http://www.langual.org/langual_thesaurus.asp?termid=B1276 - Lycopersicon esculentum Mill. - Lycopersicon esculentum var. esculentum P. Mill. - Solanum lycopersicum L. - gold apple - love apple - lycopersicon esculentum - lycopersicon lycopersicum - solanum lycopersicum - tomato plant - - - - - - - - - - - Kale (also called Borecole) is a form of cabbage (*Brassica oleracea* Acephala Group) in which the central leaves do not form a head. It is considered to be closer to wild cabbage than most domesticated forms. The species *Brassica oleracea* contains a wide array of vegetables, including broccoli, cauliflower, and Brussels sprouts. The Cultivar Group Acephala also includes spring greens and collard greens, which are extremely similar genetically. Kale can be classified by leaf type: Curly leaved (Scots kales), Plain leaved, Rape kale, Leaf and spear (a cross between curly leaved and plain leaved kale), Cavolo nero (also known as black cabbage, Tuscan kale, Lacinato and dinosaur kale) - WIKIPEDIA:Kale) - http://langual.org - - GRIN:319629 - ITIS:23062 - MANSFELD:23870 - http://eol.org/pages/583899 - http://www.langual.org/langual_thesaurus.asp?termid=B1281 - Brassica oleracea L. - Brassica oleracea L. var. sabellica L. - Brassica oleracea var. sabellica L. - brassica oleracea - cole - kale plant - - - - - - - - - - A vertebrate animal is any species of organism within the subphylum Vertebrata (chordates with backbones). Vertebrates represent the overwhelming majority of the phylum Chordata, with currently about 69,276 species described. - Damion Dooley - - http://langual.org - animal - http://www.langual.org/langual_thesaurus.asp?termid=B1297 - LanguaL curation note: For a unicellular animal, use *ALGAE OR FUNGUS USED AS FOOD SOURCE*. - vertebrate animal - - - - - - - - - - - http://langual.org - GRIN:25555 - MANSFELD:11672 - http://www.langual.org/langual_thesaurus.asp?termid=B1299 - Olea europaea L. - manzanilla olive - olea europaea - olive plant - - - - - - - - - - - - The onion (*Allium cepa *L), also known as the bulb onion or common onion, is a vegetable that is the most widely cultivated species of the genus *Allium*. Its close relatives include the garlic, shallot, leek, chive,[2] and Chinese onion. - This genus also contains several other species variously referred to as onions and cultivated for food, such as the Japanese bunching onion (*Allium fistulosum*), the tree onion (*A. ×proliferum*), and the Canada onion (*Allium canadense*). The name "wild onion" is applied to a number of *Allium* species, but *A. cepa* is exclusively known from cultivation. [https://en.wikipedia.org/wiki/Onion] - http://langual.org - GRIN:300022 - PLANTS:ALLIU - http://eol.org/pages/8187 - http://www.langual.org/langual_thesaurus.asp?termid=B1300 - Allium - Allium L. - Allium sp. - allium spp. - bulb onion - cebolla - garden onion - onion plant - - - - - - - - - - - Wheat (*Triticum* spp.) is a domesticated grass from the Levant that is cultivated worldwide. Major cultivated species of wheat: - - * Common wheat or Bread wheat (*Triticum aestivum*) A hexaploid species that is the most widely cultivated in the world. - - * Durum (*Triticum durum*) The only tetraploid form of wheat widely used today, and the second most widely cultivated wheat. - - * Einkorn (*Triticum monococcum*) A diploid species with wild and cultivated variants. Domesticated at the same time as emmer wheat, but never reached the same importance. - - * Emmer (*Triticum dicoccon*) A tetraploid species, cultivated in ancient times but no longer in widespread use. - - * Spelt (*Triticum spelta*) Another hexaploid species cultivated in limited quantities. - WIKIPEDIA:Wheat - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1312 - triticum spp. - wheat plant - - - - - - - - - - - - - - - - *Oryza sativa*, commonly known as Asian rice, is the plant species most commonly referred to in English as rice. *Oryza sativa* contains two major subspecies: the sticky, short-grained *japonica* or *sinica* variety, and the nonsticky, long-grained *indica* variety. - http://langual.org - GRIN:26077 - ITIS:41976 - MANSFELD:20986 - PLANTS:ORSA - http://eol.org/pages/1115098 - http://www.langual.org/langual_thesaurus.asp?termid=B1322 - lowland rice - upland rice - Rice occurs in a variety of colors, including white, brown, black, purple, and red rices. Black rice (also known as purple rice) is a range of rice types, some of which are glutinous rice. Varieties include Indonesian black rice and Thai jasmine black rice. - rice plant - - - - - - - - - - Any grass cultivated (grown) for the edible components of its grain. - Damion Dooley - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1324 - grain plant - - - - - - - - - - - - *Vitis* (grapevines) is a genus of 79 accepted species of vining plants in the flowering plant family *Vitaceae*. The genus is made up of species predominantly from the Northern hemisphere. It is economically important as the source of grapes, both for direct consumption of the fruit and for fermentation to produce wine. [https://en.wikipedia.org/wiki/Vitis] - http://langual.org - http://eol.org/pages/38383 - http://www.langual.org/langual_thesaurus.asp?termid=B1329 - Vitis - vitis spp. - grape plant - - - - - - - - - - Crustaceans form a large, diverse arthropod taxon which includes such familiar animals as crabs, lobsters, crayfish, shrimp, krill, woodlice, and barnacles. [https://en.wikipedia.org/wiki/Crustacean] - http://langual.org - http://eol.org/pages/2598871 - http://www.langual.org/langual_thesaurus.asp?termid=B1374 - crustacea - crustacean - - - - - - - - - - http://langual.org - GRIN:32617 - MANSFELD:35616 - http://www.langual.org/langual_thesaurus.asp?termid=B1378 - Saccharum officinarum L. - saccharum officinarum - sugar cane plant - - - - - - - - - - - - - Field corn is maize of varieties that (in contrast with sweet corn and popcorn) are not, in the United States, grown primarily for consumption as human food in the form of fresh kernels. More than 98% of corn-growing land in the U.S. is in use for field-corn production. Principal field corn varieties are Dent corn, Flint corn, Flour corn (including blue corn (*Zea mays amylacea*), and Waxy corn. - WIKIPEDIA:Field_corn - http://langual.org - GRIN:311987 - PLANTS:ZEMAM2 - http://eol.org/pages/8223 - http://www.langual.org/langual_thesaurus.asp?termid=B1379 - Zea mays L. ssp. mays - Zea mays L. subsp. mays - Zea mays ssp. mays L. - corn, field - dent corn - flint corn - maize - podcorn - zea mays var. indentata (not acc.) - zea mays var. indurata (not acc.) - Field corn is a general term used in North America for corn varieties other than sweet corn, popcorn, yellow food grade corn used for yellow corn meal or flour and corn starch, and white food-grade corn used for white meal or flour and corn starch. Source: https://en.wikipedia.org/wiki/Field_corn - -LanguaL curation note: Searching note--use 'field corn' for any breakfast cereal or snack food having 'corn' as the first ingredient. - field corn plant - - - - - - - - - - http://langual.org - GRIN:11523 - MANSFELD:1118 - http://www.langual.org/langual_thesaurus.asp?termid=B1381 - Coriandrum sativum L. - chinese parsley - cilantro - coriandrum sativum - coriander plant - - - - - - - - - - Lettuce (Lactuca sativa) is an annual plant of the daisy family, Asteraceae. It is most often grown as a leaf vegetable, but sometimes for its stem and seeds. - https://en.wikipedia.org/wiki/Lettuce - http://langual.org - GRIN:21360 - ITIS:36607 - PLANTS:LASA3 - http://eol.org/pages/468144 - http://www.langual.org/langual_thesaurus.asp?termid=B1390 - Lactuca sativa L. - lactuca sativa - lettuce plant - - - - - - - - - - - - - Cucumber (Cucumis sativus) is a widely cultivated plant in the gourd family, Cucurbitaceae. It is a creeping vine that bears cucumiform fruits that are used as vegetables. There are three main varieties of cucumber: slicing, pickling, and seedless. - https://en.wikipedia.org/wiki/Cucumber - http://langual.org - GRIN:12580 - MANSFELD:3698 - http://www.langual.org/langual_thesaurus.asp?termid=B1404 - Cucumis sativus L. ssp. sativus - cucumis sativus - cucumber plant - - - - - - - - - - http://langual.org - GRIN:300050 - MANSFELD:25827 - http://www.langual.org/langual_thesaurus.asp?termid=B1415 - Asparagus officinalis L. - asparagus officinalis - asparagus plant - - - - - - - - - - Turmeric is a flowering plant, Curcuma longa of the ginger family, Zingiberaceae, the roots of which are used in cooking. - - http://langual.org - GRIN:12676 - MANSFELD:3244 - http://www.langual.org/langual_thesaurus.asp?termid=B1425 - Curcuma longa L. - curcuma domestica - curcuma longa - turmeric plant - - - - - - - - - - - - The term shellfish is used both broadly and specifically. For regulatory purposes it is often narrowly defined as filter-feeding molluscs such as clams, mussels, and oyster to the exclusion of crustaceans and all else. Although their shells may differ, all shellfish are invertebrates. - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1433 - Covers both freshwater and saltwater organisms - shellfish - - - - - - - - - - http://langual.org - ITIS:176086 - http://eol.org/pages/1049263 - http://www.langual.org/langual_thesaurus.asp?termid=B1457 - Gallus gallus (Linnaeus, 1758) - chicken - chicken - - - - - - - - - - The zucchini or courgette is a summer squash which can reach nearly a meter in length, but which is usually harvested at half that size or less. Along with certain other squashes, it belongs to the species Cucurbita pepo. Zucchini can be dark or light green. A related hybrid, the golden zucchini, is a deep yellow or orange color. - - - courgette - cucurbita pepo var. melopepo cv. zucchini - zucchini plant - - - - - - - - - - - - - - - - - - The shallot is a type of onion, specifically a botanical variety of the species *Allium cepa*. The shallot was formerly classified as a separate species,* A. ascalonicum*, a name now considered a synonym of the currently accepted name. - Like garlic, shallots are formed in clusters of offsets with a head composed of multiple cloves. The skin colour of shallots can vary from golden brown to gray to rose red, and their off-white flesh is usually tinged with green or magenta. [https://en.wikipedia.org/wiki/Shallot] - http://langual.org - - GRIN:101652 - ITIS:42720 - MANSFELD:110 - http://eol.org/pages/8187 - http://www.langual.org/langual_thesaurus.asp?termid=B1538 - Allium cepa L. - Allium cepa L. var. aggregatum G. Don - Allium cepa L. var. aggregatum G.Don - allium cepa var. aggregatum - shallot plant - - - - - - - - - - - - - - - - - - This "or" class is just to represent an equivalency with a commonly used classification outside of FoodOn. It should not have subclasses under it. (2022-11-30) - http://langual.org - https://orcid.org/0000-0002-9578-0788 - http://www.langual.org/langual_thesaurus.asp?termid=B1563 - fjerkrae - gamebird - fowl - game birds - poultry or game bird - - - - - - - - - - This is a hierarchy of organisms, grouped minimally in a combination of taxonomy and consumer-oriented food groups. - http://langual.org - - http://www.langual.org/langual_thesaurus.asp?termid=B1564 - This was LanguaL definition: Individual plant or animal from which the food product or its major ingredient is derived; also a chemical food source [FDA CFSAN 1995]. - food product organismal source - - - - - - - - - - Leaf vegetables, also called leafy greens, salad greens, pot herbs, vegetable greens, or simply greens, are plant leaves eaten as a vegetable, sometimes accompanied by tender petioles and shoots. - https://en.wikipedia.org/wiki/Leaf_vegetable - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1566 - leafy green - leafy vegetable plant - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1579 - vegetable-producing plant - - - - - - - - - - A type of fruit produced by flowering plants in the subfamily *Maloideae* of the family *Rosaceae*. - Damion Dooley - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1599 - maloideae - pome fruit plant - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1607 - nut or edible seed producing plant - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1643 - capsicum annuum, longum group - capsicum chile pepper - cayenne pepper - chile pepper - chili pepper - long pepper - red pepper (chile pepper) - hot pepper plant - - - - - - - - - - - - - - - - - - - A mature female chicken (usually more than 10 months of age) with meat less tender than that of a roaster, and with a nonflexible breastbone tip. - http://langual.org - hen - http://www.langual.org/langual_thesaurus.asp?termid=B1713 - stewing chicken - stewing hen - chicken hen - - - - - - - - - - The Decapoda or decapods (literally "ten-footed") are an order of crustaceans within the class Malacostraca, including many familiar groups, such as crayfish, crabs, lobsters, prawns, and shrimp. Most decapods are scavengers. [https://en.wikipedia.org/wiki/Decapoda] - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1998 - decapoda - decapod - - - - - - - - - - - - - - - - - Cucurbita (Latin for gourd) is a genus of herbaceous vines in the gourd family, Cucurbitaceae, also known as cucurbits, native to the Andes and Mesoamerica. Five species are grown worldwide for their edible fruit, variously known as squash, pumpkin, or gourd depending on species, variety, and local parlance, and for their seeds. - - http://langual.org - GRIN:12957 - MANSFELD:4048 - http://www.langual.org/langual_thesaurus.asp?termid=B2091 - Cucurbita maxima L. (Duch.) - pumpkin plant - cucurbita spp. - pumpkin, squash or gourd - squash, gourd or pumpkin plant - - - - - - - - - - *Mollusca* is a large phylum of invertebrate animals whose members are known as molluscs or mollusks. Molluscs are the largest marine phylum, comprising about 23% of all the named marine organisms. Numerous molluscs also live in freshwater and terrestrial habitats. [https://en.wikipedia.org/wiki/Mollusca] - http://langual.org - EC:No 216/2009 MOL - FAO ASFIS:MOL - http://eol.org/pages/2195 - http://www.langual.org/langual_thesaurus.asp?termid=B2112 - Mollusca - mollusk - mollusc - - - - - - - - - - *Bivalvia*, in previous centuries referred to as the *Lamellibranchiata* and *Pelecypoda*, is a class of marine and freshwater molluscs that have laterally compressed bodies enclosed by a shell consisting of two hinged parts. Bivalves as a group have no head and they lack some usual molluscan organs like the radula and the odontophore. They include the clams, oysters, cockles, mussels, scallops, and numerous other families that live in saltwater, as well as a number of families that live in freshwater.[https://en.wikipedia.org/wiki/Bivalvia] - http://langual.org - http://eol.org/pages/2215 - http://www.langual.org/langual_thesaurus.asp?termid=B2113 - bivalvia - lamellibranchiata - pelecypod - pelecypoda - bivalve - - - - - - - - - - - Echinoderm is the common name given to any member of the phylum *Echinodermata* of marine animals. The adults are recognizable by their (usually five-point) radial symmetry, and include such well-known animals as sea stars, sea urchins, sand dollars, and sea cucumbers, as well as the sea lilies or "stone lilies". [https://en.wikipedia.org/wiki/Echinoderm] - http://langual.org - EC:No 1637/2001 ECH - FAO ASFIS:ECH - http://www.langual.org/langual_thesaurus.asp?termid=B2115 - Echinodermata - Echinodermata Klein, 1734 - echinodermata - echinoderm - - - - - - - - - - - - - - - - - - - Black pepper consists of unripe whole fruit that are sundried. White pepper consists of the seeds only of ripe fruit. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B2255 - piper nigrum - black or white pepper plant - - - - - - - - - - - *Coelenterata* is an obsolete term encompassing the animal phyla *Cnidaria* (coral animals, true jellies, sea anemones, sea pens, and their allies) and *Ctenophora* (comb jellies). [https://en.wikipedia.org/wiki/Coelenterata] - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B2409 - coelenterata - coelenterate - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B2559 - pepper, poblano - poblano pepper plant - - - - - - - - - - - - - - - - - - - - - - - - - The bell pepper (also known as sweet pepper or pepper in the United Kingdom, Canada and Ireland, and capsicum in Australia, India, Pakistan, Bangladesh, Singapore and New Zealand) is a cultivar group of the species *Capsicum annuum*. Bell peppers are sometimes grouped with less pungent pepper varieties as "sweet peppers". [https://en.wikipedia.org/wiki/Bell_pepper] - http://langual.org - - GRIN:311784 - GRIN:8904 - ITIS:30492 - MANSFELD:6120 - PLANTS:CAAN4 - http://eol.org/pages/581098 - http://www.langual.org/langual_thesaurus.asp?termid=B2628 - sweet pepper plant - Capsicum annuum L. - Capsicum anuum L. - capsicum frutescens var. grossum - bell pepper plant - - - - - - - - - - Unripe fruit of red or yellow bell pepper varieties. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B2629 - green pepper plant - green bell pepper plant - - - - - - - - - - Ripe fruit of red bell pepper varieties. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B2630 - red bell sweet pepper plant - red sweet pepper plant - LanguaL curation note: Do not confuse with *RED PEPPER*. - red bell pepper plant - - - - - - - - - - Ripe fruit of yellow bell pepper varieties. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B2631 - yellow bell pepper plant - - - - - - - - - - Grouped together because of similar use. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B2633 - paprika, hot - red pepper (pungent pepper variety) - pungent pepper variety plant - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B3357 - LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term. - plant according to family - - - - - - - - - - http://langual.org - CCPR: - GRIN:30008 - GRIN:300085 - PLANTS:BRASS2 - http://eol.org/pages/4219 - http://www.langual.org/langual_thesaurus.asp?termid=B3372 - Brassica - Brassica L. - Brassica sp. - Brassica spp. - brassica spp. - brassica species - - - - - - - - - - http://langual.org - CCPR: - GRIN:12546 - http://www.langual.org/langual_thesaurus.asp?termid=B3407 - Cucumis sativus L.; pickling cucumber cultivars - bur cucumber - bur gherkin - cucumis anguria - west indian gherkin plant - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B4168 - plant used for dietary supplements - - - - - - - - - - *Allium* is a genus of monocotyledonous flowering plants that includes hundreds of species, including the cultivated onion, garlic, scallion, shallot, leek, and chives. [https://en.wikipedia.org/wiki/Allium] - http://langual.org - http://eol.org/pages/8187 - http://www.langual.org/langual_thesaurus.asp?termid=B4302 - allium - onion - wild onion - allium species - - - - - - - - - - The biological subfamily *Bovinae* includes a diverse group of 10 genera of medium- to large-sized ungulates, including domestic cattle, the bison, African buffalo, the water buffalo, the yak, and the four-horned and spiral-horned antelopes. The evolutionary relationship between the members of the group is obscure, and their classification into loose tribes rather than formal subgroups reflects this uncertainty. General characteristics include cloven hoofs and usually at least one of the sexes of a species having true horns. - WIKIPEDIA:Bovinae - http://langual.org - http://eol.org/pages/2851454 - http://www.langual.org/langual_thesaurus.asp?termid=B4374 - bovinae - bovine - - - - - - - - - - A bovid (family *Bovidae*) is any of almost 140 species of cloven-hoofed, ruminant mammal which has males with characteristic unbranching horns covered in a permanent sheath of keratin. - -The family is widespread, being native to Asia, Africa, Europe and North America, and diverse: members include bison, African buffalo, water buffalo, antelopes, gazelles, sheep, goats, muskoxen, and domestic cattle. - WIKIPEDIA:Bovidae - http://langual.org - http://eol.org/pages/7687 - http://www.langual.org/langual_thesaurus.asp?termid=B4381 - bovidae - bovid - - - - - - - - - - *Cucumis* is a genus of twining, tendril-bearing plants in the *Cucurbitaceae* family which includes the cucumber (*Cucumis sativus*), muskmelons (*Cucumis melo*, including cantaloupe and honeydew), the horned melon (*Cucumis metuliferus*), and the West Indian gherkin (*Cucumis anguria*). [https://en.wikipedia.org/wiki/Cucumis] - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B4459 - cucumis species - - - - - - - - - - The *Cucurbitaceae*, also called cucurbits and the gourd family, are a plant family consisting of about 965 species in around 95 genera, the most important of which are: - *Cucurbita* - squash, pumpkin, zucchini, some gourds; - *Lagenaria* - calabash, and others that are inedible; - *Citrullus* - watermelon (*C. lanatus, C. colocynthis*) and others; - *Cucumis* - cucumber (*C. sativus*), various melons; - *Luffa* - luffa, loofah - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B4460 - cucurbitaceae - gourd/squash family - - - - - - - - - - Tunicates, previously known as *Urochordata* or urochordates, are members of the *Tunicata*, a subphylum of the phylum *Chordata*. They are marine filter feeders with a saclike morphology. In their respiration and feeding they take in water through an incurrent (or inhalant) siphon and expel the filtered water through an excurrent (or exhalant) siphon. Most adult tunicates are sessile and attached to rocks or similarly suitable surfaces on the ocean floor; others such as salps, doliolids and pyrosomes swim in the pelagic zone as adults. Various species are commonly known as sea squirts or sea pork. - WIKIPEDIA:Tunicate - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B4466 - oopah - sea squirt - tunicata - tunicate - - - - - - - - - - Pattypan squash, sunburst squash, cibleme in Cajun French, white squash, scallopini or yellow squash in Australian English, is a summer squash (species *Cucurbita pepo*) notable for its small size, round and shallow shape, and scalloped edges, somewhat resembling a small toy top, or flying saucer. - WIKIPEDIA:Pattypan_squash - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B4505 - pattypan squash plant - scallop squash plant - - - - - - - - - - The *Solanaceae*, or nightshades, are an economically important family of flowering plants. Many members of the family contain potent alkaloids, and some are highly toxic, but many, including tomatoes, potatoes, eggplant, bell/chili peppers, and tobacco are widely used. The *Solanaceae* consists of about 98 genera and some 2,700 species, with a great diversity of habitats, morphology and ecology. [https://en.wikipedia.org/wiki/Solanaceae] - http://langual.org - http://eol.org/pages/4437 - http://www.langual.org/langual_thesaurus.asp?termid=B4934 - nightshade family - solanaceae plant - - - - - - - - - - *Solanum* is a large and diverse genus of flowering plants, which include two food crops of high economic importance, the potato and the tomato. It also contains the nightshades and horse nettles, as well as numerous plants cultivated for their ornamental flowers and fruit. - *Solanum* species show a wide range of growing habits, such as annual and perennials, vines, subshrubs, shrubs, and small trees. Many formerly independent genera like *Lycopersicon* (the tomatoes) and *Cyphomandra* are now included in *Solanum* as subgenera or sections. Thus, the genus today contains roughly 1,500-2,000 species. - - http://langual.org - GRIN:300568 - PLANTS:SOLAN - http://eol.org/pages/4437 - http://www.langual.org/langual_thesaurus.asp?termid=B5104 - Solanum - Solanum L. - Solanum spp. - solanum plant - - - - - - - - - - - - - - - - - - Edible flesh of any type of animal, including poultry and seafood. Excludes parts containing only animal fat, which is indexed under *FAT OR OIL* or under *FAT, TRIM*. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0103 - Damion Dooley Feb 6, 2017: Good meat cut resources to incorporate for Canada: The CFIA Meat Cuts Manual -http://www.inspection.gc.ca/food/labelling/meat-cuts/eng/1300126276015/1300126372856 - meat part of animal - - - - - - - - - - A broad term that includes the nutritive sweeteners dextrose, fructose, galactose, lactose, maltose and sucrose, which are simple carbohydrates with molecules composed of one or two saccharide units. Note that on a product label or in a recipe, 'sugar' means *SUCROSE* and should be so indexed. Use the broad term *SUGAR* only if the specific sugar used is not known or not listed in the vocabulary. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0108 - sugar - sugar - - - - - - - - - - Anatomical part of the plant or animal from which a food product or its major ingredient is derived. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0116 - LanguaL curation note: "e.g. *LEAF*, *ROOT OR TUBER*, *ORGAN MEAT*, *MILK* OR *EGG*; it also includes components of parts, such as *CREAM*, and extracts, concentrates or isolates, such as *PROTEIN EXTRACT* or *SUGAR*." - part of organism - - - - - - - - - - Bone, feathers, shell, skin or trim fat. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0122 - LanguaL curation note: *BLOOD* AND *INK, AQUATIC ANIMAL* are now listed under organism substance. - nonmeat part of animal - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0125 - boneless meat - skeletal meat part, without bone, skin undetermined - skeletal meat part, without bone or shell - - - - - - - - - - Includes carcass meat, organ meat, and nonmeat parts of animals, as well as the whole animal. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0127 - LanguaL curation note: Includes carcass meat, organ meat, and nonmeat parts of animals, as well as the whole animal. - animal body or body part - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0138 - LanguaL curation note: Renamed from *FRUIT OR BERRY, PEEL REMOVED* in LanguaL 2008. - fruit, peel removed - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0144 - LanguaL curation note: This broad term is used for the plant as a whole, excluding the root and the fruit; for any piece consisting of two or more individual parts (e.g., a celery stalk with the leaf blades attached); or for any mixture of two or more individual parts (e.g., mushroom stems and pieces). - plant above surface, excluding fruit and seed - - - - - - - - - - The parts of a plant that are not fruit or seed. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0148 - flower, root, stem or leaf - leaf, flower, root or stem - stem, leaf, flower or root - root, stem, leaf or flower - - - - - - - - - Extract, concentrate or isolate high in sugar, oligosaccharide or polysaccharide. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0152 - carbohydrate extract, concentrate, or isolate - - - - - - - - - - - - - - - - - - - - - - - Soft sugar whose crystals are covered by a film of refined dark syrup that imparts color, flavor, and moisture. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0156 - brown sugar - brown sugar - - - - - - - - - - - - - - - - - White sugar is highly refined crystalline sugar, mostly sucrose, that appears white in color. White sugar is commonly used in North America and Europe, made either of beet sugar or cane sugar, that has undergone a refining process which removes molasses. - Damion Dooley - https://en.wikipedia.org/wiki/White_sugar - http://langual.org - 2019-06-18T21:52:36Z - https://upload.wikimedia.org/wikipedia/commons/thumb/0/04/A_Bowl_of_Sugar_2.jpg/320px-A_Bowl_of_Sugar_2.jpg - SUBSET_SIREN:F4298 - http://www.langual.org/langual_thesaurus.asp?termid=C0157 - subset_siren - SIREN DB annotation: -* has quality 'crystal' (http://purl.obolibrary.org/obo/FOODON_03430143) -* derives from 'white sugar' (http://purl.obolibrary.org/obo/FOODON_03420157) - - white sugar - white sugar - - - - - - - - - - Anatomical part of an animal; includes eggs and milk that, although separated from the animal, are produced as integral parts and are affected by the animal's food intake and metabolism. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0164 - part of animal - - - - - - - - - - - - - - - - - - - - - - The fleshy fruit of any plant. *FRUIT* includes vegetables berries and pods as well. The bulk of a fruit is its fleshy part, which is covered by a peel (skin) and which encloses a core, pit or seeds. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0167 - berry - berry or fruit (anatomical part) - fruit or berry, peel undetermined - hip (fruit) - infructescence - LanguaL curation note: The descriptors under *FRUIT* are arrayed so that the indexer can check first whether the peel is present, removed or undetermined; then check the same informationfor the core, pit or seeds. For juices, beverages or jellies made from fruit, Index the entire part from which the product is derived. - -Renamed from *FRUIT OR BERRY* in LanguaL 2008. - fruit part - - - - - - - - - - - Carcass meat from any type of animal including poultry and seafood. Includes retail and wholesale cuts other than organ meat. Refers to the whole carcass or parts. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0175 - skeletal meat part - - - - - - - - - - - - - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0178 - seed part - - - - - - - - - - Poultry, game bird or turtle eggs. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0194 - LanguaL curation note: Fish roe are indexed under *OVARY, ROE*. - egg or egg component - - - - - - - - - - Edible organ meat, including blood and bone marrow. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0218 - variety meat - organ meat - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The egg yolk and albumen component of one or more eggs with shell removed. - Damion Dooley - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0225 - egg (without shell) - - - - - - - - - - A physical-chemical component separated from the food source or its parts by extraction, centrifugation, filtration, heat processing, expressing or a similar process. The separated component may be converted through further processing. If this is done, the final substance is indexed. A water-extracted component may remain in aqueous dispersion. The extract, concentrate or isolate is indexed in preference to the anatomic part from which it is derived. For example, peanut oil is indexed under *PEANUT* combined wih *FAT OR OIL* rather than with *SEED OR KERNEL*. On the other hand, fruit and vegetable juices can be indexed under *FRUIT JUICE OR NECTAR* or *VEGETABLE JUICE* (A. PRODUCT TYPE); therefore the anatomic part of the plant should be indexed. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0228 - Damion Dooley's note: Items in this branch will be merged into foodon food product branch. - extract, concentrate or isolate of plant or animal - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0229 - flesh of fruit - LanguaL curation note: Renamed from *FRUIT OR BERRY, PEEL REMOVED, CORE, PIT OR SEED REMOVED* in LanguaL 2008. - fruit, peel removed, core, pit or seed removed - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0238 - bulb, root or tuber - tuber, bulb or root - root, tuber or bulb - - - - - - - - - - The oil produced by pressing or extracting lipids from plant seeds (e.g. grapeseed oil, rapeseed oil, linseed oil) /AM - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0307 - seed oil - - - - - - - - - - The physical state of the food product (liquid, semiliquid, semisolid, or solid). Solid food products are further subdivided by shape or form. Terms are provided for products that have both liquid and solid components or that incorporate air or other gases. [FDA CFSAN 1995] - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=E0113 - Damion Dooley's note: these categories need to be mapped over to PATO phenotypic categories, with a suitable treatment of mixtures of solids that are divided into parts. - food physical quality - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=E0122 - LanguaL curation note: The distinctions in this category are based on size characteristics, primarily thickness, which are important for heat transfer and for diffusion of chemicals in processing. *DIVIDED INTO HALVES, QUARTERS OR SEGMENTS* should be examined first and if one of the descriptors listed applies it should be used regardless of the size of the pieces. If none of these are applicable, other *DIVIDED OR DISINTEGRATED* descriptors should be examined. Do not use any of these descriptors if dividing or disintegrating results in a semiliquid or semisolid product. - divided or disintegrated - - - - - - - - - - - - - - - - - - - - - - - - - - - A state of matter between a solid and a gas, in which a substance has the capacity to flow and conforms to the shape of the container. Liquids range from water to honey, corresponding to a range in viscosity (or apparent viscosity) from 1 to 500 centipoise (viscosity is a measure of a liquid's resistance to flow). Products that are pourable but have a higher viscosity are *SEMILIQUID*. - http://langual.org - SUBSET_SIREN:F5105 - http://www.langual.org/langual_thesaurus.asp?termid=E0130 - fluid - SIREN DB annotation: -* has quality 'liquid' (http://purl.obolibrary.org/obo/FOODON_03430130) - - food (liquid) - - - - - - - - - - - - - - - - - - - - - - - - - - - A solid product is a hard or soft product capable of retaining its own shape at room temperature (20 degrees C.). A soft product that is spreadable or formable is considered semisolid. - http://langual.org - SUBSET_SIREN:F17643 - http://www.langual.org/langual_thesaurus.asp?termid=E0151 - solid - food (solid) - - - - - - - - - - Divided into pieces whose shape bears little or no relation to the shape of the whole. If all dimensions are below 0.2 cm., use *DISINTEGRATED OR GROUND*. Examples are: bread slice, cubed beef, sliced carrot, cut green beans, apple ring, shredded cabbage or cheese. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=E0152 - divided into pieces - - - - - - - - - - - - - - - http://www.langual.org/langual_thesaurus.asp?termid=G0002 - food cooking - - - - - - - - - Cooked at moderate to high levels of heat in which no liquid is added and only small amounts of fat may be added to prevent sticking. - http://www.langual.org/langual_thesaurus.asp?termid=G0004 - dry cooked - LanguaL - cooking by dry heat - - - - - - - - - - - - - - - Cooked without moisture, covered or uncovered, in an oven. - Damion Dooley - http://www.langual.org/langual_thesaurus.asp?termid=G0005 - roasting - food baking - - - - - - - - - Used to specifically characterize a food product based on the treatment or processes applied to the product or any indexed ingredient. The processes include adding, substituting or removing components or modifying the food or component, e.g., through fermentation. - http://www.langual.org/langual_thesaurus.asp?termid=H0111 - LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term. - food treatment process - - - - - - - - - A food modification process by microbial or enzymatic action which results in molecular changes in any food component. - http://www.langual.org/langual_thesaurus.asp?termid=H0119 - fermented, unspecified - LanguaL curation note: If salt, sugar or other food additive is used to aid in the modification process, index it by the appropriate term under *INGREDIENT ADDED*. - microbial/enzymatic modification process - - - - - - - - - A food modification process where physical or chemical changes are effected in any food ingredient through a physical or non-enzymatic chemical process. - http://www.langual.org/langual_thesaurus.asp?termid=H0130 - physical/chemical modification process - - - - - - - - - http://www.langual.org/langual_thesaurus.asp?termid=H0141 - LanguaL curation note: Used when the food product underwent mechanical, chemical or enzymatic modification that has affected the texture, flavor or other characteristic of the product. - food modification process - - - - - - - - - - - - - - - - - - - - - - requires curation - A food product which is output of a salting process where salt is dissolved or absorbed into the food as an ingredient or flavourant. - http://langual.org - - - http://www.langual.org/langual_thesaurus.asp?termid=H0173 - salted - compounded food - LanguaL curation note: Used when it is necessary to distinguish one product from another (e.g., salted vs. unsalted peanuts), or for salt-fermented products (e.g. soy sauce). It can also be used for other products known to contain at least 4% added and naturally present salt (sodium chloride). -When salting is used as preservation method, index *preservation by SALTING [J0103]* or narrower term. - food (salted) - salted - - - - - - - - - - - - - - - - - - This disjunction is provided for food indexers who used the LanguaL category per guidelines. Currently, by specifying the more specific nut or seed as ingredient instead, this category can be inferred. - nut or seed added - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=H0177 - LanguaL curation note: With the exception of peanut (see *PEANUT OR PEANUT BUTTER ADDED*), used when a nut or seed ingredient is the second ingredient in order of predominance. - plant seed or nut food product - - - - - - - - - Treated with acid that may be produced by fermentation or added and/or with salt brine, often in the presence of spices or herbs, producing changes in flavor and texture. - http://www.langual.org/langual_thesaurus.asp?termid=H0190 - LanguaL curation note: Also index by other applicable terms from *MICROBIALLY/ ENZYMATICALLY MODIFIED*. - pickling - - - - - - - - - - - - - - - - - - A fat or oil derived from vegetable material - Damion Dooley - vegetable fat or oil added - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=H0263 - This is a convenience class inherited from LanguaL - vegetable fat or oil - - - - - - - - - Preservation by adding chemical preservatives (e.g., sorbic acid, sodium benzoate, BHT, calcium proprionate) to suppress or inhibit undesirable microorganisms or enzyme activity. - http://www.langual.org/langual_thesaurus.asp?termid=J0100 - preservation by adding chemicals - - - - - - - - - - - http://www.langual.org/langual_thesaurus.asp?termid=J0103 - LanguaL curation note: Used when salting is used for preservation. The salt content of the food is generally 8% or higher (e.g. salted fish, etc.). - food salting - - - - - - - - - The methods contributing to the prevention or retardation of microbial, enzymatic or oxidative spoilage and thus to the extension of shelf life. Index all methods for which information is available, even if a corresponding descriptor has already been used in *H. TREATMENT APPLIED*. Preservation descriptors refer to the finished food as a whole with these exceptions: (1) if the components of a multi-component food, such as cream pie, are preservation by different methods, index all methods; (2) if chemical preservatives are declared on the label, always index them even if it is known that the preservative was introduced through or is only present in a component or ingredient of the food; and (3) if the preservation method for an ingredient is declared on the label (such as brie cheese made from pasteurized milk) index it. Also use *INGREDIENT preservation by THERMAL PROCESSING* or *INGREDIENT preservation by IRRADIATION* when ingredients have been pasteurized, ultrapasteurized, sterilized or irradiated. - http://www.langual.org/langual_thesaurus.asp?termid=J0107 - LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term. - food preservation process - - - - - - - - - Preservation by use of chemical to destroy, suppress or inhibit undesirable microorganisms or enzyme activity. - http://www.langual.org/langual_thesaurus.asp?termid=J0109 - chemical food preservation process - - - - - - - - - http://www.langual.org/langual_thesaurus.asp?termid=J0119 - LanguaL curation note: Used when sufficient radiation (e.g. 10 kGy) is applied to destroy most patho-genic and food spoilage organisms. Also index *preservation by CHILLING*. - pasteurization by irradiation - - - - - - - - - Preservation by the use of high temperature for a time sufficient to reduce or destroy undesirable microorganisms and enzyme activity. [FDA CFSAN 1995] - http://www.langual.org/langual_thesaurus.asp?termid=J0120 - heat treatment food preservation - - - - - - - - - Preservation by irradiation, primarily by gamma radiation. - http://www.langual.org/langual_thesaurus.asp?termid=J0122 - preservation by ionizing radiation - - - - - - - - - http://www.langual.org/langual_thesaurus.asp?termid=J0135 - LanguaL curation note: Used when the product is held at a temperature of 60-150 °C (140-300 °F) for a time sufficient to destroy most pathogenic and food spoilage organisms. When followed by refrigeration, also index *preservation by CHILLING*. - pasteurization by heating - - - - - - - - - Preservation by the use of radiation to destroy or suppress undesirable microorganisms or enzyme activity. - http://www.langual.org/langual_thesaurus.asp?termid=J0138 - preservation by irradiation - - - - - - - - - Preservation method that lowers the water activity (relative humidity) of a food product. This is accomplished by using mechanical dehydration equipment, by natural drying, by adding salt, sugar or other agents to the food or by surface drying during a refrigeration or freezing operation. This method of preservation may be used in conjunction with other preservation methods such as preservation by thermal processing. - http://www.langual.org/langual_thesaurus.asp?termid=J0145 - preservation by reducing water activity - - - - - - - - - http://www.langual.org/langual_thesaurus.asp?termid=J0149 - preservation by adding acid - - - - - - - - - Preservation by adding inorganic acids or salts (e.g. SO2, H2SO4, KNO4, NaNO3) to suppress or inhibit undesirable micro-organisms or enzyme activity. - http://www.langual.org/langual_thesaurus.asp?termid=J0154 - preservation by adding inorganic acids or salts - - - - - - - - - - A food contact material which encloses the food and can be in the type of a container, packaging or wrapping. - Previous definition was a legacy definition, not ontological and has been moved to comments. - http://orcid.org/0000-0001-8008-8249 - https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/food-packaging - http://langual.org - container - packaging - wrapping - http://www.langual.org/langual_thesaurus.asp?termid=M0100 - food container - food wrap - food wrapping - Previous definition: Type of container or wrapping defined by the main container material, the container form and the material of the liner lids of ends. Also type of container or wrapping by form; prefer description by material first, then by form. [FDA CFSAN 1995]. - food packaging - - - - - - - - - - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=M0194 - bottle, jar or can - jar, bottle or can - can, bottle or jar - - - - - - - - - - Classification corresponding to FSTA Thesaurus Packaging 3.1 Package Types - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=M0195 - container or wrapping by form - - - - - - - - - - - - - - - - - - - - A container which is a bottle or a jar. - https://en.wikipedia.org/wiki/Container - http://langual.org - - http://www.langual.org/langual_thesaurus.asp?termid=M0203 - jar - bottle or jar - - - - - - - - - - A container which is made of a thin metal and and is used for the distribution or storage of goods. - http://langual.org - - http://www.langual.org/langual_thesaurus.asp?termid=M0204 - canister - canned (packed in a can) - can (container) - - - - - - - - - - - A narrow-necked container typically made of glass or plastic that is used to store and transport liquids. - https://en.wikipedia.org/wiki/Bottle - http://langual.org - - http://www.langual.org/langual_thesaurus.asp?termid=M0214 - bottle - - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=M0215 - wide-necked bottle - wide-necked jar - jar - jar - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=M0218 - jug or demijohn - - - - - - - - - - The specific container or coating materials in direct contact with the food. [FDA CFSAN 1995] - - - http://langual.org - surface - http://www.langual.org/langual_thesaurus.asp?termid=N0010 - food product contact surface - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=N0050 - food contact surface from natural material - - - - - - - - - - - An uncured cheese food product which is soft and acid set and can be made from cow or buffalo milk. - https://en.wikipedia.org/wiki/Paneer - 2022-10-20T17:11:49.301Z - https://orcid.org/0000-0001-5193-0062 - https://orcid.org/0000-0001-8008-8249 - - ponir - paneer - paneer - - - - - - - - - requires discussion - An avian animal which is any of a number of species of wild birds which are hunted, killed and eaten by humans. - https://simple.wikipedia.org/wiki/Game_bird#:~:text=A%20game%20bird%20is%20any,so%20there%20are%20gun%20laws. - - 2022-11-03T01:40:18.746Z - game bird - - - - - - - - - Population category defined using ancestry informative markers (AIMs) based on genetic/genomic data - - ancestral group - ancestry category - - - - - - - - - Includes individuals who either self-report or have been described by authors as South Asian or one of the sub-populations from this region (e.g Asian Indian). This category also includes individuals who genetically cluster with reference populations from this region, for example 1000 Genomes and/or HapMap -BEB, GIH, ITU, PJL and STU populations. - - South Asian - - - - - - - - - Includes individuals who either self-report or have been described by authors as South East Asian or one of the sub-populations from this region (e.g Vietnamese). This category also includes includes individuals who genetically cluster with reference populations from this region, for example 1000 Genomes KHV population. We note that East Asian and South East Asian populations are often conflated. However, recent studies indicate a unique genetic background for South East Asian populations. - - South East Asian - - - - - - - - - Includes individuals that either self-report or have been described as Asian but there was not sufficient information to allow classification as East Asian, Central Asian, South Asian or South-East Asian. - - Asian unspecified - Asian - - - - - - - - - Includes individuals who either self-report or are described by authors as Hispanic, Latino, Latin American or one of the sub-populations -from this region. This category includes individuals with known admixture of primarily European, African and Native American ancestries, though some may have also a degree of Asian (e.g. Peru). We also note that the levels of admixture vary depending on the country, with Caribbean countries carrying higher levels of African admixture when compared to South American countries, for example. This category also includes individuals who genetically cluster with reference populations from this region, for example 1000 Genomes and/or HapMap CLM, MXL, PEL and PUR populations - Jackie MacArthur - Joannella Morales - - Hispanic or Latin American - - - - - - - - - - Mexican - Mexican - - - - - - - - - - American - American - - - - - - - - - - Asian Indian - Indian Asian - Indian - Indian - - - - - - - - - - Thai - Thai - - - - - - - - - Population for which insufficient information is available to allocate it to a specific ancestral group or which contain individuals from a range of known ancestry categories, eg American - - undefined ancestry population - - - - - - - - - data item - - An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. - - data item - - - - - - - - - symbol - - An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. - based on Oxford English Dictionary - - symbol - - - - - - - - - information content entity - - A generically dependent continuant that is about some thing. - PERSON: Chris Stoeckert - OBI_0000142 - - information content entity - - - - - - - - - curation status specification - - The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - OBI_0000266 - - curation status specification - - - - - - - - - data about an ontology part - Data about an ontology part is a data item about a part of an ontology, for example a term - - data about an ontology part - - - - - - - - - - Benincaseae - - - - - - - - - - bony vertebrates - Euteleostomi - - - - - - - - - - stalk celery plant - - http://langual.org - GRIN:102051 - ITIS:182185 - MANSFELD:1236 - PLANTS:APGRD - http://eol.org/pages/1245043 - http://www.langual.org/langual_thesaurus.asp?termid=B3729 - celery - stalk celery - Apium graveolens L. var. dulce (Mill.) DC. - Apium graveolens var. dulce (Mill.) Pers. - Apium graveolens var. dulce (P. Mill.) DC. - apium graveolens var. dulce - Apium graveolens Dulce Group - - - - - - - - - - Archelosauria - - - - - - - - - - Dipnotetrapodomorpha - - - - - - - - - - turmeric - Curcuma longa - - - - - - - - - - Boreoeutheria - - - - - - - - - - Acrogymnospermae - - - - - - - - - - Mesangiospermae - - - - - - - - - - Petrosaviidae - - - - - - - - - - Pentapetalae - - - - - - - - - - Panicoideae - - - - - - - - - - PACMAD clade - - - - - - - - - - Oryzeae - - - - - - - - - - Andropogoneae - - - - - - - - - - Galloanserae - - - - - - - - - - Fabeae - - - - - - - - - - Andropogonodae - - - - - - - - - - walnut family - Juglandaceae - - - - - - - - - - - *Juglans* is a plant genus of the family *Juglandaceae*, the seeds of which are known as walnuts. - - WIKIPEDIA:Juglans - - http://langual.org - 2022-02-01T00:18:43Z - http://eol.org/pages/38394 - http://www.langual.org/langual_thesaurus.asp?termid=B1290 - walnuts - juglans spp. - LanguaL curation note: When indexing the walnut fruit (drupe, seed) index both *WALNUT [B1290]* and *FRUIT [C0167]* (or its more precise narrower terms). - Juglans - - - - - - - - - - Amygdaloideae - - - - - - - - - - Aurantioideae - - - - - - - - - - NPAAA clade - - - - - - - - - - 50 kb inversion clade - - - - - - - - - - Hologalegina - - - - - - - - - - IRL clade - - - - - - - - - - magnoliids - Magnoliidae - - - - - - - - - - rue family - Rutaceae - - - - - - - - - - Apioideae - - - - - - - - - - apioid superclade - - - - - - - - - - Scandiceae - - - - - - - - - - Apieae - - - - - - - - - - Daucinae - - - - - - - - - - Citrus - - - - - - - - - - Citrus x limon - lemon - Citrus limon - - - - - - - - - - eucaryotes - eukaryotes - Eukaryota - - - - - - - - - - Bovinae - - - - - - - - - - - "Miller intended Malus pumila (from the Latin pumilus – small) to denote the Paradise Apple, a weak, low-growing form of M. domestica used as a rootstock, which he took to be a distinct species (Bean 1981). Until very recently it has been widely used for all forms of orchard apple (otherwise known as M. domestica), and sometimes also for their primary wild progenitor (for example by Juniper & Mabberley 2006; Grimshaw & Bayton 2009). While M. pumila is the earlier name, M. domestica has been conserved (Qian et al. 2010, Applequist 2017)." - from https://treesandshrubsonline.org/articles/malus/malus-domestica/ - paradise apple plant - - http://langual.org - GRIN:23261 - ITIS:25262 - PLANTS:MAPU - http://eol.org/pages/629943 - http://www.langual.org/langual_thesaurus.asp?termid=B3346 - paradise apple - ping guo - Malus pumila Mill. - Malus pumila P. Mill. - malus pumila - malus pumila var. niedzwetzkyana - malus sylvestris var. niedzwetskyana - malus sylvestris var. paradisiaca - Malus pumila - - - - - - - - - - shallot - Allium cepa var. aggregatum - - - - - - - - - - Laurasiatheria - - - - - - - - - - tetrapods - Tetrapoda - - - - - - - - - - amniotes - Amniota - - - - - - - - - - Theria - Theria <mammals> - - - - - - - - - - diapsids - Sauria - - - - - - - - - - Chlorophyta/Embryophyta group - chlorophyte/embryophyte group - green plants - Viridiplantae - - - - - - - - - - Opisthokonta - - - - - - - - - - Bilateria - - - - - - - - - - deuterostomes - Deuterostomia - - - - - - - - - - Gnetaceae - - - - - - - - - - Gnetum - - - - - - - - - - angiosperms - flowering plants - Magnoliopsida - - - - - - - - - - Laurales - - - - - - - - - - laurel family - Lauraceae - - - - - - - - - - avocado - Persea americana - - - - - - - - - - Fagales - - - - - - - - - - Pecora - - - - - - - - - - BEP clade - BOP clade - - - - - - - - - - Apiineae - - - - - - - - - - cucumber family - Cucurbitaceae - - - - - - - - - - Cucumis - - - - - - - - - - cucumber - cucumbers - Cucumis sativus - - - - - - - - - - marrows - pumpkins - squashes - Cucurbita - - - - - - - - - - - - - - - http://langual.org - GRIN:12606 - ITIS:22373 - PLANTS:CUPE - Cucurbita pepo L. - Cucurbita pepo - - - - - - - - - - Brassicales - - - - - - - - - - Cruciferae - mustard family - Brassicaceae - - - - - - - - - - Brassica - - - - - - - - - - Rosales - - - - - - - - - - rose family - Rosaceae - - - - - - - - - - Malus - - - - - - - - - - apple - apple tree - cultivated apple - Malus domestica - - - - - - - - - - Prunus - - - - - - - - - - pea family - Fabaceae - - - - - - - - - - Indian corn - Zea mays subsp. sacharata - corn - maize - Zea mays subsp. mays - - - - - - - - - - Papilionoideae - - - - - - - - - - lentil - Lens culinaris - - - - - - - - - - Poales - - - - - - - - - - carrot family - Apiaceae - - - - - - - - - - Daucus - - - - - - - - - - Queen Anne's lace - carrot - carrots - Daucus carota - - - - - - - - - - - A marshland plant in the family Apiaceae that has been cultivated as a vegetable since antiquity. - - celery plant - - - GRIN:300034 - MANSFELD:1212 - http://www.langual.org/langual_thesaurus.asp?termid=B1282 - Apium graveolens L. - Apium graveolens - - - - - - - - - - asparagus family - Asparagaceae - - - - - - - - - - mammals - Mammalia - - - - - - - - - - Solanales - - - - - - - - - - nightshade family - Solanaceae - - - - - - - - - - peppers - Capsicum - - - - - - - - - - - ancho pepper plant - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B2550 - C annuum - Capsicum annuum - - - - - - - - - - - WIKIPEDIA:Tomato - - http://langual.org - GRIN:101442 - ITIS:521671 - ITIS:529044 - MANSFELD:6054 - http://eol.org/pages/392557 - tomato - Lycopersicon esculentum Mill. - Lycopersicon esculentum var. esculentum P. Mill. - Solanum lycopersicum L. - lycopersicon esculentum - Solanum lycopersicum - - - - - - - - - - Solanum - - - - - - - - - - Sapindales - - - - - - - - - - Solanoideae - - - - - - - - - - monocots - monocotyledons - Liliopsida - - - - - - - - - - grass family - Poaceae - - - - - - - - - - Gnetum africanum - - - - - - - - - - Oryza - - - - - - - - - - - Asian cultivated rice - asian rice - red rice - rice - Oryza sativa - - - - - - - - - - maize - FoodOn Note: the NCBITaxon exact synonym "maize" is more appropriate for "Zea mays subsp. mays" - Zea mays - - - - - - - - - - Zingiberales - - - - - - - - - - ginger family - Zingiberaceae - - - - - - - - - - Zingiber - - - - - - - - - - amaryllis family - Amaryllidaceae - - - - - - - - - - Allium - - - - - - - - - - - - http://langual.org - GRIN:2244 - ITIS:42720 - PLANTS:ALCE - http://eol.org/pages/8187 - onion - Allium cepa L. - pickling onion - allium cepa - Allium cepa - - - - - - - - - - - - - Garlic (*Allium sativum*) is a species in the onion genus, *Allium*.Its close relatives include the onion, shallot, leek, chive, and Chinese onion. Garlic is native to Central Asia and northeastern Iran, and has long been a common seasoning worldwide, with a history of several thousand years of human consumption and use. [https://en.wikipedia.org/wiki/Garlic] - garlic plant - - http://langual.org - GRIN:2368 - GRIN:315611 - ITIS:42652 - MANSFELD:212 - PLANTS:ALSA2 - http://eol.org/pages/1084926 - http://www.langual.org/langual_thesaurus.asp?termid=B1233 - garlic - Allium sativum L. - allium sativum - Allium sativum - - - - - - - - - - Asparagus - - - - - - - - - - garden asparagus - Asparagus officinalis - - - - - - - - - - commelinids - - - - - - - - - - cumin - Cuminum cyminum - - - - - - - - - - vascular plants - Tracheophyta - - - - - - - - - - seed plants - Spermatophyta - - - - - - - - - - Eumetazoa - - - - - - - - - - Asteridae - asterids - - - - - - - - - - rosids - - - - - - - - - - Fabales - - - - - - - - - - Maleae - - - - - - - - - - Asparagales - - - - - - - - - - chordates - Chordata - - - - - - - - - - Vertebrata - vertebrates - Vertebrata <vertebrates> - - - - - - - - - - Gnathostomata - jawed vertebrates - Gnathostomata <vertebrates> - - - - - - - - - - euphyllophytes - Euphyllophyta - - - - - - - - - - Archosauria - - - - - - - - - - birds - avian - Aves - - - - - - - - - - Neognathae - - - - - - - - - - landfowls - Galliformes - - - - - - - - - - turkeys - Phasianidae - - - - - - - - - - Gallus domesticus - bantam - chicken - chickens - gallus gallus domesticus - Gallus gallus - - - - - - - - - - Phasianinae - - - - - - - - - - Meleagris - - - - - - - - - - whales, hippos, ruminants, pigs, camels etc. - Artiodactyla - - - - - - - - - - fabids - - - - - - - - - - malvids - - - - - - - - - - campanulids - - - - - - - - - - lamiids - - - - - - - - - - eutherian mammals - placental mammals - placentals - Eutheria - - - - - - - - - - ginger - Zingiber officinale - - - - - - - - - - Brassiceae - - - - - - - - - - boars - pigs - Suidae - - - - - - - - - - - A suid native to much of Eurasia and North Africa. - - Damion Dooley - - - http://langual.org - 2020-04-01T23:10:20Z - pig - pigs - swine - wild boar - Sus scrofa - - - - - - - - - - Bovidae - - - - - - - - - - oxen, cattle - Bos - - - - - - - - - - Cattle (colloquially cows) are the most common type of large domesticated ungulates. They are a prominent modern member of the subfamily *Bovinae*, are the most widespread species of the genus *Bos*, and are most commonly classified collectively as *Bos taurus*... with three subspecies: *Bos taurus primigenius, Bos taurus indicus, Bos taurus taurus*. - cattle - - - - - ITIS:183838 - MSW3:14200687 - Bos taurus Linnaeus, 1758 - bovine - cattle - cow - dairy cow - domestic cattle - domestic cow - ox - oxen - Bos taurus - - - - - - - - - - - Curcuma - - - - - - - - - processed material - Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples - - Is a material entity that is created or changed during material processing. - PERSON: Alan Ruttenberg - - - processed material - - - - - - - - - organism - - A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. - WEB: http://en.wikipedia.org/wiki/Organism - - organism - - - - - - - - - A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities - - quality - - - - - - - - - A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. - - physical quality - - - - - - - - - A quality which inheres in a continuant. - - physical object quality - - - - - - - - - A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity characterized by particles arranged such that their shape and volume are relatively stable. - - quality of a solid - - - - - - - - - A physical quality inhering in an entity exhibiting the physical characteristics of an amorphous (non-crystalline) form of matter between a gas and a solid that has a definite volume, but no definite shape. - - quality of a liquid - - - - - - - - - A quality inhering in a bearer by virtue of its constitution. - - quality of a substance - - - - - - - - - - A plant structure (PO:0005679) which is a whole organism. - - genet (broad) - ramet (broad) - - PO_GIT:538 - PO_GIT:69 - planta entera (Spanish, exact) - 植物体全体 (Japanese, exact) - bush (narrow) - frutex (narrow) - frutices (narrow) - gametophyte (narrow) - herb (narrow) - liana (narrow) - prothalli (narrow) - prothallium (narrow) - prothallus (narrow) - seedling (narrow) - shrub (narrow) - sporophyte (narrow) - suffrutex (narrow) - suffrutices (narrow) - tree (narrow) - vine (narrow) - woody clump (narrow) - plant_anatomy - clonal colony (related) - colony (related) - PO:0000003 - - - Examples include plant embryo (PO:0009009), megagametophyte (PO:0025279) and microgametophyte (PO:0025280). - whole plant - - - - - - - - - - - - - - - - - - - - - A phyllome primordium (PO:0025128) that develops from a vascular leaf anlagen (PO:0025431) and is part of a vegetative shoot apex (PO:0025223) and is committed to the development of a vascular leaf (PO:0009025). - - PO_GIT:466 - leaf primordium (exact) - portion of vascular leaf primordium tissue (exact) - primordio de hoja (Spanish, exact) - vascular leaf primordia (exact, plural) - 葉原基 (Japanese, exact) - plant_anatomy - PO:0000017 - vascular leaf primordium - - - - - - - - - A floral structure primordium (PO:0025477) that is committed to the development of an ovule (PO:0020003). - - PO_GIT:465 - portion of ovule primordium tissue (exact) - primordio de &#243vulo (Spanish, exact) - 胚珠原基（可視的） (Japanese, exact) - plant_anatomy - PO:0000018 - The transition from ovule primordium to ovule occurs when an integument (PO:0020021) begins to develop from the protoderm (PO:0006210). - ovule primordium - - - - - - - - - A floral structure primordium (PO:0025477) that is committed to the development of a gynoecium (PO:0009062). - - PO_GIT:465 - pistil primordium (exact) - portion of gynoecium primordium tissue (exact) - primordio de gineceo (Spanish, exact) - 雌蕊原基(可視的） (Japanese, exact) - plant_anatomy - PO:0000019 - Use carpel primordium (PO:0004703) for the primordium (PO:0025127) of an individual carpel (PO:0009030). - gynoecium primordium - - - - - - - - - A shoot axis (PO:0025029) that is the most distal part of a shoot system (PO:0009006) and has as parts a shoot apical meristem (PO:0020148) and the youngest primordia (PO:0025127). - - PO_GIT:234 - &#225pice del epiblasto (epiblastema) (Spanish, exact) - シュート頂、茎頂 (Japanese, exact) - plant_anatomy - PO:0000037 - - shoot axis apex - - - - - - - - - A root (PO:0009005) that is initiated in a developing plant embryo (PO:0009009). - - PO_GIT:594 - embryonic root (exact) - ra&#237z embri&#243nica (Spanish, exact) - 初期の根、胚根 (Japanese, exact) - plant_anatomy - PO:0000045 - - embryo root - - - - - - - - - - - - - - - A portion of meristem tissue (PO:0009013) which is the organogenic region of the meristem, characterized by higher rates of cell division. - - zona perif&#233rica (Spanish, exact) - 周辺帯 (Japanese, exact) - plant_anatomy - peripheral meristem (related) - PO:0000225 - peripheral zone - - - - - - - - - A portion of reproductive shoot apical meristem tissue (PO:0008028) that gives rise to the floral organs (PO:0025395). - - PO:0006329 - PO:0006373 - PO:0006374 - PO:0025091 - floral meristem (exact) - mersitema floral (Spanish, exact) - 花芽分裂組織 (Japanese, exact) - Poaceae floret meristem (narrow) - ear floret meristem (narrow) - floret meristem (narrow) - tassel floret meristem (narrow) - plant_anatomy - floral apical meristem (related) - PO:0000229 - In Zea mays and other grasses, the floret meristem is part of a spikelet and develops into a specific type of floret. If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the spikelet type that the meristem is part of. Choose the most specific term possible from: spikelet (PO:0009051), ear spikelet (PO:0006320), ear pedicellate spikelet (PO:0006348), ear sessile spikelet (PO:0006349), tassel spikelet (PO:0006309), tassel pedicellate spikelet (PO:0006312), tassel sessile spikelet (PO:0006311). - flower meristem - - - - - - - - - A native plant cell (PO:0025606) synthesizing protoplasm and producing new cells by division and with only a primary cell wall. - - CL:0000034 - PO_GIT:272 - c&#233lula meristem&#225tica (Spanish, exact) - stem cell (exact) - 分裂組織細胞 (Japanese, exact) - plant_anatomy - PO:0004010 - - meristematic cell - - - - - - - - - - - - - - - A primordium (PO:0025127) that develops from a root anlagen (PO:0025433) and is committed to the development of a root (PO:0009005). - - PO_GIT:467 - portion of root primordium tissue (exact) - primordio de ra&#237z (Spanish, exact) - root primordia (exact, plural) - 根原基（可視的） (Japanese, exact) - plant_anatomy - PO:0005029 - A root primordium may arise from cells of a pericycle (PO:0006203) in a root in most seed plant (pericyclic lateral root primordium; PO:0025492), from cells of an endodermis (PO:0000252) in ferns and some seed plants (non-pericyclic lateral root primordium: PO:0025493), or from cells of a shoot axis (PO:0025029), in the case of a basal root primordium (PO:0025479) or shoot-borne root primordium (PO:0025480). Transition from root primordium to root occurs with the formation of a root cap (PO:0020123), shortly after the development of a root apical meristem (PO:0020147). - root primordium - - - - - - - - - - - - - - - - - - - - - A lateral plant organ (PO:0009008) produced by a shoot apical meristem (PO:0020148). - - filoma (Spanish, exact) - フィロム、葉(的）器官 (Japanese, exact) - plant_anatomy - PO:0006001 - - - phyllome - - - - - - - - - - - - - - - A portion of meristem tissue (PO:0009013) that is part of a shoot system (PO:0009006). - - PO_GIT:472 - PO_GIT:583 - meristema del epiblasto (epiblastema) (Spanish, exact) - シュート分裂組織 (Japanese, exact) - plant_anatomy - PO:0006079 - - shoot system meristem - - - - - - - - - A portion of meristem tissue (PO:0009013) that is the outer layer of an apical meristem (PO:0020144), or the outer layer of a plant embryo proper (PO:0000001), and gives rise to a portion of epidermis (PO:0005679). - - PO_GIT:125 - portion of protoderm tissue (exact) - protodermis (Spanish, exact) - 前表皮、原表皮 (Japanese, exact) - plant_anatomy - dermatogen cell (related) - PO:0006210 - A protoderm may or may not arise from independent initial cells (PO:0004011). Some researchers also refer to it as an epidermis in a meristematic state. - protoderm - - - - - - - - - - - - - - - A plant structure development stage (PO:0009012) that has as primary participant a whole plant (PO:0000003). - - PO_GIT:390 - plant_structure_development_stage - Solanaceae whole plant growth stages (SGN:0000001) (related) - cereal plant growth stage ontology (GRO:0007199) (related) - maize growth stage (GRO:0007002) (related) - plant growth stages in Arabidopsis (TAIR:0000021) (related) - rice growth stage (GRO:0007040) (related) - sorghum growth stage (GRO:0007124) (related) - wheat, barley and oat growth stage (GRO:0007156) (related) - PO:0007033 - - whole plant development stage - - - - - - - - - A shoot apical meristem (PO:0020148) that gives rise to the apical growth of vegetative tissues and organs. - - PO_GIT:36 - meristema vegetativo apical del epiblasto (epiblastema) (Spanish, exact) - 栄養シュート頂端分裂組織 (Japanese, exact) - plant_anatomy - vegetative meristem (related) - PO:0008016 - vegetative shoot apical meristem - - - - - - - - - - - - - - - A shoot apical meristem (PO:0020148) that gives rise to the apical growth of reproductive tissues and organs. - - PO_GIT:36 - meristema apical reproductivo del epiblasto (epiblastema) (Spanish, exact) - 生殖シュート頂端 分裂組織 (Japanese, exact) - plant_anatomy - PO:0008028 - reproductive shoot apical meristem - - - - - - - - - - - - - - - A multi-tissue plant structure (PO:0025496) that develops from a gynoecium (PO:0009062), or a single carpel (PO:0009030), and at maturity may have as parts one or more seeds (PO:0009010). - - PO:0020067 - PO:0020068 - PO:0020069 - PO:0020070 - PO:0020071 - PO:0020072 - PO:0020073 - PO:0020074 - PO:0020076 - PO:0020077 - PO:0020078 - PO:0020079 - PO:0020080 - PO:0020082 - PO:0020083 - PO:0020087 - PO:0020107 - aggregate fruit (broad) - compound fruit (broad) - dehiscent fruit (broad) - diaspore (broad) - indehiscent fruit (broad) - multiple fruit (broad) - propagule (broad) - PO_GIT:76 - frucht (exact, German) - fruto (exact, Spanish) - 果実 (exact, Japanese) - coenocarp (narrow) - syncarp (narrow) - plant_anatomy - PO:0009001 - - - - - - - A fruit (PO:0009001) may contain additional plant structures (PO:0009011) that were part of a flower (PO:0009046) and mature along with the gynoecium, such as a receptacle (PO:0009064). A fruit may develop without fertilization in cases of parthenocarpy, apomixis, or other hormone-induced conditions and may not always contain seeds (PO:0009010). When annotating to fruit (PO:0009001) that are referred to as ‘aggregate’, ‘multiple’, or ‘compound’, please annotate directly to the appropriate plant structure, such as receptacle, hypanthium (PO:0009065) or infructescence (PO:0006342). Fruits only occur in angiosperms. - fruit - https://en.wikipedia.org/wiki/Fruit_anatomy - - - - - - - - - A cell which is a plant structure (PO:0009011). - - cell (broad) - GO:0005623 - PO_GIT:56 - c&#233lula vegetal (Spanish, exact) - 植物細胞 (Japanese, exact) - plant_anatomy - PO:0009002 - - - - Applies to cells that are living or dead at maturity (e.g., fiber cell or tracheid) and includes any external encapsulating structures (if present) such as the plasma membrane and the plant-type cell wall. Definition of cell GO:0005623: "The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope". GO:0009505. Definition of plant-type cell wall (GO:0009505): A more or less rigid structure lying outside the cell membrane of a cell and composed of cellulose and pectin and other organic and inorganic substances, synonym; exact: cellulose and pectin-containing cell wall. - plant cell - - - - - - - - - - - - - - - - - - - - - A plant axis (PO:0025004) that lacks shoot axis nodes (PO:0005004) and usually grows indeterminately. - - PO:0003006 - PO_GIT:578 - ra&#237z (Spanish, exact) - radices (exact, plural) - radix (exact) - 根 (Japanese, exact) - aerial root (narrow) - climbing root (narrow) - plant_anatomy - PO:0009005 - - - - - - - - - - Roots function in the absorption of water and inorganic nutrients, anchoring the plant body to the substrate and supporting it, storage of food and nutrients, and vegetative reproduction. The roots of most vascular plant species enter into symbiosis with soil-borne microorganisms. Roots are usually positively geotropic and found underground, although there are many exceptions such as the aerial roots of orchids. Roots often form secondary thickening from the root lateral meristem (PO:0006308). Commonly thought of as one of the three basic parts of the plant body, along with the shoot axis (PO:0025029) and leaves (PO:0025034). - root - - - - - - - - - A collective plant organ structure (PO:0025007) that produces shoot-borne portions of meristem tissue (PO:0009013) and the plant structures (PO:0009011) that arise from them. - - PO_GIT:135 - sistema de epiblasto (epiblastema) (Spanish, exact) - シュート系、苗条系 (Japanese, exact) - tree crown (narrow) - plant_anatomy - Poaceae crown (related) - shoot (related) - thalli (related) - thallus (related) - PO:0009006 - - - The shoot system is generally used to refer to the above-ground plant parts, although some plants have parts of their shoot system underground. For example, a rhizome (PO:0004542), bulb (PO:0025356), a corm (PO:0025355) or a subterranean tuber (PO:0004547), as in Solanum tuberosum (potato) or yam, are all part of the shoot system. - shoot system - - - - - - - - - A plant structure (PO:0009011) that consists predominantly of similarly specialized plant cells (PO:0009002) of one or more types. - - portion of tissue (broad) - tissue (broad) - PO_GIT:59 - porci&#243n de un tejido vegetal (Spanish, exact) - 植物組織の一部 (Japanese, exact) - plant_anatomy - plant tissue (related) - PO:0009007 - - - A portion of plant tissue may contain one or several types of cells that are organized in a specific spatial arrangement into a structural unit (which includes a mass of callus) and may include an intercellular matrix. May include other types of isolated cells, such as idioblasts. - portion of plant tissue - - - - - - - - - A multi-tissue plant structure (PO:0025496) that is a functional unit, is a proper part of a whole plant (PO:0000003), and includes portions of plant tissue (PO:0009007) of at least two different types that derive from a common developmental path. - - organ (broad) - PO_GIT:55 - &#243rgano vegetal (Spanish, exact) - 植物 器官 (Japanese, exact) - plant_anatomy - compound plant organ (related) - simple plant organ (related) - PO:0009008 - - Examples include stem (PO:0009047), leaf (PO:0025034), and root (PO:0009005). May include individual plant cells (PO:0009002) that are not part of a portion of plant tissue (e.g., idioblasts, PO:0000283). A plant organ may have one or more different plant organs as parts, such as a sporophyll (PO:0009026) that may have as part a sporangium (PO:0025094) or a carpel (PO:0009030) that may have as part a plant ovule (PO:0020003). - plant organ - - - - - - - - - A whole plant (PO:0000003) that participates in the plant embryo stage (PO:0007631). - - embryo (broad) - PO_GIT:92 - embri&#243n (Spanish, exact) - 植物胚 (Japanese, exact) - plant_anatomy - germ (related) - PO:0009009 - A plant embryo is generally formed after the first division of a plant zygote (PO:0000423), but in the case of a nucellar (adventitious) plant embryo (PO:0004537), somatic plant embryo (PO:0025302), microspore-derived cultured plant embryo (PO:0025305), and other embryos that arise through apogamy, it begins after the division of a single cell that is not a zygote. The end of the embryo stage varies among taxa; the beginning of a seed germination stage (PO:0007057) in seed plants, formation of the first vascular leaf (PO:0009025) in pteridophytes, the beginning of development of a sporangium (PO:0025094) in bryophytes, or the beginning of the formation of a plant organ (PO:0009008) such as a root (PO:0009005), shoot axis (PO:0025029), or vascular leaf (PO:0009025) in a cultured plant embryo (PO:0000010). - plant embryo - - - - - - - - - - - - - - - - - - - - - A multi-tissue plant structure (PO:0025496) that develops from a plant ovule (PO:0020003) and has as parts a plant embryo (PO:0009009) enclosed in a seed coat (PO:0009088). - - diaspore (broad) - PO_GIT:405 - semilla (Spanish, exact) - 種子 (Japanese, exact) - pyrene (narrow) - plant_anatomy - PO:0009010 - - - - - - - - - - A seed generally develops from an ovule (PO:0020003) after fertilization, but may develop without fertilization in the case of apogamy (e.g., adventitious embryos or somatic embryos). A seed is a reproductive unit of seed plants (gymnosperms, angiosperms, and fossil pteridosperms). - seed - - - - - - - - - - A plant anatomical entity (PO:0025131) that is, or was, part of a plant, or was derived from a part of a plant. - - - PO_GIT:57 - estructura vegetal (Spanish, exact) - 植物 構造 (Japanese, exact) - plant_anatomy - PO:0009011 - - 'Part' includes both proper parts and the whole plant. CARO:0000003 'connected anatomical structure' is defined as: Material anatomical entity that is a single connected structure with inherent 3D shape, generated by coordinated expression of the organism's own genome. - plant structure - - - - - - - - - A stage in the life of a plant structure (PO:0009011) during which the plant structure undergoes developmental processes. - - PO:0007021 - PO_GIT:185 - etapa de desarrollo de estructura vegetal (Spanish, exact) - plant growth and development stage (exact) - plant_structure_development_stage - Arabidopsis growth (related) - PO:0009012 - - Refers to GO:0032502 'developmental process', which includes growth, differentiation, and senescence, and BFO:0000003 'ocurrent'. - plant structure development stage - - - - - - - - - - - - - - - A portion of plant tissue (PO:0009007) in which plant cells (PO:0009002) have retained their embryonic characteristics, or have reverted to them secondarily, and that divide to produce new cells that can undergo differentiation to form mature tissues, i.e. they have a capacity for morphogenesis and growth. - - PO_GIT:472 - meristem (exact) - meristema (Spanish, exact) - meristematic tissue (exact) - 分裂組織 (Japanese, exact) - plant_anatomy - PO:0009013 - - portion of meristem tissue - - - - - - - - - - - - - - - - - - - - - A leaf (PO:0025034) in a vascular plant. - - PO_GIT:137 - foliage leaf (exact) - hoja vascular (Spanish, exact) - leaf, vascular (exact) - vascular leaves (exact, plural) - 維管束のある葉, または維管束植物の葉 (Japanese, exact) - ascidia (narrow) - ascidium (narrow) - fiddlehead (narrow) - frond (narrow) - needle-like leaf (narrow) - pitcher (narrow) - pitcher blade (narrow) - pitcher-blade (narrow) - scale-like leaf (narrow) - sterile frond (narrow) - trophophyll (narrow) - plant_anatomy - crozier (related) - macrophyll (related) - megaphyll (related) - PO:0009025 - - - - - - - - - - - - - Has vascular tissue. From APweb Glossary: In angiosperms, commonly thought of as one of the three basic parts of the seed plant body, a structure usually of determinate growth, without secondary thickening, and of superficial origin, often flattened and photosynthetic in part, and in the axil of which is found a bud. Occurs in the sporophytic phase of a plant life cycle. - vascular leaf - - - - - - - - - - - - - - - A determinate reproductive shoot system (PO:0025082) that has as part at least one carpel (PO:0009030) or at least one stamen (PO:0009029) and does not contain any other determinate shoot system (PO:0009006) as a part. - - PO:0004541 - PO_GIT:160 - PO_GIT:259 - flor (Spanish, exact) - 花 (Japanese, exact) - Asteraceae floret (narrow) - basal flower (narrow) - double flower (narrow) - hermaphrodite flower (narrow) - monoclinous flower (narrow) - perfect flower (narrow) - plant_anatomy - floret (related) - PO:0009046 - - - - The characteristic reproductive structure of angiosperms. May have as part one or more petals, sepals or tepals. May contain one or more pistillode (PO:0009078), staminode (PO:0009077) or other aborted organs that don't show up in mature form. - flower - - - - - - - - - A shoot axis (PO:0025029) that is the primary axis of a plant. - - PO_GIT:52 - PO_GIT:96 - ca&#241a (Spanish, exact) - culm (exact) - eje primario (Spanish, exact) - primary axis (exact) - primary stem (exact) - tallo (Spanish, exact) - tronco (Spanish, exact) - 茎 (Japanese, exact) - bole (narrow) - cane (narrow) - caudex (narrow) - caudices (narrow) - core (narrow) - primocane (narrow) - scape (narrow) - stalk (narrow) - trunk (narrow) - plant_anatomy - PO:0009047 - - - A stem often bears leaves and buds. It is usually above ground, and is more or less negatively geotropic. - stem - - - - - - - - - - - - - - - - - - - - - A collective phyllome structure (PO:0025023) composed all of the carpels (PO:0009030) in a flower (PO:0009046). - - PO:0006317 - PO:0006357 - PO:0006365 - PO:0006384 - PO:0006391 - PO:0006394 - PO:0006403 - PO:0006404 - PO:0006423 - PO:0006424 - PO:0006425 - PO:0006426 - PO:0025089 - pistil (broad) - PO_GIT:470 - PO_GIT:71 - PO_GIT:98 - ginoecio (Spanish, exact) - gynaecium (exact) - gynoecia (exact, plural) - 雌蕊群 (Japanese, exact) - Poaceae gynoecium (narrow) - Zea gynoecium (narrow) - apocarpous gynoecium (narrow) - gynoecium of ear floret (narrow) - gynoecium of lower floret of pedicellate spikelet of ear (narrow) - gynoecium of lower floret of pedicellate spikelet of tassel (narrow) - gynoecium of lower floret of sessile spikelet of ear (narrow) - gynoecium of lower floret of sessile spikelet of tassel (narrow) - gynoecium of tassel floret (narrow) - gynoecium of upper floret of pedicellate spikelet of ear (narrow) - gynoecium of upper floret of pedicellate spikelet of tassel (narrow) - gynoecium of upper floret of sessile spikelet of ear (narrow) - gynoecium of upper floret of sessile spikelet of tassel (narrow) - syncarpous gynoecium (narrow) - plant_anatomy - PO:0009062 - - - If annotating gene expression to a gynoecium with a single carpel (PO:0009030), the annotation should go on carpel. A gynoecium with two or more carpels may be either syncarpous (carpels fused) or apopcarpous (carpels free) or the carpels may be partially fused. The word pistil is used synonymously with gynoecium for a synocarpous gynoecium, and synonymously with carpel for an apocarpous gynoecium, whether it has one or more carpels. In Zea mays, gynoecia of tassel florets and of the lower florets of ear spikelets usually do not develop fully, and they are present in a rudimentary state. If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the corresponding floret type. Choose the most specific term possible from: spikelet floret (PO:0009082), ear floret (PO:0006354), lower floret of pedicellate spikelet of ear (PO:0006353), lower floret of sessile spikelet of ear (PO:0006351), upper floret of pedicellate spikelet of ear (PO:0006350), upper floret of sessile spikelet of ear (PO:0006352), tassel floret (PO:0006310), lower floret of pedicellate spikelet of tassel (PO:0006313), lower floret of sessile spikelet of tassel (PO:0006315), upper floret of pedicellate spikelet of tassel (PO:0006314), upper floret of sessile spikelet of tassel (PO:0006316). - gynoecium - - - - - - - - - - - - - - - A plant organ (PO:0009008) that has as parts a nucellus (PO:0020020) in which a female gametophyte (PO:0025279) is located, one or two integuments (PO:0020021), and a funicle (PO:0020006). - - PO:0006457 - PO:0006491 - PO_GIT:464 - PO_GIT:70 - &#243vulo vegetal (Spanish, exact) - 胚珠 (Japanese, exact) - Poaceae ovule (narrow) - Zea ovule (narrow) - plant_anatomy - PO:0020003 - - - A seed (PO:0009010) develops from a plant ovule. In angiosperms, a plant ovule is part of a plant ovary (PO:0009072). In conifers, a plant ovule is part of an ovuliferous scale (add term). If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the corresponding floret type. Choose the most specific term possible from: spikelet floret (PO:0009082), ear floret (PO:0006354), upper floret of pedicellate spikelet of ear (PO:0006350), upper floret of sessile spikelet of ear (PO:0006352). - plant ovule - - - - - - - - - An embryo root (PO:0000045) that is the basal continuation of a hypocotyl (PO:0020100) in a plant embryo (PO:0009009) or a seedling (PO:0000003). - - PO_GIT:344 - rad&#237cula (Spanish, exact) - 幼根 (Japanese, exact) - plant_anatomy - PO:0020031 - - May develop into the primary root (PO:0020127) and eventually the root system (PO:0025025) of an adult plant. Sometimes abortive. - radicle - - - - - - - - - - - - - - - A stalk (PO:0025066) of a vascular leaf (PO:0009025). - - http://www.langual.org/langual_thesaurus.asp?termid=C0304 - pec&#237olo (Spanish, exact) - 葉柄 (Japanese, exact) - plant_anatomy - PO:0020038 - - LanguaL definition: Leafstalk, the slender, usually cylindrical portion of a leaf, which supports the blade and is attached to the stem (Source: Webster's) - petiole - - - - - - - - - - - - - - - A root (PO:0009005) that develops directly from a seedling radicle (PO:0020127). - - PO:0020089 - PO_GIT:161 - ra&#237z primaria (Spanish, exact) - tap root (exact) - 一次根 (Japanese, exact) - plant_anatomy - PO:0020127 - - The first root of a plant. In dicots and gymnosperms it becomes the tap root, the central axis of a root system (PO:0025025). - primary root - - - - - - - - - - - - - - - A maximal portion of meristem tissue (PO:0009013) located at a shoot apex (PO:0000037) or root tip (PO:0000025). - - promeristem (broad) - PO_GIT:579 - AM (exact) - meristema apical (Spanish, exact) - 頂端分裂組織 (Japanese, exact) - plant_anatomy - primary meristem (related) - PO:0020144 - - apical meristem - - - - - - - - - - - - - - - - A shoot system meristem (PO:0006079) formed at the apex of the shoot axis (PO:0025029), including those originating from an axillary bud meristem (PO:0000232). - - promeristem (broad) - PO_GIT:472 - SAM (exact) - meristema apical del epiblasto (epiblastema) (Spanish, exact) - 茎頂分裂組織 (Japanese, exact) - plant_anatomy - primary shoot meristem (related) - PO:0020148 - - shoot apical meristem - - - - - - - - - - - - - - - - - - - - - - - - - - A cardinal part of multi-tissue plant structure (PO:0025498) that is a proper part of a plant organ (PO:0009008) and includes portions of plant tissue (PO:0009007) of at least two different types. - - rwalls - 2010-02-11T01:18:24Z - PO_GIT:52 - PO_GIT:60 - cardinal part of plant organ (exact) - parte de un &#243rgano cardinal (Spanish, exact) - 基本的な（主要な）器官部 (Japanese, exact) - plant_anatomy - PO:0025001 - - - Cardinal refers to the fact that these are biologically meaningful and not arbitrary parts. Examples include petiole (PO:0020038), lamina (PO:0025060), and leaflet (PO:0020049). See also collective organ part structure (PO:0025269), for plant structures composed of parts of multiple organs. - cardinal organ part - - - - - - - - - An axial plant organ (PO:0009008). - - rwalls - 2010-07-01T03:44:41Z - eje de la planta (Spanish, exact) - plant axes (exact, plural) - 植物軸（軸柱） (Japanese, exact) - plant_anatomy - PO:0025004 - - Includes roots and shoots. - plant axis - - - - - - - - - - - - - - - A collective plant structure (PO:0025497) that is a proper part of a whole plant (PO:0000003), and is composed of two or more adjacent plant organs (PO:0009008) and the associated portions of plant tissue (PO:0009007). - - rwalls - 2010-02-09T04:12:11Z - PO_GIT:63 - estructura vegetal colectiva de &#243rgano (Spanish, exact) - 集合植物器官構造 (Japanese, exact) - plant_anatomy - PO:0025007 - - Organs can be of the same type or different types. Examples include flower (PO:0009046), perianth (PO:0009058), and inflorescence (PO:0009049). See also collective organ part structure (PO:0025269), for plant structures composed of parts of multiple organs, but no complete plant organs. This was formerly named collective plant structure. - collective plant organ structure - - - - - - - - - A collective plant organ structure (PO:0025007) that consists of two or more phyllomes (PO:0006001) originating from the same node or from one or more adjacent nodes with compressed shoot internodes (PO:0005005). - - Laurel_Cooper - 2010-04-28T11:04:34Z - PO:0008033 - cycle (broad) - verticil (broad) - PO_GIT:90 - PO_GIT:99 - estructura colectiva del filoma (Spanish, exact) - 葉的器官が集まった構造 (Japanese, exact) - floral whorl (narrow) - whorl (narrow) - plant_anatomy - phyllome whorl (related) - PO:0025023 - - collective phyllome structure - - - - - - - - - - - - - - - A collective plant organ structure (PO:0025007) that produces root meristems (PO:0006085), the plant structures (PO:0009011) that arise from them and the parts thereof. - - rwalls - 2010-07-01T02:11:26Z - root (broad) - PO_GIT:136 - sistema de ra&#237z (Spanish, exact) - 根系 (Japanese, exact) - plant_anatomy - PO:0025025 - - Generally the below ground portion of a vascular plant. - root system - - - - - - - - - - - - - - - A plant axis (PO:0025004) that is part of a shoot system (PO:0009006). - - rwalls - 2010-07-01T03:46:35Z - caullome (exact) - eje del epiblasto (epiblastema) (Spanish, exact) - シュート軸 (Japanese, exact) - plant_anatomy - shoot (related) - PO:0025029 - - - - - - - Often bears leaves and branches. In vascular plants, has at least one node and one internode. - shoot axis - - - - - - - - - - A phyllome (PO:0006001) that is not associated with a reproductive structure. - - http://langual.org - rwalls - 2010-07-12T01:31:44Z - PO_GIT:274 - PO_GIT:301 - http://www.langual.org/langual_thesaurus.asp?termid=C0200 - hoja (Spanish, exact) - 葉 (Japanese, exact) - plant_anatomy - PO:0025034 - - LanguaL definition: The flat or fleshy expanded blade (lamina) including a small and insignificant leafstalk but excluding a large and fleshy leafstalk such as celery stalks or rhubarb stalks. - -LanguaL curation note: If the part indexed consists of a large leafstalk and a leaf blade, use *PLANT ABOVE SURFACE, EXCLUDING FRUIT OR SEED*. Compare *STEM, STALK (WITHOUT LEAVES)*. - leaf - - - - - - - - - A cardinal organ part (PO:0025001) that is elongated and sub-cylindrical to cylindrical and supports another cardinal organ part. - - Laurel_Cooper - 2009-12-18T10:09:17Z - PATO:0001873 - PATO:0002226 - PO_GIT:52 - PO_GIT:78 - tallo de alto orden (secundario, terciario, etc) (Spanish, exact) - 柄 (Japanese, exact) - plant_anatomy - stipe (related) - PO:0025066 - - Some stalks may be ridged or grooved. - stalk - - - - - - - - - - - - - - - A shoot system (PO:0009006) in the sporophytic phase that has as part at least one sporangium (PO:0025094). - - rwalls - 2010-09-17T09:49:10Z - sistema de brote reproductivo (Spanish, exact) - 生殖シュート 系、苗条系 (Japanese, exact) - plant_anatomy - PO:0025082 - - reproductive shoot system - - - - - - - - - - - - - - - - - - - - - - - - - - A plant structure (PO:0009011) that is part of an plant embryo (PO:0009009). - - rwalls - 2010-11-05T01:36:24Z - PO_GIT:245 - PO_GIT:339 - embryonic plant structure (exact) - estructura vegetal embri&#243nica (Spanish, exact) - 胚性植物構造 (Japanese, exact) - plant_anatomy - PO:0025099 - Includes plant structures that only occur in embryos (such as suspensor) as well as plant structures that are part of an embryo when a plant is in the embryonic phase (such as embryonic radicle). - embryo plant structure - - - - - - - - - A portion of meristem tissue (PO:0009013) that has as parts protoderm (PO:0006210) and sub-epidermal meristematic tissue and is committed to the development of a particular plant structure (PO:0009011). - - rwalls - 2010-11-15T09:10:22Z - PO_GIT:186 - portion of primordial tissue (exact) - portion of primordium tissue (exact) - primordia (exact, plural) - primordio (Spanish, exact) - 原基（可視的） (Japanese, exact) - plant_anatomy - PO:0025127 - A primordium appears as a protrusion and is the first distinct form of a plant organ (PO:0009008), cardinal organ part (PO:0025001), or collective plant organ structure (PO:0025007). The transition from a primordium to the plant structure it develops into is marked by the development of non-meristematic cells, although meristematic cells may be present after the transition. - primordium - - - - - - - - - - - - - - - - - - - - - A primordium (PO:0025127) that develops from a phyllome anlagen (PO:0025430) and is part of a shoot apex (PO:0000037) and is committed to the development of a phyllome (PO:0006001). - - rwalls - 2010-11-15T09:27:11Z - PO_GIT:466 - phyllome primordia (exact, plural) - portion of phyllome primordium tissue (exact) - primordio del filoma (Spanish, exact) - フィロム原基（可視的） (Japanese, exact) - plant_anatomy - PO:0025128 - The transition from phyllome primordium to phyllome occurs when the first non-meristematic tissue develops begins to develop. - phyllome primordium - - - - - - - - - An anatomical entity that is or was part of a plant. - - rwalls - 2010-11-15T11:41:38Z - PO_GIT:224 - entidad anat&#243mica vegetal (Spanish, exact) - 植物 解剖学（形態）的実体 (Japanese, exact) - plant_anatomy - PO:0025131 - Includes both material entities such as plant structures and immaterial entities such as plant anatomical spaces. CARO:0000000 'anatomical entity' is defined as: A part of a cellular organism that is either an immaterial entity or a material entity with granularity aboove the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. Refers to BFO:0000004 'independent continuant'. - plant anatomical entity - - - - - - - - - A shoot apex that has as part a reproductive shoot apical meristem. - - rwalls - 2010-12-20T08:47:03Z - &#225pice reproductivo del epiblasto (epiblastema) (Spanish, exact) - 生殖シュート頂、茎頂 (Japanese, exact) - plant_anatomy - PO:0025222 - reproductive shoot apex - - - - - - - - - - - - - - - A shoot apex PO:0000037) that has as part a vegetative shoot apical meristem (PO:0008016). - - rwalls - 2010-12-20T08:47:03Z - PO_GIT:234 - &#225pice vegetativo del epiblasto (epiblastema) (Spanish, exact) - 栄養シュート頂、栄養枝頂 (Japanese, exact) - plant_anatomy - PO:0025223 - vegetative shoot apex - - - - - - - - - - - - - - - - - - - - - A portion of plant tissue (PO:0009007) that is part of a plant embryo (PO:0009009). - - rwalls - 2010-12-20T12:27:10Z - portion of embryo tissue (broad) - PO_GIT:338 - portion of embryonic plant tissue (exact) - tejido embri&#243nico vegetal (Spanish, exact) - 植物胚性組織 の一部 (Japanese, exact) - plant_anatomy - PO:0025233 - This class is for tissues that only occur as part of an embryo. - portion of embryo plant tissue - - - - - - - - - - A radicle (PO:0020031) that is part of a plant embryo (PO:0009009). - - rwalls - 2011-04-25T10:41:14Z - PO_GIT:344 - embryonic radicle (exact) - rad&#237cula del embri&#243n (Spanish, exact) - 胚幼根 (Japanese, exact) - plant_anatomy - PO:0025296 - - May eventually develop into the root system (PO:0025025) of an adult plant. Sometimes is abortive. - plant embryo radicle - - - - - - - - - - - - - - - A radicle (PO:0020031) that is part of a whole plant (PO:0000003) in the seedling development stage (PO:0007131). - - rwalls - 2011-04-25T10:41:48Z - PO_GIT:344 - rad&#237cula de la pl&#225ntula (Spanish, exact) - 実生幼根 (Japanese, exact) - plant_anatomy - PO:0025297 - Develops from an embryo radicle (PO:0025296). May develop into the root system (PO:0025025) of an adult plant. Sometimes is abortive. - seedling radicle - - - - - - - - - A maximal whole plant development stage. - - rwalls - 2011-10-19T10:54:37Z - PO_GIT:230 - vida de la planta entera (Spanish, exact) - 植物体の一生 (Japanese, exact) - plant_structure_development_stage - PO:0025337 - There are only two types of life of whole plant. Every life of a whole plant is either a maximal gametophyte stage or a maximal sporophyte stage. - life of whole plant stage - - - - - - - - - - - - - - - A plant structure development stage (PO:0009012) that has as primary participant a collective plant structure (PO:0025497). - - rwalls - 2011-10-19T11:12:49Z - PO_GIT:391 - etapa de desarrollo de una estructura colectiva de la planta (Spanish, exact) - 集合的植物構造の発生過程 (Japanese, exact) - plant_structure_development_stage - PO:0025338 - Includes flower development stage (PO:0007615), corolla development stage (PO:0007604), and inflorescence development stage (PO:0001083). - collective plant organ structure development stage - - - - - - - - - A short, enlarged shoot system (PO:0009006) that has as parts a short stem (PO:0009047) in which the shoot internodes (PO:0005005) do not elongate, and one or more buds (PO:0000055) enclosed by fleshy leaves (PO:0009025) or leaf bases (PO:0020040). - - rwalls - 2011-11-16T03:39:15Z - diaspore (broad) - PO_GIT:173 - bulbo (Spanish, exact) - 球根、鱗茎 (Japanese, exact) - bulblet (narrow) - plant_anatomy - PO:0025356 - May serve as a storage and/or perennating organ. Usually underground. A bulb differs from a corm (PO:0025355) by having fleshy leaves or leaf bases. The outer leaves of a bulb are often dry and membranous, rather than fleshy. May bear adventitious roots. Examples include Alium and Tulipa. Not the same structure as a bulbil. - bulb - - - - - - - - - - - - - - - - - - - - - - - - - - A plant organ (PO:0009008) that is part of a flower (PO:0009046). - - rwalls - 2012-01-19T11:44:36Z - PO_GIT:423 - &#243rgano floral (Spanish, exact) - flower organ (exact) - 花器官 (Japanese, exact) - plant_anatomy - PO:0025395 - Includes phyllomes such as anthers and petals, as well as shoot axes such as androphores and gynophores. - floral organ - - - - - - - - - - - - - - - A portion of meristem tissue (PO:0009013) that is part of a peripheral zone (PO:0000225) of a shoot apical meristem (PO:0020148) and will give rise to a phyllome primordium (PO:0025128). - - Laurel_Cooper - 2012-02-07T08:20:10Z - phyllome meristem (broad) - PO_GIT:427 - フィロム原基 (Japanese, exact) - plant_anatomy - PO:0025430 - The phyllome anlagen is only detectable by gene expression, not morphology. - phyllome anlagen - - - - - - - - - - - - - - - A phyllome anlagen (PO:0025430) that will give rise to a vascular leaf primordium (PO:0000017) and is part of a peripheral zone (PO:0000225) of a shoot apical meristem (PO:0020148). - - Laurel_Cooper - 2012-02-07T08:40:37Z - leaf meristem (broad) - PO_GIT:407 - 維管束系葉原基 (Japanese, exact) - plant_anatomy - PO:0025431 - This is the region where you have the maximum concentration of auxin in the SAM (at least in a few species that have been studied). - vascular leaf anlagen - - - - - - - - - A portion of meristem tissue (PO:0009013) that is committed to the development of a root primordium (PO:0005029). - - Laurel_Cooper - 2012-02-08T01:00:56Z - PO_GIT:427 - precursor de ra&#237 (Spanish, exact) - 根原基 (Japanese, exact) - plant_anatomy - PO:0025433 - Only detectable by gene expression, not morphology. May arise in a pericycle (PO:0006203), as for lateral roots in most seed plants, an endodermis (PO:0000252), as for lateral roots in ferns, or from parenchyma cells (PO:0000074) that are part a shoot axis (PO:0025029), in the case of a basal root (PO:0025002) or shoot-borne root (PO:0000042). - root anlagen - - - - - - - - - - - - - - - A primordium (PO:0025127) that is committed to the development of a floral organ (PO:0025395) and is part of a reproductive shoot apex (PO:0025222). - - rwalls - 2012-04-26T03:57:09Z - PO_GIT:465 - floral structure primordia (exact, plural) - portion of floral structure primordium tissue (exact) - primordio de organo floral (Spanish, exact) - 花器官原基 (Japanese, exact) - plant_anatomy - PO:0025477 - - If annotating to a primordium of a floral structure, it is better to use the more specific term, such as petal primordium (PO:0000021) or anther primordium (PO:0006089). - floral organ primordium - - - - - - - - - A plant structure (PO:0009011) that has as parts two or more portions of plant tissue (PO:0009007) of at least two different types and which through specific morphogenetic processes forms a single structural unit demarcated by primarily bona-fide boundaries from other structural units of different types. - - Laurel_Cooper - 2012-06-11T14:57:00Z - PO_GIT:480 - estructura vegetal con m&#250ltiples tejidos (Spanish, exact) - 複数の組織からなる植物構造 (Japanese, exact) - plant_anatomy - PO:0025496 - Most multi-tissue plant structures have at least a small connection to other plant structures via a fiat boundary, such as where a leaf (PO:0025034) connects to a shoot axis (PO:0025029), a petal (PO:0009032) connects to a receptacle (PO:0009064), or a branch (PO:0025073) connects to a stem (PO:0009047). Refers to CARO:0000055 multi-tissue structure, def'n: Anatomical structure that has as parts two or more portions of tissue of at least two different types, and which through specific morphogenetic processes, form a single distinct structural unit demarcated by bona-fide boundries from other structural units of differnt types. - multi-tissue plant structure - - - - - - - - - A plant structure (PO:0009011) that is a proper part of a whole plant (PO:0000003) and includes two or more adjacent plant organs (PO:0009008) or adjacent cardinal organ parts (PO:0025001), along with any associated portions of plant tissue (PO:0009007). - - Laurel_Cooper - 2012-06-11T15:09:20Z - PO_GIT:479 - estructura vegetal colectiva (Spanish, exact) - 集合的植物構造 (Japanese, exact) - plant_anatomy - PO:0025497 - This is a parent term to describe both collective organ part structure (PO:0025269) (e.g. septum), as well as collective plant organ structure (PO:0025007) (which was formerly named collective plant structure), for example shoot system (PO:0009006). - collective plant structure - - - - - - - - - - - - - - - A plant structure (PO:0009011) that is a proper part of a multi-tissue plant structure (PO:0025496) and includes portions of plant tissues (PO:0009007) of at least two different types. - - Laurel_Cooper - 2012-06-11T15:28:44Z - PO_GIT:485 - parte cardinal de estructura vegetal con m&#250ltiples tejidos (Spanish, exact) - 複数の組織からなる植物構造の基本（主要）部分 (Japanese, exact) - plant_anatomy - PO:0025498 - Includes cardinal parts of plant organs (PO:0025001) as well as parts of other multi-tissue plant structures. Cardinal refers to the fact that these are biologically meaningful and not arbitrary parts. Most cardinal parts of multi-tissue plant structures have both fiat and bona-fide boundaries, including parts with large fiat boundaries, such as leaf base (PO:0020040) or fruit distal end (PO:0008001), and parts with primarily bona-fide boundaries, such as leaflet (PO:0020049). - cardinal part of multi-tissue plant structure - - - - - - - - - A plant axis (PO:0025004) that is radially enlarged. - - Laurel_Cooper - 2012-11-20T18:35:45Z - PO_GIT:127 - 塊茎 (Japanese, exact) - plant_anatomy - PO:0025522 - - Functions in storage of photosynthate metabolites. May develop from a branch (PO:0025073) or a root (PO:0009005). If you are annotating to tuber, you should pick the more specific child term: shoot axis tuber (PO:0004543) or tuberous root tuber (PO:0025476). - tuber - - - - - - - - - - - - - - - A collective plant organ structure development stage (PO:0025338) that begins with the onset of the plant organ development stage (PO:0025339) and ends with either gametophyte senescent stage (PO:0025343) or sporophyte senescent stage (PO:0007017) or death. - - Laurel_Cooper - 2012-12-13T18:21:19Z - PO_GIT:517 - plant_structure_development_stage - PO:0025527 - The shoot system (PO:0009006) develops fron the shoot apical meristem (PO:0020148) in the plant embryo (PO:0009009) in vascular plants. In lower plants the gametophore (PO:0030018) arises from a gametophore meristematic apical cell (PO:0030019) in the protonema (PO:0030003). - shoot system development stage - - - - - - - - - A shoot system development stage (PO:0025527) that has as primary participant a reproductive shoot system (PO:0025082). - - Laurel_Cooper - 2012-12-13T19:01:14Z - PO_GIT:517 - plant_structure_development_stage - PO:0025530 - reproductive shoot system development stage - - - - - - - - - A plant cell (PO:0009002) that is either part of a multicellular whole plant (PO:0000003) 'in vivo' or a unicellular organism 'in natura' (i.e. part of a natural environment). - - Laurel_Cooper - 2014-05-13T16:51:47Z - PO_GIT:586 - plant_anatomy - PO:0025606 - A native plant cell is one that is not grown or maintained in vitro, nor part of an in vitro plant structure (PO:0000004). - native plant cell - - - - - - - - - - - - - - - A whole plant development stage (PO:0007033) that has as primary participant a whole plant (PO:0000003) during the interval between fertilization (or apogamy) and death. - - rwalls - 2010-07-15T02:56:11Z - PO_GIT:139 - PO_GIT:68 - fase esporof&#237tica (Spanish, exact) - sporophytic development stage (exact) - sporophytic phase (exact) - sporphyte phase (exact) - 胞子体発生過程 (Japanese, exact) - plant_structure_development_stage - PO:0028002 - - A whole plant (PO:0000003) in the sporophyte development stage usually has twice the chromosome complement of a plant in the gametophytic phase, but may not in the case of apogamy. Examples of apogamy include both naturally occurring instances (such as sporophytes arising form haploid cells as in bryophytes or ferns) as well as in vitro instances (such as haploid embryo culture or in vitro fusion of non-gamete cells or protoplasts). During the sporophyte development stage, a plant may produce meiospores by meiosis. - sporophyte development stage - - - - - - - - - A fruit (PO:0009001) which develops from a carpel (PO:0009030) and at maturity comprises a fleshy exocarp (PO:0009085), fleshy mesocarp (PO:0009087), and a stony endocarp (PO:0009086). - - indehiscent fruit (broad) - PO_GIT:647 - drupa (exact, Spanish) - drupe (exact) - steinfrucht (exact, German) - stone fruit (exact) - whole pit fruit - plant_anatomy - PO:0030103 - May develop from an inferior or superior carpel (PO:0009030) and may contain one or more seeds (PO:0009010). Examples: Amborella trichopoda (basal angiosperm), coffee (Coffea canephora), Cornaceae (Davidia spp.), cashew (Anacardium occidentale), coconut (Cocos nucifera), and almond, peach and plum (Prunus spp.). - drupe fruit - - - - - - - - - A fruit (PO:0009001) which at maturity comprises a fleshy endocarp (PO:0009086), fleshy mesocarp (PO:0009087), and fleshy exocarp (PO:0009085). - - indehiscent fruit (broad) - PO_GIT:652 - bacca (exact) - baya (exact, Spanish) - beere (exact, German) - berry (exact) - pyrine (narrow) - plant_anatomy - PO:0030108 - Examples: pepper (Capsicum annuum), papaya (Carica papaya), avocado (Persea americana), may apple (Podophyllum peltatum), date palm (Phoenix dactylifera), tomato (Solanum lycopersicum), potato (Solanum tuberosum), chocolate (Theobroma cacao), blueberry (Vaccinium spp.), and grape (Vitis vinifera). - berry fruit - - - - - - - - - A berry fruit (PO:0030108) which develops from a superior gynoecium (PO:0009062) and at maturity comprises a thickened exocarp (PO:0009085), thickened mesocarp (PO:0009087), and endocarp (PO:0009086), and has as parts juice sacs (PO:0006013) on a carpel adaxial epidermis (PO:0025618). - - indehiscent fruit (broad) - panzerbeere (broad, German) - PO_GIT:652 - citrus fruit (exact) - hesperide (exact, German) - hesperidio (exact, Spanish) - hesperidium (exact) - plant_anatomy - PO:0030109 - A hesperidium fruit (PO:0030109) develops from a superior gynoecium (PO:0009062), and therefore is not surrounded by receptacle (PO:0009064) tissue. Examples: orange, grapefruit, lemon, and lime (Citrus spp.). - hesperidium fruit - - - - - - - - - - - - - - - - - - - - - - - - - - A berry fruit (PO:0030108) which develops from an inferior gynoecium (PO:0009062) and at maturity comprises a fleshy exocarp (PO:0009085), fleshy mesocarp (PO:0009087), and hardened endocarp (PO:0009086) and has as a part a fleshy hypanthium (PO:0009065) which is indistinct from the exocarp (PO:0009085). - - indehiscent fruit (broad) - PO_GIT:652 - apfelfrucht (exact, German) - kernfrucht (exact, German) - kernobst (exact, German) - pome (exact) - pomo (exact, Spanish) - plant_anatomy - PO:0030110 - A pome fruit (PO:0030110) is a specialized type of berry fruit (PO:0030108) which is encapsuled in persistent, accrescent receptacle (PO:0009064) and/or hypanthium (PO:0009065) tissue. Examples: Apple, crab apple, and pear (Malus spp. and Pyrus spp.) - pome fruit - - - - - - - - - A berry fruit (PO:0030108) which develops from an inferior carpel (PO:0009030) and at maturity comprises a fleshy exocarp (PO:0009085), fleshy mesocarp (PO:0009087), and fleshy endocarp (PO:0009086), and has as a part a hard receptacle (PO:0009064) which surrounds, and is indistinct from, the exocarp (PO:0009085). - - indehiscent fruit (broad) - panzerbeere (broad, German) (broad) - PO_GIT:652 - kürbisfrucht (exact, German) - pepo (exact) - pepónide (exact, Spanish) - plant_anatomy - PO:0030111 - A pepo fruit (PO:0030111) is specialized type of berry fruit (PO:0030108) which is encapsuled by persistent, accrescent receptacle (PO:0009064) tissue. The rind, or tough outer covering, of pepo fruits comprises receptical tissue and at least the exocarp (PO:0009085) layer of the pericarp (PO:0009084). Examples: pumpkin (Cucurbita pepo), cucumber (Cucumis sativus), and watermelon (Citrullus lanatus) and banana (Musa acuminata). - pepo fruit - - - - - - - - - - - - - - - Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body. - organism substance - - - - - - - - - Anatomical structure that is an individual member of a species and consists of more than one cell. - - multi-cellular organism - multicellular organism - - - - - - - - - A specialized accessory gland of the skin of mammals that secretes milk. The gland is typically only developed in females, and regresses in males. - - glandula mammaria - lactiferous gland - mammary gland - - - - - - - - - - - - - - - - An emulsion of fat globules within a fluid that is secreted by the mammary gland during lactation. - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0235 - mammal milk - mammary gland milk - LanguaL curation note: See scope note for *MILK OR MILK COMPONENT*. for lowfat milk use *FAT PARTIALLY REMOVED*; for skim milk, use *FAT FULLY REMOVED* (both found in D3. TREATMENT APPLIED). - milk - - - - - - - - - Gonochoristic organism that can produce female gametes. - - female organism - - - - - - - - - - - - - - - - - - - A product of the somatic follicle cell epithelium and a structure that supports the egg in a hostile environment, minimizing water loss whilst allowing gas exchanges essential for embryonic respiration[GO]. - egg shell - - http://langual.org - - http://www.langual.org/langual_thesaurus.asp?termid=C0278 - egg shell - shell (egg) - LanguaL term definition: The covering of a bird or reptile egg. - eggshell - - - - - - - - - Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not. - - fluid - body fluid - bodily fluid - - - - - - - - - A multicellular organism that existence_ends_with a post-juvenile adult stage and existence_starts_with a post-juvenile adult stage. - - adults - adult organism - - - - - - - - - - - - - - - - - - The yellow spheroidal mass of stored food that forms the inner portion of the egg of a bird or reptile and is surrounded by the white. - egg yolk - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0215 - egg yolk - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - egg (with shell) - The hard-shelled reproductive body produced by a bird (especially by the common domestic chicken) or a reptile; also: its contents used as food. - whole egg in shell - - http://langual.org - Note that this is cross referenced to both LanguaL "egg" as well as "whole egg in shell" - http://www.langual.org/langual_thesaurus.asp?termid=C0128 - http://www.langual.org/langual_thesaurus.asp?termid=C0274 - LanguaL curation note: The egg shell functions as a container. Therefore, the physical state of a raw egg in the shell is *LIQUID, HIGH VISCOSITY, WITH NO VISIBLE PARTICLES*. - shelled egg - - - - - - - - - - - - - - - - - - Albumen is the clear liquid contained within an egg and consists of water and proteins, among which are ovomucin and ovomucoid. It protects the egg yolk and provides additional nutrition for the growth of the embryo. - egg white, albumen - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0241 - egg white - egg white - albumen - - - - - - - - - - unit - - - - - - - - - - length unit - - - - - - - - - - mass unit - - - - - - - - - - base unit - - - - - - - - - - volume unit - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tablespoon - tablespoons - - - - - - - - - - inch based unit - - - - - - - - - - quart based unit - - - - - - - - - - ounce based unit - - - - - - - - - - pound based unit - - - - - - - - - - teaspoon based unit - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - a - - - - - - - - - - - - - - - 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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diced - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - This is a traditional Mexican soup that can be made with a rotisserie chicken or poached chicken. It is full of flavor and garnished with cilantro, lime juice, sour cream, cheese, avocado, and corn chips. - - - Tortilla Soup - - - - - - - - - - - - - - - - - - - - - - - - - - - - beaten - - - - - - - - - - - - - - - - - chopped, diced - - - - - - - - - - - - - - - - - - - - - - - - - - 10 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - 4 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - ground - - - - - - - - - - - - - - - - - - - - minced - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - - - - - - - - ________ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 8 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - medium-high - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - temperature - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - no longer pink in the center - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Chopped/Diced - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - beaten - - - - - - - - - - - - - - - - - chopped, diced - - - - - - - - - - - - - - - - - - - - - - - - - - - - 10 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - 4 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - ground - - - - - - - - - - - - - - - - - - - - - - minced - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - - - - - - - - - - ________ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 8 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - medium-high - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - temperature - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - no longer pink in the center - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Chopped/Diced - - - - - - - - - - - - - - - Patties are made of ground turkey, spinach, feta, eggs and garlic and grilled until no longer pink in the center. - - - Spinach and Feta Turkey Burgers - - - - - - - - - - - - - - - - - - - - - - - - - - - - to taste - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - fresh spears - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - olive oil - - - - - - - - - - - - - - - - - spears - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tender - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - high heat, oil - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - to taste - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - fresh spears - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - olive oil - - - - - - - - - - - - - - - - - spears - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tender - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - high heat, oil - - - - - - - - - - - - - - - - - - - - - - - - A delicious and easy side dish of grilled asparagus. - - - Grilled Asparagus - - - - - - - - - - - - - - - - - - - - - - - - - - - - 3 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - 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- - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - browned - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - heated - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - 1/2 teaspoon - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 3/4 cup - - - - - - - - - - - - - - - - - 3 tablespoons - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - drained - - - - - - - - - - - - - - - - - N/A - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - to - - - - - - - - - - - - - - - - - thickens - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - lightly salted water - - - - - - - - - - - - - - - - - boil - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Chopped - - - - - - - - - - - - - - - - - heated - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - stirred - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - boil - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - whisked - - - - - - - - - - - - - - - This stir-fry combines noodles with pork, vegetables, and a flavorful sauce to create a delicious meal. - - - - - - Sweet and Spicy Pork and Napa Cabbage Stir-Fry with Spicy Noodles - - - - - - - - - - - - - - - - - - - - - - - - - - - - 0.5 - - - - - - - - - - - - - - - - - diced - - - - - - - - - - - - - - - - - - - - - - - - - - 0.5 - - - - - - - - - - - - - - - - - diced - - - - - - - - - - - - - - - - - - - - - - - - - - 0.75 - - - - - - - - - - - - - - - - - chopped, diced - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - chopped raw - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - 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- - - - - - - - - - - - - - - - - - temperature - - - - - - - - - - - - - - - - - - - - - - - - - - - 3 ingredients - - - - - - - - - - - - - - - - - water - - - - - - - - - - - - - - - - - dissolved - - - - - - - - - - - - - - - - - dissolved - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ½ - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - thinly - - - - - - - - - - - - - - - - - Chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 ½ - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - mixture - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - be made 2 weeks ahead - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - temperature - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 3 ingredients - - - - - - - - - - - - - - - - - water - - - - - - - - - - - - - - - - - dissolved - - - - - - - - - - - - - - - - - dissolved - - - - - - - - - - - - - - - A recipe for quick-pickled red onions involving whisking of apple cider vinegar, sugar and salt, adding onions to a jar, and letting sit for one hour. - - - - Quick-Pickled Red Onions - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1/4 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 8 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 8 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - 1/2 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - 1/2 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1/4 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - whole - - - - - - - - - - - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - Fried - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - dried - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1/4 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 8 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 8 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1/2 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1/2 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1/4 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - whole - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - Fried - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - dried - - - - - - - - - - - - - - - A guide to making corn dogs at home by combining various ingredients and following a series of steps. - - - - How To Make Easy Homemade Corn Dogs - - - - - - - - - - - - - - - - - - - - - - example to be eventually removed - example to be eventually removed - - - - - - - - - metadata complete - Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. - metadata complete - - - - - - - - - organizational term - Term created to ease viewing/sort terms for development purpose, and will not be included in a release - organizational term - - - - - - - - - ready for release - Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." - ready for release - - - - - - - - - metadata incomplete - Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. - metadata incomplete - - - - - - - - - uncurated - Nothing done yet beyond assigning a unique class ID and proposing a preferred term. - uncurated - - - - - - - - - pending final vetting - All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. - pending final vetting - - - - - - - - - to be replaced with external ontology term - Terms with this status should eventually replaced with a term from another ontology. - group:OBI - to be replaced with external ontology term - - - - - - - - - requires discussion - A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. - group:OBI - requires discussion - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Breakfast - - - Brunch - - - Gluten-Free - - - Grilling - - - Main - - - Recipe - - - Seafood - - - Snacks - - - Stir-Fry - - - Vegetarian - - - Main Course - - - Main Dish - - - Main dish - - - Side Dish - - - - inch - - - - quart - quarts - - - - ounce - ounces - - - - pound - pounds - - - - teaspoon - teaspoons - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/tests/output/reaction-20657015.pickle b/tests/output/reaction-20657015.pickle deleted file mode 100644 index 4df38ebcc..000000000 Binary files a/tests/output/reaction-20657015.pickle and /dev/null differ diff --git a/tests/output/reaction-20657015.yaml b/tests/output/reaction-20657015.yaml deleted file mode 100644 index 328478c23..000000000 --- a/tests/output/reaction-20657015.yaml +++ /dev/null @@ -1,105 +0,0 @@ -input_id: /Users/cjm/repos/ontogpt/tests/input/cases/reaction-20657015.txt -input_text: "Title: Molecular identification of N-acetylaspartylglutamate synthase\ - \ and beta-citrylglutamate synthase\n\nAbstract\nThe purpose of the present work\ - \ was to determine the identity of the enzymes that synthesize N-acetylaspartylglutamate\ - \ (NAAG), the most abundant dipeptide present in vertebrate central nervous system\ - \ (CNS), and \u03B2-citrylglutamate, a structural analogue of NAAG present in testis\ - \ and immature brain. Previous evidence suggests that NAAG is not synthesized on\ - \ ribosomes but presumably is synthesized by a ligase. As attempts to detect this\ - \ ligase in brain extracts failed, we searched the mammalian genomes for putative\ - \ enzymes that could catalyze this type of reaction. Mammalian genomes were found\ - \ to encode two putative ligases homologous to Escherichia coli RIMK, which ligates\ - \ glutamates to the C terminus of ribosomal protein S6. One of them, named RIMKLA,\ - \ is almost exclusively expressed in the CNS, whereas RIMKLB, which shares 65% sequence\ - \ identity with RIMKLA, is expressed in CNS and testis. Both proteins were expressed\ - \ in bacteria or HEK293T cells and purified. RIMKLA catalyzed the ATP-dependent\ - \ synthesis of N-acetylaspartylglutamate from N-acetylaspartate and l-glutamate.\ - \ RIMKLB catalyzed this reaction as well as the synthesis of \u03B2-citrylglutamate.\ - \ The nature of the reaction products was confirmed by mass spectrometry and NMR.\ - \ RIMKLA was shown to produce stoichiometric amounts of NAAG and ADP, in agreement\ - \ with its belonging to the ATP-grasp family of ligases. The molecular identification\ - \ of these two enzymes will facilitate progress in the understanding of the function\ - \ of NAAG and \u03B2-citrylglutamate." -raw_completion_output: "genes: RIMKLB; RIMKLA;\nreactions: N-acetylaspartate + l-glutamate\ - \ = N-acetylaspartylglutamate + ADP; N-acetylaspartate + l-glutamate = beta-citrylglutamate;\ - \ \ngene_reaction_pairings: RIMKLB: N-acetylaspartate + l-glutamate = N-acetylaspartylglutamate\ - \ + ADP; RIMKLB: N-acetylaspartate + l-glutamate = beta-citrylglutamate; RIMKLA:\ - \ N-acetylaspartate + l-glutamate = N-acetylaspartylglutamate + ADP; \norganism:\ - \ mammalian" -prompt: 'From the text below, extract the following entities in the following format: - - - gene: - - reaction: - - - - Text: - - RIMKLA: N-acetylaspartate + l-glutamate = N-acetylaspartylglutamate + ADP - - - === - - - ' -extracted_object: - genes: - - HGNC:29228 - - HGNC:28725 - reactions: - - label: N-acetylaspartate + l-glutamate reaction - description: A chemical reaction between N-acetylaspartate and l-glutamate, resulting - in the production of N-acetylaspartylglutamate and ADP - synonyms: - - NA - subclass_of: AUTO:Chemical%20Reaction - left_side: - - AUTO:N-acetylaspartate - - CHEBI:29988 - right_side: - - CHEBI:76931 - - CHEBI:16761 - - label: N-acetylaspartate synthesis - description: A reaction in which N-acetylaspartate is converted to beta-citrylglutamate - synonyms: - - N-acetylaspartic acid synthesis - - NAA synthesis - subclass_of: GO:0009058 - left_side: - - AUTO:N-acetylaspartate - - CHEBI:29988 - right_side: - - CHEBI:76942 - gene_reaction_pairings: - - gene: HGNC:29228 - reaction: AUTO:N-acetylaspartate%20%2B%20l-glutamate%20%3D%20N-acetylaspartylglutamate%20%2B%20ADP - - gene: HGNC:29228 - reaction: AUTO:N-acetylaspartate%20%2B%20l-glutamate%20%3D%20beta-citrylglutamate - - gene: HGNC:28725 - reaction: AUTO:N-acetylaspartate%20%2B%20l-glutamate%20%3D%20N-acetylaspartylglutamate%20%2B%20ADP - organism: AUTO:mammalian -named_entities: -- id: HGNC:29228 - label: RIMKLB -- id: HGNC:28725 - label: RIMKLA -- id: CHEBI:29988 - label: l-glutamate -- id: CHEBI:76931 - label: N-acetylaspartylglutamate -- id: CHEBI:16761 - label: ADP -- id: GO:0009058 - label: Anabolism -- id: CHEBI:29988 - label: l-glutamate -- id: CHEBI:76942 - label: beta-citrylglutamate -- id: HGNC:29228 - label: RIMKLB -- id: HGNC:29228 - label: RIMKLB -- id: HGNC:28725 - label: RIMKLA diff --git a/tests/output/reaction-21290071.pickle b/tests/output/reaction-21290071.pickle deleted file mode 100644 index 9d02f2e9a..000000000 Binary files a/tests/output/reaction-21290071.pickle and /dev/null differ diff --git a/tests/output/reaction-21290071.yaml b/tests/output/reaction-21290071.yaml deleted file mode 100644 index 27cafa1cf..000000000 --- a/tests/output/reaction-21290071.yaml +++ /dev/null @@ -1,114 +0,0 @@ -input_id: /Users/cjm/repos/ontogpt/tests/input/cases/reaction-21290071.txt -input_text: 'Title: Substrate specificity of Rv3378c, an enzyme from Mycobacterium - - tuberculosis, and the inhibitory activity of the bicyclic diterpenoids - - against macrophage phagocytosis - - - Abstract - - The Rv3378c gene product from Mycobacterium tuberculosis encodes a diterpene synthase - to produce tuberculosinol (3), 13R-isotuberculosinol (4a), and 13S-isotuberculosinol - (4b) from tuberculosinyl diphosphate (2). The product distribution ratios are 1 - : 1 for 3 to 4 and 1 : 3 for 4a to 4b. The substrate specificity of the Rv3378c-encoded - enzyme was examined. The 3 labdadienyl diphosphates, copalyl diphosphate (CDP) (7), - ent-CDP (8), and syn-CDP (9), underwent the conversion reaction, with good yields - (67-78%). Copalol (23) and manool (24) were produced from 7, ent-copalol (25) and - ent-manool (26) from 8, and syn-copalol (27) and vitexifolin A (28) from 9. The - ratio of 23 to 24 was 40 : 27, that of 25:26 was 22 : 50, and that of 27:28 was - 16 : 62. Analysis on a GC-MS chromatograph equipped with a chiral column revealed - that 24, 26, and 28 consisted of a mixture of 13R- (a) and 13S-stereoisomers (b) - in the following ratio: ca. 1 : 1 for 24a to 24b, ca. 1 : 5 for 26a to 26b, and - ca. 1 : 19 for 28a to 28b. The structures of these products indicate that the reactions - of the 3 CDPs proceeded in the same fashion as that of 2. This is the first report - on the enzymatic synthesis of natural diterpenes manool, ent-manool, and vitexifolin - A. Both Rv3377c and Rv3378c genes are found in virulent Mycobacterium species, but - not in avirulent species. We found that 3 and 4 inhibited the phagocytosis of opsonized - zymosan particles by human macrophage-like cells. Interestingly, the inhibitory - activity was synergistically increased by the coexistence of 3 and 4b. Other labdane-related - diterpenes, 13-16 and 23-28, had little or no inhibitory activity. This synergistic - inhibition by 3 and 4 may provide further advantage to the impairment of phagocyte - function, which might contribute to pathogenicity of M. tuberculosis. - - ' -raw_completion_output: ' - - Gene: Rv3378c - - Reactions: 2 -> 3 + 4; 7 -> 23 + 24; 8 -> 25 + 26; 9 -> 27 + 28 - - Organism: Mycobacterium tuberculosis' -prompt: 'Split the following piece of text into fields in the following format: - - - label: - - description: - - synonyms: - - subclass_of: - - left_side: - - right_side: - - - - Text: - - 9 -> 27 + 28 - - - === - - - ' -extracted_object: - gene: AUTO:Rv3378c - reactions: - - label: 2 to 3 + 4 - description: A reaction involving the transfer of 2 atoms to yield 3 and 4 atoms. - synonyms: - - None - subclass_of: AUTO:Reaction - left_side: - - AUTO:2 - right_side: - - AUTO:3 - - AUTO:4 - - label: reaction_7-23+24 - description: Reaction between 7 and 23, resulting in the production of 24 - synonyms: - - N/A - subclass_of: AUTO:Chemical%20Reaction - left_side: - - AUTO:7 - right_side: - - AUTO:23 - - AUTO:24 - - label: 8 to 25 and 26 - description: Chemical reaction that involves conversion of 8 to 25 and 26. - synonyms: - - n/a - subclass_of: AUTO:Conversion%20reaction - left_side: - - AUTO:8 - right_side: - - AUTO:25 - - AUTO:26 - - label: 9 to 27 and 28 reaction - description: A reaction in which 9 combines to form both 27 and 28 - synonyms: - - N/A - subclass_of: AUTO:Combination%20reaction - left_side: - - AUTO:9 - right_side: - - AUTO:27 - - AUTO:28 - organism: NCBITaxon:1773 -named_entities: -- id: MESH:D009169 - label: Mycobacterium tuberculosis diff --git a/tests/output/recipe-egg-noodles.pickle b/tests/output/recipe-egg-noodles.pickle deleted file mode 100644 index ef1d26ffc..000000000 Binary files a/tests/output/recipe-egg-noodles.pickle and /dev/null differ diff --git a/tests/output/recipe-egg-noodles.yaml b/tests/output/recipe-egg-noodles.yaml deleted file mode 100644 index e21717354..000000000 --- a/tests/output/recipe-egg-noodles.yaml +++ /dev/null @@ -1,354 +0,0 @@ -input_id: /Users/cjm/repos/ontogpt/tests/input/cases/recipe-egg-noodles.txt -input_text: "Homemade Egg Noodles\n\nGather the ingredients.\n\nCombine the flour\ - \ and salt in a large shallow bowl or on a clean work surface. Make a well in the\ - \ center, almost like a \"bowl\" of flour, to hold the eggs. Crack the eggs into\ - \ it.\n\nFlour with eggs cracked into the well in the center\nUse a fork to beat\ - \ the eggs and then gradually start incorporating the flour into the eggs. As you\ - \ beat them, they will slowly but surely take up some flour from the edges.\n\n\ - Eggs beat with a fork in a well in the center of flour\nKeep stirring and pulling\ - \ in more flour until a solid dough forms. The dough will be sticky. Don't worry;\ - \ you'll be working in more flour in a moment. Add too much flour now, and the extra\ - \ flour needed to roll out the noodles will lead to a dry rather than tender noodle.\n\ - \nMixed egg and flour kneaded together to form a shaggy dough\nTurn the dough out\ - \ onto a well-floured work surface. With well-floured hands, knead the dough, incorporating\ - \ more flour as necessary to keep it from sticking to either the work surface or\ - \ your hands, until the dough is smooth and firm and no longer sticky. This takes\ - \ roughly 5 to 10 minutes.\n\nFormed dough ball for egg pasta\nWrap the dough with\ - \ plastic wrap and chill it for at least 30 minutes and up to overnight.\n\nBall\ - \ of egg pasta dough in glass bowl covered with plastic wrap\nDivide the chilled\ - \ dough into 2 pieces and work with one half of the dough at a time.\n\nBall of\ - \ egg pasta dough cut in half with a knife\nOn a well-floured surface, roll out\ - \ the dough to the desired thickness (anywhere from 1/4 inch to paper-thin, depending\ - \ on your preference). Be sure to rotate or otherwise move the dough between each\ - \ pass of the rolling pin to keep the dough from sticking to the work surface underneath.\ - \ Sprinkle everything with flour\u2014including the work surface when you lift the\ - \ dough\u2014as necessary to keep the dough from sticking.\n\nEgg pasta dough rolled\ - \ out with wooden rolling pin\nUse a sharp knife or pizza cutting wheel to cut the\ - \ noodles. You can make them as narrow or wide as you like. Be sure to cut them\ - \ as evenly as possible to ensure a uniform cooking time. If you fold the dough\ - \ to cut, make sure it is floured so it does not stick together.\n\nFresh pasta\ - \ cut into noodles with a knife\nLay the noodles on a cooling or drying rack and\ - \ let them sit until ready to cook. Repeat rolling and cutting with the remaining\ - \ half of the dough.\n\nFresh homemade egg pasta noodles on a marble counter \n\ - Boil the noodles in well-salted water until tender to the bite (2 to 10 minutes\ - \ for fresh noodles depending on the thickness). Drain and use in your favorite\ - \ recipe. Enjoy!\n\nEgg pasta noodles with pesto and Parmesan cheese on a plate\n\ - \n" -raw_completion_output: "\nLabel: Homemade Egg Noodles \nDescription: Homemade egg\ - \ noodles that are boiled until tender for use in your favorite recipe.\nCategories:\ - \ Pasta; Noodles \nIngredients: Flour; Salt; Eggs \nSteps: Gather the ingredients;\ - \ Combine the flour and salt in a bowl/on a work surface and make a well in the\ - \ center; Beat eggs with a fork and gradually incorporate flour; Knead dough with\ - \ well-floured hands until smooth and firm; Wrap dough in plastic wrap and chill;\ - \ Divide chilled dough into two and roll out; Cut noodles; Boil in salted water\ - \ and drain; Enjoy." -prompt: 'Split the following piece of text into fields in the following format: - - - food: - - state: - - - - Text: - - none - - - === - - - ' -extracted_object: - label: Homemade Egg Noodles - description: Homemade egg noodles that are boiled until tender for use in your favorite - recipe. - categories: - - FOODON:03306347 - - FOODON:03306944 - ingredients: - - food_item: - food: FOODON:03301116 - - food_item: - food: AUTO:Salt - state: Chopped - - food_item: - food: FOODON:03316061 - steps: - - action: AUTO:Gather%3B - inputs: - - food: FOODON:00004272 - state: N/A - utensils: - - AUTO:N/A. - - action: AUTO:Combine - inputs: - - food: FOODON:03301116 - - food: AUTO:Salt - state: Chopped - outputs: - - food: AUTO:Well - utensils: - - AUTO:Bowl - - AUTO:Work%20surface - - action: AUTO:Beat%3B%20incorporate - inputs: - - food: FOODON:03316061 - - food: FOODON:03301116 - outputs: - - food: FOODON:03316061 - state: beaten - - food: FOODON:03301116 - state: incorporated - utensils: - - AUTO:fork - - action: AUTO:knead%3B - inputs: - - food: FOODON:03311552 - outputs: - - food: FOODON:03311552 - state: smooth and firm - utensils: - - AUTO:hands. - - action: AUTO:Wrap%3B%20Chill - inputs: - - food: FOODON:03311552 - outputs: - - food: FOODON:03311552 - utensils: - - AUTO:None - - action: AUTO:divide%3B%20roll%20out - inputs: - - food: FOODON:03311552 - state: chilled - outputs: - - food: AUTO:two%20pieces%20of%20dough - utensils: - - AUTO:none - - action: FOODON:00002777 - inputs: - - food: FOODON:03306944 - outputs: - - food: FOODON:03306944 - state: cut - utensils: - - AUTO:none - - action: AUTO:Boil%3B%20Drain - inputs: - - food: FOODON:00002340 - - food: AUTO:Salt - state: Chopped - outputs: - - food: AUTO:Boiled%20Water - state: Boiled - utensils: - - AUTO:Pot - - action: AUTO:none - inputs: - - food: AUTO:none - outputs: - - food: AUTO:none - utensils: - - AUTO:none -named_entities: -- id: AUTO:Main - label: Main -- id: FOODON:03306347 - label: Pasta -- id: FOODON:03301704 - label: onion -- id: AUTO:small%20%28chopped%29 - label: small (chopped) -- id: FOODON:00003485 - label: bell pepper -- id: AUTO:cups - label: cups -- id: FOODON:00003582 - label: garlic -- id: UO:0010042 - label: tablespoons -- id: FOODON:03310351 - label: butter -- id: AUTO:salt - label: salt -- id: UO:0010040 - label: teaspoon -- id: FOODON:00001649 - label: pepper -- id: FOODON:03000227 - label: tomato -- id: AUTO:%2815%20ounce%29%20cans - label: (15 ounce) cans -- id: AUTO:1%20%2816%20ounce%29%20box%20spaghetti%20noodles - label: 1 (16 ounce) box spaghetti noodles -- id: FOODON:00001282 - label: hamburger meat -- id: AUTO:lbs - label: lbs -- id: AUTO:Melt%3B%20Saut%C3%A9 - label: "Melt; Saut\xE9" -- id: AUTO:Pan - label: Pan -- id: AUTO:add%3B%20cook - label: add; cook -- id: AUTO:well%20done - label: well done -- id: AUTO:pan - label: pan -- id: AUTO:Add - label: Add -- id: AUTO:adjust%3B - label: adjust; -- id: FOODON:03460173 - label: salted -- id: AUTO:none - label: none -- id: AUTO:Cook - label: Cook -- id: FOODON:03306944 - label: noodles -- id: AUTO:Mix%3B - label: Mix; -- id: FOODON:03311146 - label: sauce -- id: HANCESTRO:0415 - label: Mexican -- id: AUTO:Soup - label: Soup -- id: AUTO:poached%20chicken - label: poached chicken -- id: AUTO:1%20%2815%20oz%29%20can%20fire%20roasted%20tomatoes - label: 1 (15 oz) can fire roasted tomatoes -- id: AUTO:N/A - label: N/A -- id: AUTO:red%20enchilada%20sauce - label: red enchilada sauce -- id: AUTO:oz - label: oz -- id: FOODON:03310943 - label: zucchini -- id: AUTO:medium%2C%20sliced%20into%201/4-inch%20half%20circles - label: medium, sliced into 1/4-inch half circles -- id: AUTO:1%20%284%20oz%29%20can%20green%20chilies - label: 1 (4 oz) can green chilies -- id: FOODON:03411457 - label: chicken -- id: AUTO:creamed%20corn - label: creamed corn -- id: AUTO:ground%20cumin - label: ground cumin -- id: AUTO:tsp - label: tsp -- id: FOODON:03302030 - label: chili powder -- id: AUTO:sea%20salt - label: sea salt -- id: AUTO:freshly%20ground%20black%20pepper - label: freshly ground black pepper -- id: AUTO:bay%20leaves - label: bay leaves -- id: AUTO:cilantro - label: cilantro -- id: AUTO:Tbsp - label: Tbsp -- id: FOODON:00003661 - label: lime -- id: FOODON:03302515 - label: sour cream -- id: FOODON:00001013 - label: cheese -- id: FOODON:00003600 - label: avocado -- id: AUTO:large%2C%20sliced - label: large, sliced -- id: FOODON:03310710 - label: Tortilla chips -- id: AUTO:Pick%3B - label: Pick; -- id: AUTO:pre-cooked%20chicken - label: pre-cooked chicken -- id: AUTO:meat - label: meat -- id: dbpediaont:Square - label: Place -- id: AUTO:large%20stock%20pot - label: large stock pot -- id: AUTO:Pot - label: Pot -- id: AUTO:add%3B - label: add; -- id: FOODON:03304007 - label: enchilada sauce -- id: FOODON:03317304 - label: chilis -- id: AUTO:corn - label: corn -- id: FOODON:00003024 - label: cumin -- id: AUTO:pot - label: pot -- id: AUTO:Stir%3B - label: Stir; -- id: AUTO:combine - label: combine -- id: AUTO:- - label: '-' -- id: AUTO:cook%3B - label: cook; -- id: AUTO:soup - label: soup -- id: AUTO:none. - label: none. -- id: AUTO:topping%3B - label: topping; -- id: AUTO:fresh%20lime%20juice - label: fresh lime juice -- id: FOODON:03302052 - label: corn chips -- id: FOODON:03301116 - label: Flour -- id: AUTO:Salt - label: Salt -- id: FOODON:03316061 - label: Eggs -- id: AUTO:Gather%3B - label: Gather; -- id: FOODON:00004272 - label: ingredients -- id: AUTO:N/A. - label: N/A. -- id: AUTO:Combine - label: Combine -- id: AUTO:Well - label: Well -- id: AUTO:Bowl - label: Bowl -- id: AUTO:Work%20surface - label: Work surface -- id: AUTO:Beat%3B%20incorporate - label: Beat; incorporate -- id: AUTO:fork - label: fork -- id: AUTO:knead%3B - label: knead; -- id: FOODON:03311552 - label: dough -- id: AUTO:hands. - label: hands. -- id: AUTO:Wrap%3B%20Chill - label: Wrap; Chill -- id: AUTO:None - label: None -- id: AUTO:divide%3B%20roll%20out - label: divide; roll out -- id: AUTO:two%20pieces%20of%20dough - label: two pieces of dough -- id: FOODON:00002777 - label: Cut -- id: AUTO:Boil%3B%20Drain - label: Boil; Drain -- id: FOODON:00002340 - label: Water -- id: AUTO:Boiled%20Water - label: Boiled Water diff --git a/tests/output/recipe-palak-paneer.owl b/tests/output/recipe-palak-paneer.owl deleted file mode 100644 index 71630dadd..000000000 --- a/tests/output/recipe-palak-paneer.owl +++ /dev/null @@ -1,337 +0,0 @@ -Prefix( owl: = ) -Prefix( rdf: = ) -Prefix( rdfs: = ) -Prefix( xsd: = ) -Prefix( xml: = ) -Prefix( linkml: = ) -Prefix( recipe: = ) -Prefix( FOODON: = ) -Prefix( UO: = ) -Prefix( dcterms: = ) -Prefix( HANCESTRO: = ) -Prefix( BFO: = ) -Prefix( AUTO: = ) -Prefix( RO: = ) -Prefix( qudt: = ) -Prefix( dbpediaont: = ) -Prefix( core: = ) -Prefix( shex: = ) - -Ontology( - EquivalentClasses( - AUTO:_ROOT - ObjectIntersectionOf( - recipe:Recipe - ObjectSomeValuesFrom( recipe:steps ObjectIntersectionOf( - AUTO:melt%3B%20saut%C3%A9 - ObjectSomeValuesFrom( ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "chopped" ) - ) ) - ObjectSomeValuesFrom( AUTO:pan ) - ) ) - ObjectSomeValuesFrom( recipe:steps ObjectIntersectionOf( - AUTO:add%3B%20cook - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "chopped/diced" ) - ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( AUTO:meat ) - DataHasValue( recipe:state "well done" ) - ) ) - ObjectSomeValuesFrom( AUTO:pan ) - ) ) - ObjectSomeValuesFrom( recipe:steps ObjectIntersectionOf( - AUTO:add%3B - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "sauce" ) - ) ) - ObjectSomeValuesFrom( ObjectSomeValuesFrom( AUTO:salt ) ) - ObjectSomeValuesFrom( ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "powder" ) - ) ) - ObjectSomeValuesFrom( ObjectSomeValuesFrom( AUTO:none ) ) - ObjectSomeValuesFrom( AUTO:none ) - ) ) - ObjectSomeValuesFrom( recipe:steps ObjectIntersectionOf( - AUTO:adjust - ObjectSomeValuesFrom( ObjectSomeValuesFrom( AUTO:salt ) ) - ObjectSomeValuesFrom( ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "powder" ) - ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( AUTO:inputs ) - DataHasValue( recipe:state "adjusted" ) - ) ) - ObjectSomeValuesFrom( AUTO:none ) - ) ) - ObjectSomeValuesFrom( recipe:steps ObjectIntersectionOf( - AUTO:Cook - ObjectSomeValuesFrom( ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( ObjectSomeValuesFrom( AUTO:as%20directed ) ) - ) ) - ObjectSomeValuesFrom( recipe:steps ObjectIntersectionOf( - AUTO:mix%3B - ObjectSomeValuesFrom( ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "+" ) - ) ) - ObjectSomeValuesFrom( AUTO:none ) - ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectIntersectionOf( - ObjectSomeValuesFrom( AUTO:small%20onion ) - DataHasValue( recipe:state "chopped" ) - ) ) - ObjectSomeValuesFrom( recipe:amount ObjectIntersectionOf( - DataHasValue( recipe:value "1" ) - ObjectSomeValuesFrom( qudt:unit ) - ) ) - ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "chopped" ) - ) ) - ObjectSomeValuesFrom( recipe:amount ObjectIntersectionOf( - DataHasValue( recipe:value "1" ) - ObjectSomeValuesFrom( qudt:unit ) - ) ) - ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "powder" ) - ) ) - ObjectSomeValuesFrom( recipe:amount ObjectIntersectionOf( - DataHasValue( recipe:value "2" ) - ObjectSomeValuesFrom( qudt:unit ) - ) ) - ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( recipe:amount ObjectIntersectionOf( - DataHasValue( recipe:value "3" ) - ObjectSomeValuesFrom( qudt:unit ) - ) ) - ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectSomeValuesFrom( AUTO:salt ) ) - ObjectSomeValuesFrom( recipe:amount ObjectIntersectionOf( - DataHasValue( recipe:value "1" ) - ObjectSomeValuesFrom( qudt:unit ) - ) ) - ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( recipe:amount ObjectIntersectionOf( - DataHasValue( recipe:value "1" ) - ObjectSomeValuesFrom( qudt:unit ) - ) ) - ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "canned" ) - ) ) - ObjectSomeValuesFrom( recipe:amount DataHasValue( recipe:value "2" ) ) - ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectIntersectionOf( - ObjectSomeValuesFrom( AUTO:1%20%2816%20ounce%29%20box%20spaghetti%20noodles ) - DataHasValue( recipe:state "uncooked" ) - ) ) - ObjectSomeValuesFrom( recipe:amount DataHasValue( recipe:value "1" ) ) - ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "chopped/diced" ) - ) ) - ObjectSomeValuesFrom( recipe:amount ObjectIntersectionOf( - DataHasValue( recipe:value "1 - 1 1⁄2" ) - ObjectSomeValuesFrom( qudt:unit AUTO:lb ) - ) ) - ) ) - ) - ) - Declaration( Class( AUTO:_ROOT ) ) - AnnotationAssertion( rdfs:label AUTO:_ROOT "Simple Spaghetti" ) - AnnotationAssertion( dcterms:description AUTO:_ROOT "An easy to make and delicious spaghetti dish." ) - AnnotationAssertion( dcterms:subject AUTO:_ROOT AUTO:Main%20dishes ) - AnnotationAssertion( dcterms:subject AUTO:_ROOT AUTO:Italian%20recipes ) - SubClassOf( AUTO:_ROOT ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectIntersectionOf( - ObjectSomeValuesFrom( AUTO:small%20onion ) - DataHasValue( recipe:state "chopped" ) - ) ) - ObjectSomeValuesFrom( recipe:amount ObjectIntersectionOf( - DataHasValue( recipe:value "1" ) - ObjectSomeValuesFrom( qudt:unit ) - ) ) - ) ) ) - SubClassOf( AUTO:_ROOT ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "chopped" ) - ) ) - ObjectSomeValuesFrom( recipe:amount ObjectIntersectionOf( - DataHasValue( recipe:value "1" ) - ObjectSomeValuesFrom( qudt:unit ) - ) ) - ) ) ) - SubClassOf( AUTO:_ROOT ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "powder" ) - ) ) - ObjectSomeValuesFrom( recipe:amount ObjectIntersectionOf( - DataHasValue( recipe:value "2" ) - ObjectSomeValuesFrom( qudt:unit ) - ) ) - ) ) ) - SubClassOf( AUTO:_ROOT ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( recipe:amount ObjectIntersectionOf( - DataHasValue( recipe:value "3" ) - ObjectSomeValuesFrom( qudt:unit ) - ) ) - ) ) ) - SubClassOf( AUTO:_ROOT ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectSomeValuesFrom( AUTO:salt ) ) - ObjectSomeValuesFrom( recipe:amount ObjectIntersectionOf( - DataHasValue( recipe:value "1" ) - ObjectSomeValuesFrom( qudt:unit ) - ) ) - ) ) ) - SubClassOf( AUTO:_ROOT ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( recipe:amount ObjectIntersectionOf( - DataHasValue( recipe:value "1" ) - ObjectSomeValuesFrom( qudt:unit ) - ) ) - ) ) ) - SubClassOf( AUTO:_ROOT ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "canned" ) - ) ) - ObjectSomeValuesFrom( recipe:amount DataHasValue( recipe:value "2" ) ) - ) ) ) - SubClassOf( AUTO:_ROOT ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectIntersectionOf( - ObjectSomeValuesFrom( AUTO:1%20%2816%20ounce%29%20box%20spaghetti%20noodles ) - DataHasValue( recipe:state "uncooked" ) - ) ) - ObjectSomeValuesFrom( recipe:amount DataHasValue( recipe:value "1" ) ) - ) ) ) - SubClassOf( AUTO:_ROOT ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "chopped/diced" ) - ) ) - ObjectSomeValuesFrom( recipe:amount ObjectIntersectionOf( - DataHasValue( recipe:value "1 - 1 1⁄2" ) - ObjectSomeValuesFrom( qudt:unit AUTO:lb ) - ) ) - ) ) ) - SubClassOf( AUTO:_ROOT ObjectSomeValuesFrom( recipe:steps ObjectIntersectionOf( - AUTO:melt%3B%20saut%C3%A9 - ObjectSomeValuesFrom( ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "chopped" ) - ) ) - ObjectSomeValuesFrom( AUTO:pan ) - ) ) ) - SubClassOf( AUTO:_ROOT ObjectSomeValuesFrom( recipe:steps ObjectIntersectionOf( - AUTO:add%3B%20cook - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "chopped/diced" ) - ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( AUTO:meat ) - DataHasValue( recipe:state "well done" ) - ) ) - ObjectSomeValuesFrom( AUTO:pan ) - ) ) ) - SubClassOf( AUTO:_ROOT ObjectSomeValuesFrom( recipe:steps ObjectIntersectionOf( - AUTO:add%3B - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "sauce" ) - ) ) - ObjectSomeValuesFrom( ObjectSomeValuesFrom( AUTO:salt ) ) - ObjectSomeValuesFrom( ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "powder" ) - ) ) - ObjectSomeValuesFrom( ObjectSomeValuesFrom( AUTO:none ) ) - ObjectSomeValuesFrom( AUTO:none ) - ) ) ) - SubClassOf( AUTO:_ROOT ObjectSomeValuesFrom( recipe:steps ObjectIntersectionOf( - AUTO:adjust - ObjectSomeValuesFrom( ObjectSomeValuesFrom( AUTO:salt ) ) - ObjectSomeValuesFrom( ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "powder" ) - ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( AUTO:inputs ) - DataHasValue( recipe:state "adjusted" ) - ) ) - ObjectSomeValuesFrom( AUTO:none ) - ) ) ) - SubClassOf( AUTO:_ROOT ObjectSomeValuesFrom( recipe:steps ObjectIntersectionOf( - AUTO:Cook - ObjectSomeValuesFrom( ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( ObjectSomeValuesFrom( AUTO:as%20directed ) ) - ) ) ) - SubClassOf( AUTO:_ROOT ObjectSomeValuesFrom( recipe:steps ObjectIntersectionOf( - AUTO:mix%3B - ObjectSomeValuesFrom( ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "+" ) - ) ) - ObjectSomeValuesFrom( AUTO:none ) - ) ) ) - AnnotationAssertion( rdfs:label "bell pepper" ) - AnnotationAssertion( rdfs:label "garlic" ) - AnnotationAssertion( rdfs:label "tablespoons" ) - AnnotationAssertion( rdfs:label "butter" ) - AnnotationAssertion( rdfs:label "tablespoons" ) - AnnotationAssertion( rdfs:label "teaspoon" ) - AnnotationAssertion( rdfs:label "pepper" ) - AnnotationAssertion( rdfs:label "teaspoon" ) - AnnotationAssertion( rdfs:label "tomato sauce" ) - AnnotationAssertion( rdfs:label "hamburger meat" ) - AnnotationAssertion( rdfs:label "butter" ) - AnnotationAssertion( rdfs:label "onion" ) - AnnotationAssertion( rdfs:label "bell peppers" ) - AnnotationAssertion( rdfs:label "hamburger meat" ) - AnnotationAssertion( rdfs:label "tomato" ) - AnnotationAssertion( rdfs:label "pepper" ) - AnnotationAssertion( rdfs:label "garlic" ) - AnnotationAssertion( rdfs:label "pepper" ) - AnnotationAssertion( rdfs:label "garlic" ) - AnnotationAssertion( rdfs:label "noodles" ) - AnnotationAssertion( rdfs:label "sauce" ) - AnnotationAssertion( rdfs:label "noodles" ) - AnnotationAssertion( rdfs:label "noodles" ) -) \ No newline at end of file diff --git a/tests/output/recipe-spaghetti.owl b/tests/output/recipe-spaghetti.owl deleted file mode 100644 index 71630dadd..000000000 --- a/tests/output/recipe-spaghetti.owl +++ /dev/null @@ -1,337 +0,0 @@ -Prefix( owl: = ) -Prefix( rdf: = ) -Prefix( rdfs: = ) -Prefix( xsd: = ) -Prefix( xml: = ) -Prefix( linkml: = ) -Prefix( recipe: = ) -Prefix( FOODON: = ) -Prefix( UO: = ) -Prefix( dcterms: = ) -Prefix( HANCESTRO: = ) -Prefix( BFO: = ) -Prefix( AUTO: = ) -Prefix( RO: = ) -Prefix( qudt: = ) -Prefix( dbpediaont: = ) -Prefix( core: = ) -Prefix( shex: = ) - -Ontology( - EquivalentClasses( - AUTO:_ROOT - ObjectIntersectionOf( - recipe:Recipe - ObjectSomeValuesFrom( recipe:steps ObjectIntersectionOf( - AUTO:melt%3B%20saut%C3%A9 - ObjectSomeValuesFrom( ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "chopped" ) - ) ) - ObjectSomeValuesFrom( AUTO:pan ) - ) ) - ObjectSomeValuesFrom( recipe:steps ObjectIntersectionOf( - AUTO:add%3B%20cook - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "chopped/diced" ) - ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( AUTO:meat ) - DataHasValue( recipe:state "well done" ) - ) ) - ObjectSomeValuesFrom( AUTO:pan ) - ) ) - ObjectSomeValuesFrom( recipe:steps ObjectIntersectionOf( - AUTO:add%3B - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "sauce" ) - ) ) - ObjectSomeValuesFrom( ObjectSomeValuesFrom( AUTO:salt ) ) - ObjectSomeValuesFrom( ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "powder" ) - ) ) - ObjectSomeValuesFrom( ObjectSomeValuesFrom( AUTO:none ) ) - ObjectSomeValuesFrom( AUTO:none ) - ) ) - ObjectSomeValuesFrom( recipe:steps ObjectIntersectionOf( - AUTO:adjust - ObjectSomeValuesFrom( ObjectSomeValuesFrom( AUTO:salt ) ) - ObjectSomeValuesFrom( ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "powder" ) - ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( AUTO:inputs ) - DataHasValue( recipe:state "adjusted" ) - ) ) - ObjectSomeValuesFrom( AUTO:none ) - ) ) - ObjectSomeValuesFrom( recipe:steps ObjectIntersectionOf( - AUTO:Cook - ObjectSomeValuesFrom( ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( ObjectSomeValuesFrom( AUTO:as%20directed ) ) - ) ) - ObjectSomeValuesFrom( recipe:steps ObjectIntersectionOf( - AUTO:mix%3B - ObjectSomeValuesFrom( ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "+" ) - ) ) - ObjectSomeValuesFrom( AUTO:none ) - ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectIntersectionOf( - ObjectSomeValuesFrom( AUTO:small%20onion ) - DataHasValue( recipe:state "chopped" ) - ) ) - ObjectSomeValuesFrom( recipe:amount ObjectIntersectionOf( - DataHasValue( recipe:value "1" ) - ObjectSomeValuesFrom( qudt:unit ) - ) ) - ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "chopped" ) - ) ) - ObjectSomeValuesFrom( recipe:amount ObjectIntersectionOf( - DataHasValue( recipe:value "1" ) - ObjectSomeValuesFrom( qudt:unit ) - ) ) - ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "powder" ) - ) ) - ObjectSomeValuesFrom( recipe:amount ObjectIntersectionOf( - DataHasValue( recipe:value "2" ) - ObjectSomeValuesFrom( qudt:unit ) - ) ) - ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( recipe:amount ObjectIntersectionOf( - DataHasValue( recipe:value "3" ) - ObjectSomeValuesFrom( qudt:unit ) - ) ) - ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectSomeValuesFrom( AUTO:salt ) ) - ObjectSomeValuesFrom( recipe:amount ObjectIntersectionOf( - DataHasValue( recipe:value "1" ) - ObjectSomeValuesFrom( qudt:unit ) - ) ) - ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( recipe:amount ObjectIntersectionOf( - DataHasValue( recipe:value "1" ) - ObjectSomeValuesFrom( qudt:unit ) - ) ) - ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "canned" ) - ) ) - ObjectSomeValuesFrom( recipe:amount DataHasValue( recipe:value "2" ) ) - ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectIntersectionOf( - ObjectSomeValuesFrom( AUTO:1%20%2816%20ounce%29%20box%20spaghetti%20noodles ) - DataHasValue( recipe:state "uncooked" ) - ) ) - ObjectSomeValuesFrom( recipe:amount DataHasValue( recipe:value "1" ) ) - ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "chopped/diced" ) - ) ) - ObjectSomeValuesFrom( recipe:amount ObjectIntersectionOf( - DataHasValue( recipe:value "1 - 1 1⁄2" ) - ObjectSomeValuesFrom( qudt:unit AUTO:lb ) - ) ) - ) ) - ) - ) - Declaration( Class( AUTO:_ROOT ) ) - AnnotationAssertion( rdfs:label AUTO:_ROOT "Simple Spaghetti" ) - AnnotationAssertion( dcterms:description AUTO:_ROOT "An easy to make and delicious spaghetti dish." ) - AnnotationAssertion( dcterms:subject AUTO:_ROOT AUTO:Main%20dishes ) - AnnotationAssertion( dcterms:subject AUTO:_ROOT AUTO:Italian%20recipes ) - SubClassOf( AUTO:_ROOT ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectIntersectionOf( - ObjectSomeValuesFrom( AUTO:small%20onion ) - DataHasValue( recipe:state "chopped" ) - ) ) - ObjectSomeValuesFrom( recipe:amount ObjectIntersectionOf( - DataHasValue( recipe:value "1" ) - ObjectSomeValuesFrom( qudt:unit ) - ) ) - ) ) ) - SubClassOf( AUTO:_ROOT ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "chopped" ) - ) ) - ObjectSomeValuesFrom( recipe:amount ObjectIntersectionOf( - DataHasValue( recipe:value "1" ) - ObjectSomeValuesFrom( qudt:unit ) - ) ) - ) ) ) - SubClassOf( AUTO:_ROOT ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "powder" ) - ) ) - ObjectSomeValuesFrom( recipe:amount ObjectIntersectionOf( - DataHasValue( recipe:value "2" ) - ObjectSomeValuesFrom( qudt:unit ) - ) ) - ) ) ) - SubClassOf( AUTO:_ROOT ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( recipe:amount ObjectIntersectionOf( - DataHasValue( recipe:value "3" ) - ObjectSomeValuesFrom( qudt:unit ) - ) ) - ) ) ) - SubClassOf( AUTO:_ROOT ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectSomeValuesFrom( AUTO:salt ) ) - ObjectSomeValuesFrom( recipe:amount ObjectIntersectionOf( - DataHasValue( recipe:value "1" ) - ObjectSomeValuesFrom( qudt:unit ) - ) ) - ) ) ) - SubClassOf( AUTO:_ROOT ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( recipe:amount ObjectIntersectionOf( - DataHasValue( recipe:value "1" ) - ObjectSomeValuesFrom( qudt:unit ) - ) ) - ) ) ) - SubClassOf( AUTO:_ROOT ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "canned" ) - ) ) - ObjectSomeValuesFrom( recipe:amount DataHasValue( recipe:value "2" ) ) - ) ) ) - SubClassOf( AUTO:_ROOT ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectIntersectionOf( - ObjectSomeValuesFrom( AUTO:1%20%2816%20ounce%29%20box%20spaghetti%20noodles ) - DataHasValue( recipe:state "uncooked" ) - ) ) - ObjectSomeValuesFrom( recipe:amount DataHasValue( recipe:value "1" ) ) - ) ) ) - SubClassOf( AUTO:_ROOT ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "chopped/diced" ) - ) ) - ObjectSomeValuesFrom( recipe:amount ObjectIntersectionOf( - DataHasValue( recipe:value "1 - 1 1⁄2" ) - ObjectSomeValuesFrom( qudt:unit AUTO:lb ) - ) ) - ) ) ) - SubClassOf( AUTO:_ROOT ObjectSomeValuesFrom( recipe:steps ObjectIntersectionOf( - AUTO:melt%3B%20saut%C3%A9 - ObjectSomeValuesFrom( ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "chopped" ) - ) ) - ObjectSomeValuesFrom( AUTO:pan ) - ) ) ) - SubClassOf( AUTO:_ROOT ObjectSomeValuesFrom( recipe:steps ObjectIntersectionOf( - AUTO:add%3B%20cook - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "chopped/diced" ) - ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( AUTO:meat ) - DataHasValue( recipe:state "well done" ) - ) ) - ObjectSomeValuesFrom( AUTO:pan ) - ) ) ) - SubClassOf( AUTO:_ROOT ObjectSomeValuesFrom( recipe:steps ObjectIntersectionOf( - AUTO:add%3B - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "sauce" ) - ) ) - ObjectSomeValuesFrom( ObjectSomeValuesFrom( AUTO:salt ) ) - ObjectSomeValuesFrom( ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "powder" ) - ) ) - ObjectSomeValuesFrom( ObjectSomeValuesFrom( AUTO:none ) ) - ObjectSomeValuesFrom( AUTO:none ) - ) ) ) - SubClassOf( AUTO:_ROOT ObjectSomeValuesFrom( recipe:steps ObjectIntersectionOf( - AUTO:adjust - ObjectSomeValuesFrom( ObjectSomeValuesFrom( AUTO:salt ) ) - ObjectSomeValuesFrom( ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "powder" ) - ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( AUTO:inputs ) - DataHasValue( recipe:state "adjusted" ) - ) ) - ObjectSomeValuesFrom( AUTO:none ) - ) ) ) - SubClassOf( AUTO:_ROOT ObjectSomeValuesFrom( recipe:steps ObjectIntersectionOf( - AUTO:Cook - ObjectSomeValuesFrom( ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( ObjectSomeValuesFrom( AUTO:as%20directed ) ) - ) ) ) - SubClassOf( AUTO:_ROOT ObjectSomeValuesFrom( recipe:steps ObjectIntersectionOf( - AUTO:mix%3B - ObjectSomeValuesFrom( ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "+" ) - ) ) - ObjectSomeValuesFrom( AUTO:none ) - ) ) ) - AnnotationAssertion( rdfs:label "bell pepper" ) - AnnotationAssertion( rdfs:label "garlic" ) - AnnotationAssertion( rdfs:label "tablespoons" ) - AnnotationAssertion( rdfs:label "butter" ) - AnnotationAssertion( rdfs:label "tablespoons" ) - AnnotationAssertion( rdfs:label "teaspoon" ) - AnnotationAssertion( rdfs:label "pepper" ) - AnnotationAssertion( rdfs:label "teaspoon" ) - AnnotationAssertion( rdfs:label "tomato sauce" ) - AnnotationAssertion( rdfs:label "hamburger meat" ) - AnnotationAssertion( rdfs:label "butter" ) - AnnotationAssertion( rdfs:label "onion" ) - AnnotationAssertion( rdfs:label "bell peppers" ) - AnnotationAssertion( rdfs:label "hamburger meat" ) - AnnotationAssertion( rdfs:label "tomato" ) - AnnotationAssertion( rdfs:label "pepper" ) - AnnotationAssertion( rdfs:label "garlic" ) - AnnotationAssertion( rdfs:label "pepper" ) - AnnotationAssertion( rdfs:label "garlic" ) - AnnotationAssertion( rdfs:label "noodles" ) - AnnotationAssertion( rdfs:label "sauce" ) - AnnotationAssertion( rdfs:label "noodles" ) - AnnotationAssertion( rdfs:label "noodles" ) -) \ No newline at end of file diff --git a/tests/output/recipe-spaghetti.pickle b/tests/output/recipe-spaghetti.pickle deleted file mode 100644 index df48e1075..000000000 Binary files a/tests/output/recipe-spaghetti.pickle and /dev/null differ diff --git a/tests/output/recipe-spaghetti.yaml b/tests/output/recipe-spaghetti.yaml deleted file mode 100644 index d01824103..000000000 --- a/tests/output/recipe-spaghetti.yaml +++ /dev/null @@ -1,207 +0,0 @@ -input_id: /Users/cjm/repos/ontogpt/tests/input/cases/recipe-spaghetti.txt -input_text: "SIMPLE SPAGHETTI\n\nDIRECTIONS\nOn medium heat melt the butter and sautee\ - \ the onion and bell peppers.\nAdd the hamburger meat and cook until meat is well\ - \ done.\nAdd the tomato sauce, salt, pepper and garlic powder.\nSalt, pepper and\ - \ garlic powder can be adjusted to your own tastes.\nCook noodles as directed.\n\ - Mix the sauce and noodles if you like, I keep them separated.\n\nINGREDIENTS\nUNITS:\ - \ US\n1\nsmall onion (chopped)\n1\nbell pepper (chopped)\n2\ntablespoons garlic\ - \ powder\n3\ntablespoons butter\n1\nteaspoon salt\n1\nteaspoon pepper\n2\n(15 ounce)\ - \ cans tomato sauce\n1\n(16 ounce) box spaghetti noodles\n1 - 1 1\u20442\nlb hamburger\ - \ meat.\n" -raw_completion_output: "\nurl: \nlabel: Simple Spaghetti\ndescription: A recipe for\ - \ a simple spaghetti featuring saut\xE9ed onions, bell peppers and hamburger meat.\n\ - categories: Main; Pasta\ningredients: 1 small onion (chopped); 1 bell pepper (chopped);\ - \ 2 tablespoons garlic powder; 3 tablespoons butter; 1 teaspoon salt; 1 teaspoon\ - \ pepper; 2 (15 ounce) cans tomato sauce; 1 (16 ounce) box spaghetti noodles; 1\ - \ - 1 1\u20442 lb hamburger meat\nsteps: On medium heat melt the butter and saut\xE9\ - \ the onion and bell peppers; Add the hamburger meat and cook until well done; Add\ - \ the tomato sauce, salt, pepper and garlic powder; Salt, pepper and garlic powder\ - \ can be adjusted to own tastes; Cook noodles as directed; Mix the sauce and noodles\ - \ if desired." -prompt: 'Split the following piece of text into fields in the following format: - - - food: - - state: - - - - Text: - - noodles - - - === - - - ' -extracted_object: - label: Simple Spaghetti - description: "A recipe for a simple spaghetti featuring saut\xE9ed onions, bell\ - \ peppers and hamburger meat." - categories: - - AUTO:Main - - FOODON:03306347 - ingredients: - - food_item: - food: FOODON:03301704 - amount: - value: '1' - unit: AUTO:small%20%28chopped%29 - - food_item: - food: FOODON:00003485 - state: chopped - amount: - value: '4' - unit: AUTO:cups - - food_item: - food: FOODON:00003582 - state: powder - amount: - value: '2' - unit: UO:0010042 - - food_item: - food: FOODON:03310351 - amount: - value: '3' - unit: UO:0010042 - - food_item: - food: AUTO:salt - amount: - value: '1' - unit: UO:0010040 - - food_item: - food: FOODON:00001649 - amount: - value: '1' - unit: UO:0010040 - - food_item: - food: FOODON:03000227 - state: sauce - amount: - value: '2' - unit: AUTO:%2815%20ounce%29%20cans - - food_item: - food: AUTO:1%20%2816%20ounce%29%20box%20spaghetti%20noodles - state: uncooked - amount: - value: '1' - - food_item: - food: FOODON:00001282 - state: chopped - amount: - value: "1 - 1 1\u20442" - unit: AUTO:lbs - steps: - - action: AUTO:Melt%3B%20Saut%C3%A9 - inputs: - - food: FOODON:03310351 - - food: FOODON:03301704 - - food: FOODON:00003485 - state: diced - utensils: - - AUTO:Pan - - action: AUTO:add%3B%20cook - inputs: - - food: FOODON:00001282 - state: chopped - outputs: - - food: AUTO:well%20done - state: done - utensils: - - AUTO:pan - - action: AUTO:Add - inputs: - - food: FOODON:03000227 - state: sauce - - food: AUTO:salt - - food: FOODON:00001649 - - food: FOODON:00003582 - state: powder - - action: AUTO:adjust%3B - inputs: - - food: AUTO:salt - - food: FOODON:00001649 - - food: FOODON:00003582 - state: powder - outputs: - - food: FOODON:03460173 - - food: FOODON:00001649 - state: peppered - - food: FOODON:00003582 - state: flavoured - utensils: - - AUTO:none - - action: AUTO:Cook - inputs: - - food: FOODON:03306944 - outputs: - - food: AUTO:none - utensils: - - AUTO:none - - action: AUTO:Mix%3B - inputs: - - food: FOODON:03311146 - - food: FOODON:03306944 -named_entities: -- id: AUTO:Main - label: Main -- id: FOODON:03306347 - label: Pasta -- id: FOODON:03301704 - label: onion -- id: AUTO:small%20%28chopped%29 - label: small (chopped) -- id: FOODON:00003485 - label: bell pepper -- id: AUTO:cups - label: cups -- id: FOODON:00003582 - label: garlic -- id: UO:0010042 - label: tablespoons -- id: FOODON:03310351 - label: butter -- id: AUTO:salt - label: salt -- id: UO:0010040 - label: teaspoon -- id: FOODON:00001649 - label: pepper -- id: FOODON:03000227 - label: tomato -- id: AUTO:%2815%20ounce%29%20cans - label: (15 ounce) cans -- id: AUTO:1%20%2816%20ounce%29%20box%20spaghetti%20noodles - label: 1 (16 ounce) box spaghetti noodles -- id: FOODON:00001282 - label: hamburger meat -- id: AUTO:lbs - label: lbs -- id: AUTO:Melt%3B%20Saut%C3%A9 - label: "Melt; Saut\xE9" -- id: AUTO:Pan - label: Pan -- id: AUTO:add%3B%20cook - label: add; cook -- id: AUTO:well%20done - label: well done -- id: AUTO:pan - label: pan -- id: AUTO:Add - label: Add -- id: AUTO:adjust%3B - label: adjust; -- id: FOODON:03460173 - label: salted -- id: AUTO:none - label: none -- id: AUTO:Cook - label: Cook -- id: FOODON:03306944 - label: noodles -- id: AUTO:Mix%3B - label: Mix; -- id: FOODON:03311146 - label: sauce diff --git a/tests/output/recipe-tortilla-soup.pickle b/tests/output/recipe-tortilla-soup.pickle deleted file mode 100644 index 58e540545..000000000 Binary files a/tests/output/recipe-tortilla-soup.pickle and /dev/null differ diff --git a/tests/output/recipe-tortilla-soup.yaml b/tests/output/recipe-tortilla-soup.yaml deleted file mode 100644 index fc574b578..000000000 --- a/tests/output/recipe-tortilla-soup.yaml +++ /dev/null @@ -1,444 +0,0 @@ -input_id: /Users/cjm/repos/ontogpt/tests/input/cases/recipe-tortilla-soup.txt -input_text: 'Tortilla Soup - - - Ingredients - - 1 rotisserie chicken or 3-4 cups poached chicken - - 1 (15 oz) can fire roasted tomatoes, diced - - 1 (10 oz) can red enchilada sauce, mild - - 1 small onion, chopped - - 1 medium zucchini, sliced into 1/4-inch half circles - - 1 (4 oz) can green chilies - - 4 cloves garlic, minced - - 4 cups chicken broth - - 1 (14.5 oz) can creamed corn, undrained (can sub with 1 can sweet corn, drained) - - 1 tsp ground cumin - - 1 tsp chili powder - - 1 tsp sea salt - - 1/4 tsp freshly ground black pepper - - 3 bay leaves - - - Garnish - - 4 Tbsp chopped cilantro - - 1 lime cut into wedges - - sour cream - - cheese, shredded (cheddar, mozzarella, Mexican blend) - - 1 large avocado, sliced - - Tortilla chips, crushed - - - Method - - While rotisserie chicken is still warm, pick all meat of the bones, discard skin. - Place the chicken meat in a large stock pot. Discard bones, or save if you like - to make homemade stock. - - Add to the pot the tomatoes, enchilada sauce, chicken broth, onion, zucchini, chilis, - garlic, corn, cumin, chili powder, salt, pepper and bay leaves. Stir to combine - and turn the heat to high. - - As soon as soup begins to boil, turn the heat to medium-low heat and continue to - cook, uncovered, until the onions are translucent and zucchini is tender, about - 30 minutes. - - Serve the soup topped with chopped cilantro, a squeeze of fresh lime juice, sour - cream, cheese, avocado and corn chips. - - ' -raw_completion_output: "\nurl: \nlabel: Tortilla Soup\ndescription: This is a traditional\ - \ Mexican soup that can be made with a rotisserie chicken or poached chicken. It\ - \ is full of flavor and garnished with cilantro, lime juice, sour cream, cheese,\ - \ avocado, and corn chips. \ncategories: Mexican; Soup\ningredients: 1 rotisserie\ - \ chicken or 3-4 cups poached chicken; 1 (15 oz) can fire roasted tomatoes, diced;\ - \ 1 (10 oz) can red enchilada sauce, mild; 1 small onion, chopped; 1 medium zucchini,\ - \ sliced into 1/4-inch half circles; 1 (4 oz) can green chilies; 4 cloves garlic,\ - \ minced; 4 cups chicken broth; 1 (14.5 oz) can creamed corn, undrained (can sub\ - \ with 1 can sweet corn, drained); 1 tsp ground cumin; 1 tsp chili powder; 1 tsp\ - \ sea salt; 1/4 tsp freshly ground black pepper; 3 bay leaves; 4 Tbsp chopped cilantro;\ - \ 1 lime cut into wedges; sour cream; cheese, shredded (cheddar, mozzarella, Mexican\ - \ blend); 1 large avocado, sliced; Tortilla chips, crushed\nsteps: Pick all meat\ - \ of the bones from pre-cooked chicken, discard skin and bones; Place chicken meat\ - \ into large stock pot; Add tomatoes, enchilada sauce, chicken broth, onion, zucchini,\ - \ chilis, garlic, corn, cumin, chili powder, salt, pepper and bay leaves to pot;\ - \ Stir to combine and turn the heat to high; As soon as soup begins to boil, turn\ - \ the heat to medium-low and cook uncovered until onions are translucent and zucchini\ - \ is tender, about 30 minutes; Serve soup topped with chopped cilantro, a squeeze\ - \ of fresh lime juice, sour cream, cheese, avocado and corn chips." -prompt: 'Split the following piece of text into fields in the following format: - - - food: - - state: - - - - Text: - - soup - - - === - - - ' -extracted_object: - label: Tortilla Soup - description: This is a traditional Mexican soup that can be made with a rotisserie - chicken or poached chicken. It is full of flavor and garnished with cilantro, - lime juice, sour cream, cheese, avocado, and corn chips. - categories: - - HANCESTRO:0415 - - AUTO:Soup - ingredients: - - food_item: - food: AUTO:poached%20chicken - state: poached - amount: - value: 3-4 - unit: AUTO:cups - - food_item: - food: AUTO:1%20%2815%20oz%29%20can%20fire%20roasted%20tomatoes - state: chopped - amount: - value: diced - unit: AUTO:N/A - - food_item: - food: AUTO:red%20enchilada%20sauce - state: chopped - amount: - value: '10' - unit: AUTO:oz - - food_item: - food: FOODON:03301704 - state: small - amount: - value: chopped - unit: AUTO:N/A - - food_item: - food: FOODON:03310943 - state: chopped - amount: - value: '1' - unit: AUTO:medium%2C%20sliced%20into%201/4-inch%20half%20circles - - food_item: - food: AUTO:1%20%284%20oz%29%20can%20green%20chilies - state: chopped, diced - amount: - value: '1' - - food_item: - food: FOODON:00003582 - state: cloves - amount: - value: minced - - food_item: - food: FOODON:03411457 - state: broth - amount: - value: '4' - unit: AUTO:cups - - food_item: - food: AUTO:creamed%20corn - state: creamed - amount: - value: '14.5' - unit: AUTO:oz - - food_item: - food: AUTO:ground%20cumin - state: ground - amount: - value: '1' - unit: AUTO:tsp - - food_item: - food: FOODON:03302030 - state: chopped - amount: - value: '1' - unit: AUTO:tsp - - food_item: - food: AUTO:sea%20salt - state: diced - amount: - value: '1' - unit: AUTO:tsp - - food_item: - food: AUTO:freshly%20ground%20black%20pepper - state: ground - amount: - value: 1/4 - unit: AUTO:tsp - - food_item: - food: AUTO:bay%20leaves - state: chopped - - food_item: - food: AUTO:cilantro - state: chopped - amount: - value: '4' - unit: AUTO:Tbsp - - food_item: - food: FOODON:00003661 - amount: - value: '1' - - food_item: - food: FOODON:03302515 - state: chopped - - food_item: - food: FOODON:00001013 - state: shredded (cheddar, mozzarella, Mexican blend) - - food_item: - food: FOODON:00003600 - amount: - value: '1' - unit: AUTO:large%2C%20sliced - - food_item: - food: FOODON:03310710 - state: Chopped - amount: - value: crushed - steps: - - action: AUTO:Pick%3B - inputs: - - food: AUTO:pre-cooked%20chicken - state: pre-cooked - outputs: - - food: AUTO:meat - utensils: - - AUTO:none - - action: dbpediaont:Square - inputs: - - food: FOODON:03411457 - state: meat - outputs: - - food: AUTO:large%20stock%20pot - utensils: - - AUTO:Pot - - action: AUTO:add%3B - inputs: - - food: FOODON:03000227 - - food: FOODON:03304007 - - food: FOODON:03411457 - state: broth - - food: FOODON:03301704 - - food: FOODON:03310943 - state: chopped - - food: FOODON:03317304 - state: chopped - - food: FOODON:00003582 - - food: AUTO:corn - - food: FOODON:00003024 - state: chopped - - food: FOODON:03302030 - state: chopped - - food: AUTO:salt - - food: FOODON:00001649 - - food: AUTO:bay%20leaves - outputs: - - food: AUTO:pot - utensils: - - AUTO:pot - - action: AUTO:Stir%3B - inputs: - - food: AUTO:combine - utensils: - - AUTO:- - - action: AUTO:cook%3B - inputs: - - food: AUTO:soup - outputs: - - food: FOODON:03310943 - state: diced - utensils: - - AUTO:none. - - action: AUTO:topping%3B - inputs: - - food: AUTO:cilantro - state: chopped - - food: AUTO:fresh%20lime%20juice - state: chopped - - food: FOODON:03302515 - state: chopped - - food: FOODON:00001013 - - food: FOODON:00003600 - - food: FOODON:03302052 - state: chopped - outputs: - - food: AUTO:soup - utensils: - - AUTO:none -named_entities: -- id: AUTO:Main - label: Main -- id: FOODON:03306347 - label: Pasta -- id: FOODON:03301704 - label: onion -- id: AUTO:small%20%28chopped%29 - label: small (chopped) -- id: FOODON:00003485 - label: bell pepper -- id: AUTO:cups - label: cups -- id: FOODON:00003582 - label: garlic -- id: UO:0010042 - label: tablespoons -- id: FOODON:03310351 - label: butter -- id: AUTO:salt - label: salt -- id: UO:0010040 - label: teaspoon -- id: FOODON:00001649 - label: pepper -- id: FOODON:03000227 - label: tomato -- id: AUTO:%2815%20ounce%29%20cans - label: (15 ounce) cans -- id: AUTO:1%20%2816%20ounce%29%20box%20spaghetti%20noodles - label: 1 (16 ounce) box spaghetti noodles -- id: FOODON:00001282 - label: hamburger meat -- id: AUTO:lbs - label: lbs -- id: AUTO:Melt%3B%20Saut%C3%A9 - label: "Melt; Saut\xE9" -- id: AUTO:Pan - label: Pan -- id: AUTO:add%3B%20cook - label: add; cook -- id: AUTO:well%20done - label: well done -- id: AUTO:pan - label: pan -- id: AUTO:Add - label: Add -- id: AUTO:adjust%3B - label: adjust; -- id: FOODON:03460173 - label: salted -- id: AUTO:none - label: none -- id: AUTO:Cook - label: Cook -- id: FOODON:03306944 - label: noodles -- id: AUTO:Mix%3B - label: Mix; -- id: FOODON:03311146 - label: sauce -- id: HANCESTRO:0415 - label: Mexican -- id: AUTO:Soup - label: Soup -- id: AUTO:poached%20chicken - label: poached chicken -- id: AUTO:1%20%2815%20oz%29%20can%20fire%20roasted%20tomatoes - label: 1 (15 oz) can fire roasted tomatoes -- id: AUTO:N/A - label: N/A -- id: AUTO:red%20enchilada%20sauce - label: red enchilada sauce -- id: AUTO:oz - label: oz -- id: FOODON:03310943 - label: zucchini -- id: AUTO:medium%2C%20sliced%20into%201/4-inch%20half%20circles - label: medium, sliced into 1/4-inch half circles -- id: AUTO:1%20%284%20oz%29%20can%20green%20chilies - label: 1 (4 oz) can green chilies -- id: FOODON:03411457 - label: chicken -- id: AUTO:creamed%20corn - label: creamed corn -- id: AUTO:ground%20cumin - label: ground cumin -- id: AUTO:tsp - label: tsp -- id: FOODON:03302030 - label: chili powder -- id: AUTO:sea%20salt - label: sea salt -- id: AUTO:freshly%20ground%20black%20pepper - label: freshly ground black pepper -- id: AUTO:bay%20leaves - label: bay leaves -- id: AUTO:cilantro - label: cilantro -- id: AUTO:Tbsp - label: Tbsp -- id: FOODON:00003661 - label: lime -- id: FOODON:03302515 - label: sour cream -- id: FOODON:00001013 - label: cheese -- id: FOODON:00003600 - label: avocado -- id: AUTO:large%2C%20sliced - label: large, sliced -- id: FOODON:03310710 - label: Tortilla chips -- id: AUTO:Pick%3B - label: Pick; -- id: AUTO:pre-cooked%20chicken - label: pre-cooked chicken -- id: AUTO:meat - label: meat -- id: dbpediaont:Square - label: Place -- id: AUTO:large%20stock%20pot - label: large stock pot -- id: AUTO:Pot - label: Pot -- id: AUTO:add%3B - label: add; -- id: FOODON:03304007 - label: enchilada sauce -- id: FOODON:03317304 - label: chilis -- id: AUTO:corn - label: corn -- id: FOODON:00003024 - label: cumin -- id: AUTO:pot - label: pot -- id: AUTO:Stir%3B - label: Stir; -- id: AUTO:combine - label: combine -- id: AUTO:- - label: '-' -- id: AUTO:cook%3B - label: cook; -- id: AUTO:soup - label: soup -- id: AUTO:none. - label: none. -- id: AUTO:topping%3B - label: topping; -- id: AUTO:fresh%20lime%20juice - label: fresh lime juice -- id: FOODON:03302052 - label: corn chips diff --git a/tests/output/spires-extract-spaghetti.owl b/tests/output/spires-extract-spaghetti.owl deleted file mode 100644 index 59ac5c179..000000000 --- a/tests/output/spires-extract-spaghetti.owl +++ /dev/null @@ -1,7689 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - label - label - label - label - - - - - - - - - - - - - - - - - - - - - - - - - is part of - a core relation that holds between a part and its whole - - part of - part of - part_of - - - - - - - - - - has part - a core relation that holds between a whole and its part - - - has part - has part - has_part - - - - - - - - - A defining ingredient defines what a food is principally categorized as, rather than an ingredient listed by percentage of weight or volume. A food may have more than one defining ingredient. - Damion Dooley - FoodOn - For example, 'bean soup' has a defining ingredient of some 'bean (whole)'. Similarly, spicy chicken wings require a defining ingredient of (usually minute) amounts of chilli. - -A soup may 'has ingredient' some bean, but that doesn't make it a 'bean soup', i.e. there should be no inference to that category. However, some classes may have that simple ingredient "necessary and sufficient" equivalency. - has defining ingredient - - - - - - - - - - - A relation attaching between a food material and another food material that has been added to it at some point in its history. - Damion Dooley - FoodOn - has ingredient - - - - - - - - - participates in - a relation between a continuant and a process, in which the continuant is somehow involved in the process - - - participates in - participates_in - - - - - - - - has participant - a relation between a process and a continuant, in which the continuant is somehow involved in the process - - has participant - has_participant - - - - - - - - a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence - - has quality - - - - - - - - a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence - - has role - - - - - - - - - a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity - - derives from - - - - - - - - - x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. - - - - in taxon - - - - - - - - - develops from - develops from - develops_from - - - - - - - - - p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. - - has input - - - - - - - - - p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. - - has output - - - - - - - - - An organism that is a member of a population of organisms - is member of is a mereological relation between a item and a collection. - is member of - member part of - SIO - - - member of - - - - - - - - - has member is a mereological relation between a collection and an item. - SIO - - has member - - - - - - - - - - - - - - - a produced_by b iff some process that occurs_in b has_output a. - - produced by - - - - - - - - - - "has substance added" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time. - Damion Dooley - - has substance added - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - canned - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - 1-1 1⁄2 - - - - - - - - - - - - - - - - - chopped/diced - - - - - - - - - - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - chopped, diced - - - - - - - - - - - - - - - - - - - - - - - - powder - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - powder - - - - - - - - - - - - - - - - - sauce - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chopped/diced - - - - - - - - - - - - - - - - - well done - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - powder - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - to own tastes - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - canned - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1-1 1⁄2 - - - - - - - - - - - - - - - - - chopped/diced - - - - - - - - - - - - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - chopped, diced - - - - - - - - - - - - - - - - - - - - - - - - - - powder - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - powder - - - - - - - - - - - - - - - - - sauce - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chopped/diced - - - - - - - - - - - - - - - - - well done - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - powder - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - to own tastes - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A classic spaghetti recipe made with onion, bell peppers, garlic powder, butter, salt, pepper, tomato sauce, and hamburger meat. - - - Simple Spaghetti - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - entity - Entity - Julius Caesar - Verdi’s Requiem - the Second World War - your body mass index - BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 - Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf - - - - - - An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) - - entity - entity - - - - - Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf - - per discussion with Barry Smith - - - - - - An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) - - - - - - - - - - - - - - - - - continuant - Continuant - continuant - An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. - An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. - BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 - Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants - - - - - A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) - if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) - if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) - if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) - (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] - (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] - (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] - (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] - - continuant - continuant - - - - - Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants - - - - - - A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) - - - - - - if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) - - - - - - if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) - - - - - - if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) - - - - - - (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] - - - - - - (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] - - - - - - (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] - - - - - - (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] - - - - - - - - - - occurrent - Occurrent - An entity that has temporal parts and that happens, unfolds or develops through time. - An entity that has temporal parts and that happens, unfolds or develops through time. - BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region - BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. - Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. - Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. - - - - - An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) - Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) - b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) - (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] - (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] - - occurrent - occurrent - - - - - Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. - - per discussion with Barry Smith - - - - - Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. - - - - - - An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) - - - - - - Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) - - - - - - b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) - - - - - - (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] - - - - - - (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] - - - - - - - - - - - - - - - - - - ic - IndependentContinuant - a chair - a heart - a leg - a molecule - a spatial region - an atom - an orchestra. - an organism - the bottom right portion of a human torso - the interior of your mouth - A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. - A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) - - - - - For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) - For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) - (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] - (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] - (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] - - independent continuant - independent continuant - - - - - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) - - - - - - For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) - - - - - - For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) - - - - - - (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] - - - - - - (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] - - - - - - (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] - - - - - - - - - - t-region - TemporalRegion - Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional - A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) - All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) - Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) - (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] - (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] - (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] - - temporal region - - - - - Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional - - per discussion with Barry Smith - - - - - A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) - - - - - - All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) - - - - - - Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) - - - - - - (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] - - - - - - (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] - - - - - - (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] - - - - - - - - - - sdc - SpecificallyDependentContinuant - Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key - of one-sided specifically dependent continuants: the mass of this tomato - of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. - the disposition of this fish to decay - the function of this heart: to pump blood - the mutual dependence of proton donors and acceptors in chemical reactions [79 - the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction - the pink color of a medium rare piece of grilled filet mignon at its center - the role of being a doctor - the shape of this hole. - the smell of this portion of mozzarella - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. - (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] - - specifically dependent continuant - - - - - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - - - - - - Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. - - per discussion with Barry Smith - - - - - (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] - - - - - - - - - - fiat-object-part - FiatObjectPart - or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29 - the FMA:regional parts of an intact human body. - the Western hemisphere of the Earth - the division of the brain into regions - the division of the planet into hemispheres - the dorsal and ventral surfaces of the body - the upper and lower lobes of the left lung - BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions - - b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) - (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] - - fiat object - fiat object part - - - - - b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) - - - - - - (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] - - - - - - - - - - gdc - GenericallyDependentContinuant - The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. - the pdf file on your laptop, the pdf file that is a copy thereof on my laptop - the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - - (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] - - generically dependent continuant - - - - - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - - - - - - (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] - - - - - - - - - - 1d-t-region - OneDimensionalTemporalRegion - the temporal region during which a process occurs. - BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks). - A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) - (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] - - one-dimensional temporal region - - - - - A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) - - - - - - (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] - - - - - - - - - - material - MaterialEntity - material entity - material entity - a flame - a forest fire - a human being - a hurricane - a photon - a puff of smoke - a sea wave - a tornado - an aggregate of human beings. - an energy wave - an epidemic - the undetached arm of a human being - An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. - BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 - BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. - BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. - - - - - A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) - Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) - every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) - (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] - bfo - BFO:0000040 - - material entity - material entity - - - - - A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) - - - - - - Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) - - - - - - every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) - - - - - - (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] - - - - - - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] - - - - - - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] - - - - - - - - - - A role played by the molecular entity or part thereof within a biological context. - - biological role - - - - - - - - - food role - A physiological role played by any substance of either plant, animal or artificial origin which contains essential body nutrients that can be ingested by an organism to provide energy, promote growth, and maintain the processes of life. - - food - - - - - - - - role (CHEBI) - A role is particular behaviour which a material entity may exhibit. - - role - - - - - - - - - - physiological role - - - - - - - - - A portion of environmental material is a fiat object part which forms the medium or part of the medium of an environmental system. - - environmental - environmental material - - - - - - - - - Food material for humans and animals which is processed with the intention that it be consumable as a whole or added to other food products. - Damion Dooley - Foodon product type - https://en.wikipedia.org/wiki/Food - The FoodOn "food product" class is provided as a branch under which new food product categories and food products themselves can be placed. Here classes are provided to differentiate a food product by its food composition, processing and/or consumption characteristics. This avoids brand name products but it may include generic food dish categories. It has a much greater depth and polyhierarchy than other agency product type schemes have in an effort to group related products together. The upper level basis of this tree originated in the environment ontology (ENVO) and from the US Code of Federal Regulations. - food product - - - - - - - - - - - - - - - - - - - - - - A food product made of meat, the skeletal muscle and associated fat, and other edible tissues such as organs, livers, skin, brains, bone marrow, kidneys, or lungs, of mammals. - - SUBSET_SIREN:F17332 - mammalian meat food product - - - - - - - - - - - - - - - - - - - - - - - - - - - This class includes food products which are derived from or produced by a plant. - plant food product - - - - - - - - - - - - - - - - - - - - - - - - - - Meat from bovines, especially domestic cattle (cows). - beef food product - - - - - Meat from bovines, especially domestic cattle (cows). - http://en.wikipedia.org/wiki/Beef - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A food product derived from plant fruit. - plant fruit food product - - - - - - - - - - - - - - - - - - - - - - - - - - - A food product which is derived from or produced by an animal that has a vertibrae. - Damion Dooley - vertebrate animal food product - - - - - - - - - bovine dairy food product - - - - - - - - - - - - - - - cattle dairy food product - - - - - - - - - - - - - - - A relish, sauce, or seasoning added to food to impart a particular flavour or to complement the dish. - Damion Dooley - https://en.wikipedia.org/wiki/Condiment - condiment - condiment food product - - - - - - - - - - - - - - - - - - - - - - - - - - bovine meat food product - - - - - - - - - A food product derived from or produced by a plant root. - plant root food product - - - - - - - - - - solanaceous fruit food product - - - - - - - - - - - - - - - - A food product deriving from one or more tomatoes. - tomato food product - - - - - - - - - solanaceous food product - - - - - - - - - - - - - - - - - - - - - - - - - - invertebrate animal food product - - - - - - - - - - - - - - - - - A vegetable product such as leaves, flowers, seeds and roots that is rich in essential oils and aromatic principles. Used mainly a a condiment. - Damion Dooley - http://www.fao.org/WAICENT/faoinfo/economic/faodef/fdef10e.htm#1.01 - http://www.langual.org/langual_thesaurus.asp?termid=H0151 - herb and spice - herb or spice - spice or herb - - - - - - - - - - - - - - - - - - - - - - A dairy food product has mammilian milk or a milk component as an ingredient. - Damion Dooley - http://www.langual.org/langual_thesaurus.asp?termid=H0242 - dairy product - milk product - dairy food product - - - - - - - - - milk or milk based food product - - - - - - - - - - - - - - - - - - - - - - Any plant food product which, typically, is constituted by intact parts from one or more annual plants cultivated as field and garden crops in the open and under glass, and used almost exclusively for food. - - vegetable food product - - - - - - - - - - A ground beef product is made of beef that has been finely chopped with a knife or a meat grinder (American English) or mincing machine (British English). Ground beef is used in many recipes including hamburgers and spaghetti Bolognese. - - - beef mince - beef mince - ground beef - hamburger meat - minced beef - ground beef food product - - - - - - - - - pepper - black or white pepper product - - - - - - - - - A food product which normally exists as an ingredient to another food product, rather than eaten on its own, and is more complex than a chemical food component. - food product component - - - - - - - - - - - - - - - - - - - - - - - - - - - cow milk based food product - - - - - - - - - cow milk butter food product - - - - - - - - - - - - - - - - - - - - - - - - - - - garlic food product - - - - - - - - - - - - - - - - - - - - - - - - - - ginger - ginger food product - - - - - - - - - - - - - - - gravy or sauce - - - - - - - - - - - - - - - - - - - - - - - - - - green bell pepper food product - - - - - - - - - - - - - - - - - - - - - - - - - - red pepper - hot pepper food product - - - - - - - - - - - - - - - - - - - - - - - - - - milk based gravy or sauce food product - - - - - - - - - - - - - - - - - - - - - - - - - - - onion flavouring food product - - - - - - - - - - - - - - - - - - - - - - - - - - onion food product - - - - - - - - - - - - - - - A food product deriving from one or more sweet or hot peppers. - pepper vegetable food product - - - - - - - - - plant based gravy or sauce food product - - - - - - - - - - - - - - - A plant fruit food product which is labeled (in common language or by regulation) as a vegetable food product. - plant fruit as vegetable food product - - - - - - - - - - - - - - - - - - - - - - - - - - - - A food product harvested from underground plant parts. - plant root vegetable food product - - - - - - - - - - - - - - - - - - - - - - - - - - red bell pepper food product - - - - - - - - - - - - - - - tomato based gravy or sauce food product - - - - - - - - - - - - - - - tomato substance - - - - - - - - - vegetable based gravy or sauce food product - - - - - - - - - - - - - - - A food product consisting of food material derived primarily from a single organism. - Damion Dooley - food product by organism - - - - - - - - - - - - - - - - - - - - - - - - - - Any substance that can be consumed by an organism to satisfy nutritional or other health needs, or to provide a social or organoleptic food experience - - - food - foodstuff - nourishment - sustenance - food material - - - - - - - - - Familiar examples of invertebrates include arthropods (insects, arachnids, crustaceans, and myriapods), mollusks (chitons, snails, bivalves, squids, and octopuses), annelids (earthworms and leeches), and cnidarians (hydras, jellyfishes, sea anemones, and corals).[wikipedia] - - Invertebrates are animals that neither possess nor develop a vertebral column (commonly known as a backbone or spine), derived from the notochord. This includes all animals apart from the subphylum Vertebrata. - Damion Dooley - https://en.wikipedia.org/wiki/Invertebrate - animal - invertebrate animal - - - - - - - - - - A class which contains food product categories qualified by a quality such as granularity or temperature, which is useful for tasks like food inspection where little prior knowledge of how the food came to be is available. Some terms like "food (frozen)" are both a quality descriptor and the output of a process. - Damion Dooley - food product by quality - - - - - - - - - - - - - - - - - - - - - - A food product consisting of food material derived from ingredients sourced from multiple organisms. - Damion Dooley - 2019-01-23T22:40:32Z - multi-ingredient - The definition of this is being discussed in issue: https://github.com/FoodOntology/foodon/issues/57 - -Namely, how to characterize the threshold of ingredients that make for multi-component classification? Salt, pepper, spices wouldn't normally make a food multi-component? - multi-component food product - - - - - - - - - - Dairy cattle are a type of cattle bred for the ability to produce large quantities of milk, from which dairy products are made. This class covers both male and female members of a dairy breed. - Damion Dooley - https://en.wikipedia.org/wiki/Dairy_cattle - 2019-01-26T22:49:27Z - dairy cattle - https://en.wikipedia.org/wiki/List_of_dairy_cattle_breeds - - - - - - - - - - Taurine cattle (Bos taurus taurus), also called European cattle, are a subspecies of domesticated cattle originating in the Near East. Both taurine cattle and indicine cattle (zebus) are descended from the aurochs. Taurine cattle were originally considered a distinct species, but are now typically grouped with zebus and aurochs into one species, Bos taurus. Most modern breeds of cattle are taurine cattle. - Damion Dooley - https://en.wikipedia.org/wiki/Taurine_cattle - 2019-01-28T02:41:04Z - http://www.langual.org/langual_thesaurus.asp?termid=B5186 - taurine cattle - - - - - - - - - Damion Dooley - 2019-06-28T00:25:22Z - ginger - ginger root - - - - - - - - - - - - - - - - - - - - - - - - - - - The poblano (Capsicum annuum) is a mild chili pepper originating in the state of Puebla, Mexico. Dried, it is called ancho or chile ancho, from the Spanish word ancho ("wide"). - - Emma Griffiths - 2019-08-13T04:55:19Z - ancho - ancho pepper - chile ancho - poblano - ancho pepper - - - - - - - - - - A multicellular eukaryotic heterotrophic organism within the kingdom Animalia. - - - 2019-08-14T18:02:36Z - - animal - - - - - - - - - - - - - - - - - - - - - - - - - - - A bell pepper is a fruits in different colours - including red, yellow, orange, green, white, and purple - from a bell pepper plant cultivar. Bell peppers are sometimes grouped with less pungent pepper varieties as "sweet peppers". - - - 2019-08-22T18:01:49Z - - pepper - bell pepper food product - - - - - - - Kham Tran - www.khamtran.com - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A food product not including meat and animal tissue products (such as gelatin or animal-derived rennet). - - https://en.wikipedia.org/wiki/Vegetarian_cuisine - 2019-09-11T21:12:43Z - vegetarian food - vegetarian food product - - - - - - - - - - A food product made from black, white, pink or similar peppercorns. - - 2019-11-15T23:03:24Z - peppercorn food product - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A ripened red colored berry fruit of a bell pepper plant cultivar. - - https://orcid.org/0000-0001-5275-8866 - 2020-10-14T12:37:01 - bell pepper - capsicum - pepper - sweet pepper - sweet red bell pepper - sweet red bell pepper (whole) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A berry fruit of a pepper plant (Capsicum) - - https://orcid.org/0000-0001-5275-8866 - https://www.britannica.com/plant/pepper-plant-Capsicum-genus - 2020-10-14T02:39:11 - pepper - peppers - pepper (whole) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A berry fruit in the Grossum cultivar group of a bell pepper plant. - - 2020-11-19T01:08:58Z - bell pepper - capsicum - pepper - sweet pepper - bell pepper (whole) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An immature green colored berry fruit of a bell pepper plant cultivar. - - https://orcid.org/0000-0001-5275-8866 - 2020-10-14T07:08:14 - bell pepper - capsicum - pepper - sweet green pepper - sweet pepper - sweet green bell pepper (whole) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A mature yellow colored berry fruit of a bell pepper plant cultivar. - - 2020-11-19T01:24:18Z - bell pepper - capsicum - pepper - sweet pepper - sweet yellow pepper - sweet yellow bell pepper (whole) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A bulb of a garlic plant (Allium sativum) - - https://en.wikipedia.org/wiki/Garlic - 2020-11-30T04:49:32 - garlic - garlic bulb - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A root of a ginger plant (Zingiber officinale) - - https://en.wikipedia.org/wiki/Ginger - 2021-02-11T17:33:19 - elephant ginger - elephant ginger root - ginger - ginger root - ginger root (whole) - - - - - - - - - - An anatomical part of a plant that is consumed by humans or other animals as food. - - https://en.wikipedia.org/wiki/Vegetable - 2021-02-12T18:49:32 - vegetable (whole) - - - - - - - - - - A plan specification for making a food product, which may have ingredient, device, action and objective specifications. - - 2021-11-29T21:52:28Z - food recipe - - - - - - - - - A food product deriving from one or more animals. - - 2022-09-01T16:31:09Z - animal food product - - - - - - - - - - - - - - - - - - - - - - - - - - - - A whole ginger root or some substance made from a processed ginger root. - https://orcid.org/0000-0001-5275-8866 - https://en.wikipedia.org/wiki/Ginger - ginger - ginger root - ginger root (whole or parts) - - - - - - - - - - - - - - - - - - - - - - - - - - - - A whole tomato or some substance made from a processed tomato. - https://orcid.org/0000-0001-5275-8866 - https://en.wikipedia.org/wiki/Tomato - 2022-04-13T12:27:40Z - tomato - tomato (whole or parts) - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F1217 - subset_siren - SIREN DB annotation: -* has quality 'liquid, high viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430139) -* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) -* derives from 'fruit, peel present, core, pit or seed present' (http://purl.obolibrary.org/obo/FOODON_03420140) - - tomato sauce - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A berry fruit of a tomato plant (Solanum lycopersicum). - http://orcid.org/0000-0002-8844-9165 - http://langual.org - SUBSET_SIREN:F1453 - tomato - subset_siren - tomato (whole) - - - - - - - - - - http://langual.org - SUBSET_SIREN:F1704 - onion - subset_siren - SIREN DB annotation: -* has quality 'solid' (http://purl.obolibrary.org/obo/FOODON_03430151) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'root, tuber or bulb, with peel' (http://purl.obolibrary.org/obo/FOODON_03420239) - - onion (whole, raw) - - - - - - - - - - - - - - - - - - - - http://langual.org - 2019-08-26T14:29:56Z - SUBSET_SIREN:F1886 - SUBSET_SIREN:F5599 - raw beef hamburger - subset_siren - SIREN DB annotation: -* has quality 'divided or disintegrated' (http://purl.obolibrary.org/obo/FOODON_03430122) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'skeletal meat part, without bone, without skin' (http://purl.obolibrary.org/obo/FOODON_03420268) - - ground beef (raw) - - - - - - - - - - - - - - - - - - - - - - - - - - - - Fruit which has not been subjected to heat treatment, but which may have other mechanical processes such as slicing applied to it. - http://langual.org - SUBSET_SIREN:F2007 - subset_siren - SIREN DB annotation: -* has quality 'solid' (http://purl.obolibrary.org/obo/FOODON_03430151) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'fruit part' (http://purl.obolibrary.org/obo/FOODON_03420167) - - fruit (raw) - - - - - - - - - - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F2008 - subset_siren - SIREN DB annotation: -* has quality 'solid' (http://purl.obolibrary.org/obo/FOODON_03430151) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'part of plant' (http://purl.obolibrary.org/obo/FOODON_03420174) - - vegetable (raw) - - - - - - - - - - - http://langual.org - milk - SUBSET_SIREN:F2116 - cow milk - subset_siren - SIREN DB annotation: -* has quality 'liquid, low viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430123) -* derives from 'milk (mammary secretion)' (http://purl.obolibrary.org/obo/UBERON_0001913) - - cow milk (liquid) - - - - - - - - - - - - - - - - - - - Note that this allows for several kinds of fruit in one sample, e.g. "some fruit (whole,raw)" allows "apple (whole, raw)" and "orange (whole, raw)". - Damion Dooley - http://langual.org - SUBSET_SIREN:F4644 - fruit - fruits - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'fruit part' (http://purl.obolibrary.org/obo/FOODON_03420167) - - fruit (whole, raw) - - - - - - - - - - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F6429 - subset_siren - SIREN DB annotation: -* has quality 'solid' (http://purl.obolibrary.org/obo/FOODON_03430151) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'skeletal meat part' (http://purl.obolibrary.org/obo/FOODON_03420175) - - meat (raw) - - - - - - - - - - - - - - - - - - - - - - - - - - - - http://langual.org - raw milk - SUBSET_SIREN:F7455 - milk - subset_siren - SIREN DB annotation: -* has quality 'liquid, low viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430123) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'milk (mammary secretion)' (http://purl.obolibrary.org/obo/UBERON_0001913) -* has consumer 'not pasteurized claim or use' (http://purl.obolibrary.org/obo/FOODON_03510121) - - cow milk (raw) - - - - - - - - - - http://langual.org - SUBSET_SIREN:F9840 - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'root, tuber or bulb, with peel' (http://purl.obolibrary.org/obo/FOODON_03420239) - - ginger root (whole, raw) - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F9927 - garden tomato - tomato - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'fruit, peel present, core, pit or seed present' (http://purl.obolibrary.org/obo/FOODON_03420140) - - tomato (whole, raw) - - - - - - - - - - http://langual.org - SUBSET_SIREN:F10351 - subset_siren - SIREN DB annotation: -* has quality 'semisolid with smooth consistency' (http://purl.obolibrary.org/obo/FOODON_03430119) -* has quality 'partially heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440018) -* derives from 'butter' (http://purl.obolibrary.org/obo/FOODON_00001023) -* formed as a result of 'pasteurization by heating' (http://purl.obolibrary.org/obo/FOODON_03470135) - - butter - - - - - - - - - - - A food product that has not been cooked. - http://langual.org - SUBSET_SIREN:F11126 - subset_siren - SIREN DB annotation: -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) - - food (raw) - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F11146 - subset_siren - SIREN DB annotation: -* has quality 'liquid' (http://purl.obolibrary.org/obo/FOODON_03430130) - - sauce - - - - - - - - - - http://langual.org - SUBSET_SIREN:F15150 - subset_siren - SIREN DB annotation: -* derives from 'milk (mammary secretion)' (http://purl.obolibrary.org/obo/UBERON_0001913) - - mammalian milk product - - - - - - - - - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F15295 - subset_siren - SIREN DB annotation: -* has quality 'semiliquid with smooth consistency' (http://purl.obolibrary.org/obo/FOODON_03430135) -* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) -* derives from 'part of plant' (http://purl.obolibrary.org/obo/FOODON_03420174) -* formed as a result of 'alcohol-acetic acid fermentation process' (http://purl.obolibrary.org/obo/FOODON_03460123) -* formed as a result of 'acidified' (http://purl.obolibrary.org/obo/FOODON_03460200) -* has substance added 'sugar or sugar syrup added' (http://purl.obolibrary.org/obo/FOODON_03460136) -* has substance added 'flavoring, spice or herb added' (http://purl.obolibrary.org/obo/FOODON_03460227) - - catsup - - - - - - - - - - - - - - - - - - - - - - - - - - - - A whole vegetable or some substance made from a processed vegetable. - https://orcid.org/0000-0001-5275-8866 - https://en.wikipedia.org/wiki/Vegetable - 2022-04-13T09:20:12Z - vegetable - vegetable (whole or parts) - - - - - - - - - - http://langual.org - SUBSET_SIREN:F15615 - subset_siren - SIREN DB annotation: -* derives from 'fruit part' (http://purl.obolibrary.org/obo/FOODON_03420167) - - fruit food product - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A bulb of an onion plant (Allium cepa). - https://orcid.org/0000-0001-5275-8866 - http://langual.org - 2020-10-21T05:43:41 - SUBSET_SIREN:F16347 - bulb onion - common onion - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* derives from 'root, tuber or bulb, with peel' (http://purl.obolibrary.org/obo/FOODON_03420239) - - onion (whole) - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F16522 - subset_siren - SIREN DB annotation: -* derives from 'part of plant' (http://purl.obolibrary.org/obo/FOODON_03420174) - - tomato multi-component product - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F16579 - subset_siren - SIREN DB annotation: -* derives from 'part of plant' (http://purl.obolibrary.org/obo/FOODON_03420174) - - multi-component plant food product - - - - - - - - - - A meat product is a product organized by the form of - or processing done to - its meat component (a skeletal meat part of an animal or crustacean). - http://langual.org - SUBSET_SIREN:F17170 - subset_siren - SIREN DB annotation: -* derives from 'animal body or body part' (http://purl.obolibrary.org/obo/FOODON_03420127) - - meat (whole or parts) - - - - - - - - - - Seasoned product that contains multiple ingredients and that is used in limited amounts to accompany other foods; excludes flavors, spices and herbs. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0105 - condiment, dressing, gravy or sauce - gravy, condiment, dressing or sauce - sauce, condiment, dressing or gravy - dressing, condiment, gravy or sauce (us cfr) - - - - - - - - - - Aromatic or pungent plant product used whole or ground as a seasoning in food products. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0113 - herb or spice - spice or herb (us cfr) - - - - - - - - - - Product that imparts or helps to impart a taste or aroma in food (21 CFR.170.3(n)(26). [FDA CFSAN 1995] - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0133 - seasoning or flavoring - flavoring or seasoning (us cfr) - - - - - - - - - - A multiple-component food product typically containing a protein source, a vegetable, and a potato, rice or cereal-based component packaged to be served after heating, either as separate items or courses or mixed as recipe components; see 21 CFR 102.26, 102.28 and 104.47 for nutritional quality guidelines. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0139 - compartmentalized dinner - dinner with components separated in serving containers - dinner, compartmentalized - food packs with separate components - heat and serve dinner - multiple-course dinner - tv dinner - multicomponent meal (us cfr) - - - - - - - - - - Fruit in all forms; includes fruit juices and fruit juice drinks, fruit butters, jellies, preserves, and related products. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0143 - pie filling, fruit - fruit or fruit product (us cfr) - - - - - - - - - - Milk in all forms, milk-based beverage, cultured milk product, or milk or milk product analog. Index infant formula under *MEAL REPLACEMENT*. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0148 - milk or milk product (us cfr) - - - - - - - - - - Meat (flesh and organs including blood and bone marrow) from mammals. Used for meat in all forms including cured meat, sausage or luncheon meat and meat product analogs. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0150 - meat or meat product (from mammal) (us cfr) - - - - - - - - - - Vegetables in all forms except where a use-related product type descriptior (such as *PREPARED FOOD PRODUCT* or *SNACK FOOD*) takes precedence. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0152 - vegetable or vegetable product (us cfr) - - - - - - - - - - Milk, a product derived from milk, or a dairy product analog; includes cheese and frozen dairy desserts. [FDA CFSAN 1995] - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0164 - dairy product (us cfr) - - - - - - - - - - Food product that is 1) ready or nearly ready for consumption; 2) usually a composite of several foods or ingredients that often belong to distinct product types; 3) usually formulated, mixed and partially or fully cooked. Prepared foods often undergo several of the processes listed in *F. EXTENT OF HEAT TREATMENT* and *H. TREATMENT APPLIED*; these factors should be carefully considered in indexing. The classification of prepared food products emphasizes consumption characteristics. [FDA CFSAN 1995] - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0172 - prepared dish - prepared food product (us cfr) - - - - - - - - - - Food product that is usually pungent, tart, salty, or spicy and is used to enhance the flavors of other foods; includes catsup, relish, prepared mustard, prepared horseradish, and condiment sauces. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0179 - relish or condiment - condiment or relish (us cfr) - - - - - - - - - - Products of the flesh of animals. [FDA CFSAN 1995] - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0217 - meat, poultry, seafood or related product (us cfr) - - - - - - - - - - Fruits and vegetables in all forms. [FDA CFSAN 1995] - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0257 - fruit or vegetable product (us cfr) - - - - - - - - - - Nonstandardized food product used as a meal accompaniment and consisting of a mixture of fats or oils, starch, liquid and other optional ingredients specified by the recipe; excludes condiment sauce (q.v.) and tomato or spaghetti sauce, which are vegetable products. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0286 - sauce or gravy - gravy or sauce (us cfr) - - - - - - - - - - Food group having common consumption, functional or manufacturing characteristics, e.g. *FRUIT OR VEGETABLE PRODUCT*, *DAIRY PRODUCT*, *CONFECTIONARY*, *PREPARED FOOD PRODUCT*, etc. [FDA CFSAN 1995] - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0289 - LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term. - USA agency food product type - - - - - - - - - - An agency food product type is a class of food product defined by an agency or consortium. - Damion Dooley - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0361 - This class is designed to hold 3rd party food classification schemes which are being mapped to FoodOn classes using the 'has member' relation. The two hierarchies are not melded into a subclass polyhierarchy because of possible logical inconsistencies in the agency schemes. The hierarchies of agency schemes are as true to their agency representation as possible. - agency food product type - - - - - - - - - - Food and Drugs, title 21, Code of Federal Regulations. Original food classification in LanguaL. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A1270 - LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term. - U.S. code of federal regulations, title 21 food product type - https://www.ecfr.gov/cgi-bin/text-idx?SID=87f720ce0d0b6c4548f4bbfd1f8e4c3d&mc=true&tpl=/ecfrbrowse/Title21/21chapterI.tpl - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1006 - fruit plant used as vegetable - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1018 - vegetable-producing plant, root, tuber or bulb - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1057 - vegetable-producing plant, above-ground parts - - - - - - - - - - Mammals (from Latin mamma "breast") are vertebrate animals constituting the class Mammalia, and characterized by the presence of mammary glands which in females produce milk for feeding (nursing) their young, a neocortex (a region of the brain), fur or hair, and three middle ear bones. - Damion Dooley - https://en.wikipedia.org/wiki/Mammal - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1134 - mammal - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1140 - fruit-producing plant - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1179 - flavor-producing plant - herb-producing plant - spice or flavor-producing plant - - - - - - - - - - - - - - - - - - - - - A dairy cow is an adult female member of a dairy cattle breed - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1201 - cow - domesticated cattle - dairy cow - - - - - - - - - - - - The taxonomies given vary widely. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1250 - capsicum - capsicum annuum - green or red pepper plant - - - - - - - - - - - - - - - - - The word "tomato" may refer to the plant (*Solanum lycopersicum*) or the edible, typically red, fruit that it bears. Originating in South America, the tomato was spread around the world following the Spanish colonization of the Americas, and its many varieties are now widely grown, often in greenhouses in cooler climates.See also the list of tomato cultivars - WIKIPEDIA:List_of_tomato_cultivars - http://langual.org - - GRIN:101442 - ITIS:521671 - ITIS:529044 - MANSFELD:6054 - PLANTS:SOLY2 - http://eol.org/pages/392557 - http://www.langual.org/langual_thesaurus.asp?termid=B1276 - Lycopersicon esculentum Mill. - Lycopersicon esculentum var. esculentum P. Mill. - Solanum lycopersicum L. - gold apple - love apple - lycopersicon esculentum - lycopersicon lycopersicum - solanum lycopersicum - tomato plant - - - - - - - - - - A vertebrate animal is any species of organism within the subphylum Vertebrata (chordates with backbones). Vertebrates represent the overwhelming majority of the phylum Chordata, with currently about 69,276 species described. - Damion Dooley - - http://langual.org - animal - http://www.langual.org/langual_thesaurus.asp?termid=B1297 - LanguaL curation note: For a unicellular animal, use *ALGAE OR FUNGUS USED AS FOOD SOURCE*. - vertebrate animal - - - - - - - - - - - - The onion (*Allium cepa *L), also known as the bulb onion or common onion, is a vegetable that is the most widely cultivated species of the genus *Allium*. Its close relatives include the garlic, shallot, leek, chive,[2] and Chinese onion. - This genus also contains several other species variously referred to as onions and cultivated for food, such as the Japanese bunching onion (*Allium fistulosum*), the tree onion (*A. ×proliferum*), and the Canada onion (*Allium canadense*). The name "wild onion" is applied to a number of *Allium* species, but *A. cepa* is exclusively known from cultivation. [https://en.wikipedia.org/wiki/Onion] - http://langual.org - GRIN:300022 - PLANTS:ALLIU - http://eol.org/pages/8187 - http://www.langual.org/langual_thesaurus.asp?termid=B1300 - Allium - Allium L. - Allium sp. - allium spp. - bulb onion - cebolla - garden onion - onion plant - - - - - - - - - - This is a hierarchy of organisms, grouped minimally in a combination of taxonomy and consumer-oriented food groups. - http://langual.org - - http://www.langual.org/langual_thesaurus.asp?termid=B1564 - This was LanguaL definition: Individual plant or animal from which the food product or its major ingredient is derived; also a chemical food source [FDA CFSAN 1995]. - food product organismal source - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1579 - vegetable-producing plant - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1643 - capsicum annuum, longum group - capsicum chile pepper - cayenne pepper - chile pepper - chili pepper - long pepper - red pepper (chile pepper) - hot pepper plant - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B2559 - pepper, poblano - poblano pepper plant - - - - - - - - - - - - - - - - - - - - - - - - - The bell pepper (also known as sweet pepper or pepper in the United Kingdom, Canada and Ireland, and capsicum in Australia, India, Pakistan, Bangladesh, Singapore and New Zealand) is a cultivar group of the species *Capsicum annuum*. Bell peppers are sometimes grouped with less pungent pepper varieties as "sweet peppers". [https://en.wikipedia.org/wiki/Bell_pepper] - http://langual.org - - GRIN:311784 - GRIN:8904 - ITIS:30492 - MANSFELD:6120 - PLANTS:CAAN4 - http://eol.org/pages/581098 - http://www.langual.org/langual_thesaurus.asp?termid=B2628 - sweet pepper plant - Capsicum annuum L. - Capsicum anuum L. - capsicum frutescens var. grossum - bell pepper plant - - - - - - - - - - Unripe fruit of red or yellow bell pepper varieties. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B2629 - green pepper plant - green bell pepper plant - - - - - - - - - - Ripe fruit of red bell pepper varieties. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B2630 - red bell sweet pepper plant - red sweet pepper plant - LanguaL curation note: Do not confuse with *RED PEPPER*. - red bell pepper plant - - - - - - - - - - Ripe fruit of yellow bell pepper varieties. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B2631 - yellow bell pepper plant - - - - - - - - - - Grouped together because of similar use. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B2633 - paprika, hot - red pepper (pungent pepper variety) - pungent pepper variety plant - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B3357 - LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term. - plant according to family - - - - - - - - - - *Allium* is a genus of monocotyledonous flowering plants that includes hundreds of species, including the cultivated onion, garlic, scallion, shallot, leek, and chives. [https://en.wikipedia.org/wiki/Allium] - http://langual.org - http://eol.org/pages/8187 - http://www.langual.org/langual_thesaurus.asp?termid=B4302 - allium - onion - wild onion - allium species - - - - - - - - - - The biological subfamily *Bovinae* includes a diverse group of 10 genera of medium- to large-sized ungulates, including domestic cattle, the bison, African buffalo, the water buffalo, the yak, and the four-horned and spiral-horned antelopes. The evolutionary relationship between the members of the group is obscure, and their classification into loose tribes rather than formal subgroups reflects this uncertainty. General characteristics include cloven hoofs and usually at least one of the sexes of a species having true horns. - WIKIPEDIA:Bovinae - http://langual.org - http://eol.org/pages/2851454 - http://www.langual.org/langual_thesaurus.asp?termid=B4374 - bovinae - bovine - - - - - - - - - - A bovid (family *Bovidae*) is any of almost 140 species of cloven-hoofed, ruminant mammal which has males with characteristic unbranching horns covered in a permanent sheath of keratin. - -The family is widespread, being native to Asia, Africa, Europe and North America, and diverse: members include bison, African buffalo, water buffalo, antelopes, gazelles, sheep, goats, muskoxen, and domestic cattle. - WIKIPEDIA:Bovidae - http://langual.org - http://eol.org/pages/7687 - http://www.langual.org/langual_thesaurus.asp?termid=B4381 - bovidae - bovid - - - - - - - - - - The *Solanaceae*, or nightshades, are an economically important family of flowering plants. Many members of the family contain potent alkaloids, and some are highly toxic, but many, including tomatoes, potatoes, eggplant, bell/chili peppers, and tobacco are widely used. The *Solanaceae* consists of about 98 genera and some 2,700 species, with a great diversity of habitats, morphology and ecology. [https://en.wikipedia.org/wiki/Solanaceae] - http://langual.org - http://eol.org/pages/4437 - http://www.langual.org/langual_thesaurus.asp?termid=B4934 - nightshade family - solanaceae plant - - - - - - - - - - *Solanum* is a large and diverse genus of flowering plants, which include two food crops of high economic importance, the potato and the tomato. It also contains the nightshades and horse nettles, as well as numerous plants cultivated for their ornamental flowers and fruit. - *Solanum* species show a wide range of growing habits, such as annual and perennials, vines, subshrubs, shrubs, and small trees. Many formerly independent genera like *Lycopersicon* (the tomatoes) and *Cyphomandra* are now included in *Solanum* as subgenera or sections. Thus, the genus today contains roughly 1,500-2,000 species. - - http://langual.org - GRIN:300568 - PLANTS:SOLAN - http://eol.org/pages/4437 - http://www.langual.org/langual_thesaurus.asp?termid=B5104 - Solanum - Solanum L. - Solanum spp. - solanum plant - - - - - - - - - - Anatomical part of the plant or animal from which a food product or its major ingredient is derived. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0116 - LanguaL curation note: "e.g. *LEAF*, *ROOT OR TUBER*, *ORGAN MEAT*, *MILK* OR *EGG*; it also includes components of parts, such as *CREAM*, and extracts, concentrates or isolates, such as *PROTEIN EXTRACT* or *SUGAR*." - part of organism - - - - - - - - - - Bone, feathers, shell, skin or trim fat. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0122 - LanguaL curation note: *BLOOD* AND *INK, AQUATIC ANIMAL* are now listed under organism substance. - nonmeat part of animal - - - - - - - - - - Includes carcass meat, organ meat, and nonmeat parts of animals, as well as the whole animal. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0127 - LanguaL curation note: Includes carcass meat, organ meat, and nonmeat parts of animals, as well as the whole animal. - animal body or body part - - - - - - - - - - The parts of a plant that are not fruit or seed. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0148 - flower, root, stem or leaf - leaf, flower, root or stem - stem, leaf, flower or root - root, stem, leaf or flower - - - - - - - - - - Anatomical part of an animal; includes eggs and milk that, although separated from the animal, are produced as integral parts and are affected by the animal's food intake and metabolism. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0164 - part of animal - - - - - - - - - - - - - - - - - - - - - - The fleshy fruit of any plant. *FRUIT* includes vegetables berries and pods as well. The bulk of a fruit is its fleshy part, which is covered by a peel (skin) and which encloses a core, pit or seeds. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0167 - berry - berry or fruit (anatomical part) - fruit or berry, peel undetermined - hip (fruit) - infructescence - LanguaL curation note: The descriptors under *FRUIT* are arrayed so that the indexer can check first whether the peel is present, removed or undetermined; then check the same informationfor the core, pit or seeds. For juices, beverages or jellies made from fruit, Index the entire part from which the product is derived. - -Renamed from *FRUIT OR BERRY* in LanguaL 2008. - fruit part - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0238 - bulb, root or tuber - tuber, bulb or root - root, tuber or bulb - - - - - - - - - - - - - - - - - - - - - - - - - - - A state of matter between a solid and a gas, in which a substance has the capacity to flow and conforms to the shape of the container. Liquids range from water to honey, corresponding to a range in viscosity (or apparent viscosity) from 1 to 500 centipoise (viscosity is a measure of a liquid's resistance to flow). Products that are pourable but have a higher viscosity are *SEMILIQUID*. - http://langual.org - SUBSET_SIREN:F5105 - http://www.langual.org/langual_thesaurus.asp?termid=E0130 - fluid - SIREN DB annotation: -* has quality 'liquid' (http://purl.obolibrary.org/obo/FOODON_03430130) - - food (liquid) - - - - - - - - - data item - - An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. - - data item - - - - - - - - - information content entity - - A generically dependent continuant that is about some thing. - PERSON: Chris Stoeckert - OBI_0000142 - - information content entity - - - - - - - - - directive information entity - - An information content entity whose concretizations indicate to their bearer how to realize them in a process. - PERSON: Alan Ruttenberg - PERSON: Bjoern Peters - - directive information entity - - - - - - - - - curation status specification - - The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - OBI_0000266 - - curation status specification - - - - - - - - - data about an ontology part - Data about an ontology part is a data item about a part of an ontology, for example a term - - data about an ontology part - - - - - - - - - plan specification - - A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. - OBI Plan and Planned Process branch - OBI_0000344 - - - plan specification - - - - - - - - - - bony vertebrates - Euteleostomi - - - - - - - - - - Dipnotetrapodomorpha - - - - - - - - - - Boreoeutheria - - - - - - - - - - Mesangiospermae - - - - - - - - - - Petrosaviidae - - - - - - - - - - Pentapetalae - - - - - - - - - - eucaryotes - eukaryotes - Eukaryota - - - - - - - - - - Bovinae - - - - - - - - - - Laurasiatheria - - - - - - - - - - tetrapods - Tetrapoda - - - - - - - - - - amniotes - Amniota - - - - - - - - - - Theria - Theria <mammals> - - - - - - - - - - Chlorophyta/Embryophyta group - chlorophyte/embryophyte group - green plants - Viridiplantae - - - - - - - - - - Opisthokonta - - - - - - - - - - Bilateria - - - - - - - - - - deuterostomes - Deuterostomia - - - - - - - - - - angiosperms - flowering plants - Magnoliopsida - - - - - - - - - - Pecora - - - - - - - - - - mammals - Mammalia - - - - - - - - - - Solanales - - - - - - - - - - nightshade family - Solanaceae - - - - - - - - - - peppers - Capsicum - - - - - - - - - - - ancho pepper plant - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B2550 - C annuum - Capsicum annuum - - - - - - - - - - - WIKIPEDIA:Tomato - - http://langual.org - GRIN:101442 - ITIS:521671 - ITIS:529044 - MANSFELD:6054 - http://eol.org/pages/392557 - tomato - Lycopersicon esculentum Mill. - Lycopersicon esculentum var. esculentum P. Mill. - Solanum lycopersicum L. - lycopersicon esculentum - Solanum lycopersicum - - - - - - - - - - Solanum - - - - - - - - - - Solanoideae - - - - - - - - - - monocots - monocotyledons - Liliopsida - - - - - - - - - - Zingiberales - - - - - - - - - - ginger family - Zingiberaceae - - - - - - - - - - Zingiber - - - - - - - - - - amaryllis family - Amaryllidaceae - - - - - - - - - - Allium - - - - - - - - - - - - http://langual.org - GRIN:2244 - ITIS:42720 - PLANTS:ALCE - http://eol.org/pages/8187 - onion - Allium cepa L. - pickling onion - allium cepa - Allium cepa - - - - - - - - - - - - - Garlic (*Allium sativum*) is a species in the onion genus, *Allium*.Its close relatives include the onion, shallot, leek, chive, and Chinese onion. Garlic is native to Central Asia and northeastern Iran, and has long been a common seasoning worldwide, with a history of several thousand years of human consumption and use. [https://en.wikipedia.org/wiki/Garlic] - garlic plant - - http://langual.org - GRIN:2368 - GRIN:315611 - ITIS:42652 - MANSFELD:212 - PLANTS:ALSA2 - http://eol.org/pages/1084926 - http://www.langual.org/langual_thesaurus.asp?termid=B1233 - garlic - Allium sativum L. - allium sativum - Allium sativum - - - - - - - - - - commelinids - - - - - - - - - - vascular plants - Tracheophyta - - - - - - - - - - seed plants - Spermatophyta - - - - - - - - - - Eumetazoa - - - - - - - - - - Asteridae - asterids - - - - - - - - - - Asparagales - - - - - - - - - - chordates - Chordata - - - - - - - - - - Vertebrata - vertebrates - Vertebrata <vertebrates> - - - - - - - - - - Gnathostomata - jawed vertebrates - Gnathostomata <vertebrates> - - - - - - - - - - euphyllophytes - Euphyllophyta - - - - - - - - - - whales, hippos, ruminants, pigs, camels etc. - Artiodactyla - - - - - - - - - - lamiids - - - - - - - - - - eutherian mammals - placental mammals - placentals - Eutheria - - - - - - - - - - ginger - Zingiber officinale - - - - - - - - - - Bovidae - - - - - - - - - - oxen, cattle - Bos - - - - - - - - - - Cattle (colloquially cows) are the most common type of large domesticated ungulates. They are a prominent modern member of the subfamily *Bovinae*, are the most widespread species of the genus *Bos*, and are most commonly classified collectively as *Bos taurus*... with three subspecies: *Bos taurus primigenius, Bos taurus indicus, Bos taurus taurus*. - cattle - - - - - ITIS:183838 - MSW3:14200687 - Bos taurus Linnaeus, 1758 - bovine - cattle - cow - dairy cow - domestic cattle - domestic cow - ox - oxen - Bos taurus - - - - - - - - - - organism - - A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. - WEB: http://en.wikipedia.org/wiki/Organism - - organism - - - - - - - - - A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities - - quality - - - - - - - - - A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. - - physical quality - - - - - - - - - A quality which inheres in a continuant. - - physical object quality - - - - - - - - - A physical quality inhering in an entity exhibiting the physical characteristics of an amorphous (non-crystalline) form of matter between a gas and a solid that has a definite volume, but no definite shape. - - quality of a liquid - - - - - - - - - A quality inhering in a bearer by virtue of its constitution. - - quality of a substance - - - - - - - - - - A plant structure (PO:0005679) which is a whole organism. - - genet (broad) - ramet (broad) - - PO_GIT:538 - PO_GIT:69 - planta entera (Spanish, exact) - 植物体全体 (Japanese, exact) - bush (narrow) - frutex (narrow) - frutices (narrow) - gametophyte (narrow) - herb (narrow) - liana (narrow) - prothalli (narrow) - prothallium (narrow) - prothallus (narrow) - seedling (narrow) - shrub (narrow) - sporophyte (narrow) - suffrutex (narrow) - suffrutices (narrow) - tree (narrow) - vine (narrow) - woody clump (narrow) - plant_anatomy - clonal colony (related) - colony (related) - PO:0000003 - - - Examples include plant embryo (PO:0009009), megagametophyte (PO:0025279) and microgametophyte (PO:0025280). - whole plant - - - - - - - - - A floral structure primordium (PO:0025477) that is committed to the development of a gynoecium (PO:0009062). - - PO_GIT:465 - pistil primordium (exact) - portion of gynoecium primordium tissue (exact) - primordio de gineceo (Spanish, exact) - 雌蕊原基(可視的） (Japanese, exact) - plant_anatomy - PO:0000019 - Use carpel primordium (PO:0004703) for the primordium (PO:0025127) of an individual carpel (PO:0009030). - gynoecium primordium - - - - - - - - - A shoot axis (PO:0025029) that is the most distal part of a shoot system (PO:0009006) and has as parts a shoot apical meristem (PO:0020148) and the youngest primordia (PO:0025127). - - PO_GIT:234 - &#225pice del epiblasto (epiblastema) (Spanish, exact) - シュート頂、茎頂 (Japanese, exact) - plant_anatomy - PO:0000037 - - shoot axis apex - - - - - - - - - A portion of reproductive shoot apical meristem tissue (PO:0008028) that gives rise to the floral organs (PO:0025395). - - PO:0006329 - PO:0006373 - PO:0006374 - PO:0025091 - floral meristem (exact) - mersitema floral (Spanish, exact) - 花芽分裂組織 (Japanese, exact) - Poaceae floret meristem (narrow) - ear floret meristem (narrow) - floret meristem (narrow) - tassel floret meristem (narrow) - plant_anatomy - floral apical meristem (related) - PO:0000229 - In Zea mays and other grasses, the floret meristem is part of a spikelet and develops into a specific type of floret. If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the spikelet type that the meristem is part of. Choose the most specific term possible from: spikelet (PO:0009051), ear spikelet (PO:0006320), ear pedicellate spikelet (PO:0006348), ear sessile spikelet (PO:0006349), tassel spikelet (PO:0006309), tassel pedicellate spikelet (PO:0006312), tassel sessile spikelet (PO:0006311). - flower meristem - - - - - - - - - A native plant cell (PO:0025606) synthesizing protoplasm and producing new cells by division and with only a primary cell wall. - - CL:0000034 - PO_GIT:272 - c&#233lula meristem&#225tica (Spanish, exact) - stem cell (exact) - 分裂組織細胞 (Japanese, exact) - plant_anatomy - PO:0004010 - - meristematic cell - - - - - - - - - - - - - - - A primordium (PO:0025127) that develops from a root anlagen (PO:0025433) and is committed to the development of a root (PO:0009005). - - PO_GIT:467 - portion of root primordium tissue (exact) - primordio de ra&#237z (Spanish, exact) - root primordia (exact, plural) - 根原基（可視的） (Japanese, exact) - plant_anatomy - PO:0005029 - A root primordium may arise from cells of a pericycle (PO:0006203) in a root in most seed plant (pericyclic lateral root primordium; PO:0025492), from cells of an endodermis (PO:0000252) in ferns and some seed plants (non-pericyclic lateral root primordium: PO:0025493), or from cells of a shoot axis (PO:0025029), in the case of a basal root primordium (PO:0025479) or shoot-borne root primordium (PO:0025480). Transition from root primordium to root occurs with the formation of a root cap (PO:0020123), shortly after the development of a root apical meristem (PO:0020147). - root primordium - - - - - - - - - - - - - - - A portion of meristem tissue (PO:0009013) that is part of a shoot system (PO:0009006). - - PO_GIT:472 - PO_GIT:583 - meristema del epiblasto (epiblastema) (Spanish, exact) - シュート分裂組織 (Japanese, exact) - plant_anatomy - PO:0006079 - - shoot system meristem - - - - - - - - - A portion of meristem tissue (PO:0009013) that is the outer layer of an apical meristem (PO:0020144), or the outer layer of a plant embryo proper (PO:0000001), and gives rise to a portion of epidermis (PO:0005679). - - PO_GIT:125 - portion of protoderm tissue (exact) - protodermis (Spanish, exact) - 前表皮、原表皮 (Japanese, exact) - plant_anatomy - dermatogen cell (related) - PO:0006210 - A protoderm may or may not arise from independent initial cells (PO:0004011). Some researchers also refer to it as an epidermis in a meristematic state. - protoderm - - - - - - - - - - - - - - - A plant structure development stage (PO:0009012) that has as primary participant a whole plant (PO:0000003). - - PO_GIT:390 - plant_structure_development_stage - Solanaceae whole plant growth stages (SGN:0000001) (related) - cereal plant growth stage ontology (GRO:0007199) (related) - maize growth stage (GRO:0007002) (related) - plant growth stages in Arabidopsis (TAIR:0000021) (related) - rice growth stage (GRO:0007040) (related) - sorghum growth stage (GRO:0007124) (related) - wheat, barley and oat growth stage (GRO:0007156) (related) - PO:0007033 - - whole plant development stage - - - - - - - - - - - - - - - A shoot apical meristem (PO:0020148) that gives rise to the apical growth of reproductive tissues and organs. - - PO_GIT:36 - meristema apical reproductivo del epiblasto (epiblastema) (Spanish, exact) - 生殖シュート頂端 分裂組織 (Japanese, exact) - plant_anatomy - PO:0008028 - reproductive shoot apical meristem - - - - - - - - - - - - - - - A multi-tissue plant structure (PO:0025496) that develops from a gynoecium (PO:0009062), or a single carpel (PO:0009030), and at maturity may have as parts one or more seeds (PO:0009010). - - PO:0020067 - PO:0020068 - PO:0020069 - PO:0020070 - PO:0020071 - PO:0020072 - PO:0020073 - PO:0020074 - PO:0020076 - PO:0020077 - PO:0020078 - PO:0020079 - PO:0020080 - PO:0020082 - PO:0020083 - PO:0020087 - PO:0020107 - aggregate fruit (broad) - compound fruit (broad) - dehiscent fruit (broad) - diaspore (broad) - indehiscent fruit (broad) - multiple fruit (broad) - propagule (broad) - PO_GIT:76 - frucht (exact, German) - fruto (exact, Spanish) - 果実 (exact, Japanese) - coenocarp (narrow) - syncarp (narrow) - plant_anatomy - PO:0009001 - - - - - - - A fruit (PO:0009001) may contain additional plant structures (PO:0009011) that were part of a flower (PO:0009046) and mature along with the gynoecium, such as a receptacle (PO:0009064). A fruit may develop without fertilization in cases of parthenocarpy, apomixis, or other hormone-induced conditions and may not always contain seeds (PO:0009010). When annotating to fruit (PO:0009001) that are referred to as ‘aggregate’, ‘multiple’, or ‘compound’, please annotate directly to the appropriate plant structure, such as receptacle, hypanthium (PO:0009065) or infructescence (PO:0006342). Fruits only occur in angiosperms. - fruit - https://en.wikipedia.org/wiki/Fruit_anatomy - - - - - - - - - A cell which is a plant structure (PO:0009011). - - cell (broad) - GO:0005623 - PO_GIT:56 - c&#233lula vegetal (Spanish, exact) - 植物細胞 (Japanese, exact) - plant_anatomy - PO:0009002 - - - - Applies to cells that are living or dead at maturity (e.g., fiber cell or tracheid) and includes any external encapsulating structures (if present) such as the plasma membrane and the plant-type cell wall. Definition of cell GO:0005623: "The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope". GO:0009505. Definition of plant-type cell wall (GO:0009505): A more or less rigid structure lying outside the cell membrane of a cell and composed of cellulose and pectin and other organic and inorganic substances, synonym; exact: cellulose and pectin-containing cell wall. - plant cell - - - - - - - - - - - - - - - - - - - - - A plant axis (PO:0025004) that lacks shoot axis nodes (PO:0005004) and usually grows indeterminately. - - PO:0003006 - PO_GIT:578 - ra&#237z (Spanish, exact) - radices (exact, plural) - radix (exact) - 根 (Japanese, exact) - aerial root (narrow) - climbing root (narrow) - plant_anatomy - PO:0009005 - - - - - - - - - - Roots function in the absorption of water and inorganic nutrients, anchoring the plant body to the substrate and supporting it, storage of food and nutrients, and vegetative reproduction. The roots of most vascular plant species enter into symbiosis with soil-borne microorganisms. Roots are usually positively geotropic and found underground, although there are many exceptions such as the aerial roots of orchids. Roots often form secondary thickening from the root lateral meristem (PO:0006308). Commonly thought of as one of the three basic parts of the plant body, along with the shoot axis (PO:0025029) and leaves (PO:0025034). - root - - - - - - - - - A collective plant organ structure (PO:0025007) that produces shoot-borne portions of meristem tissue (PO:0009013) and the plant structures (PO:0009011) that arise from them. - - PO_GIT:135 - sistema de epiblasto (epiblastema) (Spanish, exact) - シュート系、苗条系 (Japanese, exact) - tree crown (narrow) - plant_anatomy - Poaceae crown (related) - shoot (related) - thalli (related) - thallus (related) - PO:0009006 - - - The shoot system is generally used to refer to the above-ground plant parts, although some plants have parts of their shoot system underground. For example, a rhizome (PO:0004542), bulb (PO:0025356), a corm (PO:0025355) or a subterranean tuber (PO:0004547), as in Solanum tuberosum (potato) or yam, are all part of the shoot system. - shoot system - - - - - - - - - A plant structure (PO:0009011) that consists predominantly of similarly specialized plant cells (PO:0009002) of one or more types. - - portion of tissue (broad) - tissue (broad) - PO_GIT:59 - porci&#243n de un tejido vegetal (Spanish, exact) - 植物組織の一部 (Japanese, exact) - plant_anatomy - plant tissue (related) - PO:0009007 - - - A portion of plant tissue may contain one or several types of cells that are organized in a specific spatial arrangement into a structural unit (which includes a mass of callus) and may include an intercellular matrix. May include other types of isolated cells, such as idioblasts. - portion of plant tissue - - - - - - - - - A multi-tissue plant structure (PO:0025496) that is a functional unit, is a proper part of a whole plant (PO:0000003), and includes portions of plant tissue (PO:0009007) of at least two different types that derive from a common developmental path. - - organ (broad) - PO_GIT:55 - &#243rgano vegetal (Spanish, exact) - 植物 器官 (Japanese, exact) - plant_anatomy - compound plant organ (related) - simple plant organ (related) - PO:0009008 - - Examples include stem (PO:0009047), leaf (PO:0025034), and root (PO:0009005). May include individual plant cells (PO:0009002) that are not part of a portion of plant tissue (e.g., idioblasts, PO:0000283). A plant organ may have one or more different plant organs as parts, such as a sporophyll (PO:0009026) that may have as part a sporangium (PO:0025094) or a carpel (PO:0009030) that may have as part a plant ovule (PO:0020003). - plant organ - - - - - - - - - - A plant anatomical entity (PO:0025131) that is, or was, part of a plant, or was derived from a part of a plant. - - - PO_GIT:57 - estructura vegetal (Spanish, exact) - 植物 構造 (Japanese, exact) - plant_anatomy - PO:0009011 - - 'Part' includes both proper parts and the whole plant. CARO:0000003 'connected anatomical structure' is defined as: Material anatomical entity that is a single connected structure with inherent 3D shape, generated by coordinated expression of the organism's own genome. - plant structure - - - - - - - - - A stage in the life of a plant structure (PO:0009011) during which the plant structure undergoes developmental processes. - - PO:0007021 - PO_GIT:185 - etapa de desarrollo de estructura vegetal (Spanish, exact) - plant growth and development stage (exact) - plant_structure_development_stage - Arabidopsis growth (related) - PO:0009012 - - Refers to GO:0032502 'developmental process', which includes growth, differentiation, and senescence, and BFO:0000003 'ocurrent'. - plant structure development stage - - - - - - - - - - - - - - - A portion of plant tissue (PO:0009007) in which plant cells (PO:0009002) have retained their embryonic characteristics, or have reverted to them secondarily, and that divide to produce new cells that can undergo differentiation to form mature tissues, i.e. they have a capacity for morphogenesis and growth. - - PO_GIT:472 - meristem (exact) - meristema (Spanish, exact) - meristematic tissue (exact) - 分裂組織 (Japanese, exact) - plant_anatomy - PO:0009013 - - portion of meristem tissue - - - - - - - - - - - - - - - A determinate reproductive shoot system (PO:0025082) that has as part at least one carpel (PO:0009030) or at least one stamen (PO:0009029) and does not contain any other determinate shoot system (PO:0009006) as a part. - - PO:0004541 - PO_GIT:160 - PO_GIT:259 - flor (Spanish, exact) - 花 (Japanese, exact) - Asteraceae floret (narrow) - basal flower (narrow) - double flower (narrow) - hermaphrodite flower (narrow) - monoclinous flower (narrow) - perfect flower (narrow) - plant_anatomy - floret (related) - PO:0009046 - - - - The characteristic reproductive structure of angiosperms. May have as part one or more petals, sepals or tepals. May contain one or more pistillode (PO:0009078), staminode (PO:0009077) or other aborted organs that don't show up in mature form. - flower - - - - - - - - - - - - - - - - - - - - - A collective phyllome structure (PO:0025023) composed all of the carpels (PO:0009030) in a flower (PO:0009046). - - PO:0006317 - PO:0006357 - PO:0006365 - PO:0006384 - PO:0006391 - PO:0006394 - PO:0006403 - PO:0006404 - PO:0006423 - PO:0006424 - PO:0006425 - PO:0006426 - PO:0025089 - pistil (broad) - PO_GIT:470 - PO_GIT:71 - PO_GIT:98 - ginoecio (Spanish, exact) - gynaecium (exact) - gynoecia (exact, plural) - 雌蕊群 (Japanese, exact) - Poaceae gynoecium (narrow) - Zea gynoecium (narrow) - apocarpous gynoecium (narrow) - gynoecium of ear floret (narrow) - gynoecium of lower floret of pedicellate spikelet of ear (narrow) - gynoecium of lower floret of pedicellate spikelet of tassel (narrow) - gynoecium of lower floret of sessile spikelet of ear (narrow) - gynoecium of lower floret of sessile spikelet of tassel (narrow) - gynoecium of tassel floret (narrow) - gynoecium of upper floret of pedicellate spikelet of ear (narrow) - gynoecium of upper floret of pedicellate spikelet of tassel (narrow) - gynoecium of upper floret of sessile spikelet of ear (narrow) - gynoecium of upper floret of sessile spikelet of tassel (narrow) - syncarpous gynoecium (narrow) - plant_anatomy - PO:0009062 - - - If annotating gene expression to a gynoecium with a single carpel (PO:0009030), the annotation should go on carpel. A gynoecium with two or more carpels may be either syncarpous (carpels fused) or apopcarpous (carpels free) or the carpels may be partially fused. The word pistil is used synonymously with gynoecium for a synocarpous gynoecium, and synonymously with carpel for an apocarpous gynoecium, whether it has one or more carpels. In Zea mays, gynoecia of tassel florets and of the lower florets of ear spikelets usually do not develop fully, and they are present in a rudimentary state. If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the corresponding floret type. Choose the most specific term possible from: spikelet floret (PO:0009082), ear floret (PO:0006354), lower floret of pedicellate spikelet of ear (PO:0006353), lower floret of sessile spikelet of ear (PO:0006351), upper floret of pedicellate spikelet of ear (PO:0006350), upper floret of sessile spikelet of ear (PO:0006352), tassel floret (PO:0006310), lower floret of pedicellate spikelet of tassel (PO:0006313), lower floret of sessile spikelet of tassel (PO:0006315), upper floret of pedicellate spikelet of tassel (PO:0006314), upper floret of sessile spikelet of tassel (PO:0006316). - gynoecium - - - - - - - - - - - - - - - A maximal portion of meristem tissue (PO:0009013) located at a shoot apex (PO:0000037) or root tip (PO:0000025). - - promeristem (broad) - PO_GIT:579 - AM (exact) - meristema apical (Spanish, exact) - 頂端分裂組織 (Japanese, exact) - plant_anatomy - primary meristem (related) - PO:0020144 - - apical meristem - - - - - - - - - - - - - - - - A shoot system meristem (PO:0006079) formed at the apex of the shoot axis (PO:0025029), including those originating from an axillary bud meristem (PO:0000232). - - promeristem (broad) - PO_GIT:472 - SAM (exact) - meristema apical del epiblasto (epiblastema) (Spanish, exact) - 茎頂分裂組織 (Japanese, exact) - plant_anatomy - primary shoot meristem (related) - PO:0020148 - - shoot apical meristem - - - - - - - - - An axial plant organ (PO:0009008). - - rwalls - 2010-07-01T03:44:41Z - eje de la planta (Spanish, exact) - plant axes (exact, plural) - 植物軸（軸柱） (Japanese, exact) - plant_anatomy - PO:0025004 - - Includes roots and shoots. - plant axis - - - - - - - - - - - - - - - A collective plant structure (PO:0025497) that is a proper part of a whole plant (PO:0000003), and is composed of two or more adjacent plant organs (PO:0009008) and the associated portions of plant tissue (PO:0009007). - - rwalls - 2010-02-09T04:12:11Z - PO_GIT:63 - estructura vegetal colectiva de &#243rgano (Spanish, exact) - 集合植物器官構造 (Japanese, exact) - plant_anatomy - PO:0025007 - - Organs can be of the same type or different types. Examples include flower (PO:0009046), perianth (PO:0009058), and inflorescence (PO:0009049). See also collective organ part structure (PO:0025269), for plant structures composed of parts of multiple organs, but no complete plant organs. This was formerly named collective plant structure. - collective plant organ structure - - - - - - - - - A collective plant organ structure (PO:0025007) that consists of two or more phyllomes (PO:0006001) originating from the same node or from one or more adjacent nodes with compressed shoot internodes (PO:0005005). - - Laurel_Cooper - 2010-04-28T11:04:34Z - PO:0008033 - cycle (broad) - verticil (broad) - PO_GIT:90 - PO_GIT:99 - estructura colectiva del filoma (Spanish, exact) - 葉的器官が集まった構造 (Japanese, exact) - floral whorl (narrow) - whorl (narrow) - plant_anatomy - phyllome whorl (related) - PO:0025023 - - collective phyllome structure - - - - - - - - - - - - - - - A collective plant organ structure (PO:0025007) that produces root meristems (PO:0006085), the plant structures (PO:0009011) that arise from them and the parts thereof. - - rwalls - 2010-07-01T02:11:26Z - root (broad) - PO_GIT:136 - sistema de ra&#237z (Spanish, exact) - 根系 (Japanese, exact) - plant_anatomy - PO:0025025 - - Generally the below ground portion of a vascular plant. - root system - - - - - - - - - - - - - - - A plant axis (PO:0025004) that is part of a shoot system (PO:0009006). - - rwalls - 2010-07-01T03:46:35Z - caullome (exact) - eje del epiblasto (epiblastema) (Spanish, exact) - シュート軸 (Japanese, exact) - plant_anatomy - shoot (related) - PO:0025029 - - - - - - - Often bears leaves and branches. In vascular plants, has at least one node and one internode. - shoot axis - - - - - - - - - - - - - - - A shoot system (PO:0009006) in the sporophytic phase that has as part at least one sporangium (PO:0025094). - - rwalls - 2010-09-17T09:49:10Z - sistema de brote reproductivo (Spanish, exact) - 生殖シュート 系、苗条系 (Japanese, exact) - plant_anatomy - PO:0025082 - - reproductive shoot system - - - - - - - - - A portion of meristem tissue (PO:0009013) that has as parts protoderm (PO:0006210) and sub-epidermal meristematic tissue and is committed to the development of a particular plant structure (PO:0009011). - - rwalls - 2010-11-15T09:10:22Z - PO_GIT:186 - portion of primordial tissue (exact) - portion of primordium tissue (exact) - primordia (exact, plural) - primordio (Spanish, exact) - 原基（可視的） (Japanese, exact) - plant_anatomy - PO:0025127 - A primordium appears as a protrusion and is the first distinct form of a plant organ (PO:0009008), cardinal organ part (PO:0025001), or collective plant organ structure (PO:0025007). The transition from a primordium to the plant structure it develops into is marked by the development of non-meristematic cells, although meristematic cells may be present after the transition. - primordium - - - - - - - - - An anatomical entity that is or was part of a plant. - - rwalls - 2010-11-15T11:41:38Z - PO_GIT:224 - entidad anat&#243mica vegetal (Spanish, exact) - 植物 解剖学（形態）的実体 (Japanese, exact) - plant_anatomy - PO:0025131 - Includes both material entities such as plant structures and immaterial entities such as plant anatomical spaces. CARO:0000000 'anatomical entity' is defined as: A part of a cellular organism that is either an immaterial entity or a material entity with granularity aboove the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. Refers to BFO:0000004 'independent continuant'. - plant anatomical entity - - - - - - - - - A shoot apex that has as part a reproductive shoot apical meristem. - - rwalls - 2010-12-20T08:47:03Z - &#225pice reproductivo del epiblasto (epiblastema) (Spanish, exact) - 生殖シュート頂、茎頂 (Japanese, exact) - plant_anatomy - PO:0025222 - reproductive shoot apex - - - - - - - - - A maximal whole plant development stage. - - rwalls - 2011-10-19T10:54:37Z - PO_GIT:230 - vida de la planta entera (Spanish, exact) - 植物体の一生 (Japanese, exact) - plant_structure_development_stage - PO:0025337 - There are only two types of life of whole plant. Every life of a whole plant is either a maximal gametophyte stage or a maximal sporophyte stage. - life of whole plant stage - - - - - - - - - - - - - - - A plant structure development stage (PO:0009012) that has as primary participant a collective plant structure (PO:0025497). - - rwalls - 2011-10-19T11:12:49Z - PO_GIT:391 - etapa de desarrollo de una estructura colectiva de la planta (Spanish, exact) - 集合的植物構造の発生過程 (Japanese, exact) - plant_structure_development_stage - PO:0025338 - Includes flower development stage (PO:0007615), corolla development stage (PO:0007604), and inflorescence development stage (PO:0001083). - collective plant organ structure development stage - - - - - - - - - A short, enlarged shoot system (PO:0009006) that has as parts a short stem (PO:0009047) in which the shoot internodes (PO:0005005) do not elongate, and one or more buds (PO:0000055) enclosed by fleshy leaves (PO:0009025) or leaf bases (PO:0020040). - - rwalls - 2011-11-16T03:39:15Z - diaspore (broad) - PO_GIT:173 - bulbo (Spanish, exact) - 球根、鱗茎 (Japanese, exact) - bulblet (narrow) - plant_anatomy - PO:0025356 - May serve as a storage and/or perennating organ. Usually underground. A bulb differs from a corm (PO:0025355) by having fleshy leaves or leaf bases. The outer leaves of a bulb are often dry and membranous, rather than fleshy. May bear adventitious roots. Examples include Alium and Tulipa. Not the same structure as a bulbil. - bulb - - - - - - - - - - - - - - - - - - - - - - - - - - A plant organ (PO:0009008) that is part of a flower (PO:0009046). - - rwalls - 2012-01-19T11:44:36Z - PO_GIT:423 - &#243rgano floral (Spanish, exact) - flower organ (exact) - 花器官 (Japanese, exact) - plant_anatomy - PO:0025395 - Includes phyllomes such as anthers and petals, as well as shoot axes such as androphores and gynophores. - floral organ - - - - - - - - - A portion of meristem tissue (PO:0009013) that is committed to the development of a root primordium (PO:0005029). - - Laurel_Cooper - 2012-02-08T01:00:56Z - PO_GIT:427 - precursor de ra&#237 (Spanish, exact) - 根原基 (Japanese, exact) - plant_anatomy - PO:0025433 - Only detectable by gene expression, not morphology. May arise in a pericycle (PO:0006203), as for lateral roots in most seed plants, an endodermis (PO:0000252), as for lateral roots in ferns, or from parenchyma cells (PO:0000074) that are part a shoot axis (PO:0025029), in the case of a basal root (PO:0025002) or shoot-borne root (PO:0000042). - root anlagen - - - - - - - - - - - - - - - A primordium (PO:0025127) that is committed to the development of a floral organ (PO:0025395) and is part of a reproductive shoot apex (PO:0025222). - - rwalls - 2012-04-26T03:57:09Z - PO_GIT:465 - floral structure primordia (exact, plural) - portion of floral structure primordium tissue (exact) - primordio de organo floral (Spanish, exact) - 花器官原基 (Japanese, exact) - plant_anatomy - PO:0025477 - - If annotating to a primordium of a floral structure, it is better to use the more specific term, such as petal primordium (PO:0000021) or anther primordium (PO:0006089). - floral organ primordium - - - - - - - - - A plant structure (PO:0009011) that has as parts two or more portions of plant tissue (PO:0009007) of at least two different types and which through specific morphogenetic processes forms a single structural unit demarcated by primarily bona-fide boundaries from other structural units of different types. - - Laurel_Cooper - 2012-06-11T14:57:00Z - PO_GIT:480 - estructura vegetal con m&#250ltiples tejidos (Spanish, exact) - 複数の組織からなる植物構造 (Japanese, exact) - plant_anatomy - PO:0025496 - Most multi-tissue plant structures have at least a small connection to other plant structures via a fiat boundary, such as where a leaf (PO:0025034) connects to a shoot axis (PO:0025029), a petal (PO:0009032) connects to a receptacle (PO:0009064), or a branch (PO:0025073) connects to a stem (PO:0009047). Refers to CARO:0000055 multi-tissue structure, def'n: Anatomical structure that has as parts two or more portions of tissue of at least two different types, and which through specific morphogenetic processes, form a single distinct structural unit demarcated by bona-fide boundries from other structural units of differnt types. - multi-tissue plant structure - - - - - - - - - A plant structure (PO:0009011) that is a proper part of a whole plant (PO:0000003) and includes two or more adjacent plant organs (PO:0009008) or adjacent cardinal organ parts (PO:0025001), along with any associated portions of plant tissue (PO:0009007). - - Laurel_Cooper - 2012-06-11T15:09:20Z - PO_GIT:479 - estructura vegetal colectiva (Spanish, exact) - 集合的植物構造 (Japanese, exact) - plant_anatomy - PO:0025497 - This is a parent term to describe both collective organ part structure (PO:0025269) (e.g. septum), as well as collective plant organ structure (PO:0025007) (which was formerly named collective plant structure), for example shoot system (PO:0009006). - collective plant structure - - - - - - - - - - - - - - - A collective plant organ structure development stage (PO:0025338) that begins with the onset of the plant organ development stage (PO:0025339) and ends with either gametophyte senescent stage (PO:0025343) or sporophyte senescent stage (PO:0007017) or death. - - Laurel_Cooper - 2012-12-13T18:21:19Z - PO_GIT:517 - plant_structure_development_stage - PO:0025527 - The shoot system (PO:0009006) develops fron the shoot apical meristem (PO:0020148) in the plant embryo (PO:0009009) in vascular plants. In lower plants the gametophore (PO:0030018) arises from a gametophore meristematic apical cell (PO:0030019) in the protonema (PO:0030003). - shoot system development stage - - - - - - - - - A shoot system development stage (PO:0025527) that has as primary participant a reproductive shoot system (PO:0025082). - - Laurel_Cooper - 2012-12-13T19:01:14Z - PO_GIT:517 - plant_structure_development_stage - PO:0025530 - reproductive shoot system development stage - - - - - - - - - A plant cell (PO:0009002) that is either part of a multicellular whole plant (PO:0000003) 'in vivo' or a unicellular organism 'in natura' (i.e. part of a natural environment). - - Laurel_Cooper - 2014-05-13T16:51:47Z - PO_GIT:586 - plant_anatomy - PO:0025606 - A native plant cell is one that is not grown or maintained in vitro, nor part of an in vitro plant structure (PO:0000004). - native plant cell - - - - - - - - - - - - - - - A whole plant development stage (PO:0007033) that has as primary participant a whole plant (PO:0000003) during the interval between fertilization (or apogamy) and death. - - rwalls - 2010-07-15T02:56:11Z - PO_GIT:139 - PO_GIT:68 - fase esporof&#237tica (Spanish, exact) - sporophytic development stage (exact) - sporophytic phase (exact) - sporphyte phase (exact) - 胞子体発生過程 (Japanese, exact) - plant_structure_development_stage - PO:0028002 - - A whole plant (PO:0000003) in the sporophyte development stage usually has twice the chromosome complement of a plant in the gametophytic phase, but may not in the case of apogamy. Examples of apogamy include both naturally occurring instances (such as sporophytes arising form haploid cells as in bryophytes or ferns) as well as in vitro instances (such as haploid embryo culture or in vitro fusion of non-gamete cells or protoplasts). During the sporophyte development stage, a plant may produce meiospores by meiosis. - sporophyte development stage - - - - - - - - - A fruit (PO:0009001) which at maturity comprises a fleshy endocarp (PO:0009086), fleshy mesocarp (PO:0009087), and fleshy exocarp (PO:0009085). - - indehiscent fruit (broad) - PO_GIT:652 - bacca (exact) - baya (exact, Spanish) - beere (exact, German) - berry (exact) - pyrine (narrow) - plant_anatomy - PO:0030108 - Examples: pepper (Capsicum annuum), papaya (Carica papaya), avocado (Persea americana), may apple (Podophyllum peltatum), date palm (Phoenix dactylifera), tomato (Solanum lycopersicum), potato (Solanum tuberosum), chocolate (Theobroma cacao), blueberry (Vaccinium spp.), and grape (Vitis vinifera). - berry fruit - - - - - - - - - - - - - - - Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body. - organism substance - - - - - - - - - Anatomical structure that is an individual member of a species and consists of more than one cell. - - multi-cellular organism - multicellular organism - - - - - - - - - A specialized accessory gland of the skin of mammals that secretes milk. The gland is typically only developed in females, and regresses in males. - - glandula mammaria - lactiferous gland - mammary gland - - - - - - - - - - - - - - - - An emulsion of fat globules within a fluid that is secreted by the mammary gland during lactation. - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0235 - mammal milk - mammary gland milk - LanguaL curation note: See scope note for *MILK OR MILK COMPONENT*. for lowfat milk use *FAT PARTIALLY REMOVED*; for skim milk, use *FAT FULLY REMOVED* (both found in D3. TREATMENT APPLIED). - milk - - - - - - - - - Gonochoristic organism that can produce female gametes. - - female organism - - - - - - - - - Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not. - - fluid - body fluid - bodily fluid - - - - - - - - - A multicellular organism that existence_ends_with a post-juvenile adult stage and existence_starts_with a post-juvenile adult stage. - - adults - adult organism - - - - - - - - - - - - - - - - - - - - - - - - - - - - example to be eventually removed - example to be eventually removed - - - - - - - - - metadata complete - Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. - metadata complete - - - - - - - - - organizational term - Term created to ease viewing/sort terms for development purpose, and will not be included in a release - organizational term - - - - - - - - - ready for release - Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." - ready for release - - - - - - - - - metadata incomplete - Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. - metadata incomplete - - - - - - - - - uncurated - Nothing done yet beyond assigning a unique class ID and proposing a preferred term. - uncurated - - - - - - - - - pending final vetting - All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. - pending final vetting - - - - - - - - - to be replaced with external ontology term - Terms with this status should eventually replaced with a term from another ontology. - group:OBI - to be replaced with external ontology term - - - - - - - - - requires discussion - A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. - group:OBI - requires discussion - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/tests/output/test-output.html b/tests/output/test-output.html deleted file mode 100644 index 07bb61c22..000000000 --- a/tests/output/test-output.html +++ /dev/null @@ -1,795 +0,0 @@ -

Results: /Users/cjm/repos/ontogpt/tests/input/cases/recipe-spaghetti.txt - -

-

Input

-SIMPLE SPAGHETTI - -DIRECTIONS -On medium heat melt the butter and sautee the onion and bell peppers. -Add the hamburger meat and cook until meat is well done. -Add the tomato sauce, salt, pepper and garlic powder. -Salt, pepper and garlic powder can be adjusted to your own tastes. -Cook noodles as directed. -Mix the sauce and noodles if you like, I keep them separated. - -INGREDIENTS -UNITS: US -1 -small onion (chopped) -1 -bell pepper (chopped) -2 -tablespoons garlic powder -3 -tablespoons butter -1 -teaspoon salt -1 -teaspoon pepper -2 -(15 ounce) cans tomato sauce -1 -(16 ounce) box spaghetti noodles -1 - 1 1⁄2 -lb hamburger meat. - -

Results

-
-

url

-N/A -

label

-Simple Spaghetti -

description

-An easy to make and delicious spaghetti dish. -

categories

-
    -
  • item: 1:
    • -AUTO:Main%20dishes -
  • item: 2:
    • -AUTO:Italian%20recipes -
-

ingredients

- -

steps

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  • item: 1:
    • -
    -
      -
    • action:
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      • item: 1:
        • -
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          -
        • food:
          • -AUTO:meat -
        • state:
          • -well done -
            -
        -
      -
    • utensils:
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        • -AUTO:pan -
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        • state:
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      • item: 3:
        • -
        -
        -
      • item: 4:
        • -
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      -
    • outputs:
      • -
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      • item: 1:
        • -
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          -
        • food:
          • -AUTO:none -
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      • item: 1:
        • -AUTO:none -
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      • -AUTO:adjust -
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        • food:
          • -AUTO:salt -
        • state:
          • -None -
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        -
      • item: 3:
        • -
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      -
    • outputs:
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        -
      • item: 1:
        • -
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          -
        • food:
          • -AUTO:inputs -
        • state:
          • -adjusted -
            -
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        • -AUTO:none -
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  • item: 5:
    • -
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      -
    • action:
      • -AUTO:Cook -
    • inputs:
      • - -
    • outputs:
      • -
        -
      • item: 1:
        • -
        -
          -
        • food:
          • -AUTO:as%20directed -
        • state:
          • -None -
            -
        -
      -
    • utensils:
      • -
        -
      -
        -
    -
  • item: 6:
    • -
    -
      -
    • action:
      • -AUTO:mix%3B -
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      • - -
    • outputs:
      • - -
    • utensils:
      • -
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      • item: 1:
        • -AUTO:none -
      -
        -
    -
-
-

YAML Object

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-
-extracted_object:
-  categories:
-  - AUTO:Main%20dishes
-  - AUTO:Italian%20recipes
-  description: An easy to make and delicious spaghetti dish.
-  ingredients:
-  - amount:
-      unit: AUTO:%28chopped%29
-      value: '1'
-    food_item:
-      food: AUTO:small%20onion
-      state: chopped
-  - amount:
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-      value: '1'
-    food_item:
-      food: FOODON:00003485
-      state: chopped
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-    food_item:
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-      state: null
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-      value: '1'
-    food_item:
-      food: AUTO:salt
-      state: null
-  - amount:
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-      value: '1'
-    food_item:
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-      state: null
-  - amount:
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-    food_item:
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-      state: canned
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-    food_item:
-      food: AUTO:1%20%2816%20ounce%29%20box%20spaghetti%20noodles
-      state: uncooked
-  - amount:
-      unit: AUTO:lb
-      value: "1 - 1 1\u20442"
-    food_item:
-      food: FOODON:00001282
-      state: chopped/diced
-  label: Simple Spaghetti
-  steps:
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-      state: null
-    - food: FOODON:03301704
-      state: null
-    - food: FOODON:00003485
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-  - action: AUTO:add%3B%20cook
-    inputs:
-    - food: FOODON:00001282
-      state: chopped/diced
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-      state: well done
-    utensils:
-    - AUTO:pan
-  - action: AUTO:add%3B
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-      state: +
-    utensils:
-    - AUTO:none
-  url: N/A
-input_id: /Users/cjm/repos/ontogpt/tests/input/cases/recipe-spaghetti.txt
-input_text: "SIMPLE SPAGHETTI\n\nDIRECTIONS\nOn medium heat melt the butter and sautee\
-  \ the onion and bell peppers.\nAdd the hamburger meat and cook until meat is well\
-  \ done.\nAdd the tomato sauce, salt, pepper and garlic powder.\nSalt, pepper and\
-  \ garlic powder can be adjusted to your own tastes.\nCook noodles as directed.\n\
-  Mix the sauce and noodles if you like, I keep them separated.\n\nINGREDIENTS\nUNITS:\
-  \ US\n1\nsmall onion (chopped)\n1\nbell pepper (chopped)\n2\ntablespoons garlic\
-  \ powder\n3\ntablespoons butter\n1\nteaspoon salt\n1\nteaspoon pepper\n2\n(15 ounce)\
-  \ cans tomato sauce\n1\n(16 ounce) box spaghetti noodles\n1 - 1 1\u20442\nlb hamburger\
-  \ meat.\n"
-input_title: null
-named_entities:
-- id: FOODON:00003485
-  label: bell pepper
-- id: FOODON:00003582
-  label: garlic
-- id: UO:0010042
-  label: tablespoons
-- id: FOODON:03310351
-  label: butter
-- id: UO:0010042
-  label: tablespoons
-- id: UO:0010040
-  label: teaspoon
-- id: FOODON:00001649
-  label: pepper
-- id: UO:0010040
-  label: teaspoon
-- id: FOODON:03301217
-  label: tomato sauce
-- id: FOODON:00001282
-  label: hamburger meat
-- id: FOODON:03310351
-  label: butter
-- id: FOODON:03301704
-  label: onion
-- id: FOODON:00003485
-  label: bell peppers
-- id: FOODON:00001282
-  label: hamburger meat
-- id: FOODON:03000227
-  label: tomato
-- id: FOODON:00001649
-  label: pepper
-- id: FOODON:00003582
-  label: garlic
-- id: FOODON:00001649
-  label: pepper
-- id: FOODON:00003582
-  label: garlic
-- id: FOODON:03306944
-  label: noodles
-- id: FOODON:03311146
-  label: sauce
-- id: FOODON:03306944
-  label: noodles
-- id: FOODON:03306944
-  label: noodles
-prompt: 'Split the following piece of text into fields in the following format:
-
-
-  food: <the food item>
-
-  state: <the state of the food item (e.g. chopped, diced)>
-
-
-
-  Text:
-
-  sauce + noodles
-
-
-  ===
-
-
-  '
-raw_completion_output: "\nurl: N/A\nlabel: Simple Spaghetti\ndescription: An easy\
-  \ to make and delicious spaghetti dish.\ncategories: Main dishes; Italian recipes\n\
-  ingredients: 1 small onion (chopped); 1 bell pepper (chopped); 2 tablespoons garlic\
-  \ powder; 3 tablespoons butter; 1 teaspoon salt; 1 teaspoon pepper; 2 (15 ounce)\
-  \ cans tomato sauce; 1 (16 ounce) box spaghetti noodles; 1 - 1 1\u20442 lb hamburger\
-  \ meat.\nsteps: On medium heat melt the butter and saut\xE9 the onion and bell peppers;\
-  \ Add the hamburger meat and cook until meat is well done; Add the tomato sauce,\
-  \ salt, pepper and garlic powder; Salt, pepper and garlic powder can be adjusted\
-  \ to your own taste; Cook noodles as directed; Mix the sauce and noodles if you\
-  \ like, I keep them separated."
-
-
- -
-

Prompt

-
-
-Split the following piece of text into fields in the following format:
-
-food: <the food item>
-state: <the state of the food item (e.g. chopped, diced)>
-
-
-Text:
-sauce + noodles
-
-===
-
-
-
- -
-

Completion

-
-
-
-url: N/A
-label: Simple Spaghetti
-description: An easy to make and delicious spaghetti dish.
-categories: Main dishes; Italian recipes
-ingredients: 1 small onion (chopped); 1 bell pepper (chopped); 2 tablespoons garlic powder; 3 tablespoons butter; 1 teaspoon salt; 1 teaspoon pepper; 2 (15 ounce) cans tomato sauce; 1 (16 ounce) box spaghetti noodles; 1 - 1 1⁄2 lb hamburger meat.
-steps: On medium heat melt the butter and sauté the onion and bell peppers; Add the hamburger meat and cook until meat is well done; Add the tomato sauce, salt, pepper and garlic powder; Salt, pepper and garlic powder can be adjusted to your own taste; Cook noodles as directed; Mix the sauce and noodles if you like, I keep them separated.
-
- -
diff --git a/tests/output/test-output.md b/tests/output/test-output.md deleted file mode 100644 index e9668ee33..000000000 --- a/tests/output/test-output.md +++ /dev/null @@ -1,704 +0,0 @@ -# /Users/cjm/repos/ontogpt/tests/input/cases/recipe-spaghetti.txt - -## Input - -_SIMPLE SPAGHETTI_ - -__ - -_DIRECTIONS_ - -_On medium heat melt the butter and sautee the onion and bell peppers._ - -_Add the hamburger meat and cook until meat is well done._ - -_Add the tomato sauce, salt, pepper and garlic powder._ - -_Salt, pepper and garlic powder can be adjusted to your own tastes._ - -_Cook noodles as directed._ - -_Mix the sauce and noodles if you like, I keep them separated._ - -__ - -_INGREDIENTS_ - -_UNITS: US_ - -_1_ - -_small onion (chopped)_ - -_1_ - -_bell pepper (chopped)_ - -_2_ - -_tablespoons garlic powder_ - -_3_ - -_tablespoons butter_ - -_1_ - -_teaspoon salt_ - -_1_ - -_teaspoon pepper_ - -_2_ - -_(15 ounce) cans tomato sauce_ - -_1_ - -_(16 ounce) box spaghetti noodles_ - -_1 - 1 1⁄2_ - -_lb hamburger meat._ - -__ - -## Results - - - -### url - - -- N/A - - -### label - - -- Simple Spaghetti - - -### description - - -- An easy to make and delicious spaghetti dish. - - -### categories - - -- AUTO:Main%20dishes - -- AUTO:Italian%20recipes - - -### ingredients - - -- food_item: - - food: - - AUTO:small%20onion - - - state: - - chopped - - -- amount: - - value: - - 1 - - - unit: - - AUTO:%28chopped%29 - - - -- food_item: - - food: - - bell pepper [FOODON:00003485](https://bioregistry.io/FOODON:00003485) - - - state: - - chopped - - -- amount: - - value: - - 1 - - - unit: - - AUTO:%28chopped%29 - - - -- food_item: - - food: - - garlic [FOODON:00003582](https://bioregistry.io/FOODON:00003582) - - - state: - - powder - - -- amount: - - value: - - 2 - - - unit: - - tablespoons [UO:0010042](https://bioregistry.io/UO:0010042) - - - -- food_item: - - food: - - butter [FOODON:03310351](https://bioregistry.io/FOODON:03310351) - - - state: - - None - - -- amount: - - value: - - 3 - - - unit: - - tablespoons [UO:0010042](https://bioregistry.io/UO:0010042) - - - -- food_item: - - food: - - AUTO:salt - - - state: - - None - - -- amount: - - value: - - 1 - - - unit: - - teaspoon [UO:0010040](https://bioregistry.io/UO:0010040) - - - -- food_item: - - food: - - pepper [FOODON:00001649](https://bioregistry.io/FOODON:00001649) - - - state: - - None - - -- amount: - - value: - - 1 - - - unit: - - teaspoon [UO:0010040](https://bioregistry.io/UO:0010040) - - - -- food_item: - - food: - - tomato sauce [FOODON:03301217](https://bioregistry.io/FOODON:03301217) - - - state: - - canned - - -- amount: - - value: - - 2 - - - unit: - - None - - - -- food_item: - - food: - - AUTO:1%20%2816%20ounce%29%20box%20spaghetti%20noodles - - - state: - - uncooked - - -- amount: - - value: - - 1 - - - unit: - - None - - - -- food_item: - - food: - - hamburger meat [FOODON:00001282](https://bioregistry.io/FOODON:00001282) - - - state: - - chopped/diced - - -- amount: - - value: - - 1 - 1 1⁄2 - - - unit: - - AUTO:lb - - - - -### steps - - -- action: - - AUTO:melt%3B%20saut%C3%A9 - -- inputs: - - food: - - butter [FOODON:03310351](https://bioregistry.io/FOODON:03310351) - - - state: - - None - - - - food: - - onion [FOODON:03301704](https://bioregistry.io/FOODON:03301704) - - - state: - - None - - - - food: - - bell pepper [FOODON:00003485](https://bioregistry.io/FOODON:00003485) - - - state: - - chopped - - -- outputs: -- utensils: - - AUTO:pan - - -- action: - - AUTO:add%3B%20cook - -- inputs: - - food: - - hamburger meat [FOODON:00001282](https://bioregistry.io/FOODON:00001282) - - - state: - - chopped/diced - - -- outputs: - - food: - - AUTO:meat - - - state: - - well done - - -- utensils: - - AUTO:pan - - -- action: - - AUTO:add%3B - -- inputs: - - food: - - tomato [FOODON:03000227](https://bioregistry.io/FOODON:03000227) - - - state: - - sauce - - - - food: - - AUTO:salt - - - state: - - None - - - - food: - - pepper [FOODON:00001649](https://bioregistry.io/FOODON:00001649) - - - state: - - None - - - - food: - - garlic [FOODON:00003582](https://bioregistry.io/FOODON:00003582) - - - state: - - powder - - -- outputs: - - food: - - AUTO:none - - - state: - - None - - -- utensils: - - AUTO:none - - -- action: - - AUTO:adjust - -- inputs: - - food: - - AUTO:salt - - - state: - - None - - - - food: - - pepper [FOODON:00001649](https://bioregistry.io/FOODON:00001649) - - - state: - - None - - - - food: - - garlic [FOODON:00003582](https://bioregistry.io/FOODON:00003582) - - - state: - - powder - - -- outputs: - - food: - - AUTO:inputs - - - state: - - adjusted - - -- utensils: - - AUTO:none - - -- action: - - AUTO:Cook - -- inputs: - - food: - - noodles [FOODON:03306944](https://bioregistry.io/FOODON:03306944) - - - state: - - None - - -- outputs: - - food: - - AUTO:as%20directed - - - state: - - None - - -- utensils: - -- action: - - AUTO:mix%3B - -- inputs: - - food: - - sauce [FOODON:03311146](https://bioregistry.io/FOODON:03311146) - - - state: - - None - - - - food: - - noodles [FOODON:03306944](https://bioregistry.io/FOODON:03306944) - - - state: - - None - - -- outputs: - - food: - - noodles [FOODON:03306944](https://bioregistry.io/FOODON:03306944) - - - state: - - + - - -- utensils: - - AUTO:none - - - - -YAML: - -
-```yaml -extracted_object: - categories: - - AUTO:Main%20dishes - - AUTO:Italian%20recipes - description: An easy to make and delicious spaghetti dish. - ingredients: - - amount: - unit: AUTO:%28chopped%29 - value: '1' - food_item: - food: AUTO:small%20onion - state: chopped - - amount: - unit: AUTO:%28chopped%29 - value: '1' - food_item: - food: FOODON:00003485 - state: chopped - - amount: - unit: UO:0010042 - value: '2' - food_item: - food: FOODON:00003582 - state: powder - - amount: - unit: UO:0010042 - value: '3' - food_item: - food: FOODON:03310351 - state: null - - amount: - unit: UO:0010040 - value: '1' - food_item: - food: AUTO:salt - state: null - - amount: - unit: UO:0010040 - value: '1' - food_item: - food: FOODON:00001649 - state: null - - amount: - unit: null - value: '2' - food_item: - food: FOODON:03301217 - state: canned - - amount: - unit: null - value: '1' - food_item: - food: AUTO:1%20%2816%20ounce%29%20box%20spaghetti%20noodles - state: uncooked - - amount: - unit: AUTO:lb - value: "1 - 1 1\u20442" - food_item: - food: FOODON:00001282 - state: chopped/diced - label: Simple Spaghetti - steps: - - action: AUTO:melt%3B%20saut%C3%A9 - inputs: - - food: FOODON:03310351 - state: null - - food: FOODON:03301704 - state: null - - food: FOODON:00003485 - state: chopped - outputs: [] - utensils: - - AUTO:pan - - action: AUTO:add%3B%20cook - inputs: - - food: FOODON:00001282 - state: chopped/diced - outputs: - - food: AUTO:meat - state: well done - utensils: - - AUTO:pan - - action: AUTO:add%3B - inputs: - - food: FOODON:03000227 - state: sauce - - food: AUTO:salt - state: null - - food: FOODON:00001649 - state: null - - food: FOODON:00003582 - state: powder - outputs: - - food: AUTO:none - state: null - utensils: - - AUTO:none - - action: AUTO:adjust - inputs: - - food: AUTO:salt - state: null - - food: FOODON:00001649 - state: null - - food: FOODON:00003582 - state: powder - outputs: - - food: AUTO:inputs - state: adjusted - utensils: - - AUTO:none - - action: AUTO:Cook - inputs: - - food: FOODON:03306944 - state: null - outputs: - - food: AUTO:as%20directed - state: null - utensils: [] - - action: AUTO:mix%3B - inputs: - - food: FOODON:03311146 - state: null - - food: FOODON:03306944 - state: null - outputs: - - food: FOODON:03306944 - state: + - utensils: - - AUTO:none - url: N/A -input_id: /Users/cjm/repos/ontogpt/tests/input/cases/recipe-spaghetti.txt -input_text: "SIMPLE SPAGHETTI\n\nDIRECTIONS\nOn medium heat melt the butter and sautee\ - \ the onion and bell peppers.\nAdd the hamburger meat and cook until meat is well\ - \ done.\nAdd the tomato sauce, salt, pepper and garlic powder.\nSalt, pepper and\ - \ garlic powder can be adjusted to your own tastes.\nCook noodles as directed.\n\ - Mix the sauce and noodles if you like, I keep them separated.\n\nINGREDIENTS\nUNITS:\ - \ US\n1\nsmall onion (chopped)\n1\nbell pepper (chopped)\n2\ntablespoons garlic\ - \ powder\n3\ntablespoons butter\n1\nteaspoon salt\n1\nteaspoon pepper\n2\n(15 ounce)\ - \ cans tomato sauce\n1\n(16 ounce) box spaghetti noodles\n1 - 1 1\u20442\nlb hamburger\ - \ meat.\n" -input_title: null -named_entities: -- id: FOODON:00003485 - label: bell pepper -- id: FOODON:00003582 - label: garlic -- id: UO:0010042 - label: tablespoons -- id: FOODON:03310351 - label: butter -- id: UO:0010042 - label: tablespoons -- id: UO:0010040 - label: teaspoon -- id: FOODON:00001649 - label: pepper -- id: UO:0010040 - label: teaspoon -- id: FOODON:03301217 - label: tomato sauce -- id: FOODON:00001282 - label: hamburger meat -- id: FOODON:03310351 - label: butter -- id: FOODON:03301704 - label: onion -- id: FOODON:00003485 - label: bell peppers -- id: FOODON:00001282 - label: hamburger meat -- id: FOODON:03000227 - label: tomato -- id: FOODON:00001649 - label: pepper -- id: FOODON:00003582 - label: garlic -- id: FOODON:00001649 - label: pepper -- id: FOODON:00003582 - label: garlic -- id: FOODON:03306944 - label: noodles -- id: FOODON:03311146 - label: sauce -- id: FOODON:03306944 - label: noodles -- id: FOODON:03306944 - label: noodles -prompt: 'Split the following piece of text into fields in the following format: - - - food: - - state: - - - - Text: - - sauce + noodles - - - === - - - ' -raw_completion_output: "\nurl: N/A\nlabel: Simple Spaghetti\ndescription: An easy\ - \ to make and delicious spaghetti dish.\ncategories: Main dishes; Italian recipes\n\ - ingredients: 1 small onion (chopped); 1 bell pepper (chopped); 2 tablespoons garlic\ - \ powder; 3 tablespoons butter; 1 teaspoon salt; 1 teaspoon pepper; 2 (15 ounce)\ - \ cans tomato sauce; 1 (16 ounce) box spaghetti noodles; 1 - 1 1\u20442 lb hamburger\ - \ meat.\nsteps: On medium heat melt the butter and saut\xE9 the onion and bell peppers;\ - \ Add the hamburger meat and cook until meat is well done; Add the tomato sauce,\ - \ salt, pepper and garlic powder; Salt, pepper and garlic powder can be adjusted\ - \ to your own taste; Cook noodles as directed; Mix the sauce and noodles if you\ - \ like, I keep them separated." - -``` - -
- - -Prompt: - -
-``` -Split the following piece of text into fields in the following format: - -food: -state: - - -Text: -sauce + noodles - -=== - - -``` - -
- - -Completion: - -
-``` - -url: N/A -label: Simple Spaghetti -description: An easy to make and delicious spaghetti dish. -categories: Main dishes; Italian recipes -ingredients: 1 small onion (chopped); 1 bell pepper (chopped); 2 tablespoons garlic powder; 3 tablespoons butter; 1 teaspoon salt; 1 teaspoon pepper; 2 (15 ounce) cans tomato sauce; 1 (16 ounce) box spaghetti noodles; 1 - 1 1⁄2 lb hamburger meat. -steps: On medium heat melt the butter and sauté the onion and bell peppers; Add the hamburger meat and cook until meat is well done; Add the tomato sauce, salt, pepper and garlic powder; Salt, pepper and garlic powder can be adjusted to your own taste; Cook noodles as directed; Mix the sauce and noodles if you like, I keep them separated. -``` - -
diff --git a/tests/output/training-drugmechdb.yaml b/tests/output/training-drugmechdb.yaml deleted file mode 100644 index a0e1cbd63..000000000 --- a/tests/output/training-drugmechdb.yaml +++ /dev/null @@ -1,4132 +0,0 @@ -base_model: text-davinci-003 -examples: -- completion: 'disease: MESH:D000073605 - - drug: Tetracycline - - mechanism_links: Tetracycline - disrupts - ribosomal subunit; ribosomal subunit - - location of - translation; translation - in taxon - NCBITaxon:780; NCBITaxon:780 - - causes - MESH:D000073605 - - references: https://en.wikipedia.org/wiki/Tetracycline#Mechanism_of_action' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Tetracycline passively diffuses through porin channels in the bacterial membrane - and reversibly binds to the 30S ribosomal subunit, preventing binding of tRNA - to the mRNA-ribosome complex, and thus interfering with protein synthesis. - - - === - - - disease: MESH:D000073605 - - drug: Tetracycline - - ' -- completion: 'disease: Depressive Disorder, Major - - drug: Protriptyline - - mechanism_links: Protriptyline - decreases activity of - sodium-dependent noradrenaline - transporter (human); sodium-dependent noradrenaline transporter (human) - decreases - abundance of - Norepinephrine; Norepinephrine - participates in - neuronal signal - transduction; neuronal signal transduction - negatively correlated with - Depressive - Disorder, Major' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Protriptyline acts by decreasing the reuptake of norepinephrine and serotonin - (5-HT). - - - === - - - disease: Depressive Disorder, Major - - drug: Protriptyline - - ' -- completion: 'disease: Urinary Tract Infections - - drug: Loracarbef - - mechanism_links: loracarbef - decreases activity of - InterPro:IPR005311; InterPro:IPR005311 - - prevents - peptidoglycan-protein cross-linking; peptidoglycan-protein cross-linking - - contributes to - cell wall; cell wall - in taxon - Escherichia coli; Escherichia - coli - causes - Urinary Tract Infections - - references: https://go.drugbank.com/drugs/DB00447#mechanismofaction' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Loracarbef is an oral, synthetic beta-lactam antibiotic of the carbacephem class. - Chemically, carbacephems differ from cephalosporin-class antibiotics in the dihydrothiazine - ring where a methylene group has been substituted for a sulfur atom. Loracarbef - has a spectrum of activity similar to that of the second generation cephalosporins. - It is structurally identical to cefaclor except for a sulfur atom that has been - replaced by a methylene group. This change gives greater chemical stability in - solution and allows storage at room temperature. Loracarbef, like all b-lactams - and cephalosporins, inhibits penicillin binding proteins, enzymes that create - the cross-linkage of the peptidoglycan polymer. This binding leads to interference - with the formation and remodeling of the cell wall structure. - - - === - - - disease: Urinary Tract Infections - - drug: Loracarbef - - ' -- completion: 'disease: Opioid-Related Disorders - - drug: Naloxone - - mechanism_links: Naloxone - decreases activity of - delta-type opioid receptor - (human); delta-type opioid receptor (human) - negatively regulates - InterPro:IPR000276; - Naloxone - decreases activity of - mu-type opioid receptor (human); mu-type opioid - receptor (human) - negatively regulates - InterPro:IPR000276; Naloxone - decreases - activity of - kappa-type opioid receptor (human); kappa-type opioid receptor (human) - - negatively regulates - InterPro:IPR000276; InterPro:IPR000276 - decreases activity - of - InterPro:IPR000274; InterPro:IPR000274 - decreases abundance of - Cyclic - AMP; Cyclic AMP - causes - Substance Withdrawal Syndrome; Substance Withdrawal - Syndrome - correlated with - Opioid-Related Disorders - - references: https://go.drugbank.com/drugs/DB01183#mechanismofaction; DOI:10.18773/austprescr/1996.063; - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3999180/' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - While the mechanism of action of naloxone is not fully understood, the preponderance - of evidence suggests that naloxone antagonizes the opioid effects by competing - for the same receptor sites, especially the mu-opioid receptor. Recently, naloxone - has been shown to bind all three opioid receptors (mu, kappa and gamma) but the - strongest binding is to the mu receptor. - - - === - - - disease: Opioid-Related Disorders - - drug: Naloxone - - ' -- completion: 'disease: Organophosphate Poisoning - - drug: Pralidoxime - - mechanism_links: pralidoxime - increases activity of - acetylcholinesterase (human); - acetylcholinesterase (human) - positively regulates - acetylcholine catabolic - process; acetylcholine catabolic process - decreases abundance of - Acetylcholine; - Acetylcholine - contributes to - positive regulation of synaptic transmission, - cholinergic; positive regulation of synaptic transmission, cholinergic - occurs - in - Organophosphate Poisoning - - references: https://go.drugbank.com/drugs/DB00733; https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL1420/; - https://en.wikipedia.org/wiki/Organophosphate_poisoning#Signs_and_symptoms' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Pralidoxime is an antidote to organophosphate pesticides and chemicals. Organophosphates - bind to the esteratic site of acetylcholinesterase, which results initially in - reversible inactivation of the enzyme. Acetylcholinesterase inhibition causes - acetylcholine to accumulate in synapses, producing continuous stimulation of cholinergic - fibers throughout the nervous systems. If given within 24 hours after organophosphate - exposure, pralidoxime reactivates the acetylcholinesterase by cleaving the phosphate-ester - bond formed between the organophosphate and acetylcholinesterase. - - - === - - - disease: Organophosphate Poisoning - - drug: Pralidoxime - - ' -- completion: 'disease: Wilms Tumor - - drug: Dactinomycin - - mechanism_links: Dactinomycin - negatively regulates - DNA-templated transcription; - DNA-templated transcription - precedes - translation; Dactinomycin - directly - interacts with - DNA; DNA - participates in - DNA replication; DNA replication - - positively correlated with - HP:0031377; translation - occurs in - HP:0031377; - HP:0031377 - causes - Wilms Tumor - - references: https://go.drugbank.com/drugs/DB00970; https://drugs.ncats.io/drug/1CC1JFE158' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Good evidence exists that this drug bind strongly, but reversibly, to DNA, interfering - with synthesis of RNA (prevention of RNA polymerase elongation) and, consequently, - with protein synthesis. - - - === - - - disease: Wilms Tumor - - drug: Dactinomycin - - ' -- completion: 'disease: Mevalonate Kinase Deficiency - - drug: Canakinumab - - mechanism_links: canakinumab - decreases activity of - interleukin-1 beta (human); - interleukin-1 beta (human) - positively regulates - HP:0001945; interleukin-1 - beta (human) - positively regulates - inflammatory response; HP:0001945 - manifestation - of - Mevalonate Kinase Deficiency; inflammatory response - occurs in - Mevalonate - Kinase Deficiency - - references: https://go.drugbank.com/drugs/DB06168; https://en.wikipedia.org/wiki/Mevalonate_kinase_deficiency#Treatment' - prompt: "From the text below, extract the following entities in the following format:\n\ - \ndisease: \ndrug: \nmechanism_links: \n\ - \n\nText:\nIn inflammatory diseases involving Cryopyrin-Associated Periodic Syndromes\ - \ (CAPS), interleukin-1 beta (IL-1\u03B2) is excessively activated and drives\ - \ inflammation. The protein cryopyrin controls the activation of IL-1\u03B2, and\ - \ mutations in cryopyrin's gene, NLRP-3, up-regulate IL-1\u03B2 activation. Canakinumab\ - \ is a human monoclonal anti-human IL-1\u03B2 antibody of the IgG1/\u03BA isotype.\ - \ Canakinumab binds to human IL-1\u03B2 and neutralizes its inflammatory activity\ - \ by blocking its interaction with IL-1 receptors, but it does not bind IL-1\u03B1\ - \ or IL-1 receptor antagonist (IL-1ra).\n\n===\n\ndisease: Mevalonate Kinase Deficiency\n\ - drug: Canakinumab\n" -- completion: 'disease: Hypercholesterolemia - - drug: Simvastatin - - mechanism_links: Simvastatin - decreases activity of - 3-hydroxy-3-methylglutaryl-coenzyme - A reductase (human); 3-hydroxy-3-methylglutaryl-coenzyme A reductase (human) - - negatively regulates - REACT:R-HSA-191273; REACT:R-HSA-191273 - decreases abundance - of - Cholesterol; Cholesterol - contributes to - Hypercholesterolemia - - references: https://go.drugbank.com/drugs/DB00641#mechanismofaction; https://pubchem.ncbi.nlm.nih.gov/compound/Simvastatin' - prompt: "From the text below, extract the following entities in the following format:\n\ - \ndisease: \ndrug: \nmechanism_links: \n\ - \n\nText:\nSimvastatin is a prodrug in which the 6-membered lactone ring of simvastatin\ - \ is hydrolyzed <i>in vivo</i> to generate the beta,delta-dihydroxy\ - \ acid, an active metabolite structurally similar to HMG-CoA (hydroxymethylglutaryl\ - \ CoA). Once hydrolyzed, simvastatin competes with HMG-CoA for HMG-CoA reductase,\ - \ a hepatic microsomal enzyme, which catalyzes the conversion of HMG-CoA to mevalonate,\ - \ an early rate-limiting step in cholesterol biosynthesis.[A181421] Simvastatin\ - \ acts primarily in the liver, where decreased hepatic cholesterol concentrations\ - \ stimulate the upregulation of hepatic low density lipoprotein (LDL) receptors\ - \ which increases hepatic uptake of LDL. Simvastatin also inhibits hepatic synthesis\ - \ of very low density lipoprotein (VLDL).[F4655, F4658] The overall effect is\ - \ a decrease in plasma LDL and VLDL. Statins have also been found to bind allosterically\ - \ to \u03B22 integrin function-associated antigen-1 (LFA-1), which plays an important\ - \ role in leukocyte trafficking and in T cell activation.[A181559]\n\n===\n\n\ - disease: Hypercholesterolemia\ndrug: Simvastatin\n" -- completion: 'disease: Pneumonia, Bacterial - - drug: Ceftazidime - - mechanism_links: Ceftazidime - negatively regulates - Pfam:PF00905; Pfam:PF00905 - - positively regulates - peptidoglycan biosynthetic process; peptidoglycan biosynthetic - process - positively correlated with - peptidoglycan-based cell wall biogenesis; - peptidoglycan-based cell wall biogenesis - in taxon - Streptococcus pneumoniae; - Streptococcus pneumoniae - causes - Pneumonia, Bacterial - - references: https://go.drugbank.com/drugs/DB00438; https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL44354/' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - The bactericidal activity of ceftazidime results from the inhibition of cell wall - synthesis via affinity for penicillin-binding proteins (PBPs). - - - === - - - disease: Pneumonia, Bacterial - - drug: Ceftazidime - - ' -- completion: 'disease: Meningitis - - drug: Erythromycin - - mechanism_links: Erythromycin Ethylsuccinate - negatively regulates - RNA, Ribosomal, - 23S; RNA, Ribosomal, 23S - participates in - translation; translation - occurs - in - Bacteria; Bacteria - causes - Meningitis - - references: https://go.drugbank.com/drugs/DB00199#mechanism-of-action; https://www.rxlist.com/erythromycin-ethylsuccinate-drug.htm; - https://en.wikipedia.org/wiki/Meningitis' - prompt: "From the text below, extract the following entities in the following format:\n\ - \ndisease: \ndrug: \nmechanism_links: \n\ - \n\nText:\nIn order to replicate, bacteria require a specific process of protein\ - \ synthesis, enabled by ribosomal proteins.[A6505] Erythromycin acts by inhibition\ - \ of protein synthesis by binding to the 23S ribosomal RNA molecule in the 50S\ - \ subunit of ribosomes in susceptible bacterial organisms. It stops bacterial\ - \ protein synthesis by inhibiting the transpeptidation/translocation step of protein\ - \ synthesis and by inhibiting the assembly of the 50S ribosomal subunit.[L7261,A14179]\ - \ This results in the control of various bacterial infections.[A174193,L7261]\ - \ The strong affinity of macrolides, including erythromycin, for bacterial ribosomes,\ - \ supports their broad\u2010spectrum antibacterial activities.[A174193]\n\n===\n\ - \ndisease: Meningitis\ndrug: Erythromycin\n" -- completion: 'disease: Staphylococcal Infections - - drug: Teicoplanin - - mechanism_links: Teicoplanin - negatively regulates - alanylalanine; alanylalanine - - participates in - peptidoglycan biosynthetic process; peptidoglycan biosynthetic - process - positively regulates - peptidoglycan-based cell wall biogenesis; peptidoglycan-based - cell wall biogenesis - positively correlated with - cell division; cell division - - occurs in - Staphylococcus; Staphylococcus - causes - Staphylococcal Infections - - references: https://go.drugbank.com/drugs/DB06149' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Teicoplanin inhibits peptidoglycan polymerization, resulting in inhibition of - bacterial cell wall synthesis and cell death. - - - === - - - disease: Staphylococcal Infections - - drug: Teicoplanin - - ' -- completion: 'disease: Muscle Spasticity - - drug: Chlorphenesin - - mechanism_links: Chlorphenesin - causes - relaxation of muscle; relaxation of - muscle - negatively correlated with - Muscle Spasticity - - references: https://go.drugbank.com/drugs/DB14656; https://www.ebi.ac.uk/chebi/chebiOntology.do?chebiId=CHEBI:3643' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - The mechanism of action of chlorphenesin is not well defined, and its effects - are measured mainly by subjective responses. It is known that chlorphenesin acts - in the central nervous system (CNS) rather than directly on skeletal muscle. - - - === - - - disease: Muscle Spasticity - - drug: Chlorphenesin - - ' -- completion: 'disease: Rhinitis, Allergic, Seasonal - - drug: Brompheniramine - - mechanism_links: Brompheniramine - decreases activity of - histamine H1 receptor - (human); histamine H1 receptor (human) - positively correlated with - Histamine; - Histamine - positively regulates - regulation of vascular permeability; regulation - of vascular permeability - correlated with - Rhinitis, Allergic, Seasonal - - references: https://go.drugbank.com/drugs/DB00835#mechanism-of-action; https://www.uniprot.org/uniprot/P35367#function; - https://en.wikipedia.org/wiki/Allergic_rhinitis' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Brompheniramine is an antagonist of the H1 histamine receptors with moderate antimuscarinic - actions, as with other common antihistamines such as diphenhydramine. Due to its - anticholindergic effects, brompheniramine may cause drowsiness, sedation, dry - mouth, dry throat, blurred vision, and increased heart rate. - - - === - - - disease: Rhinitis, Allergic, Seasonal - - drug: Brompheniramine - - ' -- completion: 'disease: Lennox Gastaut Syndrome - - drug: Rufinamide - - mechanism_links: rufinamide - decreases activity of - sodium channel protein type - 9 subunit alpha (human); sodium channel protein type 9 subunit alpha (human) - - positively regulates - neuronal action potential; neuronal action potential - - positively correlated with - neurotransmitter secretion; neurotransmitter secretion - - positively correlated with - HP:0032792; HP:0032792 - positively correlated - with - Lennox Gastaut Syndrome - - references: https://go.drugbank.com/drugs/DB06201#mechanism-of-action; https://en.wikipedia.org/wiki/Rufinamide; - https://pubmed.ncbi.nlm.nih.gov/30391662/; https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7461817/; - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7461817/; https://en.wikipedia.org/wiki/Lennox%E2%80%93Gastaut_syndrome#Seizures' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Rufinamide is a triazole derivative antiepileptic that prolongs the inactive state - of voltage gated sodium channels thus stabilizing membranes, ultimately blocking - the spread of partial seizure activity. - - - === - - - disease: Lennox Gastaut Syndrome - - drug: Rufinamide - - ' -- completion: 'disease: Dyspareunia - - drug: Dienestrol - - mechanism_links: Dienestrol - chemically similar to - Estrogens; Estrogens - increases - activity of - estrogen receptor (human); estrogen receptor (human) - positively - regulates - REACT:R-HSA-9018519; REACT:R-HSA-9018519 - negatively correlated with - - HP:0030016; HP:0030016 - manifestation of - Dyspareunia - - references: https://go.drugbank.com/drugs/DB00890' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Dienestrol is a synthetic, non-steroidal estrogen. Estrogens passively diffuse - into target cells of responsive tissues, complex with the estrogen receptors, - and enter the cell''s nucleus to initiate or enhance gene transcription of protein - synthesis after binding to DNA. - - - === - - - disease: Dyspareunia - - drug: Dienestrol - - ' -- completion: 'disease: Dysentery, Bacillary - - drug: Norfloxacin - - mechanism_links: Norfloxacin - decreases activity of - PR:P0AES5; Norfloxacin - - decreases activity of - PR:P0AFI4; PR:P0AES5 - positively regulates - DNA replication; - PR:P0AFI4 - positively regulates - DNA replication; DNA replication - occurs in - - Shigella flexneri; Shigella flexneri - causes - Dysentery, Bacillary - - references: https://go.drugbank.com/drugs/DB01059#mechanism-of-action; https://www.uniprot.org/uniprot/P0AES5#function; - https://www.uniprot.org/uniprot/P0AFI4#function; https://en.wikipedia.org/wiki/Shigellosis' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - The bactericidal action of Norfloxacin results from inhibition of the enzymes - topoisomerase II (DNA gyrase) and topoisomerase IV, which are required for bacterial - DNA replication, transcription, repair, and recombination. Norfloxacin is a broad-spectrum - antibiotic agent that is shown to be effective against various Gram-positive and - Gram-negative bacterial species. The fluorine atom at the 6 position increases - potency against gram-negative organisms, and the piperazine moiety at the 7 position - is responsible for anti-pseudomonal activity - - - === - - - disease: Dysentery, Bacillary - - drug: Norfloxacin - - ' -- completion: 'disease: Breast Neoplasms - - drug: Drostanolone propionate - - mechanism_links: dromostanolone propionate - increases activity of - androgen - receptor (human); androgen receptor (human) - negatively regulates - intracellular - estrogen receptor signaling pathway; intracellular estrogen receptor signaling - pathway - positively regulates - cell population proliferation; cell population - proliferation - positively correlated with - Breast Neoplasms - - references: https://go.drugbank.com/drugs/DB14655; https://en.wikipedia.org/wiki/Drostanolone_propionate; - https://en.wikipedia.org/wiki/Anabolic_steroid#Mechanism_of_action' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Dromostanolone is a synthetic androgenic anabolic steroid and is approximately - 5 times as potent as natural methyltestosterone. Like testosterone and other androgenic - hormones, dromostanolone binds to the androgen receptor. This causes downstream - genetic transcriptional changes. This ultimately causes retention of nitrogen, - potassium, and phosphorus; increases protein anabolism; and decreases amino acid - catabolism. The antitumour activity of dromostanolone appears related to reduction - or competitive inhibition of prolactin receptors or estrogen receptors or production. - - - === - - - disease: Breast Neoplasms - - drug: Drostanolone propionate - - ' -- completion: 'disease: Sneezing - - drug: Methdilazine - - mechanism_links: methdilazine - decreases activity of - histamine H1 receptor - (human); histamine H1 receptor (human) - positively regulates - histamine receptor - activity; histamine receptor activity - participates in - histamine secretion - involved in inflammatory response; histamine secretion involved in inflammatory - response - positively correlated with - Sneezing - - references: https://go.drugbank.com/drugs/DB00902' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Methdilazine binds to the histamine H<sub>1</sub> receptor. This blocks - the action of endogenous histamine, which subsequently leads to temporary relief - of the negative symptoms brought on by histamine. - - - === - - - disease: Sneezing - - drug: Methdilazine - - ' -- completion: 'disease: Hypercholesterolemia - - drug: Inositol nicotinate - - mechanism_links: Inositol Niacinate - increases activity of - hydroxycarboxylic - acid receptor 3 (human); Inositol Niacinate - increases activity of - hydroxycarboxylic - acid receptor 2 (human); hydroxycarboxylic acid receptor 3 (human) - participates - in - REACT:R-HSA-418594; hydroxycarboxylic acid receptor 2 (human) - participates - in - REACT:R-HSA-418594; REACT:R-HSA-418594 - decreases abundance of - Triglycerides; - Triglycerides - positively correlated with - low density lipoprotein triglyceride; - Triglycerides - positively correlated with - Cholesterol, LDL; Triglycerides - - positively correlated with - Lipoproteins, LDL; low density lipoprotein triglyceride - - positively correlated with - Hypercholesterolemia; Cholesterol, LDL - positively - correlated with - Hypercholesterolemia; Lipoproteins, LDL - positively correlated - with - Hypercholesterolemia - - references: https://go.drugbank.com/drugs/DB08949#mechanism-of-action; https://en.wikipedia.org/wiki/Hypercholesterolemia#Medication; - https://pubmed.ncbi.nlm.nih.gov/15083592/; https://www.sciencedirect.com/science/article/pii/B978032329738700037X; - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5441126/' - prompt: "From the text below, extract the following entities in the following format:\n\ - \ndisease: \ndrug: \nmechanism_links: \n\ - \n\nText:\nInositol nicotinate and other niacins directly and noncompetitively\ - \ inhibit microsomal enzyme diacylglycerol acyltransferase 2 (DGAT2) responsible\ - \ for esterification of fatty acids to form triglycerides, resulting in decreased\ - \ triglyceride synthesis and hepatic atherogenic lipoprotein secretion. Inhibitied\ - \ triglyceride synthesis results in accelerated intracellular hepatic apo B degradation\ - \ and the decreased secretion of VLDL and LDL particles [A19555]. Niacin also\ - \ inhibits hepatic expression of beta-chain adenosine triphosphate synthase which\ - \ inhibits the removal or uptake of HDL\u2013apo A-I. It is also suggested that\ - \ niacin increases vascular endothelial cell redox state, resulting in the inhibition\ - \ of oxidative stress and vascular inflammatory genes or key cytokines involved\ - \ in atherosclerosis. It acts as a ligand on G-protein coupled receptor 109A (HCAR2/HM74A)\ - \ and 109B (HCAR3/HM74) which mediates the anti-lipolytic and lipid-lowering effects\ - \ of nicotinic acid. Niacin-mediated signalling of GPR109A expressed on adipocytes\ - \ and G(i)-mediated decrease in cAMP levels result in decreased lipolysis, fatty\ - \ acid mobilization, and triglyceride synthesis. The action of inositol nicotinate\ - \ on GPR109A expressed on skin and macrophages to cause increased prostaglandin\ - \ D2/E2 activity is thought to be less significant compared to other niacin molecules\ - \ as it involves sustained release that leads to less flushing [A19555].\n\n===\n\ - \ndisease: Hypercholesterolemia\ndrug: Inositol nicotinate\n" -- completion: 'disease: Enterobacteriaceae Infections - - drug: Ticarcillin - - mechanism_links: Ticarcillin - negatively regulates - InterPro:IPR001460; InterPro:IPR001460 - - positively regulates - peptidoglycan biosynthetic process; peptidoglycan biosynthetic - process - positively correlated with - peptidoglycan-based cell wall biogenesis; - peptidoglycan-based cell wall biogenesis - in taxon - Enterobacteriaceae; Enterobacteriaceae - - causes - Enterobacteriaceae Infections - - references: https://go.drugbank.com/drugs/DB01607' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Ticarcillin''s principal mechanism of action revolves around its capacity to prevent - the cross-linking of peptidoglycan during bacterial cell wall synthesis. Consequently, - when the offending bacteria attempt to undergo cell division, cell death occurs. - - - === - - - disease: Enterobacteriaceae Infections - - drug: Ticarcillin - - ' -- completion: 'disease: Hypotension - - drug: Dopamine - - mechanism_links: Dopamine - increases activity of - alpha-1A adrenergic receptor - (human); alpha-1A adrenergic receptor (human) - positively regulates - vasoconstriction; - vasoconstriction - negatively correlated with - Hypotension; Dopamine - increases - activity of - beta-1 adrenergic receptor (human); beta-1 adrenergic receptor (human) - - positively regulates - cardiac muscle contraction; cardiac muscle contraction - - negatively correlated with - Hypotension - - references: https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL59/; https://en.wikipedia.org/wiki/Dopamine#Medical_uses' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Dopamine is a precursor to norepinephrine in noradrenergic nerves and is also - a neurotransmitter in certain areas of the central nervous system. Dopamine produces - positive chronotropic and inotropic effects on the myocardium, resulting in increased - heart rate and cardiac contractility. This is accomplished directly by exerting - an agonist action on beta-adrenoceptors and indirectly by causing release of norepinephrine - from storage sites in sympathetic nerve endings. In the brain, dopamine actas - as an agonist to the five dopamine receptor subtypes (D!, D2, D3, D4, D5). - - - === - - - disease: Hypotension - - drug: Dopamine - - ' -- completion: 'disease: Hypertension - - drug: Torasemide - - mechanism_links: torsemide - decreases activity of - solute carrier family 12 - member 1 (human); solute carrier family 12 member 1 (human) - positively regulates - - sodium ion transport; sodium ion transport - regulates - renal water retention; - renal water retention - positively correlated with - HP:0032263; HP:0032263 - - manifestation of - Hypertension - - references: https://go.drugbank.com/drugs/DB00214#BE0000502; https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL1148/' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - As mentioned above, torasemide is part of the loop diuretics and thus, it acts - by reducing the oxygen demand in the medullary thick ascending loop of Henle by - inhibiting the Na+/K+/Cl- pump on the luminal cell membrane surface.[A174466] - This action is obtained by the binding of torasemide to a chloride ion-binding - site of the transport molecule.[L5257] Torasemide is known to have an effect in - the renin-angiotensin-aldosterone system by inhibiting the downstream cascade - after the activation of angiotensin II. This inhibition will produce a secondary - effect marked by the reduction of the expression of aldosterone synthase, TGF-B1 - and thromboxane A2 and a reduction on the aldosterone receptor binding.[A174466, - A174472] - - - === - - - disease: Hypertension - - drug: Torasemide - - ' -- completion: 'disease: Hyperuricemia - - drug: Lesinurad - - mechanism_links: lesinurad - decreases activity of - solute carrier family 22 - member 12 (human); solute carrier family 22 member 12 (human) - negatively correlated - with - renal urate salt excretion; renal urate salt excretion - decreases activity - of - Uric Acid; lesinurad - decreases activity of - solute carrier family 22 member - 11 (human); solute carrier family 22 member 11 (human) - negatively correlated - with - renal urate salt excretion; Uric Acid - positively correlated with - Hyperuricemia - - references: https://go.drugbank.com/drugs/DB11560#BE0000879; https://en.wikipedia.org/wiki/Lesinurad#Mechanism_of_action' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Lesinurad inhibits the activity of uric acid transporter 1 (URAT1) and organic - anion transporter 4 (OAT4). URAT1 is a major transporter enzyme responsible for - reuptake of uric acid from the renal tubules; inhibition of URAT1 function thereby - increases excretion of uric acid. - - - === - - - disease: Hyperuricemia - - drug: Lesinurad - - ' -- completion: 'disease: Parkinson Disease, Postencephalitic - - drug: Bromocriptine - - mechanism_links: Bromocriptine - positively regulates - D(2) dopamine receptor - (human); Bromocriptine - positively regulates - D(3) dopamine receptor (human); - D(2) dopamine receptor (human) - positively correlated with - Dopamine; D(3) dopamine - receptor (human) - positively correlated with - Dopamine; Dopamine - located in - - dopaminergic cell groups; dopaminergic cell groups - located in - substantia - nigra; substantia nigra - participates in - nigrostriatal tract; nigrostriatal - tract - affected by - Parkinson Disease, Postencephalitic - - references: https://go.drugbank.com/drugs/DB01200#BE000058; https://en.wikipedia.org/wiki/Postencephalitic_parkinsonism#:~:text=the%20free%20encyclopedia-,Postencephalitic%20parkinsonism,degeneration%20leads%20to%20clinical%20parkinsonism' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - The dopamine D<sub>2</sub> receptor is a 7-transmembrane G-protein - coupled receptor associated with G<sub>i</sub> proteins. In lactotrophs, - stimulation of dopamine D<sub>2</sub> receptor causes inhibition of - adenylyl cyclase, which decreases intracellular cAMP concentrations and blocks - IP3-dependent release of Ca<sup>2+</sup> from intracellular stores. - Decreases in intracellular calcium levels may also be brought about via inhibition - of calcium influx through voltage-gated calcium channels, rather than via inhibition - of adenylyl cyclase. Additionally, receptor activation blocks phosphorylation - of p42/p44 MAPK and decreases MAPK/ERK kinase phosphorylation. Inhibition of MAPK - appears to be mediated by c-Raf and B-Raf-dependent inhibition of MAPK/ERK kinase. - Dopamine-stimulated growth hormone release from the pituitary gland is mediated - by a decrease in intracellular calcium influx through voltage-gated calcium channels - rather than via adenylyl cyclase inhibition. Stimulation of dopamine D<sub>2</sub> - receptors in the nigrostriatal pathway leads to improvements in coordinated muscle - activity in those with movement disorders. - - - === - - - disease: Parkinson Disease, Postencephalitic - - drug: Bromocriptine - - ' -- completion: 'disease: Crohn Disease - - drug: Betamethasone - - mechanism_links: Betamethasone - increases activity of - glucocorticoid receptor - (human); glucocorticoid receptor (human) - decreases abundance of - cytosolic - phospholipase A2 (human); cytosolic phospholipase A2 (human) - positively regulates - - inflammatory response; inflammatory response - positively correlated with - - Crohn Disease' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Glucocorticoids inhibit neutrophil apoptosis and demargination, and inhibit NF-Kappa - B and other inflammatory transcription factors.[A187463] They also inhibit phospholipase - A2, leading to decreased formation of arachidonic acid derivatives.[A187463] In - addition, glucocorticoids promote anti-inflammatory genes like interleukin-10.[A187463] - Corticosteroids like betamethasone can act through nongenomic and genomic pathways.[A31458] - The genomic pathway is slower and occurs when glucocorticoids activate glucocorticoid - receptors and initiate downstream effects that promote transcription of anti-inflammatory - genes including phosphoenolpyruvate carboxykinase (PEPCK), IL-1-receptor antagonist, - and tyrosine amino transferase (TAT).[A31458] On the other hand, the nongenomic - pathway is able to elicit a quicker response by modulating T-cell, platelet and - monocyte activity through the use of existing membrane-bound receptors and second - messengers.[A31458] - - - === - - - disease: Crohn Disease - - drug: Betamethasone - - ' -- completion: 'disease: Hypercholesterolemia - - drug: Colestipol - - mechanism_links: Colestipol - decreases abundance of - Bile Acids and Salts; Bile - Acids and Salts - derives from - Cholesterol; Cholesterol - positively correlated - with - Hypercholesterolemia; Colestipol - increases activity of - low-density - lipoprotein receptor (human); low-density lipoprotein receptor (human) - positively - regulates - low-density lipoprotein particle clearance; low-density lipoprotein - particle clearance - decreases abundance of - Lipoproteins, LDL; Lipoproteins, - LDL - positively correlated with - Hypercholesterolemia - - references: https://go.drugbank.com/drugs/DB00375#BE0004809' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Colestipol is a lipid-lowering polymer that binds with bile acids in the intestine - forming a complex that is excreted in the feces [FDA Label, F4555, F4567]. This - non-systemic action results in a continuous, partial removal of bile acids from - the enterohepatic circulation preventing their reabsorption [FDA Label, F4555, - F4567]. This increased fecal loss of bile acids due to colestipol hydrochloride - administration leads to increased oxidation of cholesterol to bile acids [FDA - Label, F4555, F4567]. This results in an increase in the number of hepatic low-density - lipoprotein (LDL) receptors, and consequently an increased uptake of LDL and a - decrease in serum/plasma beta lipoprotein or total and LDL cholesterol levels - [FDA Label, F4555, F4567]. Although hydrochloride produces an increase in the - hepatic synthesis of cholesterol in man, serum cholesterol levels fall [FDA Label, - F4555, F4567]. - - - === - - - disease: Hypercholesterolemia - - drug: Colestipol - - ' -- completion: 'disease: HIV Infections - - drug: Lopinavir - - mechanism_links: Lopinavir - negatively regulates - PR:Q72874; PR:Q72874 - negatively - correlated with - negative regulation of peptidase activity; negative regulation - of peptidase activity - decreases activity of - gag polyprotein (human immunodeficiency - virus type 1 group M subtype B (isolate HXB2)); gag polyprotein (human immunodeficiency - virus type 1 group M subtype B (isolate HXB2)) - participates in - virion assembly; - virion assembly - in taxon - NCBITaxon:11676; NCBITaxon:11676 - causes - HIV Infections - - references: https://go.drugbank.com/drugs/DB01601#mechanism-of-action; https://www.uniprot.org/uniprot/P04591#function; - https://pubmed.ncbi.nlm.nih.gov/23266279/' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - The HIV lifecycle is comprised of 3 distinct stages: assembly, involving creation - and packaging of essential viral components; budding, wherein the viral particle - crosses the host cell plasma membrane and forms a lipid envelope; and maturation, - wherein the viral particle alters its structure and becomes infectious.[A191712] - At the center of this lifecycle is the Gag polyprotein which, along with the products - of its proteolysis, coordinate these stages and function as the major structural - proteins of the virus. The HIV-1 protease enzyme, a dimeric aspartic protease, - is the enzyme responsible for cleaving the Gag polyprotein and thus plays a critical - role in many aspects of the HIV viral lifecycle.[A191712] Lopinavir is an inhibitor - of the HIV-1 protease enzyme.[L11163] Its design is based on the "peptidomimetic" - principle, wherein the molecule contains a hydroxyethylene scaffold which mimics - the normal peptide linkage (cleaved by HIV protease) but which itself cannot be - cleaved.[A191757] By preventing HIV-1 protease activity, and thus the proteolysis - of the Gag polyprotein, lopinavir results in the production of immature, non-infectious - viral particles. - - - === - - - disease: HIV Infections - - drug: Lopinavir - - ' -- completion: 'disease: Herpes Zoster - - drug: Valaciclovir - - mechanism_links: valacyclovir - has metabolite - Acyclovir; Acyclovir - negatively - regulates - PR:P09252; PR:P09252 - positively regulates - viral DNA genome replication; - viral DNA genome replication - in taxon - NCBITaxon:10335; NCBITaxon:10335 - causes - - Herpes Zoster - - references: https://go.drugbank.com/drugs/DB00577' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Valacyclovir is the L-valine ester of aciclovir. It is classified as a nucleoside - analog DNA polymerase enzyme inhibitor. Aciclovir is a purine (guanine) nucleoside - analog is a metabolite that heavily contributes to the pharmacological actions - of valacyclovir. In fact, most of valacyclovir''s activity is attributed to acyclovir - [A175885]. 3) inactivation of the viral DNA polymerase. The higher level of antiviral - activity of acyclovir against HSV compared with VZV is attributed to its more - efficient phosphorylation by viral thymidine kinase (TK). - - - === - - - disease: Herpes Zoster - - drug: Valaciclovir - - ' -- completion: 'disease: Hyperuricemia - - drug: Sulfinpyrazone - - mechanism_links: Sulfinpyrazone - decreases activity of - solute carrier family - 22 member 12 (human); solute carrier family 22 member 12 (human) - negatively - correlated with - renal urate salt excretion; renal urate salt excretion - negatively - correlated with - Hyperuricemia - - references: https://go.drugbank.com/drugs/DB01138' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Sulfinpyrazone is an oral uricosuric agent (pyrazolone derivative) used to treat - chronic or intermittent gouty arthritis. Sulfinpyrazone competitively inhibits - the reabsorption of uric acid at the proximal convoluted tubule, thereby facilitating - urinary excretion of uric acid and decreasing plasma urate concentrations. This - is likely done through inhibition of the urate anion transporter (hURAT1) as well - as the human organic anion transporter 4 (hOAT4). Sulfinpyrazone is not intended - for the treatment of acute attacks because it lacks therapeutically useful analgesic - and anti-inflammatory effects. Sulfinpyrazone and its sulfide metabolite possess - COX inhibitory effects. Sulfinpyrazone has also been shown to be a UDP-glucuronsyltransferase - inhibitor and a very potent CYP2C9 inhibitor. Sulfinpyrazone is also known to - be a cystic fibrosis transmembrane conductance regulator (CFTR) inhibitor as well - as an inhibitor of several multridrug resistance proteins (MRPs). - - - === - - - disease: Hyperuricemia - - drug: Sulfinpyrazone - - ' -- completion: 'disease: Crohn Disease - - drug: Budesonide - - mechanism_links: Budesonide - molecularly interacts with - glucocorticoid receptor - (human); glucocorticoid receptor (human) - increases abundance of - annexin A1 - (human); annexin A1 (human) - decreases activity of - InterPro:IPR001211; glucocorticoid - receptor (human) - increases abundance of - interleukin-10 (human); interleukin-10 - (human) - decreases activity of - InterPro:IPR001211; InterPro:IPR001211 - prevents - - arachidonic acid secretion; arachidonic acid secretion - negatively regulates - - leukotriene biosynthetic process; leukotriene biosynthetic process - prevents - - inflammatory response; arachidonic acid secretion - negatively regulates - prostaglandin - biosynthetic process; prostaglandin biosynthetic process - prevents - inflammatory - response; inflammatory response - correlated with - Crohn Disease - - references: https://go.drugbank.com/drugs/DB01222#mechanismofaction; https://pubchem.ncbi.nlm.nih.gov/compound/Budesonide#section=Pharmacology; - doi:10.1165/rcmb.2016-0068OC' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - The short term effects of corticosteroids are decreased vasodilation and permeability - of capillaries, as well as decreased leukocyte migration to sites of inflammation.[A187463] - Corticosteroids binding to the glucocorticoid receptor mediates changes in gene - expression that lead to multiple downstream effects over hours to days.[A187463] - Lower doses of corticosteroids provide an anti-inflammatory effect, while higher - doses are immunosuppressive.[A187463] High doses of glucocorticoids for an extended - period bind to the mineralocorticoid receptor, raising sodium levels and decreasing - potassium levels.[A187463] - - - === - - - disease: Crohn Disease - - drug: Budesonide - - ' -- completion: 'disease: Rhinitis, Vasomotor - - drug: Carbinoxamine - - mechanism_links: carbinoxamine - decreases activity of - histamine H1 receptor - (human); histamine H1 receptor (human) - positively regulates - cellular response - to histamine; cellular response to histamine - positively correlated with - Histamine; - Histamine - participates in - inflammatory response; inflammatory response - contributes - to - Rhinitis, Vasomotor - - references: https://go.drugbank.com/drugs/DB00748#mechanism-of-action; https://www.uniprot.org/uniprot/P35367#function' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Carbinoxamine competes with free histamine for binding at HA-receptor sites. This - antagonizes the effects of histamine on HA-receptors, leading to a reduction of - the negative symptoms brought on by histamine HA-receptor binding. Carbinoxamine''s - anticholinergic action appears to be due to a central antimuscarinic effect, which - also may be responsible for its antiemetic effects, although the exact mechanism - is unknown. - - - === - - - disease: Rhinitis, Vasomotor - - drug: Carbinoxamine - - ' -- completion: 'disease: Protoporphyria, Erythropoietic - - drug: Afamelanotide - - mechanism_links: afamelanotide - increases activity of - melanocyte-stimulating - hormone receptor (human); melanocyte-stimulating hormone receptor (human) - participates - in - melanocortin receptor activity; melanocortin receptor activity - positively - regulates - melanin biosynthetic process; melanin biosynthetic process - positively - correlated with - UV protection; UV protection - negatively correlated with - - HP:0000992; HP:0000992 - manifestation of - Protoporphyria, Erythropoietic - - references: https://go.drugbank.com/drugs/DB04931#BE0002447; https://en.wikipedia.org/wiki/Erythropoietic_protoporphyria' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Patients with erythropoietic porphyria (EPP) have a deficiency of ferrochelatase - (FECH), an enzyme involved in the final step of heme biosynthesis. FECH is required - to insert iron into protoporphyrin IX (PPIX) to generate heme, and a deficiency - in FECH results in accumulation of PPIX (particularly in the liver and superficial - skin vasculature). PPIX molecules are photodynamic - exposure to UV radiation - causes these molecules to form reactive oxygen species that lead to subsequent - tissue damage.[A187199] Activation of MC1R signalling by afamelanotide also instigates - other protective processes, including an increase in antioxidant activity, DNA - repair, and secretion of immunomodulatory proteins such as interleukin-10.[A187202] - - - === - - - disease: Protoporphyria, Erythropoietic - - drug: Afamelanotide - - ' -- completion: 'disease: Prostatitis - - drug: Cephalexin - - mechanism_links: Cephalexin - decreases activity of - PR:Q8DR59; PR:Q8DR59 - positively - regulates - peptidoglycan biosynthetic process; peptidoglycan biosynthetic process - - in taxon - Escherichia coli; Escherichia coli - causes - Prostatitis - - references: https://go.drugbank.com/drugs/DB00567; https://en.wikipedia.org/wiki/Cefalexin#Mechanism_of_action; - https://medlineplus.gov/ency/article/000519.htm' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Cephalexin is a first generation cephalosporin antibiotic.[A179071,A179074] Cephalosporins - contain a beta lactam and dihydrothiazide.[A179071] Unlike penicillins, cephalosprins - are more resistant to the action of beta lactamase.[A179071] Cephalexin inhibits - bacterial cell wall synthesis, leading breakdown and eventualy cell death.[Label] - - - === - - - disease: Prostatitis - - drug: Cephalexin - - ' -- completion: 'disease: Candidiasis, Oral - - drug: Ketoconazole - - mechanism_links: Ketoconazole - decreases activity of - lanosterol 14-alpha demethylase - (Candida albicans SC5314); lanosterol 14-alpha demethylase (Candida albicans SC5314) - - positively regulates - ergosterol biosynthetic process; ergosterol biosynthetic - process - positively correlated with - cell wall biogenesis; cell wall biogenesis - - occurs in - Candida albicans; Candida albicans - causes - Candidiasis, Oral - - references: https://go.drugbank.com/drugs/DB01026#mechanism-of-action; https://drugs.ncats.io/substances?q=%22KETOCONAZOLE%22; - https://www.uniprot.org/uniprot/P10613#function; https://en.wikipedia.org/wiki/Oral_candidiasis' - prompt: "From the text below, extract the following entities in the following format:\n\ - \ndisease: \ndrug: \nmechanism_links: \n\ - \n\nText:\nKetoconazole interacts with 14-&alpha;-sterol demethylase, a cytochrome\ - \ P-450 enzyme necessary for the conversion of lanosterol to ergosterol.[A181802,T116]\ - \ This results in inhibition of ergosterol synthesis and increased fungal cellular\ - \ permeability due to reduced amounts of ergosterol present in the fungal cell\ - \ membrane. This metabolic inhibition also results in accumulation of 14\u03B1\ - -methyl-3,6-diol, a toxic metabolite. The increase in membrane fluidity is also\ - \ thought to produce impairment of membrane-bound enzyme systems as components\ - \ become less closely packed.\n\n===\n\ndisease: Candidiasis, Oral\ndrug: Ketoconazole\n" -- completion: 'disease: Tennis Elbow - - drug: Triamcinolone - - mechanism_links: Triamcinolone - increases activity of - glucocorticoid receptor - (human); glucocorticoid receptor (human) - increases activity of - annexin A1 - (human); glucocorticoid receptor (human) - decreases activity of - prostaglandin - G/H synthase 1 (human); glucocorticoid receptor (human) - decreases activity of - - prostaglandin G/H synthase 2 (human); annexin A1 (human) - decreases activity - of - cytosolic phospholipase A2 (human); prostaglandin G/H synthase 1 (human) - - positively regulates - prostaglandin biosynthetic process; prostaglandin G/H - synthase 2 (human) - positively regulates - prostaglandin biosynthetic process; - cytosolic phospholipase A2 (human) - positively regulates - leukotriene biosynthetic - process; cytosolic phospholipase A2 (human) - positively regulates - prostaglandin - biosynthetic process; leukotriene biosynthetic process - positively correlated - with - inflammatory response; prostaglandin biosynthetic process - positively - correlated with - inflammatory response; inflammatory response - has phenotype - - HP:0012531; inflammatory response - positively correlated with - HP:0100261; - HP:0012531 - manifestation of - Tennis Elbow; HP:0100261 - manifestation of - - Tennis Elbow - - references: https://go.drugbank.com/drugs/DB00620#mechanism-of-action; https://www.cancer.gov/publications/dictionaries/cancer-drug/def/triamcinolone; - https://www.ncbi.nlm.nih.gov/books/NBK544309/; https://www.uniprot.org/uniprot/P04150#function; - https://www.uniprot.org/uniprot/P04083#function; https://www.uniprot.org/uniprot/P47712#function; - https://www.uniprot.org/uniprot/P23219#function; https://www.uniprot.org/uniprot/P35354#function; - https://en.wikipedia.org/wiki/Tennis_elbow' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Corticosteroids like triamcinolone inhibit phospholipase A2 on cell membranes, - preventing the breakdown of lysosomal membranes of leukocytes, which in turn prevent - the formation of arachidonic acid, which decrease expression of cyclooxygenase - and lipoxygenase, inhibiting synthesis of prostaglandins and leukotrienes.[A184463] - Anti-inflammatory activity occurs via reversal of vascular dilation and reducing - permeability, which prevents macrophage and leukocyte migration.[A184463] Triamcinolone - also inhibits nuclear factor kappa-B, which decreases the production of pro-inflammatory - signals such as interleukin-6, interleukin-8, and monocyte chemoattractant protein-1.[A184463] - - - === - - - disease: Tennis Elbow - - drug: Triamcinolone - - ' -- completion: 'disease: Esotropia - - drug: Echothiophate - - mechanism_links: Echothiophate Iodide - decreases activity of - acetylcholinesterase - (human); Echothiophate Iodide - decreases activity of - cholinesterase (human); - cholinesterase (human) - positively regulates - acetylcholinesterase activity; - acetylcholinesterase activity - decreases abundance of - Acetylcholine; acetylcholinesterase - (human) - positively regulates - acetylcholine catabolic process; acetylcholine - catabolic process - decreases abundance of - Acetylcholine; Acetylcholine - negatively - correlated with - HP:0000549; HP:0000549 - manifestation of - Esotropia - - references: https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL1201341/; - https://go.drugbank.com/drugs/DB01057#BE0002180' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Echothiophate Iodide is a long-acting cholinesterase inhibitor for topical use - which enhances the effect of endogenously liberated acetylcholine in iris, ciliary - muscle, and other parasympathetically innervated structures of the eye. Echothiophate - iodide binds irreversibly to cholinesterase, and is long acting due to the slow - rate of hydrolysis by cholinesterase. It causes miosis, increase in facility of - outflow of aqueous humor, fall in intraocular pressure, and potentiation of accommodation. - - - === - - - disease: Esotropia - - drug: Echothiophate - - ' -- completion: 'disease: Gastroesophageal Reflux - - drug: Potassium bicarbonate - - mechanism_links: potassium bicarbonate - negatively regulates - Gastric Acid; - Gastric Acid - positively correlated with - Gastroesophageal Reflux - - references: https://go.drugbank.com/drugs/DB11098' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - The antacid potential of potassium bicarbonate is attained by increasing the gastrointestinal - pH by neutralizing hydrochloric acid.[T144] The increase in pH results in suppression - of the action of pepsin which is the enzyme that exacerbates ulceration due to - the presence of acid.[T143] - - - === - - - disease: Gastroesophageal Reflux - - drug: Potassium bicarbonate - - ' -- completion: 'disease: Obesity - - drug: Fenfluramine - - mechanism_links: Fenfluramine - increases activity of - 5-hydroxytryptamine receptor - 1D (human); 5-hydroxytryptamine receptor 1D (human) - positively correlated with - - Serotonin; Serotonin - negatively regulates - positive regulation of appetite; - positive regulation of appetite - positively correlated with - Obesity - - references: https://go.drugbank.com/drugs/DB00574; https://pubmed.ncbi.nlm.nih.gov/2692639/' - prompt: "From the text below, extract the following entities in the following format:\n\ - \ndisease: \ndrug: \nmechanism_links: \n\ - \n\nText:\nDravet syndrome is a complex pediatric encephalopathy characterized\ - \ by recurrent pharmacoresistant seizures of variable type, delayed development,\ - \ and in many cases, impairment in speech, language, gait, and other neurocognitive\ - \ functions.[A214694, A214709, A214712, A214715] Despite substantial variation\ - \ in presentation and severity, roughly 80% of patients with Dravet syndrome have\ - \ mutations in the _SCN1A_ gene, which encodes the alpha subunit of a voltage-gated\ - \ sodium channel (Na<sub>v</sub>1.1).[A214685, A214688, A214691, A214700,\ - \ A214709, A214715] This channel is predominantly localized in inhibitory GABAergic\ - \ interneurons as well as in excitatory pyramidal neurons; it is thought that\ - \ dysfunction of neurotransmission regulation results in the seizures and other\ - \ corresponding symptoms of Dravet syndrome.[A214700, A214709] Although the exact\ - \ mechanism by which stimulation/inhibition of various receptors leads to the\ - \ observed therapeutic benefit is unclear, it is hypothesized to be two-fold.\ - \ Stimulation of 5-HT<sub>1D</sub> and 5-HT<sub>2C</sub>\ - \ may result in increased GABAergic neurotransmission, while \u03C31 receptor\ - \ antagonism may help to modulate responses to _N_-methyl-D-aspartate (NMDA).[A214700]\n\ - \n===\n\ndisease: Obesity\ndrug: Fenfluramine\n" -- completion: 'disease: Enterocolitis - - drug: Clidinium - - mechanism_links: clidinium - negatively regulates - muscarinic acetylcholine receptor - M1 (human); muscarinic acetylcholine receptor M1 (human) - positively regulates - - smooth muscle contraction; smooth muscle contraction - positively correlated - with - gastric acid secretion; smooth muscle contraction - positively correlated - with - HP:0003394; gastric acid secretion - correlated with - Enterocolitis; HP:0003394 - - correlated with - Enterocolitis - - references: https://go.drugbank.com/drugs/DB00771#mechanism-of-action; https://en.wikipedia.org/wiki/Clidinium_bromide#Mechanism_of_action' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Inhibits muscarinic actions of acetylcholine at postganglionic parasympathetic - neuroeffector sites primarily by inhibiting the M1 muscarinic receptors. - - - === - - - disease: Enterocolitis - - drug: Clidinium - - ' -- completion: 'disease: Common Cold - - drug: Carbinoxamine - - mechanism_links: carbinoxamine - decreases activity of - histamine H1 receptor - (human); histamine H1 receptor (human) - positively regulates - cellular response - to histamine; cellular response to histamine - positively correlated with - Histamine; - Histamine - participates in - inflammatory response; inflammatory response - caused - by - NCBITaxon:12058; NCBITaxon:12058 - causes - Common Cold - - references: https://go.drugbank.com/drugs/DB00748#mechanism-of-action; https://www.uniprot.org/uniprot/P35367#function' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Carbinoxamine competes with free histamine for binding at HA-receptor sites. This - antagonizes the effects of histamine on HA-receptors, leading to a reduction of - the negative symptoms brought on by histamine HA-receptor binding. Carbinoxamine''s - anticholinergic action appears to be due to a central antimuscarinic effect, which - also may be responsible for its antiemetic effects, although the exact mechanism - is unknown. - - - === - - - disease: Common Cold - - drug: Carbinoxamine - - ' -- completion: 'disease: Nausea - - drug: Triflupromazine - - mechanism_links: Triflupromazine - decreases activity of - muscarinic acetylcholine - receptor M2 (human); muscarinic acetylcholine receptor M2 (human) - located in - - upper digestive tract; upper digestive tract - decreases activity of - gastric - acid secretion; gastric acid secretion - correlated with - Nausea - - references: https://go.drugbank.com/drugs/DB00508#mechanismofaction' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Triflupromazine binds to the dopamine D1 and dopamine D2 receptors and inhibits - their activity. The mechanism of the anti-emetic effect is due predominantly to - blockage of the dopamine D2 neurotransmitter receptors in the chemoreceptor trigger - zone (CTZ) and vomiting centre. Triflupromazine blocks the neurotransmitter dopamine - and the vagus nerve in the gastrointestinal tract. Triflupromazine also binds - the muscarinic acetylcholine receptors (M1 and M2) and the tryptamine D receptors - (5HT<sub>2B</sub>). - - - === - - - disease: Nausea - - drug: Triflupromazine - - ' -- completion: 'disease: Angina Pectoris - - drug: Bepridil - - mechanism_links: Bepridil - decreases activity of - sodium/potassium-transporting - ATPase subunit alpha-1 (human); sodium/potassium-transporting ATPase subunit alpha-1 - (human) - positively regulates - sodium ion export across plasma membrane; sodium - ion export across plasma membrane - positively correlated with - calcium ion import; - calcium ion import - positively correlated with - Myocardial Ischemia; Myocardial - Ischemia - positively correlated with - Angina Pectoris - - references: https://go.drugbank.com/drugs/DB01244#BE0000732 https://www.ahajournals.org/doi/full/10.1161/01.STR.29.3.705' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Bepridil has inhibitory effects on both the slow calcium (L-type) and fast sodium - inward currents in myocardial and vascular smooth muscle, interferes with calcium - binding to calmodulin, and blocks both voltage and receptor operated calcium channels. - Bepridil inhibits the transmembrane influx of calcium ions into cardiac and vascular - smooth muscle. This has been demonstrated in isolated myocardial and vascular - smooth muscle preparations in which both the slope of the calcium dose response - curve and the maximum calcium-induced inotropic response were significantly reduced - by bepridil. In cardiac myocytes <i>in vitro</i>, bepridil was shown - to be tightly bound to actin. Bepridil regularly reduces heart rate and arterial - pressure at rest and at a given level of exercise by dilating peripheral arterioles - and reducing total peripheral resistance (afterload) against which the heart works. - - - === - - - disease: Angina Pectoris - - drug: Bepridil - - ' -- completion: 'disease: Lymphoma, Non-Hodgkin - - drug: Pixantrone - - mechanism_links: pixantrone - increases abundance of - DNA Adducts; DNA Adducts - - decreases activity of - DNA topoisomerase 2-alpha (human); DNA topoisomerase - 2-alpha (human) - positively regulates - cellular response to DNA damage stimulus; - cellular response to DNA damage stimulus - positively regulates - apoptotic chromosome - condensation; apoptotic chromosome condensation - positively correlated with - - cell death; cell death - decreases abundance of - neoplastic cell; neoplastic - cell - manifestation of - Lymphoma, Non-Hodgkin - - references: https://go.drugbank.com/drugs/DB06193; https://en.wikipedia.org/wiki/Pixantrone' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Pixantrone is an aza-anthracenedione which acts as a DNA intercalator. By intercalating - between DNA, with modest affinity, it stimulates DNA cleavage by topoisomerase - II. (Pixantrone acts as a poison to topoisomerase II by stabilizing protein-DNA - complexes which are usually transient, giving rise to double stranded DNA breaks.) - The first line agent doxorubicin is cardiotoxic, in part, due to its ability to - redox activate the superoxide anion and hydrogen peroxide, and form a long-lived - secondary alcohol metabolite: doxorubicinol. [3] Clearance of doxorubicin from - myocardial tissue is incomplete, and it can be found months or years after the - last administration. [3] In doxorubicin treated ex vivo cardiac strips, pixantrone - formed an N-dealkylated product that inhibited metabolism of residual doxorubicin - into doxorubicinol. Additionally, in ex vivo human myocardial strips (doxorubicin - naive, and doxorubicin pretreated) pixantrone showed high cardiac uptake without - formation of superoxide anion or hydrogen peroxide. Pixantrones lack of cardiotoxicity - is thus attributed to its redox inactivity and inhibition of doxorubicinol formation. - [3] - - - === - - - disease: Lymphoma, Non-Hodgkin - - drug: Pixantrone - - ' -- completion: 'disease: Dermatitis, Seborrheic - - drug: Halcinonide - - mechanism_links: Halcinonide - positively regulates - glucocorticoid receptor - (human); glucocorticoid receptor (human) - negatively correlated with - HP:0001019; - HP:0001019 - manifestation of - Dermatitis, Seborrheic - - references: https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL1200845/; - https://en.wikipedia.org/wiki/Halcinonide; https://pubchem.ncbi.nlm.nih.gov/compound/443943#section=Mechanism-of-Action; - https://en.wikipedia.org/wiki/Corticosteroid#Pharmacology' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - The precise mechanism of action of topical corticosteroids is unclear. However - they possess anti-inflammatory, antipruritic, and vasoconstrictive actions. New - research indicates that halcinonide activates MBP (myelin basic protein) expression - via smoothened receptor activation. This finding suggests that halcinonide could - be used in the treatment of multiple sclerosis therapy as an alternative to Dexamethasone - or Methylprednisolone. - - - === - - - disease: Dermatitis, Seborrheic - - drug: Halcinonide - - ' -- completion: 'disease: Hyperglycemia - - drug: Inulin - - mechanism_links: Inulin - positively regulates - negative regulation of appetite; - negative regulation of appetite - prevents - Hyperglycemia' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - As a diagnostic agent, inulin is readily soluble and essentially indigestible. - It readily passes through the blood and into the urine. It is neither secreted - nor resorbed by the kidney making it an excellent indicator for renal clearance - rates. The inulin clearance test has largely been succeeded by the creatinine - clearance test as a measure of glomerular filtration rate. Inulin is a hypoglycemic - agent. Since it is not digestible by human enzymes ptyalin and amylase, inulin - passes through much of the digestive system intact. It is only in the colon that - bacteria metabolise inulin, with the release of significant quantities of carbon - dioxide and/or methane. Because inulin is not broken down into simple sugars (monosaccharides) - by normal digestion, it does not elevate blood sugar levels, hence, helping diabetics - regulate blood sugar levels. - - - === - - - disease: Hyperglycemia - - drug: Inulin - - ' -- completion: 'disease: Tinea Pedis - - drug: Benzocaine - - mechanism_links: Benzocaine - decreases activity of - sodium channel protein type - 10 subunit alpha (human); sodium channel protein type 10 subunit alpha (human) - - participates in - voltage-gated sodium channel activity; voltage-gated sodium - channel activity - increases transport of - Sodium; Sodium - positively correlated - with - membrane depolarization; membrane depolarization - positively regulates - - neuronal action potential; neuronal action potential - occurs in - pain receptor - cell; pain receptor cell - participates in - sensory perception of pain; sensory - perception of pain - occurs in - Tinea Pedis - - references: https://go.drugbank.com/drugs/DB01086; https://en.wikipedia.org/wiki/Benzocaine' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Benzocaine binds to sodium channels and reversibly stabilizes the neuronal membrane - which decreases its permeability to sodium ions. Depolarization of the neuronal - membrane is inhibited thereby blocking the initiation and conduction of nerve - impulses. - - - === - - - disease: Tinea Pedis - - drug: Benzocaine - - ' -- completion: 'disease: Depressive Disorder - - drug: Amoxapine - - mechanism_links: Amoxapine - negatively regulates - sodium-dependent serotonin - transporter (human); sodium-dependent serotonin transporter (human) - positively - regulates - serotonin uptake; serotonin uptake - positively correlated with - - Depressive Disorder - - references: https://go.drugbank.com/drugs/DB00543#mechanism-of-action; https://en.wikipedia.org/wiki/Amoxapine#Pharmacology' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Amoxapine acts by decreasing the reuptake of norepinephrine and serotonin (5-HT). - - - === - - - disease: Depressive Disorder - - drug: Amoxapine - - ' -- completion: 'disease: HIV Infections - - drug: Abacavir - - mechanism_links: abacavir - increases abundance of - carbovir triphosphate; carbovir - triphosphate - decreases activity of - gag-pol polyprotein (human immunodeficiency - virus type 1 group M subtype B (isolate HXB2)); gag-pol polyprotein (human immunodeficiency - virus type 1 group M subtype B (isolate HXB2)) - participates in - viral DNA genome - replication; viral DNA genome replication - causes - HIV Infections' - prompt: "From the text below, extract the following entities in the following format:\n\ - \ndisease: \ndrug: \nmechanism_links: \n\ - \n\nText:\nAbacavir is a carbocyclic synthetic nucleoside analogue and an antiviral\ - \ agent. Intracellularly, abacavir is converted by cellular enzymes to the active\ - \ metabolite carbovir triphosphate, an analogue of deoxyguanosine-5'-triphosphate\ - \ (dGTP). Carbovir triphosphate inhibits the activity of HIV-1 reverse transcriptase\ - \ (RT) both by competing with the natural substrate dGTP and by its incorporation\ - \ into viral DNA. Viral DNA growth is terminated because the incorporated nucleotide\ - \ lacks a 3'-OH group, which is needed to form the 5\u2032 to 3\u2032 phosphodiester\ - \ linkage essential for DNA chain elongation.\n\n===\n\ndisease: HIV Infections\n\ - drug: Abacavir\n" -- completion: 'disease: Humoral Hypercalcemia Of Malignancy - - drug: Pamidronic acid - - mechanism_links: pamidronate - decreases activity of - farnesyl pyrophosphate - synthase (human); pamidronate - decreases activity of - geranylgeranyl pyrophosphate - synthase (human); pamidronate - molecularly interacts with - hydroxylapatite; - hydroxylapatite - positively correlated with - ossification; hydroxylapatite - - positively correlated with - bone regeneration; farnesyl pyrophosphate synthase - (human) - positively correlated with - isoprenoid biosynthetic process; geranylgeranyl - pyrophosphate synthase (human) - positively correlated with - isoprenoid biosynthetic - process; isoprenoid biosynthetic process - positively regulates - osteoclast; - osteoclast - positively correlated with - bone resorption; bone resorption - positively - correlated with - Humoral Hypercalcemia Of Malignancy; ossification - negatively - correlated with - Humoral Hypercalcemia Of Malignancy; bone regeneration - negatively - correlated with - Humoral Hypercalcemia Of Malignancy - - references: https://go.drugbank.com/drugs/DB00282; https://pubchem.ncbi.nlm.nih.gov/compound/4674' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Bisphosphonates are taken into the bone where they bind to hydroxyapatite. Bone - resorption by osteoclasts causes local acidification, releasing the bisphosphonate, - which is taken into the osteoclast by fluid-phase endocytosis.[A959] Endocytic - vesicles become acidified, releasing bisphosphonates into the cytosol of osteoclasts - where they act.[A959] Nitrogen containing bisphosphonates such as pamidronate - are known to induce apoptosis of hematopoietic tumor cells by inhibiting the components - of the mevalonate pathway farnesyl diphosphate synthase, farnesyl diphosphate, - and geranylgeranyl diphosphate.[A202769,A203123,A203111] These components are - essential for post-translational prenylation of GTP-binding proteins like Rap1.[A202769,A203123] - The lack of prenylation of these proteins interferes with their function, and - in the case of Rap1, leads to apoptosis.[A202769,A203123] pamidronate also activated - caspases 3 and 9 which further contribute to apoptosis.[A202769,A203123,A203177] - - - === - - - disease: Humoral Hypercalcemia Of Malignancy - - drug: Pamidronic acid - - ' -- completion: 'disease: Stevens-Johnson Syndrome - - drug: Prednisolone - - mechanism_links: Prednisolone - increases activity of - glucocorticoid receptor - (human); glucocorticoid receptor (human) - increases activity of - annexin A1 - (human); glucocorticoid receptor (human) - decreases activity of - prostaglandin - G/H synthase 1 (human); glucocorticoid receptor (human) - decreases activity of - - prostaglandin G/H synthase 2 (human); annexin A1 (human) - decreases activity - of - cytosolic phospholipase A2 (human); prostaglandin G/H synthase 1 (human) - - positively regulates - prostaglandin biosynthetic process; prostaglandin G/H - synthase 2 (human) - positively regulates - prostaglandin biosynthetic process; - cytosolic phospholipase A2 (human) - positively regulates - leukotriene biosynthetic - process; cytosolic phospholipase A2 (human) - positively regulates - prostaglandin - biosynthetic process; leukotriene biosynthetic process - positively correlated - with - inflammatory response; prostaglandin biosynthetic process - positively - correlated with - inflammatory response; inflammatory response - contributes to - - HP:0008066; HP:0008066 - manifestation of - Stevens-Johnson Syndrome - - references: https://go.drugbank.com/drugs/DB00860#mechanism-of-action; https://www.uniprot.org/uniprot/P04150#function; - https://www.uniprot.org/uniprot/P04083#function; https://www.uniprot.org/uniprot/P47712#function; - https://www.uniprot.org/uniprot/P23219#function; https://www.uniprot.org/uniprot/P35354#function; - https://en.wikipedia.org/wiki/Stevens%E2%80%93Johnson_syndrome' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - The short term effects of corticosteroids are decreased vasodilation and permeability - of capillaries, as well as decreased leukocyte migration to sites of inflammation.[A187463] - Corticosteroids binding to the glucocorticoid receptor mediates changes in gene - expression that lead to multiple downstream effects over hours to days.[A187463] - Lower doses of corticosteroids provide an anti-inflammatory effect, while higher - doses are immunosuppressive.[A187463] High doses of glucocorticoids for an extended - period bind to the mineralocorticoid receptor, raising sodium levels and decreasing - potassium levels.[A187463] - - - === - - - disease: Stevens-Johnson Syndrome - - drug: Prednisolone - - ' -- completion: 'disease: Carcinoma, Non-Small-Cell Lung - - drug: Vinorelbine - - mechanism_links: vinorelbine - decreases activity of - InterPro:IPR000217; InterPro:IPR000217 - - positively regulates - G2/M transition of mitotic cell cycle; G2/M transition - of mitotic cell cycle - positively correlated with - cell division; cell division - - positively correlated with - HP:0031377; HP:0031377 - positively correlated - with - Carcinoma, Non-Small-Cell Lung - - references: https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL553025/; https://go.drugbank.com/drugs/DB00361#mechanism-of-action; - https://en.wikipedia.org/wiki/Vinorelbine#Pharmacology' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Vinca alkaloids are structurally similar compounds composed of two multi-ringed - units, _vindoline_, and _catharanthine_. _Vinorelbine tartrate_ is a vinca alkaloid - in which the catharanthine component is the target of structural modification - [L2005], [L2006]. - - - === - - - disease: Carcinoma, Non-Small-Cell Lung - - drug: Vinorelbine - - ' -- completion: 'disease: Bronchial Spasm - - drug: Dyphylline - - mechanism_links: Dyphylline - decreases activity of - InterPro:IPR043371; InterPro:IPR043371 - - increases abundance of - Cyclic AMP; Cyclic AMP - causes - response to bronchodilator; - response to bronchodilator - enables - relaxation of smooth muscle; relaxation - of smooth muscle - located in - bronchus; bronchus - contributes to - vasodilation; - vasodilation - correlated with - Bronchial Spasm - - references: https://go.drugbank.com/drugs/DB00651#mechanismofaction' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - The bronchodilatory action of dyphylline, as with other xanthines, is thought - to be mediated through competitive inhibition of phosphodiesterase with a resulting - increase in cyclic AMP producing relaxation of bronchial smooth muscle as well - as antagonism of adenosine receptors. - - - === - - - disease: Bronchial Spasm - - drug: Dyphylline - - ' -- completion: 'disease: Urticaria - - drug: Azatadine - - mechanism_links: azatadine - decreases activity of - histamine H1 receptor (human); - histamine H1 receptor (human) - positively regulates - histamine receptor activity; - histamine receptor activity - participates in - cellular response to histamine; - cellular response to histamine - positively correlated with - inflammatory response; - inflammatory response - causes - Urticaria - - references: https://go.drugbank.com/drugs/DB00719; https://en.wikipedia.org/wiki/Antihistamine#H1-antihistamines; - https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL946/' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Antihistamines such as azatadine appear to compete with histamine for histamine - H1- receptor sites on effector cells. The antihistamines antagonize those pharmacological - effects of histamine which are mediated through activation of H1- receptor sites - and thereby reduce the intensity of allergic reactions and tissue injury response - involving histamine release. - - - === - - - disease: Urticaria - - drug: Azatadine - - ' -- completion: 'disease: Heart Failure - - drug: Levosimendan - - mechanism_links: simendan - increases stability of - troponin C, slow skeletal - and cardiac muscles (human); troponin C, slow skeletal and cardiac muscles (human) - - positively regulates - heart contraction; heart contraction - negatively correlated - with - Heart Failure; simendan - increases activity of - ATP-sensitive inward - rectifier potassium channel 11 (human); simendan - increases activity of - ATP-sensitive - inward rectifier potassium channel 8 (human); ATP-sensitive inward rectifier potassium - channel 11 (human) - positively regulates - relaxation of smooth muscle; ATP-sensitive - inward rectifier potassium channel 8 (human) - positively regulates - relaxation - of smooth muscle; relaxation of smooth muscle - positively regulates - vasodilation; - vasodilation - negatively correlated with - HP:0000822; HP:0000822 - affects risk - for - Heart Failure - - references: https://go.drugbank.com/drugs/DB00922' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Levosimendan appears to increase myofilament calcium sensitivity by binding to - cardiac troponin C in a calcium-dependent manner. This stabilizes the calcium-induced - conformational change of troponin C, thereby (1) changing actin-myosin cross-bridge - kinetics apparently without increasing the cycling rate of the cross-bridges or - myocardial ATP consumption, (2) increasing the effects of calcium on cardiac myofilaments - during systole and (3) improving contraction at low energy cost (inotropic effect). - Calcium concentration and, therefore, sensitization decline during diastole, allowing - normal or improved diastolic relaxation. Levosimendan also leads to vasodilation - through the opening of ATP-sensitive potassium channels. By these inotropic and - vasodilatory actions, levosimendan increases cardiac output without increasing - myocardial oxygen demand. Levosimendan also has a selective phosphodiesterase - (PDE)-III inhibitory action that may contribute to the inotropic effect of this - compound under certain experimental conditions. It has been reported that levosimendan - may act preferentially as a Ca<sup>2+</sup> sensitizer at lower concentrations, - whereas at higher concentrations its action as a PDE-III inhibitor becomes more - prominent in experimental animals and humans. - - - === - - - disease: Heart Failure - - drug: Levosimendan - - ' -- completion: 'disease: Dacryocystitis - - drug: Fusidic acid - - mechanism_links: Fusidic Acid - decreases activity of - PR:P68790; PR:P68790 - - positively regulates - translation; translation - occurs in - Staphylococcus aureus; - Staphylococcus aureus - causes - Dacryocystitis - - references: https://go.drugbank.com/drugs/DB02703#mechanism-of-action; https://en.wikipedia.org/wiki/Fusidic_acid; - https://www.uniprot.org/uniprot/P68790#function; https://en.wikipedia.org/wiki/Dacryocystitis' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Fusidic acid works by interfering with bacterial protein synthesis, specifically - by preventing the translocation of the elongation factor G (EF-G) from the ribosome. - It also can inhibit chloramphenicol acetyltransferase enzymes. - - - === - - - disease: Dacryocystitis - - drug: Fusidic acid - - ' -- completion: 'disease: Hypertension, Pulmonary - - drug: Epoprostenol - - mechanism_links: Epoprostenol - positively correlated with - prostacyclin receptor - (human); prostacyclin receptor (human) - positively regulates - prostacyclin receptor - activity; prostacyclin receptor activity - positively regulates - vasodilation; - vasodilation - negatively correlated with - HP:0032263; HP:0032263 - manifestation - of - Hypertension, Pulmonary - - references: https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL1139/; https://go.drugbank.com/drugs/DB01240#BE0000475' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Prostaglandins are present in most body tissues and fluids and mediate many biological - functions. Epoprostenol (PGI2) is a member of the family of prostaglandins that - is derived from arachidonic acid. The major pharmacological actions of epoprostenol - is ultimately inhibition of platelet aggregation. Prostacycline (PGI2) from endothelial - cells activate G protein-coupled receptors on platelets and endothelial cells. - This activation causes adenylate cyclase to produce cyclic AMP which inhibits - further platelet activation and activates protein kinase A. Cyclic AMP also prevents - coagulation by preventing an increase in intracellular calcium from thromboxane - A2 binding. PKA then continues the cascade by phosphorylating and inhibiting myosin - light-chain kinase which leads to smooth muscle relaxation and vasodilation. Notably, - PGI2 and TXA2 work as physiological antagonists. - - - === - - - disease: Hypertension, Pulmonary - - drug: Epoprostenol - - ' -- completion: 'disease: Hepatic Encephalopathy - - drug: Erythromycin - - mechanism_links: Erythromycin Ethylsuccinate - negatively regulates - RNA, Ribosomal, - 23S; RNA, Ribosomal, 23S - participates in - translation; translation - occurs - in - Bacteria; Bacteria - causes - Hepatic Encephalopathy - - references: https://go.drugbank.com/drugs/DB00199#mechanism-of-action; https://www.rxlist.com/erythromycin-ethylsuccinate-drug.htm; - https://en.wikipedia.org/wiki/Hepatic_encephalopathy' - prompt: "From the text below, extract the following entities in the following format:\n\ - \ndisease: \ndrug: \nmechanism_links: \n\ - \n\nText:\nIn order to replicate, bacteria require a specific process of protein\ - \ synthesis, enabled by ribosomal proteins.[A6505] Erythromycin acts by inhibition\ - \ of protein synthesis by binding to the 23S ribosomal RNA molecule in the 50S\ - \ subunit of ribosomes in susceptible bacterial organisms. It stops bacterial\ - \ protein synthesis by inhibiting the transpeptidation/translocation step of protein\ - \ synthesis and by inhibiting the assembly of the 50S ribosomal subunit.[L7261,A14179]\ - \ This results in the control of various bacterial infections.[A174193,L7261]\ - \ The strong affinity of macrolides, including erythromycin, for bacterial ribosomes,\ - \ supports their broad\u2010spectrum antibacterial activities.[A174193]\n\n===\n\ - \ndisease: Hepatic Encephalopathy\ndrug: Erythromycin\n" -- completion: 'disease: Chlamydial Pneumonia - - drug: Sparfloxacin - - mechanism_links: sparfloxacin - decreases activity of - PR:Q9Z7I9; sparfloxacin - - decreases activity of - PR:Q54A16; PR:Q9Z7I9 - participates in - bacterial-type - DNA replication; PR:Q54A16 - participates in - bacterial-type DNA replication; - bacterial-type DNA replication - occurs in - NCBITaxon:83558; NCBITaxon:83558 - - causes - Chlamydial Pneumonia - - references: https://go.drugbank.com/drugs/DB01208#mechanism-of-action' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - The bactericidal action of sparfloxacin results from inhibition of the enzymes - topoisomerase II (DNA gyrase) and topoisomerase IV, which are required for bacterial - DNA replication, transcription, repair, and recombination. - - - === - - - disease: Chlamydial Pneumonia - - drug: Sparfloxacin - - ' -- completion: 'disease: Hypertension - - drug: Eprosartan - - mechanism_links: eprosartan - negatively regulates - type-1 angiotensin II receptor - (human); type-1 angiotensin II receptor (human) - positively correlated with - - Angiotensin II; Angiotensin II - positively regulates - Vasoconstriction; Vasoconstriction - - positively correlated with - HP:0032263; HP:0032263 - positively correlated - with - Hypertension - - references: https://go.drugbank.com/drugs/DB00876' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Eprosartan blocks the vasoconstrictor and aldosterone-secreting effects of angiotensin - II by selectively blocking the binding of angiotensin II to the AT<sub>1</sub> - receptor found in many tissues (e.g., vascular smooth muscle, adrenal gland). - There is also an AT<sub>2</sub> receptor found in many tissues but - it is not known to be associated with cardiovascular homeostasis. Eprosartan does - not exhibit any partial agonist activity at the AT<sub>1</sub> receptor. - Its affinity for the AT<sub>1</sub> receptor is 1,000 times greater - than for the AT<sub>2</sub> receptor. In vitro binding studies indicate - that eprosartan is a reversible, competitive inhibitor of the AT<sub>1</sub> - receptor. Eprosartan has also been shown to bind to AT<sub>1</sub> - receptors both presynaptically and synaptically. Its action on presynaptic AT<sub>1</sub> - receptors results in the inhibition of sympathetically stimulated noradrenaline - release. Unlike ACE inhibitors, eprosartan and other ARBs do not interfere with - response to bradykinins and substance P, which allows for the absence of adverse - effects that are present in ACE inhibitors (eg. dry cough). - - - === - - - disease: Hypertension - - drug: Eprosartan - - ' -- completion: 'disease: Tinea Pedis - - drug: Luliconazole - - mechanism_links: 4-(2,4-dichlorophenyl)-1,3-dithiolan-2-ylidene-1-imidazolylacetonitrile - - negatively regulates - InterPro:IPR001128; InterPro:IPR001128 - positively regulates - - ergosterol biosynthetic process; ergosterol biosynthetic process - in taxon - - NCBITaxon:5551; NCBITaxon:5551 - causes - Tinea Pedis - - references: https://go.drugbank.com/drugs/DB08933; https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL2105689/; - https://en.wikipedia.org/wiki/Antifungal#Azoles' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - The exact mechanism of action for luliconazole''s anti-fungal activity is still - not known, but luliconazole is thought to inhibit the enzyme lanosterol demethylase. - Lanosterol demethylase is needed for the synthesis of ergosterol, which is a major - component of the fungus cell membranes. - - - === - - - disease: Tinea Pedis - - drug: Luliconazole - - ' -- completion: 'disease: Adenocarcinoma, Follicular - - drug: Lenvatinib - - mechanism_links: lenvatinib - decreases activity of - platelet-derived growth - factor receptor alpha (human); platelet-derived growth factor receptor alpha (human) - - disrupts - cellular process; cellular process - located in - malignant cell; - malignant cell - participates in - Adenocarcinoma, Follicular - - references: https://go.drugbank.com/drugs/DB09078#mechanismofaction' - prompt: "From the text below, extract the following entities in the following format:\n\ - \ndisease: \ndrug: \nmechanism_links: \n\ - \n\nText:\nLenvatinib is a receptor tyrosine kinase (RTK) inhibitor that inhibits\ - \ the kinase activities of vascular endothelial growth factor (VEGF) receptors\ - \ VEGFR1 (FLT1), VEGFR2 (KDR), and VEGFR3 (FLT4). Lenvatinib also inhibits other\ - \ RTKs that have been implicated in pathogenic angiogenesis, tumor growth, and\ - \ cancer progression in addition to their normal cellular functions, including\ - \ fibroblast growth factor (FGF) receptors FGFR1, 2, 3, and 4; the platelet derived\ - \ growth factor receptor alpha (PDGFR\u03B1), KIT, and RET.\n\n===\n\ndisease:\ - \ Adenocarcinoma, Follicular\ndrug: Lenvatinib\n" -- completion: 'disease: Constipation - - drug: Magnesium hydroxide - - mechanism_links: Magnesium Hydroxide - subclass of - Laxatives; Laxatives - positively - correlated with - defecation; defecation - negatively correlated with - Constipation - - references: https://go.drugbank.com/drugs/DB09104' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - The suspension of magnesium hydroxide is ingested and enters the stomach. According - to the amount ingested, the magnesium hydroxide will either act as an antacid - or a laxative. Through the ingestion of 2-5 grams (in adults) the magnesium hydroxide - acts as a laxative in the colon. The majority of the suspension is not absorbed - in the intestinal tract and will create an osmotic effect to draw water into the - gut from surrounding tissues. With this increase of water in the intestines, the - feces will soften and the intraluminal volume of the feces will increase. These - effects still stimulate intestinal motility and induce the urge to defecate. Magnesium - hydroxide will also release cholecystokinin (CKK) in the intestines which will - accumulate water and electrolytes in the lumen and furthermore increase intestinal - motility. - - - === - - - disease: Constipation - - drug: Magnesium hydroxide - - ' -- completion: 'disease: Atrial Fibrillation - - drug: Quinidine - - mechanism_links: Quinidine - disrupts - InterPro:PR001696; InterPro:PR001696 - - positively regulates - cardiac conduction; cardiac conduction - positively correlated - with - cardiac muscle contraction; cardiac muscle contraction - positively correlated - with - Atrial Fibrillation - - references: https://pubchem.ncbi.nlm.nih.gov/compound/441074; https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL1294/; - https://www.drugs.com/pro/quinidine-gluconate.html#s-34090-1' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Quinidine acts on sodium channels on the neuronal cell membrane, limiting the - spread of seizure activity and reducing seizure propagation. The antiarrhythmic - actions are mediated through effects on sodium channels in Purkinje fibers. Quinidine - may also act on the slow inward calcium current (ICa), the rapid (IKr) and slow - (IKs) components of the delayed potassium rectifier current, the inward potassium - rectifier current (IKI), the ATP-sensitive potassium channel (IKATP) and Ito. - - - === - - - disease: Atrial Fibrillation - - drug: Quinidine - - ' -- completion: 'disease: Avitaminosis - - drug: Sodium fluoride - - mechanism_links: Sodium Fluoride - contraindicated for - Avitaminosis - - references: https://go.drugbank.com/drugs/DB09325; https://www.sciencedirect.com/science/article/abs/pii/S0736574815300630' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - The prevention of dental caries by topical fluoride is achieved by various mechanisms.[A181703] - Sodium fluoride kills bacteria that cause caries, such a Streptococcus mutans - and lactobacilli[A181718] by interfering with their metabolic activities that - result in the formation of lactic acid. Fluoride ions cause the inhibition of - glycolytic and other enzymes involved in bacterial metabolism. It changes the - permeability of cell membranes, lowering the pH in the cytoplasm of the cell, - leading to a decrease in acidity, which is normally implicated in tooth decay.[A181652] When - administered at low topical doses, fluoride in both saliva and plaque and saliva - prevent the demineralization of healthy tooth enamel while remineralizing teeth - that have previously been demineralized. Sodium fluoride is absorbed by the surface - of hydroxyapatite crystals on the teeth, which are necessary for mineralization. - This renders the teeth more resistant to demineralization by changing the apatite - crystal solubility.[A181670,A181694] Sodium fluoride inhibits the demineralization - of teeth in a pH-related manner. When used in high doses, in formulations such - as the fluoride varnishes or gels, sodium fluoride forms a layer on the surface - of tooth enamel. When the pH of the mouth is reduced due to acid production by - bacteria such as S.mutans, fluoride is released, interfering with bacterial metabolism, - and then acts to remineralize the teeth.[A181652,A181694,L7688] - - - === - - - disease: Avitaminosis - - drug: Sodium fluoride - - ' -- completion: 'disease: Endocarditis, Bacterial - - drug: Cefapirin - - mechanism_links: Cephapirin - decreases activity of - InterPro:IPR001460; InterPro:IPR001460 - - positively regulates - peptidoglycan-protein cross-linking; peptidoglycan-protein - cross-linking - positively regulates - peptidoglycan-based cell wall biogenesis; - peptidoglycan-based cell wall biogenesis - has output - cell wall; cell wall - - occurs in - Staphylococcus aureus; Staphylococcus aureus - causes - Endocarditis, - Bacterial - - references: https://go.drugbank.com/drugs/DB01139; https://en.wikipedia.org/wiki/Infective_endocarditis#Cause' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - The bactericidal activity of cephapirin results from the inhibition of cell wall - synthesis via affinity for penicillin-binding proteins (PBPs). - - - === - - - disease: Endocarditis, Bacterial - - drug: Cefapirin - - ' -- completion: 'disease: Ovarian Neoplasms - - drug: Cisplatin - - mechanism_links: Cisplatin - negatively regulates - DNA synthesis involved in - DNA replication; Cisplatin - negatively regulates - DNA-templated transcription; - Cisplatin - disrupts - DNA; DNA synthesis involved in DNA replication - part of - - HP:0031377; DNA-templated transcription - part of - HP:0031377; DNA - participates - in - HP:0031377; HP:0031377 - positively correlated with - Ovarian Neoplasms - - references: https://go.drugbank.com/drugs/DB00515' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Alkylating agents work by three different mechanisms: 1) attachment of alkyl groups - to DNA bases, resulting in the DNA being fragmented by repair enzymes in their - attempts to replace the alkylated bases, preventing DNA synthesis and RNA transcription - from the affected DNA, 2) DNA damage via the formation of cross-links (bonds between - atoms in the DNA) which prevents DNA from being separated for synthesis or transcription, - and 3) the induction of mispairing of the nucleotides leading to mutations. - - - === - - - disease: Ovarian Neoplasms - - drug: Cisplatin - - ' -- completion: 'disease: Bipolar Disorder - - drug: Doxepin - - mechanism_links: Doxepin - decreases activity of - sodium-dependent serotonin - transporter (human); Doxepin - decreases activity of - sodium-dependent noradrenaline - transporter (human); sodium-dependent serotonin transporter (human) - participates - in - serotonin uptake; sodium-dependent noradrenaline transporter (human) - participates - in - norepinephrine uptake; norepinephrine uptake - decreases abundance of - Norepinephrine; - serotonin uptake - decreases abundance of - Serotonin; Serotonin - positively - correlated with - serotonin secretion, neurotransmission; Norepinephrine - positively - correlated with - norepinephrine secretion, neurotransmission; serotonin secretion, - neurotransmission - negatively regulates - Bipolar Disorder; norepinephrine secretion, - neurotransmission - negatively regulates - Bipolar Disorder - - references: https://go.drugbank.com/drugs/DB01142; https://en.wikipedia.org/wiki/Doxepin; - https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL1628227/' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Doxepin exact mechanism of action is not very clear. However, doxepin is known - to be a selective histamine H1 receptor blocker.[A177163] This effect on histamine - receptors indicates effectiveness in skin conditions.[T249] It is known that the - lack of dopamine transporters in the frontal cortex and the transmission of dopamine - in this region is largely inactivated by the effect of norepinephrine reuptake. - Hence, doxepin action on the frontal cortex is suggested to increase dopamine - neurotransmission in this area.[T249] - - - === - - - disease: Bipolar Disorder - - drug: Doxepin - - ' -- completion: 'disease: Chancroid - - drug: Ofloxacin - - mechanism_links: Ofloxacin - negatively regulates - InterPro:IPR013759; InterPro:IPR013759 - - positively regulates - DNA topological change; DNA topological change - in taxon - - NCBITaxon:730; NCBITaxon:730 - causes - Chancroid - - references: https://en.wikipedia.org/wiki/Ofloxacin#Mode_of_action; https://www.ebi.ac.uk/chembl/target_report_card/CHEMBL2311224/; - https://go.drugbank.com/drugs/DB01165' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Ofloxacin acts on DNA gyrase and toposiomerase IV, enzymes which, like human topoisomerase, - prevents the excessive supercoiling of DNA during replication or transcription. - By inhibiting their function, the drug thereby inhibits normal cell division. - - - === - - - disease: Chancroid - - drug: Ofloxacin - - ' -- completion: 'disease: Bronchiectasis - - drug: Acetylcysteine - - mechanism_links: Acetylcysteine - has metabolite - cysteine; cysteine - decreases - abundance of - mucus; cysteine - subclass of - mucolytic; mucolytic - negatively - correlated with - Bronchiectasis; mucus - positively correlated with - Bronchiectasis - - references: https://en.wikipedia.org/wiki/Acetylcysteine#Pharmacodynamics; https://pubchem.ncbi.nlm.nih.gov/compound/12035#section=Mechanism-of-Action; - https://en.wikipedia.org/wiki/Acetylcysteine#Lungs; https://en.wikipedia.org/wiki/Bronchiectasis#Airway_clearance' - prompt: "From the text below, extract the following entities in the following format:\n\ - \ndisease: \ndrug: \nmechanism_links: \n\ - \n\nText:\nAcetylcysteine protects against acetaminophen overdose-induced hepatotoxicity\ - \ by maintaining or restoring hepatic concentrations of glutathione. It does this\ - \ by producing the glutathione precursor L-cysteine. Glutathione is required to\ - \ inactivate an intermediate metabolite (N-acetyl-p-benzoquinoneimine or NAPQI)\ - \ of acetaminophen that is thought to be hepatotoxic. In acetaminophen overdose\ - \ cases, excessive quantities of this metabolite are formed because the primary\ - \ metabolic (glucuronide and sulfate conjugation) pathways become saturated. Acetylcysteine\ - \ may act by reducing the metabolite to the parent compound and/or by providing\ - \ sulfhydryl for conjugation of the metabolite. Experimental evidence also suggests\ - \ that a sulfhydryl-containing compound such as acetylcysteine may also directly\ - \ inactivate the metabolite. The mechanisms of action for acetylcysteine\u2019\ - s well-known mucolytic effects are different. In particular, when inhaled, acetylcysteine\ - \ (and its metabolic byproduct cysteine) exerts its mucolytic action through its\ - \ free sulfhydryl group, which reduces the disulfide bonds in the mucus matrix\ - \ and lowers mucus viscosity. This action increases with increasing pH and is\ - \ most significant at pH 7 to 9. The mucolytic action of acetylcysteine is not\ - \ affected by the presence of DNA. Acetylcysteine is also an antioxidant and reduces\ - \ oxidative stress. Acetylcysteine serves as a prodrug to L-cysteine which is\ - \ a precursor to the biologic antioxidant, glutathione and hence administration\ - \ of acetylcysteine replenishes glutathione stores. L-cysteine also serves as\ - \ a precursor to cystine which in turn serves as a substrate for the cystine-glutamate\ - \ antiporter on astrocytes hence increasing glutamate release into the extracellular\ - \ space. This glutamate in turn acts on mGluR2/3 receptors, and at higher doses\ - \ of acetylcysteine, mGluR5. Glutathione also modulates the NMDA receptor by acting\ - \ at the redox site. These effects on glutamate and NMDA signaling appear to explain\ - \ some of the positive neuropsychotropic effects associated with NAC. Acetylcysteine\ - \ also possesses some anti-inflammatory effects possibly via inhibiting NF-\u03BA\ - B through redox activation of the nuclear factor kappa kinases thereby modulating\ - \ cytokine synthesis.\n\n===\n\ndisease: Bronchiectasis\ndrug: Acetylcysteine\n" -- completion: 'disease: Intraabdominal Infections - - drug: Ticarcillin - - mechanism_links: Ticarcillin - negatively regulates - InterPro:IPR001460; InterPro:IPR001460 - - positively regulates - peptidoglycan biosynthetic process; peptidoglycan biosynthetic - process - positively correlated with - peptidoglycan-based cell wall biogenesis; - peptidoglycan-based cell wall biogenesis - in taxon - Escherichia coli; Escherichia - coli - causes - Intraabdominal Infections - - references: https://go.drugbank.com/drugs/DB01607' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Ticarcillin''s principal mechanism of action revolves around its capacity to prevent - the cross-linking of peptidoglycan during bacterial cell wall synthesis. Consequently, - when the offending bacteria attempt to undergo cell division, cell death occurs. - - - === - - - disease: Intraabdominal Infections - - drug: Ticarcillin - - ' -- completion: 'disease: Cough - - drug: Benzocaine - - mechanism_links: Benzocaine - decreases activity of - sodium channel protein type - 10 subunit alpha (human); sodium channel protein type 10 subunit alpha (human) - - participates in - voltage-gated sodium channel activity; voltage-gated sodium - channel activity - increases transport of - Sodium; Sodium - positively correlated - with - membrane depolarization; membrane depolarization - positively regulates - - neuronal action potential; neuronal action potential - occurs in - pain receptor - cell; pain receptor cell - participates in - sensory perception of pain; sensory - perception of pain - occurs in - Cough - - references: https://go.drugbank.com/drugs/DB01086; https://en.wikipedia.org/wiki/Benzocaine' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Benzocaine binds to sodium channels and reversibly stabilizes the neuronal membrane - which decreases its permeability to sodium ions. Depolarization of the neuronal - membrane is inhibited thereby blocking the initiation and conduction of nerve - impulses. - - - === - - - disease: Cough - - drug: Benzocaine - - ' -- completion: 'disease: Arthritis, Juvenile - - drug: Etodolac - - mechanism_links: Etodolac - decreases activity of - prostaglandin G/H synthase - 2 (human); Etodolac - decreases activity of - prostaglandin G/H synthase 1 (human); - prostaglandin G/H synthase 2 (human) - increases abundance of - Prostaglandins; - prostaglandin G/H synthase 1 (human) - increases abundance of - Prostaglandins; - Prostaglandins - participates in - inflammatory response; inflammatory response - - causes - Pain; Pain - occurs in - Arthritis, Juvenile - - references: https://go.drugbank.com/drugs/DB00749; https://pubmed.ncbi.nlm.nih.gov/1714278/' - prompt: "From the text below, extract the following entities in the following format:\n\ - \ndisease: \ndrug: \nmechanism_links: \n\ - \n\nText:\nSimilar to other NSAIDs, the anti-inflammatory effects of etodolac\ - \ result from inhibition of the enzyme cycooxygenase (COX). This decreases the\ - \ synthesis of peripheral prostaglandins involved in mediating inflammation. Etodolac\ - \ binds to the upper portion of the COX enzyme active site and prevents its substrate,\ - \ arachidonic acid, from entering the active site. Etodolac was previously thought\ - \ to be a non-selective COX inhibitor, but it is now known to be 5 \u2013 50 times\ - \ more selective for COX-2 than COX-1. Antipyresis may occur by central action\ - \ on the hypothalamus, resulting in peripheral dilation, increased cutaneous blood\ - \ flow, and subsequent heat loss.\n\n===\n\ndisease: Arthritis, Juvenile\ndrug:\ - \ Etodolac\n" -- completion: 'disease: Endometritis - - drug: Imipenem - - mechanism_links: Imipenem - decreases activity of - InterPro:IPR005311; InterPro:IPR005311 - - positively regulates - peptidoglycan biosynthetic process; peptidoglycan biosynthetic - process - positively regulates - peptidoglycan-based cell wall biogenesis; peptidoglycan-based - cell wall biogenesis - positively correlated with - cell division; cell division - - in taxon - Bacteria; Bacteria - causes - Endometritis - - references: https://go.drugbank.com/drugs/DB01598#mechanismofaction; https://en.wikipedia.org/wiki/Imipenem#Mechanism_of_action; - https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL148/; https://pubchem.ncbi.nlm.nih.gov/compound/104838' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Imipenem acts as an antimicrobial through the inhibition of cell wall synthesis - of various gram-positive and gram-negative bacteria.[L7526,L7568] This inhibition - of cell wall synthesis in gram-negative bateria is attained by binding to penicillin-binding - proteins (PBPs). In E. coli and selected strains of P. aeruginosa, imipenem has - shown to have the highest affinity to PBP-2, PBP-1a, and PBP-1b.[A15388] This - inhibition of PBPs prevents the bacterial cell from adding to the peptidoglycan - polymer which forms the bacterial cell wall eventually leading to cell death.[T116] - - - === - - - disease: Endometritis - - drug: Imipenem - - ' -- completion: 'disease: Appendicitis - - drug: Piperacillin - - mechanism_links: Piperacillin - negatively regulates - Pfam:PF00905; Pfam:PF00905 - - positively regulates - peptidoglycan biosynthetic process; peptidoglycan biosynthetic - process - positively correlated with - peptidoglycan-based cell wall biogenesis; - peptidoglycan-based cell wall biogenesis - in taxon - Escherichia coli; Escherichia - coli - causes - Appendicitis - - references: https://go.drugbank.com/drugs/DB00319; https://pubmed.ncbi.nlm.nih.gov/23231389/' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - By binding to specific penicillin-binding proteins (PBPs) located inside the bacterial - cell wall, Piperacillin inhibits the third and last stage of bacterial cell wall - synthesis. Cell lysis is then mediated by bacterial cell wall autolytic enzymes - such as autolysins; it is possible that Piperacillin interferes with an autolysin - inhibitor. - - - === - - - disease: Appendicitis - - drug: Piperacillin - - ' -- completion: 'disease: Scrub Typhus - - drug: Fusidic acid - - mechanism_links: Fusidic Acid - decreases activity of - PR:B3CTE7; PR:B3CTE7 - - positively regulates - translation; translation - occurs in - NCBITaxon:784; NCBITaxon:784 - - causes - Scrub Typhus - - references: https://go.drugbank.com/drugs/DB02703#mechanism-of-action; https://en.wikipedia.org/wiki/Fusidic_acid; - https://www.uniprot.org/uniprot/B3CTE7#function; https://en.wikipedia.org/wiki/Scrub_typhus' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Fusidic acid works by interfering with bacterial protein synthesis, specifically - by preventing the translocation of the elongation factor G (EF-G) from the ribosome. - It also can inhibit chloramphenicol acetyltransferase enzymes. - - - === - - - disease: Scrub Typhus - - drug: Fusidic acid - - ' -- completion: 'disease: MESH:D000080223 - - drug: Astemizole - - mechanism_links: Astemizole - decreases activity of - histamine H1 receptor (human); - histamine H1 receptor (human) - positively regulates - histamine receptor activity; - histamine receptor activity - participates in - cellular response to histamine; - cellular response to histamine - positively correlated with - inflammatory response; - cellular response to histamine - positively correlated with - positive regulation - of vascular permeability; cellular response to histamine - positively correlated - with - HP:0000969; HP:0000969 - manifestation of - MESH:D000080223; positive regulation - of vascular permeability - manifestation of - MESH:D000080223; inflammatory response - - causes - MESH:D000080223 - - references: https://go.drugbank.com/drugs/DB00637' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Astemizole competes with histamine for binding at H<sub>1</sub>-receptor - sites in the GI tract, uterus, large blood vessels, and bronchial muscle. This - reversible binding of astemizole to H<sub>1</sub>-receptors suppresses - the formation of edema, flare, and pruritus resulting from histaminic activity. - As the drug does not readily cross the blood-brain barrier and preferentially - binds at H1 receptors in the peripehery rather than within the brain, CNS depression - is minimal. Astemizole may also act on H<sub>3</sub>-receptors, producing - adverse effects. - - - === - - - disease: MESH:D000080223 - - drug: Astemizole - - ' -- completion: 'disease: Klinefelter Syndrome - - drug: Fluoxymesterone - - mechanism_links: Fluoxymesterone - increases activity of - androgen receptor (human); - androgen receptor (human) - positively regulates - androgen receptor signaling - pathway; androgen receptor signaling pathway - positively correlated with - development - of secondary male sexual characteristics; development of secondary male sexual - characteristics - negatively correlated with - Klinefelter Syndrome - - references: https://go.drugbank.com/drugs/DB01185; https://en.wikipedia.org/wiki/Fluoxymesterone; - https://en.wikipedia.org/wiki/Androgen' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Fluoxymesterone is a synthetic androgenic anabolic steroid and is approximately - 5 times as potent as natural methyltestosterone. Like testosterone and other androgenic - hormones, fluoxymesterone binds to the androgen receptor. It produces retention - of nitrogen, sodium, potassium, and phosphorus; increases protein anabolism; decreases - amino acid catabolism and decreased urinary excretion of calcium. The antitumour - activity of fluoxymesterone appears related to reduction or competitive inhibition - of prolactin receptors or estrogen receptors or production. - - - === - - - disease: Klinefelter Syndrome - - drug: Fluoxymesterone - - ' -- completion: 'disease: Klebsiella Infections - - drug: Moxifloxacin - - mechanism_links: MESH:D000077266 - decreases activity of - PR:A6TBT6; MESH:D000077266 - - decreases activity of - PR:A6TE12; PR:A6TBT6 - positively regulates - DNA replication; - PR:A6TE12 - positively regulates - DNA replication; DNA replication - occurs in - - NCBITaxon:570; NCBITaxon:570 - causes - Klebsiella Infections - - references: https://go.drugbank.com/drugs/DB00218#mechanism-of-action; https://www.uniprot.org/uniprot/A6TBT6#function; - https://www.uniprot.org/uniprot/A6TE12#function; https://en.wikipedia.org/wiki/Klebsiella#In_humans' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - The bactericidal action of moxifloxacin results from inhibition of the enzymes - topoisomerase II (DNA gyrase) and topoisomerase IV. DNA gyrase is an essential - enzyme that is involved in the replication, transcription and repair of bacterial - DNA. Topoisomerase IV is an enzyme known to play a key role in the partitioning - of the chromosomal DNA during bacterial cell division. - - - === - - - disease: Klebsiella Infections - - drug: Moxifloxacin - - ' -- completion: 'disease: Tuberculosis, Pulmonary - - drug: Ethambutol - - mechanism_links: Ethambutol - decreases activity of - PR:P9WNL5; Ethambutol - - decreases activity of - PR:P9WNL7; Ethambutol - decreases activity of - probable - arabinosyltransferase A (Mycobacterium tuberculosis H37Rv); PR:P9WNL5 - positively - regulates - Actinobacterium-type cell wall biogenesis; PR:P9WNL7 - positively - regulates - Actinobacterium-type cell wall biogenesis; probable arabinosyltransferase - A (Mycobacterium tuberculosis H37Rv) - positively regulates - Actinobacterium-type - cell wall biogenesis; Actinobacterium-type cell wall biogenesis - positively correlated - with - cell division; cell division - in taxon - Mycobacterium tuberculosis; Mycobacterium - tuberculosis - causes - Tuberculosis, Pulmonary - - references: https://go.drugbank.com/drugs/DB00330' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Ethambutol inhibits arabinosyl transferases which is involved in cell wall biosynthesis. - By inhibiting this enzyme, the bacterial cell wall complex production is inhibited. - This leads to an increase in cell wall permeability. - - - === - - - disease: Tuberculosis, Pulmonary - - drug: Ethambutol - - ' -- completion: 'disease: Tendinopathy - - drug: Triamcinolone - - mechanism_links: Triamcinolone Acetonide - increases activity of - glucocorticoid - receptor (human); glucocorticoid receptor (human) - increases activity of - annexin - A1 (human); glucocorticoid receptor (human) - decreases activity of - prostaglandin - G/H synthase 1 (human); glucocorticoid receptor (human) - decreases activity of - - prostaglandin G/H synthase 2 (human); annexin A1 (human) - decreases activity - of - cytosolic phospholipase A2 (human); prostaglandin G/H synthase 1 (human) - - positively regulates - prostaglandin biosynthetic process; prostaglandin G/H - synthase 2 (human) - positively regulates - prostaglandin biosynthetic process; - cytosolic phospholipase A2 (human) - positively regulates - leukotriene biosynthetic - process; cytosolic phospholipase A2 (human) - positively regulates - prostaglandin - biosynthetic process; leukotriene biosynthetic process - positively correlated - with - inflammatory response; prostaglandin biosynthetic process - positively - correlated with - inflammatory response; inflammatory response - has phenotype - - HP:0012531; HP:0012531 - located in - tendon; tendon - location of - Tendinopathy - - references: https://go.drugbank.com/drugs/DB00620#mechanism-of-action; https://www.uniprot.org/uniprot/P04150#function; - https://www.uniprot.org/uniprot/P04083#function; https://www.uniprot.org/uniprot/P47712#function; - https://www.uniprot.org/uniprot/P23219#function; https://www.uniprot.org/uniprot/P35354#function; - https://en.wikipedia.org/wiki/Tendinopathy' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Corticosteroids like triamcinolone inhibit phospholipase A2 on cell membranes, - preventing the breakdown of lysosomal membranes of leukocytes, which in turn prevent - the formation of arachidonic acid, which decrease expression of cyclooxygenase - and lipoxygenase, inhibiting synthesis of prostaglandins and leukotrienes.[A184463] - Anti-inflammatory activity occurs via reversal of vascular dilation and reducing - permeability, which prevents macrophage and leukocyte migration.[A184463] Triamcinolone - also inhibits nuclear factor kappa-B, which decreases the production of pro-inflammatory - signals such as interleukin-6, interleukin-8, and monocyte chemoattractant protein-1.[A184463] - - - === - - - disease: Tendinopathy - - drug: Triamcinolone - - ' -- completion: 'disease: Hot Flashes - - drug: Paroxetine - - mechanism_links: Paroxetine - decreases activity of - sodium-dependent serotonin - transporter (human); sodium-dependent serotonin transporter (human) - positively - regulates - serotonin uptake; serotonin uptake - decreases abundance of - Serotonin; - Serotonin - positively correlated with - serotonin secretion, neurotransmission; - serotonin secretion, neurotransmission - treats - Hot Flashes - - references: https://go.drugbank.com/drugs/DB00715#BE0000749; https://drugs.ncats.io/drug/41VRH5220H; - https://en.wikipedia.org/wiki/Hot_flash#Mechanism' - prompt: "From the text below, extract the following entities in the following format:\n\ - \ndisease: \ndrug: \nmechanism_links: \n\ - \n\nText:\nParoxetine enhances serotonergic activity via the inhibition presynaptic\ - \ reuptake of serotonin by the serotonin (SERT) receptor.[A5492,A181772] This\ - \ inhibition raises the level of serotonin in the synaptic cleft, relieving various\ - \ symptoms. This drug has been demonstrated to be a stronger inhibitor of serotonin\ - \ reuptake than other members of the same drug class, including [Citalopram],\ - \ [Fluoxetine], and [Fluvoxamine].[A31914] The mechanism of action of paroxetine\ - \ in relieving the vasomotor symptoms of menopause is unknown, according to the\ - \ Brisdelle prescribing information[L7703], but may occur due to its effects on\ - \ thermoregulation.[A181973] Paroxetine shows a clinically insignificant affinity\ - \ for adrenergic alpha-1 and alpha-2 receptors and \u03B2-adrenergic receptors,\ - \ dopamine D1 and D2 receptors, histamine H1 receptors and serotonin 5-HT1A, 5-HT2A\ - \ and 5-HT2C receptors.[A31914] This drug shows some affinity for muscarinic cholinergic\ - \ receptors and 5-H2B receptors.[A181829,A181847] The delayed onset of paroxetine\ - \ therapeutic effects may be explained by the initial paroxetine actions on the\ - \ 5-HT neurons. In rats, paroxetine activates 5-HT1A receptors when it is first\ - \ administered, inhibiting the stimulation of the 5-HT neurons and subsequent\ - \ release of serotonin at the synaptic cleft.[A31914]\n\n===\n\ndisease: Hot Flashes\n\ - drug: Paroxetine\n" -- completion: 'disease: Lymphoma, Non-Hodgkin - - drug: Thiotepa - - mechanism_links: Thiotepa - disrupts - DNA; DNA - participates in - DNA replication; - DNA replication - precedes - lymphocyte proliferation; lymphocyte proliferation - - positively correlated with - Lymphoma, Non-Hodgkin - - references: https://go.drugbank.com/drugs/DB04572; https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL671/' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - The alkyl group is attached to the guanine base of DNA, at the number 7 nitrogen - atom of the imidazole ring. They stop tumor growth by crosslinking guanine nucleobases - in DNA double-helix strands, directly attacking DNA. This makes the strands unable - to uncoil and separate. As this is necessary in DNA replication, the cells can - no longer divide. These drugs act nonspecifically. - - - === - - - disease: Lymphoma, Non-Hodgkin - - drug: Thiotepa - - ' -- completion: 'disease: Nephrotic Syndrome - - drug: Prednisone - - mechanism_links: Prednisone - has metabolite - Prednisolone; Prednisolone - increases - activity of - glucocorticoid receptor (human); glucocorticoid receptor (human) - - increases activity of - annexin A1 (human); glucocorticoid receptor (human) - - decreases activity of - prostaglandin G/H synthase 1 (human); glucocorticoid - receptor (human) - decreases activity of - prostaglandin G/H synthase 2 (human); - annexin A1 (human) - decreases activity of - cytosolic phospholipase A2 (human); - prostaglandin G/H synthase 1 (human) - positively regulates - prostaglandin biosynthetic - process; prostaglandin G/H synthase 2 (human) - positively regulates - prostaglandin - biosynthetic process; cytosolic phospholipase A2 (human) - positively regulates - - leukotriene biosynthetic process; cytosolic phospholipase A2 (human) - positively - regulates - prostaglandin biosynthetic process; leukotriene biosynthetic process - - positively correlated with - inflammatory response; prostaglandin biosynthetic - process - positively correlated with - inflammatory response; inflammatory response - - positively correlated with - Nephrotic Syndrome - - references: https://go.drugbank.com/drugs/DB00635#mechanism-of-action; https://en.wikipedia.org/wiki/Prednisone; - https://www.uniprot.org/uniprot/P04150#function; https://www.uniprot.org/uniprot/P04083#function; - https://www.uniprot.org/uniprot/P47712#function; https://www.uniprot.org/uniprot/P23219#function; - https://www.uniprot.org/uniprot/P35354#function; https://en.wikipedia.org/wiki/Nephrotic_syndrome' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Prednisone is first metabolized in the liver to its active form, prednisolone, - a glucocorticoid agonist corticosteroid.[L10502] Lower doses of corticosteroids - provide an anti-inflammatory effect, while higher doses are immunosuppressive.[A187463] - High doses of glucocorticoids for an extended period bind to the mineralocorticoid - receptor, raising sodium levels and decreasing potassium levels.[A187463] - - - === - - - disease: Nephrotic Syndrome - - drug: Prednisone - - ' -- completion: 'disease: Arthralgia - - drug: Acetaminophen - - mechanism_links: Acetaminophen - decreases activity of - prostaglandin G/H synthase - 1 (human); Acetaminophen - decreases activity of - prostaglandin G/H synthase - 2 (human); Acetaminophen - decreases activity of - prostaglandin E synthase 3 - (human); prostaglandin G/H synthase 1 (human) - positively regulates - prostaglandin - biosynthetic process; prostaglandin G/H synthase 2 (human) - positively regulates - - prostaglandin biosynthetic process; prostaglandin E synthase 3 (human) - positively - regulates - prostaglandin biosynthetic process; prostaglandin biosynthetic process - - increases abundance of - Prostaglandins; Prostaglandins - positively correlated - with - Arthralgia - - references: https://go.drugbank.com/drugs/DB00316#mechanism-of-action; https://www.uniprot.org/uniprot/P23219#function; - https://www.uniprot.org/uniprot/P35354#function; https://www.uniprot.org/uniprot/Q15185#function; - https://en.wikipedia.org/wiki/Arthralgia' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - According to its FDA labeling, acetaminophen''s exact mechanism of action has - not been fully established[Label] - despite this, it is often categorized alongside - NSAIDs (nonsteroidal anti-inflammatory drugs) due to its ability to inhibit the - cyclooxygenase (COX) pathways.[T518] It is thought to exert central actions which - ultimately lead to the alleviation of pain symptoms.[T518] One theory is that - acetaminophen increases the pain threshold by inhibiting two isoforms of cyclooxygenase, - COX-1 and COX-2, which are involved in prostaglandin (PG) synthesis. Prostaglandins - are responsible for eliciting pain sensations.[A176366] Acetaminophen does not - inhibit cyclooxygenase in peripheral tissues and, therefore, has no peripheral - anti-inflammatory effects. Though acetylsalicylic acid (aspirin) is an irreversible - inhibitor of COX and directly blocks the active site of this enzyme, studies have - shown that acetaminophen (paracetamol) blocks COX indirectly.[F4133] Studies also - suggest that acetaminophen selectively blocks a variant type of the COX enzyme - that is unique from the known variants COX-1 and COX-2.[A468] This enzyme has - been referred to as _COX-3_. The antipyretic actions of acetaminophen are likely - attributed to direct action on heat-regulating centers in the brain, resulting - in peripheral vasodilation, sweating, and loss of body heat.[F4133] The exact - mechanism of action of this drug is not fully understood at this time, but future - research may contribute to deeper knowledge.[F4133] - - - === - - - disease: Arthralgia - - drug: Acetaminophen - - ' -- completion: 'disease: Acne Vulgaris - - drug: Clotrimazole - - mechanism_links: Adapalene - positively regulates - Receptors, Retinoic Acid; - Receptors, Retinoic Acid - negatively regulates - keratinization; keratinization - - increases abundance of - HP:0025249; HP:0025249 - positively correlated with - - Acne Vulgaris - - references: https://go.drugbank.com/drugs/DB00210#mechanism-of-action; https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2374937/; - https://en.wikipedia.org/wiki/Adapalene#Pharmacodynamics; https://pubmed.ncbi.nlm.nih.gov/19929446/' - prompt: "From the text below, extract the following entities in the following format:\n\ - \ndisease: \ndrug: \nmechanism_links: \n\ - \n\nText:\nClotrimazole acts primarily by damaging the permeability barrier in\ - \ the cell membrane of fungi. Clotrimazole causes inhibition of ergosterol biosynthesis,\ - \ an essential constituent of fungal cell membranes. If ergosterol synthesis is\ - \ either completely or partially inhibited, the cell is no longer able to construct\ - \ an intact and functional cell membrane [F3088],[F3100]. Because ergosterol directly\ - \ promotes the growth of fungal cells in a hormone\u2010like fashion, rapid onset\ - \ of the above events leads to dose-dependent inhibition of fungal growth [A174094].\ - \ Though decreased ergosterol, due to the inhibition of lanosterol 14-demethylase\ - \ (also known as _CYP51_) [A174094] is accepted to be primarily responsible for\ - \ the antimycotic properties of clotrimazole, this drug also shows other pharmacological\ - \ effects. These include the inhibition of sarcoplasmic reticulum Ca2+\u2010ATPase,\ - \ depletion of intracellular calcium, and blocking of calcium\u2010dependent\ - \ potassium channels and voltage\u2010dependent calcium channels [A174094]. The\ - \ action of clotrimazole on these targets accounts for other effects of this drug\ - \ that are separate from its antimycotic activities [A174094].\n\n===\n\ndisease:\ - \ Acne Vulgaris\ndrug: Clotrimazole\n" -- completion: 'disease: Irritable Bowel Syndrome - - drug: Dicyclomine - - mechanism_links: Dicyclomine - decreases activity of - muscarinic acetylcholine - receptor M3 (human); muscarinic acetylcholine receptor M3 (human) - participates - in - response to acetylcholine; response to acetylcholine - positively regulates - - smooth muscle contraction; smooth muscle contraction - positively regulates - - intestinal motility; smooth muscle contraction - positively regulates - defecation; - intestinal motility - occurs in - Irritable Bowel Syndrome; defecation - occurs - in - Irritable Bowel Syndrome; Dicyclomine - negatively regulates - response to - histamine; response to histamine - positively correlated with - Irritable Bowel - Syndrome - - references: https://go.drugbank.com/drugs/DB00804; https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL1123/; - https://drugs.ncats.io/drug/4KV4X8IF6V' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Dicyclomine achieves its action partially through direct antimuscarinic activity - of the M1 and M2 receptors, and partially through antagonism of bradykinin and - histamine.[A6556,A182555,L7967] Dicyclomine non-competitively inhibits the action - of bradykinin and histamine, resulting in direct action on the smooth muscle, - and decreased strength of contractions seen in spasms of the ileum.[A182555] - - - === - - - disease: Irritable Bowel Syndrome - - drug: Dicyclomine - - ' -- completion: 'disease: Alcohol Withdrawal Delirium - - drug: Diazepam - - mechanism_links: Diazepam - positively regulates - GABA receptor activity; GABA - receptor activity - positively regulates - GABA-gated chloride ion channel activity; - GABA receptor activity - positively correlated with - gamma-aminobutyric acid - secretion, neurotransmission; GABA-gated chloride ion channel activity - negatively - regulates - neuronal action potential; neuronal action potential - positively - regulates - glutamate secretion, neurotransmission; gamma-aminobutyric acid secretion, - neurotransmission - negatively correlated with - Alcohol Withdrawal Delirium; - glutamate secretion, neurotransmission - positively correlated with - Seizures; - Seizures - manifestation of - Alcohol Withdrawal Delirium - - references: https://go.drugbank.com/drugs/DB00829#BE0004797; https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1312739/' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Diazepam is a benzodiazepine tranquilliser with anticonvulsant, sedative, muscle - relaxant and amnesic properties [F3157, F3160, L5188]. Benzodiazepines, such as - diazepam, bind to receptors in various regions of the brain and spinal cord. This - binding increases the inhibitory effects of gamma-aminobutyric acid (GABA) [F3157, - F3160, L5188]. GABAs functions include CNS involvement in sleep induction. Also - involved in the control of hypnosis, memory, anxiety, epilepsy and neuronal excitability - [F3157, F3160, L5188]. - - - === - - - disease: Alcohol Withdrawal Delirium - - drug: Diazepam - - ' -- completion: 'disease: Nausea - - drug: Triflupromazine - - mechanism_links: Triflupromazine - decreases activity of - D(2) dopamine receptor - (human); D(2) dopamine receptor (human) - located in - area postrema; area postrema - - negatively regulates - vagus nerve; vagus nerve - located in - upper digestive - tract; upper digestive tract - prevents - Nausea - - references: https://go.drugbank.com/drugs/DB00508#mechanismofaction' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Triflupromazine binds to the dopamine D1 and dopamine D2 receptors and inhibits - their activity. The mechanism of the anti-emetic effect is due predominantly to - blockage of the dopamine D2 neurotransmitter receptors in the chemoreceptor trigger - zone (CTZ) and vomiting centre. Triflupromazine blocks the neurotransmitter dopamine - and the vagus nerve in the gastrointestinal tract. Triflupromazine also binds - the muscarinic acetylcholine receptors (M1 and M2) and the tryptamine D receptors - (5HT<sub>2B</sub>). - - - === - - - disease: Nausea - - drug: Triflupromazine - - ' -- completion: 'disease: Psoriasis - - drug: Cortisone acetate - - mechanism_links: Cortisone - increases activity of - glucocorticoid receptor (human); - glucocorticoid receptor (human) - increases activity of - annexin A1 (human); - glucocorticoid receptor (human) - decreases activity of - prostaglandin G/H synthase - 1 (human); glucocorticoid receptor (human) - decreases activity of - prostaglandin - G/H synthase 2 (human); annexin A1 (human) - decreases activity of - cytosolic - phospholipase A2 (human); prostaglandin G/H synthase 1 (human) - positively regulates - - prostaglandin biosynthetic process; prostaglandin G/H synthase 2 (human) - positively - regulates - prostaglandin biosynthetic process; cytosolic phospholipase A2 (human) - - positively regulates - leukotriene biosynthetic process; cytosolic phospholipase - A2 (human) - positively regulates - prostaglandin biosynthetic process; leukotriene - biosynthetic process - positively correlated with - inflammatory response; prostaglandin - biosynthetic process - positively correlated with - inflammatory response; inflammatory - response - positively correlated with - HP:0011123; HP:0011123 - positively correlated - with - Psoriasis - - references: https://go.drugbank.com/drugs/DB01380#mechanism-of-action; https://www.uniprot.org/uniprot/P04150#function; - https://www.uniprot.org/uniprot/P04083#function; https://www.uniprot.org/uniprot/P47712#function; - https://www.uniprot.org/uniprot/P23219#function; https://www.uniprot.org/uniprot/P35354#function; - https://en.wikipedia.org/wiki/Psoriasis' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Cortisone acetate binds to the cytosolic glucocorticoid receptor. After binding - the receptor the newly formed receptor-ligand complex translocates itself into - the cell nucleus, where it binds to many glucocorticoid response elements (GRE) - in the promoter region of the target genes. The DNA bound receptor then interacts - with basic transcription factors, causing the increase in expression of specific - target genes. The anti-inflammatory actions of corticosteroids are thought to - involve lipocortins, phospholipase A2 inhibitory proteins which, through inhibition - arachidonic acid, control the biosynthesis of prostaglandins and leukotrienes. - Specifically glucocorticoids induce lipocortin-1 (annexin-1) synthesis, which - then binds to cell membranes preventing the phospholipase A2 from coming into - contact with its substrate arachidonic acid. This leads to diminished eicosanoid - production. The cyclooxygenase (both COX-1 and COX-2) expression is also suppressed, - potentiating the effect. In other words, the two main products in inflammation - Prostaglandins and Leukotrienes are inhibited by the action of Glucocorticoids. - Glucocorticoids also stimulate the lipocortin-1 escaping to the extracellular - space, where it binds to the leukocyte membrane receptors and inhibits various - inflammatory events: epithelial adhesion, emigration, chemotaxis, phagocytosis, - respiratory burst and the release of various inflammatory mediators (lysosomal - enzymes, cytokines, tissue plasminogen activator, chemokines etc.) from neutrophils, - macrophages and mastocytes. Additionally the immune system is suppressed by corticosteroids - due to a decrease in the function of the lymphatic system, a reduction in immunoglobulin - and complement concentrations, the precipitation of lymphocytopenia, and interference - with antigen-antibody binding. - - - === - - - disease: Psoriasis - - drug: Cortisone acetate - - ' -- completion: 'disease: Mycosis Fungoides - - drug: Mechlorethamine - - mechanism_links: Mechlorethamine - disrupts - DNA; DNA - participates in - DNA - replication; DNA replication - occurs in - HP:0031377; HP:0031377 - occurs in - - Mycosis Fungoides - - references: https://go.drugbank.com/drugs/DB00888' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Alkylating agents work by three different mechanisms: 1) attachment of alkyl groups - to DNA bases, resulting in the DNA being fragmented by repair enzymes in their - attempts to replace the alkylated bases, preventing DNA synthesis and RNA transcription - from the affected DNA, 2) DNA damage via the formation of cross-links (bonds between - atoms in the DNA) which prevents DNA from being separated for synthesis or transcription, - and 3) the induction of mispairing of the nucleotides leading to mutations. Mechlorethamine - is cell cycle phase-nonspecific. - - - === - - - disease: Mycosis Fungoides - - drug: Mechlorethamine - - ' -- completion: 'disease: Chorioretinitis - - drug: Sulfadiazine - - mechanism_links: Sulfadiazine - negatively regulates - InterPro:IPR006390; InterPro:IPR006390 - - positively regulates - folic acid biosynthetic process; folic acid biosynthetic - process - in taxon - NCBITaxon:5811; NCBITaxon:5811 - causes - Chorioretinitis - - references: https://go.drugbank.com/drugs/DB00359; https://en.wikipedia.org/wiki/Sulfadiazine#Mechanism_of_action' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Sulfadiazine is a competitive inhibitor of the bacterial enzyme dihydropteroate - synthetase. This enzyme is needed for the proper processing of para-aminobenzoic - acid (PABA) which is essential for folic acid synthesis. The inhibited reaction - is necessary in these organisms for the synthesis of folic acid. - - - === - - - disease: Chorioretinitis - - drug: Sulfadiazine - - ' -- completion: 'disease: Ascites - - drug: Spironolactone - - mechanism_links: Spironolactone - negatively regulates - mineralocorticoid receptor - (human); mineralocorticoid receptor (human) - positively correlated with - Aldosterone; - Aldosterone - contributes to - renal sodium ion absorption; renal sodium ion absorption - - positively correlated with - renal water retention; renal water retention - - contributes to - Ascites - - references: https://go.drugbank.com/drugs/DB00421; https://en.wikipedia.org/wiki/Ascites#:~:text=Ascites%20is%20the%20abnormal%20buildup,discomfort%2C%20and%20shortness%20of%20breath' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Spironolactone competitively inhibits aldosterone dependant sodium potassium exchange - channels in the distal convoluted tubule.[Label] This action leads to increased - sodium and water excretion, but more potassium retention.[Label] The increased - excretion of water leads to diuretic and also antihypertensive effects.[Label] - - - === - - - disease: Ascites - - drug: Spironolactone - - ' -- completion: 'disease: Intraabdominal Infections - - drug: Imipenem - - mechanism_links: Imipenem - decreases activity of - InterPro:IPR005311; InterPro:IPR005311 - - positively regulates - peptidoglycan biosynthetic process; peptidoglycan biosynthetic - process - positively regulates - peptidoglycan-based cell wall biogenesis; peptidoglycan-based - cell wall biogenesis - positively correlated with - cell division; cell division - - in taxon - Bacteria; Bacteria - causes - Intraabdominal Infections - - references: https://go.drugbank.com/drugs/DB01598#mechanismofaction; https://en.wikipedia.org/wiki/Imipenem#Mechanism_of_action; - https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL148/; https://pubchem.ncbi.nlm.nih.gov/compound/104838' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Imipenem acts as an antimicrobial through the inhibition of cell wall synthesis - of various gram-positive and gram-negative bacteria.[L7526,L7568] This inhibition - of cell wall synthesis in gram-negative bateria is attained by binding to penicillin-binding - proteins (PBPs). In E. coli and selected strains of P. aeruginosa, imipenem has - shown to have the highest affinity to PBP-2, PBP-1a, and PBP-1b.[A15388] This - inhibition of PBPs prevents the bacterial cell from adding to the peptidoglycan - polymer which forms the bacterial cell wall eventually leading to cell death.[T116] - - - === - - - disease: Intraabdominal Infections - - drug: Imipenem - - ' -- completion: 'disease: Trachoma - - drug: Meclocycline - - mechanism_links: meclocycline - decreases activity of - InterPro:IPR000235; InterPro:IPR000235 - - positively regulates - tRNA aminoacylation; tRNA aminoacylation - participates - in - translation; translation - in taxon - Chlamydia trachomatis; Chlamydia trachomatis - - causes - Trachoma - - references: https://go.drugbank.com/drugs/DB13092' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - As a tetracycline, meclocycline likely works by reversably associating with the - 30s subint of the bacterial ribosome [A19429]. A likely binding site for tetracyclines - has been identified on protein S7 of this subunit. This association blocks the - association of aminoacyl-tRNA with the ribosome, inhibiting protein synthesis. - Ultimately this inhibits bacterial growth due to a lack of proteins necessary - for reproduction. - - - === - - - disease: Trachoma - - drug: Meclocycline - - ' -- completion: 'disease: Dacryocystitis - - drug: Tobramycin - - mechanism_links: Tobramycin - negatively regulates - RNA, Ribosomal, 16S; Tobramycin - - negatively regulates - RNA, Ribosomal, 23S; RNA, Ribosomal, 16S - located in - - ribosome; RNA, Ribosomal, 23S - located in - ribosome; ribosome - positively - regulates - translation; translation - occurs in - Bacteria; Bacteria - causes - - Dacryocystitis - - references: https://go.drugbank.com/drugs/DB00684#mechanism-of-action; https://en.wikipedia.org/wiki/16S_ribosomal_RNA; - https://en.wikipedia.org/wiki/23S_ribosomal_RNA; https://en.wikipedia.org/wiki/Dacryocystitis' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Tobramycin binds irreversibly to one of two aminoglycoside binding sites on the - 30 S ribosomal subunit, inhibiting bacterial protein synthesis. Tobramycin may - also destabilize bacterial memebrane by binding to 16 S 16 S r-RNA. An active - transport mechanism for aminoglycoside uptake is necessary in the bacteria in - order to attain a significant intracellular concentration of tobramycin. - - - === - - - disease: Dacryocystitis - - drug: Tobramycin - - ' -- completion: 'disease: Rhinitis, Vasomotor - - drug: Cyclizine - - mechanism_links: Cyclizine - decreases activity of - histamine H1 receptor (human); - histamine H1 receptor (human) - positively regulates - histamine receptor activity; - histamine receptor activity - participates in - cellular response to histamine; - cellular response to histamine - positively correlated with - inflammatory response; - inflammatory response - causes - Rhinitis, Vasomotor - - references: https://go.drugbank.com/drugs/DB01176; https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL648/; - https://en.wikipedia.org/wiki/Cyclizine' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Vomiting (emesis) is essentially a protective mechanism for removing irritant - or otherwise harmful substances from the upper GI tract. Emesis or vomiting is - controlled by the vomiting centre in the medulla region of the brain, an important - part of which is the chemotrigger zone (CTZ). The vomiting centre possesses neurons - which are rich in muscarinic cholinergic and histamine containing synapses. These - types of neurons are especially involved in transmission from the vestibular apparatus - to the vomiting centre. Motion sickness principally involves overstimulation of - these pathways due to various sensory stimuli. Hence the action of cyclizine which - acts to block the histamine receptors in the vomiting centre and thus reduce activity - along these pathways. Furthermore since cyclizine possesses anti-cholinergic properties - as well, the muscarinic receptors are similarly blocked. - - - === - - - disease: Rhinitis, Vasomotor - - drug: Cyclizine - - ' -- completion: 'disease: Syphilis, tertiary - - drug: Benzylpenicillin - - mechanism_links: Penicillin G - decreases activity of - InterPro:IPR001460; InterPro:IPR001460 - - participates in - peptidoglycan biosynthetic process; peptidoglycan biosynthetic - process - positively regulates - peptidoglycan-based cell wall biogenesis; peptidoglycan-based - cell wall biogenesis - occurs in - NCBITaxon:160; NCBITaxon:160 - causes - Syphilis, - tertiary - - references: https://go.drugbank.com/drugs/DB01053#mechanism-of-action; https://en.wikipedia.org/wiki/Syphilis#Tertiary' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - By binding to specific penicillin-binding proteins (PBPs) located inside the bacterial - cell wall, penicillin G inhibits the third and last stage of bacterial cell wall - synthesis. Cell lysis is then mediated by bacterial cell wall autolytic enzymes - such as autolysins; it is possible that penicillin G interferes with an autolysin - inhibitor. - - - === - - - disease: Syphilis, tertiary - - drug: Benzylpenicillin - - ' -- completion: 'disease: Rhinoscleroma - - drug: Amikacin - - mechanism_links: Amikacin - decreases activity of - PR:B5XN85; Amikacin - negatively - regulates - RNA, Ribosomal, 16S; PR:B5XN85 - part of - small ribosomal subunit; - RNA, Ribosomal, 16S - located in - small ribosomal subunit; small ribosomal subunit - - participates in - translation; translation - occurs in - NCBITaxon:39831; NCBITaxon:39831 - - causes - Rhinoscleroma - - references: https://go.drugbank.com/drugs/DB00479#mechanism-of-action; https://drugs.ncats.io/drug/84319SGC3C; - https://en.wikipedia.org/wiki/Amikacin#Mechanism_of_action; https://www.uniprot.org/uniprot/B5XN85#function; - https://en.wikipedia.org/wiki/Prokaryotic_small_ribosomal_subunit; https://en.wikipedia.org/wiki/Rhinoscleroma' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - The primary mechanism of action of amikacin is the same as that for all aminoglycosides. - It binds to bacterial 30S ribosomal subunits and interferes with mRNA binding - and tRNA acceptor sites, interfering with bacterial growth. This leads to disruption - of normal protein synthesis and production of non-functional or toxic peptides. - Other actions have been postulated for drugs of this class.[Label,F1949,F1950] - Amikacin, as well as the rest of the aminoglycosides, are generally bacteriocidal - against gram-positive and gram-negative bacteria.[L4680,F1954] - - - === - - - disease: Rhinoscleroma - - drug: Amikacin - - ' -- completion: 'disease: Menorrhagia - - drug: Tranexamic acid - - mechanism_links: Tranexamic Acid - negatively regulates - plasminogen (human); - plasminogen (human) - positively regulates - fibrinolysis; Tranexamic Acid - decreases - activity of - Fibrinolysin; Fibrinolysin - positively regulates - fibrinolysis; - fibrinolysis - correlated with - HP:0001892; HP:0001892 - positively correlated - with - Menorrhagia - - references: https://go.drugbank.com/drugs/DB00302#mechanism-of-action; https://en.wikipedia.org/wiki/Tranexamic_acid#Mechanism_of_action' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Tranexamic acid competitively inhibits activation of plasminogen (via binding - to the kringle domain), thereby reducing conversion of plasminogen to plasmin - (fibrinolysin), an enzyme that degrades fibrin clots, fibrinogen, and other plasma - proteins, including the procoagulant factors V and VIII. Tranexamic acid also - directly inhibits plasmin activity, but higher doses are required than are needed - to reduce plasmin formation. - - - === - - - disease: Menorrhagia - - drug: Tranexamic acid - - ' -- completion: 'disease: Urticaria - - drug: Methdilazine - - mechanism_links: methdilazine - decreases activity of - histamine H1 receptor - (human); histamine H1 receptor (human) - positively regulates - histamine receptor - activity; histamine receptor activity - participates in - histamine secretion - involved in inflammatory response; histamine secretion involved in inflammatory - response - positively correlated with - Urticaria - - references: https://go.drugbank.com/drugs/DB00902' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Methdilazine binds to the histamine H<sub>1</sub> receptor. This blocks - the action of endogenous histamine, which subsequently leads to temporary relief - of the negative symptoms brought on by histamine. - - - === - - - disease: Urticaria - - drug: Methdilazine - - ' -template: drug.DrugMechanism diff --git a/tests/output/treatment-schiz.pickle b/tests/output/treatment-schiz.pickle deleted file mode 100644 index da37e5bda..000000000 Binary files a/tests/output/treatment-schiz.pickle and /dev/null differ diff --git a/tests/output/treatment-schiz.yaml b/tests/output/treatment-schiz.yaml deleted file mode 100644 index 77d817e21..000000000 --- a/tests/output/treatment-schiz.yaml +++ /dev/null @@ -1,110 +0,0 @@ -input_id: /Users/cjm/repos/ontogpt/tests/input/cases/treatment-schiz.txt -input_text: "According to the American Psychiatric Association, second-generation\ - \ (atypical) antipsychotics (SGAs)\u2014with the exception of clozapine\u2014are\ - \ the agents of choice for first-line treatment of schizophrenia.16,25 Clozapine\ - \ is not recommended because of its risk of agranulocytosis.2 SGAs are usually preferred\ - \ over first-generation (typical) antipsychotics (FGAs) because they are associated\ - \ with fewer extrapyramidal symptoms.2 However, SGAs tend to have metabolic side\ - \ effects, such as weight gain, hyperlipidemia, and diabetes mellitus.26 These adverse\ - \ effects can contribute to the increased risk of cardiovascular mortality observed\ - \ in schizophrenia patients.26\n\nThe Texas Medication Algorithm Project (TMAP)\ - \ has provided a six-stage pharmacotherapeutic algorithm for the treatment of schizophrenia.\ - \ Stage 1 is first-line monotherapy with an SGA. If the patient shows little or\ - \ no response, he or she should proceed to stage 2, which consists of monotherapy\ - \ with either another SGA or an FGA. If there is still no response, the patient\ - \ should move to stage 3, which consists of clozapine monotherapy with monitoring\ - \ of the white blood cell (WBC) count.24 If agranulocytosis occurs, clozapine should\ - \ be discontinued. If stage-3 therapy fails to elicit a response, the patient should\ - \ proceed to stage 4, which combines clozapine with an FGA, an SGA, or electroconvulsive\ - \ therapy (ECT).24 If the patient still shows no response to treatment, stage 5\ - \ calls for monotherapy with an FGA or an SGA that has not been tried.24 Finally,\ - \ if stage 5 treatment is unsuccessful, stage 6 consists of combination therapy\ - \ with an SGA, an FGA, ECT, and/or a mood stabilizer." -raw_completion_output: "\ndisease: Schizophrenia \ndrugs: Second-generation (atypical)\ - \ antipsychotics; Clozapine; First-generation (typical) antipsychotics; \ntreatments:\ - \ Monotherapy with an SGA; Monotherapy with either another SGA or an FGA; Clozapine\ - \ monotherapy; Combining clozapine with an FGA, an SGA, or electroconvulsive therapy;\ - \ Monotherapy with an FGA or an SGA that has not been tried; Combination therapy\ - \ with an SGA, an FGA, electroconvulsive therapy, and/or a mood stabilizer.\ncontraindications:\ - \ Clozapine \ntreatment_mechanisms: \ntreatment_efficacies: \ntreatment_adverse_effects:\ - \ Clozapine*Agranulocytosis; SGAs*Weight gain; Hyperlipidemia; Diabetes mellitus" -prompt: 'Split the following piece of text into fields in the following format: - - - treatment: - - adverse_effects: - - - - Text: - - Diabetes mellitus - - - === - - - ' -extracted_object: - disease: MONDO:0005090 - drugs: - - AUTO:Second-generation%20%28atypical%29%20antipsychotics - - CHEBI:3766 - - AUTO:First-generation%20%28typical%29%20antipsychotics - treatments: - - AUTO:Monotherapy%20with%20an%20SGA - - AUTO:Monotherapy%20with%20either%20another%20SGA%20or%20an%20FGA - - AUTO:Clozapine%20monotherapy - - AUTO:Combining%20clozapine%20with%20an%20FGA%2C%20an%20SGA%2C%20or%20electroconvulsive%20therapy - - AUTO:Monotherapy%20with%20an%20FGA%20or%20an%20SGA%20that%20has%20not%20been%20tried - - AUTO:Combination%20therapy%20with%20an%20SGA%2C%20an%20FGA%2C%20electroconvulsive%20therapy%2C%20and/or%20a%20mood%20stabilizer. - contraindications: - - NCIT:C28936 - treatment_adverse_effects: - - treatment: NCIT:C28936 - adverse_effects: - - HP:0012234 - - treatment: NCIT:C87122 - adverse_effects: - - HP:0004324 - - treatment: NCIT:C34707 - adverse_effects: - - NCIT:C18902 - - treatment: HP:0000819 -named_entities: -- id: MONDO:0005090 - label: Schizophrenia -- id: AUTO:Second-generation%20%28atypical%29%20antipsychotics - label: Second-generation (atypical) antipsychotics -- id: CHEBI:3766 - label: Clozapine -- id: AUTO:First-generation%20%28typical%29%20antipsychotics - label: First-generation (typical) antipsychotics -- id: AUTO:Monotherapy%20with%20an%20SGA - label: Monotherapy with an SGA -- id: AUTO:Monotherapy%20with%20either%20another%20SGA%20or%20an%20FGA - label: Monotherapy with either another SGA or an FGA -- id: AUTO:Clozapine%20monotherapy - label: Clozapine monotherapy -- id: AUTO:Combining%20clozapine%20with%20an%20FGA%2C%20an%20SGA%2C%20or%20electroconvulsive%20therapy - label: Combining clozapine with an FGA, an SGA, or electroconvulsive therapy -- id: AUTO:Monotherapy%20with%20an%20FGA%20or%20an%20SGA%20that%20has%20not%20been%20tried - label: Monotherapy with an FGA or an SGA that has not been tried -- id: AUTO:Combination%20therapy%20with%20an%20SGA%2C%20an%20FGA%2C%20electroconvulsive%20therapy%2C%20and/or%20a%20mood%20stabilizer. - label: Combination therapy with an SGA, an FGA, electroconvulsive therapy, and/or - a mood stabilizer. -- id: NCIT:C28936 - label: Clozapine -- id: HP:0012234 - label: Agranulocytosis -- id: NCIT:C87122 - label: SGAs -- id: HP:0004324 - label: Weight gain -- id: NCIT:C34707 - label: Hyperlipidemia -- id: NCIT:C18902 - label: N/A -- id: HP:0000819 - label: Diabetes mellitus diff --git a/tests/output/unit_test_cache.db b/tests/output/unit_test_cache.db deleted file mode 100644 index 100db9e29..000000000 Binary files a/tests/output/unit_test_cache.db and /dev/null differ diff --git a/tests/unit/test_clients/__init__.py b/tests/unit/test_clients/__init__.py deleted file mode 100644 index e69de29bb..000000000 diff --git a/tests/unit/test_clients/test_pubmed_client_unit.py b/tests/unit/test_clients/test_pubmed_client_unit.py deleted file mode 100644 index 3239ebb1c..000000000 --- a/tests/unit/test_clients/test_pubmed_client_unit.py +++ /dev/null @@ -1,23 +0,0 @@ -"""PubMed client tests.""" -import unittest - -from ontogpt.clients import PubmedClient - - -class TestCompletion(unittest.TestCase): - """Test annotation.""" - - def setUp(self) -> None: - """Set up.""" - self.client = PubmedClient() - - def test_lookup(self): - """Test PMID lookup.""" - text = self.client.text("PMID:28449677") - print(text) - - def test_search(self): - """Test PMID search.""" - print("Testing...") - results = list(self.client.search("Long covid", ["review", "treatment", "therapies"])) - print(results) diff --git a/tests/unit/test_clients/test_unit_openai_client.py b/tests/unit/test_clients/test_unit_openai_client.py deleted file mode 100644 index 5356b4937..000000000 --- a/tests/unit/test_clients/test_unit_openai_client.py +++ /dev/null @@ -1,47 +0,0 @@ -"""Open AI client tests.""" -import re -import unittest - -import yaml - -from ontogpt.clients.openai_client import OpenAIClient -from tests import PROMPTS_FILE -from tests.unit import UNIT_CACHE_DB - - -class TestCompletion(unittest.TestCase): - """Test annotation.""" - - def _client(self, engine: str) -> OpenAIClient: - # TODO: use a mock - # for now we have a pseudo-mock test; the test uses cached responses - # in UNIT_CACHE_DB. - # if the test changes (e.g. a new prompt is added) then - # 1. temporarily remove the setting for api_key (it will be set from your env) - # 2. run the test - # 3. commit the new cache db - client = OpenAIClient( - model=engine, - api_key="fake", - cache_db_path=UNIT_CACHE_DB, - ) - return client - - def test_all_prompts(self): - """Test all prompts.""" - prompt_doc = yaml.safe_load(open(PROMPTS_FILE)) - default_engine = prompt_doc.get("default_engine", "gpt-3.5-turbo") - for prompt in prompt_doc["prompts"]: - prompt_text = prompt["prompt"] - if not isinstance(prompt_text, str): - prompt_text = yaml.dump(prompt_text) - engine = prompt.get("engine", default_engine) - client = self._client(engine) - pre_prompt = prompt.get("pre_prompt", "") - prompt_text = "".join([pre_prompt, prompt_text]) - print(f"## Testing prompt [{engine}: [{len(prompt_text)}] {prompt_text}") - ann = client.complete(prompt_text) - print(f"## Response: len={len(ann)}") - print(ann) - for expected in prompt.get("expected", []): - self.assertTrue(re.search(expected, ann, re.IGNORECASE)) diff --git a/tests/unit/test_converters/__init__.py b/tests/unit/test_converters/__init__.py deleted file mode 100644 index e69de29bb..000000000 diff --git a/tests/unit/test_converters/test_ontology_converter.py b/tests/unit/test_converters/test_ontology_converter.py deleted file mode 100644 index 1d4884d21..000000000 --- a/tests/unit/test_converters/test_ontology_converter.py +++ /dev/null @@ -1,63 +0,0 @@ -"""Core tests.""" -import logging -import unittest - -import yaml -from oaklib import get_implementation_from_shorthand -from oaklib.datamodels.vocabulary import IS_A, PART_OF -from oaklib.interfaces.obograph_interface import OboGraphInterface - -from ontogpt.converters.ontology_converter import OntologyConverter -from ontogpt.engines import halo_engine -from ontogpt.io.yaml_wrapper import dump_minimal_yaml -from tests import INPUT_DIR, OUTPUT_DIR - -TEST_ONTOLOGY_OAK = INPUT_DIR / "go-nucleus.db" -TEST_ONTOLOGY_HALO = INPUT_DIR / "go-nucleus.halo.yaml" -TEST_ONTOLOGY_OUTPUT = OUTPUT_DIR / "go-nucleus.halo.yaml" -HALLUCINATED_ONTOLOGY_OUTPUT = OUTPUT_DIR / "go-nucleus.hallucinated.halo.yaml" - -logger = logging.getLogger(halo_engine.__name__) -logger.setLevel(level=logging.INFO) - - -class TestOntologyConverter(unittest.TestCase): - """Test ability to convert from OAK to native HALO form.""" - - def setUp(self) -> None: - """Set up.""" - self.adapter = get_implementation_from_shorthand(str(TEST_ONTOLOGY_OAK)) - self.converter = OntologyConverter(self.adapter) - - def test_ontology_from_obograph(self): - """Test ontology from obograph.""" - oi = self.adapter - if not isinstance(oi, OboGraphInterface): - raise ValueError("Not an OboGraphInterface") - graph = oi.as_obograph() - converter = self.converter - ontology = converter.from_obograph(graph) - # print(yaml.dump(ontology.dict())) - [nucleus] = [x for x in ontology.elements if x.name == "Nucleus"] - self.assertCountEqual(["NuclearEnvelope", "NuclearMembrane"], nucleus.parts) - self.assertCountEqual(["IntracellularMembrane-boundedOrganelle"], nucleus.subclass_of) - self.assertCountEqual(["cell nucleus", "horsetail nucleus"], nucleus.synonyms) - self.assertIn("A membrane-bounded organelle", nucleus.description) - - def test_extract_seed_ontology(self): - """Test extract seed ontology.""" - converter = self.converter - preds = [IS_A, PART_OF] - ontology = converter.extract_seed_ontology( - ["GO:0031965", "GO:0005635", "GO:0006793"], preds - ) - [nucleus] = [x for x in ontology.elements if x.name == "Nucleus"] - self.assertCountEqual(["NuclearEnvelope", "NuclearMembrane"], nucleus.parts) - self.assertCountEqual(["IntracellularMembrane-boundedOrganelle"], nucleus.subclass_of) - self.assertCountEqual(["cell nucleus", "horsetail nucleus"], nucleus.synonyms) - self.assertIn("A membrane-bounded organelle", nucleus.description) - [nm] = [x for x in ontology.elements if x.name == "NuclearMembrane"] - print(yaml.dump(nm.dict())) - self.assertEqual("Membrane and part of some Nucleus", nm.equivalent_to) - with open(TEST_ONTOLOGY_OUTPUT, "w") as f: - f.write(dump_minimal_yaml(ontology)) diff --git a/tests/unit/test_exporters/__init__.py b/tests/unit/test_exporters/__init__.py deleted file mode 100644 index 3cd856bdd..000000000 --- a/tests/unit/test_exporters/__init__.py +++ /dev/null @@ -1,3 +0,0 @@ -from tests import INPUT_DIR - -TEST_PICKLED_RESULTS = str(INPUT_DIR / "recipe-spaghetti.pickle") diff --git a/tests/unit/test_exporters/test_html_exporter.py b/tests/unit/test_exporters/test_html_exporter.py deleted file mode 100644 index 1e59b99ac..000000000 --- a/tests/unit/test_exporters/test_html_exporter.py +++ /dev/null @@ -1,23 +0,0 @@ -"""Core tests.""" -import pickle -import unittest - -from ontogpt.io.html_exporter import HTMLExporter -from tests import OUTPUT_DIR -from tests.unit.test_exporters import TEST_PICKLED_RESULTS - - -@unittest.skip("Not yet fully compatible with linkml exporters and test fixtures") -class TestExportHTML(unittest.TestCase): - """Test annotation.""" - - def setUp(self) -> None: - """Set up.""" - self.exporter = HTMLExporter() - with open(TEST_PICKLED_RESULTS, "rb") as f: - self.extraction_result = pickle.load(f) - - def test_export(self): - """Test export.""" - with open(str(OUTPUT_DIR / "test-output.html"), "w", encoding="utf-8") as f: - self.exporter.export(self.extraction_result, f) diff --git a/tests/unit/test_exporters/test_markdown_exporter.py b/tests/unit/test_exporters/test_markdown_exporter.py deleted file mode 100644 index 6e1feebab..000000000 --- a/tests/unit/test_exporters/test_markdown_exporter.py +++ /dev/null @@ -1,24 +0,0 @@ -"""Core tests.""" -import pickle -import unittest - -from ontogpt.io.markdown_exporter import MarkdownExporter -from tests import OUTPUT_DIR -from tests.unit.test_exporters import TEST_PICKLED_RESULTS - - -@unittest.skip("Not yet fully compatible with linkml exporters and test fixtures") -class TestExport(unittest.TestCase): - """Test annotation.""" - - def setUp(self) -> None: - """Set up.""" - self.exporter = MarkdownExporter() - with open(TEST_PICKLED_RESULTS, "rb") as f: - self.extraction_result = pickle.load(f) - # print(yaml.dump(self.extraction_result.dict())) - - def test_export(self): - """Test export.""" - with open(str(OUTPUT_DIR / "test-output.md"), "w", encoding="utf-8") as f: - self.exporter.export(self.extraction_result, f) diff --git a/tests/unit/test_exporters/test_owl_exporter.py b/tests/unit/test_exporters/test_owl_exporter.py deleted file mode 100644 index 8c1d31661..000000000 --- a/tests/unit/test_exporters/test_owl_exporter.py +++ /dev/null @@ -1,34 +0,0 @@ -"""Core tests.""" -import pickle -import unittest - -from linkml_runtime import SchemaView - -from ontogpt.io.owl_exporter import OWLExporter -from ontogpt.templates import PATH_TO_TEMPLATES -from tests import OUTPUT_DIR -from tests.unit.test_exporters import TEST_PICKLED_RESULTS - - -@unittest.skip("Not yet fully compatible with linkml exporters and test fixtures") -class TestExportOWL(unittest.TestCase): - """Test exporting from pre-made results to OWL.""" - - def setUp(self) -> None: - """Set up.""" - self.exporter = OWLExporter() - self.schemaview = SchemaView(str(PATH_TO_TEMPLATES / "recipe.yaml")) - with open(TEST_PICKLED_RESULTS, "rb") as f: - self.extraction_result = pickle.load(f) - - def test_export(self): - """Test export.""" - print(f"URL={self.extraction_result.extracted_object.url}") - print(f"Label={self.extraction_result.extracted_object.label}") - with open(str(OUTPUT_DIR / "recipe-spaghetti.owl"), "w", encoding="utf-8") as f: - self.exporter.export(self.extraction_result, f, self.schemaview, id_value="AUTO:_ROOT") - - def test_export2(self): - """Test export.""" - with open(str(OUTPUT_DIR / "recipe-palak-paneer.owl"), "w", encoding="utf-8") as f: - self.exporter.export(self.extraction_result, f, self.schemaview, id_value="AUTO:_ROOT") diff --git a/tests/unit/test_exporters/test_rdf_exporter.py b/tests/unit/test_exporters/test_rdf_exporter.py deleted file mode 100644 index 558d332ee..000000000 --- a/tests/unit/test_exporters/test_rdf_exporter.py +++ /dev/null @@ -1,27 +0,0 @@ -"""Core tests.""" -import pickle -import unittest - -from linkml_runtime import SchemaView - -from ontogpt.io.rdf_exporter import RDFExporter -from ontogpt.templates import PATH_TO_TEMPLATES -from tests import OUTPUT_DIR -from tests.unit.test_exporters import TEST_PICKLED_RESULTS - - -@unittest.skip("Not yet fully compatible with linkml exporters and test fixtures") -class TestExportRDF(unittest.TestCase): - """Test RDF export.""" - - def setUp(self) -> None: - """Set up.""" - self.exporter = RDFExporter() - self.schemaview = SchemaView(str(PATH_TO_TEMPLATES / "recipe.yaml")) - with open(TEST_PICKLED_RESULTS, "rb") as f: - self.extraction_result = pickle.load(f) - - def test_export(self): - """Test export.""" - with open(str(OUTPUT_DIR / "test-output.ttl"), "w", encoding="utf-8") as f: - self.exporter.export(self.extraction_result, f, self.schemaview) diff --git a/tests/unit/test_ontex/__init__.py b/tests/unit/test_ontex/__init__.py deleted file mode 100644 index e69de29bb..000000000 diff --git a/tests/unit/test_ontex/test_extract.py b/tests/unit/test_ontex/test_extract.py deleted file mode 100644 index f7455d3e0..000000000 --- a/tests/unit/test_ontex/test_extract.py +++ /dev/null @@ -1,176 +0,0 @@ -"""Core tests.""" -import csv -import logging -import unittest -from typing import Iterator, List, Tuple - -import yaml -from oaklib import get_adapter -from oaklib.datamodels.vocabulary import IS_A, PART_OF -from oaklib.interfaces.obograph_interface import OboGraphInterface - -from ontogpt.io.yaml_wrapper import dump_minimal_yaml -from ontogpt.ontex import extractor -from ontogpt.ontex.extractor import OntologyExtractor, Task, TaskCollection -from tests import ( - CELLULAR_ANATOMICAL_ENTITY, - ENVELOPE, - FUNGI, - IMBO, - INPUT_DIR, - INTRACELLULAR_ORGANELLE, - MEMBRANE_BOUNDED_ORGANELLE, - NUCLEAR_ENVELOPE, - NUCLEAR_MEMBRANE, - NUCLEUS, - ORGANELLE, - OUTPUT_DIR, - VACUOLE, -) - -TEST_ONTOLOGY_OAK = INPUT_DIR / "go-nucleus.db" -TEST_ONTOLOGY_ABOX = INPUT_DIR / "fhkb.db" - - -logger = logging.getLogger(extractor.__name__) -logger.setLevel(level=logging.INFO) - -IS_ANCESTOR_OF = "fhkb:isAncestorOf" -HAS_ANCESTOR = "fhkb:hasAncestor" -HAS_PARENT = "fhkb:hasParent" -IS_PARENT_OF = "fhkb:isParentOf" -HAS_FATHER = "fhkb:hasFather" -HAS_MOTHER = "fhkb:hasMother" -HAS_PARENT = "fhkb:hasParent" -HAS_SIBLING = "fhkb:hasSibling" -HAS_BROTHER = "fhkb:hasBrother" -HAS_SISTER = "fhkb:hasSister" - - -class TestOntologyExtractor(unittest.TestCase): - """Test ability to convert from OAK to native HALO form.""" - - def setUp(self) -> None: - """Set up.""" - self.adapter = get_adapter(str(TEST_ONTOLOGY_OAK)) - self.abox_adapter = get_adapter(str(TEST_ONTOLOGY_ABOX)) - if not isinstance(self.adapter, OboGraphInterface): - raise ValueError("Not an OboGraphInterface") - self.extractor = OntologyExtractor(adapter=self.adapter) - self.abox_extractor = OntologyExtractor(adapter=self.abox_adapter) - self.abox_extractor.query_predicates = [HAS_ANCESTOR, HAS_SIBLING] - - def cases(self) -> Iterator[Tuple[Task, List[str]]]: - extractor = self.extractor - # yield extractor.extract_indirect_superclasses_task(select_random=True), None - yield extractor.extract_transitive_superclasses_task( - subclass=NUCLEUS, siblings=[VACUOLE], roots=[ORGANELLE] - ), [ORGANELLE, IMBO, INTRACELLULAR_ORGANELLE, MEMBRANE_BOUNDED_ORGANELLE] - yield extractor.extract_indirect_superclasses_task( - subclass=NUCLEUS, siblings=[VACUOLE], roots=[ORGANELLE] - ), [ORGANELLE, INTRACELLULAR_ORGANELLE, MEMBRANE_BOUNDED_ORGANELLE] - yield extractor.extract_most_recent_common_subsumers_task( - subclass1=NUCLEUS, subclass2=VACUOLE, siblings=[NUCLEAR_MEMBRANE], roots=[] - ), [IMBO] - yield extractor.extract_incoherent_ontology_task( - incoherents=[NUCLEUS], - siblings=[VACUOLE], - disjoints=[(ORGANELLE, ENVELOPE)], - spiked_relationships=[(NUCLEUS, IS_A, NUCLEAR_MEMBRANE)], - roots=[CELLULAR_ANATOMICAL_ENTITY], - ), [NUCLEUS] - yield extractor.extract_subclass_of_expression_task( - superclass=NUCLEUS, - predicate=PART_OF, - siblings=[VACUOLE], - ), [NUCLEAR_MEMBRANE, NUCLEAR_ENVELOPE] - yield extractor.extract_subclass_of_expression_task( - superclass=IMBO, - predicate=PART_OF, - siblings=[FUNGI], - ), [NUCLEAR_MEMBRANE, NUCLEAR_ENVELOPE] - - def test_extract(self): - """Test extract tasks.""" - extractor = self.extractor - for task, expected in self.cases(): - if not task.ontology.axioms: - raise ValueError(f"Task {task} has no axioms") - print(yaml.dump(task.dict(), sort_keys=False)) - answer_texts = [a.text for a in task.answers] - if expected is not None: - self.assertCountEqual(answer_texts, [extractor._name(x) for x in expected]) - - @unittest.skip("Non-deterministic") - def test_random_taxon_constraints(self): - """Test extract random tasks.""" - extractor = self.extractor - task = extractor.extract_taxon_constraint_task(select_random=True, never_in=True) - print(dump_minimal_yaml(task)) - - @unittest.skip("Non-deterministic") - def test_random(self): - """Test extract random tasks.""" - extractor = self.extractor - abox_extractor = self.abox_extractor - abox_tc = abox_extractor.create_random_tasks(20, abox=True) - tc = extractor.create_random_tasks(20, abox=False) - tc.tasks.extend(abox_tc.tasks) - for task in tc.tasks: - if not task.answers: - print(f"Task {task} has no answers") - # raise ValueError(f"Task {task} has no answers") - if not task.ontology.axioms: - raise ValueError(f"Task {task} has no axioms") - # raise ValueError(f"Task {task} has no axioms") - path = OUTPUT_DIR / "random-reasoner-tasks.yaml" - with open(path, "w") as f: - f.write(dump_minimal_yaml(tc)) - tc = TaskCollection.load(path) - task_types = {type(obj) for obj in tc.tasks} - print(len(tc.tasks)) - print(task_types) - # increase this every time you add a new task type - self.assertEqual(len(task_types), 7) - - @unittest.skip("Non-deterministic") - def test_random_obfuscated(self): - extractor = self.extractor - extractor.obfuscate = True - abox_extractor = self.abox_extractor - abox_extractor.obfuscate = True - abox_tc = abox_extractor.create_random_tasks(20, abox=True) - tc = extractor.create_random_tasks(20, abox=False) - # merge - tc.tasks.extend(abox_tc.tasks) - for task in tc.tasks: - if not task.answers: - print(f"Task {task} has no answers") - # raise ValueError(f"Task {task} has no answers") - if not task.ontology.axioms: - raise ValueError(f"Task {task} has no axioms") - # raise ValueError(f"Task {task} has no axioms") - path = OUTPUT_DIR / "obfuscated-reasoner-tasks.yaml" - with open(path, "w") as f: - f.write(dump_minimal_yaml(tc)) - tc = TaskCollection.load(path) - task_types = {type(obj) for obj in tc.tasks} - print(len(tc.tasks)) - print(task_types) - # increase this every time you add a new task type - self.assertEqual(len(task_types), 6) - self.assertGreater(len(tc.obfuscated_curie_map.keys()), 20) - - def test_introspect(self): - """Test introspection.""" - root_class = Task - with open(OUTPUT_DIR / "task-classes.tsv", "w") as f: - writer = csv.DictWriter(f, fieldnames=["code", "task", "description"], delimiter="\t") - writer.writeheader() - for subclass in root_class.__subclasses__(): - row = { - "code": subclass._code, - "task": subclass.__name__, - "description": subclass.__doc__.replace("\n", " ").strip(), - } - writer.writerow(row) diff --git a/tests/unit/test_unit_cli.py b/tests/unit/test_unit_cli.py index 6593664ac..23a53b696 100644 --- a/tests/unit/test_unit_cli.py +++ b/tests/unit/test_unit_cli.py @@ -3,7 +3,7 @@ from click.testing import CliRunner -from ontogpt.cli import main +from talisman.cli import main from tests import OUTPUT_DIR CLI_OUTPUT_DIR = OUTPUT_DIR / "cli" diff --git a/tests/unit/test_utils/test_gene_set_utils.py b/tests/unit/test_utils/test_gene_set_utils.py index a77b60680..26558644d 100644 --- a/tests/unit/test_utils/test_gene_set_utils.py +++ b/tests/unit/test_utils/test_gene_set_utils.py @@ -4,8 +4,8 @@ import unittest from pathlib import Path -from ontogpt.utils import gene_set_utils -from ontogpt.utils.gene_set_utils import ( +from talisman.utils import gene_set_utils +from talisman.utils.gene_set_utils import ( fill_missing_gene_set_values, load_gene_sets, parse_gene_set, diff --git a/tests/unit/test_utils/test_yaml_wrapper.py b/tests/unit/test_utils/test_yaml_wrapper.py deleted file mode 100644 index 1d482be79..000000000 --- a/tests/unit/test_utils/test_yaml_wrapper.py +++ /dev/null @@ -1,39 +0,0 @@ -"""Tests YAML utils.""" -import io -import unittest - -from ruamel.yaml import YAML, RoundTripRepresenter - - -def repr_str(dumper: RoundTripRepresenter, data: str): - if "\n" in data: - return dumper.represent_scalar("tag:yaml.org,2002:str", data, style="|") - return dumper.represent_scalar("tag:yaml.org,2002:str", data) - - -class TestYAML(unittest.TestCase): - def test_dump_load(self): - # previous versions of ruamel.yaml would generate unparsable yaml - # for certain combinations of whitespace and embedded yaml tokens - cases = [ - "\nfoo: bar", - " \nfoo: bar", - " \n foo: bar", - " \n foo: bar\n{}", - " \n foo: bar\n{} ", - " \n foo: bar\n{}\n|\n{", - ] - for case in cases: - obj = {"a": case} - # yaml = YAML(typ="safe") - yaml = YAML() - yaml.representer.add_representer(str, repr_str) - yaml.default_flow_style = False - yaml.indent(sequence=4, offset=2) - file = io.StringIO() - yaml.dump(obj, file) - ys = file.getvalue() - # print(ys) - yaml = YAML() - r = yaml.load(ys) - self.assertEqual(r, obj) diff --git a/util/ctd-train2obo.pl b/util/ctd-train2obo.pl deleted file mode 100755 index ddd6b2c0f..000000000 --- a/util/ctd-train2obo.pl +++ /dev/null @@ -1,12 +0,0 @@ -#!/usr/bin/perl - -while(<>) { - chomp; - @toks = split(/\t/, $_); - if (scalar(@toks) == 6) { - print "[Term]\n"; - print "id: MESH:$toks[-1]\n"; - print "synonym: \"$toks[-3]\" EXACT []\n\n"; - - } -} diff --git a/util/ctd-train2tsv.pl b/util/ctd-train2tsv.pl deleted file mode 100755 index 7fb15d237..000000000 --- a/util/ctd-train2tsv.pl +++ /dev/null @@ -1,11 +0,0 @@ -#!/usr/bin/perl - -while(<>) { - chomp; - @toks = split(/\t/, $_); - if (scalar(@toks) == 6) { - print "- id: MESH:$toks[-1]\n"; - print " - synonym: $toks[-3]\n"; - - } -} diff --git a/util/ctd-train2yaml.pl b/util/ctd-train2yaml.pl deleted file mode 100755 index 0e3cf3c72..000000000 --- a/util/ctd-train2yaml.pl +++ /dev/null @@ -1,11 +0,0 @@ -#!/usr/bin/perl - -while(<>) { - chomp; - @toks = split(/\t/, $_); - if (scalar(@toks) == 6) { - print "- id: MESH:$toks[-1]\n"; - print " synonym: \"$toks[-3]\"\n"; - - } -} diff --git a/util/dump-omim2pmid.pl b/util/dump-omim2pmid.pl deleted file mode 100755 index c719299b2..000000000 --- a/util/dump-omim2pmid.pl +++ /dev/null @@ -1,2 +0,0 @@ -#!/usr/bin/perl -sqlite3 $db/omim.db -cmd "select subject,object from statements where predicate='IAO:0000142'" diff --git a/util/filter-hpoa.pl b/util/filter-hpoa.pl deleted file mode 100755 index 862638ca1..000000000 --- a/util/filter-hpoa.pl +++ /dev/null @@ -1,16 +0,0 @@ -#!/usr/bin/perl - -@files = split(/\n/, `ls -1 src/semantic_llama/evaluation/hpoa/test_cases/*.txt`); -%ids = {}; -foreach $file (@files) { - if ($file =~ m@omim-(\d+)@) { - $ids{"OMIM:$1"} = 1; - } -} -while (<>) { - if (m@^(OMIM:\d+)@) { - if ($ids{$1}) { - print; - } - } -}